# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Mycobacterium_bovis_BCG_Pasteur_1173P2_uid58781/NC_008769.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Mycobacterium_bovis_BCG_Pasteur_1173P2_uid58781/NC_008769.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Mycobacterium_bovis_BCG_Pasteur_1173P2_uid58781/NC_008769.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|121635884|ref|YP_976107.1|  [L=507]
Description: chromosomal replication initiation protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-103  345.7   0.1   2.5e-103  344.6   0.0    1.6  2  Bac_DnaA      Bacterial dnaA  protein
      4e-27   94.0   0.0    8.4e-27   93.0   0.0    1.6  1  Bac_DnaA_C    Bacterial dnaA protein helix-turn-helix
    5.4e-10   39.3   0.0    1.1e-09   38.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
    8.5e-06   26.2   0.0    0.00023   21.6   0.0    3.2  4  AAA           ATPase family associated with various cellular 
     0.0011   19.2   0.3        1.4    9.2   0.0    2.9  2  AAA_22        AAA domain
     0.0091   15.7   0.0      0.033   13.9   0.0    2.0  2  DnaA_N        DnaA N-terminal domain
  ------ inclusion threshold ------
      0.012   14.5   0.0       0.54    9.1   0.0    2.2  2  AFG1_ATPase   AFG1-like ATPase
      0.015   15.7   0.4       0.25   11.7   0.0    2.7  3  AAA_16        AAA ATPase domain
      0.076   13.4   0.0       0.21   12.0   0.0    1.8  1  RNA_helicase  RNA helicase
      0.082   12.7   0.0       0.28   11.0   0.0    2.0  1  HTH_38        Helix-turn-helix domain
       0.13   12.2   0.0       0.45   10.4   0.0    1.8  1  ATPase_2      ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.6   0.0  1.5e-106  2.5e-103       1     218 [.     168     385 ..     168     386 .. 0.99
   2 ?   -2.6   0.0       2.5     4e+03     180     207 ..     405     433 ..     389     443 .. 0.66

  Alignments for each domain:
  == domain 1  score: 344.6 bits;  conditional E-value: 1.5e-106
                                    --SS-SGGG----TTTHHHHHHHHHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHH CS
                       Bac_DnaA   1 LnkrytFetFviGasnrlAlaaalkvaeapgkkynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelv 80 
                                    Ln+rytF+tFviGasnr+A+aaal++aeap+++ynPlfi+ge+GlGktHLl+a+gn++++ +p +rv+Y+++eeF+n+++
  gi|121635884|ref|YP_976107.1| 168 LNRRYTFDTFVIGASNRFAHAAALAIAEAPARAYNPLFIWGESGLGKTHLLHAAGNYAQRLFPGMRVKYVSTEEFTNDFI 247
                                    89****************************************************************************** PP

                                    HHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEE CS
                       Bac_DnaA  81 kalrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlv 160
                                    ++lrd+++ +fk+++r+vDvLl+DDiqf++gke++qee+fhtfn+l++++kq+v+ssDr+Pk+l++ledrlr+rfe+Gl+
  gi|121635884|ref|YP_976107.1| 248 NSLRDDRKVAFKRSYRDVDVLLVDDIQFIEGKEGIQEEFFHTFNTLHNANKQIVISSDRPPKQLATLEDRLRTRFEWGLI 327
                                    ******************************************************************************** PP

                                    EE-----HHHHHHHHHHHHHHTT----TTHHHHHHHH--S-HHHHHHHHHHHHHHHHH CS
                       Bac_DnaA 161 vdieppdletrlailkkkieaeklevpeevlefiaervtdnvRelegalnrlkayasl 218
                                    +d++pp+letr+ail+kk+++e+l vp++vle+ia+++++n+Relegal+r++a+asl
  gi|121635884|ref|YP_976107.1| 328 TDVQPPELETRIAILRKKAQMERLAVPDDVLELIASSIERNIRELEGALIRVTAFASL 385
                                    ******************************************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                    HHTT----.TTHHHHHHHH--S-HHHHHH CS
                       Bac_DnaA 180 eaeklevp.eevlefiaervtdnvReleg 207
                                    +a+ +++    ++   ae++++ v el+g
  gi|121635884|ref|YP_976107.1| 405 DANTMQISaATIMAATAEYFDTTVEELRG 433
                                    34455554156788888999999999887 PP

>> Bac_DnaA_C  Bacterial dnaA protein helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   5.1e-30   8.4e-27       3      69 .]     415     480 ..     413     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 5.1e-30
                                    HHHHTHHHHTT--HHHHHS----CSSHHHHHHHHHHHHHTS---HHHHHHHHT-STTHHHHHHHHHH CS
                     Bac_DnaA_C   3 kIieaVaeyfgvsvedlkskkRkkeiveaRqiamylareltdlslpeIGkefggrdHsTVihaikki 69 
                                    +I++a+aeyf+ +ve+l+++ +++ +++ Rqiamyl+reltdlslp+IG++f grdH+TV++a +ki
  gi|121635884|ref|YP_976107.1| 415 TIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAF-GRDHTTVMYAQRKI 480
                                    79**************************************************.8***********98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   6.5e-13   1.1e-09      48     153 ..     202     310 ..     165     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 6.5e-13
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavr..aglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqa 125
                                    + + + G sG GK+hl  a g  a r   g++v +v++e++ +      rd++     +++  vd+l++Dd+ + + ++ 
  gi|121635884|ref|YP_976107.1| 202 NPLFIWGESGLGKTHLLHAAGNYAQRlfPGMRVKYVSTEEFTNDFINSLRDDRKVAFKRSYRDVDVLLVDDIQFIEGKEG 281
                                    557899*****************999778*******************999999999*********************** PP

                      IstB_IS21 126 eaellfeviekrye.rrsiiitsnlpfae 153
                                     +e++f+  +   + ++ i+i+s+ p ++
  gi|121635884|ref|YP_976107.1| 282 IQEEFFHTFNTLHNaNKQIVISSDRPPKQ 310
                                    *********99887257899999998776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.94   1.5e+03       7      23 ..       5      21 ..       3      88 .. 0.81
   2 ?   -1.2   0.0       1.6   2.6e+03     102     112 ..     175     185 ..     131     192 .. 0.60
   3 !   21.6   0.0   1.4e-07   0.00023       2     129 ..     205     323 ..     204     326 .. 0.83
   4 ?   -2.2   0.1       3.3   5.4e+03      19      39 ..     399     424 ..     387     448 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.94
                                   TTSSHHHHHHHHHHHHT CS
                            AAA  7 pGtGKTllakavakelg 23
                                   pG G T++ +av++el+
  gi|121635884|ref|YP_976107.1|  5 PGSGFTTVWNAVVSELN 21
                                   999**********9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                    TEEEEEEESSG CS
                            AAA 102 kvivigatnrp 112
                                    +++viga+nr 
  gi|121635884|ref|YP_976107.1| 175 DTFVIGASNRF 185
                                    46788888885 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.4e-07
                                    EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                            AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                     ++G  G GKT l +a  + +     g+++  +s  e++++++    ++ +  fk+  +     +l++D+i  + +++  
  gi|121635884|ref|YP_976107.1| 205 FIWGESGLGKTHLLHAAGNYAqrlfpGMRVKYVSTEEFTNDFINSLRDDRKVAFKRSYRD--VDVLLVDDIQFIEGKE-- 280
                                    579*****************955555699**************99999999999997665..49**********8888.. PP

                                    CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                            AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                            +++++++ ++ + + ++   +++ + rp k    l  +R+  ++e
  gi|121635884|ref|YP_976107.1| 281 -------GIQEEFFHTFNTLHNANK--QIVISSDRPPKQLATLE-DRLRTRFE 323
                                    .......899999999999999644..66777888777777777.77776665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.3
                                    HHHH..THEEEEEETTTCSSS...ST CS
                            AAA  19 akel..gvefleisgsellsk...yv 39 
                                     ++l  +++ ++is+++++     y+
  gi|121635884|ref|YP_976107.1| 399 LRDLiaDANTMQISAATIMAAtaeYF 424
                                    33323356666666666663222233 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00087       1.4       8      25 ..     204     221 ..     199     240 .. 0.85
   2 !    6.6   0.1    0.0056       9.1      91     118 ..     259     296 ..     235     304 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00087
                         AAA_22   8 lvvtGesGtGKTtllrrl 25 
                                    l+++GesG GKT+ll   
  gi|121635884|ref|YP_976107.1| 204 LFIWGESGLGKTHLLHAA 221
                                    789***********9765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0056
                         AAA_22  91 v.....ielliiDEaqhlr..s...eealeeLrsllnl 118
                                    +     + +l++D++q++   +   ee + ++ +l+n 
  gi|121635884|ref|YP_976107.1| 259 KrsyrdVDVLLVDDIQFIEgkEgiqEEFFHTFNTLHNA 296
                                    04444689**********87615559999999999994 PP

>> DnaA_N  DnaA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.9   9.6e+03       2      11 ..      11      20 ..      11      21 .. 0.84
   2 !   13.9   0.0     2e-05     0.033      21      63 ..      45      87 ..      35      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.9
                         DnaA_N  2 elWsavlerL 11
                                   ++W+av ++L
  gi|121635884|ref|YP_976107.1| 11 TVWNAVVSEL 20
                                   58****9987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2e-05
                         DnaA_N 21 dtWikplklfalknngltlivpneFardwiesnYldriaellk 63
                                   + W+  +++  + ++   l+vp++F+++ ie++    i+++l+
  gi|121635884|ref|YP_976107.1| 45 RAWLNLVQPLTIVEGFALLSVPSSFVQNEIERHLRAPITDALS 87
                                   57999999999*8888*****************9999998875 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00033      0.54      59     109 ..     198     252 ..     152     261 .. 0.70
   2 ?    3.2   0.0      0.02        32     287     343 ..     266     322 ..     257     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtylmdlf..f..eslpvekkrrvhfhafmarvhdeltk 109
                                     ++ + l++wG  G GKt+l+  +  +  +  p+ + + v + +f  +  + l+ 
  gi|121635884|ref|YP_976107.1| 198 ARAYNPLFIWGESGLGKTHLLHAAgnYaqRLFPGMRVKYVSTEEFTNDFINSLRD 252
                                    557788***************7652231144677777777777777776666665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                    AFG1_ATPase 287 htvlledVpvltkakedaarRfiaLvDelYdadvklvvsaevaleelye.agrlefef 343
                                      +l++d++ ++ +ke  +  f     +l +a+ ++v+s + ++++l + ++rl+  f
  gi|121635884|ref|YP_976107.1| 266 DVLLVDDIQFIE-GKEGIQEEFFHTFNTLHNANKQIVISSDRPPKQLATlEDRLRTRF 322
                                    556788888887.99999****************************975266776666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.4   5.5e+03      57      91 ..      66     100 ..      45     144 .. 0.65
   2 ?   11.7   0.0   0.00015      0.25      22      51 ..     199     228 ..     186     319 .. 0.78
   3 ?    0.9   0.1      0.33   5.3e+02      46     124 ..     363     444 ..     356     492 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.4
                         AAA_16  57 rgkcdqlesaipysa.laqalareellrqlldeaes 91 
                                       ++q+e ++++ a +++al+r +l  q+    + 
  gi|121635884|ref|YP_976107.1|  66 PSSFVQNEIERHLRApITDALSR-RLGHQIQLGVRI 100
                                    55666666666664447777755.666666655333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd 51 
                                       + +++ GesG GK+ l+ ++ +++++ 
  gi|121635884|ref|YP_976107.1| 199 RAYNPLFIWGESGLGKTHLLHAAGNYAQRL 228
                                    333889**************9988655544 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.33
                         AAA_16  46 ralekd....ggiflrgkcdqlesaipysa.laqalareellrqllde......aesaeleawrekleealaavpelaga 114
                                     ++e++    +g ++r ++  +  ++p +  la++  r +l+++ +++        +a +e+++++       v el+g 
  gi|121635884|ref|YP_976107.1| 363 SSIERNirelEGALIRVTAFASLNKTPIDKaLAEIVLR-DLIADANTMqisaatIMAATAEYFDTT-------VEELRGP 434
                                    45555544444445555555554567776668888855.888888888443333222223333332.......3344444 PP

                         AAA_16 115 easrllellk 124
                                    +++r l++ +
  gi|121635884|ref|YP_976107.1| 435 GKTRALAQSR 444
                                    4433333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.21       2      84 ..     205     301 ..     204     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..........klkkkdsvys...rnpeddfwdgYtgqevvvidDfgqvkdee..n 66 
                                    +++G+sg GK++l +  a + +++l           ++ +++++       +  f  +Y++ +v+++dD+  ++ +e  +
  gi|121635884|ref|YP_976107.1| 205 FIWGESGLGKTHLLHA-AGNYAQRLfpgmrvkyvsTEEFTNDFINslrDDRKVAFKRSYRDVDVLLVDDIQFIEGKEgiQ 283
                                    89**************.77777777899999999955555555554312333445599*************999665544 PP

                   RNA_helicase  67 psdlaelirlvsstpypl 84 
                                    ++ +++++ l + ++ ++
  gi|121635884|ref|YP_976107.1| 284 EEFFHTFNTLHNANKQIV 301
                                    448888888888777665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.28      20      39 ..     456     475 ..     440     478 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                         HTH_38  20 GlslreIArrLgrspsTIsR 39 
                                    +lsl +I++  gr+++T+ +
  gi|121635884|ref|YP_976107.1| 456 DLSLPKIGQAFGRDHTTVMY 475
                                    69***************975 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00028      0.45      19     122 ..     200     302 ..     192     306 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl..edkdkyviyyi..alreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                     ++++fi+G  g GKt Ll  + +    +  + +v y++  ++ +++i++l++     +++    k    +v    ++ i
  gi|121635884|ref|YP_976107.1| 200 AYNPLFIWGESGLGKTHLLHAAGNYAqrLFPGMRVKYVSteEFTNDFINSLRDD----RKVA--FKRSYRDVDVLLVDDI 273
                                    5799***************98866552144455555554112333333333333....2222..2222233333333333 PP

                       ATPase_2  95 lk.eksklvfkaielllekikkkgkkiii 122
                                       e ++ +++ +   ++ + +  k+i+i
  gi|121635884|ref|YP_976107.1| 274 QFiEGKEGIQEEFFHTFNTLHNANKQIVI 302
                                    22355555666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2970.14
//
Query:       gi|121635885|ref|YP_976108.1|  [L=402]
Description: DNA polymerase III subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-44  149.9   0.0    5.2e-36  123.4   0.0    2.4  3  DNA_pol3_beta    DNA polymerase III beta subunit, N-terminal 
    2.6e-36  124.4   0.0      2e-33  115.0   0.0    2.7  3  DNA_pol3_beta_2  DNA polymerase III beta subunit, central dom
    1.4e-34  118.6   0.0    1.3e-33  115.4   0.0    2.3  2  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.21   11.5   0.0    1.3  1  SEF14_adhesin    SEF14-like adhesin


Domain annotation for each model (and alignments):
>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.0   1.2e-39   5.2e-36       2     121 .]      14     130 ..      13     130 .. 0.98
   2 !   24.0   0.0   7.6e-09   3.4e-05       9      91 ..     143     227 ..     139     259 .. 0.86
   3 ?   -3.3   0.0       2.1   9.2e+03      59      90 ..     324     354 ..     295     361 .. 0.60

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.2e-39
                                    EEEEEHHHHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHH CS
                  DNA_pol3_beta   2 kftiereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivka 81 
                                     f++ re++++++++vak +++R+ +p+Lsgvll+ +d++l+++g+D+e+s+e+++ ae+  ++g+vlv++rll+di++a
  gi|121635885|ref|YP_976108.1|  14 TFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIV-SPGSVLVSGRLLSDITRA 92 
                                    68999********************************************************.9***************** PP

                                    SSTTSEEEEEEETTEEEEEEETTEEEEEE-BEGGGS---- CS
                  DNA_pol3_beta  82 Lpndkkvkisvneqklliiksgssrfslstlsaeeypnlp 121
                                    Lpn k+v ++v++++++++ +g++rfsl+t+++e+yp+lp
  gi|121635885|ref|YP_976108.1|  93 LPN-KPVGVHVEGNRVALT-CGNARFSLPTMPVEDYPTLP 130
                                    ***.***************.*****************997 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 7.6e-09
                                    HHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEE..EEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTS CS
                  DNA_pol3_beta   9 ellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisi..estisaeseeeegkvlvparllldivkaLpndk 86 
                                     +++++++va +  +  tlp+L+g+ +e+  +++ l +tD+   +  e + sa+s++ e +vlvpa++l+++ ka   ++
  gi|121635885|ref|YP_976108.1| 143 LFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAvrELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGS 222
                                    58899***********************************96554124456677778999*************9977777 PP

                                    EEEEE CS
                  DNA_pol3_beta  87 kvkis 91 
                                    +v +s
  gi|121635885|ref|YP_976108.1| 223 DVRLS 227
                                    77776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.1
                                    SEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEE CS
                  DNA_pol3_beta  59 aeseeeegkvlvparllldivkaLpndkkvki 90 
                                       + e+ ++  ++ +l d +++L   + v++
  gi|121635885|ref|YP_976108.1| 324 VDYAGEPLTIAFNPTYLTDGLSSLRS-ERVSF 354
                                    33445666777777888887777777.66666 PP

>> DNA_pol3_beta_2  DNA polymerase III beta subunit, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0029        13      20     105 ..      35     116 ..      17     123 .. 0.82
   2 !  115.0   0.0   4.5e-37     2e-33       2     116 .]     139     260 ..     138     260 .. 0.98
   3 ?   -1.4   0.0      0.61   2.7e+03      76     101 ..     286     311 ..     274     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                                    SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTCEEEEEEEHHHHHHHHHHHTSSSSEEEEEEESSEEEEE CS
                DNA_pol3_beta_2  20 edetrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeqvklalsegkirfe 99 
                                       + pvL Gv l  +++ l+++  d    a +++ +e  ++   sv+v  + l +++++l +  + v + ++ +++ ++
  gi|121635885|ref|YP_976108.1|  35 ARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSP--GSVLVSGRLLSDITRALPN--KPVGVHVEGNRVALT 110
                                    555678999**9999999999999997777777777777777..69***************99..999999999999999 PP

                                    ETTEEE CS
                DNA_pol3_beta_2 100 vgnvrl 105
                                    +gn+r+
  gi|121635885|ref|YP_976108.1| 111 CGNARF 116
                                    999987 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 4.5e-37
                                    EEHHHHHHHHHCCGGGS-SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTC.EEEEEEEHHHHHHHHHHH CS
                DNA_pol3_beta_2   2 lkqkelkelieqvafaasedetrpvLtGvrleieedklllaaTdghRlavrkleleeeeed.easvivPaktlaelakll 80 
                                    l+++ ++e+i+qva+aa++d+t+p+LtG+r+ei +++++laaTd++Rlavr+l+++++++d ea+v+vPaktlae+ak+ 
  gi|121635885|ref|YP_976108.1| 139 LPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDiEAAVLVPAKTLAEAAKAG 218
                                    68899*************************************************************************** PP

                                    TSSSSEEEEEEE.......SSEEEEEETTEEEEEE-BSS---B CS
                DNA_pol3_beta_2  81 edneeqvklals.......egkirfevgnvrltsrlldgkfPd 116
                                       +++v+l+l+       +g ++++ +++r+t+rlld++fP+
  gi|121635885|ref|YP_976108.1| 219 IG-GSDVRLSLGtgpgvgkDGLLGISGNGKRSTTRLLDAEFPK 260
                                    99.***************************************7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.61
                                    HHHHHTSSSSEEEEEEESSEEEEEET CS
                DNA_pol3_beta_2  76 laklledneeqvklalsegkirfevg 101
                                    l  l++d + qv++ +++g +r+++g
  gi|121635885|ref|YP_976108.1| 286 LVALVADRGAQVRMEFADGSVRLSAG 311
                                    44456677888899888888888766 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.13   5.9e+02       5      34 ..     130     158 ..     128     193 .. 0.80
   2 !  115.4   0.0   2.9e-37   1.3e-33       1     111 [.     262     371 ..     262     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.13
                                    -SS-SEEEEEEHHHHHHHHHHHHTTSSTST CS
                DNA_pol3_beta_3   5 PkefkkkvtvdlkelkealkRvalladekn 34 
                                    P+  +++ ++  + ++ea++ va+ a ++ 
  gi|121635885|ref|YP_976108.1| 130 PTLPEETGLLPAELFAEAISQVAIAA-GRD 158
                                    6666666677788999*******998.555 PP

  == domain 2  score: 115.4 bits;  conditional E-value: 2.9e-37
                                    CCCS-SS-SEEEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETTSEEEEEEEEEBEESS-EEEEEEHHHH CS
                DNA_pol3_beta_3   1 krllPkefkkkvtvdlkelkealkRvalladeknrkvrLsleegqlklsaensevgeaeEevdvnyeGeeleiafNvsYl 80 
                                    ++llP+e+++++t+d++el ea+k val+ad + ++vr+++ +g+++lsa++++vg+aeE++ v+y Ge+l+iafN++Yl
  gi|121635885|ref|YP_976108.1| 262 RQLLPTEHTAVATMDVAELIEAIKLVALVAD-RGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYL 340
                                    69****************************5.************************************************ PP

                                    HHHHHHH-SSEEEEEESSTTS-EEEEETTEE CS
                DNA_pol3_beta_3  81 ldalkaleteevelqltdstkpvllsevede 111
                                    +d+l++l +e+v++ +t++ kp+ll++v+ +
  gi|121635885|ref|YP_976108.1| 341 TDGLSSLRSERVSFGFTTAGKPALLRPVSGD 371
                                    **************************98755 PP

>> SEF14_adhesin  SEF14-like adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.21      67     136 ..      45     114 ..      21     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                  SEF14_adhesin  67 irltGshasvsvaGddasvsGGlitvpfkdtaGqvlfrGrinaeiiqdqattivdglapGwrlassqetl 136
                                    + ltGs +++ ++G d  vs          + G vl  Gr+ ++i+++  +  v+    G r+a +  + 
  gi|121635885|ref|YP_976108.1|  45 VLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVGVHVEGNRVALTCGNA 114
                                    679*****************998888888899***********************9999***99876553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2603.22
//
Query:       gi|121635886|ref|YP_976109.1|  [L=385]
Description: recombination protein F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-16   57.9   0.0    1.5e-15   57.2   0.0    1.3  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.3e-07   32.3   0.0    1.7e-07   32.0   0.0    1.2  1  AAA_23       AAA domain
    2.2e-06   27.7   0.1    0.00011   22.1   0.0    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.2e-06   26.7   0.0    5.6e-06   26.3   0.0    1.1  1  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.025   15.1   0.0      0.042   14.4   0.0    1.4  1  ABC_tran     ABC transporter
      0.074   13.0   0.0       0.15   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.077   12.7   0.0       0.17   11.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.081   13.2   0.1        0.2   11.9   0.1    1.7  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.14   11.4   0.0       0.23   10.7   0.0    1.3  1  DUF2813      Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   7.7e-19   1.5e-15       1     196 [.       2     353 ..       2     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 7.7e-19
                                    EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80 
                                    ++++l +++F+s+a   v+l+++++ t+ vGpNG GK+nl++A+ +        + r +    li        +++a ++
  gi|121635886|ref|YP_976109.1|   2 YVRHLGLRDFRSWA--CVDLELHPGRTVFVGPNGYGKTNLIEALWYSTTLG---SHRVSADLPLIRV-----GTDRAVIS 71 
                                    688999*******5..9***************************6643332...4488888889998.....78888899 PP

                                    EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx........................ RF
                          SMC_N  81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtk.kevsellesagiske........................ 135
                                     ++ n++++       + +  ++ ++  ++ ++n+++v++ ++v  +l+ + + +e                        
  gi|121635886|ref|YP_976109.1|  72 TIVVNDGRE-------CAVDLEIATGRVNKARLNRSSVRStRDVVGVLRAVLFAPEdlglvrgdpadrrrylddlaivrr 144
                                    888888888.......99999999999999********9989************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121635886|ref|YP_976109.1| 145 paiaavraeyervvrqrtallksvpgaryrgdrgvfdtlevwdsrlaehgaelvaaridlvnqlapevkkayqllapesr 224
                                    ******************************************************************************** PP

                                    ...................................................................CS-HHHHHHHHHH CS
                                    ...................................................................xxxxxxxxxxxxx RF
                          SMC_N 136 ...................................................................lLSgGektLvala 148
                                                                                                         S Ge   +a+a
  gi|121635886|ref|YP_976109.1| 225 sasigyrasmdvtgpseqsdtdrqllaarllaalaarrdaelergvclvgphrddlilrlgdqpakgFASHGEAWSLAVA 304
                                    ******************************************************************************** PP

                                    HHHH....HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                    xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfA....iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                    L++A    ++    +p+ llD++ a+LD ++++++a+  ++++   Q++v++
  gi|121635886|ref|YP_976109.1| 305 LRLAayqlLRVDGGEPVLLLDDVFAELDVMRRRALATAAESAE---QVLVTA 353
                                    ****77744445679*********************9988887...999886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   8.5e-11   1.7e-07       2      55 ..       6      65 ..       5     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8.5e-11
                         AAA_23  2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks......g 55
                                   L ++ frs+  +++++++g t+++GpNG GKT +++A+ + ++  ++r s +        
  gi|121635886|ref|YP_976109.1|  6 LGLRDFRSWACVDLELHPGRTVFVGPNGYGKTNLIEALWYSTTLGSHRVSADLplirvgT 65
                                   56889***********************************99987777666545554432 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.5e-08   0.00011       2      22 ..      26      46 ..      25      91 .. 0.83
   2 ?   -0.8   0.0      0.55   1.1e+03     142     255 ..     176     262 ..     157     273 .. 0.58
   3 ?    2.2   0.0     0.067   1.3e+02     246     287 ..     308     348 ..     300     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   +v++GpNg GK+nL++al++ 
  gi|121635886|ref|YP_976109.1| 26 TVFVGPNGYGKTNLIEALWYS 46
                                   8*****************975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.55
                         AAA_21 142 kaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergv 221
                                    ++ +++t + w+++l  +g    +   ++i   +   +++k+  q l ++++ + i +++++++   ++           
  gi|121635886|ref|YP_976109.1| 176 DRGVFDTLEVWDSRLAEHGA---ELVAARIDLVNQLAPEVKKAYQLLAPESRSASIGYRASMDVTGPSE----------- 241
                                    44555555555555555544...4444444444555556666666666666666666666654444432........... PP

                         AAA_21 222 vflengdgqelparelSdGtkrll..alltallral 255
                                                    Sd  ++ll  +ll+al++++
  gi|121635886|ref|YP_976109.1| 242 ---------------QSDTDRQLLaaRLLAALAARR 262
                                    ...............388888886667777776665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.067
                         AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                    a + +l  + ++ ++ll+D++ + L+  + r l++  +++++
  gi|121635886|ref|YP_976109.1| 308 AAYQLLRVDGGE-PVLLLDDVFAELDVMRRRALATAAESAEQ 348
                                    444444444444.*************9999999987776654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.8e-09   5.6e-06       1      44 [.       1      44 [.       1      51 [. 0.95

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.8e-09
                         AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileald 44
                                   M+++ + ++ FRs   v+++l +  tv++G+N+ GK++++eal+
  gi|121635886|ref|YP_976109.1|  1 MYVRHLGLRDFRSWACVDLELHPGRTVFVGPNGYGKTNLIEALW 44
                                   8888899999*********************************8 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.1e-05     0.042       4      35 ..      17      47 ..      15     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  4 vslklkegekvaivGenGaGKStLlkllagll 35
                                   v+l+l++g++ ++vG+nG GK+ L+++l   +
  gi|121635886|ref|YP_976109.1| 17 VDLELHPGRT-VFVGPNGYGKTNLIEALWYST 47
                                   6778888865.689************997655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05      0.15      96     133 ..      20      57 ..       7      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                    HCTTSEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpelelktgevsek 133
                                    +l+   +v+vG+ G GK+ Li+al  +++l  + vs++
  gi|121635886|ref|YP_976109.1|  20 ELHPGRTVFVGPNGYGKTNLIEALWYSTTLGSHRVSAD 57 
                                    5777889*****************99999888888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.6e-05      0.17      17      42 ..      19      43 ..      10      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                   +e+++   t+++Gp+G GK+ l+ A+
  gi|121635886|ref|YP_976109.1| 19 LELHPG-RTVFVGPNGYGKTNLIEAL 43
                                   556655.5***************997 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001       0.2      33      87 ..     293     342 ..     287     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                        SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                     S Ge+   +++al +a+ +l++ +        +++LD+ F++lD  ++++l  +
  gi|121635886|ref|YP_976109.1| 293 ASHGEA-WSLAVALRLAAYQLLRVD----GGEPVLLLDDVFAELDVMRRRALATA 342
                                    7999*9.*****************5....3556899*********9999988766 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.23       1      44 [.       1      45 [.       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                        DUF2813  1 myLerieisGFRGinrLSlslee.ntvLiGENaWGKSSLldALsl 44
                                   my +++ +  FR      l+l++  tv++G N +GK  L++AL+ 
  gi|121635886|ref|YP_976109.1|  1 MYVRHLGLRDFRSWACVDLELHPgRTVFVGPNGYGKTNLIEALWY 45
                                   999999999************984699****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2529.72
//
Query:       gi|121635887|ref|YP_976110.1|  [L=187]
Description: hypothetical protein BCG_0004 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-23   83.3   1.2    1.9e-23   82.7   1.2    1.3  1  DciA      Dna[CI] antecedent, DciA
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.15   12.2   0.0    1.2  1  DUF962    Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   1.2   2.1e-27   1.9e-23       1      89 []      75     162 ..      75     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 2.1e-27
                           DciA   1 slgdllerllskrglkkkalalarllqaWeeivGpelaahcrpvklrdgtLvvevesgawateLryqkpqllerlneelg 80 
                                    +lg+++++l++krg++  ++a+ ++l +W+++vG+++a+h+rp  l+dg+L v +es+awat+Lr +++qll+++++++g
  gi|121635887|ref|YP_976110.1|  75 PLGKAARELAKKRGWS-VRVAEGMVLGQWSAVVGHQIAEHARPTALNDGVLSVIAESTAWATQLRIMQAQLLAKIAAAVG 153
                                    6899************.8************************************************************** PP

                           DciA  81 eeavrriri 89 
                                    + +vr+++i
  gi|121635887|ref|YP_976110.1| 154 NDVVRSLKI 162
                                    *******97 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.15      51      88 ..      97     134 ..      46     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                         DUF962  51 fvvgyifafvGHfvfEkrkPAlfknplqsllidplmvl 88 
                                    +v+g   a vGH + E+ +P+ +++ + s++++   ++
  gi|121635887|ref|YP_976110.1|  97 MVLGQWSAVVGHQIAEHARPTALNDGVLSVIAESTAWA 134
                                    566777789****************9999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1188.57
//
Query:       gi|121635888|ref|YP_976111.1|  [L=714]
Description: DNA gyrase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-63  213.9   2.1      2e-63  213.0   2.1    1.5  1  DNA_gyraseB    DNA gyrase B
    2.7e-26   91.5   0.0    6.1e-26   90.4   0.0    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    1.7e-20   73.6   0.0    4.7e-20   72.2   0.0    1.8  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.3e-16   59.0   0.0    1.5e-15   57.2   0.0    1.9  2  Toprim         Toprim domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.033   14.0   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   2.1   5.6e-67     2e-63       1     173 [.     295     464 ..     295     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 5.6e-67
                    DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneya 80 
                                    Gl dfv+++n+ k+++++++++++g+   +   eve+a+qw+ +yse++++F+N+i+t+eGGtH++gf+salt+++n+ya
  gi|121635888|ref|YP_976111.1| 295 GLVDFVKHINRTKNAIHSSIVDFSGKG--TG-HEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYA 371
                                    89************************9..77.89********************************************** PP

                    DNA_gyraseB  81 kkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekave 160
                                    k++kllk+k+ +++g+diregl av+svk+ epqFeGQTK+kLgn+evks+v+kv +e+l++++e n++++k +++kav+
  gi|121635888|ref|YP_976111.1| 372 KDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVS 451
                                    ******************************************************************************** PP

                    DNA_gyraseB 161 aakareaarkare 173
                                    +a+ar+aarkare
  gi|121635888|ref|YP_976111.1| 452 SAQARIAARKARE 464
                                    ***********98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.7e-29   6.1e-26       5      62 ..     645     702 ..     641     703 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.7e-29
                  DNA_gyraseB_C   5 eiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefi 62 
                                     iqR+KGLGEm++++LweTTmdp+ R L qvt++da++adelfs+LmG++v++Rr+fi
  gi|121635888|ref|YP_976111.1| 645 GIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFI 702
                                    69*******************************************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.3e-23   4.7e-20       3     110 ..      78     216 ..      76     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.3e-23
                                    HHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.............GTCSTTCHHCST CS
                      HATPase_c   3 ekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk.............klfekfsqddst 67 
                                    e++L+++i+++vdNav++  a++a+++ v +   e d  ++v D+G+Gip++ +              + ++kf++ d++
  gi|121635888|ref|YP_976111.1|  78 ERGLHHLIWEVVDNAVDEamAGYATTVNVVLL--E-DGGVEVADDGRGIPVATHAsgiptvdvvmtqlHAGGKFDS-DAY 153
                                    899***************65559999999999..6.******************************666666****.*** PP

                                    CHTSTSSSHHHHHHHHHHHHTTTEEEE..........EEET..........TTEEEEEEEEES CS
                      HATPase_c  68 krggggtGlGlsivkklvelmgGeiwv..........esep..........grGttftftlpl 110
                                    +++gg +G+G+s+v++l+++++ ei++          +sep          + G+t++f+++ 
  gi|121635888|ref|YP_976111.1| 154 AISGGLHGVGVSVVNALSTRLEVEIKRdgyewsqvyeKSEPlglkqgaptkKTGSTVRFWADP 216
                                    ****************9999999999999999999985555555544445567******9986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   4.2e+03       8      45 ..     149     193 ..     149     216 .. 0.78
   2 !   57.2   0.0   4.3e-19   1.5e-15       1     101 [.     493     603 ..     493     605 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                    HHHHHHHHHTHTSTEEEEEEESSSSEEEHS.....TTEEEEE..E CS
                         Toprim   8 psdaktiakalgsgfqavtaslGhildlet.....efkpvye..e 45 
                                    +sda +i+  l + ++ v+  l + l++e      e+++vye  e
  gi|121635888|ref|YP_976111.1| 149 DSDAYAISGGLHGVGVSVVNALSTRLEVEIkrdgyEWSQVYEksE 193
                                    589999999999888889988888888888888999999988441 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 4.3e-19
                                    EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEECSS CS
                         Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiilatDp 72 
                                    el++vEg+s+ +++++ ++s fqa+++++G+i+++e+ ++++v++  e++ ++++l++     ++  ++r+++i+l+ D+
  gi|121635888|ref|YP_976111.1| 493 ELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKaRIDRVLKntEVQAIITALGTgihdeFDIGKLRYHKIVLMADA 572
                                    69***********************************8888888888899999999989999999999************ PP

                                    SHHHHHHHHHHHHHHT....HHHTTTEEEEEES CS
                         Toprim  73 DreGeaiawellevlk....ellenkigrvefs 101
                                    D++G++i+++ll++l     +l+en  g+v+ +
  gi|121635888|ref|YP_976111.1| 573 DVDGQHISTLLLTLLFrfmrPLIEN--GHVFLA 603
                                    ************9988777788888..887766 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.3e-06     0.033       7      50 ..      85     128 ..      80     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.3e-06
                    HATPase_c_3   7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseeel 50 
                                    + e+vdN++d    + a++v++++ ++    g + + DdG G++ ++ 
  gi|121635888|ref|YP_976111.1|  85 IWEVVDNAVDeamaGYATTVNVVLLED----GGVEVADDGRGIPVATH 128
                                    6799****9997767788999999996....69**********97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 4497.39
//
Query:       gi|121635889|ref|YP_976112.1|  [L=838]
Description: DNA gyrase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.2e-147  491.4   0.0   2.8e-147  491.1   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
      3e-70  231.5  12.9    4.7e-12   45.2   0.1    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.086   12.5   0.4       0.16   11.6   0.4    1.3  1  TPD52          Tumour protein D52 family
       0.11   12.3   0.4          1    9.1   0.0    2.7  3  dCache_1       Cache domain
       0.49   10.8   2.5        1.1    9.6   2.5    1.7  1  Nnf1           Nnf1


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.1   0.0  7.7e-151  2.8e-147       1     425 [.      39     483 ..      39     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 491.1 bits;  conditional E-value: 7.7e-151
                  DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGs 79 
                                    Ra+P+vrDGlKPv+Rr+Lyamf+   ++d+++ K+a+ v+e++g+YhPHGdas+yd++vr+aq +++++pl+d+qGnfGs
  gi|121635889|ref|YP_976112.1|  39 RALPEVRDGLKPVHRRVLYAMFDSgFRPDRSHAKSARSVAETMGNYHPHGDASIYDTLVRMAQPWSLRYPLVDGQGNFGS 118
                                    9******************************************************************************* PP

                  DNA_topoisoIV  80 ildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkei 159
                                       +d++Aa+RY+e+rL+++a e+l+eid+etvd+ +nyDg+ +EP+vlp+++PnlL+nG+ GIavGmat+ipphnl+e+
  gi|121635889|ref|YP_976112.1| 119 P-GNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLREL 197
                                    *.99999************************************************************************* PP

                  DNA_topoisoIV 160 idaliallkgeea.......ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie....e.ktivitElPig 227
                                     da+   l++++a        ++  v+gPdfpt g i+g++++++ay+tgrG+i++r+ ve+e    + +++vitElP++
  gi|121635889|ref|YP_976112.1| 198 ADAVFWALENHDAdeeetlaAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEedsrGrTSLVITELPYQ 277
                                    **********9999999787778889************************************99998459********** PP

                  DNA_topoisoIV 228 vntskliekieelvkkkkik.isdirde.sdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpkyls 304
                                    vn +++i +i+e v+++k+  is+i+d+ sdr g+rivie+kr+a +++v+++lyk+t+L++s+ +n+l+++d+ p++l 
  gi|121635889|ref|YP_976112.1| 278 VNHDNFITSIAEQVRDGKLAgISNIEDQsSDRvGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLR 357
                                    ****************************9999************************************************ PP

                  DNA_topoisoIV 305 lkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeylle 382
                                    l ++++++++++l+v+ rr++y+l+k++er++il+gl+kal+ +devi++ir+s++ + a++ Lie   ++e qa+++l+
  gi|121635889|ref|YP_976112.1| 358 LDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELldIDEIQAQAILD 437
                                    ******************************************************************98899********* PP

                  DNA_topoisoIV 383 mrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                    m+lrrL+++e++++ ++++++e+ei++le++lak   ++ ++++el
  gi|121635889|ref|YP_976112.1| 438 MQLRRLAALERQRIIDDLAKIEAEIADLEDILAKperQRGIVRDEL 483
                                    ********************************99776666666665 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   1.3e-15   4.7e-12       1      48 []     515     562 ..     515     562 .. 0.97
   2 !   33.9   0.0   4.4e-12   1.6e-08       1      41 [.     565     608 ..     565     615 .. 0.83
   3 !   33.5   0.0   6.1e-12   2.2e-08       2      48 .]     622     666 ..     621     666 .. 0.96
   4 !   40.6   0.0   3.7e-14   1.3e-10       1      47 [.     669     717 ..     669     718 .. 0.97
   5 !   43.7   0.3   3.8e-15   1.4e-11       2      48 .]     722     769 ..     721     769 .. 0.96
   6 !   38.4   0.4   1.7e-13     6e-10       2      45 ..     773     816 ..     772     818 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.3e-15
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                    d +++iT+ Gy+kr++ + +++q+Rg+kGv+g  lk +d + + +v+s
  gi|121635889|ref|YP_976112.1| 515 DVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCS 562
                                    679******************************************996 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4.4e-12
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdkl 41 
                                    d +l++T +G+v+r ++++lpe +R+a+G+++     + +++++
  gi|121635889|ref|YP_976112.1| 565 DLILFFTTQGRVYRAKAYDLPEASRTARGQHVAnllAFQPEERI 608
                                    779*****************************955555555555 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 6.1e-12
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                    +l+l+T+nG vk+ +l ++ + + g  G+ +++l+++d+lv+++++s
  gi|121635889|ref|YP_976112.1| 622 YLVLATRNGLVKKSKLTDFDSNRSG--GIVAVNLRDNDELVGAVLCS 666
                                    89*********************99..****************9986 PP

  == domain 4  score: 40.6 bits;  conditional E-value: 3.7e-14
                                    SEEEEEETTSEEEEEEG..GGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfpl..selpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    d+lll++ nG+ +rf++  + l+++gR+++Gv+g++++ +d+l s+ vv
  gi|121635889|ref|YP_976112.1| 669 DDLLLVSANGQSIRFSAtdEALRPMGRATSGVQGMRFNIDDRLLSLNVV 717
                                    89********************************************998 PP

  == domain 5  score: 43.7 bits;  conditional E-value: 3.8e-15
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEES CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvvs 48 
                                    +ll++Ts Gy+kr+ ++e+p+qgRg+kGv  + ++ + ++lv++l+v+
  gi|121635889|ref|YP_976112.1| 722 YLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRrGRLVGALIVD 769
                                    8*******************************999999*******995 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 1.7e-13
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEE CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvl 45 
                                    el  +Ts G v+r+ + +++  gR +kGv++++l egd l +++
  gi|121635889|ref|YP_976112.1| 773 ELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIA 816
                                    57789***********************************9986 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   4.5e-05      0.16      17      58 ..     438     477 ..     424     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                          TPD52  17 vsaseptlteeereeLkseLakleeeivtLrqvLaakekhla 58 
                                    +++    l+  er+ +  +Lak+e+ei+ L+++La  e++  
  gi|121635889|ref|YP_976112.1| 438 MQLR--RLAALERQRIIDDLAKIEAEIADLEDILAKPERQRG 477
                                    3333..59999************************9999865 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.58   2.1e+03     122     152 ..     270     298 ..     258     302 .. 0.72
   2 ?    9.1   0.0   0.00028         1      12     118 ..     441     542 ..     429     556 .. 0.76
   3 ?   -1.1   0.1      0.37   1.3e+03      76      85 ..     670     679 ..     606     769 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.58
                       dCache_1 122 visdp.yvdqtggkpvitiavpiyddsgkfiG 152
                                    vi+++ y+ +  ++ +++ia++++d  gk  G
  gi|121635889|ref|YP_976112.1| 270 VITELpYQVNH-DNFITSIAEQVRD--GKLAG 298
                                    55555254444.89*********97..88777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00028
                       dCache_1  12 lglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGqviassd 91 
                                      la +  + i d+l+++e      a+  +l d l +p+r     r ++++ l +i++++ d +   ++ adG+v   sd
  gi|121635889|ref|YP_976112.1| 441 RRLAALERQRIIDDLAKIE------AEIADLEDILAKPER----QRGIVRDELAEIVDRHGDDRRTRIIAADGDV---SD 507
                                    5556666666666666666......666789999***998....9******************************...33 PP

                       dCache_1  92 pssppnleg........tddpadrdwykealaggg 118
                                    ++ +    +        +++ +++d+y+  + gg+
  gi|121635889|ref|YP_976112.1| 508 EDLIAREDVvvtitetgYAKRTKTDLYRSQKRGGK 542
                                    33333333345666667778888888888777774 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.37
                       dCache_1  76 gvylvdadGq 85 
                                    ++ lv+a+Gq
  gi|121635889|ref|YP_976112.1| 670 DLLLVSANGQ 679
                                    3344444444 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.5   0.00031       1.1      29     106 ..     392     470 ..     368     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                                    TTHHHHHHHHHHHHHHHHCCHH-T..............TTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  29 rdvvekLneLDdlieeAkerreegeeeasrpe....vpphtLpPeeliaahlapakkeeqeeLearlqeleaenaelaee 104
                                    r++v+ L++LD++i+  +  +     +  r+      ++++ +++ +++ +l+++ + e++++   l+++eae a+l++ 
  gi|121635889|ref|YP_976112.1| 392 RGLVKALDALDEVIALIRASETV---DIARAGlielLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDI 468
                                    789********999966654443...22233345579999************************************9987 PP

                                    HH CS
                           Nnf1 105 ve 106
                                    ++
  gi|121635889|ref|YP_976112.1| 469 LA 470
                                    65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 5135.00
//
Query:       gi|121635890|ref|YP_976113.1|  [L=304]
Description: hypothetical protein BCG_0007 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-41  139.9   6.5    5.6e-41  139.6   6.5    1.1  1  DUF3566    Transmembrane domain of unknown function (DUF3566)
  ------ inclusion threshold ------
      0.034   14.4   4.5      0.047   13.9   4.0    1.5  1  DUF2189    Predicted integral membrane protein (DUF2189)
       0.22   10.3   0.0        0.3    9.9   0.0    1.0  1  Anoctamin  Calcium-activated chloride channel
        2.4    8.4   5.4       0.42   10.8   0.5    1.9  2  DUF3270    Protein of unknown function (DUF3270)


Domain annotation for each model (and alignments):
>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   6.5   1.2e-44   5.6e-41       2     118 .]     187     302 ..     186     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.2e-44
                        DUF3566   2 rrarlqlsrvdpwSvlklsfllsvalfivlvvavavlylvldalgvfdkvnslvkdlvgeessldleevlslgrvlslaa 81 
                                     ra++q++r+dpwS+lk+s+llsvalf+v+++ va+lylvl ++gv+ k+ns v+dl +++s  + +e++s g++++ a+
  gi|121635890|ref|YP_976113.1| 187 VRASMQIRRIDPWSTLKVSLLLSVALFFVWMITVAFLYLVLGGMGVWAKLNSNVGDLLNNAS-GSSAELVSSGTIFGGAF 265
                                    599*********************************************************95.556699*********** PP

                        DUF3566  82 lvgvvnvvlltalatlaallYNlvadlvGGlevtLad 118
                                    l+g+vn+vl+talat++a++YNl++dl+GG+evtLad
  gi|121635890|ref|YP_976113.1| 266 LIGLVNIVLMTALATIGAFVYNLITDLIGGIEVTLAD 302
                                    ***********************************98 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.0     1e-05     0.047      43     111 ..     198     267 ..     174     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                        DUF2189  43 anassllllglllallfllWvraaallfallfgtapleslsafledvlltpeg..laflivgllvGavlAa 111
                                     ++  l +  ll ++lf++W++++a+l+ +l g ++ ++l++ + d+l ++ g   +++  g+++G+++ +
  gi|121635890|ref|YP_976113.1| 198 PWS-TLKVSLLLSVALFFVWMITVAFLYLVLGGMGVWAKLNSNVGDLLNNASGssAELVSSGTIFGGAFLI 267
                                    222.3444445667899****************99999999999998877665225688889999998865 PP

>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   6.6e-05       0.3      89     185 ..     174     290 ..     163     292 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.6e-05
                      Anoctamin  89 prpefrgelkrespvtgee.efyyppwkrrlfrllvslplvllliclavvgvlilrclal.qelvssvke.......... 156
                                     r +  ++++r  pv  ++    ++pw+ + + ll+s++l++++++++ +  l+l+ + + ++l s+v +          
  gi|121635890|ref|YP_976113.1| 174 ARVQLSARRSRG-PVRASMqIRRIDPWSTLKVSLLLSVALFFVWMITVAFLYLVLGGMGVwAKLNSNVGDllnnasgssa 252
                                    567777666643.4544441345699**9999******988855554444444444355446666666667777777777 PP

                      Anoctamin 157 .......lls...flptvlnlvlililnevykklaiwlt 185
                                           +     fl  ++n+vl+++l+ +   +   +t
  gi|121635890|ref|YP_976113.1| 253 elvssgtI-FggaFLIGLVNIVLMTALATIGAFVYNLIT 290
                                    76555441.045699999999999999877666655555 PP

>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   9.5e-05      0.42      43      70 ..     208     235 ..     203     245 .. 0.87
   2 ?   -0.7   0.4      0.37   1.7e+03      58      78 ..     272     292 ..     264     299 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                        DUF3270  43 ariAvFsvitvlvsfillalklatllAf 70 
                                    + +A+F v ++ v+f++l+l    ++A 
  gi|121635890|ref|YP_976113.1| 208 LSVALFFVWMITVAFLYLVLGGMGVWAK 235
                                    579*****************99999985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                        DUF3270  58 illalklatllAfllAilisl 78 
                                    i l + lat+ Af+  +++ l
  gi|121635890|ref|YP_976113.1| 272 IVLMTALATIGAFVYNLITDL 292
                                    455566999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1991.15
//
Query:       gi|121635891|ref|YP_976114.1|  [L=145]
Description: hypothetical protein BCG_0008c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-66  220.2   6.9    9.3e-66  220.0   6.9    1.0  1  CwsA      Cell wall synthesis protein CwsA
     0.0065   16.2   0.8     0.0087   15.8   0.8    1.1  1  DotU      Type VI secretion system protein DotU
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.039   13.8   0.0    1.3  1  VirB8     VirB8 protein
      0.055   13.4   0.2      0.073   13.0   0.2    1.1  1  RUN       RUN domain


Domain annotation for each model (and alignments):
>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.0   6.9   2.1e-69   9.3e-66       1     132 []       9     145 .]       9     145 .] 0.99

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 2.1e-69
                           CwsA   1 ltprerltrGlkysavGPvdvtrGv....vglgvesaqstaeelrrryresrlarelaaaqeaiaqelaaaqevvaglPq 76 
                                    ltprerltrGl+ysavGPvdvtrG+    vglg++sa+sta+ lrrryre+rlare+aaaqe++aqel+aaq+vva+lPq
  gi|121635891|ref|YP_976114.1|   9 LTPRERLTRGLAYSAVGPVDVTRGLlelgVGLGLQSARSTAAGLRRRYREGRLAREVAAAQETLAQELTAAQDVVANLPQ 88 
                                    8***********************9898899************************************************* PP

                           CwsA  77 aledarkkrrrkrp.lllagvavavlaGGavafsivrrssrPePsslpPsvdvsPkp 132
                                    al+dar++rr+k++ +++ag+a+a+laGGavafsivrrssrPePs++pPsv+v+P+p
  gi|121635891|ref|YP_976114.1|  89 ALQDARTQRRSKHHlWIFAGIAAAILAGGAVAFSIVRRSSRPEPSPRPPSVEVQPRP 145
                                    ************9989***************************************98 PP

>> DotU  Type VI secretion system protein DotU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   1.9e-06    0.0087     126     203 ..      51     122 ..      46     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                           DotU 126 GFeGryrleadgeeelealrqrlyeeirrlrgeaeealsphwqagdeaarrllrrelplwvilalallvllllflgls 203
                                    G + ryr e + ++e +a  ++l++e++++++ ++ +l ++ q  d++ +r++  +  lw+++++a+++l++  +++s
  gi|121635891|ref|YP_976114.1|  51 GLRRRYR-EGRLAREVAAAQETLAQELTAAQDVVA-NLPQALQ--DARTQRRS--KHHLWIFAGIAAAILAGGAVAFS 122
                                    6666898.44677799************7665555.4555544..44444443..4469************8877776 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-06     0.039      11      49 ..      94     132 ..      88     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          VirB8  11 gsarvqarnwrlvafvslliavlavgavvlllplktveP 49 
                                    + +r+++++++++a+++++i ++ ++a+ ++ +++++eP
  gi|121635891|ref|YP_976114.1|  94 RTQRRSKHHLWIFAGIAAAILAGGAVAFSIVRRSSRPEP 132
                                    6789****************9999999999999998888 PP

>> RUN  RUN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.6e-05     0.073      12      85 ..      50     114 ..      42     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                            RUN  12 hGLrrssesllralglkkessfwallekvakllteaesllsav.qelealhsskkrsadgkfrawirlaLnekkL 85 
                                     GLrr      r+++ +  ++++a+ e +a+ lt a++++ ++ q+l++++++     ++k ++wi ++  +  L
  gi|121635891|ref|YP_976114.1|  50 AGLRR------RYREGRLAREVAAAQETLAQELTAAQDVVANLpQALQDARTQ----RRSKHHLWIFAGIAAAIL 114
                                    69999......9**************************988874566666666....8*********99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 975.32
//
Query:       gi|121635892|ref|YP_976115.1|  [L=182]
Description: iron-regulated peptidyl-prolyl cis-trans isomerase A ppiA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-48  164.0   0.1    3.7e-48  163.8   0.1    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.1     2e-52   3.7e-48       2     157 ..      17     180 ..      16     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2e-52
                  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkeg................fYdgttFhRvikgfmvqgGdptgktsageq 65 
                                    ++++t+ +G+i+i Lf+++aPktv+nF+ l++ g                fYdg +FhRvi+gfm+qgGdptg+++    
  gi|121635892|ref|YP_976115.1|  17 ATLHTN-RGDIKIALFGNHAPKTVANFVGLAQ-GtkdystqnasggpsgpFYDGAVFHRVIQGFMIQGGDPTGTGR---- 90 
                                    578997.************************6.55788888888999999***********************966.... PP

                  Pro_isomerase  66 ekkggesiraipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVv..eGmdvvekiekvet 142
                                       gg   ++++dE++++l++ k+++lama++g  p ++gsqFfIt++++phl++++t+FG+V+  e+++vve+i+k+ t
  gi|121635892|ref|YP_976115.1|  91 ---GG-PGYKFADEFHPELQFdKPYLLAMANAG--PGTNGSQFFITVGKTPHLNRRHTIFGEVIdaESQRVVEAISKTAT 164
                                    ...33.23689*****77676699*******98..8****************************999************* PP

                  Pro_isomerase 143 de.erpkknvkivsae 157
                                    d+ +rp+++v+i+s++
  gi|121635892|ref|YP_976115.1| 165 DGnDRPTDPVVIESIT 180
                                    ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1348.04
//
Query:       gi|121635893|ref|YP_976116.1|  [L=111]
Description: hypothetical protein BCG_0010c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-12   45.0   0.7    1.5e-11   44.2   0.7    1.4  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.7   8.4e-16   1.5e-11       1      45 [.      58     108 ..      58     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.4e-16
                          bPH_6   1 RprvrvdpdGvevrnlfrtrrlpWsaiagvrfpegrrl......arldlrd 45 
                                    Rpr++++pdG+++r++frt++l+ s i+ +r++e+rr+      +++++ +
  gi|121635893|ref|YP_976116.1|  58 RPRLAITPDGLAIRGWFRTQLLRHSNIKIIRIDEFRRYgrlvrlLEIETVS 108
                                    9******************************99999998888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 820.70
//
Query:       gi|121635894|ref|YP_976117.1|  [L=93]
Description: septation inhibitor protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  101.5   4.4    2.2e-29  101.3   4.4    1.0  1  CrgA          Cell division protein CrgA
     0.0029   17.0   1.1     0.0033   16.8   0.1    1.5  2  DUF3273       Protein of unknown function (DUF3273)
  ------ inclusion threshold ------
          8    6.3   5.8        4.9    7.0   4.4    1.5  2  Myc_target_1  Myc target protein 1


Domain annotation for each model (and alignments):
>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   4.4   3.8e-33   2.2e-29       1      88 []       1      93 []       1      93 [] 0.94

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3.8e-33
                           CrgA  1 mpkskvrkkaeytpkaaertpvkakaakpsprwyvpvmlglmllGllwlvvyYlage......eipfmaelgawNlliGfgl 76
                                   mpkskvrkk+++t +a +rtp k+k   ps+ w+v +++glml+Gl+wl+v+ la+        +++ma+lg wN++i+f++
  gi|121635894|ref|YP_976117.1|  1 MPKSKVRKKNDFTVSAVSRTPMKVK-VGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIgsqaptALNWMAQLGPWNYAIAFAF 81
                                   9**********************98.****************************987775555556**************** PP

                           CrgA 77 iivGllmttrWr 88
                                   +i+Gll+t+rW+
  gi|121635894|ref|YP_976117.1| 82 MITGLLLTMRWH 93
                                   ***********7 PP

>> DUF3273  Protein of unknown function (DUF3273)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.6e-07    0.0033      51      90 ..      14      53 ..       4      56 .. 0.83
   2 ?   -2.1   0.1      0.31   1.8e+03     185     199 ..      73      87 ..      71      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-07
                        DUF3273 51 aldlvklaeevkvgsaptlvvslliglyllGtlllmvfqv 90
                                   +  +  ++ +vkvg ++++ vsl+igl+l+G + lmvfq 
  gi|121635894|ref|YP_976117.1| 14 VSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQL 53
                                   34456678999***************************95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.31
                        DUF3273 185 lgylnlvlfvlagll 199
                                    + y+ +++f+++gll
  gi|121635894|ref|YP_976117.1|  73 WNYAIAFAFMITGLL 87 
                                    667777777777776 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.4   0.00082       4.9      25      44 ..      32      51 ..      10      66 .. 0.87
   2 ?   -1.9   0.0      0.43   2.5e+03      10      35 ..      64      88 ..      53      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00082
                   Myc_target_1 25 FcvSmvvGLllgaliyvllt 44
                                   ++vS+ +GL+l +li++++ 
  gi|121635894|ref|YP_976117.1| 32 WFVSLFIGLMLIGLIWLMVF 51
                                   579*************9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                   Myc_target_1 10 leilesfdledlilaFcvSmvvGLll 35
                                   l++  +++  +  +aF+  m+ GLll
  gi|121635894|ref|YP_976117.1| 64 LNWMAQLGPWNYAIAFAF-MITGLLL 88
                                   555556666667778865.7788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 706.59
//
Query:       gi|121635895|ref|YP_976118.1|  [L=262]
Description: hypothetical protein BCG_0012 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-37  128.4   0.0    2.8e-37  127.8   0.0    1.3  1  DUF881      Bacterial protein of unknown function (DUF881)
  ------ inclusion threshold ------
       0.13   12.1   0.1       0.22   11.4   0.1    1.3  1  DASH_Spc19  Spc19


Domain annotation for each model (and alignments):
>> DUF881  Bacterial protein of unknown function (DUF881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.0   3.1e-41   2.8e-37       4     145 .]     105     255 ..     102     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 3.1e-41
                         DUF881   4 elkllaGltpveGpGvtitlddakkaeeeaeee........vhdedLldvvneLraaGAeaIsingqRivatsaircagn 75 
                                    el+  a++ pv+GpG+++tl+da+++++ +  +        vh++d+ +v+n+L++aGAeaI++++qRi+a s  rc+gn
  gi|121635895|ref|YP_976118.1| 105 ELAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRdaspddlvVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGN 184
                                    6777899****************9996665555999******************************************** PP

                         DUF881  76 ailvdgrrispPyeikaIGdpekLesalniseavggllellke.glsvtvekseevtipayrgplelkyak 145
                                    ++l++gr++spPy+i aIGd++++++al++ + v  + +++ + gl ++ e + +++i  y +p+++++a+
  gi|121635895|ref|YP_976118.1| 185 TLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRfGLGYREEVHPDLQIVGYADPVRMHFAQ 255
                                    *****************************************9889********************999885 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.4e-05      0.22      62     100 ..      56      94 ..      49     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                                    TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                     DASH_Spc19  62 ePqieellekaekeleklerreetLkaklelqegrlsna 100
                                    +P + +l+++a++++++l++++e+L ++++   gr  ++
  gi|121635895|ref|YP_976118.1|  56 APRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDT 94 
                                    689999**************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1816.08
//
Query:       gi|121635896|ref|YP_976119.1|  [L=232]
Description: para-aminobenzoate synthase component II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-48  165.1   0.0    1.8e-48  164.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.4e-12   47.9   0.1    8.1e-12   45.3   0.1    2.0  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.0     2e-52   1.8e-48       2     187 ..       5     189 ..       4     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 2e-52
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETH CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspg.vegkieaikearenkiPiLGICL 79 
                                    ++Dnyds++ nlv++l +lg++ ev+++d   +  +   + ++dg+l+s+Gpg+p+ ++ ++++++ ++ +++P+LG+CL
  gi|121635896|ref|YP_976119.1|   5 VVDNYDSFVFNLVQYLGQLGIEAEVWRNDDHRLSDEAaVAGQFDGVLLSPGPGTPErAGASVSMVHACAAAHTPLLGVCL 84 
                                    89***************************988888655699*************************************** PP

                                    HHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEE CS
                         GATase  80 GmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiie 159
                                    G+Q+++ +fg++v ++  +  hg+t+ + +++ ++l+gl+++++++++H++++ p +++pa l+vta+++++  +m++++
  gi|121635896|ref|YP_976119.1|  85 GHQAIGVAFGATVDRAP-ELLHGKTSSVFHTNVGVLQGLPDPFTATRYHSLTILP-KSLPAVLRVTARTSSG-VIMAVQH 161
                                    *****************.9***********999*********************9.99***********988.9****** PP

                                    ETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                         GATase 160 kknpfvgvQFHPEststpegpellfnfl 187
                                       p++gvQFHPEs++t++g+++l+n l
  gi|121635896|ref|YP_976119.1| 162 TGLPIHGVQFHPESILTEGGHRILANWL 189
                                    ************************9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   9.1e-16   8.1e-12      86     216 .]      57     174 ..      50     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 9.1e-16
                  Peptidase_C26  86 adpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgs 165
                                     +peR   ++ +++a+ ++++P+lg+C+G+q + va+G t+ ++ e    l  h       ++ +v  ++ ++l+ l   
  gi|121635896|ref|YP_976119.1|  57 GTPERAGASVSMVHACAAAHTPLLGVCLGHQAIGVAFGATVDRAPE----LL-HG------KTSSVFHTNVGVLQGLPD- 124
                                    57899999*****************************988766555....33.32......334455566788999988. PP

                  Peptidase_C26 166 eeievnslHhqai..kelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                      +  + +H+ +i  k l   lrv+A+++ gvi a++++    ++ gvQ+HPE
  gi|121635896|ref|YP_976119.1| 125 -PFTATRYHSLTIlpKSLPAVLRVTARTSSGVIMAVQHTG--LPIHGVQFHPE 174
                                    .899999*****96667***********************..56********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1547.16
//
Query:       gi|121635897|ref|YP_976120.1|  [L=196]
Description: RNA polymerase sigma factor SigM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-16   59.7   3.0    3.6e-16   58.7   3.0    1.5  1  Sigma70_r2    Sigma-70 region 2
    1.3e-15   56.8   0.5    1.3e-15   56.8   0.5    2.2  3  Sigma70_r4_2  Sigma-70, region 4
    9.6e-09   35.4   4.3    3.1e-05   23.9   0.3    2.1  2  Sigma70_ECF   ECF sigma factor
    1.4e-07   30.9   0.1    3.6e-07   29.6   0.1    1.7  1  Sigma70_r4    Sigma-70, region 4
     0.0056   16.5   0.3      0.019   14.7   0.3    2.0  1  HTH_23        Homeodomain-like domain
     0.0056   16.8   1.5      0.011   15.8   0.3    2.2  2  HTH_28        Helix-turn-helix domain
     0.0084   16.0   0.0      0.021   14.7   0.0    1.7  1  Terminase_5   Putative ATPase subunit of terminase (gpP-like)
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.084   12.7   0.0    1.6  1  DUF746        Domain of Unknown Function (DUF746)
      0.064   12.8   0.0       0.21   11.1   0.0    1.8  2  GerE          Bacterial regulatory proteins, luxR family
      0.099   13.2   0.1       0.16   12.5   0.1    1.3  1  DUF134        Protein of unknown function  DUF134


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   3.0     2e-19   3.6e-16       1      69 [.      39     105 ..      39     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2e-19
                                    HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69 
                                    l++r++++++rlar   + ++da+D +Q+a+l ++r++ +f+ + +  +s+wl+ri+ na++drlR+++
  gi|121635897|ref|YP_976120.1|  39 LFRRHHRQLHRLARLTSRTSEDADDALQDAMLSAHRGAGSFRYDAA--VSSWLHRIVVNACLDRLRRAK 105
                                    79************99**************************5555..*******************87 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1     2e+03      41      49 ..      83      91 ..      82      93 .. 0.85
   2 ?   -3.5   0.3         5   8.9e+03      46      53 ..     100     107 ..      99     107 .. 0.75
   3 !   56.8   0.5     7e-19   1.3e-15       3      54 .]     130     181 ..     128     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHH CS
                   Sigma70_r4_2 41 gtVksrlsR 49
                                   ++V s+l+R
  gi|121635897|ref|YP_976120.1| 83 AAVSSWLHR 91
                                   689*****9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                                    HHHHHHHH CS
                   Sigma70_r4_2  46 rlsRArkk 53 
                                    rl+RA+++
  gi|121635897|ref|YP_976120.1| 100 RLRRAKAH 107
                                    68888875 PP

  == domain 3  score: 56.8 bits;  conditional E-value: 7e-19
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    a+++al +Lp +qr++++  +++g+s++++A++lg+ egtVksr +RAr++L
  gi|121635897|ref|YP_976120.1| 130 AVQRALMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    799***********************************************98 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   3.5e-05     0.062       5      54 ..      22      73 ..      18      81 .. 0.90
   2 !   23.9   0.3   1.7e-08   3.1e-05     129     181 ..     130     183 ..      98     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                    Sigma70_ECF  5 telleqvkdGdaeaaeqllelvydeLrrlagskl.knerreetledtaL.vf 54
                                   +ell +   Gd  a +ql+++ + +L rla+     +e +++ l+d  L ++
  gi|121635897|ref|YP_976120.1| 22 AELLAAHVAGDRYAFDQLFRRHHRQLHRLARLTSrTSEDADDALQDAMLsAH 73
                                   678999999**********************99989999*******999666 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.7e-08
                    Sigma70_ECF 129 aler.llsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawler 181
                                    a++r l++l++eq+  v    ++G+s++++A  lgv++ tv+ r a aRa+l+r
  gi|121635897|ref|YP_976120.1| 130 AVQRaLMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARLAR 183
                                    455426679*****************************************9976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1     2e-10   3.6e-07       1      48 [.     134     181 ..     134     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2e-10
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    aL +Lp ++r  ++ +  +g++ ++++++lg+ +++V+++ +rA+ +L
  gi|121635897|ref|YP_976120.1| 134 ALMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    799******************************************999 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.1e-05     0.019      10      40 ..     145     176 ..     133     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                         HTH_23  10 illlla.eGlsvreIAreLgvsrrTvyrwlkr 40 
                                    ++ +++ +G+s+++ Ar+Lgv + Tv     r
  gi|121635897|ref|YP_976120.1| 145 AVVAVDmQGYSIADTARMLGVAEGTVKSRCAR 176
                                    56666667******************855555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   4.5e+03      28      35 ..      84      91 ..      81      92 .. 0.83
   2 !   15.8   0.3   6.2e-06     0.011       6      40 ..     146     180 ..     129     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                         HTH_28 28 tvyrWikr 35
                                    v++W++r
  gi|121635897|ref|YP_976120.1| 84 AVSSWLHR 91
                                   6899*998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.2e-06
                         HTH_28   6 iklla.aGhsvreaArelgisrrtvyrWikryeegG 40 
                                    + ++  +G s++++Ar lg+ + tv++ + r ++  
  gi|121635897|ref|YP_976120.1| 146 VVAVDmQGYSIADTARMLGVAEGTVKSRCARARA-R 180
                                    455554788**********************998.4 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.021      12      38 ..     152     178 ..     142     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                    Terminase_5  12 qGyrvaeIAeelglkeatVysWkkrde 38 
                                    qGy++a+ A++lg+ e tV s + r +
  gi|121635897|ref|YP_976120.1| 152 QGYSIADTARMLGVAEGTVKSRCARAR 178
                                    9*******************9888866 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05     0.084      11      43 ..     152     184 ..     141     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                         DUF746  11 qplslaeaadllgtdegiiakwvreFrewllqL 43 
                                    q  s+a+ a++lg+ eg+++ + ++ r++l++L
  gi|121635897|ref|YP_976120.1| 152 QGYSIADTARMLGVAEGTVKSRCARARARLARL 184
                                    6679*************************9987 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.77   1.4e+03      39      55 ..     132     148 ..     129     150 .. 0.84
   2 ?   11.1   0.0   0.00012      0.21      15      45 ..     151     181 ..     142     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.77
                                    HHHHHHHT-SSHHHHHH CS
                           GerE  39 snimkKLnvksrvelvr 55 
                                    ++++++L v+ r+++v 
  gi|121635897|ref|YP_976120.1| 132 QRALMRLPVEQRAAVVA 148
                                    68999*****9999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                                    CTTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                           GerE  15 aeGksnkeIAeelniSekTVkvhksnimkKL 45 
                                    ++G+s  + A+ l+++e TVk+  +++  +L
  gi|121635897|ref|YP_976120.1| 151 MQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    79*********************99998887 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.9e-05      0.16      34      80 ..     137     183 ..     114     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                         DUF134  34 aisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiak 80 
                                     + +++  a+  vd + ++  ++a+++G+++ t+ +  + ar ++a 
  gi|121635897|ref|YP_976120.1| 137 RLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARLAR 183
                                    566788889999********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1476.65
//
Query:       gi|121635898|ref|YP_976121.1|  [L=254]
Description: hypothetical protein BCG_0018 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1729.61
//
Query:       gi|121635899|ref|YP_976122.1|  [L=335]
Description: thioredoxin reductase trxB2 (TRXR) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-48  165.6   0.6    1.6e-48  165.4   0.6    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-23   83.7   0.0      2e-19   70.0   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.5e-20   72.3   1.3    5.6e-19   68.5   0.1    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   34.0   9.4     0.0056   16.3   0.0    4.1  4  DAO             FAD dependent oxidoreductase
      5e-08   32.5  11.9    7.8e-05   21.9   0.8    4.6  5  FAD_binding_2   FAD binding domain
    8.2e-08   31.7   1.7     0.0054   15.9   0.7    3.8  4  GIDA            Glucose inhibited division protein A
      4e-07   29.8   4.9    1.6e-06   27.7   0.7    3.0  3  FAD_oxidored    FAD dependent oxidoreductase
    1.7e-06   27.4   0.2     0.0039   16.4   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    7.8e-06   24.8   0.1     0.0035   16.1   0.1    3.4  4  HI0933_like     HI0933-like protein
    3.6e-05   23.1   0.0    0.00069   18.9   0.0    2.3  2  Thi4            Thi4 family
    0.00012   22.2   0.1     0.0081   16.4   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.001   18.2   2.4       0.77    8.7   0.0    3.0  4  Lycopene_cycl   Lycopene cyclase protein
     0.0094   16.4   0.2      0.088   13.3   0.0    2.2  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.011   15.0   1.8       0.96    8.6   0.1    2.9  3  FAD_binding_3   FAD binding domain
       0.02   13.7   0.3          1    8.1   0.1    2.8  3  Trp_halogenase  Tryptophan halogenase
      0.035   14.7   2.6        0.1   13.3   0.9    2.6  3  SnoaL_2         SnoaL-like domain
       0.11   12.5   7.4       0.76    9.8   0.0    3.5  4  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.6   1.6e-51   1.6e-48       2     294 .]      16     304 ..      15     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1.6e-51
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgielllg 72 
                                    dv+viG+GpAG++aal++a+a++  +++  egt ++g  + ++ +++++++++ ++         e+   l+ g +l+++
  gi|121635899|ref|YP_976122.1|  16 DVIVIGSGPAGYTAALYAARAQLAPLVF--EGTSFGGALMTTTGVENYPGFRNGITgpelmdemrEQ--ALRFGADLRME 91 
                                    8***************************..99999999********************666655444..23333333333 PP

                                    CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGy 152
                                      v ++   ++ +k    ++ d+++  + +++lA+G+ +r l++pG++e  g++v+++++++++    ++  i+v+GgG 
  gi|121635899|ref|YP_976122.1|  92 -DVESVSL-HGPLKS--VVTADGQTHRARAVILAMGAAARYLQVPGEQELLGRGVSSCATCDGFFFRDQD--IAVIGGGD 165
                                    .3333332.224444..4458999*****************************************99998..******** PP

                                    HHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxx RF
                    Pyr_redox_2 153 iGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle.vvledgeei 226
                                     ++E A +l++++  vtlv++rd++       +s+++ ++ +++ ++++ ++++v+++dg+++    +++ + ++ ++++
  gi|121635899|ref|YP_976122.1| 166 SAMEEATFLTRFARSVTLVHRRDEFR------ASKIMLDRARNNdKIRFLTNHTVVAVDGDTTvtglRVRdTNTGAETTL 239
                                    *************************7......9999999999988******************9966555899999999* PP

                                    EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    ++  v+va+G +p++ l+  +  + +d++g+++v  +   t+ pg++a+GD +  ++++++a++A  +G
  gi|121635899|ref|YP_976122.1| 240 PVTGVFVAIGHEPRSGLV--REAIDVDPDGYVLVQGRTtSTSLPGVFAAGDLV--DRTYRQAVTAAGSG 304
                                    **************9775..7778889*****9988874788***********..9********99876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1    0.0001      0.11       1      34 [.      18      50 ..      18      57 .. 0.89
   2 !   70.0   0.0   1.9e-22     2e-19     101     305 .]      90     287 ..      65     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                   i+iG GPaG +aa+ + +a+l   l+ E  + g 
  gi|121635899|ref|YP_976122.1| 18 IVIGSGPAGYTAALYAARAQL-APLVFEGTSFGG 50
                                   89*******************.689999887775 PP

  == domain 2  score: 70.0 bits;  conditional E-value: 1.9e-22
                    Pyr_redox_3 101 feeVesvkkedeg.fevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefh..kyagqkvvViGgknSa 176
                                     e+Vesv+ ++    +v+++ +t +A+ vi+A+G     ++l++pGe++ l    s    ++   +++q+++ViGg++Sa
  gi|121635899|ref|YP_976122.1|  90 MEDVESVSLHGPLkSVVTADGQTHRARAVILAMGA--AARYLQVPGEQElLGRGVSSCATCDgfFFRDQDIAVIGGGDSA 167
                                    4789999998755266777778************9..99********97555545555544400567************* PP

                    Pyr_redox_3 177 vDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkve 256
                                    ++ A+ l r   +Vt+v+r++e ++++   +   +++++++++ l +++ + v  +++v+ ++ +++    +t  ++++ 
  gi|121635899|ref|YP_976122.1| 168 MEEATFLTRFARSVTLVHRRDEFRASKIMLD---RARNNDKIRFLTNHTVVAVDGDTTVTGLRVRDT----NTGAETTLP 240
                                    *********************9888753333...677888888888888888888988888887654....344445555 PP

                    Pyr_redox_3 257 vkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    v + v++a+G +p   +++ + ++ d dg+++++  t +t +pg+f aG
  gi|121635899|ref|YP_976122.1| 241 V-TGVFVAIGHEPRSGLVR-EAIDVDPDGYVLVQGRTTSTSLPGVFAAG 287
                                    5.678889*********99.9999***********************99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.21   2.2e+02       2      21 ..      17      36 ..      16     109 .. 0.88
   2 !   68.5   0.1   5.3e-22   5.6e-19       2      80 ..     158     230 ..     157     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                                   EEEECSSHHHHHHHHHHHHT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalael 21
                                   v+v+G+G  g  +A ++a+ 
  gi|121635899|ref|YP_976122.1| 17 VIVIGSGPAGYTAALYAARA 36
                                   89******999999988765 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 5.3e-22
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklkd 80 
                                    ++v+GgG++++E+A++l++++ +Vt+v+r+d+++      aski+ ++ ++n +i++l+n++v++++g++  v++++++d
  gi|121635899|ref|YP_976122.1| 158 IAVIGGGDSAMEEATFLTRFARSVTLVHRRDEFR------ASKIMLDRARNNdKIRFLTNHTVVAVDGDTT-VTGLRVRD 230
                                    89********************************......***************************9998.99999985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   6.2e-05     0.066       1      42 [.      16      57 ..      16      67 .. 0.85
   2 !   16.3   0.0   5.3e-06    0.0056     147     206 ..      72     129 ..      63     146 .. 0.79
   3 ?    3.0   0.0      0.06        63       1      32 [.     157     190 ..     157     194 .. 0.84
   4 ?    5.3   0.1     0.012        12     152     207 ..     196     257 ..     188     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsg 42
                                   dv++iG+G +G ++A+++ar+    +++e    +g ga   ++g
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQlaPLVFEGT-SFG-GALMTTTG 57
                                   9*****************9998888888888.777.77655555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.3e-06
                                    HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.H CS
                            DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.l 206
                                    +l+  ++++a + G++++ +  v++++ ++  ++ v  +t+ g++++a+av++a+Ga ++ l
  gi|121635899|ref|YP_976122.1|  72 ELMDEMREQALRFGADLRME-DVESVSLHG-PLKSV--VTAdGQTHRARAVILAMGAAARyL 129
                                    69999**************9.****98864.45566..4555988777*********99842 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.06
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32 
                                    d+++iGGG   +  A +L+r    Vtl+ ++d++
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFArsVTLVHRRDEF 190
                                    8*****************874336****999876 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.012
                                    HHHHHHHTT.-EEEESECEEEEEEEETCEEEEE.EECT.EEEE..EEEEEEE--GGGHH..HH CS
                            DAO 152 laraaealG.veilegtevtgleeedgkvwgve.rttp.gend..aadavVnaaGawsd..ll 207
                                    ++++a+++  +++l++++v+++ + d  v+g++ r+t+ g+++   ++ v +a G+  +  l+
  gi|121635899|ref|YP_976122.1| 196 MLDRARNNDkIRFLTNHTVVAV-DGDTTVTGLRvRDTNtGAETtlPVTGVFVAIGHEPRsgLV 257
                                    67778777659**********9.4457788888988888887324555599999988665333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.8   7.4e-08   7.8e-05       1      40 [.      16      54 ..      16      63 .. 0.84
   2 !    8.4   1.1   0.00096         1     111     227 ..      43     150 ..      41     174 .. 0.67
   3 ?    2.3   0.0     0.067        71       1      35 [.     157     191 ..     157     196 .. 0.92
   4 !    5.7   0.5    0.0061       6.5     146     204 ..     195     253 ..     191     287 .. 0.82
   5 ?    1.2   0.0      0.14   1.5e+02     378     404 ..     263     292 ..     260     306 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.4e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataw 40
                                   DviViGsG AG++AAl aa+a l  +v e ++ fgga+  
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTS-FGGALMT 54
                                   9**********************988888877.5777655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00096
                                    B-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEEC..TTEEEEEEEEETTTTCEE CS
                  FAD_binding_2 111 vdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLive..dgrvtGavvenpesgrev 188
                                    + ++ +Gg   t  t+ +++   +++ +tg++l+  + e+a++ g d+    +++++      g    +v +   +g+++
  gi|121635899|ref|YP_976122.1|  43 FEGTSFGGALMT-TTGVENYP-GFRNGITGPELMDEMREQALRFGADL----RMEDVESVslHGPLKSVVTA---DGQTH 113
                                    668999999999.88886666.47999**************6666555....44444221116677776666...77766 PP

                                    EEEESEEEE-----GG..........GSSSBSSGTT-S- CS
                  FAD_binding_2 189 rirakavvlatgGfgrallkellgaaaeaettnapavtG 227
                                    r  a+av+la g++ r l  +  +++  + +++ ++++G
  gi|121635899|ref|YP_976122.1| 114 R--ARAVILAMGAAARYLQVPGEQELLGRGVSSCATCDG 150
                                    5..9***********933333345555666666666666 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.067
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                    D+ ViG+G + +  A+ +++  ++v++v   +ef+
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDEFR 191
                                    899*************************9998887 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0061
                                    HHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 146 rlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                     ++++ar+++ ++f++++ ++++   d  vtG  v++ ++g e+++  ++v +a g  +r
  gi|121635899|ref|YP_976122.1| 195 IMLDRARNNDkIRFLTNHTVVAV-DGDTTVTGLRVRDTNTGAETTLPVTGVFVAIGHEPR 253
                                    57788888888***********9.3355**************999988888888776555 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.14
                                    BETTSBE...STTEEESSBTEEE-STCEES CS
                  FAD_binding_2 378 tdengrv...ldadgqpipGLYAaGevaag 404
                                    +d++g v    + + + +pG +AaG     
  gi|121635899|ref|YP_976122.1| 263 VDPDGYVlvqGRTTSTSLPGVFAAGDLVDR 292
                                    66666665555668999********88754 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7   5.1e-06    0.0054       1      25 [.      16      40 ..      16      79 .. 0.86
   2 !    8.2   0.0    0.0011       1.1     113     156 ..      88     130 ..      75     149 .. 0.78
   3 ?    3.4   0.0     0.031        33       1      34 [.     157     189 ..     157     211 .. 0.85
   4 ?   -0.1   0.1      0.36   3.8e+02     354     388 ..     279     315 ..     270     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--E CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakv 25
                                   dviViG G AG+ AAl aar+ +  
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQLAP 40
                                   8*******************98765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                    EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EE CS
                           GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGtflkgki 156
                                    ++ e ve++++ ++ +k vvt+dg+t +a+av++a G+  +   
  gi|121635899|ref|YP_976122.1|  88 LRMEDVESVSL-HGPLKSVVTADGQTHRARAVILAMGAAARYLQ 130
                                    55677788866.8999*********************9444443 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.031
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                    d+ ViGgG + +e A  + r   +v+L+ h+ d+
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLV-HRRDE 189
                                    799************************9.44444 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.36
                                    SSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHH CS
                           GIDA 354 kvkgLflAGqinGteGY...eEaaaqGllAGinaarka 388
                                    + +g+f+AG++   + Y   + aa++G+ A+i a r +
  gi|121635899|ref|YP_976122.1| 279 SLPGVFAAGDLVDRT-YrqaVTAAGSGCAAAIDAERWL 315
                                    568899999988887.6222345669999999998765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.7   1.6e-09   1.6e-06       1      66 [.      16      80 ..      16     128 .. 0.82
   2 ?    0.9   0.0      0.22   2.3e+02       1      32 [.     157     188 ..     157     190 .. 0.94
   3 ?    1.2   0.0      0.18   1.9e+02      90     130 ..     194     234 ..     187     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.6e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtg..iarefler 66
                                   Dv+V+G+gpaG++AA+ Aara    l+ e + + G l+t  +v +  g++   + +tg  +++e++e+
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTSFGGALMTTTGVENYPGFR---NGITGpeLMDEMREQ 80
                                   9*******************************************999999...666663344444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                    D+ V+GGg + +  A    r  ++v Lv++r+
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRD 188
                                    9***************************9986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.18
                   FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske.g 130
                                    k +l+   ++++++ l+n+++v+v+ +  ++++++v++ + g
  gi|121635899|ref|YP_976122.1| 194 KIMLDRARNNDKIRFLTNHTVVAVDGDT-TVTGLRVRDTNtG 234
                                    45555556889**************985.8****99887755 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.27   2.8e+02       3      34 ..      15      44 ..      10      49 .. 0.72
   2 !   16.4   0.0   3.7e-06    0.0039     134     230 ..     104     192 ..      73     195 .. 0.66
   3 !    6.8   0.0     0.003       3.1     288     341 ..     199     251 ..     193     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                    K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalfle 34
                                    D+i iG Gp+  + a+ ++ ++  l+ l++e
  gi|121635899|ref|YP_976122.1| 15 RDVIVIGSGPAGYTAALYAARAQ--LAPLVFE 44
                                   58999999998877666665555..6666666 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.7e-06
                    K_oxygenase 134 tveskdaegeeeelearnlvlgvGtep...kiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                    +v     + + ++++ar+++l++G  +   ++P   e l    r v s  +        + ++iaV+G+G Sa e +  l
  gi|121635899|ref|YP_976122.1| 104 SVV----TADGQTHRARAVILAMGAAArylQVPGEQELLG---RGVSSCATCDGF--FFRDQDIAVIGGGDSAMEEATFL 174
                                    333....3467899**********7762224565555443...444444433333..67789*************99888 PP

                    K_oxygenase 211 lrrqkkvelklvtrsealep 230
                                    +r ++  +++lv r++++++
  gi|121635899|ref|YP_976122.1| 175 TRFAR--SVTLVHRRDEFRA 192
                                    87766..999*****99986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.003
                    K_oxygenase 288 kvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                    + ++++++r+l+n++v +++ +++  + l +r++++g+e+tl v  v++A G +
  gi|121635899|ref|YP_976122.1| 199 RARNNDKIRFLTNHTVVAVDGDTT-VTGLRVRDTNTGAETTLPVTGVFVAIGHE 251
                                    6677889**************996.999**********************9975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.3e-06    0.0035       2      36 ..      16      50 ..      15      59 .. 0.84
   2 ?    1.2   0.0      0.11   1.2e+02     130     165 ..      91     125 ..      71     127 .. 0.62
   3 ?    2.6   0.0     0.041        43       2      35 ..     157     190 ..     156     198 .. 0.86
   4 ?   -2.1   0.0       1.1   1.2e+03     372     386 ..     277     291 ..     271     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   dviviG G+AG  aA+ aa+++   l++e ++  g
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTSFGG 50
                                   8***************************9875544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                    --EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 130 tevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    ++v+sv+ +   k  v+  ++++ +a++++lA+G +
  gi|121635899|ref|YP_976122.1|  91 EDVESVSLHGPLKSVVT-ADGQTHRARAVILAMGAA 125
                                    34555555555544455.59**************86 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.041
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                    d++viGgG + +  A  + +  ++V+l+ + +++
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDEF 190
                                    89************************99887765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.1
                                    BTTSTTEEE-GGGBS CS
                    HI0933_like 372 skkvpgLffaGEvlD 386
                                    s ++pg+f aG ++D
  gi|121635899|ref|YP_976122.1| 277 STSLPGVFAAGDLVD 291
                                    7889********999 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.6e-07   0.00069      13      56 ..      10      51 ..       1      59 [. 0.83
   2 ?    1.5   0.0      0.14   1.4e+02      15      38 ..     153     176 ..     142     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                                   HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                           Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                    ++ + Dv+++G+G++G taa y a++ +l  +++e   s+GG 
  gi|121635899|ref|YP_976122.1| 10 AHHPVRDVIVIGSGPAGYTAALYAARA-QLAPLVFEG-TSFGGA 51
                                   566689********************9.999999996.478875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                    HTEEEEEEE--SHHHHHHHHHHHH CS
                           Thi4  15 yaesDvvivGaGssGLtaayylak 38 
                                    + ++D++++G+G s +  a  l++
  gi|121635899|ref|YP_976122.1| 153 FRDQDIAVIGGGDSAMEEATFLTR 176
                                    5679**********9999988876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.7e-06    0.0081       1      37 [.      19      54 ..      19      80 .. 0.81
   2 ?    3.0   0.0      0.12   1.2e+02       1      30 [.     160     189 ..     160     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                   ++G+G +G +aA ++a+a++  l++e   ++GG + +
  gi|121635899|ref|YP_976122.1| 19 VIGSGPAGYTAALYAARAQLAPLVFEGT-SFGGALMT 54
                                   8************************865.55655444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    ++G+G s++  A +L++  ++v+l+ +rd 
  gi|121635899|ref|YP_976122.1| 160 VIGGGDSAMEEATFLTRFARSVTLVHRRDE 189
                                    8****************9999*99988876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0014       1.5       1      24 [.      16      39 ..      16      47 .. 0.80
   2 !    8.7   0.0   0.00073      0.77      88     157 ..      72     139 ..      64     147 .. 0.78
   3 ?   -1.1   0.0      0.71   7.4e+02       1      30 [.     157     184 ..     157     194 .. 0.78
   4 ?   -2.9   0.0       2.6   2.7e+03     119     157 ..     212     249 ..     196     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpg 24
                                   Dv+viG+GpAg   A   ++a+ +
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARAQLA 39
                                   9***********999888555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00073
                  Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyG 157
                                    +l  e+ e+    g+ l+   vesv  +    ++vv+++g++ rar+v+ a g a+++  +  g Q  +G
  gi|121635899|ref|YP_976122.1|  72 ELMDEMREQALRFGADLRMEDVESVSLHGP-LKSVVTADGQTHRARAVILAMG-AAARYLQVPGEQELLG 139
                                    677788888888899999999999987666.899*******************.5555444555555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.71
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                    D++viG+G   +  A  l   + + +v+l+
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFL--TRFARSVTLV 184
                                    99******9999888888..6666666666 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 2.6
                  Lycopene_cycl 119 eslvvleggrkirarlvvdarglaslkkarrlglQtfyG 157
                                    +++v+++g+ ++ +  v d    ++++  + +g+ ++ G
  gi|121635899|ref|YP_976122.1| 212 HTVVAVDGDTTVTGLRVRDTNT-GAETTLPVTGVFVAIG 249
                                    5567778888888888888776.5555555555555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.77   8.1e+02       8      29 ..      15      36 ..      13      54 .. 0.82
   2 !   13.3   0.0   8.4e-05     0.088       5      72 ..     153     221 ..     151     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.77
                  NAD_binding_7  8 kkvlvvGgGevAarkvrkllea 29
                                   + v+v+G G+ +++ +   ++a
  gi|121635899|ref|YP_976122.1| 15 RDVIVIGSGPAGYTAALYAARA 36
                                   6799******999877665555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.4e-05
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdle..gadlviaatddr 72 
                                    ++++ + v+GgG+ A++ +  l ++   vt+v  +  e+  +++ l +   ++++     ++v+a+  d+
  gi|121635899|ref|YP_976122.1| 153 FRDQDIAVIGGGDSAMEEATFLTRFARSVTLVHRR-DEFRASKIMLDRARNNDKIRflTNHTVVAVDGDT 221
                                    68999***************************999.6666666666655544443311344666655555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00091      0.96       3      19 ..      16      32 ..      15      42 .. 0.89
   2 ?    1.7   0.0      0.12   1.3e+02       3      35 ..     157     189 ..     155     193 .. 0.90
   3 ?    2.3   0.1     0.077        82     108     153 ..     193     239 ..     190     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00091
                                   EEEEE--SHHHHHHHHH CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlall 19
                                   dV+++G+GpaG ++al 
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALY 32
                                   8*************975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                    d++++G+G + +  a++L++   +v+lv +r++
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDE 189
                                    789******************889999999876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.077
                                    HHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                  FAD_binding_3 108 eriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetv 153
                                     +i++++a++   +++  ++ v+++  d++    +vrd +tg+e+t+
  gi|121635899|ref|YP_976122.1| 193 SKIMLDRARNNDkIRFLTNHTVVAVDGDTTVTGLRVRDTNTGAETTL 239
                                    689999999999899999999**999999999999*******99986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.001         1       1      21 [.      16      36 ..      16      43 .. 0.89
   2 ?   -0.1   0.0      0.31   3.3e+02     160     211 ..      77     126 ..      72     131 .. 0.84
   3 ?    1.7   0.0     0.089        93       1      33 [.     157     186 ..     157     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                                   EEEEE--SHHHHHHHHHHHHH CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalaka 21
                                   +++++G G+aG++aA + a+a
  gi|121635899|ref|YP_976122.1| 16 DVIVIGSGPAGYTAALYAARA 36
                                   699*************99887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                                    HHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG- CS
                 Trp_halogenase 160 LrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrg 211
                                    +r+ a + G + +  +v++v l+  g  +s+ ++dg++  a+ +i + G ++
  gi|121635899|ref|YP_976122.1|  77 MREQALRFGADLRMEDVESVSLH--GPLKSVVTADGQTHRARAVILAMGAAA 126
                                    78889999999999999999886..8999*********99999998888765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.089
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                    +i ++GGG ++   A+ l +      +vtlv  
  gi|121635899|ref|YP_976122.1| 157 DIAVIGGGDSAMEEATFLTRFA---RSVTLVHR 186
                                    699*****************99...56888875 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.8   5.1e+03      32      57 ..      16      45 ..       7      58 .. 0.72
   2 ?   -1.3   0.0       3.2   3.4e+03      62      62 ..      97      97 ..      50     160 .. 0.56
   3 ?   13.3   0.9   9.6e-05       0.1      32      92 ..     179     245 ..     153     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                                   E....EESHHHHHHHHHHHHHHEEEEEEEE CS
                        SnoaL_2 32 e....lrGreairaffralfaafpdlrfei 57
                                   +     +G++++ a++ a++a++  l fe 
  gi|121635899|ref|YP_976122.1| 16 DviviGSGPAGYTAALYAARAQLAPLVFEG 45
                                   344557889999998888888777777765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                                   E CS
                        SnoaL_2 62 a 62
                                    
  gi|121635899|ref|YP_976122.1| 97 S 97
                                   1 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 9.6e-05
                                    E....EESHHHHHH...HHHHHHHHEEEEEEE.EEEE.EEETTEEEEEEEEEEEEETTSSEEEEEEEEEE CS
                        SnoaL_2  32 e....lrGreaira...ffralfaafpdlrfe.ihdv.vadgdrvavewtvtgtipatgrgvtvrgvdvf 92 
                                    +    ++ r+++ra   ++ ++++  + +rf   h v ++dgd+ ++  +v+     tg+++t+++++vf
  gi|121635899|ref|YP_976122.1| 179 RsvtlVHRRDEFRAskiMLDRARN-NDKIRFLtNHTVvAVDGDTTVTGLRVRD--TNTGAETTLPVTGVF 245
                                    34556889999***9999999987.55555541555589************95..9**********9998 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.27   2.9e+02       2      19 ..      19      36 ..      18      59 .. 0.71
   2 ?    9.8   0.0   0.00072      0.76     122     155 ..      91     124 ..      72     125 .. 0.79
   3 ?   -2.5   0.0       4.2   4.4e+03       1      17 [.     159     175 ..     159     203 .. 0.68
   4 ?    3.7   0.3     0.052        55     108     155 ..     197     250 ..     189     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                  NAD_binding_9  2 ivGaGprGlavlerLlar 19
                                   ++G Gp+G +++   ++ 
  gi|121635899|ref|YP_976122.1| 19 VIGSGPAGYTAALYAARA 36
                                   8*******9998766555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                  NAD_binding_9 122 aevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    ++v++++ ++    v++adg++++a+aV+LA+G 
  gi|121635899|ref|YP_976122.1|  91 EDVESVSLHGPLKSVVTADGQTHRARAVILAMGA 124
                                    566677777777789*****************95 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.2
                  NAD_binding_9   1 aivGaGprGlavlerLl 17 
                                    a++G+G +++  ++ L 
  gi|121635899|ref|YP_976122.1| 159 AVIGGGDSAMEEATFLT 175
                                    67888877765544444 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.052
                  NAD_binding_9 108 larlpegvtvevh.raevvdleera..dgqavlladg...aslaadaVvLAlGh 155
                                    l+r++++ +++++ +++vv+++ +   +g +v+ ++    ++l +  V++A+Gh
  gi|121635899|ref|YP_976122.1| 197 LDRARNNDKIRFLtNHTVVAVDGDTtvTGLRVRDTNTgaeTTLPVTGVFVAIGH 250
                                    6778888899997355788777766335557776433233568**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 2465.87
//
Query:       gi|121635900|ref|YP_976123.1|  [L=116]
Description: thioredoxin trxC (TRX) (MPT46) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-33  113.3   0.0    5.1e-33  113.1   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.3e-09   38.5   0.1    1.7e-08   34.9   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    1.1e-06   28.8   0.0    0.00018   21.7   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    1.1e-05   25.0   0.0    1.7e-05   24.4   0.0    1.3  1  KaiB           KaiB domain
      5e-05   23.1   0.0    5.6e-05   22.9   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    7.9e-05   22.8   0.0    0.00012   22.1   0.0    1.3  1  Thioredoxin_7  Thioredoxin-like
    0.00011   21.9   0.1    0.00013   21.7   0.1    1.3  1  Redoxin        Redoxin
    0.00038   20.4   0.0     0.0015   18.4   0.0    1.7  2  AhpC-TSA       AhpC/TSA family
     0.0011   18.4   0.0     0.0012   18.3   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0015   18.5   0.0      0.002   18.1   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0021   17.9   0.0     0.0026   17.6   0.0    1.1  1  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.066   13.4   0.0       0.11   12.7   0.0    1.5  1  Glutaredoxin   Glutaredoxin
      0.083   13.3   0.0        0.1   13.0   0.0    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.0   3.7e-36   5.1e-33       2     101 ..       9     108 ..       8     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.7e-36
                                    EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEET CS
                    Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkn 81 
                                    ++++t+++F ++v +++k+vlv+F+A+wCg+Ck++aP+le++a+e + ++++ak+dvd+n+++a++++v +iPtl+lfk+
  gi|121635900|ref|YP_976123.1|   9 TIKVTDASFATDVLSSNKPVLVDFWATWCGPCKMVAPVLEEIATERATDLTVAKLDVDTNPETARNFQVVSIPTLILFKD 88 
                                    57899*************************************************************************** PP

                                    TEEEEEEESS-HHHHHHHHH CS
                    Thioredoxin  82 gkevkkyegarekeklaafl 101
                                    g+ vk+++ga+ k++l + l
  gi|121635900|ref|YP_976123.1|  89 GQPVKRIVGAKGKAALLREL 108
                                    ************99998766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.2e-11   1.7e-08       3     105 ..      23     104 ..      21     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.2e-11
                  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                    +++kpvlv+f++++C+ Ck    +l+e+               + + a+++  ak  +      ++n e ar ++v + P
  gi|121635900|ref|YP_976123.1|  23 SSNKPVLVDFWATWCGPCKMVAPVLEEI---------------ATERATDLTVAKLDV------DTNPETARNFQVVSIP 81 
                                    579*************************...............344455555555553......5666899********* PP

                  Thioredoxin_2  83 tiv.fldgkeivarlpGyvpaeel 105
                                    t++ f dg+ +v r++G+  ++ l
  gi|121635900|ref|YP_976123.1|  82 TLIlFKDGQ-PVKRIVGAKGKAAL 104
                                    *66599999.999****9866555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00018       1      28 [.      25      52 ..      25      68 .. 0.88
   2 ?    5.6   0.0     0.014        19      70      90 ..      67      87 ..      54      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                   .SEEEEEE--SSSHHHHHHHHHHHHHHH CS
                  Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelye 28
                                   +k vl+ f+a+wc pck + p l e+ +
  gi|121635900|ref|YP_976123.1| 25 NKPVLVDFWATWCGPCKMVAPVLEEIAT 52
                                   799********************99865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                                   -HHHHTT-S--TT-SEEEEE- CS
                  Thioredoxin_8 70 krnklkkkynvkaiPtlvvld 90
                                    + + +++++v +iPtl++ +
  gi|121635900|ref|YP_976123.1| 67 TNPETARNFQVVSIPTLILFK 87
                                   4557899**********9976 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.2e-08   1.7e-05      28      77 ..      56     106 ..      41     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                    TTEEEEEEETTTSHCHHCCTCEESCCCCCCC.CSCCHCCCCCCHHHCCHHC CS
                           KaiB  28 fqyeLqvvdvleqPelaeedrlvatPaLikl.sPePkqrlaGdlilqqlkl 77 
                                       ++  +dv ++Pe a+++++v +P+Li   + +P++r++G + ++ l +
  gi|121635900|ref|YP_976123.1|  56 TDLTVAKLDVDTNPETARNFQVVSIPTLILFkDGQPVKRIVGAKGKAALLR 106
                                    34555557*********************862579*******998776665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     4e-08   5.6e-05      48     107 ..      32      89 ..       6     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4e-08
                                    E--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                  Thioredoxin_9  48 ltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                    + + wCg + ++ Pvl++ia e + +++v  l  d n+e+ ++++     +iPtli+++++
  gi|121635900|ref|YP_976123.1|  32 FWATWCGPCKMVAPVLEEIAtERATDLTVAKLDVDTNPETARNFQV---VSIPTLILFKDG 89 
                                    5689***************9666779999999************66...9******98654 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     9e-08   0.00012      15      81 ..      23      86 ..      16      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                                   HHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                  Thioredoxin_7 15 ergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81
                                   +++kpvlv+f a+wc++C+ ++ ++++  +  +  a +  + ++dv+++ +  ++++   +P+++++
  gi|121635900|ref|YP_976123.1| 23 SSNKPVLVDFWATWCGPCKMVAPVLEEIAT--E-RATDLTVAKLDVDTNPETARNFQVVSIPTLILF 86
                                   689*****************9998877633..3.568888888888777776655555668888776 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   9.7e-08   0.00013      27      75 ..      24      70 ..       6     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.7e-08
                                   TTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                        Redoxin 27 kgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75
                                    +k+v+v f+++ +c++C+  +p le++a++ ++ + +v  + +d+++ 
  gi|121635900|ref|YP_976123.1| 24 SNKPVLVDFWAT-WCGPCKMVAPVLEEIATE-RATDLTVAKLDVDTNPE 70
                                   5899********.***************888.77777776666666665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0015      22      69 ..      20      67 ..       5      78 .. 0.74
   2 ?    1.6   0.0      0.17   2.4e+02      88     116 ..      65      87 ..      48      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                   HH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSS CS
                       AhpC-TSA 22 dy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvds 69
                                   d+  ++kpv++ f+++ wc +C+  +p l++ + e +  +++v  + vd+
  gi|121635900|ref|YP_976123.1| 20 DVlsSNKPVLVDFWAT-WCGPCKMVAPVLEEIATERA-TDLTVAKLDVDT 67
                                   4445779*********.**********9999886655.556666665554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                                    E-TTSHHHHHTT-EETTTTECSCEEEEE- CS
                       AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvid 116
                                     D++ ++a++++v+       +++ ++++
  gi|121635900|ref|YP_976123.1|  65 VDTNPETARNFQVV------SIPTLILFK 87 
                                    69999999999999......677766665 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.8e-07    0.0012      45     104 ..      36      88 ..       2     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.8e-07
                      OST3_OST6  45 kCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                     C +C+ ++p +e +a    +d       l  ak+d+d ++++ + +++ s+P l+lf+ 
  gi|121635900|ref|YP_976123.1|  36 WCGPCKMVAPVLEEIATERATD-------LTVAKLDVDTNPETARNFQVVSIPTLILFKD 88 
                                    4999999999999999888777.......99***************************87 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-06     0.002       9      55 ..      36      85 ..      28     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                   SSTTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEEC CS
                  Thioredoxin_3  9 gCakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvi 55
                                    C  C+ ++ +++e+a+e+ ++++v k    +++e   +++V s+P+l++
  gi|121635900|ref|YP_976123.1| 36 WCGPCKMVAPVLEEIATERATDLTVAKLdvDTNPETaRNFQVVSIPTLIL 85
                                   59*****************999988775446666667**********975 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0026     132     210 ..      28      97 ..      17     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                           TraF 132 gLlfFyrgkcpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpv 209
                                     L+ F +  c+ c++ ap+l+++a +    l+v   +vd +p   ++          +++v ++P+l+l++  +    +v
  gi|121635900|ref|YP_976123.1|  28 VLVDFWATWCGPCKMVAPVLEEIATERatDLTVAKLDVDTNPE--TAR---------NFQVVSIPTLILFKDGQPVKRIV 96 
                                    577788999**************98762267777777777766..666.........8************9997666666 PP

                           TraF 210 a 210
                                    +
  gi|121635900|ref|YP_976123.1|  97 G 97 
                                    5 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-05      0.11       5      41 ..      33      75 ..      26      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                                   ESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHH CS
                   Glutaredoxin  5 tkptCpyCkkakrlLkelg......vkfeeidvdkdeeireel 41
                                     ++C+ Ck++  +L+e        + ++  dvd ++e     
  gi|121635900|ref|YP_976123.1| 33 WATWCGPCKMVAPVLEEIAteratdLTVAKLDVDTNPETARNF 75
                                   5589***********8777444444669********9988776 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05       0.1      10      54 ..      37      84 ..      32     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                   -HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCT.TTTEEE CS
                         DUF836 10 ChlCeqakekLkelkleeg..leleviDIakdeeleakYgl.eipvla 54
                                   C+ C+ +  +L+e+++e    l++ + D+++++e  + +++  ip l 
  gi|121635900|ref|YP_976123.1| 37 CGPCKMVAPVLEEIATERAtdLTVAKLDVDTNPETARNFQVvSIPTLI 84
                                   9************77666656999************999953667665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 730.25
//
Query:       gi|121635901|ref|YP_976124.1|  [L=406]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-30  105.3   3.2    4.7e-16   58.7   0.1    3.0  3  PG_binding_1  Putative peptidoglycan binding domain
    1.2e-29  103.6   0.0      2e-29  103.0   0.0    1.3  1  Amidase_3     N-acetylmuramoyl-L-alanine amidase
    1.7e-08   34.6   0.1       0.12   12.7   0.0    3.5  3  PG_binding_3  Predicted Peptidoglycan domain
    1.9e-05   24.9   0.4    0.00042   20.6   0.1    2.8  2  PG_binding_2  Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> PG_binding_1  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.3   9.5e-16   4.3e-12       2      57 .]      18      83 ..      17      83 .. 0.87
   2 !   58.7   0.1   1.1e-19   4.7e-16       2      57 .]     105     160 ..     104     160 .. 0.97
   3 ?   -2.0   0.0      0.95   4.3e+03       7      26 ..     367     385 ..     355     386 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 9.5e-16
                                   SHHHHHHHHHHHHTT--..SSSS.........SB--HHHHHHHHHHHHHTTST-SSSBSHHHHHHH CS
                   PG_binding_1  2 gedvkelqryLsrlGyl.sgpad.........gtfgpateeaVkefQqffgLpvtGildpaTlaal 57
                                   +++v+e++ +L++lG l  +++d           f++++ +aV++fQq++gL v+Gi+++aT++al
  gi|121635901|ref|YP_976124.1| 18 SAAVTEIRAALTALGMLdHQEEDlttgrnvalELFDAQLDQAVRAFQQHRGLLVDGIVGEATYRAL 83
                                   689*************9844444445677777*******************************997 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 1.1e-19
                                    SHHHHHHHHHHHHTT--.SSSSSB--HHHHHHHHHHHHHTTST-SSSBSHHHHHHH CS
                   PG_binding_1   2 gedvkelqryLsrlGylsgpadgtfgpateeaVkefQqffgLpvtGildpaTlaal 57 
                                    g+dv +lq +L+ lG+++g +dg+fg +t +a+  +Q+ +gL ++Gi +p+Tl+ l
  gi|121635901|ref|YP_976124.1| 105 GDDVATLQARLQDLGFYTGLVDGHFGLQTHNALMSYQREYGLAADGICGPETLRSL 160
                                    79***************************************************976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.95
                                    HHHHHHHHTT--.SSSSSB- CS
                   PG_binding_1   7 elqryLsrlGylsgpadgtf 26 
                                    ++ ++L  lG + + ++gtf
  gi|121635901|ref|YP_976124.1| 367 AAVKRLYLLGKN-DRPTGTF 385
                                    455566666655.7777776 PP

>> Amidase_3  N-acetylmuramoyl-L-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   4.4e-33     2e-29       1     174 [.     193     370 ..     193     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 4.4e-33
                      Amidase_3   1 ividpGHGgkdpGavg...knglkEkdlnlkvalklaklLeakgaeVvltrdddksvslkeranianksradlfvsiHad 77 
                                    i+idpG Gg d G ++   ++ ++E+dl +++a +l+ +++a g+e +l+r +++s s  era+ an+ +adl++s+ + 
  gi|121635901|ref|YP_976124.1| 193 IIIDPGRGGVDHGLIAqgpAGPISEADLLWDLASRLEGRMAAIGMETHLSRPTNRSPSDAERAATANAVGADLMISLRCE 272
                                    89***********777667777********************************************************** PP

                      Amidase_3  78 saanssasGvevfy..leknekkaeskrlaksiqkelkkklglknrgvkeannlyvlrktkipavlvElgfisnpedakl 155
                                      ++ +a+Gv  f   + + + ++  ++la  iq+e+++++gl++  v+ ++ + +lr t++p v v++g+i+np d+ +
  gi|121635901|ref|YP_976124.1| 273 TQTSLAANGVASFHfgNSHGSVSTIGRNLADFIQREVVARTGLRDCRVHGRT-WDLLRLTRMPTVQVDIGYITNPHDRGM 351
                                    999999********98899999999***************************.*************************** PP

                      Amidase_3 156 lkseeyqeklakaiaegik 174
                                    l s+++++++a++i  ++k
  gi|121635901|ref|YP_976124.1| 352 LVSTQTRDAIAEGILAAVK 370
                                    ***************9986 PP

>> PG_binding_3  Predicted Peptidoglycan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.6e-05      0.12       2      32 ..      59      84 ..      58      97 .. 0.82
   2 !   10.3   0.0   0.00014      0.64       5      32 ..     110     138 ..     107     145 .. 0.75
   3 !    8.3   0.0   0.00061       2.7      13      31 ..     142     160 ..     138     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHT.....S---S---HHHHHHH. CS
                   PG_binding_3  2 aivilQriLgklgydvkvDGiiGpkTlaAve 32
                                   a++ +Q+  g     + vDGi+G +T +A++
  gi|121635901|ref|YP_976124.1| 59 AVRAFQQHRG-----LLVDGIVGEATYRALK 84
                                   6788888888.....9**************5 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                                    HHHHHHT......S---S---HHHHHHH. CS
                   PG_binding_3   5 ilQriLgklg.ydvkvDGiiGpkTlaAve 32 
                                     lQ  L +lg y+  vDG +G +T +A++
  gi|121635901|ref|YP_976124.1| 110 TLQARLQDLGfYTGLVDGHFGLQTHNALM 138
                                    57777755543899**************6 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00061
                                    ....S---S---HHHHHHH CS
                   PG_binding_3  13 lgydvkvDGiiGpkTlaAv 31 
                                    + y +++DGi Gp+Tl+ +
  gi|121635901|ref|YP_976124.1| 142 REYGLAADGICGPETLRSL 160
                                    567799**********988 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   5.1e+02      18      32 ..      21      35 ..       7      65 .. 0.77
   2 !   20.6   0.1   9.3e-08   0.00042      12      51 ..     102     141 ..      97     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                   PG_binding_2 18 aeevqaaLsrLGyyd 32
                                   + e++aaL +LG  d
  gi|121635901|ref|YP_976124.1| 21 VTEIRAALTALGMLD 35
                                   679999999999833 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 9.3e-08
                   PG_binding_2  12 vlaedvaeevqaaLsrLGyydgeaggafrealrdALrafi 51 
                                    +l +d +  +qa L+ LG+y g  +g f+ ++++AL +++
  gi|121635901|ref|YP_976124.1| 102 PLYGDDVATLQARLQDLGFYTGLVDGHFGLQTHNALMSYQ 141
                                    78899999******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2796.54
//
Query:       gi|121635902|ref|YP_976125.1|  [L=244]
Description: hypothetical protein BCG_0022c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1598.44
//
Query:       gi|121635903|ref|YP_976126.1|  [L=344]
Description: chromosome partitioning protein parB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-26   91.4   0.2    6.4e-26   90.5   0.2    1.5  1  ParBc      ParB-like nuclease domain
    4.6e-16   58.3   0.4    9.8e-16   57.3   0.4    1.5  1  HTH_ParB   HTH domain found in ParB protein
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.056   13.3   0.0    1.6  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.076   13.4   0.1        7.1    7.1   0.1    2.5  2  HOASN      Haem-oxygenase-associated N-terminal helices
      0.084   12.9   0.3       0.64   10.0   0.1    2.6  2  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.11   12.6   0.0       0.25   11.5   0.0    1.5  1  SoPB_HTH   Centromere-binding protein HTH domain
       0.13   12.3   0.0        2.2    8.4   0.0    2.2  2  KorB       KorB domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.2   2.5e-29   6.4e-26       2      90 .]      62     155 ..      61     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.5e-29
                          ParBc   2 evplseirpnplqprkd.spekieelvasIkkkGllqPiivrktr....qgryeiiaGerRlrAakrlglkevpvivlei 76 
                                    e+p+s i+ np+qpr+  ++e+++elv+sI++ GllqPi+vr  +    + ry+i++GerR+rAa+++gl ++p+iv+e+
  gi|121635903|ref|YP_976126.1|  62 EIPPSAIEANPRQPRQVfDEEALAELVHSIREFGLLQPIVVRSLAgsqtGVRYQIVMGERRWRAAQEAGLATIPAIVRET 141
                                    8**********************************************9999***************************** PP

                          ParBc  77 ddeeamalslieni 90 
                                     d++ ++ +l eni
  gi|121635903|ref|YP_976126.1| 142 GDDNLLRDALLENI 155
                                    ************97 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.4   3.8e-19   9.8e-16       2      50 ..     206     255 ..     205     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.8e-19
                       HTH_ParB   2 evqeavsegkiseGHARaLlslkde.elqlqlaekiieegLsVRetEklv 50 
                                    +vq+ v +g +s+GHARaLlsl+   e q++la +i++egLsVR tE+ v
  gi|121635903|ref|YP_976126.1| 206 PVQRRVAAGVLSAGHARALLSLEAGpEAQEELASRIVAEGLSVRATEETV 255
                                    599*********************99*********************977 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056      10      46 ..     165     201 ..     162     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                                    CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHH CS
                           TrmB  10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsL 46 
                                    Ea +Y+ Ll +   t de+a ++g++r+ + +++r L
  gi|121635903|ref|YP_976126.1| 165 EAAAYQQLLDEFGVTHDELAARIGRSRPLITNMIRLL 201
                                    99**************************999998866 PP

>> HOASN  Haem-oxygenase-associated N-terminal helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.033        86      58      77 ..     167     186 ..     160     197 .. 0.85
   2 ?    7.1   0.1    0.0028       7.1      18      40 ..     238     260 ..     228     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                    HHHHHHHHHHHH---GGGHH CS
                          HOASN  58 aayqalllvlslsddvateq 77 
                                    aayq+ll ++ ++ d  +++
  gi|121635903|ref|YP_976126.1| 167 AAYQQLLDEFGVTHDELAAR 186
                                    89**********99976665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                                    HHHHHHHHTSTT--HHHHHHHHH CS
                          HOASN  18 eaalladalkvgasldqidlale 40 
                                    +++++a+ l v a+ + ++la +
  gi|121635903|ref|YP_976126.1| 238 ASRIVAEGLSVRATEETVTLANH 260
                                    79*****************9975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00025      0.64      17      46 ..     173     202 ..     150     203 .. 0.79
   2 ?   -1.4   0.0      0.94   2.4e+03       5      31 ..     222     241 ..     220     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                    EEEEEHHHHHHHHHTTSSHHHHHHHHHHHH CS
                      HTH_Crp_2  17 eielpltqeelAsmlGltretvsrilseLk 46 
                                      e+ +t++elA+++G +r  ++ +++ Lk
  gi|121635903|ref|YP_976126.1| 173 LDEFGVTHDELAARIGRSRPLITNMIRLLK 202
                                    346899**************9999999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                                    HHHHHHHCTTTCEEEEEHHHHHHHHHT CS
                      HTH_Crp_2   5 rfLlrlaeraggeielpltqeelAsml 31 
                                    r Ll l++++         qeelAs++
  gi|121635903|ref|YP_976126.1| 222 RALLSLEAGP-------EAQEELASRI 241
                                    6666664432.......2466666654 PP

>> SoPB_HTH  Centromere-binding protein HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.25       5      49 ..     164     207 ..     161     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                       SoPB_HTH   5 eRarrYalaLkdeyannlsalaeaeklskkilskmlrvaklPdav 49 
                                    e a  Y  +L de++     la +   s+ +++ m+r  klP  v
  gi|121635903|ref|YP_976126.1| 164 EEAAAYQ-QLLDEFGVTHDELAARIGRSRPLITNMIRLLKLPIPV 207
                                    5566664.6789*****************************9765 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   3.3e+02      26      84 ..     131     156 ..     123     173 .. 0.58
   2 ?    8.4   0.0   0.00087       2.2       3      77 ..     177     258 ..     175     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                           KorB  26 lldvpdylrelydseviadirtLyeLrraaekhpaevrafvaengeagltrsavrrflk 84 
                                    l+ +p+                                 +v+e g+++l r+a  +++ 
  gi|121635903|ref|YP_976126.1| 131 LATIPA---------------------------------IVRETGDDNLLRDALLENIH 156
                                    444455.................................55555555555555544443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00087
                           KorB   3 gvkqadIAkaLGksksfvslylklldvpdylrelydsevia..dirtLyeLrraaekhpaevrafv.....aengeaglt 75 
                                    gv+  + A++ G+s+  ++    ll++p  ++  +  +v +    r+L +L    e +++ ++++v      ++ e+++t
  gi|121635903|ref|YP_976126.1| 177 GVTHDELAARIGRSRPLITNMIRLLKLPIPVQRRVAAGVLSagHARALLSLEAGPEAQEELASRIVaeglsVRATEETVT 256
                                    78999**************************9999999975337999999999999999999999955544455555555 PP

                           KorB  76 rs 77 
                                    ++
  gi|121635903|ref|YP_976126.1| 257 LA 258
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2279.53
//
Query:       gi|121635904|ref|YP_976127.1|  [L=347]
Description: chromosome partitioning protein parA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-58  195.5   0.0    9.4e-58  195.0   0.0    1.2  1  AAA_31       AAA domain
    1.8e-28   99.1   0.0    2.5e-28   98.7   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-10   40.6   2.0    3.1e-09   36.7   2.0    2.1  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.1e-09   38.0   0.2    1.5e-07   31.0   0.1    2.4  3  MipZ         ATPase MipZ
    1.4e-09   37.8   0.1    4.3e-05   23.1   0.2    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.3e-08   33.6   0.2    7.2e-08   32.0   0.2    1.7  1  ArsA_ATPase  Anion-transporting ATPase
    7.4e-05   22.3   0.1    0.00049   19.6   0.1    2.0  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0058   16.3   0.4       0.74    9.4   0.4    2.3  2  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.035   13.4   0.3      0.076   12.3   0.1    1.6  2  VirC1        VirC1 protein
      0.058   13.0   0.9       0.16   11.6   0.4    2.0  2  AAA_25       AAA domain
        0.1   11.6   0.2       0.24   10.4   0.2    1.6  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.17   11.7   0.6       0.57    9.9   0.0    2.1  3  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0   0.0   6.3e-61   9.4e-58       2     177 .]      85     263 ..      84     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 6.3e-61
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi.ekneiektlyevlieeknikeaiiktk.ve 79 
                                    +v++ianqKGGvGKTTt+vn+aaala +g k+L++DlDpQ+na+t+lgi ++++ + + ye+li e++++ a+ ++  +e
  gi|121635904|ref|YP_976127.1|  85 RVLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGItDRQSGTPSSYEMLIGEVSLHTALRRSPhSE 164
                                    799**********************************************66778999*****************998678 PP

                         AAA_31  80 nldlipssidLaeaeielvelekkeeilkellekvkd.eYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGle 158
                                    +l  ip++idLa+aeielv++  +e++l+++l ++++ ++Dy+++DcpPsLgllt+naLva+ +v+ip+q+e+yaleG++
  gi|121635904|ref|YP_976127.1| 165 RLFCIPATIDLAGAEIELVSMVARENRLRTALAALDNfDFDYVFVDCPPSLGLLTINALVAAPEVMIPIQCEYYALEGVS 244
                                    88*********************************9857***************************************** PP

                         AAA_31 159 qllktieevkkklnpklei 177
                                    ql+++ie vk +lnp+le+
  gi|121635904|ref|YP_976127.1| 245 QLMRNIEMVKAHLNPQLEV 263
                                    ****************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   1.7e-31   2.5e-28       1     127 [.      87     313 ..      87     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.7e-31
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    ++ia++kGGvGKTt+a+n+a+ala +gl++l++D+Dpq+n+++ + g   +  +                          
  gi|121635904|ref|YP_976127.1|  87 LTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNAST-ALGITDR--Qsgtpssyemligevslhtalrrsphs 163
                                    58****************************************9.3333333..2358999999***************** PP

                                    ..............................................................................CC CS
                                    ..............................................................................xx RF
                           CbiA  55 ..............................................................................dl 56 
                                                                                                                  ++
  gi|121635904|ref|YP_976127.1| 164 erlfcipatidlagaeielvsmvarenrlrtalaaldnfdfdyvfvdcppslglltinalvaapevmipiqceyyaleGV 243
                                    ******************************************************************************** PP

                                    HCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEE.EEE--CCHCCCCHHTS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxx RF
                           CbiA  57 krllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlg.viprdeavaeapargep 127
                                    ++l + +e+++ +++++l++  v+l+++dg+   t+l ++++++ ++y g +vl  vipr+++v+eap   ++
  gi|121635904|ref|YP_976127.1| 244 SQLMRNIEMVKAHLNPQLEVTTVILTMYDGR---TKLADQVADEVRQYfGSKVLRtVIPRSVKVSEAPGYSMT 313
                                    ******************************9...889999999999999******************987765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   2.0   2.1e-12   3.1e-09       3     151 ..      84     241 ..      82     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.1e-12
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.............ekpeqsekkliPve 69 
                                    ++v++++  KGGVGK+t+avn+A+aLa +glk+ ++D+D  G    + lg+++                         v+
  gi|121635904|ref|YP_976127.1|  84 RRVLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNA-STALGITDrqsgtpssyemliG----------EVS 152
                                    57899*************************************76.5566776623333322211110..........111 PP

                           ParA  70 a........kgikvmSigfllesedeavvwrGpm.kskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagav 140
                                             ++ ++  i   ++   + +   + +  ++ ++  l+  +  + Dy+++D+PP  g   lt+   +   +++
  gi|121635904|ref|YP_976127.1| 153 LhtalrrspHSERLFCIPATIDLAGAEIELVSMVaRENRLRTALAALDNFDFDYVFVDCPPSLG--LLTINALVAAPEVM 230
                                    1222333444444555555555444444443333134567777777777788888888888877..45555555555555 PP

                           ParA 141 iVttpqevala 151
                                    i    +  al+
  gi|121635904|ref|YP_976127.1| 231 IPIQCEYYALE 241
                                    55555555555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1     1e-10   1.5e-07       2      42 ..      86     126 ..      85     146 .. 0.89
   2 ?    4.7   0.0     0.011        16      74     133 ..     179     237 ..     158     270 .. 0.78
   3 ?   -3.6   0.0       3.5   5.2e+03      29      56 ..     309     336 ..     301     338 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1e-10
                                    EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                           MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqr 42 
                                    v+ ++n+kGG Gk+ttav +a aL+ +G++  +idld + +
  gi|121635904|ref|YP_976127.1|  86 VLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGN 126
                                    6789*********************************7654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                                    HHHHTTS-HHHHHHHHHHHHHHHHH.H-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSH CS
                           MipZ  74 eeaeveeeeeaevaeleelvadlea.eldfividtPGsdsalsrlahsladtlvtPlndsf 133
                                    e + v+  + +  ++l++++a+l + ++d++ +d+P s   l+  a   a  ++ P+   +
  gi|121635904|ref|YP_976127.1| 179 EIELVSMVARE--NRLRTALAALDNfDFDYVFVDCPPSLGLLTINALVAAPEVMIPIQCEY 237
                                    44444444444..488888888865389**********99999999999999999997665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                                    T--EEEEE--TTT-HHHHHHHHHHHHHH CS
                           MipZ  29 Garvaaidldlrqrtlarylenraatae 56 
                                    G +++ id d   r    yl+  ++ ae
  gi|121635904|ref|YP_976127.1| 309 GYSMTIIDYDPGSRGAMSYLDASRELAE 336
                                    6666677777777777777776666655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   2.9e-08   4.3e-05       8      45 ..      93     131 ..      87     140 .. 0.85
   2 !   12.6   0.0   4.6e-05     0.069     140     248 ..     225     338 ..     196     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.9e-08
                      Fer4_NifH   8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaD.strl 45 
                                    kGG+Gk+tt+ n++aala +g k l++  DP+ + st l
  gi|121635904|ref|YP_976127.1|  93 KGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNaSTAL 131
                                    9******************************97624544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.6e-05
                      Fer4_NifH 140 kaqevyivtsgelmalyaanniakgieky.aksgg.vrlgGliinsr..kvddereliekfaeelgtkvle.vvPrdeiv 214
                                     a ev+i  ++e  al    ++ + ie   a+ ++ ++++ +i      +++  ++++++  +  g+kvl  v+Pr+ +v
  gi|121635904|ref|YP_976127.1| 225 AAPEVMIPIQCEYYALEGVSQLMRNIEMVkAHLNPqLEVTTVILTMYdgRTKLADQVADEVRQYFGSKVLRtVIPRSVKV 304
                                    4778999999999999999999999986514444458899888763300355556666777777899*996368****** PP

                      Fer4_NifH 215 rkaelrkktvieyapeseqakeyrelarkilenk 248
                                     +a    +t+i+y+p s+ a  y + +r+++e +
  gi|121635904|ref|YP_976127.1| 305 SEAPGYSMTIIDYDPGSRGAMSYLDASRELAERD 338
                                    ***********************99999998877 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.2   4.8e-11   7.2e-08       8     144 ..      92     220 ..      85     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.8e-11
                                    ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSCC CS
                    ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeeal 87 
                                     KGGVGKtt +  +a+ l+ +g k+l+i +DP  + s ++     ++ t  +  + + E+  +++l++  ++   +    
  gi|121635904|ref|YP_976127.1|  92 QKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGITDRQSGTPSSYEMLIGEVSLHTALRRSPHSERLF---- 167
                                    59**************************************999999999888888899999998888877654433.... PP

                                    HHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGH CS
                    ArsA_ATPase  88 lgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllsl 144
                                      +  + d+   e + +  +     + + l  +++ ++d+v +D +P    l+ll +
  gi|121635904|ref|YP_976127.1| 168 -CIPATIDLAGAEIELVSMVARENRLRTALAALDNFDFDYVFVDCPPS---LGLLTI 220
                                    .33333333333333333445556677777778888888888888885...333333 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.3e-07   0.00049       4     138 ..      87     226 ..      85     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                       CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregw..araeldgapwrqaale..yapgl 79 
                                    l++   +GGvG+t+ ++ +a al  +g + lviDl p+    +   +  +q+ +    + ++ +  +++a  +    + l
  gi|121635904|ref|YP_976127.1|  87 LTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGITDRQSGTPssYEMLIGEVSLHTALRRspHSERL 166
                                    6667779******************************9998888888744443331133444555555554442234557 PP

                       CBP_BcsQ  80 dllPfG.elnveekenlqqlaekaeallaalkelk.eqyrwillDlpagasaltrellala 138
                                      +P    l+ +e e l ++ +++++l +al++l   +++++++D+p     lt ++l  a
  gi|121635904|ref|YP_976127.1| 167 FCIPATiDLAGAEIE-LVSMVARENRLRTALAALDnFDFDYVFVDCPPSLGLLTINALVAA 226
                                    777876245555555.66788899999999999997899*******999888887776655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.4   0.00049      0.74      11      38 ..      95     122 ..      88     130 .. 0.91
   2 ?    4.3   0.0     0.019        28     135     156 ..     256     277 ..     223     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                                    TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54  11 GaGKTttlaKLaallkkegkkvllvaaD 38 
                                    G+GKTtt+  +aa l  +g k+l++ +D
  gi|121635904|ref|YP_976127.1|  95 GVGKTTTAVNIAAALAVQGLKTLVIDLD 122
                                    9**********************99888 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                                    HHHHHSSCSEEEEESTTSSSST CS
                          SRP54 135 aFkeavgitgviltklDgdakg 156
                                    + + ++++t+vilt  Dg++k 
  gi|121635904|ref|YP_976127.1| 256 HLNPQLEVTTVILTMYDGRTKL 277
                                    567789************9986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.1e-05     0.076       3      36 ..      86     119 ..      84     128 .. 0.86
   2 ?   -2.5   0.0       1.7   2.5e+03      82     114 ..     202     234 ..     187     285 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                          VirC1   3 litfcslkGGaGkttalmglcsalasdgkrvalf 36 
                                    ++t++  kGG Gktt+ + + +ala +g +  + 
  gi|121635904|ref|YP_976127.1|  86 VLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVI 119
                                    799**********************999776555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                          VirC1  82 eGfdyaladtrg..GsselnntiiassdllliPtm 114
                                      fdy+++d     G   +n+ + a   +  iP  
  gi|121635904|ref|YP_976127.1| 202 FDFDYVFVDCPPslGLLTINALVAAPEVM--IPIQ 234
                                    55666666654311444444444433333..3333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4    0.0001      0.16      35      66 ..      87     120 ..      80     210 .. 0.75
   2 ?   -1.2   0.0      0.84   1.3e+03      76     107 ..     237     265 ..     215     316 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                         AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlg.p 66 
                                    l++    +g+GKtt a+++a+a+a +G + l  +
  gi|121635904|ref|YP_976127.1|  87 LTIANQKGGVGKTTTAVNIAAALAvQGLKTLViD 120
                                    56666679****************9998776554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.84
                         AAA_25  76 yvsaEdsedelrrRlravgealrddarllvld 107
                                    y+++E+   +l r ++ v ++l++  +l v++
  gi|121635904|ref|YP_976127.1| 237 YYALEGVS-QLMRNIEMVKAHLNP--QLEVTT 265
                                    66666666.666666666666622..222222 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00016      0.24      23      71 ..      78     127 ..      58     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                    GGG-S-SEEEEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEEEE------ CS
                           MeaB  23 lakaGraqvvGltGv.PGaGkstlvealglelrrrGkrvavlavDPsspf 71 
                                    l++ Gr +v+ +     G+Gk t+  ++++ l+ +G +  v+ +DP  + 
  gi|121635904|ref|YP_976127.1|  78 LQRPGRRRVLTIANQkGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNA 127
                                    567899999999875268****************************8765 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00038      0.57       4      34 ..      95     125 ..      93     133 .. 0.89
   2 ?   -1.9   0.0       1.6   2.4e+03      26      52 ..     207     233 ..     200     267 .. 0.74
   3 ?   -3.9   0.0       6.8     1e+04      22      34 ..     309     321 ..     308     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                         CLP1_P   4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34 
                                     +GK+T a +++  ++ +g k++++DlD+  
  gi|121635904|ref|YP_976127.1|  95 GVGKTTTAVNIAAALAVQGLKTLVIDLDPQG 125
                                    59**************************964 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                         CLP1_P  26 vyvDlDvGqseispPgtislalverpi 52 
                                    v+vD+ +  + +++++ +++  v  pi
  gi|121635904|ref|YP_976127.1| 207 VFVDCPPSLGLLTINALVAAPEVMIPI 233
                                    788888888888888888887776666 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6.8
                         CLP1_P  22 grkpvyvDlDvGq 34 
                                    g++ +++D D+G 
  gi|121635904|ref|YP_976127.1| 309 GYSMTIIDYDPGS 321
                                    567899*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2379.51
//
Query:       gi|121635905|ref|YP_976128.1|  [L=224]
Description: 16S rRNA methyltransferase GidB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-55  187.9   0.0    1.3e-55  187.6   0.0    1.0  1  GidB             rRNA small subunit methyltransferase G
     0.0022   17.6   0.0     0.0036   16.9   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.08   12.0   0.0      0.098   11.8   0.0    1.1  1  VP40             Matrix protein VP40
       0.12   13.0   0.0       0.24   12.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
       0.15   11.7   0.0       0.21   11.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.16   11.0   0.0       0.23   10.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   4.4e-59   1.3e-55       5     179 ..      19     194 ..      15     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 4.4e-59
                                    HHHHHHHHHHHHHHS---S--SHHHHHHHCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHH CS
                           GidB   5 lkkYlelllkwNkkinLtsikepeellerhlldslsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekk 84 
                                    +++Y+e l+  + +++L++++e+ +l++rhll+++++ ell++ + +v+D+GsGaGlPG+pLaiarp+l+++Lle+l ++
  gi|121635905|ref|YP_976128.1|  19 ARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGD-RVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRR 97 
                                    689******************************************.9********************************* PP

                                    HHHHHHHHHHCT-SSEEEEES-CCC...TTTTT-EEEEEEC-SSSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCCHC CS
                           GidB  85 iaFLeevkeelklenveivearaee...kqeeekydvvtsRAlaslnelteillkllkegglilalKGksaedeleekek 161
                                    ++FL+e++++l+++ veiv+ raee   +++    d+++sRA+a+l++lt+++++l++++g++la+KG++a+de++e+++
  gi|121635905|ref|YP_976128.1|  98 TEFLREMVTDLGVA-VEIVRGRAEEswvQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRR 176
                                    **************.************999************************************************** PP

                                    CCCCCCEEEEEEEEEE-T CS
                           GidB 162 alqlskvevlsvkslkek 179
                                     +++s++++++v++++++
  gi|121635905|ref|YP_976128.1| 177 VMIASGAVDVRVVTCGAN 194
                                    *************99765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06    0.0036      31      93 ..      61     123 ..      51     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTS CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleev 93 
                                    + ++v+D+G+GaG+ g+ la + p+++v+l++   r  e+ +e +++ +++ve+v   + e +
  gi|121635905|ref|YP_976128.1|  61 RGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESW 123
                                    4678***************************************99999999999887766655 PP

>> VP40  Matrix protein VP40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05     0.098     118     218 ..      64     167 ..      49     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                    EEEEEEECS---TT-SSHHHHCSEEEEEHHHCS-CCG-STTEEEEEEEEEEEEEEE-TTBT---HHHHHTT..-EEEEEE CS
                           VP40 118 klvrvnrlGtGipdhplrllreGnqaflqelvlprvfltnqftydltalklivqklpddawrpsddkliGs..alrpavs 195
                                    ++v +   G+G+p  pl + r   q  l e +l r+   + +  dl   + iv+   +++w   +d+l Gs  a+  av+
  gi|121635905|ref|YP_976128.1|  64 RVVDIG-SGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESW--VQDQLGGSdaAVSRAVA 140
                                    444443.4899************************999999999*****************..9******9999999**9 PP

                                    SSTTS-....-EE---B-GGGGSS-S- CS
                           VP40 196 ihpklr....pillptvkkqayksgkk 218
                                       kl     p++ p+ +  a k ++ 
  gi|121635905|ref|YP_976128.1| 141 ALDKLTkwsmPLIRPNGRMLAIKGERA 167
                                    999996333477777766666654443 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.24       1      71 [.      65     137 ..      65     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvss 71 
                                    v+d+G G G     la + ++ +v+ +++  +  e  re + + g+ ve+v+g ae+  ++ + g  D+ vs+
  gi|121635905|ref|YP_976128.1|  65 VVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEEswVQDQLGGSDAAVSR 137
                                    89********99999988679**********************************983334455577777774 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.1e-05      0.21      47      75 ..      62      90 ..      43     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.1e-05
                Methyltransf_16 47 klsvlELGsGtGlvGlavaellpeakvil 75
                                   + +v+++GsG+Gl G+ +a + p+++v+l
  gi|121635905|ref|YP_976128.1| 62 GDRVVDIGSGAGLPGVPLAIARPDLQVVL 90
                                   678*****************999999986 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.8e-05      0.23      13      75 ..      44     109 ..      43     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                                    E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TC CS
                         RrnaAD  13 lknkkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kd 75 
                                    l+++ ++n ++    le  + v++ig+G G+  ++La      qvv+lE   r  ++l++ ++ ++
  gi|121635905|ref|YP_976128.1|  44 LWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARpdLQVVLLEPLLRRTEFLREMVTdLG 109
                                    78999999999999999*******************5444589******98888888888776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1670.83
//
Query:       gi|121635906|ref|YP_976129.1|  [L=187]
Description: hypothetical protein BCG_0026c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-15   54.9   0.1    1.4e-14   53.8   0.1    1.6  2  R3H       R3H domain
    5.6e-07   29.3   0.0    9.3e-07   28.6   0.0    1.4  1  KH_4      KH domain


Domain annotation for each model (and alignments):
>> R3H  R3H domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   9.1e+03      29      36 ..      98     105 ..      91     105 .. 0.69
   2 !   53.8   0.1   1.5e-18   1.4e-14       2      59 ..     127     185 ..     126     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                                    HHHHHHHH CS
                            R3H  29 yeRriiHe 36 
                                      R+++H+
  gi|121635906|ref|YP_976129.1|  98 LTRLAVHQ 105
                                    56999996 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 1.5e-18
                                    HHHHHHHHHHHHHH-S--EEE-----SHHHHHHHHHHHHSS.EEEEEE--SS-SEEEEE CS
                            R3H   2 fllrvekklaefvkdtgrslefppmssyeRriiHelaeayg.leseSvGeepkRrvvvt 59 
                                     l ++++++a++v +tg + e+ pm+++eR+i+H++++a + ++seS+G ep+Rrvvv 
  gi|121635906|ref|YP_976129.1| 127 ELAALADEVARRVAETGDREELVPMTPFERKIVHDAVAAVPgVHSESEGVEPERRVVVL 185
                                    68899****************************************************95 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     1e-10   9.3e-07       6      65 ..      47     106 ..      43     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-10
                           KH_4   6 dilkalvddpe.evevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaaanke 65 
                                    d+l++l+d  + + +++++ e ++ ++ ++  ++dl +++G+ G++ldAlq l+ +a++++
  gi|121635906|ref|YP_976129.1|  47 DYLEELLDVLDfDGDIDLDVEGNRAVVSID-GSDDLNKLVGRGGEVLDALQELTRLAVHQK 106
                                    677777777766777777777888888888.7889**********************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1262.86
//
Query:       gi|121635907|ref|YP_976130.1|  [L=366]
Description: preprotein translocase subunit YidC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-49  165.6   0.4    1.2e-48  165.1   0.4    1.1  1  60KD_IMP        60Kd inner membrane protein
     0.0084   15.8   0.1       0.28   10.8   0.0    2.2  2  Wzy_C           O-Antigen ligase
  ------ inclusion threshold ------
      0.082   12.9   0.2       0.21   11.6   0.0    1.7  2  SicP-binding    SicP binding
       0.13   11.0   1.6        1.7    7.3   0.6    2.1  2  DUF2207         Predicted membrane protein (DUF2207)
       0.25   11.4   1.4       0.62   10.1   0.3    2.1  2  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
        2.9    7.8   7.4         36    4.3   3.3    3.0  2  LapA_dom        Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.4     4e-52   1.2e-48       1     164 [.      40     273 ..      40     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 4e-52
                       60KD_IMP   1 yglaIilltiivrlillpltlkqlkssakmqelqPelkeiqekykkdkqklqqemmklYkkegvnplaGclplLiqlpif 80 
                                    ++l++++l++++r++l++ +++q++++++mqelqP++k++q+ky kd+q+++ em+kl++++g+np+ Gclp+L q+p+f
  gi|121635907|ref|YP_976130.1|  40 WALSVMFLVFTLRALLYKPFVRQIRTTRQMQELQPQIKALQKKYGKDRQRMALEMQKLQREHGFNPILGCLPMLAQIPVF 119
                                    89****************************************************************************** PP

                       60KD_IMP  81 ialyrvlrsla....................................sfwikdLsapd...................... 102
                                    ++ly+vlrs++                                      ++++++a+                       
  gi|121635907|ref|YP_976130.1| 120 LGLYHVLRSFNrttggfgqphlsvienrltgnyvfspvdvghfldanL-FGAPIGAYMtqrsgldvfvdfsrpaliavgv 198
                                    *********999999999998888888888887777777775555530.3333333225566666777777777999999 PP

                       60KD_IMP 103 .lpillavttflqqkls...ksk..........kmqkmmlyvmplmilffslsfpaglvlYwlvsnllsiaqqlii 164
                                     ++il++++t+++++ s   + +          +m+k+ lyv+pl +++ + ++p +++lYw+ +n+++++qq+++
  gi|121635907|ref|YP_976130.1| 199 pVMILAGIATYFNSRASiarQ-SaeaaanpqtaMMNKLALYVFPLGVVVGGPFLPLAIILYWFSNNIWTFGQQHYV 273
                                    999**********99995541.134445555535599************************************986 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.028        83      18      59 ..      18      65 ..       2     132 .. 0.64
   2 !   10.8   0.0   9.4e-05      0.28      10      89 ..     184     290 ..     178     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.028
                          Wzy_C 18 giigllvalivlliifykrripfllllgilvgvilliilfv........l 59
                                   ++i  +   ++++++++ ++++++l   ++ +v +l +l++         
  gi|121635907|ref|YP_976130.1| 18 SWIMWVWYRLFAFVLGPSNFFAWALS--VMFLVFTLRALLYkpfvrqirT 65
                                   55555555666777777777744433..5555555555555555553331 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.4e-05
                          Wzy_C  10 lflstsRsgiigl.lvalivlliifykrri..........................pfllllgilvgvilliilfvlstn 62 
                                    +f+  sR ++i++ +  +i++ i++y + +                            l+++++   + l+iil ++s+n
  gi|121635907|ref|YP_976130.1| 184 VFVDFSRPALIAVgVPVMILAGIATYFNSRasiarqsaeaaanpqtammnklalyvFPLGVVVGGPFLPLAIILYWFSNN 263
                                    788899*******533466667777777777*****************98777555222222222224578888889999 PP

                          Wzy_C  63 letlknitkafgkldkkkgkdksgssR 89 
                                    + t++++ + fg  +k++++ k+   R
  gi|121635907|ref|YP_976130.1| 264 IWTFGQQHYVFGMIEKEEEAKKQEAVR 290
                                    999999999999999885554444443 PP

>> SicP-binding  SicP binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     7e-05      0.21      28      66 ..      59      98 ..      35     105 .. 0.82
   2 ?   -3.5   0.0       3.5     1e+04      20      30 ..     284     294 ..     272     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                                   HHHCS--S-H.HHHHHHHHHHHHTTSCHHHHHHHHHHHH- CS
                   SicP-binding 28 yaeqvrvedr.kiLevfllaLskkyGeeavkdaldysair 66
                                   +  q+r   + + L+  ++aL kkyG++  + al++ + +
  gi|121635907|ref|YP_976130.1| 59 FVRQIRTTRQmQELQPQIKALQKKYGKDRQRMALEMQKLQ 98
                                   6678997655378**********************98866 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                                    T-HHHHHHHHH CS
                   SicP-binding  20 kntevvrkyae 30 
                                    k+ e+vr+ a 
  gi|121635907|ref|YP_976130.1| 284 KKQEAVRRRAA 294
                                    77888888775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.6   0.00058       1.7     381     453 ..       8      81 ..       6      94 .. 0.72
   2 ?    2.7   0.0     0.014        43     184     231 ..     211     260 ..     172     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                        DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrr..teeGaellakwkgFkk 453
                                    ++l +++  + ++++++  l++++l++ ++f+++ l + +l++ + +ll++ ++++   t++ +el  ++k+++k
  gi|121635907|ref|YP_976130.1|   8 FSLDFIYYPVSWIMWVWYRLFAFVLGP-SNFFAWALSVMFLVFTLRALLYKPFVRQIrtTRQMQELQPQIKALQK 81 
                                    567777778889999999999999998.5555555555555555555555566666457*************965 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.014
                        DUF2207 184 nkldeilkeeqk..ntreraarlslallillilllillllllllllikll 231
                                    n++++i ++ ++  ++ + a  ++lal+++++ +++   +l+l ++++++
  gi|121635907|ref|YP_976130.1| 211 NSRASIARQSAEaaANPQTAMMNKLALYVFPLGVVVGGPFLPLAIILYWF 260
                                    56666666666666777778888888888888888888888888888843 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00021      0.62       6      91 ..      17      90 ..      12     101 .. 0.78
   2 ?   -0.9   0.0      0.48   1.4e+03      28      49 ..     194     217 ..     172     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                 Halogen_Hydrol  6 lsiliavivalvsffllgfsfflalliailggilvyvasrknkkkkhlkksglsrkelkyiretlkeakekikrlekalkrv 87
                                   +s++++v++ l++f+l   +ff++    +l+ +++ ++ r      ++k+     +++   +++++e + +ik+l+k + + 
  gi|121635907|ref|YP_976130.1| 17 VSWIMWVWYRLFAFVLGPSNFFAW----ALSVMFLVFTLR----ALLYKP---FVRQI-RTTRQMQELQPQIKALQKKYGKD 86
                                   899************999999999....999999999999....677777...34444.56789999999999999999887 PP

                 Halogen_Hydrol 88 rsle 91
                                   r++ 
  gi|121635907|ref|YP_976130.1| 87 RQRM 90
                                   7654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.48
                 Halogen_Hydrol  28 la..lliailggilvyvasrknkk 49 
                                    +a  + ++il+gi++y+ sr    
  gi|121635907|ref|YP_976130.1| 194 IAvgVPVMILAGIATYFNSRASIA 217
                                    342344569999999999883333 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.3     0.012        36      40      62 ..      60      82 ..      27      83 .. 0.69
   2 ?    4.0   0.0     0.015        43      27      57 ..     194     224 ..     192     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                       LapA_dom 40 wsylrlrrelrrlkkkikkleke 62
                                   ++++r+ r++++l+ +ik+l+k+
  gi|121635907|ref|YP_976130.1| 60 VRQIRTTRQMQELQPQIKALQKK 82
                                   56779****************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                       LapA_dom  27 fgiGallgwllslwsylrlrrelrrlkkkik 57 
                                    +++G+ +++l+++ +y+  r  + r+  + +
  gi|121635907|ref|YP_976130.1| 194 IAVGVPVMILAGIATYFNSRASIARQSAEAA 224
                                    689999******************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 2490.33
//
Query:       gi|121635908|ref|YP_976131.1|  [L=120]
Description: hypothetical protein BCG_0028c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-27   92.6   0.1    1.3e-26   92.2   0.1    1.2  1  YidD      Putative membrane protein insertion efficiency fact


Domain annotation for each model (and alignments):
>> YidD  Putative membrane protein insertion efficiency factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.1   7.3e-31   1.3e-26       4      65 ..      23      85 ..      20      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 7.3e-31
                           YidD  4 lialirlYqkvispll.ksCrfyptCSeYaleaiekyGllkGlllalkRilrCnplskgGyDp 65
                                   li++i++Y++++spl+ +sCrf+ptCS+Ya++a+++yGll+G++l++ R+++C p+++gG+Dp
  gi|121635908|ref|YP_976131.1| 23 LIFVIQVYRHMLSPLRpASCRFVPTCSQYAVDALTEYGLLRGSWLTMIRLAKCGPWHRGGWDP 85
                                   899***********7779********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 950.28
//
Query:       gi|121635909|ref|YP_976132.1|  [L=125]
Description: ribonuclease P [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-23   81.4   0.3    5.3e-23   81.2   0.3    1.0  1  Ribonuclease_P  Ribonuclease P


Domain annotation for each model (and alignments):
>> Ribonuclease_P  Ribonuclease P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.3     3e-27   5.3e-23       2     109 ..      12     117 ..      11     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 3e-27
                 Ribonuclease_P   2 pkkerLkkraeFqavfregkrvaskdlvlyalknsleksslrlGlsvskkvgkAvvRNrikRllReafrlnkdelpagld 81 
                                    + ++r++++a+F++++++g r  ++d+v+y++  s + +  r+Gl+++k vg+Av+R+r+ R+lR+++   ++el ++ +
  gi|121635909|ref|YP_976132.1|  12 RARNRMRRSADFETTVKHGMRTVRSDMVVYWWRGSGGGP--RVGLIIAKSVGSAVERHRVARRLRHVAGSIVKELHPSDH 89 
                                    6789*****************************666665..*************************************** PP

                 Ribonuclease_P  82 lvviakkgaaeadfaelekelekllkkl 109
                                    +v++a ++ + +++a+le++l+  l+++
  gi|121635909|ref|YP_976132.1|  90 VVIRALPSSRHVSSARLEQQLRCGLRRA 117
                                    ************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 965.14
//
Query:       gi|121635910|ref|YP_976133.1|  [L=47]
Description: 50S ribosomal protein L34 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-18   65.2  14.6      4e-18   65.1  14.6    1.0  1  Ribosomal_L34  Ribosomal protein L34


Domain annotation for each model (and alignments):
>> Ribosomal_L34  Ribosomal protein L34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1  14.6   2.2e-22     4e-18       2      44 .]       5      47 .]       4      47 .] 0.98

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.2e-22
                                   --S----HHHHHCSSSHHHHHHSHHHHHHHHHHHTTSSS-SCC CS
                  Ribosomal_L34  2 krtyqPskrkRkrkhGFraRmstknGrkvLkrRraKGRkrLsv 44
                                   krt+qP++r+R+r+hGFr Rm+t++Gr ++++Rr+KGR +Ls+
  gi|121635910|ref|YP_976133.1|  5 KRTFQPNNRRRARVHGFRLRMRTRAGRSIVSSRRRKGRRTLSA 47
                                   9****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 374.02
//
Query:       gi|121635911|ref|YP_976134.1|  [L=507]
Description: chromosomal replication initiation protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-103  345.7   0.1   2.5e-103  344.6   0.0    1.6  2  Bac_DnaA      Bacterial dnaA  protein
      4e-27   94.0   0.0    8.4e-27   93.0   0.0    1.6  1  Bac_DnaA_C    Bacterial dnaA protein helix-turn-helix
    5.4e-10   39.3   0.0    1.1e-09   38.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
    8.5e-06   26.2   0.0    0.00023   21.6   0.0    3.2  4  AAA           ATPase family associated with various cellular 
     0.0011   19.2   0.3        1.4    9.2   0.0    2.9  2  AAA_22        AAA domain
     0.0091   15.7   0.0      0.033   13.9   0.0    2.0  2  DnaA_N        DnaA N-terminal domain
  ------ inclusion threshold ------
      0.012   14.5   0.0       0.54    9.1   0.0    2.2  2  AFG1_ATPase   AFG1-like ATPase
      0.015   15.7   0.4       0.25   11.7   0.0    2.7  3  AAA_16        AAA ATPase domain
      0.076   13.4   0.0       0.21   12.0   0.0    1.8  1  RNA_helicase  RNA helicase
      0.082   12.7   0.0       0.28   11.0   0.0    2.0  1  HTH_38        Helix-turn-helix domain
       0.13   12.2   0.0       0.45   10.4   0.0    1.8  1  ATPase_2      ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.6   0.0  1.5e-106  2.5e-103       1     218 [.     168     385 ..     168     386 .. 0.99
   2 ?   -2.6   0.0       2.5     4e+03     180     207 ..     405     433 ..     389     443 .. 0.66

  Alignments for each domain:
  == domain 1  score: 344.6 bits;  conditional E-value: 1.5e-106
                                    --SS-SGGG----TTTHHHHHHHHHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHH CS
                       Bac_DnaA   1 LnkrytFetFviGasnrlAlaaalkvaeapgkkynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelv 80 
                                    Ln+rytF+tFviGasnr+A+aaal++aeap+++ynPlfi+ge+GlGktHLl+a+gn++++ +p +rv+Y+++eeF+n+++
  gi|121635911|ref|YP_976134.1| 168 LNRRYTFDTFVIGASNRFAHAAALAIAEAPARAYNPLFIWGESGLGKTHLLHAAGNYAQRLFPGMRVKYVSTEEFTNDFI 247
                                    89****************************************************************************** PP

                                    HHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEE CS
                       Bac_DnaA  81 kalrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlv 160
                                    ++lrd+++ +fk+++r+vDvLl+DDiqf++gke++qee+fhtfn+l++++kq+v+ssDr+Pk+l++ledrlr+rfe+Gl+
  gi|121635911|ref|YP_976134.1| 248 NSLRDDRKVAFKRSYRDVDVLLVDDIQFIEGKEGIQEEFFHTFNTLHNANKQIVISSDRPPKQLATLEDRLRTRFEWGLI 327
                                    ******************************************************************************** PP

                                    EE-----HHHHHHHHHHHHHHTT----TTHHHHHHHH--S-HHHHHHHHHHHHHHHHH CS
                       Bac_DnaA 161 vdieppdletrlailkkkieaeklevpeevlefiaervtdnvRelegalnrlkayasl 218
                                    +d++pp+letr+ail+kk+++e+l vp++vle+ia+++++n+Relegal+r++a+asl
  gi|121635911|ref|YP_976134.1| 328 TDVQPPELETRIAILRKKAQMERLAVPDDVLELIASSIERNIRELEGALIRVTAFASL 385
                                    ******************************************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                    HHTT----.TTHHHHHHHH--S-HHHHHH CS
                       Bac_DnaA 180 eaeklevp.eevlefiaervtdnvReleg 207
                                    +a+ +++    ++   ae++++ v el+g
  gi|121635911|ref|YP_976134.1| 405 DANTMQISaATIMAATAEYFDTTVEELRG 433
                                    34455554156788888999999999887 PP

>> Bac_DnaA_C  Bacterial dnaA protein helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   5.1e-30   8.4e-27       3      69 .]     415     480 ..     413     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 5.1e-30
                                    HHHHTHHHHTT--HHHHHS----CSSHHHHHHHHHHHHHTS---HHHHHHHHT-STTHHHHHHHHHH CS
                     Bac_DnaA_C   3 kIieaVaeyfgvsvedlkskkRkkeiveaRqiamylareltdlslpeIGkefggrdHsTVihaikki 69 
                                    +I++a+aeyf+ +ve+l+++ +++ +++ Rqiamyl+reltdlslp+IG++f grdH+TV++a +ki
  gi|121635911|ref|YP_976134.1| 415 TIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAF-GRDHTTVMYAQRKI 480
                                    79**************************************************.8***********98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   6.5e-13   1.1e-09      48     153 ..     202     310 ..     165     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 6.5e-13
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavr..aglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqa 125
                                    + + + G sG GK+hl  a g  a r   g++v +v++e++ +      rd++     +++  vd+l++Dd+ + + ++ 
  gi|121635911|ref|YP_976134.1| 202 NPLFIWGESGLGKTHLLHAAGNYAQRlfPGMRVKYVSTEEFTNDFINSLRDDRKVAFKRSYRDVDVLLVDDIQFIEGKEG 281
                                    557899*****************999778*******************999999999*********************** PP

                      IstB_IS21 126 eaellfeviekrye.rrsiiitsnlpfae 153
                                     +e++f+  +   + ++ i+i+s+ p ++
  gi|121635911|ref|YP_976134.1| 282 IQEEFFHTFNTLHNaNKQIVISSDRPPKQ 310
                                    *********99887257899999998776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.94   1.5e+03       7      23 ..       5      21 ..       3      88 .. 0.81
   2 ?   -1.2   0.0       1.6   2.6e+03     102     112 ..     175     185 ..     131     192 .. 0.60
   3 !   21.6   0.0   1.4e-07   0.00023       2     129 ..     205     323 ..     204     326 .. 0.83
   4 ?   -2.2   0.1       3.3   5.4e+03      19      39 ..     399     424 ..     387     448 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.94
                                   TTSSHHHHHHHHHHHHT CS
                            AAA  7 pGtGKTllakavakelg 23
                                   pG G T++ +av++el+
  gi|121635911|ref|YP_976134.1|  5 PGSGFTTVWNAVVSELN 21
                                   999**********9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                    TEEEEEEESSG CS
                            AAA 102 kvivigatnrp 112
                                    +++viga+nr 
  gi|121635911|ref|YP_976134.1| 175 DTFVIGASNRF 185
                                    46788888885 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.4e-07
                                    EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                            AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                     ++G  G GKT l +a  + +     g+++  +s  e++++++    ++ +  fk+  +     +l++D+i  + +++  
  gi|121635911|ref|YP_976134.1| 205 FIWGESGLGKTHLLHAAGNYAqrlfpGMRVKYVSTEEFTNDFINSLRDDRKVAFKRSYRD--VDVLLVDDIQFIEGKE-- 280
                                    579*****************955555699**************99999999999997665..49**********8888.. PP

                                    CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                            AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                            +++++++ ++ + + ++   +++ + rp k    l  +R+  ++e
  gi|121635911|ref|YP_976134.1| 281 -------GIQEEFFHTFNTLHNANK--QIVISSDRPPKQLATLE-DRLRTRFE 323
                                    .......899999999999999644..66777888777777777.77776665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.3
                                    HHHH..THEEEEEETTTCSSS...ST CS
                            AAA  19 akel..gvefleisgsellsk...yv 39 
                                     ++l  +++ ++is+++++     y+
  gi|121635911|ref|YP_976134.1| 399 LRDLiaDANTMQISAATIMAAtaeYF 424
                                    33323356666666666663222233 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00087       1.4       8      25 ..     204     221 ..     199     240 .. 0.85
   2 !    6.6   0.1    0.0056       9.1      91     118 ..     259     296 ..     235     304 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00087
                         AAA_22   8 lvvtGesGtGKTtllrrl 25 
                                    l+++GesG GKT+ll   
  gi|121635911|ref|YP_976134.1| 204 LFIWGESGLGKTHLLHAA 221
                                    789***********9765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0056
                         AAA_22  91 v.....ielliiDEaqhlr..s...eealeeLrsllnl 118
                                    +     + +l++D++q++   +   ee + ++ +l+n 
  gi|121635911|ref|YP_976134.1| 259 KrsyrdVDVLLVDDIQFIEgkEgiqEEFFHTFNTLHNA 296
                                    04444689**********87615559999999999994 PP

>> DnaA_N  DnaA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.9   9.6e+03       2      11 ..      11      20 ..      11      21 .. 0.84
   2 !   13.9   0.0     2e-05     0.033      21      63 ..      45      87 ..      35      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.9
                         DnaA_N  2 elWsavlerL 11
                                   ++W+av ++L
  gi|121635911|ref|YP_976134.1| 11 TVWNAVVSEL 20
                                   58****9987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2e-05
                         DnaA_N 21 dtWikplklfalknngltlivpneFardwiesnYldriaellk 63
                                   + W+  +++  + ++   l+vp++F+++ ie++    i+++l+
  gi|121635911|ref|YP_976134.1| 45 RAWLNLVQPLTIVEGFALLSVPSSFVQNEIERHLRAPITDALS 87
                                   57999999999*8888*****************9999998875 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00033      0.54      59     109 ..     198     252 ..     152     261 .. 0.70
   2 ?    3.2   0.0      0.02        32     287     343 ..     266     322 ..     257     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtylmdlf..f..eslpvekkrrvhfhafmarvhdeltk 109
                                     ++ + l++wG  G GKt+l+  +  +  +  p+ + + v + +f  +  + l+ 
  gi|121635911|ref|YP_976134.1| 198 ARAYNPLFIWGESGLGKTHLLHAAgnYaqRLFPGMRVKYVSTEEFTNDFINSLRD 252
                                    557788***************7652231144677777777777777776666665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                    AFG1_ATPase 287 htvlledVpvltkakedaarRfiaLvDelYdadvklvvsaevaleelye.agrlefef 343
                                      +l++d++ ++ +ke  +  f     +l +a+ ++v+s + ++++l + ++rl+  f
  gi|121635911|ref|YP_976134.1| 266 DVLLVDDIQFIE-GKEGIQEEFFHTFNTLHNANKQIVISSDRPPKQLATlEDRLRTRF 322
                                    556788888887.99999****************************975266776666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.4   5.5e+03      57      91 ..      66     100 ..      45     144 .. 0.65
   2 ?   11.7   0.0   0.00015      0.25      22      51 ..     199     228 ..     186     319 .. 0.78
   3 ?    0.9   0.1      0.33   5.3e+02      46     124 ..     363     444 ..     356     492 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.4
                         AAA_16  57 rgkcdqlesaipysa.laqalareellrqlldeaes 91 
                                       ++q+e ++++ a +++al+r +l  q+    + 
  gi|121635911|ref|YP_976134.1|  66 PSSFVQNEIERHLRApITDALSR-RLGHQIQLGVRI 100
                                    55666666666664447777755.666666655333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd 51 
                                       + +++ GesG GK+ l+ ++ +++++ 
  gi|121635911|ref|YP_976134.1| 199 RAYNPLFIWGESGLGKTHLLHAAGNYAQRL 228
                                    333889**************9988655544 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.33
                         AAA_16  46 ralekd....ggiflrgkcdqlesaipysa.laqalareellrqllde......aesaeleawrekleealaavpelaga 114
                                     ++e++    +g ++r ++  +  ++p +  la++  r +l+++ +++        +a +e+++++       v el+g 
  gi|121635911|ref|YP_976134.1| 363 SSIERNirelEGALIRVTAFASLNKTPIDKaLAEIVLR-DLIADANTMqisaatIMAATAEYFDTT-------VEELRGP 434
                                    45555544444445555555554567776668888855.888888888443333222223333332.......3344444 PP

                         AAA_16 115 easrllellk 124
                                    +++r l++ +
  gi|121635911|ref|YP_976134.1| 435 GKTRALAQSR 444
                                    4433333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.21       2      84 ..     205     301 ..     204     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..........klkkkdsvys...rnpeddfwdgYtgqevvvidDfgqvkdee..n 66 
                                    +++G+sg GK++l +  a + +++l           ++ +++++       +  f  +Y++ +v+++dD+  ++ +e  +
  gi|121635911|ref|YP_976134.1| 205 FIWGESGLGKTHLLHA-AGNYAQRLfpgmrvkyvsTEEFTNDFINslrDDRKVAFKRSYRDVDVLLVDDIQFIEGKEgiQ 283
                                    89**************.77777777899999999955555555554312333445599*************999665544 PP

                   RNA_helicase  67 psdlaelirlvsstpypl 84 
                                    ++ +++++ l + ++ ++
  gi|121635911|ref|YP_976134.1| 284 EEFFHTFNTLHNANKQIV 301
                                    448888888888777665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.28      20      39 ..     456     475 ..     440     478 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                         HTH_38  20 GlslreIArrLgrspsTIsR 39 
                                    +lsl +I++  gr+++T+ +
  gi|121635911|ref|YP_976134.1| 456 DLSLPKIGQAFGRDHTTVMY 475
                                    69***************975 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00028      0.45      19     122 ..     200     302 ..     192     306 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl..edkdkyviyyi..alreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                     ++++fi+G  g GKt Ll  + +    +  + +v y++  ++ +++i++l++     +++    k    +v    ++ i
  gi|121635911|ref|YP_976134.1| 200 AYNPLFIWGESGLGKTHLLHAAGNYAqrLFPGMRVKYVSteEFTNDFINSLRDD----RKVA--FKRSYRDVDVLLVDDI 273
                                    5799***************98866552144455555554112333333333333....2222..2222233333333333 PP

                       ATPase_2  95 lk.eksklvfkaielllekikkkgkkiii 122
                                       e ++ +++ +   ++ + +  k+i+i
  gi|121635911|ref|YP_976134.1| 274 QFiEGKEGIQEEFFHTFNTLHNANKQIVI 302
                                    22355555666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3177.22
//
Query:       gi|121635912|ref|YP_976135.1|  [L=402]
Description: DNA polymerase III subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-44  149.9   0.0    5.2e-36  123.4   0.0    2.4  3  DNA_pol3_beta    DNA polymerase III beta subunit, N-terminal 
    2.6e-36  124.4   0.0      2e-33  115.0   0.0    2.7  3  DNA_pol3_beta_2  DNA polymerase III beta subunit, central dom
    1.4e-34  118.6   0.0    1.3e-33  115.4   0.0    2.3  2  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.21   11.5   0.0    1.3  1  SEF14_adhesin    SEF14-like adhesin


Domain annotation for each model (and alignments):
>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.0   1.2e-39   5.2e-36       2     121 .]      14     130 ..      13     130 .. 0.98
   2 !   24.0   0.0   7.6e-09   3.4e-05       9      91 ..     143     227 ..     139     259 .. 0.86
   3 ?   -3.3   0.0       2.1   9.2e+03      59      90 ..     324     354 ..     295     361 .. 0.60

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.2e-39
                                    EEEEEHHHHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHH CS
                  DNA_pol3_beta   2 kftiereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivka 81 
                                     f++ re++++++++vak +++R+ +p+Lsgvll+ +d++l+++g+D+e+s+e+++ ae+  ++g+vlv++rll+di++a
  gi|121635912|ref|YP_976135.1|  14 TFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIV-SPGSVLVSGRLLSDITRA 92 
                                    68999********************************************************.9***************** PP

                                    SSTTSEEEEEEETTEEEEEEETTEEEEEE-BEGGGS---- CS
                  DNA_pol3_beta  82 Lpndkkvkisvneqklliiksgssrfslstlsaeeypnlp 121
                                    Lpn k+v ++v++++++++ +g++rfsl+t+++e+yp+lp
  gi|121635912|ref|YP_976135.1|  93 LPN-KPVGVHVEGNRVALT-CGNARFSLPTMPVEDYPTLP 130
                                    ***.***************.*****************997 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 7.6e-09
                                    HHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEE..EEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTS CS
                  DNA_pol3_beta   9 ellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisi..estisaeseeeegkvlvparllldivkaLpndk 86 
                                     +++++++va +  +  tlp+L+g+ +e+  +++ l +tD+   +  e + sa+s++ e +vlvpa++l+++ ka   ++
  gi|121635912|ref|YP_976135.1| 143 LFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAvrELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGS 222
                                    58899***********************************96554124456677778999*************9977777 PP

                                    EEEEE CS
                  DNA_pol3_beta  87 kvkis 91 
                                    +v +s
  gi|121635912|ref|YP_976135.1| 223 DVRLS 227
                                    77776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.1
                                    SEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEE CS
                  DNA_pol3_beta  59 aeseeeegkvlvparllldivkaLpndkkvki 90 
                                       + e+ ++  ++ +l d +++L   + v++
  gi|121635912|ref|YP_976135.1| 324 VDYAGEPLTIAFNPTYLTDGLSSLRS-ERVSF 354
                                    33445666777777888887777777.66666 PP

>> DNA_pol3_beta_2  DNA polymerase III beta subunit, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0029        13      20     105 ..      35     116 ..      17     123 .. 0.82
   2 !  115.0   0.0   4.5e-37     2e-33       2     116 .]     139     260 ..     138     260 .. 0.98
   3 ?   -1.4   0.0      0.61   2.7e+03      76     101 ..     286     311 ..     274     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                                    SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTCEEEEEEEHHHHHHHHHHHTSSSSEEEEEEESSEEEEE CS
                DNA_pol3_beta_2  20 edetrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeqvklalsegkirfe 99 
                                       + pvL Gv l  +++ l+++  d    a +++ +e  ++   sv+v  + l +++++l +  + v + ++ +++ ++
  gi|121635912|ref|YP_976135.1|  35 ARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSP--GSVLVSGRLLSDITRALPN--KPVGVHVEGNRVALT 110
                                    555678999**9999999999999997777777777777777..69***************99..999999999999999 PP

                                    ETTEEE CS
                DNA_pol3_beta_2 100 vgnvrl 105
                                    +gn+r+
  gi|121635912|ref|YP_976135.1| 111 CGNARF 116
                                    999987 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 4.5e-37
                                    EEHHHHHHHHHCCGGGS-SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTC.EEEEEEEHHHHHHHHHHH CS
                DNA_pol3_beta_2   2 lkqkelkelieqvafaasedetrpvLtGvrleieedklllaaTdghRlavrkleleeeeed.easvivPaktlaelakll 80 
                                    l+++ ++e+i+qva+aa++d+t+p+LtG+r+ei +++++laaTd++Rlavr+l+++++++d ea+v+vPaktlae+ak+ 
  gi|121635912|ref|YP_976135.1| 139 LPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDiEAAVLVPAKTLAEAAKAG 218
                                    68899*************************************************************************** PP

                                    TSSSSEEEEEEE.......SSEEEEEETTEEEEEE-BSS---B CS
                DNA_pol3_beta_2  81 edneeqvklals.......egkirfevgnvrltsrlldgkfPd 116
                                       +++v+l+l+       +g ++++ +++r+t+rlld++fP+
  gi|121635912|ref|YP_976135.1| 219 IG-GSDVRLSLGtgpgvgkDGLLGISGNGKRSTTRLLDAEFPK 260
                                    99.***************************************7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.61
                                    HHHHHTSSSSEEEEEEESSEEEEEET CS
                DNA_pol3_beta_2  76 laklledneeqvklalsegkirfevg 101
                                    l  l++d + qv++ +++g +r+++g
  gi|121635912|ref|YP_976135.1| 286 LVALVADRGAQVRMEFADGSVRLSAG 311
                                    44456677888899888888888766 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.13   5.9e+02       5      34 ..     130     158 ..     128     193 .. 0.80
   2 !  115.4   0.0   2.9e-37   1.3e-33       1     111 [.     262     371 ..     262     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.13
                                    -SS-SEEEEEEHHHHHHHHHHHHTTSSTST CS
                DNA_pol3_beta_3   5 PkefkkkvtvdlkelkealkRvalladekn 34 
                                    P+  +++ ++  + ++ea++ va+ a ++ 
  gi|121635912|ref|YP_976135.1| 130 PTLPEETGLLPAELFAEAISQVAIAA-GRD 158
                                    6666666677788999*******998.555 PP

  == domain 2  score: 115.4 bits;  conditional E-value: 2.9e-37
                                    CCCS-SS-SEEEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETTSEEEEEEEEEBEESS-EEEEEEHHHH CS
                DNA_pol3_beta_3   1 krllPkefkkkvtvdlkelkealkRvalladeknrkvrLsleegqlklsaensevgeaeEevdvnyeGeeleiafNvsYl 80 
                                    ++llP+e+++++t+d++el ea+k val+ad + ++vr+++ +g+++lsa++++vg+aeE++ v+y Ge+l+iafN++Yl
  gi|121635912|ref|YP_976135.1| 262 RQLLPTEHTAVATMDVAELIEAIKLVALVAD-RGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYL 340
                                    69****************************5.************************************************ PP

                                    HHHHHHH-SSEEEEEESSTTS-EEEEETTEE CS
                DNA_pol3_beta_3  81 ldalkaleteevelqltdstkpvllsevede 111
                                    +d+l++l +e+v++ +t++ kp+ll++v+ +
  gi|121635912|ref|YP_976135.1| 341 TDGLSSLRSERVSFGFTTAGKPALLRPVSGD 371
                                    **************************98755 PP

>> SEF14_adhesin  SEF14-like adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.21      67     136 ..      45     114 ..      21     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                  SEF14_adhesin  67 irltGshasvsvaGddasvsGGlitvpfkdtaGqvlfrGrinaeiiqdqattivdglapGwrlassqetl 136
                                    + ltGs +++ ++G d  vs          + G vl  Gr+ ++i+++  +  v+    G r+a +  + 
  gi|121635912|ref|YP_976135.1|  45 VLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVGVHVEGNRVALTCGNA 114
                                    679*****************998888888899***********************9999***99876553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2903.09
//
Query:       gi|121635913|ref|YP_976136.1|  [L=385]
Description: recombination protein F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-16   57.9   0.0    1.5e-15   57.2   0.0    1.3  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.3e-07   32.3   0.0    1.7e-07   32.0   0.0    1.2  1  AAA_23       AAA domain
    2.2e-06   27.7   0.1    0.00011   22.1   0.0    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.2e-06   26.7   0.0    5.6e-06   26.3   0.0    1.1  1  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.025   15.1   0.0      0.042   14.4   0.0    1.4  1  ABC_tran     ABC transporter
      0.074   13.0   0.0       0.15   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.077   12.7   0.0       0.17   11.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.081   13.2   0.1        0.2   11.9   0.1    1.7  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.14   11.4   0.0       0.23   10.7   0.0    1.3  1  DUF2813      Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   7.7e-19   1.5e-15       1     196 [.       2     353 ..       2     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 7.7e-19
                                    EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80 
                                    ++++l +++F+s+a   v+l+++++ t+ vGpNG GK+nl++A+ +        + r +    li        +++a ++
  gi|121635913|ref|YP_976136.1|   2 YVRHLGLRDFRSWA--CVDLELHPGRTVFVGPNGYGKTNLIEALWYSTTLG---SHRVSADLPLIRV-----GTDRAVIS 71 
                                    688999*******5..9***************************6643332...4488888889998.....78888899 PP

                                    EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx........................ RF
                          SMC_N  81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtk.kevsellesagiske........................ 135
                                     ++ n++++       + +  ++ ++  ++ ++n+++v++ ++v  +l+ + + +e                        
  gi|121635913|ref|YP_976136.1|  72 TIVVNDGRE-------CAVDLEIATGRVNKARLNRSSVRStRDVVGVLRAVLFAPEdlglvrgdpadrrrylddlaivrr 144
                                    888888888.......99999999999999********9989************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121635913|ref|YP_976136.1| 145 paiaavraeyervvrqrtallksvpgaryrgdrgvfdtlevwdsrlaehgaelvaaridlvnqlapevkkayqllapesr 224
                                    ******************************************************************************** PP

                                    ...................................................................CS-HHHHHHHHHH CS
                                    ...................................................................xxxxxxxxxxxxx RF
                          SMC_N 136 ...................................................................lLSgGektLvala 148
                                                                                                         S Ge   +a+a
  gi|121635913|ref|YP_976136.1| 225 sasigyrasmdvtgpseqsdtdrqllaarllaalaarrdaelergvclvgphrddlilrlgdqpakgFASHGEAWSLAVA 304
                                    ******************************************************************************** PP

                                    HHHH....HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                    xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfA....iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                    L++A    ++    +p+ llD++ a+LD ++++++a+  ++++   Q++v++
  gi|121635913|ref|YP_976136.1| 305 LRLAayqlLRVDGGEPVLLLDDVFAELDVMRRRALATAAESAE---QVLVTA 353
                                    ****77744445679*********************9988887...999886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   8.5e-11   1.7e-07       2      55 ..       6      65 ..       5     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8.5e-11
                         AAA_23  2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks......g 55
                                   L ++ frs+  +++++++g t+++GpNG GKT +++A+ + ++  ++r s +        
  gi|121635913|ref|YP_976136.1|  6 LGLRDFRSWACVDLELHPGRTVFVGPNGYGKTNLIEALWYSTTLGSHRVSADLplirvgT 65
                                   56889***********************************99987777666545554432 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.5e-08   0.00011       2      22 ..      26      46 ..      25      91 .. 0.83
   2 ?   -0.8   0.0      0.55   1.1e+03     142     255 ..     176     262 ..     157     273 .. 0.58
   3 ?    2.2   0.0     0.067   1.3e+02     246     287 ..     308     348 ..     300     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   +v++GpNg GK+nL++al++ 
  gi|121635913|ref|YP_976136.1| 26 TVFVGPNGYGKTNLIEALWYS 46
                                   8*****************975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.55
                         AAA_21 142 kaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergv 221
                                    ++ +++t + w+++l  +g    +   ++i   +   +++k+  q l ++++ + i +++++++   ++           
  gi|121635913|ref|YP_976136.1| 176 DRGVFDTLEVWDSRLAEHGA---ELVAARIDLVNQLAPEVKKAYQLLAPESRSASIGYRASMDVTGPSE----------- 241
                                    44555555555555555544...4444444444555556666666666666666666666654444432........... PP

                         AAA_21 222 vflengdgqelparelSdGtkrll..alltallral 255
                                                    Sd  ++ll  +ll+al++++
  gi|121635913|ref|YP_976136.1| 242 ---------------QSDTDRQLLaaRLLAALAARR 262
                                    ...............388888886667777776665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.067
                         AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                    a + +l  + ++ ++ll+D++ + L+  + r l++  +++++
  gi|121635913|ref|YP_976136.1| 308 AAYQLLRVDGGE-PVLLLDDVFAELDVMRRRALATAAESAEQ 348
                                    444444444444.*************9999999987776654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.8e-09   5.6e-06       1      44 [.       1      44 [.       1      51 [. 0.95

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.8e-09
                         AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileald 44
                                   M+++ + ++ FRs   v+++l +  tv++G+N+ GK++++eal+
  gi|121635913|ref|YP_976136.1|  1 MYVRHLGLRDFRSWACVDLELHPGRTVFVGPNGYGKTNLIEALW 44
                                   8888899999*********************************8 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.1e-05     0.042       4      35 ..      17      47 ..      15     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  4 vslklkegekvaivGenGaGKStLlkllagll 35
                                   v+l+l++g++ ++vG+nG GK+ L+++l   +
  gi|121635913|ref|YP_976136.1| 17 VDLELHPGRT-VFVGPNGYGKTNLIEALWYST 47
                                   6778888865.689************997655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05      0.15      96     133 ..      20      57 ..       7      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                    HCTTSEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpelelktgevsek 133
                                    +l+   +v+vG+ G GK+ Li+al  +++l  + vs++
  gi|121635913|ref|YP_976136.1|  20 ELHPGRTVFVGPNGYGKTNLIEALWYSTTLGSHRVSAD 57 
                                    5777889*****************99999888888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.6e-05      0.17      17      42 ..      19      43 ..      10      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                   +e+++   t+++Gp+G GK+ l+ A+
  gi|121635913|ref|YP_976136.1| 19 LELHPG-RTVFVGPNGYGKTNLIEAL 43
                                   556655.5***************997 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001       0.2      33      87 ..     293     342 ..     287     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                        SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                     S Ge+   +++al +a+ +l++ +        +++LD+ F++lD  ++++l  +
  gi|121635913|ref|YP_976136.1| 293 ASHGEA-WSLAVALRLAAYQLLRVD----GGEPVLLLDDVFAELDVMRRRALATA 342
                                    7999*9.*****************5....3556899*********9999988766 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.23       1      44 [.       1      45 [.       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                        DUF2813  1 myLerieisGFRGinrLSlslee.ntvLiGENaWGKSSLldALsl 44
                                   my +++ +  FR      l+l++  tv++G N +GK  L++AL+ 
  gi|121635913|ref|YP_976136.1|  1 MYVRHLGLRDFRSWACVDLELHPgRTVFVGPNGYGKTNLIEALWY 45
                                   999999999************984699****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2423.46
//
Query:       gi|121635914|ref|YP_976137.1|  [L=187]
Description: hypothetical protein BCG_0034 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-23   83.3   1.2    1.9e-23   82.7   1.2    1.3  1  DciA      Dna[CI] antecedent, DciA
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.15   12.2   0.0    1.2  1  DUF962    Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   1.2   2.1e-27   1.9e-23       1      89 []      75     162 ..      75     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 2.1e-27
                           DciA   1 slgdllerllskrglkkkalalarllqaWeeivGpelaahcrpvklrdgtLvvevesgawateLryqkpqllerlneelg 80 
                                    +lg+++++l++krg++  ++a+ ++l +W+++vG+++a+h+rp  l+dg+L v +es+awat+Lr +++qll+++++++g
  gi|121635914|ref|YP_976137.1|  75 PLGKAARELAKKRGWS-VRVAEGMVLGQWSAVVGHQIAEHARPTALNDGVLSVIAESTAWATQLRIMQAQLLAKIAAAVG 153
                                    6899************.8************************************************************** PP

                           DciA  81 eeavrriri 89 
                                    + +vr+++i
  gi|121635914|ref|YP_976137.1| 154 NDVVRSLKI 162
                                    *******97 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.15      51      88 ..      97     134 ..      46     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                         DUF962  51 fvvgyifafvGHfvfEkrkPAlfknplqsllidplmvl 88 
                                    +v+g   a vGH + E+ +P+ +++ + s++++   ++
  gi|121635914|ref|YP_976137.1|  97 MVLGQWSAVVGHQIAEHARPTALNDGVLSVIAESTAWA 134
                                    566777789****************9999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1252.89
//
Query:       gi|121635915|ref|YP_976138.1|  [L=714]
Description: DNA gyrase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-63  213.9   2.1      2e-63  213.0   2.1    1.5  1  DNA_gyraseB    DNA gyrase B
    2.7e-26   91.5   0.0    6.1e-26   90.4   0.0    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    1.7e-20   73.6   0.0    4.7e-20   72.2   0.0    1.8  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.3e-16   59.0   0.0    1.5e-15   57.2   0.0    1.9  2  Toprim         Toprim domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.033   14.0   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   2.1   5.6e-67     2e-63       1     173 [.     295     464 ..     295     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 5.6e-67
                    DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneya 80 
                                    Gl dfv+++n+ k+++++++++++g+   +   eve+a+qw+ +yse++++F+N+i+t+eGGtH++gf+salt+++n+ya
  gi|121635915|ref|YP_976138.1| 295 GLVDFVKHINRTKNAIHSSIVDFSGKG--TG-HEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYA 371
                                    89************************9..77.89********************************************** PP

                    DNA_gyraseB  81 kkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekave 160
                                    k++kllk+k+ +++g+diregl av+svk+ epqFeGQTK+kLgn+evks+v+kv +e+l++++e n++++k +++kav+
  gi|121635915|ref|YP_976138.1| 372 KDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVS 451
                                    ******************************************************************************** PP

                    DNA_gyraseB 161 aakareaarkare 173
                                    +a+ar+aarkare
  gi|121635915|ref|YP_976138.1| 452 SAQARIAARKARE 464
                                    ***********98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.7e-29   6.1e-26       5      62 ..     645     702 ..     641     703 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.7e-29
                  DNA_gyraseB_C   5 eiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefi 62 
                                     iqR+KGLGEm++++LweTTmdp+ R L qvt++da++adelfs+LmG++v++Rr+fi
  gi|121635915|ref|YP_976138.1| 645 GIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFI 702
                                    69*******************************************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.3e-23   4.7e-20       3     110 ..      78     216 ..      76     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.3e-23
                                    HHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.............GTCSTTCHHCST CS
                      HATPase_c   3 ekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk.............klfekfsqddst 67 
                                    e++L+++i+++vdNav++  a++a+++ v +   e d  ++v D+G+Gip++ +              + ++kf++ d++
  gi|121635915|ref|YP_976138.1|  78 ERGLHHLIWEVVDNAVDEamAGYATTVNVVLL--E-DGGVEVADDGRGIPVATHAsgiptvdvvmtqlHAGGKFDS-DAY 153
                                    899***************65559999999999..6.******************************666666****.*** PP

                                    CHTSTSSSHHHHHHHHHHHHTTTEEEE..........EEET..........TTEEEEEEEEES CS
                      HATPase_c  68 krggggtGlGlsivkklvelmgGeiwv..........esep..........grGttftftlpl 110
                                    +++gg +G+G+s+v++l+++++ ei++          +sep          + G+t++f+++ 
  gi|121635915|ref|YP_976138.1| 154 AISGGLHGVGVSVVNALSTRLEVEIKRdgyewsqvyeKSEPlglkqgaptkKTGSTVRFWADP 216
                                    ****************9999999999999999999985555555544445567******9986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   4.2e+03       8      45 ..     149     193 ..     149     216 .. 0.78
   2 !   57.2   0.0   4.3e-19   1.5e-15       1     101 [.     493     603 ..     493     605 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                    HHHHHHHHHTHTSTEEEEEEESSSSEEEHS.....TTEEEEE..E CS
                         Toprim   8 psdaktiakalgsgfqavtaslGhildlet.....efkpvye..e 45 
                                    +sda +i+  l + ++ v+  l + l++e      e+++vye  e
  gi|121635915|ref|YP_976138.1| 149 DSDAYAISGGLHGVGVSVVNALSTRLEVEIkrdgyEWSQVYEksE 193
                                    589999999999888889988888888888888999999988441 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 4.3e-19
                                    EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEECSS CS
                         Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiilatDp 72 
                                    el++vEg+s+ +++++ ++s fqa+++++G+i+++e+ ++++v++  e++ ++++l++     ++  ++r+++i+l+ D+
  gi|121635915|ref|YP_976138.1| 493 ELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKaRIDRVLKntEVQAIITALGTgihdeFDIGKLRYHKIVLMADA 572
                                    69***********************************8888888888899999999989999999999************ PP

                                    SHHHHHHHHHHHHHHT....HHHTTTEEEEEES CS
                         Toprim  73 DreGeaiawellevlk....ellenkigrvefs 101
                                    D++G++i+++ll++l     +l+en  g+v+ +
  gi|121635915|ref|YP_976138.1| 573 DVDGQHISTLLLTLLFrfmrPLIEN--GHVFLA 603
                                    ************9988777788888..887766 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.3e-06     0.033       7      50 ..      85     128 ..      80     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.3e-06
                    HATPase_c_3   7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseeel 50 
                                    + e+vdN++d    + a++v++++ ++    g + + DdG G++ ++ 
  gi|121635915|ref|YP_976138.1|  85 IWEVVDNAVDeamaGYATTVNVVLLED----GGVEVADDGRGIPVATH 128
                                    6799****9997767788999999996....69**********97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 4609.00
//
Query:       gi|121635916|ref|YP_976139.1|  [L=838]
Description: DNA gyrase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.2e-147  491.4   0.0   2.8e-147  491.1   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
      3e-70  231.5  12.9    4.7e-12   45.2   0.1    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.086   12.5   0.4       0.16   11.6   0.4    1.3  1  TPD52          Tumour protein D52 family
       0.11   12.3   0.4          1    9.1   0.0    2.7  3  dCache_1       Cache domain
       0.49   10.8   2.5        1.1    9.6   2.5    1.7  1  Nnf1           Nnf1


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.1   0.0  7.7e-151  2.8e-147       1     425 [.      39     483 ..      39     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 491.1 bits;  conditional E-value: 7.7e-151
                  DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGs 79 
                                    Ra+P+vrDGlKPv+Rr+Lyamf+   ++d+++ K+a+ v+e++g+YhPHGdas+yd++vr+aq +++++pl+d+qGnfGs
  gi|121635916|ref|YP_976139.1|  39 RALPEVRDGLKPVHRRVLYAMFDSgFRPDRSHAKSARSVAETMGNYHPHGDASIYDTLVRMAQPWSLRYPLVDGQGNFGS 118
                                    9******************************************************************************* PP

                  DNA_topoisoIV  80 ildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkei 159
                                       +d++Aa+RY+e+rL+++a e+l+eid+etvd+ +nyDg+ +EP+vlp+++PnlL+nG+ GIavGmat+ipphnl+e+
  gi|121635916|ref|YP_976139.1| 119 P-GNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLREL 197
                                    *.99999************************************************************************* PP

                  DNA_topoisoIV 160 idaliallkgeea.......ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie....e.ktivitElPig 227
                                     da+   l++++a        ++  v+gPdfpt g i+g++++++ay+tgrG+i++r+ ve+e    + +++vitElP++
  gi|121635916|ref|YP_976139.1| 198 ADAVFWALENHDAdeeetlaAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEedsrGrTSLVITELPYQ 277
                                    **********9999999787778889************************************99998459********** PP

                  DNA_topoisoIV 228 vntskliekieelvkkkkik.isdirde.sdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpkyls 304
                                    vn +++i +i+e v+++k+  is+i+d+ sdr g+rivie+kr+a +++v+++lyk+t+L++s+ +n+l+++d+ p++l 
  gi|121635916|ref|YP_976139.1| 278 VNHDNFITSIAEQVRDGKLAgISNIEDQsSDRvGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLR 357
                                    ****************************9999************************************************ PP

                  DNA_topoisoIV 305 lkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeylle 382
                                    l ++++++++++l+v+ rr++y+l+k++er++il+gl+kal+ +devi++ir+s++ + a++ Lie   ++e qa+++l+
  gi|121635916|ref|YP_976139.1| 358 LDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELldIDEIQAQAILD 437
                                    ******************************************************************98899********* PP

                  DNA_topoisoIV 383 mrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                    m+lrrL+++e++++ ++++++e+ei++le++lak   ++ ++++el
  gi|121635916|ref|YP_976139.1| 438 MQLRRLAALERQRIIDDLAKIEAEIADLEDILAKperQRGIVRDEL 483
                                    ********************************99776666666665 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   1.3e-15   4.7e-12       1      48 []     515     562 ..     515     562 .. 0.97
   2 !   33.9   0.0   4.4e-12   1.6e-08       1      41 [.     565     608 ..     565     615 .. 0.83
   3 !   33.5   0.0   6.1e-12   2.2e-08       2      48 .]     622     666 ..     621     666 .. 0.96
   4 !   40.6   0.0   3.7e-14   1.3e-10       1      47 [.     669     717 ..     669     718 .. 0.97
   5 !   43.7   0.3   3.8e-15   1.4e-11       2      48 .]     722     769 ..     721     769 .. 0.96
   6 !   38.4   0.4   1.7e-13     6e-10       2      45 ..     773     816 ..     772     818 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.3e-15
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                    d +++iT+ Gy+kr++ + +++q+Rg+kGv+g  lk +d + + +v+s
  gi|121635916|ref|YP_976139.1| 515 DVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCS 562
                                    679******************************************996 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4.4e-12
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdkl 41 
                                    d +l++T +G+v+r ++++lpe +R+a+G+++     + +++++
  gi|121635916|ref|YP_976139.1| 565 DLILFFTTQGRVYRAKAYDLPEASRTARGQHVAnllAFQPEERI 608
                                    779*****************************955555555555 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 6.1e-12
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                    +l+l+T+nG vk+ +l ++ + + g  G+ +++l+++d+lv+++++s
  gi|121635916|ref|YP_976139.1| 622 YLVLATRNGLVKKSKLTDFDSNRSG--GIVAVNLRDNDELVGAVLCS 666
                                    89*********************99..****************9986 PP

  == domain 4  score: 40.6 bits;  conditional E-value: 3.7e-14
                                    SEEEEEETTSEEEEEEG..GGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfpl..selpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    d+lll++ nG+ +rf++  + l+++gR+++Gv+g++++ +d+l s+ vv
  gi|121635916|ref|YP_976139.1| 669 DDLLLVSANGQSIRFSAtdEALRPMGRATSGVQGMRFNIDDRLLSLNVV 717
                                    89********************************************998 PP

  == domain 5  score: 43.7 bits;  conditional E-value: 3.8e-15
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEES CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvvs 48 
                                    +ll++Ts Gy+kr+ ++e+p+qgRg+kGv  + ++ + ++lv++l+v+
  gi|121635916|ref|YP_976139.1| 722 YLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRrGRLVGALIVD 769
                                    8*******************************999999*******995 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 1.7e-13
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEE CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvl 45 
                                    el  +Ts G v+r+ + +++  gR +kGv++++l egd l +++
  gi|121635916|ref|YP_976139.1| 773 ELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIA 816
                                    57789***********************************9986 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   4.5e-05      0.16      17      58 ..     438     477 ..     424     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                          TPD52  17 vsaseptlteeereeLkseLakleeeivtLrqvLaakekhla 58 
                                    +++    l+  er+ +  +Lak+e+ei+ L+++La  e++  
  gi|121635916|ref|YP_976139.1| 438 MQLR--RLAALERQRIIDDLAKIEAEIADLEDILAKPERQRG 477
                                    3333..59999************************9999865 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.58   2.1e+03     122     152 ..     270     298 ..     258     302 .. 0.72
   2 ?    9.1   0.0   0.00028         1      12     118 ..     441     542 ..     429     556 .. 0.76
   3 ?   -1.1   0.1      0.37   1.3e+03      76      85 ..     670     679 ..     606     769 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.58
                       dCache_1 122 visdp.yvdqtggkpvitiavpiyddsgkfiG 152
                                    vi+++ y+ +  ++ +++ia++++d  gk  G
  gi|121635916|ref|YP_976139.1| 270 VITELpYQVNH-DNFITSIAEQVRD--GKLAG 298
                                    55555254444.89*********97..88777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00028
                       dCache_1  12 lglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGqviassd 91 
                                      la +  + i d+l+++e      a+  +l d l +p+r     r ++++ l +i++++ d +   ++ adG+v   sd
  gi|121635916|ref|YP_976139.1| 441 RRLAALERQRIIDDLAKIE------AEIADLEDILAKPER----QRGIVRDELAEIVDRHGDDRRTRIIAADGDV---SD 507
                                    5556666666666666666......666789999***998....9******************************...33 PP

                       dCache_1  92 pssppnleg........tddpadrdwykealaggg 118
                                    ++ +    +        +++ +++d+y+  + gg+
  gi|121635916|ref|YP_976139.1| 508 EDLIAREDVvvtitetgYAKRTKTDLYRSQKRGGK 542
                                    33333333345666667778888888888777774 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.37
                       dCache_1  76 gvylvdadGq 85 
                                    ++ lv+a+Gq
  gi|121635916|ref|YP_976139.1| 670 DLLLVSANGQ 679
                                    3344444444 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.5   0.00031       1.1      29     106 ..     392     470 ..     368     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                                    TTHHHHHHHHHHHHHHHHCCHH-T..............TTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  29 rdvvekLneLDdlieeAkerreegeeeasrpe....vpphtLpPeeliaahlapakkeeqeeLearlqeleaenaelaee 104
                                    r++v+ L++LD++i+  +  +     +  r+      ++++ +++ +++ +l+++ + e++++   l+++eae a+l++ 
  gi|121635916|ref|YP_976139.1| 392 RGLVKALDALDEVIALIRASETV---DIARAGlielLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDI 468
                                    789********999966654443...22233345579999************************************9987 PP

                                    HH CS
                           Nnf1 105 ve 106
                                    ++
  gi|121635916|ref|YP_976139.1| 469 LA 470
                                    65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5242.87
//
Query:       gi|121635917|ref|YP_976140.1|  [L=304]
Description: hypothetical protein BCG_0037 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-41  139.9   6.5    5.6e-41  139.6   6.5    1.1  1  DUF3566    Transmembrane domain of unknown function (DUF3566)
  ------ inclusion threshold ------
      0.034   14.4   4.5      0.047   13.9   4.0    1.5  1  DUF2189    Predicted integral membrane protein (DUF2189)
       0.22   10.3   0.0        0.3    9.9   0.0    1.0  1  Anoctamin  Calcium-activated chloride channel
        2.4    8.4   5.4       0.42   10.8   0.5    1.9  2  DUF3270    Protein of unknown function (DUF3270)


Domain annotation for each model (and alignments):
>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   6.5   1.2e-44   5.6e-41       2     118 .]     187     302 ..     186     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.2e-44
                        DUF3566   2 rrarlqlsrvdpwSvlklsfllsvalfivlvvavavlylvldalgvfdkvnslvkdlvgeessldleevlslgrvlslaa 81 
                                     ra++q++r+dpwS+lk+s+llsvalf+v+++ va+lylvl ++gv+ k+ns v+dl +++s  + +e++s g++++ a+
  gi|121635917|ref|YP_976140.1| 187 VRASMQIRRIDPWSTLKVSLLLSVALFFVWMITVAFLYLVLGGMGVWAKLNSNVGDLLNNAS-GSSAELVSSGTIFGGAF 265
                                    599*********************************************************95.556699*********** PP

                        DUF3566  82 lvgvvnvvlltalatlaallYNlvadlvGGlevtLad 118
                                    l+g+vn+vl+talat++a++YNl++dl+GG+evtLad
  gi|121635917|ref|YP_976140.1| 266 LIGLVNIVLMTALATIGAFVYNLITDLIGGIEVTLAD 302
                                    ***********************************98 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.0     1e-05     0.047      43     111 ..     198     267 ..     174     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                        DUF2189  43 anassllllglllallfllWvraaallfallfgtapleslsafledvlltpeg..laflivgllvGavlAa 111
                                     ++  l +  ll ++lf++W++++a+l+ +l g ++ ++l++ + d+l ++ g   +++  g+++G+++ +
  gi|121635917|ref|YP_976140.1| 198 PWS-TLKVSLLLSVALFFVWMITVAFLYLVLGGMGVWAKLNSNVGDLLNNASGssAELVSSGTIFGGAFLI 267
                                    222.3444445667899****************99999999999998877665225688889999998865 PP

>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   6.6e-05       0.3      89     185 ..     174     290 ..     163     292 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.6e-05
                      Anoctamin  89 prpefrgelkrespvtgee.efyyppwkrrlfrllvslplvllliclavvgvlilrclal.qelvssvke.......... 156
                                     r +  ++++r  pv  ++    ++pw+ + + ll+s++l++++++++ +  l+l+ + + ++l s+v +          
  gi|121635917|ref|YP_976140.1| 174 ARVQLSARRSRG-PVRASMqIRRIDPWSTLKVSLLLSVALFFVWMITVAFLYLVLGGMGVwAKLNSNVGDllnnasgssa 252
                                    567777666643.4544441345699**9999******988855554444444444355446666666667777777777 PP

                      Anoctamin 157 .......lls...flptvlnlvlililnevykklaiwlt 185
                                           +     fl  ++n+vl+++l+ +   +   +t
  gi|121635917|ref|YP_976140.1| 253 elvssgtI-FggaFLIGLVNIVLMTALATIGAFVYNLIT 290
                                    76555441.045699999999999999877666655555 PP

>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   9.5e-05      0.42      43      70 ..     208     235 ..     203     245 .. 0.87
   2 ?   -0.7   0.4      0.37   1.7e+03      58      78 ..     272     292 ..     264     299 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                        DUF3270  43 ariAvFsvitvlvsfillalklatllAf 70 
                                    + +A+F v ++ v+f++l+l    ++A 
  gi|121635917|ref|YP_976140.1| 208 LSVALFFVWMITVAFLYLVLGGMGVWAK 235
                                    579*****************99999985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                        DUF3270  58 illalklatllAfllAilisl 78 
                                    i l + lat+ Af+  +++ l
  gi|121635917|ref|YP_976140.1| 272 IVLMTALATIGAFVYNLITDL 292
                                    455566999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2082.81
//
Query:       gi|121635918|ref|YP_976141.1|  [L=145]
Description: hypothetical protein BCG_0038c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-66  220.2   6.9    9.3e-66  220.0   6.9    1.0  1  CwsA      Cell wall synthesis protein CwsA
     0.0065   16.2   0.8     0.0087   15.8   0.8    1.1  1  DotU      Type VI secretion system protein DotU
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.039   13.8   0.0    1.3  1  VirB8     VirB8 protein
      0.055   13.4   0.2      0.073   13.0   0.2    1.1  1  RUN       RUN domain


Domain annotation for each model (and alignments):
>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.0   6.9   2.1e-69   9.3e-66       1     132 []       9     145 .]       9     145 .] 0.99

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 2.1e-69
                           CwsA   1 ltprerltrGlkysavGPvdvtrGv....vglgvesaqstaeelrrryresrlarelaaaqeaiaqelaaaqevvaglPq 76 
                                    ltprerltrGl+ysavGPvdvtrG+    vglg++sa+sta+ lrrryre+rlare+aaaqe++aqel+aaq+vva+lPq
  gi|121635918|ref|YP_976141.1|   9 LTPRERLTRGLAYSAVGPVDVTRGLlelgVGLGLQSARSTAAGLRRRYREGRLAREVAAAQETLAQELTAAQDVVANLPQ 88 
                                    8***********************9898899************************************************* PP

                           CwsA  77 aledarkkrrrkrp.lllagvavavlaGGavafsivrrssrPePsslpPsvdvsPkp 132
                                    al+dar++rr+k++ +++ag+a+a+laGGavafsivrrssrPePs++pPsv+v+P+p
  gi|121635918|ref|YP_976141.1|  89 ALQDARTQRRSKHHlWIFAGIAAAILAGGAVAFSIVRRSSRPEPSPRPPSVEVQPRP 145
                                    ************9989***************************************98 PP

>> DotU  Type VI secretion system protein DotU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   1.9e-06    0.0087     126     203 ..      51     122 ..      46     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                           DotU 126 GFeGryrleadgeeelealrqrlyeeirrlrgeaeealsphwqagdeaarrllrrelplwvilalallvllllflgls 203
                                    G + ryr e + ++e +a  ++l++e++++++ ++ +l ++ q  d++ +r++  +  lw+++++a+++l++  +++s
  gi|121635918|ref|YP_976141.1|  51 GLRRRYR-EGRLAREVAAAQETLAQELTAAQDVVA-NLPQALQ--DARTQRRS--KHHLWIFAGIAAAILAGGAVAFS 122
                                    6666898.44677799************7665555.4555544..44444443..4469************8877776 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-06     0.039      11      49 ..      94     132 ..      88     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          VirB8  11 gsarvqarnwrlvafvslliavlavgavvlllplktveP 49 
                                    + +r+++++++++a+++++i ++ ++a+ ++ +++++eP
  gi|121635918|ref|YP_976141.1|  94 RTQRRSKHHLWIFAGIAAAILAGGAVAFSIVRRSSRPEP 132
                                    6789****************9999999999999998888 PP

>> RUN  RUN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.6e-05     0.073      12      85 ..      50     114 ..      42     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                            RUN  12 hGLrrssesllralglkkessfwallekvakllteaesllsav.qelealhsskkrsadgkfrawirlaLnekkL 85 
                                     GLrr      r+++ +  ++++a+ e +a+ lt a++++ ++ q+l++++++     ++k ++wi ++  +  L
  gi|121635918|ref|YP_976141.1|  50 AGLRR------RYREGRLAREVAAAQETLAQELTAAQDVVANLpQALQDARTQ----RRSKHHLWIFAGIAAAIL 114
                                    69999......9**************************988874566666666....8*********99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1050.67
//
Query:       gi|121635919|ref|YP_976142.1|  [L=182]
Description: iron-regulated peptidyl-prolyl cis-trans isomerase a ppiA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-48  164.0   0.1    3.7e-48  163.8   0.1    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.1     2e-52   3.7e-48       2     157 ..      17     180 ..      16     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2e-52
                  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkeg................fYdgttFhRvikgfmvqgGdptgktsageq 65 
                                    ++++t+ +G+i+i Lf+++aPktv+nF+ l++ g                fYdg +FhRvi+gfm+qgGdptg+++    
  gi|121635919|ref|YP_976142.1|  17 ATLHTN-RGDIKIALFGNHAPKTVANFVGLAQ-GtkdystqnasggpsgpFYDGAVFHRVIQGFMIQGGDPTGTGR---- 90 
                                    578997.************************6.55788888888999999***********************966.... PP

                  Pro_isomerase  66 ekkggesiraipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVv..eGmdvvekiekvet 142
                                       gg   ++++dE++++l++ k+++lama++g  p ++gsqFfIt++++phl++++t+FG+V+  e+++vve+i+k+ t
  gi|121635919|ref|YP_976142.1|  91 ---GG-PGYKFADEFHPELQFdKPYLLAMANAG--PGTNGSQFFITVGKTPHLNRRHTIFGEVIdaESQRVVEAISKTAT 164
                                    ...33.23689*****77676699*******98..8****************************999************* PP

                  Pro_isomerase 143 de.erpkknvkivsae 157
                                    d+ +rp+++v+i+s++
  gi|121635919|ref|YP_976142.1| 165 DGnDRPTDPVVIESIT 180
                                    ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1412.90
//
Query:       gi|121635920|ref|YP_976143.1|  [L=111]
Description: hypothetical protein BCG_0040c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-12   45.0   0.7    1.5e-11   44.2   0.7    1.4  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.7   8.4e-16   1.5e-11       1      45 [.      58     108 ..      58     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.4e-16
                          bPH_6   1 RprvrvdpdGvevrnlfrtrrlpWsaiagvrfpegrrl......arldlrd 45 
                                    Rpr++++pdG+++r++frt++l+ s i+ +r++e+rr+      +++++ +
  gi|121635920|ref|YP_976143.1|  58 RPRLAITPDGLAIRGWFRTQLLRHSNIKIIRIDEFRRYgrlvrlLEIETVS 108
                                    9******************************99999998888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 880.15
//
Query:       gi|121635921|ref|YP_976144.1|  [L=93]
Description: septation inhibitor protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  101.5   4.4    2.2e-29  101.3   4.4    1.0  1  CrgA          Cell division protein CrgA
     0.0029   17.0   1.1     0.0033   16.8   0.1    1.5  2  DUF3273       Protein of unknown function (DUF3273)
  ------ inclusion threshold ------
          8    6.3   5.8        4.9    7.0   4.4    1.5  2  Myc_target_1  Myc target protein 1


Domain annotation for each model (and alignments):
>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   4.4   3.8e-33   2.2e-29       1      88 []       1      93 []       1      93 [] 0.94

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3.8e-33
                           CrgA  1 mpkskvrkkaeytpkaaertpvkakaakpsprwyvpvmlglmllGllwlvvyYlage......eipfmaelgawNlliGfgl 76
                                   mpkskvrkk+++t +a +rtp k+k   ps+ w+v +++glml+Gl+wl+v+ la+        +++ma+lg wN++i+f++
  gi|121635921|ref|YP_976144.1|  1 MPKSKVRKKNDFTVSAVSRTPMKVK-VGPSSVWFVSLFIGLMLIGLIWLMVFQLAAIgsqaptALNWMAQLGPWNYAIAFAF 81
                                   9**********************98.****************************987775555556**************** PP

                           CrgA 77 iivGllmttrWr 88
                                   +i+Gll+t+rW+
  gi|121635921|ref|YP_976144.1| 82 MITGLLLTMRWH 93
                                   ***********7 PP

>> DUF3273  Protein of unknown function (DUF3273)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.6e-07    0.0033      51      90 ..      14      53 ..       4      56 .. 0.83
   2 ?   -2.1   0.1      0.31   1.8e+03     185     199 ..      73      87 ..      71      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-07
                        DUF3273 51 aldlvklaeevkvgsaptlvvslliglyllGtlllmvfqv 90
                                   +  +  ++ +vkvg ++++ vsl+igl+l+G + lmvfq 
  gi|121635921|ref|YP_976144.1| 14 VSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQL 53
                                   34456678999***************************95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.31
                        DUF3273 185 lgylnlvlfvlagll 199
                                    + y+ +++f+++gll
  gi|121635921|ref|YP_976144.1|  73 WNYAIAFAFMITGLL 87 
                                    667777777777776 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.4   0.00082       4.9      25      44 ..      32      51 ..      10      66 .. 0.87
   2 ?   -1.9   0.0      0.43   2.5e+03      10      35 ..      64      88 ..      53      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00082
                   Myc_target_1 25 FcvSmvvGLllgaliyvllt 44
                                   ++vS+ +GL+l +li++++ 
  gi|121635921|ref|YP_976144.1| 32 WFVSLFIGLMLIGLIWLMVF 51
                                   579*************9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                   Myc_target_1 10 leilesfdledlilaFcvSmvvGLll 35
                                   l++  +++  +  +aF+  m+ GLll
  gi|121635921|ref|YP_976144.1| 64 LNWMAQLGPWNYAIAFAF-MITGLLL 88
                                   555556666667778865.7788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 710.86
//
Query:       gi|121635922|ref|YP_976145.1|  [L=262]
Description: hypothetical protein BCG_0042 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-37  128.4   0.0    2.8e-37  127.8   0.0    1.3  1  DUF881      Bacterial protein of unknown function (DUF881)
  ------ inclusion threshold ------
       0.13   12.1   0.1       0.22   11.4   0.1    1.3  1  DASH_Spc19  Spc19


Domain annotation for each model (and alignments):
>> DUF881  Bacterial protein of unknown function (DUF881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.0   3.1e-41   2.8e-37       4     145 .]     105     255 ..     102     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 3.1e-41
                         DUF881   4 elkllaGltpveGpGvtitlddakkaeeeaeee........vhdedLldvvneLraaGAeaIsingqRivatsaircagn 75 
                                    el+  a++ pv+GpG+++tl+da+++++ +  +        vh++d+ +v+n+L++aGAeaI++++qRi+a s  rc+gn
  gi|121635922|ref|YP_976145.1| 105 ELAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRdaspddlvVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGN 184
                                    6777899****************9996665555999******************************************** PP

                         DUF881  76 ailvdgrrispPyeikaIGdpekLesalniseavggllellke.glsvtvekseevtipayrgplelkyak 145
                                    ++l++gr++spPy+i aIGd++++++al++ + v  + +++ + gl ++ e + +++i  y +p+++++a+
  gi|121635922|ref|YP_976145.1| 185 TLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRfGLGYREEVHPDLQIVGYADPVRMHFAQ 255
                                    *****************************************9889********************999885 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.4e-05      0.22      62     100 ..      56      94 ..      49     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                                    TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                     DASH_Spc19  62 ePqieellekaekeleklerreetLkaklelqegrlsna 100
                                    +P + +l+++a++++++l++++e+L ++++   gr  ++
  gi|121635922|ref|YP_976145.1|  56 APRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDT 94 
                                    689999**************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1991.42
//
Query:       gi|121635923|ref|YP_976146.1|  [L=232]
Description: para-aminobenzoate synthase component II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-48  165.1   0.0    1.8e-48  164.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.4e-12   47.9   0.1    8.1e-12   45.3   0.1    2.0  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.0     2e-52   1.8e-48       2     187 ..       5     189 ..       4     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 2e-52
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETH CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspg.vegkieaikearenkiPiLGICL 79 
                                    ++Dnyds++ nlv++l +lg++ ev+++d   +  +   + ++dg+l+s+Gpg+p+ ++ ++++++ ++ +++P+LG+CL
  gi|121635923|ref|YP_976146.1|   5 VVDNYDSFVFNLVQYLGQLGIEAEVWRNDDHRLSDEAaVAGQFDGVLLSPGPGTPErAGASVSMVHACAAAHTPLLGVCL 84 
                                    89***************************988888655699*************************************** PP

                                    HHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEE CS
                         GATase  80 GmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiie 159
                                    G+Q+++ +fg++v ++  +  hg+t+ + +++ ++l+gl+++++++++H++++ p +++pa l+vta+++++  +m++++
  gi|121635923|ref|YP_976146.1|  85 GHQAIGVAFGATVDRAP-ELLHGKTSSVFHTNVGVLQGLPDPFTATRYHSLTILP-KSLPAVLRVTARTSSG-VIMAVQH 161
                                    *****************.9***********999*********************9.99***********988.9****** PP

                                    ETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                         GATase 160 kknpfvgvQFHPEststpegpellfnfl 187
                                       p++gvQFHPEs++t++g+++l+n l
  gi|121635923|ref|YP_976146.1| 162 TGLPIHGVQFHPESILTEGGHRILANWL 189
                                    ************************9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   9.1e-16   8.1e-12      86     216 .]      57     174 ..      50     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 9.1e-16
                  Peptidase_C26  86 adpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgs 165
                                     +peR   ++ +++a+ ++++P+lg+C+G+q + va+G t+ ++ e    l  h       ++ +v  ++ ++l+ l   
  gi|121635923|ref|YP_976146.1|  57 GTPERAGASVSMVHACAAAHTPLLGVCLGHQAIGVAFGATVDRAPE----LL-HG------KTSSVFHTNVGVLQGLPD- 124
                                    57899999*****************************988766555....33.32......334455566788999988. PP

                  Peptidase_C26 166 eeievnslHhqai..kelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                      +  + +H+ +i  k l   lrv+A+++ gvi a++++    ++ gvQ+HPE
  gi|121635923|ref|YP_976146.1| 125 -PFTATRYHSLTIlpKSLPAVLRVTARTSSGVIMAVQHTG--LPIHGVQFHPE 174
                                    .899999*****96667***********************..56********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1555.28
//
Query:       gi|121635924|ref|YP_976147.1|  [L=626]
Description: Ser/Thr protein kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-54  179.1   9.0    4.2e-17   61.7   0.4    4.3  4  PASTA           PASTA domain
    1.2e-50  172.3   0.0    1.6e-50  171.9   0.0    1.1  1  Pkinase         Protein kinase domain
    1.5e-35  122.7   0.0    2.1e-35  122.3   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    1.4e-06   28.5   2.0      0.013   15.4   0.0    2.7  3  APH             Phosphotransferase enzyme family
    2.4e-05   23.3   0.0    3.8e-05   22.6   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.082   12.5   0.0        6.1    6.4   0.0    2.3  2  SMC_ScpB        Segregation and condensation complex subunit 
       0.24   10.7   0.0       0.39   10.0   0.0    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.4   1.7e-20   4.2e-17       1      63 []     360     422 ..     360     422 .. 0.98
   2 !   35.4   0.2   2.8e-12   7.1e-09       2      61 ..     428     488 ..     427     490 .. 0.92
   3 !   47.0   1.7   6.7e-16   1.7e-12       3      63 .]     497     557 ..     495     557 .. 0.95
   4 !   36.6   0.0   1.2e-12     3e-09       2      61 ..     562     624 ..     561     626 .] 0.82

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.7e-20
                                    EE--TTTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTBEEEECS-TTSEECTTS-EEEEEEE CS
                          PASTA   1 vtvPdvtGmsvdeAkatLkalGlkiktveetsddvpeGtVisQsPeaGtevskgskvtltvsk 63 
                                    v+vPdv+G+s ++A+atL++ G+ki+t +++++++p++ Vi+++P+a+t+vs+g+++t+ vs+
  gi|121635924|ref|YP_976147.1| 360 VQVPDVRGQSSADAIATLQNRGFKIRTLQKPDSTIPPDHVIGTDPAANTSVSAGDEITVNVST 422
                                    79**********************************************************995 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 2.8e-12
                                    E--TTTTSBHHHHHHHHHHTT-.-CCCEEEECTCCGTTBEEEECS-TTSEECTTS-EEEEE CS
                          PASTA   2 tvPdvtGmsvdeAkatLkalGl.kiktveetsddvpeGtVisQsPeaGtevskgskvtltv 61 
                                    ++Pdv  ++++eA++ L+a+G+ ++k+ +++s +   G+Vi+++P+a+++      v+++v
  gi|121635924|ref|YP_976147.1| 428 EIPDVSTLTYAEAVKKLTAAGFgRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIV 488
                                    69*********************************************99987777777776 PP

  == domain 3  score: 47.0 bits;  conditional E-value: 6.7e-16
                                    --TTTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTBEEEECS-TTSEECTTS-EEEEEEE CS
                          PASTA   3 vPdvtGmsvdeAkatLkalGlkiktveetsddvpeGtVisQsPeaGtevskgskvtltvsk 63 
                                    +Pdv+G++vd A+++L+ +G++   + +++++ p+G V++++P+aGt+v+ +s ++l vsk
  gi|121635924|ref|YP_976147.1| 497 IPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSK 557
                                    8********************7777777********************************8 PP

  == domain 4  score: 36.6 bits;  conditional E-value: 1.2e-12
                                    E--TTTTSBHHHHHHHHHHTT--CCCEEE...ECTCCGTTBEEEECS-TTSEECTTS-EEEEE CS
                          PASTA   2 tvPdvtGmsvdeAkatLkalGlkiktvee...tsddvpeGtVisQsPeaGtevskgskvtltv 61 
                                     +Pd+ Gm + +A+  L+alG++   ++    +   +  ++V+ Q+P+aGt v+++  +tl++
  gi|121635924|ref|YP_976147.1| 562 VMPDLSGMFWVDAEPRLRALGWTGMLDKGadvDAGGSQHNRVVYQNPPAGTGVNRDGIITLRF 624
                                    6*********************5555555422666666666*******************987 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.9   0.0   6.3e-54   1.6e-50       1     255 [.      11     265 ..      11     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 6.3e-54
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEE....SSEEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfee....kdelyl 75 
                                    ye  e lG G++++V  a++ + ++ vAvK+++ + a++ +   +++rE +  + l+hp iv +y++ e         y+
  gi|121635924|ref|YP_976147.1|  11 YELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLARDPSFyLRFRREAQNAAALNHPAIVAVYDTGEAetpaGPLPYI 90 
                                    78899******************************999877779************************99555445569* PP

                                    EEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS.. CS
                        Pkinase  76 vleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk.. 153
                                    v+eyv+g +l d+++++g +++++a ++++  +++l++ H++giiHrD+Kp+Ni+i+ ++ +K++DFG+a+ +  s +  
  gi|121635924|ref|YP_976147.1|  91 VMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARAIADSGNsv 170
                                    *************************************************************************9999889 PP

                                    ..BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHT CS
                        Pkinase 154 ..ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeas 231
                                      +  ++gt +Yl+PE  ++ ++++ +Dv+slG++lye+ltg+ppf g++  + +++++++         +    +++++
  gi|121635924|ref|YP_976147.1| 171 tqTAAVIGTAQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVAYQHVRE---------DPIPPSARHE 241
                                    989999*****************************************77777766666666.........6678899999 PP

                                    TS-HHHHHHHHHHT-SSGCCSTTH CS
                        Pkinase 232 eiseeakdllkkllkkdpkkRlta 255
                                     +s ++  ++ k l+k+p++R+  
  gi|121635924|ref|YP_976147.1| 242 GLSADLDAVVLKALAKNPENRYQT 265
                                    9********************864 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0   8.1e-39   2.1e-35       3     251 ..      13     264 ..      11     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 8.1e-39
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSS....E CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeep....l 76 
                                    lg+ lG G  ++V+ ++      + + +VavK+l+++  ++     ++ +ea+   +l+hp iv+++     e p     
  gi|121635924|ref|YP_976147.1|  13 LGEILGFGGMSEVHLARDL----RLHRDVAVKVLRADLARDPsfYLRFRREAQNAAALNHPAIVAVYDTGEAETPagplP 88 
                                    6788999999999988877....7899*******8876665535899********************9998666666679 PP

                                    EEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                    Pkinase_Tyr  77 livteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                    +iv+eyv+g +L++ ++++   ++t k+ ++++++ ++++++ +++ ++Hrd+   N+++s ++ vk+ DfG+ar+i ++
  gi|121635924|ref|YP_976147.1|  89 YIVMEYVDGVTLRDIVHTE--GPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARAIADS 166
                                    *****************98..9*******************************************************888 PP

                                    SEEEETTSST.SGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTS.HHHHHHHHHHTTEE..S-BBTTSBH CS
                    Pkinase_Tyr 157 deyvkkeeak.lpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypgl.kneevleklkegkr..lekpekcpe 232
                                     + v+++ a     ++++pE  +  ++  +sDv+s G +l+E++t ge p++g    + ++++++e+     ++ e  ++
  gi|121635924|ref|YP_976147.1| 167 GNSVTQTAAViGTAQYLSPEQARGDSVDARSDVYSLGCVLYEVLT-GEPPFTGDsPVSVAYQHVREDPIppSARHEGLSA 245
                                    777555555416899******************************.******993455567777777652255678899* PP

                                    HHHHHHHHHT-SSGGGS-- CS
                    Pkinase_Tyr 233 elyelmkkcweedpeeRpt 251
                                    +l  ++ k ++++pe+R +
  gi|121635924|ref|YP_976147.1| 246 DLDAVVLKALAKNPENRYQ 264
                                    ****************975 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   3.1e-05     0.078      22      96 ..      36     120 ..      28     127 .. 0.67
   2 !   15.4   0.0   5.1e-06     0.013     152     197 ..     119     161 ..     106     165 .. 0.77
   3 ?   -2.0   0.0       1.1   2.7e+03      91     118 ..     259     285 ..     223     331 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                    -EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTE...EEEEEE----EE-SS......HHHHHH CS
                            APH  22 ryvlrrnppa..raaeeirrevallrlLakagvpvPevlagdtddeeigl...lfalieyvpgrsllr......klsaaq 90 
                                    ++++++ ++   r + +  r+ ++ ++ a+++ p+ ++++ dt+++e +    ++ ++eyv+g +l++      +++++ 
  gi|121635924|ref|YP_976147.1|  36 DVAVKVLRADlaRDPSFYLRFRREAQNAAALNHPAIVAVY-DTGEAETPAgplPYIVMEYVDGVTLRDivhtegPMTPKR 114
                                    5666666666445777777888888888888775555544.566666666778**************9776555555444 PP

                                    HHHHHH CS
                            APH  91 lpelle 96 
                                    + e+++
  gi|121635924|ref|YP_976147.1| 115 AIEVIA 120
                                    444444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 152 vlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                    +++a+ al   + + +++H+D +p N+++ +++     v Df+ a+
  gi|121635924|ref|YP_976147.1| 119 IADACQALNF-SHQNGIIHRDVKPANIMISATNAVK--VMDFGIAR 161
                                    4555555555.699****************777777..****9887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHCCHHCH.-STTTB-SH CS
                            APH  91 lpellealgeflaalhqvdpaalpladf 118
                                     ++ ++ ++e++a+l +v ++  p++ +
  gi|121635924|ref|YP_976147.1| 259 PENRYQTAAEMRADLVRV-HNGEPPEAP 285
                                    333344444444444444.332333322 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-08   3.8e-05     304     394 ..     111     196 ..     105     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-08
                 Pkinase_fungal 304 spkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesga..rertGTleFm 381
                                    +pk+++e+++Da ++++  + + gi+HrD+   Ni+i      +++   + D+ +a  ++d s +s+      +GT++++
  gi|121635924|ref|YP_976147.1| 111 TPKRAIEVIADACQALNFSH-QNGIIHRDVKPANIMIS-----ATNAVKVMDFGIARAIAD-SGNSVTqtAAVIGTAQYL 183
                                    68999************999.*****************.....67888999****999996.777754448899****99 PP

                 Pkinase_fungal 382 aievlkgeeHsyr 394
                                    + e  +g +   r
  gi|121635924|ref|YP_976147.1| 184 SPEQARGDSVDAR 196
                                    9887776555555 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0024       6.1      86     123 ..     342     382 ..     338     393 .. 0.79
   2 ?    3.5   0.0     0.019        48      57     128 ..     452     522 ..     444     531 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
                       SMC_ScpB  86 letLaiIaykq..pvtr.aeieeiRGvnsdsvvrtLlergl 123
                                    l ++  Ia++    +tr  ++ ++RG++s +++ tL++rg+
  gi|121635924|ref|YP_976147.1| 342 LTVVVTIAINTfgGITRdVQVPDVRGQSSADAIATLQNRGF 382
                                    66677777775558998459*******************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                       SMC_ScpB  57 yrlvtkpelaevvkklvkekkktrLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekg 128
                                    ++ + +p   e+v k++ ++ +++ ++a   ++ iI+   p t+ +i ++ G+++d + ++L   g+ + ++
  gi|121635924|ref|YP_976147.1| 452 FKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATK-DIPDVAGQTVDVAQKNLNVYGFTKFSQ 522
                                    6666778888999******999999999*************997.899999999999998888777766655 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00015      0.39      33     167 ..      31     158 ..      16     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                            Kdo  33 rkyyrggllgklskdlyrfklgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakw 112
                                     +++r   ++ l  dl r +  ++r++rE ++  +L++  + + +    ++   g+     +++e ++g+  L d++ + 
  gi|121635924|ref|YP_976147.1|  31 LRLHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPL--PYIVMEYVDGVT-LRDIVHTE 107
                                    556777777777777666667788888888888887776665555555554444444..5699****9985.99999873 PP

                            Kdo 113 aelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                      +  ++  + + +  ++ +  h+ g+ H+d+ + ni++ +++     + ++D+ 
  gi|121635924|ref|YP_976147.1| 108 GPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATN----AVKVMDFG 158
                                    33555555555555555555569*****************998....77888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3992.38
//
Query:       gi|121635925|ref|YP_976148.1|  [L=431]
Description: Ser/Thr protein kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-46  158.8   0.0    2.2e-46  158.4   0.0    1.1  1  Pkinase         Protein kinase domain
      2e-32  112.5   0.0    2.7e-32  112.1   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    2.3e-06   27.7   0.1     0.0003   20.8   0.0    2.5  2  APH             Phosphotransferase enzyme family
    8.4e-06   25.3   0.0    1.2e-05   24.8   0.0    1.1  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0016   17.3   0.0     0.0021   16.9   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.014   14.3   0.0      0.019   13.9   0.0    1.1  1  Haspin_kinase   Haspin like kinase domain
      0.021   14.4   0.0       0.04   13.5   0.0    1.3  1  RIO1            RIO1 family
      0.049   12.9   0.0       0.12   11.7   0.0    1.6  2  Kinase-like     Kinase-like
      0.059   13.5   0.0       0.11   12.7   0.0    1.4  1  ABC1            ABC1 family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.0   1.1e-49   2.2e-46       1     253 [.      13     261 ..      13     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 1.1e-49
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEE.....SSEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfee.....kdely 74 
                                    y+ ++ + +G++G+V +av+++ g+ vAvK++k e  ++ +  +++++E +  + l+hp i  + ++ e+      ++ y
  gi|121635925|ref|YP_976148.1|  13 YRLQRLIATGGMGQVWEAVDNRLGRRVAVKVLKSEFSSDPEFiERFRAEARTTAMLNHPGIASVHDYGESqmngeGRTAY 92 
                                    566788999*************************998887778***********************999988888999** PP

                                    EEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS. CS
                        Pkinase  75 lvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk. 153
                                    lv+e+v+g+ l+++l+r g ls ++a ++++q+ ++l+  H++g++HrD+Kp NiLi  +g++KitDFG+ak ++     
  gi|121635925|ref|YP_976148.1|  93 LVMELVNGEPLNSVLKRTGRLSLRHALDMLEQTGRALQIAHAAGLVHRDVKPGNILITPTGQVKITDFGIAKAVDAAPVt 172
                                    **************************************************************************998875 PP

                                    .BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTT CS
                        Pkinase 154 .ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpease 232
                                     +  ++gt +Y+APE   +++ s+++Dv+slGv+ ye ++gk pf+g+   +     +++          ++   p + +
  gi|121635925|ref|YP_976148.1| 173 qTGMVMGTAQYIAPEQALGHDASPASDVYSLGVVGYEAVSGKRPFAGDGALT---VAMKH---------IKEPPPPLPPD 240
                                    577799****************************************444444...33333.........3356889999* PP

                                    S-HHHHHHHHHHT-SSGCCST CS
                        Pkinase 233 iseeakdllkkllkkdpkkRl 253
                                    +++++++l++  l k+p  R+
  gi|121635925|ref|YP_976148.1| 241 LPPNVRELIEITLVKNPAMRY 261
                                    *****************9996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   1.4e-35   2.7e-32       3     249 ..      15     260 ..      13     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1.4e-35
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEE.....SSSS CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvct.....keep 75 
                                    l++ ++ G  G+V+e+  +    +   +VavK+lk+e +++    e++  ea++   l+hp i +++         ++++
  gi|121635925|ref|YP_976148.1|  15 LQRLIATGGMGQVWEAVDN----RLGRRVAVKVLKSEFSSDPefIERFRAEARTTAMLNHPGIASVHDYGEsqmngEGRT 90 
                                    6788999*********988....88999******987766554589*****************99876665445556666 PP

                                    EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTT CS
                    Pkinase_Tyr  76 llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiek 155
                                     ++v+e+v+g  L++ L+++   +l+l++ l++  q  ++++  ++  lvHrd+   N+L++ + +vki+DfG+a+++ +
  gi|121635925|ref|YP_976148.1|  91 AYLVMELVNGEPLNSVLKRT--GRLSLRHALDMLEQTGRALQIAHAAGLVHRDVKPGNILITPTGQVKITDFGIAKAV-D 167
                                    *******************8..9*******************************************************.6 PP

                                    SSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHH CS
                    Pkinase_Tyr 156 ddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpeely 235
                                        ++++      +++apE    +  + +sDv+s Gv+ +E ++ g++p++g  + +v+ k  ++   + p + p+++ 
  gi|121635925|ref|YP_976148.1| 168 AAPVTQTGMVMGTAQYIAPEQALGHDASPASDVYSLGVVGYEAVS-GKRPFAGDGALTVAMKHIKEPPPPLPPDLPPNVR 246
                                    6677888999999********************************.********88888888888889999999****** PP

                                    HHHHHHT-SSGGGS CS
                    Pkinase_Tyr 236 elmkkcweedpeeR 249
                                    el++  + ++p+ R
  gi|121635925|ref|YP_976148.1| 247 ELIEITLVKNPAMR 260
                                    ***99999999888 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00053       1.1      13     106 ..      27     133 ..      17     135 .. 0.80
   2 !   20.8   0.0   1.5e-07    0.0003     148     198 ..     115     165 ..     105     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00053
                                    EEEEEETT.-.-EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTE..EEEEEE----EE-SS. CS
                            APH  13 tylvttpa.g.ryvlrrnppa..raaeeirrevallrlLakagv.pvPevlagdtddeeigl..lfalieyvpgrsllr. 84 
                                    +++ ++ + g r+++++   +    +e+i+r+ a+ r  a ++   ++ v+++++++   +    ++++e v g++l   
  gi|121635925|ref|YP_976148.1|  27 VWEAVDNRlGrRVAVKVLKSEfsSDPEFIERFRAEARTTAMLNHpGIASVHDYGESQMNGEGrtAYLVMELVNGEPLNSv 106
                                    6777777775477788877777779999999999998888666645899999998776665568*************999 PP

                                    .....HHHHHHHHHHHHHHHHHHCCHH CS
                            APH  85 .....klsaaqlpellealgeflaalh 106
                                         +ls +++ ++le+ g++l   h
  gi|121635925|ref|YP_976148.1| 107 lkrtgRLSLRHALDMLEQTGRALQIAH 133
                                    999999999999999999999997655 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.5e-07
                                    HHHHHHHHHHHH--S...SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 148 leeqvlaalaallpg...elptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    l++ +l++l+++ ++   + +++l+H+D +pgN+l++p+++    + Df+ a++
  gi|121635925|ref|YP_976148.1| 115 LRH-ALDMLEQTGRAlqiAHAAGLVHRDVKPGNILITPTGQVK--ITDFGIAKA 165
                                    455.788888888888889******************886666..999998876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     6e-09   1.2e-05      57     165 ..      57     159 ..      25     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6e-09
                            Kdo  57 ravrEfrllkrLeeagvavpkpvaagavkvgle.yrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklh 135
                                    r+++E r    L++ g+a      +g+ ++++e ++A l++e ++g + L+ +l++  +l+ +    +l+++gr+ +  h
  gi|121635925|ref|YP_976148.1|  57 RFRAEARTTAMLNHPGIASVHD--YGESQMNGEgRTAYLVMELVNG-EPLNSVLKRTGRLSLRHALDMLEQTGRALQIAH 133
                                    6667777777777777776654..5666777777*******97765.89******9888999****************** PP

                            Kdo 136 ragvnHadlyaknillqqeeeeeaeiwliD 165
                                    +ag+ H+d+ + nil+  ++    ++ + D
  gi|121635925|ref|YP_976148.1| 134 AAGLVHRDVKPGNILITPTG----QVKITD 159
                                    ****************9998....555555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0021     305     390 ..     115     193 ..      79     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                 Pkinase_fungal 305 pkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaie 384
                                     +++l  l++  ++++  +  ag++HrD+  +Nilit     ++ +  + D+ +ak ++      + +  +GT++++a e
  gi|121635925|ref|YP_976148.1| 115 LRHALDMLEQTGRALQIAH-AAGLVHRDVKPGNILIT-----PTGQVKITDFGIAKAVDAAPV-TQTGMVMGTAQYIAPE 187
                                    5677778888888888888.9****************.....7888999**********7444.456999******9988 PP

                 Pkinase_fungal 385 vlkgee 390
                                       g++
  gi|121635925|ref|YP_976148.1| 188 QALGHD 193
                                    766555 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.7e-06     0.019     182     257 ..      87     166 ..      65     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                  Haspin_kinase 182 qqlflvlllk.dkGtdLeev....klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRl 256
                                    +  + +l+++  +G++L+ v       s ++al ++ q+   L++a ++  + HRd + +niL+  +++v + d+ ++++
  gi|121635925|ref|YP_976148.1|  87 EGRTAYLVMElVNGEPLNSVlkrtGRLSLRHALDMLEQTGRALQIAHAA-GLVHRDVKPGNILITPTGQVKITDFGIAKA 165
                                    4455666666358999998875444568999999999999999999875.899**********************99987 PP

                  Haspin_kinase 257 e 257
                                     
  gi|121635925|ref|YP_976148.1| 166 V 166
                                    5 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     2e-05      0.04      82     150 ..      92     161 ..      87     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                    EEEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                           RIO1  82 vlvmefigedgvaapklkdve.e..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                     lvme+++  g ++  + + + +   ++a +++e++ ++++ + + aglvH D+   N+l++   +v i D++
  gi|121635925|ref|YP_976148.1|  92 YLVMELVN--GEPLNSVLKRTgRlsLRHALDMLEQTGRALQ-IAHAAGLVHRDVKPGNILITPTgQVKITDFG 161
                                    69******..8888876666522233344444555555444.44599***************98799999986 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   3.2e+03      18      52 ..      17      51 ..      12      67 .. 0.74
   2 ?   11.7   0.0   5.8e-05      0.12     157     190 ..     129     162 ..      97     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                    Kinase-like 18 ellkkgdrsvvfevkdqetgeplavkvfllpseas 52
                                    l+  g+ + v+e+ d+  g  +avkv  ++    
  gi|121635925|ref|YP_976148.1| 17 RLIATGGMGQVWEAVDNRLGRRVAVKVLKSEFSSD 51
                                   67888899999999999999999999876654444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.8e-05
                    Kinase-like 157 aanLqakglvhgkftvdnllldekgglmlggfta 190
                                     +  +a glvh ++++ n+l  + g++++++f+ 
  gi|121635925|ref|YP_976148.1| 129 LQIAHAAGLVHRDVKPGNILITPTGQVKITDFGI 162
                                    5566899*************************74 PP

>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.4e-05      0.11      19      47 ..      19      48 ..      15      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                           ABC1 19 iAaASiaqVhrAklk.sgeeVavKvqrpgv 47
                                   iA++ ++qV++A+ +  g++VavKv + + 
  gi|121635925|ref|YP_976148.1| 19 IATGGMGQVWEAVDNrLGRRVAVKVLKSEF 48
                                   899**********9966********87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2874.44
//
Query:       gi|121635926|ref|YP_976149.1|  [L=491]
Description: penicillin-binding protein pbpA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-75  254.6   0.0    1.4e-75  254.3   0.0    1.1  1  Transpeptidase  Penicillin binding protein transpeptidase dom


Domain annotation for each model (and alignments):
>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.3   0.0     8e-80   1.4e-75       1     306 []     160     484 ..     160     484 .. 0.96

  Alignments for each domain:
  == domain 1  score: 254.3 bits;  conditional E-value: 8e-80
                                    EEEEEEETTT-BEEEEEEESE-TTTHHCC................TCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSST CS
                 Transpeptidase   1 gaavvldaktgevlamaskpsydpnakvg................kneplanravqsqyePGStfKvvtaaaaleagvik 64 
                                    ga+v+l+++tg++la++s+psydpn  ++                +++pl+nra++++y+PGStfKv+t+aaal ag+ +
  gi|121635926|ref|YP_976149.1| 160 GAVVALEPSTGKILALVSSPSYDPNLLAShnpevqaqawqrlgdnPASPLTNRAISETYPPGSTFKVITTAAALAAGATE 239
                                    79****************************************************************************** PP

                                    TSEEEEETCCEETTSS..ECTCCCC-SSSSEE.EHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS...-SSSSST CS
                 Transpeptidase  65 pdetlddsggkiqggqs.ikdweqdnkgsegi.tlrealekSsntyfvklaqklgadklrkylkkfglGn...ktgidlp 139
                                    +++ +  +++   g+++ ++++  + +g+e++ +lrea+ kS+nt+fv+l  ++gad lr+++++fgl++   +t+++ +
  gi|121635926|ref|YP_976149.1| 240 TEQLTAAPTIPLPGSTAqLENYGGAPCGDEPTvSLREAFVKSCNTAFVQLGIRTGADALRSMARAFGLDSpprPTPLQVA 319
                                    99999999999999999*****************************************************999******* PP

                                    T-B--B--SSHHHHHHHHHTTT...SBB-HHHHHHHHHHHHTTTEEE--BSEEEEEECTT.EEEESS-EEEEE-S-HHHH CS
                 Transpeptidase 140 gesaGvptrkwlegatisfgiG...ltvtplqlaqayaaiangGklvkPhlvkaivdpdg.vrkvkpkelnklpisketa 215
                                    +++ G p + +  +a+ +++iG   +++tpl  a+++a+iangG++++P+lv ++++pd  +++++  +++++++s++ a
  gi|121635926|ref|YP_976149.1| 320 ESTVG-PIPDS--AALGMTSIGqkdVALTPLANAEIAATIANGGITMRPYLVGSLKGPDLaNISTTVGYQQRRAVSPQVA 396
                                    *****.66666..56677899999******************************************************** PP

                                    HHHHHHHHHHHHCTTTTGCGTCTTS--EEEEEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEEEECTCS...SSS CS
                 Transpeptidase 216 ekvkeglkgvvsrgsgtataavegykvagKTGTAevagkkgngkkegakiswfvgyapadnpkyavavlieqpk...eaa 292
                                     k++e++ g ++    + ++a++g+++a KTGTAe+ ++ +++  +    +w++++apa+ pk+avavl+e+++   +a+
  gi|121635926|ref|YP_976149.1| 397 AKLTELMVGAEKVA--QQKGAIPGVQIASKTGTAEHGTDPRHTPPH----AWYIAFAPAQAPKVAVAVLVENGAdrlSAT 470
                                    **************..5555******************99998766....6***************************** PP

                                    SCCHHHHHHHHHHH CS
                 Transpeptidase 293 ggkaaapiakkile 306
                                    gg+ aapi ++++e
  gi|121635926|ref|YP_976149.1| 471 GGALAAPIGRAVIE 484
                                    **********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3269.17
//
Query:       gi|121635927|ref|YP_976150.1|  [L=469]
Description: cell division protein rodA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-105  351.9  17.3   5.9e-105  351.2  17.3    1.3  1  FTSW_RODA_SPOVE  Cell cycle protein
  ------ inclusion threshold ------
       0.47   10.5   3.9         46    4.1   0.0    3.6  4  DUF3278          Protein of unknown function (DUF3278)


Domain annotation for each model (and alignments):
>> FTSW_RODA_SPOVE  Cell cycle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.2  17.3  6.6e-109  5.9e-105       3     357 ..      81     444 ..      79     446 .. 0.94

  Alignments for each domain:
  == domain 1  score: 351.2 bits;  conditional E-value: 6.6e-109
                FTSW_RODA_SPOVE   3 llllvllllvilGlvmiysaslveslvlfgdsfvlfirqlvylllglivfvlllriplkfleklakllliislllLvlvk 82 
                                    ll +v+ll+  lGlvmi++++lv+++   +  + ++ +q++++l+g+++f l++++ lk++++la++++i +l  Lv+++
  gi|121635927|ref|YP_976150.1|  81 LLPVVALLNG-LGLVMIHRLDLVDNEIGEH-RHPSANQQMLWTLVGVAAFALVVTF-LKDHRQLARYGYICGLAGLVFLA 157
                                    5566777777.***********87765555.8999*********************.*********************** PP

                FTSW_RODA_SPOVE  83 vp.....lgssanGAkrWirlggisiqPsEfvkialilflAavlskk...........kkevksrlrellillvivllil 146
                                    vp       s++nGAk Wirl+g+siqP+Ef+ki+l++f++avl++k             ++ +r+r+l++ll+++++++
  gi|121635927|ref|YP_976150.1| 158 VPallpaALSEQNGAKIWIRLPGFSIQPAEFSKILLLIFFSAVLVAKrglftsagkhlLGMTLPRPRDLAPLLAAWVISV 237
                                    *9977666789********************************************98888******************** PP

                FTSW_RODA_SPOVE 147 vlillqpdlgtavllliillvvlflsglsl.klilaivlalilviaivllilledyqvkrvtslldpfkdplgsgYqviq 225
                                    +++++++dlg ++ll+ ++lvv++l+++++ ++++ + l +++ + ++++i+ +  ++ rv ++ldpf+dp g+gYq++q
  gi|121635927|ref|YP_976150.1| 238 GVMVFEKDLGASLLLYTSFLVVVYLATQRFsWVVIGLTL-FAAGTLVAYFIFEHV-RL-RVQTWLDPFADPDGTGYQIVQ 314
                                    ******************************666666666.899999999998888.66.********************* PP

                FTSW_RODA_SPOVE 226 sliAigsGGllGkGlgnsqqkleyLPeahtDfIfavigEelGlvGvllllllffllivrglriarkakdrfgsllavgiv 305
                                    sl+++++GG++G+Glgn+q   + +P+a+tDfI+a +gEelGlvG++++l+l++++i+rglr+a++++d+fg+lla+g++
  gi|121635927|ref|YP_976150.1| 315 SLFSFATGGIFGTGLGNGQP--DTVPAASTDFIIAAFGEELGLVGLTAILMLYTIVIIRGLRTAIATRDSFGKLLAAGLS 392
                                    ********************..********************************************************** PP

                FTSW_RODA_SPOVE 306 llivvqsfinigmvlGllPvtGltlPflSyGGsSllalliligillnisree 357
                                    +++++q+fi++g+v+ l+P+tGlt+P++SyGGsSlla++il++il++is+ +
  gi|121635927|ref|YP_976150.1| 393 STLAIQLFIVVGGVTRLIPLTGLTTPWMSYGGSSLLANYILLAILARISHGA 444
                                    ************************************************9965 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0051        46      36      79 ..      20      63 ..      17      74 .. 0.78
   2 ?    4.1   0.0    0.0051        46      87     127 ..      95     135 ..      81     137 .. 0.90
   3 ?   -2.8   0.2      0.68   6.1e+03      71      85 ..     249     263 ..     232     273 .. 0.63
   4 ?    1.0   0.1     0.048   4.3e+02      29      78 ..     352     404 ..     350     414 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0051
                        DUF3278 36 nafillwlyllilslvalllakktpeselilglvltnlllvvlv 79
                                   na +ll+++ +++++ all++++ +++ +  +l +  l + +l 
  gi|121635927|ref|YP_976150.1| 20 NAELLLLCFAAVITFAALLVVQANQDQGVPWDLTSYGLAFLTLF 63
                                   78899*****************9999888878887665554443 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0051
                        DUF3278  87 askklglatkeveakdyekavkkivlksikfglyfaivlyl 127
                                      ++l l+++e+ ++  ++a +++ +  ++++ +  +v++l
  gi|121635927|ref|YP_976150.1|  95 MIHRLDLVDNEIGEHRHPSANQQMLWTLVGVAAFALVVTFL 135
                                    568999*************************9999999886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.68
                        DUF3278  71 tnlllvvlvsglYil 85 
                                    + ll++ + + +Y++
  gi|121635927|ref|YP_976150.1| 249 SLLLYTSFLVVVYLA 263
                                    345555555555554 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.048
                        DUF3278  29 einrignnafillwlyllilslvalllakktpeselilglvl...tnlllvvl 78 
                                    e++ +g +a ++l+ + +i  l + +  + +  ++l+ gl +   ++l++vv+
  gi|121635927|ref|YP_976150.1| 352 ELGLVGLTAILMLYTIVIIRGLRTAIATRDSFGKLLAAGLSStlaIQLFIVVG 404
                                    67788999999999999998888877777777777776665421234444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3470.26
//
Query:       gi|121635928|ref|YP_976151.1|  [L=514]
Description: Serine/threonine phosphatase PPP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   51.1   0.4    2.2e-13   50.4   0.4    1.3  1  PP2C_2    Protein phosphatase 2C
    8.2e-08   32.2   0.0      7e-06   25.9   0.0    2.1  2  PP2C      Protein phosphatase 2C


Domain annotation for each model (and alignments):
>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.4   2.4e-17   2.2e-13      10     183 ..      21     201 ..      16     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.4e-17
                         PP2C_2  10 lpcqDalavwtdsggsllaVaDGaGSakrSerGariaveavvealaelleseeee..eeallraleaailadvlkeeaea 87 
                                    ++++D++     +g++lla aDG+G ++ +e++++++  a+  +l +     +     +a++ra  +ai        a+ 
  gi|121635928|ref|YP_976151.1|  21 ANNEDSVY----AGARLLALADGMGGHAAGEVASQLVIAAL-AHLDDDEPGGDLLakLDAAVRAGNSAIA-------AQV 88 
                                    56777776....899999***********999888766544.3444444333333334444444444444.......655 PP

                         PP2C_2  88 q.daelkdyatTllaavvtpdeivalqiGDGaivvrdrdgevqllgepds................geyanq......tt 144
                                    + + +l+ ++tTl a++++++++ +++iGD+   +  rdge+ +++++d+                +            +
  gi|121635928|ref|YP_976151.1|  89 EmEPDLEGMGTTLTAILFAGNRLGLVHIGDSRG-YLLRDGELTQITKDDTfvqtlvdegritpeeaHS---HpqrsliMR 164
                                    54669****************************.679**********888888888886666633333...245689999 PP

                         PP2C_2 145 fltsedaeeelrirrlkledgdalllmTDGlanslrdee 183
                                    +lt +++e++l +r+ +  +gd+ ll++DGl++ ++de 
  gi|121635928|ref|YP_976151.1| 165 ALTGHEVEPTLTMREAR--AGDRYLLCSDGLSDPVSDET 201
                                    99999999999999988..79***********9998775 PP

>> PP2C  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   7.8e-10     7e-06      29     140 ..      26     136 ..      11     142 .. 0.82
   2 !    4.2   0.0    0.0031        28     192     230 ..     171     208 ..     167     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.8e-10
                                    CCCCCCEEEEEEEEESSSHHHHHHHHHHHHHHHHHHHCHTTHHHHHHHHHHHHHHHHHHHHHHHHHC.HCCT-EEEEEEE CS
                           PP2C  29 sgkssvsffavfdghggseaakyarehleeilksqksfeelekleqalrksfladtdeelksskant.epsksGstavva 107
                                    s +   +++a  dg+gg+ a ++a++ +   l+  +++e++ +l + l  +++a   + ++ + +++   +  G+t + +
  gi|121635928|ref|YP_976151.1|  26 SVYAGARLLALADGMGGHAAGEVASQLVIAALAHLDDDEPGGDLLAKLDAAVRA-GNSAIAAQVEMEpDLEGMGTTLTAI 104
                                    566777899********************9999999999888888888888888.445555545776567899******* PP

                                    EEETTEEEEEEESS-EEEEEETTEEEEECS--- CS
                           PP2C 108 lirgtklyvAnvGDSravLcrkgnakkeltedH 140
                                    l+ g++l + + GDSr  L r+g+   ++t+d 
  gi|121635928|ref|YP_976151.1| 105 LFAGNRLGLVHIGDSRGYLLRDGELT-QITKDD 136
                                    ***********************998.999985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0031
                                    ---EEEEEEE-TTEEEEEEE-HHHHTTSHHHHHHHHHHH CS
                           PP2C 192 aePdvtsvklteedefliLacdGlwdvlsdqeavdlvrd 230
                                     eP +t+++    d +l L +dGl d +sd+++ +  + 
  gi|121635928|ref|YP_976151.1| 171 VEPTLTMREARAGDRYL-LCSDGLSDPVSDETILEALQI 208
                                    58999999999999997.89************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 3836.32
//
Query:       gi|121635929|ref|YP_976152.1|  [L=155]
Description: hypothetical protein BCG_0049c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-16   59.8   0.0    3.2e-16   59.4   0.0    1.1  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
    2.2e-15   56.7   0.0    3.4e-15   56.2   0.0    1.3  1  FHA           FHA domain


Domain annotation for each model (and alignments):
>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   3.5e-20   3.2e-16       2      89 ..      66     154 ..      65     155 .] 0.94

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 3.5e-20
                                    EECCCCTT-EEEETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC.--TTSEEE CS
                   Yop-YscD_cpl   2 vlsGpdkGaeveLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveele.lrpgdvle 80 
                                    v +G+  Ga+++L+e+ v+iG+++d+ +vL+D+  s +h++L+++ +++ +edlgs+ng++++  +v+++  +  g+ + 
  gi|121635929|ref|YP_976152.1|  66 VTEGALTGARITLSEQPVLIGRADDSTLVLTDDYASTRHARLSMRGSEWYVEDLGSTNGTYLDRAKVTTAVrVPIGTPVR 145
                                    568999**************************************************************5555******** PP

                                    ETTEEEEEE CS
                   Yop-YscD_cpl  81 lGttelalv 89 
                                    +G t + l+
  gi|121635929|ref|YP_976152.1| 146 IGKTAIELR 154
                                    ***998775 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   3.7e-19   3.4e-15       2      69 .]      84     147 ..      83     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.7e-19
                                    EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                     iGR++d+++vl d   S++Ha+++++++  ++y+eDlgS+nGt++++ ++++   v++  g+ +++G
  gi|121635929|ref|YP_976152.1|  84 LIGRADDSTLVLTDDYASTRHARLSMRGS--EWYVEDLGSTNGTYLDRAKVTT--AVRVPIGTPVRIG 147
                                    7****************************..*********************9..9999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1188.82
//
Query:       gi|121635930|ref|YP_976153.1|  [L=521]
Description: hypothetical protein BCG_0050c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-35  119.5   0.0    1.3e-34  119.0   0.0    1.2  1  DUF3662       Protein of unknown function (DUF2662)
    1.2e-16   60.8   0.0      2e-16   60.1   0.0    1.4  1  FHA           FHA domain
    2.3e-14   53.5   0.1    3.5e-14   52.9   0.1    1.3  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d


Domain annotation for each model (and alignments):
>> DUF3662  Protein of unknown function (DUF2662)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0   2.1e-38   1.3e-34       2     114 ..       9     121 ..       8     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 2.1e-38
                        DUF3662   2 qrfErrlerlvegafarvfrgevqpvEiakaLrremddnarvvsrgrvlaPneYtveLspeDyerlasleeelaeeladl 81 
                                    qr+Er+le++v++afar+f+g+++p+E+++ Lrre++d ++ ++++r+laPneY ++L+ +D+e+l ++ e  ++ +a+ 
  gi|121635930|ref|YP_976153.1|   9 QRVERKLEQTVGDAFARIFGGSIVPQEVEALLRREAADGIQSLQGNRLLAPNEYIITLGVHDFEKLGADPELKSTGFARD 88 
                                    89****************************************************************************** PP

                        DUF3662  82 laehareqgytlvgpvtVeleedeslktGqfrv 114
                                    la++++eqg++++g+v+V++e++++l+tGqfr+
  gi|121635930|ref|YP_976153.1|  89 LADYIQEQGWQTYGDVVVRFEQSSNLHTGQFRA 121
                                    *******************************97 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   3.4e-20     2e-16       2      69 .]     450     512 ..     449     512 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 3.4e-20
                                    EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                    +iGR +d++++l+d  +Sr+H++i++d++     l Dl+S+nGt vN+ +++     +L++gdvi+lG
  gi|121635930|ref|YP_976153.1| 450 IIGRGQDAQFRLPDTGVSRRHLEIRWDGQ--VALLADLNSTNGTTVNNAPVQE---WQLADGDVIRLG 512
                                    79***************************..*********************8...**********98 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   5.9e-18   3.5e-14       8      87 ..     438     517 ..     436     521 .] 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 5.9e-18
                                    TT-EEEETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC--TTSEEEETTEEEE CS
                   Yop-YscD_cpl   8 kGaeveLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveelelrpgdvlelGttela 87 
                                    +G++++L+eg  +iG+++d+   L D +vsr+hl+++ + +   l dl+s+ng++vn+ +v+e +l++gdv+ lG  e+ 
  gi|121635930|ref|YP_976153.1| 438 SGRTYQLREGSNIIGRGQDAQFRLPDTGVSRRHLEIRWDGQVALLADLNSTNGTTVNNAPVQEWQLADGDVIRLGHSEII 517
                                    699************************************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3298.65
//
Query:       gi|121635931|ref|YP_976154.1|  [L=322]
Description: hypothetical protein BCG_0051c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-40  137.8   6.4    1.2e-29  103.8   0.8    2.2  2  NMO           Nitronate monooxygenase
    1.9e-10   40.3   4.6      9e-05   21.6   0.0    2.4  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    5.2e-08   32.3   4.5    8.4e-08   31.6   4.5    1.3  1  FMN_dh        FMN-dependent dehydrogenase
    0.00048   19.7   0.1    0.00076   19.0   0.1    1.4  1  His_biosynth  Histidine biosynthesis protein
      0.008   15.4   1.2      0.015   14.5   1.2    1.4  1  DHO_dh        Dihydroorotate dehydrogenase
     0.0094   15.3   0.9     0.0094   15.3   0.9    1.9  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.5   7.5e-13   2.2e-09       3      53 ..       6      56 ..       4      64 .. 0.92
   2 !  103.8   0.8   3.9e-33   1.2e-29     106     326 ..      81     306 ..      70     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.5e-13
                            NMO  3 lltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlake 53
                                   + +++++i +p+v ++m  i++ +Laaavs aGgLG++++gy+  D la +
  gi|121635931|ref|YP_976154.1|  6 AFSQMFGIDYPIVSAPMDLIAGGELAAAVSGAGGLGLIGGGYGDRDWLARQ 56
                                   668899**************************************9999876 PP

  == domain 2  score: 103.8 bits;  conditional E-value: 3.9e-33
                            NMO 106 vevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLv 185
                                    +++ l++++ +v + fg+p     ++ k ag+ l+  i   ++a  + + GaD+l++qG eaGGh      g +++++Lv
  gi|121635931|ref|YP_976154.1|  81 LDLALQYEPVAVMLSFGDP-AVFADAIKSAGTRLVCQIQNRTQAERALQVGADVLVAQGTEAGGHGH----GPRSTLTLV 155
                                    67888999999********.5667889999***********************************66....34689**** PP

                            NMO 186 pqvldavd.....iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkklleaklddteltsavs.... 256
                                    p+++d v      iPviAaGGi d+rg+aaaL lGA+gv +gtrf +t e+   + ++  ll a  dd+  t+  +    
  gi|121635931|ref|YP_976154.1| 156 PEIVDLVTargtdIPVIAAGGIADGRGLAAALMLGAAGVLVGTRFYATVEALSTPQARDPLLAATGDDMCRTTIYDqlrr 235
                                    *******9999****************************************99999999999999888877776541111 PP

                            NMO 257 .....GrpaRalatelleeleeakiatlalpeahelakkiraalveagnteegllwagqgidrldkiisvkeLie 326
                                         G  + +l + l+ + e+++   l  +  + +a   ra  v a +    ++ agq+++ ++ +++++++i 
  gi|121635931|ref|YP_976154.1| 236 ypwpqGHTMSVLSNALTDQFEDTELDILHRE--EAMARYWRA--VPARDYSIANVTAGQAAGLVNAVLPAADVIT 306
                                    1111155555555555555553333333222..223333332..3333566666666666666666666666665 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     3e-08     9e-05      23      63 ..       3      43 ..       1      49 [. 0.95
   2 !   18.7   2.2   2.4e-07   0.00071     202     246 ..     163     207 ..     117     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3e-08
                                   --EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 23 lktkltkkiklniPlvsaamdtvtesemAialareGgigvi 63
                                   l+t +++ + +  P+vsa+md +++ e+A a++ +Gg+g+i
  gi|121635931|ref|YP_976154.1|  3 LSTAFSQMFGIDYPIVSAPMDLIAGGELAAAVSGAGGLGLI 43
                                   789999*********************************98 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.4e-07
                                    HHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 202 aakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEsp 246
                                    +a+ +++pvia GGi   + ++ Al +Ga  v++G  + +t E+ 
  gi|121635931|ref|YP_976154.1| 163 TARGTDIPVIAAGGIADGRGLAAALMLGAAGVLVGTRFYATVEAL 207
                                    567789********************************9999986 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   4.5   2.8e-11   8.4e-08     223     305 ..     116     202 ..     103     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.8e-11
                                    EE-SHHHHHHHHHTTESEEEE..--GGGTSSTT---HHHCHHHHHHHH.....SS-EEEESS--SHHHHHHHHHTT-SEE CS
                         FMN_dh 223 GvltaedakraveaGvdgivv..SNHGGRqldgapatidvLpeiveavgg...rievlvDgGirrGsDvlkAlalGAdav 297
                                     +++   a+ra+++G+d +v      GG+   g  +t+   peiv+ v     +i+v++ gGi  G   + Al lGA +v
  gi|121635931|ref|YP_976154.1| 116 QIQNRTQAERALQVGADVLVAqgTEAGGHG-HGPRSTLTLVPEIVDLVTArgtDIPVIAAGGIADGRGLAAALMLGAAGV 194
                                    589999***********8877445678865.899**********8877643449************************** PP

                                    EESHHHHH CS
                         FMN_dh 298 llGRpfly 305
                                    l+G  f  
  gi|121635931|ref|YP_976154.1| 195 LVGTRFYA 202
                                    ***98854 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.6e-07   0.00076     144     225 ..     114     202 ..      57     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                                    EEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHH..HHHH.....HHHHSSEEEEESS--SHHHHHHHHHTTCSE CS
                   His_biosynth 144 etgldavelakkleelgageilltdidrdGtlsGpdlel..tkel.....aeavkipviasGGvgsledlkelksegvda 216
                                      +++    a+++ ++ga  ++ +  ++ G  +Gp  +l  + e+     a+ ++ipvia+GG+++   l+++   g+++
  gi|121635931|ref|YP_976154.1| 114 VCQIQNRTQAERALQVGADVLVAQGTEAGGHGHGPRSTLtlVPEIvdlvtARGTDIPVIAAGGIADGRGLAAALMLGAAG 193
                                    5666666777888888888888888888888888876542244541111134569************************* PP

                                    EEESHHHHT CS
                   His_biosynth 217 vivgsalye 225
                                    v+vg+ +y 
  gi|121635931|ref|YP_976154.1| 194 VLVGTRFYA 202
                                    ******996 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.2     5e-06     0.015     196     278 ..     118     201 ..      88     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                    ...BSEE--CTTCCGCCCCTT.SSEEEE.EGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEES CS
                         DHO_dh 196 tNttvqrlaidlkseknvkan.ktGGls.GkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvy 273
                                    +N t    a+++ +   v +  ++GG + G+    + +  i +l +    +ip+I+ GGi  g+     ++ GA+ v v+
  gi|121635931|ref|YP_976154.1| 118 QNRTQAERALQVGADVLVAQGtEAGGHGhGPRSTLTLVPEIVDLVTARGTDIPVIAAGGIADGRGLAAALMLGAAGVLVG 197
                                    45555555455555444444345666543666666667779999999999****************************** PP

                                    HHHHH CS
                         DHO_dh 274 talvf 278
                                    t + +
  gi|121635931|ref|YP_976154.1| 198 TRF-Y 201
                                    *98.4 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   3.1e-06    0.0094     133     206 ..     119     199 ..      96     219 .. 0.80
   2 ?   -3.0   1.7       1.2   3.5e+03     195     226 ..     287     318 ..     280     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                                    -HHHHHHHHHTT-SEBEEBSSST.TS----S-.....HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESH CS
                           ThiG 133 DlvlarrleevGcaavmPlaapi.GsglGlln.....kealkiiieea.kvPvivDAGigspsdaaqamelGadavllnt 205
                                    +   a+r  +vG+ +++  ++   G g+G ++     +e + +++++  ++Pvi   Gi      a+a+ lGa +vl+ t
  gi|121635931|ref|YP_976154.1| 119 NRTQAERALQVGADVLVAQGTEAgGHGHGPRStltlvPEIVDLVTARGtDIPVIAAGGIADGRGLAAALMLGAAGVLVGT 198
                                    5677999999****99999987625789988711111344566666556*****************************98 PP

                                    H CS
                           ThiG 206 a 206
                                     
  gi|121635931|ref|YP_976154.1| 199 R 199
                                    5 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                    HTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                           ThiG 195 elGadavllntavaeakdpvamArafklavea 226
                                      G  a l+n+ +  a+ +  mA+  + +++a
  gi|121635931|ref|YP_976154.1| 287 TAGQAAGLVNAVLPAADVITGMAQQAARTLTA 318
                                    56888999998888888888999877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2254.06
//
Query:       gi|121635932|ref|YP_976155.1|  [L=139]
Description: transcriptional regulatory protein whiB-like whiB5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-13   50.3   1.6    3.9e-13   49.8   1.6    1.2  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   1.6   2.2e-17   3.9e-13       1      64 []      12      83 ..       5      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.2e-17
                           Whib  1 WreraaCrgedpelffpekgdreeeAkavC.arCpV..rreCleealeegeeyGvwGGl.....tereRraL 64
                                   W+ +++ +g+d ++     ++++++A+  C +rCp+  +r+C+++a+e+++eyGvw+G+     ++r+R++L
  gi|121635932|ref|YP_976155.1| 12 WFGYPDDDGSDGAAKARAYERSATQARIQClRRCPLlqQRRCAQHAVEHRVEYGVWAGIklpggQYRKREQL 83
                                   888888888888777766669***************9999*******************9999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1057.46
//
Query:       gi|121635933|ref|YP_976156.1|  [L=256]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.1   0.0    1.3e-10   41.2   0.0    2.2  2  HTH_3     Helix-turn-helix
    6.7e-11   42.4   5.7    1.4e-09   38.1   0.5    2.7  2  HTH_31    Helix-turn-helix domain
    0.00043   20.1   0.0      0.008   16.0   0.0    2.8  2  HTH_25    Helix-turn-helix domain
      0.008   16.2   0.0      0.014   15.4   0.0    1.4  1  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.4   0.1         10    6.3   0.0    3.0  3  HTH_35    Winged helix-turn-helix DNA-binding
      0.043   13.8   0.0       0.11   12.4   0.0    1.7  1  HTH_37    Helix-turn-helix domain
      0.063   13.1   2.6        4.7    7.1   0.1    3.1  3  HTH_IclR  IclR helix-turn-helix domain
        0.1   12.8   0.5       0.32   11.2   0.2    1.9  2  DUF5130   Domain of unknown function (DUF5130)


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   5.8e-14   1.3e-10       1      52 [.      10      61 ..      10      64 .. 0.97
   2 !    5.6   0.0    0.0072        16      19      46 ..      57      83 ..      53      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5.8e-14
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52
                                   +++lR+ +++s+++LA+++Gvs   +s +E+G r+P  +t++k+++ Lg+++
  gi|121635933|ref|YP_976156.1| 10 IRALRESRDWSLADLAAATGVSTMGLSYLERGARKPHKSTVQKVENGLGLPP 61
                                   89***********************************************997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0072
                                   HTSSHHHHHHHHTTSSCSBHHHHHHHHH CS
                          HTH_3 19 lGvsrstisriEnGernPsletlkklak 46
                                   lG+++ t+sr+    + P+ e + ++a 
  gi|121635933|ref|YP_976156.1| 57 LGLPPGTYSRLLVA-ADPDAELARLIAA 83
                                   89************.88******99995 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.5   6.4e-13   1.4e-09       2      58 ..       6      61 ..       5      67 .. 0.95
   2 !    6.2   0.6     0.006        13       3      59 ..     193     250 ..     168     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.4e-13
                         HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                    Ga  ralRe + +s++++A+++gvs   ls lE+G+r  p  +++ ++ ++lgl+p
  gi|121635933|ref|YP_976156.1|  6 AGAAIRALRESRDWSLADLAAATGVSTMGLSYLERGAR-KPHKSTVQKVENGLGLPP 61
                                   58999*********************************.6***************98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.006
                         HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspa..vlealaralgldpa 59 
                                     a+  ++ +++ L  + vA+++gv ++ + ++ +    +p  a   ++a+++a  ++ +
  gi|121635933|ref|YP_976156.1| 193 SARFDRACAQSSLPEAVVAALIGVGADEMWDIRNRGV-IPAGAlpRVRAFVDAIEASHD 250
                                    4555555566689999****************99777.574444499999998888654 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.6e-06     0.008       2      34 ..      10      42 ..       9      70 .. 0.91
   2 ?    0.5   0.0      0.25   5.7e+02      25      40 ..     172     187 ..     165     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                         HTH_25  2 LraaRearglsleevaketkIrkdylealEedd 34
                                    ra Re+r +sl ++a+ t +++  l  lE++ 
  gi|121635933|ref|YP_976156.1| 10 IRALRESRDWSLADLAAATGVSTMGLSYLERGA 42
                                   699********************9999999885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                                    HHHHHHHCT--TTSS- CS
                         HTH_25  25 dylealEeddfdalpe 40 
                                    ++l+alE+ + ++l+ 
  gi|121635933|ref|YP_976156.1| 172 EHLRALEATRGALLER 187
                                    68*****998887765 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.1e-06     0.014       1      56 [.       7      61 ..       7      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.1e-06
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56
                                   G  ++++Re + +++++la  +g+s   +s +E g + +p  ++++k+ + lg+++
  gi|121635933|ref|YP_976156.1|  7 GAAIRALRESRDWSLADLAAATGVSTMGLSYLERGAR-KPHKSTVQKVENGLGLPP 61
                                   789********************************99.9999***99999999986 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.017        37       7      32 ..      10      35 ..       6      62 .. 0.75
   2 ?   -0.4   0.0      0.53   1.2e+03      15      45 ..      47      77 ..      42      87 .. 0.79
   3 ?    6.3   0.0    0.0045        10      43      62 ..     206     225 ..     183     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.017
                         HTH_35  7 IiAaLrkrgttLaalsreaglssstl 32
                                   I A  + r ++La+l+ + g s   l
  gi|121635933|ref|YP_976156.1| 10 IRALRESRDWSLADLAAATGVSTMGL 35
                                   55555679************987554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                         HTH_35 15 gttLaalsreaglssstlsnaltrpwpkgEa 45
                                   ++t++++   +gl + t s+ l    p +E 
  gi|121635933|ref|YP_976156.1| 47 KSTVQKVENGLGLPPGTYSRLLVAADPDAEL 77
                                   5788899999999999999999999999985 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0045
                         HTH_35  43 gEalIAeaLgvppeeiwPsR 62 
                                     Ea++A ++gv + e+w  R
  gi|121635933|ref|YP_976156.1| 206 PEAVVAALIGVGADEMWDIR 225
                                    49***************755 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.1e-05      0.11      21      54 ..       8      41 ..       2      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                         HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                   +ai++l+e+r++s +++a+++g++   +s l+rg
  gi|121635933|ref|YP_976156.1|  8 AAIRALRESRDWSLADLAAATGVSTMGLSYLERG 41
                                   68***********************999999987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0021       4.7      10      31 ..      11      31 ..       6      32 .. 0.81
   2 ?    5.0   0.0    0.0096        21      13      40 ..      42      69 ..      35      70 .. 0.83
   3 ?   -2.1   0.1       1.5   3.4e+03       9      18 ..     174     183 ..     168     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0021
                                   CT-CTTBSS-BHHHHHHHHTS- CS
                       HTH_IclR 10 dalaeapqeltlselArrtglp 31
                                   +al+e +  ++l++lA++tg++
  gi|121635933|ref|YP_976156.1| 11 RALRESRD-WSLADLAAATGVS 31
                                   56666666.9**********86 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0096
                                   CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLq 40
                                   a+ p   t++ + + +glp+ t +RlL 
  gi|121635933|ref|YP_976156.1| 42 ARKPHKSTVQKVENGLGLPPGTYSRLLV 69
                                   45556679999999************95 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                                    HCT-CTTBSS CS
                       HTH_IclR   9 Ldalaeapqe 18 
                                    L+al++++++
  gi|121635933|ref|YP_976156.1| 174 LRALEATRGA 183
                                    5566666555 PP

>> DUF5130  Domain of unknown function (DUF5130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00014      0.32      66     115 ..      65     114 ..      55     128 .. 0.85
   2 ?   -1.6   0.0       1.3   2.9e+03      71     109 ..     140     176 ..     117     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                        DUF5130  66 areilakvpepenavLiavsPnqraievvsGaevadrvadrvaqlGvtaa 115
                                    +r ++a  p++e a Lia  P + + + ++Ga v dr +d+ +  G + a
  gi|121635933|ref|YP_976156.1|  65 SRLLVAADPDAELARLIAAQPSNPTAVRRAGAVVVDRHSDTDVLEGYAEA 114
                                    56678899********************************9888887655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                        DUF5130  71 akvpepenavLiavsPnqraievvsGaevadrvadrvaq 109
                                    + + +  +a ++a s  +  + v +Ga+ ++r+ ++  +
  gi|121635933|ref|YP_976156.1| 140 SVIAQCVKAEMLAAS--SWRVAVNAGADSTGRLMEHLRA 176
                                    555555555556555..4567788888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1824.85
//
Query:       gi|121635934|ref|YP_976157.1|  [L=277]
Description: hypothetical protein BCG_0054 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2147.43
//
Query:       gi|121635935|ref|YP_976158.1|  [L=120]
Description: hypothetical protein BCG_0056 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-38  130.5  12.4    3.4e-38  130.3  12.4    1.0  1  DUF4226   Domain of unknown function (DUF4226)
  ------ inclusion threshold ------
      0.022   14.5   2.1      0.051   13.4   0.4    1.9  2  SKA2      Spindle and kinetochore-associated protein 2
        6.3    7.4  12.3         45    4.6   0.1    3.0  2  Rnk_N     Rnk N-terminus


Domain annotation for each model (and alignments):
>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3  12.4   5.7e-42   3.4e-38       1     111 []       4     115 ..       4     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 5.7e-42
                        DUF4226   1 qrGsaadAarareaaLaqrlsataelDrqlaevlrsahakaaegrrrLdalqaeidqavatqa.laldTpaGarqfqrfL 79 
                                    q+Gs+++++++r+a La++++a+ae+Dr+la+vl+saha+++e+ rrLda++ae+d+av +q+ la+dT +Gar+fq+fL
  gi|121635935|ref|YP_976158.1|   4 QAGSSVAVIQERQALLARQHDAVAEADRELADVLASAHAAMRESVRRLDAIAAELDRAVPDQDqLAVDTLMGAREFQTFL 83 
                                    78****************************************************************************** PP

                        DUF4226  80 iaklreiakvVadasedsrskaalveaLtaqY 111
                                    +ak+rei +vVa+a+e++r+k+a++++L+aqY
  gi|121635935|ref|YP_976158.1|  84 VAKQREIVAVVAAAHELDRAKSAVLKRLRAQY 115
                                    *******************************9 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   8.5e-06     0.051      47     107 ..       9      71 ..       6      74 .. 0.87
   2 ?    0.8   0.1     0.068   4.1e+02      51      78 ..      87     114 ..      78     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                           SKA2  47 lkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elppls.eeeqeaae 107
                                    ++ ++e+ + L +q+++++++ +el+d + +  +a+re +++L a a el  +  +++q a++
  gi|121635935|ref|YP_976158.1|   9 VAVIQERQALLARQHDAVAEADRELADVLASAHAAMRESVRRLDAIAaELDRAVpDQDQLAVD 71 
                                    5679****************************************9888887777677777665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.068
                           SKA2  51 keelqaLkeqceellaekkelidkirtt 78 
                                    ++e+ a+ + ++el  +k  + +++r++
  gi|121635935|ref|YP_976158.1|  87 QREIVAVVAAAHELDRAKSAVLKRLRAQ 114
                                    6778888888888888888888888877 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   7.6     0.014        85      17      38 ..      37      61 ..      16      62 .. 0.74
   2 ?    4.6   0.1    0.0075        45      32      38 ..      97     103 ..      87     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.014
                                   HHCT..TTT.SSTTHHHHHHHHHCS CS
                          Rnk_N 17 ldsl..adr.dppaaeaLeaELdRA 38
                                   l+s+  a r +   ++a +aELdRA
  gi|121635935|ref|YP_976158.1| 37 LASAhaAMReSVRRLDAIAAELDRA 61
                                   44443533337778888*******9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0075
                                    HHHHHCS CS
                          Rnk_N  32 eaELdRA 38 
                                    ++ELdRA
  gi|121635935|ref|YP_976158.1|  97 AHELDRA 103
                                    79***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 897.82
//
Query:       gi|121635936|ref|YP_976159.1|  [L=477]
Description: hypothetical protein BCG_0057 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-36  122.9   5.7      1e-35  122.3   3.9    2.0  2  DUF4226          Domain of unknown function (DUF4226)
  ------ inclusion threshold ------
      0.091   12.7   0.2        1.4    8.8   0.1    2.2  2  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.21   1.9e+03      40      58 ..      44      62 ..      38      69 .. 0.72
   2 !  122.3   3.9   1.2e-39     1e-35       1     111 []      75     184 ..      75     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.21
                        DUF4226 40 kaaegrrrLdalqaeidqa 58
                                   +++   ++Lda+ ++i+q 
  gi|121635936|ref|YP_976159.1| 44 TSTTRSEQLDAILRKIRQR 62
                                   5556667899999999875 PP

  == domain 2  score: 122.3 bits;  conditional E-value: 1.2e-39
                        DUF4226   1 qrGsaadAarareaaLaqrlsataelDrqlaevlrsahakaaegrrrLdalqaeidqavatqalaldTpaGarqfqrfLi 80 
                                    ++G+aa+A++++eaaLa+ +sata+lD q+++++++ah k++eg ++L++lq+ei++av+ ++ +ldTpaGar+fqrfLi
  gi|121635936|ref|YP_976159.1|  75 EQGDAARAIADAEAALAHPNSATAQLDLQVVSAILNAHLKTVEGGESLHELQQEIEAAVRIRS-DLDTPAGARDFQRFLI 153
                                    68*************************************************************.**************** PP

                        DUF4226  81 aklreiakvVadasedsrskaalveaLtaqY 111
                                    +kl++i++vVa+as d++sk+al++a+t++Y
  gi|121635936|ref|YP_976159.1| 154 GKLKDIREVVATASLDAASKSALMAAWTSLY 184
                                    *****************************99 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00016       1.4      26      97 ..      62     135 ..      39     149 .. 0.71
   2 ?    1.3   0.0     0.032   2.9e+02      41      78 ..     369     429 ..     350     446 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00016
                2_5_RNA_ligase2  26 pHitLlypfvededl.......adlaellsrlaketepfevrldgfgvFehkksvvylsvsdsealqalraallealpe 97 
                                     H +L+yp ++d+         ad++++l++  + t+++++++ ++    h        v++ e+l++l++++++a+  
  gi|121635936|ref|YP_976159.1|  62 RHSNLYYPAPPDREQgdaaraiADAEAALAHPNSATAQLDLQVVSAILNAH-----LKTVEGGESLHELQQEIEAAVRI 135
                                    699**********99777555555555555555455555555544444333.....444499**********9999865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.032
                2_5_RNA_ligase2  41 adlaellsrlak........................etepfevrldgfgvFehkksvvylsv 78 
                                    ++la++++++a+                          +p +++ + +gvF+ + +++ l +
  gi|121635936|ref|YP_976159.1| 369 PQLAAAIKAAASgtpiadafqqqgiaiplpgtavanPVDPARISAGDVGVFT-DRHALALGP 429
                                    55555555555566666666666666666666666699999**********7.466999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3119.33
//
Query:       gi|121635937|ref|YP_976160.1|  [L=105]
Description: hypothetical protein BCG_0058 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-29  100.4   1.7    6.9e-29  100.3   1.7    1.0  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
  ------ inclusion threshold ------
      0.034   14.4   4.1       0.93    9.8   4.1    2.2  1  WXG100         Proteins of 100 residues with WXG
      0.096   13.0   0.8       0.17   12.2   0.3    1.7  2  KxDL           Uncharacterized conserved protein
       0.11   12.5   0.4       0.36   10.9   0.0    1.9  2  DUF3775        Protein of unknown function (DUF3775)


Domain annotation for each model (and alignments):
>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   1.7   1.5e-32   6.9e-29       1      99 [.       1      98 [.       1      99 [. 0.99

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 1.5e-32
                  T7SS_ESX_EspC  1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLra 82
                                   mtd+++V+p+hlr++aa+h+++a++++++++++ +a +++lds Gpi+++++d+ ++++++r+++++++a++++++a++Lr+
  gi|121635937|ref|YP_976160.1|  1 MTDRIHVQPAHLRQAAAHHQQTADYLRTVPSSH-DAIRESLDSLGPIFSELRDTGRELLELRKQCYQQQADNHADIAQNLRT 81
                                   9********************************.************************************************ PP

                  T7SS_ESX_EspC 83 AAaaYeatDeeaagald 99
                                   +Aa++e+++++a+++l+
  gi|121635937|ref|YP_976160.1| 82 SAAMWEQHERAASRSLG 98
                                   **************997 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.1   0.00021      0.93       2      85 ..       5      90 ..       4      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                                   HCSHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeelede...lqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80
                                   i v+p+ lrqaaa+ q++a+ l+++   +++++ ++d+l+  +s + +d+ ++ +e  kq  q+ +d+ ++i+++l+++a+ 
  gi|121635937|ref|YP_976160.1|  5 IHVQPAHLRQAAAHHQQTADYLRTVpssHDAIRESLDSLGPIFS-ELRDTGRELLELRKQCYQQQADNHADIAQNLRTSAAM 85
                                   789****************9877652226777777777777777.5678888888888888899999999999999999888 PP

                                   HHHHH CS
                         WXG100 81 fedaD 85
                                    e+++
  gi|121635937|ref|YP_976160.1| 86 WEQHE 90
                                   88877 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.43   1.9e+03      43      59 ..      12      28 ..       5      45 .. 0.54
   2 ?   12.2   0.3   3.8e-05      0.17      21      60 ..      46      85 ..      31      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.43
                           KxDL 43 laklrarfkqgtkllke 59
                                   l ++ a+ +q +  l+ 
  gi|121635937|ref|YP_976160.1| 12 LRQAAAHHQQTADYLRT 28
                                   44444444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.8e-05
                           KxDL 21 tsgrlnkknreLlelnalsqerlaklrarfkqgtkllkev 60
                                   +  +l ++ reLlel++++ ++ a+ +a+++q+ +++  +
  gi|121635937|ref|YP_976160.1| 46 IFSELRDTGRELLELRKQCYQQQADNHADIAQNLRTSAAM 85
                                   567899*****************************99887 PP

>> DUF3775  Protein of unknown function (DUF3775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     8e-05      0.36      42      72 ..      15      44 ..      10      45 .. 0.86
   2 ?   -0.4   0.1      0.27   1.2e+03      44      51 ..      66      73 ..      47      96 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                        DUF3775 42 AreeesertadyLlgkplladyLeeGLealg 72
                                   A+ ++ ++tadyL   p  +d ++e L+ lg
  gi|121635937|ref|YP_976160.1| 15 AA-AHHQQTADYLRTVPSSHDAIRESLDSLG 44
                                   44.566799********************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                        DUF3775 44 eeeserta 51
                                   +++++++a
  gi|121635937|ref|YP_976160.1| 66 QQQADNHA 73
                                   33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 566.28
//
Query:       gi|121635938|ref|YP_976161.1|  [L=101]
Description: hypothetical protein BCG_0059 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-61  203.3   1.1    3.8e-61  203.2   1.1    1.0  1  DUF2694   Protein of unknown function (DUF2694)


Domain annotation for each model (and alignments):
>> DUF2694  Protein of unknown function (DUF2694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   1.1   2.1e-65   3.8e-61       1      97 []       1      97 [.       1      97 [. 0.99

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 2.1e-65
                        DUF2694  1 mteanpafdtvhpsgdvlvrscrggylhsvalseaameadaerlaeaillaadvsylkallevrneivaaghspsaavpttd 82
                                   mt+anpafdtvhpsg++lvrscrggy+hsv+lseaame+dae+laeaill+advs+lkallevrneivaagh+psa+vpttd
  gi|121635938|ref|YP_976161.1|  1 MTDANPAFDTVHPSGHILVRSCRGGYMHSVSLSEAAMETDAETLAEAILLTADVSCLKALLEVRNEIVAAGHTPSAQVPTTD 82
                                   9********************************************************************************* PP

                        DUF2694 83 dlrvaiekllahrlr 97
                                   dl+vaiekllah+lr
  gi|121635938|ref|YP_976161.1| 83 DLNVAIEKLLAHQLR 97
                                   *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 551.90
//
Query:       gi|121635939|ref|YP_976162.1|  [L=365]
Description: hypothetical protein BCG_0060 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-36  124.0   0.4    6.4e-36  122.6   0.4    1.8  1  DUF5631       Family of unknown function (DUF5631)
    1.9e-35  120.8   0.3    7.2e-35  118.9   0.3    2.1  1  DUF5632       Family of unknown function (DUF5632)
  ------ inclusion threshold ------
       0.19   12.1   0.0       0.87   10.0   0.0    2.1  2  Ribosomal_L5  Ribosomal protein L5


Domain annotation for each model (and alignments):
>> DUF5631  Family of unknown function (DUF5631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.4   1.1e-39   6.4e-36       2      96 .]     269     361 ..     268     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 1.1e-39
                        DUF5631   2 delgvelseatrrrdgLPrlvhtlakaaaagtgvldeEvdllrehldtirkqvlaaYPdvdaalvlnwlLLAaiealvag 81 
                                      l+vel  at+r+dgLP++vh++a+aa  g+g + eEvdllr+h+dt+ ++vla+YP+vd+al+ln++LLAa+e++v+g
  gi|121635939|ref|YP_976162.1| 269 AGLSVELGIATQRHDGLPKIVHAMATAA--GNGAAAEEVDLLRVHVDTALHHVLAQYPRVDPALLLNCMLLAATERSVTG 346
                                    6799********************9998..999*********************************************** PP

                        DUF5631  82 devaAnYHlaWfral 96 
                                    d++aAnYH+aWfr+l
  gi|121635939|ref|YP_976162.1| 347 DPIAANYHFAWFREL 361
                                    ************985 PP

>> DUF5632  Family of unknown function (DUF5632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.3   1.2e-38   7.2e-35       2      81 .]     164     243 ..     163     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.2e-38
                        DUF5632   2 seeqrLqRlldavaRqeprLaWavGeraDgttllvtDlasGWiPpgvelpagvtLleParrsgeleallGevavaaayep 81 
                                     +e+rLqRll++vaRqeprL+WavG  aDgtt+lvtD+a+GWiPpg++lp+gv+Ll Parr g++ +l+G ++   +y+p
  gi|121635939|ref|YP_976162.1| 164 DDEARLQRLLAFVARQEPRLNWAVGVNADGTTVLVTDVAHGWIPPGIALPEGVRLLAPARRAGRAPELVGITTCCKTYTP 243
                                    5899**************************************************************************98 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00015      0.87      22      43 ..     104     122 ..      94     126 .. 0.84
   2 ?   -2.3   0.0         1   6.1e+03      17      39 ..     275     297 ..     270     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                                    SCHHHHHCCHHHHCCCHSS--E CS
                   Ribosomal_L5  22 edkkllekaakeLaeItGQkPv 43 
                                    ++   +e+a++eL++ItG  Pv
  gi|121635939|ref|YP_976162.1| 104 RR---VESAMRELRQITGRVPV 122
                                    44...9*************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1
                                    -SSSSSCHHHHHCCHHHHCCCHS CS
                   Ribosomal_L5  17 vGeagedkkllekaakeLaeItG 39 
                                    +G a++++  l k +  +a+ +G
  gi|121635939|ref|YP_976162.1| 275 LGIATQRHDGLPKIVHAMATAAG 297
                                    67788998889998888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2406.14
//
Query:       gi|121635940|ref|YP_976163.1|  [L=109]
Description: hypothetical protein BCG_0061 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-63  211.9   2.1    1.4e-63  211.8   2.1    1.0  1  DUF2710      Protein of unknown function (DUF2710)
    0.00051   20.2   0.0    0.00083   19.5   0.0    1.3  1  YbaB_DNA_bd  YbaB/EbfC DNA-binding family
     0.0012   19.0   4.2       0.51   10.6   0.2    2.1  2  DUF4129      Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> DUF2710  Protein of unknown function (DUF2710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.8   2.1   2.4e-67   1.4e-63       1     104 []       3     106 ..       3     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 2.4e-67
                        DUF2710   1 sgsdsraepsqlsdkdlvesvlrdlseaaekwealvaeaetvtysvdlgdvravansdgrlleltlhpgvvsdyaysela 80 
                                    sgsdsr+epsqlsd+dlvesvlrdlseaa+kwealv++aetvtysvdlgdvravansdgrlleltlhpgv+++ya++ela
  gi|121635940|ref|YP_976163.1|   3 SGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELA 82 
                                    8******************************************************************************* PP

                        DUF2710  81 erlnlvitalreeveaefearygs 104
                                    +r+nl+italr+eveae++aryg+
  gi|121635940|ref|YP_976163.1|  83 DRVNLAITALRDEVEAENRARYGG 106
                                    **********************97 PP

>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-07   0.00083      20      83 ..      41     104 ..      24     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                                    TSEEEEEETTTTEEEEEETT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    YbaB_DNA_bd  20 ekevegssggglVkVtvngkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaeeem 83 
                                    +++v+ s   g V++++n +g+++++++ p ++       L+d +  A+ + ++++e+e++++ 
  gi|121635940|ref|YP_976163.1|  41 AETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARY 104
                                    567888888899********************99666778*******************99876 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   8.6e-05      0.51      22      60 ..      16      52 ..       9      67 .. 0.84
   2 !   10.3   0.6   0.00011      0.64      22      54 ..      78     107 ..      62     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.6e-05
                        DUF4129 22 prEyarrv.riapspaaalaalaelfeearYGgrpasaee 60
                                    r++++ v r   ++a+ ++al++  e + Y+   ++ ++
  gi|121635940|ref|YP_976163.1| 16 DRDLVESVlRDLSEAADKWEALVTQAETVTYS---VDLGD 52
                                   699****************************5...44444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                        DUF4129  22 prEyarrv..riapspaaalaalaelfeearYGgr 54 
                                     +E+a rv  +      +al++ +e+ ++arYGgr
  gi|121635940|ref|YP_976163.1|  78 HGELADRVnlA-----ITALRDEVEAENRARYGGR 107
                                    68999999544.....4899999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 746.12
//
Query:       gi|121635941|ref|YP_976164.1|  [L=70]
Description: remnant of a transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 508.82
//
Query:       gi|121635942|ref|YP_976165.1|  [L=771]
Description: 8-amino-7-oxononanoate synthase bioF2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-55  188.2   0.0      3e-55  187.8   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    5.6e-08   33.0   1.2    5.6e-08   33.0   1.2    2.5  3  Acetyltransf_6   Acetyltransferase (GNAT) domain
      6e-07   29.0   0.1    1.1e-06   28.2   0.1    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
      3e-06   26.8   0.1    5.1e-06   26.0   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.1e-05   23.2   0.0    3.4e-05   22.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00012   21.2   0.0    0.00019   20.5   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0047   15.7   0.1      0.096   11.4   0.1    2.1  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
      0.018   14.2   0.0      0.027   13.6   0.0    1.2  1  FemAB_like       Peptidogalycan biosysnthesis/recognition


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.0   1.4e-58     3e-55       3     361 ..     418     755 ..     416     757 .. 0.95

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 1.4e-58
                                    EEESSSSSTTSTTSS.HHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                  Aminotran_1_2   3 vinLgsneylgdsgk.ptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                    ++ Lg+n ylg++ + +++++ a+a+++ g + +g+    g+ d++ +le++la flg       k+  av++++G++++
  gi|121635942|ref|YP_976165.1| 418 IVLLGTNSYLGLATHpEVVEASAEATRRyGTGCSGSPLLNGTLDLHVSLEQELACFLG-------KPA-AVLCSTGYQSN 489
                                    789************9999999999999******************************.......555.*********** PP

                                    HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TT CS
                  Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNP 160
                                    ++a+ +l++   gd i+ +++++ s  +++rlsg+ +  y+       h+d+++l + l++  eg+   ++i+v  ++++
  gi|121635942|ref|YP_976165.1| 490 LAAISALCE--SGDMIIQDALNHRSLFDAARLSGADFTLYR-------HNDMDHLARVLRRT-EGRR--RIIVVDAVFSM 557
                                    *****9998..******************************.......************94.4444..7********** PP

                                    T--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS..HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHH CS
                  Aminotran_1_2 161 tGtvatleeleklldlakkynlllfvDeaYagfvfgsl..davatranveeepnllivgslsKafGlaGeRvGyilgnaa 238
                                     Gtva+l+++ +l   a++++++++vDe +a +v+g+   +a ++ ++v ++ + +++g++sK+f+++G   G+i+g+  
  gi|121635942|ref|YP_976165.1| 558 EGTVADLATIAEL---ADRHGCRVYVDESHALGVLGPDgrGA-SAALGVLARMD-VVMGTFSKSFASVG---GFIAGDRP 629
                                    *************...********************777444.44999999999.**************...******** PP

                                    HHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHH CS
                  Aminotran_1_2 239 vvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetak 318
                                    vv+++r   ++  +s++l++a+aaa+++al++ ++  ++r+r+ + ++++  +La+ g +     ++++++ ++++  a+
  gi|121635942|ref|YP_976165.1| 630 VVDYIRHNGSGHVFSASLPPAAAAATHAALRVSRREPDRRARVLAAAEYMATGLARQGYQAEYHGTAIVPVILGNPTVAH 709
                                    ******************************************************99999999999************999 PP

                                    HHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHH CS
                  Aminotran_1_2 319 elskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelve 361
                                    + +  L    gvyv p+ ++ v   ++ +R ++ A + +++l+++++
  gi|121635942|ref|YP_976165.1| 710 AGYLRLMRS-GVYVNPVAPPAVpeeRSGFRTSYlADHRQSDLDRALH 755
                                    99999**99.************999777****************997 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   1.2   2.5e-11   5.6e-08      20     139 ..     186     308 ..     168     311 .. 0.84
   2 ?   -0.8   0.3      0.71   1.6e+03      29      75 ..     530     580 ..     511     605 .. 0.71
   3 ?   -3.7   0.1       5.3   1.2e+04      27      49 ..     668     689 ..     650     703 .. 0.45

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                 Acetyltransf_6  20 vrf.rvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgd.rlyy 97 
                                    +++ ++++ +e +  l +l+r+ +++ +d+ +++l+ +f+++  ++l  +g+ rl+  r +g+p+A++l+++  d  +++
  gi|121635942|ref|YP_976165.1| 186 IEVeELDEYAEHAPVLARLWRNVKTEAKDYQREDLNPEFFAACSRHL--HGRSRLWLFRYQGTPIAFFLNVWGADeNYIL 263
                                    34425566667777788888888888789999***************..***********************99967778 PP

                 Acetyltransf_6  98 wlggydpe...laklspgllllweliedaaeeGlrrfdlgggdee 139
                                    +  g+d++   ++k  +++  l+  ++da+ ++ rr+++g+ ++ 
  gi|121635942|ref|YP_976165.1| 264 LEWGIDRDfehYRKANLYRAALMLSLKDAISRDKRRMEMGITNYF 308
                                    999****966667999************************99875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.71
                 Acetyltransf_6  29 edleallelfraqwarr.....pdvfadpltraflrdllaalaargalrlyv 75 
                                     d++ l + +r++ +rr      +vf+ + t a l+ + a+la+r  +r+yv
  gi|121635942|ref|YP_976165.1| 530 NDMDHLARVLRRTEGRRriivvDAVFSMEGTVADLATI-AELADRHGCRVYV 580
                                    45666666666666666788888888888877777666.5556777788876 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.3
                 Acetyltransf_6  27 dpedleallelfraqwarrpdvf 49 
                                    +++ + a+ e ++   ar+ ++ 
  gi|121635942|ref|YP_976165.1| 668 RRARVLAAAEYMATGLARQ-GYQ 689
                                    2222223333333334444.444 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   4.7e-10   1.1e-06      36     221 ..     465     636 ..     457     692 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.7e-10
                                    HHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHH CS
                Beta_elim_lyase  36 rLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekle 115
                                     Le+++a  +gk aa+ + +G ++n  ++++l+++g+ +i +  +h     +   a l+g+   +l+  +    d++ l+
  gi|121635942|ref|YP_976165.1| 465 SLEQELACFLGKPAAVLCSTGYQSNLAAISALCESGDMIIQDALNHRSLFDA---ARLSGAD-FTLYRHN----DMDHLA 536
                                    69999***********************************999999888765...4568884.5677777....799*** PP

                                    HHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH...HHHTS-CHHHHTTSSEE CS
                Beta_elim_lyase 116 aaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa...kslgeivkemfsyvDsv 192
                                    +++++++    + ++i++  ++ ++ G+v     l+ +a++a+++g ++ +D    +         +  +  +++ +D+v
  gi|121635942|ref|YP_976165.1| 537 RVLRRTEG---RRRIIVVD-AVFSMEGTVA---DLATIAELADRHGCRVYVDESHALGVLgpdGRGASAALGVLARMDVV 609
                                    *****666...55555554.4444578876...56678899***********999888888764555555566799**** PP

                                    EEESSSTT--SS-EEEEE-HH....HHHH CS
                Beta_elim_lyase 193 tmslkKdllanvGgvlafrddeledylae 221
                                    +  ++K  +a vGg++a+++    dy+++
  gi|121635942|ref|YP_976165.1| 610 MGTFSKS-FASVGGFIAGDRP-VVDYIRH 636
                                    ******9.778*********9.8899887 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   2.3e-09   5.1e-06      27     151 ..     465     588 ..     458     604 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.3e-09
                                    HHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGG CS
                DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaiea 106
                                    ++E+++a +lg+  a+ +s+G ++++ a++al  + gd +I  +l+  +   a++ +ga+  +   +  ++    a++ +
  gi|121635942|ref|YP_976165.1| 465 SLEQELACFLGKPAAVLCSTGYQSNLAAISALCES-GDMIIQDALNHRSLFDAARLSGADFTLYRHNDMDH---LARVLR 540
                                    68*****************************9877.9**********************988876664333...344445 PP

                                    G--TTEEEEEEB-....GGGB---HHHHHHHHHHCT-EEEEE-TT-TT- CS
                DegT_DnrJ_EryC1 107 aitertkaIlpVh....lyGqvadmdalkaiaakhglkvieDaAhAlGa 151
                                      + r++ I++V+    + G vad++ + ++a++hg  v  D +hAlG 
  gi|121635942|ref|YP_976165.1| 541 RTEGRRR-IIVVDavfsMEGTVADLATIAELADRHGCRVYVDESHALGV 588
                                    5555555.55554222267****************************95 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-08   3.4e-05      55     180 ..     464     588 ..     458     592 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-08
                                    HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHC CS
                Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekai 134
                                      le+++a   g  aa+++s+G  +  aai al+++Gd i+ +   +++ ++  +     + + +++ d+++l+++ +  
  gi|121635942|ref|YP_976165.1| 464 VSLEQELACFLGKPAAVLCSTGYQSNLAAISALCESGDMIIQDALNHRSLFDAARLSGADFTL-YRHNDMDHLARVLRRT 542
                                    579***********************************9998877666666555555555533.4566677777777777 PP

                                    CTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTT CS
                Cys_Met_Meta_PP 135 kentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspl 180
                                    + + +++ ++++ +    v+D+++ia+la  +g+ v vD + a ++
  gi|121635942|ref|YP_976165.1| 543 EGRRRIIVVDAVFSMEGTVADLATIAELADRHGCRVYVDESHALGV 588
                                    779************************************9887666 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.6e-08   0.00019      47     181 ..     465     587 ..     430     592 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.6e-08
                                    HHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSC CS
                    Aminotran_5  47 earekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeege 126
                                      ++++a +++ +     + + +t+ + nl+a+s++   + gd i+  +++h + +    ++a+  ga+ + ++ ++  +
  gi|121635942|ref|YP_976165.1| 465 SLEQELACFLGKPA---AV-LCSTGYQSNLAAISAL--CESGDMIIQDALNHRSLF----DAARLSGADFTLYRHNDMDH 534
                                    55666666666665...23.3457778899888885..8*****************....88888899999998887777 PP

                                    BEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                    Aminotran_5 127 ldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                    l   ++    + + +++ + +v ++ Gt+ +++ i++la ++g+ v vD + a+g
  gi|121635942|ref|YP_976165.1| 535 LA--RVLRRTEGRRRIIVVDAVFSMEGTVADLATIAELADRHGCRVYVDESHALG 587
                                    66..777778899************************************998876 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   4.3e-05     0.096      93     129 ..     487     523 ..     479     588 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EE CS
                       OKR_DC_1  93 ssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgat 129
                                     sn + + a++++gd+++ d  +H+S++ a  lsga 
  gi|121635942|ref|YP_976165.1| 487 QSNLAAISALCESGDMIIQDALNHRSLFDAARLSGAD 523
                                    58999******************************96 PP

>> FemAB_like  Peptidogalycan biosysnthesis/recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.027     170     289 ..     156     275 ..      89     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                     FemAB_like 170 yasfddfLaalssrkRknirkerrkvaeqgitievltgeeiteeewdafyefYqetyskkwgspyLtreffellaerlae 249
                                    ++s ++ L  ls+++R  ++   +  ++ gi++e l+  + ++  + ++++   +t +k  +++ L+ eff+  +++l+ 
  gi|121635942|ref|YP_976165.1| 156 WSSVEEALGCLSHKRRLPLKTSLEFRERFGIEVEELDEYAEHAPVLARLWRNV-KTEAKDYQREDLNPEFFAACSRHLHG 234
                                    6788999999************************9998877666666666654.466666799***************** PP

                     FemAB_like 250 kvllvlaeregeliagalnligedtlyG.RyWGaleelpfL 289
                                    +  l l + +g++ia  ln+ g+d  y    WG  +++++ 
  gi|121635942|ref|YP_976165.1| 235 RSRLWLFRYQGTPIAFFLNVWGADENYIlLEWGIDRDFEHY 275
                                    **********************9998862468887766644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5135.35
//
Query:       gi|121635943|ref|YP_976166.1|  [L=87]
Description: acyl carrier protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-11   44.0   0.4    2.3e-11   43.8   0.4    1.1  1  PP-binding     Phosphopantetheine attachment site
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.016   14.9   0.0    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.4   2.6e-15   2.3e-11       3      64 ..       5      66 ..       3      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.6e-15
                     PP-binding  3 lrelvaevlgvpleeidpdtdlf.dlGlDSllavellaaleeefgveiplsdlfehptlaela 64
                                   + + ++++l+++   i++++ l  dlG+DSl + +l+ +le+ef+++i+ +d  + +t+++++
  gi|121635943|ref|YP_976166.1|  5 INATIQRILRTDRG-ITANQVLVdDLGFDSLKLFQLITELEDEFDIAISFRDAQNIKTVGDVY 66
                                   6688999***8765.6999999967****************************88*****987 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-06     0.016      29      64 ..      34      69 ..      22      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-06
                  Guanylate_cyc 29 ievvklLnelyarfdelldekkvykvktiGdaymvv 64
                                    ++++l+ el  +fd  ++ ++ +++kt+Gd y  v
  gi|121635943|ref|YP_976166.1| 34 LKLFQLITELEDEFDIAISFRDAQNIKTVGDVYTSV 69
                                   68899****************************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 705.15
//
Query:       gi|121635944|ref|YP_976167.1|  [L=131]
Description: hypothetical protein BCG_0065 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-11   42.5   1.1      1e-10   42.2   1.1    1.1  1  SnoaL_2   SnoaL-like domain
    9.8e-05   22.7   0.2    0.00016   22.1   0.2    1.4  1  DUF4440   Domain of unknown function (DUF4440)
     0.0028   17.8   0.1     0.0033   17.5   0.1    1.2  1  SnoaL_4   SnoaL-like domain
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.025   14.8   0.0    1.2  1  SnoaL_3   SnoaL-like domain
      0.088   12.6   0.1       0.16   11.7   0.1    1.5  1  SnoaL     SnoaL-like polyketide cyclase
       0.11   12.3   0.0       0.14   12.0   0.0    1.1  1  TMV_coat  Virus coat protein (TMV like)


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   1.1   3.4e-14     1e-10       1     101 [.      10     115 ..      10     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.4e-14
                                    HHHHHHHHHTTCHHHHHHTEEEEEEEEETTSE.....EESHHHHHHHHHHHHH.HEEEEEEEEEEEEEE.TTEEEEEEEE CS
                        SnoaL_2   1 vraflaalnagdldalaalfapdvvwedpgge.....lrGreairaffralfa.afpdlrfeihdvvad.gdrvavewtv 73 
                                    vr+ +aa+++gdl++l ++fapdv++  pg       +rG + + a +    a a ++++++++dv+ + + +v++ +++
  gi|121635944|ref|YP_976167.1|  10 VRRTFAAFARGDLAELTQCFAPDVEQFVPGKHalagvFRGVDNVVACLGDTAAaADGTMTVTLEDVLSNtDGQVIAVYRL 89 
                                    89************************98855557778*********6666555599**********55514577778888 PP

                                    EEEEETTSSEEEEEEEEEEEEETTEEEE CS
                        SnoaL_2  74 tgtipatgrgvtvrgvdvfrvrdGkive 101
                                    ++   + g+ ++ r + + +v++G+i++
  gi|121635944|ref|YP_976167.1|  90 RA--SRAGKVLDQREAILVTVAGGRITR 115
                                    85..899999999*************97 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   5.3e-08   0.00016       4      83 ..       9      95 ..       7     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.3e-08
                                   HHHHHHHHHHCT-HHHHHHCEEEEEEEE-TT.....S-EEEHHHHHHHHHC.CHCEEEEEEEEEEEEEEE.TTEEEEEEEEE CS
                        DUF4440  4 leealeeafvagdaealaallapdavlvgps.....gtvldkeellealea.gfaagrslelteeevrvl.gdlAvvtgryt 78
                                   l+++ ++af++gd+++l +++apd++ + p+     g +++ +++++ l + ++aa+ ++++t e+v    ++ +++++r +
  gi|121635944|ref|YP_976167.1|  9 LVRRTFAAFARGDLAELTQCFAPDVEQFVPGkhalaGVFRGVDNVVACLGDtAAAADGTMTVTLEDVLSNtDGQVIAVYRLR 90
                                   7899************************888889988889*********664668889999999998877466888888888 PP

                                   EEECC CS
                        DUF4440 79 fegrg 83
                                   +++ g
  gi|121635944|ref|YP_976167.1| 91 ASRAG 95
                                   87643 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.1e-06    0.0033      11      82 ..       8      82 ..       4     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS.....--EESHHHHHHHHHSHHHHHH-EEEEE---EEEE.ETT CS
                        SnoaL_4 11 dlvarygyylDtkdweeladlFtedavvdytgvg...egvlegrdairaalrealdgfaltqHllsnpliel.dgd 82
                                   dlv r + +  ++d +el ++F++d++  ++g +    gv++g+d ++a l + +++ + t+ ++   + +  dg+
  gi|121635944|ref|YP_976167.1|  8 DLVRRTFAAFARGDLAELTQCFAPDVEQFVPG-KhalAGVFRGVDNVVACLGDTAAAADGTMTVTLEDVLSNtDGQ 82
                                   789999999999***************77775.569****************999888887777666666654554 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.5e-06     0.025       4      77 ..       9      86 ..       7     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-06
                        SnoaL_3  4 lldafyeaaaegdfdalfalwaddivfigtgadel...ltgreevrrslkqifakg.egisfeltdvrvtesgdvawv 77
                                   l+++ ++a+a+gd+++l + +a+d+  + +g++ l   ++g + v+++l +  a++  + + +l+dv    +g+v+ v
  gi|121635944|ref|YP_976167.1|  9 LVRRTFAAFARGDLAELTQCFAPDVEQFVPGKHALagvFRGVDNVVACLGDTAAAAdGTMTVTLEDVLSNTDGQVIAV 86
                                   6678899***************999999999987644477***********999996699999999988888777655 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.5e-05      0.16       3      86 ..      10      98 ..       8     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                                   HHHHHHHHHHTT-HHHHHGTEEEEEEETCCTT....TCECHHHHHHHHHHHHHHHCTTCEE..EEEEEEEET.TEEEEEEEE CS
                          SnoaL  3 vlrfyeevwnsgdldaldelvaedvvdhnpee....eparGlegfrafveelfkafPDlkv..evedlvaeg.dkvaarltf 77
                                   v+r+++++  +gdl++l + +a+dv++  p++    ++ rG++++ a + ++ +a  D ++  + ed+++    +v a  ++
  gi|121635944|ref|YP_976167.1| 10 VRRTFAAF-ARGDLAELTQCFAPDVEQFVPGKhalaGVFRGVDNVVACLGDTAAAA-DGTMtvTLEDVLSNTdGQVIAVYRL 89
                                   45555555.9*****************99998888899999999999998887766.4333247788887773466666666 PP

                                   EEEESSEBT CS
                          SnoaL 78 tGthtgefl 86
                                   +++  g++l
  gi|121635944|ref|YP_976167.1| 90 RASRAGKVL 98
                                   666666555 PP

>> TMV_coat  Virus coat protein (TMV like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05      0.14      51     126 ..      22     109 ..       4     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                    -...B--S.BTTC-S.S...S.TT.....SSSEEEEHHHHHHHHHHHCHHHS....S-SCCCCCCCCS...........S CS
                       TMV_coat  51 g...rdlpvsvterF.pgartslG.....dkeflllldkrvtaalsrladaad...deknrvvelnkaeaegkttrtten 118
                                         ++++   e+F pg ++  G     d+ +++l d+++ a  +    + d   ++  +v+++ + +a+ + ++  ++
  gi|121635944|ref|YP_976167.1|  22 LaelTQCFAPDVEQFvPGKHALAGvfrgvDNVVACLGDTAAAADGTMTVTLEDvlsNTDGQVIAVYRLRASRAGKVLDQR 101
                                    0444689999999998999*********999999996666554433333333344499999******************* PP

                                    ST-SSTTT CS
                       TMV_coat 119 qaatatae 126
                                    +a+  t++
  gi|121635944|ref|YP_976167.1| 102 EAILVTVA 109
                                    **998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 860.87
//
Query:       gi|121635945|ref|YP_976168.1|  [L=562]
Description: fatty-acid-CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-52  177.6   0.0    3.8e-52  177.3   0.0    1.1  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
       0.11   10.8   0.0       0.17   10.3   0.0    1.1  1  PLA2_B       Lysophospholipase catalytic domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.0   4.2e-56   3.8e-52       7     422 ..      17     436 ..      11     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 4.2e-56
                                    HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHH CS
                    AMP-binding   7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeel 86 
                                       d++  + +++ + ++Y++l +r+ +    Lr+l++k+g+ V+i +++ +e++  +l+++  Gav+vp+ p+   ++ 
  gi|121635945|ref|YP_976168.1|  17 ACTDRTLTITCEDSEVISYQDLIARAAACIPPLRRLDLKRGEPVLITAHTNLEFLSCFLGLMLHGAVPVPIPPREALKTT 96 
                                    455778777788999**********************************************************9999888 PP

                                    HHHHHHHTE.....SEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSE CS
                    AMP-binding  87 ayiledsea.....kvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddl 161
                                    +  ++  ++     +vli  +  ++ +++++aa+++ + +  + l +++ ++  ++ +++ ++ +     + + ++ dd 
  gi|121635945|ref|YP_976168.1|  97 ERFMTRLGPllrhhRVLI--CTPAEHDEIRAAASTDCQISRFTALAEAGDEQFGRATAQQLADTA---TADWPLCTLDDD 171
                                    888888877444446777..767778888888888888888888887776666555554444433...336668999*** PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.C CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa.l 240
                                    ay++YTSG+T  P GV+++ rnl++n++++++  +  ++++dv+ s+lpl+h++gl+ +l++al++  + v+ ++  +  
  gi|121635945|ref|YP_976168.1| 172 AYVQYTSGSTAAPRGVVITYRNLLSNMRAMAVGSQ--FQHGDVMGSWLPLHHDMGLVGSLFAALFNSVSAVFTTPHRFlY 249
                                    *****************************875544..5589*************************************88 PP

                                    HHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC......EEEE CS
                    AMP-binding 241 dpklllelieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfge......evle 313
                                    dp  +l+l++  ++t+++ ++ +le l+++ +++ a+ +  dl ++r ++++ ep+ +e +r+f a+f +      ++  
  gi|121635945|ref|YP_976168.1| 250 DPLGFLRLLTSSGATHTFMPNFALEWLINAYHRRgADIEGIDLHKMRRLIIASEPVHAEGMRRFAATFAGvglaptALGS 329
                                    899999*******************9999555555788899**********************************99*** PP

                                    EEEEGGGSSECEE.......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS.-SEBTT-HHHH CS
                    AMP-binding 314 gYGlTEttgvvtv.......lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgv.mkgYlkkpeat 385
                                    gYGl+E+t++v++        ++ +  + + + G++lpg ev+i D +     p    G + +rg +v +k Y +   + 
  gi|121635945|ref|YP_976168.1| 330 GYGLAEATVAVSMsapntgfRTETHAAAEVVTGGRVLPGYEVRI-DAA-----PGARAGTIKLRGDSVaAKAYVGG--KK 401
                                    ***********7778899985556666777788***********.766.....33344********8725778877..55 PP

                                    HHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 386 aeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                     +a+d e+++  T Dlg+l  d ++ i+gR ++++++
  gi|121635945|ref|YP_976168.1| 402 LDALD-EEGFCDTHDLGFLV-DDEIVILGRQDEVFIV 436
                                    56787.547*********87.679**********987 PP

>> PLA2_B  Lysophospholipase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   1.9e-05      0.17     198     244 ..     199     243 ..     188     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.9e-05
                         PLA2_B 198 pveylGtklsnGtvvkkgkcvagfdnaGflmgtsstlFnevlleins 244
                                        +G++++ G v+  g+  + +  +G++++ +++lFn v  ++++
  gi|121635945|ref|YP_976168.1| 199 RAMAVGSQFQHGDVM--GSWLPLHHDMGLVGSLFAALFNSVSAVFTT 243
                                    55669**********..***********************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3936.03
//
Query:       gi|121635946|ref|YP_976169.1|  [L=226]
Description: hypothetical protein BCG_0067c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-31  108.2  21.2    8.3e-31  107.6  21.2    1.3  1  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
    6.9e-08   33.1   6.4    6.9e-08   33.1   6.4    1.6  1  DinB_2    DinB superfamily
  ------ inclusion threshold ------
       0.08   12.9   0.0        0.1   12.5   0.0    1.3  1  DinB      DinB family


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6  21.2   1.4e-34   8.3e-31       1     141 []      11     147 ..      11     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 1.4e-34
                        MDMPI_N   1 lreewaalaalvagLtdeqwaapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaas 80 
                                    lr+e ++l+alva L+ + wa p+p+pGWt+a++++Hl +++r +++a+++e+ +++l++ aaa++  ++ + a+ + a+
  gi|121635946|ref|YP_976169.1|  11 LRAESDDLDALVAHLPADRWADPTPAPGWTIAHQIGHLLWTDRVALTAVTDEAGFAELMTAAAANPAGFV-DDAATELAA 89 
                                    799*******************************************************************.999999999 PP

                        MDMPI_N  81 lapeallaafraavtrlaaalaalppdaiadrlgipggprslgeflrtrlvEavvHglDla 141
                                     +p++ll ++r ++ rl ++l a+p+++  +++g+p++++s   ++++rl+E+++HglD+a
  gi|121635946|ref|YP_976169.1|  90 VSPAELLTDWRVTRGRLHEELLAVPDGRKLAWFGPPMSAAS---MATARLMETWAHGLDVA 147
                                    9********************************99999999...***************96 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   6.4   1.2e-11   6.9e-08       3      93 ..      12     117 ..      10     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.2e-11
                         DinB_2   3 erararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlr...........geeap.......rpgldplt 64 
                                    ++  ++l al++ l+++ +  + + ++w+ia++++Hl ++ +++l ++                +       +++ ++l+
  gi|121635946|ref|YP_976169.1|  12 RAESDDLDALVAHLPADRWADPTPAPGWTIAHQIGHLLWTDRVALTAVTdeagfaelmtaA---AanpagfvDDAATELA 88 
                                    5667899******************************************877666555541...0333455567888888 PP

                         DinB_2  65 ppsaaealaylaevrarllallealtdad 93 
                                      s+ae+l  ++ +r+rl++ l a +d +
  gi|121635946|ref|YP_976169.1|  89 AVSPAELLTDWRVTRGRLHEELLAVPDGR 117
                                    8*********************9999943 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05       0.1      10      61 ..       7      58 ..       1     116 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHHHHHHHHHCT--CCCTT--SSTTS--HHHHHHHHHHHHHHHHHH CS
                           DinB 10 llqynqwardrtldaiaaLpdeelkaengegfqsvkqtlnHvldveelwlsr 61
                                   +++ ++++ d ++ ++a Lp++ ++ +  + ++++++++ H+l +++  l++
  gi|121635946|ref|YP_976169.1|  7 FVADLRAESDDLDALVAHLPADRWADPTPAPGWTIAHQIGHLLWTDRVALTA 58
                                   56778889999*******************************9877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1792.39
//
Query:       gi|121635947|ref|YP_976170.1|  [L=441]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-10   39.3  43.0    3.6e-10   39.3  43.0    2.2  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3  43.0     2e-14   3.6e-10      29     339 ..      65     383 ..      39     384 .. 0.72
   2 !    6.4   5.8    0.0002       3.6      86     167 ..     345     426 ..     344     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2e-14
                          MFS_1  29 ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll.fa..sslw.lllvlrvlqGlgagalf 103
                                    ++p +i  ++++ +l ++++ +++G+l+dr+ rr+vl+ + ++ ++  + +++ +a  ++   ll+ + v  Gl+  +++
  gi|121635947|ref|YP_976170.1|  65 ADPMAIAGAFAVLFLPYSLLGPFAGALMDRWDRRWVLVGANTGRLALiAGVGTiLAvgAGDVpLLVGALVANGLA-RFVA 143
                                    66677777999**************************99887776663333334334655554999999999999.6*** PP

                          MFS_1 104 pagaaliadwfpkeergraigllsagfslGailg...pllggllasslg...Wravfyilaivsllafvlfllllpeepp 177
                                    ++  a++ +++p+e+   +++++ a+ +++a lg   +ll  +l+ s+       vf+++ +vs+ +  l  + l+  p+
  gi|121635947|ref|YP_976170.1| 144 SGLSAALPHVVPREQVVTMNSVAIASGAVSAFLGanfMLLPRWLLGSGDegaSAIVFLVAIPVSIAL--L--WSLRFGPR 219
                                    *********************************9777788889997777886666677777777777..4..55555555 PP

                          MFS_1 178 erkrkspkeee....kgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevlgls.....glllag 247
                                      +++ +++      +  + ++++ + + ++  p     ++a l++ +++ + + + + l+l  v++ +     gl +a+
  gi|121635947|ref|YP_976170.1| 220 VLGPDDTERAIhgsaVYAVVTGWLHGARTVVQLP----TVAAGLSGLAAHRMvVGINSLLILLLVRHVTaravgGLGTAL 295
                                    5555555555433333344444444444444444....666666666666667445555555788888888898988888 PP

                          MFS_1 248 lllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasd 327
                                    l++a+++l+++ + +l+   ++r+gr  + + al++++++ ++ a l v+    ++++  +l+G+++ +v  ++ ++++ 
  gi|121635947|ref|YP_976170.1| 296 LFFAATGLGAFLANVLTPTAIRRWGRYATANGALAAAATIQVAAAGLLVP----VMVVCGFLLGVAGQVVKLCADSAMQM 371
                                    889999999988899999999*****999999999999999999999999....33334444566666667777777777 PP

                          MFS_1 328 lappeeagtasg 339
                                     +    +g++++
  gi|121635947|ref|YP_976170.1| 372 DVDDALRGHVFA 383
                                    777788887776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0002
                          MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                    ++++v+ +l G+++ ++   + +++   + +  rg ++++  a f +++il   ++++l+   g   vf++++ +  la+
  gi|121635947|ref|YP_976170.1| 345 PVMVVCGFLLGVAGQVVKLCADSAMQMDVDDALRGHVFAVQDALFWVSYILSITVAAALIPEHGHAPVFVLFGSAIYLAG 424
                                    5799**********99999999999999999*****************************88888889999988888887 PP

                          MFS_1 166 vl 167
                                    ++
  gi|121635947|ref|YP_976170.1| 425 LV 426
                                    74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3267.46
//
Query:       gi|121635948|ref|YP_976171.1|  [L=202]
Description: hypothetical protein BCG_0069 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-35  123.0   0.0    1.4e-35  122.6   0.0    1.1  1  DUF179    Uncharacterized ACR, COG1678


Domain annotation for each model (and alignments):
>> DUF179  Uncharacterized ACR, COG1678
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   7.7e-40   1.4e-35       3     159 ..      31     185 ..      29     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 7.7e-40
                                    STTTTSTTEEEEEEEEETTEEEEEESSSEEEEEHHHHHHHGCTSSSST-CHHHSEEEES-SEEEEEEEEEEES....... CS
                         DUF179   3 ledpnFersVvlllehdeegalGlvlNrpleltlkelleelleleaepateklssvylGGPveqdrlfvlhsle...... 76 
                                    l +p+F+rsV++++eh++ g+lG+vlNrp+e+++ ++l+++++l+a+p+t     +++GGPv++d+ ++l  l+      
  gi|121635948|ref|YP_976171.1|  31 LLEPTFRRSVIYIVEHNDGGTLGVVLNRPSETAVYNVLPQWAKLAAKPKT-----MFIGGPVKRDAALCLAVLRvgadpe 105
                                    789*********************************************99.....**********666666534445566 PP

                                    .SSSEEECSTTEEEE-SSHHHHHHCSTTSCSSEEEEEEEEEECTTHHHHHHHTTSEEEEE-.HHHHHCTSTSSHHHHHHH CS
                         DUF179  77 elessleisdglylttsldilealagkagpeklrvflGyagWeagQLeeEieegaWlvvpassedllfetppeelWeeal 156
                                    ++++  +++  l++       e l   a  e +r+++Gy+gW+ gQLe Eie+++W+v++a ++d+l + p ++lW ++l
  gi|121635948|ref|YP_976171.1| 106 GVPGLRHVAGRLVMVDLDADPEVL--AAAVEGVRIYAGYSGWTIGQLEGEIERDDWIVLSALPSDVLVG-PRADLWGQVL 182
                                    788888888877774333333333..456799*************************************.********** PP

                                    HCC CS
                         DUF179 157 rrl 159
                                    rr+
  gi|121635948|ref|YP_976171.1| 183 RRQ 185
                                    996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1498.71
//
Query:       gi|121635949|ref|YP_976172.1|  [L=115]
Description: hypothetical protein BCG_0070c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.8   2.2      0.027   14.8   2.2    2.1  2  DUF308    Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.027   4.9e+02       8      22 ..       3      17 ..       1      29 [. 0.54
   2 ?   14.8   2.2   1.5e-06     0.027       2      50 ..      46      96 ..      45     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.027
                         DUF308  8 vlGilalllPvaall 22
                                   ++G+l++   +a++l
  gi|121635949|ref|YP_976172.1|  3 LAGVLCMCAAAASAL 17
                                   445555544444443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.5e-06
                         DUF308  2 lGillivlGilalllPvaallalvllf...GilllvsGivqiiaafaarkkn 50
                                    ++ l++ G++a++ P+ ++l++v++    ++  l++G +q +++   r+++
  gi|121635949|ref|YP_976172.1| 46 AAVMLAAGGVVAVAAPGHTALMVVIVCiagAVGTLAAGSWQSAQYA-LRRET 96
                                   57999*******************999999999********99887.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 858.06
//
Query:       gi|121635950|ref|YP_976173.1|  [L=310]
Description: hypothetical protein BCG_0071c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-63  210.9   0.0    1.1e-62  210.6   0.0    1.1  1  Lpp-LpqN  Probable lipoprotein LpqN


Domain annotation for each model (and alignments):
>> Lpp-LpqN  Probable lipoprotein LpqN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.6   0.0     6e-67   1.1e-62       2     173 ..     103     270 ..     102     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 6e-67
                                    SS-HHHHHHHTT-EEEE--STT--SEEEE----TT-EE-SS---TTEEEEEEETT.SSSSS-EEEEEEEEEEES---HHH CS
                       Lpp-LpqN   2 svtladYleengvteepvaagdlgaltvdlplPegWedagdpnledayaviaktqpesgedtptavllvskLtGdvDpae 81 
                                    s+tl+d+l+e+gv+ e+++++ ++al+++lp+P++W++++dpn++da+ via+ + +++ +t++a+l+v++L Gd+Dpae
  gi|121635950|ref|YP_976173.1| 103 SGTLRDHLREKGVKLEAQRPHGFKALDITLPMPPRWTQVPDPNVPDAFVVIAD-RLGNSVYTSNAQLVVYRLIGDFDPAE 181
                                    579**************************************************.5699********************** PP

                                    HHCCTTHHHHTSTT-EEEEEE---BTTB-EEEEEEEEECTTEEEEEEEEEEEEEETT...EEEEEEEEEEEEGGGTTTTH CS
                       Lpp-LpqN  82 alehapvdaqnlpgfkatdgstadlsGfpssqieGtYdkdgkrlavaqrtViitgappdaqrYlvqLtvttledqaeala 161
                                    a++h++ d+q+l ++++t++s+a+++Gfpss+ieGtY++++++l++++r+Vi+t++    ++Ylv+L+vtt+ +qa+++ 
  gi|121635950|ref|YP_976173.1| 182 AITHGYIDSQKLLAWQTTNASMANFDGFPSSIIEGTYRENDMTLNTSRRHVIATSGA---DKYLVSLSVTTALSQAVTDG 258
                                    *******************************************************88...79****************** PP

                                    HHHHHHHHH-EE CS
                       Lpp-LpqN 162 dateaIiegftv 173
                                    +at+aI++gf+v
  gi|121635950|ref|YP_976173.1| 259 PATDAIVNGFQV 270
                                    **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2352.16
//
Query:       gi|121635951|ref|YP_976174.1|  [L=969]
Description: leucyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-55  186.1   0.0    1.4e-54  184.4   0.0    1.8  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    2.3e-34  118.6   0.0    7.6e-18   64.1   0.0    5.2  4  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.6e-15   56.8   0.0    3.6e-12   45.7   0.0    2.9  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.6e-13   48.9   0.0    1.3e-12   47.9   0.0    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
       0.31   10.8   1.0       0.93    9.3   0.0    2.2  2  S4             S4 domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.0   3.9e-58   1.4e-54       1     185 []     305     504 ..     305     504 .. 0.93

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 3.9e-58
                  tRNA-synt_1_2   1 rnWIGrseGleiefkveesee.....klevfttrpdtlfGvtfvalapehplvekl.................aekkkel 58 
                                    rnWIGrs+G+   f+ +  ++     ++evfttrpdtlfG+t+++lapeh+lv++l                  +  +++
  gi|121635951|ref|YP_976174.1| 305 RNWIGRSTGAVALFSARAASDdgfevDIEVFTTRPDTLFGATYLVLAPEHDLVDELvaaswpagvnplwtyggGTPGEAI 384
                                    8*************9988843366669****************************99999999988888777767789** PP

                  tRNA-synt_1_2  59 aafieevkkksesereletkekeGvftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikq 138
                                    aa+ + ++ ks+ er +e++ek+Gvf g++ai+P +ge +pi++a+yvl++ygtga+mavP+hdqrD++Fa+ ++lpi +
  gi|121635951|ref|YP_976174.1| 385 AAYRRAIAAKSDLER-QESREKTGVFLGSYAINPANGEPVPIFIADYVLAGYGTGAIMAVPGHDQRDWDFARAFGLPIVE 463
                                    **************9.67889*********************************************************** PP

                  tRNA-synt_1_2 139 vikpedeekkleeseeayteegilvnsgefdglkskeakekiakkle 185
                                    vi+  +      +se+ayt++gilvns+ ++g+++ +ak++i+++le
  gi|121635951|ref|YP_976174.1| 464 VIAGGN------ISESAYTGDGILVNSDYLNGMSVPAAKRAIVDRLE 504
                                    ***644......4589**************************99875 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.1e-08     4e-05      29      83 ..      75     130 ..      66     185 .. 0.78
   2 !   64.1   0.0   2.1e-21   7.6e-18     154     350 ..     231     507 ..     225     515 .. 0.87
   3 !   12.7   0.1   7.7e-06     0.028     416     439 ..     517     540 ..     511     551 .. 0.88
   4 !   12.1   0.0   1.2e-05     0.043     563     589 ..     739     765 ..     733     775 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-08
                    tRNA-synt_1  29 dgPPyvtGs.lHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekk 83 
                                    d  Py  G+ lH+Gh l  +  d+  ry rm G +vl+  G+D  Gl+ e+   ++
  gi|121635951|ref|YP_976174.1|  75 DMFPYPSGEgLHVGHPLGYIATDVYARYFRMVGRNVLHALGFDAFGLPAEQYAVQT 130
                                    55688888669*************************************99765444 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 2.1e-21
                    tRNA-synt_1 154 gliyrgkklvnwstklktalselEveykdkk................................................. 184
                                     l+yr+  lvnw++ l t+l++ Ev     +                                                 
  gi|121635951|ref|YP_976174.1| 231 RLVYRADSLVNWCPGLGTVLANEEVTADGRSdrgnfpvfrkrlrqwmmritayadrllddldvldwpeqvktmqrnwigr 310
                                    58***********************776666779**********************************999999999998 PP

                    tRNA-synt_1 185 ..dalihvafpl..adkeevklviaTTtPeTllgdtavavnpeldyv.....................itkeklilaeal 239
                                      +a+  ++  +  +d+ ev +++ TT+P Tl+g t ++++pe d v                     + +e+   + a 
  gi|121635951|ref|YP_976174.1| 311 stGAVALFSARAasDDGFEVDIEVFTTRPDTLFGATYLVLAPEHDLVdelvaaswpagvnplwtygggTPGEA---IAAY 387
                                    7744444444443466777**************************************9999988765433333...3344 PP

                    tRNA-synt_1 240 lkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinilde 319
                                     ++++ k++ ++ + +e+   + g ++++p +++ +pi   dyv +  GtG++   P+hd+ D+  ++ ++l+++ ++ +
  gi|121635951|ref|YP_976174.1| 388 RRAIAAKSDLERQESREKTGVFLGSYAINPANGEPVPIFIADYVLAGYGTGAIMAVPGHDQRDWDFARAFGLPIVEVI-A 466
                                    55666666666677788888999*************************************************999888.5 PP

                    tRNA-synt_1 320 dgtlteea..........aefeglkvfdarkkvveelkekg 350
                                     g+++e+a             +g++v +a++++v+ l+  g
  gi|121635951|ref|YP_976174.1| 467 GGNISESAytgdgilvnsDYLNGMSVPAAKRAIVDRLESAG 507
                                    799999999********66679***************9988 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 7.7e-06
                    tRNA-synt_1 416 iqdWciSRqrwWGhriplfvsket 439
                                     +dW + Rqr+WG++ p+ ++++ 
  gi|121635951|ref|YP_976174.1| 517 LRDWLFARQRYWGEPFPIVYDSDG 540
                                    58****************999885 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 1.2e-05
                    tRNA-synt_1 563 KmSKslgNvidpldvikkygadalRlt 589
                                    K+ Ksl+N ++p+++ ++ygad lR +
  gi|121635951|ref|YP_976174.1| 739 KIGKSLKNSVSPDEICDAYGADTLRVY 765
                                    899**********************87 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0     1e-15   3.6e-12       5     109 ..      75     182 ..      71     192 .. 0.89
   2 ?   -0.5   0.0      0.11   3.9e+02     156     219 ..     247     309 ..     239     319 .. 0.77
   3 !    6.9   0.0   0.00062       2.2     326     369 ..     738     781 ..     733     787 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1e-15
                                    E--B--SS-.--HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT- CS
                   tRNA-synt_1g   5 talpYangk.lHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklni 83 
                                      +pY++g+ lH+Gh l +i++D++aRy r+ g++vl+  g D++G p e+ A + g++p+  +e +  ++++++ +l+ 
  gi|121635951|ref|YP_976174.1|  75 DMFPYPSGEgLHVGHPLGYIATDVYARYFRMVGRNVLHALGFDAFGLPAEQYAVQTGTHPRTRTEANVVNFRRQLGRLGF 154
                                    56899998758********************************************************************9 PP

                                    --SEEE..ETTSHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1g  84 sfdkyg..rttseehkelvqeifkklke 109
                                     +d+    +tt+ + ++ +q if ++++
  gi|121635951|ref|YP_976174.1| 155 GHDSRRsfSTTDVDFYRWTQWIFLQIYN 182
                                    9997542257778888888888888765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.11
                                    SSB-E................EEE.E.EEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHH CS
                   tRNA-synt_1g 156 gkkleptelinpksaisgskpevket.ehlffklskfekklkewieeeekeleenvkkivkewlk 219
                                    g+ l  +e++    +  g+ p+++++ +++++++ +++++l + +  +  +++e+vk++ ++w+ 
  gi|121635951|ref|YP_976174.1| 247 GTVLANEEVTADGRSDRGNFPVFRKRlRQWMMRITAYADRLLDDL--DVLDWPEQVKTMQRNWIG 309
                                    555555566555555567778777653789***********9999..6667************96 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00062
                                    ------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                   tRNA-synt_1g 326 kKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                                    +K+ kS ++ v ++e+ + + ad+lR y ++ +p +    + ++
  gi|121635951|ref|YP_976174.1| 738 GKIGKSLKNSVSPDEICDAYGADTLRVYEMSMGPLEASRPWATK 781
                                    799*************************9999988776655555 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.6e-16   1.3e-12       5     149 ..     818     933 ..     814     938 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.6e-16
                    Anticodon_1   5 lselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfi 84 
                                    l+ l++++  v+e+++ +r n+a ++l e  +n l        k+r             +v + ++e l+++laP +P+i
  gi|121635951|ref|YP_976174.1| 818 LRALHRTIVGVSEDFAALRNNTATAKLIEY-TNHL------TKKHRD------------AVPRAAVEPLVQMLAPLAPHI 878
                                    7889*************************6.6767......334443............677899*************** PP

                    Anticodon_1  85 tEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselk 149
                                    +Eelw     +lg+ +s+ + ++p+ +a++l +e     ve+    v++++k+r++  ++ +++++
  gi|121635951|ref|YP_976174.1| 879 AEELW----LRLGNTTSLAHGPFPKaDAAYLVDE----TVEY---PVQVNGKVRGRVVVAADTDEE 933
                                    *****....99*************8666665433....5899...***********9999888754 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00026      0.93       5      28 ..     674     697 ..     673     698 .. 0.93
   2 ?   -1.4   0.5      0.55     2e+03      28      35 ..     914     921 ..     914     923 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                    HHHHHTTSSSSHHHHHHHHHTTTE CS
                             S4   5 kvlarlglassrreArqlIehGrV 28 
                                    kvl+ lg +ssr   r+l+++G +
  gi|121635951|ref|YP_976174.1| 674 KVLYDLGHVSSREPYRRLVNQGYI 697
                                    8*********************76 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.55
                                    EEETTEEE CS
                             S4  28 VlVNGkvv 35 
                                    V+VNGkv+
  gi|121635951|ref|YP_976174.1| 914 VQVNGKVR 921
                                    89****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (969 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5915.78
//
Query:       gi|121635952|ref|YP_976175.1|  [L=208]
Description: transcriptional regulatory protein (marR-family) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   63.6   1.0    3.1e-17   62.2   0.4    1.9  2  MarR             MarR family
    1.6e-09   37.5   2.0    3.1e-09   36.6   1.3    1.9  2  MarR_2           MarR family
    8.2e-06   26.2   0.2      2e-05   25.0   0.1    1.8  2  HTH_27           Winged helix DNA-binding domain
    0.00063   19.2   0.8     0.0012   18.4   0.1    1.8  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00093   19.0   0.0      0.002   18.0   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.025   14.4   0.1    1.5  1  HxlR             HxlR-like helix-turn-helix
      0.016   15.4   0.0      0.063   13.5   0.0    1.9  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.12   12.1   0.1       0.35   10.7   0.1    1.8  1  MerR             MerR family regulatory protein
       0.16   12.2   0.0       0.37   11.0   0.0    1.7  1  HTH_34           Winged helix DNA-binding domain
       0.21   10.1   0.0       0.26    9.8   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.85    9.6   4.0       0.25   11.4   0.6    1.9  2  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.81   1.3e+03      17      40 ..      49      72 ..      45      72 .. 0.77
   2 !   62.2   0.4   1.9e-20   3.1e-17       1      59 []      83     141 ..      83     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.81
                                   TEEHHHHHHHHTS-HHHHHHHHHH CS
                           MarR 17 plsvseLakklgvskstvtrvldr 40
                                   ++ v++La+ l+   s +  +l+r
  gi|121635952|ref|YP_976175.1| 49 APEVTQLAEGLHRALSKLISMLRR 72
                                   678999999999888877777765 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 1.9e-20
                                    --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                           MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59 
                                    ltl+q++iL++l +qgp+++++La +  v ++t+t +++rLek Gl++Rs++p+D R+v
  gi|121635952|ref|YP_976175.1|  83 LTLAQLSILVTLLDQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRDPSDLRAV 141
                                    89*******************************************************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.9   6.4e+03      24      32 ..      52      60 ..      46      64 .. 0.59
   2 !   36.6   1.3   1.9e-12   3.1e-09       2      62 .]      82     140 ..      81     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.9
                                   HHHHHHHHT CS
                         MarR_2 24 vgelarrlg 32
                                   v++la+ l+
  gi|121635952|ref|YP_976175.1| 52 VTQLAEGLH 60
                                   445555544 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 1.9e-12
                                    T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                         MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62 
                                    +lt+aq+ +L  L + ++  +++++la++ ++  ++++ +++rL++ GLv r+++p D+Ra
  gi|121635952|ref|YP_976175.1|  82 DLTLAQLSILVTLLDQGP--IRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRDPSDLRA 140
                                    79****************..****************************************7 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.2e-08     2e-05      37      68 .]     118     149 ..      84     149 .. 0.86
   2 ?   -3.1   0.0       7.4   1.2e+04      18      39 ..     161     183 ..     158     188 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
                         HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                     ++++L++ GLv+r++d+ d r+++v +T+ G
  gi|121635952|ref|YP_976175.1| 118 VAIRRLEKIGLVKRSRDPSDLRAVLVDITPQG 149
                                    69****************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                         HTH_27  18 rkkladlcgrlnvedshis.ysl 39 
                                    r++la+l   l ++d  +  ++l
  gi|121635952|ref|YP_976175.1| 161 RAALAALLSQLPRSDLETLrKAL 183
                                    55555555555555555444554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.4   2.2e+03      22      38 ..      54      70 ..      52      72 .. 0.61
   2 !   18.4   0.1   7.2e-07    0.0012       5      48 .]      87     130 ..      83     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                         HTH_24 22 eLAerlglSpstvnrrl 38
                                   +LAe l+  +s +   l
  gi|121635952|ref|YP_976175.1| 54 QLAEGLHRALSKLISML 70
                                   67777776666665555 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 7.2e-07
                         HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    ++ IL +L +++ i +++LA +  +  +t++  ++rLe+ Gl+k
  gi|121635952|ref|YP_976175.1|  87 QLSILVTLLDQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVK 130
                                    789***************************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06     0.002       6      57 ..      83     134 ..      80     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                    HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                           TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                    L+    ++ ++Ll +gp +++++a +  v  ++   ++r+Le+ GlV+r++ 
  gi|121635952|ref|YP_976175.1|  83 LTLAQLSILVTLLDQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRD 134
                                    777788999****************************************975 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.5e-05     0.025       9      73 ..      89     153 ..      87     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                    HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGH CS
                           HxlR   9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsle 73 
                                     ilv+ll+ g+ R+++l+++   + + + +  +r+Le+ gl++r+  p+    v   +t++Gr+++
  gi|121635952|ref|YP_976175.1|  89 SILVTLLDqGPIRMTDLAAHE-RVRTPTTTVAIRRLEKIGLVKRSRDPSDLRAVLVDITPQGRAVH 153
                                    578888877********9886.9***************************************9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   3.3e+03      19      33 ..      46      60 ..      41      72 .. 0.68
   2 ?   13.5   0.0   3.9e-05     0.063      19      54 ..      96     131 ..      89     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                   HHSSB-HHHHHHHHT CS
                 Fe_dep_repress 19 ekkvvktkdlaerLn 33
                                   e   +++++lae L 
  gi|121635952|ref|YP_976175.1| 46 EFTAPEVTQLAEGLH 60
                                   556678899999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.9e-05
                                    HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                 Fe_dep_repress  19 ekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54 
                                    ++++++ +dla    v+ ++ +  +++Lek G+v+ 
  gi|121635952|ref|YP_976175.1|  96 DQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKR 131
                                    7899******************************86 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.35      12      33 ..     116     136 ..     113     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                                    THHHHHHHHHTTSSTSEEETTT CS
                           MerR  12 sprtLRyYEreGLipppeRteg 33 
                                    ++ ++R++E++GL+ +  R+++
  gi|121635952|ref|YP_976175.1| 116 TTVAIRRLEKIGLV-KRSRDPS 136
                                    6779**********.6666655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.37       3      68 ..      88     152 ..      86     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                         HTH_34   3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68 
                                    l++l +L+++  + +++l +  ++ +    v ++ Lek g ++++ + ++  +  l+ iTp+Gr+ 
  gi|121635952|ref|YP_976175.1|  88 LSILVTLLDQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRDPSDL-RAVLVDITPQGRAV 152
                                    78888888888888888888888888899999***************9988.9***********86 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00016      0.26      54     151 ..      60     162 ..      34     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHT-SEEEEESSH.HHHHHHHHHTTS-TT....EEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHH CS
                Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssG.maAiaaailallkaG....deivvsddlYggtqrllkkvlkklgievkfvdtsdle 128
                                    +++l + i+ L +g+   a +   + A+ +++++ll +G    +++ +++ +  +t  +  + l+k+g+  +  d+sdl 
  gi|121635952|ref|YP_976175.1|  60 HRALSKLISMLRRGDPNGAAAGDlTLAQLSILVTLLDQGpirmTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRDPSDLR 139
                                    5778888999999965555544414577899999***9944444599999999*************************** PP

                                    HHHHHCCTTEEEEEEESS-TTTT CS
                Cys_Met_Meta_PP 129 elekaikentklvylEtptnpll 151
                                    ++   i+++ ++v+ E+++n   
  gi|121635952|ref|YP_976175.1| 140 AVLVDITPQGRAVHGESLANRRA 162
                                    *******************9765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00015      0.25      20      55 ..      94     133 ..      60     141 .. 0.77
   2 ?   -2.2   0.2       2.6   4.2e+03       3      12 ..     164     173 ..     160     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                    E....EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                      HTH_Crp_2  20 l....pltqeelAsmlGltretvsrilseLkreglisrgr 55 
                                    l    p+ +++lA++  ++  t++ ++++L++ gl++r+r
  gi|121635952|ref|YP_976175.1|  94 LldqgPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSR 133
                                    23444999*****************************865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                    HHHHHHHHHC CS
                      HTH_Crp_2   3 lArfLlrlae 12 
                                    lA++L +l +
  gi|121635952|ref|YP_976175.1| 164 LAALLSQLPR 173
                                    6666666633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1462.54
//
Query:       gi|121635953|ref|YP_976176.1|  [L=244]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-13   48.4   0.1    8.9e-13   47.7   0.1    1.4  1  GntR            Bacterial regulatory proteins, gntR family
    7.4e-05   23.2   2.0    0.00012   22.5   2.0    1.3  1  FCD             FCD domain
     0.0014   18.6   0.0     0.0028   17.6   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0024   17.5   0.0     0.0035   17.0   0.0    1.3  1  HTH_41          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.049   14.0   0.0      0.097   13.0   0.0    1.4  1  Rrf2            Transcriptional regulator
      0.051   13.5   0.0       0.11   12.3   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.12   12.6   0.0       0.21   11.8   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   3.5e-16   8.9e-13       3      64 .]      11      71 ..       9      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.5e-16
                                   HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR  3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                   +qv++++ +++l+g lr Gd+    +e+a  +gVsr +++eAL +Le +g+v  r  rG+f+
  gi|121635953|ref|YP_976176.1| 11 DQVVAHILNLLLTGKLRSGDRV-DRNEIAHGLGVSRVPIQEALVQLEHDGIVSTRYHRGAFI 71
                                   79********************.************************************997 PP

>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.0   4.6e-08   0.00012       4     119 ..      84     194 ..      81     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.6e-08
                            FCD   4 elRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlrrlr 83 
                                    el  lL + a ++aa + t++ l +l++++++l+   ++++   fae+ +++ r++++    p+l ++++  ++ + r+ 
  gi|121635953|ref|YP_976176.1|  84 ELDGLLNGIASARAAANPTPRILGQLDAVMRSLRNSKESRA---FAECVWEYRRTVNDEYAGPRLHATIRASQNLIPRVF 160
                                    67789999***************************988666...**********************************88 PP

                            FCD  84 rlalssperleeslaeHraildAirardadaAraam 119
                                    +++   ++ ++++l   ++  +Ai +r+++aAraa+
  gi|121635953|ref|YP_976176.1| 161 WMT--YQNSRDDVLPFYEEENAAIHRREPEAARAAC 194
                                    877..7788888888888888*************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.1e-06    0.0028      21      55 ..      31      66 ..      13      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.E CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg.r 55
                                   ++ + e+A+ lG++r+ +  +l +L+ +g++s++ +
  gi|121635953|ref|YP_976176.1| 31 RVDRNEIAHGLGVSRVPIQEALVQLEHDGIVSTRyH 66
                                   6789****************************5523 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-06    0.0035       2      39 ..      28      64 ..      27      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                         HTH_41  2 vGdRlktIeelakeleLSvGlvQkALklLeddkaisle 39
                                    GdR+++ +e+a+ l++S+  +Q AL  Le d+++s+ 
  gi|121635953|ref|YP_976176.1| 28 SGDRVDR-NEIAHGLGVSRVPIQEALVQLEHDGIVSTR 64
                                   6999999.89************************9974 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05     0.097       8      58 ..      12      64 ..       7      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHHH...HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           Rrf2  8 eyalhallyL...akeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   +++ h+l  L   +++++++ v  +eia+  ++s++ ++  l +L++ g+v ++
  gi|121635953|ref|YP_976176.1| 12 QVVAHILNLLltgKLRSGDR-VDRNEIAHGLGVSRVPIQEALVQLEHDGIVSTR 64
                                   55667766665545566666.******************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.11      25      56 ..      34      65 ..      25      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                   HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerek 56
                                    +eia+ lgv+r  ++e+L +Le  G+V ++ 
  gi|121635953|ref|YP_976176.1| 34 RNEIAHGLGVSRVPIQEALVQLEHDGIVSTRY 65
                                   589*************************9876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.3e-05      0.21      19      60 .]      28      69 ..      18      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                                   HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                 Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                   +++ v + ++a  L+vs   ++e l  Le dG v +   +g+
  gi|121635953|ref|YP_976176.1| 28 SGDRVDRNEIAHGLGVSRVPIQEALVQLEHDGIVSTRYHRGA 69
                                   5677999***************************99988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1581.53
//
Query:       gi|121635954|ref|YP_976177.1|  [L=264]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-33  114.1   0.1    2.4e-32  112.6   0.1    1.6  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.1   1.3e-36   2.4e-32      10     220 ..      12     214 ..       9     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.3e-36
                 Bac_luciferase  10 rqggalgaas.aslrylvelaraaEelGfdavwvaehhggpgga.....ldaftllaalaaaTerirlgtavtplytrhP 83 
                                    r+g++l+ +  + +r +++ +r+ E+ G d +++ +h ++ +g+     ++++t+l+a a++T++i++g+ vt+   r+P
  gi|121635954|ref|YP_976177.1|  12 RIGVQLQPQHaPHYRAVRDAVRRCEDIGVDIAFTWDHFFPLYGDpdgphFECWTVLGAWAEQTSHIEIGALVTCNSYRNP 91 
                                    5555555555689******************************9************************************ PP

                 Bac_luciferase  84 avlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpg 163
                                     +lA +a t+dh+sgGR++lg+g+g+ +++++ +G ++ +   rl++   +l r+ ++      G+          p+p 
  gi|121635954|ref|YP_976177.1|  92 ELLADMARTVDHISGGRLILGIGSGWKQKDYDEYGYRFGTAGSRLDDLAAALPRIKAR-----LGKL--------NPPPT 158
                                    ***************************************************9999933.....5666........78898 PP

                 Bac_luciferase 164 qgpiPvyvaaas.paglelaarhadglllag.eppeeaaelierlragaaeagrdpadi 220
                                     + iPv++++++  ++l+l a++ad+++++   + + a+ ++ +     +  gr pa+i
  gi|121635954|ref|YP_976177.1| 159 RD-IPVLIGGGGeRKTLRLVAEYADIWHSFTaGDSYLAKSAVLS--THCSTVGRNPATI 214
                                    88.*************************9994333333322222..2245566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1838.03
//
Query:       gi|121635955|ref|YP_976178.1|  [L=298]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-19   71.3   9.6      2e-19   71.1   9.6    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.2e-11   42.7   0.4    5.7e-10   39.3   0.4    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    5.5e-06   25.8   0.7    3.7e-05   23.1   0.7    2.2  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.014   15.0   0.0    1.4  1  Esterase       Putative esterase
      0.011   14.5   0.0       0.21   10.2   0.0    2.0  2  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   9.6   5.7e-23     2e-19       1     219 [.      52     289 ..      52     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.7e-23
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTST.S-GGCS--HHH...CHHHHHHHCCTT..TTSE.EEEEETCH CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhG.rsdpppldled...ladlaalldelaagggpv.vlvGHSlG 75 
                                    v++lHG+g +a+ W    +   l++    la+DlpGhG ++++ + ++++    ++la +l+ela   + + ++vG SlG
  gi|121635955|ref|YP_976178.1|  52 VIFLHGGGQNAHTWD--TVIVGLGEPA--LAVDLPGHGhSAWREDGNYSPqlnSETLAPVLRELA---PGAeFVVGMSLG 124
                                    79************6..5555557777..9********555999999999644477788999996...4446******** PP

                                    HHHHHHHHHCC...EE..EEES-................----TTT.....S----TTHHHHHHTT-CCCCHCCH..... CS
                  Abhydrolase_6  76 Galalaaapla.lvvg..vlldppp..............talpagl.....laaalelllallallrllawlsre..... 128
                                    G+ a ++a+ a ++vg  vl+d +p              +           + + ++ ++a l+                
  gi|121635955|ref|YP_976178.1| 125 GLTAIRLAAMApDLVGelVLVDVTPsalqrhaeltaeqrG-----TvalmhGEREFPSFQAMLD----------Ltiaaa 189
                                    ******7777778888999999955554444333322221.....1222122222222222222..........011222 PP

                                    ......S-HSCCCCHHH..CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE..C....TT-CHHHHCHHCCCHST CS
                  Abhydrolase_6 129 ......plprlfladed..adaawrarlarlaallaglgllpaaawadlpvpllvl..g....geDplvprllerllaqa 194
                                          +l+r+ +++    +   w++r+++ + + ++ g   ++++ +l +p+ ++  g     +D+  ++l +r+    
  gi|121635955|ref|YP_976178.1| 190 phrdvkSLRRGVFHNSRrlDNGNWVWRYDAIRTFGDFAG--LWDDVDALSAPITLVrgGssgfVTDQDTAELHRRAT--H 265
                                    233344455544444443336***********9999999..566999999999777752455666777676666555..5 PP

                                    TEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 195 garlpvvlpgaGHlphleepdevae 219
                                     +++ ++++ +GH+++ ++p++++e
  gi|121635955|ref|YP_976178.1| 266 FRGV-HIVEKSGHSVQSDQPRALIE 289
                                    6666.99**********9*998876 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.4   1.6e-13   5.7e-10       1     255 [.      50     282 ..      50     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.6e-13
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHH.SHHHHHHHHH.HHHHHCTTSSEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddy.gtasvaddld.rildalgddkltlv 78 
                                    p +++lhG++ +++ w    ++ +L   g   +++Dl+G+g+S  + +    +y +  +  + l   +++  +  ++ +v
  gi|121635955|ref|YP_976178.1|  50 PRVIFLHGGGQNAHTWDT--VIVGL---GEPALAVDLPGHGHSAWRED---GNYsPQLN-SETLApVLRELAPGAEF-VV 119
                                    679***************..*****...66*************55555...55533433.33444366777777777.** PP

                                    EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHH CS
                  Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlv 158
                                    G S+GG++a  +aa++p+ V  lvl++            + +++++ +     +   a  ++ + + + +a+l++  ++ 
  gi|121635955|ref|YP_976178.1| 120 GMSLGGLTAIRLAAMAPDLVGELVLVDV----------TPSALQRHAELTAEQRGTVALMHGEREFPSFQAMLDLTIAAA 189
                                    ****************************..........777777777777777777777777777777777777777776 PP

                                    HHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHC.. CS
                  Abhydrolase_1 159 dalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaql.. 236
                                          + +k+++++ + n+  l+ g + ++  +  t+ +   l+++  ++ +ap+ ++ g s + v+++   +l +   
  gi|121635955|ref|YP_976178.1| 190 P----HRDVKSLRRGVFHNSRRLDNGNWVWRYDAIRTFGDFAGLWDDV-DALSAPITLVRGGSSGFVTDQDTAELHRRat 264
                                    5....7888888889999999999999999999999999999999997.8888899999999999999988888888845 PP

                                    .HTSEEEEEEETCSSSHHHH CS
                  Abhydrolase_1 237 .lpkkrlvvisdagHlafle 255
                                     +++  +++++++gH ++ +
  gi|121635955|ref|YP_976178.1| 265 hFRG--VHIVEKSGHSVQSD 282
                                    5555..99999999998865 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.7     1e-08   3.7e-05       6     237 ..      51     282 ..      48     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-08
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhS 84 
                                     v+++HG ++ +   + ++  L +     +a+D  GhG+s+  + g   s +      +++   ++e  p+++ f++G S
  gi|121635955|ref|YP_976178.1|  51 RVIFLHGGGQNAHTWDTVIVGLGEP---ALAVDLPGHGHSAwREDG-NYSPQ---LNSETLAPVLRELAPGAE-FVVGMS 122
                                    5899999999999999999888776...5678********754444.22222...334556666777779996.****** PP

                    Hydrolase_4  85 mGGliallyllrypdkvaglils...aPalkikaklkappllklllkllgkllpklqv.snnlkadslsrdpevvaayea 160
                                    +GGl+a++++++ pd v  l+l+    +al+ +a+l a +   ++l    + +p++q   + + a+   rd + +++   
  gi|121635955|ref|YP_976178.1| 123 LGGLTAIRLAAMAPDLVGELVLVdvtPSALQRHAELTAEQRGTVALMHGEREFPSFQAmLDLTIAAAPHRDVKSLRRGVF 202
                                    ***************88899986332467777777656666666777777888888885333444555555555554444 PP

                    Hydrolase_4 161 dplv.hgkitvrlllelldamkr...leeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHelln 236
                                    +     ++  + + ++++++  +   l+++++++++P+ l+ G++   v  ++++el++r+++    +++ ++  H++  
  gi|121635955|ref|YP_976178.1| 203 HNSRrLDNGNWVWRYDAIRTFGDfagLWDDVDALSAPITLVRGGSSGFVTDQDTAELHRRATH-FRGVHIVEKSGHSVQS 281
                                    44444666666666776666533222789999999***********99999*********997.8888999998888776 PP

                    Hydrolase_4 237 E 237
                                    +
  gi|121635955|ref|YP_976178.1| 282 D 282
                                    6 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.9e-06     0.014     113     154 ..     112     227 ..      52     293 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-06
                                    ECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC....................................... CS
                       Esterase 113 apdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps....................................... 153
                                    ap +  v+G S+GGl+A+ la+ +pd+ g        v ps                                       
  gi|121635955|ref|YP_976178.1| 112 APGAEFVVGMSLGGLTAIRLAAMAPDLVGELVLVD--VTPSalqrhaeltaeqrgtvalmhgerefpsfqamldltiaaa 189
                                    333467********************999877766..6666666666666666666655555555555555555555555 PP

                                    .....................................H CS
                       Esterase 154 .....................................n 154
                                                                         +
  gi|121635955|ref|YP_976178.1| 190 phrdvkslrrgvfhnsrrldngnwvwrydairtfgdfA 227
                                    55555555555555555555555555555555555554 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.9e-05      0.21      60     136 ..      78     151 ..      75     169 .. 0.88
   2 ?    2.3   0.0     0.016        57     220     270 ..     238     289 ..     203     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.9e-05
                                    EEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S- CS
                            Ndr  60 hvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitska 136
                                     vd PG+ + a     ++  p l+  +++l  vl  +   +   +G+  G     r a+  p++v  lvL+++t++a
  gi|121635955|ref|YP_976178.1|  78 AVDLPGHGHSAWRED-GNYSPQLN--SETLAPVLRELAPGAEFVVGMSLGGLTAIRLAAMAPDLVGELVLVDVTPSA 151
                                    689999998887654.44678887..59**********************************************987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.016
                                    S-EEEEEETTSTTHHH..HHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHH CS
                            Ndr 220 vkvllvvGdkspfvde..vvevnskldkkkttllkvadsgglvleeqPdklae 270
                                     +  lv G +s fv +  + e++++  + +     v++sg  v+++qP +l+e
  gi|121635955|ref|YP_976178.1| 238 APITLVRGGSSGFVTDqdTAELHRRATHFRGV-HIVEKSGHSVQSDQPRALIE 289
                                    55667777777776541134444443333322.237899***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1903.99
//
Query:       gi|121635956|ref|YP_976179.1|  [L=367]
Description: myo-inositol-1-phosphate synthase INO1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-32  111.7   0.0    1.1e-31  109.3   0.0    2.0  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.048   13.9   0.0       0.17   12.1   0.0    1.9  2  DUF1611_N       Domain of unknown function (DUF1611_N) Rossma
       0.11   11.9   0.0       0.23   10.8   0.0    1.6  2  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.23   1.4e+03      65     102 ..      48      93 ..      27      97 .. 0.73
   2 !  109.3   0.0   1.8e-35   1.1e-31       1     109 []     203     311 ..     203     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.23
                                    E...........EEEEE-GGGT.TEEEEEEEEEEEEGGGEEEEEEE CS
                 Inos-1-P_synth  65 y.......vdhevvikYvpylg.DsKvaldeieseiflggkntiel 102
                                            ++h   +k+v + + D K+    ++  if   +nti++
  gi|121635956|ref|YP_976179.1|  48 GlmhvrfgPYHVRDVKFVAAFDvDAKKVGFDLSDAIFASENNTIKI 93 
                                    0455555566777889988775599999999999999999999997 PP

  == domain 2  score: 109.3 bits;  conditional E-value: 1.8e-35
                                    SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GG CS
                 Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpy 77 
                                    G+T++++vLa+l+++rg++++++++lN++Gn+D++n+ e+er++sKkisK+++v++ +k++  +   + v+i   ++v +
  gi|121635956|ref|YP_976179.1| 203 GATITHRVLAKLFEDRGVQLDRTMQLNVGGNMDFLNMLERERLESKKISKTQAVTSNLKREFKT---KDVHIgpsDHVGW 279
                                    9**********************************************************95543...4699999****** PP

                                    GTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                 Inos-1-P_synth  78 lgDsKvaldeieseiflggkntielkleceDS 109
                                    l+D+K+a++++e+++f++++ ++e+kle++DS
  gi|121635956|ref|YP_976179.1| 280 LDDRKWAYVRLEGRAFGDVPLNLEYKLEVWDS 311
                                    *******************************9 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.5e+03      25      40 ..      11      25 ..       5      31 .. 0.78
   2 ?   12.1   0.0   2.8e-05      0.17      10      88 ..     121     193 ..     113     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                      DUF1611_N 25 ealaagaevlviGiap 40
                                   ea + +++v ++G+++
  gi|121635956|ref|YP_976179.1| 11 EA-STEVRVAIVGVGN 25
                                   34.7899999999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.8e-05
                      DUF1611_N  10 ellddrgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpelaalakkkgvki 88 
                                    el d   ++vv+ l+ea + ++ v +++++ e+ +       +++ A++aG+  v+ l  ++++dp +a+     gv i
  gi|121635956|ref|YP_976179.1| 121 ELSDAEPVDVVQALKEA-KVDVLVSYLPVGSEEADK-----FYAQCAIDAGVAFVNALPVFIASDPVWAKKFTDAGVPI 193
                                    44444788888888888.666666667776666554.....79**************************9988888877 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.35   2.1e+03       3      21 ..      18      35 ..      16      51 .. 0.73
   2 ?   10.8   0.0   3.9e-05      0.23     208     252 ..     156     287 ..     129     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.35
                                   xxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_5  3 vllvGlgGnngtTlvagvl 21
                                   v +vG+ Gn ++ lv gv 
  gi|121635956|ref|YP_976179.1| 18 VAIVGV-GNCASSLVQGVE 35
                                   678888.888888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.9e-05
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx................................... RF
                  NAD_binding_5 208 iyavAailegvpyingsPqntl.vpglvelAekkgvfiaGdDfKt................................... 251
                                     ya  ai +gv+++n  P      p   +  +  gv+i+GdD+K+                                   
  gi|121635956|ref|YP_976179.1| 156 FYAQCAIDAGVAFVNALPVFIAsDPVWAKKFTDAGVPIVGDDIKSqvgatithrvlaklfedrgvqldrtmqlnvggnmd 235
                                    79****************9999566677788999***********77777777766666666666666666666666666 PP

                                    ...................................................x RF
                  NAD_binding_5 252 ...................................................l 252
                                                                                        
  gi|121635956|ref|YP_976179.1| 236 flnmlererleskkisktqavtsnlkrefktkdvhigpsdhvgwlddrkwaY 287
                                    5555555555555555555555555555555555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2661.21
//
Query:       gi|121635957|ref|YP_976180.1|  [L=180]
Description: hypothetical protein BCG_0078c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-22   78.7   0.0    3.8e-22   78.0   0.0    1.4  1  PadR             Transcriptional regulator PadR-like family
    0.00011   22.8   0.6    0.00021   21.9   0.6    1.4  1  Vir_act_alpha_C  Virulence activator alpha C-term
     0.0061   16.3   0.0      0.008   15.9   0.0    1.2  1  AphA_like        Putative AphA-like transcriptional regulator
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.24   11.2   0.0    1.5  1  HxlR             HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   8.5e-26   3.8e-22       1      74 [.       6      81 ..       6      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8.5e-26
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S..TSSS-EEEEEESHCCCHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees..gegpprkyYrlTdaGrrela 74
                                   iL+ll e+p++Gye++k+l+ l++ ++++s+GslYpaL+r++++gl++++ +++   ++++r++Y+lTd+Grr++ 
  gi|121635957|ref|YP_976180.1|  6 ILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAgtPVRRARRVYQLTDKGRRRFG 81
                                   89**************************************************998899***************975 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.6   4.7e-08   0.00021       5      74 ..      97     168 ..      95     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.7e-08
                Vir_act_alpha_C   5 lllKlfaaavldpealieeLerrreeheekLaeyeeieerl..eeargqylvLrrgiryeeawieWcdeale 74 
                                    + + l +    + ea ++ Le rr++ ee+ + ++e  +r   + +r+ +   + g++  e +++W++e ++
  gi|121635957|ref|YP_976180.1|  97 FGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARAssSFDRYTRQLHQLGLESSEREVKWLNELIA 168
                                    678899999********************************86669***********************998 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-06     0.008      13     174 ..       3     166 ..       1     168 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                      AphA_like  13 rLvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLve...avdGeGmednalL.aiteaGrrelqa 88 
                                     L++LGl+  +p+   el +    l++     s   l+ +l  ++ +GL+    a  G  + +  ++  +t++Grr++ +
  gi|121635957|ref|YP_976180.1|   3 ELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAenaAPAGTPVRRARRVyQLTDKGRRRFGE 82 
                                    699***9999***************************************952223457777777665379********** PP

                      AphA_like  89 LltanlraplsdlsklviaLklrfLdLlevaerraqidlllelvetelarlvdlraavsedGp.lleeWLdhdieqleer 167
                                    L++        +++  +  + l+f +  +++ r +  +   + ve     l ++ a  s+  + ++++  +  +e  e  
  gi|121635957|ref|YP_976180.1|  83 LVADTGP---HNYTDDGFGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARASSSFDrYTRQLHQLGLESSERE 159
                                    **98643...4577778888999999999999999999999999877766766666666665546666667788999999 PP

                      AphA_like 168 lewleel 174
                                    ++wl+el
  gi|121635957|ref|YP_976180.1| 160 VKWLNEL 166
                                    9999887 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.24      19      71 ..      22      78 ..       9      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                                   EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS.SS-...EEEEEE-TCGGG CS
                           HxlR 19 kRfselkralpkisqkmLaqrLreLeqdglierevype.vPp...kveYsltekGrs 71
                                   kR + l  a+   s   L   Lr++++dgli  ++ p  +P+   +  Y+lt+kGr 
  gi|121635957|ref|YP_976180.1| 22 KRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAgTPVrraRRVYQLTDKGRR 78
                                   566666666666777788999**********99998863565323568*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1211.87
//
Query:       gi|121635958|ref|YP_976181.1|  [L=289]
Description: hypothetical protein BCG_0079c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-17   62.0   6.2    7.5e-17   61.1   6.2    1.4  1  DUF1707   Domain of unknown function (DUF1707)


Domain annotation for each model (and alignments):
>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   6.2   4.2e-21   7.5e-17       1      53 []      17      69 ..      17      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 4.2e-21
                        DUF1707  1 lRasdadReravelLrealaeGrLtldEfdeRleaalaArtrgeLaalvaDLP 53
                                   +Ra+d+dR++a+++L++al +G L+++E++eR++aa++A t+g+L++lvaDL+
  gi|121635958|ref|YP_976181.1| 17 TRAKDSDRQDACRILDDALRDGELSMEEHRERVSAATKAVTLGDLQRLVADLQ 69
                                   5***************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2210.84
//
Query:       gi|121635959|ref|YP_976182.1|  [L=137]
Description: hypothetical protein BCG_0080 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-58  195.6   0.1    2.7e-58  195.4   0.1    1.0  1  DUF5318   Family of unknown function (DUF5318)


Domain annotation for each model (and alignments):
>> DUF5318  Family of unknown function (DUF5318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.1   1.5e-62   2.7e-58       8     124 ..       1     117 [.       1     123 [. 0.97

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 1.5e-62
                        DUF5318   8 vdyalqrrallaevragrvgvaevcdaspyllraakfhGeptdvacPvcrkenltlvsyvyGdelkqaaGsartaeeler 87 
                                    +dy+l+rr+llaev++gr+gv+evcda+pyllraakfhG+p+ v cP+crke+ltlvs+v+G++l+ ++Gsartaeel  
  gi|121635959|ref|YP_976182.1|   1 MDYTLRRRSLLAEVYSGRTGVSEVCDANPYLLRAAKFHGKPSRVICPICRKEQLTLVSWVFGEHLGAVSGSARTAEELIL 80 
                                    59****************************************************************************** PP

                        DUF5318  88 laatleefsvyvvevcrscswnhlvesyvlGkeeeak 124
                                    la+ ++ef+v+vvevcr+cswnhlv+syvlG+   a+
  gi|121635959|ref|YP_976182.1|  81 LATRFSEFAVHVVEVCRTCSWNHLVKSYVLGAARPAR 117
                                    *******************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1049.88
//
Query:       gi|121635960|ref|YP_976183.1|  [L=681]
Description: bifunctional penicillin-binding protein 1A/1B PONA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-56  190.8   0.0    2.3e-56  190.1   0.0    1.4  1  Transgly        Transglycosylase
    7.9e-27   94.2   1.6    1.3e-26   93.6   1.6    1.3  1  Transpeptidase  Penicillin binding protein transpeptidase dom


Domain annotation for each model (and alignments):
>> Transgly  Transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   0.0   2.5e-60   2.3e-56       4     177 ..      40     217 ..      37     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 2.5e-60
                       Transgly   4 llael.eeeenrelvkleeippalkkavvaiEDrrFyehkGvdlkgiarAvlknlksgkssqGgSTitqQlvknlflsee 82 
                                     +a++   e nr+ v+l+++p ++++av+a+EDr+Fy+++G+++ g+arAv +nl  g+  qGgSTitqQ+vkn+++ ++
  gi|121635960|ref|YP_976183.1|  40 EIAKIvPPEGNRVDVNLSQVPMHVRQAVIAAEDRNFYSNPGFSFTGFARAVKNNLF-GGDLQGGSTITQQYVKNALVGSA 118
                                    56666446899********************************************5.55669************988655 PP

                       Transgly  83 ....rtlerKlkeavlAlklekklsKdeILeaYlNsvylgrevyGieaAarayFgkdakdLtlaeaalLagllkaPsryn 158
                                        + l rK+ke+v+A k+  ++sKd++L+aYlN +y+gr++yGi aA++ayF+k++++Lt+ae alLa+l+++Ps+++
  gi|121635960|ref|YP_976183.1| 119 qhgwSGLMRKAKELVIATKMSGEWSKDDVLQAYLNIIYFGRGAYGISAASKAYFDKPVEQLTVAEGALLAALIRRPSTLD 198
                                    3456679************************************************************************* PP

                       Transgly 159 plenpeeakkrrkvvlerm 177
                                    p+ +pe a++r+++vl+ m
  gi|121635960|ref|YP_976183.1| 199 PAVDPEGAHARWNWVLDGM 217
                                    *****************99 PP

>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   1.6   1.4e-30   1.3e-26       2     289 ..     311     578 ..     310     600 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.4e-30
                                    EEEEEETTT-BEEEEEEESE-TTTHHCCTCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS. CS
                 Transpeptidase   2 aavvldaktgevlamaskpsydpnakvgkneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqs 81 
                                    a+v +d+ +g+v a+++    + n++           +q   + GS fKv++++aale+g i    ++d+s+ ++ g   
  gi|121635960|ref|YP_976183.1| 311 AVVSIDPHNGAVRAYYGGD--NANGFDF---------AQAGLQTGSSFKVFALVAALEQG-IGLGYQVDSSPLTVDG--- 375
                                    7999**************6..6788877.........***********************.777888******9988... PP

                                    ECTCCCC-SSSSEEEHHHHHHTT-HHHHHHHHH..HH-HHHHHHHHHHTTTTS...-SSSSSTT-B--B--SSH.HHHHH CS
                 Transpeptidase  82 ikdweqdnkgsegitlrealekSsntyfvklaq..klgadklrkylkkfglGn...ktgidlpgesaGvptrkw.legat 155
                                    ik  +++ +g ++ ++ eal+ S nt +++l    + g++ + +++++ g+ +        l++  +G p+++  + g+ 
  gi|121635960|ref|YP_976183.1| 376 IKITNVEGEGCGTCNIAEALKMSLNTSYYRLMLklNGGPQAVADAAHQAGIASsfpGVAHTLSEDGKGGPPNNGiVLGQ- 454
                                    66666666667889*****************962355999***********9943333344444444533332245555. PP

                                    HHHTTTSBB-HHHHHHHHHHHHTTTEEE--BSEEEEEECTT...EEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTT CS
                 Transpeptidase 156 isfgiGltvtplqlaqayaaiangGklvkPhlvkaivdpdg...vrkvkpkelnklpisketaekvkeglkgvvsrgsgt 232
                                           +   + +a+aya++a  G++ +Ph+v+++v+ +g    +  + ++ + + i k  a++v+ +++  +   +g+
  gi|121635960|ref|YP_976183.1| 455 ------YQTRVIDMASAYATLAASGIYHPPHFVQKVVSANGqvlFDASTADNTGDQRIPKAVADNVTAAMEPIAGYSRGH 528
                                    ......89999******************************998788888999************************999 PP

                                    GCGTCTTS--EEEEEEEEECSSSTTSEEEEEEEEEEEEEEST.TS-SEEEEEEECTCS CS
                 Transpeptidase 233 ataavegykvagKTGTAevagkkgngkkegakiswfvgyapa.dnpkyavavlieqpk 289
                                    + a   g + a+KTGT+++ +   n+       +w+vgy+p+ +  +++ +v  ++p 
  gi|121635960|ref|YP_976183.1| 529 NLA--GGRDSAAKTGTTQFGDTTANK------DAWMVGYTPSlSTAVWVGTVKGDEPL 578
                                    988..899************966665......36********9999998888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 5235.85
//
Query:       gi|121635961|ref|YP_976184.1|  [L=560]
Description: hypothetical protein BCG_0082 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-14   54.2  36.9    1.6e-14   54.2  36.9    3.1  3  GT87            Glycosyltransferase family 87
  ------ inclusion threshold ------
      0.046   13.6  13.9       0.12   12.2   0.0    3.0  3  Mannosyl_trans  Mannosyltransferase (PIG-M)


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.041   3.7e+02     130     145 ..      63      78 ..       8     105 .. 0.62
   2 !   54.2  36.9   1.8e-18   1.6e-14      16     234 ..     181     409 ..     171     414 .. 0.71
   3 ?   -2.0   7.5      0.26   2.3e+03       4      41 ..     413     450 ..     411     488 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.041
                           GT87 130 aaaaatalvltalpll 145
                                     +++a+alv+ al++ 
  gi|121635961|ref|YP_976184.1|  63 RVMFAIALVFLALGWS 78 
                                    2333344444444333 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 1.8e-18
                           GT87  16 llpyglalalwallnlaalllalrlllrrlgral..asavalalllaalalepvlstlgfGqinllllllvlldllllrr 93 
                                    + p+++ + +++++n+aa+ lal++l++ ++++    + ++ a   a++a +p+   + f+++++l + l+  +ll++ r
  gi|121635961|ref|YP_976184.1| 181 VAPLPVVAEVVMFFNVAAFGLALAWLTTVWATSGlaGRRIWDA---ALVAASPLVIFQIFTNFDALATGLATSGLLAWAR 257
                                    5667777778888999999888877777766555533333333...589999**9************************* PP

                           GT87  94 rrpllaGlliGlaaaiKltPalfllylll....rrrwralaaaaatalvltal...pllllppssleyfletlfdtseri 166
                                    rrp+laG+liGl+ a Kl+P+lfl  lll    ++r+ ala ++a a+++ +l   p++ll p  ++ f+++ ++ ++ +
  gi|121635961|ref|YP_976184.1| 258 RRPVLAGVLIGLGSAAKLYPLLFLYPLLLlgirAGRLNALARTMAAAAATWLLvnlPVMLLFPRGWSEFFRLNTRRGDDM 337
                                    *************************777779999*******9955555555555999999999********777776766 PP

                           GT87 167 aedvgnqsllslagllaralalgl.s.avtllwlvlvllv..valaavaawrlrrrerllalaaallvall..a 234
                                     ++++ +   s +g       lg+ + +  l  +v +l+v   a++a++a+ +  r r++ l++++++++l   
  gi|121635961|ref|YP_976184.1| 338 DSLYNVVK--SFTGWRGFDPTLGFwEpPLVLNTVVTLLFVlcCAAIAYIALTAPHRPRVAQLTFLTVASFLlvN 409
                                    33333333..3333333333344443233333333333332255555555555599999999998898885344 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.26
                           GT87   4 PPfaallfaplallpyglalalwallnlaalllalrll 41 
                                     P + l ++pla+l ++  ++l+a++++ al+++ r+ 
  gi|121635961|ref|YP_976184.1| 413 SPQFSLWLVPLAVLALPHRRILLAWMTIDALVWVPRMY 450
                                    589999*********************99999995543 PP

>> Mannosyl_trans  Mannosyltransferase (PIG-M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       0.1   8.9e+02      43     217 ..     157     207 ..     147     215 .. 0.49
   2 ?   12.2   0.0   1.3e-05      0.12       6      54 ..     239     287 ..     237     324 .. 0.80
   3 ?    5.3   5.7    0.0018        16     149     206 ..     378     438 ..     363     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.1
                 Mannosyl_trans  43 YPliyalalalslskkkeqsvaakllrllki.avlvlvlvalisllaltlllyklYGqefleeaylYhlvrkDhrhnfsl 121
                                    YP++  +  +ls+   k+ + ++k+  l  + +v+++                                           
  gi|121635961|ref|YP_976184.1| 157 YPVLTGIYQYLSMAIAKTYTALSKVAPLPVVaEVVMFFN----------------------------------------- 195
                                    555555555555555555555555553322212333333......................................... PP

                 Mannosyl_trans 122 yflllYleeaskvaassilkllaflPqlvllllvslkfrrnlafalfvqtfvfvtfnkvctsqYfvWylvlLplllskvk 201
                                                                                                                    
  gi|121635961|ref|YP_976184.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                 Mannosyl_trans 202 llswkkalvllllWla 217
                                        + a++l+l+Wl+
  gi|121635961|ref|YP_976184.1| 196 ----VAAFGLALAWLT 207
                                    ....444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.3e-05
                 Mannosyl_trans   6 nadsivailvlltlyllekrkiasaalvlGlavhlkiYPliyalalals 54 
                                    n d++ + l    l   ++r+ + a+++ Gl    k+YPl+++ +l+l 
  gi|121635961|ref|YP_976184.1| 239 NFDALATGLATSGLLAWARRRPVLAGVLIGLGSAAKLYPLLFLYPLLLL 287
                                    667888888888899999***9***********************9883 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0018
                 Mannosyl_trans 149 lvllllvslkf..rrnlafalfvqtfvfvtfnkvctsqYfvWylvlLplllskvkll.swk 206
                                       + +++l+   r  +a+ +f++   f   nkv   q+ +W ++l  l l++ ++l +w 
  gi|121635961|ref|YP_976184.1| 378 CAAIAYIALTAphRPRVAQLTFLTVASFLLVNKVWSPQFSLWLVPLAVLALPHRRILlAWM 438
                                    333444444434488899999*99999******************9999999887731443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3891.62
//
Query:       gi|121635962|ref|YP_976185.1|  [L=187]
Description: hypothetical protein BCG_0083 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-21   75.7   0.0    4.3e-21   75.4   0.0    1.1  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   2.4e-25   4.3e-21      28     164 ..       4     140 ..       2     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.4e-25
                                    EEEEEEESSTSEEEETTS.EEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                      DJ-1_PfpI  28 ikvdvvsvdkeevkgsrG.lkvtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                                    ++v+ v+  ++ev++ +  l + +da++d+    + D+++ pGG     +l  ++ v+++v+e+++   l  ++C+g ++
  gi|121635962|ref|YP_976185.1|   4 FDVVFVGHRRGEVRSDNAmLGLLCDAAFDE--LTRPDVVIFPGGIG-TRTLIHDQTVLDWVREAHRHTLLTTSVCTGGLV 80 
                                    6788999999999998887899*******8..6678*********9.88888889************************* PP

                                    HHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEE..TTEEEESSGGGHHHHHHHHHH CS
                      DJ-1_PfpI 107 LaaagvlkgrrvTsypavkdklekagakyvdkrvvvd..gnlvTsrgpgaaiefalelle 164
                                    Laaag+l+g ++T+++ v+d  +  ga+yv +rvv    ++++T++g+ + i+++l l+e
  gi|121635962|ref|YP_976185.1|  81 LAAAGLLNGLTATTHWRVQDLFNSLGARYVPQRVVEHlpERVITAAGVSSGIDMGLRLVE 140
                                    ***********************************973366***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1207.24
//
Query:       gi|121635963|ref|YP_976186.1|  [L=96]
Description: 30S ribosomal protein S6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-28   97.5   0.0    4.4e-28   97.4   0.0    1.0  1  Ribosomal_S6  Ribosomal protein S6


Domain annotation for each model (and alignments):
>> Ribosomal_S6  Ribosomal protein S6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   2.4e-32   4.4e-28       2      90 .]       4      92 ..       3      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 2.4e-32
                                   EEEEEEE-TTS-HHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEESCCHHHHHHHHHHCSTTE CS
                   Ribosomal_S6  2 YElvfilrpelseeevkelvekvgklilenggvvrkveswGkrkLaypikkkteGyyvlmnfdaspevikelertlrlderv 83
                                   YE+++il+p+l+e +v+  +e++ +++ + gg+v+kv+ wGkr+Lay+i k+ eG+yv+++++a p++++el+r+l l+e+v
  gi|121635963|ref|YP_976186.1|  4 YEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIYVVIDVKAAPATVSELDRQLSLNESV 85
                                   ********************************************************************************** PP

                                   EEEEEEE CS
                   Ribosomal_S6 84 lRylivk 90
                                   lR+ +++
  gi|121635963|ref|YP_976186.1| 86 LRTKVMR 92
                                   **99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 749.58
//
Query:       gi|121635964|ref|YP_976187.1|  [L=164]
Description: single-stranded DNA-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-30  105.6   0.0    1.5e-30  105.3   0.0    1.1  1  SSB              Single-strand binding protein family
    1.6e-05   24.8   0.1    2.7e-05   24.1   0.1    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.019   15.1   0.0    1.3  1  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.014   15.9   0.1      0.021   15.3   0.1    1.3  1  Ribosomal_S3_C   Ribosomal protein S3, C-terminal domain


Domain annotation for each model (and alignments):
>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   3.3e-34   1.5e-30       3     101 ..       6     106 ..       4     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 3.3e-34
                                    EEEEEEEESSS-EEEEETTSEEEEEEEEEEEEEEEE..TTCCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEEE CS
                            SSB   3 kvilvGrlgkdpelrqtesGnavarftlatnrrfkd..qegekdeetewhrvvvfgklaevvaeylkkGslvyveGrlqt 80 
                                     +++vG+l++dpelr+t+sG+ava+ft+a++ r+ d  + ++kd+e+ ++r+ +++++ae+vae+l++G++v+v+Grl++
  gi|121635964|ref|YP_976187.1|   6 TITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDrqTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQ 85 
                                    689*****************************99999888999************************************* PP

                                    EEEECTTSCEEEEEEEEEEEE CS
                            SSB  81 rkyedqegqkrysteivaeev 101
                                    r++e +eg+kr++ e+ ++e+
  gi|121635964|ref|YP_976187.1|  86 RSFETREGEKRTVIEVEVDEI 106
                                    ******************997 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     6e-09   2.7e-05      29      73 ..      54     106 ..      39     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6e-09
                                    EEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.....TTS....SEEEEEEEE CS
                tRNA_anti-codon  29 riqvvlfreeatklaenlkeGdvvrvtGrvkrr.....pgg....elelkveei 73 
                                     +++ ++re+a+++ae+l++G  v v+Gr+k r     + g     +e+ v+ei
  gi|121635964|ref|YP_976187.1|  54 FLRCNIWREAAENVAESLTRGARVIVSGRLKQRsfetrE-GekrtVIEVEVDEI 106
                                    689******************************886651.14455577766665 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.3e-06     0.019      44      79 ..      48      84 ..      28     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                    tRNA_anti_2 44 kD.ekakisavifrsraaklkftledGmkVlvkgrls 79
                                   kD e   +++ i+r++a+++  +l+ G++V+v grl+
  gi|121635964|ref|YP_976187.1| 48 KDgEALFLRCNIWREAAENVAESLTRGARVIVSGRLK 84
                                   67444569**************************986 PP

>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   4.8e-06     0.021      16      51 ..      61      96 ..      56     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEE CS
                 Ribosomal_S3_C 16 kkairramkagakGikiqvsGrLggaeiarsekyke 51
                                   ++a +++ ++  +G++++vsGrL+  +   +e  k+
  gi|121635964|ref|YP_976187.1| 61 REAAENVAESLTRGARVIVSGRLKQRSFETREGEKR 96
                                   5688899999999***********544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1056.03
//
Query:       gi|121635965|ref|YP_976188.1|  [L=84]
Description: 30S ribosomal protein S18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-22   79.2   0.5    2.5e-22   78.8   0.5    1.2  1  Ribosomal_S18  Ribosomal protein S18


Domain annotation for each model (and alignments):
>> Ribosomal_S18  Ribosomal protein S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.5   1.4e-26   2.5e-22       3      52 .]      28      77 ..      26      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.4e-26
                  Ribosomal_S18  3 ekidYkdvelLsqFiterGkIlprriTGlcakhQrklakaIkrARhlaLL 52
                                   + idYkd+ lL+ +i+erGkI  rr+TG+c +hQr +a a+k+AR++aLL
  gi|121635965|ref|YP_976188.1| 28 QAIDYKDTALLRTYISERGKIRARRVTGNCVQHQRDIALAVKNAREVALL 77
                                   67***********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 619.02
//
Query:       gi|121635966|ref|YP_976189.1|  [L=152]
Description: 50S ribosomal protein L9 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-23   80.9   0.3    9.9e-23   80.4   0.3    1.2  1  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
    4.5e-20   70.9   0.0    7.4e-20   70.3   0.0    1.4  1  Ribosomal_L9_N  Ribosomal protein L9, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.3   1.1e-26   9.9e-23       1      86 []      63     150 ..      63     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.1e-26
                                    HHHHHHHHHHSS..-EEEE--B-T.T-BBSS---HHHHHHHHHHHT-----GGGEE-TT.T-SBSSEEEEEEESSSS-EE CS
                 Ribosomal_L9_C   1 eeaealaekLeakvkvtikakage.dgklFGsVtakdIaealkkklgieidkkkielee.piktlGeyevtvkLhkevta 78 
                                    e+a+++++++ea   + + +k+++ +gklFGsVta+d+++a+kk+ g ++dk+ ++l++ +ik++G++ v+v+Lh+e+ +
  gi|121635966|ref|YP_976189.1|  63 EHANEIKAAIEALGPIALPVKTSAdSGKLFGSVTAADVVAAIKKAGGPNLDKRIVRLPKtHIKAVGTHFVSVHLHPEIDV 142
                                    689********84479999999776**********************************55******************* PP

                                    EEEEEEE- CS
                 Ribosomal_L9_C  79 kikveVva 86 
                                    ++ ++Vva
  gi|121635966|ref|YP_976189.1| 143 EVSLDVVA 150
                                    ******85 PP

>> Ribosomal_L9_N  Ribosomal protein L9, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   8.2e-24   7.4e-20       1      46 [.       1      46 [.       1      47 [. 0.98

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 8.2e-24
                                   -EEEESSCBTTTBSSS-EEE--HHHHHHTTTTTTSEEE-SHHHHHH CS
                 Ribosomal_L9_N  1 MkVILlkdVkglGkkGdvveVkdGyaRNyLipqglAvyAtpenlke 46
                                   Mk IL+ dV++lG  Gd veVkdGy+RN+L+p+glA+ A++++ k+
  gi|121635966|ref|YP_976189.1|  1 MKLILTADVDHLGSIGDTVEVKDGYGRNFLLPRGLAIVASRGAQKQ 46
                                   9****************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1334.59
//
Query:       gi|121635967|ref|YP_976190.1|  [L=173]
Description: hypothetical protein BCG_0088 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1192.09
//
Query:       gi|121635968|ref|YP_976191.1|  [L=874]
Description: replicative DNA helicase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-96  321.1   0.0    5.4e-96  320.8   0.0    1.1  1  DnaB_C           DnaB-like helicase C terminal domain
    9.7e-34  115.6   0.0    3.2e-33  113.9   0.0    1.9  2  DnaB             DnaB-like helicase N terminal domain
    1.8e-20   73.3   0.0      3e-20   72.5   0.0    1.4  1  Intein_splicing  Intein splicing domain
    7.8e-19   67.8   0.0    2.2e-18   66.3   0.0    1.8  2  LAGLIDADG_3      LAGLIDADG-like domain
    1.9e-15   56.9   0.0    4.9e-15   55.6   0.0    1.7  1  AAA_25           AAA domain
    1.9e-05   24.1   0.0    3.5e-05   23.3   0.0    1.4  1  ATPase           KaiC
  ------ inclusion threshold ------
      0.015   14.7   0.2       0.05   13.0   0.1    1.8  2  TniB             Bacterial TniB protein
      0.026   13.7   0.1      0.042   13.1   0.1    1.2  1  TIP49            TIP49 P-loop domain
      0.037   14.3   0.0      0.088   13.1   0.0    1.6  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8   0.0   2.7e-99   5.4e-96       1     255 []     201     871 ..     201     871 .. 0.99

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 2.7e-99
                                    SBXSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C   1 GlstgfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklr 80 
                                    G++tgf++LD++t+Gl++g+++i+Aarp++Gk++l l++++++ +++++  ++fslems++++v+Rlls+ea+i+++++r
  gi|121635968|ref|YP_976191.1| 201 GVATGFTELDEVTNGLHPGQMVIVAARPGVGKSTLGLDFMRSCSIRHRMASVIFSLEMSKSEIVMRLLSAEAKIKLSDMR 280
                                    9******************************************************************************* PP

                                    HTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSCSSSCCCHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  81 tgklkeedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegseekenreqevseisrs 160
                                    +g+++++dw++l+++++e+sea+lfidd+p+lt++eir+karrl+++ +l+liv+DyLqlm++ ++ e+r+ evse sr+
  gi|121635968|ref|YP_976191.1| 281 SGRMSDDDWTRLARRMSEISEAPLFIDDSPNLTMMEIRAKARRLRQKANLKLIVVDYLQLMTSGKKYESRQVEVSEFSRH 360
                                    **************************************************************877799************ PP

                                    HHHHHHHCTSXEEEEEEXSGGGCCSCCHSXXHHHHCCTT......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                         DnaB_C 161 LkalakelnvpvialsqLsravesredkrPvlsDLreSg......................................... 199
                                    Lk lakel+vpv+a+sqL+r  e+r+dk+P+l+DLreSg                                         
  gi|121635968|ref|YP_976191.1| 361 LKLLAKELEVPVVAISQLNRGPEQRTDKKPMLADLRESGcltastrilradtgaevafgelmrsgerpmvwslderlrmv 440
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         DnaB_C 200 ................................................................................ 199
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 441 arpminvfpsgrkevfrlrlasgreveatgshpfmkfegwtplaqlkvgdriaaprrvpepidtqrmpeselislarmig 520
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         DnaB_C 200 ................................................................................ 199
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 521 dgsclknqpiryepvdeanlaavtvsaahsdgaairddylaarvpslrparqrlprgrctpiaawlaglglftkrshekc 600
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         DnaB_C 200 ................................................................................ 199
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 601 vpeavfrapndqvalflrhlwsaggsvrwdptngqgrvyygstsrrliddvaqlllrvgifswithapklgghdswrlhi 680
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         DnaB_C 200 ................................................................................ 199
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 681 hgakdqvrflrhvgvhgaeavaaqemlrqlkgpvrnpnldsapkkvwaqvrnrlsakqmmdiqlheptmwkhspsrsrph 760
                                    ******************************************************************************** PP

                                    .......................................................SCCCCXSEEEEEEECCHHHHHHCHH CS
                                    .......................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 200 .......................................................sieqdADvvlflyrdeyykedseek 224
                                                                                           s+eqdADvv++l+r++ +++d+++ 
  gi|121635968|ref|YP_976191.1| 761 raeariedraihelargdaywdtvveitsigdqhvfdgtvsgthnfvangislhnSLEQDADVVILLHRPDAFDRDDPRG 840
                                    **************************************************************************999889 PP

                                    CEEEEEEEEETTSXXEEEEEEEETTTTEEEX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 225 gkaeiiiaKhRnGptgtvklafekeytrFen 255
                                    g+a++i+aKhRnGpt+tv++a++ +++rF n
  gi|121635968|ref|YP_976191.1| 841 GEADFILAKHRNGPTKTVTVAHQLHLSRFAN 871
                                    99***************************87 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0   1.6e-36   3.2e-33       1     103 []      23     125 ..      23     125 .. 0.99
   2 ?   -2.4   0.0       2.6   5.2e+03      16      41 ..     826     851 ..     823     852 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 1.6e-36
                                    HHHHHHHHHHHHHHHHHHSTTHHHHHHCC--GGGSSSHHHHHHHHHHHHHHHTTTS-SHHHHHHHSCSSS-GGHGT.HHH CS
                           DnaB   1 eppqsieaEqavLgalLldpeaidevadilkpedFyepahrliFeailelyekgepiDlvtvkeelekkgkledvggaay 80 
                                    +ppq++ aEq+vLg++Ll+++ai +v + l+p dFy+pah+++++ail+ly +gep+D+vtv++el+++g+l ++gga y
  gi|121635968|ref|YP_976191.1|  23 QPPQDLAAEQSVLGGMLLSKDAIADVLERLRPGDFYRPAHQNVYDAILDLYGRGEPADAVTVAAELDRRGLLRRIGGAPY 102
                                    69****************************************************************************** PP

                                    HHHHHHC-S-CCCHHHHHHHHHH CS
                           DnaB  81 laelvaavpsaanieeyaeivke 103
                                    l++l++ vp+aan+ +ya iv+e
  gi|121635968|ref|YP_976191.1| 103 LHTLISTVPTAANAGYYASIVAE 125
                                    *********************87 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                    HHHSTTHHHHHHCC--GGGSSSHHHH CS
                           DnaB  16 lLldpeaidevadilkpedFyepahr 41 
                                    lL+ p+a+d+      + dF  ++hr
  gi|121635968|ref|YP_976191.1| 826 LLHRPDAFDRDDPRGGEADFILAKHR 851
                                    78889999999999999*****9998 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.5e-23     3e-20       4     134 .]     410     815 ..     407     815 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.5e-23
                                    CTTCEEEEHHHHCC.ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECC CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing   4 edgeekvkieelve.kegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkrad 82 
                                    +d++ +v  +el+   e   v+sl+ e l++ +    +++ ++ ke+++++l+sgr++ aT+ H+++ +  eg+  + + 
  gi|121635968|ref|YP_976191.1| 410 ADTGAEVAFGELMRsGERPMVWSLD-ERLRMVARPMINVFPSGRKEVFRLRLASGREVEATGSHPFMKF--EGW--TPLA 484
                                    6888899999998823334689999.6667777777899999***************************..9**..9*** PP

                                    C--TT-EEEEE..................................................................... CS
                                    xxxxxxxxxxx..................................................................... RF
                Intein_splicing  83 eLkegdliavp..................................................................... 93 
                                    +Lk+gd ia p                                                                     
  gi|121635968|ref|YP_976191.1| 485 QLKVGDRIAAPrrvpepidtqrmpeselislarmigdgsclknqpiryepvdeanlaavtvsaahsdgaairddylaarv 564
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 565 pslrparqrlprgrctpiaawlaglglftkrshekcvpeavfrapndqvalflrhlwsaggsvrwdptngqgrvyygsts 644
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|121635968|ref|YP_976191.1| 645 rrliddvaqlllrvgifswithapklgghdswrlhihgakdqvrflrhvgvhgaeavaaqemlrqlkgpvrnpnldsapk 724
                                    ******************************************************************************** PP

                                    ...................................................HSCEEEEEEEEEEEEECEEEEEEEEETTT CS
                                    ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  94 ...................................................dadvvwdkvksievedeeeyVYdltvedn 122
                                                                                       ++d++wd v++i+  ++++ V+d tv ++
  gi|121635968|ref|YP_976191.1| 725 kvwaqvrnrlsakqmmdiqlheptmwkhspsrsrphraeariedraihelaRGDAYWDTVVEITSIGDQH-VFDGTVSGT 803
                                    ********************************************************************99.********* PP

                                    -EEEECTTEEE- CS
                                    xxxxxxxxxxxx RF
                Intein_splicing 123 hNFvangiivHN 134
                                    hNFvangi +HN
  gi|121635968|ref|YP_976191.1| 804 HNFVANGISLHN 815
                                    ***********9 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.1e-21   2.2e-18       1      83 []     611     694 ..     611     694 .. 0.98
   2 ?   -3.6   0.0       7.6   1.5e+04      14      32 ..     797     816 ..     797     819 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.1e-21
                                    HHHHHHHHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGG CS
                    LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvs.isltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFl 79 
                                    +++a fLr+l++a Gsv+++ ++g++ ++++s+s++l++dv++lLlr GI+s i++  k +g++++rl i + ++  rFl
  gi|121635968|ref|YP_976191.1| 611 DQVALFLRHLWSAGGSVRWDPTNGQGrVYYGSTSRRLIDDVAQLLLRVGIFSWITHAPKLGGHDSWRLHIHGAKDQVRFL 690
                                    5799*******************999****************************************************** PP

                                    TTTX CS
                    LAGLIDADG_3  80 ekig 83 
                                    +++g
  gi|121635968|ref|YP_976191.1| 691 RHVG 694
                                    *998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.6
                                    CCECCECSTTTTS.EEEEES CS
                    LAGLIDADG_3  14 DGsvskskkkgvs.isltss 32 
                                    DG+vs++ +   + isl +s
  gi|121635968|ref|YP_976191.1| 797 DGTVSGTHNFVANgISLHNS 816
                                    999*9999887778888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   2.5e-18   4.9e-15      14     191 ..     201     380 ..     191     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.5e-18
                         AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlrav 93 
                                    ++a+  ++++ +  gl p g  +++a++pg+GK+tl ld + +++  +         +++ ++ s+E+s +e+  Rl  +
  gi|121635968|ref|YP_976191.1| 201 GVATGFTELDEVTNGLHP-GQMVIVAARPGVGKSTLGLDFMRSCSIRH---------RMASVIFSLEMSKSEIVMRLLSA 270
                                    566667778888888865.**************************433.........5799******************* PP

                         AAA_25  94 geal..........rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensn 162
                                     +++          +dd++ ++  ++++  + pLf +d+ + +   +++a ++++++ ++++l+v+D l+ +++g + ++
  gi|121635968|ref|YP_976191.1| 271 EAKIklsdmrsgrmSDDDWTRLARRMSEiSEAPLFIDDSPNLTM-MEIRAKARRLRQKANLKLIVVDYLQLMTSGKKYES 349
                                    ***9**********99********************99888875.5689999*****999***************77777 PP

                         AAA_25 163 sdv..galvealeriarrtgaavllvhHvgK 191
                                    ++v  +++  +l+ +a+++ + v+++ ++++
  gi|121635968|ref|YP_976191.1| 350 RQVevSEFSRHLKLLAKELEVPVVAISQLNR 380
                                    77556********************998875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.8e-08   3.5e-05       1     165 [.     202     379 ..     202     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.8e-08
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle.e 79 
                                    v tg  +lDe++ +G+  g++v ++  pG GK++++l F+ +   +   + v+ ++e +++++  +  s    ++    +
  gi|121635968|ref|YP_976191.1| 202 VATGFTELDEVT-NGLHPGQMVIVAARPGVGKSTLGLDFMRSCSIRHRMASVIFSLEMSKSEIVMRLLSAEAKIKLSDmR 280
                                    679********7.9**************************998888899***********99999888777666544313 PP

                         ATPase  80 egklaiidasesaeesaee..........kdkedleelieelaeaikeikakrvviDsitglayeekeavaRe.ilrqlv 148
                                    +g++   d ++ a+ + +e          + +  ++e+ ++ ++  ++ + k +v+D ++ + ++ k+ + R+ ++ ++ 
  gi|121635968|ref|YP_976191.1| 281 SGRMSDDDWTRLAR-RMSEiseaplfiddSPNLTMMEIRAKARRLRQKANLKLIVVDYLQLM-TSGKKYESRQvEVSEFS 358
                                    44555544444333.33334556888876677777888888888888888899999999888.55555555542333333 PP

                         ATPase 149 r...vl.kklgvTailvseks 165
                                    r    l k+l+v  + +s+ +
  gi|121635968|ref|YP_976191.1| 359 RhlkLLaKELEVPVVAISQLN 379
                                    300033466666666666655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5     3e+03      37      60 ..     221     244 ..     206     255 .. 0.77
   2 ?   13.0   0.1   2.5e-05      0.05     100     160 ..     310     375 ..     302     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                           TniB  37 nlllvGdsnnGKtmivekFarlhp 60 
                                     ++++ ++ +GK+++   F+r+ +
  gi|121635968|ref|YP_976191.1| 221 MVIVAARPGVGKSTLGLDFMRSCS 244
                                    4667789999****9999988765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.5e-05
                           TniB 100 ararvskleqqvlrllrelkvrvLiiDEihnllagsarkqr.....eflnalksLgnelkipivlv 160
                                    ++ ++ ++++++ rl ++ +++++++D ++ + +g+  + r     ef   lk L  el++p+v++
  gi|121635968|ref|YP_976191.1| 310 PNLTMMEIRAKARRLRQKANLKLIVVDYLQLMTSGKKYESRqvevsEFSRHLKLLAKELEVPVVAI 375
                                    6667889999999999*******************9876652222267899*************86 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.1e-05     0.042      46     112 ..     215     277 ..     198     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  46 kklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvrik 112
                                    +   G+ v++a  +g Gk+ l +   ++ +      +  +s ++sle++k+e++++ l    ++++ 
  gi|121635968|ref|YP_976191.1| 215 GLHPGQMVIVAARPGVGKSTLGLDFMRSCS----IRHRMASVIFSLEMSKSEIVMRLLSAEAKIKLS 277
                                    555799*****************9998877....5566799**************999877777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.088       5     104 ..     219     342 ..     216     377 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..................erpevvfvtlpsstsskdllrellralgl 66 
                                     ++++v + +G+GK+tl   ++++  ++   +                   +++++ + ++ s+  s+d +++l+r + +
  gi|121635968|ref|YP_976191.1| 219 GQMVIVAARPGVGKSTLGLDFMRSCSIRHRMASvifslemskseivmrllsAEAKIKLSDMRSGRMSDDDWTRLARRMSE 298
                                    57999*******************98754444466666665554444444433333344444444444445555555554 PP

                         AAA_22  67 elka.......erlsseellealeqalraravielliiDEaqhlr 104
                                      +a       ++l+  e++++ ++  +++   +l+++D  q ++
  gi|121635968|ref|YP_976191.1| 299 ISEAplfiddsPNLTMMEIRAKARRLRQKANL-KLIVVDYLQLMT 342
                                    44446666654444444444444444444444.777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 6035.86
//
Query:       gi|121635969|ref|YP_976192.1|  [L=230]
Description: hypothetical protein BCG_0090 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-55  185.6   0.0      1e-54  185.4   0.0    1.0  1  DarT      ssDNA thymidine ADP-ribosyltransferase, DarT


Domain annotation for each model (and alignments):
>> DarT  ssDNA thymidine ADP-ribosyltransferase, DarT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.0   5.8e-59     1e-54       1     200 []      29     230 .]      29     230 .] 0.97

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 5.8e-59
                           DarT   1 yhithidNLpsIlasggllsdnkveeeginytnigdsgikqrrlk.kevpi..ppggtlgdYvpfYfaprspmlyrierg 77 
                                    +h+th+dNLp I+++g ll+d++v    +++t+++++ +k+ r++ ++ p+  +p ++ +d+vpfY+a+rspmly++++g
  gi|121635969|ref|YP_976192.1|  29 WHFTHADNLPGIITAGRLLADSAV----TPTTEVAYNPVKELRRHkVVAPDsrYPASMASDHVPFYIAARSPMLYVVCKG 104
                                    8***********************....789**************77777789*************************** PP

                           DarT  78 nhaeykg..edivvLvidleil.asgercvftdgnaaasgtefrngledl.eeidwdlvyakswknteedsdrkerkqAE 153
                                    +++ y+g   ++v+L++ l  + +++  ++ +dgnaaas+t+f+ + + l + +d+dl+++++w+nt++d++r++r+ AE
  gi|121635969|ref|YP_976192.1| 105 HSG-YSGgaGPLVHLGVALGDIiDADLTWCASDGNAAASYTKFSRQVDTLgTFVDFDLLCQRQWHNTDDDPNRQSRRAAE 183
                                    *87.9999***********************************************************99*********** PP

                           DarT 154 vLvkdsiplelitgigvrneevkkqveelldkagvsppvevkpdwyf 200
                                    +Lv++++p el++ ++++n e++++v++lld +g  +++ +kp++y+
  gi|121635969|ref|YP_976192.1| 184 ILVYGHVPFELVSYVCCYNTETMTRVRTLLDPVGGVRKYVIKPGMYY 230
                                    **********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1809.92
//
Query:       gi|121635970|ref|YP_976193.1|  [L=352]
Description: hypothetical protein BCG_0091 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-23   83.6   0.0    1.6e-23   83.0   0.0    1.3  1  Macro     Macro domain
    0.00087   18.5   0.0     0.0012   18.0   0.0    1.1  1  DUF1719   Domain of unknown function (DUF1719)


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.8e-27   1.6e-23       1     117 [.      18     131 ..      18     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.8e-27
                                    EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSS.SSEEEEEESE-TTTSTSTTHHHHHH CS
                          Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlp.akyvihtvgplftsskskeeeella 79 
                                    Vn++N+ + +g+g+a +++r++++ ++++ k++++  g++++G+++v+++++l+  k++i++  p+ ++++  ++ + + 
  gi|121635970|ref|YP_976193.1|  18 VNTVNCVGVMGKGIALQFKRRYPEMFTAYEKACKR--GEVTIGKMFVVDTGQLDgPKHIINF--PTKKHWRAPSKLAYID 93 
                                    9********************************65..88***********************..**************** PP

                                    HHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHH CS
                          Macro  80 kayknalelaeekgiksvafPaistGifgvpweeaarv 117
                                    + + ++++  +e +i sva+P ++ G +g++we++++ 
  gi|121635970|ref|YP_976193.1|  94 AGLIDLIRVIRELNIASVAVPPLGVGNGGLDWEDVEQR 131
                                    ***********************************985 PP

>> DUF1719  Domain of unknown function (DUF1719)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-07    0.0012      38     128 ..     204     292 ..     185     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-07
                        DUF1719  38 rfAdgAseFlrfvelGgtprrylffdplirhLlaGkeleyklvq.gsklllflirpvsleerGveaklifvyedrkapek 116
                                     fA++A+    ++ l  tp ry + +  +rhLl+G e  + +    +  ++++ +p+sl  +G++a   +  +d  a   
  gi|121635970|ref|YP_976193.1| 204 YFANEADP---DLALDFTPGRYGPYSERVRHLLQGMEGAFTVGLgDGTARVLANQPISLTTKGTDAITDYLATDAAADRV 280
                                    56666654...5566779999999******************662566677778************************** PP

                        DUF1719 117 sfvlglmLrlse 128
                                    s  + ++Lr+ e
  gi|121635970|ref|YP_976193.1| 281 SAAVDTVLRVIE 292
                                    *********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2955.07
//
Query:       gi|121635971|ref|YP_976194.1|  [L=141]
Description: hypothetical protein BCG_0092 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1062.61
//
Query:       gi|121635972|ref|YP_976195.1|  [L=380]
Description: cellulase celA1 (endoglucanase) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-71  239.8   0.0    6.6e-71  239.5   0.0    1.1  1  Glyco_hydro_6  Glycosyl hydrolases family 6


Domain annotation for each model (and alignments):
>> Glyco_hydro_6  Glycosyl hydrolases family 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.5   0.0   3.7e-75   6.6e-71       8     305 ..     105     363 ..      98     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 239.5 bits;  conditional E-value: 3.7e-75
                  Glyco_hydro_6   8 qaaakldaalaakaakvakvptavWldriakieelrkaldeavaqakaegavvvlVvYnlPgRDCaaqaSaGelasaaal 87 
                                     +aa++++  +a++++va++p+  Wld++ + +++  ++++++ +a+a+ga++vl +Y +P+RDC + +++G++a+ ++ 
  gi|121635972|ref|YP_976195.1| 105 MVAARNANPPNAELTSVANTPQSYWLDQAFPPATVGGTVARYTGAAQAAGAMPVLTLYGIPHRDC-GSYASGGFATGTD- 182
                                    444555667788999************99999*********************************.************9. PP

                  Glyco_hydro_6  88 ekYkeyidaiaagigkysdlravvvlEpDslanlvtnlsvekCaeaaaaaerlaglayAvkkLkalpnvavYlDaghsgw 167
                                      Y+ +ida+a+g+g+   + a++++EpD+la +       +C +  +++er+++++yAv++L + p  avY+Daghs  
  gi|121635972|ref|YP_976195.1| 183 --YRGWIDAVASGLGS---SPATIIVEPDALAMA-------DCLSPDQRQERFDLVRYAVDTLTRDPAAAVYVDAGHS-- 248
                                    ..**************...************988.......6**999999****************************.. PP

                  Glyco_hydro_6 168 lgWeknleeaaellakvvkaaagvakvdGfalnvsnynateeateanksvdekkYakalskalvaaglpalahfviDtsR 247
                                      W  ++e +a++l++      gv +++Gf+lnvsn+ +t+         +e  Y++a+s       + +  h+viDtsR
  gi|121635972|ref|YP_976195.1| 249 -RW-LSAEAMAARLND-----VGVGRARGFSLNVSNFYTTD---------EEIGYGEAISGLT----NGS--HYVIDTSR 306
                                    .55.55699*******.....89******************.........*********9865....444..******** PP

                  Glyco_hydro_6 248 nGkqgkerkdageWCNppgrglGerpttstgdplvdaylWvKppGeSDGtcdrsaaea 305
                                    nG +++  +++ +WCNp+gr+lG++ptt+t+ ++ daylW+K+pGeSDGtc+r++++a
  gi|121635972|ref|YP_976195.1| 307 NGAGPA-PDAPLNWCNPSGRALGAPPTTATAGAHADAYLWIKRPGESDGTCGRGEPQA 363
                                    ***987.66789*****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2841.41
//
Query:       gi|121635973|ref|YP_976196.1|  [L=479]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-30  105.4   5.9    1.9e-30  105.4   4.1    2.0  2  FAD_binding_4  FAD binding domain
    3.8e-08   33.3   0.1      8e-08   32.3   0.1    1.5  1  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   4.1   2.1e-34   1.9e-30       1     138 [.      74     209 ..      74     210 .. 0.98
   2 ?   -2.2   0.0      0.34   3.1e+03      63      81 ..     386     404 ..     376     442 .. 0.61

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.1e-34
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    pa++v+p+s+ +v++a+++a++++l+v +rGgG+s++g+++a+g++vldl++l + +++d+++g++tv + + l ++++ 
  gi|121635973|ref|YP_976196.1|  74 PAVIVTPTSQLDVQKAMAFAAANNLKVAPRGGGHSYVGASTANGAMVLDLRQLPGDINYDATTGRVTVTPATGLYAMHQV 153
                                    899**************************************9********99**************************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                    laa+g+ ++  +g++ +++v+G+ ++++ G +s+ +Gl++d+++++ vvl+ G+ v++
  gi|121635973|ref|YP_976196.1| 154 LAAAGRGIP--TGTCPTVGVAGHALGGGLGANSRHAGLLCDQLTSASVVLPSGQAVTA 209
                                    *********..9*****************************************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.34
                                    TTEEEEETTSBHHHHHHHH CS
                  FAD_binding_4  63 egtatveaGvtlgdlveal 81 
                                    +  atv +G+t     ++ 
  gi|121635973|ref|YP_976196.1| 386 GALATVSPGATAFPWRRQS 404
                                    6677777777765544444 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   8.9e-12     8e-08       2      38 ..     439     472 ..     438     474 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 8.9e-12
                                    -TTS--GGG-HHHHHHHHGGGHHHHHHHHHHH-TT-- CS
                            BBE   2 YvNyrdldlgkewgerYFggNferLvkvKtkyDPdNv 38 
                                    YvNy  +  +   ++rYFg N++rL  v++kyDP+ v
  gi|121635973|ref|YP_976196.1| 439 YVNYLEVNQP---PARYFGPNLSRLSAVRQKYDPSRV 472
                                    **********...*********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3541.01
//
Query:       gi|121635974|ref|YP_976197.1|  [L=979]
Description: hypothetical protein BCG_0095 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-272  905.3   0.0   3.4e-272  905.1   0.0    1.0  1  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  905.1   0.0  1.9e-276  3.4e-272       7     758 .]      25     819 ..      19     819 .. 0.95

  Alignments for each domain:
  == domain 1  score: 905.1 bits;  conditional E-value: 1.9e-276
                        UPF0182   7 vlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlell........eklerl 78 
                                     +++lll+   l+++y+++lwf e+g++sv++t lltrl+++++v+l++a ++l++llla+r++ +        ++++ l
  gi|121635974|ref|YP_976197.1|  25 GMLALLLFGPRLVDIYVDWLWFGEVGFRSVWITVLLTRLAIVAAVALVVAGIVLAALLLAYRSRPFfvpdepqrDPVAPL 104
                                    456677789******************************************************4446677777799**** PP

                        UPF0182  79 realekklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvllali 158
                                    r+a++++++l+ ++ia+ l++++gl+as +w kv+lf+++ +fg+ Dp fg Di+F+vF+lPf++ +l++l+++v+la++
  gi|121635974|ref|YP_976197.1| 105 RSAVMRRPRLFGWGIAVTLGVVCGLIASFDWVKVQLFVHGGTFGIVDPEFGYDIGFFVFDLPFYRSVLNWLFVAVVLAFL 184
                                    ******************************************************************************** PP

                        UPF0182 159 avllvyllsgeslgirl..kfaelskaarrhlsvllallllllalsywLdryellys..krg.vvtGagYtdvnavlpak 233
                                    a+ll+++l+g   g+rl      l++aar++l+v++++++ll+a++ywLdryell s  k + ++tGagYtd++a+lpak
  gi|121635974|ref|YP_976197.1| 185 ASLLTHYLFG---GLRLttGRGMLTQAARVQLAVFAGAVVLLKAVAYWLDRYELLSSgrK-EpTFTGAGYTDIHAELPAK 260
                                    **********...44454466789*********************************744.459**************** PP

                        UPF0182 234 tilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTreAygL.. 311
                                    ++l++ia+++av +++ai+l++l++p++a+allvl+ail+g+++p l+++f+V+Pn+++ E+pYi+rnIeaTreAy +  
  gi|121635974|ref|YP_976197.1| 261 LVLVAIAVLCAVSFFTAIFLRDLRIPAMAAALLVLSAILVGGLWPLLMEQFSVRPNAADVERPYIQRNIEATREAYRIgg 340
                                    *******************************************************************************9 PP

                        UPF0182 312 dkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkF.edldvdrYtidgeerqvviaaREldy 390
                                    d v++++++  ++ +++d+  + +ti+++rLlDp++l++tf+q+qq++n+++F e ld+drY+idge +++++++REl+ 
  gi|121635974|ref|YP_976197.1| 341 DWVQYRSYPGIGTKQPRDVPVDVTTIAKVRLLDPHILSRTFTQQQQLKNFFSFaEILDIDRYRIDGELQDYIVGVRELSP 420
                                    *****************************************************9999*********************** PP

                        UPF0182 391 salpeeaktwvnkhlvYTHGyGvvaspvnkvt............eeGlpeflvkdip..see.eeslkieepriYfGel. 454
                                    ++l+ ++++w+nkh+vYTHG+G+va+p+n+v+            ++G+p + v+di     + ++ +++e+pr+Y+Ge+ 
  gi|121635974|ref|YP_976197.1| 421 KSLTGNQTDWINKHTVYTHGNGFVAAPANRVNaaardaenisdsNSGYPIYAVSDIAslG-SgRQVIPVEQPRVYYGEVi 499
                                    ******************************************9999***********642.369**************99 PP

                        UPF0182 455 ...tndyvivgt.kvk....EfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnik 526
                                       ++dy+ivg         E+d++    + ++tY+G gGv+ig++++r++fa+k+ + k+l+s+ei sesk+l++R++k
  gi|121635974|ref|YP_976197.1| 500 aqaDPDYAIVGGaP-GsaprEYDTD----TSKYTYTGAGGVSIGNWFNRTVFATKFAQHKFLFSREIGSESKVLIHRDPK 574
                                    9999*******952.3356799998....4569*********************************************** PP

                        UPF0182 527 eRvekvaPfLtlDsdpYlvvadgrlyWivDaYTtsdrYPySepeeats..........geeevnYiRNSVKvvvDAydGt 596
                                    eRv++vaP+Lt+D++pY+vv++gr++WivDaYTt d+YPy+++++ +           + ++v+Y+RNSVK++vDAydGt
  gi|121635974|ref|YP_976197.1| 575 ERVQRVAPWLTTDDNPYPVVVNGRIVWIVDAYTTLDTYPYAQRSSLEGpvtsptgivrQGKQVSYVRNSVKATVDAYDGT 654
                                    *******************************************444413456788888889******************* PP

                        UPF0182 597 vklYvvdeeDPiikawskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpke...ee 673
                                    v+l+++d++DP++++w+++Fpg++k+ +++p+eLr+h+rYPedlF+vq++llakYHv++p++F++++ +W+vp++   + 
  gi|121635974|ref|YP_976197.1| 655 VTLFQFDRDDPVLRTWMRAFPGTVKSEDQIPDELRAHFRYPEDLFEVQRSLLAKYHVDEPREFFTTNAFWSVPSDptnDA 734
                                    ***************************************************************************87656 PP

                        UPF0182 674 eqpvePyYlilklpgeekeefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqiearinqdpeisq 753
                                    + +++P Y+++  +++ +++f l s+++  +re+l+a+++a+sd+ nygkl+++elp+++l++Gp+qi++++ +d+++++
  gi|121635974|ref|YP_976197.1| 735 NATQPPFYVLVGDQQSAQPSFRLASAMVGYNREFLSAYISAHSDPANYGKLTVLELPTDTLTQGPQQIQNSMISDTRVAS 814
                                    666***************************************************************************** PP

                        UPF0182 754 qlsLw 758
                                    + +L+
  gi|121635974|ref|YP_976197.1| 815 ERTLL 819
                                    *9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (979 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.27s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 6402.51
//
Query:       gi|121635975|ref|YP_976198.1|  [L=79]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 514.49
//
Query:       gi|121635976|ref|YP_976199.1|  [L=133]
Description: hypothetical protein BCG_0096 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-06   26.5   0.1    8.6e-06   26.3   0.1    1.1  1  PIN       PIN domain
      0.009   16.2   0.0      0.015   15.5   0.0    1.3  1  PIN_2     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   9.6e-10   8.6e-06       2     119 ..       5     122 ..       4     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 9.6e-10
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHH..HHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvl..aEllyvlarrkskrekaaelvelllllsalkilp.idaeia 78 
                                    v+D+ +++++l g+  ++ +++ l    e +++a +l  aE+ + l+r  ++ e ++e  ++ l++    i +   ++ +
  gi|121635976|ref|YP_976199.1|   5 VVDAAAVVDALAGKGASAIVLRGLL--KESISNAPHLldAEVGHALRRAVLSDEISEEQARAALDALPYLIDNrYPHSPR 82 
                                    89*********99999988888776..566666666657*********77777777777777777666666664555555 PP

                                    HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                    ++ + + l+++++ +Dal +A+A + + +l+ t D++++ +
  gi|121635976|ref|YP_976199.1|  83 LIEYTWQLRHNVTFYDALYVALATALDVPLL-TGDSRLAAA 122
                                    56666666666********************.*****9876 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06     0.015       1     116 [.       5     120 ..       5     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                          PIN_2   1 VvdaNivvsallksrikkrlilvekaleli.apeeaveeiekhkealvkksklseeeleellelletkikiveeslyesk 79 
                                    Vvda +vv al ++ +  +++    + ++  ap+ + +e+ +     v   ++see++ ++l++l   i+    ++    
  gi|121635976|ref|YP_976199.1|   5 VVDAAAVVDALAGKGASAIVLRGLLKESISnAPHLLDAEVGHALRRAVLSDEISEEQARAALDALPYLIDNRYPHSP-RL 83 
                                    89999999998874444444444444444414444555999999999999*************99999986554444.44 PP

                          PIN_2  80 ikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdli 116
                                    i+   ++ ++v   D+ +vAla +l+ p+ T+D+ l 
  gi|121635976|ref|YP_976199.1|  84 IEYTWQLRHNVTFYDALYVALATALDVPLLTGDSRLA 120
                                    44445555566789*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 957.99
//
Query:       gi|121635977|ref|YP_976200.1|  [L=745]
Description: isocitrate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
          0 1249.5   0.0          0 1249.3   0.0    1.0  1  IDH       Monomeric isocitrate dehydrogenase


Domain annotation for each model (and alignments):
>> IDH  Monomeric isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1249.3   0.0         0         0       1     733 [.       7     740 ..       7     741 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1249.3 bits;  conditional E-value: 0
                                    EEEEEE-SHHHHHHHHHHHHHHHHHHGGGT-EEEEEE-SHHHHHHHH-GGGS-TTT----HHHHHHHHTTSTT-EEEE-- CS
                            IDH   1 kiiytktDeaPalatysllPivkaftkaagievetkdislagrilaafpelLkeeqrvedaLaelgelakkpeaniiklP 80 
                                    +iiyt tDeaP laty++lPiv+af++ agi++e++dis+a+rila+fp++L+eeqrv+d+Laelg+l++ p++niiklP
  gi|121635977|ref|YP_976200.1|   7 TIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQRVPDNLAELGRLTQLPDTNIIKLP 86 
                                    69****************************************************************************** PP

                                    ---B-HHHHHHHHHHHHTTT-------SS-SSHHHHHHHHHHGCCSBS-SHHHH--B-EEEE--HHHHHHHHHS------ CS
                            IDH  81 nisasvpqlkaaikeLqekGyklpdypeepktdeekeikarydkvlGsavnPvLreGnsdrrapkavkeyakknPhsmge 160
                                    nisasvpql aaikeLq+kGy++pdyp++p+td+ek+ik+ry+++lGsavnPvLr+Gnsdrrapkavkeya+k+Phsmge
  gi|121635977|ref|YP_976200.1|  87 NISASVPQLVAAIKELQDKGYAVPDYPADPNTDQEKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGE 166
                                    ******************************************************************************** PP

                                    --TT---EEE--SSSSHHHH-EEEE-SS-EEEEEEEEETTS-EEEEEEEEEE-TT-EEEEEEE-HHHHHHHHHHHHHHHH CS
                            IDH 161 wskdsktkvatmeegDfyeseksvtlekatkvkiefvakdgevtvlkeklkleagevidatvlsakalkefleeqieeak 240
                                    ws +s+t+va+m++gDfy+ eks+tl++a++v++e+ ak+g++ vlk +++l++g+vid++++s+kal++f+eeq+++a 
  gi|121635977|ref|YP_976200.1| 167 WSMASRTHVAHMRHGDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQMQDAF 246
                                    ******************************************************************************** PP

                                    HHT-EEEE-B-CCCS-TTS-HHHHHHHHHHTHHHHHCTHHHHHHTT--GGGHHHHHHHHSSTS-HHHHHHHHHHHHHHGG CS
                            IDH 241 eegvlfslhlkatmmkvsdPiifGhavkvffkdvfekyaeelkelgvnannGlgdllakieklpeekkeeieadieavle 320
                                    e+gv+fslh+katmmkvs+Pi+fGhav++f+kd+f+k++e +++lgvn+nnGl+dl++kie+lp+++++ei +d+++++e
  gi|121635977|ref|YP_976200.1| 247 ETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLSDLYSKIESLPASQRDEIIEDLHRCHE 326
                                    ******************************************************************************** PP

                                    GS--B-EEETTTTEETTS-TTTSBHHHHHHHHHHTTSEEE-TTS-EEEEEEE-S--TTTHHHHHHHHHHHHH-S--TTT- CS
                            IDH 321 krpelamvdsdkgitnlhvpsdviiDasmpavirdsgkmwnkdgkekdtkaviPdrsyakvyqeviedckkngafdpttm 400
                                    +rpelamvds +gi+n+h psdvi+Dasmpa+ir++gkm+++dgk+kdtkav P+++++++yqe+i++ck+ng+fdpttm
  gi|121635977|ref|YP_976200.1| 327 HRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTM 406
                                    ******************************************************************************** PP

                                    ----EEE--TTT-CGGGGGGSEEE-SSSEEEEEEE.TT--EEEEEEE-TT-EEEEEEE-HHHHHHHHHHHHHHHHHH--- CS
                            IDH 401 GsvsnvGLmaqkaeeYGshdktfeieadGtvrvvd.eegevllehevekgDiwracqtkdapirdWvklaverarasgtp 479
                                    G+v+nvGLmaq+aeeYGshdktfei++dG+ ++vd ++gevll+++ve+gDiwr+c +kdapirdWvklav+rar sg+p
  gi|121635977|ref|YP_976200.1| 407 GTVPNVGLMAQQAEEYGSHDKTFEIPEDGVANIVDvATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARISGMP 486
                                    ***********************************999****************************************** PP

                                    EEEE--TTSHHHHHHHHHHHHHHCCS--TT--EEEE-HHHHHHHHHHHHTTT---EEEE-HHHHHHHHHHHHHHHHSSGG CS
                            IDH 480 avfWLdeerahdaelikkvekylkehdtegldikilspveatklslerirkgkdtisvtGnvlrDyltDlfPilelgtsa 559
                                    ++fWLd  r+h++elikkv++ylk+hdtegldi+i+s+v+++++++er+ +g dti+ tGn+lrDyltDlfPilelgtsa
  gi|121635977|ref|YP_976200.1| 487 VLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTIAATGNILRDYLTDLFPILELGTSA 566
                                    ******************************************************************************** PP

                                    GSEEEEEBTTS-EEEESSSS---HHHHHHHHHHS------HHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHT CS
                            IDH 560 kmlsivpllaGGglfetGaGGsaPkhvqqlleenhLrWdslgeflalaasleelaekkenkkakvladtldkateklLen 639
                                    kmls+vpl+aGGg++etGaGGsaPkhv+ql+eenhLrWdslgeflal a +e++  k++n++ak+l++tld+a++klL+n
  gi|121635977|ref|YP_976200.1| 567 KMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEENHLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDN 646
                                    ******************************************************************************** PP

                                    T-S--SSTTS--HHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHHHHHHHTHHHHHHHHHHTTTS----S-SSS--HHHH CS
                            IDH 640 dksPsrkvgelDnrgshfylalywaealaaqtedaelkakfakvakeleeneekiveelaaaqgkpvdigGyykpdeekv 719
                                    dksPsrk+gelDnrgs+fyla+ywa++laaqt+d++l+++fa++a+ l++ne+ iv+el+++qg+pvdigGyy+pd++++
  gi|121635977|ref|YP_976200.1| 647 DKSPSRKTGELDNRGSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYAPDSDMT 726
                                    ******************************************************************************** PP

                                    HHHH---HHHHHHH CS
                            IDH 720 ekamrpsatlnail 733
                                    +++mrps+t+na+l
  gi|121635977|ref|YP_976200.1| 727 TAVMRPSKTFNAAL 740
                                    ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5011.37
//
Query:       gi|121635978|ref|YP_976201.1|  [L=189]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.1e-15   54.4   0.1    1.7e-14   53.3   0.1    1.6  1  TetR_N     Bacterial regulatory proteins, tetR family
    0.00048   20.2   0.0     0.0011   19.1   0.0    1.5  2  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.024   14.7   0.1    2.2  3  TetR_C_21  Tetracyclin repressor-like, C-terminal domain
      0.027   14.6   0.1      0.083   13.0   0.1    1.9  1  DprA_WH    DprA winged helix domain
       0.12   12.2   0.0       0.43   10.4   0.0    2.0  1  LacI       Bacterial regulatory proteins, lacI family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   4.8e-18   1.7e-14       2      47 .]      20      64 ..      19      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.8e-18
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   l++A + fa  G + + v+eIA+rAGv++g++Yr+Fp+Ke+L++a+
  gi|121635978|ref|YP_976201.1| 20 LEVAYQTFAADGLS-VPVDEIARRAGVGAGTVYRHFPTKEALFQAV 64
                                   899***********.*****************************97 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.7   9.6e+03      50      62 ..      65      77 ..      56      78 .. 0.69
   2 !   19.1   0.0     3e-07    0.0011      37     100 ..     116     179 ..     110     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHH CS
                      TetR_C_29 50 liekleeilerGq 62
                                   + +++ +i+++G+
  gi|121635978|ref|YP_976201.1| 65 IADRMHRIIDKGH 77
                                   4567788888876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3e-07
                                    -TTS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHHHHHHHHTHHHHHHHH-- CS
                      TetR_C_29  37 lkksesirelnspliekleeilerGqaagvFrpgvdaldlyllisslcffrvsnrhtlsalfgr 100
                                    ++ s++++e ++ +++ l ++l+  q+ag  rp+vd+l++ +l ++   ++  n +   ++ ++
  gi|121635978|ref|YP_976201.1| 116 IEISSAAPEAEADFLDLLTDLLRAAQRAGTVRPDVDVLEVKTLLVGCQAMQSYNAELAAKVTDV 179
                                    556888999999*******************************999999988888877776665 PP

>> TetR_C_21  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       4.1   1.5e+04      95     107 ..       9      21 ..       4      23 .. 0.57
   2 ?   -0.1   0.0      0.27   9.6e+02      45      85 ..      65     104 ..      49     113 .. 0.74
   3 ?   14.7   0.1   6.8e-06     0.024      50      86 ..     135     171 ..     117     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.1
                      TetR_C_21  95 aeerarrraavve 107
                                    ++++ar ra v e
  gi|121635978|ref|YP_976201.1|   9 RADAARNRARVLE 21 
                                    4556666666655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                      TetR_C_21  45 leekvaairaaQraGtvdaswkpedlltlvlalasawaaap 85 
                                    +++++ +i +   +  ++++ + + l++++ +++  w a+ 
  gi|121635978|ref|YP_976201.1|  65 IADRMHRIIDK-GHALLKSKHPGDALFAFLRSMVLQWGATD 104
                                    55555555555.45678888888999999999999997765 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6.8e-06
                      TetR_C_21  50 aairaaQraGtvdaswkpedlltlvlalasawaaapa 86 
                                    + +raaQraGtv+++++  ++ tl+++  ++ + +++
  gi|121635978|ref|YP_976201.1| 135 DLLRAAQRAGTVRPDVDVLEVKTLLVGCQAMQSYNAE 171
                                    679***********************99999887777 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.3e-05     0.083      11      43 ..      13      51 ..       2      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                        DprA_WH 11 ddlerrvLaaLgpe......PvhvDqLvrrtglpaaevs 43
                                   +  ++rvL+   ++      +v+vD+++rr+g+ a++v 
  gi|121635978|ref|YP_976201.1| 13 ARNRARVLEVAYQTfaadglSVPVDEIARRAGVGAGTVY 51
                                   5566666666633333335689**************996 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.43       3      18 ..      37      52 ..      36      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                                   HHHHHHCTS-HHHHHH CS
                           LacI  3 kDVArlAGVSkaTVSr 18
                                   +++Ar+AGV + TV r
  gi|121635978|ref|YP_976201.1| 37 DEIARRAGVGAGTVYR 52
                                   69***********966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1325.75
//
Query:       gi|121635979|ref|YP_976202.1|  [L=303]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-29  100.8   0.8    8.3e-28   97.2   0.8    2.0  1  adh_short       short chain dehydrogenase
    5.1e-20   72.0   1.6    2.6e-19   69.7   1.6    1.9  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.8e-10   41.1   0.9    2.6e-10   40.5   0.9    1.3  1  KR              KR domain
     0.0022   17.5   0.1     0.0028   17.1   0.1    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
        0.3   11.0   3.6       0.46   10.3   3.6    1.5  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.8   2.3e-31   8.3e-28       2     190 ..      16     218 ..      15     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.3e-31
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79 
                                    ++++tGa  G+G ++a +la+ Ga+vv++ r+ +k +++a+ + e+  ga++   ++D+t+ ++v+a+ ++ +++++++d
  gi|121635979|ref|YP_976202.1|  16 TAVITGANTGLGFETAAALAAHGAHVVLAVRNLDKGKQAAARITEAtpGAEVELQELDLTSLASVRAAAAQLKSDHQRID 95 
                                    79*******************************************99********************************* PP

                                    EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGT.............SB-TTB CS
                      adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagk.............vpvagv 146
                                    +L+nNAG+  + +  +++++ +e  + +N  g f lt ++++ +l   + r+v++sSv  +              ++  v
  gi|121635979|ref|YP_976202.1|  96 LLINNAGV--MYTPRQTTADGFEMQFGTNHLGHFALTGLLIDRLLPVAGSRVVTISSVGHRiraaihfddlqweRRYRRV 173
                                    ********..34444556666************************************97651111122222222457789 PP

                                    HHHHHHHHHHHHHHHHHHHHHGGGTEEEE.EEEESSBSSHHHHHH CS
                      adh_short 147 aaYsAsKaavagltrslakelaptgirvn.avaPGlvdTdmakel 190
                                    aaY+ +K a   +t +l++ lap g ++  a +PG+ +T+++++ 
  gi|121635979|ref|YP_976202.1| 174 AAYGQAKLANLLFTYELQRRLAPGGTTIAvASHPGVSNTELVRNM 218
                                    *************************6665145788888*998775 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   1.6   7.4e-23   2.6e-19       1     182 [.      21     218 ..      21     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 7.4e-23
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT.SEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelg.aev..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                    Ga  g+G+++A ala++Ga+vvl+ +n ++ k+++++++e+++ aev   e+D t+ ++v+a++++++++++++D l+nn
  gi|121635979|ref|YP_976202.1|  21 GANTGLGFETAAALAAHGAHVVLAVRNLDKgKQAAARITEATPgAEVelQELDLTSLASVRAAAAQLKSDHQRIDLLINN 100
                                    8899***********************999999999**999984557779****************************** PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH..HCTSCCEEEEEEEGGGTSBST..........TTT...HH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp..lmkeggsivnlssvgaervvp..........nyn...ay 141
                                    ag++ +      +t+ ++f+  + +n  + f+l+  ++   l  +g+++v++ssvg ++  +           y    ay
  gi|121635979|ref|YP_976202.1| 101 AGVMYT----PRQTTADGFEMQFGTNHLGHFALTGLLIDrlLPVAGSRVVTISSVGHRIRAAihfddlqwerRYRrvaAY 176
                                    *****9....469**************************844456799*******8764322111111111112122266 PP

                                    HHHHHHHHHHHHHHHHHHGGGTEEEEEEE.E--BHCTGGGGS CS
                   adh_short_C2 142 gaaKaalealtrylAvelgpkgiRvNavs.pgpikTlaasgi 182
                                    g aK a   +t  l + l+p g ++ + s pg+ +T++++++
  gi|121635979|ref|YP_976202.1| 177 GQAKLANLLFTYELQRRLAPGGTTIAVAShPGVSNTELVRNM 218
                                    666666666666666666666665554444566666666555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.9   7.2e-14   2.6e-10       3      94 ..      17     106 ..      15     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 7.2e-14
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     +itG+  gLG e+a  la++ga h+vl  R+  + ++++a+i+e +  gaeve+ ++D+++ ++v+a+ +++k+++++i
  gi|121635979|ref|YP_976202.1|  17 AVITGANTGLGFETAAALAAHGA-HVVLAVRNLDKGKQAAARITEATP-GAEVELQELDLTSLASVRAAAAQLKSDHQRI 94 
                                    68********************8.799999996666777767766443.******************************* PP

                                    -EEEE------- CS
                             KR  83 kGvihaAgvlrd 94 
                                       i+ Agv+ +
  gi|121635979|ref|YP_976202.1|  95 DLLINNAGVMYT 106
                                    ********9864 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   7.9e-07    0.0028       2      81 ..      18     110 ..      17     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.9e-07
                                    EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHH....H.T-SE CS
                      Epimerase   2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl........elveldltdrsalerlfke....e.qpda 67 
                                    ++tGa+  +G  ++ al+++g + v+++ +l ++++ a++  +        el eldlt  ++++++ ++    + ++d 
  gi|121635979|ref|YP_976202.1|  18 VITGANTGLGFETAAALAAHGAHvVLAVRNLDKGKQAAARI-TeatpgaevELQELDLTSLASVRAAAAQlksdHqRIDL 96 
                                    79*******************66377777775555444433.3589**************99877766541111457888 PP

                                    EEE--S---HHHHH CS
                      Epimerase  68 vihlAavggvaass 81 
                                     i+ A+v   +++ 
  gi|121635979|ref|YP_976202.1|  97 LINNAGVMYTPRQT 110
                                    88888855444443 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.6   0.00013      0.46       1      59 [.      21      85 ..      21     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.......HHHCTTTCEEEE--TT-CCHHHHHHT CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekla.......eleaeeglevvegdvtdvedlaealk 59
                                   GA+ + G + ++ l+a+ g +v++ vRn +k +       e    +++e+ e+d+t+ +++++a +
  gi|121635979|ref|YP_976202.1| 21 GANTGLGFETAAALAAH-GAHVVLAVRNLDKGKqaaaritEATPGAEVELQELDLTSLASVRAAAA 85
                                   89999999999999999.59********55544112211133334788899**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2240.45
//
Query:       gi|121635980|ref|YP_976203.1|  [L=461]
Description: l-serine dehydratase sdaA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-96  323.0   6.3    1.5e-95  319.8   4.8    2.1  2  SDH_alpha  Serine dehydratase alpha chain
    3.5e-54  183.4   0.0    6.5e-54  182.5   0.0    1.5  1  SDH_beta   Serine dehydratase beta chain


Domain annotation for each model (and alignments):
>> SDH_alpha  Serine dehydratase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.012   1.1e+02      91     110 ..     149     168 ..     142     180 .. 0.79
   2 !  319.8   4.8   1.7e-99   1.5e-95       4     260 .]     187     451 ..     184     451 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.012
                      SDH_alpha  91 ggrvvtaptsGaaGilPavl 110
                                    gg +vt  tsG++G  P  +
  gi|121635980|ref|YP_976203.1| 149 GGFIVTEQTSGNSGQHPCSV 168
                                    688***********966543 PP

  == domain 2  score: 319.8 bits;  conditional E-value: 1.7e-99
                      SDH_alpha   4 leilelvteneeeaakrlsaeeidakleeiwevmdeaieeglsnkaiaeegllpgelkvkr.ayaalgkrll........ 74 
                                    ++i+e++++ne + + r +++e++a l ++++vm e+ ++++     a+egllpg+l+v+r a +  ++rl         
  gi|121635980|ref|YP_976203.1| 187 VSISEAALRNE-TCC-R-TENEVRAALLHLRDVMVECEQRSI-----AREGLLPGGLRVRRrA-KVWYDRLNaedptrkp 257
                                    68999999988.555.7.59******************9555.....68***********977.99*****555555555 PP

                      SDH_alpha  75 ....dklsaaAlavaemnaaggrvvtaptsGaaGilPavlvalleelkas.....eellraLllaaligilikrnasisg 145
                                        d+++++Alav+e+na+ggrvvtapt+GaaGi+Pavl+++++ ++a      + ++r+Ll+a++ig+l+k++asisg
  gi|121635980|ref|YP_976203.1| 258 efaeDWVNLVALAVNEENASGGRVVTAPTNGAAGIVPAVLHYAIHYTSAGagdpdDVTVRFLLTAGAIGSLFKERASISG 337
                                    55558*************************************888555559***9999********************** PP

                      SDH_alpha 146 AecGcqaevGvacamAAaglaallggspeqienAaeialehllGltCDpvaGlvkipCiernalgavkAvtaarlalagd 225
                                    Ae+Gcq+evG+a+amAAagla++lgg+p+q+enAaeia+eh lGltCDp+aGlv+ipCierna++a kA++aar+al+gd
  gi|121635980|ref|YP_976203.1| 338 AEVGCQGEVGSAAAMAAAGLAEILGGTPRQVENAAEIAMEHSLGLTCDPIAGLVQIPCIERNAISAGKAINAARMALRGD 417
                                    *******************************************************************************9 PP

                      SDH_alpha 226 ggegivsldevietmrntgkdmsekyketseggLa 260
                                    g  ++v+ld+vi+tmr tg+dm++kykets ggLa
  gi|121635980|ref|YP_976203.1| 418 G-IHRVTLDQVIDTMRATGADMHTKYKETSAGGLA 451
                                    9.9******************************97 PP

>> SDH_beta  Serine dehydratase beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.0   7.3e-58   6.5e-54       1     154 [.       4     156 ..       4     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 7.3e-58
                                    XXXXXXXXXXXXX-TTTHHHHHHHHHHHHHHHHTT-TTT--EEEEEEEHHHHHS-TTSSHHHHHHHHHTT--TTTS-GGG CS
                       SDH_beta   1 SvfdlfkiGiGPSSShTvgpmraaaaFveelkekelleevarirveLyGsLaatgkghgtdeAvllGLegeepetvdpda 80 
                                    Svfdlf+iGiGPSSShTvgpmraa++Fv +l+++++l++++ +rv+L+GsLaatg+ghgt++A+llGLeg++pet+ +++
  gi|121635980|ref|YP_976203.1|   4 SVFDLFTIGIGPSSSHTVGPMRAANQFVVALRRRGHLDDLEAMRVDLFGSLAATGAGHGTMSAILLGLEGCQPETITTEH 83 
                                    9******************************************************************************* PP

                                    HHHHHHHHHHHTEEEETTTEEEE--HHHHEEEETT---SS-SSEEEEEEE-TTS-EEEEEEEEEETTTEEEETT CS
                       SDH_beta  81 vesrleeieeekklklagekeiefdeeedivlekkkslplhsnglelsaldeegellleetyySiGGGfiveee 154
                                     e+rl+ei++++  +++g   ++++e+ di l+++ +lp+h+ng++++a   +g++l++ety+S+GGGfiv+e+
  gi|121635980|ref|YP_976203.1|  84 KERRLAEIAASGVTRIGGVIPVPLTER-DIDLHPDIVLPTHPNGMTFTAAGPHGRVLATETYFSVGGGFIVTEQ 156
                                    ******************989999887.*******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3115.28
//
Query:       gi|121635981|ref|YP_976204.1|  [L=425]
Description: serine hydroxymethyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.8e-159  529.2   0.0   5.7e-159  529.0   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    3.9e-09   36.1   0.0    7.5e-09   35.2   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
      1e-05   25.0   1.0    1.4e-05   24.6   1.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00013   21.3   0.5    0.00044   19.6   0.5    1.7  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.011   14.3   0.0      0.016   13.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.0   0.0  1.6e-162  5.7e-159       2     399 .]       9     390 ..       8     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 529.0 bits;  conditional E-value: 1.6e-162
                                    HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                           SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                    ++ dp++a +i+ e +rq++++e+iasen++  av++a+GsvltnkyaeGyPG+ryyGGcefvd ve+la+dr k lf++
  gi|121635981|ref|YP_976204.1|   9 TAFDPDIAALIDGELRRQESGLEMIASENYAPLAVMQAQGSVLTNKYAEGYPGRRYYGGCEFVDGVEQLAIDRVKALFGA 88 
                                    678***************************************************************************** PP

                                    STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHH CS
                           SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydel 161
                                    +    ++nvqp+sG+ an+a  +all+pgd+ilgl+la+GGhlthG+++++     s+kl++++ y+v+ke+ l+d+d++
  gi|121635981|ref|YP_976204.1|  89 E----YANVQPHSGATANAATMHALLNPGDTILGLSLAHGGHLTHGMRINF-----SGKLYHATAYEVSKEDYLVDMDAV 159
                                    *....******************************************9999.....************************ PP

                                    HHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EE CS
                           SHMT 162 ekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprggl 241
                                     + a++++Pk+i+aG say+r++d+ar+r iadev+a l+vdmah+aGlvaagv+psP+++a+vvt+tthktl Gprgg+
  gi|121635981|ref|YP_976204.1| 160 AEAARTHRPKMIIAGWSAYPRQLDFARFRAIADEVDAVLMVDMAHFAGLVAAGVHPSPVPHAHVVTSTTHKTLGGPRGGI 239
                                    ******************************************************************************** PP

                                    EEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHH.... CS
                           SHMT 242 illrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealk.... 317
                                    il++             +  ++kkinsavfPg+qGGPl hviaaka+a+k a++pef + q++ l+ a+ la  l+    
  gi|121635981|ref|YP_976204.1| 240 ILCN-------------DPAIAKKINSAVFPGQQGGPLGHVIAAKATAFKMAAQPEFAQRQQRCLDGARILAGRLTqpdv 306
                                    ****.............5789**************************************************998863333 PP

                                    .HTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT--HHHHHHH CS
                           SHMT 318 .ekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrgfkeedlekv 395
                                     e+g+++++gGtd hlvlvdlr+ +ldG++ae  l +v+it+n+n+vP+d + +++tsGlr+Gtpal++rgf+++d++ v
  gi|121635981|ref|YP_976204.1| 307 aERGIAVLTGGTDVHLVLVDLRDAELDGQQAEDRLAAVDITVNRNAVPFDpRPPMITSGLRIGTPALAARGFSHNDFRAV 386
                                    379***********************************************9***************************** PP

                                    HHHH CS
                           SHMT 396 akfi 399
                                    a++i
  gi|121635981|ref|YP_976204.1| 387 ADLI 390
                                    9986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   2.1e-12   7.5e-09      67     347 ..      89     369 ..      52     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.1e-12
                                    GGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THH.HHHHHHTTSE.EEEEEBEET..TTTEE-HHHHHHHHTTH CS
                  Aminotran_1_2  67 reaavvvgsGagaliealifllklnpgdeilvpdptyasy.knilrlsgge.vvryplyse..edfhldlealeealkea 142
                                      a+v+  sGa+a++++  +ll+  pgd il  ++ ++ + +++ r++ +  ++    y+   ed+ +d++a+ ea +++
  gi|121635981|ref|YP_976204.1|  89 EYANVQPHSGATANAATMHALLN--PGDTILGLSLAHGGHlTHGMRINFSGkLYHATAYEVskEDYLVDMDAVAEAARTH 166
                                    4459*************999995..************99834567766544344444443257************99995 PP

                                    HCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSST CS
                  Aminotran_1_2 143 pegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKa 222
                                         ++k+i+      P    ++ +  +++   a++  ++l+vD+a+ ++   +     +++   ++ + +++++  K 
  gi|121635981|ref|YP_976204.1| 167 -----RPKMIIAGWSAYP--RQLDFARFRAI---ADEVDAVLMVDMAHFAGLVAA----GVHPSPVPHAH-VVTSTTHKT 231
                                    .....6688887765555..57777889999...99999*********9998872....23555555555.777777899 PP

                                    TSSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHS..... CS
                  Aminotran_1_2 223 fGlaGeRvGyilg.naavvsqlrklsrpflsssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLael..... 295
                                    +G +  R G+il+ ++a+++ +++++ p+    +l +++aa + ++++ ++ e+ +++qr  + ++ l  +L+++     
  gi|121635981|ref|YP_976204.1| 232 LGGP--RGGIILCnDPAIAKKINSAVFPGQQGGPLGHVIAAKATAFKMAAQpEFAQRQQRCLDGARILAGRLTQPdvaer 309
                                    8855..58*****666999999999999999888888888888888887778********************99988898 PP

                                    TEEEECCSCSS.EEEEEETHH......CHHHHHHH..HHHTCTEEEEEGGGGTSTTEEEEE CS
                  Aminotran_1_2 296 glkvlasqsgm.flltdlsae......takelskk..LleevgvyvtpgtsftvpgrlRit 347
                                    g++vl+  + + ++l+dl+ +      +++ l+ +   +++ + + +  +++ +++ lRi 
  gi|121635981|ref|YP_976204.1| 310 GIAVLTGGTDVhLVLVDLRDAeldgqqAEDRLAAVdiTVNR-NAVPFDPRPPMITSGLRIG 369
                                    88888765322133334433346555544444444534444.4444444666665556665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.0     4e-09   1.4e-05      89     203 ..     144     260 ..      80     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-09
                                    EE-B-TTTSSB-GGGCGGG-.-TTEEEEEE.B-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEE CS
                DegT_DnrJ_EryC1  89 fvDvdpdtynidpaaieaai.tertkaIlp.VhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaav 166
                                      +v +++y +d +a+++a  t r k I++   +y +  d+++ +aia++ + +++ D Ah  G   +g +   +  a v
  gi|121635981|ref|YP_976204.1| 144 AYEVSKEDYLVDMDAVAEAArTHRPKMIIAgWSAYPRQLDFARFRAIADEVDAVLMVDMAHFAGLVAAGVHPSPVPHAHV 223
                                    568999*********977662666688886258999999******************************99999999999 PP

                                    EE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCE CS
                DegT_DnrJ_EryC1 167 fSFyptKnlttGeGGavvtndeelaekarvlrnhGlk 203
                                    +     K+l    GG+++ nd+++a+k++     G++
  gi|121635981|ref|YP_976204.1| 224 VTSTTHKTLGGPRGGIILCNDPAIAKKINSAVFPGQQ 260
                                    999*************************987777765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   1.2e-07   0.00044      39     279 ..      80     350 ..      60     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                                    HHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-...EBTTTBE-HHHH CS
                Beta_elim_lyase  39 davaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlk...nkeaGkmdlekl 114
                                    d+v++lfg+e+a +  ++G  An+  + +ll++g+ ++  + ah+   + g    ++g   +      +ke+  +d++++
  gi|121635981|ref|YP_976204.1|  80 DRVKALFGAEYAnVQPHSGATANAATMHALLNPGDTILGLSLAHGGHLTHGMRINFSGKLYHATAyevSKEDYLVDMDAV 159
                                    899*******6626789*********************************999999776433332133445577899999 PP

                                    HHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEE CS
                Beta_elim_lyase 115 eaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtm 194
                                    ++a +       ++k+i+           + +    ++ +aia++ +  l++D A fa   ++ g++++ +  ++ +vt 
  gi|121635981|ref|YP_976204.1| 160 AEAART-----HRPKMIIAGWSAY-----PRQ-LDFARFRAIADEVDAVLMVDMAHFAGL-VAAGVHPSPV-PHAHVVTS 226
                                    999998.....4678998766655.....333.4578899****************9975.5888888765.67889*** PP

                                    ESSSTT--SS-EEEEE-HH.....................................HHHHHHHH...HHHHT---SSTHH CS
                Beta_elim_lyase 195 slkKdllanvGgvlafrddel.................................edylaerveq...rkylggglrqagv 238
                                       K l+ + Gg+++ +d  +                                  ++ ++  +    ++ l+g+l+q +v
  gi|121635981|ref|YP_976204.1| 227 TTHKTLGGPRGGIILCNDPAIakkinsavfpgqqggplghviaakatafkmaaqPEFAQRQQRCldgARILAGRLTQPDV 306
                                    ******************96677777777777777777777777777777777744433333333346667777776666 PP

                                    HHH..HHHHHHHHS......STTHHHHHHHHHHHHHHHHHCT--EEE CS
                Beta_elim_lyase 239 laaleagiraleeg......laslerdhktaeqlaeklelvrlaipr 279
                                          gi +l+ g      l  l+++   ++q  ++l++v+++++r
  gi|121635981|ref|YP_976204.1| 307 AER---GIAVLTGGtdvhlvLVDLRDAELDGQQAEDRLAAVDITVNR 350
                                    544...44444444333333566666666666666677777766665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-06     0.016      60     224 ..      81     252 ..      74     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                                    HHHHHHT-SEEEEE.SSHHHHHHHHHHTTS-TTEEEEEESTSSHH..HH....HHHHHTHHHTTCEEEEEST.TSHHHHH CS
                Cys_Met_Meta_PP  60 riaaLeggeaalav.ssGmaAiaaailallkaGdeivvsddlYgg..tq....rllkkvlkklgievkfvdt.sdleele 131
                                    r+ aL g+e a +   sG +A aa++ all+ Gd i+  + ++gg  t+    ++  k+++ +  ev+  d   d+++++
  gi|121635981|ref|YP_976204.1|  81 RVKALFGAEYANVQpHSGATANAATMHALLNPGDTILGLSLAHGGhlTHgmriNFSGKLYHATAYEVSKEDYlVDMDAVA 160
                                    7888999988866526*********************9999998844331111344455555556666555444666666 PP

                                    HHCCT.TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT....-SEEEEETTTTTTCSSS- CS
                Cys_Met_Meta_PP 132 kaike.ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg....aDivvhSaTKylgGhsdv 206
                                    +a +  + k++     + p    +D+++  ++a +++++++vD +  ++l+   ++      a +v+  + K lgG    
  gi|121635981|ref|YP_976204.1| 161 EAARThRPKMIIAGWSAYPR--QLDFARFRAIADEVDAVLMVDMAHFAGLVAAGVHPSpvphAHVVTSTTHKTLGGPR-- 236
                                    65554499999999888886..59*******************99999988766655444458899999999999976.. PP

                                    -EEEEEESSCHHHHHHHH CS
                Cys_Met_Meta_PP 207 vaGvivvkgkeelkkelk 224
                                     +G+i++++ ++++k+++
  gi|121635981|ref|YP_976204.1| 237 -GGIILCND-PAIAKKIN 252
                                    .78888888.77777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3050.83
//
Query:       gi|121635982|ref|YP_976205.1|  [L=250]
Description: maturase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.4   0.0    1.3e-17   64.0   0.0    1.1  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   7.5e-22   1.3e-17       1     105 [.      86     189 ..      86     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 7.5e-22
                                    EE-TT..S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCG CS
                          RVT_1   1 ipKkg.pgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkka 79 
                                    ipK+g +g++R +++++v +++++++++  L++++e  +++ ++gfrp r  +d + +++ +   +++++++l+ D+k +
  gi|121635982|ref|YP_976205.1|  86 IPKPGgLGKVRRLGIPTVADRVVQAALKLVLEPIFETDFEPVSYGFRPARRAHDTIAEIHLF--GTQEYRWVLDADIKAC 163
                                    8*****************************************************99777777..88************** PP

                                    CCCSBB-GGGGGGG-EEET....... CS
                          RVT_1  80 Fdsvpleellrkltafkvptklinli 105
                                    Fd+++++ l+ ++ +   ++++++l+
  gi|121635982|ref|YP_976205.1| 164 FDRIDHADLMDRVRHRIKDKRVLRLV 189
                                    **********9988866665533332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1802.96
//
Query:       gi|121635983|ref|YP_976206.1|  [L=349]
Description: glutamine ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   22.5  10.2    0.00012   22.5  10.2    3.4  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.1    0.0067   1.2e+02       6      41 ..       5      40 ..       2     105 .. 0.82
   2 ?    0.3   3.4     0.056     1e+03      62      83 ..     229     250 ..     158     259 .. 0.67
   3 !   22.5  10.2   6.5e-09   0.00012       2      95 ..     259     341 ..     258     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0067
                           FtsX  6 ilralGmkkkqvlllllteillitlvalviGlglgl 41
                                    lr + ++k++++  +++ +l++++   + Gl++g+
  gi|121635983|ref|YP_976206.1|  5 ALRDMQWRKRRLVITIISTGLIFGMTLVLTGLANGF 40
                                   566666889999999999999999999999999976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.056
                           FtsX  62 isidlitvliiivlllllalla 83 
                                     si++ +vl+ iv +l++ +++
  gi|121635983|ref|YP_976206.1| 229 NSISIVAVLLWIVAVLIVGSVV 250
                                    3344444444444444444444 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 6.5e-09
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                    r +++++a+G  +++++ +l +++l+i+l+a+v+G++l+ ++a l           + + + +++ ++l++ v ++++ l
  gi|121635983|ref|YP_976206.1| 259 RDFAVFKAIGTPTRSIMAGLALQALVIALLAAVVGVVLAQVLAPL-----------FPMIVAVPVGAYLALPVAAIVIGL 327
                                    6799*******************************9999999999...........99********************** PP

                           FtsX  82 lagllsiskilkke 95 
                                    +a+++ + ++   +
  gi|121635983|ref|YP_976206.1| 328 FASVAGLKRVVTVD 341
                                    **999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2563.14
//
Query:       gi|121635984|ref|YP_976207.1|  [L=330]
Description: glutamine ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-32  113.0   0.0    2.9e-32  112.1   0.0    1.5  1  ABC_tran      ABC transporter
    3.4e-19   68.7   0.5    9.2e-19   67.3   0.2    1.8  2  cNMP_binding  Cyclic nucleotide-binding domain
    9.6e-09   35.5   0.2    0.00061   19.7   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.2e-08   33.8   0.0    6.9e-08   32.2   0.0    1.7  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00016   22.1   0.2    0.00036   21.0   0.2    1.6  1  AAA_16        AAA ATPase domain
    0.00073   19.0   0.0     0.0014   18.1   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0038   17.2   0.0      0.017   15.1   0.0    2.0  2  Urease_beta   Urease beta subunit
      0.004   17.6   0.2      0.016   15.6   0.2    2.0  1  AAA           ATPase family associated with various cellular 
     0.0044   16.6   2.5     0.0068   16.0   0.1    2.2  2  AAA_25        AAA domain
     0.0066   17.0   0.0     0.0099   16.4   0.0    1.2  1  AAA_23        AAA domain
     0.0069   16.1   0.1      0.015   15.0   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0074   16.6   1.5      0.061   13.6   1.5    2.1  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.018   15.0   0.1    1.2  1  Rad17         Rad17 P-loop domain
      0.014   15.3   0.0      0.029   14.3   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.017   14.8   0.2      0.077   12.7   0.2    1.9  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.022   14.7   1.1       0.21   11.5   0.3    2.1  2  NACHT         NACHT domain
      0.027   15.0   0.3        1.2    9.7   0.0    2.6  3  AAA_18        AAA domain
       0.12   12.4   0.2       0.27   11.2   0.2    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.21   11.7   0.3       0.21   11.7   0.3    2.1  2  AAA_33        AAA domain
       0.21   10.4   0.0       0.33    9.7   0.0    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
       0.24   11.1   0.0        8.2    6.0   0.0    2.0  2  AAA_15        AAA ATPase domain
       0.25   11.0   0.0       0.49   10.1   0.0    1.4  1  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   3.5e-35   2.9e-32       2     137 .]      24     172 ..      23     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 3.5e-35
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                    + ++l++ +g++v ++G++G+GK+tLl++l g l+p++G i++d+ d+++    +  +  r+++g+++q  +l p lt+ 
  gi|121635984|ref|YP_976207.1|  24 NGLNLDVAAGSLVMLLGPSGCGKTTLLSCLGGILRPKSGAIKFDEVDITTlqgaELANYRRNKVGIVFQAFNLVPSLTAV 103
                                    789***********************************************999777788899****************99 PP

                                    HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    en             +s++++e++l++++l e  +++       LSgGq+qrva+ara++ +p+l+l+DEpta
  gi|121635984|ref|YP_976207.1| 104 ENvmvplrsagmsrrASRRRAEELLARVNLAERMNHRP----GDLSGGQQQRVAVARAIALDPPLILADEPTA 172
                                    99***********9999999**********99666666....*****************************97 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.6   3.8e+03      28      42 ..     183     197 ..     164     204 .. 0.67
   2 !   67.3   0.2   1.1e-21   9.2e-19       2      84 ..     229     311 ..     228     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.6
                                    EEEEEEETTS.EEEE CS
                   cNMP_binding  28 vrvyrlsedgkevvl 42 
                                    +r+ r  +dg++vv+
  gi|121635984|ref|YP_976207.1| 183 LRLIRELADGERVVV 197
                                    678888889988443 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 1.1e-21
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    ++++agev+f+q + +d +y+v +Ge+++++  +dg e +++v gpGd+fGe+++l + pr+atv+A++d++ +  + ++
  gi|121635984|ref|YP_976207.1| 229 VHLQAGEVLFEQSTMGDLIYVVSEGEFEIVHELADGGEELVKVAGPGDYFGEIGVLFHLPRSATVRARSDATAVGYTVQA 308
                                    689*****************************************************99**************99999999 PP

                                    HHH CS
                   cNMP_binding  82 fle 84 
                                    f+e
  gi|121635984|ref|YP_976207.1| 309 FRE 311
                                    886 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     4e-05     0.033       2      25 ..      36      59 ..      35      88 .. 0.75
   2 !   19.7   0.0   7.5e-07   0.00061     207     299 ..     132     203 ..     110     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                    +l Gp g+GK++LL +l ++ r 
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCLGGILRP 59
                                   689***************998663 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.5e-07
                         AAA_21 207 eliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                    +l ++ ++r                  + +lS G+++  a++ a++ ++   +l+l DEp ++L+   ++++l+l++el+
  gi|121635984|ref|YP_976207.1| 132 NLAERMNHR------------------PGDLSGGQQQRVAVARAIALDP---PLILADEPTAHLDFIQVEEVLRLIRELA 190
                                    555555555..................5679999999989999999988...**************************** PP

                         AAA_21 287 rngaQviltTHSp 299
                                    ++   v+++TH+ 
  gi|121635984|ref|YP_976207.1| 191 DGERVVVVATHDS 203
                                    *77777*****96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   8.4e-11   6.9e-08      26     213 ..      35     217 ..      28     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.4e-11
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                    + +++Gp G+GK+ ll  +  +L  +s  +++ ++++    + +e a+  + +v i+f+  +   +  +   ++++ + +
  gi|121635984|ref|YP_976207.1|  35 LVMLLGPSGCGKTTLLSCLGGILRPKSG-AIKFDEVDITTLQGAELANYRRNKVGIVFQAFNLV-PSLTAVENVMVPLRS 112
                                    66899*************9999998777.99999998777777899999999999999988876.333344455555566 PP

                                    TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                     g s+ +  ++  +     +l e+++  +  LSgG+++ va+a  +A+      pl l De  a+LD+ +v++v +l++e
  gi|121635984|ref|YP_976207.1| 113 AGMSRRASRRRAEELLARVNLAERMNHRPGDLSGGQQQRVAVARAIALD----PPLILADEPTAHLDFIQVEEVLRLIRE 188
                                    666665555555566677778888888899*************999985....6************************** PP

                                    HCTTSEEE.EE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 186 ksknaQfi.vislreemlekadklvgvtk 213
                                      +   ++ v +++++ml  ad++v +t 
  gi|121635984|ref|YP_976207.1| 189 LADGERVVvVATHDSRMLPMADRVVELTP 217
                                    *99876651568999********999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   4.4e-07   0.00036      20      89 ..      31     112 ..      23     202 .. 0.52

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.4e-07
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd.........ggiflrgkcdqlesaipy.....salaqalareellrql 85 
                                    ++g  +lv+l G+sG+GK++l+ +l   l+ +         ++ +l+g    +     y      ++ qa+    l+  l
  gi|121635984|ref|YP_976207.1|  31 AAG--SLVMLLGPSGCGKTTLLSCLGGILRPKsgaikfdevDITTLQGAELAN-----YrrnkvGIVFQAF---NLVPSL 100
                                    455..79******************9877777433333333222222222222.....2333312244444...333333 PP

                         AAA_16  86 lde........a 89 
                                     +         +
  gi|121635984|ref|YP_976207.1| 101 TAVenvmvplrS 112
                                    333333444442 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0014      17      66 ..      28      77 ..      21      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                   Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66
                                   + +a g  ++l+Gp+G+GKt l ++l ++l p s +  ++   i++++g+
  gi|121635984|ref|YP_976207.1| 28 LDVAAGSLVMLLGPSGCGKTTLLSCLGGILRPKSGAIKFDEVDITTLQGA 77
                                   55556667999********************9999888888888877774 PP

>> Urease_beta  Urease beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.3   4.3e+03      55      67 ..      24      36 ..      21      51 .. 0.83
   2 !   15.1   0.0   2.1e-05     0.017      36      81 ..     172     217 ..     169     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.3
                                   TTEEE-SSTT-EE CS
                    Urease_beta 55 lGlrldipagtav 67
                                    Gl ld++ag  v
  gi|121635984|ref|YP_976207.1| 24 NGLNLDVAAGSLV 36
                                   589999*999866 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                                    TTS-GGGS-TTEES-HHHHTTEEE-SSTT-EEEE-TT-EEEEEEEE CS
                    Urease_beta  36 shyhflevnkaLefdRekalGlrldipagtavrfepgeekevelve 81 
                                    +h+ f++v + L++ Re a G r+ + a+   r+ p++ + vel +
  gi|121635984|ref|YP_976207.1| 172 AHLDFIQVEEVLRLIRELADGERVVVVATHDSRMLPMADRVVELTP 217
                                    7******************************************975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2     2e-05     0.016       1      51 [.      36      92 ..      36     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                   EEEESSTTSSHHHHHHHHHHHH....T.HEEEEEETTTCS.SSSTTHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel....g.vefleisgsell.skyvgesekkirelfk 51
                                   v+l Gp G+GKT+l + +   l    g ++f e++ ++l   ++   + +k+  +f+
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCLGGILrpksGaIKFDEVDITTLQgAELANYRRNKVGIVFQ 92
                                   689***************999855441455555555555433344445555555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   8.3e-06    0.0068      29      53 ..      30      53 ..      17      57 .. 0.84
   2 ?   -0.2   0.2      0.77   6.3e+02      93     106 ..     185     198 ..     101     224 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.3e-06
                         AAA_25 29 llpagelallaGapgtGKttlaldl 53
                                   + +ag+l++l G++g+GKttl++ l
  gi|121635984|ref|YP_976207.1| 30 V-AAGSLVMLLGPSGCGKTTLLSCL 53
                                   4.69*****************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.77
                         AAA_25  93 vgealrddarllvl 106
                                    + ++l+d +r+ v+
  gi|121635984|ref|YP_976207.1| 185 LIRELADGERVVVV 198
                                    22223333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0099       8      43 ..      21      57 ..      19      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                         AAA_23  8 rsfrdqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                   r++++ ++d     l+ + Gp G+GKTT+l ++  +L
  gi|121635984|ref|YP_976207.1| 21 RPINGLNLDVaAGSLVMLLGPSGCGKTTLLSCLGGIL 57
                                   56666667774346999***************98776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.8e-05     0.015      18      52 ..      29      64 ..      23      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                         AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak.kv 52
                                   ++   g  ++l GpsG GK+Tll  +  +L p++  +
  gi|121635984|ref|YP_976207.1| 29 DVAA-GsLVMLLGPSGCGKTTLLSCLGGILRPKSgAI 64
                                   5553.44899*************99999998887555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.5   7.4e-05     0.061       6     122 ..      34     194 ..      31     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfvtlpss 50 
                                    +++++ G+sG+GKTtll  l   l   + a +                                     +e v v l s 
  gi|121635984|ref|YP_976207.1|  34 SLVMLLGPSGCGKTTLLSCLGGILRPKSGAIKfdevdittlqgaelanyrrnkvgivfqafnlvpslTAVENVMVPLRSA 113
                                    678999*************9999976666666888999999999999988877777766666665555555556666666 PP

                         AAA_22  51 t....sskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr..s.eealeeLrsllnl 118
                                    +     s+  ++ell  ++l     +++  +l   + ++ + ara    ++l++ DE    l+  + ee+l+ +r+l++ 
  gi|121635984|ref|YP_976207.1| 114 GmsrrASRRRAEELLARVNLAERM-NHRPGDLSgGQQQRVAVARAIaldPPLILADEPTAhLDfiQvEEVLRLIRELAD- 191
                                    553333333334444444443333.666666665555555555555888899999995544766546888888888888. PP

                         AAA_22 119 srkg 122
                                        
  gi|121635984|ref|YP_976207.1| 192 -GER 194
                                    .444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.2e-05     0.018      43      71 ..      31      59 ..      23      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                          Rad17 43 rkkriLLisGPsGCgkstvvkvLskelgi 71
                                   +   ++++ GPsGCgk+t +  L  +l +
  gi|121635984|ref|YP_976207.1| 31 AAGSLVMLLGPSGCGKTTLLSCLGGILRP 59
                                   555689999***********999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.5e-05     0.029      98     127 ..      32      61 ..      20      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                    TTSEEEEECSTTSSHHHHHHHHCTT----- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelkt 127
                                    ++++++l+G+SG GK+tL+  l + l+ k 
  gi|121635984|ref|YP_976207.1|  32 AGSLVMLLGPSGCGKTTLLSCLGGILRPKS 61 
                                    56899**************99977665555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.5e-05     0.077       4      22 ..      36      54 ..      34      75 .. 0.83
   2 ?   -1.1   0.0       1.8   1.4e+03      88     121 ..      82     116 ..      72     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                      PduV-EutP  4 illiGkvgsGKttLtqalk 22
                                   ++l+G++g+GKttL   l 
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCLG 54
                                   8*************88775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                      PduV-EutP  88 fnkeviGiitk.idlaedeenieaveelLksaGae 121
                                     +++ +Gi+ +  +l+ +  ++e+v   L+saG++
  gi|121635984|ref|YP_976207.1|  82 YRRNKVGIVFQaFNLVPSLTAVENVMVPLRSAGMS 116
                                    56888999987358999999999999999999987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00026      0.21       2      18 ..      35      51 ..      34      58 .. 0.90
   2 ?    1.7   0.0      0.27   2.2e+02      38     127 ..     108     201 ..      99     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                   CEEEEC-TTTCHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlq 18
                                   lv+l G++G+GKTtLl 
  gi|121635984|ref|YP_976207.1| 35 LVMLLGPSGCGKTTLLS 51
                                   799************96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.27
                                    EEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.....CHHHHCCSCCCEE....EEEE-STT-SS-TCH......... CS
                          NACHT  38 Fflslrelsrsgnarsladllfsqlpepaapvse.....vwavllelperlL....lilDglDelvtdlgqkekqpvrtl 108
                                      l+++ +sr+   r+  +ll+++ +++ +++++     + + ++++++ +     lil  +De  ++l++ + ++v +l
  gi|121635984|ref|YP_976207.1| 108 VPLRSAGMSRRASRRRAEELLARVNLAERMNHRPgdlsgGQQQRVAVARAIAldppLIL--ADEPTAHLDFIQVEEVLRL 185
                                    56677778888888999999999999999999996666644444444444446777777..7888888888666666666 PP

                                    HHHHHCTTTTT--EEEEEE CS
                          NACHT 109 Lselirkkllpeasllltv 127
                                    ++el  +    ++ +++t 
  gi|121635984|ref|YP_976207.1| 186 IRELADG---ERVVVVATH 201
                                    6666555...444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0014       1.2       1      18 [.      36      53 ..      36      95 .. 0.88
   2 ?   -1.7   0.0         5   4.1e+03     103     120 ..     124     141 ..     121     159 .. 0.80
   3 ?    2.8   0.0       0.2   1.7e+02      49      94 ..     171     213 ..     129     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                         AAA_18  1 IlltGtpGvGKttlakeL 18
                                   ++l G++G+GKttl   L
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCL 53
                                   789**********98765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5
                         AAA_18 103 peelleRlekRgyeeaki 120
                                     eell R++  +++++++
  gi|121635984|ref|YP_976207.1| 124 AEELLARVNLAERMNHRP 141
                                    588999998888888876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                         AAA_18  49 skrldedkldklldaleenssaleegknlvidghlaeleseaakdi 94 
                                    +  ld  +++++l++++e ++    + ++v+  h + ++++a++  
  gi|121635984|ref|YP_976207.1| 171 TAHLDFIQVEEVLRLIRELAD---GERVVVVATHDSRMLPMADRVV 213
                                    566788889999999999875...566669********99988743 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00033      0.27       2      19 ..      36      53 ..      35      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                                   EEEE--SSSSHHHHHHHG CS
                          AAA_5  2 vlLvGppGtgKselaerl 19
                                   v+L+Gp+G+gK++l   l
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCL 53
                                   89***********98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00026      0.21       1      17 [.      35      51 ..      35      61 .. 0.91
   2 ?   -1.1   0.1       2.4     2e+03      86     121 ..     104     139 ..      69     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                         AAA_33  1 lvllvGlpGsGKstlae 17
                                   lv+l G++G+GK+tl+ 
  gi|121635984|ref|YP_976207.1| 35 LVMLLGPSGCGKTTLLS 51
                                   89************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                         AAA_33  86 arflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                    ++++  +r +g+ +r+   ++ e +++ +la+R+++
  gi|121635984|ref|YP_976207.1| 104 ENVMVPLRSAGMSRRASRRRAEELLARVNLAERMNH 139
                                    444445555555555555555555555566666555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0004      0.33      24      54 ..      32      62 ..      27      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                           DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkG 54
                                   +g  v++lG +g+Gkttl++ l G+  +k G
  gi|121635984|ref|YP_976207.1| 32 AGSLVMLLGPSGCGKTTLLSCLGGILRPKSG 62
                                   67789********************999988 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.01       8.2      25      62 ..      35      68 ..      22      94 .. 0.74
   2 ?    3.1   0.0      0.08        66     324     368 ..     162     205 ..     149     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                         AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiek 62
                                   l  l G+ ++GK+++l  l  +l  k    + +ik+++
  gi|121635984|ref|YP_976207.1| 35 LVMLLGPSGCGKTTLLSCLGGILRPK----SGAIKFDE 68
                                   88999*************99988888....33333333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.08
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    + ++l +EP ahL   + +++ +l++ela+ ++  v++ TH + +
  gi|121635984|ref|YP_976207.1| 162 PPLILADEPTAHLDFIQVEEVLRLIRELADGER-VVVVATHDSRM 205
                                    668999*******7777777789*********9.9******9877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0006      0.49       5      22 ..      36      53 ..      33      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   +++ Gpsg GKTtl++ l
  gi|121635984|ref|YP_976207.1| 36 VMLLGPSGCGKTTLLSCL 53
                                   789***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2519.12
//
Query:       gi|121635985|ref|YP_976208.1|  [L=411]
Description: hypothetical protein BCG_0105 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-52  177.0   0.1    7.7e-52  176.7   0.1    1.0  1  Amidohydro_1  Amidohydrolase family
    5.3e-21   75.6  14.1    1.9e-16   60.6   9.0    2.2  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.056   12.9   0.0    1.4  1  PTE           Phosphotriesterase family
      0.052   13.1   1.8       0.11   12.1   1.8    1.5  1  HMGL-like     HMGL-like


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.7   0.1   1.7e-55   7.7e-52       1     344 []      65     398 ..      65     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 1.7e-55
                                    EEEE-EEEEEEECETTECSSS.GHHHHH.STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHT.SSSEE CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.tledwl.vppetaaealesgiktalksGtttvadmgattstgiealleaaee.lplgl 77 
                                    ++lPGl+DaH Hl++++   + + ed+  +p+  +   +++++++al+sG+tt++d g  +++++ al+e++++ + +g+
  gi|121635985|ref|YP_976208.1|  65 TLLPGLVDAHAHLCWDP---DgRPEDLAgDPHAVLVGRARRHAAAALRSGITTIRDLGD-RDYAALALREEYRQkTTVGP 140
                                    589***********995...256778779******************************.789************99*** PP

                                    EEEEESSEGGS.............GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHH CS
                   Amidohydro_1  78 rilggkvsldr.............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkr 144
                                    ++++++++l+r             +++e   a+ e+ ++g a++ik++a+g++ ++  ++++p+++  +l++++ +a++ 
  gi|121635985|ref|YP_976208.1| 141 ELVVSGPPLTRsgghcwflggvadSVEELVDAVQERAARG-ADWIKVMATGGFVTTASDPWQPQYGSGQLAAVVAAAEQV 219
                                    ***********************76667677777777777.8************************************** PP

                                    TTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHH CS
                   Amidohydro_1 145 dlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsi 224
                                    +lpv++Ha+ t g+  +a+aa++++ieh+t+l+    ++ +d++ +i+a+gv++ +t + ++   + e+ v        +
  gi|121635985|ref|YP_976208.1| 220 GLPVTAHAHATAGIA-AAVAAGVDGIEHCTFLSEGSAAASPDVVEAIVAQGVWCGMT-IPRVYPEMPENLV-------AV 290
                                    ********8888886.***************************************88.3333333333344.......48 PP

                                    SEHHHHHHHHHHHHTSCEEEEEE.CTTSSCCGGHHHH.HHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTT CS
                   Amidohydro_1 225 lrsgrealrkaldeGvkvglgtD.gaasgnslnllee.lrlalklqrgllyedeegglslkealrmaTingAkalglddk 302
                                    +++g++++r+++d+G++v+l+tD g+a g+  ++l + l ++            ++g++  e+l+ aT  +A ++gl ++
  gi|121635985|ref|YP_976208.1| 291 VQDGWRNIRRLIDAGARVALSTDaGVAPGRRHDVLPDdLVYLS-----------RHGFTSTEVLTGATAAAAASCGLGHR 359
                                    9**********************55577777788777699999...........999*********************** PP

                                    SSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                   Amidohydro_1 303 vGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                    +G+i++G+dADl +v+     + +gl +   vk v+ +G++v
  gi|121635985|ref|YP_976208.1| 360 KGRIAPGYDADLLAVAAGVDHDPAGLCD---VKAVWRSGTQV 398
                                    ***************8866677777755...77777777665 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   3.2e-07    0.0015       2      43 ..      58      90 ..      57     102 .. 0.87
   2 !   60.6   9.0   4.3e-20   1.9e-16     161     472 ..      99     398 ..      86     399 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-07
                   Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtsleg 43
                                    +D+   ++lPG+vD+H+H         l+++pd r+ +l+g
  gi|121635985|ref|YP_976208.1| 58 LVDLGESTLLPGLVDAHAH---------LCWDPDGRPEDLAG 90
                                   59*****************.........78899988887765 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 4.3e-20
                   Amidohydro_3 161 avaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi...............ikelldaaerlglplspg 225
                                     +++ +aa+ + Git++  +  ++   ++l++  e+ ++++   +++                ++++d++e+l   +   
  gi|121635985|ref|YP_976208.1|  99 RARRHAAAALRSGITTI--RDLGDRDYAALALREEYRQKTTVGPELVvsgppltrsgghcwfLGGVADSVEELVDAVQ-E 175
                                    56778889999999999..55555566667777777777754444448999999999999999999999999999999.7 PP

                   Amidohydro_3 226 seeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngn 305
                                    +++  ++ +k+ a    g+ + ++++p    +p + +++la++vaaa ++gl+v  ha+ +a ++        aa + g+
  gi|121635985|ref|YP_976208.1| 176 RAARGADWIKVMAT---GGFVTTASDP---WQPQYGSGQLAAVVAAAEQVGLPVTAHAHATAGIA--------AAVAAGV 241
                                    78888888999888...8999999998...559999*****************************........3345666 PP

                   Amidohydro_3 306 qdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgperargs........tpvkellnagvkvalgs 374
                                        ++eh++++   +++   +v +  va gv +++++       r+ pe+++++         ++++l++ag +val++
  gi|121635985|ref|YP_976208.1| 242 D---GIEHCTFLsegSAAASPDVVEAIVAQGVWCGMTI------PRVYPEMPENLvavvqdgwRNIRRLIDAGARVALST 312
                                    6...79******99977777777777777777777777......6666777777777788888***************** PP

                   Amidohydro_3 375 DapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdp 454
                                    Da v+p  ++  + + +         v+  ++ ++ +e+l   T+ +A+ +gl +rkG++++G+dADl    a+ +d dp
  gi|121635985|ref|YP_976208.1| 313 DAGVAPGRRHDVLPDDL---------VYLSRHGFTSTEVLTGATAAAAASCGLGHRKGRIAPGYDADLLAV-AAGVDHDP 382
                                    *7777776666655444.........5677889************************************99.69999999 PP

                   Amidohydro_3 455 pelaearvrltvvdGrvv 472
                                    + l +  v++++ +G +v
  gi|121635985|ref|YP_976208.1| 383 AGLCD--VKAVWRSGTQV 398
                                    97777..99999999877 PP

>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.056      99     248 ..     163     314 ..     158     344 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                    CS-CHCHHHHHHHHHHT-STTTS--E..EEEEEEE-CTBS-HHHHHHHHHHHHHHHHH---EEEEEGCCTTCHHHHHHHH CS
                            PTE  99 arsveeltdvlvdeiehGidgteika..GiikeigtsgkltpseekvleavaqahkqtGaPisihtsaslragleqlril 176
                                    a+sveel d + +   +G+d  ++ a  G ++ +++ ++   +  + l av  a +q+G P++ h++a+ +     ++  
  gi|121635985|ref|YP_976208.1| 163 ADSVEELVDAVQERAARGADWIKVMAtgGFVTTASDPWQPQYGSGQ-LAAVVAAAEQVGLPVTAHAHATAG-----IAAA 236
                                    789*******99999*****99887655888888888887666665.788888999***********9984.....3334 PP

                                    HHTT--.GGGEE.ETTGGCS--HHHHHHHHHTT-EEEE--T......T-TTTS-HHHHHHHHHHHHHTT-GGGEEE---- CS
                            PTE 177 qeeGvD.lsrvv.vghldtktdvkellelidlGaYleyDlf......gvdlispdekRirivhalvdrGyedrillshDi 248
                                     ++GvD + + + ++        + ++ +++ G + ++           +l+   ++  r + +l+d G   r+ ls D+
  gi|121635985|ref|YP_976208.1| 237 VAAGVDgIEHCTfLSEGSAAASPDVVEAIVAQGVWCGMTIPrvypemPENLVAVVQDGWRNIRRLIDAGA--RVALSTDA 314
                                    4566664444331344445566666666777777766654333444455556666666677777777663..66666665 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   2.4e-05      0.11     144     236 ..     165     261 ..     161     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                                    -HHHHHHHHHHHHHHT-SEEEEEETTS---.......HHHHHHHHHHHHHHS-..GGGEEEEEB-TTS-HHHHHHHHHHT CS
                      HMGL-like 144 dleflaevveaaeeaGatriniaDtvGvlt.......Pneaaelisalkervk.dkvilsvHcHndlGlAvantlaAvea 215
                                    ++e+l++ v++ ++ Ga+ i++ +t G++t       P+    +++a+++  +   +++  H+H++ G+A     aAv a
  gi|121635985|ref|YP_976208.1| 165 SVEELVDAVQERAARGADWIKVMATGGFVTtasdpwqPQYGSGQLAAVVAAAEqVGLPVTAHAHATAGIA-----AAVAA 239
                                    578889999999999************9864444333666667777777777755578888999888877.....68999 PP

                                    T--EEEEB.TTS--SSBBB-BH CS
                      HMGL-like 216 Gadrvdgt.vnGlGeraGnaal 236
                                    G+d ++ +  ++ G +a  +++
  gi|121635985|ref|YP_976208.1| 240 GVDGIEHCtFLSEGSAAASPDV 261
                                    *****96515566655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2834.62
//
Query:       gi|121635986|ref|YP_976209.1|  [L=390]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-32  112.9   0.0    2.2e-32  112.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.078   12.6   0.4       0.14   11.7   0.4    1.4  1  DisA_N           DisA bacterial checkpoint controller nucleot
      0.088   12.7   0.0        7.6    6.5   0.0    2.5  2  NIR_SIR_ferr     Nitrite/Sulfite reductase ferredoxin-like ha
       0.18   11.1   0.0       0.22   10.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   4.9e-36   2.2e-32      79     363 .]      98     381 ..      40     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 4.9e-36
                                    HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET..TTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                  Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse..edfhldlealeealkeapegnkktkvilves 156
                                     + ++++fl++  p++ + +p p y ++ ++l   g + v++p+ ++    + ldl+al++a  +          +++++
  gi|121635986|ref|YP_976209.1|  98 GMEVVVEFLTR--PESPVALPVPAYMPFFDVLHVTGRQRVEVPMVQQdsGRYLLDLDALQAAFVR------GAGSVIICN 169
                                    56678899999..******************************99884466789*******9999......6689***** PP

                                    S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEE CS
                  Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyil 234
                                    p+NP Gt++t++el++++d+a +++++++ De+ a  v+gs   va  a v+e+ +  ++++ s sK ++l+G+ ++ ++
  gi|121635986|ref|YP_976209.1| 170 PNNPLGTAFTEAELRAIVDIAARHGARVIADEIWAPVVYGSRH-VA-AASVSEAAAevVVTLVSASKGWNLPGLMCAQVI 247
                                    ****************************************764.44.566666655668**************9999998 PP

                                    EEH....HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEE CS
                  Aminotran_1_2 235 gna....avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmfl 308
                                     +     +  +   ++  ++  s+++ +a  aa ++ +    +l+e    l ++r++l  +L el  g++v a+++++++
  gi|121635986|ref|YP_976209.1| 248 LSNrrdaHDWDR-INMLHRMGASTVGIRANIAAYHHGES---WLDELLPYLRANRDHLARALPELapGVEVNAPDGTYLS 323
                                    854354211222.2233334449*************996...************************************** PP

                                    EEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 309 ltdlsae.takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelveal 363
                                    +++++a+   +e ++ Ll + +v+++pg +f++   +g+ R+++ ++t++ l++++ea+
  gi|121635986|ref|YP_976209.1| 324 WVGFRALaLPSEPAEYLLSKAKVALSPGIPFGAavgSGFARLNF-ATTRAILDRAIEAI 381
                                    *******767777888****************************.************98 PP

>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   3.1e-05      0.14      82     108 ..     207     234 ..     187     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                    T-SHHHHHHHHHHHHSSSEEEE.E-TTT CS
                         DisA_N  82 elGtRHraAlgiseetdalviv.VSeet 108
                                     +G+RH aA+++se   ++v++ VS ++
  gi|121635986|ref|YP_976209.1| 207 VYGSRHVAAASVSEAAAEVVVTlVSASK 234
                                    58************99777765266665 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.016        72      41      57 ..     127     143 ..     124     148 .. 0.89
   2 ?    6.5   0.0    0.0017       7.6      16      37 ..     172     194 ..     162     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                   NIR_SIR_ferr  41 irlTtrQnlqlhgvpee 57 
                                    +++T rQ ++++ v+++
  gi|121635986|ref|YP_976209.1| 127 LHVTGRQRVEVPMVQQD 143
                                    89*********999876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                   NIR_SIR_ferr  16 vpnGri.taeqlraladiaekyg 37 
                                     p G   t ++lra+ dia ++g
  gi|121635986|ref|YP_976209.1| 172 NPLGTAfTEAELRAIVDIAARHG 194
                                    5678888999************9 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.22     109     167 ..     149     200 ..     100     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                                    E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    +dl++l+aa  + ga     + +++ + nn   G++ + +elr++ +ia ++g +++ D
  gi|121635986|ref|YP_976209.1| 149 LDLDALQAAFVR-GA-----GSVIICNPNNP-LGTAFTEAELRAIVDIAARHGARVIAD 200
                                    788888888877.34.....67777788884.7***********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2760.91
//
Query:       gi|121635987|ref|YP_976210.1|  [L=129]
Description: hypothetical protein BCG_0107c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 982.52
//
Query:       gi|121635988|ref|YP_976211.1|  [L=276]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-14   53.7   0.0    3.7e-14   53.0   0.0    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
      1e-12   49.2   9.3    1.2e-12   49.0   9.3    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.3e-06   27.8   0.2    3.6e-06   26.4   0.2    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00044   19.0   0.1    0.00072   18.3   0.1    1.2  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.015   15.0   0.1        2.4    7.8   0.0    2.3  2  PGAP1          PGAP1-like protein
       0.19   10.2   0.1       0.29    9.7   0.1    1.2  1  ADP_PFK_GK     ADP-specific Phosphofructokinase/Glucokinase c


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.2e-17   3.7e-14       2     252 ..      23     257 ..      22     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEET CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhS 81 
                                    ++v++hG+ +++ +w++  + + La +g ++i++ ++  ++ +p       d ++  va ++  +l+al ++ ++lvG +
  gi|121635988|ref|YP_976211.1|  23 PVVFVHGYMMGGQLWRR--VSERLAGRGLRCIAPTWPLGAHPKPLRPG--ADQTIGGVAGIVADVLAALELKDVVLVGND 98 
                                    8****************..******************99999999988..999*************************** PP

                                    HHHHHHHHHHHHHGGGEEEEEEESE..CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHH CS
                  Abhydrolase_1  82 mGGmialayaaeyperVkalvllga..idpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvd 159
                                     GG +   +a  yper  alvl++    + ++ +i      a++  + f+       +   +p + +++ a +++h++ +
  gi|121635988|ref|YP_976211.1|  99 TGGVVTQLVAVHYPERLGALVLTSCdaFEHFPPPILKPVILAAKSATLFRA----AIQVMRAPAARNRAYAGLSHHNIDH 174
                                    *************************87777777777777777777777665....4556666666677777777777766 PP

                                    HHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS CS
                  Abhydrolase_1 160 alkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpk 239
                                           ++ +p  + +    + ++ ++s+ +  tt+ a++l ++++      p+l+ ++++D  +  +++ +la+ +p+
  gi|121635988|ref|YP_976211.1| 175 L----TRAWVRPALSNPAIAEDLRQLSLSLRTEVTTAVAARLPEFDK------PALIAWSADDVFFALENGQRLAATIPR 244
                                    4....4555555666778999999***********************......*************************** PP

                                    EEEEEEETCSSSH CS
                  Abhydrolase_1 240 krlvvisdagHla 252
                                    +r +vi++a  ++
  gi|121635988|ref|YP_976211.1| 245 ARFEVIEGARTFS 257
                                    *****99987665 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   9.3   3.9e-16   1.2e-12       1     219 [.      24     267 ..      24     268 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.9e-16
                                    EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--T..TSTS-....GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlp..GhGrs....dpppldledladl.aalldelaagggpvvlvGH 72 
                                    v+++HG  +++  W+  ++ ++la++  +++ap +p   h  +    ++++ +   +a + a++l++l    ++vvlvG+
  gi|121635988|ref|YP_976211.1|  24 VVFVHGYMMGGQLWR--RVSERLAGRgLRCIAPTWPlgAH--PkplrPGADQTIGGVAGIvADVLAALE--LKDVVLVGN 97 
                                    8*****888888998..9977777777888******5444..222335555777668888888999996..9******** PP

                                    TCHHHHHHH.HHHCC..EE..EEES-..........----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCC CS
                  Abhydrolase_6  73 SlGGalala.aaplalvvg..vlldp........pptalpagllaaalelllallallrllawlsreplprlfladedad 141
                                    + GG++ ++ a++++ + g  vl  +        pp   p  l+a  ++l++a++++ r++a ++r+ ++ l +++ d  
  gi|121635988|ref|YP_976211.1|  98 DTGGVVTQLvAVHYPERLGalVLT-ScdafehfpPPILKPVILAAKSATLFRAAIQVMRAPAARNRA-YAGLSHHNID-- 173
                                    *****9999666677667754444.358899985444555555666666666666655554444332.2224444333.. PP

                                    CCHCHCCCGHH..............HHCCHHCHTTCCHHTT-TTGCEEECTT-C....HHHHCHHCCCH.STTEEETCE. CS
                  Abhydrolase_6 142 aawrarlarla..............allaglgllpaaawadlpvpllvlggeDp....lvprllerlla.qagarlpvvl 202
                                       ra++++++               l++ + +  aa+++    p l+ +++D+    l     +rl+a +++ar+ +v+
  gi|121635988|ref|YP_976211.1| 174 HLTRAWVRPALsnpaiaedlrqlslSLRTEVTTAVAARLPEFDKPALIAWSADDvffaLEN--GQRLAAtIPRARF-EVI 250
                                    3333333333322233322221112333344455688888888888888999998775333..33444488*****.*** PP

                                    ..SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 203 pgaGHlphleepdevae 219
                                    +ga  + + ++pd++a+
  gi|121635988|ref|YP_976211.1| 251 EGARTFSMVDSPDRLAD 267
                                    ***************97 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   1.2e-09   3.6e-06       7     230 ..      24     253 ..      18     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.2e-09
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    vv+vHG+    +   ++ e+La +G  ++a  +   G ++ k    p  d+ +  +a +v  v +  + + ++l+G  +G
  gi|121635988|ref|YP_976211.1|  24 VVFVHGYMMGGQLWRRVSERLAGRGLRCIAPTWP-LGAHP-KPL-RPGADQTIGGVAGIVADVLAALELKDVVLVGNDTG 100
                                    8999***999999999*********999999887.67774.222.35677777777777777777778889********* PP

                    Hydrolase_4  87 GliallyllrypdkvaglilsaP.alkikaklkappllklllkllgkllpklqv.............snnlkadslsrdp 152
                                    G++++l++ +yp+++ +l+l++  a++  ++ ++ + + l++k +  +   +qv              ++++ d l+r  
  gi|121635988|ref|YP_976211.1| 101 GVVTQLVAVHYPERLGALVLTSCdAFEHFPP-PILKPVILAAKSATLFRAAIQVmrapaarnrayagLSHHNIDHLTR-- 177
                                    ********************88625554433.3444455567777777777777888887555444433344444444.. PP

                    Hydrolase_4 153 evvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypgl 230
                                    + v+   ++p + ++++   l   ++++ ++ +r ++++ P l+  +++D     e+ ++l+++++  + ++++++g+
  gi|121635988|ref|YP_976211.1| 178 AWVRPALSNPAIAEDLRQLSLSLRTEVTTAVAARLPEFDKPALIAWSADDVFFALENGQRLAATIP--RARFEVIEGA 253
                                    334445566777677776667777889999999999999***************************..5888888887 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.4e-07   0.00072      81     134 ..      72     125 ..      65     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-07
                                    -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES--- CS
                            Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinits 134
                                    ++ ++a  +  vl  ++lk v+ +G   G  +  + a+++per+ +lvL ++++
  gi|121635988|ref|YP_976211.1|  72 TIGGVAGIVADVLAALELKDVVLVGNDTGGVVTQLVAVHYPERLGALVLTSCDA 125
                                    6678888999****************************************9985 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00082       2.4       3      25 ..      20      42 ..      18      48 .. 0.87
   2 ?    5.0   0.0    0.0059        18      90     111 ..      89     110 ..      80     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00082
                          PGAP1  3 sGipVlFvpGnagsykqvrslAs 25
                                   +G+pV+Fv+G ++  + +r +++
  gi|121635988|ref|YP_976211.1| 20 TGRPVVFVHGYMMGGQLWRRVSE 42
                                   79***********9999998776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0059
                          PGAP1  90 ptsviliGHSmGGivaraaltl 111
                                     ++v+l+G   GG+v ++++++
  gi|121635988|ref|YP_976211.1|  89 LKDVVLVGNDTGGVVTQLVAVH 110
                                    579**************99876 PP

>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   9.6e-05      0.29      83     109 ..      69      96 ..      65     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.6e-05
                                    SEEEEESHHHHHHHHHCCTT-.EEEEE- CS
                     ADP_PFK_GK  83 aelrmGGnagimanrlakega.kvllga 109
                                    a++++GG agi+a +la++++ +v+l++
  gi|121635988|ref|YP_976211.1|  69 ADQTIGGVAGIVADVLAALELkDVVLVG 96 
                                    6789*****************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2017.48
//
Query:       gi|121635989|ref|YP_976212.1|  [L=201]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-15   56.4   0.1    4.4e-15   55.2   0.1    1.7  1  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   2.4e-19   4.4e-15       1      46 [.      19      64 ..      19      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.4e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   ++ +Ar+l++ rGy++++++eIA +AGv++ga+Y++F++K++L++ 
  gi|121635989|ref|YP_976212.1| 19 LITGARKLWGLRGYAEVGTPEIATEAGVTRGAMYHQFADKAALFRD 64
                                   6889****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1553.31
//
Query:       gi|121635990|ref|YP_976213.1|  [L=197]
Description: hypothetical protein BCG_0110c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-08   34.0   2.7    4.7e-08   33.3   2.7    1.4  1  AbiEii         Nucleotidyl transferase AbiEii toxin, Type IV 
    0.00088   19.4   0.1     0.0015   18.7   0.1    1.4  1  Gasdermin_C    Gasdermin PUB domain
  ------ inclusion threshold ------
       0.09   13.3   1.3         11    6.7   0.0    2.2  2  Hrs_helical    Hepatocyte growth factor-regulated tyrosine ki
       0.17   12.5   1.5       0.43   11.3   0.1    2.2  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
        1.2    9.1   9.4      0.038   14.0   2.4    2.0  2  DUF2514        Protein of unknown function (DUF2514)


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   2.7   1.3e-11   4.7e-08       9     190 ..      16     182 ..       9     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.3e-11
                         AbiEii   9 saladklvFkGGTaLslayglipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigegedyeglrl 88 
                                      l++++++ GG+a s +    pRf++D+D+++      +  +a + +++++  ++ + +  v+++a +    +   +rl
  gi|121635990|ref|YP_976213.1|  16 TGLRQRWALVGGFAVSARSE--PRFTRDVDIVVA----VANDDAAESLVRQLLTQQYHLLASVEQDAAR----RLAAVRL 85 
                                    57899***********8777..*********985....4445555566666666666655555544433....4555555 PP

                         AbiEii  89 rypaefggyarqkikieigfreavppaerreippyleelggpafevpvysleellaeKllalldrgrdrsraRDlyDlal 168
                                      +a+ +   +  + +++ f +   ++e  e  + +e l  p+   pv + + l+a Klla    ++d +r++D  Dl +
  gi|121635990|ref|YP_976213.1|  86 --GAT-A-DTAANVVVDLLFASCGIEPEIAEAAEEIEIL--PDLVAPVATTAHLIAMKLLA----RDDDRRPQDRSDLRA 155
                                    ..554.3.3444777888888777666666666666666..999*****************....569999********* PP

                         AbiEii 169 Lle....aeldaea.laeallaylasr 190
                                    L +    +++ +++   e++ ++  +r
  gi|121635990|ref|YP_976213.1| 156 LVDaaspQDIQDARkAIELITLRGFHR 182
                                    ***985544444442335555544444 PP

>> Gasdermin_C  Gasdermin PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   4.2e-07    0.0015     109     169 ..      55     109 ..      53     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.2e-07
                                    HHCCTTCCHHHHHHHHHHHHHTSSTTS-EEEB--GGGGTSS-STT..SHHHHHHHCCT-EE- CS
                    Gasdermin_C 109 kclelqvlpalleLvesllednvlyqeespfsLkpelLaplkdeer.aitqrLlescglele 169
                                    ++l  q+l ++ +L+ s+ +d ++        L   +L+  +d+    ++  L++scg+e e
  gi|121635990|ref|YP_976213.1|  55 ESLVRQLLTQQYHLLASVEQDAAR-------RLAAVRLGATADTAAnVVVDLLFASCGIEPE 109
                                    688899******************.......***************7788889******998 PP

>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.003        11      26      61 ..      47      82 ..      37      92 .. 0.89
   2 ?    5.4   0.3    0.0074        27      54      87 ..     146     183 ..     127     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.003
                    Hrs_helical 26 sianDsavqslFqkltamhsqllkriqeqeekraey 61
                                    +anD+a +sl  +l + + +ll+ +++   +r   
  gi|121635990|ref|YP_976213.1| 47 AVANDDAAESLVRQLLTQQYHLLASVEQDAARRLAA 82
                                   69**************************99999765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0074
                    Hrs_helical  54 qeekraeyeslqdkl..aqikeareald..alreehke 87 
                                    + ++r+++ +l d    + i++ar+a++  +lr  h++
  gi|121635990|ref|YP_976213.1| 146 RPQDRSDLRALVDAAspQDIQDARKAIEliTLRGFHRD 183
                                    3466788888888763368*******984456777765 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.43      50      87 ..      34      69 ..       4      82 .. 0.81
   2 ?    0.2   0.2      0.31   1.1e+03      59      72 ..     152     165 ..      72     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                   -HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE CS
                  NAD_binding_3 50 dlddliahldpdvvVEcasseavaelvlkaLkagkdvv 87
                                   + +++++  d+d+vV +a ++a+++lv + L++  +++
  gi|121635990|ref|YP_976213.1| 34 SEPRFTR--DVDIVVAVANDDAAESLVRQLLTQQYHLL 69
                                   4556666..9***********************99976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.31
                                    S-EEEEE-S--HHH CS
                  NAD_binding_3  59 dpdvvVEcasseav 72 
                                    d + +V++as++ +
  gi|121635990|ref|YP_976213.1| 152 DLRALVDAASPQDI 165
                                    33335555555554 PP

>> DUF2514  Protein of unknown function (DUF2514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.4   1.1e-05     0.038      75     144 ..      46     116 ..      31     124 .. 0.79
   2 ?   -1.2   0.7       0.5   1.8e+03      65      97 ..     140     172 ..     127     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                        DUF2514  75 aAradavgaaaaadrLrqeaakL.aaaksavaadsaaaargkaaaraavvLadlLsraaerarelAeaaDr 144
                                    +A a+ + a++ + +L ++  +L a  ++  a+  aa+  g +a  aa v  dlL  + +   e+Aeaa +
  gi|121635990|ref|YP_976213.1|  46 VAVANDDAAESLVRQLLTQQYHLlASVEQDAARRLAAVRLGATADTAANVVVDLLFASCGIEPEIAEAAEE 116
                                    4666666677777777766666636666667888899999*****************99999999999976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.5
                        DUF2514  65 avkdaqekaaaAradavgaaaaadrLrqeaakL 97 
                                    a++d ++ +++    a+  aa+ + +++  +++
  gi|121635990|ref|YP_976213.1| 140 ARDDDRRPQDRSDLRALVDAASPQDIQDARKAI 172
                                    566677777777777777777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1346.20
//
Query:       gi|121635991|ref|YP_976214.1|  [L=70]
Description: hypothetical protein BCG_0111c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00097   19.0   0.0     0.0014   18.5   0.0    1.3  1  DUF3717   Protein of unknown function (DUF3717)


Domain annotation for each model (and alignments):
>> DUF3717  Protein of unknown function (DUF3717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.6e-08    0.0014       4      25 ..      38      59 ..      35      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.6e-08
                        DUF3717  4 siteiEaAINyWRerspsadde 25
                                    ++eiEaAI +WR  +p a+++
  gi|121635991|ref|YP_976214.1| 38 DVVEIEAAIDAWRMTRPGAEEG 59
                                   689**************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 506.53
//
Query:       gi|121635992|ref|YP_976215.1|  [L=273]
Description: hypothetical protein BCG_0112 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-16   59.4   0.0      4e-10   39.2   0.0    2.2  2  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 
  ------ inclusion threshold ------
      0.082   12.6   0.7       0.39   10.4   0.7    1.9  1  Pilus_CpaD       Pilus biogenesis CpaD protein (pilus_cpaD)


Domain annotation for each model (and alignments):
>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   4.5e-14     4e-10       3      50 ..     132     179 ..     130     186 .. 0.93
   2 !   18.2   0.0   1.6e-07    0.0014      18      57 .]     221     260 ..     212     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 4.5e-14
                                    XX-EEEEE-S--S-B-HHHHHHHHHHHT-SEEEEEETTTTEEEEEEEE CS
                Ribosom_S30AE_C   3 epeivrtkrfelkpmsveeAilqmellghdFfvFrnaetgevnVvYrr 50 
                                    e  ++r+k + l+  ++ +Ai  m+ +++d+++F++aetge  VvYr 
  gi|121635992|ref|YP_976215.1| 132 EALVTRRKPVVLRRATPLQAIAAMDAMDYDVHLFTDAETGEDAVVYRA 179
                                    56799*****************************************96 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.6e-07
                                    -HHHHHHHHHHHT-SEEEEEETTTTEEEEEEEETTSCEEE CS
                Ribosom_S30AE_C  18 sveeAilqmellghdFfvFrnaetgevnVvYrrkdgnYGL 57 
                                    ++  A+ +  + g +F+ F++++tg+ + +Y r dgn GL
  gi|121635992|ref|YP_976215.1| 221 TEAAAVDRAREHGLPFLFFTDQATGRGQLLYSRYDGNLGL 260
                                    555566666677889***********************98 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   4.3e-05      0.39      83     147 ..      30     122 ..      23     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.3e-05
                     Pilus_CpaD  83 gssneaaaaaaaaeiravlaaaGvpaseisvrayqaaap............................edaapvrlsyeri 134
                                    g++n+++a+++a+++ +vla++Gv++ + +vr + a+ +                             + a +rl  + +
  gi|121635992|ref|YP_976215.1|  30 GRANASQAERLARAVGRVLADRGVTGGA-RVRLTMANCAdgptlvqinlqvgdtplraqaatagiddLRPALIRLDRQIV 108
                                    678999******************9876.555555444446899999999999999999999999887788899999999 PP

                     Pilus_CpaD 135 eAkvpeCgl.wped 147
                                    +A+++ C++ wp+ 
  gi|121635992|ref|YP_976215.1| 109 RASAQWCPRpWPDR 122
                                    99999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1813.47
//
Query:       gi|121635993|ref|YP_976216.1|  [L=152]
Description: hypothetical protein BCG_0113 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-22   80.2   2.8    1.7e-22   79.9   2.8    1.1  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   2.8   9.7e-27   1.7e-22       1     140 [.      20     143 ..      20     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 9.7e-27
                                    -HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC.T--.ECEEEEEEEEEEE-SEGGEEE CS
                   Pyridox_ox_2   1 dreeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalr.gap.vcvvvtevdglvlarsfnsln 78 
                                    dr+e+++lL+++ +g ++f++ + p+i+Pvn+ v ++++++++  +++   a r  a+   vv++e+d+l++ r+    +
  gi|121635993|ref|YP_976216.1|  20 DRDEAMRLLASVDHGCVVFTRAALPAIRPVNHLVVDGRVIVRTRLTAKVSVAVRsSADaGVVVAYEADDLDPRRR----T 95 
                                    89****************************************************85557****************....7 PP

                                    .EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEE CS
                   Pyridox_ox_2  79 .yrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgr 140
                                     + SVvv+G a+ev+d+e+ a++++ll     p  w n         + ++v+++++e v+g 
  gi|121635993|ref|YP_976216.1|  96 gW-SVVVTGLATEVSDPEQVARYQRLL----HP--WVNM--------AMDTVVAIEPEIVTGI 143
                                    7*.*********************998....56..8844........4678999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1230.70
//
Query:       gi|121635994|ref|YP_976217.1|  [L=114]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-10   39.8   2.2    4.7e-09   36.2   0.5    2.2  2  HTH_20     Helix-turn-helix domain
    1.6e-08   34.3   0.3    3.1e-08   33.4   0.3    1.5  1  HTH_5      Bacterial regulatory protein, arsR family
     0.0055   16.6   1.0       0.98    9.4   0.2    2.3  2  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0087   16.2   0.2      0.017   15.3   0.0    1.5  2  HTH_34     Winged helix DNA-binding domain
     0.0098   15.8   0.0      0.016   15.0   0.0    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.02   14.8   4.9       0.23   11.4   4.9    2.2  1  MarR_2     MarR family
      0.033   14.5   0.3        1.2    9.6   0.1    2.2  2  Rrf2       Transcriptional regulator
       0.16   11.6   0.9        0.3   10.7   0.2    1.8  2  HTH_24     Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.5   2.1e-12   4.7e-09       2      60 ..      12      70 ..      11      71 .. 0.91
   2 ?    3.3   0.0      0.04        89      27      50 ..      79     106 ..      76     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.1e-12
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHH.HHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselae.rldlskntlsyHLrvLeeagLvevvreg 60
                                   + ++ LahP R ril +L  ++ ++++el    ++l  ++ls++L vL++ag v  +r g
  gi|121635994|ref|YP_976217.1| 12 EFFKTLAHPARIRILELL-VERDRSVGELLSsDVGLESSNLSQQLGVLRRAGVVAARRDG 70
                                   789***************.*********8651569**********************987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.04
                                    HHHHHHHH....TS-HHHHHHHHHHHHH CS
                         HTH_20  27 aselaerl....dlskntlsyHLrvLee 50 
                                    a+++ae+l     +    ls++++vLe+
  gi|121635994|ref|YP_976217.1|  79 APDIAELLavarKVLARVLSDRVAVLED 106
                                    7888999955544777778999999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.3   1.4e-11   3.1e-08       1      45 [.      19      64 ..      19      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.4e-11
                                   SHHHHHHHHHHTTSSEEHHHH.HHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  1 dptRlkILklLaegelcvcel.aeelglsqstvShHLkkLreaGLV 45
                                   +p+R++IL lL e+ ++v+el + ++gl  s++S++L +Lr aG+V
  gi|121635994|ref|YP_976217.1| 19 HPARIRILELLVERDRSVGELlSSDVGLESSNLSQQLGVLRRAGVV 64
                                   599*****************6499*********************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2   0.00044      0.98      27      54 ..      40      68 ..      24      79 .. 0.85
   2 !    6.2   0.0    0.0045        10      26      44 ..      81      99 ..      72     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00044
                                   HHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2 27 lAsmlGltretvsrilseLkreglis.rg 54
                                   l+s +Gl  + +s+ l+ L+r+g++  r+
  gi|121635994|ref|YP_976217.1| 40 LSSDVGLESSNLSQQLGVLRRAGVVAaRR 68
                                   778899999****************9754 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0045
                                   HHHHHTTSSHHHHHHHHHH CS
                      HTH_Crp_2 26 elAsmlGltretvsrilse 44
                                   ++A++l + r  + r+ls+
  gi|121635994|ref|YP_976217.1| 81 DIAELLAVARKVLARVLSD 99
                                   9***************986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.5e-06     0.017       2      47 ..      22      67 ..      21      73 .. 0.93
   2 ?   -2.4   0.0       2.5   5.6e+03       8      24 ..      85     101 ..      82     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.5e-06
                         HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                   R+ +l +L++ d+   + l++ +++ ++nLs +l +L  ag +  +
  gi|121635994|ref|YP_976217.1| 22 RIRILELLVERDRSVGELLSSDVGLESSNLSQQLGVLRRAGVVAAR 67
                                   889**************************************88766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                         HTH_34   8 yLasvdeadfvelkeal 24 
                                    +La+++++ ++ l++ +
  gi|121635994|ref|YP_976217.1|  85 LLAVARKVLARVLSDRV 101
                                    57778888888877765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.4e-06     0.016      12      67 ..      24      80 ..      21      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                                   CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                           TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                   ++   L++++++  + +++++g++ s+  + L  L ++G+V  ++ g+ ++Y+ + p
  gi|121635994|ref|YP_976217.1| 24 RILELLVERDRSVGELLSSDVGLESSNLSQQLGVLRRAGVVAARRdGNAMIYSIAAP 80
                                   6677899**********************************9888577999998766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.9    0.0001      0.23       5      57 ..      20      70 ..      16     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHHCTTTSEEEHHHHHH.HHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                         MarR_2  5 paqarvLaaLgrrpgrdltvgelar.rlglsksavsrilkrLvaaGLverrpgp 57
                                   pa  r+L  L  r++   +vgel     gl+ s++s+ l  L +aG v  r++ 
  gi|121635994|ref|YP_976217.1| 20 PARIRILELLVERDR---SVGELLSsDVGLESSNLSQQLGVLRRAGVVAARRDG 70
                                   8999**********6...****99889*********************888765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00051       1.2      29      59 ..      38      68 ..      21      75 .. 0.84
   2 ?    3.2   0.0     0.049   1.1e+02      26      47 ..      77      98 ..      69      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 29 eeiaerqnispsylekilakLrkaglvksvr 59
                                   e +++ ++++ s l++ l  Lr+ag+v ++r
  gi|121635994|ref|YP_976217.1| 38 ELLSSDVGLESSNLSQQLGVLRRAGVVAARR 68
                                   5578899********************9997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.049
                                   B-HHHHHHHHTS-HHHHHHHHH CS
                           Rrf2 26 vsseeiaerqnispsylekila 47
                                   +++ +iae   + +++l+++l+
  gi|121635994|ref|YP_976217.1| 77 IAAPDIAELLAVARKVLARVLS 98
                                   67789**************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00013       0.3       5      47 ..      22      64 ..      20      65 .. 0.95
   2 ?   -1.8   0.0         1   2.3e+03      22      33 ..      81      92 ..      77     103 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                         HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +++ILelL +  r     L+  +gl +s+++++l  L ++G++
  gi|121635994|ref|YP_976217.1| 22 RIRILELLVERDRSVGELLSSDVGLESSNLSQQLGVLRRAGVV 64
                                   589**************************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                         HTH_24 22 eLAerlglSpst 33
                                   ++Ae l + +  
  gi|121635994|ref|YP_976217.1| 81 DIAELLAVARKV 92
                                   566666555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 782.22
//
Query:       gi|121635995|ref|YP_976218.1|  [L=159]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-24   85.9   1.2    2.4e-24   85.6   1.2    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   1.2   1.3e-28   2.4e-24       1     130 [.      45     155 ..      45     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1.3e-28
                                    -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEES CS
                    Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavG 80 
                                    C+Gc++++  +  +++d+     +r++ +l+a+++         +ad l+v+G vt++++  l+++ e+++++++via+G
  gi|121635995|ref|YP_976218.1|  45 CNGCEVEISGAFGPVYDA-----ERFGARLVASPR---------HADALLVTGVVTHNMAGPLRKTLEATPRPRVVIACG 110
                                    ******************.....************.........************************************ PP

                                    HHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                    Oxidored_q6  81 tCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                    +CA + G++  a+  ++g  vg++ evvpvd++i+GCPp+p+ai+++l +
  gi|121635995|ref|YP_976218.1| 111 DCALNRGVF--AD--AYG-VVGAVGEVVPVDVEIAGCPPTPAAIMAALRS 155
                                    *********..55..455.3689***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1151.79
//
Query:       gi|121635996|ref|YP_976219.1|  [L=642]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-52  178.6  17.7    1.5e-52  178.6  17.7    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.19   10.5   0.2       0.29    9.9   0.2    1.3  1  Anoctamin        Calcium-activated chloride channel


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6  17.7   1.7e-56   1.5e-52       1     278 [.     101     384 ..     101     399 .. 0.92
   2 ?   -2.5   1.3      0.26   2.4e+03     117     140 ..     470     494 ..     395     518 .. 0.56

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.7e-56
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    a+++ ++ l++El+ +++++L+    ++p+  +A+l ++++t lg +++L+g+++l ++ g+  f  l  +         
  gi|121635996|ref|YP_976219.1| 101 AGSVTTFLLAWELMAIASLILVLSEHARPQVRSAGLWYAVMTQLGFIAILVGLVVLAAAGGSDRFAGLGAV-----CDGV 175
                                    678999***************************************************************99.....6667 PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiisml 159
                                    + ++++l lvg+  K+++vplh Wlp a+ eaP pvsal++a +v++g+++++r+ l l      ++   ll+++ +s+l
  gi|121635996|ref|YP_976219.1| 176 RAAVFMLTLVGFGSKAGLVPLHAWLPRAHPEAPSPVSALMSAAMVNLGIYGIVRFDLQLLgPGPRWWGLALLAVGGTSAL 255
                                    788899999*******************************888************99999788899************** PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialav......at.....qygveaaiihllthalfkallFllagsviyerek 228
                                    +g l a +  d+KrllAyS+   +G++++al++      ++     +++ +aa++h+++ha fk+l F++agsv  + + 
  gi|121635996|ref|YP_976219.1| 256 YGVLQASVAADLKRLLAYSTTENMGLITLALGAatlfadTGaygpaSIAAAAAMLHMIAHAAFKSLAFMAAGSV-LAATG 334
                                    ******************************9984333332222222456889**********************.5666* PP

                Proton_antipo_M 229 trdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                     rd++ +ggLa +mP + + + v++l+ +GlP+ agF+s++l+ ++++++
  gi|121635996|ref|YP_976219.1| 335 LRDLDLLGGLARRMPATTVFFGVAALGACGLPLGAGFVSEWLLVQSLIHA 384
                                    *******************************************9998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.26
                Proton_antipo_M 117 sall.Aatlvkagvlllirllllla 140
                                     a l Aa +vk  +l+ +++l+ ++
  gi|121635996|ref|YP_976219.1| 470 AATLpAAQAVKFTGLGAVVRLPAMS 494
                                    2334466667777777776666666 PP

>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   3.2e-05      0.29     329     395 ..      90     158 ..      84     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.2e-05
                      Anoctamin 329 lFsaafPlapl......lallnniieirldafklvtelrRpvperaesiGiWqkilealgvlavitnallial 395
                                    lF+aa  l+p+      + l + ++ i +  +  + e+ Rp   +++s G W+ +++ lg++a+++  +++a 
  gi|121635996|ref|YP_976219.1|  90 LFVAAMLLVPAagsvttFLLAWELMAIASLILV-LSEHARP---QVRSAGLWYAVMTQLGFIAILVGLVVLAA 158
                                    666666666654444446777777777766554.4577899...9*********************9998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 4320.96
//
Query:       gi|121635997|ref|YP_976220.1|  [L=316]
Description: formate hydrogenlyase hycD (FHL) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-41  141.0  13.4    6.3e-41  140.6  13.4    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6  13.4   3.5e-45   6.3e-41      10     293 ..      13     305 ..       6     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 3.5e-45
                                    HHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS-SS CS
                         NADHdh  10 lllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviPfg 89 
                                    +++ + l++++ R+v Ar++ R G       Gllqp+ D+lK l K++i+p+++ +++f +apv++  ++ll+ a+ P+ 
  gi|121635997|ref|YP_976220.1|  13 VMVGAPLVIGMTRQVRARWEGRAGA------GLLQPWRDLLKQLGKQQITPAGT-TIVFAAAPVIVAGTTLLIAAIAPLV 85 
                                    4555559******************......********************999.9**********************99 PP

                                    S..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCC CS
                         NADHdh  90 e..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqe 167
                                    +     d +++l+ ++ l+ lg++++ laG++++  +  +Ga R++++   +E +++l+++a+ + ags +l  +v++  
  gi|121635997|ref|YP_976220.1|  86 AtgSPLDPSADLFAVVGLLFLGTVALTLAGIDTGTSFGGMGASREITIAALVEPTILLAVFALSIPAGSANLGALVASTI 165
                                    6456777788******************************************************************9997 PP

                                    TT...-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSS...SSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT. CS
                         NADHdh 168 ei...wfillqllafiifliallaetnraPFDlpeaesEL...vaGfhtEYsgmkfalfflaeyanmvlvsalavllFlg 241
                                    ++    + l+ +laf++++i+++aet+r P D p  + EL    +++  EY+g ++al+ +a  ++++++ al++ lFl 
  gi|121635997|ref|YP_976220.1| 166 DHpghVVSLAGVLAFVALVIVIVAETGRLPVDNPATHLELtmvHEAMVLEYAGPRLALVEWAAGMRLTVLLALLANLFL- 244
                                    66665457778*****************************66668999*******************************. PP

                                    SS-HCCS.............HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHH CS
                         NADHdh 242 Gwllpfs.............gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplala 293
                                     w    +             g++ +++Kv++l +l++ ++  l++lR+ ++ +l    +l   la
  gi|121635997|ref|YP_976220.1| 245 PW----GiagaaptaldvltGVVAVAAKVAILAVLLATFEVFLAKLRLFRVPELLAGSFLLALLA 305
                                    34....33344668899*********************************999988776655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2374.94
//
Query:       gi|121635998|ref|YP_976221.1|  [L=220]
Description: hydrogenase hycP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.094   12.3   3.8       0.21   11.1   3.8    1.6  1  TM140            TM140 protein family
        3.3    6.8   8.3       0.66    9.1   2.1    2.2  2  Choline_transpo  Plasma-membrane choline transporter


Domain annotation for each model (and alignments):
>> TM140  TM140 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.8   2.3e-05      0.21      84     165 ..      64     148 ..      56     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                          TM140  84 galvltlf.vplplllaqcnkdegeWkl.avgfl.aassvllagGlglflsyvwkWvrlsllGpgflalvlaqallilll 160
                                    g  vl+l  + lp lla+  + e   +  a  ++ +ass+l+++Gl+l  + +++ v     G ++ a+ +a a++++ l
  gi|121635998|ref|YP_976221.1|  64 GIAVLALRaLVLPWLLARAVGAEAAAQReATPLVnTASSLLITAGLTLTAFAITQPVVNLEPGVTINAVPAAFAVVLIAL 143
                                    5567777514689999999988876655144454257788899**************************99988777776 PP

                          TM140 161 laivl 165
                                    +++++
  gi|121635998|ref|YP_976221.1| 144 FVMTT 148
                                    66554 PP

>> Choline_transpo  Plasma-membrane choline transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7     0.017   1.5e+02       7      41 ..      16      50 ..      11      88 .. 0.74
   2 ?    9.1   2.1   7.3e-05      0.66     238     313 ..      80     156 ..      71     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.017
                Choline_transpo  7 avllllllivlrkrirlaiallkvaskaiksnpsl 41
                                   +++l+ +liv+r+ +r +++ll     a+ ++p l
  gi|121635998|ref|YP_976221.1| 16 GLVLASVLIVWRRDLRAIVRLLAWQGAALAAIPLL 50
                                   6789999**************99777777776654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 7.3e-05
                Choline_transpo 238 lkrnglrvavldsvvdfvlflgkllialltgliaylllkatltnpe...elnsplvpllvvfiiayliasiflsvyesa 313
                                     ++ g+ +a+    + +v + ++lli+++ +l+a+ +++   +  e   ++n++  +++ v++ia++++++ l+ ++ a
  gi|121635998|ref|YP_976221.1|  80 ARAVGAEAAAQREATPLVNTASSLLITAGLTLTAFAITQPVVNL-EpgvTINAV-PAAFAVVLIALFVMTTRLHAVSQA 156
                                    44555678888889999*****************9888744444.367555555.444445556677766666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1793.17
//
Query:       gi|121635999|ref|YP_976222.1|  [L=488]
Description: hydrogenase hycQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-45  154.5  20.3    3.3e-45  154.5  20.3    1.6  2  Proton_antipo_M  Proton-conducting membrane transporter
    0.00014   21.9   3.2    0.00024   21.1   0.1    2.9  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2      0.42   3.8e+03     267     283 ..      35      51 ..      14      82 .. 0.60
   2 !  154.5  20.3   3.7e-49   3.3e-45       1     288 [.     124     419 ..     124     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.42
                Proton_antipo_M 267 skfliLeaavavslill 283
                                    s  ++L++ava++ ++ 
  gi|121635999|ref|YP_976222.1|  35 SATTVLACAVAMGFWMG 51 
                                    33333334443333333 PP

  == domain 2  score: 154.5 bits;  conditional E-value: 3.7e-49
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg........tlefeelskal 72 
                                    an++  +++++E++ + + +L+g ++++  +leA+ k++++ ++g  + +lg +lly ++          l+++ l++  
  gi|121635999|ref|YP_976222.1| 124 ANNIGVIWVAIEATTVITAFLVGHRRTR-TALEATWKYVVICSVGIAVAFLGTVLLYFAARdsgaaaagALNLDILAEH- 201
                                    788899*******************888.***************************97643333444459999999998. PP

                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssnei.sqll 150
                                     +gl+   + l+  lll+g  +K++++p+h+Wl+da+ +aP+pvsal++++l++++  +lirl ++l  vs++++ ++ l
  gi|121635999|ref|YP_976222.1| 202 AAGLDPGVARLAGGLLLIGYGAKAGLFPFHTWLADAHSQAPAPVSALMSGVLLAVAFSVLIRLRPILDaVSGPAYlRNGL 281
                                    89999999999********************************************************976666643789* PP

                Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektr 230
                                    l+++++++l++ l+  ++ d+Kr+lAySs+ h+G++ ia+a++t  +++a+++h+l+h++ k  lFl+ g++ ++ ++++
  gi|121635999|ref|YP_976222.1| 282 LVVGLATLLVAVLMLTVTGDVKRMLAYSSMEHMGLIAIAAAAGTTLAIAALLLHVLAHGIGKTVLFLAGGQL-QAAHDST 360
                                    *******************************************************************99887.7888*** PP

                Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vv 288
                                     i+++ g + + +++ + ++v+l+ l GlPp+a F s+++i  ++ +  l +++ a ++
  gi|121635999|ref|YP_976222.1| 361 AIADITGVMRRSRLIGVSFAVGLIVLLGLPPFAMFASELAIARSLANERLAWVLGAaLL 419
                                    *****************************************999988887777766444 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.7e-08   0.00024       4      47 ..      49      93 ..      47     110 .. 0.79
   2 ?   -1.3   0.8      0.27   2.4e+03      20      38 ..     244     262 ..     243     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.7e-08
                Proton_antipo_N  4 Wlsvgg.lsieigfllDklsalmllvvtfvsllvhlYSigYMadd 47
                                   W+ +g  + +   ++ D l+++ml+v+ +v++l    SigY + +
  gi|121635999|ref|YP_976222.1| 49 WMGSGAqFGLGGLLRADALTVVMLVVIGIVGTLATAASIGYIDTE 93
                                   5555533444445899*************************9654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.27
                Proton_antipo_N  20 klsalmllvvtfvsllvhl 38 
                                    ++salm  v   v++ v++
  gi|121635999|ref|YP_976222.1| 244 PVSALMSGVLLAVAFSVLI 262
                                    689***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3379.92
//
Query:       gi|121636000|ref|YP_976223.1|  [L=492]
Description: formate hydrogenase hycQ (FHL) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-22   78.9   0.0    4.2e-18   65.4   0.0    2.2  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    5.8e-17   62.5   0.0    1.2e-16   61.4   0.0    1.4  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    6.5e-11   41.8   0.5    8.6e-08   31.5   0.1    2.1  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0     7e-22   4.2e-18       1     165 [.     256     411 ..     256     423 .. 0.88
   2 !   11.5   0.0     2e-05      0.12     206     264 ..     427     485 ..     420     491 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 7e-22
                                    HTT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHH CS
                 Complex1_49kDa   1 DlGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRt 80 
                                    D+G       a r Re++l+   +vtG Rl    ir GGva    +++ e     l  l   l+e+ +l   n+++ +R 
  gi|121636000|ref|YP_976223.1| 256 DVGYSLANAHAQRIRENLLRRNAAVTGHRLLRGAIRAGGVALRALPDTDE-----LAALAVDLAEVATLTLANSVVYDRF 330
                                    66777777788999**************************9765555544.....456677899**************** PP

                                    SSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT-- CS
                 Complex1_49kDa  81 kgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklp 160
                                     g +vl+ ++a +lg+ G v+RasG++ D R ++p  +    +       +gDv++Ry+vr +E+  S+ + + ++e+ +
  gi|121636000|ref|YP_976223.1| 331 AGTAVLHPDDASALGCLGYVARASGLRSDARVEHPTIVLPITEIGA---PDGDVLARYTVRRDEFAASAALAQHIVESHT 407
                                    ************************************9988887765...59*******************9999998875 PP

                                    .S-SB CS
                 Complex1_49kDa 161 egpvl 165
                                     gp+ 
  gi|121636000|ref|YP_976223.1| 408 -GPIE 411
                                    .6665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2e-05
                                    EEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT-- CS
                 Complex1_49kDa 206 aavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldi 264
                                      vE  +G++++ +  d + +  r+k+ +ps+ n  al+  + ++ + D++ +  s++ 
  gi|121636000|ref|YP_976223.1| 427 GIVEGWRGTIVHRVEIDVDGRITRAKVVDPSWFNWPALPVAMADTIVPDFPLANKSFNQ 485
                                    569999********************************************998888875 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0     2e-20   1.2e-16       8     116 ..      16     120 ..      10     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2e-20
                                    HHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHHHHHHHHHHH CS
                 Complex1_30kDa   8 llevakflkdeeelgfdvlsdltavDekeerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgadwyEREayDm 87 
                                    l+++a+ l  + +++   l+ + a D  +++++vvy +l    ++r+ ++  v++++pe+ S++ l   a ++ERE+ D+
  gi|121636000|ref|YP_976223.1|  16 LIATAEQLWAD-SFR---LALVAAHDD-GDSLRVVYLFLAGYPDRRVELEYVVPADNPEIRSLAYLSFPAGRFEREMADL 90 
                                    56666666662.222...444555554.699********877789******99*************************** PP

                                    SHHBCTTSSTSS-SSSSTTS.SS-TTSTTS CS
                 Complex1_30kDa  88 fGivfeghpdlrrillpedf.eghPLRkdf 116
                                    +Gi+  ghp++rr+++++ +   hP+R d 
  gi|121636000|ref|YP_976223.1|  91 YGIRPVGHPKPRRLVRHAHWpDWHPMRTDA 120
                                    ****************88887779***996 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   1.4e-11   8.6e-08       1      67 [.     181     247 ..     181     254 .. 0.96
   2 !    8.6   0.1   0.00012      0.74     418     458 ..     421     460 ..     381     473 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.4e-11
                                    --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhi 67 
                                    RG+E++ +gr    a  l++Ri G    +Hala   a+edAlgi++p++ + +r li   + l +h 
  gi|121636000|ref|YP_976223.1| 181 RGIEKLFHGRPATAAVDLAERISGDTSAAHALAHSLAIEDALGIELPHEIHRLRALIVELERLYNHA 247
                                    9********************************************************9999988885 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00012
                                    S-SEEEEEEEEEETTEEEEEEEEEE.TTEEEEEEEE-HHHHH CS
                   NiFeSe_Hases 418 vpkeakGvglveapRGaLsHwikik.dgkienYqavvPsTWn 458
                                         +G+g+ve  RG++ H ++i+ dg+i++ ++v Ps  n
  gi|121636000|ref|YP_976223.1| 421 A--PSSGIGIVEGWRGTIVHRVEIDvDGRITRAKVVDPSWFN 460
                                    3..358******************66************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3342.75
//
Query:       gi|121636001|ref|YP_976224.1|  [L=224]
Description: hypothetical protein BCG_0121 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-09   38.4   0.1    1.3e-09   38.4   0.1    1.9  2  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.014   15.6   0.3        0.2   11.9   0.3    2.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
      0.024   14.9   0.0       0.04   14.1   0.0    1.4  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
      0.069   13.4   0.0       0.13   12.5   0.0    1.4  1  DPBB_1           Lytic transglycolase


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.28   1.3e+03      38      70 ..      19      54 ..       4      73 .. 0.59
   2 !   38.4   0.1     3e-13   1.3e-09       3     139 ..      77     216 ..      75     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
                                   ECSE.STSSSTTTEEEEECCCS....SEEEEEEEEEET CS
                Polyketide_cyc2 38 eleg.gggpargvegtvrvggr....gtvreelvevdp 70
                                   ++++ + g+   ++++vr g +    +  ree  +v p
  gi|121636001|ref|YP_976224.1| 19 TVVKgRSGS--LSWRRVRTGDLglavWGGREEYRAVKP 54
                                   333312233..333333333334455557777776666 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 3e-13
                                    EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECS.ESTSSS....TTTEEEEECCCS.SEEEEEEEEEETTTTEEE CS
                Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarvele.ggggpa....rgvegtvrvggr.gtvreelvevdpegrlls 76 
                                    +v++sv++aap+++ +a+v+d++  ++ + +  +v++  + + ++    +++  +++  g+  +++ +++++ p + l++
  gi|121636001|ref|YP_976224.1|  77 RVSRSVEVAAPAAELFAIVADPRRHRELDGSG-TVRGNiKVPAKLvvgsKFS-TKMKLFGLpYRITSRVTALKP-NELVE 153
                                    89*******************99999874422.2333311233334221244.55555555977**********.***** PP

                                    EEEE.SSS-TSEEEEEEEEECCET.EEEEEEEEEEE.E--T...T--HHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  77 yrivkpvpvanyvatwtvtpdggg.trvtwtgefda.gplg...gpfekpaaakavkgdleagLerLk 139
                                    +      p++ ++++w+++   +  trvt t++++a g+++   ++ e++ +ak  ++ +ea+L++L 
  gi|121636001|ref|YP_976224.1| 154 WSH----PLG-HRWRWEFESLSPTlTRVTETFDYHAaGAIKnglKFYEMTGFAKSNAAGIEATLAKLS 216
                                    **8....777.88*********999**********854444333555788888888888999999986 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   4.5e-05       0.2       1     106 [.      84     185 ..      84     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E........EEECSTTSSCEEEEEEEEEEETTTEEECTTCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsa........dlevgfggltesftarvtldppeeitfklveg 72 
                                    v+apa++++a+vad  +  e+      +  ++ + + + a        +++ + +gl+ + t+rvt  +p+e    lve 
  gi|121636001|ref|YP_976224.1|  84 VAAPAAELFAIVADPRRHRELDG----SGTVRGNIK-VPAklvvgskfSTKMKLFGLPYRITSRVTALKPNE----LVE- 153
                                    68999999999999988887654....333333332.11233345555888999******************....333. PP

                                    CCCEE..EEEEEECTECCEEECEEEEEEEEEEEE-S CS
                 Polyketide_cyc  73 dfksl..egkWtieslppnsggtrtkvalevdfkfa 106
                                    + + l  + +W++esl+p    t t+v+ ++d+  a
  gi|121636001|ref|YP_976224.1| 154 WSHPLghRWRWEFESLSP----TLTRVTETFDYHAA 185
                                    444430155788999995....77777777776544 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.9e-06      0.04       2      96 ..      86     180 ..      85     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.9e-06
                                    S-HHHHHHHHH-HHHHHHH......EEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEE CS
                          AHSA1   2 apperVfraltdpellkrW......ftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrledepeee 75 
                                    ap++++f+   dp + +          + ++  +l +G+kf+++++  g  + ++ ++++++p+e ++++        + 
  gi|121636001|ref|YP_976224.1|  86 APAAELFAIVADPRRHRELdgsgtvRGNIKVPAKLVVGSKFSTKMKLFGLPYRITSRVTALKPNELVEWSH-------PL 158
                                    89*****************997754444455555577******66699999999999*************4.......45 PP

                                    EEEEEEEEEE.ETTEEEEEEEE CS
                          AHSA1  76 estvtielee.egggTrltlth 96 
                                      + ++e+e   ++ Tr+t t 
  gi|121636001|ref|YP_976224.1| 159 GHRWRWEFESlSPTLTRVTETF 180
                                    5677788888777778877766 PP

>> DPBB_1  Lytic transglycolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.13      42      75 ..      63     100 ..      48     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                    --EEEEEEEE----STTECEEE-HHHHHHHT-T....T CS
                         DPBB_1  42 gksvtVtitDrgpfppgrhiDLSkaAfeklakp....r 75 
                                    g  +tVt++D gp + +r   ++++A+e +a++    r
  gi|121636001|ref|YP_976224.1|  63 GDMMTVTVVDAGPGRVSRSVEVAAPAAELFAIVadprR 100
                                    6889************************9998755550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1712.11
//
Query:       gi|121636002|ref|YP_976225.1|  [L=197]
Description: methyltransferase/methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-20   71.4   0.0    1.1e-19   70.9   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.4e-19   70.6   0.0    2.1e-19   70.0   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    4.2e-14   53.1   0.0    6.3e-14   52.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.4e-13   49.7   0.0    3.9e-13   49.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.1e-12   48.1   0.0    1.4e-12   47.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.9e-10   39.5   0.0    5.6e-10   39.0   0.0    1.1  1  MTS              Methyltransferase small domain
    9.9e-10   38.4   0.0    1.3e-09   38.0   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    4.4e-09   36.0   0.0    6.1e-09   35.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-08   33.5   0.0    2.3e-08   33.4   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    6.5e-06   25.6   0.0      8e-06   25.3   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    1.3e-05   24.3   0.0    1.9e-05   23.8   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    2.3e-05   23.9   0.0      3e-05   23.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0017   18.3   0.0     0.0024   17.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
     0.0019   17.8   0.0     0.0025   17.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
     0.0061   15.9   0.0     0.0076   15.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.032   14.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
        0.1   12.4   0.0       0.13   12.0   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.11   12.8   0.0       0.29   11.5   0.0    1.7  1  TOBE             TOBE domain
       0.24   10.8   0.0       0.35   10.3   0.0    1.2  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.1e-22   1.1e-19       1      96 []      27     120 ..      27     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.1e-22
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    LdvGcG G+la+ la+r   v++vD+++ +l++a+++  +++  +++++ad+ +  ++++ fD+vvs+ +lhh+ed + a
  gi|121636002|ref|YP_976225.1|  27 LDVGCGDGLLAARLARRIPYVTAVDIDAPVLRRAQTRFANAP--IRWLHADIMTAELPNAGFDAVVSNAALHHIEDTRTA 104
                                    8****************************************9..99********************************** PP

                                    HHHHHHHEEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                    l+ +  ++ pgG+l++
  gi|121636002|ref|YP_976225.1| 105 LSRLGGLVTPGGTLAV 120
                                    ************9975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   2.2e-22   2.1e-19       1      97 []      26     116 ..      26     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.2e-22
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLd+GcG G l+++la+r+    vt+vDi++  l++a++r+  +++ ++++++d+ + +++++ fD+vvs+ alhh++  
  gi|121636002|ref|YP_976225.1|  26 VLDVGCGDGLLAARLARRI--PYVTAVDIDAPVLRRAQTRF--ANAPIRWLHADIMTAELPNAGFDAVVSNAALHHIE-- 99 
                                    9*****************9..7*******************..5679***********************777***98.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    d+++al+++  +++pgG
  gi|121636002|ref|YP_976225.1| 100 DTRTALSRLGGLVTPGG 116
                                    789*************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   6.7e-17   6.3e-14       1      99 []      27     118 ..      27     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 6.7e-17
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L++GcG+G l+++l+++     +t+vDi++ ++ +a++++a     ++ + ++ + +l    +++ fD+vv++ +lhh++
  gi|121636002|ref|YP_976225.1|  27 LDVGCGDGLLAARLARR--IPYVTAVDIDAPVLRRAQTRFANAPI-RWLHADIMTAEL----PNAGFDAVVSNAALHHIE 99 
                                    8*************999..55566*********888888887774.333333333332....2369************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d+r +l+++  l++pgG l
  gi|121636002|ref|YP_976225.1| 100 DTRTALSRLGGLVTPGGTL 118
                                    *****************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   4.1e-16   3.9e-13       7     113 ..      26     124 ..      22     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.1e-16
                Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                    vlD+GCG G l+ +la+++     v+ +Di++ ++++A+++ ++  +   +  ++di ++e  l  + fD ++sn++l++
  gi|121636002|ref|YP_976225.1|  26 VLDVGCGDGLLAARLARRIP---YVTAVDIDAPVLRRAQTRFANAPI---RWLHADIMTAE--LPNAGFDAVVSNAALHH 97 
                                    8***************6654...49***************9987666...69999999988..8889************* PP

                Methyltransf_31  87 ladpdkileeiervlkpggilliedpr 113
                                    + d   +l ++  +++pgg l++ ++ 
  gi|121636002|ref|YP_976225.1|  98 IEDTRTALSRLGGLVTPGGTLAVVTFV 124
                                    **********************99988 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.5e-15   1.4e-12      24     124 ..      24     127 ..      10     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.5e-15
                Methyltransf_23  24 grvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd 97 
                                    + vLd+GcG+G l+  l+++   vt+vD++     +a+       +   +   +d + a+ p++ fd +v++  l+h++d
  gi|121636002|ref|YP_976225.1|  24 QCVLDVGCGDGLLAARLARRIPYVTAVDIDAPVLRRAQtrfanaPI---RWLHADIMTAELPNAGFDAVVSNAALHHIED 100
                                    58***************99999*******98777766454332111...111122336666******************* PP

                Methyltransf_23  98 ppellrqiatllkpgGylllseplasl 124
                                       +l++++ l+ pgG l + ++  ++
  gi|121636002|ref|YP_976225.1| 101 TRTALSRLGGLVTPGGTLAVVTFVTPS 127
                                    ******************999986654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   5.9e-13   5.6e-10      23     116 ..      14     104 ..      11     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 5.9e-13
                                    HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-ST.TTTSTTS-EEEE CS
                            MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdv.leeveekkfdli 101
                                    Ll+++    ++ vlD+GcG G+l+a la++ p   vt+vd+da  l+ a++ +++    ++ ++ d+ ++e++++ fd++
  gi|121636002|ref|YP_976225.1|  14 LLDAMVPLGTQCVLDVGCGDGLLAARLARRIPY--VTAVDIDAPVLRRAQTRFANAP--IRWLHADImTAELPNAGFDAV 89 
                                    677777767778*********************..9***********9998887655..67777776167899******* PP

                                    EE---STTTCHCHHH CS
                            MTS 102 vsNPPfhagkatela 116
                                    vsN  +h+ ++t++a
  gi|121636002|ref|YP_976225.1|  90 VSNAALHHIEDTRTA 104
                                    *******99885554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.4e-12   1.3e-09      46     142 ..      25     118 ..       6     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                           NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfst.dekfdlivvaevlyyiedvae 124
                                     +l+vGc  G l+ rla     +t vd+    + ra++r  + + i w+ +d+   ++ ++ fd +v    l++ied   
  gi|121636002|ref|YP_976225.1|  25 CVLDVGCGDGLLAARLARRIPYVTAVDIDAPVLRRAQTRFAN-APIRWLHADIMTAELpNAGFDAVVSNAALHHIED--- 100
                                    589***************************************.88********999853889*******99988877... PP

                           NodS 125 lraavrnlvsllapdgql 142
                                     r+a+  l  l++p+g+l
  gi|121636002|ref|YP_976225.1| 101 TRTALSRLGGLVTPGGTL 118
                                    589999999999999987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.5e-12   6.1e-09      39     158 ..      14     127 ..       6     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.5e-12
                                    HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                    + + + ++  + vlDv +G g la++l++ +     v+ +Di++ +L+ ++ +  +     i++l+a+ +  +  +  fD
  gi|121636002|ref|YP_976225.1|  14 LLDAMVPLGTQCVLDVGCGDGLLAARLARRIP---YVTAVDIDAPVLRRAQTRFAN---APIRWLHADIMTAELPNAGFD 87 
                                    567788888999***************99886...68999***********99866...579****************** PP

                                    EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE---- CS
                Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskve 158
                                     v     l  + D+ +aL  +   + pGG+l v+ f  + 
  gi|121636002|ref|YP_976225.1|  88 AVVSNAALHHIEDTRTALSRLGGLVTPGGTLAVVTFVTPS 127
                                    **********************************998776 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.4e-11   2.3e-08      18      97 ..      10      95 ..       5     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.4e-11
                                   HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCT... CS
                         RrnaAD 18 vineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevte... 96
                                   +++  ld++ +  ++ vl++g G G+l ++La r+  v+++ +d   + + q+++  + ++ ++h+D++++e+p+   +   
  gi|121636002|ref|YP_976225.1| 10 HYDALLDAMVPLGTQCVLDVGCGDGLLAARLARRIPYVTAVDIDAPVLRRAQTRFA-NAPIRWLHADIMTAELPNAGFDavv 90
                                   567777888888999**************************************998.*****************96555555 PP

                                   ....T CS
                         RrnaAD 97 ....k 97
                                        
  gi|121636002|ref|YP_976225.1| 91 snaaL 95
                                   55541 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   8.4e-09     8e-06      53     175 ..      13     131 ..       5     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.4e-09
                                    HHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS-----..SE CS
                 Methyltransf_2  53 kvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslPea..Da 130
                                     +l a+   g + ++DvG G G la+  ++  P ++++  D p V ++A++++   ++  +++   d++  +lP+a  Da
  gi|121636002|ref|YP_976225.1|  13 ALLDAMVPLGTQCVLDVGCGDGLLAARLARRIPYVTAVDIDAP-VLRRAQTRF---ANAPIRWLHADIMTAELPNAgfDA 88 
                                    555555555678899**************************88.889999994...56789*************88779* PP

                                    EEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS-- CS
                 Methyltransf_2 131 illkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsg 175
                                    ++ +  lh  +d   ++ L r+   + +gG + vv  v +  ++g
  gi|121636002|ref|YP_976225.1|  89 VVSNAALHHIEDT--RTALSRLGGLVTPGGTLAVVTFVTPSLRNG 131
                                    ********99886..5679***************99998876665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     2e-08   1.9e-05      95     222 ..       2     125 ..       1     132 [. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2e-08
                                    --SEEHHHHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHHHHHHHHHCCTTTTSSEEEE--- CS
                 Methyltransf_9  95 dteWrsdwkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfliqfeavrkllgedqrahllplg 173
                                    d  W ++  +d +l  + +l  + +ldvGcg+G    r++ + +  ++v id   l     +a  ++ +   r  +  + 
  gi|121636002|ref|YP_976225.1|   2 DQPWNANIHYDALLDAMVPLGTQCVLDVGCGDGLLAARLARRIPYvTAVDIDAPVLR----RAQTRFANAPIRWLHADIM 77 
                                    778***********************************9888765146777776665....4556777777777777778 PP

                                    GGGS-T---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-B CS
                 Methyltransf_9 174 ieqlpeleafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletlvi 222
                                      +lp+ ++fd+v s   l+h +     l++l   ++ gG+l + t v 
  gi|121636002|ref|YP_976225.1|  78 TAELPN-AGFDAVVSNAALHHIEDTRTALSRLGGLVTPGGTLAVVTFVT 125
                                    888886.79*************************9******99998876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.2e-08     3e-05     161     241 ..      22     100 ..      13     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.2e-08
                           PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNILaevl 239
                                    +++ vlDvG+G G+La a +      v+avDiD   ++ a+  ++   ++  + ++ +++el++ + +d +v+N   + +
  gi|121636002|ref|YP_976225.1|  22 GTQCVLDVGCGDGLLA-ARLARRIPYVTAVDIDAPVLRRAQTRFANAPIRWlHADI-MTAELPN-AGFDAVVSNAALHHI 98 
                                    45689**********8.444556789**************9988777776644443.7799999.89*******766665 PP

                           PrmA 240 ie 241
                                     +
  gi|121636002|ref|YP_976225.1|  99 ED 100
                                    54 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-06    0.0024      10      60 ..      17      66 ..      13      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                Methyltransf_18 10 slvekgs.rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniek 60
                                   ++v+ g+  v+D+G+  g+l++ l+  ++++ v+a+Di +  l++a++  ++
  gi|121636002|ref|YP_976225.1| 17 AMVPLGTqCVLDVGCGDGLLAARLA--RRIPYVTAVDIDAPVLRRAQTRFAN 66
                                   5777766599**************9..68999**************998766 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.6e-06    0.0025      10      98 ..      18     108 ..      11     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                           MetW  10 likpgsr.vldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqg..dldkdlenfedksfdyvvlsqtlq 86 
                                    +++ g++ vld+GcGdG l   l+  +      +++d+  + ++ ++  +       +d   ++ ++  fd vv + +l 
  gi|121636002|ref|YP_976225.1|  18 MVPLGTQcVLDVGCGDGLLAARLAR-RIPYVTAVDIDAPVLRRAQTRFANAPIRwlHADIMTAELPNAGFDAVVSNAALH 96 
                                    555554339**********999965.4445567788888888888776665444014555567899************** PP

                           MetW  87 atrnpkevldel 98 
                                     + ++++ l+ l
  gi|121636002|ref|YP_976225.1|  97 HIEDTRTALSRL 108
                                    **9999988765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     8e-06    0.0076      64     170 ..      24     126 ..       9     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8e-06
                                    -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGG CS
                           CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgke 143
                                    + +Ld+GcG G l+ r ++r    v ++ + +   ++a+ r++++ + r  + +++  e  +  +d+vvs  a+ h+   
  gi|121636002|ref|YP_976225.1|  24 QCVLDVGCGDGLLAARLARR-IPYVTAVDIDAPVLRRAQTRFANAPI-RWLHADIMTAELPNAGFDAVVSNAALHHIEDT 101
                                    469*****************.678999*****************995.4555566654444559************9877 PP

                                    GHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                           CMAS 144 nydtffkklkkllkedGllllhtitsl 170
                                    +  t  ++l  l+ ++G+l++ t +++
  gi|121636002|ref|YP_976225.1| 102 R--TALSRLGGLVTPGGTLAVVTFVTP 126
                                    6..457899999999999888777655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05     0.032      26      72 ..      23      65 ..      10     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekrae 72
                                    + v+DvG+G g L+ +la    +   +v+++d+ + + ++a++r +
  gi|121636002|ref|YP_976225.1| 23 TQCVLDVGCGDGLLAARLAR---R-IPYVTAVDIDAPVLRRAQTRFA 65
                                   56799***************...4.779*******999999998755 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.13      75     155 ..      24      98 ..       7     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                    -EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS CS
                           PCMT  75 arvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaape 154
                                    + vL+vG+G G l+a lar +  ++   +++  + + ++a+ +  +  +      ++D  +   ++a +da++  aa ++
  gi|121636002|ref|YP_976225.1|  24 QCVLDVGCGDGLLAARLARRIPYVT---AVDIDAPVLRRAQTRFANAPI---RWLHADIMTAELPNAGFDAVVSNAALHH 97 
                                    469***************9998776...556566777777777665544...4455666666667777777777777666 PP

                                    - CS
                           PCMT 155 i 155
                                    i
  gi|121636002|ref|YP_976225.1|  98 I 98 
                                    6 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.29      14      40 ..      18      43 ..      15      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                           TOBE 14 veplgseveVrvdlgggatLtArvtrr 40
                                    +plg +++++v +g+g  L+Ar+ rr
  gi|121636002|ref|YP_976225.1| 18 MVPLGTQCVLDVGCGDGL-LAARLARR 43
                                   689***************.*****987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00037      0.35       4      48 ..      25      67 ..      23      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC CS
                 Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal 48
                                    vl++GcG G +  +lA + P ++  +++i  +v++++  + ++ 
  gi|121636002|ref|YP_976225.1| 25 CVLDVGCGDGLLAARLARRIPYVT--AVDIDAPVLRRAQTRFANA 67
                                   689******************876..6777788888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1411.51
//
Query:       gi|121636003|ref|YP_976226.1|  [L=256]
Description: hypothetical protein BCG_0123 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-35  119.9  10.9    1.3e-34  119.5  10.9    1.2  1  DUF2127   Predicted membrane protein (DUF2127)


Domain annotation for each model (and alignments):
>> DUF2127  Predicted membrane protein (DUF2127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5  10.9     7e-39   1.3e-34       2     139 ..      83     224 ..      82     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 7e-39
                        DUF2127   2 lrliallklvkglllllaglallfllssr.dlaalaer...larelhldpesslvelllekasnlspstlklvalallaY 77 
                                    +r++ +++lv++l+l la++a++ ++ +r  ++a++ r   ++r  +++ ++  v ++leka  ++pstl+l++ +l+aY
  gi|121636003|ref|YP_976226.1|  83 IRALGVERLVRALVLALAAWAVWEFRGARgAIQATLDRdlpVLRAAGFKVDQMTVIHALEKALAAKPSTLALITGMLAAY 162
                                    799************************9995555554443678999********************************** PP

                        DUF2127  78 allklieavgLwrekrWaeylavvstaifiplEiyelvrkvsvlkiallliNlaivvyllre 139
                                    a+l+++e+vgLw+ krW+ey+avv+t+if+plE+++l++ +++++++++ iN+a+vvyll++
  gi|121636003|ref|YP_976226.1| 163 AVLQAVEGVGLWLLKRWGEYFAVVATSIFLPLEVHDLAKGITTTRVVTFSINVAAVVYLLIS 224
                                    ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1728.68
//
Query:       gi|121636004|ref|YP_976227.1|  [L=255]
Description: bifunctional MTA/SAH nucleosidase mtn [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-45  154.5   0.2      3e-45  154.3   0.2    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.021   14.0   0.0       0.12   11.6   0.0    1.9  2  NUP        Purine nucleoside permease (NUP)


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.2   3.3e-49     3e-45       2     233 ..       5     249 ..       4     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 3.3e-49
                                    EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEE CS
                      PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGg 81 
                                    +++i+++p+e++ l+   l + + + + +++ f  G+l  ++vv++  G+Gk+n+  ++++ l ++fg+++i+++G+aGg
  gi|121636004|ref|YP_976227.1|   5 VGVICAIPQELAYLRGV-LVDAKRQQV-AQILFDSGQLDAHRVVLAAAGMGKVNTG-LTATLLADRFGCRTIVFTGVAGG 81 
                                    89***************.999999999.9***************************.*********************** PP

                                    SSTTT-TT-EEEEEEEEESSSCCGCCTHHCC........TCCCCTTSSEE--HHHHHHHHH............CHHTTT. CS
                      PNP_UDP_1  82 lnpdlkvGDvvipddainfdgrsplygpkee........gqyfpdsydapadpelrallke............aaealg. 140
                                    l+p+l +GD+vi+d+++++d++       ++        +++     ++ +dp+ ++++k+            a      
  gi|121636004|ref|YP_976227.1|  82 LDPELCIGDIVIADRVVQHDFGLLTDERLRPyqpghipfIEPTERLGYP-VDPAVIDRVKHrldgftlaplstA----Ag 156
                                    ******************7776663222222555666987777777777.9**********9999999876422....13 PP

                                    .....TTEEEEEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCC CS
                      PNP_UDP_1 141 .....ikvhrGvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeve 215
                                         +++ +G+++t+d+  ++ + ++rl+++lg  aveME+ avaq+++ ++ip+++ir++sdla+ + +      ++ 
  gi|121636004|ref|YP_976227.1| 157 gggrqPRIYYGTILTGDQYLHCERTRNRLHHELGGMAVEMEGGAVAQICASFDIPWLVIRALSDLAGADSG-----VDFN 231
                                    468*************************************************************6666444.....7788 PP

                                    HHHHHHHHHHHHHHHHHH CS
                      PNP_UDP_1 216 efaqeaaknaaalllall 233
                                     f  e a  +a++ll+ll
  gi|121636004|ref|YP_976227.1| 232 RFVGEVAASSARVLLRLL 249
                                    888888888888888776 PP

>> NUP  Purine nucleoside permease (NUP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.12      44     117 ..      42     111 ..      22     130 .. 0.80
   2 ?   -0.2   0.0      0.05   4.5e+02     184     207 ..     159     182 ..     154     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                            NUP  44 dgsvcqlvtGegeinaaasimaLvlsprFdLtktYfliaGiaGvnPkaatiGsvafaryavqvdlqyeidarel 117
                                    ++ v+   +G+g++n    ++a +l +rF  +    +++G+aG    +  iG++++a+ +vq d     d+r  
  gi|121636004|ref|YP_976227.1|  42 AHRVVLAAAGMGKVNTG--LTATLLADRFGCRT--IVFTGVAGGLDPELCIGDIVIADRVVQHDFGLLTDERLR 111
                                    345899999***99976..567788899*9987..566899876444568**************9999998855 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.05
                            NUP 184 qkpPsvvkcdtltsdtywsGklls 207
                                     ++P ++ +  lt+d+y + ++  
  gi|121636004|ref|YP_976227.1| 159 GRQPRIYYGTILTGDQYLHCERTR 182
                                    589**************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1797.03
//
Query:       gi|121636005|ref|YP_976228.1|  [L=761]
Description: cation transporter p-type atpase A ctpA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-49  168.7   4.5      2e-49  168.7   4.5    3.0  3  Hydrolase     haloacid dehalogenase-like hydrolase
    1.8e-45  154.7   3.9    1.8e-45  154.7   3.9    2.4  2  E1-E2_ATPase  E1-E2 ATPase
    3.6e-11   43.4   0.0    8.2e-11   42.2   0.0    1.7  1  HMA           Heavy-metal-associated domain
    0.00026   20.8   0.2      0.024   14.4   0.1    2.4  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    0.00084   19.8   1.3      0.018   15.5   0.2    3.4  3  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.81   2.9e+03     120     152 ..      60      92 ..      40     109 .. 0.73
   2 ?    1.3   0.7       0.1   3.6e+02     103     152 ..     291     391 ..     161     398 .. 0.61
   3 !  168.7   4.5   5.6e-53     2e-49       1     210 []     437     649 ..     437     649 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.81
                                    HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraa 152
                                      +aa ++++ ++ag++  l+t d ++  +  a
  gi|121636005|ref|YP_976228.1|  60 AVDAAALCQAVRRAGYQADLCTDDGRSASDPDA 92 
                                    457888888889999988888888776655544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                    H......................................................TTHHHHHHHHHHTHHBHTTHHHHHH CS
                                    x......................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 103 l......................................................qaralavftiadplkvkpeaaeava 128
                                    +                                                       ++a+a   +    +v+  a+ ++a
  gi|121636005|ref|YP_976228.1| 291 DmsamtgeakptrvrpggqviggttvldgrliveaaavgadtqfagmvrlveqaqAQKADAQRLADRISSVFVPAVLVIA 370
                                    04444444444444444444444444445555555555555555555555666632233333344444568888889999 PP

                                    HHHHTTEEEEEEESSEHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 129 sLkaagievvlltgdnpetaeraa 152
                                    +L aag+   l+ g++p  a +aa
  gi|121636005|ref|YP_976228.1| 371 ALTAAGW---LIAGGQPDRAVSAA 391
                                    9999988...88888888777655 PP

  == domain 3  score: 168.7 bits;  conditional E-value: 5.6e-53
                                    SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE....... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakarsgaltgfatfigrg....... 67 
                                    ++tvvfDk+GTLttg+ +v  v++         lalaa  e +seh  + a+ aaa  r+ a+t+f++++grg       
  gi|121636005|ref|YP_976228.1| 437 VDTVVFDKTGTLTTGRLQVSAVTAAPgweadqVLALAATVEAASEHSVALAI-AAATTRRDAVTDFRAIPGRGvsgtvsg 515
                                    68**************999999999977777777788888888*********.8888888******************** PP

                                    .HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSE CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 .ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdn 144
                                     a+ +gkp w+ +   +p+++aa   a+s g+t++++  +++ ++v+++ad   vk+ a++ava+L ++g+++ lltgdn
  gi|121636005|ref|YP_976228.1| 516 rAVRVGKPSWIGSSSCHPNMRAARRHAESLGETAVFVevDGEPCGVIAVADA--VKDSARDAVAALADRGLRTMLLTGDN 593
                                    *************************************99*************..************************** PP

                                    HHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 145 petaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    pe a ++a ++G          ++e++a  +pegkv +i++L+ +++ vamVGDg+nD +ala+A+
  gi|121636005|ref|YP_976228.1| 594 PESAAAVATRVG----------IDEVIADILPEGKVDVIEQLRDRGHVVAMVGDGINDGPALARAD 649
                                    ************..........6666**************************************98 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4      0.48   1.7e+03     117     157 ..     126     142 ..      93     193 .. 0.63
   2 !  154.7   3.9     5e-49   1.8e-45       4     179 ..     243     419 ..     240     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.48
                                    HHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                   E1-E2_ATPase 117 klgkvlvpvvlliallvflialllgkslaeallralallva 157
                                    +++++                        +++l+alal v+
  gi|121636005|ref|YP_976228.1| 126 RFTGW------------------------QWVLSALALPVV 142
                                    33333........................444444444333 PP

  == domain 2  score: 154.7 bits;  conditional E-value: 5e-49
                                    --EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEE CS
                   E1-E2_ATPase   4 pptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeak 82 
                                    ++++ v+  dg+e+ i+a+el+     ++++g++v+aDg  v+gsa vd sa+TGE++p ++  g +v++Gt+v++g+++
  gi|121636005|ref|YP_976228.1| 243 AKEVAVLlPDGSEMVIPADELKEQQRFVVRPGQIVAADGLAVDGSAAVDMSAMTGEAKPTRVRPGGQVIGGTTVLDGRLI 322
                                    55555555************************************************************************ PP

                                    EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TT CS
                   E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPca 162
                                    +++ a+g dt+++ ++rlve+a+++k++ q+ +d++++v+vp+vl+ia+l+++ +l+ g+++ +a+  ala+lv+a+Pca
  gi|121636005|ref|YP_976228.1| 323 VEAAAVGADTQFAGMVRLVEQAQAQKADAQRLADRISSVFVPAVLVIAALTAAGWLIAGGQPDRAVSAALAVLVIACPCA 402
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 163 Lplavplalalgarrla 179
                                    L+la+p+a++++ +r a
  gi|121636005|ref|YP_976228.1| 403 LGLATPTAMMVASGRGA 419
                                    *************9987 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   2.3e-14   8.2e-11       2      62 .]      18      76 ..      17      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.3e-14
                            HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                   +r+sgm C +Ca +ve++L +lpgV  + v+++t+ +t++++++  +  ++ +a++ agy+
  gi|121636005|ref|YP_976228.1| 18 LRISGMSCSACAHRVESTLNKLPGV-RAAVNFGTRVATIDTSEAV-DAAALCQAVRRAGYQ 76
                                   79***********************.788************9988.5589*********95 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0098        35      16      58 ..     568     610 ..     562     613 .. 0.90
   2 !   14.4   0.1   6.8e-06     0.024     205     247 ..     631     673 ..     617     681 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0098
                                    --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                    +++++++a++ l ++g   ++ TG +++++  v+  +g+d  +
  gi|121636005|ref|YP_976228.1| 568 VKDSARDAVAALADRGLRTMLLTGDNPESAAAVATRVGIDEVI 610
                                    78999*********************************99544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.8e-06
                                    GEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                    Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                     v+ +GDg ND + L +a+lg+A+g +++ ++ aAd +    +
  gi|121636005|ref|YP_976228.1| 631 VVAMVGDGINDGPALARADLGMAIGRGTDVAIGAADIILVRDH 673
                                    57889*******************************9976655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.42   1.5e+03      46     110 ..      20      83 ..      10      93 .. 0.74
   2 ?   -2.5   0.0       1.6   5.6e+03       1      41 [.     440     474 ..     440     519 .. 0.62
   3 !   15.5   0.2     5e-06     0.018      89     187 ..     571     645 ..     560     646 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.42
                            HAD  46 llrldraglaelleallagls.eelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgg 110
                                    ++ ++++++a+ +e++l  l+  + a  ++  va++ +  +   +a +l++a+r+aG++  +++  
  gi|121636005|ref|YP_976228.1|  20 ISGMSCSACAHRVESTLNKLPgVRAAVNFGTRVATIDTSEAV--DAAALCQAVRRAGYQADLCTDD 83 
                                    556666777777777777777666666677777666666643..9999*********998888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralrekllla 41 
                                    ++fD  gTL++g      ++      a + w+a ++ +l+a
  gi|121636005|ref|YP_976228.1| 440 VVFDKTGTLTTGRLQVSAVT------AAPGWEADQVLALAA 474
                                    67888889988854442222......222244444444444 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 5e-06
                            HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegeg 168
                                     a++++aa +++G r+ +++g + + + +++ ++g+dev+a                   +  egkv+++++ l ++g  
  gi|121636005|ref|YP_976228.1| 571 SARDAVAALADRGLRTMLLTGDNPESAAAVATRVGIDEVIAD------------------ILPEGKVDVIEQ-LRDRG-- 629
                                    5788888888*************************9999999..................233345555555.22233.. PP

                            HAD 169 idleevvayGDspsDlpll 187
                                       + v  +GD+++D p+l
  gi|121636005|ref|YP_976228.1| 630 ---HVVAMVGDGINDGPAL 645
                                    ...2344448888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 5524.69
//
Query:       gi|121636006|ref|YP_976229.1|  [L=282]
Description: hypothetical protein BCG_0126c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-10   39.3   4.8      1e-09   38.5   4.8    1.5  1  zf-HC2           Putative zinc-finger
  ------ inclusion threshold ------
        3.2    7.8  10.2        8.1    6.5  10.1    1.7  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   4.8   1.1e-13     1e-09       1      35 []      49      83 ..      49      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.1e-13
                                   HCCHHHHHHHHHCCT-SCCCHCCCHHHHCHTCHHC CS
                         zf-HC2  1 CeevrelLsaYlDGeLspeerarveaHLaeCpdCr 35
                                   Ce +re+Lsa+lDGe +p   arv++HL eC++Cr
  gi|121636006|ref|YP_976229.1| 49 CEVAREALSARLDGERAPVPSARVDEHLGECSACR 83
                                   **********************************9 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  10.1    0.0009       8.1      38     100 ..     190     252 ..     167     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0009
                Phage_holin_3_6  38 gllgaagvlallalllllvala..lalaa.....lwlaalivaavllvlagvlalvglkklkkakplper 100
                                    +      + +l ++l+++va++  +++ +     +   + i++ + +v+++vla++ ++ +++ +p p++
  gi|121636006|ref|YP_976229.1| 190 A------AAGLAGVLTAFVAILtgYVI-VdalsgAVSTTRILTHLPVVIGAVLAIMVWRSASGPRPRPDA 252
                                    2......33333333333333322222.12245566777789******************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2315.83
//
Query:       gi|121636007|ref|YP_976230.1|  [L=317]
Description: hypothetical protein BCG_0127c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-64  217.2   3.4    4.3e-64  216.9   3.4    1.1  1  DUF222    Domain of unknown function (DUF222)
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.015   15.5   0.1    2.2  3  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   3.4   4.8e-68   4.3e-64     103     301 .]       2     223 ..       1     223 [. 0.97

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 4.8e-68
                         DUF222 103 atvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltk.dedGmsrisgeldaeaaaaldavLd 181
                                    +t+++aea+l+++aa+++p+eLa+ ++r++++l+pDg+ +d+e+ar+r++tl++ + dGmsr+sg+l+++a+a+++avL+
  gi|121636007|ref|YP_976230.1|   2 STRQAAEADLAGKAAQYRPDELARYAQRVMDWLHPDGDLTDTERARKRGITLSNqQYDGMSRLSGYLTPQARATFEAVLA 81 
                                    799***************************************************9************************* PP

                         DUF222 182 slaap.vcap..............dgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvhvtaeeltaaagga 246
                                    +laap   +p              ++++D+Rs+aqr++D+Lla+lr+++a+g+l++h+g+p+++vv++t+++l++ ag+ 
  gi|121636007|ref|YP_976230.1|  82 KLAAPgATNPddhtpvidttpdaaAIDRDTRSQAQRNHDGLLAGLRALIASGELGQHNGLPVSIVVTTTLTDLQTGAGK- 160
                                    *****88888*********************************************************************. PP

                         DUF222 247 altgggglLpasdvrrLAkdAt..........laifdepagrpldlgrtkrtasaalrralraRD 301
                                    + tggg+lLp++dv+r+ ++A+           aifd+  g+pl+l++tkr+as+a+r++l a D
  gi|121636007|ref|YP_976230.1| 161 GFTGGGTLLPMADVIRMTSHAHhyspasgrypQAIFDH--GTPLALYHTKRLASPAQRIMLFAND 223
                                    **************************999986668888..*********************9877 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.61   5.5e+03      14      23 ..     179     188 ..     173     203 .. 0.65
   2 ?   15.5   0.1   1.6e-06     0.015       4      42 ..     226     266 ..     224     271 .. 0.85
   3 ?   -3.7   0.8       1.7   1.5e+04      15      23 ..     289     297 ..     279     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.61
                            HNH  14 levdHiipis 23 
                                    ++ +H  p s
  gi|121636007|ref|YP_976230.1| 179 SHAHHYSPAS 188
                                    5667765544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-06
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHn 42 
                                    C +++ +   + ++ +H+  +   g++di +l+l+C   ++
  gi|121636007|ref|YP_976230.1| 226 CTKPGCDApaYHSQAHHVTGWTSTGRTDITDLTLACDPDNR 266
                                    6666666666889***********************98887 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.7
                            HNH  15 evdHiipis 23 
                                    + dH +p+ 
  gi|121636007|ref|YP_976230.1| 289 HLDHGQPWT 297
                                    566666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.18s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2790.63
//
Query:       gi|121636008|ref|YP_976231.1|  [L=260]
Description: hypothetical protein BCG_0128c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-19   70.0   2.4    3.1e-19   69.6   2.4    1.3  1  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   2.4   1.7e-23   3.1e-19       3      97 ..      76     180 ..      74     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.7e-23
                         DUF222   3 aaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lpa 71 
                                    + le+le + rrl+av+++l+++l+ ++s+ee g++ ++ ++a+rlri+  +A+ r++ A++l++r           L+a
  gi|121636008|ref|YP_976231.1|  76 RSLERLECLVRRLPAVGHTLINQLDTQASEEELGGT-LCCALANRLRITKPDAALRIADAADLGPRraltgeplapqLTA 154
                                    6799********************************.******************************************* PP

                         DUF222  72 vaaalraGdidlrqvrvIaartdllp 97 
                                    +a+a+r+G i++ +++vI+a ++   
  gi|121636008|ref|YP_976231.1| 155 TATAQRQGLIGEAHIKVIRALFRPPA 180
                                    *******************9988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2088.05
//
Query:       gi|121636009|ref|YP_976232.1|  [L=463]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-59  199.2  19.3    8.5e-59  198.2  19.3    1.5  1  PPE       PPE family
  ------ inclusion threshold ------
       0.21   11.9   3.3       0.51   10.6   3.3    1.7  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.2  19.3   9.5e-63   8.5e-59       1     157 [.       2     158 ..       2     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.2 bits;  conditional E-value: 9.5e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+s ll+aG g+g+ll Aa++W++L++++a a ael ++l e++a++WqG+++++++aa+ pylaWL+++a +++
  gi|121636009|ref|YP_976232.1|   2 AIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAATQYVAAHGPYLAWLEQTAINSA 81 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     +Aaq+ aaaaaY +Alaam++pae+aan+a + +l+atnffG+nt++Ia +ea+y +mw+q+a++maaY+a++ aa
  gi|121636009|ref|YP_976232.1|  82 VTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIATNFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAA 158
                                    **************************************************************************998 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.3   5.7e-05      0.51      11      61 ..      23      74 ..      18      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHH CS
                         WXG100 11 qaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaq 61
                                    aa++ q+ +++   + ++l + + ++ +s+W+G+aa+++ a+   + + ++
  gi|121636009|ref|YP_976232.1| 23 VAAQQWQELSDQYALACAELGQLLGEVqASSWQGTAATQYVAAHGPYLAWLE 74
                                   58999999999999999**********999**********998765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3850.73
//
Query:       gi|121636010|ref|YP_976233.1|  [L=289]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-31  107.9   0.0    9.7e-31  107.5   0.0    1.0  1  TauD      Taurine catabolism dioxygenase TauD, TfdA family


Domain annotation for each model (and alignments):
>> TauD  Taurine catabolism dioxygenase TauD, TfdA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   5.4e-35   9.7e-31       9     254 ..      10     263 ..       3     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 5.4e-35
                           TauD   9 fgaegvdlsdleslddelkeelrellaeygvvvfrgfplspeqqlefarrfG...plygtpgrgtntkygevldvssvye 85 
                                    +ga+ v + d+++ldd +++e+r+++++ ++vv+++++ sp +++++ r +G   p y +  +++ ++++e++++s+++ 
  gi|121636010|ref|YP_976233.1|  10 LGAQ-VTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIGqivPYYEP--MYHHEDHPEIFVSSTEEG 86 
                                    6777.7778888899999*********************************976544444..478889999999665333 PP

                           TauD  86 sadianlayttllwHtDlsylesppgiqlLhcleapatGGetpfvDgraaynaLpeelpellegltavrvyyhyrg.... 161
                                    ++    + +t+++wH D +++++p  +++   l +p +   t+f D ++++++Lp++ ++  +g   ++++++ ++    
  gi|121636010|ref|YP_976233.1|  87 QG----VPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGHDRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKirps 162
                                    33....3367999******************************************************************* PP

                           TauD 162 ..gglrteqelpavdkhprtghpvvrthpvltgrkallvnppfatri.eglgtpeskelldaleelled......pefty 232
                                      ++   e  ++  ++ p+ ++p v +hp+ tg++ l++ +  +t+i + +g p   e+l++l +++ +        f +
  gi|121636010|ref|YP_976233.1| 163 dvYRPIGEVWDEINRTTPPIKWPTVIRHPK-TGQEILYICATGTTKIeDKDGNPVDPEVLQELMAATGQldpeyqSPFIH 241
                                    99888888889999***************7.*********9888889556666999999999999998887444225556 PP

                           TauD 233 rfqwqeGdlvifdNrrvlHgrt 254
                                        q Gd++++dNr ++H+++
  gi|121636010|ref|YP_976233.1| 242 TQHYQVGDIILWDNRVLMHRAK 263
                                    777888**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2254.01
//
Query:       gi|121636011|ref|YP_976234.1|  [L=183]
Description: hypothetical protein BCG_0131 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-61  205.6   0.0    3.5e-61  205.4   0.0    1.0  1  FcoT      FcoT-like thioesterase domain


Domain annotation for each model (and alignments):
>> FcoT  FcoT-like thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   1.9e-65   3.5e-61       1     155 [.      28     178 ..      28     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 1.9e-65
                                    HHCCCCH.CCG--EEEEEEEEETTEETTS.EEEEEEE--SS-SSCS--SS--CHHHHHHHHHHHHHHHHHHHHCT-SCCC CS
                           FcoT   1 rvLepYk.kncrYLksaevesesdavdegkavakgeFeipescYiddtGHfnavElniCynqlaYvllAkavkeklleal 79 
                                    rvLepY+ k crYL +a++++++d+v     +a+g+F+i+es+Yi++tGHfnavEl++C+nqlaY+++A av ++++++l
  gi|121636011|ref|YP_976234.1|  28 RVLEPYScKGCRYLIDAQYSATEDSV-----LAYGNFTIGESAYIRSTGHFNAVELILCFNQLAYSAFAPAVLNEEIRVL 102
                                    8*********************9999.....9************************************************ PP

                                    TT--HHHHHHCCCCCEEEEEEEEEEEC---TTSEEEEEEEEEEEEE-SSS-EEEEEEEEEEE-SSS-EEEEEEEEE CS
                           FcoT  80 aawtledylerqLsdilitkfssrfrkainprkFsgeleikkvrerekgarllilktkieflDeegGeaeGevela 155
                                    ++w+++dy+++qLs++li+k+ssrfrk++np+kFs++l +++++ +e+++r+l++ + ief+De+gG+a+Ge+ela
  gi|121636011|ref|YP_976234.1| 103 RGWSIDDYCQHQLSSMLIRKASSRFRKPLNPQKFSARLLCRDLQVIERTWRYLKVPCVIEFWDENGGAASGEIELA 178
                                    **************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1288.09
//
Query:       gi|121636012|ref|YP_976235.1|  [L=540]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-74  251.1   0.0    1.8e-74  250.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.2e-11   45.5   0.2    3.9e-11   43.8   0.2    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.9   0.0     2e-78   1.8e-74       2     422 ..      21     430 ..      20     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 250.9 bits;  conditional E-value: 2e-78
                                    HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                    AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                     eqa+++p+++al ++++   l Yrel ++v  lAa Lr+  v +g+rV+++++n+pe ++++la++k+Ga++v+ + +l
  gi|121636012|ref|YP_976235.1|  21 FEQARQQPEAIALRRCDGTSALRYRELVAEVGGLAADLRAQSVSRGSRVLVISDNGPETYLSVLACAKLGAIAVMADGNL 100
                                    689**********88999*********************99*************************************** PP

                                    -HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSE CS
                    AMP-binding  82 taeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddl 161
                                    + ++++  ++ +++ + +  v     +++ +a ++  ++  vi +d +++ +e  ++++ ++++ a     ++ + ++d+
  gi|121636012|ref|YP_976235.1| 101 PIAAIERFCQITDPAAAL--VAPGS-KMASSAVPEALHSIPVIAVDIAAVTRE--SEHSLDAASLA----GNADQGSEDP 171
                                    ******************..54333.444445554445556677776666555..33333333322....3446789*** PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTT..T-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTC CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklke..ddvvlsilplahifglilelllallsGatvvllpkd 237
                                    + +i+TSGTTG+PK+V l  r + a    l  +++   ++++  +++ +s lp  hi gl +++l++l++G+ +v   ++
  gi|121636012|ref|YP_976235.1| 172 LAMIFTSGTTGEPKAVLLANRTFFAVPDIL--QKEglNWVTWvvGETTYSPLPATHIGGL-WWILTCLMHGGLCVTGGEN 248
                                    **********************98874444..33333334447799*************8.***********77775544 PP

                                    GCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEE CS
                    AMP-binding 238 aaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYG 316
                                     ++    lle +++  v ++++vP++l +l++  ++      +   +slrlv  gg++  ++ +rf++a++ +   ++YG
  gi|121636012|ref|YP_976235.1| 249 -TT---SLLEILTTNAVATTCLVPTLLSKLVSeLKSA-----NATVPSLRLVGYGGSRAIAADVRFIEATGVR-TAQVYG 318
                                    .43...489*********************9944333.....33899*****99**********9****9876.9***** PP

                                    EGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE.....EEEEEEETTS-SEBTT-HHHHHHH CS
                    AMP-binding 317 lTEttgvvtv...lpleedkkklgsvGkplpgvevkivDeetgepvpdgee.....GellvrgpgvmkgYlkkpeataea 388
                                    l+Et++ + +   ++ +  k  +g vG+p pgv+v+++  ++ +p ++g       G l++++p +m gY+++pe+tae+
  gi|121636012|ref|YP_976235.1| 319 LSETGCTALClptDDGSIVKIEAGAVGRPYPGVDVYLAATDGIGPTAPGAGpsasfGTLWIKSPANMLGYWNNPERTAEV 398
                                    ******9966655444444456799****************999999888778889************************ PP

                                    EEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 389 fdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    ++  ++w++TGDl +++edG ++i gR+ ++i++
  gi|121636012|ref|YP_976235.1| 399 LI--DGWVNTGDLLERREDGFFYIKGRSSEMIIC 430
                                    *9..57**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.2   4.4e-15   3.9e-11       1      76 []     439     519 ..     439     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.4e-15
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE.---..---....HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvl.kdg..sea....leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                    ev  +   + +V+eaa++ +pde  G alv++ v  +++  + +    l++++ a+ r+e +p a+p+++v+v ++p+t+
  gi|121636012|ref|YP_976235.1| 439 EVDRIAEGVSGVREAACYEIPDEEFG-ALVGLAVVaSAEldE-SaaraLKHTIAARFRRESEPMARPSTIVIVTDIPRTQ 516
                                    678888999**************888.666665551333332.13567******************************** PP

                                    TS- CS
                  AMP-binding_C  74 sGK 76 
                                    sGK
  gi|121636012|ref|YP_976235.1| 517 SGK 519
                                    **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3701.19
//
Query:       gi|121636013|ref|YP_976236.1|  [L=78]
Description: hypothetical protein BCG_0133 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-12   45.9   0.3    5.9e-12   45.8   0.3    1.1  1  PP-binding  Phosphopantetheine attachment site
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.15   12.3   0.0    1.2  1  PND         FANCM pseudonuclease domain


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.3   6.6e-16   5.9e-12       1      65 [.       3      68 ..       3      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.6e-16
                     PP-binding  1 eklrelvaevlgvpleei.d.pdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaa 65
                                   ++++++v++vl +++ ++ d ++tdl+dlGlDS+ +v l+ +l    + e+p++   ++p++a +++
  gi|121636013|ref|YP_976236.1|  3 DRILAAVCDVLYIDEADLiDgDETDLRDLGLDSVRFVLLMKQLGVNRQSELPSRLA-ANPSIAGWLR 68
                                   689**********999955669********************************88.9****99877 PP

>> PND  FANCM pseudonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05      0.15      41      63 ..       4      26 ..       1      56 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                   EECSSSEEEEEEEHHHHHH-STT CS
                            PND 41 fylsndtavlyiseadiiegngy 63
                                     l++ + vlyi+ead+i+g + 
  gi|121636013|ref|YP_976236.1|  4 RILAAVCDVLYIDEADLIDGDET 26
                                   567789*************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 569.58
//
Query:       gi|121636014|ref|YP_976237.1|  [L=2512]
Description: peptide synthetase nrp [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.2e-121  404.2   3.9    1.7e-83  280.6   0.1    2.6  2  AMP-binding      AMP-binding enzyme
    2.1e-87  293.7   0.0    1.7e-85  287.4   0.0    2.1  2  Condensation     Condensation domain
    8.9e-60  202.0   0.0    1.3e-59  201.5   0.0    1.3  1  NAD_binding_4    Male sterility protein
    1.8e-23   82.6   0.5    1.8e-13   50.6   0.1    2.7  2  PP-binding       Phosphopantetheine attachment site
    2.8e-09   37.8   2.3    1.6e-08   35.4   0.5    3.5  2  AMP-binding_C    AMP-binding enzyme C-terminal domain
    8.9e-07   28.6   0.0      2e-06   27.4   0.0    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00022   20.3   0.0    0.00084   18.4   0.0    1.8  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0031   16.4   0.0      0.062   12.1   0.0    2.4  3  GH3              GH3 auxin-responsive promoter
  ------ inclusion threshold ------
      0.098   11.7   0.0         13    4.7   0.0    2.4  2  RmlD_sub_bind    RmlD substrate binding domain
       0.14   12.4   0.1        3.9    7.7   0.1    2.9  2  HTH_17           Helix-turn-helix domain
       0.25   10.5   0.0        1.2    8.2   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   1.3   4.7e-39   7.6e-36      37     422 ..     473     828 ..     471     829 .. 0.78
   2 !  280.6   0.1     1e-86   1.7e-83       2     423 .]    1499    1882 ..    1498    1882 .. 0.87

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 4.7e-39
                                    HHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSC CS
                    AMP-binding  37 agLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvliatvdselleklleaaak 116
                                    a+L ++G+ +gd+ ++  + +   + +l+a+  aG+ +++++++        ++++ +  +l+  +       + ++aa+
  gi|121636014|ref|YP_976237.1| 473 AWLVQRGAAPGDVLVFTDDDTDKTIDLLIACHLAGCGYSVCDTADEISVRTNAITEHGDGILV--T-------VVDVAAT 543
                                    688888999999888888999999999999999999999999999999999999999999999..3.......2222221 PP

                                    C-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC CS
                    AMP-binding 117 leavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr 196
                                         +  v+ +del+k   ++e+     ++  ++++++l +  +ayi+ TSGTTG+PK V +sh++l+ ++ +++ + +
  gi|121636014|ref|YP_976237.1| 544 -----QLAVVGHDELRKV--VDER-----VT--QVTHDALLATKTAYIMPTSGTTGQPKLVRISHGSLAVFCDAIS-RAY 608
                                    .....1223333333333..2211.....22..33555678999******************************95.334 PP

                                    .SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHH CS
                    AMP-binding 197 .fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalk 274
                                     +  +++d+vl+++pl  ++++  e+++  ++Ga++v +   ++ d ++l++++ + + t++ ++ +v++ l +  +a++
  gi|121636014|ref|YP_976237.1| 609 gW--GAHDTVLQCAPLTSDISV-EEIFGGAACGARLVRSAAMKTGDLAALVDDLVARETTIVDLPTAVWQLLCAdGDAID 685
                                    34..479**************8.***************9999998888999*******************9988565555 PP

                                    CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.....CHCTTTCTSTTS-BEE-TTE CS
                    AMP-binding 275 aakkakdlsslrlvllggeplspellrffralfge...evlegYGlTEttgvvtv.....lpleedkkklgsvGkplpgv 346
                                        a   s+lr++++gge+++ ++++++ +       ++l +YG+TE+t+v+t+     +++  d +   + G+p+  +
  gi|121636014|ref|YP_976237.1| 686 ----AIGRSRLRQIVIGGEAIRCSAVDKWLESAASqgiSLLSSYGPTEATVVATFlpivcDQTTMDGAL-LRLGRPILPN 760
                                    ....557889**************999999998888999**************9844443222222222.2355555444 PP

                                    EEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT.-HHHHHHHEEE...T.CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 347 evkivDeetgepvpdgeeGellvrgpgvmkgYlk.kpeataeafds...e.grwlrTGDlgrldedGyleivgRkkdlik 421
                                     v +              Ge+++ g  v+ gYl+ + +    + ++   +  r + TGD +++d++G   + gRk+ ++k
  gi|121636014|ref|YP_976237.1| 761 TVFL------------AFGEVVIVGDLVADGYLGiDGDGFGTV-TAadgSrRRAFATGDRVTVDAEGFPVFSGRKDAVVK 827
                                    4444............23****************553443333.323443356*************************** PP

                                    E CS
                    AMP-binding 422 l 422
                                    +
  gi|121636014|ref|YP_976237.1| 828 I 828
                                    8 PP

  == domain 2  score: 280.6 bits;  conditional E-value: 1e-86
                                     HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                    AMP-binding    2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79  
                                     ++q+a+ p++ a+    ++ ++TYrelde++nrlA+ L   G+++g++Va+l ++++  vva++a+lk Ga++ p++p
  gi|121636014|ref|YP_976237.1| 1499 AAQVARIPEAEAVCC--GDASMTYRELDEASNRLAHRLAGCGAGPGECVALLFERCAPAVVAMVAVLKTGAAYLPIDP 1574
                                     5789999******98..99********************88************************************* PP

                                     TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-B CS
                    AMP-binding   80 tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelk 157 
                                     + +++++a++l d+ + + +  + +     l++  a  ++  ++ v+da   l      +  +        ++++ + 
  gi|121636014|ref|YP_976237.1| 1575 ANPPPRVAFMLGDAVPVAAV--TTAG----LRSRLAG-HDLPIIDVVDA---L-----AAYPG--------TPPPMPA 1629
                                     ********************..5333....3333332.22223333332...2.....21221........1234688 PP

                                     TTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                    AMP-binding  158 pddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllp 235 
                                     + +layi+YTSGTTG+PKGV ++hrn++   asl  + r  l++ +v+ ++ ++ ++++  +e+++all G+++v++p
  gi|121636014|ref|YP_976237.1| 1630 AVNLAYILYTSGTTGEPKGVGITHRNVTRLFASL--PAR--LSAAQVWSQCHSYGFDASA-WEIWGALLGGGRLVIVP 1702
                                     99****************************9996..444..456889999*********8.***************** PP

                                     TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEE CS
                    AMP-binding  236 kdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevle 313 
                                     ++ a++p+ +++l+ +++v+v++ +P+++ +l  +           l s+ lv ++ge+++++l++++    +  +l+
  gi|121636014|ref|YP_976237.1| 1703 ESVAASPNDFHGLLVAEHVSVLTQTPAAVAMLPTQ----------GLESVALV-VAGEACPAALVDRWAPG-RV-MLN 1767
                                     **9999999***********************886..........57789885.7*************997.44.9** PP

                                     EEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEE CS
                    AMP-binding  314 gYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafd 390 
                                     +YG+TEtt+++++ +p  ++ +  + +G p+ g+ + ++D   ++pvp g+ Gel++ g+gv  gY+++  +ta++f+
  gi|121636014|ref|YP_976237.1| 1768 AYGPTETTICAAIsAP-LRPGSGMPPIGVPVSGAALFVLDSW-LRPVPAGVAGELYIAGAGVGVGYWRRAGLTASRFV 1843
                                     ***********88533.455556778***************9.*********************************** PP

                                     E.....T.CCEEEEEEEEEEETTSEEEEEEECCCEEEET CS
                    AMP-binding  391 s.....e.grwlrTGDlgrldedGyleivgRkkdliklr 423 
                                     +     +  r++rTGDl+ +++dG+le++gR++d++k+r
  gi|121636014|ref|YP_976237.1| 1844 AcpfggSgARMYRTGDLVCWRADGQLEFLGRTDDQVKIR 1882
                                     8999974457***************************96 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.01        17     117     157 ..     101     142 ..      98     155 .. 0.79
   2 !  287.4   0.0     1e-88   1.7e-85       5     456 ..    1023    1475 ..    1020    1475 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                                    -SEEEEEEESSTTEEEEEEEE..ECCT--TTTHHHHHHHHHHH CS
                   Condensation 117 pLfraalfkiaenrlllllsv..HHiivDGvSlgillrdlakl 157
                                    pL+r+ +++ + n+++  l+v  HHi++DG  +g++  dla+ 
  gi|121636014|ref|YP_976237.1| 101 PLVRHTVHT-DPNGYVTGLDVhtHHILLDGGATGTIEADLARY 142
                                    899999999.88888876665228*************999975 PP

  == domain 2  score: 287.4 bits;  conditional E-value: 1e-88
                                     EEXXCCHHHHHHHHHHSSSSSTTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT----- CS
                   Condensation    5 yplspaQkrmwflekleeessaynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevel 82  
                                     +pls aQ+r+wfl +l++    ynm+++l+l+g+ld e+l  a+  ++ rh++LRtvf    +g p+Q + e+r ++l
  gi|121636014|ref|YP_976237.1| 1023 IPLSFAQRRLWFLDQLQRPAPVYNMAVALRLRGYLDTEALGAAVADVVGRHESLRTVFP-AVDGVPRQLVIEARRADL 1099
                                     89********************************************************6.55*********9999988 PP

                                     ..EEEE-T..TSSSHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHH CS
                   Condensation   83 ..evleisdleeseeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklY 158 
                                        +++++ + +++ ++aiee+a+    ++fdL++++++r  lf+ia+++++l++  HHi +DG+S+  l+ dl+++Y
  gi|121636014|ref|YP_976237.1| 1100 gcDIVDATAWPADRLQRAIEEAAR----HSFDLATEIPLRTWLFRIADDEHVLVAVAHHIAADGWSVAPLTADLSAAY 1173
                                     446666666667777777777777....7************************************************* PP

                                     HHHHTT-------S--.HHHHHHHHHHHHCSHH.....HHHHHHHHHHHHH......S---BSS---SS---S-EEEE CS
                   Condensation  159 qqlekgeelplpqktp.Ykdyaeweqqyleskd.....lekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsi 230 
                                     ++   g+ ++  + +  Y dy  w++++l+  d     +  + aYW++ l+g  + l Lp+ ++ p++ + ++ +l++
  gi|121636014|ref|YP_976237.1| 1174 ASRCAGRAPDWAPLPVqYVDYTLWQREILGDLDdsdspIAAQLAYWENALAGMPERLRLPTARPYPPVADQRGASLVV 1251
                                     ********999888878***********9864422333889*********************999************* PP

                                     EEEE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT CS
                   Condensation  231 kldeeteeklrklakeqgvtlndvllaalgllLskytgqddivvgteisgReseikdiermvGlFvntlPlridvkea 308 
                                     ++++++++++r++a+++++t  +v  a l++lLsk++g+ d++vg++i+gR ++  ++++ vG+Fvntl lr++++++
  gi|121636014|ref|YP_976237.1| 1252 DWPASVQQQVRRIARQHNATSFMVVAAGLAVLLSKLSGSPDVAVGFPIAGRSDP--ALDNLVGFFVNTLVLRVNLAGD 1327
                                     ******************************************************..********************** PP

                                     -BHHHHHHHHHHHHHHHHCCTTS-HHHHHHCSS.SS-SSSS-S-SEEEEESSS-HHCCCEEECCCCSEEECEE....E CS
                   Condensation  309 ktfselikrvkedllkaephqgypleeLvkdlelqrkesrspLfdpvfsfenylgqeseeeesqlselklsvssve.a 385 
                                      +f+el+ +v+++ l a+++q++p+e Lv++l+ +r++  +pL+++++  +        +   ql+ ++l+ ++++ +
  gi|121636014|ref|YP_976237.1| 1328 PSFAELLGQVRARSLAAYENQDVPFEVLVDRLKPTRAMTHHPLIQVMLAWQD-------NPVGQLNLGDLQATPMPiD 1398
                                     **************************************************88.......6666666666666677777 PP

                                     .....SSEEEEEEE......TTSSEEEEEEEETTTS-HHHHHHHHHHHHHHHHHHHHSTTSBCCC-----HHHHHHH CS
                   Condensation  386 eeeskydlslease......tngkltikieYntslFdeetierflerlkelleqviehpeqklselkllsdaekekL 456 
                                      +++  dl +++ e      +  ++   +eY+t++F+ + i+ ++erl+++l +v++ pe ++s+++ l+ +e++ L
  gi|121636014|ref|YP_976237.1| 1399 TRTARMDLVFSLAErfsegsEPAGIGGAVEYRTDVFEAQAIDVLIERLRKVLVAVAAAPERTVSSIDALDGTERARL 1475
                                     888888998888887754544558999******************************************99998876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.5   0.0   8.1e-63   1.3e-59       1     257 []    2112    2372 ..    2112    2372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 8.1e-63
                                     EE-TTSHHHHHHHHHHHHHS-.T.EEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHH...HHTTTEEEEE--TTSGGG CS
                  NAD_binding_4    1 lTGaTGFLGkvLlekLLrttpev.kiyllvRaksgesaeeRleeelekkelfsallk...elaerikvveGDlseprl 74  
                                     lTGaTGFLG++L+ +LLr+ +   ++++lvRa+s+e+a++Rle+++++ + +    +    +a+r++vv+GD sep+l
  gi|121636014|ref|YP_976237.1| 2112 LTGATGFLGRYLVLELLRRLDVDgRLICLVRAESDEDARRRLEKTFDSGDPELLR-HfkeLAADRLEVVAGDKSEPDL 2188
                                     8******************98669******************9999987654333.234599**************** PP

                                     G--HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS CS
                  NAD_binding_4   75 GLseedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekv 151 
                                     GL++  +++lae+vd+i++saA vn   py+el+ +Nv Gt e++++a ++k + ++ +vST  + +  + ++++e+ 
  gi|121636014|ref|YP_976237.1| 2189 GLDQPMWRRLAETVDLIVDSAAMVN-AFPYHELFGPNVAGTAELIRIALTTKLK-PFTYVSTaDVGAAIEPSAFTED- 2263
                                     *************************.679********************99888.*******667777777777666. PP

                                     -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST---TTSHHHHHHHHH CS
                  NAD_binding_4  152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwingsdlgirgllgl 228 
                                           + ++ + +r+ ++g++ +Y  sK+++E l+rea++ + lpv+++R+++i++  s  G++n sd+++r++l+l
  gi|121636014|ref|YP_976237.1| 2264 -----ADIRVISPTRTVDGGWAGGYGTSKWAGEVLLREANDLCALPVAVFRCGMILAdTSYAGQLNMSDWVTRMVLSL 2336
                                     .....5679************************************************55666**************** PP

                                     HHH-EEES-SB---TT.......--EEEHHHHHHHH CS
                  NAD_binding_4  229 iakgvlpeilgdkeav.......ldlvpvDyvanai 257 
                                     +a+g+ p+ +++++++       +d +pv +va+ai
  gi|121636014|ref|YP_976237.1| 2337 MATGIAPRSFYEPDSEgnrqrahFDGLPVTFVAEAI 2372
                                     *************99999***************997 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     4e-10   6.6e-07       3      66 ..     938     998 ..     936     999 .. 0.96
   2 !   50.6   0.1   1.1e-16   1.8e-13       2      67 .]    1992    2055 ..    1991    2055 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4e-10
                     PP-binding   3 lrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaay 66 
                                    l ++++++lg++   i+pd++l   G+ Sl+++++l + ++ +g++++l dl   +t a+la+y
  gi|121636014|ref|YP_976237.1| 938 LSQIWSRQLGRA---IGPDSSLLGEGIGSLDLIRILPETRRYLGWRLSLLDLIGADTAANLADY 998
                                    789********8...99*********************************************98 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 1.1e-16
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     ++  ++a+vlg++  ++++d+++f+lG+DSl+a++++aa++ +++ ++p++ l+  ++ + l+++l
  gi|121636014|ref|YP_976237.1| 1992 TVAGIFARVLGLE--RVGVDDSFFELGGDSLAAMRVIAAINTTLNADLPVRALLHASSTRGLSQLL 2055
                                     6889*******98..678*******************************************99975 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.3   8.7e+03      43      72 ..    1439    1470 ..    1427    1473 .. 0.77
   2 !   35.4   0.5   9.8e-12   1.6e-08       1      76 []    1890    1965 ..    1890    1965 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.3
                                     HHHHHHHHHHHT-TTT.S-S.EEEE-S---B- CS
                  AMP-binding_C   43 eeeLkahvrkelgpya.vpk.kvvfvdelpkt 72  
                                      + L++++rk l ++a +p+ +v  +d+l+ t
  gi|121636014|ref|YP_976237.1| 1439 IDVLIERLRKVLVAVAaAPErTVSSIDALDGT 1470
                                     6889999****999955999555588888766 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 9.8e-12
                                     HHHHHHHSSTTEEEEEEE-----TTS.---EEEEEE.---.---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                  AMP-binding_C    1 evEsalvshpaVaeaaVvGvpdevkG.ealvafVvl.kdg.sealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75  
                                     ev  al++  +V +a+V++  d   G ++lv++ +  ++g ++  ++ L+a+++++l+ y vp +vv++d+lp+t +G
  gi|121636014|ref|YP_976237.1| 1890 EVATALAELAGVGQAVVIAREDR-PGdKRLVGYATEiAPGaVD--PAGLRAQLAQRLPGYLVPAAVVVIDALPLTVNG 1964
                                     78899*************99888.77699******53567433..6******************************** PP

                                     - CS
                  AMP-binding_C   76 K 76  
                                     K
  gi|121636014|ref|YP_976237.1| 1965 K 1965
                                     9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.2e-09     2e-06       1     190 [.    2110    2333 ..    2110    2359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                                     EEEETTTSHHHHHHHHHHHHCT...SEEEEEES-STTTTCHHCHHC.....................EEEE--TT-HH CS
                      Epimerase    1 ilVtGatGfiGsalvkallekg...yevigldrlssasntarledl.....................elveldltdrs 54  
                                     +l+tGatGf+G++lv +ll++     ++i+l r +s++   r+ ++                     e+v +d  +++
  gi|121636014|ref|YP_976237.1| 2110 VLLTGATGFLGRYLVLELLRRLdvdGRLICLVRAESDEDARRRLEKtfdsgdpellrhfkelaadrlEVVAGDKSEPD 2187
                                     699************99999988666688888887766665555556********************77777776666 PP

                                     ......HHHHHHHHHT-SEEEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSS CS
                      Epimerase   55 ......alerlfkeeqpdavihlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeq 125 
                                            ++rl +   +d ++  Aa v     ++    +++  n++gt +l+  a ++++k + ++s++ v  + +++
  gi|121636014|ref|YP_976237.1| 2188 lgldqpMWRRLAE--TVDLIVDSAAmV-----NAFPYHELFGPNVAGTAELIRIALTTKLKPFTYVSTADVGAAIEPS 2258
                                     5554447777777..899999998844.....44444788999*************************9998866664 PP

                                     SBSTCSTTS--........--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT..S-TTSTTSHHHHHH CS
                      Epimerase  126 pkeettltgpl........kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr..ngegevsrvipali 190 
                                       +e+++   +             Y+ +K age l++++++   l++ ++r+  +       g+ ++s  +++++
  gi|121636014|ref|YP_976237.1| 2259 AFTEDADIRVIsptrtvdgGWAGGYGTSKWAGEVLLREANDLCALPVAVFRCGMILADTsyAGQLNMSDWVTRMV 2333
                                     333333333332111123355678***************************998887776655555666666665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-07   0.00084       2     162 ..    2112    2299 ..    2111    2308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-07
                      3Beta_HSD    2 vtGgaGFlGralvkeLvrleelkevrvlD.........................lrespelleelskvnvkkviegDv 54  
                                     +tG++GFlGr+lv eL+r+ ++ + r +                          lr+ +el  +  +v   +  e D+
  gi|121636014|ref|YP_976237.1| 2112 LTGATGFLGRYLVLELLRRLDV-DGRLIClvraesdedarrrlektfdsgdpelLRHFKELAADRLEVVAGDKSEPDL 2188
                                     79***************99873.3333333445567999999998875555555444444444444444444555566 PP

                      3Beta_HSD   55 .tdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeil. 130 
                                      +d++  ++  e vd+++  a++v+ +      e+   nv GT +++  ++++ ++ + Y+S+a+v     +  +++ 
  gi|121636014|ref|YP_976237.1| 2189 gLDQPMWRRLAETVDLIVDSAAMVNAFP---YHELFGPNVAGTAELIRIALTTKLKPFTYVSTADVGAA-IEPSAFTe 2262
                                     4567777888899999998877776665...556899****************************8544.33333330 PP

                      3Beta_HSD  131 ngdEeleyesl.....hqdaypesKalaEklvlkaNg 162 
                                     ++d +   ++      +   y +sK   E l+ +aN+
  gi|121636014|ref|YP_976237.1| 2263 DADIRVISPTRtvdggWAGGYGTSKWAGEVLLREAND 2299
                                     3333222222233444777888888888888888887 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   3.8e-05     0.062      45     101 ..     542     598 ..     519     618 .. 0.76
   2 ?   -3.7   0.0       2.3   3.8e+03     392     419 ..     817     844 ..     803     852 .. 0.82
   3 ?    1.0   0.0     0.091   1.5e+02      77     104 ..    1634    1660 ..    1630    1683 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                    HHHS--BEHHHHHHHHH.HHHTTCC.CTSSSS-SEEEEECCEETTEEEEEEESHHHHH CS
                            GH3  45 kkkvPivtYedlepyie.riakGeqnvLtsepiklfalsSGTtsgksKliPvteeslk 101
                                      ++ +v +++l++ ++ r+ +   + L+++++ ++  +SGTt g++Kl+ +++ sl 
  gi|121636014|ref|YP_976237.1| 542 ATQLAVVGHDELRKVVDeRVTQVTHDALLATKTAYIMPTSGTT-GQPKLVRISHGSLA 598
                                    578999**********6266666888*****************.*****977776665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.3
                                    EEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                            GH3 392 eFvgRknvvlsidgeklteeelqkavee 419
                                     F+gRk+ v++i g  ++  e+++ ++e
  gi|121636014|ref|YP_976237.1| 817 VFSGRKDAVVKISGKRVDIAEVTRRIAE 844
                                    489*******************998875 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.091
                                     SEEEEECCEETTEEEEEEESHHHHHHHH CS
                            GH3   77 klfalsSGTtsgksKliPvteeslkela 104 
                                      +++ +SGTt g++K + +t++++ +l 
  gi|121636014|ref|YP_976237.1| 1634 AYILYTSGTT-GEPKGVGITHRNVTRLF 1660
                                     56789*****.******99999888843 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.01        17       2      55 ..    2109    2165 ..    2108    2169 .. 0.82
   2 ?    4.7   0.0    0.0082        13      24     151 ..    2175    2313 ..    2166    2333 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                                     EEEEESTTSHHHH....HHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEE CS
                  RmlD_sub_bind    2 kilvtGanGqlGs....eLakqlaeeglevlaltreeldltdaeavaellkeakpdvv 55  
                                     ++l+tGa+G lG+    eL ++l+ +g  ++ l r+e d + + ++++++++ +p+++
  gi|121636014|ref|YP_976237.1| 2109 TVLLTGATGFLGRylvlELLRRLDVDG-RLICLVRAESDEDARRRLEKTFDSGDPELL 2165
                                     699********9744446777888788.788888****************99999876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0082
                                     SEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEE CS
                  RmlD_sub_bind   24 glevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvS 100 
                                      lev+a +++e dl   + + + l+e   d++v+ AA  + +      ++ +  n+ ++++l + a  ++  ++ +vS
  gi|121636014|ref|YP_976237.1| 2175 RLEVVAGDKSEPDLGLDQPMWRRLAE-TVDLIVDSAAMVNAFP----YHELFGPNVAGTAELIRIALTTKLkPFTYVS 2247
                                     55666666666666555555555555.4556666666655554....3445666777777777777666643677777 PP

                                     EGGGS-S-TTS-B-TTS--...--S........SHHHHHHHHHHHHHHHH-S....SEEEEEE-SE CS
                  RmlD_sub_bind  101 tDyVFdGekkrpYeeddet...sPl........nvYGrtKlaGEqavlaagk....kalivRtswv 151 
                                     t  V  + ++++++ed+     sP         + YG +K+aGE   ++a++     ++++R + +
  gi|121636014|ref|YP_976237.1| 2248 TADVGAAIEPSAFTEDADIrviSPTrtvdggwaGGYGTSKWAGEVLLREANDlcalPVAVFRCGMI 2313
                                     77777777777777776531224532222222267*************987622223456666655 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0024       3.9      14      48 ..       9      44 ..       5      46 .. 0.79
   2 ?    0.9   0.0      0.33   5.4e+02      38      49 ..     702     713 ..     695     715 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                         HTH_17 14 srstvyrlirrgelpaak.iGrrwriprsdleewle 48
                                   s++ +y+ +r+   pa+  iG+++r++r +l ++l+
  gi|121636014|ref|YP_976237.1|  9 SQRNLYNGVRQDNNPALYlIGKSYRFRRLELARFLA 44
                                   55666666777777777669**************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.33
                         HTH_17  38 iprsdleewlek 49 
                                    i++s++++wle+
  gi|121636014|ref|YP_976237.1| 702 IRCSAVDKWLES 713
                                    9*********97 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.74   1.2e+03     190     207 ..    1647    1664 ..    1642    1676 .. 0.85
   2 ?    8.2   0.0   0.00073       1.2       1     129 [.    2110    2249 ..    2110    2260 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.74
                                     SSEEES-TT-EEEEE-HH CS
                Polysacc_synt_2  190 gpvtvTdpemtRyfmtie 207 
                                     + v +T++++tR f +++
  gi|121636014|ref|YP_976237.1| 1647 KGVGITHRNVTRLFASLP 1664
                                     5699**********9987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00073
                                     EEEETTTSHHHHHHHHHHHHH...B-SEEEEE..ES-HHHHHHHHHH.............-TTEEEE.....E--TT- CS
                Polysacc_synt_2    1 vlvtGagGsiGselvrqilkk...kpkkiill..erdElklyeieke.......leeelkkkklkve.ivpvigdvrd 65  
                                     vl+tGa+G +G+ lv ++l++   + + i l+  e+dE +  ++ek+       l +++k+  l ++ + +v gd  +
  gi|121636014|ref|YP_976237.1| 2110 VLLTGATGFLGRYLVLELLRRldvDGRLICLVraESDEDARRRLEKTfdsgdpeLLRHFKE--LAADrLEVVAGDKSE 2185
                                     7999999999999999999887533333433322667778888888766655553233333..323303344555554 PP

                                     HHH.HHHHTT.....T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG CS
                Polysacc_synt_2   66 ker.lekalee...lkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD 129 
                                      +  l++ + +    +vd+++ +AA+       +  +e +  Nv gt ++i++a++++ k + ++St 
  gi|121636014|ref|YP_976237.1| 2186 PDLgLDQPMWRrlaETVDLIVDSAAMV--N--AFPYHELFGPNVAGTAELIRIALTTKLKPFTYVSTA 2249
                                     3322333332211158999**999973..2..2334678899************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 1.28u 0.33s 00:00:01.61 Elapsed: 00:00:00.56
# Mc/sec: 13545.65
//
Query:       gi|121636015|ref|YP_976238.1|  [L=661]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-80  269.9  25.5    1.6e-80  269.9  25.5    3.2  3  Caa3_CtaG  Cytochrome c oxidase caa3 assembly factor (Caa3_Ct
    1.7e-12   47.6  15.4    1.7e-12   47.6  15.4    5.9  6  CopD       Copper resistance protein D


Domain annotation for each model (and alignments):
>> Caa3_CtaG  Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.3  12.3         2   1.8e+04     127     184 ..     175     233 ..      44     266 .. 0.59
   2 ?   -3.8  18.8      0.78     7e+03      85     193 ..     231     342 ..     159     362 .. 0.73
   3 !  269.9  25.5   1.8e-84   1.6e-80       2     233 .]     381     625 ..     380     625 .. 0.98

  Alignments for each domain:
  == domain 1  score: -10.3 bits;  conditional E-value: 2
                      Caa3_CtaG 127 ealhalmhlhfllaGllfwwpvl.gpdpeprrlspllrllylfaamvlhaflgallmfa 184
                                        +l h+++l+  +l +++ +    p++   ++ +  +++++a+++ ++ g+ ++ a
  gi|121636015|ref|YP_976238.1| 175 LYTRWLGHVVLLVPTVLAVVATAvTGNPGQGPDHDYATSAAIVFAVAFATLTGLKIAAA 233
                                    33333444444444443332222133344444555555555566666666666666555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.78
                      Caa3_CtaG  85 llrllrsrvlrv.lthPlvalllfvallyllylpplfdaalrsealhalmhlhfllaGllfw..wpvlgpdpeprrlspl 161
                                    + +l  +++ r+ l   +++ +l +a   +l +  +  +a+ s ++   + + ++l++++++  w +l + p+  r+  +
  gi|121636015|ref|YP_976238.1| 231 AAALAGTTPSRAvLVTQVTCGALALAYGAMLLYLFIPGWAVDSDFARLGLLAGVILTSVWLFdcWRLLVRPPHAGRRRGG 310
                                    333333344443344444444444444444444567799*******************9999999999887877777777 PP

                      Caa3_CtaG 162 lrllylfaamvlhaflgallmfastvlypayy 193
                                    +  ++l +++++  ++++++m a++ l +a++
  gi|121636015|ref|YP_976238.1| 311 GSGAALAMMAAMASIAAMAVMTAPRFLTHAFT 342
                                    77777777778888899999*******99995 PP

  == domain 3  score: 269.9 bits;  conditional E-value: 1.8e-84
                      Caa3_CtaG   2 lYllgvrrlrrrgd.wpvgrtvaFllGllllalalgspldvyghalfsaHmvqhllllmvaPpllvlGaPvtlllralpr 80 
                                    +Y++g++ lrrrg+ wpvgr +a+l+G+++l+++ gs++ +yg a+fs+Hm++h++l m++P+llvlG Pvtl+lr+lp 
  gi|121636015|ref|YP_976238.1| 381 GYAAGFAALRRRGNsWPVGRLIAWLTGCAALVFTSGSGVRAYGSAMFSVHMAEHMTLNMFIPVLLVLGGPVTLALRVLPV 460
                                    7***********966****************************************************************9 PP

                      Caa3_CtaG  81 al.......re.llrllrsrvlrvlthPlvalllfvallyllylpplfdaalrsealhalmhlhfllaGllfwwpvlgpd 152
                                    ++       re l+ ll+srv  +l+hP++a++lfva++y++y++plfd+ +r++++h++m +hfl++G+lf+w+++g d
  gi|121636015|ref|YP_976238.1| 461 TGdgrppgaREwLTWLLHSRVTTFLSHPITAFVLFVASPYIVYFTPLFDTFVRYHWGHEFMAIHFLVVGYLFYWAIIGID 540
                                    88*******999******************************************************************** PP

                      Caa3_CtaG 153 peprrlspllrllylfaamvlhaflgallmfastvlypayy..la.swg.splaDqqlGGlimwvlgelvyllvllalfv 228
                                    p+prrl++++r+++lfa m++haf+g++lm +s+ +++++y  ++ +w  s +aDq+lGG+i+w l el+ ++v++al+ 
  gi|121636015|ref|YP_976238.1| 541 PGPRRLPYPGRIGLLFAVMPFHAFFGIALMTMSSTVGATFYrsVNlPWLsSIIADQHLGGGIAWSLTELPVIMVIVALVT 620
                                    *****************************************97669********************************** PP

                      Caa3_CtaG 229 rwlrs 233
                                    +w+r+
  gi|121636015|ref|YP_976238.1| 621 QWARQ 625
                                    **985 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.0      0.23   2.1e+03      14      66 ..      34      90 ..      21     116 .. 0.59
   2 !   47.6  15.4   1.9e-16   1.7e-12       9     105 .]     117     234 ..     110     234 .. 0.92
   3 ?   -6.8  12.3         2   1.8e+04      35      69 ..     234     269 ..     224     337 .. 0.72
   4 ?   -1.2   1.3       0.3   2.7e+03      50      84 ..     373     401 ..     369     419 .. 0.53
   5 ?   -1.2   1.5       0.3   2.7e+03       5      54 ..     399     446 ..     395     479 .. 0.60
   6 ?   -2.0   0.0      0.52   4.7e+03      93     100 ..     611     618 ..     560     641 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                           CopD 14 avavvlvtGvvnallrvg.....lagllttayGrlllaKlalllvllalaalnrfrlv 66
                                   + avv++ G+v +++r+      ++g++  + +  +    a l+ +l+l+al++ +++
  gi|121636015|ref|YP_976238.1| 34 VCAVVAAFGLVSGARRYAeagnpYPGAFV-SVAEPVGFFAASLAGALCLGALIHVVMT 90
                                   33666677777776664444354333333.2234555666666666666666665555 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 1.9e-16
                           CopD   9 rlalaavavvl....vtGvvnallrvg.....lagllttayGrlllaKlalllvllalaalnrf.....rlvprleaa.. 72 
                                    +l+laa++vv+    +tGv++a l+++      ++++++a+G +++a +++l+v++al++++r+     +lvp++ a   
  gi|121636015|ref|YP_976238.1| 117 WLGLAATMVVIqaahDTGVGPARLLASgalsdSVAASEMARG-WIVAAICALVVATALRLYTRWlghvvLLVPTVLAVva 195
                                    89********************9998888655588889****.**************************9****977788 PP

                           CopD  73 ...tgaggqalrhrlrrsaalelvlalvvll...laaal 105
                                       tg++gq+++h++++saa+++++a+++l+   +aaal
  gi|121636015|ref|YP_976238.1| 196 tavTGNPGQGPDHDYATSAAIVFAVAFATLTglkIAAAL 234
                                    889**************************9988877776 PP

  == domain 3  score: -6.8 bits;  conditional E-value: 2
                           CopD  35 llt.tayGrlllaKlalllvllalaalnrfrlvprl 69 
                                    l++ t+   +l+  + +++++la++a+  ++ +p  
  gi|121636015|ref|YP_976238.1| 234 LAGtTPSRAVLVTQVTCGALALAYGAMLLYLFIPGW 269
                                    333355556888999999999999999999988866 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.3
                           CopD  50 lllvllalaalnrfrlvprleaatgaggqalrhrl 84 
                                    +  v+la++ ++ f+ ++r      ++++  + rl
  gi|121636015|ref|YP_976238.1| 373 AAGVVLAIGYAAGFAALRRR-----GNSWPVG-RL 401
                                    45566666666666666665.....2333333.33 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.3
                           CopD   5 rrFsrlalaavavvlvtGvvnallrvglagllttayG.rlllaKlalllvl 54 
                                     r  ++ + + a+v+++G +  +     +++++   +  + l + + +l++
  gi|121636015|ref|YP_976238.1| 399 GRLIAWLTGCAALVFTSGSGVRAYG---SAMFSVHMAeHMTLNMFIPVLLV 446
                                    5667889999999999998883333...44544333313334444444444 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 0.52
                           CopD  93 vlalvvll 100
                                    v++++v l
  gi|121636015|ref|YP_976238.1| 611 VIMVIVAL 618
                                    22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4361.29
//
Query:       gi|121636016|ref|YP_976239.1|  [L=752]
Description: cation-transporter P-type atpase B ctpB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-44  152.7   6.8    2.2e-44  152.3   5.1    2.0  2  Hydrolase     haloacid dehalogenase-like hydrolase
    8.7e-44  149.2   4.7    8.7e-44  149.2   4.7    1.9  2  E1-E2_ATPase  E1-E2 ATPase
    3.9e-10   40.0   0.9    9.3e-10   38.8   0.3    2.1  2  HMA           Heavy-metal-associated domain
    2.7e-05   24.6   0.4    0.00011   22.7   0.4    2.0  1  HAD           haloacid dehalogenase-like hydrolase
    0.00011   22.0   0.1      0.015   15.1   0.0    2.5  2  Hydrolase_3   haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.6   2.1e+03      91     137 ..     209     251 ..     192     265 .. 0.65
   2 !  152.3   5.1     6e-48   2.2e-44       1     210 []     440     658 ..     440     658 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.6
                                    HHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHH.HHHHHHHHTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                      Hydrolase  91 gsaqsqgrtvallqaralavftiadplkvkpeaa.eavasLkaagiev 137
                                    + + ++g tv++l   a ++f++  +   k + a  a+a+L a+++ v
  gi|121636016|ref|YP_976239.1| 209 YLEVAAGVTVFVL---AGRYFEARAK--SKAGSAlRALAELGAKNVAV 251
                                    5555666666666...5555665555..66666666666666666633 PP

  == domain 2  score: 152.3 bits;  conditional E-value: 6e-48
                                    SSEEEEESBTTTBCHHHHHHHHHHHH..........CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa..........alalaaaletgsehpigkalvaaakarsgaltgfatfigrg... 67 
                                    i+tvvfDk+GTLt g+  v +v+              l laaa e +seh  ++a+vaa  +  g++ gf +++g+g   
  gi|121636016|ref|YP_976239.1| 440 IDTVVFDKTGTLTVGQLAVSTVTMAGsgtserdreeVLGLAAAVESASEHAMAAAIVAASPDP-GPVNGFVAVAGCGvsg 518
                                    79**************8888888877999*99999999999999999*********9999885.9*************** PP

                                    .....HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                    .....xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 .....ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievv 138
                                         ++ +gkp w+t+        l +a  + +s+g+tv+++  ++ ++a +tiad+  +k+ aa ava+L+++g++++
  gi|121636016|ref|YP_976239.1| 519 evgghHVEVGKPSWITRTtpCHDAALVSARLDGESRGETVVFVsvDGVVRAALTIADT--LKDSAAAAVAALRSRGLRTI 596
                                    ******************999999999999999*********99999999999999**..******************** PP

                                    EEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 139 lltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    lltgdn++ a+++a q+G          ++++va  +pegkv +i++L+++++ vamVGDg+nD +al  A+
  gi|121636016|ref|YP_976239.1| 597 LLTGDNRAAADAVAAQVG----------IDSAVADMLPEGKVDVIQRLREEGHTVAMVGDGINDGPALVGAD 658
                                    ******************..........5566************************************9886 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.85     3e+03     122     139 ..     135     152 ..      88     180 .. 0.63
   2 !  149.2   4.7   2.4e-47   8.7e-44       6     179 ..     249     422 ..     243     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.85
                                    HHHHHHHHHHHHHHS-ST CS
                   E1-E2_ATPase 122 lvpvvlliallvfliall 139
                                    +++++l++ +++++++++
  gi|121636016|ref|YP_976239.1| 135 YILTALAAPVVTWAAWPF 152
                                    444455555555555555 PP

  == domain 2  score: 149.2 bits;  conditional E-value: 2.4e-47
                                    EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEE CS
                   E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavV 85 
                                     a ++ dg e  i+a+el+     + ++g++++aDg++v+gsa +d sa+TGE++pv+     +v +Gtvv++g++++++
  gi|121636016|ref|YP_976239.1| 249 VAVLLPDGAELVIPASELKKRQRFVTRPGETIAADGVVVDGSAAIDMSAMTGEAKPVRAYPAASVVGGTVVMDGRLVIEA 328
                                    455559************************************************************************** PP

                                    EE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHH CS
                   E1-E2_ATPase  86 tatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpl 165
                                    ta+g dt+++ ++rlve+a+ +k++ q+ +d +++v+vpvv++ia l+ +++l+ g ++ +a+  +l++lv+a+PcaL+l
  gi|121636016|ref|YP_976239.1| 329 TAVGADTQFAAMVRLVEQAQTQKARAQRLADHIAGVFVPVVFVIAGLAGAAWLVSGAGADRAFSVTLGVLVIACPCALGL 408
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHH CS
                   E1-E2_ATPase 166 avplalalgarrla 179
                                    a+p+a++++ +r a
  gi|121636016|ref|YP_976239.1| 409 ATPTAMMVASGRGA 422
                                    **********9987 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   2.6e-13   9.3e-10       2      62 .]      19      76 ..      18      76 .. 0.89
   2 ?   -2.8   0.0       2.5   8.9e+03      18      40 ..     432     453 ..     432     453 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.6e-13
                            HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                   ++vsgm Ca+Ca++ve  L ++pgV  ++v++at+ +t++ +  ++   ++   +ekagy+
  gi|121636016|ref|YP_976239.1| 19 LDVSGMSCAACASRVETKLNKIPGV-RASVNFATRVATIDAVGMAA--DELCGVVEKAGYH 76
                                   79***********************.89*************66662..5699999999997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                            HMA  18 kvLselpgVesvkvdlatktvtV 40 
                                    ++L+++ ++++v++d   +t+tV
  gi|121636016|ref|YP_976239.1| 432 RALETIRSIDTVVFDKT-GTLTV 453
                                    68999999999999854.66665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4     3e-08   0.00011      85     187 ..     576     654 ..     557     654 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3e-08
                            HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                    +l+  a +++aa r++G r+++++g +r  + +++a++g    +++       +             egkv+++++ l +
  gi|121636016|ref|YP_976239.1| 576 TLKDSAAAAVAALRSRGLRTILLTGDNRAAADAVAAQVG----IDS------AVADM--------LPEGKVDVIQR-LRE 636
                                    45567888999999*************************....999......55556........55667777777.333 PP

                            HAD 165 egegidleevvayGDspsDlpll 187
                                    eg+     +v  +GD+++D p+l
  gi|121636016|ref|YP_976239.1| 637 EGH-----TVAMVGDGINDGPAL 654
                                    443.....35666******9886 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0074        27      15      58 ..     576     619 ..     561     622 .. 0.90
   2 !   15.1   0.0   4.1e-06     0.015     195     254 ..     630     689 ..     625     690 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0074
                                    ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                    ++++++++a++ l+++g   ++ TG +  a+  v+ ++g+d++v
  gi|121636016|ref|YP_976239.1| 576 TLKDSAAAAVAALRSRGLRTILLTGDNRAAADAVAAQVGIDSAV 619
                                    6789999*********************************9776 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.1e-06
                                    HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHH CS
                    Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVaka 254
                                    ++++l+ +   v+ +GDg ND + L  a+lg A+g +++ +  aAd +    + + V +a
  gi|121636016|ref|YP_976239.1| 630 VIQRLREEGHTVAMVGDGINDGPALVGADLGLAIGRGTDVALGAADIILVRDDLNTVPQA 689
                                    67888888999***********************************99877776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (752 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 5094.29
//
Query:       gi|121636017|ref|YP_976240.1|  [L=504]
Description: hypothetical protein BCG_0137 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-18   65.9   0.0    6.2e-18   64.7   0.0    1.7  1  cNMP_binding  Cyclic nucleotide-binding domain
  ------ inclusion threshold ------
      0.031   14.8   0.0      0.081   13.4   0.0    1.7  1  XdhC_C        XdhC Rossmann domain
       0.15   11.8   0.1       0.35   10.6   0.1    1.6  1  Cupin_2       Cupin domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0     1e-21   6.2e-18       2      86 ..     396     475 ..     395     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1e-21
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                     +++ g+++frqG++ad++++++sGe++      dg  +v+ +lg+Gd+fGe  ll+g +r atv+A ++s+l++l+ ++
  gi|121636017|ref|YP_976240.1| 396 LQVRSGHTLFRQGERADHFFVIESGELEA---LVDG--KVILRLGAGDHFGEACLLGGMRRIATVRACEPSVLWELDGKA 470
                                    57899************************...6999..56777************************************* PP

                                    HHHHH CS
                   cNMP_binding  82 flell 86 
                                    f ++l
  gi|121636017|ref|YP_976240.1| 471 FGDAL 475
                                    98876 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.081       2      45 ..     201     246 ..     200     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..- CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..t 45 
                                    +i Gag ++ ala++++ l  rv v+d+r+   t+ ++p+a    +
  gi|121636017|ref|YP_976240.1| 201 LITGAGAIGTALADVLRPLHDRVDVYDTRSGCMTPIDLPNAIGgyD 246
                                    79****************************9999999996644542 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.9e-05      0.35      18      46 ..     410     439 ..     395     442 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.9e-05
                                    SEEEEEEEEESEEEEEECTE.EEEEETTEE CS
                        Cupin_2  18 gedeffyVleGegeltvdge.eveleaGds 46 
                                    ++d+ff++ +Ge+e  vdg+   +l+aGd 
  gi|121636017|ref|YP_976240.1| 410 RADHFFVIESGELEALVDGKvILRLGAGDH 439
                                    6689****************7789999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3857.12
//
Query:       gi|121636018|ref|YP_976241.1|  [L=94]
Description: 50S ribosomal protein L28 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-20   72.7   0.2    2.7e-20   72.3   0.2    1.2  1  Ribosomal_L28  Ribosomal L28 family
  ------ inclusion threshold ------
       0.71   10.1   5.0          2    8.6   0.2    2.2  2  Tat            Transactivating regulatory protein (Tat)


Domain annotation for each model (and alignments):
>> Ribosomal_L28  Ribosomal L28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.2     3e-24   2.7e-20       2      59 ..       4      61 ..       3      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 3e-24
                                   --TTT------------S-..-SSS-BTTEEEEEEEE.TTTEEEEEEEEHHHHHH--. CS
                  Ribosomal_L28  2 vCeltGkkpqfGnnvshsknkTkRtwkPNlqkvrlwseelgrkvrikvstkcLRtidk 59
                                   +C++tG+++ fG+ vshs+++T+R+w PN+q + +++++++r ++++vs+++++ id+
  gi|121636018|ref|YP_976241.1|  4 RCQITGRTVGFGKAVSHSHRRTRRRWPPNIQLKAYYLPSEDRRIKVRVSAQGIKVIDR 61
                                   8*******************************************************96 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00023         2      32      61 ..       4      33 ..       1      35 [. 0.88
   2 ?    3.6   0.9    0.0081        73      46      60 ..      59      73 ..      46      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00023
                                   SSHHHHHHCTT---S-XXXXXXXXXXXXXX CS
                            Tat 32 hcqvcfikkalGisyerkkrrqrrrahrks 61
                                    cq+   + ++G +    +rr rrr + + 
  gi|121636018|ref|YP_976241.1|  4 RCQITGRTVGFGKAVSHSHRRTRRRWPPNI 33
                                   7************************88765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0081
                                   S-XXXXXXXXXXXXX CS
                            Tat 46 yerkkrrqrrrahrk 60
                                    +r + r rrra r 
  gi|121636018|ref|YP_976241.1| 59 IDRDGHRGRRRAARA 73
                                   589999*****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 683.28
//
Query:       gi|121636019|ref|YP_976242.1|  [L=398]
Description: hypothetical protein BCG_0139 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-15   56.5   0.0    3.6e-15   55.7   0.0    1.4  1  CobW_C    Cobalamin synthesis protein cobW C-terminal domain
    1.6e-09   37.6   0.0    2.5e-09   37.0   0.0    1.2  1  cobW      CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> CobW_C  Cobalamin synthesis protein cobW C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0     4e-19   3.6e-15       4      94 .]     238     351 ..     235     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4e-19
                         CobW_C   4 fvfrarrpfdperleelleeelpegilRaKGivwlagkpd.alvlqgvggrlrlepagawwaa................. 65 
                                    + f+arrpf+p+rl+++++  l +g++R +G +wla++pd ++ l+ +gg lr+ +ag+w aa                 
  gi|121636019|ref|YP_976242.1| 238 VEFSARRPFHPQRLHAAVDL-LLDGVVRTRGRLWLANRPDqVMWLESAGGGLRVASAGKWLAAmaasevayvdlerrlfa 316
                                    6799****************.*******************9*************************************** PP

                         CobW_C  66 ......ededrrseLVfIGrdldkealeeaLdacl 94 
                                          +++dr++ + ++  + d+  + +aL+a+l
  gi|121636019|ref|YP_976242.1| 317 dlmwvyPFGDRHTAMTVLVCGADPTDIVNALNAAL 351
                                    *******************************9986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   2.8e-13   2.5e-09      52     149 ..      52     174 ..      29     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.8e-13
                                    .....EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEEECTTTTHHHH..HTT............SHHHHHCCCEC CS
                           cobW  52 e....ivelenGciCctlredllkelealeereerldviliEttGlaePapv..aft............eeelksdltld 113
                                         ++e++ Gc+ ct+r+dll  l++l +r  ++ +i++     +eP+p+  a              +   + d+++ 
  gi|121636019|ref|YP_976242.1|  52 IttedALEFAHGCVSCTIRDDLLVLLRRLHRRD-NVGRIVVHLAPWLEPQPIcwA-IdhvrvcvghgypDGPAALDVRVA 129
                                    0333499**************************.9*****************642.1577788899988888889***** PP

                                    EEEEEEETTTH..........CCHCCHHHHHHHHHHTSSEEEEE- CS
                           cobW 114 avvavvDaknl.........eaeeekieekaedqlaaadllvlnK 149
                                    avv++vD+ ++           ++++ ++    q ++adllvl+ 
  gi|121636019|ref|YP_976242.1| 130 AVVTCVDCVRWlpqslgedeLPDGRTVAQVTVGQAEFADLLVLTH 174
                                    ********999******9998899******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3104.08
//
Query:       gi|121636020|ref|YP_976243.1|  [L=1625]
Description: cation-transporter atpase I ctpI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-37  128.7   4.8    4.5e-37  127.3   4.8    1.8  1  E1-E2_ATPase     E1-E2 ATPase
    3.5e-26   92.8   3.2    3.5e-26   92.8   3.2    3.9  4  Hydrolase        haloacid dehalogenase-like hydrolase
    1.3e-16   60.9   0.6    3.4e-16   59.5   0.6    1.7  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    6.5e-08   32.6   0.0    1.5e-07   31.4   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
  ------ inclusion threshold ------
      0.017   15.2   0.3       0.17   12.0   0.3    2.9  1  Ldr_toxin        Toxin Ldr, type I toxin-antitoxin system
      0.033   14.6   1.3       0.15   12.4   0.7    2.5  2  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   4.8   1.5e-40   4.5e-37      11     179 ..     851    1029 ..     840    1031 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 1.5e-40
                                     -TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-..........G-TTEE-TT-EEE CS
                   E1-E2_ATPase   11 rdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek..........ekgdmvfsGtvvv 77  
                                     +++++ ++ ak l++GD++ l a ++vpaD+r++  ++ evdes+LTGEslpv+k          ++ +m+f G+++v
  gi|121636020|ref|YP_976243.1|  851 HATRTATVSAKSLRVGDVIDLAAPEVVPADARLLVAEDlEVDESFLTGESLPVDKqvdpvavndpDRASMLFEGSTIV 928 
                                     5668899*******************************************************9999************ PP

                                     E-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                   E1-E2_ATPase   78 sgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155 
                                     +g+a+a+V+atg  t  ++++++v++  ++ + +q  l++l++ + p+ l+ +++v ++all++ sl++a+  ++a++
  gi|121636020|ref|YP_976243.1|  929 AGHARAIVVATGVGTAAHRAISAVADV-ETAAGVQARLRELTSKVLPMTLAGGAAVTALALLRRASLRQAVADGVAIA 1005
                                     ***************************.99************************************************ PP

                                     HHHS-TTHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase  156 vaaiPcaLplavplalalgarrla 179 
                                     vaa+P++Lpl+++l+ +++a+rl 
  gi|121636020|ref|YP_976243.1| 1006 VAAVPEGLPLVATLSQLAAAQRLT 1029
                                     *********************996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.5      0.14     4e+02      85     209 ..     244     380 ..     182     381 .. 0.71
   2 ?   -3.0   0.0       2.4   7.2e+03     171     181 ..     465     475 ..     391     537 .. 0.57
   3 ?   -3.2   0.2       2.8   8.3e+03      81     127 ..     841     885 ..     759     890 .. 0.57
   4 !   92.8   3.2   1.2e-29   3.5e-26       1     210 []    1047    1352 ..    1047    1352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE.EEE...SSEHHHHH.HHHHHTT..G CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...xxxxxxxx.xxxxxxx..x RF
                      Hydrolase  85 dlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievv.llt...gdnpetae.raanqlG..d 157
                                       aa+g  qs g     l +r l++ ++a  ++v+ + + a+as ++   +vv +++     ++e+ +  aa  +G   
  gi|121636020|ref|YP_976243.1| 244 TTAAANGLTQSLGTPLLDLVQRSLQISEAAAHRRVWRDREPALASPRRPQAPVVpIISsagAKSQEPRHsWAAAAAGeaS 323
                                    45566777777777777777789999999999999999999999999888865514445645556888855566699664 PP

                                    GGE.SEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxx.xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 158 dyf.daviasdiet....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                    + +  ++i++ i+t     a+p  + +++a++   +  +  ++ G g  Daa++  A
  gi|121636020|ref|YP_976243.1| 324 HVVvGGSIDAAIDTakgsRAGPVEQYVNQAANGSLIAAASALVAGGGTEDAAGAILA 380
                                    444466666666667777777777777777766667777788888888888877666 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                    STTTSHHHHHH CS
                                    xxxxxxxxxxx RF
                      Hydrolase 171 vakpspegkva 181
                                      +p+p+ + a
  gi|121636020|ref|YP_976243.1| 465 APEPDPDELPA 475
                                    44444444433 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                                    HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeav 127
                                    +    l+aa ++  ++  ++  l  r+  v+ +a p  v  +a+ +v
  gi|121636020|ref|YP_976243.1| 841 TTRRRLEAARHATRTATVSAKSL--RVGDVIDLAAPEVVPADARLLV 885
                                    22233444444444444444444..6666666666666666666555 PP

  == domain 4  score: 92.8 bits;  conditional E-value: 1.2e-29
                                     SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase    1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78  
                                     ++t++fDk+GTLt+ + +v+ +++s + a++  l   ++ p ++ l aaa a + +  g ++     a a  +  + +
  gi|121636020|ref|YP_976243.1| 1047 VDTICFDKTGTLTENRLRVVCALPSSTAAERDPLPQTTDAPSAEVLRAAARASTQPHNGEGH-----AHATDEAILAA 1119
                                     68**************9999999999888888888889999999999999998555544444.....44444444444 PP

                                     HHHCHHHHHHHHHHHHHHCHHHHHH..................................................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                      Hydrolase   79 aldippdlgaaigsaqsqgrtvall..................................................... 103 
                                     a        a  gs+ sqg ++ ++                                                     
  gi|121636020|ref|YP_976243.1| 1120 AS-------ALAGSLSSQGDSEWVVlaevpfessrgyaaaigrvgtdgipmlmlkgapetilprcrladpgvdhehae 1190
                                     44.......6666666666666666666666666666666667777777777779*********************** PP

                                     .........................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEE CS
                                     .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  104 .........................................qaralavftiadplkvkpeaaeavasLkaagievvll 140 
                                                                              + ++ +++ +ad+   +p  + ++++L +a  +vvl+
  gi|121636020|ref|YP_976243.1| 1191 svvrhlaeqglrvlavaqrtwdngtthddetdadavdavahDLELIGYVGLADT--ARPSSRPLIEALLDAERNVVLI 1266
                                     *********************************9999999999***********..***************99***** PP

                                     ESSEHHHHHHHHHHTT................GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHH CS
                                     xxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  141 tgdnpetaeraanqlG................ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnD 202 
                                     tgd+p ta+++a+qlG                d+  +a++a+d  ++a +spe+kv+++  Lq  ++ +amVGDg+nD
  gi|121636020|ref|YP_976243.1| 1267 TGDHPITARAIARQLGlpadarvvtgaelavlDEEAHAKLAADMQVFARVSPEQKVQIVASLQRCGRVTAMVGDGAND 1344
                                     *******************965555555555444445555555555*****************88888********** PP

                                     HHHHHHTT CS
                                     xxxxxxxx RF
                      Hydrolase  203 aaalaaAg 210 
                                     aaa+++A+
  gi|121636020|ref|YP_976243.1| 1345 AAAIRMAD 1352
                                     ******98 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.6   1.1e-19   3.4e-16       4     178 ..    1426    1597 ..    1423    1602 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.1e-19
                Cation_ATPase_C    4 lsaiqiLwinLvtDllpalaLaleppe..........kdimkrpPr.kkkepli......skkmlrriliqgllqalv 64  
                                       + q+L++nL+tD++pala a+  +           +d  +r +r ++++ li      +  +lr+i+  g+++a+ 
  gi|121636020|ref|YP_976243.1| 1426 VGTRQLLLVNLLTDMFPALAVAVTSQFaepddaeyptDDAAERAQReHRRAVLIgptpslDAPLLRQIVNRGVVTAAG 1503
                                     5678******************7443222334555559*****99988888776222222567*************** PP

                Cation_ATPase_C   65 tllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvli 142 
                                     + ++++++ +  g++            tm +++lv++q++++l +r+             ++l++  +l+s++++v i
  gi|121636020|ref|YP_976243.1| 1504 ATAAWAIGRWTPGTERR--------TATMGLTALVMTQLAQTLLTRR------------HSPLVIATALGSAGVLVGI 1561
                                     *********97776664........89********************............5899*************** PP

                Cation_ATPase_C  143 vyvpglnavfgtaplsleewlialllalvvllvdel 178 
                                     +++p++ ++fg++pl++  w++++   +  ++v  l
  gi|121636020|ref|YP_976243.1| 1562 IQTPVISHFFGCTPLGPVAWTGVFSATAGATAVSAL 1597
                                     ***********************9999998887554 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   4.9e-11   1.5e-07      20      89 ..    1108    1178 ..    1091    1179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.9e-11
                  Cation_ATPase   20 lGnktEsALlvlaekl.gldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCt 89  
                                     +  +t+ A+l +a++l g   ++ ++e+  ++e+pF+ssr +++ + +  +++  +l+ KGApe il rC 
  gi|121636020|ref|YP_976243.1| 1108 HAHATDEAILAAASALaGSLSSQGDSEWVVLAEVPFESSRGYAAAIGRVGTDGIPMLMLKGAPETILPRCR 1178
                                     5679***********9777788999************************9********************5 PP

>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   5.7e-05      0.17       2      29 ..     759     790 ..     758     791 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                                    -HHHHHHHHHHHHH...HHHHH.HHHHHHHHH CS
                      Ldr_toxin   2 TlAelaMaFWHDLA...APvlA.GIlaaaIVn 29 
                                    TlA+la a  H LA    P+lA G  a+aIV+
  gi|121636020|ref|YP_976243.1| 759 TLAQLAVATRHELAdplTPILAvGAAASAIVG 790
                                    9*************555579998999****98 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   3.5e+03      56      96 ..     373     419 ..     351     425 .. 0.64
   2 ?   12.4   0.7     5e-05      0.15      86     186 ..    1245    1347 ..    1183    1349 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                            HAD  56 elleallaglseelaaelerfv....aevirpk.......lldpgalellaa 96 
                                     +  a+lag + + +   ++f     +             +ldpgal++l++
  gi|121636020|ref|YP_976243.1| 373 DAAGAILAGVPRAAHMGRQAFAavlgR-----GlantgqlVLDPGALRRLDR 419
                                    455566666666555555555533331.....133334446999**999984 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5e-05
                            HAD   86 ldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlatelevdd.......rltgelglegkpvrge 152 
                                      +p  + l++a ++a   vv+++g + + +++++++lg    a  v + el+v d         +++++ + +p    
  gi|121636020|ref|YP_976243.1| 1245 ARPSSRPLIEALLDAERNVVLITGDHPITARAIARQLGlpadARVVTGAELAVLDeeahaklAADMQVFARVSPE--- 1319
                                     457777888888899999**********************87777888899999999988555555544444444... PP

                            HAD  153 gkvaalrewlaaegegidleevvayGDspsDlpl 186 
                                     +kv+ +++   +++       +  +GD+ +D ++
  gi|121636020|ref|YP_976243.1| 1320 QKVQIVAS--LQRCGRV----TAMVGDGANDAAA 1347
                                     66666666..4445444....7888******877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.45
# Mc/sec: 10765.83
//
Query:       gi|121636021|ref|YP_976244.1|  [L=69]
Description: hypothetical protein BCG_0141c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 469.04
//
Query:       gi|121636022|ref|YP_976245.1|  [L=496]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-32  109.4  19.0    1.3e-31  108.8  19.0    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8  19.0   7.2e-36   1.3e-31       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 7.2e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms ++++P ++aaaa++lagigsals+anaaaaaptta+  a+aDeVS+ iAalf+a+aqeyqalsaqa afh+qfvqal+ 
  gi|121636022|ref|YP_976245.1|  1 MSLLITSPATVAAAATHLAGIGSALSTANAAAAAPTTALSVAGADEVSVLIAALFEAYAQEYQALSAQALAFHDQFVQALNM 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a  YaaaE+a
  gi|121636022|ref|YP_976245.1| 83 GAVCYAAAETA 93
                                   *********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3132.78
//
Query:       gi|121636023|ref|YP_976246.1|  [L=249]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-34  116.8  17.0    8.3e-34  116.8  17.0    2.3  3  Rhomboid     Rhomboid family
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.27   11.0   0.0    1.5  1  Shugoshin_C  Shugoshin C terminus
       0.34   11.5   0.1       0.34   11.5   0.1    2.8  3  DUF1751      Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.7   4.2e+03     101     122 ..      34      55 ..      17      64 .. 0.57
   2 !  116.8  17.0   1.4e-37   8.3e-34       3     145 ..      72     204 ..      70     209 .. 0.92
   3 ?    3.6   0.4      0.01        61      81     113 ..     198     230 ..     198     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                                    -HC...CCCCCCCCCCHHHCTS CS
                       Rhomboid 101 iiallllllfillnlvlgllpr 122
                                       +++ +++i+ln+++ +++ 
  gi|121636023|ref|YP_976246.1|  34 SATPVVTYTLISLNALVFVMQV 55 
                                    4445556666666666655554 PP

  == domain 2  score: 116.8 bits;  conditional E-value: 1.4e-37
                                    GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHH CS
                       Rhomboid   3 krgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgl 82 
                                    ++g+ +rl+ts+flH g +Hll+Nm+al+v+G+ple+ lG+lrf++ly++s+l+gs+l++l+ + ++  ++GaSGa+fgl
  gi|121636023|ref|YP_976246.1|  72 ASGQTYRLVTSAFLHYGAMHLLLNMWALYVVGPPLEMWLGRLRFGALYAVSALGGSVLVYLIAPLNT-ATAGASGAVFGL 150
                                    689**************************************************************85.************ PP

                                    HHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHH CS
                       Rhomboid  83 lgallvlvprnrkllrkliiallllllfillnlvlgllpraggvsnlAHlgGllaGlllglll 145
                                    +ga+++   r +  +r        ++++i++nl++ +l++a  +s+++H+gGl++G+l++++ 
  gi|121636023|ref|YP_976246.1| 151 FGATFMVARRLHLDVRW-------VVALIVINLAFTFLAPA--ISWQGHVGGLVTGALVAATY 204
                                    ****9999888887773.......45779**********98..**************998875 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHCCCCGS----HC...CCCCCCC CS
                       Rhomboid  81 gllgallvlvprnrkllrkliiallllllfill 113
                                    +l++a+ v  pr+r++l ++ + +++l++f++l
  gi|121636023|ref|YP_976246.1| 198 ALVAATYVYAPRERRNLIQATVTITVLVAFVVL 230
                                    688999999999999999988885555555444 PP

>> Shugoshin_C  Shugoshin C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.6e-05      0.27       3      20 ..      31      48 ..      29      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                    Shugoshin_C  3 psRrarkvvsYKEPSLns 20
                                   ++R+a++vv Y + SLn+
  gi|121636023|ref|YP_976246.1| 31 RQRSATPVVTYTLISLNA 48
                                   79**************96 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.56   3.3e+03      11      30 ..      38      57 ..      35      64 .. 0.70
   2 ?   11.5   0.1   5.6e-05      0.34       9      73 ..      77     141 ..      69     158 .. 0.87
   3 ?    0.2   0.5      0.19   1.2e+03      60      96 ..     194     230 ..     185     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.56
                        DUF1751 11 lltasfveqnvwkvlvsllt 30
                                   ++t++++ +n + ++++++ 
  gi|121636023|ref|YP_976246.1| 38 VVTYTLISLNALVFVMQVTV 57
                                   67777887777777777655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.6e-05
                        DUF1751   9 wtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvt 73 
                                    + l+t++f     +++l+++ +l+++g  lE   g+  +    +v +++ ++lv+l++ l  ++ 
  gi|121636023|ref|YP_976246.1|  77 YRLVTSAFLHYGAMHLLLNMWALYVVGPPLEMWLGRLRFGALYAVSALGGSVLVYLIAPLNTATA 141
                                    789****************************9999**9*9999*********9999988776655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.19
                        DUF1751  60 llvvlltlllylvtkseelllvpisGlagilagflva 96 
                                    l++ +l  ++y+   +e+  l++   ++++l++f+v 
  gi|121636023|ref|YP_976246.1| 194 LVTGALVAATYVYAPRERRNLIQATVTITVLVAFVVL 230
                                    5555555555555555554457777788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1846.89
//
Query:       gi|121636024|ref|YP_976247.1|  [L=685]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-24   86.0  23.4    3.9e-24   85.3  23.4    1.3  1  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3  23.4   2.2e-28   3.9e-24       2     335 ..      34     385 ..      33     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2.2e-28
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxx RF
                  Acyl_transf_3   2 aylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla......amlyrrrglskli 75 
                                    ++lD+lR+iA+ lV + H  i+ +                    g +gv+ FF+lSGf+++        ++ r +ls ++
  gi|121636024|ref|YP_976247.1|  34 PALDGLRAIAVALVLASHGGIPGM------------------GGGFIGVDAFFVLSGFLITsllldeLGRTGRIDLSGFW 95 
                                    68*******************876..................67889********************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  76 krRilrlliplliwllliillialvaghiqanasanvtlfdet..........kglmfllfefpatghlWfLwalfvlyl 145
                                     rR++rll +l+++ l++ +  al+ +    +   +   ++ +          ++    + +  +  h+W+L ++ ++y+
  gi|121636024|ref|YP_976247.1|  96 IRRARRLLPALVLMVLTVSAARALFPDQALTGLRSDAIAAFLWtanwrfvaqnTDYFTQGAPPSPLQHTWSLGVEEQYYV 175
                                    ********999999999999999999998888888888887778999***99988888899999**************** PP

                                    xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxx RF
                  Acyl_transf_3 146 llpll.........lrllrkvrkshlllllilllllslvfirhelfgpatsvgllplpsvla...........llfflfG 205
                                    + pll         +   r +r+  ++ + ++ ++ +l++ + ++   + ++ +++ ++               + ++  
  gi|121636024|ref|YP_976247.1| 176 VWPLLligatlllaA---RARRRCRRATVGGVRFAAFLIASLGTM--ASATAAVAFTSAATRdriyfgtdtraQALLIGS 250
                                    *********974431...333333333333333333333333333..222222222222222455566777874444445 PP

                                    xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 206 alladaddrdrnlsr.........glkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllfa 276
                                    a +a + + + +l+r         g+ i++ll +++la+  +   + t       sv  + + ll+v++g+++++++++a
  gi|121636024|ref|YP_976247.1| 251 AAAALLVRDWPSLNRgwclirtrwGRRIARLLPFVGLAGLAVTTHVAT------GSVGEFRHGLLIVVAGAAVIVVASVA 324
                                    555555555566666689996555555555566666665555555555......9************************* PP

                                    xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 277 lpsrsafk......llrylgkiSygiYliHlpllmllqkllrdwglnlgevlllvlllvvsvivs 335
                                    + +r a+        l++lg iSyg+Yl+H+p+  +l      w+ +     l+ + + ++v+++
  gi|121636024|ref|YP_976247.1| 325 MEQRGAVArilawrPLVWLGTISYGVYLWHWPIFLALNGQRTGWSGP----ALFAARCAATVVLA 385
                                    *****888888999******************************555....44444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 5095.68
//
Query:       gi|121636025|ref|YP_976248.1|  [L=318]
Description: GDP-mannose 4,6-dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-59  201.2   0.0    4.6e-59  200.5   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.3e-47  160.3   0.0    7.1e-47  159.9   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.1e-11   42.2   0.0    7.1e-11   41.7   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.7e-07   30.0   0.1    0.00013   21.2   0.2    3.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.4e-05   24.4   0.3       0.17   11.0   0.1    2.6  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.058   13.4   0.0    2.1  2  B12-binding      B12 binding domain
      0.017   14.1   0.0      0.025   13.6   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.053   13.0   0.1        3.9    6.9   0.0    2.5  3  adh_short        short chain dehydrogenase
      0.099   12.8   0.0       0.22   11.7   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.12   12.2   0.0       0.25   11.2   0.0    1.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.0   2.6e-62   4.6e-59       2     332 .]       5     304 ..       4     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 2.6e-62
                                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                    iTG  G  Gs+lae+Ll+ g++v+ +  r +      i+      +   + +++  ++D+tD  s+ + +a  +pd+v++
  gi|121636025|ref|YP_976248.1|   5 ITGAGGMMGSHLAEMLLAAGHDVYATYCRPT------IDP-----S---DLQFNGAEVDITDWCSVYDSIATFRPDAVFH 70 
                                    9**********************99866554......332.....1...22467789*********************** PP

                                    --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S..SSSB-TTS-----SHHHHHHHH CS
                  GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq..evpqtEttpfyPrsPYaaaKly 159
                                    LAAqs  +vs+  P +t+ +n++Gt+ ++ea r++   ++++++ a++s  YG v+  evp++E+  ++P  PY+++K++
  gi|121636025|ref|YP_976248.1|  71 LAAQSYPAVSWARPVETLTTNMVGTAIVFEALRRVR--PHAKIIVAGSSAEYGFVDpsEVPINERRELRPLHPYGVSKAA 148
                                    **********************************75..79*************996559********************* PP

                                    HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                  GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq 239
                                     d+++ +y+++yg+++v++++fn  +pr+  +     + r+    ++ +q+ +++Gnl+ kR    v+D  +a+ lml +
  gi|121636025|ref|YP_976248.1| 149 TDMLAYQYHKSYGMHTVVARIFNCTGPRKVGDALSDFVRRCTWLEHHPEQSAIRVGNLKTKRTIVDVRDLNRALMLMLDK 228
                                    ********************************99999999999999999******************************* PP

                                    SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH-- CS
                  GDP_Man_Dehyd 240 dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgW 319
                                    ++        g  ++v++ +  ++ ++ k++++            +  ++v evdp+  rp++++ ++gd+sk+    gW
  gi|121636025|ref|YP_976248.1| 229 GE-------AGADYNVGGSIAYEMGDVLKQVIAAC----------KRDDIVPEVDPALLRPTDEKIIYGDCSKLAAITGW 291
                                    99.......69999999999999999998876642..........34568899*************************** PP

                                    --SS-HHHHHHHH CS
                  GDP_Man_Dehyd 320 kpkvsfeelvrem 332
                                    ++++ +++++++m
  gi|121636025|ref|YP_976248.1| 292 QQEICLTQTIADM 304
                                    **********998 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.0   3.9e-50   7.1e-47       2     241 .]       4     238 ..       3     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 3.9e-50
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                     +tGa G++Gs+l++ ll++g++v +   +++ +++ ++   +  e+d+td  ++ + +++++pdav+hlAa++ +a+s+
  gi|121636025|ref|YP_976248.1|   4 WITGAGGMMGSHLAEMLLAAGHDVYATYCRPTIDPSDLQF--NGAEVDITDWCSVYDSIATFRPDAVFHLAAQSYPAVSW 81 
                                    69****************************7777766655..999*********************************** PP

                                    HSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSS..SSBSTCSTTS----SSHHHHHHHHHHHHHHHHHH CS
                      Epimerase  82 edpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdae..qpkeettltgplkpnspYaaaKlageklveayaa 158
                                     +p +++ +n++gt  ++ea+r+  ++ +++ ++Ss+ YG +++  +p +e     +l+p  pY+++K+a + l+ +y++
  gi|121636025|ref|YP_976248.1|  82 ARPVETLTTNMVGTAIVFEALRRVRPHaKIIVAGSSAEYGFVDPseVPINERR---ELRPLHPYGVSKAATDMLAYQYHK 158
                                    ***********************97777************7777535899999...99********************** PP

                                    HHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTS....SSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-ST CS
                      Epimerase 159 qyglnaiilrlfnlyGprngegevsrvipalirkilegk....qevtllgdgtalRdflyveDvaeaillvlehvdagdk 234
                                    +yg+++++ r+fn  Gpr    +v   ++ ++r++   +    q+ + +g+++ +R  ++v+D+ +a++l+l++   g++
  gi|121636025|ref|YP_976248.1| 159 SYGMHTVVARIFNCTGPR----KVGDALSDFVRRCTWLEhhpeQSAIRVGNLKTKRTIVDVRDLNRALMLMLDK---GEA 231
                                    ******************....99999999999997744456689*****************************...888 PP

                                    TEEEEES CS
                      Epimerase 235 geiyniG 241
                                    g +yn+G
  gi|121636025|ref|YP_976248.1| 232 GADYNVG 238
                                    99****9 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0     4e-14   7.1e-11       1     138 [.       1     155 [.       1     175 [. 0.87

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 4e-14
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------HHHH CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytavDka 67 
                                    mk+ +tGa+G++Gs+La+ l ++g++v+a+  +             e+d+td  +v + ++ ++pd+v ++AA       
  gi|121636025|ref|YP_976248.1|   1 MKVWITGAGGMMGSHLAEMLLAAGHDVYATYCRptidpsdlqfngaEVDITDWCSVYDSIATFRPDAVFHLAAQSYPAVS 80 
                                    899***************************65569**************************************7777777 PP

                                    HHSHHHHHHHHTHHHHHHHHHHHHC....T-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH CS
                  RmlD_sub_bind  68 EseeeaayavnaeavealAeaaaav....galLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla 138
                                       + +    n+ +++ + ea ++v    ++ +   S +y F    + p +e  e  Pl  YG +K+a      +
  gi|121636025|ref|YP_976248.1|  81 WARPVETLTTNMVGTAIVFEALRRVrphaKIIVAGSSAEYGFVDPSEVPINERRELRPLHPYGVSKAATDMLAYQ 155
                                    77889999999999998888887753321566667899****************************998766555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   7.4e-08   0.00013       2     118 ..       4     105 ..       3     119 .. 0.72
   2 ?    1.9   0.0     0.057     1e+02     132     157 ..     136     161 ..     126     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.4e-08
                                    EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                     +tGagG +Gs+l + +l+        + r                + ++l+++      d++d  ++ + + ++++d+v
  gi|121636025|ref|YP_976248.1|   4 WITGAGGMMGSHLAEMLLAAGHDVYATYCRPTI-------------DPSDLQFN--GAEVDITDWCSVYDSIATFRPDAV 68 
                                    677888888877777776665444333333322.............23333333..3346999***************** PP

                                    EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHT CS
                Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaiea 118
                                    fh AA     +    p+e+++tN++gt  v ea  + 
  gi|121636025|ref|YP_976248.1|  69 FHLAAQSYPAVSWARPVETLTTNMVGTAIVFEALRRV 105
                                    *****9877777789***************9997665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.057
                                    SS--SHHHHHHHHHHHHHHHGGG--S CS
                Polysacc_synt_2 132 vnPtnvmGatKrlaekllqalakese 157
                                     +P   +G++K+++++l+ +++k+ +
  gi|121636025|ref|YP_976248.1| 136 LRPLHPYGVSKAATDMLAYQYHKSYG 161
                                    579999************99998874 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00012      0.21       1      27 [.       5      32 ..       5      35 .. 0.88
   2 !   11.0   0.1   9.6e-05      0.17      89     208 ..      66     174 ..      57     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                   EE-TTSHHHHHHHHHHHHHS-.T.EEEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.kiyl 27
                                   +TGa G++G++L e LL    +v   y+
  gi|121636025|ref|YP_976248.1|  5 ITGAGGMMGSHLAEMLLAAGHDVyATYC 32
                                   8****************99988766666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.6e-05
                                    -EEEE--SS....-S.STTSSEEHHHHHHHHHHHHHHHTSSS--..-EEEEEEGGGTTS-TTT--SSS-H......HHH- CS
                  NAD_binding_4  89 dviihsaAt....vnfdepykellrvNveGtrevlelakklkkl.kvllhvSTayvngeregeveekvyeegekeeklde 163
                                    d+++h aA+    v++ +p+++ l +N+ Gt  v+e  ++++   k ++  S+a     + +e                 
  gi|121636025|ref|YP_976248.1|  66 DAVFHLAAQsypaVSWARPVET-LTTNMVGTAIVFEALRRVRPHaKIIVAGSSAEYGFVDPSE---------------VP 129
                                    6777777754444667666655.4578888888877777655542455555553222222222...............23 PP

                                    -EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                  NAD_binding_4 164 deraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                     +++++    + Y  sKa+ ++l  +++++ g+ +v+ R+ + tg
  gi|121636025|ref|YP_976248.1| 130 INERRELRPLHPYGVSKAATDMLAYQYHKSYGMHTVVARIFNCTG 174
                                    344455555679***************************877776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.058      20      91 ..      16     118 ..      10     122 .. 0.76
   2 ?   -2.1   0.0       2.1   3.8e+03       5      27 ..     238     260 ..     236     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                    B12-binding  20 laaalrdagfeVqll.........ganven............edivaairaekpdvvglSal..............ltsq 64 
                                    la++l +ag++V+ +         +                   + ++i+ ++pd+v   a               lt++
  gi|121636025|ref|YP_976248.1|  16 LAEMLLAAGHDVYATycrptidpsD----LqfngaevditdwCSVYDSIATFRPDAVFHLAAqsypavswarpvetLTTN 91 
                                    7788888888776553344444441....0333344445777789***********99955567778888899999**** PP

                    B12-binding  65 leavkelvellkrirprvkvvvGGahp 91 
                                    + +++ + e+l+r+rp++k++v G  +
  gi|121636025|ref|YP_976248.1|  92 MVGTAIVFEALRRVRPHAKIIVAGSSA 118
                                    **********************99765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                    B12-binding   5 latvggdlhplGlavlaaalrda 27 
                                    ++++++++ ++ ++v+aa++rd+
  gi|121636025|ref|YP_976248.1| 238 GGSIAYEMGDVLKQVIAACKRDD 260
                                    67788888899999999999985 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.025       2     151 ..       5     147 ..       4     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                      3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealeg..vdvvihlaslv.d 78 
                                    +tG++G +G++l ++L+ +++  +v +   r       +  ++n     e+D+td  ++ + +     d+v+hla+ + +
  gi|121636025|ref|YP_976248.1|   5 ITGAGGMMGSHLAEMLLAAGH--DVYATYCRPTIDP--SDLQFN---GAEVDITDWCSVYDSIATfrPDAVFHLAAQSyP 77 
                                    8*******************6..6666655544444..333444...4489999999998866651169*****987625 PP

                      3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvka..gvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                      +  +  e  + n+ GT  v ea ++     +++v  Ssae  + +  + +i      +++e  + ++y  sKa
  gi|121636025|ref|YP_976248.1|  78 AVSWARPVETLTTNMVGTAIVFEALRRVrpHAKIIVAGSSAEYGFVDPSEVPIN-----ERRELRPLHPYGVSKA 147
                                    5667888999**************865422688899999988777644444444.....3444445556666665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0022       3.9       3      30 ..       3      30 ..       1      61 [. 0.89
   2 ?   -3.1   0.0       2.6   4.6e+03     105     138 ..      88     118 ..      82     123 .. 0.65
   3 ?    3.4   0.0     0.025        46     147     173 ..     140     166 ..     131     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEE CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvv 30
                                   v +tGa++ +G  +a+ l+++G +v+++
  gi|121636025|ref|YP_976248.1|  3 VWITGAGGMMGSHLAEMLLAAGHDVYAT 30
                                   78***********************984 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                                    HHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGG CS
                      adh_short 105 ievNltgvflltravlpamlkqssGrIvnvsSva 138
                                    + +N++g+  + +a+ +    +  ++I+  +S a
  gi|121636025|ref|YP_976248.1|  88 LTTNMVGTAIVFEALRRV---RPHAKIIVAGSSA 118
                                    556666666555554444...6777777777765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.025
                                    HHHHHHHHHHHHHHHHHHHHHGGGTEE CS
                      adh_short 147 aaYsAsKaavagltrslakelaptgir 173
                                     +Y+ sKaa ++l+ + +k +  + + 
  gi|121636025|ref|YP_976248.1| 140 HPYGVSKAATDMLAYQYHKSYGMHTVV 166
                                    58****************999999864 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.22       1      33 [.       1      32 [.       1      55 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEE CS
                         DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavd 33
                                   +kv ++Ga G mG+++++++ + +++ + a + 
  gi|121636025|ref|YP_976248.1|  1 MKVWITGAGGMMGSHLAEMLLA-AGHDVYATYC 32
                                   89*****************998.6666666555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.25       2      30 ..       3      32 ..       2      52 .. 0.87
   2 ?   -4.0   0.0       6.4   1.1e+04      94     105 ..      96     107 ..      81     117 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                   EEEE--.SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  2 vaviGa.GtmGagiaavfasagleVvlvdi 30
                                   v + Ga G+mG+ +a+++++ag++V  + +
  gi|121636025|ref|YP_976248.1|  3 VWITGAgGMMGSHLAEMLLAAGHDVYATYC 32
                                   67889978*****************98765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.4
                                    HHHHHHHHCCS- CS
                        3HCDH_N  94 rkvfaelekiak 105
                                    + vf++l ++ +
  gi|121636025|ref|YP_976248.1|  96 AIVFEALRRVRP 107
                                    334555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1827.55
//
Query:       gi|121636026|ref|YP_976249.1|  [L=196]
Description: phosphoheptose isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-25   90.3   0.5    1.4e-25   89.9   0.5    1.3  1  SIS_2     SIS domain
    6.1e-10   39.1   0.3    4.6e-09   36.2   0.0    2.1  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.5   1.5e-29   1.4e-25      23     138 .]      33     148 ..      11     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.5e-29
                                    HHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHHTT-TTHHHHHHHHTT-. CS
                          SIS_2  23 kaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeatkssalerdegyakqilrlvrl. 101
                                    +  + + +  ++g +v+++G+G+Saa+a+++aa++ g   f+r+ l a alh+++  ++ +a+++d  y++ ++r  ++ 
  gi|121636026|ref|YP_976249.1|  33 AIGDRLIAGYRAGARVFMCGNGGSAADAQHFAAELTGHLIFDRPPLGAEALHANS--SHLTAVANDYDYDTVFARALEGs 110
                                    45566778889******************************************99..77777777777777777775554 PP

                                    .-TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                          SIS_2 102 .kpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                     +pgD+L+ iS+sGn+ +v+ aa+ a+e+g++v+A+t+
  gi|121636026|ref|YP_976249.1| 111 aRPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTG 148
                                    5***********************************97 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.04   3.6e+02       7      27 ..      47      67 ..      42      75 .. 0.84
   2 !   36.2   0.0   5.2e-13   4.6e-09      51     106 ..     111     166 ..      80     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.04
                                   EEEEEESHHHHHHHHHHHHHH CS
                            SIS  7 riyvlGaGtsyaiakelalkl 27
                                   r+++ G G s+a a+ +a+ l
  gi|121636026|ref|YP_976249.1| 47 RVFMCGNGGSAADAQHFAAEL 67
                                   99**********999999877 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 5.2e-13
                                    -STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEE CS
                            SIS  51 ideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyina 106
                                    ++++d +++is+sg++ ++++aa+ a+e g++++a+T+++g +la++ad  + +++
  gi|121636026|ref|YP_976249.1| 111 ARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFLINVPS 166
                                    689*********************************************87766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1380.52
//
Query:       gi|121636027|ref|YP_976250.1|  [L=190]
Description: dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0027   17.8   0.4      0.011   15.9   0.1    2.0  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
     0.0063   16.8   0.0     0.0098   16.2   0.0    1.3  1  HAD_SAK_2       HAD domain in Swiss Army Knife RNA repair pro
      0.007   16.4   0.0      0.015   15.4   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.18   11.9   0.0    2.0  2  HAD_2           Haloacid dehalogenase-like hydrolase
      0.019   15.4   0.0      0.039   14.4   0.0    1.5  1  HAD             haloacid dehalogenase-like hydrolase
      0.022   14.5   0.0      0.032   13.9   0.0    1.3  1  PNK3P           Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.6e-06     0.011       2      41 ..      13      63 ..      12      88 .. 0.88
   2 ?   -0.4   0.0       0.4   1.2e+03       6      18 ..      88     100 ..      83     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                                   EEESTTTSE...........ETTEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                    Hydrolase_6  2 lfDidGvLw...........rgdkaipgaaealnalraagkpvvllTNnss 41
                                   ++D dGv+            r+ + +pgaa+al+ lra    +v++TN+ +
  gi|121636027|ref|YP_976250.1| 13 FLDRDGVINrqvvgdyvrnwRQFEWLPGAARALKKLRAWAPYIVVVTNQQG 63
                                   688999999777777777778999************************975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                                    TTTSEETTEE-TT CS
                    Hydrolase_6   6 dGvLwrgdkaipg 18 
                                    dGvL++g +++p+
  gi|121636027|ref|YP_976250.1|  88 DGVLIDGFQVCPH 100
                                    9*****9998886 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.3e-06    0.0098       2     106 ..      12     127 ..      11     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                      HAD_SAK_2   2 iFLDiDGVLnpekskkrregeedealdpe..averlkriveatgakiVlsstWrrred............eelkallkaa 67 
                                    +FLD DGV+n++ + +  +++  +++++   a+++lk++  a    iV+ ++ +                ++l+ +l+++
  gi|121636027|ref|YP_976250.1|  12 LFLDRDGVINRQVVGDYVRNW--RQFEWLpgAARALKKLR-AWAPYIVVVTNQQGVGAglmsavdvmvihRHLQMQLASD 88 
                                    8***********999977755..55777445999999955.555567777777766667998877655544455555555 PP

                      HAD_SAK_2  68 grpriigvtpdlpeeeseeekk...sRaqeilewlrrheeve 106
                                    g   +i+  +  p+++s+        R   +l+wlrrh++ e
  gi|121636027|ref|YP_976250.1|  89 G--VLIDGFQVCPHHRSQRC-GcrkPRPGLVLDWLRRHPDSE 127
                                    5..55665555555543332.13559999*********5444 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.9e-06     0.015       2      41 ..     108     147 ..     107     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.9e-06
                                    .STTSSHHHHHHHHHH.---GGGEEEEES-TTTHHHHHHHC CS
                 Hydrolase_like   2 lgKPepemydfalevl.gsdpeevlmiGDrlatDiagAnna 41 
                                    ++KP p+++   l+++ +s+p  ++++GD+  +D++ A+n+
  gi|121636027|ref|YP_976250.1| 108 CRKPRPGLVLDWLRRHpDSEPLLSIVVGDS-LSDLELAHNV 147
                                    89******999999987788889*******.********96 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.06   1.8e+02      69     105 ..      28      62 ..      13      90 .. 0.80
   2 ?   11.9   0.0     6e-05      0.18     130     173 ..     105     149 ..      95     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.06
                          HAD_2  69 yneekkkkevkpydgvkelLeeLkeagyklgivTsks 105
                                    y+ +  +  ++ ++g+  +L++L++    + +vT+++
  gi|121636027|ref|YP_976250.1|  28 YVRNWRQ--FEWLPGAARALKKLRAWAPYIVVVTNQQ 62 
                                    5555555..8999**********99999999999985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6e-05
                          HAD_2 130 dvekkKPdpeviekalekl.klkkeeviyvGDsptDieaakkagi 173
                                     ++ +KP p +++ +l++  + ++   i+vGDs +D+e a+++  
  gi|121636027|ref|YP_976250.1| 105 RCGCRKPRPGLVLDWLRRHpDSEPLLSIVVGDSLSDLELAHNVAA 149
                                    56678***********9988999******************9765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.039      71     187 ..      27     144 ..      12     145 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                            HAD  71 aelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplveplla.elg.adevlatelevdd......rltgel 142
                                    ++++ ++    +   + pga ++l++ ra    +vvv++     +  + a  +  +++ l  +l++d+       +  ++
  gi|121636027|ref|YP_976250.1|  27 DYVRNWR----QFE-WLPGAARALKKLRAWAPYIVVVTNQQGVGAGLMSAvDVMvIHRHLQMQLASDGvlidgfQVCPHH 101
                                    3444444....555.55888888887776666777778776666666663222244444444555555511124444445 PP

                            HAD 143 glegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                    + +   +r+  ++  + +wl +++   +l  ++++GDs sDl+l+
  gi|121636027|ref|YP_976250.1| 102 RSQRCGCRK-PRPGLVLDWLRRHPDSEPLL-SIVVGDSLSDLELA 144
                                    555666666.55566666888888666664.8999*******998 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.032      21     112 ..      29     125 ..      12     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                          PNK3P  21 akdaddwkllsesvlekLkklkeegykivifsNqggvvekktkkslekfkekieallkeldvp...llvyaatkkd.... 93 
                                     ++  ++++l       Lkkl      iv+++Nq+gv +  +  s+ +++   ++l  +l  +   +  +  + +     
  gi|121636027|ref|YP_976250.1|  29 VRNWRQFEWLP-GAARALKKLRAWAPYIVVVTNQQGVGA--GLMSAVDVMVIHRHLQMQLASDgvlIDGFQVCPHHrsqr 105
                                    44556666664.578899999999999***********9..666666666666666666644443433333333221233 PP

                          PNK3P  94 .kyRKPetGmweelkkdlee 112
                                       RKP++G++    ++  +
  gi|121636027|ref|YP_976250.1| 106 cGCRKPRPGLVLDWLRRHPD 125
                                    489******98776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1402.87
//
Query:       gi|121636028|ref|YP_976251.1|  [L=355]
Description: sugar kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-11   43.8   3.6    2.4e-11   43.7   0.8    2.5  2  GHMP_kinases_N  GHMP kinases N terminal domain
    2.1e-09   37.6   0.1    2.1e-09   37.6   0.1    1.9  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.31   2.8e+03       5      20 ..       5      20 ..       2      21 .. 0.78
   2 !   43.7   0.8   2.7e-15   2.4e-11       6      66 .]     106     169 ..     101     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.31
                                   EESSHTTSSSCHHHHH CS
                 GHMP_kinases_N  5 kseiPvgaGLGSSAAl 20
                                   +++ P+  GLG+++++
  gi|121636028|ref|YP_976251.1|  5 RGRAPLRLGLGGGGTD 20
                                   67778889***99876 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 2.7e-15
                                    ESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.H..HHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   6 seiPvgaGLGSSAAlavalvaAllallgls.l..eeaklaleaerlaqggngsggDvaasvyGg 66 
                                     + P+g+GLGSS+Al+va+++  +al g s    e+a+la e+er   g  g+++D +a+++Gg
  gi|121636028|ref|YP_976251.1| 106 VDAPPGSGLGSSSALVVAMLLTTCALIGSSpGpyELARLAWEIERVDLGMAGGWQDHYAAAFGG 169
                                    578************************988534477*********999999************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3         1   9.4e+03      54      64 ..     110     120 ..     109     123 .. 0.79
   2 !   37.6   0.1   2.4e-13   2.1e-09       3      82 ..     245     323 ..     237     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                 GHMP_kinases_C  54 sGaGgGptvfa 64 
                                    +G+G+G++ + 
  gi|121636028|ref|YP_976251.1| 110 PGSGLGSSSAL 120
                                    69****98665 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 2.4e-13
                 GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralree 82 
                                    ++l  gd++ +++ l ++++ ++++ ++i++p++e + + +++ G  ++k+sGaGgG+++ +++ d+ +  +var+l +e
  gi|121636028|ref|YP_976251.1| 245 DLLVVGDIPGFADSLLRGWQAKKRTSTRISNPAIEHAYQVAQSSGMVAGKVSGAGGGGFLMMIV-DPRRRIEVARSLERE 323
                                    567779**************99999***************************************.99999*****99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2477.97
//
Query:       gi|121636029|ref|YP_976252.1|  [L=251]
Description: hypothetical protein BCG_0150c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-23   81.7   0.3    8.7e-23   81.2   0.3    1.2  1  Big_10    Bacterial Ig domain
    1.6e-19   70.7   0.0    2.8e-19   70.0   0.0    1.3  1  YkuD      L,D-transpeptidase catalytic domain
     0.0026   18.4   0.2     0.0063   17.2   0.2    1.7  1  Big_5     Bacterial Ig-like domain


Domain annotation for each model (and alignments):
>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.3   1.5e-26   8.7e-23      86     180 ..      40     137 ..      23     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.5e-26
                         Big_10  86 atltpedgstvGvgqpisikFdkpvedkaavekalkvttspavegafaWlsdsevdwRpkeYwkpgtkVtvkak..lygv 163
                                    a+++p +g++vGv+ p+ ++F++pv+d++ave++++++t ++++g+f W+ ++ v+w p+ Yw+p+t+V+v ++  ++g 
  gi|121636029|ref|YP_976252.1|  40 ASVSPANGAVVGVAHPVVVTFTTPVTDRRAVERSIRISTPHNTTGHFEWVASNVVRWVPHRYWPPHTRVSVGVQelTEGF 119
                                    6789****************************************************************998775448999 PP

                         Big_10 164 elgdgvygkedksv.sft 180
                                    e+gd + g ++ s+ +ft
  gi|121636029|ref|YP_976252.1| 120 ETGDALIGVASISAhTFT 137
                                    999999998876541455 PP

>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   4.7e-23   2.8e-19       6     146 .]     129     249 ..     125     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 4.7e-23
                                    EETTTTEEEEEEETTEEEEEEE-BEBTTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEEECCCTT CS
                           YkuD   6 vdlaeqrllvlyengklvlsfpvsvGgkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyldkknskv 85 
                                     ++++ +++++ +ng++++++p+s+G   +++r+TP+G+f   sk+r     + +  ++ ++   +++  +++       
  gi|121636029|ref|YP_976252.1| 129 ASISA-HTFTVSRNGEVLRTMPASLG---KPSRPTPIGSFHAMSKERTVV--MDSRTIGIPLNSSDGYLLTAHY------ 196
                                    57888.567888**************...66************8888887..8888888888888888777766...... PP

                                    CECCCCEEE-STTS-EEEE.ETCSS...CTHHC.BSSSEEE-HHHHHHHHHHHHTTEEEEE CS
                           YkuD  86 algkvkfvfpngsgiyiHgtgapdlfergkgarrShGCirlseedakelyelvlvgtpvvi 146
                                          +v  ++sg+y+H  ++  + ++   a+ ShGCi+ls+++a + ++ v+vg+p+++
  gi|121636029|ref|YP_976252.1| 197 ------AVRVTWSGVYVHSAPWSVNSQG--YANVSHGCINLSPDNAAWYFDAVTVGDPIEV 249
                                    ......99**********5555555444..4666************************987 PP

>> Big_5  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.1e-06    0.0063       5      83 ..      37     112 ..      35     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                          Big_5   5 PtvvstsPadgatgvavnaeitvtFseav.dastvtaatvialsdsettavtgsydasgktvtitpsaeLaanttYtvti 83 
                                    P v s+sPa+ga+ v v  +++vtF+ +v d   v+ ++ i  s++++t+  +   ++++ v   p   + ++t+ +v +
  gi|121636029|ref|YP_976252.1|  37 PGVASVSPANGAV-VGVAHPVVVTFTTPVtDRRAVERSIRI--STPHNTTGHFE-WVASNVVRWVPHRYWPPHTRVSVGV 112
                                    7799********9.67778**********888888888888..66666666665.4888888888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1945.85
//
Query:       gi|121636030|ref|YP_976253.1|  [L=314]
Description: oxidative stress response regulatory protein oxyS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-26   90.5   5.5    1.5e-25   89.8   5.5    1.3  1  LysR_substrate  LysR substrate binding domain
    1.7e-19   69.5   0.2    3.3e-19   68.6   0.2    1.5  1  HTH_1           Bacterial regulatory helix-turn-helix protein


Domain annotation for each model (and alignments):
>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   5.5   1.7e-29   1.5e-25       2     206 ..      87     296 ..      86     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.7e-29
                                    TTSCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESH.HHHHHHHHTTSSSEEEEESSS.CCTTEEEEEEEEEE CS
                 LysR_substrate   2 gglrgrLrigapptlaryllppllarfraryPevelelvegds.eelldllaegelDlairagpp.edsglearpLaeep 79 
                                    +g +g+Lr+g++pt a++    +l++f+ ++P  ++++ +    +el ++l+e elD++i++ +  ++++++ +pL+ee+
  gi|121636030|ref|YP_976253.1|  87 SGITGTLRLGTVPT-ASTTASLVLSAFCSAHPLAKVQVCSRLAaTELYRRLREFELDAVIVHPETqDSDDVDLVPLYEEQ 165
                                    5789**********.88999******************9998879*******************9999************ PP

                                    EEEEEETTSGGGGSSSE.CGGGGCTSEEEEESTTSTHHHHHHHHHHCTTEECEEEEEESSHHHHHHHHHTTS-BEEEEGG CS
                 LysR_substrate  80 lvlvaspdhpLargepv.sledLadeplilleegsglrdlledalreaglkprvalevnsleallalvaaGlGiallprs 158
                                    +vl+ ++d  L  g+++  ++d a++pl ll+++ + r+ +++a++++ +++ + +e++s+++l a va G   +++p+ 
  gi|121636030|ref|YP_976253.1| 166 YVLLSPADM-LPPGTSTlVWRDAAQLPLALLTADMRDRQVIDAAFADHAVSAIPQVETDSVASLFAQVATGNWASIVPHT 244
                                    ********9.99966666************************************************************** PP

                                    GHHCCC....HTTTEEEEEESSTTCEEEEEEEEETTCCCHHHHHHHHHHHHH CS
                 LysR_substrate 159 avrdel....adgrlvalplpepplprelylvyrkgrelspavrafidflre 206
                                    ++ + +      g+++a++l +p l+++++l++++  + sp +ra+i ++++
  gi|121636030|ref|YP_976253.1| 245 WLWAMPmsgpTGGEIRAVELVDPVLKAQIALATNALGPGSPVARALITCAQA 296
                                    *998885555789*********9999*********************98865 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.2   3.7e-23   3.3e-19       1      60 []       3      62 ..       3      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3.7e-23
                                   HHHHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.EEE-HHHH CS
                          HTH_1  1 lrqlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.lrLTeaGe 60
                                   +rql++fvava+e++f+rAAe++++sqpa+s +i++LE+el+v+L++R g++   LT +Ge
  gi|121636030|ref|YP_976253.1|  3 FRQLEYFVAVAQERHFARAAEKCYVSQPALSSAIAKLERELNVTLINR-GHSfEGLTREGE 62
                                   69**********************************************.777459999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2073.23
//
Query:       gi|121636031|ref|YP_976254.1|  [L=582]
Description: oxalyl-CoA decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-49  166.1   2.4    2.9e-48  163.7   0.1    3.1  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.7e-34  117.1   0.0    8.2e-34  116.3   0.0    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    1.1e-26   93.4   0.3    4.1e-26   91.6   0.0    2.1  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.1   4.8e-52   2.9e-48       3     170 ..      15     182 ..      13     184 .. 0.97
   2 ?   -3.2   0.1      0.95   5.6e+03     137     155 ..     203     220 ..     202     223 .. 0.74
   3 ?    0.8   0.0     0.056   3.4e+02      82     106 ..     436     460 ..     425     556 .. 0.66

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 4.8e-52
                                    HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                   TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                    + +++v+aLka++v++++gv+G  i++l +a++++ gir++ +rhE +a++aA +   +t +pgv+l+tsgpG++n+l+a
  gi|121636031|ref|YP_976254.1|  15 GCHLVVDALKANDVDTIYGVVGIPITDLARAAQAS-GIRYIGFRHEASAGNAAAAAGFLTARPGVCLTTSGPGFLNGLPA 93 
                                    6789*******************************.7******************************************* PP

                                    HHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                   TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                    la+A ++ +P++ +sg++++ +++  +g  q  ldql+ +rp++k+a+r+ +++++ + ++rAirta+sgrpg vyl++p
  gi|121636031|ref|YP_976254.1|  94 LANATTNCFPMIQISGSSSRPMVDlqRGDYQ-DLDQLNAARPFVKAAYRIGQVQDIGRGVARAIRTATSGRPGGVYLDIP 172
                                    ************************9777777.9*********************************************** PP

                                    HHHCC-EEEH CS
                   TPP_enzyme_N 161 kdvlleevde 170
                                     dvl ++v++
  gi|121636031|ref|YP_976254.1| 173 GDVLGQAVEA 182
                                    ******9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.95
                                    HHHHHHHHHHHHSSS--EE CS
                   TPP_enzyme_N 137 pealrrAirtalsgrpgPv 155
                                    pea++rA++++  + ++P 
  gi|121636031|ref|YP_976254.1| 203 PEAIDRALDVL-AQAQRPL 220
                                    89999999999.5555565 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.056
                                    HHHHHHHHT--EEEEEEE--CCCHH CS
                   TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg 106
                                    a+a A  ++ P++++ gd++    g
  gi|121636031|ref|YP_976254.1| 436 AIAAAVETGRPVVAIEGDSAFGFSG 460
                                    6677777777777777777666555 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   1.4e-37   8.2e-34       1     137 []     206     335 ..     206     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 1.4e-37
                                    HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SE CS
                   TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDl 80 
                                    i++a++ l++a+rp++++G+g+a+++a + +re++e++giP++ + m+kg++p++hp++       +++a++ a+++aD+
  gi|121636031|ref|YP_976254.1| 206 IDRALDVLAQAQRPLLVLGKGAAYAQADNVIREFVEHTGIPFLPMSMAKGLLPDSHPQS-------AAAARSLAMARADV 278
                                    799******************************************************99.......79999********* PP

                                    EEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                   TPP_enzyme_M  81 vlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                    vl++Gar+++    g++p+++ +ak+i++di+++e++ n+++  ++ gd++ +++aL
  gi|121636031|ref|YP_976254.1| 279 VLLVGARLNWLLGNGESPQWSADAKFIQVDIEASEFDSNRPIVAPLTGDIGSVMSAL 335
                                    **********99999999**********************************99987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.49     3e+03      34      71 ..      65     100 ..      36     107 .. 0.55
   2 !   91.6   0.0   6.8e-30   4.1e-26       7     153 .]     405     552 ..     400     552 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.49
                                    HHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHT CS
                   TPP_enzyme_C  34 lpaAiGaklakpdrevvaivGDGgflmi.lqelatavrr 71 
                                     +aA G   a   r+ v+++  G  + + l++la+a  +
  gi|121636031|ref|YP_976254.1|  65 AAAAAGFLTA---RPGVCLTTSGPGFLNgLPALANATTN 100
                                    2333333334...35566666665555556666666666 PP

  == domain 2  score: 91.6 bits;  conditional E-value: 6.8e-30
                                    HHHHHH.HTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBC CS
                   TPP_enzyme_C   7 lwaarl.lkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegy 85 
                                    l++ar  ++++ pr+ l+sg++g mG g+++Ai+a++   +r+vvai GD++f ++++e++t++r++lp+tvv+lnN+g 
  gi|121636031|ref|YP_976254.1| 405 LDLARNiIDMHLPRHRLDSGTWGVMGIGMGYAIAAAVE-TGRPVVAIEGDSAFGFSGMEFETICRYRLPVTVVILNNGGV 483
                                    555665477888*************************5.689***********************************987 PP

                                    CCHHHH.HHHHTCCTTTTSBB........BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  86 gmtggq.qepfggkrksgpagk.......dlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       +g   + f +        +            +++ +aea+G kg+ v+++   ele al +al+++gp+li++
  gi|121636031|ref|YP_976254.1| 484 --YRGDeATIFRSAAP---VWRhdpaptvLNAHARHELIAEAFGGKGYHVSTP--TELESALTDALASNGPSLIDC 552
                                    ..44442333332222...222234566667778***************9999..*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3791.60
//
Query:       gi|121636032|ref|YP_976255.1|  [L=525]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-81  272.8   0.1    4.9e-81  272.5   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    1.2e-17   64.6   0.3    3.8e-17   63.0   0.3    1.9  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.5   0.1   5.5e-85   4.9e-81       3     422 ..      15     427 ..      13     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 5.5e-85
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                     +a + p+++alv +++   ++ r+l + v++lA  L++ G+ +gdrVa+ +   +e+vvalla+ +a +vvvpl+p+l+
  gi|121636032|ref|YP_976255.1|  15 VAATRLPEAPALVVTADRIAISHRDLARLVDELAGQLTRSGLLPGDRVALRMGSNAEFVVALLAASRADLVVVPLDPALP 94 
                                    5788999*****99999*********************88**************************************** PP

                                    HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSE CS
                    AMP-binding  83 aeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddl 161
                                      e +   ++++a+v++  +d++   +++++++      ++ +  d++++  +  ++ ++ +e +     ++e l+pdd 
  gi|121636032|ref|YP_976255.1|  95 ITEQRVRSQAAGARVVL--IDADGpHDRAEPTTR-WWPLTVNVGGDSGPSGGTLSVHLDAATEPNP-ATSTPEGLRPDD- 169
                                    *****************..777775555544443.3333444444444444443333333333332.344777899999. PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                    a+i++T+GTTG PK V  +h+n++++v+++   t  +l+++d  ++++pl+h  gli++ll++l+sG++v l+ +  + +
  gi|121636032|ref|YP_976255.1| 170 AMIMFTGGTTGLPKMVPWTHANIASSVRAI--ITGYRLSPRDATVAVMPLYHGHGLIASLLATLASGGAVSLPARGRF-S 246
                                    9****************************8..33456789********************************887755.6 PP

                                    HHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGG CS
                    AMP-binding 242 pklllelieklkvtviagvPrvlealle.sgalkaakkakdlss.lrlvllggeplspellrffralfgeevlegYGlTE 319
                                    +++++++i++ ++t  ++vP++ + lle s ++     + + ++ lr++ ++ +pl ++++ +++  f  +v+ ++G+TE
  gi|121636032|ref|YP_976255.1| 247 AHTFWDDIKAVGATWYTAVPTIHQILLErSATEP----SGRKPAaLRFIRSCSAPLTAQAALALQTEFAAPVVCAFGMTE 322
                                    67889*********************99665554....3455556****9****************************** PP

                                    GSSECEE......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETC CS
                    AMP-binding 320 ttgvvtv......lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdseg 393
                                    +t+ vt+      +++e++ +++g vG+   g++++iv  + g p+p g +Ge+++rg +v +gYl++p  ta  f+  +
  gi|121636032|ref|YP_976255.1| 323 ATHQVTTtqiegiDQTETPVVSTGLVGRS-TGAQIRIVGSD-GLPLPAGAVGEIWLRGTTVVRGYLGDPTITAANFT--D 398
                                    *****878999987778888889999999.8*********9.99********************************9..5 PP

                                    CEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 394 rwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +wlrTGDlg l + G l i gR+k+li++
  gi|121636032|ref|YP_976255.1| 399 GWLRTGDLGSLSAAGDLSIRGRIKELINR 427
                                    7**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.3   4.3e-21   3.8e-17       2      75 ..     437     510 ..     436     511 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 4.3e-21
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                    vE +l+shp+V eaaV+Gvp+++ Gea++a++v+++  ++++eeL++++r++l+++  p  +   + lp t+ G
  gi|121636032|ref|YP_976255.1| 437 VEGVLASHPNVMEAAVFGVPHQLYGEAVAAVIVPRESAPPTREELVQFCRERLAAFEIPASFQEASGLPHTAKG 510
                                    8*********************************8554569******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3538.59
//
Query:       gi|121636033|ref|YP_976256.1|  [L=714]
Description: elongation factor G [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-41  139.3   0.0      9e-41  138.4   0.0    1.5  1  EFG_IV         Elongation factor G, domain IV
    1.8e-37  128.8   0.0    2.6e-37  128.3   0.0    1.2  1  GTP_EFTU       Elongation factor Tu GTP binding domain
    1.4e-24   85.9   0.0    5.5e-23   80.8   0.0    2.4  2  EFG_C          Elongation factor G C-terminus
    1.7e-23   82.5   0.0    2.9e-23   81.8   0.0    1.4  1  EFG_II         Elongation Factor G, domain II
    7.9e-13   48.6   0.0    2.9e-12   46.8   0.0    2.1  1  GTP_EFTU_D2    Elongation factor Tu domain 2
    2.6e-07   30.7   0.0    7.9e-07   29.2   0.0    1.8  2  MMR_HSR1       50S ribosome-binding GTPase
    2.3e-05   23.8   0.0    3.5e-05   23.2   0.0    1.2  1  Septin         Septin
     0.0038   17.1   0.0     0.0058   16.5   0.0    1.2  1  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0047   17.3   0.1      0.013   15.9   0.1    1.7  1  AAA_16         AAA ATPase domain
     0.0048   16.8   0.1      0.039   13.9   0.2    2.3  2  RsgA_GTPase    RsgA GTPase
      0.006   16.7   0.2       0.28   11.2   0.1    2.3  2  Dynamin_N      Dynamin family
     0.0083   16.6   0.0      0.017   15.6   0.0    1.4  1  ABC_tran       ABC transporter
  ------ inclusion threshold ------
       0.01   15.5   0.2      0.021   14.5   0.2    1.5  1  AAA_29         P-loop containing region of AAA domain
      0.013   15.1   0.0      0.086   12.4   0.0    2.2  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.017   15.6   0.0      0.034   14.7   0.0    1.4  1  AAA_23         AAA domain
      0.019   14.9   0.0      0.041   13.9   0.0    1.5  1  AAA_5          AAA domain (dynein-related subfamily)
      0.023   14.1   0.0      0.051   13.0   0.0    1.5  1  SRPRB          Signal recognition particle receptor beta subu
      0.025   14.8   0.5      0.053   13.8   0.5    1.5  1  AAA_28         AAA domain
      0.051   13.3   0.0      0.088   12.5   0.0    1.3  1  IstB_IS21      IstB-like ATP binding protein
      0.053   13.7   0.0        0.2   11.8   0.0    2.0  1  AAA_33         AAA domain
      0.069   13.4   0.0       0.33   11.2   0.1    2.0  2  AAA_22         AAA domain
      0.086   12.2   0.1       0.15   11.4   0.1    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.091   12.5   0.2       0.17   11.6   0.2    1.5  1  AAA_30         AAA domain
       0.12   12.1   0.0       0.19   11.4   0.0    1.3  1  Guanylate_kin  Guanylate kinase
       0.12   12.6   0.0       0.23   11.7   0.0    1.5  1  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.13   12.6   0.2        0.4   11.1   0.0    1.9  2  AAA            ATPase family associated with various cellular
       0.15   11.8   0.0        1.6    8.5   0.0    2.2  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.22   11.4   0.1       0.51   10.2   0.1    1.6  1  NACHT          NACHT domain


Domain annotation for each model (and alignments):
>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   1.4e-43     9e-41       2     119 ..     501     617 ..     500     619 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 1.4e-43
                                    CCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS- CS
                         EFG_IV   2 qVayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplage 81 
                                    +V+ rEt++ ++k  +++++kqsgg+gqy+ + +e+ePl+egsg+ef d+++gg+vp+++i++vekG++ ++++G++ag+
  gi|121636033|ref|YP_976256.1| 501 RVPLRETFAGNAK-GHGRHIKQSGGHGQYGVCDIEVEPLPEGSGFEFLDKVVGGAVPRQFIPSVEKGVRAQMDKGVHAGY 579
                                    5999*********.****************************************************************** PP

                                    -EESEEEEEEEEE--TTTC-HHHHHHHHCHHHHHHHHC CS
                         EFG_IV  82 pvtdvkvtLldgslhevdsseaafkpaarralkeallk 119
                                    pv+d++vtLldg+ h+vdss+ af++a+  al+ea+++
  gi|121636033|ref|YP_976256.1| 580 PVVDIRVTLLDGKAHSVDSSDFAFQMAGALALREAAAA 617
                                    ***********************************976 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.0   4.1e-40   2.6e-37       3     193 ..      23     286 ..      22     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 4.1e-40
                                    EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                       GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                    +rn++++g    GKtTL+++Ll +++  s+ g+++e+++v+D+ ++E +++ ++  a++sl   ++  ++nl+DtPG +d
  gi|121636033|ref|YP_976256.1|  23 VRNVVLVGPSGGGKTTLIEALLVAAKVLSRPGSVTEGTTVCDFDEAEIRQQRSVGLAVASLA--YDGIKVNLVDTPGYAD 100
                                    69************************************************************..**************** PP

                                    GHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH......... CS
                       GTP_EFTU  83 FskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk......... 153
                                    F+ e  +glr++D+a++v++a+eGv + t+ +++ ++++g+p+ v+i+K+D+++a+++e  +++++ + +k         
  gi|121636033|ref|YP_976256.1| 101 FVGELWAGLRAADCALFVIAANEGVDEPTKSLWQECSQVGMPRAVVITKLDHARANYREALTAAQDAFGDKvlplylpsg 180
                                    ********************************************************************999********* PP

                                    ...................................................................HHHHHHHHHTTTT CS
                       GTP_EFTU 154 ...................................................................eeklekygekgek 166
                                                                                                        ++lek++++g+ 
  gi|121636033|ref|YP_976256.1| 181 dgligllsqalyeyadgkrttrtpaesdterieeargaliegiieesedeslmerylggetidesvlIQDLEKAVARGS- 259
                                    **************************************************************99999999999999995. PP

                                    TEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 167 evpvvfgSalkgegvktllealvellp 193
                                    ++pv+++++ +g g  +lle+ ++ +p
  gi|121636033|ref|YP_976256.1| 260 FFPVIPVCSSTGVGTLELLEVATRGFP 286
                                    ********************9887766 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.22   1.4e+02      10      55 ..     460     508 ..     458     513 .. 0.84
   2 !   80.8   0.0   8.6e-26   5.5e-23       1      86 [.     621     706 ..     621     709 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.22
                                    EEEEECCCCCCHHHHHHH.CT-EEEEEEEE...TTEEEEEEEEEGGG-T CS
                          EFG_C  10 eievpeeyvgkvisdlss.rrGeiedmeqd..asgrviieaeiPlaeli 55 
                                     ie ++e  + v+  + + + G ++d+  +  + +  +ie ++Pl+e++
  gi|121636033|ref|YP_976256.1| 460 RIEQNQETHQVVLWCMGEaHAGVVLDTLANryGVSVDTIELRVPLRETF 508
                                    6777888889999999987888999998888888999**********98 PP

  == domain 2  score: 80.8 bits;  conditional E-value: 8.6e-26
                                    EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE CS
                          EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYee 80 
                                    +llEPi ++ + vp+++vg+v++dlssrrG+++++e+ + +r++i+ae+P  el  +a +Lrsl +G +sf+ +f++Ye+
  gi|121636033|ref|YP_976256.1| 621 ILLEPIDEISVLVPDDFVGAVLGDLSSRRGRVLGTETAGHDRTVIKAEVPQVELTRYAIDLRSLAHGAASFTRSFARYEP 700
                                    59****************************************************************************** PP

                                    --HHHH CS
                          EFG_C  81 vpgdkl 86 
                                    +p++ +
  gi|121636033|ref|YP_976256.1| 701 MPESAA 706
                                    **9876 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   4.5e-26   2.9e-23       1      73 [.     425     497 ..     425     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.5e-26
                         EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                                    +PeP++ +ai ++ k+dedkls  L rl++EDptlr+e+++eT++++l++mGe+H  +v++ l ++y+v+v++
  gi|121636033|ref|YP_976256.1| 425 MPEPLLPIAIAAHAKTDEDKLSVGLGRLAAEDPTLRIEQNQETHQVVLWCMGEAHAGVVLDTLANRYGVSVDT 497
                                    6*********************************************************************987 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.5e-15   2.9e-12       1      73 [.     329     411 ..     329     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.5e-15
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEE..........EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSST CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke..........ivtrissletfhededeavaganaGvivaikgledaiiv 69 
                                    G+v+l+rv+sGt++++ +v++ g  ++   +          + +ri+ l  + ++++ + a ++aG+i+ai +l+ a ++
  gi|121636033|ref|YP_976256.1| 329 GRVSLVRVFSGTIRPDTTVHVSGhFSSFFGGgtsnthpdhdEDERIGVLSFPLGKQQRPAAAVVAGDICAIGKLSRA-ET 407
                                    89*******************8888775555*********************************************8.** PP

                                    TCEE CS
                    GTP_EFTU_D2  70 Gdtl 73 
                                    Gdtl
  gi|121636033|ref|YP_976256.1| 408 GDTL 411
                                    ***9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.2e-09   7.9e-07       1     113 [.      25     148 ..      25     149 .. 0.65
   2 ?   -2.4   0.0       7.9     5e+03      25      82 ..     193     248 ..     183     256 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-09
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE......ETTEE...............EEEEECGGCSSH CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk......lkgke...............ielvDtpGlieg 59 
                                    +v++vG +  GK+tLi al+ ++   s+   +T  ++   ++          +               ++lvDtpG +  
  gi|121636033|ref|YP_976256.1|  25 NVVLVGPSGGGKTTLIEALLVAAKVLSRPGSVTEGTTVCDFDeaeirqQ---RsvglavaslaydgikVNLVDTPG-YA- 99 
                                    599****************986333344445666666666653332230...1344444444444444********.76. PP

                                    HHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                       MMR_HSR1  60 aseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                       +  +g+ ++ l+ ad +l+v+ a+ e++++  ++l +  ++ + p  +v++
  gi|121636033|ref|YP_976256.1| 100 ---D-FVGELWAGLRAADCALFVIAAN-EGVDEPTKSLWQECSQVGMPRAVVIT 148
                                    ...3.488888888899*******977.66766666655554445556666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.9
                                    EESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEE CS
                       MMR_HSR1  25 ivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflaleeadlillv 82 
                                    + +d + tTr++ e   +  + +e + + + G+ie +se+++l +++l  e  d  +l+
  gi|121636033|ref|YP_976256.1| 193 EYADGKRTTRTPAESDTE--RiEEARGALIEGIIE-ESEDESLMERYLGGETIDESVLI 248
                                    556666777777766655..223444444556665.56666677777765555555555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.4e-08   3.5e-05       6      76 ..      25     102 ..      21     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.4e-08
                                    EEEEEEBTTSSCCCCCCTTSSSS----.........--------------S-EEEEEEEEETTCEEEEEEEE---BSSSS CS
                         Septin   6 tlmvvGesglGkttlintlfetdliee.........ekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdav 76 
                                    ++++vG sg Gkttli++l+    + +         +  +  + +++++ ++  + +++  dg+k+  +++Dtpg+ d+v
  gi|121636033|ref|YP_976256.1|  25 NVVLVGPSGGGKTTLIEALLVAAKVLSrpgsvtegtTVCDFDEAEIRQQRSVGLAVASLAYDGIKV--NLVDTPGYADFV 102
                                    899***************987766555589888885444445558888888888889999998765..67********97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.1e-06    0.0058       3      26 ..      27      52 ..      26      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.1e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl..d 26
                                   vl+Gp g GK++L++al ++a +  +
  gi|121636033|ref|YP_976256.1| 27 VLVGPSGGGKTTLIEALLVAAKVlsR 52
                                   9****************999876441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     2e-05     0.013      24      46 ..      20      45 ..       8      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
                         AAA_16 24 p...elvllsGesGvGKsslvrellr 46
                                   p   ++v+l+G+sG GK++l+++ll 
  gi|121636033|ref|YP_976256.1| 20 PggvRNVVLVGPSGGGKTTLIEALLV 45
                                   33469*****************9984 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   6.1e-05     0.039     101     122 ..      25      46 ..       6     102 .. 0.73
   2 ?   -0.6   0.0       1.7   1.1e+03      42      82 ..     136     175 ..     113     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                                    EEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                     +vlvG+SG GK+tLi+all  
  gi|121636033|ref|YP_976256.1|  25 NVVLVGPSGGGKTTLIEALLVA 46 
                                    689***************9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                    HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                    RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeelealgyevllv 82 
                                    + + g++  +v++K+D +  +   e+l ++  a+g +vl +
  gi|121636033|ref|YP_976256.1| 136 CSQVGMPRAVVITKLDHARANY-REALTAAQDAFGDKVLPL 175
                                    5666788899******999988.788888888887777765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00044      0.28       1      44 [.      26      69 ..      26      82 .. 0.86
   2 ?    3.2   0.0      0.13        83     102     142 ..      89     125 ..      79     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeee 44
                                   +++vG    GK+++++aLl ++   + p+ +T  +++   +e e
  gi|121636033|ref|YP_976256.1| 26 VVLVGPSGGGKTTLIEALLVAAKVLSRPGSVTEGTTVCDFDEAE 69
                                   799*******************999*******999887776655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                    SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-C CS
                      Dynamin_N 102 gltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdl 142
                                    +++lvD+PG+ +   +        ++ ad  l+v +an  +
  gi|121636033|ref|YP_976256.1|  89 KVNLVDTPGYADFVGEL----WAGLRAADCALFVIAANEGV 125
                                    689******98854444....44556666666666666654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.7e-05     0.017      13      45 ..      25      58 ..      23      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-05
                                   EEEEEESTTSSHHHHHHHHTTSS--..SEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkp..teGeilld 45
                                    v++vG++G GK+tL+++l+   k     G++  +
  gi|121636033|ref|YP_976256.1| 25 NVVLVGPSGGGKTTLIEALLVAAKVlsRPGSV-TE 58
                                   589**************998766655555555.33 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.3e-05     0.021      24      44 ..      25      45 ..      16      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                         AAA_29 24 atlltGpsGsGKSTllDAiqa 44
                                   +++l+GpsG GK+Tl+ A+ +
  gi|121636033|ref|YP_976256.1| 25 NVVLVGPSGGGKTTLIEALLV 45
                                   689*************88654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.086       3      29 ..      26      53 ..      24      84 .. 0.69
   2 ?   -0.7   0.0       1.5   9.4e+02     113     156 ..     113     156 ..     101     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                   EEEEESTTCCHHHHHHHHH.CT--SS-E CS
                           cobW  3 tvltGflGsGKTtLlnhll.enraglkl 29
                                   +vl+G+ G GKTtL+++ll + +   + 
  gi|121636033|ref|YP_976256.1| 26 VVLVGPSGGGKTTLIEALLvAAKVLSRP 53
                                   699***************9744444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                    CEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                           cobW 113 davvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                    d+ ++v+ a++  +e +k+  +  +q+ +   +v++K D + ++
  gi|121636033|ref|YP_976256.1| 113 DCALFVIAANEGVDEPTKSLWQECSQVGMPRAVVITKLDHARAN 156
                                    66777888877766667777777789999999*******99887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.3e-05     0.034      23      42 ..      27      46 ..      24      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-05
                         AAA_23 23 lItGpNGaGKTTildAikla 42
                                   +++Gp G GKTT+++A+  a
  gi|121636033|ref|YP_976256.1| 27 VLVGPSGGGKTTLIEALLVA 46
                                   89**************9876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.4e-05     0.041       1      47 [.      25      76 ..      25      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                                   EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B-- CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrrei 47
                                   +v+LvGp+G gK++l+e l+ a        +v++     d  e++++++r++
  gi|121636033|ref|YP_976256.1| 25 NVVLVGPSGGGKTTLIEALLVAAkvlsrPGSVTEGTTVCDFDEAEIRQQRSV 76
                                   69***************99888766666566666666667777777777776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05     0.051       4      70 ..      24     109 ..      22     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                                    -EEEEE-STTSSHHHHHHHHHHS.................S---B---SS-EEETTG.....GGTT-SEEEETT-GCCSH CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttd.................svkktvtSqessaalkv..ksekgskltliDfPGheklrq 64 
                                    ++v+lvG+s  GKT+l++ L+                    + ++ + q+ s+ l v   + +g k++l+D PG   +  
  gi|121636033|ref|YP_976256.1|  24 RNVVLVGPSGGGKTTLIEALLVAakvlsrpgsvtegttvcDFDEAEIRQQRSVGLAVasLAYDGIKVNLVDTPGYADFVG 103
                                    689***************99988889999998855555553333333333333333344456999*********999988 PP

                                    HHHHHH CS
                          SRPRB  65 kllekl 70 
                                    +l   l
  gi|121636033|ref|YP_976256.1| 104 ELWAGL 109
                                    887765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   8.3e-05     0.053       1      19 [.      25      43 ..      25      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-05
                         AAA_28  1 kivitGgestGKTtlleaL 19
                                   ++v++G++++GKTtl+eaL
  gi|121636033|ref|YP_976256.1| 25 NVVLVGPSGGGKTTLIEAL 43
                                   59****************9 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.088      48      71 ..      24      47 ..      22     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                      IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                    n+vl+GpsG GK+ l  al v+a
  gi|121636033|ref|YP_976256.1| 24 RNVVLVGPSGGGKTTLIEALLVAA 47
                                   59*****************97766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031       0.2       2      22 ..      26      46 ..      26      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                         AAA_33  2 vllvGlpGsGKstlaerllkk 22
                                   v+lvG++G GK+tl+e ll +
  gi|121636033|ref|YP_976256.1| 26 VVLVGPSGGGKTTLIEALLVA 46
                                   789**************9844 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00052      0.33       8      26 ..      26      44 ..      22      78 .. 0.89
   2 ?   -1.5   0.0       4.5   2.9e+03      29      70 ..     161     200 ..      93     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                         AAA_22  8 lvvtGesGtGKTtllrrll 26
                                   +v++G+sG GKTtl++ ll
  gi|121636033|ref|YP_976256.1| 26 VVLVGPSGGGKTTLIEALL 44
                                   79*************9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                         AAA_22  29 ldeeakaee.....erpevvfvtlpsstsskdllrellralglelka 70 
                                    l       +      +++v+  +lps+ ++  ll++ l ++ +++ +
  gi|121636033|ref|YP_976256.1| 161 L-------TaaqdaFGDKVLPLYLPSGDGLIGLLSQALYEYADGKRT 200
                                    2.......122244677888888888888888888888887777766 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00023      0.15      40      73 ..      24      57 ..       7      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                   .SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEE CS
                   FtsK_SpoIIIE 40 shllvaGatgsGKStalntLilSlatthtPeeVq 73
                                    +++++G +g GK+t + +L++++ + + P  V+
  gi|121636033|ref|YP_976256.1| 24 RNVVLVGPSGGGKTTLIEALLVAAKVLSRPGSVT 57
                                   69************************99999985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00027      0.17       2      40 ..       5      45 ..       4      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                         AAA_30  2 lnaeQaaavealltsgdrv..avltGpAGtGKttalkalre 40
                                   +na+Q aa++ +++++  v  +vl+Gp G GKtt+++al  
  gi|121636033|ref|YP_976256.1|  5 VNASQGAAAAPTANGPGGVrnVVLVGPSGGGKTTLIEALLV 45
                                   578899999888888776522799************99844 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0003      0.19       3      35 ..      24      57 ..      22      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTEE.E--E CS
                  Guanylate_kin  3 rpvvlvgpsgaGksslkkaLlselpekfg.vsvs 35
                                   r vvlvgpsg Gk +l++aLl   +      sv+
  gi|121636033|ref|YP_976256.1| 24 RNVVLVGPSGGGKTTLIEALLVAAKVLSRpGSVT 57
                                   88******************98777555445555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.23       2      90 ..      26     122 ..      25     152 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                    EEEESSTTSSHHHHHHCHCT-CC..C-E...EETTTTEEEEEEECGGSGGCT...TBTTTTCEEEEEEEE-SGGCTTTT- CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkf..sek...ekstigvdfltkevtkikgve...ndkkvkkvklniWDtaGqerfrslh 73 
                                    vvlvG sg GKt+l++ ++      s+    ++ t+ +df + e+ + ++v     + + + +k+n+ Dt G  +f    
  gi|121636033|ref|YP_976256.1|  26 VVLVGPSGGGKTTLIEALLVAAKvlSRPgsvTEGTTVCDFDEAEIRQQRSVGlavASLAYDGIKVNLVDTPGYADFVGEL 105
                                    89**************9876433123331113344445555555544443321112334455777888888877777766 PP

                                    HHHHCTSCEEEEEEEGH CS
                            Roc  74 plylreaalailvydsr 90 
                                       lr+a++a++v+ ++
  gi|121636033|ref|YP_976256.1| 106 WAGLRAADCALFVIAAN 122
                                    66677777777776644 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00063       0.4       1      23 [.      26      48 ..      26      89 .. 0.76
   2 ?   -2.3   0.0       8.9   5.7e+03      55      70 ..     613     629 ..     582     639 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00063
                                   EEEESSTTSSHHHHHHHHHHHHT CS
                            AAA  1 vllyGppGtGKTllakavakelg 23
                                   v+l+Gp G GKT+l++a+   ++
  gi|121636033|ref|YP_976256.1| 26 VVLVGPSGGGKTTLIEALLVAAK 48
                                   689**************987764 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.9
                                    HTS.TSEEEEEETGGGH CS
                            AAA  55 eka.kpsilfiDEidal 70 
                                    e a ++++++++ id++
  gi|121636033|ref|YP_976256.1| 613 EAAaATKVILLEPIDEI 629
                                    23344577777777665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0024       1.6       2      21 ..      24      43 ..      23      51 .. 0.90
   2 ?    0.6   0.0      0.68   4.4e+02      39     104 ..      91     155 ..      84     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                      PduV-EutP  2 kkilliGkvgsGKttLtqal 21
                                   ++++l+G++g GKttL +al
  gi|121636033|ref|YP_976256.1| 24 RNVVLVGPSGGGKTTLIEAL 43
                                   689*************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.68
                      PduV-EutP  39 eviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasv.fnkeviGiitkidlaed 104
                                    +++DtPG      +l   l+++ +   via    ++e+++ + ++ ++v + + v  +itk+d a+ 
  gi|121636033|ref|YP_976256.1|  91 NLVDTPGYADFVGELWAGLRAADCALFVIAANEGVDEPTKSLWQECSQVgMPRAV--VITKLDHARA 155
                                    6799999555566788899988888889999999999887777766655255655..7999999843 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0008      0.51       2      25 ..      25      48 ..      24      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0008
                                   CEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                    v+l G++G GKTtL++ l +a++
  gi|121636033|ref|YP_976256.1| 25 NVVLVGPSGGGKTTLIEALLVAAK 48
                                   699**************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4431.70
//
Query:       gi|121636034|ref|YP_976257.1|  [L=144]
Description: hypothetical protein BCG_0155c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-18   66.0   0.1    4.3e-18   65.3   0.1    1.4  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.069   13.1   0.0          7    6.7   0.0    2.2  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.1   4.8e-22   4.3e-18       9      88 .]      10     106 ..       4     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 4.8e-22
                                    HHHSSEEEEEEEETTSEEEEEEEEEEEETTT.......TEEEEEEETTS......HHHHHHHHH-EEEEEEEETT....G CS
                 Putative_PNPOx   9 laeskavvlATvdedGrPnvspvllkagdgr.......dgivfatnads......rklrnleenprvallfldde....l 71 
                                    +a+s++++lAT ++dG+P+++pv ++ g +r       d+i++a++a++      r+l+nle+npr+++l+++++    +
  gi|121636034|ref|YP_976257.1|  10 FAQSPVARLATSTPDGTPHLVPVVFALGARRpaeatgaDVIYTAVDAKRkttqrlRRLANLEHNPRASVLVDSYAddwtQ 89 
                                    4567**********************99999*****9999999999999999999************************* PP

                                    SEEEEEEEEEEEESCHH CS
                 Putative_PNPOx  72 grgvrieGtaelvsdge 88 
                                     ++vr +G a+++ dge
  gi|121636034|ref|YP_976257.1|  90 LWWVRADGVAAIHRDGE 106
                                    **************997 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0041        36      15      45 ..      45      75 ..      38      80 .. 0.84
   2 ?    6.7   0.0   0.00078         7       6      40 ..      97     134 ..      94     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0041
                                   ------EE-B--S---SS--EEEEEEE--TT CS
                   Ribosomal_L2 15 gGhkkkyrlidfkrnkekvkgkVveieyDpg 45
                                   +G++  y ++d kr+ ++   +++++e++p 
  gi|121636034|ref|YP_976257.1| 45 TGADVIYTAVDAKRKTTQRLRRLANLEHNPR 75
                                   567888********88888899*******96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00078
                                    --BSSTT--------EE-B--S-.--SS..--EEEEEE CS
                   Ribosomal_L2   6 gritvrhrggGhkkkyrlidfkr.nkek..vkgkVvei 40 
                                    g +++++ g  +++ yrl+  k+ ++++  ++g V+ i
  gi|121636034|ref|YP_976257.1|  97 GVAAIHRDGEVMRAAYRLLRAKYaQYQSvpLNGPVIAI 134
                                    8899*****************99665556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1077.41
//
Query:       gi|121636035|ref|YP_976258.1|  [L=122]
Description: hypothetical protein BCG_0156 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   10.8   0.0       0.16   10.6   0.0    1.0  1  DUF5005   Domain of unknown function (DUF5005)


Domain annotation for each model (and alignments):
>> DUF5005  Domain of unknown function (DUF5005)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     9e-06      0.16     258     333 ..      12      88 ..       3     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-06
                        DUF5005 258 ghiylyvtennydvl..varttthdltseweyyvrdlsgnfswqksypteeeskrsrilennyvcsmpwvfkkgdlyy 333
                                    g + l vte n+d    v rtt   lt + ey v+    +    +    +  + + ri+ +   c +p +   g lyy
  gi|121636035|ref|YP_976258.1|  12 GWVGLNVTETNRDQCyrVERTTVDALTHP-EYRVHTRGVQRVRVTRNARKHRVSKHRIVAAMRHCGVPVIQEDGSLYY 88 
                                    66778899999986433889999888877.9*99998888888999999999*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 778.11
//
Query:       gi|121636036|ref|YP_976259.1|  [L=122]
Description: hypothetical protein BCG_0157 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00064   19.6   0.3     0.0021   17.9   0.1    2.0  2  RHH_1          Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.26   11.5   0.0    1.5  1  Ribosomal_S18  Ribosomal protein S18


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.39   3.5e+03      11      18 ..      38      45 ..      37      48 .. 0.77
   2 !   17.9   0.1   2.3e-07    0.0021       2      37 ..      76     111 ..      75     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.39
                                   HHHHHHHH CS
                          RHH_1 11 lerLdela 18
                                   +er++++a
  gi|121636036|ref|YP_976259.1| 38 DERVEQMA 45
                                   68999998 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.3e-07
                                    EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1   2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37 
                                    v++ +++ + ++L elar r++S+S l+R  l e++
  gi|121636036|ref|YP_976259.1|  76 VQVVVSKATHAKLKELARSRKMSVSKLLRPVLDEFV 111
                                    66778888999******************8888876 PP

>> Ribosomal_S18  Ribosomal protein S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.26      12      27 ..     106     122 .]     104     122 .] 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                  Ribosomal_S18  12 lLsqFi.terGkIlprr 27 
                                    +L +F+ +e+G+Ilprr
  gi|121636036|ref|YP_976259.1| 106 VLDEFVqRETGRILPRR 122
                                    7999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 896.76
//
Query:       gi|121636037|ref|YP_976260.1|  [L=538]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-37  127.7  25.0    1.6e-37  127.7  25.0    1.7  2  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7  25.0   9.1e-42   1.6e-37       1      92 [.       1      92 [.       1      93 [. 0.99
   2 ?   -2.5   0.0      0.38   6.7e+03      47      60 ..     517     530 ..     514     531 .. 0.87

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 9.1e-42
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+vaPe++ aaa+dlagigsa+saanaaaaapttavlaa+aDeVSaaiAalfs haq+yqalsaqaaafh+qfvq+la+
  gi|121636037|ref|YP_976260.1|  1 MSFVSVAPEIVVAAATDLAGIGSAISAANAAAAAPTTAVLAAGADEVSAAIAALFSGHAQAYQALSAQAAAFHQQFVQTLAG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +ag+YaaaEa
  gi|121636037|ref|YP_976260.1| 83 GAGAYAAAEA 92
                                   *********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHHH CS
                             PE  47 VSaaiAalfsahaq 60 
                                    VS  + alf+a +q
  gi|121636037|ref|YP_976260.1| 517 VSGLVTALFGAPGQ 530
                                    9999*****99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 3588.75
//
Query:       gi|121636038|ref|YP_976261.1|  [L=355]
Description: serine protease pepA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-22   80.5  10.9    2.3e-22   80.5  10.9    2.2  2  Trypsin_2      Trypsin-like peptidase domain
      2e-13   50.4   0.2    4.3e-13   49.4   0.2    1.6  1  PDZ_2          PDZ domain
    7.8e-09   35.7   3.5    1.5e-08   34.7   3.5    1.4  1  Trypsin        Trypsin
      3e-08   33.4   0.2    8.4e-08   31.9   0.2    1.8  1  PDZ_6          PDZ domain
    1.7e-06   28.3   1.6    3.5e-06   27.3   0.3    2.2  2  PDZ            PDZ domain
    0.00018   21.4   0.1    0.00043   20.2   0.1    1.6  1  Tricorn_PDZ    Tricorn protease PDZ domain
  ------ inclusion threshold ------
      0.016   13.9   2.8        1.3    7.5   0.1    2.1  2  Peptidase_S46  Peptidase S46


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       0.4     1e+03      63      95 ..      38      71 ..      15      77 .. 0.74
   2 !   80.5  10.9   9.2e-26   2.3e-22       1     150 []      79     222 ..      79     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.4
                      Trypsin_2 63 ssderaglpplplgpse.alkggepvyvvGyplg 95
                                   s+d+ a++p+lpl+ps+  +++g +v+ +   lg
  gi|121636038|ref|YP_976261.1| 38 SQDRFADFPALPLDPSAmVAQVGPQVVNINTKLG 71
                                   5677899********9976777777777655555 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 9.2e-26
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsea 80 
                                    G+G++++++g++lTn+Hv+++a++ ++        +   +g+++ + vv++d   D+A+l++  + + glp + +g+   
  gi|121636038|ref|YP_976261.1|  79 GTGIVIDPNGVVLTNNHVIAGATDINA--------FSVGSGQTYGVDVVGYDRTQDVAVLQL--RGAGGLPSAAIGG--G 146
                                    9**************************........8999*************666*******..*************..6 PP

                      Trypsin_2  81 lkggepvyvvGyplggeksgsvssGivsgvve......sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                    +++gepv+++G+ +g+++ + +  G+v ++ +      s + a+++ ++++q daa++pG SGGp+++  G+vvG+
  gi|121636038|ref|YP_976261.1| 147 VAVGEPVVAMGNSGGQGGTPRAVPGRVVALGQtvqasdSLTGAEETLNGLIQFDAAIQPGDSGGPVVNGLGQVVGM 222
                                    78899*******655555558888888888888777778888888888888************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.2   1.7e-16   4.3e-13       2      71 ..     269     337 ..     268     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.7e-16
                                    ...XX------..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEE CS
                          PDZ_2   2 ylGvsvsdeedtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlR 71 
                                    +lG  v+d+++ +g+ v+ V  + Paa  g+ +gDvi++vdg +++s + +  +l+++ pGd +++t + 
  gi|121636038|ref|YP_976261.1| 269 FLGLGVVDNNG-NGARVQRVVGSAPAASLGISTGDVITAVDGAPINSATAMADALNGHHPGDVISVTWQT 337
                                    79********8.******************************************************9764 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   3.5   5.9e-12   1.5e-08      27     200 ..      79     228 ..      59     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.9e-12
                                    EEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBH CS
                        Trypsin  27 CgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvr 105
                                     +G++i++n  vlT++H++ +a+d++       ++  +g  q++ v+ v    +y+  +   D+a+l+l+     g    
  gi|121636038|ref|YP_976261.1|  79 GTGIVIDPNgVVLTNNHVIAGATDINA------FSVGSG--QTYGVDVV----GYDRTQ---DVAVLQLRGA--GGLPSA 141
                                    58*******9999*******9555544......777777..67777773....588887...*********9..333333 PP

                                    CCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHH.....TTTTSTTTEEEEESTTSSSBCTTTT CS
                        Trypsin 106 piclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksa.....ykgkvtenmlcagakeggkdacqGD 180
                                     i         +vg    v+++g+   +g   t + v  +vv   +  +a       +++ +  ++ +a     ++ +GD
  gi|121636038|ref|YP_976261.1| 142 AIGGGV-----AVG--EPVVAMGNSGGQG--GTPRAVPGRVVALGQTVQAsdsltGAEETLNGLIQFDA-----AIQPGD 207
                                    333333.....555..6677778877777..45555555555555333322345333337788999999.....****** PP

                                    TTSEEEETTTEEEEEEEEE.S CS
                        Trypsin 181 SGGPlvcsdgelvGivswg.k 200
                                    SGGP+v++ g++vG++++  +
  gi|121636038|ref|YP_976261.1| 208 SGGPVVNGLGQVVGMNTAAsD 228
                                    ****************98752 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.2   3.3e-11   8.4e-08       1      56 []     283     337 ..     283     337 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.3e-11
                          PDZ_6   1 vVtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlvvrr 56 
                                    +V+ V+   PA+  G+  GD+i++v+G p+   s +  a++l   ++g  +++++++
  gi|121636038|ref|YP_976261.1| 283 RVQRVVGSAPAASLGISTGDVITAVDGAPI--NSATAMADALNgHHPGDVISVTWQT 337
                                    69999999**********************..***********999*********96 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.6   6.6e+03      36      53 ..     137     156 ..     110     160 .. 0.59
   2 !   27.3   0.3   1.3e-09   3.5e-06       9      65 ..     267     319 ..     260     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                                    T.SHHHHHT.SSTTEEEEEE CS
                            PDZ  36 g.gaaeadg.lkvGDkIlsv 53 
                                    g ++a+ +g + vG  ++++
  gi|121636038|ref|YP_976261.1| 137 GlPSAAIGGgVAVGEPVVAM 156
                                    45555555556666666555 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.3e-09
                                    TSESSEEEEEETTSSSSSSEEEEEECTT.SHHHHHTSSTTEEEEEETTEETTTSHHHH CS
                            PDZ   9 rgglGfslkggsdqrgdkgifvsevlpg.gaaeadglkvGDkIlsvNgvdvenvshee 65 
                                    + +lG+ ++ ++ +    g+ v++v+   +aa  + ++ GD+I++v+g ++++ + ++
  gi|121636038|ref|YP_976261.1| 267 TAFLGLGVVDNNGN----GARVQRVVGSaPAASLG-ISTGDVITAVDGAPINSATAMA 319
                                    6799*****99996....**********6666666.****************998765 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.7e-07   0.00043      32      85 ..     292     344 ..     280     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                                    GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE-STT-EEE CS
                    Tricorn_PDZ  32 PLaepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvkrkdgkarr 85 
                                    P a  G+   +Gd+i+avdg p+++ + +a +L g+  g+ +++t ++k+g++r+
  gi|121636038|ref|YP_976261.1| 292 PAASLGIS--TGDVITAVDGAPINSATAMADALNGHHpGDVISVTWQTKSGGTRT 344
                                    66777887..9***********************986368889999999998886 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00052       1.3      46      70 ..      76     100 ..      62     107 .. 0.85
   2 ?    6.7   0.4   0.00093       2.4     630     651 ..     202     223 ..     163     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00052
                                    TTTEE-EE-STT-EEEE-HHHHHHH CS
                  Peptidase_S46  46 lggCtasfVSpeGLvlTNHHCayga 70 
                                     g  t+ ++ p+G vlTN H++ ga
  gi|121636038|ref|YP_976261.1|  76 VGAGTGIVIDPNGVVLTNNHVIAGA 100
                                    4779****************99876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00093
                                    ---TT-TT-EEE-TTS-EEEEE CS
                  Peptidase_S46 630 DitGGNSGSPvlngkgelvGla 651
                                     i  G SG Pv+ng g++vG++
  gi|121636038|ref|YP_976261.1| 202 AIQPGDSGGPVVNGLGQVVGMN 223
                                    5677****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2682.68
//
Query:       gi|121636039|ref|YP_976262.1|  [L=601]
Description: trehalose synthase treS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-76  258.4   0.0    5.5e-76  256.3   0.0    1.8  1  Alpha-amylase   Alpha amylase, catalytic domain
    1.5e-22   79.5   0.0    2.9e-22   78.6   0.0    1.5  1  Malt_amylase_C  Maltogenic Amylase, C-terminal domain
    4.3e-06   27.0   0.0    2.8e-05   24.3   0.0    2.3  2  DUF3459         Domain of unknown function (DUF3459)
  ------ inclusion threshold ------
       0.03   13.4   0.0      0.042   12.9   0.0    1.1  1  hDGE_amylase    Glycogen debranching enzyme, glucanotransfera


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.3   0.0   1.2e-79   5.5e-76       1     333 [.      66     422 ..      66     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 1.2e-79
                                    --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TT CS
                  Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsde 80 
                                    GDL+G+i++LdYl+ LG++ iwl P+++sp  d gYdi+d++k+ pefGt +d+ +L+++ah +gi++i+DlV+NHts++
  gi|121636039|ref|YP_976262.1|  66 GDLRGLIDRLDYLQWLGIDCIWLPPFYDSPLRDGGYDIRDFYKVLPEFGTVDDFVALVDAAHRRGIRIITDLVMNHTSES 145
                                    9******************************************************************************* PP

                                    SCCCHCCHHSTTSGGGCCC-E......ESS-STTC-.TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCCCCCCC CS
                  Alpha-amylase  81 hewfkeslkkkgepkrdyyiwkegkeekeppnnwks.lfdgsaweydekaqeyylhlflkklpdLnteneevrkelkdvv 159
                                    h wf+es++ ++ p++dyy+w +  e + +++   +  +++s+w++d  + ++y h f++++pdLn++n++v++++ dv+
  gi|121636039|ref|YP_976262.1| 146 HPWFQESRRDPDGPYGDYYVWSDTSE-RYTDARIIFvDTEESNWSFDPVRRQFYWHRFFSHQPDLNYDNPAVQEAMIDVI 224
                                    **********************9954.44444444447889*************************************** PP

                                    CCCCTTT-SEEEETTCCCTTTCCCC.HCCHCCHHHHHHHHHHHTC.CGTT-EEEEE-TT-SCC..CHCCCC-CGG-SICE CS
                  Alpha-amylase 160 kfwlekgidGfRlDvvkhvskveal.esngeflheftqalnetva.srkevmtvgEvssdase..dlrvyttearlelem 235
                                    +fwl  gidGfRlD+v+++ ++e++  +n +  h f + + ++v+ +   +++++E ++   +  +  ++ +++  e +m
  gi|121636039|ref|YP_976262.1| 225 RFWLGLGIDGFRLDAVPYLFEREGTnCENLPETHAFLKRVRKVVDdEFPGRVLLAEANQWPGDvvEYFGDPNTGGDECHM 304
                                    *********************998867999**************977888999999877555400455667777777777 PP

                                    CCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTTTT............ CS
                  Alpha-amylase 236 vldfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsaea............ 303
                                     ++fp +     +    +    s   ++e++++    +++   +  +fl nHD   +  ++ +++  +            
  gi|121636039|ref|YP_976262.1| 305 AFHFPLMPRI--FM---AVRRESRFPISEIIAQT-PPIPD-MAQWGIFLRNHDELTLEMVTDEERD-Ymyaeyakdprmk 376
                                    7777654322..22...22222233333433332.23333.3333455555555544444444442.2244555555555 PP

                                    ................HHHHHHHHHCCCTSSSEEEEETTCCCT--- CS
                  Alpha-amylase 304 ................ekklklaaillltlrGvpviYyGeEigmtg 333
                                                     ++++l+++lll+l+G pv YyG+Eigm +
  gi|121636039|ref|YP_976262.1| 377 anvgirrrlaplldndRNQIELFTALLLSLPGSPVLYYGDEIGMGD 422
                                    55555555569***9999**************************77 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   6.5e-26   2.9e-22       1      75 []     501     581 ..     501     581 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 6.5e-26
                                    -EEEE---S-TTEEEEEEEETT...EEEEEEEE..SS-EEEEE--GGGTT-EEEETTTTEE-----SS.EEEEE-TT-EE CS
                 Malt_amylase_C   1 GsfefleadnrkvlaYlReyed...etilvvaN..rsaqaveldlselagrvpvelfggeefpaigel.ytltLppygfy 74 
                                    G f+ l  +n++vlaY+R+  +   +t+l+v+N  r++q+ eldl+++ +++pvel g+ efp ig+  y+ltLp +gfy
  gi|121636039|ref|YP_976262.1| 501 GAFQELGGSNPSVLAYVRQVAGddgDTVLCVNNlsRFPQPIELDLQQWTNYTPVELTGHVEFPRIGQVpYLLTLPGHGFY 580
                                    8999***************988888******************************************************* PP

                                    E CS
                 Malt_amylase_C  75 w 75 
                                    w
  gi|121636039|ref|YP_976262.1| 581 W 581
                                    * PP

>> DUF3459  Domain of unknown function (DUF3459)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.6   2.7e+03      60      78 ..     269     287 ..     253     297 .. 0.78
   2 !   24.3   0.0   6.3e-09   2.8e-05       1      64 [.     484     547 ..     484     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                                    SS---SEEEEECT--S... CS
                        DUF3459  60 pegaagkllfsseaaragg 78 
                                    +++ +g++l++  +++ g+
  gi|121636039|ref|YP_976262.1| 269 DDEFPGRVLLAEANQWPGD 287
                                    56789*********99765 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 6.3e-09
                                    HHHHHHHHHHHHCCCTT--CGGEEEEEEECTCEEEEEEE..ETTEEEEEEEE-SSCGCCS-SS--- CS
                        DUF3459   1 lyrdLLaLRreePaLadarrgglevavlgdgallvrwrl..gdgrllrllaNLgdepvtlppegaa 64 
                                    ++r++La+Rr++Pa+a  ++++l +    +  l+ ++++  +dg++++++ NL++ p++++ + ++
  gi|121636039|ref|YP_976262.1| 484 FTRTMLAVRRRHPAFAVGAFQELGG--SNPSVLAYVRQVagDDGDTVLCVNNLSRFPQPIELDLQQ 547
                                    68**********************8..899999999999978888999*******77777633433 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.4e-06     0.042      35     113 ..      82     152 ..      66     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-06
                                    T--EEEES--EEE-TT--TTSEEEEEEE-TTT-.....SSC.HHHHHHHHHHHHHH--EEEEEE--SEEETT-CCCCC- CS
                   hDGE_amylase  35 gYnmiHftPlqelGesnSpYSiadqleldkelfeekdkeekeedveklvkklekeygllsltDvVlnHtannskwleeh 113
                                    g ++i + P+      +  Y i+d  ++ +e+        +++d+ +lv+ ++   g+  +tD+V+nHt++  +w +e 
  gi|121636039|ref|YP_976262.1|  82 GIDCIWLPPFYDSPLRDGGYDIRDFYKVLPEF-------GTVDDFVALVDAAH-RRGIRIITDLVMNHTSESHPWFQES 152
                                    55666666666666666677777777777776.......35677777777665.569******************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4053.04
//
Query:       gi|121636040|ref|YP_976263.1|  [L=455]
Description: hypothetical protein BCG_0161 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-15   56.3   1.1    1.2e-14   55.0   1.1    1.7  1  Mak_N_cap  Maltokinase N-terminal cap domain
    5.6e-05   23.2   0.1    0.00013   22.0   0.1    1.6  1  APH        Phosphotransferase enzyme family
     0.0084   15.5   0.0      0.016   14.6   0.0    1.4  1  APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance k


Domain annotation for each model (and alignments):
>> Mak_N_cap  Maltokinase N-terminal cap domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   1.1   2.1e-18   1.2e-14       1      87 []      16      96 ..      16      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.1e-18
                                   CCTTSTT-STTTT-EEEEEEEEEEEC.......TEEEEEEEEEETT...EEEEEEEEECSS--CCGHC.CEEEEE.EETTCC CS
                      Mak_N_cap  1 WLprqrWfagkgrpvtglrlvsatelddpagevglehllvrveeag...dvYqvpLgyreappeglep.aligtaehgplgg 78
                                   WLprqrW+ag++r+++ +++  ++ l     + +l+++lv+v++++   ++Yqv++g+  +p+ ++   a ig a     ++
  gi|121636040|ref|YP_976263.1| 16 WLPRQRWYAGRNRELATVKPGVVVAL-----RHNLDLVLVDVTYTDgatERYQVLVGWDFEPASEYGTkAAIGVA-----DD 87
                                   **************************.....789**********97789****************9888******.....88 PP

                                   EEEEEGGGS CS
                      Mak_N_cap 79 rtvyDAlhD 87
                                   rt +DAl+D
  gi|121636040|ref|YP_976263.1| 88 RTGFDALYD 96
                                   99*****99 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.1e-08   0.00013      96     211 ..     252     367 ..     237     403 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-08
                                    HHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SG CS
                            APH  96 ealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselldlleeleeqvlaalaallpgelptvllHgDlhp 175
                                    ++lge+ a +h++ +++l+ a  + + ++    + s+t   + +el++ +  +e+   ++laa++      + +HgDlh+
  gi|121636040|ref|YP_976263.1| 252 YRLGEAVASVHATLADSLGTAQATFP-VDRMLARLSST-VAVVPELREYAPTIEQ-QFQKLAAEAI---TVQRVHGDLHL 325
                                    46777777777776666777777744.44444444444.4566677774666666.5777887777...6********** PP

                                    GGEEEC..TTEEEEE---.........TT-EEEECCHHHHCCHHH CS
                            APH 176 gNllvdpddgrvtGviDf.........edaglgpplyDlavllrs 211
                                    g +l +p+ +    +iDf         e+  +  pl D+a +lrs
  gi|121636040|ref|YP_976263.1| 326 GQVLRTPESWL---LIDFegepgqpldERRAPDSPLRDVAGVLRS 367
                                    ******88555...8***777777777777777777777777755 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-06     0.016     150     188 ..     307     344 ..     264     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                      APH_6_hur 150 aeLleepselrpLHgdlhhenvLagerrgWlaidPkglv 188
                                    ++L +e+  ++  Hgdlh  +vL ++ + Wl id +g  
  gi|121636040|ref|YP_976263.1| 307 QKLAAEAITVQRVHGDLHLGQVLRTP-ESWLLIDFEGEP 344
                                    567788889999**************.9******77654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3013.78
//
Query:       gi|121636041|ref|YP_976264.1|  [L=259]
Description: hypothetical protein BCG_0162 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-26   93.2  22.5    2.2e-26   93.0  22.5    1.0  1  DUF1275    Protein of unknown function (DUF1275)
      0.008   16.5   0.2      0.017   15.4   0.2    1.5  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.024   14.8   1.6      0.051   13.8   1.0    1.8  2  DUF3397    Protein of unknown function (DUF3397)


Domain annotation for each model (and alignments):
>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0  22.5   3.7e-30   2.2e-26       2     190 ..      13     212 ..      12     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 3.7e-30
                        DUF1275   2 llllafvaGllDavaflaaggvfvsaqTGNtvllglal.aegnakaalaalvsllaFvlGaalagllarrg..grrrrlv 78 
                                     ++la++aG+l a+af ++ g+fv+++TGN  + +l+l  + ++ ++ a+l+ +l+Fv+G+++a++++r++   + +  +
  gi|121636041|ref|YP_976264.1|  13 SWVLAALAGILGATAFTHSAGYFVTFMTGNSQRAVLGLfGDDAWMSVTASLL-ILFFVAGVVIASVCRRHFwaAHPHGPT 91 
                                    689**********************************945566688888888.**************9887766666666 PP

                        DUF1275  79 llleallllaaallvpagsvsp.....lalallafamGlqnalfsrlsga.eitttvlTgnltdlgidlarll.kkrkla 151
                                    +l++  l++aa++ +  g +++     +++++++f +G+ n++f +  g+ +++  ++Tg+l+++g+++ r+l  ++  +
  gi|121636041|ref|YP_976264.1|  92 VLTTFSLIFAAGVDIMLGGWHEsmldfVPILFVVFGIGALNTSFVK-DGEvSVPLSYVTGTLVKMGQGIERHLaGGK-VE 169
                                    6666777777775555444434799*******************99.6666**********************6433.22 PP

                        DUF1275 152 .rnrrlaiilafllGavvGallvks...aaalwlaaallllva 190
                                     +  ++++ ++f+lGa++G+++++     ++l++aa+++++++
  gi|121636041|ref|YP_976264.1| 170 dWLGYFLLHASFVLGAAAGGAISMVvtgPQMLAVAAVVCAATT 212
                                    4999************************99*******999876 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.8e-06     0.017      21      79 ..     194     251 ..     185     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-06
                      TetR_C_11  21 alaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadv 79 
                                     +++p++ a+ + + a+ +  + l++ +r  l+++ r +  ++l rA +rGel+ ++ +
  gi|121636041|ref|YP_976264.1| 194 VVTGPQMLAVAAVVCAATTGYTYLHADRRG-LVNQKRPQPGKRLFRALRRGELDSGTST 251
                                    678887888888888888889999999999.***********************98865 PP

>> DUF3397  Protein of unknown function (DUF3397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.0   8.6e-06     0.051       6      85 ..      62     143 ..      57     147 .. 0.82
   2 ?   -2.1   0.0      0.74   4.4e+03      47      73 ..     190     215 ..     167     229 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                        DUF3397   6 llpllvlllvyiivkkfslkkkkaklkalDvttpf.lilavhl.lseelfgksflpllllvllllaillliiqarkkgei 83 
                                     l++l++++ ++i+++ +++ + a+ + + v+t f li+a+ + ++   + +s+l ++ +++ + +i  l ++++k+ge+
  gi|121636041|ref|YP_976264.1|  62 SLLILFFVAGVVIASVCRRHFWAAHPHGPTVLTTFsLIFAAGVdIMLGGWHESMLDFVPILFVVFGIGALNTSFVKDGEV 141
                                    5778888888888899977779999999998776625555544489999******************************9 PP

                        DUF3397  84 sy 85 
                                    s+
  gi|121636041|ref|YP_976264.1| 142 SV 143
                                    87 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.74
                        DUF3397  47 llseelfgksflpllllvllllailll 73 
                                    ++s +++g ++l  +  v++ +++  +
  gi|121636041|ref|YP_976264.1| 190 AISMVVTGPQML-AVAAVVCAATTGYT 215
                                    445555555553.33344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1736.17
//
Query:       gi|121636042|ref|YP_976265.1|  [L=340]
Description: hypothetical protein BCG_0163c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-73  245.2   0.7    9.2e-73  245.0   0.7    1.0  1  Esterase  Putative esterase


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.7   5.1e-77   9.2e-73       1     251 []      61     322 ..      61     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 5.1e-77
                                    ETTTTEEEEEEEEE.CC.GGTTTEEEEEEE--T......THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSB CS
                       Esterase   1 SealgreikvqvyLPedyspgrkypvvylldGl......tgwdqnfrakelleslaregeiaeviivvvprggessfysd 74 
                                    S+++gr+ikvq++       g+++++vylldGl      +gwd+n++a+e +++++ +        v++p+gg+ssfy+d
  gi|121636042|ref|YP_976265.1|  61 SASMGRDIKVQFQ-------GGGPHAVYLLDGLraqddyNGWDINTPAFEEYYQSGLS--------VIMPVGGQSSFYTD 125
                                    89***********.......9*************************************........************** PP

                                    TTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC. CS
                       Esterase  75 wdlgarfyenategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps. 153
                                    w+++    ++ + +++++++etflt e++ +l+an+ ++p+g+a++G Sm+G +ALila+++p++F +++s+S+++nps 
  gi|121636042|ref|YP_976265.1| 126 WYQP----SQSNGQNYTYKWETFLTREMPAWLQANKGVSPTGNAAVGLSMSGGSALILAAYYPQQFPYAASLSGFLNPSe 201
                                    ****....************************************************************************ PP

                                    ...................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCC CS
                       Esterase 154 ...................namWgqeekeawqendpvllakelsaslkalriyldvGtseddlgeqlsveilevlarnre 214
                                                       n+mWg+++++aw++ndp++++++l+a+++++++y+ +Gt++d +g++ ++++le l+  ++
  gi|121636042|ref|YP_976265.1| 202 gwwptliglamndsggynaNSMWGPSSDPAWKRNDPMVQIPRLVANNTRIWVYCGNGTPSDLGGDNIPAKFLEGLTLRTN 281
                                    ******************************************************************************** PP

                                    HHHHCCCCCCTT-SCCCC....--SSHHHHHHHHHHCHHHH CS
                       Esterase 215 lkeqlaargvegedheyd....GghsweyWraqLiaaladl 251
                                    ++++ ++++ +g++++++    G+hsw yW++qL+a++ad+
  gi|121636042|ref|YP_976265.1| 282 QTFRDTYAADGGRNGVFNfppnGTHSWPYWNEQLVAMKADI 322
                                    *************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2407.76
//
Query:       gi|121636043|ref|YP_976266.1|  [L=151]
Description: hypothetical protein BCG_0164 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-33  115.5   0.1    1.3e-33  115.2   0.1    1.1  1  MaoC_dehydratas  MaoC like domain
    1.3e-07   31.9   0.1    1.7e-07   31.4   0.1    1.1  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.1   1.4e-37   1.3e-33       3     121 ..      11     131 ..       9     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 1.4e-37
                                    CCCTTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT...EGGGEE CS
                MaoC_dehydratas   3 qnaigekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn...vvarvg 79 
                                    ++a gekv +++++t+t+++++l+a ++gD+++iHvdpe A++++fg++IahG++tla++ +l +++++ +    ++++g
  gi|121636043|ref|YP_976266.1|  11 AAAAGEKVGQSDWVTITQEEVNLFADATGDHQWIHVDPERAAAGPFGTTIAHGFMTLALLPRLQHQMYTVKgvkLAINYG 90 
                                    56789****************************************************************9999999**** PP

                                    EEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                MaoC_dehydratas  80 eikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtkevte 121
                                     +kvrF++pV++g++++++   vg++d  +  +v++t+++t+
  gi|121636043|ref|YP_976266.1|  91 LNKVRFPAPVPVGSRVRATSSLVGVEDLGNG-TVQATVSTTV 131
                                    ************************9999876.6777776665 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   1.9e-11   1.7e-07       3     126 ..      14     135 ..      12     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.9e-11
                MaoC_dehydrat_N   3 iGaefepvk.aevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqe 81 
                                     G ++++ +  ++++e+v+ fa a+g+ + +++d+e a+a  +++ ia    + +l  + ++ + ++++    +  g ++
  gi|121636043|ref|YP_976266.1|  14 AGEKVGQSDwVTITQEEVNLFADATGDHQWIHVDPERAAAGPFGTTIAHGFMTLALLPRLQHQMYTVKGVKLAINYGLNK 93 
                                    566775544489**************************9999999999877777777655456777766666677888** PP

                MaoC_dehydrat_N  82 feyhepiraGDelttesriadvydkkgvGalefivvettvtnqrG 126
                                    +++ +p+ +G +++ +s++  v+d    G + ++ + +t+++ +G
  gi|121636043|ref|YP_976266.1|  94 VRFPAPVPVGSRVRATSSLVGVED---LGNGTVQATVSTTVEVEG 135
                                    ************************...488888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1096.49
//
Query:       gi|121636044|ref|YP_976267.1|  [L=447]
Description: acyl-CoA dehydrogenase fadE1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-29  103.4   7.5    1.9e-29  102.8   7.5    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.4e-21   74.9   0.0    7.8e-21   74.1   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.1e-18   65.0   0.0    4.3e-17   62.8   0.0    2.1  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.3e-10   40.9   3.6    7.7e-10   39.2   0.8    2.3  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    0.00048   19.9   0.0     0.0012   18.6   0.0    1.7  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   7.5   5.3e-33   1.9e-29       5     149 ..     262     409 ..     258     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 5.3e-33
                                    HHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-------- CS
                  Acyl-CoA_dh_1   5 rvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd 84 
                                     +a+++l  +R+ +a++ ++larra++ + e+a +r++  ++l+d q  +ek+a+ ++++e+ rllv+r+a+++d++++ 
  gi|121636044|ref|YP_976267.1| 262 MIAQTRLGGGRIHHAMRTIALARRAFDMMCERALSRQTRHGRLADLQMTQEKIADSWIQIEQFRLLVLRTAWLIDKHHDY 341
                                    67999**********************************************************************99998 PP

                                    ...HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  85 ...raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       r +++++K+  ++++++v+++am+l+G+ G+++e+p+ +++ +a +l i++G++e +++++arr 
  gi|121636044|ref|YP_976267.1| 342 qkvRRDIAAVKVAMPQVLHDVVQRAMHLHGALGVSDEMPFVKMMLAAESLGIADGATELHKMTVARRT 409
                                    999***************************************************************96 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   2.2e-24   7.8e-21       1      96 [.     145     245 ..     145     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 2.2e-24
                                    EEE---SS-SS-GGG---EE.EEETT..EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE. CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvktta.aerdg.geyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsv. 75 
                                    ++ +TEpq+Gsd   + t a  + +g g++++nGeK+++tna++a++++v+a  +kp+  +++++slf+vp+d+pg+++ 
  gi|121636044|ref|YP_976267.1| 145 CYSMTEPQGGSDPGLFVTAAtRDAAGnGDWIINGEKWFSTNAKHASFFIVMAV-TKPEarTYEKMSLFIVPADTPGIEIv 223
                                    999***************88666666345************************.5555589*****************95 PP

                                    ----.-BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  76 rrie.eklGlrglptgelvfed 96 
                                    r +      +r +++g+++++d
  gi|121636044|ref|YP_976267.1| 224 RNVGvGAESTRHASHGYIRYHD 245
                                    5554333344555566666655 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.2e-20   4.3e-17       8     113 .]      27     141 ..      20     141 .. 0.82
   2 ?   -1.0   0.0      0.75   2.7e+03      59      80 ..     379     400 ..     344     412 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.2e-20
                                    HHHHHHHHHHHTHH...H.HHHHHHHTS....GHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHH CS
                  Acyl-CoA_dh_N   8 rdtvrefaeeelap...h.aaewdeege....fprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagla 79 
                                     d+v +f++eel+p   +  + +d++++    + r l+++++++Gl++ ++  e gG+g++ +  a++ e ++r  ++ +
  gi|121636044|ref|YP_976267.1|  27 LDWVEKFMAEELEPldlVaLDPYDKKNAdtmaILRPLQRQVKDQGLWAAHLRPELGGQGFGQVKLALLNEIIGRSRWAPS 106
                                    689***********55523333332222222255889*************************************777555 PP

                                    H.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  80 l.llgvhsslvapailrfGteeqkrryLpklasge 113
                                    + + ++ +s +a++++ fGt+eqk+ryL++l++ge
  gi|121636044|ref|YP_976267.1| 107 AfGCQAPDSGNAEILALFGTDEQKARYLRPLLDGE 141
                                    549999***************************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.75
                                    S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N  59 ldyleaaivaeelaradaglal 80 
                                    + ++ ++++ae l+ ad +++l
  gi|121636044|ref|YP_976267.1| 379 MPFVKMMLAAESLGIADGATEL 400
                                    5678888888888888888765 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.8   2.2e-13   7.7e-10       3     115 ..     275     380 ..     273     381 .. 0.91
   2 ?    2.0   0.1     0.064   2.3e+02       2      27 ..     385     410 ..     384     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.2e-13
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    +a+ ++ +Ar+a++ + e+a  r++   + +lad ++tq ++a++  ++++ r+l++r+a+     ++++  +  + r++
  gi|121636044|ref|YP_976267.1| 275 HAMRTIALARRAFDMMCERALSRQT--RHGRLADLQMTQEKIADSWIQIEQFRLLVLRTAWL----IDKHHDY-QKVRRD 347
                                    67777889*****************..9**********************************....5555554.566*** PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-H CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesp 115
                                    +++ +++  +   ++v++++ ++G+ ++ +e p
  gi|121636044|ref|YP_976267.1| 348 IAAVKVAMPQVLHDVVQRAMHLHGALGVSDEMP 380
                                    ****************************99876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.064
                                    HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervr 27 
                                    ++aa  lG+A +a + +   +++r+ 
  gi|121636044|ref|YP_976267.1| 385 MLAAESLGIADGATELHKMTVARRTL 410
                                    68999********9999998888876 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.3e-07    0.0012     165     236 ..     157     230 ..     125     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.3e-07
                                    TTSB-EEEEE-SSE...EEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE------ CS
                         HpaB_N 165 pdvyvrvveetddG...ivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfed 236
                                    p ++v    ++++G    +++G k + T+a  a  ++v+ + ++ ++   +    f+vp+d+pG++++       
  gi|121636044|ref|YP_976267.1| 157 PGLFVTAATRDAAGngdWIINGEKWFSTNAKHASFFIVMAVTKP-EARTYEKMSLFIVPADTPGIEIVRNVGVGA 230
                                    5555555555555533449**********************888.7777788889***********986655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3339.48
//
Query:       gi|121636045|ref|YP_976268.1|  [L=360]
Description: F420-dependent glucose-6-phosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-55  189.4   7.1    1.3e-55  189.1   7.1    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   7.1   7.3e-60   1.3e-55       8     245 ..      49     281 ..      27     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 7.3e-60
                 Bac_luciferase   8 ptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply.trh 82 
                                    +++q        ++ ++lv++a+aaE++Gf +vw+++h+++++ +    + ++ +la + + T+ i +gt+vt++  ++h
  gi|121636045|ref|YP_976268.1|  49 SHEQ--------FRTDRLVAHAQAAEQAGFRYVWASDHLQPWQDNeghsMFPWLTLALVGNSTSSILFGTGVTCPIyRYH 120
                                    3333........799****************************99****99*********************98887*** PP

                 Bac_luciferase  83 PavlAqqaatLdhlsgGRfglglgtggpaveerrfGv..dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllp 160
                                    Pa++Aq++a+L  l +GR+ lglgtg++ +e+++     +++er++rl E++ ++r+lw+ge+++f G++f+++++ l  
  gi|121636045|ref|YP_976268.1| 121 PATVAQAFASLAILNPGRVFLGLGTGERLNEQAATDTfgNYRERHDRLIEAIVLIRQLWSGERISFTGHYFRTDELKLYD 200
                                    *******************************88774466**********************************8888888 PP

                 Bac_luciferase 161 rpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeArae 240
                                     p+ + +P++vaa++p+++ la+r++dg++ +  +  +a +l++ ++aga++agrdp ++   + l+ +v+d+ ++Ara 
  gi|121636045|ref|YP_976268.1| 201 TPAMP-PPIFVAASGPQSATLAGRYGDGWIAQARDINDA-KLLAAFAAGAQAAGRDPTTLGKRAELFAVVGDDKAAARAA 278
                                    88555.89***********************99777765.68889999*************************9999986 PP

                 Bac_luciferase 241 arali 245
                                      +l+
  gi|121636045|ref|YP_976268.1| 279 --DLW 281
                                    ..455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2543.34
//
Query:       gi|121636046|ref|YP_976269.1|  [L=160]
Description: acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00033   20.9   0.0    0.00039   20.6   0.0    1.4  1  Acetyltransf_1  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.25   11.8   0.0    1.6  1  Acetyltransf_7  Acetyltransferase (GNAT) domain
       0.14   12.2   0.0        1.9    8.5   0.0    2.2  2  FR47            FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   6.6e-08   0.00039      49      94 ..     115     158 ..      26     160 .] 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.6e-08
                                    EEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                 Acetyltransf_1  49 sllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                    ++  + +++++++y+  +  +p+ rg+G G+ L++  ++r+  e +
  gi|121636046|ref|YP_976269.1| 115 MM--RVHPEEPHWYLAAIGSDPTVRGQGFGQVLMRSRLDRCDAEHC 158
                                    33..333679***************************999988766 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.2e-05      0.25      30      48 ..     130     148 ..      96     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                                    EEE-GGGTTSSHHHHHHHH CS
                 Acetyltransf_7  30 laVdpeyrgkGiGraLlea 48 
                                    +  dp  rg+G G+ L++ 
  gi|121636046|ref|YP_976269.1| 130 IGSDPTVRGQGFGQVLMRS 148
                                    66799************95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.051   3.1e+02      43      69 ..      13      40 ..      11      59 .. 0.86
   2 ?    8.5   0.0   0.00031       1.9      22      45 ..     125     148 ..     100     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.051
                                   HHHHHHHHHH.S-S-EEEEEETT-HHHH CS
                           FR47 43 vkalakeiae.rgktvllvvvasNtpsi 69
                                   v++l++ +a+   +++++ +  sN++++
  gi|121636046|ref|YP_976269.1| 13 VRELSRTMARaFYDDPFMSWLLSNDNAR 40
                                   6788888888677899999999999997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00031
                                    SSEEEEEE-GGG-SSSHHHHHHHH CS
                           FR47  22 gelgalqvlpehrrrGlgsrlvka 45 
                                     +l a+  +p++r++G+g++l ++
  gi|121636046|ref|YP_976269.1| 125 WYLAAIGSDPTVRGQGFGQVLMRS 148
                                    57999999************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1269.17
//
Query:       gi|121636047|ref|YP_976270.1|  [L=201]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-15   55.1   0.0    1.4e-14   53.6   0.0    1.8  2  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.064   14.0   0.0       0.16   12.8   0.0    1.7  1  TetR_C_15  Tetracyclin repressor-like, C-terminal domain
      0.078   13.2   0.0       0.13   12.5   0.0    1.5  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
       0.11   11.4   0.0       0.15   11.0   0.0    1.1  1  GRAS       GRAS domain family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0     3e-18   1.4e-14       1      47 []      20      66 ..      20      66 .. 0.95
   2 ?   -2.5   0.0       1.1   4.7e+03      10      18 ..     128     136 ..     121     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3e-18
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +ld+ ++ ++erGy+attv++I+++A +sk+++Y +F+sKe+++++l
  gi|121636047|ref|YP_976270.1| 20 LLDGLVASIGERGYRATTVSDIVRHARTSKRTFYDRFTSKEQCFLEL 66
                                   68888999************************************996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                    HHHHTTT-- CS
                         TetR_N  10 aerGydatt 18 
                                    ++rG++++t
  gi|121636047|ref|YP_976270.1| 128 QRRGMEQLT 136
                                    689999887 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05      0.16       1      55 [.      87     139 ..      87     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                      TetR_C_15   1 pLeealdalvdallaahrenpalrrvlleeapslgelelvealeqriaealaalL 55 
                                    ++ + +++ v+a++   +++pa+   + +e+pslg++  +  +++r  e+l++lL
  gi|121636047|ref|YP_976270.1|  87 DWHDQIRQAVEAYVTHIESRPAVTLSWIREFPSLGAA--AYPVQRRGMEQLTSLL 139
                                    78999****************************9999..4444455555555555 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05      0.13       2      55 ..      86     139 ..      85     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                    SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHH CS
                      TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerll 55 
                                    +++++++r++v+a+v +i ++++ ++  +re+ +L ++++   r+  +++++ll
  gi|121636047|ref|YP_976270.1|  86 ADWHDQIRQAVEAYVTHIESRPAVTLSWIREFPSLGAAAYPVQRRGMEQLTSLL 139
                                    5789*****************************999988875544444444444 PP

>> GRAS  GRAS domain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05      0.15     246     350 ..      45     149 ..      31     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                                    S-S.SSHHHHHHHHHHHHHHHHHHHHHHHS-TT-HHHHHHHHHTHHHHHHHHHCTTCCCTSS---.HCHHHHHHHCTTEE CS
                           GRAS 246 anhnsesFlerflealeyysalfdsleaklpreseerikveeellgreivnvvacegaerrerhetlekWrerleeaGFk 325
                                    a +++ +F +rf+++ +++  l+ + +++l++  ++ +   +     +i+++v +  ++ + r     +W + + + G  
  gi|121636047|ref|YP_976270.1|  45 ARTSKRTFYDRFTSKEQCFLELLLADNETLGNSIRAAVDPNAD-WHDQIRQAVEAYVTHIESRPAVTLSWIREFPSLGAA 123
                                    6678899***************999999987666666666666.789************99******************* PP

                                    EE--TCHHHHHHHHHHTTSS.-TTEE CS
                           GRAS 326 pvplsekaakqaklllrkvk.sdgyk 350
                                    ++p++ + ++q  +ll + + s g++
  gi|121636047|ref|YP_976270.1| 124 AYPVQRRGMEQLTSLLIELSaSPGFR 149
                                    *************9999988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1546.32
//
Query:       gi|121636048|ref|YP_976271.1|  [L=441]
Description: cytochrome p450 138 cyp138 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-62  209.5   0.0    2.4e-61  207.9   0.0    1.6  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   1.3e-65   2.4e-61      28     442 ..      41     416 ..      18     435 .. 0.85

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1.3e-65
                                    HHHHHH-SEEEEEETT.EEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHHH CS
                           p450  28 klqkkygpifrlklgs.kpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltptl 106
                                    ++ ++yg+ f+  + +  +vvv+ +p+++++v+  + ee  +   ++ l+    +f   +v+  +g+++++ Rr+l p +
  gi|121636048|ref|YP_976271.1|  41 RFVRRYGKAFTANILMyGRVVVVADPQLARQVFTSSPEELGN--IQPNLSR---MFGSGSVFALDGDDHRRRRRLLAPPF 115
                                    56689999999887662689999*************988888..6788887...9************************* PP

                                    TSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHTTTSSHHHHHHHHHHHHHHHHH CS
                           p450 107 tsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdlledeklselvkaveelsslls 185
                                    +++ ++ ++e ++eee+ +  +++ +   ++  + + + + +++l++i + +Fga  +   d    el +++   ++l  
  gi|121636048|ref|YP_976271.1| 116 HGK-SMkNYETIIEEETLRETANWPQG--QA--FATLPSMMHITLNAILRAIFGAGGS-ELD----ELRRLIPPWVTLG- 184
                                    ***.777********987766666555..55..559*******************744.444....5666666665444. PP

                                    CHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHH CS
                           p450 186 kssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdfldalllakkekkgesklsdeelaa 265
                                    ++   l ++++  +y   + + +l e +++++ ++dklie  r++ + a  +r d l+++l ++  ++++s +s++++  
  gi|121636048|ref|YP_976271.1| 185 SRLAALPKPKR--DYGRLSPWGRLAEWRRQYDTVIDKLIEAERADPNFA--DRTDVLALMLRST--YDDGSIMSRKDIGD 258
                                    66656666666..6777788888888***********************..999*999999996..88889********* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEE CS
                           p450 266 tvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikEtLRlhpvvplllpRe 345
                                    ++l+ll+aG++Tt++tl wa+  L ++P+v ++l eE+d+  ++             + +a+i E++R ++v+++   R+
  gi|121636048|ref|YP_976271.1| 259 ELLTLLAAGHETTAATLGWAFERLSRHPDVLAALVEEVDNGGHE-------------LRQAAILEVQRARTVIDFAARRV 325
                                    *************************************9985444.............679**************777777 PP

                                    SSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHH CS
                           p450 346 vtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGerlArmelklf 425
                                     +  +++++ +ip G+ +i+n+  +h dp+vfp+P++Fdp+R+   k     ++fa++PFG G R C+G  +A me+ ++
  gi|121636048|ref|YP_976271.1| 326 NPPVYQLGEWVIPRGYSIIINIAQIHGDPDVFPQPDRFDPQRYIGSKP----SPFAWIPFGGGTRRCVGAAFANMEMDVV 401
                                    777888999************************************975....7*************************** PP

                                    HHHHHHHEEEEESTSTS CS
                           p450 426 latlLqnFevelqpetd 442
                                    l t+L++F++e+    +
  gi|121636048|ref|YP_976271.1| 402 LRTVLRHFTLETTT--A 416
                                    ***********743..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3054.55
//
Query:       gi|121636049|ref|YP_976272.1|  [L=182]
Description: methionine sulfoxide reductase A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-56  190.5   0.0    2.2e-56  190.3   0.0    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   1.2e-60   2.2e-56       1     152 [.       6     153 ..       6     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 1.2e-60
                                    EEEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT-S CS
                           PMSR   1 eavlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDptql 80 
                                    +a+lagGCFWg+++l+++++Gv+st+vGY gG+ +n+tY++       haEave+++dp+++++++lle+ff+ihDpt++
  gi|121636049|ref|YP_976272.1|   6 KAILAGGCFWGLQDLIRNQPGVVSTRVGYSGGNIPNATYRNH----GTHAEAVEIIFDPTVTDYRTLLEFFFQIHDPTTK 81 
                                    589************************************987....579******************************* PP

                                    SEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS-- CS
                           PMSR  81 nrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpegyc 152
                                    +rqgnD+Gt+Yrsai+y +e+qk++a +++++++++  + +k+vte++p+++f++ae +Hq+Yl++ p+gy+
  gi|121636049|ref|YP_976272.1|  82 DRQGNDRGTSYRSAIFYFDEQQKRIALDTIADVEASGLWPGKVVTEVSPAGDFWEAEPEHQDYLQRYPNGYT 153
                                    **********************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1243.46
//
Query:       gi|121636050|ref|YP_976273.1|  [L=167]
Description: hypothetical protein BCG_0174 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-08   33.7   0.2    7.9e-08   32.9   0.2    1.5  1  SnoaL_2   SnoaL-like domain
    0.00017   21.7   0.0    0.00021   21.4   0.0    1.2  1  SnoaL_4   SnoaL-like domain
     0.0018   18.5   0.1     0.0025   18.1   0.1    1.4  1  SnoaL_3   SnoaL-like domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.018   14.8   0.0    1.3  1  SnoaL     SnoaL-like polyketide cyclase


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.2   1.8e-11   7.9e-08       6     100 ..      24     125 ..      18     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.8e-11
                                    HHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEE.EEEE..EEETTEEEEEEEEEEE..EET CS
                        SnoaL_2   6 aalnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfe.ihdv..vadgdrvavewtvtgt..ipa 79 
                                    +a +++d+d ++++++pdv++  + +g  rGr+++ra++++   +fp+ ++  +  +  v d+ +  +  +++     p 
  gi|121636050|ref|YP_976273.1|  24 RAAATRDWDCWVQHYTPDVEYIEHaAGIMRGRQRVRAWIQETMTTFPGSHMVaFPSLwsVIDESTGRIICELDNPmlDPG 103
                                    5899*****************9888999****************999998874444444333333333222222233666 PP

                                    TSSEEEEEEEEEEEEE.TTEEE CS
                        SnoaL_2  80 tgrgvtvrgvdvfrvr.dGkiv 100
                                    +g+ ++ + +++++ + +G+++
  gi|121636050|ref|YP_976273.1| 104 DGSVISATNISIITYAgNGQWC 125
                                    6666666777777664246665 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.6e-08   0.00021      14      90 ..      20      95 ..       7     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.6e-08
                                   HHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEE.ETTEEEEEEEE CS
                        SnoaL_4 14 arygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnpliel.dgdtAtgrayl 90
                                    ++++++ t+dw+ +++ +t+d+++   +   g ++gr+++ra+++e ++ f+ ++ + +  l ++ d+ t + ++ l
  gi|121636050|ref|YP_976273.1| 20 KTVARAAATRDWDCWVQHYTPDVEYIEHA--AGIMRGRQRVRAWIQETMTTFPGSHMVAFPSLWSViDESTGRIICEL 95
                                   56789999**************8864443..6*****************99999888888888888787777777766 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   5.5e-07    0.0025       9      63 ..      23      76 ..      16     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                        SnoaL_3  9 yeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfel 63
                                    +aaa++d+d  ++++++d+ +i+ +a   ++gr+ vr+++++ +  ++g ++++
  gi|121636050|ref|YP_976273.1| 23 ARAAATRDWDCWVQHYTPDVEYIEHAA-GIMRGRQRVRAWIQETMTTFPGSHMVA 76
                                   679*********************888.7889*************9998888765 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.1e-06     0.018       8      59 ..      23      74 ..      16     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                                   HHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEE CS
                          SnoaL  8 eevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkv 59
                                   + ++ ++d+d + +++++dv++   +++  rG++ +ra ++e++++fP  ++
  gi|121636050|ref|YP_976273.1| 23 ARAAATRDWDCWVQHYTPDVEYIEHAAGIMRGRQRVRAWIQETMTTFPGSHM 74
                                   556689*****************9999*********************8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1204.95
//
Query:       gi|121636051|ref|YP_976274.1|  [L=340]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-25   87.4   0.0    2.1e-24   86.3   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.8e-18   64.5   0.0    9.9e-18   64.1   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.1e-17   62.4   0.2    8.1e-17   61.7   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
    4.2e-15   56.0   0.0      2e-14   53.8   0.0    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.8e-11   43.1   0.0    3.1e-07   29.8   0.0    2.2  2  NAD_binding_4    Male sterility protein
    9.9e-07   28.5   0.0    1.9e-06   27.6   0.0    1.4  1  NmrA             NmrA-like family
     0.0022   18.0   0.0        2.2    8.2   0.0    2.6  2  KR               KR domain
     0.0031   16.7   0.0      0.012   14.8   0.0    1.9  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.22   10.3   0.0        0.3    9.9   0.0    1.2  1  HcyBio           Homocysteine biosynthesis enzyme, sulfur-inc


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   1.1e-27   2.1e-24       2     240 ..       6     234 ..       5     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1.1e-27
                                    EEETTTSHHHHHHHHHHHHCT....SEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                      Epimerase   2 lVtGatGfiGsalvkallekg....yevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAavg 75 
                                    lV+Ga+Gf+Gs+++++l +       ev ++ r   a nt +++dl  +  ++d+ d + ++++++  ++d v+ +  v 
  gi|121636051|ref|YP_976274.1|   6 LVIGANGFLGSHVTRQLVADCapqkGEVRAMVRP--AANTRSIDDLplTRFHGDVFDTATVAEAMA--GCDDVYYC--VV 79 
                                    8****************98776755678888888..888888888888999***************..********..** PP

                                    -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSS.SBSTCSTTS----SSHHHHHHHHHHHHHH CS
                      Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeq.pkeettltgplkpnspYaaaKlageklve 154
                                    + +a+  dp+ ++++n++g +n+l++a +a ++r++f sS ++ G+      +ee+     ++  +pY ++ +a+e lv 
  gi|121636051|ref|YP_976274.1|  80 DTRAWLRDPSPLFRTNVAGLRNVLDVATDASLRRFVFTSSYATVGRRRGHvATEEDR--VDTRKVTPYVRSRVAAEDLVL 157
                                    *********************************************999942333333..255999*************** PP

                                    HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-ST CS
                      Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdk 234
                                    +ya++ gl+a+++ +++ yG ++     +    a+i+ +  g+ ++t+ g    + + + v+D+a+a++l++e+   g++
  gi|121636051|ref|YP_976274.1| 158 QYAHDAGLPAVAMCVSTTYGGGDW---GRTPHGAFIAGAVFGRLPFTMRG---IRLEAVGVDDAARALILAAER---GRN 228
                                    **********************22...33334457777777776888888...777899**************9...777 PP

                                    TEEEEE CS
                      Epimerase 235 geiyni 240
                                    ge y i
  gi|121636051|ref|YP_976274.1| 229 GERYLI 234
                                    888876 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0     5e-21   9.9e-18       1     185 [.       6     179 ..       6     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5e-21
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee..lkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                    +v+G+ GFlG+++ ++Lv      + evr++ +r   ++  ++  +  +   +gDv d++++ ea+ g d v +  ++vd
  gi|121636051|ref|YP_976274.1|   6 LVIGANGFLGSHVTRQLVADCApqKGEVRAM-VRPAANT-RSIDDLPLT-RFHGDVFDTATVAEAMAGCDDVYY--CVVD 80 
                                    69****************7443258899988.4444444.355556555.578*****************9987..5999 PP

                      3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklv 157
                                     +        + + nv G rnvl+ +++a++r++v+tSs+  vg   +  ++  + Ee ++++  + +y +s+  aE+lv
  gi|121636051|ref|YP_976274.1|  81 TRAwLRDPSPLFRTNVAGLRNVLDVATDASLRRFVFTSSYATVGR--RRGHV--ATEEDRVDTRKVTPYVRSRVAAEDLV 156
                                    999445556799*********************************..33344..58999********************* PP

                      3Beta_HSD 158 lkaNgrtlknggrlyTcaLRpagiyGeg 185
                                    l+           l  +a+  ++ yG g
  gi|121636051|ref|YP_976274.1| 157 LQYAH---DA--GLPAVAMCVSTTYGGG 179
                                    *8655...22..3666666666666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.2     4e-20   8.1e-17       1     131 [.       9     156 ..       9     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4e-20
                                    TTTSHHHHHHHHHHHHC-...T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg...ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                    GA+G  G++++++l+a+    + ev+a+vR ++ + ++  +  l+ ++gdv d++++aea++g+d V+ ++  ++     
  gi|121636051|ref|YP_976274.1|   9 GANGFLGSHVTRQLVADCapqKGEVRAMVRPAANTRSID-DLPLTRFHGDVFDTATVAEAMAGCDDVYYCVVDTRAwlrd 87 
                                    9***************9888889************9885.789************************9999777777765 PP

                                    .......HHHH..HHHHHHHHHHCT--EEEEEEETTT.TS...GCGCHHHHHHHHCCHHHHHHHHHHHHHH CS
                 NAD_binding_10  74 .......deeg..aknivdaakeagvkRfvlvsaigv.gd...evpgefgewnkellkaylaakraaeell 131
                                           +  +   +n++d+a  a  +Rfv+ s+  + g+   +v++e ++++++ + +y++   aae+l+
  gi|121636051|ref|YP_976274.1|  88 psplfrtN--VagLRNVLDVATDASLRRFVFTSSYATvGRrrgHVATEEDRVDTRKVTPYVRSRVAAEDLV 156
                                    55555333..167*******************99655154333466677888999999***9999999986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   9.8e-18     2e-14       1     327 [.       6     318 ..       6     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 9.8e-18
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEE..EESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivr..rsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                    L+ G +Gf Gs+++++L++      g vr     + nt++i+ l           l+ ++gD+ D++ + +++a +  d 
  gi|121636051|ref|YP_976274.1|   6 LVIGANGFLGSHVTRQLVADCAPQKGEVRamVRPAANTRSIDDLP----------LTRFHGDVFDTATVAEAMAGC--DD 73 
                                    899***************986665555542122344677777774..........34578**************98..9* PP

                                    EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----..SHHHHH CS
                  GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPr..sPYaaa 156
                                    vy   +    +  + +P   +++nv G  ++L+++ ++ l+   rf+++S+    G+ + +  tE+ +++ r   PY  +
  gi|121636051|ref|YP_976274.1|  74 VYY--CVVDTRAWLRDPSPLFRTNVAGLRNVLDVATDASLR---RFVFTSSYATVGRRRGHVATEEDRVDTRkvTPYVRS 148
                                    **7..778888999***********************9986...9**************9999999887765228***** PP

                                    HHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHH CS
                  GDP_Man_Dehyd 157 KlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlm 236
                                    +++a+ +v +y +  gl+av   ++ +++     + +      ++a +  g+ + +  G          v+D ++a+ l+
  gi|121636051|ref|YP_976274.1| 149 RVAAEDLVLQYAHDAGLPAVAMCVSTTYGGGDWGRTPHG---AFIAGAVFGRLPFTMRGIR---LEAVGVDDAARALILA 222
                                    *****************************9976665544...4677778999888866633...245789********** PP

                                    HHCSS---EEE-TT-EEECHHCHHCCHHCCCH.HHHHH...................TTG.GCCCEECGG--SS--SB-- CS
                  GDP_Man_Dehyd 237 lqqdkpedyviatgethsvrefvelaflelgk.tiewegkgeeevg.......rakesgk.vvvevdpkyfrpgevdlll 307
                                     +++++ + ++ + + + ++e+v++a+ e+g     w+ +     +       ra+ +gk ++ ++  +++  +e+    
  gi|121636051|ref|YP_976274.1| 223 AERGRNGERYLISERMMPLQEVVRIAADEAGVpPPRWSISVPVLYAlgalgslRARLTGKdTELSLASVRMMRSEA---D 299
                                    *****999999999*************9999744456544332222333333322223330233333333333333...3 PP

                                    B-THHHHHHH----SS-HHH CS
                  GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfee 327
                                     d  ka +eLgW+p+  +ee
  gi|121636051|ref|YP_976274.1| 300 VDHGKAVRELGWQPR-PVEE 318
                                    6999999*****998.4555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   5.9e-05      0.12       3      36 ..       9      44 ..       7      68 .. 0.79
   2 !   29.8   0.0   1.6e-10   3.1e-07     101     216 ..      85     185 ..      59     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                                   -TTSHHHHHHHHHHHHHS-.T..EEEEEE-SSSHHH CS
                  NAD_binding_4  3 GaTGFLGkvLlekLLrttpev..kiyllvRaksges 36
                                   Ga GFLG+++ ++L+ +++    ++ ++vR+  ++ 
  gi|121636051|ref|YP_976274.1|  9 GANGFLGSHVTRQLVADCAPQkgEVRAMVRPAANTR 44
                                   9**************76654449*******877654 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.6e-10
                                    STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHH CS
                  NAD_binding_4 101 depykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeekldederaklkglpntYeqs 179
                                     ++ + l+r+Nv G r+vl+ a+  +    +++ S+ a+v g r+g+v            +++ed  ++ k   + Y++s
  gi|121636051|ref|YP_976274.1|  85 LRDPSPLFRTNVAGLRNVLDVATDASLR-RFVFTSSyATV-GRRRGHV------------ATEEDRVDTRK--VTPYVRS 148
                                    55667799***************88666.*******5555.5555576............23333333333..457**** PP

                                    HHHHHHHHHHHHHHH---EEEEEE-EEE--SSST--- CS
                  NAD_binding_4 180 KalaEklvrearrrsglpvvivRpsiitgesktGwin 216
                                     ++aE+lv ++++  glp+v + +s+ +g    G + 
  gi|121636051|ref|YP_976274.1| 149 RVAAEDLVLQYAHDAGLPAVAMCVSTTYGGGDWGRTP 185
                                    ******************9988777776643333333 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   9.6e-10   1.9e-06       2     105 ..       6     122 ..       6     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.6e-10
                                    EESSTTSHHHHHHHHHHHH....HT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEE.E---GG. CS
                           NmrA   2 lviGaTGrqGksvvrallk....aghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvf.svtgfy. 75 
                                    lviGa G +G++v+r l++    ++ +vra+vR     + +s+ + + +  +gd+ d + ++ea+ g d v+ +v+ +  
  gi|121636051|ref|YP_976274.1|   6 LVIGANGFLGSHVTRQLVAdcapQKGEVRAMVRPA--ANTRSIDDLPLTRFHGDVFDTATVAEAMAGCDDVYyCVVDTRa 83 
                                    7****************999999999*******76..56789*************************9877615544437 PP

                                    .........S-HHHHHHHHHHHHHHHS-SEEEEEE---G CS
                           NmrA  76 .........skeiedgkklvdAakeaGvkhfiySslgdd 105
                                             +++++   ++ d+a  a  ++f++ s  + 
  gi|121636051|ref|YP_976274.1|  84 wlrdpsplfRTNVAGLRNVLDVATDASLRRFVFTSSYAT 122
                                    7********9***********************776554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0025         5       4      25 ..       6      27 ..       3      49 .. 0.91
   2 !    8.2   0.0    0.0011       2.2     109     145 ..      92     128 ..      85     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                                   EEETTTSHHHHHHHHHHHHHHS CS
                             KR  4 litGGlGgLGlelarwlaekga 25
                                   l++G+ G LG +++r+l++++a
  gi|121636051|ref|YP_976274.1|  6 LVIGANGFLGSHVTRQLVADCA 27
                                   9*****************9997 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                    HTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT CS
                             KR 109 lapKvkGawnLhelledesldffvlfSSiagllgsag 145
                                    ++  v+G++n+  + +d sl  fv++SS a++   +g
  gi|121636051|ref|YP_976274.1|  92 FRTNVAGLRNVLDVATDASLRRFVFTSSYATVGRRRG 128
                                    67789*************************9876666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     6e-06     0.012       2     128 ..       6     119 ..       6     124 .. 0.74
   2 ?   -2.7   0.0       1.2   2.4e+03     206     229 ..     212     235 ..     205     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-06
                                    EEETTTSHHHHHHHHHHHHH.B-S..EEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkk.kpk..kiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                    lv Ga G +Gs+++rq+++   p+  +++ + r   +  +i++              ++ + gdv d++++++a+   ++
  gi|121636051|ref|YP_976274.1|   6 LVIGANGFLGSHVTRQLVADcAPQkgEVRAMVRPAANTRSIDDL------------PLTRFHGDVFDTATVAEAMA--GC 71 
                                    67888888888888888776544411344444444444444432............223446**************..** PP

                                    SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                    d v+ +    +     + p   ++tNv g +nv+++a++a  +++v+ S+
  gi|121636051|ref|YP_976274.1|  72 DDVYYCVVDTRA--WLRDPSPLFRTNVAGLRNVLDVATDASLRRFVFTSS 119
                                    ****99876665..45677888*************************997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHH--SS-EEEE- CS
                Polysacc_synt_2 206 ieeavqLvlqalalakggeifvld 229
                                    +++a++ ++ a++++++ge ++  
  gi|121636051|ref|YP_976274.1| 212 VDDAARALILAAERGRNGERYLIS 235
                                    678888888899999999987764 PP

>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00015       0.3     286     336 ..     101     155 ..      58     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                    xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio 286 pvvDvserrrerktlgevsYael....GkieiegkevktarlsslkrareiaeeL 336
                                    +v+Dv+++   r+ +++ sYa +    G++  e+++v t +++ + r+r +ae L
  gi|121636051|ref|YP_976274.1| 101 NVLDVATDASLRRFVFTSSYATVgrrrGHVATEEDRVDTRKVTPYVRSRVAAEDL 155
                                    68899999888899999999999****************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2332.46
//
Query:       gi|121636052|ref|YP_976275.1|  [L=126]
Description: hypothetical protein BCG_0176 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-30  103.6   0.7    4.6e-30  103.4   0.7    1.1  1  NTP_transf_9  Domain of unknown function (DUF427)
  ------ inclusion threshold ------
      0.097   13.1   0.0       0.12   12.8   0.0    1.2  1  RAMA          Restriction Enzyme Adenine Methylase Associated


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.7   5.1e-34   4.6e-30       1      92 [.      24     116 ..      24     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 5.1e-34
                                    EEEE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEE.TTEEEEEEEEEESS--T CS
                   NTP_transf_9   1 vrvklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslav.dgkevkdaaWsYpeptp 79 
                                    v+v++ng+vva+t +a+ ++e+++p + Y+p +dv  + l +++t+t+Cp+KGeasyys+++ +g+ v+d++W+Y++p+p
  gi|121636052|ref|YP_976275.1|  24 VQVRVNGEVVADTAAALCLQEASYPAVQYIPLADVVQDRLIRTETSTYCPFKGEASYYSVTTdAGDIVDDVMWTYENPYP 103
                                    79*********************************99***********************9845568************* PP

                                    T-GGGTT-BEE-T CS
                   NTP_transf_9  80 eaaeikgyvaFya 92 
                                    ++a+i+g+va y+
  gi|121636052|ref|YP_976275.1| 104 AVAAIAGHVACYP 116
                                    ***********98 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.12      24      79 ..      51     111 ..      16     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                           RAMA  24 r.vtlkdLleagllepGekllieykgr.thkAdlladGkIk....gqefgspsaaakalvGn 79 
                                    + + l+d++++ l++  +  +  +kg+  +  + ++ G I+    + ++++p+ a +a+ G 
  gi|121636052|ref|YP_976275.1|  51 QyIPLADVVQDRLIRTETSTYCPFKGEaSYYSVTTDAGDIVddvmW-TYENPYPAVAAIAGH 111
                                    2599*****************7777753566777999****75533.49****999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 911.15
//
Query:       gi|121636053|ref|YP_976276.1|  [L=136]
Description: hypothetical protein BCG_0177c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.6   0.0    1.4e-08   35.3   0.0    1.1  1  SnoaL_2   SnoaL-like domain
    0.00086   19.4   0.0     0.0011   19.1   0.0    1.1  1  LEH       Limonene-1,2-epoxide hydrolase catalytic domain
     0.0046   16.7   0.0     0.0094   15.7   0.0    1.5  1  SnoaL     SnoaL-like polyketide cyclase
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.046   13.8   0.0    1.4  1  WI12      Wound-induced protein WI12


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.1e-12   1.4e-08       7     100 ..      19     111 ..      14     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.1e-12
                                    HHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEE CS
                        SnoaL_2   7 alnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvt 85 
                                     ++ gdld+  al++ d++++   + +   ++ +r+++++   +++++++e+ + v +g++v+ve++++g + a+ ++++
  gi|121636053|ref|YP_976276.1|  19 LCEGGDLDEGFALLSNDFTYWSIvTRTELDKKTFRRAVERRK-QVFEVNIELIRCVNEGETVVVEGHCDG-VSADRTRYD 96 
                                    56789**************9988577788999*****99997.59************************9.********* PP

                                    EEEEEEEEEETTEEE CS
                        SnoaL_2  86 vrgvdvfrvrdGkiv 100
                                     ++v +f+ rdG i 
  gi|121636053|ref|YP_976276.1|  97 SPFVCIFETRDGMII 111
                                    ************996 PP

>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.3e-07    0.0011      18     121 ..      24     124 ..       8     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-07
                                    -HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT.TTT-EEEEEEEEEEEETTEEEEEEEEEEEE..TTEEEEEEEE CS
                            LEH  18 dydaavrrlatdlevyeneglstihGraeaiallerlsadilavevkilriaadgsaVltERlDrliladGplivqltvm 97 
                                    d+d   + l +d +++  +  +++  +   +a+ +r  +++ +v+++++r   +g+ V+ E     + ad   + + + +
  gi|121636053|ref|YP_976276.1|  24 DLDEGFALLSNDFTYWSIVTRTELDKKTFRRAVERR--KQVFEVNIELIRCVNEGETVVVEGHCDGVSADR-TRYDSPFV 100
                                    566666666666666666555444444433444333..6999*****************997655555587.67788888 PP

                                    EEEEEETTEEEEEEEE--HHHHHH CS
                            LEH  98 GvfeVedgrivlWRdYfDvndllk 121
                                     +fe  dg i+  R+Y D + l +
  gi|121636053|ref|YP_976276.1| 101 CIFETRDGMIISLREYSDTQSLAE 124
                                    8******************99875 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-06    0.0094       6     122 ..      15     122 ..      10     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-06
                                    HHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEB CS
                          SnoaL   6 fyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgef 85 
                                    f++ + + gdld+   l+++d+ + + +++    ++ fr++ve+  + f + ++e  ++v eg++v+++ ++        
  gi|121636053|ref|YP_976276.1|  15 FLQSLCEGGDLDEGFALLSNDFTYWSIVTRTELDKKTFRRAVERRKQVF-EVNIELIRCVNEGETVVVEGHC-------- 85 
                                    78888999*****************999999999**********99999.9*****************9886........ PP

                                    TTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHH CS
                          SnoaL  86 lGipptGkkvkfeeitllrvedGkIveewdviDllgl 122
                                     G+ +   + +   +++++ +dG I + +++ D ++l
  gi|121636053|ref|YP_976276.1|  86 DGVSADRTRYDSPFVCIFETRDGMIISLREYSDTQSL 122
                                    6777777788888888888888888888888887765 PP

>> WI12  Wound-induced protein WI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     1e-05     0.046      13      62 ..      62     120 ..      53     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                           WI12  13 sfefkprsvdaf..gstviaeGtdetrkly.......WvhaWtvkdGvitqvreyfnts 62 
                                     fe + + + ++  g+tv++eG  ++ +         +v ++   dG+i  +rey++t+
  gi|121636053|ref|YP_976276.1|  62 VFEVNIELIRCVneGETVVVEGHCDGVSADrtrydspFVCIFETRDGMIISLREYSDTQ 120
                                    5666666666666699*****9544332211111334899****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 978.83
//
Query:       gi|121636054|ref|YP_976277.1|  [L=308]
Description: hypothetical protein BCG_0178 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2481.39
//
Query:       gi|121636055|ref|YP_976278.1|  [L=492]
Description: hypothetical protein BCG_0179c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-81  274.5  30.2    1.4e-81  274.5  30.2    2.0  2  Voltage_CLC      Voltage gated chloride channel
  ------ inclusion threshold ------
        7.2    6.8  10.3        3.2    8.0   0.4    3.9  4  NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit 


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.3   0.3    0.0088        78     162     187 ..      46      71 ..      25      89 .. 0.79
   2 !  274.5  30.2   1.6e-85   1.4e-81       2     352 ..     113     461 ..     112     463 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0088
                                    GGHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Voltage_CLC 162 lelilfvllGilgGllgalfvrlllk 187
                                    ++++l + +G+++Gl +++f   l  
  gi|121636055|ref|YP_976278.1|  46 KWFLLGITIGVIAGLGAVVFYLALKY 71 
                                    57888899999999999999766554 PP

  == domain 2  score: 274.5 bits;  conditional E-value: 1.6e-85
                                    HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT. CS
                    Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllkl 81 
                                    g++l++l+v ++apea+g+G++e ++ ++g+ + ++ r +lvk++as+lt+gsG+s GreGp+ qi+A ++s+l r+l+l
  gi|121636055|ref|YP_976278.1| 113 GAVLSALIVAKLAPEATGHGTDEAIESVHGDPRAIRGRAVLVKMVASALTIGSGGSGGREGPTAQISAGFCSLLTRRLNL 192
                                    6899***************************************************************************9 PP

                                    --SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T---....- CS
                    Voltage_CLC  82 srndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafgeveslf.al 159
                                    s++d  r+ va G++AGi+A+F aPlgG+ ++  + ++++f++r+llp f+as +a+ vl ++lg  p fg +++ + + 
  gi|121636055|ref|YP_976278.1| 193 SNED-GRTAVALGIGAGIGAIFAAPLGGAALGASIpYRDDFDYRNLLPGFIASGTAYAVLGAFLGFDPLFGYIDAEYrFE 271
                                    9777.999***************************************************************966655456 PP

                                    -GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCHHHHHCTT- CS
                    Voltage_CLC 160 sllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyeliasllegs 239
                                    + + l++fv++G++++++g+l++r+++++  + r+l   +  ++l+pa++gllvgllgl++p+ +l++gy++++ ++++ 
  gi|121636055|ref|YP_976278.1| 272 KAWPLLWFVVIGLIAAAVGYLYARVFHASVAITRRL---PGGPVLKPAIGGLLVGLLGLPIPQ-ILSSGYGWAQLAADRG 347
                                    778899****************************99...888999******************.**********999665 PP

                                    S-.HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCTHHHHHCC CS
                    Voltage_CLC 240 tl.llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGmaaflagvt 318
                                    tl  ++l+++++l ++k+lat+l++g+g +gG+f P +viGA +G+++  + +l     ++++pg+f++v+m+a+++ v+
  gi|121636055|ref|YP_976278.1| 348 TLlSIPLWIVIVLPIAKILATSLSIGTGGSGGLFGPGIVIGAFVGAAIWRLGELTELPGVPHEPGIFVVVAMMACFGSVS 427
                                    55599*******************************************9998888667788899**************** PP

                                    S-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHH CS
                    Voltage_CLC 319 rapltaiviviEltgdlelllplmlavliAkava 352
                                    rapl+++++v E+tg++++++  ++av iA ++ 
  gi|121636055|ref|YP_976278.1| 428 RAPLAVMIMVAEMTGSFSVVPGAIIAVGIAALLL 461
                                    ******************************9875 PP

>> NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.2   1.8e+03      70      84 ..      50      64 ..      35      75 .. 0.64
   2 ?    2.6   0.1     0.016   1.5e+02      49      85 ..     174     213 ..     173     217 .. 0.70
   3 ?   -1.2   0.1      0.25   2.3e+03      76      94 ..     280     297 ..     246     308 .. 0.77
   4 ?    8.0   0.4   0.00035       3.2      46      72 ..     445     472 ..     413     476 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                NiFe_hyd_3_EhaA 70 dGlllaiiiGvlsal 84
                                    G+++++i+G+ + +
  gi|121636055|ref|YP_976278.1| 50 LGITIGVIAGLGAVV 64
                                   355566666654443 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.016
                NiFe_hyd_3_EhaA  49 PtavlalGllalvfk.lgveiydGll.laiiiGv.lsalf 85 
                                    Pta ++ G+++l++  l+++  dG + +a+ iG  ++a+f
  gi|121636055|ref|YP_976278.1| 174 PTAQISAGFCSLLTRrLNLSNEDGRTaVALGIGAgIGAIF 213
                                    9**********99877999977774314444443356666 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.25
                NiFe_hyd_3_EhaA  76 iiiGvlsalfskyllekvf 94 
                                    ++iG+++a  + yl+ +vf
  gi|121636055|ref|YP_976278.1| 280 VVIGLIAAA-VGYLYARVF 297
                                    678888775.456667766 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.00035
                NiFe_hyd_3_EhaA  46 vifPtavlalGllalvfk.lgveiydGl 72 
                                     + P a++a+G+ al+ +  +v+iy+  
  gi|121636055|ref|YP_976278.1| 445 SVVPGAIIAVGIAALLLSrTNVTIYETQ 472
                                    478************9887888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3328.45
//
Query:       gi|121636056|ref|YP_976279.1|  [L=280]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-16   58.2   0.1    8.5e-16   57.5   0.1    1.4  1  TetR_N      Bacterial regulatory proteins, tetR family
    4.9e-06   26.8   2.5    1.3e-05   25.4   2.5    1.8  1  TetR_C_11   Tetracyclin repressor-like, C-terminal domain
    3.2e-05   24.1   2.6    6.8e-05   23.1   2.4    1.7  1  TetR_C_6    BetI-type transcriptional repressor, C-terminal
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.066   12.8   0.0    1.4  1  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   1.9e-19   8.5e-16       1      47 []      93     139 ..      93     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.9e-19
                                    HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N   1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47 
                                    Il+aAr++f+erGyd++t++eIA rA ++++a+ +yF++K+ L++++
  gi|121636056|ref|YP_976279.1|  93 ILHAARQVFSERGYDGATFQEIAVRADLTRPAINHYFANKRVLYQEV 139
                                    9******************************************9996 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.5     3e-09   1.3e-05      19      89 ..     173     243 ..     155     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3e-09
                      TetR_C_11  19 aealas.pragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgp 89 
                                    +ea a+ p+ +a l+  + e+qr+pel +   +  ++  r+ l   +  A++rGel+ad+dv  ++++ll +
  gi|121636056|ref|YP_976279.1| 173 MEADAQyPASTAFLATTVLESQRHPELSRTEND-AVRATREFLVWAVNDAIERGELAADVDVSSLAETLLVV 243
                                    44444458999****************999999.*****************************999998765 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   2.4   1.5e-08   6.8e-05       4      86 ..     164     247 ..     161     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                    HHHHHHHCCSTHSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHHHHHHHHHH CS
                       TetR_C_6   4 rlraileallpldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaeaaAerlaAl 82 
                                    rl  +++ ++ +d++ +a +a     + e++r+pel +  +++ ++ r+ l+ ++ ++ e g+l+ad+d+   Ae+l  +
  gi|121636056|ref|YP_976279.1| 164 RLAVVVDFAMEADAQYPASTAFLATTVLESQRHPELSRTENDAVRATREFLVWAVNDAIErGELAADVDVSSLAETLLVV 243
                                    788899999********99999999999**************************************************99 PP

                                    HHHH CS
                       TetR_C_6  83 idGL 86 
                                    + G 
  gi|121636056|ref|YP_976279.1| 244 LCGV 247
                                    9885 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.066      10      35 ..      98     123 ..      95     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHTTT--HHHHHHHHTS-HH CS
                     Sigma70_r4  10 revlelrfgeglTleEIgerlgiSre 35 
                                    r+v++ r ++g T++EI+ r +++r 
  gi|121636056|ref|YP_976279.1|  98 RQVFSERGYDGATFQEIAVRADLTRP 123
                                    9*********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2155.40
//
Query:       gi|121636057|ref|YP_976280.1|  [L=317]
Description: hypothetical protein BCG_0181 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-61  208.2   0.5    1.7e-61  207.5   0.5    1.3  1  LCM              Leucine carboxyl methyltransferase
     0.0055   16.2   0.1     0.0085   15.6   0.1    1.3  1  Methyltransf_19  S-adenosyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.5   0.5   1.9e-65   1.7e-61       1     187 [.      31     213 ..      31     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 1.9e-65
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    algvaaara+e+ +  ++li+D++a+ lvs+ag ++  r ad +l++ + ++  ++ ++   +++avRt+ffd+++ aa+
  gi|121636057|ref|YP_976280.1|  31 ALGVAAARAVETAAT-NPLIRDEFAKVLVSSAGTAW-ARLADADLAWLDGDQLGRRVHRVACDYQAVRTHFFDEYFGAAV 108
                                    789**********98.****************9986.8888888888875677788899999****************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     +ag+rqvViL+AGlD+rayRl+w+ag++v+E+Dqp+vle+K+ +l+ +ga p+a+++ v+vDlr ddwp+aL aagfd 
  gi|121636057|ref|YP_976280.1| 109 -DAGVRQVVILAAGLDARAYRLNWPAGTVVYEIDQPSVLEYKAGILQSHGAVPTARRHAVAVDLR-DDWPAALIAAGFDG 186
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleai 187
                                    ++ptaw+aeG+l+YL+ +a+d+l++++
  gi|121636057|ref|YP_976280.1| 187 TQPTAWLAEGLLPYLPGDAADRLFDMV 213
                                    ************************987 PP

>> Methyltransf_19  S-adenosyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.5e-07    0.0085      67     202 ..     109     238 ..      78     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-07
                Methyltransf_19  67 eaGirqflDiGtGlPtednvHqvaqrvaPesRvvYvDnDPivlaharallest...peGatdyieaDlrdpeeilespea 143
                                    +aG+rq + + +Gl          +   P+  vvY  + P vl++   +l+s+   p  + + +++Dlrd         +
  gi|121636057|ref|YP_976280.1| 109 DAGVRQVVILAAGLDARA-----YRLNWPAGTVVYEIDQPSVLEYKAGILQSHgavPTARRHAVAVDLRDDWPAA---LI 180
                                    457777777777766543.....34457999********************984445667789999**9954433...36 PP

                Methyltransf_19 144 revlDldrPvAlllvailhfveDeedaaaivrelvdalpaGsllvlshltedlnpeeve 202
                                    ++ +D  +P A l   +l +++  + a ++ + +++  ++Gs +++  +t +++ ++++
  gi|121636057|ref|YP_976280.1| 181 AAGFDGTQPTAWLAEGLLPYLPG-DAADRLFDMVTALSAPGSQVAVEAFTMNTKGNTQR 238
                                    699******************97.788899999999999********999998766644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2299.83
//
Query:       gi|121636058|ref|YP_976281.1|  [L=310]
Description: hypothetical protein BCG_0182 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-62  210.1   0.5    3.6e-62  209.7   0.5    1.2  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.7   0.5     2e-66   3.6e-62       1     187 [.      18     204 ..      18     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.7 bits;  conditional E-value: 2e-66
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHH.CHCCCHCHHCHG.C.HCCCCT--HHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglell.erkadkelekek.e.eekkekkapelnrgiavRtrffddllk 77 
                                    a++vaaara+e+ r+ d+li+Dp+a+ lv +ag  ++ e++ d +l ++  + ++++++ +  l+ ++avRt ffd++++
  gi|121636058|ref|YP_976281.1|  18 AVMVAAARAVETDRP-DPLIRDPYARLLVTNAGAGAIwEAMLDPTLVAKAaAiDAETAAIVAYLRSYQAVRTNFFDTYFA 96 
                                    89*************.*****************999876666777666664468889999999999************** PP

                                    HHHHCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHT CS
                            LCM  78 aalsaagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaag 157
                                    +a+ aagirqvViL++GlD+rayRl+w+ag+ v+E+Dqp+vl++K +tl+e g +p+a +r vp+Dlr +dwp+aL++ag
  gi|121636058|ref|YP_976281.1|  97 SAV-AAGIRQVVILASGLDSRAYRLDWPAGTIVYEIDQPKVLSYKSTTLAENGVTPSAGRREVPADLR-QDWPAALRDAG 174
                                    ***.7***************************************************************.*********** PP

                                    T-TTSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 158 fdpekptawvaeGvlvYLtpeasdalleai 187
                                    fdp+++taw+aeG+l+YL++ea+d+l+ ++
  gi|121636058|ref|YP_976281.1| 175 FDPTARTAWLAEGLLMYLPAEAQDRLFTQV 204
                                    ***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2164.10
//
Query:       gi|121636059|ref|YP_976282.1|  [L=506]
Description: aldehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-95  319.3   0.0      4e-95  319.0   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.0   0.0   2.2e-99     4e-95      21     462 .]      38     477 ..      20     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 319.0 bits;  conditional E-value: 2.2e-99
                                    EEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH.HHHHHHHHHHH CS
                         Aldedh  21 akvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara.eveeaidvlry 99 
                                    a v++ +++dv + va+ +++f + ++ ++e R++ Lr++++l+ e+++ +a++++ +   +  ea   +++ +   ++y
  gi|121636059|ref|YP_976282.1|  38 APVSDEKQTDVAKTVARLRKTFASGRTRSVEWRKQQLRALQKLMDENEDAIAAALAEDLDRNPFEAYLaDIATTSAEAKY 117
                                    568889999**************************************************9998888888*********** PP

                                    HHHHHHH.HSEEE....EEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHH CS
                         Aldedh 100 yaelaek.legev....lpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalllae 174
                                    +a+ +++ ++ +     +p+    + +v +eP+G+v++I +WN+P+ l+++ ++ a+aaGN+vvlKP+e +++sa l++e
  gi|121636059|ref|YP_976282.1| 118 AAKRVRRwMRRRYllleVPQ-LPGRGWVEYEPYGTVLIIGAWNYPFYLTLGPAVGAIAAGNAVVLKPSEIAAASAHLMTE 196
                                    *******6666666633333.56889****************************************************** PP

                                    HHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHH CS
                         Aldedh 175 lfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDldkav 254
                                    l+ +  l+ +++ vv+g+g+ v+++l++ +++d v+ftG+te+grk+++ aa +l++vtlElGGk+p+iv +daD+d a+
  gi|121636059|ref|YP_976282.1| 197 LVYR-YLDTEAIAVVQGDGA-VSQELIA-QGFDRVMFTGGTEIGRKVYEGAAPHLTPVTLELGGKSPVIVAADADVDVAA 273
                                    ****.9***********997.6666665.49************************************************* PP

                                    HHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHH....T CS
                         Aldedh 255 eaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeake....e 330
                                    ++i++  ++naGQ+C+a+  +l    + de+v+k+++a++k++ g p  + + +   ++++q++++ +y++ ak     +
  gi|121636059|ref|YP_976282.1| 274 KRIAWIKLLNAGQTCVAPDYVLADATVRDELVSKITAALTKFRSGAP--QGMRI---VNQRQFDRLSGYLAAAKTdaaaD 348
                                    ***********************************************..45666...*************9877611115 PP

                                    TSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHH CS
                         Aldedh 331 gaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdlerae 410
                                    g  +++Gg    + ++++  ++Ptv+ + +pd +++ +EiFGP+l+v+++k++++ai+ +N+ +  L+a++ftk+ +  e
  gi|121636059|ref|YP_976282.1| 349 GGGVVVGG----DCDASNLRIQPTVVVDPDPDGPLMSNEIFGPILPVVTVKSLDDAIRFVNSRPKPLSAYLFTKSRAVRE 424
                                    66678888....56788999************************************************************ PP

                                    HHHHHS-SSEEEESSSST--TTT.SEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 411 rvaerleaGnvyiNdsttgaaea.lpfgGvkqSglGreggkegleeytevktv 462
                                    rv++++ aG +++N+ + +   a lpfgGv++Sg+G+ +g++g+ee+++ k+v
  gi|121636059|ref|YP_976282.1| 425 RVIREVPAGGMMVNHLAFQVSTAkLPFGGVGASGMGAYHGRWGFEEFSHRKSV 477
                                    ***************9666666679***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3065.48
//
Query:       gi|121636060|ref|YP_976283.1|  [L=286]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-37  129.5   1.6    1.8e-37  128.7   1.6    1.3  1  adh_short     short chain dehydrogenase
    1.3e-30  106.7   2.4    3.8e-30  105.2   2.4    1.8  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.4e-21   77.3   0.8      2e-21   76.7   0.8    1.2  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   1.6     3e-41   1.8e-37       2     190 ..       8     204 ..       7     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 3e-41
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH.........HHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseek.........leevakelkeegakalaiqvDvtdreevealvekav 72 
                                    v++vtGa++G+Gr++a +la eGa+vvv d   ++         + ev++e++++g +a+a    v++++ + +++++a 
  gi|121636060|ref|YP_976283.1|   8 VIVVTGAGGGLGREYALTLAGEGASVVVNDLGGARdgtgagsamADEVVAEIRDKGGRAVANYDSVATEDGAANIIKTAL 87 
                                    89**************************87654322222222227899999999999*********************** PP

                                    HHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short  73 kklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                    +++g ++ +v NAGi ++g+f+++s e+w++v++v l g +++ ra+ p++ +qs Gr+v  +S+ g+ +++g++ Y+A+
  gi|121636060|ref|YP_976283.1|  88 DEFGAVHGVVSNAGILRDGTFHKMSFENWDAVLKVHLYGGYHVLRAAWPHFREQSYGRVVVATSTSGLFGNFGQTNYGAA 167
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                    K +++gl+++la e a+++i  na+aP + +T m++++
  gi|121636060|ref|YP_976283.1| 168 KLGLVGLINTLALEGAKYNIHANALAP-IAATRMTQDI 204
                                    **************************9.4568888765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   2.4   6.4e-34   3.8e-30       1     192 [.      13     213 ..      13     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 6.4e-34
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGG.........H.HHHHHHHHHHTTSEEEE--.TTSHHHHHHHHHHHHHHHSS CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlnee.........a.kkrveelaeelgaevlecD.Vtdeeqvealveevvekfgk 69 
                                    Ga  g+Gr+ A +la eGa+vv+ dl+ +           ++ v+e+ +++g++v + D V+ e+  +++++++ ++fg 
  gi|121636060|ref|YP_976283.1|  13 GAGGGLGREYALTLAGEGASVVVNDLGGArdgtgagsaMaDEVVAEIRDKGGRAVANYDsVATEDGAANIIKTALDEFGA 92 
                                    7889*********************98651111111112346677777777788877777999999************** PP

                                    EEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHH CS
                   adh_short_C2  70 lDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaa 147
                                    ++++v nagi ++  g f+++s e++d +l+v ly+ +++++aa p+++e+  g++v  +s+++  +  +++ ygaaK +
  gi|121636060|ref|YP_976283.1|  93 VHGVVSNAGILRD--GTFHKMSFENWDAVLKVHLYGGYHVLRAAWPHFREQsyGRVVVATSTSGLFGNFGQTNYGAAKLG 170
                                    *************..*******************************999999**************************** PP

                                    HHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHH CS
                   adh_short_C2 148 lealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleel 192
                                    l++l+ +lA e ++++i  Na +p + +T+++++i   +e+le+l
  gi|121636060|ref|YP_976283.1| 171 LVGLINTLALEGAKYNIHANALAPIA-ATRMTQDIL-PPEVLEKL 213
                                    ***********************965.678888887.56666654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.8   3.3e-25     2e-21       3     161 ..       9     176 ..       8     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 3.3e-25
                                    EEEETTTSHHHHHHHHHHHHHHS-EEE..EE-SS.....--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlv..llsRsa...aadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                     ++tG+ GgLG+e a +la +ga+ +v  l + +    a ++ +++ +ae++++g +  +    v+ +d  +++++++ +
  gi|121636060|ref|YP_976283.1|   9 IVVTGAGGGLGREYALTLAGEGASVVVndLGGARDgtgAGSAMADEVVAEIRDKGGRAVANYDSVATEDGAANIIKTALD 88 
                                    58**********************9995444444346666777789********9999999999**************** PP

                                    HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHH.TTT...S--SEEEEEEEHHHHH--TT-HHHHHHH CS
                             KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhel.led...esldffvlfSSiagllgsagqanYaaaN 153
                                    e+++++Gv+  Ag+lrd+++ +m+ e++++vl+  + G  ++ ++  ++   +s   +v+ +S +gl+g++gq+nY aa 
  gi|121636060|ref|YP_976283.1|  89 EFGAVHGVVSNAGILRDGTFHKMSFENWDAVLKVHLYGGYHVLRAaWPHfreQSYGRVVVATSTSGLFGNFGQTNYGAAK 168
                                    ***********************************99887765542443555999***********************97 PP

                                    HHHHHHHH CS
                             KR 154 aflDalae 161
                                      l +l++
  gi|121636060|ref|YP_976283.1| 169 LGLVGLIN 176
                                    66655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1899.77
//
Query:       gi|121636061|ref|YP_976284.1|  [L=322]
Description: quinone oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-26   92.0   1.3    2.8e-26   92.0   1.3    1.9  2  ADH_zinc_N    Zinc-binding dehydrogenase
    2.9e-13   51.0   0.1    4.4e-12   47.2   0.0    2.6  2  ADH_zinc_N_2  Zinc-binding dehydrogenase
    3.1e-09   36.7   0.0    1.7e-08   34.3   0.0    2.1  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.014   14.7   1.9      0.022   14.0   1.9    1.3  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   4.5e+03      50      74 ..      20      43 ..      13      46 .. 0.74
   2 !   92.0   1.3   6.2e-30   2.8e-26       1     125 [.     150     274 ..     150     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                                   HHHHTTTSSEEEEEESSCSHHHHHH CS
                     ADH_zinc_N 50 ikeltggegvdvvfecvGsgatlea 74
                                   i e   g+g +vv+++ ++g ++++
  gi|121636061|ref|YP_976284.1| 20 IDEVS-GDGGKVVIDVRAAGVCFPD 43
                                   55555.7789999999888888876 PP

  == domain 2  score: 92.0 bits;  conditional E-value: 6.2e-30
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    gvG+aavq+Aka+ a +via+++ e  ++++++lGad+v+  +e  + ++++++t g+gvd+v++ +G g t+++al +l
  gi|121636061|ref|YP_976284.1| 150 GVGTAAVQIAKAMQAgKVIAMVHREGAIDYVASLGADVVLPLTE-GWAQQVRDHTYGQGVDIVVDPIG-GPTFDDALGVL 227
                                    9*****************************************78.***********************.*********** PP

                                    EEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkeal 125
                                    + +G+l ++G+  g  + +++++ll +++s++G+ +g + ++++   
  gi|121636061|ref|YP_976284.1| 228 AIDGKLLLIGFAAGAVPtLKVNRLLVRNISVVGVGWGEYLNAVPGSA 274
                                    ***********6666666******************99877776655 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.25   1.1e+03      85     103 ..     151     168 ..      99     181 .. 0.53
   2 !   47.2   0.0   9.8e-16   4.4e-12       1     133 []     183     320 ..     183     320 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.25
                                    .-HHHHHHHHHHHHHHH-- CS
                   ADH_zinc_N_2  85 aqadileelaalieeGklr 103
                                    +++    ++a+ +++Gk+ 
  gi|121636061|ref|YP_976284.1| 151 VGTA-AVQIAKAMQAGKVI 168
                                    2233.34455555555544 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 9.8e-16
                                    TT-SEEE..ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.....S-EEE-CHHHCTTT-E CS
                   ADH_zinc_N_2   1 lGAdevi..dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp....lsaallkpakkrkgrs 72 
                                    lGAd v+      +++++++t g+gvD+v+d +gg+++ +++l vl+  G+l+ ig +      + +  + + ++ +  +
  gi|121636061|ref|YP_976284.1| 183 LGADVVLplTEGwAQQVRDHTYGQGVDIVVDPIGGPTF-DDALGVLAIDGKLLLIGfA-AgavpTLKVNRLLVRNISVVG 260
                                    89**999775555777779999****************.*******777***999944.335553333334444455555 PP

                                    EEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                    v +  ++ + ++  a +++  ++ +    lrp++ +++pl+ea+ A++ l  g + GK+Vl
  gi|121636061|ref|YP_976284.1| 261 VGWGEYLNAVPG-SAALFAWGLNQLVFLGLRPPPPQRYPLSEAQAALQSLDDGGVLGKVVL 320
                                    555555555555.5554554444444444*******************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   3.9e-12   1.7e-08       2      61 ..      28      86 ..      27      94 .. 0.92
   2 ?    0.1   0.0      0.16   7.3e+02      91     107 ..      89     105 ..      85     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.9e-12
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                          ADH_N  2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvv 61
                                   g+v+i+v+aag+C  Dl + kg+ +l+  +p+++G E++G+v ++ ++  +++vG+rV +
  gi|121636061|ref|YP_976284.1| 28 GKVVIDVRAAGVCFPDLLLTKGEYQLKLTPPFVPGMETAGVVRSAPSD-AGFHVGERVSA 86
                                   689****************************************98776.59******976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                    S-SSSBSEEEECGGGEE CS
                          ADH_N  91 ldGgfaeyvvvpekklv 107
                                    + Gg+ae++ vp +++v
  gi|121636061|ref|YP_976284.1|  89 VLGGYAEQIAVPVANVV 105
                                    56**********98887 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.9     5e-06     0.022      24      76 ..     135     189 ..     114     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                                    TCB---.EEEEEST.SHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTCECE CS
                    AlaDh_PNT_C  24 pgvepa.kvlviGg.GvaGlqAiatakglga.kVtvlDvrparleqleslgakfve 76 
                                       +p+ +vlv+G+ G +G++A+++ak+++a kV ++  r+ ++ ++ slga +v 
  gi|121636061|ref|YP_976284.1| 135 A-LRPGdTVLVLGAaGGVGTAAVQIAKAMQAgKVIAMVHREGAIDYVASLGADVVL 189
                                    4.55652699***559**************97899999999*********999554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2260.97
//
Query:       gi|121636062|ref|YP_976285.1|  [L=95]
Description: hypothetical protein BCG_0186c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 759.24
//
Query:       gi|121636063|ref|YP_976286.1|  [L=588]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-70  235.2   2.0    1.5e-69  234.0   2.0    1.5  1  PE-PPE         PE-PPE domain
    2.5e-30  104.6  20.3    5.1e-30  103.7  20.3    1.5  1  PE             PE family
  ------ inclusion threshold ------
       0.23   11.9  12.1       0.54   10.7  12.1    1.6  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   2.0   2.5e-73   1.5e-69       6     226 ..     196     415 ..     190     416 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 2.5e-73
                         PE-PPE   6 elvsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa.pdqlsfv 84 
                                    +++ +P++++p+tg+ksl ++ Sv+ G++ L+ ai ++ +ag++v+vfGySq+a++as e+++l++l+ +a  p+ql+f+
  gi|121636063|ref|YP_976286.1| 196 KALVTPEELYPITGVKSLPFQTSVQLGLQILDGAIWEQINAGNHVTVFGYSQSAVIASLEMQHLISLGPNAPsPSQLNFI 275
                                    5788**************************************************************9998889******* PP

                         PE-PPE  85 lvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvHtnyet 164
                                    l+gn ++pngg+lar+pg l +  lg+ f gatp++  y+T++++ +YDg+adfP+yplN+l+d+Na+ Gi +vHt+y +
  gi|121636063|ref|YP_976286.1| 276 LIGNEMNPNGGILARIPG-LNVTTLGLPFYGATPDNP-YPTTTYTLEYDGFADFPRYPLNVLSDINAVFGILTVHTTYAD 353
                                    *****************9.***************987.****************************************99 PP

                         PE-PPE 165 evaeqlpanirttvnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgY 226
                                     +++q +++ + ++++ +  +tyy+i+te+lPLl plr ++ ++ pl+++++++L v+v+lgY
  gi|121636063|ref|YP_976286.1| 354 LTPAQIASATQLPTQGTT-SNTYYIIETEHLPLLAPLRAIPvIGPPLAALVEPNLEVIVNLGY 415
                                    999999999998888877.899*******************99******************** PP

>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7  20.3   8.5e-34   5.1e-30       2      92 ..      40     130 ..      39     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 8.5e-34
                                    XXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE   2 sfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqala 81 
                                    s+v ++P +laaaa+dlagigsa+++a+aa+aaptt+++aaaaDeVS+a A+lf+a++q++qa+saq+aafh++f q la
  gi|121636063|ref|YP_976286.1|  40 SYVFAQPSVLAAAATDLAGIGSAINQATAAVAAPTTGLAAAAADEVSTALATLFGAYGQQFQAISAQVAAFHNEFTQRLA 119
                                    89****************************************************************************** PP

                                    HHHHHHHS--X CS
                             PE  82 aaagsYaaaEa 92 
                                    aaa+++ +aEa
  gi|121636063|ref|YP_976286.1| 120 AAANAFVNAEA 130
                                    **********9 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  12.1   9.1e-05      0.54       7      98 ..      44     136 ..      41     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                  T7SS_ESX_EspC   7 Vdpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAa 85 
                                     +p++l ++a+++ ++ + i++a+aa+ a+++   +     ++ a+++ + a+ +  +a  +++aa ++e+ ++L aAA 
  gi|121636063|ref|YP_976286.1|  44 AQPSVLAAAATDLAGIGSAINQATAAVaAPTTGLAAAAADEVSTALATLFGAYGQQFQAISAQVAAFHNEFTQRLAAAAN 123
                                    699***********************96677777777788899************************************* PP

                  T7SS_ESX_EspC  86 aYeatDeeaagal 98 
                                    a+ +++ ++ +al
  gi|121636063|ref|YP_976286.1| 124 AFVNAEATNTSAL 136
                                    *********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4131.85
//
Query:       gi|121636064|ref|YP_976287.1|  [L=525]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-69  231.5   0.4      2e-68  230.4   0.4    1.6  1  PE-PPE    PE-PPE domain


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.4   0.4   1.1e-72     2e-68       5     226 ..     111     335 ..     108     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.4 bits;  conditional E-value: 1.1e-72
                         PE-PPE   5 aelvsyPasflpvtglksltvdeSvaeGtenLeaairaela.agekvvvfGySqgalvasnekarlaalsepaa.pdqls 82 
                                     ++v++P++++p+tg+ sl ++ Sv+eG++ L++ai+ ela +g++v+vfG+Sq+a++as e++r +a++  a  +++l+
  gi|121636064|ref|YP_976287.1| 111 LQAVFTPEELYPLTGVRSLVLNTSVEEGLTILHDAIMVELAtTGNAVTVFGWSQSAIIASLEMQRFTAMGGAAPsASDLN 190
                                    589**********************************999867888**********************98877788**** PP

                         PE-PPE  83 fvlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvHtny 162
                                    fvlvgn ++pngg+larfp  lt+p l++tf gatp d+ y+T +++ +YDg+adf +yplN+++d+Na++Gi +vHt+y
  gi|121636064|ref|YP_976287.1| 191 FVLVGNEMNPNGGMLARFPD-LTLPTLDLTFYGATPSDTIYPTAIYTLEYDGFADFSRYPLNFISDLNAVAGITFVHTKY 269
                                    ********************.*********************************************************** PP

                         PE-PPE 163 etevaeqlpanirtt.vnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgY 226
                                     + +++q++ + + + + + ++ t+yy+i+te+ PLlqplr ++ +++pl+d+++++L+v+v+lgY
  gi|121636064|ref|YP_976287.1| 270 LDLTPAQVEGATKLPtSPGYTGVTDYYIIRTENRPLLQPLRAVPvIGDPLADLIQPNLKVIVNLGY 335
                                    999999999998888899**************************99******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3419.90
//
Query:       gi|121636065|ref|YP_976288.1|  [L=276]
Description: phosphotyrosine protein phosphatase ptpB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-58  197.9   0.0    2.7e-58  197.7   0.0    1.0  1  Y_phosphatase3  Tyrosine phosphatase family
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.02   14.5   0.0    1.3  1  Y_phosphatase2  Tyrosine phosphatase family
      0.026   14.1   0.0      0.035   13.7   0.0    1.1  1  Y_phosphatase   Protein-tyrosine phosphatase
       0.14   11.9   0.0       0.21   11.4   0.0    1.3  1  DSPc            Dual specificity phosphatase, catalytic domai


Domain annotation for each model (and alignments):
>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.0   6.1e-62   2.7e-58       2     231 ..       5     275 ..       4     276 .] 0.93

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 6.1e-62
                 Y_phosphatase3   2 plegvsNfRDlGgyptadgrkvrpgvlyRsaelsklteadlakLadlgirtviDLRspeEreaeap...legaryvhlpv 78 
                                    +l+g++NfRD+   +ta    +rpg+l+Rs+els+l++a++a+L++lgi++v DLRs++E++++ p   ++g++++ lp+
  gi|121636065|ref|YP_976288.1|   5 ELPGAWNFRDVADTATA----LRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSREVARRGPgrvPDGIDVHLLPF 80 
                                    589**********9875....***************************************8775666666888******* PP

                 Y_phosphatase3  79 ...........................e.ea.aeeekeeeeaeetlaelYrelle..sakkayrkvfealadeepvlfHC 127
                                                               + e+ +++++ +++a++++++ Yr++++   a++a+++v++ la+ +pvl HC
  gi|121636065|ref|YP_976288.1|  81 pdladddaddsaphetafkrlltnggsNgESgESSQSINDAATRYMTDEYRQFPTrnGAQRALHRVVTLLAAGRPVLTHC 160
                                    ***********************999735555889999999**************88888************55****** PP

                 Y_phosphatase3 128 taGKDRTGvlaalllsllGvdeedivaDYlltneyleelrerlkakleeellaea............leellsvrpeyle 195
                                     aGKDRTG+++al+l+++G+d+++ivaDYl++n+ + +lr+r+++ ++++++ e              + +l+vr+eyl+
  gi|121636065|ref|YP_976288.1| 161 FAGKDRTGFVVALVLEAVGLDRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELapevvtftkarlSDGVLGVRAEYLA 240
                                    *******************************************888888877777999********99************ PP

                 Y_phosphatase3 196 aaldaieekygsvegYlreelglseeeiealrerll 231
                                    aa ++i+e+ygs+ gYlr++ g+s+++++++r  ll
  gi|121636065|ref|YP_976288.1| 241 AARQTIDETYGSLGGYLRDA-GISQATVNRMRGVLL 275
                                    *****************976.***********8876 PP

>> Y_phosphatase2  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.5e-06      0.02      75     133 ..     139     195 ..     113     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                                    -HHHHHHHHHHHH-GGG-SEEEE-SSSSSHHHHHHHHHHHHTTB-HHHHHHHHHHHHCC CS
                 Y_phosphatase2  75 ksdllkkalklllnkenypvllhckrGkhrtglvigclRklqkWslasilnEyrrFsgs 133
                                     +  l++++ ll   +  pvl hc  Gk rtg v++ +    + +  +i+++y r + s
  gi|121636065|ref|YP_976288.1| 139 AQRALHRVVTLL--AAGRPVLTHCFAGKDRTGFVVALVLEAVGLDRDVIVADYLRSNDS 195
                                    555566666555..3557*****************998887787888888877776655 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-06     0.035     169     200 ..     152     183 ..     121     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                                    TSS-EEEECSSSSHHHHHHHHHHHHHHHHHHH CS
                  Y_phosphatase 169 ksgpvvVhCsaGvgRtgtfvaldillqqleae 200
                                       pv+ hC aG  Rtg +val + +  l+++
  gi|121636065|ref|YP_976288.1| 152 AGRPVLTHCFAGKDRTGFVVALVLEAVGLDRD 183
                                    567*****************998777666663 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.21      65      92 ..     145     172 ..     114     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                                    HHHHHHHTT-EEEEEESSSSSHHHHHHH CS
                           DSPc  65 fidkakqkgkkvlVHCqaGisRSatlii 92 
                                     + ++   g+ vl HC aG  R++ +++
  gi|121636065|ref|YP_976288.1| 145 RVVTLLAAGRPVLTHCFAGKDRTGFVVA 172
                                    556678899***************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1878.63
//
Query:       gi|121636066|ref|YP_976289.1|  [L=403]
Description: acyl-CoA dehydrogenase fadE2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-41  141.0   4.2    4.9e-41  140.4   4.2    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.5e-19   69.0   6.0    7.9e-19   68.3   6.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    7.4e-19   67.8   0.0    1.3e-18   67.0   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      2e-08   34.9   0.1    6.1e-08   33.3   0.0    1.9  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.055   13.8   0.0    1.7  1  DUF4169        Domain of unknown function (DUF4169)


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.4   4.2   1.4e-44   4.9e-41       1     149 [.     240     390 ..     240     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 1.4e-44
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+Gf++a+ +l  +R+ ++++alg+a+ral  +++++r+r afg+pl+++ +v++ +a+ + e+++arll+++aa+++d+
  gi|121636066|ref|YP_976289.1| 240 GSGFAIAQARLGPGRIHHCMRALGAAERALALMVNRVRNRVAFGRPLAEQGVVQQAIAQSRNEIDQARLLCEKAAWTIDQ 319
                                    68****************************************************************************** PP

                                    ----..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    ++++  r  ++m+K++a+++a++v+d+a+q++G+aG+++++p++rly + r++ri++G++e++++ iar+ 
  gi|121636066|ref|YP_976289.1| 320 HGNKeaRHLVAMIKAVAPRVACDVIDRAIQVHGAAGVSDDTPLARLYGWHRAMRIFDGPDEVHLRSIARAE 390
                                    *999999*************************************************************985 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   6.0   2.2e-22   7.9e-19       3     120 ..     257     366 ..     255     375 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.2e-22
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    +++ alGaA++ala +v ++r+rv   +g++la++ ++q+a+a+++ ++d+Ar+l e+aa++    ++++ +   e r  
  gi|121636066|ref|YP_976289.1| 257 HCMRALGAAERALALMVNRVRNRVA--FGRPLAEQGVVQQAIAQSRNEIDQARLLCEKAAWT----IDQHGN--KEARHL 328
                                    7899*********************..***********************************....444433..36799* PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHH CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlw 120
                                     ++ +a+a + a +++d++++++G+ ++ ++ pl Rl+
  gi|121636066|ref|YP_976289.1| 329 VAMIKAVAPRVACDVIDRAIQVHGAAGVSDDTPLARLY 366
                                    ************************************86 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   3.6e-22   1.3e-18       1      96 [.     128     227 ..     128     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.6e-22
                                    EEE---SS-.SS-GGG---EEEEETT.EEEEEEEEEEEETTTT..-SEEEEEEETS---.----EEEEEEE..GGGEEE- CS
                  Acyl-CoA_dh_M   1 afalTEpqa.GsdvasvkttaaerdggeyvlnGeKiwitnaai..atlalvlartekpd.rarglslflvprdapgvsvr 76 
                                    af +TEp +  sd+++++t +++rdg +yv+nG+K+w ++aa+  +++++v++rt+ ++ ++++ s++lvp d+pgv++ 
  gi|121636066|ref|YP_976289.1| 128 AFSMTEPAVaSSDARNIET-TISRDGADYVINGRKWWTSGAADprCKILIVMGRTNPDAaAHQQQSMVLVPIDTPGVTIV 206
                                    799****9989********.99999999***************99999******5444489******************7 PP

                                    ----BSS-TTS-.EEEEEEE. CS
                  Acyl-CoA_dh_M  77 rieeklGlrglp.tgelvfed 96 
                                    r  +  G ++ + ++e+ +++
  gi|121636066|ref|YP_976289.1| 207 RSTPVFGWQDRHgHCEIDYHN 227
                                    777889977654477776665 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.7e-11   6.1e-08       6     112 ..       7     123 ..       2     124 .. 0.79
   2 ?   -2.2   0.0       1.8   6.3e+03      89     101 ..     313     325 ..     279     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.7e-11
                                    HHHHHHHHHHHHHTHHHHHHHH..HHTS.........GHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_N   6 alrdtvrefaeeelaphaaewd..eege.........fprelwkklaelGllgitvpeeygGagldyleaaivaeelara 74 
                                    ++r ++ +f+ e++   +a++d  ++++         + +el  k+++ Gl+++ +  e    gl++le+a +ae  +  
  gi|121636066|ref|YP_976289.1|   7 DYRTRLSDFMTEHVFGAEADYDdyRRAAgpadhtappIIEELKTKAKDRGLWNLFLSAES---GLTNLEYAPLAEMTGW- 82 
                                    57899999*****97767777655444456676654444788**************9996...5888999999999998. PP

                                    -HHHHH.HHHH..HHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  75 daglal.llgv..hsslvapailrfGteeqkrryLpklasg 112
                                    ++ +a+ +l++   ++ +++++  fGte+q++++L++l++g
  gi|121636066|ref|YP_976289.1|  83 SMEIAPeALNCaaPDTGNMEILHMFGTEQQRAQWLRPLLDG 123
                                    4555555665555888899********************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                    THHHHHHHS-HHH CS
                  Acyl-CoA_dh_N  89 vapailrfGteeq 101
                                    +a++i ++G++e 
  gi|121636066|ref|YP_976289.1| 313 AAWTIDQHGNKEA 325
                                    3467788888776 PP

>> DUF4169  Domain of unknown function (DUF4169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.055      24      55 .]     277     308 ..     276     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                        DUF4169  24 eNRakFGrtKaekeleeaeaerakrrlDghrl 55 
                                    +NR++FGr+ ae    ++  ++++ ++D++rl
  gi|121636066|ref|YP_976289.1| 277 RNRVAFGRPLAEQGVVQQAIAQSRNEIDQARL 308
                                    6*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2872.15
//
Query:       gi|121636067|ref|YP_976290.1|  [L=366]
Description: NAD(p) transhydrogenase (subunit alpha) pntAa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-66  222.1   0.6    6.5e-66  221.7   0.6    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    9.8e-39  132.8   0.3    2.7e-38  131.4   0.1    1.8  2  AlaDh_PNT_N     Alanine dehydrogenase/PNT, N-terminal domain
    1.7e-05   24.3   0.0     0.0081   15.5   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0045   17.0   0.8       0.02   14.9   0.4    2.3  2  ADH_zinc_N      Zinc-binding dehydrogenase
     0.0097   16.1   0.3      0.044   14.0   0.3    2.2  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.049   13.5   4.0       0.22   11.4   0.1    2.8  3  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.6   2.2e-69   6.5e-66       1     207 [.     146     362 ..     146     365 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.2e-69
                                    HHHHHHHHCSCGCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE... CS
                    AlaDh_PNT_C   1 AvleaakalekffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev... 77 
                                    Avl+aa++ ++ff++ +t+aG+v+   pa+vlv+G+GvaGlqA+atak+lga++t +Dvrp+++ q++s+ga+++++   
  gi|121636067|ref|YP_976290.1| 146 AVLLAASESTRFFPMLTTAAGTVK---PATVLVLGVGVAGLQALATAKRLGARTTGYDVRPEVADQVRSVGAQWLDLgis 222
                                    89**********************...***************************************************** PP

                                    ...............HCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETTGGGT-SBTT--TBB CS
                    AlaDh_PNT_C  78 ...............lksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvAidqGGnvetsrltt 142
                                                   +++q+++l+ea++  dvvi+t+l+pG++aP+Lvt++ v++MkpgsV+vD+A ++GGn+e   lt+
  gi|121636067|ref|YP_976290.1| 223 asgeggyareltddeRAQQQKALEEAISGFDVVITTALVPGRPAPTLVTAAAVEAMKPGSVVVDLAGETGGNCE---LTE 299
                                    ***************9**********************************************************...*** PP

                                    TTSEEEEETTEEEEEBSTGGGGSHHHHHHHHHHHHHHHHHHHCHHHTCCHHHCTSHHHHCCEEEE CS
                    AlaDh_PNT_C 143 hgepvveekgvvhygvanlpgavprtasalltnntlpyleelladkglkkalkedealrkglvvk 207
                                    +g++vv+ ++v++ +  nlp+++p++as+l+++n++++l  l++d++l + + +de++++ +v++
  gi|121636067|ref|YP_976290.1| 300 PGRTVVK-HDVTIAAPLNLPATMPEHASELYSKNITALLDLLIKDGRL-APDFDDEVIAQSCVTR 362
                                    *****99.****************************************.***********99986 PP

>> AlaDh_PNT_N  Alanine dehydrogenase/PNT, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.1   8.9e-42   2.7e-38       1     135 [.      12     141 ..      12     142 .. 0.98
   2 ?   -2.1   0.0       1.5   4.5e+03      95     110 ..     319     334 ..     270     338 .. 0.55

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 8.9e-42
                                    EE---SSTT----SS-HHHHHHHHHTT-EEEEETTTTGGGTC-HHHHHHTTEEEESCHHHHCTTSSEEEESS--.CHCGG CS
                    AlaDh_PNT_N   1 gvpkEikagErRvaltPatvkkLvkaGhevlVesgaGegagfsdeeYeeaGaeivesaeevlaeadlilkVkepseeele 80 
                                    gv++E+ ++ErRval+P+ v++Lv++G+ v+Ve+gaGe+a ++de Y+++Ga+i     +++a ad+++kV +p+++e+ 
  gi|121636067|ref|YP_976290.1|  12 GVVAESGPDERRVALVPKAVASLVNRGVAVVVEAGAGERALLPDELYTAVGASIG----DAWA-ADVVVKVAPPTAAEVG 86 
                                    799***************************************************9....6899.**************** PP

                                    GS-TTCEEEEE--GGCHHHHHHHHHHCTEEEEEGGG-BSSGCCGGGTHHHHHHHH CS
                    AlaDh_PNT_N  81 llkegqtlisflhlaanpellealaekgvtaialElvprisraqsldaLssmaei 135
                                    +l+ gqtli+fl + +  + + al ++gv+a+alE++prisraq +daLss+a++
  gi|121636067|ref|YP_976290.1|  87 RLRGGQTLIGFLAPRNADNSIGALTQAGVQAFALEAIPRISRAQVMDALSSQANV 141
                                    *****************************************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                    GCHHHHHHHHHHCTEE CS
                    AlaDh_PNT_N  95 aanpellealaekgvt 110
                                    a+ pe +++l +k++t
  gi|121636067|ref|YP_976290.1| 319 ATMPEHASELYSKNIT 334
                                    1355555555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-06    0.0081      33      85 ..     167     219 ..     150     224 .. 0.88
   2 !    6.4   0.0    0.0017       5.1      76     127 ..     236     288 ..     227     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                                    -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSH CS
                   2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsl 85 
                                    +++  tv ++G+G  G ++  ++k +g++ ++yd++++  ++++++g+++ +l
  gi|121636067|ref|YP_976290.1| 167 TVKPATVLVLGVGVAGLQALATAKRLGARTTGYDVRPEVADQVRSVGAQWLDL 219
                                    57789********************************9999888888887665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                                    HHHTCEECSHHHHHHH-SEEEE-S-.-STTTTTSBSHHHHHCSTTTEEEEESS CS
                   2-Hacid_dh_C  76 eelgvelvsleellaesDivslhlp.ltpetrhlinaeelakmkkgailiNta 127
                                    +e   +   lee+++  D+v+ ++         l++a++ ++mk+g++++  a
  gi|121636067|ref|YP_976290.1| 236 DERAQQQKALEEAISGFDVVITTALvPGRPAPTLVTAAAVEAMKPGSVVVDLA 288
                                    344456789*********987654313445678****************9876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   3.2e+03      47      66 ..      28      46 ..      16      55 .. 0.70
   2 !   14.9   0.4   6.7e-06      0.02       3      91 ..     182     292 ..     177     327 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                   HHHHHHHTTTSSEEEEEESS CS
                     ADH_zinc_N 47 verikeltggegvdvvfecv 66
                                    +++++l   +gv vv+e+ 
  gi|121636067|ref|YP_976290.1| 28 PKAVASLV-NRGVAVVVEAG 46
                                   46666777.55777777764 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.7e-06
                                    HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET................TTCHHHHHHHHHTTTSSEEEEEESS CS
                     ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGadeviny................keadlverikeltggegvdvvfecv 66 
                                    Gl a++ Ak lGa++++ d+ +e ++++++ Ga  +                   ++a+ +++++e+    g+dvv+ ++
  gi|121636067|ref|YP_976290.1| 182 GLQALATAKRLGARTTGYDVRPEVADQVRSVGAQWLDLGisasgeggyareltddERAQQQKALEEAI--SGFDVVITTA 259
                                    666777899**********************7765533344466666666665534437788888888..5999999875 PP

                                    C.....SHH.HHHHHHHCEEEEEEEEECSC..T CS
                     ADH_zinc_N  67 G.....sga.tleaalkllkpgGrlvvvGg..g 91 
                                          +++ +  aa++++kpg  +v  +g  g
  gi|121636067|ref|YP_976290.1| 260 LvpgrpAPTlVTAAAVEAMKPGSVVVDLAGetG 292
                                    422233333133456778888888877777543 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   1.5e-05     0.044       4      89 ..     175     287 ..     172     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.........................EEE-SSHHHHHHHCSE CS
                  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.........................akaaesieelvasldv 58 
                                    ++G+Gv G +     ++ g ++++y++++e ++++ + g                         a+  + +ee++++ dv
  gi|121636067|ref|YP_976290.1| 175 VLGVGVAGLQALATAKRLGARTTGYDVRPEVADQVRSVGaqwldlgisasgeggyareltdderAQQQKALEEAISGFDV 254
                                    79*********************************999999********************9999999999*******99 PP

                                    EEE..-SSSHHHHHHHHHSHCCC--TT-EEEE- CS
                  NAD_binding_2  59 vit..mvkagkavdeviegllealkkgdilidg 89 
                                    vit  +v+  +a   v+   +ea+k+g++++d 
  gi|121636067|ref|YP_976290.1| 255 VITtaLVPGRPAPTLVTAAAVEAMKPGSVVVDL 287
                                    88632355555555555559***********97 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.19   5.6e+02      77      95 ..      94     120 ..      25     146 .. 0.64
   2 ?    2.1   0.2     0.052   1.6e+02      38      73 ..     121     156 ..      91     196 .. 0.73
   3 ?   11.4   0.1   7.2e-05      0.22      49      86 ..     240     279 ..     233     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.19
                                    H........HHHHHHHHHHCT--EEEE CS
                 NAD_binding_10  77 g........aknivdaakeagvkRfvl 95 
                                             a+n + a+ +agv+ f l
  gi|121636067|ref|YP_976290.1|  94 LigflaprnADNSIGALTQAGVQAFAL 120
                                    033333444788888888888877765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.052
                                    TTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                 NAD_binding_10  38 eeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                    e+  ++  ++v+d+ + ++ ++g+ aV+ a++ + +
  gi|121636067|ref|YP_976290.1| 121 EAIPRISRAQVMDALSSQANVSGYKAVLLAASESTR 156
                                    456677788888999999999999999999977665 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 7.2e-05
                                    T-CCHHHHHHTT-SEEEES---TCC..HHHHHHHHHHHHH CS
                 NAD_binding_10  49 tdvedlaealkgadaVvsalggggk..deegaknivdaak 86 
                                    +++++l+ea++g d+V++++   g+   + +++++v+a+k
  gi|121636067|ref|YP_976290.1| 240 QQQKALEEAISGFDVVITTALVPGRpaPTLVTAAAVEAMK 279
                                    67899***********999955555224445********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2586.13
//
Query:       gi|121636068|ref|YP_976291.1|  [L=110]
Description: NAD(p) transhydrogenase (subunit alpha) pntAb [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-31  107.5   8.5      4e-31  107.3   8.5    1.0  1  PNTB_4TM  4TM region of pyridine nucleotide transhydrogenase,
  ------ inclusion threshold ------
      0.014   15.6   4.7      0.019   15.2   4.7    1.3  1  TrbC      TrbC/VIRB2 family
      0.024   14.4   4.2      0.029   14.2   4.2    1.0  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1
        6.6    7.4   7.5         35    5.1   7.5    2.0  1  DUF2627   Protein of unknown function (DUF2627)


Domain annotation for each model (and alignments):
>> PNTB_4TM  4TM region of pyridine nucleotide transhydrogenase, mitoch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   8.5     9e-35     4e-31       2      81 ..       9      93 ..       8      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 9e-35
                       PNTB_4TM  2 ltvfvLalfvGyeviwkVtpaLhtPLmsvtnaisgiiivgallalg.....stlakvlgaiavvlasinvvGGFlvtqrmLk 78
                                   l+++vL+ fvG+ vi+kV+++LhtPLms+tnai+gi+++gal+++g     s + +v+ ++avv++++nv+GGF+vt+rmL 
  gi|121636068|ref|YP_976291.1|  9 LAILVLSGFVGFAVISKVPNTLHTPLMSGTNAIHGIVVLGALVVFGeiehpSLVLQVILFVAVVFGTLNVIGGFIVTDRMLG 90
                                   89********************************************9999888899************************** PP

                       PNTB_4TM 79 mFk 81
                                   mFk
  gi|121636068|ref|YP_976291.1| 91 MFK 93
                                   **8 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   4.7   4.3e-06     0.019      42      96 ..      23      79 ..       9      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                           TrbC 42 lqnivdfltgpla.kviatiaiivaGimlafgrls.wrtlvmvviGiviifgAssiv 96
                                   + ++ ++l+ pl   + a+ +i+v+G+ ++fg+++    +++v+++++++fg  +++
  gi|121636068|ref|YP_976291.1| 23 ISKVPNTLHTPLMsGTNAIHGIVVLGALVVFGEIEhPSLVLQVILFVAVVFGTLNVI 79
                                   66777777777651456899***************777789**********976665 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.2   6.5e-06     0.029      47     118 ..      10      84 ..       5      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-06
                         Bax1-I  47 aplalv.flslsaarlkkkssalalallllftlleGlslspillvyt....gaiilqaflltaaifgglslyalttk 118
                                    a+l+l  f  +++a + k +++l ++l+ +  ++ G+++   l+v+     ++++lq++l  a++fg l +++ +  
  gi|121636068|ref|YP_976291.1|  10 AILVLSgF--VGFAVISKVPNTLHTPLMSGTNAIHGIVVLGALVVFGeiehPSLVLQVILFVAVVFGTLNVIGGFIV 84 
                                    44555544..34455777899988************988777666666*********************99987763 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.5    0.0078        35      14      61 ..      38      84 ..       4      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0078
                        DUF2627 14 llaayGiklmrd.alfgilsspfsslwlqflaGlllfaiglgfiaGfil 61
                                     a  Gi ++    +fg+++   +sl+lq+++ ++++ + l +i+Gfi 
  gi|121636068|ref|YP_976291.1| 38 TNAIHGIVVLGAlVVFGEIE--HPSLVLQVILFVAVVFGTLNVIGGFIV 84
                                   55666776665413455544..56789*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 857.72
//
Query:       gi|121636069|ref|YP_976292.1|  [L=475]
Description: NAD(p) transhydrogenase (subunit beta) pntB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-173  578.5  27.8   1.2e-173  578.3  27.8    1.0  1  PNTB            NAD(P) transhydrogenase beta subunit
  ------ inclusion threshold ------
      0.082   12.6   0.0       0.16   11.7   0.0    1.4  1  DUF3830         Protein of unknown function (DUF3830)
        1.9    8.7   8.9        3.2    8.0   2.8    3.1  3  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> PNTB  NAD(P) transhydrogenase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.3  27.8    2e-177  1.2e-173       2     459 ..       8     470 ..       7     471 .. 0.93

  Alignments for each domain:
  == domain 1  score: 578.3 bits;  conditional E-value: 2e-177
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           PNTB   2 elaylvaallfilglkglsspktarrgnllgavgmllavvatlllllkeaaseelalillalvigaviGlllakkvemte 81 
                                    e++y+++  lfi+gl gl+ pkta+rgnl++a+gm++av+atl+++ ++   +++ li+++lv+g v+G+  a+ ++mt+
  gi|121636069|ref|YP_976292.1|   8 EILYIISFSLFIYGLMGLTGPKTAVRGNLIAAAGMTIAVAATLVMIRHT---SQWPLIIAGLVVGVVLGVPPARLTKMTA 84 
                                    689***************************************7655333...458999********************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                           PNTB  82 mPqlvallnslvGlAavlvalaelleeeaekaee...aleavelvelvlgvliGavtftGslvAflKLqgllsskplkl. 157
                                    mPqlva++n+++G++ +l+al+e+++++  +a +   + ++   v+ +++++iG+++f+Gs+vAf+KLq+++s++p+ l 
  gi|121636069|ref|YP_976292.1|  85 MPQLVAFFNGVGGGTVALIALSEFIDTTGFSAFQhgeSPTVHIVVASLFAAIIGSISFWGSIVAFGKLQEIISGRPIGLg 164
                                    **************************98876544675666667788899*****************************98 PP

                                    XXXXXXXXXXXXXXXXXX..X................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           PNTB 158 pgrkllnlllllalvvllvlfvla.......asslllllllvlalllGvllvlpiggaDmpvvisllnsysGlaaaaaGf 230
                                    ++++ +nllll+++v+++v++ l+        + ++++ llv+a +lG+++vlpiggaDmpvvis+ln+++Gl+aaaaG+
  gi|121636069|ref|YP_976292.1| 165 KAQQPINLLLLAVAVAAAVVIGLHahpgsggVALWWMIGLLVAAGVLGLMVVLPIGGADMPVVISMLNAMTGLSAAAAGL 244
                                    89**********99999888777678888766666678899999************************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X--S-EESHHHHHHHHHC-SEEEE CS
                           PNTB 231 vlenklLiivGalvgasGaiLsyimckamNrsllnvllggfgaaassekaeeeekeekevkeisaedvaellkeakkvii 310
                                    +l+n+++i++G++vgasG+iL+++m+kamNrs+ ++++ggfg +  + +  +   ++k+vk++sa+d+a ++++a++vi+
  gi|121636069|ref|YP_976292.1| 245 ALNNTAMIVAGMIVGASGSILTNLMAKAMNRSIPAIVAGGFGGGGVAPSGGG---DDKHVKATSAADAAIQMAYANQVIV 321
                                    *****************************************75555554444...4669********************* PP

                                    EE-HHHHHCTTHHHHHHHHHHHHHTT-EEEEEE-TTSSSSTTHHHHHHHHCT--GGGEEEHHHHCCGGGG-SEEEEES-S CS
                           PNTB 311 vPGYGlavaqAqhavaelaklLeekgveVkfaiHPvAGRmPGhmnVLLAeadvpydkvlemdeineefaetDvalViGAn 390
                                    vPGYGlavaqAqhav++la+lLe++gv Vk+aiHPvAGRmPGhmnVLLAea+v+yd +++md+in+efa+tDv++ViGAn
  gi|121636069|ref|YP_976292.1| 322 VPGYGLAVAQAQHAVKDLATLLEDRGVPVKYAIHPVAGRMPGHMNVLLAEAEVDYDAMKDMDDINDEFARTDVTIVIGAN 401
                                    ******************************************************************************** PP

                                    CCC-CHHCCSTTSTTTTSS---GGGSSEEEEEESSS--TTT--S-GGGGSTTEEEEES-HHHHHHHHHH CS
                           PNTB 391 DvvnpaakedpnspiagmPvlevekakkvivlkrslasGYagveNplFykentsmlfgdakksleellk 459
                                    Dv+npaa+++++spi+gmP+l+v+k+++vivlkrs++sG+ag++NplFy++ t+mlfgdakks++e+ +
  gi|121636069|ref|YP_976292.1| 402 DVTNPAARNETSSPIYGMPILNVDKSRSVIVLKRSMNSGFAGIDNPLFYADGTTMLFGDAKKSVTEVSE 470
                                    ****************************************************************99875 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.16      39     105 ..     387     460 ..     367     473 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                                    -SSSSSEEEEEEE--SSS---S-SEESS--TTEEEEEEEEHHHH......SSTTT---......EEEE-SSS---EETT CS
                        DUF3830  39 akyagneiyvllpefaatelpaENaTvtPipGdvvlfsfektel......gnpgygye......laifygrgnlllngd 105
                                      +a+ ++ + + + + t++ a N+T+ Pi+G  +l   ++ ++         +            +fy+ g ++l gd
  gi|121636069|ref|YP_976292.1| 387 DEFARTDVTIVIGANDVTNPAARNETSSPIYGMPILNVDKSRSVivlkrsM--N---SgfagidNPLFYADGTTMLFGD 460
                                    579*****************************8777755554444544221..2...1233444889999999998666 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.091   5.4e+02      76      99 ..      30      53 ..      19      58 .. 0.82
   2 ?    8.0   2.8   0.00053       3.2      20      93 ..     244     314 ..     184     320 .. 0.82
   3 ?    1.6   0.0     0.053   3.2e+02      26     103 ..     319     400 ..     308     410 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.091
                                   HHHHHTEEE-TT--HHHHHHHHHH CS
                 Asparaginase_C 76 elerlgvisaddmtpeaarikLml 99
                                    + r ++i+a  mt++ a +++m+
  gi|121636069|ref|YP_976292.1| 30 TAVRGNLIAAAGMTIAVAATLVMI 53
                                   55677899999**********996 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00053
                                    HHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE-TT--HHHH CS
                 Asparaginase_C  20 lkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvisaddmtpeaa 93 
                                    l+ +  + +++g+ vG+  s l +++++a++r i+ +++     g+v++s   +g +++  ++ sa d  ++ a
  gi|121636069|ref|YP_976292.1| 244 LALNNTAMIVAGMIVGASGSILTNLMAKAMNRSIPAIVAGGFGGGGVAPS---GGGDDKHVKATSAADAAIQMA 314
                                    45577899******************************************...566777777777776666655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.053
                                    EEEEEEBTTTB--H..HHHHHHHHHHTTT-EEEEEESSSBS-----H........HHHHHTEEE-TT--HHHHHHHHHHH CS
                 Asparaginase_C  26 GvvlegtGvGnlps..allealkeakargivvvatsqcpsgsvsnseye...agkelerlgvisaddmtpeaarikLmll 100
                                     +v+ g+G   ++   a+ +++  + +rg++v  +   + g++ ++  +   a+ e +   +   dd++ e ar+ + ++
  gi|121636069|ref|YP_976292.1| 319 VIVVPGYGLAVAQAqhAVKDLATLLEDRGVPVKYAIHPVAGRMPGHM-NvllAEAEVDYDAMKDMDDINDEFARTDVTIV 397
                                    5888899988887666888888888899***9999999999998873.33554444444444555577777777777666 PP

                                    CTT CS
                 Asparaginase_C 101 lgk 103
                                    +g 
  gi|121636069|ref|YP_976292.1| 398 IGA 400
                                    665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3243.49
//
Query:       gi|121636070|ref|YP_976293.1|  [L=214]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-21   77.2   0.2    1.7e-21   76.6   0.2    1.3  1  TetR_C_24    Tetracyclin repressor-like, C-terminal domain
      3e-13   49.3   0.2    9.2e-13   47.8   0.2    1.9  1  TetR_N       Bacterial regulatory proteins, tetR family
    0.00017   21.8   0.0    0.00025   21.2   0.0    1.3  1  TetR_C_5     QacR-like protein, C-terminal region
  ------ inclusion threshold ------
      0.016   15.4   0.0       0.11   12.7   0.0    2.1  2  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.028   14.5   0.2       0.07   13.2   0.1    1.9  1  TetR_C_27    Tetracyclin repressor-like, C-terminal domain
      0.088   12.9   0.0       0.14   12.2   0.0    1.4  1  TetR_C_17    Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.2   5.6e-25   1.7e-21       3     114 .]      81     196 ..      79     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 5.6e-25
                                    SHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-H....HHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHH CS
                      TetR_C_24   3 spaerLralvrahveviaeereeaavllrelraLsp....ehreeiralrreyerllrdlieeGvaagefedldpklaal 78 
                                    +++e L +   +++ +ia+++e+aav+++e  + ++    e+ +e+r++++++ +++  li++G+a+gef ++d +++al
  gi|121636070|ref|YP_976293.1|  81 TAREALYQYTVRLLTAIASNPERAAVYFQEQPYITEwftsEQVAEVREKEQQVYEHVHGLIDRGIASGEFYECDSHVVAL 160
                                    68999*************************9886544444**************************************** PP

                                    HHHHHHHCHHHC--TTSSS-HHHHHHHHHHHHHH-S CS
                      TetR_C_24  79 ailgmlnwvyrWyrpdGplspeeiadqyadlllrgl 114
                                      +gm+ ++yrW rp+G+ +++eia+++   llrgl
  gi|121636070|ref|YP_976293.1| 161 GYIGMTLGSYRWLRPSGRRTAKEIAAEFSTALLRGL 196
                                    **********************************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.2   3.1e-16   9.2e-13       1      41 [.      16      56 ..      16      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.1e-16
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKe 41
                                   +l++A +lfa rGy++t ++++A+  G++k+++Y+y++sK 
  gi|121636070|ref|YP_976293.1| 16 LLAVATKLFAARGYHGTRMDDVADVIGLNKATVYHYYASKS 56
                                   799*************************************7 PP

>> TetR_C_5  QacR-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   8.4e-08   0.00025      18     128 ..      81     195 ..      75     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.4e-08
                       TetR_C_5  18 tateklYalaelsleeyktPlsnaieelaseqvksks.ilekllkLerkslkay...ekileeGiqsGefrienvedvsk 93 
                                    ta+e lY ++   l+ +    ++a   ++ +++ ++  + e++ ++ +k  ++y   + +++ Gi sGef++ + + v++
  gi|121636070|ref|YP_976293.1|  81 TAREALYQYTVRLLTAIASNPERAAVYFQEQPYITEWfTSEQVAEVREKEQQVYehvHGLIDRGIASGEFYECDSHVVAL 160
                                    899********99****99999**999*99999887425566666665555555111679***********988776665 PP

                       TetR_C_5  94 ivasllsGlvvliheleieelkklfnkaidilLkg 128
                                       ++  G    +     +  k +  ++++ lL+g
  gi|121636070|ref|YP_976293.1| 161 GYIGMTLGSYRWLRPSGRRTAKEIAAEFSTALLRG 195
                                    55555555555555555566666666666666665 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05      0.11      15      54 ..      20      59 ..      10      73 .. 0.88
   2 ?   -0.2   0.0      0.35     1e+03      64      82 ..     126     144 ..     103     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHHH-HHHHH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWkkkkeFie 54
                                   a +l + + y+ + +d++a+ +g++++T y++   k  i 
  gi|121636070|ref|YP_976293.1| 20 ATKLFAARGYHGTRMDDVADVIGLNKATVYHYYASKSLIL 59
                                   6688999************************998877765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                                    HHTTHHHHHHHHHHHHHSS CS
                    HTH_Tnp_1_2  64 leeeraevykaLlrkilkg 82 
                                    + e+ ++vy++  ++i+ g
  gi|121636070|ref|YP_976293.1| 126 VREKEQQVYEHVHGLIDRG 144
                                    3455566777777776655 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05      0.07      34      74 ..     119     159 ..      82     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                    HHH-HHHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHH CS
                      TetR_C_27  34 ieeelevvekhieeleeqlaeIireGvaaGeFkaadpeaaa 74 
                                    ++e+++ v++  +++ e++  +i++G+a+GeF + d ++ a
  gi|121636070|ref|YP_976293.1| 119 TSEQVAEVREKEQQVYEHVHGLIDRGIASGEFYECDSHVVA 159
                                    5677788888889999******************9998876 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.8e-05      0.14      25      66 ..     110     151 ..      85     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                                    HHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-- CS
                      TetR_C_17  25 yEyfltsyreeerrayleeRyerlvealkellqeGvergEfk 66 
                                       ++t++ + e+ a + e+ +++ e+++ l+++G+++gEf+
  gi|121636070|ref|YP_976293.1| 110 EQPYITEWFTSEQVAEVREKEQQVYEHVHGLIDRGIASGEFY 151
                                    44589************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1588.52
//
Query:       gi|121636071|ref|YP_976294.1|  [L=468]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-70  235.8   1.7    4.2e-70  235.8   1.7    1.6  2  PE-PPE         PE-PPE domain
    4.9e-31  106.9  19.8    9.9e-31  105.9  19.8    1.5  1  PE             PE family


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.8   1.7   4.7e-74   4.2e-70       5     226 ..     154     375 ..     151     376 .. 0.95
   2 ?   -2.8   0.1      0.41   3.7e+03      10      30 ..     384     402 ..     378     412 .. 0.47

  Alignments for each domain:
  == domain 1  score: 235.8 bits;  conditional E-value: 4.7e-74
                         PE-PPE   5 aelvsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa..pdqls 82 
                                    +++ ++P++ +p+  +++l++d+S+a+G++ L++ i+ael+ g +vvvfGySq+a+va+ne++ l+al   +a  p++l 
  gi|121636071|ref|YP_976294.1| 154 PVAQYTPEQWWPF--IGNLSLDQSIAQGVTLLNNGINAELQNGHDVVVFGYSQSAAVATNEIRALMALPPGQApdPSRLA 231
                                    56678*******8..****************************************************98888899***** PP

                         PE-PPE  83 fvlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvHtny 162
                                    f+l+gn+n+pngg+l+r+ g l++ +l+++f+gatp ds+y+T+ ++ qYDg a+ P+yplN+l+d+Na++Gi  vH++y
  gi|121636071|ref|YP_976294.1| 232 FTLIGNINNPNGGVLERYVG-LYLTFLDMSFNGATPPDSPYQTYMYTGQYDGYAHNPQYPLNILSDLNAFMGIRWVHNAY 310
                                    ******************99.********************************************************999 PP

                         PE-PPE 163 etevaeqlpanirtt.vnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgY 226
                                         + ++++++ + + + +++t+yy++ t++lPLlqp+r ++ v++p++++++++LrvlvdlgY
  gi|121636071|ref|YP_976294.1| 311 PFTA-AEVANAVPLPtSPGYTGNTHYYMFLTQDLPLLQPIRAIPfVGTPIAELIQPDLRVLVDLGY 375
                                    6665.555666666669************************************************* PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.41
                         PE-PPE  10 yPasflpvtglksltvdeSva 30 
                                    +Pas++++  ++ + v +++a
  gi|121636071|ref|YP_976294.1| 384 TPASLFAP--INPIAVASALA 402
                                    33333332..33333333333 PP

>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9  19.8   1.1e-34   9.9e-31       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 1.1e-34
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+v++aPe+la+aaad++gigsa++aa+a aa+ptt++laaaaDeVS a+Aalfs++a+e+q++ +qaaafh +f +alaa
  gi|121636071|ref|YP_976294.1|  1 MSYVIAAPEMLATAAADVDGIGSAIRAASASAAGPTTGLLAAAADEVSSAAAALFSEYARECQEVLKQAAAFHGEFTRALAA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   a+++Ya+aEa
  gi|121636071|ref|YP_976294.1| 83 AGAAYAQAEA 92
                                   *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3203.76
//
Query:       gi|121636072|ref|YP_976295.1|  [L=502]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-79  264.3   3.4    1.3e-78  263.6   3.4    1.3  1  PE-PPE         PE-PPE domain
    4.6e-31  107.0  18.8    8.1e-31  106.2  18.8    1.4  1  PE             PE family
     0.0027   18.1  13.9     0.0041   17.6  13.9    1.3  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
     0.0088   16.0   0.6      0.024   14.6   0.0    1.9  2  Cutinase       Cutinase


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.6   3.4     3e-82   1.3e-78       1     226 [.     172     398 ..     172     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 263.6 bits;  conditional E-value: 3e-82
                         PE-PPE   1 PgadaelvsyPasflpvtg.lksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaapd 79 
                                    Pga  + +++P++f+pvt+ l++lt+++Sv+eG++ L++ ++++la ++kvv+fGySq+a++++n++++l+a+++p+  d
  gi|121636072|ref|YP_976295.1| 172 PGAVSQGLFTPEQFWPVTPdLGNLTFNQSVTEGVALLNTTVNNQLALDNKVVAFGYSQSATIINNYINSLMAMGSPNP-D 250
                                    7888999********************************************************************999.* PP

                         PE-PPE  80 qlsfvlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvH 159
                                    ++sfv++g  n+p ggllarfpg ++ip+l++ f+gatp++s+y+T++++aqYDg+a++P++pl +l+d+Na++G+++vH
  gi|121636072|ref|YP_976295.1| 251 DISFVMIGSGNNPVGGLLARFPG-FYIPFLDVPFNGATPANSPYPTHIYTAQYDGIAHAPQFPLRILSDINAFMGYFYVH 329
                                    **********************9.******************************************************** PP

                         PE-PPE 160 tnyetevaeqlpanirtt.vnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgY 226
                                    ++y + +a+q++++++ + + + +++t+yy++ t++lPLlqp+r+++  + p++d+++++LrvlvdlgY
  gi|121636072|ref|YP_976295.1| 330 NTYPELMATQVDNAVPLPtSPGYTGNTQYYMFLTQDLPLLQPIRDIPyAGPPIADLFQPQLRVLVDLGY 398
                                    *****************9999**************************99******************** PP

>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2  18.8   1.8e-34   8.1e-31       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.8e-34
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms++v+aP++la+aaa++++i+s+l+aanaaaa+pt ++laaa DeVSaa+Aalfsa+++eyqa+ +qaaafh +f ++l+a
  gi|121636072|ref|YP_976295.1|  1 MSHLVTAPDMLATAAAHVDEIASTLRAANAAAAGPTCNLLAAAGDEVSAATAALFSAYGREYQAVVKQAAAFHSEFTRTLEA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a+++Ya+aEaa
  gi|121636072|ref|YP_976295.1| 83 AGNAYAHAEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  13.9   9.1e-07    0.0041       5      98 ..       4      98 ..       1     100 [. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.1e-07
                  T7SS_ESX_EspC  5 LsVdpdhlrelaakhdevaaeiasavaaaagasaavldshG.picaatndavaaaeaarraagealaaasteLadkLraAAa 85
                                   L   pd l ++aa++de+a+++++a+aaaag + ++l   G  ++aat++ ++a+ +  +a +++ aa ++e+ + L aA  
  gi|121636072|ref|YP_976295.1|  4 LVTAPDMLATAAAHVDEIASTLRAANAAAAGPTCNLLAAAGdEVSAATAALFSAYGREYQAVVKQAAAFHSEFTRTLEAAGN 85
                                   666799***********************************5599999999******************************* PP

                  T7SS_ESX_EspC 86 aYeatDeeaagal 98
                                   aY  ++ ++a ++
  gi|121636072|ref|YP_976295.1| 86 AYAHAEAANAARV 98
                                   *********9876 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.53   2.4e+03      96     117 ..      30      51 ..      26     100 .. 0.55
   2 !   14.6   0.0   5.4e-06     0.024      59     113 ..     202     252 ..     190     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.53
                                    HHTT.....S-HHHHHHEEEEE CS
                       Cutinase  96 aieggatatlpaavadkvaavv 117
                                    a+++g t +l aa+ d+v+a+ 
  gi|121636072|ref|YP_976295.1|  30 AAAAGPTCNLLAAAGDEVSAAT 51 
                                    5555555666666666665542 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.4e-06
                                    HHHHHHHHHHHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.....S-HHHHHHE CS
                       Cutinase  59 eagakeaaalvqslaskCPdtkivlgGYSqGaqvidnaieggatatlpaavadkv 113
                                     +g++ +++ v++  +   d+k+v+ GYSq a++i+n i+    +++ +   d++
  gi|121636072|ref|YP_976295.1| 202 TEGVALLNTTVNNQLA--LDNKVVAFGYSQSATIINNYINS--LMAMGSPNPDDI 252
                                    5555555555555444..49******************998..444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3338.84
//
Query:       gi|121636073|ref|YP_976296.1|  [L=449]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-55  186.5   0.0    9.7e-55  185.9   0.0    1.3  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    3.1e-34  117.7   5.9    5.8e-34  116.8   5.9    1.4  1  FAD_binding_4  FAD binding domain
    0.00038   20.2   0.4     0.0007   19.4   0.4    1.4  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9   0.0   1.6e-58   9.7e-55       1     247 [.     211     444 ..     211     447 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 1.6e-58
                                    --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHH CS
                  FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeel 80 
                                    +p++r++a+++f++++a v+a r +++  +++aalel+d +a  l+++++g+  ++p e+++lllve+++d+ ++ ++ +
  gi|121636073|ref|YP_976296.1| 211 TPSHRVTAVCGFAELAALVDAGRMFRDV-EGIAALELIDGRAAALTREHLGV--RPPVEADWLLLVELAADH-DQTDRLA 286
                                    599*************************.***********************..******************.6666667 PP

                                    HH.HHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH.. CS
                  FAD-oxidase_C  81 ea.lveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyg.. 157
                                         ++++++ +++      d+a++++lw+ R+++ +     +l+ ++ +l++D+s+P+s+++ + rd+ al++++   
  gi|121636073|ref|YP_976296.1| 287 DLlGGARMCGEPAVGV-----DAAAQQRLWRTRESLAE-----VLGVYGPPLKFDVSLPLSAISGFARDAVALVHRHVpd 356
                                    7657788888888887.....*****************.....9************************************ PP

                                    ...EEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHH CS
                  FAD-oxidase_C 158 ...levvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrr 234
                                       +   lfgH+g+gnlhl++l      +  +r  +l+++++ l++e+gG++s EHGvG +k+ayl ++++ +++a+mrr
  gi|121636073|ref|YP_976296.1| 357 speALPLLFGHIGEGNLHLNVLR-----CPPDREPALYAKMMGLIAECGGNVSSEHGVGSRKRAYLGMSRQANDVAAMRR 431
                                    **********************9.....78889999******************************************** PP

                                    HHHHH-TT--BST CS
                  FAD-oxidase_C 235 iKaalDPkgiLNP 247
                                    +KaalDP g+LN 
  gi|121636073|ref|YP_976296.1| 432 VKAALDPTGYLNA 444
                                    ************6 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   5.9   9.6e-38   5.8e-34       2     137 ..      37     173 ..      36     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 9.6e-38
                                    EEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   2 aavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    +a+vrp+s+eeva++lr++++ag+ v+v+Gg +sl+ + v + ++v+l+++rl  + ++d  e++++++aGvtl+++++a
  gi|121636073|ref|YP_976296.1|  37 SALVRPGSAEEVAEVLRVCRDAGAYVTVQGGRTSLVAGTVpEHDDVLLSTERLCVVSDVDTVERRIEIGAGVTLAAVQHA 116
                                    689*********************************777669************************************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvr 137
                                    ++ +gl++g++ ++ +++tvGG+ +tnagG +  +yG++ ++v+gl+v l+dG+v+r
  gi|121636073|ref|YP_976296.1| 117 ASTAGLVFGVDLSARDTATVGGMASTNAGGLRTVRYGNMGEQVVGLDVALPDGTVLR 173
                                    *******************************************************86 PP

>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   1.2e-07    0.0007       5     110 ..      39     138 ..      34     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                                    EEE-SSHHHHHHHHHH...CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHHH CS
                  FAD_binding_5   5 ylrpasleealallaa...epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaaea 81 
                                    ++rp s ee++++l+          v Gg + +v  +      + l++ +++  +++++  e+ +eiGA+vtl+++  +a
  gi|121636073|ref|YP_976296.1|  39 LVRPGSAEEVAEVLRVcrdAGAYVTVQGGRTSLVAGTVPE-HDDVLLSTERLCVVSDVDTVERRIEIGAGVTLAAVQ-HA 116
                                    6788888888888877665667778889988888888777.469********************************3.33 PP

                                    HHHHHHHHSHHHHHTSS-HHHHHH-BHHH CS
                  FAD_binding_5  82 lvrerypalsealekiAspqiRnvaTiGG 110
                                    +        +  l  + +   R +aT+GG
  gi|121636073|ref|YP_976296.1| 117 A-------STAGLVFGVDLSARDTATVGG 138
                                    3.......345666777778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3284.29
//
Query:       gi|121636074|ref|YP_976297.1|  [L=383]
Description: zinc-type alcohol dehydrogenase (e subunit) adhE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-26   90.0   1.5    1.9e-25   88.9   1.5    1.6  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.9e-16   60.2   0.1    3.9e-16   59.2   0.1    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    7.8e-07   28.8   0.1    1.6e-06   27.8   0.1    1.4  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    3.1e-06   28.3   0.0    6.7e-06   27.2   0.0    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   1.5   4.1e-29   1.9e-25       2     109 .]      48     174 ..      47     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 4.1e-29
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                    gevl++++aag+C+sDl +++g     ++ p+ lGHE++G+ve+vg++v++++vG+rVv+ +l  cg+CaaC ++ ++ C
  gi|121636074|ref|YP_976297.1|  48 GEVLVRIEAAGVCHSDLSVVDG--TRVRPVPILLGHEAAGIVEQVGDGVDGVAVGQRVVLVFLPRCGQCAACATDGRTPC 125
                                    79*******************9..68999*************************************************** PP

                                    ........................TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                          ADH_N  82 ........................eeakllgvsldGgfaeyvvvpekklvkl 109
                                                            + ++ lgvs   gfa++vvv+++++v++
  gi|121636074|ref|YP_976297.1| 126 epgsaankagtllgggirlsrggrPVYHHLGVS---GFATHVVVNRASVVPV 174
                                    999999988888888888877766666666666...8899999998888875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   8.8e-20   3.9e-16       1     127 [.     216     339 ..     212     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 8.8e-20
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    gvG+aav  A  +   +v+avd  +ekl  ak lGa+e+++++        ++  gg ++ vv+e+vG++a+l +a+ l+
  gi|121636074|ref|YP_976297.1| 216 GVGMAAVLTALTYTDvRVVAVDQLPEKLSAAKALGAHEIYTPQ--------QATAGGVKAAVVVEAVGHPAALHTAIGLT 287
                                    8999999999955545**************************3........3444688999******************* PP

                                    EEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSC..HHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgs..lreefkealdl 127
                                    +pgGr  +vG++  +    +++ +++ + +s++Gs lgs  +++++++++ l
  gi|121636074|ref|YP_976297.1| 288 APGGRTITVGLPPPDVRisLSPLDFVTEGRSLIGSYLGSavPSHDIPRFVSL 339
                                    ***********555454237777799*************9888888887665 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   3.6e-10   1.6e-06      32     205 ..     207     370 ..     201     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.6e-10
                    Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTGsa 111
                                    +s+ v+G G +G+ a  +l+a   ++++v v++  + p  ++   ++lGa  + +   p  + ++   +  +vvEa G++
  gi|121636074|ref|YP_976297.1| 207 QSVAVVGLGGVGMAA--VLTA--LTYTDVRVVAVDQLP-EKLSAAKALGAHEIYT---PQ-QATAGGVKAAVVVEAVGHP 277
                                    6899********988..7765..68999*999975555.57889******88754...43.3445678999********* PP

                    Glu_dehyd_C 112 khafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsv.Nanr.rhfeaavdtLaalpeslldelvtkv 189
                                    +++  ai   ap G ++ +G+p +  v +  + l  ++v e + l+Gs   + + +h      +L +  +  +++lvt+ 
  gi|121636074|ref|YP_976297.1| 278 AALHTAIGLTAPGGRTITVGLPPPD-VRISLSPL--DFVTEGRSLIGSYlGSAVpSHDIPRFVSLWQSGRLPVESLVTST 354
                                    **********************997.78888777..89**********6234441444445667777777789******* PP

                    Glu_dehyd_C 190 vdldeleeAfedddet 205
                                    + ld+++eA ++  + 
  gi|121636074|ref|YP_976297.1| 355 IRLDDINEAMDHLADG 370
                                    *******999876655 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.5e-09   6.7e-06       1     125 [.     249     370 ..     249     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.5e-09
                                    TT-SEEEETTSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----...S-EEE-CHHHCTTT-EEEE--G CS
                   ADH_zinc_N_2   1 lGAdevidyrtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpp..lsaallkpakkrkgrsvkyefl 78 
                                    lGA+e++  + ++++  +gg +  vv+++vg +a+l+ ++ + ++gGr +++g pp  ++  l+++ +  +grs+  + l
  gi|121636074|ref|YP_976297.1| 249 LGAHEIY--TPQQAT--AGGVKAAVVVEAVGHPAALHTAIGLTAPGGRTITVGLPPpdVRISLSPLDFVTEGRSLIGSYL 324
                                    7888876..433332..3566799*******999989999999888*******666587777788888777777777777 PP

                                    GG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS CS
                   ADH_zinc_N_2  79 fsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesg 125
                                     s+ +s  +d + + + l ++G+  ++  v+++  l++++eA+++l+ g
  gi|121636074|ref|YP_976297.1| 325 GSAVPS--HD-IPRFVSLWQSGRlpVESLVTSTIRLDDINEAMDHLADG 370
                                    754444..66.************6667889***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2711.76
//
Query:       gi|121636075|ref|YP_976298.1|  [L=151]
Description: hypothetical protein BCG_0199 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-14   52.1   0.0    9.7e-14   51.5   0.0    1.3  1  4HBT         Thioesterase superfamily
    7.4e-11   42.6   0.0    9.7e-11   42.2   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
      3e-05   23.4   0.0     0.0061   15.9   0.1    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.6e-17   9.7e-14       1      76 [.      31     111 ..      31     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.6e-17
                                    TSSB-HHHHHHHHHHHHHHHHHHTTST.....TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                           4HBT   1 gGvvhgGvylallDeaagaalrslggr.....gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                    +G+++++vy++l+D+a  a++++  g        l  v+e  +++++  r+++ l+v   v+rlgr+s++++  v++e++
  gi|121636075|ref|YP_976298.1|  31 FGHLNNAVYYQLFDTAINAWINTSTGVdplamPVLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVTYRLGVFKEPD 110
                                    7*****************************************************************************98 PP

                                    C CS
                           4HBT  76 r 76 
                                     
  gi|121636075|ref|YP_976298.1| 111 D 111
                                    6 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.6e-14   9.7e-11       2     120 ..      24     141 ..      23     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.6e-14
                         4HBT_2   2 rpndvDlnghlnnarylryleearvkfle.rtglksrsiarrgiglilssahvryrrplkfpdrltvefrvididaktli 80 
                                    r+ d D++ghlnna y + +++a+  ++   tg++  +++   ++ i++++ +ry ++l+fp+ l v + v++  ++++ 
  gi|121636075|ref|YP_976298.1|  24 RWADNDMFGHLNNAVYYQLFDTAINAWINtSTGVDPLAMP---VLGIVAESGCRYFSELRFPESLMVGLAVTRLGRSSVT 100
                                    899*************************644444444444...78899******************************** PP

                         4HBT_2  81 iehrfls.nadgkk.aarveerivvmdygkrskkapvPpell 120
                                        + + ++d++  +a ++ ++v++d+++r +++p+P++++
  gi|121636075|ref|YP_976298.1| 101 YRLGVFKePDDAGViTALGHWVHVYVDRTSR-RPVPIPEAIR 141
                                    *999999777777799**************9.******9986 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     1e-06    0.0061     161     181 ..      23      43 ..      12      58 .. 0.84
   2 !    5.8   0.0    0.0012       7.4     100     132 ..     113     145 ..      81     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                    Acyl-ACP_TE 161 vrysDlDlnqHvNNvkYlewi 181
                                     r++D D+++H+NN++Y +  
  gi|121636075|ref|YP_976298.1|  23 TRWADNDMFGHLNNAVYYQLF 43 
                                    69***************9865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0012
                    Acyl-ACP_TE 100 gekiieaksvfvl..mdqetrrlsrvtdeilaeye 132
                                    g  +i+a   +v+  +d+ +rr++ +++ i++ ++
  gi|121636075|ref|YP_976298.1| 113 G--VITALGHWVHvyVDRTSRRPVPIPEAIRSLLS 145
                                    3..77777777763379************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1250.21
//
Query:       gi|121636076|ref|YP_976299.1|  [L=161]
Description: hypothetical protein BCG_0200 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-13   49.2   0.0    8.6e-13   48.6   0.0    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    3.2e-07   30.7   0.1    4.1e-07   30.4   0.1    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.047   13.8   0.2      0.065   13.4   0.2    1.3  1  DUF1997          Protein of unknown function (DUF1997)


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.4e-16   8.6e-13       1     130 []      25     152 ..      25     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.4e-16
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE.....E..EEECSTTSSCEEEEEEEEEEETTTEEECT.TCCCCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes..glsa..dlevgfggltesftarvtldppeeitfkl.vegdfk 75 
                                    v a+a++++a+vad+e+ype++ +++ + vl++ ++        +l  + +g+  ++   v+   +++i+  +  + +f 
  gi|121636076|ref|YP_976299.1|  25 VTADAASIMAIVADIERYPEWNEGVKGAWVLARYDDgrP--SqvRLDTAVQGIEGTYIHAVYYPGENQIQTVMqQGELFA 102
                                    689********************************8652..145667777777777777777777777443330344777 PP

                                    EEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  76 slegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldellaale 130
                                    + e   +++  +    ++ ++v ++v+  +++p+++++v++++++vl++l+++l+
  gi|121636076|ref|YP_976299.1| 103 KQEQLFSVVATGA---ASLLTVDMDVQ--VTMPVPEPMVKMLLNNVLEHLAENLK 152
                                    7777777777766...78777777755..59********************9985 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   6.9e-11   4.1e-07       4     142 ..      19     155 ..      16     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.9e-11
                                    EEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEE.ECSE..STSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE CS
                Polyketide_cyc2   4 vtvsvviaappekVwalvsdfenwprWhpevarv.eleg..gggpargvegtvrvggrgtvreelvevdpegrllsyriv 80 
                                    ++++v++ a+++ + a+v+d e +p+W ++v+ +  l+    g p ++v+  ++v+g    +     + p +  ++  ++
  gi|121636076|ref|YP_976299.1|  19 LSKTVEVTADAASIMAIVADIERYPEWNEGVKGAwVLARydDGRP-SQVRLDTAVQG-IEGTYIHAVYYPGENQIQTVMQ 96 
                                    689*****************************9942333312444.66668888999.5678888888899999999996 PP

                                    .SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  81 kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarl 142
                                    +   +a+ +  ++v ++g+ + +t ++++++     p+ +p+++ ++   le   e+Lk+r+
  gi|121636076|ref|YP_976299.1|  97 QGELFAKQEQLFSVVATGAASLLTVDMDVQV---TMPVPEPMVKMLLNNVLEHLAENLKQRA 155
                                    67888889999****************9995...3444455566666666666666666666 PP

>> DUF1997  Protein of unknown function (DUF1997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.1e-05     0.065      99     143 ..     119     156 ..      62     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                        DUF1997  99 legdldlkvsvelppflallPesllestgnsvlkqvlkqvkprlt 143
                                    l+  +d+ v+v        +Pe+++++  n+vl+ + +++k+r  
  gi|121636076|ref|YP_976299.1| 119 LT--VDMDVQV-----TMPVPEPMVKMLLNNVLEHLAENLKQRAE 156
                                    22..2222222.....2347999*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1311.58
//
Query:       gi|121636077|ref|YP_976300.1|  [L=271]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-20   73.2   5.6    4.8e-20   72.2   5.6    1.4  1  FCD       FCD domain
    1.4e-13   50.2   0.2      3e-13   49.2   0.2    1.6  1  GntR      Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.066   12.6   0.0       0.14   11.5   0.0    1.5  2  RtcR      Regulator of RNA terminal phosphate cyclase
       0.08   12.7   0.1        0.3   10.9   0.0    2.0  3  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.081   12.6   0.0       0.14   11.8   0.0    1.4  1  HTH_41    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   5.6   1.4e-23   4.8e-20       1     115 [.     133     245 ..     133     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.4e-23
                            FCD   1 dlyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlr 80 
                                    d+++l+a++  e+a  a+ ++td +++el++++ al+ a+++gd + +a +++aFHr++++a+++  la++l + ++++ 
  gi|121636077|ref|YP_976300.1| 133 DIFWLQATIAQELATSATAHITDVEIDELDRINNALAGAIGSGDAKTIASIEFAFHRVFNKASRRIKLAWFLLNAARYMP 212
                                    89****************************************************************************** PP

                            FCD  81 rlrrlalssperleeslaeHraildAirardadaA 115
                                    ++   a  +p++ ++++  Hr++++A+r+rd +a+
  gi|121636077|ref|YP_976300.1| 213 AQVFAA--DPRWGADAVNSHRQLIAALRRRDTAAV 245
                                    988887..************************997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.2   8.4e-17     3e-13       1      64 []      61     123 ..      61     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 8.4e-17
                                    HHHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR   1 lyeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64 
                                    l+++v+ +Lr+ I+sg lr G+ + +  e aae+gVs t+vReAL +L  eg+v  ++ rG +V
  gi|121636077|ref|YP_976300.1|  61 LSDEVAGHLRAAIMSGALRSGTFI-RLDETAAELGVSVTPVREALLKLRGEGMVGLEPHRGHVV 123
                                    5789********************.***********************************9876 PP

>> RtcR  Regulator of RNA terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1     4e+03     145     167 ..     144     166 ..     137     169 .. 0.70
   2 ?   11.5   0.0     4e-05      0.14     119     144 ..     199     224 ..     192     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                           RtcR 145 eeeaagkyeiiDldLsrydkiae 167
                                    e +++++ +i D+++ + d+i++
  gi|121636077|ref|YP_976300.1| 144 ELATSATAHITDVEIDELDRINN 166
                                    44566777888888888888865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4e-05
                           RtcR 119 qiclfLltearylParllqtsPpkke 144
                                    ++++fLl  ary+Pa++  + P+   
  gi|121636077|ref|YP_976300.1| 199 KLAWFLLNAARYMPAQVFAADPRWGA 224
                                    689****************9999332 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.2e-05       0.3       1      43 [.      70     112 ..      70     125 .. 0.85
   2 ?   -2.9   0.0       1.6   5.8e+03       3      19 ..     139     155 ..     138     156 .. 0.76
   3 ?   -2.6   0.0       1.3   4.7e+03       2      18 ..     230     246 ..     230     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.2e-05
                       HTH_DeoR   1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgl 43 
                                    R + +   l++ ++++++e +++lgvS + +R  L +L  +g+
  gi|121636077|ref|YP_976300.1|  70 RAAIMSGALRSGTFIRLDETAAELGVSVTPVREALLKLRGEGM 112
                                    5666777899999*******************99999998887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                       HTH_DeoR   3 eqilellkqqgklsvee 19 
                                    + i + l+ + + ++++
  gi|121636077|ref|YP_976300.1| 139 ATIAQELATSATAHITD 155
                                    67888898888888876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                       HTH_DeoR   2 ieqilellkqqgklsve 18 
                                    + q++  l+++++  v 
  gi|121636077|ref|YP_976300.1| 230 HRQLIAALRRRDTAAVI 246
                                    56888899999888775 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.14       9      43 ..      86     121 ..      82     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                         HTH_41   9 IeelakeleLSvGlvQkALklLeddkaisle.rrGr 43 
                                     +e a el++Sv  v  AL +L  +++++le  rG+
  gi|121636077|ref|YP_976300.1|  86 LDETAAELGVSVTPVREALLKLRGEGMVGLEpHRGH 121
                                    68999*************************956888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1925.52
//
Query:       gi|121636078|ref|YP_976301.1|  [L=554]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     1e-103  347.2   0.0   1.2e-103  347.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    5.6e-18   65.7   0.1    1.8e-17   64.1   0.1    1.9  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.0   0.0  1.3e-107  1.2e-103       1     422 [.      32     436 ..      32     437 .. 0.87

  Alignments for each domain:
  == domain 1  score: 347.0 bits;  conditional E-value: 1.3e-107
                                    HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                    le++a  +pd++al +   g+t+T+++l++rv +lA +L  +Gv+ gdrV+il+ n+ e+v ++la+ ++Ga++vpln +
  gi|121636078|ref|YP_976301.1|  32 LERHAMMQPDAPALRF--VGNTMTWADLRRRVAALAGALSGRGVGFGDRVMILMLNRTEFVESVLAANMIGAIAVPLNFR 109
                                    589999********99..9*********************88************************************** PP

                                    S-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTS CS
                    AMP-binding  81 ltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpdd 160
                                    lt+ e+a ++ed+ a v++  ++++l++ +  ++   +   +viv+  ++++++  +  e+  +e+ ++ +e++ + +d+
  gi|121636078|ref|YP_976301.1| 110 LTPTEIAVLVEDCAAHVML--TEAALAPVAIGVRN-IQPLLSVIVVAGGSSQDS-VFGYEDLLNEA-GDVHEPVDIPNDS 184
                                    *******************..66555444444443.334445555555554444.33333333333.2356777899*** PP

                                    EEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC CS
                    AMP-binding 161 layiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaa 239
                                    +a+i+YT GTTG+PKG++l+h+nl+ ++ ++ l+t   ++ ++dv ++ +pl+hi+g+  ++l+ ll G   v++p  a 
  gi|121636078|ref|YP_976301.1| 185 PALIMYTAGTTGRPKGAVLTHANLTGQAMTA-LYTSgANI-NSDVGFVGVPLFHIAGI-GNMLTGLLLGLPTVIYPLGA- 260
                                    ***************************9996.45443444.58999999********7.*****************775. PP

                                    CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEE CS
                    AMP-binding 240 ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGl 317
                                    +dp++ll+++e++kvt i++vP+ ++a+   ++a+      +d  +lr++  g++p + +llr+++a+f+e ++l ++G+
  gi|121636078|ref|YP_976301.1| 261 FDPGQLLDVLEAEKVTGIFLVPAQWQAVCTeQQARP-----RD-LRLRVLSWGAAPAPDALLRQMSATFPEtQILAAFGQ 334
                                    5999**********************8866354333.....24.34888777**************************** PP

                                    GGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEE CS
                    AMP-binding 318 TEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlr 397
                                    TE+++v+++l  e+  +k+gsvG+++p v +++vD++ ++ vp ge+Ge++ r p++m++Y+++peataeaf   g+w++
  gi|121636078|ref|YP_976301.1| 335 TEMSPVTCMLLGEDAIAKRGSVGRVIPTVAARVVDQN-MNDVPVGEVGEIVYRAPTLMSCYWNNPEATAEAFA--GGWFH 411
                                    *******998889999********************9.**********************************8..57*** PP

                                    EEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 398 TGDlgrldedGyleivgRkkdlikl 422
                                    +GDl+r+d dGy+++v+Rkkd+i++
  gi|121636078|ref|YP_976301.1| 412 SGDLVRMDSDGYVWVVDRKKDMIIS 436
                                    ***********************96 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.1     2e-21   1.8e-17       1      76 []     445     519 ..     445     519 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2e-21
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E++l+shp++ae+aV+G  de++Ge+++a+    ++ ++  e+L ++++++l+ y+ pk++++vd+lp++  GK
  gi|121636078|ref|YP_976301.1| 445 ELENVLASHPDIAEVAVIGRADEKWGEVPIAVAAVTND-DLRIEDLGEFLTDRLARYKHPKALEIVDALPRNPAGK 519
                                    89******************************998423.3358********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3922.09
//
Query:       gi|121636079|ref|YP_976302.1|  [L=265]
Description: integral membrane protein YrbE1a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-56  190.6  25.3    3.2e-56  190.4  25.3    1.1  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4  25.3   1.8e-60   3.2e-56       1     211 [.      46     256 ..      46     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 1.8e-60
                           MlaE   1 lveqlefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtm 80 
                                    ++ q++f++   ++++++++++++++l++ +  +l+qfga +  gs  a+  v +lgP++t l+vag+ ++ai+A+lG++
  gi|121636079|ref|YP_976302.1|  46 FILQCWFIMRVGFLPTIMVSIPLTVLLIFTLNILLAQFGAADISGSGAAIGAVTQLGPLTTVLVVAGAGSTAICADLGAR 125
                                    578***************************************************************************** PP

                           MlaE  81 rvteeidAlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgll 160
                                    +++eeidA+ev+gidpi++lvvPrvlA+++++ lL+ ++++vg++gg+l++v+l+++s gayl++++ ++ l++++++ +
  gi|121636079|ref|YP_976302.1| 126 TIREEIDAMEVLGIDPIHRLVVPRVLASMLVATLLNGLVITVGLVGGFLFGVYLQNVSGGAYLATLTLITGLPEVVIATI 205
                                    ******************************************************************************** PP

                           MlaE 161 KalvfGliialiacyqGltakggaegvgrattravvtsivlilvvdlvltl 211
                                    Ka+ fGli +l++cy+Glt++gg++g+g+a++++vv +++++++v+++lt 
  gi|121636079|ref|YP_976302.1| 206 KAATFGLIAGLVGCYRGLTVRGGSKGLGTAVNETVVLCVIALFAVNVILTT 256
                                    *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1861.95
//
Query:       gi|121636080|ref|YP_976303.1|  [L=289]
Description: integral membrane protein YrbE1b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-50  170.8  25.8    3.8e-50  170.5  25.8    1.1  1  MlaE      Permease MlaE
  ------ inclusion threshold ------
        4.9    7.2   8.5       0.48   10.4   0.1    3.1  3  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5  25.8   4.2e-54   3.8e-50       5     210 ..      70     275 ..      66     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 4.2e-54
                           MlaE   5 lefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtmrvte 84 
                                    +++v+++++ iv++++l  + ++a+qg+  l ++g+e+++g++ al+ vr  gPv+t++ +a+ vG++ +AelG+mr++e
  gi|121636080|ref|YP_976303.1|  70 AMAVVGGTVAIVGFVTLSGSSLVAIQGFASLGNIGVEAFTGFFAALINVRIAGPVVTGVALAATVGAGATAELGAMRISE 149
                                    5788999************************************************************************* PP

                           MlaE  85 eidAlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllKalv 164
                                    eidAlevmgi++i++l  +r++A++++++ L+++a+++++l+  +++++l+g+s g+y +++q++l++ d+++++l al+
  gi|121636080|ref|YP_976303.1| 150 EIDALEVMGIKSISFLASTRIMAGLVVIIPLYALAMIMSFLSPQITTTVLYGQSNGTYEHYFQTFLRPDDVFWSFLEALI 229
                                    ******************************************************************************** PP

                           MlaE 165 fGliialiacyqGltakggaegvgrattravvtsivlilvvdlvlt 210
                                    + +i+++ +cy+G++a+gg+ gvg+a+ r++  s+v + vv l+ +
  gi|121636080|ref|YP_976303.1| 230 ITAIVMVSHCYYGYAAGGGPVGVGEAVGRSMRFSLVSVQVVVLFAA 275
                                    **************************************99988765 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8      0.29   2.6e+03      15      23 ..      78      86 ..      71     121 .. 0.67
   2 ?   10.4   0.1   5.4e-05      0.48       9      38 ..     163     192 ..     160     215 .. 0.84
   3 ?    0.3   0.1     0.076   6.8e+02      17      33 ..     264     280 ..     259     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.29
                         OppC_N 15 lAvvglvil 23
                                   +A+vg+v l
  gi|121636080|ref|YP_976303.1| 78 VAIVGFVTL 86
                                   455555544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.4e-05
                         OppC_N   9 rFkrNklAvvglvilllllliaifaPliaP 38 
                                    +F+   + ++glv+++ l+++a +  +++P
  gi|121636080|ref|YP_976303.1| 163 SFLASTRIMAGLVVIIPLYALAMIMSFLSP 192
                                    68889999*************988877766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.076
                         OppC_N  17 vvglvilllllliaifa 33 
                                    +v+  +++l++++a+++
  gi|121636080|ref|YP_976303.1| 264 LVSVQVVVLFAALALYG 280
                                    56666677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2027.07
//
Query:       gi|121636081|ref|YP_976304.1|  [L=454]
Description: MCE-family protein mce1A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.2e-109  365.7   0.2   1.6e-109  365.3   0.2    1.2  1  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
      6e-14   52.1   0.1    1.2e-13   51.2   0.1    1.5  1  MlaD       MlaD protein


Domain annotation for each model (and alignments):
>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.3   0.2  1.8e-113  1.6e-109       1     257 []     154     454 .]     154     454 .] 0.99

  Alignments for each domain:
  == domain 1  score: 365.3 bits;  conditional E-value: 1.8e-113
                      Mce4_CUP1   1 enllplleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLd 80 
                                    ++l++++e+vdP+kLn tLsA+aeAL+G+G+++Ges++++n+vLd+lN+r+pq r+di++la+l+dvYadaapdl+d+Ld
  gi|121636081|ref|YP_976304.1| 154 QTLTSIAEKVDPVKLNLTLSAAAEALTGLGDKFGESIVNANTVLDDLNSRMPQSRHDIQQLAALGDVYADAAPDLFDFLD 233
                                    799***************************************************************************** PP

                      Mce4_CUP1  81 navttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLakYspeltCllrnladvepkvakal 160
                                    ++vtt+rTi++qqaeLd++llaa+g++nt+ad+++r+g++L+r++adl+pt++lL++Yspel+C++rn+ d++p +++a+
  gi|121636081|ref|YP_976304.1| 234 SSVTTARTINAQQAELDSALLAAAGFGNTTADVFDRGGPYLQRGVADLVPTATLLDTYSPELFCTIRNFYDADPLAKAAA 313
                                    *******************************************************************************9 PP

                      Mce4_CUP1 161 ggtngyslrld...............................................atlllgarnpYvypedlPrvna 193
                                    gg+ngyslr++                                                +++ ga+npY+ype+lPrvna
  gi|121636081|ref|YP_976304.1| 314 GGGNGYSLRTNseilsgigisllsplalatngaaigiglvagliasplavaanlagalPGIVGGAPNPYTYPENLPRVNA 393
                                    999******99**********************************************9999******************* PP

                      Mce4_CUP1 194 kgGPggapgcgslqditrd.wperelvsdtlapagvsiap..hleigvPawaeYvvgrqvgslligP 257
                                    +gGPggapgc  +q+itrd wp+++lv+dt    g+s+ap  h+e+g+P+++eYv+grqvg+++i+P
  gi|121636081|ref|YP_976304.1| 394 RGGPGGAPGC--WQPITRDlWPAPYLVMDT----GASLAPynHMEVGSPYAVEYVWGRQVGDNTINP 454
                                    **********..******************....99999999************************9 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1   1.3e-17   1.2e-13       3      79 ..      45     124 ..      43     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.3e-17
                           MlaD   3 ytvtaqfdnang.LkvgapVryrGvtvGrVtsi.tldp.dtrrvtvtvdldkksetsipedsraqvstggllgekyiald 79 
                                     ++t+   +a+  + +g++V+y+Gv++GrV++i ++    +  +++ +d+d++++ +ip+++ a ++ ++++g+ky++l+
  gi|121636081|ref|YP_976304.1|  45 TQLTMLSARAGLvMDPGSKVTYNGVEIGRVDTIsEVTRdGESAAKFILDVDPRYIHLIPANVNADIKATTVFGGKYVSLT 124
                                    5678888899999********************65555355555**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3235.62
//
Query:       gi|121636082|ref|YP_976305.1|  [L=346]
Description: MCE-family protein mce1B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-19   68.1   0.2    1.2e-18   67.2   0.2    1.5  1  MlaD           MlaD protein
    1.4e-06   28.0   4.4    1.8e-06   27.6   3.8    1.3  1  Mce4_CUP1      Cholesterol uptake porter CUP1 of Mce4, putati
     0.0036   16.8   0.0     0.0051   16.3   0.0    1.1  1  FAM92          FAM92 protein
  ------ inclusion threshold ------
      0.029   14.1   0.1       0.04   13.6   0.1    1.1  1  DUF745         Protein of unknown function (DUF745)
      0.033   14.6   0.4        7.2    7.1   0.2    2.3  2  DASH_Dad2      DASH complex subunit Dad2
      0.076   12.9   0.5        0.1   12.5   0.5    1.1  1  SIKE           SIKE family
       0.11   10.9   0.4       0.14   10.6   0.4    1.2  1  Hemagglutinin  Haemagglutinin
       0.18   11.8   0.1       0.31   11.1   0.1    1.3  1  Sipho_Gp157    Siphovirus Gp157
        0.2   11.9   0.3       0.83    9.9   0.3    2.0  2  DASH_Dad1      DASH complex subunit Dad1


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.2   5.9e-22   1.2e-18       3      80 ..      37     112 ..      35     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 5.9e-22
                           MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    + +ta+f+n++gL +g+ Vr +Gv++G+V++++l + +rrv+v++++d   +++++++++aq++ ++l+g++y++l+ 
  gi|121636082|ref|YP_976305.1|  37 NGYTAEFSNVSGLRQGQFVRASGVEIGKVKALHLVDGGRRVRVEFNID--RSVPLYQSTTAQIRYSDLIGNRYVELKR 112
                                    569*********************************************..*************************986 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   3.8     9e-10   1.8e-06       5     126 ..     148     269 ..     146     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9e-10
                      Mce4_CUP1   5 plleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavt 84 
                                    p+ +a dPak n + +A+ + ++G+G  + ++l++  ++ +++ +r   + e +++l+ + d+  +  +++ ++++n+  
  gi|121636082|ref|YP_976305.1| 148 PVFRALDPAKVNNIANALITVFQGQGGTINDTLDQTAQLTSQIAERDQAIGEVVKNLNIVLDTTVKHRKEFDETVNNLEN 227
                                    7899**************************************************************************** PP

                      Mce4_CUP1  85 tsrTiveqqaeLdalllaavglsntgadllerngdnLirlaa 126
                                      + + +++++L+  l+++ + + t+adll++n++ + ++++
  gi|121636082|ref|YP_976305.1| 228 LITGLRNHSDQLAGGLAHISNGAGTVADLLAENRTLVRKAVS 269
                                    *********************************987766665 PP

>> FAM92  FAM92 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.5e-06    0.0051      10     117 ..     176     283 ..     169     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                          FAM92  10 letkddrvkilneavsivekhlgelcsifalvvrktaklrdkadelvkevkayadde.eineklcqGlksfadevaklqd 88 
                                    +++  d++ +l  +++  ++ +ge+ + + +v   t k r ++de v++++       +   +l+ Gl   ++    + d
  gi|121636082|ref|YP_976305.1| 176 INDTLDQTAQLTSQIAERDQAIGEVVKNLNIVLDTTVKHRKEFDETVNNLENLITGLrNHSDQLAGGLAHISNGAGTVAD 255
                                    667779********************************************998776505557899********9999999 PP

                          FAM92  89 yrdieverleakvveelktyetlvkskrd 117
                                       +e + l  k v  l   ++ v  +r 
  gi|121636082|ref|YP_976305.1| 256 LL-AENRTLVRKAVSYLDAIQQPVIDQRV 283
                                    87.56677888888888888777666665 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-05      0.04      66     175 ..     185     298 ..     180     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                         DUF745  66 qleqelreaeavvqeekkslq....sseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqll 141
                                    ql+++++e ++++ e+ k+l+    ++ +  k   +++++ ++ ++ l++  ++    l+++ + a  ++  lae ++l+
  gi|121636082|ref|YP_976305.1| 185 QLTSQIAERDQAIGEVVKNLNivldTTVKHRKEFDETVNNLENLITGLRNHSDQLAGGLAHISNGAGTVADLLAENRTLV 264
                                    777788888777777777665111166677777777777778888888888888888899******************** PP

                         DUF745 142 eaAkkRveeLkkqlkearkdlektkkaAykAacA 175
                                     +A + ++ +++ + + r +l++  +++  A +A
  gi|121636082|ref|YP_976305.1| 265 RKAVSYLDAIQQPVIDQRVELDDLLHKTPTALTA 298
                                    ***************9999999887777777666 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0036       7.2      19      58 ..     171     210 ..     163     224 .. 0.86
   2 ?    5.8   0.0    0.0093        19      13      58 ..     221     266 ..     212     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                      DASH_Dad2  19 dlsdslakqleeLeeklstladgteavasVlanWqnvlra 58 
                                     + +++++ l++ ++  s++a+  +a+ +V++n + vl +
  gi|121636082|ref|YP_976305.1| 171 GQGGTINDTLDQTAQLTSQIAERDQAIGEVVKNLNIVLDT 210
                                    566789999*************************999976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0093
                      DASH_Dad2  13 aLkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlra 58 
                                    + ++l++l   l++  ++L+  l+ +++g+ +va+ la+  + +r 
  gi|121636082|ref|YP_976305.1| 221 TVNNLENLITGLRNHSDQLAGGLAHISNGAGTVADLLAENRTLVRK 266
                                    5677888888888999999999999999999999998877666554 PP

>> SIKE  SIKE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   5.2e-05       0.1       3      96 ..     175     274 ..     174     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                           SIKE   3 tieqiladakkLverLkehdtaAdsLleqaq.alnkkiesmkqyqeevkelneiak.ekprseL....iagiqqenrqir 76 
                                    ti+  l ++ +L++++ e+d+a  +++++ +  l++ ++  k++ e v++l++     + +s+     +a+i++    + 
  gi|121636082|ref|YP_976305.1| 175 TINDTLDQTAQLTSQIAERDQAIGEVVKNLNiVLDTTVKHRKEFDETVNNLENLITgLRNHSDQlaggLAHISNGAGTVA 254
                                    7899999***************99999999626788999999*********97666567777651222356888999*** PP

                           SIKE  77 eLqqENreLrasleehqsaL 96 
                                    +L  ENr L      + +a+
  gi|121636082|ref|YP_976305.1| 255 DLLAENRTLVRKAVSYLDAI 274
                                    *******9976655555555 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   6.9e-05      0.14     368     435 ..     192     262 ..     163     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                                    HHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                  Hemagglutinin 368 stqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvdd...gfldvityniellvlleneri 435
                                       +ai ++ k++n + +  +k+ +   + +n+le+ i  l ++ d    g + +      ++ ll ++r+
  gi|121636082|ref|YP_976305.1| 192 ERDQAIGEVVKNLNIVLDTTVKHRKEFDETVNNLENLITGLRNHSDQlagGLAHISNGAGTVADLLAENRT 262
                                    4578********************************99988877665111344444444445555555555 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00015      0.31      24      83 ..     172     234 ..     156     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                    Sipho_Gp157  24 eeeeikdtLesle...eeieeKaeniakviknleaeaeaikeeekrLaerkkslenkaenLKe 83 
                                    + ++i+dtL++ +   ++i+e+ + i+ v+knl+   +   ++ k+++e    len +  L++
  gi|121636082|ref|YP_976305.1| 172 QGGTINDTLDQTAqltSQIAERDQAIGEVVKNLNIVLDTTVKHRKEFDETVNNLENLITGLRN 234
                                    3469*****8755555******************************************99998 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   3.4e+03      33      47 ..      35      49 ..      32      49 .. 0.78
   2 ?    9.9   0.3   0.00041      0.83       5      43 ..     182     220 ..     180     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                      DASH_Dad1 33 eviavgkeFesVaaL 47
                                    +++ + eF++V+ L
  gi|121636082|ref|YP_976305.1| 35 RTNGYTAEFSNVSGL 49
                                   5677789*****976 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00041
                      DASH_Dad1   5 qRdrliqeIaesmeevlnnlnaLNRsLEeviavgkeFes 43 
                                    q ++l+++Iae  + + + +  LN+ L+++++  keF++
  gi|121636082|ref|YP_976305.1| 182 QTAQLTSQIAERDQAIGEVVKNLNIVLDTTVKHRKEFDE 220
                                    56799********************************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2430.64
//
Query:       gi|121636083|ref|YP_976306.1|  [L=515]
Description: MCE-family protein mce1C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-11   44.1   0.1    3.1e-11   43.4   0.1    1.4  1  MlaD          MlaD protein
    6.9e-06   25.7   1.6    3.3e-05   23.5   1.7    1.9  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
     0.0036   17.5   0.5       0.14   12.4   0.2    2.3  2  DUF948        Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.016   15.7   1.2          3    8.4   0.1    2.3  2  NPV_P10       Nucleopolyhedrovirus P10 protein
      0.067   13.6   0.0       0.33   11.4   0.0    2.2  1  PLAC9         Placenta-specific protein 9
      0.082   13.0   0.1       0.28   11.2   0.1    1.8  2  DUF1664       Protein of unknown function (DUF1664)
       0.77    9.8   5.2        2.2    8.3   5.0    1.7  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   1.2e-14   3.1e-11       3      80 ..      40     112 ..      38     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-14
                           MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                      ++ qf++++gL++g++Vr++G+ vG+V+ +++  d++++ v++++    ++ i + sr  ++t ++lg k+++++p
  gi|121636083|ref|YP_976306.1|  40 PSYYGQFTDSGGLHKGDRVRIAGLGVGTVEGLKI--DGDHIVVKFSIG---TNTIGTESRLAIRTDTILGRKVLEIEP 112
                                    57899***************************99..************...999**********************98 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.7   1.3e-08   3.3e-05      19     157 ..     158     295 ..     150     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                      Mce4_CUP1  19 LsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLda 98 
                                    L+ ++e ++    +l  +l+ + ++ d++ +r +q+++ + + +++a + +d ++++ + L na t  ++ +e+ +++da
  gi|121636083|ref|YP_976306.1| 158 LNVLSETVDQTYPHLSAALDGVAKFSDTIGKRDEQITHLLAQANQVASILGDRSDQVDRLLVNAKTLIAAFNERGRAVDA 237
                                    566666666666677778888889999999************************************************** PP

                      Mce4_CUP1  99 lllaavglsntgadllerngdnLirlaadlrptlelLakYspeltCllrnladvepkva 157
                                    ll ++  +s ++++l+++n +nL +++++lr  ++lL + ++ l+ +l+ l ++  +++
  gi|121636083|ref|YP_976306.1| 238 LLGNISAFSAQVQNLINDN-PNLNHVLEQLRILTDLLVDRKEDLAETLTILGRFSASFG 295
                                    **************99887.9***************99888877777766666665555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.012        30      29      80 ..     152     203 ..     148     207 .. 0.72
   2 !   12.4   0.2   5.4e-05      0.14      30      87 ..     195     252 ..     186     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                         DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                    + +++++++l + vd++   + ++l+ v +  + + ++ e++ +l ++++++
  gi|121636083|ref|YP_976306.1| 152 ETVKRSLNVLSETVDQTYPHLSAALDGVAKFSDTIGKRDEQITHLLAQANQV 203
                                    4566777777777777777777777777777777777888888877777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.4e-05
                         DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    ++ a+ +++ + ++  +++v++ll ++++l +  ne+  +vd+l  ++   +++v++l
  gi|121636083|ref|YP_976306.1| 195 HLLAQANQVASILGDRSDQVDRLLVNAKTLIAAFNERGRAVDALLGNISAFSAQVQNL 252
                                    5667788888889999999************************************998 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0067        17      12      66 ..     150     208 ..     149     217 .. 0.85
   2 ?    8.4   0.1    0.0012         3      12      63 ..     234     285 ..     232     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0067
                        NPV_P10  12 dikavddkVdalqqqvdd....vqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                    di+ v+  +++l++ vd+    +++ l  v + ++ + +  +q+++l ++ +++ +iL 
  gi|121636083|ref|YP_976306.1| 150 DIETVKRSLNVLSETVDQtyphLSAALDGVAKFSDTIGKRDEQITHLLAQANQVASILG 208
                                    8999999999999999653333899999999**********************999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                        NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                    ++ a+   ++a ++qv+++ ++ p+++++ e+L  +++ L + ++ + +   
  gi|121636083|ref|YP_976306.1| 234 AVDALLGNISAFSAQVQNLINDNPNLNHVLEQLRILTDLLVDRKEDLAETLT 285
                                    6778888999**************************9999887776665555 PP

>> PLAC9  Placenta-specific protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.33      22      48 ..     153     179 ..     140     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                          PLAC9  22 avqsrldvieetvektvehleaevkGl 48 
                                    +v++ l+v+ etv++t  hl a + G+
  gi|121636083|ref|YP_976306.1| 153 TVKRSLNVLSETVDQTYPHLSAALDGV 179
                                    7999******************99886 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.28      34     113 ..     142     221 ..     134     231 .. 0.86
   2 ?    4.4   0.1     0.014        37      43     117 ..     186     263 ..     180     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                    vTk      +e+v ++l+ +se++ +t  hLs+ +d v k  d   +  ++i++ ++++++  s +g+ +++v+++  + 
  gi|121636083|ref|YP_976306.1| 142 VTKAASGWDIETVKRSLNVLSETVDQTYPHLSAALDGVAKFSDTIGKRDEQITHLLAQANQVASILGDRSDQVDRLLVNA 221
                                    677777777899**********************************************9999999999999999877665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                        DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeike...evtevredlseigedvesvkeavegleskl 117
                                    + +  +q++++ ++ +++   L +r d+vd+ l + k ++++ +e    v+++ +++s+++ +v+++ +   +l++ l
  gi|121636083|ref|YP_976306.1| 186 IGKRDEQITHLLAQANQVASILGDRSDQVDRLLVNAKTLIAAFNErgrAVDALLGNISAFSAQVQNLINDNPNLNHVL 263
                                    444456788888888888889999999999999888888877765111677777777777777777766555566555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.19   4.9e+02      41      68 ..     152     179 ..     144     204 .. 0.51
   2 ?    8.3   5.0   0.00086       2.2      42     111 ..     192     266 ..     158     285 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.19
                   Baculo_PEP_C  41 daietqLnalsedlksllaeldtrldtl 68 
                                    ++++++Ln lse + +  ++l+++ld +
  gi|121636083|ref|YP_976306.1| 152 ETVKRSLNVLSETVDQTYPHLSAALDGV 179
                                    4555555555555555555555544432 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00086
                   Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinstLnnl 111
                                    +i   L a ++++ s l + ++++d ll n ++ ++a++      d+l  ++ +  +++ nL ++ +N+n  L+ l
  gi|121636083|ref|YP_976306.1| 192 QITHLL-AQANQVASILGDRSDQVDRLLVNAKTLIAAFNergravDALLGNISAFSAQVQNLINDNPNLNHVLEQL 266
                                    222222.223345555555666999999999999999999999999999999999***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 3499.52
//
Query:       gi|121636084|ref|YP_976307.1|  [L=530]
Description: MCE-family protein mce1D [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-13   49.3   0.2    1.7e-12   47.4   0.0    2.0  2  MlaD          MlaD protein
    1.1e-06   28.3   1.6    2.1e-06   27.4   1.6    1.4  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
  ------ inclusion threshold ------
       0.02   14.7   0.1      0.033   13.9   0.1    1.4  1  RIX1          rRNA processing/ribosome biogenesis
       0.28   11.2   8.0        5.7    7.0   0.5    2.4  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   3.8e-16   1.7e-12       3      80 ..      47     120 ..      45     121 .. 0.97
   2 ?   -1.0   0.0      0.51   2.3e+03      23      33 ..     435     445 ..     434     452 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.8e-16
                           MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    +tv+a+f++an L vg++V+++G++vG++++i  +p +++++vt+  +   + ++p++++a + + +l+ ++ i+l+p
  gi|121636084|ref|YP_976307.1|  47 NTVVAYFTQANALYVGDKVQIMGLPVGSIDKI--EPAGDKMKVTFHYQ--NKYKVPANASAVILNPTLVASRNIQLEP 120
                                    79******************************..88************..**************************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                           MlaD  23 yrGvtvGrVts 33 
                                    ++Gv+vG +t+
  gi|121636084|ref|YP_976307.1| 435 MQGVQVGPITQ 445
                                    89*****9986 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   1.6   4.7e-10   2.1e-06      18     135 ..     173     291 ..     169     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.7e-10
                      Mce4_CUP1  18 tLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLd 97 
                                    +++A+a++L+G+G+++ ++l+ l + L++lN+   ++ + +r+la + ++ ++  ++++   +n++  ++ +++  a+L+
  gi|121636084|ref|YP_976307.1| 173 VIEAFADGLAGKGKQINTTLNSLSQALNALNEGRGDFFAVVRSLALFVNALHQDDQQFVALNKNLAEFTDRLTHSDADLS 252
                                    789***************************************************************************** PP

                      Mce4_CUP1  98 alllaavglsntgadllerngdnLirlaadlrp.tlelL 135
                                    +++++  +l   ++ ++++n++ L++ +++l   t++lL
  gi|121636084|ref|YP_976307.1| 253 NAIQQFDSLLAVARPFFAKNREVLTHDVNNLATvTTTLL 291
                                    *************************99999876144454 PP

>> RIX1  rRNA processing/ribosome biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   7.5e-06     0.033      98     160 ..     240     311 ..     218     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.5e-06
                           RIX1  98 p.....dppavlelaistlsriftltrgkptltREiltpnlpkfitallqlleee....letvlealstllp 160
                                          +++a l+ ai+  + ++  +r + +  RE+lt+ + +++t   +ll+ +    letvl+++ tl  
  gi|121636084|ref|YP_976307.1| 240 FtdrltHSDADLSNAIQQFDSLLAVARPFFAKNREVLTHDVNNLATVTTTLLQPDpldgLETVLHIFPTLAA 311
                                    35555566778999***************************************7799999999998887765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0013       5.7     104     121 ..     188     205 ..     175     208 .. 0.89
   2 ?    6.0   2.7    0.0026        12      34     104 ..     231     313 ..     211     318 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                   Baculo_PEP_C 104 instLnnllqalnnldlg 121
                                    in+tLn+l qaln+l++g
  gi|121636084|ref|YP_976307.1| 188 INTTLNSLSQALNALNEG 205
                                    999**********99987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0026
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldt.......rldtlltnLtdalnalq...dtlrn..eLtnlnsiltnLlssv 101
                                     +l++ l++   +L++ ++dl+++++++d+        ++++ + Lt+ +n+l+   +tl +   L++l+++l    +  
  gi|121636084|ref|YP_976307.1| 231 VALNKNLAEFTDRLTHSDADLSNAIQQFDSllavarpFFAKNREVLTHDVNNLAtvtTTLLQpdPLDGLETVLHIFPTLA 310
                                    45555555555555555555555555555555555557888888888888888755444432123566666665544444 PP

                   Baculo_PEP_C 102 tNi 104
                                    +Ni
  gi|121636084|ref|YP_976307.1| 311 ANI 313
                                    555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 3670.46
//
Query:       gi|121636085|ref|YP_976308.1|  [L=390]
Description: mce family lipoprotein LprK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-11   44.3   0.0      3e-11   43.4   0.0    1.5  1  MlaD          MlaD protein
  ------ inclusion threshold ------
      0.011   15.8   2.1      0.093   12.8   0.5    2.3  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
      0.012   15.1   0.7      0.022   14.2   0.6    1.5  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
      0.077   12.3   0.0       0.11   11.8   0.0    1.2  1  TMEM132       Transmembrane protein family 132
       0.15   12.3   0.1       0.41   10.9   0.0    1.8  2  DUF948        Bacterial protein of unknown function (DUF948)
       0.17   11.8   1.6       0.45   10.4   1.6    1.8  1  LPAM_2        Prokaryotic lipoprotein-attachment site


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0     1e-14     3e-11       2      79 ..      51     124 ..      50     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1e-14
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyiald 79 
                                    +yt+++q+++   ++ +++V+++ v vG++++i+l   +  +t+t++l+  +++ +p++++a++ +++llg++ ++l 
  gi|121636085|ref|YP_976308.1|  51 SYTIYVQMPDTLAINGNSRVMVADVWVGSIRAIKL--KNWVATLTLSLK--KDVTLPKNATAKIGQTSLLGSQHVELA 124
                                    79*********************************..999999999999..************************986 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   3.1e-05     0.093      46     114 ..     169     236 ..     150     243 .. 0.74
   2 ?    2.6   0.0     0.044   1.3e+02      42      80 ..     246     284 ..     224     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                   Baculo_PEP_C  46 qLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqa 114
                                    +L+ +++++++ ++  ++++ ++l +L++   +l+   d+++ +++++n     Ll+ v++  + Ln +l++
  gi|121636085|ref|YP_976308.1| 169 NLEGIQQEINAIVTGRADQIRAFLGKLDTFTDELNqqrDDITRAIDSTNR----LLAYVGGRSEVLNRVLTD 236
                                    5999***********************99999999666677777777765....555666666666666655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.044
                   Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                    + ++ L + s+++ +l+++ d+ l+++   L++ l+alq
  gi|121636085|ref|YP_976308.1| 246 DKQELLINASDAVGRLSQSADQYLSAARGDLHQDLQALQ 284
                                    445556677888888888888888888888888888887 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   7.5e-06     0.022      26     141 ..     181     296 ..     170     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                      Mce4_CUP1  26 LeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavg 105
                                    ++Gr +++   l +l+++ delN++ +++++ i + ++l +  +  ++ l ++L+++    +  +++q+ L ++  a+  
  gi|121636085|ref|YP_976308.1| 181 VTGRADQIRAFLGKLDTFTDELNQQRDDITRAIDSTNRLLAYVGGRSEVLNRVLTDLPPLIKHFADKQELLINASDAVGR 260
                                    78999*************************************************************************** PP

                      Mce4_CUP1 106 lsntgadllerngdnLirlaadlrptlelLakYspe 141
                                    ls+++ + l++ + +L + +++l+  l+ L + +p 
  gi|121636085|ref|YP_976308.1| 261 LSQSADQYLSAARGDLHQDLQALQCPLKELRRAAPY 296
                                    ****************99999998877777666665 PP

>> TMEM132  Transmembrane protein family 132
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.11     198     270 ..      46     120 ..      34     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                        TMEM132 198 GrevGrtevqVlsplsdsvlgekevrvlddkv.siteLsv.qvvsglslslspssgseraivattsaqevltaek 270
                                    G  +G+ ++ V  p + ++ g++ v v d  v si+++++ + v+ l+lsl+++ +  + ++a++  ++ l +++
  gi|121636085|ref|YP_976308.1|  46 GTGPGSYTIYVQMPDTLAINGNSRVMVADVWVgSIRAIKLkNWVATLTLSLKKDVTLPKNATAKIGQTSLLGSQH 120
                                    7899***********************************8357999*********99999999999998887776 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.41      21      85 ..     167     231 ..     157     235 .. 0.90
   2 ?   -2.9   0.0       2.9   8.7e+03      39      55 ..     255     271 ..     240     284 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                         DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    l++l+ + +e++a +++  +q+++ l ++++ +++ n+  +d+++ +++ ++l + v+  +e ++
  gi|121636085|ref|YP_976308.1| 167 LVNLEGIQQEINAIVTGRADQIRAFLGKLDTFTDELNQQRDDITRAIDSTNRLLAYVGGRSEVLN 231
                                    67888999999999**************************************9999988887765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                         DUF948  39 ekqvdpilkevedllak 55 
                                     + v+ +++ +++ l+ 
  gi|121636085|ref|YP_976308.1| 255 SDAVGRLSQSADQYLSA 271
                                    34444445555554444 PP

>> LPAM_2  Prokaryotic lipoprotein-attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.6   0.00015      0.45       2      18 ..      19      35 ..      19      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                         LPAM_2  2 llllallllLaGCGqKG 18
                                   l+ll+l+llL+ CG +G
  gi|121636085|ref|YP_976308.1| 19 LVLLVLALLLSSCGWRG 35
                                   79************665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2970.34
//
Query:       gi|121636086|ref|YP_976309.1|  [L=515]
Description: MCE-family protein mce1F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-17   62.4   0.2    6.4e-17   61.6   0.2    1.4  1  MlaD       MlaD protein
    7.2e-05   22.4   0.7    0.00012   21.7   0.7    1.2  1  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
     0.0011   19.2   0.1        1.6    9.1   0.0    2.5  2  DUF948     Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.2   1.1e-20   6.4e-17       2      79 ..      39     112 ..      38     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.1e-20
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyiald 79 
                                     yt++a ++ ++gL + a+V+yrG+t+G+Vt++  +p++++++vt+++   s+ +ip d++a v++ + +ge+yi+l+
  gi|121636086|ref|YP_976309.1|  39 QYTLKADLPASGGLYPTANVTYRGITIGKVTAV--EPTDQGARVTMSIA--SNYKIPVDASANVHSVSAVGEQYIDLV 112
                                    69*******************************..88************..*************************97 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.7     2e-08   0.00012      10     140 ..     150     280 ..     146     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-08
                      Mce4_CUP1  10 vdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTi 89 
                                       +k+   L  +a+A+ G+G  l + ++  ++++ ++ +++ ++++ i++   + d   +  +++ +  +++   ++  
  gi|121636086|ref|YP_976309.1| 150 LPTEKIGLLLDETAQAVGGLGPALQRLVDSTQAIVGDFKTNIGDVNDIIENSGPILDSQVNTGDQIERWARKLNNLAAQT 229
                                    56788999999************************************************************999999999 PP

                      Mce4_CUP1  90 veqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLakYsp 140
                                    +++ ++++++l++a+ ++++++ +++  +d+L +++a+l+   ++L++Y+ 
  gi|121636086|ref|YP_976309.1| 230 ATRDQNVRSILSQAAPTADEVNAVFSGVRDSLPQTLANLEVVFDMLKRYHA 280
                                    99***********************************************85 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00027       1.6      20      85 ..     151     216 ..     146     220 .. 0.89
   2 !    8.2   0.1   0.00048       2.9      26      76 ..     220     274 ..     210     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                         DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    +  k++ +lde+a+++ +l+  ++ +++ +++++   ++   dvn+ +e+  p+ ++  ++g++++
  gi|121636086|ref|YP_976309.1| 151 PTEKIGLLLDETAQAVGGLGPALQRLVDSTQAIVGDFKTNIGDVNDIIENSGPILDSQVNTGDQIE 216
                                    56688889**************************************99999999999888888775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00048
                         DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvne....klekvdpltea 76 
                                    + l+++aa+ ++  ++v++il +++ + ++vn++ ++v++     l++++ +++ 
  gi|121636086|ref|YP_976309.1| 220 RKLNNLAAQTATRDQNVRSILSQAAPTADEVNAVFSGVRDslpqTLANLEVVFDM 274
                                    5566777777777788888888888888888888888877444455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3691.32
//
Query:       gi|121636087|ref|YP_976310.1|  [L=213]
Description: mce associated membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1479.21
//
Query:       gi|121636088|ref|YP_976311.1|  [L=322]
Description: mce associated transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.8   8.3    3.9e-16   59.5   8.3    1.7  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   8.3   2.2e-20   3.9e-16       2     139 ..      21     143 ..      20     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.2e-20
                            RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllgl 81 
                                    a +  R +Af+iD++  l++ +  al +       + +++a+ ++ + ll+l  +l+l+v  lll   +g++lG+ l+g+
  gi|121636088|ref|YP_976311.1|  21 APWHVRAGAFAIDVLPGLAVAATMALTALT-----VPPGSAWRWLCACLLGL-TILLLAVNRLLLPTITGWSLGRALTGI 94 
                                    78999**********988887776666666.....44555555544444443.344555666666666************ PP

                            RDD  82 kvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDkl 139
                                    +vv++dg+ +g +++l+R l          +lv  l l++g+l++l++++r+++ D+l
  gi|121636088|ref|YP_976311.1|  95 RVVRRDGSAIGPWRLLVRDL---------AHLVDTLSLFVGWLWPLWDSRRRTFADLL 143
                                    ********************.........9**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2357.11
//
Query:       gi|121636089|ref|YP_976312.1|  [L=184]
Description: mce associated protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1352.00
//
Query:       gi|121636090|ref|YP_976313.1|  [L=244]
Description: MCE associated membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1738.00
//
Query:       gi|121636091|ref|YP_976314.1|  [L=369]
Description: lipoprotein lprO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.9   0.6    6.5e-08   33.0   0.6    1.9  1  NAGPA     Phosphodiester glycosidase


Domain annotation for each model (and alignments):
>> NAGPA  Phosphodiester glycosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.6   3.6e-12   6.5e-08       5     167 ..     150     366 ..     147     369 .] 0.54

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.6e-12
                          NAGPA   5 aavnGgffdpksgg...........plglvisdgkilkkangeeaagalait............................ 45 
                                    +avn++ffd + ++           plg ++ + +             +                               
  gi|121636091|ref|YP_976314.1| 150 IAVNANFFDVRGQKggswrstgcssPLGAYVDNTRGQG---------RANQAvtgtvayagkqglsggnelwsslttmil 220
                                    78999999999887888885555554444444332222.........222220001111122222222233332323333 PP

                          NAGPA  46 .kdgklvv.slqeldeanvkeavgagplLvkngkivktsadggs................................grap 91 
                                      +g+++v + ++++++++ +                                                        +a+
  gi|121636091|ref|YP_976314.1| 221 pVGGAPYVlRPKSRQDYDLATP---------------------ViedllnknarfvavagigllspgntgqlhdggPSAA 279
                                    3444444443333333333333.....................22233333333334444444444455556677679** PP

                          NAGPA  92 RtaiGvtadgtllllvvdgrqsaGatlkelaellkklGavnAlnLDGGgSttmvv..............egkv.innp.s 155
                                    Rta+++ +++  +++   g      t + +++l++ lG ++A+ LDGGgS++ v+              +g+   ++  +
  gi|121636091|ref|YP_976314.1| 280 RTALAYAKQKDEMYIFQGG----NYTPDNIQDLFRGLGSDTAILLDGGGSSAIVLrrdtggmwagagspKGSCdTRQVlC 355
                                    *******999888888776....799999999**99******************98887766655555433332222213 PP

                          NAGPA 156 daegerpvanal 167
                                    d+  er++++ l
  gi|121636091|ref|YP_976314.1| 356 DSH-ERALPSWL 366
                                    333.66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2547.04
//
Query:       gi|121636092|ref|YP_976315.1|  [L=452]
Description: hypothetical protein BCG_0217c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-46  157.3   0.2    6.2e-46  157.0   0.2    1.1  1  DUF3533          Protein of unknown function (DUF3533)
    6.3e-16   58.4  11.5      2e-15   56.8  11.5    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
      0.005   16.3  22.2      0.005   16.3  22.2    3.2  3  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> DUF3533  Protein of unknown function (DUF3533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.2     1e-49   6.2e-46       5     376 ..      32     403 ..      28     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 1e-49
                        DUF3533   5 lavlilails.lywGalyrrsdrlknlnvlvVneDeggseltpvvgeavaqainettssslgtwtvvnpsefkeseeeve 83 
                                    +++  +++l+ ly G+++++ ++l+++++++VneD g     p+ +++v+ +++ +  +++ +++vv       s++e +
  gi|121636092|ref|YP_976315.1|  32 TTLALMSALAaLYLGGILNPMTNLRHFPIALVNEDAG-----PAGQQIVDGLVSGLD-KNKFDIRVV-------SPDEAR 98 
                                    55666777766**************************.....888888888888888.578888888.......699*** PP

                        DUF3533  84 elvhkekywgaivvkenateklyaalsangassynstelleliyesgRdattvssyilpaltqleaaalakygsqllqql 163
                                    +l+++  ++g+  +++ ++++l++   a+  +++++ + + +i +++R  t  +s+  ++lt   ++++ k+g++l+ ++
  gi|121636092|ref|YP_976315.1|  99 RLLDTAAVYGSALIPPTFSSQLRDFG-ASAVTPTRTDRPAITISTNPRAGTLAASIAGQTLTRALTVVNGKVGERLTAEV 177
                                    *************************9.8888899999***********7555556666777777777777********** PP

                        DUF3533 164 iqslsntaqaaqlsnallaspiafnsidlrPftdgvalaplqvgliyliiltffq.........faflgklhaemg.... 230
                                    ++++   a a   + a laspi+++s  ++P+++g++ +++++++++l++l++f+         +++lg++ ae+g    
  gi|121636092|ref|YP_976315.1| 178 AAQTGGVALAGA-AAAGLASPIDVKSTAYNPLPNGTGNGLSAFYYALLLLLAGFTgsivvstlvDSMLGYVPAEFGpvyr 256
                                    ***998777776.4458***********************************************************9887 PP

                        DUF3533 231 ..lsrkl.kfkqllvyrllisvvslfvlSlffslvslafqvdftvafGragFvvyWmitwlvmaavglanenvasilgpp 307
                                       + ++ +f++ l+++++++vv+++  S ++ ++   +++++++ +       +W++ +++++avg++  +++++lg  
  gi|121636092|ref|YP_976315.1| 257 faEQVNIsRFRT-LLVKWAVMVVLALLTSGVYLAIAHGLGMPIPLGW------QVWLYGVFAIIAVGVTSSSLIAVLGSM 329
                                    443334434444.666***************************4443......56************************* PP

                        DUF3533 308 ylpvwllfwvilNvss..tfvPlelspgFYrygyal.PlhniveilrvI.ffdtak.gqlgrnlgiLlawvvvn 376
                                    +l+v +l++vil ++s  ++vPle+ p+F+r+++++ P+h+++ ++r+  ++++ + + l ++l+++ + ++++
  gi|121636092|ref|YP_976315.1| 330 GLLVSMLIFVILGLPSagATVPLEAVPAFFRWLAQFePMHQVFLGVRSLlYLNGNAdAGLSQALTMTSIGLIIG 403
                                    ****************999******************************8777777699999999988877765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8  11.5   3.3e-19     2e-15      10     343 ..      36     407 ..      30     410 .. 0.67

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 3.3e-19
                ABC2_membrane_3  10 lPiilvlllglifsnsveddentpiavvdednsslsqqlvealea...spsvelvyevdseeeakkalkngdidgilvip 86 
                                    l+  l++l++  + n  ++ ++ pia+v+ed  +  qq+v+ l +    ++++  ++v s +ea+++l+   ++g   ip
  gi|121636092|ref|YP_976315.1|  36 LMSALAALYLGGILNPMTNLRHFPIALVNEDAGPAGQQIVDGLVSgldKNKFD--IRVVSPDEARRLLDTAAVYGSALIP 113
                                    443444443333344455899***********999999997777653234477..9************************ PP

                ABC2_membrane_3  87 kgfskdll..................kgesatvtvlinssnlnsskailnalns.llqqlnasalv.............. 133
                                      fs +l                    ++++ + +l  s   ++ + +l  +n+ +                        
  gi|121636092|ref|YP_976315.1| 114 PTFSSQLRdfgasavtptrtdrpaitISTNPRAGTLAASIAGQTLTRALTVVNGkVG--------Erltaevaaqtggva 185
                                    ****9999*******987554444444444444444444444444555555554333........122233344666787 PP

                ABC2_membrane_3 134 .lqseatstsaninvestql...eeelsnvasflvgliliilifitasfiav........siveE..kesrikelqlvsg 199
                                         a+  + +i+v+st++   ++ + n  s ++ ++l++l+ +t+s++++        ++  E     r  e+     
  gi|121636092|ref|YP_976315.1| 186 lAGAAAAGLASPIDVKSTAYnplPNGTGNGLSAFYYALLLLLAGFTGSIVVStlvdsmlgYVPAEfgPVYRFAEQVN--- 262
                                    75666666778888888887777777766666666677777778888877773444433333355225668999975... PP

                ABC2_membrane_3 200 vsplqywlskilgdflvyllqlllilllafglgipfg....nlglllllfllfglayialgyllsslfknsetaqilifi 275
                                    +s++  +l+k   +++++ll++ ++l++a glg+p+      +++ ++ ++  g ++++l+++l+s+      + ++ ++
  gi|121636092|ref|YP_976315.1| 263 ISRFRTLLVKWAVMVVLALLTSGVYLAIAHGLGMPIPlgwqVWLYGVFAIIAVGVTSSSLIAVLGSM------GLLVSML 336
                                    66**************************655435554414333444444555555555555555543......4555555 PP

                ABC2_membrane_3 276 villlsgffggl.fpledlpsalkwifsiiPffapglgllrli..tgdplweillsliilalfavvyllla 343
                                    ++++l++ ++g  +ple++p +++w++ + P+++++lg  +l+  +g+  + + ++l++  +  ++ lll+
  gi|121636092|ref|YP_976315.1| 337 IFVILGLPSAGAtVPLEAVPAFFRWLAQFEPMHQVFLGVRSLLylNGNADAGLSQALTMTSIGLIIGLLLG 407
                                    555666666666478***************************96655533445588888888888888875 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2     0.082   4.9e+02     160     185 ..      30      55 ..      15      63 .. 0.64
   2 !   16.3  22.2   8.3e-07     0.005      55     210 .]     227     380 ..     202     380 .. 0.78
   3 ?    0.8   0.1     0.045   2.7e+02      23      42 ..     389     408 ..     382     432 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.082
                  ABC2_membrane 160 dasqlaslvllpllllsGffipidsm 185
                                     a++la +  l  l+l+G++ p +++
  gi|121636092|ref|YP_976315.1|  30 IATTLALMSALAALYLGGILNPMTNL 55 
                                    45566666666666666666666655 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.3e-07
                  ABC2_membrane  55 llffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflfl 134
                                    l +f+   ++ +++ s+  +++ e g ++r       s++  +l k++v+++++ll + ++l+i++ l g+++  ++ ++
  gi|121636092|ref|YP_976315.1| 227 LAGFTGSIVVSTLVDSMLGYVPAEFGPVYRFAEQVNISRFRTLLVKWAVMVVLALLTSGVYLAIAHGL-GMPIPLGWQVW 305
                                    4444444444456777778899999999999999999******************************9.99997346666 PP

                  ABC2_membrane 135 llllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                    l+ ++ ++a+   +  ++a++ s+   + +  +v+l  l  +G+ +p++++p +++w+a++ P+  ++ ++rs l+
  gi|121636092|ref|YP_976315.1| 306 LYGVFAIIAVGVTSSSLIAVLGSMGLLVSMLIFVILG-LPSAGATVPLEAVPAFFRWLAQFEPMHQVFLGVRSLLY 380
                                    6666666666666666666666666666666655555.4778*****************************99875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.045
                  ABC2_membrane  23 lwrliqplllalvfgtvfgn 42 
                                    l++ +++  ++l++g++ g+
  gi|121636092|ref|YP_976315.1| 389 LSQALTMTSIGLIIGLLLGG 408
                                    44555555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3301.07
//
Query:       gi|121636093|ref|YP_976316.1|  [L=244]
Description: hypothetical protein BCG_0218c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-38  128.8   0.3    1.2e-37  128.2   0.3    1.2  1  Pirin      Pirin
    1.8e-07   31.2   0.0    3.7e-07   30.2   0.0    1.5  1  Pirin_C_2  Quercetinase C-terminal cupin domain
  ------ inclusion threshold ------
      0.016   14.9   0.4        1.2    8.9   0.1    2.5  2  Cupin_2    Cupin domain


Domain annotation for each model (and alignments):
>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.3   1.9e-41   1.2e-37       5     108 .]      12     122 ..       7     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 1.9e-41
                                    CCGTCC.TTCCEECTCEECCEEESS.S.ETT.....EEEE..T-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT CS
                          Pirin   5 rralgkaaelqsvdpFlfldefdpaelevge.....edvi..gagfpphphrgletvtylleGevehrDslGnkgvirpG 77 
                                    +ra++++++l+s+++F+f d++dp+++++g      +d++  + gf+phphr++e+vt++l+G+++h+Ds+Gn+gvi+pG
  gi|121636093|ref|YP_976316.1|  12 DRAVTTTSWLKSRHSFSFGDHYDPDNTHHGLllvnnDDQMepASGFDPHPHRDMEIVTWVLRGALRHQDSAGNSGVIYPG 91 
                                    5777889*********************999999999999999************************************* PP

                                    -EEEEE-TT-EEEEEEE-SSSS-EEEEEEEE CS
                          Pirin  78 dvqwmtAgsGivhsEmneeeeesleglqlWv 108
                                     +q+m+Ag+Gi+hsEmn++++e+++++q+Wv
  gi|121636093|ref|YP_976316.1|  92 LAQRMSAGTGILHSEMNDSATEPVHFVQMWV 122
                                    ******************************8 PP

>> Pirin_C_2  Quercetinase C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.1e-11   3.7e-07       7      86 .]     156     235 ..     149     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.1e-11
                      Pirin_C_2   7 grdgslkinQ.darlyaakldegesleyelaagrkaYlqvieGevevn.geslaagDGlaiedesslsltaeedaevLlf 84 
                                    g+d +l+++  +a+l+ a+l++g ++++  a+   + l+v+ G+++++ g +la+gD++ ++d+++  lta+e++evL+ 
  gi|121636093|ref|YP_976316.1| 156 GQDAALTLHNsSASLHGARLRPGATVSLPCAPF--LHLFVAYGRLTLEgGGELADGDAVRFTDADARGLTANEPSEVLIW 233
                                    7889999975279******************98..99**********8357***************************97 PP

                      Pirin_C_2  85 Dl 86 
                                    ++
  gi|121636093|ref|YP_976316.1| 234 EM 235
                                    75 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0002       1.2       5      67 ..      51     117 ..      48     123 .. 0.77
   2 ?    3.7   0.0    0.0084        50      24      55 ..     192     220 ..     190     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                                    EETTEEEEEECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT..-EEEEEE-SSS.-EEE CS
                        Cupin_2   5 lppGesapshrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpag..tpHrfrNtgde.parl 67 
                                    ++p   + +h H++ + +  Vl+G ++ +   g+  ++ +G +    ag    H   N++ + p+++
  gi|121636093|ref|YP_976316.1|  51 MEPASGFDPHPHRDMEIVTWVLRGALRHQdSAGNSGVIYPGLAQRMSAGtgILHSEMNDSATePVHF 117
                                    78888999*******99*********99977788888888877777776445666666666656666 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0084
                                    EEEESEEEEEECTEEEEEETTEEEEE-TT-EE CS
                        Cupin_2  24 yVleGegeltvdgeeveleaGdsvyfpagtpH 55 
                                    +V  G+++l+ +ge   l +Gd+v f      
  gi|121636093|ref|YP_976316.1| 192 FVAYGRLTLEGGGE---LADGDAVRFTDADAR 220
                                    78889999999999...******999765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1740.96
//
Query:       gi|121636094|ref|YP_976317.1|  [L=370]
Description: RNA polymerase factor sigma-70 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-20   72.3   2.1    2.5e-20   72.0   0.4    2.0  2  Sigma70_r2      Sigma-70 region 2
    9.5e-15   54.0   0.2    2.1e-14   52.9   0.2    1.6  1  Sigma70_r4_2    Sigma-70, region 4
    1.8e-08   34.9   0.4    6.5e-08   33.2   0.2    2.1  2  SnoaL_2         SnoaL-like domain
    1.1e-06   28.0   0.2    1.9e-06   27.3   0.2    1.4  1  Sigma70_r4      Sigma-70, region 4
    3.5e-06   27.2   0.0      6e-06   26.4   0.0    1.4  1  SnoaL_4         SnoaL-like domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.022   15.3   0.0    1.5  1  NTF2            Nuclear transport factor 2 (NTF2) domain
      0.019   15.2   0.0      0.045   14.0   0.0    1.7  2  SnoaL_3         SnoaL-like domain
       0.13   12.5   2.6       0.12   12.5   0.5    2.1  2  Acetyltransf_6  Acetyltransferase (GNAT) domain
       0.39   10.9   1.3        3.6    7.8   0.1    2.5  2  Tetradecapep    Myoactive tetradecapeptides family


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.4   1.3e-23   2.5e-20       3      71 .]      63     129 ..      62     129 .. 0.97
   2 ?   -1.6   0.1       1.2   2.4e+03      17      27 ..     245     255 ..     220     270 .. 0.64

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.3e-23
                                    HHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST. CS
                     Sigma70_r2   3 erylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrrr 71 
                                    e y++ +++ ++r++gs +daeDlvQe++lr+w+a e f  +++ s+++wl+ria+n+++++l  rrrr
  gi|121636094|ref|YP_976317.1|  63 EPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFA-GKS-SLRTWLHRIATNTCLTALEGRRRR 129
                                    689*************************************.***.******************999985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                    T-THHHHHHHH CS
                     Sigma70_r2  17 lgsgadaeDlv 27 
                                    ++++ +a+Dl+
  gi|121636094|ref|YP_976317.1| 245 APDSPEAQDLL 255
                                    44555555554 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.2     1e-17   2.1e-14       2      54 .]     180     232 ..     179     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1e-17
                                    HHHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   2 qalrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    +a+ +al++L++rqr+++llr++ +++ +E+A  +g+s ++V+s l+RAr +L
  gi|121636094|ref|YP_976317.1| 180 LAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQL 232
                                    68899*********************************************987 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   5.5e+03      41      61 ..      93     115 ..      53     135 .. 0.57
   2 !   33.2   0.2   3.2e-11   6.5e-08       2      75 ..     256     331 ..     255     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                                    HHHHHHHH..HEEEEEEEEEEEE CS
                        SnoaL_2  41 affralfa..afpdlrfeihdvv 61 
                                    ++++a+    +++ lr  +h+++
  gi|121636094|ref|YP_976317.1|  93 RAWKAYEGfaGKSSLRTWLHRIA 115
                                    22333222224455555555554 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 3.2e-11
                                    HHHHHHHHTTCHHHHHHTEEEEEEEEET..TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEE CS
                        SnoaL_2   2 raflaalnagdldalaalfapdvvwedp..ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtg 75 
                                     +++aa++a+d+d+l++lf++++ we p  +g ++G +ai   + +   a++  ++++  ++a+g+ +a+ +   g
  gi|121636094|ref|YP_976317.1| 256 ARYIAAFEAYDIDRLVELFTAEAIWEMPpyTGWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAG 331
                                    69**************************65555***********************************99865544 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   9.5e-10   1.9e-06       1      49 [.     185     233 ..     185     234 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.5e-10
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    aL++L++r+r vl lr +  +  +E+++  g S  +V +++ rA+ +L+
  gi|121636094|ref|YP_976317.1| 185 ALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQ 233
                                    8****************9999************************9996 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0     3e-09     6e-06       8      63 ..     250     304 ..     244     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3e-09
                                    HHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHH CS
                        SnoaL_4   8 aIrdlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalreald 63 
                                    + +dl+ary  +  ++d + l++lFt++a++++++  +g ++g++ai++++++  +
  gi|121636094|ref|YP_976317.1| 250 EAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPY-TGWYQGAQAIVTLIHQQCP 304
                                    679*******************************97.************9998543 PP

>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.1e-05     0.022       2      51 ..     251     300 ..     250     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHH CS
                           NTF2   2 akafvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffr 51 
                                    a+ ++ +Y aa++a+d + l++l++a+a  ++p+   + +g++aI++ + 
  gi|121636094|ref|YP_976317.1| 251 AQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGWYQGAQAIVTLIH 300
                                    677899***************************************98765 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.5     9e+03      35      55 ..      97     117 ..      78     124 .. 0.75
   2 ?   14.0   0.0   2.3e-05     0.045       3      63 ..     253     313 ..     251     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.5
                        SnoaL_3  35 adelltgreevrrslkqifak 55 
                                    a e + g+  +r++l++i  +
  gi|121636094|ref|YP_976317.1|  97 AYEGFAGKSSLRTWLHRIATN 117
                                    567788888888888887766 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.3e-05
                        SnoaL_3   3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfel 63 
                                    +ll+++++a+++ d+d+l++l++ ++++  +  + ++ g +++++ ++q++ +  + +++l
  gi|121636094|ref|YP_976317.1| 253 DLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGWYQGAQAIVTLIHQQCPAYSPGDMRL 313
                                    689*************************9999999999*****999999887766655555 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.4   2.8e+03      44      65 ..      54      73 ..      19      97 .. 0.57
   2 ?   12.5   0.5   5.9e-05      0.12      27     114 ..     263     354 ..     224     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                 Acetyltransf_6 44 rrpdvfadpltraflrdllaal 65
                                   rr + f +++t+ + r+lla++
  gi|121636094|ref|YP_976317.1| 54 RR-GDF-SAHTEPYRRELLAHC 73
                                   22.444.355555556665555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.9e-05
                 Acetyltransf_6  27 dpedleallelf..raqwarr...pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyywlgg 101
                                    ++ d+++l+elf  +a w++      +   ++   ++++ ++a  ++g+ rl  l ++g+p+A++++   + +l ++l  
  gi|121636094|ref|YP_976317.1| 263 EAYDIDRLVELFtaEAIWEMPpytGWYQGAQAIVTLIHQQCPAY-SPGDMRLISLIANGQPAAAMYMRAGDVHLPFQLHV 341
                                    45579999999955567999977544555556666666666666.49*******************98888888899999 PP

                 Acetyltransf_6 102 ydpelaklspgll 114
                                     d +++++s+   
  gi|121636094|ref|YP_976317.1| 342 LDMAADRVSHVVA 354
                                    9999999998655 PP

>> Tetradecapep  Myoactive tetradecapeptides family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.24   4.7e+02       6      11 ..     239     244 ..     236     245 .. 0.88
   2 ?    7.8   0.1    0.0018       3.6       4      12 ..     343     351 ..     342     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.24
                   Tetradecapep   6 aADRIS 11 
                                    aADR S
  gi|121636094|ref|YP_976317.1| 239 AADRLS 244
                                    9***98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                   Tetradecapep   4 DGaADRISH 12 
                                    D aADR+SH
  gi|121636094|ref|YP_976317.1| 343 DMAADRVSH 351
                                    569****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2425.95
//
Query:       gi|121636095|ref|YP_976318.1|  [L=279]
Description: lysophospholipase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-79  266.3   0.1    2.1e-79  266.1   0.1    1.0  1  Hydrolase_4    Serine aminopeptidase, S33
    8.3e-16   59.3   7.1    1.1e-15   58.9   7.1    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.4e-13   50.3   0.2    9.5e-10   38.5   0.3    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.5e-05   24.6   0.1      0.018   14.5   0.0    2.6  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00011   22.1   0.0       0.57    9.9   0.0    2.6  3  Abhydrolase_2  Phospholipase/Carboxylesterase
    0.00014   21.5   0.0      0.015   14.9   0.0    2.7  2  DLH            Dienelactone hydrolase family
     0.0065   16.1   0.1      0.012   15.3   0.0    1.4  2  Esterase       Putative esterase
  ------ inclusion threshold ------
      0.052   12.1   0.2       0.19   10.2   0.0    1.8  2  PAF-AH_p_II    Platelet-activating factor acetylhydrolase, is
       0.19   11.4   0.0       0.32   10.6   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
        0.2   11.8   0.1        1.6    8.9   0.0    2.1  2  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.1   0.1   1.2e-82   2.1e-79       2     239 .]      28     263 ..      27     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 266.1 bits;  conditional E-value: 1.2e-82
                    Hydrolase_4   2 epkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfll 81 
                                    +p+avvvl+HGl+eh++ry+++a++L a+G  +yalDhrGhGrs+gkr+ v+++++y++D++++v  + +e+p+ ++++l
  gi|121636095|ref|YP_976318.1|  28 APQAVVVLAHGLGEHARRYDHVAQRLGAAGLVTYALDHRGHGRSGGKRVLVRDISEYTADFDTLVGIATREYPGCKRIVL 107
                                    799***************************************************************************** PP

                    Hydrolase_4  82 GhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayead 161
                                    GhSmGG i+++y+ ++pd+++ ++lsaPa++ +    ++p++++++kllg ++p l+v ++l+++ +srdpevv+ay++d
  gi|121636095|ref|YP_976318.1| 108 GHSMGGGIVFAYGVERPDNYDLMVLSAPAVAAQDL--VSPVVAVAAKLLGVVVPGLPV-QELDFTAISRDPEVVQAYNTD 184
                                    *******************************9976..9********************.99******************* PP

                    Hydrolase_4 162 plv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEpd 239
                                    plv hg++ +++++ ll++++++ +ra+++t+Pll+lhG++D++++ e+sr+l+e +gs+d++lk ypglyHe++nEp+
  gi|121636095|ref|YP_976318.1| 185 PLVhHGRVPAGIGRALLQVGETMPRRAPALTAPLLVLHGTDDRLIPIEGSRRLVECVGSADVQLKEYPGLYHEVFNEPE 263
                                    *****************************************************************************96 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   7.1     6e-19   1.1e-15       1     215 [.      33     263 ..      33     269 .. 0.65

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6e-19
                                    EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT...........TTSEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhGrsdpppldledladlaalldelaa.........gggpvvlv 70 
                                    v+l+HG+g +a+ +   ++ ++l+aag  ++a+D +GhGrs ++   ++d+ ++    +++++          g++ +++
  gi|121636095|ref|YP_976318.1|  33 VVLAHGLGEHARRYD--HVaQRLGAAGLVTYALDHRGHGRSGGKRVLVRDISEY---TADFDTlvgiatreyPGCKRIVL 107
                                    8*******9999996..7768888888888*********776666555555555...33333333367788889999*** PP

                                    EETCHHHHHHHHHHCC........EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCH......S-HS....CC CS
                  Abhydrolase_6  71 GHSlGGalalaaapla......lvvgvlldppptalpagllaaalelllallallrllawlsre......plpr....lf 134
                                    GHS+GG ++ a   +        +  vl +p   ++  +l++++++++++ll++ ++ ++++ e      ++++     +
  gi|121636095|ref|YP_976318.1| 108 GHSMGGGIVFA---YGverpdnYDLMVLSAP--AVAAQDLVSPVVAVAAKLLGVVVP-GLPVQEldftaiSRDPevvqAY 181
                                    ******99999...66555666333377777..344444444444444444443333.2222221111122222111133 PP

                                    CCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHH.....HCHHCCCHSTTEEETCE...SSS- CS
                  Abhydrolase_6 135 ladedadaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvp.....rllerllaqagarlpvvlpgaGHl 208
                                      d+   ++ ++  a+  + l ++g+  +++ ++l++pllvl g++D+l+p     rl+e+ +  a+++l +++pg  H 
  gi|121636095|ref|YP_976318.1| 182 NTDPL--VHHGRVPAGIGRALLQVGETMPRRAPALTAPLLVLhGTDDRLIPiegsrRLVECVGS-ADVQL-KEYPGLYHE 257
                                    33333..666666666667777888777889999999999996688886665445588888888.*****.********7 PP

                                    HHHHSHH CS
                  Abhydrolase_6 209 phleepd 215
                                    ++  ep+
  gi|121636095|ref|YP_976318.1| 258 VFN-EPE 263
                                    776.664 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.3   5.3e-13   9.5e-10       2     106 ..      32     135 ..      31     154 .. 0.88
   2 !    9.9   0.0    0.0003      0.53     210     253 ..     214     259 ..     171     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.3e-13
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...CHHSHHHHHHHHHHHHHHCTTSSEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin..ddygtasvaddldrildalgddkltlvG 79 
                                    v+v+ hGl++ +  +    +a+ L  +g  +++lD+rG+g+S      +   ++y+  ++   +  +   ++  k +++G
  gi|121636095|ref|YP_976318.1|  32 VVVLAHGLGEHARRYDH--VAQRLGAAGLVTYALDHRGHGRSGGKRVLVRdiSEYTA-DFDTLVGIATREYPGCKRIVLG 108
                                    79**********99999..***********************999998879888887.5999999887777777777*** PP

                                    ETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  80 hSmGGmialayaaeyperVkalvllga 106
                                    hSmGG i++ay  e p++ + +vl ++
  gi|121636095|ref|YP_976318.1| 109 HSMGGGIVFAYGVERPDNYDLMVLSAP 135
                                    ************************999 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0003
                                    HHSEEEEEEETTCSSSCHHHHHHHHHCHTS..EEEEEEETCSSSHH CS
                  Abhydrolase_1 210 vlaptlvisgtsDplvppkaledlaqllpk..krlvvisdagHlaf 253
                                     +ap lv++gt+D+l+p++ +++l +   +  ++l+ +++ +H +f
  gi|121636095|ref|YP_976318.1| 214 LTAPLLVLHGTDDRLIPIEGSRRLVECVGSadVQLKEYPGLYHEVF 259
                                    567*********************9995555599999999999987 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0018       3.3      64      99 ..     103     137 ..      44     144 .. 0.73
   2 !   14.5   0.0   9.9e-06     0.018     142     207 ..     214     277 ..     202     279 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                                    GGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE-- CS
                   Peptidase_S9  64 erlaitGgSyGGyltgaalnqrpdlFkaavaevpvv 99 
                                    +r ++ G+S GG  + a   +rpd ++ +v ++p v
  gi|121636095|ref|YP_976318.1| 103 KR-IVLGHSMGGGIVFAYGVERPDNYDLMVLSAPAV 137
                                    44.468***********999***********99977 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.9e-06
                                    ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHH CS
                   Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlke 207
                                     ++plL++hG+ D  +p++ + +lv+ + ++  +v+l+ +p+  H v ++  +++ l +++a+l e
  gi|121636095|ref|YP_976318.1| 214 LTAPLLVLHGTDDRLIPIEGSRRLVECVGSA--DVQLKEYPGLYHEVFNEPERNQVLDDVVAWLTE 277
                                    689**********************999885..57899*********9999999*********987 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00066       1.2       6      28 ..      22      44 ..      19      58 .. 0.83
   2 ?   -1.4   0.0      0.97   1.7e+03     108     131 ..     105     128 ..      80     152 .. 0.75
   3 !    9.9   0.0   0.00032      0.57     152     203 ..     213     260 ..     197     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00066
                                   EE--SS---EEEEEE--TT--SH CS
                  Abhydrolase_2  6 vvspkdkaqavviflHGlGdsgh 28
                                   v  p+ ++qavv++ HGlG+ + 
  gi|121636095|ref|YP_976318.1| 22 VWTPDTAPQAVVVLAHGLGEHAR 44
                                   6679999************9874 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.97
                                    EEEEETHHHHHHHHHHHT-SS--S CS
                  Abhydrolase_2 108 iigGFSqGaalalylaltlpkklg 131
                                    i+ G S+G+ ++ + ++  p  + 
  gi|121636095|ref|YP_976318.1| 105 IVLGHSMGGGIVFAYGVERPDNYD 128
                                    456899999998888887777664 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00032
                                    GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--H CS
                  Abhydrolase_2 152 avtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHside 203
                                    a+t   p l +Hg++D ++p+  + ++ e   ++  +v+lk y+gl H+  +
  gi|121636095|ref|YP_976318.1| 213 ALT--APLLVLHGTDDRLIPIEGSRRLVECVGSA--DVQLKEYPGLYHEVFN 260
                                    444..69999***********9999998887665..68**********9765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.029        52      76     119 ..      82     123 ..      21     152 .. 0.56
   2 !   14.9   0.0   8.3e-06     0.015     139     194 ..     210     263 ..     188     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.029
                            DLH  76 ekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                    ++ ++d+ +++  ++++++   k++ v G  mGG +++++  e 
  gi|121636095|ref|YP_976318.1|  82 SEYTADF-DTLVGIATREYPGCKRI-VLGHSMGGGIVFAYGVER 123
                                    3444555.33333333333344554.568888888888876665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.3e-06
                            DLH 139 eaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsr 194
                                    +a+ + ap+l+l+g+ D  ip +   +l e +    +d++lk Ypg +H  +n+ +
  gi|121636095|ref|YP_976318.1| 210 RAPALTAPLLVLHGTDDRLIPIEGSRRLVECV--GSADVQLKEYPGLYHEVFNEPE 263
                                    578899************************99..8899***********8666544 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   5.8e+03      21      67 ..      27      40 ..      18      61 .. 0.54
   2 !   15.3   0.0   6.4e-06     0.012     116     150 ..     102     137 ..      89     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                                   TTTEEEEEEE--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS- CS
                       Esterase 21 grkypvvylldGltgwdqnfrakelleslaregeiaeviivvvprgg 67
                                   + +  vv+l +Gl                                 g
  gi|121636095|ref|YP_976318.1| 27 TAPQAVVVLAHGL---------------------------------G 40
                                   4444555555555.................................2 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.4e-06
                                    C.EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S CS
                       Esterase 116 g.ravaGqSmGGlgALilalkhpdrFgsvssfSpiv 150
                                      r v+G+SmGG +   +++++pd +      +p v
  gi|121636095|ref|YP_976318.1| 102 CkRIVLGHSMGGGIVFAYGVERPDNYDLMVLSAPAV 137
                                    2599**********************8877777765 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00011      0.19     101     138 ..      31      68 ..      18      90 .. 0.88
   2 ?   -0.7   0.0      0.22     4e+02     230     242 ..     104     116 ..      99     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                    EEEEEE--TT--TTTTHHHHHHHHHTT-EEEEE---SS CS
                    PAF-AH_p_II 101 PlivFsHGLgafRtlYsalcielAskGfvvaavEHrDe 138
                                     ++v +HGLg     Y  ++  l + G+v  a++Hr +
  gi|121636095|ref|YP_976318.1|  31 AVVVLAHGLGEHARRYDHVAQRLGAAGLVTYALDHRGH 68 
                                    489*********************************76 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                                    EEEEEETHHHHHH CS
                    PAF-AH_p_II 230 vaviGHsFGgAtv 242
                                     +v+GHs Gg  v
  gi|121636095|ref|YP_976318.1| 104 RIVLGHSMGGGIV 116
                                    589******9766 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018      0.32     157     198 ..     211     253 ..     192     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                           FSH1 157 edkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlkHpg 198
                                     + ++ p L ++G++D +++ e s++L+e++ +   ++ ++pg
  gi|121636095|ref|YP_976318.1| 211 APALTAPLLVLHGTDDRLIPIEGSRRLVECVGSAdVQLKEYPG 253
                                    567899************************9886666666666 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.43   7.7e+02      55      82 ..      48      76 ..      26      87 .. 0.74
   2 ?    8.9   0.0   0.00087       1.6      33      69 ..     214     250 ..     199     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.43
                  Abhydrolase_4 55 klakalggavlvtvege..GHgalaagntC 82
                                   ++a++lg a lvt+  +  GHg + +g++ 
  gi|121636095|ref|YP_976318.1| 48 HVAQRLGAAGLVTYALDhrGHGRS-GGKRV 76
                                   678899999999885433499887.45554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00087
                  Abhydrolase_4  33 gaapvLllqnerDpaTPyegakklakalggavlvtve 69 
                                     +ap L+l ++ D   P eg ++l +  g+a +  +e
  gi|121636095|ref|YP_976318.1| 214 LTAPLLVLHGTDDRLIPIEGSRRLVECVGSADVQLKE 250
                                    269***********************99988655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1790.39
//
Query:       gi|121636096|ref|YP_976319.1|  [L=249]
Description: hypothetical protein BCG_0221 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   49.7   0.9    5.1e-13   48.7   0.9    1.6  1  DUF2786   Protein of unknown function (DUF2786)


Domain annotation for each model (and alignments):
>> DUF2786  Protein of unknown function (DUF2786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.9   2.8e-17   5.1e-13       1      39 [.       5      43 ..       5      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.8e-17
                        DUF2786  1 kilekIrKLLalAesstneaEAeaAlakAqeLmarynld 39
                                   k+l++I++LL++Ae ++n++EA+a+++ Aq+L +  ++d
  gi|121636096|ref|YP_976319.1|  5 KMLARIAALLRQAEGTDNPHEADAFMSTAQRLATAASID 43
                                   8*********************************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1835.93
//
Query:       gi|121636097|ref|YP_976320.1|  [L=169]
Description: hypothetical protein BCG_0222 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1226.69
//
Query:       gi|121636098|ref|YP_976321.1|  [L=691]
Description: beta-glucosidase bglS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-54  185.3   0.0    2.5e-54  184.3   0.0    1.5  1  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
      8e-47  160.2   0.0    1.2e-46  159.6   0.0    1.2  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
    9.9e-17   60.8   0.0    1.9e-16   59.9   0.0    1.5  1  Fn3-like         Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0   4.2e-58   2.5e-54       1     204 []     325     574 ..     325     574 .. 0.86

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 4.2e-58
                                    -EEEEEGSS--S-.S-STEEEEEESGGGSSS-SS-BSSS----S---.......................HHHHHHHHHH CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxx RF
                Glyco_hydro_3_C   1 iVLLkNennlLPL.kkklkkiaviGpnadetlklGggsgtvtvsylv.......................splegirerl 56 
                                    iVLL+N  +lLPL ++++ +iaviG  a+  +  G gs++vt++                          spl+++r+rl
  gi|121636098|ref|YP_976321.1| 325 IVLLQNR-GLLPLaPESAGRIAVIGGYAHLGVPAGYGSSAVTPPGGYagvipiggsglaaglrnlyllpsSPLSELRKRL 403
                                    8*****9.*****999999**********99999999999955433344556666666666666667777********** PP

                                    H.........-HHHHHHHHHHHTSEEEEEEEES...SB-TTSCSGHHSSTTHHHHHHHHHHTTSSEEEEEEESSGG--TT CS
                                    xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_3_C  57 es.......eegideaveaakeaDvavvvvgedpeiegEgvDrtdlalpeaqdelikavaaanknvvvvlqsggpvavep 129
                                    ++         + +eav aa++aD+a+v++ +    egEg+D +dl+lp +qd+li+ava+an n+vvvl++g+pv++ p
  gi|121636098|ref|YP_976321.1| 404 PNaqfefdpGINPAEAVLAARRADIAIVFAIRA---EGEGFDSADLSLPWGQDALIAAVASANANTVVVLETGNPVTM-P 479
                                    99*****9977899*******************...******************************************.8 PP

                                    TGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx.................... RF
                Glyco_hydro_3_C 130 wkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpddyyeek..dt.................... 187
                                    w  ++v+Ai++aw+pGq+gG+a+a+ ++G+vnPsG+Lp+tfp +l+++p+ ++ ++   +                    
  gi|121636098|ref|YP_976321.1| 480 W-RDSVNAIMQAWYPGQAGGQAVAESVTGQVNPSGRLPITFPVDLGQTPR-SQPRElgAPwgtsttihytegadvgyrwf 557
                                    9.66********************************************88.22222341144566788889999998884 PP

                                    .S-----SETTTT-BCH CS
                                    xxxxxxxxxxxxxxxxx RF
                Glyco_hydro_3_C 188 ykfegtplYpeGlglsY 204
                                    +++++tp++ +G+glsY
  gi|121636098|ref|YP_976321.1| 558 ASTNQTPMFAFGHGLSY 574
                                    44788899*******99 PP

>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.0     2e-50   1.2e-46      63     318 ..      43     292 ..      40     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 2e-50
                                    ...S--EEEE---BTTB-...--SSS.---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSSSG CS
                  Glyco_hydro_3  63 rlgiPlllavDqegGlvq...rlgeg.tlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprngig 138
                                    rlg+P+ll +D+  G+ +   r g++ t +P+ lalaa++++ l++  g++i++e+r  g ++++a  ++++rdprng++
  gi|121636098|ref|YP_976321.1|  43 RLGVPALLMSDAGLGVTNpgyRPGDTaTALPAGLALAASFNPVLARSSGKAIGREARSRGFNVQLAGAINLARDPRNGRN 122
                                    799**********99986444678888***************************************************** PP

                                    GGSS-SSHHHHHHHHHHHHHHHHHTT-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHH.HTT-SEEEE CS
                  Glyco_hydro_3 139 vrsFsedpelvaalaaamvkGlqgagvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaai.eagvdsVMt 217
                                    +++ sedp l a++aa+ + G+q++gv+at KHF     +  ++++++ +  ++ ++ re dl+ f+  i +++ ++VM+
  gi|121636098|ref|YP_976321.1| 123 FEYLSEDPLLSATMAAESIIGIQQQGVIATTKHFSL---NCNETNRHWLDAVIDPDAHRESDLLAFEIVIeRSQPGAVMA 199
                                    ************************************...599****************************99******** PP

                                    ---B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHHHCCS-HHHHHHHHHHHT-SBEES-S---SGHHHHHH CS
                  Glyco_hydro_3 218 aHvqfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkeiadrggkeeavvlaLkAGvDilLvpeertseikalkk 297
                                    a   +++++g+ a+g+  ll dvL+  +G+ G v+sD+    +     +      +   A++D  L+++e    +++l +
  gi|121636098|ref|YP_976321.1| 200 A---YNKVNGDYAAGNDHLLNDVLKGAWGYRGWVMSDWG---GTPSWECALAGLDQECGAQIDAVLWQSEAF--TDRLRA 271
                                    *...**********************************9...66777778888889999*********9996..8***** PP

                                    HHHTTSS-HHHHHHHHHHHHH CS
                  Glyco_hydro_3 298 avkeGeltearidesvrrvlr 318
                                    a ++G+l++ r+ + vrr+lr
  gi|121636098|ref|YP_976321.1| 272 AYADGNLPKGRLSDMVRRILR 292
                                    *******************97 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   3.2e-20   1.9e-16       2      70 ..     607     672 ..     606     673 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.2e-20
                                    EEEEEEEESS-STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGGG-EEETTTTEEE--SCEEEEEEESS CS
                       Fn3-like   2 vvqlYvsdpessverpvkeLkgFekveLapGesktvtftldrkdlsvwdeekqkwvvepGeytvlvgts 70 
                                    v qlY+ + ++   +   +L gFe+veL+pG++++v+++ d++ l+ +d e+ +w++epG ytv vg+s
  gi|121636098|ref|YP_976321.1| 607 VPQLYMIAAPG---ESRLRLLGFERVELEPGQTRRVRIEADPRLLARYDGEARSWRIEPGGYTVAVGAS 672
                                    89999988887...799**************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 5017.38
//
Query:       gi|121636099|ref|YP_976322.1|  [L=220]
Description: o-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-33  114.2   0.0    5.8e-33  113.9   0.0    1.0  1  Methyltransf_3   O-methyltransferase
    4.3e-18   66.3   0.0    7.3e-18   65.5   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
    3.6e-08   33.4   0.1    5.7e-08   32.8   0.1    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-07   31.6   0.0    1.8e-07   31.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.4e-06   28.9   0.0    2.8e-06   27.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00068   19.4   0.0    0.00086   19.0   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0051   16.5   0.0     0.0059   16.3   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.052   13.5   0.0      0.073   13.0   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
       0.18   11.1   0.0       0.23   10.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.22   11.1   0.0       0.29   10.7   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0   3.3e-36   5.8e-33      24     182 ..      37     189 ..      22     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 3.3e-36
                                    T.TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEE CS
                 Methyltransf_3  24 tdlsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekiel 103
                                     +l+++ vs+++g+fL lL   ++a+rvleiG+  G+s + +a +  + G++++++ +++++e+a+  +q+agva+++e+
  gi|121636099|ref|YP_976322.1|  37 AELPRIAVSAQQGKFLCLLAGAIQARRVLEIGTLGGFSTIWLARGAGPQGRVVTLEYQPKHAEVARVNLQRAGVADRVEV 116
                                    458999************************************************************************** PP

                                    EES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG-SS--SHHHHH.....H CS
                 Methyltransf_3 104 iegdalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvveeddeeakalreyravl 182
                                     +g+al +L  l  +     fD++f+DaDk++ v y + +++L ++G +i++Dn++  G +++e d++  + +  r  l
  gi|121636099|ref|YP_976322.1| 117 VVGPALDTLPTLAGGP----FDLVFIDADKENNVVYIQWAIRLARRGAVIVVDNVIRGGGILAESDDADAVAA--RRTL 189
                                    ***********98776....*************************************9999888554443333..3344 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   4.1e-21   7.3e-18       1     106 []      65     167 ..      65     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 4.1e-21
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDggh 79 
                                    +EiG+  G+st+wl+r +   g  r+v+++ +p+ ae a+ ++++ag++drv+++++++ ++l++la g++Dl+fiD++ 
  gi|121636099|ref|YP_976322.1|  65 LEIGTLGGFSTIWLARGAGPQG--RVVTLEYQPKhAEVARVNLQRAGVADRVEVVVGPALDTLPTLAGGPFDLVFIDAD- 141
                                    7**************9999998..6*******9533334455556********************************98. PP

                Methyltransf_24  80 aaeavledleallprlapggvvlfdDi 106
                                     +e    +++++ ++ ++g+v+++d++
  gi|121636099|ref|YP_976322.1| 142 -KENNVVYIQWAIRLARRGAVIVVDNV 167
                                    .66666779****************85 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   3.2e-11   5.7e-08      71     152 ..      58     142 ..      34     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.2e-11
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-..SEEEEE CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeeka..PYdaih 147
                                      +  rvLe+G+  G+ t  lar  g++grvv++e++++ +e a+ nl++ +++ +v vvvg      +  a  P+d ++
  gi|121636099|ref|YP_976322.1|  58 AIQARRVLEIGTLGGFSTIWLARGAGPQGRVVTLEYQPKHAEVARVNLQRAGVAdRVEVVVGPALDTLPTLAggPFDLVF 137
                                    446789*********************************************98779******999999987766999999 PP

                                    ESSBB CS
                           PCMT 148 vgaaa 152
                                    + a  
  gi|121636099|ref|YP_976322.1| 138 IDADK 142
                                    98865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   9.8e-11   1.8e-07       5     111 ..      62     166 ..      60     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 9.8e-11
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsne 82 
                                     rvl++G+  G+ t+ la+ +gp+++vv ++++++  e+Ar n+q+ g+  +ve+ +g++ + l++l +  +fDl++ + 
  gi|121636099|ref|YP_976322.1|  62 RRVLEIGTLGGFSTIWLARGAGPQGRVVTLEYQPKHAEVARVNLQRAGVAdRVEVVVGPALDtLPTL-AGGPFDLVFID- 139
                                    589**********************************************99**************95.669******99. PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggillied 111
                                      ++  ++  +++ ++r+ + g ++++++
  gi|121636099|ref|YP_976322.1| 140 --ADKENNVVYIQWAIRLARRGAVIVVDN 166
                                    ..566666667777777777666666654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.6e-09   2.8e-06       1      70 [.      64     138 ..      64     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.6e-09
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BS.SSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaed.lp.fedgsfDlvvs 70 
                                    vL++G+  G  t++la+  g +++v+ ++++++  e ar +++++g+  +ve+v+g a d lp ++ g fDlv++
  gi|121636099|ref|YP_976322.1|  64 VLEIGTLGGFSTIWLARGAGpQGRVVTLEYQPKHAEVARVNLQRAGVadRVEVVVGPALDtLPtLAGGPFDLVFI 138
                                    8****************9966*************************************5548846889*****98 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.8e-07   0.00086      42      97 ..      62     117 ..      52     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.8e-07
                          GCD14  42 svvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvt 97 
                                     +v+e Gt  g  +  +ar  +P+G++ t+e+  + ae ar ++++ ++++ v v 
  gi|121636099|ref|YP_976322.1|  62 RRVLEIGTLGGFSTIWLARGAGPQGRVVTLEYQPKHAEVARVNLQRAGVADRVEVV 117
                                    589*****99988899*********************************9999886 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0059      65     121 ..      86     140 ..      50     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                    SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                  Cons_hypoth95  65 kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                     ++v +e +++ +++ + nl++ ++ +++++++  al+ l++l  ++++fd+vf+D 
  gi|121636099|ref|YP_976322.1|  86 GRVVTLEYQPKHAEVARVNLQRAGVADRVEVVVGPALDTLPTL--AGGPFDLVFIDA 140
                                    4899***************************************..6789******95 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     4e-05     0.073      13      78 ..      60     125 ..      50     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                    +  +rv+ iGt  g+ +i+l++  g   +v+  + +++  e a+ n+++ag+ d++ev+++  l++l
  gi|121636099|ref|YP_976322.1|  60 Q-ARRVLEIGTLGGFSTIWLARgAGPQGRVVTLEYQPKHAEVARVNLQRAGVADRVEVVVGPALDTL 125
                                    4.67999*************973567889********************************999987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.23      43     123 ..      56     139 ..      46     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TT.T-TTS-.T-EEE CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanae.eLpfed.dsfDv 119
                                     +  ++++vl++ +  g  ++ l++ +g +g+vv l+++++  +v++  l++ g+  ++e +++ a   Lp    + fD+
  gi|121636099|ref|YP_976322.1|  56 AGAIQARRVLEIGTLGGFSTIWLARGAGPQGRVVTLEYQPKHAEVARVNLQRAGVAdRVEVVVGPALdTLPTLAgGPFDL 135
                                    5556677899999889999************************************989*****99852588766578888 PP

                                    EEEE CS
                Ubie_methyltran 120 vtvs 123
                                    v + 
  gi|121636099|ref|YP_976322.1| 136 VFID 139
                                    8765 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.29      22      77 ..      85     138 ..      61     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                Methyltransf_15  22 fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                      +v+++e+++++ ++a  N +  gv+d++ +v+g  +++l +l       dlvf+
  gi|121636099|ref|YP_976322.1|  85 QGRVVTLEYQPKHAEVARVNLQRAGVADRVEVVVGPALDTLPTLAGGPF--DLVFI 138
                                    45899******************************99999988776666..77775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1539.07
//
Query:       gi|121636100|ref|YP_976323.1|  [L=143]
Description: hypothetical protein BCG_0225 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-34  114.7  26.6    8.6e-18   63.7  13.6    2.1  2  SPW       SPW repeat
  ------ inclusion threshold ------
      0.017   14.8   0.6      0.059   13.2   0.6    1.9  1  PHBC_N    Poly-beta-hydroxybutyrate polymerase N terminal


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   5.0   9.7e-20   8.7e-16       2      47 ..      35      80 ..      34      81 .. 0.97
   2 !   63.7  13.6   9.6e-22   8.6e-18       1      47 [.      88     135 ..      88     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 9.7e-20
                            SPW  2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafaaa 47
                                   +++ll+Gl++++SPW++Gfsat+g+ ++++ivG++va La++fa+a
  gi|121636100|ref|YP_976323.1| 35 GLALLAGLYVAASPWIVGFSATRGLPTCDLIVGIAVAYLAYGFASA 80
                                   689*****************************************97 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 9.6e-22
                            SPW   1 eWanlllGlwlivSPWvl.GfsattgaawnnvivGavvavLalafaaa 47 
                                    +W++++lG+w+i+SPWvl G++ t+g++w+++i+GavvavL+++f+++
  gi|121636100|ref|YP_976323.1|  88 TWTLPVLGVWVIFSPWVLpGVAVTAGMMWSHIIAGAVVAVLGFYFGMR 135
                                    6*********************************************97 PP

>> PHBC_N  Poly-beta-hydroxybutyrate polymerase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   6.5e-06     0.059       5      25 ..      20      40 ..      16      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-06
                         PHBC_N  5 alDralhAalArlTgGlSPas 25
                                    +Dra++ ++A++T Gl   +
  gi|121636100|ref|YP_976323.1| 20 SFDRAAESTIAHFTFGLALLA 40
                                   49***************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1047.91
//
Query:       gi|121636101|ref|YP_976324.1|  [L=575]
Description: dihydroxy-acid dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-206  687.1   0.6   1.6e-206  686.9   0.6    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.9   0.6    9e-211  1.6e-206       1     517 []      49     572 ..      49     572 .. 0.97

  Alignments for each domain:
  == domain 1  score: 686.9 bits;  conditional E-value: 9e-211
                       ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqll 80 
                                    kp+ig+a+s++e++pc+  l++la+avkegv +agg+p+ef ti+vsDgi+mg+egm++sL+sRe+iadsve++++a++l
  gi|121636101|ref|YP_976324.1|  49 KPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERL 128
                                    8******************************************************************************* PP

                       ILVD_EDD  81 DalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk.......kldlssvfeavgalaagkiseeeleeleeaac 153
                                    D+ vl++gCDK++Pg+lmaaarl++ a+f+++G++++g++k       +++++++feavga+++g +s+++++++e+a+c
  gi|121636101|ref|YP_976324.1| 129 DGSVLLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKlsdgserDVTIIDAFEAVGACSRGLMSRADVDAIERAIC 208
                                    *************************************77555666667999***************************** PP

                       ILVD_EDD 154 pgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalG 233
                                    pg G+C+gm+TAntma++aealG+slpgsa+ pat+++r+ +a+++g+++vel+++ +++rdiltkeafeNAi+v++a G
  gi|121636101|ref|YP_976324.1| 209 PGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARDILTKEAFENAIAVVMAFG 288
                                    ******************************************************************************** PP

                       ILVD_EDD 234 GStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktl 313
                                    GStNavlHllAiA+ea+v l+l+df+++++ vp+la++kP g++ m+d++++GGvp+v+k Ll+agllhgd+ltvtg+t+
  gi|121636101|ref|YP_976324.1| 289 GSTNAVLHLLAIAHEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTM 368
                                    ******************************************************************************** PP

                       ILVD_EDD 314 aenlee..aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkika 391
                                    aenl++      + +v+r l++p++++gg+++L+G+LapeGavvKt++ +    +feg+Arvfd e++a++a+++g+i+ 
  gi|121636101|ref|YP_976324.1| 369 AENLAAitPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFD--SDVFEGTARVFDGERAALDALEDGTITV 446
                                    ****886444599*************************************..56789*********************** PP

                       ILVD_EDD 392 gdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidie 471
                                    gd vviryeGPkGgpGm+Eml++t a++g+glgk+v l+tDGRfSG+++gl++gh++PEA++gGpial+++GD+i++d++
  gi|121636101|ref|YP_976324.1| 447 GDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVA 526
                                    ******************************************************************************** PP

                       ILVD_EDD 472 krtlelevseeelaaRraawkpekkvktrgllakyaklvssaseGA 517
                                     r l+++ + +e+a+R+++++p +  +t+g+l+ky klvssa+ GA
  gi|121636101|ref|YP_976324.1| 527 GRVLDVLADPAEFASRQQDFSPPPPRYTTGVLSKYVKLVSSAAVGA 572
                                    *********************9544556***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4213.49
//
Query:       gi|121636102|ref|YP_976325.1|  [L=96]
Description: hypothetical protein BCG_0227 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-31  106.8   0.3    6.4e-31  106.5   0.3    1.0  1  Trns_repr_metal  Metal-sensitive transcriptional repressor


Domain annotation for each model (and alignments):
>> Trns_repr_metal  Metal-sensitive transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   0.3   3.6e-35   6.4e-31       2      76 ..      11      91 ..      10      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 3.6e-35
                                   HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHH CS
                Trns_repr_metal  2 kkkllnrLkrieGQvrgiqrmieedryCidiltQlaAvrsalnkvglelledhlkhcvaeaiee......ekieeliellk 76
                                   k+++ +rL+r+eGQvrgi+rmieed+yCid+ltQ++Av+sal++v+l ll++hl+hcv++a++e       k++e++++++
  gi|121636102|ref|YP_976325.1| 11 KDNYAKRLRRVEGQVRGIARMIEEDKYCIDVLTQISAVTSALRSVALNLLDEHLSHCVTRAVAEggpgadGKLAEASAAIA 91
                                   8999**********************************************************8889999889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 679.76
//
Query:       gi|121636103|ref|YP_976326.1|  [L=413]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-31  108.6  56.4    4.7e-22   78.4  26.7    2.0  2  MFS_1            Major Facilitator Superfamily
    0.00098   18.5  38.7    0.00098   18.5  38.7    1.6  2  MFS_4            Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4  26.7   5.2e-26   4.7e-22       1     213 [.      26     222 ..      26     242 .. 0.85
   2 !   33.9  25.3   1.8e-12   1.6e-08       4     171 ..     227     397 ..     224     412 .. 0.71

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 5.2e-26
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l++aaf++ +a  +   al+ a+a++l +s+  +g+ll+ yal+aav+++pl r++  + rrr l+++l+++ ++ l+ +
  gi|121636103|ref|YP_976326.1|  26 LACAAFIYVTAEILPVGALS-AIARNLRVSVVLVGTLLSWYALVAAVTTVPLVRWTAHWPRRRALVVSLVCLTVSQLVSA 104
                                    68999999999999999999.******************************************************66666 PP

                          MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                    +a+++ +l+++rvl++++ g+l++++a ++++++p+++ gra+  +++g+sl+ ++g +l ++++  +gWr++ + ++++
  gi|121636103|ref|YP_976326.1| 105 LAPNFAVLAAGRVLCAVTHGLLWAVIAPIATRLVPPSHAGRATTSIYIGTSLALVVGSPLTAAMSLMWGWRLAAVCVTGA 184
                                    668877*******************************************************************9999999 PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwill 213
                                    ++ +++ + l lpe   +    +++ ++            ++ ++++    l+
  gi|121636103|ref|YP_976326.1| 185 AAAVALAARLALPEMVLRADQLEHVGRR-----------ARHHRNPR----LV 222
                                    9999998888888877777777766662...........23333333....33 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 1.8e-12
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                    +++++ ++ ++ ++ +  ++ +  g+ +  + +ll++y+++ +v++++++r  dr+ ++  +++g++++ ++++ll+ +a
  gi|121636103|ref|YP_976326.1| 227 LTMIAVTGHFVSYTYIVVIIRDVVGVRGPNLAWLLAAYGVAGLVSVPLVARPLDRW-PKGAVIVGMTGLTAAFTLLTaLA 305
                                    55666666666666666688999*********************************.77766666666666645555443 PP

                          MFS_1  83 ....sslw.lllvlrvlqGlga.galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                        ++   +ll   ++  +ga +++++ ++  +a  + +++   a gl+ ++f++G++ g+llggll++    ++++++
  gi|121636103|ref|YP_976326.1| 306 fgerHTAAtALLGTGAIVLWGAlATAVSPMLQSAAMRSGGDDPDGASGLYVTAFQIGIMAGALLGGLLYER---SLAMML 382
                                    44774444455555555555554666666666667777777****************************44...455666 PP

                          MFS_1 157 laivsllafvlflll 171
                                     a ++l+++ lf++ 
  gi|121636103|ref|YP_976326.1| 383 TASAGLMGVALFGMT 397
                                    666666654454443 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3     0.091   8.2e+02      43      80 ..      41      75 ..      16      82 .. 0.55
   2 !   18.5  38.7   1.1e-07   0.00098      52     354 ..      79     388 ..      57     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.091
                          MFS_4 43 vGallaafalsagaeRlr.llagllatvllllamaltes 80
                                   vGal a     a++ R+  +l+g+l++  +l+a + t  
  gi|121636103|ref|YP_976326.1| 41 VGALSA----IARNLRVSvVLVGTLLSWYALVAAVTTVP 75
                                   455555....33333443445555555555555444444 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.1e-07
                          MFS_4  52 lsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGi 130
                                    + a+  R r l ++l+  +++ l +al+ +fa++++ R+l  v+ ++   +++ ++ + + ++ ++r    ++ G  l  
  gi|121636103|ref|YP_976326.1|  79 WTAHWPRRRaLVVSLVCLTVSQLVSALAPNFAVLAAGRVLCAVTHGLLWAVIAPIATRLVPPSHAGRATTSIYIGTSLAL 158
                                    544444444399999999************************************************************** PP

                          MFS_4 131 avsgllvlll.lqlglsasslWlalavlsavllllvalllpraalreas.aaaeaakaeqkslpllalllaYglaGfGYi 208
                                    +v++ l +++ l  g+  +++ + +++ +a++ l+  l lp+  lr+ + ++   ++ ++++  l+++ ++  +a  G  
  gi|121636103|ref|YP_976326.1| 159 VVGSPLTAAMsLMWGWRLAAVCV-TGA-AAAVALAARLALPEMVLRADQlEHVGRRARHHRNPRLVKVSVLTMIAVTGHF 236
                                    *9986655440555555554433.333.333334444445533333332033333356678888999999999******* PP

                          MFS_4 209 itatFlvaiardgaggalleallWll..vGlaaivgvlvwlrvakrsglrralaaallieavgvllslls......pspl 280
                                    +  t++v i+rd   g    +l+Wll  +G+a +v+v +  r  +r+  +++++ +  + a+  ll+ l        + +
  gi|121636103|ref|YP_976326.1| 237 VSYTYIVVIIRD-VVGVRGPNLAWLLaaYGVAGLVSVPLVARPLDRWPKGAVIVGMTGLTAAFTLLTALAfgerhtAATA 315
                                    ************.6777789999987447********8888888899999888888888777777776542222112344 PP

                          MFS_4 281 glivssvll.GltflaitalvlqlarelappatrrllglmTasfgigQilGpllasllaeatgslalallvaaaa 354
                                    +l  ++++l G+  +a+ ++   +a +  ++ +  + gl  ++f ig ++G+ll +ll+e++ ++ l   ++a++
  gi|121636103|ref|YP_976326.1| 316 LLGTGAIVLwGALATAVSPMLQSAAMRSGGDDPDGASGLYVTAFQIGIMAGALLGGLLYERSLAMMLT--ASAGL 388
                                    44455655516666666666666667777788899************************997555443..33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2673.39
//
Query:       gi|121636104|ref|YP_976327.1|  [L=352]
Description: hypothetical protein BCG_0229 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-23   83.3   0.0    3.7e-23   82.5   0.0    1.4  1  Big_10    Bacterial Ig domain
    6.1e-19   68.9   0.2    9.8e-19   68.2   0.2    1.3  1  YkuD      L,D-transpeptidase catalytic domain


Domain annotation for each model (and alignments):
>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   4.1e-27   3.7e-23      86     162 ..     123     199 ..     116     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.1e-27
                         Big_10  86 atltpedgstvGvgqpisikFdkpvedkaavekalkvttspavegafaWlsdsevdwRpkeYwkpgtkVtvkaklyg 162
                                     t++p dg+ vGv++pi i+F  p++d+a +e+a+++++ p+v g+f+W+s ++v+wRp e+w+++t V+++a+ + 
  gi|121636104|ref|YP_976327.1| 123 PTFNPVDGAMVGVAKPIVINFAVPIADRAMAESAIHISSIPPVPGKFYWMSPTQVRWRPFEFWPANTAVNIDAAGTK 199
                                    5899*******************************************************************997554 PP

>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.2   1.1e-22   9.8e-19       6     146 .]     212     334 ..     207     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.1e-22
                                    EETTTTEEEEEEETTEEEEEEE-BEBTTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEEECCCTT CS
                           YkuD   6 vdlaeqrllvlyengklvlsfpvsvGgkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyldkknskv 85 
                                     d a++++ ++ +ng + ++fp s+G   +g+++TP+Gt+++ +k++     + +s ++ ++    +++ +++d      
  gi|121636104|ref|YP_976327.1| 212 ADDATHQM-TITRNGVVQKTFPMSMG-MVSGGHQTPNGTYYVLEKFATVV--MDSSTYGVPVNSAQGYKLTASD------ 281
                                    67788888.777**************.9999************7777776..8888888888888888888877...... PP

                                    CECCCCEEE-STTS-EEEE.ETCSS...CTHHC.BSSSEEE-HHHHHHHHHHHHTTEEEEE CS
                           YkuD  86 algkvkfvfpngsgiyiHgtgapdlfergkgarrShGCirlseedakelyelvlvgtpvvi 146
                                          +v  ++sg ++H  ++  ++++  +++ +hGCi+ls+++ak++y++   g+pvv+
  gi|121636104|ref|YP_976327.1| 282 ------AVRIDNSGNFVHSAPWSVADQG--KRNVTHGCINLSPANAKWFYDNFGSGDPVVV 334
                                    ......9999********5555555544..5667*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2528.32
//
Query:       gi|121636105|ref|YP_976328.1|  [L=615]
Description: hypothetical protein BCG_0230c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.4   0.1        0.4   11.0   0.1    1.7  1  DUF5071   Domain of unknown function (DUF5071)


Domain annotation for each model (and alignments):
>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   2.2e-05       0.4      25      94 ..     485     557 ..     471     568 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                                    GGHHHHHGGGS-TTSTTHHHHHHHHHHTGGGTHHHHHHHH...HSS-H..HHHHHHHHHHGGGS-HHHHHHHHHH CS
                        DUF5071  25 plvpeLLeWlqDlNwPiaspiaelLarfpeelvkeiaeiL...eknDe..ewkyfvleflveklpveskkklkee 94 
                                     l + LL+Wl+D+  P   ++++ L+ +  +l++e+ + L   e +D    w++ +l +   ++  ++k  l++ 
  gi|121636105|ref|YP_976328.1| 485 RLYERLLGWLADIQQPRPADCLRPLQIH--ALISEVLKTLpldEDQDPpaDWHFDLLGMSHAEAARSVKHLLEDV 557
                                    46789******************99866..467777777676655663336888888877777777666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3871.90
//
Query:       gi|121636106|ref|YP_976329.1|  [L=1194]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-65  220.1   9.1    2.1e-37  129.3   0.1    2.1  2  ABC_membrane     ABC transporter transmembrane region
    3.4e-60  202.5   0.0    1.5e-29  103.2   0.0    2.3  2  ABC_tran         ABC transporter
    1.5e-10   40.7   0.2     0.0011   18.2   0.0    3.5  4  Zeta_toxin       Zeta toxin
      8e-07   29.6   4.3     0.0084   16.5   0.2    3.1  2  AAA_16           AAA ATPase domain
      3e-06   26.9   0.5      0.034   13.9   0.0    2.8  2  AAA_29           P-loop containing region of AAA domain
    6.6e-06   25.7   0.0       0.95    8.9   0.0    4.0  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.2e-05   24.7  18.3      0.015   14.6   2.8    2.9  2  ABC_membrane_3   ABC transporter transmembrane region
    4.5e-05   23.6   2.6       0.18   11.9   0.2    3.3  3  AAA_33           AAA domain
    4.7e-05   23.4   0.0      0.016   15.1   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
    9.4e-05   22.7   0.6       0.52   10.6   0.0    2.9  2  AAA_22           AAA domain
    0.00018   21.3   4.1       0.17   11.6   0.7    3.7  3  AAA_30           AAA domain
    0.00036   20.5   0.2      0.093   12.6   0.0    3.1  3  Ploopntkinase3   P-loop Nucleotide Kinase3
    0.00064   19.8   0.1        1.5    8.9   0.0    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0013   18.4   7.4      0.071   12.7   0.0    3.4  3  AAA_25           AAA domain
     0.0019   18.5   2.4        1.1    9.5   0.4    2.9  2  AAA_28           AAA domain
     0.0019   17.3   0.0       0.83    8.6   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
     0.0027   18.1   0.1          2    8.8   0.0    3.0  2  AAA              ATPase family associated with various cellul
     0.0028   17.6   0.3       0.78    9.6   0.1    2.7  2  NTPase_1         NTPase
     0.0037   17.2   0.2        3.9    7.3   0.0    2.8  2  NACHT            NACHT domain
     0.0045   17.5   0.1        1.5    9.4   0.1    2.4  2  AAA_18           AAA domain
     0.0047   16.2   1.2        1.2    8.2   0.0    2.8  3  NB-ARC           NB-ARC domain
     0.0056   16.4   0.3        7.2    6.3   0.0    3.3  4  IstB_IS21        IstB-like ATP binding protein
     0.0068   16.4   0.1        5.8    6.9   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0068   15.9   0.1       0.25   10.8   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
     0.0069   16.2   4.2        1.5    8.5   0.1    3.9  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0096   15.3   0.1        2.8    7.2   0.0    2.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.013   15.3   0.0        1.3    8.7   0.0    2.3  2  AAA_24           AAA domain
      0.014   15.0   0.1        3.5    7.2   0.0    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.015   15.4   0.7        3.8    7.5   0.1    2.2  2  DUF87            Helicase HerA, central domain
      0.021   15.3   0.6        2.7    8.4   0.1    2.5  2  AAA_17           AAA domain
      0.021   14.2   0.1        3.5    7.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.025   14.3   0.2        7.8    6.2   0.1    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.029   13.3   0.4        1.7    7.6   0.0    2.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.04   14.3   0.0          7    7.1   0.0    2.4  2  RNA_helicase     RNA helicase
      0.046   13.5   0.7        8.9    6.0   0.1    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.05   13.5   0.1         10    6.0   0.0    2.4  2  APS_kinase       Adenylylsulphate kinase
      0.057   12.6   0.0       0.53    9.4   0.0    2.0  2  G-alpha          G-protein alpha subunit
      0.075   12.3   0.1        9.8    5.4   0.0    2.2  2  AAA_8            P-loop containing dynein motor region D4
       0.11   12.9   0.2        1.2    9.6   0.1    2.0  2  AAA_23           AAA domain
       0.21   10.5   0.0        2.9    6.7   0.0    2.1  2  AAA_10           AAA-like domain
       0.71    9.9   3.1         21    5.2   0.1    3.5  2  CytB6-F_Fe-S     Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.1   4.7e-40   2.1e-37       1     270 [.      20     285 ..      20     288 .. 0.95
   2 !   93.4   4.6   4.2e-29   1.9e-26       2     273 ..     628     897 ..     627     898 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 4.7e-40
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrkl 80 
                                    l+l++ +a++++v+++l+plv++r++d+ +  +d++   l+ ++++l++++ a  +l++++ y+   ++  + ++lr ++
  gi|121636106|ref|YP_976329.1|  20 LLLGFGAALAGTVIAVLVPLVTKRVIDDAIA-ADHRP--LAPWAVVLVAAAGATYLLTYVRRYYGGRIAHLVQHDLRMDA 96 
                                    5789999***********************9.99999..***************************************** PP

                                    HHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  81 fkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsav 160
                                    f+++lr + +  d+ s+G+l+ r tnd++ ++ +l +   ++ + +lt++ g++vm +l++ l+l+ + ++p+i l++  
  gi|121636106|ref|YP_976329.1|  97 FQALLRWDGRQQDRWSSGQLIVRTTNDLQLVQALLFDVPNVL-RHVLTLLLGVAVMTWLSVPLALLAVLLVPVIGLIAHR 175
                                    *****************************9999999988765.6666666699999999999****************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 161 iakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsya 240
                                      ++l  ++   q++ a ++ v+  ++ gir+Vkafg ee+++ k   a++  + a++++a++n+ +++ +q l+ l ++
  gi|121636106|ref|YP_976329.1| 176 SRRLLAAATHCAQEHKAAVTGVVDAAVCGIRVVKAFGQEERETVKLVMASRALYAAQLRVARLNAHFGPLLQTLPALGQM 255
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHTTSSTHHHHHHHHHHHHHH CS
                   ABC_membrane 241 lalwfGttlvisgelsvgdlvvflslfail 270
                                    +++ +G+++  +g ++vg++v+f + +++l
  gi|121636106|ref|YP_976329.1| 256 AVFALGGWMAAQGSITVGTFVAFWACLTLL 285
                                    *********************998777765 PP

  == domain 2  score: 93.4 bits;  conditional E-value: 4.2e-29
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                     l++ll ++++++ +l pl++ + +d+ +     +   l   +l+ ++ +++++++ +++ ++  +tge++ +rlr+ +f
  gi|121636106|ref|YP_976329.1| 628 ALSLLLVAVQTCAGLLPPLLIRHGIDVGIRRHVLSA--LWWAALAGTATVVIRWVVQWGSAMVAGYTGEQVLFRLRSVVF 705
                                    68999************************9777777..99999999********************************** PP

                                    HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsavi 161
                                     +  r+ +  f++    ++++ +t dv+ +  +l + l++ + s++t+vg+l+ ++ +  +l l+++ ++p+++l ++ +
  gi|121636106|ref|YP_976329.1| 706 AHAQRLGLDAFEDDGDAQIVTAVTADVEAIVAFLRTGLVVAVISVVTLVGILVALLAIRARLVLLIFTTMPVLALATWQF 785
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 162 akilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyal 241
                                     + ++   ++   +++ +++ ++E   g+r  +af++e + l+ +   ++++++ g++ +++ +l  ++  ll +l+++l
  gi|121636106|ref|YP_976329.1| 786 RRASNWTYRRARHRLGTVTATLREYAAGLRIAQAFRAEYRGLQSYFAHSDDYRRLGVRGQRLLALYYPFVALLCSLATTL 865
                                    ******************************************************************************** PP

                                    HHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 242 alwfGttlvisgelsvgdlvvflslfailfga 273
                                    +l+ G+  v +g +svg lv++l+++ +l ++
  gi|121636106|ref|YP_976329.1| 866 VLLDGAREVRAGVISVGALVTYLLYIELLYTP 897
                                    ***************************99987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   3.5e-32   1.5e-29       1     137 []     350     499 ..     350     499 .. 0.95
   2 !   97.2   0.0   2.5e-30   1.1e-27       2     136 ..     960    1107 ..     959    1108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.5e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+++sl++++ge++a+vG  G+GKStL++l ++ ++ t+G +++ g+d++e +l slr+ ig +p+++ lf+++ ++ n 
  gi|121636106|ref|YP_976329.1| 350 LREISLSVRAGETLAVVGAPGSGKSTLASLATRCYDVTQGAVRIGGQDVRELTLDSLRSAIGLVPEDAVLFSGT-IGANi 428
                                    6789**********************************************************************.99999 PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   ++ ++ie+++++l + +  +t v+ ++ +LSgGq+qr+alarall +p+ll++D+pt+
  gi|121636106|ref|YP_976329.1| 429 aygrpdatpeqiataARAAHIEEFVNTLPDGY--QTAVGARGLTLSGGQRQRIALARALLHQPRLLIMDDPTS 499
                                    *****999999887777777999999999888..99999999*****************************96 PP

  == domain 2  score: 97.2 bits;  conditional E-value: 2.5e-30
                                     EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran    2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79  
                                       ++l + +g++v++vG++G+GKStL+kl+a+ ++pt G++++dg dl+e +   +r+++g+++qe+ +f ++ vr+ 
  gi|121636106|ref|YP_976329.1|  960 AGINLRIPAGQTVVFVGSTGSGKSTLIKLVARFYDPTHGTVRVDGCDLREFDVDGYRNRLGIVTQEQYVFAGT-VRDA 1036
                                     679********************************************************************99.**** PP

                                     .......HHHTCHHHHHHHSTTGG........TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                     .......xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   80 .......esdeeiekalsklglke........lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136 
                                            + d+++e+a++++g +           ++v + ++++LS Gq q +alara l +p++lllDE+t
  gi|121636106|ref|YP_976329.1| 1037 iaygrpdATDAQVERAAREVGAHPmitaldngYLHQV-TAGGRNLSAGQLQLLALARARLVDPDILLLDEAT 1107
                                     *******888888888888887777776555433333.2566*****************************9 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3   5.7e+02      11      55 ..      53      93 ..      43     100 .. 0.81
   2 !   17.3   0.1   5.1e-06    0.0022      20      57 ..     364     401 ..     355     406 .. 0.94
   3 ?   -2.3   0.0       5.1   2.2e+03      51      71 ..     552     572 ..     522     583 .. 0.60
   4 !   18.2   0.0   2.6e-06    0.0011      19      57 ..     972    1010 ..     967    1026 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                     Zeta_toxin 11 psqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                                   ++   P +++l++  +AG ++l+++++++   +g++ +l + dlR
  gi|121636106|ref|YP_976329.1| 53 HRPLAPWAVVLVA--AAGATYLLTYVRRYY--GGRIAHLVQHDLR 93
                                   4567788888886..5666**********9..9999999999998 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.1e-06
                     Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                     ++G+pG+GKs+la+l+++  + ++++vr+ + d+Rel
  gi|121636106|ref|YP_976329.1| 364 AVVGAPGSGKSTLASLATRCYDVTQGAVRIGGQDVREL 401
                                    589*********************************97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.1
                     Zeta_toxin  51 pDdlRelhPeyeeilkadpkk 71 
                                    pD++ e+ P+y+e+l   p+ 
  gi|121636106|ref|YP_976329.1| 552 PDEVWERCPRYRELLSPAPDL 572
                                    566666666666666554444 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 2.6e-06
                     Zeta_toxin   19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57  
                                     ++ +G++G+GKs+l++l+++  +++ + vr+d+ dlRe+
  gi|121636106|ref|YP_976329.1|  972 VVFVGSTGSGKSTLIKLVARFYDPTHGTVRVDGCDLREF 1010
                                     7789*********************************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.6    0.0002     0.087      19      51 ..     357     387 ..     349     524 .. 0.57
   2 !   16.5   0.2   1.9e-05    0.0084       5      63 ..     952    1008 ..     950    1144 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0002
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd 51 
                                    vr+g  e + ++G++G+GKs+l+  + r +  +
  gi|121636106|ref|YP_976329.1| 357 VRAG--ETLAVVGAPGSGKSTLASLATRCYDVT 387
                                    5666..6799*************8887733333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.9e-05
                         AAA_16    5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63  
                                     R +e+ +L+ +  r+ +g  + v+++G  G+GKs+l++ ++r +  ++g +    cd  
  gi|121636106|ref|YP_976329.1|  952 RTREVPALAGINLRIPAG--QTVVFVGSTGSGKSTLIKLVARFYDPTHGTVRVDGCDLR 1008
                                     778888887777777777..57*******************999999887766666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0012      0.51      20      38 ..     358     376 ..     350     379 .. 0.79
   2 !   13.9   0.0   7.7e-05     0.034      22      39 ..     968     986 ..     960     996 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                         AAA_29  20 dlkg.atlltGpsGsGKSTl 38 
                                    + +g +  ++G+ GsGKSTl
  gi|121636106|ref|YP_976329.1| 358 R-AGeTLAVVGAPGSGKSTL 376
                                    4.3448899**********8 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.7e-05
                         AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                    +g +++++G +GsGKSTl+
  gi|121636106|ref|YP_976329.1| 968 AGqTVVFVGSTGSGKSTLI 986
                                    455899************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.25   1.1e+02      27      40 ..     363     376 ..     351     380 .. 0.84
   2 !    8.9   0.0    0.0022      0.95     111     209 ..     391     539 ..     377     544 .. 0.78
   3 ?    2.5   0.2      0.19        81      26      42 ..     971     987 ..     958     993 .. 0.79
   4 ?    6.2   0.0     0.014       6.2     135     210 ..    1078    1149 ..     999    1156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.25
                                    EEEEESTTSSHHHH CS
                                    xxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnl 40 
                                     a+vG+ GSGKs l
  gi|121636106|ref|YP_976329.1| 363 LAVVGAPGSGKSTL 376
                                    589*********87 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0022
                                    EEETTEEE-HHHHHHHHHCTT-STT......................................................C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx......................................................x RF
                          SMC_N 111 ykingkevtkkevsellesagiske......................................................l 136
                                    ++i g++v++  + +l +  g+ +e                                                      +
  gi|121636106|ref|YP_976329.1| 391 VRIGGQDVRELTLDSLRSAIGLVPEdavlfsgtiganiaygrpdatpeqiataaraahieefvntlpdgyqtavgarglT 470
                                    66667777777777777777777777777777777777777777777777777777777777777777788888888889 PP

                                    S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                    LSgG+++ +ala    +   ++  l ++D+  +a D+     + e+l+e+  +   ++ + r+ ml+ ad++ 
  gi|121636106|ref|YP_976329.1| 471 LSGGQRQRIALARA--L--LHQPRLLIMDDPTSAVDAVIECGIQEVLREAIADRTAVIFTRRRSMLTLADRVA 539
                                    ******98887754..3..3445599******************************************99875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.19
                                    EEEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlld 42 
                                      + vG+ GSGKs l+ 
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIK 987
                                    45669********9986 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.014
                                     TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210 
                                      +LS G+ +L+ala     + v+p  + llDe   aLD +  + v +   +   +   +++++   + e+ad++v 
  gi|121636106|ref|YP_976329.1| 1078 RNLSAGQLQLLALARA---RLVDP-DILLLDEATVALDPATEAVVQRATLTLAARRTTLIVAHGLAIAEHADRIVV 1149
                                     489****999998754...45555.5789**********9988888877788888889999999999999998875 PP

>> ABC_membrane_3  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.8   3.3e-05     0.015       6     155 ..      14     173 ..       9     183 .. 0.77
   2 !   14.4   7.7   3.8e-05     0.017       1     166 [.     616     793 ..     616     877 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                 ABC_membrane_3   6 kkarkrlavtfllvlaenvlllayPlligfaiddllagkvaqlliyalvvll....liligaarrivDTRaysrIyaela 81 
                                     ++r  l + f   la+ v+ +++Pl+    idd +a +   l+ +a+v++       l+  +rr +  R+   +  +l 
  gi|121636106|ref|YP_976329.1|  14 MRHRRDLLLGFGAALAGTVIAVLVPLVTKRVIDDAIAADHRPLAPWAVVLVAaagaTYLLTYVRRYYGGRIAHLVQHDLR 93 
                                    5788999999*****************************9988877777775222267999**********999998886 PP

                 ABC_membrane_3  82 vevv...l..eqrqqdldtS.kvaarlalsrelvdFlEkhlPtlitavvsivgavvmllvlefslglsallillllllll 155
                                       +   l  + rqqd   S +   r +   +lv+ l  ++P ++  v++++ +v ++  l++ l+l+a+l++ ++ l++
  gi|121636106|ref|YP_976329.1|  94 MDAFqalLrwDGRQQDRWSSgQLIVRTTNDLQLVQALLFDVPNVLRHVLTLLLGVAVMTWLSVPLALLAVLLVPVIGLIA 173
                                    553311121134444444331334555555679**********************9999***999999999887776665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-05
                 ABC_membrane_3   1 lktiakkarkrlavtfllvlaenvlllayPlligfaiddllagkvaqlliyalv.....vllliligaarrivDTRaysr 75 
                                    l+++++++r  la+ +llv++     l+ Plli   id  ++++v  +l++a++     v++ ++++    +v   +  +
  gi|121636106|ref|YP_976329.1| 616 LRRLLREFRGPLALSLLLVAVQTCAGLLPPLLIRHGIDVGIRRHVLSALWWAALagtatVVIRWVVQWGSAMVAGYTGEQ 695
                                    7899**********************************988888877777765433333788899988777777766666 PP

                 ABC_membrane_3  76 Iyaelavevvleqr.......qqdldtSkvaarlalsrelvdFlEkhlPtlitavvsivgavvmllvlefslglsallil 148
                                    +   l + v+++ +       + d d  +v+a  a ++ +v Fl + l + +++vv++vg +v ll +   l l++++ +
  gi|121636106|ref|YP_976329.1| 696 VLFRLRSVVFAHAQrlgldafEDDGDAQIVTAVTADVEAIVAFLRTGLVVAVISVVTLVGILVALLAIRARLVLLIFTTM 775
                                    666665555544430111111566677889999999******************************************99 PP

                 ABC_membrane_3 149 lllllllprFarrnerln 166
                                     +l+l   +F r ++  +
  gi|121636106|ref|YP_976329.1| 776 PVLALATWQFRRASNWTY 793
                                    999999999998876555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0015      0.65       4      17 ..     365     378 ..     363     417 .. 0.81
   2 ?   -2.0   0.0       8.4   3.7e+03      72     113 ..     515     558 ..     480     569 .. 0.78
   3 !   11.9   0.2   0.00042      0.18       2      30 ..     972    1004 ..     971    1151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                         AAA_33   4 lvGlpGsGKstlae 17 
                                    +vG+pGsGKstla 
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLAS 378
                                    89**********97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.4
                         AAA_33  72 nvildatnlsrrerarflklarrlgvpv..rivvvetdeetlke 113
                                     +i+d t +   +r+ +l la r  v +  r+++v t++e++++
  gi|121636106|ref|YP_976329.1| 515 EAIADRTAVIFTRRRSMLTLADRVAVLDsgRLLDVGTPDEVWER 558
                                    56788887777777777777777777654477888888888775 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00042
                         AAA_33    2 vllvGlpGsGKstlaerllkklg....avllss 30  
                                     v++vG  GsGKstl++ +++  +    +v+++ 
  gi|121636106|ref|YP_976329.1|  972 VVFVGSTGSGKSTLIKLVARFYDpthgTVRVDG 1004
                                     79*************998764444444555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.03        13      92     121 ..     352     382 ..     331     397 .. 0.76
   2 !   15.1   0.0   3.8e-05     0.016      98     120 ..     968     990 ..     947    1003 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                                    HHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallp 121
                                    e++  ++  +t ++vG  G GKStL    + 
  gi|121636106|ref|YP_976329.1| 352 EISLSVRAgETLAVVGAPGSGKSTLASLATR 382
                                    55555555599**************876555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.8e-05
                                    TTSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                    +++t+v+vG++G GKStLi+ ++
  gi|121636106|ref|YP_976329.1| 968 AGQTVVFVGSTGSGKSTLIKLVA 990
                                    469****************9765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.003       1.3       7      27 ..     362     382 ..     357     410 .. 0.85
   2 !   10.6   0.0    0.0012      0.52       8      30 ..     972     994 ..     968    1018 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                         AAA_22   7 ilvvtGesGtGKTtllrrlle 27 
                                     l+v+G +G+GK+tl+   ++
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASLATR 382
                                    589************987665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                         AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                    +v +G +G+GK+tl++ +++ +d
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLVARFYD 994
                                    6889**************99986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0068         3      20      49 ..     362     391 ..     353     405 .. 0.82
   2 ?   -1.1   0.0         3   1.3e+03     124     141 ..     906     923 ..     901     931 .. 0.82
   3 !   11.6   0.7   0.00039      0.17      19     113 ..     970    1122 ..     963    1133 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0068
                         AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                    + +++G++G+GK+t+ + +++ ++  +g v
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASLATRCYDVTQGAV 391
                                    6789***********999999888765444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                         AAA_30 124 DerQlasVeaGgvlrdlv 141
                                    D+ Q a+V aG++ ++l 
  gi|121636106|ref|YP_976329.1| 906 DDYQRAAVAAGRIRSLLS 923
                                    999*********999883 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00039
                         AAA_30   19 rvavltGpAGtGKttalkalreaweaa.g.........................grviglAptgkaAkvLa..eelgi 68  
                                     +++v +G  G+GK+t++k +++ ++   g                         ++  ++A t + A + +  +++++
  gi|121636106|ref|YP_976329.1|  970 QTVVFVGSTGSGKSTLIKLVARFYDPThGtvrvdgcdlrefdvdgyrnrlgivtQEQYVFAGTVRDAIAYGrpDATDA 1047
                                     47899*******************999557555555555555555554444444222233333332222222223333 PP

                         AAA_30   69 eastiakllkrlk..............................grarlepgtllivDEagmvdtkqlaallkaae 113 
                                     + ++ a+ + ++                               +rarl + ++l+ DEa ++    ++a++++a+
  gi|121636106|ref|YP_976329.1| 1048 QVERAAREVGAHPmitaldngylhqvtaggrnlsagqlqllalARARLVDPDILLLDEATVALDPATEAVVQRAT 1122
                                     444444444444477777777777777888888888888888877778888888888888887777777777776 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       7.5   3.3e+03      59      93 ..      16      51 ..      11      75 .. 0.61
   2 !   12.6   0.0   0.00021     0.093       8      31 ..     365     388 ..     361     407 .. 0.88
   3 ?    4.1   0.0      0.09        39       6      29 ..     972     995 ..     969    1013 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.5
                 Ploopntkinase3 59 krreafsGt.dalassiidkavPwvetkPydlllae 93
                                   +rr+++ G   ala ++i   vP v+ +  d  +a 
  gi|121636106|ref|YP_976329.1| 16 HRRDLLLGFgAALAGTVIAVLVPLVTKRVIDDAIAA 51
                                   566666664146777777777777777665544443 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00021
                 Ploopntkinase3   8 lvGqPGaGkstlmaeltkgfdrsk 31 
                                    +vG+PG+Gkstl +  t+++d ++
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASLATRCYDVTQ 388
                                    89******************9765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.09
                 Ploopntkinase3   6 iylvGqPGaGkstlmaeltkgfdr 29 
                                    + +vG+ G+Gkstl+  +++ +d 
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLVARFYDP 995
                                    5679**********9888887775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0057       2.5       2      20 ..     363     381 ..     362     411 .. 0.84
   2 !    8.9   0.0    0.0034       1.5       2      19 ..     972     989 ..     971    1003 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0057
                                    EEEEESTTSSHHHHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinalt 20 
                                     a+vG p +GKStL +  t
  gi|121636106|ref|YP_976329.1| 363 LAVVGAPGSGKSTLASLAT 381
                                    69************87666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0034
                                    EEEEESTTSSHHHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinal 19 
                                    v++vG + +GKStLi+  
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLV 989
                                    89*************865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00016     0.071      28      54 ..     356     381 ..     330     392 .. 0.74
   2 ?   -2.5   0.1       7.2   3.1e+03      82     138 ..     672     737 ..     658     746 .. 0.54
   3 !    8.5   0.0     0.003       1.3      29      50 ..     965     986 ..     955     993 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                         AAA_25  28 gllpagelallaGapgtGKttlaldla 54 
                                     + +age+ +++Gapg+GK+tla+   
  gi|121636106|ref|YP_976329.1| 356 SV-RAGETLAVVGAPGSGKSTLASLAT 381
                                    44.69*****************98655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                         AAA_25  82 sedelrrRlravgeal...........rddarllvldlagveslpLfakdrggtlltadvdaleaaie 138
                                    ++  + r++ ++g a+           r+ + + + ++++   l+ f++d + +++ta+++++ea + 
  gi|121636106|ref|YP_976329.1| 672 TATVVIRWVVQWGSAMvagytgeqvlfRL-RSVVFAHAQRL-GLDAFEDDGDAQIVTAVTADVEAIVA 737
                                    55555566667776666666666555322.22233333332.44555555555557777777666554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.003
                         AAA_25  29 llpagelallaGapgtGKttla 50 
                                     +pag +++++G +g+GK+tl 
  gi|121636106|ref|YP_976329.1| 965 RIPAGQTVVFVGSTGSGKSTLI 986
                                    69******************96 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0079       3.5       3      21 ..     364     381 ..     362     409 .. 0.81
   2 !    9.5   0.4    0.0024       1.1       2      27 ..     972    1002 ..     971    1157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0079
                         AAA_28   3 vitGgestGKTtlleaLaa 21 
                                    +++G++++GK+tl++ La 
  gi|121636106|ref|YP_976329.1| 364 AVVGAPGSGKSTLAS-LAT 381
                                    789*********985.555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0024
                         AAA_28    2 ivitGgestGKTtlleaLa.....argypvv 27  
                                     +v++G  ++GK+tl++  a      +g++ v
  gi|121636106|ref|YP_976329.1|  972 VVFVGSTGSGKSTLIKLVArfydpTHGTVRV 1002
                                     8***************999555444466544 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.014       6.2     103     150 ..     334     381 ..     317     422 .. 0.81
   2 !    8.6   0.0    0.0019      0.83     127     193 ..     967    1034 ..     940    1044 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                          T2SSE 103 ltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                    l+++ +++    +  + + ++ +vr+  ++ v G+ gsGK+tl+  + 
  gi|121636106|ref|YP_976329.1| 334 LEFQRVSFGYVADRPVLREISLSVRAGETLAVVGAPGSGKSTLASLAT 381
                                    55666666666777788889999*******************987665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                          T2SSE  127 rerglilvsGgTgsGKttllyallkeinksderivtvE..DpvEiqleg.anqvqlnakkakvtfadllr 193 
                                      + +++++ G TgsGK+tl+  +  + + + +  v v   D +E +++g  n++ ++++ ++  fa  +r
  gi|121636106|ref|YP_976329.1|  967 PAGQTVVFVGSTGSGKSTLIKLVARFYDPT-HGTVRVDgcDLREFDVDGyRNRLGIVTQ-EQYVFAGTVR 1034
                                     466789999**********98887777666.4444443336666666542456666666.5555666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.04        17       3      22 ..     365     384 ..     363     424 .. 0.71
   2 !    8.8   0.0    0.0047         2       1      35 [.     972    1008 ..     972    1111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.04
                                    EESSTTSSHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakel 22 
                                    ++G pG GK++la+   +  
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASLATRCY 384
                                    79***********8765544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0047
                                     EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                            AAA    1 vllyGppGtGKTllakavakelg..vefleisgsell 35  
                                     v+++G  G GK++l+k va+  +     ++++g +l+
  gi|121636106|ref|YP_976329.1|  972 VVFVGSTGSGKSTLIKLVARFYDptHGTVRVDGCDLR 1008
                                     689****************987533445777777766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.038        17       2      32 ..     363     395 ..     362     412 .. 0.70
   2 !    9.6   0.1    0.0018      0.78       3      52 ..     973    1024 ..     971    1056 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.038
                                    EEEE--TTSSHHHHHHHHHHHH.....GGGEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellk..ssgvkvgG 32 
                                    +++ G pG+GK+Tl + +++  +  +  v++gG
  gi|121636106|ref|YP_976329.1| 363 LAVVGAPGSGKSTLASLATRCYDvtQGAVRIGG 395
                                    5788**********9988765430033466666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                     EEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-------EEEEEET CS
                       NTPase_1    3 fiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrrigFkivdl 52  
                                     +  G+ G+GK+Tl+k v++  +     v+v+G   +e   +g r    iv+ 
  gi|121636106|ref|YP_976329.1|  973 VFVGSTGSGKSTLIKLVARFYDPThgTVRVDGCDLREFDVDGYRNRLGIVTQ 1024
                                     56799*************99875543799*************9999998875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0     0.009       3.9       2      17 ..     362     377 ..     361     384 .. 0.90
   2 ?    6.8   0.0     0.013       5.6       2      21 ..     971     990 ..     970     994 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                                    CEEEEC-TTTCHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLl 17 
                                    ++++ G++GsGK+tL+
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLA 377
                                    789***********98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    +v+  G  GsGK+tL++ +a
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIKLVA 990
                                    899************98665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0033       1.5       3      18 ..     365     380 ..     363     405 .. 0.82
   2 ?    5.7   0.0     0.046        20       1      20 [.     972     991 ..     972    1026 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0033
                         AAA_18   3 ltGtpGvGKttlakeL 18 
                                    + G+pG+GK+tla   
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASLA 380
                                    89**********9865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.046
                         AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                    ++  G  G+GK+tl k +++
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLVAR 991
                                    577899**********9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0028       1.2      22      45 ..     362     385 ..     354     392 .. 0.83
   2 ?   -1.1   0.0         2   8.7e+02      95     142 ..     480     531 ..     471     559 .. 0.67
   3 ?    5.3   0.1     0.022       9.6      22      42 ..     971     991 ..     964    1000 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                                    EEEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                                     +a+vG +G+GK+tla+ + + +d
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASLATRCYD 385
                                    589*************98877655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                                    HHHHHCCCTTEEEEEEEE-SHHH....H......HHHHCHTTSEEEEEESBCC CS
                         NB-ARC  95 klvrlLltkrfllvlDDVweeed....wdkig.vvlparenrlrvllTTRdee 142
                                     l r+Ll++  ll++DD    +d       i+ v + a   r  v++T R   
  gi|121636106|ref|YP_976329.1| 480 ALARALLHQPRLLIMDDPTSAVDavieC-GIQeVLREAIADRTAVIFTRRRSM 531
                                    578999999999999*977776654222.233134456677888888887654 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.022
                                    EEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqiln 42 
                                     v +vG  G+GK+tl+k + +
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIKLVAR 991
                                    57899**********998766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.016       7.2      44      65 ..     357     378 ..     344     393 .. 0.86
   2 ?   -2.1   0.0       6.3   2.7e+03     102     137 ..     482     516 ..     473     534 .. 0.59
   3 ?    6.0   0.0      0.02       8.9      29      63 ..     950     985 ..     932     991 .. 0.81
   4 ?   -2.6   0.0       9.2     4e+03     103     130 ..    1092    1118 ..    1082    1144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                      IstB_IS21  44 iekkenivllGpsGvGKshlai 65 
                                    +++ e ++++G +G GKs la 
  gi|121636106|ref|YP_976329.1| 357 VRAGETLAVVGAPGSGKSTLAS 378
                                    67899***************94 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.3
                      IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                    a + l +++lli+Dd     +d   +  + ev+ ++
  gi|121636106|ref|YP_976329.1| 482 ARALLHQPRLLIMDDPT-SAVDAVIECGIQEVLREA 516
                                    44556778999999853.445555555555555444 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.02
                      IstB_IS21  29 sldkrkvkeLatlsf.iekkenivllGpsGvGKshl 63 
                                    s+  r+v +La+ +  i + + +v++G +G GKs l
  gi|121636106|ref|YP_976329.1| 950 SYRTREVPALAGINLrIPAGQTVVFVGSTGSGKSTL 985
                                    56678899999888658999**************87 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 9.2
                      IstB_IS21  103 lkrllkvdllilDdlgllpldqaeaell 130 
                                      +rl+ +d+l+lD+   + ld a ++++
  gi|121636106|ref|YP_976329.1| 1092 RARLVDPDILLLDEAT-VALDPATEAVV 1118
                                     578999999***9964.45666555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.018       7.8       4      23 ..     365     384 ..     362     399 .. 0.84
   2 ?    6.9   0.0     0.013       5.8       2      23 ..     972     993 ..     971    1006 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                                    EE--SSSSHHHHHHHGGGGB CS
                          AAA_5   4 LvGppGtgKselaerlaaal 23 
                                    +vG+pG+gKs+la    + +
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASLATRCY 384
                                    79***********9887765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                    EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                    v+ vG +G+gKs+l++ +a+++
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLVARFY 993
                                    789***************9987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.18        77      28      51 ..     355     378 ..     351     390 .. 0.83
   2 !   10.8   0.0   0.00057      0.25      29      58 ..     965     994 ..     958    1002 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                          AAA_7  28 lllknkkpvllvGptGtGKtviik 51 
                                    l ++++  + +vG  G+GK+++++
  gi|121636106|ref|YP_976329.1| 355 LSVRAGETLAVVGAPGSGKSTLAS 378
                                    6688899999**********9986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00057
                          AAA_7  29 llknkkpvllvGptGtGKtviikdllkkld 58 
                                     + +++ v++vG+tG+GK+++ik + + +d
  gi|121636106|ref|YP_976329.1| 965 RIPAGQTVVFVGSTGSGKSTLIKLVARFYD 994
                                    5678899***************98776655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1         1   4.5e+02       3      17 ..     364     378 ..     363     405 .. 0.81
   2 ?    1.0   0.0       0.7   3.1e+02     220     272 ..     452     503 ..     391     526 .. 0.76
   3 !    8.5   0.1    0.0035       1.5       3      22 ..     973     992 ..     971    1018 .. 0.85
   4 ?    4.2   0.1     0.071        31     235     274 ..    1078    1113 ..    1006    1135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
                         AAA_21   3 vliGpNgsGKSnLLd 17 
                                    +++G+ gsGKS+L  
  gi|121636106|ref|YP_976329.1| 364 AVVGAPGSGKSTLAS 378
                                    689*********965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.7
                         AAA_21 220 gvvflengdgqelparel..SdGtkrllalltallralkkgsllliDEpEngLHP 272
                                    +v +l +g+   + ar l  S G+++ +al+ all ++   +ll+ D+p +  + 
  gi|121636106|ref|YP_976329.1| 452 FVNTLPDGYQTAVGARGLtlSGGQRQRIALARALLHQP---RLLIMDDPTSAVDA 503
                                    566666666677777777779*****99*******999...********998876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0035
                         AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                    v++G  gsGKS+L+++   +
  gi|121636106|ref|YP_976329.1| 973 VFVGSTGSGKSTLIKLVARF 992
                                    99*************98665 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.071
                         AAA_21  235 relSdGtkrllalltallralkkgsllliDEpEngLHPkl 274 
                                     r+lS G+++llal+ a l ++   ++ll+DE    L+P +
  gi|121636106|ref|YP_976329.1| 1078 RNLSAGQLQLLALARARLVDP---DILLLDEATVALDP-A 1113
                                     467999999966666666666...*******9999999.3 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0064       2.8      40      55 ..     361     376 ..     338     381 .. 0.77
   2 ?    5.2   0.0     0.027        12      41      56 ..     971     986 ..     923     989 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0064
                                    .SEEEE--TTSSHHHH CS
                   FtsK_SpoIIIE  40 shllvaGatgsGKSta 55 
                                      l v+Ga+gsGKSt 
  gi|121636106|ref|YP_976329.1| 361 ETLAVVGAPGSGKSTL 376
                                    4688**********95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                                    SEEEE--TTSSHHHHH CS
                   FtsK_SpoIIIE  41 hllvaGatgsGKStal 56 
                                     ++ +G+tgsGKSt +
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLI 986
                                    46779********986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0     0.003       1.3       4      45 ..     362     400 ..     359     462 .. 0.82
   2 ?    4.3   0.0     0.066        29       3      22 ..     970     989 ..     968    1046 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                         AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpd 45 
                                     ++++G +g+GK+tla+ +   + + d+ +G+ ++ + ++ +
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASLA---TRCYDVTQGAVRIGGQDVRE 400
                                    5799*************99...77778877777777776655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    + ++ +G+ g+GK+tl+k  
  gi|121636106|ref|YP_976329.1| 970 QTVVFVGSTGSGKSTLIKLV 989
                                    67899************987 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.035        15       3      31 ..     363     391 ..     361     406 .. 0.80
   2 ?    7.2   0.0    0.0079       3.5       2      21 ..     971     990 ..     970    1016 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.035
                                    EEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                           cobW   3 tvltGflGsGKTtLlnhllenraglklav 31 
                                    + ++G +GsGK+tL +  +++ +  + av
  gi|121636106|ref|YP_976329.1| 363 LAVVGAPGSGKSTLASLATRCYDVTQGAV 391
                                    5799**********888888877777666 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0079
                                    EEEEEESTTCCHHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll 21 
                                    ++v++G+ GsGK+tL++ + 
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIKLVA 990
                                    5799************8765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.026        11      25      42 ..     362     379 ..     340     383 .. 0.84
   2 ?    7.5   0.1    0.0086       3.8      29      42 ..     975     988 ..     972    1000 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                          DUF87  25 HlAilgsTGsGKSntvav 42 
                                     lA++g  GsGKS+++++
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASL 379
                                    58************9975 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0086
                          DUF87  29 lgsTGsGKSntvav 42 
                                    +gsTGsGKS+++++
  gi|121636106|ref|YP_976329.1| 975 VGSTGSGKSTLIKL 988
                                    69*********986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0062       2.7       1      21 [.     366     386 ..     366     392 .. 0.84
   2 ?    4.6   0.1      0.09        40       1      23 [.     975     997 ..     975    1000 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0062
                                    EE-TTSSHHHHHHHHHHHHTE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygf 21 
                                    +G PGsGK+t+++   + y++
  gi|121636106|ref|YP_976329.1| 366 VGAPGSGKSTLASLATRCYDV 386
                                    7***********877776665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.09
                                    EE-TTSSHHHHHHHHHHHHTEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfth 23 
                                    +G  GsGK+t+++ +++ y+ th
  gi|121636106|ref|YP_976329.1| 975 VGSTGSGKSTLIKLVARFYDPTH 997
                                    6889********88888887666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.008       3.5      16      40 ..     354     378 ..     345     386 .. 0.81
   2 ?    4.5   0.0     0.046        20      22      43 ..     969     990 ..     958    1000 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.008
                   Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmlak 40 
                                     +++  g  l +vG+pGsGK+ la+
  gi|121636106|ref|YP_976329.1| 354 SLSVRAGETLAVVGAPGSGKSTLAS 378
                                    556666778999***********97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.046
                   Mg_chelatase  22 gHnlllvGppGsGKtmlakrlp 43 
                                    g  +++vG+ GsGK+ l+k ++
  gi|121636106|ref|YP_976329.1| 969 GQTVVFVGSTGSGKSTLIKLVA 990
                                    45799***********998765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.018       7.8       3      17 ..     365     378 ..     363     393 .. 0.76
   2 ?    5.7   0.0     0.025        11       4      21 ..     975     992 ..     972    1013 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                Viral_helicase1   3 vhGvpGcGKStlirk 17 
                                    v G+pG+GKStl  +
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTL-AS 378
                                    88*********4.44 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                Viral_helicase1   4 hGvpGcGKStlirkllrt 21 
                                     G  G+GKStli+ ++r 
  gi|121636106|ref|YP_976329.1| 975 VGSTGSGKSTLIKLVARF 992
                                    5889*********99987 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0039       1.7      16      47 ..     347     378 ..     335     391 .. 0.81
   2 ?    2.9   0.1       0.1        45      30      50 ..     970     990 ..     954    1002 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                                    HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHH CS
                           MeaB  16 kellerllakaGraqvvGltGvPGaGkstlve 47 
                                    + +l++++ +    + + + G PG+Gkstl +
  gi|121636106|ref|YP_976329.1| 347 RPVLREISLSVRAGETLAVVGAPGSGKSTLAS 378
                                    6678888777777788999**********976 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                                    EEEEEEE-TTSSHHHHHHHHH CS
                           MeaB  30 qvvGltGvPGaGkstlvealg 50 
                                    q v + G+ G+Gkstl++ ++
  gi|121636106|ref|YP_976329.1| 970 QTVVFVGSTGSGKSTLIKLVA 990
                                    567789**********97654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.085        37       3      17 ..     365     379 ..     363     390 .. 0.85
   2 ?    7.1   0.0     0.016         7       1      20 [.     972     991 ..     972    1025 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.085
                   RNA_helicase   3 lyGpsgeGKStlake 17 
                                    ++G++g GKStla  
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASL 379
                                    89**********975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                   RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                    ++++G++g GKStl+k +a+
  gi|121636106|ref|YP_976329.1| 972 VVFVGSTGSGKSTLIKLVAR 991
                                    6899***********98543 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.031        14       1      17 [.     365     381 ..     365     392 .. 0.81
   2 ?    6.0   0.1      0.02       8.9       2      22 ..     975     995 ..     974    1003 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                     ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                    vvG +GsGK+t+ +  +
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLASLAT 381
                                    89*********987655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                     ATP_bind_1   2 vGpaGsGKttfvgalseilel 22 
                                    vG  GsGK+t+++ ++ +++ 
  gi|121636106|ref|YP_976329.1| 975 VGSTGSGKSTLIKLVARFYDP 995
                                    8************99988765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.046        20       3      43 ..     361     400 ..     359     416 .. 0.78
   2 ?    6.0   0.0     0.023        10       2      42 ..     969    1008 ..     968    1018 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.046
                                    EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                     APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43 
                                     ++ + G  gsGKst+a     +  +  + ++++ G+ vR+
  gi|121636106|ref|YP_976329.1| 361 ETLAVVGAPGSGKSTLASLAT-RCYDVTQGAVRIGGQDVRE 400
                                    678889***********8655.5566666777888888885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.023
                                     -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT CS
                     APS_kinase    2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvR 42  
                                     g +v + G +gsGKst+ + +++   +  + ++++dG  +R
  gi|121636106|ref|YP_976329.1|  969 GQTVVFVGSTGSGKSTLIKLVAR-FYDPTHGTVRVDGCDLR 1008
                                     6899*************988875.55556666667776666 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.58   2.5e+02      25      47 ..     362     384 ..     346     410 .. 0.82
   2 ?    9.4   0.0    0.0012      0.53      25      51 ..     971     997 ..     961    1008 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.58
                                    EEEEEESTTSSHHHHHHHHHHHC CS
                        G-alpha  25 kllllGqseSGKsTilkqlklly 47 
                                    +l ++G+ +SGKsT+     + y
  gi|121636106|ref|YP_976329.1| 362 TLAVVGAPGSGKSTLASLATRCY 384
                                    57899*********987666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                    EEEEEESTTSSHHHHHHHHHHHCS--- CS
                        G-alpha  25 kllllGqseSGKsTilkqlkllykkgf 51 
                                    +++++G+ +SGKsT++k + ++y++++
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIKLVARFYDPTH 997
                                    5899*******************9986 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.046        20      24      50 ..     359     386 ..     353     396 .. 0.78
   2 ?    5.4   0.0     0.022       9.8      21      58 ..     965    1003 ..     963    1031 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.046
                          AAA_8  24 rghaL.lvGvgGsGrqsltkLAafiael 50 
                                     g++L +vG  GsG+ +l++LA+   ++
  gi|121636106|ref|YP_976329.1| 359 AGETLaVVGAPGSGKSTLASLATRCYDV 386
                                    56666258**************987655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                          AAA_8   21 rqprgh.aLlvGvgGsGrqsltkLAafiaelelfqievt 58  
                                     r+p g+ +  vG  GsG+ +l+kL a   + +  +++v+
  gi|121636106|ref|YP_976329.1|  965 RIPAGQtVVFVGSTGSGKSTLIKLVARFYDPTHGTVRVD 1003
                                     5666652568**************998877776666664 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.3   5.9e+02      24      36 ..     365     377 ..     352     399 .. 0.87
   2 ?    9.6   0.1    0.0027       1.2      21      37 ..     971     987 ..     962     991 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                         AAA_23  24 ItGpNGaGKTTil 36 
                                    ++G  G+GK+T+ 
  gi|121636106|ref|YP_976329.1| 365 VVGAPGSGKSTLA 377
                                    68999******85 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                         AAA_23  21 ltlItGpNGaGKTTild 37 
                                     ++++G +G+GK+T++ 
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIK 987
                                    5799***********96 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.31   1.4e+02      21      42 ..     359     381 ..     349     393 .. 0.77
   2 ?    6.7   0.0    0.0067       2.9      23      44 ..     971     992 ..     957    1001 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.31
                         AAA_10  21 asas.liiGdlGnGKSvlakllv 42 
                                    a ++ +++G +G GKS la l+ 
  gi|121636106|ref|YP_976329.1| 359 AGETlAVVGAPGSGKSTLASLAT 381
                                    444449**********9998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0067
                         AAA_10  23 asliiGdlGnGKSvlakllvly 44 
                                     ++++G++G GKS l+kl+  +
  gi|121636106|ref|YP_976329.1| 971 TVVFVGSTGSGKSTLIKLVARF 992
                                    349**************98765 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5      0.28   1.2e+02       8      32 ..      17      40 ..      14      41 .. 0.80
   2 ?    5.2   0.1     0.049        21       8      26 ..     657     675 ..     656     682 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                   CytB6-F_Fe-S  8 rRqllNlllvGaialtaaaaLyPvv 32
                                   rR ll l  ++a+a+t  a L+P v
  gi|121636106|ref|YP_976329.1| 17 RRDLL-LGFGAALAGTVIAVLVPLV 40
                                   55555.56799************87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                   CytB6-F_Fe-S   8 rRqllNlllvGaialtaaa 26 
                                    rR +l+ l+ +a+a+ta+ 
  gi|121636106|ref|YP_976329.1| 657 RRHVLSALWWAALAGTATV 675
                                    9****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.96u 0.30s 00:00:01.26 Elapsed: 00:00:00.48
# Mc/sec: 7545.90
//
Query:       gi|121636107|ref|YP_976330.1|  [L=211]
Description: LuxR family two component transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-13   49.9   0.3    3.6e-13   48.8   0.3    1.6  1  GerE        Bacterial regulatory proteins, luxR family
    0.00012   21.8   0.1    0.00045   19.9   0.1    2.1  1  HTH_23      Homeodomain-like domain
    0.00072   19.5   0.2     0.0023   17.9   0.1    1.9  2  HTH_29      Winged helix-turn helix
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.052   13.3   0.0    1.6  1  HTH_38      Helix-turn-helix domain
      0.023   15.1   0.1      0.044   14.2   0.1    1.5  1  GcrA        GcrA cell cycle regulator
       0.04   13.4   0.1      0.084   12.4   0.1    1.5  1  Sigma70_r4  Sigma-70, region 4
      0.079   13.8   0.0       0.18   12.7   0.0    1.7  1  EF-hand_11  EF-hand domain


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.3   1.4e-16   3.6e-13       2      57 .]     150     205 ..     149     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.4e-16
                                    SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHHH CS
                           GerE   2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrla 57 
                                     L +RE+ vLrlla+G+s+ ++A +ln  e+T+k+ +  i ++L++++r+++v +a
  gi|121636107|ref|YP_976330.1| 150 ALAEREVAVLRLLADGLSTHQVAVQLNYCERTIKNIVHDIVTRLKLRNRTHAVAHA 205
                                    5899************************************************9986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.8e-07   0.00045       8      39 ..     156     187 ..     149     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.8e-07
                         HTH_23   8 lrillllaeGlsvreIAreLgvsrrTvyrwlk 39 
                                      +l+lla+Gls++++A +L+  +rT+ ++++
  gi|121636107|ref|YP_976330.1| 156 VAVLRLLADGLSTHQVAVQLNYCERTIKNIVH 187
                                    468999999*********************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   4.6e+03       5      19 ..     113     127 ..     110     134 .. 0.64
   2 !   17.9   0.1     9e-07    0.0023       3      36 ..     157     189 ..     156     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                         HTH_29   5 llllaeGvstvsqiA 19 
                                    ++l+aeG  +  + +
  gi|121636107|ref|YP_976330.1| 113 IRLSAEGRLRLPERV 127
                                    778888876555555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 9e-07
                         HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrf 36 
                                    ++l+lla+G+s + q+A +l++++rt+ +++++ 
  gi|121636107|ref|YP_976330.1| 157 AVLRLLADGLS-THQVAVQLNYCERTIKNIVHDI 189
                                    69********8.*****************99976 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.052      13      42 ..     158     187 ..     150     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                         HTH_38  13 IerllaeGlslreIArrLgrspsTIsRElk 42 
                                      rlla Gls  ++A +L++   TI + ++
  gi|121636107|ref|YP_976330.1| 158 VLRLLADGLSTHQVAVQLNYCERTIKNIVH 187
                                    46899********************99986 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.7e-05     0.044       9      55 ..     156     205 ..     151     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                           GcrA   9 elLkklwleGlSasqiaaqlg...gvsRnAViGkvhRLglsgrakalept 55 
                                     +  +l  +GlS+ q+a ql+      +n V   v RL+l  r +a+ ++
  gi|121636107|ref|YP_976330.1| 156 VAVLRLLADGLSTHQVAVQLNyceRTIKNIVHDIVTRLKLRNRTHAVAHA 205
                                    44456889*************55445569999*********999887655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.3e-05     0.084       9      49 ..     153     194 ..     149     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                    HHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   9 erevlelrf.geglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    erev +lr   +gl+ ++++ +l+  + +++ i ++ + +L+
  gi|121636107|ref|YP_976330.1| 153 EREVAVLRLlADGLSTHQVAVQLNYCERTIKNIVHDIVTRLK 194
                                    7888888888899***************************98 PP

>> EF-hand_11  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.1e-05      0.18      55      99 ..     103     147 ..      77     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                                    HHHHHHHHHTS-B-TTS-EEHHHHHHHHCS-.--------S-... CS
                     EF-hand_11  55 deqfdrlwselpvnakgrlkyqdflsklsiervaatpmaagdsge 99 
                                    +  fd + + + + a grl+ ++ + ++ + r+ +tp a  d+  
  gi|121636107|ref|YP_976330.1| 103 QSTFDCIVETIRLSAEGRLRLPERVQRYLVGRIKSTPTAEPDTPC 147
                                    4579***********************************999643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1336.83
//
Query:       gi|121636108|ref|YP_976331.1|  [L=194]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-07   31.0   0.0    3.7e-07   29.8   0.0    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
    0.00049   20.0   0.0    0.00081   19.3   0.0    1.3  1  TetR_C_13  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   4.1e-11   3.7e-07       5      44 ..      12      52 ..       9      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.1e-11
                                   HHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTS.SHHHHH CS
                         TetR_N  5 ArelfaerGydattvreIAkrAGvskgalYryFp.sKeeLl 44
                                   A+ l+ erG +at ++++ ++ G  +g+ Y+yFp ++ +Ll
  gi|121636108|ref|YP_976331.1| 12 AALLIRERGAHATAISDVLQHSGAPRGSAYHYFPgGRTQLL 52
                                   7779******************************8888887 PP

>> TetR_C_13  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     9e-08   0.00081       5     110 ..      76     181 ..      73     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9e-08
                                    HHHHHHHHHHHHHHTTTT----HHHHHHHTGGGS-TTHHHHHHHHHHH...HHHHHHHHHHHHHCTTSS-TTS-HHHHHH CS
                      TetR_C_13   5 rlrafvedakagmeryefkrGCLvGnLgqEvaalpesfrerleevled...wqkrvaacleeaqeageiaadadaeelae 81 
                                     l a++++ ++++   +f+ GC +  +  E+++ +++   r+  v+++     +r ++   +   a+ i +d  a+ela 
  gi|121636108|ref|YP_976331.1|  76 LLDALIDKYRQQLLSTDFRAGCPIAAVSVEAGDEQDRE--RMAPVIARaaaVFDRWSDLTAQRFIADGIPPD-RAHELAV 152
                                    5788899999999****************999876654..44444443000334555555566667778665.56789** PP

                                    HHHHHHHHHHHHHHHHTSSHHHHHHHHHH CS
                      TetR_C_13  82 ffwigWeGAvlRaklerstqPlelfletf 110
                                    +  ++ eGA+l a++ r+ +Pl+l  + +
  gi|121636108|ref|YP_976331.1| 153 LATSTLEGAILLARVRRDLTPLDLVHRQL 181
                                    **********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1430.58
//
Query:       gi|121636109|ref|YP_976332.1|  [L=748]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-30  106.1   0.0    3.1e-30  105.5   0.0    1.2  1  Molybdopterin    Molybdopterin oxidoreductase
      6e-15   55.2   0.1    1.1e-14   54.4   0.1    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    4.2e-10   39.5   0.6    7.5e-10   38.6   0.6    1.4  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   5.2e-34   3.1e-30       1     398 [.      61     430 ..      61     452 .. 0.83

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 5.2e-34
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEE.EEBTSSCSHHHHHHHHHHHHHTT-EEE-BEEC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvag.fssgplmsmeslaslkkllsllggknlsfydw 79 
                                    Rl  Pm R   r +G ++++ Wd+A  +ia+ +k++++++g d+++  ++ g+ + +   +s++ +l++lg+      + 
  gi|121636109|ref|YP_976332.1|  61 RLSSPMRR---RADGTYEEIDWDTAIVEIAEGFKQIRDTHGGDKIFYyGGGGQGNHLGGAYSGA-FLKALGSR--YRSNA 134
                                    9*******...************************************99999999999999775.99999994..44555 PP

                                    CGGGTTHHHH...CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC..-EEEEECSSB-HC CS
                  Molybdopterin  80 yadlppasaq...qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkk..akvivigpryael 154
                                    +a+ ++++a    q +g+            +++en+++ + +G N+   +    ar+    + k+    +ivi+p ++++
  gi|121636109|ref|YP_976332.1| 135 LAQEKTGEAWvdfQLYGGHT---------RGEFENAEVSVFVGKNPWMSQSFPRARVVLNEIAKDpgRSMIVIDPVVTDT 205
                                    66666677633444444443.........468***************99999989888777777789************* PP

                                    GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHH CS
                  Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaakt 234
                                    +k ad +l ++pg da  ++a++ v++qe++ +++fl+ +  g + ++  l+++     ++ ++v  +  r  ar++  +
  gi|121636109|ref|YP_976332.1| 206 AKMADFHLRVQPGCDAWCLAALAAVLVQENLCNEAFLAAHVHGVDTVRAALQEVPVADYAQRCGVDEELLRAAARRIGTA 285
                                    ****************************************************9999999999999999999999999999 PP

                                    TSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCC CS
                  Molybdopterin 235 agksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkeekikfaae 314
                                    a  s +    g+++  +++        L +l+gn  ++gG+  h      +a           + s  + +++++ +a  
  gi|121636109|ref|YP_976332.1| 286 ASVSVFE-DLGIQQAPNSTVCSYLNKLLWILTGNFAKKGGQHLHSS----FAPLF-------SQVSGRTPVTGAPIIAGL 353
                                    9944444.66888888887666666666788887777766555522....22222.......333555788999999999 PP

                                    TTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCG CS
                  Molybdopterin 315 qpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyE 394
                                     pgn++   ++ ++e+        ++++ +   np ++ ad      a++ l+l vv+d+ +t+ta+ a+++LPaa+ +E
  gi|121636109|ref|YP_976332.1| 354 IPGNVVP--EEILTEHP-----DRFRAMIVESGNPAHSLADSAACRAAFQALELMVVVDVAMTETARLAHYVLPAASQFE 426
                                    9999987..55555544.....55668888888*********************************************** PP

                                    SEEE CS
                  Molybdopterin 395 kedl 398
                                    k + 
  gi|121636109|ref|YP_976332.1| 427 KPEA 430
                                    9653 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   1.9e-18   1.1e-14      18     110 ..     634     734 ..     617     735 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.9e-18
                                    CGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC.............S- CS
                Molydop_binding  18 trpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe........agekggn 89 
                                     +p++r+++ ++  ++++ edA+alG++dG l +++++ Gs+e+ ++vte++  G +++p g++         ++  g++
  gi|121636109|ref|YP_976332.1| 634 RDPSWRKRDANG-ALRVSVEDAQALGLADGCLARITTAAGSAEATVEVTETMLAGHAALPNGFGLdytgddgrTVVAGVA 712
                                    456666667677.9*************************************************99********9****** PP

                                    GHCTS.--SCSTTT--CSTT-E CS
                Molydop_binding  90 aNalt.ddatdplsgtpefksv 110
                                     Nalt  +  dp++gtp  k+v
  gi|121636109|ref|YP_976332.1| 713 PNALTsTRWRDPYAGTPWHKHV 734
                                    *****************99987 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.6   1.3e-13   7.5e-10       3      54 ..       6      57 ..       4      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.3e-13
                                   EEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCC CS
                 Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervy 54
                                   + +taC  C ++Cg+ v+v d +  +++gd+ hp + g +C K  +l  + +
  gi|121636109|ref|YP_976332.1|  6 WLPTACILCECNCGIVVQVDDRRLARIRGDKAHPGSAGYTCNKALRLDHYQN 57
                                   779****************************************988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5056.62
//
Query:       gi|121636110|ref|YP_976333.1|  [L=663]
Description: zinc metalloprotease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-98  330.2   0.0    3.3e-98  329.9   0.0    1.1  1  Peptidase_M13_N  Peptidase family M13
    3.4e-81  271.7   0.0    1.3e-80  269.8   0.0    1.9  2  Peptidase_M13    Peptidase family M13
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.029   14.1   0.0    1.5  1  Peptidase_M48    Peptidase family M48
       0.21   10.2   0.0       0.29    9.7   0.0    1.1  1  Glyco_transf_18  Glycosyltransferase family 18


Domain annotation for each model (and alignments):
>> Peptidase_M13_N  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.9   0.0  7.3e-102   3.3e-98       1     382 []      20     400 ..      20     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 329.9 bits;  conditional E-value: 7.3e-102
                Peptidase_M13_N   1 PCdDFYeyaCGnWlkehpipadkssygtfeelqeelekqlreileekpsskedak.avkkaktlYksCmdedaieklglk 79 
                                    P+dD + +++G+Wl+eh+ipad+++ g+f+ l ++ e q+r+++ +++++ ++     +++++lY+s++de+a+e++g++
  gi|121636110|ref|YP_976333.1|  20 PQDDLFGHVNGRWLAEHEIPADRATDGAFRSLFDRAETQVRDLIIQASQAGAAVGtDAQRIGDLYASFLDEEAVERAGVQ 99 
                                    99***********************************99*****6655554444425559******************** PP

                Peptidase_M13_N  80 plldllkelggldsnwkdkfdllellaklrrygidilfslgvdpdpkdpsknvlyldqpglglpdreyylkerdekeeei 159
                                    pl+d l++++++     d ++l+++l++l+r g+   ++++vd+d kd++++ +++ q+g+glpd++yy   rde+++ +
  gi|121636110|ref|YP_976333.1| 100 PLHDELATIDSA----ADATELAAALGTLQRAGVGGGIGVYVDTDSKDSTRYLVHFTQSGIGLPDESYY---RDEQHAAV 172
                                    **********97....7899**************999********************************...788999** PP

                Peptidase_M13_N 160 leaykeylakllkll.ge...eaaelaeevvefekklakitldseerrdpeklynpmtlaelqklapqidwkaylsalle 235
                                    l+ay  ++a+++ l  g    + a+ a+++v++e+kla +++d ++rrd++  yn  t+a+lq+    +dw ++++al +
  gi|121636110|ref|YP_976333.1| 173 LAAYPGHIARMFGLVyGGesrDHAKTADRIVALETKLADAHWDVVKRRDADLGYNLRTFAQLQTEGAGFDWVSWVTALGS 252
                                    *************9444423334889*************************************76699*********433 PP

                Peptidase_M13_N 236 rt.sssekvivtepeylkklskllaettpkrtlanYllwrlvrelapylsdefrdakfefyk.tlsgreer.prwkrCvs 312
                                     + +  ++++v++p+yl  +++l+a+  + ++++ +  wrl+r++ap l++ ++++ fefy+ tl+g+++  +rwkr vs
  gi|121636110|ref|YP_976333.1| 253 -ApDAMTELVVRQPDYLVTFASLWAS-VNVEDWKCWARWRLIRARAPWLTRALVAEDFEFYGrTLTGAQQLrDRWKRGVS 330
                                    .34799******************77.899***************************************8889******* PP

                Peptidase_M13_N 313 qvnsllgmalgrlyvkkyfpeeskkdveemvedikeafkerlkeldWmdeetkkkAleKldamklkigyP 382
                                    +v++l+g+a+g+lyv+++fp+++k++++++v++++ea++ +++eldWm+++t+++Al+Kl++++ k+gyP
  gi|121636110|ref|YP_976333.1| 331 LVENLMGDAVGKLYVQRHFPPDAKSRIDTLVDNLQEAYRISISELDWMTPQTRQRALAKLNKFTAKVGYP 400
                                    *********************************************************************9 PP

>> Peptidase_M13  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.33   1.5e+03      72     120 ..      72     125 ..      58     150 .. 0.82
   2 !  269.8   0.0     3e-84   1.3e-80       1     205 []     452     659 ..     452     659 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.33
                  Peptidase_M13  72 efkekakclieqfsevtepektk.....avngaltlgEniADlggleiAyrayk 120
                                    ++++ a+ + + ++ + ++e+++      + ++l   + +AD   l++A+ + +
  gi|121636110|ref|YP_976333.1|  72 AVGTDAQRIGDLYASFLDEEAVEragvqPLHDELATIDSAADATELAAALGTLQ 125
                                    5667788888888888888888777777899999999999**999999998776 PP

  == domain 2  score: 269.8 bits;  conditional E-value: 3e-84
                  Peptidase_M13   1 NAyYqpeensivfpaailqppffdleypeavNyggiGaviaHEltHgfddqgvqfdkegnlaswltdedaeefkekakcl 80 
                                    NAyY+p +n+ivfpaailqppffd++++ea+NyggiGavi+HE++Hgfddqg+++d +gnl++w+td+d++ef++++k+l
  gi|121636110|ref|YP_976333.1| 452 NAYYNPGMNEIVFPAAILQPPFFDPQADEAANYGGIGAVIGHEIGHGFDDQGAKYDGDGNLVDWWTDDDRTEFAARTKAL 531
                                    9******************************************************************************* PP

                  Peptidase_M13  81 ieqfsevtepektk.....avngaltlgEniADlggleiAyraykklksakeerlpelenltkdqlfFisyAqiwcekqs 155
                                    ieq++++t+++ ++     +v+ga+t+gEni+Dlggl+iA+ ay+   s +++ +p +++lt +q++F+++Aqiw++k++
  gi|121636110|ref|YP_976333.1| 532 IEQYHAYTPRDLVDhpgppHVQGAFTIGENIGDLGGLSIALLAYQ--LSLNGNPAPVIDGLTGMQRVFFGWAQIWRTKSR 609
                                    *********************************************..9******************************** PP

                  Peptidase_M13 156 deellrqllvdvHspaelRvngvlsnlpaFaeaFnckegskmypekekrv 205
                                    ++e++r+l+vd+Hsp+e+R+ngv++n++aF++aF+++e++++++++++rv
  gi|121636110|ref|YP_976333.1| 610 AAEAIRRLAVDPHSPPEFRCNGVVRNVDAFYQAFDVTEDDALFLDPQRRV 659
                                    **********************************************9986 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.5e-06     0.029      33      74 ..     449     497 ..     432     502 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-06
                                    GGT-EEEEESSS-EEEEEEHHHH.........-SSB-HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  33 pkrNAFalgggknkrivltdgLl.........kqllseeelaaVlGHElGH 74 
                                    +++NA+  +g   + iv+  ++l          ++ +   + aV+GHE+GH
  gi|121636110|ref|YP_976333.1| 449 QTVNAYYNPGM--NEIVFPAAILqppffdpqaDEAANYGGIGAVIGHEIGH 497
                                    345********..79***************999999*************** PP

>> Glyco_transf_18  Glycosyltransferase family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   6.5e-05      0.29     421     473 ..     610     662 ..     605     663 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.5e-05
                Glyco_transf_18 421 aikeilktkvkpylPyeftceGmLeRvaayiekqdfCskssklWpPlsalrvl 473
                                    a ++i +  v+p+ P ef c+G+++ v a+ +  d+  + +    P++ +r++
  gi|121636110|ref|YP_976333.1| 610 AAEAIRRLAVDPHSPPEFRCNGVVRNVDAFYQAFDVTEDDALFLDPQRRVRIW 662
                                    667777889***************************99999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4263.52
//
Query:       gi|121636111|ref|YP_976334.1|  [L=219]
Description: hypothetical protein BCG_0236 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.9   0.4       0.07   13.2   0.4    1.3  1  DUF2567   Protein of unknown function (DUF2567)


Domain annotation for each model (and alignments):
>> DUF2567  Protein of unknown function (DUF2567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   3.9e-06      0.07      47     101 ..      45      94 ..      33     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-06
                        DUF2567  47 aalllgllavlavvaavlvW.qaRahRGpvmvaalaiglvaaaalaaevGallvkl 101
                                    a +llg+l+v avv   ++W + R   G  ++++  + l+aa  +a+      +++
  gi|121636111|ref|YP_976334.1|  45 ASTLLGVLSVAAVVLGAMIWsAHRDDSGERTYLTR-VMLTAAEWTAVL-----INM 94 
                                    56899***************778888888887653.334444444443.....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1701.82
//
Query:       gi|121636112|ref|YP_976335.1|  [L=229]
Description: hypothetical protein BCG_0237 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        1.1    8.9   3.9        2.4    7.7   3.9    1.6  1  ABC_membrane  ABC transporter transmembrane region


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.9   0.00013       2.4     111     160 ..       1      50 [.       1      55 [. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00013
                                    HHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 111 lrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsav 160
                                    +r+++   +++++ +l+t+ ++ +++++lgw l +v ++ ++++++v  v
  gi|121636112|ref|YP_976335.1|   1 MRNAWRLVVFDVLAPLATIAALAAIGVLLGWPLWWVSTCSVLVLLVVEGV 50 
                                    67899999***********************************9999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.33
# Mc/sec: 2052.94
//
Query:       gi|121636113|ref|YP_976336.1|  [L=167]
Description: hypothetical protein BCG_0238c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0025   17.9   0.1      0.021   14.9   0.0    2.3  3  HTH_3           Helix-turn-helix
     0.0026   18.1   2.6      0.014   15.8   1.0    2.6  2  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.24   11.8   0.0    1.5  2  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.17     1e+03      38      51 ..      45      58 ..      38      61 .. 0.79
   2 ?   -1.1   0.0      0.35   2.1e+03       4      22 ..      56      75 ..      54      81 .. 0.73
   3 !   14.9   0.0   3.6e-06     0.021       6      44 ..     111     149 ..     101     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHTSE CS
                          HTH_3 38 letlkklakaLgvs 51
                                   + t +++a aL+ +
  gi|121636113|ref|YP_976336.1| 45 IATWQRIAAALKRD 58
                                   67889999999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.35
                                   HHHHTTHHHHHHHHHHT.SS CS
                          HTH_3  4 lRkqlglsqeeLAeklG.vs 22
                                   +R+  g + +++ e+l  ++
  gi|121636113|ref|YP_976336.1| 56 KRDPYGRTARQVEEVLEgIP 75
                                   68888999999988876555 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.6e-06
                                    HHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                          HTH_3   6 kqlglsqeeLAeklGvsrstisriEnGernPsletlkkl 44 
                                    +  gl+++e+A ++Gv+ + ++++  G+ +Ps + ++++
  gi|121636113|ref|YP_976336.1| 111 DRSGLQRQEFASRIGVTAQDLTAYLDGIVSPSASLMIRM 149
                                    578******************************999886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7      0.12   7.4e+02      37      62 ..      78     103 ..      44     105 .. 0.74
   2 !   15.8   1.0   2.3e-06     0.014      11      49 ..     111     148 ..      86     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                         HTH_31  37 Grrgrpspavlealaralgl.dpaera 62 
                                    G   +  ++vl+++ + l++ ++ae+a
  gi|121636113|ref|YP_976336.1|  78 GIA-NAFWEVLDRARTHLDAnERAEVA 103
                                    444.35677888887888876677776 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.3e-06
                         HTH_31  11 eraGLsqeevAerlgvsestlsrlEqGrrgrpspavlea 49 
                                     r+GL ++e A r+gv++  l+ +  G    ps +   +
  gi|121636113|ref|YP_976336.1| 111 DRSGLQRQEFASRIGVTAQDLTAYLDGIV-SPSASLMIR 148
                                    467**************************.6*9986655 PP

>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.1e-05      0.24       3      58 ..      18      69 ..      16      74 .. 0.78
   2 ?   -3.8   0.0       2.9   1.8e+04      59      72 ..     148     161 ..     145     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                                   SS-HHHHHHHHHHHHH..HHHHHHH..SS--HHHHHHHHHHHHHHC----HHHHHH CS
                 Myb_DNA-bind_4  3 kWteeetklLieawgerilelrfqergkkrnkklWeevaeamaergykrspeqCke 58
                                    W+e  ++  +e+w +   ++ ++    +   ++W+ +a+a+++  y r++ q++e
  gi|121636113|ref|YP_976336.1| 18 AWSEPDVDRRVEFWPTVAIRSALE----SGDIATWQRIAAALKRDPYGRTARQVEE 69
                                   699999999999999933444443....233347*******************986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHCSSS CS
                 Myb_DNA-bind_4  59 KienLkkrYkkeke 72 
                                    +++ L+ r+ ++k+
  gi|121636113|ref|YP_976336.1| 148 RMRRLSDRFVRAKS 161
                                    66777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1083.98
//
Query:       gi|121636114|ref|YP_976337.1|  [L=966]
Description: transmembrane transport protein mmpL11 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-73  245.3  38.4    3.5e-37  128.1  14.4    2.3  2  MMPL            MMPL family
    9.9e-07   26.8  13.0    9.9e-07   26.8  13.0    2.6  3  ACR_tran        AcrB/AcrD/AcrF family
    0.00084   19.2  25.9      0.017   14.9   8.1    2.7  3  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1  14.4   5.8e-41   3.5e-37      90     330 ..     117     369 ..      43     372 .. 0.84
   2 !  122.9  16.0   2.2e-39   1.3e-35      55     321 ..     450     704 ..     402     712 .. 0.84

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 5.8e-41
                           MMPL  90 alvtlegdpgsteadesvaairaaveear......pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLliv 163
                                    ++v+l++d+ +  + + ++++r+ +          +   ++ +v G++a+ a  +  +++d++ +e   l +il++L+ v
  gi|121636114|ref|YP_976337.1| 117 YVVSLRLDARNAGTSDVAKKLRDRIGVKGdqsgqtANGKVRLYVIGQGALSAAAAANTKHDIANAERWNLPIILMVLVAV 196
                                    56777777777777777777777654433346677889999*************************************** PP

                           MMPL 164 yrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavira 243
                                    ++Sl+aa++pl+ +v  +++++gl  ++ l  + ++s fv++ +++++ia ++DY l+++ Ryreel+ g++  +av  a
  gi|121636114|ref|YP_976337.1| 197 FGSLAAAAIPLALAVCTVVITMGL--VFVLSMHTTMSVFVTSTVSMFGIALAVDYSLFILMRYREELRCGRRPPDAVDAA 274
                                    ************************..666666799********************************************* PP

                           MMPL 244 vastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraala......kprrkrkk. 316
                                    +a++g +v+ +G+tv++++ g  +++ p+l+++++ + l+v+v++l + Tl+PA+l+++ raa +      ++rr +++ 
  gi|121636114|ref|YP_976337.1| 275 MATSGLAVVLSGMTVIASLTGIYLINTPALRSMATGAILAVAVAMLTSATLTPAVLATFARAAAKrsalvhWSRRPASTq 354
                                    *************************************************************9644466666555544445 PP

                           MMPL 317 .rwWrrlgrlvvrrP 330
                                      +W r    v rrP
  gi|121636114|ref|YP_976337.1| 355 sWFWSRWVGWVMRRP 369
                                    556677777788887 PP

  == domain 2  score: 122.9 bits;  conditional E-value: 2.2e-39
                           MMPL  55 delkkdtkhvgevsdflsdpdvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatl 134
                                     ++ +++++v +v+++           ++D+ +a +   l  dp++  a ++++  r+ + +      ++v v+Gp+a++
  gi|121636114|ref|YP_976337.1| 450 HRI-AQAPNVVSVAPP---------RFADDNGSALLSAVLSVDPEDLGARDTITWMRTQLPRVA--GAAQVDVGGPTALI 517
                                    333.444445555554.........667777777888888889999999999999999999999..99************ PP

                           MMPL 135 adlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilall....lgl....elstfvlg 205
                                    +d+ d ++    l+ v  +v+++++Lli  rS+  a+  +l+ ++s++aa+g+ v++++      lg+     + ++v++
  gi|121636114|ref|YP_976337.1| 518 KDFDDRVSATQPLVLVFVAVIAFLMLLISIRSVFLAFKGVLMTLLSVAAAYGSlVMVFQWGwargLGFpalhSIDSTVPP 597
                                    *****************************************************999987541111333211257899*** PP

                           MMPL 206 llvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvl 285
                                    l+ +++++ + DY ++L++R+re+  +  ++++av+  v+++++++t a+l++++ ++g+++a +p +a++Gva+a++++
  gi|121636114|ref|YP_976337.1| 598 LVLAMTFGLSMDYEIFLLTRIRERFLQTGQTRDAVAYGVRTSARTITSAALIMIAVFCGFAFAGMPLVAEIGVACAVAIA 677
                                    ***********************998888888************************************************ PP

                           MMPL 286 vdvlivlTll.PAllvllGraalakprrkrkkrwW.rr 321
                                    vd+ +v+ +l PAl++++ r+           +wW +r
  gi|121636114|ref|YP_976337.1| 678 VDATVVRLVLvPALMAMFDRW-----------NWWlPR 704
                                    ******99999**********...........777555 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  13.0   1.7e-10   9.9e-07     344     558 ..     189     402 ..     174     415 .. 0.78
   2 ?   -4.0   0.0      0.33     2e+03      40      67 ..     424     450 ..     422     461 .. 0.74
   3 !    6.9   5.0   0.00017         1     390     489 ..     601     695 ..     585     697 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.7e-10
                                    HHHHHHHHHSSHHHHHHHH.HHHH.HHHHHHHHHHHHTT.....--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ACR_tran 344 vvlvvflFLqnlratlipa.iavP.lsllgtfavlkalg.....fslNlltLfgLvlAiGlvvDdAiVvvEnierkleee 416
                                    +++v+    ++l a+ ip+ +av  +++ ++++++  +      f   + ++fg++l     vD +  ++    ++l+  
  gi|121636114|ref|YP_976337.1| 189 ILMVLVAVFGSLAAAAIPLaLAVCtVVITMGLVFVLSMHttmsvFVTSTVSMFGIAL----AVDYSLFILMRYREELRC- 263
                                    445555555777777776413443144444444443333111113445667777777....69****************. PP

                                    TS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHS---STT CS
                       ACR_tran 417 gekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPalcallLkerkee 496
                                    g  p  a+ ++m + + a+v + ++++a +  i +++       r++a   +la+++++l + tltPa+ a++ ++  ++
  gi|121636114|ref|YP_976337.1| 264 GRRPPDAVDAAMATSGLAVVLSGMTVIASLTGIYLIN---TPALRSMATGAILAVAVAMLTSATLTPAVLATFARAAAKR 340
                                    ***************************9999998876...5668*******************************99998 PP

                                    -CTSHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHH..HHHHCS-BESS----T CS
                       ACR_tran 497 kekkffrefnrlfealeraYakllekvlrhravvllvalvllvlsv..llfvripkeflPeede 558
                                     +  + +++ r  +  +  + + + +v+r+++++ l+a  +l++++  + ++ +++++l ++d 
  gi|121636114|ref|YP_976337.1| 341 SA--LVHWSRRPASTQSWFWSRWVGWVMRRPWITALAASTVLLVMAapATLMVLGNSLLRQFDS 402
                                    85..9***************************99988766665554115667788888888775 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 0.33
                                    --EEEEEEE-TTC-HHHHHHHTHHHHHC CS
                       ACR_tran  40 pptvqvstsypGaspevvesevtqplEq 67 
                                    p++v v+ ++ Gas+ +  +++++ + +
  gi|121636114|ref|YP_976337.1| 424 PVQVLVRFDAGGASAPEHSQTIAA-IRH 450
                                    789999999999999999999975.444 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHH CS
                       ACR_tran 390 gLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivl 469
                                    ++++  Gl  D  i  +  i ++  +   + + a+++++++ ++++ + al+++avf  ++f  G+   l ++++++ ++
  gi|121636114|ref|YP_976337.1| 601 AMTF--GLSMDYEIFLLTRIRERFLQ-TGQTRDAVAYGVRTSARTITSAALIMIAVFCGFAF-AGM--PLVAEIGVACAV 674
                                    4444..99999999999999877776.46678999***********************9876.566..488999999999 PP

                                    HHHH.HHHHHHCCHHHHHHHH CS
                       ACR_tran 470 aill.svlvaltltPalcall 489
                                    ai++ +++v l+l+Pal a++
  gi|121636114|ref|YP_976337.1| 675 AIAVdATVVRLVLVPALMAMF 695
                                    9987578999*******9986 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   8.1   2.9e-06     0.017      14     140 ..     208     337 ..     198     348 .. 0.78
   2 ?   -0.8   0.2       0.2   1.2e+03      36      58 ..     532     554 ..     529     559 .. 0.78
   3 !   11.6   7.3   3.1e-05      0.18       6     130 ..     550     688 ..     547     698 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                                    HHHHCCHHHHCCHHHHHHHHHHH..HHHHHHHHHHHHHCHHC.CHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCC CS
                 Sterol-sensing  14 iivllsvasslgllaylgltltl..iilevlPflvlavgvdn.ifvlvkavqrtsrsldeseriaealgevgpsilltsl 90 
                                    + ++++v+ ++gl+++l +++t+   ++  +    +a  vd   f+l++  +++    + ++ +  a+ + g +++l+ +
  gi|121636114|ref|YP_976337.1| 208 ALAVCTVVITMGLVFVLSMHTTMsvFVTSTVSMFGIALAVDYsLFILMRYREELRCGRRPPDAVDAAMATSGLAVVLSGM 287
                                    456788888999988888877762223333444445556665056777777777777888******************** PP

                                    HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                 Sterol-sensing  91 tellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre 140
                                    t +++l+  +l++ pa+++ ++ a++av+v  l  +t+  avL+   r  
  gi|121636114|ref|YP_976337.1| 288 TVIASLTGIYLINTPALRSMATGAILAVAVAMLTSATLTPAVLATFARAA 337
                                    *******667**********************************988766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHCHHCCHHCH CS
                 Sterol-sensing  36 liilevlPflvlavgvdnifvlv 58 
                                    l+ + v+ fl l++++  +f+  
  gi|121636114|ref|YP_976337.1| 532 LVFVAVIAFLMLLISIRSVFLAF 554
                                    56778999999999999998765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 3.1e-05
                                    HHHHHHHHHHHHCCHHHHCCHHHH.........HHHHHHHHHHHHHHHHHHHH....CHH.CCHHCHHHHHHHHTTTCHH CS
                 Sterol-sensing   6 fgLglagviivllsvasslgllay.........lgltltliilevlPflvlav....gvd.nifvlvkavqrtsrsldes 71 
                                    ++L++ gv+++llsva+++g l +         lg ++ + i   +P lvla+    ++d +if+l++  +r  ++ +  
  gi|121636114|ref|YP_976337.1| 550 VFLAFKGVLMTLLSVAAAYGSLVMvfqwgwargLGFPALHSIDSTVPPLVLAMtfglSMDyEIFLLTRIRERFLQTGQTR 629
                                    679999999999999999885444222233333567777888899******98443345678****************** PP

                                    HHHHHHHHHHCCCCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHH CS
                 Sterol-sensing  72 eriaealgevgpsilltsltellall.lgaltdvpavqeFclfaavavlvdFllqitfFv 130
                                    + +a ++++ +  i++ +l  ++++  ++ +  +p v e  + +ava++vd  +  ++ v
  gi|121636114|ref|YP_976337.1| 630 DAVAYGVRTSARTITSAALIMIAVFCgFA-FAGMPLVAEIGVACAVAIAVDATVVRLVLV 688
                                    **************************666.*********************876555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (966 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 6198.58
//
Query:       gi|121636115|ref|YP_976338.1|  [L=136]
Description: hypothetical protein BCG_0240 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-26   92.1   0.1    2.4e-26   91.8   0.1    1.1  1  MHB       Haemophore, haem-binding


Domain annotation for each model (and alignments):
>> MHB  Haemophore, haem-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1   1.3e-30   2.4e-26       1      76 [.      39     115 ..      39     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.3e-30
                            MHB   1 pnCtaadlarvvsgVaastsaYLdthPdvnqaltslkgqpr.dqaraavkaYfdanPqvaadLrgIrqPltdlknrC 76 
                                    ++C+a+++ar+v++Va+s+++YLd+hP++nq++t++ +q+  + + a+++a+f+anP+va+dL++++qPltdl++rC
  gi|121636115|ref|YP_976338.1|  39 DPCAASEVARTVGSVAKSMGDYLDSHPETNQVMTAVLQQQVgPGSVASLTAHFEANPKVASDLHALSQPLTDLSTRC 115
                                    79**********************************999999*********************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 919.74
//
Query:       gi|121636116|ref|YP_976339.1|  [L=427]
Description: hypothetical protein BCG_0241c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-37  127.4  42.4    9.6e-37  127.1  42.4    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1  42.4   5.4e-41   9.6e-37       9     301 .]      62     361 ..      52     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 5.4e-41
                LPG_synthase_TM   9 alllalllrgvdl...aalaaalrsldpwwlllalllallsvl..lralrWrlllrslgarislrrllrayliglfvnnv 83 
                                    +++++ +   +++   a+++ +l ++ +wwll+a++ a  s +  +  +  r+ll+s+g++++ +r+ +a+++++ ++++
  gi|121636116|ref|YP_976339.1|  62 VAIVLAIEVALGWdqlAKAWVSLYRAKWWWLLAAVAAAGAS-MhsFAQIQ-RTLLKSAGVHVKQWRSEAAFYAANSLSTT 139
                                    222222233445533388888888888*********66666.52454443.89*************************** PP

                LPG_synthase_TM  84 tPgalgGevvrayllkr...kegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavla 160
                                    +Pg   G+v+ a +l r    +g s+  a + +v+  +l+ ++l+llgl ++++lg+++++++ +l++l++++     ++
  gi|121636116|ref|YP_976339.1| 140 LPG---GPVLSATFLLRqqrIWGASTVVASWQLVMSGVLQAVGLALLGLGGAFFLGAKNNPFS-LLFTLGGFV-----TL 210
                                    **7...9999999999977789999999******************************98864.333333333.....34 PP

                LPG_synthase_TM 161 lllllllrrrlarlarvlkrlarllarfarklasakr..........klvlasprrlllafllslliwllealtlylllr 230
                                    lll+ ++  r+  +  + +r++++++++++++a a            + v   +r l++af++sl+ w++++++l ++++
  gi|121636116|ref|YP_976339.1| 211 LLLAQAVASRPELIEGIGRRVLSWANSVRGRPADAGLpkwretlmqlESVSLGRRDLGVAFGWSLFNWIADVACLGFAAY 290
                                    77788999999999999999999999999999988889999******888888999************************ PP

                LPG_synthase_TM 231 algvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                    a g ++s+++l+++++a+ +vg++p++PgGl v+Ea+l+  l++ G++   a++a+l+yrli+++l++++G
  gi|121636116|ref|YP_976339.1| 291 AAGDHASVGGLAVAYAAARAVGTIPLMPGGLLVVEAVLVPGLVSSGMPLPSAISAMLIYRLISWLLIAAIG 361
                                    *******************************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2977.87
//
Query:       gi|121636117|ref|YP_976340.1|  [L=367]
Description: hypothetical protein BCG_0242 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-81  272.0  31.3    7.3e-81  271.8  31.3    1.0  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
      0.061   13.4   0.4      0.061   13.4   0.4    3.6  5  DUF3742          Protein of unknown function (DUF3742)
       0.15   12.2   0.1       0.15   12.2   0.1    4.8  5  HemY_N           HemY protein N-terminus
        1.5    7.8   8.5       0.33   10.0   3.5    2.1  2  XK-related       XK-related protein


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.8  31.3   1.6e-84   7.3e-81       2     325 ..      22     346 ..      21     348 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.8 bits;  conditional E-value: 1.6e-84
                AI-2E_transport   2 llilvllllllalypfis...elllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaq 78 
                                    +++lv+l+ ++al+++++    +++p+l+Al+l+ ll p+v++L++rg++r +av+lvll+ +++l ++++++v+++ia+
  gi|121636117|ref|YP_976340.1|  22 WRFLVILAAMVALLWVLNkfeVIVVPVLLALMLSALLVPPVDWLDSRGLPRAVAVTLVLLSGFAVLGGILTFVVSQFIAG 101
                                    8999**************9999********************************************************** PP

                AI-2E_transport  79 ltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllffll 158
                                    l +lv++++++ids  ++l e p +l  ++  i++ ++++++ l+n + ++++ +ls +a++++l++ +vlvl++l+f+l
  gi|121636117|ref|YP_976340.1| 102 LPHLVTEVERSIDSARRWLIEGPAHLRGEQ--IDNAGNAAIEALRNNQAKLTSGALSTAATITELVTAAVLVLFTLIFFL 179
                                    *****************************6..************************************************ PP

                AI-2E_transport 159 ldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiG 238
                                    + g+ ++q+++k++p++vr+rv+a+ r+ + +l gy+r+++lval  +  v++gl+++gvp+al la lv++ ++iP+iG
  gi|121636117|ref|YP_976340.1| 180 YGGRSIWQYVTKAFPASVRDRVRAAGRAGYASLIGYARATFLVALTDAAGVGAGLAVMGVPLALPLASLVFFGAFIPLIG 259
                                    ******************************************************************************** PP

                AI-2E_transport 239 avivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltav 318
                                    av++ + ++++all +gi ++li + ++++v+++e ++l+P +mg+++++hpl+++l++ agg l+G+vG +lavp++a+
  gi|121636117|ref|YP_976340.1| 260 AVVAGFLAVVVALLAKGIGYALITVGLLIAVNQLEAHLLQPLVMGRAVSIHPLAVVLAIAAGGVLAGVVGALLAVPTAAF 339
                                    ******************************************************************************** PP

                AI-2E_transport 319 ikailea 325
                                    +++++++
  gi|121636117|ref|YP_976340.1| 340 FNNAVQV 346
                                    ***9987 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   3.7       1.2   5.3e+03      65      82 ..      21      39 ..       3      56 .. 0.69
   2 ?   13.4   0.4   1.4e-05     0.061      33      64 ..      63      95 ..      61     109 .. 0.87
   3 ?   -2.6   0.0       1.3   5.7e+03      39      61 ..     153     176 ..     130     180 .. 0.53
   4 ?   -6.5   5.8         4   1.8e+04      42      42 ..     260     260 ..     214     293 .. 0.57
   5 ?   -3.3   0.5       2.2   9.7e+03      35      51 ..     318     334 ..     305     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                        DUF3742 65 fWlal.llvvvvlvawaar 82
                                   +W  l +l+++v+ +w+ +
  gi|121636117|ref|YP_976340.1| 21 AWRFLvILAAMVALLWVLN 39
                                   4666645555666666654 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                        DUF3742 33 swlvakGvpaavatavlwvvklavlG.vllyva 64
                                    wl+++G+p+ava  ++++   avlG +l +v+
  gi|121636117|ref|YP_976340.1| 63 DWLDSRGLPRAVAVTLVLLSGFAVLGgILTFVV 95
                                   6************************63788876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                        DUF3742  39 Gvpaavatavlwv.vklavlGvll 61 
                                    G+ + +at   +v + + vl +l+
  gi|121636117|ref|YP_976340.1| 153 GALSTAATITELVtAAVLVLFTLI 176
                                    443344443333302233444444 PP

  == domain 4  score: -6.5 bits;  conditional E-value: 4
                        DUF3742  42 a 42 
                                    a
  gi|121636117|ref|YP_976340.1| 260 A 260
                                    1 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 2.2
                        DUF3742  35 lvakGvpaavatavlwv 51 
                                    ++a Gv a+v+ a+l v
  gi|121636117|ref|YP_976340.1| 318 IAAGGVLAGVVGALLAV 334
                                    44555666666665554 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   5.0       3.4   1.5e+04      17      34 ..      22      39 ..      17      58 .. 0.74
   2 ?   12.2   0.1   3.5e-05      0.15      17      95 ..      76     151 ..      71     163 .. 0.77
   3 ?    7.2   1.9    0.0012       5.5      15      79 ..     160     224 ..     150     235 .. 0.81
   4 ?   -2.8   2.9       1.7   7.5e+03      18      33 ..     259     274 ..     245     294 .. 0.63
   5 ?   -1.1   1.5      0.49   2.2e+03      21      46 ..     312     337 ..     306     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.4
                         HemY_N 17 vvavlllvllfvllylll 34
                                   + ++++l+++++ll++l 
  gi|121636117|ref|YP_976340.1| 22 WRFLVILAAMVALLWVLN 39
                                   556666666666666664 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.5e-05
                         HemY_N  17 vvavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAekaaakaaklseaplla 95 
                                    v++vll   +++  +l + + +++ +lp+ v +   +r  + ar+ l eG  +l +++   A +aa +a+++ +a+ l+
  gi|121636117|ref|YP_976340.1|  76 VTLVLLSGFAVLGGILTFVVSQFIAGLPHLVTEV--ERSIDSARRWLIEGPAHLRGEQIDNAGNAAIEALRNNQAK-LT 151
                                    3455555555566666667777888889999997..999**********************************996.33 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0012
                         HemY_N  15 slvvavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAe 79 
                                    +++ +v ++vl++++l+++l   r +++  +++   + r r r+a +a    li +a   f  A 
  gi|121636117|ref|YP_976340.1| 160 TITELVTAAVLVLFTLIFFLYGGRSIWQYVTKAFPASVRDRVRAAGRAGYASLIGYARATFLVAL 224
                                    67788999999999999999999999999999999999999999888888888777766666665 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.7
                         HemY_N  18 vavlllvllfvllyll 33 
                                     av++ +l++v+++l+
  gi|121636117|ref|YP_976340.1| 259 GAVVAGFLAVVVALLA 274
                                    3444444444444443 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.49
                         HemY_N  21 lllvllfvllylllrllrlllrlpar 46 
                                    l++vl++++  +l  ++++ll++p++
  gi|121636117|ref|YP_976340.1| 312 LAVVLAIAAGGVLAGVVGALLAVPTA 337
                                    57788888888888888888888876 PP

>> XK-related  XK-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.5   7.3e-05      0.33     185     272 ..       4      97 ..       1     110 [. 0.81
   2 ?   -0.2   0.2      0.09     4e+02     214     240 ..     154     186 ..     152     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.3e-05
                     XK-related 185 srpdkkklsllavilqflWrlltiasRvlalalfasvfklwvllvlllhwlvmtl.....Wivsqkt.dfckskveeilf 258
                                    s++d     l + +    Wr+l+i + ++al  ++  f+++v++vll+++l  +l     W+ s    +++  +++ +  
  gi|121636117|ref|YP_976340.1|   4 SLDDASVAPLVRKTAAWAWRFLVILAAMVALLWVLNKFEVIVVPVLLALMLSALLvppvdWLDSRGLpRAVAVTLVLLSG 83 
                                    66777777888888999***********************************9999998888665554556667777777 PP

                     XK-related 259 rlvvgiiyiFcwfn 272
                                     +v+g i+ F+ ++
  gi|121636117|ref|YP_976340.1|  84 FAVLGGILTFVVSQ 97 
                                    77888888887765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.09
                     XK-related 214 alalfasvfklwvllvlllhwlvmtl......W 240
                                    al++ a++ +l +++vl+l  l+++l      W
  gi|121636117|ref|YP_976340.1| 154 ALSTAATITELVTAAVLVLFTLIFFLyggrsiW 186
                                    678888888888888888888888885555333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2250.63
//
Query:       gi|121636118|ref|YP_976341.1|  [L=944]
Description: transmembrane transport protein mmpL3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-66  223.8  28.8      7e-39  133.7   4.9    2.7  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   4.9   3.9e-43     7e-39       7     309 ..      48     368 ..      43     399 .. 0.80
   2 !   95.0  16.0   2.2e-31     4e-27       3     324 ..     427     738 ..     425     746 .. 0.79

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 3.9e-43
                           MMPL   7 aesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpd..vaaafvSkD 84 
                                     +sv+a  + ++       s  i+ +++a+ ++++ + a ++ v + ++++++d++  ++v  + +      a+++  +D
  gi|121636118|ref|YP_976341.1|  48 SQSVQASVLGDQVYGR-DRSGHIVAIFQAPAGKTVDDPAWSKKVVDELNRFQQDHP--DQVLGWAGYLRasQATGMATAD 124
                                    5666666544444444.788899999*********998888888888888866655..67777743333448899999** PP

                           MMPL  85 gkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivy 164
                                    +k + + + l+gd ++t   ++++ai+  +++++   g +v+++G  ++++ l+ + + d + +ev++l +++v+L+ v+
  gi|121636118|ref|YP_976341.1| 125 KKYTFVSIPLKGDDDDTIL-NNYKAIAPDLQRLD---GGTVKLAGLQPVAEALTGTIATDQRRMEVLALPLVAVVLFFVF 200
                                    ***********98655554.66666666666666...******************************************* PP

                           MMPL 165 rSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavirav 244
                                    + ++aa+lp+++ ++ ++ alg++ +la +    ++ f+++ ++++++++++DY l++vsR+ree+a+g d+e+av r+v
  gi|121636118|ref|YP_976341.1| 201 GGVIAAGLPVMVGGLCIAGALGIMRFLAIF--GPVHYFAQPVVSLIGLGIAIDYGLFIVSRFREEIAEGYDTETAVRRTV 278
                                    ***************999999996655554..78********************************************** PP

                           MMPL 245 astgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.la............... 308
                                     ++g++vt++++ ++++ +gL++   ++l+++  a   +v++++ +++T+lPA l +lG+ +                  
  gi|121636118|ref|YP_976341.1| 279 ITAGRTVTFSAVLIVASAIGLLLFPQGFLKSLTYATIASVMLSAILSITVLPACLGILGKHVdALgvrtlfrvpflanwk 358
                                    *********************************************************99986433444444444444444 PP

                           MMPL 309 .........k 309
                                             +
  gi|121636118|ref|YP_976341.1| 359 isaaylnwlA 368
                                    4444444440 PP

  == domain 2  score: 95.0 bits;  conditional E-value: 2.2e-31
                           MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf...lsdpdvaaa 79 
                                    +p+ +++ +a ++ ++ fp+   ++++ +v+++ +++ +++ a+ a ++  + ++   ++ ++   d+   +++  + a+
  gi|121636118|ref|YP_976341.1| 427 LPPTNSVRQAQEEFDKLFPG-YRTNPLTLVIQTSNHQPVTE-AQIADIRSKAMAI---GGFIEPDNDPanmWQER-AYAV 500
                                    67778888899999999999.88889999999888888888.4444444443333...44444444442213332.6677 PP

                           MMPL  80 fvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilvi 159
                                      SkD +   ++   +g  +  +a ++++++ra     +p++g++v v+G++a+  d  ++   ++ l++v+ l   +v+
  gi|121636118|ref|YP_976341.1| 501 GASKDPSVRVLQ---NGLINPADASKKLTELRA----ITPPKGITVLVGGTPALELDSIHGLFAKMPLMVVILLTTTIVL 573
                                    788888773333...333333334445555554....458**************************************** PP

                           MMPL 160 LlivyrSlvaallplltvvvsllaalgl.vlilalllglelstf........vlgllvvlliavGtDYallLvsRyreel 230
                                    ++++++S+v ++   l+ ++ l+ ++g+ + i+ + ++ +  +f        v+gl ++l+++ +tDY ++LvsR+ e++
  gi|121636118|ref|YP_976341.1| 574 MFLAFGSVVLPIKATLMSALTLGSTMGIlTWIFVDGHFSKWLNFtptpltapVIGLIIALVFGLSTDYEVFLVSRMVEAR 653
                                    ****************************8888888776554444111222227889************************ PP

                           MMPL 231 aagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraalak 309
                                    ++g +++ea+    a tg+ +taa+l+va+   ++v+++l +++ +++ +  ++l+d+ +v+ +l P+++ llG   + +
  gi|121636118|ref|YP_976341.1| 654 ERGMSTQEAIRIGTAATGRIITAAALIVAVVAGAFVFSDLVMMKYLAFGLMAALLLDATVVRMFLvPSVMKLLGDDCWWA 733
                                    ***************************************************************************95443 PP

                           MMPL 310 prrkrkkrwWrrlgr 324
                                    p          r +r
  gi|121636118|ref|YP_976341.1| 734 P----------RWAR 738
                                    3..........3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (944 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.36s 00:00:01.14 Elapsed: 00:00:00.49
# Mc/sec: 5750.56
//
Query:       gi|121636119|ref|YP_976342.1|  [L=242]
Description: hypothetical protein BCG_0244c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-07   30.8   0.0    4.8e-07   30.3   0.0    1.2  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.7e-11   4.8e-07       1     146 [.      39     202 ..      39     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.7e-11
                            NYN   1 rvavfiDgenlpvpak..........gke.vdyrklleeirs..........kgelvraraygn...wedeeqnkfqdal 56 
                                    rv + +D+ nl +  +          ++  +d+   +  +r+            e  +a++++n    ++e  + + dal
  gi|121636119|ref|YP_976342.1|  39 RVLLVWDAPNLDMGLGsilgrrptalERPrFDALGRWLLARTaeivagrpgiSTEP-EATVFTNiapGSAEVVRPWVDAL 117
                                    56777888888888778888777744333444444333333377888776654446.88999998744455579****** PP

                            NYN  57 sstgikvkhkplkkrggsgkkavDvelavdalelaydnkydtivLvsgDgD.FaplveklrergkrVevllaeeastsse 135
                                    ++ g++v  kp++      + +vD  +   + e   +  ++ +v+ s Dg  F +++e++ + g  V vl+++ +++s +
  gi|121636119|ref|YP_976342.1| 118 RNVGFAVFAKPKVD----EDSDVDRDMLAHIDERYREG-LAALVVASADGQaFRQPLEAVARSGTPVQVLGFR-EHASWA 191
                                    **********9975....67999999999998888555.8*********777*******************98.799999 PP

                            NYN 136 Lisaadefisl 146
                                    L s   ef++l
  gi|121636119|ref|YP_976342.1| 192 LASDTLEFVDL 202
                                    99888788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2055.47
//
Query:       gi|121636120|ref|YP_976343.1|  [L=263]
Description: tRNA (guanine-N(7)-)-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-54  183.6   0.0    2.4e-54  183.4   0.0    1.1  1  Methyltransf_4   Putative methyltransferase
    0.00055   20.6   0.0    0.00095   19.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00058   19.1   0.0     0.0008   18.6   0.0    1.1  1  Methyltransf_3   O-methyltransferase
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.042   13.7   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
      0.026   14.3   0.0       0.04   13.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      0.031   14.0   0.0      0.051   13.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.07   14.2   0.0       0.18   12.8   0.0    1.9  1  Methyltransf_24  Methyltransferase domain
       0.16   11.5   0.1       0.24   10.9   0.1    1.2  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.4   0.0   1.1e-57   2.4e-54       2     172 ..      77     247 ..      76     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 183.4 bits;  conditional E-value: 1.1e-57
                                    -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC..TTSSEEEEES-CCCHHHHCS-TTSEEEEEEE CS
                 Methyltransf_4   2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal..elkNlrilrgdalkvllelledgslekifil 79 
                                    apvvleiG+G+G++++a+Ak++P++++++++++++++a++l++i++   +  N+r++ g+a++vl++l++++sl++++++
  gi|121636120|ref|YP_976343.1|  77 APVVLEIGSGSGTSTLAMAKAEPHVDVIAVDVYRRGLAQLLCAIDKVgsDGINIRLILGNAVDVLQHLIAPDSLCGVRVF 156
                                    79********************************************988899**************************** PP

                                    S-----SGGGGGGSTTSHHHHHHHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEEESSCCCSCCTCHCHHCCCSSTT CS
                 Methyltransf_4  80 FPDPwfKkrhhKrRllqpellkelarvLkkgGvlelaTDveeyaeemlkvleeeplferlskeeeleeeplsvlriatky 159
                                    FPDPw+K+rhhKrRllqp++++ +a++L+++Gvl++aTD++ yae++++  ++ep+++r++ ++el +  +sv+r+atky
  gi|121636120|ref|YP_976343.1| 157 FPDPWPKARHHKRRLLQPATMALIADRLVPSGVLHAATDHPGYAEHIAAAGDAEPRLVRVDPDTELLP--ISVVRPATKY 234
                                    ******************************************************************97..678******* PP

                                    CCCCCCTTSS-EE CS
                 Methyltransf_4 160 eqkvqskgkeiye 172
                                    e+k+q  g++++e
  gi|121636120|ref|YP_976343.1| 235 ERKAQLGGGAVIE 247
                                    *****99999876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.2e-07   0.00095       1      58 [.      80     140 ..      80     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.2e-07
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHH...HHHHHHHTTTTEEEEESBCCGB CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemlea...areraeeeglnvefvqgdaedl 58 
                                    vL++G G+G+ tla+ak+ ++ +v++vD+  + l++   a  ++ ++g+n++++ g+a d+
  gi|121636120|ref|YP_976343.1|  80 VLEIGSGSGTSTLAMAKAEPHVDVIAVDVYRRGLAQllcAIDKVGSDGINIRLILGNAVDV 140
                                    9****************9769*********9999883334466666888999999998664 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.6e-07    0.0008      48     121 ..      77     150 ..      75     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.6e-07
                                    --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GG.GEEEEES-HHHHHHHHHTSSS- CS
                 Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvae.kieliegdalkvLeelvkdkkl 121
                                    a  vleiG   G s La+a a P    ++a+d+ r   +  l  i+k g +   i li g+a+ vL++l+  ++l
  gi|121636120|ref|YP_976343.1|  77 APVVLEIGSGSGTSTLAMAKAEPH-VDVIAVDVYRRGLAQLLCAIDKVGSDGiNIRLILGNAVDVLQHLIAPDSL 150
                                    5679*****************997.5799******99999999*****9975389*************9987765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.042      22      62 ..      76     157 ..      40     223 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                Methyltransf_23  22 aggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae...................................... 61 
                                        vL+iG G+G ++l  ++++++ +v++vD +++  ++a+                                      
  gi|121636120|ref|YP_976343.1|  76 DAPVVLEIGSGSGtSTLAMAKAEPHvDVIAVDVYRR--GLAQllcaidkvgsdginirlilgnavdvlqhliapdslcgv 153
                                    3349*********4455555777878******9975..444455666666666666655555555555555555555555 PP

                Methyltransf_23  62 ...k 62 
                                        
  gi|121636120|ref|YP_976343.1| 154 rvfF 157
                                    5551 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05      0.04       4      65 ..      77     139 ..      75     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee 65 
                                    + +vl++G+G+G+ t+++a ++ p+ +v+ +D   + + +     +k g+d  n+++  g++ +
  gi|121636120|ref|YP_976343.1|  77 APVVLEIGSGSGTSTLAMA-KAEPHVDVIAVDVYRRGLAQLLCAIDKVGSDgiNIRLILGNAVD 139
                                    5689***************.999*********98887777666666666666666666666555 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.051      49      78 ..      79     108 ..      72     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                Methyltransf_16  49 svlELGsGtGlvGlavaellpeakviltDl 78 
                                     vlE+GsG+G   la+a++ p+++vi  D+
  gi|121636120|ref|YP_976343.1|  79 VVLEIGSGSGTSTLAMAKAEPHVDVIAVDV 108
                                    69***********************99886 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05      0.18       1      82 [.      81     165 ..      81     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddr.vrlikadseealasla....agsiDllf 74 
                                    +EiG+ sG stl++++a  + +   ++avd  ++  ++    +++ g d + +rli +++ ++l++l        + ++f
  gi|121636120|ref|YP_976343.1|  81 LEIGSGSGTSTLAMAKAEPHVD---VIAVDVYRRgLAQLLCAIDKVGSDGInIRLILGNAVDVLQHLIapdsLCGVRVFF 157
                                    7**********99998755554...89***99943223333333455555349999999999999888654433355666 PP

                Methyltransf_24  75 iDgghaae 82 
                                     D  ++a+
  gi|121636120|ref|YP_976343.1| 158 PDPWPKAR 165
                                    66555554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00011      0.24      34      69 ..      79     114 ..      71     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                    EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHH CS
                            MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAle 69 
                                     vl +G+G G  ++a+ak++p+++v +vdv  r l+
  gi|121636120|ref|YP_976343.1|  79 VVLEIGSGSGTSTLAMAKAEPHVDVIAVDVYRRGLA 114
                                    4899*************************9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1938.34
//
Query:       gi|121636121|ref|YP_976344.1|  [L=361]
Description: hypothetical protein BCG_0246 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.7   0.2      0.065   13.0   0.2    1.3  1  Pox_Ag35  Pox virus Ag35 surface protein
      0.098   12.3   0.1       0.13   11.9   0.1    1.2  1  DUF885    Bacterial protein of unknown function (DUF885)


Domain annotation for each model (and alignments):
>> Pox_Ag35  Pox virus Ag35 surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.3e-06     0.065     137     184 ..     224     271 ..     220     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-06
                       Pox_Ag35 137 kdlkkltarvsAvstvLedvQAasisRqftslvkaieelkalaeeGke 184
                                    ++l++l  rvs v +v++ v Aa+ +  +  l+ a+ el+ala + ke
  gi|121636121|ref|YP_976344.1| 224 AQLRTLLRRVSGVDAVIDKVTAAGSEVRYRRLLDAVAELEALAAQAKE 271
                                    689***************************************998775 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.5e-05      0.13       5     151 ..     134     275 ..     131     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                                    HHCT-.-S.TT-----SHHHHHHHHHHHHHHHHHHCT.S-CCHHHH.HHHHHHHHHHHHHHHHHHHHHSHHHHTT-CCCC CS
                         DUF885   5 tslGi.ydkddrlpdlspaaeaaraarlraalaeldaaidrdklse.erldldllrerleleletaeagypleqlralag 82 
                                    t lG+    ++ ++ l  aa +   + lraal +l+    +d+ ++ +r  +  l   l    e + + +++ +l    g
  gi|121636121|ref|YP_976344.1| 134 TLLGVpM--ESMIGLLAVAALDDLDDTLRAALRALA--AHPDGFDAlDRAVAGFLAAALPVPTEVRLRLLDTLDL---FG 206
                                    6666632..666777778888999999999999994..4666662225555555555444444444444655555...89 PP

                                    HHHHHHHHHCGTTSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHTT.-S-HHHHHHHHHHHHHHHGT CS
                         DUF885  83 pvqqlpsllseepfateedleaylarlaavpaaldqaranlregaaaglvpprrqvekvieqlrgllag 151
                                    +  +++     +p +t+++l+++l+r+++v+a++d ++a  +e   + l+ +  ++e+ ++q++++   
  gi|121636121|ref|YP_976344.1| 207 IALGMAAFRPGRPSRTPAQLRTLLRRVSGVDAVIDKVTAAGSEVRYRRLLDAVAELEALAAQAKEIGGP 275
                                    999999999999****************************99988888888888899988888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2654.58
//
Query:       gi|121636122|ref|YP_976345.1|  [L=492]
Description: hypothetical protein BCG_0247 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.1   0.9      0.015   15.1   0.9    2.1  3  Activator-TraM  Transcriptional activator TraM


Domain annotation for each model (and alignments):
>> Activator-TraM  Transcriptional activator TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.3   5.3e+03      75     100 ..      86     111 ..      78     132 .. 0.74
   2 ?   15.1   0.9   8.6e-07     0.015      34     116 ..     165     247 ..     156     262 .. 0.89
   3 ?   -2.7   0.2      0.27   4.8e+03     115     129 ..     412     426 ..     392     463 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.3
                 Activator-TraM  75 aalaaskealvkllqegakeaaevvr 100
                                    +al+ s   l  +  e + + ++vv 
  gi|121636122|ref|YP_976345.1|  86 TALTESDCVLLDTAAEHTDAVVAVVS 111
                                    46777777777788888877777664 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.6e-07
                 Activator-TraM  34 rllqdsakaqqelldqfkeeleaiasrWgddakekaervlnaalaaskealvkllqegakeaaevvrkeveaalarlkss 113
                                    + l d a+a++++l ++ + l  +a+r++ da++   r    al   + ++ +  ++   e + ++r ++++a ++l  +
  gi|121636122|ref|YP_976345.1| 165 KQLADPAVARRNMLRAWESRLLMVARRFDGDAQSAGRRARVDALRQQRRTVLRQGRQSKSEHTIALRAQIQHARVKLSYF 244
                                    4467999********************************************99999999999999********9999988 PP

                 Activator-TraM 114 ire 116
                                    +r+
  gi|121636122|ref|YP_976345.1| 245 ARN 247
                                    876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.27
                 Activator-TraM 115 rearrvallnlvasa 129
                                     ++r va+ +l+++a
  gi|121636122|ref|YP_976345.1| 412 VATRVVAVETLLSTA 426
                                    333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3881.41
//
Query:       gi|121636123|ref|YP_976346.1|  [L=606]
Description: phosphoenolpyruvate carboxykinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   8.6e-171  567.6   0.0   1.1e-170  567.3   0.0    1.1  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
   4.4e-102  340.3   0.0   5.7e-102  339.9   0.0    1.1  1  PEPCK_N    Phosphoenolpyruvate carboxykinase N-terminal domai


Domain annotation for each model (and alignments):
>> PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.3   0.0  1.2e-174  1.1e-170       1     358 []     245     605 ..     245     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: 567.3 bits;  conditional E-value: 1.2e-174
                                    -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---SSTT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE-TT- CS
                      PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamleptlegwkvetvgdDiawlkfgedgrlraiNpeaGfFgvapgt 80 
                                    wLaEhmlil++ spe+k +y+aaafpsacGKtnlaml+pt++gw+ et+gdDiaw++fg+dgrl+a+Npe+GfFgvapgt
  gi|121636123|ref|YP_976346.1| 245 WLAEHMLILKLISPENKAYYFAAAFPSACGKTNLAMLQPTIPGWRAETLGDDIAWMRFGKDGRLYAVNPEFGFFGVAPGT 324
                                    9******************************************************************************* PP

                                    STTT-HHHHHHT.TBS-EEES-EEETTS-EE-TT--------EE-TTSSEE-T...T-SSS-TT-EEEEEGGGSTTB-TT CS
                      PEPCK_GTP  81 nektnpnalktl.kkntiftNvaltedgdvwWegleeeapaelidwkgkkwtke..kekaahpnsrftvpakqlpiiape 157
                                    n+k+npna++t+ + nt+ftNvalt+dgdvwWegle + p++lidwkg++w  +  +++aahpnsr+++p++q+pi+ape
  gi|121636123|ref|YP_976346.1| 325 NWKSNPNAMRTIaAGNTVFTNVALTDDGDVWWEGLEGD-PQHLIDWKGNDWYFRetETNAAHPNSRYCTPMSQCPILAPE 403
                                    ************8899*******************865.66**********98755666********************* PP

                                    TT-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHHHHT-EEE--TTSSS-TT-EEE-GGG-GGG-SS-HHHHHHHHHH CS
                      PEPCK_GTP 158 wedpeGvpisaiifggrrsetvplvleafdwehGvflgatlesetTaaaegkvgvvrrdPfamlpFlgynlgdYlehwle 237
                                    w+dp+Gvpis i+fggrr++tvplv+ea+dw+hGvf+gatl+se+Taaaegkvg+vrrdP+amlpFlgyn+gdY++hw++
  gi|121636123|ref|YP_976346.1| 404 WDDPQGVPISGILFGGRRKTTVPLVTEARDWQHGVFIGATLGSEQTAAAEGKVGNVRRDPMAMLPFLGYNVGDYFQHWIN 483
                                    ******************************************************************************** PP

                                    HTTST.T-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE-BTTC--TT-..TT--HHH CS
                      PEPCK_GTP 238 lgkkl.ekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvPkkedldlkgldlskedlee 316
                                    lgk++ e+klPk+f vNwfr++++g+flWPGfgen+rvlkWi++r+e++a   +tpiG+vP+ edldl+gld++++d+++
  gi|121636123|ref|YP_976346.1| 484 LGKHAdESKLPKVFFVNWFRRGDDGRFLWPGFGENSRVLKWIVDRIEHKAGGATTPIGTVPAVEDLDLDGLDVDAADVAA 563
                                    **999899******************************************99**************************** PP

                                    HS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                      PEPCK_GTP 317 llsvdkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                    +l+vd++ew++e+  iee+++ +geklP+ +++e+++l++rl
  gi|121636123|ref|YP_976346.1| 564 ALAVDADEWRQELPLIEEWLQFVGEKLPTGVKDEFDALKERL 605
                                    ***************************************997 PP

>> PEPCK_N  Phosphoenolpyruvate carboxykinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.9   0.0  6.4e-106  5.7e-102       2     217 ..      22     240 ..      21     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.9 bits;  conditional E-value: 6.4e-106
                                    HHHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-..TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS-- CS
                        PEPCK_N   2 fveevaelcqPdkvvvcdgseeeneellkelvekgelikl..ekypnsylarsdpkDvARvesrTfictekeedagplnn 79 
                                    +veevael+qPd+vv+ dgseee ++l+++lve+g++i+l  ek++nsyla sdp+DvARvesrT+ic+ ke dagp+nn
  gi|121636123|ref|YP_976346.1|  22 WVEEVAELTQPDRVVFTDGSEEEFQRLCDQLVEAGTFIRLnpEKHKNSYLALSDPSDVARVESRTYICSAKEIDAGPTNN 101
                                    ******************************************************************************** PP

                                    EE-HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TSEEEEE CS
                        PEPCK_N  80 wmdpeemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeefvkclH 159
                                    wmdp em++ +k+l++gcm+GrtmyV+pf+mGp+g++  k+gveiTds+YVv+smr+mtr+gk++lek+g+++ fvk+lH
  gi|121636123|ref|YP_976346.1| 102 WMDPGEMRSIMKDLYRGCMRGRTMYVVPFCMGPLGAEDPKLGVEITDSEYVVVSMRTMTRMGKAALEKMGDDGFFVKALH 181
                                    ******************************************************************************** PP

                                    E-S--S.S-SS-BTB---GG-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHH CS
                        PEPCK_N 160 svgapl.egqkdvkWpcnekkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasvia 217
                                    svgapl +gqkdv+Wpc e+kyi+hfpe+rei+s+gsgYgGNaLlgKkc++lRias++a
  gi|121636123|ref|YP_976346.1| 182 SVGAPLePGQKDVAWPCSETKYITHFPETREIWSYGSGYGGNALLGKKCYSLRIASAMA 240
                                    ****9999**************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4052.43
//
Query:       gi|121636124|ref|YP_976347.1|  [L=323]
Description: transcriptional regulator NadR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-28  100.2   0.1    2.8e-28   99.2   0.1    1.6  2  AAA_28           AAA domain
    0.00083   19.8   0.0     0.0013   19.1   0.0    1.3  1  AAA              ATPase family associated with various cellul
     0.0016   18.6   0.0      0.038   14.2   0.0    2.3  2  CTP_transf_like  Cytidylyltransferase-like
     0.0078   16.6   0.1      0.016   15.6   0.1    1.7  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.068   12.9   0.0        0.1   12.3   0.0    1.2  1  Cytidylate_kin   Cytidylate kinase
       0.11   12.6   0.0       0.25   11.5   0.0    1.6  1  AAA_33           AAA domain
       0.13   12.0   0.1        0.2   11.4   0.1    1.2  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.16   12.3   0.0       0.47   10.7   0.0    1.8  2  AAA_22           AAA domain
       0.19   11.6   0.0       0.28   11.1   0.0    1.3  1  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3   6.6e+03      24      39 ..      17      32 ..      14      69 .. 0.64
   2 !   99.2   0.1   1.4e-31   2.8e-28       1     163 []     154     307 ..     154     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                         AAA_28 24 ypvvpEaareileekl 39
                                   ++++ E+ar+ ++e++
  gi|121636124|ref|YP_976347.1| 17 HVYLCEFARRWVDELT 32
                                   5556677777777765 PP

  == domain 2  score: 99.2 bits;  conditional E-value: 1.4e-31
                         AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcD 79 
                                    ++ i+G+estGKTtl++a a++  +++vpE a ++ e ++ +  + l+w+ ++++ ++     + ee+ a++a++vl+cD
  gi|121636124|ref|YP_976347.1| 154 RVSIIGPESTGKTTLAQAVAEKlRTKWVPERAKMLRELNGGSLIG-LEWA-EIVRGQI-----ASEEALARDADRVLICD 226
                                    689*****************998**********999999999987.9**6.4444444.....44455556899****** PP

                         AAA_28  80 rglldtlaYarayggeaeaeleaaarekrydlvfllppapeidddgeRredleereaiderlrealrelgipviivpsgd 159
                                    +++l+t+++a+++ g +++el + ar+  ydl +l+ p+ ++d d+ R+  + +r  + +r+++alr++g +++++ +g 
  gi|121636124|ref|YP_976347.1| 227 TDPLATTVWAEFLAGGCPQELRDLARR-PYDLTLLTTPDVPWDADDGRCV-PGARGTFFARCEQALRAAGRSFVVI-TGG 303
                                    *********************999887.9********************9.899**********************.*** PP

                         AAA_28 160 veeR 163
                                    +eeR
  gi|121636124|ref|YP_976347.1| 304 WEER 307
                                    ***9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.7e-07    0.0013       3      35 ..     157     197 ..     155     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.7e-07
                                    EESSTTSSHHHHHHHHHHHHTHE........EEEEETTTCS CS
                            AAA   3 lyGppGtGKTllakavakelgve........fleisgsell 35 
                                    ++Gp  tGKT+la+ava++l ++        + e++g +l+
  gi|121636124|ref|YP_976347.1| 157 IIGPESTGKTTLAQAVAEKLRTKwvperakmLRELNGGSLI 197
                                    79*****************9644333344446778877777 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.9e-05     0.038       3      74 ..       7      71 ..       5     134 .. 0.70
   2 ?    2.1   0.0       0.1   2.1e+02      50      99 ..     183     234 ..     173     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                   EE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH CS
                CTP_transf_like  3 gGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr 74
                                    G F p+H GH  l e a++ ++e l + v s         ++++ ++R++ ++++   d+v++ +   ++r
  gi|121636124|ref|YP_976347.1|  7 LGKFMPPHAGHVYLCEFARRWVDE-LTIVVGSTAA------EPIPGAQRVAWMRELFPFDRVVHLANENPQR 71
                                   699*********************.7776655332......3455666666666665666666555555555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                                    HHHHHHHHHTTCTTEEEEEEESEHH......HHHHHTTTT.EEEEEEEHHHHHHHHC CS
                CTP_transf_like  50 eRlemlelakevdevisvdpweltr......evlkklkpd.klylvigadvledfse 99 
                                    eR +ml+++   +  i  +  e++r      e l +   d + +l+++ d+l+++  
  gi|121636124|ref|YP_976347.1| 183 ERAKMLRELNGGSL-IGLEWAEIVRgqiaseEALAR---DaDRVLICDTDPLATT-V 234
                                    89999999966665.999999999985544333333...3567********9996.4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.8e-06     0.016      26      61 ..     154     186 ..     140     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.8e-06
                         AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                     v ++G+  +GK++l++++++ l+++   ++ ++++
  gi|121636124|ref|YP_976347.1| 154 RVSIIGPESTGKTTLAQAVAEKLRTK---WVPERAK 186
                                    5889*****************99999...3333333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05       0.1       1      27 [.     155     181 ..     155     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                                    EEEE-STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   1 iaiDGPagsGKssvaralaeklglkyl 27 
                                    ++i GP ++GK ++a+a+aekl  k++
  gi|121636124|ref|YP_976347.1| 155 VSIIGPESTGKTTLAQAVAEKLRTKWV 181
                                    5788******************99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.25       4      24 ..     157     177 ..     155     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                         AAA_33   4 lvGlpGsGKstlaerllkklg 24 
                                    ++G+  +GK+tla+ +++kl 
  gi|121636124|ref|YP_976347.1| 157 IIGPESTGKTTLAQAVAEKLR 177
                                    79***************9987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001       0.2       2      23 ..     153     174 ..     152     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkg 23 
                                    k++ +iG+  +GKttL+qa+ +
  gi|121636124|ref|YP_976347.1| 153 KRVSIIGPESTGKTTLAQAVAE 174
                                    8999**************9976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.47       9      30 ..     156     177 ..     154     226 .. 0.87
   2 ?   -2.6   0.0       3.1   6.1e+03      78      97 ..     282     300 ..     274     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                         AAA_22   9 vvtGesGtGKTtllrrlleqld 30 
                                     ++G+  tGKTtl++ ++e+l 
  gi|121636124|ref|YP_976347.1| 156 SIIGPESTGKTTLAQAVAEKLR 177
                                    59*****************983 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                         AAA_22  78 llealeqalraraviellii 97 
                                    +++++eqalra+++ ++++i
  gi|121636124|ref|YP_976347.1| 282 FFARCEQALRAAGR-SFVVI 300
                                    56899999999999.88887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.28       2      29 ..     155     182 ..     154     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                    EEEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvk 29 
                                    v i Gp  +GKtTl + v+e+l+ + v+
  gi|121636124|ref|YP_976347.1| 155 VSIIGPESTGKTTLAQAVAEKLRTKWVP 182
                                    7799******************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2397.24
//
Query:       gi|121636125|ref|YP_976348.1|  [L=437]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-13   49.8   0.1    1.8e-11   44.1   0.0    2.5  2  B12-binding  B12 binding domain
    5.7e-13   49.6   0.0      1e-12   48.8   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0     2e-15   1.8e-11      45     120 ..      37     110 ..       1     111 [. 0.85
   2 !    3.2   0.0    0.0098        88      30      77 ..     295     344 ..     269     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2e-15
                    B12-binding  45 aairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    aa+ +  p++vg+S+    ++++v  l+++++++ ++v++v+G a ++l +e++l+++  +d+vvvg+ge a+  l
  gi|121636125|ref|YP_976348.1|  37 AAALSGTPRLVGFSC--IDTFPEVLWLAQRARQAWDGVRIVIGNAMATLNYERILRQHDCFDYVVVGDGEVAFTKL 110
                                    4556668********..999***********************************977999***********9877 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0098
                    B12-binding  30 eVqllganvenedivaairaekpdvvglSal..ltsqleavkelvellkr 77 
                                    + q+l   ++++d+++a++++  dv+  +++  +t q ++ +e+v+ll++
  gi|121636125|ref|YP_976348.1| 295 RKQILTRGQDAADTINALQQLGIDVIPGTIMfhPTVQPDELRETVRLLRA 344
                                    455665566679*************9888886678888888888888654 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.1e-16     1e-12       3     167 .]     170     342 ..     168     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.1e-16
                                    EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS........TTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx........xxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekg.vkevilgggeplly........pdfvellerla 71 
                                     trgC++rC+fC ++ +      + +r +sv+ +++e+++l +++  v+++ ++ +  +          +df+ +++r+ 
  gi|121636125|ref|YP_976348.1| 170 STRGCPYRCTFCGTGAMsaMLGKDSYRAKSVDAVVDEIDYL-VSDYdVNFLSITDDLFISKhpgsqqraADFANAVLRRG 248
                                    69***************887778888999************.67766888888855444444444444455555555555 PP

                                    HTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH...HHHHHHHHHHHHTTSETEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  72 klavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf...eevlealeklreagikrvvdr 148
                                         ++ + +    +++  +  + l ++g+ rv +g+e++++e  l+   r++ +   ++  +++ +l ++gi+++  +
  gi|121636125|ref|YP_976348.1| 249 IS--VNFMVDIRLDSVVD-LDLFKHLHRAGLRRVFIGVETGSYE-QLRAY-RKQILtrgQDAADTINALQQLGIDVIPGT 323
                                    54..67777777777775.99999999999**************.55555.32222345888899*************** PP

                                    EEEBTTTSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 149 ivglpGendeeleellell 167
                                    i+ +p +  +el+e+++ll
  gi|121636125|ref|YP_976348.1| 324 IMFHPTVQPDELRETVRLL 342
                                    ***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3399.43
//
Query:       gi|121636126|ref|YP_976349.1|  [L=537]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-74  251.0   0.0    2.1e-74  250.6   0.0    1.1  1  AMP-binding     AMP-binding enzyme
    4.1e-17   62.9   0.0    9.3e-17   61.8   0.0    1.7  1  AMP-binding_C   AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.05   13.4   0.0    1.8  2  DUF5111         Domain of unknown function (DUF5111)
      0.032   14.2   0.0       0.07   13.1   0.0    1.4  1  PAC2            PAC2 family
       0.16   11.8   0.0       0.25   11.2   0.0    1.3  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6   0.0     6e-78   2.1e-74       9     422 ..      41     438 ..      35     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 6e-78
                                    TTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHH CS
                    AMP-binding   9 pdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelay 88 
                                     dk+a++ + +g+ +++ el++r+nrlA+++r++G++++d+Vail++n  +  +++ a+ + G+ +vp+n++lta e ay
  gi|121636126|ref|YP_976349.1|  41 ADKPAVILYPSGTVISFDELEARANRLAHWFRQAGLREDDVVAILMENNEHVHAVMWAARRSGLYYVPINTHLTASEAAY 120
                                    589999887889********************99********************************************** PP

                                    HHHHHTESEEE.....ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEE CS
                    AMP-binding  89 iledseakvli.....atvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlay 163
                                    i+++s+ak+++     ++      + l+e+ +        ++l  ++l    + +e+  ++     p +++  ++ +  +
  gi|121636126|ref|YP_976349.1| 121 IVDNSGAKAIVgsaalRE----TCHGLAEHLPG--GLPDLLMLAGGGLVGWMTYPECVADQ-----P-DTPIEDEREGDL 188
                                    ***********7532212....13555555553..22334566666665555555555333.....3.333566677779 PP

                                    EEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                    AMP-binding 164 iiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                    ++Y+SGTTG+PKG+  +   ++  +a   ++    f++++d+v+ls +p++h +  +++++ al++G t v+++k++a  
  gi|121636126|ref|YP_976349.1| 189 LQYSSGTTGRPKGIKRELPHVSPDAAPGMMPALldFWMDADSVYLSPAPMYHTAP-SVWTMSALAAGVTTVVMEKFDA-- 265
                                    ******************9999998875577667788999***************.5*******************99.. PP

                                    HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGS CS
                    AMP-binding 242 pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEtt 321
                                    +++ l++i++++vt+ + vP+++ ++l+ ++    ++++d+sslr v+ +++p++ ++ +++    g+ + e Y  +E++
  gi|121636126|ref|YP_976349.1| 266 EGA-LDAIQRYRVTHAQFVPAMFVRMLKLPEAV--RNSYDMSSLRRVIHAAAPCPVQIKEQMIHWWGPIIDEYYASSEAS 342
                                    444.6***********************64333..5677*****************************9*********** PP

                                    SECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEE CS
                    AMP-binding 322 gvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDl 401
                                    g + + + e+  + +gsvGkp+ g  v+iv  + g ++p++++Ge+++ g   +  Yl++p++ta + + + +w+  GD+
  gi|121636126|ref|YP_976349.1| 343 GSTLI-TAEDWLTHPGSVGKPIQG-GVHIVGAD-GSELPPNQPGEIYFEGGYPF-EYLNDPAKTAASRN-KHGWVTVGDV 417
                                    ***74.334444789******998.9*****99.99**************9998.5************9.646******* PP

                                    EEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 402 grldedGyleivgRkkdlikl 422
                                    g+ld+dGyl+++gR  ++i++
  gi|121636126|ref|YP_976349.1| 418 GYLDDDGYLFLTGRRHHMIIS 438
                                    *******************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   2.6e-20   9.3e-17       1      76 []     447     525 ..     447     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.6e-20
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e E+ lv+hp+V +aaV+Gvpd+  G++++a V   d         + eL a++r++l ++++p+ + f ++lp+t +GK
  gi|121636126|ref|YP_976349.1| 447 EAENLLVAHPKVLDAAVFGVPDDEMGQRVMAAVQTVDSadA-NdqFAGELLAWLRDRLSHFKCPRSIAFEPQLPRTDTGK 525
                                    67*******************************98544322.13599********************************9 PP

>> DUF5111  Domain of unknown function (DUF5111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05      0.05      76     114 ..      83     122 ..      65     126 .. 0.82
   2 ?   -2.5   0.0       1.2   4.4e+03      49      69 ..     435     455 ..     432     475 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                        DUF5111  76 afkltnd.esawnlWfPgqsGiyyvvvntkakewsalyik 114
                                    a  ++n+ + +  +W   +sG+yyv +nt+    +a yi 
  gi|121636126|ref|YP_976349.1|  83 AILMENNeHVHAVMWAARRSGLYYVPINTHLTASEAAYIV 122
                                    55666662556779*****************999999985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                        DUF5111  49 lsvssWlniylkeadgtiWgn 69 
                                    + +s+ +niy +ea++ + ++
  gi|121636126|ref|YP_976349.1| 435 MIISGGVNIYPQEAENLLVAH 455
                                    77889999*****99987665 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05      0.07      28      93 ..     417     500 ..     414     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                    EEEEEHCCHSBCCCC.SEEEEETTEEE-SEEE...EEE.TTT...............SEEEEEEE..E-HSCHHHHHHHH CS
                           PAC2  28 vgeidsdyllpfvgprpvvlveegrelepprl...yak.dsg..............srdllvlqg..repilqyeefaka 87 
                                    vg++d+d++l   g+r+++++++g+ + p +    +   +++              ++++++ ++   + +++ + fa +
  gi|121636126|ref|YP_976349.1| 417 VGYLDDDGYLFLTGRRHHMIISGGVNIYPQEAenlL-VaHPKvldaavfgvpddemGQRVMAAVQtvDSADANDQ-FAGE 494
                                    9***********************666666665543.3366689999*********7777777775555555555.**** PP

                                    HHHHHH CS
                           PAC2  88 lldwae 93 
                                    ll w++
  gi|121636126|ref|YP_976349.1| 495 LLAWLR 500
                                    ****97 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     7e-05      0.25      12      85 ..      45     119 ..      39     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                 DEDD_Tnp_IS110  12 acvidaegkvllservpndeegleallek.laakagevlvvveatghygallvaflleagitvvvvnp.lavkrlr 85 
                                    a+++ ++g+v+   +++   ++l+ ++ +  +++++ v + +e ++h +a + a ++  g+ +v +n  l++++++
  gi|121636126|ref|YP_976349.1|  45 AVILYPSGTVISFDELEARANRLAHWFRQaGLREDDVVAILMENNEHVHAVMWA-ARRSGLYYVPINThLTASEAA 119
                                    67788999999999***************77789999************86555.566666666655526666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3519.34
//
Query:       gi|121636127|ref|YP_976350.1|  [L=388]
Description: acyl-CoA dehydrogenase fadE3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-47  160.8   4.6    2.6e-47  160.8   4.6    1.7  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.8e-29  102.7   0.8    4.7e-29  101.3   0.1    2.1  3  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      2e-24   85.6   0.0    4.4e-24   84.5   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    8.3e-20   71.4   3.1    1.4e-19   70.7   3.1    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.1     5e+03      97     114 ..      71      88 ..      68     105 .. 0.79
   2 !  160.8   4.6   5.9e-51   2.6e-47       1     148 [.     234     381 ..     234     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHGGGT CS
                  Acyl-CoA_dh_1  97 elaqevadlamqllGgaG 114
                                    ++ qe+a+  m l G++G
  gi|121636127|ref|YP_976350.1|  71 QVTQELARGWMSLAGAMG 88 
                                    567888888888888888 PP

  == domain 2  score: 160.8 bits;  conditional E-value: 5.9e-51
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+Gf ++m++l+ +R+ vaa+alg+a +ale +l+ya++r++fg+p+ +hq+v   la+ma++l+aar l++ aae++d 
  gi|121636127|ref|YP_976350.1| 234 GQGFSQMMKGLETGRIQVAARALGVATAALEDSLAYAQQRESFGRPIWQHQAVGNYLADMATKLTAARQLTRYAAERYDS 313
                                    79****************************************************************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                    g+   +ea maKlfase+a+e+a  a+ ++Gg+Gy++ey ver++rd+ ++ +geGt+eiqrn+ia +
  gi|121636127|ref|YP_976350.1| 314 GQRCDMEAGMAKLFASEVAMEIALNAVRIHGGYGYSTEYDVERYFRDSPLMILGEGTNEIQRNVIAGQ 381
                                    *****************************************************************966 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.1     1e-32   4.7e-29       1     113 []       6     117 ..       6     117 .. 0.97
   2 ?   -1.7   0.1      0.99   4.4e+03      75      75 ..     271     271 ..     221     310 .. 0.56
   3 ?   -2.8   0.0       2.2   9.8e+03      15      30 ..     299     314 ..     282     333 .. 0.57

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 1e-32
                                    THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                    ++++ +l +tvr+f+++ ++p ++e+++++ +p++++++++  G++g+++ e+ygG+ +++ +++ v++elar++++la 
  gi|121636127|ref|YP_976350.1|   6 NDDEAMLVATVRAFIDRDVKPTVREVEHANSYPEAWIEQMKHIGIYGLAIDEQYGGSPVSMPCYVQVTQELARGWMSLAG 85 
                                    58999**********************999************************************************** PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasge 113
                                    ++g h+ +va+ +  fGteeq+r yLp++asge
  gi|121636127|ref|YP_976350.1|  86 AMGGHT-VVAKLLTLFGTEEQRRTYLPPMASGE 117
                                    **9998.5559*********************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.99
                                    - CS
                  Acyl-CoA_dh_N  75 d 75 
                                     
  gi|121636127|ref|YP_976350.1| 271 Q 271
                                    1 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.2
                                    HHHHTHHHHHHHHHHT CS
                  Acyl-CoA_dh_N  15 aeeelaphaaewdeeg 30 
                                    a+++l  +aae +++g
  gi|121636127|ref|YP_976350.1| 299 AARQLTRYAAERYDSG 314
                                    3344444555555444 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   9.9e-28   4.4e-24       2      96 ..     122     220 ..     121     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 9.9e-28
                                    EE---SS-SS-GGG---EE.EEETT.E..EEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE- CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvktta.aerdgge..yvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvr 76 
                                    +alTEp++Gsd+++++tta a++ +g+    +nG K+wi+na+ + l+ vl++t+ ++  r++g+s++lv+   pg++v+
  gi|121636127|ref|YP_976350.1| 122 MALTEPGGGSDLQNMSTTAlADGPEGSagLLINGCKTWISNARRSGLFAVLCKTDPNAtpRHQGMSIVLVE-PGPGLTVS 200
                                    89*****************9999998888************************43333578**********.799****8 PP

                                    ----BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  77 rieeklGlrglptgelvfed 96 
                                    r  +klG++g++++el f++
  gi|121636127|ref|YP_976350.1| 201 RDLPKLGYKGVESCELSFDN 220
                                    8889**************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   3.1   3.1e-23   1.4e-19       3     123 ..     251     361 ..     249     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3.1e-23
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    +aa alG+A aal++ +++a++r +  +g+++++++a+   la++a++l AAr+l++ aa+r     + g+++      e
  gi|121636127|ref|YP_976350.1| 251 VAARALGVATAALEDSLAYAQQRES--FGRPIWQHQAVGNYLADMATKLTAARQLTRYAAER----YDSGQRC----DME 320
                                    799**********************..***********************************....9******....789 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHH CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDa 123
                                    a +a+++a+e a +++ ++++++Gg+++ +e+ ++R++RD 
  gi|121636127|ref|YP_976350.1| 321 AGMAKLFASEVAMEIALNAVRIHGGYGYSTEYDVERYFRDS 361
                                    99**************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2603.94
//
Query:       gi|121636128|ref|YP_976351.1|  [L=337]
Description: hypothetical protein BCG_0253 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00013   21.5   0.0       0.36   10.4   0.0    2.2  2  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     2e-05      0.36      42     105 ..      57     119 ..      45     128 .. 0.81
   2 !    8.8   0.0   6.4e-05       1.1      51     106 ..     246     300 ..     243     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2e-05
                                    HHHHTTTSSSB--H..HHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEE CS
                MaoC_dehydratas  42 fAkkagfggpIahG..mltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkr 105
                                     A+++g +gp ah    + +ai  + ++++  +   a++    +rF +   +gdtl++++evvg r
  gi|121636128|ref|YP_976351.1|  57 CAAVTGMPGPLAHPglVCDVAIGQSTLATQRVK---ANLFYRGLRFHRFPAVGDTLYTRTEVVGLR 119
                                    799999999999962235567777777666666...99*9***********************965 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 6.4e-05
                                    SB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEE CS
                MaoC_dehydratas  51 pIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrd 106
                                    + + G +t +++ +  ++ l++  ++ +  +++  t+pV  gdtl+ el  +  ++
  gi|121636128|ref|YP_976351.1| 246 RLVYGGHTIGLALAQATRLLPN-LATVLDWESCDHTAPVHEGDTLYSELHIESAQA 300
                                    5677889999999888877777.9999*******************9998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2230.83
//
Query:       gi|121636129|ref|YP_976352.1|  [L=302]
Description: esterase lipW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-60  203.7   0.2    3.7e-60  203.4   0.2    1.1  1  Abhydrolase_3  alpha/beta hydrolase fold
    2.5e-06   26.7   0.0    7.9e-06   25.0   0.0    1.6  1  COesterase     Carboxylesterase family
    3.1e-06   26.1   0.1    2.6e-05   23.1   0.1    1.9  2  AXE1           Acetyl xylan esterase (AXE1)
    8.2e-05   22.2   0.3    0.00068   19.2   0.0    2.3  3  Peptidase_S9   Prolyl oligopeptidase family
    0.00062   19.4   0.0       0.56    9.7   0.0    2.1  2  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
       0.02   14.4   0.2       0.04   13.4   0.2    1.4  1  Esterase_phd   Esterase PHB depolymerase
       0.09   12.7   0.0       0.16   11.8   0.0    1.3  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.4   0.2   1.5e-63   3.7e-60       1     209 [.      74     271 ..      74     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: 203.4 bits;  conditional E-value: 1.5e-63
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    l+++H GG+v+g+++++d+lc +++++lg++v svdYrlAPe+p+Paa+ d+++al wla+     ++dp+r++++G Sa
  gi|121636129|ref|YP_976352.1|  74 LLWIHAGGYVMGTAQQDDRLCLRFSSRLGITVASVDYRLAPENPYPAALGDCYSALTWLASLP---AVDPARVAIGGASA 150
                                    69***********************************************************95...8************* PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                    GG laaa+al ard+g++++a+q+l+yP++d  rt   si    ++ ++ l++ +a +  wr+yl++ad     a p ++
  gi|121636129|ref|YP_976352.1| 151 GGGLAAALALLARDRGGITPAFQLLVYPMLDD-RT---SIA--PANPHYRLWNGRANRFGWRAYLGDAD--ARVAVPGRR 222
                                    *****************************977.65...552..34567789**************7555..558889988 PP

                                    S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTG CS
                  Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgf 209
                                    +dl gl+p+++ v+++D+l+de+ ayaerl aagv+++++++eg++Hgf
  gi|121636129|ref|YP_976352.1| 223 DDLGGLAPAWIGVGTHDLLHDEDLAYAERLTAAGVPCQVEVVEGAFHGF 271
                                    89**********************************************9 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.1e-09   7.9e-06      93     209 ..      62     165 ..      42     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.1e-09
                                    EEESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHH CS
                     COesterase  93 ytPkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlAL 170
                                    y P+ +   ++  P l wih gg+++g+a++    +  + ++ ++ v ++ YRl +         e p  ++l D   AL
  gi|121636129|ref|YP_976352.1|  62 YRPAGS---NEPAPALLWIHAGGYVMGTAQQddRLCLRFSSRLGITVASVDYRLAP---------ENPYPAALGDCYSAL 129
                                    777654...444599**************99555566778888***********86.........678889999****** PP

                                    HHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSGGGT CS
                     COesterase 171 rWVkenIasFGGdpervtlfGesAGaasvsllllsplsr 209
                                    +W+    a    dp rv + G sAG+ ++++l l    r
  gi|121636129|ref|YP_976352.1| 130 TWLASLPAV---DPARVAIGGASAGGGLAAALALLARDR 165
                                    ***876654...****************99998876666 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.059   1.5e+02      70     118 ..      58     111 ..      53     116 .. 0.72
   2 !   23.1   0.1     1e-08   2.6e-05     157     203 ..     124     170 ..     112     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.059
                                    EEEEEEES.SSSSEEEEEEEE..-TT--GGGHHHHH..HHHH.TT-EEEEEE-T CS
                           AXE1  70 kaklvlPkekeeklPavvefh..GYegsrgeihdll..nyaa.aGyavvvmdvR 118
                                      +l +P+ ++e+ Pa++  h  GY +++ +  d l   +++  G++v+++d R
  gi|121636129|ref|YP_976352.1|  58 GVRLYRPAGSNEPAPALLWIHagGYVMGTAQQDDRLclRFSSrLGITVASVDYR 111
                                    568899*********997555449***999998876114443247777666655 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEE CS
                           AXE1 157 DavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavva 203
                                    D + ++  +aslp vD+ Rva+ Gas GG+la a a l ++   +++
  gi|121636129|ref|YP_976352.1| 124 DCYSALTWLASLPAVDPARVAIGGASAGGGLAAALALLARDRGGITP 170
                                    88999999***************************999887666655 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   3.8e+03      73      83 ..      79      89 ..      79      92 .. 0.83
   2 !   19.2   0.0   2.6e-07   0.00068      45      83 ..     122     160 ..     115     166 .. 0.89
   3 ?   -0.3   0.0      0.24   6.2e+02     160     189 ..     243     272 ..     231     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHH CS
                   Peptidase_S9 73 yGGyltgaaln 83
                                   +GGy++g+a+ 
  gi|121636129|ref|YP_976352.1| 79 AGGYVMGTAQQ 89
                                   7******9987 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.6e-07
                                    HHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH CS
                   Peptidase_S9  45 fdDfiaaaealakegyvdserlaitGgSyGGyltgaaln 83 
                                    + D+  a+ +la+   vd+ r+ai G+S+GG l++a++ 
  gi|121636129|ref|YP_976352.1| 122 LGDCYSALTWLASLPAVDPARVAIGGASAGGGLAAALAL 160
                                    56999**************************99988765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHH--S-SEEEEEETTS-SSTT CS
                   Peptidase_S9 160 aealklvaaLqkkgknvlllifpdegHgvg 189
                                     e l ++++L+ +g++ ++ +  ++ Hg+ 
  gi|121636129|ref|YP_976352.1| 243 DEDLAYAERLTAAGVPCQVEVVEGAFHGFD 272
                                    566788999999999999999999999876 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.001       2.6      79     117 ..     122     160 ..     111     172 .. 0.88
   2 !    9.7   0.0   0.00022      0.56     145     192 ..     229     274 ..     223     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
                            DLH  79 lddlkaavaylksvpevstkkvgvvGfCmGGalalllaa 117
                                    l d   a+ +l+s p v++ +v++ G   GG la +la 
  gi|121636129|ref|YP_976352.1| 122 LGDCYSALTWLASLPAVDPARVAIGGASAGGGLAAALAL 160
                                    55667899**************************99985 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                            DLH 145 apilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFand 192
                                    ap  + +g++D   + d     +e l+aa+v+++++v +ga H+F + 
  gi|121636129|ref|YP_976352.1| 229 APAWIGVGTHDLLHDEDL--AYAERLTAAGVPCQVEVVEGAFHGFDRV 274
                                    577888888888888884..78999********************765 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.6e-05      0.04      90     121 ..     134     165 ..     124     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                   Esterase_phd  90 dehrvdaarvyvaGlsaGaaladllalhypdv 121
                                    +   vd+arv + G saG++la  lal   d+
  gi|121636129|ref|YP_976352.1| 134 SLPAVDPARVAIGGASAGGGLAAALALLARDR 165
                                    55679********************9987776 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.4e-05      0.16       9      41 ..     128     160 ..     125     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                                    HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHH CS
                         BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllas 41 
                                    a+++l + p v   ++++ G S Gg la +la 
  gi|121636129|ref|YP_976352.1| 128 ALTWLASLPAVDPARVAIGGASAGGGLAAALAL 160
                                    899**************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2391.62
//
Query:       gi|121636130|ref|YP_976353.1|  [L=442]
Description: hypothetical protein BCG_0255 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-18   66.4   0.0    3.4e-18   65.9   0.0    1.2  1  Oxidored_molyb   Oxidoreductase molybdopterin binding domain
    9.8e-05   22.0  12.7     0.0049   16.5   0.6    2.4  2  Ni_hydr_CYTB     Prokaryotic cytochrome b561
  ------ inclusion threshold ------
       0.17   11.6   0.3       0.38   10.4   0.2    1.6  1  DUF3236          Protein of unknown function (DUF3236)
        5.2    6.9   9.5        3.1    7.6   0.1    3.0  3  Phage_holin_2_3  Bacteriophage holin family HP1
        7.9    7.1  18.7       0.53   10.9   1.9    3.2  2  DUF4405          Domain of unknown function (DUF4405)


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   9.4e-22   3.4e-18      11     165 ..     310     441 ..     300     442 .] 0.89

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 9.4e-22
                                    C-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHHTTB-ET CS
                 Oxidored_molyb  11 kwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLekagvkkp 90 
                                    +wrl + g    ++ l  + L  lp+++    l+C++              +w    ++  +W+Gv+l+++   agv  p
  gi|121636130|ref|YP_976353.1| 310 DWRLVLRG-GPAEVVLDRATLAGLPQRTARLPLACVE--------------GW----SAVRTWSGVPLAELALLAGV--P 368
                                    69999999.67788999999*99**************..............79....9999****************..8 PP

                                    T..EEEEEEEEE-TCCTEEE.EEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEES CS
                 Oxidored_molyb  91 earhvvfegadeeleeskyg.asiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievsd 165
                                     ar + ++++++    +++g a++  +++ + d+lLA++++g +L+ +hGyP R++vp l g+ ++Kw+  ie+++
  gi|121636130|ref|YP_976353.1| 369 AARSARVTSLQR---GGAFGeAKLAANQIADPDALLALRVDGADLSLNHGYPARIIVPALPGVHNTKWVAGIEFHK 441
                                    9********985...55665167788888877*****************************************986 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.4e-06    0.0049      88     157 ..      25     121 ..      16     124 .. 0.68
   2 !    9.4   8.8   0.00021      0.76      42     169 ..     106     204 ..      92     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                    --------------TT..........THHHHHHHHHHHHHHHHHHHT...............HHHHHHHH.......... CS
                   Ni_hydr_CYTB  88 rgrkpeagknnplqkl..........vhlllyvllvvliltGlllsf...............aatagfpll........l 134
                                    + ++p+a +   + +           ++l+l+v+l+++i+tGll +                        l         
  gi|121636130|ref|YP_976353.1|  25 QRHPPPALHRLTRFRSplrgpwltsvFGLVLLVALPFVIITGLLSYIayapqlgqaipgdvgW-------LrlpaftwpT 97 
                                    4555555555555555666666666699****************9996666666644444330.......366666666* PP

                                    .HTS-THHHHHHH.HHHHHHH.HH CS
                   Ni_hydr_CYTB 135 ddkggaqlarelHellaaall.af 157
                                    +++++ +l   lH  l+ +++ ++
  gi|121636130|ref|YP_976353.1|  98 RPSWLYRLTQGLHVGLGLVIIpVV 121
                                    *************66666666444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                                    HHHHHHHHHHHHHHHHHHHHHHH------------STTTSSSSS----------------TTTHHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB  42 aralHklaGlvllalllfrllwlkkakkpspriifrqikrdltlllrgrkpeagknnplqklvhlllyvllvvliltGll 121
                                    +  lH  +Glv++ ++l+ l+                        l  ++p+++    l++l +l+l+  ++++i+tG+l
  gi|121636130|ref|YP_976353.1| 106 TQGLHVGLGLVIIPVVLAKLWSV-------------------IPRLFVWPPARSIAQVLERLSVLMLVGGILFQIVTGVL 166
                                    46678888888888888888777...................77789999999999999999****************** PP

                                    HHTHHHHHHHH...HTS-THHHHHHH.HHHHHHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB 122 lsfaatagfplllddkggaqlarelHellaaallafvvlHiaaallhg 169
                                                  d  +  ++ + H + a++++a ++lHi+  + h 
  gi|121636130|ref|YP_976353.1| 167 NIQY----------DYIFGFSFYTGHYFGAWVFIAGFLLHIVVKIPHM 204
                                    9776..........9999999*****9**************8766665 PP

>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00011      0.38      68     121 ..     217     269 ..     195     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                    STGGGGGGSSSHHHHHHHHHHHHS--SEEEEEEESSSTTS-EEEEEEETTS-EE CS
                        DUF3236  68 ietnsaDltriPalskalialdisdadlviaRGRLGvpGsGsllvildekgril 121
                                    + tn+aD+   P    +l++++  +a l   RG LG+ G+G ll+ + + g+ l
  gi|121636130|ref|YP_976353.1| 217 LGTNVADTRAQPCDPDGLVSVNPGEATLS-RRGALGLVGAGVLLIGVLTVGQTL 269
                                    469***********************986.8*************9877777666 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00087       3.1      28      45 ..     153     170 ..     147     172 .. 0.89
   2 ?   -4.0   0.4       3.6   1.3e+04      26      35 ..     187     196 ..     183     198 .. 0.75
   3 ?    4.6   0.5    0.0079        28      11      32 ..     347     367 ..     346     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00087
                Phage_holin_2_3  28 iviGIicgvvTfliNwyy 45 
                                    +v GI++ +vT ++N+ y
  gi|121636130|ref|YP_976353.1| 153 LVGGILFQIVTGVLNIQY 170
                                    799*************99 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.6
                Phage_holin_2_3  26 WAiviGIicg 35 
                                    W+ + G ++ 
  gi|121636130|ref|YP_976353.1| 187 WVFIAGFLLH 196
                                    9999998765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0079
                Phage_holin_2_3  11 sSavavvlGllsLseWAiviGI 32 
                                    +Sav + +G+  L+e A++ G+
  gi|121636130|ref|YP_976353.1| 347 WSAVRTWSGV-PLAELALLAGV 367
                                    9*********.*********96 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9   0.00015      0.53       4      35 ..      53      93 ..      50     123 .. 0.71
   2 ?    0.2   9.2      0.32   1.1e+03       4      64 ..     151     199 ..     148     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                        DUF4405  4 lllllsflvlaiSGillsfavlpsgrgaywa.........f 35
                                   l+ll++  +++i+G+l ++a+ p+ ++a  +         f
  gi|121636130|ref|YP_976353.1| 53 LVLLVALPFVIITGLLSYIAYAPQLGQAIPGdvgwlrlpaF 93
                                   89*********************998888878884444431 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                        DUF4405   4 lllllsflvlaiSGillsfavlpsgrgaywa...flglskhqwrdiHeilgllflilvvlHlgl 64 
                                    l+l+  +l+++++G+l  +           +   f           H + +++f++  +lH+++
  gi|121636130|ref|YP_976353.1| 151 LMLVGGILFQIVTGVLNIQY---------DYifgF------SFYTGHYFGAWVFIAGFLLHIVV 199
                                    45555666666666666544.........333222......46778***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3371.80
//
Query:       gi|121636131|ref|YP_976354.1|  [L=182]
Description: hypothetical protein BCG_0256 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.23   11.1   0.1       0.23   11.1   0.1    1.6  2  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.32   5.8e+03      71      82 ..      19      30 ..      17      37 .. 0.61
   2 ?   11.1   0.1   1.3e-05      0.23      36      95 ..     109     169 ..     101     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHHH CS
                    Oxidored_q2 71 Ltaivigaaeta 82
                                   L+a+v g+a + 
  gi|121636131|ref|YP_976354.1| 19 LLAMVSGFALLG 30
                                   667777776654 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHHHHC..............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                    Oxidored_q2  36 avnlllvlagvftegtlvi.tnpatefadplpqalvLtaivigaaetavgLallvrlyrey 95 
                                    ++ ll++l g   +g++ + + + ++ +  l+  l Lta+++g++ +a ++ l+v+  r +
  gi|121636131|ref|YP_976354.1| 109 GLTLLVFLPGIIRQGAPTYlDATGQTQEPFLGRWLLLTAVAFGISAAAYAIRLVVAHVRRR 169
                                    666777777777777777678888888999********************99999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1378.94
//
Query:       gi|121636132|ref|YP_976355.1|  [L=413]
Description: esterase lipC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-25   87.7   0.1    1.6e-24   86.9   0.1    1.4  1  Abhydrolase_3  alpha/beta hydrolase fold
    3.8e-11   42.9   0.0    7.5e-10   38.6   0.0    2.3  1  Peptidase_S9   Prolyl oligopeptidase family
      1e-09   37.9   0.2    7.7e-09   34.9   0.2    1.9  1  COesterase     Carboxylesterase family
     0.0044   16.3   0.1      0.087   12.1   0.0    2.4  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0048   17.0   0.0      0.046   13.8   0.0    2.2  2  Abhydrolase_4  TAP-like protein
     0.0053   16.7   0.0      0.024   14.6   0.0    1.9  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
  ------ inclusion threshold ------
      0.022   14.3   0.0        1.4    8.4   0.0    2.3  2  Esterase_phd   Esterase PHB depolymerase
      0.031   13.8   0.0       0.11   12.0   0.0    2.1  2  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.1   7.2e-28   1.6e-24       2     209 ..     160     369 ..     159     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 7.2e-28
                                    EEE--STTTS--TTTT.HHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   2 vyfHGGGfvlgsldth.dalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    +++ GG++v gs + +  a++++la+  g v++s+dYr AP h++P  + d+ +a+ w++++  ++g d + i++aG Sa
  gi|121636132|ref|YP_976355.1| 160 IFVPGGAWVHGSRAIQgYAVLSRLAA-QGWVCLSIDYRVAPHHRWPRHILDVKTAIAWARANVDKFGGDRNFIAVAGCSA 238
                                    6778***********99999999998.599********************************99**************** PP

                                    HHHHHHHHHHHHHHTT---..........EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGG CS
                  Abhydrolase_3  81 GGnlaaavalrardegepk..........vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadr 150
                                    GG+l+a + l a d +  +          v ++v iy   d e+ +++++   +++          +d + r+++++   
  gi|121636132|ref|YP_976355.1| 239 GGHLSALAGLTANDPQ-YQaelpegsdtsVDAVVGIYGRYDWEDRSTPER---ARF----------VDFLERVVVQRTID 304
                                    *************985.3346999999999*******9777755555555...222..........24444555542222 PP

                                    GST....TTSGGGCS-SST---EEEEEETT-TT..HHHHHHHHHHHHH.TT--EEEEEETTEETTG CS
                  Abhydrolase_3 151 ddp....laspllaedlsglpptlvvvaefDpl..rdegeayaerlra.agvevelieyegmvHgf 209
                                    ++p     asp+++   +++pp lv+ + +D     ++++ + erlra    +v + e +g+ Hgf
  gi|121636132|ref|YP_976355.1| 305 RHPevfrDASPIQR-VTRNAPPFLVIHGSRDCVipVEQARSFVERLRAvSRSQVGYLELPGAGHGF 369
                                    24433445788866.7999************9833579999******967889************9 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   3.4e-13   7.5e-10      45     188 ..     210     369 ..     179     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.4e-13
                                    HHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH.H-GGG-SE............EEEESE---CCCHHCSTTS. CS
                   Peptidase_S9  45 fdDfiaaaealakegyvdserlaitGgSyGGyltgaaln.qrpdlFka............avaevpvvdvlrydsdtdl. 110
                                    ++  ia+a+a ++++  d++ +a+ G S+GG l++ a    ++  ++a            +v  ++ +d+    + +++ 
  gi|121636132|ref|YP_976355.1| 210 VKTAIAWARANVDKFGGDRNFIAVAGCSAGGHLSALAGLtANDPQYQAelpegsdtsvdaVVGIYGRYDWEDRSTPERAr 289
                                    556799*************************9998875437777787522222222212166667778888887777778 PP

                                    ...THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-S CS
                   Peptidase_S9 111 ...lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegH 186
                                       + e++  + + ++ +e ++++sp++ +++  + pp+L+ihG  D  +p+++a  +v++L+      v +l  p++gH
  gi|121636132|ref|YP_976355.1| 290 fvdFLERVVVQRTIDRHPEVFRDASPIQRVTR--NAPPFLVIHGSRDCVIPVEQARSFVERLRAVSRSqVGYLELPGAGH 367
                                    8887777777777778****************..*****************************6666669********** PP

                                    ST CS
                   Peptidase_S9 187 gv 188
                                    g+
  gi|121636132|ref|YP_976355.1| 368 GF 369
                                    87 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   3.4e-12   7.7e-09      90     198 ..     143     242 ..     138     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.4e-12
                                    EEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG...S-THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHH CS
                     COesterase  90 LnvytPkekkeakkklPVlVwihGggfqtgsase...ydgsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDq 166
                                    L+v+  k+    +k  PVl+++ Gg+ + gs      +  s Laa+ + +  +i YR+ +   +            +lD+
  gi|121636132|ref|YP_976355.1| 143 LDVWRRKD--MPTKPAPVLIFVPGGAWVHGSRAIqgyAVLSRLAAQ-GWVCLSIDYRVAPHHRWPR---------HILDV 210
                                    78888433..456666**************9977564556677777.9**********99644443.........48*** PP

                                    HHHHHHHHHHGGGGTEEEEEEEEEEETHHHHH CS
                     COesterase 167 vlALrWVkenIasFGGdpervtlfGesAGaas 198
                                     +A+ W + n+ +FGGd + + ++G sAG+ +
  gi|121636132|ref|YP_976355.1| 211 KTAIAWARANVDKFGGDRNFIAVAGCSAGGHL 242
                                    *****************************976 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.056   1.3e+02      53      96 ..     201     249 ..     153     259 .. 0.58
   2 !   12.1   0.0   3.9e-05     0.087     188     220 ..     320     352 ..     301     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.056
                    Hydrolase_4  53 psfddyvdDlaafvekvkeehpel.....plfllGhSmGGliallyllr 96 
                                    +++ +++ D+++++  ++++  +       + + G S GG +++l++l+
  gi|121636132|ref|YP_976355.1| 201 HRWPRHILDVKTAIAWARANVDKFggdrnFIAVAGCSAGGHLSALAGLT 249
                                    3455555566666543332222212223467788999999999888844 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.9e-05
                    Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgsk 220
                                    ++   P+l++hG++D v++ e++r ++erl++ 
  gi|121636132|ref|YP_976355.1| 320 TRNAPPFLVIHGSRDCVIPVEQARSFVERLRAV 352
                                    444479*******************99998764 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.35   7.9e+02      44      62 ..     208     226 ..     205     254 .. 0.80
   2 !   13.8   0.0     2e-05     0.046      28      74 ..     317     368 ..     304     378 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                  Abhydrolase_4  44 rDpaTPyegakklakalgg 62 
                                     D  T  ++a++  +++gg
  gi|121636132|ref|YP_976355.1| 208 LDVKTAIAWARANVDKFGG 226
                                    7999************997 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                  Abhydrolase_4  28 estakgaapvLllqnerDpaTPyegakklakalgg.a....vlvtvegeGHg 74 
                                    +   ++a+p L++ + rD + P e+a+++ ++l+  +      +   g+GHg
  gi|121636132|ref|YP_976355.1| 317 QRVTRNAPPFLVIHGSRDCVIPVEQARSFVERLRAvSrsqvGYLELPGAGHG 368
                                    3334467**************************9654444444666666666 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.024      22     163 ..     229     369 ..     212     371 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                    SSEEEEEETHHHHHHHHHHHHSSSEEEEE.EES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT-B--TT CS
                         BAAT_C  22 dkigllGiSkGgelalllasflkkisavv.lingsavvvegklvykdeskvlpelklsmeklkvnknglldivdvlallk 100
                                    + i++ G S Gg l  l + + ++++    l  gs + v +      +     + + +  ++    + +++++ + + ++
  gi|121636132|ref|YP_976355.1| 229 NFIAVAGCSAGGHLSALAGLTANDPQYQAeLPEGSDTSVDAVVGIYGRYDWEDRSTPERARFVDFLERVVVQRTIDRHPE 308
                                    67888888888888888888888666554144566554433333222323333333444444446667777777777777 PP

                                    TGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S-- CS
                         BAAT_C 101 eklaekalipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHli 163
                                       +   + +v +   p+l++ g  D ++p +e a+  +erL++  ++ +v +l  p+aGH +
  gi|121636132|ref|YP_976355.1| 309 VFRDASPIQRVTRNAPPFLVIHGSRDCVIP-VEQARSFVERLRAVSRS-QVGYLELPGAGHGF 369
                                    77777778899999************9999.56788************.************65 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00062       1.4      81     120 ..     213     252 ..     201     266 .. 0.88
   2 ?    3.4   0.0      0.02        45     169     199 ..     323     353 ..     297     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00062
                   Esterase_phd  81 vvalvdalvdehrvdaarvyvaGlsaGaaladllalhypd 120
                                     +a ++a vd+ + d   + vaG saG+ l+ l +l+  d
  gi|121636132|ref|YP_976355.1| 213 AIAWARANVDKFGGDRNFIAVAGCSAGGHLSALAGLTAND 252
                                    56889999**********************9999987665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                   Esterase_phd 169 glpalvvqGdadtvvavknaeslvvalrrls 199
                                    + p lv++G  d v+ v +a s+v +lr  s
  gi|121636132|ref|YP_976355.1| 323 APPFLVIHGSRDCVIPVEQARSFVERLRAVS 353
                                    45899******************99998765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.7     6e+03      31      44 ..     178     191 ..     152     194 .. 0.74
   2 ?   12.0   0.0   4.9e-05      0.11     121     190 ..     298     370 ..     203     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                            DLH  31 diserlaeeGYval 44 
                                     + +rla +G+v l
  gi|121636132|ref|YP_976355.1| 178 AVLSRLAAQGWVCL 191
                                    47789999999877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.9e-05
                            DLH 121 evdaavafYG..lspekeleeaakikapilalfgeeDefipadevekleealkaa.nvdlelkvYpgagHaFa 190
                                     v++++  ++   +  ++++++++ + p l+++g +D +ip +++  + e l+a    ++     pgagH+F 
  gi|121636132|ref|YP_976355.1| 298 VVQRTIDRHPevFRDASPIQRVTRNAPPFLVIHGSRDCVIPVEQARSFVERLRAVsRSQVGYLELPGAGHGFD 370
                                    45666666667667789999999****************************987514455666689******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2919.26
//
Query:       gi|121636133|ref|YP_976356.1|  [L=257]
Description: hypothetical protein BCG_0258 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-71  241.6   0.8    1.4e-71  241.4   0.8    1.0  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
  ------ inclusion threshold ------
       0.13   10.9   0.0       0.18   10.5   0.0    1.1  1  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.8   1.6e-75   1.4e-71       1     231 [.       4     230 ..       4     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 1.6e-75
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    Ls++Da++l++e+++ +mh++++av+e +s++++   ++++re i+ r+++ ++l +++v++pl++++p+W+e++++Dl+
  gi|121636133|ref|YP_976356.1|   4 LSGWDAVLLYSETPNVHMHTLKVAVIELDSDRQEF-GVDAFREVIAGRLHKLEPLGYQLVDVPLKFHHPMWREHCQVDLN 82 
                                    899********************************.7******************************************* PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yH+R ++l+aPG++rel e+v+++as+pL+r++PlWe++++EGl+++riA+++k+HHAl+DGv++++++ar +dl p ++
  gi|121636133|ref|YP_976356.1|  83 YHIRPWRLRAPGGRRELDEAVGEIASTPLNRDHPLWEMYFVEGLANHRIAVVAKIHHALADGVASANMMARGMDLLPGPE 162
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaal.earslvlpfaaprtplnt 231
                                      +++p+ p+++  ++ql + +a+ +++++lg+++++++++++ +gr++++++  + +l++pf++p+t++n+
  gi|121636133|ref|YP_976356.1| 163 VGRYVPD-PAPT--KRQLLS-AAFIDHLRHLGRIPATIRYTTQGLGRVRRSSRkLSPALTMPFTPPPTFMNR 230
                                    *******.6666..344443.579****************************9999**************96 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     2e-05      0.18     113     147 ..     111     147 ..      94     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2e-05
                                    CCCS.-SEEEEEEE.SSTTEEEEEEEEECCT--TTTH CS
                   Condensation 113 Lekg.pLfraalfk.iaenrlllllsvHHiivDGvSl 147
                                    L+++ pL+ ++ ++ +a++r  +++++HH ++DGv  
  gi|121636133|ref|YP_976356.1| 111 LNRDhPLWEMYFVEgLANHRIAVVAKIHHALADGVAS 147
                                    66666999999996489999**************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1946.13
//
Query:       gi|121636134|ref|YP_976357.1|  [L=269]
Description: aldehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-81  273.1   0.3    3.9e-81  272.9   0.3    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.086   11.9   0.0       0.11   11.6   0.0    1.1  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.9   0.3   4.4e-85   3.9e-81      98     332 ..       2     235 ..       1     250 [. 0.96

  Alignments for each domain:
  == domain 1  score: 272.9 bits;  conditional E-value: 4.4e-85
                                    HHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHHH CS
                         Aldedh  98 ryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalllaelfe 177
                                    +y+a++a+k++ + + + +  +++v re +GvvgaI++WN+Pl+la+ k+apal+aG+t+vlKPa etpl+a +lae+f+
  gi|121636134|ref|YP_976357.1|   2 NYFAGAADKVTWTETRTGSYGQSIVSRESVGVVGAIVAWNVPLFLAVNKIAPALLAGCTIVLKPAAETPLTANALAEVFA 81 
                                    79*******9996666656999********************************************************** PP

                                    HTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHHHHH CS
                         Aldedh 178 eaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDldkaveai 257
                                    e+glP+gvl+vv+g g e+g+al+++p++d+ +ftGs++vgr++ ++aa+ lk++tlElGGk+++i+led+Dl +a+  +
  gi|121636134|ref|YP_976357.1|  82 EVGLPEGVLSVVPG-GIETGQALTSNPDIDMFTFTGSSAVGREVGRRAAEMLKPCTLELGGKSAAIILEDVDLAAAIPMM 160
                                    **************.***************************************************************** PP

                                    HHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTTS CS
                         Aldedh 258 vkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakeega 332
                                    v++ ++naGQ C++ +r+l ++s yde+v+++++ +++l vg p d++ ++GPlise+q+ +ve++  +++  g 
  gi|121636134|ref|YP_976357.1| 161 VFSGVMNAGQGCVNQTRILAPRSRYDEIVAAVTNFVTALPVGPPSDPAAQIGPLISEKQRTRVEALHRQGHRGGR 235
                                    *****************************************************************9999887664 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05      0.11      88     144 ..      29      86 ..      12     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                           LuxC  88 qprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvden 144
                                       g+v  +++ Nvpl l+v  i+ +lL++  ++lk+ ++ p +a+al+  +a+v   
  gi|121636134|ref|YP_976357.1|  29 ESVGVVGAIVAWNVPLfLAVNKIAPALLAGCTIVLKPAAETPLTANALAEVFAEVGLP 86 
                                    456888889999***857999********************************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1899.45
//
Query:       gi|121636135|ref|YP_976358.1|  [L=116]
Description: aldehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-19   68.2   0.1    5.4e-19   68.0   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.1     3e-23   5.4e-19       1      83 [.      17     102 ..      17     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3e-23
                                    EET-SSSE.EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH..HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                         Aldedh   1 wveseset.ievinPatgeviakvpaataedvdaavaaAkeafk..awaklpaeeRaeiLrkaadlleerkeelaeletl 77 
                                    w++++++  iev +Patge ++kvp a a+dvdaavaaA++af+   w ++p++eRa+++++a ++l+erk+ +++l+++
  gi|121636135|ref|YP_976358.1|  17 WTKPSTSDvIEVRCPATGEYVGKVPMAAAADVDAAVAAARAAFDngPWPSTPPHERAAVIAAAVKMLAERKDLFTKLLAA 96 
                                    788888555***********************************888********************************* PP

                                    HH---H CS
                         Aldedh  78 etGkpl 83 
                                    etG+p 
  gi|121636135|ref|YP_976358.1|  97 ETGQPP 102
                                    ***985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1012.25
//
Query:       gi|121636136|ref|YP_976359.1|  [L=254]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-15   57.7   0.0    2.6e-15   56.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    6.4e-10   39.6   0.0    1.2e-09   38.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.5e-07   30.7   0.0    3.5e-07   30.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    8.4e-06   26.5   0.0    2.1e-05   25.2   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    0.00014   21.7   0.0    0.00091   19.0   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
    0.00073   18.9   0.0      0.003   16.9   0.0    1.8  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
       0.58    9.1   2.1       0.79    8.6   2.1    1.1  1  Peptidase_M66    Peptidase M66


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0     1e-18   2.6e-15       1      95 [.      63     155 ..      63     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1e-18
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    LdvG G G++a a+ ++g  ++gv++++  + +a  +  +++    fv+a+   lp++d+s+D+++ss+v +hv++p ++
  gi|121636136|ref|YP_976359.1|  63 LDVGGGPGYFATAFSDAGVGYIGVEPDPDEMHAAGPAFTGRP--GMFVRASGMALPLADDSVDICLSSNVAEHVPRPWQL 140
                                    8****************************9999988888888..579********************************* PP

                                    HHHHHHHEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllv 95 
                                      e+ Rv kpgGl+v
  gi|121636136|ref|YP_976359.1| 141 GTEMLRVTKPGGLVV 155
                                    ************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   4.6e-13   1.2e-09       2      97 .]      63     152 ..      62     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 4.6e-13
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+G G+G ++ a+++++    ++gv+++++ + aa   +   g    fv+++  +lp++d+s+D+++ss++ +h++++ 
  gi|121636136|ref|YP_976359.1|  63 LDVGGGPGYFATAFSDAG--VGYIGVEPDPDEMHAAGPAF--TGRPGMFVRASGMALPLADDSVDICLSSNVAEHVPRP- 137
                                    9****************5..99***************999..46689**********************999***9855. PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                      ++  e+ rv+kpgG
  gi|121636136|ref|YP_976359.1| 138 -WQLGTEMLRVTKPGG 152
                                    .589***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.4e-10   3.5e-07      21     119 ..      57     158 ..      19     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.4e-10
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg.................kf 83 
                                    + g  +Ld+G G G+++  +++ g+ ++gv+++p   + a                a+  +                 + 
  gi|121636136|ref|YP_976359.1|  57 PVGRTLLDVGGGPGYFATAFSDAGVGYIGVEPDPDEMHAA--------------GPAFTGRpgmfvrasgmalpladdSV 122
                                    344599**************************98644433..............333322233333333444444445** PP

                Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllse 119
                                    d+  +++v ehvp p  l + + + +kpgG+++ls+
  gi|121636136|ref|YP_976359.1| 123 DICLSSNVAEHVPRPWQLGTEMLRVTKPGGLVVLSY 158
                                    **********************************98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   8.2e-09   2.1e-05       1      98 [.      63     153 ..      63     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.2e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L++G+G G ++ a+ ++  ++ y+gv+++p+ +++a   +  r +  + +    al l+d+    s+D+ ++snv +h++
  gi|121636136|ref|YP_976359.1|  63 LDVGGGPGYFATAFSDA--GVGYIGVEPDPDEMHAAGPAFTGRPG-MFVRASGMALPLADD----SVDICLSSNVAEHVP 135
                                    8****************..**************666666666665.445555555555554....*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                     + ++  ++ ++ kpgG 
  gi|121636136|ref|YP_976359.1| 136 RPWQLGTEMLRVTKPGGL 153
                                    *****************7 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.6e-07   0.00091       6     115 ..      61     162 ..      58     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.6e-07
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                    ++lD+G G G+++ ++ +    +  ++G++ +++    A             F +++  +l+  l+d+++D+ ls +v  
  gi|121636136|ref|YP_976359.1|  61 TLLDVGGGPGYFATAFSDA---GVGYIGVEPDPDEMHAAGPAFTGR---PGMFVRASGMALP--LADDSVDICLSSNVAE 132
                                    5788888888888887743...234888888888887777743322...3457777777899..99************** PP

                Methyltransf_31  86 aladpdkileeiervlkpggilliedprll 115
                                    +++ p +   e+ rv kpgg +++++  +l
  gi|121636136|ref|YP_976359.1| 133 HVPRPWQLGTEMLRVTKPGGLVVLSYTVWL 162
                                    ************************998844 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06     0.003      49     150 ..      60     155 ..      48     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                    TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG CS
                Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrn 128
                                    +++lDv gG g +a ++sd+    g + v    ++m   g +   + g     f+ a++++Lp  dds D+   s     
  gi|121636136|ref|YP_976359.1|  60 RTLLDVGGGPGYFATAFSDAG--VGYIGVEPDPDEMHAAGPAFTGRPG----MFVRASGMALPLADDSVDICLSSNVAEH 133
                                    556666666666666666542..2333333333445555555444444....49*****************999988889 PP

                                    -S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 129 vtDklkaLkeayrvlkpGGrlv 150
                                    v+   +   e+ rv kpGG +v
  gi|121636136|ref|YP_976359.1| 134 VPRPWQLGTEMLRVTKPGGLVV 155
                                    998888889**********876 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.1   0.00031      0.79     200     227 ..     166     192 ..     151     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                  Peptidase_M66 200 qGHalGLpHylageaaskgsypyaegsl 227
                                     GH +GL Hyl g +a+   y+ ++g  
  gi|121636136|ref|YP_976359.1| 166 GGHEMGLSHYLGGARAA-ARYVRKHGHP 192
                                    6************5555.8898887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1936.77
//
Query:       gi|121636137|ref|YP_976360.1|  [L=384]
Description: hypothetical protein BCG_0262 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.0   0.0    2.2e-29  102.2   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    6.1e-22   78.5   0.0    9.7e-22   77.8   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.5e-17   63.4   2.2    2.5e-17   63.4   2.2    2.2  2  Glyco_transf_4   Glycosyltransferase Family 4
      1e-15   58.5  13.6      1e-15   58.5  13.6    2.2  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    4.5e-10   39.8   0.0    7.7e-10   39.0   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   6.3e-33   2.2e-29      16     171 ..     200     353 ..     193     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 6.3e-33
                                    EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESE CS
                Glycos_transf_1  16 kiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadi 95 
                                    + +++++rl+++K ++ ++ a+a+l+ +  p ++l i+G+g ++++l ++++ l + d v+f+g+v++  ++++l+++ +
  gi|121636137|ref|YP_976360.1| 200 PRVVVLSRLVPHKQIEDALAAVAELQPR-IPGLHLDIVGGGWWRQRLVDHVHRLDIADAVTFHGHVDDVTKHHVLQSSWV 278
                                    678999*******************988.*************************************************** PP

                                    EEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                Glycos_transf_1  96 fvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                     +lps++Eg+G++++EA + g+p+i +  +gg+a+ ++dg+tG+lv+    ++l++ +++ll+d+ lr++lg +a+ 
  gi|121636137|ref|YP_976360.1| 279 HLLPSRKEGWGLAVIEAAQHGVPTIGYRsSGGLADSIVDGVTGILVDDR--AELVAWLEQLLSDSVLRDQLGAKAQA 353
                                    *************************************************..*********************99986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   2.7e-25   9.7e-22       2     134 .]     200     340 ..     199     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 2.7e-25
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH-S CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaaad 74 
                                    p+++ ++rl+++ k+++  l av++l+ + + ++l ivG+g  r ++l + ++  ++++ v+f+G+v+d  +  +l++++
  gi|121636137|ref|YP_976360.1| 200 PRVVVLSRLVPH-KQIEDALAAVAELQPRiPgLHLDIVGGGWwR-QRLVDHVHrlDIADAVTFHGHVDDvtKHHVLQSSW 277
                                    799******655.**************88758*******87755.68888886588899********88677888***** PP

                                    EEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvg.giaevv..gengllvppgdpealaeailrLled 134
                                    v ++Ps  eg+gl+++Ea+ +g+p++  + + g+a+ +  g++g+lv+  d ++l++ +++Ll+d
  gi|121636137|ref|YP_976360.1| 278 VHLLPSrkEGWGLAVIEAAQHGVPTIGYRSSgGLADSIvdGVTGILVD--DRAELVAWLEQLLSD 340
                                    ******999*******************88538999888********9..9************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   2.2   6.9e-21   2.5e-17       2     168 ..      21     186 ..      20     188 .. 0.80
   2 ?    1.6   0.7     0.068   2.4e+02      41     109 ..     201     275 ..     189     303 .. 0.65

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.9e-21
                 Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllr...slaflrrlrrllkrekpDvv.H 77 
                                    GG e ++ ++  +La+ G+ Vt+ t +++g+++ e +++vr+ r     +  +l+    +a++r     l+r +pDvv  
  gi|121636137|ref|YP_976360.1|  21 GGSEAYLQRIGAQLAASGIAVTLRTARYPGAPRHELVDGVRISRAG-GRYSVYLWallAMAAARCGLGPLRRVRPDVVvD 99 
                                    9**********************************53333333333.22222223000223333334469999*****99 PP

                 Glyco_transf_4  78 ahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl...lrradrviavSeatadelrerygv 154
                                    +++ ++++a ll+ r  + + lV+++H       ++   ++  rl +++e  l   l+r ++ ++vS   a++l++ +gv
  gi|121636137|ref|YP_976360.1| 100 TQNGWPFVARLLYGR--RSLVLVHHCHREQ----WPVAGRMMGRLGWYVESMLsprLHRRNQYVTVSLPSARDLIA-LGV 172
                                    999999988888888..6***********9....88888888899988888888889*******************.*** PP

                 Glyco_transf_4 155 ppekitVipnGvDl 168
                                    ++e+i+V+ nG D 
  gi|121636137|ref|YP_976360.1| 173 DSERIAVVRNGLDE 186
                                    ************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.068
                 Glyco_transf_4  41 vrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr...rlgiplVltvHglye......... 108
                                    + v+  +l+++k+    la++  l+ ++   + D+v       +g+   +l     rl+i   +t+Hg+ +         
  gi|121636137|ref|YP_976360.1| 201 RVVVLSRLVPHKQIEDALAAVAELQPRIPGLHLDIV------GGGWWRQRLVDhvhRLDIADAVTFHGHVDdvtkhhvlq 274
                                    455556666777777778888888888888888888......22333333333566899999999999997664333332 PP

                 Glyco_transf_4 109 k 109
                                    +
  gi|121636137|ref|YP_976360.1| 275 S 275
                                    1 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5  13.6   2.9e-19     1e-15       1     160 []      21     183 ..      21     183 .. 0.86
   2 ?   -4.5   4.7         5   1.8e+04      95     102 ..     252     259 ..     187     333 .. 0.58

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 2.9e-19
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrl..lrqrrerpdvvh 78 
                                    gG++ y +++ ++Laa G  Vt+ t++++++++++  dgvr+ r   +++  ++a la+++a  +l  l  rr rpdvv+
  gi|121636137|ref|YP_976360.1|  21 GGSEAYLQRIGAQLAASGIAVTLRTARYPGAPRHELVDGVRISRAGGRYSVYLWALLAMAAARCGLgpL--RRVRPDVVV 98 
                                    8*******************************************9999887655555554444443224..9******** PP

                Glyco_trans_4_4  79 ahsptaglaarlarrrrgiplvvtlhg..lllrrg.sgavrrlyralerrllrradavlvvseaeaeelralgvpadrvv 155
                                      +   +++arl+  rr++ lv+++h   + ++++ +g++++++  + +  l+r  + ++vs   a++l+algv+ +r++
  gi|121636137|ref|YP_976360.1|  99 DTQNGWPFVARLLYGRRSLVLVHHCHReqWPVAGRmMGRLGWYVESMLSPRLHRRNQYVTVSLPSARDLIALGVDSERIA 178
                                    98877799999998799*********542555544899******99999999999999999999**************** PP

                Glyco_trans_4_4 156 vvpng 160
                                    vv+ng
  gi|121636137|ref|YP_976360.1| 179 VVRNG 183
                                    ****8 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 5
                Glyco_trans_4_4  95 rgiplvvt 102
                                     +i   vt
  gi|121636137|ref|YP_976360.1| 252 LDIADAVT 259
                                    22222333 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   2.1e-13   7.7e-10       2      90 ..     279     367 ..     278     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.1e-13
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeerraiaeaarervlae 80 
                                     L psr+e+  l + Eaa  G++ +  ++  gl++ + +g ++il++d +el++ +++ll++  +r++++++a++r   e
  gi|121636137|ref|YP_976360.1| 279 HLLPSRKEGWGLAVIEAAQHGVPTIGYRSsGGLADSIVDGVTGILVDDRAELVAWLEQLLSDSVLRDQLGAKAQAR-SGE 357
                                    689************************9999*********************************************.99* PP

                Glyco_trans_1_2  81 htydhraeql 90 
                                    +++++ ae l
  gi|121636137|ref|YP_976360.1| 358 FSWRQSAEAL 367
                                    *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2719.74
//
Query:       gi|121636138|ref|YP_976361.1|  [L=576]
Description: hypothetical protein BCG_0263c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3596.03
//
Query:       gi|121636139|ref|YP_976362.1|  [L=421]
Description: hypothetical protein BCG_0264c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-96  322.2   3.8    3.8e-96  321.9   3.8    1.0  1  PorA             Porin PorA
  ------ inclusion threshold ------
      0.063   11.8   0.1        0.1   11.1   0.1    1.2  1  CD36             CD36 family


Domain annotation for each model (and alignments):
>> PorA  Porin PorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.9   3.8  4.2e-100   3.8e-96       2     299 ..       6     336 ..       5     337 .. 0.96

  Alignments for each domain:
  == domain 1  score: 321.9 bits;  conditional E-value: 4.2e-100
                           PorA   2 sllllalGvallvlAillptyvvpklkklPldldattvtegttatlldaaalaak.aka.edapvtsqrtvtaeepsdkd 79 
                                    ++ +++lG+all++A+ll ty++ +++++Pld+dat+ ++g t+t ld+a+la++     +d+p+ sq++vt+e+p+++d
  gi|121636139|ref|YP_976362.1|   6 ACGAIGLGAALLIAALLLSTYTTRRIAEIPLDIDATLISDG-TGTALDSASLATEhIVVnQDVPLVSQQQVTVESPANAD 84 
                                    7889*************************************.************864448******************** PP

                           PorA  80 evtlqvgttvsrtdkkeaeddlsasvdrvtldRktgepv...........seakvsdekaspaeevpreGlqykFPfdte 148
                                    +vtlqvg++++rtdk++++++l a+vd+vtl+Rkt+++v           +++  +de++++a +++++Gl y+FPf+te
  gi|121636139|ref|YP_976362.1|  85 VVTLQVGSSLRRTDKQKDSGLLLAIVDTVTLNRKTAMAVsddthtggavqKPRGLNDENPPTAIPLRHDGLSYRFPFHTE 164
                                    **************************************************999*************************** PP

                           PorA 149 kksYqyFDptlrkavpadfvgeeevdGlevyrFeqev...pptkla............aklrltvPaslw.........v 204
                                    kk+Y+yFDp+++ka++a+++gee+v+Gl++yrF+q+v   p+ kl             ++ ++t  a++w         +
  gi|121636139|ref|YP_976362.1| 165 KKTYPYFDPIAQKAFDANYEGEEDVNGLTTYRFTQNVgytPEGKLVaplkypslyagdEDGKVTTSAAMWglpgdpneqI 244
                                    *************************************77744444467777799999999999999***9********** PP

                           PorA 205 tmtryysatrtlwVepeTGviVkgeekirqylardgdeaeeaavtlldadlawdeetveaqveqakegrdklkllgrtlp 284
                                    tmtryy+a+rt+wV+p++G+iVk++e+ ++y+ard  ++e   vt+ d++++ +eetve+qv+ a+++rd+l+l++r+lp
  gi|121636139|ref|YP_976362.1| 245 TMTRYYAAQRTFWVDPVSGTIVKETERANHYFARDPLKPE---VTFADYQVTSTEETVESQVNAARDERDRLALWSRVLP 321
                                    ***************************************9...************************************* PP

                           PorA 285 ivllvlGlvllvagl 299
                                    i+++++Glv+lv+g 
  gi|121636139|ref|YP_976362.1| 322 ITFTAAGLVALVGGG 336
                                    ************996 PP

>> CD36  CD36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.2e-05       0.1     261     299 ..     160     198 ..     152     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           CD36 261 pfltkddtltiFssdlcRslpleyekevevkgipayryt 299
                                    pf t+++t  +F +   ++++++ye+e++v+g+++yr+t
  gi|121636139|ref|YP_976362.1| 160 PFHTEKKTYPYFDPIAQKAFDANYEGEEDVNGLTTYRFT 198
                                    78999*********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3067.48
//
Query:       gi|121636140|ref|YP_976363.1|  [L=407]
Description: integral membrane acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-26   93.2  31.3    1.9e-26   93.0  31.3    1.0  1  Acyl_transf_3    Acyltransferase family
  ------ inclusion threshold ------
       0.32   11.1   1.0        0.8    9.8   1.0    1.6  1  DUF357           Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0  31.3   2.1e-30   1.9e-26       3     335 ..      38     370 ..      36     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.1e-30
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxx RF
                  Acyl_transf_3   3 ylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla.......amlyrrrglskli 75 
                                    +++++R++A++ Vv+ H++   ++  g g   +          +  +v +FF +SGf+l+       ++l++++ +  ++
  gi|121636140|ref|YP_976363.1|  38 AVEGMRACAAVGVVVTHVAFQTGHSSGVGGRLF--------GRFDLAVAVFFAVSGFLLWrghaaaaRDLRSHPRTGPYL 109
                                    689*****************9999999988776........78999********************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  76 krRilrlliplliwllliillialvaghiqanasanvtlfdetkglmfllfefpatghlWfLwalfvlylllplllrllr 155
                                    ++R+ r++ ++++  ++i+ l     + +   + an+tl       +++l  +++  ++W+L++++ +y++lp+l+ l r
  gi|121636140|ref|YP_976363.1| 110 RSRVARIMPAYVVAVVVILSLLPDADHASLTVWLANLTLT----QIYVPLTLTGGLTQMWSLSVEVAFYAALPVLALLGR 185
                                    ********99999999999999998888888888888888....46********************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 156 kvrkshlllllilllllslvfirhelfgpatsvgllplpsvla.llfflfGalladaddrdrnlsrglkislllslllla 234
                                    +++   ++ ++++l++ls+ ++++ l       g +pl + +a ++ f++G+lla +      l++++ +++++ +++++
  gi|121636140|ref|YP_976363.1| 186 RIPVGARVPAIAALAALSWAWGWLPLDAG---SGINPLTWPPAfFSWFAAGMLLAEWAYSPVGLPHRWARRRVAMAVTAL 262
                                    *****************999999998433...344444444445*****************************9999999 PP

                                    xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 235 lillalfgqtdg.....gglvasvliqsaslllvslgimllllllfalpsrsafk..llrylgkiSygiYliHlpllmll 307
                                    l++l++++   g      g  a  +  +a  +lv++++ + l+l +  +s++     +++ lg+ Syg++++Hl  l ++
  gi|121636140|ref|YP_976363.1| 263 LGYLVAASPLAGpeglvPGTAAQFAVKTAMGSLVAFALVAPLVLDRPDTSHRLLGspAMVTLGRWSYGLFIWHLAALAMV 342
                                    9999999999998888888888888888888888888888888888888888777************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 308 qkllrdwglnlgevlllvlllvvsvivs 335
                                      ++ ++ +   ++++lvl l++ ++++
  gi|121636140|ref|YP_976363.1| 343 FPVIGAFPFTGRMPTVLVLTLIFGFAIA 370
                                    *******666333333333333333333 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0   8.9e-05       0.8      51      67 ..     196     214 ..     194     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.9e-05
                                    HHHHHHHHHHHHHH..HHH CS
                         DUF357  51 vnAlasfsYaeGwL..Dag 67 
                                    + Ala++s+a+GwL  Dag
  gi|121636140|ref|YP_976363.1| 196 IAALAALSWAWGWLplDAG 214
                                    68***********633666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2790.05
//
Query:       gi|121636141|ref|YP_976364.1|  [L=226]
Description: hypothetical protein BCG_0266c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   38.2   0.3    1.8e-09   38.2   0.3    1.4  2  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1      0.81   1.4e+04      95     111 ..       9      25 ..       9      25 .. 0.84
   2 !   38.2   0.3     1e-13   1.8e-09       1     120 [.      94     209 ..      94     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.81
                                    HHHHHHHHHHT-EEE.E CS
                            PIN  95 aliaAtAkehgikliat 111
                                    a+ +A++++ g  li+t
  gi|121636141|ref|YP_976364.1|   9 AMGLALCIYIGSLLIYT 25 
                                    56689999999999987 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 1e-13
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    ++lDTsv+ +l r+ +++  a++ l+e+++++ ++++  E+ y +++       ++e  +l+  lsa+ +++ +a++ ++
  gi|121636141|ref|YP_976364.1|  94 YLLDTSVIKRLSRPAVRR--AVEPLAEAGAVARTQITDLEVGYSARN-------ETEWQRLMVALSAFDLIESTASHHRR 164
                                    68*******999888877..56666667*******************.......************************** PP

                                    HHHHHHHHH......SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  81 aaeialkyg......llpnDaliaAtAkehgikliatfDedfrrva 120
                                    a+ i + +       +++ D+liaA  +ehg+ ++ ++D df+ +a
  gi|121636141|ref|YP_976364.1| 165 ALGIQRLLAarsqrgRKIPDLLIAAAGEEHGLVVL-HYDADFDLIA 209
                                    *999999999999*******************777.******9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1516.20
//
Query:       gi|121636142|ref|YP_976365.1|  [L=326]
Description: phosphotriesterase PHP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-145  484.5   0.2   1.4e-145  484.4   0.2    1.0  1  PTE           Phosphotriesterase family
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.065   13.0   0.1    1.9  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   0.2  1.5e-149  1.4e-145       1     298 []      11     320 ..      11     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 1.5e-149
                                    EEGGCTSCEEEEE-SCEE-HHHHCHCCCCC--HHHHHHHHHHHHHHHHHTTEEEEEE---CCCT--HHHHHHHHCCHSSE CS
                            PTE   1 vetsdlGvtLahehltitldefkqnvpealevedkevaaiieellelkarGvdalveltttglgRdvqtlkrvaeetgvn 80 
                                    ++t+dlGvtL+heh++i+++e++qn+pea+++edk+va++i++l+elkarGvd++v+lt++glgR++++++rva++t++n
  gi|121636142|ref|YP_976365.1|  11 IDTADLGVTLMHEHVFIMTTEIAQNYPEAWGDEDKRVAGAIARLGELKARGVDTIVDLTVIGLGRYIPRIARVAAATELN 90 
                                    799***************************************************************************** PP

                                    EEEEECB--CCG--.......TCCCCS-CHCHHHHHHHHHHT-STTTS--EEEEEEEE-CTBS-HHHHHHHHHHHHHHHH CS
                            PTE  81 ivaatGfYvdatvp.......eaararsveeltdvlvdeiehGidgteikaGiikeigtsgkltpseekvleavaqahkq 153
                                    iv+atG+Y++++vp       ++a+++++e++td++v++iehGi++t+ikaGi+k+++++++ltp++e+vl+avaqahk+
  gi|121636142|ref|YP_976365.1|  91 IVVATGLYTYNDVPfyfhylgPGAQLDGPEIMTDMFVRDIEHGIADTGIKAGILKCATDEPGLTPGVERVLRAVAQAHKR 170
                                    ******************************************************************************** PP

                                    H---EEEEEGCCTTCHHHHHHHHHHTT--GGGEEETTGGCS--HHHHHHHHHTT-EEEE--TT-TTTS-HHHHHHHHHHH CS
                            PTE 154 tGaPisihtsaslragleqlrilqeeGvDlsrvvvghldtktdvkellelidlGaYleyDlfgvdlispdekRirivhal 233
                                    tGaPis+ht+a+lr+gl+q+ri++eeGv+lsrvv+gh++++tdv++l+eli++G+Yl++D+fgvd+isp+++R++iv+++
  gi|121636142|ref|YP_976365.1| 171 TGAPISTHTHAGLRRGLDQQRIFAEEGVELSRVVIGHCGDSTDVGYLEELIAAGSYLGMDRFGVDVISPFQDRVNIVARM 250
                                    ******************************************************************************** PP

                                    HHTT-GGGEEE-----SEECCCSCCCCCHH.TTH....HHHTHHHHHHHTT--HHHHHHHHTHHHHHHHH CS
                            PTE 234 vdrGyedrillshDittkfralkkelvgya.ydl....lltdviPklkqrGlteeqldkiLvenPkqile 298
                                    ++rG++d+++lshD++++f+al++elv++a +++    +++dviP+lkq+G+t+eql+++Lv+nP++i+e
  gi|121636142|ref|YP_976365.1| 251 CERGHADKMVLSHDACCYFDALPEELVPVAmPNWhylhIHNDVIPALKQHGVTDEQLHTMLVDNPRRIFE 320
                                    ******************************999999********************************96 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.2e-06     0.065      98     289 ..     126     319 ..      21     321 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-06
                                    HHHHHHHHHHHTTECE..EEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCH CS
                   Amidohydro_2  98 aaaeleraveelgfkG..vrlnphvggddllgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgv 175
                                     ++ +e+ +++ g+k+  ++  ++ +g  +  +r  r + +a +++g+p+  h         ++++ +    q  ++++ 
  gi|121636142|ref|YP_976365.1| 126 FVRDIEHGIADTGIKAgiLKCATDEPGLTPGVERVLRAVAQAHKRTGAPISTH---------THAGLRRGLDQQRIFAEE 196
                                    55555555566666653333333334444444444466666666666666666.........344444444444444444 PP

                                    HHHCTTSEEEESGGGTT..TTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--... CS
                   Amidohydro_2 176 arkfPnlkivlaHgGgp..serlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdrilfGsD... 250
                                     +++   ++v+ H+G      +l++++++ + +    ++  g    ++   + +++ +++ar  e   +d+++ + D   
  gi|121636142|ref|YP_976365.1| 197 GVELS--RVVIGHCGDStdVGYLEELIAAGSYLG---MDRFG----VDVISPFQDRVNIVARMCERGHADKMVLSHDacc 267
                                    45554..688888888865333333333322222...22222....23345556666999******************** PP

                                    .........BTSTTSTSCTTHHHHCHHHHH....SSHHHHHHHHTHHHHHHC CS
                   Amidohydro_2 251 .........yPhptleaepealalldlval....lsdeerekilggNAarly 289
                                              P+  + +++  +++   +al     +de+++ +l++N++r++
  gi|121636142|ref|YP_976365.1| 268 yfdalpeelVPVAMPNWHYLHIHNDVIPALkqhgVTDEQLHTMLVDNPRRIF 319
                                    *********5555555555555555555555566****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2470.58
//
Query:       gi|121636143|ref|YP_976366.1|  [L=568]
Description: acyl-CoA dehydrogenase fadE4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-13   51.3   0.8    8.8e-13   48.7   0.2    2.2  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      5e-08   33.0   0.0    9.7e-08   32.1   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
       0.01   16.1   1.3      0.016   15.5   0.2    1.8  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.2   1.5e-16   8.8e-13       4     147 ..     238     385 ..     236     387 .. 0.95
   2 ?    0.1   0.0      0.14   8.3e+02     101     123 ..     513     537 ..     506     545 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.5e-16
                                    HHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH------- CS
                  Acyl-CoA_dh_1   4 frvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkp 83 
                                    f++a++t n+   +++++a+g++  al e++ +a +r+ +g+ + d+ +vr+ l + +++l a++l + ra   +  +  
  gi|121636143|ref|YP_976366.1| 238 FHAALNTVNVCKYNLGWGAIGMCTHALYESVTHAANRHLYGTVVTDFSHVRRLLTDAYVRLIAMKLVASRASDYMRSASA 317
                                    6788999999999************************************************************8888877 PP

                                    -....HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                  Acyl-CoA_dh_1  84 d....raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    +       + ++K++++   ++v++   +++ ++G+++++ +e  +r++ +l+ +eGt  i + ++++
  gi|121636143|ref|YP_976366.1| 318 AdrryLLYSPLTKAKVTSEGERVITALWDVIAAKGVEKDTFFETVAREIGLLPRLEGTVHINIGLLGK 385
                                    77888999**************************************************9999888776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHGGGTTSGGGH..HHH CS
                  Acyl-CoA_dh_1 101 evadlamqllGgaGyleeyp..ver 123
                                    ++ + a++l+G  ++++e++    r
  gi|121636143|ref|YP_976366.1| 513 DFNTHAVELHGRSATTAEQArfAMR 537
                                    5667899*****9999666543334 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.6e-11   9.7e-08       1      70 [.     131     199 ..     131     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.6e-11
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS-------EEEEEEE..G CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpdrarglslflvprda 70 
                                    af+l+E+++G dv + ++   + ++g+++ nGeK +i+na+ a ++ ++++ +++p+ +++  +f+ ++++
  gi|121636143|ref|YP_976366.1| 131 AFGLSEQTHGADVYQTDM-ILTPSDGGWTANGEKYYIGNANVARMVSTFGKiAGTPE-SQEYVFFVADSQH 199
                                    79***************9.65555559************************988888.8888777776554 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   2.6e-06     0.016       7     122 ..     256     365 ..     252     371 .. 0.89
   2 ?   -2.8   0.0       1.2   7.3e+03      31      61 ..     463     493 ..     445     496 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                  Acyl-CoA_dh_2   7 alGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearra 86 
                                    a+G++  al e v +a++r     g+ ++d++ +   l++a  rl A +++  ra + +  ++aa+++      + + ++
  gi|121636143|ref|YP_976366.1| 256 AIGMCTHALYESVTHAANRHL--YGTVVTDFSHVRRLLTDAYVRLIAMKLVASRASDYMRSASAADRR----YLLYSPLT 329
                                    79*******************..8999********************999999999886555555555....59****** PP

                                    HHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHH CS
                  Acyl-CoA_dh_2  87 aalavelaiaavdalfeaaGgsalrkesplqRlwRD 122
                                    +a ++++  +++ al ++++++++ k+   + + R+
  gi|121636143|ref|YP_976366.1| 330 KAKVTSEGERVITALWDVIAAKGVEKDTFFETVARE 365
                                    ************************999877766666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                    -------HHHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  31 gekladdpatqlalaeaaarldAArallera 61 
                                     ++++ d  + + ++++ a++  A+++le+a
  gi|121636143|ref|YP_976366.1| 463 DAAQQKDIDFAFGVGQLFANVPYAQLILEEA 493
                                    4555666667788888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4142.86
//
Query:       gi|121636144|ref|YP_976367.1|  [L=229]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-12   47.6   1.0    1.1e-12   47.6   1.0    1.8  2  TetR_N     Bacterial regulatory proteins, tetR family
    9.6e-05   22.7   3.7    9.6e-05   22.7   3.7    2.3  3  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
       0.13   12.3   1.4       0.94    9.6   0.0    2.5  3  TetR_C_29  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   1.0   1.8e-16   1.1e-12       2      44 ..      18      60 ..      17      62 .. 0.96
   2 ?   -2.3   0.1      0.69   4.1e+03      11      35 ..     109     133 ..     108     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.8e-16
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLl 44
                                   ++aA++ f+ +G+++ +++ IA+rAGv+kg+l++yF++K++L+
  gi|121636144|ref|YP_976367.1| 18 VEAAEAEFGAHGFSRGSLNVIARRAGVAKGSLFQYFADKRDLY 60
                                   69***************************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                                    HHHTTT--HHHHHHHHTSSHHHHHH CS
                         TetR_N  11 erGydattvreIAkrAGvskgalYr 35 
                                    er  +a+ + e+   A +s +++ +
  gi|121636144|ref|YP_976367.1| 109 ERALHAAATLEVDTDARISVRSVLH 133
                                    5667777777777777777777765 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.2   1.2e+03      11      46 ..      59      90 ..      56     102 .. 0.60
   2 !   22.7   3.7   1.6e-08   9.6e-05      11      87 ..      92     167 ..      90     178 .. 0.80
   3 ?   -2.7   0.1       1.2   7.4e+03      82      89 ..     203     210 ..     195     224 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                      TetR_C_11 11 Lrallralaealaspragallrallaeaqrdpelae 46
                                   L a++ ++    as+r ++ + +l+ e+  +  + e
  gi|121636144|ref|YP_976367.1| 59 LYAFIADI----ASQRVRSYMEDLIRELDPNRPFFE 90
                                   44444444....455677777777777766655555 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.6e-08
                      TetR_C_11  11 Lrallralaealas.pragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlll 87 
                                    L+ ll+  ++ +a+ pr++al +a   e+  d++++  +r  l +   + lr ++r A+arG+lrad d+ ++++lll
  gi|121636144|ref|YP_976367.1|  92 LTDLLDGWVAYFAEhPRERALHAAATLEV--DTDARISVRSVLHRHYLDVLRPLVRDAHARGDLRADSDTGALMSLLL 167
                                    56778888887777366666666666666..8888889999777778**************************99987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.2
                      TetR_C_11  82 vldlllgp 89 
                                    ++++l+++
  gi|121636144|ref|YP_976367.1| 203 LVAVLAAA 210
                                    22222222 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.092   5.5e+02      61      88 ..      43      71 ..      35      82 .. 0.78
   2 ?    9.6   0.0   0.00016      0.94       5      77 ..      92     163 ..      89     175 .. 0.86
   3 ?   -1.5   0.1      0.44   2.6e+03       1      18 [.     196     213 ..     196     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.092
                                   HHHTT.SS-SS--HHHHHHHHHHHHHHHH CS
                      TetR_C_29 61 Gqaag.vFrpgvdaldlyllisslcffrv 88
                                   G+a+g +F+   d +dly+ i+ ++  rv
  gi|121636144|ref|YP_976367.1| 43 GVAKGsLFQYFADKRDLYAFIADIASQRV 71
                                   66666357777899999999998887766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHHH-HHHHHHHHHHHHS-TT--TTS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHH CS
                      TetR_C_29   5 lrrlveftfdyhaanpefvrLvsiEnlhrgrhlkksesirelnspliekleeilerGqaagvFrpgvdaldly 77 
                                    l+ l++  + y+a++p   +L +   l    ++ + +  + l++  ++ l+ +++  +a+g +r++ d   l+
  gi|121636144|ref|YP_976367.1|  92 LTDLLDGWVAYFAEHPRERALHAAATLEVDTDA-RISVRSVLHRHYLDVLRPLVRDAHARGDLRADSDTGALM 163
                                    6788899999***********999999999998.55556677************************9987665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHHHHHHH CS
                      TetR_C_29   1 Pvealrrlveftfdyhaa 18 
                                    P  a+rrlv+++   ++a
  gi|121636144|ref|YP_976367.1| 196 PALAVRRLVAVLAAAFDA 213
                                    778999*99998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1238.19
//
Query:       gi|121636145|ref|YP_976368.1|  [L=314]
Description: ribonucleotide-diphosphate reductase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-18   65.5   0.0    6.8e-18   65.1   0.0    1.1  1  Ribonuc_red_sm   Ribonucleotide reductase, small chain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.017   14.9   0.1    1.4  1  Haem_oxygenas_2  Iron-containing redox enzyme
      0.052   14.0   0.2        4.4    7.7   0.1    2.6  3  Rubrerythrin     Rubrerythrin


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.1e-21   6.8e-18      20     261 ..      28     269 ..      21     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.1e-21
                                    HCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBS...SHHHHHHHHHHHHHHHHHH CS
                 Ribonuc_red_sm  20 eanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevq...ipearafygfqaamEniHa 96 
                                    +a fW p ++d++ D +dw+ kLs+de++  +++ + +++ +  v+e +   ++s ++       +++++ +a++E+ H+
  gi|121636145|ref|YP_976368.1|  28 NAKFWDPADIDFTRDRADWE-KLSDDERDYATRLCTQFIAGEEAVTEDIQ-PFMSAMRaegRLADEMYLTQFAFEEAKHT 105
                                    689****************9.6**************************54.7777777333345689************* PP

                                    HHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTT.SC...HHHHHHHHHHHHHHHCCCHHHHHHHHHHH CS
                 Ribonuc_red_sm  97 esYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskk.de...ekfaerlvafallegilfysgFaailwlk 172
                                    +++ + l++++  +++ +++++ +  + ++        ++++  + d+    ++  ++  + ++eg+l   g++a   + 
  gi|121636145|ref|YP_976368.1| 106 QVFRMWLDAVG-ISEDLHRYLDDLPAYRQIFYAELP--ECLNALSaDPspaAQVRASVTYNHIVEGMLALTGYYAWHKIC 182
                                    ***********.667778888888888887765432..233333323344555555666667*****************9 PP

                                    .HTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHTTT.BTTCHHHH CS
                 Ribonuc_red_sm 173 .krgllpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikeavel.Ekefitdalpvellglnked 250
                                     +r +lpg+ e ++ i  De  H+  +  ++++ ++  + +   +e++++eli  a++l E+ f+  + +   + l+k+ 
  gi|121636145|ref|YP_976368.1| 183 vERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLiEEGFA-LYGDQPPFDLSKD- 260
                                    9*******************************998887666667999999999888875255554.2223333345533. PP

                                    HHHHHHHHHHH CS
                 Ribonuc_red_sm 251 vkqYieyvadr 261
                                      ++++y +d+
  gi|121636145|ref|YP_976368.1| 261 --DFLQYSTDK 269
                                    ..455555555 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.9e-06     0.017      48      85 ..     101     143 ..      77     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                Haem_oxygenas_2  48 ernHvelyrrllkalGldeeplealpelpetlalinl.....f 85 
                                    e++H++++r +l a+G++e+ +++l+ lp+ +++  +     +
  gi|121636145|ref|YP_976368.1| 101 EAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAelpecL 143
                                    567*************************766555444555551 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3    0.0047        28      83     134 ..      58     109 ..      43     110 .. 0.76
   2 ?    7.7   0.1   0.00074       4.4      34      62 ..      93     121 ..      65     136 .. 0.82
   3 ?    2.8   0.0     0.024   1.4e+02     109     129 ..     185     205 ..     174     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0047
                                    HHHH.HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  83 knLe.eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                    + L  + i+g++a+ e++ +f++ +  + + +  + ++ + a +E kH + +r
  gi|121636145|ref|YP_976368.1|  58 TRLCtQFIAGEEAVTEDIQPFMSAMRAEGRLA-DEMYLTQFAFEEAKHTQVFR 109
                                    44434789999999999999998887755555.67777888888999999887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00074
                                    HHHHHHHHHHHHHHHHHHHHHHCSTTHH. CS
                   Rubrerythrin  34 lFeelAeeEreHakilnklleklepelel 62 
                                    ++ ++A eE++H ++++ +l+++  +++l
  gi|121636145|ref|YP_976368.1|  93 YLTQFAFEEAKHTQVFRMWLDAVGISEDL 121
                                    57899***************999999884 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.024
                                    HTTSHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin 109 kegneeakklfkklaeaEkkH 129
                                    ++  +  ++l++++ ++E++H
  gi|121636145|ref|YP_976368.1| 185 RAILPGMQELVRRIGDDERRH 205
                                    455566677777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2128.38
//
Query:       gi|121636146|ref|YP_976369.1|  [L=511]
Description: succinate-semialdehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.4e-144  479.7   1.2   9.2e-144  479.4   1.2    1.0  1  Aldedh          Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.035   13.1   0.0      0.079   12.0   0.0    1.5  1  LuxC            Acyl-CoA reductase (LuxC)
       0.94    9.6   5.5        0.7   10.0   3.3    1.9  2  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.4   1.2  1.5e-147  9.2e-144       9     462 .]      57     508 ..      49     508 .. 0.97

  Alignments for each domain:
  == domain 1  score: 479.4 bits;  conditional E-value: 1.5e-147
                                    EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                         Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                    i++inPatge++ +++aat ++vdaa+a+A++ f  ++++++++Ra+  +++adlle+++++ a+++tle+Gk+la a+a
  gi|121636146|ref|YP_976369.1|  57 IATINPATGETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQRARWANATADLLEAEADQAAAMMTLEMGKTLAAAKA 136
                                    899***************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHH.HSEEEEEE.C.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTS CS
                         Aldedh  89 eveeaidvlryyaelaek.legevlps.s.egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeet 165
                                    e  ++++ +ryyae ae  l++e +   +   + a+ r++PlGv++a++PWNfPl  a++ +apal+aGN+ +lK a+++
  gi|121636146|ref|YP_976369.1| 137 EALKCAKGFRYYAENAEAlLADEPADAaKvGASAAYGRYQPLGVILAVMPWNFPLWQAVRFAAPALMAGNVGLLKHASNV 216
                                    ******************66667666644789999********************************************* PP

                                    HHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE- CS
                         Aldedh 166 plsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivl 245
                                    p +al+la ++++ g+P+g ++ +    s + ea++++p+v++ ++tGs + g+ + + a++++k+++lElGG +p+iv+
  gi|121636146|ref|YP_976369.1| 217 PQCALYLADVIARGGFPDGCFQTLLV-SSGAVEAILRDPRVAAATLTGSEPAGQSVGAIAGNEIKPTVLELGGSDPFIVM 295
                                    ************************98.7889************************************************* PP

                                    TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHH CS
                         Aldedh 246 edaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyve 325
                                    ++aDld+av+ +v+g + n+GQ Ciaa+r++v+ +iyd+fv+k+v+++++l+vgdp d+dtdvGPl++e+ +++v k+ve
  gi|121636146|ref|YP_976369.1| 296 PSADLDAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRVGDPTDPDTDVGPLATEQGRNEVAKQVE 375
                                    ******************************************************************************** PP

                                    HHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SB CS
                         Aldedh 326 eakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkd 405
                                    +a ++ga + +Gg   ++ ++ g+f+ Ptv++++++dm++++eE+FGPV+sv+++ +++ea+eiaN+t +GL++  +t+d
  gi|121636146|ref|YP_976369.1| 376 DAAAAGAVIRCGG---KRLDRPGWFYPPTVITDISKDMALYTEEVFGPVASVFRAANIDEAVEIANATTFGLGSNAWTRD 452
                                    *************...7899************************************************************ PP

                                    HHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 406 leraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                    +++ +r+++++ aG+v iN +t++ +e  pfgGvk+Sg+Gre +++g++e++++ktv
  gi|121636146|ref|YP_976369.1| 453 ETEQRRFIDDIVAGQVFINGMTVSYPEL-PFGGVKRSGYGRELSAHGIREFCNIKTV 508
                                    *********************9999999.**************************98 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05     0.079      82     137 ..     170     226 ..     156     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                           LuxC  82 ksyekaqprglvlhvlsgNvpllp.vmsilqglLvknvnllkvSssdpflaaallks 137
                                      y ++qp g++l v++ N pl   v   + +l+++nv llk  s+ p+ a  l+  
  gi|121636146|ref|YP_976369.1| 170 AAYGRYQPLGVILAVMPWNFPLWQaVRFAAPALMAGNVGLLKHASNVPQCALYLADV 226
                                    4799******************86155677899************999998888765 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3   0.00012       0.7      22      85 ..      71     134 ..      62     149 .. 0.73
   2 ?   -3.8   0.0       2.2   1.3e+04      60      77 ..     330     347 ..     320     350 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                 Acetyltransf_6  22 frvatdpedleallelfraqwarr..pdvfadpltraflrdllaalaargalrlyvlrldgrpvAv 85 
                                    f+ a+++++++a++++  +++a    ++ +++++     +dll+a  a++a+ +++l+++ +++A+
  gi|121636146|ref|YP_976369.1|  71 FT-AATDDEVDAAIARAHRRFADYrqTSFAQRARWANATADLLEAE-ADQAAAMMTLEMGKTLAAA 134
                                    43.5577778887777766655555225555556666999999998.5999**********99997 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                 Acetyltransf_6  60 dllaalaargalrlyvlr 77 
                                    d+++++ +++ +r+ +lr
  gi|121636146|ref|YP_976369.1| 330 DIYDDFVDKFVARMAALR 347
                                    344444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3421.91
//
Query:       gi|121636147|ref|YP_976370.1|  [L=482]
Description: hypothetical protein BCG_0272c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-125  419.7  18.8    3.9e-66  224.0   4.1    2.2  2  LMF1      Lipase maturation factor


Domain annotation for each model (and alignments):
>> LMF1  Lipase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.4   7.1   1.6e-63   2.8e-59       1     162 [.     121     272 ..     121     290 .. 0.96
   2 !  224.0   4.1   2.2e-70   3.9e-66     259     440 ..     293     472 ..     280     473 .. 0.94

  Alignments for each domain:
  == domain 1  score: 201.4 bits;  conditional E-value: 1.6e-63
                           LMF1   1 lsFqwdslLLEvGflaillapfkllsklpkslplpslvvwlvrwLlfRlmfgsGlvKlrsgdptWwdLtaldyhyetqpl 80 
                                    +sF+w+slLLE+Gfl+i+l + ++        ++p l+++l rwLlfR+ fg+Gl+K+r gd++W++Lt+l+yh+etqp+
  gi|121636147|ref|YP_976370.1| 121 YSFGWESLLLETGFLMIFLGNERT--------APPILTLLLARWLLFRVEFGAGLIKMR-GDSCWRSLTCLYYHHETQPM 191
                                    89*****************97766........8**************************.******************** PP

                           LMF1  81 PtplawyahqlpswlhkletvvtlvvelvvpfllllPirklrlfggviqvllqlliilsGNynflnlltivlalslldDq 160
                                    P pl+w++h+lp+ lh++e++++++++lvvpf l++P ++++ ++++i v++ql++++sGN+++ln+lti+la+s++d +
  gi|121636147|ref|YP_976370.1| 192 PGPLSWFFHHLPKPLHRIEVAGNHFAQLVVPFGLFTP-QPAASIAAAIIVVTQLWLVASGNFSWLNWLTILLACSAIDTS 270
                                    *************************************.***************************************986 PP

                           LMF1 161 fl 162
                                    + 
  gi|121636147|ref|YP_976370.1| 271 SA 272
                                    65 PP

  == domain 2  score: 224.0 bits;  conditional E-value: 2.2e-70
                           LMF1 259 lvllllavlvftlslvpksklasvrnllskrqlmnsslnpfrlvnsYglfrrvtkeRpeviiegtndse....tkWkeye 334
                                     ++++++++v++ls+ p       rnlls++q+mn s+npf+lvn+Yg+f+++ ++R ev+iegt++s     t Wk ye
  gi|121636147|ref|YP_976370.1| 293 GLVVVFTAAVLLLSYWPA------RNLLSSHQRMNMSFNPFHLVNTYGAFGSICRTRREVVIEGTDESPiteqTVWKAYE 366
                                    456666777777777775......59*****************************************999999******* PP

                           LMF1 335 FkykPgdvsrrprlvaPyqprLDwqmwfaalgkyeqnpWllsLlyrLLqnskevlkLlaenPfekkppkyvRaelYkYrf 414
                                    Fk kPgd++r pr++aPy+ rLDw+mwfaa+++    pW++ +l+rLL+n++++lkLl++nPf+++pp+yvRa+lY+Yrf
  gi|121636147|ref|YP_976370.1| 367 FKGKPGDPRRLPRQWAPYHLRLDWLMWFAAISPGYALPWMTPFLNRLLRNDPATLKLLRHNPFPQSPPRYVRAQLYQYRF 446
                                    *******************************999999**************************999************** PP

                           LMF1 415 tkkeesrargawWtRelvgeyvPpls 440
                                    t+ +e r+++awW+R+l+g+yvPp+s
  gi|121636147|ref|YP_976370.1| 447 TTVAELRRDRAWWHRTLIGRYVPPMS 472
                                    **99999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3494.16
//
Query:       gi|121636148|ref|YP_976371.1|  [L=1400]
Description: hypothetical protein BCG_0273c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.4e-280  931.2  27.7   2.4e-280  931.2  27.7    2.4  3  DUF3367       Alpha-(1->3)-arabinofuranosyltransferase
    9.6e-11   41.9   0.0    5.4e-06   26.6   0.0    2.5  2  F5_F8_type_C  F5/8 type C domain


Domain annotation for each model (and alignments):
>> DUF3367  Alpha-(1->3)-arabinofuranosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  931.2  27.7  2.6e-284  2.4e-280       2     666 ..      16     692 ..      15     693 .. 0.99
   2 ?   -1.9   0.1     0.061   5.4e+02     430     479 ..    1199    1248 ..    1196    1266 .. 0.90
   3 ?   -4.7   5.7      0.45     4e+03     139     193 ..    1267    1334 ..    1248    1383 .. 0.64

  Alignments for each domain:
  == domain 1  score: 931.2 bits;  conditional E-value: 2.6e-284
                        DUF3367   2 llllaflqspglivaDTKldltanPlgFLaralhlWtdtaplGqlqnQayGYlfPhglFfalldllglpaWvtqRlWwal 81 
                                    +l+l+f+qspg++++DTKldltanPl+FLara++lW++++p+Gq qnQayGYlfPhg+Ff++++llg+p WvtqRlWwa+
  gi|121636148|ref|YP_976371.1|  16 ALALTFAQSPGQVSPDTKLDLTANPLRFLARATNLWNSDLPFGQAQNQAYGYLFPHGTFFVIGHLLGVPGWVTQRLWWAV 95 
                                    789***************************************************************************** PP

                        DUF3367  82 llvvaflGvvrlaealgigspasrvlaalayaLsPrvlttlgaiSsealpvalaPWvllPlvsal..reraslrraaals 159
                                    ll+v+f+G++r+aealg+g p+srv++a+a+aLsPrvlttlg+iSse+lp++laPWvllP + al  ++ +s+r +aa++
  gi|121636148|ref|YP_976371.1|  96 LLTVGFWGLLRVAEALGVGGPSSRVVGAVAFALSPRVLTTLGSISSETLPMMLAPWVLLPTILALrgTSGRSVRALAAQA 175
                                    ***************************************************************9977788999******* PP

                        DUF3367 160 alavalmGavNAvatlaallvavlwlltrrrerralrllawWlvavvlatlWWivpLlllgrysppFldfiEsaavTtew 239
                                    +lavalmGavNA+atla +l+av+w++++r++r ++r++awWl a++latlWW+++L  l  +sppFldfiEs++vTt+w
  gi|121636148|ref|YP_976371.1| 176 GLAVALMGAVNAIATLAGCLPAVIWWACHRPNRLWWRYTAWWLLAMALATLWWVMALTQLHGVSPPFLDFIESSGVTTQW 255
                                    ******************************************************************************** PP

                        DUF3367 240 lslaevlrGttsWtpfvsperpagaelvtepvlvlatalvaalGLaGLarrdlparrllllillvgvvllaagyagelgs 319
                                     sl+evlrGt+sWtpfv+p+++aga lvt ++++l t+lvaa+GLaGL+   +par++l+++llvgvvlla+g+ g l s
  gi|121636148|ref|YP_976371.1| 256 SSLVEVLRGTDSWTPFVAPNATAGAPLVTGSAAILGTCLVAAAGLAGLTSPAMPARGRLVTMLLVGVVLLAVGHRGGLAS 335
                                    ******************************************************************************** PP

                        DUF3367 320 plaeavrelLdgagapLRNvhKfdplvrLplvlGlahllaavslpasaraaaaakalahp.rerrvaaallvvvvvaaav 398
                                    p+a++v+++Ld+ag+pLRNvhK+ p++rLplvlGla+ll++v+lp+sa++ a+ +a+ahp r++rva+a+++++++++++
  gi|121636148|ref|YP_976371.1| 336 PVAHPVQAFLDAAGTPLRNVHKVGPVIRLPLVLGLAQLLSRVPLPGSAPRPAWLRAFAHPeRDKRVAVAVVALTALVVST 415
                                    ******************************************************************************** PP

                        DUF3367 399 apawtgrllpegayeevPdyWeeaadwLnekaag....eraLvvPgapfaeqeWGltrDeplqaLldvpwavrdavPlvp 474
                                    ++awtgr++p+g++ ++P+yW+eaadwL++++a     +r+LvvPgapfa+q WG+++Deplq+L d pw+vrd++Pl+p
  gi|121636148|ref|YP_976371.1| 416 SLAWTGRVAPPGTFGALPQYWQEAADWLRTHHAAtptpGRVLVVPGAPFATQVWGTSHDEPLQVLGDGPWGVRDSIPLTP 495
                                    ******************************99998999****************************************** PP

                        DUF3367 475 pgaiRlldgveralaegrasagladtLarqGvgyvlvRnDLdeeasdsaraalvhraleespGltrvaeFGpevekeele 554
                                    p++iR+ld+v+r +a+gr+sagladtLarqG++yvlvRnDLd+e+s+sar+ l+hr++++spGl++ aeFG +v+++ l+
  gi|121636148|ref|YP_976371.1| 496 PQTIRALDSVQRLFAAGRPSAGLADTLARQGISYVLVRNDLDPETSRSARPILLHRSIAGSPGLAKLAEFGAPVGPDPLA 575
                                    ***************************************************************************9999* PP

                        DUF3367 555 elvadeglrekvpaveiyevdea..aagaalvdadevavvaggpEallrlae....qglleadrpallaadaeaaelpae 628
                                    ++v+d+glr+++pa+eiy+v+++  + +++++++d++a+v+ggpE+llrl+e    qg+++ + p+l++ada+aa+lp+ 
  gi|121636148|ref|YP_976371.1| 576 GFVNDSGLRPRYPAIEIYRVSAPanPGAPYFAATDQLARVDGGPEVLLRLDErrrlQGQPPLG-PVLMTADARAAGLPVP 654
                                    *********************99556999***********************99999998887.**************** PP

                        DUF3367 629 evvvtDtprrretnygrvddasSailaaddarrslnav 666
                                    +v+vtDtp +ret+ygrvd++sSai+a++dar++ n+v
  gi|121636148|ref|YP_976371.1| 655 QVAVTDTPVARETDYGRVDHHSSAIRAPGDARHTYNRV 692
                                    **********************************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.061
                        DUF3367  430 aageraLvvPgapfaeqeWGltrDeplqaLldvpwavrdavPlvppgaiR 479 
                                     +a++r+LvvP++  +     +++   l +++   w +   vP ++pg+i 
  gi|121636148|ref|YP_976371.1| 1199 SATSRVLVVPESINSGWVARTSTGARLTPIAVNGWQQAWVVPAGNPGTIT 1248
                                     5679********99999989999999********************9985 PP

  == domain 3  score: -4.7 bits;  conditional E-value: 0.45
                        DUF3367  139 llPlvsal...........reraslrraaalsalavalmGavNAvatlaallvav..lwlltrrrerr 193 
                                     llPl+  l           ++ + ++r  a++a+ v+  Gav A    + ++ ++  + +++rrrer 
  gi|121636148|ref|YP_976371.1| 1267 LLPLLALLafwrtgrrqlaDRPTPPWRPGAWAAAGVLAAGAVIASIAGVMVMGTAlgVRYALRRRERL 1334
                                     45555444555667777766677889999999999999999977544433333330122333333333 PP

>> F5_F8_type_C  F5/8 type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     6e-10   5.4e-06       7      70 ..     717     791 ..     711     807 .. 0.79
   2 !   12.6   0.0   1.2e-05      0.11      12      58 ..     958    1008 ..     943    1023 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6e-10
                                    C.........SSTTTGGGGGGSSSTTSSEEESSSSTT..EEEEEEEEEEEEEEEEEEEECSSTTSSEEEEEEEEE CS
                   F5_F8_type_C   7 e.........esgewpaaaaldGnkntaWsssssddk..qwlqvdLgkpkkidgvvtqgrqdggnayvksykiqv 70 
                                    +         +++   +aaa+dG+++taW s++ ++   qwlqvd+ +p +   v++++   + +a v++  i++
  gi|121636148|ref|YP_976371.1| 717 SsadatampdVAPASAPAAAVDGDPATAWVSNALQAAvgQWLQVDFDRPVTNAVVTLTPSATAVGAQVRRILIET 791
                                    33355555555666699*************999888899************999999988666688888777765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.2e-05
                                     TGGGGGGSSSTTSSEE.ESSSSTT...EEEEEEEEEEEEEEEEEEEECSST CS
                   F5_F8_type_C   12 wpaaaaldGnkntaWs.ssssddk...qwlqvdLgkpkkidgvvtqgrqdg 58  
                                     ++a aa dG+++taW+ +++  ++   ++l++ L +p+ ++g+++   ++ 
  gi|121636148|ref|YP_976371.1|  958 GSAYAAADGDPATAWTaPQRVVQHktpPTLTLALPRPTVVTGLRLAASRSM 1008
                                     5799************74444444799****************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.44
# Mc/sec: 9487.34
//
Query:       gi|121636149|ref|YP_976372.1|  [L=57]
Description: hypothetical protein BCG_0274c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-22   77.1   1.1    8.8e-22   77.0   1.1    1.0  1  DUF2613   Protein of unknown function (DUF2613)


Domain annotation for each model (and alignments):
>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   1.1   4.9e-26   8.8e-22       1      55 []       3      56 ..       3      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 4.9e-26
                        DUF2613  1 rflgPaaaSaVaGivlGvvavfgvtavvqqdsrPstdravnadsalLgsveYGsR 55
                                   r + PaaaS+V+G++lG++a+fgvt++vqqd++P+    ++++s++L++veYG+R
  gi|121636149|ref|YP_976372.1|  3 RIVAPAAASVVVGLLLGAAAIFGVTLMVQQDKKPPLP-GGDPSSSVLNRVEYGNR 56
                                   7899*********************************.****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 373.21
//
Query:       gi|121636150|ref|YP_976373.1|  [L=388]
Description: lipoprotein lpqI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-83  278.7   0.0    7.8e-83  278.5   0.0    1.0  1  Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.5   0.0   4.3e-87   7.8e-83       3     318 ..      62     378 ..      60     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 278.5 bits;  conditional E-value: 4.3e-87
                                    HHHHHHTEE-B-SE-S--HHHHHHHHHH--SEEE--GGGTSSHHHHHHHHHHHHHH-SS....S--EEEE---BTTB--- CS
                  Glyco_hydro_3   3 dekigqLlvvevseekkseeaaellkkyqvGgiilfaenledtkqleelieaarqaseksrlgiPlllavDqegGlvqrl 82 
                                    ++k++qLlvv v   +++++a++++++y+vGgi+++        +  +++++a +++     ++Pl+++vD+egG+ +rl
  gi|121636150|ref|YP_976373.1|  62 RDKLAQLLVVGV---RDAADAQAVVTNYHVGGILIG------SDTDLTIFDGALAEIVAGGGPLPLAVSVDEEGGRLSRL 132
                                    689******998...8999****************7......666678999999999999******************** PP

                                    SSS..---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSS.SGGGSS-SSHHHHHHHHHHHHHH CS
                  Glyco_hydro_3  83 geg..tlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprng.igvrsFsedpelvaalaaamvkG 159
                                    ++   +  Psa+ la+t++++++++l+r +++++r+lgi+idfaPvvdv+++p++  ig+rsF++dp+ v+a+a+a+++G
  gi|121636150|ref|YP_976373.1| 133 RSLigGTGPSARELAQTRTVQQVRDLARDRGRQMRKLGITIDFAPVVDVTDAPDDTvIGDRSFGSDPATVTAYAGAYAQG 212
                                    **888999************************************************************************ PP

                                    HHHTT-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHH.HTT-SEEEE---B-TTT---.BGGG-HHHH CS
                  Glyco_hydro_3 160 lqgagvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaai.eagvdsVMtaHvqfpaldgt.patgskkll 237
                                    l++agv++++KHFpghG g+ dsh + +t++ + ++l  +dlvp+++++ +a+v+ VM++H+q+p l+g+ pa++sk+++
  gi|121636150|ref|YP_976373.1| 213 LRDAGVLPVLKHFPGHGRGSGDSHNGGVTTP-PLDDLVGDDLVPYRTLVtQAPVG-VMVGHLQVPGLTGSePASLSKAAV 290
                                    ******************************9.*****************99***9.*************99********* PP

                                    IIIIIIIS-.....--SEEEES-T.TSHHHHCCS-HHHHHHHHHHHT-SBEES-S---SG..HHHHHHHHHTTSS-HHHH CS
                  Glyco_hydro_3 238 tdvLRkelG.....FdGvvvsDal.amkeiadrggkeeavvlaLkAGvDilLvpeertse..ikalkkavkeGelteari 309
                                     ++LR+  G     FdG v+sD+l +m++i+dr+g +eav ++L+AG Di+L++++++++  +++l++a+++Gel+++++
  gi|121636150|ref|YP_976373.1| 291 -NLLRTGTGygappFDGPVFSDDLsGMAAISDRFGVSEAVLRTLQAGADIALWVTTKEVPavLDRLEQALRAGELPMSAV 369
                                    .***********************99*******************************99899****************** PP

                                    HHHHHHHHH CS
                  Glyco_hydro_3 310 desvrrvlr 318
                                    d+sv rv++
  gi|121636150|ref|YP_976373.1| 370 DRSVVRVAT 378
                                    *******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2857.29
//
Query:       gi|121636151|ref|YP_976374.1|  [L=204]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-17   61.6   0.0    9.7e-17   60.5   0.0    1.6  1  TetR_N       Bacterial regulatory proteins, tetR family
    2.6e-06   27.7   0.1    4.6e-06   26.9   0.1    1.5  1  TetR_C_24    Tetracyclin repressor-like, C-terminal domain
    0.00025   21.8   1.1     0.0004   21.1   0.4    1.8  2  TetR_C_15    Tetracyclin repressor-like, C-terminal domain
      0.002   18.3   0.0     0.0045   17.1   0.0    1.6  2  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
     0.0055   16.9   0.5     0.0097   16.1   0.5    1.5  1  TetR_C_6     BetI-type transcriptional repressor, C-terminal
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.063   13.3   0.1    1.4  1  TetR_C_32    Tetracyclin repressor-like, C-terminal domain
      0.072   13.8   1.1       0.12   13.2   0.4    1.7  2  TetR_C_33    Tetracyclin repressor-like, C-terminal domain
       0.13   11.2   0.0       0.16   11.0   0.0    1.1  1  DUF4837      Domain of unknown function (DUF4837)


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   4.3e-20   9.7e-17       2      47 .]      18      63 ..      17      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.3e-20
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   ldaA+++f+ +Gy++t++++IA++A++sk+ lY y++sKe+L+ a+
  gi|121636151|ref|YP_976374.1| 18 LDAAVQMFSVNGYHETSMDAIAAEAQISKPMLYLYYGSKEDLFGAC 63
                                   8******************************************885 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1     2e-09   4.6e-06       2      89 ..      83     168 ..      82     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2e-09
                                    SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHH CS
                      TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalail 81 
                                    +sp++ Lr+ + +++++i  +r+++ v++++    s++ + ++r+ r+++ +l+++l+++G + g ++d++ +++a a++
  gi|121636151|ref|YP_976374.1|  83 QSPKDLLRNTIVSFLRYIDANRASWIVMYTQ-ATSSQAFAHTVREGREQIVQLVAELVRAGTR-GPLTDAEIEMMAVALV 160
                                    78999**********************9988.6678888999******************986.667899********** PP

                                    HHHHCHHH CS
                      TetR_C_24  82 gmlnwvyr 89 
                                    g+   v++
  gi|121636151|ref|YP_976374.1| 161 GAGEAVAT 168
                                    *9988875 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.5   7.8e+03       8      17 ..      16      25 ..       9      32 .. 0.62
   2 !   21.1   0.4   1.8e-07    0.0004       2      90 ..      85     175 ..      84     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.5
                      TetR_C_15  8 alvdallaah 17
                                   +++da+++++
  gi|121636151|ref|YP_976374.1| 16 QMLDAAVQMF 25
                                   3444444444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.8e-07
                      TetR_C_15   2 Leealdalvdallaahrenpalrrvlleeapslgel.elvealeqriaealaalLa..rrrpelppedlelaafvaveav 78 
                                    ++++l+  +  +l++  +n a   v++ +a+s++++ + v++ +++i++++a+l++  +r p ++ +++e+ a  +v a 
  gi|121636151|ref|YP_976374.1|  85 PKDLLRNTIVSFLRYIDANRASWIVMYTQATSSQAFaHTVREGREQIVQLVAELVRagTRGPLTD-AEIEMMAVALVGAG 163
                                    56889999999*******************************************98434777777.************** PP

                      TetR_C_15  79 eallhlaleedp 90 
                                    ea+  ++   d 
  gi|121636151|ref|YP_976374.1| 164 EAVATRLGIGDT 175
                                    *99877665555 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06    0.0045      15      71 ..      21      79 ..       6      91 .. 0.85
   2 ?   -2.3   0.0       2.1   4.6e+03      67      86 ..     112     131 ..      94     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH..H-HHHHHHHHHHHHHHHHTTHHHH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWk..kkkeFieyvnelaeefleeeraev 71
                                   a+++   n y+++++d ia+e ++s+  ly +   k+  F + +n+  ++f+++ r+ +
  gi|121636151|ref|YP_976374.1| 21 AVQMFSVNGYHETSMDAIAAEAQISKPMLYLYYgsKEDLFGACLNREMSRFIDALRSSI 79
                                   67888999**********************9987455559999********99988776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                                    THHHHHHHHHHHHHSSS--H CS
                    HTH_Tnp_1_2  67 eraevykaLlrkilkgrssv 86 
                                     +a+  +a  +++++gr ++
  gi|121636151|ref|YP_976374.1| 112 TQATSSQAFAHTVREGREQI 131
                                    33344444555555554433 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   4.3e-06    0.0097      23      91 ..     104     171 ..      85     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHHHHHHHHHH CS
                       TetR_C_6  23 lavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaAerlaAlidGLwlraa 91 
                                     a w+ ++ +a+++ ++a   re  +++ +++++l++++ + g ++da+ e +A +l+   +  ++r+ 
  gi|121636151|ref|YP_976374.1| 104 RASWIVMYTQATSSQAFAHTVREGREQIVQLVAELVRAGTR-GPLTDAEIEMMAVALVGAGEAVATRLG 171
                                    478**********************************9999.777777777777777654444444444 PP

>> TetR_C_32  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.8e-05     0.063       1      81 [.      85     161 ..      85     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                      TetR_C_32   1 arerLrafirrllarllseeesewwakfmaREqlePtealeriyqeeirPlhealerivaellgedaedeevrlrtlsiv 80 
                                    ++++Lr  i ++l+++ ++ + +w+++     q+  ++a+   ++e  +   ++++++v++ +  + +d+e+ + ++++v
  gi|121636151|ref|YP_976374.1|  85 PKDLLRNTIVSFLRYIDAN-RASWIVMYT---QATSSQAFAHTVREGREQIVQLVAELVRAGTRGPLTDAEIEMMAVALV 160
                                    6899*********976666.677766555...9*********************************************** PP

                      TetR_C_32  81 G 81 
                                    G
  gi|121636151|ref|YP_976374.1| 161 G 161
                                    9 PP

>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.9   1.5e+04      22      33 ..      24      33 ..      15      45 .. 0.57
   2 ?   13.2   0.4   5.2e-05      0.12       6     102 ..      94     186 ..      89     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.9
                                   CCSS--TT-S-H CS
                      TetR_C_33 22 lfgspvpgyaap 33
                                   +f   v gy+++
  gi|121636151|ref|YP_976374.1| 24 MF--SVNGYHET 33
                                   44..55566665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHH-HHHHHHCCSS--TT-S-.HGHHCCCCHHHHHHHHHHHGGG---TH--CCHHHHHHHHHHHHHHHHHHHHC CS
                      TetR_C_33   6 rayrrfAlahpaeYallfgspvpgyaa.pdelaaagarvlalllaalaalvaaglppadavaaaralwaalhGlvsLelf 84 
                                      ++r+  a++a + +++ +++   +a ++ +++  +++++l++++++a       ++ + a + ++ +al G +   ++
  gi|121636151|ref|YP_976374.1|  94 VSFLRYIDANRASWIVMY-TQATSSQAfAHTVREGREQIVQLVAELVRAG----TRGPLTDAEIEMMAVALVG-AGEAVA 167
                                    578999************.3333334422356666666666666666554....4344233445555556666.566777 PP

                                    TTTTS.SS-HHHHHHHHHH CS
                      TetR_C_33  85 ghfgl.padpdalferlvd 102
                                     ++g+ ++d+d+ +e ++ 
  gi|121636151|ref|YP_976374.1| 168 TRLGIgDTDVDEAAEMMIN 186
                                    7888888899998888875 PP

>> DUF4837  Domain of unknown function (DUF4837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     7e-05      0.16      51     119 ..      66     137 ..      26     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                        DUF4837  51 ekfsglvkkvRnilvvkidse...eeketsvkvekdvyAkpQivveikapsaeelaelleknkdsiinlfek 119
                                    +++s ++  +R+ ++ + +++   +++ +s+    d ++ + iv++ +a+s +++a+++ + +++i++l+ +
  gi|121636151|ref|YP_976374.1|  66 REMSRFIDALRSSINFDQSPKdllRNTIVSFLRYIDANRASWIVMYTQATSSQAFAHTVREGREQIVQLVAE 137
                                    56677777777777777655433356777888888********************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1440.80
//
Query:       gi|121636152|ref|YP_976375.1|  [L=77]
Description: hypothetical protein BCG_0277 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.7   0.0       0.13   12.2   0.0    1.3  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.2e-06      0.13       3      30 ..       3      30 ..       1      35 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-06
                          RHH_5  3 RvnvtLPeelleeLeewAdeegRsvSnl 30
                                   R++v LP+el+ + ++ A e + +++ +
  gi|121636152|ref|YP_976375.1|  3 RTQVQLPDELYRDAKRVAHEHEMTLAEV 30
                                   99****************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 560.88
//
Query:       gi|121636153|ref|YP_976376.1|  [L=145]
Description: hypothetical protein BCG_0278 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-09   37.2   0.0    3.9e-09   37.1   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   2.2e-13   3.9e-09       3     114 ..       4     126 ..       2     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.2e-13
                                    E-HHHHHHHH.TTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEEB CS
                            PIN   3 lDTsvliall.rgeekaeaarklleel...eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkilpi 73 
                                    +DT++l+++  r+ ++++aa++ l e     ++++++lvl El+  l++     r+++  +aae+  ++ + ++  +l+ 
  gi|121636153|ref|YP_976376.1|   4 IDTNILLYAQnRDCPEHDAAAAFLVECsgrADVAVCELVLMELYQLLRNptvvtRPLEGPEAAEVCQTFRRNRRWALLE- 82 
                                    8*****************************************************8888888888888888888888888. PP

                                    CHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESST CS
                            PIN  74 daeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDe 114
                                    +a++  e++ +a+  +   ++++Da +a t ++hg + +at++ 
  gi|121636153|ref|YP_976376.1|  83 NAPVMNEVWVLAATPRiarRRLFDARLALTLRHHGVDEFATRNI 126
                                    5555555555554444444**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1057.54
//
Query:       gi|121636154|ref|YP_976377.1|  [L=280]
Description: hypothetical protein BCG_0279c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-28   97.0   0.0    3.9e-26   91.0   0.0    2.3  2  MaoC_dehydratas  MaoC like domain
    1.5e-06   28.4   0.3       0.04   14.1   0.1    2.2  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
     0.0054   16.3   0.0     0.0076   15.8   0.0    1.1  1  Cas9_a           Cas9 alpha-helical lobe domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0077        46       9      31 ..      31      52 ..      23      53 .. 0.80
   2 !   91.0   0.0   6.5e-30   3.9e-26       7     103 ..     162     256 ..     157     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0077
                                   EEEEEEEEEEEHHHHHHHHHHHT CS
                MaoC_dehydratas  9 kvetekeitvteadialyalvsg 31
                                   +v   +e+++ +a +a ya+v+g
  gi|121636154|ref|YP_976377.1| 31 TVT-VEELPIDPANVAAYAAVTG 52
                                   444.4899999**********98 PP

  == domain 2  score: 91.0 bits;  conditional E-value: 6.5e-30
                                    TSEEEEEEEEEEE...HHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEE CS
                MaoC_dehydratas   7 gekvetekeitvt...eadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikv 83 
                                    ++k++  ++  v    +a+i++ya+v gD+npiH++p +Ak++gf+++IahGm+t+a+v +++e++++d        ++v
  gi|121636154|ref|YP_976377.1| 162 QKKPKLPPPAAVLritPAKIRRYAAVGGDHNPIHTNPIAAKLFGFPTVIAHGMFTAAAVLANIEARFPD-----AVRYSV 236
                                    5555555555443444*****************************************************.....88**** PP

                                    EE-S--BTTCEEEEEEEEEE CS
                MaoC_dehydratas  84 rFtkpVlpgdtlkvelevvg 103
                                    rF+kpVl + t   ++ + +
  gi|121636154|ref|YP_976377.1| 237 RFAKPVLLPATAGLYVAEGD 256
                                    **********9988876655 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   2.2e-05      0.13      46     112 ..      56     124 ..      34     139 .. 0.76
   2 !   14.1   0.1   6.6e-06      0.04      13      57 ..     175     219 ..     170     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                MaoC_dehydrat_N  46 sliaPptflivlatkapell.....ealgidlsrllhgeqefeyhepiraGDelttesriadvydkkgvGal 112
                                    + ++P t++++l +    ++     ++++    + +h+e+ ++  +pi + D + ++ r + +++    G l
  gi|121636154|ref|YP_976377.1|  56 GNQVPLTYPFALTFPS--VMslvtgFDFPFAAMGAIHTENHITQYRPIAVTDAVGVRVRAENLREHR-RGLL 124
                                    579***********66..34123345556669999***********************999999954.3444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.6e-06
                MaoC_dehydrat_N  13 evereavrefakavgetnpayldeeaaraagyrsliaPptflivl 57 
                                     ++  ++r++a   g+ np+++++ aa+  g+ ++ia  +f+ ++
  gi|121636154|ref|YP_976377.1| 175 RITPAKIRRYAAVGGDHNPIHTNPIAAKLFGFPTVIAHGMFTAAA 219
                                    58999********************************99996643 PP

>> Cas9_a  Cas9 alpha-helical lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06    0.0076      20      89 ..      89     156 ..      80     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                         Cas9_a  20 lkaslaFqryrivavlanLrirekgeerkLtveekqkvfdfLlslkskeeltWedvaekLgieRrelrGt 89 
                                     ++++   +yr +av + + +r+++  ++L  + +  ++d +++++  +++ W++v+  L+ +R++l+G 
  gi|121636154|ref|YP_976377.1|  89 IHTENHITQYRPIAVTDAVGVRVRA--ENLREHRRGLLVDLVTNVSVGNDVAWHQVTTFLHQQRTSLSGE 156
                                    566777889*********9999876..569999***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1903.21
//
Query:       gi|121636155|ref|YP_976378.1|  [L=454]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-51  173.7  10.0    1.1e-49  169.1   6.1    2.9  3  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    2.1e-44  151.3   5.0    4.5e-44  150.3   3.7    1.9  2  adh_short     short chain dehydrogenase
    4.9e-13   49.4   2.6    4.9e-13   49.4   2.6    1.7  2  KR            KR domain
    0.00047   19.7   0.2    0.00082   18.9   0.2    1.5  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.027   14.3   0.4       0.08   12.8   0.3    1.9  2  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.045   1.6e+02     142     166 ..     135     158 ..      99     177 .. 0.73
   2 ?    3.2   0.0     0.015        53     209     229 ..     176     196 ..     168     198 .. 0.89
   3 !  169.1   6.1   3.1e-53   1.1e-49       1     231 [.     220     448 ..     220     448 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.045
                                    HHHHHHHHHHHHHHHHHHGGGTEEE CS
                   adh_short_C2 142 gaaKaalealtrylAvelgpkgiRv 166
                                     +a  ale++tr+l +el + g + 
  gi|121636155|ref|YP_976378.1| 135 RIAQRALEGFTRSLGKELRR-GATT 158
                                    567889***********987.5555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                                    HHHHHHCSGGGTT--SEEEEE CS
                   adh_short_C2 209 eaalfLasdeasyitGqtlvv 229
                                    +++ fL+s +++y+ Gq++ v
  gi|121636155|ref|YP_976378.1| 176 STMRFLLSAKSAYVDGQVFSV 196
                                    6889**************987 PP

  == domain 3  score: 169.1 bits;  conditional E-value: 3.1e-53
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHH.SSEEEEEE---- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekf.gklDilvnnagi 79 
                                    Gaa+gIG+ iA+ +a+ Ga+vv+ d++ +a ++++e a+++g ++l +DVt +++v+++ e++++++ gk Dilvnnagi
  gi|121636155|ref|YP_976378.1| 220 GAARGIGATIAEVFARDGAHVVAIDVESAA-ENLAETASKVGGTALWLDVTADDAVDKISEHLRDHHgGKADILVNNAGI 298
                                    9****************************8.89999*******************************99*********** PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH..HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalp..lmkeggsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                    +++  + +++++++ +d +l+vnl + ++l++ ++    + egg+++ lss+++  +  +++ y+++Ka+++++t++lA 
  gi|121636155|ref|YP_976378.1| 299 TRD--KLLANMDDARWDAVLAVNLLAPLRLTEGLVGngSIGEGGRVIGLSSIAGIAGNRGQTNYATTKAGMIGITQALAP 376
                                    ***..***************************99998999**************************************** PP

                                    HHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEEST CS
                   adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDg 231
                                     l++kgi++Nav+pg+i+T+++++i+   + +e  ++   l + g+p +vaea++++as++++++tG+++ v g
  gi|121636155|ref|YP_976378.1| 377 GLAAKGITINAVAPGFIETQMTAAIP--LATREVGRRLNSLLQGGQPVDVAEAIAYFASPASNAVTGNVIRVCG 448
                                    *************************9..5566666677777777*************************99865 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.19   6.7e+02     155     169 ..     140     154 ..     118     163 .. 0.90
   2 !  150.3   3.7   1.2e-47   4.5e-44       1     190 [.     214     401 ..     214     405 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHGG CS
                      adh_short 155 avagltrslakelap 169
                                    a++g+trsl kel++
  gi|121636155|ref|YP_976378.1| 140 ALEGFTRSLGKELRR 154
                                    899*********986 PP

  == domain 2  score: 150.3 bits;  conditional E-value: 1.2e-47
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESC..HHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHH.SS CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrs..eekleevakelkeegakalaiqvDvtdreevealvekavkkl.gk 77 
                                    kv++vtGa++GIG  ia+ +a++Ga+vv++d +  +e+l+e+a++++      +a+ +Dvt  ++v+++ e+ ++++ gk
  gi|121636155|ref|YP_976378.1| 214 KVAIVTGAARGIGATIAEVFARDGAHVVAIDVEsaAENLAETASKVGG-----TALWLDVTADDAVDKISEHLRDHHgGK 288
                                    89***************************6655005555555555554.....68899*******************99* PP

                                    ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
                      adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                                     d+LvnNAGit+++  +++++++w++v++vNl +++ lt+ ++ +   +++Gr++  sS+ag  ++ g++ Y+++Ka+++
  gi|121636155|ref|YP_976378.1| 289 ADILVNNAGITRDKLLANMDDARWDAVLAVNLLAPLRLTEGLVGNGSIGEGGRVIGLSSIAGIAGNRGQTNYATTKAGMI 368
                                    *********************************************999******************************** PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakel 190
                                    g+t++la  la +gi++navaPG+++T+m++++
  gi|121636155|ref|YP_976378.1| 369 GITQALAPGLAAKGITINAVAPGFIETQMTAAI 401
                                    *****************************9875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   6.7e+03       9      38 ..     141     170 ..     140     180 .. 0.77
   2 !   49.4   2.6   1.4e-16   4.9e-13       4     154 ..     217     365 ..     214     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                                    TSHHHHHHHHHHHHHHS-EEEEE-SS..-- CS
                             KR   9 lGgLGlelarwlaekgarhlvllsRsaaad 38 
                                    l g+ ++l + l + + + lv+ls +a++ 
  gi|121636155|ref|YP_976378.1| 141 LEGFTRSLGKELRRGATTALVYLSPDAKPA 170
                                    567888888899888899999999996554 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 1.4e-16
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS.S-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee.ppi 82 
                                    ++tG++ g+G ++a+  a++ga+ +++   s     ++ +++ae ++  +  +++ +Dv+  dav ++ e++++++ ++ 
  gi|121636155|ref|YP_976378.1| 217 IVTGAARGIGATIAEVFARDGAHVVAIDVES-----AA-ENLAETAS-KVGGTALWLDVTADDAVDKISEHLRDHHgGKA 289
                                    8*********************988887766.....22.33443333.455578889****************9998999 PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNa 154
                                       ++ Ag++rdkll++m+++++++vla  + +   L e l       +   ++ +SSiag+ g++gq+nYa++ a
  gi|121636155|ref|YP_976378.1| 290 DILVNNAGITRDKLLANMDDARWDAVLAVNLLAPLRLTEGLVGngsiGEGGRVIGLSSIAGIAGNRGQTNYATTKA 365
                                    999***********************************98877677778899********************9876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   2.3e-07   0.00082       2      61 ..     217     279 ..     216     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-07
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfk 61 
                                    +VtGa+  iG+ +++ +++ g +v+++d +s a+n a+ + +   +   ld+t ++a++++ +
  gi|121636155|ref|YP_976378.1| 217 IVTGAARGIGATIAEVFARDGAHVVAIDVESAAENLAETASKvggTALWLDVTADDAVDKISE 279
                                    8**********************************99999999***************99865 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   4.8e+03      28      54 ..     130     156 ..     118     171 .. 0.55
   2 ?   12.8   0.3   2.2e-05      0.08      10      41 ..     225     256 ..     214     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                    E-S-HHHHHHHHHHHHHHHHCCTTTTS CS
                        3HCDH_N  28 vdiseealekalekieksleklvekgk 54 
                                      ++e+++++ale  ++sl k  ++g+
  gi|121636155|ref|YP_976378.1| 130 ASTNERIAQRALEGFTRSLGKELRRGA 156
                                    334555555555555555555555554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
                                    CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                        3HCDH_N  10 mGagiaavfasagleVvlvdiseealekalek 41 
                                    +Ga ia+vfa+ g +Vv +d++++a + a+ +
  gi|121636155|ref|YP_976378.1| 225 IGATIAEVFARDGAHVVAIDVESAAENLAETA 256
                                    8********************87765555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3127.41
//
Query:       gi|121636156|ref|YP_976379.1|  [L=440]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-43  148.2   0.0    4.1e-43  147.6   0.0    1.3  1  Thiolase_N     Thiolase, N-terminal domain
      6e-29  100.2   0.2    1.2e-28   99.2   0.2    1.5  1  Thiolase_C     Thiolase, C-terminal domain
     0.0042   16.7   0.1     0.0094   15.6   0.1    1.5  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   6.9e-47   4.1e-43       1     260 []      15     283 ..      15     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 6.9e-47
                                    EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEE CS
                     Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavt 80 
                                    v++ +++r+p+ ++ g+++d+s +++ ++al++l+++ g++ e +d v+ G vl+   + n++r+ +l ++++  +pa  
  gi|121636156|ref|YP_976379.1|  15 VAVLGGNRIPFARSDGAYADASNQDMFTAALSGLVDRFGLAGERLDMVVGGAVLKHSRDFNLMRECVLGSELSPYTPAFD 94 
                                    78999*************************************************************************** PP

                                    EEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT........TGGSSSSEEEEEHHHHH......HT CS
                     Thiolase_N  81 vnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr........sglklgdekakdllipd......gl 146
                                    ++++c+ gl+a ++aa+ iaag+++v+ agGv + s+ p+    d+r        s+ ++++ k++++l  +      + 
  gi|121636156|ref|YP_976379.1|  95 LQQACGTGLQAAIAAADGIAAGRYEVAAAGGVDTTSDPPIGLGDDLRrtllklrrSRSNVQRLKLVGTLPASlgveipAN 174
                                    **********************************************99***99997777777777777765563323334 PP

                                    EETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHH CS
                     Thiolase_N 147 adafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekL 226
                                     +  ++  mG +a  +ak+++i R +qde A++sh++ a+a + g F+d + P+            +d+ +r+++++ekL
  gi|121636156|ref|YP_976379.1| 175 SEPRTGLSMGEHAAVTAKQMGIKRVDQDELAAASHRNMADAYDRGFFDDLVSPFLGL--------YRDDNLRPNSSVEKL 246
                                    5777899**************************************999989777654........57899********** PP

                                    HTS-BSSSTT.S..S-BTTSB--BEEEEEEEEEEEHH CS
                     Thiolase_N 227 aklkpaFkke.G..tvtAgnasqisDGaaavllmses 260
                                    a+l+p+F  + G  t+tAgn+ +++DGa+  ll+se+
  gi|121636156|ref|YP_976379.1| 247 ATLRPVFGVKaGdaTMTAGNSTPLTDGASVALLASEQ 283
                                    *******87777669*******************985 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.2     2e-32   1.2e-28       2     122 ..     291     439 ..     290     440 .] 0.90

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 2e-32
                                    --SEEEEEEEEEE--G....GGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G........... CS
                     Thiolase_C   2 kplakirsyaevgvdp....eilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl........... 66 
                                     pla++++  +++vd     + l ++P+ya++++l ++gl+++d d++Ei+EAFa+++La + a ++++           
  gi|121636156|ref|YP_976379.1| 291 APLAYLVDAETAAVDYvngnDGLLMAPTYAVPRLLARNGLSLQDFDFYEIHEAFASVVLAHLAAWESEEyckrrlgldaa 370
                                    6899999999999985333478*********************************************99*********** PP

                                    ......GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCTTSE.......EEEEEEETTTEEEEEEEE CS
                     Thiolase_C  67 ......ekvNvnGGaialGHPlGasGaRivvtllselkkeggkl.......gvaalCigggqgvalvie 122
                                          +k+NvnG ++a GHP+ a+G Ri+++ +++l ++++ +       g++++C++ggqgva+++e
  gi|121636156|ref|YP_976379.1| 371 lgsidrSKLNVNGSSLAAGHPFAATGGRILAQTAKQLAEKKAAKkgggplrGLISICAAGGQGVAAILE 439
                                    *************************************988754323334448***************98 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.6e-06    0.0094     167     208 ..      91     132 ..      82     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                                    SEEEEESGGGHH.HHHHHHHHHHHHTTS-SEEEEEEEE---SH CS
                  ketoacyl-synt 167 psvtvdtACsSs.lvavhaavqslrsgeadvalaGGvellltp 208
                                    p++ ++ AC ++  +a++aa + + +g+ +va aGGv+++  p
  gi|121636156|ref|YP_976379.1|  91 PAFDLQQACGTGlQAAIAAA-DGIAAGRYEVAAAGGVDTTSDP 132
                                    6777788*****66666666.*****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3012.74
//
Query:       gi|121636157|ref|YP_976380.1|  [L=611]
Description: acyl-CoA dehydrogenase fadE5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-30  103.8   1.1    1.8e-29  102.4   1.1    1.8  1  Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
    7.1e-17   61.4   0.0    1.6e-16   60.3   0.0    1.7  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.5e-14   54.5   1.3    1.4e-13   51.3   1.3    2.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    6.1e-09   35.8   0.0    1.4e-08   34.6   0.0    1.7  1  AcylCoA_DH_N   Acyl-CoA dehydrogenase N terminal
     0.0002   22.0   0.0     0.0008   20.1   0.0    2.0  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.087   13.1   0.0    2.6  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   1.1   5.9e-33   1.8e-29       3     124 .]     475     607 ..     473     607 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 5.9e-33
                  Acyl-CoA_dh_C   3 aeieatvara....alkelaaaleaalealqeateallakaakgdp.....eealaaavpyLelfGdvvigwlllrqala 73 
                                    ++i+a+v++     +lk+++a l++al+++q +++al ++++++++     +++++++v++L+ +Gd++igwll rqa++
  gi|121636157|ref|YP_976380.1| 475 GQIQAFVDSGagngRLKTERALLAKALTNVQGMAAALTGYLMAAQQdvtslYKVGLGSVRFLMSVGDLIIGWLLQRQAAV 554
                                    69******4334457***************************995566888***************************** PP

                  Acyl-CoA_dh_C  74 Aqakla..agekdaafyegKlatarfFaervLPraaalaaaieagddslmeld 124
                                    A a+l+  a  ++++fyegK+a+a fFa++ LP +++ +++ie+ d+++meld
  gi|121636157|ref|YP_976380.1| 555 AVAALDagATGDERSFYEGKVAVASFFAKNFLPLLTSTREVIETLDNDIMELD 607
                                    ******776677888***********************************996 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   5.4e-20   1.6e-16       2      95 ..     162     272 ..     161     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 5.4e-20
                                    EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEE.....EEEEE..TS-------EEEEEEE......G CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatla.....lvlar..tekpdrarglslflvp....rda 70 
                                    + lTEp+aGsdv + +t+a+++++g++ ++G K++it++   +l+     lvlar   ++p +++glsl +vp    +  
  gi|121636157|ref|YP_976380.1| 162 MVLTEPDAGSDVGAARTKAVQQADGSWHIDGVKRFITSGDSGDLFenifhLVLARpeGAGP-GTKGLSLYFVPkflfD-- 238
                                    789**************************************777777777*****644444.6**********66551.. PP

                                    G.........GEEE-----BSS-TTS-EEEEEEE CS
                  Acyl-CoA_dh_M  71 p.........gvsvrrieeklGlrglptgelvfe 95 
                                              gv v+ +e+k+Gl+  +t+el f 
  gi|121636157|ref|YP_976380.1| 239 VetgepgernGVFVTNVEHKMGLKVSATCELAFG 272
                                    1445669999*********************996 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.3   4.8e-17   1.4e-13       2     143 ..     288     455 ..     287     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 4.8e-17
                                    BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTS............B-CC-BGGGSHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrr............kafgkplidhqlvreklaemaaeleaarl 69 
                                    +G++++ e +++ R++v+  a++++   + +al+ya++r            +a   ++  h+ vr+ l + +a +e++r+
  gi|121636157|ref|YP_976380.1| 288 NGIAQMFEVIEQARMMVGTKAIATLSTGYLNALQYAKSRvqgadltqmtdkTAPRVTITHHPDVRRSLMTQKAYAEGLRA 367
                                    6999999********************************777666665553444467899******************** PP

                                    HHHHHHH--------..............HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS CS
                  Acyl-CoA_dh_1  70 lvyraaealdagkpd..............raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige 135
                                    l + +a  +da+  +                   ++K ++se a    ++ +q lGg G+l++yp+e+++rda++++++e
  gi|121636157|ref|YP_976380.1| 368 LYLYTATFQDAAVAEvvhgvdaklavrvnDLMLPVVKGVGSEQAYAKLTESLQTLGGSGFLQDYPIEQYIRDAKIDSLYE 447
                                    *******99999999999******99998888999********************************************* PP

                                    S-HHHHHH CS
                  Acyl-CoA_dh_1 136 Gtseiqrn 143
                                    Gt+ iq +
  gi|121636157|ref|YP_976380.1| 448 GTTAIQAQ 455
                                    *****975 PP

>> AcylCoA_DH_N  Acyl-CoA dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.6e-12   1.4e-08       1      32 []       3      34 ..       3      34 .. 0.98

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.6e-12
                   AcylCoA_DH_N  1 qYkAPlRDmrFvLyEvLdaealaalPgfadad 32
                                   +Y++++RD  F+L+EvL++++ ++++ f+d+d
  gi|121636157|ref|YP_976380.1|  3 HYRSNVRDQVFNLFEVLGVDKALGHGEFSDVD 34
                                   8*****************************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.7e-07    0.0008      31     103 ..      75     148 ..      36     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.7e-07
                                    SGHHHH...HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH.HHHHHHHTTHHHHHHHS-HHHHH CS
                  Acyl-CoA_dh_N  31 efprel...wkklaelGllgitvpeeygGagldyleaaivaeelaradaglal.llgvhsslvapailrfGteeqkr 103
                                      p+++   ++++ e+G+  + + e+ gG+ +    a+++a      +a  a+ +++ + +  a+++++ Gteeqk+
  gi|121636157|ref|YP_976380.1|  75 MLPESFkksVNAMLEAGWDKVGIDEALGGMPMP--KAVVWALHEHILGANPAVwMYAGG-AGFAQILYHLGTEEQKK 148
                                    35544345699******************9974..333333333333443345255554.45569***********7 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.76   2.3e+03      43      92 ..     289     334 ..     285     345 .. 0.55
   2 ?   13.1   0.0   2.9e-05     0.087      69     132 ..     387     449 ..     316     451 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  43 alaeaaarldAAralleraaaraealaaagkevtvedraearraaalave 92 
                                     +a++   +++Ar+++  +a +          +++ + a++r++ a +++
  gi|121636157|ref|YP_976380.1| 289 GIAQMFEVIEQARMMVGTKAIA----TLSTGYLNALQYAKSRVQGADLTQ 334
                                    5677777777777777666655....233333344455555554444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.9e-05
                                    HHTT----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG CS
                  Acyl-CoA_dh_2  69 aaagkevtvedraearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaal 132
                                    ++a+ +v v+d +   + + + +e a a   +  ++ Ggs+ ++++p++ + RDa++ + ++++
  gi|121636157|ref|YP_976380.1| 387 VDAKLAVRVND-LMLPVVKGVGSEQAYAKLTESLQTLGGSGFLQDYPIEQYIRDAKIDSLYEGT 449
                                    44444443333.3334557777888888899999*********************998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3992.20
//
Query:       gi|121636158|ref|YP_976381.1|  [L=162]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-25   88.7   0.2    4.5e-25   88.5   0.2    1.0  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.15   10.4   0.0       0.18   10.1   0.0    1.1  1  DUF4815        Domain of unknown function (DUF4815)


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.2     5e-29   4.5e-25       2     153 ..      17     159 ..      16     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 5e-29
                                    TTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SC CS
                  Flavin_Reduct   2 rrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgpr 81 
                                    ++++++v+ + + + ++ + g+ +s+f+++sl+Pplv+f++++ s t+ +l     + i++l e + a+++ +++    +
  gi|121636158|ref|YP_976381.1|  17 GHFPTGVVAIAA-EVDGVRQGLAASTFVPVSLEPPLVSFCVQNTSTTWPKLTGVPMLGISVLGEAHDAAVRTLAA----K 91 
                                    689*********.5577777*******************************************************....6 PP

                                    CCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEEE CS
                  Flavin_Reduct  82 tddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrryag 153
                                    t d+  fagl++ +++ ga +++g  ++le  + + v++gdh++++++V +vkv+ +    p +++r+ +++
  gi|121636158|ref|YP_976381.1|  92 TGDR--FAGLETVSNDAGAVFIKGTSVWLESAIEQLVPAGDHTIVVLRVNQVKVDPNVA--PIVFHRSVLRR 159
                                    8899..**************************************************965..99*99987765 PP

>> DUF4815  Domain of unknown function (DUF4815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     2e-05      0.18      41      85 ..      84     127 ..      75     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2e-05
                        DUF4815  41 riadvvfkdGdilsGaelvvdkdkgavtveagsvYlkgkvrdvee 85 
                                    ++  + +k Gd+ +G e+v  +d+gav+++ +sv+l+ ++ ++  
  gi|121636158|ref|YP_976381.1|  84 AVRTLAAKTGDRFAGLETVS-NDAGAVFIKGTSVWLESAIEQLVP 127
                                    56677899*********988.9****************9988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1148.24
//
Query:       gi|121636159|ref|YP_976382.1|  [L=436]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   11.9  49.6        1.9    7.4  20.4    2.9  2  MFS_1     Major Facilitator Superfamily
        3.6    7.5   5.2        7.1    6.6   0.3    3.7  2  PsbN      Photosystem II reaction centre N protein (psbN)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  23.5   0.00041       3.7       8     228 ..      31     253 ..      26     263 .. 0.69
   2 ?    7.4  20.4   0.00021       1.9      34     172 ..     269     413 ..     242     434 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00041
                          MFS_1   8 salarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fa... 82 
                                    +al+ ++++++lp ++  +l +    + l++ ++++g a++++++ + +  + rr  ++++   l +l+++ +l  +   
  gi|121636159|ref|YP_976382.1|  31 AALQLGNVSIVLP-FVVAELDAELWIAALIFPAFTAGGAIGNVVAPPAVAAVPRRHrLFIIVSCLAVLAGVNALcATigk 109
                                    5778888889999.999999988888999999999999999999999999998777776666666666644444222457 PP

                          MFS_1  83 sslw..lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.......Wrav 153
                                     s+   ll+v   l G+ ++++f a a l+a++ +++ r+r +    + +++Ga+l++++++ l+            ++ 
  gi|121636159|ref|YP_976382.1| 110 GSVAgiLLVVNVTLIGVVSAISFVAFADLVAAMPSGTARARIL---LTEVGVGAALTAVVAATLSFVPDqhplsrnIHL- 185
                                    4444433555556***********************9999977...777788888888888888844447778554222. PP

                          MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..illialllfffgfsgllt 228
                                     + +a+++++++    +    +++  +r+  ++      ++ +  +w+a++++   w   +l++ +lf+ ++ g ++
  gi|121636159|ref|YP_976382.1| 186 LWTAAVAMAISAA---ICRALPHRIVPRVHAAPG----LHKLVYVGWTAIRTNG--WyrRYLLVQVLFGSVVLGSSF 253
                                    5555555555544...333334444444444444....3344444699999999..999677777766666665544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00021
                          MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllf..a...sslwlllvlrvlqGlgagalfpaga 107
                                    +  ++ ++ +g + ++ ++ r+ +rfG   +++ ++l+++++ +l ++f  a   +++ ++ ++ +l +++  ++f+ag+
  gi|121636159|ref|YP_976382.1| 269 VVAVVLFVCVGLLGGIALWNRVRERFGLVGLFVGSALVSIAAaVLSIAFdlAgawPNVVAIGLVIALVSIANQSVFTAGQ 348
                                    444666677789999***************999999999999555555655444566556666666999*********** PP

                          MFS_1 108 aliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                     +ia+ + +  r++ i++ ++ +++G +   l+ gl+a+     ++ +i+ ++ l a+  +  + 
  gi|121636159|ref|YP_976382.1| 349 LWIARDAEPGLRTSLISFGQLVINAGLVGMGLALGLIAQDHDAVWPVMIVLLLNLTAAYSATRFA 413
                                    **************************987778888888999999999999999999866333333 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.7     0.095   8.5e+02       9      26 ..     299     316 ..     296     318 .. 0.60
   2 ?    6.6   0.3   0.00079       7.1       6      26 ..     326     346 ..     324     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.095
                           PsbN   9 isiaavlvaiTgfsiYta 26 
                                    ++++++lv+i++  + +a
  gi|121636159|ref|YP_976382.1| 299 LFVGSALVSIAAAVLSIA 316
                                    566666777666655555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00079
                           PsbN   6 vlsisiaavlvaiTgfsiYta 26 
                                    v++i ++++lv+i+  s++ta
  gi|121636159|ref|YP_976382.1| 326 VVAIGLVIALVSIANQSVFTA 346
                                    799*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3142.78
//
Query:       gi|121636160|ref|YP_976383.1|  [L=248]
Description: fumarate reductase iron-sulfur subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-27   93.8   0.1      1e-26   93.0   0.1    1.4  1  Fer2_3         2Fe-2S iron-sulfur cluster binding domain
    1.7e-15   57.2   9.3    2.5e-15   56.6   6.3    2.3  2  Fer4_8         4Fe-4S dicluster domain
    2.2e-06   27.5   0.9    2.2e-06   27.5   0.9    2.1  2  Fer2           2Fe-2S iron-sulfur cluster binding domain
    0.00024   21.6   7.0    0.00024   21.6   7.0    2.2  2  Fer4_17        4Fe-4S dicluster domain
    0.00048   20.3   6.5       0.19   11.9   0.3    2.6  3  Fer4_18        4Fe-4S dicluster domain
     0.0036   17.9   6.2     0.0036   17.9   6.2    2.8  4  Fer4_7         4Fe-4S dicluster domain
     0.0051   16.9   9.7       0.18   12.0   0.2    3.3  3  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.049   14.6   8.0       0.77   10.7   0.2    3.0  3  Fer4_16        4Fe-4S double cluster binding domain
       0.06   13.5   0.1       0.13   12.4   0.1    1.5  1  Thioredoxin_7  Thioredoxin-like
        0.1   12.7   0.2        0.1   12.7   0.2    1.9  2  Fer2_4         2Fe-2S iron-sulfur cluster binding domain
        0.2   11.8  16.0       0.77    9.9  11.1    3.0  3  Fer4_10        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.1   6.4e-30     1e-26       3     105 ..       8     105 ..       6     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 6.4e-30
                         Fer2_3   3 kvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakq 82 
                                    +v+R d+    +   + e++ve++e++ vld++l+++++++p la r++C++g CGsc+++inGkp+l+C +++++++++
  gi|121636160|ref|YP_976383.1|   8 RVWRGDE----SCGELREFTVEVNEGEVVLDVILRLQQTQTPDLAVRWNCKAGKCGSCSAEINGKPRLMCMTRMSTFDED 83 
                                    6777776....568899************************************************************988 PP

                         Fer2_3  83 kseieleplpkfpvirDLvvDid 105
                                    +  ++++p+++fpvirDLv+D++
  gi|121636160|ref|YP_976383.1|  84 E-IVTVTPMRTFPVIRDLVTDVS 105
                                    7.7******************86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.35   5.6e+02      53      58 ..      57      62 ..      28     105 .. 0.81
   2 !   56.6   6.3   1.6e-18   2.5e-15       1      65 []     140     216 ..     140     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.35
                         Fer4_8 53 tcgaCt 58
                                    cg+C+
  gi|121636160|ref|YP_976383.1| 57 KCGSCS 62
                                   344443 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 1.6e-18
                         Fer4_8   1 elekCieCgaCqsaCpvlrr...................tkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevC 61 
                                    e++kCieC++Cq+ C+v+r+                     +h+ld+r+++++ +qee++      l++C+++++CtevC
  gi|121636160|ref|YP_976383.1| 140 EFRKCIECFLCQNVCHVVRDheenkdafagprflmriaeLEMHPLDTRDRRSQ-AQEEHG------LGYCNITKCCTEVC 212
                                    589*****************999999999999999999666************.999999......************** PP

                         Fer4_8  62 pvgi 65 
                                    p++i
  gi|121636160|ref|YP_976383.1| 213 PENI 216
                                    **97 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.9   1.3e-09   2.2e-06       7      77 ..      21      77 ..      14      78 .. 0.86
   2 ?   -2.2   1.2       2.5     4e+03      56      56 ..     170     170 ..     148     212 .. 0.52

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.3e-09
                                   EEEEEEETTTHBHHHHHH....HTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2  7 evevevadgettlldaae....enggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                   e++vev++ge +l  +++    + ++++++++C++g+Cg+C +e++            g++      rl+C+t++
  gi|121636160|ref|YP_976383.1| 21 EFTVEVNEGEVVLDVILRlqqtQTPDLAVRWNCKAGKCGSCSAEIN------------GKP------RLMCMTRM 77
                                   7899******9776667688877899******************99............787......79**9998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                                    S CS
                           Fer2  56 e 56 
                                    +
  gi|121636160|ref|YP_976383.1| 170 P 170
                                    0 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.55   8.9e+02       5       9 ..      58      62 ..      38     104 .. 0.72
   2 !   21.6   7.0   1.5e-07   0.00024       1      60 [.     143     216 ..     143     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                        Fer4_17  5 CgyCl 9 
                                   Cg C 
  gi|121636160|ref|YP_976383.1| 58 CGSCS 62
                                   33333 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.5e-07
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepk......kllraakl........glleeaekeekaslCieCgeCerkCPqgl 60 
                                    +Ci+C  C ++C   ++++++++       l+r a+l         +  +a++e+  + C+  + C+++CP+++
  gi|121636160|ref|YP_976383.1| 143 KCIECFLCQNVCHVVRDHEENKDafagprFLMRIAELemhpldtrDRRSQAQEEHGLGYCNITKCCTEVCPENI 216
                                    6****************99975523332156666655888887644444456669*****************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       8.5   1.4e+04      57      64 ..      54      61 ..      38      69 .. 0.60
   2 !   11.8   0.2   0.00013      0.21      42      74 ..     125     157 ..      82     165 .. 0.79
   3 !   11.9   0.3   0.00012      0.19      46      79 ..     187     220 ..     175     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.5
                        Fer4_18 57 gagdcidc 64
                                   +ag+c +c
  gi|121636160|ref|YP_976383.1| 54 KAGKCGSC 61
                                   34444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                        Fer4_18  42 kekkalkekeerkekgagdcidcescvkvcPtg 74 
                                    +++  +++++  ++++  +ci+c  c +vc + 
  gi|121636160|ref|YP_976383.1| 125 PSEYRMAQVDVARSQEFRKCIECFLCQNVCHVV 157
                                    455667788889999999999999999999765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00012
                        Fer4_18  46 alkekeerkekgagdcidcescvkvcPtgidirk 79 
                                      ++++ ++e+g g c   + c +vcP +i i +
  gi|121636160|ref|YP_976383.1| 187 RDRRSQAQEEHGLGYCNITKCCTEVCPENIKITD 220
                                    45566777888999****************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.5      0.71   1.2e+03      29      42 ..      49      62 ..      23      77 .. 0.68
   2 ?   -2.0   2.0       3.4   5.6e+03       4       9 ..      57      62 ..      52      91 .. 0.76
   3 !    9.5   3.1   0.00092       1.5      35      49 ..     141     155 ..     108     158 .. 0.69
   4 !   17.9   6.2   2.2e-06    0.0036       1      51 [.     143     215 ..     143     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.71
                         Fer4_7 29 ekveidpekClgCg 42
                                    +++ ++ kC +C 
  gi|121636160|ref|YP_976383.1| 49 VRWNCKAGKCGSCS 62
                                   44555555555553 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                         Fer4_7  4 gCgaCv 9 
                                   +Cg C 
  gi|121636160|ref|YP_976383.1| 57 KCGSCS 62
                                   344443 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00092
                         Fer4_7  35 pekClgCgaCvavCP 49 
                                     +kC+ C  C++vC 
  gi|121636160|ref|YP_976383.1| 141 FRKCIECFLCQNVCH 155
                                    568888888888885 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 2.2e-06
                         Fer4_7   1 rCigCgaCvaaC...............pvkaieldeeenek.......gtekveidpekClgCgaCvavCPtg 51 
                                    +Ci+C  C+++C               p   +++ e e ++        +++ e+   +C  ++ C +vCP +
  gi|121636160|ref|YP_976383.1| 143 KCIECFLCQNVChvvrdheenkdafagPRFLMRIAELEMHPldtrdrrSQAQEEHGLGYCNITKCCTEVCPEN 215
                                    7***********8888888888887774333333332222222222224466688899*************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5     0.081   1.3e+02      33      43 ..      44      62 ..      14      76 .. 0.73
   2 !   12.0   0.2   0.00011      0.18      34      47 ..     142     155 ..     107     171 .. 0.75
   3 !    7.2   0.3    0.0034       5.5       6      23 ..     206     223 ..     183     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.081
                         Fer4_9 33 e......eaC..igCgaCv 43
                                          ++C   +Cg+C 
  gi|121636160|ref|YP_976383.1| 44 TpdlavrWNCkaGKCGSCS 62
                                   2556666888433599886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                         Fer4_9  34 eaCigCgaCveaCp 47 
                                     +Ci+C  C ++C 
  gi|121636160|ref|YP_976383.1| 142 RKCIECFLCQNVCH 155
                                    56888888888885 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0034
                         Fer4_9   6 gaCveaCpagvvvedaae 23 
                                    + C+e+Cp ++ + d+a 
  gi|121636160|ref|YP_976383.1| 206 KCCTEVCPENIKITDNAL 223
                                    448888888888877765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       2.3   3.8e+03       3       8 ..      56      61 ..      41      64 .. 0.67
   2 ?   10.7   0.2   0.00048      0.77      34      64 ..     124     154 ..     101     157 .. 0.75
   3 ?    7.9   0.1    0.0037         6      54      67 .]     202     215 ..     161     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                        Fer4_16  3 gtCgkC 8 
                                   g+Cg C
  gi|121636160|ref|YP_976383.1| 56 GKCGSC 61
                                   344444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                        Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                    +  e + ++ d ++ ++  +++ C  Cq+vC
  gi|121636160|ref|YP_976383.1| 124 QPSEYRMAQVDVARSQEFRKCIECFLCQNVC 154
                                    45666777788888889999*********** PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0037
                        Fer4_16  54 itgCdiCqdvCPan 67 
                                    +   + C++vCP n
  gi|121636160|ref|YP_976383.1| 202 CNITKCCTEVCPEN 215
                                    22223455555543 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   8.1e-05      0.13      26      67 ..     144     191 ..     141     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                                    -TT-HHHHHHHHHHHH-HHHHH.HH.HT-EEEEESS.....--S-GGG CS
                  Thioredoxin_7  26 aswcftCqalerdflsdeevkaala.ekfvllrvdv.....terdani 67 
                                    + +cf Cq +  ++ ++ee+k a+a  +f ++ ++      ++rd++ 
  gi|121636160|ref|YP_976383.1| 144 CIECFLCQNVCHVVRDHEENKDAFAgPRFLMRIAELemhplDTRDRRS 191
                                    668**********************88888888887889997777765 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   6.2e-05       0.1      12      69 ..      23      75 ..      21      90 .. 0.83
   2 ?   -2.7   0.5         4   6.6e+03      41      54 ..     137     150 ..     130     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                         Fer2_4 12 evtvpeGdtvasAllangvd.vprsckygrprgelcaggeCrnClVevegepnvracst 69
                                   +v+v eG+ v++++l+ +++ +p +          c  g+C  C  e++g+p++  c+t
  gi|121636160|ref|YP_976383.1| 23 TVEVNEGEVVLDVILRLQQTqTPDLAVR-----WNCKAGKCGSCSAEINGKPRLM-CMT 75
                                   699************9998637788888.....89*****************874.444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4
                         Fer2_4  41 prgelcaggeCrnC 54 
                                    +++e+    eC+ C
  gi|121636160|ref|YP_976383.1| 137 RSQEFRKCIECFLC 150
                                    46778888888888 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.11   1.8e+02      41      53 ..      49      63 ..      36      64 .. 0.70
   2 ?    9.9  11.1   0.00047      0.77       6      56 .]     141     213 ..     136     213 .. 0.84
   3 ?    4.7   2.6      0.02        33       9      30 ..     202     223 ..     199     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                        Fer4_10 41 kvekCtg..cgaCve 53
                                   + ++C +  cg+C +
  gi|121636160|ref|YP_976383.1| 49 VRWNCKAgkCGSCSA 63
                                   567777777999976 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00047
                        Fer4_10   6 ddtCirCgkCvkaCPadl........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                      +Ci+C  C+++C  ++                         +   +  +  +++++++++ C     C+e+CP
  gi|121636160|ref|YP_976383.1| 141 FRKCIECFLCQNVC--HVvrdheenkdafagprflmriaeleMHPLDTRDRRSQAQEEHGLGYCNITKCCTEVCP 213
                                    579***********..8889********************97444444455555556668**************9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.02
                        Fer4_10   9 CirCgkCvkaCPadltsvgakg 30 
                                    C   + C+++CP +++  ++  
  gi|121636160|ref|YP_976383.1| 202 CNITKCCTEVCPENIKITDNAL 223
                                    5555679999*99875544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1830.67
//
Query:       gi|121636161|ref|YP_976384.1|  [L=646]
Description: succinate dehydrogenase flavoprotein subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-87  292.9   4.6    5.4e-87  292.6   4.6    1.1  1  FAD_binding_2   FAD binding domain
    3.4e-21   75.6   0.0    6.7e-21   74.6   0.0    1.5  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    8.6e-08   31.7   3.7    3.3e-05   23.3   1.2    2.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-05   24.5   4.0    0.00036   20.2   4.0    2.8  1  DAO             FAD dependent oxidoreductase
    0.00037   19.3   4.3    0.00083   18.2   0.5    2.5  3  HI0933_like     HI0933-like protein
      0.001   18.4   2.1      0.015   14.6   0.2    2.8  3  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.012   14.7   2.8      0.012   14.7   2.8    2.2  3  GIDA            Glucose inhibited division protein A
       0.08   12.2   0.6       0.17   11.1   0.6    1.6  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.13   11.6   0.3       0.23   10.7   0.3    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.16   10.9   0.1       0.27   10.3   0.1    1.4  1  Lycopene_cycl   Lycopene cyclase protein
       0.33   10.2   4.4       0.47    9.7   4.4    1.4  1  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.6   4.6   3.3e-90   5.4e-87       1     417 []      10     429 ..      10     429 .. 0.96

  Alignments for each domain:
  == domain 1  score: 292.6 bits;  conditional E-value: 3.3e-90
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HH CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqp 80 
                                    Dv+ViG+G+AGL+A +ea+e+Glkvavv k    + +t++++Gg +a+  +++   + kd+++ h+ dt+ ++  l++ +
  gi|121636161|ref|YP_976384.1|  10 DVVVIGAGGAGLRAVIEARERGLKVAVVCKSLFGKAHTVMAEGGCAAAM-GNA---NPKDNWKTHFGDTMRGGKFLNNWR 85 
                                    9******************************99888*********9999.776...677********************* PP

                                    HHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT..... CS
                  FAD_binding_2  81 lveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag..... 155
                                    ++e+ +++ap+ v eLe +g+ f+rt+dg++ +r +Gg++ + r +h ++d+      tg +l+ +l +++ +++     
  gi|121636161|ref|YP_976384.1|  86 MAELHAKEAPDRVWELETYGALFDRTDDGRISQRNFGGHTYP-RLAH-VGDR------TGLELIRTLQQKVVSLQqedha 157
                                    ******************************************.****.****......*************888888899 PP

                                    ........EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S- CS
                  FAD_binding_2 156 ........vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtG 227
                                            +++++++ ++eL+ ++g + Ga    +esgr   ++a avvlatgG+g+           ++ t+n    tG
  gi|121636161|ref|YP_976384.1| 158 elgdyearIKVFAECTITELLKDQGAIAGAFGYWRESGRFIVFEAPAVVLATGGIGK----------SFKVTSNSWEYTG 227
                                    9********************************99*********************9..........9************ PP

                                    HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH..................... CS
                  FAD_binding_2 228 dglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm..................... 286
                                    dg+alalraga l +  me+vqfhPt++v + + +giL+te++rg+Gg+l +++  rFm                     
  gi|121636161|ref|YP_976384.1| 228 DGHALALRAGATLIN--MEFVQFHPTGMVWPPSVKGILVTEGVRGDGGVLKNSENSRFMfdyippvfkgqyaeteeeadq 305
                                    ************999..************55555677******************************************* PP

                                    ...........GGGS-HHHHHHHHH.HHHHTTTS..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTT CS
                  FAD_binding_2 287 ...........nelasrdvvsrailekeiaeggs..eanvyldashgldaegleatleaineeaangldkdfgrgidpad 353
                                                +l +rd+v+rai   e++ g++     vyld++++l ++ ++++l+ +++++++ ++      +d+++
  gi|121636161|ref|YP_976384.1| 306 wlkdndsarrtPDLLPRDEVARAIN-SEVKAGRGtpHGGVYLDIASRLTPAEIKRRLPSMYHQFKELAE------VDITT 378
                                    ***********9999**********.77777777686789**************************999......9**** PP

                                    SEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                  FAD_binding_2 354 rpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                    + +        v p++hy mgGve+d+++ +      ++pGL+AaGe+a gg+hg nrlgGnsl
  gi|121636161|ref|YP_976384.1| 379 QAME-------VGPTCHYVMGGVEVDADTGA-----ATVPGLFAAGECA-GGMHGSNRLGGNSL 429
                                    *777.......*****************999.....9************.************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   4.1e-24   6.7e-21       1     102 [.     488     587 ..     488     599 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 4.1e-24
                                    .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTT CS
                 Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGa 80 
                                    + +L+ +m++ vg+ R+++++++al+ l+el +r++nv v+++  ++N  +   + l+n+l ++e++a++Al+R+ESrG+
  gi|121636161|ref|YP_976384.1| 488 HMDLQYVMNDLVGIIRNADEISRALTLLAELWSRYHNVLVEGHR-QYNPGWNLSIDLRNMLLVSECVARAALQRTESRGG 566
                                    779*************************************9886.59********************************* PP

                                    BEBTTS-SEETTT-SEEEEE.. CS
                 Succ_DH_flav_C  81 HaredfperdDenwlkhtlasl 102
                                    H+r+d+p   D nw++  l+  
  gi|121636161|ref|YP_976384.1| 567 HTRDDHP-GMDPNWRRILLVCR 587
                                    *******.8899****999843 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.2     2e-08   3.3e-05       1      40 [.       9      54 ..       9     229 .. 0.66
   2 !    8.3   0.1   0.00076       1.2     256     281 ..     392     418 ..     379     427 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2e-08
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEE.....E.TTHCHHHCSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlv.....e.legtclnggc 40
                                   +dvvviG+G AGl+a +++++ g+kv++v     + + + +  ggc
  gi|121636161|ref|YP_976384.1|  9 YDVVVIGAGGAGLRAVIEARERGLKVAVVckslfGkAHTVMAEGGC 54
                                   69***************************44333233333334444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00076
                                    TEEE--TTS.BESSTTEEE-GGGCTEC CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 256 ggivvdefl.rtnvpgiyaiGDvaggk 281
                                    gg++vd    + +vpg++a+G +agg 
  gi|121636161|ref|YP_976384.1| 392 GGVEVDADTgAATVPGLFAAGECAGGM 418
                                    8899998875677***********544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.0   2.2e-07   0.00036       1     141 [.      10     343 ..      10     359 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.2e-07
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS..STHHSTH..................HHH CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl..rylpeas..................ela 58 
                                    dvv+iG+G +Gl +  e+ +rg  V++++k+  +g++ +  + g +++++  +  p+                       
  gi|121636161|ref|YP_976384.1|  10 DVVVIGAGGAGLRAVIEARERGlkVAVVCKS-LFGKAHTVMAEGGCAAAMgnA-NPK-DnwkthfgdtmrggkflnnW-- 84 
                                    9*****************999**********.999866666666666656443.333.23567777554444444440.. PP

                                    HHHHHHHHHH.HHHHHHHSSTTSEEEEEEEEEESS............................................. CS
                            DAO  59 rlslealeel.releeelgididyrrtGllslaad............................................. 92 
                                             + +el +++++d  ++  ++  l++                                              
  gi|121636161|ref|YP_976384.1|  85 ---------RmAELHAKEAPDRVWELETYGALFDRtddgrisqrnfgghtyprlahvgdrtglelirtlqqkvvslqqed 155
                                    .........34444444455555555555555421123333333333333444444444444444444444444444444 PP

                                    ................................................................................ CS
                            DAO  93 ................................................................................ 92 
                                                                                                                    
  gi|121636161|ref|YP_976384.1| 156 haelgdyearikvfaectitellkdqgaiagafgywresgrfivfeapavvlatggigksfkvtsnsweytgdghalalr 235
                                    44444444444444444444444446666666666666666666666667777777777777777777777777777777 PP

                                    ..............................................................HHHHHHHHHHHHHHHHTT CS
                            DAO  93 ..............................................................eeelealdkllallleag 110
                                                                                                  e  +e+ d++l++  +a 
  gi|121636161|ref|YP_976384.1| 236 agatlinmefvqfhptgmvwppsvkgilvtegvrgdggvlknsensrfmfdyippvfkgqyaE-TEEEADQWLKDNDSAR 314
                                    777777777777777777777777777777777777777766666666666666666666632.3444556666653333 PP

                                    TTEEEEEHHHHHHHSTTSTTTSEEEEETTEE CS
                            DAO 111 ldaelldaeevrelepalpgllgalfypdtg 141
                                        ll ++ev++     ++++++ ++p++g
  gi|121636161|ref|YP_976384.1| 315 RTPDLLPRDEVARAIN--SEVKAGRGTPHGG 343
                                    2224677765554442..3566666666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   5.1e-07   0.00083       1      46 [.       9      53 ..       9      89 .. 0.79
   2 ?   -2.0   0.0      0.68   1.1e+03     153     165 ..     200     212 ..     163     245 .. 0.66
   3 ?    1.7   0.1     0.051        83     354     384 ..     388     414 ..     361     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGr 46
                                   +dv+viG+G AGl a i+a++rg +V+++ k   +g+   +  +G+
  gi|121636161|ref|YP_976384.1|  9 YDVVVIGAGGAGLRAVIEARERGLKVAVVCKS-LFGKAHTVMAEGG 53
                                   59*************************99765.5555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.68
                                    EEESEEEE----S CS
                    HI0933_like 153 leadklvlAtGGl 165
                                    +ea ++vlAtGG 
  gi|121636161|ref|YP_976384.1| 200 FEAPAVVLATGGI 212
                                    68899******84 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.051
                                    SEEEEEE-GGGB-TTT-BBTTSTTEEE-GGG CS
                    HI0933_like 354 evTaGGVdlkevssktmeskkvpgLffaGEv 384
                                       +GGV   ev+++t  + +vpgLf aGE+
  gi|121636161|ref|YP_976384.1| 388 HYVMGGV---EVDADTG-AATVPGLFAAGEC 414
                                    5567887...5677776.889*********8 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   8.9e-06     0.015      17      51 ..       8      41 ..       3      54 .. 0.85
   2 ?    0.6   0.0      0.17   2.7e+02     175     229 ..     348     403 ..     335     409 .. 0.75
   3 ?    1.1   0.1      0.12     2e+02     210     232 ..     403     425 ..     398     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersv 51
                                     Dvv++GaG +GL a     ++ +lkva++ +s+
  gi|121636161|ref|YP_976384.1|  8 SYDVVVIGAGGAGLRAVIEARER-GLKVAVVCKSL 41
                                   57************998776555.******98876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                    HHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTE..EE-THHHHHHHT-E CS
                           Thi4 175 vvvkkikleakiekvkgeksldaekaedaivkktrevvpnl..yvaGmevaevdgan 229
                                    ++  +++ ++ + +++ +   + e ae +i  ++ ev p    +++G+ev +  ga 
  gi|121636161|ref|YP_976384.1| 348 IA-SRLTPAEIKRRLPSMYHQFKELAEVDITTQAMEVGPTChyVMGGVEVDADTGAA 403
                                    44.4555566689999999******************99753156789998877765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.12
                                    EEETTEEE-THHHHHHHT-EB-- CS
                           Thi4 210 evvpnlyvaGmevaevdganRmG 232
                                    + vp+l++aG  +  ++g nR+G
  gi|121636161|ref|YP_976384.1| 403 ATVPGLFAAGECAGGMHGSNRLG 425
                                    679*******************9 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.8   7.6e-06     0.012       1      45 [.      10      59 ..      10      66 .. 0.81
   2 ?   -1.2   0.0      0.51   8.4e+02     117     151 ..     173     212 ..     144     239 .. 0.66
   3 ?   -2.2   0.1         1   1.7e+03     354     367 ..     404     417 ..     396     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE.....ES-GGGTT--SSSSEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.....thkldtiaelsCnpsig 45
                                   dv+ViG+G AG+ A ++a ++G+kv+ +      +    +ae +C  ++g
  gi|121636161|ref|YP_976384.1| 10 DVVVIGAGGAGLRAVIEARERGLKVAVVckslfGKAHTVMAEGGCAAAMG 59
                                   79************************997777644555566666666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                                    -EEEEEECTTEEEEEE...ETTS-..EEEECEEEE--TT- CS
                           GIDA 117 eveeliveekkvkgvv...tedge..tikakavviatGtf 151
                                    +++el+ +++ ++g      e+g+  +++a avv+atG  
  gi|121636161|ref|YP_976384.1| 173 TITELLKDQGAIAGAFgywRESGRfiVFEAPAVVLATGGI 212
                                    45666666666666441114455511456679*****983 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                                    SSBTEEE-CGGGTB CS
                           GIDA 354 kvkgLflAGqinGt 367
                                    +v+gLf+AG+  G 
  gi|121636161|ref|YP_976384.1| 404 TVPGLFAAGECAGG 417
                                    689*******9985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00011      0.17       1      29 [.      12      39 ..      12      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                   ++iGaG aGl a ie+++ gl ++ ++ k
  gi|121636161|ref|YP_976384.1| 12 VVIGAGGAGLRAVIEARERGL-KVAVVCK 39
                                   79*******************.5777755 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00014      0.23      30      56 ..      10      36 ..       3      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                   EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                                    v+viG+G aGl A+  a++ g kV v
  gi|121636161|ref|YP_976384.1| 10 DVVVIGAGGAGLRAVIEARERGLKVAV 36
                                   69*****************99999987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00016      0.27       1      43 [.      10      47 ..      10      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyv 43
                                   DvvviGaG Agl+   +    + glkv ++    ++lf+  ++
  gi|121636161|ref|YP_976384.1| 10 DVVVIGAGGAGLRAVIEA--RERGLKVAVV--C-KSLFGKAHT 47
                                   9************99998..8999999999..4.444776665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.4   0.00029      0.47       1      31 [.      10      40 ..      10     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                   DvvV+G+g aG+ A i A ++G kv++v ++
  gi|121636161|ref|YP_976384.1| 10 DVVVIGAGGAGLRAVIEARERGLKVAVVCKS 40
                                   9*************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4174.18
//
Query:       gi|121636162|ref|YP_976385.1|  [L=273]
Description: succinate dehydrogenase membrane anchor subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2120.44
//
Query:       gi|121636163|ref|YP_976386.1|  [L=97]
Description: hypothetical protein BCG_0288c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 674.18
//
Query:       gi|121636164|ref|YP_976387.1|  [L=159]
Description: heat shock protein hsp [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-14   53.3   0.0    2.9e-14   53.1   0.0    1.1  1  HSP20       Hsp20/alpha crystallin family
    5.3e-07   29.1   0.3    2.4e-06   27.0   0.3    1.9  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   3.2e-18   2.9e-14       2     101 ..      47     157 ..      46     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.2e-18
                                    --SSEEEEEEEEE-TT--.CCCEEEEEETTE....EEEEEE--.....---TT-..---SS---EEEEEE--STTB-TTT CS
                          HSP20   2 ikeeeeefevkldvpglk.keelkvkvednr....vlvkgehe...eeeedekg..likerssrkFsrkftLPenvdadk 71 
                                    i+++ +   v+l++pg++  ++++v+++ ++    ++++geh+   +++ ++k+    +e ++++F+r+f+LP  v  ++
  gi|121636164|ref|YP_976387.1|  47 IVKDGDDAVVRLELPGIDvDKDVNVELDPGQpvsrLVIRGEHRdehTQDAGDKDgrTLREIRYGSFRRSFRLPAHVTSEA 126
                                    778889999*********777******98877777********8884444444411456899****************** PP

                                    -EEEEETTEEEEEEEBSS--...-------- CS
                          HSP20  72 vkaslkdGvLtvtvpkkepekk.kkerkiqi 101
                                    ++as++ GvLtv v    ++++  + ++i+i
  gi|121636164|ref|YP_976387.1| 127 IAASYDAGVLTVRVAGAYKAPAeTQAQRIAI 157
                                    **************97766555478999988 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.3   2.7e-10   2.4e-06       2      62 ..      52     139 ..      51     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.7e-10
                     ArsA_HSP20   2 deyvlkldLPfvdke.eidlsrs....gdeLtIkig.......................nfrRqitLPsvlarkevtsAk 53 
                                    d+ v++l+LP++d + +++++ +     + L+I+ +                       +frR++ LP ++  + +  A+
  gi|121636164|ref|YP_976387.1|  52 DDAVVRLELPGIDVDkDVNVELDpgqpVSRLVIRGEhrdehtqdagdkdgrtlreirygSFRRSFRLPAHVTSEAI-AAS 130
                                    7889********766467777665344789********************************************88.*** PP

                     ArsA_HSP20  54 fedgvLeIr 62 
                                    +  gvL++r
  gi|121636164|ref|YP_976387.1| 131 YDAGVLTVR 139
                                    *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1217.04
//
Query:       gi|121636165|ref|YP_976388.1|  [L=853]
Description: nitrite reductase NAD(P)H] large subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-47  159.7   2.6    1.3e-46  159.1   2.6    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-20   72.6   0.1    6.3e-20   71.3   0.0    1.7  2  NIR_SIR        Nitrite and sulphite reductase 4Fe-4S domain
    1.3e-17   64.1   4.9    4.4e-16   59.2   0.3    3.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.4e-14   54.1   6.7    2.5e-09   37.3   5.2    3.0  2  Fer2_BFD       BFD-like [2Fe-2S] binding domain
    2.8e-10   39.9   0.0    1.8e-09   37.3   0.0    2.3  2  NIR_SIR_ferr   Nitrite/Sulfite reductase ferredoxin-like half
    6.6e-09   35.6   0.1    1.8e-08   34.2   0.1    1.7  1  Rubredoxin_C   Rubredoxin NAD+ reductase C-terminal domain
    7.9e-06   25.3   0.0       0.51    9.6   0.1    3.0  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      6e-05   22.3   0.7      0.041   13.0   0.2    3.1  3  GIDA           Glucose inhibited division protein A
    6.6e-05   22.2   4.0      0.028   13.5   0.5    2.5  2  FAD_binding_2  FAD binding domain
    0.00056   19.6   7.4      0.023   14.3   0.0    3.5  3  DAO            FAD dependent oxidoreductase
     0.0072   15.7   0.9        1.9    7.7   0.0    3.0  3  Amino_oxidase  Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.016   14.0   0.5          5    5.7   0.0    2.7  3  HI0933_like    HI0933-like protein
      0.019   15.2   0.4      0.071   13.3   0.4    2.1  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.027   14.9   1.1        3.1    8.3   0.1    2.6  2  NAD_binding_7  Putative NAD(P)-binding
      0.054   12.7   0.7        0.1   11.8   0.7    1.4  1  FAD_binding_3  FAD binding domain
       0.11   12.8   0.7         19    5.6   0.1    2.9  2  TrkA_N         TrkA-N domain
       0.27   11.2   9.4        1.4    8.9   0.2    3.7  4  NAD_binding_9  FAD-NAD(P)-binding
       0.29   10.4   5.7      0.048   12.9   1.1    1.9  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.93    8.6   1.9        3.5    6.7   0.1    2.4  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
        2.1    8.2   3.8        2.6    7.9   0.6    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.1   2.6   1.5e-49   1.3e-46       2     278 ..      15     302 ..      14     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 1.5e-49
                                    SEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCH CS
                                    xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielll 71 
                                    ++vv+G G+ G+++ + +++     ++++t++ +eg   ++++ l++  +++ ++   +       +      q ++lll
  gi|121636165|ref|YP_976388.1|  15 EIVVVGHGMVGHRLVEAVRArdadGSLRITVLAEEGDAAYDRVGLTSYTESWDRALLALPgndyagD------QRVRLLL 88 
                                    69************9999998876699******************9999999988865558755433......58***** PP

                                    CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.......SE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx RF
                    Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.......kr 144
                                    ++ v++id++ k v+        +++  yd+lvlAtGs ++ +++pG    ++++ rt+d+ +a++   ++       + 
  gi|121636165|ref|YP_976388.1|  89 NTRVTQIDRATKSVVT-----AAGQRHRYDTLVLATGSYAFVPPVPGHDLPACHVYRTFDDLDAIRAGAQRtldgghtDG 163
                                    *99********99998.....567899*********************99999999**************9888866555 PP

                                    EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.....EEE. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx. RF
                    Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge.....kle. 217
                                     vv+GgG+ G+E A al+++g ++++ve ++rl+ ++ d++ +a l++ + + G++v++gt  + i++ ++         
  gi|121636165|ref|YP_976388.1| 164 GVVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMaQQIDEAGGALLARMIADLGIAVHVGTGTESIESVKHsdgsvW-Ar 242
                                    5**************************************************************99998888777533.26 PP

                                    EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva 278
                                    v l+dge+ida  v++a+G+rp++el+ +++gl++ +rgg+++d ++rt++p+iya+G va
  gi|121636165|ref|YP_976388.1| 243 VRLSDGEVIDAGVVIFAAGIRPRDELA-RAAGLAIGDRGGVLTDLSCRTSDPDIYAVGEVA 302
                                    ***************************.********************************9 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.8   5.2e+03      65      87 ..     214     261 ..     197     267 .. 0.69
   2 !   71.3   0.0     7e-23   6.3e-20       2     153 ..     645     782 ..     644     786 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.8
                                    SSEEEEEEEETTCEE.........................EEEEEE-- CS
                                    xxxxxxxxxxxxxxx.........................xxxxxxxx RF
                        NIR_SIR  65 nDiglvgvkkdekei.........................gfnilvGG 87 
                                     D+g+ +++  ++e                          g+ i+  G
  gi|121636165|ref|YP_976388.1| 214 ADLGIAVHVGTGTESiesvkhsdgsvwarvrlsdgevidaGVVIFAAG 261
                                    477777777766666666677777777777777777777777777666 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 7e-23
                                    SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigf 81 
                                    g+ +r+v++c+g+ +c+    D+ +la ++e     +y+  + P+K K  vsgc + c++++ +D+g+++++k     g+
  gi|121636165|ref|YP_976388.1| 645 GKAVRTVKSCVGSDWCRYGQQDSVQLAIDLE----LRYRGLRAPHKIKLGVSGCARECAEARGKDVGVIATEK-----GW 715
                                    789****************************....9*************************************.....** PP

                                    EEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH.HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                        NIR_SIR  82 nilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv.ee 153
                                    n++v G+ g t++ ++ +a    +++e ++++++  + +y     r++ + +R + +ve lG+++ re+v e 
  gi|121636165|ref|YP_976388.1| 716 NLYVAGNGGMTPKHAQLLA--SDLDKETLIRYIDRFLIYYI----RTADRLQRTAPWVESLGLDHVREVVcED 782
                                    *******************..6899999*************....************************9554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.1   9.6e+02       2      20 ..      16      34 ..      15      50 .. 0.79
   2 ?    4.1   0.0     0.077        69      49      73 ..      78     103 ..      75     108 .. 0.81
   3 !   59.2   0.3   4.9e-19   4.4e-16       3      78 ..     165     245 ..     163     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                   EEEECSSHHHHHHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalae 20
                                   +vvvG G +g  l +a ++
  gi|121636165|ref|YP_976388.1| 16 IVVVGHGMVGHRLVEAVRA 34
                                   8*********887777665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.077
                                    HHHHTTEEEECSEEEEEEEEETTS.E CS
                      Pyr_redox  49 klekngievllntkveeiegsedg.v 73 
                                    +  ++ +++llnt+v++i+  ++  v
  gi|121636165|ref|YP_976388.1|  78 YAGDQRVRLLLNTRVTQIDRATKSvV 103
                                    566889*************8888633 PP

  == domain 3  score: 59.2 bits;  conditional E-value: 4.9e-19
                                    EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE..EETTS..EEEEE CS
                      Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeie..gsedg..vesvk 77 
                                    vv+GgG++glE+A+al+++g +++vve++++l+ +++De+ +++l++ + ++gi v+ +t +e+ie  +++dg  + +v+
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMaQQIDEAGGALLARMIADLGIAVHVGTGTESIEsvKHSDGsvWARVR 244
                                    9****************************************************************977444443556666 PP

                                    E CS
                      Pyr_redox  78 l 78 
                                    l
  gi|121636165|ref|YP_976388.1| 245 L 245
                                    6 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   5.2   2.8e-12   2.5e-09       2      50 ..     441     488 ..     440     489 .. 0.97
   2 !   15.1   0.0   2.4e-05     0.022       6      50 ..     502     546 ..     498     547 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.8e-12
                       Fer2_BFD   2 VCrCegvtegeIrdairraglttveevkrrtkagtgCggCrpaieeiLa 50 
                                    +C+C++vt+ge++ ai ++g  +v ++k  t agt Cg+C+p ++++L+
  gi|121636165|ref|YP_976388.1| 441 ICSCNNVTKGELKCAI-ADGCGDVPALKSCTAAGTSCGSCVPLLKQLLE 488
                                    9***************.99****************************97 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
                       Fer2_BFD   6 egvtegeIrdairraglttveevkrrtkagtgCggCrpaieeiLa 50 
                                    ++ ++ e+ + i++ +++t+ ++ +r + g gC  C+p ++ iLa
  gi|121636165|ref|YP_976388.1| 502 FSQSRAELFEIITATEVRTFSGLLDRFGRGKGCDICKPVVASILA 546
                                    5567788999998888****************************8 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.8   2.5e+03      21      39 ..     513     531 ..     512     533 .. 0.90
   2 !   37.3   0.0     2e-12   1.8e-09       3      66 ..     573     633 ..     571     635 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                   NIR_SIR_ferr  21 itaeqlraladiaekygsg 39 
                                    ita + r +  + +++g+g
  gi|121636165|ref|YP_976388.1| 513 ITATEVRTFSGLLDRFGRG 531
                                    79999************98 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2e-12
                   NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66 
                                    qk+g   y+v  rvp+G+i +e l  + +ia+++g  + ++T  Q + l+g + ++l+ i+++L
  gi|121636165|ref|YP_976388.1| 573 QKNGS--YSVVPRVPGGDIKPEHLILIGQIAQDFG-LYTKITGGQRIDLFGARVDQLPLIWQRL 633
                                    88987..8***************************.**************************98 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1     2e-11   1.8e-08       2      60 ..     339     400 ..     339     409 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2e-11
                                    --EEEETTEEEEEES--TT---.SEEEEEE-SS-..EEEEEEETT..EEEEEEEES-HHHHH CS
                   Rubredoxin_C   2 vtiLkvsgidlfSvGdieeeek.aeelveedkekgkYkklfikng..klvGAiliGDtkesa 60 
                                    +t+Lk +g+d+ S+Gd  +  + + e+v +d+ k++Y kl++ ++   l G +l+GD + + 
  gi|121636165|ref|YP_976388.1| 339 STKLKLLGVDVASFGDAMGATEnCLEVVINDAVKRTYAKLVLSDDatTLLGGVLVGDASSYG 400
                                    699*************9998777********************9844699*******99875 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00087      0.78      93     160 ..      81     146 ..      75     156 .. 0.80
   2 !    9.6   0.1   0.00056      0.51       1      29 [.     165     192 ..     165     202 .. 0.89
   3 ?    3.1   0.0     0.052        47     232     305 .]     226     299 ..     207     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00087
                    Pyr_redox_3  93 sfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefh 160
                                     ++++  l+++V++++++  + +v++  +  + +++++AtG + +  ++ +pG +   + +y+++++++
  gi|121636165|ref|YP_976388.1|  81 DQRVRLLLNTRVTQIDRAT-KSVVTAAGQRHRYDTLVLATGSYAF--VPPVPGHDLpACHVYRTFDDLD 146
                                    567778899*******985.56888999999999********877..7889**9964788888887775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEk 29 
                                    ++iG+G  Gl+aa +l+++gl+   ++E 
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQ-THVVEM 192
                                    79*******************6.568885 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.052
                    Pyr_redox_3 232 naevkeikekeeey..kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    +++++++k+++ ++  +v+ +dg+       v++a G +p  ++ +++++++  d+  vlt+  + t  p+++ +G
  gi|121636165|ref|YP_976388.1| 226 TESIESVKHSDGSVwaRVRLSDGEV-IDAGVVIFAAGIRPRDELARAAGLAI-GDRGGVLTDLSCRTSDPDIYAVG 299
                                    4567888888887766889999865.556999*************9999999.77778899999999999999988 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0089       7.9     115     152 ..      89     123 ..      81     133 .. 0.84
   2 !   13.0   0.2   4.5e-05     0.041       3      29 ..     165     198 ..     164     210 .. 0.82
   3 ?   -1.0   0.0      0.77   6.9e+02     116     149 ..     227     261 ..     220     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0089
                                    ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-B CS
                           GIDA 115 eeeveeliveekkvkgvvtedgetikakavviatGtfl 152
                                    + +v++++   + +k vvt+ g+  + ++ v+atG++ 
  gi|121636165|ref|YP_976388.1|  89 NTRVTQID---RATKSVVTAAGQRHRYDTLVLATGSYA 123
                                    56677774...5999*********************85 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.5e-05
                                    EEE-SSHHHHHHHHHHHHTT--EEEE.......E CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLi.......t 29 
                                    +ViGgG+ G+eAA a+ + G+++  +       +
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVemmprlmA 198
                                    7**********************99855555444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.77
                                    S-EEEEEECTTEEEE.EEETTS-EEEECEEEE--T CS
                           GIDA 116 eeveeliveekkvkg.vvtedgetikakavviatG 149
                                    e++e+++ ++++v + v+++dge+i a +v+ a+G
  gi|121636165|ref|YP_976388.1| 227 ESIESVKHSDGSVWArVRLSDGEVIDAGVVIFAAG 261
                                    5667777777777777*****************99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.5   3.2e-05     0.028       3      43 ..     165     206 ..     164     212 .. 0.85
   2 !    9.2   0.2   0.00062      0.56     368     403 ..     274     303 ..     248     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                    EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGGG--S CS
                  FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg.atawsqG 43 
                                    +ViG+Gl GL AA ++++ Gl++ vve +++    ++  ++G
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMAqQIDEAGG 206
                                    8**************************999865555555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00062
                                    EEEEES-EEEBETTSBESTTEEESSBTEEE-STCEE CS
                  FAD_binding_2 368 aqhytmgGvetdengrvldadgqpipGLYAaGevaa 403
                                     + +  gGv td+++r+        p+ YA+Gevaa
  gi|121636165|ref|YP_976388.1| 274 LAIGDRGGVLTDLSCRT------SDPDIYAVGEVAA 303
                                    556678***********......99*********93 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.6e-05     0.023     158     212 ..      81     127 ..      58     156 .. 0.77
   2 ?    4.7   0.1      0.02        18       3      29 ..     165     193 ..     165     208 .. 0.83
   3 ?    2.9   0.2     0.077        69     152     207 ..     209     268 ..     197     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                                    HTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCT CS
                            DAO 158 alGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllke 212
                                    ++ v++l++t+vt +++     + v  +t+ g+++++d++V+a+G ++ ++   ++
  gi|121636165|ref|YP_976388.1|  81 DQRVRLLLNTRVTQIDRA---TKSV--VTAaGQRHRYDTLVLATGSYA-FV---PP 127
                                    5679***********875...4445..4454988778********997.44...33 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                                    EEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO   3 viiGGGiiGlstAyeLarrg..Vtllekg 29 
                                    v+iGGG  Gl +A +L + g  + ++e+ 
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGlqTHVVEMM 193
                                    8***************5559999999976 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.077
                                    HHHHHHHTT-EEEESECEEEEEE...EETCEEEEEEECTEEEEEEEE..EEE--GGGHH.HH CS
                            DAO 152 laraaealGveilegtevtglee...edgkvwgverttpgendaada..vVnaaGawsd.ll 207
                                    lar +++lG+ ++ gt  +++e     dg vw   r ++ge+  +da  v+ aaG+  + +l
  gi|121636165|ref|YP_976388.1| 209 LARMIADLGIAVHVGTGTESIESvkhSDGSVWARVRLSDGEV--IDAgvVIFAAGIRPRdEL 268
                                    566677888777777666666432226688887755555887..67777******8766644 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0021       1.9     220     265 ..      81     124 ..      60     137 .. 0.81
   2 ?    0.9   0.0      0.24   2.2e+02       3      25 ..     173     195 ..     173     196 .. 0.92
   3 ?    3.5   0.1     0.039        35     212     262 ..     208     262 ..     196     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                    TTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHH CS
                  Amino_oxidase 220 lrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvl 265
                                      +++++lntrV++i+r + + +v +  g+  ++D  v+++  ++ 
  gi|121636165|ref|YP_976388.1|  81 DQRVRLLLNTRVTQIDR-ATK-SVVTAAGQRHRYDTLVLATGSYAF 124
                                    56799************.444.4445578888*******9988765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHTTEEEEEEESSSS CS
                  Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardr 25 
                                    GL aA+ L ++G+++ v+E  +r
  gi|121636165|ref|YP_976388.1| 173 GLEAANALRQFGLQTHVVEMMPR 195
                                    999****************8777 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.039
                                    HHHHHHHTTTTEEEETSEEEEEEEE..ETTC...EEEEETTSTEEEESEEEE-S-H CS
                  Amino_oxidase 212 lpealaeelrgldirlntrVkeikr..egdg...vtvtledgevveaDaVvvTvpl 262
                                    l  ++ +  +g  ++++t   +i+   ++dg    +v+l+dgev++a  V+ ++ +
  gi|121636165|ref|YP_976388.1| 208 LLARMIA-DLGIAVHVGTGTESIESvkHSDGsvwARVRLSDGEVIDAGVVIFAAGI 262
                                    5555666.699999999999999999966666699****************99876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0056         5     121     166 ..      81     123 ..      76     128 .. 0.83
   2 ?    5.4   0.2    0.0071       6.4       4      35 ..     165     196 ..     163     208 .. 0.87
   3 ?   -3.7   0.0       4.1   3.7e+03     376     391 ..     293     308 ..     290     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0056
                                    HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                    HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                    +++v+l l+t+v+++++ +++   v++  +++ + d+lvlAtG+ +
  gi|121636165|ref|YP_976388.1|  81 DQRVRLLLNTRVTQIDRATKS--VVTA-AGQRHRYDTLVLATGSYA 123
                                    689************776666..5555.899************865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0071
                                    EEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like   4 iviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                    +viGgG  Gl aA ++++ g ++ ++e +++l
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEMMPRL 196
                                    8**************************99886 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.1
                                    TTEEE-GGGBSEEE-T CS
                    HI0933_like 376 pgLffaGEvlDvegvt 391
                                    p+++ +GEv  ++g +
  gi|121636165|ref|YP_976388.1| 293 PDIYAVGEVAAIDGRC 308
                                    899*******999976 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4     8e-05     0.071       1      31 [.     166     196 ..     166     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                    ++G+Gl Gl aA +L++ g++ +++e+ +rl
  gi|121636165|ref|YP_976388.1| 166 VIGGGLLGLEAANALRQFGLQTHVVEMMPRL 196
                                    8*************************98886 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0035       3.1       8      46 ..      14      69 ..      11     122 .. 0.61
   2 ?    4.7   0.1     0.044        40      11      38 ..     165     192 ..     161     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                  NAD_binding_7  8 kkvlvvGgGevAarkvrklleag....akvtvvapevkeele.............e 46
                                   ++++vvG G v+ r v+ + + +     ++tv+a+e  ++ +              
  gi|121636165|ref|YP_976388.1| 14 REIVVVGHGMVGHRLVEAVRARDadgsLRITVLAEEGDAAYDrvgltsyteswdrA 69
                                   789**************999888223346999999954444355444444444442 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                  NAD_binding_7  11 lvvGgGevAarkvrklleagakvtvvap 38 
                                    +v+GgG ++++ ++ l ++g + +vv  
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEM 192
                                    79*******************9999854 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00011       0.1       5      34 ..     165     194 ..     163     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                    +++G+G+ Gl +a+ L++ G ++++ve + 
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEMMP 194
                                    69************************9875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.021        19       1      21 [.      16      36 ..      16      54 .. 0.78
   2 ?    4.5   0.1     0.045        40       2      35 ..     165     198 ..     164     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                                   EEEES-SHHHHHHHHHHHHTT CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLsegg 21
                                   i+++G+G vG +l+e ++++ 
  gi|121636165|ref|YP_976388.1| 16 IVVVGHGMVGHRLVEAVRARD 36
                                   89**************99954 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.045
                                    EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerve 35 
                                    ++iG G +G + a+ L++ g  +  v++  ++ ++
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQfGL-QTHVVEMMPRLMA 198
                                    89****************776.6999998887644 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.74   6.6e+02       1      31 [.      17      46 ..      17      71 .. 0.85
   2 ?    8.9   0.2    0.0016       1.4     116     154 ..      83     120 ..      69     122 .. 0.84
   3 ?   -1.1   0.1       1.9   1.7e+03       1      18 [.     165     182 ..     165     195 .. 0.84
   4 ?    5.5   0.1     0.017        15     104     154 ..     209     261 ..     206     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.74
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlf 31
                                   ++vG G+ G  ++e++ ar + + +l+it+ 
  gi|121636165|ref|YP_976388.1| 17 VVVGHGMVGHRLVEAVRAR-DADGSLRITVL 46
                                   699**********999999.59999999997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                  NAD_binding_9 116 tvevh.raevvdleeradgqavlladgaslaadaVvLAlG 154
                                    +v+++ +++v++++++ ++  v++a g+++++d +vLA+G
  gi|121636165|ref|YP_976388.1|  83 RVRLLlNTRVTQIDRATKS--VVTAAGQRHRYDTLVLATG 120
                                    5555438999999998876..799***************9 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                  NAD_binding_9   1 aivGaGprGlavlerLla 18 
                                    +++G+G  Gl ++++L +
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQ 182
                                    69*********9999865 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.017
                  NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgq..avlladgaslaadaVvLAlG 154
                                    +++++a+l   v+v   ++++++++ +++++  +v+l+dg+ ++a  V+ A G
  gi|121636165|ref|YP_976388.1| 209 LARMIADLGIAVHVGTGTESIESVKHSDGSVwaRVRLSDGEVIDAGVVIFAAG 261
                                    5666777766667777788999999999996458*****************99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       1.5   1.3e+03      28      43 ..      13      28 ..       4      38 .. 0.76
   2 ?   12.9   1.1   5.4e-05     0.048      32      75 ..     165     209 ..     147     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                   --EEEEESTSHHHHHH CS
                    AlaDh_PNT_C 28 pakvlviGgGvaGlqA 43
                                   + +++v+G G++G   
  gi|121636165|ref|YP_976388.1| 13 AREIVVVGHGMVGHRL 28
                                   4579*********765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.4e-05
                                    EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHHTTTCEC CS
                    AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDvrparl.eqleslgakfv 75 
                                    +viGgG  Gl+A+++ +++g ++ v+++ p+ + +q+++ g+  +
  gi|121636165|ref|YP_976388.1| 165 VVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMaQQIDEAGGALL 209
                                    79**************************99976256666777644 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.49   4.4e+02     188     221 ..      10      43 ..       4      57 .. 0.79
   2 ?    6.7   0.1    0.0039       3.5     288     340 ..      77     121 ..      72     124 .. 0.81
   3 ?    3.3   0.2     0.042        38     143     223 ..     106     193 ..      90     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.49
                    K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkvelkl 221
                                     +a+++i+VvG G  +  ++e + +r ++ +l++
  gi|121636165|ref|YP_976388.1|  10 PAAAREIVVVGHGMVGHRLVEAVRARDADGSLRI 43 
                                    67899*********99999999988877655544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                    K_oxygenase 288 kvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                    ++ g++r+rll n++v+++++ +k +         + + +++++d++vlATG 
  gi|121636165|ref|YP_976388.1|  77 DYAGDQRVRLLLNTRVTQIDRATK-S-------VVTAAGQRHRYDTLVLATGS 121
                                    577899***************997.2.......2233456899*********5 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.042
                    K_oxygenase 143 eeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee..........llakkriaVvGsGqSaaeifedllr 212
                                      ++++  +lvl++G+ + +P+v  +  +    +H  ++  + ++            + +  +V+G+G  + e ++ l +
  gi|121636165|ref|YP_976388.1| 106 AGQRHRYDTLVLATGSYAFVPPVPGHDLP---ACHVYRTFDDLDAiragaqrtldGGHTDGGVVIGGGLLGLEAANALRQ 182
                                    44566667799999999999988776554...444444444444444466676654455566788888888888887777 PP

                    K_oxygenase 213 rqkkvelklvt 223
                                       ++++  ++
  gi|121636165|ref|YP_976388.1| 183 FGLQTHVVEMM 193
                                    65555544444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.79   7.1e+02       2      19 ..      16      33 ..      15      53 .. 0.83
   2 ?    7.9   0.6    0.0029       2.6       4      42 ..     166     204 ..     165     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.79
                                   EEEE--SCCHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfa 19
                                   + v+G G++G+ + +++ 
  gi|121636165|ref|YP_976388.1| 16 IVVVGHGMVGHRLVEAVR 33
                                   78*********9987765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                                    EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                        3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekaleki 42 
                                    viG G++G + a+++ + gl++++v++ ++ +++  +++
  gi|121636165|ref|YP_976388.1| 166 VIGGGLLGLEAANALRQFGLQTHVVEMMPRLMAQQIDEA 204
                                    9**************************998887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (853 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.77u 0.27s 00:00:01.04 Elapsed: 00:00:00.42
# Mc/sec: 6076.75
//
Query:       gi|121636166|ref|YP_976389.1|  [L=118]
Description: nitrite reductase [NAD(P)H] small subunit nirD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-35  120.4   0.0    3.1e-35  120.3   0.0    1.0  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   1.7e-39   3.1e-35       2     103 ..      10     113 ..       9     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.7e-39
                                    EEEEEECCCS-TTB-EEEEE.TTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-B CS
                       Rieske_2   2 wvpvckledlvketgvaalv.dgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGe 80 
                                    w++ c++++l++++gv +l+ dg+qvalfrl++++v+A++n+dp+s+a+v+srG+vgd++g+ +v+sP+ kq f L++G+
  gi|121636166|ref|YP_976389.1|  10 WTTACAYDHLIPGRGVGVLLdDGSQVALFRLDDGSVHAVGNVDPFSGAAVMSRGIVGDRGGRAMVQSPILKQAFALDDGS 89 
                                    ********************889********************************************************* PP

                                    BSS-TTSB-BEE-EEES.TSEEEE CS
                       Rieske_2  81 cledeevslkvypvrve.dgkvev 103
                                    cl+d++vs++vyp+rv+ +g+++v
  gi|121636166|ref|YP_976389.1|  90 CLDDPRVSVPVYPARVTpEGRIQV 113
                                    *****************999*999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 670.45
//
Query:       gi|121636167|ref|YP_976390.1|  [L=174]
Description: bifunctional cobalamin biosynthesis protein cobU: cobinamide kinase + cobinamide phosphate guanylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-49  168.1   0.0    1.4e-49  167.9   0.0    1.0  1  CobU       Cobinamide kinase / cobinamide phosphate guanyltra
  ------ inclusion threshold ------
      0.059   13.4   0.0        0.1   12.7   0.0    1.4  1  Dynamin_N  Dynamin family


Domain annotation for each model (and alignments):
>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.0   1.6e-53   1.4e-49       1     169 []       3     174 .]       3     174 .] 0.94

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.6e-53
                           CobU   1 ilvtGgarSGKSefAeklaeeskekvvYiATaeal...DeemaeRiarHrerRpaeWetveepldlaealkeeekkevvL 77 
                                    ilvtGg+rSGKS++Ae+l+ + +++vvY+A +++    D ++++R+a Hr+rRp +W tve+ +d+a+al+e++  ++vL
  gi|121636167|ref|YP_976390.1|   3 ILVTGGVRSGKSTHAEALLGD-AADVVYVAPGRPAagsDPDWDARVALHRARRPPTWLTVET-ADVATALSEAR--SPVL 78 
                                    79****************986.699********99999************************.9******7775..7*** PP

                           CobU  78 vDcltlwltnllleeeaek.....veekleeeveellealkelkatvvlVsnEvglgvvpenalgrlfrdllGrlnqrla 152
                                    vDcl++wlt +++ e  ++     v + le++++ l++al+ l+ t ++V+nEvglgvvp++++g lfrdllG++n+r+a
  gi|121636167|ref|YP_976390.1|  79 VDCLGTWLTAIMDGEALWSaatadVYAVLEARLDGLCAALTGLP-TAIVVTNEVGLGVVPSHSSGVLFRDLLGTINRRVA 157
                                    *************999888988888889999*********9987.6788******************************* PP

                           CobU 153 aeadevvlvvaGlplkl 169
                                    a +dev+lv+aG  lkl
  gi|121636167|ref|YP_976390.1| 158 AVCDEVHLVIAGRVLKL 174
                                    ************99886 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05       0.1       1      22 [.       3      24 ..       3      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                   i+v G + sGKS+ ++aLlg++
  gi|121636167|ref|YP_976390.1|  3 ILVTGGVRSGKSTHAEALLGDA 24
                                   89******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1317.86
//
Query:       gi|121636168|ref|YP_976391.1|  [L=494]
Description: cobyric acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-44  150.0   0.0      9e-44  149.4   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.7e-23   82.4   0.0    4.2e-23   81.8   0.0    1.2  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-20   74.3   0.0    4.4e-20   72.3   0.0    1.8  1  AAA_26         AAA domain
     0.0067   16.1   0.0     0.0095   15.6   0.0    1.2  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.37   10.6   0.0    1.7  2  GATase         Glutamine amidotransferase class-I
       0.15   11.8   0.0       0.27   11.0   0.0    1.4  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.0     3e-47     9e-44       1     193 [.     255     429 ..     255     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 3e-47
                       GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlg 80 
                                    ++av+rlp+isn+td+d+L  ep+ +v f++   ++l +dadl++lpG++ ti+dla+lr+++ld+a+  +++ag+p+lg
  gi|121636168|ref|YP_976391.1| 255 RVAVVRLPRISNFTDVDALGLEPDLDVVFAS-DPRAL-DDADLIVLPGTRATIADLAWLRARDLDRALLVHVAAGKPLLG 332
                                    69*****************************.9****.56**************************************** PP

                       GATase_3  81 iCGGlqmLGeeiedpegveg...eageveglglLdietefekekltgqvegevelaaegeevkGyEiHsGrtilkekakp 157
                                    iCGG+qmLG+ i+dp+g+eg   +++eveglglLd+et+f+ +k+++  +ge      g + +GyEiH+Gr +++++a++
  gi|121636168|ref|YP_976391.1| 333 ICGGFQMLGRVIRDPYGIEGpggQVTEVEGLGLLDVETAFSPHKVLRLPRGE----GLGVPASGYEIHHGRITRGDTAEE 408
                                    *******************9988888********************999999....5689**********9999987777 PP

                       GATase_3 158 llkvkvggnngekdGavkksedgnvlGtYlHglfdn 193
                                    +l             a     dg v+Gt  Hg ++ 
  gi|121636168|ref|YP_976391.1| 409 FLGG-----------AR----DGPVFGTMWHGSLEG 429
                                    6643...........33....346689999988776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   1.4e-26   4.2e-23       1     118 [.       4     233 ..       4     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.4e-26
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.....HTTEB-HHHH..................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxx..................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.....leglendiep..................... 54 
                                    +++a+t++++GK+ ++a+L+ralarrg rV++++a++++nn+++       g+e+ +++                     
  gi|121636168|ref|YP_976391.1|   4 LLVAGTTSDAGKSAVTAGLCRALARRGVRVAPFKAQNMSNNSMVcrgpdGTGVEIGRAQwvqalaarttpeaamnpvllk 83 
                                    589*****************************************766555555555555********************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121636168|ref|YP_976391.1|  84 pasdhrshvvlmgkpwgevassswcagrralaeaacrafdalaarydvvvaegagspaeinlragdyvnmglarhaglpt 163
                                    ******************************************************************************** PP

                                    ....CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCH CS
                                    ....xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ....dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeav 118
                                        d++r +++++a+ +++all      ++ag+v+n+++g+  + ll  +l++l++ +g++v+g +p+  ++
  gi|121636168|ref|YP_976391.1| 164 ivvgDIDR-GGVFAAFLGTVALLaaedqALVAGFVVNKFRGD--SDLLAPGLRDLERVTGRRVYGTLPWHPDL 233
                                    ********.9*********9999*******************..***********9988**********9987 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   1.5e-23   4.4e-20       2     194 ..       3     233 ..       2     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.5e-23
                         AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie............ededselikellgldqtyelpeplal 69 
                                    +++v+gt+ ++GK++v++gL+ral r+gv+v+ fK  +  ++            e +++++++ l+  ++++ +++p++l
  gi|121636168|ref|YP_976391.1|   3 GLLVAGTTSDAGKSAVTAGLCRALARRGVRVAPFKAQNMSNNsmvcrgpdgtgvEIGRAQWVQALAARTTPEAAMNPVLL 82 
                                    589********************************8766666788988877776667*********************99 PP

                         AAA_26  70 saplspelaarqegedidlekiv.......................kelekdadivvVEGagglgvpitee..llnadia 124
                                    + p+s++ +       + + k +                       ++l++++d+vv EGag+  +  ++    +n  +a
  gi|121636168|ref|YP_976391.1|  83 K-PASDHRSHV-----VLMGKPWgevassswcagrralaeaacrafDALAARYDVVVAEGAGSPAEINLRAgdYVNMGLA 156
                                    7.666665443.....333333333333444799999999999********************99775554479****** PP

                         AAA_26 125 knlgapvilVarggl.gtinqllltiealrqknvr.vlGvilNkvrnpe.....nvetlekksgipvlGvvPylpdl 194
                                    ++ g+p+i+V+ +++ g +++ l t+++l  ++   v+G ++Nk+r +       ++ le  +g +v+G++P+ pdl
  gi|121636168|ref|YP_976391.1| 157 RHAGLPTIVVGDIDRgGVFAAFLGTVALLAAEDQAlVAGFVVNKFRGDSdllapGLRDLERVTGRRVYGTLPWHPDL 233
                                    *************9945889*********8765544***********95577779********************98 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.2e-06    0.0095      74     163 ..     288     376 ..     269     420 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-06
                                    HHHHHHHHHSSEEEE--S.-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG-S---B-- CS
                  Peptidase_S51  74 eeieeklleadviyvgGG.ntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsysdspikapesfeaL 152
                                    +++++    ad+i++ G   t+  l+ l+ ++ld++l+ +v++g+++ G+  G  + g+ i+     + p  + +++e+L
  gi|121636168|ref|YP_976391.1| 288 RALDD----ADLIVLPGTrATIADLAWLRARDLDRALLVHVAAGKPLLGICGGFQMLGRVIRDPYGIEGPGGQVTEVEGL 363
                                    55555....7888777762466668889**********************************9999999*9999****** PP

                                    --SSS..EEETTT CS
                  Peptidase_S51 153 gLvkf..qivPHy 163
                                    gL++    + PH 
  gi|121636168|ref|YP_976391.1| 364 GLLDVetAFSPHK 376
                                    **87511567886 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   3.3e+03       4      31 ..      12      40 ..      11      54 .. 0.69
   2 ?   10.6   0.0   0.00012      0.37      64      86 ..     321     342 ..     269     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                   ESSTS.THHHHHHHHHHTT-EEEEEETTS CS
                         GATase  4 Dnyds.vtenlvhalvelgvkvevvpida 31
                                   D+++s vt  l++al+++gv+v  ++ + 
  gi|121636168|ref|YP_976391.1| 12 DAGKSaVTAGLCRALARRGVRVAPFKAQN 40
                                   5555426778999***9998887776654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                    HHHHCTSTS-EEEETHHHHHHHH CS
                         GATase  64 ikearenkiPiLGICLGmQllai 86 
                                    + +++ +++P+LGIC G+Q+l+ 
  gi|121636168|ref|YP_976391.1| 321 LVHVA-AGKPLLGICGGFQMLGR 342
                                    33334.59************986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.9e-05      0.27      97     118 ..     321     340 ..     300     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.9e-05
                  Peptidase_C26  97 LiraalergvPilgiCrGlqll 118
                                    L+   +++g+P+lgiC G+q+l
  gi|121636168|ref|YP_976391.1| 321 LV--HVAAGKPLLGICGGFQML 340
                                    33..35789***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3313.91
//
Query:       gi|121636169|ref|YP_976392.1|  [L=556]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-57  191.5  21.0    9.7e-57  191.5  21.0    2.3  2  PPE            PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5  21.0   5.4e-61   9.7e-57       1     157 [.       8     164 ..       8     165 .. 0.99
   2 ?   -1.2   0.1      0.11     2e+03      30      67 ..     428     465 ..     419     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 5.4e-61
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall++Gpg+gpll +a+ W++L+  +a++a+el+++la+++a++W+Gp++a ++aa++pylaWL +a+a+++
  gi|121636169|ref|YP_976392.1|   8 ASPPEVHSALLSSGPGPGPLLVSAEGWHSLSIAYAETADELAALLAAVQAGTWDGPTAAVYVAAHTPYLAWLVQASANSA 87 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    ++A++ e+aa+aY +Alaam+++ae+ an+a + +l+atnffG+nt++Ia +e +y++mw+q+a++ma+Y+a+s+aa
  gi|121636169|ref|YP_976392.1|  88 AMATRQETAATAYGTALAAMPTLAELGANHALHGVLMATNFFGINTIPIALNESDYARMWIQAATTMASYQAVSTAA 164
                                    **************************************************************************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHH CS
                            PPE  30 LaaelasaaaelesvlaelaaeaWqGpssaamaaaaap 67 
                                    L  +l+saa++ ++v +++++++ +  s++a aaaaap
  gi|121636169|ref|YP_976392.1| 428 LVGDLNSAAQARKAVGTGVRKKTPEPDSAEAPAAAAAP 465
                                    66788999999999999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3725.81
//
Query:       gi|121636170|ref|YP_976393.1|  [L=72]
Description: hypothetical protein BCG_0295 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 560.76
//
Query:       gi|121636171|ref|YP_976394.1|  [L=151]
Description: hypothetical protein BCG_0296c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-25   87.3   0.1      9e-25   87.0   0.1    1.1  1  TetR_C_16  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.1     5e-29     9e-25       2     107 .]      39     144 ..      38     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 5e-29
                                    THHHHHHHHHHHHHHHHT-HHHHHHHHH--------HHHHHHHHHHHHHHCTTTS-STTHHHHHHHHHHHHHHHHHHHHT CS
                      TetR_C_16   2 elGerlvravlevwepearepllallrsalsseeaaellrefleeqvlaplaarlggpdaelRaalvasqllGlalaRyv 81 
                                    ++G+r +  ++++w++++++p++a   + ++  ++ae++++++   v+ pl + lg+++ + Ra+l+a+ql+Gl+++Ry 
  gi|121636171|ref|YP_976394.1|  39 QVGRRTLYVLITTWDAAGGGPFAASAIATTGLAKTAEIVQSMFIGPVFNPLLKMLGADKIAIRASLCAAQLVGLGIMRYG 118
                                    79****************************************************************************** PP

                                    S--TTCCCS-HHHHHHHHHHHHHHHH CS
                      TetR_C_16  82 lrleplasasreelvalvgptlqryL 107
                                    +r epl s+s+e lv+ +gpt+qryL
  gi|121636171|ref|YP_976394.1| 119 VRSEPLHSMSVEMLVDAIGPTMQRYL 144
                                    *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1042.99
//
Query:       gi|121636172|ref|YP_976395.1|  [L=247]
Description: hypothetical protein BCG_0297c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-26   92.0   0.3    6.9e-17   61.7   0.1    2.8  2  CbiX      CbiX


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.1   3.8e-21   6.9e-17       1     106 [.       8     104 ..       8     105 .. 0.96
   2 !   26.9   0.0   2.5e-10   4.5e-06       2     106 ..     124     220 ..     123     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.8e-21
                                    -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--S CS
                           CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeae 80 
                                    HG+r+p++ + ++++a+++ +  + ++v+++f+++  ps  e+l++l    ++  +vvP+fl++G+hv++D+p  +++  
  gi|121636172|ref|YP_976395.1|   8 HGTRRPSGVAMIADIAAQVSALVD-RTVQVAFVDVLGPSPSEVLSAL---SCRPAIVVPAFLSRGYHVRTDLPAHVAA-- 81 
                                    ************************.*******************999...*************************987.. PP

                                    SSS-TTEEEEE---CCCSCCHHHHHH CS
                           CbiX  81 eahpkdveieytepLGthplvaevlk 106
                                    +ahp   ++++t++LG+  ++a+++ 
  gi|121636172|ref|YP_976395.1|  82 SAHP---HVTVTPALGPCREIAQIVT 104
                                    7777...78*************9986 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 2.5e-10
                                    STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-.....SBSEEEEEEESSSSSHHHHTHHHHHC CS
                           CbiX   2 GSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeq.....gvkrivvvPlflfaGvhvkeDIpeel 76 
                                    G++d+++++++++    + e  +  +v +gf+    p++++a+++++++     g++r+vv  ++l++G + ++      
  gi|121636172|ref|YP_976395.1| 124 GASDRRARADLHTTRTLVSELTG-SWVDMGFAGTGGPDVRTAVQRARDRaeanrGARRVVVASFLLAEGLFQER------ 196
                                    899**********9999999999.*******************99998899999*****************999...... PP

                                    T--SSSS-TTEEEEE---CCCSCCHHHHHH CS
                           CbiX  77 eeaeeahpkdveieytepLGthplvaevlk 106
                                     + ++  +     ++t+pLGthp +a++++
  gi|121636172|ref|YP_976395.1| 197 -LRASGAD-----VVTRPLGTHPGLAQLVA 220
                                    .4445555.....689********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1813.89
//
Query:       gi|121636173|ref|YP_976396.1|  [L=381]
Description: bifunctional uroporphyrinogen-III synthetase/response regulator domain-containing protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-38  132.3   0.0    2.5e-38  131.7   0.0    1.2  1  HEM4         Uroporphyrinogen-III synthase HemD
    1.6e-12   47.3   0.0      6e-12   45.5   0.0    2.0  2  Trans_reg_C  Transcriptional regulatory protein, C terminal


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.0   2.8e-42   2.5e-38       2     230 ..      24     268 ..      23     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 2.8e-42
                                    HHHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH...HTT---HHHHHCSEEE CS
                           HEM4   2 elaealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealk...reeedvkalaslkvaa 78 
                                    el ++l+++Gae++ +P+i++ + +d++el++  ++l a+ +d+l++ +  +++ +++a++    ++e++++l+s+++++
  gi|121636173|ref|YP_976396.1|  24 ELCALLRRQGAEVCSAPAIKMIALPDDDELQNNTEALIADPPDILVAHTGIGFRGWLAAAEgwgLANELLESLSSARIIS 103
                                    7889**************************************************************************** PP

                                    SSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---E.EEEEE.-SS.S-....-HHHHHHHHHTTEEEEEE-SEEEE CS
                           HEM4  79 vGpaTaraLeelglrvdlvpseegtaegLaeelaeslag.krvll.lrgeia....rddlaegLeergaevdevevYetv 152
                                    +Gp+++ aL+++glr ++ p  ++++ +++e+l es  + +r+ + l+g        +++  gL+ +ga+v+ + vY+++
  gi|121636173|ref|YP_976396.1| 104 RGPKATGALRAAGLREEWSPD-SESSHEVLEYLLESGVSrTRIAVqLHGAADswdpFPEFLGGLRFAGAQVVPIRVYRWK 182
                                    ********************9.888899999888877776997777554433344499999******************4 PP

                                    E-HH..HHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH.......HHHCTSEEEEESHHHHHHHHHTT---SEEET CS
                           HEM4 153 paee..epeelkealkagevdavvftSpstvrnllellkdeg.......delkevkvaaiGptTaealkklglkvdvvae 223
                                    pa      ++l++ + ++++dav+ftS+ +++++le++++         +  ++v+++++Gp+T++ l + g+++   +e
  gi|121636173|ref|YP_976396.1| 183 PAPLggVFDHLVTGIARRQFDAVTFTSAPAAAAVLERSRELDiedqllaALRTDVHAMCVGPVTSRPLIRKGVPT-SAPE 261
                                    44334599*******************************999******9999***********************.999* PP

                                    S--HHHH CS
                           HEM4 224 eptaegl 230
                                    +++ ++l
  gi|121636173|ref|YP_976396.1| 262 RMRLGAL 268
                                    9999987 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   9.6e+03      11      20 ..     129     138 ..     125     151 .. 0.67
   2 !   45.5   0.0   6.6e-16     6e-12       5      77 .]     306     372 ..     302     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                    HHHHHHHHHT CS
                    Trans_reg_C  11 fklLelLlen 20 
                                     ++Le+Lle+
  gi|121636173|ref|YP_976396.1| 129 HEVLEYLLES 138
                                    5677777764 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 6.6e-16
                                    E-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   5 eltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                     l+p  +++L++L+++pg vvsr +Ll+ + g+ +  d+++vd+++ rLR  L+d    ++ + tv ++GYrl
  gi|121636173|ref|YP_976396.1| 306 PLSPSGMAILRALVHRPGGVVSRGDLLRVLPGDGS--DTHAVDTAVLRLRTALGD----KNIVATVVKRGYRL 372
                                    68999************************999997..******************....57**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2706.98
//
Query:       gi|121636174|ref|YP_976397.1|  [L=469]
Description: integral membrane nitrite extrusion protein narK3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-15   54.8  53.7      7e-15   54.8  53.7    2.3  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8  53.7   3.9e-19     7e-15       9     350 ..      40     407 ..      38     408 .. 0.77
   2 !    1.2   9.7    0.0078   1.4e+02     118     174 ..     390     447 ..     383     466 .. 0.63

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 3.9e-19
                          MFS_1   9 alarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllllfa... 82 
                                    +++ + l++++ l + ++ +g+s+    ll ++ +l+ a + +p+ + + +fG r  +++ +l+l++ + + +ll+a   
  gi|121636174|ref|YP_976397.1|  40 GFSVWSLWSVMVLfMPTSVYGFSAGDKFLLGATATLVGACLRFPYTFATAKFGGRNwTIFSALVLLIPTvGSILLLAnpg 119
                                    5667778888888777999*********************************9888466666666666655666666645 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                     +lw+ lv+ +l+Glg g+ f+a+++ i + fp++ +g a++l ++g +lG+ +  l+g l+++ +g r +++++ai ++
  gi|121636174|ref|YP_976397.1| 120 LPLWPYLVCGALAGLG-GGNFAASMTNINAFFPQRLKGAALALNAGGGNLGVPMVQLVGLLVIATAGDREPYWVCAIYLV 198
                                    55889***********.89999999******************************************************* PP

                          MFS_1 163 lafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgl 240
                                    l++v  l+++l++++ +e + +               +  +a+++ p+ w  +i+ll+++  f ++  +++ +  +vl +
  gi|121636174|ref|YP_976397.1| 199 LLAVagLGAALYMDNLTEYRIELN-------------T-MRAVVSEPHTW--VISLLYIG-TFGSFIGFSFAF-GQVLQI 260
                                    **9988888888777777777644.............2.779999**996..55555554.333333333333.555555 PP

                          MFS_1 241 s..........glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.........ssav 301
                                    +          + l a+ +  l+ l+g  +++ +g+l+dr+g  r +l a+ ++lla+ +l+ ++++         + ++
  gi|121636174|ref|YP_976397.1| 261 NfiasgqstaqASLHAAQIAFLGPLLGSLSRIYGGKLADRIGGGRVTLAAFCAMLLATGILISASTFgdhlagpmpTATM 340
                                    555557778895599999999999999999*************9999999999999999999999999999998883333 PP

                          MFS_1 302 llll.....vlvliGfglgfv...fpsllalasdla..........ppeeagtasglfntagslgga 350
                                    ++++     +++l G+g g v    ps++ + s+++          +++++g+++gl++ +g+lgg+
  gi|121636174|ref|YP_976397.1| 341 VGYVigftaLFILSGIGNGSVykmIPSIFEARSHSLqiseaerrqwSRSMSGALIGLAGAVGALGGV 407
                                    3333455545555777888885555555555555555544444444448888999999988888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.0078
                          MFS_1 118 ergraigllsagfslGa.ilgpllggllasslgWravfyilaivsllafvlfllllpe 174
                                      g  igl++a  +lG   +  +l    ++s+  +++f+++++++l+a vl ++ +++
  gi|121636174|ref|YP_976397.1| 390 MSGALIGLAGAVGALGGvGVNLALRESYLTSGTATSAFWAFGVFYLVASVLTWAIYVR 447
                                    5666677777766666633334444444457779**************9964444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3192.16
//
Query:       gi|121636175|ref|YP_976398.1|  [L=181]
Description: aminoglycoside 2'-n-acetyltransferase aac [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-11   42.9   0.1    6.6e-11   42.4   0.1    1.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      3e-07   30.7   0.1    3.7e-07   30.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.5e-05   23.5   0.1    8.9e-05   22.8   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00043   20.2   0.0    0.00055   19.9   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   13.7   0.1       0.13   12.2   0.1    1.6  2  DEK_C            DEK C terminal domain


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.1   1.8e-14   6.6e-11       7     125 ..      18     131 ..      13     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.8e-14
                                    GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGT CS
                 Acetyltransf_9   7 eedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehr 86 
                                    +e  +++ +++  aF+ + +++      ++ +l+   + +++ +g +++++a+++++l  +G+ l++++v gVav ++ r
  gi|121636175|ref|YP_976398.1|  18 SETRQDIRQMVTGAFAGDFTET-----DWEHTLGG-MHALIWHHGAIIAHAAVIQRRLIYRGNALRCGYVEGVAVRADWR 91 
                                    5667889999999999999986.....34566665.45566779************************************ PP

                                    TS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT- CS
                 Acetyltransf_9  87 grgvlskLlaraleemreegqplsllfP..ssipiYrrfGy 125
                                    g+ ++s+Ll+++ + mr   ++l  l    +++++Y + G+
  gi|121636175|ref|YP_976398.1|  92 GQRLVSALLDAVEQVMRG-AYQLGALSSsaRARRLYASRGW 131
                                    *****************7.6667777664466899*99999 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1     1e-10   3.7e-07      34     116 ..      47     130 ..      16     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1e-10
                                    EEEE.EEETTEEEEEEEEEEEET....TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHH CS
                 Acetyltransf_1  34 gllv.aeedgeliGfisllkipd....ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaa 108
                                    g  + + + g +i+++ + ++      ++ +++y+e++aV+ ++rg+ l saLl+a+e+ +r        l   ++  +a
  gi|121636175|ref|YP_976398.1|  47 GMHAlIWHHGAIIAHAAVIQRRLiyrgNALRCGYVEGVAVRADWRGQRLVSALLDAVEQVMRGA----YQLGALSSSARA 122
                                    33334778899*****99999999999889*****************************99999....5666668999** PP

                                    HHHHHHTT CS
                 Acetyltransf_1 109 irlYeklG 116
                                    +rlY   G
  gi|121636175|ref|YP_976398.1| 123 RRLYASRG 130
                                    ****7677 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.5e-08   8.9e-05      24      74 ..      68     131 ..      46     132 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                                    S..........TCTEEEEE-GGGTTSSHHHHHHHHTT...SE.EEEEEEEETHH.HHHHHHHHTTE CS
                 Acetyltransf_7  24 d..........aeitrlaVdpeyrgkGiGraLleaae...kg.iileqlelnae.kaikfYeklGF 74 
                                               ++ +++aV+ ++rg+ + +aLl+a+e   +g ++l    l+++ +a+++Y++ G+
  gi|121636175|ref|YP_976398.1|  68 RliyrgnalrcGYVEGVAVRADWRGQRLVSALLDAVEqvmRGaYQLG--ALSSSaRARRLYASRGW 131
                                    2344444444446667******************8444666622223..232224999*****995 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.5e-07   0.00055      27     106 ..      54     131 ..      18     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.5e-07
                Acetyltransf_10  27 eegealllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGF 106
                                    ++g+ + ++a  + +++  ++  + ++++ ++V+ ++rgq + +aLl+ave+ + +  ++    + +s  a+++Y + G+
  gi|121636175|ref|YP_976398.1|  54 HHGAIIAHAAVIQRRLIYRGNALRCGYVEGVAVRADWRGQRLVSALLDAVEQVM-RGAYQ-LGALSSSARARRLYASRGW 131
                                    44455555555555555444444445***************************9.55566.78999999**********9 PP

>> DEK_C  DEK C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.6e-05      0.13      14      40 ..      11      37 ..       8      40 .. 0.88
   2 ?   -2.1   0.0         1   3.7e+03       6      17 ..      99     110 ..      97     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                          DEK_C 14 LreaDLdtvTkkkvReqLeeklgvdLs 40
                                     +aDLd+ T+ ++R++++  + +d +
  gi|121636175|ref|YP_976398.1| 11 VHTADLDSETRQDIRQMVTGAFAGDFT 37
                                   568*****************9999865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                          DEK_C   6 irkaireiLrea 17 
                                    + +a+++++r a
  gi|121636175|ref|YP_976398.1|  99 LLDAVEQVMRGA 110
                                    667999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1379.80
//
Query:       gi|121636176|ref|YP_976399.1|  [L=300]
Description: hypothetical protein BCG_0301c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-82  274.5   0.1    1.1e-81  274.3   0.1    1.0  1  CT_A_B    Carboxyltransferase domain, subdomain A and B


Domain annotation for each model (and alignments):
>> CT_A_B  Carboxyltransferase domain, subdomain A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.3   0.1   6.3e-86   1.1e-81       1     263 [.      26     283 ..      26     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 274.3 bits;  conditional E-value: 6.3e-86
                                    GT----S-SSHHHHHHHHHHTTS-TTS-EEEEESC-EEEEES.S-EEEEEEESCEEEEETTEEE-SSCEEEE-TT-EEEE CS
                         CT_A_B   1 lGvprsGamDrlalrlANrlvgNeegaaaLEitlggpelrfe.edavvavtGadleatldgepvplwepvevkaGdvLkl 79 
                                    lGv rsGa+Dr++++lANrlv N+++ a++E+t+gg++ r++ +d+ +avtGad+++t++g  v +++ ++v++G+v++l
  gi|121636176|ref|YP_976399.1|  26 LGVGRSGAADRRSHTLANRLVANPDDWATVEVTFGGFSARVRgGDVDIAVTGADTDPTVNGIMVGTNSIHHVRDGQVISL 105
                                    6****************************************6499*********************************** PP

                                    EEESSECEEEEEETT-BE---BTTB-S-BTTTTBSTTTTS---TT-EEEBSSSTT--S-C.BGGCS---SSCSEEEEEEE CS
                         CT_A_B  80 gaakaGlraYLavaGgldvpevlgSrStdllaglGgleGraLkagdvLplgeaaaaaaakakeleaaapeeseeeevrvv 159
                                    g+++aGlr+YLav+Gg+ v++vlgSrS d+++++G+    +L+agdvLp+ge++++ ++    +++ a+ e++  e+rvv
  gi|121636176|ref|YP_976399.1| 106 GTPRAGLRTYLAVRGGVCVEPVLGSRSYDVMSAIGPS---PLRAGDVLPVGEHTDDYPEL--DQAPVAAIEEHLVELRVV 180
                                    ************************************9...******************96..333333333344457*** PP

                                    E-TTGCCB-HHHHHHHHHS-EEEECEECSSEEEEESGG.SSC..S.TEEEEEE--TTEEEE-CTTEEEEE-TTS-SEEEE CS
                         CT_A_B 160 pGpqadlfteealeallssewtvsaesdRmGvrLdGeagler..kesellsegvvlGaiqvppdgqpivllaDhqttGGY 237
                                    pGp++d++   + +al+++ w  s++sdR+G+rL+G++ l++   +++l+ egv++Gaiqvpp+g p++l++Dh+ tG Y
  gi|121636176|ref|YP_976399.1| 181 PGPRDDWLV--DPDALVHTIWMASNRSDRVGMRLQGRP-LQHrwPDRQLPGEGVTRGAIQVPPNGLPVILGPDHPITGSY 257
                                    ********5..6689*********************55.66635337********************************* PP

                                    EEEEEE-GGGHHHHTT--TTSEEEEE CS
                         CT_A_B 238 pkiatvisadldklaQlrpgdkvrFe 263
                                    p++++++++d+dk+aQ+rpg+ vr++
  gi|121636176|ref|YP_976399.1| 258 PVVGVITDEDIDKVAQIRPGQYVRLH 283
                                    ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2290.28
//
Query:       gi|121636177|ref|YP_976400.1|  [L=210]
Description: hypothetical protein BCG_0302c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-52  178.8   0.1    1.2e-52  178.6   0.1    1.0  1  CT_C_D    Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.1   6.7e-57   1.2e-52       2     202 .]       8     199 ..       7     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 6.7e-57
                                    EEEEETTTEEEEEE-SS--HHHHHHHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH.---- CS
                         CT_C_D   2 rirplGdeallvefgeeisealskrvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkalleeaeeea 81 
                                    +++ +Gd+al++++      ++ +++ a+++alra+alpgvv++v a r++lv++d  ++ +   +++l++l  ++e+ a
  gi|121636177|ref|YP_976400.1|   8 TVLDYGDHALMLQC------DSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPRY-QGVTRQRLRRLRVTPEAVA 80 
                                    57789*********......788899******************************9994.7788899999988866666 PP

                                    -----E.EEEEEEESTTT-TTHHHHHHHHTS-HHHHHHHHHHS-EEEEEE-SSTT-EEE----GGG-----SS--S-B-T CS
                         CT_C_D  82 aeesrl.veipvcYdgevgpDLeevaelnglsveevirlhtaaeyrvaflGfapGfaylggldprlavpRrasPrtrvpa 160
                                    a++ r+ + i+v+Yd   gpDL+eva+++gl++++vi++hta+ +r  f G apGfayl + dp+l+vpRr + rt++p 
  gi|121636177|ref|YP_976400.1|  81 AADHRCdLVIDVVYD---GPDLAEVARCTGLTTAAVINAHTATGWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPP 157
                                    66666559*******...************************************************************** PP

                                    TEEEEETTEEEEE-S-B---SEEEEEE-S-SB-TTSSSSBS- CS
                         CT_C_D 161 gsVgiageqtgiyplesPGGWqliGrTplplfdpdreppall 202
                                    gsV++a+ +++iyp ++P+ Wq+iG+T++ l+d dr +pall
  gi|121636177|ref|YP_976400.1| 158 GSVALADGFSAIYPSQAPSDWQIIGHTDAVLWDVDRPQPALL 199
                                    ***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1688.25
//
Query:       gi|121636178|ref|YP_976401.1|  [L=330]
Description: periplasmic iron-transport lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-40  138.0   0.5    4.3e-40  137.8   0.5    1.0  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.035   13.9   1.9      0.035   13.9   1.9    2.1  2  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   0.5   4.8e-44   4.3e-40       2     234 ..      60     297 ..      59     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 4.8e-44
                                    EE-SHHHHHHHHHT....T-GGGEEEB-GGG--GGGGGGT...TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGH CS
                   Peripla_BP_2   2 aslspsvteillal....Gatdkvvgvdtttsdpldadklee.aivevgadgeidvEklaalkPDlvilskglgltdede 76 
                                    +s +++  + lla+     a   ++g++ ++++p++a+kl    +++++ d+ i ++++aalkPDl+++ + + + ++++
  gi|121636178|ref|YP_976401.1|  60 VSAGYTEQDDLLAVdvvpIAVTDWFGDQPFAVWPWAAPKLGGaRPAVLNLDNGIQIDRIAALKPDLIVAINAG-VDADTY 138
                                    566666666666666777777889***************999*******************************.****** PP

                                    HHHHHHS-EEE----TTS.HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE- CS
                   Peripla_BP_2  77 ellksgiptvivessntg.eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvag 155
                                    ++l++++ptv++  + ++ e +k+q+r +g+++   d+++ l++ +d+k+aa+ ++++ +  k++l++ g  ++g vva+
  gi|121636178|ref|YP_976401.1| 139 QQLSAIAPTVAQSGGDAFfEPWKDQARSIGQAVFAADRMRSLIEAVDQKFAAVAQRHPRWRGKKALLLQGRLWQGNVVAT 218
                                    *************999999************************************************************* PP

                                    TTSTTTHHHHTS--EESTTT--..STT-EEE-HHHHHH..H--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-E CS
                   Peripla_BP_2 156 snsyigdlldalgieniaaesk..kseyeeisaEqila..sdpdvifvsgraeadnktgleflkenpllaelpAvkngrV 231
                                      ++ +d+l+++g+ ++++ ++   ++++ i++++i+a  +++dv+++++       ++ ++l+++p+ a+  A +++r 
  gi|121636178|ref|YP_976401.1| 219 LAGWRTDFLNDMGLVIADSIKPfaVDQRGVIPRDHIKAvlDAADVLIWMTE----SPEDEKALLADPEIAASQATAQRRH 294
                                    *****************9999999***************************....*******************999987 PP

                                    EEE CS
                   Peripla_BP_2 232 yal 234
                                    + +
  gi|121636178|ref|YP_976401.1| 295 IFT 297
                                    766 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.9     4e-06     0.035       3      25 ..       6      28 ..       4      29 .. 0.90
   2 ?   -4.1   0.8       1.9   1.7e+04      10      14 ..      37      41 ..      37      42 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-06
                     TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                   SRR FL+ + AaaA ++++gc++
  gi|121636178|ref|YP_976401.1|  6 SRRGFLQVAEAAAATGLFAGCSS 28
                                   9********99999999999987 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.9
                     TAT_signal 10 gsAAa 14
                                   g+AA+
  gi|121636178|ref|YP_976401.1| 37 GGAAV 41
                                   45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2630.94
//
Query:       gi|121636179|ref|YP_976402.1|  [L=1209]
Description: 5-oxoprolinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     2e-203  676.5   4.9     2e-203  676.5   4.9    1.6  2  Hydantoinase_B  Hydantoinase B/oxoprolinase
   6.2e-115  383.4   2.7   6.2e-115  383.4   2.7    1.8  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.6e-60  203.9   0.2    2.5e-58  196.7   0.0    2.6  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.24   1.4e+03       5      50 ..     422     468 ..     419     478 .. 0.76
   2 !  676.5   4.9  3.3e-207    2e-203       1     515 [.     694    1200 ..     694    1201 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.24
                 Hydantoinase_B   5 levfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadg.elv 50 
                                    ++ ++n++++i  + g+ + r a +++    +  +ca+ da g ++v
  gi|121636179|ref|YP_976402.1| 422 VANMANAVKKISVQKGHDVTRYALTTFGGAGGQHACAVADALGiRTV 468
                                    56677888888888888888888888888888888888888775555 PP

  == domain 2  score: 676.5 bits;  conditional E-value: 3.3e-207
                 Hydantoinase_B    1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegel 78  
                                     Dp+ le+f+n +msiae+mg  l+ ta S+ni+erlDfscalfd+dg+lva+aphipvhlgsm ++vk+v++++ +++
  gi|121636179|ref|YP_976402.1|  694 DPVLLEIFNNLFMSIAEQMGFRLEATAQSVNIRERLDFSCALFDPDGNLVANAPHIPVHLGSMGTTVKEVIRRRLSGM 771 
                                     9**********************************************************************999889* PP

                 Hydantoinase_B   79 kpGDvlltNdPyaggtHlpDitvitPvfhege..lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklvee 154 
                                     kpGDv+++NdPy+ggtHlpDitvitPvf  g   ++ffvasr+Hha+iGGitpGsmp+d++ei+eEG++++++ l e+
  gi|121636179|ref|YP_976402.1|  772 KPGDVYAVNDPYHGGTHLPDITVITPVFNTGGedVLFFVASRGHHAEIGGITPGSMPADSREIHEEGVLFDNWLLAEN 849 
                                     ****************************988789******************************************** PP

                 Hydantoinase_B  155 ge.leedvlelllanv...RtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelp 228 
                                     g+ +e++  +ll++++   R+p+ nl+Dl+Aqiaanq+g +++ ++i+++G d+v a+m++++dnae+avr+++ +l 
  gi|121636179|ref|YP_976402.1|  850 GRfREAETRRLLTEAPfgsRNPDTNLADLRAQIAANQKGVDEVGKMIDHFGRDVVAAYMRHVQDNAEEAVRRVIDRLD 927 
                                     **99999999999999************************************************************** PP

                 Hydantoinase_B  229 dgtyeaedylddgipikvtvtidgde..atvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpie 304 
                                     +g y+++  +d g +i+v++t+d+    at+Dftgts q+++n+Nap++v+ +av+yv+r+lv++diplN+Gclrp++
  gi|121636179|ref|YP_976402.1|  928 NGAYRYR--MDSGATIAVRITVDRAArsATIDFTGTSAQLDTNFNAPTSVVNAAVLYVFRTLVADDIPLNDGCLRPLR 1003
                                     **99977..999*********9998889************************************************** PP

                 Hydantoinase_B  305 vklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGa 382 
                                     +++pegs+l p++paavv+gnvetsq ++ ++++al+      v+A+++gtmnn+tfg   +  +++ +yyet++ G+
  gi|121636179|ref|YP_976402.1| 1004 IVVPEGSMLAPTHPAAVVAGNVETSQAITGALFAALG------VQAEGSGTMNNVTFG---N--ERH-QYYETVGSGS 1069
                                     *************************************......***************...4..455.9********* PP

                 Hydantoinase_B  383 GArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvf 460 
                                     GA+ g +Gas v++hmtn+r td+E+lE ryPvl+++f++r++sgGaG++rGGdG+vr++ef+ep +tvs+ls +r++
  gi|121636179|ref|YP_976402.1| 1070 GAGDGYHGASVVQTHMTNSRLTDPEVLEWRYPVLLREFAVRQGSGGAGRWRGGDGAVRRLEFTEP-MTVSTLSGHRRV 1146
                                     ****************************************************************9.************ PP

                 Hydantoinase_B  461 apwGlaGGepGargrvvlnllvr..geeenlggkatvelkagdvlvietpGGGGyGd 515 
                                     +p+G+aGG pG+ gr   n+++r  g++++l+g  ++++++gd+lvietpGGGGyG 
  gi|121636179|ref|YP_976402.1| 1147 RPYGMAGGSPGELGR---NRVERadGSTVELAGCGSTHVEPGDTLVIETPGGGGYGP 1200
                                     ***************...9999999*******************************6 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.4   2.7    1e-118  6.2e-115       1     289 [.     202     489 ..     202     491 .. 0.99
   2 ?   -3.5   0.0      0.81   4.9e+03     194     233 ..     884     923 ..     873     934 .. 0.73

  Alignments for each domain:
  == domain 1  score: 383.4 bits;  conditional E-value: 1e-118
                 Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                    r++t+vv+Aylsp+lr+y+++v ++++      rlm+mqs+Ggl++a ++r+k  ++ilSGPa+G+vg++++s lag+++
  gi|121636179|ref|YP_976402.1| 202 RGDTTVVDAYLSPVLRRYINQVADQMRG----VRLMFMQSNGGLAQAGHFRGK--DAILSGPAGGIVGMVRMSALAGFDH 275
                                    899************************9....79*******************..************************* PP

                 Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGg 160
                                    vI+fDmGGTstDvs+++ ge+e+++ t++agv++r+p+ldi+tv+agGgsil +++g+++rvgp+sagadpgpacyr+Gg
  gi|121636179|ref|YP_976402.1| 276 VIGFDMGGTSTDVSHYA-GEYERVFTTQVAGVRLRAPMLDIHTVAAGGGSIL-HFDGSRYRVGPDSAGADPGPACYRGGG 353
                                    *****************.**********************************.*************************** PP

                 Hydantoinase_A 161 teltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvavenmanavrkl 232
                                     +l+vTDan++LGr+qp +f+s  gp+gdq+ld  ++rr f++la+ +         +e+vAeg l++av nmanav+k+
  gi|121636179|ref|YP_976402.1| 354 -PLCVTDANVMLGRIQPTHFPSvfGPSGDQPLDAGTVRRGFTDLAADIAARtgddrsPEQVAEGYLRIAVANMANAVKKI 432
                                    .***********************************************99999*************************** PP

                 Hydantoinase_A 233 svergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                    sv++g+d+++++l+ fGGaG+qha+a+a++lg+++v++pp+agvlsalG++lAd ++
  gi|121636179|ref|YP_976402.1| 433 SVQKGHDVTRYALTTFGGAGGQHACAVADALGIRTVLIPPMAGVLSALGIGLADTTA 489
                                    ******************************************************876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.81
                 Hydantoinase_A 194 larrafeelakelnlkveevAegilsvavenmanavrkls 233
                                    + ++ ++e++k +     +v ++ ++ +++n  +avr+++
  gi|121636179|ref|YP_976402.1| 884 ANQKGVDEVGKMIDHFGRDVVAAYMRHVQDNAEEAVRRVI 923
                                    4556667777777777788888888888888888888874 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.7   0.0   4.2e-62   2.5e-58       2     178 .]       8     183 ..       7     183 .. 0.97
   2 !    4.5   0.1    0.0041        25       2      23 ..     277     298 ..     276     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 196.7 bits;  conditional E-value: 4.2e-62
                     Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllst.....pdavaegirealeevleesiprtskidvvrmGTTvatNallerkg 76 
                                    +++D+GGTfTD+va +++ +++ ++Klls      +da++ gir +l++ +     + +++d+vrmGTTvatNaller+g
  gi|121636179|ref|YP_976402.1|   8 FWVDRGGTFTDVVARRPD-GRLLTHKLLSDnparyRDAAVAGIRALLANGE-----AGTRVDAVRMGTTVATNALLERTG 81 
                                    89**************98.99**************************9963.....3689******************** PP

                     Hydant_A_N  77 ervaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavv 156
                                    er+ L++t+gf d+l+i++qnrp++f++ri+ p++lye+vvevderv+adg+vl++ d e++ e++++++a+g++++avv
  gi|121636179|ref|YP_976402.1|  82 ERTLLVITRGFGDALRIAYQNRPRIFDRRIVLPEMLYERVVEVDERVTADGRVLRAPDLEALGEKMRQAHADGIRAVAVV 161
                                    ******************************************************************************** PP

                     Hydant_A_N 157 llhSylnpehElrvaeiareig 178
                                    +lhSyl+p hE++++++a++ig
  gi|121636179|ref|YP_976402.1| 162 CLHSYLYPGHEREIGTLAQRIG 183
                                    ******************9985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0041
                     Hydant_A_N   2 igIDvGGTfTDavaldekeeev 23 
                                    ig D+GGT TD+  + ++ e+v
  gi|121636179|ref|YP_976402.1| 277 IGFDMGGTSTDVSHYAGEYERV 298
                                    899********98887665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.26s 00:00:01.07 Elapsed: 00:00:00.44
# Mc/sec: 8267.76
//
Query:       gi|121636180|ref|YP_976403.1|  [L=463]
Description: integral membrane nitrite extrusion protein narU [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-13   49.0  58.5    4.2e-13   49.0  58.5    2.2  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.027   14.4   0.4      0.027   14.4   0.4    4.8  5  DUF485    Protein of unknown function, DUF485
      0.068   11.7  24.9     0.0083   14.7  14.3    2.4  2  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0  58.5     7e-17   4.2e-13      10     351 ..      58     414 ..      47     416 .. 0.73
   2 ?    1.1   5.5     0.024   1.4e+02     117     176 ..     395     456 ..     389     460 .. 0.69

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 7e-17
                          MFS_1  10 larsilgpalplalaed.lg........ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    ++ ++l++++   ++ +  g        +s+s++  l+++ + + a++ lp+ + +  fG r +  ++++l+++ +lll+
  gi|121636180|ref|YP_976403.1|  58 FSVWMLWSIVVVQMTAAaPGhpaasgwaLSASQALCLVAVPSGVGAFLRLPYTFAIPIFGGRNWTTVSAALLVIPCLLLA 137
                                    444445555554332221221111222245555555777788888******************99999999999988888 PP

                          MFS_1  81 fa...sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslg..Wrav 153
                                    +a   +sl+ ++lv+ + ++ ++g+ f++++a i+  +p++++g a+gl +ag ++G+++   ++ +++++  g   + +
  gi|121636180|ref|YP_976403.1| 138 WAvshPSLPfAVLVVIAATAGFGGGNFASSMANISFFYPEKDKGWALGLNAAGGNIGVAVVqKIIPPIVVAGSGvaLSRA 217
                                    866778888888888888888889**********************************9997999999997777555555 PP

                          MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                     +++ ++++ a+v+++l++     +++ ++p              +w++l++    wi+ +  +++f  f g+++ +p++
  gi|121636180|ref|YP_976403.1| 218 GLFFVPLAVAAAVCAFLFMNNLTEAKADVKP--------------VWQSLRHAD-TWIMSLLYIGTFGSFIGYSAAFPTL 282
                                    8888888888888855555444444444433..............577788777.57555555555666666******** PP

                          MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfg 313
                                    l++v+g +   l+     l+a +g  +++l+g+l+dr+g  r++  +++ l+++a++ ++   + + +++ ++++++ ++
  gi|121636180|ref|YP_976403.1| 283 LKTVFGRGDIALG--WAFLGAGIGSLVRPLGGKLADRIGGARITAASFVMLAAGAAAALWSVQSVNLPVFFVSFMFLFVA 360
                                    ********32333..366666777777*************9999999999999999999999999999999977777778 PP

                          MFS_1 314 lgfvfpsllalasdlapp................eeagtasglfntagslggal 351
                                     g+ ++s+  ++s+ +                  ++a+ a+g+++++g++gg++
  gi|121636180|ref|YP_976403.1| 361 TGIGNGSSYRMISRIFQVkgevaggdpetmvnmrRQAAGALGIISSIGAFGGFV 414
                                    888888888888888833444455555566655444445666666666666666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.024
                          MFS_1 117 eergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpeep 176
                                    ++ + a+g++s+  ++G  + pl+ ++   ++g     + fy++ +++ll+ v ++++l+++ 
  gi|121636180|ref|YP_976403.1| 395 RQAAGALGIISSIGAFGGFVVPLAYAWSKVHFGniePALHFYVAFFLALLV-VTWYCYLRRTT 456
                                    567788899999888888888666555558888764444477777777776.55788887765 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4     0.074   4.4e+02      40      71 ..     109     139 ..      91     142 .. 0.87
   2 ?   -2.9   0.2       1.1   6.8e+03      16      32 ..     220     236 ..     215     240 .. 0.67
   3 ?   14.4   0.4   4.5e-06     0.027      13      57 ..     254     298 ..     249     306 .. 0.90
   4 ?   -1.4   4.6       0.4   2.4e+03      30      71 ..     327     363 ..     323     363 .. 0.80
   5 ?    4.8   1.8    0.0045        27      13      74 ..     394     453 ..     388     457 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.074
                         DUF485  40 dllatkvgegnitvglllgllqivltflltgl 71 
                                      +a +++ g  ++  + ++l+++ + ll+++
  gi|121636180|ref|YP_976403.1| 109 YTFAIPIF-GGRNWTTVSAALLVIPCLLLAWA 139
                                    578999**.77999999999999999999985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                         DUF485  16 fafpltaiflvvYfgfv 32 
                                    f +pl++++ v+ f+f+
  gi|121636180|ref|YP_976403.1| 220 FFVPLAVAAAVCAFLFM 236
                                    66677777776666665 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.5e-06
                         DUF485  13 rrrfafpltaiflvvYfgfvllvafapdllatkvgegnitvglll 57 
                                    r + +++++++ ++ + +f+  +a +p+ll+t +g+g i +g+++
  gi|121636180|ref|YP_976403.1| 254 RHADTWIMSLLYIGTFGSFIGYSAAFPTLLKTVFGRGDIALGWAF 298
                                    55668**************************************87 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.4
                         DUF485  30 gfvllvafapdllatkvgegnitvglllgllqivltflltgl 71 
                                    +fv+l+a a    a+ ++ ++ +v l++ ++ +++ f++tg+
  gi|121636180|ref|YP_976403.1| 327 SFVMLAAGA----AAALW-SVQSVNLPVFFVSFMFLFVATGI 363
                                    677888877....66677.77889999999999999999986 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.0045
                         DUF485  13 rrrfafpl.taiflvvYfgfvllvafapdllatkvgegnitvglllgllqivltflltgl.Yvr 74 
                                    rr+ a  l ++  ++++ gfv+ +a+a      kv  gni  +l + ++ ++   ++t++ Y r
  gi|121636180|ref|YP_976403.1| 394 RRQAAGALgIISSIGAFGGFVVPLAYA----WSKVHFGNIEPALHFYVAFFLALLVVTWYcYLR 453
                                    444444440555678999*********....567777999999999999999999999852555 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.6    0.0068        41     286     337 ..     116     167 ..      83     171 .. 0.67
   2 ?   14.7  14.3   1.4e-06    0.0083     143     377 ..     191     415 ..     175     447 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0068
                          MFS_2 286 lgkk.ntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpws 337
                                    +g +  t++++all+i+ l+l++++     l+f vl+via ++  + + ++ s
  gi|121636180|ref|YP_976403.1| 116 FGGRnWTTVSAALLVIPCLLLAWAV-SHPSLPFAVLVVIAATAGFGGGNFASS 167
                                    5655256777788899999999999.777777777777666654444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-06
                          MFS_2 143 svlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfr 222
                                     ++g +++  +++++v++ +g      + + ++l+++ L++++++ ++l+  + +e+       ++   +++    +++r
  gi|121636180|ref|YP_976403.1| 191 GNIGVAVVQKIIPPIVVAGSG-----VALSRAGLFFVPLAVAAAVCAFLFMNNLTEA-------KADVKPVW----QSLR 254
                                    456666666666666666555.....689999999**************99998654.......33333333....4566 PP

                          MFS_2 223 nraflillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivl 302
                                    +   +i+ ll++ ++ ++  + +++   l+ v g g+ a  ++++    + l+ pl  +la r+g  +++++++++++++
  gi|121636180|ref|YP_976403.1| 255 HADTWIMSLLYIGTFGSFIGYSAAFPTLLKTVFGRGDIALGWAFLGAGIGSLVRPLGGKLADRIGGARITAASFVMLAAG 334
                                    778888888899999999************************************************************** PP

                          MFS_2 303 lvlvlll.qpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregv.....ffavlsfisklatgiglgv 376
                                     + +l+  q  nl +f+v ++  ++++g+ +   + m++ ++ +     G   e++      +a  + i   ++++g++v
  gi|121636180|ref|YP_976403.1| 335 AAAALWSvQSVNLPVFFVSFMFLFVATGIGNGSSYRMISRIFQVKGEVAGGDPETMvnmrrQAAGALGIISSIGAFGGFV 414
                                    ******98899999999999999999999***********9998877777777776455554444444444455555555 PP

                          MFS_2 377 s 377
                                    +
  gi|121636180|ref|YP_976403.1| 415 V 415
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3237.56
//
Query:       gi|121636181|ref|YP_976404.1|  [L=169]
Description: hypothetical protein BCG_0306c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-14   51.9   0.2    9.5e-14   51.0   0.2    1.4  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
  ------ inclusion threshold ------
      0.022   14.6   0.7      0.062   13.2   0.2    1.9  2  DUF2249          Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.2   1.1e-17   9.5e-14       4      59 ..      90     143 ..      88     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.1e-17
                                    EEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSH CS
                PhdYeFM_antitox   4 vsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslp 59 
                                    v+isea+a+ls+l++e ++++  v++ ++G+p+a l+s+e ye+l+e+ e+l++ +
  gi|121636181|ref|YP_976404.1|  90 VPISEARAHLSRLVRESADDD--VVLMNHGRPAAILISAERYESLMEELEDLRDRL 143
                                    89*****************99..************************988888765 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   6.9e-06     0.062      23      62 ..      41      80 ..      23      81 .. 0.88
   2 ?   -1.6   0.0      0.28   2.5e+03      11      24 ..     127     140 ..     124     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-06
                        DUF2249 23 LapGetlelvndhdPkpLlyqLearrpgffsweylergpg 62
                                   L+++e l+ +++h P+ L + L +rr+ +++++y++r+p 
  gi|121636181|ref|YP_976404.1| 41 LREDEWLRHHLPHPPRQLSRCLHRRRRSACHHRYSRRTPK 80
                                   89999********************************995 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                        DUF2249  11 erhaaIfeafeaLa 24 
                                    er +  +e++e+L+
  gi|121636181|ref|YP_976404.1| 127 ERYESLMEELEDLR 140
                                    78888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1423.14
//
Query:       gi|121636182|ref|YP_976405.1|  [L=397]
Description: hypothetical protein BCG_0307c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-06   26.4   0.0    2.2e-05   24.6   0.0    1.9  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.2e-09   2.2e-05      11      73 ..     141     201 ..     132     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-09
                                    .TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHH CS
                  DNA_primase_S  11 cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraa 73 
                                    ++ +    + w+ v++++ v++e+l ed+g   +++ +sg+rGfH++ +   ++++ + + aa
  gi|121636182|ref|YP_976405.1| 141 VDLDPMPGVAWQRVVEVALVVREVL-EDYGLT-AWPKTSGSRGFHVYARIAPCWSFPQVRLAA 201
                                    5566666688***************.*****9.******************999999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2975.00
//
Query:       gi|121636183|ref|YP_976406.1|  [L=560]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-76  256.2   0.0    5.8e-76  255.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    8.3e-21   74.8   0.1      3e-20   73.0   0.1    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.8   0.0   6.4e-80   5.8e-76       3     422 ..      69     467 ..      68     468 .. 0.88

  Alignments for each domain:
  == domain 1  score: 255.8 bits;  conditional E-value: 6.4e-80
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                    ++a++ p++ a++d  e  tlT++elde+++++A+gL+++Gv+ g+ Vail++n   +v+a ++++++Ga ++ ln++++
  gi|121636183|ref|YP_976406.1|  69 HNARRAPNRAAVID--EEGTLTFSELDEAAHAVANGLLAKGVRAGEGVAILARNHRWFVIANYGAARVGARIILLNSEFS 146
                                    6899**********..99********************99**************************************** PP

                                    HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSE CS
                    AMP-binding  83 aeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddl 161
                                     ++++ + +  +akv+i  +d+e   + +l++ +  + ++l +  d+d+++ ++++  +e  ++++   + +++  +   
  gi|121636183|ref|YP_976406.1| 147 GPQIKEVSDREGAKVII--YDDEYtKAVSLAQPPLGKLRALGVNPDDDKPSGSSDETLAELIAHSS---TAPAPKASRRA 221
                                    *****************..78777566666666655556666666666666665555555555543...35667888999 PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                     +ii TSGTTG+PKG+   +  ++a +  + l+ +  +k+++v l   p++h++g+ +   la++ G+t+vl ++++   
  gi|121636183|ref|YP_976406.1| 222 SIIILTSGTTGTPKGANRNTPPTLAPIGGI-LS-HVPFKAGEVTLLPSPMFHALGY-MHAALAMFLGSTLVLRRRFK--- 295
                                    **************************9998.44.4446689**************8.***************99775... PP

                                    HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGS CS
                    AMP-binding 242 pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEtt 321
                                    p+l+le+iek+k+t +++vP +l ++l++ +++  + + dlssl++v++ g++l +el++++   +g+ ++++YG TE +
  gi|121636183|ref|YP_976406.1| 296 PALVLEDIEKHKATSMVVVPVMLSRILDQLEKT--EPKPDLSSLKIVFVSGSQLGAELATRALGDLGPVIYNMYGSTEVA 373
                                    5788**********************9964444..4566***************************************** PP

                                    SECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEE CS
                    AMP-binding 322 gvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDl 401
                                     +++ + +++ + ++++vG+++ gv vki+De+ g++vp+g +G ++v+ +  ++gY +      + ++  +++l +GD+
  gi|121636183|ref|YP_976406.1| 374 FATI-AGPKDLQFNPSTVGPVVKGVTVKILDEN-GNEVPQGAVGRIFVGNAFPFEGYTGG---GGKQII--DGLLSSGDV 446
                                    **99.7778888999*****************9.************************98...334455..37******* PP

                                    EEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 402 grldedGyleivgRkkdlikl 422
                                    g++de+G l++ gR +++i++
  gi|121636183|ref|YP_976406.1| 447 GYFDERGLLYVSGRDDEMIVS 467
                                    *******************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.1   3.3e-24     3e-20       1      76 []     476     551 ..     476     551 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.3e-24
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE  ++ hp+V eaa++Gv+d+  G +l afVv k+g ++ e+++k++vr++l+ y+vp++v+f+delp++ +GK
  gi|121636183|ref|YP_976406.1| 476 EVEDLISGHPDVVEAAAIGVDDKEFGARLRAFVVKKPGADLDEDTIKQYVRDHLARYKVPREVIFLDELPRNPTGK 551
                                    8*********************************998966689********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3826.89
//
Query:       gi|121636184|ref|YP_976407.1|  [L=731]
Description: acyl-CoA dehydrogenase fadE6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-44  152.1   5.8    4.2e-24   85.5   4.9    2.4  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      4e-24   85.4   0.2    7.2e-11   42.8   0.1    2.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    7.2e-20   71.0   0.0      1e-18   67.3   0.0    2.3  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    5.5e-08   33.2   8.5    5.5e-08   33.2   8.5    2.1  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   4.9   9.4e-28   4.2e-24      17     134 ..     217     338 ..     206     345 .. 0.95
   2 !   65.1   0.0   1.7e-21   7.8e-18       1     150 []     575     725 ..     575     725 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 9.4e-28
                                    ---..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------....HHHHHHHH CS
                  Acyl-CoA_dh_1  17 avaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd....raeasmaK 92 
                                    ++ a a+g+ar a ++a +ya+ r++fg+p++++q++++k+aem a++e a ++v++aa+ald+++++    + +a++a 
  gi|121636184|ref|YP_976407.1| 217 LLSAEAVGVARWATDTASAYAKIREQFGRPIGQFQAIKHKCAEMIADTERATAAVWDAARALDDAGESssdvEFAAAVAA 296
                                    57899***************************************************************9**99******* PP

                                    HHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHS CS
                  Acyl-CoA_dh_1  93 lfaselaqevadlamqllGgaGyleeypverlyrdarvlrig 134
                                     +a+ +aq+++++++q++Gg G+++e+    +yr+a++l   
  gi|121636184|ref|YP_976407.1| 297 TLAPATAQRCTQDCIQVHGGIGFTWEHDTNVYYRRALMLAAC 338
                                    ************************************998765 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 1.7e-21
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++G++v  +tl+ eR++++ ++  ++   l e ++++r+ +  g+    +q+ r++ +++ ae +a++ll++r + +  a
  gi|121636184|ref|YP_976407.1| 575 NRGWEVSRNTLTAERVSIG-GSDSTFLPTLGEFVDFVRDYRFEGQF---DQVARHRAGQLIAEGHATKLLNLRSTLLTLA 650
                                    89****************7.889999999***************86...******************************* PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGH.....HHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeyp.....verlyrdarvlrigeGtseiqrniiarrll 150
                                    g+++ a a++ Kl+  ++ q  a+ a+  +G++++  +++     +  ++ ++r+++i++Gtse+q+niia+rll
  gi|121636184|ref|YP_976407.1| 651 GGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTErlpgkWGEYLLASRATTIYGGTSEVQLNIIAERLL 725
                                    ***********************************6444445688****************************86 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.6e-14   7.2e-11       1      96 [.       6     100 ..       6     114 .. 0.78
   2 !   40.1   0.0   1.1e-13   4.9e-10      21     113 .]     375     465 ..     368     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.6e-14
                                    THHHHHHHHHHHHHHHHHTHHHHHHHH.HHT.SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewd.eeg.efprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                    t+e+ +l d+vr+++++ ++  + ++  e+  e p   w+++ae+Gl g+++ e +gG+g+++le a+v+ e++++ ++ 
  gi|121636184|ref|YP_976407.1|   6 TPEHYELADSVRSLVARVAPSEVLHAAlESPvENPPPYWQAAAEQGLQGVHLAESVGGQGFGILELAVVLAEFGYGAVP- 84 
                                    79***************886655555444444556667*************************************8888. PP

                                    HHHHHHHHHTTHHHHHHH CS
                  Acyl-CoA_dh_N  79 alllgvhsslvapailrf 96 
                                      ++ v s++++  i+++
  gi|121636184|ref|YP_976407.1|  85 --GPFVPSAIASALIAAH 100
                                    ..5567777776545443 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 1.1e-13
                                    HHHHHHHHHTSGHHH.HHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-H CS
                  Acyl-CoA_dh_N  21 phaaewdeegefpre.lwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrfGte 99 
                                    +  ae+ + +++pre +  ++ae G++  ++p+ +g a ++++e++i+a+e++++ +  ++ +++ + +v p i++fGt+
  gi|121636184|ref|YP_976407.1| 375 QIRAEVAALKAMPREpRTVAIAEGGWVLPYLPKPWGRA-ASPVEQIIIAQEFTAGRVK-RPQIAIATWIV-PSIVAFGTD 451
                                    445566566689988447777**************765.59************97776.77899999999.89******* PP

                                    HHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N 100 eqkrryLpklasge 113
                                     qk+r Lp+  +g+
  gi|121636184|ref|YP_976407.1| 452 NQKQRLLPPTFRGD 465
                                    *********99995 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   5.1e+02      18      51 ..     123     157 ..     107     193 .. 0.71
   2 !   67.3   0.0   2.3e-22     1e-18       1      89 [.     469     557 ..     469     563 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                    -EE.EEETT.EEEEEEEEEEEETTTT-SEEEEEEE CS
                  Acyl-CoA_dh_M  18 tta.aerdggeyvlnGeKiwitnaaiatlalvlar 51 
                                    + + a+r g+  v++Ge + +  aa+a+++++ + 
  gi|121636184|ref|YP_976407.1| 123 SGLtATRHGDVLVIRGEVRAVPAAAQASVLVLPVA 157
                                    44558899999******999999999888766444 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 2.3e-22
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE--- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvrri 78 
                                    +  ++Ep+aGsd+as++t+a++ dg +++++G+Kiw t+a+++++  +lart+ p+  +++g++ fl++ +++gv+v+++
  gi|121636184|ref|YP_976407.1| 469 CQLFSEPGAGSDLASLATKATRVDG-GWRITGQKIWTTGAQYSQWGALLARTD-PSapKHNGITYFLLDMKSEGVQVKPL 546
                                    67789*************8888888.8************************44.44489********************* PP

                                    --BSS-TTS-E CS
                  Acyl-CoA_dh_M  79 eeklGlrglpt 89 
                                    +e +G  + +t
  gi|121636184|ref|YP_976407.1| 547 RELTGKEFFNT 557
                                    *9999887664 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.3       3.4   1.5e+04       4      25 ..     108     129 ..     106     135 .. 0.68
   2 !   33.2   8.5   1.2e-11   5.5e-08       3     114 ..     218     323 ..     216     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2   4 aavalGaAraalaefvelarer 25 
                                    a  a+GaA aa+a    l+++r
  gi|121636184|ref|YP_976407.1| 108 AELATGAAIAAYALDSGLTATR 129
                                    6678888888877666666555 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.2e-11
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    ++a a+G+Ar a + + ++a+ r +  +g+++ +++a++++ ae+ a+ + A a + +aa++   l +ag++ + +    
  gi|121636184|ref|YP_976407.1| 218 LSAEAVGVARWATDTASAYAKIREQ--FGRPIGQFQAIKHKCAEMIADTERATAAVWDAARA---LDDAGES-SSDVEFA 291
                                    7899*********************..*****************************999999...4455555.6777899 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT- CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkes 114
                                    a++aa+la  +a+++++++++++Gg + + e+
  gi|121636184|ref|YP_976407.1| 292 AAVAATLAPATAQRCTQDCIQVHGGIGFTWEH 323
                                    99***********************9987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 5004.89
//
Query:       gi|121636185|ref|YP_976408.1|  [L=377]
Description: hypothetical protein BCG_0310c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-06   25.3   0.1     0.0015   17.8   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0015   18.0   0.1      0.079   12.4   0.0    2.4  2  Peptidase_S9   Prolyl oligopeptidase family
     0.0046   16.6   0.0        1.6    8.3   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0016       9.3      55      96 ..      89     130 ..      43     174 .. 0.74
   2 !   17.8   0.0   2.5e-07    0.0015     173     228 ..     295     350 ..     244     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0016
                    Hydrolase_4  55 fddyvdDlaafvekvkeehpelplfllGhSmGGliallyllr 96 
                                    +d+ + D+   v+ ++e ++ + ++llG S GG + ++y  +
  gi|121636185|ref|YP_976408.1|  89 LDHALVDIGVGVRWLREVQGVETVVLLGNSGGGSLMAAYQSQ 130
                                    5778888888899999999999*************9999743 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.5e-07
                    Hydrolase_4 173 llelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                    +++l  a+ r+  + a+it P l+l +eaD+ + p++++++y+ l+s+dkt   ++
  gi|121636185|ref|YP_976408.1| 295 MWSLRVAQTRAAPHLARITCPALVLNAEADTGIFPSDAQQIYDGLASSDKTQVSID 350
                                    344555789999999***********************************987765 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.1    0.0097        58      64      85 ..     110     131 ..      61     134 .. 0.79
   2 !   12.4   0.0   1.3e-05     0.079     135     207 ..     307     374 ..     292     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0097
                                    GGEEEEEETHHHHHHHHHHHH- CS
                   Peptidase_S9  64 erlaitGgSyGGyltgaalnqr 85 
                                    e +++ G S GG l++a + q+
  gi|121636185|ref|YP_976408.1| 110 ETVVLLGNSGGGSLMAAYQSQA 131
                                    7899************988765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.3e-05
                                    -CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHH CS
                   Peptidase_S9 135 spldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlke 207
                                     +l++  +++p L++ ++aD+ + p+ a ++++ L + +k+   ++  d +H + +p a+ e+  ++++++++
  gi|121636185|ref|YP_976408.1| 307 PHLAR--ITCPALVLNAEADTGIFPSDAQQIYDGLASSDKT---QVSIDTDHYFTTPGARSEQADTIAKWIAK 374
                                    45555..99***************************99986...6777889*******************986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00027       1.6      63      94 ..     100     131 ..      64     142 .. 0.88
   2 !    6.4   0.0     0.001       6.1     206     251 ..     292     354 ..     188     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                                    HHHHHHHCTTSSEEEEEETHHHHHHHHHHHHH CS
                  Abhydrolase_1  63 ldrildalgddkltlvGhSmGGmialayaaey 94 
                                    ++++++  g++ ++l+G S GG +++ay +++
  gi|121636185|ref|YP_976408.1| 100 VRWLREVQGVETVVLLGNSGGGSLMAAYQSQA 131
                                    78999***********************8887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                                    C................THHHHSEEEEEEE.TTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                  Abhydrolase_1 206 e................lknvlaptlvisg.tsDplvppkaledlaqllpkkrlvvisdagHl 251
                                    +                l  +++p+lv+ + ++ +++p +a+  +++l ++ +  v  d+ H+
  gi|121636185|ref|YP_976408.1| 292 WlgmwslrvaqtraaphLARITCPALVLNAeADTGIFPSDAQQIYDGLASSDKTQVSIDTDHY 354
                                    044455666667777778899*********556667777*********777688888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2678.82
//
Query:       gi|121636186|ref|YP_976409.1|  [L=206]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-10   40.7   0.3      4e-10   39.3   0.3    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.018   15.1   0.1       0.16   12.0   0.0    2.4  2  TetR_C_27  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.3   4.5e-14     4e-10       3      45 ..      18      60 ..      16      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.5e-14
                                   HHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  3 daArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   +aAr +  ++G+ attv++I ++AG s++++Y y++sKe++++
  gi|121636186|ref|YP_976409.1| 18 AAARTVVVRNGILATTVADITAEAGRSAASFYNYYDSKEAMVR 60
                                   69999***********************************986 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.062   5.6e+02      41      63 ..      63      85 ..      29     108 .. 0.76
   2 ?   12.0   0.0   1.8e-05      0.16      52      95 ..     134     177 ..     112     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.062
                                   HHHHHHHHHHHHHHHHHHHHHCT CS
                      TetR_C_27 41 vekhieeleeqlaeIireGvaaG 63
                                   + ++++++++   ++ir+G ++ 
  gi|121636186|ref|YP_976409.1| 63 ALRFRDDANQRALSVIRHGLSDR 85
                                   55788888888899999998765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                      TetR_C_27  52 laeIireGvaaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                    ++e +++++a G+   +dp+ +a+a+++++++f+  +l  + s+
  gi|121636186|ref|YP_976409.1| 134 ITETVKRAQAHGYCVGDDPQLMAEAIVAMFNQFCYLQLSGKRSR 177
                                    78999*****************************9988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1370.80
//
Query:       gi|121636187|ref|YP_976410.1|  [L=193]
Description: hypothetical protein BCG_0312 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-23   83.6   0.0    1.6e-23   83.3   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    4.4e-06   26.9   0.0    2.1e-05   24.7   0.0    2.0  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.036   14.9   0.0      0.085   13.7   0.0    1.7  1  Glyoxalase_6  Glyoxalase-like domain
       0.13   12.4   0.0        4.5    7.3   0.0    2.2  2  Glyoxalase_3  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   3.6e-27   1.6e-23       1     128 []      15     163 ..      15     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 3.6e-27
                                    EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCC......BSC.. CS
                     Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkk......iee.. 72 
                                    gi+hval+++d+++++dFY ++LG+ l+k  d  ++++g+++ f   +g++++++++  ++++ ++  +      i +  
  gi|121636187|ref|YP_976410.1|  15 GINHVALVCSDMARTVDFYSNILGMPLIKALD-LPGGQGQHFFFDAGNGDCVAFFWFADAPDRVPGLSSpvaipgI-Gdi 92 
                                    79******************************.9999******************************776666551.055 PP

                                    .....TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE...........EEEETTSEEEEE CS
                     Glyoxalase  73 .....tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysf...........yfrDpdGillei 128
                                         t++h+af++ ++   +++ +rlk++gv+v ++++++  +  +s+           yf+DpdGi+le+
  gi|121636187|ref|YP_976410.1|  93 tsavsTMNHLAFHVPAERF-DAYRQRLKDKGVRVGPVLNHDDSETQVSAvvhpgvyvrsfYFQDPDGITLEF 163
                                    667889**********999.***************************************************8 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.7e-09   2.1e-05       1      93 [.      17     125 ..      17     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.7e-09
                                    EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETT...........EEE.EEEEESSTT..-THHHTS CS
                   Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgs...........vqi.eLieplegp..eflaehg 66 
                                    +++++v+ D+ ++v+++s++lG+  ++    +  + +  f+++g+g+            ++  L +p+  p    +    
  gi|121636187|ref|YP_976410.1|  17 NHVALVCSDMARTVDFYSNILGMPLIKALDLPGGQGQHFFFDAGNGDcvaffwfadapDRVpGLSSPVAIPgiGDITSAV 96 
                                    6*********************87665555554433333444444432110000000012214555555556677777** PP

                                    -EEEEEEEEE..S-HHHHHHHHCTTTEEE CS
                   Glyoxalase_4  67 eglhhlaywv..ddldaavarleeqGfev 93 
                                      ++hla++v  + +da  +rl+++G++v
  gi|121636187|ref|YP_976410.1|  97 STMNHLAFHVpaERFDAYRQRLKDKGVRV 125
                                    *********95569*************98 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.085       2     101 ..      19     158 ..      18     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                   Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree................aaledpegvgpaaedaatllfqrvpe........... 54 
                                    v+l ++d+a+ ++F++ +lg+++ +                               +  a ++f  +p+           
  gi|121636187|ref|YP_976410.1|  19 VALVCSDMARTVDFYSNILGMPLIKALdlpggqgqhfffdagnG------------DCVAFFWFADAPDrvpglsspvai 86 
                                    7888******************9998877777665543332220............233456666666677777777788 PP

                   Glyoxalase_6  55 ........paknrvHldlav..edldaevarlvalGArvlreprdgthgr...............vlaDPeG 101
                                            ++ +  Hl ++v  e  da  +rl + G rv    ++++ ++                ++DP+G
  gi|121636187|ref|YP_976410.1|  87 pgigditsAVSTMNHLAFHVpaERFDAYRQRLKDKGVRVGPVLNHDDSETqvsavvhpgvyvrsfYFQDPDG 158
                                    888889885556667777776588899999999999888766666655555668777777777777777777 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.001       4.5       2      30 ..      17      50 ..      16      67 .. 0.82
   2 ?    3.4   0.0     0.016        71       3      37 ..     101     136 ..      74     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                   Glyoxalase_3  2 DHvvlavpdleeaaarfarrlGftvt.....pgg 30
                                    Hv l+++d++++++ + + lG+ ++     pgg
  gi|121636187|ref|YP_976410.1| 17 NHVALVCSDMARTVDFYSNILGMPLIkaldlPGG 50
                                   6**********************99966666444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                   Glyoxalase_3   3 Hvvlavp..dleeaaarfarrlGftvtpggehpglgt 37 
                                    H+ ++vp    ++ ++r+ ++ G++v p  +h +  t
  gi|121636187|ref|YP_976410.1| 101 HLAFHVPaeRFDAYRQRL-KDKGVRVGPVLNHDDSET 136
                                    444444444555555555.444555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1177.75
//
Query:       gi|121636188|ref|YP_976411.1|  [L=241]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-06   25.3   0.0    2.7e-05   23.8   0.0    1.9  1  TetR_N    Bacterial regulatory proteins, tetR family
     0.0027   17.8   0.0     0.0084   16.2   0.0    1.8  2  TetR_C_8  Transcriptional regulator C-terminal region
  ------ inclusion threshold ------
      0.024   14.7   0.1        0.1   12.7   0.0    2.0  2  HTH_AraC  Bacterial regulatory helix-turn-helix proteins, Ara


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.6e-09   2.7e-05      11      45 ..      36      70 ..      24      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.6e-09
                                   HHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N 11 erGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   ++ ++++t+r I +rAG+s + +Y  F++K+e + 
  gi|121636188|ref|YP_976411.1| 36 QHDIAELTIRTICRRAGLSVRYFYESFTDKDEFVG 70
                                   8999***************************9875 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.36   2.1e+03      65      83 ..      58      77 ..      50      87 .. 0.75
   2 !   16.2   0.0   1.4e-06    0.0084      59     102 ..     155     198 ..      95     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.36
                                   HHHHHH.HHHHHHHHHHHHH CS
                       TetR_C_8 65 fiadfy.sygfvgvildWle 83
                                   f+ +f  +  fvg + dW+ 
  gi|121636188|ref|YP_976411.1| 58 FYESFTdKDEFVGRVFDWVV 77
                                   55556656689999999986 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-06
                                    -HHHHHHHHHHHHHHHHHHHHHHHHTTS-S-HHHHHHHHHHHHH CS
                       TetR_C_8  59 seedkefiadfysygfvgvildWlengmkespeeiaellsklin 102
                                     +++ + +a+f ++g+ ++i  Wl ++ + +p++++++l  l++
  gi|121636188|ref|YP_976411.1| 155 ANDHVKAVAHFAVGGVGQTISAWLAGDVRLDPDQLVDQLAALLD 198
                                    34677889*******************************99975 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1       8      29 ..      41      62 ..      38      63 .. 0.93
   2 ?   -1.8   0.0      0.61   3.6e+03      33      41 ..     170     178 ..     170     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                   T--HHHHHHHTTSSHHHHHHHH CS
                       HTH_AraC  8 nltiediAdelgfSrsyFsrlF 29
                                   +lti+ i+  +g+S +yF+  F
  gi|121636188|ref|YP_976411.1| 41 ELTIRTICRRAGLSVRYFYESF 62
                                   58*****************988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                                    SSS-HHHHH CS
                       HTH_AraC  33 tGmtPsqyr 41 
                                    +G+t+s+++
  gi|121636188|ref|YP_976411.1| 170 VGQTISAWL 178
                                    59*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1696.11
//
Query:       gi|121636189|ref|YP_976412.1|  [L=306]
Description: hypothetical protein BCG_0314 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-49  168.8   6.5    2.8e-49  168.4   6.5    1.1  1  DUF2236   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   6.5   1.6e-53   2.8e-49       7     226 ..      44     273 ..      42     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 1.6e-53
                        DUF2236   7 elilllgalaalllqaahplvltgvldh...s.tfad.plrRllrTaqfiltvvygsgeeaeaaaarVrllHaavrgtda 81 
                                    ++++ll+++a++++++a p+v+ gvl++   s ++++ p++R ++T+++++ +v gs +++ a  + V+++Ha+v +t  
  gi|121636189|ref|YP_976412.1|  44 MGVALLAGPANVIMELAMPGVGYGVLESrveSgRLDRhPIKRARTTFTYVAVAVAGSDDQKAAFRRAVNKVHAQVYSTPE 123
                                    7999**99******************777776688556****************************************99 PP

                        DUF2236  82 sgerygainpedllwvhatfsasflraygrtvgpltaeeeeayyhewrrvgrllGvpdrllpatraafdayldemvlael 161
                                    s+  y+a++pe++lwv+a+++++ +++y+ +vg++++ee++  y+    +g++l+vp++++p +raafd+y+ +  l+++
  gi|121636189|ref|YP_976412.1| 124 SPVSYHAFDPELQLWVAACLYKGGVDVYRTFVGEMDDEEADHHYRAGMAMGTTLQVPPQMWPPDRAAFDRYWRQS-LDRV 202
                                    99***********************************************************99**********99.6*** PP

                        DUF2236 162 evdeearel........gdarll.......parpalpllrvitrgllppalrellglpvpwssrdellvvalralvrlar 226
                                    ++d+ +r++             +       ++r++  +  +it+g+lp+++r+ ++lp  w ++ +++   + al++++r
  gi|121636189|ref|YP_976412.1| 203 HIDDVVRDYlypivalrI----RgialpgpLRRLSEGIALLITTGFLPQRFRDEMRLP--WDATKQRR---FDALMAVLR 273
                                    *********777755440....2556666677999***********************..********...******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2383.63
//
Query:       gi|121636190|ref|YP_976413.1|  [L=142]
Description: hypothetical protein BCG_0315c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-11   44.0   0.0      3e-11   43.9   0.0    1.0  1  PIN       PIN domain
      0.005   16.6   0.0       0.01   15.6   0.0    1.6  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   3.4e-15     3e-11       2     120 ..       3     133 ..       2     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.4e-15
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkil 71 
                                    ++D +vl+a++  ++++++++r ++++l    +   +++lv+a +l+  ++      +s r  a ++ve+    + +   
  gi|121636190|ref|YP_976413.1|   3 LIDVNVLLAAHrGDHPNHRTVRPWFDRLlaadDPFTVPNLVWASFLRLTTNrrifeIPSPRADAFAFVEAVNAQPHHLPT 82 
                                    79***********************************************************************9999999 PP

                                    EBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  72 pidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                    + + +++   +++ ++++    l+ Da++ A A eh ++++ + D+df+r a
  gi|121636190|ref|YP_976413.1|  83 SPGPRHLVLLRKLCDEADasgDLIPDAVLGAIAVEHHCAVV-SLDRDFARFA 133
                                    99************************************999.*******987 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-06      0.01      33      67 ..     102     139 ..      88     142 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                        DUF5615  33 eg..asDeeileyAkeedriivTkDkDFgel.lllggp 67 
                                    +g  ++D    ++A e+ +++v+ D+DF +  + ++ +
  gi|121636190|ref|YP_976413.1| 102 SGdlIPDAVLGAIAVEHHCAVVSLDRDFARFaSVRHIR 139
                                    4456999999******************9986555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1149.57
//
Query:       gi|121636191|ref|YP_976414.1|  [L=85]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-06   27.7   2.7    2.8e-06   27.1   2.7    1.4  1  RHH_1           Ribbon-helix-helix protein, copG family
    0.00095   19.0   0.7     0.0018   18.1   0.7    1.5  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
     0.0097   16.3   1.7      0.022   15.2   0.6    2.1  2  CcdA            Post-segregation antitoxin CcdA
  ------ inclusion threshold ------
      0.011   16.5   0.9      0.015   16.0   0.9    1.2  1  PSK_trans_fac   Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   2.7   6.2e-10   2.8e-06       1      37 [.       2      38 ..       2      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.2e-10
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   r+++++++ell++  ++ar+rg+S +++I++Alr+ l
  gi|121636191|ref|YP_976414.1|  2 RTTVSISDELLATAKRRARERGQSLGAVIEDALRREL 38
                                   89********************************988 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.7     4e-07    0.0018       1      34 [.       1      36 [.       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKr..EaVnlALre 34
                                   Mrt++ i DeLla A r+++ ++++  ++++ ALr+
  gi|121636191|ref|YP_976414.1|  1 MRTTVSISDELLATAKRRARERGQSlgAVIEDALRR 36
                                   9*******************8888766999999985 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   4.9e-06     0.022       3      39 ..       2      42 ..       1      47 [. 0.81
   2 ?   -2.1   0.0       1.2   5.3e+03      23      32 ..      71      80 ..      68      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-06
                           CcdA  3 avnlsldsdllaqA....ralgiNlSatleeaLaeevkeek 39
                                   ++++s++ +lla+A    r+ g +l a++e+aL++e+++++
  gi|121636191|ref|YP_976414.1|  2 RTTVSISDELLATAkrraRERGQSLGAVIEDALRRELAAAR 42
                                   699********976111156799*************99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                           CcdA 23 lSatleeaLa 32
                                   lS++l+e+L+
  gi|121636191|ref|YP_976414.1| 71 LSEVLDEGLE 80
                                   7888888886 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.9   3.4e-06     0.015      13      46 ..      14      47 ..       8      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                  PSK_trans_fac 13 lareLarltgeskteAvrrAleerlerlrrerae 46
                                    a++ ar +g+s+ +++++Al+++l+  r   a+
  gi|121636191|ref|YP_976414.1| 14 TAKRRARERGQSLGAVIEDALRRELAAARTGGAR 47
                                   678889********************99865444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 599.05
//
Query:       gi|121636192|ref|YP_976415.1|  [L=916]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-33  115.5  26.6    1.9e-33  114.6  26.6    1.5  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  26.6   1.1e-37   1.9e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.1e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe++aaaa+dla++ s+++aanaaaaa tta+laa+aDeVS+a+Aalf+ah+q+yqalsaqa+afh+qf qal++
  gi|121636192|ref|YP_976415.1|  1 MSFVIAAPEVIAAAATDLASLESSIAAANAAAAANTTALLAAGADEVSTAVAALFGAHGQAYQALSAQAQAFHAQFTQALTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++g+YaaaEaa
  gi|121636192|ref|YP_976415.1| 83 GGGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (916 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.09u 0.30s 00:00:01.39 Elapsed: 00:00:00.54
# Mc/sec: 5138.82
//
Query:       gi|121636193|ref|YP_976416.1|  [L=899]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-35  120.7  25.2    3.7e-35  120.1  25.2    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1  25.2   2.1e-39   3.7e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 2.1e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe++aaaa+dla++gs++saanaaaaa tta++aa+aDeVS+aiAalf+ah+q+yqalsaqa+afh+qfvqal++
  gi|121636193|ref|YP_976416.1|  1 MSFVIAAPEVIAAAATDLASLGSSISAANAAAAANTTALMAAGADEVSTAIAALFGAHGQAYQALSAQAQAFHAQFVQALTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++g+YaaaEaa
  gi|121636193|ref|YP_976416.1| 83 GGGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (899 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.07u 0.35s 00:00:01.42 Elapsed: 00:00:00.58
# Mc/sec: 4703.38
//
Query:       gi|121636194|ref|YP_976417.1|  [L=834]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-34  117.5  26.6    3.8e-34  116.9  26.6    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9  26.6   2.1e-38   3.8e-34       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 2.1e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe++aaaa+dla++ s+++aanaaaaa tta+laa+aDeVS+a+Aalf+ah+q+yqalsaqa+afh+qfvqal++
  gi|121636194|ref|YP_976417.1|  1 MSFVIAAPEVIAAAATDLASLESSIAAANAAAAANTTALLAAGADEVSTAVAALFGAHGQAYQALSAQAQAFHAQFVQALTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++g+YaaaEaa
  gi|121636194|ref|YP_976417.1| 83 GGGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.01u 0.37s 00:00:01.38 Elapsed: 00:00:00.56
# Mc/sec: 4463.91
//
Query:       gi|121636195|ref|YP_976418.1|  [L=536]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-58  197.7  23.1    1.2e-58  197.7  23.1    2.8  3  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7  23.1   6.8e-63   1.2e-58       1     157 [.       6     162 ..       6     163 .. 0.99
   2 ?   -4.9   4.3         1   1.8e+04      71      91 ..     341     361 ..     286     378 .. 0.52
   3 ?   -4.0   4.1      0.76   1.4e+04      76      96 ..     406     426 ..     401     438 .. 0.49

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 6.8e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall++Gpg+g++l Aa  W++L+ae+a++a+el  +l +++++aWqGps+aa++aa+apylaWL +a++ ++
  gi|121636195|ref|YP_976418.1|   6 ASPPEVHSALLSSGPGPGSVLSAAGVWSSLSAEYAAVADELIGLLGAVQTGAWQGPSAAAYVAAHAPYLAWLMRASETSA 85 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    eaAa++e++aaaY++A+aam+++ e+aan++ + +lvatnffG+nt++Ia +ea+y++mw+q+a++ma+Y+a+++aa
  gi|121636195|ref|YP_976418.1|  86 EAAARHETVAAAYTTAVAAMPTLVELAANHTLHGVLVATNFFGINTIPIALNEADYARMWTQAASTMATYQAVAEAA 162
                                    **************************************************************************998 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHH CS
                            PPE  71 WLsaaaaqaeeaAaqaeaaaa 91 
                                     ++ a + a+  Aa+a+aaa 
  gi|121636195|ref|YP_976418.1| 341 AVAMAPTMAAPGAAVASAAAP 361
                                    333333333333333333333 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHHHHHHHHHHH CS
                            PPE  76 aaqaeeaAaqaeaaaaaYeaA 96 
                                    +a+a+++A q ++aaaa  aA
  gi|121636195|ref|YP_976418.1| 406 SASAQRKAPQPDSAAAAAAAA 426
                                    444444444444444432222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3203.92
//
Query:       gi|121636196|ref|YP_976419.1|  [L=302]
Description: hypothetical protein BCG_0321 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-60  204.4   0.2    1.9e-60  204.1   0.2    1.1  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.2     1e-64   1.9e-60       1     187 [.      18     198 ..      18     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 1e-64
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    al va arale++++ d+l+ Dp+ae++++a+g  +  +  d++l ++k   k+    +++ +++ +Rt++fd+++++a+
  gi|121636196|ref|YP_976419.1|  18 ALFVATARALEAQKS-DPLVVDPYAEAFCRAVGGSW-ADVLDGKLPDHK--LKSTDFGEHFVNFQGARTKYFDEYFRRAA 93 
                                    7889*********98.****************9987.888899998887..346667899******************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     aag+rqvViL+AGlD+rayRlpw++g++vfE+D+p+vl+fKre+l+ +ga+p+a +r ++vDlr ddwp+aL+++gfd+
  gi|121636196|ref|YP_976419.1|  94 -AAGARQVVILAAGLDSRAYRLPWPDGTTVFELDRPQVLDFKREVLASHGAQPRALRREIAVDLR-DDWPQALRDSGFDA 171
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleai 187
                                    ++p+aw+aeG+l+YL+++a+++l+  i
  gi|121636196|ref|YP_976419.1| 172 AAPSAWIAEGLLIYLPATAQERLFTGI 198
                                    ***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2149.36
//
Query:       gi|121636197|ref|YP_976420.1|  [L=631]
Description: hypothetical protein BCG_0322 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-19   69.2   0.0    8.3e-19   68.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
    6.4e-13   48.7   0.2    1.7e-12   47.3   0.2    1.8  1  AAA_lid_6        AAA lid domain
    1.4e-06   27.9   0.2    8.3e-05   22.1   0.1    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.6e-05   24.0   0.0    8.7e-05   22.3   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00061   20.2   1.1     0.0014   19.1   0.1    2.1  2  AAA_16           AAA ATPase domain
    0.00092   19.8   0.0     0.0023   18.5   0.0    1.7  1  AAA_18           AAA domain
     0.0011   18.9   0.0     0.0031   17.5   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0055   16.5   0.2       0.03   14.1   0.0    2.3  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.3       0.26   11.5   0.1    2.5  2  AAA_22           AAA domain
      0.019   14.7   0.2       0.26   11.0   0.2    2.2  1  Sigma54_activat  Sigma-54 interaction domain
      0.021   15.1   0.1      0.097   12.9   0.0    2.3  2  AAA_28           AAA domain
      0.022   14.9   0.1       0.08   13.1   0.1    2.1  1  AAA_33           AAA domain
      0.034   13.9   0.0      0.065   13.0   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.041   14.0   0.0      0.088   12.9   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.052   13.5   0.0      0.078   12.9   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.061   12.5   0.1        4.5    6.4   0.0    2.3  2  DUF815           Protein of unknown function (DUF815)
      0.067   13.5   0.1        0.2   12.0   0.1    1.8  1  AAA_19           AAA domain
       0.13   12.1   0.1       0.87    9.4   0.0    2.3  3  AAA_3            ATPase family associated with various cellul
       0.17   11.3   0.0       0.29   10.6   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
        0.2   11.4   0.0       0.38   10.5   0.0    1.4  1  AAA_11           AAA domain
       0.27   10.8   3.0        1.4    8.4   0.6    2.8  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   9.7e-22   8.3e-19       2     131 ..     382     513 ..     381     514 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 9.7e-22
                                    EEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA   2 llyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                    ++ GppGtGKT++a+ vak           ++ e+  ++l+ +++ge+e+k+++++++a       +lf+DE++al+ + 
  gi|121636197|ref|YP_976420.1| 382 VFAGPPGTGKTTIARVVAKIYcglgllkRENIREVHRADLIGQHIGETEAKTNAIIDSA--L--DGVLFLDEAYALVATG 457
                                    799*****************544444434889************************997..3..38***********999 PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..GGGSTHHHH.S.TTSSEEEETT CS
                            AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnr..pdkldpall.r.gRfdrkieie 131
                                      ++++++  ++++Ll+ +++ ++   +++vi+a++r   dk+ +    + +Rf+r i ++
  gi|121636197|ref|YP_976420.1| 458 --AKNDFGLVAIDTLLARMENDRD---RLVVIIAGYRadLDKFLDTNEgLrSRFTRNIDFP 513
                                    ..99*******************9...6*********776776665554459999999886 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.2     2e-15   1.7e-12      15      62 .]     564     614 ..     538     614 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2e-15
                      AAA_lid_6  15 rrdenfGNARfVRnllekairrqadRlatt...ddseltredlmtLtaeDi 62 
                                    r  + +GN+RfVRn++e+++++++ Rl+++    ++e ++e+lmt+ta+D+
  gi|121636197|ref|YP_976420.1| 564 RSLDIAGNGRFVRNIVERSEEEREFRLDHSehaGSGEFSDEELMTITADDV 614
                                    444559********************************************7 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   9.7e-08   8.3e-05      13      50 ..     370     406 ..     363     434 .. 0.72
   2 ?    4.5   0.0     0.023        20      82     115 ..     417     450 ..     406     456 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.7e-08
                   Mg_chelatase  13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                    r l++a   +H+l+++GppG+GKt +a+ ++++ + l 
  gi|121636197|ref|YP_976420.1| 370 RGLTVAQ-RTHHLVFAGPPGTGKTTIARVVAKIYCGLG 406
                                    5566654.58********************99977653 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                   Mg_chelatase  82 hhsaskaalvGggskpkpGeislahnGvLfLDEl 115
                                    h++      +G  +  +   i  a  GvLfLDE+
  gi|121636197|ref|YP_976420.1| 417 HRADLIGQHIGETEAKTNAIIDSALDGVLFLDEA 450
                                    44444444566666777778899**********7 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     1e-07   8.7e-05       5      55 ..     340     400 ..     338     455 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                         RuvB_N   5 sleeyigqekvkeklk.....ifieaa.kkre....ealdhvllyGpPGlGkttlakiiak 55 
                                    +l+e+ig ++vk +++     +++e   k+r+    +   h++++GpPG Gktt+a+++ak
  gi|121636197|ref|YP_976420.1| 340 QLAEFIGLDEVKRQVSrlkssVAMELVrKQRGltvaQRTHHLVFAGPPGTGKTTIARVVAK 400
                                    5789999999988764222225555441345422225678*******************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.5   3.8e+03      53     106 ..     255     308 ..     242     345 .. 0.57
   2 !   19.1   0.1   1.6e-06    0.0014      21     141 ..     375     485 ..     352     511 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                         AAA_16  53 giflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeala 106
                                    +++lr++ d+  sa + ++ l  a  ++e ++q l++++   +   + ++e+++ 
  gi|121636197|ref|YP_976420.1| 255 ALVLRAHVDEE-SASEVLQdLYAAHPENEQVEQALSDTSFGIVTTTAGRIEARTD 308
                                    46666666665.4444444477777777777777777555555444444444444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.6e-06
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                    ++r++ +++ G++G+GK++++r +++ +++  g++ r++            + ++  r +l+ q   e+e++  +  + +
  gi|121636197|ref|YP_976420.1| 375 AQRTHHLVFAGPPGTGKTTIARVVAKIYCGL-GLLKREN------------IREVH-RADLIGQHIGETEAKTNAIIDSA 440
                                    567799*******************966654.2222222............44556.77999999999888888888888 PP

                         AAA_16 101 leeala...avpelagaea..srllellkrllallsrderplvlvl 141
                                    l+++l    a  +l + +a     l ++  lla++++d++ lv+++
  gi|121636197|ref|YP_976420.1| 441 LDGVLFldeA-YALVATGAknDFGLVAIDTLLARMENDRDRLVVII 485
                                    8877775532.22222222534445555555588888777777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.7e-06    0.0023       3      91 ..     383     479 ..     381     492 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-06
                         AAA_18   3 ltGtpGvGKttlakeLskrl.gf....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                     +G+pG+GKtt+a+ ++k   g+     +n+r+v++ + +     ++ + e++       d++ld++   ++        
  gi|121636197|ref|YP_976420.1| 383 FAGPPGTGKTTIARVVAKIYcGLgllkRENIREVHRADLI----GQH-IGETEAKTNAIIDSALDGVLFLDEayalvatg 457
                                    69***************99655566776666666655332....222.22233333333344444444444444455555 PP

                         AAA_18  70 aleegknlvidghlaeleseaa 91 
                                    a  + + + id +la +e +++
  gi|121636197|ref|YP_976420.1| 458 AKNDFGLVAIDTLLARMENDRD 479
                                    4444455566666666666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.6e-06    0.0031       1      73 [.     380     449 ..     380     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEES CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDE 73 
                                    +++  GppGtgK+++a+ +a+ + +  ++   + r   ++dl+g+     g+t+ + +++ ++a  g +l+lDE
  gi|121636197|ref|YP_976420.1| 380 HLVFAGPPGTGKTTIARVVAKIYcGLGLLKRENIREVHRADLIGQHI---GETEAKTNAIIDSALDG-VLFLDE 449
                                    68899******************999999999999999999999998...66666666666565554.566666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.8   1.5e+03      43      77 ..     237     271 ..     228     311 .. 0.68
   2 !   14.1   0.0   3.5e-05      0.03      17      42 ..     377     402 ..     364     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.8
                         AAA_30  43 eaaggrviglAptgkaAkvLaeelgieastiakll 77 
                                    e+  g+v+++A  g+ Ak+L   + ++ ++  ++l
  gi|121636197|ref|YP_976420.1| 237 EEPDGPVAVAAVDGALAKALVLRAHVDEESASEVL 271
                                    44467899999999999997755555333333333 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaw 42 
                                    +    v  Gp+GtGKtt+ +++++++
  gi|121636197|ref|YP_976420.1| 377 RTHHLVFAGPPGTGKTTIARVVAKIY 402
                                    33467899**************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00031      0.26       6      28 ..     379     401 ..     374     430 .. 0.85
   2 ?    1.8   0.0       0.3   2.6e+02      87     135 ..     438     494 ..     405     496 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                         AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                     +lv  G++GtGKTt +r +++ 
  gi|121636197|ref|YP_976420.1| 379 HHLVFAGPPGTGKTTIARVVAKI 401
                                    689999***********988765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                         AAA_22  87 raravielliiDEaqhlr....s....eealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                    +++   ++l +DEa  l     +      a+ +L  +++++r+ + +i++G + +l+k
  gi|121636197|ref|YP_976420.1| 438 DSAL-DGVLFLDEAYALVatgaKndfgLVAIDTLLARMENDRDRLVVIIAGYRaDLDK 494
                                    3333.59*********987655167778888888777777999999999998777776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2    0.0003      0.26      16     105 ..     372     453 ..     357     503 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                    HHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTS CS
                Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgG 95 
                                     +va+ + +++  G  GtGK+++ar + +      + + + n     +e+ +++L G + G  t A++  +  +++a +G
  gi|121636197|ref|YP_976420.1| 372 LTVAQRTHHLVFAGPPGTGKTTIARVVAKIYC-GLGLLKREN----IREVHRADLIGQHIGE-TEAKT--NAIIDSALDG 443
                                    3567777889999************9977443.222233333....3455667777777764.44444..4578888888 PP

                                    EEEEETGGGS CS
                Sigma54_activat  96 tlfLDeigel 105
                                    +lfLDe   l
  gi|121636197|ref|YP_976420.1| 444 VLFLDEAYAL 453
                                    8888887665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.3   2.8e+03      26      44 ..     261     280 ..     251     306 .. 0.72
   2 ?   12.9   0.0   0.00011     0.097       3      36 ..     382     418 ..     380     471 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                         AAA_28  26 vv.pEaareileeklakged 44 
                                    +v +E+a e+l++++a + +
  gi|121636197|ref|YP_976420.1| 261 HVdEESASEVLQDLYAAHPE 280
                                    45689999999999966543 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                         AAA_28   3 vitGgestGKTtlleaLaar..gypvv.pEaareile 36 
                                    v+ G+++tGKTt+++  a+   g   + +E  re+ +
  gi|121636197|ref|YP_976420.1| 382 VFAGPPGTGKTTIARVVAKIycGLGLLkRENIREVHR 418
                                    899************9998667666666666666654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.4e-05      0.08       3      21 ..     382     400 ..     381     491 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                         AAA_33   3 llvGlpGsGKstlaerllk 21 
                                    ++ G+pG+GK+t a+ ++k
  gi|121636197|ref|YP_976420.1| 382 VFAGPPGTGKTTIARVVAK 400
                                    799************9886 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05     0.065      27      71 ..     358     402 ..     328     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                      IstB_IS21  27 arsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgvea 71 
                                    + s+  + v++ ++l   ++ + +v+ Gp+G+GK+ +a  +++  
  gi|121636197|ref|YP_976420.1| 358 KSSVAMELVRKQRGLTVAQRTHHLVFAGPPGTGKTTIARVVAKIY 402
                                    34566667777889999999*****************98877655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.088       5      76 ..     380     449 ..     376     458 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                    -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEET CS
                          AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDE 76 
                                     + ++gp g+Gkt +a+ +a++        l r + +e+  ++ + + + + + + ++++  + +G+++lDE
  gi|121636197|ref|YP_976420.1| 380 HLVFAGPPGTGKTTIARVVAKIYC--GLGLLKRENIREVHRADLIGQHIGETEAKTNAIIDSALDGVLFLDE 449
                                    5789******************97..578999*********99999*************************9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.2e-05     0.078      44      70 ..     377     403 ..     350     481 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                          Rad17  44 kkriLLisGPsGCgkstvvkvLskelg 70 
                                    + + L+ +GP+G gk+t+ +v++k++ 
  gi|121636197|ref|YP_976420.1| 377 RTHHLVFAGPPGTGKTTIARVVAKIYC 403
                                    2346899*****************963 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0052       4.5      39      91 ..     364     420 ..     324     449 .. 0.72
   2 ?    3.7   0.0     0.033        28     182     223 ..     502     543 ..     475     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0052
                         DUF815  39 alventeqfleglpannvLLwGarGtGKSslvkallneyaeegL....rlieveked 91 
                                    +lv+  + +   ++++++++ G  GtGK ++ + + + y+  gL     + ev++ d
  gi|121636197|ref|YP_976420.1| 364 ELVRKQRGLTVAQRTHHLVFAGPPGTGKTTIARVVAKIYCGLGLlkreNIREVHRAD 420
                                    4556666677778899********************999988842222344555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                         DUF815 182 LsdRFGlwlgFykldqeeYleiveklakklglelekeeleee 223
                                    L  RF  ++ F + + +e +ei +k+a++++  +e+++l++ 
  gi|121636197|ref|YP_976420.1| 502 LRSRFTRNIDFPSYTSHELVEIAHKMAEQRDSVFEQSALHDL 543
                                    778***************************999999887764 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023       0.2       8      37 ..     376     405 ..     369     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvel 37 
                                     + ++l+  ++pGtGKT++ + + +++  l
  gi|121636197|ref|YP_976420.1| 376 QRTHHLVFAGPPGTGKTTIARVVAKIYCGL 405
                                    344556666779*******99988877655 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.52   4.4e+02      63     100 ..     342     381 ..     327     382 .. 0.76
   2 ?    9.4   0.0     0.001      0.87       1      53 [.     380     433 ..     379     452 .. 0.79
   3 ?   -3.3   0.0       8.7   7.4e+03      86     117 ..     527     560 ..     522     563 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.52
                          AAA_3  63 anllladeinrappktqsal.leam.eerqvtvegethkl 100
                                    a+++  de+ r  ++ +s++ +e + ++r +tv+++th+l
  gi|121636197|ref|YP_976420.1| 342 AEFIGLDEVKRQVSRLKSSVaMELVrKQRGLTVAQRTHHL 381
                                    677778********99988634544145669999999887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.001
                          AAA_3   1 hvllegvPGlaktllvkalaka.ldlefkriqftpdllPsdilGtevfeekeke 53 
                                    h+++ g PG++kt++++ +ak+  +l + +     ++  +d++G+++ e+++k+
  gi|121636197|ref|YP_976420.1| 380 HLVFAGPPGTGKTTIARVVAKIyCGLGLLKRENIREVHRADLIGQHIGETEAKT 433
                                    88999***************9735777777777888999999999888777655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.7
                          AAA_3  86 meerq..vtvegethklpepflvlatqnPieqeG 117
                                    m+e++  v  +++ h+l+  f  la++   +++G
  gi|121636197|ref|YP_976420.1| 527 MAEQRdsVFEQSALHDLEALFAKLAAESTPDTNG 560
                                    5555411445666789999999998877666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.29      29      51 ..     374     396 ..     363     402 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                          AAA_7  29 llknkkpvllvGptGtGKtviik 51 
                                    + ++ +++++ Gp GtGKt+i++
  gi|121636197|ref|YP_976420.1| 374 VAQRTHHLVFAGPPGTGKTTIAR 396
                                    578899**************987 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00044      0.38      15      36 ..     376     397 ..     365     436 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                         AAA_11  15 seseitliqGPPGtgKTktive 36 
                                    ++++  ++ GPPGtgKT+    
  gi|121636197|ref|YP_976420.1| 376 QRTHHLVFAGPPGTGKTTIARV 397
                                    44555899*********54333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.2   1.9e+03      53     115 ..     144     200 ..     140     219 .. 0.54
   2 ?    8.4   0.6    0.0017       1.4      36      58 ..     381     403 ..     371     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                         AAA_25  53 lalava.tGkpwlgpvapeqgkVlyvsaEdsedelr.rRlravgealrddarllvldlagveslp 115
                                     a+a+a tG p   ++  +   V+   +E ++ ++r  R  av  ++r+ ++ +v++l +    p
  gi|121636197|ref|YP_976420.1| 144 YAAALAsTGGPE--EF-AKANHVVSGITERRA-GWRaARWLAVVINYRAERWSDVVKLLT----P 200
                                    455555566654..33.355556666666666.444356666667777777777777633....3 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                         AAA_25  36 allaGapgtGKttlaldlalava 58 
                                     ++aG+pgtGKtt+a  +a  ++
  gi|121636197|ref|YP_976420.1| 381 LVFAGPPGTGKTTIARVVAKIYC 403
                                    679***********977765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 4155.27
//
Query:       gi|121636198|ref|YP_976421.1|  [L=538]
Description: hypothetical protein BCG_0323 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.6e-177  591.0   2.6   1.8e-177  590.8   2.6    1.0  1  T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM


Domain annotation for each model (and alignments):
>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.8   2.6    1e-181  1.8e-177       2     473 ..      35     522 ..      34     523 .. 0.98

  Alignments for each domain:
  == domain 1  score: 590.8 bits;  conditional E-value: 1e-181
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSSEEEETTT-- CS
                 T7SS_ESX1_EccB   2 qlttrdqvsgyrFllrRlehAlvrrdvrmlddplrsqsrallvGvvlavvvlagaavlallkPqgkvgdskivadkesga 81 
                                    +++tr+qv+g+rF++rR++++++ +d+rml dplr+qsra+l+Gv+++++ l+g +v++l++P+g++g+++++ad++++a
  gi|121636198|ref|YP_976421.1|  35 GFVTRHQVTGWRFVMRRIAAGIALHDTRMLVDPLRTQSRAVLMGVLIVITGLIGSFVFSLIRPNGQAGSNAVLADRSTAA 114
                                    799***************************************************************************** PP

                                    EEEEETTEEEEES-HHHHHHHCTS-B--EEE-HHHHHTS-B--EBS-TTS-S---B-SS.SSCEEEEEEEECSTTSS..- CS
                 T7SS_ESX1_EccB  82 lYvvvdgtLhPvlNlaSArLilgkaakpttvkdseLdklprGplvGIpgAPealpqsadldeskWtvCDtvssaasa..s 159
                                    lYv+v+++LhPvlNl+SArLi+g++ +pttvk++eLd++prG+l+GIpgAPe+++q+++ ++++WtvCD  +++++   +
  gi|121636198|ref|YP_976421.1| 115 LYVRVGEQLHPVLNLTSARLIVGRPVSPTTVKSTELDQFPRGNLIGIPGAPERMVQNTS-TDANWTVCDGLNAPSRGgaD 193
                                    ***********************************************************.***********999888889 PP

                                    EEEEEEEES.----BTTEEE--TTEEEEEEETTEEEEEETTEEEEE-TTSHHHHHCCT--..TS--EE--HHHHHHS-EE CS
                 T7SS_ESX1_EccB 160 avettviag.klalgaraaelaadqavLvsadgktyLvydgkraeidladravtrAlgle..gakprpvsagllnalpev 236
                                     v++tviag  +++garaa+l ++qavLv++++ t+L++dgkr+ idlad+avt+ lgl+   ++pr +++gl+na+pe+
  gi|121636198|ref|YP_976421.1| 194 GVGVTVIAGpLEDTGARAAALGPGQAVLVDSGAGTWLLWDGKRSPIDLADHAVTSGLGLGadVPAPRIIASGLFNAIPEA 273
                                    *********88999*********************************************9878889************** PP

                                    EESS----TTTTSB-TTSS-TTSBTT-EEEEEET........TEEEEEEEETTEEEEE-HHHHHHHHHHT-TT-SS--EE CS
                 T7SS_ESX1_EccB 237 pplkaPaipgaGkpaglelggkarvGsvvkvsdad.......geeeyYvvlsdglqrvtevvadllrnansqgltepptv 309
                                    ppl+aP ip+aG+pa++ ++   ++G+vv++++ +       ++ +yY+vl+dglq++++v+a++lrn+ns+gl++pp++
  gi|121636198|ref|YP_976421.1| 274 PPLTAPIIPDAGNPASFGVPA--PIGAVVSSYALKdsgktisDTVQYYAVLPDGLQQISPVLAAILRNNNSYGLQQPPRL 351
                                    *************99997777..69*****998877889998899*********************************** PP

                                    -CCHCCCS-E-----...--SS--EEE-TTTS-EEEEEEEE-STTSS-EEEEEEESS-SS-GCCGEEE-TTSSEE..... CS
                 T7SS_ESX1_EccB 310 epdvlaklpvveelpvdayPekppkivdvkeapvlCaswekgagdarakvallagaalPvpekaktvelvsadgsgatvd 389
                                    ++d++aklpv++ l++++yP++p+++vdv+++pv+Ca w+k+ g+a+++++llag+alPvp+  +tvelv a g+g  ++
  gi|121636198|ref|YP_976421.1| 352 GADEVAKLPVSRVLDTRRYPSEPVSLVDVTRDPVTCAYWSKPVGAATSSLTLLAGSALPVPDAVHTVELVGA-GNGGVAT 430
                                    ***********************************************************************9.77999** PP

                                    .EEESSBE..EEEEEECSTT..CEEEEEEEETTSEEEEE-SH........HHHHHCT--S.-EE--HHHHTTSEEEEEE- CS
                 T7SS_ESX1_EccB 390 avylppgtgalvqatgaepaseargslfyvsdtGvRYgipde........etakaLGlkeepepaPwsilkllpaGPtLs 461
                                    +v+l+ gtg++ q++g  p+++ +gslf+vsdtGvRYgi++e        ++++aLGl+ +p+p+Pws+l+l+++GPtLs
  gi|121636198|ref|YP_976421.1| 431 RVALAAGTGYFTQTVGGGPDAPGAGSLFWVSDTGVRYGIDNEpqgvagggKAVEALGLNPPPVPIPWSVLSLFVPGPTLS 510
                                    ******************************************************************************** PP

                                    CCCCT-EESSXX CS
                 T7SS_ESX1_EccB 462 radAlvahDglp 473
                                    radAl+ahD+l 
  gi|121636198|ref|YP_976421.1| 511 RADALLAHDTLV 522
                                    *********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3574.14
//
Query:       gi|121636199|ref|YP_976422.1|  [L=1330]
Description: hypothetical protein BCG_0324 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-102  342.4   0.0    8.2e-73  244.7   0.0    4.5  3  FtsK_SpoIIIE     FtsK/SpoIIIE family
    4.3e-10   40.0   0.0      0.032   14.5   0.0    3.9  3  AAA_22           AAA domain
    5.9e-09   36.5   0.1      0.043   14.2   0.0    4.2  3  AAA_16           AAA ATPase domain
    3.5e-08   33.5   0.0      0.011   15.6   0.0    3.8  3  NACHT            NACHT domain
    9.2e-06   26.1   0.0        1.2    9.5   0.0    3.5  3  AAA_19           AAA domain
    9.2e-06   25.7   0.0     0.0039   17.1   0.0    3.0  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00017   21.4   0.0        3.5    7.3   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00021   20.5   0.1        4.2    6.3   0.1    3.5  3  T2SSE            Type II/IV secretion system protein
    0.00023   20.9   1.9        2.8    7.7   0.3    3.5  3  AAA_29           P-loop containing region of AAA domain
    0.00036   19.5   0.1        0.1   11.5   0.0    2.9  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    0.00079   19.6   0.0     0.0085   16.2   0.0    2.2  2  DUF87            Helicase HerA, central domain
     0.0008   19.8   0.0        5.1    7.5   0.0    3.7  4  RNA_helicase     RNA helicase
     0.0022   18.5   0.0        1.9    9.0   0.0    3.2  3  ABC_tran         ABC transporter
     0.0027   17.8   0.0       0.81    9.7   0.0    3.6  3  AAA_14           AAA domain
     0.0049   16.5   0.1        2.9    7.5   0.0    2.7  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0052   16.9   0.0         13    6.0   0.0    3.7  3  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.027   14.7   0.0       0.34   11.1   0.0    2.6  3  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.031   14.7   0.0        0.1   13.0   0.0    1.9  1  GspH             Type II transport protein GspH
      0.043   13.5   0.0         12    5.5   0.0    2.9  3  AAA_24           AAA domain
      0.057   12.3   0.1          5    5.9   0.0    2.6  3  AAA_10           AAA-like domain
      0.072   13.6   0.0         29    5.1   0.0    3.1  3  AAA_23           AAA domain
      0.078   12.4   0.0        5.4    6.4   0.0    3.0  3  TniB             Bacterial TniB protein
      0.093   12.8   0.0        8.4    6.5   0.0    3.1  3  MMR_HSR1         50S ribosome-binding GTPase
       0.19   10.5   0.0       0.32    9.8   0.0    1.3  1  RHSP             Retrotransposon hot spot protein
       0.22   12.1   0.0          3    8.4   0.0    2.7  3  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   3.1e-22   2.2e-19      13     241 ..     441     635 ..     435     637 .. 0.91
   2 !  244.7   0.0   1.1e-75   8.2e-73       4     241 ..     787    1037 ..     785    1039 .. 0.98
   3 !   17.4   0.0   3.1e-06    0.0023      29      79 ..    1091    1140 ..    1075    1185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.1e-22
                                    T---TTEEEEEEETTS-EEEEEGGGS-......SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS.SCGG CS
                   FtsK_SpoIIIE  13 tessqlpvalgkeisgnplvldlkkma.....shllvaGatgsGKStalntLilSlatthtPeeVqliliDykgv.elsa 86 
                                    +++++l v +g+ ++g+pl++dlk  a     +h+l +G tgsGKS +l++++lSl+tth++e++  i  D+kg     +
  gi|121636199|ref|YP_976422.1| 441 RRDEELRVPIGVTGTGEPLMFDLKDEAeggmgPHGLMIGMTGSGKSQTLMSILLSLLTTHSAERLIVIYADFKGEaGADS 520
                                    5678899999***************************************************************9977789 PP

                                    GTT-TTBSS...S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-........... CS
                   FtsK_SpoIIIE  87 lediphlls..vavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddlaaene 164
                                    + d p++++   ++a+    a r+ + L  e+ +r+ l+reag +   ++ + + e+++ i                   
  gi|121636199|ref|YP_976422.1| 521 FRDFPQVVAviSNMAEKKSLADRFADTLRGEVARREMLLREAGRKVQGSAFNSVLEYENAI------------------- 581
                                    9999999997779******************************998888555556666664................... PP

                                    ...........-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                   FtsK_SpoIIIE 165 ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrl 241
                                                      +ag  l + p+l+v+ de+  L+la+  +      ++++  arkgr+ ++H l+a q l
  gi|121636199|ref|YP_976422.1| 582 ------------------AAGHSLPPIPTLFVVADEF-TLMLADHPE----YAELFDYVARKGRSFRIHILFASQTL 635
                                    ..................5889999**********99.599999999....99*******************99975 PP

  == domain 2  score: 244.7 bits;  conditional E-value: 1.1e-75
                                     HHHTSHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTS CS
                   FtsK_SpoIIIE    4 evleskkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykg 81  
                                     +++   +++++++ +++++++e++++plv+d++++a++++++G+++sGKStal+t+ilS+a+ h+P+eV+++++Dy+g
  gi|121636199|ref|YP_976422.1|  787 ARAGVGPRQWRWPLGEIDRPFEMRRDPLVFDARSSAGNMVIHGGPKSGKSTALQTFILSAASLHSPHEVSFYCLDYGG 864 
                                     56778899********************************************************************** PP

                                     SSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHH..HHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-.... CS
                   FtsK_SpoIIIE   82 velsalediphllsvavatdperalraleeLvkemeery..alfreagvrsiaaydgeiaedpldifgdvflvlDnyd 157 
                                     ++l+al+d++h++sva+a +per++r++ eL++++ +r+  ++fr++g++ ++  d++++e++l+i++++ + +Dn+d
  gi|121636199|ref|YP_976422.1|  865 GQLRALQDLAHVGSVASALEPERIRRTFGELEQLLLSRQqrEVFRDRGANGSTP-DDGFGEVFLVIDNLYGFGRDNTD 941 
                                     ***************************************999********9999.*********************** PP

                                     .....................-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHH...... CS
                   FtsK_SpoIIIE  158 dlaaene...ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlark...... 226 
                                     +++++n+   r+t+L+n+g++yg+hv++t++++le + +++++++ r+eLrl++++ds+v+v +a++R+a++      
  gi|121636199|ref|YP_976422.1|  942 QFNTRNPllaRVTELVNVGLAYGIHVIITTPSWLEVPLAMRDGLGLRLELRLHDARDSNVRVVGALRRPADAvphdqp 1019
                                     ************************************************************************999999 PP

                                     CG...GGTEEEEEEES-- CS
                   FtsK_SpoIIIE  227 gr...aaglHlllatqrl 241 
                                     gr   +a+ H+l+a+++l
  gi|121636199|ref|YP_976422.1| 1020 GRgltMAAEHFLFAAPEL 1037
                                     88999*********9975 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.1e-06
                                     -EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-T CS
                   FtsK_SpoIIIE   29 nplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDy 79  
                                      p++ldl+ ++  l+v G   sGK+t l+ +i  +   +t+++V++ ++D 
  gi|121636199|ref|YP_976422.1| 1091 APVILDLAANP-LLMVFGDARSGKTTLLRHIIRTVREHSTADRVAFTVLDR 1140
                                     5899*******.*************************************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0052       3.7       7      67 ..     474     551 ..     470     634 .. 0.66
   2 !   14.5   0.0   4.4e-05     0.032       3      99 ..     820     931 ..     818     973 .. 0.65
   3 !   12.7   0.0   0.00016      0.11       7      48 ..    1102    1148 ..    1099    1213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdllrellralgle 67 
                                    +++ +G +G+GK+ +l  +l +l    +ae+                 ++ ++v   +++  + k+l+ +++  l  e
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSQTLMSILLSLLTTHSAERliviyadfkgeagadsfRDFPQVVAVISNMAEKKSLADRFADTLRGE 551
                                    7889*********99999999997655555455555555555555555555555555555555555555555555443 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.4e-05
                         AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka.erlsseelle 80 
                                    ++ag +v++G + +GK+t l+++  ++        ++p+ v f++l  ++++   l++l++ +g+ ++a e+ + ++ + 
  gi|121636199|ref|YP_976422.1| 820 SSAGNMVIHGGPKSGKSTALQTFILSAA-----SLHSPHEVsFYCLDYGGGQLRALQDLAH-VGSVASAlEPERIRRTFG 893
                                    6899*********************983.....3344444425555555555555555543.444444444556666666 PP

                         AAA_22  81 aleqalrarav...................ielliiDE 99 
                                     leq l +r+                     ++l+iD+
  gi|121636199|ref|YP_976422.1| 894 ELEQLLLSRQQrevfrdrgangstpddgfgEVFLVIDN 931
                                    66666665555333333333444444445555566655 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00016
                         AAA_22    7 ilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlp 48  
                                     +l+v+G + +GKTtllr + ++  e++ a++      ++++ +v+ p
  gi|121636199|ref|YP_976422.1| 1102 LLMVFGDARSGKTTLLRHIIRTVREHSTADRvaftvLDRRLHLVDEP 1148
                                     689*******************9999888887777744444455444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0016       1.1      18     113 ..     466     568 ..     456     622 .. 0.62
   2 !    7.2   0.0    0.0086       6.2      22      88 ..     820     894 ..     812     959 .. 0.66
   3 !   14.2   0.0   5.9e-05     0.043      25     152 ..    1101    1212 ..    1085    1242 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                         AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdql.esaipysalaqalareellrqllde.aes 91 
                                     +  g ++  l +G+ G+GKs  + ++l +l ++    + i+++++++   + a       + +   ++++ + ++ +++
  gi|121636199|ref|YP_976422.1| 466 EAEGGMGPHGLMIGMTGSGKSQTLMSILLSLLTThsaeRLIVIYADFKGEaG-A----DSFRDF-P-QVVAVISNMaEKK 538
                                    556667799999*********9998888877777788679999999998821.1....133333.2.2222222222334 PP

                         AAA_16  92 aeleawrekleeala........avpelag 113
                                    +++++++++l++++a        a++++ g
  gi|121636199|ref|YP_976422.1| 539 SLADRFADTLRGEVArremllreAGRKVQG 568
                                    455555555555555444433333333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0086
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesa........ipysalaqalareellrqllde 88 
                                    ++ ++++++G + +GKs+ ++++  ++   +  + ++  c +++ +        ++   +a+al+  e +r    e
  gi|121636199|ref|YP_976422.1| 820 SSAGNMVIHGGPKSGKSTALQTFILSAASLHsPHEVSFYCLDYGGGqlralqdlAHVGSVASALEP-ERIRRTFGE 894
                                    3448999*************8887444333336667777777733323233332233336666655.333333333 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.9e-05
                         AAA_16   25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102 
                                     +l+++ G++ +GK++l+r++ r ++++       ++d+           ++l+r      l de+     +++ + ++
  gi|121636199|ref|YP_976422.1| 1101 PLLMVFGDARSGKTTLLRHIIRTVREH------STADRV--------AFTVLDR---RLHLVDEPLF-PDNEYTANID 1160
                                     7899*****************988888......333333........2233322...2233333333.3344444444 PP

                         AAA_16  103 ealaavpelagaea.srllellkrll.allsrderplvlvlDdlqwadeasl 152 
                                     + + a   la  ++ +r  + ++++  ++ +  +++ +l++Dd++++ ++++
  gi|121636199|ref|YP_976422.1| 1161 RIIPAMLGLANLIEaRRPPAGMSAAElSRWTFAGHTHYLIIDDVDQVPDSPA 1212
                                     4433222222211135555555555544444445555666666666655554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.27   1.9e+02       5      31 ..     477     503 ..     475     514 .. 0.78
   2 !   10.8   0.0   0.00046      0.33       3     127 ..     825     971 ..     824     983 .. 0.74
   3 !   15.6   0.0   1.6e-05     0.011       3     100 ..    1103    1218 ..    1101    1270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.27
                                    EEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT   5 lqGeaGsGKTtLlqklalawaegklpq 31 
                                    + G  GsGK+  l ++ l + + +  +
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMSILLSLLTTHSAE 503
                                    6899******99999998887776555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEE......ETTTTTTS-...-HCHHHCCCCTS--SSS-C..... CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFfl......slrelsrsgnarsladllfsqlpepaapvse..... 71 
                                    ++++G + sGK+t lq ++l +a+ + p+   +++F+       +lr          l+dl +    ++a ++++     
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFILSAASLHSPH---EVSFYCldygggQLR---------ALQDLAHVGSVASALEPERirrtf 892
                                    789*************************9...577774222222333.........444444433333333333322333 PP

                                    ..CHHHHCCSCCCEE...................EEEE-STT-SS-TCH...........HHHHHCTTTTT--EEEEEE CS
                          NACHT  72 ..vwavllelperlL...................lilDglDelvtdlgq..kekqpvrtlLselirkkllpeasllltv 127
                                        ++ll++++r +                   l++D l  + +d+    ++++p+    +el++  l  + ++++t+
  gi|121636199|ref|YP_976422.1| 893 geLEQLLLSRQQREVfrdrgangstpddgfgevfLVIDNLYGFGRDNTDqfNTRNPLLARVTELVNVGLAYGIHVIITT 971
                                    3344677777777779999999999999999999999999999998887789999999999999999999999999887 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.6e-05
                                     EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....................-HCHHHCCCC CS
                          NACHT    3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..................rsladllfsql 62  
                                     +++ G+a sGKTtLl++++++ +e        ++ F +  r+l    +                   ++la+l+ +  
  gi|121636199|ref|YP_976422.1| 1103 LMVFGDARSGKTTLLRHIIRTVREHSTAD---RVAFTVLDRRLHLVDEPlfpdneytanidriipamLGLANLIEARR 1177
                                     6788*******************999666...8999999999888877778899999999999999999999999999 PP

                                     TS--SSS-CCHHHHCCSCCCEE.EEEE-STT-SS-TCH..... CS
                          NACHT   63 pepaapvsevwavllelperlL.lilDglDelvtdlgq....k 100 
                                     p+ ++   e    +++ +  +  li+D++D++++ +       
  gi|121636199|ref|YP_976422.1| 1178 PPAGMSAAE--LSRWTFAGHTHyLIIDDVDQVPDSPAMtgpyI 1218
                                     999999988..66666665554599999999998665555543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.037        27      12      41 ..     474     503 ..     467     530 .. 0.82
   2 ?    6.9   0.0      0.01       7.2       8      41 ..     820     853 ..     815     892 .. 0.82
   3 !    9.5   0.0    0.0016       1.2       8      40 ..    1098    1130 ..    1093    1142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                         AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvk 41 
                                    + l+++  G+GK+++l+ i+  l+ +++ +
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSQTLMSILLSLLTTHSAE 503
                                    5688999*************9999999764 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvk 41 
                                    ++++++++ +Gp +GK++ l++ +  + +l++ +
  gi|121636199|ref|YP_976422.1| 820 SSAGNMVIHGGPKSGKSTALQTFILSAASLHSPH 853
                                    57889*****************998888777544 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0016
                         AAA_19    8 lkekvllvtaGpGtGKTrvlkhivallvelggv 40  
                                     +++++l+v + + +GKT++l+hi++ + e  + 
  gi|121636199|ref|YP_976422.1| 1098 AANPLLMVFGDARSGKTTLLRHIIRTVREHSTA 1130
                                     5678899******************99988765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.097        70      24      87 ..     476     549 ..     462     605 .. 0.67
   2 ?    1.2   0.0      0.41   2.9e+02      23      54 ..     825     858 ..     818     908 .. 0.82
   3 !   17.1   0.0   5.5e-06    0.0039      14      51 ..    1094    1133 ..    1085    1155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.097
                       ATPase_2  24 fiYGpegsGKtaLlkeiienledkdk....yviyyialreesiskldefie......eeeekkklekalgiavp 87 
                                    +  G  gsGK++ l+ i+  l+  +      viy +   e   +++++f +      +  ekk+l++ ++++++
  gi|121636199|ref|YP_976422.1| 476 LMIGMTGSGKSQTLMSILLSLLTTHSaerlIVIYADFKGEAGADSFRDFPQvvavisNMAEKKSLADRFADTLR 549
                                    567999*****999988888766655577778888888888888888886688888866666666666633332 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                       ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdk..yviyy 54 
                                    ++i G  +sGK++ l+ +i    +++   +v +y
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFILSAASLHSphEVSFY 858
                                    699**************99877665554455555 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.5e-06
                       ATPase_2   14 ilerepneiyfiYGpegsGKtaLlkeiienledkdk..yv 51  
                                     il+   n+ ++++G  +sGKt+Ll++ii   ++++   +v
  gi|121636199|ref|YP_976422.1| 1094 ILDLAANPLLMVFGDARSGKTTLLRHIIRTVREHSTadRV 1133
                                     5666778999******************998776653344 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.083        60       4      28 ..     478     500 ..     475     525 .. 0.77
   2 !    6.9   0.0    0.0064       4.6       2      21 ..     826     845 ..     825     864 .. 0.83
   3 !    7.3   0.0    0.0048       3.5       5      40 ..    1107    1149 ..    1103    1167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.083
                Viral_helicase1   4 hGvpGcGKStlirkllrtsliltvn 28 
                                     G+ G+GKS+ + ++l +   lt++
  gi|121636199|ref|YP_976422.1| 478 IGMTGSGKSQTLMSILLS--LLTTH 500
                                    599************988..44444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0064
                Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                                    v+hG p +GKSt++++++ +
  gi|121636199|ref|YP_976422.1| 826 VIHGGPKSGKSTALQTFILS 845
                                    8***************9987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0048
                Viral_helicase1    5 GvpGcGKStlirkllrts.liltvnrptaelltegk......p 40  
                                     G + +GK+tl+r+++rt   + t++r ++ +l +++       
  gi|121636199|ref|YP_976422.1| 1107 GDARSGKTTLLRHIIRTVrEHSTADRVAFTVLDRRLhlvdepL 1149
                                     55669************99888888888888888875554443 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0059       4.2     134     163 ..     477     508 ..     474     511 .. 0.76
   2 ?    3.6   0.0     0.042        30     127     150 ..     820     843 ..     811     851 .. 0.84
   3 !    5.9   0.0     0.008       5.7     118     156 ..    1091    1127 ..    1073    1141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0059
                          T2SSE 134 vsGgTgsGKttll.yallkeinks.derivtv 163
                                    + G TgsGK+ +l  +ll+ + ++  er++++
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLmSILLSLLTTHsAERLIVI 508
                                    5699******8874667777777777777765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.042
                          T2SSE 127 rerglilvsGgTgsGKttllyall 150
                                    ++ g++++ Gg  sGK+t l + +
  gi|121636199|ref|YP_976422.1| 820 SSAGNMVIHGGPKSGKSTALQTFI 843
                                    4679****************8876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.008
                          T2SSE  118 iaevlrkavrerglilvsGgTgsGKttllyallkeinks 156 
                                        +l  a  ++ l++v G   sGKttll  ++ ++ ++
  gi|121636199|ref|YP_976422.1| 1091 APVILDLA--ANPLLMVFGDARSGKTTLLRHIIRTVREH 1127
                                     44445545..788999******************99998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.3     0.004       2.8      24      48 ..     474     499 ..     464     504 .. 0.74
   2 !    7.0   0.1    0.0068       4.9      21      44 ..     821     842 ..     814     851 .. 0.77
   3 ?    3.1   0.0      0.11        82      24      39 ..    1102    1117 ..    1093    1122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
                         AAA_29  24 atlltGpsGsGKS.TllDAiqalLvp 48 
                                      l++G +GsGKS Tl+  +  lL+ 
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSqTLMSILLSLLTT 499
                                    459**********6666555566655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0068
                         AAA_29  21 lkgatlltGpsGsGKSTllDAiqa 44 
                                     +g++++ G   sGKST l  +++
  gi|121636199|ref|YP_976422.1| 821 SAGNMVIHGGPKSGKSTAL--QTF 842
                                    3579*************88..444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.11
                         AAA_29   24 atlltGpsGsGKSTll 39  
                                       ++ G+  sGK+Tll
  gi|121636199|ref|YP_976422.1| 1102 LLMVFGDARSGKTTLL 1117
                                     56889**********8 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00014       0.1      17      58 ..     474     519 ..     468     541 .. 0.75
   2 ?   -0.6   0.0      0.67   4.8e+02      11      37 ..     818     844 ..     812     850 .. 0.83
   3 ?    4.0   0.0     0.027        19      19      43 ..    1104    1128 ..    1100    1147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairarg..draivl..DltGafvsr 58 
                                    h l++G tGsGK+q+l ++l ++      +r iv+  D++G+  ++
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSQTLMSILLSLLTTHsaERLIVIyaDFKGEAGAD 519
                                    889************9998877655433377776434999987554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.67
                  TrwB_AAD_bind  11 keretqhilivGttGsGKtqalekllr 37 
                                     ++ +  ++i G+  sGK++al+ ++ 
  gi|121636199|ref|YP_976422.1| 818 ARSSAGNMVIHGGPKSGKSTALQTFIL 844
                                    56677889**************99985 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.027
                  TrwB_AAD_bind   19 livGttGsGKtqalekllrairarg 43  
                                     +++G + sGKt+ l++++r++r+  
  gi|121636199|ref|YP_976422.1| 1104 MVFGDARSGKTTLLRHIIRTVREHS 1128
                                     7789999***************976 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0085      25      81 ..     474     533 ..     466     552 .. 0.76
   2 ?    0.4   0.0      0.79   5.7e+02      12      49 ..    1091    1126 ..    1071    1140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                          DUF87  25 HlAilgsTGsGKSntvavLleellekkga.tilil..DpHGEYgkalekllsekvkvitp 81 
                                    H + +g+TGsGKS t  ++l +ll +++a +++++  D  GE g+ + + +++ v vi++
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSQTLMSILLSLLTTHSAeRLIVIyaDFKGEAGADSFRDFPQVVAVISN 533
                                    77789******************9966665555544477777666665666666666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.79
                          DUF87   12 vpvyldlnklvtrHlAilgsTGsGKSntvavLleelle 49  
                                      pv ldl  + +  l ++g + sGK+++ + +++ + e
  gi|121636199|ref|YP_976422.1| 1091 APVILDL--AANPLLMVFGDARSGKTTLLRHIIRTVRE 1126
                                     6777777..44677889***************997765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.31   2.2e+02       3      33 ..     477     507 ..     476     557 .. 0.75
   2 ?    4.9   0.0     0.048        34       2      35 ..     826     858 ..     825     863 .. 0.77
   3 !    7.5   0.0    0.0071       5.1       2      26 ..    1104    1128 ..    1103    1142 .. 0.86
   4 ?   -2.3   0.0         8   5.8e+03      51      64 ..    1197    1210 ..    1188    1215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkds 33 
                                    + G +g GKS++  ++  +ll++   ++   
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMSILLSLLTTHSAERLIV 507
                                    6799******999998888776654444444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.048
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvy 35 
                                    +++G +  GKSt+ ++++ + + +l ++++ s+y
  gi|121636199|ref|YP_976422.1| 826 VIHGGPKSGKSTALQTFILSAA-SLHSPHEVSFY 858
                                    79**************887766.44466666666 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0071
                   RNA_helicase    2 wlyGpsgeGKStlakeLakallkkl 26  
                                     +++G+++ GK+tl +++++++ +++
  gi|121636199|ref|YP_976422.1| 1104 MVFGDARSGKTTLLRHIIRTVREHS 1128
                                     799*****************99887 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 8
                   RNA_helicase   51 evvvidDfgqvkde 64  
                                      +++idD+ qv+d+
  gi|121636199|ref|YP_976422.1| 1197 HYLIIDDVDQVPDS 1210
                                     5789*******998 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.041        29      16      36 ..     477     498 ..     471     545 .. 0.82
   2 ?   -0.8   0.2       2.8     2e+03      14      32 ..     825     843 ..     820     847 .. 0.84
   3 !    9.0   0.0    0.0026       1.9       4      37 ..    1093    1126 ..    1090    1149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.041
                                    EEESTTSSHH.HHHHHHTTSS- CS
                                    xxxxxxxxxx.xxxxxxxxxxx RF
                       ABC_tran  16 ivGenGaGKS.tLlkllagllk 36 
                                    ++G +G+GKS tL+++l+ ll+
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSqTLMSILLSLLT 498
                                    79********666777766655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                                    EEEEESTTSSHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  14 vaivGenGaGKStLlklla 32 
                                    ++i G   +GKSt l++++
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFI 843
                                    67999999*****999875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0026
                                     EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran    4 vslklkegekvaivGenGaGKStLlkllagllkp 37  
                                     v l+l ++ ++ ++G+  +GK+tLl+ +++ ++ 
  gi|121636199|ref|YP_976422.1| 1093 VILDLAANPLLMVFGDARSGKTTLLRHIIRTVRE 1126
                                     66889999999******************99876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.2   8.3e+02       7      45 ..     477     519 ..     475     542 .. 0.63
   2 ?    2.3   0.0      0.22   1.6e+02       5      25 ..     825     845 ..     822     865 .. 0.80
   3 !    9.7   0.0    0.0011      0.81       3      43 ..    1101    1143 ..    1099    1266 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                         AAA_14   7 itGaRrvGKTtllkqlikell....vkkesilyinldderdkk 45 
                                    + G+  +GK+  l  ++ +ll    +++  ++y +++ e  ++
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMSILLSLLtthsAERLIVIYADFKGEAGAD 519
                                    579999****999999988888855555556666666655433 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                         AAA_14   5 lvitGaRrvGKTtllkqlike 25 
                                    +vi G  ++GK+t l+++i +
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFILS 845
                                    6899999**********9854 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                         AAA_14    3 kilvitGaRrvGKTtllkqlikell..vkkesilyinldderd 43  
                                     ++l++ G  r+GKTtll+++i++     +++++ +  ld+   
  gi|121636199|ref|YP_976422.1| 1101 PLLMVFGDARSGKTTLLRHIIRTVRehSTADRVAFTVLDRRLH 1143
                                     678899999************9988754555555555555433 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.011       7.8       5      37 ..     477     513 ..     473     530 .. 0.83
   2 ?   -2.5   0.0       4.7   3.3e+03       4      23 ..     826     845 ..     825     850 .. 0.79
   3 !    7.5   0.0     0.004       2.9       5      27 ..    1105    1127 ..    1101    1147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                                    EEESTTCCHHHHHHHHH....CT--SS-EEEEESS-S CS
                           cobW   5 ltGflGsGKTtLlnhll....enraglklavivNefg 37 
                                    + G  GsGK+  l ++l    + ++ ++l vi  +f+
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMSILlsllTTHSAERLIVIYADFK 513
                                    57999*****8888877798899999*********96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                    EEEESTTCCHHHHHHHHHCT CS
                           cobW   4 vltGflGsGKTtLlnhllen 23 
                                    v+ G + sGK+t l++ +  
  gi|121636199|ref|YP_976422.1| 826 VIHGGPKSGKSTALQTFILS 845
                                    7788888*******998854 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.004
                                     EEESTTCCHHHHHHHHHCT--SS CS
                           cobW    5 ltGflGsGKTtLlnhllenragl 27  
                                     + G   sGKTtLl+h+++  ++ 
  gi|121636199|ref|YP_976422.1| 1105 VFGDARSGKTTLLRHIIRTVREH 1127
                                     5666669**********543333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.018        13       3      20 ..     476     493 ..     475     539 .. 0.85
   2 ?    2.6   0.0      0.19   1.4e+02       3      78 ..     826     972 ..     825    1005 .. 0.76
   3 ?    3.5   0.0       0.1        72       1      63 [.    1102    1170 ..    1102    1194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                         AAA_33   3 llvGlpGsGKstlaerll 20 
                                    l++G+ GsGKs+ + ++l
  gi|121636199|ref|YP_976422.1| 476 LMIGMTGSGKSQTLMSIL 493
                                    69*********9988765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt.................................................. 32 
                                    +++G p sGKst ++  +  l a  l s+                                                   
  gi|121636199|ref|YP_976422.1| 826 VIHGGPKSGKSTALQTFI--LSAASLHSPHevsfycldygggqlralqdlahvgsvasaleperirrtfgeleqlllsrq 903
                                    678999999999999988..777777777777777777788888888888888888888888877777777777777777 PP

                         AAA_33  33 ........................lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat 78 
                                                            ++++l+g ++++ td+ + ++ l +++ el++  l+ g++vi+  +
  gi|121636199|ref|YP_976422.1| 904 qrevfrdrgangstpddgfgevflVIDNLYGFGRDN-TDQFNTRNPLLARVTELVNVGLAYGIHVIITTP 972
                                    777777777777777777777777777777776654.466777777777777888888888888888766 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                         AAA_33    1 lvllvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqq..sktdytrvldrlyqilnela 63  
                                     l+++ G + sGK+tl++++++       a +++  +l rrl   d++  ++++yt   dr++  + +la
  gi|121636199|ref|YP_976422.1| 1102 LLMVFGDARSGKTTLLRHIIRTVRehstADRVAFTVLDRRLHLVDEPlfPDNEYTANIDRIIPAMLGLA 1170
                                     678889999********9964322222566665555555555433333345555555555555555555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       9.4   6.7e+03       4      18 ..     477     491 ..     476     502 .. 0.81
   2 ?   -0.4   0.0       1.8   1.3e+03       2      25 ..     825     848 ..     824     862 .. 0.80
   3 ?   11.1   0.0   0.00048      0.34       2      41 ..    1103    1142 ..    1102    1154 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.4
                                    EESSTTSSHHHHHHC CS
                            Roc   4 lvGdsgvGKtsllkr 18 
                                    ++G +g+GK+  l +
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMS 491
                                    89*******986655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                    EEEESSTTSSHHHHHHCHCT-CCC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfs 25 
                                    +v+ G  ++GK++ l+ f+ +  s
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFILSAAS 848
                                    678899***********9976655 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00048
                                     EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEEC CS
                            Roc    2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkev 41  
                                     +++ Gd+++GKt+ll+++++   ++++   ++ ++l++++
  gi|121636199|ref|YP_976422.1| 1103 LMVFGDARSGKTTLLRHIIRTVREHSTADRVAFTVLDRRL 1142
                                     6899***************999999999888888887765 PP

>> GspH  Type II transport protein GspH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014       0.1      20      73 ..     336     414 ..     330     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                    SS-EEEECTT....E...................EE.ESCEESSSCCCCEETTTCSSEEEEEESSSSTTESSEC.TT-- CS
                           GspH  20 grpvtlcpss....g...................wq.ggWrvfvdanangtldggedvlrrgaaldggdtltga.akgt 73 
                                    g++v  c++s    +                   wq ggW+++ da+++ ++d  + + rr + +d++ t+ g  +++t
  gi|121636199|ref|YP_976422.1| 336 GVTVVHCSASaphrEqysdpekpilrvahgaierWQtGGWQPYIDAADQFSADEAAHLARRLSRWDSNPTHAGLrSAAT 414
                                    556666644455441445566666667777788899999*****************************99988754444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         2   1.4e+03       4      22 ..     474     492 ..     471     542 .. 0.65
   2 ?    4.4   0.0     0.037        27       4      22 ..     824     842 ..     821     869 .. 0.82
   3 ?    5.5   0.0     0.017        12       5      45 ..    1103    1152 ..    1099    1209 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                      l++G  g+GK+ ++ ++
  gi|121636199|ref|YP_976422.1| 474 HGLMIGMTGSGKSQTLMSI 492
                                    56899********998877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.037
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    +++i G +++GK+t + ++
  gi|121636199|ref|YP_976422.1| 824 NMVIHGGPKSGKSTALQTF 842
                                    799************9998 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                         AAA_24    5 iliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpd 45  
                                     ++++G++ +GKTtl++++          ++++f  +++ l+ +d   fpd
  gi|121636199|ref|YP_976422.1| 1103 LMVFGDARSGKTTLLRHIirtvrehstADRVAFTVLDRRLHLVDEPLFPD 1152
                                     689*************9977777777777777777666666666666665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.043        31      22      60 ..     473     515 ..     464     538 .. 0.68
   2 ?    5.9   0.0     0.007         5     247     295 ..     598     647 ..     591     665 .. 0.73
   3 ?   -2.9   0.0       3.4   2.4e+03      18      43 ..     819     844 ..     817     850 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.043
                         AAA_10  22 sasliiGdlGnGKSvlakllvlyisllg....gkaliiDpkke 60 
                                    ++ l+iG +G GKS +   + l ++         +++ D k e
  gi|121636199|ref|YP_976422.1| 473 PHGLMIGMTGSGKSQTLMSILLSLLTTHsaerLIVIYADFKGE 515
                                    7889**********98776665554443342223444566666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.007
                         AAA_10 247 DE.awiftssaeGkkllkelvRiGRsynaavylvtqsadDv.lkeelknni 295
                                    DE   ++++ +e ++l + + R+GRs+   +++++q   Dv + +++ +n 
  gi|121636199|ref|YP_976422.1| 598 DEfTLMLADHPEYAELFDYVARKGRSFRIHILFASQTL-DVgKIKDIDKNT 647
                                    662357899999***********************975.441333334444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.4
                         AAA_10  18 ktnasasliiGdlGnGKSvlakllvl 43 
                                    ++ a +++i G++  GKS   ++ +l
  gi|121636199|ref|YP_976422.1| 819 RSSAGNMVIHGGPKSGKSTALQTFIL 844
                                    6789999***********99988776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.31   2.2e+02      23      43 ..     476     496 ..     473     524 .. 0.83
   2 ?    2.0   0.0      0.37   2.6e+02      17      37 ..     818     840 ..     805     847 .. 0.77
   3 ?    5.1   0.0      0.04        29      18      39 ..    1099    1120 ..    1089    1124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.31
                         AAA_23  23 lItGpNGaGKTTildAiklaL 43 
                                    l +G++G+GK+  l  i l L
  gi|121636199|ref|YP_976422.1| 476 LMIGMTGSGKSQTLMSILLSL 496
                                    568********8888887766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.37
                         AAA_23  17 F..skgltlItGpNGaGKTTild 37 
                                       s g  +I+G   +GK+T l+
  gi|121636199|ref|YP_976422.1| 818 ArsSAGNMVIHGGPKSGKSTALQ 840
                                    35567889************997 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.04
                         AAA_23   18 skgltlItGpNGaGKTTildAi 39  
                                      ++l  ++G+  +GKTT+l+ i
  gi|121636199|ref|YP_976422.1| 1099 ANPLLMVFGDARSGKTTLLRHI 1120
                                     579999*************877 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         3   2.2e+03      36      53 ..     473     490 ..     462     522 .. 0.77
   2 ?    2.0   0.0      0.16   1.1e+02      34      56 ..     821     843 ..     812     856 .. 0.82
   3 ?    6.4   0.0    0.0076       5.4      36      73 ..    1101    1138 ..    1096    1268 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                           TniB  36 pnlllvGdsnnGKtmive 53 
                                    p+ l++G +  GK++ + 
  gi|121636199|ref|YP_976422.1| 473 PHGLMIGMTGSGKSQTLM 490
                                    788999*******98765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                           TniB  34 rmpnlllvGdsnnGKtmivekFa 56 
                                       n++++G ++ GK++ ++ F 
  gi|121636199|ref|YP_976422.1| 821 SAGNMVIHGGPKSGKSTALQTFI 843
                                    55699***************996 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0076
                           TniB   36 pnlllvGdsnnGKtmivekFarlhppekdedaekvpvl 73  
                                     p l+++Gd   GKt+++++  r+ ++++ +d+  + vl
  gi|121636199|ref|YP_976422.1| 1101 PLLMVFGDARSGKTTLLRHIIRTVREHSTADRVAFTVL 1138
                                     6799****************999999988888777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         2   1.4e+03       4      20 ..     477     493 ..     475     513 .. 0.76
   2 ?    1.9   0.0      0.32   2.3e+02       2      22 ..     825     845 ..     824     856 .. 0.81
   3 ?    6.5   0.0     0.012       8.4       3      40 ..    1104    1144 ..    1102    1162 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
                                    EEESTTSSHHHHHHHHH CS
                       MMR_HSR1   4 ivGrpNvGKStLinalt 20 
                                     +G++ +GKS  + +++
  gi|121636199|ref|YP_976422.1| 477 MIGMTGSGKSQTLMSIL 493
                                    69********6555544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.32
                                    EEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                    ++i G p +GKSt +++ + +
  gi|121636199|ref|YP_976422.1| 825 MVIHGGPKSGKSTALQTFILS 845
                                    6899*********99987655 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.012
                                     EEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEE CS
                       MMR_HSR1    3 aivGrpNvGKStLinaltge...kaivsdkpgtTrdinegr 40  
                                     +++G   +GK+tL++ ++++   ++ + + ++t +d + + 
  gi|121636199|ref|YP_976422.1| 1104 MVFGDARSGKTTLLRHIIRTvreHSTADRVAFTVLDRRLHL 1144
                                     7899999**********996433456666666666665554 PP

>> RHSP  Retrotransposon hot spot protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00045      0.32     125     168 ..     472     516 ..     444     546 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00045
                           RHSP 125 ipn.vlvGtpGiGkslavGsfllykllhydaellriiayvvkGka 168
                                     p+ +++G +G Gks +  s ll  l  + ae l +i   +kG+a
  gi|121636199|ref|YP_976422.1| 472 GPHgLMIGMTGSGKSQTLMSILLSLLTTHSAERLIVIYADFKGEA 516
                                    567799****************************999889***98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.4   1.7e+03       4      14 ..     478     488 ..     476     562 .. 0.75
   2 ?   -1.5   0.0       4.7   3.4e+03       3      16 ..     827     840 ..     826     862 .. 0.86
   3 ?    8.4   0.0    0.0042         3       2      84 ..    1104    1206 ..    1103    1214 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                         AAA_18   4 tGtpGvGKttl 14 
                                     G+ G+GK++ 
  gi|121636199|ref|YP_976422.1| 478 IGMTGSGKSQT 488
                                    699*****964 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.7
                         AAA_18   3 ltGtpGvGKttlak 16 
                                    + G p +GK+t  +
  gi|121636199|ref|YP_976422.1| 827 IHGGPKSGKSTALQ 840
                                    77999******876 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0042
                         AAA_18    2 lltGtpGvGKttlakeL....skrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss..... 69  
                                     ++ G +++GKttl +++    +++  +  +++ +++ +++l l ++p   d++  +++d+   ++ +l + ++     
  gi|121636199|ref|YP_976422.1| 1104 MVFGDARSGKTTLLRHIirtvREH--StADRVAFTVLDRRLHLVDEPLFPDNEYTANIDRIIPAMLGLANLIEarrpp 1179
                                     689**************6664222..2478888888888888888877556666777777777777777776677777 PP

                         AAA_18   70 ............aleegknlvidghla 84  
                                                   ++ + l+id++ +
  gi|121636199|ref|YP_976422.1| 1180 agmsaaelsrwtFAGHTHYLIIDDVDQ 1206
                                     777777777777667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 1.08u 0.37s 00:00:01.45 Elapsed: 00:00:00.59
# Mc/sec: 6805.91
//
Query:       gi|121636200|ref|YP_976423.1|  [L=102]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-22   78.3  12.8    5.1e-22   78.0  12.8    1.1  1  PE             PE family
  ------ inclusion threshold ------
        1.4    9.4   8.3        3.1    8.3   8.3    1.8  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0  12.8   5.7e-26   5.1e-22       4      93 .]       3      92 ..       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 5.7e-26
                                   XXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  4 vvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaag 85
                                   ++v+Pe laaa+a +++++++l+aa+a aa+++tav+++aaD VS ++Aa fsa++ e+  ++a++++++ +++  + ++++
  gi|121636200|ref|YP_976423.1|  3 LRVVPEGLAAASAAVEALTARLAAAHASAAPVITAVVPPAADPVSLQTAAGFSAQGVEHAVVTAEGVEELGRAGVGVGESGA 84
                                   89******************************************************************************** PP

                                   HHHS--XX CS
                             PE 86 sYaaaEaa 93
                                   sY a +aa
  gi|121636200|ref|YP_976423.1| 85 SYLAGDAA 92
                                   ******97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.3   0.00035       3.1       4      58 ..       2      57 ..       1      97 [. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00035
                  T7SS_ESX_EspC  4 nLsVdpdhlrelaakhdevaaeiasavaaaagasaavld.shGpicaatndavaaa 58
                                   +L+V+p+ l +++a +++  a++a+a a+aa+  +av++    p++++t++ ++a 
  gi|121636200|ref|YP_976423.1|  2 TLRVVPEGLAAASAAVEALTARLAAAHASAAPVITAVVPpAADPVSLQTAAGFSAQ 57
                                   49******************************999988625568888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 570.00
//
Query:       gi|121636201|ref|YP_976424.1|  [L=513]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-61  205.3  24.5    5.3e-61  205.3  24.5    2.9  3  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3  24.5     3e-65   5.3e-61       1     157 [.       8     164 ..       8     165 .. 0.99
   2 ?    0.6   0.6     0.031   5.6e+02       9      42 ..     176     209 ..     174     221 .. 0.83
   3 ?   -8.8   8.1         1   1.8e+04      17      48 ..     306     337 ..     303     363 .. 0.47

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 3e-65
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall+ Gpg+g+l+aAa+aW++L+ae+as+aael+ +l ++ + aWqGps+++++aa++py+aWL++a+a+a+
  gi|121636201|ref|YP_976424.1|   8 ASPPEVHSALLSNGPGPGSLVAAATAWSQLSAEYASTAAELSGLLGAVPGWAWQGPSAEWYVAAHLPYVAWLTQASADAA 87 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aAaq+eaaaaaY++Alaam+++ae+aan+  +++lvatnffG+nt++I  +ea+y +mw+q+aa+m  Y+aas aa
  gi|121636201|ref|YP_976424.1|  88 GAAAQHEAAAAAYTTALAAMPTLAELAANHVIHTVLVATNFFGINTIPITLNEADYVRMWLQAAAVMGLYQAASGAA 164
                                    *************************************************************************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.031
                                    HHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE   9 allyaGpgsgpllaAaaaWdgLaaelasaaaele 42 
                                    ++++ G g+++ + A + W+ L a l++  ++++
  gi|121636201|ref|YP_976424.1| 176 TVMNPGGGAASTVGAVNPWQWLLALLQQLWNAYT 209
                                    57999***************99998887766665 PP

  == domain 3  score: -8.8 bits;  conditional E-value: 1
                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                            PPE  17 sgpllaAaaaWdgLaaelasaaaelesvlael 48 
                                    s+pl aAa a  ++   +++a +   +  a++
  gi|121636201|ref|YP_976424.1| 306 STPLAAAAVAAGSVWPAVSMAVTGAGTAGAAT 337
                                    55666666555544444444444333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3082.99
//
Query:       gi|121636202|ref|YP_976425.1|  [L=97]
Description: hypothetical protein BCG_0327 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-07   28.9   6.6    1.2e-06   28.7   6.6    1.1  1  WXG100         Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.038   14.5  13.4      0.046   14.2  13.4    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
      0.086   13.1   0.1       0.14   12.5   0.1    1.4  1  KORA           TrfB plasmid transcriptional repressor


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   6.6   1.9e-10   1.2e-06       8      85 ..      10      87 ..       4      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.9e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  8 elrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85
                                   +l ++ ++f+++a+ ++  + + ++   + q+  +G+++ afqa+ +++ +aa+k++++L+  + +l +aa ++  aD
  gi|121636202|ref|YP_976425.1| 10 QLVASQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQGESSAAFQAAHARFVAAAAKVNTLLDVAQANLGEAAGTYVAAD 87
                                   677888999999****************************************************************99 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.4   7.7e-06     0.046      10      96 ..       6      92 ..       1      94 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                  T7SS_ESX_EspC 10 dhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYeatD 91
                                   +h+ +l a + + aa++   + +  +a +a ++       ++ +a++aa+a   aa++++++ ++   ++L +AA++Y a+D
  gi|121636202|ref|YP_976425.1|  6 AHIPQLVASQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQGESSAAFQAAHARFVAAAAKVNTLLDVAQANLGEAAGTYVAAD 87
                                   7888999999999999999999996666777777788899****************************************** PP

                  T7SS_ESX_EspC 92 eeaag 96
                                    +aa+
  gi|121636202|ref|YP_976425.1| 88 AAAAS 92
                                   **997 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05      0.14      33      63 ..      14      44 ..      11      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                           KORA 33 kqadvatelgltkqavsqavkrvwaahaere 63
                                   +q+ +a++ gl ++ ++qa++ +++a a ++
  gi|121636202|ref|YP_976425.1| 14 SQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQ 44
                                   799**********************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 691.98
//
Query:       gi|121636203|ref|YP_976426.1|  [L=96]
Description: low molecular weight protein antigen 7 cfp7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-16   60.2   7.1      2e-16   60.0   7.1    1.1  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.038   13.7   1.8      0.045   13.5   1.8    1.1  1  FTO_CTD   FTO C-terminal domain
       0.13   12.3   0.0        0.2   11.7   0.0    1.3  1  Xpo1      Exportin 1-like protein


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   7.1   3.3e-20     2e-16       1      85 [.       3      87 ..       3      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 3.3e-20
                                   CHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  1 qikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82
                                   qi++++ ++  +a ++++ a++l+++ ++++ e++alqs+W+G+++ ++qa++++w+qa+++lv+a++ +s+++++++ a+ 
  gi|121636203|ref|YP_976426.1|  3 QIMYNYPAMLGHAGDMAGYAGTLQSLGAEIAVEQAALQSAWQGDTGITYQAWQAQWNQAMEDLVRAYHAMSSTHEANTMAMM 84
                                   79*******************************************************************************9 PP

                                   HHH CS
                         WXG100 83 daD 85
                                     D
  gi|121636203|ref|YP_976426.1| 85 ARD 87
                                   988 PP

>> FTO_CTD  FTO C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.8   7.5e-06     0.045      61      99 ..      48      86 ..      33      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-06
                        FTO_CTD 61 GsrhaklhdyWkrkieeLeeawkkmElltrlvLdalrka 99
                                   G  ++++++ W++++e+L  a+++m ++ ++   a+ + 
  gi|121636203|ref|YP_976426.1| 48 GITYQAWQAQWNQAMEDLVRAYHAMSSTHEANTMAMMAR 86
                                   778**********************98877655554333 PP

>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05       0.2      15      44 ..      49      78 ..      47      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                                   HHHHHTTTTSTTHHHHHHHHHCT.HHHHHH CS
                           Xpo1 15 lflqeypnnWpsffddllsllssspsglel 44
                                   + +q ++++W+++++dl+++ ++  s+ e+
  gi|121636203|ref|YP_976426.1| 49 ITYQAWQAQWNQAMEDLVRAYHAMSSTHEA 78
                                   789***************999984333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 668.13
//
Query:       gi|121636204|ref|YP_976427.1|  [L=295]
Description: hypothetical protein BCG_0329 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-64  215.8   5.2    8.1e-64  215.6   5.2    1.0  1  ESX-1_EspG  EspG family


Domain annotation for each model (and alignments):
>> ESX-1_EspG  EspG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.6   5.2   4.5e-68   8.1e-64       1     244 [.      11     269 ..      11     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 4.5e-68
                                    EHHHHHHHHHHHT----CGGGCC--STSSHHHHHHHHHHHHHHHHHTTSBETT.EB-HHHHHHHHHHHS-SEEEEEEEEE CS
                     ESX-1_EspG   1 svdeldvlwealglgelPvpLevpspgataeeraalreraaaeLaerGLadgr.rvdpeladaLrlLarpdrevdarvvr 79 
                                    +vd +++++e  g+g++P++L+++ p+++a++r a+++r+++eL+++GL++ +  ++p++ad++++++ pdr++d+r+v 
  gi|121636204|ref|YP_976427.1|  11 TVDNAWFIAETIGAGTFPWVLAITMPYSDAAQRGAFVDRQRDELTRMGLLSPQgVINPAVADWIKVVCFPDRWLDLRYVG 90 
                                    799***************************************************************************** PP

                                    ...--STTCEEEEEEEEETTEE.........EEEEEETTEEEEEEE-TSG...HHHHHHTTSH.--B-SS--EEEEHHHH CS
                     ESX-1_EspG  80 ...rdlgdeelralvarrgrqa.........vlavrdgddvtlepvrpds...laaalvalLpeappgrgrsvslpadel 144
                                        d+  e lr++va r +++         v+a+r+++ vt+++++ d+   l++ l  +L ++pp+r++++slp++++
  gi|121636204|ref|YP_976427.1|  91 pasADGACELLRGIVALRTGTGktsnktgngVVALRNAQLVTFTAMDIDDpraLVPILGVGLAHRPPARFDEFSLPTRVG 170
                                    ***99999*****9999999999*************************878***************************** PP

                                    HHHHHHHHT..GHHHHHHHHT--CCCHHHHHHHTSSTSEEEEEEEEEEECCCECEEECESS-EEEEEETTEEEEEEEEEE CS
                     ESX-1_EspG 145 eeaaerara..alaaalralgasaadaralarllasprsrvgqfivavardrggrrtradrplswfDteaGRylvspsra 222
                                    ++a+er r+   l++++++lg++a+++ ++++++++prs+v+  iva++ ++ gr+t+++++ls++Dt+aGR+lvspsra
  gi|121636204|ref|YP_976427.1| 171 ARADERLRSgvPLGEVVDYLGIPASARPVVESVFSGPRSYVE--IVAGCNRD-GRHTTTEVGLSIVDTSAGRVLVSPSRA 247
                                    *******99**999****************************..****8888.99************************* PP

                                    TTS--E.EEEEE--HHHHHHHHH CS
                     ESX-1_EspG 223 adgeew.ltvaPadparlarale 244
                                     dge w +t++P++p ++a a++
  gi|121636204|ref|YP_976427.1| 248 FDGE-WvSTFSPGTPFAIAVAIQ 269
                                    ***9.66**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1984.03
//
Query:       gi|121636205|ref|YP_976428.1|  [L=472]
Description: hypothetical protein BCG_0330 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-22   79.4   1.6    6.6e-22   78.0   1.6    1.8  1  YukD      WXG100 protein secretion system (Wss), protein YukD


Domain annotation for each model (and alignments):
>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   1.6   3.7e-26   6.6e-22       1      76 []       8      90 ..       8      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 3.7e-26
                                   EEEEEEE-TTTEEEEEEETTSBTTHHHHHHHHHS-..........--S---TT-EEEEGGGEEEETTSBCGGGT--TT-EEE CS
                           YukD  1 lvrVtvlagnrrvDlaLPadvpvaellpalvrllg.......epddeagrpggwsLarvggapLsgdrtLaeagVrDGdlLv 75
                                   +vrV++la+ r +++aLPa++p++e+lpa++rl+        +  ++ g++ ++sLa+vgg+p+s+d++L+++gV+DGdlLv
  gi|121636205|ref|YP_976428.1|  8 IVRVAILADSRLTEMALPAELPLREILPAVQRLVVpsaqngdGGQADSGAAVQLSLAPVGGQPFSLDASLDTVGVVDGDLLV 89
                                   69********************************777888997888889********************************9 PP

                                   E CS
                           YukD 76 L 76
                                   L
  gi|121636205|ref|YP_976428.1| 90 L 90
                                   8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 3461.41
//
Query:       gi|121636206|ref|YP_976429.1|  [L=461]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-36  125.3   5.4    5.1e-36  124.5   5.4    1.4  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   5.4   2.8e-40   5.1e-36       1     298 []      86     389 ..      86     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 2.8e-40
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeeg 80 
                                    g+g lva++DtGv+p+    +                  + +g+  e+t+   ++d+      HGt vAGi+a++ p + 
  gi|121636206|ref|YP_976429.1|  86 GEGQLVAIIDTGVQPGPRLPN-----------------VDAGGDFVESTDGLTDCDG------HGTLVAGIVAGQ-PGND 141
                                    799**********99887777.................2377888888999999998......************.**** PP

                                    SSB-SSTTSEEEEEE-SSTTSB-HH....HHHHHH..........HHHHHHCT-SEEEE-EESCETTCHHCHHHHHH..H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                   Peptidase_S8  81 ekngvapgakilsvkvldtsggsmetg..telira..........ieeaaedkvdvinmslgestslpktgrsieal..a 146
                                    +++gvap a++ls+++++t+++  ++g  ++l++a          i  aa  +++vin+s       ++ +++ + l  a
  gi|121636206|ref|YP_976429.1| 142 GFSGVAPAARLLSIRAMSTKFSPRTSGgdPQLAQAtldvavlagaIVHAADLGAKVINVSTITCLPADRMVDQAA-LgaA 220
                                    *************************99978888887777777776666777777799999886666666666543.489* PP

                                    HHHHH.CCT-EEEEE--SS-T-HH....................EEE-TTCEECTTTSTTCEEEEEES............ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxx............ RF
                   Peptidase_S8 147 inravnkkgvlvviSaGNngktgs....................slqagspvgtpstsknvitvgayt............ 194
                                    i++a  +k+ ++v++aGN g +gs                    +               + +v +++            
  gi|121636206|ref|YP_976429.1| 221 IRYAAVDKDAVIVAAAGNTGASGSvsascdsnpltdlsrpddprN---------------WAGVTSVSipswwqpyvlsv 285
                                    ********************9999999995555555555544444...............44444444444555555555 PP

                                    ....TTSSB-TT--B-TT.......-EEEE-S-..CCCCCCCCCHHHTTTHH........EEEE-SHHHCHHHHHHHHHH CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 195 ....tegkiapfSsrGpssdgklkpdivapGgn..ivstwsrqsnnsaglss........yqsmsGTSmAsPnaagaaAl 260
                                        ++g+ + fS  Gp +       i+apG+n  +vs+ +  +       +        + + sGTS A+  ++g+aAl
  gi|121636206|ref|YP_976429.1| 286 asltSAGQPSKFSMPGPWV------GIAAPGENiaSVSNSGDGA---LA--NglpdahqkLVALSGTSYAAGYVSGVAAL 354
                                    5555*************87......7*******44333333333...22..134668899******************** PP

                                    HHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 261 llsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                    ++s++p l++++v + l  tA    +  + +s+++GaG
  gi|121636206|ref|YP_976429.1| 355 VRSRYPGLNATEVVRRLTATA---HRGARESSNIVGAG 389
                                    *********************...66677899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3305.56
//
Query:       gi|121636207|ref|YP_976430.1|  [L=331]
Description: hypothetical protein BCG_0332 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-15   54.9   4.9    8.7e-15   54.9   4.9    2.1  2  EccE      Putative type VII ESX secretion system translocon, 
  ------ inclusion threshold ------
      0.025   14.8   0.8        3.7    7.7   0.8    2.5  2  DUF3631   Protein of unknown function (DUF3631)


Domain annotation for each model (and alignments):
>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   4.9   9.7e-19   8.7e-15       2      99 .]     127     214 ..     126     214 .. 0.95
   2 ?   -2.7   0.0      0.85   7.7e+03       6      11 ..     234     239 ..     219     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 9.7e-19
                           EccE   2 aaqRttWlalrldpeenvaalsaRgggtegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaapadvr 81 
                                     ++ +tW+ l++ +++n aal+aR +++  ++++a++aarRla++Lre G++a  +  +e++a++aa +          r
  gi|121636207|ref|YP_976430.1| 127 SGDCRTWVGLTVVADDNLAALQAR-SARIPLQETAQVAARRLADHLREIGWEAGTAAPDEIPALVAADS----------R 195
                                    67899*******************.*****************************************998..........7 PP

                           EccE  82 eewrtirtrd.gylttYav 99 
                                    e+wr++r++d  y+++Y+v
  gi|121636207|ref|YP_976430.1| 196 ETWRGMRHTDsDYVAAYRV 214
                                    ******998879****986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.85
                           EccE   6 ttWlal 11 
                                    +tW+al
  gi|121636207|ref|YP_976430.1| 234 ETWIAL 239
                                    344444 PP

>> DUF3631  Protein of unknown function (DUF3631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0051        46     144     168 ..     101     126 ..      92     132 .. 0.81
   2 ?    7.7   0.8   0.00041       3.7      17      83 ..     192     258 ..     180     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0051
                        DUF3631 144 arkLakkLkeydiksktlrlene.qa 168
                                     + +a+ L++y+i+++t+r++++ +a
  gi|121636207|ref|YP_976430.1| 101 LTLIARYLDRYGIRADTIRITSRvTA 126
                                    566899**************987555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00041
                        DUF3631  17 rrdeeelealrdrLaawaesvaeevaeaepempegveDRaa.dvwepLlavadlaggewpetaraAcv 83 
                                    ++++e ++ +r++  +++++++ +++++ p++ ++++ R+a ++w +L  +a +ag ++  t  aAc+
  gi|121636207|ref|YP_976430.1| 192 ADSRETWRGMRHTDSDYVAAYRVSADAELPDTLPAIRSRPAqETWIAL-EIAYAAGSSTRYTVAAACA 258
                                    5667788888888899999999999999****99*****753899886.8************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2329.88
//
Query:       gi|121636208|ref|YP_976431.1|  [L=400]
Description: hypothetical protein BCG_0333c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-05   23.5   0.5     0.0001   22.1   0.4    1.7  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00034   21.3   2.8    0.00034   21.3   2.8    2.3  2  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.028   13.5   0.0      0.096   11.8   0.0    1.7  2  DUF2048        Abhydrolase domain containing 18
      0.072   13.0   0.0       0.11   12.4   0.0    1.3  1  UPF0227        Uncharacterised protein family (UPF0227)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.4   2.3e-08    0.0001       1     117 [.     170     301 ..     170     331 .. 0.79
   2 ?   -1.7   0.0      0.41   1.8e+03     215     237 ..     343     373 ..     331     382 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-08
                                    SEEEEE-STTTCGGG....GTTGHHHHHHHHT.......TSEEEEEEETTSTTSSSTTTGB..........CHH..SHHH CS
                  Abhydrolase_1   1 pvlvilhGlpgssdv....waerglapaLakd.......gfdvillDlrGvgySspapacin.........ddy..gtas 58 
                                    p+l+++hG+ gss++    ++          +       g+dv+l+ l+ +g+     ++ +         + +   +a 
  gi|121636208|ref|YP_976431.1| 170 PTLCVIHGFMGSSYLlnglFF----------SlpwyyrsGYDVLLYTLPFHGQRAEKFSPFSgfgyftsglSGFaeAMAQ 239
                                    6899**********7554433..........33333445**************877777776877777777445334444 PP

                                    HHHHHHHH...HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHH CS
                  Abhydrolase_1  59 vaddldri...ldalgddkltlvGhSmGGmialayaaeyperVkalvllga.idpaaslieaq 117
                                       d++ i   l + g+d+++l   S+GG +++ +a+   +r  a++  ++ ++pa  ++e+ 
  gi|121636208|ref|YP_976431.1| 240 AVYDFRSIvdyLRHIGVDRIALTSISLGGYTSALLASV-ESRLEAVIPNCPvVMPAKLFDEWF 301
                                    4555555568899************************8.999999999999888888777775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.41
                                    EEEEETTCSSSCH.HHHHHHHHC.......H CS
                  Abhydrolase_1 215 lvisgtsDplvpp.kaledlaql.......l 237
                                    ++i g  D+++pp +a   ++q+       +
  gi|121636208|ref|YP_976431.1| 343 MIITGLGDRMAPPeHAVTLWKQWdrcalhwF 373
                                    7899999999999888877777755444444 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.7      0.14   6.3e+02      89     149 ..      58     127 ..      13     170 .. 0.50
   2 !   21.3   2.8   7.6e-08   0.00034       4     156 ..     175     374 ..     172     395 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                    EEEEES-..----TTTS----TTHHHHHHTT-C.CCCHCCH.S-HSCCCCHHH.......C...CCCHCHCCC CS
                  Abhydrolase_6  89 vgvlldppptalpagllaaalelllallallrl.lawlsre.plprlfladed.......a...daawrarla 149
                                    ++vl ++   ++pa  ++a++ + ++  ++    +a l+++ +++++f a+++       +    ++w+ar +
  gi|121636208|ref|YP_976431.1|  58 ASVLSAT---VTPAVVANALRHVNEGSERSNLNfYAELAAAhDPAKSFPAPTElpkvtsrPaspLTEWVARGT 127
                                    3355555...666666555555555555533331111111122333555544432222221222333333332 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 7.6e-08
                                    E--GC.....G....CHHHHHHHHCCTCEEEEE--TTST.....................S-GGCS--HHHCHHHHHHHC CS
                  Abhydrolase_6   4 lHGagssassW....lvapLaallaagvhvlapDlpGhG.....................rsdpppldledladlaalld 58 
                                    +HG  + +ss+    l+ +L  ++++g+ vl + lp hG                     +++ ++ ++ d + ++++l+
  gi|121636208|ref|YP_976431.1| 175 IHG--FMGSSYllngLFFSLPWYYRSGYDVLLYTLPFHGqraekfspfsgfgyftsglsgFAEAMAQAVYDFRSIVDYLR 252
                                    799..5556664333144889999999999******99977777655555555544444433555566666688888899 PP

                                    CTT..TTSEEEEEETCHHHHHHHHHHCC...EEEEES-..----TTTS----TTHHHHHHTT-C...........CCCH. CS
                  Abhydrolase_6  59 elaagggpvvlvGHSlGGalalaaapla.lvvgvlldppptalpagllaaalelllallallrl...........lawl. 125
                                    +++   +++ l   SlGG+ ++++a++  ++++v+ + p+ + pa l++ +++  + +   lrl           la++ 
  gi|121636208|ref|YP_976431.1| 253 HIG--VDRIALTSISLGGYTSALLASVEsRLEAVIPNCPV-VMPAKLFDEWFPANKLVKLGLRLtnisrdeliagLAYHg 329
                                    995..9999**********999944444655556666644.444444333333333222222221111212222223332 PP

                                    ..CCH.............S-HSCCCCHHHCCCCHCHCCCGHHHHCC CS
                  Abhydrolase_6 126 ..sre.............plprlfladedadaawrarlarlaalla 156
                                      + +              l++++ ++e a + w ++++ +++ ++
  gi|121636208|ref|YP_976431.1| 330 plN-YrpllpkdrrmiitGLGDRMAPPEHAVTLWKQWDRCALHWFP 374
                                    211.012222112222222222333333347777777766665555 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05     0.096     160     205 ..     241     286 ..     198     294 .. 0.85
   2 ?   -1.3   0.0       0.2   9.1e+02     299     333 ..     345     379 ..     337     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                        DUF2048 160 ilEslvllhwlereGyGplgltGlSmGGhmaslaasnwpkplvlvp 205
                                    + + ++++ +l + G  +++lt +S+GG  ++l as+  +  +++p
  gi|121636208|ref|YP_976431.1| 241 VYDFRSIVDYLRHIGVDRIALTSISLGGYTSALLASVESRLEAVIP 286
                                    56778899999999**********************9999888777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.2
                        DUF2048 299 vaAkdDayvpresvaslqeiwpgsevryldgGHvs 333
                                    ++   D+  p e   +l + w  +  +++ g H+ 
  gi|121636208|ref|YP_976431.1| 345 ITGLGDRMAPPEHAVTLWKQWDRCALHWFPGSHLL 379
                                    55667888888888999999***********9974 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.11      42     103 ..     237     303 ..     231     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                        UPF0227  42 pqqalkeleklv...aelgddnillvGssLGGyyatrlger.fglrqvlln.Palkplenlagklge 103
                                    ++qa+    ++v    ++g d+i+l   sLGGy+++ l+     l++v+ n P + p + +++   +
  gi|121636208|ref|YP_976431.1| 237 MAQAVYDFRSIVdylRHIGVDRIALTSISLGGYTSALLASVeSRLEAVIPNcPVVMPAKLFDEWFPA 303
                                    5555555555551114566788****************97626788888877888898888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2664.16
//
Query:       gi|121636209|ref|YP_976432.1|  [L=261]
Description: trans-aconitate 2-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-13   48.6   0.0    1.1e-12   48.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.4e-12   48.2   0.0    2.4e-12   47.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.6e-11   43.6   0.0    6.7e-11   42.7   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.8e-08   34.3   0.0    2.1e-08   34.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.4e-08   33.5   0.0    1.2e-07   32.4   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    4.9e-06   26.2   0.0    8.5e-06   25.4   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0002   21.5   0.0    0.00057   20.0   0.0    1.6  2  FtsJ             FtsJ-like methyltransferase
     0.0003   20.1   0.0    0.00047   19.5   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    0.00069   19.6   0.0      0.001   19.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00075   19.2   0.0      0.001   18.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.17   11.2   0.0       0.23   10.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   6.8e-16   1.1e-12       5     125 ..      14     135 ..      10     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 6.8e-16
                Methyltransf_23   5 reeelsdklerllpklraggrvLdiGcGtGillevlren..gfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepq 80 
                                    r + + +++ r++  l++  rv+d+GcG G+l+++l+++  g+ +++ D spe+v+ a+  +    ++  +    +++p+
  gi|121636209|ref|YP_976432.1|  14 RNRPFYELVSRVG--LERARRVVDLGCGPGHLTRYLARRwpGAVIEALDSSPEMVAAAAerG----IDATTGDLRDWKPK 87 
                                    5555566777777..8999*****************6662566999**********995433....33333334689999 PP

                Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl...k 125
                                      +d++v++  l++vp +  ll +  + l+pg ++ ++ p++     +
  gi|121636209|ref|YP_976432.1|  88 PDTDVVVSNAALHWVPEHSDLLVRWVDELAPGSWIAVQIPGNFEtpsH 135
                                    9**************************************986434442 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.5e-15   2.4e-12       1      94 [.      33     117 ..      33     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.5e-15
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    v+dlGcG+G+lt++la+r++ a + ++D s+em++aa+er       ++  +gd++d++ +    D+vvs+ alh++++ 
  gi|121636209|ref|YP_976432.1|  33 VVDLGCGPGHLTRYLARRWPGAVIEALDSSPEMVAAAAERG------IDATTGDLRDWKPKP-DTDVVVSNAALHWVPE- 104
                                    89*****************55999****************9......99*********8655.79*****777**9884. PP

                                    HHHHHHHHHHHHEE CS
                Methyltransf_25  81 dlekalkeiarvLk 94 
                                     + ++l ++ + L 
  gi|121636209|ref|YP_976432.1| 105 -HSDLLVRWVDELA 117
                                    .4466655555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   4.1e-14   6.7e-11       1      95 [.      34     123 ..      34     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.1e-14
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhvedp 77 
                                    +d+GcG G l+++la+r   a + ++D s+em+++a e++ ++        +d+++  p +d   D+vvs+ +lh+v+++
  gi|121636209|ref|YP_976432.1|  34 VDLGCGPGHLTRYLARRWpgAVIEALDSSPEMVAAAAERGIDA------TTGDLRDWkPKPD--TDVVVSNAALHWVPEH 105
                                    59*************998989999*********9998777665......79*****878888..9*************** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                    +++l  ++  L pg +++
  gi|121636209|ref|YP_976432.1| 106 SDLLVRWVDELAPGSWIA 123
                                    *********999998876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-11   2.1e-08       3     113 ..      29     128 ..      27     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                    ++ rv+DlGCG G+lt  la +  p+a +  +D s+e++  A e+    g+d  +    d+  ++    d   D+++sn+
  gi|121636209|ref|YP_976432.1|  29 RARRVVDLGCGPGHLTRYLA-RRWPGAVIEALDSSPEMVAAAAER----GIDATTGDLRDWKPKP----D--TDVVVSNA 97 
                                    5679****************.7799*******************7....8887777777777777....3..7******* PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                    +l+ +++  + l +  + l pg+ ++++ p 
  gi|121636209|ref|YP_976432.1|  98 ALHWVPEHSDLLVRWVDELAPGSWIAVQIPG 128
                                    ********99999999999998888887665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   7.4e-11   1.2e-07       1      98 [.      34     121 ..      34     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7.4e-11
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    +++GcG G+l+r+l+++ p++ + ++D sp+++++a+e+  +      +  +++ +           D+vv++ +lh+++
  gi|121636209|ref|YP_976432.1|  34 VDLGCGPGHLTRYLARRWPGAVIEALDSSPEMVAAAAERGIDATT--GDLRDWKPKP--------DTDVVVSNAALHWVP 103
                                    59***************9***************777777666554..4455566555........67************* PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    +  ++l +  + L+pg +
  gi|121636209|ref|YP_976432.1| 104 EHSDLLVRWVDELAPGSW 121
                                    *******99999999976 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.2e-09   8.5e-06      28     105 ..      26      97 ..      20     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.2e-09
                                    HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE-- CS
                            MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNP 105
                                      e++++v+DlGcG G l+  la+++p a ++++d + + +++a e        +++++ d+ +  ++ + d++vsN 
  gi|121636209|ref|YP_976432.1|  26 GLERARRVVDLGCGPGHLTRYLARRWPGAVIEALDSSPEMVAAAAER------GIDATTGDLRDWKPKPDTDVVVSNA 97 
                                    5557899**********************999999999888776432......2445556666666666666666665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.5e-07   0.00057      11      77 ..      20      88 ..      17     108 .. 0.80
   2 ?   -1.6   0.0       1.5   2.5e+03      31      38 ..     117     124 ..     115     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                                   HHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....HHHTTEEEECS-CCCSSHHH CS
                           FtsJ 11 eidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....aplpgvttiqgditdpetie 77
                                   e+ ++++ +++ ++vvDlg++PG  + +l++r   ++++ a+D  p     a   g+   +gd +d + ++
  gi|121636209|ref|YP_976432.1| 20 ELVSRVG-LERARRVVDLGCGPGHLTRYLARRWP-GAVIEALDSSPEmvaaAAERGIDATTGDLRDWKPKP 88
                                   5667777.88999*******************85.699******666586444499999999998876665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                    TTSHHHHH CS
                           FtsJ  31 aPGgwsqv 38 
                                    aPG+w+ v
  gi|121636209|ref|YP_976432.1| 117 APGSWIAV 124
                                    89999987 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.9e-07   0.00047      55     148 ..      22     109 ..      16     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.9e-07
                                    HHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTT.S-----SEEE CS
                 Methyltransf_2  55 leafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffk.dslPeaDail 132
                                    +  + le+ +++vD+G G G l +  ++ +P+  +  +D  pe v+aA e+       +++ + Gd+++ ++ P++D+++
  gi|121636209|ref|YP_976432.1|  22 VSRVGLERARRVVDLGCGPGHLTRYLARRWPGAVIEALDSsPEMVAAAAER-------GIDATTGDLRDwKPKPDTDVVV 94 
                                    56778999******************************9548888888887.......9*********645667888888 PP

                                    EESSGGGS-HHHHHHH CS
                 Methyltransf_2 133 lkrvlhDwsdekcvkl 148
                                     +  lh w  e+   l
  gi|121636209|ref|YP_976432.1|  95 SNAALH-WVPEHSDLL 109
                                    888887.666665544 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.2e-07     0.001      24      70 ..      28      72 ..      16      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.2e-07
                Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekr 70
                                   ++a +vvD+G+G g+L++ la    +  +  + ++d++ e+v++a +r
  gi|121636209|ref|YP_976432.1| 28 ERARRVVDLGCGPGHLTRYLAR---RwPGAVIEALDSSPEMVAAAAER 72
                                   46889*****************...65788899******999998876 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.2e-07     0.001      12      65 ..      28      82 ..      16     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.2e-07
                           MetW 12 kpgsrvldlGcGdGellellkee.kqvdgrGleldeegvaecvakGlsviqgdld 65
                                   +   rv+dlGcG G+l ++l+ +  +   + l+ + e va++ ++G+    gdl 
  gi|121636209|ref|YP_976432.1| 28 ERARRVVDLGCGPGHLTRYLARRwPGAVIEALDSSPEMVAAAAERGIDATTGDLR 82
                                   55679*************9976414566678889999*************99984 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.23      55      90 ..      22      57 ..      14      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEE CS
                           CMAS 55 leklelkpGmtlLdiGcGWGslvrraverydvkvvg 90
                                   + +++l+   +++d+GcG G+l+r+ ++r+   v+ 
  gi|121636209|ref|YP_976432.1| 22 VSRVGLERARRVVDLGCGPGHLTRYLARRWPGAVIE 57
                                   67899************************9777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1941.13
//
Query:       gi|121636210|ref|YP_976433.1|  [L=267]
Description: hypothetical protein BCG_0335c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.8e-106  352.7   0.3   1.1e-105  352.5   0.3    1.0  1  Sulphotransf     Stf0 sulphotransferase
    0.00017   22.1   0.2       0.34   11.2   0.0    2.2  2  Sulfotransfer_3  Sulfotransferase family


Domain annotation for each model (and alignments):
>> Sulphotransf  Stf0 sulphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.5   0.3  1.2e-109  1.1e-105       2     244 .]       8     259 ..       7     259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 352.5 bits;  conditional E-value: 1.2e-109
                   Sulphotransf   2 YlvcasqRsGstLLvelLratgvaGePdeffq.......apqlreWaeeve........lpleegtsdlalaeayleaal 66 
                                    Ylv+a+qRsGstLLve+Lratg+aGeP+effq       apq+reW+++v+        +pl++gt+d+a+++a++e+++
  gi|121636210|ref|YP_976433.1|   8 YLVLATQRSGSTLLVESLRATGCAGEPQEFFQylpstgmAPQPREWFAGVDddtilqllDPLDPGTPDTATPVAWREHVR 87 
                                    9******************************************************************************* PP

                   Sulphotransf  67 taGrtengvfGlklmreqlglllerldklyPdlsgdalr..iedvlGk.tlyihlsRedkvaqAvslvrAkqtglWriap 143
                                    t+Grt+ngv+G+klm++q++ll++r+++l Pd+sgd+lr  i+dv+G+ ++++h++R+d+v+qAvs++rA+qt++Wr++p
  gi|121636210|ref|YP_976433.1|  88 TSGRTPNGVWGGKLMWNQTALLQQRAAQL-PDRSGDGLRaaIRDVIGNePVFVHVHRPDVVSQAVSFWRAVQTQVWRGHP 166
                                    *****************************.************************************************** PP

                   Sulphotransf 144 dgtelerlapardaeYdaeaiasqvraleaqeeeWraWFaeegiepldisyealvaapvavvaavlealgldpelakdvk 223
                                    d++++++      a+Y+a+aia+ +r+l++qe++WraWFaeegi+p+di+y++l+++++a+va+vl+a+g+dp+la+  +
  gi|121636210|ref|YP_976433.1| 167 DPKRDSQ------AVYHAGAIAHIIRNLRDQENGWRAWFAEEGIDPIDIAYPVLWRNLTAIVASVLDAIGQDPKLAP--A 238
                                    ******8......****************************************************************..* PP

                   Sulphotransf 224 palekladerskeWveRyrad 244
                                    p+le++a++rs+eWv+Ryra+
  gi|121636210|ref|YP_976433.1| 239 PMLERQANQRSDEWVDRYRAE 259
                                    *******************85 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   3.8e-05      0.34       1      47 [.       7      59 ..       7      95 .. 0.69
   2 !    9.0   0.0   0.00019       1.7     127     212 ..     137     230 ..     128     234 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                   -EEEE--TTSSHHHHHHHHHT.....STT..EE--S--.--TT.-SBHHHHHHH CS
                Sulfotransfer_3  1 PifivGlpRSGTTlLhrlLaa.....hpd..vripeetlfvaprllalleawsk 47
                                   P  ++ ++RSG+TlL + L a      p+  ++  + t  +ap+ +++++  ++
  gi|121636210|ref|YP_976433.1|  7 PYLVLATQRSGSTLLVESLRAtgcagEPQefFQYLPST-GMAPQPREWFAGVDD 59
                                   67899***************988888666665555555.666655555554444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00019
                                    EEEEEE--H.HHHHHHHHHTT-.-------......--..-HHH.HHHHHHHHHHHHHHHHHHH.S-TTSE..EEEEHHH CS
                Sulfotransfer_3 127 kfihlvRdpvdtvlssyvslfg.kkresys......edsldele.daleewarayerllaarar.lppdrf..ldvrYed 195
                                     f+h++R p  +v+s+ vs+++  +++ ++      +ds + ++ +a+++  r +++ ++ ++  + ++ +  +d+ Y  
  gi|121636210|ref|YP_976433.1| 137 VFVHVHR-P--DVVSQAVSFWRaVQTQVWRghpdpkRDSQAVYHaGAIAHIIRNLRDQENGWRAwFAEEGIdpIDIAYPV 213
                                    69*****.7..588888888772567899977776533333444445555555554444444445333333448999999 PP

                                    HHH-HHHHHHHHHHHHT CS
                Sulfotransfer_3 196 Lvadpegtlrriyeflg 212
                                    L ++  + + ++++ +g
  gi|121636210|ref|YP_976433.1| 214 LWRNLTAIVASVLDAIG 230
                                    99999999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2108.02
//
Query:       gi|121636211|ref|YP_976434.1|  [L=465]
Description: sulfatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-43  149.4   0.1    7.8e-42  143.7   0.1    2.1  1  Sulfatase     Sulfatase
    1.9e-10   40.9   0.2    3.6e-08   33.4   0.2    2.4  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    1.2e-06   28.7   0.0      0.014   15.7   0.0    2.3  2  DUF4976       Domain of unknown function (DUF4976)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.1   1.3e-45   7.8e-42       2     307 ..      12     286 ..      11     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 1.3e-45
                                    EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTT CS
                      Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggglpqt 81 
                                    n++++ + dlg+ +lg+y+++  + p+ldrla+eg++ft+++++aplc+psr +l+tgryp+++g +    +g ++    
  gi|121636211|ref|YP_976434.1|  12 NLLIVHWHDLGR-YLGVYHHPDVYSPRLDRLAAEGILFTRAHATAPLCTPSRGSLFTGRYPQSNGLVGLAHHG-WEYRTG 89 
                                    8999******88.****************************************************88888777.****** PP

                                    S-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTCSHHHHHHHHH CS
                      Sulfatase  82 eatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrvppeggysddrlldea 161
                                    ++tLp+ll e G ++a++g  h + +     +k+ gfd+f      s+ +++     y               +++l + 
  gi|121636211|ref|YP_976434.1|  90 VQTLPQLLSESGWYSALFGMQHETSY-----PKRLGFDEFDV----SNSYCE-----YVV----------AKAQDWLHNR 145
                                    ***********************988.....35789999887....555555.....221..........4455666666 PP

                                    HHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.........HHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sulfatase 162 lefllarndkpfflylatlapHappeapdeyakkyatffddgseaar.........qlleaylnsveyvDdligrvlaaL 232
                                    +  l   +++ f+l+  + ++H p++ ++  ++ +a+ + +               q ++++++s++ +D+++gr+l++L
  gi|121636211|ref|YP_976434.1| 146 VPAL---DGQRFLLTAGFFETHRPYPHERYRPADSAAVELP-----DylpdtpevrQDVAEFYGSIATADEAVGRLLDTL 217
                                    6664...599************9764444444444444333.....0233446688************************ PP

                                    HHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC..EEECSEEEGGGHHHHHHHHT CS
                      Sulfatase 233 eenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap..rvseelvshiDlfptildla 307
                                     ++gl+  t+vvf+ Dhg++           k+ + y+ gt + l+++ p + a   rv++el s +Dl+pt+ldl+
  gi|121636211|ref|YP_976434.1| 218 ADTGLDASTWVVFVTDHGPAF-------PRAKS-TLYDAGTGIALIIRPPTRRAMapRVYDELFSGVDLVPTLLDLL 286
                                    *******************77.......67787.****************9999899******************97 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.2     6e-12   3.6e-08      20     233 ..      34     235 ..      24     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6e-12
                                    TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEETTTTGGGGGCTTS-HHHHH CS
                   Phosphodiest  20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvtededaprwwqgepiwdta 99 
                                      p l++La eg+ +++ ++++P  T p+  sl TG+yP ++G vg   +  ++ e   ++t+ +  p+ + +e  w  a
  gi|121636211|ref|YP_976434.1|  34 YSPRLDRLAAEGILFTRAHATAPLCT-PSRGSLFTGRYPQSNGLVG---LAHHGWE---YRTGVQTLPQ-LLSESGWYSA 105
                                    6799*******************999.7899***************...6555655...5555444344.5556666666 PP

                                    HHTHTTCEE...EESETTTTSEBTTCT.SC.TBHHSBTCT.CSTTSCHHHHHHHHHHHHHHHCHTHSHHHHHCT.SSESE CS
                   Phosphodiest 100 akarglkaa...alfwpgsevdystyyylvsetppryleddfnakvpledkvdkavlqtwldaafakvvlekel.ekpdl 175
                                     + + + ++    l++   e+d+s+ y    e+   +++d  ++ vp  d     ++  +++++  +   ++e  +  d 
  gi|121636211|ref|YP_976434.1| 106 LFGMQHETSypkRLGF--DEFDVSNSYC---EYVVAKAQDWLHNRVPALDGQRFLLTAGFFETHRPY---PHERyRPADS 177
                                    6665665332334444..4555554433...222222223345555444433333444567766654...6667445599 PP

                                    EEEEECC..CHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                   Phosphodiest 176 llvylee..tDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                     +v l++  +Dt   ++  d  e+   ++++D+a+g+Ll+ l ++gl+a+t ++ v DHG
  gi|121636211|ref|YP_976434.1| 178 AAVELPDylPDTPEVRQ--DVAEFYGSIATADEAVGRLLDTLADTGLDASTWVVFVTDHG 235
                                    99977765567776666..6689************************************9 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   7.4e-05      0.45       1      74 [.     290     363 ..     290     371 .. 0.74
   2 !   15.7   0.0   2.3e-06     0.014      62     101 ..     376     419 ..     369     421 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.4e-05
                        DUF4976   1 ipadmqGksllpllk..gkkkkewrkalyYhyyeyPaehavkrhygvrteryklihfykdidewel.yDlkkDpkel 74 
                                    +pad++G s +p l   + +++++r+++y     y  +++  + +++rt++y  i+ y      +l +D+++ p+ +
  gi|121636211|ref|YP_976434.1| 290 VPADVEGVSHAPALLapDTENAAVRDHVYT-AKTY--HDSFDPIRAIRTKEYSYIENYAPRPLLDLpWDIQESPAGM 363
                                    599******998544114555556665543.3333..557899***************9998888877888888766 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.3e-06
                        DUF4976  62 welyDlkkDpkelknlyddpe....yeevvkelkkkleelrkky 101
                                     elyDl++Dp+e +nl+  ++    +++++++l  +l++ r+++
  gi|121636211|ref|YP_976434.1| 376 RELYDLRADPTETNNLLAGDDstqgVAAIAADLAVRLHDWRQRT 419
                                    69*************98644301114567777888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3329.09
//
Query:       gi|121636212|ref|YP_976435.1|  [L=606]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-32  110.8  28.8    5.4e-32  110.0  28.8    1.5  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0  28.8     3e-36   5.4e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 3e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pe++aaaa++la+i+sa++aanaaaaa tt+v++aaaDeVS+a+Aalfs+haq+yqa+saqaaafh+q+v++l+ 
  gi|121636212|ref|YP_976435.1|  1 MSFVIAQPEMIAAAAGELASIRSAINAANAAAAAQTTGVMSAAADEVSTAVAALFSSHAQAYQAASAQAAAFHAQVVRTLTV 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                    ag+Ya+aEaa
  gi|121636212|ref|YP_976435.1| 83 DAGAYASAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.95u 0.32s 00:00:01.27 Elapsed: 00:00:00.51
# Mc/sec: 3574.73
//
Query:       gi|121636213|ref|YP_976436.1|  [L=75]
Description: hypothetical protein BCG_0338 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-11   42.1   2.2    4.5e-10   39.1   1.2    2.1  2  RHH_1            Ribbon-helix-helix protein, copG family
    0.00054   20.3   0.9    0.00075   19.9   0.9    1.4  1  CcdA             Post-segregation antitoxin CcdA
     0.0016   18.5   0.1      0.003   17.6   0.0    1.5  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.058   13.4   0.2       0.17   11.8   0.0    1.7  2  RHH_3            Ribbon-helix-helix domain
      0.087   13.3   0.4        0.1   13.1   0.4    1.1  1  AvrPtoB_bdg      Avirulence AvrPtoB, BAK1-binding domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   1.2   1.3e-13   4.5e-10       2      37 ..       6      41 ..       5      43 .. 0.95
   2 !    6.1   0.1    0.0031        11      25      36 ..      38      49 ..      38      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.3e-13
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   +s+++d+ +l+++d+ ar+ g +rSe+I++Alr+ +
  gi|121636213|ref|YP_976436.1|  6 ISVTVDAAVLAAIDADARAAGLNRSEMIEQALRNEH 41
                                   8********************************976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0031
                                   HHHHHHHHHHHH CS
                          RHH_1 25 rSelIReAlrey 36
                                   r e++R Alr+y
  gi|121636213|ref|YP_976436.1| 38 RNEHLRVALRDY 49
                                   89*********9 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.9   2.1e-07   0.00075       1      37 [.       3      43 ..       3      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.1e-07
                           CcdA  1 Kkavnlsldsdlla....qAralgiNlSatleeaLaeevke 37
                                   K ++++++d+++la     Ara+g+N S+++e+aL++e  +
  gi|121636213|ref|YP_976436.1|  3 KEKISVTVDAAVLAaidaDARAAGLNRSEMIEQALRNEHLR 43
                                   78899*****999633336****************998654 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.5e-07     0.003      88     122 ..       2      36 ..       1      37 [. 0.94
   2 ?   -2.2   0.0       1.2   4.3e+03      81      86 ..      58      63 ..      43      71 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.5e-07
                HicB_lk_antitox  88 kaeriNitlpervlkriDaavkaagesRSgflaka 122
                                    ++e+i +t+ + vl+ iDa ++aag +RS ++ +a
  gi|121636213|ref|YP_976436.1|   2 TKEKISVTVDAAVLAAIDADARAAGLNRSEMIEQA 36 
                                    579****************************9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                HicB_lk_antitox 81 dlskld 86
                                   d++ + 
  gi|121636213|ref|YP_976436.1| 58 DIDAYA 63
                                   222333 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.17       2      37 ..       3      38 ..       2      39 .. 0.95
   2 ?   -1.0   0.0      0.51   1.8e+03      33      43 ..      43      53 ..      40      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                          RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAie 37
                                   k++++v++d   ++  +a  ++ + +rS+ +++A+ 
  gi|121636213|ref|YP_976436.1|  3 KEKISVTVDAAVLAAIDADARAAGLNRSEMIEQALR 38
                                   99********************************95 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                          RHH_3 33 deAiellLekY 43
                                   + A+ ++++k+
  gi|121636213|ref|YP_976436.1| 43 RVALRDYTAKT 53
                                   66888888875 PP

>> AvrPtoB_bdg  Avirulence AvrPtoB, BAK1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.8e-05       0.1       3      59 ..       9      66 ..       7      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                   ---HHHHHHHHHHHHHHHHH..HHHCTT--HHHHHHHHHHHHHH-----HHHHHHHHCT CS
                    AvrPtoB_bdg  3 rvdraamrnrgndeadaalr..glvqqgvnlehlrtalerhvmqrlpipldigsalqnv 59
                                    vd a +     d   a l    +++q +  ehlr al  +  + +p  ldi +  q v
  gi|121636213|ref|YP_976436.1|  9 TVDAAVLAAIDADARAAGLNrsEMIEQALRNEHLRVALRDYTAKTVP-ALDIDAYAQRV 66
                                   6777777777777666666422589**************99999999.59998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 503.38
//
Query:       gi|121636214|ref|YP_976437.1|  [L=100]
Description: hypothetical protein BCG_0339 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 645.96
//
Query:       gi|121636215|ref|YP_976438.1|  [L=73]
Description: hypothetical protein BCG_0340 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-05   24.3   3.0    3.2e-05   23.7   0.5    2.4  2  RHH_1          Ribbon-helix-helix protein, copG family
     0.0025   17.9   0.2     0.0031   17.6   0.2    1.1  1  Pcc1           Transcription factor Pcc1
  ------ inclusion threshold ------
      0.013   15.3   0.7      0.013   15.3   0.7    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.048   14.0   0.0      0.054   13.9   0.0    1.1  1  ParD           Antitoxin ParD


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.5   7.1e-09   3.2e-05       6      34 ..       9      37 ..       8      41 .. 0.92
   2 ?    0.6   0.1      0.13   5.9e+02      26      32 ..      65      71 ..      43      71 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.1e-09
                                   EEHHHHHHHHHHHHHHTSSHHHHHHHHHH CS
                          RHH_1  6 ldeellerLdelarrrgrSrSelIReAlr 34
                                   +++++l+ Ld++a+r+g Sr e IR+ l+
  gi|121636215|ref|YP_976438.1|  9 IPDDVLASLDAIAARLGLSRTEYIRRRLA 37
                                   79***********************9665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                   HHHHHHH CS
                          RHH_1 26 SelIReA 32
                                    el+R+A
  gi|121636215|ref|YP_976438.1| 65 PELMRQA 71
                                   5777776 PP

>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2     7e-07    0.0031      19      62 ..      18      62 ..      10      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7e-07
                                   HHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHH CS
                           Pcc1 19 rtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngf 62
                                    +++    ls+ + ++r l  ++++ +v+++A ++r LR av g+
  gi|121636215|ref|YP_976438.1| 18 DAIAARLGLSRTEyIRRRLAQDAQTARVTVTAADLRRLRGAVAGL 62
                                   56667778999999****************************886 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.7     3e-06     0.013      15      40 ..      12      35 ..       4      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                  HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvrr 40
                                   d  +s  ++A+r+GlS+++ +rR  r
  gi|121636215|ref|YP_976438.1| 12 DVLASLDAIAARLGLSRTEYIRR--R 35
                                   5678999************9999..5 PP

>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.054       5      50 ..       6      51 ..       1      60 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                           ParD  5 sIditpeqhqrlkAvAAlqGksikeYvLerlleepkeadedealke 50
                                     di ++   +l A+AA  G s  eY+  rl +++++a     +++
  gi|121636215|ref|YP_976438.1|  6 IRDIPDDVLASLDAIAARLGLSRTEYIRRRLAQDAQTARVTVTAAD 51
                                   449999999*******************999988877754444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 485.54
//
Query:       gi|121636216|ref|YP_976439.1|  [L=141]
Description: hypothetical protein BCG_0341 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.8   0.0    1.5e-10   41.6   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   8.3e-15   1.5e-10       2     121 ..       7     125 ..       6     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 8.3e-15
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                    ++D s+l++l ++ ++  ++ + +e+ + ++++ ++  E+ + ++        +++++e ++  lsa+ +  ++ +i ++
  gi|121636216|ref|YP_976439.1|   7 LIDKSALVRLTDSPDMEIWSNR-IER-GLVHITGVTRLEVGFSAEC------GEIARREFREPpLSAMPVEYLTPRIEDR 78 
                                    69******99966666665555.666.9******************......5555555555559*************** PP

                                    HHHHHHHHH.......SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  81 aaeialkyg.......llpnDaliaAtAkehgikliatfDedfrrvak 121
                                    a+e+   +         ++ D+liaAtA+ +g++++ + D+df+ +a+
  gi|121636216|ref|YP_976439.1|  79 ALEVQTLLAdrghhrgPSIPDLLIAATAELSGLTVL-HVDKDFDAIAA 125
                                    *****9999999*********************999.*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 999.54
//
Query:       gi|121636217|ref|YP_976440.1|  [L=210]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-17   62.5   0.0    4.6e-17   61.5   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
    6.1e-08   32.9   2.0    6.1e-08   32.9   2.0    1.5  2  TetR_C_6   BetI-type transcriptional repressor, C-terminal
  ------ inclusion threshold ------
       0.11   12.8   6.1       0.04   14.1   3.2    1.8  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
       0.27   12.0   4.0        3.6    8.4   3.8    2.5  1  TetR_C_15  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0     1e-20   4.6e-17       1      47 []      19      65 ..      19      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1e-20
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Ilda+++l+a +Gy+at++++I +++G++++++Y++F+sKe+ l+a+
  gi|121636217|ref|YP_976440.1| 19 ILDATERLMATKGYAATSISDIRDACGLAPSSIYWHFGSKEGVLAAM 65
                                   9*******************************************996 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.1   1.4e+04      65      81 ..      12      28 ..       9      29 .. 0.56
   2 !   32.9   2.0   1.4e-11   6.1e-08       3     114 ..      89     203 ..      87     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.1
                                   TSCTTSTHHHHHHHHHH CS
                       TetR_C_6 65 glradadaeaaAerlaA 81
                                   g+r+++   +a+erl+A
  gi|121636217|ref|YP_976440.1| 12 GERSRESILDATERLMA 28
                                   45555555566666655 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.4e-11
                                    HHHHHHHHCCSTHSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH...TTSCTTSTHHHHHHHH CS
                       TetR_C_6   3 erlraileallpldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae...gglradadaeaaAerl 79 
                                    +r ++ l++l++l  + +++l+++  +  e   dp++a++ r+  ++  +++r+++ +l++       ad  +++ ++  
  gi|121636217|ref|YP_976440.1|  89 QRSERQLTELVSLQSQHPDFLRLFYLLSMERSQDPAVAAVVRRVRNTAIARFRDSITHLLPsdiPPGKADLVVAELTAFA 168
                                    688889999**************************************************996555566677788999999 PP

                                    HHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                       TetR_C_6  80 aAlidGLwlraalapeeldaeraralvrrhldall 114
                                    +Al dG +  ++l+p+++d er+++ +r+ l+al+
  gi|121636217|ref|YP_976440.1| 169 VALSDGVYFAGHLEPDTTDVERMYRRLRQALEALI 203
                                    9*******************************997 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.5   1.1e+04      47      61 ..      15      29 ..      13      35 .. 0.61
   2 ?   14.1   3.2   8.9e-06      0.04       9     105 ..      94     203 ..      88     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHHHHHH CS
                      TetR_C_31 47 lrralrealaallaa 61
                                   +r+ +++a+++l+a 
  gi|121636217|ref|YP_976440.1| 15 SRESILDATERLMAT 29
                                   556666666666665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.9e-06
                                    HHHHHCCCCCTTHHHHHHHHHHHHHHCCSCHHHHHHHHHH....HHHHHHHHHHHHHHCS.S-HH.....HHHHHHHHHH CS
                      TetR_C_31   9 lladlldraladrertlAryelfleaarrPeLraalarlr....ralrealaallaalGl.pdpe.....eaarllvaal 78 
                                     l++l+    ++++ +   y l +e + +P+++a+++r r    +++r+ ++ ll  +   p+ +     e ++  va+ 
  gi|121636217|ref|YP_976440.1|  94 QLTELVSLQSQHPDFLRLFYLLSMERSQDPAVAAVVRRVRntaiARFRDSITHLLP-SDIpPGKAdlvvaELTAFAVALS 172
                                    68899988788****************************98888999999999887.55535444333323555577888 PP

                                    HHHHHHHHHSG.TS-H....HHHHHHHHHHHT CS
                      TetR_C_31  79 dGllldrLagp.aadp....raevrellrall 105
                                    dG+ +    +p ++ +     + +r++l+al+
  gi|121636217|ref|YP_976440.1| 173 DGVYFAGHLEPdTT-DvermYRRLRQALEALI 203
                                    ******99999422.23435466777777776 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.8    0.0008       3.6       2      62 ..      87     147 ..      86     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0008
                      TetR_C_15   2 LeealdalvdallaahrenpalrrvlleeapslgelelvealeqriaealaalLarrrpel 62 
                                     e+  ++ + +l+ +++++p+++r+++  + +  +  +v+a+ +r++ ++ a ++   ++l
  gi|121636217|ref|YP_976440.1|  87 VEQRSERQLTELVSLQSQHPDFLRLFYLLSMERSQDPAVAAVVRRVRNTAIARFRDSITHL 147
                                    56777888999*****************997777776666666666666555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1590.22
//
Query:       gi|121636218|ref|YP_976441.1|  [L=302]
Description: dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-21   74.6   0.0    4.7e-18   65.4   0.0    2.1  2  adh_short       short chain dehydrogenase
    3.5e-10   39.8   0.0    1.7e-09   37.6   0.0    1.9  2  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    4.7e-07   29.9   0.0    7.1e-07   29.3   0.0    1.2  1  KR              KR domain
    0.00085   19.3   0.0     0.0017   18.3   0.0    1.5  2  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0     1e-21   4.7e-18       2     138 ..       5     140 ..       4     149 .. 0.90
   2 !    7.3   0.0   0.00066       2.9     143     182 ..     171     212 ..     167     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1e-21
                                    EEEEESTTSHHHHHHHHHHHHTT-..EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHH.SSE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGa..kvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkkl.gkl 78 
                                    ++++tGassG+G+++a++l++++a  +vv++ r +++ +++++el+e  ++  +++vD+++ ++v+ +ve+++     ++
  gi|121636218|ref|YP_976441.1|   5 TAVITGASSGLGLQCARALLRRDAswHVVLAVRDPARGRAAMEELGE-PNRCSVLEVDLASVRSVRSFVETVRTTPlPPI 83 
                                    69*******************987336888999*************8.689*********************98755*** PP

                                    SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGG CS
                      adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSva 138
                                     +Lv NAG++ +++   ++++ +e ++ vN  g f l+  +l+ +   + +rIv vsS +
  gi|121636218|ref|YP_976441.1|  84 RALVCNAGLQ-VVSGIAFTDDGVEMTFGVNHLGHFALVTGILDWLA--RPARIVVVSSGT 140
                                    *********5.66666889999**********************77..99********75 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00066
                                    -TTBHHHHHHHHHHHHHHHHHHH..HHGGGTEEEEEEEESSB CS
                      adh_short 143 vagvaaYsAsKaavagltrslak..elaptgirvnavaPGlv 182
                                     +g   Y++sK   + +t +l +  ++ ++g+ vna  PGl+
  gi|121636218|ref|YP_976441.1| 171 AEGRRRYTTSKLCNVLFTYELDRrlDHGEQGVMVNAFDPGLM 212
                                    566778*************996511677888*********97 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   3.9e-13   1.7e-09       1     129 [.      10     139 ..      10     150 .. 0.94
   2 ?   -0.2   0.0      0.14   6.1e+02     158     175 ..     196     213 ..     192     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.9e-13
                                    TTTTSHHHHHHHHHHHTT-E..EEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHH.SSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGae..vvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekf.gklDilvnn 76 
                                    Ga sg+G ++A+al ++ a+  vvl+ ++ ++ ++++eel e    +vle+D ++  +v+++ve+v+ +    +  lv n
  gi|121636218|ref|YP_976441.1|  10 GASSGLGLQCARALLRRDASwhVVLAVRDPARgRAAMEELGEPNRCSVLEVDLASVRSVRSFVETVRTTPlPPIRALVCN 89 
                                    899************99986659******999999999**9999999*******************99877********* PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEG CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssv 129
                                    ag       + + +++++++ ++ vn  + f+l+  +l  +++ ++iv +ss 
  gi|121636218|ref|YP_976441.1|  90 AGLQVV---SGIAFTDDGVEMTFGVNHLGHFALVTGILDWLARPARIVVVSSG 139
                                    ****99...778999***********************************995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.14
                                    HHGGGTEEEEEEEE--BH CS
                   adh_short_C2 158 elgpkgiRvNavspgpik 175
                                    + g++g+ vNa  pg++ 
  gi|121636218|ref|YP_976441.1| 196 DHGEQGVMVNAFDPGLMP 213
                                    679999999999999875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.6e-10   7.1e-07       1      91 [.       4      92 ..       4     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.6e-10
                                   SEEEEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS.S CS
                             KR  1 gtylitGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee.p 80
                                   gt +itG+  gLGl+ ar l+++    h+vl  R+ +a  + +a ++el +   +++v+++D+++  +v++ +e+++++  p
  gi|121636218|ref|YP_976441.1|  4 GTAVITGASSGLGLQCARALLRRDaSWHVVLAVRD-PA--RGRAAMEELGE-PNRCSVLEVDLASVRSVRSFVETVRTTPlP 81
                                   789******************98736699999999.33..33446788877.568999*******************9999* PP

                                   ---EEEE---- CS
                             KR 81 pikGvihaAgv 91
                                   pi+  +  Ag+
  gi|121636218|ref|YP_976441.1| 82 PIRALVCNAGL 92
                                   *****999986 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.8e-07    0.0017       1      59 [.      10      73 ..      10     103 .. 0.89
   2 ?   -3.5   0.0       1.8     8e+03      91     102 ..     131     142 ..     127     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-07
                                   TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHC....HHHHCTTTCEEEE--TT-CCHHHHHHT CS
                 NAD_binding_10  1 GAtGkvGrllvkellarg.ghevtalvRnpekl....aeleaeeglevvegdvtdvedlaealk 59
                                   GA+ + G + ++ ll+r+  ++v++ vR+p++     +el + ++++v+e+d+ +v ++++ ++
  gi|121636218|ref|YP_976441.1| 10 GASSGLGLQCARALLRRDaSWHVVLAVRDPARGraamEELGEPNRCSVLEVDLASVRSVRSFVE 73
                                   9****************************97652122688899***************998776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                                    -EEEEEEETTTT CS
                 NAD_binding_10  91 kRfvlvsaigvg 102
                                     R+v+vs+   +
  gi|121636218|ref|YP_976441.1| 131 ARIVVVSSGTHD 142
                                    588888875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2324.48
//
Query:       gi|121636219|ref|YP_976442.1|  [L=1147]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.3e-120  391.7 575.0    4.3e-12   45.7  24.0   25.1 27  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2  27.1   3.5e-11   6.2e-07       6      40 .]       2      36 ..       1      36 [. 0.97
   2 !   34.8  30.7   5.9e-13   1.1e-08       1      40 []      27      66 ..      27      66 .. 0.98
   3 !   31.2  24.9   8.3e-12   1.5e-07       2      40 .]      68     106 ..      67     106 .. 0.98
   4 ?   -1.1  14.1       0.1   1.8e+03      11      38 ..     237     265 ..     229     267 .. 0.72
   5 !    8.2   6.2   0.00012       2.2      13      38 ..     273     298 ..     266     310 .. 0.70
   6 !   23.2  27.1   2.7e-09   4.8e-05       2      39 ..     337     374 ..     331     375 .. 0.81
   7 !   30.6  23.8   1.2e-11   2.2e-07       2      40 .]     347     385 ..     346     385 .. 0.98
   8 !   32.7  18.1   2.8e-12     5e-08       2      40 .]     357     395 ..     356     395 .. 0.98
   9 !   32.0  19.0   4.5e-12     8e-08       3      39 ..     378     414 ..     378     420 .. 0.97
  10 !   37.8  25.4     7e-14   1.2e-09       3      39 ..     420     456 ..     418     457 .. 0.97
  11 !   32.8  24.3   2.5e-12   4.5e-08       1      40 []     458     497 ..     458     497 .. 0.98
  12 !   45.7  24.0   2.4e-16   4.3e-12       2      39 ..     489     526 ..     488     527 .. 0.98
  13 !   38.9  19.9   3.2e-14   5.7e-10       2      40 .]     519     557 ..     518     557 .. 0.98
  14 !   25.5  14.5   4.9e-10   8.8e-06       2      36 ..     529     563 ..     528     567 .. 0.68
  15 !    5.5  25.7   0.00085        15       4      39 ..     685     722 ..     673     724 .. 0.79
  16 !   12.6   6.3   5.4e-06     0.097       1      28 [.     725     752 ..     723     757 .. 0.75
  17 !    4.3  15.9     0.002        36       3      40 .]     764     805 ..     761     805 .. 0.82
  18 !   22.1  19.5   5.7e-09    0.0001       2      39 ..     780     819 ..     779     819 .. 0.78
  19 !   28.5  20.2   5.8e-11     1e-06       2      39 ..     812     849 ..     811     850 .. 0.98
  20 !   38.6  13.1   4.1e-14   7.3e-10       3      40 .]     848     885 ..     847     885 .. 0.96
  21 !   27.8  22.3   9.1e-11   1.6e-06       1      39 [.     881     919 ..     881     920 .. 0.89
  22 !   37.8  25.8   6.9e-14   1.2e-09       3      39 ..     920     956 ..     918     957 .. 0.97
  23 !   37.2  23.1   1.1e-13     2e-09       1      40 []     958     997 ..     958     997 .. 0.98
  24 !   38.2  15.8   5.4e-14   9.7e-10       2      40 .]     999    1037 ..     998    1037 .. 0.98
  25 ?    1.9   9.2     0.012   2.1e+02       8      30 ..    1069    1092 ..    1063    1093 .. 0.63
  26 !   10.6  11.2   2.3e-05      0.42       3      38 ..    1085    1120 ..    1084    1122 .. 0.93
  27 ?   -2.2   2.4      0.22   3.9e+03       4      14 ..    1133    1143 ..    1132    1145 .. 0.40

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.5e-11
                 Pentapeptide_2  6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40
                                   +NsG gN+GffN+G+gN+G +N+G+gN+G+gn+Gs
  gi|121636219|ref|YP_976442.1|  2 FNSGDGNIGFFNSGTGNFGIGNTGTGNFGIGNSGS 36
                                   8*********************************6 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 5.9e-13
                 Pentapeptide_2  1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40
                                   gN+G++NsGs+ tG+fN+G gNtG fN G++NtG++ntGs
  gi|121636219|ref|YP_976442.1| 27 GNFGIGNSGSTSTGLFNSGDGNTGGFNPGNFNTGNFNTGS 66
                                   8**************************************6 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 8.3e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG +N+G++NtG fN+G+ NtG +N+G++ tG++ +G+
  gi|121636219|ref|YP_976442.1|  68 NTGGFNAGNTNTGHFNTGNYNTGIANTGDVSTGAFISGN 106
                                    *************************************96 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.1
                 Pentapeptide_2  11 gNtGffNlGsg.NtGsfNlGsgNtGsgnt 38 
                                      +GffN+G g   G++N+G + +G  n+
  gi|121636219|ref|YP_976442.1| 237 PSSGFFNTGAGtASGFGNVGGNTSGLWNL 265
                                    46899999987257999999988888775 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.00012
                 Pentapeptide_2  13 tGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +G++N+G    G +N+G+  +G+ nt
  gi|121636219|ref|YP_976442.1| 273 SGLLNVGALGSGVANVGNTISGIYNT 298
                                    56777777777777777777776665 PP

  == domain 6  score: 23.2 bits;  conditional E-value: 2.7e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G +N+G  N+G +N+G  N+G++N+G+ N+G  n+G
  gi|121636219|ref|YP_976442.1| 337 NVGLANLGGSNFGIGNTGIFNVGFANVGNHNIGLANLG 374
                                    88888888888888888888888888888888888888 PP

  == domain 7  score: 30.6 bits;  conditional E-value: 1.2e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+G +N+Gf+N+G+ N+G +NlG++ +G+ n+G+
  gi|121636219|ref|YP_976442.1| 347 NFGIGNTGIFNVGFANVGNHNIGLANLGNYSVGFANSGN 385
                                    *************************************96 PP

  == domain 8  score: 32.7 bits;  conditional E-value: 2.8e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+G++N+G++NlG+ ++G++N+G++ +G+ ntGs
  gi|121636219|ref|YP_976442.1| 357 NVGFANVGNHNIGLANLGNYSVGFANSGNYHIGIANTGS 395
                                    9*************************************6 PP

  == domain 9  score: 32.0 bits;  conditional E-value: 4.5e-12
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G++NsG+ ++G +N+Gs+N+G++N+GsgN+G+g tG
  gi|121636219|ref|YP_976442.1| 378 VGFANSGNYHIGIANTGSANIGFANTGSGNIGIGLTG 414
                                    69********************************999 PP

  == domain 10  score: 37.8 bits;  conditional E-value: 7e-14
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +Gs+NsGs+N+G+fN+G gN+G+fN+G+gN+G+gntG
  gi|121636219|ref|YP_976442.1| 420 FGSFNSGSHNIGLFNSGDGNVGFFNSGTGNVGIGNTG 456
                                    8***********************************9 PP

  == domain 11  score: 32.8 bits;  conditional E-value: 2.5e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +N+G++NsGs+NtG++N+Gs+Nt  fN G++NtG gntGs
  gi|121636219|ref|YP_976442.1| 458 ANFGIANSGSFNTGLGNTGSTNTSLFNPGNVNTGVGNTGS 497
                                    6**************************************6 PP

  == domain 12  score: 45.7 bits;  conditional E-value: 2.4e-16
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N+Gs NtG+fN+Gs+NtGsfNlG+ NtGs+n+G
  gi|121636219|ref|YP_976442.1| 489 NTGVGNTGSINTGSFNTGSTNTGSFNLGDHNTGSFNSG 526
                                    *************************************9 PP

  == domain 13  score: 38.9 bits;  conditional E-value: 3.2e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtGs+NsG  NtG fN G  NtG +N+G++NtG++ +G+
  gi|121636219|ref|YP_976442.1| 519 NTGSFNSGDYNTGYFNAGDYNTGVANTGNVNTGAFISGN 557
                                    *************************************96 PP

  == domain 14  score: 25.5 bits;  conditional E-value: 4.9e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36 
                                    NtG++N+G  NtG +N+G++NtG f +G++  G++
  gi|121636219|ref|YP_976442.1| 529 NTGYFNAGDYNTGVANTGNVNTGAFISGNYSNGFF 563
                                    77777777777777777777777777777777776 PP

  == domain 15  score: 5.5 bits;  conditional E-value: 0.00085
                 Pentapeptide_2   4 GslNsGsgNt.GffNlGsgNt.GsfNlGsgNtGsgntG 39 
                                    G++ +G g++ Gf+N G gN+ G++N+G gN+G++n+G
  gi|121636219|ref|YP_976442.1| 685 GFFHTGAGHVsGFGNFGAGNMsGFGNFGAGNSGFFNAG 722
                                    77777777744888888888558888888888888887 PP

  == domain 16  score: 12.6 bits;  conditional E-value: 5.4e-06
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNl 28 
                                    gN+G lN+G   +G++NlG++  G +N+
  gi|121636219|ref|YP_976442.1| 725 GNSGLLNFGALQSGLANLGNTISGVYNT 752
                                    6777777777777777777777777776 PP

  == domain 17  score: 4.3 bits;  conditional E-value: 0.002
                 Pentapeptide_2   3 tGslNsGsgNtGff..NlGs..gNtGsfNlGsgNtGsgntGs 40 
                                    +G++N+G    G+f  N+G+   N+G +N G  N G+gn+Gs
  gi|121636219|ref|YP_976442.1| 764 SGIANIGANLAGLFldNTGNltLNFGVANQGGLNAGIGNLGS 805
                                    588899988888888899974459999999999999999995 PP

  == domain 18  score: 22.1 bits;  conditional E-value: 5.7e-09
                 Pentapeptide_2   2 NtGs..lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG+  lN+G +N G +N G gN Gs N+G++NtG+ n+G
  gi|121636219|ref|YP_976442.1| 780 NTGNltLNFGVANQGGLNAGIGNLGSVNIGFVNTGDSNLG 819
                                    6665226889999999999999999999999999988887 PP

  == domain 19  score: 28.5 bits;  conditional E-value: 5.8e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG+ N+G gN+G++N G +N+G +N+G +NtG++ +G
  gi|121636219|ref|YP_976442.1| 812 NTGDSNLGIGNLGDLNFGGVNIGGNNIGIANTGIFDIG 849
                                    ***********************************998 PP

  == domain 20  score: 38.6 bits;  conditional E-value: 4.1e-14
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G +N+Gs N+G++NlG  N G++N+Gs+N+G+ n+Gs
  gi|121636219|ref|YP_976442.1| 848 IGLANLGSYNIGLANLGDDNLGFGNAGSYNIGFANFGS 885
                                    799*********************************96 PP

  == domain 21  score: 27.8 bits;  conditional E-value: 9.1e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+Gs N+G +NtG++N+G++NtG++N+G g tG+g +G
  gi|121636219|ref|YP_976442.1| 881 ANFGSDNLGFANTGSYNIGFANTGNNNIGVGLTGNGQIG 919
                                    699999999999999999999999999999999999887 PP

  == domain 22  score: 37.8 bits;  conditional E-value: 6.9e-14
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +GslNsGs N+G+fN+GsgN+G+fN+G+gN+G++n+G
  gi|121636219|ref|YP_976442.1| 920 IGSLNSGSNNIGLFNSGSGNIGFFNSGTGNVGIFNAG 956
                                    8***********************************9 PP

  == domain 23  score: 37.2 bits;  conditional E-value: 1.1e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G +NsG +NtG +N Gs+NtG fN G+ NtGs+n+Gs
  gi|121636219|ref|YP_976442.1| 958 GNFGLANSGGFNTGIGNAGSTNTGVFNPGDLNTGSFNPGS 997
                                    8*************************************96 PP

  == domain 24  score: 38.2 bits;  conditional E-value: 5.4e-14
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG +N GsgNtG +N+G  NtG +N+G+++tG++ tGs
  gi|121636219|ref|YP_976442.1|  999 NTGGFNPGSGNTGYLNTGDYNTGVANTGDVDTGAFITGS 1037
                                     *************************************96 PP

  == domain 25  score: 1.9 bits;  conditional E-value: 0.012
                 Pentapeptide_2    8 sGsgNtGffNlGsgNt.GsfNlGs 30  
                                     +G   +GffN+G g++ G+ N+G 
  gi|121636219|ref|YP_976442.1| 1069 TGGPSSGFFNSGAGSVsGFVNSGA 1092
                                     355567888888877547888776 PP

  == domain 26  score: 10.6 bits;  conditional E-value: 2.3e-05
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     +G++NsG g +G +N+G    G +N+G+  +G +n+
  gi|121636219|ref|YP_976442.1| 1085 SGFVNSGAGLSGYLNTGALGSGVANVGNTISGWLNA 1120
                                     59**************************99998886 PP

  == domain 27  score: -2.2 bits;  conditional E-value: 0.22
                 Pentapeptide_2    4 GslNsGsgNtG 14  
                                     G++N+G+   G
  gi|121636219|ref|YP_976442.1| 1133 GIGNFGTNLAG 1143
                                     44444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                       96  (0.00535445); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 7917.59
//
Query:       gi|121636220|ref|YP_976443.1|  [L=1975]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.4e-183  594.5 871.5    2.9e-11   43.1  23.9   36.6 41  Pentapeptide_2  Pentapeptide repeats (8 copies)
    1.2e-56  191.2  27.9    1.2e-56  191.2  27.9    2.0  2  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7  23.2   9.8e-11   8.8e-07       2      40 .]     199     237 ..     196     237 .. 0.88
   2 !   35.7  19.3   6.5e-13   5.9e-09       2      40 .]     219     257 ..     218     257 .. 0.98
   3 !   24.8  28.2   1.6e-09   1.5e-05       2      40 .]     239     277 ..     238     282 .. 0.94
   4 !   35.4  26.0   8.1e-13   7.3e-09       3      39 ..     282     318 ..     280     319 .. 0.97
   5 !   35.4  32.7   7.7e-13   6.9e-09       1      40 []     310     349 ..     310     349 .. 0.98
   6 !   38.9  30.7   6.3e-14   5.7e-10       1      40 []     320     359 ..     320     359 .. 0.98
   7 !   38.3  21.2     1e-13   9.1e-10       2      40 .]     351     389 ..     350     389 .. 0.98
   8 ?   -0.8  16.7      0.16   1.4e+03       4      38 ..     505     541 ..     504     547 .. 0.76
   9 ?   -2.0  23.6      0.39   3.5e+03       3      40 .]     526     566 ..     525     579 .. 0.83
  10 !   24.7  23.0   1.8e-09   1.6e-05       2      39 ..     599     636 ..     598     637 .. 0.98
  11 !   31.0  14.3   1.9e-11   1.7e-07       1      39 [.     613     651 ..     613     652 .. 0.97
  12 !   27.2  24.8   2.9e-10   2.6e-06       1      39 [.     633     671 ..     628     672 .. 0.90
  13 !   33.2  23.9   3.8e-12   3.4e-08       2      40 .]     649     687 ..     648     687 .. 0.98
  14 !   37.3  23.0     2e-13   1.8e-09       3      39 ..     692     728 ..     690     729 .. 0.97
  15 !   30.3  29.2   3.2e-11   2.9e-07       1      39 [.     720     758 ..     720     759 .. 0.98
  16 !   42.6  21.3   4.4e-15     4e-11       2      39 ..     761     798 ..     760     799 .. 0.98
  17 !   34.1  23.7     2e-12   1.8e-08       2      40 .]     781     819 ..     780     819 .. 0.97
  18 ?    1.0  18.2     0.044     4e+02       4      38 ..     939     975 ..     938     977 .. 0.86
  19 ?    2.3  16.0     0.018   1.6e+02       4      30 ..     984    1010 ..     976    1032 .. 0.61
  20 !   17.6  16.6   2.9e-07    0.0026       3      39 ..    1039    1075 ..    1037    1076 .. 0.95
  21 !   20.2  20.2   4.5e-08    0.0004       1      39 [.    1047    1085 ..    1047    1085 .. 0.98
  22 !   26.8  15.3   3.9e-10   3.5e-06       3      39 ..    1069    1105 ..    1068    1105 .. 0.92
  23 !   34.4  20.2   1.6e-12   1.4e-08       3      40 .]    1084    1121 ..    1083    1121 .. 0.96
  24 !   32.4  26.8   7.1e-12   6.3e-08       2      40 .]    1103    1141 ..    1102    1141 .. 0.98
  25 !   24.1  31.9   2.8e-09   2.5e-05       2      40 .]    1123    1161 ..    1122    1166 .. 0.96
  26 !   36.1  27.5   4.7e-13   4.2e-09       3      40 .]    1166    1203 ..    1164    1203 .. 0.97
  27 !   39.9  24.9   3.1e-14   2.8e-10       2      40 .]    1205    1243 ..    1204    1243 .. 0.98
  28 !   34.4  18.9   1.7e-12   1.5e-08       2      40 .]    1245    1283 ..    1244    1283 .. 0.98
  29 ?    1.8  19.4     0.025   2.3e+02       4      38 ..    1400    1436 ..    1399    1439 .. 0.77
  30 !   10.1   4.6   6.6e-05      0.59      11      38 ..    1442    1469 ..    1436    1471 .. 0.64
  31 ?   -2.1   0.1      0.42   3.8e+03      16      22 ..    1479    1485 ..    1476    1488 .. 0.49
  32 !   36.6  19.5   3.3e-13     3e-09       1      39 [.    1508    1546 ..    1508    1547 .. 0.98
  33 !   32.1  20.0   8.3e-12   7.4e-08       1      39 [.    1548    1586 ..    1544    1587 .. 0.94
  34 !   31.5  25.4   1.3e-11   1.2e-07       2      39 ..    1584    1621 ..    1583    1622 .. 0.97
  35 !   37.7  28.9   1.5e-13   1.4e-09       3      39 ..    1627    1663 ..    1625    1664 .. 0.97
  36 !   37.9  29.0   1.4e-13   1.2e-09       1      40 []    1655    1694 ..    1655    1694 .. 0.98
  37 !   43.1  23.9   3.2e-15   2.9e-11       1      39 [.    1665    1703 ..    1665    1704 .. 0.98
  38 !   40.7  12.7   1.7e-14   1.6e-10       2      40 .]    1696    1734 ..    1695    1734 .. 0.98
  39 ?   -1.1   8.1       0.2   1.8e+03       4      33 ..    1846    1877 ..    1843    1880 .. 0.62
  40 !    4.1   8.0    0.0048        43      13      38 ..    1880    1905 ..    1867    1907 .. 0.68
  41 !   29.9  20.4   4.2e-11   3.7e-07       2      39 ..    1930    1967 ..    1929    1968 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.8e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N G +N+G  N+G++N+G  N+G++NlGs+N G+ n+Gs
  gi|121636220|ref|YP_976443.1| 199 NLGLANVGANNVGNGNVGVFNVGFGNLGSYNLGFANLGS 237
                                    889999999999999999999999999999999999985 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 6.5e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+Gs N+Gf+NlGs N G +NlG  N+G+ ntGs
  gi|121636220|ref|YP_976443.1| 219 NVGFGNLGSYNLGFANLGSDNLGLANLGGHNIGFANTGS 257
                                    9*************************************6 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.6e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N G +N+G +N+Gf+N+Gs N+G++N+Gs+N+G+g tG+
  gi|121636220|ref|YP_976443.1| 239 NLGLANLGGHNIGFANTGSNNVGFGNTGSNNVGIGLTGN 277
                                    99********************************99996 PP

  == domain 4  score: 35.4 bits;  conditional E-value: 8.1e-13
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +Gs+NsGs+N+G+fN+GsgN+G fN+G+gN+G+gn+G
  gi|121636220|ref|YP_976443.1| 282 FGSFNSGSHNIGLFNSGSGNVGLFNSGTGNFGIGNSG 318
                                    8***********************************9 PP

  == domain 5  score: 35.4 bits;  conditional E-value: 7.7e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++NsG+gN+G++N+Gs+NtG+fN+G++NtG++ntG+
  gi|121636220|ref|YP_976443.1| 310 GNFGIGNSGTGNFGLGNTGSTNTGWFNTGDVNTGNFNTGN 349
                                    8**************************************6 PP

  == domain 6  score: 38.9 bits;  conditional E-value: 6.3e-14
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G +N+Gs+NtG+fN+G +NtG+fN+G++NtGs+n+G+
  gi|121636220|ref|YP_976443.1| 320 GNFGLGNTGSTNTGWFNTGDVNTGNFNTGNYNTGSFNAGN 359
                                    8*************************************96 PP

  == domain 7  score: 38.3 bits;  conditional E-value: 1e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtGs+N+G+ NtG fN+G  NtG +N+G++NtG++ +G+
  gi|121636220|ref|YP_976443.1| 351 NTGSFNAGNYNTGYFNTGDYNTGVANTGNVNTGAFIAGN 389
                                    ************************************996 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 0.16
                 Pentapeptide_2   4 GslNsG.sgNtGffNlGsg.NtGsfNlGsgNtGsgnt 38 
                                    G++Ns  s  +GffN G g   G++N+G g +G+ n+
  gi|121636220|ref|YP_976443.1| 505 GFGNSTtSPSSGFFNAGAGtASGFGNFGGGASGFWNL 541
                                    5666541457899999987257999999999999886 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 0.39
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgN...tGsfNlGsgNtGsgntGs 40 
                                    +G++N+G g +Gf+Nl s+     G++N+G   +G  n+G+
  gi|121636220|ref|YP_976443.1| 526 SGFGNFGGGASGFWNLASATsglSGFGNVGALGSGVANVGN 566
                                    59*************98766222568898888888888885 PP

  == domain 10  score: 24.7 bits;  conditional E-value: 1.8e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G +N+G  N+G +N G  N+G +NlG++N+G+gn+G
  gi|121636220|ref|YP_976443.1| 599 NFGLANVGGNNVGGANAGIFNVGLANLGDYNIGFGNLG 636
                                    9***********************************99 PP

  == domain 11  score: 31.0 bits;  conditional E-value: 1.9e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N G++N+G +N+G++N+G+gN G  NlG++  Gs n+G
  gi|121636220|ref|YP_976443.1| 613 ANAGIFNVGLANLGDYNIGFGNLGGDNLGFAHAGSYNIG 651
                                    6*************************************9 PP

  == domain 12  score: 27.2 bits;  conditional E-value: 2.9e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN G  N+G ++ G++N+G++NtGs+NlG++NtG++n+G
  gi|121636220|ref|YP_976443.1| 633 GNLGGDNLGFAHAGSYNIGFANTGSNNLGFANTGDNNIG 671
                                    799999999999999999999999999999999999999 PP

  == domain 13  score: 33.2 bits;  conditional E-value: 3.8e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+Gs N+Gf+N+G  N+G++N+Gs+N+G+g tGs
  gi|121636220|ref|YP_976443.1| 649 NIGFANTGSNNLGFANTGDNNIGFANIGSNNIGIGLTGS 687
                                    9************************************96 PP

  == domain 14  score: 37.3 bits;  conditional E-value: 2e-13
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +GslNsGs+N+G+fN+G gN+G fN+GsgN+G+gn+G
  gi|121636220|ref|YP_976443.1| 692 FGSLNSGSHNIGLFNSGDGNIGLFNSGSGNFGIGNAG 728
                                    8***********************************9 PP

  == domain 15  score: 30.3 bits;  conditional E-value: 3.2e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+G+gN+G +N+G gN+G +N+Gs NtG +n+G
  gi|121636220|ref|YP_976443.1| 720 GNFGIGNAGTGNWGIGNSGAGNFGIGNAGSTNTGLFNSG 758
                                    8*************************************9 PP

  == domain 16  score: 42.6 bits;  conditional E-value: 4.4e-15
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtGslN Gs NtG++N+Gs+NtG fN+G++NtG +ntG
  gi|121636220|ref|YP_976443.1| 761 NTGSLNPGSYNTGSVNTGSVNTGGFNAGNYNTGYFNTG 798
                                    *************************************9 PP

  == domain 17  score: 34.1 bits;  conditional E-value: 2e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG +N+G+ NtG fN+G  NtG +N+G++NtG++ +G+
  gi|121636220|ref|YP_976443.1| 781 NTGGFNAGNYNTGYFNTGDYNTGMANTGNINTGAFISGN 819
                                    *************************************96 PP

  == domain 18  score: 1.0 bits;  conditional E-value: 0.044
                 Pentapeptide_2   4 GslN.sGsgNtGffNlGsgN.tGsfNlGsgNtGsgnt 38 
                                    G++N +G   +GffN+G g+  G++N+G + +G+ n+
  gi|121636220|ref|YP_976443.1| 939 GFGNsTGGLSSGFFNSGAGSaSGFGNFGGAASGFMNL 975
                                    6777358999********9846************996 PP

  == domain 19  score: 2.3 bits;  conditional E-value: 0.018
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNlGs 30  
                                     G+lN+G   +G +N+G++  G +N+G+
  gi|121636220|ref|YP_976443.1|  984 GFLNVGALGSGVANVGNTISGIYNVGT 1010
                                     555555555555555555555555553 PP

  == domain 20  score: 17.6 bits;  conditional E-value: 2.9e-07
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     t   N+G +N+G++N+G+++ G fN+G + +G++n+G
  gi|121636220|ref|YP_976443.1| 1039 TAAINLGLANHGNLNVGFASLGGFNFGGATIGHNNVG 1075
                                     7789*******************************99 PP

  == domain 21  score: 20.2 bits;  conditional E-value: 4.5e-08
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +N+G+lN+G + +G fN G + +G +N+G gNtG++ +G
  gi|121636220|ref|YP_976443.1| 1047 ANHGNLNVGFASLGGFNFGGATIGHNNVGIGNTGIFDVG 1085
                                     6***********************************998 PP

  == domain 22  score: 26.8 bits;  conditional E-value: 3.9e-10
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +G  N+G gNtG f++G +N Gs+N+G+gN G+ n+G
  gi|121636220|ref|YP_976443.1| 1069 IGHNNVGIGNTGIFDVGLANLGSYNIGFGNLGDDNLG 1105
                                     6889999999999999999999999999999999998 PP

  == domain 23  score: 34.4 bits;  conditional E-value: 1.6e-12
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +G +N+Gs N+Gf+NlG  N G++N+Gs+N+G+gn+G+
  gi|121636220|ref|YP_976443.1| 1084 VGLANLGSYNIGFGNLGDDNLGFGNFGSYNIGFGNVGN 1121
                                     699*********************************96 PP

  == domain 24  score: 32.4 bits;  conditional E-value: 7.1e-12
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     N G++N+Gs N+Gf+N+G+ N G++N+G gN+G+ ntGs
  gi|121636220|ref|YP_976443.1| 1103 NLGFGNFGSYNIGFGNVGNDNLGFANAGGGNIGFANTGS 1141
                                     99************************************6 PP

  == domain 25  score: 24.1 bits;  conditional E-value: 2.8e-09
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     N G++N+G gN+Gf+N+Gs N+G++N+Gs+N+G+g tG+
  gi|121636220|ref|YP_976443.1| 1123 NLGFANAGGGNIGFANTGSNNVGFGNTGSNNVGIGLTGN 1161
                                     99*********************************9996 PP

  == domain 26  score: 36.1 bits;  conditional E-value: 4.7e-13
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +Gs+NsGsgN+G+fN+Gs N+G+fN+GsgN+G+ n+Gs
  gi|121636220|ref|YP_976443.1| 1166 FGSFNSGSGNIGLFNSGSNNIGFFNSGSGNFGIANSGS 1203
                                     8************************************6 PP

  == domain 27  score: 39.9 bits;  conditional E-value: 3.1e-14
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG++N+G++NtG+fN+G +NtG fN Gs+NtGs+ntGs
  gi|121636220|ref|YP_976443.1| 1205 NTGIGNTGNTNTGLFNSGDVNTGAFNPGSFNTGSFNTGS 1243
                                     **************************************6 PP

  == domain 28  score: 34.4 bits;  conditional E-value: 1.7e-12
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG +N G++NtG +N+G+ NtG +N+G+++tG++ tG+
  gi|121636220|ref|YP_976443.1| 1245 NTGGFNPGNTNTGYLNIGNYNTGIANTGDVDTGAFITGN 1283
                                     *************************************96 PP

  == domain 29  score: 1.8 bits;  conditional E-value: 0.025
                 Pentapeptide_2    4 GslNsGsg.NtGffNlGsgN.tGsfNlGsgNtGsgnt 38  
                                     G++Ns +   +GffN+G g   G++N+G +N+G+ n+
  gi|121636220|ref|YP_976443.1| 1400 GFGNSTTNpSSGFFNTGAGGaSGFGNFGGANSGFWNL 1436
                                     66666543278******87537***********9996 PP

  == domain 30  score: 10.1 bits;  conditional E-value: 6.6e-05
                 Pentapeptide_2   11 gNtGffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     g +G++N+G    G +N+G+  +G+ nt
  gi|121636220|ref|YP_976443.1| 1442 GASGLLNVGALGSGLANVGTTVSGFYNT 1469
                                     5566666666666666666666666665 PP

  == domain 31  score: -2.1 bits;  conditional E-value: 0.42
                 Pentapeptide_2   16 fNlGsgN 22  
                                     fN+G +N
  gi|121636220|ref|YP_976443.1| 1479 FNSGLAN 1485
                                     2333333 PP

  == domain 32  score: 36.6 bits;  conditional E-value: 3.3e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +N+G+lN+G +N+G++N+G++N Gs+N+Gs+N+G +n+G
  gi|121636220|ref|YP_976443.1| 1508 ANHGTLNVGIANLGDYNIGFANLGSANFGSANIGGNNIG 1546
                                     6************************************99 PP

  == domain 33  score: 32.1 bits;  conditional E-value: 8.3e-12
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +NtG++ +G +N+G++N+G+gN+G+ NlG+gN Gs n+G
  gi|121636220|ref|YP_976443.1| 1548 ANTGIFDIGLANLGSYNIGFGNFGDDNLGFGNLGSYNVG 1586
                                     69***********************************99 PP

  == domain 34  score: 31.5 bits;  conditional E-value: 1.3e-11
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G+ N+Gf+N+Gs N+G++N+Gs+N+G+g tG
  gi|121636220|ref|YP_976443.1| 1584 NVGFGNLGNDNLGFANTGSNNIGFANTGSNNIGIGLTG 1621
                                     9***********************************99 PP

  == domain 35  score: 37.7 bits;  conditional E-value: 1.5e-13
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +GslNsGsgN+G+fN+GsgN+G+fN+G+gN+G+gntG
  gi|121636220|ref|YP_976443.1| 1627 FGSLNSGSGNIGLFNSGSGNIGFFNSGNGNVGIGNTG 1663
                                     8***********************************9 PP

  == domain 36  score: 37.9 bits;  conditional E-value: 1.4e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     gN+G++N+G++N+G++N+Gs+NtG+fN+G++NtG+gntGs
  gi|121636220|ref|YP_976443.1| 1655 GNVGIGNTGTANFGLGNTGSTNTGFFNSGDVNTGIGNTGS 1694
                                     8**************************************6 PP

  == domain 37  score: 43.1 bits;  conditional E-value: 3.2e-15
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +N+G +N+Gs+NtGffN+G +NtG +N+Gs+NtGs+n+G
  gi|121636220|ref|YP_976443.1| 1665 ANFGLGNTGSTNTGFFNSGDVNTGIGNTGSFNTGSFNPG 1703
                                     6*************************************9 PP

  == domain 38  score: 40.7 bits;  conditional E-value: 1.7e-14
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtGs+N G  NtG+fN Gs NtG +N+G+++tG++ +Gs
  gi|121636220|ref|YP_976443.1| 1696 NTGSFNPGDSNTGDFNPGSYNTGLGNTGDVDTGAFISGS 1734
                                     *************************************96 PP

  == domain 39  score: -1.1 bits;  conditional E-value: 0.2
                 Pentapeptide_2    4 GslNsG.sgNtGffNlGsgN.tGsfNlGsgNt 33  
                                     G++Ns  s  +GffN+G g+  G+ N+  g +
  gi|121636220|ref|YP_976443.1| 1846 GFGNSTtSPSSGFFNSGAGSaSGFLNVVAGAS 1877
                                     66665414467888888876347777655555 PP

  == domain 40  score: 4.1 bits;  conditional E-value: 0.0048
                 Pentapeptide_2   13 tGffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     +G +N+G    G +N+G+  +G+ n+
  gi|121636220|ref|YP_976443.1| 1880 SGYLNVGALGSGVTNVGHTVSGFYNA 1905
                                     56677777777777777777777765 PP

  == domain 41  score: 29.9 bits;  conditional E-value: 4.2e-11
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N G +N+Gs N Gf+N+G   +G +NlG++N+G+gn+G
  gi|121636220|ref|YP_976443.1| 1930 NLGLANLGSNNAGFGNTGIFDVGVANLGNYNIGFGNFG 1967
                                     99***********************************9 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2  27.9   1.3e-60   1.2e-56       2     157 ..       6     161 ..       5     162 .. 0.99
   2 ?    2.0   0.7     0.023   2.1e+02      58      91 ..     158     191 ..     157     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 1.3e-60
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    + PEvns ++y G+gsgp+laAaaaWdgLa+ela aa+ + sv+++la++aW+Gp++ ama+a+apyl WL  a+aqae+
  gi|121636220|ref|YP_976443.1|   6 SAPEVNSLRMYLGAGSGPMLAAAAAWDGLADELAVAASWFGSVTSGLADAAWRGPAAVAMARAVAPYLGWLISATAQAEQ 85 
                                    57****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    aAaqa++a+a +eaA+aa+v+pa +aanra l++lv++n++G n+paIaatea+ye+mwaqd+aam +Y+a ++aa
  gi|121636220|ref|YP_976443.1|  86 AAAQARVAVATFEAARAATVHPAIVAANRAVLVSLVSSNLLGFNAPAIAATEAAYERMWAQDVAAMVGYHAGASAA 161
                                    *************************************************************************998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.023
                                    HHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  58 saamaaaaapylaWLsaaaaqaeeaAaqaeaaaa 91 
                                    + a+++a +p+++ L++ a  +e+  + a+aaa 
  gi|121636220|ref|YP_976443.1| 158 ASAAVSALMPFTQQLKKLAGLSERLTSAAAAAAG 191
                                    67899*******************9999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1975 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.02u 0.30s 00:00:01.32 Elapsed: 00:00:00.46
# Mc/sec: 13010.24
//
Query:       gi|121636221|ref|YP_976444.1|  [L=223]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-24   86.4   0.0    3.1e-24   85.9   0.0    1.2  1  Nitroreductase  Nitroreductase family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   1.7e-28   3.1e-24       1     169 [.      14     178 ..      14     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.7e-28
                                    HHH--B---B-S--.--HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHH CS
                 Nitroreductase   1 irkRrSiRkFddep.vpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeel 79 
                                    i++Rr  R F +   v++++l+++l+aa+ aPs g +qpwrf+ ++d+ l++++  ++ ++ l   +++  + ++     
  gi|121636221|ref|YP_976444.1|  14 IAERRDMRRFVPGGvVSEDVLARLLHAAHAAPSVGLMQPWRFIRITDETLKRRIHALVDDERLLTAEALGAREEE----F 89 
                                    789******************************************999999998888887777666666555554....4 PP

                                    HHHHHHHHHHSSEEEEE.---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S. CS
                 Nitroreductase  80 klkaqkalagapvlivi.vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpd 158
                                     +++ + + +++ l+v+   +   s     +   + +l+++++a+qnl+LaA+++Glg+ +++ fd ++  +++ll +p 
  gi|121636221|ref|YP_976444.1|  90 LALKVEGILDCAELLVVaLCDRRGSYIFGRRTLPQMDLASVSCAIQNLWLAARSEGLGMGWVSLFDPQR--LAALLAMPA 167
                                    5666666666665555535555556677788889999********************************..********9 PP

                                    .SEEEEEEEEE CS
                 Nitroreductase 159 eeeivvliavG 169
                                    + e+v+++++G
  gi|121636221|ref|YP_976444.1| 168 DAEPVAILCLG 178
                                    9********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1905.18
//
Query:       gi|121636222|ref|YP_976445.1|  [L=160]
Description: hypothetical protein BCG_0347c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1253.11
//
Query:       gi|121636223|ref|YP_976446.1|  [L=238]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-14   53.9  13.0    1.5e-14   53.9  13.0    2.3  2  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
        2.1    8.0  24.0       0.18   11.5  17.9    2.3  2  PAP2_3    PAP2 superfamily


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.6      0.87   7.8e+03      96      97 ..      16      17 ..       6      27 .. 0.39
   2 !   53.9  13.0   1.7e-18   1.5e-14       3     130 ..      92     204 ..      87     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.87
                           PAP2 96 vl 97
                                   + 
  gi|121636223|ref|YP_976446.1| 16 AT 17
                                   11 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 1.7e-18
                           PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkki 82 
                                    l ll +l l a+ t ++K++  rpRP ++ +   ++                sfPSgH++ a+a++l+l  +l ++ + +
  gi|121636223|ref|YP_976446.1|  92 LLLLACLPLNAIMTIAAKSVAHRPRPATALVSAHST----------------SFPSGHALEATASVLALLTVLLPMLHSR 155
                                    55666666677777888*********9987654332................89*****777776666555554444443 PP

                           PAP2  83 g.lvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                      +++++++ +l+++ v+++R++l+vH+++Dv+aG+++G++ ++++  +
  gi|121636223|ref|YP_976446.1| 156 FtRHIAITVGALCVLTVGVARVALNVHHPTDVVAGWALGYLYFLVCLCV 204
                                    3479**************************************9998765 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3      0.44   3.9e+03     153     168 ..       9      24 ..       2      27 .. 0.49
   2 ?   11.5  17.9     2e-05      0.18      98     189 ..     107     199 ..      66     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.44
                         PAP2_3 153 vlalllnvlmivatva 168
                                    ++ l++++  ++a+++
  gi|121636223|ref|YP_976446.1|   9 AVSLAFVATAVYAVMW 24 
                                    4444444444444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2e-05
                         PAP2_3  98 aaaslagalrdgasravllrgtienglaafPSlHvawallvalalwr....lrrkr....llrvlalllnvlmivatvat 169
                                    aa s+a+       r  ++++ ++++  +fPS H+  a+  +lal +    + ++r    +   +++l ++ + va va+
  gi|121636223|ref|YP_976446.1| 107 AAKSVAH-------RPRPATALVSAHSTSFPSGHALEATASVLALLTvllpMLHSRftrhIAITVGALCVLTVGVARVAL 179
                                    4444444.......555666777889999*****98766655554431111334442344677778888888899***** PP

                         PAP2_3 170 gnHYlvDviaGvalalvaia 189
                                      H  +Dv+aG+al+++ ++
  gi|121636223|ref|YP_976446.1| 180 NVHHPTDVVAGWALGYLYFL 199
                                    **************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1830.01
//
Query:       gi|121636224|ref|YP_976447.1|  [L=218]
Description: hypothetical protein BCG_0349 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.7e-05   23.3   0.1    9.8e-05   22.8   0.1    1.4  1  YkuD       L,D-transpeptidase catalytic domain
  ------ inclusion threshold ------
       0.17   11.6   0.1       0.31   10.9   0.1    1.3  1  zf-H2C2_5  C2H2-type zinc-finger domain


Domain annotation for each model (and alignments):
>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.1e-08   9.8e-05      31     144 ..      78     214 ..      39     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                                    B......TTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEEECCCTT................... CS
                           YkuD  31 G......gkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyldkknskv................... 85 
                                    G        k+g+  TP G++ ++s++     + p++  + ++ + +  + +++  +ns +                   
  gi|121636224|ref|YP_976447.1|  78 GsagmapEAKSGYPATPMGVYSLDSAF----GTAPNPGGGLPYTQVG-PNHWWSGDDNSPTfnsmqvcqksqcpfstads 152
                                    155566734445779*********332....2233444333433333.34444444444445778889999999999*** PP

                                    .............CECCCCEEE-STTS-EEEE.ETCSS...CTHHC.BSSSEEE-HHHHHHHHHHHHTTEEE CS
                           YkuD  86 .............algkvkfvfpngsgiyiHgtgapdlfergkgarrShGCirlseedakelyelvlvgtpv 144
                                                    +  +v ++gs++++H   ++           + GC++++++ + ++ +++ +g  +
  gi|121636224|ref|YP_976447.1| 153 enlqipqykhsvvMGVNKAKVPGKGSAFFFH--TTD--------GGPTAGCVAIDDATLVQIIRWLRPGAVI 214
                                    ************6556666777788889999..444........355********************99766 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.4e-05      0.31       4      17 ..     143     156 ..     143     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.4e-05
                      zf-H2C2_5   4 sqCDYstawksnLk 17 
                                    sqC++sta + nL+
  gi|121636224|ref|YP_976447.1| 143 SQCPFSTADSENLQ 156
                                    7***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1512.96
//
Query:       gi|121636225|ref|YP_976448.1|  [L=163]
Description: hypothetical protein BCG_0350c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-28   97.4   1.9    8.6e-28   97.0   1.9    1.1  1  SnoaL_4   SnoaL-like domain
    6.4e-06   26.7   1.4    8.7e-06   26.3   1.4    1.2  1  SnoaL_2   SnoaL-like domain
  ------ inclusion threshold ------
      0.015   15.5   0.2      0.044   14.1   0.2    1.7  1  SnoaL_3   SnoaL-like domain
      0.069   13.6   0.4       0.12   12.8   0.4    1.4  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   1.9   1.9e-31   8.6e-28       5     124 ..      14     134 ..      12     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 1.9e-31
                                    HHHHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS....--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEETT CS
                        SnoaL_4   5 dreaIrdlvarygyylDtkdweeladlFtedavvdytgvg..egvlegrdairaalrealdgfaltqHllsnplieldgd 82 
                                    d++aI++l++ry ++lDtk w+++ d+ +ed++ dy+++   e  ++ r++++++lr+al++++ t H +++p i+++gd
  gi|121636225|ref|YP_976448.1|  14 DIAAIKQLKYRYLRALDTKHWDDFTDTLAEDVTGDYGSSVgtELHFTNRADLVDYLRQALGPGVITEHRVTHPEITVTGD 93 
                                    899**********************************87699999999******************************** PP

                                    EEEEEEEEEEEEEETTEEEEEE..EEEEEEEEEEETTEEEEE CS
                        SnoaL_4  83 tAtgrayllatlvrdgdggrqvlaggryedelvredggWris 124
                                    tAtg++yl++   +++  +  ++ +++y+d+++r+ +gWris
  gi|121636225|ref|YP_976448.1|  94 TATGIWYLQDRVIVAE-FNFMLIGAAFYHDQYRRTTDGWRIS 134
                                    ***********88775.56677788****************8 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   1.4   1.9e-09   8.7e-06       3      77 ..      24     124 ..      23     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                                    HHHHHHHTTCHHHHHHTEEEEEE.EEET.TSE...EESHHHHHHHHHHHHH..HEEEEEEEEEEEEEETTEEEEEEEEEE CS
                        SnoaL_2   3 aflaalnagdldalaalfapdvv.wedp.gge...lrGreairaffralfa..afpdlrfeihdvvadgdrvavewtvtg 75 
                                    ++l+al+++ +d++ +++a+dv+  ++  +g+   ++ r+++ +++r+++    + + r++  ++++ gd++   w ++ 
  gi|121636225|ref|YP_976448.1|  24 RYLRALDTKHWDDFTDTLAEDVTgDYGSsVGTelhFTNRADLVDYLRQALGpgVITEHRVTHPEITVTGDTATGIWYLQD 103
                                    89*********************5455577777*****************977777777777888*******99998887 PP

                                    E...................E CS
                        SnoaL_2  76 t...................i 77 
                                    +                   +
  gi|121636225|ref|YP_976448.1| 104 RvivaefnfmligaafyhdqY 124
                                    766666555555555555553 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   9.7e-06     0.044       1      83 [.      18     103 ..      18     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                        SnoaL_3   1 vealldafyeaaaegdfdalfalwa.....ddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdva 75 
                                    +++l  ++++a+ ++ +d + +++a     d+ + +g  +  ++t+r++++++l+q +  g  ++ ++t+ ++t+ gd+a
  gi|121636225|ref|YP_976448.1|  18 IKQLKYRYLRALDTKHWDDFTDTLAedvtgDYGSSVG--TELHFTNRADLVDYLRQALGPGVITEHRVTHPEITVTGDTA 95 
                                    56777789999**************777777777777..55699**************9998889999999999999888 PP

                        SnoaL_3  76 wvtelldv 83 
                                         l+ 
  gi|121636225|ref|YP_976448.1|  96 TGIWYLQD 103
                                    76655544 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.7e-05      0.12       1     107 []      18     133 ..      18     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                    HHHHHHHHHHHHHCT-HHHHHHCEEEEEEEE.-TT....S-EEEHHHHHHHHHC..CHCEEEEEEEEEEEEEEETTEEEE CS
                        DUF4440   1 iaaleealeeafvagdaealaallapdavlv.gps....gtvldkeellealea..gfaagrslelteeevrvlgdlAvv 73 
                                    i++l  ++ +a+ ++ ++ + + la+d++   g+s      ++++++l++ l++  g+   ++ ++t +e+ v+gd+A+ 
  gi|121636225|ref|YP_976448.1|  18 IKQLKYRYLRALDTKHWDDFTDTLAEDVTGDyGSSvgteLHFTNRADLVDYLRQalGPGVITEHRVTHPEITVTGDTATG 97 
                                    67788899999999999999999999996543444522133346999999999955556667779999***********9 PP

                                    EEEEEEEECCTTEEEE....EEEEEEEEEEEETTEEEE CS
                        DUF4440  74 tgrytfegrgdgepve....grgrftsvwrkegggWri 107
                                    +++ + ++  ++  +     g + +   +r++ +gWri
  gi|121636225|ref|YP_976448.1|  98 IWYLQDRVIVAE--FNfmliGAAFYHDQYRRTTDGWRI 133
                                    999887776665..333356899999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1036.35
//
Query:       gi|121636226|ref|YP_976449.1|  [L=409]
Description: hypothetical protein BCG_0351 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2696.12
//
Query:       gi|121636227|ref|YP_976450.1|  [L=620]
Description: hypothetical protein BCG_0352 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   63.4   0.0    1.6e-17   63.0   0.0    1.1  1  HSP70     Hsp70 protein
      0.009   14.9   0.1      0.019   13.8   0.0    1.5  2  MreB_Mbl  MreB/Mbl protein
  ------ inclusion threshold ------
       0.01   15.6   0.3      0.032   13.9   0.2    1.8  2  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   2.6e-21   1.6e-17     182     372 ..     158     347 ..      61     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.6e-21
                                    SSSCEEEEEEEEXSSXEEEEEEEEETT....EEE.EEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHH..HH CS
                          HSP70 182 kdkernvlvyDlGggtfdvSilelekG....vfe.vkaTagDthlGGedfDealvehlveefkkkegidlskdkka..lq 254
                                         +v ++D+Gg+++ v ++e ++      f+ v aTa  +++ G + D+al+  ++++f    ++d ++   +  l 
  gi|121636227|ref|YP_976450.1| 158 G---GVVGLLDFGGSATYVTLVETKSDsrtsDFQpVSATARYQDFSGSQIDQALLLRVIDQFGYGDDVDPASTAAVgqLG 234
                                    3...47889**************9854222356559*********************************98887652277 PP

                                    HHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEES CS
                          HSP70 255 rlkeaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvG 334
                                    +l+e++  aK  LS+  +te+  e+          s++++R+++e+l++d l   + ++  +l+  + +  ++ +vv vG
  gi|121636227|ref|YP_976450.1| 235 QLREQCRAAKERLSTDVATELFAELAGC-----SSSIEMTREQLEDLIQDPLTGFIYAFDDMLARHNASWADLAAVVTVG 309
                                    9**************6666665555555.....559******************************************** PP

                                    GGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHH CS
                          HSP70 335 GstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqa 372
                                    G + iP v+++++  ++++  ++ +p  a a+GA + a
  gi|121636227|ref|YP_976450.1| 310 GGANIPLVTQRLSFHTRRPVLTASQPGCAAAMGALLLA 347
                                    **********************************8766 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1      0.63   3.7e+03     125     161 ..     137     175 ..      89     179 .. 0.65
   2 !   13.8   0.0   3.2e-06     0.019     229     316 ..     260     344 ..     235     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.63
                                    EEEEHHHHHHHHTT--TTSSS-EEE..EEE-SS-EEEEE CS
                       MreB_Mbl 125 llieeplaAAiGaglpveepsgnmv..vdiGggttevav 161
                                     l+++++aA    + ++  p+g +v  +d Gg +t v++
  gi|121636227|ref|YP_976450.1| 137 RLVSDAIAALTAVNSELGLPHGGVVglLDFGGSATYVTL 175
                                    456666666666677777777777655788888887766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.2e-06
                                    TTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTT CS
                       MreB_Mbl 229 tglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpl 308
                                     g   ++e++ e++++ +++p++  + a   +L +  +   ad++  ++v +GGga +  + + ls +t+ pv +a++p 
  gi|121636227|ref|YP_976450.1| 260 AGCSSSIEMTREQLEDLIQDPLTGFIYAFDDMLARHNASW-ADLA--AVVTVGGGANIPLVTQRLSFHTRRPVLTASQPG 336
                                    6888999***************************999875.6776..68999**************************** PP

                                    THHHHHHH CS
                       MreB_Mbl 309 tcvakGtg 316
                                     ++a G+ 
  gi|121636227|ref|YP_976450.1| 337 CAAAMGAL 344
                                    *9999986 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.43   2.6e+03       4      57 ..       8      73 ..       7     160 .. 0.66
   2 ?   13.9   0.2   5.4e-06     0.032     125     195 ..     278     348 ..     251     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.43
                         FGGY_C  4 slGTssflll.vgtkpvisehglltpva............gedgkpeyalegsiavagslvawlldn 57
                                   s+GT+ ++ + +g  pv    ++lt ++            +   +p  ++ g++   g++va +  +
  gi|121636227|ref|YP_976450.1|  8 SIGTTNLVAAgNGGPPV-TRRAVLTLYPhcapkigvpsqnPNLIEPGALMSGFVERIGDAVALVSPD 73
                                   67788888777777777.7777777777677777777665555777777777777777777766555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.4e-06
                         FGGY_C 125 rAaleavalqlrailealekdsgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAilAa 195
                                    +  l +  +++ + l   +++  ++l+ ++++GGg++ +l+ q l   + +pV ++ +   a+a+Ga +lA+
  gi|121636227|ref|YP_976450.1| 278 QDPLTGFIYAFDDMLARHNAS-WADLAAVVTVGGGANIPLVTQRLSFHTRRPVLTASQpGCAAAMGALLLAN 348
                                    444555556666666666555.889*******************************999999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 4016.79
//
Query:       gi|121636228|ref|YP_976451.1|  [L=128]
Description: hypothetical protein BCG_0353 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 895.11
//
Query:       gi|121636229|ref|YP_976452.1|  [L=220]
Description: hypothetical protein BCG_0354c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-23   80.0   4.6    7.6e-23   80.0   4.6    1.8  2  DUF3060   Protein of unknown function (DUF3060)
  ------ inclusion threshold ------
      0.014   15.7   2.3      0.015   15.5   0.7    1.9  3  DUF3040   Protein of unknown function (DUF3040)
      0.027   14.6   0.6      0.056   13.6   0.6    1.5  1  CwsA      Cell wall synthesis protein CwsA


Domain annotation for each model (and alignments):
>> DUF3060  Protein of unknown function (DUF3060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.51     3e+03      34      40 ..     137     143 ..     133     153 .. 0.62
   2 !   80.0   4.6   1.3e-26   7.6e-23       1      56 [.     157     212 ..     157     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.51
                        DUF3060  34 itvsGld 40 
                                    ++vsG++
  gi|121636229|ref|YP_976452.1| 137 LSVSGVN 143
                                    4444443 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 1.3e-26
                        DUF3060   1 vsGssNtvtltGeCeavtVsGssNtVtvdsvdkitvsGldNtVtyksGePkvsdtG 56 
                                    vsG sNtv +tG+C+++tVsG++N+Vt+dsvd+i++ G++N Vty+sG+Pk+s+ G
  gi|121636229|ref|YP_976452.1| 157 VSGMSNTVVITGHCTSLTVSGMRNSVTADSVDTIEAAGFNNEVTYHSGSPKISNAG 212
                                    8*****************************************************99 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7     1e+04      11      22 ..      20      29 ..      17      47 .. 0.66
   2 ?   15.5   0.7   2.6e-06     0.015      36      75 ..      66     106 ..      58     112 .. 0.66
   3 ?   -2.7   0.0       1.2   7.2e+03      58      73 ..     137     158 ..     120     170 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                        DUF3040 11 LeeiEraLaaeD 22
                                    +e+Er La  D
  gi|121636229|ref|YP_976452.1| 20 IRELERPLA--D 29
                                   578888885..4 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.6e-06
                        DUF3040  36 arrrslrrlavlavllfvaGllllvlG.vaaaavvlgvvGf 75 
                                     r++s  r+ ++ ++++v+G+l+lv+G +a +a  l+   f
  gi|121636229|ref|YP_976452.1|  66 PRSSSGNRAWWILAAVVVVGVLVLVGGiAAFSAQRLSQGNF 106
                                    4455556766777777778********66655544444444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.2
                        DUF3040  58 llvlGvaaaa......vvlgvv 73 
                                    l v Gv ++        +++v 
  gi|121636229|ref|YP_976452.1| 137 LSVSGVNVNRtiacndSIVSVS 158
                                    4444433333233333344444 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   9.3e-06     0.056      86     117 ..      71     105 ..      64     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                           CwsA  86 rrkrplllag...vavavlaGGavafsivrrssrP 117
                                     ++  ++la+   v+v vl+GG +afs  r s+  
  gi|121636229|ref|YP_976452.1|  71 GNRAWWILAAvvvVGVLVLVGGIAAFSAQRLSQGN 105
                                    46677999996556788***********9998543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1757.17
//
Query:       gi|121636230|ref|YP_976453.1|  [L=294]
Description: beta-1,3-glucanase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-14   53.3   0.2    1.2e-13   50.9   0.2    1.9  1  Glyco_hydro_16  Glycosyl hydrolases family 16
  ------ inclusion threshold ------
        0.1   11.6   5.3       0.14   11.2   5.3    1.1  1  DEC-1_N         DEC-1 protein, N-terminal region


Domain annotation for each model (and alignments):
>> Glyco_hydro_16  Glycosyl hydrolases family 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.2   1.3e-17   1.2e-13      14     130 ..     106     227 ..      97     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.3e-17
                                    EEEETTSEEEEEEEE....EEEEEEEECCEESSE.EEEEEEE--.-STTEEEEEEEETGGTSTTEEEEE.EEETT-TTEE CS
                 Glyco_hydro_16  14 vsvengetltltldk....esgsrikskksflyG.kvearikaa.ksaGvvtafylssedekahdEiDi.EflGndtgkv 86 
                                    v  + +++l+l++++    + g+ +    +   G ++earik++    G+++a +ls++d   ++EiD+ E+ Gn t+  
  gi|121636230|ref|YP_976453.1| 106 VFLDGNSNLVLRATRegnrYFGGLVHGLWRGGIGtTWEARIKFNcLAPGMWPAWWLSNDDPGRSGEIDLiEWYGNGTWPS 185
                                    4444345677777666665667777776666666579*****661578**********99******************** PP

                                    EEEEEBTTBSGEEEEEETSS-TTTS-EEEEEEEETTEEEEEETT CS
                 Glyco_hydro_16  87 qtnvygkGkgkrekrlslwfdptedfHtYaieWtpdkikfyVDg 130
                                     t+v+++ +g++ ++ +     +  +H++ + W+p+ + f++D 
  gi|121636230|ref|YP_976453.1| 186 GTTVHANPDGTAFETCP--IGVDGGWHNWRVTWNPSGMYFWLDY 227
                                    *********99966777..4589*****************9884 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.3   1.5e-05      0.14     111     148 ..      18      61 ..       6     108 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                        DEC-1_N 111 gllGaaapapalaaapppapapvpddpapapaapqaa........a 148
                                    g l aa pap+  a+p  + ap+   p+papaap aa         
  gi|121636230|ref|YP_976453.1|  18 GALAAALPAPTAWADPSRPAAPAG--PTPAPAAPAAAtggllfhdE 61 
                                    456677888888888887778776..66666666665333433330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2132.39
//
Query:       gi|121636231|ref|YP_976454.1|  [L=204]
Description: muconolactone isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-60  201.3   0.0    2.4e-31  107.8   0.0    2.0  2  MIase     Muconolactone delta-isomerase


Domain annotation for each model (and alignments):
>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   0.0   1.3e-35   2.4e-31       1      90 []       1      93 [.       1      93 [. 0.99
   2 !   91.8   0.0   1.2e-30   2.2e-26       2      90 .]     108     199 ..     108     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 1.3e-35
                          MIase  1 mlFlvemtvklpedlpaeevaelkarekaraqelqrqGklvrlwrv...vgeyanisifdvedndeLhelLssLPlfpymti 79
                                   m+Flv+mt+++p+++pa++v++++are+ar++el++qGkl rlwr+   +ge++++++f+++dn eL++lL+s+P +++ t 
  gi|121636231|ref|YP_976454.1|  1 MEFLVTMTTRVPDSMPADAVERVRAREAARSRELAAQGKLLRLWRPplrPGEWRTLGLFAADDNGELEQLLASMPPRSWRTD 82
                                   9*********************************************999********************************* PP

                          MIase 80 evtpLarHpsd 90
                                   +vtpL  Hp+d
  gi|121636231|ref|YP_976454.1| 83 DVTPLGAHPND 93
                                   *********97 PP

  == domain 2  score: 91.8 bits;  conditional E-value: 1.2e-30
                          MIase   2 lFlvemtvklpedlpaeevaelkarekaraqelqrqGklvrlwrv...vgeyanisifdvedndeLhelLssLPlfpymt 78 
                                    +Fl+++t+ +p+++pa++v+++ are++ra el+ +G+lvrlw++   ++  +++++++++d+ eL+++L+sLPl+ +mt
  gi|121636231|ref|YP_976454.1| 108 EFLIATTIMVPPGTPAQVVDDTVAREARRAPELAGRGHLVRLWALpdgPDGQRTLGLWRARDPGELMAILESLPLAGWMT 187
                                    7********************************************8888999**************************** PP

                          MIase  79 ievtpLarHpsd 90 
                                    ie+tpL+ Hp+d
  gi|121636231|ref|YP_976454.1| 188 IETTPLSPHPDD 199
                                    **********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1466.61
//
Query:       gi|121636232|ref|YP_976455.1|  [L=256]
Description: glycerophosphoryl diester phosphodiesterase glpQ2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-40  137.9   0.0    5.9e-40  137.6   0.0    1.1  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
    1.8e-06   28.2   1.6    6.2e-06   26.5   0.9    2.3  3  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   6.6e-44   5.9e-40       1     258 [.      14     241 ..      14     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 6.6e-44
                                    TTTTTT.TSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCC CS
                           GDPD   1 HRGasg.nlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenka 79 
                                    HRG+ + +lp n++ +f++Aa+lG +yiE+Dv+ T+Dgv+V+lHD++l+  ++ +g   v  l++ ++++++  ++++  
  gi|121636232|ref|YP_976455.1|  14 HRGFTSfRLPMNSMGAFQEAAKLGFRYIETDVRATRDGVAVILHDRRLAPGVGLSG--AVDRLDWRDVRKAQ-LGAGQ-- 88 
                                    9999772667**********************************************..**************.77777.. PP

                                    CSCCCSSGCCB...BHHHHHHH....HHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEE CS
                           GDPD  80 qlsenrvrlefpfptleevlkk....pqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifss 155
                                               ++ptle++l        n ++++   i+++++++e+ +  +++ ++ s++e++       + r + + +
  gi|121636232|ref|YP_976455.1|  89 -----------SIPTLEDLLTAlpdmRVNIDIKAASAIEPTVNVIERCN-AHNRVLIGSFSERR-------RRRALRLLT 149
                                    ...........56888888877332224555555556899999999999.899*********99.......567777779 PP

                                    STHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-T CS
                           GDPD 156 fnpdilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnn 235
                                     ++++   +  ++ +l    l + +++a++    +r++++++ ++ lg v+ ++++     +V+ ++++g +vh++tv++
  gi|121636232|ref|YP_976455.1| 150 KRVASSAGTGALLAWLTARPLGS-RAYAWRM---MRDIDCVQLPSRLGGVPVITPA-----RVRGFHAAGRQVHAWTVDE 220
                                    **********************8.4444444...69********************.....******************* PP

                                    HSHHHHHHHHCCC-SEEEES-HH CS
                           GDPD 236 edeeemkrlleagvdgvitDfpd 258
                                    +  + m++ll++ vdg+itD+ d
  gi|121636232|ref|YP_976455.1| 221 P--DVMHTLLDMDVDGIITDRAD 241
                                    *..*****************987 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.61   5.5e+03      14      28 ..      31      45 ..      29      45 .. 0.78
   2 ?   -3.0   0.0       1.3   1.2e+04      12      20 ..      75      83 ..      72      84 .. 0.76
   3 !   26.5   0.9   6.9e-10   6.2e-06       1      28 [.     212     239 ..     212     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.61
                         GDPD_2 14 relvgaGVdgInTDd 28
                                   +e+ ++G ++I TD+
  gi|121636232|ref|YP_976455.1| 31 QEAAKLGFRYIETDV 45
                                   566689999**9995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                         GDPD_2 12 vwrelvgaG 20
                                   +wr  ++a 
  gi|121636232|ref|YP_976455.1| 75 DWRDVRKAQ 83
                                   899988875 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 6.9e-10
                         GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTDd 28 
                                    +v +Wt+d ++v+ +l+++ VdgI+TD+
  gi|121636232|ref|YP_976455.1| 212 QVHAWTVDEPDVMHTLLDMDVDGIITDR 239
                                    688************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1822.73
//
Query:       gi|121636233|ref|YP_976456.1|  [L=264]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.3  10.1    1.8e-09   37.3  10.1    2.0  2  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.9    0.0032        58     257     330 ..      39     102 ..      13     105 .. 0.59
   2 !   37.3  10.1     1e-13   1.8e-09     194     329 ..     131     263 ..     108     264 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0032
                            Zip 257 plGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalml 330
                                    ++Gil G++    s  + + ++ + ++ ++aG+ +     e+lp +l +           l ++g+ +G+a+++
  gi|121636233|ref|YP_976456.1|  39 LAGILGGVV---PSVRTPSAAMVSGVQHFAAGIVMAAVAGEVLP-DLRSRGP------LWLIVVGFSAGVAVLV 102
                                    333333333...33344444445556889999999999999999.7766652......4555666666666665 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1e-13
                            Zip 194 ilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGiliGilvrsise 271
                                     ++ fidGL ++  +++ss t+i+++iA+++  l+ +l++ ++L+ +g++r  a     +++l+  +G + G +      
  gi|121636233|ref|YP_976456.1| 131 AVDLFIDGLLVAtgATVSSRTAIIITIALTVEVLFLGLAVALRLAGSGMPRIRAAATTSALSLVIAVGGVSGAV----AL 206
                                    46779***955555*****************************************9999999999999999999....78 PP

                            Zip 272 ssgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalm 329
                                    ++  + v +++la++a  +l   + ell  E ++  +  ++  ++ + +++l G ++m
  gi|121636233|ref|YP_976456.1| 207 GRAGNTVLTLVLAFAAAALLWLVVEELLV-EAHETPERPWMAVMFFAGFLILYGLGVM 263
                                    8999999*********************9.8888887778899999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1724.19
//
Query:       gi|121636234|ref|YP_976457.1|  [L=222]
Description: pyrrolidone-carboxylate peptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-87  290.5   0.1    1.1e-86  290.2   0.1    1.0  1  Peptidase_C15  Pyroglutamyl peptidase


Domain annotation for each model (and alignments):
>> Peptidase_C15  Pyroglutamyl peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.2   0.1     6e-91   1.1e-86       2     201 ..       3     207 ..       2     208 .. 0.99

  Alignments for each domain:
  == domain 1  score: 290.2 bits;  conditional E-value: 6e-91
                                    EEEEEEE---TT-S--HHHHHHHHHTT-EETTEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT--SEEEE-E CS
                  Peptidase_C15   2 kvLvtGfdPfgkekinPaleavkeLdgaeiaeativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrsaitverv 81 
                                    kvLvtGf+P+g +++nPa+ +++eLdg++ia+at+++r+vP++f++s++++++aiaei+p++v+++G+++Grs+itver+
  gi|121636234|ref|YP_976457.1|   3 KVLVTGFGPYGVTPVNPAQLTAEELDGRTIAGATVISRIVPNTFFESIAAAQQAIAEIEPALVIMLGEYPGRSMITVERL 82 
                                    9******************************************************************************* PP

                                    EES-BE-.S..S--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHHHHHHHS- CS
                  Peptidase_C15  82 ainldDa.r..ipDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvlylldkklp 158
                                    a+n++D+ r  ++D++g++l++ep++p+g++aY++t+Pv+amv a+++aGvPa+vs++aGtfvCnhl+Y+vl++l++k++
  gi|121636234|ref|YP_976457.1|  83 AQNVNDCgRygLADCAGRVLVGEPTDPAGPVAYHATVPVRAMVLAMRKAGVPADVSDAAGTFVCNHLMYGVLHHLAQKGL 162
                                    *******8899********************************************************************* PP

                                    -SEEEEEEE-B-GGGTHHHHHT..-B--HHHHHHHHHHHHHHHHH CS
                  Peptidase_C15 159 evraGfihiPylpeqvidkpet..pslsldkevagvkaaieaive 201
                                    +vraG+ih+P+lp++++ +++   ps+s++++vagv+a+iea+++
  gi|121636234|ref|YP_976457.1| 163 PVRAGWIHLPCLPSVAALDHNLgvPSMSVQTAVAGVTAGIEAAIR 207
                                    ********************9999******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1534.64
//
Query:       gi|121636235|ref|YP_976458.1|  [L=220]
Description: hypothetical protein BCG_0360 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1473.59
//
Query:       gi|121636236|ref|YP_976459.1|  [L=190]
Description: deoxycytidine triphosphate deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-12   46.0   0.0    4.8e-07   28.9   0.0    2.1  2  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
    8.7e-11   41.6   0.0    1.2e-10   41.1   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.6e-09   6.8e-05       5     116 ..       3     112 ..       1     115 [. 0.77
   2 !   28.9   0.0   5.4e-11   4.8e-07     243     353 ..      69     175 ..      63     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.6e-09
                            DCD   5 lpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvras..FlpgkgekvaekleelklheldLtegavlekgc 82 
                                    l+d++++a i++g +   +p++++ +qP+s+D+rL    +rv     +   + +k +++l++l  + +d  e  vl  g 
  gi|121636236|ref|YP_976459.1|   3 LSDRDLRAEISSGRL-GIDPFDDTLVQPSSIDVRLD-CLFRVFNNtrYTHIDPAKQQDELTSLV-QPVD-GEPFVLHPGE 78 
                                    788888888999998.5579***************6.579995441133333334444444442.3344.4778****** PP

                            DCD  83 vYivplleslaLpadlsaaanpksstGRlDvftR 116
                                      +   le ++Lp++l+++ + kss GRl ++t 
  gi|121636236|ref|YP_976459.1|  79 FVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTH 112
                                    *****************************99985 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 5.4e-11
                            DCD 243 geklildpdeFYilasreavkvppdlaaemv..pfdalvGefRvhYaGffDpGFGlaeaggegsravLevR.srevPFil 319
                                    ge ++l p+eF + ++ e  ++p +la  +       ++G +    aGf+DpGF  +          Le+    + P  l
  gi|121636236|ref|YP_976459.1|  69 GEPFVLHPGEFVLGSTLELFTLPDNLAGRLEgkSSLGRLGLLTHSTAGFIDPGFSGH--------ITLELSnVANLPITL 140
                                    5669*******999999**********9776114455788888889********743........44666414689**** PP

                            DCD 320 edgqivgrlvyermaekpealYGee.lgsnYqgqg 353
                                      g  +g+l   r+++ +e+ YG++ +gs+Yqgq+
  gi|121636236|ref|YP_976459.1| 141 WPGMKIGQLCMLRLTSPSEHPYGSSrAGSKYQGQR 175
                                    ***********************86267*****96 PP

>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   1.4e-14   1.2e-10      22     125 ..      70     177 ..      67     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.4e-14
                                    SSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE..EEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEE CS
                        dUTPase  22 kdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvp..gvidsdyrGevkvvlfnltkkdvkikkgdRiAqL 99 
                                    +++++ pge vl +t   ++lpd+la+++ ++S+l ++gl+ +   g id  + G++ + l n  + ++++  g +i qL
  gi|121636236|ref|YP_976459.1|  70 EPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHStaGFIDPGFSGHITLELSNVANLPITLWPGMKIGQL 149
                                    578999************************************9999********************************** PP

                                    EEEEBECGEEEEESST..TTESSBTTXT CS
                        dUTPase 100 ifariltaeleevetl..katergeggf 125
                                     + r+  ++ +++ +    ++++g++g 
  gi|121636236|ref|YP_976459.1| 150 CMLRLTSPSEHPYGSSraGSKYQGQRGP 177
                                    ***9999777776554245666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1269.73
//
Query:       gi|121636237|ref|YP_976460.1|  [L=443]
Description: udp-glucose 6-dehydrogenase udgA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-61  205.6   0.0      7e-61  205.1   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.6e-31  108.4   0.0    4.5e-31  106.9   0.0    1.8  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    2.9e-28   98.4   0.1    7.1e-28   97.1   0.0    1.7  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      8e-07   29.6   0.3      0.099   13.2   0.0    3.6  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0004   20.6   0.7       0.18   11.9   0.1    3.4  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
       0.01   15.7   0.0       0.03   14.2   0.0    1.8  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.0   2.3e-64     7e-61       1     183 [.       1     181 [.       1     187 [. 0.97

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 2.3e-64
                                    SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEE CS
                 UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvi 80 
                                    m++sv+G+GY+G+++a+ +a++ghev+gvDid  kv+kl  g+ip+yepgL++l+++++++grl+fttd+++a++ adv+
  gi|121636237|ref|YP_976460.1|   1 MRCSVFGTGYLGATHAVGMAQLGHEVVGVDIDPGKVAKLAGGDIPFYEPGLRKLLTDNLAAGRLRFTTDYDMAADFADVH 80 
                                    89****************************************************************************** PP

                                    EE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE------TTS CS
                 UDPG_MGDP_dh_N  81 fiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEflregs 160
                                    f+ VgTP+k  +  aDl++v+++++++ + l + +++v kSTvpvgta el ++  + a++  gvd+++++nPEflreg 
  gi|121636237|ref|YP_976460.1|  81 FLGVGTPQKIGEYGADLRHVHAVIDALVPRLVRASILVGKSTVPVGTAAELGHRAGALAPR--GVDVEIAWNPEFLREGF 158
                                    **********9999***********************************999999998887..79*************** PP

                                    HHHHHHS-S-EEEEESSCHHHHH CS
                 UDPG_MGDP_dh_N 161 avkdllnpdrvviGveekkaeaa 183
                                    av+d+lnpdr+v+Gv++++++a 
  gi|121636237|ref|YP_976460.1| 159 AVHDTLNPDRIVLGVQDDSTRAE 181
                                    *****************999844 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   1.5e-34   4.5e-31       1      93 [.     204     298 ..     204     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1.5e-34
                   UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgl 80 
                                    +tAEl+K+ aNaflatkIsfiN ++++cea g+dv+++++a+g dprig+++l++glG+GG clpkD++a++a+a elg 
  gi|121636237|ref|YP_976460.1| 204 QTAELVKVSANAFLATKISFINAISEVCEAAGADVSQLADALGYDPRIGRQCLNAGLGFGGGCLPKDIRAFMARAGELGA 283
                                    59*****************************************************************************9 PP

                   UDPG_MGDP_dh  81 e..aelleavrevNe 93 
                                    +  +++l++v+ +N 
  gi|121636237|ref|YP_976460.1| 284 DqaLTFLREVDSINM 298
                                    988899999999995 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.7   1.1e+04      22      68 ..     187     235 ..     181     238 .. 0.59
   2 !   97.1   0.0   2.4e-31   7.1e-28       1     104 [.     322     422 ..     322     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                                    HHHHHHHCTSEEEEE-SSTHHCCCCHHGG..BTCCEEES-CHHHHTT-S CS
                 UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaele..ekgvevvdsleealkgad 68 
                                    +++ Ll++g+   + D ++ e  +    +  ++++++++ ++e ++ a 
  gi|121636237|ref|YP_976460.1| 187 LYAPLLAAGVPFLVTDLQTAELVKVSANAflATKISFINAISEVCEAAG 235
                                    5566666666666666666665544333355566777777777766665 PP

  == domain 2  score: 97.1 bits;  conditional E-value: 2.4e-31
                                    EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGG CS
                 UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefk 80 
                                    a+lG afK+++dD+R+Spal+++ +L+ +ga v++yDPk+ ++a +      +++++ s++ea++ ada+++lte++ef 
  gi|121636237|ref|YP_976460.1| 322 AVLGAAFKPESDDVRDSPALNVAGQLQLNGATVHVYDPKALDNAHRL---FPTLNYAVSVAEACERADAVLVLTEWREFI 398
                                    89*******************************************99...67899*99********************** PP

                                    GS-HHHHHHCCSS-EEEESSS-CC CS
                 UDPG_MGDP_dh_C  81 eldlaklkelmkpavvfDgrnvld 104
                                    +l+ a+l+++++++v++Dgrn+ld
  gi|121636237|ref|YP_976460.1| 399 DLEPADLANRVRARVIVDGRNCLD 422
                                    **********************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   3.3e-05     0.099       4      95 ..       5     107 ..       2     109 .. 0.82
   2 ?    4.4   0.1     0.019        55      15      77 ..     155     227 ..     152     241 .. 0.84
   3 !    7.9   0.0    0.0016       4.7      35      93 ..     358     416 ..     340     419 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...................-EEECECHHHHHHH-SE CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...................vkvtavdneeaaeeadv 64 
                                    + G+G +g++ a g+++ g   he+v + + +p k+++la                        + t+ d+  aa+ adv
  gi|121636237|ref|YP_976460.1|   5 VFGTGYLGATHAVGMAQLG---HEVV-GVDIDPGKVAKLAGGDIpfyepglrklltdnlaagrLRFTT-DYDMAADFADV 79 
                                    78*****************...****.99**********954335999*************9777777.9********** PP

                                    EEE-S-.HHHHHHHHHHCGHHHHTTSEEEEES CS
                  F420_oxidored  65 vvlavk.pedveevlselakdalkgklvisvl 95 
                                     +l v  p+++ e  ++l     + + vi++l
  gi|121636237|ref|YP_976460.1|  80 HFLGVGtPQKIGEYGADL----RHVHAVIDAL 107
                                    ***995256666666555....5666666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                                    HHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                  F420_oxidored  15 asgllaaga.qpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlavkpedveev 77 
                                     +g++ +++ +p  iv++ + +  +ae + +el+           vt  +++e+++ +   +la k + + ++
  gi|121636237|ref|YP_976460.1| 155 REGFAVHDTlNPDRIVLGVQDDSTRAEVAVRELYapllaagvpFLVTDLQTAELVKVSANAFLATKISFINAI 227
                                    56778888889999999999999999999999999999999999999999****************9876554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0016
                                    SCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                  F420_oxidored  35 npekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                    +p+ ++ +++ +     av+ +ea+e+ad v++   ++ + ++  +  ++  + +++++
  gi|121636237|ref|YP_976460.1| 358 DPKALDNAHRLFPTLNYAVSVAEACERADAVLVLTEWREFIDLEPADLANRVRARVIVD 416
                                    444444455555555566688*****************999986554466666666665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   6.2e-05      0.18       3     106 ..       4     137 ..       2     148 .. 0.75
   2 ?   -3.1   0.0       2.5   7.6e+03      19      55 ..     192     233 ..     186     238 .. 0.55
   3 ?    4.0   0.0     0.018        53      13      62 ..     342     391 ..     341     421 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                                    EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHHC... CS
                  NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvasl... 56 
                                     + G+G +G+  a  +++ g++v++++ ++ kv +l+                              ++   +++ +   
  gi|121636237|ref|YP_976460.1|   4 SVFGTGYLGATHAVGMAQLGHEVVGVDIDPGKVAKLAGGDipfyepglrklltdnlaagrlrfT---TDYDMAADFAdvh 80 
                                    689**********************************888899999999999999998874432...3333333333222 PP

                                    .......SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHH CS
                  NAD_binding_2  57 .......dvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelke 106
                                           +++     + ++v +vi+ l+++l + +il+  st+ + ++ el +++ +
  gi|121636237|ref|YP_976460.1|  81 flgvgtpQKIGEYGADLRHVHAVIDALVPRLVRASILVGKSTVPVGTAAELGHRAGA 137
                                    445555555555556667788888889999999999999999999888888777655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                    HHTT-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHH CS
                  NAD_binding_2  19 lkagykvavynrtkekveelvaeg.....akaaesieelvas 55 
                                    l+ag    v +++++++ ++ a+      ++ ++ i+e++++
  gi|121636237|ref|YP_976460.1| 192 LAAGVPFLVTDLQTAELVKVSANAflatkISFINAISEVCEA 233
                                    556666666666655554444443333336666666666655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.018
                                    HHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE- CS
                  NAD_binding_2  13 nmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitm 62 
                                    n a +l+ +g +v+vy+ ++    + +   ++ a s++e+++++d+v+++
  gi|121636237|ref|YP_976460.1| 342 NVAGQLQLNGATVHVYDPKALDNAHRLFPTLNYAVSVAEACERADAVLVL 391
                                    578899999********7765544444466999************99986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05      0.03       3      77 ..       4      74 ..       2      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77
                                    v G+G +Ga  a  +a+ g+eVv vdi++ +++k +      +e     g  k  + + a+ r++fttd++ a+
  gi|121636237|ref|YP_976460.1|  4 SVFGTGYLGATHAVGMAQLGHEVVGVDIDPGKVAKLAGGDIPFYEP----GLRKLLTDNLAAGRLRFTTDYDMAA 74
                                   699***************************9998876654443333....3333223344566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3233.52
//
Query:       gi|121636238|ref|YP_976461.1|  [L=223]
Description: hypothetical protein BCG_0363c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-26   92.0   0.2    6.3e-26   91.6   0.2    1.2  1  PIG-L     GlcNAc-PI de-N-acetylase


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.2   3.5e-30   6.3e-26       1     130 [.      14     137 ..      14     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 3.5e-30
                                    EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH-HHHHHHHHHHHHHHHHCTE..EEEEECCCBT CS
                          PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleekeelaeiRekEaraaakhlgvadedvffldfpD 80 
                                    l+v+AHpDDe+++ g+ + +++a+g +++ +c t G+a++   t    ++l+e+R++E+ aaa++lgv  ++v  l +pD
  gi|121636238|ref|YP_976461.1|  14 LAVFAHPDDESFGLGAVLGDFTAQGTRLRGLCFTHGEASTLGRTD---RNLGEVRREELAAAAQVLGV--DHVQLLAYPD 88 
                                    789************************************555554...4*******************..********** PP

                                    T-STTS-CHHHHHHHHHHHHHH--SEEEEE-TTTT.H-HHHHHHHHHHHHH CS
                          PIG-L  81 gslesydedellddlaklieryrPdvvltldpegd.dhpDHtavasaavaa 130
                                    ++l++ + +el+++++++++    d++l++d++g  +hpDH+ + +aa aa
  gi|121636238|ref|YP_976461.1|  89 NGLAQIPLNELTQRVVDALAGA--DLLLVFDDNGVtGHPDHRRATEAALAA 137
                                    *******************888..*****************9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1617.80
//
Query:       gi|121636239|ref|YP_976462.1|  [L=226]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-17   61.9   0.0    1.5e-16   60.9   0.0    1.5  2  Rhodanese      Rhodanese-like domain
      4e-09   36.4   2.7    1.3e-08   34.7   0.7    2.5  2  HTH_20         Helix-turn-helix domain
    2.6e-07   30.4   0.0    4.4e-07   29.7   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
    3.5e-06   26.7   0.8    3.5e-06   26.7   0.8    2.7  3  HTH_IclR       IclR helix-turn-helix domain
      7e-05   22.6   0.0    0.00016   21.5   0.0    1.6  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0081   16.0   1.2     0.0081   16.0   1.2    2.2  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.011   15.8   0.3      0.028   14.4   0.3    1.8  1  HTH_29         Winged helix-turn helix
      0.011   15.3   0.3      0.079   12.5   0.1    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.014   15.4   0.2      0.028   14.4   0.1    1.5  1  Dimerisation2  Dimerisation domain
      0.017   15.2   0.6      0.061   13.5   0.1    2.2  2  HTH_28         Helix-turn-helix domain
      0.033   14.0   0.9      0.087   12.7   0.1    2.2  2  HTH_23         Homeodomain-like domain
      0.062   13.4   0.8      0.062   13.4   0.8    2.6  3  DprA_WH        DprA winged helix domain
      0.084   12.8   0.0       0.14   12.1   0.0    1.3  1  HTH_43         Winged helix-turn helix
       0.11   12.9   0.1       0.29   11.5   0.1    1.7  1  Rrf2           Transcriptional regulator
       0.13   12.1   0.0       0.26   11.1   0.0    1.5  1  TFIIE_alpha    TFIIE alpha subunit
       0.14   12.2   1.2       0.33   11.0   0.2    2.1  3  HTH_Crp_2      Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.2     1e+04      10      25 ..      24      39 ..      17      64 .. 0.62
   2 !   60.9   0.0   1.3e-19   1.5e-16       2     106 ..     121     211 ..     120     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.2
                      Rhodanese 10 ekgkvallDvRppeeY 25
                                   + ++ ++lD  ++ e 
  gi|121636239|ref|YP_976462.1| 24 NGRRLQILDLLAQGER 39
                                   5556667776655554 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 1.3e-19
                      Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aa 80 
                                     +el +++e+g+v l+DvRp eeY++ghIpgA+n+             p +el ++l+el    ++ +v yc+g+ + + 
  gi|121636239|ref|YP_976462.1| 121 RAELLRRREAGEVTLVDVRPHEEYQAGHIPGAINI-------------PIAELADRLAEL--AGDRDIVAYCRGAYCvM- 184
                                    578999999***99*********************.............9999******99..99*************53. PP

                      Rhodanese  81 aa..aallkklGyknvsvldGGfkawke 106
                                    a    ++++ +G  +v+ ld G+ +w  
  gi|121636239|ref|YP_976462.1| 185 APdaVRIARDAG-REVKRLDDGMLEWRL 211
                                    4445779999**.99***********75 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.7   1.2e-11   1.3e-08       2      60 ..      17      74 ..      13      75 .. 0.94
   2 ?    0.7   0.0      0.48   5.4e+02      35      53 ..     154     173 ..     116     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.2e-11
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   ++ +ALa+  R+ il++L   +++ ++++a + ++  +t+s +L++L + gLve +reg
  gi|121636239|ref|YP_976462.1| 17 RVGKALANGRRLQILDLL-AQGERAVEAIATATGMNLTTASANLQALKSGGLVEARREG 74
                                   45599*************.***************************************8 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                                    TS-HHHHHHHHHHHHH.CTT CS
                         HTH_20  35 dlskntlsyHLrvLee.agL 53 
                                     ++ ++l ++L++L+   ++
  gi|121636239|ref|YP_976462.1| 154 NIPIAELADRLAELAGdRDI 173
                                    57778888888888655555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   3.9e-10   4.4e-07       3      46 ..      26      69 ..      24      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.9e-10
                                   HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                    Rl+IL lLa+ge+ v  +a ++g++  t S  L +L+  GLVe
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVE 69
                                   7******************************************7 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       0.7   7.8e+02       3      19 ..       6      22 ..       6      26 .. 0.79
   2 !   26.7   0.8   3.1e-09   3.5e-06       4      49 ..      26      69 ..      25      72 .. 0.95
   3 ?   -2.6   0.0       4.4     5e+03      21      29 ..     157     165 ..     154     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.7
                                   HHHHHHHCT-CTTBSS- CS
                       HTH_IclR  3 dRalaiLdalaeapqel 19
                                   dR +a+Ld++a+ + +l
  gi|121636239|ref|YP_976462.1|  6 DRKAALLDQVARVGKAL 22
                                   67799*****9977665 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.1e-09
                                   HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  4 RalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   R l+iLd+la++ ++  +  +A +tg++ +t++  Lq L   G+ve
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQGERA--VEAIATATGMNLTTASANLQALKSGGLVE 69
                                   569***********8..****************************9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                                    HHHHHHHHT CS
                       HTH_IclR  21 lselArrtg 29 
                                    ++elA+r++
  gi|121636239|ref|YP_976462.1| 157 IAELADRLA 165
                                    789999975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.4e-07   0.00016      16      63 ..      32      80 ..      30      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63
                                    Ll++g+  ++ ia ++g   +++   L+ L++ GlVe +++  +++Yr
  gi|121636239|ref|YP_976462.1| 32 DLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVEARREGtRQYYR 80
                                   79************************************99977255665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.2   7.3e-06    0.0081       7      55 ..      27      72 ..      21      77 .. 0.89
   2 ?   -1.4   0.1         2   2.2e+03      20      31 ..     152     164 ..     122     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.3e-06
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                    +++L  L+ +++   +v ++a ++g+   ++s  l+ L + GLve r+
  gi|121636239|ref|YP_976462.1| 27 RLQILDLLAQGER---AVEAIATATGMNLTTASANLQALKSGGLVEARR 72
                                   6789999999996...*****************************9886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                    S.EEEHHHHHHHH CS
                         MarR_2  20 r.dltvgelarrl 31 
                                      ++ ++ela+rl
  gi|121636239|ref|YP_976462.1| 152 AiNIPIAELADRL 164
                                    2455677888776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   2.5e-05     0.028       1      53 [.      27      77 ..      27      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                         HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrp 53
                                   R+q+l lla+G+  v  iA ++g+  +t    l +   gGl    + rr++ r 
  gi|121636239|ref|YP_976462.1| 27 RLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGL---VEaRREGTRQ 77
                                   99**************************************5...5545555554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.1e-05     0.079       5      48 .]      27      69 ..      24      69 .. 0.88
   2 ?    0.3   0.0      0.48   5.4e+02      18      27 ..     155     164 ..     154     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.1e-05
                         HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +++IL lL + +      +A ++g+ ++t ++ l+ L++ Gl++
  gi|121636239|ref|YP_976462.1| 27 RLQILDLLAQ-GERAVEAIATATGMNLTTASANLQALKSGGLVE 69
                                   6778888887.7788899***********************996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                         HTH_24  18 isqreLAerl 27 
                                    i+++eLA+rl
  gi|121636239|ref|YP_976462.1| 155 IPIAELADRL 164
                                    899*****98 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.5e-05     0.028      11      74 ..      18      79 ..      14      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                  Dimerisation2 11 aSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalY 74
                                   + kaL    +L++ dlL++ ++  +e++a++ g+++   +  l+a+ + gL e ++ e++++ Y
  gi|121636239|ref|YP_976462.1| 18 VGKALANGRRLQILDLLAQ-GERAVEAIATATGMNLTTASANLQALKSGGLVEARR-EGTRQYY 79
                                   678999999**********.9999*****************************774.4444566 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.4e-05     0.061       1      41 [.      26      67 ..      26      74 .. 0.89
   2 ?   -2.0   0.0       3.6   4.1e+03      33      46 ..     125     137 ..     121     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                         HTH_28  1 qRleiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                   +Rl+i+ lla+G+ +v ++A + g++ +t +  ++++ +gG+
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQGErAVEAIATATGMNLTTASANLQALKSGGL 67
                                   7***********999***********9999998888888885 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                         HTH_28  33 ikryeegGiagLvp 46 
                                    ++r +e G+  Lv+
  gi|121636239|ref|YP_976462.1| 125 LRR-REAGEVTLVD 137
                                    555.4447777777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.7e-05     0.087       6      46 ..      26      67 ..      25      72 .. 0.89
   2 ?   -2.9   0.1       5.8   6.5e+03       4      15 ..     118     129 ..     115     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                         HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   +Rl+il lla+    v++IA++ g++  T +  l++ + +Gl
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQgERAVEAIATATGMNLTTASANLQALKSGGL 67
                                   7**********9889***************999999866764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                         HTH_23   4 ereRlrilllla 15 
                                    ++ R++ l+   
  gi|121636239|ref|YP_976462.1| 118 AITRAELLRRRE 129
                                    566777777655 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   5.5e-05     0.062      13      56 ..      26      69 ..      17      74 .. 0.87
   2 ?   -2.5   0.0       5.2   5.9e+03      41      58 ..     159     167 ..     154     169 .. 0.50
   3 ?   -1.2   0.0       2.1   2.3e+03      31      54 ..     191     214 ..     190     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                        DprA_WH 13 lerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                    + ++L++L++  ++v++++ +tg+   + sa L  L   Glve
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVE 69
                                   6789****************************998886666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                        DprA_WH  41 evsaaLleLELaGlverl 58 
                                    e++  L e         l
  gi|121636239|ref|YP_976462.1| 159 ELADRLAE---------L 167
                                    44444444.........4 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                        DprA_WH  31 LvrrtglpaaevsaaLleLELaGl 54 
                                    ++r++g ++ ++    le+ LaGl
  gi|121636239|ref|YP_976462.1| 191 IARDAGREVKRLDDGMLEWRLAGL 214
                                    789999999999999999999996 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.14       8      48 ..      26      66 ..      20      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT CS
                         HTH_43  8 RrlylaylideeeanvpklieltgmPRRtlqDtlkalaeld 48
                                   Rrl +  l++++e++v ++ ++tgm   t+   l+al+  +
  gi|121636239|ref|YP_976462.1| 26 RRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGG 66
                                   9***********************************98755 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00026      0.29      22      59 ..      36      72 ..      26      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                   TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   ++e  ++e+ia+ ++++ + ++  l+ L+  glv+++r
  gi|121636239|ref|YP_976462.1| 36 QGE-RAVEAIATATGMNLTTASANLQALKSGGLVEARR 72
                                   333.479****************************987 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.26      12      62 ..      24      73 ..      11      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                   -HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                    TFIIE_alpha 12 geeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                   ++   ++ld L+ +ge + e +a  ++++l+     L +L++ +lv+ +r+
  gi|121636239|ref|YP_976462.1| 24 NGRRLQILDLLA-QGERAVEAIATATGMNLTTASANLQALKSGGLVEARRE 73
                                   567789999999.9*********************************9985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.8   6.4e+03      53      62 ..      24      33 ..      17      38 .. 0.74
   2 ?   11.0   0.2   0.00029      0.33      25      54 ..      42      74 ..      39      92 .. 0.78
   3 ?   -2.2   0.0       3.8   4.3e+03      19      31 ..     152     164 ..     122     166 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.8
                                   ETEEEEES-H CS
                      HTH_Crp_2 53 rgrririldl 62
                                   +grr++ildl
  gi|121636239|ref|YP_976462.1| 24 NGRRLQILDL 33
                                   4545999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00029
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..T CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.r..g 54
                                   e +A   G++  t s  l++Lk  gl++ r  g
  gi|121636239|ref|YP_976462.1| 42 EAIATATGMNLTTASANLQALKSGGLVEaRreG 74
                                   679*************************85232 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.8
                                    EEEHHHHHHHHHT CS
                      HTH_Crp_2  19 elpltqeelAsml 31 
                                     +++  +elA++l
  gi|121636239|ref|YP_976462.1| 152 AINIPIAELADRL 164
                                    2455556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1743.36
//
Query:       gi|121636240|ref|YP_976463.1|  [L=229]
Description: hypothetical protein BCG_0365 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-17   61.5   0.1    1.4e-16   60.9   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    1.1e-13   51.6   0.0    1.8e-13   51.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.8e-07   31.2   0.0    2.1e-07   30.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      1e-06   29.4   0.0    1.4e-06   28.9   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    1.1e-06   28.5   0.0    1.7e-06   27.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00013   21.4   0.0    0.00024   20.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0011   18.7   0.0     0.0023   17.6   0.0    1.6  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0096   15.1   0.1       0.03   13.5   0.1    1.7  1  Methyltransf_20  Putative methyltransferase
  ------ inclusion threshold ------
      0.013   14.1   0.0      0.014   13.9   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.013   15.3   0.0      0.018   14.8   0.0    1.1  1  DUF938           Protein of unknown function (DUF938)
      0.013   15.1   0.0      0.017   14.7   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.013   14.8   0.0      0.018   14.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.028   14.3   0.1      0.053   13.4   0.0    1.4  2  Methyltransf_8   Hypothetical methyltransferase
      0.038   13.1   0.0       0.58    9.2   0.0    2.0  1  Pox_MCEL         mRNA capping enzyme
       0.17   11.6   0.4          6    6.6   0.0    2.4  2  He_PIG_assoc     He_PIG associated, NEW1 domain of bacterial 


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   1.2e-19   1.4e-16       1      97 []      58     156 ..      58     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.2e-19
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEEESTGGG. CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvssgalhh. 76 
                                    vL+l++G+Gr+tl++a ++   +v+++D+s+ ++++ r+ a+++g+  +v+ +++d+++ lp + gs+D  ++ +al++ 
  gi|121636240|ref|YP_976463.1|  58 VLELAAGHGRDTLYFAGQG--FTVVATDFSDVAVAQLRRSAQARGVsaRVQPIVHDLRQpLPVKTGSIDGAFAHMALCMa 135
                                    9***************995..*************************99*********887*************9995555 PP

                                    SSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                    ls ++++++++e+ rvL+pgG
  gi|121636240|ref|YP_976463.1| 136 LSTSEIHAVVAEVGRVLRPGG 156
                                    ********************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.5e-16   1.8e-13       1      95 [.      59     159 ..      59     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.5e-16
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.TSS-TT-EEEEEEES-CCC-... CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaek.lpfednsfDlvvssevlhhv... 74 
                                    L++++G Gr + ++a +g +vv++D+s+ ++++ ++ a+ +g+  +v+ +v d+++ lp++ +s+D  +++++l+     
  gi|121636240|ref|YP_976463.1|  59 LELAAGHGRDTLYFAGQGFTVVATDFSDVAVAQLRRSAQARGVsaRVQPIVHDLRQpLPVKTGSIDGAFAHMALCMAlst 138
                                    7999*************************************99999999******988******************9999 PP

                                    CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                     + +++++e+ RvL+pgG+++
  gi|121636240|ref|YP_976463.1| 139 SEIHAVVAEVGRVLRPGGKFI 159
                                    9*****************997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.8e-10   2.1e-07      23     120 ..      55     163 ..      25     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.8e-10
                Methyltransf_23  23 ggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                                     +rvL++++G+G+ + +++ +gf+v++ D s++av+ ++        +a+ ++ +   +q  +++ g++d + + + l+ 
  gi|121636240|ref|YP_976463.1|  55 VQRVLELAAGHGRDTLYFAGQGFTVVATDFSDVAVAQLRrsaqargvSARVQPIVHDLRQPLPVKTGSIDGAFAHMALCM 134
                                    459*********************************9996666666644444444444556666999************9 PP

                Methyltransf_23  95 vpd...ppellrqiatllkpgGylllsep 120
                                      +    +++++ +++ l+pgG ++ ++ 
  gi|121636240|ref|YP_976463.1| 135 ALStseIHAVVAEVGRVLRPGGKFIYTVR 163
                                    99644588***************998885 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.2e-09   1.4e-06       1      99 []      59     158 ..      59     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnvlhh 78 
                                    Le+ +G G+ + +++ +  + +++++D+s  a+  a+ + +++ +   ++v+  + dl +  +   +s D  +a+ +l+ 
  gi|121636240|ref|YP_976463.1|  59 LELAAGHGRDTLYFAGQ--GFTVVATDFSDVAV--AQLRRSAQARGVSARVQPIVHDLRQPLPVktGSIDGAFAHMALCM 134
                                    89***************..**************..8888888888999999999999877776699*********88887 PP

                Methyltransf_12  79 l...kdirevldnirklLkpgGrl 99 
                                         +i++v++++ ++L+pgG++
  gi|121636240|ref|YP_976463.1| 135 AlstSEIHAVVAEVGRVLRPGGKF 158
                                    7799******************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.5e-09   1.7e-06       6     109 ..      57     160 ..      53     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.5e-09
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnev 83 
                                    rvl+l++G G++t+ +a   g++ +vv  D+s  a+ + r  aq  g++ +v+  + d  + l+  ++  ++D  +++ +
  gi|121636240|ref|YP_976463.1|  57 RVLELAAGHGRDTLYFA---GQGFTVVATDFSDVAVAQLRRSAQARGVSaRVQPIVHDLRQpLP--VKTGSIDGAFAHMA 131
                                    89***************...77889************************9**************..999*********99 PP

                Methyltransf_31  84 l...naladpdkileeiervlkpggilli 109
                                    l     +++  ++  e+ rvl+pgg ++ 
  gi|121636240|ref|YP_976463.1| 132 LcmaLSTSEIHAVVAEVGRVLRPGGKFIY 160
                                    987778888899999***********995 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     2e-07   0.00024      32     128 ..      56     156 ..      42     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-T.TEEEEE--GGG.----S.-EEEEEEE.SSGGG CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlk.nistalydine.aklde.rydfilst.vvlmf 107
                                     +vl+l  g+gr++ly++ +g+ v a d  + ++a l++ ++   ++  ++  + d+ + + ++    d  ++   + m 
  gi|121636240|ref|YP_976463.1|  56 QRVLELAAGHGRDTLYFAGQGFTVVATDFSDVAVAQLRRSAQARGVSaRVQPIVHDLRQpLPVKTgSIDGAFAHmALCMA 135
                                    479**********************************9998877665146666667654222221133333333034466 PP

                                    S-GGGHHHHHHHHHHTEEEEE CS
                           TehB 108 leaeripsiienmqectkvgg 128
                                    l +  i  +++++ +  ++gg
  gi|121636240|ref|YP_976463.1| 136 LSTSEIHAVVAEVGRVLRPGG 156
                                    666666666666666666666 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0023      34      87 ..      51     104 ..      19     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                    T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGG CS
                           TPMT  34 kakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvke 87 
                                    +a   +rvl    G + d   +A qg +vv+ ++s+ Av++  + a+ +  + +
  gi|121636240|ref|YP_976463.1|  51 NADGVQRVLELAAGHGRDTLYFAGQGFTVVATDFSDVAVAQLRRSAQARGVSAR 104
                                    4555667888889****************************8776665433333 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   2.5e-05      0.03     131     246 ..      52     161 ..      44     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                Methyltransf_20 131 egrpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgdafdeeslaalePrptl 210
                                    ++   r+l++aaGhGr  l     a +   +++  d+s++ v+q r+ ++++g+++ ++    d  ++  +++ +    +
  gi|121636240|ref|YP_976463.1|  52 ADGVQRVLELAAGHGRDTL---YFAGQ-GFTVVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQPLPVKTGSIDGAF 127
                                    555679**********655...55544.5568899*******************99887666665555555444444444 PP

                Methyltransf_20 211 aivsGlyelfpdndlvkrslaGlaeavepgglliyt 246
                                    a ++    l      +++ +a ++++++pgg +iyt
  gi|121636240|ref|YP_976463.1| 128 AHMALCMAL--STSEIHAVVAEVGRVLRPGGKFIYT 161
                                    433333333..2344556666666666666666666 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.014     149     220 ..      86     163 ..      48     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                Methyltransf_29 149 Deheaqvq.faLeRgvpaila.vlgtkrlpyPsr..sfd..lihCsrCridwteedgilllevdRvlRpgGyfvlsap 220
                                    D+  aq+   a  Rgv a +  ++   r p P +  s d  ++h + C    t+e  +++ ev RvlRpgG f+++  
  gi|121636240|ref|YP_976463.1|  86 DVAVAQLRrSAQARGVSARVQpIVHDLRQPLPVKtgSIDgaFAHMALCMALSTSEIHAVVAEVGRVLRPGGKFIYTVR 163
                                    555555542467788888876244555666665411555446899****999999999****************9865 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.018      25     135 ..      53     156 ..      41     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                         DUF938  25 tte.rvLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappapasi 103
                                     +  rvLE+a+G G+   +fA +    +  ++d  +   + ++  a++ ++s   +P+  d  ++  pv+        si
  gi|121636240|ref|YP_976463.1|  53 DGVqRVLELAAGHGRDTLYFAGQ--GFTVVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQP-LPVK------TGSI 123
                                    33338****************85..5566788888888888999999999999999999998887.5555......3344 PP

                         DUF938 104 dailsinllH.ispwsaveglfagagellkkka 135
                                    d  ++   l    + s +++++a +g++l++++
  gi|121636240|ref|YP_976463.1| 124 DGAFAHMALCmALSTSEIHAVVAEVGRVLRPGG 156
                                    444433332202345556666666666666665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.4e-05     0.017       3      61 ..      57     122 ..      55     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe.......l 61 
                                     +l l +G G ++  fa ++ +v+a + +   +a+  + a++ gvs ++++++ d+ +        
  gi|121636240|ref|YP_976463.1|  57 RVLELAAGHGRDTLYFAGQGFTVVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQplpvktgS 122
                                    78999**************99*********************************998855544440 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.018      48     150 ..      55     159 ..      18     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                    TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--.TTT-TTS-T-EE....EEE CS
                Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqan.aeeLpfeddsfD....vvt 121
                                     ++vl++a+G g  ++ +   +g+ ++vv  D+++  + + ++ ++ +g++ +++ ++ +  + Lp + +s D     ++
  gi|121636240|ref|YP_976463.1|  55 VQRVLELAAGHGRDTLYF---AGQGFTVVATDFSDVAVAQLRRSAQARGVSaRVQPIVHDlRQPLPVKTGSIDgafaHMA 131
                                    468999999999888776...6899************************9988986555416779988766661111555 PP

                                    EES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                    +   l  +++++ ++ e+ rvl+pGG+++
  gi|121636240|ref|YP_976463.1| 132 LCMAL-STSEIHAVVAEVGRVLRPGGKFI 159
                                    55555.5899****************985 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.4   7.7e+03      32      56 ..       8      32 ..       6      33 .. 0.78
   2 ?   13.4   0.0   4.4e-05     0.053     109     154 ..     108     158 ..      80     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.4
                                   HHHHH-HHHHHHHHHHHHHHHCTSS CS
                 Methyltransf_8 32 dlfkedpeafdlyhkgfrsqvkkWP 56
                                   +l k +pe++   h+ +++  +  P
  gi|121636240|ref|YP_976463.1|  8 RLVKRQPELLVAQHEHWQDTYRAHP 32
                                   6889999999999999988766555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.4e-05
                                    EES-T.TS-S--TT-EEEEE....EES---SS-HHHHHHHHHHHEEEEEEE CS
                 Methyltransf_8 109 vacdl.akvPledesvdvav....fclslmgtnladflkeanrvlkvGGll 154
                                    ++ dl + +P++ +s+d a     +c++l + +++  + e+ rvl++GG +
  gi|121636240|ref|YP_976463.1| 108 IVHDLrQPLPVKTGSIDGAFahmaLCMALSTSEIHAVVAEVGRVLRPGGKF 158
                                    4568844599999999976422237************************86 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00049      0.58      59     105 ..      50      94 ..      43     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
                       Pox_MCEL  59 kldesnklkvLdldcgkGgDLeKyekgeIsklvatDiaeesieecke 105
                                    ++      +vL+l+ g G D   y++g+  + vatD +++++++ ++
  gi|121636240|ref|YP_976463.1|  50 FN-ADGVQRVLELAAGHGRDTL-YFAGQGFTVVATDFSDVAVAQLRR 94 
                                    54.444568***********65.99999999**********998643 PP

>> He_PIG_assoc  He_PIG associated, NEW1 domain of bacterial glycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.081        97       6      19 ..      32      45 ..      31      47 .. 0.83
   2 ?    6.6   0.0     0.005         6      12      26 ..     153     167 ..     151     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.081
                                   --EEEE-TTSEEEE CS
                   He_PIG_assoc  6 PkVfGarPgnpFLf 19
                                   P  +G rP  p ++
  gi|121636240|ref|YP_976463.1| 32 PVLYGTRPSEPGVY 45
                                   678******99777 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.005
                                    -TTSEEEEE--EESS CS
                   He_PIG_assoc  12 rPgnpFLftIPasGe 26 
                                    rPg  F++t+  +G+
  gi|121636240|ref|YP_976463.1| 153 RPGGKFIYTVRHTGD 167
                                    9*********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1738.76
//
Query:       gi|121636241|ref|YP_976464.1|  [L=449]
Description: cytochrome P450 135A1 cyp135A1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-63  214.7   0.0    5.1e-63  213.4   0.0    1.5  1  p450      Cytochrome P450
  ------ inclusion threshold ------
      0.092   11.4   0.1       0.13   11.0   0.1    1.1  1  Cas_Csd1  CRISPR-associated protein (Cas_Csd1)


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.4   0.0   5.7e-67   5.1e-63       1     449 [.      10     420 ..      10     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 5.7e-67
                                    --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETT..EEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHH CS
                           p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgs..kpvvvlsgpeavkevlikkgeefsgrpdeallats 78 
                                    Ppgp +lp +   + +   + +  +l  +++kyg++f+l++ +   + vv+++pe++ke++ ++  +  +  +    ++ 
  gi|121636241|ref|YP_976464.1|  10 PPGP-RLPRYLQSVLYL--RFREWFLPAMHRKYGDVFSLRVPPyaDNLVVYTRPEHIKEIFAADPRSLHAG-E---GNHI 82 
                                    5555.566555555555..3445566899***********98844689****************7444443.3...3333 PP

                                    HHTTTTSSSTTCGH.HHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHH CS
                           p450  79 rkpfkgkgvlfang.ekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsi 156
                                     ++ +g++ ++++  ++  ++R++l+p++t   +l  +++++ ++a+++++++r++a+ +      ++++  +ld+i ++
  gi|121636241|ref|YP_976464.1|  83 LGFVMGEHSVLMTDeAEYARMRSLLMPAFTRA-ALrGYRDMIASVAREHITRWRPHATIN----SLDHMNALTLDIILRV 157
                                    446666666666655****************9.999**********************99....799************* PP

                                    HHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSC CS
                           p450 157 lFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakk 236
                                    +Fg+     + +   el    ++++++  ++      ++p lk +    ++++ + + k++++l + i  rr + d +  
  gi|121636241|ref|YP_976464.1| 158 VFGVT----DPKVKAELTSRLQQIINI--HPAILAGVPYPSLKRMN--PWKRFFHNQTKIDEILYREIASRRIDSDLT-- 227
                                    ****6....344445666666666433..57778999999666433..4666666779********************.. PP

                                    SSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHH CS
                           p450 237 srrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyd 316
                                     r d l+ ll++k +   +  l+d+el+ ++++ll+aG++Tt+++lsw+L eLa+ Pe+q+++      ++g+++     
  gi|121636241|ref|YP_976464.1| 228 ARTDVLSRLLQTK-DTPTK-PLTDAELRDQLITLLLAGHETTAAALSWTLWELAHAPEIQSQVVWA---AVGGDD----- 297
                                    9***********8.66665.9******************************************776...885545..... PP

                                    HCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTE CS
                           p450 317 dlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnsk 396
                                          +l+av+kE +R h+v+  ++ R+vt + +i+g  +p+Gt+v +++   h ++   p+P eF+p+RFld ++   
  gi|121636241|ref|YP_976464.1| 298 -----GFLEAVLKEGMRRHTVIA-STARKVTAPAEIGGWRLPAGTVVNTSILLAHASEVSHPKPTEFRPSRFLDGSV--- 368
                                    .....6*****************.***************************************************76... PP

                                    SSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEESS CS
                           p450 397 rksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpppilek 449
                                      +  +lPFG G+R C+G ++A  e  ++l  ++++F+++    ++ +++l +
  gi|121636241|ref|YP_976464.1| 369 -APNTWLPFGGGVRRCLGFGFALTEGAVILQEIFRRFTITAAGPSKGETPLVR 420
                                    .799**********************************998766666666655 PP

>> Cas_Csd1  CRISPR-associated protein (Cas_Csd1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.4e-05      0.13     312     395 ..     107     192 ..      81     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.4e-05
                       Cas_Csd1 312 LapnagRlsvrfyreltlgeflknlkrwfedlaivkkkkeevgapslkrllkala...ddksklknv.ppnlagrllrai 387
                                    L p  +R ++r yr++ ++   +++ rw  +  i + +   ++a++l  +l+ ++   d+k k++ +   +++ ++ +ai
  gi|121636241|ref|YP_976464.1| 107 LMPAFTRAALRGYRDMIASVAREHITRWRPHATINSLD--HMNALTLDIILRVVFgvtDPKVKAELTsRLQQIINIHPAI 184
                                    478899****************************7544..7999**********99986665555332456677899*** PP

                       Cas_Csd1 388 legtpyPe 395
                                    l g pyP+
  gi|121636241|ref|YP_976464.1| 185 LAGVPYPS 192
                                    *******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2902.50
//
Query:       gi|121636242|ref|YP_976465.1|  [L=200]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-16   59.4   0.0    3.9e-16   58.6   0.0    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family
    3.9e-11   43.2   1.0    7.2e-11   42.3   1.0    1.4  1  TetR_C_6        BetI-type transcriptional repressor, C-termin
    1.7e-07   31.4   3.6    2.5e-07   30.9   2.4    1.9  2  TetR_C_31       Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.051   14.3   0.3       0.15   12.8   0.3    1.9  2  TetR_C_15       Tetracyclin repressor-like, C-terminal domain
      0.054   13.6   0.0      0.078   13.1   0.0    1.2  1  TetR_C_17       Tetracyclin repressor-like, C-terminal domain
       0.13   12.3   0.1       0.36   10.9   0.0    1.8  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.3e-19   3.9e-16       1      46 [.      11      56 ..      11      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.3e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   +ld+A++++ erGy +t+ r+IA++AGv+ +++ ++F+sK++Ll+ 
  gi|121636242|ref|YP_976465.1| 11 LLDGALACLRERGYGNTSSRDIARAAGVNIASINYHFGSKDALLDD 56
                                   79*****************************************985 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   1.0   2.4e-14   7.2e-11       2     100 ..      82     181 ..      81     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.4e-14
                                    HHHHHHHHHCCSTHSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHHHHHHHH CS
                       TetR_C_6   2 rerlraileallpldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaeaaAerla 80 
                                    + ++ a+lea ++  ++ r ++ + ++ +a a+r+++l+e++++ ya +r++ ++l  ++++   +++++ + ++ + l+
  gi|121636242|ref|YP_976465.1|  82 AGQILAVLEATVDSFEQIRPAVYACVESYAPALRSEALRERLAAGYADVRQHSVDLAGAALAgTDIAPPENLSTIVSVLM 161
                                    567899*******8888888**************************************999999**************** PP

                                    HHHHHHHHHHHHTCTTCHHH CS
                       TetR_C_6  81 AlidGLwlraalapeeldae 100
                                    A+idGL ++++ +p  +++ 
  gi|121636242|ref|YP_976465.1| 162 AVIDGLMIQWIADPSATPRS 181
                                    *************9655532 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.18   5.4e+02      40      75 ..      54      89 ..      51      94 .. 0.72
   2 !   30.9   2.4   8.4e-11   2.5e-07       5     101 ..      84     188 ..      80     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHH CS
                      TetR_C_31 40 LraalarlrralrealaallaalGlpdpeeaarllv 75
                                   L +al r++ +  ++++++++ + +++p+ ++ +++
  gi|121636242|ref|YP_976465.1| 54 LDDALGRCFSTWNQRVQEAFDHSRAAGPAGQILAVL 89
                                   667888888888888888888888877776665544 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 8.4e-11
                                    HHHHHHHHHCCCCCTTHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCS....S-HH...HHHHHHHHH CS
                      TetR_C_31   5 eladlladlldraladrertlAryelfleaarrPeLraalarlrralrealaallaalGl....pdpe...eaarllvaa 77 
                                    ++ ++l++ +d +++ r ++ A  e +  a r ++Lr+ la++++++r++ ++l  a+ +    + pe   + + +l+a+
  gi|121636242|ref|YP_976465.1|  84 QILAVLEATVDSFEQIRPAVYACVESYAPALRSEALRERLAAGYADVRQHSVDLAGAALAgtdiAPPEnlsTIVSVLMAV 163
                                    56688899999999999***************************77777666655444443011335555458889**** PP

                                    HHHHHHHHHHSGTS-H.HHHHHHHH CS
                      TetR_C_31  78 ldGllldrLagpaadp.raevrell 101
                                    +dGl+++ +a+p a+p  +ev ++l
  gi|121636242|ref|YP_976465.1| 164 IDGLMIQWIADPSATPrSTEVIRAL 188
                                    ************7777534444444 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.1   9.3e+03      55      76 ..      20      41 ..       6      44 .. 0.64
   2 ?   12.8   0.3     5e-05      0.15      23      92 ..     110     178 ..      87     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                      TetR_C_15 55 Larrrpelppedlelaafvave 76
                                    +r   +++++d+++aa v ++
  gi|121636242|ref|YP_976465.1| 20 RERGYGNTSSRDIARAAGVNIA 41
                                   4455566777888888877665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5e-05
                      TetR_C_15  23 lrrvlleeapslgelelvealeqriaealaalLarrrpelppedlelaafvaveaveallhlaleedpad 92 
                                    +  +l++ea + ++++  ++++q+ ++++ a La    + p e+l +++ v+++++++l+ + ++++ a+
  gi|121636242|ref|YP_976465.1| 110 YAPALRSEALRERLAAGYADVRQHSVDLAGAALAGTDIAPP-ENLSTIVSVLMAVIDGLMIQWIADPSAT 178
                                    56688889988888899999**************9998888.********************99999843 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.078       5      89 ..      88     171 ..      84     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                    HHHCHHHHTTTGGGSSHHHHHHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHH CS
                      TetR_C_17   5 yleeqkeeleeideslllakyEyfltsyreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldG 84 
                                     le   +++e+i ++ ++a +E +  + r e+ r+ l++ y  + ++ ++l  +  +  +  P   l++i+++l++++dG
  gi|121636242|ref|YP_976465.1|  88 VLEATVDSFEQI-RPAVYACVESYAPALRSEALRERLAAGYADVRQHSVDLAGAALAGTDIAPPENLSTIVSVLMAVIDG 166
                                    566666666665.46678888989999999999999999999999999999999999999******************** PP

                                    HHHHH CS
                      TetR_C_17  85 lilet 89 
                                    l+++ 
  gi|121636242|ref|YP_976465.1| 167 LMIQW 171
                                    **975 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.36      17      43 ..      16      42 ..      14      44 .. 0.87
   2 ?   -2.5   0.0       1.8   5.5e+03      30      46 ..     116     132 ..     114     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                   HHHHHHTT--EE-HHHHHHHCTS-HHH CS
                 Put_DNA-bind_N 17 LeelkeegveriSSteLaealgvtaaq 43
                                   L  l+e+g  ++SS+++a+a+gv+ a 
  gi|121636242|ref|YP_976465.1| 16 LACLRERGYGNTSSRDIARAAGVNIAS 42
                                   666999*****************9765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                    HHHHHHHCTS-HHHHHH CS
                 Put_DNA-bind_N  30 SteLaealgvtaaqvRK 46 
                                    S+ L e+l  + a vR+
  gi|121636242|ref|YP_976465.1| 116 SEALRERLAAGYADVRQ 132
                                    77788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1544.56
//
Query:       gi|121636243|ref|YP_976466.1|  [L=208]
Description: hypothetical protein BCG_0368c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-15   57.2   0.0    2.9e-15   56.7   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    2.6e-13   50.5   0.0    3.8e-13   49.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.7e-08   34.5   0.0    2.5e-08   33.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.9e-07   31.0   0.0    2.2e-07   30.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    5.9e-06   25.8   0.0    7.2e-06   25.5   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.3e-06   26.7   0.0    1.2e-05   25.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   14.7   0.0       0.12   11.8   0.0    2.1  1  Methyltransf_4   Putative methyltransferase
       0.05   12.5   0.0      0.091   11.7   0.0    1.4  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.11   12.3   0.1       0.22   11.2   0.1    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   1.4e-18   2.9e-15       2      96 .]      55     151 ..      54     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.4e-18
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHH CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpek 79 
                                    ++G G Gr +  la +ga+v gv++s++m+++a +++ ++     +++ ++d  +lp++d+s D v+  + + + +dp++
  gi|121636243|ref|YP_976466.1|  55 EIGFGPGRTLGLLAAAGAQVSGVEVSTTMIAIAAHHNAKAIAagLISLYHGDGVTLPVADHSLDKVLGVHNFYFSPDPRA 134
                                    79*******************************99999988899999********************************* PP

                                    HHHHHHHHEEEEEEEEE CS
                Methyltransf_11  80 alkeiaRvLkpgGllvi 96 
                                     l  iaR L+pgG+lv+
  gi|121636243|ref|YP_976466.1| 135 SLCDIARALRPGGRLVL 151
                                    **************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   1.9e-16   3.8e-13       1      97 []      53     147 ..      53     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.9e-16
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                    v ++G G+Gr++  la+++  a+v gv++s +m+++a+++++++ +   +++++gd  +lp +d+s D v+ ++++  +s
  gi|121636243|ref|YP_976466.1|  53 VCEIGFGPGRTLGLLAAAG--AQVSGVEVSTTMIAIAAHHNAKAIAagLISLYHGDGVTLPVADHSLDKVLGVHNFY-FS 129
                                    789**************95..****************999987544679***********************97765.55 PP

                                    HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                     +d ++ l  iar+L+pgG
  gi|121636243|ref|YP_976466.1| 130 -PDPRASLCDIARALRPGG 147
                                    .688999***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.3e-11   2.5e-08      14     131 ..      43     165 ..      29     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-11
                Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqg.. 81 
                                    e l+    +g rv++iG G G++l +l++ g++v gv+ s  +++ia+                                
  gi|121636243|ref|YP_976466.1|  43 ELLA--PGPGERVCEIGFGPGRTLGLLAAAGAQVSGVEVSTTMIAIAAhhnakaiaagL------------------Isl 102
                                    4344..57899***********************************8333333333322..................022 PP

                Methyltransf_23  82 .............kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrlll 131
                                                 + d +   + ++  pdp + l  ia+ l+pgG+l+l+ +  +++ + +++
  gi|121636243|ref|YP_976466.1| 103 yhgdgvtlpvadhSLDKVLGVHNFYFSPDPRASLCDIARALRPGGRLVLTSISDDQPLAARFD 165
                                    2333344444444*************************************9987777666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.1e-10   2.2e-07       4     119 ..      50     159 ..      47     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.1e-10
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre.naqklgldnveFeqgdieeleklledekfDlilsne 82 
                                    g rv+++G G G+ +  la     +a+v G++ s ++i  A   na+      +++ +gd  +l+  ++d + D +l   
  gi|121636243|ref|YP_976466.1|  50 GERVCEIGFGPGRTLGLLA---AAGAQVSGVEVSTTMIAIAAHhNAKAIAAGLISLYHGDGVTLP--VADHSLDKVLGVH 124
                                    789************9999...4579***************9944554555599***********..99*********99 PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedprllaelp 119
                                     ++  +dp + l  i r+l+pgg+l++++++  +++p
  gi|121636243|ref|YP_976466.1| 125 NFYFSPDPRASLCDIARALRPGGRLVLTSIS--DDQP 159
                                    99****************************9..3333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   3.6e-09   7.2e-06      47     156 ..      49     156 ..      26     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.6e-09
                                    -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH.HHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge.kklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                    +g++v ++  G g  ++ l+ ++g   +v +++++ +m+ ++  + +k  +   i + ++++  Lp  d s D v   + 
  gi|121636243|ref|YP_976466.1|  49 PGERVCEIGFGPGR-TLGLLAAAG--AQVSGVEVSTTMIAIAAhHNAKAIAAGLISLYHGDGVTLPVADHSLDKVLGVHN 125
                                    45566666666553.555655555..4799*********99761567888888*********************975566 PP

                                    GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                Ubie_methyltran 126 lrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                    +   +D   +L ++ r l+pGGrlv   +s 
  gi|121636243|ref|YP_976466.1| 126 FYFSPDPRASLCDIARALRPGGRLVLTSISD 156
                                    66669*******************9877764 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   6.3e-09   1.2e-05       2      99 .]      55     149 ..      54     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.3e-09
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlk 80 
                                    eiG G G++l  l+++  ++++ gv++s+ +i+ a+ + ak ++     + l + d   l+   +s D v+  + +   +
  gi|121636243|ref|YP_976466.1|  55 EIGFGPGRTLGLLAAA--GAQVSGVEVSTTMIAIAAHHNAKAIAAG--LISLYHGDGVTLPVAdHSLDKVLGVHNFYFSP 130
                                    89**************..**************99999888888644..55555555444433378*************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d+r++l  i+++L+pgGrl
  gi|121636243|ref|YP_976466.1| 131 DPRASLCDIARALRPGGRL 149
                                    *****************97 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.3e-05      0.12       5      76 ..      53     120 ..      50     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.3e-05
                                    EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCCHHHHCS-TTSEEEE CS
                 Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalkvllelledgsleki 76 
                                    v+eiG+G G+ l  lA + ++++  G+E++++++a + ++ ++   +  + + +gd ++     ++d+sl+k+
  gi|121636243|ref|YP_976466.1|  53 VCEIGFGPGRTLGLLAAAGAQVS--GVEVSTTMIAIAAHHNAKAiAAGLISLYHGDGVT---LPVADHSLDKV 120
                                    89**************9988765..*******999877665554355556666666632...23555555555 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.6e-05     0.091      97     266 ..      29     192 ..       9     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                                    SEEHHH.HHHHHG.GGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE--.. CS
                 Methyltransf_9  97 eWrsdw.kWdrvl.phlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllpl.. 172
                                     Wr++    +r+  + l++  g ++ ++G g G  l  ++++ga+ v G++ s+   i   a ++  +     + l    
  gi|121636243|ref|YP_976466.1|  29 IWRAETaDVNRIAvELLAPGPGERVCEIGFGPGRTLGLLAAAGAQ-VSGVEVSTTM-IAIAAHHNAKAIAAGLISLYHgd 106
                                    577664246777513467888999999999999887766666665.6788877654.44445444444444444443311 PP

                                    -GGGS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-TT-EE--SS-BTTBSS---EEBHHHH CS
                 Methyltransf_9 173 gieqlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletlvieGdenavlvPedryakmrnvyfiPsaaal 251
                                    g+  lp   +++d v+ +  +y    P   l ++  +l+ gG lvl +  i  d+  +     r+     +y +P +   
  gi|121636243|ref|YP_976466.1| 107 GV-TLPVaDHSLDKVLGVHNFYFSPDPRASLCDIARALRPGGRLVLTS--ISDDQPLA----ARFD--PAIYRVPPTLDT 177
                                    44.46664789***********************************76..55666543....3443..5799******** PP

                                    HHHHHHTT-EEEEEE CS
                 Methyltransf_9 252 kvWlekvgfvdvriv 266
                                      Wl  +gf+dv i 
  gi|121636243|ref|YP_976466.1| 178 AAWLGAAGFIDVGIK 192
                                    ***********9875 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.22      64     134 ..      40     108 ..      34     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHH.HHHHHHHHHCTTCSEEEEES-GG CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelv.eeakrnlkkldlenvivvvgDGr 134
                                    +a+ell   +g+rv e+G G G    +la    ++    ++e +  ++  +a++n k+ ++  +++ +gDG 
  gi|121636243|ref|YP_976466.1|  40 IAVELLAPGPGERVCEIGFGPGRTLGLLAAAGAQV---SGVEVSTTMIaIAAHHNAKAIAAGLISLYHGDGV 108
                                    578999999*************9988888765444...599988776516678899999999********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1597.62
//
Query:       gi|121636244|ref|YP_976467.1|  [L=246]
Description: hypothetical protein BCG_0369c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-12   46.1   3.1      6e-12   45.2   3.1    1.5  1  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.062   13.3   0.0    1.9  2  TetR_C_7  AefR-like transcriptional repressor, C-terminal dom


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   3.1   6.6e-16     6e-12       1      47 []      13      59 ..      13      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.6e-16
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   I++a +++f+ +Gy++t+v+++A+++ ++kg+lY y ++K++L++a+
  gi|121636244|ref|YP_976467.1| 13 IVAASARVFIAHGYQRTQVQDVADALALAKGTLYGYAQGKAALFAAA 59
                                   899*****************************************996 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.55   4.9e+03     108     115 ..      16      23 ..       5      39 .. 0.57
   2 ?   13.3   0.0   6.9e-06     0.062      30      81 ..     148     200 ..     121     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.55
                                    HHHHHHHH CS
                       TetR_C_7 108 saVdmFla 115
                                    +  ++F+a
  gi|121636244|ref|YP_976467.1|  16 ASARVFIA 23 
                                    33333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.9e-06
                                    HHT-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB-SS-HH.HHHHHHHHHH CS
                       TetR_C_7  30 aerfPelarafyeagpgrveealaayLeaavaaGrLridDpe.lAAeqflgll 81 
                                    a+  P+la+ ++  g +  ++a++ayL +  +aG L  + p+ + A+  ++l+
  gi|121636244|ref|YP_976467.1| 148 APELPDLAEVWFGTGRNAQVDAVQAYLVHRERAGLLILPGPApMVARTIVELC 200
                                    6788********************************98865325556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1751.70
//
Query:       gi|121636245|ref|YP_976468.1|  [L=388]
Description: dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-22   78.1   0.0    2.4e-21   76.2   0.0    1.7  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0031   17.1   0.5      0.098   12.2   0.0    2.3  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.024   15.2   0.0        2.7    8.6   0.0    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.061   13.6   0.1       0.37   11.1   0.0    2.3  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   5.4e-25   2.4e-21       2     294 .]       4     312 ..       3     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 5.4e-25
                                    SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                    xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                     v+++G+G++Gl++a tl+q    + +++lv+ +    + g +l  +l+g++++ +++ + +     g+e++++ +v +i
  gi|121636245|ref|YP_976468.1|   4 TVLILGAGVGGLTTADTLRQllpPEDRIILVD-RSFDGTLGLSLLWVLRGWRRPDDVRVRPTAASLPGVEMVTA-TVAHI 81 
                                    699*****************8777*******4.44444556677779999999999999666666779999999.9**** PP

                                    EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC......TTBEECCSECHHHHHHCCSS-T...SEEEEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                    Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.....aenvgklvrtldsaealklkllp...krivvvGg 150
                                    d +++ v+  +        i yd+lv+A G+  ++  +pG+     a+ +g++  tld a +l+ k       ri+v  +
  gi|121636245|ref|YP_976468.1|  82 DIAAQVVHTDN------SVIGYDALVIALGAALNTDAVPGLsdaldADVAGQF-YTLDGAAELRAKVEAlehGRIAVAIA 154
                                    ****7777744......46***********99998899999999965556555.89999999999999887766655544 PP

                                    SHHHHHHHHH........HHHHT-.......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEE CS
                                    xxxxxxxxxx........xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 151 GyiGvElAaa........laklgk.......evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngek 215
                                    G+    + aa        +a+lg+       ++      + +++  ++e+++al   l+++Gv ++ ++   ++d+  + 
  gi|121636245|ref|YP_976468.1| 155 GVP-FKCPAApfeaafliAAQLGDryatgtvQIDTFTPDPLPMPVAGPEVGEALVSMLKDHGVGFHPRKALARVDEAAR- 232
                                    431.222222222222344666667777643444455555555********************************9998. PP

                                    EEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGC.....TECCSS--HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                    Pyr_redox_2 216 levvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDva.....ggkggpelaqa 289
                                     +++ +dg++++ dl+ v     ps +   +++gl   e g+i vd++   t+ ++++aiGD +     +gk  p+ a+ 
  gi|121636245|ref|YP_976468.1| 233 -TMHFGDGTSEPFDLLAVVPPHVPSAAA--RSAGLS--ESGWIPVDPRTlSTSADNVWAIGDATvltlpNGKPLPKAAVF 307
                                    .9****************9999999766..799996..5*******9876999*********99***************9 PP

                                    HHHHH CS
                                    xxxxx RF
                    Pyr_redox_2 290 AvqqG 294
                                    A +q+
  gi|121636245|ref|YP_976468.1| 308 AEAQA 312
                                    99987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.2e-05     0.098       2      49 ..       5      54 ..       4      68 .. 0.76
   2 ?    3.1   0.1     0.013        57     159     229 ..      69     133 ..      62     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                   EEEECTSHHHHHHHHHHHHT.T....EEEEESSSSTTSSGGGSSEEEEESSSS CS
                            DAO  2 vviiGGGiiGlstAyeLarr.g....VtllekgdiagsgaSgrnsgllhsglr 49
                                   v+i G+G+ Gl+tA  L +  +    ++l++++  +  g+ g +  ++  g+r
  gi|121636245|ref|YP_976468.1|  5 VLILGAGVGGLTTADTLRQLlPpedrIILVDRS--FD-GTLGLSLLWVLRGWR 54
                                   89***************544745889******9..44.666666666666665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                                    TT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH.HTT.CTTTSEEEEEEEEEEEEEE CS
                            DAO 159 lGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll.gll.keldlpispvrgqvlvlkp 229
                                     Gve+++  +v +++     ++ v  +t++++  +da+V+a Ga  +  + ++l   l      v gq ++l+ 
  gi|121636245|ref|YP_976468.1|  69 PGVEMVTA-TVAHIDI---AAQVV--HTDNSVIGYDALVIALGAALNtDAvPGLsDAL---DADVAGQFYTLDG 133
                                    58999998.8999955...34444..4543343579*******997663333332223...2556677666644 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.018        81       2      21 ..       5      24 ..       4      38 .. 0.78
   2 ?    8.6   0.0   0.00059       2.7      31      71 ..     192     232 ..     170     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                                   EEEECSSHHHHHHHHHHHHT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalael 21
                                   v+++G+G+ gl  A +l++l
  gi|121636245|ref|YP_976468.1|  5 VLILGAGVGGLTTADTLRQL 24
                                   89***************997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00059
                                    SSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                      Pyr_redox  31 sdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                     + ++++ ++e++++l   l+++g+ ++  + ++++++ ++
  gi|121636245|ref|YP_976468.1| 192 DPLPMPVAGPEVGEALVSMLKDHGVGFHPRKALARVDEAAR 232
                                    45567999***************************997665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.3e-05      0.37       1      18 [.       7      24 ..       7      39 .. 0.81
   2 ?   -1.3   0.1      0.57   2.6e+03      28      51 ..     320     346 ..     305     355 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                                   EE--SHHHHHHHHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka 18
                                   I+GaG++Gl++A +L++ 
  gi|121636245|ref|YP_976468.1|  7 ILGAGVGGLTTADTLRQL 24
                                   89*************984 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.57
                                    SSSSSGGG-EECETT...CEECTS--- CS
                  NAD_binding_8  28 rdrlGGraasyevpg...vrvdygahi 51 
                                    +++lG ++a +++ g   + v++g h 
  gi|121636245|ref|YP_976468.1| 320 ARHLGYDVAERHFTGtgaCYVETGDHQ 346
                                    456777777777754456777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2590.66
//
Query:       gi|121636246|ref|YP_976469.1|  [L=261]
Description: hypothetical protein BCG_0371 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-22   79.8   4.7    3.1e-22   79.8   4.7    2.0  2  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
    9.4e-18   64.9   6.8    9.4e-18   64.9   6.8    2.2  2  MDMPI_C   MDMPI C-terminal domain
  ------ inclusion threshold ------
      0.016   15.7   1.0      0.024   15.1   0.4    1.6  2  DinB_2    DinB superfamily


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   4.7   5.1e-26   3.1e-22       4     141 .]      20     140 ..      17     140 .. 0.87
   2 ?   -0.0   0.4      0.22   1.3e+03      26      53 ..     196     223 ..     183     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 5.1e-26
                        MDMPI_N   4 ewaalaalvagLtdeqwaapsp.cpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaasla 82 
                                    +++a+ +l + +   + ++p+p cpGW++++l++H++r +r++a++++++ +  ++ ++          +  +  +++ +
  gi|121636246|ref|YP_976469.1|  20 QTHAFGELIRNV---DQSTPVPtCPGWSLGQLFRHVGRGDRWAAQIVRDRLD--HFLDP----------RSVEGGKPPPD 84 
                                    444444444444...569*****************************99633..33333..........8899999**** PP

                        MDMPI_N  83 peallaafraavtrlaaalaalppdaiadrlgipggprslgeflrtrlvEavvHglDla 141
                                    p++ ++++ ++++ l +a++++  + +++++   +gpr++g+++r+rl+E++vH++D+a
  gi|121636246|ref|YP_976469.1|  85 PDDAISWLYGGARLLVDAVEQTGVETPVWTF---LGPRPAGWWVRRRLHEVAVHRADVA 140
                                    *******************************...***********************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.22
                        MDMPI_N  26 cpGWtvadlvaHlarsaralaaalaaeg 53 
                                    + GWtv+   + +++s+r   +a+a +g
  gi|121636246|ref|YP_976469.1| 196 AGGWTVRRDERGVTWSHRHGKGAVALRG 223
                                    5688888766666666666666655444 PP

>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.0      0.54   3.2e+03      44      44 ..      97      97 ..      57     146 .. 0.49
   2 !   64.9   6.8   1.6e-21   9.4e-18       2      90 ..     153     253 ..     152     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.54
                        MDMPI_C 44 g 44
                                   +
  gi|121636246|ref|YP_976469.1| 97 R 97
                                   2 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 1.6e-21
                        MDMPI_C   2 laadgvdellatvvarraaapdsrvvlelegprtvhlhatdggrarlalwadg..............adatvrGtaadll 67 
                                    +aadg++e+l+++++++++++   ++l+le+++t+hlhatd+g+ +++ w+++              +++++rG a++ll
  gi|121636246|ref|YP_976469.1| 153 VAADGISEFLERIAVQAGSGG---TPLPLEDDDTLHLHATDPGLLEAGGWTVRrdergvtwshrhgkGAVALRGGATELL 229
                                    8*****************987...*******************987777777788888********************** PP

                        MDMPI_C  68 lllwGRlspddt.levdGdralla 90 
                                    l++ +Rls++dt +e+ Gd+++++
  gi|121636246|ref|YP_976469.1| 230 LAMVRRLSVADTgIELLGDAGVWQ 253
                                    **********************98 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.4   4.1e-06     0.024      24     126 ..      37     137 ..      17     139 .. 0.75
   2 ?   -2.2   0.0      0.93   5.6e+03      72      72 ..     219     219 ..     163     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-06
                         DinB_2  24 qpspgkwsiawllaHlgnveelllerlrgeeap.....rpgldpltppsaaealaylaevrarllallealtdadldrpl 98 
                                     p  ++ws+++l++H+g   + +++ +r+ + +     r+    ++pp++++a+ +l    + l + +e++        +
  gi|121636246|ref|YP_976469.1|  37 VPTCPGWSLGQLFRHVGRGDRWAAQIVRD-RLDhfldpRSVEGGKPPPDPDDAISWLYGGARLLVDAVEQTG-------V 108
                                    566689************65555555553.332233323333334459**********************44.......4 PP

                         DinB_2  99 tap.hpglgkltlgdvllfvlqHeqhHle 126
                                     +p + +lg++++g++++  l++ + H++
  gi|121636246|ref|YP_976469.1| 109 ETPvWTFLGPRPAGWWVRRRLHEVAVHRA 137
                                    4555667***********99999999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                         DinB_2  72 l 72 
                                    +
  gi|121636246|ref|YP_976469.1| 219 V 219
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1933.31
//
Query:       gi|121636247|ref|YP_976470.1|  [L=124]
Description: hypothetical protein BCG_0372 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.9   2.5    2.1e-07   31.5   2.5    1.2  1  SnoaL_2   SnoaL-like domain
     0.0042   17.3   0.2     0.0057   16.9   0.2    1.5  1  SnoaL_3   SnoaL-like domain
  ------ inclusion threshold ------
      0.069   13.6   0.5       0.12   12.8   0.5    1.6  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   2.5   3.4e-11   2.1e-07       1     100 [.       9     100 ..       9     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.4e-11
                                    HHHHHHHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE.... CS
                        SnoaL_2   1 vraflaalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt.... 76 
                                    v a+ +alna d+++l+al ++d+   d+ g+++G++a+r +  +l     + + e+ +++++   v+ve  +t      
  gi|121636247|ref|YP_976470.1|   9 VLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDALRGWASSL-----TTTAELGRMYVHHGVVVVEQKITSGedpg 83 
                                    679**************************99**********96666.....789*********999*9*98887534555 PP

                                    EETTSSEEEEEEEEEEEEETTEEE CS
                        SnoaL_2  77 ipatgrgvtvrgvdvfrvrdGkiv 100
                                    i         +g++ frv ++ ++
  gi|121636247|ref|YP_976470.1|  84 I-------ARTGAAAFRVVQDHVA 100
                                    3.......4444444444333332 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   9.5e-07    0.0057       5      57 ..       9      59 ..       6     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.5e-07
                        SnoaL_3  5 ldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakge 57
                                   + a+++a+ ++d+++l+al +ddi + g +a+  + g++++r +++     +e
  gi|121636247|ref|YP_976470.1|  9 VLAWHDALNAADIETLVALSTDDIDI-G-DAHGAVQGHDALRGWASSLTTTAE 59
                                   669********************997.5.798999*********998876655 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5     2e-05      0.12       3      43 ..       7      47 ..       6     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHH CS
                        DUF4440  3 aleealeeafvagdaealaallapdavlvgpsgtvldkeel 43
                                   a++ a+ +a++a d+e+l al ++d+ +  + g v++ ++l
  gi|121636247|ref|YP_976470.1|  7 ATVLAWHDALNAADIETLVALSTDDIDIGDAHGAVQGHDAL 47
                                   67789*************************99*99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 897.49
//
Query:       gi|121636248|ref|YP_976471.1|  [L=288]
Description: glucose-1-phosphate thymidylyltransferase rmlA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-65  219.1   0.0    8.3e-65  218.8   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    1.2e-10   42.0   0.0    1.6e-10   41.6   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   9.3e-69   8.3e-65       2     245 ..       3     236 ..       2     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 9.3e-69
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    ++ILaGGsGtRL+P+t+ ++k+l+pv++k ++i+++l++l+ +gi++i +++t+++++ +++ l++g+++gv++++a+++
  gi|121636248|ref|YP_976471.1|   3 GIILAGGSGTRLYPITMGISKQLLPVYDK-PMIYYPLTTLMMAGIRDIQLITTPHDAPGFHRLLGDGAHLGVNISYATQD 81 
                                    7****************************.************************************************** PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEE CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrver 161
                                    +++g+A+A++++a+ ++ ++    +lvLg++++++  + + +k++++ +     ++++++v+++++yGv+e++ eg + +
  gi|121636248|ref|YP_976471.1|  82 QPDGLAQAFVIGANHIGADSV---ALVLGDNIFYGPGLGTSLKRFQSISG---GAIFAYWVANPSAYGVVEFGAEGMALS 155
                                    *****************9995...**********************9999...8999*********************** PP

                                    EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
                NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                                    ++EKP ++k s++a+ G+Y+++++v++++ + l++++rge eit++++ +l++g+ a+++l+++++ W D+Gt+dsll+a
  gi|121636248|ref|YP_976471.1| 156 LEEKPVTPK-SNYAVPGLYFYDNDVIEIA-RGLKKSARGEYEITEVNQVYLNQGRLAVEVLARGTA-WLDTGTFDSLLDA 232
                                    *********.******************9.67********************************96.************* PP

                                    HHHH CS
                NTP_transferase 242 nekl 245
                                    ++++
  gi|121636248|ref|YP_976471.1| 233 ADFV 236
                                    9887 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   1.8e-14   1.6e-10       1     107 [.       3     120 ..       3     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.8e-14
                                    EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC......HHHHHHTTCTS-EEE-.TTS CS
                   NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggde......evlaalarlgvrvved.edp 68 
                                    ++iLAGG ++R+     g  K+llp+ +kp++ + l +l  ag++++ +++ ++       +l + a+lgv + +  +d+
  gi|121636248|ref|YP_976471.1|   3 GIILAGGSGTRLypitmGISKQLLPVYDKPMIYYPLTTLMMAGIRDIQLITTPHdapgfhRLLGDGAHLGVNISYAtQDQ 82 
                                    79*********96666555****************************999877523333344445566676664441334 PP

                                    S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHH CS
                   NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPlltpelverl 107
                                      g ++++  +++++ +ad v+++++D +++ p l   l
  gi|121636248|ref|YP_976471.1|  83 PDGLAQAFVIGANHI-GADSVALVLGDNIFYGPGLGTSL 120
                                    58*************.9*************998765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2200.99
//
Query:       gi|121636249|ref|YP_976472.1|  [L=171]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   59.4   4.4    5.2e-16   58.8   4.4    1.3  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   4.4   2.9e-20   5.2e-16      37      92 ..      70     125 ..      66     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.9e-20
                                    H----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--X CS
                             PE  37 tavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaagsYaaaEa 92 
                                    t vlaaa+DeVSaa+Aal sah++ +++l+ qaaafh qf+q l+ +ags a+aE+
  gi|121636249|ref|YP_976472.1|  70 TRVLAAAEDEVSAAVAALISAHGRRHHSLNNQAAAFHGQFAQNLNVGAGSCASAET 125
                                    78****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1200.35
//
Query:       gi|121636250|ref|YP_976473.1|  [L=503]
Description: hypothetical protein BCG_0375 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-92  310.9  21.6      1e-92  310.9  21.6    1.4  2  DUF222      Domain of unknown function (DUF222)
     0.0034   17.2   0.9     0.0067   16.3   0.9    1.5  1  HNH_5       HNH endonuclease
  ------ inclusion threshold ------
      0.024   14.8   3.0      0.045   13.9   3.0    1.5  1  HNH         HNH endonuclease
       0.16   12.3   0.0       0.32   11.3   0.0    1.4  1  Invasin_D3  Invasin, domain 3


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.9  21.6   2.3e-96     1e-92       1     301 []      33     339 ..      33     339 .. 0.99
   2 ?   -4.3   1.3       2.3     1e+04     157     168 ..     468     479 ..     442     489 .. 0.43

  Alignments for each domain:
  == domain 1  score: 310.9 bits;  conditional E-value: 2.3e-96
                         DUF222   1 llaaleeleaaarrlaavevllvael...aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalr 77 
                                    ++a+++e++aaa++l a+++l+++++   ++re++ +d+++avaa+vaa+lris++ A++r+r+Ara+rerLp++a+++ 
  gi|121636250|ref|YP_976473.1|  33 CSATRAENRAAAAQLVALGELFAYRWsrcGGREEWVMDTMAAVAAEVAAALRISQGLAASRLRYARAMRERLPKTAEVFS 112
                                    5789*********************99999************************************************** PP

                         DUF222  78 aGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltkd 157
                                    aGdi++ ++++I++rtdl+ d ++la+vd+++aa+++r++++++a+La +vd++var+d+D+vrr++e +++r+++++++
  gi|121636250|ref|YP_976473.1| 113 AGDIGYLMFATIVYRTDLIVDPDVLAAVDAQLAANVARWPSMTKARLAGQVDKIVARADADAVRRRKEYQAQRQFWVGES 192
                                    ******************************************************************************** PP

                         DUF222 158 edGmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlall....rlalaagaldchagvp...atv 230
                                    +dG+++i g+l a++a+alda+L++la +vc++    DpRs++qrraDAL+al+    rl++++g++dc+ag++   + v
  gi|121636250|ref|YP_976473.1| 193 QDGVCQIGGSLLAVDAHALDARLSALAGTVCEH----DPRSREQRRADALGALAggadRLGCGCGRADCAAGKRpaaPPV 268
                                    *********************************....*************************************999*** PP

                         DUF222 231 vvhvtaeeltaaagg...aaltgggglLpasdvrrLAkdAtlaifdepagrpld.lgrtkrtasaalrralraRD 301
                                    v+h++ae +t +++g   a  ++++gl++a+ v++LAk+Atl     p  +p d  ++ ++++s+al++++r+RD
  gi|121636250|ref|YP_976473.1| 269 VIHLIAEAATINGTGsapASQMNADGLITAELVAELAKTATLV----PLVHPGDaPPEPGYAPSKALADFVRCRD 339
                                    *******************************************....******9889*****************9 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 2.3
                         DUF222 157 dedGmsrisgel 168
                                    +++  +r + ++
  gi|121636250|ref|YP_976473.1| 468 RQNHAARQRAQV 479
                                    222222222222 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   1.5e-06    0.0067       8      37 ..     349     378 ..     342     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                          HNH_5   8 iaekelseeHIiPeslGGkltisnlvtlCk 37 
                                     + ++   +H iP + GG ++ snl ++C+
  gi|121636250|ref|YP_976473.1| 349 EPATNCDLDHTIPYAAGGPTHASNLKCYCR 378
                                    45778999*********************8 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.0     1e-05     0.045       4      43 ..     342     383 ..     337     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHnk 43 
                                    C +++ ++  + +  dH ip++ gg++  +Nl + C++ H  
  gi|121636250|ref|YP_976473.1| 342 CRWPGCDEpaTNCDLDHTIPYAAGGPTHASNLKCYCRTHHLV 383
                                    666766666688999*********************987765 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.32      47      81 ..     281     315 ..     269     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                     Invasin_D3  47 sagtlsavtdngdGtytatLtattagtatitptvn 81 
                                     +g+  a + n+dG  ta+L a+ a+tat+ p v 
  gi|121636250|ref|YP_976473.1| 281 GTGSAPASQMNADGLITAELVAELAKTATLVPLVH 315
                                    3356667889**********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3424.97
//
Query:       gi|121636251|ref|YP_976474.1|  [L=429]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-45  155.8   0.0    1.9e-45  155.6   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-05   23.6   0.0    4.1e-05   23.1   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00074   18.6   0.0     0.0014   17.6   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.035   12.7   0.0      0.054   12.0   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.044   13.1   0.0      0.074   12.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.6   0.0   5.3e-49   1.9e-45       4     348 ..      60     406 ..      57     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 5.3e-49
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    ++L+++++    g + ++++++  ++   a + +  y++++g  +++ a+   +   ++ +    + v +g+G ++li +
  gi|121636251|ref|YP_976474.1|  60 LKLNIGNPAPF-GFEAPDVIMRDIIQ---ALPYAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITM 135
                                    67777777666.55566666666654...99999*********************66666555555************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                      ++l l+ gd++l+p+p y+  +    l+gg+ v y +++ ++++ d+ +le +++e      +tk ++v +p+NPtG+
  gi|121636251|ref|YP_976474.1| 136 TLQAL-LDNGDQVLIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITE------RTKALVVINPNNPTGA 208
                                    *****.****************************************************......**************** PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH...... CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgna...... 237
                                    v+++e l++++dla+k+ lll+ De+Y +  +++ ++++ +a ++++  +l+ ++lsKa+ +aG R G+++++       
  gi|121636251|ref|YP_976474.1| 209 VYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHIS-LASIAPDMLCLTFNGLSKAYRVAGYRAGWLAITGpkehas 287
                                    *********************************776656.888888888***********************87799999 PP

                                    HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH CS
                  Aminotran_1_2 238 avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae 315
                                     +++ +  l++  l    ++q+a+  al   +  +++l     rl ++r+    +L+e+ g++++++ ++++ + +l++e
  gi|121636251|ref|YP_976474.1| 288 SFIEGIGLLANMRLCpNVPAQHAIQVALGGHQ-SIEDLVLPGGRLLEQRDIAWTKLNEIpGVSCVKPAGALYAFPRLDPE 366
                                    99999999998888846666666666666666.557999999************************************** PP

                                    .....CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEEC CS
                  Aminotran_1_2 316 .....takelskkLleevgvyvtpgtsftv..pgrlRitv 348
                                         ++++l   Ll  ++++vt+gt f    p +lR+  
  gi|121636251|ref|YP_976474.1| 367 vydidDDEQLVLDLLLSEKILVTQGTGFNWpaPDHLRLVT 406
                                    ***998899988866666************9999999866 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.1e-08   4.1e-05      52     144 ..     134     232 ..     123     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.1e-08
                                    HHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEEEB-...GGGB--.. CS
                DegT_DnrJ_EryC1  52 hlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIlpVh...lyGqva.. 125
                                     ++L+al +++gd+V++ps  +    ++ + +g +pv    d+ + +++d a++e++itertka ++++     G+v   
  gi|121636251|ref|YP_976474.1| 134 TMTLQAL-LDNGDQVLIPSPDYPLWTASTSLAGGTPVHYLCDEtQGWQPDIADLESKITERTKALVVINpnnPTGAVYsc 212
                                    3556664.5569**********9999999999999997666551679*****************9988622246765422 PP

                                    .-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 126 .dmdalkaiaakhglkvieD 144
                                      + ++ ++a+kh+l ++ D
  gi|121636251|ref|YP_976474.1| 213 eILTQMVDLARKHQLLLLAD 232
                                    34789999********9998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     4e-07    0.0014      76     175 ..     132     232 ..     121     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-07
                                    HHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE.EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                    Aminotran_5  76 lvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi.pldeegeldldelekllnektklvaithvsnvtGt 154
                                    l+ ++l++ l++gd++++ + ++   + +   l  + g  v+++   +++++ d+ +le++++e+tk++ +   +n tG 
  gi|121636251|ref|YP_976474.1| 132 LITMTLQALLDNGDQVLIPSPDYPLWT-ASTSL--AGGTPVHYLcDETQGWQPDIADLESKITERTKALVVINPNNPTGA 208
                                    444444434888888888888887666.44444..47999999867788899***************************9 PP

                                    ...B--HHHHHHHHHHTT-EEEEE CS
                    Aminotran_5 155 ...iqpveeigklakkkgalvlvD 175
                                       ++ + ++++la+k++ l+l+D
  gi|121636251|ref|YP_976474.1| 209 vysCEILTQMVDLARKHQLLLLAD 232
                                    4434557789999********999 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05     0.054      81     174 ..     134     233 ..     126     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                    HHHHHTTS-TTEEEEEESTSS...HHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----.. CS
                Cys_Met_Meta_PP  81 aaailallkaGdeivvsddlY...ggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvD.. 155
                                    +++++all +Gd++++ +  Y     + +l   +  +   + +   + d+++le++i+e+tk++ +  p np+  v    
  gi|121636251|ref|YP_976474.1| 134 TMTLQALLDNGDQVLIPSPDYplwTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAVYSce 213
                                    678889999999999887654111555566655555544444444456899*********************98776522 PP

                                    .HHHHHHHHHHTT-EEEEEG CS
                Cys_Met_Meta_PP 156 .iekiaklakkagvlvvvDn 174
                                     ++++++la+k+++l++ D 
  gi|121636251|ref|YP_976474.1| 214 iLTQMVDLARKHQLLLLADE 233
                                    2578999*******999996 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05     0.074     108     167 ..     180     232 ..     154     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                                    BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    + d+++le++i+e      ++k++++ + nn   G v+s e l ++ ++a+k+++ l+ D
  gi|121636251|ref|YP_976474.1| 180 QPDIADLESKITE------RTKALVVINPNNP-TGAVYSCEILTQMVDLARKHQLLLLAD 232
                                    6799999999999......4666666677774.7*********************99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2973.42
//
Query:       gi|121636252|ref|YP_976475.1|  [L=882]
Description: iron-sulfur-binding reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-38  130.4   1.3    7.1e-18   64.6   0.2    2.6  2  CCG       Cysteine-rich domain
    2.9e-12   46.8   4.9    4.8e-12   46.1   3.4    2.2  2  Fer4_8    4Fe-4S dicluster domain
    1.3e-10   41.2   4.0    1.3e-10   41.2   4.0    3.0  3  Fer4_10   4Fe-4S dicluster domain
    2.4e-10   40.4   4.3    3.3e-10   40.0   2.3    2.3  2  Fer4_9    4Fe-4S dicluster domain
    1.1e-07   32.3   4.9     0.0035   17.9   0.2    3.0  3  Fer4_7    4Fe-4S dicluster domain
      5e-07   30.2   2.9      0.025   15.1   0.1    2.7  2  Fer4_17   4Fe-4S dicluster domain
      2e-05   25.5   4.8      0.082   13.8   0.3    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00022   21.1  16.8     0.0019   18.2   1.4    3.0  2  Fer4_2    4Fe-4S binding domain
    0.00045   19.9  18.9      0.015   15.1   5.9    2.7  3  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.023   15.6  17.6       0.14   13.1   5.7    2.8  2  Fer4_3    4Fe-4S binding domain
      0.027   15.0  19.3       0.15   12.6   3.1    2.9  2  Fer4_4    4Fe-4S binding domain
      0.073   13.2  10.9        0.5   10.5   1.6    2.7  2  Fer4_21   4Fe-4S dicluster domain
      0.096   12.8  13.6          2    8.6   1.8    2.8  2  Fer4_6    4Fe-4S binding domain
       0.22   12.4  13.4       0.55   11.1   0.9    3.4  3  Fer4_22   4Fe-4S dicluster domain
        1.2    9.9   8.0         10    7.0   0.3    3.5  3  Fer4_15   4Fe-4S single cluster domain
        1.5    9.0   7.7       0.86    9.8   0.9    2.6  2  Fer4_18   4Fe-4S dicluster domain
        5.8    7.5  14.3        5.1    7.7   0.7    3.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1     8e-21   8.5e-18       1      84 [.     477     568 ..     477     569 .. 0.92
   2 !   64.6   0.2   6.7e-21   7.1e-18       1      84 [.     607     693 ..     607     694 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 8e-21
                            CCG   1 vayfdgCh.llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaee..tg....ada 72 
                                    +++++gC+ ++++++++++ka+++ll+++gv++ +l ++e+C+G++++rsg+e l+++la++ vet++   +g    +++
  gi|121636252|ref|YP_976475.1| 477 YLFWVGCAgAYDDKAKKTTKAVAELLAVAGVKYLVLgAGETCNGDSARRSGNEFLFQQLAQQAVETLDGlfEGvetvDRK 556
                                    68*****9999999******************************************************96512555599* PP

                            CCG  73 ivtacpgCllql 84 
                                    iv++cp+C++++
  gi|121636252|ref|YP_976475.1| 557 IVVTCPHCFNTI 568
                                    *********998 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 6.7e-21
                            CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivta 76 
                                    ++y+d+C+l+r++  y+++r+++ +  +a ++e++++ +++ CCGagg r+++ee + +++++++v++a  t+a ai+ta
  gi|121636252|ref|YP_976475.1| 607 ITYHDPCYLGRHNkvYEAPRELIGAA-GASLTEMPRHaDRSFCCGAGGARMWMEEhIGKRINHERVDEALATDATAIATA 685
                                    69************999999988888.****************************9************************ PP

                            CCG  77 cpgCllql 84 
                                    cp+C +++
  gi|121636252|ref|YP_976475.1| 686 CPFCRVMV 693
                                    ****9986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   3.4   4.6e-15   4.8e-12       2      65 .]     292     406 ..     291     406 .. 0.65
   2 ?   -2.3   0.0         6   6.4e+03      14      33 ..     685     704 ..     683     743 .. 0.60

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.6e-15
                         Fer4_8   2 lekCieCgaCqsaCpvlrr.....................................tkkhlldargeaaedvqeeqvlee 44 
                                    +  C+eCg+Cqs+Cp++++                                                            +
  gi|121636252|ref|YP_976475.1| 292 FATCTECGRCQSQCPAWNTgkplspklvimdlrdhwmakapyilgqkdasaggeagH----------------------Q 349
                                    678************777767776666666666665555555533333333333321......................0 PP

                         Fer4_8  45 ....................................eealwsCttcgaCtevCpvgi 65 
                                                                         + lwsC+tcgaC+e+Cpv+i
  gi|121636252|ref|YP_976475.1| 350 ehhhvpesgfgrvpghgpeqatrplvgteeqggvidPDVLWSCVTCGACVEQCPVDI 406
                                    2333333455555555555555666666677788889*****************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                         Fer4_8  14 aCpvlrrtkkhlldargeaa 33 
                                    aCp++r +  +  + r+e a
  gi|121636252|ref|YP_976475.1| 685 ACPFCRVMVTDGVNDRQEEA 704
                                    68887775544444333333 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   4.0   1.3e-13   1.3e-10       4      56 .]     290     403 ..     287     403 .. 0.94
   2 ?   -1.0   0.0       1.9     2e+03      35      50 ..     551     566 ..     545     569 .. 0.80
   3 ?   -1.9   0.0       3.5   3.7e+03      17      36 ..     684     703 ..     683     711 .. 0.54

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.3e-13
                        Fer4_10   4 idddtCirCgkCvkaCPadl............................................................ 23 
                                    +d  tC++Cg+C++ CPa++                                                            
  gi|121636252|ref|YP_976475.1| 290 LDFATCTECGRCQSQCPAWNtgkplspklvimdlrdhwmakapyilgqkdasaggeaghqehhhvpesgfgrvpghgpeq 369
                                    57789*************88***********************************************************9 PP

                        Fer4_10  24 .tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     t+  +  e+ ++  + +++++C +cgaCve+CP
  gi|121636252|ref|YP_976475.1| 370 aTRPLVGTEEQGGVIDPDVLWSCVTCGACVEQCP 403
                                    877777888888888888***************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                        Fer4_10  35 eeavrkkvekCtgcga 50 
                                    e ++rk v  C++c++
  gi|121636252|ref|YP_976475.1| 551 ETVDRKIVVTCPHCFN 566
                                    6688999999999976 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.5
                        Fer4_10  17 kaCPadltsvgakgeaseee 36 
                                    +aCP++  +v     + +ee
  gi|121636252|ref|YP_976475.1| 684 TACPFCRVMVTDGVNDRQEE 703
                                    68999774444444444444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   2.3   3.1e-13   3.3e-10       2      49 ..     295     405 ..     294     407 .. 0.98
   2 ?   -2.7   0.0       6.5   6.9e+03      34      40 ..     684     690 ..     656     696 .. 0.63

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.1e-13
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase................................................ 33 
                                    Ct+Cg+C+++Cpa+ + +  +++ + ++ ++                                                 
  gi|121636252|ref|YP_976475.1| 295 CTECGRCQSQCPAWNTGKPLSPKLVIMDLRDHwmakapyilgqkdasaggeaghqehhhvpesgfgrvpghgpeqatrpl 374
                                    ***************************998889*********************************************** PP

                         Fer4_9  34 ...............eaCigCgaCveaCpkg 49 
                                                   ++C++CgaCve Cp +
  gi|121636252|ref|YP_976475.1| 375 vgteeqggvidpdvlWSCVTCGACVEQCPVD 405
                                    *****************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                         Fer4_9  34 eaCigCg 40 
                                    +aC +C+
  gi|121636252|ref|YP_976475.1| 684 TACPFCR 690
                                    5676664 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.3e-05     0.024      33      50 ..     290     307 ..     265     310 .. 0.81
   2 !   17.9   0.2   3.3e-06    0.0035      33      52 .]     384     406 ..     346     406 .. 0.77
   3 ?   -2.4   0.0         7   7.4e+03      45      50 ..     683     688 ..     651     707 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                         Fer4_7  33 idpekClgCgaCvavCPt 50 
                                    +d  +C+ Cg+C++ CP+
  gi|121636252|ref|YP_976475.1| 290 LDFATCTECGRCQSQCPA 307
                                    577899999999999995 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.3e-06
                         Fer4_7  33 idpe...kClgCgaCvavCPtga 52 
                                    idp+   +C++CgaCv+ CP+++
  gi|121636252|ref|YP_976475.1| 384 IDPDvlwSCVTCGACVEQCPVDI 406
                                    44433338************985 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7
                         Fer4_7  45 vavCPt 50 
                                    +++CP+
  gi|121636252|ref|YP_976475.1| 683 ATACPF 688
                                    445543 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3     4e-05     0.042      42      58 ..     291     307 ..     269     308 .. 0.83
   2 !   15.1   0.1   2.4e-05     0.025      36      60 ..     382     406 ..     364     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                        Fer4_17  42 kaslCieCgeCerkCPq 58 
                                     + +C+eCg+C+++CP+
  gi|121636252|ref|YP_976475.1| 291 DFATCTECGRCQSQCPA 307
                                    5789************5 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
                        Fer4_17  36 eaekeekaslCieCgeCerkCPqgl 60 
                                    ++++ ++  +C++Cg C+++CP ++
  gi|121636252|ref|YP_976475.1| 382 GVIDPDVLWSCVTCGACVEQCPVDI 406
                                    4556678889************887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.5   0.00019       0.2       1      19 [.     294     312 ..     294     329 .. 0.83
   2 !   13.8   0.3   7.8e-05     0.082       2      16 ..     392     406 ..     391     432 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                        Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                    +C++Cg+C + CP+    +
  gi|121636252|ref|YP_976475.1| 294 TCTECGRCQSQCPAWNTGK 312
                                    5************876655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.8e-05
                        Fer4_16   2 CgtCgkCaevCPtna 16 
                                    C+tCg+C+e CP++ 
  gi|121636252|ref|YP_976475.1| 392 CVTCGACVEQCPVDI 406
                                    ************975 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   1.8e-06    0.0019       4      22 .]     289     307 ..     286     307 .. 0.88
   2 !   12.1   3.0   0.00016      0.17       5      21 ..     384     403 ..     382     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                         Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                      d ++C++Cg C+s CPa
  gi|121636252|ref|YP_976475.1| 289 MLDFATCTECGRCQSQCPA 307
                                    57889*************8 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                         Fer4_2   5 vdtd...rCigCgaCvsaCP 21 
                                    +d+d   +C+ CgaCv  CP
  gi|121636252|ref|YP_976475.1| 384 IDPDvlwSCVTCGACVEQCP 403
                                    67777779************ PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.4   4.2e-05     0.045       4      19 ..     291     306 ..     289     307 .. 0.89
   2 !   15.1   5.9   1.4e-05     0.015       8      21 ..     392     405 ..     391     406 .. 0.93
   3 ?   -3.3   0.1       8.9   9.4e+03      16      20 ..     684     688 ..     683     688 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                    ETTTSSS-THHHHHST CS
                           Fer4   4 deekCigCGaCvevCP 19 
                                    d   C+ CG+C + CP
  gi|121636252|ref|YP_976475.1| 291 DFATCTECGRCQSQCP 306
                                    7788************ PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.4e-05
                                    SSS-THHHHHSTTT CS
                           Fer4   8 CigCGaCvevCPvg 21 
                                    C+ CGaCve CPv+
  gi|121636252|ref|YP_976475.1| 392 CVTCGACVEQCPVD 405
                                    *************8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.9
                                    HHSTT CS
                           Fer4  16 evCPv 20 
                                     +CP+
  gi|121636252|ref|YP_976475.1| 684 TACPF 688
                                    79**6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.0    0.0096        10       1      12 [.     295     306 ..     295     310 .. 0.94
   2 ?   13.1   5.7   0.00014      0.14       1      14 [.     392     405 ..     392     406 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0096
                         Fer4_3   1 CtgCgaCvevCP 12 
                                    Ct Cg+C   CP
  gi|121636252|ref|YP_976475.1| 295 CTECGRCQSQCP 306
                                    ************ PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+ CgaCve CPv+
  gi|121636252|ref|YP_976475.1| 392 CVTCGACVEQCPVD 405
                                    ************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.1   0.00014      0.15       3      16 ..     294     307 ..     292     312 .. 0.91
   2 ?   12.6   2.5   0.00015      0.16       3      16 ..     391     404 ..     390     410 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                    +C++Cg+C + CP 
  gi|121636252|ref|YP_976475.1| 294 TCTECGRCQSQCPA 307
                                    7************5 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00015
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                    +C+ Cg+Cv  CP+
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCPV 404
                                    6************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0022       2.3       6      19 ..     293     306 ..     273     310 .. 0.74
   2 ?   10.5   1.6   0.00048       0.5      40      54 ..     391     405 ..     378     411 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                        Fer4_21   6 dkCigCgkCliaCe 19 
                                    ++C +Cg+C   C+
  gi|121636252|ref|YP_976475.1| 293 ATCTECGRCQSQCP 306
                                    55666666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                        Fer4_21  40 eCvGCnlCssvCPve 54 
                                    +Cv C  C++ CPv+
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCPVD 405
                                    6************94 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8    0.0019         2       8      21 ..     294     307 ..     293     311 .. 0.91
   2 ?    8.4   4.4    0.0022       2.4       8      22 ..     391     405 ..     391     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                         Fer4_6   8 kCigCgdCvrvCPe 21 
                                     C+ Cg+C + CP+
  gi|121636252|ref|YP_976475.1| 294 TCTECGRCQSQCPA 307
                                    6************6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                         Fer4_6   8 kCigCgdCvrvCPeg 22 
                                    +C+ Cg+Cv  CP +
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCPVD 405
                                    6************75 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00052      0.55      73      94 ..     286     307 ..     278     308 .. 0.81
   2 ?    8.3   1.0     0.004       4.3      81      96 .]     391     406 ..     384     406 .. 0.89
   3 ?   -2.1   0.0       6.9   7.3e+03       9      27 ..     683     701 ..     678     714 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                        Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                    +k   +  +C+ CgRC+++cp+
  gi|121636252|ref|YP_976475.1| 286 WKGMLDFATCTECGRCQSQCPA 307
                                    555668899***********96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.004
                        Fer4_22  81 gCvGCgRCieacpvki 96 
                                    +Cv Cg C+e+cpv+i
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCPVDI 406
                                    699*********9986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.9
                        Fer4_22   9 tlvCptCsCfdvedetkee 27 
                                    +++Cp C  + +  +++++
  gi|121636252|ref|YP_976475.1| 683 ATACPFCRVMVTDGVNDRQ 701
                                    6889999987766665433 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.066        69       3      20 ..     290     307 ..     289     317 .. 0.89
   2 ?    7.0   0.3    0.0096        10       6      30 ..     390     413 ..     384     432 .. 0.71
   3 ?    1.1   0.1      0.66   6.9e+02      38      61 ..     665     688 ..     650     689 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.066
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    +D  +C+ cg+C   +p 
  gi|121636252|ref|YP_976475.1| 290 LDFATCTECGRCQSQCPA 307
                                    67889*********9985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0096
                        Fer4_15   6 daCigcglCvaeapevfeldedgla 30 
                                    + C  cg+Cv+ +p  +e   d++ 
  gi|121636252|ref|YP_976475.1| 390 WSCVTCGACVEQCPVDIEHV-DHIV 413
                                    57***********9444433.5554 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.66
                        Fer4_15  38 eiaegevpddeeeaaqeAaraCPv 61 
                                    +i+ ++v++ + ++a   a aCP 
  gi|121636252|ref|YP_976475.1| 665 RINHERVDEALATDATAIATACPF 688
                                    566789*****************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.15   1.6e+02      58      73 ..     292     307 ..     280     309 .. 0.87
   2 ?    9.8   0.9   0.00082      0.86      60      76 ..     391     407 ..     369     415 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                        Fer4_18  58 agdcidcescvkvcPt 73 
                                     + c++c+ c + cP 
  gi|121636252|ref|YP_976475.1| 292 FATCTECGRCQSQCPA 307
                                    578***********95 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00082
                        Fer4_18  60 dcidcescvkvcPtgid 76 
                                     c++c++cv+ cP++i+
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCPVDIE 407
                                    6************9986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.7    0.0048       5.1       4      18 ..     293     307 ..     290     320 .. 0.91
   2 ?    4.2   3.0      0.06        63       5      17 ..     391     403 ..     389     406 .. 0.94
   3 ?    1.3   0.1      0.47     5e+02      29      52 ..     664     687 ..     658     689 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                        Fer4_13   4 dtCiacgaCvelaPd 18 
                                     tC++cg C + +P 
  gi|121636252|ref|YP_976475.1| 293 ATCTECGRCQSQCPA 307
                                    79************6 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.06
                        Fer4_13   5 tCiacgaCvelaP 17 
                                    +C+ cgaCve +P
  gi|121636252|ref|YP_976475.1| 391 SCVTCGACVEQCP 403
                                    6***********9 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.47
                        Fer4_13  29 svvaeqptseeekadaeeAadaCP 52 
                                     ++ +++++e++  da++ a aCP
  gi|121636252|ref|YP_976475.1| 664 KRINHERVDEALATDATAIATACP 687
                                    478899999*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5700.65
//
Query:       gi|121636253|ref|YP_976476.1|  [L=832]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-14   51.7   0.0    1.2e-13   50.4   0.0    1.8  1  GerE          Bacterial regulatory proteins, luxR family
    5.3e-07   29.2   0.4    5.9e-05   22.7   0.1    2.9  2  Sigma70_r4_2  Sigma-70, region 4
     0.0027   17.5   0.5     0.0027   17.5   0.5    3.6  3  AAA_30        AAA domain
      0.007   16.1   1.2       0.27   11.1   0.1    3.5  3  HTH_23        Homeodomain-like domain
      0.008   15.7   0.1       0.34   10.5   0.1    2.7  2  Sigma70_r4    Sigma-70, region 4
      0.008   16.1   0.5      0.014   15.3   0.5    1.3  1  NTPase_1      NTPase
  ------ inclusion threshold ------
      0.011   15.9   0.0        7.3    6.8   0.1    3.4  2  HTH_28        Helix-turn-helix domain
       0.03   13.8   0.0        7.8    6.0   0.1    3.2  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.065   13.0   0.0       0.27   11.0   0.0    2.1  1  HTH_38        Helix-turn-helix domain
       0.12   11.7   0.1       0.24   10.7   0.1    1.4  1  Zeta_toxin    Zeta toxin
       0.13   12.5   2.9        3.2    8.0   0.2    2.8  2  AAA_22        AAA domain
       0.14   11.9   0.1        0.3   10.8   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.27   11.5   3.9        0.3   11.4   1.3    2.3  2  AAA_19        AAA domain
       0.71    9.8  12.8      0.094   12.6   0.3    4.6  4  MarR_2        MarR family
        1.5    9.1   4.6       0.61   10.3   0.6    2.4  3  AAA_28        AAA domain
        1.7    9.0  17.9       0.14   12.5   8.7    3.8  2  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   1.1e-16   1.2e-13       2      56 ..     762     816 ..     761     817 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.1e-16
                                    SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHH CS
                           GerE   2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrl 56 
                                    +Ls+RErev +ll  G+   +I+++l+iS+kTV+ h+++i ++L++ sr+e   +
  gi|121636253|ref|YP_976476.1| 762 PLSDREREVAELLLLGMPYRDIGARLFISAKTVEHHVARIRQRLGAGSRSEMLSM 816
                                    7*************************************************99887 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.051        57      18      43 ..     197     222 ..     180     229 .. 0.82
   2 !   22.7   0.1   5.2e-08   5.9e-05      11      54 .]     763     805 ..     762     805 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.051
                                    HHHHHHTS---HHHHHHHHT--HHHH CS
                   Sigma70_r4_2  18 ifllryleglsykEIAellgisegtV 43 
                                     ++++  ++l   ++A+ lgis++  
  gi|121636253|ref|YP_976476.1| 197 LLMMSLTHELGVSDVAAALGISVTDA 222
                                    678999999*************9865 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 5.2e-08
                                    S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    L+ r+re+ +l  l g++y++I ++l is +tV+++++R r++L
  gi|121636253|ref|YP_976476.1| 763 LSDREREVAEL-LLLGMPYRDIGARLFISAKTVEHHVARIRQRL 805
                                    899999**9**.7****************************998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   2.4e-06    0.0027      21      52 ..      45      76 ..      31      82 .. 0.90
   2 ?    2.5   0.2     0.091     1e+02      88     121 ..      84     117 ..      80     124 .. 0.88
   3 ?   -2.3   0.1       2.7   3.1e+03     133     181 ..     647     692 ..     643     701 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrvigl 52
                                   +++tG+ GtGKtt+l+a+r++++++g +v+++
  gi|121636253|ref|YP_976476.1| 45 VLITGGIGTGKTTVLAAARDTLRRSGLTVLAC 76
                                   579***********************999876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.091
                         AAA_30  88 pgtllivDEagmvdtkqlaallkaaekagakvil 121
                                    p+t l++D a ++  ++l +l+++++++  +v+ 
  gi|121636253|ref|YP_976476.1|  84 PETALVIDDAQLLTDTELLRLTERVADSRLTVVA 117
                                    5699**********************98888875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                         AAA_30 133 a.GgvlrdlveaagigtaeLtevvRqkeseeraaalalregdaeealeal 181
                                    + G++l  +v a+ + +  L++  R    + r +a+++  +++++a ++l
  gi|121636253|ref|YP_976476.1| 647 PhGQALGAMV-AHSTLAQALSDAGRT---WLRVLAENVDADEVTAAARSL 692
                                    4488888887.477778888888887...888888888887777665555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.27   3.1e+02      19      31 ..     207     219 ..     197     220 .. 0.80
   2 ?   -2.1   0.1       3.4   3.8e+03      10      27 ..     282     299 ..     279     300 .. 0.72
   3 !   11.1   0.1   0.00024      0.27      10      41 ..     770     801 ..     763     808 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                         HTH_23  19 svreIAreLgvsr 31 
                                     v+++A++Lg+s 
  gi|121636253|ref|YP_976476.1| 207 GVSDVAAALGISV 219
                                    5899*******96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                         HTH_23  10 illllae.GlsvreIAreL 27 
                                    +l+l+ e Gl+ ++ A++L
  gi|121636253|ref|YP_976476.1| 282 ALRLA-EhGLRDERLADIL 299
                                    44455.55*****999987 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00024
                         HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                    ++ ll+ G+++r+I ++L +s  Tv + + r 
  gi|121636253|ref|YP_976476.1| 770 VAELLLLGMPYRDIGARLFISAKTVEHHVARI 801
                                    4555666******************9888775 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.12   1.3e+02      13      44 ..     198     229 ..     189     231 .. 0.82
   2 !   10.5   0.1    0.0003      0.34       5      48 ..     763     805 ..     761     807 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                                    HHHHHTTT--HHHHHHHHTS-HHHHHHHHHHH CS
                     Sigma70_r4  13 lelrfgeglTleEIgerlgiSrerVrqiekrA 44 
                                    l ++  ++l  +++++ lgiS   +r +  rA
  gi|121636253|ref|YP_976476.1| 198 LMMSLTHELGVSDVAAALGISVTDARGLVDRA 229
                                    566677888999*********98887776666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0003
                                    S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    L++rerev el  +   ++ +Ig+rl iS  +V  + +r +++L
  gi|121636253|ref|YP_976476.1| 763 LSDREREVAELLLLGM-PYRDIGARLFISAKTVEHHVARIRQRL 805
                                    89******99998765.9*********************99998 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   1.3e-05     0.014       1      30 [.      44      73 ..      44      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                   kv+iTG  G+GKtT++  + ++l++sg++v
  gi|121636253|ref|YP_976476.1| 44 KVLITGGIGTGKTTVLAAARDTLRRSGLTV 73
                                   689************************987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.026        29      12      41 ..     204     234 ..     197     238 .. 0.85
   2 ?    6.8   0.1    0.0065       7.3       4      38 ..     769     803 ..     768     808 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                         HTH_28  12 Gh.svreaArelgisrrtvyrWikryeegGi 41 
                                    ++  v+++A++lgis +  ++++ r  + G+
  gi|121636253|ref|YP_976476.1| 204 HElGVSDVAAALGISVTDARGLVDRAHASGL 234
                                    456899*******************999884 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0065
                         HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWikryee 38 
                                    e+ +ll+ G+++r++ ++l is  tv   + r ++
  gi|121636253|ref|YP_976476.1| 769 EVAELLLLGMPYRDIGARLFISAKTVEHHVARIRQ 803
                                    67888888**********************99998 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.007       7.8      19      50 ..     197     228 ..     193     230 .. 0.80
   2 ?    3.9   0.0     0.031        35      18      45 ..     768     795 ..     761     796 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.007
                   HTH_Tnp_ISL3  19 yilelllesrsvkavArqlgvSwtTVwrildr 50 
                                      +++l++   v++vA+ lg+S t  +  +dr
  gi|121636253|ref|YP_976476.1| 197 LLMMSLTHELGVSDVAAALGISVTDARGLVDR 228
                                    56788999999***********9977766666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.031
                   HTH_Tnp_ISL3  18 ayilelllesrsvkavArqlgvSwtTVw 45 
                                    + ++elll +++ +++ ++l +S++TV+
  gi|121636253|ref|YP_976476.1| 768 REVAELLLLGMPYRDIGARLFISAKTVE 795
                                    66777777777***************96 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.27       5      43 ..     763     800 ..     759     800 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                         HTH_38   5 LsleeReeIerllaeGlslreIArrLgrspsTIsRElkR 43 
                                    Ls  eR e + ll  G+ +r+I+ rL  s  T+  ++ R
  gi|121636253|ref|YP_976476.1| 763 LSDRER-EVAELLLLGMPYRDIGARLFISAKTVEHHVAR 800
                                    899999.77778889******************999988 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.24      14      44 ..      40      70 ..      30      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                     Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqg 44
                                     P+ +l+ G+ G GK++++++++d l+r g
  gi|121636253|ref|YP_976476.1| 40 TVPVKVLITGGIGTGKTTVLAAARDTLRRSG 70
                                   679**********************997554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0029       3.2       9      30 ..      46      67 ..      44      85 .. 0.78
   2 ?    3.7   0.2     0.061        69      94     117 ..      87     109 ..      81     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                         AAA_22  9 vvtGesGtGKTtllrrlleqld 30
                                   ++tG  GtGKTt+l+  +++l 
  gi|121636253|ref|YP_976476.1| 46 LITGGIGTGKTTVLAAARDTLR 67
                                   79**************999984 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.061
                         AAA_22  94 lliiDEaqhlrseealeeLrslln 117
                                    +l+iD+aq l +++ l  L +++ 
  gi|121636253|ref|YP_976476.1|  87 ALVIDDAQLL-TDTELLRLTERVA 109
                                    79********.8777766655554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00027       0.3      25      41 ..      45      61 ..      36      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                         AAA_29 25 tlltGpsGsGKSTllDA 41
                                   +l+tG +G+GK+T+l A
  gi|121636253|ref|YP_976476.1| 45 VLITGGIGTGKTTVLAA 61
                                   8*************966 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.3   0.00027       0.3      12      37 ..      44      69 ..      34      79 .. 0.83
   2 ?   -1.4   0.1       2.3   2.6e+03     104     133 ..      86     114 ..      71     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                         AAA_19 12 vllvtaGpGtGKTrvlkhivallvel 37
                                    +l+t+G GtGKT+vl ++   l + 
  gi|121636253|ref|YP_976476.1| 44 KVLITGGIGTGKTTVLAAARDTLRRS 69
                                   479*************9987777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                         AAA_19 104 ellivDEfqdvd.elqyrLlkallgekkkll 133
                                    ++l++D +q ++     rL +++++++  l+
  gi|121636253|ref|YP_976476.1|  86 TALVIDDAQLLTdTELLRLTERVADSR--LT 114
                                    589******999889999999999444..33 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.3e+02       3      26 ..      24      45 ..      22      49 .. 0.85
   2 ?   12.6   0.3   8.4e-05     0.094      20      54 ..     192     238 ..     177     242 .. 0.77
   3 ?   -3.0   0.4       6.4   7.2e+03      11      42 ..     333     363 ..     327     369 .. 0.67
   4 ?   -0.5   0.0       1.1   1.2e+03      25      45 ..     781     801 ..     765     804 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                   --HHHHHHHHHHHCTTTSEEEHHH CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvge 26
                                   ++pa +r+L++L+++p   + v+ 
  gi|121636253|ref|YP_976476.1| 24 VPPAARRALLELANAPT--VPVKV 45
                                   689*************8..77765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.4e-05
                                    S............EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  20 r............dltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    +            +l v+++a++lg+s   +  +++r+ a GL+e +
  gi|121636253|ref|YP_976476.1| 192 PtldtllmmslthELGVSDVAAALGISVTDARGLVDRAHASGLIESS 238
                                    5555555555555577****************************976 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.4
                                    HHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHH CS
                         MarR_2  11 LaaLgrrpgrdl.tvgelarrlglsksavsril 42 
                                      aL+r ++  + +++ la+ l  s+ a+ r+ 
  gi|121636253|ref|YP_976476.1| 333 ADALARTGD--CtAAATLADDLLSSPDATERAA 363
                                    455666655..4488888888888888777765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.1
                                    HHHHHHHTSSHHHHHHHHHHH CS
                         MarR_2  25 gelarrlglsksavsrilkrL 45 
                                    +++ +rl +s  +v  +++r 
  gi|121636253|ref|YP_976476.1| 781 RDIGARLFISAKTVEHHVARI 801
                                    79***********99999986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00054      0.61       1      18 [.      44      61 ..      44      77 .. 0.85
   2 ?   -3.2   0.0       7.7   8.7e+03      99     143 ..     567     613 ..     546     623 .. 0.54
   3 ?   -2.1   0.1       3.6   4.1e+03      13      34 ..     659     680 ..     658     715 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                         AAA_28  1 kivitGgestGKTtllea 18
                                   k+ itGg +tGKTt+l+a
  gi|121636253|ref|YP_976476.1| 44 KVLITGGIGTGKTTVLAA 61
                                   699************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.7
                         AAA_28  99 eleaaar.ekrydl.vfllppapeidddgeRredleereaiderlre 143
                                    ++ aa++   +y l  f l p +e+   ++R  ++++ + + ++ + 
  gi|121636253|ref|YP_976476.1| 567 HWYAAMEaLAEYSLdLFALLPLGELWVAAARMRQVDQLQHTLDQALT 613
                                    44443331444666666666666442233333334444444444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.6
                         AAA_28  13 TtlleaLaargypvvpEaarei 34 
                                    +tl++aL++ g ++++  a  +
  gi|121636253|ref|YP_976476.1| 659 STLAQALSDAGRTWLRVLAENV 680
                                    7999999999888875554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   8.7   0.00013      0.14      24     155 ..      41     197 ..      28     312 .. 0.73
   2 ?   -0.7   0.9       1.4   1.6e+03      84      84 ..     556     556 ..     411     692 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                         AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipysa.laqalareellrqllde..........ae 90 
                                        vl++G  G+GK++++ ++++ l+++g  +l++   +  + ++++++  aq+l+  ellr  ++           ae
  gi|121636253|ref|YP_976476.1|  41 VpVKVLITGGIGTGKTTVLAAARDTLRRSGLTVLACPPPDGePPETALVIdDAQLLTDTELLRLTERVadsrltvvaaAE 120
                                    44679************************777777777666544466655577777777777766666554444432222 PP

                         AAA_16  91 saeleawrekleeala.............avpelagaea.....srllellkrll.allsrderp.lvlvlDdlqwadea 150
                                    ++e+ ++        +             + ++l+ ae+        l  l +++ a+++ +++   v +++ l ++de 
  gi|121636253|ref|YP_976476.1| 121 AREHHRAL-------RaltmalerdrpriSLGPLPVAEHlrdctA-GLPFLIHAVsARAQAPAQAaKVALIERLRRLDEP 192
                                    22222222.......133344557777775555555555666632.2333333333444444443456667777777776 PP

                         AAA_16 151 slqll 155
                                    +l+ l
  gi|121636253|ref|YP_976476.1| 193 TLDTL 197
                                    66664 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                         AAA_16  84 q 84 
                                     
  gi|121636253|ref|YP_976476.1| 556 R 556
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (832 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 5493.30
//
Query:       gi|121636254|ref|YP_976477.1|  [L=179]
Description: hypothetical protein BCG_0379 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 1173.05
//
Query:       gi|121636255|ref|YP_976478.1|  [L=479]
Description: isoniazid inductible gene protein iniB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3178.37
//
Query:       gi|121636256|ref|YP_976479.1|  [L=640]
Description: isoniazid inductible gene protein iniA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-08   34.4   0.0    5.1e-08   33.1   0.0    1.7  1  Dynamin_N        Dynamin family
    9.3e-05   22.5   0.0    0.00062   19.8   0.0    2.3  2  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.02   14.6   0.8       0.02   14.6   0.8    2.5  3  MukF_M           MukF middle domain
        0.2   10.9   0.6       0.33   10.2   0.6    1.2  1  Cas_Csa4         CRISPR-associated protein (Cas_Csa4)
        1.1    9.4   6.3       0.23   11.6   0.5    2.4  3  GCN5L1           GCN5-like protein 1 (GCN5L1)
        1.7    8.8   8.4       0.64   10.2   0.4    3.3  4  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
        3.2    8.1  14.5        5.8    7.3   0.1    4.8  4  TetR_C_11        Tetracyclin repressor-like, C-terminal domai


Domain annotation for each model (and alignments):
>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0     2e-11   5.1e-08       1     152 [.      73     220 ..      73     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2e-11
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEE..T-EB--CHHHHHHHHHHHHH CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkek..ekkledfsevreeieketek 78 
                                    +++ G  ++GKS +l +Ll  +   +g    T  +++++++ +++a+   v +   ++  ++ +  ++++ + ++++   
  gi|121636256|ref|YP_976479.1|  73 VVIAGLLKQGKSQLLSSLLNLPAARVGDDEATVVITVVSYSAQPSAR--LVLAAGPDGttAAVDIPVDDISTDVRRAPHA 150
                                    6889999**************************************55..5666666663355555666666666555555 PP

                                    HHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHH CS
                      Dynamin_N  79 iagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealflar 152
                                          +   +v++  + +ll+ gl ++D+PG+    + + + +  ++ +ad++l+v++ ++++++ e  f+++
  gi|121636256|ref|YP_976479.1| 151 GG----REVLRVEVGAPSPLLRGGLAFIDTPGVGGLGQPHLSATLGLLPEADAVLVVSDTSQEFTEPEMWFVRQ 220
                                    44....6667899****************************************************988777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.4e-07   0.00062       1      91 [.      72     211 ..      72     234 .. 0.77
   2 ?   -1.1   0.0      0.75   1.9e+03      64      93 ..     532     577 ..     515     597 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                                    EEEEEESTTSSHHHHHHHHHTS.TEEESSST.TSSSSEEEEEEEETTEE............................... CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkp.gtTrdinegrvklkgke............................... 47 
                                    +v+i+G    GKS L+++l++  +a+v+d    + ++++ +  +    +                               
  gi|121636256|ref|YP_976479.1|  72 RVVIAGLLKQGKSQLLSSLLNLpAARVGDDEaTVVITVVSYSAQ----Psarlvlaagpdgttaavdipvddistdvrra 147
                                    699******************97889976651333444444444....22456777777888899999999999999999 PP

                                    .......................EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSH CS
                       MMR_HSR1  48 .......................ielvDtpGliegaseek.glgkaflaleeadlillvvdaseeklk 91 
                                                           + ++DtpG + g   ++  l+ ++  l ead++l+v d s+e ++
  gi|121636256|ref|YP_976479.1| 148 phaggrevlrvevgapspllrggLAFIDTPG-VGGL--GQpHLSATLGLLPEADAVLVVSDTSQE-FT 211
                                    999****************************.8733..33346666666778*********8855.43 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                                    H..HHHHHHHHHHC..TSEEEEEEETT............TTCSHHH CS
                       MMR_HSR1  64 k..glgkaflalee..adlillvvdas............eeklkpl 93 
                                    +  +++ + +a+ +  +d i +vv+ +            +++++++
  gi|121636256|ref|YP_976479.1| 532 RllRVRSEAKANVRrfVDDISFVVSKQsrdrlkmiqrllRDHYREI 577
                                    2344444444444446788888886334444444433332234444 PP

>> MukF_M  MukF middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.56   1.4e+03      46      81 ..      48      87 ..      42     110 .. 0.69
   2 ?   -4.0   0.1       4.3   1.1e+04      12      34 ..     340     363 ..     338     367 .. 0.54
   3 ?   14.6   0.8   7.8e-06      0.02      40     102 ..     551     614 ..     524     626 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHGGGGH CS
                         MukF_M 46 eildridltqrvmdeqqq....qvkeeiaellnkdWreai 81
                                   ++ +r dl qr+   +q+    qv+  ia ll++   + +
  gi|121636256|ref|YP_976479.1| 48 KLNERGDLVQRLTRARQRitdpQVRVVIAGLLKQGKSQLL 87
                                   5556667777777666643334677778888887665555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.3
                                    HHHHHHHHHHHHHT-.-SHHHHHH CS
                         MukF_M  12 vadeleraaeaaeeg.gdekaWrk 34 
                                    +a++ler +  a+++ ++++ W++
  gi|121636256|ref|YP_976479.1| 340 LASDLERRKREAQQAvQQTALWQQ 363
                                    566666655444444155555654 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 7.8e-06
                                    HHHTHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHH CS
                         MukF_M  40 lkysvae.ildridltqrvmdeqqqqvkeeiaellnkdWreaisscekllsetsstlrelqdtl 102
                                    + + v++   dr+ + qr++ ++ +++ eei++ l++  +++i++ +   +e  + +relq  l
  gi|121636256|ref|YP_976479.1| 551 ISFVVSKqSRDRLKMIQRLLRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQL 614
                                    556665414699*************************************************877 PP

>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00013      0.33     258     348 ..     525     617 ..     519     623 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                       Cas_Csa4 258 Yalefkvgnnqrirsfrevelsklldfiaelkardfastiklvddllre.....dleillrLieallygdlrevysalrv 332
                                    Y  + k+ +  r+rs  + ++ + +d i+ +  ++ ++  k+++ llr      + ei   L+e+l   ++ +  +  + 
  gi|121636256|ref|YP_976479.1| 525 YKED-KQNRLLRVRSEAKANVRRFVDDISFVVSKQSRDRLKMIQRLLRDhyreiAEEITRSLTESLQATIAAAQVA--ET 601
                                    4444.99999**************************************9877777777777887775555333322..22 PP

                       Cas_Csa4 333 lkkagvrldaelvdal 348
                                    +  + +r+ ++++++l
  gi|121636256|ref|YP_976479.1| 602 ERDNRIRELQRQLGIL 617
                                    2444466666666666 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.46   1.2e+03      16      77 ..     302     365 ..     294     373 .. 0.62
   2 ?   -1.6   0.7       1.2     3e+03      63      75 ..     351     363 ..     336     426 .. 0.63
   3 ?   11.6   0.5     9e-05      0.23       7      72 ..     558     623 ..     555     630 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.46
                         GCN5L1  16 qekakkeaiesaaaltealvdklnsgvaeayan..qkklekeakalqanvakfakqtdqWlalv 77 
                                    +e+ ++ ++ ++++ te+l  +l s+++ +       +l +++ + ++++++  +qt+ W ++ 
  gi|121636256|ref|YP_976479.1| 302 TERVRAGVLGEIRSATEQLAVSLGSELSVVNDPnlRDRLASDLERRKREAQQAVQQTALWQQVL 365
                                    5666666666666666666666666666655431145666666777777777777777777665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                         GCN5L1  63 vakfakqtdqWla 75 
                                    +++  +qt+ W +
  gi|121636256|ref|YP_976479.1| 351 AQQAVQQTALWQQ 363
                                    3333333333333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 9e-05
                         GCN5L1   7 akqaerreeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdq 72 
                                    +++ +++  q  ++++  e a+++t++l+++l++ +a+a + + + ++ +++lq+++  +++ +d+
  gi|121636256|ref|YP_976479.1| 558 QSRDRLKMIQRLLRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQLGILSQVNDN 623
                                    5667788899999*******************************************9988887766 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.57   1.5e+03      46      78 ..     251     283 ..     229     289 .. 0.69
   2 ?   10.2   0.4   0.00025      0.64      37      98 ..     299     359 ..     259     362 .. 0.75
   3 ?   -2.7   0.0       2.5   6.5e+03      34      51 ..     382     399 ..     370     421 .. 0.57
   4 ?    1.1   0.7      0.16   4.2e+02      31      99 ..     528     600 ..     513     610 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.57
                                    HHHHHHHHH....T-HHHHHHHHHHHHHHT-HHHHHH CS
                PEP-utilisers_N  46 elealaeka....lgeeeaaifeahlmlleDpellee 78 
                                    +l++++  +    +    +++++ h+  l+D+el ee
  gi|121636256|ref|YP_976479.1| 251 HLQRARVPMpiiaV----SSLLRSHAVTLNDKELNEE 283
                                    44444333344322....569999********99886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                                    HHHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHT--HHHHHHHHH CS
                PEP-utilisers_N  37 eeAlekvreelea.laekalgeeeaaifeahlmlleDpelleeveerIregglnaeaAveevv 98 
                                     +A e+vr+ +   ++ + + e+ a  +   l+ ++Dp+l++++ + ++ ++  a++Av++++
  gi|121636256|ref|YP_976479.1| 299 SRATERVRAGVLGeIR-S-ATEQLAVSLGSELSVVNDPNLRDRLASDLERRKREAQQAVQQTA 359
                                    4444444444433122.1.22223557889999***************************985 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.5
                                    HHHHHHHHHHHHHHHHHH CS
                PEP-utilisers_N  34 erleeAlekvreeleala 51 
                                    +r+++  e +++++++  
  gi|121636256|ref|YP_976479.1| 382 TRFRTVTEDAERQIDSCD 399
                                    466666666666666533 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHHHHHHHHHH...T-HHHHHHHHHHHHHHT-..HHHHHHHHHHHHHHT--HHHHHHHHHH CS
                PEP-utilisers_N  31 aelerleeAlekvreelealaeka...lgeeeaaifeahlmlleD..pelleeveerIregglnaeaAveevve 99 
                                    + ++rl + + ++++ +++  +++   +++++++ +++ + ll+D  +e++ee+++ ++ + l+a  A ++v+e
  gi|121636256|ref|YP_976479.1| 528 DKQNRLLRVRSEAKANVRRFVDDIsfvVSKQSRDRLKMIQRLLRDhyREIAEEITRSLT-ESLQATIAAAQVAE 600
                                    55667777777888888887777778766677889999999999955588999999998.66688888888877 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0023       5.8       8      38 ..      52      82 ..      50     107 .. 0.91
   2 ?    1.1   0.4      0.18   4.7e+02      27      66 ..     317     357 ..     303     362 .. 0.65
   3 ?    1.0   0.5       0.2   5.2e+02      34     110 ..     372     442 ..     356     444 .. 0.53
   4 ?    4.6   0.4     0.015        38       7      50 ..     570     613 ..     569     624 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
                      TetR_C_11  8 rgDLrallralaealaspragallrallaea 38
                                   rgDL++ l+++++ +++p+ + ++++ll + 
  gi|121636256|ref|YP_976479.1| 52 RGDLVQRLTRARQRITDPQVRVVIAGLLKQG 82
                                   9**************************9776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                      TetR_C_11  27 agallrallaea..qrdpelaealrerlleprraalravlrr 66 
                                    +++l  +l +e+   +dp l+++l    le+r++++++ +++
  gi|121636256|ref|YP_976479.1| 317 TEQLAVSLGSELsvVNDPNLRDRLAS-DLERRKREAQQAVQQ 357
                                    5555555555541157********99.666666666665554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.2
                      TetR_C_11  34 llaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgpllyrllltgeplddafaerlv 110
                                    l a++  d +l++++r+ ++e+  ++++     A+   e+   +dve ++++++g  + ++  + e+l d+ a++++
  gi|121636256|ref|YP_976479.1| 372 LTADV--DHDLRTRFRT-VTEDAERQIDSCDPTAHW-AEIG--NDVENAIATAVGDNFVWAYQRSEALADDVARSFA 442
                                    55555..5566666666.666666555544333332.2333..3555555555555555555555555555555555 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.015
                      TetR_C_11   7 lrgDLrallralaealaspragallrallaeaqrdpelaealre 50 
                                    lr+  r++++++ ++l++  ++ + +a +ae +rd +++e  r+
  gi|121636256|ref|YP_976479.1| 570 LRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQ 613
                                    55666788889999999999999999999999999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 4201.49
//
Query:       gi|121636257|ref|YP_976480.1|  [L=493]
Description: isoniazid inductible gene protein iniC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-09   38.7   0.0    9.5e-08   32.3   0.0    2.2  2  Dynamin_N    Dynamin family
    9.6e-07   28.9   0.0    2.4e-06   27.6   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.019   14.9   0.0       0.32   10.9   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
      0.054   13.0   0.0        1.1    8.7   0.0    2.2  2  FeoB_N       Ferrous iron transport protein B
      0.055   12.8   0.0        3.7    6.8   0.0    2.2  2  AIG1         AIG1 family
        0.1   12.4   0.9       0.23   11.3   0.9    1.6  1  BPS          BPS (Between PH and SH2)
       0.13   12.2   0.0       0.37   10.8   0.0    1.7  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.22   10.5   0.0       0.48    9.4   0.0    1.4  2  IIGP         Interferon-inducible GTPase (IIGP)


Domain annotation for each model (and alignments):
>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.3e-11   9.5e-08       1      47 [.      47      93 ..      47     110 .. 0.91
   2 ?    4.2   0.0     0.018        41     102     118 ..     138     154 ..     120     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.3e-11
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---C CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeas 47
                                   ia+ G+ ++GKS+++naL+g+di p++++  Tr ++  ++g +++++
  gi|121636257|ref|YP_976480.1| 47 IALAGTLKAGKSTLVNALVGDDIAPTDATEATRIVTWFRHGPTPRVT 93
                                   8999*************************************999976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                                    SEEEEE---B-SSSGTT CS
                      Dynamin_N 102 gltlvDlPGldsvnkrd 118
                                    + t+vD+PG  s +   
  gi|121636257|ref|YP_976480.1| 138 DATIVDTPGTSSLACDA 154
                                    679******99876555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.1e-09   2.4e-06       1      84 [.      46     179 ..      46     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.1e-09
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke................................. 47 
                                    ++a++G   +GKStL+nal+g+    +d   +Tr ++++r      +                                 
  gi|121636257|ref|YP_976480.1|  46 RIALAGTLKAGKSTLVNALVGDDIAPTDATEATRIVTWFRHGPT--Prvtanhrggrranvpitrrgglsfdlrrinpae 123
                                    699*******************999999999*******987622..1344555677788899999999999999999999 PP

                                    ...............EEEEECGGCSS...HHHHHH.HHHHHHHHHHCTSEEEEEEE CS
                       MMR_HSR1  48 ...............ielvDtpGlie...gaseek.glgkaflaleeadlillvvd 84 
                                                    ++vDtpG  +   +ase+  +l      + ++d+++++++
  gi|121636257|ref|YP_976480.1| 124 lidlevewpaeelidATIVDTPGTSSlacDASERTlRLLVPADGVPRVDAVVFLLR 179
                                    9999999999999999*******432333333333333333334556777777775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.32      91     129 ..      35      74 ..      19      81 .. 0.80
   2 ?    1.4   0.0      0.12   2.6e+02     152     164 ..     138     150 ..     132     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                    +++ ++l++   ++l+G   +GKStL+nal++++ + t +
  gi|121636257|ref|YP_976480.1|  35 DRIGARLAEpLRIALAGTLKAGKSTLVNALVGDDIAPTDA 74 
                                    5666667775567899***************997666655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                                    TEEEESS-SSSS- CS
                    RsgA_GTPase 152 gglliDtPGfrel 164
                                    +++++DtPG ++l
  gi|121636257|ref|YP_976480.1| 138 DATIVDTPGTSSL 150
                                    678******9987 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00051       1.1       2      23 ..      46      67 ..      45      70 .. 0.91
   2 ?    1.9   0.0     0.066   1.5e+02      48      67 ..     138     157 ..     128     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00051
                                   EEEEEESTTSSHHHHHHHHHTT CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                   ++al+G   +Gk+tl+nal g 
  gi|121636257|ref|YP_976480.1| 46 RIALAGTLKAGKSTLVNALVGD 67
                                   69*****************985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.066
                                    EEEEEE----SSSSSSSHHH CS
                         FeoB_N  48 eveivDlPGiYslsayseee 67 
                                    +++ivD PG+ sl   ++e 
  gi|121636257|ref|YP_976480.1| 138 DATIVDTPGTSSLACDASER 157
                                    578*********97666554 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.015        34       1      25 [.      45      69 ..      45      85 .. 0.84
   2 ?    6.8   0.0    0.0016       3.7      51     142 ..     139     228 ..     128     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.015
                                   EEEEEESSTTSSHHHHHHHHHTS-- CS
                           AIG1  1 ltivlvGktgnGkSaTgNsilgkka 25
                                   l+i l G   +GkS+ +N+++g+++
  gi|121636257|ref|YP_976480.1| 45 LRIALAGTLKAGKSTLVNALVGDDI 69
                                   5899*****************9876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                                    EEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEE.EEEEGGGG CS
                           AIG1  51 inViDTPglfdlsvsadkiskeivrclllseegihalllvlslgrfteedekalktlkelFGekilkyliv.vftrkddl 129
                                      ++DTPg  +l  +a+   +   r l  ++  + +  +v+ l+ +++ d ++lk++  l G ++    i+ v  r+d++
  gi|121636257|ref|YP_976480.1| 139 ATIVDTPGTSSLACDAS---ERTLRLLVPADGVPRVDAVVFLLRTLNAADVALLKQIGGLVGGSVGALGIIgVASRADEI 215
                                    579*****999987665...44455445555555666788999999*******************998776588899999 PP

                                    TTCCHHHHHHHHH CS
                           AIG1 130 eddsledylskss 142
                                    ++  ++ +ls ++
  gi|121636257|ref|YP_976480.1| 216 GAGRIDAMLSAND 228
                                    9999999999543 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9    0.0001      0.23      23      47 ..     443     467 ..     442     468 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                            BPS  23 NptEalsaaleegqaWRkksslRls 47 
                                    N +Ea  aal ++q WR++ ++ l+
  gi|121636257|ref|YP_976480.1| 443 NSREAPRAALAAAQHWRRRAAHPLN 467
                                    899****************998765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.37       7      40 ..      34      65 ..      31      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHH CS
                           TsaE  7 tealgkklakalgdvilLeGdLGaGKTtlvrgla 40
                                   ++++g++la+     i+L G L aGK+tlv +l+
  gi|121636257|ref|YP_976480.1| 34 LDRIGARLAE--PLRIALAGTLKAGKSTLVNALV 65
                                   5678999998..557***************9986 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00021      0.48      34      89 ..      43      93 ..      33      96 .. 0.90
   2 ?   -3.5   0.0       1.8     4e+03     227     255 ..     343     371 ..     339     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                                   --EEEEEEESTTSSHHHHHHHHTT--TTSTTS--SSCHSHHTS-EEEE-SS-TTEE CS
                           IIGP 34 aklkiavtGdsGnGkssFinaLRliGheeedsAptGvvettkkrtpYssskfPnvv 89
                                    +l+ia  G   +Gks+ +naL  +G   +d Apt + e t+  t +++   P+v+
  gi|121636257|ref|YP_976480.1| 43 EPLRIALAGTLKAGKSTLVNAL--VG---DDIAPTDATEATRIVTWFRHGPTPRVT 93
                                   6899*****************9..55...789*****************9999996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                                    HHS---SHHHHHHHHHHHHHHHHHHHHHT CS
                           IIGP 227 eslsnvtdkvieekreslkqkialealka 255
                                    + l nv+d+   ++ ++lk + al +l+ 
  gi|121636257|ref|YP_976480.1| 343 VALRNVIDQQFAQRSDMLKAHTALVSLRR 371
                                    67899999999999999999988877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3575.58
//
Query:       gi|121636258|ref|YP_976481.1|  [L=186]
Description: lipoprotein lpqJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          3    7.8   9.7        6.9    6.6   9.7    1.7  1  DUF3558   Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   9.7   0.00039       6.9       1      37 [.      18      54 ..      18      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00039
                        DUF3558  1 lllaGCssttdGtapaasssassssttsssaapav.pl 37
                                   +l+aGC +t+dG  p as+++ ++ +t ++++p++ p 
  gi|121636258|ref|YP_976481.1| 18 ALVAGCNTTIDGR-PVASPGSGPTEPTFPTPRPTTaPP 54
                                   68***********.444444444444444444444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1212.68
//
Query:       gi|121636259|ref|YP_976482.1|  [L=136]
Description: hypothetical protein BCG_0384 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-14   52.7   4.5    7.9e-14   52.3   4.5    1.2  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   4.5   4.4e-18   7.9e-14       1     114 [.       8     116 ..       8     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 4.4e-18
                                    EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaal 80 
                                    +v+LA+G+++ +g++K l++     +l+ ++ alr+ g+++v++v g+ ev    a+ gv+ ++ +d+++g +as++a+l
  gi|121636259|ref|YP_976482.1|   8 GVLLAAGAGRWYGKPKVLVD----GWLDTAVGALRDGGCNDVILVLGAVEVS---APAGVTAITAPDWQQGLSASVRAGL 80 
                                    79**************9995....69**********************9987...689********************** PP

                                    HHH...SSSCEEEEETT-TT--HHHHHHHHHCHHHH CS
                   NTP_transf_3  81 raaa..dadavlvlacDmPlltpelverllaaaaas 114
                                    ++a   +ad++++   D+P +++++v+r+l +a  s
  gi|121636259|ref|YP_976482.1|  81 AQADreHADYAVLHVIDTPDVNAKVVARVLGRALVS 116
                                    **77779**********************9988544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 929.97
//
Query:       gi|121636260|ref|YP_976483.1|  [L=487]
Description: l-asparagine permease ansP2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.4e-100  335.0  36.4   7.7e-100  334.7  36.4    1.0  1  AA_permease    Amino acid permease
    1.1e-37  129.9  35.8    1.3e-37  129.7  35.8    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.7  36.4  8.6e-104  7.7e-100       2     432 ..      27     435 ..      26     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: 334.7 bits;  conditional E-value: 8.6e-104
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                    +++ialgg+iGtglf+g g  l++aGp g++l+y ++g+++fl+ ++lge++ + p+sg+f  ya++f g++++fv G++
  gi|121636260|ref|YP_976483.1|  27 LQMIALGGAIGTGLFLGAGGRLASAGP-GLFLVYGICGIFVFLILRALGELVLHRPSSGSFVSYAREFYGEKVAFVAGWM 105
                                    79*************************.**************************************************** PP

                    AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiill 161
                                    y+++w+++ ++++ta++++ ++w  ++ +p +w  +++ l+v+l +nl++v+++ge ef+++lik+ia++ f+ivg ++l
  gi|121636260|ref|YP_976483.1| 106 YFLNWAMTGIVDTTAIAHYCHYWRAFQPIP-QWTLALIALLVVLSMNLISVRLFGELEFWASLIKVIALVTFLIVGTVFL 184
                                    ******************************.************************************************* PP

                    AA_permease 162 aggkpnkga..gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                    ag  + +g+  g++ ++++g+    ++p g        ++ ++ v + vvfa++ ielv+i+agE+++P+k +P+ai++v
  gi|121636260|ref|YP_976483.1| 185 AGRYKIDGQetGVSLWSSHGG----IVPTG--------LLPIVLVTSGVVFAYAAIELVGIAAGETAEPAKIMPRAINSV 252
                                    *******9999**********....99999........****************************************** PP

                    AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlysla 319
                                    v+ri+ fYv+s++l+ ll+p+++ +         spfv+f+++ g+ ++++++n+v+ltaalss+n++lys+ R+l s+a
  gi|121636260|ref|YP_976483.1| 253 VLRIACFYVGSTVLLALLLPYTAYKEHV------SPFVTFFSKIGIDAAGSVMNLVVLTAALSSLNAGLYSTGRILRSMA 326
                                    ***********************55444......9********************************************* PP

                    AA_permease 320 kdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgr 399
                                     +g  P++ + +sk gvP+ +ill++ i+ll+++l++++++  ++f+++l i+a   ++ w  i +++lr+ +   ++  
  gi|121636260|ref|YP_976483.1| 327 INGSGPRFTAPMSKTGVPYGGILLTAGIGLLGIILNAIKPS--QAFEIVLHIAATGVIAAWATIVACQLRLHRM--ANAG 402
                                    *****************************************..**************************99888..8888 PP

                    AA_permease 400 sieelgfkaallplgvilvlaaliiillilaly 432
                                    ++++ +f+++l p+  +l+la+l  +l+++ + 
  gi|121636260|ref|YP_976483.1| 403 QLQRPKFRMPLSPFSGYLTLAFLAGVLILMYFD 435
                                    8899***********************999876 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7  35.8   1.5e-41   1.3e-37       5     419 ..      26     447 ..      22     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 1.5e-41
                  AA_permease_2   5 safalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsaw 82 
                                    ++ ++++g +ig+g f     ++as+gp l+l++ i  + + +  l ++ El  + p+sg  ++y+++++g+kvaf+++w
  gi|121636260|ref|YP_976483.1|  26 QLQMIALGGAIGTGLFLGAggRLASAGPGLFLVYGICGIFV-FLILRALGELVLHRPSSGSFVSYAREFYGEKVAFVAGW 104
                                    667899**********9999999999998666554433333.45677999*9877************************* PP

                  AA_permease_2  83 fnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliil 162
                                    ++++ ++ +  + ++++a y+ + +   +q+  +++  +a + l++v  +n+++++  + + ++  ++k+ + l++++i+
  gi|121636260|ref|YP_976483.1| 105 MYFLNWAMTGIVDTTAIAHYCHY-WR-AFQP--IPQWTLALIALLVVLSMNLISVRLFGELEFWASLIKV-IALVTFLIV 179
                                    ********997777778888877.54.4544..3455556677777788899999999************.89999999* PP

                  AA_permease_2 163 glitvdgggfsslstetdt......ffpngwpg....vllgllivlwsfdGfesaanvseevkk..kdvpkaifiglliv 230
                                    g +++ g++  +    ++t      +++++ p+    ++l+ ++v+++++++e +   + e  +  k +p+ai++++l +
  gi|121636260|ref|YP_976483.1| 180 GTVFLAGRYKIDG---QETgvslwsSHGGIVPTgllpIVLVTSGVVFAYAAIELVGIAAGETAEpaKIMPRAINSVVLRI 256
                                    *****99999855...3333333223333333322225778888*****************5554477************ PP

                  AA_permease_2 231 lvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPr 310
                                    +++y++ +++++  +p    ++    +s++  ff + g +++ +++++++  ++l ++n+ ++++ r+l+++a  g  Pr
  gi|121636260|ref|YP_976483.1| 257 ACFYVGSTVLLALLLPYTAYKE--H-VSPFVTFFSKIGIDAAGSVMNLVVLTAALSSLNAGLYSTGRILRSMAINGSGPR 333
                                    ****************988874..3.35799************************************************* PP

                  AA_permease_2 311 ffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigal.ilrkkrphl.krpgk.ilv 387
                                    f a ++k+g p+++i lta + l+ ++l ++ +s a+ ++l +++ g+i  ++ ++++ l ++r+ +  + +rp++ +++
  gi|121636260|ref|YP_976483.1| 334 FTAPMSKTGVPYGGILLTAGIGLLGIILNAIKPSQAFEIVLHIAATGVIAAWATIVACQLrLHRMANAGQlQRPKFrMPL 413
                                    **********************88888888888**********************8888879999999666664444444 PP

                  AA_permease_2 388 aiig.alfllfllvalf.fppkgpatqssliyti 419
                                    + ++  l+l fl  +l+ ++ ++++ +  ++ t+
  gi|121636260|ref|YP_976483.1| 414 SPFSgYLTLAFLAGVLIlMYFDEQHGPWMIAATV 447
                                    4444355555554333303345555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3209.62
//
Query:       gi|121636261|ref|YP_976484.1|  [L=328]
Description: hypothetical protein BCG_0386 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2476.52
//
Query:       gi|121636262|ref|YP_976485.1|  [L=217]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00043   20.0   0.4     0.0015   18.2   0.1    2.0  2  HTH_23     Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.021   14.9   0.0    1.5  1  HTH_3      Helix-turn-helix
      0.033   14.3   0.1      0.084   13.0   0.1    1.8  1  HTH_28     Helix-turn-helix domain
      0.047   14.0   0.0        0.1   12.9   0.0    1.5  1  HTH_Tnp_1  Transposase
      0.054   13.9   1.5        2.1    8.8   0.9    2.9  2  HTH_31     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.3e-07    0.0015       9      40 ..      79     111 ..      70     120 .. 0.85
   2 ?   -1.3   0.0      0.59   2.1e+03       5      15 ..     117     127 ..     114     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-07
                         HTH_23   9 rillllae.GlsvreIAreLgvsrrTvyrwlkr 40 
                                    ++l  la+ G  +r+IAr  gvs   + +w+k 
  gi|121636262|ref|YP_976485.1|  79 HALEQLADyGFAWRDIARVVGVSVPAITKWRKG 111
                                    46677777***********************95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                         HTH_23   5 reRlrilllla 15 
                                    ++Rl+i++lla
  gi|121636262|ref|YP_976485.1| 117 ENRLKIARLLA 127
                                    57889988886 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.8e-06     0.021       9      49 ..      88     127 ..      81     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.8e-06
                                    THHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                          HTH_3   9 glsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                    g   +++A+++Gvs+ +i+++ +G +  + e+ +k+a+ L 
  gi|121636262|ref|YP_976485.1|  88 GFAWRDIARVVGVSVPAITKWRKG-AGVTGENRLKIARLLA 127
                                    566789******************.6699999999999875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.3e-05     0.084       4      44 ..      79     120 ..      78     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                         HTH_28   4 eiikllaa.GhsvreaArelgisrrtvyrWikryeegGiagL 44 
                                    +++++la+ G + r++Ar +g+s   + +W+k     G++ L
  gi|121636262|ref|YP_976485.1|  79 HALEQLADyGFAWRDIARVVGVSVPAITKWRKGAGVTGENRL 120
                                    67888888677********************98777777666 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05       0.1      15      61 ..      80     126 ..      78     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                      HTH_Tnp_1  15 iVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspaefelt 61 
                                    ++++  + g+  +++Ar  gvs  +  kWr+ +   ge  +++  +l+
  gi|121636262|ref|YP_976485.1|  80 ALEQLADYGFAWRDIARVVGVSVPAITKWRKGAGvTGENRLKIA-RLL 126
                                    67788899***********************9965555555555.555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9   0.00057       2.1      13      56 ..      75     128 ..      51     134 .. 0.75
   2 ?    2.0   0.0     0.073   2.6e+02      23      41 ..     149     167 ..     145     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00057
                         HTH_31  13 a............GLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                    +            G   ++ A+ +gvs+  ++++  G+   ++ +   ++ar+l l
  gi|121636262|ref|YP_976485.1|  75 CapmhaleqladyGFAWRDIARVVGVSVPAITKWRKGAG--VTGENRLKIARLLAL 128
                                    16666666666666666899****************999..788888888888875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.073
                         HTH_31  23 rlgvsestlsrlEqGrrgr 41 
                                    ++gv  +++  lE+Gr ++
  gi|121636262|ref|YP_976485.1| 149 QAGVGITRMDLLERGRYDL 167
                                    68999***********874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1648.11
//
Query:       gi|121636263|ref|YP_976486.1|  [L=219]
Description: hypothetical protein BCG_0388 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1533.59
//
Query:       gi|121636264|ref|YP_976487.1|  [L=625]
Description: molecular chaperone DnaK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-247  823.1  14.5   1.6e-219  730.1   7.8    2.0  2  HSP70     Hsp70 protein
    1.5e-16   60.2   0.9    4.8e-16   58.5   0.9    1.8  1  MreB_Mbl  MreB/Mbl protein
    5.8e-05   22.5   0.1       0.22   10.7   0.0    2.6  2  StbA      StbA protein
  ------ inclusion threshold ------
      0.015   15.7   5.5         19    5.7   0.0    4.0  3  FtsA      Cell division protein FtsA
       0.45    9.7   6.7          1    8.5   6.7    1.6  1  ISG65-75  Invariant surface glycoprotein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.3   7.9e-32   2.8e-28       1      74 [.       4      78 ..       4      81 .. 0.97
   2 !  730.1   7.8  4.5e-223  1.6e-219     102     599 .]      80     583 ..      77     583 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 7.9e-32
                                   EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTT CS
                          HSP70  1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfs 74
                                   ++GiDLGttnsvv+v+egg++ v+an+eg+rttPs+vaF+++ e lvG++Ak+qavtn+++tv svKr++G ++s
  gi|121636264|ref|YP_976487.1|  4 AVGIDLGTTNSVVSVLEGGDPVVVANSEGSRTTPSIVAFARNgEVLVGQPAKNQAVTNVDRTVRSVKRHMGSDWS 78
                                   59**********************************************************************987 PP

  == domain 2  score: 730.1 bits;  conditional E-value: 4.5e-223
                                    EETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCC CS
                          HSP70 102 eaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldk 181
                                    e+ g+k+t+ +isa++L+klk++aeaylg+++tdavit PaYfndaqRqatkdAg+iAGLnvlRivNepTAaalaYGldk
  gi|121636264|ref|YP_976487.1|  80 EIDGKKYTAPEISARILMKLKRDAEAYLGEDITDAVITTPAYFNDAQRQATKDAGQIAGLNVLRIVNEPTAAALAYGLDK 159
                                    5679**************************************************************************** PP

                                    SSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHH CS
                          HSP70 182 kdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaae 261
                                     +ke+ +lv+DlGggtfdvS+le+++Gv+ev+aT+gD+hlGG+d+D+++v++lv++fk ++gidl+kdk+a+qrl+eaae
  gi|121636264|ref|YP_976487.1| 160 GEKEQRILVFDLGGGTFDVSLLEIGEGVVEVRATSGDNHLGGDDWDQRVVDWLVDKFKGTSGIDLTKDKMAMQRLREAAE 239
                                    ******************************************************************************** PP

                                    HHHHHTTTSSCSEEEEEEEEEETTT..EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGS CS
                          HSP70 262 kaKkeLSsskqteinleietvdedg..kdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvGGstRi 339
                                    kaK+eLSss++t+inl+++tvd+d+    l+e+l+Ra+f+++++dll+rt +p++++++d++++++eid+vvlvGGstR+
  gi|121636264|ref|YP_976487.1| 240 KAKIELSSSQSTSINLPYITVDADKnpLFLDEQLTRAEFQRITQDLLDRTRKPFQSVIADTGISVSEIDHVVLVGGSTRM 319
                                    ***********************8777889************************************************** PP

                                    HHHHHHHHHHTT.CHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEE CS
                          HSP70 340 Pkvqelvkelfg.kepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkks 418
                                    P+v++lvkel+g kep+k+vnpDe+va+GAA+qagvl+g  evkd+lllDvtpLslgiet+ggvmt+liernttiptk+s
  gi|121636264|ref|YP_976487.1| 320 PAVTDLVKELTGgKEPNKGVNPDEVVAVGAALQAGVLKG--EVKDVLLLDVTPLSLGIETKGGVMTRLIERNTTIPTKRS 397
                                    ***********99**************************..*************************************** PP

                                    EEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEEC CS
                          HSP70 419 qvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitiea 498
                                    ++f+ta+dnq++v+i+v+qgere++++nkllgsfel+gippaprG pqieVtfdidanGi++v+akdk+tgke++i+i++
  gi|121636264|ref|YP_976487.1| 398 ETFTTADDNQPSVQIQVYQGEREIAAHNKLLGSFELTGIPPAPRGIPQIEVTFDIDANGIVHVTAKDKGTGKENTIRIQE 477
                                    ******************************************************************************** PP

                                    CSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....GGGSTHHHHHHHHHHHHHHHCHTTS CS
                          HSP70 499 seglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee.....aekvseaekekvesaieeLkeelee 573
                                     +gls+e+i++m+kdae++aeed+k++e+++ +n+ae+lvy++ek ++e+     ++kv+e++ +kv++a++e k++l +
  gi|121636264|ref|YP_976487.1| 478 GSGLSKEDIDRMIKDAEAHAEEDRKRREEADVRNQAETLVYQTEKFVKEQreaegGSKVPEDTLNKVDAAVAEAKAALGG 557
                                    *************************************************988887889999999**************** PP

                                    SCHHHHHHHHHHHHHHHHHHHHHHHH CS
                          HSP70 574 eekeeieakteelkkvvekiaeklye 599
                                    +++++i++++e+l ++++++++++ye
  gi|121636264|ref|YP_976487.1| 558 SDISAIKSAMEKLGQESQALGQAIYE 583
                                    *********************99985 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.9   1.3e-19   4.8e-16       3     315 ..       4     349 ..       2     357 .. 0.71

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.3e-19
                                    EEEEEE-SSEEEEEETTTE..EEEEE.......ES-EEEETTT--EEEESHHHHT.TTTS-GTTEEEE.-SE.ETTEES. CS
                       MreB_Mbl   3 dlgiDLGtantlvyvkgkg..ivlne.......psvvAikkktkkvlavGeeAkk.mlgktpgnikav.rPl.kdGvia. 69 
                                     +giDLGt+n +v v + g  +v+ +       ps+vA+ ++ +    vG+ Ak+  +    ++++ v r + +d  i+ 
  gi|121636264|ref|YP_976487.1|   4 AVGIDLGTTNSVVSVLEGGdpVVVANsegsrttPSIVAFARNGEV--LVGQPAKNqAVTNVDRTVRSVkRHMgSDWSIEi 81 
                                    69**********987655533555322333444999999877554..478888752455566666554144522333322 PP

                                    .SHHH.HHHHHHHHHHHHHT....SS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTS CS
                       MreB_Mbl  70 .dlev.aeellkyfikkvkk....kkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpvee 143
                                       ++ a e+  +++ k+k+          +  vi++P   ++ +r+A k+a + aG +   +++ep aAA+  gl+  e
  gi|121636264|ref|YP_976487.1|  82 dGKKYtAPEISARILMKLKRdaeaYLGEDITDAVITTPAYFNDAQRQATKDAGQIAGLNVLRIVNEPTAAALAYGLDKGE 161
                                    122221223333444444442200333466788********************************************987 PP

                                    SS-E.EEEEE-SS-EEEEEEETT.EEEEEEEE....S-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHH CS
                       MreB_Mbl 144 psgn.mvvdiGggttevavislg.givtsksv....rvaGdeldeaiikyirkkynlliGertaekikieigsavkeeee 217
                                     +   +v d+Gggt +v+++ +g g+v+ ++     +++Gd++d+ +++++  k++ + G   +++ k+++  + + +e+
  gi|121636264|ref|YP_976487.1| 162 KEQRiLVFDLGGGTFDVSLLEIGeGVVEVRATsgdnHLGGDDWDQRVVDWLVDKFKGTSGIDLTKD-KMAMQRLREAAEK 240
                                    76542789**************9456655544233379******************9999887654.8889999999999 PP

                                    HEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHH..HHHHHHHHHTS-HHHHHHHHHH-E........EEESGGGGSB CS
                       MreB_Mbl 218 ekmeikGrdlvtglpkevevsseevrealkepvsai..veavkevLektppeLaadivdrgi........vltGGgallk 287
                                     k+e++  + ++     ++v++++    l e++++       +  L++t     + i+d gi        vl+GG++ + 
  gi|121636264|ref|YP_976487.1| 241 AKIELSSSQSTSINLPYITVDADKNPLFLDEQLTRAefQRITQDLLDRTRKPFQSVIADTGIsvseidhvVLVGGSTRMP 320
                                    99999988777666667999999999999999876421455677899999999999999997444444447889999999 PP

                                    THHHHHHHHHSS-.EEE-SSTTTHHHHHH CS
                       MreB_Mbl 288 gldkllseetglp.vkvaedpltcvakGt 315
                                     + +l++e tg +  + + +p ++va G+
  gi|121636264|ref|YP_976487.1| 321 AVTDLVKELTGGKePNKGVNPDEVVAVGA 349
                                    99999988886541455667777777776 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0001      0.37     157     228 ..     158     233 ..     127     254 .. 0.69
   2 !   10.7   0.0   6.1e-05      0.22     214     293 ..     249     330 ..     199     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                           StbA 157 keldeleslLiiDlGGttLDvak..vrgklegiskvkgdskiGvslitdavkealet..aktrtssfladeliknr 228
                                    ++ ++ ++ L+ DlGG t Dv+   +   + ++  + gd+++G     + v + l    + t +   + d++  +r
  gi|121636264|ref|YP_976487.1| 158 DKGEKEQRILVFDLGGGTFDVSLleIGEGVVEVRATSGDNHLGGDDWDQRVVDWLVDkfKGTSGIDLTKDKMAMQR 233
                                    445778899************9711445677788888999999887777777766542334444445555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.1e-05
                           StbA 214 trtssfladeliknrkdeeyLkrrindedkresvlevinekvkkLkerviravsefsgythvmvvGGGael..iaeaikk 291
                                      ts  l    +++ k+  +L ++++ ++ +    + +++  k  ++ + ++  ++s++ hv++vGG + +  +++ +k+
  gi|121636264|ref|YP_976487.1| 249 QSTSINLPYITVDADKNPLFLDEQLTRAEFQRITQDLLDRTRKPFQSVIADTGISVSEIDHVVLVGGSTRMpaVTDLVKE 328
                                    33333333445778888899**9999999999999999999999********9**************9987557777777 PP

                           StbA 292 at 293
                                     t
  gi|121636264|ref|YP_976487.1| 329 LT 330
                                    66 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0093        33       1      22 [.       5      26 ..       5      47 .. 0.86
   2 ?    5.7   0.0    0.0054        19       4      87 ..     170     334 ..     167     350 .. 0.56
   3 ?    4.6   0.6     0.012        43      17      85 ..     464     570 ..     450     600 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0093
                                   EEEEE-SSSEEEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                           FtsA  1 alvDiGagktdvavaedgalvh 22
                                   +++D+G++ + v+v+e+g +v 
  gi|121636264|ref|YP_976487.1|  5 VGIDLGTTNSVVSVLEGGDPVV 26
                                   68***************98775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0054
                                    EE-SSSEEEEEEETTEEEE.................EEEES-........-HHHHHHH..HHHHHT--HHHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxx.................xxxxxx........xxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                           FtsA   4 DiGagktdvavaedgalvh.................lrvigv........ggngitkd..iakalrtaveeAerikikyG 56 
                                    D+G+g+ dv+++e g+ v                   rv+           g  +tkd  +   ++   e+Ae+ ki+  
  gi|121636264|ref|YP_976487.1| 170 DLGGGTFDVSLLEIGEGVVevratsgdnhlggddwdQRVVDWlvdkfkgtSGIDLTKDkmA---MQRLREAAEKAKIELS 246
                                    7777777777777765222223333333333444443333333333343355555666444...4555566677776555 PP

                                    -S--...................EEEEEHHHHH...........................................GGGG CS
                                    xxxx...................xxxxxxxxxx...........................................xxxx RF
                           FtsA  57 sala...................ekeigrkels...........................................ggsa 74 
                                    s  +                   +        +                                           g++ 
  gi|121636264|ref|YP_976487.1| 247 SSQStsinlpyitvdadknplflD--------EqltraefqritqdlldrtrkpfqsviadtgisvseidhvvlvgGSTR 318
                                    555455555666555555555552........044444444566666667778888888888888888889999999999 PP

                                    STTHHHHHHHHH...T CS
                                    xxxxxxxxxxxx...x RF
                           FtsA  75 lpnleelaeral...s 87 
                                    +p +++l+++ +   +
  gi|121636264|ref|YP_976487.1| 319 MPAVTDLVKELTggkE 334
                                    9999999988864443 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.012
                                    TTEEEEEEEES-.-HHHHHHH.HHHHHT--HHHHHHHHHHH--S--..............EEEEEHHHHH.......... CS
                                    xxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxx.......... RF
                           FtsA  17 dgalvhlrvigv.ggngitkd.iakalrtaveeAerikikyGsala..............ekeigrkels.......... 70 
                                    d++  + ++i + +g+g++k+ i ++++ a + Ae+  ++   a                         +          
  gi|121636264|ref|YP_976487.1| 464 DKGTGKENTIRIqEGSGLSKEdIDRMIKDAEAHAEEDRKRREEADVrnqaetlvyqtekfV--------Keqreaeggsk 535
                                    4445556677777666666655************998854434333444554444544440........04444454444 PP

                                    ....................GGGGSTTHHHHHHHH CS
                                    ....................xxxxxxxxxxxxxxx RF
                           FtsA  71 ....................ggsalpnleelaera 85 
                                                        ggs +  ++ ++e+ 
  gi|121636264|ref|YP_976487.1| 536 vpedtlnkvdaavaeakaalGGSDISAIKSAMEKL 570
                                    54555557777788888888888888877777776 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.7   0.00029         1      48     144 ..     491     595 ..     484     604 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00029
                       ISG65-75  48 reetadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkak........nkkareka 119
                                    + ++a    ++ ++++a + n+ e + y++ek+ +  +ea++ ++  e++ +k++ a++eAka+        +k+a ek 
  gi|121636264|ref|YP_976487.1| 491 KDAEAHAEEDRKRREEADVRNQAETLVYQTEKFVKEQREAEGGSKVPEDTLNKVDAAVAEAKAAlggsdisaIKSAMEKL 570
                                    44555556667788999*********************************************863333333367788888 PP

                       ISG65-75 120 kkalekaekaskkakeaakkAlGee 144
                                     ++ ++  +a+ +a++aa++A G+ 
  gi|121636264|ref|YP_976487.1| 571 GQESQALGQAIYEAAQAASQATGAA 595
                                    8888888899999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 4479.44
//
Query:       gi|121636265|ref|YP_976488.1|  [L=235]
Description: heat shock protein GrpE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-30  104.9   0.0    5.2e-30  104.3   0.0    1.3  1  GrpE             GrpE
    0.00093   18.2   0.6     0.0013   17.7   0.6    1.2  1  DUF3375          Protein of unknown function (DUF3375)
  ------ inclusion threshold ------
      0.037   13.8   0.1      0.051   13.3   0.1    1.2  1  FAM184           Family with sequence similarity 184, A and B
      0.046   13.6   0.1       0.12   12.3   0.1    1.7  1  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   1.2e-33   5.2e-30      20     165 ..      47     187 ..      17     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 1.2e-33
                                    CTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC...HHH-HHHHHHHHHHH CS
                           GrpE  20 eleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksak.eneeekslleGvemt 98 
                                    + +  e++v+el+ +l+r +a+f n+rkr+ +++++a++ a+ +++ +LL vlD+lera k+   e+         ++ +
  gi|121636265|ref|YP_976488.1|  47 DAAHTEDKVAELTADLQRVQADFANYRKRALRDQQAAADRAKASVVSQLLGVLDDLERARKHGDlESG-------PLKSV 119
                                    5667899******************************************************9532222.......26789 PP

                                    HHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC....TBEEEEEE--EEETTEEEE-EEEEEE CS
                           GrpE  99 lkqllkiLekhgvekiepkgepFDpnlheavstveddekee.gtvvevvqkGYklkdrvlRpAmVkVs 165
                                    +++l+++L   g++ + ++ge+FDp lheav+++ d  + +   +  v+++GY+l+++vlR+A V+V+
  gi|121636265|ref|YP_976488.1| 120 ADKLDSALTGLGLVAFGAEGEDFDPVLHEAVQHEGDGGQGSkPVIGTVMRQGYQLGEQVLRHALVGVV 187
                                    99**********************************99666267779*******************97 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.6     3e-07    0.0013     147     227 ..      21     102 ..      18     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-07
                        DUF3375 147 iaeidaeidrlrageveelddeqvlerireilnlareLpaDFrrVeeefrel.drelreriaeeegskgevLeevlegyd 225
                                    +++id e  ++r+     +   ++   + +  + ++eL+aD+ rV+++f +  +r+lr++ a+++++k  v+ ++l+  d
  gi|121636265|ref|YP_976488.1|  21 KRRIDPETGEVRHVPPGDMPGGTAAADAAHTEDKVAELTADLQRVQADFANYrKRALRDQQAAADRAKASVVSQLLGVLD 100
                                    667777777777744444555555555666788899*************9973589******************998766 PP

                        DUF3375 226 al 227
                                     l
  gi|121636265|ref|YP_976488.1| 101 DL 102
                                    65 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.051      88     136 ..      44     101 ..      38     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                         FAM184  88 lkleaehs.qkvvelsreveevkrkFee.klrqfaqlqeqleqekeka.......Lee 136
                                    +++ a+h+ +kv+el ++++ v+++F + + r++ ++q+++++ k++        L++
  gi|121636265|ref|YP_976488.1|  44 AAADAAHTeDKVAELTADLQRVQADFANyRKRALRDQQAAADRAKASVvsqllgvLDD 101
                                    6677778626****************86588999999999999998884444444444 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.7e-05      0.12       7      30 ..      54      77 ..      49      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                Surfac_D-trimer  7 rveaLeGklqrLqnafsqYkKavL 30
                                   +v  L   lqr q+ f+ Y+K +L
  gi|121636265|ref|YP_976488.1| 54 KVAELTADLQRVQADFANYRKRAL 77
                                   7889999**************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1793.44
//
Query:       gi|121636266|ref|YP_976489.1|  [L=395]
Description: chaperone protein DnaJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-37  126.9   0.0    1.6e-36  125.6   0.0    1.6  1  DnaJ_C           DnaJ C terminal domain
    7.7e-25   86.8   0.1    1.2e-24   86.2   0.1    1.3  1  DnaJ             DnaJ domain
    5.5e-13   49.1  15.0    8.8e-13   48.4  15.0    1.3  1  DnaJ_CXXCXGXG    DnaJ central domain
    4.3e-06   26.6  15.5    0.00089   19.2   4.6    2.6  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
  ------ inclusion threshold ------
        1.1    9.6   5.5         12    6.4   5.5    2.4  1  Lar_restr_allev  Restriction alleviation protein Lar
        2.4    8.4  19.1        1.1    9.5   4.0    4.1  3  DUF5351          Family of unknown function (DUF5351)


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   5.3e-40   1.6e-36       2     148 .]     151     362 ..     150     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 5.3e-40
                                    EEEEEE-HHHHHH-.EEE.EEEE......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                         DnaJ_C   2 eveleisleelykGktkkikikrnvi...................................................... 27 
                                    e+e e+++ e++kG+   ++++                                                          
  gi|121636266|ref|YP_976489.1| 151 ETETELDFVEAAKGVAMPLRLTSPAPctnchgsgarpgtspkvcptcngsgvinrnqgafgfsepctdcrgsgsiiehpc 230
                                    78999*************9998877799999************************************************* PP

                                    ............TEEEEEE-TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  28 ........kkekktlevkipaGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyveveislaeallG 97 
                                            +++++t++v+ip+G++dgq+irl+g+G+   +g+++GDl+v ++v+p+++F r+g+dl v+v++s++e +lG
  gi|121636266|ref|YP_976489.1| 231 eeckgtgvTTRTRTINVRIPPGVEDGQRIRLAGQGEagLRGAPSGDLYVAVHVRPDKIFGRDGDDLTVTVPVSFTELALG 310
                                    ******9877777**********************955444*************************************** PP

                                    EEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  98 gklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                     +l+vptldg+v +++   t  g++lr++g+G+pk   +g+ Gdl+v+vkv++P
  gi|121636266|ref|YP_976489.1| 311 STLSVPTLDGTVGVRVpkgTADGRILRVRGRGVPKR--SGGSGDLLVTVKVAVP 362
                                    **************99999****************9..7*************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.1   3.9e-28   1.2e-24       1      63 []      10      72 ..      10      72 .. 0.99

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.9e-28
                                   HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   d+Y+ Lgvs+das +eIk+aYrkla+ +HPD np++p a e+Fk ++eA++vLsdp kRk+YD
  gi|121636266|ref|YP_976489.1| 10 DFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAAGERFKAVSEAHNVLSDPAKRKEYD 72
                                   79************************************************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4  15.0   2.9e-16   8.8e-13       1      67 []     177     237 ..     177     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.9e-16
                  DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                    C++C+Gsga++g+ +k C+tC+GsGv++++q   g f   ++++C++C+G+G++i  +++C++CkG+g
  gi|121636266|ref|YP_976489.1| 177 CTNCHGSGARPGTsPKVCPTCNGSGVINRNQ---GAFG--FSEPCTDCRGSGSII--EHPCEECKGTG 237
                                    **********9776999********877776...2322..468************..889******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.6     3e-07   0.00089      12      47 ..     176     208 ..     173     210 .. 0.90
   2 !   12.4   3.1   3.8e-05      0.11      11      42 ..     214     239 ..     211     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-07
                                    E-TTTTTTSEETTE......E-TTTTTSSEEE-HHH CS
                      Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkglipTaqG 47 
                                    +C +C+gsG  +++ p     CP C+G g+i  +qG
  gi|121636266|ref|YP_976489.1| 176 PCTNCHGSGARPGTSP---KVCPTCNGSGVINRNQG 208
                                    8*************55...57**********99998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.8e-05
                                    EE-TTTTTTSEETTE......E-TTTTTSSEE CS
                      Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                    ++C  C gsG i         +C +C+G g+ 
  gi|121636266|ref|YP_976489.1| 214 EPCTDCRGSGSIIEH------PCEECKGTGVT 239
                                    79***********99......********985 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.5    0.0039        12       4      36 ..     192     221 ..     190     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0039
                Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyCadCga 36 
                                    k CP C+g +v+ r+q+     ++   C+dC  
  gi|121636266|ref|YP_976489.1| 192 KVCPTCNGSGVINRNQGAFGFSEP---CTDCRG 221
                                    67****************998555...555544 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.7     0.077   2.3e+02      20      28 ..     177     185 ..     176     186 .. 0.86
   2 ?    9.5   4.0   0.00037       1.1       1      28 [.     194     224 ..     194     225 .. 0.90
   3 ?    4.6   0.9     0.012        36      20      28 ..     230     238 ..     228     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.077
                        DUF5351  20 CesCeGtgk 28 
                                    C+ C+G+g 
  gi|121636266|ref|YP_976489.1| 177 CTNCHGSGA 185
                                    999999995 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00037
                        DUF5351   1 CpYCeGkGYf...qLlLGGSETCesCeGtgk 28 
                                    Cp C+G G +   q + G SE C+ C G+g+
  gi|121636266|ref|YP_976489.1| 194 CPTCNGSGVInrnQGAFGFSEPCTDCRGSGS 224
                                    999*****98666899*************96 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.012
                        DUF5351  20 CesCeGtgk 28 
                                    Ce+C+Gtg+
  gi|121636266|ref|YP_976489.1| 230 CEECKGTGV 238
                                    *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3083.12
//
Query:       gi|121636267|ref|YP_976490.1|  [L=126]
Description: heat shock protein transcriptional regulator HspR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-17   62.4   0.0    5.5e-17   61.6   0.0    1.3  1  MerR_1      MerR HTH family regulatory protein
    2.6e-11   43.1   0.4    4.4e-11   42.3   0.4    1.4  1  MerR        MerR family regulatory protein
    3.9e-07   29.8   0.2    4.6e-07   29.6   0.2    1.1  1  MerR_2      MerR HTH family regulatory protein
    0.00076   19.2   0.2     0.0012   18.6   0.2    1.3  1  Lebercilin  Ciliary protein causing Leber congenital amaurosi
  ------ inclusion threshold ------
      0.029   14.7   0.1       0.14   12.5   0.3    1.8  2  CCDC-167    Coiled-coil domain-containing protein 167
       0.64   10.4   4.6       0.41   11.1   0.4    2.3  2  DASH_Hsk3   DASH complex subunit Hsk3 like
        1.8    9.0   6.1         19    5.7   6.1    2.4  1  LPP         Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   2.2e-20   5.5e-17       3      67 ..      15      80 ..      13      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.2e-20
                                   HHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHHHHHHHHH.TT--GGG---XXX CS
                         MerR_1  3 igevakilgvtthtlrywekegllkpkrteggrryYtdedierLklikyLlk.rGltlkgikklln 67
                                   i+ +a+++g+ + tlr +++ gl+ p rt+gg r+Y+ +d+e L+++++L + +G++l+gik++++
  gi|121636267|ref|YP_976490.1| 15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQdEGVNLAGIKRIIE 80
                                   8889************************99999******************************985 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.4   1.7e-14   4.4e-11       2      38 .]      15      50 ..      14      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.7e-14
                                   HHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEEE CS
                           MerR  2 IgevAeltGvsprtLRyYEreGLipppeRtegGyRlY 38
                                   I+ +Ael+G++++tLR Y+r GL+ +p+Rt+gG R+Y
  gi|121636267|ref|YP_976490.1| 15 ISVAAELAGMHAQTLRTYDRLGLV-SPRRTSGGGRRY 50
                                   899*********************.***********9 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.2   1.8e-10   4.6e-07       8      82 ..      20      95 ..      13      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.8e-10
                         MerR_2  8 ertgieeeflieLvelgliepeiee.eewyfdesqlarlekavRLqrDLeinleGiavildLLdrieqLqrelesL 82
                                   e  g +++ l +   lgl++p++++   ++ + ++++ l+++++L +D ++nl+Gi+ i++L  ++e+Lq++l+++
  gi|121636267|ref|YP_976490.1| 20 ELAGMHAQTLRTYDRLGLVSPRRTSgGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSRLQEM 95
                                   5667788888999999*****877747888*******************************************987 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   4.6e-07    0.0012       8      45 ..      73     110 ..      67     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.6e-07
                     Lebercilin   8 arllkikeLqnelaelqskleelrkEnklLkrlqkrqe 45 
                                    a  ++i eL+++++ lqs+l+e+ +E+ +L++ q+r  
  gi|121636267|ref|YP_976490.1|  73 AGIKRIIELTSQVEALQSRLQEMAEELAVLRANQRREV 110
                                    677899*****************************975 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.67   1.7e+03       1      23 [.      16      38 ..      12      44 .. 0.84
   2 ?   12.5   0.3   5.5e-05      0.14      19      71 ..      51     112 ..      47     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.67
                       CCDC-167  1 svaseIdkleeklascrerLeav 23
                                   sva e+ ++  +++++++rL  v
  gi|121636267|ref|YP_976490.1| 16 SVAAELAGMHAQTLRTYDRLGLV 38
                                   68999999999999999999766 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.5e-05
                       CCDC-167  19 rLeaverrlrkeelseee.........ResleeEeaslkeqleenekeLksLrkeNrksmll 71 
                                    +L +ve   + ++ls++e           +l+   ++l+++l+e  +eL+ Lr   r+++++
  gi|121636267|ref|YP_976490.1|  51 SLHDVELLRQVQHLSQDEgvnlagikrIIELTSQVEALQSRLQEMAEELAVLRANQRREVAV 112
                                    56666666666667777755555554223566999**********************99987 PP

>> DASH_Hsk3  DASH complex subunit Hsk3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3      0.34   8.7e+02       2       9 ..      59      66 ..      58      67 .. 0.89
   2 ?   11.1   0.4   0.00016      0.41       7      27 ..      81     101 ..      78     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.34
                      DASH_Hsk3  2 RqyshLas 9 
                                   Rq +hL++
  gi|121636267|ref|YP_976490.1| 59 RQVQHLSQ 66
                                   9*****86 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                      DASH_Hsk3   7 LasqLaqLqaNLadteellev 27 
                                    L sq++ Lq++L+++ e+l v
  gi|121636267|ref|YP_976490.1|  81 LTSQVEALQSRLQEMAEELAV 101
                                    89**************99986 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.1    0.0075        19       4      41 ..      80     105 ..      54     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0075
                            LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaakeEAaRAN 41 
                                    eL+sqV++L+s  ++++++++ ++a            N
  gi|121636267|ref|YP_976490.1|  80 ELTSQVEALQSRLQEMAEELAVLRA------------N 105
                                    5666666666666666666555544............3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      897  (0.0500307); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 938.87
//
Query:       gi|121636268|ref|YP_976491.1|  [L=3507]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1035.3 1718.7    1.8e-10   40.5  23.0   70.7 76  Pentapeptide_2  Pentapeptide repeats (8 copies)
    4.6e-58  195.8  28.3    8.3e-58  195.0  28.3    1.4  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  23.0   5.3e-10   4.8e-06       7      40 .]     196     229 ..     194     229 .. 0.77
   2 !   27.2  27.2     3e-10   2.7e-06       1      36 [.     210     245 ..     210     248 .. 0.89
   3 !   25.7  32.8   8.8e-10   7.9e-06       2      40 .]     252     290 ..     251     290 .. 0.97
   4 !   24.9  31.1   1.5e-09   1.4e-05       3      40 .]     295     332 ..     293     332 .. 0.97
   5 !   39.2  25.1   5.2e-14   4.6e-10       2      40 .]     335     373 ..     334     373 .. 0.98
   6 !   32.1  23.5   8.8e-12   7.9e-08       2      40 .]     375     413 ..     374     413 .. 0.98
   7 !    7.2  18.5   0.00052       4.7       3      30 ..     443     471 ..     430     476 .. 0.52
   8 !    6.4   7.5   0.00091       8.2       1      28 [.     475     502 ..     475     505 .. 0.75
   9 ?    1.4  25.7     0.033     3e+02       6      38 ..     533     567 ..     514     567 .. 0.91
  10 !   17.9  31.3   2.4e-07    0.0022       1      40 []     560     601 ..     549     601 .. 0.94
  11 !   27.1  23.9     3e-10   2.7e-06       1      40 []     571     611 ..     571     611 .. 0.95
  12 !   32.7  21.7   5.7e-12   5.1e-08       1      39 [.     592     630 ..     592     630 .. 0.99
  13 !   31.8  21.4   1.1e-11   9.5e-08       3      39 ..     604     640 ..     602     641 .. 0.95
  14 !   27.6  27.2   2.1e-10   1.9e-06       2      39 ..     628     665 ..     627     666 .. 0.97
  15 !   24.7  22.5   1.7e-09   1.6e-05       7      39 ..     678     710 ..     672     710 .. 0.95
  16 !   35.2  18.6     9e-13   8.1e-09       1      39 [.     702     740 ..     702     741 .. 0.98
  17 !   38.5  25.2   8.7e-14   7.8e-10       2      39 ..     733     770 ..     732     771 .. 0.98
  18 !   38.5  24.7   8.7e-14   7.8e-10       2      39 ..     743     780 ..     742     781 .. 0.98
  19 !   31.5  15.3   1.3e-11   1.2e-07       1      39 [.     772     810 ..     772     811 .. 0.95
  20 ?    1.8  18.3     0.025   2.2e+02      11      39 ..     926     955 ..     918     956 .. 0.82
  21 !   14.6  10.2   2.4e-06     0.022       1      32 [.     961     992 ..     961     994 .. 0.93
  22 ?   -5.2   1.9         2   1.8e+04      29      36 ..    1001    1008 ..     998    1011 .. 0.52
  23 !   31.9  12.8     1e-11     9e-08       5      38 ..    1020    1053 ..    1017    1055 .. 0.93
  24 !   29.6  20.8   5.3e-11   4.8e-07       1      39 [.    1056    1094 ..    1052    1094 .. 0.70
  25 !   28.1  27.0   1.5e-10   1.4e-06       2      39 ..    1082    1119 ..    1081    1120 .. 0.97
  26 !   23.3  27.0   4.9e-09   4.4e-05       4      40 .]    1129    1165 ..    1126    1165 .. 0.96
  27 !   40.5  23.0     2e-14   1.8e-10       1      39 [.    1166    1204 ..    1166    1205 .. 0.98
  28 !   37.7  13.7   1.5e-13   1.4e-09       1      39 [.    1206    1244 ..    1206    1245 .. 0.97
  29 ?   -3.3  11.2      0.98   8.8e+03       3      38 ..    1370    1407 ..    1368    1409 .. 0.81
  30 !    6.1  13.8    0.0011        10       3      39 ..    1413    1453 ..    1410    1459 .. 0.74
  31 !   31.2  15.0   1.7e-11   1.5e-07       5      40 .]    1469    1504 ..    1465    1504 .. 0.94
  32 !   25.6  23.6     9e-10   8.1e-06       1      39 [.    1495    1533 ..    1495    1539 .. 0.70
  33 !   29.2  19.7   7.1e-11   6.3e-07       1      37 [.    1515    1551 ..    1513    1552 .. 0.94
  34 !   29.0  28.3   8.1e-11   7.2e-07       2      39 ..    1541    1578 ..    1540    1579 .. 0.97
  35 !   26.4  26.6   5.1e-10   4.5e-06       4      39 ..    1588    1623 ..    1585    1623 .. 0.97
  36 !   35.4  24.3   7.8e-13     7e-09       1      40 []    1615    1654 ..    1615    1654 .. 0.98
  37 !   34.5  19.9   1.5e-12   1.3e-08       2      40 .]    1646    1684 ..    1645    1684 .. 0.97
  38 !   33.0  17.3   4.6e-12   4.1e-08       2      40 .]    1676    1714 ..    1675    1714 .. 0.97
  39 ?    2.4  17.7     0.017   1.5e+02       3      34 ..    1849    1881 ..    1839    1883 .. 0.74
  40 ?    0.0  22.5      0.09     8e+02       4      40 .]    1861    1900 ..    1860    1910 .. 0.89
  41 !    8.6  19.6    0.0002       1.8       4      39 ..    1921    1957 ..    1918    1957 .. 0.58
  42 !   27.2  28.0     3e-10   2.7e-06       2      40 .]    1940    1978 ..    1934    1978 .. 0.96
  43 !   28.4  18.1   1.2e-10   1.1e-06       1      39 [.    1974    2012 ..    1974    2013 .. 0.98
  44 !   30.6  26.2   2.5e-11   2.2e-07       2      39 ..    2010    2047 ..    2009    2048 .. 0.97
  45 !   32.0  24.5     9e-12   8.1e-08       3      39 ..    2053    2089 ..    2051    2090 .. 0.97
  46 !   34.7  27.3   1.3e-12   1.2e-08       1      39 [.    2061    2099 ..    2061    2100 .. 0.98
  47 !   27.1  23.6   3.2e-10   2.8e-06       1      39 [.    2091    2129 ..    2091    2130 .. 0.98
  48 !   35.2  23.0   9.5e-13   8.5e-09       1      40 []    2101    2140 ..    2101    2140 .. 0.98
  49 !   36.1  20.6   4.8e-13   4.3e-09       1      40 []    2121    2160 ..    2121    2160 .. 0.98
  50 !   38.0  19.8   1.3e-13   1.1e-09       2      39 ..    2132    2169 ..    2131    2170 .. 0.97
  51 !   36.4  18.9     4e-13   3.6e-09       1      39 [.    2161    2199 ..    2161    2200 .. 0.95
  52 !    5.3  18.3    0.0021        18       4      38 ..    2321    2357 ..    2320    2359 .. 0.84
  53 !   14.9   6.6     2e-06     0.018       1      28 [.    2363    2390 ..    2360    2394 .. 0.57
  54 !   31.1  15.3   1.7e-11   1.5e-07       5      39 ..    2422    2456 ..    2419    2457 .. 0.85
  55 !   25.0  21.1   1.4e-09   1.2e-05       2      34 ..    2449    2481 ..    2448    2485 .. 0.55
  56 !   22.7  32.3   7.4e-09   6.7e-05       2      39 ..    2490    2527 ..    2489    2528 .. 0.86
  57 !   28.1  18.1   1.5e-10   1.3e-06       3      40 .]    2533    2570 ..    2531    2570 .. 0.96
  58 !   21.0  29.2   2.5e-08   0.00023       2      39 ..    2552    2589 ..    2552    2595 .. 0.97
  59 !   33.1  23.8   4.3e-12   3.8e-08       4      39 ..    2596    2631 ..    2593    2631 .. 0.95
  60 !   27.2  26.6   2.9e-10   2.6e-06       1      39 [.    2613    2651 ..    2613    2652 .. 0.97
  61 !   27.2  29.0   2.9e-10   2.6e-06       3      39 ..    2657    2693 ..    2655    2694 .. 0.97
  62 !   33.6  23.6   2.9e-12   2.6e-08       1      39 [.    2695    2733 ..    2695    2734 .. 0.98
  63 !   37.0  12.7   2.6e-13   2.3e-09       2      40 .]    2736    2774 ..    2735    2774 .. 0.98
  64 ?   -4.0  11.0       1.6   1.4e+04       4      28 ..    2925    2949 ..    2914    2955 .. 0.59
  65 !   11.2  11.5   2.8e-05      0.25       1      31 [.    2955    2985 ..    2954    3002 .. 0.87
  66 !   33.3  10.4   3.6e-12   3.2e-08       6      40 .]    3013    3047 ..    3011    3047 .. 0.91
  67 !   37.9  15.4   1.3e-13   1.1e-09       1      36 [.    3048    3083 ..    3048    3086 .. 0.95
  68 !   27.6  36.3   2.3e-10     2e-06       1      39 [.    3089    3127 ..    3089    3128 .. 0.98
  69 !   27.5  29.2   2.4e-10   2.1e-06       2      39 ..    3132    3169 ..    3131    3170 .. 0.96
  70 !   23.1  37.8   5.7e-09   5.1e-05       2      39 ..    3152    3189 ..    3151    3200 .. 0.53
  71 !   36.3  25.7   4.1e-13   3.7e-09       2      40 .]    3172    3210 ..    3171    3210 .. 0.98
  72 !   39.5  23.2   4.1e-14   3.7e-10       2      40 .]    3192    3230 ..    3191    3230 .. 0.98
  73 !   30.5  18.7   2.8e-11   2.5e-07       2      39 ..    3232    3269 ..    3231    3270 .. 0.94
  74 ?    1.8   2.7     0.026   2.3e+02      14      31 ..    3398    3416 ..    3394    3425 .. 0.57
  75 !    4.1  19.7    0.0047        43       3      38 ..    3440    3476 ..    3430    3478 .. 0.82
  76 ?   -2.1   5.1      0.43   3.9e+03       4      20 ..    3489    3505 ..    3488    3506 .. 0.41

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.3e-10
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G +N+G +N+G+gN+G+fNlGs+N+G+gn+Gs
  gi|121636268|ref|YP_976491.1| 196 NLGLANVGEGNVGNGNVGNFNLGSANIGNGNIGS 229
                                    8888888888888888888888888888888885 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 3e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36 
                                    gN+G++N+Gs+N+G++N+GsgN+Gs N+G+gN+G g
  gi|121636268|ref|YP_976491.1| 210 GNVGNFNLGSANIGNGNIGSGNIGSSNIGFGNVGPG 245
                                    799999999999999999999999999999999976 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 8.8e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+Gs N+Gf+N+Gs N+G++N+G+gN G+g tGs
  gi|121636268|ref|YP_976491.1| 252 NIGFGNTGSNNIGFGNTGSNNIGFGNTGDGNRGIGLTGS 290
                                    9***********************************996 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 1.5e-09
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G lNsG+gN+G+fN+G+gN+G +N+G+gN G+gn+G+
  gi|121636268|ref|YP_976491.1| 295 FGGLNSGTGNIGLFNSGTGNVGIGNSGTGNWGIGNSGN 332
                                    89***********************************6 PP

  == domain 5  score: 39.2 bits;  conditional E-value: 5.2e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG++NsG +NtGffN+G +NtG +N+G++NtGs n+G+
  gi|121636268|ref|YP_976491.1| 335 NTGFGNSGDANTGFFNSGIANTGVGNAGNYNTGSYNPGN 373
                                    *************************************96 PP

  == domain 6  score: 32.1 bits;  conditional E-value: 8.8e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG +N+G  NtG +N+G+ NtG +N+G++NtG++ tG+
  gi|121636268|ref|YP_976491.1| 375 NTGGFNMGQYNTGYLNSGNYNTGLANSGNVNTGAFITGN 413
                                    *************************************96 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.00052
                 Pentapeptide_2   3 tGslNsGsgN.tGffNlGsgNtGsfNlGs 30 
                                    +G++NsG g  +Gf+N+G  N G+fN+ s
  gi|121636268|ref|YP_976491.1| 443 SGFFNSGAGSaSGFLNSGANNSGFFNSSS 471
                                    35555555542355555555555555555 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.00091
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNl 28 
                                    gN+G +N+G   +G  N+G++  G fN+
  gi|121636268|ref|YP_976491.1| 475 GNSGLANAGVLVSGVINSGNTVSGLFNM 502
                                    6788888888888888888888887774 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.033
                 Pentapeptide_2   6 lNsGsgNtGffN.lGsgNtGsfN.lGsgNtGsgnt 38 
                                    +N+G +N G +N lG++N+G++N lGsgN+G++n+
  gi|121636268|ref|YP_976491.1| 533 FNLGLANRGVVNiLGNANIGNYNiLGSGNVGDFNI 567
                                    89**********55*********55*******995 PP

  == domain 10  score: 17.9 bits;  conditional E-value: 2.4e-07
                 Pentapeptide_2   1 gNtGslNs.GsgNtGffN.lGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+ GsgN+G+ N lGsgN+GsfN+GsgN+G +n+Gs
  gi|121636268|ref|YP_976491.1| 560 GNVGDFNIlGSGNLGSQNiLGSGNVGSFNIGSGNIGVFNVGS 601
                                    8******55*********56********************96 PP

  == domain 11  score: 27.1 bits;  conditional E-value: 3e-10
                 Pentapeptide_2   1 gNtGslNs.GsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN Gs N+ GsgN+G+fN+GsgN+G fN+Gsg  G+ n+Gs
  gi|121636268|ref|YP_976491.1| 571 GNLGSQNIlGSGNVGSFNIGSGNIGVFNVGSGSLGNYNIGS 611
                                    8******55******************************96 PP

  == domain 12  score: 32.7 bits;  conditional E-value: 5.7e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+Gsg +G++N+GsgN G +N+G+gN+G+ n+G
  gi|121636268|ref|YP_976491.1| 592 GNIGVFNVGSGSLGNYNIGSGNLGIYNIGFGNVGDYNVG 630
                                    8************************************99 PP

  == domain 13  score: 31.8 bits;  conditional E-value: 1.1e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                     G++N+GsgN+G +N+G+gN+G++N+G+gN G++n G
  gi|121636268|ref|YP_976491.1| 604 LGNYNIGSGNLGIYNIGFGNVGDYNVGFGNAGDFNQG 640
                                    69*********************************99 PP

  == domain 14  score: 27.6 bits;  conditional E-value: 2.1e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G++N+G +N Gf+N+G+ N+G++N+G++N+G+g +G
  gi|121636268|ref|YP_976491.1| 628 NVGFGNAGDFNQGFANTGNNNIGFANTGNNNIGIGLSG 665
                                    9**********************************999 PP

  == domain 15  score: 24.7 bits;  conditional E-value: 1.7e-09
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NsG+gN+G+fN+G+ N+G fN+G+gN+G+ n+G
  gi|121636268|ref|YP_976491.1| 678 NSGTGNSGLFNSGTNNVGIFNAGTGNVGIANSG 710
                                    *******************************99 PP

  == domain 16  score: 35.2 bits;  conditional E-value: 9e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++NsG+gN+G +N G+ NtG  N+Gs+NtG++n+G
  gi|121636268|ref|YP_976491.1| 702 GNVGIANSGTGNWGIGNPGTDNTGILNAGSYNTGILNAG 740
                                    8*************************************9 PP

  == domain 17  score: 38.5 bits;  conditional E-value: 8.7e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG+lN+G +NtGf+N+Gs NtG fN+G+ NtG++n+G
  gi|121636268|ref|YP_976491.1| 733 NTGILNAGDFNTGFYNTGSYNTGGFNVGNTNTGNFNVG 770
                                    *************************************9 PP

  == domain 18  score: 38.5 bits;  conditional E-value: 8.7e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N+Gs NtG fN+G++NtG+fN+G+ NtGs n+G
  gi|121636268|ref|YP_976491.1| 743 NTGFYNTGSYNTGGFNVGNTNTGNFNVGDTNTGSYNPG 780
                                    *************************************9 PP

  == domain 19  score: 31.5 bits;  conditional E-value: 1.3e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +NtGs+N G +NtGffN G++NtG f +G++N G++ +G
  gi|121636268|ref|YP_976491.1| 772 TNTGSYNPGDTNTGFFNPGNVNTGAFDTGDFNNGFLVAG 810
                                    6**********************************9888 PP

  == domain 20  score: 1.8 bits;  conditional E-value: 0.025
                 Pentapeptide_2  11 gNtGffNlGsgNt.GsfNlGsgNtGsgntG 39 
                                      +GffN+G+g t G++N+G g +G  n+G
  gi|121636268|ref|YP_976491.1| 926 PSSGFFNSGTGGTsGFQNVGGGSSGVWNSG 955
                                    468******99877**************99 PP

  == domain 21  score: 14.6 bits;  conditional E-value: 2.4e-06
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgN 32 
                                    gN+G+ N+Gs  +G++NlG+   G+fN+ ++N
  gi|121636268|ref|YP_976491.1| 961 GNSGFQNLGSLQSGWANLGNSVSGFFNTSTVN 992
                                    89*************************98888 PP

  == domain 22  score: -5.2 bits;  conditional E-value: 2
                 Pentapeptide_2   29 GsgNtGsg 36  
                                     G +N+G +
  gi|121636268|ref|YP_976491.1| 1001 GLNNIGTN 1008
                                     44555544 PP

  == domain 23  score: 31.9 bits;  conditional E-value: 1e-11
                 Pentapeptide_2    5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     ++N+G +N+G +N+Gs+N G+fNlGsgN+Gs+n+
  gi|121636268|ref|YP_976491.1| 1020 IFNAGLANLGQLNIGSANLGDFNLGSGNVGSFNV 1053
                                     58******************************96 PP

  == domain 24  score: 29.6 bits;  conditional E-value: 5.3e-11
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gN Gs+N+G +N+G++N+G++N G++N+G+gN G++n G
  gi|121636268|ref|YP_976491.1| 1056 GNQGSYNIGPANLGNYNIGFANLGNYNIGFGNAGDFNQG 1094
                                     577777777777777777777777777777777777765 PP

  == domain 25  score: 28.1 bits;  conditional E-value: 1.5e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G +N Gf+N+G+ N+G++N+G++N+G+g +G
  gi|121636268|ref|YP_976491.1| 1082 NIGFGNAGDFNQGFANTGNNNIGFANTGNNNIGIGLSG 1119
                                     9**********************************999 PP

  == domain 26  score: 23.3 bits;  conditional E-value: 4.9e-09
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     G  NsG++N+G+fN+G+ N+G +N+G+gN G+gn+Gs
  gi|121636268|ref|YP_976491.1| 1129 GGWNSGTANIGLFNSGTNNVGIGNSGTGNWGIGNSGS 1165
                                     889*********************************6 PP

  == domain 27  score: 40.5 bits;  conditional E-value: 2e-14
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gNtG++N+Gs+NtGffN+G +NtG +N+Gs+NtG  ntG
  gi|121636268|ref|YP_976491.1| 1166 GNTGIGNTGSTNTGFFNTGIVNTGVANAGSYNTGWYNTG 1204
                                     8*************************************9 PP

  == domain 28  score: 37.7 bits;  conditional E-value: 1.5e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +NtG++N+G +NtGf+N+G+ +tG++N G++ tG++ tG
  gi|121636268|ref|YP_976491.1| 1206 TNTGIANLGDFNTGFYNTGNFSTGFANQGDIATGAFITG 1244
                                     6*************************************9 PP

  == domain 29  score: -3.3 bits;  conditional E-value: 0.98
                 Pentapeptide_2    3 tGslNsGs.gNtGffNlGsgNt.GsfNlGsgNtGsgnt 38  
                                     tG++N+ +   +GffN G g + G +N+G + +G+ n+
  gi|121636268|ref|YP_976491.1| 1370 TGFFNATTdPSSGFFNGGPGTVsGIANIGANISGFQNV 1407
                                     788887652589*****98874499***9999999997 PP

  == domain 30  score: 6.1 bits;  conditional E-value: 0.0011
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgN....tGsgntG 39  
                                     +G+ N Gs  +G++NlG +  G fN+G g     +G++n+G
  gi|121636268|ref|YP_976491.1| 1413 SGFNNYGSLQSGLANLGDTVSGVFNTGIGApanvSGMFNIG 1453
                                     58888888888888888888888888876433335777766 PP

  == domain 31  score: 31.2 bits;  conditional E-value: 1.7e-11
                 Pentapeptide_2    5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                      +N+G gN+G fN+G+ N+G+ N+G +N+Gs+n+Gs
  gi|121636268|ref|YP_976491.1| 1469 MFNLGLGNIGQFNVGFSNVGDSNAGLANIGSFNLGS 1504
                                     69********************************96 PP

  == domain 32  score: 25.6 bits;  conditional E-value: 9e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +N+Gs+N+GsgN+G+fN+  gN Gs+N+G +N G+ n+G
  gi|121636268|ref|YP_976491.1| 1495 ANIGSFNLGSGNLGSFNVFGGNQGSYNIGPANLGNYNIG 1533
                                     6***************98666655555555555555555 PP

  == domain 33  score: 29.2 bits;  conditional E-value: 7.1e-11
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37  
                                     gN Gs+N+G +N+G++N+G gN Gs+N+G+gN G++n
  gi|121636268|ref|YP_976491.1| 1515 GNQGSYNIGPANLGNYNIGLGNLGSYNFGFGNAGDFN 1551
                                     799********************************99 PP

  == domain 34  score: 29.0 bits;  conditional E-value: 8.1e-11
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G +N+Gf+N+G+ N+G++N+G++N+G+g +G
  gi|121636268|ref|YP_976491.1| 1541 NFGFGNAGDFNLGFANTGNNNIGFANTGNNNIGIGLSG 1578
                                     9**********************************999 PP

  == domain 35  score: 26.4 bits;  conditional E-value: 5.1e-10
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     G  NsGsgN+G+fN+G+ N+G fN+G+gN+G+gn+G
  gi|121636268|ref|YP_976491.1| 1588 GGWNSGSGNSGLFNSGTNNIGLFNSGTGNIGIGNSG 1623
                                     889********************************9 PP

  == domain 36  score: 35.4 bits;  conditional E-value: 7.8e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     gN+G++NsG+gN+G +N+G +NtG fN+G++NtG +n+G+
  gi|121636268|ref|YP_976491.1| 1615 GNIGIGNSGTGNWGIANTGDTNTGIFNTGDVNTGLLNAGN 1654
                                     8*************************************96 PP

  == domain 37  score: 34.5 bits;  conditional E-value: 1.5e-12
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG lN+G++NtG fN+G  NtGsfN+Gs+Nt  +n+Gs
  gi|121636268|ref|YP_976491.1| 1646 NTGLLNAGNVNTGIFNTGHYNTGSFNAGSFNTAGFNPGS 1684
                                     *************************************96 PP

  == domain 38  score: 33.0 bits;  conditional E-value: 4.6e-12
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     Nt  +N Gs NtG +N+Gs NtG +N+G++NtG + tG+
  gi|121636268|ref|YP_976491.1| 1676 NTAGFNPGSYNTGYLNTGSYNTGLANSGDVNTGGFITGN 1714
                                     99***********************************96 PP

  == domain 39  score: 2.4 bits;  conditional E-value: 0.017
                 Pentapeptide_2    3 tGslNsGsgN.tGffNlGsgNtGsfNlGsgNtG 34  
                                     +G++N+G+g  +G +N+Gs + G+fNl sg +G
  gi|121636268|ref|YP_976491.1| 1849 SGFFNAGTGTvSGVGNVGSNSSGFFNLTSGSSG 1881
                                     478888887634888888888888888777777 PP

  == domain 40  score: 0.0 bits;  conditional E-value: 0.09
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNt...GsfNlGsgNtGsgntGs 40  
                                     G++N+Gs  +GffNl sg+    G +N+G   +G +n+G+
  gi|121636268|ref|YP_976491.1| 1861 GVGNVGSNSSGFFNLTSGSSgisGVQNFGELISGGFNFGN 1900
                                     99*************99997222579************96 PP

  == domain 41  score: 8.6 bits;  conditional E-value: 0.0002
                 Pentapeptide_2    4 GslNsGsgNtGffN.lGsgNtGsfNlGsgNtGsgntG 39  
                                     G +N+G +  Gf+N +   N G++N+GsgN+G+gn+G
  gi|121636268|ref|YP_976491.1| 1921 GGGNVGATVAGFVNnTQILNLGFGNVGSGNVGHGNIG 1957
                                     6666666666665413345666666666666666665 PP

  == domain 42  score: 27.2 bits;  conditional E-value: 3e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     N G++N+GsgN+G +N+G  N+G +NlG++N+G+gn+Gs
  gi|121636268|ref|YP_976491.1| 1940 NLGFGNVGSGNVGHGNIGDSNVGLGNLGNANVGHGNIGS 1978
                                     99***********************************96 PP

  == domain 43  score: 28.4 bits;  conditional E-value: 1.2e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gN+Gs+N+ sgN G++N+G +N G++N+G gN Gs n+G
  gi|121636268|ref|YP_976491.1| 1974 GNIGSFNVFSGNRGSYNIGPANLGNYNIGLGNLGSYNFG 2012
                                     8*************************************9 PP

  == domain 44  score: 30.6 bits;  conditional E-value: 2.5e-11
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G +N+Gf+N+Gs N+G++N+G++N+G+g +G
  gi|121636268|ref|YP_976491.1| 2010 NFGFGNAGDFNLGFANSGSNNIGFANTGNNNIGIGLSG 2047
                                     9**********************************999 PP

  == domain 45  score: 32.0 bits;  conditional E-value: 9e-12
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +Gs NsG++NtG+fN+G+ N+G fN+G+gN+G+gn+G
  gi|121636268|ref|YP_976491.1| 2053 FGSWNSGTANTGLFNSGTNNIGLFNSGTGNIGIGNSG 2089
                                     8***********************************9 PP

  == domain 46  score: 34.7 bits;  conditional E-value: 1.3e-12
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +NtG +NsG+ N+G+fN+G+gN+G +N+G gNtG+gn+G
  gi|121636268|ref|YP_976491.1| 2061 ANTGLFNSGTNNIGLFNSGTGNIGIGNSGIGNTGIGNPG 2099
                                     6*************************************9 PP

  == domain 47  score: 27.1 bits;  conditional E-value: 3.2e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gNtG++N G gNtG++N+G+gN G  N G+gN+G  n+G
  gi|121636268|ref|YP_976491.1| 2091 GNTGIGNPGVGNTGLGNSGTGNWGLWNPGTGNMGVANVG 2129
                                     8*************************************9 PP

  == domain 48  score: 35.2 bits;  conditional E-value: 9.5e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     gNtG +NsG+gN+G++N G+gN+G +N+G++NtG  n+Gs
  gi|121636268|ref|YP_976491.1| 2101 GNTGLGNSGTGNWGLWNPGTGNMGVANVGTYNTGGYNVGS 2140
                                     8*************************************96 PP

  == domain 49  score: 36.1 bits;  conditional E-value: 4.8e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     gN+G++N+G+ NtG +N+Gs+NtG +N+G +NtGs ntGs
  gi|121636268|ref|YP_976491.1| 2121 GNMGVANVGTYNTGGYNVGSTNTGIANVGIANTGSYNTGS 2160
                                     8**************************************6 PP

  == domain 50  score: 38.0 bits;  conditional E-value: 1.3e-13
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     NtG +N+Gs+NtG +N+G +NtGs+N+Gs NtGs+n G
  gi|121636268|ref|YP_976491.1| 2132 NTGGYNVGSTNTGIANVGIANTGSYNTGSTNTGSFNDG 2169
                                     ************************************88 PP

  == domain 51  score: 36.4 bits;  conditional E-value: 4e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +NtGs+N G +NtGf+N+G  NtG++N+G++NtG++  G
  gi|121636268|ref|YP_976491.1| 2161 TNTGSFNDGDFNTGFYNTGDYNTGFYNTGDVNTGAFIGG 2199
                                     6**********************************9877 PP

  == domain 52  score: 5.3 bits;  conditional E-value: 0.0021
                 Pentapeptide_2    4 GslNsGsg.NtGffNlGsgN.tGsfNlGsgNtGsgnt 38  
                                     G++Ns +g  +GffN+G+g+  G++N+G +N+G+ nt
  gi|121636268|ref|YP_976491.1| 2321 GFGNSTTGpSSGFFNSGTGSsSGFGNVGANNSGFWNT 2357
                                     78888887568******99637************998 PP

  == domain 53  score: 14.9 bits;  conditional E-value: 2e-06
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNl 28  
                                     gN+G  N+Gs  +G++NlG++  G++N+
  gi|121636268|ref|YP_976491.1| 2363 GNSGLQNFGSLQSGWANLGNTVSGFYNT 2390
                                     4555555555555555555555555554 PP

  == domain 54  score: 31.1 bits;  conditional E-value: 1.7e-11
                 Pentapeptide_2    5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     ++N+G +N+G fN+Gs+N Gs+NlGs+N G+ n+G
  gi|121636268|ref|YP_976491.1| 2422 TFNAGLANLGQFNVGSANLGSANLGSANLGNSNVG 2456
                                     68999999999999999999999999999999998 PP

  == domain 55  score: 25.0 bits;  conditional E-value: 1.4e-09
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtG 34  
                                     N G+ N+G gN+G++N+G +N+G+fN+G +NtG
  gi|121636268|ref|YP_976491.1| 2449 NLGNSNVGFGNIGNANIGGANIGDFNVGIANTG 2481
                                     555555555555555555555555555555555 PP

  == domain 56  score: 22.7 bits;  conditional E-value: 7.4e-09
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G+ N+G +N+G+ N+G++N+G++N+G+g +G
  gi|121636268|ref|YP_976491.1| 2490 NIGIGNTGNYNIGVGNTGNYNIGFGNTGNNNIGIGLSG 2527
                                     89999999999999999999999999999999999888 PP

  == domain 57  score: 28.1 bits;  conditional E-value: 1.5e-10
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +G lN+G +N+G+fNlG  N+G +N+G++N G+ ntG+
  gi|121636268|ref|YP_976491.1| 2533 FGPLNAGIANMGLFNLGDNNFGMANAGNFNQGIANTGN 2570
                                     799**********************************6 PP

  == domain 58  score: 21.0 bits;  conditional E-value: 2.5e-08
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G +N+G++N G +N+G+ N+G fN+G++N+G+g tG
  gi|121636268|ref|YP_976491.1| 2552 NFGMANAGNFNQGIANTGNNNIGLFNTGNNNVGIGLTG 2589
                                     9**********************************999 PP

  == domain 59  score: 33.1 bits;  conditional E-value: 4.3e-12
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                      slNsG gNtGffN+G++NtG fN+G+gNtG +n+G
  gi|121636268|ref|YP_976491.1| 2596 SSLNSGAGNTGFFNSGTANTGLFNSGTGNTGLFNSG 2631
                                     589********************************9 PP

  == domain 60  score: 27.2 bits;  conditional E-value: 2.9e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +NtG +NsG+gNtG+fN+G+gN+G +N+G+g +G g +G
  gi|121636268|ref|YP_976491.1| 2613 ANTGLFNSGTGNTGLFNSGTGNVGIGNMGTGGFGVGLSG 2651
                                     6***********************************999 PP

  == domain 61  score: 27.2 bits;  conditional E-value: 2.9e-10
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +G +NsGs+N+G+fN+G+gN+G +N+G+gN+G+gntG
  gi|121636268|ref|YP_976491.1| 2657 IGGTNSGSFNIGLFNSGTGNVGIGNSGTGNVGIGNTG 2693
                                     89**********************************9 PP

  == domain 62  score: 33.6 bits;  conditional E-value: 2.9e-12
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gNtG++NsG+ NtG++N G +NtG +N G+ NtG +n+G
  gi|121636268|ref|YP_976491.1| 2695 GNTGIGNSGNYNTGLLNAGLVNTGIANPGNHNTGLFNIG 2733
                                     8*************************************9 PP

  == domain 63  score: 37.0 bits;  conditional E-value: 2.6e-13
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG++N G  NtG++N+Gs NtG +N+G++ tG++ tGs
  gi|121636268|ref|YP_976491.1| 2736 NTGIANPGHYNTGSYNTGSYNTGMANAGDYGTGAFITGS 2774
                                     *************************************96 PP

  == domain 64  score: -4.0 bits;  conditional E-value: 1.6
                 Pentapeptide_2    4 GslNsGsgN.tGffNlGsgNtGsfNl 28  
                                     G+lN+G g  +G++N G+ N G +N+
  gi|121636268|ref|YP_976491.1| 2925 GFLNWGAGSaSGLLNFGN-NSGLYNF 2949
                                     566666654346666665.5555554 PP

  == domain 65  score: 11.2 bits;  conditional E-value: 2.8e-05
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsg 31  
                                     gN+G+ N Gs  +G++NlG+   G +N+G g
  gi|121636268|ref|YP_976491.1| 2955 GNSGFQNYGSLQSGWANLGNSISGIYNTGLG 2985
                                     7999999999999999999999999999987 PP

  == domain 66  score: 33.3 bits;  conditional E-value: 3.6e-12
                 Pentapeptide_2    6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     + +G +N+Gf+NlGs+N+G++NlGs+N+G  n+Gs
  gi|121636268|ref|YP_976491.1| 3013 FSVGLANLGFWNLGSANIGNYNLGSANIGVYNLGS 3047
                                     679999***********************999996 PP

  == domain 67  score: 37.9 bits;  conditional E-value: 1.3e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36  
                                     +N+G++N+Gs+N+G+fNlGs+N+Gs N+G+gN+G g
  gi|121636268|ref|YP_976491.1| 3048 ANIGDFNLGSANIGDFNLGSANIGSSNIGFGNVGPG 3083
                                     6*********************************76 PP

  == domain 68  score: 27.6 bits;  conditional E-value: 2.3e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gN+G++N+G+gN+G +N+G+gN+G++N+G+gN+G+g tG
  gi|121636268|ref|YP_976491.1| 3089 GNIGFGNTGNGNIGIGNTGTGNIGFGNTGNGNIGIGLTG 3127
                                     8************************************99 PP

  == domain 69  score: 27.5 bits;  conditional E-value: 2.4e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                      +G  NsG+gN+G+fN+G+gN+G++N+G+gN G+gn+G
  gi|121636268|ref|YP_976491.1| 3132 GFGGWNSGTGNIGLFNSGTGNIGFGNSGTGNWGIGNSG 3169
                                     68999********************************9 PP

  == domain 70  score: 23.1 bits;  conditional E-value: 5.7e-09
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++NsG+gN+G +N+G  NtG +N+Gs N+G++ntG
  gi|121636268|ref|YP_976491.1| 3152 NIGFGNSGTGNWGIGNSGDYNTGIGNTGSTNSGFFNTG 3189
                                     55555555555555555555555555555555555555 PP

  == domain 71  score: 36.3 bits;  conditional E-value: 4.1e-13
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG++N+Gs+N+GffN+G +NtG +N+G++NtG +n+G+
  gi|121636268|ref|YP_976491.1| 3172 NTGIGNTGSTNSGFFNTGLVNTGIGNSGDYNTGLFNAGN 3210
                                     *************************************96 PP

  == domain 72  score: 39.5 bits;  conditional E-value: 4.1e-14
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG++NsG  NtG+fN G++NtGsfN G++NtG +n+G+
  gi|121636268|ref|YP_976491.1| 3192 NTGIGNSGDYNTGLFNAGNTNTGSFNPGDYNTGGFNPGN 3230
                                     *************************************96 PP

  == domain 73  score: 30.5 bits;  conditional E-value: 2.8e-11
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     NtG++N G+ NtGf+N+G +NtG fN+G++  G++  G
  gi|121636268|ref|YP_976491.1| 3232 NTGYFNPGNSNTGFANSGDVNTGAFNSGNYSNGFFWRG 3269
                                     9********************************99776 PP

  == domain 74  score: 1.8 bits;  conditional E-value: 0.026
                 Pentapeptide_2   14 GffNlGsg.NtGsfNlGsg 31  
                                     GffN+ ++ + G+fN+G g
  gi|121636268|ref|YP_976491.1| 3398 GFFNSTTTpSSGFFNSGAG 3416
                                     5666554435566666654 PP

  == domain 75  score: 4.1 bits;  conditional E-value: 0.0047
                 Pentapeptide_2    3 tGslNsG.sgNtGffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     +G++N+G  gN+Gf N G+   G++NlG+  +G+ nt
  gi|121636268|ref|YP_976491.1| 3440 SGFFNAGgVGNSGFQNFGNLLSGWANLGNTVSGFYNT 3476
                                     5888886258999999999999999999999998887 PP

  == domain 76  score: -2.1 bits;  conditional E-value: 0.43
                 Pentapeptide_2    4 GslNsGsgNtGffNlGs 20  
                                     G++N+G   +G +N Gs
  gi|121636268|ref|YP_976491.1| 3489 GFGNHGARLSGILNNGS 3505
                                     44444444444444444 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0  28.3   9.3e-62   8.3e-58       1     157 [.       5     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 9.3e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+nsa+ly G+g +p+l AaaaWdgLa+el saaa++++v+a+la+++W G++s+am+ aaapyl WLsaaaaqa+
  gi|121636268|ref|YP_976491.1|   5 VLPPEINSARLYVGAGLAPMLDAAAAWDGLADELGSAAASFSAVTAGLAGSSWLGAASTAMTGAAAPYLGWLSAAAAQAQ 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA+q + aaaa+eaAlaa+v+pa i anra +++lv +n++Gqn+paIaatea+ye+mwaqd+aam +Y+a ++aa
  gi|121636268|ref|YP_976491.1|  85 QAATQTRLAAAAFEAALAATVHPAIISANRALFVSLVVSNLLGQNAPAIAATEAAYEQMWAQDVAAMFGYHAGASAA 161
                                    **************************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      103  (0.00574488); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.27u 0.31s 00:00:01.58 Elapsed: 00:00:00.52
# Mc/sec: 20178.80
//
Query:       gi|121636269|ref|YP_976492.1|  [L=214]
Description: hypothetical protein BCG_0394c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-10   39.6   0.0    8.2e-10   38.9   0.0    1.4  1  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   4.6e-14   8.2e-10       3      78 ..     126     199 ..     124     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 4.6e-14
                                    SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                           4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                     vhgGv+  l+D+  g++ +  g+   +  ++ l++d++r   ++ +l v++rv+++ ++ a+v  e++d+d++l+
  gi|121636269|ref|YP_976492.1| 126 AVHGGVLPLLFDHMFGMISHAAGR--PISRTAFLHVDYRRITPIDVPLIVRGRVTNTEGRKAFVCAELFDSDETLL 199
                                    69**********************..5*********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1571.14
//
Query:       gi|121636270|ref|YP_976493.1|  [L=432]
Description: adenylosuccinate synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     4e-174  579.5   0.0   4.5e-174  579.3   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.3   0.0  2.5e-178  4.5e-174       1     419 []       4     422 ..       4     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 579.3 bits;  conditional E-value: 2.5e-178
                                    .EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEE.ETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHH CS
                Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvv.vdgkkyklhllpSGilnpgvvnviGngvvvdpealleE 79 
                                    +v++GaqwGDEGKGk +Dll  +++ vvR+qGG+nAGHtvv   g++++lhl+pSG+l+pgv+nviGngvv+dp +ll+E
  gi|121636270|ref|YP_976493.1|   4 IVLIGAQWGDEGKGKATDLLGGRVQWVVRYQGGNNAGHTVVlPTGENFALHLIPSGVLTPGVTNVIGNGVVIDPGVLLNE 83 
                                    589**************************************999************************************ PP

                                    HTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHHHHHH CS
                Adenylsucc_synt  80 ieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeeleekl 159
                                    ++ l+++gv++   +llis++ahl++pyh+a+Dk++e+  g+kkiGtT++GiGp+y+dk+ar girv+d+ld+e+l++k+
  gi|121636270|ref|YP_976493.1|  84 LRGLQDRGVDT--AKLLISADAHLLMPYHIAIDKVTERYMGSKKIGTTGRGIGPCYQDKIARIGIRVADVLDPEQLTHKV 161
                                    *********87..6*************************99*************************************** PP

                                    HHHHHHTHHHHHHT....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS CS
                Adenylsucc_synt 160 ekllelknkllekldk.eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsS 238
                                    e+++e+kn++l k+++ ++l+ +++++ ll+ ae +k+ ++dt  lln+al++g++vL+EG+qgtllD+dhGtYP+vTsS
  gi|121636270|ref|YP_976493.1| 162 EAACEFKNQVLVKIYNrKALDPAQVVDALLEQAEGFKHRIADTRLLLNAALEAGETVLLEGSQGTLLDVDHGTYPYVTSS 241
                                    **************998999*9********************************************************** PP

                                    --SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHH CS
                Adenylsucc_synt 239 nttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDlvllryavrv 318
                                    n+tagga++g+g++p++i++vlg++KAyttrvG+Gpfptel+de ge+l ++G+Efg+ttgr+RrcGw+D+v++rya+rv
  gi|121636270|ref|YP_976493.1| 242 NPTAGGAAVGSGIGPTRIGTVLGILKAYTTRVGSGPFPTELFDEHGEYLSKTGREFGVTTGRRRRCGWFDAVIARYAARV 321
                                    ******************************************************************************** PP

                                    HT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---GGGS-HHHHHHHHHH CS
                Adenylsucc_synt 319 ngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsfedlpenakkyvefi 398
                                    ng+t+  ltklDvl++l+++ vcv+Y++dg++++++p+++++l +++pvyeelpgW edisg+r+f+dlp++a++yv ++
  gi|121636270|ref|YP_976493.1| 322 NGITDYFLTKLDVLSSLESVPVCVGYEIDGRRTRDMPMTQRDLCRAKPVYEELPGWWEDISGAREFDDLPAKARDYVLRL 401
                                    ******************************************************************************** PP

                                    HHHHTS-EEEEE-SSSTT-EE CS
                Adenylsucc_synt 399 eellgvpvkiisvGpereqti 419
                                    e+l g+pv++i+vGp+reqti
  gi|121636270|ref|YP_976493.1| 402 EQLAGAPVSCIGVGPGREQTI 422
                                    *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3176.62
//
Query:       gi|121636271|ref|YP_976494.1|  [L=215]
Description: hypothetical protein BCG_0396 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.17   12.1   0.0       0.38   11.0   0.0    1.5  1  Chaperone_III  Type III secretion chaperone domain


Domain annotation for each model (and alignments):
>> Chaperone_III  Type III secretion chaperone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.1e-05      0.38      41      82 ..      22      62 ..      15      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.1e-05
                  Chaperone_III 41 cPlialPddiedlqailslnyaskvtlaadaeksvllalyrl 82
                                    Pl+ lP+  ++l +++   y+  ++++ada+ +++l+++  
  gi|121636271|ref|YP_976494.1| 22 GPLTGLPTHQDNLDTVIG-RYSRLIVVGADADLGAVLTRLLR 62
                                   69************9997.8*************999988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1459.10
//
Query:       gi|121636272|ref|YP_976495.1|  [L=259]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-07   30.2  10.3    0.00086   18.6   0.7    3.1  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
        3.8    7.6   5.8        2.4    8.3   0.1    2.4  2  SLATT_3        SMODS and SLOG-associating 2TM effector domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   3.8     1e-05     0.093       3     108 ..      50     148 ..      48     157 .. 0.82
   2 !   18.6   0.7   9.6e-08   0.00086     186     247 ..     158     214 ..     146     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                    xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   3 illlgilvvvHElGHflvAklcg...vkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                    i+  ++++ +HE+GH+++A ++g   v v+   + + p+  s+   ++   + ++ LGG + + g     +         
  gi|121636272|ref|YP_976495.1|  50 IAGWLVSLCLHEFGHAFTAWRFGdhdVAVRG-YLTLDPRRYSHPMLSLGLPMLFIALGG-IGLPGAAVYVH--------T 119
                                    56678999***********998654477766.688889999999999999999999999.88888774433........4 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv 108
                                       +   r l+ lAGp +n+ la+l++++
  gi|121636272|ref|YP_976495.1| 120 WFMTTARRTLVSLAGPTVNLALAMLLLAA 148
                                    5568899****************999875 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 9.6e-08
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 186 aglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                    a l++ +++la++ +   +lNLlPip LDG   l+  l      p  +r+ + a+++ l++l
  gi|121636272|ref|YP_976495.1| 158 AVLWAGVAFLAFLQLTALVLNLLPIPGLDGYAALEPHLR-----PETQRALAPAKQFALVFL 214
                                    55678899**********************877766554.....444444444444444444 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00027       2.4      11      60 ..       2      52 ..       1      70 [. 0.78
   2 ?    0.2   2.6     0.084   7.5e+02      22      62 ..     137     175 ..     125     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                        SLATT_3 11 slsgqreylrllrlrlvllvvAAlaaalslkv.gsvdlaallaalafllal 60
                                   s +gqre++r + + l ll + A+++al++   ++v+++a + + ++++a 
  gi|121636272|ref|YP_976495.1|  2 SETGQRESVRPSPIFLGLLGLTAVGGALAWLAgETVQPLAYAGVFVMVIAG 52
                                   789***************************995556665555555555443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.084
                        SLATT_3  22 lrlrlvllvvAAlaaalslkvgsvdlaallaalafllalvi 62 
                                    + l l++l++AA+  +++  +    l+a +a+lafl  +++
  gi|121636272|ref|YP_976495.1| 137 VNLALAMLLLAATRLLFDPIH--AVLWAGVAFLAFLQLTAL 175
                                    678899999999998888555..568999999999865444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1945.55
//
Query:       gi|121636273|ref|YP_976496.1|  [L=145]
Description: hypothetical protein BCG_0398c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-58  196.4   0.3    1.7e-58  196.2   0.3    1.0  1  DUF3151   Protein of unknown function (DUF3151)


Domain annotation for each model (and alignments):
>> DUF3151  Protein of unknown function (DUF3151)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2   0.3   9.6e-63   1.7e-58       2     125 ..      17     140 ..      16     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 9.6e-63
                        DUF3151   2 epppvlLpedeeaeaalaagedaaevaaahpasslaWallaeealaegeavaaYAyaRtGyhrgLdaLRrnGWkGaGpvp 81 
                                    +p+p+lLp d++aea+l a+e+++ vaaahp++s+aWa+lae ala++++v+aYAyaRtGyhrgLd+LRr+GWkG+Gpvp
  gi|121636273|ref|YP_976496.1|  17 GPEPILLPGDSDAEAELLANESPSIVAAAHPSASVAWAVLAEGALADDKTVTAYAYARTGYHRGLDQLRRHGWKGFGPVP 96 
                                    799***************************************************************************** PP

                        DUF3151  82 wshepnrGfLralaaLaraaeaigeedEaercrqlledsdpeaa 125
                                    +sh+pnrGfLr++aaLaraa+aige+dE+ rc +ll+d+dp+a 
  gi|121636273|ref|YP_976496.1|  97 YSHQPNRGFLRCVAALARAAAAIGETDEYGRCLDLLDDCDPAAR 140
                                    *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1061.74
//
Query:       gi|121636274|ref|YP_976497.1|  [L=275]
Description: hypothetical protein BCG_0399 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0061   16.4   0.6      0.011   15.6   0.6    1.3  1  CbtA             Probable cobalt transporter subunit (CbtA)
  ------ inclusion threshold ------
      0.015   16.0   0.2        2.6    8.8   0.1    2.3  2  Lumazine_bd_2    Putative lumazine-binding
      0.028   14.5   1.1      0.049   13.7   1.1    1.3  1  PRIMA1           Proline-rich membrane anchor 1
      0.048   13.8   2.4       0.27   11.4   0.9    2.3  2  Phage_holin_7_1  Mycobacterial 2 TMS Phage Holin (M2 Hol) Fam
      0.081   13.0   0.5       0.14   12.3   0.5    1.3  1  SecG             Preprotein translocase SecG subunit


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6     3e-06     0.011     128     173 ..     114     159 ..     108     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-06
                           CbtA 128 lPpepPgvgaadtieaRqalylatvalsavalalavflarrlaarg 173
                                     P ++P   +a ++++R++ ++++v++ ++ala++++l+  l +rg
  gi|121636274|ref|YP_976497.1| 114 VPQSIPPRTEATSVRQRTWGWALAVVVIVLALAAIAILGTVLLTRG 159
                                    5666777777777**************************9997774 PP

>> Lumazine_bd_2  Putative lumazine-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.011        38      52      98 ..     154     204 ..     136     206 .. 0.83
   2 ?    8.8   0.1   0.00071       2.6      59     111 ..     215     270 ..     205     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                                    HHHHHHHH..-TT-EE-.EEEEEEEEE...TT.EEEEEEEEEETTEEEEEE CS
                  Lumazine_bd_2  52 lalvaerespakegdprekeIesidva...gd.vAmvkvelelpdenftDy 98 
                                    + l++ ++s+ +++d+ ++ I+s+d+a   gd +A   +++  + + + Dy
  gi|121636274|ref|YP_976497.1| 154 VLLTRGKHSKMSQEDQVRQAIQSLDIAiqtGDlTALRSLTCGSTRDGYVDY 204
                                    567888999999*************95333777888888888888888887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00071
                                    H..-TT-EE-.EEEEEEEEETTEEEEEEEEEET...TEEEEEEEEEEEETTEEEEE CS
                  Lumazine_bd_2  59 espakegdprekeIesidvagdvAmvkvelelp...denftDyLslvkidgeWkIv 111
                                    + +a+++ p   +I+++ v+g  A ++v++ ++   + + t  L l  +d++WkI 
  gi|121636274|ref|YP_976497.1| 215 RVSAAKQYPVIASIDQVVVNGAHAEANVTTFMAfdpQVRSTRSLDLQFRDDQWKIC 270
                                    336788889999*****************9775445789999************95 PP

>> PRIMA1  Proline-rich membrane anchor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   1.4e-05     0.049      12      77 ..      87     153 ..      76     164 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                         PRIMA1  12 kvtescqeacqcrrypp.lpppppppppprllsltaaestvsplepwwsel.viiiavvcaslvfllv 77 
                                     +te  q + q  ++pp +p+  pp  +    +++ +e+t+++ ++w   l v++i ++ a++  l  
  gi|121636274|ref|YP_976497.1|  87 AATEVFQ-TNQAPTTPPrMPTGMPPKTAVPQSIPPRTEATSVRQRTWGWALaVVVIVLALAAIAILGT 153
                                    2333333.333333333134433333333335567788999999999555504444444555444433 PP

>> Phage_holin_7_1  Mycobacterial 2 TMS Phage Holin (M2 Hol) Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   7.4e-05      0.27      32      83 ..     130     181 ..     122     193 .. 0.87
   2 ?    1.1   0.0      0.12   4.2e+02      30      56 ..     217     243 ..     213     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.4e-05
                Phage_holin_7_1  32 adlidivvavvsvlvaaalavaavvlrkqikdattaavdkvvkslediqavl 83 
                                      ++ +++ vv vl+ aa+a+ ++vl  + k +  +  d+v ++++ ++  +
  gi|121636274|ref|YP_976497.1| 130 RTWGWALAVVVIVLALAAIAILGTVLLTRGKHSKMSQEDQVRQAIQSLDIAI 181
                                    5799999*************************************99876554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                Phage_holin_7_1  30 saadlidivvavvsvlvaaalavaavv 56 
                                    saa+   +++++  v+v +a a a v+
  gi|121636274|ref|YP_976497.1| 217 SAAKQYPVIASIDQVVVNGAHAEANVT 243
                                    567777899999999999999999887 PP

>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   3.9e-05      0.14       1      28 [.     138     165 ..     138     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                    HHHHHHHHHHHHHHHHHHHCHHCCSCCH CS
                           SecG   1 illillvivsilLillvLlQsgkgagls 28 
                                    +++i+l++++i++ + vLl +gk + +s
  gi|121636274|ref|YP_976497.1| 138 VVVIVLALAAIAILGTVLLTRGKHSKMS 165
                                    578**********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1876.56
//
Query:       gi|121636275|ref|YP_976498.1|  [L=460]
Description: Mg2+ transport transmembrane protein mgtE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-26   90.8  10.2    1.6e-25   89.9  10.2    1.5  1  MgtE        Divalent cation transporter
    1.9e-17   63.7   0.7    1.9e-17   63.7   0.7    1.8  2  MgtE_N      MgtE intracellular N domain
    8.7e-09   35.7   1.1    0.00088   19.7   0.4    2.6  2  CBS         CBS domain
    0.00083   19.5   0.5     0.0026   18.0   0.3    2.0  2  FliG_M      FliG middle domain
  ------ inclusion threshold ------
      0.017   15.2   0.2      0.039   14.1   0.2    1.5  1  sCache_3_2  Single cache domain 3


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9  10.2   4.4e-29   1.6e-25       1     124 []     326     448 ..     326     448 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 4.4e-29
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHH CS
                           MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvl 79 
                                    iP+++g+gGn+g+q a+++++a+++g+++ + +  vl+kel +++l+g++++++++++a++lg  ++++l+v+l++++++
  gi|121636275|ref|YP_976498.1| 326 IPLLIGTGGNTGTQIATTLVRAMATGQVRFRdVPAVLAKELSTGVLVGLTMAAAAVVRAWTLGVGPQVTLTVALTVAAIV 405
                                    7***************************9999************************************************ PP

                                    HHHHHH..HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHHH CS
                           MgtE  80 laaallilgvllplllwklglDPdnaaiPlltalgDllgtlllvl 124
                                    ++++l+  +++lp ll+kl +DP+++++P++++++D +g+l+++l
  gi|121636275|ref|YP_976498.1| 406 VWSSLV--AAVLPPLLKKLRIDPAIVSGPMIATIVDGTGLLIYFL 448
                                    ******..***********************************95 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.7   5.4e-21   1.9e-17       5     102 .]      37     134 ..      34     134 .. 0.98
   2 ?   -2.9   0.2       2.9     1e+04      62      72 ..     250     260 ..     243     268 .. 0.53

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 5.4e-21
                                    HHHHCHCCS-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHHHC CS
                         MgtE_N   5 diaelleelpeeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeekveellsa 84 
                                    d a+ l +l+++e  +l  ll+   a+e++e +d++l++e ++a++++ +a +le ldsD+aa++l+e +e+k+e+ll++
  gi|121636275|ref|YP_976498.1|  37 DRARELGSLSKAELGKLGPLLDGTNAVELFESIDDKLAAEALHAMDPSLAATFLEALDSDHAANILREFKEPKREALLTL 116
                                    78999*************************************************************************** PP

                                    S-HHHHHHHHHHCTS-TT CS
                         MgtE_N  85 ldeeereeieellsYped 102
                                    l+ e++  ++ lls+ped
  gi|121636275|ref|YP_976498.1| 117 LPLERAMVLRGLLSWPED 134
                                    *****************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                    -HHHHHHHHCC CS
                         MgtE_N  62 dsDdaadllee 72 
                                      D+a+d+ ee
  gi|121636275|ref|YP_976498.1| 250 AEDEAIDIAEE 260
                                    45666666555 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.5e-05     0.054       5      52 ..     140     196 ..     136     200 .. 0.74
   2 !   19.7   0.4   2.5e-07   0.00088       1      48 [.     204     251 ..     204     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                    SBSSCEEEETTSBHHHHHHHHHH........HTSSEE.EEEETTTBEEEEEEHHHHH CS
                            CBS   5 mtrdvvtvppdttleealelmre........kgvsrl.PVVdedgklvGivtlrDll 52 
                                    m ++ +tv+p++t+++a+   re        ++ +++ +V+d d +l+G++  r l+
  gi|121636275|ref|YP_976498.1| 140 MVPETLTVRPNMTVSQAVASVRErasglrsdARTTAYvYVTDADSHLLGVIAFRALV 196
                                    667789************9997534444433334566478888889*****888776 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.5e-07
                                    HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEH CS
                            CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtl 48 
                                    V+++m +d+++v+p t+ e a+++ m  +++ ++PVVd d++l+Gi+ +
  gi|121636275|ref|YP_976498.1| 204 VRELMGDDLIVVSPLTDKELAAQTiM-GHNLMAVPVVDADNRLLGIIAE 251
                                    899**************888888857.99966**************976 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   7.2e-07    0.0026       8      43 ..      78     113 ..      71     117 .. 0.86
   2 ?   -3.0   0.0       2.5   8.9e+03      29      44 ..     306     321 ..     303     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.2e-07
                                    HTTS-HHHHHHHHHTS-HHHHHHHHHTS-HHHHHHH CS
                         FliG_M   8 lknEhPqtiAliLsyLdpeqAAevLseLpeelraev 43 
                                    l+   P  +A++L  Ld+++AA++L e++e +r+ +
  gi|121636275|ref|YP_976498.1|  78 LHAMDPSLAATFLEALDSDHAANILREFKEPKREAL 113
                                    55567999**********************999865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                    HHHHHTS-HHHHHHHH CS
                         FliG_M  29 AevLseLpeelraevi 44 
                                    ++vL ++++e+ a ++
  gi|121636275|ref|YP_976498.1| 306 GSVLRAFSDEMEAVIA 321
                                    5688888888887665 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.1e-05     0.039      41     122 ..     155     249 ..     132     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                     sCache_3_2  41 qalvddvrritgvd.......yvvitDeeg........rvlahpdpaevgrkl..sgpataaalkagrayvgtvtgtlgp 103
                                    qa +   +r++g+        yv++tD++         r l  ++p++ +r l   ++   + l+  +  ++t+ g    
  gi|121636275|ref|YP_976498.1| 155 QAVASVRERASGLRsdarttaYVYVTDADShllgviafRALVLANPEQRVRELmgDDLIVVSPLTDKELAAQTIMG---- 230
                                    344445556666667777778********9777655555555599**99999944444444555555555555544.... PP

                     sCache_3_2 104 slrvklPvfdadgrviGiv 122
                                       +++Pv+dad+r+ Gi+
  gi|121636275|ref|YP_976498.1| 231 HNLMAVPVVDADNRLLGII 249
                                    6679*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3233.16
//
Query:       gi|121636276|ref|YP_976499.1|  [L=344]
Description: fructose-bisphosphate aldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-81  274.2   0.1    1.4e-81  274.1   0.1    1.0  1  F_bP_aldolase  Fructose-bisphosphate aldolase class-II


Domain annotation for each model (and alignments):
>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.1   0.1   7.8e-86   1.4e-81       3     280 .]       9     340 ..       7     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 7.8e-86
                                    HHHHHHHHHHHT--EEEEE--SHHHHHHHHHHHHHHTS-EEEEE-HHHHHHHH-........HHHHHHHHHHHHHHHHT. CS
                  F_bP_aldolase   3 lkellkkAkeegyavgafnvtnletvkavleaaeeaksPvIlqlsegaaakyag........gaealaelvraaaeaykk 74 
                                    + e+l +Ak++ ya +a+n+t++etv+a+++++++a s+ I+q+s+g+a++ +g        ga alae+ + +a +y+ 
  gi|121636276|ref|YP_976499.1|   9 YAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFGSGlgvkdmvtGAVALAEFTHVIAAKYP- 87 
                                    579**********************************************88877**********************887. PP

                                    ..-EEEEEE----G.............HHHHHHHHHH.........S-SEEEE--TTS-HHHHHHHHHHHHHHHHHTT-E CS
                  F_bP_aldolase  75 asvpvalhlDHgak.............leglkkaiea.........gfsSvMiDgSelpleeNialtkevverahalgvs 132
                                      v+valh+DH+ k                      a         +f+S+M+DgS+ p++eN+a+++e+++ a+a++++
  gi|121636276|ref|YP_976499.1|  88 --VNVALHTDHCPKdkldsyvrpllaiS--------AqrvskggnpLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKII 157
                                    ..***********988777644443320........24556677779********************************* PP

                                    EEEE-----------..TT-TTTS--HHHHHHHHHHHH.....-EEEE--SS---SS--SS...--THHHHHHHHHH... CS
                  F_bP_aldolase 133 vEaElGriggeedgv..vaeeklyTdpeeaeefveetg.....vdalAvaiGnvHGvykpk.pkLdferlkeiqkav... 201
                                    +E+E+G++ggeedgv  + +eklyT+pe+ e+ +e++g      ++lA+++GnvHGvykp+  kL++++l++ q+ +   
  gi|121636276|ref|YP_976499.1| 158 LEIEIGVVGGEEDGVanEINEKLYTSPEDFEKTIEALGagehgKYLLAATFGNVHGVYKPGnVKLRPDILAQGQQVAaak 237
                                    ***************7766788*******************99******************555**********999999 PP

                                    .........--SEE-SGTTS-HHHHHHHHHTTEEEEEE-HHHHHHHHHHH.....HHG....G.....E-HH.H-HHHHH CS
                  F_bP_aldolase 202 .........vplVlHGgsgvpdeeirkaiklGvvKiNidtdlrlaytkav.....kke....k.....enkk.ydprkll 257
                                             + +V+HGgsg+ ++ei++a ++GvvK+N+dtd+++a+t+ +     +++    k     + kk ydpr++l
  gi|121636276|ref|YP_976499.1| 238 lglpadakpFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIaghmfTNYdgvlKvdgevGVKKvYDPRSYL 317
                                    998888844447**************************************55444333555515566678888******* PP

                                    HHHHHHHHHHHHHHHHHTT-SS- CS
                  F_bP_aldolase 258 keaeeamkevvkekiellgsagk 280
                                    k+ae++m+++v +++++l++agk
  gi|121636276|ref|YP_976499.1| 318 KKAEASMSQRVVQACNDLHCAGK 340
                                    *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2429.57
//
Query:       gi|121636277|ref|YP_976500.1|  [L=227]
Description: hypothetical protein BCG_0402 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-20   71.7   5.3    7.1e-20   71.7   5.3    1.7  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   5.3   3.9e-24   7.1e-20       1     119 [.      47     174 ..      47     175 .. 0.93
   2 ?   -2.7   0.2      0.46   8.2e+03     100     109 ..     190     199 ..     176     209 .. 0.50

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.9e-24
                    SNARE_assoc   1 lPsevllvaaGvlf.......glllgtlvtslgallGaslayllgrylgr...kalrrkllsekrvkalerlverygfla 70 
                                    lP+e ll+++G+l         + +  ++++l a+lG+ +ay++gr++g+   k+  ++++++++v ++++++e+yg ++
  gi|121636277|ref|YP_976500.1|  47 LPGESLLFTGGLLSaspappvTIGVLAPCVALVAVLGDQTAYFIGRRIGPalfKKEDSRFFKKHYVTESHAFFEKYGKWT 126
                                    79************88775444444889999************************************************* PP

                    SNARE_assoc  71 llllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                    ++l+r++pi  r++v+++aG++ +++  F+++ ++G + w   ++++G+
  gi|121636277|ref|YP_976500.1| 127 IILARFVPIA-RTFVPVIAGVSYMRYPVFLGFDIVGGVAWGAGVTLAGY 174
                                    ********98.******************************99999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.46
                    SNARE_assoc 100 flatfiGsip 109
                                    +la ++ s++
  gi|121636277|ref|YP_976500.1| 190 ILALVFVSLL 199
                                    2333332332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1674.86
//
Query:       gi|121636278|ref|YP_976501.1|  [L=376]
Description: hypothetical protein BCG_0403c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-30  107.1   0.0    1.6e-30  106.8   0.0    1.1  1  Glyco_hydro_76  Glycosyl hydrolase family 76
  ------ inclusion threshold ------
       0.05   13.4   0.1       0.11   12.3   0.1    1.5  1  FTP             Fungalysin/Thermolysin Propeptide Motif


Domain annotation for each model (and alignments):
>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   1.8e-34   1.6e-30       4     359 ..       9     351 ..       6     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.8e-34
                                    HHHHHHHHHHHHHCETTECCTCTCBSCES...........-GHHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHHCCCTCE CS
                 Glyco_hydro_76   4 saaatiakgllkyYkgnesggtpgnlpdp...........yywWeagalfgalidywrltgdstyndlitqallaqagen 72 
                                    sa++++++++l+  ++  +g++   + +p           +ywW+a +l+++l+d++ + ++++ ++ i++++ +++ +n
  gi|121636278|ref|YP_976501.1|   9 SAETAVTQRHLRRLWAL-PGTQLAVVAWPstrrdrlfgswHYWWQA-HLLDCLVDAQLRDPQPQRRARINRQVRSHRVRN 86 
                                    56666666677555555.5666666666655555555554599986.*****************************9988 PP

                                    E-SSSTTCTCSSEHHHHHHHHHHHHHHHHH.....H--HHHHHHHHHHHHHHHHCB-SCSCCS-BBSEC..ESS--SEEE CS
                 Glyco_hydro_76  73 ydympanqsrtegnDDqafwglaamtaaernfpeptdepswLalAqavfntqasrwdeetcgGGlrWqiftwnsgydykn 152
                                     ++ + n     ++DD+a+ +l a+++a r      ++++  +l+    n+ ++ w  e+ gGG+ W+      ++++ n
  gi|121636278|ref|YP_976501.1|  87 -NFSWLNS----YYDDMAWLAL-ALERADRVAGV-RRRRALPKLT----NQFVEAWVPED-GGGIPWRK-----QDQFFN 149
                                    .6776666....6677777766.78888874444.4666666665....555699***97.******86.....99**** PP

                                    HHHHHHHHHHHHHHHHHH.--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCCEEEE---HHHHHHHHHHHHHHH CS
                 Glyco_hydro_76 153 sisngplfqlaarLaryt.gnetYlewAekvwdWvedvgliddedwlvyDgasvednctdinklqwtYnqGtylsgaayl 231
                                    + +ngp   +++ Lary  +  + l+ Ae++ dW+ ++ lid+e++lv+Dg+    + +++ ++q+tY+qG++l+  + l
  gi|121636278|ref|YP_976501.1| 150 APANGP---AGLFLARYPdQYGKRLKRAEQMADWIDRT-LIDPETHLVFDGI----KAGSLVRAQYTYCQGVVLGLETEL 221
                                    ******...9*******9455669*************5.99**********9....44679******************* PP

                                    HHHH--H...HHHHHHHHHHHHHHHHCEECTTEEEEEE-TTSTTCCTTHHHHHHHHHHHHHHHH..SH.HHHHHHHHHHH CS
                 Glyco_hydro_76 232 ynaTgde...kWldrvkgllnatlstffpdgnilyevacepsekcnnDqrsFkgilarwlaltaqlap.etadtiepllr 307
                                       Tg +   ++  rv++l++a+++++ p  ++l            +D  +F+gi+ar+lal+a+++p ++ad++    r
  gi|121636278|ref|YP_976501.1| 222 AVRTGPAaraRHCARVHRLVAAVNEHMAPL-GVLRG-------AGGGDGGLFAGITARYLALVATTLPgDSADDAA--AR 291
                                    ****654455********************.99955.......24689********************77776665..78 PP

                                    HHHHHHH.TTTB.....TTTSB-TTTTTSSCCHHHH....HHHHCCHHH........... CS
                 Glyco_hydro_76 308 asaeaaa.kscsggs..dgttcglkwlkgtwdgdag....lgeqmsale.viqallveek 359
                                    ++a+a++ +s+++ +  ++t  gl  +   wd+ a+     geq+  +  ++ ++ ++e+
  gi|121636278|ref|YP_976501.1| 292 DTARAIVlASAQSAWdyRQTVDGLPVFGAFWDREAElptaGGEQARSVRgAVHSSAIAER 351
                                    888888877777777444555788888777888776444445555555446666666665 PP

>> FTP  Fungalysin/Thermolysin Propeptide Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.2e-05      0.11      20      32 ..     308     320 ..     307     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                    EEEEETTEEEEEE CS
                            FTP  20 yqQtynGipVfgg 32 
                                    y+Qt++G+pVfg+
  gi|121636278|ref|YP_976501.1| 308 YRQTVDGLPVFGA 320
                                    9***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2563.23
//
Query:       gi|121636279|ref|YP_976502.1|  [L=197]
Description: hypothetical protein BCG_0404c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-13   51.1   0.1    2.2e-13   49.9   0.1    1.5  1  Zeta_toxin  Zeta toxin
    1.8e-11   44.4   0.0    2.3e-11   44.0   0.0    1.1  1  AAA_33      AAA domain
      0.002   18.7   0.0      0.011   16.2   0.0    2.0  1  ABC_tran    ABC transporter
     0.0091   15.7   0.0      0.015   15.0   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.025   15.0   0.0      0.034   14.5   0.0    1.2  1  AAA_16      AAA ATPase domain
      0.055   13.1   0.0      0.081   12.5   0.0    1.3  1  AAA_27      AAA domain
       0.14   11.8   0.0       0.25   11.0   0.0    1.4  1  CoaE        Dephospho-CoA kinase
        0.2   12.1   0.0       0.27   11.7   0.0    1.2  1  AAA_23      AAA domain
       0.22   11.2   0.0       0.33   10.7   0.0    1.2  1  AAA_24      AAA domain


Domain annotation for each model (and alignments):
>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   1.1e-16   2.2e-13      18     187 ..       4     155 ..       1     159 [. 0.87

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.1e-16
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdl.RelhPeyeeilkadpkkaseltqkdaselvekllqeaiengy 96 
                                    l l++G  GAGKs+  +l+ + l    ++v +++D++ +++ P+       dp++ +     +a ++++ +++ +i+ g+
  gi|121636279|ref|YP_976502.1|   4 LDLVAGPNGAGKSTFVALTLAPL--LPGIVFVNADEIaKQRWPD-------DPTSHAY----QAAQVAADTRARLIDLGR 70 
                                    679********************..89*********85778887.......2222222....356788999********* PP

                     Zeta_toxin  97 niivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaegRlvpkeehdeafeglresvealeee 176
                                     +i e+ +++p++++ l++ ++ aGY+v ++v+  ++ l++++v+ R+ +    g  vp++++ e +++l+e v++    
  gi|121636279|ref|YP_976502.1|  71 PFIAETVFSHPSKLE-LIRTARTAGYTVVLHVLVIPEGLAVERVRHRVAAG---GHDVPETKIRERHRRLAELVAQ--AI 144
                                    ***************.***********************************...667*************999988..44 PP

                     Zeta_toxin 177 kqldrvkikdr 187
                                    +++d  +++d+
  gi|121636279|ref|YP_976502.1| 145 TLADGATVYDN 155
                                    46677777766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.1e-14   2.3e-11       3     141 ..       6     137 ..       4     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.1e-14
                         AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnl 80 
                                    l+ G++G+GKst++   l++l    v+++ d++ ++  ++d++s  +++       q  +++ ++    gr++i+   + 
  gi|121636279|ref|YP_976502.1|   6 LVAGPNGAGKSTFVALTLAPLLpgIVFVNADEIAKQRWPDDPTSHAYQAA------QVAADTRARLIDLGRPFIAETVFS 79 
                                    578************9998887799**************99999877443......3333444444579*****986666 PP

                         AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarfe 141
                                     +++  ++++ ar +g+ v ++v+  +e ++ eR++ R a+g+++  vpe  + + ++r+ 
  gi|121636279|ref|YP_976502.1|  80 HPSKL-ELIRTARTAGYTVVLHVLVIPEGLAVERVRHRVAAGGHD--VPETKIRERHRRLA 137
                                    66665.67778889****************************986..99999988888765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.6e-06     0.011      16      67 ..       7      54 ..       3     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                                   EEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 16 ivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67
                                   + G+nGaGKSt+++l +  l p  G + ++ +++ +q  ++ +   +   q 
  gi|121636279|ref|YP_976502.1|  7 VAGPNGAGKSTFVALTLAPLLP--GIVFVNADEIAKQ--RWPDDPTSHAYQA 54
                                   57***********998887776..8888888887773..3333444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.4e-06     0.015      26      42 ..       6      21 ..       1      35 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                         AAA_29 26 lltGpsGsGKSTllDAi 42
                                   l++Gp+G+GKST++ A+
  gi|121636279|ref|YP_976502.1|  6 LVAGPNGAGKSTFV-AL 21
                                   89***********9.54 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.034      28     129 ..       6     146 ..       2     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                         AAA_16  28 llsGesGvGKsslvrellralekdggif......lrgkcdqlesaipysalaqalareellrqllde.......aesael 94 
                                    l+ G+ G GKs+ v   l +l    ++f      +++++ + +++ +y+a   a++++  l +l+++       +  ++l
  gi|121636279|ref|YP_976502.1|   6 LVAGPNGAGKSTFVALTLAPLLPG-IVFvnadeiAKQRWPDDPTSHAYQAAQVAADTRARLIDLGRPfiaetvfSHPSKL 84 
                                    89****************999987.7775666666666666666677766444444556666777767766666333344 PP

                         AAA_16  95 eawrekleeala..........................avpelagaea.....srllellkrllal 129
                                    e  r++ ++ ++                          +vpe     +     +rl+el+++++ l
  gi|121636279|ref|YP_976502.1|  85 ELIRTARTAGYTvvlhvlvipeglavervrhrvaagghDVPET----KirerhRRLAELVAQAITL 146
                                    4444444444446778888888887777777776433333333....3444467777777777655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05     0.081      26      44 ..       2      20 ..       1      37 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                         AAA_27 26 adlhliyGpNEAGKstalr 44
                                   ++l l+ GpN AGKst ++
  gi|121636279|ref|YP_976502.1|  2 KRLDLVAGPNGAGKSTFVA 20
                                   5799************875 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.25       7      82 ..       9      87 ..       6      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                   ESTTSSHHH.HHHHHHH..TT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-HHHHHHHHHTSHHHHHHH CS
                           CoaE  7 GgiasGKst.vanlfad..lgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdReaLrkkvFadpeekkaL 82
                                   G  ++GKst va ++a    g+  v aD +A+q    + +  +  +++  ++  ++   L R  ++++vF++p++ +++
  gi|121636279|ref|YP_976502.1|  9 GPNGAGKSTfVALTLAPllPGIVFVNADEIAKQRWPDDPTSHAYQAAQVAADTRARLIDLGRPFIAETVFSHPSKLELI 87
                                   66799***956667777656999*********988766666666666777777777899**************998765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.27      23      36 ..       6      19 ..       2      24 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                         AAA_23 23 lItGpNGaGKTTil 36
                                   l+ GpNGaGK+T++
  gi|121636279|ref|YP_976502.1|  6 LVAGPNGAGKSTFV 19
                                   778*********86 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.33       6      33 ..       6      37 ..       2      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                         AAA_24  6 liyGpsgiGKTtlakel....gpkplfidtek 33
                                   l+ Gp+g+GK+t+++       p ++f++ ++
  gi|121636279|ref|YP_976502.1|  6 LVAGPNGAGKSTFVALTlaplLPGIVFVNADE 37
                                   689**********9988788889999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1334.92
//
Query:       gi|121636280|ref|YP_976503.1|  [L=129]
Description: hypothetical protein BCG_0405c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-22   78.5   2.9    5.1e-22   77.7   2.9    1.4  1  ParD_like  ParD-like antitoxin of type II bacterial toxin-ant


Domain annotation for each model (and alignments):
>> ParD_like  ParD-like antitoxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   2.9   2.8e-26   5.1e-22       2      72 ..       7     106 ..       6     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.8e-26
                      ParD_like   2 givkiddeLhdsarresaaqsRSinaQiehWariGrlvesspslsyr.............................eiee 52 
                                    ++++++++L+dsa++e+a+qsRS+++Q++hWar+Gr+v+++++ s+r                             +iee
  gi|121636280|ref|YP_976503.1|   7 RVTRVAADLVDSAAAEGARQSRSAKQQLDHWARVGRAVSNQHTASRRrveaalaghlpmtdltleegvvfnaeisaAIEE 86 
                                    79****************************************************************************** PP

                      ParD_like  53 lllkaaeeeelatrgrtlve 72 
                                    +l +++++++la++g+t+v+
  gi|121636280|ref|YP_976503.1|  87 RLSRTNYGDVLAAQGITTVA 106
                                    ***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.55
# Mc/sec: 705.63
//
Query:       gi|121636281|ref|YP_976504.1|  [L=403]
Description: hypothetical protein BCG_0406c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-70  237.3   3.2    1.2e-70  237.3   3.2    1.6  2  VWA_CoxE  VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
        0.1   13.3   0.0        0.3   11.8   0.0    1.7  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.23   2.1e+03     199     219 ..      17      38 ..      11      64 .. 0.63
   2 !  237.3   3.2   1.4e-74   1.2e-70       2     222 ..     172     391 ..     171     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.23
                       VWA_CoxE 199 pe.aralrailphvdelrpleq 219
                                    ++ a++lr+++++v +   +++
  gi|121636281|ref|YP_976504.1|  17 AAlAARLRDAGIPVSASGQASL 38 
                                    5556666666666655444443 PP

  == domain 2  score: 237.3 bits;  conditional E-value: 1.4e-74
                       VWA_CoxE   2 akklaalllglarrr.rrrkrrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflal 80 
                                    + +l+a++++++rrr +r++++++g+riDlr+t++a+ ++g+e v l+r++pr r+pr+++ll+DvS+Sm+ y+ai+l+l
  gi|121636281|ref|YP_976504.1| 172 GAWLEATMARWPRRRsMRFESSPHGKRIDLRATMNASRSTGWESVLLARIRPR-RRPRRVLLLCDVSRSMQPYAAIYLHL 250
                                    6799***********************************************99.7777********************** PP

                       VWA_CoxE  81 lhAllqqlp..rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvs 158
                                    ++A++ ++   + evfaF+t+l++lT+ l++r++++aL+r++a+v+d++GgT ig+++a++l  ++ +aL r+avv++ s
  gi|121636281|ref|YP_976504.1| 251 MRAAVLRRAggHPEVFAFSTSLTRLTSVLSHRSAEMALHRANARVTDRYGGTFIGRSVAALLAPPHGNAL-RGAVVIIAS 329
                                    ***9999999***********************************************************7.********* PP

                       VWA_CoxE 159 Dglergdreellaelarlvrrarrlvwlnplsdagtpgydpearalrailphvdelrpleqlas 222
                                    Dg+++++ + l+++l+r++rra  lvwlnp+  a++p+++p+a++++a+lp++d + p+++la 
  gi|121636281|ref|YP_976504.1| 330 DGWDSDPPDVLVHALTRVRRRAELLVWLNPR--AAHPEFQPRAGSMAAALPYCDLFLPAHSLAG 391
                                    *******************************..****************************986 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.8   7.2e+03      57      71 ..      33      47 ..      17      56 .. 0.67
   2 ?   11.8   0.0   3.3e-05       0.3       1     106 [.     230     331 ..     230     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.8
                          VWA_2 57 kdkakilnalrnlea 71
                                   +++a++ +al++l +
  gi|121636281|ref|YP_976504.1| 33 SGQASLVQALQQLVP 47
                                   455566666666554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.3e-05
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleak....gggt 76 
                                    ++++ D+S Sm+++       ++  ++++a + +++g +  + +fs++ ++l+++ + +++ + al++ +a+     ggt
  gi|121636281|ref|YP_976504.1| 230 VLLLCDVSRSMQPY------AAIYLHLMRAAVLRRAGGHPEVFAFSTSLTRLTSVLS-HRSAEMALHRANARvtdrYGGT 302
                                    6899*********8......899************************9988888754.3344445555555544559999 PP

                          VWA_2  77 nlaaaLqlarkalkkrrkgekrvivlitDg 106
                                     ++  +  + +  + + + + +v+++ +Dg
  gi|121636281|ref|YP_976504.1| 303 FIGRSVAALLAPPHGN-ALRGAVVIIASDG 331
                                    9999987766655544.5999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 2267.07
//
Query:       gi|121636282|ref|YP_976505.1|  [L=171]
Description: membrane oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.3   0.2    1.4e-14   54.0   0.2    1.1  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
  ------ inclusion threshold ------
      0.051   13.8   0.1      0.064   13.5   0.1    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
      0.068   13.4   0.1       0.11   12.6   0.1    1.4  1  DAP_epimerase    Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.2   2.3e-18   1.4e-14      26     139 ..       1     116 [.       1     117 [. 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.3e-18
                                    STTEEEEEEETTEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE...EEEE.EE-SSEEEEEEEEEEEEEETTEEEEEE CS
                           COXG  26 iPGvksvekegdeykvkvklkvGplkgsfkarvelselekenstt.ieikGk.Grgagvaidfalvvlveegggtrlsws 103
                                    +PG + +  egdey  kvk+kvGp+ ++f+++v ++e + ++      +kGk +rg g a+ + + +l+e g+ tr+  +
  gi|121636282|ref|YP_976505.1|   1 MPGAQLIGHEGDEYLGKVKVKVGPVTSEFSGKVHFVEQDRNQHRAvFDAKGKeARGTGNAAATVAAQLHEVGERTRVTVD 80 
                                    69*********************************987766554438999965889999999999999999899****** PP

                                    EEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                           COXG 104 akvnvggllaslGsrlidsaarklinelfecisskl 139
                                     + ++ g+la+ Gs +++++ +kl+ +++ +++++l
  gi|121636282|ref|YP_976505.1|  81 TDLKIVGKLAQFGSGMLQQVSEKLLGQFVDSLEAEL 116
                                    ******************************999887 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.1e-05     0.064      61     142 ..      31     116 ..       4     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                    EEEEEEEEETTTTEEEEEEE...SSS-TSEEEE..EEEEECCETEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  61 vreelvevdpegrllsyriv..kpvpvanyvat..wtvtpdgggtrvtwtgefda.gplggpfekpaaakavkgdleagL 135
                                     +  +ve d ++++  +++   + ++++n  at   +++++g+ trvt + ++++ g l++++  +++    ++ l + +
  gi|121636282|ref|YP_976505.1|  31 GKVHFVEQDRNQHRAVFDAKgkEARGTGNAAATvaAQLHEVGERTRVTVDTDLKIvGKLAQFG-SGMLQQVSEKLLGQFV 109
                                    45556777777899999994477777777766634789999999**********768888887.6888999999999999 PP

                                    HHHHHHH CS
                Polyketide_cyc2 136 erLkarl 142
                                    + L+a+l
  gi|121636282|ref|YP_976505.1| 110 DSLEAEL 116
                                    9999886 PP

>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.11      43      95 ..      33      81 ..      13      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                   EEEEEEEETTEEEEEEEETTTEEESTTHCCHHHHHHHHHCTTS-S-SEEEEEE CS
                  DAP_epimerase 43 vlfvkpsgeediklryfnrdgseaemCGnGvrvfaaylreggletkkevtvet 95
                                   v+fv++  +++ +  +f + g ea+  Gn+++ +aa l e g  ++++vtv+t
  gi|121636282|ref|YP_976505.1| 33 VHFVEQ--DRNQHRAVFDAKGKEARGTGNAAATVAAQLHEVG--ERTRVTVDT 81
                                   777773..33334459*********99999999999999998..799999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1250.23
//
Query:       gi|121636283|ref|YP_976506.1|  [L=298]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-11   43.5   0.0    1.1e-10   41.7   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    1.7e-09   37.6   0.0    0.00027   20.8   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
    6.3e-09   36.3   0.0    3.6e-08   33.9   0.0    2.1  1  AAA              ATPase family associated with various cellul
    5.7e-06   26.8   0.9    6.7e-05   23.3   0.9    2.4  1  AAA_16           AAA ATPase domain
    2.3e-05   24.7   0.0    7.3e-05   23.1   0.0    1.8  1  AAA_22           AAA domain
    0.00042   20.3   0.1      0.023   14.6   0.0    2.2  2  NACHT            NACHT domain
     0.0046   17.1   0.0     0.0099   16.0   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0073   16.1   0.5       0.33   10.7   0.1    2.7  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.024   14.0   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.035   13.8   0.0      0.048   13.4   0.0    1.3  1  AAA_24           AAA domain
      0.055   13.6   0.0        0.1   12.8   0.0    1.4  1  AAA_33           AAA domain
      0.058   13.1   0.0        1.8    8.2   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
      0.073   13.0   0.1       0.21   11.5   0.1    1.9  1  NTPase_1         NTPase
      0.099   13.0   0.0       0.21   12.0   0.0    1.6  1  RNA_helicase     RNA helicase
        0.1   13.1   0.0        0.2   12.2   0.0    1.5  1  AAA_18           AAA domain
       0.14   11.7   0.0        0.2   11.1   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
       0.15   12.1   0.1       0.27   11.3   0.1    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.19   12.1   0.1        3.5    8.0   0.1    2.2  2  AAA_19           AAA domain
       0.19   11.8   0.0          1    9.4   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.1e-13   1.1e-10       1     137 [.      37     191 ..      37     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.1e-13
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--......................--------... CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.............ngttslvdsplvraar... 64 
                                    ++lL G+pG+gK++ a+ la +l +++   q+++++t+++ ++ ++++             +g    ++  l+++a    
  gi|121636283|ref|YP_976506.1|  37 PLLLEGEPGVGKTTAAKTLAVVLDTTLIRLQCYEGLTANEALYDWNYQrqllsirlaeargKGISDISEADLYTEAYlvd 116
                                    589********************************************977777777777665555556666666555999 PP

                                    ............G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTH CS
                          AAA_5  65 ............egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelsp 132
                                                ++ +l++DE++ra++e  + Ll  l e  + ++e+g+   + ++        + t+n+ +    +l  
  gi|121636283|ref|YP_976506.1| 117 rpilrcvrhrgpTPPVLLIDEIDRADDEFEALLLEFLGESAVTVPELGTFLAECPP------IAVLTSNRSR----DLHD 186
                                    99999999************************************998876666553......5666777776....6777 PP

                                    HHHTT CS
                          AAA_5 133 alrsR 137
                                    alr+R
  gi|121636283|ref|YP_976506.1| 187 ALRRR 191
                                    88888 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.9e-07   0.00027       2      36 ..      38      72 ..      37      94 .. 0.88
   2 !   14.6   0.0   2.3e-05     0.022      55     101 ..     123     168 ..      88     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                          AAA_3  2 vllegvPGlaktllvkalakaldlefkriqftpdl 36
                                   +lleg PG++kt+++k+la +ld+++ r+q+   l
  gi|121636283|ref|YP_976506.1| 38 LLLEGEPGVGKTTAAKTLAVVLDTTLIRLQCYEGL 72
                                   69****************************97666 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.3e-05
                          AAA_3  55 efkkGpvfanllladeinrappktqsalleameerqvtvegethklp 101
                                      ++Gp    +ll dei+ra    ++ lle + e+ vtv +  + l 
  gi|121636283|ref|YP_976506.1| 123 VRHRGPT-PPVLLIDEIDRADDEFEALLLEFLGESAVTVPELGTFLA 168
                                    5566774.5699**************************987655554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.8e-11   3.6e-08       1     124 [.      38     192 ..      38     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.8e-11
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.................................STTHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.................................yvgesekkir 47 
                                    +ll G pG+GKT++ak +a  l+++++++++ e l                                   +  e+    r
  gi|121636283|ref|YP_976506.1|  38 LLLEGEPGVGKTTAAKTLAVVLDTTLIRLQCYEGLTAnealydwnyqrqllsirlaeargkgisdiseadLYTEAYLVDR 117
                                    699*******************9999999998877345799999999999988866655556555555543333333333 PP

                                    HHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.........SSTEEEEEEESSGGGSTH CS
                            AAA  48 elfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.........eskvivigatnrpdkldp 117
                                     +++ +++   +p +l+iDEid+   +             + Ll++l +             e + i ++++nr ++l +
  gi|121636283|ref|YP_976506.1| 118 PILRCVRHRGpTPPVLLIDEIDRADDEF-----------EALLLEFLGESAVTvpelgtflaECPPIAVLTSNRSRDLHD 186
                                    3443344444999**********94333...........44444444444444677777777444599************ PP

                                    HHHSTTS CS
                            AAA 118 allrgRf 124
                                    al+ +R+
  gi|121636283|ref|YP_976506.1| 187 ALR-RRC 192
                                    ***.687 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.9   7.1e-08   6.7e-05      22     160 ..      35     154 ..      25     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.1e-08
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipysalaqalareellrqlldeaesaeleawrek 100
                                    g  + +ll Ge+GvGK++ +++l+  l ++   ++r +c +  +++    al +   +++ll   l+ea+ +  ++ +e+
  gi|121636283|ref|YP_976506.1|  35 G--RPLLLEGEPGVGKTTAAKTLAVVLDTT---LIRLQCYEGlTAN---EALYDWNYQRQLLSIRLAEARGKGISDISEA 106
                                    4..459******************655555...5666666662111...2244444455666666666555555555552 PP

                         AAA_16 101 leealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlr 160
                                     +   +        ea  + + + r++   +r+  p vl++D++++ad++  +ll ++l 
  gi|121636283|ref|YP_976506.1| 107 DLY--T--------EAYLVDRPILRCV--RHRGPTPPVLLIDEIDRADDEFEALLLEFLG 154
                                    222..2........1223333344444..3333457******************555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   7.7e-08   7.3e-05       7     111 ..      37     148 ..      33     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.7e-08
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl..lrellralglelka.............e 71 
                                     l++ Ge+G+GKTt +++l+  l         + ++++ ++ ++ +  +     +  r+l + + a              
  gi|121636283|ref|YP_976506.1|  37 PLLLEGEPGVGKTTAAKTLAVVL---------DTTLIRLQCYEGLTANEAlyDWNYQRQLLSIRLAeargkgisdiseaD 107
                                    57899******************.........788887777666633333112223333333333356677888899988 PP

                         AAA_22  72 rlsseell.ealeqalrarav.ielliiDEaqhlrseealee 111
                                      ++  l+ + + + +r+r+  +++l+iDE+++ + +e    
  gi|121636283|ref|YP_976506.1| 108 LYTEAYLVdRPILRCVRHRGPtPPVLLIDEIDRAD-DEFEAL 148
                                    889999998889999999999************94.333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.023       1      24 [.      36      59 ..      36      68 .. 0.89
   2 ?    3.8   0.0     0.053        50      75     134 ..     123     186 ..      87     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                   SCEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  1 rlvilqGeaGsGKTtLlqklalaw 24
                                   r+++l+Ge+G+GKTt ++ la+ +
  gi|121636283|ref|YP_976506.1| 36 RPLLLEGEPGVGKTTAAKTLAVVL 59
                                   6899****************9866 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.053
                                    HHCCSCCCEEEEEE-STT-SS-TCH...............HHHHHCTTTTT--EEEEEEECCCHHH CS
                          NACHT  75 vllelperlLlilDglDelvtdlgq......kekqpvrtlLselirkkllpeasllltvrpralrd 134
                                    v+ + p+  +l++D +D++ +++++       e + +   L++ + +  +p   +l + r+r l d
  gi|121636283|ref|YP_976506.1| 123 VRHRGPTPPVLLIDEIDRADDEFEAllleflGESAVTVPELGTFLAE--CPPIAVLTSNRSRDLHD 186
                                    4455667778**********999997776664444455556666666..66666666555555544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05    0.0099       7      94 ..      39     144 ..      36     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                    EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HH.HHTTS............... CS
                          AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvg.aeegG............... 70 
                                    ll g+ gvGkt +ak+la +l+     +lir+ + e l+  + e l +   + +   ++ ae +G               
  gi|121636283|ref|YP_976506.1|  39 LLEGEPGVGKTTAAKTLAVVLDT----TLIRLQCYEGLT--ANEALYDWNYQRQLLSIRlAEARGkgisdiseadlytea 112
                                    788999****************6....999999999998..444455544444444443144445679999999999999 PP

                                    ...................EEEEETGGG-------------HH CS
                          AAA_2  71 ...................ivllDEidKihpkessgadvSreg 94 
                                                       ++l+DEid++             +
  gi|121636283|ref|YP_976506.1| 113 ylvdrpilrcvrhrgptppVLLIDEIDRADD-----------E 144
                                    999999999999999*************998...........4 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00035      0.33      36      60 ..      38      62 ..      31      69 .. 0.88
   2 ?    2.2   0.0      0.14   1.3e+02      87     108 ..     132     153 ..     121     161 .. 0.84
   3 ?   -1.5   0.0         2   1.9e+03      38      76 ..     236     276 ..     218     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                                   +ll G PG+Gktt ak +a  l+++
  gi|121636283|ref|YP_976506.1| 38 LLLEGEPGVGKTTAAKTLAVVLDTT 62
                                   699**************99888765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                         RuvB_N  87 vlfideihrlsraveevlysam 108
                                    vl+idei r + + e +l   +
  gi|121636283|ref|YP_976506.1| 132 VLLIDEIDRADDEFEALLLEFL 153
                                    99*********99999987655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2
                         RuvB_N  38 lyGpPGlGktt..lakiiakelgvklkitsgPvlekagdla 76 
                                    l  pPG+  t   +a+++a  +     + s+P+l   g la
  gi|121636283|ref|YP_976506.1| 236 LDKPPGVAETIdwVAALVALGVADLTAADSSPALASLGALA 276
                                    55688888885447888888888888888888888777766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.024      13      47 ..      26      60 ..      21      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                   Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                    a+ +a++ g  lll G pG GKt  ak l+ +l 
  gi|121636283|ref|YP_976506.1| 26 SAIYLAVTLGRPLLLEGEPGVGKTTAAKTLAVVLD 60
                                   688899999999******************99885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.1e-05     0.048       5      31 ..      38      61 ..      35     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                         AAA_24  5 iliyGpsgiGKTtlakelgpkplfidt 31
                                   +l+ G++g+GKTt ak+l   ++++dt
  gi|121636283|ref|YP_976506.1| 38 LLLEGEPGVGKTTAAKTL---AVVLDT 61
                                   5788**************...444443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011       0.1       3      29 ..      39      65 ..      38     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         AAA_33  3 llvGlpGsGKstlaerllkklgavlls 29
                                   ll G pG+GK+t a+ l+  l+++l++
  gi|121636283|ref|YP_976506.1| 39 LLEGEPGVGKTTAAKTLAVVLDTTLIR 65
                                   789**************9777755554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0019       1.8      19      42 ..      32      55 ..      21      71 .. 0.82
   2 ?    2.7   0.0     0.097        92      96     123 ..     132     159 ..     129     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                   CTSSS-EEEECSTTSSHHHHHHHH CS
                Sigma54_activat 19 aktdlsvlitGesGtGKellarai 42
                                   ++   ++l++Ge G+GK++ a+++
  gi|121636283|ref|YP_976506.1| 32 VTLGRPLLLEGEPGVGKTTAAKTL 55
                                   5556789**************986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.097
                                    EEEEETGGGS-HHHHHHHHHHHHHSEEE CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegeve 123
                                    +l++Dei + + e+ + Ll++l e  v+
  gi|121636283|ref|YP_976506.1| 132 VLLIDEIDRADDEFEALLLEFLGESAVT 159
                                    699*******************998764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00022      0.21       3      29 ..      39      65 ..      37     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                   EEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvk 29
                                   ++ G+pGvGKtT  k ++ +l+   ++
  gi|121636283|ref|YP_976506.1| 39 LLEGEPGVGKTTAAKTLAVVLDTTLIR 65
                                   688************999999766554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.21       2      26 ..      39      63 ..      38      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                   +l G++g+GK+t+ak+La  l ++l
  gi|121636283|ref|YP_976506.1| 39 LLEGEPGVGKTTAAKTLAVVLDTTL 63
                                   689*************998877665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021       0.2       2      19 ..      39      56 ..      38      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                         AAA_18  2 lltGtpGvGKttlakeLs 19
                                   ll G pGvGKtt ak L+
  gi|121636283|ref|YP_976506.1| 39 LLEGEPGVGKTTAAKTLA 56
                                   689************996 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022       0.2      27      58 ..      29      60 ..      21      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                          AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkld 58
                                    l ++ ++p+ll G+ G+GKt+ +k+l   ld
  gi|121636283|ref|YP_976506.1| 29 YLAVTLGRPLLLEGEPGVGKTTAAKTLAVVLD 60
                                   5678889*****************99887777 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.27      14      44 ..      30      60 ..      17      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                   HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalg 44
                                   la +lg+ +lLeG+ G+GKTt ++ la  l+
  gi|121636283|ref|YP_976506.1| 30 LAVTLGRPLLLEGEPGVGKTTAAKTLAVVLD 60
                                   344446679****************998776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0037       3.5      10      33 ..      35      58 ..      25      75 .. 0.81
   2 ?    1.8   0.0      0.28   2.7e+02     105     129 ..     132     156 ..     107     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0037
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhival 33
                                    ++ll+ + pG GKT+  k+   +
  gi|121636283|ref|YP_976506.1| 35 GRPLLLEGEPGVGKTTAAKTLAVV 58
                                   6899***********988776554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                         AAA_19 105 llivDEfqdvdelqyrLlkallgek 129
                                    +l++DE+   d+   +Ll + lge+
  gi|121636283|ref|YP_976506.1| 132 VLLIDEIDRADDEFEALLLEFLGES 156
                                    79*********88888887777665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011         1      18      43 ..      32      57 ..      25      84 .. 0.83
   2 ?   -0.6   0.0       1.3   1.3e+03     117     138 .]     142     163 ..     132     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                   HT-SS-EEEEEETT--HHHHHHCC-- CS
                Sigma54_activ_2 18 aqsklpvfltGekGsgkelvArlLhk 43
                                   +    p++l Ge+G gk++ A++L+ 
  gi|121636283|ref|YP_976506.1| 32 VTLGRPLLLEGEPGVGKTTAAKTLAV 57
                                   55667*******************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                    ---HHHHHHHHSSSEEEEE--- CS
                Sigma54_activ_2 117 agafdekLlkeLselrlhvPpL 138
                                      +f++ Ll+ L e+++ vP+L
  gi|121636283|ref|YP_976506.1| 142 DDEFEALLLEFLGESAVTVPEL 163
                                    5689999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2304.77
//
Query:       gi|121636284|ref|YP_976507.1|  [L=197]
Description: hypothetical protein BCG_0409c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-31  109.1   3.9    3.3e-31  108.8   3.9    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.019   14.7   1.4      0.022   14.5   0.7    1.5  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
       0.17   11.4   0.0       0.22   11.1   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   3.9   5.5e-35   3.3e-31       1     156 [.       8     164 ..       8     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 5.5e-35
                                    EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaa 78 
                                    +v+LA+GrS R+g++K+llp++++++l  +ld +r+ag+d++++  g   ++v+aa+a  g++vv+ ed ++g +asl+ 
  gi|121636284|ref|YP_976507.1|   8 GVVLAAGRSNRLGTPKQLLPYRDTTVLGATLDVARQAGFDQLILTLGGaaSAVRAAMALDGTDVVVVEDVERGCAASLRV 87 
                                    79***************************************99996554579999***99******************** PP

                                    HHHH.H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHCHHH CS
                   NTP_transf_3  79 alra.aadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrllrr 156
                                    al++  ++a++++++++D+P + p++++r+++       +++v++y+++ ghp +f++ ++ +la+l gd+g ++l+++
  gi|121636284|ref|YP_976507.1|  88 ALARvHPRATGIVLMLGDQPQVAPATLRRIIDVGP--ATEIMVCRYADGVGHPFWFSRTVFGELARLHGDKGVWKLVHS 164
                                    ****555*************************975..6679**********************************9984 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   3.7e-06     0.022       3     114 ..       8     118 ..       6     129 .. 0.72
   2 ?   -2.8   0.0      0.73   4.3e+03      80     103 ..     144     168 ..     142     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-06
                                    EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.CCEEEEE--SS.HHHH CS
                           IspD   3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.ksiqlvaGGde.Raes 80 
                                     v+ AAG+ +R+  g+pKq+l   + t+l  t+d++ +    d++++ +        +++ ld +++++v+  +   a s
  gi|121636284|ref|YP_976507.1|   8 GVVLAAGRSNRL--GTPKQLLPYRDTTVLGATLDVARQ-AGFDQLILTLGGAASAVRAAMALDgTDVVVVEDVERgCAAS 84 
                                    5899*******8..67*******************998.66777777765554444444444435687777654314788 PP

                                    HHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHH CS
                           IspD  81 VlnglkalegeakfVLvHDaARpllkaadiaell 114
                                       +l  +++ a+ +++  +  p +++a++ +++
  gi|121636284|ref|YP_976507.1|  85 LRVALARVHPRATGIVLMLGDQPQVAPATLRRII 118
                                    8889999988885554455666667766666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.73
                                    HHHHHHHTTSSTT.SEEEE--TT-T CS
                           IspD  80 sVlnglkalegea.kfVLvHDaARp 103
                                    +V+  l  l+g++  + LvH +  p
  gi|121636284|ref|YP_976507.1| 144 TVFGELARLHGDKgVWKLVHSGRHP 168
                                    6777788888888789999998776 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.7e-05      0.22       2     111 ..       8     105 ..       7     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    +v+La G+  RL      ++k+l+p  ++ +++ atl  + ++g+++  ++lt   ++++ + + + + ++    +++e+
  gi|121636284|ref|YP_976507.1|   8 GVVLAAGRSNRL-----GTPKQLLPYRDT-TVLGATLDVARQAGFDQ--LILTLGGAASAVRAAMALDGTD---VVVVED 76 
                                    789999999998.....355666666665.*****************..5555555555555555555444...7899** PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETT CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLgg 111
                                     ++g A ++++a+  ++ ++   +vl+Lg+
  gi|121636284|ref|YP_976507.1|  77 VERGCAASLRVALARVHPRA-TGIVLMLGD 105
                                    **********9999988888.477777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1556.50
//
Query:       gi|121636285|ref|YP_976508.1|  [L=251]
Description: hypothetical protein BCG_0410c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-20   71.9   0.4      1e-19   71.2   0.4    1.3  1  XdhC_C     XdhC Rossmann domain
    1.6e-13   50.6   1.5    1.6e-13   50.6   1.5    2.3  3  XdhC_CoxI  XdhC and CoxI family


Domain annotation for each model (and alignments):
>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.4   1.2e-23     1e-19       3     125 .]     118     229 ..     116     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.2e-23
                                    EE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-HHHHH CS
                         XdhC_C   3 ifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGSrkkaa 82 
                                    i+G  ++a al++l   lg++    d+++  a+++ +p    ta+v+++h+   +ae++++al++ ++y+gl++S+ + a
  gi|121636285|ref|YP_976508.1| 118 IYGETPIADALIELCGLLGYDARR-DTDP--ADTDALP----TAIVIASHGG-PEAEIIRTALDNGVGYVGLVASTVRGA 189
                                    89******************9753.4444..4678899....99*****995.678*******999************** PP

                                    HHCTTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                         XdhC_C  83 rrlerlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                    ++l+ l   +ls++e ar+h+P+Gl+igaktp+eIAvsi+Ae+
  gi|121636285|ref|YP_976508.1| 190 SILDSL---DLSDAERARVHTPVGLAIGAKTPAEIAVSIAAEL 229
                                    ******...8999*****************************7 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   1.5   1.8e-17   1.6e-13       2      67 ..      11      76 ..      10      76 .. 0.96
   2 ?   -3.4   0.0       1.3   1.2e+04      21      32 ..      85      96 ..      83     103 .. 0.72
   3 ?   -2.4   0.1      0.65   5.8e+03      18      34 ..     235     249 ..     227     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.8e-17
                                   HHCT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHHCT--EEEEE CS
                      XdhC_CoxI  2 laagrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideArallaagrtalvry 67
                                   +aa  p++ aTVv+++ ++ +++G   ++ +dg+++G vgg c+   v ++A+++l+ag++ l+r+
  gi|121636285|ref|YP_976508.1| 11 VAARTPFVRATVVRAQQPTSARPGDEAILLADGTIEGFVGGHCAQNSVRKAAMGVLQAGESVLLRV 76
                                   7999********************************************************999885 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                   SSGTT-EEEEET CS
                      XdhC_CoxI 21 prplGakmlvrp 32
                                   p  +Ga  +v p
  gi|121636285|ref|YP_976508.1| 85 PEAPGACVVVNP 96
                                   677899888877 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.65
                                    CSSSSGTT-EEEEETTS CS
                      XdhC_CoxI  18 GsaprplGakmlvrpdg 34 
                                    G +pr  G+k l  ++g
  gi|121636285|ref|YP_976508.1| 235 GGGPR--GRKALADENG 249
                                    55555..8888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1925.83
//
Query:       gi|121636286|ref|YP_976509.1|  [L=799]
Description: carbon monoxyde dehydrogenase large chain [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-173  578.2   0.1   1.9e-173  577.9   0.1    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    3.9e-36  123.7   0.4    1.3e-35  122.1   0.4    1.9  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
      0.073   12.9   0.6        0.4   10.5   0.0    2.5  3  ECR1_N         Exosome complex exonuclease RRP4 N-terminal re


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.9   0.1  3.1e-177  1.9e-173       5     550 .]     169     729 ..     166     729 .. 0.96

  Alignments for each domain:
  == domain 1  score: 577.9 bits;  conditional E-value: 3.1e-177
                                    -STTEEEEEEEE-H...HHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT- CS
                  Ald_Xan_dh_C2   5 apdnvlakiekGdv...eaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlgl 81 
                                    ++dn+++++e Gd+   ea+fa+ad+vv++e+ ++r++++++Et++a+a++d+ +g+lt+++++qaph +r+l a v gl
  gi|121636286|ref|YP_976509.1| 169 KSDNHIFDWETGDAaatEAVFAKADVVVQQEIVYPRVHPAPMETCGAVADLDPVTGKLTLWTTSQAPHAHRTLYALVAGL 248
                                    46788889*****877799************************************************************* PP

                                    -GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEEE CS
                  Ald_Xan_dh_C2  82 penkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvdl 161
                                    pe+k+rvi+p++GGGFG+K+  +p +v+a +a++ + +pVk+++dR+e++++tg ++++++  +++a++dGki+a++ ++
  gi|121636286|ref|YP_976509.1| 249 PEHKIRVISPDIGGGFGNKVPIYPGYVCAIVASLLLDKPVKWMEDRSENLTSTGFARDYIMVGEIAANRDGKILAIRSNV 328
                                    ******************************************************************************** PP

                                    EEEESST.HHHCHCCHCCTTGGGT.TTB--SEEEEEEEEEE-SSS-EE.-SSTTTH.HHHHHHHHHHHHHHHHHHT--HH CS
                  Ald_Xan_dh_C2 162 ladaGay.adlspavleralshld.gpYkipnvrvegrvvytNtppnt.afRGfGg.pqamfalErlmdelAeelgldpl 237
                                    lad+Ga+ a+++pa   ++++ +  g Y+i+++ +++++vytN++p + a+ +  + ++a++++Erl+d lA el++dp+
  gi|121636286|ref|YP_976509.1| 329 LADHGAFnAQAAPAKYPAGFFGVFtGSYDIEAAYCHMTAVYTNKAPGGvAYACSFRiTEAVYFVERLVDCLAFELKMDPA 408
                                    *******768888877777776655***********************9999998889********************** PP

                                    HHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.....E CS
                  Ald_Xan_dh_C2 238 elRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgf....ta 310
                                    elR rNl++p+++ py+++   vydsgd++ +++k++++++ye++raeq++ +a +  +Gig+++++e++g+g+    + 
  gi|121636286|ref|YP_976509.1| 409 ELRLRNLLRPNQF-PYQSKtgwVYDSGDYETTMRKAMNMIGYEALRAEQKQRRARGELMGIGMSFFTEAVGAGPrkdmD- 486
                                    *************.**99999********************************77788***************964321. PP

                                    ETTEE......EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHH CS
                  Ald_Xan_dh_C2 311 kflnq......egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdl 384
                                               +g+++rv+++G+++++++++ +GqG+et++aqi+aeeLg+ ++d++vv+gdtd++p+g+gt++Srst +
  gi|121636286|ref|YP_976509.1| 487 ----IlglgmaDGCELRVHPTGKAVLRLSVQTQGQGHETTFAQIVAEELGIAPDDIEVVHGDTDQTPFGLGTYGSRSTPV 562
                                    ....234566699******************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.......TTSSEEEEEEE... CS
                  Ald_Xan_dh_C2 385 ngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.......ervslsatgfyktl 454
                                    +g+A++  a+k+r++++ ia+ +levs +dl++e+gk++vk   +++v++a++a++a+         + +l+a+  y   
  gi|121636286|ref|YP_976509.1| 563 SGGAAALVARKVRDKAKIIASGMLEVSVADLQWEKGKFHVKgdpSAAVTIADIAMRAHGagdlpegIEGGLDAEVCY--- 639
                                    *****************************************9999999*********9999998877889*******... PP

                                    EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEES CS
                  Ald_Xan_dh_C2 455 deetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqll 534
                                          +p++ +++yga++++V++D+ t  vkv+r+ +v+D+G+ iNp+i+egQ++GG+v GiG+almE + +dedG++l
  gi|121636286|ref|YP_976509.1| 640 ------NPSNLTYPYGAYFCVVDIDPGTAVVKVRRFLAVDDCGTRINPMIIEGQVHGGIVDGIGMALMEMIAFDEDGNCL 713
                                    ......9999********************************************************************** PP

                                    S-STTTS----GGGS- CS
                  Ald_Xan_dh_C2 535 tasladYkiPtaadiP 550
                                      sl+dY+iPta ++P
  gi|121636286|ref|YP_976509.1| 714 GGSLMDYLIPTALEVP 729
                                    **************98 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.4   2.1e-39   1.3e-35       2     109 ..      38     145 ..      37     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 2.1e-39
                                    T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEESSTT CS
                   Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvrsvg 81 
                                    G+++YvdD+++pg+l+la++rS++ahA+iv+idv+aa+a+p+V av+t++dl++++ a++++l+++ +a+la+dk+r++g
  gi|121636286|ref|YP_976509.1|  38 GRGTYVDDVALPGMLHLAILRSPYAHARIVRIDVTAAQAHPKVKAVVTGADLAAKGLAWMPTLANDVQAVLATDKTRFQG 117
                                    99**********************************************************999999************** PP

                                    -EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                   Ald_Xan_dh_C  82 qavaavvAedeetArkAaklvkveYeel 109
                                    q+va vvAed++ Ar+A++lv+v+Ye++
  gi|121636286|ref|YP_976509.1| 118 QEVASVVAEDRYSARDACELVDVDYEPR 145
                                    **************************87 PP

>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.8e-05       0.4      11      24 ..      32      45 ..      30      64 .. 0.84
   2 ?   -2.0   0.0      0.53   3.2e+03      24      33 ..     238     247 ..     237     248 .. 0.86
   3 ?   -2.5   0.1      0.79   4.7e+03       9      21 ..     543     555 ..     539     563 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.8e-05
                                   TTTSEE-TTEEEET CS
                         ECR1_N 11 deefmrGhGTYvrg 24
                                   d+ f+rG GTYv++
  gi|121636286|ref|YP_976509.1| 32 DPRFIRGRGTYVDD 45
                                   899********976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.53
                                    TTEEEESSSE CS
                         ECR1_N  24 ggtiyAsvaG 33 
                                    ++t+yA vaG
  gi|121636286|ref|YP_976509.1| 238 HRTLYALVAG 247
                                    5789*****9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.79
                                    EETTTSEE-TTEE CS
                         ECR1_N   9 ttdeefmrGhGTY 21 
                                    +++++   G GTY
  gi|121636286|ref|YP_976509.1| 543 GDTDQTPFGLGTY 555
                                    5666666699*** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5337.46
//
Query:       gi|121636287|ref|YP_976510.1|  [L=159]
Description: carbon monoxyde dehydrogenase small chain [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-29  100.9   0.2    2.8e-29  100.9   0.2    1.6  2  Fer2_2       [2Fe-2S] binding domain
    1.6e-07   31.2   0.3    1.6e-07   31.2   0.3    2.3  2  Fer2         2Fe-2S iron-sulfur cluster binding domain
    0.00076   19.5   3.9     0.0063   16.5   3.9    2.2  1  Fer2_4       2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.015   15.3   1.2      0.015   15.3   1.2    2.0  2  Fer2_3       2Fe-2S iron-sulfur cluster binding domain
      0.028   14.4   0.0          4    7.5   0.0    2.3  2  Tricorn_PDZ  Tricorn protease PDZ domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.6       2.2   7.9e+03      23      30 ..      40      47 ..      36      49 .. 0.80
   2 !  100.9   0.2   7.8e-33   2.8e-29       1      75 [.      73     146 ..      73     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                         Fer2_2 23 gasqCGyC 30
                                   + s CG C
  gi|121636287|ref|YP_976510.1| 40 DTSNCGTC 47
                                   67899999 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 7.8e-33
                         Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                    Tvegl+ +  +l+pvqe f++++++qCG+CtpG++++a all++n p+p+e++irea+sg++CRCtgY+ iv+ +
  gi|121636287|ref|YP_976510.1|  73 TVEGLAGPDGQLDPVQEGFMRCHGLQCGFCTPGMLITARALLDRN-PDPDEQTIREAISGQICRCTGYTTIVRSI 146
                                    9*****99669**********************************.89999*********************987 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.3   4.4e-11   1.6e-07       2      48 ..       6      52 ..       5      68 .. 0.84
   2 ?    2.0   0.8     0.057   2.1e+02      34      44 ..      93     103 ..      89     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.4e-11
                                   ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEE CS
                           Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevl 48
                                   t++g++v++ev +++ +l  ++++    ++++++C  ++CgtC+vev+
  gi|121636287|ref|YP_976510.1|  6 TVNGEPVTAEV-EPRMLLVHFLRDqLRLTGTHWGCDTSNCGTCVVEVD 52
                                   89*******99.555559999998899*******************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.057
                                    SSSSSSSSTTE CS
                           Fer2  34 sCggggCgtCl 44 
                                     C+g +Cg C+
  gi|121636287|ref|YP_976510.1|  93 RCHGLQCGFCT 103
                                    599888****8 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.9   1.8e-06    0.0063       3      71 ..       2      63 ..       1      76 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                         Fer2_4  3 pvtltfDGkevtvpeG.dtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpv 71
                                   +v++t++G++vt++    +++   l+ + ++  + +        c  ++C +C+Vev+g+p v++c++ +
  gi|121636287|ref|YP_976510.1|  2 QVNMTVNGEPVTAEVEpRMLLVHFLRDQLRLTGTHWG-------CDTSNCGTCVVEVDGVP-VKSCTMLA 63
                                   5788888888888754266777777777777777777.......9****************.9***9864 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.2   4.2e-06     0.015      50      76 ..      37      63 ..      27      88 .. 0.83
   2 ?   -1.5   0.4       0.7   2.5e+03      51      61 ..      93     103 ..      82     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                         Fer2_3 50 asCregiCGscavainGkptlaCtati 76
                                   + C    CG+c v+++G p   Ct   
  gi|121636287|ref|YP_976510.1| 37 WGCDTSNCGTCVVEVDGVPVKSCTMLA 63
                                   68*********************9765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.7
                         Fer2_3  51 sCregiCGsca 61 
                                     C+   CG c+
  gi|121636287|ref|YP_976510.1|  93 RCHGLQCGFCT 103
                                    688899**997 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0063        23      48      74 ..       6      32 ..       2      44 .. 0.84
   2 ?    7.5   0.0    0.0011         4      41      61 ..      43      63 ..      35      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0063
                                   EETTEE-BTTB-HHHHHHTTTTSEEEE CS
                    Tricorn_PDZ 48 avdgepvskekgiaelLvgkagkeveL 74
                                    v+gepv++e ++  lLv    ++ +L
  gi|121636287|ref|YP_976510.1|  6 TVNGEPVTAEVEPRMLLVHFLRDQLRL 32
                                   79***************9866666655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                                   .TT-EEEEETTEE-BTTB-HH CS
                    Tricorn_PDZ 41 reGdlilavdgepvskekgia 61
                                   + G ++++vdg+pv++ + +a
  gi|121636287|ref|YP_976510.1| 43 NCGTCVVEVDGVPVKSCTMLA 63
                                   57************9866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1374.29
//
Query:       gi|121636288|ref|YP_976511.1|  [L=286]
Description: carbon monoxyde dehydrogenase medium chain [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-36  125.4   0.0    2.9e-36  124.8   0.0    1.3  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
      2e-23   82.5   1.2    3.2e-23   81.9   1.2    1.3  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.0   3.2e-40   2.9e-36      12     170 ..       2     166 ..       1     167 [. 0.95

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 3.2e-40
                                    HHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTS.GGGS-E....EEESSEEEEETTSBHHHHHHHHHHHH CS
                  FAD_binding_5  12 eealallaa.epdaklvaGgtdlgvlmkekvarpehliditgi.pelkei....eeteggleiGAavtlselaaealvre 85 
                                    + a+ ll++ +++a++vaGg++l+++mk+++a+pe l+di+++ pel ++     ++ + +++GA++++ e+ +++++++
  gi|121636288|ref|YP_976511.1|   2 DHAIGLLDRlGEGARVVAGGHSLLPMMKLRIANPEYLVDINDLaPELGYVvvggINNPNLVRLGAMTRHREILDSDALAA 81 
                                    678888888899******************************956898885555567899******************** PP

                                    HHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-EEEE CS
                  FAD_binding_5  86 rypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktalepgelita 165
                                     +p +++a + iA+p +Rn++T+GG+l+ a+p+ Dl ++  +ldA    ++++gere+++++fl gp++tal ++e++ +
  gi|121636288|ref|YP_976511.1|  82 VCPIFRDAERVIADPVVRNRGTLGGSLCQADPAEDLSTVCTVLDAVCLAKGPSGEREIAIDDFLVGPYETALAHNEVLIE 161
                                    ******************************************************************************** PP

                                    EEEE- CS
                  FAD_binding_5 166 veiPa 170
                                    v+iP 
  gi|121636288|ref|YP_976511.1| 162 VRIPL 166
                                    ****6 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   1.2   3.5e-27   3.2e-23       1     102 [.     172     272 ..     172     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 3.5e-27
                                    EEE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHT CS
                  CO_deh_flav_C   1 say.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspas 79 
                                    say k++rr + d+ai +a+++v+l+++ +i  ar+++++v+p+pv   ++ a L+G+p +ee+++ea ++++++++p +
  gi|121636288|ref|YP_976511.1| 172 SAYaKVERRVG-DWAITAAGAAVTLDGQ-TILAARVGLTAVNPDPVALAELSAGLVGQPATEEVFAEAGRRAAQACTPVT 249
                                    58*9*******.*************988.*************************************************** PP

                                    CTTC-HHHHHHHHHHHHHHHHHH CS
                  CO_deh_flav_C  80 dprasaeYRrslavsllfrflle 102
                                    d+r++aeY+r+la +l+ r l++
  gi|121636288|ref|YP_976511.1| 250 DVRGTAEYKRHLAGELTVRTLRT 272
                                    *******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2000.94
//
Query:       gi|121636289|ref|YP_976512.1|  [L=380]
Description: hypothetical protein BCG_0414c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-41  142.0   1.7    3.3e-41  140.7   0.1    2.2  2  XdhC_C     XdhC Rossmann domain
      7e-40  135.1  13.5    1.9e-21   76.0   4.2    2.8  2  XdhC_CoxI  XdhC and CoxI family
  ------ inclusion threshold ------
        0.3   10.9   0.0       0.43   10.4   0.0    1.2  1  DUF4523    Protein of unknown function (DUF4523)


Domain annotation for each model (and alignments):
>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.38   2.3e+03     108     122 ..     108     122 ..     105     124 .. 0.89
   2 !  140.7   0.1   5.5e-45   3.3e-41       1     125 []     198     344 ..     198     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                                    -S---SHHHHHHHHH CS
                         XdhC_C 108 digaktpeeIAvsil 122
                                    diga++p  IA  i+
  gi|121636289|ref|YP_976512.1| 108 DIGAQRPVAIATVIA 122
                                    69*********9886 PP

  == domain 2  score: 140.7 bits;  conditional E-value: 5.5e-45
                                    EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE......................-EEEE--S-HHHHH CS
                         XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade......................tavvvlthdhklDa 58 
                                    +++fGa ++a+alar ++ lg+rvtv+d+r+ fat++rfp+ad+                      t+++vlthd+k+D 
  gi|121636289|ref|YP_976512.1| 198 MLVFGAIDFAAALARQGSFLGYRVTVCDARAVFATPARFPTADDvvvawphrylaaqaeaggiderTVICVLTHDPKFDV 277
                                    68****************************************99************************************ PP

                                    HHHHHHSSS--SEEEESS-HHHHHHHCTTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                         XdhC_C  59 ealeaalrkkaayigllGSrkkaarrlerlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                    ++le alr  ++y+g++GSrk+++ r++rlraagl+++el+rl++PiGld+ga+tpee Avsi+A+i
  gi|121636289|ref|YP_976512.1| 278 PVLEVALRLGVGYVGAMGSRKTHDDRMDRLRAAGLTDAELSRLSSPIGLDLGARTPEETAVSIAADI 344
                                    *******88899*****************************************************97 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   4.2   3.2e-25   1.9e-21       2      68 .]       4      70 ..       3      70 .. 0.98
   2 !   63.6   1.8   2.3e-21   1.4e-17       3      68 .]     110     175 ..     108     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3.2e-25
                                   HHCT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHHCT--EEEEEE CS
                      XdhC_CoxI  2 laagrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideArallaagrtalvryg 68
                                   +aag  + +aTVv+t  saprp+Ga+m+v pdg+v Gsv+ggc+E+av++ A ++ ++g ++l++yg
  gi|121636289|ref|YP_976512.1|  4 WAAGDTAGVATVVRTLRSAPRPPGAAMVVAPDGSVSGSVSGGCVEGAVYELAAEVAQTGIPRLEHYG 70
                                   799******************************99*******************************8 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 2.3e-21
                                    HCT..EEEEEEEEEECSSSSGTT-EEEEETTS-..EEE-SSSSCHHHHHHHHHHHHHHCT--EEEEEE CS
                      XdhC_CoxI   3 aagrpvalaTVvdteGsaprplGakmlvrpdgr..viGsvgggclEaavideArallaagrtalvryg 68 
                                     a+rpva+aTV++   ++ r++G+++++rpd +  v+Gs+g+ +++aavid+Ar+lla gr+++++yg
  gi|121636289|ref|YP_976512.1| 110 GAQRPVAIATVIA--HPDERRVGRRLVIRPDTKspVTGSLGSARADAAVIDDARGLLAVGRSEILEYG 175
                                    589**********..69**************65236*******************************8 PP

>> DUF4523  Protein of unknown function (DUF4523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.2e-05      0.43     110     164 ..     197     252 ..     185     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.2e-05
                        DUF4523 110 rLsvfGpiesvtlcGrqsavvvfkdiisackavsafqsrtpgt.mlqCsWqqkfls 164
                                    r++vfG i+  +++ rq + + ++ ++  ++av a + r p    +  +W +++l+
  gi|121636289|ref|YP_976512.1| 197 RMLVFGAIDFAAALARQGSFLGYRVTVCDARAVFATPARFPTAdDVVVAWPHRYLA 252
                                    789************************************997527999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2943.85
//
Query:       gi|121636290|ref|YP_976513.1|  [L=321]
Description: LysR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-23   81.1   3.0    1.3e-22   80.2   3.0    1.3  1  LysR_substrate  LysR substrate binding domain
    2.6e-16   59.3   0.2    9.7e-16   57.5   0.2    2.1  1  HTH_1           Bacterial regulatory helix-turn-helix protein
  ------ inclusion threshold ------
       0.14   12.0   1.8       0.22   11.4   0.2    2.2  2  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   3.0   2.1e-26   1.3e-22       4     204 ..      88     291 ..      85     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.1e-26
                                    SCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS....CCTTEEEEEEEEEE CS
                 LysR_substrate   4 lrgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlairagpp....edsglearpLaeep 79 
                                     r+ Lri+a++++a++  p l++ f  r  ++++el++ +++++ +l+ ++ +D+ai    +    +d ++  rp+++++
  gi|121636290|ref|YP_976513.1|  88 GRRLLRIAASSAFAEHAAPGLIELFSSRADDLSVELSVHPTSRFRELICSRAVDIAIGPASEssigSDGSIFLRPFLKYQ 167
                                    6889********************************************************99****************** PP

                                    EEEEEETTSGGGGSSSECGGGGCTSEEEEESTTSTHHHHHHHHHHCTTEECEEEEEESSHHHHHHHHHTTS-BEEEEGGG CS
                 LysR_substrate  80 lvlvaspdhpLargepvsledLadeplilleegsglrdlledalreaglkprvalevnsleallalvaaGlGiallprsa 159
                                    ++ v++p+ pLa+g p  ++ L++++++l +   +   ++   lr   ++  +   + s +a+l+ v+   G +l+  +a
  gi|121636290|ref|YP_976513.1| 168 IITVVAPNSPLAAGIPM-PALLRHQQWMLGPSAGSVDGEIATMLRGLAIPESQQRIFQSDAAALEEVMRVGGATLAIGFA 246
                                    *****************.***********888888********************************************* PP

                                    HHCCCHTTTEEEEEESSTTCEEEEEEEEETTCCCHHHHHHHHHHH CS
                 LysR_substrate 160 vrdeladgrlvalplpepplprelylvyrkgrelspavrafidfl 204
                                    v+++la+grlv +  p+++   e+++++ + + ++pav  ++ f+
  gi|121636290|ref|YP_976513.1| 247 VAKDLAAGRLVHVTGPGLDRAGEWCVATLAPSARQPAVSELVGFI 291
                                    *****************9999********************9997 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.2   1.6e-19   9.7e-16       3      59 ..       5      61 ..       3      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.6e-19
                                   HHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                          HTH_1  3 qlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                   qlr+  av++ gs+++AA eLgls + vs+++++L++el++pLf+Rtg gl  T+ G
  gi|121636290|ref|YP_976513.1|  5 QLRAYSAVVRLGSVRAAAAELGLSDAGVSMHVAALRKELDDPLFTRTGAGLAFTPGG 61
                                   89********************************************999*****988 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.7e-05      0.22       3      46 ..       1      40 [.       1      42 [. 0.87
   2 ?   -2.7   0.1      0.97   5.8e+03      27      38 ..      68      79 ..      59      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLv 46
                                   +tpaq+r+  a+ r +    +v++ a++lgls + vs +++ L 
  gi|121636290|ref|YP_976513.1|  1 MTPAQLRAYSAVVRLG----SVRAAAAELGLSDAGVSMHVAALR 40
                                   6888888888888887....9*******************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.97
                                   HHHHHTSSHHHH CS
                         MarR_2 27 larrlglsksav 38
                                    ++ lgl ++++
  gi|121636290|ref|YP_976513.1| 68 AVEILGLQQQTA 79
                                   555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2548.69
//
Query:       gi|121636291|ref|YP_976514.1|  [L=73]
Description: hypothetical protein BCG_0416 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2  42.8        1.6    8.5  42.8    2.0  1  Collagen  Collagen triple helix repeat (20 copies)


Domain annotation for each model (and alignments):
>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  42.8   9.1e-05       1.6       4      59 ..      15      71 ..       4      73 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 9.1e-05
                                   XXXXXXXXXXXXXXX-----XXXXEEEE-TTSS--.---------------BB--XX CS
                       Collagen  4 GepGepGppGppGkrGepGeaGekGekGpaGekGp.pGaaGkpGapGekGeaGapge 59
                                   G++G  G+ G+ G+ G+ G++G+ Ge G+aG++G+ +G+aG+pG+ Ge+G+ G+pg+
  gi|121636291|ref|YP_976514.1| 15 GSAGLIGSGGAGGDGGSGGATGAGGEGGDAGASGSiNGNAGDPGNSGERGAVGKPGA 71
                                   444444555555555555555555555555555543455555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                       74  (0.00412739); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 562.43
//
Query:       gi|121636292|ref|YP_976515.1|  [L=71]
Description: protein transport protein secE2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   73.6   0.9    1.3e-20   73.4   0.9    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.9     7e-25   1.3e-20       1      63 [.       3      65 ..       3      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 7e-25
                                   EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECT.TCCEEEEEEEEEEEE- CS
                        Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahved.gkiaeYqvtlkvgFrl 63
                                   VyKvi+++G+Sp+Swe+A+ +A+++A+ ++++ir++ V e+++ v+  gki+ Y+++l+v+F++
  gi|121636292|ref|YP_976515.1|  3 VYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSaGKIT-YRIKLEVSFKM 65
                                   9********************************************6626666.*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 572.46
//
Query:       gi|121636293|ref|YP_976516.1|  [L=183]
Description: rna methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-22   80.2   0.1      2e-22   79.9   0.1    1.1  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.1   1.1e-26     2e-22       2     142 .]      34     170 ..      33     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.1e-26
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvat 81 
                                    l+v++++  +  N+G+++Rta+af ++++++v++r++   n   +r a+ +  + +l+++ds+  +l+    +g+++va+
  gi|121636293|ref|YP_976516.1|  34 LHVAIENFGHDANIGSVVRTANAFAVHTVHIVGRRRW---N---RRGAMVTDRYQRLCHHDSTTGLLEFAAGAGLTVVAV 107
                                    78999****************************7776...5...5889999999999*********************** PP

                                    ST..T-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  82 sl..kgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                    ++  ++ +l++++l+++++l+fG+E+ G+++++++ a  +v+I + g+++S+N  vA++i+++
  gi|121636293|ref|YP_976516.1| 108 DNvpGAARLEQTALPRECLLLFGQEGPGITDDARAGAAVTVSIAQFGSTRSINAGVAAGIAMH 170
                                    **99999*****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1485.73
//
Query:       gi|121636294|ref|YP_976517.1|  [L=302]
Description: hypothetical protein BCG_0419c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2355.20
//
Query:       gi|121636295|ref|YP_976518.1|  [L=179]
Description: orotate phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-11   44.1   0.8      2e-11   43.7   0.8    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.02   14.3   0.1      0.026   14.0   0.1    1.2  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.8   2.2e-15     2e-11      10     132 ..      45     158 ..      39     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.2e-15
                                    -EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE........EE----TTS CS
                   Pribosyltran  10 aildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdesrlledpagk 88 
                                     +++ + rl++e+  +  +   vv g   g+ p+a+++ ++ + p++ +v +++  + g++  +          +++ g+
  gi|121636295|ref|YP_976518.1|  45 RASALIGRLMRELTAD--WDYSVVGGLTLGADPVATAIMHAPGRPIDaFVVRKSAKAHGMQRLI--------EGSEVTGQ 114
                                    4567788888888888..88889999999****************9966666666666666666........889***** PP

                                    EEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                   Pribosyltran  89 kVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                    +Vl+V+D  +tG++ l a++++ ++g e+v++a++vd+ +++ e
  gi|121636295|ref|YP_976518.1| 115 RVLVVEDTSTTGNSALTAVHAVQDVGGEVVGVATVVDRATGAAE 158
                                    **************************************998765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.9e-06     0.026     120     173 ..     112     163 ..      87     179 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
                        UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeef 173
                                    + ++vl+++ +  TG+sa +a++ +++  vg e + v++v+  + g++++ e+ 
  gi|121636295|ref|YP_976518.1| 112 TGQRVLVVEDTSTTGNSALTAVHAVQD--VGGEVVGVATVVDRATGAAEAIEAE 163
                                    6678***********************..88899*******9999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1282.46
//
Query:       gi|121636296|ref|YP_976519.1|  [L=284]
Description: hypothetical protein BCG_0421c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2123.41
//
Query:       gi|121636297|ref|YP_976520.1|  [L=848]
Description: endopeptidase ATP binding protein subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-50  171.7   0.1    3.3e-49  167.3   0.0    2.8  3  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-36  124.7   5.2    5.1e-36  122.8   0.7    2.5  2  AAA_lid_9        AAA lid domain
    8.2e-27   93.1   1.1    8.9e-13   48.2   0.1    3.3  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    2.1e-26   91.7   1.9    2.7e-26   91.4   0.1    2.3  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    1.7e-24   86.7   2.9    1.7e-12   47.9   0.0    4.3  4  AAA              ATPase family associated with various cellul
    3.8e-18   65.8   0.7    3.2e-12   46.6   0.0    4.2  3  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-09   37.7  14.6    3.3e-06   27.6   0.1    5.3  5  AAA_16           AAA ATPase domain
    3.7e-08   33.7   1.1      0.038   14.3   0.0    4.7  4  AAA_22           AAA domain
    5.2e-08   32.8   0.0    2.4e-05   24.1   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    3.3e-06   26.9   0.0      0.064   13.0   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    4.8e-06   27.2   2.4       0.54   10.7   0.0    3.4  3  AAA_23           AAA domain
    5.2e-06   26.5   2.6       0.47   10.3   0.0    3.9  3  ATPase_2         ATPase domain predominantly from Archaea
    2.6e-05   24.3   0.0       0.24   11.5   0.0    2.7  2  AAA_14           AAA domain
    4.1e-05   23.1   0.0       0.52    9.6   0.0    3.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.4e-05   23.1   0.0      0.086   12.4   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    0.00014   21.4   0.0       0.49    9.8   0.0    3.6  3  TniB             Bacterial TniB protein
    0.00015   22.3   1.0       0.45   11.1   0.0    3.4  2  AAA_18           AAA domain
    0.00016   21.6   0.1       0.74    9.7   0.0    3.8  4  AAA_3            ATPase family associated with various cellul
    0.00022   21.2   0.1        1.7    8.5   0.0    3.2  3  RsgA_GTPase      RsgA GTPase
    0.00024   21.3   0.0       0.67   10.2   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00026   21.3   0.0        1.1    9.5   0.0    3.3  2  AAA_28           AAA domain
    0.00048   20.5   0.0        1.6    9.2   0.0    2.6  2  RNA_helicase     RNA helicase
    0.00062   19.7   0.0       0.23   11.3   0.0    2.6  2  NACHT            NACHT domain
     0.0007   19.6   0.0        1.4    9.0   0.0    3.2  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0012   18.6   0.0        1.1    8.9   0.0    2.5  2  AAA_24           AAA domain
     0.0015   18.7   0.1        2.5    8.3   0.0    3.5  3  AAA_33           AAA domain
     0.0029   16.9   0.6       0.39   10.0   0.0    3.2  3  Zeta_toxin       Zeta toxin
     0.0072   16.0   0.0         11    5.8   0.0    3.2  3  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   16.2   0.2        1.9    9.0   0.0    2.9  2  ABC_tran         ABC transporter
      0.017   14.7   0.1        1.7    8.2   0.0    3.1  2  AAA_25           AAA domain
      0.018   15.1  11.4      0.046   13.8  11.4    1.7  1  NYD-SP28         Sperm tail
      0.026   13.6   0.0      0.091   11.8   0.0    2.0  1  T2SSE            Type II/IV secretion system protein
      0.035   13.3   0.0        3.1    6.9   0.0    3.2  3  DUF815           Protein of unknown function (DUF815)
      0.046   14.1   0.1        1.4    9.2   0.0    3.1  2  AAA_19           AAA domain
      0.064   13.0   0.0       0.41   10.4   0.0    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.087   12.4   0.0        3.1    7.4   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
      0.094   12.6   0.0        7.9    6.4   0.0    2.7  2  NTPase_1         NTPase
        0.1   12.5   2.8       0.19   11.6   2.8    1.4  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
       0.11   12.2   6.2        5.6    6.7   0.0    4.2  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.15   11.9   0.0         92    2.7   0.0    3.7  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
       0.17   11.6   0.0        2.2    8.0   0.0    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.17   12.0   0.0       0.77    9.9   0.0    1.9  2  Torsin           Torsin
       0.18   11.8   0.0        5.2    7.0   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
       0.52   10.4   2.9         28    4.7   0.0    3.5  3  DUF87            Helicase HerA, central domain
       0.54   10.7   8.3        1.2    9.5   8.3    1.5  1  Fez1             Fez1


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   4.8e+02       6      29 ..     202     225 ..     197     296 .. 0.70
   2 ?   -1.9   0.2       8.1   3.2e+03      43      67 ..     411     434 ..     391     437 .. 0.68
   3 !  167.3   0.0   8.2e-52   3.3e-49       1     170 [.     598     749 ..     598     750 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                    EEEE--TTSSHHHHHHHHHHHTT- CS
                          AAA_2   6 illlgptgvGktelakalaellfv 29 
                                      l+g+ gvGkt + + la+ + +
  gi|121636297|ref|YP_976520.1| 202 PVLIGEPGVGKTAIVEGLAQRIVA 225
                                    56889999*****99999987654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.1
                                    -------THHHHHHHHHTTT-HHHH CS
                          AAA_2  43 lleeeevehlvsrligappgyvgae 67 
                                    +   +eve+lv rl++++ +  + e
  gi|121636297|ref|YP_976520.1| 411 VEI-DEVERLVRRLEIEEMALSKEE 434
                                    333.677777777777766665555 PP

  == domain 3  score: 167.3 bits;  conditional E-value: 8.2e-52
                                    -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                          AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                    rp++ +++lgptgvGktelakala++lf ++e++++r+d+se+ e    +h+v+rligappgyvg+e gG          
  gi|121636297|ref|YP_976520.1| 598 RPTGAFMFLGPTGVGKTELAKALADFLF-DDERAMVRIDMSEYGE----KHTVARLIGAPPGYVGYEAGGqlteavrrrp 672
                                    68899***********************.****************....******************************* PP

                                    ..EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-STTTTSGG CS
                          AAA_2  71 ..ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrskeeeeekk 148
                                      +vl+DEi+K+hp           +V+++LLq+l++g+ltd +gr+vd++n+++I+t+++gs   ++            
  gi|121636297|ref|YP_976520.1| 673 ytVVLFDEIEKAHP-----------DVFDVLLQVLDEGRLTDGHGRTVDFRNTILILTSNLGSGGSAE------------ 729
                                    **************...........**************************************99999............ PP

                                    G--HHHHHHTT--HHHHTT--E CS
                          AAA_2 149 keeveeelkkglipEllgRlpe 170
                                      +v  +++++++pE+++Rl++
  gi|121636297|ref|YP_976520.1| 730 --QVLAAVRATFKPEFINRLDD 749
                                    ..7899**************97 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.7   1.3e-38   5.1e-36       1     103 [.     343     445 ..     343     446 .. 0.98
   2 ?    3.5   0.3      0.16        64      64     100 ..     465     502 ..     454     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 1.3e-38
                      AAA_lid_9   1 seeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklekelak 80 
                                    s+e+ti iLrglk++ye hHgv+i+d+al+aa++lS+rYi+ rflPdkAIDl+Deaa+r+r++ +s+p e++++e+ +++
  gi|121636297|ref|YP_976520.1| 343 SVEDTIGILRGLKDRYEVHHGVRITDSALVAAATLSDRYITARFLPDKAIDLVDEAASRLRMEIDSRPVEIDEVERLVRR 422
                                    689***************************************************************************** PP

                      AAA_lid_9  81 lekekealekeeekekaerlkel 103
                                    le e+ al+kee++++aerl++l
  gi|121636297|ref|YP_976520.1| 423 LEIEEMALSKEEDEASAERLAKL 445
                                    *******************9876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                      AAA_lid_9  64 keskp.eeleklekelaklekekealekeeekekaerl 100
                                    +e++  e +++l+++l++l+ e e++e++ + +ka++l
  gi|121636297|ref|YP_976520.1| 465 NEKNAiEIVRDLKEQLEALRGESERAERDGDLAKAAEL 502
                                    33333145889999999999999999999998888776 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   2.2e-15   8.9e-13       1      52 [.      17      68 ..      17      69 .. 0.96
   2 !   42.2   0.1   1.7e-13   6.7e-11       1      53 []      94     145 ..      94     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.2e-15
                                   HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHH CS
                          Clp_N  1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekll 52
                                   A + A  +g+ +i + HLL+ALl ++dG+aa+lL++ Gv ++++r+++++ll
  gi|121636297|ref|YP_976520.1| 17 ALQAASTAGNPEIRPAHLLMALLTQNDGIAAPLLEAVGVEPATVRAETQRLL 68
                                   7899********************************************9987 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 1.7e-13
                                    HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
                          Clp_N   1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekllg 53 
                                    Aq+lA +l+++y+stEH++ +L+  +d++ a+lL   G++++alr+a  k++g
  gi|121636297|ref|YP_976520.1|  94 AQQLATELDDEYVSTEHVMVGLAT-GDSDVAKLLTGHGASPQALREAFVKVRG 145
                                    9********************887.99*********************99997 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.1   6.8e-29   2.7e-26       1      80 [.     756     835 ..     756     836 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.8e-29
                                    SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTSEEE CS
                  ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegdtvr 80 
                                    L+ eel++Ivd++l++l krl++r+++l+v+  a+++la++g+dp+yGARpLrr++q+ i d+la+++l+g++++gdtv 
  gi|121636297|ref|YP_976520.1| 756 LNPEELVRIVDIQLAQLGKRLAQRRLQLQVSLPAKRWLAQRGFDPVYGARPLRRLVQQAIGDQLAKMLLAGQVHDGDTVP 835
                                    7889*************************************************************************996 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.2   4.7e+02      77     111 ..      85     119 ..      73     129 .. 0.81
   2 !   47.9   0.0   4.2e-15   1.7e-12       2     124 ..     203     334 ..     202     340 .. 0.75
   3 ?    2.7   0.3      0.39   1.6e+02      63     100 ..     412     456 ..     375     484 .. 0.84
   4 !   31.4   0.0   5.5e-10   2.2e-07       2     111 ..     604     722 ..     603     740 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                                    CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnr 111
                                    +es  + ++++qL teld++  ++++v+v +at +
  gi|121636297|ref|YP_976520.1|  85 RESLAAITTAQQLATELDDEYVSTEHVMVGLATGD 119
                                    467778999***********999888888777755 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 4.2e-15
                                    EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGG CS
                            AAA   2 llyGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDEida 69 
                                    +l+G pG+GKT++++ +a+ +          + +++ +++ +++  sky ge e++++++++++k++a++ i fiDE++ 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIvagdvpeslrDKTIVALDLGSMVagSKYRGEFEERLKAVLDDIKNSAGQIITFIDELHT 282
                                    599*****************7666555544447799999999998899******************9977********** PP

                                    HHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHS.TTS CS
                            AAA  70 laksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallr.gRf 124
                                    ++++   ++ e ++++ n + ++l + +       ++gat+     +++++   + +Rf
  gi|121636297|ref|YP_976520.1| 283 IVGAG--ATGEGAMDAGNMIKPMLARGEL-----RLVGATTLdeyRKHIEKDAALeRRF 334
                                    ****9..5555555555555555555544.....5777776655444444444443555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.39
                                    EEETGGGHHHHH.......TTCCCHHHHHHHHHHHHHHHHTTTSS CS
                            AAA  63 fiDEidalaksr.......sgseseeeervvnqLlteldgvkkke 100
                                     iDE+++l+++        s++e+e + + +++L +el ++k+k 
  gi|121636297|ref|YP_976520.1| 412 EIDEVERLVRRLeieemalSKEEDEASAERLAKLRSELADQKEKL 456
                                    599999999988999999999999999999999999999999874 PP

  == domain 4  score: 31.4 bits;  conditional E-value: 5.5e-10
                                    EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STT.HHHHHHHHHHHHHHHTSTS.EEEEE CS
                            AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvg.esekkirelfkeakekakp.silfi 64 
                                    ++ Gp G+GKT laka+a  l   ++ +++i++se  +k            yvg e+  ++ e +++    + p +++++
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLfddERAMVRIDMSEYGEKhtvarligappgYVGyEAGGQLTEAVRR----R-PyTVVLF 678
                                    789*****************9776699**********999****99999998872444555555544....2.669**** PP

                                    ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS CS
                            AAA  65 DEidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr 111
                                    DEi++ +++             ++Ll++ld+ +           +++i+i+++n 
  gi|121636297|ref|YP_976520.1| 679 DEIEKAHPDV-----------FDVLLQVLDEGRLTdghgrtvdFRNTILILTSNL 722
                                    ******9999...........*********9998888899988555888888885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   0.00012     0.049       3      24 ..     203     225 ..     201     334 .. 0.82
   2 ?   -0.4   0.1       2.6     1e+03      41     103 ..     354     420 ..     352     449 .. 0.65
   3 !   46.6   0.0     8e-15   3.2e-12       2     135 ..     603     736 ..     602     739 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                                    EEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5   3 lLvGppGtgKselaerlaaal.n 24 
                                    +L+G+pG+gK+ ++e la+++  
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIvA 225
                                    79****************99852 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.6
                                    HH--B--.........--------......G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEE CS
                          AAA_5  41 lkgrreikngttslvdsplvraar......egeilvlDEveraesevlnsLlslleerrllleeggelv 103
                                    lk r+e+   + + +ds+lv aa+      +++ l +  ++ + +e++++L + ++ r + ++e  +lv
  gi|121636297|ref|YP_976520.1| 354 LKDRYEV-HHGVRITDSALVAAATlsdryiTARFLPDKAID-LVDEAASRLRMEIDSRPVEIDEVERLV 420
                                    6677777.777788999999999888888844444444444.444555555555555555555555555 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 8e-15
                                    EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEEESGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar..egeilvlDEve 75 
                                    ++ +Gp+G+gK+ela+ la +l   +r ++ + ++++ ++ ++   +    +       + l++a+r     ++++DE+e
  gi|121636297|ref|YP_976520.1| 603 FMFLGPTGVGKTELAKALADFLfddERAMVRIDMSEYGEKHTVARLIGAPpGYVGYEAGGQLTEAVRrrPYTVVLFDEIE 682
                                    6889*******************76666666677776666666666665544445555689999999877789999**** PP

                                    G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHH CS
                          AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalr 135
                                    +a+++v+++Ll++l+e rl   +g++++   ++     + +i t+n  + +s +++ +a+r
  gi|121636297|ref|YP_976520.1| 683 KAHPDVFDVLLQVLDEGRLT--DGHGRTVDFRN-----TILILTSNLGSgGSAEQVLAAVR 736
                                    ********************..66665554444.....89999*99999766677777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       6.7   2.7e+03     127     127 ..      75      75 ..      12     171 .. 0.63
   2 !   27.6   0.1   8.3e-09   3.3e-06       2      49 ..     180     224 ..     179     235 .. 0.88
   3 ?    0.1   0.0       2.3     9e+02     118     145 ..     254     281 ..     229     304 .. 0.79
   4 !   14.7   0.0   7.3e-05     0.029       2      59 ..     572     635 ..     571     653 .. 0.80
   5 ?    0.2   0.0       2.1   8.5e+02     134     160 ..     670     697 ..     662     709 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.7
                         AAA_16 127 l 127
                                     
  gi|121636297|ref|YP_976520.1|  75 T 75 
                                    2 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.3e-09
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellrale 49 
                                    ++GR++e++++ ++l+r  ++ p   +l+Ge+GvGK+++v+ l++++ 
  gi|121636297|ref|YP_976520.1| 180 VIGRDNEIRRVVQVLSRRTKNNP---VLIGEPGVGKTAIVEGLAQRIV 224
                                    78*************98888766...899************9999876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.3
                         AAA_16 118 rllellkrllallsrderplvlvlDdlq 145
                                     + e lk+ l+ +++ + +++ ++D+l+
  gi|121636297|ref|YP_976520.1| 254 EFEERLKAVLDDIKNSAGQIITFIDELH 281
                                    4667777888888887888*******99 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 7.3e-05
                         AAA_16   2 lvGReeeleqLlsalervrsgrp......elvllsGesGvGKsslvrellralekdggiflrgk 59 
                                    ++G ++ + ++ +a++r r+g +      ++ ++ G+ GvGK+ l+++l++ l +d+   +r +
  gi|121636297|ref|YP_976520.1| 572 VIGQKAAVTAVSDAVRRSRAGVSdpnrptGAFMFLGPTGVGKTELAKALADFLFDDERAMVRID 635
                                    67888889999999998888877778889*********************99988865555544 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 2.1
                         AAA_16 134 erp.lvlvlDdlqwadeaslqllaaLlr 160
                                    +rp +v+++D++++a ++  ++l + l+
  gi|121636297|ref|YP_976520.1| 670 RRPyTVVLFDEIEKAHPDVFDVLLQVLD 697
                                    45569**********9999998655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       8.2   3.3e+03      49      84 ..      38      73 ..       9      87 .. 0.74
   2 !   13.1   0.0   0.00021     0.085       4      50 ..     198     245 ..     195     299 .. 0.69
   3 ?    0.1   0.1       2.2   8.8e+02      37     105 ..     325     408 ..     314     453 .. 0.52
   4 !   14.3   0.0   9.5e-05     0.038       6     114 ..     601     694 ..     597     703 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.2
                         AAA_22 49 sstsskdllrellralglelkaerlsseellealeq 84
                                    +t  + ++  ll+a+g+e  + r+++++ll++l q
  gi|121636297|ref|YP_976520.1| 38 LLTQNDGIAAPLLEAVGVEPATVRAETQRLLDRLPQ 73
                                   556667889999999999999988888888877755 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00021
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpss 50 
                                    t++  v++Ge+G+GKT  ++ l+++ ++   +e  +++++v  +l s 
  gi|121636297|ref|YP_976520.1| 198 TKNNPVLIGEPGVGKTAIVEGLAQRIVAGDVPESlRDKTIVALDLGSM 245
                                    778889**************9999986555444444444445554444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.2
                         AAA_22  37 e......erpevvfvtlpsstsskdllrellralglelka...................erlsseellealeqalrarav 91 
                                    e      +r ++v+v  ps ++   +lr l   +++ +                     +                 r+ 
  gi|121636297|ref|YP_976520.1| 325 EkdaaleRRFQQVYVGEPSVEDTIGILRGLKDRYEVHHGVritdsalvaaatlsdryitA-----------------RFL 387
                                    334444667777777777777777777777777776555533333333333333322221.................222 PP

                         AAA_22  92 ..ielliiDEaqh.lr....s 105
                                      +++ ++DEa   lr    s
  gi|121636297|ref|YP_976520.1| 388 pdKAIDLVDEAASrLRmeidS 408
                                    444444444444444332221 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 9.5e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                    g  +  G++G+GKT l++ l++ l  +      ++  v++++++ ++  +    ++r +g +  +      e   +l++a
  gi|121636297|ref|YP_976520.1| 601 GAFMFLGPTGVGKTELAKALADFLFDD------ERAMVRIDMSEYGEKHT----VARLIGAPPGY---VGYEAGGQLTEA 667
                                    556778*****************9532......55556888888885544....57777777777...777888888888 PP

                         AAA_22  86 lraravielliiDEaqhlrseealeeLrs 114
                                    +r+r    +++ DE+++  +++++  L +
  gi|121636297|ref|YP_976520.1| 668 VRRRPY-TVVLFDEIEKA-HPDVFDVLLQ 694
                                    888888.89999999887.7666665555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.019       7.5       2      44 ..     181     221 ..     180     248 .. 0.70
   2 !   24.1   0.0   6.1e-08   2.4e-05      23     124 ..     601     703 ..     572     740 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                                    ---SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat   2 igesealkelleqikkvaktdlsvlitGesGtGKellaraihe 44 
                                    ig++++++++++ +++ +k+  +v + Ge G+GK+ + + + +
  gi|121636297|ref|YP_976520.1| 181 IGRDNEIRRVVQVLSRRTKN-NPV-LIGEPGVGKTAIVEGLAQ 221
                                    77888888888888775443.455.56********99887766 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 6.1e-08
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE..HHHHHTTTSEEEEE CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk..GlfekadgGtlfLD 100
                                       + +G +G+GK+ la+a+ +    +e+ +v+++++++ e+   ++L G   G + G e+  +   ++++    ++++D
  gi|121636297|ref|YP_976520.1| 601 GAFMFLGPTGVGKTELAKALADFLFDDERAMVRIDMSEYGEKHTVARLIGAPPG-YVGYEAGGQltEAVRRRPYTVVLFD 679
                                    567899*********************************************999.677555433336677777899999* PP

                                    TGGGS-HHHHHHHHHHHHHSEEES CS
                Sigma54_activat 101 eigelplelQekLlrvlqegever 124
                                    ei++  +++   Ll+vl+eg+++ 
  gi|121636297|ref|YP_976520.1| 680 EIEKAHPDVFDVLLQVLDEGRLTD 703
                                    *******************98764 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00065      0.26      45      74 ..     197     226 ..     183     264 .. 0.79
   2 !   13.0   0.0   0.00016     0.064      49      76 ..     602     629 ..     598     651 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavra 74 
                                    ++k+n vl+G +GvGK+ +   l+++ v+ 
  gi|121636297|ref|YP_976520.1| 197 RTKNNPVLIGEPGVGKTAIVEGLAQRIVAG 226
                                    57899*******************998875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                      IstB_IS21  49 nivllGpsGvGKshlaialgveavragl 76 
                                    ++++lGp+GvGK+ la al+     ++ 
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALADFLFDDER 629
                                    5789***************987666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.27   1.1e+02      23      41 ..     203     221 ..     198     345 .. 0.83
   2 !    8.5   3.2    0.0065       2.6     143     195 ..     430     483 ..     365     520 .. 0.78
   3 !   10.7   0.0    0.0014      0.54      20      54 ..     601     635 ..     595     689 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.27
                         AAA_23  23 lItGpNGaGKTTildAikl 41 
                                    +++G+ G GKT+i++ +  
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQ 221
                                    678999*********9975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0065
                         AAA_23 143 feefelkdkkerleelekeleeled.ekkllekleqekekekeleeleeeleei 195
                                      ++e+++  erl++l+ el ++++  ++l  ++++ek+  +   +l+e+le +
  gi|121636297|ref|YP_976520.1| 430 LSKEEDEASAERLAKLRSELADQKEkLAELTTRWQNEKNAIEIVRDLKEQLEAL 483
                                    344555666679999988775555416666666699999999999999999866 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0014
                         AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrks 54 
                                    g + + Gp+G GKT +  A+   L+ + + + r +
  gi|121636297|ref|YP_976520.1| 601 GAFMFLGPTGVGKTELAKALADFLFDDERAMVRID 635
                                    7799*********************9988877766 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0012      0.47       4      42 ..     183     221 ..     181     227 .. 0.91
   2 !    9.2   0.0    0.0025         1     101     136 ..     254     289 ..     235     347 .. 0.81
   3 ?    4.2   0.0     0.091        36      26      60 ..     606     639 ..     597     651 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                       ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiie 42 
                                    R++e++++ ++l+r +++  ++ G  g+GKta++  +++
  gi|121636297|ref|YP_976520.1| 183 RDNEIRRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQ 221
                                    99******************************9987665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
                       ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                                    + ++ ++++l++ik+++ +ii +iDel  ++  g  
  gi|121636297|ref|YP_976520.1| 254 EFEERLKAVLDDIKNSAGQIITFIDELHTIVGAGAT 289
                                    567899************************966555 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.091
                       ATPase_2  26 YGpegsGKtaLlkeiienledkdkyviyyialree 60 
                                     Gp g+GKt L k ++  l d d++ +  i+++e+
  gi|121636297|ref|YP_976520.1| 606 LGPTGVGKTELAKALADFLFD-DERAMVRIDMSEY 639
                                    4************99887744.4444445555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0019      0.78       6      91 ..     203     298 ..     199     323 .. 0.79
   2 !   11.5   0.0   0.00059      0.24       6      90 ..     604     699 ..     600     705 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                         AAA_14   6 vitGaRrvGKTtllkqlikell.......vkkesilyinldderd.kkla.dpekllelileklke.ekktylflDEiqe 75 
                                    v+ G   vGKT +++ l+++          +++ i+ ++l +    +k++ ++e+ l+++l+ +k+  ++ + f+DE + 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIVagdvpesLRDKTIVALDLGSMVAgSKYRgEFEERLKAVLDDIKNsAGQIITFIDELHT 282
                                    5677778***********988899999888888999999888666534443566667777777655579999******** PP

                         AAA_14  76 vpewekalkslvdegk 91 
                                    + ++  +  + +d g+
  gi|121636297|ref|YP_976520.1| 283 IVGAGATGEGAMDAGN 298
                                    *988888888887763 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00059
                         AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe...............kllelileklkeekktylfl 70 
                                    +  G+  vGKT l+k l++ l+ +++ ++ i++ +  +k     +               +l e++++    +  t++++
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLFDDERAMVRIDMSEYGEKHTV-ARligappgyvgyeaggQLTEAVRR----RPYTVVLF 678
                                    567999***********9888888888888888886664322.1122334444444222223333333....44577*** PP

                         AAA_14  71 DEiqev.pewekalkslvdeg 90 
                                    DEi ++ p+++++l +++deg
  gi|121636297|ref|YP_976520.1| 679 DEIEKAhPDVFDVLLQVLDEG 699
                                    ***987689*****9999988 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.013       5.2      12      55 ..     188     232 ..     176     256 .. 0.70
   2 !    9.6   0.0    0.0013      0.52      25      51 ..     603     629 ..     599     752 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                   Mg_chelatase  12 kralei.aaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                    +r++++ +   + n +l+G pG GKt + + l++ + + +  e+l
  gi|121636297|ref|YP_976520.1| 188 RRVVQVlSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVAGDVPESL 232
                                    5555541445667889***********999887766555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplse 51 
                                    ++++Gp G GKt lak+l+  l + ++
  gi|121636297|ref|YP_976520.1| 603 FMFLGPTGVGKTELAKALADFLFDDER 629
                                    6899*************9999876433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0049         2      32      56 ..     198     222 ..     185     229 .. 0.78
   2 !   12.4   0.0   0.00022     0.086      35      82 ..     602     649 ..     597     652 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0049
                          AAA_7  32 nkkpvllvGptGtGKtviikdllkk 56 
                                     k++ +l+G+ G+GKt+i++ l ++
  gi|121636297|ref|YP_976520.1| 198 TKNNPVLIGEPGVGKTAIVEGLAQR 222
                                    45667899***********987765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                          AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                     +++ GptG+GKt ++k l + l +++  ++ i +s + + +++ ++i
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALADFLFDDERAMVRIDMSEYGEKHTVARLI 649
                                    589********************99***********999988888776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.015       6.2      25      57 ..     189     221 ..     184     242 .. 0.80
   2 !    9.8   0.0    0.0012      0.49      93     183 ..     244     338 ..     220     341 .. 0.71
   3 ?    0.5   0.0      0.84   3.3e+02      36      55 ..     601     620 ..     579     634 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                           TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                    +++++ +r   +n +l+G++ +GKt+ive  a+
  gi|121636297|ref|YP_976520.1| 189 RVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQ 221
                                    566666666678999*************97766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                           TniB  93 algaplkararvskleqqvlrllrelkvrvL.iiDEihnllagsar..kqreflnalksLgnelkipivlvGt.eealra 168
                                    ++ a  k r + ++  ++vl  +++   +++  iDE+h ++ + a+      + n++k +  + ++ +v++ t +e  ++
  gi|121636297|ref|YP_976520.1| 244 SMVAGSKYRGEFEERLKAVLDDIKNSAGQIItFIDELHTIVGAGATgeGAMDAGNMIKPMLARGELRLVGATTlDEYRKH 323
                                    5555555566666666666666666655655369******96555400455678****************9993456679 PP

                           TniB 169 lrtDpqlasRFepia 183
                                    +++D+ l++RF+++ 
  gi|121636297|ref|YP_976520.1| 324 IEKDAALERRFQQVY 338
                                    ***********9975 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.84
                           TniB  36 pnlllvGdsnnGKtmivekF 55 
                                       +++G++ +GKt +++  
  gi|121636297|ref|YP_976520.1| 601 GAFMFLGPTGVGKTELAKAL 620
                                    457899*********99865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0      0.01       4.1       3      22 ..     204     223 ..     203     284 .. 0.69
   2 !   11.1   0.0    0.0011      0.45       3      21 ..     605     623 ..     604     651 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.01
                         AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                                    l G pGvGKt + + L++r 
  gi|121636297|ref|YP_976520.1| 204 LIGEPGVGKTAIVEGLAQRI 223
                                    8899************9994 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                         AAA_18   3 ltGtpGvGKttlakeLskr 21 
                                      G+ GvGKt+lak+L++ 
  gi|121636297|ref|YP_976520.1| 605 FLGPTGVGKTELAKALADF 623
                                    57**************865 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.3   2.1e+03      75     111 ..       7      42 ..       2      45 .. 0.67
   2 ?    4.7   0.0     0.063        25       4      23 ..     204     223 ..     202     228 .. 0.87
   3 ?    1.5   0.0      0.65   2.6e+02       6      23 ..     607     624 ..     603     640 .. 0.79
   4 !    9.7   0.0    0.0018      0.74      64     107 ..     674     718 ..     656     724 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.3
                          AAA_3  75 ppktqsalleameerqvtvegethklpepflvlatqn 111
                                    ++ktq+al  a++    t+++   +  + ++ l tqn
  gi|121636297|ref|YP_976520.1|   7 TTKTQAALTAALQAAS-TAGNPEIRPAHLLMALLTQN 42 
                                    579*****99998765.44444445555566666666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.063
                          AAA_3   4 legvPGlaktllvkalakal 23 
                                    l g PG++kt +v+ la+ +
  gi|121636297|ref|YP_976520.1| 204 LIGEPGVGKTAIVEGLAQRI 223
                                    6789*************986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.65
                          AAA_3   6 gvPGlaktllvkalakal 23 
                                    g  G++kt l+kala+ l
  gi|121636297|ref|YP_976520.1| 607 GPTGVGKTELAKALADFL 624
                                    567************987 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0018
                          AAA_3  64 nllladeinrappktqsalleameerqvtve.gethklpepflvl 107
                                     ++l dei++a p +   ll++++e ++t + g+t ++ ++ l+l
  gi|121636297|ref|YP_976520.1| 674 TVVLFDEIEKAHPDVFDVLLQVLDEGRLTDGhGRTVDFRNTILIL 718
                                    589*************************96426777777776666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0043       1.7      88     122 ..     188     222 ..     160     235 .. 0.73
   2 ?   -0.0   0.1       1.8   7.3e+02      52     108 ..     429     487 ..     404     488 .. 0.68
   3 !    8.0   0.0    0.0063       2.5     101     121 ..     602     622 ..     566     648 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0043
                                    TTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGKStLinallpe 122
                                    + + ++ ++ +++  vl+G+ GvGK+++++ l+++
  gi|121636297|ref|YP_976520.1| 188 RRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQR 222
                                    333344444455667**************999876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.8
                                    EEE-GGG--HHHHHHHHHHHHHHTT..SEEEE--TTTHTTHHHHHHHCTTSEEEEECST CS
                    RsgA_GTPase  52 vlnKiDlleeeeeleelkeelealg..yevllvsaktkegleelkellkdktsvlvGqS 108
                                    +l+K +   ++e+l +l++el++    ++ l+++ ++++++ e+ + lk+++ +l G+S
  gi|121636297|ref|YP_976520.1| 429 ALSKEEDEASAERLAKLRSELADQKekLAELTTRWQNEKNAIEIVRDLKEQLEALRGES 487
                                    56666655555556666666665551134455666677888888899999999998887 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0063
                                    EEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallp 121
                                      +++G++GvGK+ L +al+ 
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALAD 622
                                    5689************99986 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0057       2.3       3      22 ..     203     222 ..     202     239 .. 0.86
   2 !   10.2   0.0    0.0017      0.67       3      37 ..     604     637 ..     602     647 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0057
                                    EEESSTTSSHHHHHHCHCT- CS
                            Roc   3 vlvGdsgvGKtsllkrfved 22 
                                    vl+G+ gvGKt +++ + ++
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQR 222
                                    79***********9988765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                                    EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEE CS
                            Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfl 37 
                                    +++G +gvGKt l+k + +  f+++ ++++ +d++
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLFDDE-RAMVRIDMS 637
                                    89****************9999766.466666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0028       1.1       3      33 ..     203     234 ..     201     278 .. 0.84
   2 !    8.0   0.0    0.0078       3.1       2      21 ..     603     622 ..     602     648 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                         AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaare 33 
                                    v++G ++ GKT ++e La+r     vpE+ r+
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRiVAGDVPESLRD 234
                                    89*****************9544477888775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0078
                         AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                    ++++G+ + GKT l++aLa+
  gi|121636297|ref|YP_976520.1| 603 FMFLGPTGVGKTELAKALAD 622
                                    6799**************94 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0064       2.6       3      23 ..     204     224 ..     203     282 .. 0.75
   2 !    9.2   0.0    0.0039       1.6       2      23 ..     604     625 ..     603     645 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0064
                   RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                    l G++g+GK+ +++ La+++ 
  gi|121636297|ref|YP_976520.1| 204 LIGEPGVGKTAIVEGLAQRIV 224
                                    78***************9997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0039
                   RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                    ++ Gp+g+GK+ lak La+ l 
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLF 625
                                    689*************998665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00059      0.23       4      31 ..     203     230 ..     202     250 .. 0.90
   2 ?    5.4   0.0      0.04        16       5      23 ..     605     623 ..     602     634 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00059
                                    EEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT   4 ilqGeaGsGKTtLlqklalawaegklpq 31 
                                    +l Ge+G+GKT+ +++la+ + +g+ p+
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIVAGDVPE 230
                                    689****************999998876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.04
                                    EEC-TTTCHHHHHHHHHHH CS
                          NACHT   5 lqGeaGsGKTtLlqklala 23 
                                      G+ G+GKT L++ la+ 
  gi|121636297|ref|YP_976520.1| 605 FLGPTGVGKTELAKALADF 623
                                    67*************9975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.5   3.4e+03      35      61 ..     136     166 ..     102     169 .. 0.78
   2 !    9.0   0.0    0.0034       1.4       6      43 ..     186     223 ..     182     231 .. 0.81
   3 ?    6.6   0.0     0.019       7.6      21      43 ..     602     624 ..     567     632 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.5
                                    HHHHHHHHTT------T....TTTSEEEEEE CS
                           TsaE  35 lvrglakalgveevkSP....TFtlveeYel 61 
                                    l  +++k  g ++v+SP    T++ +++Y++
  gi|121636297|ref|YP_976520.1| 136 LREAFVKVRGSARVTSPepeaTYQALQKYST 166
                                    5566777777779999988889999999965 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE   6 etealgkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                                    e++++ + l + +++  +L G+ G+GKT++v gla+ +
  gi|121636297|ref|YP_976520.1| 186 EIRRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRI 223
                                    666777777777778899*****************987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.019
                                    EEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakal 43 
                                    ++++ G+ G+GKT l+++la  l
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALADFL 624
                                    37899*************99765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0096       3.8       3      33 ..     200     230 ..     198     289 .. 0.76
   2 !    8.9   0.0    0.0029       1.1       6      82 ..     604     689 ..     602     706 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0096
                         AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtek 33 
                                    ++ +++G++g+GKT ++  l ++++  d+ +
  gi|121636297|ref|YP_976520.1| 200 NNPVLIGEPGVGKTAIVEGLAQRIVAGDVPE 230
                                    56699**********9999977776665555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                         AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...........aaeladyktlviDti 74 
                                    +  Gp g+GKT lak l  ++lf d e+ + ++d  ++ + ++++ ++ +               a   ++y ++ +D i
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKAL-ADFLF-DDERAMVRIDMSEYGEKHTVARLIGAPPGYvgyeaggqlteAVRRRPYTVVLFDEI 681
                                    568**************.77776.66777888888887755544444443333366677777777777777888888888 PP

                         AAA_24  75 deleelcl 82 
                                    +++   ++
  gi|121636297|ref|YP_976520.1| 682 EKAHPDVF 689
                                    87766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.036        15       4      22 ..     204     222 ..     203     265 .. 0.93
   2 !    8.3   0.0    0.0063       2.5       3      28 ..     604     634 ..     603     684 .. 0.83
   3 ?   -1.5   0.0       6.5   2.6e+03      91     133 ..     752     792 ..     727     797 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                         AAA_33   4 lvGlpGsGKstlaerllkk 22 
                                    l+G pG+GK+  +e+l+++
  gi|121636297|ref|YP_976520.1| 204 LIGEPGVGKTAIVEGLAQR 222
                                    89**************975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0063
                         AAA_33   3 llvGlpGsGKstlaerllkklg.....avll 28 
                                    ++ G+ G+GK+ la+ l+  l      +v++
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLFdderaMVRI 634
                                    899*************986554444455555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 6.5
                         AAA_33  91 larrlgvpvrivvvetdeetlkeRlakRaangddrsevpeeal 133
                                    +++ l+ ++++ +v+   ++l +Rla+R  + ++   +p + +
  gi|121636297|ref|YP_976520.1| 752 IFEGLNPEELVRIVDIQLAQLGKRLAQRRLQLQV--SLPAKRW 792
                                    5677776777888999999999999999886443..3555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.11        44      15      40 ..     198     223 ..     184     234 .. 0.78
   2 ?   -1.2   0.5       2.6     1e+03     150     175 ..     454     485 ..     421     493 .. 0.73
   3 !   10.0   0.0   0.00098      0.39      14      58 ..     597     643 ..     583     657 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdel 40 
                                    ++   +l G pG GK+++ e l++++
  gi|121636297|ref|YP_976520.1| 198 TKNNPVLIGEPGVGKTAIVEGLAQRI 223
                                    45555677***********9999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                     Zeta_toxin 150 e......gRlvpkeehdeafeglresvealee 175
                                    e       R+ ++++ +e+++ l+e++eal  
  gi|121636297|ref|YP_976520.1| 454 EklaeltTRWQNEKNAIEIVRDLKEQLEALRG 485
                                    13334756999999999999999999999865 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00098
                     Zeta_toxin  14 erPklill.gGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                    +rP+  ++  G +G GK+ela++l+d l   ++ +vr+d  ++ e h
  gi|121636297|ref|YP_976520.1| 597 NRPTGAFMfLGPTGVGKTELAKALADFLFdDERAMVRIDMSEYGEKH 643
                                    6776555525999**************9989999*****99998877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.029        11      20      42 ..     197     219 ..     189     227 .. 0.78
   2 ?    5.6   0.0     0.034        13      21      43 ..     599     621 ..     592     630 .. 0.81
   3 ?   -0.4   0.0       2.5   9.8e+02       4      36 ..     693     727 ..     692     736 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.029
                         AAA_29  20 dlkgatlltGpsGsGKSTllDAi 42 
                                    ++k++ +l+G+ G+GK++++  +
  gi|121636297|ref|YP_976520.1| 197 RTKNNPVLIGEPGVGKTAIVEGL 219
                                    4455789************9766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.034
                         AAA_29  21 lkgatlltGpsGsGKSTllDAiq 43 
                                    + ga+++ Gp+G+GK+ l  A++
  gi|121636297|ref|YP_976520.1| 599 PTGAFMFLGPTGVGKTELAKALA 621
                                    56899**********98877766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                         AAA_29   4 lqlvNWgtfdg.htieidlkg.atlltGpsGsGKS 36 
                                    lq+++ g +++ h  ++d ++ + +lt + GsG S
  gi|121636297|ref|YP_976520.1| 693 LQVLDEGRLTDgHGRTVDFRNtILILTSNLGSGGS 727
                                    57777777776677777777868889999999977 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.18        73      15      34 ..     203     222 ..     194     246 .. 0.86
   2 ?    9.0   0.0    0.0047       1.9      15      37 ..     604     626 ..     598     672 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.18
                                    EEEESTTSSHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllagl 34 
                                    +++Ge G GK+ +++ la+ 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQR 222
                                    79***********9988765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0047
                                    EEEESTTSSHHHHHHHHTTSS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllagllkp 37 
                                     ++G++G GK+ L+k+la  l +
  gi|121636297|ref|YP_976520.1| 604 MFLGPTGVGKTELAKALADFLFD 626
                                    689**************986544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0043       1.7      37     107 ..     203     276 ..     174     332 .. 0.78
   2 ?    2.9   0.0      0.17        69      35      55 ..     602     622 ..     576     632 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                         AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg......pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                    +l+G pg+GKt+++  la  ++ G+ +++      +  +      +v++   + e+++Rl+av+ +++  a+  ++ 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIVAGD-VPEslrdktI--VALDLGSMVAGSKYRGEFEERLKAVLDDIKNSAGQIITF 276
                                    699*******************888.6665555322..233444467777778899999999999886666555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                         AAA_25  35 lallaGapgtGKttlaldlal 55 
                                      ++ G++g+GKt la  la 
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALAD 622
                                    44677**********998885 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  11.4   0.00011     0.046       5      66 ..     426     488 ..     422     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                       NYD-SP28   5 reeerrreeeelrqerkekleeeaksseekfeeinekWr.eilrknkpqeLrkeleeqkqace 66 
                                    +e++  +ee+e+ +er++kl  e +  +ek++e++ +W+ e +++++ ++L+++le ++   e
  gi|121636297|ref|YP_976520.1| 426 EEMALSKEEDEASAERLAKLRSELADQKEKLAELTTRWQnEKNAIEIVRDLKEQLEALRGESE 488
                                    7888899*******************************966777889*********9986665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023     0.091     123     204 ..     594     676 ..     451     683 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                          T2SSE 123 rkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak..kakvtfadllraaLRlrP 200
                                    + + r  g +++ G+Tg GKt l+ al  ++ ++++ +v + D  E+  ++  +  + a    ++ ++   l +a+R+rP
  gi|121636297|ref|YP_976520.1| 594 SDPNRPTGAFMFLGPTGVGKTELAKALADFLFDDERAMVRI-DMSEYGEKHTVARLIGAPpgYVGYEAGGQLTEAVRRRP 672
                                    5555567899999*******************996666655.99999988877766666666777777778888899998 PP

                          T2SSE 201 Drim 204
                                      ++
  gi|121636297|ref|YP_976520.1| 673 YTVV 676
                                    7665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0079       3.1      44      79 ..     190     225 ..     158     281 .. 0.77
   2 ?    2.1   0.0      0.23        90      55      94 ..     602     641 ..     586     653 .. 0.83
   3 ?   -3.1   0.0         9   3.6e+03     190     232 ..     751     797 ..     745     799 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0079
                         DUF815  44 teqfleglpannvLLwGarGtGKSslvkallneyae 79 
                                    + q l+ ++ nn +L+G+ G+GK ++v  l +++ +
  gi|121636297|ref|YP_976520.1| 190 VVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVA 225
                                    44667778889999**************99998765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                         DUF815  55 nvLLwGarGtGKSslvkallneyaeegLrlievekedlke 94 
                                      ++ G  G+GK  l kal   + +++ +++ ++ ++  e
  gi|121636297|ref|YP_976520.1| 602 AFMFLGPTGVGKTELAKALADFLFDDERAMVRIDMSEYGE 641
                                    56889****************9999999999998877655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 9
                         DUF815 190 lgFykldqeeYleiveklakklglelek....eeleeeAlewalerg 232
                                    l F+ l+ ee ++iv+  +++lg +l++     +++  A +w ++rg
  gi|121636297|ref|YP_976520.1| 751 LIFEGLNPEELVRIVDIQLAQLGKRLAQrrlqLQVSLPAKRWLAQRG 797
                                    77888888999999999999998888873333344555777777766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0036       1.4      10      37 ..     199     226 ..     190     346 .. 0.88
   2 ?    0.7   0.0       1.5   6.2e+02      11      34 ..     601     624 ..     592     637 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0036
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvel 37 
                                    +++ ++++ pG GKT ++++  + +v+ 
  gi|121636297|ref|YP_976520.1| 199 KNNPVLIGEPGVGKTAIVEGLAQRIVAG 226
                                    5667899***********9998887765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                    + ++ +++ G GKT++ k+    l
  gi|121636297|ref|YP_976520.1| 601 GAFMFLGPTGVGKTELAKALADFL 624
                                    56778999******9988776665 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     0.001      0.41      16      48 ..     597     629 ..     590     642 .. 0.88
   2 ?   -1.3   0.0       4.2   1.7e+03     102     129 ..     671     698 ..     662     700 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                DNA_pol3_delta2  16 grlahayLfeGdegigkkelalnlakallceek 48 
                                    +r + a++f G++g+gk ela++la  l+ +e+
  gi|121636297|ref|YP_976520.1| 597 NRPTGAFMFLGPTGVGKTELAKALADFLFDDER 629
                                    77888***********************99876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                DNA_pol3_delta2 102 skkkiiiiedaekmtksAaNalLktlEE 129
                                      + +++ +++ek ++     lL++l E
  gi|121636297|ref|YP_976520.1| 671 RPYTVVLFDEIEKAHPDVFDVLLQVLDE 698
                                    567899*******************998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.3   1.2e+02       5      26 ..     203     224 ..     199     242 .. 0.83
   2 ?    7.4   0.0    0.0077       3.1       4      29 ..     603     628 ..     600     637 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.3
                                    EEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   5 llvGlqGaGKTttlaKLaallk 26 
                                    +l+G  G+GKT  +  La+++ 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQRIV 224
                                    799**************99875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0077
                                    EEEEESTTSSHHHHHHHHHHHHHHTT CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkeg 29 
                                    ++++G++G+GKT  +  La+ l +++
  gi|121636297|ref|YP_976520.1| 603 FMFLGPTGVGKTELAKALADFLFDDE 628
                                    79************999*99887665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.02       7.9       4      25 ..     204     225 ..     201     231 .. 0.84
   2 ?    3.3   0.0      0.17        69       6      23 ..     607     624 ..     602     633 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                                    EE--TTSSHHHHHHHHHHHH.. CS
                       NTPase_1   4 iTGppGvGKtTlvkkvlellks 25 
                                    + G+pGvGKt +v+ +++ +  
  gi|121636297|ref|YP_976520.1| 204 LIGEPGVGKTAIVEGLAQRIVA 225
                                    67************99998865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                                    --TTSSHHHHHHHHHHHH CS
                       NTPase_1   6 GppGvGKtTlvkkvlell 23 
                                    Gp GvGKt l k +++ l
  gi|121636297|ref|YP_976520.1| 607 GPTGVGKTELAKALADFL 624
                                    9**********9999877 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.8   0.00049      0.19      89     169 ..     411     488 ..     365     516 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00049
                           FTA4  89 leievnedltkeelIkeLPesweveekeaeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgsed 168
                                     ei+  e+l+++  I+e+  s+e+  +ea++e l +l+ + a+++++L+el +r q+ ++ ++  r+lk++le ++g  +
  gi|121636297|ref|YP_976520.1| 411 VEIDEVERLVRRLEIEEMALSKEE--DEASAERLAKLRSELADQKEKLAELTTRWQNEKNAIEIVRDLKEQLEALRGE-S 487
                                    4455678999999**********4..566666678999************************************9663.2 PP

                           FTA4 169 p 169
                                    +
  gi|121636297|ref|YP_976520.1| 488 E 488
                                    2 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.036        14      35      57 ..     201     223 ..     173     286 .. 0.74
   2 ?   -2.4   0.2         9   3.6e+03      89     109 ..     412     434 ..     390     437 .. 0.73
   3 ?    6.7   0.0     0.014       5.6      31      55 ..     598     622 ..     567     633 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.036
                         RuvB_N  35 hvllyGpPGlGkttlakiiakel 57 
                                      +l+G PG+Gkt++ + +a+ +
  gi|121636297|ref|YP_976520.1| 201 NPVLIGEPGVGKTAIVEGLAQRI 223
                                    34678********9977665543 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9
                         RuvB_N  89 fideihrlsra..veevlysame 109
                                     ide+ rl r   +ee+  s  e
  gi|121636297|ref|YP_976520.1| 412 EIDEVERLVRRleIEEMALSKEE 434
                                    59*****9885225677665555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.014
                         RuvB_N  31 ealdhvllyGpPGlGkttlakiiak 55 
                                    ++    ++ Gp G+Gkt lak +a+
  gi|121636297|ref|YP_976520.1| 598 RPTGAFMFLGPTGVGKTELAKALAD 622
                                    55567899*************9986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.23        92       3      62 ..     203     257 ..     203     261 .. 0.83
   2 ?    2.1   0.0      0.34   1.4e+02       4      24 ..     605     625 ..     603     650 .. 0.80
   3 ?    1.7   0.0      0.46   1.8e+02     253     285 ..     669     699 ..     662     720 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefei 62 
                                    vliG  g+GK+ + + l      +r v g+ +e+ + ++i   +  +     ++++efe 
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLA-----QRIVAGDVPESLRDKTIVALDLGSMVAGSKYRGEFEE 257
                                    89***************5.....7888888888888888888888888888888888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                         AAA_21   4 liGpNgsGKSnLLdaldllar 24 
                                    + Gp g+GK+ L +al  + +
  gi|121636297|ref|YP_976520.1| 605 FLGPTGVGKTELAKALADFLF 625
                                    78**************66543 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.46
                         AAA_21 253 ralkkgsllliDEpEngLHPkllrrllellkel 285
                                    r+++  +++l+DE+E   HP +   ll++l+e 
  gi|121636297|ref|YP_976520.1| 669 RRRPY-TVVLFDEIEKA-HPDVFDVLLQVLDEG 699
                                    44555.*********98.888888888888655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0         1   4.2e+02       5      23 ..     203     221 ..     200     227 .. 0.85
   2 ?    8.0   0.0    0.0056       2.2       4      23 ..     603     622 ..     600     631 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                      PduV-EutP   5 lliGkvgsGKttLtqalkg 23 
                                    +liG+ g+GKt++ + l +
  gi|121636297|ref|YP_976520.1| 203 VLIGEPGVGKTAIVEGLAQ 221
                                    69*********99887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0056
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                     +++G++g+GKt L++al +
  gi|121636297|ref|YP_976520.1| 603 FMFLGPTGVGKTELAKALAD 622
                                    69***************976 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         7   2.8e+03      59     117 ..     205     263 ..     195     270 .. 0.76
   2 ?    9.9   0.0    0.0019      0.77      15      80 ..     560     627 ..     555     637 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7
                                    EE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEHHHHS--GGGHHHHHHHHHHHHHHHH CS
                         Torsin  59 hGwtGtGknfvaeiiaenlyrdGlrsdyvkkfvatadfPkkkkveeykeelkeqiretl 117
                                     G +G Gk  + e +a+ +    +  +   k +   d+      ++y+ e++e+++  l
  gi|121636297|ref|YP_976520.1| 205 IGEPGVGKTAIVEGLAQRIVAGDVPESLRDKTIVALDLGSMVAGSKYRGEFEERLKAVL 263
                                    58999999999999999998877777777777777777777777777777777776655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                                    -HHHHHHHHHHH--S-HHHHHHHHHHHH.HHHT-SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHSTT CS
                         Torsin  15 nleeLekdlekklfGqhlvkklvvksvk.aylenekpkkpL.vlsfhGwtGtGknfvaeiiaenlyrd 80 
                                    +l  +e +l k+++Gq  +   v  +v+ +     +p++p  ++ f G tG Gk  +a+ +a+ l+ d
  gi|121636297|ref|YP_976520.1| 560 KLLRMEDELGKRVIGQKAAVTAVSDAVRrSRAGVSDPNRPTgAFMFLGPTGVGKTELAKALADFLFDD 627
                                    56678999******************9724455668888764789******************99976 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.81   3.2e+02      12      47 ..     187     222 ..     159     231 .. 0.83
   2 ?    7.0   0.0     0.013       5.2       8      50 ..     575     626 ..     572     634 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.81
                                    HHHHT......TTSEEEEEESTTSTHHHHHHHHHHH CS
                         ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklier 47 
                                    i+++++ l+ + +++ ++  + G+GKT +   l++r
  gi|121636297|ref|YP_976520.1| 187 IRRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQR 222
                                    667777777666778889999******998777666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                    HHHHHHHHT..............TTS.EEEEEESTTSTHHHHHHHHHHHH-S CS
                         ResIII   8 Qeeaienlleklks........krdk.rglikmaTGtGKTlvaaklierllk 50 
                                    Q+ a++++ +++          +r +  +++  +TG+GKT +a +l++ l+ 
  gi|121636297|ref|YP_976520.1| 575 QKAAVTAVSDAVRRsragvsdpNRPTgAFMFLGPTGVGKTELAKALADFLFD 626
                                    778888888777667777776655555788************9888877665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.89   3.6e+02      29      59 ..     205     241 ..     203     243 .. 0.80
   2 ?    1.6   0.8      0.62   2.5e+02     100     149 ..     426     479 ..     382     526 .. 0.53
   3 ?    4.7   0.0     0.071        28      29      60 ..     606     636 ..     603     657 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.89
                          DUF87  29 lgsTGsGKSntvavLleelle......kkgatililD 59 
                                    +g+ G+GK+  v  L +++++       ++ ti+ lD
  gi|121636297|ref|YP_976520.1| 205 IGEPGVGKTAIVEGLAQRIVAgdvpesLRDKTIVALD 241
                                    6888****************88777765555666666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.62
                          DUF87 100 eelldlleeddkpaaavqrsvleealdqaka.....keekeklssdepvekllee 149
                                    ee++   ee d+++a+++ ++  e+ dq ++     ++++++ ++ e+v  l+e+
  gi|121636297|ref|YP_976520.1| 426 EEMALSKEE-DEASAERLAKLRSELADQKEKlaeltTRWQNEKNAIEIVRDLKEQ 479
                                    222222222.222222233333333333322333332222222222333333333 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.071
                          DUF87  29 lgsTGsGKSntvavLleellekkgatililDp 60 
                                    lg TG+GK+ +++ L + l  ++   ++ +D+
  gi|121636297|ref|YP_976520.1| 606 LGPTGVGKTELAKALADFLF-DDERAMVRIDM 636
                                    899************99998.66666666665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.3     0.003       1.2      48     148 ..     393     491 ..     389     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.003
                           Fez1  48 eekeeeikeleesleektlelevcenelqrkkseaellr.ekvekleeelkelreelselsleeeeaalesdeakaqrqe 126
                                    +  +e++++l+ +++++  e++++e  ++r + e+  l+ e+ e+  e l++lr+el++++++ +e ++++++   ++++
  gi|121636297|ref|YP_976520.1| 393 DLVDEAASRLRMEIDSRPVEIDEVERLVRRLEIEEMALSkEEDEASAERLAKLRSELADQKEKLAELTTRWQN---EKNA 469
                                    567899999*********************9877766650555666677999***999987776666666655...5666 PP

                           Fez1 127 aeeleelkreverlraeLkeer 148
                                     e +++lk+++e lr+e +  +
  gi|121636297|ref|YP_976520.1| 470 IEIVRDLKEQLEALRGESERAE 491
                                    7789999999999998755443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1390  (0.077528); expected 358.6 (0.02)
Passed bias filter:                      865  (0.0482459); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.96u 0.33s 00:00:01.29 Elapsed: 00:00:00.48
# Mc/sec: 5360.91
//
Query:       gi|121636298|ref|YP_976521.1|  [L=390]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-19   70.2   0.0    2.3e-19   69.6   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    7.8e-09   36.1   0.0    1.3e-08   35.4   0.0    1.3  1  Globin         Globin
    2.1e-06   28.4   0.0    7.6e-06   26.5   0.0    1.9  1  NAD_binding_1  Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   3.9e-23   2.3e-19       3      97 ..     151     242 ..     149     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 3.9e-23
                                    EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC.ETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH.H CS
                  FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlk.ikgeaviRsYtpissenekGelellvkvypgGkmsqaL.d 80 
                                    +++e+ +vs+d+++ r++l+++ +   +++Gq+v+++++ ++++  +R+ +p+   + +G++e++v+v+pgG +s+a+  
  gi|121636298|ref|YP_976521.1| 151 TVVEHIRVSRDLAVARLQLDRPLH---YYPGQYVNVHVPqCPRR--WRYLSPAIPADPNGRIEFHVRVVPGGLVSNAIvG 225
                                    7999****************8877...************66665..********************************99 PP

                                    CS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  81 elkigdtleikGPlGkf 97 
                                    e+++gd ++++GP+G f
  gi|121636298|ref|YP_976521.1| 226 ETRPGDRWRLSGPHGAF 242
                                    9**************99 PP

>> Globin  Globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   2.1e-12   1.3e-08       5     109 ..      11     100 ..       7     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.1e-12
                                    HHHHHHHHHTHHHHHHHHHHHHHHHHSGGGGGGSTTTTTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHH CS
                         Globin   5 vkaswekvkanaeelgaeilkrlFkaypdtkklFkkfgdlssaedlksspkfkahakkvlaalgeavknldndealkaal 84 
                                    v ++  k+  + +el +++++++F+ + ++++lF+   d          ++ +a ++++ +  ge+v++   +e+  a+l
  gi|121636298|ref|YP_976521.1|  11 VLQNAFKL--DDPELVRRFYAHWFALDASVRDLFP-P-D--------MGAQRAAFGQALHWVYGELVAQR--AEEPVAFL 76 
                                    66666777..89***********************.6.6........78********************9..889***** PP

                                    HHHHHHHHCSTT--HHHHHHHHHHH CS
                         Globin  85 kklaarHaergkvdpanFklfgeal 109
                                    ++l+++H+++g v p ++++++ al
  gi|121636298|ref|YP_976521.1|  77 AQLGRDHRKYG-VLPTQYDTLRRAL 100
                                    ***********.*********9987 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.3e-09   7.6e-06       1     108 [.     253     370 ..     253     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEE...............ESS CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvav...............vsr 65 
                                    m+ag tG+aP+r+++  + +    + +v+l++G+r+ ++l+    l ++a+ +p+ l v +v               vs 
  gi|121636298|ref|YP_976521.1| 253 MVAGSTGLAPLRALIIDLSRF-AVNPRVHLFFGARYACELYDLPTLWQIAAHNPW-LSVSPVseyngdpawaadypdVSA 330
                                    9******************99.7789*****************************.888888878888888887777677 PP

                                    CTTTSSSEESSHHHHHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  66 eeagweggkgrvqdalleellslkkeethvyvCGppgMikavr 108
                                    +      ++gr+ d + ++  +   ++ ++++CG p+M++a++
  gi|121636298|ref|YP_976521.1| 331 PRGLHVRQTGRLPDVVSRY-GG--WGDRQILICGGPAMVRATK 370
                                    7777777777777777444.44..69*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2560.65
//
Query:       gi|121636299|ref|YP_976522.1|  [L=1085]
Description: LuxR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-16   59.1   0.0    4.5e-16   58.1   0.0    1.6  1  GerE           Bacterial regulatory proteins, luxR family
    1.1e-07   31.7   0.0    1.7e-06   27.8   0.0    2.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    4.8e-06   27.1   1.9    4.8e-06   27.1   1.9    4.5  2  AAA_16         AAA ATPase domain
    9.5e-06   25.0   0.0    1.6e-05   24.2   0.0    1.3  1  NB-ARC         NB-ARC domain
    3.6e-05   23.3  56.7    0.00011   21.7  26.0    3.9  4  TPR_MalT       MalT-like TPR region
    0.00012   21.8   4.1    0.00018   21.1   0.2    3.3  4  AAA_25         AAA domain
     0.0017   18.0   0.0     0.0064   16.1   0.0    2.0  1  Sigma70_r4_2   Sigma-70, region 4
     0.0019   18.5   0.1      0.015   15.6   0.0    2.4  2  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.063   13.3   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.061   12.5   0.1      0.093   11.9   0.1    1.2  1  ArsA_ATPase    Anion-transporting ATPase
      0.075   12.9   0.1       0.48   10.3   0.0    2.5  1  HTH_23         Homeodomain-like domain
       0.13   12.2   1.9       0.94    9.4   1.9    2.4  1  NACHT          NACHT domain
       0.82   10.0   4.8        3.7    7.9   4.8    2.1  1  Med25_SD1      Mediator complex subunit 25 synapsin 1


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   3.3e-19   4.5e-16       2      56 ..    1026    1080 ..    1025    1081 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.3e-19
                                     SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHH CS
                           GerE    2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrl 56  
                                     sL++ E +v rl+ eG+ nk+IA +l++S++TV++h++++++KL+ +sr +l++ 
  gi|121636299|ref|YP_976522.1| 1026 SLTPTEIDVVRLVGEGLANKDIATRLFVSPRTVQTHLTHVYTKLGFTSRLQLAQA 1080
                                     8***************************************************986 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.2e-09   1.7e-06       7     153 ..       8     135 ..       5     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.2e-09
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekk.vykvkt.iGdaymvvsglpeekaahaaklaelaLd 84 
                                     +vt+l ad++g+t l++ h p ++  +++ l + +  ++++++ v  v+   Gd+++ ++ +        ++++  aLd
  gi|121636299|ref|YP_976522.1|   8 GTVTLLLADVEGSTWLWETH-PDDMGAAVARLDKAVSGVIAAHDgVRPVEQgEGDSFVLAFACA-------SDAVAAALD 79 
                                    58******************.********************999788898549********999.......455555666 PP

                  Guanylate_cyc  85 mlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetye 153
                                    +          +   +++r+G+htG+v ++  G       + G t+n ++r+  ++++g+  +s  t +
  gi|121636299|ref|YP_976522.1|  80 LQR-------ARLAPIRLRIGVHTGEVALRDEG------NYAGPTINRTARLRDLAHGGQTVLSGVTES 135
                                    533.......345689***********988775......578*****************9999988866 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   1.9   3.5e-09   4.8e-06       1      63 [.     196     250 ..     196     322 .. 0.77
   2 ?   -1.0   0.7       1.5     2e+03      73     139 ..     574     646 ..     545     652 .. 0.61

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.5e-09
                         AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    r+vGR++++ ++++++ +      +lv l+G+ GvGK++l+ +l+ ++ ++   f r+++++l
  gi|121636299|ref|YP_976522.1| 196 RFVGRGAQITEVHRLVTDN-----RLVTLTGAGGVGKTRLAAQLAAQIAGE---FGRAWFVDL 250
                                    79*******9999988744.....8************************99...777777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                         AAA_16  73 aqalareellrqlldeaesaeleawrekleeala....avpelagaea........srllellkrllallsrderplvl 139
                                    a al +++llr   ++ + +e +aw + +++  +    +      a+a        ++ll+ + +++a +++ ++ lv+
  gi|121636299|ref|YP_976522.1| 574 ALAL-ASSLLRVWMTRGRIQEGRAWFDSILADENarhlE-----VAAAvraraladKALLDIFVDAAAGMEQAQQALVI 646
                                    4445.3477777777777777777777777776644442.....33333333355778888888888877777776666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.2e-08   1.6e-05      21     210 ..     215     395 ..     205     434 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                    EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                         NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeveslkrklvrlL 100
                                     +v+l G gGvGKt la+q   +   + g+F +  +v ++   +   +  t++  L+l+   ++         + + r+L
  gi|121636299|ref|YP_976522.1| 215 RLVTLTGAGGVGKTRLAAQLAAQ---IAGEFGRAWFVDLAPITDPDLVPVTVAGALGLH---DQPGR--S-TTDTVLRFL 285
                                    489****************9888...******************************998...22222..2.46899**** PP

                                    CCTTEEEEEEEE-SHHH.H.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--.HHHHHHHHHHCCTS-GGC CS
                         NB-ARC 101 ltkrfllvlDDVweeed.wdkigvvlparenrlrvllTTRdeevanavsatsekievelLe.kdeawellenkvfekkle 178
                                     ++  l+vlD   +  d   ++ ++l    +++r l T R+     +v++ +   +v +L+  dea e+++  + + + +
  gi|121636299|ref|YP_976522.1| 286 GGRPALVVLDNCEHLLDaTAALVLALVKACRGVRLLATCREPL---RVEG-EVSYRVPSLSlSDEAVEMFCYRAQRVRPD 361
                                    **********986665544456677777899999999999852...4455.44456666653799******998877665 PP

                                    HH....CHHHHHHHHHHCTT-HHHHHHHHHHHC- CS
                         NB-ARC 179 ekes..leevakeivekckGlPlalkvlggllst 210
                                       +    +   ei ++  GlPla+ + ++ l++
  gi|121636299|ref|YP_976522.1| 362 FRLTddNSAAVTEICKRLDGLPLAIELAAARLRS 395
                                    4433346677788899999******999877764 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.4      0.32   4.4e+02     195     240 ..     568     611 ..     548     636 .. 0.61
   2 ?    2.3   3.8     0.064        89      17      74 ..     633     691 ..     618     704 .. 0.70
   3 !   21.7  26.0   7.9e-08   0.00011       8     231 ..     664     883 ..     657     887 .. 0.88
   4 !   16.8  22.8   2.5e-06    0.0034       8     235 ..     784    1006 ..     782    1015 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.32
                       TPR_MalT 195 nfhvdwlanaeevrvrlwlaqgdlaaaerwleaaelpsdddnhfle 240
                                    n ++    ++ +  +r+w ++g++++ ++w +++  ++++   +le
  gi|121636299|ref|YP_976522.1| 568 NSDTEGALALASSLLRVWMTRGRIQEGRAWFDSILADENA--RHLE 611
                                    4444444445555678888888888888888888644332..2223 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.064
                       TPR_MalT  17 aeralelArqALallpeddllar.iaatavlGeasllqGdleaAlqalqeaeklarqad 74 
                                    a + +e+A+qAL + +e d +a    a+ + G +++   + +aA + ++ea++lar+ d
  gi|121636299|ref|YP_976522.1| 633 AAAGMEQAQQALVIAREVDEPALlSRALTACGLIAVAVARADAAASYFAEAIDLARAVD 691
                                    45578888888888877665544355566778888888888888888888888886544 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 7.9e-08
                       TPR_MalT   8 AllaiasgdaeralelArqALallpeddllar.iaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqq 86 
                                    +l+a+a  +a++a  +  +A++l +  d  +r ++++ +++  ++++Gd  aA+ a qea++la +++   +al+   ++
  gi|121636299|ref|YP_976522.1| 664 GLIAVAVARADAAASYFAEAIDLARAVDDRWRlAQILTFQAVDAVVAGDPVAARPAAQEARELAAAIGDHSNALWCRWCL 743
                                    689999999999999999*******9999999888999****************************************** PP

                       TPR_MalT  87 aeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvl 166
                                    +  + ++G+L +A+  + +    a+ +++  l  ++ l+ l a  l  +++L +A+ ++++++e +e +e   a   y +
  gi|121636299|ref|YP_976522.1| 744 GYAQLMRGELAAAAAQFGEVVDEAEASQEV-LHKANSLQGL-AFALAYQGELSAARAAADAALEAAELGEYF-AGMGYSA 820
                                    ***************999999977666554.6667777555.8778889***************99999444.44599** PP

                       TPR_MalT 167 larialaqGdleeAetllekaeelaresnfhvdwlanaeevrvrlwlaqgdlaaaerwleaaelp 231
                                    l   ala Gd+++A+++ e a + +  +    +++++a  ++ +  la gdl+aa+rw ++a ++
  gi|121636299|ref|YP_976522.1| 821 LTTAALAAGDVQTAQHASEAAWRNLSLALPLSAAVQRAFNAQAA--LAGGDLSAARRWCDDAVQS 883
                                    **********************9999877777888898999965..8***********9998776 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 2.5e-06
                       TPR_MalT    8 AllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallq 85  
                                     A+   ++g+  +a++ A +AL+  +  +++a + + ++l++a+l +Gd++ A+ a ++a + + +   +  a+++   
  gi|121636299|ref|YP_976522.1|  784 AFALAYQGELSAARAAADAALEAAELGEYFAGMGY-SALTTAALAAGDVQTAQHASEAAWRNL-SLALPLSAAVQRAF 859 
                                     667789**********************9999999.66688*********9999988888765.56666667777777 PP

                       TPR_MalT   86 qaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaal.d 162 
                                      a+ + a G+L +A +++ +a q +t ++l+      ++l+ +a++    ++ eeAe+ ++++++++ + + +  l d
  gi|121636299|ref|YP_976522.1|  860 NAQAALAGGDLSAARRWCDDAVQSMTGHHLA------MALATRARIAVAEGKREEAERDAHKALACAAESGAHLDLpD 931 
                                     89999999***************77777766......566679*************************9999999945 PP

                       TPR_MalT  163 ayvllarialaqGdleeAetllekaeelaresnfhvdwlanaeevr.vr.lwlaqgdlaaaerwleaaelpsddd 235 
                                      +  la +a   G + +A++l+  ae+  ++    ++++ +++ v+ v+ l  a g+++   +w+e a l+ +++
  gi|121636299|ref|YP_976522.1|  932 VLECLAGLASDAGTHHAAARLFGAAEAIRQQIGSVRFAIYRSDYVQsVTaLRDAMGEKDFDAAWAEGAALSIKET 1006
                                     9*************************9988877666666666666654303456677777777888877776655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.3e-07   0.00018      26      65 ..     207     248 ..     203     268 .. 0.85
   2 ?   -1.5   0.0       1.1   1.6e+03     142     156 ..     288     302 ..     269     318 .. 0.84
   3 ?   -1.9   0.1       1.5   2.1e+03      76     121 ..     899     943 ..     877     966 .. 0.57
   4 ?   -2.5   0.0       2.3   3.1e+03      54      90 ..    1006    1051 ..    1000    1069 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                         AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava..tGkpwlg 65 
                                    v++l+  + l+ l+Ga+g+GKt la +la+ +a   G+ w+ 
  gi|121636299|ref|YP_976522.1| 207 VHRLVTDNRLVTLTGAGGVGKTRLAAQLAAQIAgeFGRAWFV 248
                                    677888899************************888898886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                         AAA_25 142 gvrlvviDplsralg 156
                                    +++lvv+D++ ++l+
  gi|121636299|ref|YP_976522.1| 288 RPALVVLDNCEHLLD 302
                                    4899****9998876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                         AAA_25  76 yvsaEdsedelrrRlravgealrddarllvldlagv.eslpLfakdr 121
                                    + +aE++++e +r ++++++ ++  +  + ldl++v e+l  +a+d+
  gi|121636299|ref|YP_976522.1| 899 IAVAEGKREEAERDAHKALACAA--ESGAHLDLPDVlECLAGLASDA 943
                                    45678888888888887776653..3333445555555555444444 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.3
                         AAA_25   54 alava.tGkpwlg.......pvapeqgkVlyvsaEds.edelrrRl 90  
                                      +a+a +G++w +       ++ p+ + V+ +++E+  +++++ Rl
  gi|121636299|ref|YP_976522.1| 1006 TIAYAqRGHSWRKrpatgweSLTPTEIDVVRLVGEGLaNKDIATRL 1051
                                     5556666666666666668888889999999999987345666665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.6e-06    0.0064      10      53 ..    1026    1068 ..    1025    1069 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                     TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                   Sigma70_r4_2   10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkk 53  
                                     +L++ +  ++ l   egl  k+IA +l +s++tV+++l     k
  gi|121636299|ref|YP_976522.1| 1026 SLTPTEIDVVRL-VGEGLANKDIATRLFVSPRTVQTHLTHVYTK 1068
                                     788888889999.79***********************877666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.015       5     104 ..     214     301 ..     209     326 .. 0.79
   2 ?   -1.5   0.0         2   2.8e+03      88     117 ..     447     483 ..     436     489 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                     +++++tG  G+GKT+l+++l+ q         e  +  fv+l+  t+++ +   ++ algl  ++  +  +   +++ +
  gi|121636299|ref|YP_976522.1| 214 NRLVTLTGAGGVGKTRLAAQLAAQIAG------EFGRAWFVDLAPITDPDLVPVTVAGALGL--HD--QPGRSTTDTVLR 283
                                    67899*******************843......244555**********************5..44..456666799999 PP

                         AAA_22  85 alraravielliiDEaqhlr 104
                                     l  r +  l+++D+ +hl 
  gi|121636299|ref|YP_976522.1| 284 FLGGRPA--LVVLDNCEHLL 301
                                    9999988..*********63 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                         AAA_22  88 arav.ielliiDEaqhlr.s.....eealeeLrslln 117
                                    + av ++++ +D+aq +  s      ++l e+  l++
  gi|121636299|ref|YP_976522.1| 447 RLAVfVGCFFVDDAQAVAcSgdvqrYQVLDEITLLVD 483
                                    4444679999*****9977333445666666655555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.063       3      37 ..     218     252 ..     216     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                    EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDp 37 
                                       + GGvGKT laa La+ +a +  r   vD+ p
  gi|121636299|ref|YP_976522.1| 218 TLTGAGGVGKTRLAAQLAAQIAGEFGRAWFVDLAP 252
                                    67899****************99888888888766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.7e-05     0.093       2      27 ..     215     240 ..     214     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                                    EEEEEEESTTSSHHHHHHHHHHHHHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklse 27 
                                    ++++++G GGVGKt ++a +a++++ 
  gi|121636299|ref|YP_976522.1| 215 RLVTLTGAGGVGKTRLAAQLAAQIAG 240
                                    7899*******************985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00035      0.48      10      35 ..    1034    1059 ..    1032    1072 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                         HTH_23   10 illllaeGlsvreIAreLgvsrrTvy 35  
                                     +++l+ eGl  ++IA++L vs+rTv+
  gi|121636299|ref|YP_976522.1| 1034 VVRLVGEGLANKDIATRLFVSPRTVQ 1059
                                     57777889999**************8 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.9   0.00068      0.94       1     128 [.     215     325 ..     215     351 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00068
                                    SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                          NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavllel 79 
                                    rlv l+G+ G+GKT L+++la ++a +           f+ l+ ++++  +  ++a  l  + ++  ++ ++  +++   
  gi|121636299|ref|YP_976522.1| 215 RLVTLTGAGGVGKTRLAAQLAAQIAGEFGR------AWFVDLAPITDPDLVpVTVAGALGLHDQPGRSTTDT--VLRFLG 286
                                    7899*****************999876422......345555555555444434444443333332333333..344444 PP

                                    CCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEE CS
                          NACHT  80 perlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvr 128
                                     + +L +lD  + l +   +        l   l+++  +++++ll+t+r
  gi|121636299|ref|YP_976522.1| 287 GRPALVVLDNCEHLLDATAA--------LVLALVKA--CRGVRLLATCR 325
                                    45556666666665554444........55555555..66666666665 PP

>> Med25_SD1  Mediator complex subunit 25 synapsin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.8    0.0027       3.7      47      93 ..     787     833 ..     765     874 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                      Med25_SD1  47 vaqpgtLsaAqaAAqsAvEAAknqKagLgtRFsplknlqqaapgvGp 93 
                                     a +g LsaA+aAA  A EAA+      g  +s+l++ + aa  v +
  gi|121636299|ref|YP_976522.1| 787 LAYQGELSAARAAADAALEAAELGEYFAGMGYSALTTAALAAGDVQT 833
                                    67899****************98777777777888777766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1085 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 7157.05
//
Query:       gi|121636300|ref|YP_976523.1|  [L=443]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-62  207.9  27.1    8.5e-62  207.9  27.1    2.3  2  PPE       PPE family
    6.2e-08   33.4  11.5    6.2e-08   33.4  11.5    6.7  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9  27.1   9.4e-66   8.5e-62       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -2.2   1.1      0.44   3.9e+03      22      85 ..     182     189 ..     172     205 .. 0.49

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 9.4e-66
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+nsa++y+Gpgs+pl++AaaaW++La+el+++aa+++sv+++l+++ W Gps+ +maaaa+py+aW++a+aa+ae
  gi|121636300|ref|YP_976523.1|   5 ALPPEINSARIYSGPGSRPLMQAAAAWQRLANELTATAASYSSVISGLTGDDWLGPSALSMAAAAVPYVAWMRATAASAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aAaqa aaa+aYe+A+aa+vpp++iaanr ++ +lv+tn+fGqntpaIa+ ea+y +mwaqd+ am++Y+ asaaa
  gi|121636300|ref|YP_976523.1|  85 QAAAQAVAAANAYESAYAATVPPTVIAANRRTMLSLVKTNVFGQNTPAIATSEAQYGAMWAQDIVAMEGYAGASAAA 161
                                    **************************************************************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHH CS
                            PPE  22 aAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaeeaAaq 85 
                                     Aaa                                                        +Aaq
  gi|121636300|ref|YP_976523.1| 182 DAAA--------------------------------------------------------TAAQ 189
                                    2222........................................................2222 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -15.4  25.1         2   1.8e+04      26      61 ..      63     100 ..      21     169 .. 0.69
   2 ?  -13.1  20.1         2   1.8e+04      23      48 ..     170     195 ..     142     294 .. 0.70
   3 !   33.4  11.5   6.9e-12   6.2e-08       2      74 ..     298     368 ..     297     372 .. 0.89
   4 ?   -9.1  22.7         2   1.8e+04      25      60 ..     376     404 ..     358     436 .. 0.47

  Alignments for each domain:
  == domain 1  score: -15.4 bits;  conditional E-value: 2
                       PE_PPE_C  26 asaaaaalsgttaaaaaaaagaalg..gmPlaaagagg 61 
                                    +s aaaa++  +++ a+aa+++ ++  ++++a a +++
  gi|121636300|ref|YP_976523.1|  63 LSMAAAAVPYVAWMRATAASAEQAAaqAVAAANAYESA 100
                                    34444444333333333333322220022222222222 PP

  == domain 2  score: -13.1 bits;  conditional E-value: 2
                       PE_PPE_C  23 apaasaaaaalsgttaaaaaaaagaa 48 
                                     pa+++ a +ls+++a+aa+a  +aa
  gi|121636300|ref|YP_976523.1| 170 PPATTSGAGSLSDAAATAAQAVVPAA 195
                                    22222222222222222222222222 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 6.9e-12
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrp 74 
                                    A  G +a +G+LSVP+sW +  pa++++aa+ +g+t++ +++ +++ ++g+++a+++++g  +g + r g  p
  gi|121636300|ref|YP_976523.1| 298 ALTGYSANIGGLSVPHSW-NLPPAVRQVAAMFPGATPMYMTGSSDGSYAGLAAAGLAGTGL-AGLTARGGSAP 368
                                    77899*************.9****************************************9.66666655554 PP

  == domain 4  score: -9.1 bits;  conditional E-value: 2
                       PE_PPE_C  25 aasaaaaalsgttaaaaaaaagaalggmPlaaagag 60 
                                    a++         + +aa+  a++  +++P+aaag++
  gi|121636300|ref|YP_976523.1| 376 AGAG-------GAGPAATRPAAQQTPAVPAAAAGSA 404
                                    2222.......2222222222222223333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3063.88
//
Query:       gi|121636301|ref|YP_976524.1|  [L=419]
Description: phosphoribosylglycinamide formyltransferase 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-22   79.0   0.0    4.7e-22   78.4   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    0.00092   18.0   0.2     0.0021   16.9   0.1    1.5  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
     0.0018   17.8   0.0     0.0062   16.1   0.0    1.8  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
  ------ inclusion threshold ------
      0.061   13.4   0.0       0.14   12.2   0.0    1.6  2  ATP-grasp_3      ATP-grasp domain
       0.17   11.4   0.0        3.4    7.1   0.0    2.2  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   1.3e-25   4.7e-22       2     170 ..     139     319 ..     138     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.3e-25
                                    HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC...........GTTCEEEEE CS
                      ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal...........keekvivEe 70 
                                    ++lglp+++f++v s  el+++a + g+p++v  ++ g  G+G+svv  ++++e a++ +            + +v +E+
  gi|121636301|ref|YP_976524.1| 139 DQLGLPTAPFWFVGSLGELQAVAVHAGFPLLVS-PVAGVAGQGSSVVAGPNEVEPAWQRAaghqvqpqtggVSPRVCAES 217
                                    689*****************************9.************************999******99888889***** PP

                                    ----SEEEEEEEEE..ETTC-.EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                      ATP-grasp  71 fvpfekElsvlvvr..saeGe.tafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                    +v+ e+ ++++vv     +G  ++f++++++   d    +s++p+++s++a+  a++ia++iv++Lgg Gvf+vEl +  
  gi|121636301|ref|YP_976524.1| 218 VVEIEFLVTMIVVCsqGPNGPlIEFCAPIGHRDADAGELESWQPQKLSTAALDAAKSIAARIVKALGGRGVFGVELMIN- 296
                                    *************84455887799****************************************************999. PP

                                    TCT.EEEEEEESS--GGGGGHHHH CS
                      ATP-grasp 148 dge.llvnElapRpHnsGhvtlda 170
                                     g+ +++  +   p  s  vt+ +
  gi|121636301|ref|YP_976524.1| 297 -GDeVYFADVTVCPAGSAWVTVRS 319
                                    .555*9999998888888877765 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.9e-07    0.0021     273     351 ..      26      97 ..      20     104 .. 0.88
   2 ?   -3.4   0.0      0.84     3e+03     340     362 ..     393     415 ..     391     415 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.9e-07
                                    -EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CC CS
                 Oxidored_nitro 273 krvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdlllggsk 351
                                    +rv++ g ++ +  la +l+ lG+ev+a+  + + ++   r+ +     +++v+   d eel + i++l+pd+l++ + 
  gi|121636301|ref|YP_976524.1|  26 RRVMLLGSAEPSRELAIALQGLGAEVIAVDGYVGAPAH--RIAD-----QSVVVTMTDAEELTAVIRRLQPDFLVTVTA 97 
                                    79********************************8884..4555.....25788889*****************99765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.84
                                    HHT-SEEEE-CCHHHHHHHTT-- CS
                 Oxidored_nitro 340 elkpdlllggskeryiaeklgip 362
                                    +++p++ +++ ++r++a +l++p
  gi|121636301|ref|YP_976524.1| 393 ATAPEVAIARERAREVASRLNVP 415
                                    57899999999999999999776 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-06    0.0062       8      71 ..     137     198 ..     129     207 .. 0.85
   2 ?   -1.7   0.0      0.46   1.7e+03     133     166 ..     264     297 ..     257     307 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                                    HHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHH CS
                    CPSase_L_D2   8 alkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkal 71 
                                    a+++++ p++p   +   +l e  a+a + g+P ++ + +g+ G+G+ v+   +e++ + ++a 
  gi|121636301|ref|YP_976524.1| 137 AADQLGLPTAPFWFV--GSLGELQAVAVHAGFPLLVSPVAGVAGQGSSVVAGPNEVEPAWQRAA 198
                                    456777777777666..889999*********************************99998886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.46
                                    --HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEET CS
                    CPSase_L_D2 133 Ltdeerqalreaavkvvrevgvvgagtveflldp 166
                                    L+ ++ +a ++ a+++v+++g +g   ve +++ 
  gi|121636301|ref|YP_976524.1| 264 LSTAALDAAKSIAARIVKALGGRGVFGVELMING 297
                                    5555555556666666666666666666666664 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.5   1.2e+04      34      55 ..     168     189 ..     163     196 .. 0.75
   2 ?   12.2   0.0   3.9e-05      0.14     119     154 ..     271     305 ..     260     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.5
                                    EEEEESS-------B--SS--T CS
                    ATP-grasp_3  34 lvvKprdGaggesvrvveekee 55 
                                    l v p+ G++g++ +vv   +e
  gi|121636301|ref|YP_976524.1| 168 LLVSPVAGVAGQGSSVVAGPNE 189
                                    5677999999999888876555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.9e-05
                                    HHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEE CS
                    ATP-grasp_3 119 evvelaeevvekleglaGyvGvDlvlkdeepyviEv 154
                                     + ++a ++v++l g +G++Gv+l+++ +e y+ +v
  gi|121636301|ref|YP_976524.1| 271 AAKSIAARIVKAL-GGRGVFGVELMINGDEVYFADV 305
                                    5678999******.******************9988 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.043   1.5e+02       6      68 ..     142     197 ..     138     203 .. 0.63
   2 ?    7.1   0.0   0.00095       3.4     124     176 ..     258     309 ..     247     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.043
                                    T--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHH CS
                Dala_Dala_lig_C   6 GlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieea 68 
                                    Glp++p+ ++ + +        l++v  + g+p++V p+      G s v   +e++ a ++a
  gi|121636301|ref|YP_976524.1| 142 GLPTAPFWFVGSLGE-------LQAVAVHAGFPLLVSPVAGVAGQGSSVVAGPNEVEPAWQRA 197
                                    555666555544332.......35678889********7765555556666666666666655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00095
                                    EESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS- CS
                Dala_Dala_lig_C 124 levpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlP 176
                                       p kl+++  ++ + +a ++ kal++rG+  v ++++  +e+++ +v  +P
  gi|121636301|ref|YP_976524.1| 258 SWQPQKLSTAALDAAKSIAARIVKALGGRGVFGVELMIN-GDEVYFADVTVCP 309
                                    55688999999**************************98.6778888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2981.26
//
Query:       gi|121636302|ref|YP_976525.1|  [L=140]
Description: hypothetical protein BCG_0427 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.6e-06   26.6   0.0      1e-05   26.0   0.0    1.3  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.7e-10     1e-05       2     102 ..       9     116 ..       8     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.7e-10
                      Rhodanese   2 akelkell.ekgkvallDvRppeeYekghIpgAvnv......skdtlsrakkseapllelpeellelgidnkktvvvycd 74 
                                    + +++e+l ++++++l+DvR ++e+    +p   ++        + +s+++ ++++l+el +++ ++  +++++v+++c+
  gi|121636302|ref|YP_976525.1|   9 PLQAWEMLsDNPRAVLVDVRCEAEWRFVGVPDLSSLgrevvyVEWATSDGTHNDNFLAELRDRIPADADQHERPVIFLCR 88 
                                    567889997777777*****999985533666666666666546667777777777777777777777789********* PP

                      Rhodanese  75 gggraaaaaallkklGyknvsvldGGfk 102
                                    +g+r+  aa  ++++G +  +++  Gf+
  gi|121636302|ref|YP_976525.1|  89 SGNRSIGAAEVATEAGITPAYNVLDGFE 116
                                    ****9999999999**877888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1004.77
//
Query:       gi|121636303|ref|YP_976526.1|  [L=406]
Description: O-succinylhomoserine sulfhydrylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.9e-133  442.4   0.0   1.1e-132  442.2   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    6.4e-06   25.7   0.1    2.2e-05   24.0   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00049   19.4   0.0    0.00072   18.8   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
     0.0011   18.0   0.0     0.0022   17.0   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.051   12.9   0.1        1.4    8.2   0.1    2.5  1  Beta_elim_lyase  Beta-eliminating lyase
      0.051   12.6   0.0       0.15   11.0   0.0    1.7  2  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.2   0.0  3.7e-136  1.1e-132       2     381 ..      21     405 ..      20     406 .] 0.98

  Alignments for each domain:
  == domain 1  score: 442.2 bits;  conditional E-value: 3.7e-136
                                    HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHH CS
                Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavssGma 78 
                                    T+ v+ g+ +   ++++a+++ylts y++ +++ a   fage ++y+YsR+gnpt+sv+eer+  +eg+ aa+a++sGma
  gi|121636303|ref|YP_976526.1|  21 TVGVRGGMLRS-GFEETAEAMYLTSGYVYGSAAVAeksFAGELDHYVYSRYGNPTVSVFEERLRLIEGAPAAFATASGMA 99 
                                    77888888865.799***************98877889****************************************** PP

                                    HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHH CS
                Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiek 158
                                    A+++++ all aGd++v+ ++l+g+++ +++++l+++g+++ fvd +dl+++e+a++  t++v++Etp+np++++vDi++
  gi|121636303|ref|YP_976526.1| 100 AVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAA 179
                                    ******************************************************************************** PP

                                    HHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHH CS
                Cys_Met_Meta_PP 159 iaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfd 238
                                    +++la++ag+ vv+Dn+fa+pllq+ + lg+D+vv+S+TK+++G+++v++G+i+  ++e ++  +++l++++G+++s+f+
  gi|121636303|ref|YP_976526.1| 180 VTELAHAAGAKVVLDNVFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAIL-GDREYIDGPVQKLMRHTGPAMSAFN 258
                                    ******************************************************.566********************** PP

                                    HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHH....HHHHH CS
                Cys_Met_Meta_PP 239 awlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelksee....ekakk 314
                                    aw+ll+Gl+TL++R+++++++A+++AefL+ hp+v++v+Yp+lpshpq++lak+q++g+g+v++F l++ e    ++a +
  gi|121636303|ref|YP_976526.1| 259 AWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFALDCPEdvakQRAFE 338
                                    ********************************************************************99989999999* PP

                                    HHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                Cys_Met_Meta_PP 315 fvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                    ++d+++l+ ++++lG+++sl+++pa++th+++ +e r+a g+ d+++R+svG+Ed+dDliaD+++al
  gi|121636303|ref|YP_976526.1| 339 VLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADIDRAL 405
                                    ******************************************************************9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   7.3e-09   2.2e-05      21     157 ..      69     207 ..      54     261 .. 0.82
   2 ?   -0.9   0.0      0.26   7.7e+02     222     259 ..     254     291 ..     244     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.3e-09
                                    S..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH.TTTTTT-EEEEESS....S-THHHHHHHHTT-EEEEE-B- CS
                DegT_DnrJ_EryC1  21 s..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLra.lgvgpgdeVIvpsl....tFvatanavlelgakpvfvDvd 93 
                                    +  +p+v+ FE++++   g+  a a++sG aA+  +L a lg+g  d ++ +       Fv   +   + g ++vfvD d
  gi|121636303|ref|YP_976526.1|  69 RygNPTVSVFEERLRLIEGAPAAFATASGMAAVFTSLGAlLGAG--DRLVAARSlfgsCFVVCSEILPRWGVQTVFVDGD 146
                                    455799*********************************56655..88877654122267888888999*********** PP

                                    TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEE CS
                DegT_DnrJ_EryC1  94 pdtynidpaaieaaitertkaIl...pVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkk 157
                                          d ++ e+a+   t+a++   p + +   +d++a++++a++ g kv+ D   A     +g +
  gi|121636303|ref|YP_976526.1| 147 ------DLSQWERALSVPTQAVFfetPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLLQQGFP 207
                                    ......99**************6444789999999*******************8777766666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                                    -BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCC CS
                DegT_DnrJ_EryC1 222 lteiqAAiglaqLerldelvarRreiaelykeeLaele 259
                                    ++ ++A ++l+ Le l   v++ ++ a+++ e L++ +
  gi|121636303|ref|YP_976526.1| 254 MSAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHP 291
                                    8999999*******999999999999999998888766 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.4e-07   0.00072      32     282 ..      62     284 ..      40     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.4e-07
                                    HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                  Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                    l++  + +yg+++    +ee+l    g        + aa  + sG  a+   l +ll   +gd+ ++ +  ++s   ++ 
  gi|121636303|ref|YP_976526.1|  62 LDHYVYSRYGNPT-VSVFEERLRLIEG--------APAAFATASGMAAVFTSLGALLG--AGDRLVAARSLFGSCFVVCS 130
                                    5555555555555.4455555554444........44466677777777777777776..77776666666666544433 PP

                                    ....HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                  Aminotran_1_2 112 ....lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                          g++ v +        + dl ++e+al+       +t+ +++e+p+NP  ++ + + +++l   a++ ++ +++D
  gi|121636303|ref|YP_976526.1| 131 eilpRWGVQTVFVD-------GDDLSQWERALSV------PTQAVFFETPSNPMQSLVDIAAVTEL---AHAAGAKVVLD 194
                                    11004455555555.......779*********9......9*************************...9999******* PP

                                    ETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E..EEEEEEHHHHHH.HHHHHHHHTS..SHHHHHHHHH CS
                  Aminotran_1_2 188 eaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv..Gyilgnaavvsq.lrklsrpfls..ssllqaavaa 262
                                     ++a+  ++         ++  +++ ++v+s  K     G Rv  G+ilg+ ++++  ++kl r+     s+  ++++++
  gi|121636303|ref|YP_976526.1| 195 NVFATPLLQ--------QGFPLGVD-VVVYSGTKHIDGQG-RVlgGAILGDREYIDGpVQKLMRHTGPamSAFNAWVLLK 264
                                    ***998887........23333444.78888888887777.655678888776666533344433322467777777777 PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                  Aminotran_1_2 263 alsdallkqseleemrqrlq 282
                                     l++   + ++ ++++qr++
  gi|121636303|ref|YP_976526.1| 265 GLETLAIRVQHSNASAQRIA 284
                                    77777777777777777765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.4e-07    0.0022      70     202 ..      94     220 ..      92     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.4e-07
                                    HHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBE CS
                    Aminotran_5  70 tteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvs 149
                                    t++++++v  sl++ l +gd+ v  ++   + +v + e+  r g++ +++  d     dl++ e +l+  t++v++   s
  gi|121636303|ref|YP_976526.1|  94 TASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVFVDGD-----DLSQWERALSVPTQAVFFETPS 168
                                    55588899999988899999999999999999999999999999888887774.....6889999*************** PP

                                    TTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTT CS
                    Aminotran_5 150 nvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKl 202
                                    n +  + +++++++la+++ga v++D + a +  +  +  lgvD+++ sg K 
  gi|121636303|ref|YP_976526.1| 169 NPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLLQQGFP-LGVDVVVYSGTKH 220
                                    *******************************99998885.9*********995 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00046       1.4      12     275 ..      51     292 ..      43     307 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00046
                                    HHHHHHHHCS----CCCT..--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT.-HHHHSSTT CS
                Beta_elim_lyase  12 eamsdaqaaamlGdesYg..edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtep.ahihfdetg 88 
                                    +a+ ++ +a +l++ +Y   +++tv ++e++++ + g+ aa+ +++G aA   +l +ll  g+  ++ +     +f  + 
  gi|121636303|ref|YP_976526.1|  51 AAVAEKSFAGELDHYVYSryGNPTVSVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSlFGSCFVVCS 130
                                    55666666667777766522578888888888888888888888888888877777777777766666654455666666 PP

                                    HHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                Beta_elim_lyase  89 aiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                     i    gv+ + +++++     l + e+a+        +++++  ++  n     + sl  +++v+++a++ g +++lD 
  gi|121636303|ref|YP_976526.1| 131 EILPRWGVQTVFVDGDD-----LSQWERALSV------PTQAVFFETPSNP----MQSLVDIAAVTELAHAAGAKVVLD- 194
                                    66666666666666666.....6666666665......5667777777773....678888899999999999999988. PP

                                    TTHHHHHHHHTS-CHHHHTTSSEEEEESSS...TT--SS-EEEEE-HH....HHHHHHHH.HHHHT---SSTHHHHH..H CS
                Beta_elim_lyase 169 ARfanaakslgeivkemfsyvDsvtmslkK...dllanvGgvlafrddeledylaerveq.rkylggglrqagvlaalea 244
                                         ++ +     +    +vD+v+ s++K   + +   Gg ++++++    y++  v+  ++  g  ++   + a    
  gi|121636303|ref|YP_976526.1| 195 -----NVFATPLLQQGFPLGVDVVVYSGTKhidGQGRVLGGAILGDRE----YIDGPVQKlMRHTGPAMSA--FNAW--V 261
                                    .....4444444444444678888888888443234456788888888....8887765546777777773..3333..3 PP

                                    HHHHHHHSSTTHHHHHHHHHHHHHHHHHCT- CS
                Beta_elim_lyase 245 giraleeglaslerdhktaeqlaeklelvrl 275
                                     +  le  + +++++++ a++ ae l+ ++ 
  gi|121636303|ref|YP_976526.1| 262 LLKGLETLAIRVQHSNASAQRIAEFLNGHPS 292
                                    3555666677788888888888887776665 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.37   1.1e+03      51      92 ..      77     119 ..      70     146 .. 0.78
   2 ?   11.0   0.0   5.1e-05      0.15     191     231 ..     197     240 ..     165     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHT-SEEEEES-HHHHHHHHHHHH.HBTSEEEEET CS
                           SelA  51 lveellkeltgaedalvvnnnaaavllvLntl.aagkeviisr 92 
                                      ee l+ + ga +a+      aav+  L +l +ag   + +r
  gi|121636303|ref|YP_976526.1|  77 VFEERLRLIEGAPAAFATASGMAAVFTSLGALlGAGDRLVAAR 119
                                    56789999999***************99988624555555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.1e-05
                                    ----BHHHHHHTT-SEEEEETTSTT...-SSS-EEEEE-HHHHH CS
                           SelA 191 skePtvqealaeGvdlvsfsGDkll...GgpqaGiivGkkelie 231
                                       P +q+ +  Gvd+v +sG k +   G +  G i+G +e+i+
  gi|121636303|ref|YP_976526.1| 197 FATPLLQQGFPLGVDVVVYSGTKHIdgqGRVLGGAILGDREYID 240
                                    4579999999*************9843345779**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2881.08
//
Query:       gi|121636304|ref|YP_976527.1|  [L=470]
Description: membrane NADH dehydrogenase ndhA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-52  177.7   2.3    3.9e-52  177.3   2.3    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.5e-12   47.9   1.1    4.3e-06   27.2   0.1    3.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    5.4e-05   22.4  10.1      0.017   14.2   0.1    4.0  5  GIDA           Glucose inhibited division protein A
    9.7e-05   22.5   0.6      0.001   19.2   0.1    2.6  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00035   19.8   0.0    0.00086   18.5   0.0    1.6  1  FAD_binding_2  FAD binding domain
    0.00064   19.1   2.6       0.13   11.5   0.1    3.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00071   18.9   0.3      0.015   14.5   0.0    2.2  2  FAD_binding_3  FAD binding domain
     0.0049   16.5   5.9       0.91    9.0   0.1    3.9  4  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   15.7   2.2        3.7    7.5   0.1    3.2  3  NAD_binding_9  FAD-NAD(P)-binding
      0.024   13.9   0.1       0.71    9.1   0.1    2.5  2  Thi4           Thi4 family
      0.028   14.8   0.1       0.15   12.5   0.1    2.3  1  NAD_binding_7  Putative NAD(P)-binding
      0.043   13.1   4.1       0.07   12.4   0.1    2.8  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.09   11.5   2.6       0.88    8.2   0.0    3.1  3  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   2.3   2.8e-55   3.9e-52       1     293 [.      15     340 ..      15     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 2.8e-55
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCCTCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..evvkklnqgielllgeevvki 78 
                                    ++vv+iG+G++Gl+aa+ l++a +++tl+ +++t++++++ll+++++g+ ++++ia   + + + ++++++llg ev +i
  gi|121636304|ref|YP_976527.1|  15 HRVVIIGSGFGGLNAAKALKRADVDITLI-SKTTTHLFQPLLYQVATGILSEGDIAPttRLILRRQKNVRVLLG-EVNAI 92 
                                    58***************************.*****************************88899999*******.***** PP

                                    EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                    Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp................ 142
                                    d ++++v+  k+  + ++   yd+l++A G+++  +g +  a+ +  + +t+d+a +l+   l                 
  gi|121636304|ref|YP_976527.1|  93 DLKAQTVTS-KLM-DMTTVTPYDSLIVAAGAQQSYFGNDEFATFAPGM-KTIDDALELRGRILGafeaaevstdhaerer 169
                                    ****99999.444.678899****************999996666655.9999999999999999999999998888885 PP

                                    .SEEEEES-SHHHHHHHHHHHHHT-...............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 .krivvvGgGyiGvElAaalaklgk...............evtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                       +vvvG+G++GvE+A+++ +l++               +v l++a++ +l++++++l+  ++++lek++ ev+l+++v
  gi|121636304|ref|YP_976527.1| 170 rLTFVVVGAGPTGVEVAGQIVELAErtlagafrtitpsecRVILLDAAPAVLPPMGPKLGLKAQRRLEKMDAEVQLNAMV 249
                                    5555****************999888999999999999999*************************************** PP

                                    EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS...HCCT-EEEETTEEE--TTSBES.STTEEE-GGGCTECC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstelle...eklglelderggivvdeflrtn.vpgiyaiGDvaggkg 282
                                    +++d +g  ++ +++ +++i++ + v+a+Gv +s+ ++     ++g e+d++g++ v + l ++ +p+++++GD     g
  gi|121636304|ref|YP_976527.1| 250 TAVDYKGITIKEKDGGERRIECACKVWAAGVAASPLGKMiaeGSDGTEIDRAGRVIVEPDLTVKgHPNVFVVGDLMFVPG 329
                                    ****999855555555555****************99889999*******************989*********997788 PP

                                    SS--HHHHHHH CS
                                    xxxxxxxxxxx RF
                    Pyr_redox_2 283 gpelaqaAvqq 293
                                    +p  aq A+q 
  gi|121636304|ref|YP_976527.1| 330 VPGVAQGAIQG 340
                                    99999999885 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.7e-06    0.0051       1      32 [.      16      47 ..      16      65 .. 0.90
   2 ?   -3.1   0.0       9.1   1.3e+04      51      62 ..      78      89 ..      66     101 .. 0.71
   3 !   27.2   0.1   3.1e-09   4.3e-06       2      70 ..     173     256 ..     172     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                   +vv++G+G+ gl +A+al++   ++t++    
  gi|121636304|ref|YP_976527.1| 16 RVVIIGSGFGGLNAAKALKRADVDITLISKTT 47
                                   79**************************8765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.1
                                   HHTTEEEECSEE CS
                      Pyr_redox 51 ekngievllntk 62
                                   ++++++vll+++
  gi|121636304|ref|YP_976527.1| 78 RQKNVRVLLGEV 89
                                   456899998864 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 3.1e-09
                                    EEEECSSHHHHHHHHHHHHTT...............SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEE CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelg...............kkVtvversdkllrllDeeaskilqeklekngievllntkveei 66 
                                     vvvG+G +g+E+Ag + el+               ++V ++++++ +l+ ++++++   q++lek+  ev ln+ v+++
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIVELAertlagafrtitpseCRVILLDAAPAVLPPMGPKLGLKAQRRLEKMDAEVQLNAMVTAV 252
                                    59***************7766666777777888888******************************************** PP

                                    EEET CS
                      Pyr_redox  67 egse 70 
                                    + ++
  gi|121636304|ref|YP_976527.1| 253 DYKG 256
                                    9654 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.3e-05     0.017       2      35 ..      17      50 ..      16      69 .. 0.86
   2 !    8.9   0.0   0.00051      0.71     103     164 ..      74     132 ..      64     171 .. 0.76
   3 ?    3.8   0.2     0.018        24       2      25 ..     173     196 ..     172     209 .. 0.85
   4 ?   -0.9   0.0      0.49   6.7e+02     347     382 ..     307     341 ..     303     351 .. 0.73
   5 ?   -4.5   0.9       5.9   8.1e+03     372     389 ..     448     465 ..     447     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                   v++iG G  G+ AA a++r+ ++++Li + + ++
  gi|121636304|ref|YP_976527.1| 17 VVIIGSGFGGLNAAKALKRADVDITLISKTTTHL 50
                                   9**************************6666554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00051
                                    HHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEE CS
                           GIDA 103 eklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekels 164
                                      l++++n+ ++ +ev+ ++++ ++v+  ++++ ++   ++ ++a+G+   +++++g++e++
  gi|121636304|ref|YP_976527.1|  74 LILRRQKNVRVLLGEVNAIDLKAQTVTSKLMDMTTVTPYDSLIVAAGA---QQSYFGNDEFA 132
                                    56899****************99*****99******************...44444444443 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.018
                                    EEEE-SSHHHHHHHHHHHHTT--E CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakv 25 
                                     +V+G+G  G+e A ++ +l  ++
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIVELAERT 196
                                    58************9987776555 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.49
                                    -TTSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHH CS
                           GIDA 347 lntLetkkvkgLflAGqinGteGYeEaaaqGllAGi 382
                                    +++L +k ++++f+ G++  + G +  +aqG + G 
  gi|121636304|ref|YP_976527.1| 307 EPDLTVKGHPNVFVVGDLMFVPG-VPGVAQGAIQGA 341
                                    45899************876665.445666666665 PP

  == domain 5  score: -4.5 bits;  conditional E-value: 5.9
                                    HHHHHHHHHHHHHHHHHC CS
                           GIDA 372 EaaaqGllAGinaarkak 389
                                    E  aqG lA+   a +a+
  gi|121636304|ref|YP_976527.1| 448 EQQAQGALAAAEQAEHAE 465
                                    8899*****999888876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   7.5e-07     0.001       1      27 [.      19      45 ..      19      49 .. 0.94
   2 ?    0.6   0.1      0.51     7e+02       1       9 [.     175     183 ..     175     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.5e-07
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                   I+G+G++Gl aA +L++a++d++l+ k
  gi|121636304|ref|YP_976527.1| 19 IIGSGFGGLNAAKALKRADVDITLISK 45
                                   9***********************977 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.51
                                    EE--SHHHH CS
                  NAD_binding_8   1 IvGaGlsGl 9  
                                    +vGaG +G 
  gi|121636304|ref|YP_976527.1| 175 VVGAGPTGV 183
                                    8*****997 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.3e-07   0.00086       2      32 ..      17      47 ..      16      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.3e-07
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   v++iGsG++GL AA ++++a  ++++++k+ 
  gi|121636304|ref|YP_976527.1| 17 VVIIGSGFGGLNAAKALKRADVDITLISKTT 47
                                   9****************************86 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   9.3e-05      0.13     165     270 ..      15     124 ..      12     135 .. 0.74
   2 !    5.5   0.3    0.0062       8.6     167     186 ..     173     192 ..     153     322 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                    Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekee..sdpsy......slkpdienrleelvkeekikvlfnaevk 236
                                    ++vv+iG +  +  aA  l r++ ++t++ ++++   +   +++         + p+++  l++   +++++vl   ev+
  gi|121636304|ref|YP_976527.1|  15 HRVVIIGSGFGGLNAAKALKRADVDITLISKTTTHLFQPllYQVATgilsegDIAPTTRLILRR---QKNVRVLLG-EVN 90 
                                    6899999999999999999999999999999987665541122221111111344444444443...255888888.999 PP

                    Pyr_redox_3 237 eikekeeeykvktedgkkvevkddvvlatGykpd 270
                                    +i+ k ++++ k  d ++v+ +d  ++a G + +
  gi|121636304|ref|YP_976527.1|  91 AIDLKAQTVTSKLMDMTTVTPYDSLIVAAGAQQS 124
                                    9999999999999999999999999999998865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0062
                    Pyr_redox_3 167 vvViGgknSavDaAlelvrk 186
                                    +vV+G++ ++v++A ++v+ 
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIVEL 192
                                    55666666666666555554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.1e-05     0.015       3      36 ..      16      49 ..      14      57 .. 0.91
   2 ?    2.1   0.1     0.066        91       5      17 ..     174     186 ..     170     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                    V+I+G+G  Gl +a+ L++a v+ +l+ k +t 
  gi|121636304|ref|YP_976527.1| 16 RVVIIGSGFGGLNAAKALKRADVDITLISKTTTH 49
                                   69****************************9876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.066
                                    EEE--SHHHHHHH CS
                  FAD_binding_3   5 lIVGaGpaGlmla 17 
                                    ++VGaGp+G+  a
  gi|121636304|ref|YP_976527.1| 174 VVVGAGPTGVEVA 186
                                    79*******9666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00066      0.91       1      28 [.      16      45 ..      16      49 .. 0.89
   2 ?    2.5   0.0     0.063        87     158     203 ..      79     122 ..      69     139 .. 0.75
   3 ?    1.2   0.4      0.16   2.1e+02       2      28 ..     173     216 ..     172     220 .. 0.62
   4 ?    3.6   0.1     0.029        40     152     210 ..     232     289 ..     225     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEES CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllek 28
                                   +vviiG+G  Gl +A +L r+   +tl+ k
  gi|121636304|ref|YP_976527.1| 16 RVVIIGSGFGGLNAAKALKRADvdITLISK 45
                                   59****************777789***987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.063
                                    HTT-EEEESECEEEEEEEETCEEEEE....EECTEEEEEEEEEEE--GGG CS
                            DAO 158 alGveilegtevtgleeedgkvwgve....rttpgendaadavVnaaGaw 203
                                    ++ v++l+g ev +++ +   +++v     +    +++ +d +++aaGa+
  gi|121636304|ref|YP_976527.1|  79 QKNVRVLLG-EVNAIDLK---AQTVTsklmDM--TTVTPYDSLIVAAGAQ 122
                                    6679*****.*****665...67775543422..23347899******98 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.16
                                    EEEECTSHHHHHHHHHH...HHT...T...........EEEEES CS
                            DAO   2 vviiGGGiiGlstAyeL...arr...g...........Vtllek 28 
                                     v++G+G +G+ +A +    a+r   g           V+ll++
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIvelAERtlaGafrtitpsecrVILLDA 216
                                    69*********999766333433333344455555555666555 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.029
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHHHH.HTT CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsdll.gll 210
                                     +r++e+  +e+ +++ vt+++    k+ ++ ++++ ge+  ++ + V aaG+ ++ l +++
  gi|121636304|ref|YP_976527.1| 232 AQRRLEKMDAEVQLNAMVTAVD---YKGITI-KEKDgGERrIECACKVWAAGVAASPLgKMI 289
                                    57889999************94...357888.67776776445566******9998443555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.016        21       1      31 [.      18      43 ..      18      56 .. 0.81
   2 ?    1.1   0.1      0.25   3.4e+02     112     155 ..      77     121 ..      70     122 .. 0.76
   3 ?    7.5   0.1    0.0027       3.7       1      20 [.     174     193 ..     174     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlf 31
                                   +i+G G+ Gl ++++L +      +++itl+
  gi|121636304|ref|YP_976527.1| 18 VIIGSGFGGLNAAKALKRA-----DVDITLI 43
                                   7*************99777.....4666666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                  NAD_binding_9 112 pegvtvevhraevvdleeradgqavlladgasl.aadaVvLAlGh 155
                                    +++ +v+v+ +ev +++ +a++++  l d +++  +d++++A G 
  gi|121636304|ref|YP_976527.1|  77 RRQKNVRVLLGEVNAIDLKAQTVTSKLMDMTTVtPYDSLIVAAGA 121
                                    44557888899999999999999888877765449*******996 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0027
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    ++vGaGp+G+ v+ ++++ a
  gi|121636304|ref|YP_976527.1| 174 VVVGAGPTGVEVAGQIVELA 193
                                    69**************9987 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00051      0.71      20      49 ..      17      45 ..      13      49 .. 0.89
   2 ?    1.9   0.0      0.08   1.1e+02      20      36 ..     173     189 ..     161     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00051
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvailer 49
                                   vvi+G+G  GL aa+ l ++ d+ ++++ +
  gi|121636304|ref|YP_976527.1| 17 VVIIGSGFGGLNAAKALKRA-DVDITLISK 45
                                   9****************999.999999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.08
                                    EEEE--SHHHHHHHHHH CS
                           Thi4  20 vvivGaGssGLtaayyl 36 
                                     v+vGaG++G+  a  +
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQI 189
                                    59********9988666 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011      0.15       8      46 ..      15      67 ..      13     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                  NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele..............e 46
                                    +v+++G G  +++ ++ l +a+ ++t+++++++   +              +
  gi|121636304|ref|YP_976527.1| 15 HRVVIIGSGFGGLNAAKALKRADVDITLISKTTTHLFQpllyqvatgilsegD 67
                                   68******************************754444444444444444440 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.1e-05      0.07      29      61 ..      15      47 ..       2      99 .. 0.86
   2 ?   -2.8   0.2       2.4   3.3e+03      31      49 ..     173     191 ..     169     198 .. 0.77
   3 ?    1.0   0.0      0.16   2.2e+02     162     197 ..     428     462 ..     418     468 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                    +v++iG G  Gl+A+++ k+ + ++t++ + +
  gi|121636304|ref|YP_976527.1| 15 HRVVIIGSGFGGLNAAKALKRADVDITLISKTT 47
                                   49******************9999998876655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                                    EEEESTSHHHHHHHHHHHH CS
                    AlaDh_PNT_C  31 vlviGgGvaGlqAiatakg 49 
                                     +v+G+G  G++ +   ++
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIVE 191
                                    689****999988766555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.16
                                    GGGSHHHHHHHHHHHHHHHHHHHCHHHTCCHHHCTS CS
                    AlaDh_PNT_C 162 pgavprtasalltnntlpyleelladkglkkalked 197
                                     g+++ t+ +++++ +++++e+  a+++l++a +++
  gi|121636304|ref|YP_976527.1| 428 RGQMAITSQMIYARLVMTLMEQQ-AQGALAAAEQAE 462
                                    5899******************9.888885554444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00064      0.88       2      33 ..      16      47 ..      15      50 .. 0.92
   2 ?    1.1   0.1     0.092   1.3e+02       3      20 ..     173     190 ..     171     198 .. 0.78
   3 ?   -0.6   0.0      0.29     4e+02     117     168 ..     234     284 ..     232     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00064
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                   +v++iG G  Gl aA ++++++ +++l+ k++
  gi|121636304|ref|YP_976527.1| 16 RVVIIGSGFGGLNAAKALKRADVDITLISKTT 47
                                   79**************************9875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.092
                                    EEEE--SHHHHHHHHHHH CS
                    HI0933_like   3 viviGgGaAGlmaAisaa 20 
                                     +v+G+G+ G+  A ++ 
  gi|121636304|ref|YP_976527.1| 173 FVVVGAGPTGVEVAGQIV 190
                                    69********98887765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.29
                                    HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-G CS
                    HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiP 168
                                    ++l++ + +++l+  v++v+++   + + +  +e+++e++  v A G ++ P
  gi|121636304|ref|YP_976527.1| 234 RRLEKMDAEVQLNAMVTAVDYKGITIKEKDG-GERRIECACKVWAAGVAASP 284
                                    68899999999*******9664444333333.78899999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3273.41
//
Query:       gi|121636305|ref|YP_976528.1|  [L=441]
Description: hypothetical protein BCG_0430 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-45  154.8  13.5    6.5e-45  153.9  13.5    1.4  1  DUF222    Domain of unknown function (DUF222)
  ------ inclusion threshold ------
      0.013   15.6   1.7      0.027   14.6   1.7    1.5  1  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9  13.5   7.2e-49   6.5e-45     120     301 .]     100     281 ..      84     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 7.2e-49
                         DUF222 120 dpaeLaklvdrlvarldpDgvrrdeeaarrreltltkdedGmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRsp 199
                                    dp +La+++dr+va +dpD+vr+++e+ar+re+ + +++dGm ++  +l a++a+alda+L++l+a+vca     DpRs 
  gi|121636305|ref|YP_976528.1| 100 DPGQLAAAIDRIVAVADPDAVRQVRERARDREVSIWNSADGMGEVYAQLYATDAQALDARLNALVATVCAG----DPRST 175
                                    799********************************************************************....***** PP

                         DUF222 200 aqrraDALlall....rlalaagaldchagvp..atvvvhvtaeeltaaagg...aaltgggglLpasdvrrLAkdAtla 270
                                    +qrraDAL+al+    rla+++ ++dc+a  +  + vv+hv+ae++ ++++g   aal gg+gl+pa+ v++LAk+A l+
  gi|121636305|ref|YP_976528.1| 176 DQRRADALGALAagadRLACRCDNPDCAAEGRpvSAVVIHVVAEQASVKGHGqapAALLGGDGLIPAELVAELAKTAGLQ 255
                                    ***************************99888799********************************************* PP

                         DUF222 271 ifdepagrpldlgrtkrtasaalrralraRD 301
                                        p  +p +  + ++++s +l+ ++raRD
  gi|121636305|ref|YP_976528.1| 256 ----PIPVP-AGTEPGYRPSVKLAAFVRARD 281
                                    ....*****.5789****************9 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.7   3.1e-06     0.027       3      38 ..     288     320 ..     283     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                            HNH   3 yCgrkfhksealevdHiipisqggaddieNlqllCk 38 
                                     C+r+    +++  dH i  ++gga+   Nl +lC+
  gi|121636305|ref|YP_976528.1| 288 GCDRPA---TQCDLDHTIAFADGGATHAANLKCLCR 320
                                    466665...889***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3140.52
//
Query:       gi|121636306|ref|YP_976529.1|  [L=239]
Description: hypothetical protein BCG_0431c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.7   0.0       0.44   10.7   0.0    1.6  1  Nbs1_C    DNA damage repair protein Nbs1


Domain annotation for each model (and alignments):
>> Nbs1_C  DNA damage repair protein Nbs1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.4e-05      0.44      17      53 ..      48      84 ..      32      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.4e-05
                         Nbs1_C 17 lPriIGGsDLlvheakknseleewlkeaveeesqqar 53
                                   + + +GG+D +     kn ele  l +a+e+ ++ + 
  gi|121636306|ref|YP_976529.1| 48 ICESVGGADTVLSRIDKNPELEPLLSQAIEAATRTSM 84
                                   55668*************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1770.23
//
Query:       gi|121636307|ref|YP_976530.1|  [L=134]
Description: hypothetical protein BCG_0432 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1049.92
//
Query:       gi|121636308|ref|YP_976531.1|  [L=130]
Description: hypothetical protein BCG_0433 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.6   0.0       0.03   14.2   0.0    1.2  1  PLDc_2    PLD-like domain


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-06      0.03      89     126 ..      43      79 ..      16      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-06
                         PLDc_2  89 idgktvivGSsNltkrgldlnlElnvviedkelakele 126
                                    ++ +tv  GS+N+t r+  + lE+++ ++d++l++e +
  gi|121636308|ref|YP_976531.1|  43 FEPRTVWWGSANWTVRAG-SHLEVGFACDDPTLVEEAT 79 
                                    45789************5.788**********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 997.32
//
Query:       gi|121636309|ref|YP_976532.1|  [L=122]
Description: hypothetical protein BCG_0434 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 924.84
//
Query:       gi|121636310|ref|YP_976533.1|  [L=213]
Description: hypothetical protein BCG_0435c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1614.83
//
Query:       gi|121636311|ref|YP_976534.1|  [L=409]
Description: lipoprotein lpqK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-57  193.6   2.2      6e-57  193.4   2.2    1.0  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   2.2   3.4e-61     6e-57       2     328 ..      42     388 ..      41     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 3.4e-61
                                    HHHHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGG CS
                 Beta-lactamase   2 drlvrelmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVsk 81 
                                     r+vr++m+q ++  v v v++ gk+v++++ G  d  +g p+t+   fr + v  +++a+++l+lv+e+kl+Ldd++s+
  gi|121636311|ref|YP_976534.1|  42 IRIVRDFMTQAHLKAVLVRVTVAGKEVVTRAVG--DSMTGVPATTAMHFRNGAVAISYVATLLLKLVDEKKLRLDDKLSR 119
                                    589****************************87..********************************************* PP

                                    TSTTCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTH........HHHHHHHHHSBSSSSTTSCEE-SHHHHHHHH CS
                 Beta-lactamase  82 ylPefagpgkgkiTlrdLltHtsGlpdlfasdlleeaaada........aellralatlppkyapGtkwgYsntgygllg 153
                                    +lP+   p+++++Tl +L+++tsG+pd+   +++++a+ +a        +ell+++++ p+ y+pGt+w+Y  t+y llg
  gi|121636311|ref|YP_976534.1| 120 WLPD--FPHADRVTLGQLAQMTSGYPDYVLGNEAFDAELYAnpfrqwttQELLDQISSRPLLYDPGTNWNYAHTNYLLLG 197
                                    **65..667778**************************999*************************************** PP

                                    HHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC...........TTTBEE CS
                 Beta-lactamase 154 ellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae...........gaggli 222
                                    ++lek++g+++ +ll++++l+pLg++ t+  + ++ +++  ++ t++++ a   pa +p+++e           +++   
  gi|121636311|ref|YP_976534.1| 198 LALEKAAGQDMPTLLQRKVLSPLGLTATANSDTPAIPEPALHAFTSERRAALKIPAGVPFYEEstfwnpswtitHGAIQT 277
                                    *************************************************************************9999999 PP

                                    EEHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEEC........ECSSEEEEECCHTEEEEEEE.STEEE CS
                 Beta-lactamase 223 stardlarflglalegglllsaetlaqltaklssgttrpagiragl........glGwvladktgapgtfghtG.ggygt 293
                                    +t+ d+ + + +   g+ll+++   ++ +++l++ t +++g + ++        glG v++ +++     + +   gy +
  gi|121636311|ref|YP_976534.1| 278 TTIYDMEATAVGIGSGRLLSADSYKKMVSTELRGKTRAQPGCPTCFeqndgysyGLGIVISGHWLL----QNPMfAGYAA 353
                                    9*********554555555555555566999999999*************6666666666665555....4444789*** PP

                                    EEEEECGGTEEEEEEESBCSSHHHHHHHHHHHHHH CS
                 Beta-lactamase 294 yvfvdpeanlvvavltnrdppnedaaedarliala 328
                                    + ++ p ++++vav ++  p++ d++ ++r++a++
  gi|121636311|ref|YP_976534.1| 354 VEAYLPSQRVAVAVAVTYAPEAFDDQGNYRNQADI 388
                                    *************************9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2968.81
//
Query:       gi|121636312|ref|YP_976535.1|  [L=395]
Description: acyl-CoA dehydrogenase fadE7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-28   98.4   0.2    7.5e-28   97.6   0.2    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.3e-27   96.7   0.1    3.1e-27   95.5   0.0    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    6.6e-25   87.1   0.0    1.3e-24   86.2   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.2e-08   35.3   0.0    2.8e-08   34.1   0.0    1.6  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.2   1.7e-31   7.5e-28       2     147 ..     241     386 ..     240     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.7e-31
                                    BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                  Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                     G+r+ +  l   R +++++a+g+ar+a + al+yar+r++fg+p++ +ql + kl++ma+el+  +ll +++ ++ d+ 
  gi|121636312|ref|YP_976535.1| 241 TGLRAPLACLSEARYGIVWGAMGAARSAWQCALDYARQRTQFGRPIAGFQLTQAKLVDMAVELHKGQLLSLHLGRLKDRV 320
                                    59999999************************************************************************ PP

                                    ---HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                  Acyl-CoA_dh_1  82 kpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    + ++ ++s  Kl  ++ a ++++ a  +lGg+G++ eypv r++ +  +   +eGt e++ +++++
  gi|121636312|ref|YP_976535.1| 321 GLRPDQVSFGKLNNTREALKICRTARTILGGNGISLEYPVIRHMVNLESVLTYEGTPEMHQLVLGQ 386
                                    ***********************************************************9887765 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   6.9e-31   3.1e-27       3     113 .]      24     135 ..      22     135 .. 0.94
   2 ?   -3.2   0.0       2.9   1.3e+04      84     108 ..     361     386 ..     345     390 .. 0.61

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 6.9e-31
                                    HHHHHHHHHHHHHHHHTHHHHHHHHHHTSGH..HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   3 eqealrdtvrefaeeelaphaaewdeegefp..relwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                    ++ a+rdtvr+f++e++ ph+a w e+g  p  r+l k+++elGllg+++   +g+ g++++++ +++ el++ad+g+++
  gi|121636312|ref|YP_976535.1|  24 DEIAVRDTVRRFCAEHVTPHVAAWFEDGDLPvaRDLAKQFGELGLLGMQL-HGHGCGGASAVHYGLACRELEAADSGIRS 102
                                    67799*********************9998866889**************.578888899******************** PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasge 113
                                    l++v+ sl++ ai+ fG++eqkr++Lp +a+g+
  gi|121636312|ref|YP_976535.1| 103 LVSVQGSLAMFAIASFGSDEQKRQWLPGMATGD 135
                                    ******************************996 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                                    HHHHTTH.HHHHHHS-HHHHHHHHHH CS
                  Acyl-CoA_dh_N  84 vhsslva.pailrfGteeqkrryLpk 108
                                    + ++++   ++   Gt+e  +  L +
  gi|121636312|ref|YP_976535.1| 361 IRHMVNLeSVLTYEGTPEMHQLVLGQ 386
                                    44445543566777888888777655 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   2.9e-28   1.3e-24       1      97 []     139     229 ..     139     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 2.9e-28
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE----- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrriee 80 
                                    +f+lTEp++Gsd a++kt  a+rdg ++v++G K+witn+  a++a+v+a      +++g++ f+vp+d+pg++ + i +
  gi|121636312|ref|YP_976535.1| 139 CFGLTEPDVGSDPAAMKT-RARRDGPDWVITGGKMWITNGSVADVAIVWAA-----TDDGIRGFIVPTDTPGFTANTIGH 212
                                    9*****************.89999999************************.....468********************* PP

                                    BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  81 klGlrglptgelvfedv 97 
                                    kl lr   t+elv+++v
  gi|121636312|ref|YP_976535.1| 213 KLSLRASITSELVLDNV 229
                                    ***************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   6.2e-12   2.8e-08       4     123 ..     258     367 ..     255     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 6.2e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                  Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                    +  a GaAr+a ++++++ar+r++  +g+++a ++ tq++l ++a +l+  ++l ++  +   ++  + ++v        
  gi|121636312|ref|YP_976535.1| 258 VWGAMGAARSAWQCALDYARQRTQ--FGRPIAGFQLTQAKLVDMAVELHKGQLLSLHLGRLKDRVGLRPDQV-------- 327
                                    55689*******************..*******************************999955555555554........ PP

                                    HHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHH CS
                  Acyl-CoA_dh_2  84 rraaalavelaiaavdalfeaaGgsalrkesplqRlwRDa 123
                                    +  ++  +++a ++++ +  + Gg+++  e+p+ R++ ++
  gi|121636312|ref|YP_976535.1| 328 SFGKLNNTREALKICRTARTILGGNGISLEYPVIRHMVNL 367
                                    66777788999999999****************9997555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2556.47
//
Query:       gi|121636313|ref|YP_976536.1|  [L=123]
Description: hypothetical protein BCG_0438 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-34  117.6  17.8    4.2e-34  117.4  17.8    1.0  1  DUF3054   Protein of unknown function (DUF3054)


Domain annotation for each model (and alignments):
>> DUF3054  Protein of unknown function (DUF3054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4  17.8   2.3e-38   4.2e-34       1     109 [.      10     112 ..      10     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.3e-38
                        DUF3054   1 lvvDvvavlvfaliGrlsHgeslsllgvletawPFlvglavgWllvaplyearaaskaaralpagvvvwlvavvvGlllR 80 
                                    l++Dvvavlvf+++Gr+sH+e+ls++g+++tawPFl+g+ +gW+l      ar ++++++++p+gv+vwl+++vvG++lR
  gi|121636313|ref|YP_976536.1|  10 LAADVVAVLVFCAVGRRSHAEGLSVTGLAATAWPFLTGTGIGWVL------ARGWRRPTALAPTGVIVWLCTIVVGMVLR 83 
                                    589******************************************......79999************************ PP

                        DUF3054  81 allkggvalsFvlValvvlavlLlgwRav 109
                                    ++++ gva sFv+Va++v+avlLlgwRa+
  gi|121636313|ref|YP_976536.1|  84 KVSSAGVAASFVVVASAVTAVLLLGWRAA 112
                                    ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 968.04
//
Query:       gi|121636314|ref|YP_976537.1|  [L=367]
Description: transmembrane transport protein mmpL1b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   5.5e-102  341.1  11.6   6.3e-102  340.9  11.6    1.0  1  MMPL       MMPL family
  ------ inclusion threshold ------
        0.1   11.9   3.7       0.22   10.8   3.7    1.5  1  WBS28      Williams-Beuren syndrome chromosomal region 28 pro
       0.13   12.7   0.2       0.22   12.0   0.2    1.4  1  CENP-H     Centromere protein H (CENP-H)
       0.13   12.1   1.0       0.19   11.5   1.0    1.3  1  SKA2       Spindle and kinetochore-associated protein 2
       0.33   11.3   3.3       0.78   10.1   3.3    1.6  1  DUF1440    Protein of unknown function (DUF1440)
        1.4    8.4   3.9        2.1    7.7   3.9    1.2  1  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.9  11.6  2.1e-105  6.3e-102       2     331 ..      10     348 ..       9     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 340.9 bits;  conditional E-value: 2.1e-105
                           MMPL   2 lspadaesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.......... 70 
                                    l++++a+++++++r+++  ++ +a+ d++i ++++ +d a + ++a +++ +++++++++++++g+++d+          
  gi|121636314|ref|YP_976537.1|  10 LTEDLANLTDDTERMDTTQRQlLAQLDPTIATMQTVKDLAQTLTSAFSGLVTQMEDMTRNATVMGRTFDAannddsfylp 89 
                                    67899*****************************************************************9999999999 PP

                           MMPL  71 ...lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdas 141
                                       +++pd   + ++f+S+Dg++ar+++t++gdp+s e++++++ i++a++ea+   pl+ + ++++G++ t++d+++++
  gi|121636314|ref|YP_976537.1|  90 peaFQNPDfqrGLKLFLSPDGTCARFVITHRGDPASAEGISHIDPIMQAADEAVkgtPLQAASIYLAGTSSTYKDIHEGT 169
                                    99999***9999******************************************************************** PP

                           MMPL 142 drdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYal 220
                                     +d+++++v++l++i++i+l ++rS+va +++++tv++sl+ a+gl vli++++l++ l++ vl++++++++avG+DY+l
  gi|121636314|ref|YP_976537.1| 170 LYDVMIAVVASLCLIFIIMLGITRSVVASAVIVGTVALSLGSAFGLsVLIWQHILHMPLHWLVLPMAIIVMLAVGSDYNL 249
                                    ******************************************************************************** PP

                           MMPL 221 lLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAll 299
                                    lL++R++ee++ag ++  ++ira+a+tg+vvt+aGl++a++m ++v+++l+v++q+G++i +G+l+d+l+v++ + PAl+
  gi|121636314|ref|YP_976537.1| 250 LLIARFQEEIGAGLKT--GMIRAMAGTGRVVTIAGLVFAFTMGSMVASDLRVVGQIGTTIMIGLLFDTLVVRSYMtPALA 327
                                    ****************..************************************************************** PP

                           MMPL 300 vllGraalakprrkrkkrwWrrlgrlvvrrPl 331
                                    +llGr+           +wW+r+  + +r+P+
  gi|121636314|ref|YP_976537.1| 328 TLLGRW-----------FWWPRRVDRLARQPQ 348
                                    ******...........*************97 PP

>> WBS28  Williams-Beuren syndrome chromosomal region 28 protein homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.7   7.3e-05      0.22      72     149 ..     172     241 ..     147     246 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.3e-05
                          WBS28  72 plgralraglaLlevPvwLvlrgprLvlaa.vlgcaralglalklgaweqlGLsvatwtdlllsclhsLmLvaLLllll 149
                                     +  a+ a l+L+ +   ++l  +r v+a+ v+  + al+  l        GLsv +w+++l+  lh L+L   ++++l
  gi|121636314|ref|YP_976537.1| 172 DVMIAVVASLCLIFI---IMLGITRSVVASaVIVGTVALS--L----GSAFGLSVLIWQHILHMPLHWLVLPMAIIVML 241
                                    344444455555555...5555555444430333333333..3....4689********************87776665 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.3e-05      0.22      17      91 ..       2      79 ..       1      80 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                         CENP-H 17 klsqelrelqeeltevekenlrlkrknrelaaell.elakekesek..eklkeelekleaelkksrqrwrvvknvasa 91
                                   +   ++ +l+e+l++++ ++ r+ +++r+l+a+l    a  +  ++  ++l+++ + l +++++  ++++v+ +++ a
  gi|121636314|ref|YP_976537.1|  2 NSMDNVDKLTEDLANLTDDTERMDTTQRQLLAQLDpTIATMQTVKDlaQTLTSAFSGLVTQMEDMTRNATVMGRTFDA 79
                                   55678999**************************6477777777779989***********************99976 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   6.5e-05      0.19      45      93 ..       5      52 ..       1      71 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                           SKA2 45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa 93
                                    ++ k++e+l++L ++ e + +++++l  ++  t+ a+++++++L +++
  gi|121636314|ref|YP_976537.1|  5 DNVDKLTEDLANLTDDTERMDTTQRQLLAQLDPTI-ATMQTVKDLAQTL 52
                                   57889*****************************9.99*****999987 PP

>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.3   0.00026      0.78      59     108 ..     181     232 ..     147     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                        DUF1440  59 vhilfsivfavlYvvvaev..fpkiklwqGalfGllvtiavHlivlPllglv 108
                                    + ++f i+++++  vva    +  ++l  G +fGl+v i  H++ +Pl  lv
  gi|121636314|ref|YP_976537.1| 181 LCLIFIIMLGITRSVVASAviVGTVALSLGSAFGLSVLIWQHILHMPLHWLV 232
                                    567888899998888877645789***********************97665 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.9    0.0007       2.1      50     109 ..       6      65 ..       2      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0007
                      Mce4_CUP1  50 rlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsnt 109
                                    ++++l+ed+ +l+d ++  +    +ll  Ld ++ t +T+++ ++ L ++++ +v+  ++
  gi|121636314|ref|YP_976537.1|   6 NVDKLTEDLANLTDDTERMDTTQRQLLAQLDPTIATMQTVKDLAQTLTSAFSGLVTQMED 65 
                                    6799*********************************************99988876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2460.66
//
Query:       gi|121636315|ref|YP_976538.1|  [L=591]
Description: transmembrane transport protein mmpL1a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.2e-113  378.0   6.6   3.2e-113  378.0   6.6    2.1  2  MMPL        MMPL family
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.037   14.3   0.1    1.2  1  Troponin    Troponin
       0.13   12.2   0.6       0.24   11.2   0.6    1.4  1  Sec34       Sec34-like family
       0.22   10.1   0.4       0.31    9.6   0.4    1.1  1  AAA_13      AAA domain
       0.35    8.5  11.6      0.008   13.9   3.2    2.0  2  ACR_tran    AcrB/AcrD/AcrF family
       0.92    9.5   4.1       0.25   11.4   0.9    1.6  2  Laminin_II  Laminin Domain II
       0.99    9.3   3.2         14    5.6   0.2    2.9  2  DASH_Dam1   DASH complex subunit Dam1
        2.9    8.0   5.6        4.6    7.4   0.4    2.6  2  DUF962      Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.0   6.6  1.4e-116  3.2e-113       2     333 .]      53     381 ..      52     381 .. 0.99
   2 ?   -0.3   0.3      0.18     4e+02       7       7 ..     494     494 ..     409     580 .. 0.52

  Alignments for each domain:
  == domain 1  score: 378.0 bits;  conditional E-value: 1.4e-116
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    l p+da+s  am+r++++f++  dsd++++v+l eg+e+lg+ +a++++d lv++l++dt+hv+++ +f++dp +aa+ +
  gi|121636315|ref|YP_976538.1|  53 LGPHDAPSLIAMKRIGKDFQQ-FDSDTTAMVLL-EGQEKLGD-EAHRFYDVLVTKLSQDTTHVQHIENFWGDPLTAAGSQ 129
                                    7899*****************.***********.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    S+Dgkaa+++++l+gd+g ++a+esvaa++++v++ +p+ g+k++vtGp+++ ad   ++dr+l++i+ ++++vi+++L+
  gi|121636315|ref|YP_976538.1| 130 SADGKAAYVQLNLTGDQGGSQANESVAAVQRIVDSVPPPPGIKAYVTGPGPLGADRVVYGDRSLHTITGISIAVIAIMLF 209
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                    i+yrSl aal++lltv+++lla +g+++ +a ++ ++lstf+++ lv+l+ia++tDY ++Lv+Ry+e++a g++re+a++
  gi|121636315|ref|YP_976538.1| 210 IAYRSLSAALIMLLTVGLELLAVRGIISTFAVNDLMGLSTFTVNVLVALTIAASTDYIIFLVGRYQEARATGQNREAAYY 289
                                    ******************************************************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrr 321
                                    +++++t++vv+a+Gltva+am++L ++rlp++++++ ++a+G++ ++l++lTl PA++++++r++l++p+r+++kr+Wrr
  gi|121636315|ref|YP_976538.1| 290 TMFGGTAHVVLASGLTVAGAMYCLGFTRLPYFNTLASPCAIGLVTVMLASLTLAPAIIAVASRFGLFDPKRATTKRRWRR 369
                                    ******************************************************************************** PP

                           MMPL 322 lgrlvvrrPlpv 333
                                    +g++vvr+P pv
  gi|121636315|ref|YP_976538.1| 370 IGTVVVRWPGPV 381
                                    *********986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.18
                           MMPL   7 a 7  
                                    +
  gi|121636315|ref|YP_976538.1| 494 T 494
                                    1 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.7e-05     0.037      26      98 ..     498     568 ..     491     580 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                    XXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Troponin  26 erlrvLkerieplkeldglseeqlqelckklheridkleeekydieekvakkdkeieelkkkvndlrGkfkkp 98 
                                    e l+ Lk+r+  l++l + + + + +++++ +e  ++l +   d+++  ++ +   +el+ ++ d    f +p
  gi|121636315|ref|YP_976538.1| 498 ENLQNLKDRVADLSTLTD-QLQRMIDITQRTQELTRQLTDATHDMNAHTRQMRDNANELRDRIADFD-DFWRP 568
                                    7899***********999.99****************************************999987.56666 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00011      0.24       9      73 ..     500     564 ..     493     570 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                          Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                     +++++ +++++++ +qL+ + +  ++ +e t++l +a+ ++ ++++++++ a+e+++++  F++
  gi|121636315|ref|YP_976538.1| 500 LQNLKDRVADLSTLTDQLQRMIDITQRTQELTRQLTDATHDMNAHTRQMRDNANELRDRIADFDD 564
                                    45566667888999999***************************************999999986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00014      0.31     282     350 ..     494     561 ..     490     576 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                         AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrke 350
                                    +  +e+L++l+++v+  +  l+++l+ ++d  ++ ++  ++  +++  ++a++ q++ + ++l +++ +
  gi|121636315|ref|YP_976538.1| 494 TMTIENLQNLKDRVADLS-TLTDQLQRMIDITQRTQELTRQLTDATHDMNAHTRQMRDNANELRDRIAD 561
                                    567899********9996.799********999999999999999999999999999999999998865 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.2   3.6e-06     0.008     830     954 ..     155     287 ..     129     292 .. 0.69
   2 ?   -3.8   5.6      0.77   1.7e+03     371     488 ..     237     349 ..     235     353 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-06
                                    HHHHHHHCTT..SSTTEEEEEEHH....HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHHHHHHH..H CS
                       ACR_tran 830 eeavekiakkvklpegvtiewtgq....aeqeqeasnsllilvalalllvflvLaalyeslsepllilltvPlalvG..a 903
                                     +av++i+  v  p+g++   tg     a+       sl ++  +++ ++ ++L++ y sls++l+ lltv l l+   +
  gi|121636315|ref|YP_976538.1| 155 VAAVQRIVDSVPPPPGIKAYVTGPgplgADRVVYGDRSLHTITGISIAVIAIMLFIAYRSLSAALIMLLTVGLELLAvrG 234
                                    3455666667777777777777742222455566678999*******************************998754338 PP

                                    HHHHHHTT--BSH.HHHHHHHHHHHHHH..HHHHHHHHHHHHHHHTTTTCHHHH CS
                       ACR_tran 904 llalllrglelsv.iaqvGlilliGlav..kNaillvefakelrekegksleea 954
                                    +++++ ++  + + ++ v +++ + +a+     i lv  ++e+r+  g ++e+a
  gi|121636315|ref|YP_976538.1| 235 IISTFAVNDLMGLsTFTVNVLVALTIAAstDYIIFLVGRYQEARA-TGQNREAA 287
                                    999999998887634566666555554410456778888888888.66666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.77
                                    HHHHHHHHTT--BCHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGG CS
                       ACR_tran 371 gtfavlkalgfslNllt.LfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPi 449
                                     tfav  ++g+s  +   L++L++A      d i+ +   +++ ++   +++eaa+++m   +  +v  +   +a    +
  gi|121636315|ref|YP_976538.1| 237 STFAVNDLMGLSTFTVNvLVALTIAAST---DYIIFLVGRYQEARA-TGQNREAAYYTMFGGTAHVVLASGLTVAG--AM 310
                                    5666655555544333225677775543...444444333333333.45566667766665444444443333332..35 PP

                                    GGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH CS
                       ACR_tran 450 lflgGveGklfrqfaltivlaillsvlvaltltPalcal 488
                                      lg +    f+ +a   ++ ++  +l +ltl Pa+ a+
  gi|121636315|ref|YP_976538.1| 311 YCLGFTRLPYFNTLASPCAIGLVTVMLASLTLAPAIIAV 349
                                    555555666899***********************9986 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.7   6.1e+03       7      20 ..     150     163 ..     149     165 .. 0.82
   2 ?   11.4   0.9   0.00011      0.25      16      77 ..     500     561 ..     492     573 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                                    XXXXXXXXXXXXXX CS
                     Laminin_II   7 eanetakevleqla 20 
                                    +ane++++v++++ 
  gi|121636315|ref|YP_976538.1| 150 QANESVAAVQRIVD 163
                                    79999999999886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                     Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                    l+ l++  ++l+ + ++l+++ +  ++t+e+ ++++ a+ d +   +++  +a++L d++  
  gi|121636315|ref|YP_976538.1| 500 LQNLKDRVADLSTLTDQLQRMIDITQRTQELTRQLTDATHDMNAHTRQMRDNANELRDRIAD 561
                                    5556666677888888999888888999999***************************9865 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0063        14       3      25 ..     498     520 ..     496     526 .. 0.86
   2 ?    3.1   0.3     0.037        83       6      31 ..     532     557 ..     527     563 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0063
                      DASH_Dam1   3 pafaeLaDsletLdknledLqqi 25 
                                    +++++L+D +++L++ +++Lq++
  gi|121636315|ref|YP_976538.1| 498 ENLQNLKDRVADLSTLTDQLQRM 520
                                    67999999999999999999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
                      DASH_Dam1   6 aeLaDsletLdknledLqqihesLsd 31 
                                    ++L+D+  +++++++++ +  ++L d
  gi|121636315|ref|YP_976538.1| 532 RQLTDATHDMNAHTRQMRDNANELRD 557
                                    689**************987777765 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0021       4.6      13      52 ..       7      46 ..       3      65 .. 0.82
   2 ?    2.0   0.6     0.096   2.1e+02      21      51 ..     191     222 ..     189     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                         DUF962 13 aeHsnpinrllHfigvplilltvlllllraklklllalfv 52
                                   a H  ++ r++H++  p+il+ v+l+++   ++  l +++
  gi|121636315|ref|YP_976538.1|  7 AGHLSAAARTIHALSLPIILFWVALTIVVNVVAPQLQSVA 46
                                   67999********************999887766665555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.096
                         DUF962  21 rllHfi.gvplilltvlllllraklklllalf 51 
                                    r lH+i g+++++++++l++++ +l+ +l ++
  gi|121636315|ref|YP_976538.1| 191 RSLHTItGISIAVIAIMLFIAYRSLSAALIML 222
                                    67898834555555555555555544433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.89u 0.34s 00:00:01.23 Elapsed: 00:00:00.55
# Mc/sec: 3230.48
//
Query:       gi|121636316|ref|YP_976539.1|  [L=142]
Description: membrane protein mmpS1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-66  222.5   1.6    1.7e-66  222.4   1.6    1.0  1  Mycobact_memb  Mycobacterium membrane protein


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.4   1.6   9.7e-71   1.7e-66       2     139 .]       6     142 .]       5     142 .] 0.99

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 9.7e-71
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEB-B----TT-----B---TTS------S- CS
                  Mycobact_memb   2 krlWiplvivvvvvvggltvsrlhsifgsekrasvadklaedskpfnPkkvkyevfGpagtvadisyldadaepqridga 81 
                                    kr+Wip+viv+vv+v+++tvsrlhs+fgs+++a+++ +l +++ +f+Pk+v yevfGp+gtva+i+yldada+p+++ +a
  gi|121636316|ref|YP_976539.1|   6 KRFWIPMVIVIVVAVAAVTVSRLHSVFGSHQHAPDTGNL-DPIIAFYPKHVLYEVFGPPGTVASINYLDADAQPHEVVNA 84 
                                    9**********************************9988.9*************************************** PP

                                    SS--B--EE-SSS------B--SS-S------BBTTB---------S-TTSSS--S-- CS
                  Mycobact_memb  82 alPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevnaltyClvksa 139
                                    a+PWs+ti+ttl+avv+nvva+g+++s+gCri+v++v+++er++n+++a+t+Clvksa
  gi|121636316|ref|YP_976539.1|  85 AVPWSFTIVTTLTAVVANVVARGDGASLGCRITVNEVIREERIVNAYHAHTSCLVKSA 142
                                    ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1122.94
//
Query:       gi|121636317|ref|YP_976540.1|  [L=585]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-65  219.4   0.0      1e-64  218.8   0.0    1.3  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.083   13.2   0.0       0.17   12.3   0.0    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
       0.53   10.8   2.9        1.1    9.8   2.9    1.5  1  p12I             Human adult T cell leukemia/lymphoma virus p


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   1.7e-68     1e-64       2     421 ..       8     470 ..       7     472 .. 0.83

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 1.7e-68
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-E..EEEEESSSHHHHHHHHHHHHTT- CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdr..VaillpnspewvvallailkaGa 72 
                                    +++a +tp + a+v+       +++  ++T+++l++rv++++a+L s G   + r   ai +p+++++v+ +l++l aG 
  gi|121636317|ref|YP_976540.1|   8 RDRATTTPSDEAFVFmdydtktGDQIDRMTWSQLYSRVTAVSAYLISYGRHADRRrtAAISAPQGLDYVAGFLGALCAGW 87 
                                    689999**999999999***9988899*******************98875544455*********************** PP

                                    EEEEEET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS- CS
                    AMP-binding  73 vvvplnp...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaek 149
                                    ++vpl     +l+ ++   ++ d+ a v++  + s++  +++++ a+  a+ ++ v+  d l++       ++++     
  gi|121636317|ref|YP_976540.1|  88 APVPLPEplgSLRDKRTGLAVLDCAADVVL--TTSQAETRVRATIATHGASVTTPVIALDTLDEP------SGDN----- 154
                                    *****998889999****************..555555666666666655555555554443322......2222..... PP

                                    TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTT......T-EEEESS-TTSCHHHHHHHHH CS
                    AMP-binding 150 peeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklke......ddvvlsilplahifglilelll 223
                                     ++ +++ +d   y++YTSG+T +P GV+ls rn++ nv ++ ++++f+  e       + v+s+lpl+h++gl+++l++
  gi|121636317|ref|YP_976540.1| 155 -CDLDSQLSDWSSYLQYTSGSTANPRGVVLSMRNVTENVDQI-IRNYFRH-EggaprlPSSVVSWLPLYHDMGLMVGLFI 231
                                    .222234467789****************************9.4555432.22445778999****************** PP

                                    HHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHH CS
                    AMP-binding 224 allsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrf 302
                                    +l++G+ v+l +++a+ ++p+++++l++k+++ + a+++ +++  +++ +++ +++  dl+++ +++ g e+++p+++++
  gi|121636317|ref|YP_976540.1| 232 PLFVGCPVILTSPEAFiRKPARWMQLLAKHQAPFSAAPNFAFDLAVAKTSEE-DMAGLDLGHVNTIINGSEQVQPNTITK 310
                                    ****************999************************999965555.46778********************** PP

                                    HHHHHTC......EEEEEEEEGGGSSECEE..........................CHCTTTCTSTTS-BEE-......T CS
                    AMP-binding 303 fralfge......evlegYGlTEttgvvtv..........................lpleedkkklgsvGkpl......p 344
                                    f ++f++      +v  +YG++E+ + +++                          ++  e+      + + +       
  gi|121636317|ref|YP_976540.1| 311 FLRRFRPynlmpaAVKPSYGMAEAVVYLATtkagspptstefdadslarghaelstFE-TER------ATRLIryhsddK 383
                                    ************99**************666999999888888887777665544322.222......223334444436 PP

                                    TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT.-HHHHHHHEEE.........TCC.EEEEEEEEEEETTSEEEEE CS
                    AMP-binding 345 gvevkivDeetgepvpdgeeGellvrgpgvmkgYlk.kpeataeafds.........egr.wlrTGDlgrldedGyleiv 413
                                    +  ++ivD++ + ++++g  Ge++++g++v  gY++ ++++++++f +         +   wlrTGDlg++    +++iv
  gi|121636317|ref|YP_976540.1| 384 EPLLRIVDPDSNIELGPGRIGEIWIHGKNVSTGYHNaDDALNRDKFQAsireasagtPRSpWLRTGDLGFIV-GDEFYIV 462
                                    7789********************************88899*****978999999874345*********97.348**** PP

                                    EECCCEEE CS
                    AMP-binding 414 gRkkdlik 421
                                    gR kdli+
  gi|121636317|ref|YP_976540.1| 463 GRMKDLII 470
                                    ******97 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05      0.17       1      91 [.     473     566 ..     473     568 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----H..HHHHHHHHHHHHHHHHHHSS--.EEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdel..kelealekkiakklksklgvsv.kvel 76 
                                    Gvn +P  ie+ +ke+ +           +++ ++l +  Ev++ +  d++   + +++++ + ++l +  g++v +  l
  gi|121636317|ref|YP_976540.1| 473 GVNHYPDDIETTVKEFTGGR--VAAFSVSDDGVEHLVIAAEVRTeHGPDKVtiMDFSTIKRLVVSALSKLHGLHVtDFLL 550
                                    9**************97655..334444567899999999998843445432278999***************9648999 PP

                                    E-TT-S----.----- CS
                AMP-binding_C_2  77 vepgtlprse.gKakr 91 
                                    v+pg lp+++ gK  r
  gi|121636317|ref|YP_976540.1| 551 VPPGALPKTTsGKISR 566
                                    *******975258877 PP

>> p12I  Human adult T cell leukemia/lymphoma virus protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.9   0.00018       1.1      40      97 ..     213     271 ..     206     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                           p12I  40 lllflpfqilsnllfllflplffslplllspslpitmrfparwr..fppwrapsqpaaaf 97 
                                    ++ +lp+     l++ lf+plf+  p++l+      +r parw   +   +ap   a  f
  gi|121636317|ref|YP_976540.1| 213 VVSWLPLYHDMGLMVGLFIPLFVGCPVILTS-PEAFIRKPARWMqlLAKHQAPFSAAPNF 271
                                    4567888888899999**********98853.3456899****73346677777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3586.10
//
Query:       gi|121636318|ref|YP_976541.1|  [L=460]
Description: membrane bound polyketide synthase pks6a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-85  285.9   0.0      4e-85  285.4   0.0    1.2  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.9e-36  124.6   0.1      4e-36  123.6   0.1    1.5  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.2e-05   25.6   0.0    2.3e-05   24.7   0.0    1.5  1  PP-binding       Phosphopantetheine attachment site
    3.8e-05   23.2   0.1     0.0001   21.8   0.1    1.6  2  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.4   0.0   8.8e-89     4e-85       2     253 .]     107     346 ..     106     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 285.4 bits;  conditional E-value: 8.8e-89
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgisp 79 
                                    epva++G+g+rfPg  d +e +w+ L e++ ai+  p      +++     + ag+  +  ggfl+ v+ fd++ff i+p
  gi|121636318|ref|YP_976541.1| 107 EPVAVIGVGCRFPGDIDgPERLWDFLTEKKCAITAYP-----DRGF-----TNAGTFAE-SGGFLKdVAGFDNRFFDIPP 175
                                    89*************999*******************.....4566.....44555554.599***************** PP

                                    HHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  80 reaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagris 159
                                    +ea +mdpqqrllle++weale+ag+ pe+l+ sr+gvf+Gv++ dy  l++ + ++ ++ ++   +g  ++++ia+ris
  gi|121636318|ref|YP_976541.1| 176 DEALRMDPQQRLLLEVSWEALEHAGIIPESLRLSRTGVFVGVSSTDYVRLVSASAQQ-KSTIWD-NTGG-SSSIIANRIS 252
                                    ***********************************************8877777665.577777.8898.9********* PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlG 239
                                    y+l+++Gps+++dtACsSslvavh+a++sl + ++d+al+GG+++l++pe ++gf +ag+ls++g c+afd++adG+v+G
  gi|121636318|ref|YP_976541.1| 253 YFLDIQGPSIVIDTACSSSLVAVHLACRSLSTWDCDIALVGGTNVLISPEPWGGFREAGILSQTGCCHAFDKSADGMVRG 332
                                    ******************************************************************************** PP

                                    -EEEEEEEEECHHH CS
                  ketoacyl-synt 240 EGvGavvLkrleda 253
                                    EG+G++vL+rl+da
  gi|121636318|ref|YP_976541.1| 333 EGCGVIVLQRLSDA 346
                                    ************98 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.1     9e-40     4e-36       1     102 [.     354     456 ..     354     458 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 9e-40
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG.SCTSE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar.kqpla 79 
                                    +a+++gsavn+dg++n+++apn++aq  ++e+a+++a+vdp +++yveahgtgt+lgD+iE++al  vfg+k+  + pl+
  gi|121636318|ref|YP_976541.1| 354 LAILTGSAVNQDGKSNGIMAPNPSAQIGVLENACKSARVDPLEIGYVEAHGTGTSLGDRIEAHALGMVFGRKRPgSGPLM 433
                                    5899********************************************************************99*99*** PP

                                    EE-THHHH-B-GGGHHHHHHHHH CS
                Ketoacyl-synt_C  80 vgSvKsniGHleaAaGvaelikv 102
                                    +gS+K+niGHle+AaG+a+lik+
  gi|121636318|ref|YP_976541.1| 434 IGSIKPNIGHLEGAAGIAGLIKA 456
                                    *********************96 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.1e-09   2.3e-05       2      65 ..      14      77 ..      13      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.1e-09
                     PP-binding  2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaa 65
                                   + re +++ +++ + e+++d +++dlGl S++++++ + l ++fg+ ip+  ++++p+ ++l++
  gi|121636318|ref|YP_976541.1| 14 WFREYLSTHIECHPNEVSLDVPIRDLGLKSIDVLAIPGDLGDRFGFCIPDLAVWDNPSANDLID 77
                                   56777777788878899*********************************************97 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.89     4e+03      23      45 ..     184     206 ..     178     220 .. 0.80
   2 !   21.8   0.1   2.2e-08    0.0001      59     112 ..     244     295 ..     235     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.89
                                    HHHHHHHHHHHHHHHHTS-GGGC CS
                     Thiolase_N  23 aeeLlaealkallekagvdpeev 45 
                                     + Ll e+ +++le+ag+ pe++
  gi|121636318|ref|YP_976541.1| 184 QQRLLLEVSWEALEHAGIIPESL 206
                                    56788899999999999888765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.2e-08
                                    TSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  59 gqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                     ++ia+ ++  ++i  + p++ ++ +csS+l av+la++s+ + ++d++++gG+
  gi|121636318|ref|YP_976541.1| 244 SSIIANRISYFLDI--QGPSIVIDTACSSSLVAVHLACRSLSTWDCDIALVGGT 295
                                    55677777777777..78999********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3249.27
//
Query:       gi|121636319|ref|YP_976542.1|  [L=946]
Description: membrane bound polyketide synthase pks6b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-62  210.9   1.3    5.2e-62  210.2   1.3    1.3  1  Acyl_transf_1   Acyl transferase domain
    1.1e-16   61.3   0.0    4.1e-16   59.4   0.0    2.0  2  KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
    3.8e-15   56.6   0.0    1.9e-13   51.0   0.0    3.0  3  Thioesterase    Thioesterase domain
    5.8e-12   45.8   0.0    1.5e-11   44.4   0.0    1.8  1  PP-binding      Phosphopantetheine attachment site
     0.0061   16.4   0.4      0.049   13.5   0.0    2.3  2  Abhydrolase_3   alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.2   1.3   1.4e-65   5.2e-62       2     316 ..     177     486 ..     176     488 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 1.4e-65
                                    EEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHTT CS
                  Acyl_transf_1   2 fvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellkskG 81 
                                    fvf GqGsQw GMG eL++  ++fa+++++    +  +  + + dv+   ++ ll+ ++f+qpaL+av++al+ ll s G
  gi|121636319|ref|YP_976542.1| 177 FVFAGQGSQWLGMGSELYAAYPVFAEALDAVVDELDRHLRYPLRDVIWGHDQDLLNTTEFAQPALFAVEVALYRLLMSWG 256
                                    9************************9988888888888888*************************************** PP

                                    -TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECCCCECC CS
                  Acyl_transf_1  82 vrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavansprrvvis 161
                                    vrp++v+GHS+GElAaa+vagal + +a+  v+ r+rlm+ l   g+m av+  e e +     dv+ a++n+p +vvis
  gi|121636319|ref|YP_976542.1| 257 VRPGLVLGHSVGELAAAHVAGALCLPDAAMLVAARGRLMQALPAGGAMFAVQAREDEVAPMLGHDVSIAAVNGPASVVIS 336
                                    *****************************************************8888888899***************** PP

                                    EEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHHHHH CS
                  Acyl_transf_1 162 gsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywvanl 241
                                    g ++a++++  r++ +g+++++ +v+ a+hs+ ++++  +  +  a++    p+++ is ++ +       sa+yw++ +
  gi|121636319|ref|YP_976542.1| 337 GAHDAVSAIADRLRGQGRRVHRLAVSHAFHSALMEPMIAEFTAVAAELSVGLPTIPVISNVTGQLVADDFASADYWARHI 416
                                    ******************************************************************************** PP

                                    HCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT CS
                  Acyl_transf_1 242 rspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltg 316
                                    r  vrf + v+sa   +   f+e+ p   l+  +e  l +    ++   v++l++d  +  v + +++a+ +++g
  gi|121636319|ref|YP_976542.1| 417 RAVVRFGDSVRSAHCAGASRFIEVGPGGGLTSLIEASLAD----AQIVSVPTLRKDRPE-PVSVMTAAAQGFVSG 486
                                    *************8889999*******************6....78899********99.888888888877776 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   1.1e-19   4.1e-16       1     112 []      18     141 ..      18     141 .. 0.91
   2 ?   -2.2   0.0       1.6   5.6e+03      61     100 ..     330     368 ..     323     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.1e-19
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi.....vgvNsfGfGGsnvHviLksnkkekrkeesk......eeslprLlvlsgr 69 
                                    Pnp ip ++e+ l+Vv+e  +wp  +     +gv+sfGfGG+n+Hvi++++ +  +++ s       +      +v+sg+
  gi|121636319|ref|YP_976542.1|  18 PNPAIP-FTELGLRVVDELQEWPVVAgrprrAGVSSFGFGGTNAHVIVEEAGSVGADTVSGradvggSGGGVVAWVISGK 96 
                                    9*****.***************998888999********************966666555556788788899999***** PP

                 KAsynt_C_assoc  70 teeaveallekleehlldaellsllneilseeisr..lpyRGyav 112
                                    t++a+ a++ +l  + + ++ l++++  +s   +r  +++R+ +v
  gi|121636319|ref|YP_976542.1|  97 TASALAAQAGRLGRYVRARPALDVVDVGYSLVSTRsvFDHRAVVV 141
                                    ***************************999988887899999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                 KAsynt_C_assoc  61 prLlvlsgrteeaveallekleehlldaellsllneilse 100
                                    p  +v+sg   +av+a++++l+ + +  ++l++ +  +s 
  gi|121636319|ref|YP_976542.1| 330 PASVVISGA-HDAVSAIADRLRGQGRRVHRLAVSHAFHSA 368
                                    556777877.68999****999999999999988888765 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.057     2e+02      83     163 ..     345     431 ..     343     441 .. 0.70
   2 ?   -3.9   0.0       3.3   1.2e+04      32      59 ..     548     575 ..     544     577 .. 0.82
   3 !   51.0   0.0   5.4e-17   1.9e-13      15     230 ..     724     936 ..     711     937 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.057
                                    HHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHHT......HHHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHH CS
                   Thioesterase  83 vArqLesqGlavkslflidssapseteaqeasrraedee......fveeltdlggtepeelledeellsellpalradyr 156
                                    +A +L+ qG+ v++l ++ + ++  +e   a+ +a   e      ++  +  ++g ++++  ++ ++++ +++a+  +++
  gi|121636319|ref|YP_976542.1| 345 IADRLRGQGRRVHRLAVSHAFHSALMEPMIAEFTAVAAElsvglpTIPVISNVTGQLVADDFASADYWARHIRAVVRFGD 424
                                    799**************998888777666666666666677777755555555555344444445577777777777777 PP

                                    HHTCCS- CS
                   Thioesterase 157 aleqysl 163
                                     + ++++
  gi|121636319|ref|YP_976542.1| 425 SVRSAHC 431
                                    7777765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.3
                                    EECSTTSTSHHHCTTCHHHHHHHHHHHH CS
                   Thioesterase  32 avqlpgrerdepplesieelaaeyaeal 59 
                                    a +l+gr+ de+++  ie +++  a+ l
  gi|121636319|ref|YP_976542.1| 548 AARLAGRSADEQLAAAIEVVCEHAAAVL 575
                                    6788999999999999999999887765 PP

  == domain 3  score: 51.0 bits;  conditional E-value: 5.4e-17
                                    GGHHHHHHCTTCEEEEEEECSTTSTSHHHCTTCHHHHHHHHHHHHHHH-SSS.SEEEEEETHHHHHHHHHHHHHHHC.T- CS
                   Thioesterase  15 vfrslasklsdpvvevlavqlpgrerdepplesieelaaeyaealrqiqpeg.PyalfGhSlGgllAfevArqLesq.Gl 92 
                                     +r +a ++ ++  +v+ ++lpg++++++++++++ +++ + +a+  +      ++l G+S Gg lA++++++L  +  +
  gi|121636319|ref|YP_976542.1| 724 EYRDIANAMTGR-HSVYSLTLPGFDSSDALPQNADMIVETVSNAIIDVVGGScRFVLSGYSSGGVLAYALCSHLSVKhQR 802
                                    699999*****8.***********************************99999**********************999** PP

                                    SEEEEEEESCCCCCCHHCHHCCCHTTHHT.....HHHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHHHHTCCS..... CS
                   Thioesterase  93 avkslflidssapseteaqeasrraedee.....fveeltdlggtepeelledeellsellpalradyraleqys..... 162
                                     + ++ lid++ ps    + + +  ++++     ++e +++ + +   +l++      +   +++a ++a+e  +     
  gi|121636319|ref|YP_976542.1| 803 NPLGVALIDTYLPSQIANPSMNEGFSPNDtgkglSREVIRVAR-M-LNRLTATR---LTAAATYAAIFQAWEPGRsmapv 877
                                    *************996666666666666644554444444433.3.33333333...33334444555555555466677 PP

                                    ..-TTSCSEHHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCCHHHSHHHHHHHHHHHHH CS
                   Thioesterase 163 ..lrpeaaqklratlfngsddklkdldtlelaerweqktsgevsvhvlegdhfylledrleavleiiekk 230
                                      ++++++    at++n ++++++++    +a         + sv  ++gdhf +++  +ea++ +i+++
  gi|121636319|ref|YP_976542.1| 878 lnIVAKDRI---ATVENLREERINRWR---TA-----AAEAAYSVAEVPGDHFGMMSTSSEAIATEIHDW 936
                                    777777777...777777777777777...22.....3577899************9779********98 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   4.2e-15   1.5e-11       2      67 .]     566     632 ..     565     632 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.2e-15
                     PP-binding   2 klrelvaevlgvplee.idpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67 
                                     ++e +a vlg++  + +d+ + + d G++Sl+avel ++l +   v++p + +f+hpt+ ela+yl
  gi|121636319|ref|YP_976542.1| 566 VVCEHAAAVLGRDGAAgLDAGQAFADSGFNSLSAVELRNRLTAVTAVTLPATAIFDHPTPTELAQYL 632
                                    6999********99995588999******************************************97 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.18   6.4e+02     167     209 ..     329     368 ..     290     370 .. 0.69
   2 !   13.5   0.0   1.4e-05     0.049      71     176 ..     775     884 ..     750     915 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.18
                                    --EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTG CS
                  Abhydrolase_3 167 pptlvvvaefDplrdegeayaerlraagvevelieyegmvHgf 209
                                     p+ vv+ +    +d   a a+rlr +g +v+   ++ ++H+ 
  gi|121636319|ref|YP_976542.1| 329 GPASVVISGA---HDAVSAIADRLRGQGRRVHRLAVSHAFHSA 368
                                    3444444444...577889***********9999999999976 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                                    CEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHT.TTSSSSCHHHHHHHHHHHS..S. CS
                  Abhydrolase_3  71 srivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeel.adgplltraaldlfwrlyl..p. 146
                                     r vl G S GG la+a++  +  +++ ++ g++li   +  ++  ++s+++  +  ++g+ l+r+ ++ +  l    + 
  gi|121636319|ref|YP_976542.1| 775 CRFVLSGYSSGGVLAYALCSHLSVKHQRNPLGVALIDTYLP-SQIANPSMNEGFSPnDTGKGLSREVIRVARMLNRltAt 853
                                    5899***************8888888999999999998653.36667777655444577788998888854433221122 PP

                                    GGGGGSTTTSGGGC.S-SST---EEEEEETT CS
                  Abhydrolase_3 147 eadrddplasplla.edlsglpptlvvvaef 176
                                    + +++  +a+  +a e  + ++p+l +va+ 
  gi|121636319|ref|YP_976542.1| 854 RLTAAATYAAIFQAwEPGRSMAPVLNIVAKD 884
                                    5555555666555555677788888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 6427.73
//
Query:       gi|121636320|ref|YP_976543.1|  [L=272]
Description: beta-lactamase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-36  124.7   5.2    5.7e-36  124.4   5.2    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
      1e-06   28.4   0.1    1.5e-06   27.9   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.019   14.4   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
       0.23   12.0   0.0       0.43   11.1   0.0    1.4  1  Agglutinin_C   Agglutinin C-terminal


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   5.2   1.3e-39   5.7e-36       4     197 .]      37     245 ..      34     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1.3e-39
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                      vn++l+++d+gv+LiD+G+++++a  +  l +lg+ p dv+a++lTH+H+DH G + ++++++  pv+++aee  + +
  gi|121636320|ref|YP_976543.1|  37 HAVNWVLVTDDTGVLLIDAGYPGDRAEVLASLNKLGYTPGDVRAIVLTHAHIDHLGSAIWFAREHSTPVYCHAEEVGHAK 116
                                    579***************************************************************************** PP

                                    CHHHHHHHHHCCHH...............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEE CS
                    Lactamase_B  84 meeaddaasrkgll...............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlft 148
                                    +e+++ a++++ +l               ++g+   + +++  +l+ +a+ ++ + ++ ++++gh++g+ +y  ++vl +
  gi|121636320|ref|YP_976543.1| 117 REYRENASVFDVALrswrprvavwgihllRRGGLTGDGIPTAQPLTAEAAAGLPGQPMAIFTPGHTSGHCSYVVDGVLAS 196
                                    ******************************************************************************** PP

                                    CTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 149 GDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                    GDal +g   + ++ ++ +++ + ++++++++sl  la l++ +l+pgH
  gi|121636320|ref|YP_976543.1| 197 GDALITGHPMLRHRGPQLLPAVFSHSQQNSIRSLAALALLETNILAPGH 245
                                    ************************************************* PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   3.4e-10   1.5e-06       4      78 ..      52     123 ..      50     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.4e-10
                                    EES--TT.HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                  Lactamase_B_2   4 LiDagpd.lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                    LiDag    r+  l  l   + l  ++ ++ a++lthaH+DHl  +  +++ +  + p+y++++   + +++   +a
  gi|121636320|ref|YP_976543.1|  52 LIDAGYPgDRAEVLASL---NkLGYTPGDVRAIVLTHAHIDHLGSAIWFAREH--STPVYCHAEEVGHAKREYRENA 123
                                    77877543344423333...225788999**************5444444434..479****988888777755444 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.2e-06     0.019       3      71 ..      45     107 ..      42     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-06
                  Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvya 71 
                                    + d   +L+D G  + ++++  +l++l  +  +v +i+L+ha ++hlG+ + +  +      ++ pvy+
  gi|121636320|ref|YP_976543.1|  45 TDDTGVLLIDAGYPGDRAEVLASLNKLGYTPGDVRAIVLTHAHIDHLGSAIWFARE------HSTPVYC 107
                                    44455789*******99999899999998999****************84333322......3455555 PP

>> Agglutinin_C  Agglutinin C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.7e-05      0.43      63      88 ..      30      55 ..      13      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.7e-05
                   Agglutinin_C 63 gestkgkkayNvvlsqdlskvvffdp 88
                                     + + ++a+N+vl +d+++v+++d+
  gi|121636320|ref|YP_976543.1| 30 KVHLARGHAVNWVLVTDDTGVLLIDA 55
                                   5556789****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1927.73
//
Query:       gi|121636321|ref|YP_976544.1|  [L=336]
Description: glucose-6-phosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-65  220.6   1.5      4e-65  220.3   1.5    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.3   1.5   2.2e-69     4e-65      16     314 .]      11     307 ..       3     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 220.3 bits;  conditional E-value: 2.2e-69
                 Bac_luciferase  16 gaasaslrylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply.trhPavlAqqa 90 
                                    +a+++++r+lvela+aaE++G d++ v++h ++++++    + ++++++a+ ++T+r+ lgt+v++++ +++Pav+Aq++
  gi|121636321|ref|YP_976544.1|  11 SAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQgghaPFSLSWMTAVGERTNRLLLGTSVLTPTfRYNPAVIAQAF 90 
                                    334489*****************************99**9*99**********************9999*********** PP

                 Bac_luciferase  91 atLdhlsgGRfglglgtggpaveerrf..Gv..dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgp 166
                                    at+  l++ R+ lg+gtg++ +e +    G+  ++ er arlrE v ++r+lw+g++vdf+G+++++kga +   p+ g 
  gi|121636321|ref|YP_976544.1|  91 ATMGCLYPNRVFLGVGTGEALNEIATGyeGAwpEFKERFARLRESVGLMRQLWSGDRVDFDGDYYRLKGASIYDVPDGG- 169
                                    ***********************66544555*********************************************888. PP

                 Bac_luciferase 167 iPvyvaaaspaglelaarhadglllag..eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearal 244
                                    +Pvy+aa++pa +++a+r +dg+++++   ++   ++l++ +r+gaa+a+r+ + i+ +i + +++++++e A+ +  ++
  gi|121636321|ref|YP_976544.1| 170 VPVYIAAGGPAVAKYAGRAGDGFICTSgkGEELYTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELALNNT-RF 248
                                    ***************************977777788999*************************************8.89 PP

                 Bac_luciferase 245 iagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvG.tpeqvaerlaayaeagvde 314
                                    +            a    +a++++   d+ ++++aada+p e++a+ ++v  +p++++e++ +y+  g+++
  gi|121636321|ref|YP_976544.1| 249 W------------APLSLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVAsDPDEAVEKVGQYVTWGLNH 307
                                    9............678899999******************999999999555*************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2313.60
//
Query:       gi|121636322|ref|YP_976545.1|  [L=690]
Description: phosphate acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-134  448.9   0.1   1.4e-134  448.4   0.1    1.2  1  PTA_PTB   Phosphate acetyl/butaryl transferase
    1.3e-23   82.8   1.6    4.5e-23   81.0   0.3    2.6  2  DRTGG     DRTGG domain
      2e-23   83.3   0.1      4e-23   82.3   0.1    1.5  1  AAA_26    AAA domain


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.4   0.1  2.4e-138  1.4e-134       1     319 []     365     682 ..     365     682 .. 1.00

  Alignments for each domain:
  == domain 1  score: 448.4 bits;  conditional E-value: 2.4e-138
                                    HHHHHHHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT-EEE-TTT-CCHHHHH CS
                        PTA_PTB   1 sflerivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsgieivdpetsekleeya 80 
                                    +f++r++++a+++  rivlpeg+d+r+lk+a +ll++gi+d++++gdea+++ +a+el++dl+g+++++p+ se ++++a
  gi|121636322|ref|YP_976545.1| 365 MFTYRLLQQARSDLMRIVLPEGDDDRILKSAGRLLQRGIVDLTILGDEAKVRLRAAELGVDLDGATVIEPCASELHDQFA 444
                                    5899**************************************************************************** PP

                                    HHHHHHCCCC.S-HCCHHHHTTSHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEETTEE CS
                        PTA_PTB  81 delyelrkrkgvtieearevvrdatyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimlledrl 160
                                    d++++lrk+kg+t+e+are+++datyf++mlv++++aDg+vsGa++tta+t+rpal+iikt pg+++vSs+f+m+l+dr+
  gi|121636322|ref|YP_976545.1| 445 DQYAQLRKAKGITVEHAREIMNDATYFGTMLVHNCHADGMVSGAAHTTAHTVRPALEIIKTVPGISTVSSIFLMCLPDRV 524
                                    ******************************************************************************** PP

                                    EEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHHHH-TTSEEEEEE-HH CS
                        PTA_PTB 161 llfaDcavnvnPtaeelaeialesaktakalgeeeprvAlLSyStkgsakgesvekvrealkivkekapdlvvdGelqlD 240
                                    l+++Dca+ +nPt+e+la+ia++sa+ta+++g +eprvA+LSySt  s+kg++v+kvr+a+++v++++p+l v+G++q+D
  gi|121636322|ref|YP_976545.1| 525 LAYGDCAIIPNPTVEQLADIAICSARTAAQFG-IEPRVAMLSYSTGDSGKGADVDKVRAATELVRAREPQLPVEGPIQYD 603
                                    ********************************.*********************************************** PP

                                    HHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--HHHHHHHHHHHH CS
                        PTA_PTB 241 aAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvndlSrgasvedivnvaaita 319
                                    aA++++va++k+++s+vaG+A+vl+fPdL++gn++yk+vqr a+a+aiGP+lqGl+kPvndlSrga v+divn++aita
  gi|121636322|ref|YP_976545.1| 604 AAVEPSVAATKLRDSPVAGRATVLIFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLRKPVNDLSRGALVDDIVNTVAITA 682
                                    *****************************************************************************97 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.25   1.5e+03      40      53 ..      98     112 ..      78     139 .. 0.63
   2 !   81.0   0.3   7.6e-27   4.5e-23       1     103 [.     207     319 ..     207     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.25
                                    T.SEEEEEETT-HHH CS
                          DRTGG  40 e.gdlvivpGDRedi 53 
                                    e +++v+v+ D +d+
  gi|121636322|ref|YP_976545.1|  98 EcDAVVVVGSDYTDV 112
                                    235555555555555 PP

  == domain 2  score: 81.0 bits;  conditional E-value: 7.6e-27
                                    HHHHHTT-EEEE--..SS--.E-EEEE-SS-HHHHHHHHHTSEEEEEETT-HHHHHHHTT-T.......EEEEEEETT-- CS
                          DRTGG   1 eiaealgaevlnggeeelrr.vekvvvgamsvenmlerlkegdlvivpGDRediqlaaleag.......iaalilTggle 72 
                                    e+ +a+++ v++g+ +  +r v  v+ + m+++++lerl++g++vi+pGDR+d++la+++a+       +++++l+gg++
  gi|121636322|ref|YP_976545.1| 207 ELTQAVNGAVVSGDVALREReVMGVLAAGMTADHVLERLTDGMAVITPGDRSDVVLAVASAHaaegfpsLSCIVLNGGFQ 286
                                    67899*********9999999*********************************************************** PP

                                    --HHHHHHHHHHT..--EEE-SS-HHHHHHHHH CS
                          DRTGG  73 pseevlklaeeag..lpvlsveldtfttakrin 103
                                    +++++++l+ +++  lpv+++ l t++ta++ +
  gi|121636322|ref|YP_976545.1| 287 LHPAIAALVSGLRlrLPVIATALGTYDTASAAA 319
                                    *****************************9875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.1   6.8e-27     4e-23       2     195 ..       6     201 ..       5     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 6.8e-27
                         AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.dedselikellgldqtyelpeplalsaplspelaar 80 
                                    +i++++ + + GK++++lgL++ l++  +kvg+f+Pi   + e d+  el+   +++  +ye +  +++++      a+r
  gi|121636322|ref|YP_976545.1|   6 AIYLAAPESQTGKSTIALGLLHRLTAMVAKVGVFRPITRLSAErDYILELLLAHTSAGLPYERCVGVTYQQ----LHADR 81 
                                    69***********************************9888764776666666666666677777888874....55667 PP

                         AAA_26  81 qegedidlekivkelekdadivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealr....qk 155
                                    ++  +  ++++ +++++++d vvV G+++++v +  e  +na+ia nlgapv+l +r++++t++q++  +e++     ++
  gi|121636322|ref|YP_976545.1|  82 DDAIAEIVDSY-HAMADECDAVVVVGSDYTDVTSPTElSVNARIAVNLGAPVLLTVRAKDRTPDQVASVVEVCLaeldTQ 160
                                    77767778888.9******************9977776*********************************998555446 PP

                         AAA_26 156 nvrvlGvilNkvrnp...envetlekksgipvlGvvPylpdle 195
                                      + ++v++N++      +  ++l+ +++     vvP +p l+
  gi|121636322|ref|YP_976545.1| 161 RAHTAAVVANRCELSaipAVTDALRRFTPP--SYVVPEEPLLS 201
                                    889*******96433233455555555443..23455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4731.47
//
Query:       gi|121636323|ref|YP_976546.1|  [L=385]
Description: acetate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.4e-128  427.0   0.0   5.4e-127  423.7   0.0    1.9  1  Acetate_kinase  Acetokinase family


Domain annotation for each model (and alignments):
>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.7   0.0    3e-131  5.4e-127       2     390 .]       5     374 ..       4     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 423.7 bits;  conditional E-value: 3e-131
                 Acetate_kinase   2 vLviNaGSsSlKfqlleaeakeevllkglveeilleeaellkklegekkeaektaiadheealklilntlkeekvikdlk 81 
                                    vLviN+GSsSlKfql+e+ + +   + g+ve+i++                 +  +adh++al+++++ l e++++ ++ 
  gi|121636323|ref|YP_976546.1|   5 VLVINSGSSSLKFQLVEP-VAGMSRAAGIVERIGER----------------SSPVADHAQALHRAFKMLAEDGIDLQTC 67 
                                    8*****************.78889999999999754................346789********************** PP

                 Acetate_kinase  82 eiaaighRvvhggekftesvlitdevvekikdlielaplhNpanlegieaakkllpevknvavfDtafhqtlpeeaylya 161
                                     + a+ghRvvhgg++f +++l++d v+ k+++l+ laplhNp+ + gi++a++ll +v +vavfDtaf+++lp++a+ ya
  gi|121636323|ref|YP_976546.1|  68 GLVAVGHRVVHGGTEFHQPTLLDDTVIGKLEELSALAPLHNPPAVLGIKVARRLLANVAHVAVFDTAFFHDLPPAAATYA 147
                                    ******************************************************************************** PP

                 Acetate_kinase 162 lpeelyeehgiRrygfHgtshkyvskraakilgkpledlnlivcHlGnGaSvaavknGksvdtsmgltpLeGlvmgtRsG 241
                                    + +++++++ iRrygfHgtsh+yvs+raa  lg+pl+ ln iv HlGnGaS +a+  G+ v+tsmgltpLeGlvmgtRsG
  gi|121636323|ref|YP_976546.1| 148 IDRDVADRWHIRRYGFHGTSHQYVSERAAAFLGRPLDGLNQIVLHLGNGASASAIARGRPVETSMGLTPLEGLVMGTRSG 227
                                    ******************************************************************************** PP

                 Acetate_kinase 242 didpailvylaeteglsadeventlnkksGllglsglssDlrevedaaeegdeeaelalkvyvhrlakyigeyaavlegk 321
                                    d+dp++++yl +t+ + ++++e++ln +sG+lgl g   D+r ++  +e gd+ a+la++v++hrl+ky+g+y+avl g+
  gi|121636323|ref|YP_976546.1| 228 DLDPGVISYLWRTARMGVEDIESMLNHRSGMLGLAG-ERDFRRLRLVIETGDRSAQLAYEVFIHRLRKYLGAYLAVL-GH 305
                                    ************************************.99**************************************.8* PP

                 Acetate_kinase 322 vDaivFTgGigenaalvrelvlkalevlglevdkeknk.nrsGedelisteqskvkvivvptnEelaiaq 390
                                     D + FT+Gigen a vr+++l++l+ lg+++d+++n  + +G +  is+++s + v+vvptnEelaia+
  gi|121636323|ref|YP_976546.1| 306 TDVVSFTAGIGENDAAVRRDALAGLQGLGIALDQDRNLgPGHGAR-RISSDDSPIAVLVVPTNEELAIAR 374
                                    *************************************98899988.79********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2736.77
//
Query:       gi|121636324|ref|YP_976547.1|  [L=750]
Description: Serine/threonine-protein kinase pknG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.4e-152  506.1   6.3   4.6e-152  505.6   6.3    1.2  1  PknG_TPR       Protein kinase G tetratricopeptide repeat
    5.3e-63  211.3   0.2    9.9e-63  210.4   0.2    1.5  1  PknG_rubred    Protein kinase G rubredoxin domain
    1.4e-31  109.9   0.0    2.4e-31  109.1   0.0    1.4  1  Pkinase        Protein kinase domain
    1.3e-12   47.6   0.0    1.9e-12   47.0   0.0    1.2  1  Pkinase_Tyr    Protein tyrosine kinase
    5.8e-06   26.7   0.0      0.063   13.8   0.0    3.7  3  TPR_19         Tetratricopeptide repeat
     0.0008   19.4   0.7       0.25   11.2   0.0    3.2  3  APH            Phosphotransferase enzyme family
     0.0043   16.7   0.0     0.0074   15.9   0.0    1.3  1  RIO1           RIO1 family
     0.0071   16.4   0.1       0.22   11.7   0.0    3.3  3  TPR_2          Tetratricopeptide repeat
     0.0079   16.8   6.5      0.016   15.9   0.0    4.0  4  TPR_16         Tetratricopeptide repeat
     0.0095   15.6   0.6      0.028   14.1   0.6    1.8  1  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.044   13.5   0.0    1.3  1  RPN7           26S proteasome subunit RPN7
      0.027   14.5   0.2      0.049   13.7   0.2    1.3  1  DZR            Double zinc ribbon
      0.069   13.5   2.0         25    5.3   0.1    3.5  3  BON            BON domain
      0.088   13.5   0.1         15    6.4   0.0    3.4  2  TPR_6          Tetratricopeptide repeat
       0.14   12.5   0.3        4.8    7.5   0.0    3.5  4  TPR_12         Tetratricopeptide repeat
       0.19   11.2   5.5        1.7    8.2   0.1    2.3  2  zf-ribbon_3    zinc-ribbon domain
       0.27   12.1   0.1       0.27   12.1   0.1    4.9  4  TPR_14         Tetratricopeptide repeat
       0.76    9.5   2.7         18    5.1   0.3    2.5  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
       0.82    9.5   5.2          3    7.7   5.4    1.9  1  HscB_4_cys     Co-chaperone HscB tetracysteine metal binding 


Domain annotation for each model (and alignments):
>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.6   6.3  4.9e-155  4.6e-152       1     340 []     409     748 ..     409     748 .. 1.00

  Alignments for each domain:
  == domain 1  score: 505.6 bits;  conditional E-value: 4.9e-155
                                    ----SSB---SS--SSSCCCCGGGHHHH---------HHHHHHHS--B---TTSTTHHHHHHTTT--HHHHHHHHHHHHT CS
                       PknG_TPR   1 pglStvFspqrttfGtdelveqtdvvvdgverdeklearevvaaLpvPlvdpedpaAalLaalvhsdpaelldsleaare 80 
                                    pglSt+Fsp+r+tfG+d+lv++tdv++dg+ ++ekl+a+e+v+aL+vPlvdp+d+aA++L+a+v s+p ++ldsl+aar+
  gi|121636324|ref|YP_976547.1| 409 PGLSTIFSPSRSTFGVDLLVAHTDVYLDGQVHAEKLTANEIVTALSVPLVDPTDVAASVLQATVLSQPVQTLDSLRAARH 488
                                    89****************************************************************************** PP

                                    ---------GCC-SHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT CS
                       PknG_TPR  81 saleadgvdaseslevpLaevrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpG 160
                                     al+adgvd+ses+e+pL+evra ldlGdv++a+++Ld+l+e+v+++Wrl Wyr++aeLl+gdy++A+++F+evl+++pG
  gi|121636324|ref|YP_976547.1| 489 GALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPG 568
                                    ******************************************************************************** PP

                                    -SHHHHHHHHHHHHHT---TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS-TTSTTHHHHHHHHHHHCH CS
                       PknG_TPR 161 EiaPklaLAataElagetdeekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeVpatSrhyttArltavllll 240
                                    E+aPklaLAataElag+tde+k+Y+tVw+t++gv+sAaFGlaR+++a+gdr +Av++LdeVp+tSrh+ttArlt++++ll
  gi|121636324|ref|YP_976547.1| 569 ELAPKLALAATAELAGNTDEHKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLL 648
                                    ******************************************************************************** PP

                                    ---------HHHHHHHHHHHHTS-TTSCCHHHHHHHHHHHHHHHCTT---SSSEETTEESSHHHHHHHHHHHHHCCCHH- CS
                       PknG_TPR 241 sgrpvaeldeadlreaarrveaLpedeeralqlrvlVlgaALdWlragkassetlLgvpfterglreglEaalRalArea 320
                                    sgr+++e++e+++r+aarrveaLp +e+r+lq+r+lVlg ALdWl+++kas++++Lg+pft++glr g+Ea+lR+lAr a
  gi|121636324|ref|YP_976547.1| 649 SGRSTSEVTEEQIRDAARRVEALPPTEPRVLQIRALVLGGALDWLKDNKASTNHILGFPFTSHGLRLGVEASLRSLARVA 728
                                    ******************************************************************************** PP

                                    SSHHHCHHCCHHCCHH--XX CS
                       PknG_TPR 321 perahRyaLvdlANaiRprs 340
                                    p+++hRy+Lvd+AN++Rp+s
  gi|121636324|ref|YP_976547.1| 729 PTQRHRYTLVDMANKVRPTS 748
                                    ******************97 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.2   1.1e-65   9.9e-63       1     139 []      12     150 ..      12     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 1.1e-65
                                    XXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXXXXXXXXXXXXXXXETTTTEEEE------TT CS
                    PknG_rubred   1 patqpaedlesasaatarpvstqavfRpevddded.saslealsteastrsasatrslspvrrlGgGLveiprvveadPl 79 
                                    p+tqpa d+++a++at+rp+stqavfRp+++d+++  +++   +te+++r+a+++r+++pvrrlGgGLveipr +++dPl
  gi|121636324|ref|YP_976547.1|  12 PGTQPA-DAQTATSATVRPLSTQAVFRPDFGDEDNfPHPTLGPDTEPQDRMATTSRVRPPVRRLGGGLVEIPRAPDIDPL 90 
                                    79****.9**********************8777767888889************************************* PP

                                    GGG-CSS---GGG-B-TTT--B-S---SS----SEEE-TTT--EEE-S-SS-TT-EETTT CS
                    PknG_rubred  80 eAlltnpvvpEskRfCwrCGrpvGRsekerkgaseGtCpkCgspysFlPqLspGdvvagq 139
                                    eAl+tnpvvpEskRfCw+CGrpvGRs++e+kgaseG+Cp+CgspysFlPqL+pGd+vagq
  gi|121636324|ref|YP_976547.1|  91 EALMTNPVVPESKRFCWNCGRPVGRSDSETKGASEGWCPYCGSPYSFLPQLNPGDIVAGQ 150
                                    ***********************************************************9 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   2.5e-34   2.4e-31       1     196 [.     151     343 ..     151     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.5e-34
                                    EEEEEEEEEESSEEEEEEEETT.TTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.....SSEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveke.tgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.....kdely 74 
                                    ye++  + +G+ G +y a++++ +g+ v++K + ++ + + +   +++E ++l+++ hp iv++++++e+     +   y
  gi|121636324|ref|YP_976547.1| 151 YEVKGCIAHGGLGWIYLALDRNvNGRPVVLKGLVHSGDAEAQ-AMAMAERQFLAEVVHPSIVQIFNFVEHtdrhgDPVGY 229
                                    567777889*********998747899*******99999977.59************************97777777789 PP

                                    EEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSB CS
                        Pkinase  75 lvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskl 154
                                    +v+eyv g++l++     ++l+ +ea  ++ +il +l+ylHs g+++ DlKpeNi++  +++lK++D+G +++++s   +
  gi|121636324|ref|YP_976547.1| 230 IVMEYVGGQSLKRSKG--QKLPVAEAIAYLLEILPALSYLHSIGLVYNDLKPENIMLT-EEQLKLIDLGAVSRINS---F 303
                                    *********9999876..579999999*******************************.9***************9...6 PP

                                    CTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-S CS
                        Pkinase 155 tsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkpp 196
                                        gt+ + APE++ +++ + ++D++++G +l+ l+    p
  gi|121636324|ref|YP_976547.1| 304 GYLYGTPGFQAPEIV-RTGPTVATDIYTVGRTLAALTL-DLP 343
                                    699************.5677999**********99954.444 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0     2e-15   1.9e-12       7     158 ..     157     305 ..     151     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2e-15
                                    EEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSS.....EEEEEE CS
                    Pkinase_Tyr   7 lGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeep.....llivte 81 
                                    +++G  G ++ +  +   + +   V++K l ++ ++e +++ + e +++ ++ hp iv++  ++ ++++      +iv+e
  gi|121636324|ref|YP_976547.1| 157 IAHGGLGWIYLALDR---NVNGRPVVLKGLVHSGDAEAQAMAMAERQFLAEVVHPSIVQIFNFVEHTDRhgdpvGYIVME 233
                                    566677777777666...778899*************9**************************94444344577***** PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                                    yv g +L+    +++ +kl + + + + l++  +++yL+s  lv  dl   N++l+ +++ k+ D G  ++i++  +
  gi|121636324|ref|YP_976547.1| 234 YVGGQSLK----RSKGQKLPVAEAIAYLLEILPALSYLHSIGLVYNDLKPENIMLT-EEQLKLIDLGAVSRINSFGY 305
                                    ***98876....445999**************************************.6788999**99998844444 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.36   3.4e+02      26      53 ..     503     530 ..     489     533 .. 0.82
   2 !   13.8   0.0   6.6e-05     0.063       5      43 ..     550     588 ..     546     588 .. 0.94
   3 ?    6.3   0.0     0.014        13      12      56 ..     590     634 ..     589     646 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                         TPR_19  26 earllLAeallalgqldeAealLdalpe 53 
                                    e+ l  ++all lg++++A + Ld+l e
  gi|121636324|ref|YP_976547.1| 503 ELPLMEVRALLDLGDVAKATRKLDDLAE 530
                                    55565589***********998888876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.6e-05
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqlde 43 
                                    gdy++A ++++++l+  p+ ++ +l+LA     +g++de
  gi|121636324|ref|YP_976547.1| 550 GDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE 588
                                    9****************************9999999997 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                         TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                    ++++ +++ + +   a+ +LA+a  a g+   A ++Ld++p+  +
  gi|121636324|ref|YP_976547.1| 590 KFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPTSR 634
                                    67888899999999999***********************98765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0087       8.2      37      95 ..     192     255 ..     163     258 .. 0.64
   2 !   11.2   0.0   0.00026      0.25     150     196 ..     252     297 ..     242     301 .. 0.80
   3 ?   -1.4   0.5       1.9   1.8e+03     128     161 ..     643     673 ..     508     682 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0087
                                    HHHHHHHHHHHHHTT-..B--B-CTTB..S-EEETTEEEEEEE----EE-SS..HHHHHHHHHHH CS
                            APH  37 irrevallrlLakagv..pvPevlagd..tddeeigllfalieyvpgrsllr..klsaaqlpell 95 
                                     +   a+ ++La+  v  ++ +++ +   td+++ +  + ++eyv+g+sl r   +  +++++++
  gi|121636324|ref|YP_976547.1| 192 QAMAMAERQFLAEV-VhpSIVQIFNFVehTDRHGDPVGYIVMEYVGGQSLKRskGQKLPVAEAIA 255
                                    33444556666666.4456677776662255555556***************7655555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHH--S...SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 150 eqvlaalaallpg...elptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                    e ++a l++ lp+     + +l+ +Dl+p N+++++++ +   +iD++ +
  gi|121636324|ref|YP_976547.1| 252 E-AIAYLLEILPAlsyLHSIGLVYNDLKPENIMLTEEQLK---LIDLGAV 297
                                    3.68888888888888999****************55555...8998865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.9
                                    HHHCHHHCCCGCCTCCHHHHHHHHHHHHHHHH-- CS
                            APH 128 qlesatarllaselldlleeleeqvlaalaallp 161
                                      +    ++  se+ +  e++++ ++++++al p
  gi|121636324|ref|YP_976547.1| 643 SAVTLLSGRSTSEVTE--EQIRD-AARRVEALPP 673
                                    2222222334444444..45555.5555555555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.9e-06    0.0074      83     150 ..     230     295 ..     227     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.9e-06
                                    EEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                           RIO1  83 lvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                    +vme++g + ++  k ++++  +ea  ++ e+l ++  l +  glv  DL   N++++e+++ +ID++
  gi|121636324|ref|YP_976547.1| 230 IVMEYVGGQSLKRSKGQKLP-VAEAIAYLLEILPALSYL-HSIGLVYNDLKPENIMLTEEQLKLIDLG 295
                                    8******5555555555555.778888999999976655.5*************************86 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.8   1.7e+03       3      16 ..     158     171 ..     156     172 .. 0.84
   2 ?   -0.9   0.0       2.6   2.4e+03      10      24 ..     511     525 ..     510     530 .. 0.78
   3 !   11.7   0.0   0.00024      0.22       5      32 ..     540     567 ..     536     569 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                          TPR_2   3 alynlGlayyklgd 16 
                                    a+  lG++y++l++
  gi|121636324|ref|YP_976547.1| 158 AHGGLGWIYLALDR 171
                                    7889******9976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                          TPR_2  10 ayyklgdyeeAleaf 24 
                                    a++ lgd ++A + +
  gi|121636324|ref|YP_976547.1| 511 ALLDLGDVAKATRKL 525
                                    788999999997765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00024
                          TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                    ++++ a +  gdy+ A ++f ++l   P
  gi|121636324|ref|YP_976547.1| 540 WYRAVAELLTGDYDSATKHFTEVLDTFP 567
                                    6899********************9887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.9   4.6e+03      36      51 ..     158     173 ..     157     189 .. 0.78
   2 ?   -2.5   0.0       9.2   8.7e+03      14      31 ..     462     476 ..     461     485 .. 0.84
   3 !   15.9   0.0   1.7e-05     0.016       1      66 [.     506     568 ..     506     569 .. 0.96
   4 ?    1.8   0.0      0.42   3.9e+02      36      58 ..     605     627 ..     604     633 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.9
                         TPR_16  36 Allllgdaalrqgrla 51 
                                    A+ +lg+++l++ r  
  gi|121636324|ref|YP_976547.1| 158 AHGGLGWIYLALDRNV 173
                                    899******9987755 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.2
                         TPR_16  14 ddAaaaleaalkrdpssP 31 
                                    d Aa +l+a++ ++   P
  gi|121636324|ref|YP_976547.1| 462 DVAASVLQATVLSQ---P 476
                                    6799******9999...5 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.7e-05
                         TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                    l++ ra+l++gd ++A + l+ + +r      +++  +++++a l  g+++ A   + + l+  p+
  gi|121636324|ref|YP_976547.1| 506 LMEVRALLDLGDVAKATRKLDDLAERV---GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPG 568
                                    6899***********************...99***************************9999998 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.42
                         TPR_16  36 AllllgdaalrqgrlaeAaalyr 58 
                                    A+++l++a+ + g+  +A+  ++
  gi|121636324|ref|YP_976547.1| 605 AAFGLARARSAEGDRVGAVRTLD 627
                                    89************999995555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6     3e-05     0.028       1      22 [.     105     134 ..     105     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                  zinc_ribbon_2   1 fCpnCGael.qdnakF.......CpyCGtp 22 
                                    fC+nCG+++   ++         CpyCG+p
  gi|121636324|ref|YP_976547.1| 105 FCWNCGRPVgRSDSETkgasegwCPYCGSP 134
                                    9********76766667***********97 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.7e-05     0.044      88     157 ..     514     579 ..     506     585 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                                    -HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HHHHHHH CS
                           RPN7  88 dwdlvskylekakellekggdwerknrlkvyeGlallairkfkeAaellldilstftskellsyedlavy 157
                                    d + v k + k+ +l e+   +  + rl  y ++a+l ++++ +A++++ ++l tf  +el +   la  
  gi|121636324|ref|YP_976547.1| 514 DLGDVAKATRKLDDLAER---VGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTF-PGELAPKLALAAT 579
                                    555666666666666666...88999******************************.6888777666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.2e-05     0.049       8      37 ..      99     134 ..      95     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                            DZR   8 lppdarfCseCgtklkavaa......edrCpsCgek 37 
                                    +p+++rfC +Cg ++ +  +      e  Cp Cg++
  gi|121636324|ref|YP_976547.1|  99 VPESKRFCWNCGRPVGRSDSetkgasEGWCPYCGSP 134
                                    578899********975555899999999****987 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.027        25      30      54 ..     174     199 ..     171     208 .. 0.91
   2 ?    3.2   0.0      0.12   1.1e+02      19      55 ..     419     453 ..     414     459 .. 0.83
   3 ?    2.1   0.2      0.27   2.5e+02      34      56 ..     647     669 ..     642     671 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                                    TTC.EEEECEEECHHHHHHHHHHHHC CS
                            BON  30 nGv.VtLsGtVdseaekekAveiarn 54 
                                    nG+ V+L+G V s ++  +A+++a++
  gi|121636324|ref|YP_976547.1| 174 NGRpVVLKGLVHSGDAEAQAMAMAER 199
                                    8999******************9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                                    TTGCCCEEEEETTCEEEECEEECHHHHHHHHHHHHCC CS
                            BON  19 ldaadinVevenGvVtLsGtVdseaekekAveiarnv 55 
                                     + ++++  v + +V+L G+V  +aek +A ei+  +
  gi|121636324|ref|YP_976547.1| 419 RSTFGVDLLVAHTDVYLDGQV--HAEKLTANEIVTAL 453
                                    56678888888977*******..99999999999765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.27
                                    EEECEEECHHHHHHHHHHHHCCT CS
                            BON  34 tLsGtVdseaekekAveiarnva 56 
                                    +LsG+ +se   e++ ++ar+v+
  gi|121636324|ref|YP_976547.1| 647 LLSGRSTSEVTEEQIRDAARRVE 669
                                    69******************997 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.016        15       4      32 ..     540     568 ..     538     569 .. 0.91
   2 ?    3.0   0.0      0.21     2e+02       2      26 ..     605     629 ..     604     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                    +++a + + +gd+d A + + ++++ +P+
  gi|121636324|ref|YP_976547.1| 540 WYRAVAELLTGDYDSATKHFTEVLDTFPG 568
                                    67899999989*****************6 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealerl 26 
                                    A + la+++ + gd   A+++l+++
  gi|121636324|ref|YP_976547.1| 605 AAFGLARARSAEGDRVGAVRTLDEV 629
                                    7799*******99********9876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.5   5.2e+03      46      60 ..     157     171 ..     154     172 .. 0.83
   2 ?   -2.8   0.0       8.9   8.4e+03      46      61 ..     510     525 ..     508     527 .. 0.70
   3 ?    7.5   0.0    0.0051       4.8       9      37 ..     542     567 ..     536     588 .. 0.67
   4 ?   -0.4   0.0       1.5   1.4e+03      41      69 ..     599     627 ..     595     629 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.5
                         TPR_12  46 ttlrnLgrlyralgr 60 
                                    ++  +Lg++y+al+r
  gi|121636324|ref|YP_976547.1| 157 IAHGGLGWIYLALDR 171
                                    57889*****99876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                         TPR_12  46 ttlrnLgrlyralgry 61 
                                    ++l +Lg++  a+ ++
  gi|121636324|ref|YP_976547.1| 510 RALLDLGDVAKATRKL 525
                                    7888888887776555 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0051
                         TPR_12   9 laavlrrlgrydeAlellekaleiarrll 37 
                                    +a++++  g+yd A +++ ++l+ +   +
  gi|121636324|ref|YP_976547.1| 542 RAVAELLTGDYDSATKHFTEVLDTF---P 567
                                    6777788899999999999999888...3 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.5
                         TPR_12  41 hpltattlrnLgrlyralgryeeAlelle 69 
                                    +++++++ ++L+r+ +a g+   A++ l 
  gi|121636324|ref|YP_976547.1| 599 NDGVISAAFGLARARSAEGDRVGAVRTLD 627
                                    56789999999999999999888877665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0018       1.7       2      16 ..     103     117 ..     102     118 .. 0.82
   2 ?    4.3   1.6      0.03        29      19      24 ..     128     133 ..     127     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                    zf-ribbon_3   2 tvrCPnCGaplssdd 16 
                                    +++C+nCG p+  +d
  gi|121636324|ref|YP_976547.1| 103 KRFCWNCGRPVGRSD 117
                                    789*****9888776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.03
                    zf-ribbon_3  19 CpyCGt 24 
                                    CpyCG+
  gi|121636324|ref|YP_976547.1| 128 CPYCGS 133
                                    666665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8      0.18   1.7e+02       8      39 ..     509     541 ..     506     545 .. 0.74
   2 ?   12.1   0.1   0.00029      0.27       2      43 ..     537     578 ..     536     579 .. 0.90
   3 ?   -0.4   0.0       3.2     3e+03       6      27 ..     608     629 ..     604     642 .. 0.84
   4 ?   -1.7   0.1       7.9   7.4e+03      19      38 ..     660     679 ..     658     685 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                         TPR_14   8 aeallalGdpdeAiallrralalaPdda.eawl 39 
                                    ++all lGd ++A + l+++ ++  + +  +w+
  gi|121636324|ref|YP_976547.1| 509 VRALLDLGDVAKATRKLDDLAERVGWRWrLVWY 541
                                    689999999999999999988875555514555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    ++ + +a a+l  Gd+d A +++ ++l+++P++++  l+la 
  gi|121636324|ref|YP_976547.1| 537 RLVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAA 578
                                    567788999999*********************999999985 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3.2
                         TPR_14   6 alaeallalGdpdeAiallrra 27 
                                     la+a  a Gd  +A++ l+++
  gi|121636324|ref|YP_976547.1| 608 GLARARSAEGDRVGAVRTLDEV 629
                                    589999999*999999999876 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 7.9
                         TPR_14  19 eAiallrralalaPddaeaw 38 
                                    + ++++rr+ al P++++++
  gi|121636324|ref|YP_976547.1| 660 QIRDAARRVEALPPTEPRVL 679
                                    56788999999999998876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.019        18       3      21 ..     103     121 ..     101     121 .. 0.88
   2 ?    4.2   0.2     0.037        35       4      12 ..     126     134 ..     123     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                  zf-NADH-PPase   3 hrFCgrCGaptepaeggwa 21 
                                     rFC  CG p+ +++ +++
  gi|121636324|ref|YP_976547.1| 103 KRFCWNCGRPVGRSDSETK 121
                                    59***********999875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                  zf-NADH-PPase   4 rFCgrCGap 12 
                                     +C+ CG+p
  gi|121636324|ref|YP_976547.1| 126 GWCPYCGSP 134
                                    58******9 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.4    0.0032         3       3      14 ..     106     117 ..     105     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                    -SSS--B--SS- CS
                     HscB_4_cys   3 CWnCGgpgapgr 14 
                                    CWnCG+p +  +
  gi|121636324|ref|YP_976547.1| 106 CWNCGRPVGRSD 117
                                    *******98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.73u 0.25s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4833.37
//
Query:       gi|121636325|ref|YP_976548.1|  [L=328]
Description: glutamine-binding lipoprotein glnH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-53  180.3   0.0      5e-53  179.8   0.0    1.2  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    0.00095   19.3   0.0     0.0026   18.0   0.0    1.7  2  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.035   14.1   0.0    1.2  1  NMT1             NMT1/THI5 like


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   8.4e-57     5e-53       1     224 [.      94     313 ..      94     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 8.4e-57
                                    EEEEE-S-BTTTBEE-T.TS-EESHHHHHHHHHHHHC.T-E..EEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTE CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3   1 lrvgvdadypPfsykde.ngeltGfdvdlakaiakrl.gvk..vefvpvswdelipalksgkvDiaiaaititpeReekv 76 
                                    l+vg d +++ fs++d+ +ge+tGfdvd+a ++a+++ gv   ve+++ s +e+++al++ +vDi++ +++it eR++ v
  gi|121636325|ref|YP_976548.1|  94 LIVGLDIGSNLFSFRDPiTGEITGFDVDIAGEVARDIfGVPshVEYRILSAAERVTALQKSQVDIVVKTMSITCERRKLV 173
                                    789**********************************9**733666656******************************* PP

                                    EEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3  77 dFsqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivefdtleealqaLkngrvdav 156
                                    +Fs+ y++a+q++l+++++      i++++dL+gk+v+v +g+t+   ++e ++    iv++ + +++l aL+++++dav
  gi|121636325|ref|YP_976548.1| 174 NFSTVYLDANQRILAPRDS-----PITKVSDLSGKRVCVARGTTSLRRIREIAP-PPVIVSVVNWADCLVALQQREIDAV 247
                                    ****************653.....588888********************9776.78899999***************** PP

                                    EEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 157 vadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakisekWfg 224
                                     +d+++la+lv+++p +++v   ++ ++++y+++++ +++ L+  +n +l+++++dgt++ +++kW++
  gi|121636325|ref|YP_976548.1| 248 STDDTILAGLVEEDPYLHIVG--PDMADQPYGVGINLDNTGLVRFVNGTLERIRNDGTWNTLYRKWLT 313
                                    ********************9..*******************************************86 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   1.2e+04      28      42 ..     115     129 ..     112     141 .. 0.79
   2 !   18.0   0.0   4.3e-07    0.0026      72     111 ..     149     188 ..     143     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                    EESHHHHHHHHHHHH CS
                Lig_chan-Glu_bd  28 yeGfcidLlkelakk 42 
                                    ++Gf +d+  e+a+ 
  gi|121636325|ref|YP_976548.1| 115 ITGFDVDIAGEVARD 129
                                    689999999888775 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.3e-07
                                    HHHHTTS-SEE-SS-B--HHHHTTSEEESESEEE-EEEEE CS
                Lig_chan-Glu_bd  72 gellekkadlavapltitaeReevvdFtkpfmelgisili 111
                                      l ++++d++v  ++it eR++ v+F++ +++    il 
  gi|121636325|ref|YP_976548.1| 149 TALQKSQVDIVVKTMSITCERRKLVNFSTVYLDANQRILA 188
                                    5677899**************************9999986 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.8e-06     0.035      36     103 ..     149     212 ..     137     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-06
                                    HHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S-TT CS
                           NMT1  36 elvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvgspf 103
                                    +++ + ++d+ v+ +  +     +  ++v + +++   ++ +++ +ds+i++++DL Gkr+ +  +  
  gi|121636325|ref|YP_976548.1| 149 TALQKSQVDIVVKTMSITC----ERRKLVNFSTVYLDANQRILAPRDSPITKVSDLSGKRVCVARGTT 212
                                    5566666666666666666....4457999999****************************9887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2165.38
//
Query:       gi|121636326|ref|YP_976549.1|  [L=439]
Description: hypothetical protein BCG_0451c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   14.3   2.4      0.042   13.4   1.1    2.0  2  4HB_MCP_1  Four helix bundle sensory module for signal transd
       0.12   12.8   1.2        7.1    7.1   0.1    2.7  2  HRG        Haem-transporter, endosomal/lysosomal, haem-respon
       0.15   12.4   0.0        1.1    9.6   0.0    2.4  2  GAT        GAT domain


Domain annotation for each model (and alignments):
>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.6   3.6e+03      13      42 ..      37      66 ..      35      81 .. 0.72
   2 ?   13.4   1.1     7e-06     0.042      13     166 ..     244     394 ..     235     397 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                      4HB_MCP_1 13 lllallliivGvvGlyslkkinknletmYe 42
                                    ++ ++l+++Gv + + ++++ +  +++ +
  gi|121636326|ref|YP_976549.1| 37 MTIGIVLAALGVASAFATSTTIEHRQQVLT 66
                                   567788888888888888887776666655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7e-06
                      4HB_MCP_1  13 lllallliivGvvGlyslkkinknletmYedrllpikdlgeikanlrelradl.lelilt.kdkaekdellkdieeleae 90 
                                    l ++++++ vG + l+  +++++++++   ++l+ i+ l+   +++++ rad  l li   +++ +k++  ++i+  +++
  gi|121636326|ref|YP_976549.1| 244 LGILVMVVWVG-TALTISTTASRSAKDTAAESLKTITNLA---ITAQQARADEtLSLIRRgDEEVRKQAFYQRIDAMQRQ 319
                                    44444444444.4455555666666777777666665555...5555555554045555534555688899999998888 PP

                      4HB_MCP_1  91 idkllekyektilteeEkelleefkeqlnaYrevrkkvlelakegkkdeAyqlyetegr....parekliealeelvdln 166
                                    +++++++       + +k  l+  ++ l ++r++ +++   +  g++  A q+   +g+    pa++kl+eal + + + 
  gi|121636326|ref|YP_976549.1| 320 LNDYMAR-----RHAVDKPDLQGADQLLVRWRQANDRINSYISVGNYRAATQVALGKGEddatPAFDKLDEALTKAMGQS 394
                                    8888886.....45559999*********************************998888777799999999999888665 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.012        70       5      35 ..      37      72 ..      35      97 .. 0.72
   2 ?    7.1   0.1    0.0012       7.1       4      28 ..     234     258 ..     232     286 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                            HRG  5 iaygifgsilglsaflvylvlaivnkqgvs.....l 35
                                   + +gi+  +lg++ +++  +    ++q ++      
  gi|121636326|ref|YP_976549.1| 37 MTIGIVLAALGVASAFATSTTIEHRQQVLTavldhT 72
                                   789*********888888888455555333444553 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                            HRG   4 riaygifgsilglsaflvylvlaiv 28 
                                    ri  g+++++lg+ +++v+   a +
  gi|121636326|ref|YP_976549.1| 234 RINPGLVVGALGILVMVVWVGTALT 258
                                    5666777777888888887766544 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.49   2.9e+03       5      29 ..      63      86 ..      60      89 .. 0.82
   2 ?    9.6   0.0   0.00018       1.1      27      68 ..     307     356 ..     291     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.49
                            GAT  5 klLsemLsstepdeellenellkeL 29
                                   ++L+ +L++tep  +++ + l++ L
  gi|121636326|ref|YP_976549.1| 63 QVLTAVLDHTEPL-SFAAGRLYTTL 86
                                   6999******987.88888888777 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
                            GAT  27 keLyetckamqpriqklieet.....adeed......llaelLqlNDeLnnvl 68 
                                    + +y+++ amq+++ +++ +      +   d      ll +  q+ND +n+ +
  gi|121636326|ref|YP_976549.1| 307 QAFYQRIDAMQRQLNDYMARRhavdkP---DlqgadqLLVRWRQANDRINSYI 356
                                    679****************96554441...2444445999999*****99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.57
# Mc/sec: 2315.70
//
Query:       gi|121636327|ref|YP_976550.1|  [L=217]
Description: mutator protein MutT3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-17   62.1   0.5    9.2e-17   61.3   0.5    1.3  1  NUDIX     NUDIX domain
    1.8e-06   27.9   0.3    8.2e-06   25.8   0.2    1.9  2  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.5     1e-20   9.2e-17      14     120 ..      43     153 ..      31     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1e-20
                                    T..SE..EEEEEES.SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEEEEE CS
                          NUDIX  14 k..ge..vLlvrrs.kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd.eheily 86 
                                    +  g   vLl++r+  ++  g W lPgG  +  Etpe++A+RE  EE+Gl+ae le+ + +    + + +  d +h+ + 
  gi|121636327|ref|YP_976550.1|  43 RpdGTpaVLLQHRAlWSHQGGtWGLPGGARDSHETPEQTAVRESSEEAGLSAERLEVRATV---VTAEVCGVDdTHWTYT 119
                                    4224478*******9999999*******************************999999944...4444444552566666 PP

                                    EEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHT CS
                          NUDIX  87 vfleevegelepndenevsevrwvpleellkekl 120
                                    ++++++ + l +    e +e+rwv  +e+++ +l
  gi|121636327|ref|YP_976550.1| 120 TVVADAGELLDTVPNRESAELRWVAENEVADLPL 153
                                    666666666666699999**********944444 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   9.1e-10   8.2e-06      10     108 ..      49     161 ..      39     163 .. 0.70
   2 ?   -0.5   0.0      0.14   1.2e+03      86     101 ..     193     208 ..     171     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.1e-10
                                    EEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEEEEEE......EEEEEEETTEEEEEE.EEEE... CS
                        NUDIX_4  10 rvllekRpekgllggLwefPgge.eegeeleeala...reelgieveelep......gtvkHvftHfrltlt.vylv... 75 
                                    +vll+ R    + gg w++Pgg   + e++e+ ++    ee+g+++e+le        + +    + ++t+t v  +   
  gi|121636327|ref|YP_976550.1|  49 AVLLQHRALWSHQGGTWGLPGGArDSHETPEQTAVresSEEAGLSAERLEVratvvtAE-VCGVDDTHWTYTtVV-Adag 126
                                    69******************999444555776555577778998666443333442223.377888899999554.4667 PP

                                    ....EEE.S..---.EEEEEEGGGGGGS---CCCHCCH CS
                        NUDIX_4  76 ....rveegeeapa.elrwvtpeeleeyalptavrkll 108
                                        +v+  +++ + elrwv ++e+++++l  ++   +
  gi|121636327|ref|YP_976550.1| 127 elldTVP--NRE-SaELRWVAENEVADLPLHPGFAASW 161
                                    7554444..223.259**************98887666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                                    EEEEEEGGGGGGS--- CS
                        NUDIX_4  86 elrwvtpeeleeyalp 101
                                     + w+tp + ++++ p
  gi|121636327|ref|YP_976550.1| 193 VFLWCTPGDADQAPSP 208
                                    4678999888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1161.39
//
Query:       gi|121636328|ref|YP_976551.1|  [L=222]
Description: thiamine-phosphate pyrophosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-53  178.6   0.0    8.7e-53  178.3   0.0    1.1  1  TMP-TENI   Thiamine monophosphate synthase
     0.0069   16.0   0.0      0.011   15.3   0.0    1.4  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
        0.1   12.7   3.4       0.13   12.4   0.9    2.4  2  bPH_6      Bacterial PH domain


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   1.5e-56   8.7e-53       1     181 []      11     201 ..      11     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 1.5e-56
                       TMP-TENI   1 lylvtdskldkneellevveealkggvtlvqlRek.........eldarellelaeklaalcrkygvpliindrvdlala 71 
                                    lyl+td++++ + +l++ +e+al+ggv+++qlR+k          l+ar+ l+ +e la+++++yg+ + +ndr+d+a a
  gi|121636328|ref|YP_976551.1|  11 LYLCTDARRE-RGDLAQFAEAALAGGVDIIQLRDKgspgelrfgPLQARDELAACEILADAAHRYGALFAVNDRADIARA 89 
                                    79****8888.9***********************99888888879********************************** PP

                       TMP-TENI  72 vgadgvHlgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaeale. 150
                                    +gad +Hlgq+dlpv+ ar++l+pd +iG S+h+++++++a+a  adY++vGp++pT+tK+++++ gl +++ +ae    
  gi|121636328|ref|YP_976551.1|  90 AGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGd 169
                                    ************************************************************************99999999 PP

                       TMP-TENI 151 .iPvvaiGGitlenvaevleagadgvavvsai 181
                                     +P++aiGGi+++++++vl+aga+++ vv+ai
  gi|121636328|ref|YP_976551.1| 170 dKPWFAIGGINAQRLPAVLDAGARRIVVVRAI 201
                                    9*****************************98 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-06     0.011     150     224 ..     137     213 ..     115     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                                    TTESEEECCCHTHHHHHHTTCSCEEEHHHTT....EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 150 dfvmGfvaqetlnateedaddfihltpgigl....eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                    +f++G  +    + + ++a+ +  ++   +l    +     +g++ +  +++ + aga  i+v R+I+ a+dp+++ae+
  gi|121636328|ref|YP_976551.1| 137 YFCVGPCWPTPTK-PGRAAPGLGLVRVAAELggddKPWFAIGGINAQRLPAVLD-AGARRIVVVRAITSADDPRAAAEQ 213
                                    6666666665544.2222333333333333344555566668899999999988.99********************97 PP

>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.48   2.9e+03      55      67 ..     121     131 ..     115     135 .. 0.52
   2 ?   12.4   0.9   2.1e-05      0.13      23      68 ..     172     215 ..     156     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                          bPH_6  55 qlgddpelvadal 67 
                                    +++   ++va+a 
  gi|121636328|ref|YP_976551.1| 121 THDP--DQVAAAA 131
                                    4444..5555443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                          bPH_6  23 pWsaiagvrfpegrrl.arldlrdgelvplpavqlgddpelvadalr 68 
                                    pW ai g++   ++rl a+ld   ++ v+++a++++ddp+++a++lr
  gi|121636328|ref|YP_976551.1| 172 PWFAIGGIN---AQRLpAVLDAGARRIVVVRAITSADDPRAAAEQLR 215
                                    788888888...555559999999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1257.49
//
Query:       gi|121636329|ref|YP_976552.1|  [L=340]
Description: thiamine biosynthesis oxidoreductase thiO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-49  167.5   6.3    7.4e-49  167.2   6.3    1.0  1  DAO            FAD dependent oxidoreductase
     0.0062   16.4   0.4     0.0097   15.8   0.4    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.024   13.9   0.1    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.018   14.4   0.1      0.036   13.4   0.1    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.068   13.7   0.4       0.26   11.9   0.1    2.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.086   12.1   0.3       0.13   11.6   0.3    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.11   11.5   2.0       0.22   10.6   2.0    1.4  1  FAD_binding_2  FAD binding domain
       0.13   12.4   0.0       0.27   11.4   0.0    1.5  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
       0.16   12.5   0.7       0.39   11.3   0.2    1.9  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.2   6.3   3.7e-52   7.4e-49       2     350 ..      10     330 ..       9     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 3.7e-52
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHH..HHHHHHHSS CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeel..releeelgi 77 
                                    +++iGGG+iGls+A+ +a++g  V +  ++ +  +gaS+ ++g+l+++ +  p  ++l+rl l++l+++    + + lg+
  gi|121636329|ref|YP_976552.1|  10 LAVIGGGVIGLSVARRAAQAGwpVRVHRSD-E--RGASWVAGGMLAPHSEGWPGEERLLRLGLQSLRLWreGSFLDGLGP 86 
                                    58********************66665555.4..39***********997777767999**********76445566799 PP

                                    TTSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHHHHH CS
                            DAO  78 didyrrtGllslaadeeelealdkllall.leagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaalara 155
                                    ++ +    +l++a d+++ ++l+  +a++ +++g ++ +++++ +r++ep   +g++ ++  p++  vd ++l+ al r+
  gi|121636329|ref|YP_976552.1|  87 QL-VTAHESLVVAVDRADVADLRT-VADWlSAQGHPV-IWESA-ARDVEPLlAQGIRHGFRAPTELAVDNRALLDALCRD 162
                                    86.556778888878888999*55.555536677776.45555.9*****9544************************** PP

                                    HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEEEEECCTHS CS
                            DAO 156 aealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkeldlpispvrgqvlvlkplsekl 234
                                    +e+lGv+   +  v +l       + v          a++vV+a+G+ +  l+   + l  pi+pv+g+vl+l ++    
  gi|121636329|ref|YP_976552.1| 163 CERLGVRWSSQ--VSSL-------SDV-----D----AHTVVIANGIDAPaLW---PGL--PIRPVKGEVLRL-RWRP-- 216
                                    *******9997..8886.......557.....2....689*********9999...999..************.5544.. PP

                                    TGSGCSEEEEE....EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCG..EEEEEEE CS
                            DAO 235 vspaailpvpe....tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgd..vlrkwaG 308
                                          +p+p+     + +gr vy++pr dg v+vG+t  +e+g d+ ++    +++ll+ + +++P+lg+  + ++ aG
  gi|121636329|ref|YP_976552.1| 217 ----GCMPLPQrvirARVRGRQVYLVPRSDG-VVVGATQ-YEHGRDT-APVVSGVRDLLDDACTVLPALGEyeLAECEAG 289
                                    ....334444444559999*********988.******9.9999999.88889***************97744779**** PP

                                    EEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHH CS
                            DAO 309 lrp.lpdglpligetpgvkglylatGhsghGltlapatGklla 350
                                    lrp +pd+lpl+++    ++ ++a+Gh+++G+ lap t++ ++
  gi|121636329|ref|YP_976552.1| 290 LRPmTPDNLPLVQRL--DSRTLVAAGHGRSGFLLAPWTAEQIV 330
                                    ***55*********5..67********************9765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   4.9e-06    0.0097       2      33 ..      10      41 ..       9      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.9e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                   +aviG G++G ++a  +a+ag +V++   +e+
  gi|121636329|ref|YP_976552.1| 10 LAVIGGGVIGLSVARRAAQAGWPVRVHRSDER 41
                                   69***********************9887765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.2e-05     0.024       2      53 ..       9      62 ..       8     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHHHCHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve..legtclnggcllskallgvaeda 53
                                   +++viGgG+ Gl++a+++aqag  v +    ++g+    g +l++  +g+++++
  gi|121636329|ref|YP_976552.1|  9 SLAVIGGGVIGLSVARRAAQAGWPVRVHRsdERGASWVAGGMLAPHSEGWPGEE 62
                                   567888888888888888887666666633255555555555555555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.8e-05     0.036      32      68 ..       3      39 ..       1      48 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                   S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                   2-Hacid_dh_C 32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68
                                   ++l+   +++iG G IG +va+r+++ g  v ++   
  gi|121636329|ref|YP_976552.1|  3 SDLHTGSLAVIGGGVIGLSVARRAAQAGWPVRVHRSD 39
                                   6788999*********************999988655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013      0.26       2      26 ..      10      34 ..       9      42 .. 0.80
   2 ?   -1.7   0.0       2.3   4.6e+03      21      35 ..     231     245 ..     228     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   EEEECSSHHHHHHHHHHHHTTSEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVt 26
                                   ++v+GgG+igl +A  +a+ g  V 
  gi|121636329|ref|YP_976552.1| 10 LAVIGGGVIGLSVARRAAQAGWPVR 34
                                   79************99988885554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                    TTSEEEEEESSSSSS CS
                      Pyr_redox  21 lgkkVtvversdkll 35 
                                     g +V++v rsd + 
  gi|121636329|ref|YP_976552.1| 231 RGRQVYLVPRSDGVV 245
                                    588999999999765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   6.3e-05      0.13      27      57 ..       6      36 ..       1      46 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                   ---EEEEESTSHHHHHHHHHHHHTT-EEEEE CS
                    AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtvl 57
                                   + +   viGgGv Gl+ ++ a++ g  V+v+
  gi|121636329|ref|YP_976552.1|  6 HTGSLAVIGGGVIGLSVARRAAQAGWPVRVH 36
                                   478899******************9999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0   0.00011      0.22       3      46 ..      11      52 ..       9      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                   EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE CS
                  FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgid 46
                                    ViG+G+ GL+ A +aa+aG  v v    ++  ga+  ++G+++
  gi|121636329|ref|YP_976552.1| 11 AVIGGGVIGLSVARRAAQAGWPVRVHRSDER--GASWVAGGMLA 52
                                   7************************999998..77777766654 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.27       2      37 ..      10      44 ..       9      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHH CS
                  NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekvee 37
                                   +++iG Gv+G + a++ ++ag+ v v+  + e+  +
  gi|121636329|ref|YP_976552.1| 10 LAVIGGGVIGLSVARRAAQAGWPVRVHRSD-ERGAS 44
                                   79***********************98644.54444 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0002      0.39       2      42 ..      10      45 ..       9      52 .. 0.83
   2 ?   -3.0   0.0       5.7   1.1e+04      61      77 ..      91     107 ..      86     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeel 42
                                   +++iG+G +g ++a+++++ag     ++ + +r+ e+ +++
  gi|121636329|ref|YP_976552.1| 10 LAVIGGGVIGLSVARRAAQAG---WPVR-V-HRSDERGASW 45
                                   79*******************...8888.4.5777766655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.7
                                    H-SEEEE-S-HHHHHHH CS
                  F420_oxidored  61 eadvvvlavkpedveev 77 
                                      + +v+av  +dv+++
  gi|121636329|ref|YP_976552.1|  91 AHESLVVAVDRADVADL 107
                                    55667777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2117.48
//
Query:       gi|121636330|ref|YP_976553.1|  [L=68]
Description: sulfur carrier protein ThiS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-12   47.8   0.2      2e-12   47.5   0.2    1.1  1  ThiS       ThiS family
     0.0031   17.5   0.0      0.004   17.2   0.0    1.2  1  ThiS-like  ThiS-like ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.2   2.3e-16     2e-12       3      77 .]       5      68 .]       2      68 .] 0.89

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.3e-16
                                   ETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB-..-TTCEEEEEESTTC- CS
                           ThiS  3 lfaelrelageeelelaegstvaelleaLgerypelalerrvavavNgeivpr.lwldtel..kdgDevailppVaGG 77
                                   ++        e+++e++e++t+a+ll++Lg+ +      r++ava+N +++pr +w+++++  ++  +++++++V+GG
  gi|121636330|ref|YP_976553.1|  5 VN--------EQQVEVDEQTTIAALLDSLGFGD------RGIAVALNFSVLPRsDWATKICelRKPVRLEVVTAVQGG 68
                                   44........45555566***************......**************99****8777**************9 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.4e-07     0.004       1      24 [.       1      24 [.       1      34 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-07
                      ThiS-like  1 MkIklNekeveveegttlealkek 24
                                   M +++Ne++vev+e+tt++al ++
  gi|121636330|ref|YP_976553.1|  1 MIVVVNEQQVEVDEQTTIAALLDS 24
                                   99****************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 459.01
//
Query:       gi|121636331|ref|YP_976554.1|  [L=252]
Description: thiazole synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.8e-107  356.9   5.1   5.4e-107  356.7   5.1    1.0  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00046   19.3   4.5      0.011   14.8   1.5    2.2  2  FMN_dh        FMN-dependent dehydrogenase
     0.0014   18.2   0.1      0.026   14.0   0.1    2.2  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.041   13.1   0.2       0.17   11.0   0.1    1.9  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
       0.15   12.3   5.3       0.35   11.1   5.3    1.6  1  HPP           HPP family
       0.89    8.5   6.4       0.15   11.0   2.4    1.6  2  IMPDH         IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.7   5.1  1.8e-110  5.4e-107       2     247 .]       8     250 ..       7     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 356.7 bits;  conditional E-value: 1.8e-110
                                    ETTEEES--EEEE-STSSSHHHHHHHHHHHT-SEEEEECCGSTTTS.TTS--CCCCCHCCTSEEEEE-TT-SSHHHHHHH CS
                           ThiG   2 iagkefksrlllGtgkykslevlkeaveasgaeivtvalrRvnleekaseeellelleekevtllPntaGaktaeeAvri 81 
                                    i++++f+srl++Gtg +++l+vl++a+ asg+e++tva+rRv+++    ++ ll+ll++ ++t lPntaG+++a+eAv +
  gi|121636331|ref|YP_976554.1|   8 IGDRSFASRLIMGTGGATNLAVLEQALIASGTELTTVAIRRVDADG---GTGLLDLLNRLGITPLPNTAGCRSAAEAVLT 84 
                                    899****************************************999...789**************************** PP

                                    HHHHHHTTS-SEEEE--BCETTTTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS---- CS
                           ThiG  82 arlarevletdliklEviadektLlPdvvetlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapiGsglGl 161
                                    a+lare+l+t+++klEviade+tL+Pd+ve+++aae+Lv++GF+vlpY++dD+vlarrle++GcaavmPl++piG+glG+
  gi|121636331|ref|YP_976554.1|  85 AQLAREALNTNWVKLEVIADERTLWPDAVELVRAAEQLVDDGFVVLPYTTDDPVLARRLEDTGCAAVMPLGSPIGTGLGI 164
                                    ******************************************************************************** PP

                                    S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH------SS CS
                           ThiG 162 lnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklaveaGrlaylagriekrev 241
                                    +n++++++i++ a+vPv++DAGig++sdaa amelG+davll++av++a+dp amA+a+++av+aG+la++agri+kr +
  gi|121636331|ref|YP_976554.1| 165 ANPHNIEMIVAGARVPVVLDAGIGTASDAALAMELGCDAVLLASAVTRAADPPAMAAAMAAAVTAGYLARCAGRIPKRFW 244
                                    ******************************************************************************** PP

                                    -XTTST CS
                           ThiG 242 asassp 247
                                    a+assp
  gi|121636331|ref|YP_976554.1| 245 AQASSP 250
                                    *****8 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0036        11      96     160 ..      79     150 ..      67     163 .. 0.75
   2 !   14.8   1.5   3.6e-06     0.011     269     303 ..     176     210 ..     164     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
                                    T-SS-HHHHHHHHTT-EEEEEE-CSSHHH....HHHHHHHHHHC...TESEEEEESSTSS---BHHHHHCT- CS
                         FMN_dh  96 vastsleevaaaaegplwfqlyvpkdrel....teellkraeaa...gykalvltvDtpvlgkRerdlrngf 160
                                    +      ++a++a ++ w++l v  d+ +    + el++ ae++   g+ +l  t+D pvl +R +d+    
  gi|121636331|ref|YP_976554.1|  79 AEAVLTAQLAREALNTNWVKLEVIADERTlwpdAVELVRAAEQLvddGFVVLPYTTDDPVLARRLEDTGCAA 150
                                    44455556666666799999999988765233367888888888888*****************99986655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.6e-06
                                    ..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 269 ggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                    g r++v++D Gi + sD++ A+ lG davll+ ++
  gi|121636331|ref|YP_976554.1| 176 GARVPVVLDAGIGTASDAALAMELGCDAVLLASAV 210
                                    34899999999999999999999999999998665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.048   1.4e+02      96     128 ..      14      46 ..       5      60 .. 0.88
   2 !   14.0   0.1   8.8e-06     0.026      63     107 ..     168     212 ..     159     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.048
                                    -SEEEESHHHHH-THHHHHHHHHHCGGGEEEEE CS
                   His_biosynth  96 adkviigtaavknpelikelaekfgsqkivvai 128
                                    a+++i+gt  ++n  ++++++ + g +  +vai
  gi|121636331|ref|YP_976554.1|  14 ASRLIMGTGGATNLAVLEQALIASGTELTTVAI 46 
                                    899*******************99999999998 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.8e-06
                                    HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                   His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                    + +e i+   ++pv ++ GI + +d++ ++e+g+d v +++a+ +
  gi|121636331|ref|YP_976554.1| 168 HNIEMIVAGARVPVVLDAGIGTASDAALAMELGCDAVLLASAVTR 212
                                    557778888889999999999999999999999999999998543 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2     6e+02     139     176 ..     121     158 ..     102     172 .. 0.72
   2 ?   11.0   0.1   5.8e-05      0.17     143     180 ..     177     214 ..     166     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                                    HHHHTT--EEEES---SHHHHHHHHTT--SEEE.E-HHH CS
                           NanE 139 alseaglkviaeGrintPekakkaieiGvdavv.vGsai 176
                                    +l+++g+ v+     + P +a++  ++G +av+ +Gs i
  gi|121636331|ref|YP_976554.1| 121 QLVDDGFVVLP-YTTDDPVLARRLEDTGCAAVMpLGSPI 158
                                    56666655544.456889999999999988875367666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.8e-05
                                    TT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                           NanE 143 aglkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                    a + v+ +  i t   a+ a+e+G dav + sa+tr +
  gi|121636331|ref|YP_976554.1| 177 ARVPVVLDAGIGTASDAALAMELGCDAVLLASAVTRAA 214
                                    67789999999*************************76 PP

>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.3   0.00012      0.35      46      85 ..     189     229 ..     155     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                            HPP  46 l.sllwlaaalavalaialmlltrtlhPPagAtaliavlgk 85 
                                      s + la+ l++ + +++ ++tr+  PPa+A a+ a++++
  gi|121636331|ref|YP_976554.1| 189 TaSDAALAMELGCDAVLLASAVTRAADPPAMAAAMAAAVTA 229
                                    3445567999999***********************99976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.42   1.2e+03     182     215 ..      15      54 ..       8      57 .. 0.72
   2 ?   11.0   2.4     5e-05      0.15     202     250 ..     173     221 ..     155     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.42
                                    HHHHCSB---HHHHHHHHHHHHCTCT......-EEEEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx RF
                          IMPDH 182 trvvagvGvpqltAvaevaeaakkag......vpviaDGG 215
                                     r ++g+G +   Av+e a +a+ ++       +v aDGG
  gi|121636331|ref|YP_976554.1|  15 SRLIMGTGGATNLAVLEQALIASGTElttvaiRRVDADGG 54 
                                    5889999999999999999888888744433334456766 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5e-05
                                    HHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 202 aakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevi 250
                                    +++ a vpv+ D Gi +  d + A+ +G dav+l s +++  + p+   
  gi|121636331|ref|YP_976554.1| 173 IVAGARVPVVLDAGIGTASDAALAMELGCDAVLLASAVTRAADPPAMAA 221
                                    455678*******************************999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1653.65
//
Query:       gi|121636332|ref|YP_976555.1|  [L=500]
Description: lipoprotein aminopeptidase lpqL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-47  160.8   0.0    4.3e-47  160.4   0.0    1.2  1  Peptidase_M28  Peptidase family M28
    3.9e-13   49.2   0.8    1.2e-12   47.7   0.8    1.9  1  PA             PA domain
    1.9e-06   27.7   0.0    3.2e-06   27.0   0.0    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0057   15.7   0.0      0.044   12.8   0.0    2.1  2  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
       0.04   13.4   0.0       0.07   12.6   0.0    1.4  1  Nicastrin      Nicastrin


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.0   1.2e-50   4.3e-47       1     196 [.     252     471 ..     252     473 .. 0.95

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 1.2e-50
                                    EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHH CS
                  Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSka 80 
                                    Nvia+++ +++++v++ gAH+Dsv++  gp   G++Dn+sgvaa+Le+a +l +s+ +  + vrf+f++aEE+gl+GS++
  gi|121636332|ref|YP_976555.1| 252 NVIAQTKTGSSANVVMAGAHLDSVPE--GP---GINDNGSGVAAVLETAVQLGNSP-HVSNAVRFAFWGAEEFGLIGSRN 325
                                    9******9998**************9..**...*********************88.99********************* PP

                                    HHH..HHCCCTTEEEEEEECS-SSSS--EEE..............HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESS CS
                  Peptidase_M28  81 fak..akpelkkiaavlnlDmvgsggkellf..............esgdkssselekelkalakpvgraaaedpfdersg 144
                                    +++  + ++lk ia++ln+Dm++s+++ +++               + +++s+++e+++ a+ k++g++      +++s+
  gi|121636332|ref|YP_976555.1| 326 YVEslDIDALKGIALYLNFDMLASPNPGYFTydgdqslpldargqPVVPEGSAGIERTFVAYLKMAGKT-----AQDTSF 400
                                    **865555************************************9999*******************96.....578899 PP

                                    TT-STTHHHHTTT--EEEE...................CTSSS-TTTTSTTSSGGGB-HHHHHHHHHHHHH CS
                  Peptidase_M28 145 rgrsDhspflkagvpvldl...................aetgfpevyHtprDtldnidkdtlariaelvle 196
                                    +grsD+  f+ ag+p   l                   a+++f+++yH++ Dtld+id ++l+ ++  v++
  gi|121636332|ref|YP_976555.1| 401 DGRSDYDGFTLAGIPSGGLfsgaevkksaeqaelwggtADEPFDPNYHQKTDTLDHIDRTALGINGAGVAY 471
                                    *************************************************************9998888776 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.8   3.3e-16   1.2e-12       1      88 [.     140     229 ..     140     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.3e-16
                             PA   1 vtgplVy.....s..cfagygisadfegvdvkGkivLvqr...tfaeKarnAqaaGAagviivndgelgaatgasgnege 70 
                                    vtgplV+     s  c+ +++     ++ +v+G +vLv+r    fa+K  +A++ GA+++ii+++    ++ + +g+ g 
  gi|121636332|ref|YP_976555.1| 140 VTGPLVAapaddSpgCSPSDY-----DRLPVSGAVVLVDRgvcPFAQKEDAAAQRGAVALIIADNI---DEQAMGGTLGA 211
                                    89****887765257866666.....3569*********999999******************543...44455556667 PP

                             PA  71 pdgitiPavgvsredgea 88 
                                    ++++ iP+v+v++++g +
  gi|121636332|ref|YP_976555.1| 212 NTDVKIPVVSVTKSVGFQ 229
                                    778***********9965 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   8.8e-10   3.2e-06       3      94 ..     269     335 ..     267     433 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.8e-10
                                    EEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20   3 gsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakall 82 
                                    g+HlD+Vp                     G+G +d+  gv+a+le + +l  + +     ++++f+++EE g  G+++++
  gi|121636332|ref|YP_976555.1| 269 GAHLDSVP-----------------E---GPGINDNGSGVAAVLETAVQLGNSPHV-SNAVRFAFWGAEEFGLIGSRNYV 327
                                    79999999.................1...59********************99765.79***********877******* PP

                                    HHHHTTTCESEE CS
                                    xxxxxxxxxxxx RF
                  Peptidase_M20  83 egleerekvdav 94 
                                    e+l     +da+
  gi|121636332|ref|YP_976555.1| 328 ESLD----IDAL 335
                                    *544....4443 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12   4.1e+02       2      25 ..     252     275 ..     252     276 .. 0.86
   2 !   12.8   0.0   1.2e-05     0.044     134     185 ..     283     335 ..     281     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                    -EEEEEESSTTSSEEEEEEE--B- CS
                  Peptidase_M42   2 nliakkkgkekepkvmiaAHmDei 25 
                                    n+ia+ k  +++  vm  AH+D +
  gi|121636332|ref|YP_976555.1| 252 NVIAQTKTGSSANVVMAGAHLDSV 275
                                    78888777799999********87 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHCTSS-S.SEEEEEEESTCTTTSHHHHHHHHHH--SEE CS
                  Peptidase_M42 134 Ddragvavllellkelkeeele.atvylvatvqEEvGlrGaktsaekikpdia 185
                                    D+  gva++le++ +l ++ +  + v +++   EE Gl G+++ +e++++d++
  gi|121636332|ref|YP_976555.1| 283 DNGSGVAAVLETAVQLGNSPHVsNAVRFAFWGAEEFGLIGSRNYVESLDIDAL 335
                                    9999********99998887666*************************99986 PP

>> Nicastrin  Nicastrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.07       2      77 ..     265     332 ..     264     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                      Nicastrin   2 vvlvtarlDsasmfddvslGaessvsslvallaaaealskllkdisnlkrnvlFvffnGEsydYiGSqrfvydlek 77 
                                    vv++ a lDs       ++G ++  s+++a+l  a  l +  + +sn    v F+f+  E ++ iGS+  v  l+ 
  gi|121636332|ref|YP_976555.1| 265 VVMAGAHLDSV----PEGPGINDNGSGVAAVLETAVQLGNS-PHVSNA---VRFAFWGAEEFGLIGSRNYVESLDI 332
                                    56777777775....3689999999*************999.889998...99******************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3600.98
//
Query:       gi|121636333|ref|YP_976556.1|  [L=498]
Description: lipoprotein peptidase lpqM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00016   21.2   2.6     0.0073   15.8   0.4    3.7  3  Zn_peptidase  Putative neutral zinc metallopeptidase


Domain annotation for each model (and alignments):
>> Zn_peptidase  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4     4e-07    0.0073      72     285 ..      75     278 ..      25     282 .. 0.66
   2 ?    0.2   0.0     0.023   4.1e+02     127     160 ..     343     376 ..     338     386 .. 0.79
   3 ?   -0.5   0.0     0.038   6.8e+02     226     264 ..     440     476 ..     416     480 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-07
                   Zn_peptidase  72 aqssegtaeeaedeqkefvsvvladtedtWtqifkek.gktyqk.pklvlfsrvvrsa...CGt.assatGPfyCPadrk 145
                                    a s ++ +++ + +  +++   + d ed+W  ++ e+ + t++   klv +  +  s+   C   +   +  f+    + 
  gi|121636333|ref|YP_976556.1|  75 AASGTVINTN-NGAIDKLSLLSVNDIEDYWMAVYSESlKGTFRPvGKLVSYDSNDPSSpivCHIdTYQLVNAFFSSRCNL 153
                                    3344444444.777778888888999999999998651445543257999977655532336651345678899999999 PP

                   Zn_peptidase 146 vyldlsffdelkqklgaaGdfaaayviahevGhhvqnllGilekveqarqgaseaeanqlsvrleLqadcfaGv...W.a 221
                                    +  d   f  + q++   Gd+++  v+ahe Gh +q +  ++    + +           ++  e qadcfaGv   W a
  gi|121636333|ref|YP_976556.1| 154 IAWDRGVFMAVAQEY--FGDMSVNGVLAHEFGHALQVMANLV----TRKD---------PTIVREQQADCFAGVylwWvA 218
                                    999999999999998..599*************999544433....2222.........2344589*******9553323 PP

                   Zn_peptidase 222 nsvqqkgllekgd.ieealnaakaiGddtLqkqsqgrvvPdsfthGtsqqrqrWfkrGfesGdla 285
                                    +  + +++l + d +++ l+      d  ++ +++         hG++  r++ f+ Gf +G +a
  gi|121636333|ref|YP_976556.1| 219 EGKSTRFTLSTADgLDHVLAGIITTRDPVMEADAEN-----DDEHGSALDRVSAFQLGFINGTPA 278
                                    333444577776635666665555555555555543.....347888888888888888888765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.023
                   Zn_peptidase 127 aCGtassatGPfyCPadrkvyldlsffdelkqkl 160
                                    +C  a+ +    yCPa +++ +dl    ++ +  
  gi|121636333|ref|YP_976556.1| 343 GCPDAKPSPPAAYCPATNTIVVDLPALARMGKVA 376
                                    577777777778***********98887776655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.038
                   Zn_peptidase 226 qkgllekgdieealnaakaiGddtLqkqsqgrvvPdsft 264
                                    q+ +l+ gd++ea++    + +  ++ ++ g  vP  ft
  gi|121636333|ref|YP_976556.1| 440 QQLVLTAGDLDEAVSG--LLTNRMVASDADGVSVPAGFT 476
                                    5679*********986..466777888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3493.98
//
Query:       gi|121636334|ref|YP_976557.1|  [L=136]
Description: hypothetical protein BCG_0459c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.043   13.6   0.0      0.047   13.4   0.0    1.0  1  7tm_3            7 transmembrane sweet-taste receptor of 3 GC
      0.045   13.5   1.3       0.29   10.9   0.2    2.2  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


Domain annotation for each model (and alignments):
>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-06     0.047      89     168 ..      20     120 ..       1     127 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-06
                          7tm_3  89 kskslrdkqllllvlllvlvqviillvwtlidplstrek.................see........ereevileCss.s 142
                                    ++  + + q+++ + +l+l+ + ++++w  +  ++   +                 + +        +++  + +C++  
  gi|121636334|ref|YP_976557.1|  20 HGEAVNRRQMFIGITGLLLAVIGLMALWFPVYLDQ---YdaygikvtcgsgwrsnlT-QalyadgndNTQALVTRCDTaL 95 
                                    45667779********************6554333...2335777777777655551.0566666777788889994446 PP

                          7tm_3 143 sysdiffllllgykglllllgtflaf 168
                                       +++ + +++  g ll+ g+++ +
  gi|121636334|ref|YP_976557.1|  96 LVRRAWAIPSVA-LGWLLVTGFLVMW 120
                                    788899555555.8999999999877 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   3.2e-05      0.29      34      52 ..      30      48 ..      21      53 .. 0.92
   2 ?    1.1   0.1     0.037   3.4e+02      44      53 ..     113     122 ..     102     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                Phage_holin_2_4 34 lialvGlavAliGlLvnWy 52
                                   +i++ Gl++A+iGl+  W+
  gi|121636334|ref|YP_976557.1| 30 FIGITGLLLAVIGLMALWF 48
                                   89**************997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.037
                Phage_holin_2_4  44 liGlLvnWyY 53 
                                    + G+Lv W  
  gi|121636334|ref|YP_976557.1| 113 VTGFLVMWVH 122
                                    789*****65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1055.31
//
Query:       gi|121636335|ref|YP_976558.1|  [L=209]
Description: hypothetical protein BCG_0460c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-05   24.1   0.2        0.4    9.9   0.0    3.0  3  Hydrolase_4    Serine aminopeptidase, S33
     0.0011   19.6   9.0      0.012   16.2   9.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0033   17.2   0.0     0.0059   16.4   0.0    1.4  1  Abhydrolase_5  Alpha/beta hydrolase family
     0.0079   15.8   0.0       0.56    9.7   0.0    2.0  1  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.029   14.0   0.1      0.046   13.4   0.1    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00056         2       2      37 ..      16      53 ..      15      56 .. 0.84
   2 ?    3.4   0.1     0.011        38      75     107 ..      89     121 ..      72     136 .. 0.75
   3 !    9.9   0.0   0.00011       0.4     186     234 ..     138     185 ..     133     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00056
                    Hydrolase_4  2 epkavvvlvHGla..ehsgryaelaeaLaaqGfavyal 37
                                   +p++vvvl HG +    s   ++++++++++G+  + +
  gi|121636335|ref|YP_976558.1| 16 PPHGVVVLTHGAGgsRESTLLQQVCAEWTRRGWLAVRY 53
                                   799*******98822468999***********988877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                    Hydrolase_4  75 elplfllGhSmGGliallyllrypdkvaglils 107
                                    e pl+  GhS GG  +  +++  ++ v+ l l+
  gi|121636335|ref|YP_976558.1|  89 EGPLIAGGHSYGGRQTSMVVAAGQAPVDVLTLF 121
                                    4599*********99998888777777766665 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00011
                    Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHel 234
                                    + + i +P+ + hG+aD+    ++ r +++ ++ +  ++  + g++H+l
  gi|121636335|ref|YP_976558.1| 138 HLPGIAVPTVFTHGTADPFGTLAQVRSAAAMVS-APTEVVEITGARHDL 185
                                    556789***************777777776666.5999*********97 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   9.0   3.4e-06     0.012       1     104 [.      21     148 ..      21     197 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                                    EEEE--GC.....GCHHHHHHHHCCT...CEEEEE--TTS.TS-GGCS--HHH.....CHHHHHHHCCTT..TTSEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaag...vhvlapDlpGh.Grsdpppldled.....ladlaalldelaagggpvvlvG 71 
                                    v+l HGag+s++s l  ++ a  +++      + + lp    r+++pp +        +++  +l ++la   gp ++ G
  gi|121636335|ref|YP_976558.1|  21 VVLTHGAGGSRESTLLQQVCAEWTRRgwlA--VRYNLPYRrRRPTGPPSGSGSgdragIVEAIQLCRGLA--EGPLIAGG 96 
                                    89********88886678877777778653..34666655334555554444422223355566777776..8889**** PP

                                    ETCHHHHHHH..HHHCC..EE.EEES-..................----TTT CS
                  Abhydrolase_6  72 HSlGGalala..aaplalvvg.vlldppp................talpagl 104
                                    HS+GG   ++  aa +a+v    l + p+                 a+p+ +
  gi|121636335|ref|YP_976558.1|  97 HSYGGRQTSMvvAAGQAPVDVlTLFSYPVhppgkpervrtehlpgIAVPTVF 148
                                    *****97777444445544443666652232122222222222222222222 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-06    0.0059      59     140 ..      92     183 ..      78     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                  Abhydrolase_5  59 fvvgGhslGGvvasrfaaeeekiegvvflasYPe....k.delselskk.....vlsivgteDgvlnvkslekakkflpk 128
                                    ++ gGhs GG  +s ++a  +    v+ l sYP     k + + ++  +     ++   gt D   +  +++ a+ +++ 
  gi|121636335|ref|YP_976558.1|  92 LIAGGHSYGGRQTSMVVAAGQAPVDVLTLFSYPVhppgKpERVRTEHLPgiavpTVFTHGTADPFGTLAQVRSAAAMVSA 171
                                    5779************9998866678889999963222122333333332222277789********************* PP

                  Abhydrolase_5 129 dtkvvsieGgnh 140
                                     t+vv+i G  h
  gi|121636335|ref|YP_976558.1| 172 PTEVVEITGARH 183
                                    *********999 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00016      0.56      88     169 ..      80     168 ..       6     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                            DLH  88 ylksvpevstkkvgvvGfCmGGa.lalllaaevpevdaavaf.YG.....lspekeleeaakikapilalfgeeDefipa 160
                                    +++ ++   ++ + + G   GG+  ++++aa ++ vd    f Y+     +    + e+ + i++p ++ +g++D+f + 
  gi|121636335|ref|YP_976558.1|  80 AIQLCRGLAEGPLIAGGHSYGGRqTSMVVAAGQAPVDVLTLFsYPvhppgKPERVRTEHLPGIAVPTVFTHGTADPFGTL 159
                                    34444444455566667777876245667777766776555547755553333345566778899999999999999888 PP

                            DLH 161 devekleea 169
                                    ++v   +  
  gi|121636335|ref|YP_976558.1| 160 AQVRSAAAM 168
                                    875544443 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.046       2     109 ..      20     127 ..      19     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH..HHHCTTSSEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri..ldalgddkltlvG 79 
                                    v+v+ hG +gs ++   + +     ++g+  + ++l+   + +++p    +  g  + a ++++i  +  l  ++l+  G
  gi|121636335|ref|YP_976558.1|  20 VVVLTHGAGGSRESTLLQQVCAEWTRRGWLAVRYNLPYRRRRPTGPP---SGSGSGDRAGIVEAIqlCRGLAEGPLIAGG 96 
                                    78888888888876333334444445588888888888888888887...555888899999966669999********* PP

                                    ETHHHHHHHHHHHHHGGGEEEEEEESE.CSS CS
                  Abhydrolase_1  80 hSmGGmialayaaeyperVkalvllga.idp 109
                                    hS+GG++ +++ a  + +V+ l+l +  ++p
  gi|121636335|ref|YP_976558.1|  97 HSYGGRQTSMVVAAGQAPVDVLTLFSYpVHP 127
                                    ************9999999999888874333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1533.29
//
Query:       gi|121636336|ref|YP_976559.1|  [L=265]
Description: phosphomethylpyrimidine kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-87  292.6   0.0    2.3e-87  292.5   0.0    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    3.7e-11   42.9   0.0    5.9e-11   42.2   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.5   0.0   2.5e-91   2.3e-87       1     245 [.      13     258 ..      13     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 292.5 bits;  conditional E-value: 2.5e-91
                                    ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHH CS
                   Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvae 80 
                                    Ds+GGAGiqAD++t++ lgv+++ ++ta+t+qnt gvk++h++p+++v+ q+eav++d++v+a+K+Gmlas+ i+++va+
  gi|121636336|ref|YP_976559.1|  13 DSGGGAGIQADMRTMALLGVHACVAVTAVTVQNTLGVKDIHEVPNDVVAGQIEAVVTDIGVQAAKTGMLASSRIVATVAA 92 
                                    9******************************************************************************* PP

                                    HHHH..TTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SE CS
                   Phos_pyr_kin  81 klkk..ykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgaka 158
                                    ++++   +vp+V+DPV+++ +g++ll+++a+++l+ +L+plat++tPNl+Ea+ L++ ++ ++e+ ++aak+l++lg ++
  gi|121636336|ref|YP_976559.1|  93 TWRRleLSVPLVVDPVCASMHGDPLLAPSALDSLRGQLFPLATLLTPNLDEARLLVDIEVVDAESQRAAAKALHALGPQW 172
                                    **7734555*********************************************************************** PP

                                    EEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BS CS
                   Phos_pyr_kin 159 VlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealel 238
                                    Vl+kGghl++++    d+lydg ++++++a+r++t + hG G+tl++aiaa la+g ++++Av+ +k++vte++++a+ l
  gi|121636336|ref|YP_976559.1| 173 VLVKGGHLRSSDGS-CDLLYDGVSCYQFDAQRLPTGDDHGGGDTLATAIAAALAHGFTVPDAVDFGKRWVTECLRAAYPL 251
                                    ********665554.8**************************************************************** PP

                                    TSSS-B- CS
                   Phos_pyr_kin 239 gkgagpv 245
                                    g+g+gpv
  gi|121636336|ref|YP_976559.1| 252 GRGHGPV 258
                                    ******8 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   6.6e-15   5.9e-11     166     283 ..     119     238 ..     107     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 6.6e-15
                                    CESSSHHHHHHHH.HHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG....GGEE..EEEETT CS
                           PfkB 166 ldplgaqfkeall.ellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG....keGa..lvvekd 238
                                     +++     + l+ +l++la+ll+pn +E++ l++ + +d e+  aa+++l+a g+++v+v+ G    ++G+  l+++++
  gi|121636336|ref|YP_976559.1| 119 APSAL----DSLRgQLFPLATLLTPNLDEARLLVDIEVVDAESQRAAAKALHALGPQWVLVKGGhlrsSDGScdLLYDGV 194
                                    33333....34441677*********************************************7633336777555677** PP

                                    EEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                           PfkB 239 gelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfan 283
                                      ++++a +     D  G GD+ + +++aal++g ++ +a+ f+ 
  gi|121636336|ref|YP_976559.1| 195 SCYQFDA-QRLPTGDDHGGGDTLATAIAAALAHGFTVPDAVDFGK 238
                                    *******.89*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2001.41
//
Query:       gi|121636337|ref|YP_976560.1|  [L=547]
Description: thiamine biosynthesis protein ThiC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.8e-199  660.7   0.0   9.4e-199  660.4   0.0    1.1  1  ThiC_Rad_SAM     Radical SAM ThiC family
    1.4e-09   37.6   0.1      5e-09   35.9   0.1    1.9  1  ThiC-associated  ThiC-associated domain


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  660.4   0.0  1.1e-202  9.4e-199       1     417 [.      82     502 ..      82     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 660.4 bits;  conditional E-value: 1.1e-202
                   ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdieeEve 79 
                                    tql++ar+g+it em+++a++e++++e vr+eva+Gr+vipan++h+e+ p++iGk + +kvnaniG+sa +s+i+eEv+
  gi|121636337|ref|YP_976560.1|  82 TQLQRARAGEITAEMAFIAAREDMSAELVRDEVARGRAVIPANHHHPESePMIIGKAFAVKVNANIGNSAVTSSIAEEVD 161
                                    89********************************************7777****************************** PP

                   ThiC_Rad_SAM  80 KlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdfltiHa 159
                                    K+ +a+++gadt+mdLstg++i+e+re+il++spvpvgtvpiYqale+++++ +elt+e +++++ eq+e+Gvd++t+Ha
  gi|121636337|ref|YP_976560.1| 162 KMVWATRWGADTIMDLSTGKNIHETREWILRNSPVPVGTVPIYQALEKVKGDPTELTWEIYRDTVIEQCEQGVDYMTVHA 241
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 160 gvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlae 239
                                    gv l++++l++  kR+tgivSrgGs++aaw+la+++e++ly++f+el++i+++ydvt+SlgdglRpGsiaDa+d+aq+ae
  gi|121636337|ref|YP_976560.1| 242 GVLLRYVPLTA--KRVTGIVSRGGSIMAAWCLAHHRESFLYTNFEELCDIFARYDVTFSLGDGLRPGSIADANDAAQFAE 319
                                    ***********..******************************************************************* PP

                   ThiC_Rad_SAM 240 livlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadl 319
                                    l +lgel+k a+++g qvm+eGPGH+p+++i +nv+l+++lc+eaPfy+lGpl+tDiap+YDhitsaiGaa++a+aG+++
  gi|121636337|ref|YP_976560.1| 320 LRTLGELTKIAKAHGAQVMIEGPGHIPMHKIVENVRLEEELCEEAPFYTLGPLATDIAPAYDHITSAIGAAIIAQAGTAM 399
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 320 lCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireeklpe 399
                                    lCyvtp+EHlglPd++dvk+Gvia+kiaahaadlakg+++a+erd+als+aR+e++w++qf+l+ldp++are+++e+lp+
  gi|121636337|ref|YP_976560.1| 400 LCYVTPKEHLGLPDRKDVKDGVIAYKIAAHAADLAKGHPRAQERDDALSTARFEFRWNDQFALSLDPDTAREFHDETLPA 479
                                    *****************************************************************************998 PP

                   ThiC_Rad_SAM 400 ....eeeaCsmCgek.Cavkive 417
                                        ++++CsmCg+k C+++i++
  gi|121636337|ref|YP_976560.1| 480 epakTAHFCSMCGPKfCSMRITQ 502
                                    788899********99****997 PP

>> ThiC-associated  ThiC-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   5.5e-13     5e-09       6      68 ..      18      72 ..      13      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.5e-13
                                   EEEEEE....-SSTT-EEEEEEE---GG.........G----EEEE---GGGG-TTS---TTT-S-- CS
                ThiC-associated  6 rkvyve....gsrpdirVpmreiklsptvlketkekeeenepvrvYDtSGpYtdpeveidvrkGLpr 68
                                    k y e    gs   ++Vp+r+++ls              + + +YDtSGpYtd ++ id+++GLp+
  gi|121636337|ref|YP_976560.1| 18 AKAYREieapGSGATLQVPFRRVHLSTG------------DHFDLYDTSGPYTDTDTVIDLTAGLPH 72
                                   55554433339999************99............5799*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4212.21
//
Query:       gi|121636338|ref|YP_976561.1|  [L=91]
Description: hypothetical protein BCG_0463c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 700.86
//
Query:       gi|121636339|ref|YP_976562.1|  [L=1539]
Description: metal cation transporting P-type atpase ctpH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-45  152.9   4.6    1.6e-44  151.6   0.5    3.2  2  E1-E2_ATPase     E1-E2 ATPase
    3.2e-22   79.9   5.1    1.9e-21   77.3   3.3    2.8  2  Hydrolase        haloacid dehalogenase-like hydrolase
    8.4e-16   58.2   2.7    1.7e-15   57.2   2.7    1.5  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
      0.008   16.2   0.0      0.017   15.2   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
     0.0083   16.5   0.0      0.047   14.1   0.0    2.4  2  HMA              Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.016   15.0   7.5      0.029   14.2   0.5    3.6  2  DUF742           Protein of unknown function (DUF742)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.5   5.4e-48   1.6e-44       7     179 ..     754     941 ..     748     943 .. 0.93
   2 ?    1.0   0.3     0.086   2.6e+02      35      65 ..    1255    1296 ..    1223    1405 .. 0.54

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 5.4e-48
                                    EEEE..-TT..S-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-...........G-TTEE CS
                   E1-E2_ATPase   7 akvi..rdg..teeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek...........ekgdmv 70 
                                     kv+   d+  ++ e++a+el+pGDi++++++++vpaD+r++e+ + evdesaLTGEsl v+k           e+++m+
  gi|121636339|ref|YP_976562.1| 754 RKVLagADDqpRYIEVRAEELRPGDIIEVRTHEVVPADARVIEEVDvEVDESALTGESLSVTKqveptpgvdliERRCML 833
                                    455544222346788***************************************************************** PP

                                    -TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHH CS
                   E1-E2_ATPase  71 fsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallr 150
                                    ++Gt+vvsg+a+avVta+g dt+  ++a+lv+    +   lq++l++l+++ +pv+++ ++lv  + ll++++l++a+ +
  gi|121636339|ref|YP_976562.1| 834 YAGTTVVSGTAVAVVTAVGPDTQERRAAELVSGD-LSSVGLQHQLSRLTNQAWPVSMTGGALVTGLGLLRRRGLRQAVAS 912
                                    *********************************9.88999**************************************** PP

                                    HHHHHHHHS-TTHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 151 alallvaaiPcaLplavplalalgarrla 179
                                    ++a+ vaa+P+++pl+++la  ++arrl+
  gi|121636339|ref|YP_976562.1| 913 GIAVTVAAVPEGMPLVATLAQQASARRLS 941
                                    ***************************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.086
                                     -B--SEEEEEEE-S.EEE-TTTS---S-EE-..........G CS
                   E1-E2_ATPase   35 drvpaDgrivegsa.evdesaLTGEslpvek..........e 65  
                                      rv+aD ++v+g   ++  ++L G +l+ ++          +
  gi|121636339|ref|YP_976562.1| 1255 ARVAADLVLVDGRIeSLLPAILEGRQLWQRVqaavsvllggN 1296
                                     567777777777776777777777776666633333333332 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.16   4.9e+02     122     144 ..     494     516 ..     422     530 .. 0.84
   2 !   77.3   3.3   6.4e-25   1.9e-21       2     209 ..     960    1241 ..     959    1242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
                                    THHHHHHHHHHTTEEEEEEESSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 122 eaaeavasLkaagievvlltgdn 144
                                     +a ava+L++ag  v++l++  
  gi|121636339|ref|YP_976562.1| 494 ALARAVAELRQAGRTVAVLSSVG 516
                                    34599999999999888888433 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 6.4e-25
                                     SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH..........HHCHHHHHHHHHHHHHHHHHHHHHHETTTE.. CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      Hydrolase    2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg..........sehpigkalvaaakarsgaltgfatfigrg.. 67  
                                     + v+fDk+GTL + + +v +v + a  ++ ++l+ +            h    a+v aa a   + t+ a+ +g    
  gi|121636339|ref|YP_976562.1|  960 DMVCFDKTGTLSENRLRVAQVRPVAGHSREEVLRCAahaapasngpQVHATDVAIVQAAAAAAASGTDGAE-PGAAep 1036
                                     789**********************9999999999998888888898888888887777777444444444.222234 PP

                                     ....................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH.................... CS
                                     ....................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.................... RF
                      Hydrolase   68 ....................ayaigkpewltal..dippdlgaaigsaqsqgrtvall.................... 103 
                                                            +g pe + a    i + +++a+ ++ + g  v+ +                    
  gi|121636339|ref|YP_976562.1| 1037 aahlpfrsgrsfsasvsgteLTVKGAPEVVLAAceGIGSSMDDAVAELAANGLRVIAVahrqltaqqaqsvvddpdei 1114
                                     44455555667888888888999999999999999999999999999999999999999******************* PP

                                     ......TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.........GGGE.SEEEE CS
                                     ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxx.xxxxx RF
                      Hydrolase  104 ......qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.........ddyf.davia 165 
                                           +  +++ + ++d+  ++  aa ++a L++  +++ l+tgd+p ta ++a++lG           +  da   
  gi|121636339|ref|YP_976562.1| 1115 arlcrdELSLVGFLGLSDT--PRAQAAALLADLHEHDLDIRLITGDHPITAAAIAEELGmqvspeqviSGAEwDALSR 1190
                                     *9999988***********..**************************************9999988874444355555 PP

                                     HHCES.......STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                     xxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  166 sdiet.......vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209 
                                     +d e        +a   pe kv++++ L  +++ +amVGDg nDaaa++aA
  gi|121636339|ref|YP_976562.1| 1191 KDQERavaerviFARMTPENKVQIVQTLEHSGRVCAMVGDGSNDAAAIRAA 1241
                                     5555598888899999*************99999***************99 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   2.7   5.8e-19   1.7e-15       2     177 ..    1313    1461 ..    1312    1466 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 5.8e-19
                Cation_ATPase_C    2 lplsaiqiLwinLvtDllpalaLaleppekdim..krpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77  
                                     +pl++ q+L++n++tD lpa aLa+ +p++ +   +r P        +++++r ++i g+++a+++ +++  +   f 
  gi|121636339|ref|YP_976562.1| 1313 SPLNTRQLLLVNMLTDALPAAALAVSKPSDPVTpaTRGPD-------QRELWRAVGIRGATTAAAATVAWVMAG--FT 1381
                                     8***************************866641244555.......79999999***************4444..44 PP

                Cation_ATPase_C   78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155 
                                       + +       a+t+a+++lv +q+ ++l+  +              +l++l +l+sl+ +++++ +p++ +++g++
  gi|121636339|ref|YP_976562.1| 1382 GLPRR-------ASTVALVALVAAQLGQTLVDSH-------------AWLVVLTALGSLAALATLISIPVVSQLLGCT 1439
                                     44434.......******************9988.............699**************************** PP

                Cation_ATPase_C  156 plsleewlialllalvvllvde 177 
                                     pl++  w+ a + a + ++ + 
  gi|121636339|ref|YP_976562.1| 1440 PLDPLGWAQATAAATAATVAVA 1461
                                     *******877776666665554 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.7e-06     0.017      23      89 ..    1009    1071 ..    1005    1073 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                  Cation_ATPase   23 ktEsALlvlaekl..gldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCt 89  
                                     +t++A++++a+++  +          +  +++pF s r + ++v  +e      l+vKGApe++l+ C+
  gi|121636339|ref|YP_976562.1| 1009 ATDVAIVQAAAAAaaSGTDGAEPGAAEPAAHLPFRSGRSFSASVSGTE------LTVKGAPEVVLAACE 1071
                                     6888888888877543333334455677899************98876......**************7 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.6e-05     0.047      16      59 ..      93     136 ..      90     139 .. 0.91
   2 ?   -3.1   0.0       3.9   1.2e+04      19      41 ..    1066    1092 ..    1057    1099 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                            HMA  16 vekvLselpgVesvkvdlatktvtVegdaestklrkiieaieka 59 
                                    v  +++++pgV s+++++  ++v+V  d+++t+lr++ + +++a
  gi|121636339|ref|YP_976562.1|  93 VLNAIQAHPGVGSASLNYPLSRVVVAIDDPDTSLRELCRIVDDA 136
                                    7899*******************************998888776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                            HMA   19 vLselpgV....esvkvdlatktvtVe 41  
                                     vL++++g+    ++++  la++ + V 
  gi|121636339|ref|YP_976562.1| 1066 VLAACEGIgssmDDAVAELAANGLRVI 1092
                                     688888887777777777777777776 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   9.8e-06     0.029      22      84 ..    1088    1150 ..    1078    1172 .. 0.84
   2 ?    1.9   1.4     0.061   1.8e+02      18     110 ..    1385    1469 ..    1372    1472 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                         DUF742   22 dldletlvvaeagapeaarlqpehrailrLcreplsVaelaAelklPvgvvrvLlsdLldagl 84  
                                      l+++++ +++  a +a+++ ++  +i rLcr+ ls +   +  + P + +  Ll+dL++ +l
  gi|121636339|ref|YP_976562.1| 1088 GLRVIAVAHRQLTAQQAQSVVDDPDEIARLCRDELSLVGFLGLSDTPRAQAAALLADLHEHDL 1150
                                     578888888888666699****************************************98774 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.061
                         DUF742   18 rpeedldletlvvaeagapeaarlqpehrailrLcreplsVaelaAelklPvgvvrvLls..dLldaglltvrapvtd 93  
                                     r +++++l++lv a+ g    ++l + h+ ++ L++   s a la  +++Pv  v  Ll+   L   g  ++ a++t 
  gi|121636339|ref|YP_976562.1| 1385 RRASTVALVALVAAQLG----QTLVDSHAWLVVLTA-LGSLAALATLISIPV--VSQLLGctPLDPLGWAQATAAAT- 1454
                                     5555899*******998....458999999998875.7899*********97..44444311344444444444443. PP

                         DUF742   94 raaeqpdrelLeevlsG 110 
                                       a++   ++L++vl G
  gi|121636339|ref|YP_976562.1| 1455 --AATVAVAVLNRVLTG 1469
                                     ..345566666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.85u 0.31s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 9797.51
//
Query:       gi|121636340|ref|YP_976563.1|  [L=147]
Description: hypothetical protein BCG_0465c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1042.02
//
Query:       gi|121636341|ref|YP_976564.1|  [L=291]
Description: exodeoxyribonuclease III protein xthA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-21   76.4   1.9    2.9e-21   76.1   1.9    1.1  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
       0.17   11.3   0.0       0.32   10.5   0.0    1.4  1  Msg2_C         Major surface glycoprotein 2 C terminal


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   1.9   3.2e-25   2.9e-21       1     233 []      27     281 ..      27     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 3.2e-25
                                    EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggavlsr 80 
                                    +twNvn+  ++      r dr++d+l + d Dvl++QE+++ ++++++l+l++ g++ a+       g++  ng+a++sr
  gi|121636341|ref|YP_976564.1|  27 ATWNVNSI-RT------RLDRVLDWLGRADVDVLAMQETKCPDGQFPALPLFELGYDVAHV------GFDQWNGVAIASR 93 
                                    7******7.44......8*********************************9988888765......79*********** PP

                                    STEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE..............CCCHHGHHHHHHHHHHHHHHHH.HHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                  Exo_endo_phos  81 fpltslfrrtfiefndlvaalrreplaakleqlni..............ashrdhdlvrdlqllalllqve.alnadrga 145
                                      l+ + +    +  + + +     + a  +  ++              a   +h+ +   +l+al + +e  l +d+ a
  gi|121636341|ref|YP_976564.1|  94 VGLDDVRVGFDGQPSWSGKPEVAATTEARALGATCggirvwslyvpngrALDDPHYTYKLDWLAALRDTAEgWLRDDPAA 173
                                    ******99999999999999999999999999999*************86666666666666666655555156788999 PP

                                    EEEEEEE-SSSTSGGGBSCGHHHHHHCTTTH.........H..............SSCESCETTTTTTTTTTTEB-BEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x..............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Exo_endo_phos 146 pvivaGDfNarpsdddsrvlrtrglalapap.........v..............glyllgggptptyvtraggsrlDri 202
                                    p+ ++GD N +p+ddd+ +++  ++ ++            v               ++++ + +t  + ++  g+r+D i
  gi|121636341|ref|YP_976564.1| 174 PIALMGDWNIAPTDDDVWSTEFFAGCTHVSEperkafnaiVdaqftdvvrpftpgPGVYTYWDYTQLRFPKKQGMRIDFI 253
                                    *********************9999999988888777666155566677889999************************* PP

                                    EEECHHHCCEEEEEEECCHHEECTSSCSSSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Exo_endo_phos 203 laspalalfrsgvlppplalvrrealtlSDH 233
                                    l spala ++   ++  + +    +  +SDH
  gi|121636341|ref|YP_976564.1| 254 LGSPALAARVMDAQIVREER---KGKAPSDH 281
                                    ***97776655554444333...34566666 PP

>> Msg2_C  Major surface glycoprotein 2 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.6e-05      0.32      12      24 ..     200     212 ..     199     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.6e-05
                         Msg2_C  12 vgVTEaElkAFDl 24 
                                    ++V+E+E kAF++
  gi|121636341|ref|YP_976564.1| 200 THVSEPERKAFNA 212
                                    79*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2205.76
//
Query:       gi|121636342|ref|YP_976565.1|  [L=302]
Description: hypothetical protein BCG_0467c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.22   10.6   0.0       0.32   10.1   0.0    1.1  1  Phage_Integr_2  Putative phage integrase


Domain annotation for each model (and alignments):
>> Phage_Integr_2  Putative phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   1.8e-05      0.32     196     223 ..      51      78 ..      33      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.8e-05
                 Phage_Integr_2 196 WsPvravalyvklslPlRtqqvrmlDSG 223
                                     sPv++val v++  P+Rt  +r l   
  gi|121636342|ref|YP_976565.1|  51 FSPVDVVALRVLTDAPVRTAAIRALEHA 78 
                                    6**********************99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2106.64
//
Query:       gi|121636343|ref|YP_976566.1|  [L=197]
Description: peptide deformylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-38  129.3   0.0    1.2e-37  129.0   0.0    1.0  1  Pep_deformylase  Polypeptide deformylase


Domain annotation for each model (and alignments):
>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   6.6e-42   1.2e-37       3     153 ..       5     162 ..       3     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 6.6e-42
                                    G---TT-GGGCS--B---BSS....HHHHHHHHHHHHHHHHHCT-SEEEGGGGT--BSEEEEECCSS-ETT....SEEEE CS
                Pep_deformylase   3 kivkvgdpvLrekakpvekfe....skelekllekmletmkeakgvgLAApQigvnkrlfvielpseeeeeeenkeltvl 78 
                                    +i  vgdpvL++ ++pv+        ++l++l+++m++tm++a+gvgLAA+Qig++ rlfv+++  ++  ++++  + v+
  gi|121636343|ref|YP_976566.1|   5 PIRIVGDPVLHTATTPVTVAAdgslPADLAQLIATMYDTMDAANGVGLAANQIGCSLRLFVYDCAADRAMTARR--RGVV 82 
                                    68899*************4445889788**************************************99988766..79** PP

                                    EEEEEE.....ECSCEEECCEE--TTSTT--CEEEEESCEEEEEE-TTS-EEEEEEEHHHHHHHHHHHHHCTT--GGGGC CS
                Pep_deformylase  79 iNPkit.....skseetitdeEgClSvpgieakVeRskrikvkyldltgkeveleaegllArvlqHEiDhlnGklfidri 153
                                    iNP ++     ++  +  td EgClSvpg +    R+k+ +v++ld +g +v++e +gl+Ar+lqHE+ hl+G l++dr+
  gi|121636343|ref|YP_976566.1|  83 INPVLEtseipETMPDPDTDDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYLDRL 162
                                    *****8887778888999************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1505.36
//
Query:       gi|121636344|ref|YP_976567.1|  [L=102]
Description: hypothetical protein BCG_0469 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-36  122.8   2.3    4.8e-36  122.4   2.3    1.1  1  DUF3263   Protein of unknown function (DUF3263)


Domain annotation for each model (and alignments):
>> DUF3263  Protein of unknown function (DUF3263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   2.3   2.7e-40   4.8e-36       2      73 ..      21      92 ..      20      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.7e-40
                        DUF3263  2 LserdraiLaferqwwrhagakeeaireelglsptrYyqlLnaLiddpeAlaadPvlvkRLrrlRaarrraR 73
                                   L++r+++iLaferqww+ ag keeai+e + +s+trYyq+LnaL+d+peAlaadP+lvkRLrrlRa+r++aR
  gi|121636344|ref|YP_976567.1| 21 LTRREHDILAFERQWWKFAGVKEEAIKELFSMSATRYYQVLNALVDRPEALAADPMLVKRLRRLRASRQKAR 92
                                   99*********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 777.71
//
Query:       gi|121636345|ref|YP_976568.1|  [L=164]
Description: tuberculin-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-13   51.4   2.1    1.6e-13   51.4   2.1    1.5  2  LytR_C    LytR cell envelope-related transcriptional attenuat
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.074   13.1   0.0    1.7  1  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   1.2e+04      43      43 ..      56      56 ..      38      73 .. 0.48
   2 !   51.4   2.1   1.8e-17   1.6e-13       3      81 ..      78     163 ..      76     164 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                         LytR_C 43 t 43
                                   +
  gi|121636345|ref|YP_976568.1| 56 S 56
                                   1 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 1.8e-17
                         LytR_C   3 kVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee.ttivy..reaaaaaakalaaalglgelqedsvkdas... 76 
                                     V+V+N +g  G+Aar+ad L+++Gftv++vgn +  d+  tt++y   e+++a+a+a+ ++lg +     ++++++   
  gi|121636345|ref|YP_976568.1|  78 EVRVYNISGAEGAAARTADRLKAAGFTVTDVGNLSLPDVAaTTVYYteVEGERATADAVGRTLGAAVELRLPELSDQppg 157
                                    79****************************88866665558*****86333337999******96663333333333688 PP

                         LytR_C  77 .vtvvl 81 
                                     ++vv 
  gi|121636345|ref|YP_976568.1| 158 vIVVVT 163
                                    545554 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-06     0.074       5      25 ..      25      45 ..      21      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-06
                        DUF3185  5 iiLlvaGivLlvfGynasdSl 25
                                   ++Ll++G+v+l  G++a  S 
  gi|121636345|ref|YP_976568.1| 25 MVLLFLGVVFLLLGWQALGSS 45
                                   79*************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1301.63
//
Query:       gi|121636346|ref|YP_976569.1|  [L=240]
Description: periplasmic superoxide dismutase [Cu-Zn] sodC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-28   99.0   1.3    3.4e-28   98.6   1.3    1.1  1  Sod_Cu    Copper/zinc superoxide dismutase (SODC)


Domain annotation for each model (and alignments):
>> Sod_Cu  Copper/zinc superoxide dismutase (SODC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   1.3   1.9e-32   3.4e-28       6     142 .]      81     237 ..      77     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.9e-32
                                    EEEEEEEEEEECSTTSTCEEEEEEEECS...S-STEEEEEEEESSTTTTTT...........TGGG-SB-S.TT-.CSST CS
                         Sod_Cu   6 gevsGtvtftqeeskesgsvevtvevkg...lppggkhgfHiHengdcsag...........fksagghfn.ptgkkhga 70 
                                    g+ + t++f+ ++    g ++vt+  +g   l+p g+hg+HiH++g+c+++           f saggh++ p ++    
  gi|121636346|ref|YP_976569.1|  81 GTKVATAKFEFAN----GYATVTIATTGvgkLTP-GFHGLHIHQVGKCEPNsvaptggapgnFLSAGGHYHvPGHTGT-- 153
                                    5777999999876....34556666666334666.69***********9999******************86765544.. PP

                                    TTTTCS-TTEEEEEEESTTSEEEEEEEEESC.BCSTTTBCTTEEEEEESS---TT..................SCHHHTT CS
                         Sod_Cu  71 pndeerhaGDLgnievdadgtakleittdklvslkgensilgralvihagaDdlg..................eskptgn 132
                                           +GDL +++v+ dg+a l +ttd+ +++++  s   +a++ihagaD+++                  ++++tg+
  gi|121636346|ref|YP_976569.1| 154 -----PASGDLASLQVRGDGSAMLVTTTDA-FTMDDLLSGAKTAIIIHAGADNFAnipperyvqvngtpgpdeTTLTTGD 227
                                    .....479*************999988777.8998544666********************************9****** PP

                                    SSSEEEEEEE CS
                         Sod_Cu 133 agariacGvI 142
                                    ag+r+acGvI
  gi|121636346|ref|YP_976569.1| 228 AGKRVACGVI 237
                                    *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1671.05
//
Query:       gi|121636347|ref|YP_976570.1|  [L=376]
Description: carboxylate-amine ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-94  316.3   0.2    2.3e-94  316.0   0.2    1.1  1  GCS2      Glutamate-cysteine ligase family 2(GCS2)


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.0   0.2   1.3e-98   2.3e-94       1     291 []      20     297 ..      20     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 316.0 bits;  conditional E-value: 1.3e-98
                                    EEEEEEEEEEETTTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHHTT- CS
                           GCS2   1 lgvEeeflvvdlatgdlrgwseiledeaiiglseggsvvkelpegqvElstapleslaeaaeeisadleelrsvadelGl 80 
                                    lgvE+ef++vd++t+dl+  +e+++  a+ig++  ++v+kel +++vE+ + ++e++aea+++++++l  +r++++++G+
  gi|121636347|ref|YP_976570.1|  20 LGVEWEFALVDSQTRDLS--NEATAVIAEIGEN--PRVHKELLRNTVEIVSGICECTAEAMQDLRDTLGPARQIVRDRGM 95 
                                    69****************..99***9*******..********************************************* PP

                                    EEE--SB-SS---------------THHHHHGG..G.G-S--B-EEEEEEE-SSHHHHH.HHHHHHHTTHHHHHHHH--B CS
                           GCS2  81 ellglGthPfalrsedevtpkaryrrmleymdrvGvlgrqmmvaglhvqvnidssseedVevlrlvrallPvllAlsAnS 160
                                    el+++GthPfa++s++++t+++ry+++++++++  + grqm+++g+hv+v+i+s+++ +  +++++++++P+llAlsA+S
  gi|121636347|ref|YP_976570.1|  96 ELFCAGTHPFARWSAQKLTDAPRYAELIKRTQW--W-GRQMLIWGVHVHVGIRSAHKVM-PIMTSLLNYYPHLLALSASS 171
                                    *********************************..8.**********************.******************** PP

                                    -EETTEE-S-SB-GGGCCTTSTT-CS----SSHHH.HHHHHHHHTTSTT-SSGG.G--BSEEEETTTT.EEEEEEEE--. CS
                           GCS2 161 PfleGrdtgyaStRariftqtpqagelplafedgaaferyaryaldvpvidvrrfrlwldirpsslpgttlelrihdttl 240
                                    P+++G+dtgyaS+Ra++f+q+p+ ++lp++f+++a+fe ++++++++++id+++ ++++dirps++ g tle+ri+d+++
  gi|121636347|ref|YP_976570.1| 172 PWWGGEDTGYASNRAMMFQQLPT-AGLPFHFQRWAEFEGFVYDQKKTGIIDHMD-EIRWDIRPSPHLG-TLEVRICDGVS 248
                                    ***********************.******************************.9************.*********** PP

                                    ..SSHHHHHHHHHHHHHHHHHHHHH------GGGGTT.HHHHHHHHHHHGG CS
                           GCS2 241 fPevrlrallearlldaqpadrldalpaavlvallddeaeenawdavrsgl 291
                                    +++++ + ++++++l ++ ++rlda +++ +++ +++  +en+w+a+r+gl
  gi|121636347|ref|YP_976570.1| 249 NLRELGALVALTHCLIVDLDRRLDAGETLPTMPPWHV--QENKWRAARYGL 297
                                    *************************************..**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2793.77
//
Query:       gi|121636348|ref|YP_976571.1|  [L=217]
Description: hypothetical protein BCG_0473 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-23   81.8   0.0    7.1e-23   81.6   0.0    1.0  1  LON_substr_bdg  ATP-dependent protease La (LON) substrate-bin


Domain annotation for each model (and alignments):
>> LON_substr_bdg  ATP-dependent protease La (LON) substrate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0     4e-27   7.1e-23       1     206 [.       8     204 ..       8     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 4e-27
                 LON_substr_bdg   1 elpllpldnkvlfPgitlpltvsrpksiaaierlldkdkpyigvflvkesqkdaideesiselysvGtvarIvqilrldd 80 
                                    el ++pl++ + +P   lpl++++p+++a++++++d+  p++gv+l+  s+  +    + +  ++vGt+arI+++   ++
  gi|121636348|ref|YP_976571.1|   8 ELAMFPLESAP-LPDEDLPLHIFEPRYAALVRDCMDTADPRFGVVLI--SRGREV--GGGDTRCDVGTLARITECADAGS 82 
                                    6899***9999.9************************9999******..776653..469999***************** PP

                 LON_substr_bdg  81 grikvvlegleRvkikklekekeegylvaeveiiedds.epedsdslqkelkalvqeiiekikkslarellkllleiell 159
                                    gr+ +  +  eR+++ ++ +  +++y++a+v+ + d++  p+ +++l  e+++ v  ++e+i   +ar      +e++l 
  gi|121636348|ref|YP_976571.1|  83 GRYMLRCRVGERIRVCDWLP--DDPYPRAKVRFWPDQPgHPVTAAQLL-EVEDRVVALFERIA--AARGVRLPAREVVLG 157
                                    ******************55..9***********88778888888876.777778889****9..8999999999***** PP

                 LON_substr_bdg 160 lkyedlenpyrLadlvaailpfsneekqelLeeldvedRlkkvlelL 206
                                      + d  ++++  + +a  +p+ + +++++L++ ++ dRl ++ + L
  gi|121636348|ref|YP_976571.1| 158 YPVVDPADTGQRLYALACRVPMGPADRYAVLAAPSAADRLVRLGDAL 204
                                    ***********889999999********************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1595.71
//
Query:       gi|121636349|ref|YP_976572.1|  [L=728]
Description: atpase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-56  188.2   0.0    6.6e-39  133.4   0.0    2.3  2  AAA              ATPase family associated with various cellul
      1e-22   79.6   8.0    6.4e-11   41.9   0.1    2.6  2  AAA_lid_3        AAA+ lid domain
    2.2e-14   53.4   0.1      8e-14   51.6   0.2    1.9  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.7e-11   43.7  11.3    0.00058   20.3   0.1    4.5  4  AAA_16           AAA ATPase domain
    1.1e-06   28.7   0.7    0.00041   20.4   0.0    3.3  3  AAA_5            AAA domain (dynein-related subfamily)
    6.7e-06   26.3   0.0       0.24   11.6   0.0    3.0  3  AAA_33           AAA domain
    2.1e-05   25.1   0.1      0.034   14.7   0.0    2.4  2  AAA_18           AAA domain
    4.1e-05   23.9   2.1      0.061   13.6   0.1    4.0  4  AAA_22           AAA domain
     0.0002   21.6   0.5      0.021   15.1   0.0    3.2  3  AAA_28           AAA domain
    0.00025   20.9   0.1      0.033   13.9   0.0    3.0  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00029   20.8   0.1       0.97    9.4   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00033   20.4   2.2        1.2    8.8   1.4    3.4  3  AAA_30           AAA domain
    0.00045   20.2   2.5        1.5    8.7   0.0    3.6  3  NACHT            NACHT domain
    0.00056   19.7   0.1       0.11   12.2   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00063   19.7   0.1        0.1   12.5   0.0    2.3  2  Rad17            Rad17 P-loop domain
    0.00081   19.7   0.0       0.17   12.3   0.0    2.3  2  RNA_helicase     RNA helicase
    0.00096   19.3   0.0     0.0062   16.7   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
     0.0016   18.4   0.0          1    9.2   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
      0.003   17.1   3.4      0.038   13.6   0.2    3.7  3  AAA_25           AAA domain
     0.0031   18.0   0.0        1.1    9.7   0.0    2.5  2  ABC_tran         ABC transporter
     0.0044   16.8   0.1       0.38   10.5   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
     0.0046   17.0   0.0       0.14   12.2   0.0    2.4  2  AAA_14           AAA domain
     0.0046   17.0   0.0      0.026   14.5   0.1    2.3  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0058   15.8   0.0        1.4    8.0   0.0    2.3  2  DUF815           Protein of unknown function (DUF815)
     0.0067   16.1   0.0       0.82    9.5   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
     0.0082   15.7   0.1       0.95    8.9   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0089   15.8   0.0          1    9.0   0.0    2.2  2  AAA_24           AAA domain
     0.0091   15.7   0.0        9.4    5.9   0.0    3.4  3  Sigma54_activat  Sigma-54 interaction domain
     0.0093   15.9   0.0        2.2    8.1   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.012   16.0   0.7          2    8.7   0.0    2.6  2  AAA_19           AAA domain
      0.014   14.8   0.5       0.42   10.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.014   14.2   0.1       0.93    8.2   0.0    2.1  2  Adeno_IVa2       Adenovirus IVa2 protein
      0.014   15.5   0.0        1.9    8.6   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.015   15.2   0.2        1.3    8.9   0.1    2.9  3  NTPase_1         NTPase
      0.028   14.2   0.0       0.16   11.7   0.0    1.9  2  AAA_11           AAA domain
      0.034   13.0   2.1        2.8    6.8   0.0    2.6  3  AFG1_ATPase      AFG1-like ATPase
      0.034   14.6   0.0        1.2    9.6   0.0    2.4  2  AAA_17           AAA domain
      0.057   12.6   0.2        2.3    7.3   0.1    2.2  2  NB-ARC           NB-ARC domain
       0.18   11.4   0.7        7.4    6.1   0.1    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.21   11.3   0.4        4.1    7.1   0.0    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   1.2e-16   5.5e-14       1     131 [.     250     369 ..     250     370 .. 0.94
   2 !  133.4   0.0   1.5e-41   6.6e-39       1     131 [.     501     631 ..     501     632 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.2e-16
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    vl++Gp G+GK +l++av+    +++++++g+e+     g++ k ++  +++++++    +l+i ++dal ++       
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCDG--RRLVTLDGPEIGALAAGDRVKAVASAVQAVRHEG--GVLLITDADALLPAA------ 319
                                    799*****************8..9***********99***************99998..***************...... PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                     +e v++ +l+el       + v++i+++ rpd+ld  l++ + +dr++ ++
  gi|121636349|ref|YP_976572.1| 320 -AEPVASLILSELRTAVAT-AGVVLIATSARPDQLDARLRSpELCDRELGLP 369
                                    .889999999999999886.55*******************9****998776 PP

  == domain 2  score: 133.4 bits;  conditional E-value: 1.5e-41
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    vllyGppG+GKT +++a+a++ + ++  ++gsel++k+vg sek +relf++a+ +a ps +f+DE+dala++r ++ +s
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQLSVHAVKGSELMDKWVGSSEKAVRELFRRARDSA-PSLVFLDELDALAPRRgQSFDS 579
                                    79******************************************************9.****************7777** PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    ++++rvv++Llteldg +   ++v+++gatnrpd +dpallr gR++r +++e
  gi|121636349|ref|YP_976572.1| 580 GVSDRVVAALLTELDGIDPL-RDVVMLGATNRPDLIDPALLRpGRLERLVFVE 631
                                    *******************7.66*************************99886 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   1.4e-13   6.4e-11       1      34 [.     391     424 ..     391     438 .. 0.91
   2 !   39.1   3.8   1.1e-12   4.8e-10       1      43 [.     654     698 ..     654     700 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.4e-13
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrg 34 
                                    d++l+e+A+rT+G++ ADlaal+reAal+A +r 
  gi|121636349|ref|YP_976572.1| 391 DLNLDEIASRTPGFVVADLAALVREAALRAASRA 424
                                    89****************************9985 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.1e-12
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike..itmedf 43 
                                    dvdl+e+A+  +GyS AD +al reAal A+rr+i++  +t +d+
  gi|121636349|ref|YP_976572.1| 654 DVDLDEVAAGLDGYSAADCVALLREAALTAMRRSIDAanVTAADL 698
                                    9***********************************447999886 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.2   1.8e-16     8e-14      11      84 ..      22      94 ..      13      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.8e-16
                                   CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
                        CDC48_N 11 dvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                                   d+ rg+vr++p+++++lg++++d+v ++g+r+T+a++  a+ ++   g++ +d+vt +nag++ G +V+V++++
  gi|121636349|ref|YP_976572.1| 22 DSRRGVVRLHPNAIAALGIREWDAVSLTGSRTTAAVAGLAAADTA-VGTVLLDDVTLSNAGLREGTEVIVSPVT 94
                                   799****************************99999999988865.*************************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   7.1e-06    0.0032      15      45 ..     238     268 ..     236     321 .. 0.86
   2 ?    6.2   0.5     0.028        13      38     144 ..     325     438 ..     324     457 .. 0.74
   3 !   20.3   0.1   1.3e-06   0.00058      24      46 ..     498     520 ..     488     535 .. 0.83
   4 ?    3.9   0.1      0.14        62     122     149 ..     545     571 ..     525     600 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.1e-06
                         AAA_16  15 alervrsgrpelvllsGesGvGKsslvrell 45 
                                    +l+++ +g+   vl+sG++GvGK +lvr++ 
  gi|121636349|ref|YP_976572.1| 238 LLQTLGAGTNLGVLVSGPAGVGKATLVRAVC 268
                                    7888999999******************987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.028
                         AAA_16  38 sslvrellralekdggif..lrgkcdqlesaipy...........salaqalareellrqlldeaesaeleawrekleea 104
                                    s ++ el++a+ ++g+++  ++++ dql++   +           ++l +a++r++ll++ll++  + +l+ +  + ++ 
  gi|121636349|ref|YP_976572.1| 325 SLILSELRTAVATAGVVLiaTSARPDQLDAR--LrspelcdrelgLPLPDAATRKSLLEALLNPVPTGDLNLDEIASRTP 402
                                    6688999999999987775677777777333..23344455566777999999999999999996666666555544443 PP

                         AAA_16 105 laavpelagaeasrllellkrllallsrderplvlvlDdl 144
                                          + +++a  ++e+  r+++++s d+rp  l  Ddl
  gi|121636349|ref|YP_976572.1| 403 GF----VVADLAALVREAALRAASRASADGRPPMLHQDDL 438
                                    33....5666668888889999999999999999999997 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 1.3e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellr 46 
                                    p+ vll+G++G+GK+ +vr+l+ 
  gi|121636349|ref|YP_976572.1| 498 PRGVLLYGPPGCGKTFVVRALAS 520
                                    499*****************985 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.14
                         AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                    ++++l+++++  + p +++lD+l+ + +
  gi|121636349|ref|YP_976572.1| 545 AVRELFRRARD-SAPSLVFLDELDALAP 571
                                    67888899998.888*********5544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.06        27       2      20 ..     250     268 ..     249     270 .. 0.88
   2 ?   -1.4   0.0       4.6   2.1e+03      61      89 ..     298     327 ..     283     364 .. 0.52
   3 !   20.4   0.0   9.2e-07   0.00041       1      94 [.     500     586 ..     500     620 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                                    EEEE--SSSSHHHHHHHGG CS
                          AAA_5   2 vlLvGppGtgKselaerla 20 
                                    vl+ Gp G+gK +l++ ++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVC 268
                                    8999***********9765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.6
                                    ----.G-SEEEEESGGG--HHHHHHHHHHH CS
                          AAA_5  61 raar.egeilvlDEveraesevlnsLlsll 89 
                                    +a+r eg +l++ + + + +++++ + sl+
  gi|121636349|ref|YP_976572.1| 298 QAVRhEGGVLLITDADALLPAAAEPVASLI 327
                                    555555666666555555555555444443 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 9.2e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppG+gK+++++ la+  + +v+ v +++      l  ++    g  +    +l r ar   +++++lDE++ + 
  gi|121636349|ref|YP_976572.1| 500 GVLLYGPPGCGKTFVVRALASTGQLSVHAVKGSE------LMDKWV---GSSEKAVRELFRRARdsAPSLVFLDELDALA 570
                                    59*******************9999999999877......666676...5555566677777776777788888888777 PP

                                    HHHHHHHHHHHHSSEE CS
                          AAA_5  79 sevlnsLlslleerrl 94 
                                    +   +s+ s  ++r +
  gi|121636349|ref|YP_976572.1| 571 PRRGQSFDSGVSDRVV 586
                                    6666666555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00073      0.33       2      33 ..     250     281 ..     250     361 .. 0.73
   2 !   11.6   0.0   0.00054      0.24       2      25 ..     501     525 ..     501     593 .. 0.78
   3 ?   -1.5   0.0       5.6   2.5e+03      96     139 ..     622     666 ..     595     669 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00073
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtl 33 
                                    vl+ G++G+GK+tl++ ++  +  v+l+ +++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCDGRRLVTLDGPEI 281
                                    6899***************9888999999873 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00054
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.a 25 
                                    vll G+pG+GK+++++ l+   +  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQlS 525
                                    7899*************98544352 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.6
                         AAA_33  96 gvpvrivvvetdeetlkeRlakRaang.ddrsevpeealdrqkar 139
                                    g  +r+v+ve++++ +++ + + a ++   +s+v++  + +++++
  gi|121636349|ref|YP_976572.1| 622 GRLERLVFVEPPDAAARREILRTAGKSiPLSSDVDLDEVAAGLDG 666
                                    556799999999999988776666655544456666666666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0087       3.9       1      18 [.     250     267 ..     250     300 .. 0.78
   2 !   14.7   0.0   7.6e-05     0.034       1      43 [.     501     540 ..     501     559 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0087
                         AAA_18   1 IlltGtpGvGKttlakeL 18 
                                    +l++G++GvGK tl +++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAV 267
                                    79************9987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.6e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdp 43 
                                    +ll G+pG+GKt + ++L++    g+ + + +k ++l + +  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALAST---GQLSVHAVKGSELMDKWVG 540
                                    799***************998...7888887777777776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.046        20       8      25 ..     250     267 ..     245     275 .. 0.87
   2 ?   -2.0   0.0       9.2   4.1e+03      84     117 ..     298     336 ..     273     345 .. 0.62
   3 !   13.6   0.1   0.00014     0.061       8      29 ..     501     522 ..     496     557 .. 0.79
   4 ?    1.1   0.0         1   4.5e+02      81     104 ..     545     570 ..     532     594 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                         AAA_22   8 lvvtGesGtGKTtllrrl 25 
                                    ++v G++G+GK tl+r +
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAV 267
                                    5899**********9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9.2
                         AAA_22  84 qalraravielliiDEaqhlr...s....eealeeLrslln 117
                                    qa+r+ +  ++l+i +a+ l           +l+eLr+ + 
  gi|121636349|ref|YP_976572.1| 298 QAVRHEG--GVLLITDADALLpaaAepvaSLILSELRTAVA 336
                                    4444444..48999999997544313444555555555554 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00014
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++G+GKT+++r l+++ 
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTG 522
                                    689***************9875 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1
                         AAA_22  81 aleqalrarav..ielliiDEaqhlr 104
                                    a+++ +r++++  ++l+ +DE + l 
  gi|121636349|ref|YP_976572.1| 545 AVRELFRRARDsaPSLVFLDELDALA 570
                                    334444444445557*********96 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       3.5   1.6e+03       7      30 ..     141     165 ..     141     168 .. 0.86
   2 ?    2.9   0.0      0.27   1.2e+02       2      20 ..     250     268 ..     249     315 .. 0.83
   3 !   15.1   0.0   4.6e-05     0.021       2      49 ..     501     549 ..     500     645 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                         AAA_28   7 gestGKTtlleaLaar.gypvvpEa 30 
                                    g++t ++  ++aLaa  g+++  E 
  gi|121636349|ref|YP_976572.1| 141 GPGTSTSAASRALAAAvGISWTSEL 165
                                    7889999999****988****9886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.27
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    + ++G+ + GK tl++a  
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVC 268
                                    6799***********9975 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 4.6e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                    + + G++++GKT +++aLa++ + +v++  + e++++   + e+a ++ 
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTgQLSVHAVKGSELMDKWVGSSEKAVREL 549
                                    6799****************94466667667776666656666555554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.18        79       2      22 ..     251     271 ..     250     302 .. 0.77
   2 ?   -0.9   0.0       2.5   1.1e+03      21      84 ..     349     411 ..     342     416 .. 0.64
   3 !   13.9   0.0   7.4e-05     0.033       5      70 ..     505     565 ..     501     572 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                    +v+G +G GK tl+r +++ +
  gi|121636349|ref|YP_976572.1| 251 LVSGPAGVGKATLVRAVCDGR 271
                                    79***********99988665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                Viral_helicase1  21 ts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaGyill.laa 84 
                                    ++ l+ +  +p  +++  g+   p ++  t +s+l+al+++     l lDE+ + ++G + + laa
  gi|121636349|ref|YP_976572.1| 349 PDqLDARLRSPELCDRELGL---PLPDAATRKSLLEALLNPVPTGDLNLDEIASRTPGFVVAdLAA 411
                                    54555555556566666665...44445555666666666655678899********999886766 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.4e-05
                Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                    G pGcGK+ ++r l++t  l++ +++   el  +++  +++   + ++ +  ++       +++lDE
  gi|121636349|ref|YP_976572.1| 505 GPPGCGKTFVVRALASTGqLSVHAVKG-SELMDKWVGSSEKAVRELFRRARDSAP-----SLVFLDE 565
                                    78***************9877777776.99*****95555555555554444432.....3667776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0036       1.6      14      42 ..     242     270 ..     220     279 .. 0.76
   2 !    9.4   0.0    0.0022      0.97      21      45 ..     493     524 ..     463     532 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0036
                                    HHHCHTEEEEEEESTTSSHHHHHHHHHHH CS
                           TsaE  14 lakalgdvilLeGdLGaGKTtlvrglaka 42 
                                    l++ ++  +l +G+ G+GK tlvr+++ +
  gi|121636349|ref|YP_976572.1| 242 LGAGTNLGVLVSGPAGVGKATLVRAVCDG 270
                                    3332233499***************9987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                                    E.......EEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgv 45 
                                    +       +lL+G+ G+GKT  vr+la++ ++
  gi|121636349|ref|YP_976572.1| 493 LgvepprgVLLYGPPGCGKTFVVRALASTGQL 524
                                    044455559*****************986544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.4    0.0027       1.2      16      59 ..     245     291 ..     236     343 .. 0.79
   2 ?   -1.8   0.0       4.9   2.2e+03     145     175 ..     403     431 ..     384     440 .. 0.70
   3 !    8.2   0.0    0.0042       1.9      21      41 ..     501     521 ..     489     565 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                         AAA_30  16 sgdrvavltGpAGtGKttalkal...reaweaaggrviglAptgkaA 59 
                                    ++++ +++ GpAG GK t+++a+   r++++ +g ++ +lA   ++ 
  gi|121636349|ref|YP_976572.1| 245 GTNLGVLVSGPAGVGKATLVRAVcdgRRLVTLDGPEIGALAAGDRVK 291
                                    555668899*************9777777777787777777665554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                         AAA_30 145 gigtaeLtevvRqkeseeraaalalregdae 175
                                    g+ +a L  +vR   ++ raa++a ++g+++
  gi|121636349|ref|YP_976572.1| 403 GFVVADLAALVRE--AALRAASRASADGRPP 431
                                    5567788888887..6899999999999987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0042
                         AAA_30  21 avltGpAGtGKttalkalrea 41 
                                    ++l Gp+G GKt++++al+ +
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALAST 521
                                    6899*************9865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0041       1.8       3      22 ..     250     269 ..     249     278 .. 0.90
   2 ?   -0.1   0.0       1.7   7.6e+02      77     140 ..     300     357 ..     286     367 .. 0.64
   3 !    8.7   0.0    0.0033       1.5       3      23 ..     501     521 ..     499     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0041
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    v++ G+aG+GK tL++ +++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCD 269
                                    789*************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                                    CCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSS CS
                          NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqle 140
                                    ++++  +Lli D+ D l        ++pv  l+ + +r   + +a ++l++++ +  +l   l+
  gi|121636349|ref|YP_976572.1| 300 VRHEGGVLLITDA-DALLPA----AAEPVASLILSELRT-AVATAGVVLIATSARPDQLDARLR 357
                                    5556667777776.555442....344788888888877.456666666666666656665555 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0033
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    v+l G++G+GKT  ++ la++
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALAST 521
                                    899*************99975 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.055        25      36      55 ..     250     269 ..     243     321 .. 0.82
   2 !   12.2   0.0   0.00024      0.11      33      69 ..     498     534 ..     489     619 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.055
                         RuvB_N  36 vllyGpPGlGkttlakiiak 55 
                                    vl++Gp G+Gk+tl + +++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCD 269
                                    89************987764 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00024
                         RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       vllyGpPG Gkt + + +a+  + ++++  g  l
  gi|121636349|ref|YP_976572.1| 498 PRGVLLYGPPGCGKTFVVRALASTGQLSVHAVKGSEL 534
                                    5679*****************9998888887777654 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.054        24      48      65 ..     250     267 ..     230     273 .. 0.88
   2 !   12.5   0.0   0.00023       0.1      46      69 ..     499     522 ..     489     539 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.054
                          Rad17  48 LLisGPsGCgkstvvkvL 65 
                                    +L+sGP+G gk+t v+ +
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAV 267
                                    69***********99865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00023
                          Rad17  46 riLLisGPsGCgkstvvkvLskel 69 
                                    r +L+ GP+GCgk+ vv+ L+   
  gi|121636349|ref|YP_976572.1| 499 RGVLLYGPPGCGKTFVVRALASTG 522
                                    557999**************9765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.065        29       1      19 [.     250     268 ..     250     273 .. 0.88
   2 !   12.3   0.0   0.00037      0.17       1      21 [.     501     521 ..     501     553 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.065
                   RNA_helicase   1 iwlyGpsgeGKStlakeLa 19 
                                    ++++Gp+g+GK tl++ ++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVC 268
                                    6799**********99876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00037
                   RNA_helicase   1 iwlyGpsgeGKStlakeLaka 21 
                                    ++lyGp+g+GK+ +++ La++
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALAST 521
                                    689**************9875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.6   1.2e+03       6      25 ..     250     269 ..     248     344 .. 0.63
   2 !   16.7   0.0   1.4e-05    0.0062       6     101 ..     501     591 ..     497     596 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.6
                                    EEEE--TTSSHHHHHHHHHH CS
                          AAA_2   6 illlgptgvGktelakalae 25 
                                    +l+ gp gvGk  l +a+ +
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCD 269
                                    57889999999997777654 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.4e-05
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt++ +ala++ ++    ++  +  sel+     + + s+++  ++   +a ++    v+lDE+d  +p+
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQL----SVHAVKGSELMD----KWVGSSEKAVRELFRRARDSApsLVFLDELDALAPR 572
                                    6889******************98....999*********....88888888888888888888899************* PP

                                    ..---------HHHHHHHHH CS
                          AAA_2  84 ..essgadvSregVqrdLLq 101
                                      +s  + vS   V+ +LL 
  gi|121636349|ref|YP_976572.1| 573 rgQSFDSGVSDR-VVAALLT 591
                                    988888888876.5555554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.013       5.7      11      42 ..     238     269 ..     236     275 .. 0.87
   2 !    9.2   0.0    0.0022         1      18      42 ..     496     520 ..     491     534 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                       ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiie 42 
                                    l++ l  ++n  +++ Gp g+GK +L++ +  
  gi|121636349|ref|YP_976572.1| 238 LLQTLGAGTNLGVLVSGPAGVGKATLVRAVCD 269
                                    67788899999****************98865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                       ATPase_2  18 epneiyfiYGpegsGKtaLlkeiie 42 
                                    ep + +++YGp g+GKt +++ +++
  gi|121636349|ref|YP_976572.1| 496 EPPRGVLLYGPPGCGKTFVVRALAS 520
                                    56666899**********9998776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   7.6e+02      46      97 ..     144     191 ..     123     239 .. 0.77
   2 ?   -0.7   0.1         2   8.9e+02      36      50 ..     250     264 ..     245     273 .. 0.87
   3 !   13.6   0.2   8.4e-05     0.038      36     107 ..     501     570 ..     494     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                         AAA_25  46 KttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                     +t a + ala a G +w+     e  +V  v+ +++ +  ++ l  +g+ +
  gi|121636349|ref|YP_976572.1| 144 TSTSAASRALAAAVGISWTS----ELLTVTGVDPDGPVSVQPNSLVTWGAGV 191
                                    58999999999999999977....7799999999999989889998888887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                         AAA_25  36 allaGapgtGKttla 50 
                                    +l+ G+ g+GK tl+
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLV 264
                                    5789********997 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.4e-05
                         AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                    +ll+G+pg+GKt+++  la +  +  +  +   +e +  ++ s E +  el rR+r     l + ++l++l 
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQLSVHAVK--GSELMDKWVGSSEKAVRELFRRARDSAPSLVFLDELDALA 570
                                    69*************999998884444444..2488899999999998899999988776665556655554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.048        21      15      33 ..     251     269 ..     240     302 .. 0.85
   2 !    9.7   0.0    0.0025       1.1       6      51 ..     493     536 ..     491     604 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.048
                                    EEEESTTSSHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllag 33 
                                     + G+ G GK tL+++++ 
  gi|121636349|ref|YP_976572.1| 251 LVSGPAGVGKATLVRAVCD 269
                                    456************9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0025
                                    EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                    l +++ + v + G+ G+GK+ ++++la   +     +  +g +l +
  gi|121636349|ref|YP_976572.1| 493 LGVEPPRGVLLYGPPGCGKTFVVRALASTGQLSVHAV--KGSELMD 536
                                    5677777899****************98766554444..4555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.12        52      49      67 ..     249     267 ..     238     316 .. 0.87
   2 !   10.5   0.0   0.00086      0.38      49      71 ..     500     522 ..     494     568 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                      IstB_IS21  49 nivllGpsGvGKshlaial 67 
                                    ++++ Gp+GvGK+ l  a+
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLVRAV 267
                                    68999********998876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00086
                      IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                    +++l Gp+G GK+++  al+  +
  gi|121636349|ref|YP_976572.1| 500 GVLLYGPPGCGKTFVVRALASTG 522
                                    799****************9765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.41   1.8e+02       5      23 ..     250     268 ..     246     294 .. 0.88
   2 !   12.2   0.0   0.00031      0.14       5      74 ..     501     567 ..     498     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.41
                         AAA_14   5 lvitGaRrvGKTtllkqli 23 
                                    ++++G+  vGK tl++ + 
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVC 268
                                    789***********99875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00031
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiq 74 
                                    +++ G+  +GKT++++ l+++      s+  ++  +  dk    +ek  ++++++++++  +++flDE  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQ---LSVHAVKGSELMDKWVGSSEKAVRELFRRARDSAPSLVFLDELD 567
                                    7899***************8887...889999999988888776665666666555566899******76 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.9e-05     0.026      19      74 ..      16      70 ..       1      77 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.9e-05
                                   GCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEE CS
                Molydop_binding 19 rpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvv 74
                                    ++++  ++++ vv+++p+  aalGi++ d V ++ +r ++ v      + + G+v
  gi|121636349|ref|YP_976572.1| 16 LNTSAVDSRRG-VVRLHPNAIAALGIREWDAVSLTGSRTTAAVAGLAAADTAVGTV 70
                                   33344444455.************************99988776666655666666 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.018       8.1      55      75 ..     249     269 ..     201     293 .. 0.76
   2 !    8.0   0.0    0.0032       1.4      52      76 ..     497     521 ..     459     566 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                         DUF815  55 nvLLwGarGtGKSslvkalln 75 
                                     vL+ G  G+GK +lv+a+  
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLVRAVCD 269
                                    599***************975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                         DUF815  52 pannvLLwGarGtGKSslvkallne 76 
                                    p + vLL+G  G+GK  +v+al ++
  gi|121636349|ref|YP_976572.1| 497 PPRGVLLYGPPGCGKTFVVRALAST 521
                                    6678*****************9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0018      0.82      24      42 ..     249     267 ..     232     269 .. 0.85
   2 ?    4.0   0.0     0.095        43      21      42 ..     498     518 ..     488     521 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                         AAA_29  24 atlltGpsGsGKSTllDAi 42 
                                     +l++Gp G+GK Tl+ A+
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLVRAV 267
                                    489************9775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.095
                         AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    ++g +ll Gp G GK+ ++ A+
  gi|121636349|ref|YP_976572.1| 498 PRG-VLLYGPPGCGKTFVVRAL 518
                                    356.9**********9887665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.06        27      33      53 ..     247     267 ..     237     272 .. 0.81
   2 !    8.9   0.0    0.0021      0.95      30      55 ..     495     520 ..     487     530 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.06
                          AAA_7  33 kkpvllvGptGtGKtviikdl 53 
                                    +  vl+ Gp+G+GK ++++ +
  gi|121636349|ref|YP_976572.1| 247 NLGVLVSGPAGVGKATLVRAV 267
                                    5679************99876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllk 55 
                                    ++  + vll+Gp G+GKt +++ l +
  gi|121636349|ref|YP_976572.1| 495 VEPPRGVLLYGPPGCGKTFVVRALAS 520
                                    5566789**************98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.055        25       3      30 ..     248     277 ..     246     304 .. 0.77
   2 !    9.0   0.0    0.0023         1       5      23 ..     501     520 ..     498     571 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.055
                         AAA_24   3 lkiliyGpsgiGKTtlakel..gpkplfid 30 
                                    l +l+ Gp+g+GK tl++    g + + +d
  gi|121636349|ref|YP_976572.1| 248 LGVLVSGPAGVGKATLVRAVcdGRRLVTLD 277
                                    568999***********9988777777776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                         AAA_24   5 iliyGpsgiGKTtlakel.g 23 
                                    +l+yGp+g GKT +++ l  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALaS 520
                                    79***********9998843 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.021       9.4      19      43 ..     244     268 ..     233     276 .. 0.86
   2 ?    0.3   0.0       1.1   4.9e+02      94     126 ..     458     494 ..     450     501 .. 0.68
   3 ?    4.6   0.0     0.053        24      23      44 ..     499     520 ..     489     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                                    CTSSS-EEEECSTTSSHHHHHHHHH CS
                Sigma54_activat  19 aktdlsvlitGesGtGKellaraih 43 
                                    a t+l vl+ G  G+GK +l ra+ 
  gi|121636349|ref|YP_976572.1| 244 AGTNLGVLVSGPAGVGKATLVRAVC 268
                                    567899*************999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                    TSEEEEETGGGS-HHHHH...HHHHHHHH.SEEESBT CS
                Sigma54_activat  94 gGtlfLDeigelplelQe...kLlrvlqe.gevervG 126
                                     G + LD++g++ ++ Q+    +l  lq+  ++ r+G
  gi|121636349|ref|YP_976572.1| 458 VGDVTLDDVGDMAAAKQAlteAVLWPLQHpDTFARLG 494
                                    57889********999962224555555424556666 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.053
                                    S-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  23 lsvlitGesGtGKellaraihe 44 
                                      vl+ G  G+GK+++ ra+ +
  gi|121636349|ref|YP_976572.1| 499 RGVLLYGPPGCGKTFVVRALAS 520
                                    569**************99865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.005       2.2     102     122 ..     250     270 ..     220     302 .. 0.84
   2 ?    5.1   0.0     0.042        19     102     132 ..     501     531 ..     491     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.005
                                    EEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                    +++ G+ GvGK tL+ a+   
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCDG 270
                                    4578***********998775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.042
                                    EEEECSTTSSHHHHHHHHCTT-----S---- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevse 132
                                    ++l G+ G GK+ ++ al+++ +l++++v+ 
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQLSVHAVKG 531
                                    6899**********************99986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.075        34      13      33 ..     250     270 ..     243     311 .. 0.81
   2 ?    8.7   0.0    0.0045         2      12      31 ..     500     519 ..     494     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.075
                         AAA_19  13 llvtaGpGtGKTrvlkhival 33 
                                    +lv +++G GK +++++++  
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCDG 270
                                    7999***********999865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0045
                         AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                     +l+ ++pG+GKT v+++  
  gi|121636349|ref|YP_976572.1| 500 GVLLYGPPGCGKTFVVRALA 519
                                    5899***********99765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1       0.2        92      24      42 ..     249     267 ..     237     272 .. 0.82
   2 ?   10.0   0.0   0.00094      0.42      25      43 ..     501     519 ..     495     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                   Mg_chelatase  24 nlllvGppGsGKtmlakrl 42 
                                     +l+ Gp+G GK+ l +++
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLVRAV 267
                                    5899*********999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt + ++l+
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALA 519
                                    89************99986 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.05        22      91     108 ..     251     268 ..     237     278 .. 0.83
   2 ?    8.2   0.0    0.0021      0.93      84     113 ..     494     524 ..     477     528 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.05
                     Adeno_IVa2  91 viyGPtGsGksqllrnli 108
                                    +++GP+G Gk+ l+r++ 
  gi|121636349|ref|YP_976572.1| 251 LVSGPAGVGKATLVRAVC 268
                                    479************976 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0021
                     Adeno_IVa2  84 glqPviGv.iyGPtGsGksqllrnlisskli 113
                                    g +P  Gv +yGP G+Gk+ ++r+l s+  +
  gi|121636349|ref|YP_976572.1| 494 GVEPPRGVlLYGPPGCGKTFVVRALASTGQL 524
                                    5666677636***************998655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.093        42      19      93 ..     245     327 ..     239     362 .. 0.66
   2 ?    8.6   0.0    0.0043       1.9      24      49 ..     501     526 ..     495     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.093
                                    T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHH.......H-HHHHHHHT..TTSEEEEEE-TT--HHHHHHH CS
                Sigma54_activ_2  19 qsklpvfltGekGsgkelvArlLhknsgpwleifvverla.......klpldlleqa..kggtLylkdiadlskaeqkeL 89 
                                      +l v++ G++G gk +  r+ ++ +   + +   e +a       k+ ++ ++ +  +gg+L++ d + l +a+    
  gi|121636349|ref|YP_976572.1| 245 GTNLGVLVSGPAGVGKATLVRAVCDGRRL-VTLDGPEIGAlaagdrvKAVASAVQAVrhEGGVLLITDADALLPAAAEPV 323
                                    56789*************99999886654.22322222221111111444555555466889999999888877766666 PP

                                    HHHH CS
                Sigma54_activ_2  90 lell 93 
                                    + l+
  gi|121636349|ref|YP_976572.1| 324 ASLI 327
                                    6655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                                    EEEEEETT--HHHHHHCC--TTS-EE CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwl 49 
                                    v+l G++G+gk++v r+L++ ++  +
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTGQLSV 526
                                    9*****************98876544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0029       1.3       2      21 ..     250     269 ..     249     278 .. 0.90
   2 ?   -1.8   0.0       5.5   2.5e+03      99     119 ..     461     481 ..     403     489 .. 0.78
   3 ?    2.9   0.0      0.21        94       2      22 ..     501     521 ..     500     534 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    v+++Gp GvGK Tlv+ v++
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCD 269
                                    789*************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.5
                                    EEE---STTGGG-HHHHHHHH CS
                       NTPase_1  99 iviDEiGkmElkskkfkeave 119
                                    + +D +G m    + + eav 
  gi|121636349|ref|YP_976572.1| 461 VTLDDVGDMAAAKQALTEAVL 481
                                    468999999999999999986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.21
                                    EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                    v++ GppG GKt +v+ ++++
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALAST 521
                                    6788********999887765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.8     8e+02      19      38 ..     249     268 ..     224     300 .. 0.80
   2 ?   11.7   0.0   0.00036      0.16      20      41 ..     501     522 ..     478     561 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                         AAA_11  19 itliqGPPGtgKTktivell 38 
                                     +l++GP G gK + + +++
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLVRAVC 268
                                    579**********9998775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00036
                         AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                    +l+ GPPG+gKT+++ +l s  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRALASTG 522
                                    799*************999876 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       4.4     2e+03      64      79 ..     249     264 ..     242     268 .. 0.85
   2 ?    5.1   0.1      0.02       9.1     144     172 ..     325     352 ..     318     357 .. 0.86
   3 ?    6.8   0.0    0.0062       2.8      58      79 ..     494     515 ..     461     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.4
                    AFG1_ATPase  64 glYlwGgvGrGKtylm 79 
                                    g+ + G+ G+GK+ l+
  gi|121636349|ref|YP_976572.1| 249 GVLVSGPAGVGKATLV 264
                                    78899*******9997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                    AFG1_ATPase 144 amllsrLleaLfargvtlvaTSNiaPedL 172
                                    +++ls L  a    gv+l+aTS + P++L
  gi|121636349|ref|YP_976572.1| 325 SLILSELRTAVATAGVVLIATSAR-PDQL 352
                                    689*******************65.7776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0062
                    AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                     vep+rg+ l+G+ G GKt+++
  gi|121636349|ref|YP_976572.1| 494 GVEPPRGVLLYGPPGCGKTFVV 515
                                    478*****************97 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.44     2e+02       2      39 ..     254     299 ..     253     347 .. 0.79
   2 ?    9.6   0.0    0.0026       1.2       1      33 [.     504     538 ..     504     568 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.44
                                    E-TTSSHHHHHHHHHHHH........TEEEEEHHHHHHHHHHTTTS CS
                         AAA_17   2 GgPGsGKgtqceklveky........gfthlsaGdllreeakrggl 39 
                                    G+ G+GK t+++ + +          ++  l aGd + ++a+  ++
  gi|121636349|ref|YP_976572.1| 254 GPAGVGKATLVRAVCDGRrlvtldgpEIGALAAGDRVKAVASAVQA 299
                                    999********88875333345565688889999999888877665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
                                    EE-TTSSHHHHHHHHHH..HHTEEEEEHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklve..kygfthlsaGdllree 33 
                                    +G+PG+GK+++++ l+   ++ ++ +  ++l+ + 
  gi|121636349|ref|YP_976572.1| 504 YGPPGCGKTFVVRALAStgQLSVHAVKGSELMDKW 538
                                    7************9997224555556655555444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0052       2.3      16      41 ..     246     268 ..     236     275 .. 0.77
   2 ?    2.9   0.0      0.11        51      23      40 ..     501     518 ..     494     527 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0052
                                    TTSCSEEEEEEESTTSSHHHHHHHHC CS
                         NB-ARC  16 delqslvvalvGmgGvGKttlakqil 41 
                                     +l+   v ++G +GvGK tl++ + 
  gi|121636349|ref|YP_976572.1| 246 TNLG---VLVSGPAGVGKATLVRAVC 268
                                    4555...889************9886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                                    EEEEESTTSSHHHHHHHH CS
                         NB-ARC  23 valvGmgGvGKttlakqi 40 
                                    v l+G +G+GKt +++  
  gi|121636349|ref|YP_976572.1| 501 VLLYGPPGCGKTFVVRAL 518
                                    679*********988765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.016       7.4       3      24 ..     250     271 ..     248     285 .. 0.87
   2 ?    3.2   0.1      0.13        58       4      23 ..     502     521 ..     500     535 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                    EEEEESTTCCHHHHHHHHHCT- CS
                           cobW   3 tvltGflGsGKTtLlnhllenr 24 
                                    ++++G+ G GK tL++++++ r
  gi|121636349|ref|YP_976572.1| 250 VLVSGPAGVGKATLVRAVCDGR 271
                                    579**************99554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                    EEEESTTCCHHHHHHHHHCT CS
                           cobW   4 vltGflGsGKTtLlnhllen 23 
                                    +l G++G GKT ++++l + 
  gi|121636349|ref|YP_976572.1| 502 LLYGPPGCGKTFVVRALAST 521
                                    688***********998754 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0092       4.1       1      18 [.     252     269 ..     252     276 .. 0.87
   2 ?    2.1   0.1      0.31   1.4e+02       2      23 ..     504     525 ..     503     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0092
                     ATP_bind_1   1 vvGpaGsGKttfvgalse 18 
                                    v GpaG+GK t+v+a+ +
  gi|121636349|ref|YP_976572.1| 252 VSGPAGVGKATLVRAVCD 269
                                    78************9876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelr 23 
                                     Gp+G GKt  v+al+++ +l+
  gi|121636349|ref|YP_976572.1| 504 YGPPGCGKTFVVRALASTGQLS 525
                                    69************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 4649.66
//
Query:       gi|121636350|ref|YP_976573.1|  [L=286]
Description: CDP-diacylglycerol--serine o-phosphatidyltransferase pssA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-11   42.3   0.7    9.3e-11   42.3   0.7    3.0  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.7   5.2e-15   9.3e-11       2      66 .]      16      79 ..      15      79 .. 0.90
   2 ?   -6.6   9.4         1   1.8e+04      12      17 ..     203     208 ..      85     233 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.2e-15
                                   -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   lP a+T+l+++++++ai + l  +   +a++l+ +a+++D+lDG++AR l  +s++G+ +DslaD
  gi|121636350|ref|YP_976573.1| 16 LPSAMTVLSICAGLTAIKFALEHQ-PKAAMALIAAAAILDGLDGRVARILDAQSRMGAEIDSLAD 79
                                   8****************7554444.59999999999**************99999*********9 PP

  == domain 2  score: -6.6 bits;  conditional E-value: 1
                                    HHHHHH CS
                CDP-OH_P_transf  12 llsvla 17 
                                    ll+vla
  gi|121636350|ref|YP_976573.1| 203 LLAVLA 208
                                    222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2121.33
//
Query:       gi|121636351|ref|YP_976574.1|  [L=231]
Description: phosphatidylserine decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-32  112.1   0.0    7.6e-32  110.5   0.0    1.7  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase
  ------ inclusion threshold ------
      0.043   13.8   0.1         11    6.1   0.0    3.2  3  RnfC_N          RnfC Barrel sandwich hybrid domain
      0.092   12.4   0.7       0.51   10.0   0.4    2.0  2  DUF4131         Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   1.3e-35   7.6e-32       5     199 ..      59     227 ..      55     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.3e-35
                 PS_Dcarbxylase   5 fvrklkdgaRpidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasessadsfkngyfvviyLspgdyHr 84 
                                    +  ++++++R +++ p+aiv+PaDg+i++i                  ++L +++++        +  v+i+Ls+ d H+
  gi|121636351|ref|YP_976574.1|  59 CAGFFRHPQRVPPTRPAAIVAPADGVICAIDSAAPP------------AELSMGDTP--------LPRVSIFLSILDAHV 118
                                    66799*************************777775............455566665........89************* PP

                 PS_Dcarbxylase  85 yhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkG.kvavvpvGatnvgsivlnvlkgdelkkGee 162
                                    ++aPvsg+v  ++h pG++ s++  ++++       neR+ + i+  +G +v+ v+++++++++iv++++ gd+l  G+ 
  gi|121636351|ref|YP_976574.1| 119 QRAPVSGEVIAVQHRPGRFGSADLPEASDD------NERTSVRIRmPNGaEVVAVQIAGLVARRIVCDAHVGDKLAIGDT 192
                                    ******************************......*********758*88***************************** PP

                 PS_Dcarbxylase 163 lGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                    +G+++fGS+ +++++ag   e+ v++gq+  +Ge+++
  gi|121636351|ref|YP_976574.1| 193 YGLIRFGSRLDTYLPAG--AEPIVNVGQRAVAGETVL 227
                                    *****************..99*************997 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.12   7.1e+02      67      86 ..      75      94 ..      71     101 .. 0.83
   2 ?    6.1   0.0    0.0018        11      70      86 ..     120     136 ..     112     145 .. 0.82
   3 ?    2.8   0.0     0.018   1.1e+02      40      58 ..     208     226 ..     201     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                         RnfC_N 67 apvhasvsGtVkaiekrlva 86
                                   a++ a+  G + ai++++ +
  gi|121636351|ref|YP_976574.1| 75 AAIVAPADGVICAIDSAAPP 94
                                   7899**********987765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0018
                         RnfC_N  70 hasvsGtVkaiekrlva 86 
                                     a+vsG+V+a+++r+  
  gi|121636351|ref|YP_976574.1| 120 RAPVSGEVIAVQHRPGR 136
                                    49**********99865 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.018
                         RnfC_N  40 apakplvkvgdkVlkGqki 58 
                                    a a+p+v+vg++   G+ +
  gi|121636351|ref|YP_976574.1| 208 AGAEPIVNVGQRAVAGETV 226
                                    5699********9999865 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   8.5e-05      0.51      15      63 ..      33      78 ..      24      88 .. 0.77
   2 ?    0.1   0.0     0.094   5.6e+02     117     145 ..     116     147 ..     103     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 8.5e-05
                        DUF4131 15 llllllllllrrrprrrvllllllllllallgfalrapqpnandlsqll 63
                                   ++ l+++++     r+r+l + +ll+++a++gf+ + ++ + ++ + ++
  gi|121636351|ref|YP_976574.1| 33 AAGLAIAAV---GHRYRWLRGTGLLAAAACAGFFRHPQRVPPTRPAAIV 78
                                   333333344...68999****************9999998887776655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.094
                        DUF4131 117 ae...glrpGdrlrltgrlkrprpatNpggFD 145
                                    a+   +   G+++++  r+ r+ +a  p++ D
  gi|121636351|ref|YP_976574.1| 116 AHvqrAPVSGEVIAVQHRPGRFGSADLPEASD 147
                                    4444477889**********999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1774.66
//
Query:       gi|121636352|ref|YP_976575.1|  [L=405]
Description: molybdopterin biosynthesis protein moeA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-42  145.4   5.6    1.2e-42  145.4   5.6    2.1  3  MoeA_N         MoeA N-terminal region (domain I and II)
    3.8e-25   88.2   0.1      6e-25   87.6   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
      1e-15   57.6   0.0      6e-15   55.2   0.0    2.4  2  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
        1.1    9.2   0.0        1.1    9.2   0.0    3.0  3  Phage_Coat_B   Phage Coat protein B


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   5.6   2.6e-46   1.2e-42       2     157 .]       3     166 ..       2     166 .. 0.90
   2 ?   -2.2   0.0      0.69   3.1e+03     133     150 ..     182     199 ..     175     212 .. 0.63
   3 ?   -2.5   0.1      0.85   3.8e+03      29      54 ..     215     239 ..     185     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 2.6e-46
                                    -HHHHHHHHHHH-.HH-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--................. CS
                         MoeA_N   2 sveealaiilaal.eleeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saag 72 
                                    sv+e+++ +++++   ++ +vpl ++a+g vl  dvvAp ++P fdnSamDGYAvrae++sga++++p        ++ag
  gi|121636352|ref|YP_976575.1|   3 SVQEHQRVVAEMIrACRPITVPL-TQAQGLVLGGDVVAPLSLPVFDNSAMDGYAVRAEDTSGATPQNPvmlpvaedIPAG 81 
                                    89*****9999994446666***.99**************************************************8888 PP

                                    ..-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHH CS
                         MoeA_N  73 eeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvevkavkpgenvrraGedikaGevllragtrltpaeig 151
                                    +++  +l++  a rimTGap+P+ga+a+vpvE t+   +++   +++++pg+++rr Ged++aG+++l++g+++tpa +g
  gi|121636352|ref|YP_976575.1|  82 RADMLTLQPVtAHRIMTGAPVPTGATAIVPVEATD-GGVDSVAIRQQATPGKHIRRSGEDVAAGTTVLHNGQIVTPAVLG 160
                                    88877777777**********************95.333343344899******************************** PP

                                    HHHHCT CS
                         MoeA_N 152 llasvG 157
                                    l+a++G
  gi|121636352|ref|YP_976575.1| 161 LAAALG 166
                                    ****98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.69
                                    -TTSEEE-TTBB--CCCH CS
                         MoeA_N 133 kaGevllragtrltpaei 150
                                    + G+ l++ gt l+p +i
  gi|121636352|ref|YP_976575.1| 182 STGSELASPGTPLQPGQI 199
                                    556666666666666654 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.85
                                    T-BBSS-EE-SS-BSSS-EESSSEEE CS
                         MoeA_N  29 grvlaedvvApedvPpfdnSamDGYA 54 
                                    g  +++  +A  dv +f  ++ D YA
  gi|121636352|ref|YP_976575.1| 215 GAAVVATATAGDDVAQFG-AILDRYA 239
                                    334444444444444442.3444455 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.1   1.3e-28     6e-25       2     143 ..     180     321 ..     179     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.3e-28
                                    EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH.HHHHHTSSEEEEESS-SSSTT-- CS
                  MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeal.laaleeadviittGGtGptpdDv 73 
                                    vi++G+el+       +g+i+ +n+ +la++++++g+ v ++++ +Dd +++ + l + a  +ad+iit+GG++++++ v
  gi|121636352|ref|YP_976575.1| 180 VISTGSELAspgtplqPGQIYESNSIMLAAAVRDAGAAVVATATAGDDVAQFGAILdRYA-VDADLIITSGGVSAGAYEV 258
                                    89******************************************************7666.555**************** PP

                                    HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                    +++a   + + +   +++ f +v+++pg p+gv+++a      g++i++LPG+p+++ + +e++++p l+
  gi|121636352|ref|YP_976575.1| 259 VKDAFGSA-DYRGGDHGVEFVKVAMQPGMPQGVGRVA------GTPIVTLPGNPVSALVSFEVFIRPPLR 321
                                    *****887.556789*********************4......336*******************99885 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.89     4e+03      54      67 ..     134     147 ..     133     150 .. 0.82
   2 !   55.2   0.0   1.3e-18     6e-15       2      72 .]     336     404 ..     335     404 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.89
                                    E-TT--EE-TT-EE CS
                         MoeA_C  54 ipegtegleaGeeV 67 
                                    i + +e+++aG++V
  gi|121636352|ref|YP_976575.1| 134 IRRSGEDVAAGTTV 147
                                    56778899***998 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 1.3e-18
                                    EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                         MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                    a+l+++l+s++g+r+f R+il++++g  ++ ++g   S+ L++la+Angl+ ipe++ +++aG++ +v+ l
  gi|121636352|ref|YP_976575.1| 336 AVLTASLTSPRGKRQFRRAILDHQAG--TVISYGPPASHHLRWLASANGLLDIPEDVVEVAAGTQLQVWDL 404
                                    799*******************8777..7**************************************9875 PP

>> Phage_Coat_B  Phage Coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00025       1.1      13      52 ..      24      63 ..      20      70 .. 0.86
   2 ?    1.9   0.2     0.046   2.1e+02      10      54 ..      87     133 ..      80     164 .. 0.76
   3 ?   -1.4   0.7       0.5   2.2e+03      23      46 ..     219     241 ..     198     258 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00025
                   Phage_Coat_B 13 pvasfrnlciagsvtaasslpvfaasvidtsavesaitdg 52
                                   p++  + l + g v a  slpvf  s +d  av    t g
  gi|121636352|ref|YP_976575.1| 24 PLTQAQGLVLGGDVVAPLSLPVFDNSAMDGYAVRAEDTSG 63
                                   5566678999**********************99877777 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.046
                   Phage_Coat_B  10 kfspvasfrnlciagsvtaassl.pvfaa.svidtsavesaitdgks 54 
                                     ++pv++ r +  a   t a+++ pv a+ + +d+ a+ +  t gk 
  gi|121636352|ref|YP_976575.1|  87 TLQPVTAHRIMTGAPVPTGATAIvPVEATdGGVDSVAIRQQATPGKH 133
                                    56899999999999998988875377654378999999999999985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.5
                   Phage_Coat_B  23 agsvtaasslpvfaasvidtsave 46 
                                      + ta   +  f  +++d  av+
  gi|121636352|ref|YP_976575.1| 219 VATATAGDDVAQF-GAILDRYAVD 241
                                    2233333333333.3334444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2745.88
//
Query:       gi|121636353|ref|YP_976576.1|  [L=311]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-29  100.8   0.2    8.1e-28   97.2   0.2    2.0  1  adh_short       short chain dehydrogenase
    2.3e-19   69.9   0.2      5e-19   68.8   0.2    1.6  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    2.2e-08   34.2   0.2    3.2e-08   33.7   0.2    1.3  1  KR              KR domain
    2.4e-05   23.9   0.0    3.6e-05   23.4   0.0    1.2  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.02   14.8   0.4      0.033   14.1   0.4    1.4  1  NAD_binding_10  NAD(P)H-binding
      0.022   14.1   0.0      0.046   13.1   0.0    1.6  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.2   2.7e-31   8.1e-28       2     190 ..      23     226 ..      22     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.7e-31
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79 
                                    vv+vtGa  GIG+ +a  +a +Ga+vv++ r+ ek +++ + + ++  ga+++  q+D+ + ++v+a+ ++ +  + ++d
  gi|121636353|ref|YP_976576.1|  23 VVVVTGANTGIGYHTAAVFADRGAHVVLAVRNLEKGNAARARIMAArpGAHVTLQQLDLCSLDSVRAAADALRTAYPRID 102
                                    9*******************************************99999******************************* PP

                                    EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGT.............SB-TTB CS
                      adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagk.............vpvagv 146
                                    vL+nNAG+ +  + ++++++ +e  + +N  g f lt +vl++ml   + r+v+vsS+  +              +++ v
  gi|121636353|ref|YP_976576.1| 103 VLINNAGVMW--TPKQVTKDGFELQFGTNHLGHFALTGLVLDHMLPVPGSRVVTVSSQGHRihaaihfddlqweRRYNRV 180
                                    ********54..455688999************************************86551111122222222467899 PP

                                    HHHHHHHHHHHHHHHHHHHHHGGGT...EEEEEEEESSBSSHHHHHH CS
                      adh_short 147 aaYsAsKaavagltrslakelaptg...irvnavaPGlvdTdmakel 190
                                    aaY+ +K a   +t +l++ l + g   i v a +PG+ +T+++++l
  gi|121636353|ref|YP_976576.1| 181 AAYGQAKLANLLFTYELQRRLGEAGkstIAV-AAHPGGSNTELTRNL 226
                                    *********************9999874554.678*******99875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.2   1.7e-22     5e-19       1     133 [.      28     162 ..      28     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.7e-22
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                    Ga  gIG+++A  +a++Ga+vvl+ +n e+  ++r++ +a++ ga+v   ++D  + ++v+a++++++  + ++D+l+nn
  gi|121636353|ref|YP_976576.1|  28 GANTGIGYHTAAVFADRGAHVVLAVRNLEKgnAARARIMAARPGAHVtlQQLDLCSLDSVRAAADALRTAYPRIDVLINN 107
                                    8899***********************99987778888888889997789****************************** PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTS CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaer 133
                                    ag++ +      ++++++f+  + +n  + f+l+  +l +m +   +++v++ss g ++
  gi|121636353|ref|YP_976576.1| 108 AGVMWT----PKQVTKDGFELQFGTNHLGHFALTGLVLDHMLPVpgSRVVTVSSQGHRI 162
                                    *****9....5689*************************66543338899999987654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.2   1.1e-11   3.2e-08       3      93 ..      24     112 ..      22     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.1e-11
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeepp 81 
                                    +++tG+  g+G ++a   a++ga h+vl  R+ ++ ++++a+i  ++a+ ga+v++ ++D+ + d+v+a+ +++++  p+
  gi|121636353|ref|YP_976576.1|  24 VVVTGANTGIGYHTAAVFADRGA-HVVLAVRNLEKGNAARARI--MAARpGAHVTLQQLDLCSLDSVRAAADALRTAYPR 100
                                    79********************8.7899999956555555555..55555****************************** PP

                                    --EEEE------ CS
                             KR  82 ikGvihaAgvlr 93 
                                    i   i+ Agv+ 
  gi|121636353|ref|YP_976576.1| 101 IDVLINNAGVMW 112
                                    *********985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   3.6e-05       1     195 [.      24     235 ..      24     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
                                    EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHH...H..T-S CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl........elveldltdrsalerlfke...e..qpd 66 
                                    ++VtGa+  iG +++  ++++g + v+++ +l +++n ar +          +l +ldl+  ++++++ +       ++d
  gi|121636353|ref|YP_976576.1|  24 VVVTGANTGIGYHTAAVFADRGAHvVLAVRNL-EKGNAARARIMaarpgahvTLQQLDLCSLDSVRAAADAlrtAypRID 102
                                    68********************7736666666.6666666555589**************9997776655422133689* PP

                                    EEEE--S---HHHHHHSH..HHHHHHHTHHHHHHHHHHHHHTCT....EEEEEEEGGGGTSCSSSSBSTCSTTS----SS CS
                      Epimerase  67 avihlAavggvaassedp..adfieknlqgtlnlleaarkagvk....rllflsSsevYGkdaeqpkeettltgplkpns 140
                                    + i+ A+v   + ++++   +  + +n  g   l   + ++ +     r++ +sS       a    ++   +  ++   
  gi|121636353|ref|YP_976576.1| 103 VLINNAGVMWTPKQVTKDgfELQFGTNHLGHFALTGLVLDHMLPvpgsRVVTVSSQGHRIHAAI-HFDDLQWERRYNRVA 181
                                    *****99666555555541244566999999999999999944444669999999333222222.24444446678999* PP

                                    HHHHHHHHHHHHHHHHHHHHT..-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHT CS
                      Epimerase 141 pYaaaKlageklveayaaqyg..lnaiilrlfnlyGprngegevsrvipalirkile 195
                                    +Y+ aKla    + ++++  g   + +i    +  G +   +e +r +p+lir +++
  gi|121636353|ref|YP_976576.1| 182 AYGQAKLANLLFTYELQRRLGeaGKSTIAVAAHPGGSN---TELTRNLPRLIRPVAT 235
                                    *******9999999998887644577777778888888...8899999999987765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.1e-05     0.033       1     105 [.      28     164 ..      28     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.......HHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEE CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.......eleaeeglevvegdvtdvedlaealk.......gadaVvs 66 
                                    GA+ ++G + ++  ++rg  +v++ vRn ek +       + +  +++++ ++d+ + +++++a +        +d+ + 
  gi|121636353|ref|YP_976576.1|  28 GANTGIGYHTAAVFADRG-AHVVLAVRNLEKGNaararimAARPGAHVTLQQLDLCSLDSVRAAADalrtaypRIDVLIN 106
                                    9****************5.99*******776652222222222347889999***9999998888766666667788888 PP

                                    S---TCCHHHH...................HHHHHHHHHHCT--EEEEEEETTTTSGC CS
                 NAD_binding_10  67 alggggkdeeg...................aknivdaakeagvkRfvlvsaigvgdev 105
                                    ++g  ++ +++                   +  ++d +     +R+v+vs+ g + ++
  gi|121636353|ref|YP_976576.1| 107 NAGVMWTPKQVtkdgfelqfgtnhlghfalTGLVLDHMLPVPGSRVVTVSSQGHRIHA 164
                                    8877766444444446666677777777777777888888888888888887766544 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.046       2      72 ..      26      92 ..      25     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHH CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerlla 72
                                   +TG +  iG ++a  + ++g +v+  vr+ ++ n++r + +a +p ++    ++l + Dl+  +s++ + +
  gi|121636353|ref|YP_976576.1| 26 VTGANTGIGYHTAAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAH----VTLQQLDLCSLDSVRAAAD 92
                                   9999999********************************999988765....89******99888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2039.31
//
Query:       gi|121636354|ref|YP_976577.1|  [L=540]
Description: chaperonin GroEL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-96  323.5  12.7    2.9e-96  323.1  12.7    1.2  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.1  12.7  1.6e-100   2.9e-96       1     491 []      22     522 ..      22     522 .. 0.92

  Alignments for each domain:
  == domain 1  score: 323.1 bits;  conditional E-value: 1.6e-100
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHH....HHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPa....akllveaaesqdeevGDGTttvviLageLlee 76 
                                    lad+vk+tlGPkG++++l++k g++++TnDG++i+ke+e+e+P+    a+l+ e+a+++d+ +GDGTtt+++La++L++e
  gi|121636354|ref|YP_976577.1|  22 LADAVKVTLGPKGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYekigAELVKEVAKKTDDVAGDGTTTATVLAQALVRE 101
                                    79****************************************************************************** PP

                                    HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCC CS
                     Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieen 156
                                    + + +aag++p  +++g+eka+ek+ e L + a+e++++    e++++ a++s++ +        +++l+++A+      
  gi|121636354|ref|YP_976577.1| 102 GLRNVAAGANPLGLKRGIEKAVEKVTETLLKGAKEVETK----EQIAATAAISAGDQ-------SIGDLIAEAM------ 164
                                    *****************************8888888877....89999999988776.......8*********...... PP

                                    SEECSCCCEECCCCEECEC..TTSEEESEEEESS--SST.......TSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                     Cpn60_TCP1 157 ekeldlgrikvvkieggsl..edselveGlvldkgvlsp.......dmpkklenakvllldvsLeiektetkttvvlsda 227
                                        ++g+ +v+++e+++    + el eG+ +dkg++s          +  le++++ll++ ++++ k+           
  gi|121636354|ref|YP_976577.1| 165 ---DKVGNEGVITVEESNTfgLQLELTEGMRFDKGYISGyfvtdpeRQEAVLEDPYILLVSSKVSTVKD----------- 230
                                    ...99**************55555666************9998775456666*****************........... PP

                                    CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S-...........-HHHHHHHHHHHT-- CS
                     Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrv...........kkkdlerlakatGat 296
                                                 l++llek+i +g+++++++++++ +al++l+ n+i++  +            +k++l+++a++tG++
  gi|121636354|ref|YP_976577.1| 231 -------------LLPLLEKVIGAGKPLLIIAEDVEGEALSTLVVNKIRGTFKSvavkapgfgdrRKAMLQDMAILTGGQ 297
                                    .............**************************************9999************************* PP

                                    EBSCGGGGGCGC.....-EEEEEEEECCETTCCEEEEE...................................CESSSSX CS
                     Cpn60_TCP1 297 avssledltpee.....lGtakkveeekigsekttiie...................................evksgki 336
                                    ++s+   lt e+     lG+a+kv    +++++tti+e                                     + g++
  gi|121636354|ref|YP_976577.1| 298 VISEEVGLTLENadlslLGKARKV---VVTKDETTIVEgagdtdaiagrvaqirqeiensdsdydreklqerlAKLAGGV 374
                                    *****5555433346669999999...9**********88888888887777777777666666666555555339**** PP

                                    EEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHH CS
                     Cpn60_TCP1 337 atillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktL 416
                                    a+i+ ++at+++l+e++ +iedA++ +k+a+e e++v+GGG+t+l++a  l+e   +++g+e+ ++++++ ALe+++k++
  gi|121636354|ref|YP_976577.1| 375 AVIKAGAATEVELKERKHRIEDAVRNAKAAVE-EGIVAGGGVTLLQAAPTLDEL--KLEGDEATGANIVKVALEAPLKQI 451
                                    ********************************.******************444..479********************* PP

                                    HHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXXX CS
                     Cpn60_TCP1 417 aeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiikakk 491
                                    a N+Gl+p  v +k+r+        +g+++++g ++dl++agv Dp+kv+r+al++A+++a ++L++++++ +k+
  gi|121636354|ref|YP_976577.1| 452 AFNSGLEPGVVAEKVRN---LP-AGHGLNAQTGVYEDLLAAGVADPVKVTRSALQNAASIAGLFLTTEAVVADKP 522
                                    ***************99...33.377*********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3710.01
//
Query:       gi|121636355|ref|YP_976578.1|  [L=142]
Description: hypothetical protein BCG_0480c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1028.44
//
Query:       gi|121636356|ref|YP_976579.1|  [L=479]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-55  186.6  29.2      3e-55  186.6  29.2    1.6  2  PPE             PPE family
    6.8e-22   77.1 146.6    4.6e-09   36.0  30.2    7.2  6  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.6  29.2   3.3e-59     3e-55       2     157 ..       1     156 [.       1     157 [. 0.99
   2 ?   -5.4   2.8         2   1.8e+04      10      45 ..     301     336 ..     298     359 .. 0.46

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 3.3e-59
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    +pPE+nsal++aGpgsgpl+aAa+aW +La+el ++ a+l sv++el+++aW Gps+aam+a a++ylaWLs+aaaqae+
  gi|121636356|ref|YP_976579.1|   1 MPPEINSALMFAGPGSGPLIAAATAWGELAEELLASIASLGSVTSELTSGAWLGPSAAAMMAVATQYLAWLSTAAAQAEQ 80 
                                    7******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    aAaqa a+a+a+eaAlaa+v+pa++aanr  ++ l+atn+fGqn+pa +++ea+ye+mwa d+aama+Y+  ++aa
  gi|121636356|ref|YP_976579.1|  81 AAAQAMAIATAFEAALAATVQPAVVAANRGLMQLLAATNWFGQNAPALMDVEAAYEQMWALDVAAMAGYHFDASAA 156
                                    **********************************************************************999887 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 2
                                    HHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  10 llyaGpgsgpllaAaaaWdgLaaelasaaaelesvl 45 
                                    +++aG gs+  l       g+ +    +aa  e+ l
  gi|121636356|ref|YP_976579.1| 301 TINAGLGSAGSLNTSFWNAGMQNAALGSAAGSEAAL 336
                                    555555555444444333344333222222222222 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4  32.5   2.2e-09     2e-05       4      39 ..     178     213 ..     175     214 .. 0.77
   2 !   36.0  30.2   5.1e-13   4.6e-09       1      39 [.     210     248 ..     210     249 .. 0.98
   3 !   33.9  31.3   2.3e-12     2e-08       2      40 .]     253     291 ..     252     291 .. 0.96
   4 !   17.5  14.4   3.2e-07    0.0029       1      38 [.     287     324 ..     287     325 .. 0.97
   5 ?   -4.6   8.7         2   1.8e+04       7      34 ..     376     403 ..     353     422 .. 0.64
   6 !    3.6   1.0    0.0071        64       6      17 ..     428     439 ..     413     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.2e-09
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    G  N+G gNtG++N+G+ N+G++N+GsgNtG gn+G
  gi|121636356|ref|YP_976579.1| 178 GQINLGFGNTGSGNIGNNNIGNNNIGSGNTGTGNIG 213
                                    677888888888888888888888888888888877 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 5.1e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+GsgN+G++NlG gN+G++N+GsgN+G+g tG
  gi|121636356|ref|YP_976579.1| 210 GNIGTGNTGSGNLGLGNLGDGNIGFGNTGSGNIGFGITG 248
                                    8*************************************9 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 2.3e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                     +G +NsGsgN+Gf+N+G+gN+G fN+GsgN+G+gn+Gs
  gi|121636356|ref|YP_976579.1| 253 GFGGFNSGSGNIGFGNSGTGNVGLFNSGSGNIGIGNSGS 291
                                    58************************************6 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 3.2e-07
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    gN+GslNsG g +G+ N G g+ Gs N+ + N G+ n+
  gi|121636356|ref|YP_976579.1| 287 GNSGSLNSGIGTSGTINAGLGSAGSLNTSFWNAGMQNA 324
                                    8**********************************996 PP

  == domain 5  score: -4.6 bits;  conditional E-value: 2
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtG 34 
                                    NsG +Nt  +   s+ +G   +G+ N G
  gi|121636356|ref|YP_976579.1| 376 NSGLTNTPVAAPASAPVGGLDSGNPNPG 403
                                    3333333333333333333333333333 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.0071
                 Pentapeptide_2   6 lNsGsgNtGffN 17 
                                    +NsGs  +G+ N
  gi|121636356|ref|YP_976579.1| 428 VNSGSNDSGLRN 439
                                    333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3105.18
//
Query:       gi|121636357|ref|YP_976580.1|  [L=171]
Description: hypothetical protein BCG_0482 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-41  141.7   0.8    3.4e-41  141.1   0.8    1.3  1  DUF664    Protein of unknown function (DUF664)
    1.2e-14   54.9   1.0    1.6e-14   54.5   1.0    1.2  1  DinB_2    DinB superfamily


Domain annotation for each model (and alignments):
>> DUF664  Protein of unknown function (DUF664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.8   3.8e-45   3.4e-41       2     147 ..      12     169 ..      11     171 .] 0.98

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 3.8e-45
                                    HHHHHHHHHHHHHHHHTT--GGGTT--BTTB-S-HHHH...........HHHHHHHHHHHHHHHTT-S---TTTSHH.TT CS
                         DUF664   2 LeafLdrqretllakleGLsdeqarrravpsstsllgL...........vkHvaevErgwfrrvlggeeevpldrsa.ad 69 
                                    L+++++r +e++++ ++GL+d+ a++r++ps++s+++L           v+Hva+vE++w+r+ + +++ ++l+r++  +
  gi|121636357|ref|YP_976580.1|  12 LRDAFTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLlwhsarvqdiqVAHVAGVEEVWTRDGWVDRFGLDLPRHDtGY 91 
                                    899***************************************************************************** PP

                                    TSSS---SS---HHHHHHHHHHHHHHHHHHHTT--HHHHTSB-T-......SBHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF664  70 pdadfelaedetladllaeyrravaradavvaaeldldetvrvpkapwgeevslrwvlvhlieetarHaGhadilRel 147
                                    ++++ ++a+ +++adll+ y++av++ +  + a++++de +rv++++w+++v+++++lv++++++a+H G+a++lR++
  gi|121636357|ref|YP_976580.1|  92 GHRPEDVAKVRAPADLLSGYYHAVHKLTLEYIAGMTADELSRVVDTSWNPPVTVSARLVSIVDDCAQHLGQAAYLRGI 169
                                    ******************************999*******************************************86 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   1.0   1.8e-18   1.6e-14       2     128 .]      16     163 ..      15     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.8e-18
                         DinB_2   2 lerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlrgeeaprpgldpltp................ 65 
                                    ++r ++ + +l+++lt++ + ++p p  +siawll+H + v+++ ++++ g e++++++ ++                  
  gi|121636357|ref|YP_976580.1|  16 FTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLLWHSARVQDIQVAHVAGVEEVWTRDGWVDRfgldlprhdtgyghrp 95 
                                    677889999*****************************************999995554444445555555555556777 PP

                         DinB_2  66 .......psaaealaylaevrarllallealtdadldrpltaphpglgkltlgdvllfvlqHeqhHleqi 128
                                            +a+ +  y+ +v++ +l+ ++++t+++l r + +     +++t+   l  ++   ++Hl+q+
  gi|121636357|ref|YP_976580.1|  96 edvakvrAPADLLSGYYHAVHKLTLEYIAGMTADELSRVVDTS--WNPPVTVSARLVSIVDDCAQHLGQA 163
                                    677777556667779****************************..99*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1338.08
//
Query:       gi|121636358|ref|YP_976581.1|  [L=232]
Description: hypothetical protein BCG_0483c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-24   86.6  23.9    7.5e-24   85.0  23.9    1.7  1  RskA      Anti-sigma-K factor rskA
  ------ inclusion threshold ------
       0.17   11.2   0.2       0.23   10.7   0.2    1.1  1  DUF3379   Protein of unknown function (DUF3379)


Domain annotation for each model (and alignments):
>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0  23.9   8.3e-28   7.5e-24      14     179 ..      60     228 ..      18     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 8.3e-28
                                    -X.............................XXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXX...... CS
                           RskA  14 aatpqaaaaaaaaaaapppaaapaararr..laaaaAaalllvlgqlavasaaldplrqsaaqaeavvavlaap...... 85 
                                    aat+++++a  + a  ++++++ ++++r+  +a a Aaa++++lg     + +l  l ++ ++++ + +vl+ap      
  gi|121636358|ref|YP_976581.1|  60 AATTAEPPAHLRTAILDATKPEVRRQSRWrtAAFASAAAIAVGLG-----AFDLGVLTRPSPPPTVAEQVLTAPdvrtvs 134
                                    445555555555555666666666666664455555555566666.....899*********************999877 PP

                                    .XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           RskA  86 .daagatatvvdsasggalvldvsglpalpagkvyqlWlipaggkpvslGvleaggsatltlpagpdlgaaaavaVTlEp 164
                                       +++tatvv+s++++  +l+++++++++ g vyq+Wl+   ++p+s+ +++++++++ t++++ dlga++a+a T+Ep
  gi|121636358|ref|YP_976581.1| 135 rPLGAGTATVVFSRDRNTGLLVMNNVAPPSRGTVYQMWLLGGAKGPRSAETMGTAAVTPSTTATLTDLGASTALAFTVEP 214
                                    65556***********************************999************************************* PP

                                    XXXXXXX..XXXXXX CS
                           RskA 165 aGGsqPtpsgpvvar 179
                                      Gs P p+g+++a+
  gi|121636358|ref|YP_976581.1| 215 GTGS-PQPTGTILAE 228
                                    ****.8888***985 PP

>> DUF3379  Protein of unknown function (DUF3379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   2.6e-05      0.23      11      94 ..      21     104 ..      17     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.6e-05
                        DUF3379  11 ladPkqqdeevleaakaseekakfvkdlkaldkkl...kqalkvdvPedLaeklllkqsleekaarkrktrvalAlaASv 87 
                                    ++d +++d +   aa+ s+  a+f ++++a+ +++   ++a   + P+ L   +l  ++ e ++   ++++++ A a + 
  gi|121636358|ref|YP_976581.1|  21 VSDDERADIDRRVAAAPSPVAAAFNDEVRAVRETMavvSAATTAEPPAHLRTAILDATKPEVRR---QSRWRTAAFASAA 97 
                                    667778888888999999*********99998876222577889*******9998655544443...3444444444445 PP

                        DUF3379  88 afvvgls 94 
                                    a++vgl 
  gi|121636358|ref|YP_976581.1|  98 AIAVGLG 104
                                    5666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1807.61
//
Query:       gi|121636359|ref|YP_976582.1|  [L=187]
Description: RNA polymerase sigma factor SigK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-14   53.1   2.5    3.2e-14   52.5   0.2    2.3  2  Sigma70_r2    Sigma-70 region 2
    2.7e-13   49.2   0.1    2.7e-13   49.2   0.1    2.2  4  Sigma70_r4    Sigma-70, region 4
      5e-11   42.1   0.9    9.7e-11   41.2   0.9    1.5  1  Sigma70_r4_2  Sigma-70, region 4
     0.0019   17.9   0.0     0.0046   16.7   0.0    1.6  1  HTH_38        Helix-turn-helix domain
     0.0029   17.5   1.4     0.0056   16.6   1.4    1.5  1  Sigma70_ECF   ECF sigma factor
  ------ inclusion threshold ------
       0.16   11.5   0.3       0.44   10.2   0.0    1.8  2  HTH_24        Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.2   1.1e-17   3.2e-14       1      69 [.      29      96 ..      29      98 .. 0.96
   2 ?   -0.6   0.1      0.39   1.2e+03      55      69 ..     167     181 ..     166     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.1e-17
                                   HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2  1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69
                                   ++++ + +v++l++r+l++    e+ +Qe++l +wr++  fd ++g s+ awll++a+++a dr+R ++
  gi|121636359|ref|YP_976582.1| 29 FYDHTKSRVYGLVMRVLRDTGYSEETTQEIYLEVWRNASEFDSAKG-SALAWLLTMAHRRAVDRVRCEQ 96
                                   5788899***************************************.*******************876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHHTSS CS
                     Sigma70_r2  55 riarnaaidrlRkrr 69 
                                    ++++ ++ d+lR+ r
  gi|121636359|ref|YP_976582.1| 167 STIKSRMRDALRSLR 181
                                    579999999999865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.7     8e+03      16      37 ..      16      37 ..      15      37 .. 0.65
   2 ?   -2.0   0.1      0.88   2.6e+03      15      26 ..      45      58 ..      40      58 .. 0.60
   3 ?   -3.3   0.1       2.3   6.7e+03      41      49 ..      85      93 ..      84      93 .. 0.83
   4 !   49.2   0.1   9.1e-17   2.7e-13       1      50 []     133     182 ..     133     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                                   HHTTT--HHHHHHHHTS-HHHH CS
                     Sigma70_r4 16 rfgeglTleEIgerlgiSrerV 37
                                   r++ g+ ++  +e ++ +++rV
  gi|121636359|ref|YP_976582.1| 16 RRVAGHDQAAFAEFYDHTKSRV 37
                                   5555666666677788888887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.88
                                   HHH..TTT--HHHH CS
                     Sigma70_r4 15 lrf..geglTleEI 26
                                   lr   + + T +EI
  gi|121636359|ref|YP_976582.1| 45 LRDtgYSEETTQEI 58
                                   23355777788887 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.3
                                   HHHHHHHHH CS
                     Sigma70_r4 41 ekrAlrkLR 49
                                   ++rA++++R
  gi|121636359|ref|YP_976582.1| 85 HRRAVDRVR 93
                                   689999988 PP

  == domain 4  score: 49.2 bits;  conditional E-value: 9.1e-17
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                                    +L+ L++ +r+++el ++ glT+ E+++rl   ++++++++++Alr LR+
  gi|121636359|ref|YP_976582.1| 133 CLKALTDTQRQCIELAYYGGLTYVEVSRRLAANLSTIKSRMRDALRSLRN 182
                                    699*********************************************95 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.9   3.3e-14   9.7e-11       1      54 []     127     180 ..     127     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.3e-14
                                    HHHHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   1 rqalrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    r+++ e+l +L+  qr++++l y+ gl+y E++++l  + +t+ksr++ A++ L
  gi|121636359|ref|YP_976582.1| 127 RRRVTECLKALTDTQRQCIELAYYGGLTYVEVSRRLAANLSTIKSRMRDALRSL 180
                                    57899*********************************************9976 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0046       3      37 ..     135     169 ..     133     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                         HTH_38   3 khLsleeReeIerllaeGlslreIArrLgrspsTI 37 
                                    k L+ ++R++Ie  +  Gl++ e+ rrL  + sTI
  gi|121636359|ref|YP_976582.1| 135 KALTDTQRQCIELAYYGGLTYVEVSRRLAANLSTI 169
                                    78***************************999999 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.4   1.9e-06    0.0056       9     173 ..      16     174 ..       8     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-06
                    Sigma70_ECF   9 eqvkdGdaeaaeqllelvydeLrrlagskl.knerreetledtaL.vfeaflrlvdkekfpdlsgrdhlfalaaeamrri 86 
                                    + v   d++a ++ + +  +++  l+ + l      eet +++ L v+        +++++  s ++   a ++++  r 
  gi|121636359|ref|YP_976582.1|  16 RRVAGHDQAAFAEFYDHTKSRVYGLVMRVLrDTGYSEETTQEIYLeVW--------RNASEFDSAKGSALAWLLTMAHRR 87 
                                    555555555555555555555555555555333334444444433222........233333355667777788899999 PP

                    Sigma70_ECF  87 lidhaRrrkr.qkRGGdvvraeldeeeds..vdsdspdelleLdealerllsldpeqarlvelrkleGlsveEiAeklgv 163
                                     +d+ R +++ ++R   +  a++d   d     + + de+  + e l+   +l + q++ +el++  Gl+  E++ +l  
  gi|121636359|ref|YP_976582.1|  88 AVDRVRCEQAgNQREVRYGAANVDPASDVvaDLAIAGDERRRVTECLK---ALTDTQRQCIELAYYGGLTYVEVSRRLAA 164
                                    999999876524454444444444444331112345566666666555...5677899********************** PP

                    Sigma70_ECF 164 skrtverrla 173
                                      +t++ r++
  gi|121636359|ref|YP_976582.1| 165 NLSTIKSRMR 174
                                    *****98875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   9.1e+03      34      42 ..     130     138 ..     128     139 .. 0.74
   2 ?   10.2   0.0   0.00015      0.44      16      40 ..     151     175 ..     146     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                         HTH_24  34 vnrrlkrLe 42 
                                    v+++lk L+
  gi|121636359|ref|YP_976582.1| 130 VTECLKALT 138
                                    788888886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                         HTH_24  16 prisqreLAerlglSpstvnrrlkr 40 
                                    +++++ e+++rl   +st++ r++ 
  gi|121636359|ref|YP_976582.1| 151 GGLTYVEVSRRLAANLSTIKSRMRD 175
                                    89*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1320.27
//
Query:       gi|121636360|ref|YP_976583.1|  [L=256]
Description: hypothetical protein BCG_0485c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.1e-78  261.2   1.3    9.4e-78  261.0   1.3    1.0  1  DUF1295     Protein of unknown function (DUF1295)
    4.9e-06   26.9   0.1    1.5e-05   25.3   0.1    1.8  1  PEMT        Phospholipid methyltransferase
    8.1e-05   22.6   0.0    0.00014   21.9   0.0    1.3  1  Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
    0.00022   21.6   0.4    0.00061   20.2   0.1    1.9  2  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
  ------ inclusion threshold ------
        7.1    7.0   9.6       0.98    9.7   0.4    2.6  2  DUF3040     Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.0   1.3   2.6e-81   9.4e-78       1     235 []      17     243 ..      17     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.0 bits;  conditional E-value: 2.6e-81
                        DUF1295   1 lflislltkssslvDvlwgvlfvilavltlllseaaklrrllvllLvvlWglRLalhllrrtlkkgeDkryeelrkelgk 80 
                                    +f+i+++++++++vDv+wg+ fv++av++++l++++ +rr+l+l+Lv +WglRL++h++r+t+++geD+ry++l +  g+
  gi|121636360|ref|YP_976583.1|  17 AFAIGRRIGRYNVVDVVWGLGFVAVAVAAATLGHGDPVRRWLLLALVSTWGLRLSWHMYRKTAGQGEDPRYADLLR--GA 94 
                                    599************************************************************************9..66 PP

                        DUF1295  81 tiallsllvvfvlQavllylvalpvllaaaskeeq.alkaldviglalwlvgivlealaDqQlsafkkdpankgkvldsG 159
                                    t+++ +l +vf lQ +l+++v++p++l+a++++++ +l a+  +gla+wlvgi++ea++D+Ql+ fk+dpan+g ++d+G
  gi|121636360|ref|YP_976583.1|  95 TPVQ-ALRKVFGLQGLLTLFVSFPLQLSAVTGPTPkPLLAVGGVGLAVWLVGITFEAVGDWQLWVFKSDPANRGVIMDRG 173
                                    6665.9999***********************999899****************************************** PP

                        DUF1295 160 LwrysRHPNYfgealiWwglflialealeglealaiagpllltlllvfvsgipllEkkalkkykdkeeyreYqkkt 235
                                    Lw ++RHPNYfg+a++Wwgl+li+++++++l  +++ +pll+t+llv+vsg +l+E    ++ k ++ ++eYq++t
  gi|121636360|ref|YP_976583.1| 174 LWAWTRHPNYFGDACVWWGLWLITINDWAPL--ATVGSPLLMTYLLVDVSGARLTE----RYLKGRPGFAEYQRRT 243
                                    ******************************9..***********************....777789********98 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   4.1e-09   1.5e-05       6      91 ..     133     219 ..     129     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.1e-09
                           PEMT   6 GlllialglllvlssiealgefgtfygdfFlelmd..klvtsGiYrylnnPeyvgstlgflGlaLitgsaag.lllallv 82 
                                    ++  + l ++lv  ++ea+g+++  + +   +  +   ++ +G++ ++++P y+g  ++++Gl Lit + ++ l+ +  +
  gi|121636360|ref|YP_976583.1| 133 AVGGVGLAVWLVGITFEAVGDWQLWVFKS--DPANrgVIMDRGLWAWTRHPNYFGDACVWWGLWLITINDWApLATVGSP 210
                                    56667889999999******998775554..222245999**************************98888757777777 PP

                           PEMT  83 llvylialk 91 
                                    ll++++++ 
  gi|121636360|ref|YP_976583.1| 211 LLMTYLLVD 219
                                    777777765 PP

>> Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   3.8e-08   0.00014      44     110 ..     137     204 ..     129     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.8e-08
                     Steroid_dh  44 lgivlfvlgmliniksdiiLrelrkegetkykiprgglFelvsapnyfgEilewigyalvtks.laal 110
                                    +g++++++g++ +  +d +L   + +  +  +i   gl+ +   pnyfg+++ w g+ l+t + +a l
  gi|121636360|ref|YP_976583.1| 137 VGLAVWLVGITFEAVGDWQLWVFKSDPANRGVIMDRGLWAWTRHPNYFGDACVWWGLWLITINdWAPL 204
                                    6899**************************************************99887764325544 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   6.8e+03       8      24 ..      51      67 ..      35      74 .. 0.56
   2 !   20.2   0.1   1.7e-07   0.00061      23      81 ..     154     216 ..     137     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                           ICMT  8 aqalrlvvmatlGeiwt 24
                                   +  +r + +  l + w 
  gi|121636360|ref|YP_976583.1| 51 GDPVRRWLLLALVSTWG 67
                                   33445555555555555 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.7e-07
                           ICMT  23 wttrvai...lpdhklvksglykylrHPnYll..fvilelatllLlcnakltalvllalvalll 81 
                                    w   v+    ++   ++++gl++++rHPnY++   v++ l  + +   a  +a+v ++l +  l
  gi|121636360|ref|YP_976583.1| 154 WQLWVFKsdpANRGVIMDRGLWAWTRHPNYFGdaCVWWGLWLITINDWA-PLATVGSPLLMTYL 216
                                    555555544455667899*************832355555544443333.47777777766655 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.3      0.22     8e+02      42      66 ..      22      46 ..       2      70 .. 0.58
   2 ?    9.7   0.4   0.00027      0.98      20      81 ..      82     145 ..      81     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                        DUF3040 42 rrlavlavllfvaGllllvlGvaaa 66
                                   rr +   v+ +v Gl ++ + vaaa
  gi|121636360|ref|YP_976583.1| 22 RRIGRYNVVDVVWGLGFVAVAVAAA 46
                                   2333444445555555555555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                        DUF3040  20 aeDPklaaalrggaararrrslrrlavlavllfva..Glll.lvlG.vaaaavvlgvvGfvvmlag 81 
                                     eDP+ a+ lrg ++ ++ r  +  +++++l++++  +l l  v+G +    +++g vG++v l+g
  gi|121636360|ref|YP_976583.1|  82 GEDPRYADLLRGATPVQALR--KVFGLQGLLTLFVsfPLQLsAVTGpTPKPLLAVGGVGLAVWLVG 145
                                    69********9999997777..45667777666661355544555644444477777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1778.81
//
Query:       gi|121636361|ref|YP_976584.1|  [L=427]
Description: cyclopropane-fatty-acyl-phospholipid synthase ufaA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-105  352.0   0.0   2.3e-105  351.8   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    2.6e-10   40.4   0.0    3.8e-10   39.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-09   38.4   0.0    3.1e-09   37.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.5e-08   35.1   0.0    3.1e-08   34.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    3.5e-06   27.7   0.0    6.1e-06   26.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.4e-05   24.2   0.0    3.4e-05   23.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.16   11.5   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.8   0.0  9.1e-109  2.3e-105       1     273 []     140     419 ..     140     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: 351.8 bits;  conditional E-value: 9.1e-109
                                    .XSXXXHHHHHHHHTS-HHHHCTTS-TT---S----SS.......TT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TT CS
                           CMAS   1 qkkkkevenikahYDlsndffalfldptmtYsCAyfer.......ddmtLeeAqlaKldlileklelkpGmtlLdiGcGW 73 
                                    ++++++++ni+ hYDlsnd+fa+fld+tmtYsCA+f++       ++++L++Aq++K+d++l+++++++G+++L+iG+GW
  gi|121636361|ref|YP_976584.1| 140 HSRDQARRNIAVHYDLSNDLFAAFLDETMTYSCAMFTDllaqptpAWTELAAAQRRKIDRLLDVAGVQQGSHVLEIGTGW 219
                                    578899**************************************9*********************************** PP

                                    SHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHH CS
                           CMAS  74 GslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklk 153
                                    G+l++ra++r ++++ ++TlS eq++la++rv+++++ ++ve++l+dy+d+d+++d+vvsv+++e+vg+++++++f++l+
  gi|121636361|ref|YP_976584.1| 220 GELCIRAAAR-GAHIRSVTLSVEQQRLARQRVAAAGFGHRVEIDLCDYRDVDGQYDSVVSVEMIEAVGYRSWPRYFAALE 298
                                    **********.********************************************************************* PP

                                    HHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS---BHHHHHH.HHHHTT-EEEEEEE-HHHHHHHHHHHHHH CS
                           CMAS 154 kllkedGllllhtitslhkkelaerglklkfidkeiFPgGelpsieeiee.eiseagftvvdveslrahYakTLkaWaea 232
                                    +l++++G +++++it++h+++la+r+++ ++i+k+iFPgG lps+++i++ + +++g+++vd++slr+hYa+TL++W+e+
  gi|121636361|ref|YP_976584.1| 299 QLVRPGGPVAIQAITMPHHRMLATRHTQ-TWIQKYIFPGGLLPSTQAIIDiTGQHTGLRIVDAASLRPHYAETLRLWRER 377
                                    **************************99.*******************99899*************************** PP

                                    HHHTHHHHHHH.SHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 233 lqenkdeaial.vseevarmyelYLagcaeaFrkgyidvaql 273
                                    +++++d +++l ++e +arm+elYLa++++ Fr+gy+dv+q+
  gi|121636361|ref|YP_976584.1| 378 FMQRRDGLAHLgFDEVFARMWELYLAYSEAGFRSGYLDVYQW 419
                                    ****************************************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   1.5e-13   3.8e-10       7     125 ..     191     317 ..     185     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.5e-13
                Methyltransf_23   7 eelsdklerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq....eaaepq 80 
                                     + ++k++rll+    ++g+ vL+iG+G G+l+  ++++g+++  v ls e++ +a+++  a    ++ +    + ++ +
  gi|121636361|ref|YP_976584.1| 191 AAQRRKIDRLLDVagVQQGSHVLEIGTGWGELCIRAAARGAHIRSVTLSVEQQRLARQRVAAAGFGHRVEidlcDYRDVD 270
                                    45567888888664469999******************************999999955555555554444444577788 PP

                Methyltransf_23  81 gkfdlIvlrevlehvp..dppellrqiatllkpgGylllseplaslk 125
                                    g++d +v+ e++e v   ++p++++ + +l++pgG + ++ ++ +++
  gi|121636361|ref|YP_976584.1| 271 GQYDSVVSVEMIEAVGyrSWPRYFAALEQLVRPGGPVAIQAITMPHH 317
                                    9**************9667*****************99999877764 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.2e-12   3.1e-09       1      97 []     212     305 ..     212     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.2e-12
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                    vL++G+G G+l++++a+r+  a++  v +s e+ + ar+r++++g+  +ve+  +d +d+   dg++D vvs+ +++ + 
  gi|121636361|ref|YP_976584.1| 212 VLEIGTGWGELCIRAAARG--AHIRSVTLSVEQQRLARQRVAAAGFghRVEIDLCDYRDV---DGQYDSVVSVEMIEAVG 286
                                    9*****************5..*********************999866777766666666...79*******999***** PP

                                    HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                     + ++++++ + ++++pgG
  gi|121636361|ref|YP_976584.1| 287 YRSWPRYFAALEQLVRPGG 305
                                    ******************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.2e-11   3.1e-08       1      95 [.     213     308 ..     213     309 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.2e-11
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..ed 76 
                                    L++G+G G l+   a rga++  v ls e+ +la++++  +g+  +ve+  +d ++    d+++D vvs e+++ v    
  gi|121636361|ref|YP_976584.1| 213 LEIGTGWGELCIRAAARGAHIRSVTLSVEQQRLARQRVAAAGFghRVEIDLCDYRD---VDGQYDSVVSVEMIEAVgyRS 289
                                    89*****************************************9997777777777...69****************99* PP

                                    HHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                    + ++++ + ++++pgG ++
  gi|121636361|ref|YP_976584.1| 290 WPRYFAALEQLVRPGGPVA 308
                                    ****************765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.4e-09   6.1e-06       1      98 [.     213     306 ..     213     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.4e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    LeiG+G G+l  + +++  +i+ + + + ++ +  a+++ a+ +  +  +ve++ +d  d dg  ++D vv+ + ++++ 
  gi|121636361|ref|YP_976584.1| 213 LEIGTGWGELCIRAAARGAHIRSVTLSVEQQRL--ARQRVAAAGFGH--RVEIDLCDYRDVDG--QYDSVVSVEMIEAVg 286
                                    8****************7777777777777777..*******99877..66666666556665..9*************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     + + ++++ + +l++pgG 
  gi|121636361|ref|YP_976584.1| 287 yRSWPRYFAALEQLVRPGGP 306
                                    99999*************95 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.3e-08   3.4e-05       3     113 ..     208     313 ..     206     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                    +g +vl++G+G Gel++++a +   +a++ ++  s e  +lAr++ +  g+  +ve   +d  + +      ++D ++s 
  gi|121636361|ref|YP_976584.1| 208 QGSHVLEIGTGWGELCIRAAAR---GAHIRSVTLSVEQQRLARQRVAAAGFGhRVEIDLCDYRDVD-----GQYDSVVSV 279
                                    6789****************54...89*************************9***********99.....88******* PP

                Methyltransf_31  82 evl..naladpdkileeiervlkpggilliedpr 113
                                    e +      + + ++  +e++++pgg ++i+ + 
  gi|121636361|ref|YP_976584.1| 280 EMIeaVGYRSWPRYFAALEQLVRPGGPVAIQAIT 313
                                    **97767778889999999999999999888776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.16      30     103 ..     207     278 ..     197     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                    CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
                            MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                                    ++  +vl +G+G+G l + +a++  +++ + + v+ + l+  +  ++  +++ve+  +d   +v+ +++d +vs
  gi|121636361|ref|YP_976584.1| 207 QQGSHVLEIGTGWGELCIRAAARGAHIRSVTLSVEQQRLARQRVAAAGFGHRVEIDLCDY-RDVD-GQYDSVVS 278
                                    46778********************98877777777766666666665565566666663.4555.88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2604.27
//
Query:       gi|121636362|ref|YP_976585.1|  [L=221]
Description: hypothetical protein BCG_0487c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-54  182.6   0.0      1e-53  182.5   0.0    1.0  1  DUF1365   Protein of unknown function (DUF1365)


Domain annotation for each model (and alignments):
>> DUF1365  Protein of unknown function (DUF1365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.0   5.8e-58     1e-53      15     237 ..       2     221 .]       1     221 [] 0.91

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 5.8e-58
                        DUF1365  15 khaFsYplllllldldeleel.rlfsrnrlallslrdedyl.dkke.....stslkekleellaeeggeeeelgkvwllt 87 
                                    +h+F+Y+ +++++d+d+l++l ++++       +++++d++ d        ++sl+++l++++a++g   ++ g+++ l 
  gi|121636362|ref|YP_976585.1|   2 HHSFAYRSYSWYVDVDNLPQLpWWLR----PFARFHADDHFaD--PfscppHSSLRDRLDAFFAARGLAVPD-GRITALL 74 
                                    7******************9954443....458********51..234566779*********999998875.******* PP

                        DUF1365  88 mprvlGyvfnPvsfyycydeekekleavvlEVsNTfgerhvYvlkadeagkdltfpKeFhVSPFndrdgsYrlrlkdplk 167
                                    ++rvlGyvfnP+s+++c+d++ ++l++v++EV+NT+g rh+Y+l + +      ++K+F+VSPF +++g+Y +r+ +p  
  gi|121636362|ref|YP_976585.1|  75 QARVLGYVFNPLSIFWCHDRD-GQLRHVIAEVHNTYGGRHAYLLPPAD--LPVVTAKNFYVSPFHQLAGYYLIRAPRP-- 149
                                    ********************9.99********************7753..56899*********************99.. PP

                        DUF1365 168 eserlavrikllseske...kltAtlklerkpltaasllrallryplmtlltvvrIlyqAlkLhlKrlpvypr 237
                                     +++l+v+++l++++++    +tAtl+++r+p+t+++++ + +  pl+ + + +rI +q+++L+l+r+pv+pr
  gi|121636362|ref|YP_976585.1| 150 -DRELDVTVTLHRDRRQvcpEFTATLRGQRRPATTRQIAMMQIISPLAPMVVAARIRIQGIRLWLRRVPVVPR 221
                                    .779********99866799**************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1499.39
//
Query:       gi|121636363|ref|YP_976586.1|  [L=439]
Description: hypothetical protein BCG_0488c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-38  130.6   2.4    2.4e-37  129.3   2.4    1.6  1  Amino_oxidase  Flavin containing amine oxidoreductase
    6.1e-09   36.0   0.7    2.4e-08   34.1   0.7    2.2  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.2e-05   25.0   5.3    1.5e-05   24.7   1.1    2.3  2  DAO            FAD dependent oxidoreductase
    0.00036   19.8   0.6    0.00066   18.9   0.6    1.4  1  FAD_binding_2  FAD binding domain
     0.0098   15.2   0.1      0.019   14.2   0.1    1.4  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.036   14.6   0.5       0.72   10.5   0.2    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.037   13.3   0.5      0.073   12.3   0.5    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.093   12.7   1.8         31    4.5   0.0    3.5  3  NAD_binding_9  FAD-NAD(P)-binding
       0.21   10.2   0.2       0.32    9.6   0.2    1.2  1  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   2.4   1.2e-40   2.4e-37       1     451 [.      16     423 ..      16     424 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 1.2e-40
                                    HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET..T.......EEEESS--EEET.TTHHHHHHHHHTTCCCCEEEE CS
                  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsd..G.......ylielGamwftg.agnpllellkelgledslslp 70 
                                    +aGL+aA+ L+ + ++Vt++Ea++r+GG+++t+++d  G       + ++  + ++++ +++ l +l+ elg+ ++ s  
  gi|121636363|ref|YP_976586.1|  16 VAGLTAAYILSGR-DRVTLYEADGRLGGHAHTHYLDngGgprgtdvVGVDSAFLVHNDrTYPTLCRLFAELGVATQES-- 92 
                                    69*********99.**********************8625777855555555555555*****************999.. PP

                                    SCCGCEEEEETTEECC.....TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHH CS
                  Amino_oxidase  71 dpgapkrvlskggref.....pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaeslee 145
                                    + ++  r+++ g +++     +g++   +++ +++l           l e lr++++a +   ++e d+++ + ++ +++
  gi|121636363|ref|YP_976586.1|  93 EMSMSVRADDIGLEYAgalgaRGLFACRQSLRPRYLC---------MLAEILRFHRAAAR-LLREETDNAEDKPETLEAF 162
                                    334556777777676688889*******999999999.........88999999999999.9999999999999999*** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE.TTHTHHHHHHHHHTTTTEE CS
                  Amino_oxidase 146 lgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp.rgGlsqlpealaeelrgld 224
                                    l+r+++++ + +d++i+p l a+++ ++g+ a   ++ ++ + l+++  l+ fg++++++ +gG ++ ++a+a+    ++
  gi|121636363|ref|YP_976586.1| 163 LSRHHFSQ-YFVDYFITP-LVAAVWSCGGADALRYPARYLFVFLDHHGMLSVFGSPTWRTvTGGSANYVQAIAA--QLDE 238
                                    ********.********9.***************************************999*************..999* PP

                                    EETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEEEESSGGSGC CS
                  Amino_oxidase 225 irlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvilefdrkfwed 304
                                    + ++t+V++++r +dgv v   dg ++++Da vv+v ++ +   l++ p   ++ +a+    + s+n + l++d+ +   
  gi|121636363|ref|YP_976586.1| 239 VSTRTPVHSLRRLPDGVLVGAGDGPSRRFDAAVVAVHPDQAL-LLLDEPT--PAERAVLGAIAYSTNSAQLHTDESV--- 312
                                    ******************************************.9999977..899999999999*************... PP

                                    STSECECECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHHHTGTSSTCSEEE CS
                  Amino_oxidase 305 nalgqgvlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLrklfgeevpepkatl 384
                                            +++  + +++      +++  +pg++ v+++y            s+  +++  +r+L +l g        + 
  gi|121636363|ref|YP_976586.1| 313 --------LPRHHRARAS------WNYLVTPGQHQVVVSYDI----------SRLMRLDGGRRYLVTLGG--------HD 360
                                    ........4444444444......89999***********88..........9999**************........66 PP

                                    EEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                  Amino_oxidase 385 vtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                    +++ + + +a+++ys++ ++p++ + ++l  + gd+r++fAG++     +g  e+   SGlraA+r+
  gi|121636363|ref|YP_976586.1| 361 RVDPS-SVIAEMTYSHPLYTPESVAAQRLLPTLGDNRVVFAGAYHG---WGFHEDGAASGLRAARRL 423
                                    66654.8899**********************************55...799************996 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.7   1.2e-11   2.4e-08       1      67 [.      11      84 ..      11      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.2e-11
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE..TT.......CEECTS---EEETTHHHHCHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev..pg.......vrvdygahifhgsgyypnvrrllre 67
                                   +vG+G++Gl+aAy L+ +  +v+l+e+  rlGG+a++  +  +g       v vd    + ++ + yp + rl++e
  gi|121636363|ref|YP_976586.1| 11 VVGSGVAGLTAAYILSGR-DRVTLYEADGRLGGHAHTHYLdnGGgprgtdvVGVDSAFLVHND-RTYPTLCRLFAE 84
                                   8***************75.58****************97744225656666666666666666.557777777766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.1   7.7e-09   1.5e-05       2      36 ..       9      44 ..       8      50 .. 0.89
   2 ?    1.9   0.2     0.068   1.4e+02     151     223 ..     231     293 ..     207     413 .. 0.56

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.7e-09
                                   EEEECTSHHHHHHHHHHHHTT.EEEEESSSSTTSSG CS
                            DAO  2 vviiGGGiiGlstAyeLarrg.Vtllekgdiagsga 36
                                   v+++G+G++Gl++Ay L+ r  Vtl+e++ ++g +a
  gi|121636363|ref|YP_976586.1|  9 VAVVGSGVAGLTAAYILSGRDrVTLYEADGRLGGHA 44
                                   99****************9988*******9999665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.068
                                    HHHHHHHHTT-EEEESECEEEEEE.EETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEE CS
                            DAO 151 alaraaealGveilegtevtglee.edgkvwgverttpgendaadavVnaaGawsd.llgllkeldlpispvrgq 223
                                    a+a+++     e+ ++t+v +l++ +dg ++g   +  g  +++da V+a  +    ll     ld p+ + r+ 
  gi|121636363|ref|YP_976586.1| 231 AIAAQLD----EVSTRTPVHSLRRlPDGVLVGA-GD--GPSRRFDAAVVAVHPDQAlLL-----LDEPTPAERAV 293
                                    4444443....6677888888866566665555.32..222346888888877744322.....22232222222 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.6   3.3e-07   0.00066       2      39 ..       9      45 ..       8      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-07
                                   EEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl.kvavvekeqefggata 39
                                   v V+GsG+AGL+AA+ ++   + +v++ e  ++ gg+++
  gi|121636363|ref|YP_976586.1|  9 VAVVGSGVAGLTAAYILSG--RdRVTLYEADGRLGGHAH 45
                                   89*************5544..447************876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   9.6e-06     0.019      18      55 ..       7      42 ..       1      48 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.6e-06
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                     v++vG+G +GLtaay+l+ +   +v++ e+   +GG
  gi|121636363|ref|YP_976586.1|  7 RSVAVVGSGVAGLTAAYILSGR--DRVTLYEADGRLGG 42
                                   5799***************988..47888888777776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00036      0.72       1      35 [.       8      41 ..       8      49 .. 0.88
   2 ?    1.6   0.0      0.21   4.2e+02       8      22 ..     101     115 ..     100     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +v+vvG+G+ gl +A +l+    +Vt+ e+  +l 
  gi|121636363|ref|YP_976586.1|  8 SVAVVGSGVAGLTAAYILSGRD-RVTLYEADGRLG 41
                                   699***************9987.999999888776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                    SHHHHHHHHHHHHTT CS
                      Pyr_redox   8 GyiglElAgalaelg 22 
                                    ++iglE+Agal + g
  gi|121636363|ref|YP_976586.1| 101 DDIGLEYAGALGARG 115
                                    78********96655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   3.6e-05     0.073       2      33 ..       8      38 ..       7      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   +v+v+G+G+AGl+aa  l+    +vtl+e++g
  gi|121636363|ref|YP_976586.1|  8 SVAVVGSGVAGLTAAYILSG-RDRVTLYEADG 38
                                   79************998887.88999997443 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.053     1e+02       1      36 [.      10      39 ..      10      50 .. 0.75
   2 ?    2.6   0.0     0.062   1.2e+02      83     104 ..     155     176 ..      88     184 .. 0.76
   3 ?    4.5   0.0     0.015        31     118     153 ..     239     274 ..     225     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.053
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                   a+vG G++Gl+++  L  r       ++tl++ ++ 
  gi|121636363|ref|YP_976586.1| 10 AVVGSGVAGLTAAYILSGRD------RVTLYEADGR 39
                                   89**********99888775......6666666555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.062
                  NAD_binding_9  83 eeldpddfvpRalyGrYlrdlf 104
                                    +  + ++f++R ++++Y+ d+f
  gi|121636363|ref|YP_976586.1| 155 KPETLEAFLSRHHFSQYFVDYF 176
                                    4446679**********99987 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.015
                  NAD_binding_9 118 evhraevvdleeradgqavlladgaslaadaVvLAl 153
                                       r+ v++l++ +dg+ v   dg s ++da v+A+
  gi|121636363|ref|YP_976586.1| 239 VSTRTPVHSLRRLPDGVLVGAGDGPSRRFDAAVVAV 274
                                    356899***************************996 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00016      0.32       2      36 ..       8      41 ..       7      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +v+v+G G AGl aA  + +   rV+l+e+  +lg
  gi|121636363|ref|YP_976586.1|  8 SVAVVGSGVAGLTAAYIL-SGRDRVTLYEADGRLG 41
                                   699************999.56679*****998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3282.75
//
Query:       gi|121636364|ref|YP_976587.1|  [L=967]
Description: transmembrane transport protein mmpL4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.4e-222  735.9  35.7   6.5e-121  403.3   8.3    3.4  4  MMPL            MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.5      0.21   3.7e+03     271     300 ..      22      51 ..      21      55 .. 0.73
   2 !  403.3   8.3  3.6e-125  6.5e-121       1     333 []      59     388 ..      59     388 .. 0.99
   3 !    2.6   0.1    0.0029        52       8      55 ..     506     553 ..     416     580 .. 0.58
   4 !  344.5   8.6  2.8e-107  5.1e-103       7     331 ..     613     943 ..     607     947 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.21
                           MMPL 271 pvlaqvGvaialGvlvdvlivlTllPAllv 300
                                    +++++++v+i lG l +  +v  ++P+l +
  gi|121636364|ref|YP_976587.1|  22 RMIHAFAVPIILGWLAVCVVVTVFVPSLEA 51 
                                    578888899999987776666666699855 PP

  == domain 2  score: 403.3 bits;  conditional E-value: 3.6e-125
                           MMPL   1 slspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaaf 80 
                                    slsp+da+s +am r+++ f+e +dsd+ ++v+  eg++ lg+ aa++++d lv++l++d+khv++v+d+++dp +aa++
  gi|121636364|ref|YP_976587.1|  59 SLSPKDAPSFEAMGRIGMVFKE-GDSDSFAMVII-EGNQPLGD-AAHKYYDGLVAQLRADKKHVQSVQDLWGDPLTAAGV 135
                                    589*******************.*********99.********.************************************ PP

                           MMPL  81 vSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviL 160
                                    +S+Dgkaa+++++l+g++g+++a+esv+a+r++ve+++++ g+k++vtGp+a++ad+++++dr+++ i++vt++vi+++L
  gi|121636364|ref|YP_976587.1| 136 QSNDGKAAYVQLSLAGNQGTPLANESVEAVRSIVESTPAPPGIKAYVTGPSALAADMHHSGDRSMARITMVTVAVIFIML 215
                                    ******************************************************************************** PP

                           MMPL 161 livyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeav 240
                                    l+vyrS+++++l+l+tv+v+l aa+g+v++l +  +++l+tf+++ll+ l+ia+GtDY +++++Ry+e+++aged+e+a+
  gi|121636364|ref|YP_976587.1| 216 LLVYRSIITVVLLLITVGVELTAARGVVAVLGHSGAIGLTTFAVSLLTSLAIAAGTDYGIFIIGRYQEARQAGEDKEAAY 295
                                    ******************************************************************************** PP

                           MMPL 241 iravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWr 320
                                    ++++++t++v++++Glt+a+a+++L++ar+p+++++G+++a+G+lv+v+++lTl PA+l + +r++l++p+r +k r Wr
  gi|121636364|ref|YP_976587.1| 296 YTMYRGTAHVILGSGLTIAGATFCLSFARMPYFQTLGIPCAVGMLVAVAVALTLGPAVLHVGSRFGLFDPKRLLKVRGWR 375
                                    ******************************************************************************** PP

                           MMPL 321 rlgrlvvrrPlpv 333
                                    r+g++vvr+Plpv
  gi|121636364|ref|YP_976587.1| 376 RVGTVVVRWPLPV 388
                                    **********986 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.0029
                           MMPL   8 esvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvd 55 
                                    ++  + dr++  ++++ +++++i v++++ + ++++a++   +    +
  gi|121636364|ref|YP_976587.1| 506 TIKYQRDRANDMLKQADEMATTIAVLTRMHSLMAEMASTTHRMVGDTE 553
                                    333344455555555555555555555555555555554444444444 PP

  == domain 4  score: 344.5 bits;  conditional E-value: 2.8e-107
                           MMPL   7 aesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.............ls 72 
                                      +  +++++++ +p+ +a+ ++ i ++++++++ l+++++++++ +++ e++++++++g+++d+             ++
  gi|121636364|ref|YP_976587.1| 613 GVLLGDLREMDRLMPQmVAQIPPQIEAMENMRTMILTMHSTMTGIFDQMLEMSDNATAMGKAFDAaknddsfylppevFK 692
                                    556778999********************************************************999999999999988 PP

                           MMPL  73 dpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdasdrdlk 146
                                    ++d   +++ f+S+Dg+aar+++ ++gdp+s+e+++s++air+a+ee     ple++k++++G+aa+++d+++++++dl 
  gi|121636364|ref|YP_976587.1| 693 NKDfqrAMKSFLSSDGHAARFIILHRGDPQSPEGIKSIDAIRTAAEESLkgtPLEDAKIYLAGTAAVFHDISEGAQWDLL 772
                                    999999******************************************99****************************** PP

                           MMPL 147 lievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsR 225
                                    ++ + +l++i++i+li++r+++aa+++++tv++sl+a++gl vl+++++l++ l++ vl+++v++l+avG+DY+llLvsR
  gi|121636364|ref|YP_976587.1| 773 IAAISSLCLIFIIMLIITRAFIAAAVIVGTVALSLGASFGLsVLLWQHILAIHLHWLVLAMSVIVLLAVGSDYNLLLVSR 852
                                    ******************************************************************************** PP

                           MMPL 226 yreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGr 304
                                    +++e++ag ++  ++ir +++tgkvvt+aGl++a++m++++v++l+v++qvG++i+lG+l+d+liv++++ P++++llGr
  gi|121636364|ref|YP_976587.1| 853 FKQEIGAGLKT--GIIRSMGGTGKVVTNAGLVFAVTMASMAVSDLRVIGQVGTTIGLGLLFDTLIVRSFMtPSIAALLGR 930
                                    ***********..******************************************************************* PP

                           MMPL 305 aalakprrkrkkrwWrrlgrlvvrrPl 331
                                    +           +wW+ +   v++rP+
  gi|121636364|ref|YP_976587.1| 931 W-----------FWWPLR---VRSRPA 943
                                    *...........***877...777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (967 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.47
# Mc/sec: 6241.43
//
Query:       gi|121636365|ref|YP_976588.1|  [L=140]
Description: membrane protein mmpS4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-75  249.4   0.0    8.8e-75  249.2   0.0    1.0  1  Mycobact_memb  Mycobacterium membrane protein


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.2   0.0   4.9e-79   8.8e-75       1     139 []       2     140 .]       2     140 .] 0.99

  Alignments for each domain:
  == domain 1  score: 249.2 bits;  conditional E-value: 4.9e-79
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEB-B----TT-----B---TTS------S CS
                  Mycobact_memb   1 lkrlWiplvivvvvvvggltvsrlhsifgsekrasvadklaedskpfnPkkvkyevfGpagtvadisyldadaepqridg 80 
                                    l+r+Wiplvi+vvv+vgg+tv+r++++fgse+r+s++d++ e+skpfnPk+++ye+fGp+gtvadisy+d+++epqr+dg
  gi|121636365|ref|YP_976588.1|   2 LMRTWIPLVILVVVIVGGFTVHRIRGFFGSENRPSYSDTNLENSKPFNPKHLTYEIFGPPGTVADISYFDVNSEPQRVDG 81 
                                    68****************************************************************************** PP

                                    -SS--B--EE-SSS------B--SS-S------BBTTB---------S-TTSSS--S-- CS
                  Mycobact_memb  81 aalPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevnaltyClvksa 139
                                    a lPWsl+i+t++aav+gn+vaqgnsdsigCri+vdg+v++ervsnevna+tyClvksa
  gi|121636365|ref|YP_976588.1|  82 AVLPWSLHITTNDAAVMGNIVAQGNSDSIGCRITVDGKVRAERVSNEVNAYTYCLVKSA 140
                                    *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1024.35
//
Query:       gi|121636366|ref|YP_976589.1|  [L=236]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-28   99.8   1.4    1.1e-28   99.8   1.4    1.5  2  TetR_C_34     Tetracyclin repressor-like, C-terminal domain
    1.5e-05   24.7   0.6    3.3e-05   23.6   0.6    1.6  1  TetR_N        Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.029   13.8   0.3      0.077   12.4   0.3    1.8  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> TetR_C_34  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   9.2e+03      50      60 ..      25      35 ..      17      55 .. 0.53
   2 !   99.8   1.4   1.8e-32   1.1e-28       1     120 []     100     222 ..     100     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                      TetR_C_34 50 laalleralPe 60
                                   +aal+e+a   
  gi|121636366|ref|YP_976589.1| 25 AAALVEAARSL 35
                                   44444444332 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 1.8e-32
                      TetR_C_34   1 avaaalaetlaarpllcdLlsllasvLEhnvsvealvafKrallerlerlaalleralPelseeqaaallaaalalvagl 80 
                                    +va+ala  laa pl+cdLl+ l+  LE++v+v+++++ Kr+ ++++ +l++++e+alP+l+  +a ++l aa++l+a l
  gi|121636366|ref|YP_976589.1| 100 RVAEALANGLAADPLFCDLLANLHLHLEQEVDVDRVIEVKRTSIAAVIALVDAIESALPALGRSGAFDILLAAYSLAATL 179
                                    69****************************************************************************** PP

                      TetR_C_34  81 wplahpsealreay.edpelaal..rvdFeeelrellaalltG 120
                                    w++a+p+e l +ay e+pel +    +dF+ +l++ll+a+l+G
  gi|121636366|ref|YP_976589.1| 180 WQIANPPERLTDAYaEEPELLPPewNLDFAAALTRLLTATLLG 222
                                    ********************66511789*************98 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.6   5.5e-09   3.3e-05       1      45 [.      28      72 ..      28      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.5e-09
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   +++aAr l  e G +++t+ ++A rAG+  +a+ ryF+s  e l+
  gi|121636366|ref|YP_976589.1| 28 LVEAARSLALETGVASVTLTAVAGRAGIHYSAVRRYFTSHKEVLL 72
                                   689***********************************8666665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.3e-05     0.077      20      51 ..      36      67 ..      21      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                   HTH_Tnp_ISL3 20 ilelllesrsvkavArqlgvSwtTVwrildry 51
                                   +le    s + +avA + g++ + V+r++ ++
  gi|121636366|ref|YP_976589.1| 36 ALETGVASVTLTAVAGRAGIHYSAVRRYFTSH 67
                                   5555566789*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1797.83
//
Query:       gi|121636367|ref|YP_976590.1|  [L=518]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-58  197.0  22.2    1.9e-58  197.0  22.2    2.2  2  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0  22.2   1.1e-62   1.9e-58       1     157 [.       9     165 ..       9     166 .. 0.99
   2 ?   -3.8   2.6      0.67   1.2e+04      77      99 ..     404     426 ..     401     442 .. 0.68

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 1.1e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall++Gpg+gp+laAa+ W++L  e+a++a+el ++la+++a+ WqGps++++aaa++pyl+WL++a+a+++
  gi|121636367|ref|YP_976590.1|   9 ASPPEVHSALLSSGPGPGPVLAAATGWSSLGREYAAVAEELGALLAAVQAGVWQGPSAESFAAACLPYLSWLTQASADCA 88 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aAa++ea+ aaY aAl am+++ae+aan+a++ a+vatnffG+nt++Ia++ea+y +mw+q+a++ma+Y+a++ +a
  gi|121636367|ref|YP_976590.1|  89 AAAARLEAVTAAYAAALVAMPTLAELAANHATHGAMVATNFFGINTIPIAVNEADYVRMWLQAATTMATYQAVADSA 165
                                    *************************************************************************9877 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.67
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  77 aqaeeaAaqaeaaaaaYeaAlaa 99 
                                    ++a+ aA +++a+aaa  +A+++
  gi|121636367|ref|YP_976590.1| 404 RRAQPAADNVTAVAAAQVSARHQ 426
                                    56777777777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 3945.48
//
Query:       gi|121636368|ref|YP_976591.1|  [L=116]
Description: hypothetical protein BCG_0493 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 834.86
//
Query:       gi|121636369|ref|YP_976592.1|  [L=148]
Description: hypothetical protein BCG_0494c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-55  185.4   0.7    4.4e-55  185.2   0.7    1.0  1  DUF5078   Domain of unknown function (DUF5078)


Domain annotation for each model (and alignments):
>> DUF5078  Domain of unknown function (DUF5078)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.7   2.5e-59   4.4e-55       1     119 []      33     147 ..      33     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 2.5e-59
                        DUF5078   1 tddyPiPrrllkttctaeqllaaardtePvyyerymidkknkseevqqaakdrihwffsldpadrrdyseelatnvfaeq 80 
                                    t+d+PiPrr+++ttc+aeq+laa+rdt+Pvyy+rymid +n++ ++qqa+++++hwffsl+pa+rrdyse++      ++
  gi|121636369|ref|YP_976592.1|  33 TEDFPIPRRMIATTCDAEQYLAAVRDTSPVYYQRYMIDFNNHA-NLQQATINKAHWFFSLSPAERRDYSEHFYN---GDP 108
                                    89****************************************8.9**************************755...5** PP

                        DUF5078  81 lavkwanwakiffnnkgvvakatevcakypkddmsvWdw 119
                                    l+  w n++kiffnnkgvvak tevc+ yp++dmsvW+w
  gi|121636369|ref|YP_976592.1| 109 LTFAWVNHMKIFFNNKGVVAKGTEVCNGYPAGDMSVWNW 147
                                    *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1117.74
//
Query:       gi|121636370|ref|YP_976593.1|  [L=304]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-29  102.5   0.0    2.8e-28   98.9   0.0    2.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    5.5e-17   62.3   0.0    1.2e-16   61.1   0.0    1.5  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   3.1e-32   2.8e-28       5     216 ..      16     239 ..      12     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 3.1e-32
                                    TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHH........HC.......HH CS
                          ECH_1   5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaee........ek.......ak 69 
                                     va i+lnrPe++N++ + + +E+ +a+  +e d+ ++++vL G ++aF+ G d+    ++        +        a 
  gi|121636370|ref|YP_976593.1|  16 PVATITLNRPEQLNTIVPPMPDEIEAAIGLAERDQDIKVIVLRGAGRAFSGGYDFGGGFQHwgdammtdGRwdpgkdfAM 95 
                                    69****************************************************98765531111111122333221122 PP

                                    HHHHHCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHH CS
                          ECH_1  70 qallkeevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskA 149
                                     +  +    + ++++    kpvia v G ++gG    al++Divia+++a++g + ++   + ga++t ++  ++  +k+
  gi|121636370|ref|YP_976593.1|  96 VTARETGPTQKFMAIWRASKPVIAQVHGWCVGGASDYALCADIVIASEDAVIGTPYSR---MWGAYLTGMWLYRLSLAKV 172
                                    222334456789******************************************9988...5789*************** PP

                                    HHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH CS
                          ECH_1 150 eeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeq 216
                                    +   l+g+++++  a+++ l++++vp e l+    e+a++la+ +   l++ k ++n+++e+   + 
  gi|121636370|ref|YP_976593.1| 173 KWHSLTGRPLTGVQAAEAELINEAVPFERLEARVAEIATELARIPLSQLQAQKLIVNQAYENMGLAS 239
                                    ******************************************9999999999999999999654443 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.3e-20   1.2e-16       2     187 ..      18     212 ..      17     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.3e-20
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS.........-THH.HH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakeg.........kkee.ee 71 
                                    ++itLnrp++lN +  +m +++++a+   e+d+++k++vl+gag +af+ G D+    ++  +            ++ + 
  gi|121636370|ref|YP_976593.1|  18 ATITLNRPEQLNTIVPPMPDEIEAAIGLAERDQDIKVIVLRGAG-RAFSGGYDFGGGFQHWGDAmmtdgrwdpG-KDfAM 95 
                                    78****************************************99.********987666655554554554431.12333 PP

                                    HHHHH...HHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGG.T----TTHHHHHHCSSTTHH CS
                          ECH_2  72 ffree...YklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaI.GlfPDvGgsyfLsrlpgelG 147
                                    + ++e    +   +i + +kpv+a ++G ++Gg    ++ + + +++e++v+  P  ++ G +    + ++L rl+ +  
  gi|121636370|ref|YP_976593.1|  96 VTAREtgpTQKFMAIWRASKPVIAQVHGWCVGGASDYALCADIVIASEDAVIGTPYSRMwGAY---LTGMWLYRLSLAKV 172
                                    33444111344567889**************************************99873444...4678899******* PP

                                    HHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT CS
                          ECH_2 148 lylalTGarlkgadalaaglathyvpseklealeeaLael 187
                                    ++  lTG+ l+g +a +a+l +  vp e+lea  +++a+ 
  gi|121636370|ref|YP_976593.1| 173 KWHSLTGRPLTGVQAAEAELINEAVPFERLEARVAEIATE 212
                                    **************************99987665555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2089.89
//
Query:       gi|121636371|ref|YP_976594.1|  [L=93]
Description: hypothetical protein BCG_0496c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-11   43.3   0.0    4.3e-11   43.2   0.0    1.1  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   2.4e-15   4.3e-11       2      51 ..       3      58 ..       2      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.4e-15
                                   TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHS......EEEEEEEESSSTSSG CS
                     PemK_toxin  2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekn......tvivvpltskdkdkk 51
                                   rGeI+ vdldp rgs  + rRp+v+vsnd+ n+ +      +v vvp+ts+ ++  
  gi|121636371|ref|YP_976594.1|  3 RGEIWQVDLDPARGSAANMRRPAVIVSNDRANAAAirldrgVVPVVPVTSNTEKVP 58
                                   9****************************888663357788********9997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 743.78
//
Query:       gi|121636372|ref|YP_976595.1|  [L=676]
Description: peptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-47  161.4   0.2    3.7e-47  160.6   0.2    1.4  1  Peptidase_S9    Prolyl oligopeptidase family
    9.3e-24   84.0   0.0    1.6e-23   83.2   0.0    1.2  1  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.53   10.4   0.0    1.7  2  Abhydrolase_4   TAP-like protein


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.2   6.1e-51   3.7e-47       9     209 ..     473     674 ..     468     676 .] 0.96

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 6.1e-51
                                    HHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG CS
                   Peptidase_S9   9 lladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdl 88 
                                    +l +rG  ++ anirG+g+yG  +h +  r+  ++ ++Df a+a  l+++g++++e+l+++GgS+GG+l+g +l+  p++
  gi|121636372|ref|YP_976595.1| 473 WL-ARGGTYALANIRGGGEYGPGWHTQAMREGRDKVAQDFAAVATDLVTRGITTAEQLGARGGSNGGLLMGIMLTGYPEK 551
                                    55.9**************************************************************************** PP

                                    -SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG--...---EEEEEEETT-SSS-THHHHH CS
                   Peptidase_S9  89 Fkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvk...aypplLlihGlaDdrvppaealk 164
                                    F+a+v+ vp +d+ ry++   l ++ ++ e+g+p +n+++ k +s+ysp++n+    +ypp+L+++++ Ddrv+p +a k
  gi|121636372|ref|YP_976595.1| 552 FGALVCDVPLLDMKRYHLL--LAGAsWMAEYGDP-DNPDDWKFISEYSPYQNISanrKYPPVLMTTSTRDDRVHPGHARK 628
                                    *******************..57777********.99999************99************************** PP

                                    HHHHHH--S-SEEEEEETTS-SSTTSSHHHH.HHHHHHHHHHHHHC CS
                   Peptidase_S9 165 lvaaLqkkgknvlllifpdegHgvgkprakv.eelarllaFlkeal 209
                                    + aaLq +g++v +  + + gH ++ ++a++  + a  +aFl ++l
  gi|121636372|ref|YP_976595.1| 629 MTAALQAAGHPVWYYENIEGGHAGAADNAQIaFKSALSFAFLWRML 674
                                    **********************999999999888899999998876 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   2.7e-27   1.6e-23      19     398 ..      13     394 ..       6     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.7e-27
                                    E-TTGGGGSTTSHHHHHHHHHHHHHHHHHHCTST.CHHHHHHHHHHHT-S-EE---EEETTEEEEEEE-SS-SS-EEEEE CS
                 Peptidase_S9_N  19 sDpYrWLeDddspetkayleaenkyteevlaqlkelrekikeeitklikeddisapfrkgkyyyysrneggknqsvlyrq 98 
                                    +DpY WLeD +  e+ ++++a nk t +++ + + ++    e+++ l    +i    r+g+y+y+++ +      ++ r+
  gi|121636372|ref|YP_976595.1|  13 ADPYLWLEDVTGAEALDWVRARNKPTTAAFCDAE-FERMRVEALEVLDTDARIPYVNRRGNYLYNFWRDAANPRGLWRRT 91 
                                    6********************************9.999999999999999999999************************ PP

                                    C..STS-TTS-EEEEE-GGGGST..TS-.EEEEEEEE-TTSSEEEEEEEETTSSEEEEEEEETTTTEEEEEEEEEEESEE CS
                 Peptidase_S9_N  99 d..alskegeeeevlLDpNtlse..dgtfvalgefavsedgkllAyslsksGsdwytirvkdietgedlpdeledvkfsg 174
                                    +  +   +++ + vl+D+++l    d+++v+ g+  + +d +   ++ls +Gsd+  +r +d+ t e+++d ++ +  ++
  gi|121636372|ref|YP_976595.1|  92 TldSYRTDSPGWDVLIDVDELGRadDQKWVWGGAGVIEPDYTRALIGLSPGGSDASIVREFDMLTREFVEDGFQLPPAKS 171
                                    7767777889**********9654277756666666**************************************998888 PP

                                    .EEECTTSSEEEEEESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGTTBEE.EEEE-.TTSSEEEEEEESSS CS
                 Peptidase_S9_N 175 .ivWaadekgffYtrydkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeepkwll.gaers.edgkylfissasgt 251
                                     i+W +  + ++ t+    d+ + +++    k +r+  G++  ++e +fe++  + ++  +a+r+   +++l+  + + +
  gi|121636372|ref|YP_976595.1| 172 qITWEDPDTVLLGTDFG-GDSLTTSGYPRVIKRWRR--GKPLADAETIFEGAGTDVRVNaSADRTpGFERTLLGRALDFW 248
                                    8****997777777777.566666699999999999..**************9999998788888345899999999999 PP

                                    S--EEEEEEGGGTSS...--EEEEESSSSS-EEEEEEETTEEEEEE-TT-TT-EEEEEETTSSSGG..GEEEEE--.SSC CS
                 Peptidase_S9_N 252 dtnelyvldlekesk...kvlklvdnrfdaeysvehnegdrfliltndgapnfrlvsvdlndpsps..ewkelvperekv 326
                                     ++e+y l+ ++  +   ++ + v+     ++ ++    ++++++t +  + + l++++ ++      e +++ + +e  
  gi|121636372|ref|YP_976595.1| 249 -NEEVYELRGSELIRieaPTDASVSI--HRDWLLIEL-RTDWTVATTR-YTAGSLLAAEYDEFLAGsaELQVVFEPDEHT 323
                                    .99***99999987677666666666..446777777.5899999975.4678999999996543311777777888888 PP

                                    EEEEEEECTTEEEEEEEETTEEEEEEEETTTS-..EEEEEB-SSSSEEEEEE--TT-SEEEEEEEETTCEEEE CS
                 Peptidase_S9_N 327 vleeitvfknylvvsyrkdvlsrvqvvdlkngkv.llfevplpgvgsvssasgekedselfysfsSfltPsti 398
                                     l + + ++++l++  + dv srv++ +  +g++      ++p++   + +s++ + +e+f++ s+f tPs++
  gi|121636372|ref|YP_976595.1| 324 ALYQYAWTRDRLLIVTLADVASRVEIAT--PGSWrREPLSGIPAATNTVIVSADSHGDEFFLDSSGFDTPSRL 394
                                    888************************9..56643444445555666666789999999***********986 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.5   1.5e+04      47      72 ..     350     378 ..     344     385 .. 0.66
   2 ?   10.4   0.0   8.9e-05      0.53      23      67 ..     595     641 ..     577     665 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.5
                  Abhydrolase_4  47 aTPyegakklakalgga...vlvtvegeG 72 
                                    aTP ++ ++  + ++ a   v v++++ G
  gi|121636372|ref|YP_976595.1| 350 ATPGSWRREPLSGIPAAtntVIVSADSHG 378
                                    68888888888888775533444555444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.9e-05
                  Abhydrolase_4  23 qrprdestakga.apvLllqnerDpaTPyegakklakalgga.vlvt 67 
                                      p ++++a+ + +pvL+ +++rD  + +  a+k++ al+ a + v 
  gi|121636372|ref|YP_976595.1| 595 YSPYQNISANRKyPPVLMTTSTRDDRVHPGHARKMTAALQAAgHPVW 641
                                    4455666665556***************************9633333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4594.87
//
Query:       gi|121636373|ref|YP_976596.1|  [L=507]
Description: aldehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.7e-159  530.6   0.0     3e-159  530.4   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.4   0.0  1.7e-163    3e-159       1     461 [.      28     494 ..      28     495 .. 0.96

  Alignments for each domain:
  == domain 1  score: 530.4 bits;  conditional E-value: 1.7e-163
                                    EET-SSSE.EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH CS
                         Aldedh   1 wveseset.ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletlet 79 
                                    wv++ +++ +e+  P+tg+++++vp+++a+d+d+a++aA++a ++w k+ ++eRa+iL+ +ad + +++  la +e++++
  gi|121636373|ref|YP_976596.1|  28 WVAPVHGRyFENPTPVTGQPFCEVPRSDAADIDKALDAAHAAAPGWGKTAPAERAAILNMIADRIDKNAAALAVAEVWDN 107
                                    7777785559999******************************************************************* PP

                                    ---HHHHHH.HHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEE CS
                         Aldedh  80 Gkplaeara.eveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvv 158
                                    Gkp++ea a +++ a+d++ry+a++++  eg   +++e++ a+ ++ePlGvvg+I+PWNfP+l+aawklapalaaGNt v
  gi|121636373|ref|YP_976596.1| 108 GKPVREALAaDIPLAVDHFRYFAAAIRAQEGALSQIDEDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNTAV 187
                                    *******************************998889******************************************* PP

                                    EEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-- CS
                         Aldedh 159 lKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGG 238
                                    lKPae+tp+s+l+l+ l+ +  lP+gv+nvv+g g+e+g+ l+++++++kv+ftG+t++gr i++ a++nl +vtlElGG
  gi|121636373|ref|YP_976596.1| 188 LKPAEQTPASVLYLMSLIGD-LLPPGVVNVVNGFGAEAGKPLASSDRIAKVAFTGETTTGRLIMQYASHNLIPVTLELGG 266
                                    ********************.9********************************************************** PP

                                    -EEEEE-TTS.....H.HHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---S CS
                         Aldedh 239 knplivleda.....D.ldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPli 312
                                    k+p+i ++d+     D  dka+e+  + + +n+G+vC+++sr l+q +iydef+e  + ++k++++gdpld +t +G+++
  gi|121636373|ref|YP_976596.1| 267 KSPNIFFADVlaahdDfCDKALEGFTM-FALNQGEVCTCPSRSLIQADIYDEFLELAAIRTKAVRQGDPLDTETMLGSQA 345
                                    *****8877544343434777777766.778************************************************* PP

                                    SHHHHHHHHHHHHHHHHTTSEEEE-TT..E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHH CS
                         Aldedh 313 seaqlekvekyveeakeegaklllGge..reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieia 390
                                    s++qlekv +y+e +k+ega ++ Gge  +   +l+ gy+++Pt++++ t++mri++eEiFGPV++v++f d ++ai ia
  gi|121636373|ref|YP_976596.1| 346 SNDQLEKVLSYIEIGKQEGAVIIAGGEraELGGDLSGGYYMQPTIFTG-TNNMRIFKEEIFGPVVAVTSFTDYDDAIGIA 424
                                    ***************************87667788888*********8.9****************************** PP

                                    HSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                         Aldedh 391 NdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                    Ndt yGL+agv+++d ++a r+ ++++aG v++N+++ + a+a +fgG+kqSg+Greg + +l++y ++k+
  gi|121636373|ref|YP_976596.1| 425 NDTLYGLGAGVWSRDGNTAYRAGRDIQAGRVWVNCYHLYPAHA-AFGGYKQSGIGREGHQMMLQHYQHTKN 494
                                    ************************************9999999.************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3301.71
//
Query:       gi|121636374|ref|YP_976597.1|  [L=163]
Description: hypothetical protein BCG_0499 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-44  149.9   0.0    2.3e-44  149.6   0.0    1.1  1  DUF779    Protein of unknown function (DUF779)


Domain annotation for each model (and alignments):
>> DUF779  Protein of unknown function (DUF779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   1.3e-48   2.3e-44       1      94 []      16     113 ..      16     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 1.3e-48
                         DUF779   1 llekLkakhgplmfhqsggccdgssPmcypageflvgdadvllgei....egvpfyiskeqfeywkhtqltidvvpgrgg 76 
                                    ll+ L+++hgp+mfhqsggccdgs+Pmcyp+ +flvgd+d+llg +    +gvp++is+ q+++wkhtql+idvvpgrgg
  gi|121636374|ref|YP_976597.1|  16 LLAGLQDRHGPVMFHQSGGCCDGSAPMCYPRADFLVGDRDILLGVLdvgeDGVPVWISGPQYQAWKHTQLIIDVVPGRGG 95 
                                    6889******************************************999888**************************** PP

                         DUF779  77 gfSLeapegkrflirsrl 94 
                                    gfSLeapeg+rfl r r+
  gi|121636374|ref|YP_976597.1|  96 GFSLEAPEGVRFLSRGRV 113
                                    ***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 998.52
//
Query:       gi|121636375|ref|YP_976598.1|  [L=79]
Description: hypothetical protein BCG_0500 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-39  133.2  13.3    2.9e-39  133.1  13.3    1.0  1  Holin_9   Putative holin
  ------ inclusion threshold ------
       0.42   10.3   4.6        0.7    9.5   4.6    1.3  1  NEMP      NEMP family
       0.54   10.3   6.8        1.9    8.6   1.2    2.2  2  DUF543    Domain of unknown function (DUF543)


Domain annotation for each model (and alignments):
>> Holin_9  Putative holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1  13.3   4.8e-43   2.9e-39       1      77 [.       1      77 [.       1      78 [. 0.99

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 4.8e-43
                        Holin_9  1 mllGvavGllagiaatllvkakirPdlvialvvgvPsviGlllilfssrrWvtalgafvlaiapGWfGvlvaiqvvs 77
                                   ml+G+a+Gllag+a+++lv+a+irPd+via+vvg+Ps+iGll+ilfs+rrWvt+lgaf+la+apGWfGvlvaiqv+s
  gi|121636375|ref|YP_976598.1|  1 MLVGNAIGLLAGVACSVLVHARIRPDIVIAMVVGIPSAIGLLVILFSGRRWVTMLGAFILALAPGWFGVLVAIQVAS 77
                                   9**************************************************************************87 PP

>> NEMP  NEMP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.6   0.00012       0.7      40      85 ..      29      76 ..      28      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                           NEMP 40 sgmalGi..llsllivlfqlmkllpkkslfylllygswgvslyllqql 85
                                    +m++Gi   + ll++lf + + + +   f+l+l+ +w+  l+ +q  
  gi|121636375|ref|YP_976598.1| 29 IAMVVGIpsAIGLLVILFSGRRWVTMLGAFILALAPGWFGVLVAIQVA 76
                                   69*****988899*************************8888888865 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.2   0.00031       1.9      28      59 ..       1      34 [.       1      41 [. 0.71
   2 ?    5.3   1.6    0.0033        20      33      58 ..      32      57 ..      26      59 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                         DUF543 28 llvkvglgllvGvvasvllfr..rRaapvalGaG 59
                                   +lv  ++gll+Gv++svl+    r  +++a+ +G
  gi|121636375|ref|YP_976598.1|  1 MLVGNAIGLLAGVACSVLVHAriRPDIVIAMVVG 34
                                   677889***********99543444455555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0033
                         DUF543 33 glgllvGvvasvllfrrRaapvalGa 58
                                    +g+  ++ + v+lf  R ++++lGa
  gi|121636375|ref|YP_976598.1| 32 VVGIPSAIGLLVILFSGRRWVTMLGA 57
                                   4555555555689***9*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 550.24
//
Query:       gi|121636376|ref|YP_976599.1|  [L=174]
Description: hypothetical protein BCG_0501 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1365.40
//
Query:       gi|121636377|ref|YP_976600.1|  [L=464]
Description: dihydrolipoamide dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-62  211.1   6.2    2.5e-62  210.8   6.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-34  119.0   0.0    3.5e-34  117.4   0.0    1.9  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    2.7e-21   75.9   2.2    4.4e-19   68.8   0.4    2.8  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.4e-08   33.6   9.6     0.0021   17.4   0.1    3.2  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.2e-07   31.5   0.9    1.2e-07   31.5   0.9    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
    1.1e-06   28.1   0.5    1.1e-06   28.1   0.5    3.4  3  GIDA           Glucose inhibited division protein A
    1.5e-06   27.7   2.9      0.011   15.0   0.0    3.0  3  FAD_binding_3  FAD binding domain
    2.2e-05   23.7   9.1    2.9e-05   23.3   1.1    3.1  3  FAD_binding_2  FAD binding domain
    7.2e-05   22.9   2.4       0.22   11.8   0.1    2.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00016   20.6  10.8     0.0041   15.9   0.2    3.5  4  HI0933_like    HI0933-like protein
    0.00017   20.9   1.3      0.063   12.5   0.1    2.6  2  Thi4           Thi4 family
     0.0063   16.4   0.3     0.0063   16.4   0.3    2.7  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.022   14.4   0.4      0.071   12.8   0.4    1.9  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.052   13.5   0.1        1.6    8.6   0.0    3.0  3  LpxI_N         LpxI N-terminal domain
       0.15   11.1   4.1        1.6    7.7   0.1    2.8  3  Lycopene_cycl  Lycopene cyclase protein
       0.26   10.8  14.2       0.32   10.5   0.2    3.7  4  DAO            FAD dependent oxidoreductase
        0.6   10.4   2.8        3.7    7.8   0.0    3.3  3  TrkA_N         TrkA-N domain
        2.8    7.2   8.6        2.1    7.6   0.2    3.2  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   6.2   2.5e-65   2.5e-62       1     294 []       4     324 ..       4     324 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 2.5e-65
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................... 57 
                                    +dvvv+G+Gp+G+ aa+++aq g+ +++ve    +g cln+gc++skall+ ae  +i++                    
  gi|121636377|ref|YP_976600.1|   4 YDVVVLGAGPGGYVAAIRAAQLGLSTAIVEpkyWGGVCLNVGCIPSKALLRNAELVHIFTkdakafgisgevtfdygiay 83 
                                    69****************************999*********************************************** PP

                                    ....HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCS CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ....evvkklnqgielllgeevvkidpgkkkvklekkke.....gdeekiaydklvlAtGssprdlgipGvaenvgklvr 128
                                        +v +   +g+++l+++++++ ++g +++ + ++       g +e++++d+ ++AtGss+r+   pG          
  gi|121636377|ref|YP_976600.1|  84 drsrKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTLLvdlndGGTESVTFDNAIIATGSSTRLV--PGT-SLSA---N 157
                                    ***9777788899******9966666999999998776588999999***************9997..888.3332...5 PP

                                    ECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 129 tldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvke 208
                                     ++  e++ + +lpk+i++ G+G+iG+E+  +l+++g++vt+ve ++r l++ d ++s+++e++++k Gv++ + t+v+ 
  gi|121636377|ref|YP_976600.1| 158 VVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVES 237
                                    69999*************************************************************************99 PP

                                    EEETTEEEE.EEETTSCE..EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS CS
                                    xxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 209 idgngekle.vvledgee..idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggp 284
                                    i + g++++ +v++dg    ++a+ v+ a+G+ p+ e+++ +k+g++l++r +i vd+++rtnv +iyaiGDv    g +
  gi|121636377|ref|YP_976600.1| 238 IADGGSQVTvTVTKDGVAqeLKAEKVLQAIGFAPNVEGYGlDKAGVALTDRKAIGVDDYMRTNVGHIYAIGDVN---GLL 314
                                    99999977776666664444******************************************************...*** PP

                                    --HHHHHHHH CS
                                    xxxxxxxxxx RF
                    Pyr_redox_2 285 elaqaAvqqG 294
                                    +la++A +qG
  gi|121636377|ref|YP_976600.1| 315 QLAHVAEAQG 324
                                    ********98 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0   3.6e-37   3.5e-34       2     108 ..     346     452 ..     345     454 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3.6e-37
                                    EEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                  Pyr_redox_dim   2 ptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                    p+++f++p+vas Glte++A+++g++++v+kfpf+an++a+  ++ +gfvKlvadak g++lG h+vG++++el+ el++
  gi|121636377|ref|YP_976600.1| 346 PRATFCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELLPELTL 425
                                    99****************************************************************************** PP

                                    HHHTTSBHHHHHTSBSSSSSTGGGGHC CS
                  Pyr_redox_dim  82 aikagltvedladtihihPtlsealke 108
                                    a +++lt+++la+++h+hPt+seal+e
  gi|121636377|ref|YP_976600.1| 426 AQRWDLTASELARNVHTHPTMSEALQE 452
                                    ************************997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.022        22       2      30 ..       6      34 ..       5      37 .. 0.93
   2 !   68.8   0.4   4.4e-22   4.4e-19       1      78 [.     173     249 ..     173     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                   vvv+G+G  g  +A  +a+lg ++ +ve 
  gi|121636377|ref|YP_976600.1|  6 VVVLGAGPGGYVAAIRAAQLGLSTAIVEP 34
                                   8************************9996 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 4.4e-22
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                    ++++ G+G ig+E++ +l+++g +Vt+ve  ++ l+++D+++sk+++++++k+g+++l+ tkve+i   +++v+ v++
  gi|121636377|ref|YP_976600.1| 173 SIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVT-VTV 249
                                    589****************************************************************8887765.555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.7   0.00072      0.72       1      29 [.       7      34 ..       7      41 .. 0.88
   2 !   11.8   0.4    0.0001       0.1       1      28 [.     175     201 ..     174     205 .. 0.95
   3 !   17.4   0.1   2.1e-06    0.0021     213     305 .]     213     308 ..     205     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00072
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                   ++ GaGP G  aai + ++gl +  i+E 
  gi|121636377|ref|YP_976600.1|  7 VVLGAGPGGYVAAIRAAQLGL-STAIVEP 34
                                   689******************.5789985 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilE 28 
                                    iI GaG++G+++++ lk+ g+ d++i+E
  gi|121636377|ref|YP_976600.1| 175 IIAGAGAIGMEFGYVLKNYGV-DVTIVE 201
                                    799******************.899*99 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.1e-06
                    Pyr_redox_3 213 dienrleelvkeekikvlfnaevkeikekeeeykvk.tedgkkvev.kddvvlatGykpdlsf..lkkslfeldedgrpv 288
                                    d+ +++e+  k+  +++l+ ++v++i +  ++++v+ t+dg   e   ++v+ a+G+ p+++   l+k++++l +d++  
  gi|121636377|ref|YP_976600.1| 213 DVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTvTKDGVAQELkAEKVLQAIGFAPNVEGygLDKAGVAL-TDRKAI 291
                                    566777777777559*************99999999666665555535666667*******876699999999.566666 PP

                    Pyr_redox_3 289 lteeteetnvpglflaG 305
                                      ++ + tnv  ++ +G
  gi|121636377|ref|YP_976600.1| 292 GVDDYMRTNVGHIYAIG 308
                                    66789*********998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.9   1.2e-10   1.2e-07       1      35 [.       5      39 ..       5      56 .. 0.93
   2 ?   -2.9   0.2       3.3   3.3e+03      98     139 ..     223     263 ..     211     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-10
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                   DvvV G+gp+G++AAi Aa+ G ++++ve++ + G
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGG 39
                                   9*****************************98844 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                   FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtveskeg.rktirAkvf 139
                                    ++ gvt+l+ t+++++   g     vtv +k+g  ++++A+ +
  gi|121636377|ref|YP_976600.1| 223 KKLGVTILTATKVESIADGG-SQVTVTV-TKDGvAQELKAEKV 263
                                    55689999999999998655.5666777.56677888888765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.5   1.1e-09   1.1e-06       1      54 [.       5      60 ..       5      82 .. 0.90
   2 ?    1.1   0.3      0.16   1.6e+02       2      28 ..     174     200 ..     173     239 .. 0.85
   3 ?    3.7   0.5     0.027        26     349     385 ..     296     332 ..     275     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-09
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G..GGTT--SSSSEEE-TTHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl..dtiaelsCnpsiggiakgllvr 54
                                   dv+V+G+G  G+ AA+ aa+lG++++++ +k+  + +++++C ps   + +++lv+
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYwgGVCLNVGCIPSKALLRNAELVH 60
                                   79**************************666432889*********9998888875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                                    EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                    +i+ G+G  G+e  + +++ G++v+++
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIV 200
                                    7999********************998 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.027
                                    TSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHH CS
                           GIDA 349 tLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaa 385
                                     ++t+ v ++++ G++nG   +++++a  qG++A+  +a
  gi|121636377|ref|YP_976600.1| 296 YMRTN-VGHIYAIGDVNGLL-QLAHVAeaQGVVAAETIA 332
                                    56776.999**********7.67777666*****97766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00035      0.35       2      31 ..       4      33 ..       3      38 .. 0.93
   2 !   15.0   0.0   1.1e-05     0.011       4      43 ..     174     213 ..     172     217 .. 0.87
   3 ?    1.8   0.0      0.12   1.1e+02     108     156 ..     215     261 ..     211     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlve 31
                                   +dV++ GaGp G ++a   ++ G ++ +ve
  gi|121636377|ref|YP_976600.1|  4 YDVVVLGAGPGGYVAAIRAAQLGLSTAIVE 33
                                   69**************************99 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43 
                                    ++I GaG  G+  + +L+++Gv+v++ve   ++ ++  ad
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDAD 213
                                    689*************************888777776665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                  FAD_binding_3 108 eriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                     + ++++ ++ g+++  +t+ves+ + +++vt +v++  +g  ++++a+
  gi|121636377|ref|YP_976600.1| 215 SKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVTK--DGVAQELKAE 261
                                    55667788899*************9999999988875..4666667665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.1   2.9e-08   2.9e-05       1      30 [.       5      34 ..       5      40 .. 0.95
   2 ?    2.1   0.1     0.083        82       2      29 ..     174     201 ..     173     207 .. 0.92
   3 ?    2.2   0.2     0.077        77     147     203 ..     218     271 ..     208     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                   Dv+V G+G +G++AA++aa+ Gl++a+ve 
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRAAQLGLSTAIVEP 34
                                   9***************************95 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.083
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavve 29 
                                    +i+ G+G+ G+  ++ +++ G +v++ve
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIVE 201
                                    79*************************8 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.077
                                    HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                  FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                      ++++k+gv++++ t+++++  ++g  ++++v+  ++g  ++++a +v+ a g ++
  gi|121636377|ref|YP_976600.1| 218 IEKQFKKLGVTILTATKVESIA-DGGSQVTVTVT--KDGVAQELKAEKVLQAIGFAP 271
                                    56889999*************4.46677777888..899999999999998877555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4    0.0008       0.8       1      27 [.       8      34 ..       8      44 .. 0.89
   2 !   11.8   0.1   0.00022      0.22       1      26 [.     176     201 ..     176     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0008
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                   ++GaG +G vaA ++a+ g++  ++e 
  gi|121636377|ref|YP_976600.1|  8 VLGAGPGGYVAAIRAAQLGLSTAIVEP 34
                                   89******************9999985 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                                    EE--SHHHHHHHHHHHCCTEEEEEE- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvllle 26 
                                    I GaG+ G+ + y L+++g+dv+++e
  gi|121636377|ref|YP_976600.1| 176 IAGAGAIGMEFGYVLKNYGVDVTIVE 201
                                    67**********************98 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   4.2e-06    0.0041       1      31 [.       4      34 ..       4      39 .. 0.93
   2 ?   -2.3   0.0       1.4   1.4e+03     141     163 ..     119     143 ..      73     147 .. 0.48
   3 ?    2.7   0.3     0.041        40       2      30 ..     173     201 ..     172     208 .. 0.91
   4 !    7.6   0.3    0.0014       1.3     110     164 ..     213     269 ..     203     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                   +dv+v+G+G+ G  aAi+aa+ g +++++e 
  gi|121636377|ref|YP_976600.1|  4 YDVVVLGAGPGGYVAAIRAAQLGLSTAIVEP 34
                                   59************************99985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                    E.EEEEE...TTEEEEESEEEE--- CS
                    HI0933_like 141 gkfrvkt.k.seeeleadklvlAtG 163
                                    +++ v++ + ++e+++ d+ ++AtG
  gi|121636377|ref|YP_976600.1| 119 NTLLVDLnDgGTESVTFDNAIIATG 143
                                    2233333211344555555555555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.041
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllle 30 
                                    ++i+ G+Ga G+     +++ g +V+++e
  gi|121636377|ref|YP_976600.1| 173 SIIIAGAGAIGMEFGYVLKNYGVDVTIVE 201
                                    6899***********************98 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE---- CS
                    HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.k..seeeleadklvlAtGG 164
                                    d+ + ++k+ k+ gv++ + t+v+s++   +++++v++ k   ++el+a+k++ A+G 
  gi|121636377|ref|YP_976600.1| 213 DVSKEIEKQFKKLGVTILTATKVESIAD-GGSQVTVTVtKdgVAQELKAEKVLQAIGF 269
                                    677778999*****************66.555577777443346899******99994 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   6.3e-05     0.063      17      51 ..       3      36 ..       1      61 [. 0.82
   2 !    6.7   0.1    0.0038       3.8      18      48 ..     172     201 ..     156     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersv 51
                                     Dvv+ GaG+ G  aa   a+  +l +ai+e + 
  gi|121636377|ref|YP_976600.1|  3 HYDVVVLGAGPGGYVAAIRAAQL-GLSTAIVEPKY 36
                                   57****************99999.********875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0038
                                    EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4  18 sDvvivGaGssGLtaayylakkpdlkvaile 48 
                                      ++i GaG+ G+  +y+l +  ++ v+i+e
  gi|121636377|ref|YP_976600.1| 172 KSIIIAGAGAIGMEFGYVLKNY-GVDVTIVE 201
                                    579****************888.99999998 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.4   3.9e+02       2      30 ..       6      34 ..       5      37 .. 0.91
   2 ?   -3.6   0.1       9.1     9e+03     105     116 ..     135     146 ..     131     157 .. 0.80
   3 !   16.4   0.3   6.3e-06    0.0063       2      64 ..     174     239 ..     173     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.4
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                   v v+GaG  G   a  +a+ gl++ +v+ 
  gi|121636377|ref|YP_976600.1|  6 VVVLGAGPGGYVAAIRAAQLGLSTAIVEP 34
                                   89*********************999886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.1
                                    -TTSEEEE--SS CS
                        3HCDH_N 105 kpdailasnTSs 116
                                     ++ai+a+ +S+
  gi|121636377|ref|YP_976600.1| 135 FDNAIIATGSST 146
                                    5789****9997 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 6.3e-06
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-...HHHHCCCH CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk...eeeveaal 64 
                                    + + GaG +G +  +v+ + g++V++v+  ++al +  + ++k++ek+ +k  ++   + +ve+++
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTiltATKVESIA 239
                                    5688*******************************************9999887744444444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   7.1e-05     0.071       1      27 [.     174     200 ..     174     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtli 27 
                                    i i+GaGaiG  +++ L++ g dvt++
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIV 200
                                    78***************99*****987 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.62   6.2e+02      28      74 ..      68     114 ..      59     131 .. 0.84
   2 ?    8.6   0.0    0.0016       1.6       4     120 ..     175     230 ..     172     240 .. 0.56
   3 ?   -1.6   0.0       2.3   2.3e+03      17      37 ..     363     383 ..     360     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.62
                         LpxI_N  28 vvalegeadeelekivdevaevsvgqlgklikaLkregvtevvmaGk 74 
                                    +++++ge++ ++    d+  +v  g++  +  ++k++++te+   G+
  gi|121636377|ref|YP_976600.1|  68 AFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGT 114
                                    5678888888888888999999999***************9976665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                         LpxI_N   4 liAGsGrlPllvaeaakaagrevvvvalegeadeelekivdevaevsvgqlgklikaLkregvtevvmaGkvekpklldl 83 
                                    +iAG+G++ +++   +k+ g +v +v +   a ++  + v++ +e ++++l                             
  gi|121636377|ref|YP_976600.1| 175 IIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKL----------------------------- 225
                                    566666666666666666666666666666555555555554444444444............................. PP

                         LpxI_N  84 rpDlralkllaklkdrgddalLravveelekeGikvl 120
                                                                    G+++l
  gi|121636377|ref|YP_976600.1| 226 --------------------------------GVTIL 230
                                    ................................44444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                         LpxI_N  17 eaakaagrevvvvalegeade 37 
                                    ++a+++g++vvv+++   a++
  gi|121636377|ref|YP_976600.1| 363 QQARNEGYDVVVAKFPFTANA 383
                                    68999******9988665555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0016       1.6       1      32 [.       5      34 ..       5      38 .. 0.95
   2 ?   -0.6   0.1      0.51   5.1e+02       2      35 ..     174     205 ..     173     211 .. 0.86
   3 ?    3.4   0.1     0.032        32      88     143 ..     213     271 ..     209     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                   Dvvv GaGp g   A r   a+ gl+  ++e+
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRA--AQLGLSTAIVEP 34
                                   9*****************..**********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasps 35 
                                    +++ GaG+ g+     l  +++g+ v+++e  p 
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVL--KNYGVDVTIVEFLPR 205
                                    7999***********99..99*******996665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.032
                  Lycopene_cycl  88 rlkeellerlvengvkllea.kvesveeeeageslvvleggr..kirarlvvdarglas 143
                                    +  +e+++++ + gv+ l a kves+++     ++ v+++g+  +++a  v+ a g a 
  gi|121636377|ref|YP_976600.1| 213 DVSKEIEKQFKKLGVTILTAtKVESIADGGSQVTVTVTKDGVaqELKAEKVLQAIGFAP 271
                                    567788888888888766552799999888744555677887889*********99443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4    0.0074       7.4       1      29 [.       5      35 ..       5      66 .. 0.92
   2 ?   -1.8   0.0       1.8   1.7e+03     184     207 ..     124     149 ..      89     166 .. 0.65
   3 ?    2.4   0.8     0.097        96       2      27 ..     174     201 ..     173     203 .. 0.93
   4 ?   10.5   0.2   0.00032      0.32     148     201 ..     214     268 ..     209     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0074
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                   dvv+ G+G  G  +A  +a+ g  ++++e +
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRAAQLGlsTAIVEPK 35
                                   9***************************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                    EECT.EEE.EEEEEEEE--GGGHHHH CS
                            DAO 184 rttp.gen.daadavVnaaGawsdll 207
                                    + ++ g++ +++d  ++a+G  ++l+
  gi|121636377|ref|YP_976600.1| 124 DLNDgGTEsVTFDNAIIATGSSTRLV 149
                                    34444665556788999999998877 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.097
                                    EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtlle 27 
                                    ++i G+G iG+   y L   g  Vt++e
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGvdVTIVE 201
                                    89***************77799****98 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00032
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEE..EEEEEEE--G CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gend..aadavVnaaG 201
                                    + + + +++++lGv+il+ t+v+++  ++g  ++v ++t+ g  +  +a++v  a G
  gi|121636377|ref|YP_976600.1| 214 VSKEIEKQFKKLGVTILTATKVESIA-DGGSQVTV-TVTKdGVAQelKAEKVLQAIG 268
                                    56778899*****************4.45555666.555557653244455766666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0037       3.7       1      34 [.     174     207 ..     174     218 .. 0.88
   2 ?   -0.6   0.1       1.5   1.5e+03      13      44 ..     234     265 ..     225     306 .. 0.71
   3 ?    0.1   0.3      0.95   9.4e+02      49      69 ..     308     328 ..     254     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerv 34 
                                    iii+G+G +G++    L+++g dv++++  ++++
  gi|121636377|ref|YP_976600.1| 174 IIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRAL 207
                                    89*****************7768*****988765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                    HHHHHHHTTEEEEEEESSHHHHHHHHHTTSEE CS
                         TrkA_N  13 laeeLseggkdvvvidkdeerveelreeglev 44 
                                     +e + +gg++v+v  +++ +++el++e++  
  gi|121636377|ref|YP_976600.1| 234 KVESIADGGSQVTVTVTKDGVAQELKAEKVLQ 265
                                    56666775567888888888999998887443 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.95
                                    TTSHHHHHHTTGGGESEEEE- CS
                         TrkA_N  49 atdeevLeeagiekadaviaa 69 
                                    +    +L+ a++++a++v+aa
  gi|121636377|ref|YP_976600.1| 308 GDVNGLLQLAHVAEAQGVVAA 328
                                    444578999999999999997 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0021       2.1      30      58 ..       5      33 ..       1      36 [. 0.89
   2 ?    2.3   0.2     0.085        85      29      69 ..     172     212 ..     166     266 .. 0.77
   3 ?    0.7   0.4      0.26   2.6e+02       5      50 ..     292     337 ..     289     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlD 58
                                    v+v+G+G  G  A+  a++lg ++ +++
  gi|121636377|ref|YP_976600.1|  5 DVVVLGAGPGGYVAAIRAAQLGLSTAIVE 33
                                   79********************9988876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.085
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                      +++ G+G  G++   + k+ g +Vt+++  p++l + ++
  gi|121636377|ref|YP_976600.1| 172 KSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDA 212
                                    568999*********************99988877766555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.26
                                    HHHHCSCGCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHT CS
                    AlaDh_PNT_C   5 aakalekffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakgl 50 
                                    + + + +++ g++ ++G v+g  +   +    Gv+  + ia a  l
  gi|121636377|ref|YP_976600.1| 292 GVDDYMRTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETL 337
                                    566789999999999**99997666666677888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3036.98
//
Query:       gi|121636378|ref|YP_976601.1|  [L=97]
Description: hypothetical protein BCG_0503 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 724.48
//
Query:       gi|121636379|ref|YP_976602.1|  [L=190]
Description: hypothetical protein BCG_0504c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-14   51.9   0.1    1.5e-13   50.6   0.0    1.7  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   8.4e-18   1.5e-13       3      81 ..      51     129 ..      49     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 8.4e-18
                                    HHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHH.HHHHHSHHHHH.HHH CS
                            CMD   3 llraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaq.aaayagwpaar.aAl 80 
                                    l+++++ + + ll  +g+L+  + eL++l+v++++ cey++++H r+A+++G++++  a+++a+  ++++++p+ + +A+
  gi|121636379|ref|YP_976602.1|  51 LFWTFAIYTGRLL--HGRLPGVDTELVILRVAHLRSCEYELQHHRRMARRRGLDANTQATIFAWpDVPDGDGPRKVlSAR 128
                                    7899999999999..899*********************99***********************6667777888775665 PP

                                    H CS
                            CMD  81 a 81 
                                    +
  gi|121636379|ref|YP_976602.1| 129 Q 129
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1424.52
//
Query:       gi|121636380|ref|YP_976603.1|  [L=474]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-69  233.0   0.0    2.4e-69  232.2   0.0    1.4  1  DUF2083        Predicted transcriptional regulator (DUF2083)
    2.5e-28   98.4   0.7    9.4e-28   96.6   0.1    2.1  2  Peptidase_M78  IrrE N-terminal-like domain
    7.2e-12   45.2   0.0    1.7e-11   44.0   0.0    1.7  1  HTH_3          Helix-turn-helix
    7.6e-12   45.1   0.0    2.5e-11   43.4   0.0    1.9  2  HTH_19         Helix-turn-helix domain
    4.8e-11   42.8   0.4    2.6e-10   40.5   0.1    2.5  2  HTH_31         Helix-turn-helix domain
    0.00026   20.8   0.1    0.00083   19.2   0.1    2.0  1  HTH_25         Helix-turn-helix domain
     0.0011   18.9   0.0     0.0073   16.2   0.0    2.2  2  HTH_37         Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.055   13.9   0.0    2.3  3  HTH_26         Cro/C1-type HTH DNA-binding domain
      0.052   13.7   0.0      0.096   12.8   0.0    1.3  1  AMIN           AMIN domain


Domain annotation for each model (and alignments):
>> DUF2083  Predicted transcriptional regulator (DUF2083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.2   0.0   1.2e-72   2.4e-69       1     157 []     311     469 ..     311     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.2 bits;  conditional E-value: 1.2e-72
                        DUF2083   1 tLqrpgargvPfffvrvDrAGniskrasatgfqfarfggaCPlwnvheafetpgrilvqlaelpdgeryltiartvekes 80 
                                    tLqrp++rgvPf+fvrvDrAGn+skr+satgf+f+++gg+CPlwnv+e+f++pg+ilvq+a++pdg++yl++artve ++
  gi|121636380|ref|YP_976603.1| 311 TLQRPSMRGVPFTFVRVDRAGNMSKRQSATGFHFSSSGGTCPLWNVYETFANPGKILVQIAQMPDGRNYLWVARTVELRA 390
                                    8******************************************************************************* PP

                        DUF2083  81 gafgepekrfaialgceikhaeklvyadgldle..ekaaatpiGvgCrlCeredCaqRafpplgrelevdenerglspy 157
                                    +++g+p k+fai+lgce++ha++lvy++gldl+   ++aatpiG+gCr+Cer++C+qRafp+lgr+l++de+++++spy
  gi|121636380|ref|YP_976603.1| 391 ARYGQPGKTFAIGLGCELRHAHRLVYSEGLDLSgdPNTAATPIGAGCRVCERDNCPQRAFPALGRALDLDEHRSTVSPY 469
                                    ******************************9962246789*************************************99 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.54   1.1e+03      83     105 ..     137     159 ..      91     174 .. 0.69
   2 !   96.6   0.1   4.7e-31   9.4e-28       2     123 .]     188     310 ..     187     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.54
                  Peptidase_M78  83 aelllPeeaflalaatqrkdlee 105
                                    + + +P+e++++ + +++++l+ 
  gi|121636380|ref|YP_976603.1| 137 GSITMPHEEVRDYFYQRQNYLHA 159
                                    55678888888888888888776 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 4.7e-31
                  Peptidase_M78   2 erlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlere.... 77 
                                    e +g++++ ++++  d+  +r+d+  t+++ ++s++sp +q f++a El++l++++ +d++ ++g+++++e +  +    
  gi|121636380|ref|YP_976603.1| 188 EVHGVRIN-KRIDLGDTVLHRYDPA-TNTLEISSHLSPGQQVFKMAAELAYLEFGDLIDAMVTDGKFTSAESRTLArlgl 265
                                    67999999.99*************8.****************************************************** PP

                  Peptidase_M78  78 anafAaelllPeeaflalaatqrkdleerlaeyfgVSkeavavrls 123
                                    an+fAa+ +lP+++f+++a+++r+d e+ l++++ VS+e++a+rls
  gi|121636380|ref|YP_976603.1| 266 ANYFAAATVLPYRQFHDVAENFRYDVER-LSAFYSVSYETIAHRLS 310
                                    ***************************7.***************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   8.6e-15   1.7e-11       1      54 [.      10      63 ..      10      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 8.6e-15
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                   +++lR+++g sq+ LA++l +s+s++ +iE + r  ++ +l+++ +++gv+ ++
  gi|121636380|ref|YP_976603.1| 10 VRQLRNERGFSQAALAQMLEISPSYLDQIEHDVRPLTVAVLLRITEVFGVDATF 63
                                   69************************************************9876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.2e-14   2.5e-11       1      63 [.       7      68 ..       7      70 .. 0.95
   2 ?   -2.9   0.0       3.7   7.3e+03      39      59 ..     274     294 ..     272     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-14
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqge 63
                                   G r++++R e+g++q++la++l is+s++ +iE++ +  ++  +ll+i e +g+d++ + +++
  gi|121636380|ref|YP_976603.1|  7 GSRVRQLRNERGFSQAALAQMLEISPSYLDQIEHDVR-PLTVAVLLRITEVFGVDATFFASQD 68
                                   89**********************************9.999***************9987765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                         HTH_19  39 vpsaelllkiaealgidleyl 59 
                                    v++++ + ++ae + +d+e+l
  gi|121636380|ref|YP_976603.1| 274 VLPYRQFHDVAENFRYDVERL 294
                                    567888889999999999987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   1.3e-13   2.6e-10       3      57 ..       7      60 ..       6      72 .. 0.95
   2 ?   -2.5   0.0       3.3   6.7e+03      42      58 ..     445     461 ..     441     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.3e-13
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                   G ++r+lR+++G sq+++A+ l +s+s+l ++E   r+  + avl ++ +++g+d
  gi|121636380|ref|YP_976603.1|  7 GSRVRQLRNERGFSQAALAQMLEISPSYLDQIEHDVRP-LTVAVLLRITEVFGVD 60
                                   89***********************************7.***************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                         HTH_31  42 pspavlealaralgldp 58 
                                    ++ ++  al ral+ld+
  gi|121636380|ref|YP_976603.1| 445 CPQRAFPALGRALDLDE 461
                                    55667789999999997 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.2e-07   0.00083       3      33 ..      11      41 ..       9      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.2e-07
                                   HHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                         HTH_25  3 raaRearglsleevaketkIrkdylealEed 33
                                   r+ R +rg s  ++a+ + I+++yl ++E d
  gi|121636380|ref|YP_976603.1| 11 RQLRNERGFSQAALAQMLEISPSYLDQIEHD 41
                                   999**************************97 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0073      16      72 ..       3      58 ..       2      62 .. 0.88
   2 ?   -1.0   0.0      0.88   1.8e+03      11      42 ..      96     127 ..      90     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                                   HHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTT CS
                         HTH_37 16 KaqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalG 72
                                   K+ + +++++l+ +r+ sq+ +aq+l+i+ + +++++  +++ +++  Ll++ + +G
  gi|121636380|ref|YP_976603.1|  3 KTYVGSRVRQLRNERGFSQAALAQMLEISPSYLDQIEH-DVRPLTVAVLLRITEVFG 58
                                   566678899****************************5.999999999999877766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.88
                                    HHHHHHHHHHHHHHHHHHHCT--HHHHHHHHT CS
                         HTH_37  11 eelkaKaqlalaiaeliekrelsqseaaqllg 42 
                                    e ++a   la+a+  l ++ +++++++a++++
  gi|121636380|ref|YP_976603.1|  96 EMVSAHPGLARAVVNLHRRYRITTAQLAAATE 127
                                    55556677899999999999999999998876 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.055       2      53 ..      10      60 ..       9      62 .. 0.94
   2 ?   -3.1   0.0       5.5   1.1e+04       9      19 ..     115     125 ..     110     128 .. 0.54
   3 ?   -2.3   0.0       3.2   6.4e+03       6      33 ..     168     195 ..     166     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                         HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct 53
                                    r+l  +rg +++ La++++is + l+ + ++ ++ ++  +L +i +++g++
  gi|121636380|ref|YP_976603.1| 10 VRQLRNERGFSQAALAQMLEISPSYLDQIEHD-VRPLTVAVLLRITEVFGVD 60
                                   689999*************************9.89**********9999986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.5
                         HTH_26   9 rgitkseLarg 19 
                                     +it+++La +
  gi|121636380|ref|YP_976603.1| 115 YRITTAQLAAA 125
                                    34566666555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.2
                         HTH_26   6 madrgitkseLargtgisaatlsrlvkg 33 
                                     a++++   +Lar +    + +++ + +
  gi|121636380|ref|YP_976603.1| 168 TAQMRMHHGDLARELTRRLTEVHGVRIN 195
                                    5888999999999876666555555555 PP

>> AMIN  AMIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.8e-05     0.096      20      83 ..      59     118 ..      49     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
                           AMIN  20 ekykvftlsnpnrlviDlpnaelglelkriennkpgiksvrvvgqkdpntvRvvldldksvkpq 83 
                                    ++ + f  ++++rlv+ l +++l+ +l+ i ++ + ++++  ++  +p+  R v++l   ++ +
  gi|121636380|ref|YP_976603.1|  59 VDATFFASQDDTRLVAELREVTLDRDLD-IAIDPHEVAEMV-SA--HPGLARAVVNLHRRYRIT 118
                                    66788999******************86.**********99.64..79*********9866654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3258.55
//
Query:       gi|121636381|ref|YP_976604.1|  [L=264]
Description: hypothetical protein BCG_0506 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-73  246.6   0.0    2.6e-73  246.4   0.0    1.0  1  Acyl-ACP_TE  Acyl-ACP thioesterase
    9.4e-06   25.9   0.2      0.033   14.6   0.0    3.0  3  4HBT         Thioesterase superfamily
  ------ inclusion threshold ------
      0.098   13.2   0.6        1.4    9.4   0.2    2.4  2  4HBT_2       Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.4   0.0   4.3e-77   2.6e-73       2     247 ..      16     263 ..      15     264 .] 0.97

  Alignments for each domain:
  == domain 1  score: 246.4 bits;  conditional E-value: 4.3e-77
                    Acyl-ACP_TE   2 kvfkekyevrvyevdvngtakleallnllqdvaanqveelGlsddkflkklnlvWvvakyeieierlpefgdkveietwa 81 
                                    +vf++++++rv+++d++g+++l+a+++++qd++++q++e+G      +++++++W+v+++++++ r++efgd++++++w+
  gi|121636381|ref|YP_976604.1|  16 DVFDREWPLRVGDIDRAGRLRLDAACRHIQDIGQDQLREMG------FEETHPLWIVRRTMVDLIRPIEFGDMLRCRRWC 89 
                                    79***************************************......9******************************** PP

                    Acyl-ACP_TE  82 esenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilaey.eeeseeklkkkpktkvleakeeseekelk 160
                                    +++++++c+++++v++ kg  +ie++++++++++et++++r++d++la + +++s+++l++k+++k+++++++se++e++
  gi|121636381|ref|YP_976604.1|  90 SGTSNRWCEMRVRVDGRKG-GLIESEAFWIHVNRETEMPARIADDFLAGLhRTTSVDRLRWKGYLKPGSRDDASEIHEFP 168
                                    ****************666.6*****************************8999************************** PP

                    Acyl-ACP_TE 161 vrysDlDlnqHvNNvkYlewilevlpleilkkhelkkitlkYekevqlgdkveilte..iaeseeslktkheirlse... 235
                                    vr++D+Dl++H+NN++Y+++i+++l+++++  + + ++t+++e++v+lgdk+ei+++  +a+s+e++ + +++r+ +   
  gi|121636381|ref|YP_976604.1| 169 VRVTDIDLFDHMNNAVYWSVIEDYLASHAELLRGPLRVTIEHEAPVALGDKLEIISHvhPAGSTEIFGPGLVDRAVTtlt 248
                                    *******************************************************998899**************99999 PP

                    Acyl-ACP_TE 236 ...Geeiakaktewr 247
                                       G+e++++++ ++
  gi|121636381|ref|YP_976604.1| 249 yvvGDEPKAVASLFN 263
                                    999999999999886 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.5e-06     0.033      28      74 ..      61     107 ..      39     112 .. 0.84
   2 ?   -2.2   0.0      0.92   5.5e+03      40      58 ..     152     170 ..     151     172 .. 0.78
   3 !    8.2   0.0   0.00051       3.1       3      61 ..     179     231 ..     177     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                                    TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETT CS
                           4HBT  28 gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrded 74 
                                      l+ v++  +d +rp+ +gd l+++ +++ ++++  +++v+v   +
  gi|121636381|ref|YP_976604.1|  61 HPLWIVRRTMVDLIRPIEFGDMLRCRRWCSGTSNRWCEMRVRVDGRK 107
                                    45788999*********************************996555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.92
                                    ESS-BBTTCEEEEEEEEEE CS
                           4HBT  40 flrpvrlgdeltvearvlr 58 
                                    +l+p+  +d  +++  ++r
  gi|121636381|ref|YP_976604.1| 152 YLKPGSRDDASEIHEFPVR 170
                                    99****9998888755555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00051
                                    SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEES CS
                           4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgr 61 
                                    +++++vy + ++  ++  +  l g+      ++ +i++ +pv lgd+l++  +v  +g+
  gi|121636381|ref|YP_976604.1| 179 HMNNAVYWSVIEDYLASHAELLRGP------LRVTIEHEAPVALGDKLEIISHVHPAGS 231
                                    6777777777777777777777776......7889***************999977666 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.062   3.7e+02      45      85 ..      63     103 ..      25     143 .. 0.67
   2 ?    9.4   0.2   0.00023       1.4       1      23 [.     169     191 ..     169     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.062
                         4HBT_2  45 glilssahvryrrplkfpdrltvefrvididaktliiehrf 85 
                                    + i++++ v+  rp+ f+d l+ +   +  + +++ + +r+
  gi|121636381|ref|YP_976604.1|  63 LWIVRRTMVDLIRPIEFGDMLRCRRWCSGTSNRWCEMRVRV 103
                                    67899999999999999999965544444444444444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00023
                         4HBT_2   1 vrpndvDlnghlnnarylrylee 23 
                                    vr +d+Dl+ h+nna y ++ e+
  gi|121636381|ref|YP_976604.1| 169 VRVTDIDLFDHMNNAVYWSVIED 191
                                    899**************966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2001.78
//
Query:       gi|121636382|ref|YP_976605.1|  [L=428]
Description: isocitrate lyase icl [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.6e-101  339.7   3.6    9.4e-53  179.5   0.1    2.1  2  ICL         Isocitrate lyase family
      6e-17   61.9   0.1    1.2e-16   60.9   0.1    1.5  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.22   11.5   0.0    1.5  1  DUF3338     Domain of unknown function (DUF3338)


Domain annotation for each model (and alignments):
>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.1   1.6e-56   9.4e-53       4     253 ..      12     251 ..       9     253 .. 0.86
   2 !  162.1   0.5   2.8e-51   1.7e-47     352     525 ..     252     426 ..     250     427 .. 0.91

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.6e-56
                                    XHH.HHHTSGGGGG---SS-HHHHHHH--SS----T.HHHHHHHHHHHHHHHHHHT--EEEEB--SH.HHHHHHHHH-S- CS
                            ICL   4 evk.kwwsdsrwrktkrvysaedivskrGnlkieya.sseqakklfklleeheaektasktfGaldp.vqvtqmakyldt 80 
                                    +++ +w +++rw+   r+ysaed+v+ +G++  e++ + + a+ l++ l    ++ +   + Gal   + v q+   l +
  gi|121636382|ref|YP_976605.1|  12 QIQqEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTlARRGAEVLWEQL----HDLEWVNALGALTGnMAVQQVRAGLKA 87 
                                    5651566799********************9877651334456666555....556667788999752668899999*** PP

                                    EEE-HHHHHHH--TT----SS-S-S-TTHHHHHHHHHHHHHHHHHHHHHHHHHSS-HHHHTTS--------EEEE-TT-S CS
                            ICL  81 iyvsGwqssstastsnepspdladypmdtvpnkvehlflaqlfhdrkqkeerlkvkkeereklanvdylrpiiadadtGh 160
                                    iy+sGwq +  a  s    pd + yp ++vp+ v  +  a +  d+  k e           ++  ++l pi+ad+++G+
  gi|121636382|ref|YP_976605.1|  88 IYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIE---------GDTSVENWLAPIVADGEAGF 158
                                    **********************************99988865444332222.........23444579************ PP

                                    SSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE--GGGEEEES CS
                            ICL 161 GGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvartdseaatlit 240
                                    GG   v  l k +i  G aG h edq ++ kkcGh+ Gkvl+p q+hi  l ++r++ad+ ++ ++v+artd+eaatlit
  gi|121636382|ref|YP_976605.1| 159 GGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLIT 238
                                    ******************************************************************************** PP

                                    -TT-GGGGGGEEE CS
                            ICL 241 stidtrdhafilG 253
                                    s +d+rd  fi G
  gi|121636382|ref|YP_976605.1| 239 SDVDERDQPFITG 251
                                    ***********98 PP

  == domain 2  score: 162.1 bits;  conditional E-value: 2.8e-51
                                    S--TT--EEE--SHHHHHHHHHHHTTS-SEEE---SS--HHHHHHHHHHHHTT-TT-EEEEE--SSS-GGGTS-HHHHHS CS
                            ICL 352 prvreGyyrykGgtqcsvvravafapyadliwmesklpdyaqakefaeGvkakvpeqklaynlspsfnwkkamsadeqet 431
                                     r+reG+yr k g++ ++ ra a+ap+adliwme+ +pd++ a++f+e vka +p+q+layn spsfnwkk        +
  gi|121636382|ref|YP_976605.1| 252 ERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAK 331
                                    59************************************************************************99**** PP

                                    HHHHHHHTTEEEEEETTHHHHHHHHHHHHHHHHHHHHTHHHHHHHTHHHHH...HHT-GGGSHHHHHTHHHHHHHHHHHH CS
                            ICL 432 yikrlaklGyvwqfitlaGlhtnalisdkfakdyakrGmkaygeevqeeei...dnGvdvvkhqkwsGaeyidellklvt 508
                                    + k la++G+ +qfitlaG+h+      ++a  ya++ m ay+e  qe+e    + G    khq+  Ga y+d++  +v 
  gi|121636382|ref|YP_976605.1| 332 FQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVEL-QEREFaaeERGYTATKHQREVGAGYFDRIATTVD 410
                                    ******************************************985.6666523368***********************9 PP

                                    --XXXXXXXXXXXXXXX CS
                            ICL 509 GGvsstaamGkGvtedq 525
                                       s+ta  G    e q
  gi|121636382|ref|YP_976605.1| 411 PNSSTTALTG-STEEGQ 426
                                    8866666544.334445 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1     2e-20   1.2e-16      26     199 ..      81     311 ..      59     353 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2e-20
                     PEP_mutase  26 eeagfkalatsSlava.....aslGvpDgeelpleellaavraiaevvs..................lPlivDledGyge 82 
                                     +ag ka+ +s+++va       + +pD++  p++++ ++vr+i ++++                   P+ +D e+G+g 
  gi|121636382|ref|YP_976605.1|  81 VRAGLKAIYLSGWQVAgdanlSGHTYPDQSLYPANSVPQVVRRINNALQradqiakiegdtsvenwlAPIVADGEAGFGG 160
                                    2459**********994432223579**********************99*****************************9 PP

                     PEP_mutase  83 speevaetvrrliaaGvvgvniEDk.....kknd.aerqlldieefaekiaaaraaaeeag..fvinARtdalll..... 149
                                     + +v e  + liaaGv+g + ED+     k++  +++ l++ +++ + ++ ar aa+ a+   v++ARtda        
  gi|121636382|ref|YP_976605.1| 161 -ALNVYELQKALIAAGVAGSHWEDQlasekKCGHlGGKVLIPTQQHIRTLTSARLAADVADvpTVVIARTDAEAAtlits 239
                                    .88**********************9985444455777888********************99********97768889* PP

                     PEP_mutase 150 ....................sagagleeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavd..vplnvvp 199
                                                        + ++g+e  i+Ra+aYa   Ad + +  ++ d e  +++ +av+   p  +++
  gi|121636382|ref|YP_976605.1| 240 dvderdqpfitgertregfyRTKNGIEPCIARAKAYAPF-ADLIWMETGTPDLEaARQFSEAVKaeYPDQMLA 311
                                    *******************99999************987.899988888777666899999995565655555 PP

>> DUF3338  Domain of unknown function (DUF3338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.22      62      98 ..      99     135 ..      96     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                        DUF3338  62 AeltGklpkeyPLkpgekppqvrRrvgtafkldekll 98 
                                    A+l G+  ++ +L p+ + pqv Rr+++a +  +++ 
  gi|121636382|ref|YP_976605.1|  99 ANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIA 135
                                    99***************************98877643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2983.95
//
Query:       gi|121636383|ref|YP_976606.1|  [L=286]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-59  201.5   1.6    1.3e-59  201.1   0.8    1.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    8.8e-34  116.0   0.0    3.3e-33  114.2   0.0    1.9  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
     0.0012   19.0   1.1     0.0012   19.0   1.1    1.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0037   16.7   0.6     0.0084   15.6   0.6    1.7  1  PALP             Pyridoxal-phosphate dependent enzyme
     0.0039   17.8   0.2       0.01   16.4   0.2    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0078   16.4   0.3      0.018   15.3   0.3    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0084   16.6   1.1      0.018   15.6   1.1    1.6  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0093   15.3   0.4      0.019   14.3   0.4    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.012   14.9   0.7      0.019   14.2   0.7    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.014   15.4   0.5        0.8    9.8   0.1    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.015   15.7   0.4      0.031   14.7   0.4    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.04   13.9   0.5      0.065   13.2   0.5    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.065   13.7   0.0       0.14   12.7   0.0    1.7  1  XdhC_C           XdhC Rossmann domain
       0.07   12.4   0.1      0.088   12.0   0.1    1.3  1  FAD_binding_3    FAD binding domain
       0.15   12.3   0.0       0.19   11.9   0.0    1.2  1  MutS_III         MutS domain III
       0.28   11.5   2.7        4.2    7.6   2.7    2.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
        1.2    9.2   6.2       0.35   11.0   0.4    2.9  3  DUF1707          Domain of unknown function (DUF1707)
        1.5    8.7   4.6        1.1    9.1   1.9    2.2  2  Rossmann-like    Rossmann-like domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.8   1.3e-62   1.3e-59       2     179 ..       8     187 ..       7     188 .. 0.98
   2 ?   -2.1   0.0       3.1   3.1e+03     161     161 ..     253     253 ..     214     272 .. 0.56

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.3e-62
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SE CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadl 81 
                                    v+v+GaG+mG+gia+v a+ag+eV++++ +e+ +++++++i ksle++v++gk++e e+++al  ++fttdl+++ d +l
  gi|121636383|ref|YP_976606.1|   8 VGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKVTERERDRALGLLTFTTDLNDLSDRQL 87 
                                    9******************************************************************************* PP

                                    EEE-S-SSHHHHHHHHHHHHCCS.-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHH CS
                        3HCDH_N  82 viEavvEnlelKrkvfaelekia.kpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetv 160
                                    viEavvE+ ++K ++fael++++ +pda+lasnTSs++i ++a+a+k+p+rv+glHFfnP+p+++LvE+vr+  T+e++ 
  gi|121636383|ref|YP_976606.1|  88 VIEAVVEDEAVKSEIFAELDRVVtDPDAVLASNTSSIPIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAA 167
                                    *********************98689****************************************************** PP

                                    HHHHHHHHHT.T-EEEEECS CS
                        3HCDH_N 161 atvvelakki.gktpvvvkd 179
                                    a++ e+a  + gk++v++ d
  gi|121636383|ref|YP_976606.1| 168 ARTEEFASTVlGKQVVRCSD 187
                                    *********99******987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                    H CS
                        3HCDH_N 161 a 161
                                    +
  gi|121636383|ref|YP_976606.1| 253 E 253
                                    2 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.2   4.2e+03      36      67 ..      26      57 ..      18      69 .. 0.56
   2 !  114.2   0.0   3.3e-36   3.3e-33       1      97 []     190     286 .]     190     286 .] 1.00

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.2
                                   HHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          3HCDH 36 glGlpmGpfelldlvgldvakkilevlaeelg 67
                                   ++G+ + +fe+++ +   + ++i + l+++ +
  gi|121636383|ref|YP_976606.1| 26 RAGVEVTVFEPAEALITAGRNRIVKSLERAVS 57
                                   45666666666665555555555554444433 PP

  == domain 2  score: 114.2 bits;  conditional E-value: 3.3e-36
                                    TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHH CS
                          3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspllekl 80 
                                    GFvvn +l+p+l  a+r+ve+g a++ed+D+a+ +gl +pmGp++l+dlvgld+ k i++ ++ee++e++y p+pll ++
  gi|121636383|ref|YP_976606.1| 190 GFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGLDTLKLIADKMFEEFKEPHYGPPPLLLRM 269
                                    9******************************************************************************* PP

                                    HHTT--BGGGTBSSSBC CS
                          3HCDH  81 veagrlgrktgkgfyky 97 
                                    veag+lg+k+g+gfy+y
  gi|121636383|ref|YP_976606.1| 270 VEAGQLGKKSGRGFYTY 286
                                    ***************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.1   1.2e-06    0.0012       1      43 [.       7      59 ..       7     145 .. 0.57
   2 ?   -2.6   0.0       5.5   5.5e+03      33      60 ..     172     199 ..     158     226 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........E CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........a 43
                                   ++g++G G+MGs +a+  ++ag +v+v++  ++ +++  ++            
  gi|121636383|ref|YP_976606.1|  7 RVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIvksleravsaG 59
                                   58**************************9665333332222223323333331 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                                    HHHHHHHHTTEEE-SSHHHHHHHCSEEE CS
                  NAD_binding_2  33 ekveelvaegakaaesieelvasldvvi 60 
                                    e + +++ ++++ +++ + +v ++ +v 
  gi|121636383|ref|YP_976606.1| 172 EFASTVLGKQVVRCSDRSGFVVNALLVP 199
                                    3333333334555555555555553333 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   8.4e-06    0.0084      57     105 ..       7      56 ..       3     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.4e-06
                                    EEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-..HHHHHHHHHTT-EEE CS
                           PALP  57 tvveassGNhgralAaaaallGlkvtivvpadas..pekvallrllGaevv 105
                                    +v + ++G++g ++A ++a++G++vt++ pa a   +++ +  ++l  + v
  gi|121636383|ref|YP_976606.1|   7 RVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALitAGRNRIVKSLE-RAV 56 
                                    5667899*********************9998875556666666666.333 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2     1e-05      0.01       1      36 [.       7      38 ..       7      69 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSC CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnp 36
                                   ++g++GaG+mg+++a+  ++ag    e++v  ++ +
  gi|121636383|ref|YP_976606.1|  7 RVGVVGAGQMGSGIAEVSARAG---VEVTVF-EPAE 38
                                   69********************...666543.3333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.8e-05     0.018       1      29 [.      10      38 ..      10      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                   +vGaG  G+ +A   a+ag++v+++e ++
  gi|121636383|ref|YP_976606.1| 10 VVGAGQMGSGIAEVSARAGVEVTVFEPAE 38
                                   8*************************876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.1   1.8e-05     0.018       1      41 [.       7      43 ..       7      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHH CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDee 41
                                   +v vvG+G  g   A++ a+ g +Vtv+e ++ l      +
  gi|121636383|ref|YP_976606.1|  7 RVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALI----TA 43
                                   688***************************99998....33 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.4   1.9e-05     0.019      37      70 ..       6      39 ..       4      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                   ++vG++G+G++G+ +a++ +  g++v+++++ + 
  gi|121636383|ref|YP_976606.1|  6 QRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEA 39
                                   68**************************999865 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   1.9e-05     0.019     143     193 ..       6      56 ..       2      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                    SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleeal 193
                                    +r+ vvG+G  G+ +A + a++g+evt+ e ++ l  a   ++ + le+a+
  gi|121636383|ref|YP_976606.1|   6 QRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAV 56 
                                    6899**************************999998666666666666555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0008       0.8      13      42 ..       6      34 ..       2      57 .. 0.90
   2 ?    3.6   0.0     0.064        64      57      98 ..      94     135 ..      81     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0008
                                   -EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                   Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvva 42
                                   ++v ++GaG+m++ +a+  +++gv+ v+v+
  gi|121636383|ref|YP_976606.1|  6 QRVGVVGAGQMGSGIAEVSARAGVE-VTVF 34
                                   799**************99999998.8775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                                    T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCC CS
                   Shikimate_DH  57 kgeeiealkleelkellaeadvvisataseepilekeeveea 98 
                                    ++e ++   + el++++ + d v+++  s+ pi++ ++ ++ 
  gi|121636383|ref|YP_976606.1|  94 EDEAVKSEIFAELDRVVTDPDAVLASNTSSIPIMKVAAATKQ 135
                                    55667778899**********************998877655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   3.1e-05     0.031       8      81 ..       6     105 ..       4     114 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev...keele..........elvklaeee...................l 55 
                                    ++v vvG+G+++   ++  ++ag +vtv  p+    +              +                           +
  gi|121636383|ref|YP_976606.1|   6 QRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEaliT---AgrnrivksleR-------AvsagkvtererdralglltF 75 
                                    5899***************************953330...244433333331.......122223333334455555553 PP

                  NAD_binding_7  56 ..e.kdlegadlvi.aatddrelneriaea 81 
                                      + +dl++ +lvi a+++d++++++i ++
  gi|121636383|ref|YP_976606.1|  76 ttDlNDLSDRQLVIeAVVEDEAVKSEIFAE 105
                                    222244666777773667888899888776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   6.5e-05     0.065       2      36 ..       8      42 ..       7     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHH CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelie 36
                                   ++v+GaG+ G+ +A v a++g ev+++   e+li+
  gi|121636383|ref|YP_976606.1|  8 VGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALIT 42
                                   89***********************9998886654 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.14       3      38 ..      10      45 ..       8     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                   EE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG CS
                         XdhC_C  3 ifGaghvaqalarlaaalgfrvtvvdpreefatker 38
                                   ++Gag+++  +a++ a++g++vtv++p e++ t+ r
  gi|121636383|ref|YP_976606.1| 10 VVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGR 45
                                   89*************************998764333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.8e-05     0.088       4      46 ..       8      50 ..       6     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEE CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgln 46
                                   V +VGaG  G   a + ++aGv+v++ e  +  +  +r ++++
  gi|121636383|ref|YP_976606.1|  8 VGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVK 50
                                   89**************************999999998877764 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.19      46      96 ..      77     138 ..      75     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                    S-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT.---HHHHHH.........HHHTT---HHH CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxx.........xxxxxxxxxxx RF
                       MutS_III  46 tdleeInaRldaVee.leneelreelrellrr.lpDleRlls.........rislgkakard 96 
                                    tdl+++++R+ ++e  +e+e++++e++++l r + D + +l+         ++++ + +++ 
  gi|121636383|ref|YP_976606.1|  77 TDLNDLSDRQLVIEAvVEDEAVKSEIFAELDRvVTDPDAVLAsntssipimKVAAATKQPQR 138
                                    89************99****************888999999644444444444443334433 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.7    0.0042       4.2       1      36 [.       8      40 ..       8     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHH CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskek 36
                                   v ++GaG +G+++ae+ ar + v  e+tv ++ ++ 
  gi|121636383|ref|YP_976606.1|  8 VGVVGAGQMGSGIAEVSARAG-V--EVTVFEPAEAL 40
                                   679***************998.5..79998887765 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00035      0.35       6      45 ..      43      82 ..      41      85 .. 0.88
   2 ?   -0.2   0.0       1.1   1.1e+03      35      51 ..      96     112 ..      95     113 .. 0.83
   3 ?   -2.3   0.3       4.8   4.8e+03      34      42 ..     163     171 ..     162     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                        DUF1707  6 adReravelLrealaeGrLtldEfdeRleaalaArtrgeL 45
                                   a R+r+v+ L +a+++G  t  E d+ l+  +  + + +L
  gi|121636383|ref|YP_976606.1| 43 AGRNRIVKSLERAVSAGKVTERERDRALGLLTFTTDLNDL 82
                                   66***********************999988877777777 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                        DUF1707  35 aalaArtrgeLaalvaD 51 
                                    +a + +  +eL+++v+D
  gi|121636383|ref|YP_976606.1|  96 EAVKSEIFAELDRVVTD 112
                                    567778899******99 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.8
                        DUF1707  34 eaalaArtr 42 
                                    ++a+aArt 
  gi|121636383|ref|YP_976606.1| 163 DEAAAARTE 171
                                    78999*995 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.9    0.0011       1.1      12      51 ..       7      49 ..       2     100 .. 0.77
   2 ?   -1.2   0.0       1.8   1.7e+03      76      96 ..     148     168 ..     119     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                  Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgi...saisaasrerae 51
                                    vG+++aG++G+ +++  +rag  v+      a+  a r+r  
  gi|121636383|ref|YP_976606.1|  7 RVGVVGAGQMGSGIAEVSARAGVEVTVFepaEALITAGRNRIV 49
                                   79*******************9988754111455566666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                  Rossmann-like  76 vPdaelpglvkglaatgavra 96 
                                    vP   l +lv+ l + +a  a
  gi|121636383|ref|YP_976606.1| 148 VPVLPLVELVRTLVTDEAAAA 168
                                    566666777777777655433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1978.51
//
Query:       gi|121636384|ref|YP_976607.1|  [L=286]
Description: mycolic acid synthase umaA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-112  375.8   0.5   1.2e-112  375.6   0.5    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    2.7e-09   37.1   0.0    3.4e-09   36.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    5.9e-09   36.5   0.1    2.9e-08   34.3   0.0    2.2  3  Methyltransf_25  Methyltransferase domain
    2.5e-08   34.5   0.0      6e-08   33.3   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    1.7e-06   28.6   0.0    3.8e-06   27.5   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    2.7e-05   24.0   0.1    0.00092   19.0   0.0    2.3  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.023   14.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.013   15.0   0.0      0.029   13.9   0.0    1.5  1  MTS              Methyltransferase small domain
      0.033   13.8   0.2       0.23   11.1   0.0    2.1  2  MetW             Methionine biosynthesis protein MetW
       0.06   12.8   0.0       0.55    9.7   0.0    2.2  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.6   0.5  6.9e-116  1.2e-112       5     273 .]       6     282 ..       2     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 375.6 bits;  conditional E-value: 6.9e-116
                                    XXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH CS
                           CMAS   5 kevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery 84 
                                    + +e+ ++ YD+s++ff+lfldptm+Y+CAyfer+dmtLeeAq+aK+dl+l+kl+l+pGmtlLdiGcGWG+ ++ra+e+y
  gi|121636384|ref|YP_976607.1|   6 PFYEESQSIYDVSDEFFSLFLDPTMAYTCAYFEREDMTLEEAQNAKFDLALDKLHLEPGMTLLDIGCGWGGGLQRAIENY 85 
                                    567899************************************************************************** PP

                                    --EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                           CMAS  85 dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGllll 164
                                    dv+v+g+TlS++q +++k++++++ +er+v+v+l+++ ++ +kvdr+vs+gafe++++e+y++ff++ +++l++dG++ll
  gi|121636384|ref|YP_976607.1|  86 DVNVIGITLSRNQFEYSKAKLAKIPTERSVQVRLQGWDEFTDKVDRIVSIGAFEAFKMERYAAFFERSYDILPDDGRMLL 165
                                    ******************************************************************************** PP

                                    EEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHHHT CS
                           CMAS 165 htitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealqen 236
                                    hti ++++k+++e g+k+        kfi +eiFPgG+lp  e+i + +++a+f+v++v+ l++hYa+TL++Wa++l++n
  gi|121636384|ref|YP_976607.1| 166 HTILTYTQKQMHEMGVKVtmsdvrfmKFIGEEIFPGGQLPAQEDIFKFAQAADFSVEKVQLLQQHYARTLNIWAANLEAN 245
                                    ***************99999************************************************************ PP

                                    HHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 237 kdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    kd+aial+see+++ y++YL+gc++ Frkg  +v q+
  gi|121636384|ref|YP_976607.1| 246 KDRAIALQSEEIYNKYMHYLTGCEHFFRKGISNVGQF 282
                                    *********************************9986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.9e-12   3.4e-09      17     140 ..      56     186 ..      37     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.9e-12
                Methyltransf_23  17 lpk..lraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                    l+k  l++g+ +LdiGcG G  l + ++ + ++v+g+ ls+++ e  +    k+++ +++q++ q ++e  +k d Iv++
  gi|121636384|ref|YP_976607.1|  56 LDKlhLEPGMTLLDIGCGWGgGLQRAIENYDVNVIGITLSRNQFEYSKaklaKIPTERSVQVRLQGWDEFTDKVDRIVSI 135
                                    3444479999**********667777888899********998887769999**************************** PP

                Methyltransf_23  90 evlehvp..dppellrqiatllkpgGylllseplaslkedrllldwlylvpag 140
                                      +e ++   +++ + + +++l ++G++ll+++l +    + +++++  v+++
  gi|121636384|ref|YP_976607.1| 136 GAFEAFKmeRYAAFFERSYDILPDDGRMLLHTILTY--TQKQMHEMGVKVTMS 186
                                    *******766***********************874..555556666555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.8     1e+04      50      69 ..      37      56 ..      27      62 .. 0.65
   2 !   34.3   0.0   1.6e-11   2.9e-08       2      97 .]      68     161 ..      67     161 .. 0.92
   3 ?   -2.1   0.0       3.7   6.6e+03      27      43 ..     217     233 ..     211     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                                   EEESBCCGBSSSTTTEEEEE CS
                Methyltransf_25 50 fvqgdaedlpfedgsfDlvv 69
                                   f++ d++  + ++++fDl +
  gi|121636384|ref|YP_976607.1| 37 FEREDMTLEEAQNAKFDLAL 56
                                   45555555556677888876 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.6e-11
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+GcG G  ++++ +++ + +v+g+ +s ++ e+ ++++++  +  + vq  ++ +++  +++D +vs+ga++ ++ e+
  gi|121636384|ref|YP_976607.1|  68 LDIGCGWGGGLQRAIENY-DVNVIGITLSRNQFEYSKAKLAK-IPTERSVQVRLQGWDEFTDKVDRIVSIGAFEAFKMER 145
                                    9****************8.7********************64.3577789999999998888********99******** PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +++++++ +++L ++G
  gi|121636384|ref|YP_976607.1| 146 YAAFFERSYDILPDDG 161
                                    *********9998887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                                    EESSHHHHHHHHHHHHH CS
                Methyltransf_25  27 vDiseemleaareraee 43 
                                     D+s e ++  ++++++
  gi|121636384|ref|YP_976607.1| 217 ADFSVEKVQLLQQHYAR 233
                                    67777777777777754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   3.3e-11     6e-08       1      98 [.      68     162 ..      68     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.3e-11
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L+iGcG G  l++  e+  d++++g+ +s++++e  k+klak+  ++  +v+l+  d + +    ++D +v++++++++ 
  gi|121636384|ref|YP_976607.1|  68 LDIGCGWGGGLQRAIEN-YDVNVIGITLSRNQFEYSKAKLAKIPTERSVQVRLQGWDEFTD----KVDRIVSIGAFEAFk 142
                                    8********99999888.8**************************************7765....9*************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     +  ++++++ ++ L ++Gr
  gi|121636384|ref|YP_976607.1| 143 mERYAAFFERSYDILPDDGR 162
                                    888889*********99997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.1e-09   3.8e-06       1      95 [.      68     164 ..      68     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.1e-09
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEEEEEES-CCC-.. CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDlvvssevlhhv.. 74 
                                    Ld+GcG G  ++   +++  +v+g+ ls ++ +++k+k  + +   +   v+ +++    f d ++D +vs  +++ +  
  gi|121636384|ref|YP_976607.1|  68 LDIGCGWGGGLQRAIENYdVNVIGITLSRNQFEYSKAKLAKIPTerS---VQVRLQGWdEFTD-KVDRIVSIGAFEAFkm 143
                                    8*****9999999998888****************999999887544...6666665546999.**************98 PP

                                    CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                    e+ +++++  + +L  +G+++
  gi|121636384|ref|YP_976607.1| 144 ERYAAFFERSYDILPDDGRML 164
                                    899999*******99999876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.054        98      56      81 ..      35      58 ..      30      62 .. 0.81
   2 !   19.0   0.0   5.2e-07   0.00092       2     113 ..      62     169 ..      61     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.054
                Methyltransf_31 56 veFeqgdieeleklledekfDlilsn 81
                                   + Fe++d++  e   + +kfDl l++
  gi|121636384|ref|YP_976607.1| 35 AYFEREDMTLEE--AQNAKFDLALDK 58
                                   569999**9988..6789****9987 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 5.2e-07
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G  + ++ e  + + +v+Gi  s +  e+++++++k   +  v+++ + + e+      +k+D i+s
  gi|121636384|ref|YP_976607.1|  62 EPGMTLLDIGCGWGGGLQRAIE--NYDVNVIGITLSRNQFEYSKAKLAKIPTErSVQVRLQGWDEFT-----DKVDRIVS 134
                                    5789*****************3..56899*********************99999**********88.....89****** PP

                Methyltransf_31  81 nevl..naladpdkileeiervlkpggilliedpr 113
                                     +++    +   ++++e+  + l ++g++l+ ++ 
  gi|121636384|ref|YP_976607.1| 135 IGAFeaFKMERYAAFFERSYDILPDDGRMLLHTIL 169
                                    99997767777888888888888888888877766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.023      64     129 ..      54     118 ..      40     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEE CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivv 129
                                    lal+ l+l++g+  L++G+G G    +   + + + +v++i  +++  e +k++l k  +e +v+v+
  gi|121636384|ref|YP_976607.1|  54 LALDKLHLEPGMTLLDIGCGWGG--GLQRAIENYDVNVIGITLSRNQFEYSKAKLAKIPTErSVQVR 118
                                    678999************98763..333334456778999999999999999999998877556655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.029      24     137 ..      56     165 ..      50     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                    HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEE CS
                            MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdliv 102
                                    l++l+ e   ++lD+GcG+G  g++ a e+ +++v  +  + +  e +k+ l++   e    v  ++ +e++ +k+d iv
  gi|121636384|ref|YP_976607.1|  56 LDKLHLEPGMTLLDIGCGWGG-GLQRAIENYDVNVIGITLSRNQFEYSKAKLAKIPTErSVQVRLQGWDEFT-DKVDRIV 133
                                    666777778899********7.99999999999999999999999999999999999974445567788888.8****** PP

                                    E---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                            MTS 103 sNPPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                    s   f a k    +   ++++ + ++L ++G++l+
  gi|121636384|ref|YP_976607.1| 134 SIGAFEAFKM---ERYAAFFERSYDILPDDGRMLL 165
                                    *888877666...6778999999999999999875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.23      10      53 ..      60     103 ..      51     134 .. 0.83
   2 ?    0.4   0.1      0.24   4.3e+02     149     186 ..     208     244 ..     203     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                           MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecv 53 
                                     ++pg ++ld+GcG G  l+   e+ +v+  G+ l+++    + 
  gi|121636384|ref|YP_976607.1|  60 HLEPGMTLLDIGCGWGGGLQRAIENYDVNVIGITLSRNQFEYSK 103
                                    578999********99999999999*********9998766555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                           MetW 149 kdfvelceelnlkvedrvaldekgrkvpavklvanllg 186
                                    +d  ++++  ++ ve+   l+++  +++   + anl +
  gi|121636384|ref|YP_976607.1| 208 EDIFKFAQAADFSVEKVQLLQQHY-ARTLNIWAANLEA 244
                                    6889999*******9887777665.6777788888765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0003      0.55       4      44 ..      66     105 ..      63     118 .. 0.85
   2 ?    0.6   0.0      0.19   3.4e+02      98     128 ..     189     219 ..     161     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHH CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkk 44 
                                    ++l+iGcG G+ l + A +n d+n++Gi ++++  ++  +k
  gi|121636384|ref|YP_976607.1|  66 TLLDIGCGWGGGL-QRAIENYDVNVIGITLSRNQFEYSKAK 105
                                    689*******986.679***********9999988776665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                    HHHHHHHHHEEEEEEEEEEESHHHHHHHHHH CS
                 Methyltransf_4  98 ellkelarvLkkgGvlelaTDveeyaeemlk 128
                                     ++k + + + +gG+l ++ D++++a+ +  
  gi|121636384|ref|YP_976607.1| 189 RFMKFIGEEIFPGGQLPAQEDIFKFAQAADF 219
                                    4566666777788888888887777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1710.77
//
Query:       gi|121636385|ref|YP_976608.1|  [L=287]
Description: mycolic acid synthase PcaA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-119  398.4   0.1   1.6e-119  398.2   0.1    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    1.1e-08   35.0   0.0    1.5e-08   34.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.8e-08   35.0   0.0      4e-08   33.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    1.4e-06   28.8   0.0    3.4e-06   27.6   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    2.2e-05   25.1   0.0      4e-05   24.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0055   15.7   0.0      0.012   14.6   0.0    1.6  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0073   15.6   0.0      0.012   14.9   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.084   11.9   0.0       0.13   11.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.096   12.5   0.0       0.21   11.4   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
       0.11   12.0   0.0       0.45   10.0   0.0    1.9  2  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.2   0.1    9e-123  1.6e-119       3     273 .]       5     283 ..       3     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 398.2 bits;  conditional E-value: 9e-123
                                    SXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                           CMAS   3 kkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrave 82 
                                     ++++ n++ahYDls+dff+lfldpt+tYsCAyferddmtL+eAq+aK+dl+l+kl+l+pGmtlLdiGcGWG+++rra+e
  gi|121636385|ref|YP_976608.1|   5 LTPHFGNVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIE 84 
                                    678999************************************************************************** PP

                                    HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EE CS
                           CMAS  83 rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGll 162
                                    +ydv+vvglTlS++qa +++k++d++d+ r+++v+l ++e +de+vdr+vs+gafeh+g+++y++ff++++++l++dG +
  gi|121636385|ref|YP_976608.1|  85 KYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKM 164
                                    ******************************************************************************** PP

                                    EEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHH CS
                           CMAS 163 llhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealq 234
                                    llhti++++ ke  e+gl+l        kfi  eiFPgG lpsi +++e+++++gf+v+ v+sl+ hYa+TL++Wa al+
  gi|121636385|ref|YP_976608.1| 165 LLHTIVRPTFKEGREKGLTLthelvhftKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALE 244
                                    *****************9999*********************************************************** PP

                                    HTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 235 enkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    +nkd+aia++s+ v+++y++YL+gca+ Fr+gy+dv q+
  gi|121636385|ref|YP_976608.1| 245 ANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQF 283
                                    ************************************997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   8.6e-12   1.5e-08      11     125 ..      51     186 ..      39     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 8.6e-12
                Methyltransf_23  11 dklerllpk..lraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg...... 81 
                                    +k++ +l+k  l++g+ +LdiGcG G ++ + ++++ ++v+g  ls+++ + +       +++fd+++ + + +      
  gi|121636385|ref|YP_976608.1|  51 AKIDLALGKlnLEPGMTLLDIGCGWGaTMRRAIEKYDVNVVGLTLSENQAGHV-------QKMFDQMDTPRSRRvllegw 123
                                    6777777665579999**********556666799999*********988875.......77777775555555555555 PP

                Methyltransf_23  82 .....kfdlIvlrevlehvpd..ppellrqiatllkpgGylllseplasl............k 125
                                           d Iv++  +eh+ +  +++ +   ++ l  +G +ll+++ ++             +
  gi|121636385|ref|YP_976608.1| 124 ekfdePVDRIVSIGAFEHFGHqrYHHFFEVTHRTLPADGKMLLHTIVRPTfkegrekgltltH 186
                                    55555**************976699********************988876554444443333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.2e-11     4e-08       2      97 .]      69     162 ..      68     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.2e-11
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+GcG G +++++ +++ + +v+g+ +se++  ++++ +++ +   + ++  +e ++  d+ +D +vs+ga++h+ +++
  gi|121636385|ref|YP_976608.1|  69 LDIGCGWGATMRRAIEKY-DVNVVGLTLSENQAGHVQKMFDQMD-TPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQR 146
                                    9****************9.7********************6533.56666667788888899********99******** PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    ++++++  +r L  +G
  gi|121636385|ref|YP_976608.1| 147 YHHFFEVTHRTLPADG 162
                                    **********997776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.9e-09   3.4e-06       1      95 [.      69     165 ..      69     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.9e-09
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    Ld+GcG G+ ++   +++  +vvg+ ls+++   +++   + +   + +++ +  ek    d+ +D +vs  +++h+  +
  gi|121636385|ref|YP_976608.1|  69 LDIGCGWGATMRRAIEKYdVNVVGLTLSENQAGHVQKMFDQMDTprSRRVLLEGWEK---FDEPVDRIVSIGAFEHFghQ 145
                                    8**************9999*************7776666666654543455566665...477***************99 PP

                                    CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                    + +++++  +R L  +G+++
  gi|121636385|ref|YP_976608.1| 146 RYHHFFEVTHRTLPADGKML 165
                                    999999999****9999876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.2e-08     4e-05       1      98 [.      69     163 ..      69     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.2e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L+iGcG G+++r+  ek  d++++g+ +s+++  + ++ + + +  +  +v le  + +d+     +D +v++++++h+ 
  gi|121636385|ref|YP_976608.1|  69 LDIGCGWGATMRRAIEK-YDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDE----PVDRIVSIGAFEHFg 143
                                    8****************.9*************************99999999999998776....9*************7 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     +  + +++  ++ L  +G+
  gi|121636385|ref|YP_976608.1| 144 hQRYHHFFEVTHRTLPADGK 163
                                    66666888888887777775 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.4e-06     0.012     116     261 ..      65     221 ..      49     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-06
                                    T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG- CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyhr 195
                                    g t+ld+Gcg G  + r + +    vvG+  se      + +   +++ +   +l  g e+++  e  d + s+G + h 
  gi|121636385|ref|YP_976608.1|  65 GMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFD--EPVDRIVSIGAFEHF 142
                                    6789*************************9998877666665555555555555545666655..689********9996 PP

                                    .S-HHHHHHHHHC.TEEEEEEEEEEEE-B....SS-TT-EE--SS.....-B..TTBSS---EEBHHHHHHHHHHTT-E CS
                 Methyltransf_9 196 .rsPldhllqlkd.qlvkgGelvletlvi....eGdenavlvPed.....ry..akmrnvyfiPsaaalkvWlekvgfv 261
                                     +    h+ ++ + +l ++G+++l t+v     eG e+ + + ++     ++  a++    ++Ps+ +++ + ekvgf 
  gi|121636385|ref|YP_976608.1| 143 gHQRYHHFFEVTHrTLPADGKMLLHTIVRptfkEGREKGLTLTHElvhftKFilAEIFPGGWLPSIPTVHEYAEKVGFR 221
                                    256788998886527999********98522224555443333321100022113333333677777777777777774 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.7e-06     0.012      42     175 ..      44     177 ..      32     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.7e-06
                                    HHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH....HHHHHHHHS-----TTEEEEE CS
                 Methyltransf_2  42 glqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe....VveaAkehlsageeervefvg 117
                                    +lqe +    + +l + +le+  +l+D+G G Ga+++ + ++y  ++v+ + l+e     v++  ++++++ ++rv   g
  gi|121636385|ref|YP_976608.1|  44 TLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYD-VNVVGLTLSEnqagHVQKMFDQMDTPRSRRVLLEG 122
                                    56777888888999999**************************5.55555555441111455555666888889999999 PP

                                    S-TTTS-----SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS-- CS
                 Methyltransf_2 118 GdffkdslPeaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsg 175
                                     + f++++   D i+       + +++ +++ +  +++lpa+Gk+++   v ++ ++g
  gi|121636385|ref|YP_976608.1| 123 WEKFDEPV---DRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEG 177
                                    99998876...66666666677999999999999999999999999987776554444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.13      19      56 ..      53      91 ..      49     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                   HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEE CS
                         RrnaAD 19 ineIldklnleekltvleigpGkGilTeeLakra.kqvv 56
                                   i+ +l klnle+ +t+l+ig G G++ ++  +    +vv
  gi|121636385|ref|YP_976608.1| 53 IDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYdVNVV 91
                                   667899******************998776554435555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.21       2      39 ..      63      98 ..      62     170 .. 0.83
   2 ?   -2.8   0.0       2.7   4.9e+03      54      80 ..     216     241 ..     212     260 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                Methyltransf_31  2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDisee 39
                                   + g+++lD+GCG G+   ++ e+ + + +vvG+  se+
  gi|121636385|ref|YP_976608.1| 63 EPGMTLLDIGCGWGATMRRAIEK-Y-DVNVVGLTLSEN 98
                                   5789*****************64.3.688888877776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                Methyltransf_31  54 dnveFeqgdieeleklledekfDlils 80 
                                    + v F++  +++l+ +++ ++ D++ +
  gi|121636385|ref|YP_976608.1| 216 EKVGFRVTAVQSLQLHYA-RTLDMWAT 241
                                    467788888888885577.67777665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00025      0.45      27     136 ..      60     165 ..      53     175 .. 0.68
   2 ?   -0.9   0.0      0.57     1e+03     102     129 ..     169     196 ..     148     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                    CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE--- CS
                            MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPP 106
                                    l+ e   ++lD+GcG+G+    + ++++ + v l+  + +A ++ k   +    + + v  ++ e+++ + +d ivs   
  gi|121636385|ref|YP_976608.1|  60 LNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFD-EPVDRIVSIGA 138
                                    555667789********977777777666655555555555555555555555556777777777777.88888888777 PP

                                    STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 107 fhagkatelavaeeliaeAkeaLkegGeLl 136
                                    f +  +   +  +++++  ++ L  +G++l
  gi|121636385|ref|YP_976608.1| 139 FEHFGH---QRYHHFFEVTHRTLPADGKML 165
                                    755444...467778888888888888776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.57
                                    EE---STTTCHCHHHHHHHHHHHHHHHE CS
                            MTS 102 vsNPPfhagkatelavaeeliaeAkeaL 129
                                    +  P f++g+++ l++++el++  k +L
  gi|121636385|ref|YP_976608.1| 169 IVRPTFKEGREKGLTLTHELVHFTKFIL 196
                                    5568899999999999999988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2014.10
//
Query:       gi|121636386|ref|YP_976609.1|  [L=146]
Description: hypothetical protein BCG_0511c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-07   28.7   0.5    9.2e-07   28.4   0.5    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.5   5.1e-11   9.2e-07     142     214 ..       5      77 ..       1      86 [. 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.1e-11
                           UbiA 142 sllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllll 214
                                     ++++l++l+ +ll++++++ +++  +  D+  gi+tlpv+lG+  ar + ++++++++l++++ ++++ +++
  gi|121636386|ref|YP_976609.1|   5 GWEVVLASLPYGLLCTTVLMGKHIDKIGYDEPLGIRTLPVLLGETCARTVTLAMMVGFYLLIAVNVMLAAMPW 77 
                                    5899********************************************9855555555555344444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1282.64
//
Query:       gi|121636387|ref|YP_976610.1|  [L=162]
Description: hypothetical protein BCG_0512c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.4   0.6      0.024   14.0   0.6    1.3  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.3e-06     0.024       5      63 ..      51     113 ..      30     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-06
                           UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme.....rtpnRPlvsGr 63 
                                    +++gl++ + + +d+  +l+l++   + ++a n++Nd++D + + d +     r ++ P ++G+
  gi|121636387|ref|YP_976610.1|  51 LVAGLLAIGEPGLDW-RWLVLWWESHAPHIANNLMNDLYDTDVGTDSAtyaraRYAQHPAATGA 113
                                    344455555555666.8999999999********************888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1235.48
//
Query:       gi|121636388|ref|YP_976611.1|  [L=234]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-08   34.0   0.0    3.1e-08   33.3   0.0    1.4  1  TetR_N       Bacterial regulatory proteins, tetR family
      0.002   18.8   0.0     0.0035   18.1   0.0    1.4  1  TetR_C_33    Tetracyclin repressor-like, C-terminal domain
     0.0074   16.3   0.0      0.013   15.5   0.0    1.5  1  HTH_3        Helix-turn-helix
     0.0092   15.5   0.0      0.044   13.3   0.0    2.0  2  HTH_24       Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.033   14.3   0.0    1.5  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
       0.02   14.8   0.0      0.078   12.9   0.0    2.0  2  HTH_11       HTH domain
      0.062   13.4   0.6        0.2   11.7   0.6    1.9  1  HTH_7        Helix-turn-helix domain of resolvase
      0.072   13.3   0.2          1    9.6   0.0    2.4  2  HTH_17       Helix-turn-helix domain
       0.08   13.7   0.2       0.26   12.0   0.1    1.9  2  TetR_C_15    Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.5e-11   3.1e-08       3      46 ..      32      74 ..      30      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.5e-11
                                   HHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  3 daArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   d++ e + ++G   ++++eIA++ Gvsk  lYryF +K +L  a
  gi|121636388|ref|YP_976611.1| 32 DGTIEAIRRHGRF-LSMDEIAAEIGVSKTVLYRYFVDKNDLTTA 74
                                   5566666666655.89************************9766 PP

>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0035       2      80 ..     103     210 ..     102     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                                    HHHHHHHHHHHHH-HHHHHHCCSS--TT-S-HGHHCCCCHHHHHHHHHHH..GGG---TH.................... CS
                      TetR_C_33   2 ralarayrrfAlahpaeYallfgspvpgyaapdelaaagarvlalllaal..aalvaagl.................... 59 
                                    r++ r y++ + a+p+ Y+ ++++     a+ +++ a+++r++a +la++  +++++ag                     
  gi|121636388|ref|YP_976611.1| 103 REIIRVYVETVAAQPEPYRFVMANSS---ASKSKVIADSERIIARMLAVMlrRRMQEAGMdtdgvepwaylivggvqlat 179
                                    67899*****************3333...2335899999999999999884336666666******************** PP

                                    .........--CCHHHHHHHH.HHHHHHHHH CS
                      TetR_C_33  60 .........ppadavaaaral.waalhGlvs 80 
                                             +++++++  ++l w+al G+v 
  gi|121636388|ref|YP_976611.1| 180 hswmsdprmSSDELIDYLTMLsWSALCGIVE 210
                                    *******965555666666666******994 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.7e-06     0.013      10      41 ..      45      76 ..      35      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                                   HHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHH CS
                          HTH_3 10 lsqeeLAeklGvsrstisriEnGernPsletl 41
                                   ls+ e+A+++Gvs++ ++r++ ++   +  ++
  gi|121636388|ref|YP_976611.1| 45 LSMDEIAAEIGVSKTVLYRYFVDKNDLTTAVM 76
                                   899******************99998887766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.2e-05     0.044       9      37 ..      35      64 ..      34      65 .. 0.90
   2 ?   -1.1   0.0      0.74   1.5e+03      14      24 ..     184     194 ..     183     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                         HTH_24  9 LelLqknpr.isqreLAerlglSpstvnrr 37
                                   +e++++++r +s+ e+A ++g+S++ + r+
  gi|121636388|ref|YP_976611.1| 35 IEAIRRHGRfLSMDEIAAEIGVSKTVLYRY 64
                                   689********************9987765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.74
                         HTH_24  14 knprisqreLA 24 
                                     +pr+s  eL 
  gi|121636388|ref|YP_976611.1| 184 SDPRMSSDELI 194
                                    69****99995 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.033      27      51 ..      45      70 ..      24      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                   S-HHHHHHHHTS-HHHHHHHH.H-HH CS
                    HTH_Tnp_1_2 27 ltldeiaeevgvsrsTlykWk.kkke 51
                                   l++deia+e+gvs++ ly++  +k++
  gi|121636388|ref|YP_976611.1| 45 LSMDEIAAEIGVSKTVLYRYFvDKND 70
                                   79*****************9856655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05     0.078       8      35 ..      37      64 ..      34      67 .. 0.84
   2 ?   -2.7   0.0         3     6e+03      14      25 ..     186     197 ..     184     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                         HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrd 35
                                    ++++  ++s +e+A e++vS+++ +r+
  gi|121636388|ref|YP_976611.1| 37 AIRRHGRFLSMDEIAAEIGVSKTVLYRY 64
                                   56666667******************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                         HTH_11  14 gpisgeeLAeeL 25 
                                    + +s++eL ++L
  gi|121636388|ref|YP_976611.1| 186 PRMSSDELIDYL 197
                                    45999***9998 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6    0.0001       0.2      13      44 ..      36      67 ..      14      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                   GGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                          HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRylad 44
                                   ++++++    s  +IA e ++s++ +YRy+ d
  gi|121636388|ref|YP_976611.1| 36 EAIRRHGRFLSMDEIAAEIGVSKTVLYRYFVD 67
                                   56666666667889***************965 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.24   4.7e+02      26      44 ..       4      25 ..       2      27 .. 0.80
   2 ?    9.6   0.0    0.0005         1       1      27 [.      44      71 ..      44      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.24
                         HTH_17 26 elpaa..k.iGrrwriprsdle 44
                                   ++pa+  k  Gr++r ++  +e
  gi|121636388|ref|YP_976611.1|  4 RIPAVtvKtDGRKRRWHQHKVE 25
                                   7999988889999999887666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0005
                         HTH_17  1 lltveEaAelLgvsrstvyr.lirrgel 27
                                   +l+ +E+A+  gvs++ +yr ++++++l
  gi|121636388|ref|YP_976611.1| 44 FLSMDEIAAEIGVSKTVLYRyFVDKNDL 71
                                   5899***************857788877 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.1   6.1e+03       8      23 ..      29      44 ..      25      52 .. 0.78
   2 ?   12.0   0.1   0.00013      0.26       4      98 ..     100     195 ..     100     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
                      TetR_C_15  8 alvdallaahrenpal 23
                                   +lvd  ++a r++ ++
  gi|121636388|ref|YP_976611.1| 29 ELVDGTIEAIRRHGRF 44
                                   5788888888888766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                      TetR_C_15   4 ealdalvdallaahrenpalrrvlleeapslgelelvealeqriaealaalLarrrpelpped..lelaafvaveaveal 81 
                                    e+ +++++ +++  +++p+  r +++ + s   ++  ++ e+ ia+ la +L+rr +e   ++  +e  a+++v  v+  
  gi|121636388|ref|YP_976611.1| 100 ELTREIIRVYVETVAAQPEPYRFVMANS-SASKSKVIADSERIIARMLAVMLRRRMQEAGMDTdgVEPWAYLIVGGVQLA 178
                                    57899***********************.88888899999***************9998733211444566666666666 PP

                      TetR_C_15  82 lhlaleedpadrealia 98 
                                    +h  +++++++ ++li+
  gi|121636388|ref|YP_976611.1| 179 THSWMSDPRMSSDELID 195
                                    66666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1706.02
//
Query:       gi|121636389|ref|YP_976612.1|  [L=456]
Description: hypothetical protein BCG_0514 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     5e-105  352.3   0.3   5.9e-105  352.1   0.3    1.0  1  DUF445          Protein of unknown function (DUF445)
  ------ inclusion threshold ------
      0.095   12.5   0.5       0.19   11.5   0.5    1.5  1  DUF3640         Protein of unknown function (DUF3640)
        0.2   11.5   2.7         11    5.8   0.1    2.6  2  Activator-TraM  Transcriptional activator TraM


Domain annotation for each model (and alignments):
>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.1   0.3  9.9e-109  5.9e-105       1     366 [.      92     454 ..      92     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 352.1 bits;  conditional E-value: 9.9e-109
                         DUF445   1 aeaAliGaladwfAikaLFRhPlglpiPfttglIPknkeriakklgnfVeehLLtkeslakkLkeaevasklaewlknpt 80 
                                    aea+++GaladwfA++aLF+hPlg+piP +t++I+++k+++++ lg fV+e++L++ ++++kL++a++ s+l++wl++ t
  gi|121636389|ref|YP_976612.1|  92 AEAGMVGALADWFAVTALFKHPLGIPIP-HTAIIKRKKDQLGEGLGTFVRENFLSPPVVETKLRDAQIPSRLGKWLSEAT 170
                                    69**************************.*************************************************** PP

                         DUF445  81 nkeslaaiveellkeiledlddesikellkknlkkkleevipepllgkllellleeerhkkllddlldriknllkdeevk 160
                                    +++++aa+++++l++++e l+de+i++++++++ ++++e ++ p +g++l +ll+e+r++++++ l dr+ ++  +  v 
  gi|121636389|ref|YP_976612.1| 171 HAQRVAAETATVLRVLVELLRDEDIQQVIDRMIVRRIAEPQWGPPAGRVLATLLAENRQEAFIQLLADRAFQWSLNAGVV 250
                                    ******************************************************************************** PP

                         DUF445 161 ekikelidelieeesgklvlesivsmflreltsilekvksdpdhllreeedkkvreliadllndpelaakveklkkkkls 240
                                      i++++++  +++s++++++ ++++++rel ++++kv+++pdh+lr++ ++++ ++++dl++dp++ a+++++k+++++
  gi|121636389|ref|YP_976612.1| 251 --IQRVVERDSPSWSPRFIDHLVGDRIHRELMEFTDKVRRNPDHELRRSATRFLFDFADDLQHDPATVARADAIKEELMA 328
                                    ..****************************************************************************** PP

                         DUF445 241 dlevqeyeealwealkdlllkdlneee.sllrerisklleklgeklaedpklreklnkflenaaakvlekyrldiskive 319
                                    + e ++ + a w+ lk+l+l+ +++ + s+lr+ri +++ ++ge+l++d +lr+k++ +  +aa++++ +y ++i+ i++
  gi|121636389|ref|YP_976612.1| 329 RDEIATAAAAAWKTLKRLVLEGVDD-PsSALRTRITDAVIRIGESLRDDADLRDKVDSWTVRAAQHLVSEYGVEITAIIT 407
                                    ************************9.66**************************************************** PP

                         DUF445 320 etvnafdaeeleelIelivgkeLqaIrinGtlvGgliGlllylvsll 366
                                    et++++daee++++Iel+vg++Lq+IrinGt+vG+++Gl++y++++l
  gi|121636389|ref|YP_976612.1| 408 ETIERWDAEEASRRIELHVGRDLQFIRINGTVVGAMAGLAIYAIAQL 454
                                    ********************************************987 PP

>> DUF3640  Protein of unknown function (DUF3640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   3.2e-05      0.19       9      24 ..     204     218 ..     200     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                        DUF3640   9 cRRVDkDqWGrGvhGR 24 
                                     RR++ +qWG+  +GR
  gi|121636389|ref|YP_976612.1| 204 VRRIAEPQWGPP-AGR 218
                                    4**********8.777 PP

>> Activator-TraM  Transcriptional activator TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3    0.0031        18      96     139 ..      25      70 ..      17      73 .. 0.85
   2 ?    5.8   0.1    0.0019        11      73     117 ..     332     376 ..     312     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0031
                 Activator-TraM  96 aevvrkeveaalarlkssirearrva..llnlvasalvvlaaalvl 139
                                    a  vr    ++ a + + + +arr+a  ++++va + +v a+++ l
  gi|121636389|ref|YP_976612.1|  25 ARRVRASFAESFAAADPEADAARRMAlrRMKVVAVGFLVGATGVFL 70 
                                    567889999999999*********984469***********99987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0019
                 Activator-TraM  73 lnaalaaskealvkllqegakeaaevvrkeveaalarlkssirea 117
                                    + +a aa+ ++l +l+ eg  +  +++r+++ +a++r+  s+r+ 
  gi|121636389|ref|YP_976612.1| 332 IATAAAAAWKTLKRLVLEGVDDPSSALRTRITDAVIRIGESLRDD 376
                                    45567788899**************************99998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3066.71
//
Query:       gi|121636390|ref|YP_976613.1|  [L=140]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-15   54.8   0.1    1.2e-14   54.0   0.1    1.4  1  HTH_3     Helix-turn-helix
      1e-12   48.2   0.1    1.6e-12   47.5   0.1    1.3  1  HTH_31    Helix-turn-helix domain
    1.8e-06   27.8   0.0    2.7e-06   27.3   0.0    1.3  1  HTH_19    Helix-turn-helix domain
    0.00055   20.2   0.0     0.0019   18.5   0.0    1.8  2  Rrf2      Transcriptional regulator
    0.00078   19.4   0.1     0.0014   18.5   0.1    1.4  1  HTH_37    Helix-turn-helix domain
     0.0014   18.3   0.1       0.45   10.4   0.0    2.4  2  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.017   14.9   0.2       0.16   11.9   0.2    2.1  1  HTH_25    Helix-turn-helix domain
       0.02   15.3   0.0      0.044   14.2   0.0    1.6  2  HTH_26    Cro/C1-type HTH DNA-binding domain
      0.024   14.2   0.2      0.065   12.8   0.0    1.8  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.042   13.8   0.3       0.46   10.5   0.0    2.3  2  HTH_6     Helix-turn-helix domain, rpiR family


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.1   6.9e-18   1.2e-14       1      54 [.      26      79 ..      26      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 6.9e-18
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                   ++  R+ +  s+++LAe++Gvs  ++s+ E+G r+Ps ++l  +akaL vs + 
  gi|121636390|ref|YP_976613.1| 26 IRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRKPSADVLSQIAKALRVSAEV 79
                                   8999**********************************************9876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.1   9.1e-16   1.6e-12       2      59 ..      22      78 ..      21      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 9.1e-16
                         HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59
                                   +G + r  Re a +s +++Aer+gvs  +ls++E+G r  ps +vl ++a al+++ +
  gi|121636390|ref|YP_976613.1| 22 IGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLR-KPSADVLSQIAKALRVSAE 78
                                   89************************************.6***************865 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.5e-09   2.7e-06       1      59 [.      23      80 ..      23      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.5e-09
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyl 59
                                   G +++  Re +  ++++laer g+s  ++s+ E g + +psa++l +ia+al +++e l
  gi|121636390|ref|YP_976613.1| 23 GSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLR-KPSADVLSQIAKALRVSAEVL 80
                                   7789999****************************99.9*************9999877 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0019       4      51 ..      13      60 ..      10      63 .. 0.90
   2 ?   -2.0   0.0       2.7   4.8e+03      29      42 ..      67      80 ..      65      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                   -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHH CS
                           Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrk 51
                                   ++ +++a  +  ++ +++e  +vs++++aer ++s +yl+++ + Lrk
  gi|121636390|ref|YP_976613.1| 13 TKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRK 60
                                   5667888899999999999999********************999997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                                   HHHHHHHTS-HHHH CS
                           Rrf2 29 eeiaerqnispsyl 42
                                   ++ia+   +s+++l
  gi|121636390|ref|YP_976613.1| 67 SQIAKALRVSAEVL 80
                                   57888888887766 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   7.8e-07    0.0014      15      71 ..      13      73 ..       2      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.8e-07
                                   HHHHHHHH.....HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHT CS
                         HTH_37 15 aKaqlala.....iaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltal 71
                                   +Ka+ ++      i+ ++e  + s++++a++ g++ P +s+++r  l++ s d L ++++al
  gi|121636390|ref|YP_976613.1| 13 TKASDVASdigsfIRSQRETAHVSMRQLAERSGVSNPYLSQVER-GLRKPSADVLSQIAKAL 73
                                   55444444455569*****************************9.79999999999999998 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00025      0.45      15      31 ..      33      49 ..      28      53 .. 0.82
   2 !    5.6   0.1    0.0076        14      19      35 ..      66      82 ..      62      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                   TT--HHHHHHHHTSSHH CS
                         TetR_N 15 dattvreIAkrAGvskg 31
                                   + +++r++A+r Gvs +
  gi|121636390|ref|YP_976613.1| 33 AHVSMRQLAERSGVSNP 49
                                   679***********977 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0076
                                   HHHHHHHHTSSHHHHHH CS
                         TetR_N 19 vreIAkrAGvskgalYr 35
                                   +++IAk++ vs+  lY 
  gi|121636390|ref|YP_976613.1| 66 LSQIAKALRVSAEVLYV 82
                                   589************96 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.7e-05      0.16       3      33 ..      27      57 ..      25      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                                   HHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                         HTH_25  3 raaRearglsleevaketkIrkdylealEed 33
                                   r +Re +  s++++a++  ++  yl + E++
  gi|121636390|ref|YP_976613.1| 27 RSQRETAHVSMRQLAERSGVSNPYLSQVERG 57
                                   899************************9998 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.8     1e+04       4      21 ..       6      23 ..       5      23 .. 0.65
   2 ?   14.2   0.0   2.5e-05     0.044      10      53 ..      34      76 ..      26      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.8
                         HTH_26  4 elmadrgitkseLargtg 21
                                   +l+a+   ++s++a ++g
  gi|121636390|ref|YP_976613.1|  6 KLAAKVSTKASDVASDIG 23
                                   456666668888887765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.5e-05
                         HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct 53
                                   +++  +La+++g+s + ls    g  + +s+d+L+ i++aL ++
  gi|121636390|ref|YP_976613.1| 34 HVSMRQLAERSGVSNPYLSQVERG-LRKPSADVLSQIAKALRVS 76
                                   678899******************.69**************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05     0.065      14      34 ..      31      51 ..      29      54 .. 0.87
   2 ?   -3.2   0.1       3.6   6.4e+03      22      30 ..      68      76 ..      67      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                         HTH_24 14 knprisqreLAerlglSpstv 34
                                   + ++ s+r+LAer+g+S + +
  gi|121636390|ref|YP_976613.1| 31 ETAHVSMRQLAERSGVSNPYL 51
                                   6899*************8865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.6
                         HTH_24 22 eLAerlglS 30
                                   ++A++l +S
  gi|121636390|ref|YP_976613.1| 68 QIAKALRVS 76
                                   799999887 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00026      0.46      25      54 ..      26      54 ..       5      60 .. 0.78
   2 ?    1.0   0.1      0.23   4.2e+02      37      48 ..      66      77 ..      60      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                   HHH-S---TT--HHHHHHHTT--HHHHHHH CS
                          HTH_6 25 ilaspdkaielsikalAkaaavSeativrf 54
                                   i++ + +  ++s+++lA+ ++vS++ + ++
  gi|121636390|ref|YP_976613.1| 26 IRS-QRETAHVSMRQLAERSGVSNPYLSQV 54
                                   544.456679*************9987665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                                   HHHHHHHTT--H CS
                          HTH_6 37 ikalAkaaavSe 48
                                   ++++Aka+ vS 
  gi|121636390|ref|YP_976613.1| 66 LSQIAKALRVSA 77
                                   689*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1061.82
//
Query:       gi|121636391|ref|YP_976614.1|  [L=199]
Description: Heparin binding hemagglutinin hbhA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00059   19.8  19.4    0.00059   19.8  19.4    1.9  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0045   17.2   0.7      0.015   15.5   0.7    2.1  1  SRP54_N         SRP54-type protein, helical bundle domain
     0.0053   16.9  22.5     0.0069   16.5  22.5    1.2  1  HC2             Histone H1-like nucleoprotein HC2
  ------ inclusion threshold ------
      0.015   15.3   2.6      0.031   14.4   2.6    1.6  1  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
      0.017   14.0   3.2      0.023   13.6   3.2    1.2  1  MRP-S27         Mitochondrial 28S ribosomal protein S27
      0.026   14.1   7.0      0.032   13.8   7.0    1.2  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.043   11.8   0.2       0.05   11.6   0.2    1.0  1  Prominin        Prominin
       0.12   12.5   1.7        1.5    8.9   0.2    2.7  2  SUIM_assoc      Unstructured region C-term to UIM in Ataxin3
       0.14   12.7   6.5       0.41   11.3   1.4    2.5  3  BST2            Bone marrow stromal antigen 2
       0.57    9.0  10.8       0.26   10.1   8.5    1.5  2  Spc7            Spc7 kinetochore protein
       0.66   10.6  20.9        7.4    7.3   5.4    3.7  3  DUF883          Bacterial protein of unknown function (DUF883
        2.3    7.9   7.5       0.28   10.9   1.5    2.0  2  DUF932          Domain of unknown function (DUF932)
        3.7    8.5  12.0        8.4    7.3  12.0    1.7  1  Stm1_N          Stm1
        8.9    6.2  13.7       0.62   10.0   8.4    1.7  2  MRP-S26         Mitochondrial ribosome subunit S26


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  19.4   4.6e-07   0.00059      44     175 ..      26     152 ..       7     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.6e-07
                                    HHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHH CS
                 Apolipoprotein  44 aeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyv 123
                                    a ++e+  +l ++++e ++   +++ee r+rl+ + e+l e    ++ el+e+ ++  eelr+ +e  +ea  +r  ++v
  gi|121636391|ref|YP_976614.1|  26 ATVNELITNLRERAEETRTDTRSRVEESRARLTKLQEDLPE----QLTELREKFTA--EELRKAAEGYLEAATSRYNELV 99 
                                    56788888999999999999999999999998877777766....56699999996..9999999999999999999999 PP

                                    HHHHHHHHH.HHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHHS-- CS
                 Apolipoprotein 124 eelrqklae.rleelkeslaphaeeveerlssrveelrekleeqaeelrerle 175
                                    e++ + l++ r ++  e++ ++ae + +++ +  +e+  +++ q +++ er+ 
  gi|121636391|ref|YP_976614.1| 100 ERGEAALERlRSQQSFEEVSARAEGYVDQAVELTQEALGTVASQTRAVGERAA 152
                                    99998777658899999999999999988888888888888888888877765 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   1.2e-05     0.015      22      67 ..       6      50 ..       2      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHH CS
                        SRP54_N 22 dleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqv 67
                                   +++++   l  aL  aD+++ +v +li n+++ +++e ++ +++ v
  gi|121636391|ref|YP_976614.1|  6 NIDDIKAPLLAALGAADLALATVNELITNLRE-RAEETRTDTRSRV 50
                                   56666667888999******************.5554665555554 PP

>> HC2  Histone H1-like nucleoprotein HC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  22.5   5.4e-06    0.0069      73     142 ..     128     198 ..     104     199 .] 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.4e-06
                            HC2  73 kavakkvvakkkvakKavAKKaaakKvvakkvvakKtvakkaaaakKpa.akkavakkaaarKaaakKava 142
                                    +av   + a  +va ++ A    a K v  +   k ++akkaa+akK+a akka+akka+a+KaaakK   
  gi|121636391|ref|YP_976614.1| 128 QAVELTQEALGTVASQTRAVGERAAKLVGIELPKKAAPAKKAAPAKKAApAKKAAAKKAPAKKAAAKKVTQ 198
                                    55555555555666667676667777777777767777888888887765777777777777777777654 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.6   2.4e-05     0.031       5     140 ..       8     141 ..       4     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                      ApoLp-III   5 eelqksvkkqlnlpsqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkk 84 
                                     ++++ +  +l+   ++  + t+ e  +nl ++++++   +++ + +    l+++ +++ ++++e ++k+++   e+ k+
  gi|121636391|ref|YP_976614.1|   8 DDIKAPLLAALG--AADLALATVNELITNLRERAEETRTDTRSRVEESRARLTKLQEDLPEQLTELREKFTA--EELRKA 83 
                                    556666666666..5555666777777778888888888888888888888888888888888888888888..79999* PP

                      ApoLp-III  85 aqelqekvQsgvqslvkesqklaeslkens..qeakeklakaikqayddaveaaqkla 140
                                    a+ + e   s+ ++lv+  +++ e+l ++   +e+++  +  + qa++ ++ea+  +a
  gi|121636391|ref|YP_976614.1|  84 AEGYLEAATSRYNELVERGEAALERLRSQQsfEEVSARAEGYVDQAVELTQEALGTVA 141
                                    ************************9975431256777777777777777777766665 PP

>> MRP-S27  Mitochondrial 28S ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.2   1.8e-05     0.023     284     385 ..      24     123 ..      13     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                        MRP-S27 284 vlklleeileeleeeeseqsklpeyvksfkellskleslgkvesesllklleqlvkeslaacekkdlaeyeklyqeWeee 363
                                    +l  ++e++++l e+ +e        ++++e + +l++l+   +e+l +l e++  e+l ++ +  l++ +++y+e  e+
  gi|121636391|ref|YP_976614.1|  24 ALATVNELITNLRERAEE--TRTDTRSRVEESRARLTKLQEDLPEQLTELREKFTAEELRKAAEGYLEAATSRYNELVER 101
                                    566667777777666666..56678999999999999999**************************************** PP

                        MRP-S27 364 reqliqrekerrekakreeear 385
                                     e +++r + +++ +++ + a+
  gi|121636391|ref|YP_976614.1| 102 GEAALERLRSQQSFEEVSARAE 123
                                    **********999999887765 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   7.0   2.5e-05     0.032     134     258 ..      20     146 ..      18     192 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                   Exonuc_VII_L 134 aAelvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrer 213
                                    aA+l++   +el  +l+e ++++++ +++++ee+++rl+kl+++l+++ + l   r++++   e+l++a +  l+++++r
  gi|121636391|ref|YP_976614.1|  20 AADLALATVNELITNLRERAEETRTDTRSRVEESRARLTKLQEDLPEQLTEL---REKFTA--EELRKAAEGYLEAATSR 94 
                                    89999999**********************************9996433322...222222..33333333333333333 PP

                   Exonuc_VII_L 214 leelkerlk...ekleekkerlkklkerle.....lleekkerleeleeklea 258
                                    ++el er +   e+l+  +++++++++r e      +e ++e+l +++++ +a
  gi|121636391|ref|YP_976614.1|  95 YNELVERGEaalERLR-SQQSFEEVSARAEgyvdqAVELTQEALGTVASQTRA 146
                                    3333333321211111.222334444444443333344444444444444443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   3.9e-05      0.05     645     748 ..      33     139 ..       6     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                       Prominin 645 knlkqslkneaqdlraiqqelvlplessvkklkksvkklde..ensdlqesikkllaaveraenflkkngseiinnes.k 721
                                    +nl+++ +++  d+r+  +e   +l+++ ++l +++++l e  ++++l+++ +  l+a+++  n+l ++g+  ++ ++ +
  gi|121636391|ref|YP_976614.1|  33 TNLRERAEETRTDTRSRVEESRARLTKLQEDLPEQLTELREkfTAEELRKAAEGYLEAATSRYNELVERGEAALERLRsQ 112
                                    68999999999999999999999******************999******************************998615 PP

                       Prominin 722 klldrileqfeeYidwvieevtenvgk 748
                                    +  + +    e Y+d + e ++e +g+
  gi|121636391|ref|YP_976614.1| 113 QSFEEVSARAEGYVDQAVELTQEALGT 139
                                    566788889999999999999998886 PP

>> SUIM_assoc  Unstructured region C-term to UIM in Ataxin3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.055        71      38      55 ..      59      76 ..      40      77 .. 0.86
   2 ?    8.9   0.2    0.0012       1.5      14      30 ..      75     105 ..      74     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.055
                     SUIM_assoc 38 qqqqdppgqlshprekpt 55
                                   + q+d p+ql+++rek t
  gi|121636391|ref|YP_976614.1| 59 KLQEDLPEQLTELREKFT 76
                                   6699***********976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                     SUIM_assoc  14 ltsEeLrkrreaYFEK..............q 30 
                                     t EeLrk  e Y E                
  gi|121636391|ref|YP_976614.1|  75 FTAEELRKAAEGYLEAatsrynelvergeaA 105
                                    599************8665555555555550 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.4   0.00032      0.41      35      90 ..      20      72 ..      16      73 .. 0.85
   2 ?    3.6   0.2     0.078     1e+02      24      62 ..      78     114 ..      72     141 .. 0.72
   3 ?    1.6   0.2      0.32   4.1e+02      28      63 ..     110     146 ..      96     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                           BST2 35 eaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90
                                    a+   at n+ + +L++  e+ ++     +++v+e +  ++kL++ L ++++e++
  gi|121636391|ref|YP_976614.1| 20 AADLALATVNELITNLRERAEETRTD---TRSRVEESRARLTKLQEDLPEQLTELR 72
                                   567778999*******9999888887...6678****************9999986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.078
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  24 rqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsq 62 
                                    ++L++a e+ +ea +    +n+ v+  +a+Le+ ++q+ 
  gi|121636391|ref|YP_976614.1|  78 EELRKAAEGYLEAATS--RYNELVERGEAALERLRSQQS 114
                                    6788888888776665..899999999999999999853 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                           BST2  28 qaqeslreaeaqaatcnqtvvtL.kasLekekaqsqk 63 
                                    ++q+s++e  a a  +    v+L +++L    +q++ 
  gi|121636391|ref|YP_976614.1| 110 RSQQSFEEVSARAEGYVDQAVELtQEALGTVASQTRA 146
                                    6888888888888888776666624556666666555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   8.5    0.0002      0.26     158     267 ..       7     117 ..       2     133 .. 0.71
   2 ?    1.8   1.7     0.071        91     162     260 ..      88     185 ..      77     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                           Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael...qeqleelee 234
                                    +++ ++ l ++l + +   a+++e +++l+e+aee  + ++ ++ee r +l++l++++ e+ +el e+   +e +++ e 
  gi|121636391|ref|YP_976614.1|   7 IDDIKAPLLAALGAADLALATVNELITNLRERAEETRTDTRSRVEESRARLTKLQEDLPEQLTELREKftaEELRKAAEG 86 
                                    55555556666666677788999999*********99999******************9887777775222444555666 PP

                           Spc7 235 kieelkeqkseleeeiaeaervleeckgwsese 267
                                     +e+++++++el e+ ++a + l+ ++++  +e
  gi|121636391|ref|YP_976614.1|  87 YLEAATSRYNELVERGEAALERLRSQQSF--EE 117
                                    77777777777777766665555544444..34 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.071
                           Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                     e +++ ++el+e+ ++  e+l+++q+  ee+++  + ++ ++ e  +e+  +++++ + + e+ ++l  +e   +++ +
  gi|121636391|ref|YP_976614.1|  88 LEAATSRYNELVERGEAALERLRSQQS-FEEVSARAEGYVDQAVELTQEALGTVASQTRAVGERAAKLVGIELPKKAAPA 166
                                    344455555555555555555555555.4467777788888888888888888888888888888888888888887777 PP

                           Spc7 242 qkseleeeiaeaervleec 260
                                    +k+   ++ a a++   ++
  gi|121636391|ref|YP_976614.1| 167 KKAAPAKKAAPAKKAAAKK 185
                                    7777777777777766655 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.4    0.0058       7.4       7      53 ..      28      74 ..      20      85 .. 0.52
   2 ?    5.4   0.8     0.021        27      26      56 ..      74     104 ..      67     112 .. 0.73
   3 ?    3.5   7.3     0.084   1.1e+02      23      70 ..     109     156 ..      96     199 .] 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0058
                         DUF883  7 leslladleellkeaadeageeaeelRerleerlerarerlrdaeea 53
                                   +++l+++l+e ++e+  ++++ +ee R+rl++  e++ e+l++++e+
  gi|121636391|ref|YP_976614.1| 28 VNELITNLRERAEETRTDTRSRVEESRARLTKLQEDLPEQLTELREK 74
                                   44455555555555555555555555555555555555555555444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                         DUF883  26 geeaeelRerleerlerarerlrdaeeavae 56 
                                    + +aeelR+ +e +le+a +r +++ e+ ++
  gi|121636391|ref|YP_976614.1|  74 KFTAEELRKAAEGYLEAATSRYNELVERGEA 104
                                    5578999999999999999988877666554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.084
                         DUF883  23 deageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70 
                                     +++++ ee+ +r+e ++++a e +++a  +va +++++ e+a + V 
  gi|121636391|ref|YP_976614.1| 109 LRSQQSFEEVSARAEGYVDQAVELTQEALGTVASQTRAVGERAAKLVG 156
                                    46899999999****************************999999885 PP

>> DUF932  Domain of unknown function (DUF932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.6      0.35   4.5e+02     131     150 ..      49      68 ..      14     111 .. 0.45
   2 ?   10.9   1.5   0.00022      0.28      97     165 ..     112     178 ..     103     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.35
                         DUF932 131 efeeeaealaavklteaeae 150
                                    ++ee+ ++l +++ +  e+ 
  gi|121636391|ref|YP_976614.1|  49 RVEESRARLTKLQEDLPEQL 68 
                                    22222222222222222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                         DUF932  97 dgatgevkvrHtgnvdakvieakkaLglvveefeefeeeaealaavklteaeaeafaeavlpepkeaae 165
                                    +++++ev+ r +g vd++v+  ++aLg+v+++++++ e+a++l  ++l +++a a  +   p +k a +
  gi|121636391|ref|YP_976614.1| 112 QQSFEEVSARAEGYVDQAVELTQEALGTVASQTRAVGERAAKLVGIELPKKAAPAKKA--APAKKAAPA 178
                                    56889999999************************************99887655444..222222222 PP

>> Stm1_N  Stm1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.0    0.0066       8.4      21      55 ..     161     195 ..     133     199 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                         Stm1_N  21 aapapppkevdkkstrsaKrptkpepPsqavrear 55 
                                    +++ap++k++++k++++aK ++ +++P++++ +++
  gi|121636391|ref|YP_976614.1| 161 KKAAPAKKAAPAKKAAPAKKAAAKKAPAKKAAAKK 195
                                    67889999999999999999999999999988876 PP

>> MRP-S26  Mitochondrial ribosome subunit S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.4   0.00048      0.62      40     133 ..      25     113 ..      22     133 .. 0.82
   2 ?   -1.7   0.2       1.8   2.3e+03     112     123 ..     179     190 ..     147     199 .] 0.50

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00048
                        MRP-S26  40 lrslrelfkeevekeeeeelkkeseekaeeeeeefkellaiNdewNaelaelReerlkkeaeekkeeilerieekeqkee 119
                                    l  ++el+++  e+ ee++++++s+ ++       ++l ++ +   ++l+elRe+ +++e+ +  e +le++ ++ ++  
  gi|121636391|ref|YP_976614.1|  25 LATVNELITNLRERAEETRTDTRSRVEES-----RARLTKLQEDLPEQLTELREKFTAEELRKAAEGYLEAATSRYNELV 99 
                                    55677777766666666665555544444.....4699999*************************************** PP

                        MRP-S26 120 ekkekaeeevlqek 133
                                    e+ e a e+++ ++
  gi|121636391|ref|YP_976614.1| 100 ERGEAALERLRSQQ 113
                                    ***99999999887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                        MRP-S26 112 eekeqkeeekke 123
                                    ++ + k++  k+
  gi|121636391|ref|YP_976614.1| 179 KKAAAKKAPAKK 190
                                    222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1946  (0.108539); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 1395.03
//
Query:       gi|121636392|ref|YP_976615.1|  [L=87]
Description: hypothetical protein BCG_0517 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-25   89.4   5.1    1.5e-25   89.2   5.1    1.0  1  DUF2516   Protein of unknown function (DUF2516)
  ------ inclusion threshold ------
      0.021   14.5   3.4       0.15   11.7   0.3    2.0  2  PRA1      PRA1 family protein
        0.2   11.9   4.2       0.22   11.7   3.9    1.3  1  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D
       0.24   11.9   3.0       0.36   11.4   0.4    2.1  2  Ytca      Uncharacterised protein family
        6.7    7.1  15.5        5.1    7.5   2.7    2.3  2  Tad       Putative Flp pilus-assembly TadE/G-like


Domain annotation for each model (and alignments):
>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   5.1   4.3e-29   1.5e-25       8      91 ..       1      84 [.       1      86 [. 0.90

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 4.3e-29
                        DUF2516  8 llllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlllglfgalsl.lgliavvaalvYlvDVRPavre 88
                                   +l+l ++vlv++++A+v+a+++r+da++aa+k+tKp+Wl+ilg+a++++ + l+  l++  + ++++a++vYlvDVRP++ e
  gi|121636392|ref|YP_976615.1|  1 MLVLLVAVLVTAVYAFVHAALQRPDAYTAADKLTKPVWLVILGAAVALASI-LYPVLGVlGMAMSACASGVYLVDVRPKLLE 81
                                   6899*******************************************9999.66666661566799**************99 PP

                        DUF2516 89 vgr 91
                                   +++
  gi|121636392|ref|YP_976615.1| 82 IQG 84
                                   985 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.2e-05      0.15     113     137 ..       2      26 ..       1      32 [. 0.87
   2 ?    4.2   0.3    0.0083        30      43      78 ..      39      74 ..      33      86 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                           PRA1 113 lvllwalliglllvllHAsfrkrnd 137
                                    lvll+a+l+ ++  ++HA++ +++ 
  gi|121636392|ref|YP_976615.1|   2 LVLLVAVLVTAVYAFVHAALQRPDA 26 
                                    799*****************98875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0083
                           PRA1 43 livvllvlllslltnplslivllllvlawlflyflr 78
                                   l+++ ++++l+ ++ p+  ++++++ + +  +y++ 
  gi|121636392|ref|YP_976615.1| 39 LVILGAAVALASILYPVLGVLGMAMSACASGVYLVD 74
                                   466677777777888887777777777666666654 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.9   6.2e-05      0.22       7      62 ..       3      56 ..       1      65 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                           DPM3  7 tlalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgygvl 62
                                   +l++a+l++a+++++ + l  +p +       ++ P+w+++l +a +la+++y vl
  gi|121636392|ref|YP_976615.1|  3 VLLVAVLVTAVYAFVHAALQ-RP-DAYTAADKLTKPVWLVILGAAVALASILYPVL 56
                                   57899999999999987777.55.44445555789******************997 PP

>> Ytca  Uncharacterised protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.16   5.7e+02      16      34 ..       2      23 ..       1      31 [. 0.60
   2 ?   11.4   0.4    0.0001      0.36      12      37 ..      36      61 ..      34      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                           Ytca 16 lClaiaiaLtlv...vrlvlvr 34
                                   l l++a++ t+v   v++ l+r
  gi|121636392|ref|YP_976615.1|  2 LVLLVAVLVTAVyafVHAALQR 23
                                   5667776666552225555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                           Ytca 12 PaWllClaiaiaLtlvvrlvlvrlkl 37
                                   P+Wl+ l +a+aL+++++ vl  l +
  gi|121636392|ref|YP_976615.1| 36 PVWLVILGAAVALASILYPVLGVLGM 61
                                   9*****************99976665 PP

>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.7    0.0014       5.1      12      39 ..       2      31 ..       1      32 [. 0.72
   2 ?    5.5   5.1    0.0061        22       3      30 ..      44      73 ..      38      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                            Tad 12 lplll..lvglavDvgravlartrlQnAAD 39
                                   l+ll+  lv +++++ +a l+r ++ +AAD
  gi|121636392|ref|YP_976615.1|  2 LVLLVavLVTAVYAFVHAALQRPDAYTAAD 31
                                   3444443555555999*************9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0061
                            Tad  3 aavlfalallpllllvglav.D.vgravla 30
                                   aav +a +l p+l+++g+a+ + ++ ++l+
  gi|121636392|ref|YP_976615.1| 44 AAVALASILYPVLGVLGMAMsAcASGVYLV 73
                                   455***************996677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 634.27
//
Query:       gi|121636393|ref|YP_976616.1|  [L=148]
Description: hypothetical protein BCG_0518 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-40  135.9   0.3    7.4e-40  135.5   0.3    1.1  1  DUF2599   Protein of unknown function (DUF2599)


Domain annotation for each model (and alignments):
>> DUF2599  Protein of unknown function (DUF2599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.3   4.1e-44   7.4e-40       1      93 []      46     142 ..      46     142 .. 0.99

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 4.1e-44
                        DUF2599   1 vesveWvereggkslevvPtdagrkaa....aaaaeaawaevlalepdadtagmraQfvCHwefaelvapdkasWnLepw 76 
                                    v+++eW+++++ +sl+v+P+++gr+a+    +aaa+aawaevlal+p+adtagmraQf+CHw++ae+ +p+k+sWnLepw
  gi|121636393|ref|YP_976616.1|  46 VDHTEWAQWGSLPSLRVYPSQVGRTASrrlgMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSWNLEPW 125
                                    79************************99**9************************************************* PP

                        DUF2599  77 RpavseeetvaagCnpg 93 
                                    Rp+v+++e++a+gCnpg
  gi|121636393|ref|YP_976616.1| 126 RPVVDDSEMLASGCNPG 142
                                    ****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.18s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1255.40
//
Query:       gi|121636394|ref|YP_976617.1|  [L=224]
Description: deoxyribose-phosphate aldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-18   67.6   9.7    1.4e-18   67.4   9.7    1.0  1  DeoC          DeoC/LacD family aldolase
    0.00021   20.6   1.7    0.00029   20.1   0.2    1.9  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0044   16.2   0.3     0.0083   15.3   0.3    1.5  1  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.017   14.6   1.3       0.11   12.0   0.1    2.3  2  His_biosynth  Histidine biosynthesis protein
       0.22   11.8   5.3         18    5.7   0.1    3.7  3  DUF3618       Protein of unknown function (DUF3618)


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   9.7     4e-22   1.4e-18       5     231 ..      13     218 ..       9     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4e-22
                                    EECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEETTC CS
                           DeoC   5 avDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvdeva 84 
                                    +vD++ +  + t +       d++alv+ea++ g  av++ p +++ a +  + ++a ++++++g++ ++ k      + 
  gi|121636394|ref|YP_976617.1|  13 LVDHTLLKPETTRA-------DVAALVAEAAELGVYAVCVSPSMVPVAVQAGGVRVAAVTGFPSGKHVSSVK------AH 79 
                                    56666555555555.......******************************************999999999......9* PP

                                    HHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCC CS
                           DeoC  85 sveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAarvsael 163
                                    ++++a+a GA ++++v+ + a+  ++   +  +i++v++a++ + l++i+e ++l +++      +++   +A r++ ++
  gi|121636394|ref|YP_976617.1|  80 EAAAALASGASEIDMVIDIGAALCGDIDAVRSDIEAVRAAAAGAVLKVIVEsAVLLGQS------NAHTLVDACRAAEDA 153
                                    ****************************************************9999999......799************ PP

                                    T-SEEEE--S.SCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTH..CEEEESHH CS
                           DeoC 164 GaDiiKvevp.kevvnateedaevfkdvikaapvpgvvlsGGvseedfletvedAvk..eaga..sGvlsGRa 231
                                    GaD++K++++   +  at  ++e + + ++  p  gv+ sGG+      +t+ dAv+  +aga   G++  Ra
  gi|121636394|ref|YP_976617.1| 154 GADFVKTSTGcHPAGGATVRAVELMAETVG--PRLGVKASGGI------RTAADAVAmlNAGAtrLGLSGTRA 218
                                    **********65566677777777777777..5567*******......999999988888887767766665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.15   5.5e+02     170     229 ..      20      76 ..      17     143 .. 0.61
   2 !   20.1   0.2   8.1e-08   0.00029     231     272 ..     172     213 ..     151     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                                    -SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHH CS
                         DHO_dh 170 aPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdi 229
                                     P+ t  + ++ +++++el++ ++ v+ + v      +++  ++ a  tG  sGk++ ++
  gi|121636394|ref|YP_976617.1|  20 KPETTRADVAALVAEAAELGVYAVCVSPSMVPVA---VQAGGVRVAAVTGFPSGKHVSSV 76 
                                    5666666667777777777777777666665554...55555555556666677666655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 8.1e-08
                                    HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEE CS
                         DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqv 272
                                    ++ +  +++++ +++ + ++GGi ++ Da+ +++aGA+ + +
  gi|121636394|ref|YP_976617.1| 172 VRAVELMAETVGPRLGVKASGGIRTAADAVAMLNAGATRLGL 213
                                    67888899******************************8876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.3e-06    0.0083      98     204 ..      97     206 ..      78     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                                    EEGGGGGGSHHHHHHHHHHHHCCSS...S-EEEEEESESS.TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CH CS
                            Dus  98 gaGaaLlrkpdlvaqivkavvkave...iPvtvkirigid.deeenalelakiveaaGaqaltvHgRtraqnyegtadwe 173
                                    ++GaaL  + d v + ++av+ a     ++v v+  +    ++ ++++++++++e+aGa+++     +  +   g a  +
  gi|121636394|ref|YP_976617.1|  97 DIGAALCGDIDAVRSDIEAVRAAAAgavLKVIVESAVLLGqSNAHTLVDACRAAEDAGADFVKT---STGCHPAGGATVR 173
                                    58********************999899999999888877678899**************9963...4556666688888 PP

                                    HHHHHHHH-S..S-EEEESS--SHHHHHHHHHH CS
                            Dus 174 aIkevkqavs..ipviaNGdIkdaedaqailee 204
                                    a++ + + v   + v a G+I++a da a+l+ 
  gi|121636394|ref|YP_976617.1| 174 AVELMAETVGprLGVKASGGIRTAADAVAMLNA 206
                                    888888888788999999999999999998876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.053   1.9e+02      11      55 ..      58     102 ..      49     133 .. 0.61
   2 ?   12.0   0.1     3e-05      0.11      60     101 ..     170     213 ..     137     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                                    TEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEE.EEEEHHHHC CS
                   His_biosynth  11 GkvVrlvkGdrfqelryagdpvelakryeeegadel.hvvDldaak 55 
                                    G  V  v G  + +++ + + +e+a ++ + ga e+ +v+D+ aa 
  gi|121636394|ref|YP_976617.1|  58 GVRVAAVTGFPSGKHVSSVKAHEAAAAL-ASGASEIdMVIDIGAAL 102
                                    4445566777777777777777777777.44555553667777766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEE CS
                   His_biosynth  60 anldlveeiaeevf..ipvqvGGGIrsledveelleagadkvii 101
                                    a   +ve +ae+v   + v   GGIr+  d+ ++l+aga ++ +
  gi|121636394|ref|YP_976617.1| 170 ATVRAVELMAETVGprLGVKASGGIRTAADAVAMLNAGATRLGL 213
                                    5567777788888755888999******************9865 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.029     1e+02      14      23 ..       6      15 ..       4      16 .. 0.92
   2 ?    2.9   0.4     0.036   1.3e+02      27      40 ..      24      37 ..      23      37 .. 0.88
   3 ?    5.7   0.1    0.0051        18       3      16 ..     105     118 ..     104     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.029
                        DUF3618 14 tRaeLaeTvd 23
                                   tRa+La+ vd
  gi|121636394|ref|YP_976617.1|  6 TRAQLAALVD 15
                                   9******998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.036
                        DUF3618 27 aradPkrladraka 40
                                   +rad+++l+ +a++
  gi|121636394|ref|YP_976617.1| 24 TRADVAALVAEAAE 37
                                   79********9986 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0051
                        DUF3618   3 dpeeIerdIertRa 16 
                                    d+++++ dIe+ Ra
  gi|121636394|ref|YP_976617.1| 105 DIDAVRSDIEAVRA 118
                                    89**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1708.26
//
Query:       gi|121636395|ref|YP_976618.1|  [L=348]
Description: hypothetical protein BCG_0520c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-19   69.3   0.4    7.2e-19   68.9   0.4    1.2  1  DUF2993   Protein of unknown function (DUF2993)


Domain annotation for each model (and alignments):
>> DUF2993  Protein of unknown function (DUF2993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.4     4e-23   7.2e-19       5     208 ..     130     326 ..     126     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 4e-23
                        DUF2993   5 gaaavaeqriatelrsql..elaedpeVsiggfPflt.qllaGeldsvsvaargvvv.dgpglriesveltledvrldls 80 
                                    g++++a++++ +++++++   + ++ + s+g  P l+ q+++ +++ +sv+++g ++ d++g+   +++lt+++vrl   
  gi|121636395|ref|YP_976618.1| 130 GGELYARHVANSKVAQAVacVVKDQATASFGVAPLLLwQVATRHFTNISVETAGNQIrDAKGM---QIKLTIQNVRLKNT 206
                                    7899999999999977777999************9999*******************999999...8************9 PP

                        DUF2993  81 dilgkvrlvpvgrltatvtlteadlnralasp.......llitdlq.....dlsnggvkltgnnlpvvveaglrlaagdg 148
                                          +  ++g l+at+t++ + +  +++++             +     ++++g+v+l g  l ++++a+    ++ +
  gi|121636395|ref|YP_976618.1| 207 P----NSRGTIGALDATITWSSEGIKESVQNAipilgafV-----TssvvtHPADGTVELKG--LLNNITAKP--IVAGK 273
                                    8....67788********************9987666652.....1444457**********..677777766..56666 PP

                        DUF2993 149 qlrleltdle.aglglpesavdlpaelldalleglselldlpglpfglrltevrvtdgglr 208
                                    +l l++ ++  +g  lp++         +  l+ ++ +l ++++p+g+++++v+vt+ g++
  gi|121636395|ref|YP_976618.1| 274 GLELQIINFNtLGFSLPKE-------TVQSTLNEFTSSL-TKNYPLGIHADSVQVTSTGVV 326
                                    79********777666555.......5555666666655.556***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2433.16
//
Query:       gi|121636396|ref|YP_976619.1|  [L=311]
Description: hypothetical protein BCG_0521c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-39  133.4   0.1      1e-38  133.2   0.1    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.1   5.7e-43     1e-38       1     260 [.      33     289 ..      33     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 5.7e-43
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvi 80 
                                    r+A++Q+++  +d +anlq++ +++ eAa  ga+L+v+PE+  +  +     ++ Ae ++g+ + +++++a++ gi+v++
  gi|121636396|ref|YP_976619.1|  33 RIALAQIRSG-TDPAANLQLVGKYAGEAATAGAQLVVFPEATMC--RLGVPLRQVAEPVDGPWANGVRRIATEAGITVIA 109
                                    79*******6.8********************************..889999999************************* PP

                                    EEEEEECCTTEEEEEEEEEEEETTSEE..EEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGS CS
                   CN_hydrolase  81 gliereltngklqayntavlldldgkl..vgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigf 158
                                    g++     +g++   nt +   +++     + y+K+hL    ++  +++e+ ++ pg +  v+ ++++++G+ +Cy+i+f
  gi|121636396|ref|YP_976619.1| 110 GMFTPT-GDGRV--TNTLIAAGPGTPNqpDAHYHKIHL----YDAFGFTESRTVAPGREPVVVVVDGVRVGLTVCYDIRF 182
                                    *88884.89999..9******99999999********8....799***********996556677777************ PP

                                    HHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEE........HCETTEEEE--EEEE- CS
                   CN_hydrolase 159 pellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvgg........yeqlilwpvghSaiid 230
                                    p l+  la++ga+++   +  ++  +    +qw ll+raral++  +v+aa q+          + +     vg+S +++
  gi|121636396|ref|YP_976619.1| 183 PALYTELARRGAQLIAV-C-ASWGSGPGKLEQWTLLARARALDSMSYVAAAGQADPgdartgvgASSAAPTGVGGSLVAS 260
                                    ***************99.2.4566666666899**********************9********9*************** PP

                                    TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                   CN_hydrolase 231 pdGrilaglgeeeegvliaeidladvratr 260
                                    p G++++ +g++  ++l+a+id + v+a+r
  gi|121636396|ref|YP_976619.1| 261 PLGEVVVSAGTQP-QLLVADIDVDNVAAAR 289
                                    *************.6***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2138.88
//
Query:       gi|121636397|ref|YP_976620.1|  [L=174]
Description: hypothetical protein BCG_0522c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-45  154.5   0.1    2.7e-45  154.3   0.1    1.0  1  DUF2505   Protein of unknown function (DUF2505)


Domain annotation for each model (and alignments):
>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.1   1.5e-49   2.7e-45       1     158 []       6     170 ..       6     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 1.5e-49
                        DUF2505   1 evsaeypapvdrvyaaltdeeywearleevgaeesevtseeveed.....gvtvtvtqtlpadalPeavrkvvsgdlkit 75 
                                    ++sa+y+ +v++v++a+ +++yw+arl+e+  + ++++s +v++d     +++v++ q +++++lP++v+++++gdl ++
  gi|121636397|ref|YP_976620.1|   6 DMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDsgddgTIEVVTLQMVRSHNLPGLVTQLHRGDLSVR 85 
                                    689**************************************999999999****************************** PP

                        DUF2505  76 rteswgplsdgratgtvsasvkgapvelsGtltLep..egegtrlevegevkvkiPlvGgklEklvaenleelldreaef 153
                                    r+e+wgp+++g at+++++s++ apv+l Gt++L+p  e++g+r++++++++v+iP++GgklE+l+  +l +l++ e++f
  gi|121636397|ref|YP_976620.1|  86 REETWGPVKEGIATASIAGSIVDAPVNLWGTAVLSPipESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRF 165
                                    ************************************88888*************************************** PP

                        DUF2505 154 teeWl 158
                                    t+ W+
  gi|121636397|ref|YP_976620.1| 166 TTLWI 170
                                    ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1197.75
//
Query:       gi|121636398|ref|YP_976621.1|  [L=369]
Description: UDP-N-acetylenolpyruvoylglucosamine reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-38  131.9   0.0    2.1e-38  131.0   0.0    1.4  1  MurB_C         UDP-N-acetylenolpyruvoylglucosamine reductase,
    4.3e-24   84.8   2.2    5.5e-23   81.2   2.6    2.3  2  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> MurB_C  UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.0   2.4e-42   2.1e-38       2     120 .]     230     365 ..     229     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 2.4e-42
                                    HHHHHHHHHHHHSHCHSTT..CTCEESESB---EESHHHHHHHH............EEEETTSSEEE-HHHHHHHTT-T. CS
                         MurB_C   2 ireavlelrakklmvkqpl..dtpsaGSfFknPivegeeaeelk............eyeaeegevklsagwLIeqaglk. 66 
                                    +reavl+lra+k+mv++p+  dt+s+GSfF+nP+v+++ +e+l+            +y+a +g  kl+agwL+e+ag+  
  gi|121636398|ref|YP_976621.1| 230 VREAVLALRARKGMVLDPTdhDTWSVGSFFTNPVVTQDVYERLAgdaatrkdgpvpHYPAPDGV-KLAAGWLVERAGFGk 308
                                    9*****************97888********************************666666665.*************99 PP

                                    TSEE...TTEEEESSSTTEEEESSS--HHHHHHHHHHHHHHHHHHHS----BSSEEE CS
                         MurB_C  67 Glrv...ggaqvsekhalflvNgggataadilalarevrkkVkekfgveLepEvvli 120
                                    G+      ++++s+khal+l+N+ggata+d+++lar+vr++V++ fg++L+pE+vli
  gi|121636398|ref|YP_976621.1| 309 GYPDagaAPCRLSTKHALALTNRGGATAEDVVTLARAVRDGVHDVFGITLKPEPVLI 365
                                    **875557789***********99******************************987 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   2.6   6.1e-27   5.5e-23       2     139 .]      34     167 ..      33     167 .. 0.95
   2 ?    0.1   0.0     0.066     6e+02      76     106 ..     232     261 ..     229     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 6.1e-27
                                    EEEEEESSHHHHHHHHHHHHHC.....TSCEEEESSSTTEE.STTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHH CS
                  FAD_binding_4   2 aavvrpeseeevaaalrlanea.....glpvlvrGgGssll.gqavatggvvldlsrlnrileideeegtatveaGvtlg 75 
                                    + v++++s+e+v+aalr+ ++a     ++p lv++gGs+l+  +++ t+ +v++l   n+ ++id  ++ +++eaG++++
  gi|121636398|ref|YP_976621.1|  34 RRVITCTSAEQVVAALRHLDSAaktgaDRP-LVFAGGSNLViAENL-TDLTVVRL--ANSGITID--GNLVRAEAGAVFD 107
                                    689***************999988886666.999*******99998.********..8998****..8************ PP

                                    HHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEE.TTSEEEEEE CS
                  FAD_binding_4  76 dlvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvl.adGevvrls 139
                                    d+v ++  +++l gle++sgipg++G+++++n+g+yg+e++    d+++++++++ ++Gev+++s
  gi|121636398|ref|YP_976621.1| 108 DVVVRA-IEQGLGGLECLSGIPGSAGATPVQNVGAYGAEVS----DTITRVRLLDrCTGEVRWVS 167
                                    ******.999999****************************....*****************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.066
                                    HHHHHHHHHTTECSSGGGTTCGSBHHHTTTT CS
                  FAD_binding_4  76 dlvealaakglllglepgsgipgtvGGaiat 106
                                    ++v al+a+++++ l+p+++++ +vG++  +
  gi|121636398|ref|YP_976621.1| 232 EAVLALRARKGMV-LDPTDHDTWSVGSFFTN 261
                                    5667788888888.49**********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2696.65
//
Query:       gi|121636399|ref|YP_976622.1|  [L=451]
Description: lipoprotein lprQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-65  218.0   0.2    1.3e-64  217.5   0.2    1.2  1  Big_10    Bacterial Ig domain
    5.6e-12   46.3   0.2    1.1e-11   45.4   0.2    1.5  1  YkuD      L,D-transpeptidase catalytic domain


Domain annotation for each model (and alignments):
>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.5   0.2   1.5e-68   1.3e-64       2     182 .]      76     260 ..      75     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 1.5e-68
                         Big_10   2 kdvkpeepvtvtvedgkLtevsltdeeGkevegelsadktsWtsteklgygttYtltakakdadgkavektssftTvapa 81 
                                    +dv p +p++v+v dg +++v+lt+++Gk v+g+ s+d+t +t te+lgy+ttYt++++a+++dgkav   ++ftTvap 
  gi|121636399|ref|YP_976622.1|  76 ADVVPIAPISVEVGDGWFQRVALTNSAGKVVAGAYSRDRTIYTITEPLGYDTTYTWSGSAVGHDGKAVPVAGKFTTVAPV 155
                                    7999**************************************************************************** PP

                         Big_10  82 ktvsatltpedgstvGvgqpisikFdkpvedkaavekalkvttspavegafaWlsd....sevdwRpkeYwkpgtkVtvk 157
                                    kt++a ++  dg+tvG+++p+ i+Fd+p++dkaave+al+vtt+p+veg +aWl d     +v+wRp+eY+++gt+V+v+
  gi|121636399|ref|YP_976622.1| 156 KTINAGFQLADGQTVGIAAPVIIQFDSPISDKAAVERALTVTTDPPVEGGWAWLPDeaqgARVHWRPREYYPAGTTVDVD 235
                                    ********************************************************99999******************* PP

                         Big_10 158 aklygvelgdgvygkedksvsftiG 182
                                    aklyg+ +gdg+yg++d+s++f+iG
  gi|121636399|ref|YP_976622.1| 236 AKLYGLPFGDGAYGAQDMSLHFQIG 260
                                    ************************9 PP

>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   1.2e-15   1.1e-11       4     146 .]     265     383 ..     262     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.2e-15
                                    EEEETTTTEEEEEEETTEEEEEEE-BEB....TTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEE CS
                           YkuD   4 ivvdlaeqrllvlyengklvlsfpvsvG....gkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyld 79 
                                    +   ++++r+ +++++ ++++ fp+s+G    +       T +G + +++k+++ +  + +++a+ + ++++        
  gi|121636399|ref|YP_976622.1| 265 VKAEVSSHRI-QVVTDAGVIMDFPCSYGeadlA----RNVTRNGIHVVTEKYSDFY--MSNPAAGYSHIHER-------- 329
                                    5566778788.888**************65444....56**********9999999..55555444444333........ PP

                                    ECCCTTCECCCCEEE-STTS-EEEE.ETCSS...CT.HHC.BSSSEEE-HHHHHHHHHHHHTTEEEEE CS
                           YkuD  80 kknskvalgkvkfvfpngsgiyiHgtgapdlfergk.garrShGCirlseedakelyelvlvgtpvvi 146
                                               ++v  +++g +iH  ++p   +  + +++ ++GCi+ls+e+a++ y+  + g+pv++
  gi|121636399|ref|YP_976622.1| 330 -----------WAVRISNNGEFIH--ANPMSAGA-QgNSNVTNGCINLSTENAEQYYRSAVYGDPVEV 383
                                    ...........46778999*****..88876544.248888*************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3345.36
//
Query:       gi|121636400|ref|YP_976623.1|  [L=251]
Description: short-chain type oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-45  154.7   0.6    2.4e-45  154.4   0.6    1.1  1  adh_short        short chain dehydrogenase
    7.2e-34  117.4   3.3      9e-34  117.0   3.3    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      2e-09   37.6   7.1    2.7e-09   37.2   7.1    1.4  1  NAD_binding_10   NAD(P)H-binding
    4.4e-09   36.5   2.5    6.6e-09   35.9   2.5    1.1  1  KR               KR domain
    1.3e-07   31.3   0.8    2.2e-07   30.6   0.8    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.8e-05   23.1   1.8    0.00013   22.2   1.5    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0025   17.4   4.3     0.0059   16.2   4.3    1.7  1  NmrA             NmrA-like family
     0.0095   16.2   0.7     0.0095   16.2   0.7    1.8  3  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.013   15.6   0.4      0.024   14.7   0.4    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.018   15.6   5.1      0.019   15.5   0.6    2.6  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.029   14.3   3.6      0.056   13.4   3.6    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.035   13.2   1.0      0.074   12.1   1.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
      0.053   14.5   8.8      0.055   14.5   5.2    2.7  2  LytR_C           LytR cell envelope-related transcriptional a


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.6   1.8e-48   2.4e-45       2     186 ..      10     186 ..       9     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 1.8e-48
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    v++vtGassGIG a+a++la++G++vv+v+r+++++ ++a++++      +ai +Dvtd ++veal ++      ++dvL
  gi|121636400|ref|YP_976623.1|  10 VAVVTGASSGIGEATARTLAAQGFHVVAVARRADRITALANQIGG-----TAIVADVTDDAAVEALARAL----SRVDVL 80 
                                    89******************************************7.....69*******99988887766....9***** PP

                                    EE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    vnNAG  +g + +++ + e w+ + ++N+ g++ +tra+lp+++++  G Iv+v+S+a+++ + g+a Y+A+K+a  +l 
  gi|121636400|ref|YP_976623.1|  81 VNNAGGaKGLQFVADADLEHWRWMWDTNVLGTLRVTRALLPKLIDSGDGLIVTVTSIAALEVYDGGAGYTAAKHAQGALH 160
                                    ******8899999******************************************************************* PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdm 186
                                    r+l+ el  + +r + +aPG+v+T++
  gi|121636400|ref|YP_976623.1| 161 RTLRGELLGKPVRLTEIAPGAVETEF 186
                                    ************************97 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   3.3   6.5e-37     9e-34       1     215 [.      15     221 ..      15     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 6.5e-37
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    Ga sgIG+a+A++la++G +vv++ ++ ++   +++la+++g +++ +DVtd+++veal+++    + ++D+lvnnag a
  gi|121636400|ref|YP_976623.1|  15 GASSGIGEATARTLAAQGFHVVAVARRADR---ITALANQIGGTAIVADVTDDAAVEALARA----LSRVDVLVNNAGGA 87 
                                    899*********************998887...*********************99999887....5699********** PP

                                    EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    +   + +++++ e+++ + d+n+ +++++++a+lp l+ +g g iv+++s++a  v ++ + y+aaK+a  al r+l  e
  gi|121636400|ref|YP_976623.1|  88 KG-LQFVADADLEHWRWMWDTNVLGTLRVTRALLPkLIDSGdGLIVTVTSIAALEVYDGGAGYTAAKHAQGALHRTLRGE 166
                                    *9.888999**************************9888889************************************** PP

                                    HGGGTEEEEEEEE--BHCTG.GGGSTT.HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHC CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTla.asgikg.fdelleelearaplgrlgtpeevaeaalfLa 215
                                    l  k +R   ++pg+++T+    +++g +++  +  + ++pl     + +vae++ f a
  gi|121636400|ref|YP_976623.1| 167 LLGKPVRLTEIAPGAVETEFsLVRFDGdQQRADAVYAGMTPL----VAADVAEVIGFVA 221
                                    ******************994333333122233333444444....4466777666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   7.1   1.9e-12   2.7e-09       1     106 [.      15     144 ..      15     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.9e-12
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-...CCHHHHHHTT-SEEEES---TCC.... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtd...vedlaealkgadaVvsalggggk.... 73 
                                    GA+ ++G + ++ l+a+ g++v+a++R+++++++l+++ g +++++dvtd   ve+la+al+ +d+ v ++gg ++    
  gi|121636400|ref|YP_976623.1|  15 GASSGIGEATARTLAAQ-GFHVVAVARRADRITALANQIGGTAIVADVTDdaaVEALARALSRVDVLVNNAGGAKGlqfv 93 
                                    9****************.5*****************99***********9665699**********99999888876776 PP

                                    ...HHHH.................HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                 NAD_binding_10  74 ...deeg.................aknivdaakeagvkRfvlvsaigvgdevp 106
                                       d                    +++++  +  +g   +v+v++i + +  +
  gi|121636400|ref|YP_976623.1|  94 adaD--LehwrwmwdtnvlgtlrvTRALLPKLIDSGDGLIVTVTSIAALEVYD 144
                                    6331..25566666666677777788888888888888888888888775444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   2.5   4.8e-12   6.6e-09       4     164 ..      12     164 ..      10     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.8e-12
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    ++tG+  g+G ++ar+la++g  h+v ++R+       +++i++l+++ +  +++ aDv+d +aveal ++++    ++ 
  gi|121636400|ref|YP_976623.1|  12 VVTGASSGIGEATARTLAAQGF-HVVAVARR-------ADRITALANQ-IGGTAIVADVTDDAAVEALARALS----RVD 78 
                                    89*******************7.77888888.......3577888775.33456778*************998....677 PP

                                    EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--S....EEEEEEEHHHHH--TT-HHHHHHHHHHHH CS
                             KR  84 GvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelledesld....ffvlfSSiagllgsagqanYaaaNaflDa 158
                                      ++ Ag ++  + +++ + e+++ +    v G+  + ++l ++ +d    ++v+++Sia+l    g a Y+aa + + a
  gi|121636400|ref|YP_976623.1|  79 VLVNNAGGAKgLQFVADADLEHWRWMWDTNVLGTLRVTRALLPKLIDsgdgLIVTVTSIAALEVYDGGAGYTAAKHAQGA 158
                                    777777766638999*************************999666633456899**********************999 PP

                                    HHHHHH CS
                             KR 159 laeyrr 164
                                    l ++ r
  gi|121636400|ref|YP_976623.1| 159 LHRTLR 164
                                    988766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.8   1.6e-10   2.2e-07       2     102 ..      12     119 ..      11     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.6e-10
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHH.T-SEEEE--S.---H CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkee.qpdavihlAa.vggv 77 
                                    +VtGa+  iG a+++ l+++g +v++++r+ ++    + +++  + + +d+td++a+e+l +   ++d+ ++ A+  +g 
  gi|121636400|ref|YP_976623.1|  12 VVTGASSGIGEATARTLAAQGFHVVAVARRADRITALA-NQIggTAIVADVTDDAAVEALARALsRVDVLVNNAGgAKGL 90 
                                    8*****************************55555443.33479***********9999999989********9978776 PP

                                    H....HHHHSHHHHHHHHTHHHHHHHHHH CS
                      Epimerase  78 a....assedpadfieknlqgtlnlleaa 102
                                    +    a  e+   ++++n+ gtl++  a+
  gi|121636400|ref|YP_976623.1|  91 QfvadADLEHWRWMWDTNVLGTLRVTRAL 119
                                    51111445555557889999999998886 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.5   9.4e-08   0.00013       2      83 ..      12      90 ..      11     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.4e-08
                                   EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGH CS
                Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppiss 82
                                   ++ Ga  ++G+a+a+ la+++    +++ + r  ++  ala+++ g+ + a   d + +ea La++l+  d++vn ++   +
  gi|121636400|ref|YP_976623.1| 12 VVTGAsSGIGEATARTLAAQGF---HVVAVARRADRITALANQIGGTAIVADVTDDAAVEA-LARALSRVDVLVNNAGGAKG 89
                                   56788889***********985...69999999***********99999999999999999.*************9887655 PP

                                   H CS
                Sacchrp_dh_NADP 83 l 83
                                   l
  gi|121636400|ref|YP_976623.1| 90 L 90
                                   5 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.3   4.3e-06    0.0059       2      72 ..      12      84 ..      11     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-H..HHHHHHHTT-SEEEE-- CS
                           NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddk..eslvealkgvdvvfsvt 72
                                   +v+Ga+  +G++ +r l+++g++v a+ R  ++ +a + +  G  +v++ +dd   e l++al+ vdv   + 
  gi|121636400|ref|YP_976623.1| 12 VVTGASSGIGEATARTLAAQGFHVVAVARRADRITALANQIGGTAIVADVTDDAavEALARALSRVDVLVNNA 84
                                   699**************************99888888777777777777677652256999999999987665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   6.9e-06    0.0095       8      58 ..      19      70 ..      11      85 .. 0.82
   2 ?   -3.0   0.0       6.3   8.7e+03       4      21 ..     110     127 ..     109     152 .. 0.64
   3 ?   -3.6   0.0       9.1   1.3e+04      29      50 ..     193     214 ..     188     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHT CS
                         TrkA_N  8 rvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeea 58
                                    +G++ a++L ++g +vv++ ++ +r+  l+++   +++v+d+td++++e++
  gi|121636400|ref|YP_976623.1| 19 GIGEATARTLAAQGFHVVAVARRADRITALANQIgGTAIVADVTDDAAVEAL 70
                                   59**********6646**********99998655599*********999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.3
                                    ES-SHHHHHHHHHHHHTT CS
                         TrkA_N   4 iGlGrvGrslaeeLsegg 21 
                                    +G  rv+r+l+ +L ++g
  gi|121636400|ref|YP_976623.1| 110 LGTLRVTRALLPKLIDSG 127
                                    666677777777776644 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.1
                                    SSHHHHHHHHHTTSEEEES-TT CS
                         TrkA_N  29 kdeerveelreeglevvvgdat 50 
                                     d++r++ + +  ++ v +d++
  gi|121636400|ref|YP_976623.1| 193 GDQQRADAVYAGMTPLVAADVA 214
                                    5666666666666666666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.7e-05     0.024      15      81 ..      11      82 ..       3      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                   EEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEE.....EGCGHHHHHHT-SEEEE CS
                   Shikimate_DH 15 vlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkgeeieal.....kleelkellaeadvvis 81
                                   +++ Ga   ++e +a+ L+a+g++ vv + R  +r  +la++++g+ i a      ++e l ++l+++dv++ 
  gi|121636400|ref|YP_976623.1| 11 AVVTGASSgIGEATARTLAAQGFH-VVAVARRADRITALANQIGGTAIVADvtddaAVEALARALSRVDVLVN 82
                                   45557754378999*********9.66667889**********999776541111145667788888888775 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.6   1.4e-05     0.019      10      55 ..      20      66 ..       9      82 .. 0.75
   2 ?    1.5   0.1      0.33   4.6e+02       4      30 ..     109     132 ..     107     158 .. 0.82
   3 ?   -2.4   0.0       5.3   7.3e+03      55      74 ..     207     227 ..     195     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECH CS
                  F420_oxidored 10 mgealasgllaagaqpheivvansrnpekaeelaeelg.....vkvtavdn 55
                                   +gea a+ l+a+g    ++v a  r  +++++la+++g     ++vt  ++
  gi|121636400|ref|YP_976623.1| 20 IGEATARTLAAQG---FHVV-AVARRADRITALANQIGgtaivADVTDDAA 66
                                   9************...9999.779**************5544433333333 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                                    EETTSHHHHHHHHHHHHTTS-GGCEEE CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivv 30 
                                    ++G+ ++ +al+ +l+ +g     ++v
  gi|121636400|ref|YP_976623.1| 109 VLGTLRVTRALLPKLIDSG---DGLIV 132
                                    79****************9...44443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.3
                                    HHHHHHH-SEE.EE-S-HHHH CS
                  F420_oxidored  55 neeaaeeadvv.vlavkpedv 74 
                                       aa+ a+v+ ++a +p++v
  gi|121636400|ref|YP_976623.1| 207 PLVAADVAEVIgFVATRPSHV 227
                                    344566666665777777665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.6   4.1e-05     0.056       1      70 [.      19      87 ..      19      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHH CS
                     ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseekl.elakklGadevinykea.dlverikeltggegvdvvfecvGsga 70
                                   g+G a+   ++a G++v+av++ ++++ +la ++G ++++   ++   ve+++++     vdv ++ +G ga
  gi|121636400|ref|YP_976623.1| 19 GIGEATARTLAAQGFHVVAVARRADRItALANQIGGTAIVADVTDdAAVEALARAL--SRVDVLVNNAG-GA 87
                                   89************************9788888**888888734436888888777..49****99999.44 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   5.4e-05     0.074       4      59 ..      12      84 ..       9      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                                   EEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH.--SEEEE-- CS
                  RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkea.kpdvvvnaA 59
                                   +vtGa+  +G + a+ la++g++v+a+ r+                 +d+td +av++l ++  + dv+vn A
  gi|121636400|ref|YP_976623.1| 12 VVTGASSGIGEATARTLAAQGFHVVAVARRadritalanqiggtaiVADVTDDAAVEALARALsRVDVLVNNA 84
                                   79*************************9999*************9999**********999863678999877 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.2     4e-05     0.055       3      64 ..       9      76 ..       7      97 .. 0.74
   2 ?    0.2   0.1       1.1   1.6e+03      43      65 ..     187     220 ..     138     235 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                         LytR_C  3 kVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee.......ttivy..reaaaaaakalaaalgl 64
                                   +V+V+ g++ sG+ +++a+ L+++Gf v++v+  +++ +        t iv+   +  +aa +ala+al  
  gi|121636400|ref|YP_976623.1|  9 RVAVVTGAS-SGIGEATARTLAAQGFHVVAVARRADRITAlanqiggTAIVAdvTD--DAAVEALARALSR 76
                                   577777776.9******************977655554448888888888874322..2477799999863 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                         LytR_C  43 ttivy.reaaa..........aaakalaaalglg 65 
                                    + +++ +++++            a  +a+ +g+ 
  gi|121636400|ref|YP_976623.1| 187 SLVRFdGDQQRadavyagmtpLVAADVAEVIGFV 220
                                    5555531111111222222212344666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1741.18
//
Query:       gi|121636401|ref|YP_976624.1|  [L=438]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-18   65.1   0.0    1.2e-17   64.3   0.0    1.4  1  ROK              ROK family
     0.0017   18.6   0.1     0.0035   17.5   0.1    1.5  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori
  ------ inclusion threshold ------
      0.085   12.8   0.1       0.28   11.2   0.1    1.9  1  HTH_Crp_2        Crp-like helix-turn-helix domain
        1.3    9.2   4.8       0.83    9.8   0.4    2.8  3  HTH_20           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.7e-21   1.2e-17       2     258 ..     110     378 ..     109     406 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.7e-21
                                    EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEE..EEEEEESSEEETTCCEBSSGG CS
                            ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeli..avgigspGlisdksgkivstp 79 
                                    +gi iG+  + +  +d  g +l++ + +tp++    +l  ++a+  d++ ++ + +    vg+ + G + d  ++ v  p
  gi|121636401|ref|YP_976624.1| 110 LGIHIGARTTSIVATDLFGRTLDTVETPTPRNAAGAAL-TSLADSADRYLQRWRRRRalWVGVTLGGAV-DSATGHVDHP 187
                                    79************************************.667777777777766554257999999***.78888889** PP

                                    CGCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTT...TTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GG CS
                            ROK  80 nitwenfdlvekleerlnvpvevenDvnaaalaEavfgask...dvenviyvtvgtGvGaGviingklitGrnGvagelG 156
                                    +++w++ ++   l+ +l++pv v+  v a+a aE ++g +      ++++yv+    vG + +i+g+++  ++G  g + 
  gi|121636401|ref|YP_976624.1| 188 RLGWRQAPVGPVLADALGLPVSVASHVDAMAGAELMLGMRRfapSSSTSLYVYARETVGYALMIGGRVHCPASGP-GTIA 266
                                    **************************************98633367899********************999953.4455 PP

                                    GSBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC.............CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHH CS
                            ROK 157 HiqldpegekcgCGnqgClEtlasgralekraqq.............kgekleakeiiklaekgdevaeevverlaeyla 223
                                     ++++ e      G +g lE  +s++a+ ++a++              g +  + ++++ a+ g+++a+e++ + a+ l+
  gi|121636401|ref|YP_976624.1| 267 PLPVHSE----MLGGTGQLESTVSDEAVLAAARRlriipgiasrtrtGGSATAITDLLRVARAGNQQAKELLAERARVLG 342
                                    5555555....5677888***************************988999999************************** PP

                                    HHHHHHHHHH--SEEEEEHCCC.TSTTHHHHHHHHH CS
                            ROK 224 kaiadlinlfdpqaivlgGgvs.eadklleairklv 258
                                     a+a l  l++p+ +v+gG    e ++ +e++++++
  gi|121636401|ref|YP_976624.1| 343 GAVALLRDLLNPDEVVVGGQAFtEYPEAMEQVEAAF 378
                                    *******************75403344445555544 PP

>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.7e-07    0.0035      35     118 ..     266     352 ..     259     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-07
                                    -B--EETTEE--BS-BTTTB-HHHHHHHH.HHHHHHHHHHHHHHHSSGGG-SEEEEEE..EEE-B-TT---HHHHHHHHH CS
                YjgF_endoribonc  35 fqlpylqekllyvGllGddvsvseGiaaa.rlaalnalaqlkeaaGelarvkrlirle..Gvlnvtqdyiempkvldaas 111
                                      lp   e l   G+l ++vs +  +aaa rl  + ++a   ++ G+ + +  l+r+   G  + ++   e  +vl +a 
  gi|121636401|ref|YP_976624.1| 266 APLPVHSEMLGGTGQLESTVSDEAVLAAArRLRIIPGIASRTRTGGSATAITDLLRVAraGNQQAKELLAERARVLGGAV 345
                                    5689999***************9999887369999*********************96337777888899********** PP

                                    HHHHHHH CS
                YjgF_endoribonc 112 dlllevl 118
                                     ll+++l
  gi|121636401|ref|YP_976624.1| 346 ALLRDLL 352
                                    ****998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.3e-05      0.28      17      54 ..      47      84 ..      32      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                                   EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                      HTH_Crp_2 17 eielpltqeelAsmlGltretvsrilseLkreglisrg 54
                                   +++ p+ ++ +A    l+  tv+r   +L ++gl++ +
  gi|121636401|ref|YP_976624.1| 47 RLRGPVGRDVIAGSTSLSIATVNRQVIALLEAGLLRER 84
                                   4555999***************************9954 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00019      0.83       7      57 ..      34      84 ..      32      86 .. 0.92
   2 ?   -2.0   0.0      0.87   3.9e+03      29      44 ..     199     213 ..     198     225 .. 0.69
   3 ?   -1.0   0.1      0.44     2e+03      12      38 ..     296     324 ..     289     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                   HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   L++   + ++ra + ++++    +a   +ls +t+++++ +L eagL++ +
  gi|121636401|ref|YP_976624.1| 34 LSDSAAASVFRAVRLRGPVGRDVIAGSTSLSIATVNRQVIALLEAGLLRER 84
                                   67788889999999999999999*************************976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.87
                                    HHHHHHTS-HHHHHHH CS
                         HTH_20  29 elaerldlskntlsyH 44 
                                     la++l+l+ + +s H
  gi|121636401|ref|YP_976624.1| 199 VLADALGLPVSVAS-H 213
                                    58889988887665.4 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.44
                                    HHHHHHHH..STCTTB-HHHHHHHHTS-H CS
                         HTH_20  12 RrrilraL..araegltaselaerldlsk 38 
                                    R+ri   +  +++ g +a+++ ++l++++
  gi|121636401|ref|YP_976624.1| 296 RLRIIPGIasRTRTGGSATAITDLLRVAR 324
                                    55555555667788889999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3314.12
//
Query:       gi|121636402|ref|YP_976625.1|  [L=480]
Description: mannosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-34  119.5   0.0    1.5e-34  119.0   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    4.7e-31  108.1   3.3    6.6e-31  107.6   2.0    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    9.9e-28   97.6  10.2    9.9e-28   97.6  10.2    2.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.5e-24   85.8   0.2    6.6e-24   84.9   0.2    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.8e-06   26.4   0.0    1.4e-05   25.4   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
      0.003   17.3   0.4       0.01   15.6   0.4    1.8  1  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
       0.14   12.2   0.1        0.7    9.9   0.1    2.0  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0   5.9e-38   1.5e-34       2     157 ..     252     407 ..     251     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 5.9e-38
                                    HHHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGG CS
                Glycos_transf_1   2 kekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnvi 76 
                                    ++  r+ lg++ +++++ +vgr+++ K +d +++a+a+l     p v++++aG     + +  + l +la+el++s++v+
  gi|121636402|ref|YP_976625.1| 252 RRAARAALGLPVDERVVAFVGRIQPLKAPDIVLRAAAKL-----PGVRIIVAGgpsgsGLASPDGLVRLADELGISARVT 326
                                    677899999****************************87.....89*********999889999**************** PP

                                    EEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                Glycos_transf_1  77 flgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                    fl  +s++dl +l+++ad++++ps+sE+fG+v++EA a+g+pv+a ++gg++  v+dg tG lv  +++ ++a+ai+ ll
  gi|121636402|ref|YP_976625.1| 327 FLPPQSHTDLATLFRAADLVAVPSYSESFGLVAVEAQACGTPVVAAAVGGLPVAVRDGITGTLVSGHEVGQWADAIDHLL 406
                                    *******************************************************************8888888888887 PP

                                    H CS
                Glycos_transf_1 157 e 157
                                    +
  gi|121636402|ref|YP_976625.1| 407 R 407
                                    5 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   2.0   2.6e-34   6.6e-31       1     169 [.      65     245 ..      65     246 .. 0.87
   2 ?   -1.6   0.0      0.93   2.4e+03      56     100 ..     328     370 ..     285     372 .. 0.56

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.6e-34
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkre.... 71 
                                    +GG+++++l+ a +LarrG+eV+++t+++  + +  v     +lv++v++ p+ +l ++ +  +    ++ +l++e    
  gi|121636402|ref|YP_976625.1|  65 AGGMNVYMLQSALHLARRGIEVEIFTRATASADPPVVrvapgVLVRNVVAGPFEGLDKYDLPTQLCAFAAGVLRAEavhe 144
                                    59***********************999999988888999**77777777776666666666666555555666666667 PP

                 Glyco_transf_4  72 ..kpDvvHahspaalgaallalrrrlgiplVltvHglye..krllkarlkplsrllralerrllrradrviavSeatade 147
                                       +D+vH+h++ ++ +++la   r+ +plV+t+H+l++  + +l    +p+ +l+   e+++++ adr+i++++ +a++
  gi|121636402|ref|YP_976625.1| 145 pgYYDIVHSHYWLSGQVGWLARD-RWAVPLVHTAHTLAAvkNAALADGDGPEPPLRTVGEQQVVDEADRLIVNTDDEARQ 223
                                    89************988877655.6**************99888888999****************************** PP

                 Glyco_transf_4 148 lrerygvppekitVipnGvDle 169
                                    +++++g +p++i V+++GvDl+
  gi|121636402|ref|YP_976625.1| 224 VISLHGADPARIDVVHPGVDLD 245
                                    ********************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                 Glyco_transf_4  56 rslaflrrlrrllkrekpDvvHahspaal.gaallalrrrlgiplV 100
                                    + ++++ +l+ l++    D+v + s+    g++++ +  + g p+V
  gi|121636402|ref|YP_976625.1| 328 LPPQSHTDLATLFR--AADLVAVPSYSESfGLVAVEAQ-ACGTPVV 370
                                    44555556666666..5777765554332033333333.3666666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  10.2   3.9e-31   9.9e-28       1     160 []      66     241 ..      66     241 .. 0.87
   2 ?    1.1   8.6      0.19   4.8e+02      35     136 ..     288     426 ..     241     443 .. 0.48

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 3.9e-31
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape..leedgvrvhrlpvprrps......pladlaalralrrll.rqrr 71 
                                    gG+++y+ + a +La+rG eV+++t+a a ++p+  ++++gv v+++ +++ ++      p+   a+++++ r+   ++ 
  gi|121636402|ref|YP_976625.1|  66 GGMNVYMLQSALHLARRGIEVEIFTRATASADPPvvRVAPGVLVRNVVAGPFEGldkydlPTQLCAFAAGVLRAEaVHEP 145
                                    8********************************96555899999999999887433455566667788877776645689 PP

                Glyco_trans_4_4  72 erpdvvhahsptaglaarlarrrrgiplvvtlh......glllrrgsgavrrlyralerrllrradavlvvseaeaeelr 145
                                      +d+vh+h++++g++++lar r+ +plv+t+h      +++l++g g++++l++  e+ ++  ad+++v++++ea++++
  gi|121636402|ref|YP_976625.1| 146 GYYDIVHSHYWLSGQVGWLARDRWAVPLVHTAHtlaavkNAALADGDGPEPPLRTVGEQQVVDEADRLIVNTDDEARQVI 225
                                    999******************999*********5554444668899********************************** PP

                Glyco_trans_4_4 146 a.lgvpadrvvvvpng 160
                                      +g++++r++vv++g
  gi|121636402|ref|YP_976625.1| 226 SlHGADPARIDVVHPG 241
                                    *999*********987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                Glyco_trans_4_4  35 leedgvrvhrlpvprrpspladlaal.....................ralrrllrqrrerpdvvhahspt..aglaarla 91 
                                    +  +gvr++    p ++ +la+++ l                     ++l+ l     +  d+v + s+    gl+a+ a
  gi|121636402|ref|YP_976625.1| 288 AKLPGVRIIVAGGPSGS-GLASPDGLvrladelgisarvtflppqshTDLATL----FRAADLVAVPSYSesFGLVAVEA 362
                                    33345665554444443.45554444111222222222222222222233333....58889999999654577888888 PP

                Glyco_trans_4_4  92 rrrrgiplvvtlh............glllrrg...sgavrrlyraler..........rllrradavlvv 136
                                    + + g+p+v  +             g         ++ v+++++a+++          r+++ra+a ++ 
  gi|121636402|ref|YP_976625.1| 363 Q-ACGTPVVAAAVgglpvavrdgitG-----TlvsGHEVGQWADAIDHllrlcagprgRVMSRAAARHAA 426
                                    8.999999999963333333333321.....022223344444333333333333333555555544443 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.2   2.6e-27   6.6e-24       2     132 ..     266     406 ..     265     407 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.6e-27
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---........HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rp.....eeleelaa..gleerveftGfv..edlaella 71 
                                    +v+ fvGr+ ++ k+ d++l+a+++l    vr++++G gp  +     + l +la+  g+++rv+f+     +dla l++
  gi|121636402|ref|YP_976625.1| 266 RVVAFVGRI-QPLKAPDIVLRAAAKLP--GVRIIVAG-GPsGSglaspDGLVRLADelGISARVTFLPPQshTDLATLFR 341
                                    6899*****.789*************9..79******.65433454566677666568999*******999999****** PP

                                    H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                    aad++ +Ps  e+fgl+++Ea a+g+pvVa +vgg++ +v  g +g lv+ +++ ++a+ai +Ll
  gi|121636402|ref|YP_976625.1| 342 AADLVAVPSysESFGLVAVEAQACGTPVVAAAVGGLPVAVrdGITGTLVSGHEVGQWADAIDHLL 406
                                    **********99***********************9999999********999**********98 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.4e-09   1.4e-05       5      91 ..     349     438 ..     338     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.4e-09
                Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekirylla.npeerraiaeaarervlaeh 81 
                                    ps ses+ l+ +Ea acG+++++ +  gl+  +++g ++ l++  ++ ++a++i++ll+   + r ++  +a +r  a +
  gi|121636402|ref|YP_976625.1| 349 PSYSESFGLVAVEAQACGTPVVAAAVGGLPVAVRDGITGTLVSghEVGQWADAIDHLLRlCAGPRGRVMSRAAARHAATF 428
                                    8889********************99*****************9999************98899999999999999**** PP

                Glyco_trans_1_2  82 tydhraeqll 91 
                                    ++++  + ll
  gi|121636402|ref|YP_976625.1| 429 SWENTTDALL 438
                                    ***9998887 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4     4e-06      0.01     105     175 ..     119     183 ..      65     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                 Glyco_transf_5 105 gedyednaerfalfsraalelleklgwk.pdvihahDWhtalvpallkelykerglfkkiktvftiHNlayq 175
                                    g d  d   ++ +f++++l++    + +  d++h h W ++ v+ l+++  +       +++v+t H la  
  gi|121636402|ref|YP_976625.1| 119 GLDKYDLPTQLCAFAAGVLRAEAVHEPGyYDIVHSHYWLSGQVGWLARDRWA-------VPLVHTAHTLAAV 183
                                    45667777888889999988877743335********************963.......********99875 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00027       0.7      10     111 ..      69     182 ..      63     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitpkkga...kdeleaegihvhrl.......kvdrkg..pleylk.a...fklkklikki 73 
                                    +v++l+ a  La rg+eV+++t+ + +     + +a+g+ v ++           k+  p ++ + a   ++  ++ +  
  gi|121636402|ref|YP_976625.1|  69 NVYMLQSALHLARRGIEVEIFTRATASadpPVVRVAPGVLVRNVvagpfegL--DKYdlPTQLCAfAagvLRAEAVHEPG 146
                                    5788888999************955542444466688888888855544320..33334555543333335778888999 PP

                Glyco_trans_4_2  74 kPDvvhahyakpygllgslaarlsgvipvvlsvwGldv 111
                                     +D+vh hy  + g +g la  +   +p+v +++ l  
  gi|121636402|ref|YP_976625.1| 147 YYDIVHSHYWLS-GQVGWLARDRWA-VPLVHTAHTLAA 182
                                    99*******777.778877655665.999999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3396.07
//
Query:       gi|121636403|ref|YP_976626.1|  [L=183]
Description: hypothetical protein BCG_0528 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.2   0.0      2e-23   82.8   0.0    1.2  1  YbjN      Putative bacterial sensory transduction regulator


Domain annotation for each model (and alignments):
>> YbjN  Putative bacterial sensory transduction regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   1.1e-27     2e-23       4     127 .]      11     136 ..       9     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.1e-27
                                    HHHHHHHHH--S-EEEEETTEE....EEEEEETTEEEEEEE--SSTT-EEEEEEEEES--TTHHHHHHHHHHHTTTTTTT CS
                           YbjN   4 lleevLeeagleyertedddga...ivvvgtwggyrftiallgeseelllvlafvarvpeedreallellnrwNrellfg 80 
                                    +++++Le ++l+y+    ++ga    +v+++++++++++++l  +e++ +v+afv+r+p+e+re+++++l+r+Nr+l+ +
  gi|121636403|ref|YP_976626.1|  11 VIQNALEVSQLKYSQHPRPGGAppaLIVELPGERKLKINTILSVGEHSVRVEAFVCRKPDENREDVYRFLLRRNRRLYGV 90 
                                    68999999999999999999999999****************************************************** PP

                                    -EEEEETTEEEEEEEEE-.TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                           YbjN  81 kayldedgdvlvehdldldagltpeqldrllalvleaadqffdalqe 127
                                    +++ld+ gd+++++++ l   ++++++dr l++vle +d++f+al e
  gi|121636403|ref|YP_976626.1|  91 AYTLDNVGDIYLVGQMAL-SAVDADEVDRVLGQVLEVVDSDFNALLE 136
                                    ******************.*************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1380.85
//
Query:       gi|121636404|ref|YP_976627.1|  [L=201]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-51  172.2  14.9    9.2e-51  172.1  14.9    1.0  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1  14.9   5.1e-55   9.2e-51       2     191 ..       3     187 ..       2     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 5.1e-55
                           LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrda 81 
                                    +l +++Gpqn++vl+qgi+r+  +++++++++ i+d  li +g+ G+a+L++a+p+++ + r++G+a+L+ +++la+r+a
  gi|121636404|ref|YP_976627.1|   3 TLKVAIGPQNAFVLRQGIRRE--YVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLVARFGGAAFLIGYALLAARNA 80 
                                    6889*****************..********************************************************* PP

                           LysE  82 kekkveaeksve.aslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaar 160
                                    ++++ + ++++  a+l+ +++++l+++++NP+++l+++++i+al++    ++++ r+++ ag+++as++wf++l+f+a r
  gi|121636404|ref|YP_976627.1|  81 WRPSGLVPSESGpAALIGVVQMCLVVTFLNPHVYLDTVVLIGALAN----EESDLRWFFGAGAWAASVVWFAVLGFSAGR 156
                                    **********9999********************************....79**************************** PP

                           LysE 161 lsrrlsskkvlriinvvvgvlligfavklll 191
                                    l++ ++++ ++ri++++v+v++ig+av +l+
  gi|121636404|ref|YP_976627.1| 157 LQPFFATPAAWRILDALVAVTMIGVAVVVLV 187
                                    ***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1440.78
//
Query:       gi|121636405|ref|YP_976628.1|  [L=249]
Description: phosphoglyceromutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-34  118.6   0.4    6.4e-28   97.8   0.2    2.0  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.2   3.6e-32   6.4e-28       1     124 [.       7     135 ..       7     145 .. 0.93
   2 !   19.5   0.0   3.4e-08   0.00061     115     170 ..     146     206 ..     134     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3.6e-32
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EE..EE-SSHHHHHHHHHHHHCTT...--EEE-G CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidai..ysSplkRarqTaeliaealg...lpvelde 75 
                                    l+L+RHGe++wna + + g+ dv Lt++G+++A + +e +a++++  +  y+S l+Ra+ Ta+l+++  +   +pv+   
  gi|121636405|ref|YP_976628.1|   7 LVLLRHGESDWNALNLFTGWVDVGLTDKGQAEAVRSGELIAEHDLLPDvlYTSLLRRAITTAHLALDSADrlwIPVRRSW 86 
                                    79****************************************66544444*****************999********** PP

                                    GGS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHH CS
                     His_Phos_1  76 gLrEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaa 124
                                    +L+E+++G+++gl +ae +++y ee    +r+++d +pp+ E+  ++ +
  gi|121636405|ref|YP_976628.1|  87 RLNERHYGALQGLDKAETKARYGEEQFMAWRRSYDTPPPPIERGSQFSQ 135
                                    *****************************************99999876 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.4e-08
                                    B...S-BHHHHHHHHHHHHHHHH..HHTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB- CS
                     His_Phos_1 115 g...gEsledvaaRvaaaleela..arhegetvlvVsHggvirallarllglpleelrrle 170
                                    g    E+l+dv+aR  + + +++  +   g+tvl+V+Hg  +ral+++l +++ +e+  l+
  gi|121636405|ref|YP_976628.1| 146 GgplTECLADVVARFLPYFTDVIvgDLRVGKTVLIVAHGNSLRALVKHLDQMSDDEIVGLN 206
                                    244579************99876224456777*****************999888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1789.27
//
Query:       gi|121636406|ref|YP_976629.1|  [L=410]
Description: two component sensor histidine kinase senX3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-25   87.3   0.0    1.9e-24   86.3   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.1e-14   52.4   0.4    1.1e-13   51.0   0.4    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
    0.00012   22.0   0.0    0.00028   20.7   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0014   18.6   0.3     0.0099   15.8   0.3    2.3  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.019   15.2   0.1      0.053   13.8   0.1    1.9  1  PAS_4        PAS fold
      0.054   13.4   0.0       0.12   12.3   0.0    1.6  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   6.2e-28   1.9e-24       1     110 [.     268     378 ..     268     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 6.2e-28
                                    EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                      HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                    gd++ L  ++ nlv+Na+ +++ ++ ++++ +++  +++i v+D GiGi +ed++++fe+f + d++++r +gg+GlGl+
  gi|121636406|ref|YP_976629.1| 268 GDQTLLVTALANLVSNAIAYSPRGSLVSISRRRRGANIEIAVTDRGIGIAPEDQERVFERFFRgDKARSRATGGSGLGLA 347
                                    68999***************7777777777775559***************************99999999********* PP

                                    HHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlpl 110
                                    ivk ++  ++G+i+v s+pg G+tft+ lp 
  gi|121636406|ref|YP_976629.1| 348 IVKHVAANHDGTIRVWSKPGTGSTFTLALPA 378
                                    ****9999*******************9985 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.4   3.6e-17   1.1e-13       1      66 [.     157     222 ..     157     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.6e-17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                          HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                    ++++f+a+v+HEL+tP+ a+ + aeaL  +++ +e ++++ e++  ea+rl ++v +l +lsr+++
  gi|121636406|ref|YP_976629.1| 157 ARRDFVANVSHELKTPVGAMALLAEALLASADDSETVRRFAEKVLIEANRLGDMVAELIELSRLQG 222
                                    589************************8887889*****************************986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.4e-08   0.00028       4      82 ..     274     349 ..     271     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.4e-08
                    HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklA 80 
                                     +Ala lv N++  + +   v+i+  + rg++ ei ++D G G+ +e+ ++++ r+ + +k     s+ +G  G+G  lA
  gi|121636406|ref|YP_976629.1| 274 VTALANLVSNAIAYSPRGslVSISRRR-RGANIEIAVTDRGIGIAPEDQERVFeRFFRGDKA---RSRATGGSGLG--LA 347
                                    579*******99854444227776666.4899*******************99679999999...58899999999..55 PP

                    HATPase_c_3  81 sl 82 
                                    ++
  gi|121636406|ref|YP_976629.1| 348 IV 349
                                    44 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   3.3e-06    0.0099      35     109 ..     276     353 ..     183     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                    HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalik 106
                                    a++ +++Na+ +  ++     v+++ ++++  +++ v+D+G g  pe++++  e           +     +G+Gla++k
  gi|121636406|ref|YP_976629.1| 276 ALANLVSNAIAYSPRG---SLVSISRRRRGANIEIAVTDRGIGIAPEDQERVFE--RffrgdkarSRATGGSGLGLAIVK 350
                                    5556677888887775...6689999999999***********99998665443..34688898888899999******9 PP

                    HATPase_c_2 107 glv 109
                                    +++
  gi|121636406|ref|YP_976629.1| 351 HVA 353
                                    986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.8e-05     0.053       4      53 ..      59     111 ..      56     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                          PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktla...ellpeedaarle 53 
                                    +p + av+d++  v+y+N++a el+ +++ +l ++ ++   + l  ed +   
  gi|121636406|ref|YP_976629.1|  59 MPLGAAVVDTHRDVVYLNERAKELGLVRDRQLDDQAWRaarQALGGEDVESDL 111
                                    6899****************************999999443344444444444 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05      0.12       6      90 ..     273     365 ..     269     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                    HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek.......kklesskskkeehGiGlks 73 
                                    l++ l nl  NAi  + + +     ++++ r++  ++ i ++    g     ++       +  + +++ ++  G+Gl  
  gi|121636406|ref|YP_976629.1| 273 LVTALANLVSNAIAYSPRGS----LVSISRRRRGANIEIAVTDRGIGiapedQErvferffRGDKARSRATGGSGLGLAI 348
                                    67788999999998777733....4555555555555555544433333333112232233444466788999******* PP

                    HATPase_c_5  74 ireivkkykgnlsieae 90 
                                    +++++ +++g++++  +
  gi|121636406|ref|YP_976629.1| 349 VKHVAANHDGTIRVWSK 365
                                    **********9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2826.02
//
Query:       gi|121636407|ref|YP_976630.1|  [L=227]
Description: two component sensory transduction protein RegX3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-28   99.0   0.1    6.7e-28   96.6   0.0    2.0  2  Trans_reg_C   Transcriptional regulatory protein, C terminal
    1.2e-27   96.3   0.0    1.7e-27   95.8   0.0    1.2  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.14   11.3   0.1          4    6.5   0.0    2.1  2  ALAD          Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.18   1.1e+03      47      61 ..     106     120 ..      92     126 .. 0.74
   2 !   96.6   0.0   1.1e-31   6.7e-28       2      77 .]     150     225 ..     149     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHTTT CS
                    Trans_reg_C  47 dvhisrLRkkLedde 61 
                                    +  i+r+R  L+  +
  gi|121636407|ref|YP_976630.1| 106 RELIARIRAVLRRGG 120
                                    567999999999865 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 1.1e-31
                                    EEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   2 eeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    ++++l  kef+lLe+L++n+grv++r +L+++vwg d+ +d++t+dvh++rLR k+e+d+++p ++ tvrg GY+l
  gi|121636407|ref|YP_976630.1| 150 DTITLPLKEFDLLEYLMRNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEADPANPVHLVTVRGLGYKL 225
                                    67999*********************************************************************97 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   2.8e-31   1.7e-27       1     112 []       4     113 ..       4     113 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 2.8e-31
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vliv+D++ +++ l+ ll++eg+ e ++++dg +al+ +++   d++llD+++pgm+G +++k++r+++ ++pvi++ta+
  gi|121636407|ref|YP_976630.1|   4 VLIVEDEESLADPLTFLLRKEGF-EATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRARS-SVPVIMVTAR 81 
                                    8**********************.9******************************************99.********** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkale 112
                                    ++e d+v +l++gadd+++Kp++ +eL+++++
  gi|121636407|ref|YP_976630.1|  82 DSEIDKVVGLELGADDYVTKPYSARELIARIR 113
                                    ****************************9985 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0   0.00066         4     236     266 ..      44      77 ..      32      80 .. 0.83
   2 ?    2.5   0.0     0.011        65     152     181 ..     182     211 ..     165     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00066
                                    TT-SBEEEE...S-TTGHHHHHHHHTT-SS-EEE CS
                           ALAD 236 eGADivmvK...PalaylDiirevkeefdlpvaa 266
                                     GADiv++    P+++  D+ ++++ ++++pv++
  gi|121636407|ref|YP_976630.1|  44 AGADIVLLDlmlPGMSGTDVCKQLRARSSVPVIM 77 
                                    69***9754444*******************986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.011
                                    HCT-SEEEE-S--TTHHHHHHHHHHHTT-T CS
                           ALAD 152 eaGadivapSdmmDgrvaaireaLdeagfe 181
                                      Gad v+  + +D +v+ +r++++++  +
  gi|121636407|ref|YP_976630.1| 182 VWGADYVGDTKTLDVHVKRLRSKIEADPAN 211
                                    56********************99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1538.09
//
Query:       gi|121636408|ref|YP_976631.1|  [L=629]
Description: oxidoreductase GMC-type [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-53  181.7   0.0    2.6e-53  181.3   0.0    1.1  1  GMC_oxred_N      GMC oxidoreductase
    3.9e-17   63.1   0.1    1.1e-16   61.7   0.0    1.8  1  GMC_oxred_C      GMC oxidoreductase
    2.9e-08   33.2   1.1    9.8e-05   21.6   0.6    2.6  2  FAD_binding_2    FAD binding domain
    1.1e-06   28.5   9.7    3.6e-05   23.5   8.8    2.9  2  DAO              FAD dependent oxidoreductase
    1.6e-06   27.6   0.3    0.00047   19.5   0.2    3.1  3  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    7.4e-06   25.4   0.3    1.1e-05   24.8   0.3    1.3  1  FAD_binding_3    FAD binding domain
    1.6e-05   25.1   3.3    0.00016   21.8   0.8    2.7  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0023   16.7   1.0     0.0058   15.4   0.8    1.6  2  HI0933_like      HI0933-like protein
      0.006   15.9   0.2       0.02   14.2   0.2    1.8  2  Thi4             Thi4 family
     0.0074   16.5   0.0      0.013   15.8   0.0    1.4  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
     0.0085   15.4   1.9        1.1    8.4   0.0    2.6  2  Amino_oxidase    Flavin containing amine oxidoreductase
     0.0087   15.7   0.4      0.053   13.2   0.1    2.1  2  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.012   14.7   0.4       0.19   10.7   0.1    2.4  2  Lycopene_cycl    Lycopene cyclase protein
      0.082   13.5   0.7       0.18   12.4   0.7    1.6  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.094   12.1   0.1        0.2   11.0   0.1    1.4  1  ThiF             ThiF family
       0.13   11.5   0.0       0.31   10.3   0.0    1.5  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
       0.14   11.5   3.1       0.22   10.8   3.1    1.3  1  FAD_oxidored     FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.3   0.0   2.5e-56   2.6e-53       2     296 .]     148     408 ..     147     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.3 bits;  conditional E-value: 2.5e-56
                    GMC_oxred_N   2 delveggGsagsvvAaRLsedpstsvlvleaggreknrlimvlalalklidkklntayete.pekalngrrlilpaGktl 80 
                                    d++v+g+G+ g++vA  L+  +   v+vle g r      +v  +++++ + +++  y  + ++ al + +++lp+G+++
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAG-LDVVVLEEGRRW-----TVEEFRSTHPVDRYAGLYRGAgATVALGRPAVVLPMGRAV 221
                                    889**********999998876.678888887665.....45566667777777777765426778999*********** PP

                    GMC_oxred_N  81 GGgsvvNwsayiRtpaadldeWeeeaglegwssdevlpafkkvetaqalesdlhgvdgrlgvtekgkeespln.kallka 159
                                    GG++vvN+++++R++ a+ ++W++e+gl +++ d++ + ++++e             ++l+v++   e +++n + ll+a
  gi|121636408|ref|YP_976631.1| 222 GGTTVVNSGTCFRPSLAVQRRWRDEFGLGLADPDQLGRRLDDAE-------------QTLRVAPVPLEIMGRNgRLLLQA 288
                                    ********************************************.............****************99***** PP

                    GMC_oxred_N 160 aeelGlp...vprdlngkhqcGvcllgvtcrtgarqstarawLrpalerpnleiltgakaekiilegrkkravGVeasdk 236
                                    a++lG++   +pr+++g++ c++c +g  c+++a+++++ + L++a+++ +++i+++a++e+i   +r +ra+GV+a++ 
  gi|121636408|ref|YP_976631.1| 289 AKSLGWRaapIPRNAPGCRGCCQCAIG--CPSNAKFGVHLNALPQACAA-GARIISWARVERI--LHRAGRAYGVRARRP 363
                                    ***************************..********************.*************..568************ PP

                    GMC_oxred_N 237 kgtvkrlvvaakevvvaaGalnsPqlLqrSGlGkaehLkevgvdvvvdlpvGknLqdHpv 296
                                    +gt  +l v a+ vvvaaGa ++P lL+rSGlG +++             +G+nL +Hp+
  gi|121636408|ref|YP_976631.1| 364 DGT--TLDVLADAVVVAAGATETPGLLRRSGLGGHPR-------------LGHNLALHPA 408
                                    ***..********************************.............********95 PP

>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0     1e-19   1.1e-16      22     142 ..     497     615 ..     485     617 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1e-19
                                    --TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.H.CHHCHHCHHCHHHHH-E.E-S--B-TT-B-ST CS
                    GMC_oxred_C  22 pnylsdprdlaalvealkaarkilaaaaldvleeeltpgaaeetsda.avesdealekfvkeavl.tsaHplGtcrMGad 99 
                                    ++y+  p ++a+l+ al+a+ +++ aa+     +e+  g  + ++ +   e ++ l+++  ++ + + +Hp+Gt++ Gad
  gi|121636408|ref|YP_976631.1| 497 VRYDIAPGEIAKLRVALQAIGRLFFAAG----AVEVLTGIPGAPPMRsLPELQDVLRRANPRSLHlAAFHPTGTAAAGAD 572
                                    6888999999999999999999999994....33333333333333303333344455555555569************* PP

                                    CGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHH CS
                    GMC_oxred_C 100 pkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAe 142
                                    ++   VD+++r++gv++++V+DaS++Ps+p +np+l+i+a+A 
  gi|121636408|ref|YP_976631.1| 573 EQLCPVDATGRLRGVEGVWVADASILPSCPEVNPQLSIMAMAL 615
                                    *****************************************96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.6   9.3e-08   9.8e-05       1      32 [.     148     179 ..     148     188 .. 0.93
   2 !    9.3   0.0    0.0005      0.53     153     204 ..     334     384 ..     294     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.3e-08
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                    D++V+GsG++G + A ++a+aGl+v+v+e + 
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAGLDVVVLEEGR 179
                                    89**************************9876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0005
                                    TCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 153 kagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                    +ag ++   +++++++++ gr++G+ ++ + +g++  + a+avv+a+g+ + 
  gi|121636408|ref|YP_976631.1| 334 AAGARIISWARVERILHRAGRAYGVRAR-RPDGTTLDVLADAVVVAAGATET 384
                                    66778888899*****************.67888899***********9875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.8   1.9e+03     277     300 ..      71      94 ..      30     109 .. 0.78
   2 !   23.5   8.8   3.4e-08   3.6e-05       1     231 [.     148     409 ..     148     472 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                                    STSCSHHHHHHHHHHHHHHSGGGC CS
                            DAO 277 dpevdeedidellealrklfPqlg 300
                                     p+  +++++++l+++++l+P+++
  gi|121636408|ref|YP_976631.1|  71 LPRLHPDERARVLHRIAALSPEVA 94 
                                    368889999999999999999853 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.4e-08
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEE..ESSSSTHHSTH..................... CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgll..hsglrylpeas..................... 55 
                                    d v++G+G  G+ +A+ Lar+g  V++le g++       r++  +  ++gl+  +                        
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAGldVVVLEEGRRWT-VEEFRSTHPVdrYAGLYRGA--Gatvalgrpavvlpmgravggt 224
                                    78*****************************9988.88888887773323333222..2123333344444444444433 PP

                                    .......HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHH.HHHHHHHH.............HHTTT..T CS
                            DAO  56 .......elarlslealeelreleeelgididyrrtGllslaadeeelea.ldkllall.............leagl..d 112
                                           ++ r sl             +++  +r    l la+ +++l + ld+  + l             +++ l   
  gi|121636408|ref|YP_976631.1| 225 tvvnsgtCF-RPSL-------------AVQRRWRDEFGLGLAD-PDQLGRrLDDAEQTLrvapvpleimgrnGRLLLqaA 289
                                    333333211.2222.............2223344444444432.212222122111111222222222111111111101 PP

                                    EEE.EEHHHHHHHSTTST.TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.E CS
                            DAO 113 ael.ldaeevrelepalp.gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttp.g 188
                                     +l ++a+ + + +p+ + +++ a+++p+ + +  +  ++al +a+ a+G++i+  ++v+++ ++ g+++gv+ r  p g
  gi|121636408|ref|YP_976631.1| 290 KSLgWRAAPIPRNAPGCRgCCQCAIGCPSNAKFGVH--LNALPQAC-AAGARIISWARVERILHRAGRAYGVRaR-RPdG 365
                                    122233333445555422355577777775443333..55565555.789***********98999******964.4448 PP

                                    EE.E..EEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEEEEEEEECC CS
                            DAO 189 en.d..aadavVnaaGawsdll.gllkeldlpispvrgqvlvlkpls 231
                                    ++ d  a davV+aaGa   ++ gll++  l  +p+ g+ l+l p +
  gi|121636408|ref|YP_976631.1| 366 TTlDvlA-DAVVVAAGAT--ETpGLLRRSGLGGHPRLGHNLALHPAT 409
                                    8765655.99******87..553344322234588888888885543 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   4.5e-07   0.00047       2      35 ..     148     181 ..     147     197 .. 0.87
   2 ?    2.4   0.0     0.071        75     220     243 ..     362     387 ..     334     411 .. 0.62
   3 ?    2.0   0.0     0.095     1e+02      65     119 ..     486     535 ..     391     559 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.5e-07
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtc 35 
                                    d vv+G+G++G  +a+tla+ag++v+++e+++ +
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAGLDVVVLEEGRRW 181
                                    679*************************876655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.071
                                    ETTSCE..EEESEEEE-S-EEES-HH CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 220 ledgee..idadlvvvavGvrpstel 243
                                      dg++  + ad vvva+G +  + l
  gi|121636408|ref|YP_976631.1| 362 RPDGTTldVLADAVVVAAGATETPGL 387
                                    34444433445555555555544444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.095
                                    HHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  65 qgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv 119
                                      ++ + ge+vv++d + +++             a ++l+ A G+   + gipG+
  gi|121636408|ref|YP_976631.1| 486 GTVRSVRGETVVRYDIAPGEIAKLRV-----ALQAIGRLFFAAGAVEVLTGIPGA 535
                                    34777777778888866666655322.....245669*****************9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.3   1.1e-08   1.1e-05       2      70 ..     147     216 ..     146     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEES.SSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECC CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvek.rsttvvlpradglnqrtmellrqlGledrilaegapne 70 
                                    +d ++VG+G  G+m a+ L++aG +vv++e  r++tv+++r+    +r   l+r +G    + + +++  
  gi|121636408|ref|YP_976631.1| 147 ADAVVVGSGAGGAMVARTLARAGLDVVVLEEgRRWTVEEFRSTHPVDRYAGLYRGAGATVALGRPAVVLP 216
                                    6889*************************87488999999*99999998888888887777666665555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.16   1.7e+02       4      16 ..      54      66 ..      54      82 .. 0.88
   2 !   21.8   0.8   1.5e-07   0.00016       1      30 [.     151     180 ..     151     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                   -SHHHHHHHHHHH CS
                  NAD_binding_8  4 aGlsGlvaAylLa 16
                                   aGl++l+aA++L+
  gi|121636408|ref|YP_976631.1| 54 AGLASLAAASYLT 66
                                   8**********97 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    +vG+G++G+  A++La+ag+dv++le ++r
  gi|121636408|ref|YP_976631.1| 151 VVGSGAGGAMVARTLARAGLDVVVLEEGRR 180
                                    8*************************9876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   5.5e-06    0.0058       2      34 ..     148     180 ..     147     183 .. 0.93
   2 ?   -1.9   0.0      0.97     1e+03     122     169 ..     335     386 ..     326     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                    d +v+G Ga G m A ++a++g +V++le++++
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAGLDVVVLEEGRR 180
                                    78***************************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.97
                                    HT-EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE----SS-GG CS
                    HI0933_like 122 agvklrletevksvekeedgkfrvktk....seeeleadklvlAtGGlSiPk 169
                                    ag ++    +v+++ +++++++ v+++    ++  + ad++v+A G +  P 
  gi|121636408|ref|YP_976631.1| 335 AGARIISWARVERILHRAGRAYGVRARrpdgTTLDVLADAVVVAAGATETPG 386
                                    56666677778888888888888877334334556889********988885 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.9e-05      0.02      15      49 ..     144     177 ..     132     180 .. 0.90
   2 ?   -3.2   0.0       3.9   4.1e+03     187     225 ..     582     618 ..     574     621 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                    HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4  15 yaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                                       +D v+vG+G+ G   a++la++ +l v++le+
  gi|121636408|ref|YP_976631.1| 144 VTRADAVVVGSGAGGAMVARTLARA-GLDVVVLEE 177
                                    5679*********************.*******96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                    S-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHH CS
                           Thi4 187 ekvkgeksldaekaedaivkktrevvpnlyvaGmevaev 225
                                     +++g  +++  +a+++i+    ev p+l +  m++a  
  gi|121636408|ref|YP_976631.1| 582 GRLRGVEGVW--VADASILPSCPEVNPQLSIMAMALAVA 618
                                    5666777777..477889999999999999999998765 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05     0.013      22      87 ..      26      90 ..      13     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                Gluconate_2-dh3 22 pgakeagvaafidrqladaplppeqeayrkglaaldayaraeygksFveldgaqqdalLealekea 87
                                    g   a+ ++ +dr++++ p ++ + a+r+gla l a++  + g+s  +l ++++ ++L+ +++ +
  gi|121636408|ref|YP_976631.1| 26 GGPLPAQFVQRVDRYVTRLPATS-RFAVRAGLASLAAASYLTTGRSLPRLHPDERARVLHRIAALS 90
                                   567789999*************9.************************************998764 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.4    0.0081       8.6       5      23 ..     160     178 ..     156     181 .. 0.87
   2 !    8.4   0.0    0.0011       1.1     209     262 ..     326     381 ..     317     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0081
                                    HHHHHHHHTTEEEEEEESS CS
                  Amino_oxidase   5 aaArqLlsaGfdVtvlEar 23 
                                    ++Ar+L++aG+dV+vlE  
  gi|121636408|ref|YP_976631.1| 160 MVARTLARAGLDVVVLEEG 178
                                    68***************76 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                    THHHHHHHHHTTTTEEEETSEEEEEEEE...ETTCEEEEETTSTEE..EESEEEE-S-H CS
                  Amino_oxidase 209 lsqlpealaeelrgldirlntrVkeikr...egdgvtvtledgevv..eaDaVvvTvpl 262
                                    l++lp+a a+   g +i   +rV +i +    + gv+ +  dg+++   aDaVvv++  
  gi|121636408|ref|YP_976631.1| 326 LNALPQACAA---GARIISWARVERILHragRAYGVRARRPDGTTLdvLADAVVVAAGA 381
                                    689*******...***************8777777999999***************875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.59   6.2e+02      84     110 ..      88     116 ..      83     127 .. 0.74
   2 !   13.2   0.1     5e-05     0.053       2      31 ..     150     179 ..     149     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.59
                                    HHHH.HGGGECTCEEEEEESSSSCHH.HH CS
                           ApbA  84 alee.ikplldpntvvlllqNGlghe.ee 110
                                    al++ ++++++   +++ll NG +++ +e
  gi|121636408|ref|YP_976631.1|  88 ALSPeVAAAVEGLKAIVLLANGADTYaHE 116
                                    55555888999999********9887444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5e-05
                                    EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr 31 
                                    +++G+Ga G ++a +La+ag dv+++  +r
  gi|121636408|ref|YP_976631.1| 150 VVVGSGAGGAMVARTLARAGLDVVVLEEGR 179
                                    69********************99987665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00018      0.19       1      34 [.     148     179 ..     148     188 .. 0.91
   2 ?    1.4   0.0      0.13   1.3e+02      93     145 ..     329     385 ..     325     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasp 34 
                                    D vv+G+G+ g  +A  l  a++gl vv++e + 
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTL--ARAGLDVVVLEEGR 179
                                    88****************..**********9876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                  Lycopene_cycl  93 llerlvengvklleakvesveeeea..geslvvleggr..kirarlvvdarglaslk 145
                                    l + ++ ++++   a+ve++ +       +++  ++g    + a +vv+a g+ + +
  gi|121636408|ref|YP_976631.1| 329 LPQACAAGARIISWARVERILHRAGraYGVRARRPDGTtlDVLADAVVVAAGATETP 385
                                    66889989999999******99988534567778888867788*********87766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   0.00017      0.18       2      32 ..     149     179 ..     148     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversd 32 
                                    +vvvG+G  g ++A +la+ g +V v+e + 
  gi|121636408|ref|YP_976631.1| 149 AVVVGSGAGGAMVARTLARAGLDVVVLEEGR 179
                                    69************************99875 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00019       0.2      11      43 ..     139     171 ..     128     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                    HHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  11 dgqekLrdskvllvGaGglGsellknLalsGvg 43 
                                    ++   + ++  ++vG G+ G  ++++La++G+ 
  gi|121636408|ref|YP_976631.1| 139 ADSPSVTRADAVVVGSGAGGAMVARTLARAGLD 171
                                    55666778889********************85 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.31       1      31 [.     150     179 ..     150     188 .. 0.91
   2 ?   -2.8   0.0       2.7   2.9e+03     122     141 ..     369     388 ..     342     398 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgn 31 
                                    +++G G+ G  +a +l +agl d+++lE g+
  gi|121636408|ref|YP_976631.1| 150 VVVGSGAGGAMVARTLARAGL-DVVVLEEGR 179
                                    79*******************.8*****995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                    Pyr_redox_3 122 tyeAkkviiAtGefdkPnkl 141
                                    ++ A+ v++A+G  + P +l
  gi|121636408|ref|YP_976631.1| 369 DVLADAVVVAAGATETPGLL 388
                                    34577777777776666555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.1   0.00021      0.22       1      32 [.     148     179 ..     148     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                    D vVvG+g++G + A + araG  v+++ee +
  gi|121636408|ref|YP_976631.1| 148 DAVVVGSGAGGAMVARTLARAGLDVVVLEEGR 179
                                    779**************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4454.65
//
Query:       gi|121636409|ref|YP_976632.1|  [L=109]
Description: hypothetical protein BCG_0534c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 709.73
//
Query:       gi|121636410|ref|YP_976633.1|  [L=329]
Description: hypothetical protein BCG_0535c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2335.40
//
Query:       gi|121636411|ref|YP_976634.1|  [L=242]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-18   66.2   0.5    3.3e-18   65.1   0.1    1.8  2  GntR            Bacterial regulatory proteins, gntR family
    9.5e-14   51.9   7.2    1.9e-13   50.9   7.2    1.5  1  FCD             FCD domain
    3.1e-07   30.3   0.0    5.8e-07   29.4   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00017   21.4   1.2    0.00043   20.1   0.1    2.2  2  MarR_2          MarR family
    0.00022   21.5   0.0    0.00045   20.5   0.0    1.5  1  Rrf2            Transcriptional regulator
    0.00049   20.2   0.0     0.0011   19.1   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0015   18.4   0.1     0.0038   17.2   0.1    1.6  1  HTH_11          HTH domain
     0.0035   17.2   0.0     0.0062   16.4   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0096   15.8   0.0      0.027   14.3   0.0    1.6  2  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.015   14.8   0.1      0.026   14.1   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.02   14.8   0.0      0.041   13.8   0.0    1.4  1  MarR            MarR family
       0.03   14.4   3.4      0.033   14.3   0.2    2.5  3  HTH_20          Helix-turn-helix domain
      0.037   13.9   0.0      0.081   12.8   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      0.045   13.6   0.2       0.11   12.3   0.2    1.7  1  HTH_IclR        IclR helix-turn-helix domain
       0.11   12.7   0.3       0.28   11.4   0.3    1.6  1  PaaX            PaaX-like protein


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.1   2.8e-21   3.3e-18       3      64 .]      21      82 ..      19      82 .. 0.97
   2 ?   -2.9   0.0       4.7   5.6e+03      27      46 ..      98     117 ..      94     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.8e-21
                                   HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR  3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                   e+++  + + Il+g++ pG++LP+er+La+++gV+rt++R+ L rL++ gl+e+r+g+G +V
  gi|121636411|ref|YP_976634.1| 21 ERIATTIADAILDGVFPPGSTLPPERDLAERLGVNRTSLRQGLARLQQMGLIEVRHGSGSVV 82
                                   789999*****************************************************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.7
                                    HHHHHHHHTS-HHHHHHHHH CS
                           GntR  27 ereLaaefgVsrttvReALr 46 
                                    +r+L   f V    +R AL 
  gi|121636411|ref|YP_976634.1|  98 VRKLGPDFLVELLEIRAALG 117
                                    56666666677777788876 PP

>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   7.2   1.6e-16   1.9e-13       1     124 [.     108     228 ..     108     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.6e-16
                            FCD   1 dlyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlr 80 
                                    +l+e+Ra+L p++ rlaa r t++d ++l ++le  ++a+ + +     +ad+a+ r+l++ ++n+ l  l++ +++ + 
  gi|121636411|ref|YP_976634.1| 108 ELLEIRAALGPLIGRLAAARSTPEDAEALCAALEVVQQADTAAA---RQAADLAYFRVLIHSTRNRALGLLYRWVEHAFG 184
                                    799************************************88666...79******************************* PP

                            FCD  81 rlrrlalssperleeslaeHraildAirardadaAraamrrHle 124
                                      ++    + ++++ +l + rai  A++a+d++aA+a +++ l+
  gi|121636411|ref|YP_976634.1| 185 GREHALTGAYDDADPVLTDLRAINGAVLAGDPAAAAATVEAYLN 228
                                    99999999*****************************9998876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.9e-10   5.8e-07      24      66 ..      45      89 ..      21      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.9e-10
                                   HHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.TEE.EEES-HHHHH CS
                      HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglis.r.grr.irildleaLr 66
                                    ++lA++lG++r ++ + l++L++ gli+ r g    +++d+e+L 
  gi|121636411|ref|YP_976634.1| 45 ERDLAERLGVNRTSLRQGLARLQQMGLIEvRhG-SgSVVRDPEGLT 89
                                   579**************************6533.34********95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.6e-07   0.00043      25      56 ..      46      77 ..      41      80 .. 0.93
   2 ?   -1.6   0.1       2.2   2.7e+03      24      37 ..     133     146 ..     109     159 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.6e-07
                                   HHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 25 gelarrlglsksavsrilkrLvaaGLverrpg 56
                                   ++la+rlg+ + ++ + l+rL++ GL+e r g
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIEVRHG 77
                                   59**************************9966 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                    HHHHHHHHTSSHHH CS
                         MarR_2  24 vgelarrlglsksa 37 
                                    + +l+++l + ++a
  gi|121636411|ref|YP_976634.1| 133 AEALCAALEVVQQA 146
                                    45566666665555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.7e-07   0.00045      29      62 ..      46      79 ..      39     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.7e-07
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                           Rrf2 29 eeiaerqnispsylekilakLrkaglvksvrGkg 62
                                   +++aer +++++ l++ la+L++ gl++++ G g
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIEVRHGSG 79
                                   689*****************************93 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.1e-07    0.0011      25      59 ..      45      79 ..      39      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.1e-07
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                 Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                     dlaerL+v   s  + l +L+++G++e+ + +g
  gi|121636411|ref|YP_976634.1| 45 ERDLAERLGVNRTSLRQGLARLQQMGLIEVRHGSG 79
                                   579**************************988665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.1e-06    0.0038      20      53 ..      47      79 ..      45      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-06
                         HTH_11 20 eLAeeLnvSrrtvrrdIkaLeelgvpIesepgrG 53
                                   +LAe+L+v r+  r+ +++L+ +g  Ie + g+G
  gi|121636411|ref|YP_976634.1| 47 DLAERLGVNRTSLRQGLARLQQMG-LIEVRHGSG 79
                                   7***********************.777776665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.2e-06    0.0062      26      58 ..      46      78 ..      44      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.2e-06
                                   CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   +++ae+lgv r++  + L +L ++Gl+e+++g+
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIEVRHGS 78
                                   79****************************998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.2e-05     0.027      30      60 ..      45      75 ..      31      80 .. 0.93
   2 ?   -2.0   0.0       2.8   3.3e+03       6      52 ..      81     124 ..      78     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                    TFIIE_alpha 30 eedlakelkidlnelrklLnrLyearlvkyk 60
                                   e dla+ l+++++ lr+ L+rL++ +l++++
  gi|121636411|ref|YP_976634.1| 45 ERDLAERLGVNRTSLRQGLARLQQMGLIEVR 75
                                   779*************************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                    HHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHH CS
                    TFIIE_alpha   6 vvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLy 52 
                                    vvr  +g  +  v+++L++  ++  + l ++l+i    l++l+ rL 
  gi|121636411|ref|YP_976634.1|  81 VVRDPEGLTHPAVVEALVR--KLGPDFLVELLEIR-AALGPLIGRLA 124
                                    6666666667777777773..45556666666663.45666666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.2e-05     0.026      21      48 .]      46      73 ..      44      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                   r+LAerlg+ ++ +++ l rL+++GlI+
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIE 73
                                   89*************************7 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05     0.041      21      51 ..      46      76 ..      41      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR 21 seLakklgvskstvtrvldrLekkGlieRsk 51
                                    +La++lgv+++++   l rL + Glie ++
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIEVRH 76
                                   69*************************9876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.7e-05     0.033      29      57 ..      47      75 ..      44      78 .. 0.94
   2 ?   -2.9   0.1       6.4   7.6e+03      25      33 ..     127     135 ..     111     146 .. 0.57
   3 ?   -0.6   0.0       1.2   1.5e+03       2      19 ..     158     175 ..     157     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                   HHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 29 elaerldlskntlsyHLrvLeeagLvevv 57
                                   +laerl++ +++l++ L+ L++ gL+ev+
  gi|121636411|ref|YP_976634.1| 47 DLAERLGVNRTSLRQGLARLQQMGLIEVR 75
                                   79**************************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.4
                                    B-HHHHHHH CS
                         HTH_20  25 ltaselaer 33 
                                    ++ +e ae+
  gi|121636411|ref|YP_976634.1| 127 RSTPEDAEA 135
                                    443333333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                                    HHHHHHS-HHHHHHHHHH CS
                         HTH_20   2 qiaeALahPvRrrilraL 19 
                                     ++++L h +R r l +L
  gi|121636411|ref|YP_976634.1| 158 AYFRVLIHSTRNRALGLL 175
                                    58999****997766666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.7e-05     0.081      20      46 ..      47      73 ..      46      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 20 elaeelglsqstvShHLkkLreaGLVe 46
                                   +lae lg+++  +++ L++L ++GL+e
  gi|121636411|ref|YP_976634.1| 47 DLAERLGVNRTSLRQGLARLQQMGLIE 73
                                   9************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   9.2e-05      0.11      22      49 ..      46      73 ..      41      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyve 49
                                   ++lA+r+g+++++ +  L+ L+++G++e
  gi|121636411|ref|YP_976634.1| 46 RDLAERLGVNRTSLRQGLARLQQMGLIE 73
                                   69************************98 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00023      0.28      29      55 ..      48      74 ..      46      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                           PaaX 29 llaelGiseslvRaalsRlakaGwlvr 55
                                   l + lG++ +++R +l Rl++ G++  
  gi|121636411|ref|YP_976634.1| 48 LAERLGVNRTSLRQGLARLQQMGLIEV 74
                                   7899*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1615.10
//
Query:       gi|121636412|ref|YP_976635.1|  [L=296]
Description: hypothetical protein BCG_0537c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2012.41
//
Query:       gi|121636413|ref|YP_976636.1|  [L=328]
Description: hypothetical protein BCG_0538 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-93  313.7   0.0    1.4e-93  313.4   0.0    1.1  1  Ppx-GppA  Ppx/GppA phosphatase family


Domain annotation for each model (and alignments):
>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.4   0.0     8e-98   1.4e-93       2     285 .]       2     291 ..       1     291 [. 0.99

  Alignments for each domain:
  == domain 1  score: 313.4 bits;  conditional E-value: 8e-98
                                    EEEECTTEEEEEEEEEEE--CCCCCHCCSSC-HHHHHHHHHHHHHHHHHCCCTTGCCEEEEEEHHHHHSTTHHHHHHHHC CS
                       Ppx-GppA   2 iarkaagllqivarekrkvrLaeglnesgrlqeeaiertisaLkefaellqkfkvenvrvVATsalRdavNadeFlarvk 81 
                                    +++++ g++++++++k+++rLae++++sg+++++ ++++is+++efa+++ ++++++++++ATsa+Rda+N++++l+rv+
  gi|121636413|ref|YP_976636.1|   2 VDAHRGGHPTPMSSTKATLRLAEATDSSGKITKRGADKLISTIDEFAKIAISSGCAELMAFATSAVRDAENSEDVLSRVR 81 
                                    789999************************************************************************** PP

                                    CCCSS-EEEE-HHHHHHHHHHHHHHHT.---SSEEEEEEETTEEEEEEEETTEEEEEEEES--CCHHHHHHSGCCC--HH CS
                       Ppx-GppA  82 kevglkveiisgeeEarliylgvvssl.lekgrglviDiGGGStElvlgeekevsklvSlplGavrlterfltddpltke 160
                                    ke+g++++ ++ge+E+rl++l+v++++ +++gr+l++DiGGGS+E+++g ++e++ ++SlplGa+rlt+++l+ddp++++
  gi|121636413|ref|YP_976636.1|  82 KETGVELQALRGEDESRLTFLAVRRWYgWSAGRILNLDIGGGSLEVSSGVDEEPEIALSLPLGAGRLTREWLPDDPPGRR 161
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHCTTTHHHHCCCEHHCCCCCCCHCCHHCHHHHHHCT.S.....SCEEEHHHHHHHHHHHCTSSCHHHHH CS
                       Ppx-GppA 161 eveaarkavekeleevkdevkkegewtrlvgtsgtisalaeltelhgek.....gyeitaeeleeliekllqlkkeeelk 235
                                    +v+++r+++++el+e++ +v ++g+++ +v+ts+t+++la+lt +++++     ++++ta+ l++li++++++++ ++++
  gi|121636413|ref|YP_976636.1| 162 RVAMLRDWLDAELAEPSVTVLEAGSPDLAVATSKTFRSLARLTGAAPSMagprvKRTLTANGLRQLIAFISRMTAVDRAE 241
                                    ******************************************************************************** PP

                                    STTS-CCHHCTHHHHHHHHHHHHHHCT-SEEEEES--HHHHHHHHHHHHH CS
                       Ppx-GppA 236 lagvsdeRadvivagalilsavlealeieaviisegalrEGvlyslllke 285
                                    l+gvs++Ra +ivagal+++a+++al+ieav+i+++alrEG+++++l++e
  gi|121636413|ref|YP_976636.1| 242 LEGVSADRAPQIVAGALVAEASMRALSIEAVEICPWALREGLILRKLDSE 291
                                    *********************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2526.67
//
Query:       gi|121636414|ref|YP_976637.1|  [L=310]
Description: hypothetical protein BCG_0539 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.064   12.1   5.6      0.085   11.7   5.6    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.6   4.7e-06     0.085      84     160 ..     227     302 ..     220     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-06
                  AA_permease_2  84 nwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                    +w ++++vl+sil+va+++ l++++ +l  ++ ++ l+ ++ +il  ++++r+++++  i+++l+ + + + li+l 
  gi|121636414|ref|YP_976637.1| 227 LWRGALVVLQSILAVAFGAGLFIAFDQLWRWNSIVALVLSVMVILGLVVSVRAVRKTEDIASTLIAVAV-GALITLG 302
                                    688999*******99999998888878877888999999****************************99.5766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2601.08
//
Query:       gi|121636415|ref|YP_976638.1|  [L=280]
Description: hypothetical protein BCG_0540 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-15   55.6   0.1    1.5e-14   53.9   0.1    1.8  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   8.5e-19   1.5e-14       1     209 [.      23     229 ..      23     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.5e-19
                                    HHHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaa 80 
                                    ++ a ++G+dgvEl  ++          +++++rk+ +++ + + s++++    +  + +++      + +l r +++a+
  gi|121636415|ref|YP_976638.1|  23 FEYADRLGYDGVELMVWGESVSQ-----DIDAVRKLSRRYRVPVLSVHAPCLLISQRV-WGANP----ILKLDRSVRAAE 92 
                                    57899************998886.....69*************999888888888555.68889....************ PP

                                    HHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHH.HHTSEEEEE--TTTTSSSTC.................. CS
                   AP_endonuc_2  81 aLGapllvlhpGtagagpkgseeeawerlaeslneladyae.kegvklalEtlagsgvelgd.................. 141
                                    +LGa ++v+hp          ++   +r+ae++ + ++ +e +  v++a+E++ ++ +                      
  gi|121636415|ref|YP_976638.1|  93 QLGAQTVVVHPP-------FRWQ---RRYAEGFSDQVAALEaASTVMVAVENMFPFRADRFFgagqsrermrkrgggpgp 162
                                    **********66.......5555...45555555555555546789**********98777799**************** PP

                                    ..HHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                   AP_endonuc_2 142 ..eelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                      + +a   d +d  +   +lD +H+  a++d  d+ r++++ + h+H++D+ g      d+h+ +g G+
  gi|121636415|ref|YP_976638.1| 163 aiSAFAPSYDPLDGNHAHYTLDLSHTATAGTDSLDMARRMGPGLVHLHLCDGSG---LPADEHLVPGRGT 229
                                    ******************************************************...7999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2067.38
//
Query:       gi|121636416|ref|YP_976639.1|  [L=291]
Description: hypothetical protein BCG_0541 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-37  129.1   4.2    3.7e-37  128.9   4.2    1.0  1  4HBT_3    Thioesterase-like superfamily
  ------ inclusion threshold ------
       0.16   12.3   0.7          3    8.3   0.3    2.5  2  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   4.2   4.1e-41   3.7e-37       2     248 .]      31     288 ..      30     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 4.1e-41
                                    -GGGECTTC.-HHHHHHHHHHHHHHT.........-S.SS.EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEET CS
                         4HBT_3   2 rppwtpggagyGGyvlAlalraaqrtv........pdprl.hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqg 72 
                                    +++wt+g +++GG+++Al+++aa+++                +++++Fl + d+g +++ +   ++Gr++s+  vel+qg
  gi|121636416|ref|YP_976639.1|  31 NEHWTIGPKVHGGAMVALCANAARTAYgaagqqpmR---QpVAVSASFLWAPDPGTMRLVTSIRKRGRRISVADVELTQG 107
                                    789*********************998899955433...257************************************** PP

                                    TEEEEEEEEEEE---T.....................---EE-----....--..GGGE---.--SSGGGSGG..TEE.E CS
                         4HBT_3  73 grpiftatasfgraes.................tgwelepaaapppv....ppp.deaalaadeaplplfrrvpgfle.p 129
                                    gr++++a++++g++e                          +a+p v    p+p + + +   ++ ++l+  +  +l   
  gi|121636416|ref|YP_976639.1| 108 GRTAVHAVVTLGEPEHflpgvdgsggasgtaplL-------SANPVVelmaPEPpEGVVPI--GPGHQLAG-LV-HLGeG 176
                                    ***************99*9999876643222111.......22333222223331444332..33344443.33.5555* PP

                                    E-HHT---S........S-EEEEEEEETTTS-SSHHHHHHHHTT-.-GGGGTSS-......SB--EEEEEEEE-S--S-. CS
                         4HBT_3 130 feprpaeggkpd.spagpkrvrqWvrlreggepahlaaLaylsDsfpvprvhglrldaeasgwmpsldltiyfhrepaed 208
                                    ++ rp+  + ++ ++  p+ ++ W+r+r g  p+ l +++++ D   +p+++ + +    +gw+p++ lt y+++ pa d
  gi|121636416|ref|YP_976639.1| 177 CDVRPVLSTLRSaTDGRPPVIQLWARPR-GVAPDAL-FALLCGDL-SAPVTFAVDR----TGWAPTVALTAYLRALPA-D 248
                                    ******666555366679999*******.8877777.78888999.4466666664....49*************875.7 PP

                                    ..EEEEEE-SEEETTEEEEEEEEE-TTS-EEEEEEEEEET CS
                         4HBT_3 209 eWllleaetpwagdgrglvearlwdedGrlvAtstQeglv 248
                                     Wl++ +++ ++g+ ++++++ + d+ Gr+v++++Q+++v
  gi|121636416|ref|YP_976639.1| 249 GWLRVLCTCVEIGQDWFDEDHIVVDRLGRIVVQTRQLAMV 288
                                    9************************************997 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00033         3       4      75 ..      40     109 ..      37     112 .. 0.81
   2 ?    1.6   0.0      0.04   3.6e+02      40      61 ..     241     262 ..     230     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00033
                                    B-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                           4HBT   4 vhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                    vhgG+++al+  aa  a    g    +   v+ s+ fl +  +g + ++ +++ + gr++ v +ve++++++
  gi|121636416|ref|YP_976639.1|  40 VHGGAMVALCANAARTAYGAAGQQ-PMRQPVAVSASFLWAPDPG-TMRLVTSIRKRGRRISVADVELTQGGR 109
                                    899999999988887777777776.33333445788***999**.**********************99876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.04
                                    ESS-BBTTCEEEEEEEEEEEES CS
                           4HBT  40 flrpvrlgdeltvearvlrlgr 61 
                                    +lr+   + +l+v ++++++g 
  gi|121636416|ref|YP_976639.1| 241 YLRALPADGWLRVLCTCVEIGQ 262
                                    9******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2055.94
//
Query:       gi|121636417|ref|YP_976640.1|  [L=295]
Description: pyrroline-5-carboxylate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-39  132.8   5.3    4.6e-39  132.8   5.3    2.3  2  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    5.2e-25   87.9   1.6    1.4e-24   86.5   1.6    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    5.6e-06   26.6   0.3    1.3e-05   25.4   0.3    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.8e-05   23.4   1.1    7.2e-05   22.9   0.2    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00077   20.3   0.6     0.0083   16.9   0.2    2.4  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00099   19.4   0.3     0.0021   18.3   0.3    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.001   19.4   0.5      0.001   19.4   0.5    1.8  2  NAD_binding_7    Putative NAD(P)-binding
     0.0014   18.8   0.2     0.0041   17.4   0.2    1.9  1  TrkA_N           TrkA-N domain
     0.0054   16.6   3.0     0.0054   16.6   3.0    2.6  3  Rossmann-like    Rossmann-like domain
     0.0075   15.9   3.0       0.03   14.0   3.0    2.0  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0087   15.6   0.2      0.015   14.9   0.2    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
  ------ inclusion threshold ------
       0.12   12.4   2.8        1.9    8.4   2.8    2.3  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.34   10.5   4.3        1.4    8.5   0.1    3.1  4  PrpR_N           Propionate catabolism activator


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.5   2.1e+03       7      18 ..     101     112 ..      96     126 .. 0.88
   2 !  132.8   5.3   3.3e-42   4.6e-39       1     103 []     169     290 ..     169     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                                    HHHHTTTHHHHH CS
                     P5CR_dimer   7 vtalsGsgpAyv 18 
                                    vt+++G + Ay+
  gi|121636417|ref|YP_976640.1| 101 VTVVAGITIAYF 112
                                    899999999998 PP

  == domain 2  score: 132.8 bits;  conditional E-value: 3.3e-42
                                    CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCH..........S.........HHH CS
                     P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaakllles..........e.........pae 61 
                                    E+qldavta+sGsgpAy+fll+eal+dagv  Glsr++A++laaqt+aG+a++lle+          e         ++ 
  gi|121636417|ref|YP_976640.1| 169 ESQLDAVTAVSGSGPAYFFLLVEALVDAGVGVGLSRQVATDLAAQTMAGSAAMLLERmdqdqggangElmglrvdltASR 248
                                    89***************************************************973323334444441444555677888 PP

                                    HHHHH--TTSHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                     P5CR_dimer  62 lrdkvtspgGtTiaglkeleegglraavieaveaaakrskel 103
                                    lr++vtspgGtT+a+l+ele+gg+r av++av+aa+ rs++l
  gi|121636417|ref|YP_976640.1| 249 LRAAVTSPGGTTAAALRELERGGFRMAVDAAVQAAKSRSEQL 290
                                    ***************************************986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   1.6     1e-27   1.4e-24       1      97 []       7     106 ..       7     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1e-27
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80 
                                    +i+iiG+G++geal+sgll+ag+q +++vva +r+p++a++la++++v vt+  +++a+e+a++vv+avkp+dve v+++
  gi|121636417|ref|YP_976640.1|   7 RIAIIGGGSIGEALLSGLLRAGRQVKDLVVA-ERMPDRANYLAQTYSVLVTS--AADAVENATFVVVAVKPADVEPVIAD 83 
                                    79***************************88.***************99999..************************** PP

                                    C......GHHHHTTSEEEEESSS CS
                  F420_oxidored  81 l......akdalkgklvisvlag 97 
                                    l      a+++++++++++v+ag
  gi|121636417|ref|YP_976640.1|  84 LanataaAENDSAEQVFVTVVAG 106
                                    *99999999**********9997 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   9.4e-09   1.3e-05       1      80 [.       7      88 ..       7     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.4e-09
                                   EEEEE--SHHHHHHHHHHHHTT-EE...EEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykv...avynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllea 79
                                   +i++iG G +G+ + + ll+ag +v   +v +r +++++ l+++  ++++s++++v+++ +v++ vk  ++v+ vi +l++a
  gi|121636417|ref|YP_976640.1|  7 RIAIIGGGSIGEALLSGLLRAGRQVkdlVVAERMPDRANYLAQTYSVLVTSAADAVENATFVVVAVKP-ADVEPVIADLANA 87
                                   59*******************99874447999**********************************85.89****9997766 PP

                                   - CS
                  NAD_binding_2 80 l 80
                                    
  gi|121636417|ref|YP_976640.1| 88 T 88
                                   5 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   5.2e-08   7.2e-05      12      98 ..       5      89 ..       2     104 .. 0.76
   2 ?   -3.8   0.1       8.8   1.2e+04      15      24 ..     130     139 ..     127     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.2e-08
                                   T-EEEEES-SHHHHHHHHHHHCC..T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS..S-S CS
                   Shikimate_DH 12 ekkvlliGaGemaelvakhLlak..gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatase..epi 89
                                    +++ +iG G ++e +++ Ll++  +vk++vva R  +ra+ la+ +       + +++  +++++a  v++a++    ep+
  gi|121636417|ref|YP_976640.1|  5 MARIAIIGGGSIGEALLSGLLRAgrQVKDLVVAERMPDRANYLAQTY------SVLVTSAADAVENATFVVVAVKPAdvEPV 80
                                   5899****************9865589*******************9......34678888888999999888754311555 PP

                                   B-HHHHHCC CS
                   Shikimate_DH 90 lekeeveea 98
                                   +   +   a
  gi|121636417|ref|YP_976640.1| 81 IADLANATA 89
                                   555544444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.8
                                    EEEES-SHHH CS
                   Shikimate_DH  15 vlliGaGema 24 
                                    + l+GaG +a
  gi|121636417|ref|YP_976640.1| 130 AALVGAGVTA 139
                                    6799999775 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2     6e-06    0.0083       2      83 ..       7      85 ..       6     100 .. 0.87
   2 ?    0.9   0.0      0.58     8e+02       4      34 ..     131     160 ..     129     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHH CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaal 83
                                   r+aiiG+G ig+  l  l ++ r+ +   + ++ + ra  +a+++ v + s  +++ +   + +v+va+ +   e ++ +++
  gi|121636417|ref|YP_976640.1|  7 RIAIIGGGSIGEALLSGLLRAGRQVKDLVVAERMPDRANYLAQTYSVLVTSAADAVEN---ATFVVVAVKPADVEPVIADLA 85
                                   89*******************9*998888******************99999888888...779999999976666555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                                    EEETTSHHHHHHHHHHHHTTTTEEEEEEECS CS
                   GFO_IDH_MocA   4 aiiGaGkigskhlrplnesqrleevvalldp 34 
                                    a++GaG  +   +  +  +q+leev al+d 
  gi|121636417|ref|YP_976640.1| 131 ALVGAGVTALAKG-RFVTPQQLEEVSALFDA 160
                                    7899999999999.88999999999999985 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   1.5e-06    0.0021       1      61 [.       8      79 ..       8     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...........TTTCEEEEE--TTTHHH CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...........lgvrfeaialdaenyea 61
                                   + iiG+Gs+G+a++  l+r +   ++++va+r  ++++ la++             + +f  +a+ ++++e 
  gi|121636417|ref|YP_976640.1|  8 IAIIGGGSIGEALLSGLLRAGRQVKDLVVAERMPDRANYLAQTYsvlvtsaadavENATFVVVAVKPADVEP 79
                                   789****************999878***********888876656666666666655556666666555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.5   7.5e-07     0.001       9      88 ..       7      91 ..       3     106 .. 0.79
   2 ?   -2.6   0.1       5.7   7.8e+03      11      26 ..     131     146 ..     128     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.5e-07
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvt..vvapev...keeleelvklaeeelekdlegadlviaatddrelneriaeaakar 85
                                   ++ ++GgG++++  ++ ll+ag +v+  vva+++   ++ l +++++  + + + +e+a +v++a++ ++++  ia++a a 
  gi|121636417|ref|YP_976640.1|  7 RIAIIGGGSIGEALLSGLLRAGRQVKdlVVAERMpdrANYLAQTYSVLVTSAADAVENATFVVVAVKPADVEPVIADLANAT 88
                                   789*******************999544999997443333336666777777899*********************999876 PP

                  NAD_binding_7 86 ril 88
                                    + 
  gi|121636417|ref|YP_976640.1| 89 AAA 91
                                   554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                  NAD_binding_7  11 lvvGgGevAarkvrkl 26 
                                     +vG+G  A+ k r +
  gi|121636417|ref|YP_976640.1| 131 ALVGAGVTALAKGRFV 146
                                    5799999999887765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2     3e-06    0.0041       1      51 [.       8      60 ..       8     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                   EEEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHTTSEEEES-TTS CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelreeglevvvgdatd 51
                                   i+iiG G +G++l+  L ++g   kd vv ++ ++r++ l++    v+v +a+d
  gi|121636417|ref|YP_976640.1|  8 IAIIGGGSIGEALLSGLLRAGrqvKDLVVAERMPDRANYLAQTY-SVLVTSAAD 60
                                   79*****************5559*99*************98665.444444433 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.0   3.9e-06    0.0054      13      95 ..       8      91 ..       4     111 .. 0.78
   2 ?   -2.1   0.0       2.4   3.4e+03      73      84 ..     164     175 ..     130     181 .. 0.71
   3 ?    0.4   0.2      0.41   5.7e+02       8      52 ..     246     289 ..     239     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                  Rossmann-like 13 vGiisaGrvGtalgaaleraghvvvgis.aisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaatga 93
                                   + ii+ G +G al   l rag +v  +  a     r    ++   v v +  d +++a ++++av  a++  ++++la+++a
  gi|121636417|ref|YP_976640.1|  8 IAIIGGGSIGEALLSGLLRAGRQVKDLVvAERMPDRANYLAQTYSVLVTSAADAVENATFVVVAVKPADVEPVIADLANATA 89
                                   78**********************9865144444444444556667777889*************************99877 PP

                  Rossmann-like 94 vr 95
                                     
  gi|121636417|ref|YP_976640.1| 90 AA 91
                                   54 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                  Rossmann-like  73 llavPdaelpgl 84 
                                    +l+vP+++l  +
  gi|121636417|ref|YP_976640.1| 164 VLTVPESQLDAV 175
                                    788888888655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.41
                  Rossmann-like   8 sarlsvGiisaGrvGtalgaaleraghvvvgisaisaasreraer 52 
                                     +rl   + s G   +a    ler g  + ++ a  +a++ r+e+
  gi|121636417|ref|YP_976640.1| 246 ASRLRAAVTSPGGTTAAALRELERGGFRM-AVDAAVQAAKSRSEQ 289
                                    57889999999888888888899999875.677777777777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.0   2.2e-05      0.03       1      91 [.       8      87 ..       8     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayqte 82
                                   iai+G G+iG  l   L +ag++v  ++  +r+    ++++  ++++    ++++ a++a+     e++  v+v+vK  ++e
  gi|121636417|ref|YP_976640.1|  8 IAIIGGGSIGEALLSGLLRAGRQVKDLVVAERMP--DRANYLAQTYS----VLVTSAADAV-----ENATFVVVAVKPADVE 78
                                   89*********************98777766454..34444455555....5666666666.....8999************ PP

                                   HHHHHHGGG CS
                           ApbA 83 ealeeikpl 91
                                    ++++++++
  gi|121636417|ref|YP_976640.1| 79 PVIADLANA 87
                                   **9998876 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.1e-05     0.015       6      72 ..       7      77 ..       3     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                   -EEEES-SHHHHHHHHHHHHTT-...-EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S.-HHH CS
                           IlvN  6 kiaviGyGsqGhaqalnlrdsgl...dvvvglregsksvkkAkeegfevltvaeavkkadvvmili.PDel 72
                                   +ia+iG Gs G+a    l  +g    d+vv+ r  ++    A+  ++ v+++a+av++a +v++ + P  +
  gi|121636417|ref|YP_976640.1|  7 RIAIIGGGSIGEALLSGLLRAGRqvkDLVVAERMPDRANYLAQTYSVLVTSAADAVENATFVVVAVkPADV 77
                                   79***********99999888872345689999999999*********************98876525444 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.8    0.0014       1.9       2      94 ..       8      95 ..       7     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHH CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqalr 83
                                   ia++G+Gs G al   l ++g +v+  v  e + ++ n       yL +    +  v +t  a+a+++a+++v++v  + ++
  gi|121636417|ref|YP_976640.1|  8 IAIIGGGSIGEALLSGLLRAGRQVKDLVVAERMPDRAN-------YLAQ----TYSVLVTSAADAVENATFVVVAVKPADVE 78
                                   99*******************99988887776655544.......5554....23345677788888888888888888888 PP

                                   HHHHHHCCC-......- CS
                 NAD_Gly3P_dh_N 84 evlkklkgll......k 94
                                    v+++l++ +      +
  gi|121636417|ref|YP_976640.1| 79 PVIADLANATaaaendS 95
                                   88888877764544444 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.72   9.9e+02     135     153 ..      47      65 ..      23      68 .. 0.74
   2 ?    8.5   0.1     0.001       1.4       5      56 ..      75     128 ..      71     166 .. 0.90
   3 ?    1.7   0.0      0.12   1.6e+02     112     144 ..     190     224 ..     183     227 .. 0.89
   4 ?   -2.8   0.1         3   4.1e+03     150     164 ..     272     286 ..     263     289 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.72
                         PrpR_N 135 kaGlksvlltsgkesvrqA 153
                                     a   svl+ts +++v++A
  gi|121636417|ref|YP_976640.1|  47 LAQTYSVLVTSAADAVENA 65 
                                    5566789999999999988 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                         PrpR_N   5 ldievvegdleeavelakeleaegvdviiSrGgtaellrkhv..svPVveikvs 56 
                                    +d+e v +dl +a ++a++  ae+v v + +G t ++ ++++   +PVv   ++
  gi|121636417|ref|YP_976640.1|  75 ADVEPVIADLANATAAAENDSAEQVFVTVVAGITIAYFESKLpaGTPVVRAMPN 128
                                    799**************************************9767899976665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.12
                         PrpR_N 112 vkelkaegvevvvGdgvvadlAek..aGlksvllt 144
                                    v+ l ++gv v +  +v++dlA++  aG  ++ll+
  gi|121636417|ref|YP_976640.1| 190 VEALVDAGVGVGLSRQVATDLAAQtmAGSAAMLLE 224
                                    8999******************9977888888876 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 3
                         PrpR_N 150 vrqAieeAleiarat 164
                                    +r+A++ A++ a+++
  gi|121636417|ref|YP_976640.1| 272 FRMAVDAAVQAAKSR 286
                                    466666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2129.37
//
Query:       gi|121636418|ref|YP_976641.1|  [L=78]
Description: hypothetical protein BCG_0543 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-14   52.4   0.0    5.1e-14   52.2   0.0    1.1  1  HTH_17        Helix-turn-helix domain
    0.00031   20.5   0.0    0.00061   19.5   0.0    1.5  2  HTH_23        Homeodomain-like domain
     0.0013   18.1   0.4      0.008   15.6   0.1    2.0  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.023   14.7   0.0    1.3  1  HTH_29        Winged helix-turn helix
      0.018   15.2   0.0      0.027   14.6   0.0    1.3  1  AbiEi_4       Transcriptional regulator, AbiEi antitoxin
      0.026   14.6   0.2      0.044   13.9   0.2    1.3  1  HTH_22        HTH domain
      0.037   13.8   0.0      0.064   13.0   0.0    1.4  2  HTH_38        Helix-turn-helix domain
      0.047   13.2   0.0       0.07   12.7   0.0    1.3  1  Sigma70_r4    Sigma-70, region 4
      0.055   13.3   0.2       0.07   12.9   0.2    1.3  1  LacI          Bacterial regulatory proteins, lacI family
       0.08   12.8   0.1       0.16   11.8   0.0    1.5  2  HTH_IclR      IclR helix-turn-helix domain
      0.085   12.9   0.0       0.15   12.1   0.0    1.4  1  HTH_7         Helix-turn-helix domain of resolvase
      0.094   12.5   0.1       0.16   11.7   0.1    1.3  1  HTH_DeoR      DeoR-like helix-turn-helix domain
       0.16   12.2   0.0       0.24   11.6   0.0    1.3  1  HTH_28        Helix-turn-helix domain
       0.17   12.0   0.0       0.24   11.5   0.0    1.3  1  Phage_Cox     Regulatory phage protein cox


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     4e-17   5.1e-14       1      49 [.      24      72 ..      24      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4e-17
                         HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdleewlek 49
                                   lltv+E+A+l +vs+ tvyrl+++gelpa+++Gr+ r++ +++ ++le 
  gi|121636418|ref|YP_976641.1| 24 LLTVAEVAALMRVSKMTVYRLVHNGELPAVRVGRSFRVHAKAVHDMLET 72
                                   79******************************************99985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.8e-07   0.00061      16      39 ..      23      46 ..      18      49 .. 0.89
   2 ?   -2.6   0.0       4.1   5.2e+03      19      25 ..      58      64 ..      50      70 .. 0.50

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                         HTH_23 16 eGlsvreIAreLgvsrrTvyrwlk 39
                                   + l+v+e+A+++ vs++Tvyr ++
  gi|121636418|ref|YP_976641.1| 23 QLLTVAEVAALMRVSKMTVYRLVH 46
                                   4789*****************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                         HTH_23 19 svreIAr 25
                                   s r  A+
  gi|121636418|ref|YP_976641.1| 58 SFRVHAK 64
                                   3333333 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.2e-06     0.008      26      49 ..      22      46 ..      17      48 .. 0.84
   2 ?    1.4   0.0      0.16   2.1e+02      32      48 ..      54      70 ..      44      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.2e-06
                   HTH_Tnp_ISL3 26 es.rsvkavArqlgvSwtTVwrild 49
                                       +v++vA++++vS  TV r ++
  gi|121636418|ref|YP_976641.1| 22 TQlLTVAEVAALMRVSKMTVYRLVH 46
                                   55579*****************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                   HTH_Tnp_ISL3 32 avArqlgvSwtTVwril 48
                                    v r ++v+++ V+++l
  gi|121636418|ref|YP_976641.1| 54 RVGRSFRVHAKAVHDML 70
                                   57788999999999887 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.8e-05     0.023      12      34 ..      24      46 ..      16      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                         HTH_29 12 vstvsqiAkllglsrrtvyrwlk 34
                                   + tv+++A+l+++s+ tvyr ++
  gi|121636418|ref|YP_976641.1| 24 LLTVAEVAALMRVSKMTVYRLVH 46
                                   459*****************986 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.1e-05     0.027      13      38 ..      24      50 ..      19      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                        AbiEi_4 13 lfttrelea.aGispsalrrLvrkGwL 38
                                   l+t++e++a   +s ++++rLv+ G+L
  gi|121636418|ref|YP_976641.1| 24 LLTVAEVAAlMRVSKMTVYRLVHNGEL 50
                                   89***********************98 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.4e-05     0.044      44      60 ..      27      43 ..      25      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                         HTH_22 44 vekvAekLgiSraTvYr 60
                                   v +vA+ + +S+ TvYr
  gi|121636418|ref|YP_976641.1| 27 VAEVAALMRVSKMTVYR 43
                                   899*************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     5e-05     0.064      21      43 ..      25      47 ..      18      48 .. 0.88
   2 ?   -3.1   0.0       5.3   6.9e+03      27      33 ..      52      58 ..      52      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-05
                         HTH_38 21 lslreIArrLgrspsTIsRElkR 43
                                   l+++e+A ++ +s+ T++R ++ 
  gi|121636418|ref|YP_976641.1| 25 LTVAEVAALMRVSKMTVYRLVHN 47
                                   89*****************9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                         HTH_38 27 ArrLgrs 33
                                   A r+grs
  gi|121636418|ref|YP_976641.1| 52 AVRVGRS 58
                                   6688887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.5e-05      0.07      20      43 ..      24      47 ..      18      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                   T--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4 20 glTleEIgerlgiSrerVrqiekr 43
                                    lT +E+++ + +S+++V ++ ++
  gi|121636418|ref|YP_976641.1| 24 LLTVAEVAALMRVSKMTVYRLVHN 47
                                   59****************998876 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.4e-05      0.07       1      23 [.      26      48 ..      26      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                                   -HHHHHHHCTS-HHHHHHHCTTS CS
                           LacI  1 tikDVArlAGVSkaTVSrvLnnk 23
                                   t  +VA l  VSk+TV r ++n 
  gi|121636418|ref|YP_976641.1| 26 TVAEVAALMRVSKMTVYRLVHNG 48
                                   5679*************999986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.16      15      40 ..      21      46 ..      11      47 .. 0.88
   2 ?   -2.6   0.0       3.8   4.9e+03      34      41 ..      65      72 ..      56      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   TBSS-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlLq 40
                                    +q lt++e+A+   ++k tv+Rl++
  gi|121636418|ref|YP_976641.1| 21 KTQLLTVAEVAALMRVSKMTVYRLVH 46
                                   45559*******************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                                   HHHHHHHH CS
                       HTH_IclR 34 tvhRlLqt 41
                                   +vh +L t
  gi|121636418|ref|YP_976641.1| 65 AVHDMLET 72
                                   47888876 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.15      23      43 ..      26      46 ..      25      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   -STTTSSSS---SSSS--SS- CS
                          HTH_7 23 siskIAkevnisRsTvYRyla 43
                                   +++++A    +s++TvYR  +
  gi|121636418|ref|YP_976641.1| 26 TVAEVAALMRVSKMTVYRLVH 46
                                   5789999***********766 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.16      12      31 ..      22      41 ..      19      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                       HTH_DeoR 12 qgklsveelvellgvSeaTi 31
                                    + l+v e+++l  vS++T+
  gi|121636418|ref|YP_976641.1| 22 TQLLTVAEVAALMRVSKMTV 41
                                   6779***************9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.24      14      34 ..      26      46 ..      18      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                         HTH_28 14 svreaArelgisrrtvyrWik 34
                                   +v+e+A+++ +s  tvyr+++
  gi|121636418|ref|YP_976641.1| 26 TVAEVAALMRVSKMTVYRLVH 46
                                   9*****************987 PP

>> Phage_Cox  Regulatory phage protein cox
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.24       6      43 ..      19      56 ..      15      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                   X---SEEEHHHHHHHHT--HHHHHHHHHHT-S-EEEE- CS
                      Phage_Cox  6 eiasdlvteekFAeliGKtekAvrkmikdgKLPvvelk 43
                                   + +++l+t ++ A l+  ++  v +++++g LP+v + 
  gi|121636418|ref|YP_976641.1| 19 QAKTQLLTVAEVAALMRVSKMTVYRLVHNGELPAVRVG 56
                                   556899*****************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 659.31
//
Query:       gi|121636419|ref|YP_976642.1|  [L=376]
Description: udp-glucose 4-epimerase galE2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.5   0.0    1.8e-19   70.2   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.4e-14   53.5   0.0    4.1e-13   49.4   0.0    2.1  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.6e-10   38.1   0.0    1.1e-09   37.7   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0003   20.0   0.0    0.00049   19.3   0.0    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0072   15.5   0.1        0.1   11.7   0.0    2.1  2  NAD_binding_4    Male sterility protein
     0.0076   16.2   0.0      0.012   15.5   0.0    1.2  1  UPF0227          Uncharacterised protein family (UPF0227)


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   5.9e-23   1.8e-19       1     180 [.      26     208 ..      26     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 5.9e-23
                                    EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                      Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihlAavggv 77 
                                    +lVtGa  f+G +l+ +l+++    +vi++d    ++   r+    e+v++d++++  +++++++ ++d+v+h+Aa +  
  gi|121636419|ref|YP_976642.1|  26 VLVTGACRFLGGYLTARLAQNPliNRVIAVDAIAPSKDMLRRMGRaEFVRADIRNPF-IAKVIRNGEVDTVVHAAAASYA 104
                                    79********************9555*****986555555444448********976.******99**********9999 PP

                                    HHHHHSHHHHHHHHTHHHHHHHHHHHHH.TCTEEEEEEEGGGGTSCSSSS...BSTCSTTS----SSHHHHHHHHHHHHH CS
                      Epimerase  78 aassedpadfieknlqgtlnlleaarka.gvkrllflsSsevYGkdaeqp...keettltgplkpnspYaaaKlageklv 153
                                    ++s  + a++ e n++g+++l+ a++ka  v+r++  s+sevYG +++ p   +e+++   p+  ++ +    l +e +v
  gi|121636419|ref|YP_976642.1| 105 PRSGGS-AALKELNVMGAMQLFAACQKApSVRRVVLKSTSEVYGSSPHDPvmfTEDSSSRRPF--SQGFPKDSLDIEGYV 181
                                    997776.77799****************9999****************998855555555555..88899999******* PP

                                    HHHHHHH.T-EEEEEEESEEESTTS-TT CS
                      Epimerase 154 eayaaqy.glnaiilrlfnlyGprngeg 180
                                    +a+ +   ++ ++ilrl n++Gp   ++
  gi|121636419|ref|YP_976642.1| 182 RALGRRRpDIAVTILRLANMIGPA-MDT 208
                                    ******99***************9.332 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   1.4e-16   4.1e-13       1     150 [.      27     163 ..      27     214 .. 0.79
   2 ?    2.0   0.0     0.036   1.1e+02     307     327 ..     310     330 ..     291     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.4e-16
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG   f G yl+ +L ++     +i  ++ + +    + l++       ++ +++++D+++   + +++++ ++d+v+
  gi|121636419|ref|YP_976642.1|  27 LVTGACRFLGGYLTARLAQNPLINRVIAVDAIAPS---KDMLRR------MGRAEFVRADIRN-PFIAKVIRNGEVDTVV 96 
                                    89****************99665544433333322...333332......35789********.57************** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS..B-TTS----- CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp..qtEttpfyPr 150
                                    + AA s  ++s  + ++  e nv+G+++L+ a++++      r++  StsEvYG+  + p  +tE+   + r
  gi|121636419|ref|YP_976642.1|  97 HAAAASYAPRSGGS-AALKELNVMGAMQLFAACQKAPS--VRRVVLKSTSEVYGSSPHDPvmFTED--SSSR 163
                                    ***********986.7888***************9864..5699************9887224554..4444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.036
                                    -B-THHHHHHH----SS-HHH CS
                  GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfee 327
                                    ++d+++++ eLg++pk++  e
  gi|121636419|ref|YP_976642.1| 310 VMDTTRMRVELGYQPKWTTVE 330
                                    78**************98766 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   3.7e-13   1.1e-09       1     130 [.      27     155 ..      27     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.7e-13
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeale..gvdvvihlaslvd 78 
                                    +vtG++ FlG +l  +L +   ++  rv+ ++   + ++ l+++++++++ +D+++ + + ++++  +vd v+h a+++ 
  gi|121636419|ref|YP_976642.1|  27 LVTGACRFLGGYLTARLAQNPLIN--RVIAVDAIAPSKDMLRRMGRAEFVRADIRN-PFIAKVIRngEVDTVVHAAAASY 103
                                    69***************9988555..66666666777799**************97.578888873358899**999999 PP

                      3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvka.gvrvlvYtSsaevvgpnslgeeil 130
                                          +  + + nv G  ++ +ac ka +vr++v  S+ ev g  s  ++++
  gi|121636419|ref|YP_976642.1| 104 APRSGGSAALKELNVMGAMQLFAACQKApSVRRVVLKSTSEVYGS-SPHDPVM 155
                                    999999999****************99769************999.5566665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-07   0.00049       1     128 [.      26     142 ..      26     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-07
                                    EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                    vlvtGa   +G  l+ +++++  ++++i ++    + + +++  ++e            v +d+r+   ++k++++ +vd
  gi|121636419|ref|YP_976642.1|  26 VLVTGACRFLGGYLTARLAQNpLINRVIAVDAIAPSKDMLRRMGRAE-----------FVRADIRNP-FIAKVIRNGEVD 93 
                                    67888888888888888777766777777777666655555543222...........234788875.68999999**** PP

                                    EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHT.T-SEEEEEEE CS
                Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaiea.gvkkvvliSt 128
                                    +v+haAA    P      +   + Nv+g++++  a+++a  v++vvl St
  gi|121636419|ref|YP_976642.1|  94 TVVHAAAASYAPRSGGS-AALKELNVMGAMQLFAACQKApSVRRVVLKST 142
                                    ************97765.445678***********998648******999 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.048   1.4e+02       1      27 [.      28      54 ..      28      88 .. 0.71
   2 !   11.7   0.0   3.4e-05       0.1      87     144 ..      91     150 ..      84     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.048
                                   EE-TTSHHHHHHHHHHHHHS-.T.EEEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.kiyl 27
                                   +TGa  FLG +L ++L ++   + ++++
  gi|121636419|ref|YP_976642.1| 28 VTGACRFLGGYLTARLAQNPL-InRVIA 54
                                   7**************987754.555544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                                    H--EEEE--SS-S.ST..TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-T CS
                  NAD_binding_4  87 evdviihsaAtvnfde..pykellrvNveGtrevlelakklkklkvllhvSTayvngere 144
                                    evd ++h aA     +      l++ Nv+G+ +++  ++k  + + ++  ST+ v+g + 
  gi|121636419|ref|YP_976642.1|  91 EVDTVVHAAAASYAPRsgGSAALKELNVMGAMQLFAACQKAPSVRRVVLKSTSEVYGSSP 150
                                    89*****99877665522566799****************************77776655 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.2e-06     0.012      68     105 ..      35      72 ..      19      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                        UPF0227  68 LGGyyatrlgerfglrqvllnPalkplenlagklgeea 105
                                    LGGy+ +rl++  +++ v+   a++p +++  ++g+ +
  gi|121636419|ref|YP_976642.1|  35 LGGYLTARLAQNPLINRVIAVDAIAPSKDMLRRMGRAE 72 
                                    9**********************************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2772.15
//
Query:       gi|121636420|ref|YP_976643.1|  [L=358]
Description: hypothetical protein BCG_0545 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-19   67.7   0.0    1.1e-18   67.1   0.0    1.3  1  Acyltransferase  Acyltransferase
     0.0088   15.0   0.0      0.013   14.5   0.0    1.3  1  DAGAT            Diacylglycerol acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   1.3e-22   1.1e-18       1     134 [.     129     260 ..     129     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.3e-22
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsy..lDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnar 77 
                                    +v+v+g en+p++g a++vaNH     +D l+l++++++++ ++r+++++a+++++++p++g+++r++g+  ++      
  gi|121636420|ref|YP_976643.1| 129 RVEVSGVENIPRDGAALVVANHAGVlpFDGLMLSVAVHDEHpAHRDLRLLAADMVFDLPVIGEAARKAGHTMACT----- 203
                                    689*********************9999*************888*******************************..... PP

                Acyltransferase  78 aagsleniselleegklvviFPEG.....trsregel..lpfkkGlvrlaakakkgvpivPvai 134
                                         + +++ll +g+l  +FPEG     +r+++++   +  + G+v++a+++  + pivP++i
  gi|121636420|ref|YP_976643.1| 204 -----TDAHRLLASGELTAVFPEGykglgKRFEDRYRlqRFGRGGFVSAALRT--KAPIVPCSI 260
                                    .....9999***************9999988888777688899**********..*******97 PP

>> DAGAT  Diacylglycerol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.4e-06     0.013      44     197 ..     123     270 ..     110     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-06
                          DAGAT  44 yfaeYfPvkLvktaeletdrnYliGyhPhgilsvgafvalatdatgvkekfpgirfnlatLa..gqfrtpfrreillllG 121
                                    +f ++f v++   ++++ d + l+  +  g+l+  +   l+     v++  p  r  l  La    f +p+  e     G
  gi|121636420|ref|YP_976643.1| 123 FFKSWFRVEVSGVENIPRDGAALVVANHAGVLPFDG-LMLS---VAVHDEHPAHR-DLRLLAadMVFDLPVIGEAARKAG 197
                                    666777777777777777777777777777777776.4455...44555555444.344444225677777777777777 PP

                          DAGAT 122 lievsresieyvLdkeekGravvlvvGGaeealeahpgketltLkkrkGfvkialktGadLvPvysfGendvykqv 197
                                     + +     + +L ++e     ++ + G +   +  ++   l    r Gfv  al+t a++vP+   G +++y  +
  gi|121636420|ref|YP_976643.1| 198 HTMACTTDAHRLLASGEL---TAVFPEGYKGLGKRFEDRYRLQRFGRGGFVSAALRTKAPIVPCSIIGSEEIYPML 270
                                    777777777777765544...5666777776666777777888889***************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2791.02
//
Query:       gi|121636421|ref|YP_976644.1|  [L=302]
Description: cyclopropane-fatty-acyl-phospholipid synthase 2 cmaA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-120  401.1   0.0   2.4e-120  400.9   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    4.4e-08   33.1   0.0    6.6e-08   32.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    5.1e-06   27.1   0.0    9.4e-06   26.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    5.2e-06   27.1   0.0    9.7e-06   26.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      7e-05   23.4   0.0    0.00014   22.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.14   12.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
       0.15   11.8   0.0       0.22   11.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.15   11.1   0.0       0.27   10.3   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.17   10.8   0.0       0.24   10.3   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.9   0.0  1.2e-123  2.4e-120       3     273 .]      13     298 ..      11     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 400.9 bits;  conditional E-value: 1.2e-123
                                    SXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                           CMAS   3 kkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrave 82 
                                     k+ ve++++hYD sn+ff+l+ldp+mtYsCAyfer+dmtLeeAq+aK++l+l+kl+l+pGmtlLdiGcGWGs++r+av+
  gi|121636421|ref|YP_976644.1|  13 LKPPVEAVRSHYDKSNEFFKLWLDPSMTYSCAYFERPDMTLEEAQYAKRKLALDKLNLEPGMTLLDIGCGWGSTMRHAVA 92 
                                    67899*************************************************************************** PP

                                    HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGT.......SGGGHHHHHHHHHHH CS
                           CMAS  83 rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehv.......gkenydtffkklkkl 155
                                    +ydv+v+glTlS++q+++ k+++de+d+ r++ev+++++e++de+vdr+vs+gafeh+       g+e+ydtffkk+++l
  gi|121636421|ref|YP_976644.1|  93 EYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFadgagdaGFERYDTFFKKFYNL 172
                                    ******************************************************************************** PP

                                    S-TT-EEEEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHH CS
                           CMAS 156 lkedGllllhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLk 227
                                    +++dG++llhtit+++k+e++e gl++        kfi +eiFPgG+lp+i+++++++s+ag++v+++++++a+Y+ TL+
  gi|121636421|ref|YP_976644.1| 173 TPDDGRMLLHTITIPDKEEAQELGLTSpmsllrfiKFILTEIFPGGRLPRISQVDYYSSNAGWKVERYHRIGANYVPTLN 252
                                    ************************99999*************************************************** PP

                                    HHHHHHHHTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 228 aWaealqenkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    aWa+alq++kdeaial+++e++++y++YL+gc++ Fr++y+dv+q+
  gi|121636421|ref|YP_976644.1| 253 AWADALQAHKDEAIALKGQETYDIYMHYLRGCSDLFRDKYTDVCQF 298
                                    ********************************************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   3.3e-11   6.6e-08      15     125 ..      63     189 ..      48     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.3e-11
                Methyltransf_23  15 rllpk..lraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                     +l+k  l++g+ +LdiGcG G++++++ +e+ ++v+g  ls+++ +  +    + +  + + ++ q ++e ++  d Iv
  gi|121636421|ref|YP_976644.1|  63 LALDKlnLEPGMTLLDIGCGWGSTMRHAvAEYDVNVIGLTLSENQYAHDKamfdEVDSPRRKEVRIQGWEEFDEPVDRIV 142
                                    334444379999**************99888899********99777665777777777777777779999999****** PP

                Methyltransf_23  88 lrevlehvpdpp.........ellrqiatllkpgGylllseplaslk 125
                                    +   +eh+ d +           ++++++l+ ++G++ll++++ ++k
  gi|121636421|ref|YP_976644.1| 143 SLGAFEHFADGAgdagferydTFFKKFYNLTPDDGRMLLHTITIPDK 189
                                    **********9999******9********************977654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.7e-09   9.4e-06       2      86 ..      77     159 ..      76     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.7e-09
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    Ld+GcG G +++++ +++ + +v+g+ +se++ ++ ++ ++e  + + +  +  ++ +++ d+ +D +vs ga++h+ d 
  gi|121636421|ref|YP_976644.1|  77 LDIGCGWGSTMRHAVAEY-DVNVIGLTLSENQYAHDKAMFDE--VdSPRRKEVRIQGWEEFDEPVDRIVSLGAFEHFADG 153
                                    9****************8.7************9998888854..4467777788888998899*******999***9987 PP

                                    HHHHHH CS
                Methyltransf_25  81 dlekal 86 
                                      ++ +
  gi|121636421|ref|YP_976644.1| 154 AGDAGF 159
                                    655555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.8e-09   9.7e-06       1      97 [.      77     177 ..      77     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.8e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L+iGcG Gs++r+  ++  d++++g+ +s+++ ++ k+ + + +  + ++v+++  + +d+     +D +v++++++h+ 
  gi|121636421|ref|YP_976644.1|  77 LDIGCGWGSTMRHAVAE-YDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFDE----PVDRIVSLGAFEHFa 151
                                    8***********99999.9*************************99999999999998876....9*************7 PP

                Methyltransf_12  80 ........kdirevldnirklLkpgG 97 
                                            +  + +++++++l  ++G
  gi|121636421|ref|YP_976644.1| 152 dgagdagfERYDTFFKKFYNLTPDDG 177
                                    77766666666666666666666666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     7e-08   0.00014       1      94 [.      77     179 ..      77     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7e-08
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-... CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv... 74 
                                    Ld+GcG G+ +++    +  +v+g+ ls+++ +  k+   e +   +    + +++     d+ +D +vs  +++h+   
  gi|121636421|ref|YP_976644.1|  77 LDIGCGWGSTMRHAVAEYdVNVIGLTLSENQYAHDKAMFDEVDSprR---KEVRIQGWEEFDEPVDRIVSLGAFEHFadg 153
                                    8************998888************9777666666654444...5555555544578**************544 PP

                                    ......CCHHHHHHHHHHHEEEEEEE CS
                Methyltransf_11  75 ......edpekalkeiaRvLkpgGll 94 
                                          e+ + ++k+++ +   +G++
  gi|121636421|ref|YP_976644.1| 154 agdagfERYDTFFKKFYNLTPDDGRM 179
                                    44443337777777777777666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.8e-05      0.14       2      90 ..      71     153 ..      70     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G     +  e   + +v+G+  se+   + +++ ++  +  + e++++ +ee++     e++D i+s
  gi|121636421|ref|YP_976644.1|  71 EPGMTLLDIGCGWGSTMRHAVAE--YDVNVIGLTLSENQYAHDKAMFDEVDSPrRKEVRIQGWEEFD-----EPVDRIVS 143
                                    5789**********999888844..3899*******9998888888887666668888888888888.....77999999 PP

                Methyltransf_31  81 nevlnaladp 90 
                                     +++ ++ad 
  gi|121636421|ref|YP_976644.1| 144 LGAFEHFADG 153
                                    8888555443 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.22      64      87 ..      63      86 ..      45     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                   HHHHHTT--TT-EEEEES-TTSHH CS
                           PCMT 64 lalellelkkgarvLevGsGsGyl 87
                                   lal+ l+l++g+  L++G+G G  
  gi|121636421|ref|YP_976644.1| 63 LALDKLNLEPGMTLLDIGCGWGST 86
                                   578999*************98843 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.27      22      45 ..      64      87 ..      60     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                   HHHHH-GGTTSEEEEES-TTTCCH CS
                         RrnaAD 22 IldklnleekltvleigpGkGilT 45
                                   +ldklnle+ +t+l+ig G G + 
  gi|121636421|ref|YP_976644.1| 64 ALDKLNLEPGMTLLDIGCGWGSTM 87
                                   79*****************99875 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.24     116     178 ..      73     135 ..      59     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                                    T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS- CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlp 178
                                    g t+ld+Gcg G  +   v+e    v+G+  se  +   +a+   +++ +r+ +   g e+++
  gi|121636421|ref|YP_976644.1|  73 GMTLLDIGCGWGSTMRHAVAEYDVNVIGLTLSENQYAHDKAMFDEVDSPRRKEVRIQGWEEFD 135
                                    6789****************************9999999998776666555554445666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2272.81
//
Query:       gi|121636422|ref|YP_976645.1|  [L=166]
Description: hypothetical protein BCG_0547c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-28   99.4   0.0    1.9e-28   99.2   0.0    1.1  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
    3.7e-06   26.5   0.0    4.8e-06   26.2   0.0    1.2  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   2.2e-32   1.9e-28       2     131 ..      10     140 ..       9     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 2.2e-32
                MaoC_dehydrat_N   2 liGaef.epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkap.ell..ealgidlsrllh 77 
                                    liG+++ +p+ + v+re++refa av++ +p++++e +a+aagy +l+aP tfl +++ + + e++  + ++i+++r+ h
  gi|121636422|ref|YP_976645.1|  10 LIGKHYrAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQlEIFtkFNIPINIARVFH 89 
                                    69****999**************************************************888877757888999****** PP

                MaoC_dehydrat_N  78 geqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                     +q+f++h+pi a D+l++++ +++v +  g   + + + +++vt+++G+pv+t
  gi|121636422|ref|YP_976645.1|  90 RDQKFRFHRPILANDKLYFDTYLDSVIESHG---TVLAEIRSEVTDAEGKPVVT 140
                                    ****************************864...9999**************98 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   5.3e-10   4.8e-06       2     121 ..       7     132 ..       6     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.3e-10
                                    TCCCTTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT......EG CS
                MaoC_dehydratas   2 fqnaigekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn......vv 75 
                                    +q+ ig+++++ +   v +++i+ +a++  D  p H ++  A++ag +  +a   + + + +++  e +++        +
  gi|121636422|ref|YP_976645.1|   7 AQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQLEIFTKFnipiniAR 86 
                                    577899999999999999*******************************9998777666666666666666699985444 PP

                                    GGEEEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                MaoC_dehydratas  76 arvgeikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtkevte 121
                                     + + +k+rF +p l++d+l++ +    +++   t+  e + evt+
  gi|121636422|ref|YP_976645.1|  87 VFHRDQKFRFHRPILANDKLYFDTYLDSVIESHGTVLAEIRSEVTD 132
                                    455889****************999988888887777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1278.97
//
Query:       gi|121636423|ref|YP_976646.1|  [L=373]
Description: phosphoserine phosphatase serB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-27   96.8   0.3    3.3e-27   96.1   0.3    1.3  1  HAD          haloacid dehalogenase-like hydrolase
    4.9e-10   40.0   0.2    1.6e-09   38.4   0.2    1.8  1  Hydrolase    haloacid dehalogenase-like hydrolase
    1.3e-06   28.3   0.0    5.4e-06   26.3   0.0    1.9  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.44   10.2   2.0         13    5.5   0.0    2.5  2  DUF3918      Protein of unknown function (DUF3918)


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.3   7.3e-31   3.3e-27       1     187 [.     124     310 ..     124     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 7.3e-31
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllal....frellrldraglaelleallagls.eelaaeler 75 
                                    a+fD+D TL++g+s+ ++ r l++r+    +r ++ +l+++     + +  ++d a+ ++   a+ +g s +el a  e+
  gi|121636423|ref|YP_976646.1| 124 AFFDVDNTLVQGSSAVHFGRGLAARHYFT-YRDVLGFLYAQAkfqlLGKENSNDVAAGRRKALAFIEGRSvAELVALGEE 202
                                    8*******************777776666.88888887777763333344445566667777779999999999999999 PP

                            HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegk 154
                                    +++e+i+ k++  g +el + h++aG +v+++++++ +l+  ++++lg    l+t  e++d  +tg+  l g + +g gk
  gi|121636423|ref|YP_976646.1| 203 IYDEIIADKIW-DGTRELTQMHLDAGQQVWLITATPYELAATIARRLGLTGALGTVAESVDgIFTGR--LVGEILHGTGK 279
                                    99999999999.9***********************************9999***999999******..*********** PP

                            HAD 155 vaalrewlaaegegidleevvayGDspsDlpll 187
                                    ++a+r+ + +eg ++++  + ay+Ds++D+p+l
  gi|121636423|ref|YP_976646.1| 280 AHAVRSLAIREGLNLKR--CTAYSDSYNDVPML 310
                                    ******77777777765..99***********9 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   3.6e-13   1.6e-09       3     207 ..     123     311 ..     121     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.6e-13
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH..........HHHH..HHHHHETTTEHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxx..xxxxxxxxxxxxx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar..........sgal..tgfatfigrgaya 70 
                                    + +fD+d+TL++g++ v+     a           ++        +++  r          +++l  +++        +a
  gi|121636423|ref|YP_976646.1| 123 AAFFDVDNTLVQGSSAVHFGRGLA-----------AR--------HYFTYRdvlgflyaqaKFQLlgKENSN-----DVA 178
                                    679***********7766655555...........22........222222222221112233333355555.....888 PP

                                    HTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  71 igkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpeta 148
                                     g+++ l+                 +gr+va l   +++  +  iad+  ++++++e+ +   +ag +v+l+t    e a
  gi|121636423|ref|YP_976646.1| 179 AGRRKALAFI---------------EGRSVAELvaLGEEIYDEIIADK--IWDGTRELTQMHLDAGQQVWLITATPYELA 241
                                    9999988888...............66666666335588888899999..***********999**************** PP

                                    HHHHHHTT....GGGESEEEEHHCES..STTT.SHHHHHHHHHHHT....STGGGEEEEESSHHHHHHHH CS
                                    xxxxxxxx....xxxxxxxxxxxxxx..xxxx.xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 149 eraanqlG....ddyfdaviasdiet..vakp.spegkvaaireLq....gkpeevamVGDgvnDaaala 207
                                      +a++lG      +++ +++++ ++  v++  +  gk +a+r L      + +++ +  D+ nD+++l 
  gi|121636423|ref|YP_976646.1| 242 ATIARRLGltgaLGTVAESVDGIFTGrlVGEIlHGTGKAHAVRSLAiregLNLKRCTAYSDSYNDVPMLS 311
                                    ********98875555555555555567666567888888888885444477888*************97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.31   1.4e+03       2      13 ..     125     136 ..     124     140 .. 0.81
   2 !   26.3   0.0   1.2e-09   5.4e-06     184     229 ..     275     320 ..     259     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                                    EEEIIIIIS-TT CS
                    Hydrolase_3   2 alDlDGTLlnsd 13 
                                    ++D+D TL++  
  gi|121636423|ref|YP_976646.1| 125 FFDVDNTLVQGS 136
                                    89******9865 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.2e-09
                                    TT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET CS
                    Hydrolase_3 184 kgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmg 229
                                    +g+ K++a++ la + +++l+++ a  D+ ND++ML+ +g++vA++
  gi|121636423|ref|YP_976646.1| 275 HGTGKAHAVRSLAIREGLNLKRCTAYSDSYNDVPMLSLVGTAVAIN 320
                                    5789****************************************85 PP

>> DUF3918  Protein of unknown function (DUF3918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0029        13       6      26 ..     136     156 ..     135     158 .. 0.91
   2 ?    3.0   1.0     0.017        78       5      23 ..     350     369 ..     349     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0029
                        DUF3918   6 tSllalGaGaaayqmaqkndm 26 
                                    +S++ +G G aa ++ + +d+
  gi|121636423|ref|YP_976646.1| 136 SSAVHFGRGLAARHYFTYRDV 156
                                    69*************999887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.017
                        DUF3918   5 mtSllalGa.Gaaayqmaqk 23 
                                    ++S+lalGa G a + +a++
  gi|121636423|ref|YP_976646.1| 350 VPSALALGAaGGALAALASR 369
                                    58******766666667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2764.14
//
Query:       gi|121636424|ref|YP_976647.1|  [L=147]
Description: membrane protein mmpS2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-64  214.8   0.2    4.3e-64  214.6   0.2    1.0  1  Mycobact_memb  Mycobacterium membrane protein
  ------ inclusion threshold ------
      0.081   13.0   0.0       0.15   12.2   0.0    1.4  1  DUF2953        Protein of unknown function (DUF2953)


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6   0.2   4.8e-68   4.3e-64       1     138 [.      10     146 ..      10     147 .] 0.99

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 4.8e-68
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEB-B----TT-----B---TTS------S CS
                  Mycobact_memb   1 lkrlWiplvivvvvvvggltvsrlhsifgsekrasvadklaedskpfnPkkvkyevfGpagtvadisyldadaepqridg 80 
                                    +kr+W++l+ivvv+vvggl+++rlhsifg++++++v+ k + d+ +fnPk+v+yevfGpa+t a+i+yld+da+++r+d+
  gi|121636424|ref|YP_976647.1|  10 VKRMWLLLAIVVVAVVGGLGIYRLHSIFGVHEQPTVMVKPDFDVPLFNPKRVTYEVFGPAKT-AKIAYLDPDARVHRLDS 88 
                                    69************************************************************.***************** PP

                                    -SS--B--EE-SSS------B--SS-S------BBTTB---------S-TTSSS--S- CS
                  Mycobact_memb  81 aalPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevnaltyClvks 138
                                    ++lPWs+t++ttl+av++n++aq+n+d+i+Criiv+g+vkder++++ +alt+C+v+s
  gi|121636424|ref|YP_976647.1|  89 VSLPWSVTVETTLPAVSVNLMAQSNADVISCRIIVNGAVKDERSETSPRALTSCQVSS 146
                                    ********************************************************98 PP

>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.15      28      52 ..      32      57 ..      20      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                        DUF2953 28 llsnlfni.kkpeievtPvFneevfe 52
                                   +l++ f + ++p ++v P+F+ + f+
  gi|121636424|ref|YP_976647.1| 32 RLHSIFGVhEQPTVMVKPDFDVPLFN 57
                                   678999999************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1146.53
//
Query:       gi|121636425|ref|YP_976648.1|  [L=968]
Description: transmembrane transport protein mmpL2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-215  714.6  22.4   9.4e-111  369.9   7.7    2.3  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.9   7.7  5.2e-115  9.4e-111       1     333 []      54     382 ..      54     382 .. 0.99
   2 !  350.6   6.7  4.1e-109  7.3e-105       2     331 ..     602     937 ..     601     939 .. 0.98

  Alignments for each domain:
  == domain 1  score: 369.9 bits;  conditional E-value: 5.2e-115
                           MMPL   1 slspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaaf 80 
                                    s+sp+da+s++a++r+++ f e  dsd+++++vl egd+ lg  +a++++ +l+++l++dt+hv++++df++dp +aa+ 
  gi|121636425|ref|YP_976648.1|  54 SMSPSDAASIQAIKRVGQVFGE-FDSDNAVTIVL-EGDQPLGG-DAHRFYSDLMRKLSADTRHVAHIQDFWGDPLTAAGS 130
                                    689*******************.***********.********.************************************ PP

                           MMPL  81 vSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviL 160
                                    +S+D++aa+++v+l g+ ++tea++sv+a+r++v+ ++p++g+k++vtGpaa++ad+++a+d+++++++++t +vi+++L
  gi|121636425|ref|YP_976648.1| 131 QSADDRAAYVVVYLVGN-NETEAYDSVHAVRHMVDTTPPPHGVKAYVTGPAALNADQAEAGDKSIAKVTAITSMVIAAML 209
                                    ***************86.788999******************************************************** PP

                           MMPL 161 livyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeav 240
                                    l++yrS+++a+l+l++v+++l+a +g++++la+++++ lstf+++llv+++ia++tDYa+++++Ry+e + agedre+a+
  gi|121636425|ref|YP_976648.1| 210 LVIYRSVITAVLVLIMVGIDLGAIRGFIALLADHNIFSLSTFATNLLVLMAIAASTDYAIFMLGRYHESRYAGEDRETAF 289
                                    ******************************************************************************** PP

                           MMPL 241 iravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWr 320
                                    ++++++t++v++++Glt+a+am++L++arlp+++++G +ia+G+lv+vl++lTl PA+l++ + ++l++p+r++++r+Wr
  gi|121636425|ref|YP_976648.1| 290 YTMFHGTAHVILGSGLTIAGAMYCLSFARLPYFETLGAPIAIGMLVAVLAALTLGPAVLTVGSFFKLFDPKRRMNTRRWR 369
                                    ******************************************************************************** PP

                           MMPL 321 rlgrlvvrrPlpv 333
                                    r+g+++vr+P pv
  gi|121636425|ref|YP_976648.1| 370 RVGTAIVRWPGPV 382
                                    **********986 PP

  == domain 2  score: 350.6 bits;  conditional E-value: 4.1e-109
                           MMPL   2 lspadaesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.......... 70 
                                    ls++++ +vk+md l + +p+  a+++++i ++++++d++l  + +  a+ ++ ++ +kd++++g+v+d+          
  gi|121636425|ref|YP_976648.1| 602 LSEKLEYLVKDMDILITLLPQmRAQMPPMISAMTTMRDMMLIWHGTLGAFYKQQERNNKDPGAMGRVFDAaqiddsfylp 681
                                    789999****************************************************************9999999999 PP

                           MMPL  71 ...lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdas 141
                                       +++pd   + ++f+S+Dgkaar+++ legdp+++e++ +v+ i++ ++ea    pl+g++++++G+aat++d+r+++
  gi|121636425|ref|YP_976648.1| 682 qsaFENPDfkrGLKMFLSPDGKAARFVIALEGDPATPEGICRVEPIKREAREAIkgtPLQGAAIYLGGTAATFKDIREGA 761
                                    99999***9999******************************************************************** PP

                           MMPL 142 drdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYal 220
                                    ++dl +++v+++ +il+i++i++rS+vaa+++++tvv+s++a++gl vl+++++lg+el+++vl+++v+ll+avG+DY+l
  gi|121636425|ref|YP_976648.1| 762 RYDLLIAGVAAISLILIIMMIITRSVVAAVVIVGTVVLSMGASFGLsVLVWQDILGIELYWMVLAMSVILLLAVGSDYNL 841
                                    ******************************************************************************** PP

                           MMPL 221 lLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAll 299
                                    lL+sR++ee++ag ++  ++ira+a+tg+vvtaaG+++a++m  +v+++l++++q+G++i+lG+l+d+l+v++++ P+++
  gi|121636425|ref|YP_976648.1| 842 LLISRLKEEIGAGLNT--GIIRAMAGTGGVVTAAGMVFAVTMSLFVFSDLRIIGQIGTTIGLGLLFDTLVVRSFMtPSIA 919
                                    ****************..************************************************************** PP

                           MMPL 300 vllGraalakprrkrkkrwWrrlgrlvvrrPl 331
                                    +llGr+           +wW+ +   v++rP+
  gi|121636425|ref|YP_976648.1| 920 ALLGRW-----------FWWPLR---VRPRPA 937
                                    ******...........***877...888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (968 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 6285.96
//
Query:       gi|121636426|ref|YP_976649.1|  [L=97]
Description: hypothetical protein BCG_0551 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   61.0   0.0    1.2e-16   60.9   0.0    1.0  1  DUF836        Glutaredoxin-like domain (DUF836)
     0.0046   16.8   0.0     0.0057   16.5   0.0    1.1  1  TraF          F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.051   13.8   0.0    1.8  2  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0     2e-20   1.2e-16       2      81 ..       6      83 ..       5      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2e-20
                                   EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT.....T-CCCHCCCCTTTTEEEECTTCGGB.TCCECGCCB-HHHHH CS
                         DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIa.....kdeeleakYgleipvlalegvkktsslleelswrldeeqLa 78
                                   + L+++ gC +C ++ e+L+el+ e g+++ +iD++     +++ l+a++g++ pv++l+g       +e+++w++de++L+
  gi|121636426|ref|YP_976649.1|  6 VELLTRAGCAICVRVAEQLAELSSELGFDMMTIDVDvaastGNPGLRAEFGDRLPVVLLDG-------REHSYWEVDEHRLR 80
                                   89**********************************999988888****************.......************** PP

                                   HHH CS
                         DUF836 79 ael 81
                                   a++
  gi|121636426|ref|YP_976649.1| 81 ADI 83
                                   *98 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.6e-07    0.0057     136     175 ..       9      48 ..       7      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.6e-07
                           TraF 136 FyrgkcpyceaqapilqafadkyglevraVsvdgrplpel 175
                                    + r++c +c   a+ l ++  + g++++ ++vd   +++ 
  gi|121636426|ref|YP_976649.1|   9 LTRAGCAICVRVAEQLAELSSELGFDMMTIDVDVAASTGN 48 
                                    6789*****************************8887654 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.5e-06     0.051       1      58 [.       6      67 ..       6      69 .. 0.73
   2 ?   -0.3   0.0      0.22   1.3e+03      26      44 ..      69      86 ..      63      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-06
                                   EEEEESTSSHHHHHHHHHH....HHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETTE CS
                   Glutaredoxin  1 vvlftkptCpyCkkakrlL....kelgvkfeeidvdkde.eireelkelsgvrtvPqvfidgk 58
                                   v+l t+ +C  C+++ + L     elg++  +idvd  +      l++  g   +P+v  dg+
  gi|121636426|ref|YP_976649.1|  6 VELLTRAGCAICVRVAEQLaelsSELGFDMMTIDVDVAAsTGNPGLRAEFG-DRLPVVLLDGR 67
                                   78999**************77777777888888888775534444444446.67777777775 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                                   EEEEEGCCSHHHHHHHHHH CS
                   Glutaredoxin 26 feeidvdkdeeireelkel 44
                                   + + +vd++  +r+++ + 
  gi|121636426|ref|YP_976649.1| 69 HSYWEVDEH-RLRADIARS 86
                                   567789998.888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 743.23
//
Query:       gi|121636427|ref|YP_976650.1|  [L=468]
Description: glutamyl-tRNA reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-44  150.3   2.1    5.9e-44  149.4   0.5    2.2  2  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    2.7e-30  105.3   0.4    6.4e-30  104.0   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      5e-22   78.2   0.5    1.2e-21   77.0   0.2    1.8  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    1.7e-05   24.4   1.3    6.7e-05   22.5   0.5    2.2  2  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    5.7e-05   23.4   0.6    0.00018   21.7   0.6    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0015   18.7   3.1     0.0026   17.9   0.1    2.4  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0033   16.8   3.0     0.0047   16.3   1.8    1.8  2  ThiF             ThiF family
     0.0038   17.8   1.1      0.014   16.0   0.2    2.3  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0038   16.9   0.3     0.0096   15.6   0.3    1.7  1  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
        0.1   13.1   0.4       0.29   11.6   0.4    1.8  1  NAD_binding_7    Putative NAD(P)-binding
        0.1   12.8   0.4       0.37   11.1   0.4    2.0  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.17   11.7  13.8      0.012   15.5   6.2    2.7  2  NAD_binding_10   NAD(P)H-binding
       0.49   10.1   3.5       0.82    9.4   2.4    2.1  1  TfuA             TfuA-like protein


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.5   4.3e-47   5.9e-44       2     146 .]       7     156 ..       6     156 .. 0.96
   2 ?   -0.8   0.0      0.86   1.2e+03     126     144 ..     210     228 ..     197     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 4.3e-47
                        GlutR_N   2 ginhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevs...leelke 76 
                                    g++h++apv ++e+l+++e+++ ++++++ ++  v+ea++LsTCNR+E+y+++++ +   + + ++lae+s     el++
  gi|121636427|ref|YP_976650.1|   7 GVSHRSAPVVVLEQLSIDESDQVKIIDRVlASpLVTEAMVLSTCNRVEVYAVVDAFHGGLSVIGQVLAEHSgmsMGELTK 86 
                                    89**************************97665777*************************9*****999666799999* PP

                        GlutR_N  77 klyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                    ++yv+  e+av+Hlf VasGLdS+v+GE+q+lgQv++ay+ a++++t+g+vL++l q+a++v+krv++et
  gi|121636427|ref|YP_976650.1|  87 YAYVRYSEAAVEHLFAVASGLDSAVIGEQQVLGQVRRAYAVAESNRTVGRVLHELAQRALSVGKRVHSET 156
                                    ********************************************************************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.86
                        GlutR_N 126 kvLerlfqkaikvakrvrt 144
                                    +vL+r +++a + a+r+r+
  gi|121636427|ref|YP_976650.1| 210 QVLNRSLSRAQRLARRIRE 228
                                    79***************97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   4.6e-33   6.4e-30       2     137 ..     172     314 ..     171     315 .. 0.92
   2 ?   -3.5   0.0       7.4     1e+04      24      40 ..     333     349 ..     327     365 .. 0.68

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 4.6e-33
                                    HHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHHHHT-SEE CS
                   Shikimate_DH   2 lakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkellaeadvv 79 
                                    +a++kl+sl++ ++++iGaG m+ l a hL ++gv ++ v+NR+l+ra++la+++  +g+ +eal+l+ l ++la+advv
  gi|121636427|ref|YP_976650.1| 172 MAERKLGSLAGTTAVVIGAGAMGALSAVHLTRAGVGHIQVLNRSLSRAQRLARRIreSGVPAEALALDRLANVLADADVV 251
                                    699****************************************************6667899****************** PP

                                    EE-SSSSS-SB-HHHHHCCHHH.S.......EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
                   Shikimate_DH  80 isataseepilekeeveealkkrk.....kplllvDiavPRdvepevaeledvrlytvDdLke 137
                                    +s+t++  p+++ ++v++al++ +     +pl++ D+++PRdv+p+va l  v +++vD +++
  gi|121636427|ref|YP_976650.1| 252 VSCTGAVRPVVSLADVHHALAAARrdeatRPLVICDLGMPRDVDPAVARLPCVWVVDVDSVQH 314
                                    ***************99987643333566788***************************9875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.4
                                    HHHHHHHHHCCT-CEEE CS
                   Shikimate_DH  24 aelvakhLlakgvkkvv 40 
                                    a +va++L+ +++ +v+
  gi|121636427|ref|YP_976650.1| 333 AAEVASYLVGQRMAEVT 349
                                    45667777777666664 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.2   8.3e-25   1.2e-21       2      97 .]     328     426 ..     327     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 8.3e-25
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S...--------TTHHHHHHHHHHHHHHHHHHSS CS
                    GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla.ldgedreelekltrslvnkllheptarLkea 80 
                                    A++i+++ev++++  ++  ev+pt+ alr++a e++e+el r+ ++l+ l+  +ree+ + +r++v+kllh+pt+r+k++
  gi|121636427|ref|YP_976650.1| 328 ARHIVAAEVASYLVGQRMAEVTPTVTALRQRAAEVVEAELLRLDNRLPgLQSVQREEVARTVRRVVDKLLHAPTVRIKQL 407
                                    99****************************************************************************** PP

                                    ..-TTTTHHHHHHHHH... CS
                    GlutR_dimer  81 ..edeeeellealrrlFnl 97 
                                      +  +++++ealr+lF+l
  gi|121636427|ref|YP_976650.1| 408 asAPGGDSYAEALRELFEL 426
                                    8666666**********86 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.56   7.7e+02     165     203 ..      91     129 ..      87     138 .. 0.83
   2 !   22.5   0.5   4.9e-08   6.7e-05      24     116 ..     175     263 ..     161     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.56
                    Glu_dehyd_C 165 rhfeaavdtLaalpeslldelvtkvvdldeleeAfeddd 203
                                    r  eaav++L a+ + l ++++ ++  l ++++A++  +
  gi|121636427|ref|YP_976650.1|  91 RYSEAAVEHLFAVASGLDSAVIGEQQVLGQVRRAYAVAE 129
                                    5558999********9999**************998554 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 4.9e-08
                    Glu_dehyd_C  24 rsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdl 103
                                    r+  +   ++a+v+GaG++G L++++l+    g+ ++ vl+r    +++ +l +++    v  +   +d+++++  + d+
  gi|121636427|ref|YP_976650.1| 175 RKLGSLAGTTAVVIGAGAMGALSAVHLTR--AGVGHIQVLNRS--LSRAQRLARRIRESGVPAEALALDRLANVLADADV 250
                                    4445567789*************999985..89999*****85..4577888999999999999**************** PP

                    Glu_dehyd_C 104 vvEaTGsakhafe 116
                                    vv +TG+ + ++ 
  gi|121636427|ref|YP_976650.1| 251 VVSCTGAVRPVVS 263
                                    ******9887664 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.6   1.3e-07   0.00018       2      81 ..     186     259 ..     185     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                    EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81 
                                    ++iGaG++G   a  l r +    +i v  rs++++++la  ++++ + a+al  +     La +l+++d+vv++++ + 
  gi|121636427|ref|YP_976650.1| 186 VVIGAGAMGALSAVHLTRAGVG--HIQVLNRSLSRAQRLARRIRESGVPAEALALD---R-LANVLADADVVVSCTGAVR 259
                                    89****************9976..****************7776666666666555...4.66699999******99874 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.49   6.7e+02       6      79 ..      65     144 ..      63     174 .. 0.55
   2 !   17.9   0.1   1.9e-06    0.0026       4      74 ..     187     266 ..     184     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.49
                                    --SHHHHHHHHHH..HHTT-EEEEE-S.SHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC CS
                  NAD_binding_2   6 GlGvMGsnmalnl..lkagykvavynr.tkekveelvaeg...akaaesieelvasldvvitmvkagkavdeviegllea 79 
                                    Gl v+G+ +a++      + + ++y r ++++ve+l a      +a+   ++++ +++    + ++++ v  v+ +l+++
  gi|121636427|ref|YP_976650.1|  65 GLSVIGQVLAEHSgmSMGELTKYAYVRySEAAVEHLFAVAsglDSAVIGEQQVLGQVRRAYAVAESNRTVGRVLHELAQR 144
                                    88888999998874233333444444413445555543322321222222355556677777777777777777776543 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.9e-06
                                    EE--SHHHHHHHHHHHHTT-.EEEEE-SSHHHHHHHHHTT........EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHH CS
                  NAD_binding_2   4 fiGlGvMGsnmalnllkagy.kvavynrtkekveelvaeg........akaaesieelvasldvvitmvkagkavdevie 74 
                                    +iG G MG+  a +l++ag  ++ v nr+ +++++l+ +         a a++ +++++a++dvv+ +  a ++v ++ +
  gi|121636427|ref|YP_976650.1| 187 VIGAGAMGALSAVHLTRAGVgHIQVLNRSLSRAQRLARRIresgvpaeALALDRLANVLADADVVVSCTGAVRPVVSLAD 266
                                    8*****************9758**************99866788998899999999************999988877655 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.8   3.4e-06    0.0047      12      48 ..     176     212 ..     163     216 .. 0.87
   2 ?   -3.4   0.0       3.6     5e+03     103     117 ..     241     255 ..     218     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                    HHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  12 gqekLrdskvllvGaGglGsellknLalsGvgkltlv 48 
                                     +  L+ ++ +++GaG+ G   ++ L ++Gvg++++ 
  gi|121636427|ref|YP_976650.1| 176 KLGSLAGTTAVVIGAGAMGALSAVHLTRAGVGHIQVL 212
                                    555788999*************************985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                                    -HHHHTT-SEEEEES CS
                                    xxxxxxxxxxxxxxx RF
                           ThiF 103 leellesvDlVvdal 117
                                    l ++l ++D+Vv ++
  gi|121636427|ref|YP_976650.1| 241 LANVLADADVVVSCT 255
                                    346788899999887 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.3   3.1e+03      43      75 ..     142     174 ..     112     183 .. 0.60
   2 !   16.0   0.2   9.9e-06     0.014       4      68 ..     187     254 ..     184     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                                    HHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                  F420_oxidored  43 aeelgvkvtavdneeaaeeadvvvlavkpedve 75 
                                    a+++    + v+ e+a++ a   v++v   ++e
  gi|121636427|ref|YP_976650.1| 142 AQRALSVGKRVHSETAIDAAGASVVSVALGMAE 174
                                    333332223335566666666666666555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.9e-06
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......-EEECECHHHHHHH-SEEEE- CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......vkvtavdneeaaeeadvvvla 68 
                                    +iGaG mg+  a  l++ag    +i v  +r+ ++a+ la+++        + +     + ++++advvv +
  gi|121636427|ref|YP_976650.1| 187 VIGAGAMGALSAVHLTRAG--VGHIQVL-NRSLSRAQRLARRIResgvpaeALALD-RLANVLADADVVVSC 254
                                    89*****************..7888855.*************99888775433333.566677789999876 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   6.9e-06    0.0096       2      37 ..     186     223 ..     185     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                                    EEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHH CS
                           ApbA   2 ailGaGaiGsllaakLakagad.vtlilrsr.rlealk 37 
                                    +++GaGa+G l a++L++ag   + +++rs  r+++l 
  gi|121636427|ref|YP_976650.1| 186 VVIGAGAMGALSAVHLTRAGVGhIQVLNRSLsRAQRLA 223
                                    69****************88774777777665555544 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00021      0.29       5      70 ..     180     256 ..     178     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeeleelvklaeeelekd..........legadlviaatd 70 
                                    l g + +v+G+G ++a  + +l +ag  +++v+   ++++     +++e+ ++++          l++ad+v+ +t 
  gi|121636427|ref|YP_976650.1| 180 LAGTTAVVIGAGAMGALSAVHLTRAGvGHIQVLNRSLSRAQRLARRIRESGVPAEalaldrlanvLADADVVVSCTG 256
                                    678899********************779***999964444433445555554444455555555999*****9996 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00027      0.37       1      26 [.     187     213 ..     187     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                    EE--SHHHHHHHHHHHCCTE.EEEEE- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvllle 26 
                                    ++GaG+ G++ A +L++ag+ ++++l 
  gi|121636427|ref|YP_976650.1| 187 VIGAGAMGALSAVHLTRAGVgHIQVLN 213
                                    8*****************998888875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.2      0.18   2.5e+02       9      72 ..     136     194 ..     130     201 .. 0.78
   2 ?   15.5   6.2   8.6e-06     0.012       3     111 ..     190     300 ..     189     396 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.18
                                    HHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                 NAD_binding_10   9 llvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                    ++++el++r  ++v   v ++  ++    ++g++vv++ +  +e     l+g+ aVv+ +g+ g
  gi|121636427|ref|YP_976650.1| 136 RVLHELAQR-ALSVGKRVHSETAID----AAGASVVSVALGMAERKLGSLAGTTAVVIGAGAMG 194
                                    456677777.478777777777776....58999******9999999*********99998765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.6e-06
                                    TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHH..H CS
                 NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..deeg..a 78 
                                     G  G l + +l ++g  ++ +l R+ +++++l+++ + + v ++++  + la++l++ad+Vvs++g+ +         +
  gi|121636427|ref|YP_976650.1| 190 AGAMGALSAVHLTRAGVGHIQVLNRSLSRAQRLARRIRESGVPAEALALDRLANVLADADVVVSCTGAVRPvvS--LadV 267
                                    5888889999999999557899************999*****************************99888543..3458 PP

                                    HHHHHHHHHCT--EEEEEEETTTTSGCGCHHHH CS
                 NAD_binding_10  79 knivdaakeagvkRfvlvsaigvgdevpgefge 111
                                     ++++aa++ +  R +++  +g+ ++v+ ++ +
  gi|121636427|ref|YP_976650.1| 268 HHALAAARRDEATRPLVICDLGMPRDVDPAVAR 300
                                    999999999999999999999998877766544 PP

>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.4    0.0006      0.82      23      45 ..     185     207 ..     172     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0006
                           TfuA  23 vavvGaasmGALRAaElaafGmi 45 
                                      v+Ga++mGAL A+ l++ G+ 
  gi|121636427|ref|YP_976650.1| 185 AVVIGAGAMGALSAVHLTRAGVG 207
                                    679***************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2948.50
//
Query:       gi|121636428|ref|YP_976651.1|  [L=309]
Description: porphobilinogen deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-66  223.5   0.0    2.5e-66  223.1   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    4.3e-22   78.3   1.0      1e-21   77.1   1.0    1.7  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.072   13.2   0.0    1.6  1  FrhB_FdhB_N      Coenzyme F420 hydrogenase/dehydrogenase, bet


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.0   4.1e-70   2.5e-66       1     202 [.       2     204 ..       2     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 4.1e-70
                 Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlpt 79 
                                    irigtR+S LA++qa +v++aL +  ++ e+vti+t+GD+    p+a++ g g+Ft++l+ea+ +g +d aVhS+KDlpt
  gi|121636428|ref|YP_976651.1|   2 IRIGTRGSLLATTQAATVRDALIAgGHSAELVTISTEGDRSM-APIASL-GVGVFTTALREAMEAGLVDAAVHSYKDLPT 79 
                                    89********************7745568************9.8****9.69**************************** PP

                 Porphobil_deam  80 elpeglelaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydai 157
                                    + ++++++aa+++r+dprD++v+++  +l elp g+ vgTsS+RR+aql++l   le+++lRGn+dtRl+k+++g++dai
  gi|121636428|ref|YP_976651.1|  80 AADPRFTVAAIPPRNDPRDAVVARDglTLGELPVGSLVGTSSPRRAAQLRALGLGLEIRPLRGNLDTRLNKVSSGDLDAI 159
                                    **********************866899**************************************************** PP

                 Porphobil_deam 158 iLAaAGLkRlgleerisevlspeellpavgQGalavevrkedeel 202
                                    ++A+AGL Rlg  ++++e+l+p ++lpa++QGalave+r++d++l
  gi|121636428|ref|YP_976651.1| 160 VVARAGLARLGRLDDVTETLEPVQMLPAPAQGALAVECRAGDSRL 204
                                    ***********99999999**********************9876 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   1.0   1.7e-25     1e-21       3      74 ..     219     296 ..     217     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.7e-25
                                    HHHHHHHHHHHTT--TTSSEEEEEEEE..TTE........EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHH CS
                Porphobil_deamC   3 evlaERallkeLeGGCsvPiGvyaeve..ane.......elkLkglvlsldglksaveeaeakgeleeaeelGkklaeel 73 
                                    +v+aERall++Le+GCs+P+G++aev+    +       el+L+g+v++ldg++  v++a++ g++ +a+elG+++a+el
  gi|121636428|ref|YP_976651.1| 219 AVTAERALLADLEAGCSAPVGAIAEVVesI-DedgrvfeELSLRGCVAALDGSD--VIRASGIGSCGRARELGLSVAAEL 295
                                    79************************9752.24799****************99..***********************9 PP

                                    H CS
                Porphobil_deamC  74 l 74 
                                    +
  gi|121636428|ref|YP_976651.1| 296 F 296
                                    7 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.072      19      53 ..      52      87 ..      40      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                    FrhB_FdhB_N 19 GivtallkylLeegiidgvivvaps.kdpwrpkpvi 53
                                   G+ t+ l +++e g++d++++  ++     +p+ ++
  gi|121636428|ref|YP_976651.1| 52 GVFTTALREAMEAGLVDAAVHSYKDlPTAADPRFTV 87
                                   99*******************998863344555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2287.66
//
Query:       gi|121636429|ref|YP_976652.1|  [L=565]
Description: uroporphyrin-III c-methyltransferase hemD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-63  211.6   0.0    2.7e-62  210.1   0.0    1.7  2  HEM4          Uroporphyrinogen-III synthase HemD
    1.2e-40  139.7   4.8      2e-40  139.0   4.8    1.4  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.24   2.1e+03     193     215 ..     265     287 ..     255     290 .. 0.78
   2 !  210.1   0.0     3e-66   2.7e-62       2     231 ..     309     539 ..     308     540 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.24
                                    HHHCTSEEEEESHHHHHHHHHTT CS
                           HEM4 193 delkevkvaaiGptTaealkklg 215
                                    d + +  +++iG+t++  +k + 
  gi|121636429|ref|YP_976652.1| 265 DSQAGPLIVTIGKTVTSRAKLNW 287
                                    67788899******999997655 PP

  == domain 2  score: 210.1 bits;  conditional E-value: 3e-66
                                    HHHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSH CS
                           HEM4   2 elaealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGp 81 
                                    e++e+l ++Ga p+e+P+i +ep++++a++++a++ l +g+++w++ftS+nav+a+ e+  + ++d +a + +k+a+vG+
  gi|121636429|ref|YP_976652.1| 309 EMSERLTSYGALPVEVPTIAVEPPRSPAQMERAVKGLVDGRFQWIVFTSTNAVRAVWEKFGEFGLDARAFSGVKIACVGE 388
                                    799***************************************************************************** PP

                                    HHHHHHHHTT---SEE-..SSSHHHHGGGS-....---E.EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHH CS
                           HEM4  82 aTaraLeelglrvdlvpseegtaegLaeelae...slag.krvlllrgeiarddlaegLeergaevdevevYetvpaeee 157
                                    +Ta+ ++++g+ ++lvps e+++ gL++ +++      +  rvll+r++ia ++laegL+erg e+++v++Y+tv+a + 
  gi|121636429|ref|YP_976652.1| 389 STADRVRAFGISPELVPSGEQSSLGLLDDFPPydsVFDPvNRVLLPRADIATETLAEGLRERGWEIEDVTAYRTVRAAPP 468
                                    ********************************7753333477************************************** PP

                                    HHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHHH CS
                           HEM4 158 peelkealkagevdavvftSpstvrnllellkdegdelkevkvaaiGptTaealkklglkvdvvaeeptaeglv 231
                                    p++++e++k+g +dav+ftS+stvrnl+ ++++   ++ ++ +a+iGp Tae+++++gl+vdv+++++ ++ lv
  gi|121636429|ref|YP_976652.1| 469 PATTREMIKTGGFDAVCFTSSSTVRNLVGIAGK---PHARTIIACIGPKTAETAAEFGLRVDVQPDTAAIGPLV 539
                                    ********************************8...9*****************************99988877 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   4.8   2.2e-44     2e-40       1     211 [.      11     245 ..      11     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 2.2e-44
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel...............................e 49 
                                    ++++VG GpGdp llT rA+++l++a +v++d   ++e + +l+  +l                               +
  gi|121636429|ref|YP_976652.1|  11 RIVFVGSGPGDPGLLTTRAAAVLANAALVFTDP-DVPEPVVALIGTDLppvsgpapaepvagngdaagggsaqehgraaS 89 
                                    689******************************.**********999999977766666555555555544444444444 PP

                   TP_methylase  50 leapmgkekepleea..............yeeiaealaealragkdVvllvsGDPlvygtgselvealrareagievevi 115
                                                  a               +++a++l++++r+g dVv+lv+GDPl  ++++ +v+a+++   ++++e++
  gi|121636429|ref|YP_976652.1|  90 --------------AvvsggpdirpalgdPADVAKTLTAEARSGVDVVRLVAGDPLTVDAVISEVNAVAR--THLHIEIV 153
                                    ..............055555566666666*****************************************..889***** PP

                   TP_methylase 116 PGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea.lyddttpvavv 194
                                    PG  + +a+++++g+pl+ +++v +v      ++e ++++al+a++++l+l  + ++lae a+ L+++ l + t p++v+
  gi|121636429|ref|YP_976652.1| 154 PGLAASSAVPTYAGLPLGSSHTVADVR----IDPENTDWDALAAAPGPLILQATASHLAESARSLIDHqLAEST-PCVVT 228
                                    ***************************....55899********************************888755.***** PP

                   TP_methylase 195 eragtedervvrgtlee 211
                                    ++++t ++r v++tl+ 
  gi|121636429|ref|YP_976652.1| 229 AHGTTCQQRSVETTLQG 245
                                    ***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 4400.39
//
Query:       gi|121636430|ref|YP_976653.1|  [L=329]
Description: delta-aminolevulinic acid dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.3e-130  435.2   0.0   1.5e-130  435.1   0.0    1.0  1  ALAD       Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
      0.044   13.4   1.5       0.15   11.6   0.3    2.0  2  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.1   0.0  1.6e-134  1.5e-130       2     317 .]       9     327 ..       8     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 435.1 bits;  conditional E-value: 1.6e-134
                                    --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-..S CS
                           ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp..e 79 
                                    +r+rrlr++ a+r+lv++t+l++++l+lp+fv +g +e+++i+smpgv++++ d+l ++++ +v++g+  ++lFgvp  +
  gi|121636430|ref|YP_976653.1|   9 QRPRRLRSTVAMRRLVAQTSLEPRHLVLPMFVADGIDEPRPITSMPGVVQHTRDSLRRAAAAAVAAGVGGLMLFGVPrdQ 88 
                                    79***************************************************************************644 PP

                                    S-BSS-GGGGSTTSHHHHHHHHHHHH-.TTSEEEEEE-STTTBSS-SSSEEE.SS.EEHHHHHHHHHHHHHHHHHCT-SE CS
                           ALAD  80 ekdeegsealnedglvqrairaikeev.pelvvitDvclceytshGhcgile.ekevdndetlellakvavsqaeaGadi 157
                                    +kd  gs+ +++dg+++ a+r + +++ + +v+++D+cl+e+t+hGhcg+l+ +++vdnd+t++++++ av+qae+Ga++
  gi|121636430|ref|YP_976653.1|  89 DKDGVGSAGIDPDGILNVALRDLAKDLgEATVLMADTCLDEFTDHGHCGVLDdRGRVDNDATVARYVELAVAQAESGAHV 168
                                    4**********************9999456899******************62456************************ PP

                                    EEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT CS
                           ALAD 158 vapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeG 237
                                    v+pS+mmDg+vaair+ Ld+ag+ +v il+Y+aK+aSafYgPFr+a++s+   gdr+tYq++p n+ ealre+eldl+ G
  gi|121636430|ref|YP_976653.1| 169 VGPSGMMDGQVAAIRDGLDAAGYIDVVILAYAAKFASAFYGPFREAVSSSL-SGDRRTYQQEPGNAAEALREIELDLDGG 247
                                    **************************************************9.6*************************** PP

                                    -SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH. CS
                           ALAD 238 ADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakevakl 317
                                    ADivmvKPa+ ylD+++++++ + +pvaayqvSGEYami+aaa+n+w+de+++vlEsl++i+RAGad++ltY+a ++a +
  gi|121636430|ref|YP_976653.1| 248 ADIVMVKPAMGYLDVVAAAADVSPVPVAAYQVSGEYAMIRAAAANNWIDERAAVLESLTGIRRAGADIVLTYWAVDAAGW 327
                                    ****************************************************************************9977 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   1.7e-05      0.15      47     108 ..     125     186 ..     109     206 .. 0.78
   2 ?    0.5   0.0     0.042   3.8e+02      82     106 ..     243     268 ..     231     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHT.SEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHH CS
                      OMPdecase  47 klaalarkhg.flifeDrKfaDIGntvekqatagsarikewadivtvhavaGkasvkalaeaa 108
                                      ++++ +hg + ++ Dr ++D  +tv+++++ ++a+++++a++v  ++++ ++ v+a+ +++
  gi|121636430|ref|YP_976653.1| 125 TCLDEFTDHGhCGVLDDRGRVDNDATVARYVELAVAQAESGAHVVGPSGMM-DGQVAAIRDGL 186
                                    45678889998999*******************************988888.55555555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.042
                                    HHHTTESEEEEEGTGH.HHHHHHHHH CS
                      OMPdecase  82 rikewadivtvhavaG.kasvkalae 106
                                    + + +adiv v +++G  ++v+a+a+
  gi|121636430|ref|YP_976653.1| 243 DLDGGADIVMVKPAMGyLDVVAAAAD 268
                                    56779***********5566666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2562.94
//
Query:       gi|121636431|ref|YP_976654.1|  [L=182]
Description: hypothetical protein BCG_0556 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0089   16.3   0.2      0.013   15.7   0.2    1.2  1  DUF3093   Protein of unknown function (DUF3093)


Domain annotation for each model (and alignments):
>> DUF3093  Protein of unknown function (DUF3093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   7.3e-07     0.013       9      77 ..      19      92 ..      15     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.3e-07
                        DUF3093  9 plwwWllaalvalaaalvaaevglavavlv...aavlvalavvallalsr..trieVtdgeLrvgrarlplavv 77
                                   +++w l++ l+a++++l+ +  g +v++++   ++v+v ++v++ +++ r  t++e+t++ Lr g  ++ la +
  gi|121636431|ref|YP_976654.1| 19 SWYWVLTGPLAAVSVLLLEISSGAGVGLITpaiFLVMVSAFVALQVKAARihTSVELTHDALRQGTETIRLAEI 92
                                   56666666666555666666666666666696644444444444444444114556667999999999977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1239.49
//
Query:       gi|121636432|ref|YP_976655.1|  [L=99]
Description: hypothetical protein BCG_0557 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.68   10.0   5.6        1.1    9.3   5.6    1.4  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.6   6.2e-05       1.1      59      96 ..      25      80 ..       3      91 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6.2e-05
                Phage_holin_3_6 59 a.................lala.alwlaalivaavllvlagvlalvglkklkkakp 96
                                   +                 + l+ ++    l+++++l+ +agvl +vg ++l++a++
  gi|121636432|ref|YP_976655.1| 25 WsrtrstvavapvidgqpVTLSvVYHPQPLVLTLLLATIAGVLSVVGTARLRRARA 80
                                   13333333333555555555554477778999*********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 714.32
//
Query:       gi|121636433|ref|YP_976656.1|  [L=503]
Description: hypothetical protein BCG_0558 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-92  310.9  21.6      1e-92  310.9  21.6    1.4  2  DUF222      Domain of unknown function (DUF222)
     0.0034   17.2   0.9     0.0067   16.3   0.9    1.5  1  HNH_5       HNH endonuclease
  ------ inclusion threshold ------
      0.024   14.8   3.0      0.045   13.9   3.0    1.5  1  HNH         HNH endonuclease
       0.16   12.3   0.0       0.32   11.3   0.0    1.4  1  Invasin_D3  Invasin, domain 3


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.9  21.6   2.3e-96     1e-92       1     301 []      33     339 ..      33     339 .. 0.99
   2 ?   -4.3   1.3       2.3     1e+04     157     168 ..     468     479 ..     442     489 .. 0.43

  Alignments for each domain:
  == domain 1  score: 310.9 bits;  conditional E-value: 2.3e-96
                         DUF222   1 llaaleeleaaarrlaavevllvael...aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalr 77 
                                    ++a+++e++aaa++l a+++l+++++   ++re++ +d+++avaa+vaa+lris++ A++r+r+Ara+rerLp++a+++ 
  gi|121636433|ref|YP_976656.1|  33 CSATRAENRAAAAQLVALGELFAYRWsrcGGREEWVMDTMAAVAAEVAAALRISQGLAASRLRYARAMRERLPKTAEVFS 112
                                    5789*********************99999************************************************** PP

                         DUF222  78 aGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltkd 157
                                    aGdi++ ++++I++rtdl+ d ++la+vd+++aa+++r++++++a+La +vd++var+d+D+vrr++e +++r+++++++
  gi|121636433|ref|YP_976656.1| 113 AGDIGYLMFATIVYRTDLIVDPDVLAAVDAQLAANVARWPSMTKARLAGQVDKIVARADADAVRRRKEYQAQRQFWVGES 192
                                    ******************************************************************************** PP

                         DUF222 158 edGmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlall....rlalaagaldchagvp...atv 230
                                    +dG+++i g+l a++a+alda+L++la +vc++    DpRs++qrraDAL+al+    rl++++g++dc+ag++   + v
  gi|121636433|ref|YP_976656.1| 193 QDGVCQIGGSLLAVDAHALDARLSALAGTVCEH----DPRSREQRRADALGALAggadRLGCGCGRADCAAGKRpaaPPV 268
                                    *********************************....*************************************999*** PP

                         DUF222 231 vvhvtaeeltaaagg...aaltgggglLpasdvrrLAkdAtlaifdepagrpld.lgrtkrtasaalrralraRD 301
                                    v+h++ae +t +++g   a  ++++gl++a+ v++LAk+Atl     p  +p d  ++ ++++s+al++++r+RD
  gi|121636433|ref|YP_976656.1| 269 VIHLIAEAATINGTGsapASQMNADGLITAELVAELAKTATLV----PLVHPGDaPPEPGYAPSKALADFVRCRD 339
                                    *******************************************....******9889*****************9 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 2.3
                         DUF222 157 dedGmsrisgel 168
                                    +++  +r + ++
  gi|121636433|ref|YP_976656.1| 468 RQNHAARQRAQV 479
                                    222222222222 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   1.5e-06    0.0067       8      37 ..     349     378 ..     342     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                          HNH_5   8 iaekelseeHIiPeslGGkltisnlvtlCk 37 
                                     + ++   +H iP + GG ++ snl ++C+
  gi|121636433|ref|YP_976656.1| 349 EPATNCDLDHTIPYAAGGPTHASNLKCYCR 378
                                    45778999*********************8 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.0     1e-05     0.045       4      43 ..     342     383 ..     337     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHnk 43 
                                    C +++ ++  + +  dH ip++ gg++  +Nl + C++ H  
  gi|121636433|ref|YP_976656.1| 342 CRWPGCDEpaTNCDLDHTIPYAAGGPTHASNLKCYCRTHHLV 383
                                    666766666688999*********************987765 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.32      47      81 ..     281     315 ..     269     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                     Invasin_D3  47 sagtlsavtdngdGtytatLtattagtatitptvn 81 
                                     +g+  a + n+dG  ta+L a+ a+tat+ p v 
  gi|121636433|ref|YP_976656.1| 281 GTGSAPASQMNADGLITAELVAELAKTATLVPLVH 315
                                    3356667889**********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3833.10
//
Query:       gi|121636434|ref|YP_976657.1|  [L=158]
Description: hypothetical protein BCG_0559c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-12   46.5   0.0    3.1e-12   46.2   0.0    1.1  1  STAS      STAS domain
    4.4e-08   33.3   0.9    7.5e-08   32.6   0.1    1.7  2  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.5e-16   3.1e-12       7     117 .]      35     135 ..      29     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.5e-16
                                    CTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEE CS
                           STAS   7 iegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlv 86 
                                    ++  ++++++g+id+an+e++ e+++r    +          ++++ldls++s+ + +G++ L  + +++++ gv+++lv
  gi|121636434|ref|YP_976657.1|  35 HHLATVVTIRGEIDAANVEQISEHVRRFSLGT----------NPMVLDLSELSHFSGAGISLLCILDEDCRAAGVQWALV 104
                                    566789**********************9998..........7************************************* PP

                                    S--HHHHHH...HHHTTCGGCC..SEEESSHHHH CS
                           STAS  87 nikpevrek...lektgffdeveeeklfltvhdA 117
                                         v++    +++ +   ++   ++ ++vh+A
  gi|121636434|ref|YP_976657.1| 105 ASPAVVEQLggrCDQGEHESMF---PMARSVHKA 135
                                    ********99999999999999...999999987 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   8.3e-12   7.5e-08       1      71 [.      41     111 ..      41     114 .. 0.88
   2 ?   -1.9   0.0       0.5   4.5e+03      65      76 ..     131     142 ..     128     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.3e-12
                         STAS_2   1 LsLsGeldldtaaelreqllealaagaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalr 71 
                                    ++++Ge+d++++++  e +++      ++v+Dls++  +  a+++lL+ l + +ra+g +  l++ p  + 
  gi|121636434|ref|YP_976657.1|  41 VTIRGEIDAANVEQISEHVRRFSLGTNPMVLDLSELSHFSGAGISLLCILDEDCRAAGVQWALVASPAVVE 111
                                    6799*****************764445*********************************99999555444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.5
                         STAS_2  65 glppalrrlldl 76 
                                     +++al++l+d 
  gi|121636434|ref|YP_976657.1| 131 SVHKALHDLADA 142
                                    566677776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1237.52
//
Query:       gi|121636435|ref|YP_976658.1|  [L=436]
Description: membrane acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-22   78.6  36.6    5.3e-22   78.3  36.6    1.1  1  Acyl_transf_3  Acyltransferase family
  ------ inclusion threshold ------
       0.15   12.3   2.0       0.19   12.0   0.4    1.9  2  TetR_C_16      Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3  36.6   5.9e-26   5.3e-22       3     339 ..      38     387 ..      36     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 5.9e-26
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxx RF
                  Acyl_transf_3   3 ylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla.......amlyrrrglskli 75 
                                    +l +lR++A+++Vv++H+  +++    +  + +a +       g  gv+lFF+lSGf+l+        +  + r    ++
  gi|121636435|ref|YP_976658.1|  38 ALTGLRIVAAVWVVLFHFRPMLGDASPGFRDALAPVL----DCGAQGVDLFFILSGFVLTwnyldrmGRSWSVRANLHFL 113
                                    799*****************99998888888888776....99**********************666666667888999 PP

                                    xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  76 krRilrll..iplliwllliillialvaghiqanasanvtlfdet.......kglmfllfefpatghlWfLwalfvlyll 146
                                    + R+ r++  + + + l ++++++ l++gh  +  ++++t    +       ++++ ++  + ++g+ W+++a+++ yll
  gi|121636435|ref|YP_976658.1| 114 WLRLARVWpvYLVTLHLAAVWVIFTLHVGHVPSPEAGQLTAISYVrqillvqLWFQPYFDGSSWDGPAWSISAEWLAYLL 193
                                    ********666666778999**********************999**********************************9 PP

                                    xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 147 lpll...lrllrkvrkshlllllilllllslvfirhelfgpatsvgllplpsvla..llfflfGalladaddrdrnlsrg 221
                                    + ll   +  +++  +   l++l++++ l+ v+++++  +++t+      +s+l   +  f++Gal+  a +r r+ +r+
  gi|121636435|ref|YP_976658.1| 194 FGLLilvIFRMKHATRARGLMWLAFAASLPPVVLLLASGQFYTP------WSWLPriVTQFAAGALACAAVRRLRPTDRA 267
                                    99999999999999999999**********99999999999886......55555559********************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 222 lkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllfalpsrsafkllrylgkiSygiYliHl 301
                                    + i+  ls+l+ ++i+  l++ +    l  ++  + +  +l++  ++ l + +  lp + + +l+++ g+iS+ +Y++H 
  gi|121636435|ref|YP_976658.1| 268 RRIAGYLSVLVGVAIVGILYLLHAH-PLAGVEDSGGVVDVLFVPLVISLAIGVGSLPALLSTRLMVFGGQISFCLYMVHE 346
                                    ********99999999999999953.33333333344444444444444444444444444449***************7 PP

                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 302 pllmllqkllrdwgln...lgevlllvlllvvsvivsvvll 339
                                    ++  +++ ++  + l    +++ + +v ll +++ ++++l+
  gi|121636435|ref|YP_976658.1| 347 LVHTAWGWAVQQYELAlqdQPWKWNVVGLLAIALGAAILLY 387
                                    77777777777775556676677777777777777777766 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   2.1e-05      0.19      40      91 ..     245     298 ..     242     305 .. 0.86
   2 ?   -3.0   0.0      0.99   8.8e+03       1      17 [.     391     408 ..     391     413 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHHHCTTTS-STTHHHHHHHHHHHHHHHHHH..HHTS--TTCCCS- CS
                      TetR_C_16  40 lrefleeqvlaplaarlggpdaelRaalvasqllGlala..Ryvlrleplasas 91 
                                    + +f + +++ +  +rl ++d+++R+a  +s+l+G+a++  +y+l+  pla ++
  gi|121636435|ref|YP_976658.1| 245 VTQFAAGALACAAVRRLRPTDRARRIAGYLSVLVGVAIVgiLYLLHAHPLAGVE 298
                                    67888889999999**********************996448999999998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.99
                                    TTHHHHHHHHHHHHHH.H CS
                      TetR_C_16   1 eelGerlvravlevwe.p 17 
                                    ee G+r +r++++v   +
  gi|121636435|ref|YP_976658.1| 391 EEPGRRWMRRMVDVKAaS 408
                                    667888899988887733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3061.66
//
Query:       gi|121636436|ref|YP_976659.1|  [L=231]
Description: hypothetical protein BCG_0561 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-18   67.9   1.4    1.8e-18   67.6   1.4    1.1  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    7.3e-07   29.4   0.0    1.6e-06   28.3   0.0    1.5  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   1.4     2e-22   1.8e-18       1     178 [.      42     215 ..      42     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 2e-22
                                    EEESHHHHTCTTB.CCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H....HHHHHHHHCTGGG-T.SEEEEE--C. CS
                  Lipase_GDSL_2   1 alGDSiTaGygad.gggrsypaylarllaarl...gldvvnnlgvsGatt..allrllerlrdllrlkp.dlvtiliGt. 72 
                                    ++GDS+T G      g +s+ a++ ++laar+    +dv    g  G+ +  ++ ++ e+l ++ +++p d++++++G  
  gi|121636436|ref|YP_976659.1|  42 VIGDSYTTGTDEGgLGSKSWTARTWQMLAARGvriAADVAA-EGRAGYGVpgDHGNVFEDL-TARAVQPdDALVVFFGSr 119
                                    69*******8777999****************766556655.8888888744223333333.356666789999999999 PP

                                    CCCCTT--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-H.H CS
                  Lipase_GDSL_2  73 NDlgrgvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDl.h 151
                                    ND g ++ +++  a++ ++   d +r +ap a +lv++p++pt   +++         +++++l + a++ g++fvD  +
  gi|121636436|ref|YP_976659.1| 120 NDQGMDPEDPEMLAEK-VRDTFDLARHRAPSASLLVIAPPWPTADVPGPML-------RIRDVLGAQARAAGAVFVDPiA 191
                                    ****999999999997.******************7777777777766654.......59******************95 PP

                                    HHHHHCCCCCGGBBTTS.SSB-HHHHH CS
                  Lipase_GDSL_2 152 daladsgerladlladdglHPnaaGyr 178
                                    d++  +    ++l + dg+HPn+aG++
  gi|121636436|ref|YP_976659.1| 192 DHWFVDR---PELIGADGVHPNDAGHE 215
                                    5555554...45667777********7 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.8e-10   1.6e-06       1     200 []      40     221 ..      40     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.8e-10
                                    EEEEESHHHHTT.......THHHHHHHCCCCEECCCTTC.....GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCT CS
                                    xxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL   1 ivafGDSltdGd.......gaatlntiqlktpknlnefdl....aldrianignkgasdnelqqllnkyplkseqlkalh 69 
                                    ++++GDS t G         + t+ t+q           +       ++a  g+ g+++   ++++  ++  +  ++a +
  gi|121636436|ref|YP_976659.1|  40 VAVIGDSYTTGTdegglgsKSWTARTWQMLA--------ArgvrIAADVAAEGRAGYGVPGDHGNV--FEDLT--ARAVQ 107
                                    679*******885544444333333333322........223343457788888888888888888..33333..67788 PP

                                    TS..EEEEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHH CS
                                    xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL  70 pd..lviislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefv 147
                                    pd  lv+++   ND          + +++e + + +r++ +  + + ap a  ++++pp ++            ++   +
  gi|121636436|ref|YP_976659.1| 108 PDdaLVVFFGSRNDQ-------GMDPEDPEMLAEKVRDTFDLAR-HRAPSASLLVIAPPWPTA-----------DVPGPM 168
                                    88*999999999***.......99*****************555.999************999...........555555 PP

                                    HHHHHHHHHHHHHCTEEEEC.HHHHHHHTHCCGCHCHTSSSB-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL 148 geynqrlndlaekdgfavvD.lydelqglsgieqlkaDglHpsekgyeklaell 200
                                      + ++l++ a+ +g ++vD + d++      e + aDg+Hp+++g+e la+++
  gi|121636436|ref|YP_976659.1| 169 LRIRDVLGAQARAAGAVFVDpIADHWFVD-RPELIGADGVHPNDAGHEYLADKI 221
                                    55555566666699999998456666666.5777778**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1635.73
//
Query:       gi|121636437|ref|YP_976660.1|  [L=300]
Description: hypothetical protein BCG_0562c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-08   34.3   0.2    1.7e-07   31.1   0.2    2.1  1  Esterase    Putative esterase
  ------ inclusion threshold ------
      0.033   13.2   0.3      0.045   12.7   0.3    1.1  1  Asp2        Accessory Sec system GspB-transporter
       0.14   12.1   6.2       0.44   10.5   6.2    1.9  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   2.9e-11   1.7e-07      11     250 ..      90     297 ..      81     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.9e-11
                                    EEEE.CC.GGTTTEEEEEEE..--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEEETTC CS
                       Esterase  11 qvyLPedyspgrkypvvyll..dGltgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgarfyenateg 88 
                                     +  P++ ++g+  pv+ l+  dG  g   ++ ++++l +l++eg  +  ++v+v+ g+++     w+         ++g
  gi|121636437|ref|YP_976660.1|  90 VISMPPG-QSGQLRPVIALHgkDGNAGMMLDLGVEQGLARLVKEG-KPAFAVVGVDGGNTY-----WHRR-------SSG 155
                                    5667888.7777777776654466688889999*****9999997.555666677777777.....7744.......444 PP

                                    CCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHC.STTTCCEEEEES--S-CCHCHHHCTTCCHHHC CS
                       Esterase  89 pgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalk.hpdrFgsvssfSpivnpsnamWgqeekeawqe 167
                                    + +      + +eLlp+l +    +++    +G SmGG+gAL+l+++  p r + + + Sp + +s  + g ++ +a+ +
  gi|121636437|ref|YP_976660.1| 156 GDSG---AMVLDELLPMLTSMGMDTSR-VGFLGWSMGGYGALLLGARlGPARTAGICAISPALFTS--FTG-STPGAFDS 228
                                    4443...57899******998777777.9***************9998899999999999774444..444.47788999 PP

                                    C-CCCCHCHH.CHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCCHHHHCCCCCCTT-SCCCC.--SSHHHHHHHHH CS
                       Esterase 168 ndpvllakel.saslkalriyldvGtseddlgeqlsveilevlarnrelkeqlaargvegedheyd.GghsweyWraqLi 245
                                    +d++++ + l    l  +   +d Gts++++              +r+    ++++ ++   +++  Ggh+ +yWr+qL+
  gi|121636437|ref|YP_976660.1| 229 YDDYVQHSVLgLPALNSIPLRVDCGTSDRFYF------------ATRQ----FVNQLHQPPAGSFSpGGHDASYWREQLP 292
                                    999887765416788999**********9433............3333....445566777788877************* PP

                                    HCHHH CS
                       Esterase 246 aalad 250
                                    ++la+
  gi|121636437|ref|YP_976660.1| 293 GELAW 297
                                    *9987 PP

>> Asp2  Accessory Sec system GspB-transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   7.6e-06     0.045     346     379 ..     169     202 ..     154     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-06
                           Asp2 346 kleeLgfeeeqlilsGlSMGtfgalyYgaklnph 379
                                     l  +g++ + + + G SMG +gal  ga+l p+
  gi|121636437|ref|YP_976660.1| 169 MLTSMGMDTSRVGFLGWSMGGYGALLLGARLGPA 202
                                    6899***************************986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.2   7.4e-05      0.44       2      19 ..      22      39 ..      21      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                     TAT_signal  2 lSRRdFLKgsAAaaAAaa 19
                                   l+RR +L+++A+a+A+aa
  gi|121636437|ref|YP_976660.1| 22 LTRRALLRWGAGAGAGAA 39
                                   89***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2080.98
//
Query:       gi|121636438|ref|YP_976661.1|  [L=116]
Description: methyltransferase/methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-15   56.8   0.0    3.1e-15   56.6   0.0    1.1  1  Methyltransf_11  Methyltransferase domain
    5.1e-13   49.5   0.0    6.2e-13   49.3   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    3.6e-10   39.8   0.0      4e-10   39.7   0.0    1.0  1  Methyltransf_31  Methyltransferase domain
    1.3e-08   34.4   0.0    1.6e-08   34.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.5e-07   30.5   0.0    6.3e-07   30.1   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    2.2e-06   27.6   0.0    2.3e-06   27.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    0.00084   20.3   0.0      0.001   20.1   0.0    1.1  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.083   12.4   0.0      0.094   12.2   0.0    1.1  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.21   11.4   0.0       0.24   11.2   0.0    1.1  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   1.6e-18   3.1e-15      19      96 .]       4      83 ..       1      83 [. 0.97

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.6e-18
                                   SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11 19 arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96
                                   ++++++++s+   ++ ++k++++gl  +++++++++ ++p +d+ +D+v+s+ ++ h +d++k+l+e+ RvL+pgG l++
  gi|121636438|ref|YP_976661.1|  4 CSITCLNISEVPNETNRKKNRQAGLdrSIRVIHGSFDDIPEPDSGYDVVWSQDAILHAPDRRKVLEEAFRVLRPGGELIF 83
                                   789************************9*************************************************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   3.1e-16   6.2e-13      22      97 .]       4      79 ..       1      79 [. 0.93

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 3.1e-16
                                   SEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25 22 akvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97
                                   +++t++ ise   e+ r++++++gl  ++++++g+++d+p++d+ +D+v+s+ a+ h   +d++k+l+e++rvL+pgG
  gi|121636438|ref|YP_976661.1|  4 CSITCLNISEVPNETNRKKNRQAGLdrSIRVIHGSFDDIPEPDSGYDVVWSQDAILH--APDRRKVLEEAFRVLRPGG 79
                                   789************************************************988555..4699**************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0     2e-13     4e-10      45     122 ..      20      96 ..       3     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2e-13
                Methyltransf_31  45 renaqklgld.nveFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggilliedprllaelpakv 122
                                    r++ ++ gld  +++ +g++ +++    d+ +D++ s++++ + +d  k+lee++rvl+pgg+l+ +dp  ++++p+ v
  gi|121636438|ref|YP_976661.1|  20 RKKNRQAGLDrSIRVIHGSFDDIP--EPDSGYDVVWSQDAILHAPDRRKVLEEAFRVLRPGGELIFTDPMQADDVPDGV 96 
                                    666788999989************..789****************************************9888888443 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0     8e-12   1.6e-08      75     150 ..       6      82 ..       2      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8e-12
                                    EEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran  75 vvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                    ++ l+i+e   ++ +kk ++ g   +i+ ++++  ++p+ d  +Dvv     +   +D+ k+L+ea+rvl+pGG+l+
  gi|121636438|ref|YP_976661.1|   6 ITCLNISEVPNETNRKKNRQAGLDrSIRVIHGSFDDIPEPDSGYDVVWSQDAILHAPDRRKVLEEAFRVLRPGGELI 82 
                                    67788999999999999999999879************************************************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   3.1e-10   6.3e-07      21      99 .]       4      81 ..       2      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.1e-10
                Methyltransf_12 21 ieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99
                                   +++t++ is+   e  ++k ++ + ++  +v     d++  ++ s +D+v++ +++ h +d+r+vl+++ ++L+pgG l
  gi|121636438|ref|YP_976661.1|  4 CSITCLNISEVPNETNRKKNRQAGLDRSIRVIHGSFDDI-PEPDSGYDVVWSQDAILHAPDRRKVLEEAFRVLRPGGEL 81
                                   789999999999977777777777766555544444443.223379*******************************76 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.2e-09   2.3e-06      45     124 ..       4      90 ..       2     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.2e-09
                Methyltransf_23  45 fsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGyl 115
                                    +s+t   +s++ +e  +           +  ++ +f  ++++ep+  +d++ + + + h pd  ++l  +++ l+pgG l
  gi|121636438|ref|YP_976661.1|   4 CSITCLNISEVPNETNRkknrqagldRSIRVIHGSF--DDIPEPDSGYDVVWSQDAILHAPDRRKVLEEAFRVLRPGGEL 81 
                                    666666666666665444444444444444555556..6999************************************** PP

                Methyltransf_23 116 llseplasl 124
                                    ++++p + +
  gi|121636438|ref|YP_976661.1|  82 IFTDPMQAD 90 
                                    ****96655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.1e-07     0.001      35     105 ..      16      85 ..       2      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                Methyltransf_24  35 aeeaaalareaglddrvrlikadseealaslaagsiDllfi.DgghaaeavledleallprlapggvvlfdD 105
                                     e++++  r+agld+ +r+i++ +++  ++ + + +D+++  D+   a ++++ le + ++l+pgg ++f D
  gi|121636438|ref|YP_976661.1|  16 NETNRKKNRQAGLDRSIRVIHGSFDDI-PEPD-SGYDVVWSqDAILHAPDRRKVLEEAFRVLRPGGELIFTD 85 
                                    33456666789***********98888.5555.68****9659999999*****************999866 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.7e-05     0.094     113     165 ..      39      89 ..      11      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                Methyltransf_PK 113 lqeftPeegrYdliWiqWcvghLtDedlvaflkrckkalkpnGlivvkenvak 165
                                    +++    +  Yd++W q  + h +D   v  l+ + + l+p+G ++  + +  
  gi|121636438|ref|YP_976661.1|  39 FDDIPEPDSGYDVVWSQDAILHAPDRRKV--LEEAFRVLRPGGELIFTDPMQA 89 
                                    5554444778***************9865..99**********9998887665 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.24     107     155 ..      33      82 ..       9      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                    TEEES-TTS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEEE CS
                 Methyltransf_8 107 rvvacdlakvPledesvdvavfclslm.gtnladflkeanrvlkvGGllk 155
                                    rv+   +  +P  d+  dv+    +++ + + ++ l+ea rvl++GG l 
  gi|121636438|ref|YP_976661.1|  33 RVIHGSFDDIPEPDSGYDVVWSQDAILhAPDRRKVLEEAFRVLRPGGELI 82 
                                    677777889999999999998876655267999**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 788.70
//
Query:       gi|121636439|ref|YP_976662.1|  [L=101]
Description: methyltransferase/methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 716.73
//
Query:       gi|121636440|ref|YP_976663.1|  [L=434]
Description: 4-amino butyrate transport carrier [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.8e-105  352.2  50.9   4.7e-105  351.9  50.9    1.0  1  AA_permease     Amino acid permease
    1.5e-32  113.0  53.8    1.9e-32  112.7  53.8    1.1  1  AA_permease_2   Amino acid permease
    8.8e-06   24.8  13.8    8.8e-06   24.8  13.8    2.3  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.9  50.9  7.9e-109  4.7e-105       4     436 ..       1     403 [.       1     430 [. 0.95

  Alignments for each domain:
  == domain 1  score: 351.9 bits;  conditional E-value: 7.9e-109
                    AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnyl 83 
                                    +ia+ggviG+glfvg+gvv+++ Gp +a+l y+l+g+ i+lvm++lge+a ++p++g+f+ ya++ lg ++Gf++G++y+
  gi|121636440|ref|YP_976663.1|   1 MIAIGGVIGAGLFVGSGVVIRATGP-AAFLTYALCGALIVLVMRMLGEMAAANPSTGAFADYAAKALGGWAGFSVGWLYW 79 
                                    8************************.999*************************************************** PP

                    AA_permease  84 fswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillag 163
                                    ++w++v+++e +a + ++++w    d+p +w  ++ +++++++ nlv+v  +ge+ef++a +k+ +i++f+++g  + +g
  gi|121636440|ref|YP_976663.1|  80 YFWVIVVGFEAVAGGKVLTYW---IDAP-LWLASLCLMMMMTATNLVSVSSFGEFEFWFAGVKVATIVGFLVLGTAFAFG 155
                                    *********************...5666.6********************************************999*** PP

                    AA_permease 164 gkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviri 243
                                      p +g  f++l+++g+    ++p+g        + ++++++v+++f++tG+e v+i+a+E+ dP++++ +a++ vv ri
  gi|121636440|ref|YP_976663.1| 156 LLPGHGMDFSNLSAHGG----FFPDG--------VGAVFAAIVVAIFSMTGTEVVTIAAAEAPDPQRAVQRAMSTVVARI 223
                                    9999**9**********....99999........********************************************** PP

                    AA_permease 244 tifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdgl 323
                                    +if+v+s++l+++++p+n+l l +      sp+v ++++ g+ ++ +++nav+lta+ls++ns+ly+asR+l+ la ++ 
  gi|121636440|ref|YP_976663.1| 224 VIFFVGSVFLLTVILPWNSLELGA------SPYVAALRHMGIGGADQIMNAVVLTAVLSCLNSGLYTASRMLFVLAARQE 297
                                    *******************99999......9************************************************* PP

                    AA_permease 324 aPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsiee 403
                                    aP+ l kv++rgvP  ai+ s+++++l++++a +++a  +vf fll++s++++l+v+lli+ls++++R++  ++g     
  gi|121636440|ref|YP_976663.1| 298 APAQLVKVNRRGVPTFAIMGSSVVGFLCVIMAWVSPA--TVFVFLLNSSGAVILFVYLLIALSQIVLRRQ--TSGQ---N 370
                                    *************************************..*******************************..6666...7 PP

                    AA_permease 404 lgfkaallplgvilvlaaliiillilalyaylt 436
                                    lg++++l+p ++i++++ ++++l  +a+ + ++
  gi|121636440|ref|YP_976663.1| 371 LGVRMWLFPGLSIVTVTGIVAVLARMAFDYAAR 403
                                    8***************************99887 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7  53.8   3.1e-36   1.9e-32       9     402 ..       2     396 ..       1     421 [. 0.82

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 3.1e-36
                  AA_permease_2   9 lvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwf 86 
                                    ++ig vig+g fv +  ++ ++gpa++l++ +   ++ + v+  + E+++a p+ g    y+++a g +++f ++w++w+
  gi|121636440|ref|YP_976663.1|   2 IAIGGVIGAGLFVGSgvVIRATGPAAFLTYALCGALI-VLVMRMLGEMAAANPSTGAFADYAAKALGGWAGFSVGWLYWY 80 
                                    89**************9999*****999888744444.5677799***999***************************** PP

                  AA_permease_2  87 ayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglit 166
                                    ++v+v+ + ++++++ l ++++        +  l   ++++  ++ n+++++  + + ++ + +k+  +++ +++lg ++
  gi|121636440|ref|YP_976663.1|  81 FWVIVVGFEAVAGGKVLTYWIDA-------PLWLASLCLMMMMTATNLVSVSSFGEFEFWFAGVKVA-TIVGFLVLGTAF 152
                                    ******99999999999999974.......344556688999999*********************5.666666566666 PP

                  AA_permease_2 167 vdg....ggfssl.stetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvni 239
                                    + g    +g +++   +++ ffp+g   v++++ ++++s++G e+++  + e++   + v +a+  +++ +++++++  +
  gi|121636440|ref|YP_976663.1| 153 AFGllpgHGMDFSnLSAHGGFFPDGVGAVFAAIVVAIFSMTGTEVVTIAAAEAPDpqRAVQRAMSTVVARIVIFFVGSVF 232
                                    5333333333322333444599999999************************7755499********************* PP

                  AA_permease_2 240 aflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkfg 319
                                    +++ ++p+++++  + +  ++ + ++ +g + +  i+++++  ++l ++n+ ++++sr+l+ la   + P  + kvn++g
  gi|121636440|ref|YP_976663.1| 233 LLTVILPWNSLELGA-S--PYVAALRHMGIGGADQIMNAVVLTAVLSCLNSGLYTASRMLFVLAARQEAPAQLVKVNRRG 309
                                    ************744.3..466666777999************************************************* PP

                  AA_permease_2 320 spiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr....pgkilvaiigalfl 395
                                     p+ ai+ + +v +++++  ++++++ + fll+ s   ++++yll++++ ++lr++   ++     + ++ ++i+ + ++
  gi|121636440|ref|YP_976663.1| 310 VPTFAIMGSSVVGFLCVIMAWVSPATVFVFLLNSSGAVILFVYLLIALSQIVLRRQTSGQNLgvrmWLFPGLSIVTVTGI 389
                                    *************99988888888********************************998855634444444444444444 PP

                  AA_permease_2 396 lfllval 402
                                    + +l+ +
  gi|121636440|ref|YP_976663.1| 390 VAVLARM 396
                                    4444333 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  13.8   1.5e-09   8.8e-06      13     233 ..       5     237 ..       1     289 [. 0.75
   2 ?   -2.1   2.3      0.22   1.3e+03     104     125 ..     373     394 ..     343     427 .. 0.55

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-09
                 Spore_permease  13 sfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe.ktliellkkilgkwLGsllsilfilyFll 91 
                                      ++G+g+ +  ++v+ +++p + ++  l+g +i++++ ++ ++   +p+   ++++  k lg w G+  + l+  ++++
  gi|121636440|ref|YP_976663.1|   5 GGVIGAGLFVGSGVVIRATGPAAFLTYALCGALIVLVMRMLGEMAAANPStGAFADYAAKALGGWAGFSVGWLYWYFWVI 84 
                                    5689***************************9999999999999988886156789************************ PP

                 Spore_permease  92 laafelRefseliqvflledtplwiiilllllv.ilYlvvkGieslar...eflfiivilliilllil...lfslklaei 164
                                    +++fe+   +++++ ++   + l+ ++l++++  + ++ v+++ ++     ++ +++++ +++l + +   l +   +++
  gi|121636440|ref|YP_976663.1|  85 VVGFEAVAGGKVLTYWIDAPLWLASLCLMMMMTaTNLVSVSSFGEFEFwfaGVKVATIVGFLVLGTAFafgLLPGHGMDF 164
                                    ****************9666666666655554414455566666654344444444444444444333111334455788 PP

                 Spore_permease 165 knlr...Pvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallgvlist.llyllttlivilv 233
                                     nl      + +g+  v+ ++ ++++s++g e++++      d++++++ a+  v+  + ++ + ++++  ++
  gi|121636440|ref|YP_976663.1| 165 SNLSahgGFFPDGVGAVFAAIVVAIFSMTGTEVVTIAAAEAPDPQRAVQRAMSTVVARIvIFFVGSVFLLTVI 237
                                    88873335899******************************99998887777766655404444455555444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.22
                 Spore_permease 104 iqvflledtplwiiilllllvi 125
                                    + ++l++ +++++++ ++ +++
  gi|121636440|ref|YP_976663.1| 373 VRMWLFPGLSIVTVTGIVAVLA 394
                                    5666666666666666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3228.50
//
Query:       gi|121636441|ref|YP_976664.1|  [L=131]
Description: hypothetical protein BCG_0566c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0024   18.0   0.1     0.0028   17.8   0.1    1.2  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.5e-07    0.0028      24      88 ..      27      93 ..       7     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-07
                                   -.-EEEEEE-TTT-SEEEEEEEEE.EETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEE CS
                F420H2_quin_red 24 p.vllLtttGrktgkprktplgfv.rdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldv 88
                                   p  ++L+ +Gr++gkp +tpl     d d  + va ++    + +w+ N+ a    +++  +k++ v
  gi|121636441|ref|YP_976664.1| 27 PaFAILEHVGRRSGKPYRTPLNVFsADVDGRAGVAILLTYGPNRDWLKNITAAGGGRMRRYGKTFGV 93
                                   44789***************97541444556666666666678899999999877777766666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 948.33
//
Query:       gi|121636442|ref|YP_976665.1|  [L=462]
Description: glutamate-1-semialdehyde aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-88  297.6   0.0    3.5e-88  296.0   0.0    1.6  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.0   0.0   1.9e-92   3.5e-88      10     406 .]      47     449 ..      40     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 296.0 bits;  conditional E-value: 1.9e-92
                                    CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SE CS
                    Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldk 89 
                                    + +it+a+G++l d+dg+ry+Dlv+s+ +++lGhahP+vv+av+++aa    +sfga t ++++ + e++ ++ap   ++
  gi|121636442|ref|YP_976665.1|  47 PRFITEAHGCWLIDADGNRYVDLVCSWGPMILGHAHPAVVEAVAKAAARG--LSFGAPTPAETQLAGEIIGRVAPV--ER 122
                                    489**********************************************9..9***********************..** PP

                                    EEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTT.CTTB............... CS
                    Aminotran_3  90 vflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktl.fgpf............... 153
                                    + l+nsG+eA+++A++lar        t ++ki++f+g++HG++ + l+ +gs   ++tl + +                
  gi|121636442|ref|YP_976665.1| 123 IRLVNSGTEATMSAVRLARG------FTGRAKIVKFSGCYHGHVDALLADAGSG--VATLgLCDDpqrpasprsqssrgl 194
                                    ********************......***********************99983..222201111233445666777888 PP

                                    ..-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEE CS
                    Aminotran_3 154 ..lpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlliv 231
                                      +p+v+ ++++d++vl++n+      + ++++  ++  +++aAvi+E+ +g++Gvv++ p+f+a+lr+++++h++lli 
  gi|121636442|ref|YP_976665.1| 195 psSPGVTGAAAADTIVLPYND------IDAVQQTFARFGEQIAAVITEASPGNMGVVPPGPGFNAALRAITAEHGALLIL 268
                                    8899*****************......667777778999***************************************** PP

                                    E-TTTTT..TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHH CS
                    Aminotran_3 232 DEvqtGf..GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavle 306
                                    DEv+tGf  +r+G +++++  +v++Dl++++K+++gG+p++a+ ++aevmq+lap +   +++T +Gnp+a a+ la+l+
  gi|121636442|ref|YP_976665.1| 269 DEVMTGFrvSRSG-WYGID--PVPADLFAFGKVMSGGMPAAAFGGRAEVMQRLAPLGpvyQAGTLSGNPVAVAAGLATLR 345
                                    *******99****.*****..**********************************99999******************** PP

                                    HHHH...TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCT CS
                    Aminotran_3 307 iiee...ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekG 371
                                    ++ +    +l  na++l   l+e+L+++     v +++ ++G+m+++ ++ e  v++            ++++++++++G
  gi|121636442|ref|YP_976665.1| 346 AADDavyTALDANADRLAGLLSEALTDAV----VPHQISRAGNMLSV-FFGETPVTDfasarasqtwryPAFFHAMLDAG 420
                                    **997777899999999999999999998....899***********.8888888889***********99********* PP

                                    EE-EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                    Aminotran_3 372 vlilsaGdnvirllppliitdeeidelleilkkal 406
                                    v+        ++ +++++++++  d+++ ++ +al
  gi|121636442|ref|YP_976665.1| 421 VY------PPCSAFEAWFVSAALDDAAFGRIANAL 449
                                    **......9999******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3235.36
//
Query:       gi|121636443|ref|YP_976666.1|  [L=202]
Description: hypothetical protein BCG_0568 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-38  130.8   0.2    5.4e-38  130.6   0.2    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
        2.8    8.0   6.6         16    5.6   0.8    2.5  2  Titin_Z     Titin Z


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.2     6e-42   5.4e-38       2     186 ..       8     191 ..       7     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 6e-42
                                    EEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                     His_Phos_1   2 yLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEid 81 
                                    ++vRHGe+++ +   +++   ++L+++G +qA+a+a++la+++i a+++Spl+Ra++Ta++ia++++l ve+d++L E +
  gi|121636443|ref|YP_976666.1|   8 HVVRHGEVHNPTGILYGRLPGFHLSATGAAQAAAVADALADRDIVAVIASPLQRAQETAAPIAARHDLAVETDPDLIE-S 86 
                                    68******99888779999***********************************************************.9 PP

                                    -GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH.T CS
                     His_Phos_1  82 fGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll.g 160
                                       +eg+     + + +++++ w++ ++ ++p++gE + d+aaR++ a+++++ r +g++v++VsH+ ++++l  +l+ +
  gi|121636443|ref|YP_976666.1|  87 ANFFEGRRVGPGDGA-WRDPRVWWQLRNPFTPSWGEPYVDIAARMTTAVDKARVRGAGHEVVCVSHQLPVWTLRLYLTgK 165
                                    999****65555555.77777788888889************************************************66 PP

                                    --GGGGGGB---TT-EEEEEE-SS-E CS
                     His_Phos_1 161 lpleelrrleldnaslsvlefdeggw 186
                                      ++++rr +++ as++ l +d+++ 
  gi|121636443|ref|YP_976666.1| 166 RLWHDPRRRDCALASVTSLIYDGDRL 191
                                    6678899999************9986 PP

>> Titin_Z  Titin Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6    0.0028        25      17      40 ..      54      73 ..      51      75 .. 0.85
   2 ?    5.6   0.8    0.0017        16      14      26 ..     128     140 ..     126     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0028
                        Titin_Z 17 VaAvDkarvrepladtrEEeAaeg 40
                                   V+A ++ r +e++a     +Aa++
  gi|121636443|ref|YP_976666.1| 54 VIASPLQRAQETAAP----IAARH 73
                                   9***********998....77776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0017
                        Titin_Z  14 AtVVaAvDkarvr 26 
                                    A +  AvDkarvr
  gi|121636443|ref|YP_976666.1| 128 ARMTTAVDKARVR 140
                                    55667*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1488.69
//
Query:       gi|121636444|ref|YP_976667.1|  [L=216]
Description: thioredoxin protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-16   58.5   0.0    7.9e-16   58.1   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    1.1e-15   57.6   0.0    1.5e-15   57.2   0.0    1.1  1  Redoxin        Redoxin
    2.8e-07   30.7   0.0    3.8e-07   30.3   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
    2.4e-05   24.2   0.0    4.1e-05   23.5   0.0    1.3  1  Thioredoxin    Thioredoxin
     0.0043   17.5   2.0       0.01   16.3   2.0    1.7  1  LPAM_1         Prokaryotic membrane lipoprotein lipid attachm


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   2.2e-19   7.9e-16      16     123 ..      78     184 ..      69     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 2.2e-19
                                    EEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES..SSCHHHHHHHHH-H.SSEEEE-TTSH CS
                       AhpC-TSA  16 etvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv..dspeshkkfiekeslnfpllsDeegk 93 
                                    ++vsl+d+ g++vv++++ + wc +C++e+++l+++y++ + +gv  +g+ v  ++ ++ ++fi++  +++p ++D+   
  gi|121636444|ref|YP_976667.1|  78 RSVSLDDFPGQVVVVNVWGQ-WCGPCRAEVSQLQRVYDATRGAGVSFLGIDVrdNNRQAPQDFINDRHVTYPSIYDPAMR 156
                                    78******************.*****************************9964445599******************** PP

                                    HHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  94 vakaygvlkeekglalratfvidkegkiry 123
                                    +  a+g   +  +  +++t v+d+++ +++
  gi|121636444|ref|YP_976667.1| 157 TLIAFGGKYP--TSVIPSTLVLDRQHRVAA 184
                                    *******988..599**********99875 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   4.2e-19   1.5e-15      12     133 ..      71     188 ..      59     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 4.2e-19
                                    CEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHHTT-TSEE CS
                        Redoxin  12 plaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf..vkefwgkeglkfpv 89 
                                    p++a+   svsl++f+g++vvvn++   +c++C+ae+ +l+ +++  +  gv+++++ + +++    ++f+++ ++++p 
  gi|121636444|ref|YP_976667.1|  71 PELADPARSVSLDDFPGQVVVVNVWGQ-WCGPCRAEVSQLQRVYDATRGAGVSFLGIDVRDNNRqaPQDFINDRHVTYPS 149
                                    566788899****************99.******************9**********665555559************** PP

                                    EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEES CS
                        Redoxin  90 lsDgsaaftkalGlrleedaseglrtpryavidedgkvvyleve 133
                                    ++D+      a+G ++         +p++ v+d++++v ++++ 
  gi|121636444|ref|YP_976667.1| 150 IYDPAMRTLIAFGGKYPTS-----VIPSTLVLDRQHRVAAVFLR 188
                                    *************665543.....9*************999875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-10   3.8e-07       1      95 []      87     182 ..      87     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-.SS-HHHHHHHGGGS-TTSEE.EE-TT-.HHHHTT-S CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl.dkkeeefekylkknkkpwlsvpfddkk.rnklkkky 78 
                                    g+vv++ ++  wc pc+a +++l+++y+  + + +v ++ + + d+++++ ++++++ + +  s+  +  +   ++  ky
  gi|121636444|ref|YP_976667.1|  87 GQVVVVNVWGQWCGPCRAEVSQLQRVYDATR-GAGVSFLGIDVrDNNRQAPQDFINDRHVTYPSIYDPAMRtLIAFGGKY 165
                                    689***************************9.9*********9679999*********88888877777664558899** PP

                                    --TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  79 nvkaiPtlvvldkngev 95 
                                     ++ iP+++vld++++v
  gi|121636444|ref|YP_976667.1| 166 PTSVIPSTLVLDRQHRV 182
                                    ************99987 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.1e-08   4.1e-05      19      67 ..      88     137 ..      80     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHH CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakk 67 
                                    + v+v+ + +wCg+C+a  ++l+++ +++++  v ++ +dv +n+  a +
  gi|121636444|ref|YP_976667.1|  88 QVVVVNVWGQWCGPCRAEVSQLQRVYDATRGaGVSFLGIDVRDNNRQAPQ 137
                                    679***************************99*********999887755 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.0   2.9e-06      0.01       1      18 []      14      32 ..      14      32 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-06
                         LPAM_1  1 MKKi.llalgalllLsGCs 18
                                   M+++ + a++ +llL+GCs
  gi|121636444|ref|YP_976667.1| 14 MRRLvIAAAVSALLLTGCS 32
                                   9***9*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1722.48
//
Query:       gi|121636445|ref|YP_976668.1|  [L=259]
Description: cytochrome c-type biogenesis protein ccdA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-40  137.3  17.5    8.1e-40  137.0  17.5    1.1  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
        9.7    6.0   7.0        2.9    7.7   0.1    2.4  2  Colicin   Colicin pore forming domain


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0  17.5     9e-44   8.1e-40       2     212 ..      21     236 ..      20     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 9e-44
                           DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkv........kvllkallFvlGlslvfvslglsaaflgqllkd 73 
                                    +laGl+sf sPC++pl+P ylsy++ v   d +  ++ v        +v  +a lFv G+++vfv+  +++  +++ l  
  gi|121636445|ref|YP_976668.1|  21 LLAGLVSFASPCVVPLVPGYLSYLAAVVGVDEQLPAGVVkppvaarwRVAGSAALFVAGFTTVFVLGTVAVLGMTTTLIT 100
                                    89**********************987655554444444444566669****************9877777777777779 PP

                           DsbD  74 vkevirrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaske. 152
                                     +  ++rv+g++++++Gl f+g   i +l+++ +    + ++ +sv+ga +lG +Falgw+PC gP l+ v+++a+ +e 
  gi|121636445|ref|YP_976668.1| 101 NQLLLQRVGGVLIVVMGLVFVGF--IGALQRQARF---TPRQLTSVAGAPVLGAVFALGWTPCLGPTLTGVITVASATEg 175
                                    999*******************3..5688888887...446666689**************************9998763 PP

                           DsbD 153 .slakgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvlll 212
                                     s+a g++l+++y lGl+ipf+l+++ +  +   l +l+++++a++i gg ll+ +G  l+
  gi|121636445|ref|YP_976668.1| 176 aSVARGIVLVIAYCLGLGIPFVLLAFGSAWAVAGLGWLRRHTRAIQIFGGALLIAVGAALV 236
                                    46889999*************************************************8776 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00033       2.9     138     177 ..      63     104 ..      53     109 .. 0.81
   2 ?   -0.1   2.8     0.084   7.6e+02     145     172 ..     200     236 ..     166     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00033
                        Colicin 138 iaasflssiafalavg..tplgilgfalliavvaaliddklv 177
                                    +aa + ++ + al v+  t++ +lg++ ++ ++++li ++l+
  gi|121636445|ref|YP_976668.1|  63 VAARWRVAGSAALFVAgfTTVFVLGTVAVLGMTTTLITNQLL 104
                                    577776666666666667*******************99886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.084
                        Colicin 145 siafalavg.........tplgilgfalliavvaali 172
                                    ++ +a av+          ++ i+g alliav aal+
  gi|121636445|ref|YP_976668.1| 200 AFGSAWAVAglgwlrrhtRAIQIFGGALLIAVGAALV 236
                                    4555555544555555546899999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 1848.40
//
Query:       gi|121636446|ref|YP_976669.1|  [L=529]
Description: hypothetical protein BCG_0571 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.8e-137  459.1   0.0   3.2e-137  458.3   0.0    1.4  1  ResB       ResB-like family
  ------ inclusion threshold ------
      0.018   15.0   1.4      0.051   13.5   0.0    2.4  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
       0.12   12.1   0.0       0.23   11.2   0.0    1.5  1  Big_4      Bacterial Ig-like domain (group 4)


Domain annotation for each model (and alignments):
>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.3   0.0  5.4e-141  3.2e-137       1     495 []       8     500 ..       8     500 .. 0.93

  Alignments for each domain:
  == domain 1  score: 458.3 bits;  conditional E-value: 5.4e-141
                           ResB   1 mrlAlvLLlllaiaSiiGtvlpQnepsanyvqqyiaegpflaeildkLglfdvYsswWFllilalLvvSlvgCilprlpk 80 
                                    m +AlvLL+lla+a+i+G++lpQ+  +a++v++y+a++p ++++ld+L+ fdv+ss WF++i++lL+vSlvgC++pr+++
  gi|121636446|ref|YP_976669.1|   8 MGTALVLLFLLALAAIPGALLPQRGLNAAKVDDYLAAHPLIGPWLDELQAFDVFSSFWFTAIYVLLFVSLVGCLAPRTIE 87 
                                    88**********************88888*************************************************** PP

                           ResB  81 llkalrkkrpkraekslkrlphsaelelaeapeeaveraaavLkkrgyrvrveeedgavslaAekGrlsrlGnlvfHial 160
                                    ++++lr + p +a+++l+rlp++a+++la +p++++++++ +L++  +r  +++++++v ++AekG+l+++GnlvfH+al
  gi|121636446|ref|YP_976669.1|  88 HARSLR-ATPVAAPRNLARLPKHAHARLAGEPAALAATITGRLRG--WRSITRQQGDSVEVSAEKGYLREFGNLVFHFAL 164
                                    ******.99*******************99999999*******99..99999888999********************** PP

                           ResB 161 vliligallgslfgfrgnvivpe..Gqsfnnail...dsfrdGslvqe...lpfslrldkFtveyydtkgqpkeFesdvt 232
                                    +++l+++++g+lfg++gnviv +  G +f+ a+    dsfr+G+ v++   +p ++r+++F++ y+++ gq+ +F++d++
  gi|121636446|ref|YP_976669.1| 165 LGLLVAVAVGKLFGYEGNVIVIAdgGPGFCSASPaafDSFRAGNTVDGtslHPICVRVNNFQAHYLPS-GQATSFAADID 243
                                    ***********************9999***9988****************99***************8.*********** PP

                           ResB 233 vldkgkea.......kektikVNhPlrykgvriYqssfgdggklelklvllkgksaqelelpgtvslslralelaneelr 305
                                    ++ ++  a       ++++++VNhPlr++g+r+Y++++                                          
  gi|121636446|ref|YP_976669.1| 244 YQADPATAdlianswRPYRLQVNHPLRVGGDRVYLQGH------------------------------------------ 281
                                    **9777335999**************************.......................................... PP

                           ResB 306 nvgpavqfkvrdpdgevanmepv...pqdg.nvlssgvrkp................qlafqglflPtaeesekgell.s 364
                                      g+a++f+v+ pdg++++ ++v   p++  ++ls+gv+++                q+a+qgl +Pt++ ++  +ll s
  gi|121636446|ref|YP_976669.1| 282 --GYAPTFTVTFPDGQTRT-STVqwrPDNPqTLLSAGVVRIdppagsypnpderrkhQIAIQGLLAPTEQLDG--TLLsS 356
                                    ..*************9995.4444688888899*******558**************************9984..3666* PP

                           ResB 365 lfpaledpalaleayrgdlgldagepqsvyaldtelfeqeqlnal....srygsplllq.....ldd.........fe.q 425
                                     fpal+ pa+a+++yrgd+gld+g+pqs+++ld++l+eq++l ++     r             +d+         f+ +
  gi|121636446|ref|YP_976669.1| 357 RFPALNAPAVAIDIYRGDTGLDSGRPQSLFTLDHRLIEQGRLVKEkrvnLR-------AgqqvrIDQgpaagtvvrFDgA 429
                                    ******************************************955344322.......222344333445556666999* PP

                           ResB 426 rqasgLqvsrdpgknlvllgalllvlGlvlslyvrhrRvWvrieae.dggskvelaglanknkagfekefe 495
                                    + +++Lqvs+dpg+ +vl++a+++++Gl++sl vr+rRvW+ri+++ +g+++vel+gl+++++ g+++efe
  gi|121636446|ref|YP_976669.1| 430 VPFVNLQVSHDPGQSWVLVFAITMMAGLLVSLLVRRRRVWARITPTtAGTVNVELGGLTRTDNSGWGAEFE 500
                                    *******************************************77789*********************96 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.5e-06     0.051      46      97 ..     135     186 ..     122     197 .. 0.85
   2 ?   -2.1   0.1      0.56   3.3e+03      43      57 ..     401     415 ..     393     425 .. 0.82
   3 ?   -2.7   0.1      0.88   5.2e+03      94     111 ..     447     464 ..     429     470 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-06
                      RseC_MucC  46 igakvGdkVevgieeksllkaallvYllPllllilgallgsallgssellaa 97 
                                    i  ++Gd+Vev+ e+  l +   lv+ + ll+l++++++g++++ +++++++
  gi|121636446|ref|YP_976669.1| 135 ITRQQGDSVEVSAEKGYLREFGNLVFHFALLGLLVAVAVGKLFGYEGNVIVI 186
                                    56689*************************************9755555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.56
                      RseC_MucC  43 eneigakvGdkVevg 57 
                                    e+++++++G++V++ 
  gi|121636446|ref|YP_976669.1| 401 EKRVNLRAGQQVRID 415
                                    56789999****986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.88
                      RseC_MucC  94 llaalgallglvlgfliv 111
                                    l+ a+++++gl++++l+ 
  gi|121636446|ref|YP_976669.1| 447 LVFAITMMAGLLVSLLVR 464
                                    344555556666555554 PP

>> Big_4  Bacterial Ig-like domain (group 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.23      19      48 ..     286     315 ..     285     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                          Big_4  19 tVeatysdgseeevkVtWdkipaedtskpG 48 
                                    t ++t+ dg +++ +V+W  +++  +  +G
  gi|121636446|ref|YP_976669.1| 286 TFTVTFPDGQTRTSTVQWRPDNPQTLLSAG 315
                                    569****************55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3762.05
//
Query:       gi|121636447|ref|YP_976670.1|  [L=324]
Description: cytochrome c-type biogenesis protein ccsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-45  153.6   9.9    6.1e-45  153.6   9.9    1.6  2  Cytochrom_C_asm  Cytochrome C assembly protein


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.16   2.9e+03     164     175 ..      21      32 ..       5      50 .. 0.55
   2 !  153.6   9.9   3.4e-49   6.1e-45       1     214 []     107     318 ..     107     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.16
                Cytochrom_C_asm 164 slitWlvfaall 175
                                    ++++++v++ ll
  gi|121636447|ref|YP_976670.1|  21 AVVALVVALLLL 32 
                                    222222222222 PP

  == domain 2  score: 153.6 bits;  conditional E-value: 3.4e-49
                Cytochrom_C_asm   1 lsnleesllllawilsllgllleylarklnlsllaavaliaalillgfalflllaelqesadlnpalqspilmiHvplal 80 
                                    ++n++e + l++++ ++ g ++ + ar  +l ++  v ++++l++ g +l+       ++a++ palqs++l iHv+++ 
  gi|121636447|ref|YP_976670.1| 107 WGNMYEFINLTCLSGLIAGAVVLRRARYRPLWVFLLVPVLILLTVSGRWLY------ANAAPVMPALQSYWLPIHVSVVS 180
                                    89********************77777755555555555555555555555......99********************* PP

                Cytochrom_C_asm  81 lsYatliigallsialliierql....kkkkklklsanlkllkqldrlsyriiliGfvlltigiilGsvWaeeaWGsyws 156
                                    l+ ++++++ ++si++l+ +++l     +     + ++l+  ++ld ++yr+++++f++  +g+i+G++WaeeaWG yw 
  gi|121636447|ref|YP_976670.1| 181 LGSGVFLVAGVASILFLVRTSRLgeptGEGALAGMVRRLPDAQTLDGIAYRTTIFAFPVFGFGVIFGAIWAEEAWGRYWG 260
                                    *****************999999777666677788999****************************************** PP

                Cytochrom_C_asm 157 WDpketaslitWlvfaallhsriekgwrgkkaailailgflllllayfgvrllgeglh 214
                                    WDpket+s+++W+v+aa+lh+r + gwr +kaa+++++gf+ +++  f+v+l++ glh
  gi|121636447|ref|YP_976670.1| 261 WDPKETVSFVAWVVYAAYLHARSTAGWRDRKAAWINVAGFVAMVFNLFFVNLVTVGLH 318
                                    **********************888****************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2762.55
//
Query:       gi|121636448|ref|YP_976671.1|  [L=405]
Description: hypothetical protein BCG_0573 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-12   45.4   0.0    3.7e-11   43.2   0.0    1.9  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    2.2e-08   34.2   0.0    4.9e-08   33.1   0.0    1.5  1  AAA_31         AAA domain
    9.1e-06   25.3   0.0    2.9e-05   23.7   0.0    1.7  1  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
    0.00014   21.4   0.1    0.00023   20.7   0.1    1.3  1  ParA           NUBPL iron-transfer P-loop NTPase
     0.0039   16.4   0.1     0.0056   15.9   0.1    1.2  1  ArsA_ATPase    Anion-transporting ATPase
  ------ inclusion threshold ------
      0.091   13.1   0.0        0.2   12.0   0.0    1.6  1  AAA_16         AAA ATPase domain
       0.12   11.9   0.0        0.2   11.2   0.0    1.3  1  YrbL-PhoP_reg  PhoP regulatory network protein YrbL


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   1.5e-14   3.7e-11       1      93 [.     153     340 ..     153     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.5e-14
                                    EEEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlaileglendiep......................... 54 
                                    ia+ s kGGvGKTt++a+L++ +a+ rg rV++vDa p++  l+     +  +e+                         
  gi|121636448|ref|YP_976671.1| 153 IAVLSLKGGVGKTTITATLGATFADlRGDRVVAVDANPDRGTLS----QKVPLETpatvrhllrdadgierysdvrgyts 228
                                    79***********************99************88887....33333335778899999998899999999999 PP

                                    ........................................................................CCHCCCHH CS
                                    ........................................................................xxxxxxxx RF
                           CbiA  55 ........................................................................dlkrllel 62 
                                                                                                            ++ +   +
  gi|121636448|ref|YP_976671.1| 229 kgpsglevlasdsdpassdafsaddytrtldilerfyglvltdcgtgllhsamsavlprsdvlvvvssgsidGARSAAAT 308
                                    99999999999999999999988888888888888888888888888888888888888888888888766655555555 PP

                                    HHHHCHCHHHH...EEEEEEEEESS...-TTC CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                           CbiA  63 lealgkkkall.lkiagvvlnrvdgeneetll 93 
                                    l  l+ +  +  ++    v+n v++++ +   
  gi|121636448|ref|YP_976671.1| 309 LDWLQAHGHDDqVRNSIAVVNAVRPRAGKVDV 340
                                    54444332222588888888888877544444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.9e-11   4.9e-08       4     149 ..     153     296 ..     150     320 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.9e-11
                         AAA_31   4 IaianqKGGvGKTTtsvnlaaala.klgkkvLlvDlDpQa.nattglgiekneiektlyevl.....i.eeknikeaiik 75 
                                    Ia+   KGGvGKTT +  l+a++a  +g +v  vD+ p    +++++ +e+     t+ ++l     i + ++++ +   
  gi|121636448|ref|YP_976671.1| 153 IAVLSLKGGVGKTTITATLGATFAdLRGDRVVAVDANPDRgTLSQKVPLET---PATVRHLLrdadgIeRYSDVRGYTS- 228
                                    99**********************889***********7614566665543...3455555522223312333333333. PP

                         AAA_31  76 tkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqa 149
                                    +  + l+++ s+ d a+ +        + + ++++l+ ++  Y +++ Dc   L   +++a++    v+++v +
  gi|121636448|ref|YP_976671.1| 229 KGPSGLEVLASDSDPASSDAF------SADDYTRTLDILERFYGLVLTDCGTGLLHSAMSAVLPRSDVLVVVSS 296
                                    334555666666665555433......34455677888888899999999887777666665554444554443 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.1e-08   2.9e-05       4     142 ..     153     292 ..     151     301 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                       CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhel.gesvlviDlspdnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldll 82 
                                    +a+  ++GGvG+t+++a+L+  +  l g++v+++D++pd   +l+ +v++e+ ++  + + d a+  +   +++   +  
  gi|121636448|ref|YP_976671.1| 153 IAVLSLKGGVGKTTITATLGATFADLrGDRVVAVDANPDRG-TLSQKVPLETPATVRHLLRD-ADGIERYSDVRGYTSKG 230
                                    677789*****************886489*********963.56666666666655444444.33333444444444455 PP

                       CBP_BcsQ  83 PfGelnveeken.lqqlaekaeallaalkelkeqyrwillDlpaga.saltrellaladlvl 142
                                    P G    +  ++  ++ a +a+ ++++l+ l++ y ++l D+ +g  ++ ++++l ++d+ +
  gi|121636448|ref|YP_976671.1| 231 PSGLEVLASDSDpASSDAFSADDYTRTLDILERFYGLVLTDCGTGLlHSAMSAVLPRSDVLV 292
                                    66643333333303334445666667777777777777777766541334444555555555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1     9e-08   0.00023       6      40 ..     153     188 ..     150     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9e-08
                           ParA   6 iavlSgKGGVGKStvavnlAlaLa.kkglkvgllDa 40 
                                    iavlS KGGVGK+t++++l +++a  +g +v  +Da
  gi|121636448|ref|YP_976671.1| 153 IAVLSLKGGVGKTTITATLGATFAdLRGDRVVAVDA 188
                                    99******************9998567888888886 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.2e-06    0.0056       2      35 ..     152     186 ..     151     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTT.S-EEEE CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekg.kkvlli 35 
                                    ++ +++ KGGVGKtt+ a++++  ++ +  +v+ +
  gi|121636448|ref|YP_976671.1| 152 RIAVLSLKGGVGKTTITATLGATFADLRgDRVVAV 186
                                    5667888*****************99761455555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.9e-05       0.2       5     104 ..     132     233 ..     131     278 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                         AAA_16   5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslv...rellralekdggiflrgkcdql..esaipysalaqalare 79 
                                    R + l+ L + ++r  +g  ++ +ls   GvGK+++     + +  l++d+++++ ++ d+   ++++p+    + ++ +
  gi|121636448|ref|YP_976671.1| 132 RAAHLNDLVAQVNRPLRGCYRIAVLSLKGGVGKTTITatlGATFADLRGDRVVAVDANPDRGtlSQKVPL---ETPATVR 208
                                    67788889999999999999****************9444344458888888889999988844444444...1111122 PP

                         AAA_16  80 ellrqlldeaesaeleawrekleea 104
                                    +llr+ +  ++ ++++ +  k ++ 
  gi|121636448|ref|YP_976671.1| 209 HLLRDADGIERYSDVRGYTSKGPSG 233
                                    4444444444444444444444444 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.8e-05       0.2      78      97 ..     259     278 ..     246     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-05
                  YrbL-PhoP_reg  78 splarilGlvqTdlGlGlvv 97 
                                      l+r++Glv Td+G+Gl+ 
  gi|121636448|ref|YP_976671.1| 259 DILERFYGLVLTDCGTGLLH 278
                                    5699*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2988.84
//
Query:       gi|121636449|ref|YP_976672.1|  [L=105]
Description: hypothetical protein BCG_0574 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-20   72.9  11.1    2.2e-20   72.5  11.1    1.1  1  DUF4229   Protein of unknown function (DUF4229)
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.036   14.3   0.0    1.1  1  DUF3007   Protein of unknown function (DUF3007)
       0.29   11.5   2.1       0.35   11.3   2.1    1.3  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5  11.1   3.7e-24   2.2e-20       1      68 []      17      85 ..      17      85 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.7e-24
                        DUF4229  1 llYtlaRlaLfvvltavillvarliglp.vpllvaallAlvvalplSmvllkklRdrataqvaerderR 68
                                   l+Y++aRl+L+v++ a+i++varligl+ +p++va l++l++a+pl+++++++lR+rata++a++ erR
  gi|121636449|ref|YP_976672.1| 17 LVYATARLLLVVAVSAAIFGVARLIGLTeFPVVVATLFGLIIAMPLGIWVFSPLRRRATAALAVAGERR 85
                                   79*****************************************************************99 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-06     0.036      11      81 ..      25      97 ..      15     105 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-06
                        DUF3007 11 lgvlllgglaylvlqalGldslsagiwsqavlvlgl..vgWvltYllRvvtkkmTyaqqlkdyeeavlqkrle 81
                                   l v++++++++ v +++Gl ++   +++   l++++   +Wv++ l R +t     a  +++ e++ l++rl+
  gi|121636449|ref|YP_976672.1| 25 LLVVAVSAAIFGVARLIGLTEFPVVVATLFGLIIAMplGIWVFSPLRRRATAALAVAGERRRAERERLRARLR 97
                                   5688899999*************99999866666654368**************************9999985 PP

>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.1   5.9e-05      0.35      38      70 ..      25      59 ..       9      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                                   HHHHHHHHHHHHHCSGGGHHH..HHHHHHHHHHHH CS
                           CPBP 38 tlailissilFglaHlpngps..vllaalaGlvlg 70
                                   +l++++s+++Fg+a l+      v++a+l+Gl+++
  gi|121636449|ref|YP_976672.1| 25 LLVVAVSAAIFGVARLIGLTEfpVVVATLFGLIIA 59
                                   6899**************55556999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 732.39
//
Query:       gi|121636450|ref|YP_976673.1|  [L=581]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-33  113.4  24.2    6.8e-33  112.9  24.2    1.3  1  PE              PE family
  ------ inclusion threshold ------
        3.3    8.2  13.6        5.7    7.5  13.6    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9  24.2   7.6e-37   6.8e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 7.6e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms + v+Pe++aaaaadlagigsa+ aanaaa apt+a+laa+aDeVSaa+Aa+fs++aq+yqalsa aaafh+qfv+alaa
  gi|121636450|ref|YP_976673.1|  1 MSNLLVTPELVAAAAADLAGIGSAIGAANAAAGAPTMALLAAGADEVSAAVAAVFSSYAQQYQALSAAAAAFHDQFVRALAA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya aEaa
  gi|121636450|ref|YP_976673.1| 83 GAGAYAGAEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.6   0.00064       5.7       3      94 ..       2      94 ..       1      97 [. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00064
                  T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp..icaatndavaaaeaarraagealaaasteLadkLra 82
                                    nL V+p+ + ++aa++ ++ + i +a+aaa ga++  l   G+  ++aa+++ ++++ +  +a  +a aa ++++ + L a
  gi|121636450|ref|YP_976673.1|  2 SNLLVTPELVAAAAADLAGIGSAIGAANAAA-GAPTMALLAAGAdeVSAAVAAVFSSYAQQYQALSAAAAAFHDQFVRALAA 82
                                   499****************************.99999999999755788888888888888888888888888888889999 PP

                  T7SS_ESX_EspC 83 AAaaYeatDeea 94
                                    A+aY  ++ ++
  gi|121636450|ref|YP_976673.1| 83 GAGAYAGAEAAN 94
                                   999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 3372.18
//
Query:       gi|121636451|ref|YP_976674.1|  [L=335]
Description: 3-oxoacyl-ACP synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-32  109.2   0.6    6.5e-31  106.4   0.1    2.6  3  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
      9e-23   79.9   1.0    2.3e-22   78.7   1.0    1.7  1  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    3.5e-06   26.6   0.3    3.5e-06   26.6   0.3    2.3  3  Thiolase_N       Thiolase, N-terminal domain
    1.9e-05   24.1   0.0    9.4e-05   21.8   0.0    1.9  2  FAE1_CUT1_RppA   FAE1/Type III polyketide synthase-like prote
    0.00042   19.8   1.5    0.00087   18.8   1.5    1.5  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
  ------ inclusion threshold ------
       0.78    9.3   9.0         27    4.2   5.8    3.0  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.62   1.8e+03       1      16 [.      73      88 ..      73      94 .. 0.85
   2 ?   -2.0   0.1       1.4   4.1e+03       5      18 ..     197     210 ..     194     211 .. 0.76
   3 !  106.4   0.1   2.2e-34   6.5e-31       1      90 []     242     332 ..     242     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.62
                                   HHHTT--GGG-SEEEE CS
                  ACP_syn_III_C  1 Lekagltpedidalvp 16
                                   L++agl+++did ++ 
  gi|121636451|ref|YP_976674.1| 73 LSNAGLSAADIDGVIV 88
                                   6789********9986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                    T--GGG-SEEEE-S CS
                  ACP_syn_III_C   5 gltpedidalvphq 18 
                                    +   +did++ + q
  gi|121636451|ref|YP_976674.1| 197 DAIRQDIDWITFAQ 210
                                    55679****99877 PP

  == domain 3  score: 106.4 bits;  conditional E-value: 2.2e-34
                                    HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GG.GB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpee.kvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgfGa 79 
                                    +++ag++p++id++vphqan ri++ ++k+l+l+++  v+++++++Gntsaasipla++e++ +g  kpgdl+ll+g Ga
  gi|121636451|ref|YP_976674.1| 242 MDAAGVRPDQIDVFVPHQANSRINELLVKNLQLRPDaVVANDIEHTGNTSAASIPLAMAELLTTGAAKPGDLALLIGYGA 321
                                    589*********************************6677889************************************* PP

                                    TTEEEEEEEE- CS
                  ACP_syn_III_C  80 Gltwgaallrw 90 
                                    Gl+++a+++r+
  gi|121636451|ref|YP_976674.1| 322 GLSYAAQVVRM 332
                                    *********95 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   1.0   7.5e-26   2.3e-22       1      80 []     116     193 ..     116     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 7.5e-26
                                    EEEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEESSSSCEEEEEEEEE-G CS
                    ACP_syn_III   1 fDlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleaseeegarildselgsdg 80 
                                    fDl+a+C+gf yal  A+++i+ g a ++Lv+g+e+ls  +D+ dr ++++f+DGA+Avv++++  +g  i  +  gsdg
  gi|121636451|ref|YP_976674.1| 116 FDLSAGCAGFGYALGAAADMIRGGGAATMLVVGTEKLSPTIDMYDRGNCFIFADGAAAVVVGETPFQG--IGPTVAGSDG 193
                                    9**************************************************************97667..9999998887 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   1.2e-09   3.5e-06       8     118 ..      46     155 ..      44     163 .. 0.93
   2 ?    0.4   0.1      0.11   3.4e+02     242     256 ..     162     176 ..     158     179 .. 0.83
   3 ?   -2.1   0.0      0.64   1.9e+03      32      98 ..     239     301 ..     234     309 .. 0.54

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                                    EE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGH CS
                     Thiolase_N   8 rtpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsS 87 
                                    rt i + + +  d sa  +++ea +++l++ag++++++d viv +  +  ++   a ++a  +g  + +    +   c+ 
  gi|121636451|ref|YP_976674.1|  46 RTGIKTRRFAADDESAASMATEACRRALSNAGLSAADIDGVIVTTNTHFLQTPPAAPMVAASLGA-KGILGFDLSAGCAG 124
                                    888888888999********************************999999999999999999999.9************* PP

                                    HHHHHHHHHHHHHTTSHSEEEEEEEEESTTS CS
                     Thiolase_N  88 glkavalaaqsiaageadvvvagGvEsmsna 118
                                       a+ +aa++i+ g a  ++++G+E++s +
  gi|121636451|ref|YP_976674.1| 125 FGYALGAAADMIRGGGAATMLVVGTEKLSPT 155
                                    ****************************965 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                                    TSB--BEEEEEEEEE CS
                     Thiolase_N 242 gnasqisDGaaavll 256
                                    gn+   +DGaaav++
  gi|121636451|ref|YP_976674.1| 162 GNCFIFADGAAAVVV 176
                                    6777789******98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.64
                                    HHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHH CS
                     Thiolase_N  32 kallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqs 98 
                                    +++++ agv p+++d  +  + +++  ++ + ++++l+   p+ v+a  ++++   +++++ la+ +
  gi|121636451|ref|YP_976674.1| 239 RRAMDAAGVRPDQIDVFVPHQ-ANSRINELLVKNLQLR---PDAVVANDIEHTGNTSAASIPLAMAE 301
                                    566677777777776433322.2222222333333333...45577777777777777777666655 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.2e-08   9.4e-05      78     203 ..      55     176 ..      21     182 .. 0.78
   2 ?   -0.3   0.0      0.17   5.1e+02      97     156 ..     244     301 ..     234     319 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.2e-08
                 FAE1_CUT1_RppA  78 eareE.aeevlfgavdellaktkvspkdid.ilvvncslfsptPslsamvvnryklredvksynLsgmGCsAglisidla 155
                                    +a +E a ++ ++a    l+++++s++did ++v+  + f  tP  + mv    + +  +  ++Ls+ GC+    ++  a
  gi|121636451|ref|YP_976674.1|  55 AADDEsAASMATEACRRALSNAGLSAADIDgVIVTTNTHFLQTPPAAPMVAASLGAK-GILGFDLSA-GCAGFGYALGAA 132
                                    34445145566789999************84666677889**********9999965.7*******9.****99****** PP

                 FAE1_CUT1_RppA 156 knllqvhkntlalvvstEnitlnwYvGnersmllanc.lFRvGgaavll 203
                                     ++++    ++ lvv tE++++ + + ++     +nc +F  G+aav++
  gi|121636451|ref|YP_976674.1| 133 ADMIRGGGAATMLVVGTEKLSPTIDMYDR-----GNCfIFADGAAAVVV 176
                                    ********************998766544.....344346666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
                 FAE1_CUT1_RppA  97 ktkvspkdidilvvncslfsptPslsamvvnryklredvksyn.LsgmG.CsAglisidlak 156
                                     ++v+p++id++v     ++++  + +++v++ +lr d  + n +   G  sA+ i + +a+
  gi|121636451|ref|YP_976674.1| 244 AAGVRPDQIDVFVP----HQANSRINELLVKNLQLRPDAVVANdIEHTGnTSAASIPLAMAE 301
                                    56899999999986....45566788888888888887554441444442345555555544 PP

>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.5   2.9e-07   0.00087      87     225 .]      48     180 ..      27     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-07
                Chal_sti_synt_N  87 sldarleiv.naevlklgkeaalkalkewGrPkskithlvfvs.ssevelPGadlklakklGlrpsvkrvmlyflGcygG 164
                                     +++r+  +  +    +++ea+++al + G  +++i  ++  + +  ++ P a  ++a+ lG +     +  +  Gc g 
  gi|121636451|ref|YP_976674.1|  48 GIKTRRFAAdDESAASMATEACRRALSNAGLSAADIDGVIVTTnTHFLQTPPAAPMVAASLGAKGI-LGFD-LSAGCAGF 125
                                    5555554441455689********************987665516679**************8764.4455.578***** PP

                Chal_sti_synt_N 165 atvlrlakdiaennkGarvlvvaseitvlgfrgPskdrlddlvGaalfGdGaaaviiGadP 225
                                    + +l  a d+      a +lvv +e       +P+   ++d     +f dGaaav++G  P
  gi|121636451|ref|YP_976674.1| 126 GYALGAAADMIRGGGAATMLVVGTEKL-----SPTI-DMYDRGNCFIFADGAAAVVVGETP 180
                                    ***********************9975.....4554.4677777889***********877 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.01        31      87     112 ..      60      85 ..      34      97 .. 0.80
   2 ?    4.2   5.8     0.009        27     155     210 ..     101     157 ..      96     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHHHHHHHTS-HHTCTT CS
                  ketoacyl-synt  87 pqqrllleaawealedagltpeeldg 112
                                     ++ ++ ea+++al +agl+++++dg
  gi|121636451|ref|YP_976674.1|  60 SAASMATEACRRALSNAGLSAADIDG 85 
                                    456799***************99886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.009
                                    HHHHHHHHT--SSE.EEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHH CS
                  ketoacyl-synt 155 agrisyalglrGps.vtvdtACsSslvavhaavqslrsgeadvalaGGvellltpea 210
                                    a +++ +lg++G   + +++ C+    a+ aa +++r g a ++l+ G+e l    +
  gi|121636451|ref|YP_976674.1| 101 APMVAASLGAKGILgFDLSAGCAGFGYALGAAADMIRGGGAATMLVVGTEKLSPTID 157
                                    556788888888652668888998878888888****************97655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2098.05
//
Query:       gi|121636452|ref|YP_976675.1|  [L=292]
Description: 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-29  102.2  29.8    2.8e-29  102.2  29.8    1.5  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        1.1    9.9   2.9        2.8    8.5   2.9    1.8  1  YtxH      YtxH-like protein


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2  29.8   3.1e-33   2.8e-29       2     228 ..      20     250 ..      19     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.1e-33
                           UbiA   2 lipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmert.pnRPlv.sGrispkealifaivlli 78 
                                    + p+++g  a+a+ +   ++ +ll+l+ ++++ +++n  Ndy D   + d +r  p R lv s++ +p+ +l++a+ +l+
  gi|121636452|ref|YP_976675.1|  20 IAPVVAGtGAAAWLHAAVWWKALLALAVAVALVIGVNYANDYSDGIRGTDDDRVgPVR-LVgSRLATPRSVLTAAMTSLA 98 
                                    57889999777778888888999999999999999*****************999***.776**********99999999 PP

                           UbiA  79 lgllll...alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalav 152
                                    lg+l +   all  p+++++g+++++ +++Yt g  ++++ ++ g++ ++++fg +++lg  + ++  +++  l+ a+a+
  gi|121636452|ref|YP_976675.1|  99 LGALAGlvlALLSAPWLIAVGAICIAGAWLYTgGsKPYGYAGF-GELAVFVFFGPVAVLGTQYtQALRVDWVGLAQAVAT 177
                                    98777778789999******************9899*******.*******************544455*********** PP

                           UbiA 153 flltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalall 228
                                    ++l+ ++++an+lrd+  D++a + tl+v+lG++++r l+  llav+ ++   +++++l++++ +++l++a+lal 
  gi|121636452|ref|YP_976675.1| 178 GALSCSVLVANNLRDIPTDARADKITLAVRLGDARTRMLYQGLLAVAGVL---TFVLMLATPWCVVGLVAAPLALR 250
                                    **************************************988788888777...77788888888888888887775 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.9   0.00031       2.8       2      20 ..      95     113 ..      94     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00031
                           YtxH   2 lglliGaavGaaaglLlAP 20 
                                    + l +Ga++G +++lL AP
  gi|121636452|ref|YP_976675.1|  95 TSLALGALAGLVLALLSAP 113
                                    5789**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2029.94
//
Query:       gi|121636453|ref|YP_976676.1|  [L=264]
Description: 5'-methylthioadenosine phosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-36  124.9   1.2    4.1e-36  124.4   1.2    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   1.2   2.3e-40   4.1e-36       3     233 ..       9     239 ..       8     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 2.3e-40
                                    EEEESSH..HHHHHHHHH..EEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SEE CS
                      PNP_UDP_1   3 aiivgsp..gevellaes..pleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvkai 73 
                                    ++i+gs+        +++     +tp+g +  +  +++Gt++ + v ++ ++G     +++ + ++a++++l ++gv+++
  gi|121636453|ref|YP_976676.1|   9 GVIGGSGfyT--FFGSDTrtVNSDTPYGQP--SAPITIGTIGVHDVaFLPRHGahhqYSAHAVPYRANMWALRALGVRRV 84 
                                    6777777441..222222345678******..*********7776669*******987888888**************** PP

                                    EEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESE CS
                      PNP_UDP_1  74 iriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadg 153
                                    +   ++G+l+p+l++G vv+pd++++ + ++++++++ +   + +++d+ ++p lra++      l+  v  G+ ++ +g
  gi|121636453|ref|YP_976676.1|  85 FGPCAVGSLDPELEPGAVVVPDQLVDRTSGRADTYFDFG-GVHAAFADP-YCPTLRAAVTG----LPGVVDGGTMVVIQG 158
                                    **************************8888888888887.999999999.********999....7788888******** PP

                                    SS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTB.ETTCTCH.HCCCHHHHHHHHHHHHHHHHH CS
                      PNP_UDP_1 154 fyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaag.gadaeatheeveefaqeaaknaaalllal 232
                                    ++++t+ae+++++  g+ +v+M+++++a+lArel++++aai++v+d+ ag +a++    ++v +++ e+ + +++l++a+
  gi|121636453|ref|YP_976676.1| 159 PRFSTRAESQWFAAAGCNLVNMTGYPEAVLARELELCYAAIALVTDVDAGvAAGDGVKAADVFAAFGENIELLKRLVRAA 238
                                    **********************************************9999766666666999999999999999999998 PP

                                    H CS
                      PNP_UDP_1 233 l 233
                                    +
  gi|121636453|ref|YP_976676.1| 239 I 239
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1888.81
//
Query:       gi|121636454|ref|YP_976677.1|  [L=346]
Description: UDP-glucose 4-epimerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-41  141.1   0.2    5.2e-40  137.4   0.2    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.1e-27   95.5   0.0    4.8e-17   62.4   0.0    2.5  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.5e-09   34.6   0.0    8.2e-05   21.7   0.0    2.3  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.1e-06   28.0   0.1     0.0064   15.6   0.1    2.1  2  RmlD_sub_bind    RmlD substrate binding domain
      2e-06   27.8   1.9    5.6e-06   26.4   1.9    1.8  1  NAD_binding_10   NAD(P)H-binding
    0.00012   21.3   0.0       0.17   10.9   0.0    2.9  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0004   19.6   0.0      0.013   14.7   0.0    2.5  2  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.2     2e-43   5.2e-40       1     233 [.       3     267 ..       3     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 2e-43
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S.---H CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAa.vggv 77 
                                    +l+tGa+GfiGs +  al ++g++v+g+d l  a + + ++ l     ++d++d+sal+ l++  ++d v h Aa vg  
  gi|121636454|ref|YP_976677.1|   3 VLLTGAAGFIGSRVDAALRAAGHDVVGVDALLPAAH-GPNPVLppGCQRVDVRDASALAPLLA--GVDLVCHQAAmVGAG 79 
                                    699****************************44444.33333489999***************..9*********66666 PP

                                    HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGT................................SCSSS CS
                      Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYG................................kdaeq 125
                                     + ++ pa+  ++++  t+ ll  +++agv+rl+ +sS  vYG                                     
  gi|121636454|ref|YP_976677.1|  80 VNAADAPAYGGHNDF-ATTVLLAQMFAAGVRRLVLASSMVVYGqgrydcpqhgpvdplprrradldngvfehrcpG-CGE 157
                                    666666666666666.56678888899*****************************************99997742.334 PP

                                    S.....BSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSS CS
                      Epimerase 126 p.....keettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqe 199
                                    p      +e++   pl+p+s Yaa+K+a e+++ a+ ++ g ++++lr+ n+yGp+   ++  s+v + + + + +gk +
  gi|121636454|ref|YP_976677.1| 158 PviwqlVDEDA---PLRPRSLYAASKTAQEHYALAWSEASGGSVVALRYHNVYGPGmPRDTPYSGVAAIFRSAVEKGK-P 233
                                    56533455555...******************************************5555559999999999999999.* PP

                                    EEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-S CS
                      Epimerase 200 vtllgdgtalRdflyveDvaeaillvlehvdagd 233
                                     +++ dg + Rdf++v+Dva a+l+++   +a++
  gi|121636454|ref|YP_976677.1| 234 PKVFEDGGQMRDFVHVDDVAAANLAAVHLGEADR 267
                                    ************************9998766544 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   8.7e-11   2.2e-07       1     137 [.       4     124 ..       4     136 .. 0.86
   2 !   62.4   0.0   1.9e-20   4.8e-17     141     331 ..     164     339 ..     156     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 8.7e-11
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L TG aGfiGs +   L + g++v+g++ +  +  ++  + +   p           ++D++D+s+l  lla v  d v 
  gi|121636454|ref|YP_976677.1|   4 LLTGAAGFIGSRVDAALRAAGHDVVGVDALLPA--AHGPNPVLP-P--------GCQRVDVRDASALAPLLAGV--DLVC 70 
                                    78************************9766544..334444442.3........3579***************9..99** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq 137
                                    + AA+   +v   ++ ++   n  +t+ LL  + a+g++   r++ aS+  vYG+ +
  gi|121636454|ref|YP_976677.1|  71 HQAAMVGAGVNAADAPAYGGHNDFATTVLLAQMFAAGVR---RLVLASSMVVYGQGR 124
                                    ************99999999999*************996...9***********965 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 1.9e-20
                                    B-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-E CS
                  GDP_Man_Dehyd 141 qtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldak 220
                                    ++E+ p++Prs Yaa+K ++++ + ++ ea g  +v  ++ n ++p + ++ +   +  +   + ++ ++  ++ ++ + 
  gi|121636454|ref|YP_976677.1| 164 VDEDAPLRPRSLYAASKTAQEHYALAWSEASGGSVVALRYHNVYGPGMPRDTPYSGVAAIFRSAVEKGKPPKVFEDGGQM 243
                                    58*************************************************999998866655554445666689***** PP

                                    EEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S CS
                  GDP_Man_Dehyd 221 RdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp 300
                                    Rd+ hv+D++ a  ++++ ++++       + ++v +   +++l++   i+               g    +    ++r 
  gi|121636454|ref|YP_976677.1| 244 RDFVHVDDVAAANLAAVHLGEADR---DGFTAVNVCSGRPISILQVATAICDA------------RGGSMSPAITGHYRS 308
                                    *************99999999764...34556777778888899998888753............3444455556889** PP

                                    S--SB--B-THHHHHHH----SS-HHHHHHH CS
                  GDP_Man_Dehyd 301 gevdlllgdaskakeeLgWkpkvsfeelvre 331
                                    g+v+ +++d+++a + Lg+++ v+  e++re
  gi|121636454|ref|YP_976677.1| 309 GDVRHIVADPARAARVLGFRAAVDPGEGLRE 339
                                    ***********************99999887 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.2e-08   8.2e-05       2     122 ..       5     122 ..       4     131 .. 0.76
   2 !   10.6   0.0   7.8e-05       0.2     140     229 ..     170     260 ..     160     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.2e-08
                      3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegvdvvihlaslvd 78 
                                    +tG+aGF+G+++  +L  +++  +v  +D      ll  ++  n      +  +Dv+d++ l   l gvd+v h a++v 
  gi|121636454|ref|YP_976677.1|   5 LTGAAGFIGSRVDAALRAAGH--DVVGVDA-----LLPAAHGPNPVLppgCQRVDVRDASALAPLLAGVDLVCHQAAMVG 77 
                                    79*********9999888885..5555553.....322233222222234889**********************99988 PP

                      3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                              +   n   T  +l+  + agvr+lv  Ss+ v g+
  gi|121636454|ref|YP_976677.1|  78 AGVnAADAPAYGGHNDFATTVLLAQMFAAGVRRLVLASSMVVYGQ 122
                                    766233444566788889999*******************99887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.8e-05
                      3Beta_HSD 140 slhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvp......llkqlaklglalfkigdeevls 213
                                      + + y+ sK   E++ l+  +   ++g     +aLR   +yG+g ++ +p       ++ ++ +g+      d  ++ 
  gi|121636454|ref|YP_976677.1| 170 LRPRSLYAASKTAQEHYALAWSE--ASGG---SVVALRYHNVYGPGMPRDTPysgvaaIFRSAVEKGKPPKVFEDGGQMR 244
                                    55788999*******99999887..4445...579***********9875541111113455555554444556677899 PP

                      3Beta_HSD 214 drvYvgNvawahilAa 229
                                    d+v v+ va a + A+
  gi|121636454|ref|YP_976677.1| 245 DFVHVDDVAAANLAAV 260
                                    9********9987665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.5e-06    0.0064       1      61 [.       1      75 [.       1     126 [. 0.87
   2 !   10.5   0.0   9.2e-05      0.24     115     229 ..     166     292 ..     159     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH--SEEEE---- CS
                  RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkeakpdvvvnaAAy 61
                                   m++l+tGa G +Gs + ++l+++g++v++++                  ++d++da+a+a ll+    d+v + AA 
  gi|121636454|ref|YP_976677.1|  1 MRVLLTGAAGFIGSRVDAALRAAGHDVVGVDALlpaahgpnpvlppgcqRVDVRDASALAPLLAG--VDLVCHQAAM 75
                                   89****************************988999***************************98..7899999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.2e-05
                                    TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEEE-SEESS.....SSS-HHHHHHHHH.HH-SEEEEESS..-EE- CS
                  RmlD_sub_bind 115 eddetsPlnvYGrtKlaGEqavla....agkkalivRtswvyge.....kgknfvktmlrla.kereelkvvaD..qlgs 182
                                    ed++  P+++Y+++K a E+  la    +g  ++ +R   vyg      +  + v+ ++r a ++ ++ kv++D  q++ 
  gi|121636454|ref|YP_976677.1| 166 EDAPLRPRSLYAASKTAQEHYALAwseaSGGSVVALRYHNVYGPgmprdTPYSGVAAIFRSAvEKGKPPKVFEDggQMRD 245
                                    78899**************9988766667789999*******98777665666677888877688899999999889999 PP

                                    -EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHH CS
                  RmlD_sub_bind 183 PTsardlAevllqllekaaeekelagvyHlanegetswlefArailk 229
                                      +++d+A++ l++++   ++++ +    + + + +s l++A ai +
  gi|121636454|ref|YP_976677.1| 246 FVHVDDVAAANLAAVHLGEADRDGFTAVNVCSGRPISILQVATAICD 292
                                    99999999988887776666666555555555556777777777766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   1.9   2.2e-09   5.6e-06       1     103 [.       7     121 ..       7     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.2e-09
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTC..EEEE--TT-CCHHHHHHTT-SEEEES-...--TCC.. CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeegl..evvegdvtdvedlaealkgadaVvsal...ggggk.. 73 
                                    GA G +G+++ + l a+ gh+v+ +      +a+ + ++ l      +dv d+++la  l+g+d V+  +   g+g +  
  gi|121636454|ref|YP_976677.1|   7 GAAGFIGSRVDAALRAA-GHDVVGV-DALLPAAHGP-NPVLppGCQRVDVRDASALAPLLAGVDLVCHQAamvGAGVNaa 83 
                                    9***********99999.5999766.3332222222.233311356789*****************88886774444433 PP

                                    HHHH..........HHHHHHHHHHCT--EEEEEEETTTTS CS
                 NAD_binding_10  74 deeg..........aknivdaakeagvkRfvlvsaigvgd 103
                                    d  +          +  +++ + +agv+R+vl s++ v+ 
  gi|121636454|ref|YP_976677.1|  84 D--ApaygghndfaTTVLLAQMFAAGVRRLVLASSMVVYG 121
                                    2..34477777777888999****************9985 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.088   2.3e+02       1      14 [.       3      16 ..       3      28 .. 0.85
   2 !    5.6   0.0    0.0029       7.4      61     127 ..      51     115 ..      48     117 .. 0.85
   3 !   10.9   0.0   6.8e-05      0.17     129     248 ..     167     295 ..     161     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.088
                                   EEEETTTSHHHHHH CS
                Polysacc_synt_2  1 vlvtGagGsiGsel 14
                                   vl+tGa+G iGs++
  gi|121636454|ref|YP_976677.1|  3 VLLTGAAGFIGSRV 16
                                   89*********987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0029
                                    --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliS 127
                                     dvrd++ l+ +l   +vd+v h AA+    +    +      N ++t+ ++    +agv+++vl S
  gi|121636454|ref|YP_976677.1|  51 VDVRDASALAPLLA--GVDLVCHQAAMVGAGVNAADAPAYGGHNDFATTVLLAQMFAAGVRRLVLAS 115
                                    59************..**********98877777766666677888888888888999999999888 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 6.8e-05
                                    GGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG.......TTSSHHHHHHHHHTTSSEEES.-TT-E CS
                Polysacc_synt_2 129 DKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS.......rGSviplFkkqikeggpvtvT.dpemt 200
                                    D   +P +++ a+K ++e ++ a ++ s      +v+ R+ NV g           v  +F++ +++g+p  v  d   +
  gi|121636454|ref|YP_976677.1| 167 DAPLRPRSLYAASKTAQEHYALAWSEAS---GGSVVALRYHNVYGPgmprdtpYSGVAAIFRSAVEKGKPPKVFeDGGQM 243
                                    66789*******************9999...7899********98522322223569999********998886145678 PP

                                    EEEE-HHHHHHHHHHHHHH--SS-.....EEEE--.-EEEHHHHHHHH..... CS
                Polysacc_synt_2 201 RyfmtieeavqLvlqalalakgge.....ifvldmGepvkivdlakalielsg 248
                                    R f+ +++ +   l a++l++        + v   G p++i+++a+a+++  g
  gi|121636454|ref|YP_976677.1| 244 RDFVHVDDVAAANLAAVHLGEADRdgftaVNV-CSGRPISILQVATAICDARG 295
                                    99999999777777777766654444432333.35799999999999887665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.033        86       1      11 [.       5      15 ..       5      28 .. 0.89
   2 !   14.7   0.0   4.9e-06     0.013      84     256 ..      62     255 ..      55     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.033
                                   EE-TTSHHHHH CS
                  NAD_binding_4  1 lTGaTGFLGkv 11
                                   lTGa GF+G++
  gi|121636454|ref|YP_976677.1|  5 LTGAAGFIGSR 15
                                   8********97 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.9e-06
                                    HHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHH..HHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                  NAD_binding_4  84 laeevdviihsaAtvnfdepyke...llrvNveGtrevle..lakklkklkvllhvSTayvngeregeveekvyeege.. 156
                                    l + vd+++h aA v    +  +       N  +t  +l   +a+++++l   +  S+ +v+g+ +    ++        
  gi|121636454|ref|YP_976677.1|  62 LLAGVDLVCHQAAMVGAGVNAADapaYGGHNDFATTVLLAqmFAAGVRRL---VLASSMVVYGQGRYDCPQH-----Gpv 133
                                    66677777777777766544444111444555555554432245555444...6677766666655443111.....123 PP

                                    ..........................HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST CS
                  NAD_binding_4 157 .......................keekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktG 213
                                                           ++++ +  +++        Y  sK + E+   ++++ sg  vv +R  +++g  ++ 
  gi|121636454|ref|YP_976677.1| 134 dplprrradldngvfehrcpgcgEPVIWQLVDEDAPLRPRSLYAASKTAQEHYALAWSEASGGSVVALRYHNVYGPGMPR 213
                                    445677778888888888888776666666667777777789*********************************66665 PP

                                    ---TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHHHHHHH CS
                  NAD_binding_4 214 wingsdlgirgllgliakgvlpeilgdkeavldlvpvDyvana 256
                                     +  s  +++ + ++++kg+ p++++d  +  d+v vD va a
  gi|121636454|ref|YP_976677.1| 214 DTPYSG-VAAIFRSAVEKGKPPKVFEDGGQMRDFVHVDDVAAA 255
                                    555555.7888889************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2218.91
//
Query:       gi|121636455|ref|YP_976678.1|  [L=477]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3498.33
//
Query:       gi|121636456|ref|YP_976679.1|  [L=548]
Description: hypothetical protein BCG_0582 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.73    9.8  12.7        1.2    9.0  12.7    1.5  1  TFIIA     Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  12.7   6.8e-05       1.2      69     180 ..     423     531 ..     303     539 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 6.8e-05
                          TFIIA  69 kqalqasaaaasqapastsqslpslvipagksvqslta...nssaataatfslpakleppvqipagvtlqtasg...... 139
                                    +++  +      ++p++t+ ++p+ + p+        +    +++ t   +++p+++ p    p+ v   t+ +      
  gi|121636456|ref|YP_976679.1| 423 SATT-P-----PTTPPTTPVTTPPTTPPTT----P--VttpPTTPPTTPVTTPPTTVAPTTVAPTTVAPTTVAPttvapa 490
                                    1111.1.....1223333333333333222....1..1122333333333334444444333344333333333322224 PP

                          TFIIA 140 qlykvnvqasgaqqiaaqplqqvvqqsqgsaaqssvaalqa 180
                                    +++ ++v+++ +qq  +qp qq+  q+q  a q++++a+q+
  gi|121636456|ref|YP_976679.1| 491 TATPTTVAPQPTQQPTQQPTQQMPTQQQTVAPQTVAPAPQP 531
                                    44455669999999999999999999888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.39
# Mc/sec: 4262.69
//
Query:       gi|121636457|ref|YP_976680.1|  [L=210]
Description: dolichyl-phosphate sugar synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-20   72.5   0.0    4.7e-20   72.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.03   14.8   0.0      0.056   14.0   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.044   13.7   0.0      0.079   12.9   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
        0.1   12.1   0.0       0.19   11.2   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0     1e-23   4.7e-20       4     141 ..       2     125 ..       1     151 [. 0.81

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1e-23
                                    EEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEE CS
                Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyi 83 
                                     p+ Nee+ l+++l+++ a      ++ +vvD++StD+t+ ++ ++     +  v+  ++  G+++a+ ag+ aat+ ++
  gi|121636457|ref|YP_976680.1|   2 LPCLNEEESLPAVLAAIPA-----GYRALVVDNNSTDDTATVAARH-----GAQVVVEPRP-GYGSAVHAGVLAATTPIV 70 
                                    59*************5555.....6*********************.....99******99.****************** PP

                                    EEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCC CS
                Glycos_transf_2  84 lflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfk 141
                                    +++DaD  +d ++l+klv++l+k gad+v g r+   g  +++  + +  +  + ++ 
  gi|121636457|ref|YP_976680.1|  71 AVIDADGSMDAGDLPKLVAELDK-GADLVTGRRRPVAGLHWPWVARVG--TVVMSWRL 125
                                    ***********************.**9999998776666555555433..33333333 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.056       2      47 ..       6      49 ..       5      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllh 47
                                   ne++ Lp++la++  +g++  lv+dn+stD+t+++ +++ +  +++
  gi|121636457|ref|YP_976680.1|  6 NEEESLPAVLAAI-PAGYR-ALVVDNNSTDDTATVAARHGAQVVVE 49
                                   8999999999998.55566.899*************9995533333 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.079       1     120 [.      69     180 ..      69     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaf 78 
                                    i++++DaD  +++  l +++ael+   +++v+g   ++    ++w++++ ++ ++++    ++     ++       + +
  gi|121636457|ref|YP_976680.1|  69 IVAVIDADGSMDAGDLPKLVAELDK-GADLVTGRRRPVagLHWPWVARVGTVVMSWRLRTRHRL--PVHDI----APMRV 141
                                    699********************86.8*******998745568888888888887665543222..34444....55678 PP

                Glyco_trans_2_3  79 lrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes 120
                                     rr+al ++g  d   +  +  +++ +r++++G+rv+  + s
  gi|121636457|ref|YP_976680.1| 142 ARREALLDLGVVD---RRSGYPLELLVRAAAAGWRVVELDVS 180
                                    8888888887777...66777799999999999999877655 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.2e-05      0.19      22      67 ..      58     102 ..      39     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslp 67 
                                    ++ ++ aa ++++ + D+d  +++  L +l+a+l + ++ lVt+  
  gi|121636457|ref|YP_976680.1|  58 VHAGVLAATTPIVAVIDADGSMDAGDLPKLVAELDK-GADLVTGRR 102
                                    4778999****************************6.9*****855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1842.67
//
Query:       gi|121636458|ref|YP_976681.1|  [L=220]
Description: hypothetical protein BCG_0584 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-29  100.2   0.6    1.2e-28   99.4   0.6    1.4  1  DUF2064   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.6   6.7e-33   1.2e-28       1     123 []      44     165 ..      44     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 6.7e-33
                                    HH.HHHTTSSSEEEEEE----TTHHHHHH..HH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHH CS
                        DUF2064   1 tlaelaaadaaevvlaldgaldkalaeql..alakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaal 78 
                                    tl+++aaa+++++ +al+g+ld+a+ +++  ++ k+++v++Q+g+ + +Rla+a+ +a  a++ pvl+iG+D+pq+ta+l
  gi|121636458|ref|YP_976681.1|  44 TLDAVAAAPVTARAVALTGDLDSAADSAEirRRLKSFTVFRQRGDAFADRLANAHVDA--ADGYPVLQIGMDTPQVTAEL 121
                                    7899*******************999877889999***********************..8888**************** PP

                                    HHHHHHHTTT-SEEEEEBTTSSEEEEEEEG-G...GGGTT--TTT CS
                        DUF2064  79 leqAfeaLeeadaVlgpaeDGGYyllGlkkrlapaelFegvpwst 123
                                    l+++++ L +  aVlg a DGG+++lG++ ++++ae+++ vp+s+
  gi|121636458|ref|YP_976681.1| 122 LADCARLLLQIPAVLGLAFDGGWWVLGIR-TPTAAECLRAVPMSQ 165
                                    *****************************.79999********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1532.83
//
Query:       gi|121636459|ref|YP_976682.1|  [L=449]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3202.25
//
Query:       gi|121636460|ref|YP_976683.1|  [L=362]
Description: O-succinylbenzoic acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-28   98.7   0.2    8.5e-28   97.1   0.2    1.7  1  AMP-binding    AMP-binding enzyme
    1.3e-16   61.3   0.5    3.3e-16   60.0   0.5    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.2   9.5e-32   8.5e-28     158     422 ..      30     261 ..      12     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 9.5e-32
                                    TTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTC CS
                    AMP-binding 158 pddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkd 237
                                     dd+a+++ TSGTTG PKG+ml+ ++l+a+++++    +++l+    +l  +p +hi+gl + l  ++++G+  v l+ +
  gi|121636460|ref|YP_976683.1|  30 DDDVALVVTTSGTTGPPKGAMLTAAALTASASAA----HDRLGGPGSWLLAVPPYHIAGL-AVLVRSVIAGSVPVELNVS 104
                                    59****************************9996....3444445689***********8.9999999999988877766 PP

                                    GCCHHHHHHHHHHHHT-..SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                    AMP-binding 238 aaldpklllelieklkv..tviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegY 315
                                    a +d + l ++i++l+   +++ +v + l + l ++a +       l  l  vl+gg+p ++ +l+++ a +++ v+ +Y
  gi|121636460|ref|YP_976683.1| 105 AGFDVTELPNAIKRLGSgrRYTSLVAAQLAKALTDPAAT-----AALAELDAVLIGGGPAPRPILDAAAAAGIT-VVRTY 178
                                    558877788888887642267777777777666654443.....27889**********************997.***** PP

                                    EEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCE CS
                    AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrw 395
                                    G++Et+g ++  +   d       G pl gv+++++             G + ++g++++kgY +      + f  e++w
  gi|121636460|ref|YP_976683.1| 179 GMSETSGGCV--Y---D-------GVPLDGVRLRVLAG-----------GRIAIGGATLAKGYRNP--VSPDPFA-EPGW 232
                                    ********99..3...4.......99*********874...........9**************86..4455666.547* PP

                                    EEEEEEEEEE..TTSEEEEEEECCCEEEE CS
                    AMP-binding 396 lrTGDlgrld..edGyleivgRkkdlikl 422
                                    ++T Dlg l+  + G l ++gR+++ i +
  gi|121636460|ref|YP_976683.1| 233 FHTDDLGALEsgDSGVLTVLGRADEAIST 261
                                    ********963345***********9975 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.5   3.7e-20   3.3e-16       2      76 .]     271     346 ..     270     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 3.7e-20
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    vE+al +hpaV+++aV+G  d++ G+++va +v  dg ++++ e+L+ahv+++l   a+p+++++v+ lp+   GK
  gi|121636460|ref|YP_976683.1| 271 VEAALGTHPAVRDCAVFGLADDRLGQRVVAAIVVGDGcPPPTLEALRAHVARTLDVTAAPRELHVVNVLPRRGIGK 346
                                    8*********************************777656699****************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2772.39
//
Query:       gi|121636461|ref|YP_976684.1|  [L=100]
Description: hypothetical protein BCG_0587c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-33  115.5   0.0    1.6e-33  115.3   0.0    1.0  1  DUF3349   Protein of unknown function (DUF3349)
  ------ inclusion threshold ------
      0.073   13.6   0.0      0.097   13.2   0.0    1.2  1  FliG_N    FliG N-terminal domain


Domain annotation for each model (and alignments):
>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   1.8e-37   1.6e-33       2      94 ..       4      91 ..       3      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 1.8e-37
                                   HHHHHHHHHHHH-TT-B-HHHHHHHHHHHCTT--HHHHHHHHHHHHHH--.SSS.BSHHHCHHHHHHHCTS---HHHHHHHH CS
                        DUF3349  2 llasileWLragYPegvPeqdyvpLlalLrrrLsdeevkevaeelvaeaaeadeavdeedieelitkvteeepseedvarVa 83
                                   +l+si++WLragYPeg+P++d +++lalL rrLs++evk+va+el++ +       d++di+++it++t+e ps+edv+rV+
  gi|121636461|ref|YP_976684.1|  4 FLTSIVAWLRAGYPEGIPPTDSFAVLALLCRRLSHDEVKAVANELMRLG-----DFDQIDIGVVITHFTDELPSPEDVERVR 80
                                   89**********************************************9.....79************************** PP

                                   HHHHTTT-GCC CS
                        DUF3349 84 arLaaggwpla 94
                                   arLaa+gwpl+
  gi|121636461|ref|YP_976684.1| 81 ARLAAQGWPLD 91
                                   *********98 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.097      23      67 ..      32      76 ..      28      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                   HHTTSXHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHHHCCCCH CS
                         FliG_N 23 vlkhLdeeeiekltkeiaslksvskeeveaVleefleeleaqeyl 67
                                   + ++L+ +e++++++e+++l++ ++ ++  V+ +f++el + e++
  gi|121636461|ref|YP_976684.1| 32 LCRRLSHDEVKAVANELMRLGDFDQIDIGVVITHFTDELPSPEDV 76
                                   5689********************************998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 721.86
//
Query:       gi|121636462|ref|YP_976685.1|  [L=92]
Description: hypothetical protein BCG_0588c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   13.4   0.7        0.1   13.0   0.4    1.3  1  DUF3357   Domain of unknown function (DUF3357)
       0.49    9.1   3.8       0.56    8.9   3.8    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
        5.9    7.1   7.1        1.4    9.1   0.7    2.2  2  CbtB      Probable cobalt transporter subunit (CbtB)


Domain annotation for each model (and alignments):
>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.8e-05       0.1      13      45 ..      40      70 ..      33      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                        DUF3357 13 aaaaararrpllaavliasalvvlvvlvalagv 45
                                    a a+ +rrpll+av +a  ++vl+v+  ++gv
  gi|121636462|ref|YP_976685.1| 40 GADATARRRPLLVAVSWAIFALVLAVV--IIGV 70
                                   567788999******999999988776..5555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.8   9.4e-05      0.56     386     436 ..      11      80 ..       2      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 9.4e-05
                        DUF2207 386 lglgliilglilillallllvll.....................lvfllilllillliaiivlllfsrllgr 436
                                    l ++++ l+  ++l +l+++  +                      v ++i++l+l++++i+vl++++ ++ +
  gi|121636462|ref|YP_976685.1|  11 LKILIFSLLAGALLPGLFAV--GvrlqaagdgadatarrrpllvAVSWAIFALVLAVVIIGVLYIARDFIAH 80 
                                    22222222222333333333..245889999********************************999988765 PP

>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.8     0.054   3.2e+02       8      27 ..       9      30 ..       5      37 .. 0.67
   2 ?    9.1   0.7   0.00023       1.4       9      36 ..      53      80 ..      45      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.054
                           CbtB  8 qrllqlvaAllLGlll..vylv 27
                                   ++l  l+++ll G+ll  +++v
  gi|121636462|ref|YP_976685.1|  9 ATLKILIFSLLAGALLpgLFAV 30
                                   5666777888888777444444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00023
                           CbtB  9 rllqlvaAllLGlllvylvgfsqaaalH 36
                                   ++ ++++Al+L++++++++ ++   ++H
  gi|121636462|ref|YP_976685.1| 53 AVSWAIFALVLAVVIIGVLYIARDFIAH 80
                                   6789**************9999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 618.85
//
Query:       gi|121636463|ref|YP_976686.1|  [L=417]
Description: low-affinity inorganic phosphate transporter integral membrane protein pitA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-78  261.5  39.6    4.1e-77  259.5  39.6    1.8  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.5  39.6   2.3e-81   4.1e-77       1     336 [.      22     321 ..      22     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 2.3e-81
                           PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwllla 80 
                                    +G++D++na+ats++s+al +r Av+l+a+++++Ga+l+ ++Va ti+kg++d +l++    + +++a l+g +vw+ll+
  gi|121636463|ref|YP_976686.1|  22 NGFHDTGNAMATSIASGALAPRVAVALSAVLNLIGAFLS-TAVAATIAKGLIDANLVT----LELVFAGLVGGIVWNLLT 96 
                                    8***********************************999.88**********765443....469*************** PP

                           PHO4  81 tvlglPvStthslvGaliGaalaaeggeavkwk.klvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpv 159
                                    ++lg+P+S++h+l+G+++Ga++aa g ++v w+  + k+++  v++ ll+ +++a+ ++lv r+                
  gi|121636463|ref|YP_976686.1|  97 WLLGIPSSSSHALIGGIVGATIAAVGLRGVIWSgVVSKVIVPAVVAALLATLVGAVGTWLVYRTT--------------- 161
                                    ***********************999999*9*636778**************************2............... PP

                           PHO4 160 lvlvtiailalsilfkgesk.kddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiyka.sk.ev.plwvl 235
                                                       + + +++te+ f+  q+ sa+lvs+ahG nD+++++G++++al+s   + ++ +v plwv+
  gi|121636463|ref|YP_976686.1| 162 -------------------RgVAEKRTERGFRRGQIGSASLVSLAHGTNDAQKTMGVIFLALMSYGAVsTTaSVpPLWVI 222
                                    ...................2267899********************************999987555444445568**** PP

                           PHO4 236 llgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavn 315
                                    + +++a+a+G++lgG+r+i+t+G+ +++ ++p +G+aae ++a+++ll  ++g  +StT+v++g+v+G G+ k   ++v+
  gi|121636463|ref|YP_976686.1| 223 VSCAVAMAAGTYLGGWRIIRTLGKGLVE-IKPPQGMAAESSSAAVILLSAHFGYALSTTQVATGSVLGSGVGK-PGAEVR 300
                                    ***************************5.********************************************.679*** PP

                           PHO4 316 wklvrnivlaWvlTlpvsall 336
                                    w++++++v+aW++Tlp+++l+
  gi|121636463|ref|YP_976686.1| 301 WGVAGRMVVAWLVTLPLAGLV 321
                                    ******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 2776.30
//
Query:       gi|121636464|ref|YP_976687.1|  [L=128]
Description: hypothetical protein BCG_0590c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-15   56.6   0.0    3.6e-15   56.3   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.3e-06   28.3   0.0    3.2e-06   27.1   0.0    1.5  1  Glyoxalase_2  Glyoxalase-like domain
     0.0008   20.2   0.1     0.0016   19.2   0.0    1.5  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   6.1e-19   3.6e-15       7     126 ..      10     111 ..       5     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.1e-19
                                    EEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCH CS
                     Glyoxalase   7 llvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdved 86 
                                    l+ +d+++sl+FY++  G+ + ++++         +++f ag+  +el+++  p++++ ++          + + l v d
  gi|121636464|ref|YP_976687.1|  10 LRPADYQRSLSFYRDQIGLAIAREYG--------AGTVFFAGQSLLELAGYGEPDHSRGPF---------PGALWLQVRD 72 
                                    6678**********************........9**************************.........899999999* PP

                                    HHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEE CS
                     Glyoxalase  87 vgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGill 126
                                    +++++ +l ++gv++ +ep r+++g  + + ++DpdGi+l
  gi|121636464|ref|YP_976687.1|  73 LEATQTELVSRGVSIAREPRREPWGLHEMH-VTDPDGITL 111
                                    ****************************76.*******98 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.3e-10   3.2e-06       5     109 ..       9     109 ..       6     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.3e-10
                                    --EES-HHHHHHHHHHTT---EEEE-SSEEEETTS-EEEEHHHHHH----.---S--SS-EEEEEES-HHHHHHHH..GG CS
                   Glyoxalase_2   5 llvvkdieeskkFYedvlelkikldfGenvsfetgfalkedlkelinlde.siaeqsnnfeLyFevedvdaflqklkeae 83 
                                    ll   d ++s +FY+d + l i  ++G   +f +g +    l el ++ e +         L  +v d++a+  +l + +
  gi|121636464|ref|YP_976687.1|   9 LLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQS----LLELAGYGEpDHSRGPFPGALWLQVRDLEATQTELVSRG 84 
                                    55567899********************999988865....56799997745666778899***************7776 PP

                                    GS-EEEEEEE-TTS-EEEEEE-TT-- CS
                   Glyoxalase_2  84 niellhelkekpWgqrvirfyDpDkh 109
                                     + +  e++++pWg   +++ DpD+ 
  gi|121636464|ref|YP_976687.1|  85 -VSIAREPRREPWGLHEMHVTDPDGI 109
                                    .***********************85 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.6e-07    0.0016       2     102 ..       8     109 ..       7     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-07
                   Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpepakn..rvHldlavedldaevarlval 79 
                                    + l  ad ++   F+++  g+  +re      + +v  a+++   l+    p++ +   +  l l+v dl+a+  +lv+ 
  gi|121636464|ref|YP_976687.1|   8 MLLRPADYQRSLSFYRDQIGLAIAREY----GAGTVFFAGQSLLELAGYGEPDHSRGpfPGALWLQVRDLEATQTELVSR 83 
                                    67788999*******************....5555555555555555555566444433567899*************** PP

                   Glyoxalase_6  80 GArvlreprdgthgr...vlaDPeGn 102
                                    G +  repr + +g     ++DP+G 
  gi|121636464|ref|YP_976687.1|  84 GVSIAREPRREPWGLhemHVTDPDGI 109
                                    **********9988799*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 913.17
//
Query:       gi|121636465|ref|YP_976688.1|  [L=294]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-38  131.7   0.0    2.8e-38  131.3   0.0    1.1  1  adh_short     short chain dehydrogenase
    5.8e-29  101.3   0.2    7.2e-29  101.0   0.2    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    0.00026   21.0   0.3    0.00058   19.8   0.3    1.5  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.0   4.7e-42   2.8e-38       1     190 [.      41     233 ..      41     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 4.7e-42
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    k +l tGassGIG a  k++    a vv+v+r+++ l +va+ +  +g +a+ +++D++d+e+++alve+++k++g++d+
  gi|121636465|ref|YP_976688.1|  41 KRILLTGASSGIGAAATKQFGLHRAVVVAVARRKDLLDAVADRITGDGGTAMSLPCDLSDMEAIDALVEDVEKRIGGIDI 120
                                    679***************************************************************************** PP

                                    EEE---SS--SSGGGCSHHH..HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseee..wervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAsKaava 157
                                    L+nNAG + ++p +e  e+   +er++ +N+ +++ l+r ++p ml++  G+I+nv+      ++++ +++Y AsKaa+ 
  gi|121636465|ref|YP_976688.1| 121 LINNAGRSIRRPLAESLERWhdVERTMVLNYYAPLRLIRGLAPGMLERGDGHIINVATWGVlSEASPLFSVYNASKAALS 200
                                    *******888888776554225***********************************97775799*************** PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakel 190
                                    + +r +  e+ ++g+  ++++ +lv+T+m +++
  gi|121636465|ref|YP_976688.1| 201 AVSRIIETEWGSQGVHSTTLYYPLVATPMIAPT 233
                                    ****************************98765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.2   1.2e-32   7.2e-29       1     189 [.      47     240 ..      47     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.2e-32
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIG+a+ k++  + a vv++ +++++ ++ +++++ ++g+++ l+cD +d e+++alve+v++++g++Dil+nnag
  gi|121636465|ref|YP_976688.1|  47 GASSGIGAAATKQFGLHRAVVVAVARRKDLlDAVADRITGDGGTAMsLPCDLSDMEAIDALVEDVEKRIGGIDILINNAG 126
                                    899***************************88888999999999977********************************* PP

                                    --EGCSS-GGGH..-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGT.SBSTTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpflet..sreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgae.rvvpnynaygaaKaalealtr 153
                                     + +   p++e    + +++r++  n y+ ++l++ ++p ++++g g i+n++  g    + p  ++y+a+Kaal a++r
  gi|121636465|ref|YP_976688.1| 127 RSIR--RPLAESleRWHDVERTMVLNYYAPLRLIRGLAPgMLERGdGHIINVATWGVLsEASPLFSVYNASKAALSAVSR 204
                                    ****..88888656889**********************9999999******99976526799999************** PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHH CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikgfdell 189
                                     +  e+g++g+   +    +++T++ +  k  d l 
  gi|121636465|ref|YP_976688.1| 205 IIETEWGSQGVHSTTLYYPLVATPMIAPTKAYDGLP 240
                                    *************************88777655533 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   9.7e-08   0.00058       4      99 ..      44     135 ..      42     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.7e-08
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    l+tG+  g+G + +++   + a  +v ++R++   +  +a  ++++  g + + +++D+sd +a+ al+e+++++ + i 
  gi|121636465|ref|YP_976688.1|  44 LLTGASSGIGAAATKQFGLHRA-VVVAVARRK---DLLDAVADRITGDGGTAMSLPCDLSDMEAIDALVEDVEKRIGGID 119
                                    89************99877665.566667773...344456789999***************************99**** PP

                                    EEEE---------TTT CS
                             KR  84 GvihaAgvlrdkllee 99 
                                      i+ Ag +  ++l+e
  gi|121636465|ref|YP_976688.1| 120 ILINNAGRSIRRPLAE 135
                                    ******9998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2133.70
//
Query:       gi|121636466|ref|YP_976689.1|  [L=314]
Description: naphthoate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-49  166.0   0.0    1.7e-48  165.1   0.0    1.3  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.5e-14   53.5   0.0    3.1e-14   53.2   0.0    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
       0.12   12.2   0.0        0.2   11.5   0.0    1.3  1  KdpC      K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.0   2.8e-52   1.7e-48       7     249 ..      48     308 ..      43     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.8e-52
                                    EEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTS......EEEEEB-HHHHHHHHC....HHHHHH.. CS
                          ECH_1   7 aviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdk......aFaaGadlkemaeeek....akqall.. 73 
                                    + + +nrPe+ Na+ +++++El  +l +++ ++ v++v LtG g+       aF++G+d++ + + ++     + a++  
  gi|121636466|ref|YP_976689.1|  48 VRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGnGPSpkdggwAFCSGGDQRIRGRSGYqyasGDTADTvd 127
                                    5789**************************************87654566669*******99888877544322222212 PP

                                    .....HCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETT.TEEE-GGGGGTS--CTTCHHHHHHHHHHH CS
                          ECH_1  74 .....keevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadn.asfglnelklGlipgaggtqilarkvGks 147
                                         + ++le +++++ +pk+vi  vnG a+gGG+ l+++cD++ a+++ a+f ++ + +G+++g +g+ +lar+vG++
  gi|121636466|ref|YP_976689.1| 128 varagRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREyARFKQTDADVGSFDGGYGSAYLARQVGQK 207
                                    22222567789999*********************************987488*************************** PP

                                    HHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHH CS
                          ECH_1 148 kAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.dalaeqleaeaklfes 226
                                    +A+ei  lg+ ++a+   ++G v++v  +++l+   l++a++++ ksp+a r+lk a+n   +    ++ ++ ea+ + +
  gi|121636466|ref|YP_976689.1| 208 FAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDgLVGQQLFAGEATRLAY 287
                                    ************************************************************9999**************** PP

                                    HCTSHHHHHHHHHHHTCSH---- CS
                          ECH_1 227 tfskddikeGlqaflEkrkpefe 249
                                    +++++   eG++afl kr+p++ 
  gi|121636466|ref|YP_976689.1| 288 MTDEAV--EGRDAFLQKRPPDWS 308
                                    *99977..**************5 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   5.1e-18   3.1e-14       3     186 ..      49     248 ..      47     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 5.1e-18
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSS......ECE--B--HHHHHHHHCS....-THH... CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagek......afCAGgDvralyeaakeg....kkee... 69 
                                    ++ +nrp+  Na   + v++l + l++ + +++v +v+l+g+g+       afC+GgD r   ++  +     ++++   
  gi|121636466|ref|YP_976689.1|  49 RVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSpkdggwAFCSGGDQRIRGRSGYQYasgdTADTvdv 128
                                    5789*************************************9877778888*******8766555544443332222223 PP

                                    .HHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-.TT-EEE--GGGGT----TTHHHHHHC.SSTTH CS
                          ECH_2  70 .eeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvt.ertvfAmPEtaIGlfPDvGgsyfLsr.lpgel 146
                                     ++   +  +++ li  +pk v++l++G + GgG +l v + +  ++ e ++f   +  +G f    gs +L+r + +++
  gi|121636466|ref|YP_976689.1| 129 aRAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASrEYARFKQTDADVGSFDGGYGSAYLARqVGQKF 208
                                    233444668999**********************************83557**********997655566666616779* PP

                                    HHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHT CS
                          ECH_2 147 GlylalTGarlkgadalaaglathyvpseklealeeaLae 186
                                    ++ +   G++ +++++ ++g  + + ++++le++  + a+
  gi|121636466|ref|YP_976689.1| 209 AREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAA 248
                                    ******************************9998655544 PP

>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.3e-05       0.2      44     108 ..     196     259 ..     174     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                                    TEEEEETTT------SSS--------ST-TTT-------SS-HHHHHHHHHHHHHHHHH-TTS.. CS
                           KdpC  44 gkvvGseligqeftsdkYfhgRpsavnynaaasggsnlgpsnpellerveervaalraenpekkk 108
                                    g ++ ++ +gq+f ++ +f gR  +++ ++ + g+ n  ++++el +   + +a+++a++p++++
  gi|121636466|ref|YP_976689.1| 196 GSAYLARQVGQKFAREIFFLGRTYTAE-QMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQR 259
                                    556667889***************999.5899999999999999998888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2299.44
//
Query:       gi|121636467|ref|YP_976690.1|  [L=102]
Description: hypothetical protein BCG_0594c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00032   21.2   0.0    0.00036   21.0   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     2e-08   0.00036       1      75 [.      12      84 ..      12      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-08
                                   EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                            PIN  1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75
                                   +v+D+s++++ll r +++  a+r++l++  +++ +a+  aE+l  l r    r  a ++ ++   l++l+ +p++ 
  gi|121636467|ref|YP_976690.1| 12 VVVDASAMVDLLaRTSDRCSAVRARLAR-TAMHAPAHFDAEVLSALGR--MQRAGALTVAYVDAALEELRQVPVTR 84
                                   69*************************9.*******************..99999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 565.83
//
Query:       gi|121636468|ref|YP_976691.1|  [L=88]
Description: hypothetical protein BCG_0595c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-06   27.2   0.2    5.4e-06   26.7   0.2    1.1  1  CcdA      Post-segregation antitoxin CcdA
  ------ inclusion threshold ------
      0.031   14.2   0.5       0.13   12.2   0.5    2.0  1  RHH_1     Ribbon-helix-helix protein, copG family
       0.08   13.3   0.0      0.094   13.1   0.0    1.2  1  Rimk_N    RimK PreATP-grasp domain


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   9.1e-10   5.4e-06       3      45 ..      19      61 ..      18      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.1e-10
                           CcdA  3 avnlsldsdllaqAralgiNlSatleeaLaeevkeekaerwke 45
                                   ++n+++  +l ++Ara g+N+Sa+ ++a+++e+++ ++++w+e
  gi|121636468|ref|YP_976691.1| 19 RLNVYVPDELAERARARGLNVSALTQAAISAELENSATDAWLE 61
                                   68***************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   2.2e-05      0.13       3      38 ..      21      52 ..      19      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                   EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                          RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlreyle 38
                                   ++++++e    L e+ar+rg ++S+l  +A+ + le
  gi|121636468|ref|YP_976691.1| 21 NVYVPDE----LAERARARGLNVSALTQAAISAELE 52
                                   5555555....5578**********99999998886 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.094      11      59 ..      21      73 ..      11      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                         Rimk_N 11 elystrrLveaaekrghevevldplrcylkieaekpevyykg....ekleefd 59
                                   ++y    L e a++rg +v  l +  +++++e+++ ++ ++g    +  ++ d
  gi|121636468|ref|YP_976691.1| 21 NVYVPDELAERARARGLNVSALTQAAISAELENSATDAWLEGleprSTGARHD 73
                                   689999*****************************999999866554444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 580.75
//
Query:       gi|121636469|ref|YP_976692.1|  [L=571]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-81  271.5   0.0    1.4e-80  271.0   0.0    1.1  1  AMP-binding      AMP-binding enzyme
    4.6e-20   72.4   5.0    1.1e-19   71.1   5.0    1.7  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.019   15.3   0.0    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.0   0.0   2.3e-84   1.4e-80       6     422 ..      59     461 ..      56     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 271.0 bits;  conditional E-value: 2.3e-84
                                    HHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHH CS
                    AMP-binding   6 aktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaee 85 
                                    +++ +k++l    ++++lT ++l +r++++ +++++lG++ g  V++l+ n+pe ++++ a +  G     l p  + ++
  gi|121636469|ref|YP_976692.1|  59 KRHQNKPVLFL--GDTRLTGGQLADRISQYIQAFEALGAGTGVAVGLLSLNRPEVLMIIGAGQARGYRRTALHPLGSLAD 136
                                    78999**9977..89***************************************************************** PP

                                    HHHHHHHHTESEEEETCTCCC..HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.....-TSCCCS-BT CS
                    AMP-binding  86 layiledseakvliatvdsel..leklleaaakleavklvivldadellkeeelkeeeeseekae.....kpeeeeelkp 158
                                     ay+l+d++++ li  +d +   +e++l+  +++++ ++++ +   +++++  lk+ + + +++      +p  ++ l p
  gi|121636469|ref|YP_976692.1| 137 HAYVLNDAGISSLI--IDPNPmfVERALALLEQVDSLQQILTIG--PVPDA--LKHVAVDLSAEAakyqpQPLVAADLPP 210
                                    **************..5544445555666666555555554443..33333..22222222222112234455777899* PP

                                    TSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCG CS
                    AMP-binding 159 ddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkda 238
                                    d+++ + YT+GTTGkPKGV+ + ++++++ +s++l + ++  ++ ++l++ pl+h+ +  ++   ++++G+++++l k++
  gi|121636469|ref|YP_976692.1| 211 DQVIGLTYTGGTTGKPKGVIGTAQSIATM-TSIQLAE-WEWPANPRFLMCTPLSHAGA--AFFTPTVIKGGEMIVLAKFD 286
                                    *************************9888.8877443.4434699***********99..58889999999999999887 PP

                                    CCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEG CS
                    AMP-binding 239 aldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlT 318
                                    +   + +l+ ie+ ++t +++vP++l all++++       +dlssl++v+ g+++++p  l ++ ++fg+ + + YG++
  gi|121636469|ref|YP_976692.1| 287 P---AEVLRIIEEQRITATMLVPSMLYALLDHPDSH----TRDLSSLETVYYGASAINPVRLAEAIRRFGPIFAQYYGQS 359
                                    6...5579***********************97766....56****************************99******** PP

                                    GGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEE CS
                    AMP-binding 319 Ettgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlr 397
                                    E+ +v+t+ ++ ++d+k+l s+G+p   ++v+++De+ g+pv++ge+Ge++v+gp ++ gY++ p++t+++f+  ++wl+
  gi|121636469|ref|YP_976692.1| 360 EAPMVITYlAKGDHDEKRLTSCGRPTLFARVALLDEH-GKPVKQGEVGEICVSGPLLAGGYWNLPDETSRTFK--DGWLH 436
                                    ******99999999999******************99.**********************************8..57*** PP

                                    EEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 398 TGDlgrldedGyleivgRkkdlikl 422
                                    TGDl+r d dG ++iv+R kd+i++
  gi|121636469|ref|YP_976692.1| 437 TGDLAREDSDGFYYIVDRVKDMIVT 461
                                    ***********************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   5.0   1.9e-23   1.1e-19       1      76 []     470     552 ..     470     552 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.9e-23
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---.....HHHHHHHHHHHHT-TTTS-SEEEE-S---B- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea.....leeeLkahvrkelgpyavpkkvvfvdelpkt 72 
                                    evE ++++hpaVa+++VvG pde++Gea+ a+Vvl+++     +     + +e++a v+++ g++ +pk+vv+vd+lp+t
  gi|121636469|ref|YP_976692.1| 470 EVEDVVAEHPAVAQVCVVGAPDEKWGEAVTAVVVLRSNaarD-EpaieaMTAEIQAAVKQRKGSVQAPKRVVVVDSLPLT 548
                                    8**********************************8664431.146788******************************* PP

                                    TTS- CS
                  AMP-binding_C  73 rsGK 76 
                                      GK
  gi|121636469|ref|YP_976692.1| 549 GLGK 552
                                    *999 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.2e-06     0.019       1      82 [.     463     545 ..     463     559 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHS.S--EEEEE-T CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklg.vsvkvelvep 79 
                                    G nvfP ++e+v+ e + v++   + + +e+  + ++  v ++++++++  + ea++++i++++k++ g v++  ++v  
  gi|121636469|ref|YP_976692.1| 463 GFNVFPREVEDVVAEHPAVAQVCVVGAPDEKWGEAVTAVVVLRSNAARDEPAIEAMTAEIQAAVKQRKGsVQAPKRVVVV 542
                                    89*******************9999999999899999888888877777799************9974425555555555 PP

                                    T-S CS
                AMP-binding_C_2  80 gtl 82 
                                    ++l
  gi|121636469|ref|YP_976692.1| 543 DSL 545
                                    555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3120.57
//
Query:       gi|121636470|ref|YP_976693.1|  [L=534]
Description: hypothetical protein BCG_0597 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-79  267.6   3.3    3.8e-79  267.3   3.3    1.1  1  Amidohydro_3  Amidohydrolase family
    3.4e-10   39.8   0.0    3.7e-09   36.3   0.0    2.4  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.3   3.3   4.3e-83   3.8e-79       1     473 []      50     532 ..      50     532 .. 0.94

  Alignments for each domain:
  == domain 1  score: 267.3 bits;  conditional E-value: 4.3e-83
                   Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlaggg.vnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpy 78 
                                    +viD+  + v+PGFv++H H      v   r+++ ++ +++++++v +a+r+++++   +   + +Gwd    +  + p 
  gi|121636470|ref|YP_976693.1|  50 RVIDLGAGCVMPGFVEAHGHPLLEAvVLSdRFVDIRPVTMRDADDVVAAIRGEVARR-GPAGAYLVGWDPLLQSGLGEP- 127
                                    69******************6555516669**************************6.444444469************. PP

                   Amidohydro_3  79 alaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllreg.afhlvldla..plar 155
                                    +l +ld  ++++p+ + + ++H a +ns+a  l g+t++t+dp+g+++ rd+nge + g  +e  a  ++   +   +++
  gi|121636470|ref|YP_976693.1| 128 TLTWLDSLAPNGPLVITHNSGHKAYFNSHAAWLNGLTRDTADPKGAKYGRDGNGE-LDGTAEEIgAILPL---LagVADP 203
                                    *******************************************************.******98554444...3445589 PP

                   Amidohydro_3 156 eaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrviikelldaaerlglplspgseeltigavk 235
                                        a+++a  a+l++ G+t++     +  ++  + p++e+ ++e l++r+++ e+  a   + ++ + g++ l+  ++k
  gi|121636470|ref|YP_976693.1| 204 SNFGAMLRAECARLNRAGLTTC----SEMAFDPGYRPMVEAVRAE-LTVRLCTYEISNARMCTDATPGQGDDMLRQVGIK 278
                                    99999999**************....44468889**********9.******888888888888888899********** PP

                   Amidohydro_3 236 lfadgvlgsrtalltepyf..............tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaae 301
                                    +++dg++    + lt py+              +g +++++e+lae+v a   rg+++a+h++gd+ vd +ld +e+a +
  gi|121636470|ref|YP_976693.1| 279 IWVDGSPWVGNIDLTFPYLdtpatraigvppgsRGCANYTREQLAEIVGAYFPRGWQIACHVHGDGGVDTILDVYEEALR 358
                                    *******999999999999999999******************************************************* PP

                   Amidohydro_3 302 kngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnf..edelldsrlgperargstpvkellnagvkvalgsDapv 378
                                    +n++ d+r rleh  +++++q++r+a+l+v+ ++++   +  +d  +d+ +g++r++   p ++  +ag++++l++D+pv
  gi|121636470|ref|YP_976693.1| 359 RNPRDDHRlRLEHVGAIRPDQLRRAAELGVTCSIFVDQIHywGDVIVDDLFGAQRGSRWMPAGSAVAAGMRISLHNDPPV 438
                                    ***********************************6666699999*********************************** PP

                   Amidohydro_3 379 gpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppela 458
                                    +p  p+  i  a +r + +g +vl p+e+l++e+a++++T ++A++l++ed  G+L+vG++AD vvl+adp +v+p+++a
  gi|121636470|ref|YP_976693.1| 439 TPEEPLRNISVAATRVAPSG-RVLAPEERLTVEQAIRAQTIDAAWQLFAEDAIGSLQVGKYADMVVLSADPRTVPPEQIA 517
                                    ******************99.9********************************************************** PP

                   Amidohydro_3 459 earvrltvvdGrvvy 473
                                    +  vr+t  +Gr+vy
  gi|121636470|ref|YP_976693.1| 518 DLAVRATFLAGRQVY 532
                                    **************8 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.044   3.9e+02       2      12 ..      59      69 ..      58     100 .. 0.85
   2 !   36.3   0.0   4.2e-13   3.7e-09      36     344 .]     209     531 ..     185     531 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.044
                                   EEE-EEEEEEE CS
                   Amidohydro_1  2 vlPGlIDaHvH 12
                                   v+PG++ aH H
  gi|121636470|ref|YP_976693.1| 59 VMPGFVEAHGH 69
                                   8********99 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 4.2e-13
                                    HHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGS......................GCCCS CS
                   Amidohydro_1  36 alesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsldr......................gsaet 93 
                                    +l+  ++++ ++G tt+ +m +   +g + + ea+++  l +r+++   s +r                       ++++
  gi|121636470|ref|YP_976693.1| 209 MLRAECARLNRAGLTTCSEMAFD--PGYRPMVEAVRAE-LTVRLCTYEISNARmctdatpgqgddmlrqvgikiwVDGSP 285
                                    56666778888999999999995..4999999999992.57888888777777777778888888888888888866666 PP

                                    HHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEE CS
                   Amidohydro_1  94 skasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehg 173
                                       ++    ++       +a+ ++ v  + +++  +++e+l+e++ +   r+ ++a H+++ +g v d++ +  e++ + 
  gi|121636470|ref|YP_976693.1| 286 WVGNIDLTFPYL----DTPATRAIGVPPGSRGCANYTREQLAEIVGAYFPRGWQIACHVHG-DGGV-DTILDVYEEALRR 359
                                    677777776776....777888888888888888999999999999999999999999966.4444.5555555333333 PP

                                    TTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEE..HHHHHHHH.............SEHHHHHHHHHHHH CS
                   Amidohydro_1 174 thlevaeslglldeiklilahgvhltpteaellkerlkeagva..hcpfsnsi.............lrsgrealrkalde 238
                                     + ++          +l l+h   + p+ +++ +e     gv+     +  ++              +s ++++  a+ +
  gi|121636470|ref|YP_976693.1| 360 NPRDD---------HRLRLEHVGAIRPDQLRRAAEL----GVTcsIFVDQIHYwgdvivddlfgaqRGSRWMPAGSAVAA 426
                                    33333.........3666777777776655554444....333122222222255555566667779************* PP

                                    TSCEEEEEECT.........TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TT CS
                   Amidohydro_1 239 GvkvglgtDga.........asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievG 309
                                    G++++l  D            s  +  +  ++r+++          +e  l++++a+r+ Ti++A +l  +d +Gs++vG
  gi|121636470|ref|YP_976693.1| 427 GMRISLHNDPPvtpeeplrnISVAATRVAPSGRVLA----------PEERLTVEQAIRAQTIDAAWQLFAEDAIGSLQVG 496
                                    *********558888887774444444446688888..........6777***************99999********** PP

                                    SB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                   Amidohydro_1 310 kdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                    k+AD+vv+  d+ +   ++  d  v+ ++++G++v
  gi|121636470|ref|YP_976693.1| 497 KYADMVVLSADPRTVPPEQIADLAVRATFLAGRQV 531
                                    ********999977777777888999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3736.53
//
Query:       gi|121636471|ref|YP_976694.1|  [L=326]
Description: O-succinylbenzoate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-30  107.0   6.0    1.6e-30  106.3   6.0    1.2  1  MR_MLE_C        Enolase C-terminal domain-like
    3.9e-27   93.4   1.3    7.1e-27   92.5   1.3    1.5  1  Enolase_like_N  Enolase N-terminal domain-like
  ------ inclusion threshold ------
      0.013   14.6   0.1      0.024   13.8   0.1    1.3  1  MAAL_C          Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   6.0   2.7e-34   1.6e-30      14     206 ..     103     287 ..      89     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.7e-34
                                    T-SEEEEETSSS..HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHH CS
                       MR_MLE_C  14 gfravKlkvggd..dvaedvervravreavgpgddvdlmvDanqawdlatAirvarel.eeldllwlEEPvppeddlegl 90 
                                    g r+ K+kv+++  ++a+d+erv+avre v  +    ++vDan++w +a+A+  a +l ++  l++lE+P+     +++l
  gi|121636471|ref|YP_976694.1| 103 GARTAKVKVAEPgqSLADDIERVNAVRELV--P---MVRVDANGGWGVAEAVAAAAALtADGPLEYLEQPCAT---VAEL 174
                                    68999***999999****************..5...59********************44455********86...789* PP

                                    HHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS.SHHHHHHHHH CS
                       MR_MLE_C  91 aelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs.gglglaaslh 168
                                    aelr r+ ++piaa+Es++ ++d  ++++a+a+di+ ++v+  gGi++++++aa      vpv++ s   +++g aa l 
  gi|121636471|ref|YP_976694.1| 175 AELR-RRvDVPIAADESIRKAEDPLAVVRAQAADIAVLKVAPLGGISALLDIAARI---AVPVVVSSALdSAVGIAAGLT 250
                                    ****.777****************************************99998876...588888887559********* PP

                                    HHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEEC CS
                       MR_MLE_C 169 laaaipnllileyfldaelleeelleeplevedGrvtv 206
                                     aaa+p+l++++       l ee + ep  + dG+++v
  gi|121636471|ref|YP_976694.1| 251 AAAALPELDHACGLGTGG-LFEEDVAEPAAPVDGFLAV 287
                                    **********99999887.5666666666777777776 PP

>> Enolase_like_N  Enolase N-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   1.3   1.2e-30   7.1e-27       1      52 []      17      68 ..      17      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.2e-30
                 Enolase_like_N  1 VvslPlrvrFRgitvReavlleGpaGwgEfspFleYddaeaarWlaaaieaA 52
                                   Vv+lP+rvrFRgit+Re++l+eGpaGwgEf++F+eY+ a+a +Wla+aie+A
  gi|121636471|ref|YP_976694.1| 17 VVALPMRVRFRGITTREVALIEGPAGWGEFGAFVEYQSAQACAWLASAIETA 68
                                   8*************************************************98 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     4e-06     0.024     102     181 ..     149     224 ..     144     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-06
                         MAAL_C 102 aaapyklliegPldagske.eqierlaelreklkekgikvelvaDeWcntledirefvdaeaadlvqiktPDlGginnti 180
                                     aa  +l+ +gPl+  +++ + +++laelr+      ++v + aDe     ed  + v a+aad+  +k+  lGgi+  +
  gi|121636471|ref|YP_976694.1| 149 VAAAAALTADGPLEYLEQPcATVAELAELRR-----RVDVPIAADESIRKAEDPLAVVRAQAADIAVLKVAPLGGISALL 223
                                    5677788888999876664256777777765.....578*************************************9876 PP

                         MAAL_C 181 e 181
                                    +
  gi|121636471|ref|YP_976694.1| 224 D 224
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2126.43
//
Query:       gi|121636472|ref|YP_976695.1|  [L=262]
Description: peroxidase bpoC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-23   83.4   2.8      4e-23   83.2   2.8    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.1e-22   81.0   0.0    1.3e-20   74.1   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.3e-12   47.5   0.0    6.4e-12   45.2   0.0    1.8  1  Hydrolase_4    Serine aminopeptidase, S33
      1e-07   32.0   0.0    1.8e-07   31.2   0.0    1.4  1  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.012   15.7   0.0    1.2  1  Patatin        Patatin-like phospholipase
      0.095   12.8   0.0       0.12   12.4   0.0    1.2  1  Thioesterase   Thioesterase domain


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   2.8   1.3e-26     4e-23       1     218 [.      15     250 ..      15     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 1.3e-26
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETCHHH CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHSlGGa 77 
                                    v+++ G g+ ++ W+  ++ a+laag++++++D +G G ++  + +++    +ad aal++ l+    p+ +vG S+G++
  gi|121636472|ref|YP_976695.1|  15 VVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIG-ATENAEGFTTqtmVADTAALIETLD--IAPARVVGVSMGAF 91 
                                    8*****9999****766*********************.8888888877666788899999995..999999******** PP

                                    HHHHHHHCC....EE.EEES-..----TTT.....S----TTHHHHHHTT-C.....CCCHCCHS-HSCCCCHHH....C CS
                  Abhydrolase_6  78 lalaaapla..lvvg.vlldppptalpagl.....laaalelllallallrl.....lawlsreplprlfladed....a 140
                                    +a+++  +a  lv++ vl+++    ++++        a +el++       +     +++++r+ l + f +++     a
  gi|121636472|ref|YP_976695.1|  92 IAQELMVVApeLVSSaVLMAT---RGRLDRarqffNKAEAELYD-------SgvqlpPTYDARARLLENFSRKTLnddvA 161
                                    ****777778655557*****...33333322222222222222.......12223356665442222333333332223 PP

                                    CCCHCHCC.......CGHH..HHCCHHCHTTCCHHTT-TTGCEEEC.TT-CHHHHCHHCCCH..STTEEETCE...SSS- CS
                  Abhydrolase_6 141 daawrarl.......arla..allaglgllpaaawadlpvpllvlg.geDplvprllerlla..qagarlpvvlpgaGHl 208
                                      +w a++       ++++  +l++++ +++++a++ + +p+lv+g ++D + p++l r  a  ++  r+   +p+aGHl
  gi|121636472|ref|YP_976695.1| 162 VGDWIAMFsmwpiksTPGLrcQLDCAPQTNRLPAYRNIAAPVLVIGfADDVVTPPYLGREVAdaLPNGRY-LQIPDAGHL 240
                                    444444443333322444444666677799999*********9998577779999999999999999999.9******** PP

                                    HHHHSHHHHH CS
                  Abhydrolase_6 209 phleepdeva 218
                                     ++e+p++v+
  gi|121636472|ref|YP_976695.1| 241 GFFERPEAVN 250
                                    *******997 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   4.4e-24   1.3e-20       2     257 .]      14     246 ..      13     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4.4e-24
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEET CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhS 81 
                                    ++v++ G +g +  w+ + ++  La  g+++i++D rG g ++ a       ++t ++ +d  ++ + l++ +  +vG S
  gi|121636472|ref|YP_976695.1|  14 PVVFIAGRGGAGRTWHPHQVPAFLAA-GYRCITFDNRGIGATENAEG-----FTTQTMVADTAALIETLDIAPARVVGVS 87 
                                    8***************9888888887.***************99997.....9*************************** PP

                                    HHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHH CS
                  Abhydrolase_1  82 mGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdal 161
                                    mG +ia ++   +pe V++ vl+++        +  +  a +f + ++   +d  + ++ p ++ ++++le ++r  + l
  gi|121636472|ref|YP_976695.1|  88 MGAFIAQELMVVAPELVSSAVLMAT--------RGRLDRARQFFNKAEAELYDSGV-QLPPTYDARARLLENFSR--KTL 156
                                    *************************........44444444444444444444333.233444444444444443..222 PP

                                    HH...HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHT CS
                  Abhydrolase_1 162 kf...pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllp 238
                                    ++      +  + s+ +++ s++    ++++  +p+t + + ++++        p+lvi+ ++D ++pp  +++ a++lp
  gi|121636472|ref|YP_976695.1| 157 NDdvaVGDWIAMFSM-WPIKSTPGLRCQLDC--APQTNRLPAYRNIAA------PVLVIGFADDVVTPPYLGREVADALP 227
                                    332322333333333.444444444444443..445555555566666......************************** PP

                                    SEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 239 kkrlvvisdagHlaflegp 257
                                    + r+++i+dagHl f+e+p
  gi|121636472|ref|YP_976695.1| 228 NGRYLQIPDAGHLGFFERP 246
                                    ****************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   2.1e-15   6.4e-12      19     237 ..      28     244 ..      13     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.1e-15
                    Hydrolase_4  19 ryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllryp 98 
                                    +  + + a+ a+G+ ++++D+rG G +e++ g    ++++v+D aa++e++      +p  ++G SmG++ia++++   p
  gi|121636472|ref|YP_976695.1|  28 WHPHQVPAFLAAGYRCITFDNRGIGATENAEG--FTTQTMVADTAALIETLD----IAPARVVGVSMGAFIAQELMVVAP 101
                                    344689999******************99999..67899*********9999....88999******************* PP

                    Hydrolase_4  99 dkvaglilsaPalkikaklkappllklllkllgkllpklqv........snnlkadslsrdpevvaayeadplv..hgki 168
                                    + v+ ++l+a+  +++    a+++ + +   l     +l++         +n   + l +d +v + ++  +++  + ++
  gi|121636472|ref|YP_976695.1| 102 ELVSSAVLMATRGRLDR---ARQFFNKAEAELYDSGVQLPPtydararlLENFSRKTLNDDVAVGDWIAMFSMWpiKSTP 178
                                    *999*******999985...666666666666666666666677677777778888888888888888888887533333 PP

                    Hydrolase_4 169 tvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                     +r  l++   ++rl     +i +P+l++  ++D v++p   re++++l+  + ++  +p + H  ++E
  gi|121636472|ref|YP_976695.1| 179 GLRCQLDCAPQTNRL-PAYRNIAAPVLVIGFADDVVTPPYLGREVADALP--NGRYLQIPDAGHLGFFE 244
                                    444444444444444.44556779***999999999999999**999999..68888889999988877 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   5.9e-11   1.8e-07      24      93 ..     190     259 ..     169     262 .] 0.85

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.9e-11
                  Abhydrolase_4  24 rprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                     +r  +  + aapvL+++   D +TP+  ++++a+al++++ ++  ++GH ++ +  ++v+ a+ +++++
  gi|121636472|ref|YP_976695.1| 190 TNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFAS 259
                                    333333334479*******************************************************976 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   4.2e-06     0.012      25     103 ..      77     167 ..      64     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.2e-06
                        Patatin  25 gerfdiisGtSaGAiia..............lllalgrdpaalvddlrnlllnkifdrdllirelaanlaarlsgllgkg 90 
                                     + +  ++G+S GA+ia               l+a+ +  ++ ++++  +++++  +    ++    ++ arl + + ++
  gi|121636472|ref|YP_976695.1|  77 DIAPARVVGVSMGAFIAqelmvvapelvssaVLMATRGRLDRARQFFNKAEAELYDSGV--QLPPTYDARARLLENFSRK 154
                                    678999************************98888888888889999999999999999..9999999999999999999 PP

                        Patatin  91 glfdaealrellr 103
                                    +l d+ a  ++++
  gi|121636472|ref|YP_976695.1| 155 TLNDDVAVGDWIA 167
                                    9999999999987 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.1e-05      0.12      46      83 ..      60      96 ..      22     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                   TCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHH CS
                   Thioesterase 46 esieelaaeyaealrqiqpegPyalfGhSlGgllAfev 83
                                    + ++++a  a+ +++     P +++G S+G+++A+e+
  gi|121636472|ref|YP_976695.1| 60 FTTQTMVADTAALIETLDIA-PARVVGVSMGAFIAQEL 96
                                   56788999988888776666.**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1772.82
//
Query:       gi|121636473|ref|YP_976696.1|  [L=554]
Description: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-28   98.9   0.8    5.3e-28   97.8   0.8    1.6  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.8     3e-32   5.3e-28       3     165 ..       7     185 ..       5     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3e-32
                                    HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHC CS
                   TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatna 79 
                                     a+++v+ L + gv+ v+ +pGsr+ pl  al++++   +ir+++  +E++a++ A g+a   g p++v++tsg++++n+
  gi|121636473|ref|YP_976696.1|   7 QARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADrsgRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANL 86 
                                    5789**************************************************************************** PP

                                    HHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH..............HHHH CS
                   TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealr..............rAir 145
                                     +a++eA+++r+Pl+vls++rp++l g+g+ q +++ql+ f   ++++  +  +e++pe                  A +
  gi|121636473|ref|YP_976696.1|  87 GPAVVEANYARVPLIVLSANRPYELLGTGANQ-TMEQLGYFGTQVRASISLGLAEDAPERTSalnatwrsatcrvlAAAT 165
                                    ********************************.**************************999999********9988888 PP

                                    HHHSSS--EEEEEEEHHHCC CS
                   TPP_enzyme_N 146 talsgrpgPvylelpkdvll 165
                                     a +++ gPv+ ++p+  +l
  gi|121636473|ref|YP_976696.1| 166 GARTANAGPVHFDIPLREPL 185
                                    89*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3877.32
//
Query:       gi|121636474|ref|YP_976697.1|  [L=171]
Description: hypothetical protein BCG_0601 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.4   1.0    0.00054   20.0   1.0    1.6  1  DUF3592   Protein of unknown function (DUF3592)


Domain annotation for each model (and alignments):
>> DUF3592  Protein of unknown function (DUF3592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.0     3e-08   0.00054       9     145 ..      32     151 ..      24     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-08
                        DUF3592   9 lifllaglallvlgglllvgk.....yllsgqwervpgtvlssehrhrsdgsrsstysvt.vrYrysfqgervsglysgs 82 
                                     i +l+ ++l+ l+ +llv+         ++++  ++++vls +     ++s  +  +++ ++Yr +  g  v  ++s  
  gi|121636474|ref|YP_976697.1|  32 RIAVLIVTGLVTLQSVLLVAGawrndIAIQRNMGVAQAEVLSAG----PRRSTIEFVTPDrITYRPQ-LG--VL-YPS-- 101
                                    45555555555555555555556666899***************....7777777888888888888.66..55.455.. PP

                        DUF3592  83 dnvgdyaaqlyraGnavqvyynPsnPtqavldqtvsgtkagglwlmvglgavlGliflligll 145
                                            + +  G ++ v yn  +P+  +++    +++ag ++  +g  av+++++++++l 
  gi|121636474|ref|YP_976697.1| 102 --------E-LSTGMRIYVEYNKRDPNLVRVQ----HRNAGLAIIPAGSIAVVAWLIAAAALV 151
                                    ........4.999*******************....777786666666666655544433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1110.16
//
Query:       gi|121636475|ref|YP_976698.1|  [L=378]
Description: mannosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-27   95.3   4.5    3.8e-27   95.3   4.5    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    5.8e-22   78.0   0.0    1.1e-21   77.2   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    2.7e-21   76.7  12.7    2.7e-21   76.7  12.7    3.0  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.1e-19   71.2   0.1    3.1e-19   69.7   0.1    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.2e-07   30.1   0.0    8.8e-07   29.0   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00039   20.7   0.0     0.0011   19.3   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   4.5   1.3e-30   3.8e-27       1     170 []      17     187 ..      17     187 .. 0.85
   2 ?   -0.6   0.1      0.38   1.1e+03      58     100 ..     318     358 ..     259     359 .. 0.40

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 1.3e-30
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkrekpDv 75 
                                    v+Gv ++v+ + ++L+r Ghe  v++p++++ +++++     ++v+rvp++ +p+   l++ + + +r+ r+l+ ++pDv
  gi|121636475|ref|YP_976698.1|  17 VNGVSNSVVKVLEHLRRTGHEALVIAPDTPPGEDRAErlhdgVRVHRVPSRMFPKVTTLPLGV-PTFRMLRALRGFDPDV 95 
                                    69**************************99999999889544444444444444444444444.35678889******** PP

                 Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvp 155
                                    vH  spa lg+++l ++rrlg+p+V+ + +  +  +  +   +  r+++a+ r+l+r adr++a+S at + l++  g+p
  gi|121636475|ref|YP_976698.1|  96 VHLASPALLGYGGLHAARRLGVPTVAVYQTDVPGFASSYGIPMTARAAWAWFRHLHRLADRTLAPSTATMESLIA-QGIP 174
                                    ********************************8555566666778999***************************.**** PP

                 Glyco_transf_4 156 pekitVipnGvDler 170
                                    +  ++ + +GvD++r
  gi|121636475|ref|YP_976698.1| 175 R--VHRWARGVDVQR 187
                                    6..*********987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                 Glyco_transf_4  58 laflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplV 100
                                    l ++  + ++l     ++vH ++ +al  a++++ + +  p+V
  gi|121636475|ref|YP_976698.1| 318 LLPVGEFEHRLPDAVAHLVHERQRYAL--AARRSVLGRSWPVV 358
                                    333334444444445556666665554..22222224566665 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   3.6e-25   1.1e-21      12     160 ..     203     340 ..     194     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.6e-25
                                    TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                    +++k+i+ +vgrl +eK vd+l  ++a         v+lvi+G+g ++++l++         +  f+g    ++l e + 
  gi|121636475|ref|YP_976698.1| 203 PDGKPIVGFVGRLAPEKHVDRLTGLAA------SGAVRLVIVGDGIDRARLQSA------MPTAVFTGARYGKELAEAYA 270
                                    689************************......689***********9999998......568899************** PP

                                    CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHHHHSHH CS
                Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn.naealaeairklledee 160
                                    + d+fv++ + E f+ v+ EA+a+glpvia +aggp+++++++ tGll + +   + l +a++ l+++++
  gi|121636475|ref|YP_976698.1| 271 SMDVFVHSGEHETFCQVVQEALASGLPVIAPDAGGPRDLITPHRTGLLLPVGeFEHRLPDAVAHLVHERQ 340
                                    ***************************************************9888889999999988874 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7  12.7   9.1e-25   2.7e-21       2     153 ..      19     177 ..      18     182 .. 0.82
   2 ?   -5.1  13.1         6   1.8e+04       4     105 ..     259     363 ..     177     378 .] 0.68

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 9.1e-25
                Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapgape..leedgvrvhrlpvprrpspladla..alralrrllrqrrerpdvv 77 
                                    G++  v  ++++L++ Ghe  v++p+ +pg+++  + +dgvrvhr+p +  p+ ++ +    ++++ r+l  r + pdvv
  gi|121636475|ref|YP_976698.1|  19 GVSNSVVKVLEHLRRTGHEALVIAPDTPPGEDRaeRLHDGVRVHRVPSRMFPKVTTLPLgvPTFRMLRAL--RGFDPDVV 96 
                                    89999999****************9999997752266**********88887633333311456778888..******** PP

                Glyco_trans_4_4  78 hahsp.taglaarlarrrrgiplvvtlhgll....lrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpad 152
                                    h+ sp ++g+ +++a+rr g+p v  ++++       +g +  +r+++a+ r l r ad+ l++s+a +e l+a+g+p+ 
  gi|121636475|ref|YP_976698.1|  97 HLASPaLLGYGGLHAARRLGVPTVAVYQTDVpgfaSSYGIPMTARAAWAWFRHLHRLADRTLAPSTATMESLIAQGIPRV 176
                                    ****735999999999899*********75433336678777777777777***************************65 PP

                Glyco_trans_4_4 153 r 153
                                    +
  gi|121636475|ref|YP_976698.1| 177 H 177
                                    4 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 6
                Glyco_trans_4_4   4 gryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll...rqrrerpdvvh.. 78 
                                    +ry  ela+a+a    +V v   +  +  + ++e+ +   ++ +p ++ +++dl  +++   ll   + +++ pd v   
  gi|121636475|ref|YP_976698.1| 259 ARYGKELAEAYASM--DVFVHSGEHETFCQVVQEALASGLPVIAPDAG-GPRDLITPHRTGLLLpvgEFEHRLPDAVAhl 335
                                    45555555555555..44444444444444344555554444455554.5666666555555555554467777744334 PP

                Glyco_trans_4_4  79 ahs.ptaglaarlarrrrgiplvvtlhg 105
                                    +h+    +laar+  ++r++p+v++   
  gi|121636475|ref|YP_976698.1| 336 VHErQRYALAARRSVLGRSWPVVCDELL 363
                                    5664447888888877999999998763 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.1   9.2e+03      25      42 ..      29      48 ..      10      65 .. 0.48
   2 !   69.7   0.1     1e-22   3.1e-19       2     133 ..     207     337 ..     206     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                                   HHHH.H.HEEEEEES---.. CS
                Glyco_trans_1_4 25 pllrkk.dvrlvivGdgp.r 42
                                   ++lr+  +  lvi+ d p  
  gi|121636475|ref|YP_976698.1| 29 EHLRRTgHEALVIAPDTPpG 48
                                   55553322345555555432 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 1e-22
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfva 78 
                                    p+++fvGrl +++k vd l   ++  +   vrlvivGdg  r ++l++ +    ++ +ftG +  ++lae++a++dvfv 
  gi|121636475|ref|YP_976698.1| 207 PIVGFVGRL-APEKHVDRLTGLAASGA---VRLVIVGDGIdR-ARLQSAM----PTAVFTGARygKELAEAYASMDVFVH 277
                                    899******.55699998877665544...79******9844.5887443....89********999************* PP

                                    --..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-.HHHHHHHHHHHHH CS
                Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv..gengllvppgd.pealaeailrLle 133
                                        e+f  ++ Ea+a+glpv+a d+gg+++++   ++gll+p g+ ++ l +a+++L++
  gi|121636475|ref|YP_976698.1| 278 SGehETFCQVVQEALASGLPVIAPDAGGPRDLItpHRTGLLLPVGEfEHRLPDAVAHLVH 337
                                    **888****************************999*********999999999999875 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.9e-10   8.8e-07      13     111 ..      24     127 ..       6     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.9e-10
                Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitpkkga.kdele..aegihvhrlkvdrkg.pleylka....fklkklikkikPDvvhahyak 84 
                                    ++++ + L+  g+e  vi p+++  +d+ e   +g++vhr++ +r + ++++l +    f++ + ++ + PDvvh+  + 
  gi|121636475|ref|YP_976698.1|  24 VVKVLEHLRRTGHEALVIAPDTPPgEDRAErlHDGVRVHRVP-SRMFpKVTTLPLgvptFRMLRALRGFDPDVVHLASPA 102
                                    6788999*************88876554443489*******9.55557788875446669*******************9 PP

                Glyco_trans_4_2  85 pygllgslaarlsgvipvvlsvwGldv 111
                                     +g+ g  aar++g +p+v+  + +dv
  gi|121636475|ref|YP_976698.1| 103 LLGYGGLHAARRLG-VPTVAVYQ-TDV 127
                                    999989899*****.66654333.455 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.6e-07    0.0011       7      80 ..     280     353 ..     274     364 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.6e-07
                Glyco_trans_1_2   7 rsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanp.eerraiaeaarervlae 80 
                                    ++e++ +++ Ea+a+G ++++ da g+++l+tp ++++l   + e++ ++  ++a+   er++ a aar+ vl +
  gi|121636475|ref|YP_976698.1| 280 EHETFCQVVQEALASGLPVIAPDAGGPRDLITPHRTGLLLP-VGEFEHRLPDAVAHLvHERQRYALAARRSVLGR 353
                                    5677888999*****************************97.457888888777765489999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2502.00
//
Query:       gi|121636476|ref|YP_976699.1|  [L=234]
Description: ubiquinone/menaquinone biosynthesis methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-59  198.5   0.0    1.3e-58  198.1   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.9e-17   63.1   0.1    5.5e-17   62.2   0.1    1.5  1  Methyltransf_11  Methyltransferase domain
    4.6e-14   52.9   0.1    9.5e-14   51.9   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    1.7e-08   34.5   0.0    2.3e-08   34.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.4e-08   33.9   0.0    4.6e-08   33.0   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    2.9e-05   24.7   0.0    5.1e-05   23.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0059   16.5   0.0     0.0078   16.1   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.027   14.1   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
       0.14   12.5   0.0       0.23   11.8   0.0    1.3  1  PI-PLC-Y         Phosphatidylinositol-specific phospholipase 


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.1   0.0   6.5e-62   1.3e-58       8     233 .]      11     227 ..       5     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.1 bits;  conditional E-value: 6.5e-62
                                    X.XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHH CS
                Ubie_methyltran   8 k.vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLk 86 
                                    + v+++f+ va+kyDl n vlslg+ r W++ +       +g+kvlD+a+Gt+  +++l++s       v +D++  mL 
  gi|121636476|ref|YP_976699.1|  11 RdVASMFDGVARKYDLTNTVLSLGQDRYWRRATRSALRIGPGQKVLDLAAGTAVSTVELTKSG---AWCVAADFSVGMLA 87 
                                    3499*****************************************************999764...46789********* PP

                                    HHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHH CS
                Ubie_methyltran  87 vgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqay 166
                                     g ++       ++  + ++a +Lpf dd fD vt+sfGlrnv++++ aL+e+ rv +pGGrl+v efs +++ l+ +ay
  gi|121636476|ref|YP_976699.1|  88 AGAAR-------KVPKVAGDATRLPFGDDVFDAVTISFGLRNVANQQAALREMARVTRPGGRLLVCEFSTPTNALFATAY 160
                                    99876.......678899************************************************************** PP

                                    HHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEEGGGTEEEEEEEE CS
                Ubie_methyltran 167 elyskevlPvlGkllakdldsyryLvesirafPdqetlkeliedaGfksveyesltgGvvaihigvk 233
                                    + y ++ lP++ + ++ + + y+yL+esira+Pdq  l++ i  aG++ v++++ltgG+va+h g+k
  gi|121636476|ref|YP_976699.1| 161 KEYLMRALPRVARAVSSNPEAYEYLAESIRAWPDQAVLAHQISRAGWSGVRWRNLTGGIVALHAGYK 227
                                    *****************************************************************98 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   2.8e-20   5.5e-17       1      96 []      56     145 ..      56     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2.8e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ld+++Gt   + +l+k ga +v+ D+s  ml++  ++++++      v +da++lpf d+ fD+v++s+ l +v+++++a
  gi|121636476|ref|YP_976699.1|  56 LDLAAGTAVSTVELTKSGAWCVAADFSVGMLAAGAARKVPK------VAGDATRLPFGDDVFDAVTISFGLRNVANQQAA 129
                                    89*****************************6665555554......9******************************** PP

                                    HHHHHHHEEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                    l+e+aRv +pgG+l++
  gi|121636476|ref|YP_976699.1| 130 LREMARVTRPGGRLLV 145
                                    *************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   4.8e-17   9.5e-14       1      97 []      55     141 ..      55     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 4.8e-17
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLdl++Gt   t +l k +  a  ++ D+s +ml+a ++r       v  v gda++lpf d+ fD+v++s++l  +   
  gi|121636476|ref|YP_976699.1|  55 VLDLAAGTAVSTVELTKSG--AWCVAADFSVGMLAAGAARK------VPKVAGDATRLPFGDDVFDAVTISFGLRNVA-- 124
                                    9*****************5..**************998887......7889*******************99988877.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    ++++al+e+arv++pgG
  gi|121636476|ref|YP_976699.1| 125 NQQAALREMARVTRPGG 141
                                    5679************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.1e-11   2.3e-08       7     125 ..      37     163 ..      32     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.1e-11
                Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlI 86 
                                    +++++++  +l +  +g++vLd+++Gt   + +l + g+ +++ D s  + +    a+k +k+  d+   ++ ++ fd +
  gi|121636476|ref|YP_976699.1|  37 RYWRRATRSAL-RIGPGQKVLDLAAGTAVSTVELTKSGAWCVAADFSVGMLAAG-AARKVPKVAGDATRLPFGDDVFDAV 114
                                    55666665555.367899**********99999**************7665543.77888888888889999******** PP

                Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplasl..........k 125
                                    + +++l +v +  ++lr +a+ ++pgG+ll++e+  +           +
  gi|121636476|ref|YP_976699.1| 115 TISFGLRNVANQQAALREMARVTRPGGRLLVCEFSTPTnalfataykeY 163
                                    *********************************8665555455544440 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.3e-11   4.6e-08       4     129 ..      52     182 ..      49     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.3e-11
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    g +vlDl++Gt   t el  +  ++a  v  D+s  ++    ++        v   +gd++ l+  + d+ fD ++    
  gi|121636476|ref|YP_976699.1|  52 GQKVLDLAAGTAVSTVELT-K--SGAWCVAADFSVGMLAAGAAR-------KVPKVAGDATRLP--FGDDVFDAVTISFG 119
                                    679********99999999.3..4789***********998886.......455578*******..***********999 PP

                Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr..............llaelp...akveeeskay 129
                                    l  +a+++++l+e+ rv +pgg+ll+++++              l++ lp   + v+++ +ay
  gi|121636476|ref|YP_976699.1| 120 LRNVANQQAALREMARVTRPGGRLLVCEFStptnalfataykeyLMRALPrvaRAVSSNPEAY 182
                                    9*****************************888887777777776666665544444444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.6e-08   5.1e-05       1      99 []      56     143 ..      56     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.6e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L++ +Gt+  + +l ++  ++  ++ D+s  ++  a+   +k       +v  +a+ l   d+   fD+v++s+ l +++
  gi|121636476|ref|YP_976699.1|  56 LDLAAGTAVSTVELTKS--GAWCVAADFSVGML--AAGAARKVP-----KVAGDATRLPFGDD--VFDAVTISFGLRNVA 124
                                    79999999999999999..99999*********..333333333.....44444444443333..8************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    + +++l++++++ +pgGrl
  gi|121636476|ref|YP_976699.1| 125 NQQAALREMARVTRPGGRL 143
                                    *****************97 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.9e-06    0.0078     109     161 ..      97     150 ..      82     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                                    EES-TTS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEEEEEEEGG CS
                 Methyltransf_8 109 vacdlakvPledesvdvavfclslm.gtnladflkeanrvlkvGGllkvaevks 161
                                    va d +++P  d+  d + + + l  + n +  l+e+ rv ++GG l v e ++
  gi|121636476|ref|YP_976699.1|  97 VAGDATRLPFGDDVFDAVTISFGLRnVANQQAALREMARVTRPGGRLLVCEFST 150
                                    578999***********99999996378999*******************9875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.027      11     103 ..      49     138 ..      42     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                           MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrn 90 
                                    i pg +vldl +G       l  + +      + +   +a+  a+ +  + gd+ +    f d+ fd v +s  l+++ n
  gi|121636476|ref|YP_976699.1|  49 IGPGQKVLDLAAGTAVSTVELT-KSGAWCVAADFSVGMLAAGAARKVPKVAGDATR--LPFGDDVFDAVTISFGLRNVAN 125
                                    6788999999999876655553.356777777888888999999999999998865..579******************* PP

                           MetW  91 pkevldellrigr 103
                                     +  l+e+ r++r
  gi|121636476|ref|YP_976699.1| 126 QQAALREMARVTR 138
                                    **********986 PP

>> PI-PLC-Y  Phosphatidylinositol-specific phospholipase C, Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.23      43      75 ..     151     184 ..     113     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                       PI-PLC-Y  43 eekk.lvkhnrrhlmRvyPkgtrvdssNlnpvef 75 
                                     +++ +++  +++lmR+ P+  r  ssN +  e+
  gi|121636476|ref|YP_976699.1| 151 PTNAlFATAYKEYLMRALPRVARAVSSNPEAYEY 184
                                    2345699999******************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1597.98
//
Query:       gi|121636477|ref|YP_976700.1|  [L=112]
Description: hypothetical protein BCG_0604c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-23   83.1   0.1    1.7e-23   82.8   0.1    1.0  1  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   9.2e-28   1.7e-23       2      94 ..       9     103 ..       8     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 9.2e-28
                         DUF732   2 aaallaaalllaapAaAdsaddaFlaalnqagiaygspdaaialGkavCkkldsGksaea..vvaevknd.nsglspeqa 78 
                                    ++ +++aa+ laapA+Ad++d+ F +++++ gi yg +d++++l+k  C++l++G++ +a  ++++++++  +g +++qa
  gi|121636477|ref|YP_976700.1|   9 VVGMTVAAVSLAAPAQADDYDAPFNNTIHRFGI-YGPQDYNAWLAKISCERLSRGVDGDAykSATFLQRNlPRGTTQGQA 87 
                                    678899***************************.*************************9999********7778***** PP

                         DUF732  79 aqfvgaAvsayCPeql 94 
                                     qf+gaA+++yCPe++
  gi|121636477|ref|YP_976700.1|  88 FQFLGAAIDHYCPEHV 103
                                    **************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 901.66
//
Query:       gi|121636478|ref|YP_976701.1|  [L=241]
Description: benzoquinone methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-18   67.2   0.0    1.7e-18   66.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.7e-18   67.1   0.0    3.8e-18   66.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    8.9e-16   58.3   0.0      2e-15   57.2   0.0    1.5  2  Methyltransf_11  Methyltransferase domain
    2.3e-14   53.6   0.0    3.2e-14   53.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    3.5e-13   49.7   0.0    6.6e-13   48.8   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    1.9e-11   44.5   0.0    3.1e-11   43.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      9e-08   31.8   0.0    1.3e-07   31.3   0.0    1.2  1  MTS              Methyltransferase small domain
    4.9e-06   26.1   0.0    6.3e-06   25.8   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.5e-05   24.5   0.0    2.1e-05   24.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.4e-05   23.3   0.0    4.2e-05   23.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00018   21.2   0.0    0.00025   20.7   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0023   17.9   0.0     0.0036   17.3   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0039   16.6   0.0     0.0049   16.3   0.0    1.1  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.033   14.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.027   14.1   0.0      0.037   13.6   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
      0.038   13.0   0.0      0.048   12.7   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.24   11.2   0.0       0.34   10.7   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   1.6e-21   1.7e-18       6     113 ..      65     169 ..      63     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.6e-21
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl. 84 
                                     vlD+GCG+ +++++lae+   + + vG+D s+ a+elAr +a+k gl n++Fe++d+ ++     d +fD i++  ++ 
  gi|121636478|ref|YP_976701.1|  65 DVLDVGCGEAAISLALAER---GHTTVGLDLSPAAVELARHEAAKRGLANASFEVADASSFT--GYDGRFDTIVDSTLFh 139
                                    59***************65...3469**********************************88..567********77779 PP

                Methyltransf_31  85 .naladpdkileeiervlkpggilliedpr 113
                                     + + + + +l++i r+  pg  + +  ++
  gi|121636478|ref|YP_976701.1| 140 sMPVESREGYLQSIVRAAAPGASYFVLVFD 169
                                    99999999********99999776665555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   3.6e-21   3.8e-18       1      96 [.      66     160 ..      66     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 3.6e-21
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    vLd+GcG+  ++lala+r+  ++ +g+D+s++++e ar++a+++gl n++f+++da+++   dg+fD +v s  +h ++ 
  gi|121636478|ref|YP_976701.1|  66 VLDVGCGEAAISLALAERG--HTTVGLDLSPAAVELARHEAAKRGLaNASFEVADASSFTGYDGRFDTIVDSTLFHSMPV 143
                                    9*****************5..9*************************************************977999*** PP

                                    HHHHHHHHHHHHHEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpg 96 
                                    e +e +l+ i r+  pg
  gi|121636478|ref|YP_976701.1| 144 ESREGYLQSIVRAAAPG 160
                                    ************99997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.2   9.7e+03      21      35 ..       8      22 ..       4      34 .. 0.72
   2 !   57.2   0.0   1.9e-18     2e-15       1      95 [.      67     164 ..      67     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.2
                                   EEEEES-HHHHHHHH CS
                Methyltransf_11 21 vvgvDlskemlklak 35
                                   + +vD+ + m++   
  gi|121636478|ref|YP_976701.1|  8 IRAVDIYEHMTESLD 22
                                   567899888887654 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 1.9e-18
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv..edp 77 
                                    LdvGcG  +++ ala+rg+++vg+Dls+++++la+++a ++gl + +f vada+++   d+ fD +v s  +h +  e +
  gi|121636478|ref|YP_976701.1|  67 LDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAKRGLaNASFEVADASSFTGYDGRFDTIVDSTLFHSMpvESR 146
                                    8*******************************************99**********999****************999** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                    e +l+ i+R   pg   +
  gi|121636478|ref|YP_976701.1| 147 EGYLQSIVRAAAPGASYF 164
                                    *************98765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0     3e-17   3.2e-14      21     123 ..      61     171 ..      45     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3e-17
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                                    + +g vLd+GcG+   +  l+e+g++ +g Dlsp+ave+a+      +  +a ++ +d+++ +  +g+fd+Iv + ++++
  gi|121636478|ref|YP_976701.1|  61 KFRGDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARheaakrGLANASFEVADASSFTGYDGRFDTIVDSTLFHS 140
                                    55789***************************************999999999999999999999*************** PP

                Methyltransf_23  95 vp..dppellrqiatllkpgGylllseplas 123
                                    +p  + + +l++i +  +pg+  +++++++ 
  gi|121636478|ref|YP_976701.1| 141 MPveSREGYLQSIVRAAAPGASYFVLVFDRA 171
                                    **8789**************88888888775 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   6.3e-16   6.6e-13      16     189 ..      43     200 ..      38     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.3e-16
                                    TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--.. CS
                           TPMT  16 pfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeys 95 
                                    p+  +e +p l  ++ +   k  + vl  +CG+a    +lAe+g++ vG++ls++Ave + +ea         ++     
  gi|121636478|ref|YP_976701.1|  43 PWSIGEPQPELAALIVQ--GKFRGDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAK---RGLANAS---- 113
                                    56666667777777766..6666678999*****************************96555444...2223333.... PP

                                    .........-TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEEEE---S----SS----HHHH CS
                           TPMT  96 ageiellcgdvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdgeglLvtldypqaeheGPPfsvpeael 175
                                        e+  ++ Ft      g+fd+i d   +  +p e re y +s+ +   p+++++ v + +++a  eGP  +v+e+el
  gi|121636478|ref|YP_976701.1| 114 ---FEVADASSFTG---YDGRFDTIVDSTLFHSMPVESREGYLQSIVRAAAPGASYF-VLVFDRAAIPEGPINAVTEDEL 186
                                    ...34567889993...34678*********************************55.556678999************* PP

                                    HHHHGGTEEEEEEE CS
                           TPMT 176 eallsagfkvaele 189
                                    +a +s+ + + e++
  gi|121636478|ref|YP_976701.1| 187 RAAVSKYWIIDEIK 200
                                    *****999888765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0     3e-14   3.1e-11       1      97 [.      67     161 ..      67     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3e-14
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG ++++ al+e+  + + +g+D+sp+a+e a+ + akr+  n+++   +a +    dg   fD++v s ++h + 
  gi|121636478|ref|YP_976701.1|  67 LDVGCGEAAISLALAER--GHTTVGLDLSPAAVELARHEAAKRGLANASFEVADASSFTGYDG--RFDTIVDSTLFHSMp 142
                                    8****************..99************888888888776555555555554444444..9************** PP

                Methyltransf_12  80 .kdirevldnirklLkpgG 97 
                                     + ++ +l++i ++ +pg+
  gi|121636478|ref|YP_976701.1| 143 vESREGYLQSIVRAAAPGA 161
                                    9999*************97 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.2e-10   1.3e-07      29     125 ..      60     157 ..      52     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                                    CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEEE--- CS
                            MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdlivsNPP 106
                                     +++g+vlD+GcG  ++++ala++  +   + +d + +A+e+a++ +++ +l+ +++   d+ + +  +++fd+iv    
  gi|121636478|ref|YP_976701.1|  60 GKFRGDVLDVGCGEAAISLALAERGHT--TVGLDLSPAAVELARHEAAKRGLAnASFEVADASSFTGyDGRFDTIVDSTL 137
                                    458899****************98777..899*******************998777777777766557*******9988 PP

                                    STTTC.HCHHHHHHHHHHHH CS
                            MTS 107 fhagk.atelavaeeliaeA 125
                                    fh+   + ++   + ++++A
  gi|121636478|ref|YP_976701.1| 138 FHSMPvESREGYLQSIVRAA 157
                                    88865355556666666666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     6e-09   6.3e-06     162     231 ..      63     133 ..      35     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6e-09
                           PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadviv 231
                                    +  vlDvG+G + +++a a  g+   v++D+ + Av+ a++ a++ ++++ ++eva +++ +  ++++d iv
  gi|121636478|ref|YP_976701.1|  63 RGDVLDVGCGEAAISLALAERGHT-TVGLDLSPAAVELARHEAAKRGLANaSFEVADASSFTGyDGRFDTIV 133
                                    358*****************9986.57***************999998887999965444442468888888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     2e-08   2.1e-05      49     160 ..      64     174 ..      53     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2e-08
                                    TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEE..S-G CS
                Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvs..fGl 126
                                     +vlDv +G + ++++l++      + v+lD+++  ++ +++ + ++g  n  f +a+a  +   d+ fD++  s  f  
  gi|121636478|ref|YP_976701.1|  64 GDVLDVGCGEAAISLALAER---GHTTVGLDLSPAAVELARHEAAKRGLANASFEVADASSFTGYDGRFDTIVDStlFHS 140
                                    479********999999765...446789*****************************************9987722555 PP

                                    GG-S-HHHHHHHHHHHEEEEEEEEEEEE----SH CS
                Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlvvlefskvelp 160
                                      v  ++  L+++ r   pG   +vl f +  +p
  gi|121636478|ref|YP_976701.1| 141 MPVESREGYLQSIVRAAAPGASYFVLVFDRAAIP 174
                                    566788889*****************99988765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     4e-08   4.2e-05      65     157 ..      65     158 ..      57     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4e-08
                                    EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-.EEE.EES-GGG-----SEEEEES-GGGTSG CS
                           CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk.vev.klldyedldekvdrvvsvgafehvgk 142
                                     +Ld+GcG  ++    +er +   vgl lS    +la+++ ++++l++   ev + + +   d+++d +v   +f  + +
  gi|121636478|ref|YP_976701.1|  65 DVLDVGCGEAAISLALAER-GHTTVGLDLSPAAVELARHEAAKRGLANAsFEVaDASSFTGYDGRFDTIVDSTLFHSMPV 143
                                    58*********99999999.*************************9764145525778999999**************** PP

                                    GGHHHHHHHHHHHS- CS
                           CMAS 143 enydtffkklkkllk 157
                                    e+ + + + + ++  
  gi|121636478|ref|YP_976701.1| 144 ESREGYLQSIVRAAA 158
                                    999999998877655 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.4e-07   0.00025      39     140 ..      58     161 ..      48     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                           NodS  39 laqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervke..sshiswivsdvqqfs.tdekfdlivvaev 115
                                    ++++  +d+l+vGc   a++  la   +    +d+ + a++ ar+   +   ++ s+ v+d   f   d +fd+iv    
  gi|121636478|ref|YP_976701.1|  58 VQGKFRGDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAKrgLANASFEVADASSFTgYDGRFDTIVD-ST 136
                                    45555689********************9999********999987654126899*********973688****975.56 PP

                           NodS 116 lyyiedvaelraavrnlvsllapdg 140
                                    l++   v+   + ++ +v+  ap+ 
  gi|121636478|ref|YP_976701.1| 137 LFHSMPVESREGYLQSIVRAAAPGA 161
                                    7888889999999999999888865 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.4e-06    0.0036      27      87 ..      64     117 ..      52     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                Methyltransf_32  27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87 
                                     +v+DvG+G++  s +la      ++  vg+d++ + ve a++ a+k g  + ++ sf+ +
  gi|121636478|ref|YP_976701.1|  64 GDVLDVGCGEAAISLALAE----RGHTTVGLDLSPAAVELARHEAAKRG--L-ANASFEVA 117
                                    579***************9....59**********************99..4.44444443 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.7e-06    0.0049      32     127 ..      64     160 ..      54     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--.--S-EEEEEEESSGGGS-G CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineak.lderydfilstvvlmflea 110
                                    g vld+gcg+   sl l+  g+    +d    +++  ++ + k  l n s ++ d  + +  d r+d i+ + ++  +  
  gi|121636478|ref|YP_976701.1|  64 GDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAKRGLANASFEVADASSFTgYDGRFDTIVDSTLFHSMPV 143
                                    789*******************************9999999999999988888888876547899999998888877777 PP

                                    GGHHHHHHHHHHTEEEE CS
                           TehB 111 eripsiienmqectkvg 127
                                    e+    ++ + + + +g
  gi|121636478|ref|YP_976701.1| 144 ESREGYLQSIVRAAAPG 160
                                    77666666666666666 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.033      17      71 ..      65     118 ..      52     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                Methyltransf_18  17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled.kievrl 71 
                                     v+D+G+  + ++++l+++g++   +  D+++ ++e a+++++k gl + + ev  
  gi|121636478|ref|YP_976701.1|  65 DVLDVGCGEAAISLALAERGHT--TVGLDLSPAAVELARHEAAKRGLANaSFEVAD 118
                                    699**************99876..899*****************999541344444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.037      14      80 ..      63     133 ..      52     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                           MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegva....ecvakGlsviqgdl.dkdlenfedksfdyvv 80 
                                    +  vld+GcG+  +   l+e ++ ++ Gl+l+ ++v     e+ ++Gl+    ++ d    +  d +fd +v
  gi|121636478|ref|YP_976701.1|  63 RGDVLDVGCGEAAISLALAE-RGHTTVGLDLSPAAVElarhEAAKRGLANASFEVaDASSFTGYDGRFDTIV 133
                                    567**********9988966.999********9999533337788999877766513333333577788776 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.5e-05     0.048     197     255 ..      58     116 ..      26     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                tRNA_U5-meth_tr 197 vtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiir 255
                                    v  + +gd+l++ cG+   slala++ +  +  +++ ++ve a+++ a+  + n ++  
  gi|121636478|ref|YP_976701.1|  58 VQGKFRGDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAKRGLANASFEV 116
                                    4455678**************************************99999998877655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.34      69     124 ..      59     115 ..      43     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                    TS-TTS-EEEES-TT-HHHHH--S.-..EEEEESS-SSTTEEES-TTS-S--TT-EE CS
                 Methyltransf_8  69 kkkdnlvvadlGcGeakiaeavre.kekvrsfdlvavnervvacdlakvPledesvd 124
                                    + k    v d+GcGea i+ a  e  +    +dl +   ++   + ak  l++ s +
  gi|121636478|ref|YP_976701.1|  59 QGKFRGDVLDVGCGEAAISLALAErGHTTVGLDLSPAAVELARHEAAKRGLANASFE 115
                                    555567799*********966654157788999998877776666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1907.35
//
Query:       gi|121636479|ref|YP_976702.1|  [L=408]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-17   62.8   0.2    1.8e-16   60.3   0.2    1.9  1  FAD_binding_3   FAD binding domain
    2.5e-10   40.1   0.5    1.6e-09   37.4   0.5    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.8e-10   38.2   0.2    0.00063   18.7   0.0    2.4  2  Trp_halogenase  Tryptophan halogenase
    1.5e-09   37.9   1.8    0.00032   20.4   0.2    2.3  2  DAO             FAD dependent oxidoreductase
    2.2e-09   36.9   0.2    1.2e-08   34.4   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    3.4e-07   29.3   0.4    2.4e-05   23.2   0.2    2.1  2  HI0933_like     HI0933-like protein
    1.8e-06   27.6   5.0    3.1e-06   26.8   5.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    6.1e-06   26.4   0.1    2.1e-05   24.7   0.1    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.2e-05   24.6   1.1    2.1e-05   23.8   1.1    1.4  1  FAD_binding_2   FAD binding domain
    1.7e-05   24.1   0.2    4.4e-05   22.7   0.4    1.5  2  GIDA            Glucose inhibited division protein A
    0.00029   21.3   0.1       0.23   12.0   0.0    2.7  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00037   19.9   1.0    0.00064   19.1   1.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0085   15.4   0.1      0.019   14.2   0.1    1.5  1  Thi4            Thi4 family
     0.0097   15.2   0.1      0.017   14.4   0.1    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.046   13.6   0.1      0.069   13.0   0.1    1.2  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.2   1.5e-19   1.8e-16       2     308 ..       7     307 ..       6     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.5e-19
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                    +dV++VGaGpaG  +a   ++aG +v++++  +   ++p +dgl++r +  l qlGl + ++++ + + l    +++   
  gi|121636479|ref|YP_976702.1|   7 ADVVVVGAGPAGSAAAAWAARAGRDVLVIDTATFPRDKPCGDGLTPRAVAELHQLGLGKWLADHIRHRGLRMSGFGG--- 83 
                                    69*******************************************************99888888444444444444... PP

                                    CCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                  FAD_binding_3  82 dtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                       ++++d    s p++ +++   el+  +++ ae +g+++  +++ +++++d +  + + +  ++g+e  v ++ l+ a
  gi|121636479|ref|YP_976702.1|  84 ---EVEVDWPGPSFPSYGSAVARLELDDRIRKVAEDTGARMLLGAKAVAVHHDSSR-RVVSLTLADGTE--VGCRQLIVA 157
                                    ...466666677999*********************************99999988.555555556776..********* PP

                                    -GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTC.CEEEEECCTTEE....EEEECCETEEEEEEEEECCE-G CS
                  FAD_binding_3 162 DGgrStvrktlgiefegeetvyeagvldvlfdadlsdivep.lvlilsaesrgv....mviPlentlerfyvqvearaek 236
                                    DG+rS+  ++lg +    etvy + v + l +a  +d++   +  ++s++  ++     + Pl n+++   + v    + 
  gi|121636479|ref|YP_976702.1| 158 DGARSPLGRKLGRR-WHRETVYGVAVRGYLSTAYSDDPWLTsHLELRSPDGAVLpgygWIFPLGNGEV--NIGV-GALST 233
                                    ************66.5566699999999999887777766657888888888779999999**99333..2222.23334 PP

                                    GGSCCCHHHHHHHHHHHHHHTTS.SCEEEEEEEEEEEEEEEEESSSEET.TEEE-GGGTEEE-STTSHHHHHHH CS
                  FAD_binding_3 237 eersekfteeevkarlreivgek.tldveieevsawtvaqrvaekyrkg.rvflaGDAaHihpPtgGqGlNtai 308
                                    ++r+ +   + ++  +  +  ++  ++ +++ vs++ +    a +   g + +l+GDAa ++ P +G G+  ++
  gi|121636479|ref|YP_976702.1| 234 SRRPADLALRPLISYYTDLRRDEwGFTGQPRAVSSALLPMGGAVSGVAGsNWMLIGDAAACVNPLNGEGIDYGL 307
                                    6678888888888777776655427788999999999988888888888899****************997765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.5   1.3e-12   1.6e-09       2     111 ..       8     162 ..       7     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.3e-12
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........................ 57 
                                    dvvv+G+GpAG aaa  +a+ag +v+++ ++ t++ +++       ++ ++ +++                         
  gi|121636479|ref|YP_976702.1|   8 DVVVVGAGPAGSAAAAWAARAGRDVLVI-DTATFPRDKPCGDGLTPRAVAELHQLGlgkwladhirhrglrmsgfggeve 86 
                                    8***************************.9999**999999888888888888777889999****************** PP

                                    .........................HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE CS
                                    .........................xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 .........................evvkklnqgielllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssp 111
                                                             +v     +g ++llg+++v++ +++ ++v+  ++   d++++ + +l++A G+++
  gi|121636479|ref|YP_976702.1|  87 vdwpgpsfpsygsavarlelddrirKV--AEDTGARMLLGAKAVAVHHDSsRRVVSLTL--ADGTEVGCRQLIVADGARS 162
                                    ************999988888555422..223457777777777777777555555333..7889************986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.3e-07   0.00063       1      58 [.       8      63 ..       8      70 .. 0.87
   2 !   17.0   0.0   1.8e-06    0.0021     153     336 ..     103     303 ..      93     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.3e-07
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S.S-EE--THHHHTHHHHT- CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvg.vGeatipsirkllrlLgi 58
                                   ++v+vG+G+aG+ aAa  a+a+    +v++++ +++++ +  G++++p  +  l++Lg+
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAG---RDVLVIDTATFPRDKpCGDGLTPRAVAELHQLGL 63
                                   69********************...68**********9652799****99996667776 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.8e-06
                                    HHHHHHHHHHHHHHCT-EEEE-.-EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT--- CS
                 Trp_halogenase 153 aalyakfLrrvaearGvtrveg.kvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLlt 231
                                    + ++++ +r+vae+ G +++ g k v v+ d + rv sl+l+dg+ev  +  i + G r+ l  + L  +++  + + + 
  gi|121636479|ref|YP_976702.1| 103 RLELDDRIRKVAEDTGARMLLGaKAVAVHHDSSRRVVSLTLADGTEVGCRQLIVADGARSPLGRK-LGRRWHRETVYGVA 181
                                    56778889**********99872566777777******************************998.79888888888888 PP

                                    -EEEEEEEE--H.....---SSEEEEE-SSEEEEEEEETTEEEE.EE.EE-TTTS-HHHHHHHHHHHCT--TTTS-EEEE CS
                 Trp_halogenase 232 drAlavqvesee.....lvepytrataekaGWtWkiPLqhrlgn.Gy.vyssahadddeAlaellaeldgkleaeprkir 304
                                     r+     +s++     ++e ++   a   G  W  PL +   n G+ + s ++  +d Al+ l++ +        ++  
  gi|121636479|ref|YP_976702.1| 182 VRGYLSTAYSDDpwltsHLELRSPDGAVLPGYGWIFPLGNGEVNiGVgALSTSRRPADLALRPLISYYTD---LRRDEWG 258
                                    8888888888888887777888888999999999999987766666523455555678888888887652...2222333 PP

                                    ---EE..............ES-SEETTEEE-CCCTEE--CCCS-HH CS
                 Trp_halogenase 305 fttGr..............rkqawvknvvalGlasgfvePlestsi 336
                                    ft G+               + +   n +++G+a++ v+Pl++ +i
  gi|121636479|ref|YP_976702.1| 259 FT-GQpravssallpmggaVSGVAGSNWMLIGDAAACVNPLNGEGI 303
                                    32.2223455555555555888888999999999999999988887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   2.7e-07   0.00032       1      30 [.       8      39 ..       8      70 .. 0.92
   2 !   17.1   0.1   2.7e-06    0.0033     151     296 ..     109     249 ..      94     316 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                   dvv++G+G +G+++A ++ar+g  V++++ + 
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAGrdVLVIDTAT 39
                                   9********************99*****9874 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.7e-06
                                    HHHHHHHHTT-EEEESECEEEEEEEE..TCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT.CTT.TSEEEE..EEEE CS
                            DAO 151 alaraaealGveilegtevtgleeed..gkvwgverttp.gendaadavVnaaGawsdllgll.kel.dlpisp..vrgq 223
                                     +++ ae+ G+++l+g++++++ + d   +v+ +  t + g+++ ++++++a Ga s l ++l ++  +  +++  vrg+
  gi|121636479|ref|YP_976702.1| 109 RIRKVAEDTGARMLLGAKAVAVHH-DssRRVVSL--TLAdGTEVGCRQLIVADGARSPLGRKLgRRWhRETVYGvaVRGY 185
                                    577889***************944.435677777..3333777667***********977444333344455444499*9 PP

                                    EEEEEECCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHS CS
                            DAO 224 vlvlkplseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklf 296
                                      +    +++ + +++ l  p+  + +g+g  ++p  +g+v +G  a         +++ + +d  l+ l  ++
  gi|121636479|ref|YP_976702.1| 186 LSTA-YSDDPWLTSHLELRSPDgAVLPGYG-WIFPLGNGEVNIGVGA---L-----STSRRPADLALRPLISYY 249
                                    9999.4444444445666666669999998.6667779999998765...2.....222233334444444444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1     1e-11   1.2e-08       1     274 [.       8     301 ..       8     348 .. 0.71
   2 ?   -3.4   0.0         3   3.6e+03     270     312 ..     355     399 ..     353     403 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1e-11
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieas...psll....fpnnyvWsdefedlgaleecvehsWsgtivylddg. 72 
                                    Dvvv+GaGpAg + Aa    a++g  v++i+++    + +     +++ v + ++ +lg   + +    ++  +++ ++ 
  gi|121636479|ref|YP_976702.1|   8 DVVVVGAGPAGSAAAAWA--ARAGRDVLVIDTAtfpRDKPcgdgLTPRAVAELHQLGLG---KWLADHIRHRGLRMSGFg 82 
                                    9************99999..999999999986411122220111234444444444444...444444444444444431 PP

                  Lycopene_cycl  73 kkillg......raYgr.vsskrlkeellerlv.engvklleakvesveeeea.geslvvleggrkirarlvvdarglas 143
                                     +++++        Yg+ v + +l  ++ +    ++++ ll ak+ +v++++    ++ +l++g ++ +r  ++a g a+
  gi|121636479|ref|YP_976702.1|  83 GEVEVDwpgpsfPSYGSaVARLELDDRIRKVAEdTGARMLLGAKAVAVHHDSSrRVVSLTLADGTEVGCRQLIVADG-AR 161
                                    2344446667766787549999****9999888666778899**********966677899****************.55 PP

                  Lycopene_cycl 144 lk....karrlglQtfyGvevevdnpp.f..dldkmvlMDfrveqklkgltFlYalPldsdrllvEeTelaskpeLpada 216
                                    ++     +rr    t yGv v+   +  +  d+     +  r+++ +  + ++++ Pl++  + +    l+     pad+
  gi|121636479|ref|YP_976702.1| 162 SPlgrkLGRRWHRETVYGVAVRGYLSTaYsdDPWLTSHLELRSPDGAVLPGYGWIFPLGNGEVNIGVGALSTSR-RPADL 240
                                    554766788888999******954432133388888999999****9******************999999988.56666 PP

                  Lycopene_cycl 217 lkkrlaaylra...lglkvkevvee.EqgviPvtlggslprleqk.vlaiGaaaglvhPaTGY 274
                                      + l +y  +     +      ++   +++P+  gg ++ ++ +  + iG aa  v P  G 
  gi|121636479|ref|YP_976702.1| 241 ALRPLISYYTDlrrDEWGFTGQPRAvSSALLPM--GGAVSGVAGSnWMLIGDAAACVNPLNGE 301
                                    5555655555512245666655555145679**..888887765538999*******998775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3
                  Lycopene_cycl 270 PaTGYsvarslaeapllasaiaaalres..slsarawatlwprer 312
                                    P+TG    rs a  ++   +++++   +  +  ar+w+   + +r
  gi|121636479|ref|YP_976702.1| 355 PTTGPITMRSTALMNIAVRVMSNLVTDDdrDWVARVWRGGGQLSR 399
                                    899999999999888666666666654444555667766665555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2     2e-08   2.4e-05       2      33 ..       8      39 ..       7      48 .. 0.92
   2 ?    4.2   0.0     0.012        14     117     166 ..     112     162 ..      96     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                   dv+v+G+G+AG  aA+ aa++g++Vl+++ a+
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAGRDVLVIDTAT 39
                                   8****************************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                                    HHHHHHT-EEE-S--EEEEECETTE..EEEEE.TTEEEEESEEEE----SS CS
                    HI0933_like 117 kelkeagvklrletevksvekeedgk.frvktkseeeleadklvlAtGGlS 166
                                    k ++++g ++ l  +  +v+++++++ +++++ +++e+ +++l++A G  S
  gi|121636479|ref|YP_976702.1| 112 KVAEDTGARMLLGAKAVAVHHDSSRRvVSLTLADGTEVGCRQLIVADGARS 162
                                    556778888888888888877766651456669**************9987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   5.0   2.6e-09   3.1e-06       1      33 [.       8      40 ..       8     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.6e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergv 33
                                   DvvVvG+gpaG aAA  AaraG+ vl++++  +
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAGRDVLVIDTATF 40
                                   9***************************98766 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.7e-08   2.1e-05       1      28 [.      11      38 ..      11      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                   +vGaG +G++aA+ +a+ag+dvl+++++
  gi|121636479|ref|YP_976702.1| 11 VVGAGPAGSAAAAWAARAGRDVLVIDTA 38
                                   8*************************95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.1   1.8e-08   2.1e-05       1      30 [.       8      37 ..       8      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                   Dv+V+G+G AG aAA+ aa+aG++v+v++ 
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAGRDVLVIDT 37
                                   9**************************986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   3.7e-08   4.4e-05       1      29 [.       8      36 ..       8      62 .. 0.86
   2 ?   -2.1   0.0       1.3   1.6e+03     124     150 ..     134     160 ..      91     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.7e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                   dv+V+G+G AG++AA+ aar+G +vl i 
  gi|121636479|ref|YP_976702.1|  8 DVVVVGAGPAGSAAAAWAARAGRDVLVID 36
                                   79***********************9983 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                    CTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 124 eekkvkgvvtedgetikakavviatGt 150
                                    ++++v  ++++dg+++ +++ ++a G+
  gi|121636479|ref|YP_976702.1| 134 SSRRVVSLTLADGTEVGCRQLIVADGA 160
                                    236777889999999999999999887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0    0.0002      0.23       2      36 ..       9      44 ..       8      67 .. 0.83
   2 ?   -2.4   0.0       6.3   7.5e+03      42      56 ..      63      77 ..      54      78 .. 0.83
   3 ?    6.4   0.0     0.011        13      44      80 ..     108     145 ..     102     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.T CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.r 36
                                   vvvvG+G  g  +A+ +a+ g +V v++ +  ++ +
  gi|121636479|ref|YP_976702.1|  9 VVVVGAGPAGSAAAAWAARAGRDVLVIDTATFPRdK 44
                                   8**************************998877743 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.3
                                   HHHHHHHHHHHTTEE CS
                      Pyr_redox 42 askilqeklekngie 56
                                   ++k+l+++++++g +
  gi|121636479|ref|YP_976702.1| 63 LGKWLADHIRHRGLR 77
                                   7899******99986 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
                                    HHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEEET CS
                      Pyr_redox  44 kilqeklekngievllntkveeiegsedg.vesvklkd 80 
                                    +++++  e+ g ++ll++k+++++++++  v s++l+d
  gi|121636479|ref|YP_976702.1| 108 DRIRKVAEDTGARMLLGAKAVAVHHDSSRrVVSLTLAD 145
                                    5677788999******************9999999876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.0   5.4e-07   0.00064      28      60 ..       6      38 ..       2      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                    a v+v+G+G aG +A+a a++ g +V v+D+ 
  gi|121636479|ref|YP_976702.1|  6 SADVVVVGAGPAGSAAAAWAARAGRDVLVIDTA 38
                                   699****************************85 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.6e-05     0.019      18      48 ..       7      36 ..       3      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                   +Dvv+vGaG++G +aa   a++ +  v++++
  gi|121636479|ref|YP_976702.1|  7 ADVVVVGAGPAGSAAAAWAARA-GRDVLVID 36
                                   7***********9999999998.88888886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.4e-05     0.017       1      30 [.      10      38 ..      10      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                   +++GaGPaG aaa  + +ag  d+l+++ +
  gi|121636479|ref|YP_976702.1| 10 VVVGAGPAGSAAAAWAARAGR-DVLVIDTA 38
                                   79******************9.8****975 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.8e-05     0.069       2      31 ..       9      38 ..       8      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                   v v+GaG  G+  aa +a+ag +V ++d++
  gi|121636479|ref|YP_976702.1|  9 VVVVGAGPAGSAAAAWAARAGRDVLVIDTA 38
                                   89*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2855.70
//
Query:       gi|121636480|ref|YP_976703.1|  [L=335]
Description: polyprenyl-diphosphate synthase grcC1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-63  212.3   0.0    7.5e-63  212.0   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.045   14.2   0.0        1.2    9.6   0.0    2.3  1  MitMem_reg       Maintenance of mitochondrial structure and f


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.0   8.4e-67   7.5e-63       3     254 ..      43     285 ..      41     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 8.4e-67
                                    HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHH CS
                polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnkl 82 
                                     ++++l +l++agGKr+Rpl+++l+a++   ++ +   + v+++++e++h a+L hDD+mD++++RRG+p+a++++Gn++
  gi|121636480|ref|YP_976703.1|  43 VMSDSLLHLFNAGGKRFRPLFTVLSAQIGP-QP-DAAAVTVAGAVIEMIHLATLYHDDVMDEAQVRRGAPSANAQWGNNV 120
                                    56788999*********************9.44.4699****************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHH CS
                polyprenyl_synt  83 AindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvala 162
                                    Ai++gd+lla+a++l+a+l    +e++++++++ +q+v Gq+ +++ + +++++  s+e+yl++v+ KT++l+ ++ +l+
  gi|121636480|ref|YP_976703.1| 121 AILAGDYLLATASRLVARL---GPEAVRIIADTFAQLVTGQMRETRGT-SENVD--SIEQYLKVVQEKTGSLIGAAGRLG 194
                                    *******************...56*********************555.57777..8*********************** PP

                                    HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTTSS CS
                polyprenyl_synt 163 allagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilgkk 242
                                     +++ga+de++e+l+++g  +G+aFQi DD++D+ +++++ gK  gtD++eg  tlp+l+al+++ p+  ++l+++l+  
  gi|121636480|ref|YP_976703.1| 195 GMFSGATDEQVERLSRLGGVVGTAFQIADDIIDIDSESDESGKLPGTDVREGVHTLPMLYALRESGPD-CARLRALLNGP 273
                                    ***************************************************************77666.569****9999 PP

                                    HHHHHHHHHHHH CS
                polyprenyl_synt 243 aekeedvkeale 254
                                     +++++v+eal 
  gi|121636480|ref|YP_976703.1| 274 VDDDAEVREALT 285
                                    999999999876 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00014       1.2      20      54 ..     149     183 ..      27     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                     MitMem_reg  20 stlstglnrqyyslkilqerldlikdYlkkveege 54 
                                     t ++ ++ q+   ++ +e +d+i++Ylk v+e++
  gi|121636480|ref|YP_976703.1| 149 DTFAQLVTGQMRETRGTSENVDSIEQYLKVVQEKT 183
                                    567788999********************999554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2217.94
//
Query:       gi|121636481|ref|YP_976704.1|  [L=286]
Description: heat shock protein HtpX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-37  126.8   0.3    1.3e-36  126.2   0.0    1.4  2  Peptidase_M48  Peptidase family M48
     0.0084   15.3   0.0      0.013   14.7   0.0    1.3  1  Peptidase_M56  BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.55   4.9e+03     112     112 ..      40      40 ..       9      64 .. 0.46
   2 !  126.2   0.0   1.4e-40   1.3e-36       2     195 ..      69     283 ..      68     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.55
                                    T CS
                                    x RF
                  Peptidase_M48 112 a 112
                                     
  gi|121636481|ref|YP_976704.1|  40 L 40 
                                    1 PP

  == domain 2  score: 126.2 bits;  conditional E-value: 1.4e-40
                                    --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhs 80 
                                    l+++ + ++v+ela +a+   p++++y+ +    NAFa+g++ ++  +  t+g+l + l+e+el+aVlGHEl+H+ +r+ 
  gi|121636481|ref|YP_976704.1|  69 LQAPAMYRIVRELATSAHQ--PMPRLYISDTAAPNAFATGRNPRNaAVCCTTGIL-RILNERELRAVLGHELSHVYNRDI 145
                                    56778889***********..***********************99*********.************************ PP

                                    HHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT....HHHHHHHHHHHHHHHHTTT.HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  81 vvslivsllasillllglallisraeedaagafldalavliglliillfl....alSRkrEyqADeagvellkrakdlvr 156
                                    ++s + + la ++  l+ +++ + + + ++ ++   +  l++ll+ +  +    a+SR+rEyqADe g+ l+ ++ +l++
  gi|121636481|ref|YP_976704.1| 146 LISCVAGALAAVITALANMAMWAGMFGGNRDNANPFALLLVALLGPIAATvirmAVSRSREYQADESGAVLTGDPLALAS 225
                                    *****************9999998887777766655555556565555556888************************** PP

                                    HHHHHHHHTT--S---HHHH...................HHS-SS--HHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 157 aliklakdlerqdvsaslrs...................ellstHPplleRiqalkel 195
                                    al k++ + + ++   +++                     l+stHPp+++Ri++l+++
  gi|121636481|ref|YP_976704.1| 226 ALRKISGGVQAAPLPPEPQLasqahlmianpfragerigSLFSTHPPIEDRIRRLEAM 283
                                    ***********999888877889999*****************************987 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.5e-06     0.013     104     220 ..      36     153 ..      28     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-06
                  Peptidase_M56 104 illliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgllkp.... 179
                                    +l+++++vg+ +  +y+    l l+    +  ++l+a + +++++e     + +  +++++s++   P  ++  ++    
  gi|121636481|ref|YP_976704.1|  36 MLAALFAVGMNV-YVYFNSDKLALRAMHAQPVSELQAPAMYRIVRELATSAH-QPMPRLYISDT-AAPNAFATGRNprna 112
                                    566666666666.444444444444334555556666566666655444333.23345555544.345555555432222 PP

                  Peptidase_M56 180 rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvav 220
                                     +   + +l+ l+++el  +l HEl+H+ ++D+l+  ++ +
  gi|121636481|ref|YP_976704.1| 113 AVCCTTGILRILNERELRAVLGHELSHVYNRDILISCVAGA 153
                                    466677789999*********************99887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2031.35
//
Query:       gi|121636482|ref|YP_976705.1|  [L=341]
Description: NAD(P)H-dependent glycerol-3-phosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-48  163.4   1.8    7.4e-48  162.4   1.1    1.8  2  NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogen
    6.3e-48  162.7   0.0      1e-47  162.0   0.0    1.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    3.4e-05   24.3   0.0    0.00019   21.9   0.0    2.3  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00067   18.7   0.0     0.0014   17.6   0.0    1.5  2  PDH             Prephenate dehydrogenase
  ------ inclusion threshold ------
      0.019   15.4   0.0        6.9    7.2   0.0    3.0  2  NAD_binding_7   Putative NAD(P)-binding
      0.053   13.8   0.0       0.19   12.0   0.0    2.0  2  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   4.2e+03      97     107 ..     143     154 ..     109     165 .. 0.54
   2 !  162.4   1.1   2.5e-51   7.4e-48       1     141 [.     184     324 ..     184     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                    HC.C--HHHHHH CS
                 NAD_Gly3P_dh_C  97 ln.qvleGveta 107
                                    +  +v+eG+ +a
  gi|121636482|ref|YP_976705.1| 143 IArEVAEGYAAA 154
                                    222455555554 PP

  == domain 2  score: 162.4 bits;  conditional E-value: 2.5e-51
                                    -HHHHHHHHHHHHHHHHHHHHHHHTTH-HHHHHHHHHHHHHHHHHHHHHHTSSGGGGGSTTTHHHHHHHHHSCT.HHHHH CS
                 NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglglgdntkaalitrglaEmarlakalgakpetflglaglgDlivtctsgksRNrrf 80 
                                    Dv+Gve agalKNv+Aia+G+   lg+g+nt+a +i+r+l+Em++l+ a+g+k+etf glaglgDlivtcts+ sRNr++
  gi|121636482|ref|YP_976705.1| 184 DVVGVETAGALKNVFAIAVGMGYSLGIGENTRALVIARALREMTKLGVAMGGKSETFPGLAGLGDLIVTCTSQRSRNRHV 263
                                    9******************************************************************************* PP

                                    HHHHHCT--HHHHHHHHCC--HHHHHHHHHHHHHHHTT.G.HHHHHHHHHHHS---HHHHH CS
                 NAD_Gly3P_dh_C  81 GeelgkgesleeiekelnqvleGvetakevyellkkkgvemplleavykilyegkspeeli 141
                                    Ge+lg g+ ++ei+++++qv+eGv++a  v+e++++ g++mp++++v +++++g ++e+++
  gi|121636482|ref|YP_976705.1| 264 GEQLGAGKPIDEIIASMSQVAEGVKAAGVVMEFANEFGLNMPIAREVDAVINHGSTVEQAY 324
                                    *********************************************************9985 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.0   3.4e-51     1e-47       1     156 [.       9     164 ..       9     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 3.4e-51
                                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT.----TTEEEES-HHHHHTT--EEEE---H CS
                 NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpg.iklpenlvattdlaealkgadiivlvvPs 79 
                                    k+ vlG+GswGt++A ++a++g ++ +wvr++ ++++in++h+n++yL + + l+++l+attd++ea++ ad++v+ vPs
  gi|121636482|ref|YP_976705.1|   9 KVVVLGGGSWGTTVASICARRG-PTLQWVRSAVTAQDINDNHRNSRYLGNdVVLSDTLRATTDFTEAANCADVVVMGVPS 87 
                                    799*******************.7899*********************8769**************************** PP

                                    HHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEESS--HHHHHTT--EEEEEEES-HHH CS
                 NAD_Gly3P_dh_N  80 qalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeekvavlsGpslAeEvakgkptavviaskdkea 156
                                    + +r vl +l++ l++ +++vsl+KG+e+gt++++s++iee+l+ ++ ++l+Gp++A+Eva+g  +a+v+a+ d+++
  gi|121636482|ref|YP_976705.1|  88 HGFRGVLVELSKELRPWVPVVSLVKGLEQGTNMRMSQIIEEVLPGHPAGILAGPNIAREVAEGYAAAAVLAMPDQHL 164
                                    ************************************************************************99876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   6.5e-08   0.00019       1      95 [.       9     111 ..       9     113 .. 0.80
   2 ?   -1.7   0.0       1.5   4.6e+03       8      71 ..     141     161 ..     135     175 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.5e-08
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..............-EEECECHHHHHHH-SEEE CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..............vkvtavdneeaaeeadvvv 66 
                                    k+ ++G+G+ g ++as ++++g + + +     r+  +a+ + ++                 ++t+ d  eaa+ advvv
  gi|121636482|ref|YP_976705.1|   9 KVVVLGGGSWGTTVASICARRGPTLQWV-----RSAVTAQDINDNHRnsrylgndvvlsdtLRATT-DFTEAANCADVVV 82 
                                    6889******************433434.....444444444444444447799999***999999.************* PP

                                    E-S-HHHHHHHHHHCGHHHHTTSEEEEES CS
                  F420_oxidored  67 lavkpedveevlselakdalkgklvisvl 95 
                                      v+ + +  vl el k++     v+s +
  gi|121636482|ref|YP_976705.1|  83 MGVPSHGFRGVLVELSKELRPWVPVVSLV 111
                                    ***************88888777888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                    SHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                  F420_oxidored   8 Gnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71 
                                     n+++ +a+g +aa                                            vla++ 
  gi|121636482|ref|YP_976705.1| 141 PNIAREVAEGYAAA-------------------------------------------AVLAMPD 161
                                    45555555555444...........................................4444444 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.8e-07    0.0014      35     131 ..      66     161 ..      34     174 .. 0.71
   2 ?   -3.1   0.0         1   3.1e+03      54      78 ..     272     296 ..     271     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.8e-07
                                    EEES-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE.--S--CHHHHHHHHHCC..GCEEEEEES---S-SS CS
                            PDH  35 eatdd.ieavkeadivvlavPvevilevlkelaphlkedalitD.vgsvKekvvreleellkegksfvgghPmaGteksG 112
                                     at+d  ea++ ad+vv+ vP + ++ vl el++ l++ + ++  v +  +     ++++++   ++ +ghP aG    G
  gi|121636482|ref|YP_976705.1|  66 RATTDfTEAANCADVVVMGVPSHGFRGVLVELSKELRPWVPVVSlVKGLEQGTNMRMSQIIE---EVLPGHP-AGI-LAG 140
                                    3566767888889*************************986665378999999999***999...9******.444.445 PP

                                    GGG--..TTTTTT-EEEEEE- CS
                            PDH 113 vdaar..eelfenavviLtPt 131
                                    ++ ar  +e +  a v   P+
  gi|121636482|ref|YP_976705.1| 141 PNIARevAEGYAAAAVLAMPD 161
                                    554441145566666655555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1
                                    -GGGHHHHHHHHHHHS-TT-EEEE- CS
                            PDH  54 PvevilevlkelaphlkedalitDv 78 
                                    P++ i+  + ++a+ +k + +++  
  gi|121636482|ref|YP_976705.1| 272 PIDEIIASMSQVAEGVKAAGVVMEF 296
                                    7888888888888888888888765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0023       6.9       6      93 ..       6     183 ..       1     187 [. 0.54
   2 ?    3.7   0.0     0.028        83      62      82 ..     247     267 ..     212     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0023
                  NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.................elvklaeee.............. 54 
                                    ++ kv+v GgG+ +++ ++  ++ g +++ v  +v+++                   +       +              
  gi|121636482|ref|YP_976705.1|   6 REPKVVVLGGGSWGTTVASICARRGPTLQWVRSAVTAQDIndnhrnsrylgndvvlsD-------Tlrattdfteaanca 78 
                                    6678999999999999999999999998888888622211233334444444333332.......033333334444555 PP

                  NAD_binding_7  55 .................................................................lekdleg.adlviaa 68 
                                                                                                     +++  eg a+ ++ a
  gi|121636482|ref|YP_976705.1|  79 dvvvmgvpshgfrgvlvelskelrpwvpvvslvkgleqgtnmrmsqiieevlpghpagilagpniAREVAEGyAAAAVLA 158
                                    55555555555555555555555555555555555555555555555444444444444433332222233334467777 PP

                  NAD_binding_7  69 tddrelneriaeaakarrilvnvad 93 
                                    ++d++l +r+ ++ ++rr  v  +d
  gi|121636482|ref|YP_976705.1| 159 MPDQHLATRLSAMFRTRRFRVYTTD 183
                                    7777777777777777777777776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                  NAD_binding_7  62 adlviaatddrelneriaeaa 82 
                                     dl++++t++r+ n+++ e+ 
  gi|121636482|ref|YP_976705.1| 247 GDLIVTCTSQRSRNRHVGEQL 267
                                    58**************98875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.5e-05      0.19       1     109 [.      10     124 ..      10     131 .. 0.89
   2 ?   -2.8   0.0       2.5   7.5e+03      64      97 ..     248     281 ..     248     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                                    EEEES-SHHHHHHHHHHHHTT.......EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLsegg.......kdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgdd 73 
                                    ++++G G  G+++a    ++g       + v++ d ++++ ++ r  g +vv  d  +  +     ++ ad+v+  ++++
  gi|121636482|ref|YP_976705.1|  10 VVVLGGGSWGTTVASICARRGptlqwvrSAVTAQDINDNHRNS-RYLGNDVVLSDTLRATTDFTEAANCADVVVMGVPSH 88 
                                    79*****************887999998668888888766665.88999999999999999999999************* PP

                                    HHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHT CS
                         TrkA_N  74 eanilavllakelnpkkkiiaraqdpehaellkklg 109
                                     +  ++v+l kel+p  ++++ ++  e+  +++   
  gi|121636482|ref|YP_976705.1|  89 GFRGVLVELSKELRPWVPVVSLVKGLEQGTNMRMSQ 124
                                    ***********************9999988888755 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                    SEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEES CS
                         TrkA_N  64 daviaatgddeanilavllakelnpkkkiiaraq 97 
                                    d+++++t++   n  + + +    p  +iia ++
  gi|121636482|ref|YP_976705.1| 248 DLIVTCTSQRSRNRHVGEQLGAGKPIDEIIASMS 281
                                    5677888888888888777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1877.97
//
Query:       gi|121636483|ref|YP_976706.1|  [L=486]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-17   61.9   0.0    5.3e-16   58.1   0.0    2.3  1  FMO-like       Flavin-binding monooxygenase-like
    6.9e-12   45.2   0.0    9.3e-07   28.4   0.0    2.7  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.6e-11   42.9   0.0    8.9e-11   41.6   0.0    1.6  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.5e-10   40.0   0.0    3.3e-08   33.6   0.0    2.9  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      2e-09   37.5   0.1    4.5e-06   26.5   0.0    3.3  3  DAO            FAD dependent oxidoreductase
    1.9e-08   33.8   0.0    2.2e-07   30.4   0.0    2.1  2  Thi4           Thi4 family
    2.9e-08   33.2   0.2    4.5e-05   22.8   0.0    3.0  4  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    4.3e-06   27.2   0.1       0.01   16.4   0.0    2.8  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.8e-05   23.7   0.7      0.011   15.7   0.0    3.5  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0022   16.6   0.0        1.6    7.2   0.0    2.3  2  Mqo            Malate:quinone oxidoreductase (Mqo)
     0.0057   15.8   0.1       0.02   14.0   0.0    1.9  2  FAD_binding_2  FAD binding domain
     0.0092   15.1   0.2       0.14   11.1   0.0    2.6  3  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.024   14.7   0.0       0.35   10.9   0.0    2.5  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.048   12.9   0.0        0.1   11.8   0.0    1.5  1  Amino_oxidase  Flavin containing amine oxidoreductase
      0.096   13.1   0.1       0.27   11.7   0.0    1.9  2  NAD_binding_7  Putative NAD(P)-binding
        0.1   11.9   0.1       0.22   10.8   0.1    1.6  1  FAD_oxidored   FAD dependent oxidoreductase
       0.21   10.6   0.3          2    7.4   0.0    2.0  2  GIDA           Glucose inhibited division protein A
       0.26    9.9   0.1        1.3    7.7   0.1    2.0  2  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   5.3e-19   5.3e-16       4     228 ..      12     225 ..      10     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.3e-19
                       FMO-like   4 vaviGaGvsGlasikcclee..gleptcfersddiGGlwrfkenveeGrasiyksvvsnsskemscfsdfplpedypnfl 81 
                                    v ++GaG+sGl +    +e   +l  t +er + iGG w +           y  v s+ss     f+  p   +     
  gi|121636483|ref|YP_976706.1|  12 VVIVGAGISGLGAAYRIIERnpQLTYTILERRARIGGTWDLFR---------YPGVRSDSSIFTLSFPYEPWTRE-EGIA 81 
                                    789********999999987336999*************8754.........66677777777777888887765.4678 PP

                       FMO-like  82 hnsklleylklfakefdllkyiqfkttvcsvkkrpdfstsGqwevvtekegkkesavfdavmvctGhhvnphlplesfpG 161
                                    +  ++ eyl   a+++++ ++i+f++ v + +     s++  w v+ e++g ++      v   +G++ + +     f G
  gi|121636483|ref|YP_976706.1|  82 DGAHIREYLTDMAHKYGIDRHIEFNSYVRAADW---DSSTDTWTVTFEQNGVHKHYRSRFVFFGSGYYNYDEGYTPDFGG 158
                                    999**********************99876443...367789************999999************9999**** PP

                       FMO-like 162 iekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvlsrvsdsGy 228
                                    iekf G ++h +++ e   ++gk+++viG G ++  +   l+  ae+v +  rs ++++s +  s +
  gi|121636483|ref|YP_976706.1| 159 IEKFGGAVVHPQHWPEDLDYTGKKIVVIGSGATAVTLIPSLTDRAEKVTMLQRSPTYLISASKYSTF 225
                                    *********************************************************9997654443 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   9.3e-10   9.3e-07       2     189 ..      11     229 ..      10     235 .. 0.74
   2 !   13.7   0.0   2.8e-05     0.028     216     274 ..     326     387 ..     310     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.3e-10
                                    SEEEE--SHHHHHHHHHHHH.H.TS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...................... CS
                                    xxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq.a.gakvtlvelegtclnggcllskallgvaedaeias...................... 57 
                                    dvv++G+G+ Gl aa ++ + + ++  t++  e+    gg +    + gv++d +i++                      
  gi|121636483|ref|YP_976706.1|  11 DVVIVGAGISGLGAAYRIIErNpQLTYTIL--ERRARIGGTWDLFRYPGVRSDSSIFTlsfpyepwtreegiadgahire 88 
                                    8****************9995425555555..555555555555666777777777777778888888888888888888 PP

                                    .....HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E....EE-BCTCTTC.TTBEECCS CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 .....evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs....sprdlgipGvaenvgklvr 128
                                          +   +  +ie+   + + + d    + +++ +++g ++++    ++  +G     +  +++  G ++ +g +v+
  gi|121636483|ref|YP_976706.1|  89 yltdmAHKYGIDRHIEFNSYVRAADWDSSTDTWTVTFEQNGVHKHYRSRFVFFGSGYynydEGYTPDFGGIEKFGGAVVH 168
                                    88888555556667888888888899988888888888889999999999******944444455566688777777755 PP

                                    ECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS..TTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                    Pyr_redox_2 129 tldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrll..raldkelsaal 189
                                    + +  e l +    k+ivv+G+G+++v l   l++ +++vt++++ ++ l   +  + ++a +
  gi|121636483|ref|YP_976706.1| 169 PQHWPEDLDYTG--KKIVVIGSGATAVTLIPSLTDRAEKVTMLQRSPTYLisASKYSTFAAVV 229
                                    555555555444..66*******************************9996333334555555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.8e-05
                                    EE.EEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--TTSBESSTTEEE- CS
                                    xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 216 le.vvledgeeidadlvvvavGvrpstelle..eklglelderggivvdeflrtnvpgiyai 274
                                    ++   l++g  +dad +v+a+G++ +  +      +g+e+d+r+++v + ++   vp+++ +
  gi|121636483|ref|YP_976706.1| 326 ATgIALKSGGHLDADIIVTATGLQLQALGGAaiSLDGVEIDPRDRFVYKAHMLEDVPNLFWC 387
                                    44578999******************9886689999****************999****976 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0     9e-14   8.9e-11       1     207 [.      13     223 ..      13     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9e-14
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkka.gledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeekl 78 
                                    +I+GaG  Gl+aa+ + +     +y+ilE+  +ig ++  ++      ++s     +++    +     +p ++ +e  +
  gi|121636483|ref|YP_976706.1|  13 VIVGAGISGLGAAYRIIERnPQLTYTILERRaRIGGTWDLFRYPGVRSDSSI----FTL---SF---PYEP-WTREEGIA 81 
                                    7************98754414459******999***9876666555544332....222...11...1223.33345567 PP

                    Pyr_redox_3  79 srkealeYlrevaksfel..piklfeeVesvkk..edegfevetske....tyeAkkviiAtGef..dkPnklnipGeek 148
                                     ++ + eYl+ +a+++ +  +i+ ++ V++ +   + ++ +v+ +++     y++++v+   G++  d  +++++ G ek
  gi|121636483|ref|YP_976706.1|  82 DGAHIREYLTDMAHKYGIdrHIEFNSYVRAADWdsSTDTWTVTFEQNgvhkHYRSRFVFFGSGYYnyDEGYTPDFGGIEK 161
                                    899999*********9884458888888887763267889999887656669***********972256789*******8 PP

                    Pyr_redox_3 149 ...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdps 207
                                        v+h ++ +e  +y+g+k+vViG + +av     l ++  +Vt++ r+ +   + s++s
  gi|121636483|ref|YP_976706.1| 162 fggAVVHPQHWPEDLDYTGKKIVVIGSGATAVTLIPSLTDRAEKVTMLQRSPTYLISASKYS 223
                                    766789999998888***********************************988766666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   3.3e-11   3.3e-08       1      51 [.      14      66 ..      14      77 .. 0.83
   2 ?    3.0   0.0      0.12   1.2e+02       1      28 [.     185     212 ..     185     218 .. 0.91
   3 ?   -3.0   0.0       9.3   9.2e+03      40      55 ..     365     381 ..     352     393 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.3e-11
                                   EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSSGGG-EECETTCEECTS--- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlGGraasyevpgvrvdygahi 51
                                   IvGaG+sGl aAy++ ++  ++  ++le+r r+GG +  +++pgvr d    +
  gi|121636483|ref|YP_976706.1| 14 IVGAGISGLGAAYRIIERnpQLTYTILERRARIGGTWDLFRYPGVRSDSSIFT 66
                                   9*************87765899**********************987765544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekr 28 
                                    ++G+G+++ ++   L+++  +v+ l+++
  gi|121636483|ref|YP_976706.1| 185 VIGSGATAVTLIPSLTDRAEKVTMLQRS 212
                                    8**************9999999999876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.3
                                    E.TTCEECTS---EEET CS
                  NAD_binding_8  40 v.pgvrvdygahifhgs 55 
                                    + p  r+ y ah + ++
  gi|121636483|ref|YP_976706.1| 365 IdPRDRFVYKAHMLEDV 381
                                    24567888888887775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   4.5e-09   4.5e-06       1      36 [.      11      49 ..      11     138 .. 0.88
   2 ?    3.4   0.0     0.049        48       1      61 [.     182     245 ..     182     261 .. 0.70
   3 ?    4.1   0.0      0.03        30     154     220 ..     307     368 ..     263     463 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.5e-09
                                   EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTTSSG CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekgdiagsga 36
                                   dvvi+G+Gi Gl++Ay   +r+     t+le++ ++g g+
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIIERNpqltYTILERRARIG-GT 49
                                   9******************99669*********9999.65 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.049
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE..EEEESSSSTHHSTHHHHHHH CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns..gllhsglrylpeaselarls 61 
                                    ++v+iG+G + ++    L+ r   Vt l +++     aS  ++  ++++ +l  ++  + ++r++
  gi|121636483|ref|YP_976706.1| 182 KIVVIGSGATAVTLIPSLTDRAekVTMLQRSPTYLISASKYSTfaAVVRKALP-PKTSHLIVRMY 245
                                    59****************976448****9997655566665554455555554.33344555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.03
                                    HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTT.SEEEEE CS
                            DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeld.lpispv 220
                                    +a+ ++ +e+++   + +++     ++g+   ++ g+ da d +V a+G++ + l g +  ld + i p+
  gi|121636483|ref|YP_976706.1| 307 NAITSGRAEVVTD-HIDHFD-----ATGI-ALKSgGHLDA-DIIVTATGLQLQALgGAAISLDgVEIDPR 368
                                    4555555666666.555552.....5666.4555465455.88*******99855333323322455554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   2.2e-10   2.2e-07      18      58 ..      10      50 ..       6      64 .. 0.89
   2 ?    0.6   0.0      0.27   2.7e+02      13      49 ..     176     211 ..     169     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.2e-10
                                   EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS--TTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailersvspGGGaw 58
                                    DvvivGaG sGL aay + ++ p+l  +iler+  +GG +w
  gi|121636483|ref|YP_976706.1| 10 VDVVIVGAGISGLGAAYRIIERnPQLTYTILERRARIGG-TW 50
                                   6***************9887766***********99986.44 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                                    HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4  13 lkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                                    l+y    +v++G+G++ +t    l+ +   kv++l r
  gi|121636483|ref|YP_976706.1| 176 LDYTGKKIVVIGSGATAVTLIPSLTDR-AEKVTMLQR 211
                                    6899999********999988888877.667777665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0033       3.3       3      38 ..      10      45 ..       8      51 .. 0.72
   2 !   22.8   0.0   4.5e-08   4.5e-05     109     236 ..      99     225 ..      84     242 .. 0.81
   3 ?   -1.8   0.0       1.3   1.3e+03     211     245 ..     256     290 ..     250     296 .. 0.83
   4 ?   -2.6   0.0       2.4   2.4e+03     328     340 ..     336     348 ..     324     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                    K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                   +D++++G+G s L+ a ++ e++ +l+   ler+ +
  gi|121636483|ref|YP_976706.1| 10 VDVVIVGAGISGLGAAYRIIERNPQLTYTILERRAR 45
                                   577777777777777777777777777777777765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 4.5e-08
                    K_oxygenase 109 leeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvG....tepkiPevleklegkervvHsseyler 184
                                    ++ +++f++ v++ ++d+++  + +tv+  +++g ++++++r +  g G     e + P++    +    vvH ++  e+
  gi|121636483|ref|YP_976706.1|  99 IDRHIEFNSYVRAADWDSST--DTWTVTF-EQNGVHKHYRSRFVFFGSGyynyDEGYTPDFGGIEKFGGAVVHPQHWPED 175
                                    57889*************97..5799998.689****************655557899*9955444458********999 PP

                    K_oxygenase 185 keellakkriaVvGsGqSaaeifedllrrqkkvelklvtrseal..eplddspf 236
                                       + ++k+i+V+GsG +a  ++  l++r++  +++++ rs+ +   ++ +s f
  gi|121636483|ref|YP_976706.1| 176 L--DYTGKKIVVIGSGATAVTLIPSLTDRAE--KVTMLQRSPTYliSASKYSTF 225
                                    8..89***********************998..788888887651145555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.3
                    K_oxygenase 211 lrrqkkvelklvtrsealeplddspfvneifsPey 245
                                    l+r++ v +k+++r++a++ l +   +  +f+P y
  gi|121636483|ref|YP_976706.1| 256 LSRKTPVFVKWLLRRTAIKNLPEGYDIETHFTPRY 290
                                    556666889***********999999999999988 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.4
                    K_oxygenase 328 tlevdavvlATGY 340
                                     l++d++v+ATG 
  gi|121636483|ref|YP_976706.1| 336 HLDADIIVTATGL 348
                                    6899********5 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0049       4.9       2      35 ..      12      47 ..      11      51 .. 0.80
   2 !   16.4   0.0     1e-05      0.01       1      35 [.     182     216 ..     182     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                                   EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                   vv+vG+G +gl +A  + e +     t++er+ ++ 
  gi|121636483|ref|YP_976706.1| 12 VVIVGAGISGLGAAYRIIERNpqLTYTILERRARIG 47
                                   8*************9995555326679999998886 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1e-05
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                    k+vv+G+G +++ l   l++ + kVt+++rs++ l
  gi|121636483|ref|YP_976706.1| 182 KIVVIGSGATAVTLIPSLTDRAEKVTMLQRSPTYL 216
                                    79*****************************9988 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.011       1      46 [.      13      54 ..      13     131 .. 0.80
   2 ?    3.8   0.3     0.053        53     126     154 ..     319     347 ..     184     349 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdq 46
                                   +ivGaG++Gl ++ r+++r     +l+ t+ +++    g+ w+  +
  gi|121636483|ref|YP_976706.1| 13 VIVGAGISGLGAAYRIIER---NPQLTYTILERRARI-GGTWDLFR 54
                                   7******************...599********8887.78887655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.053
                  NAD_binding_9 126 dleeradgqavlladgaslaadaVvLAlG 154
                                    d  ++ d   + l++g +l+ad +v A+G
  gi|121636483|ref|YP_976706.1| 319 DHIDHFDATGIALKSGGHLDADIIVTATG 347
                                    22222233456777777777777777777 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0016       1.6       3      39 ..      10      46 ..       8      49 .. 0.91
   2 !    7.1   0.0    0.0017       1.7     196     240 ..     101     144 ..      79     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                            Mqo  3 vdvvliGaGimsatlgvllkelepelsievlerldkv 39
                                   vdvv++GaGi     +  + e +p+l+ ++ler  ++
  gi|121636483|ref|YP_976706.1| 10 VDVVIVGAGISGLGAAYRIIERNPQLTYTILERRARI 46
                                   7*********999999999999**********98876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0017
                            Mqo 196 velklkhevkdlkre.edgkWkvkvkdlktgekkkvkakfvfiGaG 240
                                     ++++++ v+  + + ++++W+v+++  ++g +k+++++fvf G+G
  gi|121636483|ref|YP_976706.1| 101 RHIEFNSYVRAADWDsSTDTWTVTFE--QNGVHKHYRSRFVFFGSG 144
                                    35777778877764415579*****9..6788899*********99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     2e-05      0.02       1      32 [.      11      44 ..      11      52 .. 0.75
   2 ?   -2.6   0.0       2.2   2.2e+03       2      14 ..     183     195 ..     182     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                                   SEEEE--SHHHHHHHHHHHHTTT..-EEEEESSS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl..kvavvekeq 32
                                   Dv+++G+G++GL AA+++ e++   + +++e   
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIIERNPqlTYTILERRA 44
                                   9****************99965313555665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                                    EEEE--SHHHHHH CS
                  FAD_binding_2   2 viViGsGlAGLaA 14 
                                    ++ViGsG+   + 
  gi|121636483|ref|YP_976706.1| 183 IVVIGSGATAVTL 195
                                    79*****976665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00015      0.14       1      32 [.      11      42 ..      11      52 .. 0.91
   2 ?    0.6   0.0      0.23   2.3e+02       2      37 ..     183     216 ..     182     228 .. 0.74
   3 ?   -2.8   0.0       2.4   2.4e+03     115     143 ..     322     350 ..     307     360 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                   Dvv++GaG  gl  A r++e +p+l  +++e 
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIIERNPQLTYTILER 42
                                   9*************************999986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.23
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                    +vviG+G+  + l   lt+ +   kv++++ sp  l
  gi|121636483|ref|YP_976706.1| 183 IVVIGSGATAVTLIPSLTDRAE--KVTMLQRSPTYL 216
                                    89***************66555..556666666554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.4
                  Lycopene_cycl 115 eeageslvvleggrkirarlvvdarglas 143
                                    +++  + ++l+ g +++a ++v a+gl  
  gi|121636483|ref|YP_976706.1| 322 DHFDATGIALKSGGHLDADIIVTATGLQL 350
                                    34455778999999999999999999754 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.79   7.8e+02      13      37 ..      10      34 ..       2      45 .. 0.74
   2 ?   10.9   0.0   0.00035      0.35      10      46 ..     178     213 ..     172     225 .. 0.89
   3 ?   -2.2   0.0       3.8   3.8e+03      75      86 ..     338     349 ..     336     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.79
                                   -EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvk 37
                                     v+++GaG  +  +a  +++++ +
  gi|121636483|ref|YP_976706.1| 10 VDVVIVGAGISGLGAAYRIIERNPQ 34
                                   579******9998888887777654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                                    .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                   Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                    +++kk+++iG G +a  ++  L   +++kv+ + R+ 
  gi|121636483|ref|YP_976706.1| 178 YTGKKIVVIGSGATAVTLIPSLT-DRAEKVTMLQRSP 213
                                    6799******************9.67788**999986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.8
                                    T-SEEEE-SSSS CS
                   Shikimate_DH  75 eadvvisatase 86 
                                    +ad++++at+ +
  gi|121636483|ref|YP_976706.1| 338 DADIIVTATGLQ 349
                                    58*******866 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011       0.1       1      29 [.      19      49 ..      19      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHTT..EEEEEEESSSSSBTT CS
                  Amino_oxidase  1 laGLaaArqLlsaG..fdVtvlEardrvGGR 29
                                   ++GL aA++  +++  +  t+lE r r+GG 
  gi|121636483|ref|YP_976706.1| 19 ISGLGAAYRIIERNpqLTYTILERRARIGGT 49
                                   8*************9***************5 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.1   5.1e+03      10      29 ..      12      31 ..      10      38 .. 0.78
   2 ?   11.7   0.0   0.00027      0.27       4      40 ..     177     213 ..     176     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.1
                  NAD_binding_7 10 vlvvGgGevAarkvrkllea 29
                                   v++vG+G  ++  +++++e 
  gi|121636483|ref|YP_976706.1| 12 VVIVGAGISGLGAAYRIIER 31
                                   89*****9888888777776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00027
                  NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                    d +gkk++v+G G  A + + +l +   kvt++    
  gi|121636483|ref|YP_976706.1| 177 DYTGKKIVVIGSGATAVTLIPSLTDRAEKVTMLQRSP 213
                                    789****************************986654 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00022      0.22       1      37 [.      11      49 ..      11      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGa..kvlLveergvlGGl 37
                                   Dvv+vG+g++G+ AA+   ++    +  ++e+r ++GG+
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIIERNPqlTYTILERRARIGGT 49
                                   9**************998877642266899999999997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.002         2       1      20 [.      11      30 ..      11      41 .. 0.88
   2 ?    1.0   0.1      0.18   1.8e+02     126     150 ..     324     348 ..     308     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.002
                                   CEEEE-SSHHHHHHHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaaar 20
                                   dv+++G+G +G+ AA+ + +
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIIE 30
                                   79**************9865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                                    TEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 126 kkvkgvvtedgetikakavviatGt 150
                                       +g+ +++g ++ a+++v atG 
  gi|121636483|ref|YP_976706.1| 324 FDATGIALKSGGHLDADIIVTATGL 348
                                    4569********************6 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0013       1.3       2      36 ..      11      47 ..      10      49 .. 0.78
   2 ?   -0.8   0.0      0.47   4.6e+02       2      32 ..     182     212 ..     181     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                                   SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekakklg 36
                                   dv+++G+G +Gl aA ++  ++ +   ++le+  ++g
  gi|121636483|ref|YP_976706.1| 11 DVVIVGAGISGLGAAYRIieRNPQLTYTILERRARIG 47
                                   8***************994444556667888777766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.47
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllleka 32 
                                    +++viG Ga  +    s+ +r ++V++l + 
  gi|121636483|ref|YP_976706.1| 182 KIVVIGSGATAVTLIPSLTDRAEKVTMLQRS 212
                                    79*******9999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3048.78
//
Query:       gi|121636484|ref|YP_976707.1|  [L=163]
Description: nucleotide-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-62  209.6   6.4    3.1e-62  209.4   6.4    1.0  1  DUF520       Protein of unknown function (DUF520)
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.043   13.8   0.1    1.2  1  Microtub_bd  Microtubule binding


Domain annotation for each model (and alignments):
>> DUF520  Protein of unknown function (DUF520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.4   6.4   3.5e-66   3.1e-62       1     161 []       4     163 .]       4     163 .] 0.98

  Alignments for each domain:
  == domain 1  score: 209.4 bits;  conditional E-value: 3.5e-66
                         DUF520   1 psfDivsevdlqevknAvdqakkeistRfDfkgskaeielkekekeitltaesefklkqvkdilksklvkrgvdlkaldl 80 
                                    +sfDivs+vd+qev+nA++qa+ke++tRfDf+g++++i +k  +++++lt+++e+++k+ +d++k+kl++r+++lka+++
  gi|121636484|ref|YP_976707.1|   4 SSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKG-DEAVELTSSTEERVKAAVDVFKEKLIRRDISLKAFEA 82 
                                    59**************************************88.88*********************************** PP

                         DUF520  81 gkvekasgkkvkqevklkegidkekakkivklikdskl.kvqasiqgdevRvtgkkrDdLQaviallkkedldlplqftN 159
                                    g+ ++asgk++k +  lk+gi++e+akki+kli+d++   v+++iqgdevRvt+kkrDdLQavia+lkk+dld++lqf+N
  gi|121636484|ref|YP_976707.1|  83 GE-PQASGKTYKVTGALKQGISSENAKKITKLIRDAGPkNVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVN 161
                                    *9.99********************************967**************************************** PP

                         DUF520 160 fr 161
                                    +r
  gi|121636484|ref|YP_976707.1| 162 YR 163
                                    *9 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.8e-06     0.043      48     148 ..      39     141 ..       8     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-06
                                    TTEEEE-SEEEECTT.HCCCCCCCCHHHHHHHH.TT--EEEEEEES.................ST-HCHHHHHHHHHHCC CS
                    Microtub_bd  48 kkkefsFdrvfeses.eqeevfeeisqlvqsal.dgynvcifaygq.TGsGKtyTmegeeeeagmipraveeifetisel 124
                                    +k  ++ d  +e +s ++e v   + ++ +  + ++     f  g+   sGKty ++g   ++g   +  ++i++ i++ 
  gi|121636484|ref|YP_976707.1|  39 TKIAWKGDEAVELTSsTEERVKAAVDVFKEKLIrRDISLKAFEAGEpQASGKTYKVTG-ALKQGISSENAKKITKLIRDA 117
                                    5555555666665553555566666666665555555666666665237*********.88899999************* PP

                                    TSCCCCEEEEEEEEEEESS-EEET CS
                    Microtub_bd 125 kekgwkyeielqfveiynekvqDl 148
                                      k+ k +i++  v +  +k  Dl
  gi|121636484|ref|YP_976707.1| 118 GPKNVKTQIQGDEVRVTSKKRDDL 141
                                    ************999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1065.37
//
Query:       gi|121636485|ref|YP_976708.1|  [L=339]
Description: methyltransferase/methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-40  137.5   0.0      6e-40  136.8   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
      3e-13   49.5   0.0    9.5e-13   47.9   0.0    1.9  2  Dimerisation2    Dimerisation domain
    2.6e-07   30.4   0.0    4.3e-07   29.6   0.0    1.3  1  MTS              Methyltransferase small domain
    1.8e-06   28.6   0.1    3.9e-06   27.5   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    3.1e-06   27.9   0.0    5.7e-06   27.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    4.7e-06   27.2   0.1    8.5e-06   26.3   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00014   21.7   0.0     0.0002   21.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00014   21.7   0.0    0.00023   21.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0092   16.0   1.0      0.029   14.4   0.2    2.2  2  HTH_20           Helix-turn-helix domain
     0.0095   15.3   0.0      0.015   14.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.21   11.5   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
       0.12   12.9   0.0       0.35   11.4   0.0    1.8  1  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8   0.0     4e-43     6e-40       1     210 []     111     321 ..     111     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 4e-43
                                    HTTHHHHHHHTS--..HHHHHS--HHHHHTSSHHHHHHHHHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHH CS
                 Methyltransf_2   1 wseLadavregrnqiifkkafGislfeaikrdeeerakfnkglqessslvakkvleafdleglkslvDvGGGtGalakai 80 
                                    w++L++a++ g+ q    k  G++ fea + d++  + f++++   s+ + + + + f +e+ ++l+DvG   G l + +
  gi|121636485|ref|YP_976708.1| 111 WADLTEALKTGKAQ-SEVKQTGRPFFEALYADPRRLEAFMAAMDAASRRNIELLAKRFPFERYRRLCDVGCADGLLSRIV 189
                                    99**********99.445667*********************************************************** PP

                                    HHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS-----SEEEEESSGGGS-HHHHHHHHHHHHHH--TT CS
                 Methyltransf_2  81 vsayPtikvivfDlpeVveaAkehl.sageeervefvgGdffkdslPeaDaillkrvlhDwsdekcvklLkrvkkalpag 159
                                    ++a+P+++++ +Dlp V e A+++l   g+ erv+  +Gdf  d+lP aD+i + ++lhDw+ ++ ++l+++ ++al ++
  gi|121636485|ref|YP_976708.1| 190 AAAHPHLQCVSLDLPAVTEIARRKLtAEGLGERVQACAGDFLADPLPAADVITMGQILHDWNLDRKQQLVAKAYEALSKE 269
                                    *************************77899************************************************** PP

                                    -EEEEEE----TTS---HHHHHHHHHHHHC.SS-----HHHHHHHHHHCT-E CS
                 Methyltransf_2 160 Gkvivveavlgadpsgeletelvdlimlvq.teGkeRteaeyeellseaGfs 210
                                    G+ iv+e++++ +++++++  +++l+ml+   +  + ++a+++   +eaGf+
  gi|121636485|ref|YP_976708.1| 270 GAFIVIETLIDDARRENTTGLMMSLNMLIEfGDAFDYSAADFRGWCGEAGFR 321
                                    ******************************7788899**************6 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   6.4e-16   9.5e-13       2      88 ..       8      92 ..       7      94 .. 0.91
   2 ?   -3.6   0.0       7.8   1.2e+04      50      63 ..     173     186 ..     168     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 6.4e-16
                  Dimerisation2  2 llellnGFlaSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelasty 83
                                   ++ +  G+  Sk+L tA+ Lg+F  L + e ++ae++a++lg+  +    +lda+v+L+LL r+  ++ ++ Y+nt+ + ++
  gi|121636485|ref|YP_976708.1|  8 IMAIGGGYGPSKVLLTAVGLGLFTELGD-EAMTAEAIADRLGLLKRPAIDFLDALVSLDLLARD-GDGPGSHYRNTPETAHF 87
                                   6778889********************9.9****************999*************88.566679*********** PP

                  Dimerisation2 84 Lvsss 88
                                   L ++ 
  gi|121636485|ref|YP_976708.1| 88 LDEAR 92
                                   98765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.8
                  Dimerisation2  50 erLldacvaLgLLe 63 
                                    +rL+d+ +a gLL+
  gi|121636485|ref|YP_976708.1| 173 RRLCDVGCADGLLS 186
                                    68999999999997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.9e-10   4.3e-07      21     138 ..     161     275 ..     148     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.9e-10
                                    HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHH.HHHHHHHHHTTGC..EEEEE-STTTTSTTS- CS
                            MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAl.esakenleankle..vevvasdvleeveekk 97 
                                    +lL++ +p e+ +++ D+Gc  G+l+  +a+++p+  +++v  d  A+ e+a++ l+a++l   v++ a d l++     
  gi|121636485|ref|YP_976708.1| 161 ELLAKRFPFERYRRLCDVGCADGLLSRIVAAAHPH--LQCVSLDLPAVtEIARRKLTAEGLGerVQACAGDFLADPL-PA 237
                                    47777777779999*********************..788888888874689999999999888***********99.89 PP

                                    EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                            MTS  98 fdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliV 138
                                     d+i +   +h+ +    +  ++l+a+A eaL+++G ++++
  gi|121636485|ref|YP_976708.1| 238 ADVITMGQILHDWNL---DRKQQLVAKAYEALSKEGAFIVI 275
                                    9*****988887665...899****************9887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   2.6e-09   3.9e-06       3      97 .]     177     270 ..     175     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.6e-09
                                    EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSH CS
                Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.lhhlsd 79 
                                    d+Gc  G l++ +a++ ++ + + +D+ ++  e+ar+++ +egl  +v+   gd+ + p+++   D++++ g+ lh ++ 
  gi|121636485|ref|YP_976708.1| 177 DVGCADGLLSRIVAAAHPHLQCVSLDL-PAVTEIARRKLTAEGLgeRVQACAGDFLADPLPA--ADVITM-GQiLHDWNL 252
                                    9**************987899999998.7788************999999****99999886..9*****.886888999 PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                    ++ ++++++++++L ++G
  gi|121636485|ref|YP_976708.1| 253 DRKQQLVAKAYEALSKEG 270
                                    9999**********9988 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   3.8e-09   5.7e-06       2      98 ..     177     271 ..     176     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.8e-09
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.. 79 
                                    ++Gc +G l+r +++++p+++ + +D+ +     a++kl +++     +v+  a d l ++ + + D++++ + lh +  
  gi|121636485|ref|YP_976708.1| 177 DVGCADGLLSRIVAAAHPHLQCVSLDLPAVTE-IARRKLTAEGLGE--RVQACAGDFLADPLP-AADVITMGQILHDWnl 252
                                    8*************************966555.8999999998744..777777777666666.**************99 PP

                Methyltransf_12  80 kdirevldnirklLkpgGr 98 
                                    + +++++++++++L+++G 
  gi|121636485|ref|YP_976708.1| 253 DRKQQLVAKAYEALSKEGA 271
                                    9999***********9996 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   5.7e-09   8.5e-06       2      96 .]     177     274 ..     176     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.7e-09
                                    EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    dvGc  G+l++ +a +    ++v +Dl ++++++a++k   egl  +v+   +d+   p++    D++++ + lh +  +
  gi|121636485|ref|YP_976708.1| 177 DVGCADGLLSRIVAAAHphLQCVSLDL-PAVTEIARRKLTAEGLgeRVQACAGDFLADPLPA--ADVITMGQILHDWnlD 253
                                    9*************666789******6.88899***********999999999999889998..9************999 PP

                                    CHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                    + ++++++++  L ++G +++
  gi|121636485|ref|YP_976708.1| 254 RKQQLVAKAYEALSKEGAFIV 274
                                    *****************9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-07    0.0002       6     112 ..     174     277 ..     170     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevl 84 
                                    r++D+GC+ G l+   a  + p+ + v++D  + + e Ar ++   gl  +v+ ++gd+ + +  l     D+i+  ++l
  gi|121636485|ref|YP_976708.1| 174 RLCDVGCADGLLSRIVA-AAHPHLQCVSLDL-PAVTEIARRKLTAEGLGeRVQACAGDFLADP--LP--AADVITMGQIL 247
                                    68***************.999*********8.677899999999999988***********66..44..58********* PP

                Methyltransf_31  85 ..naladpdkileeiervlkpggilliedp 112
                                        l  +++   ++ ++l+++g++++ + 
  gi|121636485|ref|YP_976708.1| 248 hdWNLDRKQQLVAKAYEALSKEGAFIVIET 277
                                    665577889999999**********98764 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.5e-07   0.00023       9     161 ..     156     321 ..     144     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                Methyltransf_23   9 lsdklerllpk..lraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiaekakkaqkdqfdeq.....eaaep 79 
                                     ++++e l+++   ++  r++d+Gc++G l+++  +++++ +++  Dl p+  eia+ + +a+   ++ q     + a+p
  gi|121636485|ref|YP_976708.1| 156 SRRNIELLAKRfpFERYRRLCDVGCADGLLSRIVaAAHPHlQCVSLDL-PAVTEIARRKLTAEGLGERVQacagdFLADP 234
                                    467888777655457777**************995555668*******.8889999966666655555554444457788 PP

                Methyltransf_23  80 qgkfdlIvlrevlehvp.d.ppellrqiatllkpgGylllseplaslkedrllldwlylvpag.rhi..sffsarslkel 154
                                        d+I++ + l+    d    l++++++ l+ +G +++ e l ++++++      +  ++  + +    +sa +++ +
  gi|121636485|ref|YP_976708.1| 235 LPAADVITMGQILHDWNlDrKQQLVAKAYEALSKEGAFIVIETLIDDARRENTTGLMMSLNMLiEFGdaFDYSAADFRGW 314
                                    88************88774599999***9999977666666655555433332222222222233332145688889999 PP

                Methyltransf_23 155 leeaGle 161
                                    + eaG++
  gi|121636485|ref|YP_976708.1| 315 CGEAGFR 321
                                    9998886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   1.9e-05     0.029       7      60 ..      21      73 ..      18      74 .. 0.83
   2 ?   -1.3   0.0       1.5   2.3e+03      14      35 ..     133     153 ..     130     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                   HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   L+  v ++++ +L ++e++ta+++a+rl+l k  + + L++L++ +L+ + + g
  gi|121636485|ref|YP_976708.1| 21 LLTAVGLGLFTEL-GDEAMTAEAIADRLGLLKRPAIDFLDALVSLDLLARDGDG 73
                                   55566689999**.***************8888888889999999999887766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                    HHHHHHSTCTTB-HHHHHHHHT CS
                         HTH_20  14 rilraLaraegltaselaerld 35 
                                     ++ aL  a+++ ++++++++d
  gi|121636485|ref|YP_976708.1| 133 PFFEAL-YADPRRLEAFMAAMD 153
                                    577788.888888888888776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     1e-05     0.015      42     179 ..     151     289 ..     140     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                    -HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHH.HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES- CS
                           CMAS  42 tLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrr.averydvkvvglTlSkeqaklakkrvdeldlerkvevklld 120
                                     +++A ++ ++l+ ++   +   +l d+Gc  G l r  a+++   + v+l l +  ++ a++++ +++l ++v+    d
  gi|121636485|ref|YP_976708.1| 151 AMDAASRRNIELLAKRFPFERYRRLCDVGCADGLLSRIvAAAHPHLQCVSLDLPA-VTEIARRKLTAEGLGERVQACAGD 229
                                    6899999**************************9987614445578888888876.5789999***************** PP

                                    GGG-----SEEEEES-GGG.TSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTT CS
                           CMAS 121 yedldekvdrvvsvgafeh.vgkenydtffkklkkllkedGllllhtitslhkkelaerg 179
                                    +   + +   v+++g + h    ++ ++ ++k++++l ++G +++    + + +  +++g
  gi|121636485|ref|YP_976708.1| 230 FLADPLPAADVITMGQILHdWNLDRKQQLVAKAYEALSKEGAFIVIETLIDDARRENTTG 289
                                    *8877788889999877663799******************9987665555555555454 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.21      15      87 ..     172     242 ..     162     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                     +r++D+G+  g+l+  ++  +   +++  D+ +   e a+++++ +gl ++++++ +d l+   +  +d+++
  gi|121636485|ref|YP_976708.1| 172 YRRLCDVGCADGLLSRIVAAAHPHLQCVSLDL-PAVTEIARRKLTAEGLGERVQACAGDFLADPLPA-ADVIT 242
                                    5699***************************9.5689**********************99887655.56655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.35      16      67 ..      35      83 ..      20      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                         HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                   ++ ++++++++rl + + +++  l++L+  +L+ r g   d+  +++r T++
  gi|121636485|ref|YP_976708.1| 35 DEAMTAEAIADRLGLLKRPAIDFLDALVSLDLLARDG---DGPGSHYRNTPE 83
                                   677888***************************5554...557788888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2376.21
//
Query:       gi|121636486|ref|YP_976709.1|  [L=472]
Description: cytochrome p450 135b1 cyp135B1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-62  211.2   0.0      3e-62  210.9   0.0    1.1  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   0.0   1.7e-66     3e-62       2     458 ..      11     433 ..      10     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 1.7e-66
                                    -SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETT.EEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHH CS
                           p450   2 pgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgs.kpvvvlsgpeavkevlikkgeefsgrpdeallatsrk 80 
                                    pgp+    v  +l l+   +  ++l+ +q++yg++f+l++ +  ++v+ls+p a+k v+  + + f +   +++la    
  gi|121636486|ref|YP_976709.1|  11 PGPRLSGSVQAVLMLR---HGLRFLTACQRRYGSVFTLHVAGfGHMVYLSDPAAIKTVFAGNPSVFHAGEANSMLAG--- 84 
                                    5554444444455554...456779*************9866499*****************988888777778886... PP

                                    TTTTSSSTTCGHHHHHHHHHHHHHHHTSH.STTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHS CS
                           p450  81 pfkgkgvlfangekwkklRrfltptltsf.gklsleelveeeaedlveklrkkagesselditellskaaldvigsilFg 159
                                         ++l+ + + ++  Rr++ p ++ +  +++ e+ + e+a+  ++ +   + ++    +++ +s+++l+vi +++ g
  gi|121636486|ref|YP_976709.1|  85 LLGDSSLLLIDDDVHRDRRRLMSPPFHRDaVARQAEP-IAEIAAANIAGWPMAKAFA----VAPKMSEITLEVILRTVIG 159
                                    778889999999***************9933334444.4445555555555555555....9****************** PP

                                    SHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSC CS
                           p450 160 arfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrr 239
                                    a+    +  +l  l k++ +l+ ++  ++  l l  p l  l ++l+ +l++  ++++ ll + i +rr++ d a   r 
  gi|121636486|ref|YP_976709.1| 160 AS----DPVRLAALRKVMPRLL-NV-GPWATLALANPSL--LNNRLWSRLRRRIEEADALLYAEIADRRADPDLA--ART 229
                                    *7....3444556666666665.44.5899999999944..6999999999999999******************..9** PP

                                    SHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHC.CTTTT-HHHHC CS
                           p450 240 dfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevl.gdkreptyddl 318
                                    d l+ l+ a  +++g+ +++++el+ ++++ll+aG+dTt+++lswaL  L ++P + +k  +  d    gd         
  gi|121636486|ref|YP_976709.1| 230 DTLAMLVRAA-DEDGR-TMTERELRDQLITLLVAGHDTTATGLSWALERLTRHPVTLAKAVQAADASAaGD--------P 299
                                    *********6.99998.******************************************999999888455........3 PP

                                    CT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESS CS
                           p450 319 qklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrk 398
                                    +  +yldav kEtLR++pvv+  + R++t+ v++ gy +p+G +v++ ++ +h + +++p+Pe+Fdp+R   ++     +
  gi|121636486|ref|YP_976709.1| 300 AGDEYLDAVAKETLRIRPVVY-DVGRVLTEAVEVAGYRLPAGVMVVPAIGLVHASAQLYPDPERFDPDRMVGAT----LS 374
                                    4448*****************.************************************************9996....58 PP

                                    CTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEESSCSSEEESSS CS
                           p450 399 sfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpppileksglllppkp 458
                                    +  +lPFG G R C+G  +A++e++++l  +L++ e+++   + ++p+l+   +++p ++
  gi|121636486|ref|YP_976709.1| 375 PTTWLPFGGGNRRCLGATFAMVEMRVVLREILRRVELSTTTTSGERPKLKH-VIMVPHRG 433
                                    ***************************************888888888876.56666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3173.24
//
Query:       gi|121636487|ref|YP_976710.1|  [L=88]
Description: hypothetical protein BCG_0614 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-27   94.0   0.6    4.3e-27   93.5   0.6    1.2  1  DUF1918   Domain of unknown function (DUF1918)


Domain annotation for each model (and alignments):
>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.6   2.4e-31   4.3e-27       1      58 []       1      58 [.       1      58 [. 0.99

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.4e-31
                                   ----TTEEEEES-TTTS--EEEEEEEE-S-SSS-S-EEEEETTTTEEEEE---SS-EE CS
                        DUF1918  1 MkAkvGDrlvvegrtvgepereGeiveVrgedGaPPYlVRweddgheslvfPGpDaeV 58
                                   MkAkvGD+lv++g t+++p+++G i+eVr++dG+PPY+VRw +++h+++v+PGpDa+V
  gi|121636487|ref|YP_976710.1|  1 MKAKVGDWLVIKGATIDQPDHRGLIIEVRSSDGSPPYVVRWLETDHVATVIPGPDAVV 58
                                   9*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 639.42
//
Query:       gi|121636488|ref|YP_976711.1|  [L=710]
Description: ribonucleoside-diphosphate reductase large subunit nrdZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.7e-134  446.9   0.0   1.7e-103  347.0   0.0    2.1  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    8.7e-20   70.5   0.1    2.2e-19   69.2   0.0    1.8  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
      1e-15   58.1   0.0    2.1e-15   57.0   0.0    1.6  1  ATP-cone         ATP cone domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.0   0.0  2.8e-107  1.7e-103       2     353 ..     192     506 ..     191     510 .. 0.96
   2 !   98.2   0.0   7.1e-32   4.3e-28     381     500 ..     510     631 ..     505     638 .. 0.94

  Alignments for each domain:
  == domain 1  score: 347.0 bits;  conditional E-value: 2.8e-107
                                    EE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC   2 sCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAam 81 
                                     Cfvl +edsl+sI+ t+ +aa+l +aggG+G+ +s+lR+ g+ v++t+g+asGpvsf++l+d+ a vv+ gG+RrGA m
  gi|121636488|ref|YP_976711.1| 192 GCFVLPIEDSLQSIFATLGQAAELQRAGGGTGYAFSHLRPAGDRVASTGGTASGPVSFLRLYDSAAGVVSMGGRRRGACM 271
                                    5******************************************************************************* PP

                                    XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC  82 vylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeeeyeeleek 161
                                    ++l+v+HpDi +f++aK++       +l ++n+svgv+d F++av++++   L++Prt +                    
  gi|121636488|ref|YP_976711.1| 272 AVLDVSHPDICDFVTAKAE----SPSELPHFNLSVGVTDAFLRAVERNGLHRLVNPRTGK-------------------- 327
                                    *****************44....578*******************************322.................... PP

                                    ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 162 akikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfv 241
                                      i   +++a eLf++i ++a++ g+Pg++f DtiNr+n++     g+I+atN+CgE+pll+yes   CnL+sinLa+++
  gi|121636488|ref|YP_976711.1| 328 --I-VARMPAAELFDAICKAAHAGGDPGLVFLDTINRANPV--PGRGRIEATNPCGEVPLLPYES---CNLGSINLARML 399
                                    ..2.2489*********************************..6669******************...************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 242 kkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfarki 321
                                          + ++dwd+l++v  ++vr+Ld+vidv++yp+pe  ++++ tR+iGlGvmgla++la+lgipydseea+++a ++
  gi|121636488|ref|YP_976711.1| 400 -----ADGRVDWDRLEEVAGVAVRFLDDVIDVSRYPFPELGEAARATRKIGLGVMGLAELLAALGIPYDSEEAVRLATRL 474
                                    .....468************************************************************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 322 telltyyaykaSvelAkergpfplfekskysk 353
                                    ++ ++ +a +aS +lA+erg+fp f  s++++
  gi|121636488|ref|YP_976711.1| 475 MRRIQQAAHTASRRLAEERGAFPAFTDSRFAR 506
                                    *************************9999875 PP

  == domain 2  score: 98.2 bits;  conditional E-value: 7.1e-32
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                Ribonuc_red_lgC 381 lrnamvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkkiles..vqgleeip 458
                                     rna+vt++aPTg+iSliagt+ gieP+fa ++++  +   +levnp f +  +++g +++el ++i ++  v g +++p
  gi|121636488|ref|YP_976711.1| 510 RRNAQVTSVAPTGTISLIAGTTAGIEPMFAIAFTRAIVGRHLLEVNPCFDRLARDRGFYRDELIAEIAQRggVRGYPRLP 589
                                    69***********************************999***************************55556******** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 459 eeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpne 500
                                     e+++ f ta +i +++h+++qaa+q+++  ++Skt+nlp +
  gi|121636488|ref|YP_976711.1| 590 AEVRAAFPTAAEIAPQWHLRMQAAVQRHVEAAVSKTVNLPAT 631
                                    ***************************************765 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.5     9e+03      27      44 ..      23      40 ..      21      54 .. 0.70
   2 !   69.2   0.0   3.7e-23   2.2e-19       2      83 .]     108     188 ..     107     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                Ribonuc_red_lgN 27 spqqmfmRvAlalaiaea 44
                                   +++    R A+ +a+ + 
  gi|121636488|ref|YP_976711.1| 23 RIEAAVTRAAREVACDDP 40
                                   567778888888888664 PP

  == domain 2  score: 69.2 bits;  conditional E-value: 3.7e-23
                Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGte 81 
                                    kl+++a+ vl++rYll de+g+++Es  +++ R A+ +a ae +y +  + + +ae+f  l+ +++flp+sPtlmn+Gt+
  gi|121636488|ref|YP_976711.1| 108 KLSLAAVTVLRERYLLHDEQGRPAESTGELMDRSARCVAAAEDQY-EPGSSRRWAERFATLLRNLEFLPNSPTLMNSGTD 186
                                    7899***************************************99.5667777**************************9 PP

                Ribonuc_red_lgN  82 lg 83 
                                    lg
  gi|121636488|ref|YP_976711.1| 187 LG 188
                                    86 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   3.6e-19   2.1e-15       2      85 ..       8      92 ..       7      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.6e-19
                                   EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHH CS
                       ATP-cone  2 kViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdg.isteeIqdlvektliehpdyavaaayilyrn 82
                                   kV++RdGt +pfd+ +I++a+++A++++  +  ++  +v++ v + l +g  ++e+Iqd+ve  l e++  +va+ yi+yr+
  gi|121636488|ref|YP_976711.1|  8 KVRRRDGTLVPFDIARIEAAVTRAAREVACDDPDMPGTVAKAVADALGRGiAPVEDIQDCVEARLGEAGLDDVARVYIIYRQ 89
                                   79*************************5555555555666666777666659****************************** PP

                                   HHH CS
                       ATP-cone 83 lrk 85
                                    r 
  gi|121636488|ref|YP_976711.1| 90 RRA 92
                                   997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4925.23
//
Query:       gi|121636489|ref|YP_976712.1|  [L=443]
Description: hypothetical protein BCG_0616c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-20   71.2   0.1    1.1e-19   70.5   0.1    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
    5.3e-08   32.4   0.0    0.00065   19.0   0.0    2.5  2  Hydrolase_4     Serine aminopeptidase, S33
    1.8e-05   24.4   0.0    4.4e-05   23.1   0.0    1.6  1  DLH             Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.062   13.5   0.0       0.15   12.3   0.0    1.6  1  AAA_33          AAA domain
       0.07   12.7   0.0       0.12   12.0   0.0    1.3  1  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
      0.072   13.1   0.2       0.14   12.2   0.2    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
      0.087   12.3   0.0       0.15   11.4   0.0    1.3  1  UPRTase         Uracil phosphoribosyltransferase
      0.091   12.3   0.2       0.16   11.5   0.2    1.4  1  AA_kinase       Amino acid kinase family


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.1   4.8e-23   1.1e-19      14     156 ..       9     193 ..       2     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 4.8e-23
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...................... CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.............. 79 
                                    ++ r +a++l +  gk +vv+g +rgGvp+a ++a+ L +pl+++ ++k   + ++e a g++ e               
  gi|121636489|ref|YP_976712.1|   9 DAGRQLAQRLAQLSGKAVVVLGLPRGGVPVAFEVAKSLQAPLDVLVVRKLGVPFQPELAFGAIGEDgvrvlnddvvrgth 88 
                                    4455566666777****************************************************9************** PP

                                    ...........................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                   Pribosyltran  80 ...........................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                                               r+ + + g++ +iVDD+++tG T +aa++  +++g+ +v +av++ + + + +
  gi|121636489|ref|YP_976712.1|  89 ldaaamdaverkqlielqrraerfrrgRDRIPLTGRIAVIVDDGIATGATAKAACQVARAHGADKVVLAVPIGPDDIVAR 168
                                    ******************************************************************************** PP

                                    HHHH-TTS......EEEEEEE-SEE CS
                   Pribosyltran 133 vdknakrvfsls.pdnfvavvgfel 156
                                       +a++v++l  p  f av + + 
  gi|121636489|ref|YP_976712.1| 169 FAGYADEVVCLAtPALFFAVGQGYR 193
                                    ************9999988888765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.9e-07   0.00065       2     105 ..     251     357 ..     250     362 .. 0.85
   2 !   10.9   0.0   9.1e-05       0.2     189     233 ..     372     414 ..     364     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.9e-07
                    Hydrolase_4   2 epkavvvlvHGlae..hsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel..p 77 
                                    +p+++vvl+HG ++  hs r   +ae L+ +Gfa++ +D     ++e +r+ v +++ +   l  ++  ++++  ++  p
  gi|121636489|ref|YP_976712.1| 251 KPRGIVVLAHGSGSsrHSIRNRYVAEVLTGAGFATLLFDLLT-PEEERNRANVFDIELLASRLIDVTGWLATQPDTAslP 329
                                    89********9885448999999*****************94.555699999999999999999998777644444457* PP

                    Hydrolase_4  78 lfllGhSmGGliallyllrypdkvagli 105
                                    +  +G S+G+  al ++++ + +v++++
  gi|121636489|ref|YP_976712.1| 330 VGYFGASTGAGAALVAAADPRVNVRAVV 357
                                    *****************99999999887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.1e-05
                    Hydrolase_4 189 kitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                    ++ +P+ll+ G++D+vv + ++r + + ++  +++l++ pg+ H 
  gi|121636489|ref|YP_976712.1| 372 SVVAPTLLIVGGRDQVVLELNQR-AQAVIP-GKCQLTVVPGATHL 414
                                    5679**************66664.344444.59**********94 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     2e-08   4.4e-05       2     200 ..     243     426 ..     242     434 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2e-08
                            DLH   2 daylatpknakkpvvvviqeifGvn...dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekv 78 
                                    +++l  p+++   ++vv+    G        + ++e l  +G++ l+ dl++ ++     e+++a+++       + e +
  gi|121636489|ref|YP_976712.1| 243 AGHLTVPEKP--RGIVVLAHGSGSSrhsIRNRYVAEVLTGAGFATLLFDLLTPEE-----ERNRANVF-------DIELL 308
                                    6789999999..999999999999974423346999**************99888.....66666666.......22456 PP

                            DLH  79 lddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYGlspekeleeaakikapilalfgeeDef 157
                                     ++l +   +l+++p++ +  vg  G   G+  al+ aa     v a+v+  G +p+   +    + ap l ++g++D++
  gi|121636489|ref|YP_976712.1| 309 ASRLIDVTGWLATQPDTASLPVGYFGASTGAGAALVAAADPrVNVRAVVSRGG-RPDLAGDSLGSVVAPTLLIVGGRDQV 387
                                    667778889**************************999999667788888777.*************************9 PP

                            DLH 158 ipadevekleealkaanvdlelkvYpgagHaFandsresynee 200
                                    +     ++ ++a+     +++l v pga+H F ++   + +++
  gi|121636489|ref|YP_976712.1| 388 VLEL--NQRAQAV--IPGKCQLTVVPGATHLFEEPGTLEQVAK 426
                                    9876..4555666..3668999999*******99876665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.5e-05      0.15      25     115 ..      76     169 ..      66     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                         AAA_33  25 avllssdtlrrrlfg...tdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvri 101
                                    + +l+ d++r ++      d    ++++++  r+ ++ +++ r+ l+ +++vi+d + ++ ++ ++ +++ar +g+   +
  gi|121636489|ref|YP_976712.1|  76 VRVLNDDVVRGTHLDaaaMDAVERKQLIELQRRAERFRRGRDRIPLTGRIAVIVDDGIATGATAKAACQVARAHGADKVV 155
                                    556888888887766566334445578889999999999999999******************************99888 PP

                         AAA_33 102 vvvetdeetlkeRl 115
                                    ++v   ++ + +R 
  gi|121636489|ref|YP_976712.1| 156 LAVPIGPDDIVARF 169
                                    88877777777665 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.2e-05      0.12      87     140 ..     313     367 ..     309     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                  Peptidase_S15  87 advidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyd 140
                                     dv  Wla q + ++  Vg +G S ++  +l+aaa++   ++a+v+  +  dl+ 
  gi|121636489|ref|YP_976712.1| 313 IDVTGWLATQpDTASLPVGYFGASTGAGAALVAAADPRVNVRAVVSRGGRPDLAG 367
                                    68999*****999999***************************999877777665 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   6.3e-05      0.14      82     116 ..     122     156 ..     119     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                    TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEE CS
                 Pribosyl_synth  82 gGriaiivddliddvesfvaaaevlkerGaykiyv 116
                                    +Gria+ivdd i    +  aa +v +++Ga k++ 
  gi|121636489|ref|YP_976712.1| 122 TGRIAVIVDDGIATGATAKAACQVARAHGADKVVL 156
                                    8*******************************975 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.9e-05      0.15     121     158 ..     123     158 ..      95     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                        UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                                     r ++++D  iaTG++a aa+q+ + +g++  k++++ 
  gi|121636489|ref|YP_976712.1| 123 GRIAVIVDDGIATGATAKAACQVARAHGAD--KVVLAV 158
                                    45699*********************8874..666655 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   7.2e-05      0.16      80     179 ..      66     157 ..       5     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-05
                                    HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE- CS
                      AA_kinase  80 dalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgs 159
                                     a +++ge+ v+ l +  ++   l+aaa+da+e ++       + +++++a +    ++ +p ++ ++++ ++g  + g 
  gi|121636489|ref|YP_976712.1|  66 LAFGAIGEDGVRVLNDDVVRGTHLDAAAMDAVERKQ-------LIELQRRAERFRRGRDRIPLTGRIAVIVDDGI-ATGA 137
                                    6899**************************998777.......66666666666666678999999999999998.69** PP

                                    HHHHHHHHHHHCTSSEEEEE CS
                      AA_kinase 160 sDtiaallAealgAdkliil 179
                                    +  +a+ +A a gAdk++++
  gi|121636489|ref|YP_976712.1| 138 TAKAACQVARAHGADKVVLA 157
                                    *****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2931.37
//
Query:       gi|121636490|ref|YP_976713.1|  [L=113]
Description: hypothetical protein BCG_0617c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 805.36
//
Query:       gi|121636491|ref|YP_976714.1|  [L=463]
Description: nicotinate phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-39  135.2   0.0    1.5e-37  128.8   0.0    2.3  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N
    8.4e-12   45.2   0.0    1.3e-11   44.6   0.0    1.2  1  NAPRTase    Nicotinate phosphoribosyltransferase (NAPRTase) f
    1.9e-06   27.7   0.0    2.7e-06   27.2   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
     0.0017   18.8   0.0     0.0037   17.7   0.0    1.5  1  NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal d


Domain annotation for each model (and alignments):
>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.0   3.3e-41   1.5e-37       1     124 [.      10     132 ..      10     133 .. 0.99
   2 ?    4.2   0.0     0.012        55       9      53 ..     199     247 ..     198     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 3.3e-41
                     NAPRTase_N   1 LdtDlYkltmaqavfkkgpdvevvfelffRkkpfkgeyaivagleevieylenlrfteeeieyLkrklpyfkedfleyLr 80 
                                    L+tDlY++tmaqa++ + +  ++vfe ffRk p +++y ++agl +v+e+le +rf+e++++yL+  l++f+++fl +L+
  gi|121636491|ref|YP_976714.1|  10 LFTDLYEVTMAQAYWAERMSGTAVFEIFFRKLPPGRSYIMAAGLADVVEFLEAFRFDEQDLRYLR-GLGQFSDEFLRWLA 88 
                                    79**************************************************************9.************** PP

                     NAPRTase_N  81 tfrfkpsevaveeeevvfpgepeirveGpwieaillEtplLaiv 124
                                     +rf+++++a++e++v+fp+ep ++  +p+iea+l+Et +L+ +
  gi|121636491|ref|YP_976714.1|  89 GVRFTGDVWAAPEGTVIFPNEPAVQLIAPIIEAQLVETFVLNQI 132
                                    *****************************************976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                     NAPRTase_N   9 tmaqavfkkgpdvevvfelffRkkpfkg....eyaivagleevieylen 53 
                                    tma  +++ +  + + fe f R  p +     +y+ + g+++vie  ++
  gi|121636491|ref|YP_976714.1| 199 TMAHSFVQAFDSEVAAFEAFARLYPATMllvdTYDTLRGVDHVIELAKR 247
                                    9***********************9554555588888899988887665 PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   2.8e-15   1.3e-11       4     195 ..     155     330 ..     153     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.8e-15
                                    EE-TSTTSSSHHHHHHHHHHHHHHHTTTEEEESBHHHHHHHT--B--HHHHHHHHHHHHHHCHHHHHCCHHH......HH CS
                       NAPRTase   4 hDFGtRrrsslesqeivvkalkkahlvnflGtdnvlaaakysikaaetsahealgkeqelsafrnnlkqfqk......da 77 
                                     DFG+Rr++  +++  v++      l    Gt+n+laa++y+i+  +t+ah++++++ +  a     + f++        
  gi|121636491|ref|YP_976714.1| 155 VDFGARRAHGTDAACKVAR---TSYLAGAAGTSNLLAARQYGIPTFGTMAHSFVQAFDSEVA---AFEAFARlypatmLL 228
                                    7*****************9...7799999**************************9865444...455555555324433 PP

                                    HHHHHHHHCCHIIEEECHCCTHHHHHCCS-CCHHHSEEEEE-SS-HHHHHHHHHHHHHCTCTTTCC.CSEEEEESS-SHH CS
                       NAPRTase  78 ldlwvaiekgnlgiaLtdlvltdaflkdfrleakaylgvRpDSGdpvevieklaahygstlnskgy.tkrlifsDgldve 156
                                    +d + ++ + +  i+L + ++ +               vR DSGd  e+ ++  a   +     g  ++ +  s gld +
  gi|121636491|ref|YP_976714.1| 229 VDTYDTLRGVDHVIELAKRLGNRFDV----------RAVRLDSGDLDELSKATRARLDTA----GLeQVEIFASSGLDEN 294
                                    33333333333455555555555444..........68*******888777777777666....665788888******* PP

                                    HHHHHHHHHHHTTCEEEEEESHHHHSSECTTCTTTCCEE CS
                       NAPRTase 157 kiieilealkkkgfniaFGiGtnltqdlnrdtlefavka 195
                                    +i ++l a         FG+Gt+l+   +  +l +a+k+
  gi|121636491|ref|YP_976714.1| 295 RIAALLAARCP---IDGFGVGTQLVVAQDAPALDMAYKL 330
                                    ***99976444...558*******977776667777765 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   6.1e-10   2.7e-06       2     167 ..     139     327 ..     138     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.1e-10
                                    HHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHH..HHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHHHH CS
                      QRPTase_C   2 AtltarmveaaksakvrildTRkttPglrllekyA..vliGGgd.......nhrlgLsdmvlikdnhiaaagsiveavks 72 
                                    A+++ar+v+aa++  v+ ++ R+ + g+ ++ k A   +++G++        + +g+    ++ +  ++a+ s v a ++
  gi|121636491|ref|YP_976714.1| 139 ASKAARVVAAARGRPVVDFGARRAH-GTDAACKVArtSYLAGAAgtsnllaARQYGIPTFGTMAHSFVQAFDSEVAAFEA 217
                                    899********************98.445554444225777777788999999*************************** PP

                                    HHHHHTTTSEEEEEES.SHHHHHHHHH........HT-SEEEEES--HHHHHHHHHHH.HHHSTT.SEEEEESS--TTTH CS
                      QRPTase_C  73 vreavdkevkieveve.sleeleevle........aeadiimLDnfsveelkkaveel.keknkr.vlievSGgvtlenv 141
                                    +    + ++ + v+++ +l  +++v+e          +  ++LD  + +el ka   + + +  + v+i++S g+ ++ +
  gi|121636491|ref|YP_976714.1| 218 FARLYPATM-LLVDTYdTLRGVDHVIElakrlgnrFDVRAVRLDSGDLDELSKATRARlDTAGLEqVEIFASSGLDENRI 296
                                    *******98.9***9538899*****98777775555999**************997744444447************** PP

                                    HHH..HCTT-SEEEECH...HCHTB----EE CS
                      QRPTase_C 142 eey..aksgvdvisvga...lthsvkalDis 167
                                    +++  a+  +d ++vg+   + + ++alD++
  gi|121636491|ref|YP_976714.1| 297 AALlaARCPIDGFGVGTqlvVAQDAPALDMA 327
                                    *983344568999999733356788888886 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.2e-07    0.0037      54     106 ..     379     433 ..     374     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.2e-07
                     NAPRTase_C  54 kLlkkvfkdGklvyel.psleeireyvkeqlaelrpehkRlln.PtpYkVslsek 106
                                    +Ll +++++G+++ ++ p+l+  r+++++q+++l+pe + l+     Y+V +s++
  gi|121636491|ref|YP_976714.1| 379 PLLVPIMTNGRRIRQHaPTLDGARDWARQQIDALPPELRSLEDtGYSYPVAVSDR 433
                                    89*********99765499******************998855156899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 3005.23
//
Query:       gi|121636492|ref|YP_976715.1|  [L=380]
Description: hypothetical protein BCG_0619c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-73  247.9   0.0    1.3e-73  247.6   0.0    1.1  1  PGA_cap   Bacterial capsule synthesis protein PGA_cap


Domain annotation for each model (and alignments):
>> PGA_cap  Bacterial capsule synthesis protein PGA_cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.6   0.0   7.4e-78   1.3e-73       1     257 []       9     291 ..       9     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 247.6 bits;  conditional E-value: 7.4e-78
                        PGA_cap   1 tlafvGDvmlgralkqalkeke.............................ydfdpifaevkpllraa..DlaivNlEtp 49 
                                    t++++GDvmlgr+++q+l++++                             +d++++++e++++l++   D+ ++NlEt+
  gi|121636492|ref|YP_976715.1|   9 TVLLGGDVMLGRGVDQILPHPGkpqlrerymrdatgyvrlaervngriplpVDWRWPWGEALAVLENTatDVCLINLETT 88 
                                    6899**************************************************************9999********** PP

                        PGA_cap  50 vteegeplsgk.plfrappevlaalkeagfdvvslAnNHalDygeeGlletlealdeagikhaGagrseaearkpailev 128
                                    +t++ge +++k +++r++p++++al++++  v++lAnNH+lD+g++Gl +t++al+ agi+++Gag+++ +ar+ a+++v
  gi|121636492|ref|YP_976715.1|  89 ITADGEFADRKpVCYRMHPDNVPALTALRPHVCALANNHILDFGYQGLTDTVAALAGAGIQSVGAGADLLAARRSALVTV 168
                                    ******************************************************************************** PP

                        PGA_cap 129 .kgirvallaytegtnstaeakagepnseeakeeeagaskerpgvaskdleklladirearkeadlvivslHwgeeyqek 207
                                     +++rv + +++        +++g+p+s++a++++ g+   r+  +++ +++++a++ + +++ d+ ivs+Hwg ++++ 
  gi|121636492|ref|YP_976715.1| 169 gHERRVIVGSVA-------AESSGVPESWAARRDRPGVWLIRDPAQRDVADDVAAQVLADKRPGDIAIVSMHWGSNWGYA 241
                                    778888888888.......677999************************************99***************** PP

                        PGA_cap 208 padeqrelaralidaGadvviGhhpHvlqgieiykgklifYSlGNfifdq 257
                                     a+  +++a++lidaG+d+v+Gh++H++++ieiy+gk+i+Y++G++++d+
  gi|121636492|ref|YP_976715.1| 242 TAPGDVAFAHRLIDAGIDMVHGHSSHHPRPIEIYRGKPILYGCGDVVDDY 291
                                    ***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2707.50
//
Query:       gi|121636493|ref|YP_976716.1|  [L=378]
Description: hypothetical protein BCG_0620c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-19   68.8   0.0    7.9e-19   68.1   0.0    1.3  1  FAD_binding_3  FAD binding domain
    0.00084   19.8   0.0     0.0037   17.8   0.0    2.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00085   19.5   0.7     0.0028   17.8   0.1    2.2  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.002   17.7   0.3      0.013   15.1   0.1    2.0  2  DAO            FAD dependent oxidoreductase
     0.0048   16.2   0.0     0.0083   15.4   0.0    1.5  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.018   14.7   0.1      0.028   14.0   0.1    1.3  1  ApbA           Ketopantoate reductase PanE/ApbA
       0.17   11.1   0.0        9.6    5.4   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   3.1e-22   7.9e-19       3     342 ..       2     332 ..       1     337 [. 0.78

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.1e-22
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                    +V+I GaG aG+ la+ L++ G   +++e+  +    +    +     ++ + +G+ d+i+a g   ++ +    ++  +
  gi|121636493|ref|YP_976716.1|   2 KVAISGAGVAGAALAHWLQRTGHTPTVIERAPKFRTGGYMIDFWGVGYQVAKRMGITDQIAAAG--YHMEHVRSVGP-TG 78 
                                    79*****************************999999888888888999***************..55544444444.22 PP

                                    CCEEEEEHH....CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEE CS
                  FAD_binding_3  83 tpkaradle....lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYl 158
                                      k++adl      +  + + t +p  +l  +++    e  +++ f+  + ++ ++ +gv+  ++ ++t  +   + + +
  gi|121636493|ref|YP_976716.1|  79 --KVKADLGvdvfRRMVGDDFTSLPRGDLAAAIYTT-IEDQVETIFDDSIATIDEHRDGVR--LTFERTAPR---DFDLV 150
                                    ..334443333657899******************9.566688888889998999999976..555665666...679** PP

                                    EE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC.CEEEEECCTTEEEEEECCETEEEEEEEEECCE-G CS
                  FAD_binding_3 159 vGaDGgrStvrktlgiefegeetvyeagvldvlfda.dlsdivep.lvlilsaesrgvmviPlentlerfyvqvearaek 236
                                    +GaDG +S vr+ +  + + +e+    +v+  ++d  + +   ++ +++++++ +r ++  +l+  +   ++++ +rae 
  gi|121636493|ref|YP_976716.1| 151 IGADGLHSNVRRLVFGPERDFEHYLGCKVAACVVDGyRPR---DErSYVLYNTVDRQLARFALRGDR--TMFLFVFRAEH 225
                                    ************9986666666565555555555553333...44799*****************44..45555555555 PP

                                    GGS...CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHH CS
                  FAD_binding_3 237 eer...sekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavn 313
                                    ++    ++++ +++  +   e+ ++ ++  ++e+     v+q  ++++++grv+l+GDAa + +  gG G  +ai  a+ 
  gi|121636493|ref|YP_976716.1| 226 DNPgvaPKDELRDQFGDVGWESRDILAALDDVEDLYFDVVSQIRMDRWSRGRVLLIGDAAGCISLLGGEGTGLAITEAYV 305
                                    55434455555555555555666666666688888888899999************************************ PP

                                    HHHHHHHHHTTSS-GGGGHHHHHHHHHHH CS
                  FAD_binding_3 314 LawkLaavlkGeAkeelLdtYeeerrava 342
                                    La  La +  G   ++  d+Ye++ r++ 
  gi|121636493|ref|YP_976716.1| 306 LAGELARA--GGDHRRAFDAYEKRLRPFI 332
                                    ******97..5577888999999988876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-06    0.0037       1      35 [.       2      36 ..       2      43 .. 0.93
   2 ?   -1.6   0.0       1.6   4.1e+03      50      76 ..     113     135 ..     103     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   kv++ G+G+ g  lA  l++ g+  tv+er++k++
  gi|121636493|ref|YP_976716.1|  2 KVAISGAGVAGAALAHWLQRTGHTPTVIERAPKFR 36
                                   799******************************99 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                    HHHTTEEEECSEEEEEEEEETTSEEEE CS
                      Pyr_redox  50 lekngievllntkveeiegsedgvesv 76 
                                    +e++ +e +++ +++ i+++ dg   v
  gi|121636493|ref|YP_976716.1| 113 IEDQ-VETIFDDSIATIDEHRDG---V 135
                                    4444.777888888888888887...3 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.1e-06    0.0028       3      34 ..       7      40 ..       5      51 .. 0.88
   2 ?   -2.6   0.0       2.6   6.6e+03      37      54 ..      70      91 ..      59     100 .. 0.66
   3 ?   -3.1   0.0       3.9     1e+04      12      28 ..     307     327 ..     297     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                   --SHHHHHHHHHHHCCTEEEEEE-SSSS..SSGG CS
                  NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllekrdr..lGGr 34
                                   GaG++G+++A+ L++ g+  +++e++++  +GG 
  gi|121636493|ref|YP_976716.1|  7 GAGVAGAALAHWLQRTGHTPTVIERAPKfrTGGY 40
                                   9************************997445665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                                   EECE...TT.CEECTS---EEE CS
                  NAD_binding_8 37 syev...pg.vrvdygahifhg 54
                                    ++     g v++d+g+ +f+ 
  gi|121636493|ref|YP_976716.1| 70 HVRSvgpTGkVKADLGVDVFRR 91
                                   4444443235889999988865 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.9
                                    HHHHHCC....TEEEEEE-SS CS
                  NAD_binding_8  12 AylLaka....gfdvlllekr 28 
                                    A +La+a    ++  + +ekr
  gi|121636493|ref|YP_976716.1| 307 AGELARAggdhRRAFDAYEKR 327
                                    444555333225567777776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.1e-06     0.013       2      32 ..       3      35 ..       2      41 .. 0.88
   2 ?    0.6   0.0      0.13   3.2e+02     150     229 ..     107     186 ..      74     300 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.1e-06
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                   v+i G+G++G++ A++L+r g   t++e+++ +
  gi|121636493|ref|YP_976716.1|  3 VAISGAGVAGAALAHWLQRTGhtPTVIERAPKF 35
                                   8999*************88899*******9765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                    HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE....EECTEEEEEEEEEEE--GGGHH..HHHTT.CTT...TSEEEE CS
                            DAO 150 aalaraaealGveilegtevtgleeedgkvwgve....rttpgendaadavVnaaGawsd..llgll.kel...dlpisp 219
                                    aa++ ++e++ ve ++   +  ++e++    gv+    rt+p     +d v+ a G++s+     l+ ++    ++   +
  gi|121636493|ref|YP_976716.1| 107 AAIYTTIEDQ-VETIFDDSIATIDEHR---DGVRltfeRTAPRD---FDLVIGADGLHSNvrR--LVfGPErdfEHY-LG 176
                                    4444444444.5444444555564442...23322233333332...4667777777776321..233222211222.44 PP

                                    EEEEEEEEEE CS
                            DAO 220 vrgqvlvlkp 229
                                    ++   +v++ 
  gi|121636493|ref|YP_976716.1| 177 CKVAACVVDG 186
                                    5555555544 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.2e-06    0.0083       2      58 ..       2      69 ..       1     164 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH......HCHHHHHHHHHHHHH.....H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx.....x RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll......skallgvaedaeias.....e 58
                                   +v++ G+G+AG a+a+ l++ g+  t++e+   + +gg ++      ++++ +++   +ia+     e
  gi|121636493|ref|YP_976716.1|  2 KVAISGAGVAGAALAHWLQRTGHTPTVIERAPKFRTGGYMIdfwgvgYQVAKRMGITDQIAAagyhmE 69
                                   89999***********************9666666666555333333555555555555555666662 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.1e-05     0.028       1      41 [.       3      40 ..       3      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCE CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGl 41
                                   +ai GaG  G  la+ L+++g+++t+i r +   ++++ G+
  gi|121636493|ref|YP_976716.1|  3 VAISGAGVAGAALAHWLQRTGHTPTVIERAP---KFRTGGY 40
                                   689**************************98...5555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0037       9.6       2      30 ..       5      32 ..       4      37 .. 0.89
   2 ?    3.5   0.0     0.014        36     222     274 ..     113     163 ..      86     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0037
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                   I GaG aG a a+ l++ g  + +++E++
  gi|121636493|ref|YP_976716.1|  5 ISGAGVAGAALAHWLQRTGH-TPTVIERA 32
                                   77*****************9.578**996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                    Pyr_redox_3 222 vkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsfl 274
                                    + e++++ +f+ ++  i+e+   +++++e+ +  +  d v+ a G +++++ l
  gi|121636493|ref|YP_976716.1| 113 I-EDQVETIFDDSIATIDEHRDGVRLTFER-TAPRDFDLVIGADGLHSNVRRL 163
                                    2.26799**********************9.5556677788889999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2538.51
//
Query:       gi|121636494|ref|YP_976717.1|  [L=434]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-27   94.5   0.1    9.3e-27   93.7   0.1    1.3  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
    1.2e-13   50.7   0.0    8.5e-13   48.0   0.0    2.1  2  HTH_5            Bacterial regulatory protein, arsR family
    2.2e-12   46.8   1.3    2.2e-12   46.8   1.3    2.3  3  HTH_20           Helix-turn-helix domain
    3.9e-10   40.2   2.9    1.3e-09   38.5   2.9    1.9  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.6e-05   24.7   1.8    1.6e-05   24.7   1.8    2.3  2  MarR_2           MarR family
    8.9e-05   22.3   0.0    0.00017   21.4   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00017   22.3   6.9    0.00017   22.3   6.9    3.8  3  MDMPI_N          Mycothiol maleylpyruvate isomerase N-termina
    0.00023   20.8   0.7     0.0006   19.4   0.7    1.7  1  GntR             Bacterial regulatory proteins, gntR family
     0.0026   17.5   1.5     0.0098   15.7   1.5    2.0  1  HTH_IclR         IclR helix-turn-helix domain
     0.0033   17.6   0.0     0.0064   16.6   0.0    1.4  1  HTH_34           Winged helix DNA-binding domain
     0.0079   16.1   0.2      0.017   15.1   0.2    1.6  1  HTH_11           HTH domain
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.024   15.0   0.1    1.6  1  Rrf2             Transcriptional regulator
      0.014   15.3   0.1      0.042   13.8   0.1    1.7  1  MarR             MarR family
      0.019   14.9   0.7      0.048   13.6   0.7    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.02   14.5   0.2      0.048   13.3   0.2    1.6  1  RP-C             Replication protein C N-terminal domain
      0.076   13.2   0.2       0.16   12.2   0.2    1.5  1  PaaX             PaaX-like protein
       0.21   11.8   0.0       0.46   10.7   0.0    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.34   11.1   4.6       0.17   12.0   1.1    2.4  2  DprA_WH          DprA winged helix domain
       0.42   10.7   2.2        0.6   10.2   0.6    2.2  1  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   9.9e-30   9.3e-27       4     121 ..     115     228 ..     112     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 9.9e-30
                                    HHHHHHHHH-HHHHHHHEEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSET..EEEEEEEE CS
                          AHSA1   4 perVfraltdpellkrWftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrledepe..eeestvti 81 
                                    p   f+ +t+p++l+rW +  +a+++lr+Gg++r+   +    +   g++++v+p +r+v+tw++ed+++  ++ stvti
  gi|121636494|ref|YP_976717.1| 115 PTSTFALITQPDRLRRW-MAVAARIELRTGGAYRW---TVTPGHSAAGTVIDVDPGKRVVFTWGWEDHGDppPGGSTVTI 190
                                    56679************.*****************...788999999*******************77667788****** PP

                                    EEEEETTEEEEEEEEEEEEHCHHHHHHHHHHHHHHHHHHH CS
                          AHSA1  82 eleeegggTrltlthtglprkqkeeegveeGweqsldqLk 121
                                    +l++++ggT+++l+h+gl+++q+++  +++Gw+++ld+L 
  gi|121636494|ref|YP_976717.1| 191 TLTPVDGGTEVRLVHDGLTAQQAAR--HAKGWNHFLDRLV 228
                                    *************************..9**********96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0     9e-16   8.5e-13       2      46 ..       8      52 ..       7      53 .. 0.98
   2 ?   -0.1   0.0      0.91   8.5e+02      15      25 ..     281     291 ..     280     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 9e-16
                                   HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   ptR+++L+lLa ge++v++la ++ +++s++S+HL +L eaGLV+
  gi|121636494|ref|YP_976717.1|  8 PTRRRLLQLLAPGERTVTQLASQFTVTRSAISQHLGMLAEAGLVT 52
                                   9*******************************************6 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.91
                                    SEEHHHHHHHH CS
                          HTH_5  15 elcvcelaeel 25 
                                    e+ v++la++l
  gi|121636494|ref|YP_976717.1| 281 EYDVSQLADHL 291
                                    789******98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   1.3   2.3e-15   2.2e-12       5      61 .]       3      58 ..       1      58 [. 0.96
   2 ?   -3.2   0.0       9.5     9e+03      22      32 ..     205     215 ..     202     218 .. 0.70
   3 ?   -1.6   0.1       3.2     3e+03      27      39 ..     258     276 ..     248     296 .. 0.43

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.3e-15
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                   e+ a+P+Rrr+l++L  ++++t+++la ++ ++++ +s+HL  L+eagLv+ +++gr
  gi|121636494|ref|YP_976717.1|  3 EVAAEPTRRRLLQLL-APGERTVTQLASQFTVTRSAISQHLGMLAEAGLVTARKQGR 58
                                   67799**********.**************************************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.5
                                    CTTB-HHHHHH CS
                         HTH_20  22 aegltaselae 32 
                                     +glta + a+
  gi|121636494|ref|YP_976717.1| 205 HDGLTAQQAAR 215
                                    67888888776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                                    HHHHHHHH......TS-HH CS
                         HTH_20  27 aselaerl......dlskn 39 
                                    ++ l + l      dl+++
  gi|121636494|ref|YP_976717.1| 258 LAVLQHVLrgigasDLTRQ 276
                                    4444444422222222222 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   2.9   1.3e-12   1.3e-09       5     105 ..     106     203 ..     103     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.3e-12
                                    EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEE..E.. CS
                Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyri..v.. 80 
                                    +++vv++ +p   +al+++++ ++rW+   ar el++ gg+   + +tv+ g  + +  ++++vdp g+++ ++   +  
  gi|121636494|ref|YP_976717.1| 106 EKAVVVPLDPTSTFALITQPDRLRRWMAVAARIELRT-GGA--YR-WTVTPGH-S-AAGTVIDVDP-GKRVVFTWgwEdh 178
                                    7889********************************9.888..66.9999888.3.999*******.5555555533367 PP

                                    ..SSS-TSEEEEEEEEECCETEEEEE CS
                Polyketide_cyc2  81 .kpvpvanyvatwtvtpdgggtrvtw 105
                                        p +  ++t+t+tp++ggt+v+ 
  gi|121636494|ref|YP_976717.1| 179 gD-PPPGGSTVTITLTPVDGGTEVRL 203
                                    54.444447*************9985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.8   1.7e-08   1.6e-05       4      55 ..       7      55 ..       4      60 .. 0.91
   2 ?   -2.2   0.0       4.3   4.1e+03      24      45 ..     270     291 ..     256     294 .. 0.56

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   +p+ +r+L  L+ +++   tv++la  + +++sa+s++l  L +aGLv+ r+
  gi|121636494|ref|YP_976717.1|  7 EPTRRRLLQLLAPGER---TVTQLASQFTVTRSAISQHLGMLAEAGLVTARK 55
                                   6999*******99996...*****************************9885 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                                    HHHHHHHHTSSHHHHHHHHHHH CS
                         MarR_2  24 vgelarrlglsksavsrilkrL 45 
                                    +++l+r +  +   vs++ + L
  gi|121636494|ref|YP_976717.1| 270 ASDLTRQTPCTEYDVSQLADHL 291
                                    5555555555555555555544 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-07   0.00017      15      63 ..      14      62 ..      11      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                   l Ll+ g+ t++++a++  v rs + + L  L ++GlV+ +k+ + +Y 
  gi|121636494|ref|YP_976717.1| 14 LQLLAPGERTVTQLASQFTVTRSAISQHLGMLAEAGLVTARKQGRERYY 62
                                   789*************************************997766554 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3       1.2   1.1e+03      36     108 ..      40      83 ..       9     103 .. 0.51
   2 ?   -1.2   0.3       3.1   2.9e+03      31      61 ..     210     240 ..     195     257 .. 0.50
   3 !   22.3   6.9   1.8e-07   0.00017       5      77 ..     258     329 ..     254     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                        MDMPI_N  36 aHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaaslapeallaafraavtrlaaalaalppda 108
                                    +Hl++ a+a + +++                              ++ e+   + +++v rl+a +++++ d+
  gi|121636494|ref|YP_976717.1|  40 QHLGMLAEAGLVTARK-----------------------------QGRERYYRLDERGVLRLRALMESFWSDE 83 
                                    4444444444444443.............................3333333333333333333333333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                        MDMPI_N  31 vadlvaHlarsaralaaalaaegaesalard 61 
                                     ++ ++H  ++++ l +++ a+++++a +++
  gi|121636494|ref|YP_976717.1| 210 AQQAARHAKGWNHFLDRLVVAGQHGDAGPDE 240
                                    3333444444444444444333333333222 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.8e-07
                        MDMPI_N   5 waalaalvagLtdeqwaapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaad...aeavdl 77 
                                     a l+ +++g+   ++++++pc +++v +l+ Hl rs   + aa++a+ a++  +++    l+t+++    +  ++
  gi|121636494|ref|YP_976717.1| 258 LAVLQHVLRGIGASDLTRQTPCTEYDVSQLADHLLRSLAIIGAAAGAQLAPRDVDAP----LETQVAdaaQAVMEA 329
                                    56788899************************************9886555444433....443333221222222 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.7   6.4e-07    0.0006      17      60 ..      16      57 ..       4      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.4e-07
                                   SS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                           GntR 17 elrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                    l+pG++   + +La++f V+r+ + + L +L+++glv++r+++
  gi|121636494|ref|YP_976717.1| 16 LLAPGERT--VTQLASQFTVTRSAISQHLGMLAEAGLVTARKQG 57
                                   67888886..9****************************99885 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.5     1e-05    0.0098       7      49 ..      12      52 ..      12      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   ++L++la + +   +++lA ++ +++S+ + +L  L e G+v+
  gi|121636494|ref|YP_976717.1| 12 RLLQLLAPGERT--VTQLASQFTVTRSAISQHLGMLAEAGLVT 52
                                   589999999995..***************************97 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.8e-06    0.0064      11      53 ..      18      60 ..      11      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                         HTH_34 11 svdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                   +  e + ++l ++  +t +++s hl +L +ag ++ +k+ +++
  gi|121636494|ref|YP_976717.1| 18 APGERTVTQLASQFTVTRSAISQHLGMLAEAGLVTARKQGRER 60
                                   556678899*****************************98887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.8e-05     0.017       2      45 ..      10      51 ..       9      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                   ++ +l+lL  a g  +  +LA ++ v+r+++ +++  L e+g+ 
  gi|121636494|ref|YP_976717.1| 10 RRRLLQLL--APGERTVTQLASQFTVTRSAISQHLGMLAEAGLV 51
                                   57788999..88889********************999999943 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.6e-05     0.024      26      59 ..      22      55 ..      12      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvr 59
                                    +++++a+++ + +s +++ l +L++aglv++++
  gi|121636494|ref|YP_976717.1| 22 RTVTQLASQFTVTRSAISQHLGMLAEAGLVTARK 55
                                   4899**************************9975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.4e-05     0.042      17      48 ..      21      52 ..      12      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                                   TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR 17 plsvseLakklgvskstvtrvldrLekkGlie 48
                                   + +v++La+++ v++s+++  l  L ++Gl++
  gi|121636494|ref|YP_976717.1| 21 ERTVTQLASQFTVTRSAISQHLGMLAEAGLVT 52
                                   5689**************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   5.1e-05     0.048      23      60 ..      23      65 ..      10      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EEES CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.r..grr..iril 60
                                   t ++lAs   +tr+ +s+ l+ L ++gl++ r  gr+   r+ 
  gi|121636494|ref|YP_976717.1| 23 TVTQLASQFTVTRSAISQHLGMLAEAGLVTaRkqGREryYRLD 65
                                   5689**************************8533332345554 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   5.1e-05     0.048      75     119 ..      25      68 ..      23      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                           RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRyarrdreG 119
                                    +qL++++ +++s++++hl  L+eaGl++ r      Ry r d++G
  gi|121636494|ref|YP_976717.1|  25 TQLASQFTVTRSAISQHLGMLAEAGLVTARKQG-RERYYRLDERG 68 
                                    6899*************************9876.56888888777 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00017      0.16      29      70 .]      27      68 ..      20      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70
                                   l +++ +  s++   l  la+aG++++ k+gr+ +YrL ++g
  gi|121636494|ref|YP_976717.1| 27 LASQFTVTRSAISQHLGMLAEAGLVTARKQGRERYYRLDERG 68
                                   5566666666666677779*******************9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00049      0.46      24      56 ..      23      55 ..      20      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                   ++++la+   v  s +s+ l  L+++G+v   k
  gi|121636494|ref|YP_976717.1| 23 TVTQLASQFTVTRSAISQHLGMLAEAGLVTARK 55
                                   579**************************8766 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   0.00018      0.17       9      58 ..       5      54 ..       2      57 .. 0.91
   2 ?   -2.9   0.1       8.4   7.9e+03       3      32 ..     244     252 ..     242     266 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                        DprA_WH  9 plddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                   ++++++rr+L++L+p  ++v qL+ +  ++ +++s +L +L  aGlv+++
  gi|121636494|ref|YP_976717.1|  5 AAEPTRRRLLQLLAPGERTVTQLASQFTVTRSAISQHLGMLAEAGLVTAR 54
                                   6789***********************************99888888865 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                        DprA_WH   3 appaepplddlerrvLaaLgpePvhvDqLv 32 
                                    a                     P ++D+L+
  gi|121636494|ref|YP_976717.1| 244 A---------------------PDPLDELS 252
                                    3.....................33344432 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00064       0.6       1      59 [.      10      66 ..      10      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00064
                         HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlse 59
                                   R + l+lla G+ tv q+A +  ++r+ +  +l    e G   l   r +gr r  rl+e
  gi|121636494|ref|YP_976717.1| 10 RRRLLQLLAPGERTVTQLASQFTVTRSAISQHLGMLAEAG---LVTARKQGRERYyRLDE 66
                                   6778999*********************************...66645577777778998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2705.91
//
Query:       gi|121636495|ref|YP_976718.1|  [L=261]
Description: hypothetical protein BCG_0622 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-20   73.0   0.5    2.7e-12   47.4   0.1    2.2  2  Glyoxalase_6  Glyoxalase-like domain
    2.1e-16   60.3   0.0    5.9e-07   29.7   0.0    2.1  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    4.7e-05   23.6   0.2       0.39   11.0   0.0    2.5  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   9.4e-09   5.6e-05       4     102 ..      17     122 ..      14     126 .. 0.74
   2 !   47.4   0.1   4.4e-16   2.7e-12       6     106 ..     151     254 ..     146     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.4e-09
                   Glyoxalase_6   4 ldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe........paknr..vHldlavedldaev 73 
                                    l+++d  a+ +F+  ++gw  ++++     p g+g    + atl  + v          p+  +  + + +av+d+da v
  gi|121636495|ref|YP_976718.1|  17 LQTTDQSAAKKFYTSLFGWGYDDNP----VPGGGGV--YSMATLNGEAVAAiapmppgaPEGMPpiWNTYIAVDDVDAVV 90 
                                    6799*********************....2223332..33444444444445555557633332349************* PP

                   Glyoxalase_6  74 arlvalGArvlreprdgthgr...vlaDPeGn 102
                                    +++v  G++v  +  d + ++    ++DP G+
  gi|121636495|ref|YP_976718.1|  91 DKVVPGGGQVMMPAFDIGDAGrmsFITDPTGA 122
                                    ***********999886655569*******97 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 4.4e-16
                   Glyoxalase_6   6 aadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.paknrvHldlavedldaevarlvalGArvl 84 
                                    +++p+ + aF++a+ g++ ++ e  ++ ++ + ++a+da      + p   + n++H+ +av+d+da++a++ a+G++v+
  gi|121636495|ref|YP_976718.1| 151 TDKPDLALAFYEAVVGLTHSSME-IAAGQNYRVLKAGDAEVGGCMEPPMpGVPNHWHVYFAVDDADATAAKAAAAGGQVI 229
                                    67899999***************.5555555555555555555555555756799************************* PP

                   Glyoxalase_6  85 reprdgthgr...vlaDPeGneFcv 106
                                     ep d    +   vl DP+G+ F v
  gi|121636495|ref|YP_976718.1| 230 AEPADIPSVGrfaVLSDPQGAIFSV 254
                                    ***99887778************98 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   9.9e-11   5.9e-07       3     125 ..      13     123 ..      11     126 .. 0.95
   2 !   28.7   0.0     2e-10   1.2e-06       7     126 ..     149     252 ..     143     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.9e-11
                                    EEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEE CS
                     Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafial 82 
                                    ++v l ++d +++ +FYt  +G+   +  +  ++++g+ +++  +g+ +++++  ++  ++  +          ++ ++ 
  gi|121636495|ref|YP_976718.1|  13 NWVDLQTTDQSAAKKFYTSLFGWGYDDNPV--PGGGGVYSMATLNGEAVAAIAPMPPGAPEGMPP---------IWNTYI 81 
                                    578899************************..899*****************9999999999999.........****** PP

                                    EHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEE CS
                     Glyoxalase  83 dvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGil 125
                                    +v+dv++ +d++   g++v+++  + +  +++sf ++Dp G  
  gi|121636495|ref|YP_976718.1|  82 AVDDVDAVVDKVVPGGGQVMMPAFDIGDAGRMSF-ITDPTGAA 123
                                    *********************************9.****9976 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2e-10
                                    EEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCH CS
                     Glyoxalase   7 llvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdved 86 
                                    ll++ ++ +l+FY+ v+G++ +  +       g++++++ ag+  ++   +++ +g ++h+           +++++v+d
  gi|121636495|ref|YP_976718.1| 149 LLTDKPDLALAFYEAVVGLTHSSMEI----AAGQNYRVLKAGDAEVGGCMEPPMPGVPNHW-----------HVYFAVDD 213
                                    67888999***********9988877....89*****************************...........9999**** PP

                                    HHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEE CS
                     Glyoxalase  87 vgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGill 126
                                     +++  ++++ag++v aep + +  +++ +   Dp G  +
  gi|121636495|ref|YP_976718.1| 214 ADATAAKAAAAGGQVIAEPADIPSVGRFAV-LSDPQGAIF 252
                                    *******************99999999966.****99765 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   6.5e-05      0.39       6     104 ..      18     111 ..      15     116 .. 0.85
   2 !   10.0   0.3   0.00014      0.81      67      97 ..     202     232 ..     149     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                                    E-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES-HHHHHHH CS
                   Glyoxalase_4   6 vVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvddldaavar 85 
                                     ++D  aa ++++ l+G+g  ++  +   +v +++a+l+++   +  i+p +   +  e+ + ++   ++vdd+da+v++
  gi|121636495|ref|YP_976718.1|  18 QTTDQSAAKKFYTSLFGWGYDDNPVPGGGGV-YSMATLNGE--AVAAIAPMPPGAP--EGMPPIWNTYIAVDDVDAVVDK 92 
                                    578999************9999988888888.566666665..799*****99877..9********************* PP

                                    HCTTTEEEEEEEE-GGGTT CS
                   Glyoxalase_4  86 leeqGfevvqkgvragaag 104
                                    +   G +v++ +   g ag
  gi|121636495|ref|YP_976718.1|  93 VVPGGGQVMMPAFDIGDAG 111
                                    *******999876666554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                                    -EEEEEEEEES-HHHHHHHHCTTTEEEEEEE CS
                   Glyoxalase_4  67 eglhhlaywvddldaavarleeqGfevvqkg 97 
                                    +  +h+ ++vdd da+ a+++++G +v+ + 
  gi|121636495|ref|YP_976718.1| 202 PNHWHVYFAVDDADATAAKAAAAGGQVIAEP 232
                                    55689*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1836.63
//
Query:       gi|121636496|ref|YP_976719.1|  [L=1303]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-33  114.8  17.9    2.8e-33  114.1  17.9    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1  17.9   1.6e-37   2.8e-33       1      92 [.       1      91 [.       1      92 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 1.6e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pe+l++aa+dla+igs+++aan+aaaa+ + vl+a aDeVS+a+Aalf++haqeyq++saq+a+fh++fvq+l+a
  gi|121636496|ref|YP_976719.1|  1 MSFVIATPEMLTTAATDLAKIGSTITAANTAAAAVAK-VLPASADEVSVAVAALFGTHAQEYQTVSAQVATFHDRFVQTLSA 81
                                   9********************************9988.******************************************** PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   aa+sY aaEa
  gi|121636496|ref|YP_976719.1| 82 AASSYVAAEA 91
                                   *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.71u 0.38s 00:00:02.09 Elapsed: 00:00:00.57
# Mc/sec: 6907.55
//
Query:       gi|121636497|ref|YP_976720.1|  [L=252]
Description: hypothetical protein BCG_0624 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-45  152.8   0.0    8.4e-45  152.4   0.0    1.1  1  Mut7-C    Mut7-C RNAse domain
    9.2e-33  111.9   0.0    9.3e-32  108.7   0.0    2.1  2  Ub-Mut7C  Mut7-C ubiquitin
     0.0074   16.0   0.0      0.032   14.0   0.0    2.1  2  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.055   14.1   0.0       0.14   12.8   0.0    1.7  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.0   1.9e-48   8.4e-45       1     144 [.      97     239 ..      97     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.9e-48
                         Mut7-C   1 krfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlreviarl 80 
                                    +rf++D++lg+la++LRllG+d+ ++s ++d +l++++  e+rillTrdr+Llkr+  ++g++++s+++eeq  ev++rl
  gi|121636497|ref|YP_976720.1|  97 PRFVVDVNLGQLARLLRLLGFDTRWSSAADDPTLADISLGEQRILLTRDRGLLKRRAITHGLFVHSQHPEEQALEVLRRL 176
                                    69****************************************************************************** PP

                         Mut7-C  81 glklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwervee 144
                                    +l+ +l+p lsrC++Cngel+ v+k+ev +++++ +++++++f+rC  C++++W Gsh++r+ +
  gi|121636497|ref|YP_976720.1| 177 DLNGRLAP-LSRCLRCNGELAAVSKDEVIGQLEPLTRRYYESFSRCFGCGRIYWPGSHHARLVR 239
                                    ********.**************************************************99876 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   2.1e-35   9.3e-32       3      81 .]       4      82 ..       2      82 .. 0.98
   2 ?    0.7   0.0      0.11   4.8e+02      52      74 ..     176     198 ..     171     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.1e-35
                       Ub-Mut7C  3 titfrfyaeLndflprarreralavafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavypvfeald 81
                                   ++++r yaeLn+f++ ++r  +++++f++++tvk+v+Ea+G+PhtEV+lilvnG++++fs+++ +Gdr+a+yp+feald
  gi|121636497|ref|YP_976720.1|  4 YVDVRAYAELNEFVELQARGLTVRRPFRSHQTVKDVLEAMGIPHTEVDLILVNGDPADFSYRPVAGDRIAAYPMFEALD 82
                                   689*************************************************************************986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                       Ub-Mut7C  52 ilvnGesvgfshiledGdrvavy 74 
                                    + +nG+ +++s+ l+  + +a+ 
  gi|121636497|ref|YP_976720.1| 176 LDLNGRLAPLSRCLRCNGELAAV 198
                                    679********999755555444 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.62   2.8e+03      47      59 ..      50      63 ..      48      69 .. 0.83
   2 !   14.0   0.0   7.1e-06     0.032       2      58 ..      98     148 ..      97     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                        DUF5615 47 edriivTkD.kDFg 59
                                    d+i+v  D +DF+
  gi|121636497|ref|YP_976720.1| 50 VDLILVNGDpADFS 63
                                   58899999****97 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.1e-06
                        DUF5615   2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDF 58 
                                    ++++D nl  +l++llr +g+d+ +      + a+D++  ++   e+ri++T+D+  
  gi|121636497|ref|YP_976720.1|  98 RFVVDVNLG-QLARLLRLLGFDTRWS-----SAADDPTLADISLGEQRILLTRDRGL 148
                                    899*****9.9**********88888.....5689*******************975 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05      0.14      17      69 ..      29      73 ..       7      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                   EESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEE CS
                           ThiS 17 elaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDeva 69
                                    + + +tv+++lea+g ++      ++  ++vNg+ +++   +++  +gD++a
  gi|121636497|ref|YP_976720.1| 29 PFRSHQTVKDVLEAMGIPHT-----EVDLILVNGDPADF---SYRPVAGDRIA 73
                                   567789*************5.....9999**********...*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1920.08
//
Query:       gi|121636498|ref|YP_976721.1|  [L=163]
Description: hypothetical protein BCG_0625c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1089.79
//
Query:       gi|121636499|ref|YP_976722.1|  [L=71]
Description: hypothetical protein BCG_0626 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-08   33.6   0.3    1.1e-07   31.5   0.1    1.8  2  RHH_1           Ribbon-helix-helix protein, copG family
    9.7e-05   22.2   0.1    0.00013   21.8   0.1    1.2  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
  ------ inclusion threshold ------
      0.065   12.0   0.1       0.08   11.8   0.1    1.0  1  MreB_Mbl        MreB/Mbl protein
       0.21   12.1   0.0       0.24   12.0   0.0    1.1  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   2.5e-11   1.1e-07       2      37 ..       4      39 ..       3      40 .. 0.96
   2 ?    0.3   0.0      0.16   7.4e+02       8      17 ..      55      64 ..      54      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.5e-11
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   ++++l++el++++ + ar rg+S  ++IRe +r+++
  gi|121636499|ref|YP_976722.1|  4 TTVYLPDELKAAVKRAARQRGVSEAQVIRESIRAAV 39
                                   79*******************************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                                   HHHHHHHHHH CS
                          RHH_1  8 eellerLdel 17
                                   e +++r+del
  gi|121636499|ref|YP_976722.1| 55 EPIARRVDEL 64
                                   6789999998 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.8e-08   0.00013       1      31 [.       1      31 [.       1      39 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.8e-08
                          RHH_5  1 SkRvnvtLPeelleeLeewAdeegRsvSnla 31
                                   +++++v+LP+el+ ++++ A ++g+s ++++
  gi|121636499|ref|YP_976722.1|  1 MDKTTVYLPDELKAAVKRAARQRGVSEAQVI 31
                                   5789**********************99876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.8e-05      0.08     109     138 ..      13      42 ..       7      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHTT-SEEEEEEHHHHHHHHTT CS
                       MreB_Mbl 109 rrAvkeaakkaGarevllieeplaAAiGag 138
                                    + Avk aa++ G +e ++i e++ AA+G  
  gi|121636499|ref|YP_976722.1|  13 KAAVKRAARQRGVSEAQVIRESIRAAVGGA 42 
                                    679************************975 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.3e-05      0.24      46      77 ..       5      36 ..       1      38 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.3e-05
                 CopG_antitoxin 46 slrlpedlLealkekAnkrdvpyqslikelle 77
                                   ++ lp +l  a+k +A++r+v+  + i+e ++
  gi|121636499|ref|YP_976722.1|  5 TVYLPDELKAAVKRAARQRGVSEAQVIRESIR 36
                                   4589***********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 469.31
//
Query:       gi|121636500|ref|YP_976723.1|  [L=135]
Description: hypothetical protein BCG_0627 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-11   43.4   2.5    5.1e-11   43.1   2.5    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.29   11.9   2.2        0.4   11.5   2.2    1.3  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   2.5   5.7e-15   5.1e-11       1     116 [.       1     119 [.       1     124 [. 0.95

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.7e-15
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaei 77 
                                    +++DTs+l+a++   e++++a+ + +++  ++lv+s+ v+aEl y +a    + + +ael  l++l   a ++ + +a+ 
  gi|121636500|ref|YP_976723.1|   1 MIIDTSALLAYFdAAEPDHAAVSECIDSSaDALVVSPYVVAELDYLVAT---RVGVDAELAVLRELaGGAWELANCGAAE 77 
                                    68*************************99*******************9...89999999999999899*********** PP

                                    HHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                            PIN  78 aeeaaeialkyg...llpnDaliaAtAkehgikliatfDedf 116
                                     e+aa+i  ky+   ++++Da  +++A +++ + i+t D++ 
  gi|121636500|ref|YP_976723.1|  78 IEQAARIVTKYQdqrIGIADAANVVLADRYRTRTILTLDRRH 119
                                    ***************************************993 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.2   4.4e-05       0.4       3     115 ..       2     117 ..       1     118 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                          PIN_3   3 vlDtnvlldallfdspaarkildaletgaitlvvsprlldElervl.arelaypqfklraadkaallakvaler...kav 78 
                                    ++Dt+ ll+++   +p+ +++ +++ + a  lvvsp ++ El + + +r++++ + +  ++ +  +      e+    a 
  gi|121636500|ref|YP_976723.1|   2 IIDTSALLAYFDAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVaTRVGVDAELAVLRELAGGAW-----ELancGAA 76 
                                    79*****************************************977567766665555554442222.....22222677 PP

                          PIN_3  79 apdaelrpllkcrDp....dDqkvlelAlaaradvlVTkdr 115
                                    + ++++r++ k++D+    +D+  + lA   r + ++T dr
  gi|121636500|ref|YP_976723.1|  77 EIEQAARIVTKYQDQrigiADAANVVLADRYRTRTILTLDR 117
                                    77777777777776533335777777777777778888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 955.04
//
Query:       gi|121636501|ref|YP_976724.1|  [L=228]
Description: lipoprotein lpqN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-59  198.7   0.0      6e-59  198.4   0.0    1.1  1  Lpp-LpqN        Probable lipoprotein LpqN
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.064   13.4   0.0    1.4  1  DcrB            DcrB
       0.18   11.8   5.4       0.28   11.1   5.4    1.3  1  DUF3558         Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Lpp-LpqN  Probable lipoprotein LpqN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0     1e-62     6e-59       1     174 []      57     227 ..      57     227 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 1e-62
                                    -SS-HHHHHHHTT-EEEE--STT--SEEEE----TT-EE-SS---TTEEEEEEETT.SSSSS-EEEEEEEEEEES---HH CS
                       Lpp-LpqN   1 asvtladYleengvteepvaagdlgaltvdlplPegWedagdpnledayaviaktqpesgedtptavllvskLtGdvDpa 80 
                                    +++t+adY+++n+++e+pv++gd+g++t+dlp+P++W+  +++   + y+ i++tqp++++d+pt+v+++skLtGd+Dpa
  gi|121636501|ref|YP_976724.1|  57 PNYTIADYIRDNHIQETPVHHGDPGSPTIDLPVPDDWRLLPESSR-APYGGIVYTQPADPNDPPTIVAILSKLTGDIDPA 135
                                    589***********************************8886554.67******************************** PP

                                    HHHCCTTHHHHTSTT-E.EEEEE---BTTB-EEEEEEEEECTTEEEEEEEEEEEEEETT...EEEEEEEEEEEEGGGTTT CS
                       Lpp-LpqN  81 ealehapvdaqnlpgfk.atdgstadlsGfpssqieGtYdkdgkrlavaqrtViitgappdaqrYlvqLtvttledqaea 159
                                    ++l++ap++++nlpgf+ + dgs+a+l+Gf ++q++G+Y+k+gk ++vaq+tV+i++  ++a  +++qL++++l+d++ +
  gi|121636501|ref|YP_976724.1| 136 KVLQFAPGELKNLPGFQgSGDGSAATLGGFSAWQLGGSYSKNGKLRTVAQKTVVIPS--QGA-VFVLQLNADALDDETMT 212
                                    *********************************************************..778.***************** PP

                                    THHHHHHHHHH-EEE CS
                       Lpp-LpqN 160 ladateaIiegftvt 174
                                    l+da ++I+e++t+t
  gi|121636501|ref|YP_976724.1| 213 LMDAANVIDEQTTIT 227
                                    *************98 PP

>> DcrB  DcrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.064      26     116 ..     118     209 ..     106     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                    -EEEEEEEE---TTS-HHHHHHHHHHHHHHHSTT-EEEE.EEEEEET.TEEEEEEEEEEEETTE..EEEEEEEEE--SSS CS
                           DcrB  26 gaslvIsRdeleegetleeylerqlkqlrkrlkgfqlle.ekpatlgaglpaeelevtyrkkgk..pvyqlqvlvevprr 102
                                    ++++v   ++l  + + +++l+    +l++ l+gfq     ++atlg g  a +l  +y+k+gk  +v q+ v++  ++ 
  gi|121636501|ref|YP_976724.1| 118 PPTIVAILSKLTGDIDPAKVLQFAPGELKN-LPGFQGSGdGSAATLG-GFSAWQLGGSYSKNGKlrTVAQKTVVIPSQGA 195
                                    555555555555555666666666666666.99999876257899**.*************99644899*********** PP

                                    EEEEEEEE-CCCHH CS
                           DcrB 103 vLiftltspgefte 116
                                    v++++l++++  +e
  gi|121636501|ref|YP_976724.1| 196 VFVLQLNADALDDE 209
                                    ******98765444 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.4   4.8e-05      0.28       1      35 [.      15      49 ..      15      68 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                        DUF3558  1 lllaGCssttdGt.apaasssassssttsssaapav 35
                                   l+laGCs ++++  ap++s++++s++t s++++ a+
  gi|121636501|ref|YP_976724.1| 15 LALAGCSFNIKTDsAPTTSPTTTSPTT-STTTTSAT 49
                                   68*****66666642333322222222.22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1659.98
//
Query:       gi|121636502|ref|YP_976725.1|  [L=877]
Description: hypothetical protein BCG_0629 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.8e-137  458.4   0.0   3.5e-137  458.1   0.0    1.1  1  Glyco_hydro_92   Glycosyl hydrolase family 92
    5.1e-55  186.9   6.3    8.1e-55  186.3   6.3    1.3  1  Glyco_hydro_92N  Glycosyl hydrolase family 92 N-terminal doma


Domain annotation for each model (and alignments):
>> Glyco_hydro_92  Glycosyl hydrolase family 92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.1   0.0  3.9e-141  3.5e-137       1     460 [.     280     749 ..     280     751 .. 0.93

  Alignments for each domain:
  == domain 1  score: 458.1 bits;  conditional E-value: 3.9e-141
                                    HHHHHHHHHTTT--HHHHHHHHHHHHHHHHTTEEEESS-HHHHHHHHHHHHHHTTSSEE--EE-TTE-TTTSSEEE...S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                 Glyco_hydro_92   1 qArknleaEipdldfekvraaareaWnekLskieveggtedqkttFYtalYhallapneysdvdgeYsglddkvhk..eg 78 
                                    +Ar+nl+aE    +f+++raa++++Wn++Ls+i v g    +  tFYt+lY++ll+pn+++dvdg+Y g+d+ +h+  +g
  gi|121636502|ref|YP_976725.1| 280 GARANLDAEGGA-SFDDIRAATSSEWNAALSRIAVAGRGPGDVDTFYTCLYRSLLHPNTFNDVDGRYIGFDGVIHSvaSG 358
                                    69*******998.***********************99999*********************************997645 PP

                                    .--EESEEHHHHTTTHHHHHHHH-HHHHHHHHHHHHHHHHHHSS--SEESSS.B---S-S-THHHHHHHHHHTT---S-H CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Glyco_hydro_92  79 .ksYttfslWDtyRaqhplltlldperasdmvrslldiykeggwlpdwrlsnsetavmgGsnadvvladayvkgirdfdv 157
                                     ++Y +fs WDtyR++ pl+ ll p+rasdm++sl+++++++g  p+w+l+ns t +m+G+++++++++ y++g+rdfd+
  gi|121636502|ref|YP_976725.1| 359 hTHYANFSDWDTYRSLAPLQGLLFPQRASDMIQSLVTDAEQSGAYPRWALANSATGMMSGDSVVPLIVNLYAFGARDFDL 438
                                    577***************************************************************************** PP

                                    HHHHHHHHHHHHB-S-TT...TBTTTHHHHHHHSS--T......T.TTTHHHHHHHHHHHHHHHHHHHHHTT-HHH.HHH CS
                                    xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Glyco_hydro_92 158 ekayealvkdaeeepeaad..kerrglesylklgYvpa....ked.esesvsrtlEyaydDfaiaqlAkalgkkedaeky 230
                                    ++a++ +v++a++     d   er+g+  yl+lgY p+    + + +  ++s tlE ++dDfai+++A+ lg++++a+ +
  gi|121636502|ref|YP_976725.1| 439 KSALHYMVNAATQGGVGLDgfLERPGIAAYLRLGYGPQtaefRANgRIAGASVTLEWSVDDFAISRFADSLGDTATAAVF 518
                                    ************53322235599***************998855535899****************************** PP

                                    HTTGGGGGGGEETTTTCE--B-TTS-B-SS--TT--.....STTSSSS-HHHHTT--TT-HHHHHHHHTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Glyco_hydro_92 231 lkrsknwrnlfdpetgfmrprnadGtwaepfdpsedp....eegftEgnawqysffvphDvagLielmGGkeafvkrLds 306
                                     +rs++w+nlf+p+tg++ pr a G + +     + p    ++g+ Egna qy + vph+vagL++++GG++a+vkrLd+
  gi|121636502|ref|YP_976725.1| 519 QNRSQYWQNLFNPTTGYISPRSAAGFFPDGPGFVAYPsgfgQDGYDEGNAEQYLWWVPHNVAGLVTALGGRTAVVKRLDR 598
                                    ***************************86543334446787889************************************ PP

                                    HS----TTGHHHHHHHTSS-TT-GGGTTGGGGGGGTT-HHHHHHHHHHHHHHSB-SSTT-BSSTTTSSTTHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Glyco_hydro_92 307 lfeeeekksedsaglsgqydhgNEpsfhtpylYnyagapwktqervreildelynntpdGlpGndDaGqmsawyvfsalG 386
                                    + +     + ++  ++ ++++gNEp f +p+lYny+g+pwktq++v+++ + l+  tp+G pGndD G++s+wyv++alG
  gi|121636502|ref|YP_976725.1| 599 FTK-----KLNVGPNEPYLWAGNEPGFGVPWLYNYIGQPWKTQRTVDRV-RGLFGPTPGGAPGNDDLGALSSWYVWAALG 672
                                    *98.....35689999*******************************96.69**************************** PP

                                    EE-SSTTS-EEEE---SSSEEEEE-GGG-EEEEE-TT-BT..TB-EEEEEEETTEE---.EEEHHHHHT-EEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                 Glyco_hydro_92 387 lYpvapgspeyllgsPlfekvtirlengktltieaknnsa..envyvqsvtlnGkplkk.wlthediakGgtLefel 460
                                    lYp +pg++ +++++Plf++++i l++gk+++i+a+++s   + +y++ +t++ +p ++ +l  + + +Gg+L+f+l
  gi|121636502|ref|YP_976725.1| 673 LYPSTPGTTILTVNTPLFDRAVIALPTGKSIQITAPGASGrnRLKYIDGLTIDRQPSNQtFLPESIVRTGGDLTFSL 749
                                    ***********************************8885422458************8879**************98 PP

>> Glyco_hydro_92N  Glycosyl hydrolase family 92 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   6.3     9e-59   8.1e-55       1     237 []      44     274 ..      44     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 9e-59
                Glyco_hydro_92N   1 yVnpliGTggg......ghtfpgatlPfGmvklspdtrenwdsqagYeyddssitgFshthlsGtgggdlgdvslmPttg 74 
                                    +Vn+liGTg g       + fpga++PfGmv+ spdt    d++agY+y + + tgFs+th s +g+  +gd+s++Ptt+
  gi|121636502|ref|YP_976725.1|  44 HVNTLIGTGTGaaivgeINNFPGASVPFGMVQYSPDTV---DNYAGYDYGNPHSTGFSMTHAS-VGCPAFGDISMLPTTT 119
                                    6*******9999999888********************...9*********************.**************** PP

                Glyco_hydro_92N  75 evkldpgkkkkdkeeyrsrfskedetaspgyYsvtlddygikaelTateragllrftFpkgkeanilvdlsdslssdkvs 154
                                    ++        ++ +++++    ++e+  pgyY+v++  +g+ aelTat+r+g+ rf++p ++ +  l+ + +++s   + 
  gi|121636502|ref|YP_976725.1| 120 PLGS------QPWSAWEEIAHDDTEVGVPGYYTVRFPGTGVIAELTATTRTGVGRFRYPRNGWPA-LFHVRSGASLAGNY 192
                                    *984......4667777777779*************************************99876.7777777777799* PP

                Glyco_hydro_92N 155 ngsikvvddreisGyrtsrgfgl.agsykvYfvarfskpfksfgvwkggevtegaksasgkelgayvsFdtkegetvevr 233
                                     ++++++d+++i+G++ts+gf++ ++ y+vYf+++fs+pf+s+g+w+g +v  g++s++++ +g+yv F++  g+ +evr
  gi|121636502|ref|YP_976725.1| 193 AATLQIEDNTTITGSATSGGFCGkKNLYTVYFAMKFSQPFSSYGTWDGYAVYPGSHSMNSSYSGGYVGFPA--GSVLEVR 270
                                    ********************9998999********************************************..******* PP

                Glyco_hydro_92N 234 vGiS 237
                                    +++S
  gi|121636502|ref|YP_976725.1| 271 TALS 274
                                    **99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (877 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 6667.43
//
Query:       gi|121636503|ref|YP_976726.1|  [L=795]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-32  111.5  49.1    5.6e-32  111.5  49.1    3.2  3  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
     0.0004   19.9   1.9     0.0004   19.9   1.9    2.5  4  BRI3BP           Negative regulator of p53/TP53
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.051   12.9   0.0    1.2  1  Pkinase          Protein kinase domain


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  21.0     0.014        81     120     259 ..      78     213 ..      26     226 .. 0.82
   2 ?    0.9   0.2     0.045   2.7e+02     266     296 ..     307     337 ..     306     338 .. 0.93
   3 !  111.5  49.1   9.4e-36   5.6e-32       2     301 .]     493     782 ..     492     782 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.014
                LPG_synthase_TM 120 dllalvllgllallllggllaegaavllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasakr.. 197
                                     +lal +++l++l+   ++       ll + +a +l avl l   + + +++++   +  rla lla+f + +++ ++  
  gi|121636503|ref|YP_976726.1|  78 AILALPFVILIGLIVSRQW------KLLGAYAAAGLMAVLPLSISSSRIAAPRWHFDLSDRLATLLAQFLDDPRWIAMla 151
                                    3444445555555544444......5677777777777788888888888888888899999999999998888877799 PP

                LPG_synthase_TM 198 .......klvlasprrlllafllslliwllealtlylllralgvdvslallllillaltlvgalpplPg 259
                                            ++ a++r +++a+ll ++        + l++ a+  + sl++l++ +l+ +lv++++ +P+
  gi|121636503|ref|YP_976726.1| 152 avltvsgPWLPARWRHWWWALLLAFVP-------IHLVVSAIVPARSLLGLAVGWLVGALVVLVVGTPA 213
                                    99999**555555666***********.......99999999999999999999999999999999996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.045
                LPG_synthase_TM 266 aalalllallGvsaaealaaallyrlitlyl 296
                                    a++a +++ lG+  ++ +a++ l+r+ tly+
  gi|121636503|ref|YP_976726.1| 307 ALMAIAFGDLGMANTTVIAVSPLDRGWTLYA 337
                                    67999*********************99985 PP

  == domain 3  score: 111.5 bits;  conditional E-value: 9.4e-36
                LPG_synthase_TM   2 llglalsalllalllrgvdl.aalaaalrsldpwwlllalllallsvl.lralrWrlllrslgarislrrllrayliglf 79 
                                    l+ l+l+++l+++++  +    +++++lr++++ww ll l++++l+++ + a+ W++    +++ +++++l  ++ +++f
  gi|121636503|ref|YP_976726.1| 493 LIQLVLIGALVYVAYPFISTvPTFFSQLRTANWWWALLGLAVSALTYVgAAAALWAC----ADGLVGFWKLSIMQVANTF 568
                                    7899999999999977776559************************88444446633....3899*************** PP

                LPG_synthase_TM  80 vnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa.....vllllalall 154
                                    + ++tP+++gG ++  ++l++  g+++ +a+a+v +++ +++++ ++l++l+ +l g   +  ++     +    +l l+
  gi|121636503|ref|YP_976726.1| 569 AATTTPAGVGGLALSTRFLQK-GGLTAVRATAAVALQQSVQVIVHLVLLILFSALAGTSTDL-SHfvpnaT----VLYLI 642
                                    *********************.*******************999877776666555554333.34324322....22222 PP

                LPG_synthase_TM 155 llavla.lllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralg 233
                                    ++++l+ + ++l++++ +++la  ++   ++l+++   l +     +++ p+rl+l++l ++++ l +al+l++ + a+g
  gi|121636503|ref|YP_976726.1| 643 AGVALGiVGTFLFVPKLRRWLATAVR---PKLREVTNDLIA-----LAREPKRLALIVLGCAGTTLGAALALWASIEAFG 714
                                    22223324445555555555553333...333333333333.....4569****************************** PP

                LPG_synthase_TM 234 vdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                      ++++ + +++++  +++ + p+PgG+G++Eaal+  la++Gv+aa+++  +llyrl+t +l++++G
  gi|121636503|ref|YP_976726.1| 715 GGTTFVTVTVVTMVGGTLASAAPTPGGVGAVEAALIGGLAAFGVPAALGVPSVLLYRLLTCWLPVFAG 782
                                    *****************************************************************998 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       0.9   5.4e+03      61     120 ..      15      39 ..       8      45 .. 0.44
   2 ?   -3.0   0.2      0.72   4.3e+03     131     167 ..     189     224 ..     159     228 .. 0.53
   3 !   19.9   1.9   6.7e-08    0.0004       7     119 ..     426     540 ..     421     564 .. 0.92
   4 ?   -3.3   0.3      0.92   5.5e+03      49      49 ..     620     620 ..     584     659 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.9
                         BRI3BP  61 llslaalspeevqalllwgllAllayWlLslllgllvallgrvlwllkvvlfllaflyil 120
                                    l +l++ +++ ++a+                                   l+++  + ++
  gi|121636503|ref|YP_976726.1|  15 LQPLTRRTNDIIRAV-----------------------------------LAAIYLVAVI 39 
                                    334444444444444...................................4444433333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.72
                         BRI3BP 131 allLlglvavyvLlgslglyaksseesgasleakvrs 167
                                    a  Llgl av  L g l + ++++++ +  l+ ++r 
  gi|121636503|ref|YP_976726.1| 189 ARSLLGL-AVGWLVGALVVLVVGTPALEVPLDGAIRA 224
                                    3345555.33344444445555555555555555555 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 6.7e-08
                         BRI3BP   7 qtlesllGeenvrallkfLsk..llellvsgvssalevlarivtdlLdalGidasnllslaalspeevqalllwgllAll 84 
                                        +++G++ v a+++ L+k  + +++ +++    +v+a++ +++++ +G d  +    +++s  +   l+l+g+l  +
  gi|121636503|ref|YP_976726.1| 426 TAAIDTFGKQAVLAASRRLTKsaVPKRIRESITDPNAVIASTRAEVMRQTGADQIKAETITRFSRGQLIQLVLIGALVYV 505
                                    556789*************8733679****************************9999********************** PP

                         BRI3BP  85 ayWlLslllgllvallgrvlwllkvvlfllaflyi 119
                                    ay ++s +  ++  l     w++ + l++ a  y+
  gi|121636503|ref|YP_976726.1| 506 AYPFISTVPTFFSQLRTANWWWALLGLAVSALTYV 540
                                    ***********999999999*********999998 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 0.92
                         BRI3BP  49 d 49 
                                     
  gi|121636503|ref|YP_976726.1| 620 S 620
                                    1 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.5e-06     0.051      94     153 ..     345     403 ..     314     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                                    S--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                        Pkinase  94 slseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                     +se++    ++++ e+l+ lH+++i H Dl ++ i +d +g +  + FG a+   ++ +
  gi|121636503|ref|YP_976726.1| 345 GISECTKTTPTAHVWEALRTLHDQQISHGDLCSAEITVD-NGAVLFGGFGEAEYGATDAQ 403
                                    478888888899***************************.99999999999987666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5258.14
//
Query:       gi|121636504|ref|YP_976727.1|  [L=240]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-20   70.8   0.7    5.6e-20   70.8   0.7    1.9  2  GntR            Bacterial regulatory proteins, gntR family
    5.8e-09   36.4   0.8    5.8e-09   36.4   0.8    1.7  2  FCD             FCD domain
      8e-07   28.9   0.6    1.8e-06   27.8   0.1    1.9  1  MarR_2          MarR family
    1.6e-05   25.0   0.0    3.5e-05   23.9   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.9e-05   24.6   0.0    3.9e-05   23.5   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    2.6e-05   24.0   0.0    5.2e-05   23.0   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00016   21.2   0.2    0.00037   20.0   0.2    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00023   21.2   0.6     0.0021   18.1   0.1    2.4  2  HTH_20          Helix-turn-helix domain
    0.00062   19.6   0.0     0.0013   18.6   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00075   19.4   0.1     0.0017   18.2   0.1    1.6  1  HTH_11          HTH domain
     0.0028   18.0   0.0     0.0066   16.8   0.0    1.6  1  Rrf2            Transcriptional regulator
     0.0038   17.2   0.0     0.0083   16.1   0.0    1.5  1  HTH_36          Helix-turn-helix domain
     0.0041   17.0   0.0       0.01   15.8   0.0    1.6  1  MarR            MarR family
     0.0049   17.1   0.1      0.012   15.9   0.1    1.6  1  PaaX            PaaX-like protein
     0.0074   15.5   0.9      0.011   14.9   0.9    1.4  1  pPIWI_RE_X      pPIWI_RE module N-terminal domain
     0.0082   15.9   1.3      0.024   14.5   1.3    1.9  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.036   14.1   0.0    1.6  1  HTH_29          Winged helix-turn helix
      0.016   15.0   0.1      0.054   13.3   0.1    1.9  1  LexA_DNA_bind   LexA DNA binding domain
      0.017   14.9   0.7      0.036   13.9   0.1    1.9  1  HTH_IclR        IclR helix-turn-helix domain
       0.03   14.1   0.0      0.067   13.0   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.034   14.0   0.0       0.09   12.6   0.0    1.7  1  TFIIE_alpha     TFIIE alpha subunit
      0.039   14.1   0.5       0.65   10.1   0.0    2.4  2  Sigma70_r3      Sigma-70 region 3
      0.054   13.4   0.1       0.14   12.0   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.061   13.1   0.4       0.17   11.7   0.4    1.8  1  HTH_8           Bacterial regulatory protein, Fis family
      0.068   12.8   2.0      0.077   12.7   0.0    2.2  4  RP-C            Replication protein C N-terminal domain
      0.079   12.5   0.1        0.2   11.2   0.1    1.6  1  HTH_CodY        CodY helix-turn-helix domain
      0.089   12.5   4.0         18    5.2   0.3    4.4  5  CysG_dimeriser  Sirohaem synthase dimerisation region
      0.094   12.3   0.0       0.34   10.5   0.0    1.9  1  HTH_50          Helix-turn-helix domain
       0.12   12.2   0.0       0.16   11.9   0.0    1.2  1  FadR_C          FadR C-terminal domain
       0.71   10.8   4.9         15    6.8   0.1    3.9  4  TPR_14          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.7   9.3e-23   5.6e-20       3      64 .]      13      74 ..      12      74 .. 0.96
   2 ?   -2.8   0.0       8.7   5.2e+03      25      33 ..     113     121 ..     104     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 9.3e-23
                                   HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR  3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                   e+v e++  d+l+ge  pG++LPser La+ +gVsr+ vReAL+rL+a+glve+rqg  t+V
  gi|121636504|ref|YP_976727.1| 13 EEVFEQIATDVLTGEMPPGEALPSERRLAELLGVSRPAVREALKRLSAAGLVEVRQGDVTTV 74
                                   689******************************************************87776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.7
                                    --HHHHHHH CS
                           GntR  25 PsereLaae 33 
                                    P++ eLaae
  gi|121636504|ref|YP_976727.1| 113 PKVAELAAE 121
                                    889999986 PP

>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.8   4.1e+03      13      30 ..      50      67 ..      45      79 .. 0.73
   2 !   36.4   0.8   9.6e-12   5.8e-09       2     124 ..     104     223 ..     103     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.8
                            FCD 13 aarlaarratdadlaele 30
                                   a+r+a +r ++a l e +
  gi|121636504|ref|YP_976727.1| 50 AVREALKRLSAAGLVEVR 67
                                   677777777776666555 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 9.6e-12
                            FCD   2 lyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlrr 81 
                                    ++e+R    p +a+laa+r  ++  + l++ l+al+     +d+  + ++ ++F   +++ ag+ v + +++ +ra  + 
  gi|121636504|ref|YP_976727.1| 104 ILEARLRNFPKVAELAAERNEPELAELLQDSLRALDTE---EDPIVWQRHTLDFWDHVVDSAGSIVDRLMYNAFRAAYEP 180
                                    67788888899***********9999998888888885...56667*********************************9 PP

                            FCD  82 lrrlalssperleeslaeHraildAirardadaAraamrrHle 124
                                     ++   ++   +++   + r+++dAi ++d+ +A++a+++ le
  gi|121636504|ref|YP_976727.1| 181 TLAALTTTMTAAAKRPSDYRKLADAICSGDPTGAKKAAQDLLE 223
                                    777777899******************************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.9e-09   1.8e-06      26      56 ..      39      69 ..      26      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.9e-09
                                   HHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 26 elarrlglsksavsrilkrLvaaGLverrpg 56
                                    la+ lg+s++av  +lkrL+aaGLve r g
  gi|121636504|ref|YP_976727.1| 39 RLAELLGVSRPAVREALKRLSAAGLVEVRQG 69
                                   69*************************9976 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.9e-08   3.5e-05      21      55 ..      33      67 ..      29      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.9e-08
                                   SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                 Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                   + ++  +lae L+vs + V e lk+L+ +G+ve+ 
  gi|121636504|ref|YP_976727.1| 33 ALPSERRLAELLGVSRPAVREALKRLSAAGLVEVR 67
                                   567889**************************985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   6.6e-08   3.9e-05      23      62 ..      36      77 ..      30      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.6e-08
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES-H CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.rgrr.irildl 62
                                   + + lA++lG++r  v  +l++L+ +gl++ r+++  +++d 
  gi|121636504|ref|YP_976727.1| 36 SERRLAELLGVSRPAVREALKRLSAAGLVEvRQGDvTTVRDF 77
                                   5678**************************554455667775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.7e-08   5.2e-05      26      59 ..      38      71 ..      35      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.7e-08
                                   CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                           TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                   + +ae lgv+r+ v e+L++L+ +GlVe+++g  
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRLSAAGLVEVRQGDV 71
                                   689***************************9974 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   6.2e-07   0.00037      21      48 .]      38      65 ..      36      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.2e-07
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                   r LAe lg+S+++v++ lkrL  +Gl++
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRLSAAGLVE 65
                                   67************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   3.5e-06    0.0021      27      57 ..      37      67 ..      14      69 .. 0.89
   2 ?    0.5   0.1         1   6.3e+02      19      38 ..     118     135 ..     100     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-06
                                   HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 27 aselaerldlskntlsyHLrvLeeagLvevv 57
                                      lae+l++s+  ++  L+ L+ agLvev+
  gi|121636504|ref|YP_976727.1| 37 ERRLAELLGVSRPAVREALKRLSAAGLVEVR 67
                                   5569*************************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                                    HSTCTTB-HHHHHHHHTS-H CS
                         HTH_20  19 Laraegltaselaerldlsk 38 
                                    L  a+++  +elae+l+ s 
  gi|121636504|ref|YP_976727.1| 118 L--AAERNEPELAELLQDSL 135
                                    4..88889999999996554 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.2e-06    0.0013      21      46 ..      40      65 ..      38      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                   HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 21 laeelglsqstvShHLkkLreaGLVe 46
                                   lae lg+s+++v++ Lk+L  aGLVe
  gi|121636504|ref|YP_976727.1| 40 LAELLGVSRPAVREALKRLSAAGLVE 65
                                   89***********************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.9e-06    0.0017      20      46 ..      39      64 ..      36      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                         HTH_11 20 eLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                   +LAe L+vSr +vr  +k+L+++g  +
  gi|121636504|ref|YP_976727.1| 39 RLAELLGVSRPAVREALKRLSAAG-LV 64
                                   7**********************9.34 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-05    0.0066      27      60 ..      36      69 ..      23      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           Rrf2 27 sseeiaerqnispsylekilakLrkaglvksvrG 60
                                   s + +ae  ++s++ ++  l++L+ aglv++++G
  gi|121636504|ref|YP_976727.1| 36 SERRLAELLGVSRPAVREALKRLSAAGLVEVRQG 69
                                   55789***************************99 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05    0.0083      22      55 .]      31      64 ..      30      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                         HTH_36 22 ggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                   g++ ps ++la++lg+s+  v+ a+k L  +G++
  gi|121636504|ref|YP_976727.1| 31 GEALPSERRLAELLGVSRPAVREALKRLSAAGLV 64
                                   4588999**********************99985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05      0.01      21      51 ..      38      68 ..      32      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR 21 seLakklgvskstvtrvldrLekkGlieRsk 51
                                     La+ lgvs+++v ++l+rL  +Gl+e ++
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRLSAAGLVEVRQ 68
                                   579************************9887 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-05     0.012      28      56 ..      39      67 ..      31      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                           PaaX 28 rllaelGiseslvRaalsRlakaGwlvre 56
                                   rl + lG+s  +vR al Rl++aG++   
  gi|121636504|ref|YP_976727.1| 39 RLAELLGVSRPAVREALKRLSAAGLVEVR 67
                                   678889******************98765 PP

>> pPIWI_RE_X  pPIWI_RE module N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.9   1.9e-05     0.011      63     131 ..      73     158 ..      40     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                     pPIWI_RE_X  63 vlnrnaglr..edep.WlyateplppavlrllikaWlrnl............eekpelvaellaelekad..llwepeev 125
                                    ++ ++++    +  p  l+   +l+ +v+r +++a lrn+            +e  el+++ l++l++++  ++w+++++
  gi|121636504|ref|YP_976727.1|  73 TVRDFRRHAglDLLPrLLFRNGELDISVVRSILEARLRNFpkvaelaaernePELAELLQDSLRALDTEEdpIVWQRHTL 152
                                    4433333333334445899999********************************************544446889***** PP

                     pPIWI_RE_X 126 dllkap 131
                                    d+  + 
  gi|121636504|ref|YP_976727.1| 153 DFWDHV 158
                                    *98774 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.3     4e-05     0.024      21      41 ..      38      58 ..      36      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                  HTH_AsnC-type 21 aeLAervGlSestvlrRvrrL 41
                                   ++LAe +G+S+++v++ ++rL
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRL 58
                                   68******************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-05     0.036      16      41 ..      38      63 ..      31      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                         HTH_29 16 sqiAkllglsrrtvyrwlkrfeegGl 41
                                   +++A+llg+sr+ v+ +lkr  + Gl
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRLSAAGL 63
                                   789*****************999995 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     9e-05     0.054       9      61 ..      13      69 ..       4      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                                   HHHHHHHHHHHHHHSS-.....--HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                  LexA_DNA_bind  9 revldlikasieetgyp.....PsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                   +ev++ i   + +  +p     Ps r +a+ lg++   av e Lk+L+  G++e+ +g
  gi|121636504|ref|YP_976727.1| 13 EEVFEQIATDVLTGEMPpgealPSERRLAELLGVS-RPAVREALKRLSAAGLVEVRQG 69
                                   5888888888888888844444599********97.779***************9876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     6e-05     0.036      22      49 ..      38      65 ..      25      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyve 49
                                   + lA+ +g+++++v+  L+ L   G+ve
  gi|121636504|ref|YP_976727.1| 38 RRLAELLGVSRPAVREALKRLSAAGLVE 65
                                   579************************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.067      20      46 ..      37      63 ..      36      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                         HTH_23 20 vreIAreLgvsrrTvyrwlkryreeGl 46
                                    r+ A++Lgvsr  v+  lkr  + Gl
  gi|121636504|ref|YP_976727.1| 37 ERRLAELLGVSRPAVREALKRLSAAGL 63
                                   5889*****************876775 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015      0.09      29      61 ..      36      68 ..      11      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                   BHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                    TFIIE_alpha 29 teedlakelkidlnelrklLnrLyearlvkykr 61
                                   +e  la++l++ ++ +r++L rL  a+lv++++
  gi|121636504|ref|YP_976727.1| 36 SERRLAELLGVSRPAVREALKRLSAAGLVEVRQ 68
                                   57789************************9985 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.65      21      56 ..      35      70 ..      31      77 .. 0.86
   2 ?    1.6   0.1      0.49   2.9e+02      13      30 ..     105     122 ..      97     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                   XXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSS CS
                     Sigma70_r3 21 PtpeEiAeeLglseekVrevleaarepvSldlpvge 56
                                   P++  +Ae Lg+s   Vre+l+    + +++++ g+
  gi|121636504|ref|YP_976727.1| 35 PSERRLAELLGVSRPAVREALKRLSAAGLVEVRQGD 70
                                   99*******************998877777777665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.49
                                    HHHHHSSXXXHHHHHHHH CS
                     Sigma70_r3  13 LeqelgrePtpeEiAeeL 30 
                                    Le +l   P+++E+A+e 
  gi|121636504|ref|YP_976727.1| 105 LEARLRNFPKVAELAAER 122
                                    788888889999999874 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.14       8      30 ..      34      56 ..      31      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                 YdaS_antitoxin  8 vGgqkaLAealgvsqqaVsqWlk 30
                                   + + ++LAe+lgvs++aV+  lk
  gi|121636504|ref|YP_976727.1| 34 LPSERRLAELLGVSRPAVREALK 56
                                   56889*************98873 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00029      0.17      23      42 .]      39      58 ..      38      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                   HHHHHHTS-HHHHHHHHHHT CS
                          HTH_8 23 kAArlLGisRrtLyrKLkkY 42
                                   + A+lLG+sR  ++  Lk++
  gi|121636504|ref|YP_976727.1| 39 RLAELLGVSRPAVREALKRL 58
                                   56****************96 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.077      71     104 ..      34      67 ..      22      97 .. 0.90
   2 ?   -3.2   0.0       9.7   5.8e+03     133     151 ..     106     124 ..     103     141 .. 0.65
   3 ?   -2.6   0.0       6.2   3.7e+03      61      72 ..     137     148 ..     127     151 .. 0.81
   4 ?   -2.5   0.0       5.9   3.5e+03      10      37 ..     187     210 ..     180     233 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                           RP-C  71 fpsNaqLsralglsestlrrhlaaLveaGliirr 104
                                     ps ++L++ lg+s+ ++r+ l++L  aGl+  r
  gi|121636504|ref|YP_976727.1|  34 LPSERRLAELLGVSRPAVREALKRLSAAGLVEVR 67 
                                    599***************************9766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.7
                           RP-C 133 laRaeElealaeevraerr 151
                                     aR++++ ++ae ++++++
  gi|121636504|ref|YP_976727.1| 106 EARLRNFPKVAELAAERNE 124
                                    5777777777776555443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.2
                           RP-C  61 dlseearlivfp 72 
                                    +l++e+++iv+ 
  gi|121636504|ref|YP_976727.1| 137 ALDTEEDPIVWQ 148
                                    68899999*997 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 5.9
                           RP-C  10 aqrlaeaieakkkgvdkwqllralkeak 37 
                                    + ++a a    +   d ++l+ a+++  
  gi|121636504|ref|YP_976727.1| 187 TTMTAAAK--RP--SDYRKLADAICSGD 210
                                    33333322..11..34445555555443 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00033       0.2      10      37 ..      40      67 ..      33      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                       HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiiesr 37
                                   +a+ +G+ r  +  aL++L +aG++e r
  gi|121636504|ref|YP_976727.1| 40 LAELLGVSRPAVREALKRLSAAGLVEVR 67
                                   68899*********************98 PP

>> CysG_dimeriser  Sirohaem synthase dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.4     2e+03      25      47 ..       7      28 ..       4      34 .. 0.78
   2 ?    5.2   0.3      0.03        18       4      23 ..      39      58 ..      38      60 .. 0.90
   3 ?    2.0   0.2      0.29   1.7e+02      37      58 .]     114     135 ..     110     135 .. 0.91
   4 ?   -0.4   0.0       1.7     1e+03      28      37 ..     153     162 ..     153     169 .. 0.84
   5 ?    1.9   0.0       0.3   1.8e+02      37      58 .]     201     222 ..     199     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                                   HHHHHHHHHT-HHHHHHHHTT-H CS
                 CysG_dimeriser 25 aRRrFWerffdgpvaelvlaGde 47
                                    RR   e++f +++a  vl G++
  gi|121636504|ref|YP_976727.1|  7 TRRSVPEEVF-EQIATDVLTGEM 28
                                   6888889999.899999998875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHHHHHH-SSH CS
                 CysG_dimeriser  4 rLAelagrlRdrVkarlpdv 23
                                   rLAel+g  R++V+++l+ +
  gi|121636504|ref|YP_976727.1| 39 RLAELLGVSRPAVREALKRL 58
                                   8***************9876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.29
                                    HHHHHHHTT-HHHHHHHHHHHH CS
                 CysG_dimeriser  37 pvaelvlaGdeeeAealleqaL 58 
                                    +vael+++ +e e  +ll++ L
  gi|121636504|ref|YP_976727.1| 114 KVAELAAERNEPELAELLQDSL 135
                                    589***************9976 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.7
                                    HHHHHHT-HH CS
                 CysG_dimeriser  28 rFWerffdgp 37 
                                    +FW++++d++
  gi|121636504|ref|YP_976727.1| 153 DFWDHVVDSA 162
                                    5*****9875 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.3
                                    HHHHHHHTT-HHHHHHHHHHHH CS
                 CysG_dimeriser  37 pvaelvlaGdeeeAealleqaL 58 
                                    ++a+++ +Gd   A+++ +++L
  gi|121636504|ref|YP_976727.1| 201 KLADAICSGDPTGAKKAAQDLL 222
                                    58999**************987 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00057      0.34      24      46 ..      35      57 ..      32      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00057
                         HTH_50 24 pStRklAkrLGvShtaianklrk 46
                                   pS R lA+ LGvS  a+   l++
  gi|121636504|ref|YP_976727.1| 35 PSERRLAELLGVSRPAVREALKR 57
                                   8**************99776665 PP

>> FadR_C  FadR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.16       2     127 ..      76     204 ..      75     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                         FadR_C   2 nfwetsglniletlirldedkvpelvedllsaRtnisaiyireavknnpekslevlaevkeledkaea...faefDYklf 78 
                                    +f   +gl++l  l+  + +   ++v  +l+aR +  +   + a + n+ + +e+l++  +  d++e+   ++++  +++
  gi|121636504|ref|YP_976727.1|  76 DFRRHAGLDLLPRLLFRNGELDISVVRSILEARLRNFPKVAELAAERNEPELAELLQDSLRALDTEEDpivWQRHTLDFW 155
                                    5677899*******999***************************************98776666654322288889999* PP

                         FadR_C  79 relafasgnkiYvLilNglkklYsrvgslyFsneearelalkfYrelke 127
                                     ++  ++g  +  L+ N+++  Y+   +++ +  +a     + Yr+l  
  gi|121636504|ref|YP_976727.1| 156 DHVVDSAGSIVDRLMYNAFRAAYEPTLAALTTTMTAAAKRPSDYRKLAD 204
                                    ***********************97666666666665555556666655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       8.6   5.1e+03      24      24 ..      58      58 ..      37      76 .. 0.60
   2 ?    3.2   0.0      0.34     2e+02       9      38 ..      88     119 ..      80     122 .. 0.78
   3 ?    0.0   0.3       3.5   2.1e+03      17      38 ..     124     147 ..     116     150 .. 0.54
   4 ?    6.8   0.1     0.025        15      14      38 ..     208     232 ..     191     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 8.6
                         TPR_14 24 l 24
                                   l
  gi|121636504|ref|YP_976727.1| 58 L 58
                                   2 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.34
                         TPR_14   9 eallalGdpde..AiallrralalaPddaeaw 38 
                                    ++l+++G++d    + +l+++l+ +P+ ae+ 
  gi|121636504|ref|YP_976727.1|  88 RLLFRNGELDIsvVRSILEARLRNFPKVAELA 119
                                    678889988855556699999*****998875 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 3.5
                         TPR_14  17 pdeAiallrrala..laPddaeaw 38 
                                      e ++ll++ l+  +  +d+ +w
  gi|121636504|ref|YP_976727.1| 124 EPELAELLQDSLRalDTEEDPIVW 147
                                    346677888877732234555555 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.025
                         TPR_14  14 lGdpdeAiallrralalaPddaeaw 38 
                                    +Gdp +A ++++++l+la +++ a 
  gi|121636504|ref|YP_976727.1| 208 SGDPTGAKKAAQDLLELANTSLMAV 232
                                    7****************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1795.96
//
Query:       gi|121636505|ref|YP_976728.1|  [L=265]
Description: integral membrane protein YrbE2a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-56  190.2  24.8    4.2e-56  190.0  24.8    1.1  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0  24.8   2.4e-60   4.2e-56       2     211 ..      47     256 ..      46     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 2.4e-60
                           MlaE   2 veqlefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtmr 81 
                                    +eq +f++  sl+++l +++++++++++ +  +l++fga +  g+  al  v +lgP++t l++ag+ ++ai+A+lG+++
  gi|121636505|ref|YP_976728.1|  47 IEQGWFITSVSLLPTLAVSIPLTVLIIFTLNILLAEFGAADISGAGAALGAVTQLGPLTTVLVIAGAGATAICADLGART 126
                                    6899**************************************************************************** PP

                           MlaE  82 vteeidAlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllK 161
                                    ++eeidA+ev+gidpi++lvvPrv+A++i++ lL+  ++++g++gg++++v+++++s+gay+ +++ ++ l++++++++K
  gi|121636505|ref|YP_976728.1| 127 IREEIDAMEVLGIDPIHRLVVPRVVAATIVAALLNGAVITIGLVGGFVFSVFIQHVSAGAYVGTLTLVTGLPEVIISVVK 206
                                    ******************************************************************************** PP

                           MlaE 162 alvfGliialiacyqGltakggaegvgrattravvtsivlilvvdlvltl 211
                                    ++ fGli +l++cy+Glt+kgg++gvg+a++++ v ++++++++++vlt 
  gi|121636505|ref|YP_976728.1| 207 SATFGLIAGLVGCYRGLTTKGGPKGVGTAVNETLVLCVIALFATNVVLTT 256
                                    ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1928.63
//
Query:       gi|121636506|ref|YP_976729.1|  [L=295]
Description: integral membrane protein YrbE2b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-50  172.3  26.9    1.3e-50  172.0  26.9    1.1  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0  26.9   7.3e-55   1.3e-50       5     208 ..      76     279 ..      72     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 7.3e-55
                           MlaE   5 lefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtmrvte 84 
                                    +++v+++++ i+++++l  G ++a+qg+  l ++g+e+++g++ ala +r  +P++ ++ +a+ vG++ +A+lG+mr++e
  gi|121636506|ref|YP_976729.1|  76 AMAVVGGTVAIIGFVTLSGGSLIAIQGFASLGNIGVEAFTGFFAALANTRVAAPIVSGVALAATVGAGATAQLGAMRISE 155
                                    5788999************************************************************************* PP

                           MlaE  85 eidAlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllKalv 164
                                    eidAlevmgi++i++lv +r+l+++++++ L+++a+ +++++g +v+++++g+s g+y ++++++l+++d+ ++++  ++
  gi|121636506|ref|YP_976729.1| 156 EIDALEVMGIKSISFLVSTRILGGLVVIMPLYALALDMAFTSGQVVTTVFYGQSNGTYEHYFRTFLRPEDVGWSVVEVVI 235
                                    ******************************************************************************** PP

                           MlaE 165 fGliialiacyqGltakggaegvgrattravvtsivlilvvdlv 208
                                    +++++++++cy+G+ta+gg+ gvg+a+ r++  s+v ++vv l+
  gi|121636506|ref|YP_976729.1| 236 IAVVVMITHCYYGYTASGGPVGVGQAVGRSMRFSLVSVVVVVLL 279
                                    ***************************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2184.58
//
Query:       gi|121636507|ref|YP_976730.1|  [L=404]
Description: mce-family protein mce2A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.5e-103  345.0   0.0   7.1e-103  343.5   0.1    1.6  2  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
    4.9e-14   52.4   0.1    9.9e-14   51.4   0.1    1.5  1  MlaD       MlaD protein


Domain annotation for each model (and alignments):
>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.15   1.4e+03     197     222 ..      55      93 ..      29     115 .. 0.67
   2 !  343.5   0.1  7.9e-107  7.1e-103       1     257 []     153     404 .]     153     404 .] 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.15
                      Mce4_CUP1 197 P..............ggapgcgslqditrd.wperelvsdt 222
                                                    g++g+  + +i+rd  p+ +lv d+
  gi|121636507|ref|YP_976730.1|  55 LvmeagskvtyngveIGRVGS--ISEIERDgRPAAKLVLDV 93 
                                    444444444444444688888..559999999999999887 PP

  == domain 2  score: 343.5 bits;  conditional E-value: 7.9e-107
                      Mce4_CUP1   1 enllplleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLd 80 
                                    e++++++e+vdP++LnatLsAva+A +G+G ++Ges++++n++L++lNprlpql  d+r+ladl++vY da+pdl+++L+
  gi|121636507|ref|YP_976730.1| 153 ETITSIAEKVDPIELNATLSAVAQAPDGLGGKFGESIVNGNQILAQLNPRLPQLGYDVRRLADLGEVYVDASPDLWSFLQ 232
                                    689***************************************************************************** PP

                      Mce4_CUP1  81 navttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLakYspeltCllrnladvepkvakal 160
                                    na tt+rT+++qq++Lda+llaa+g++ntg+d+++r+g++L+r+aadl+pt++lL++Yspel+C++rn++d++pkva+a+
  gi|121636507|ref|YP_976730.1| 233 NALTTARTLTSQQRDLDAALLAATGAGNTGEDVFARGGPYLARAAADLVPTATLLDTYSPELFCMIRNFHDAAPKVADAV 312
                                    *******************************************************************************9 PP

                      Mce4_CUP1 161 ggtngyslrldatlllgarnpYvypedlPrvnakgGPggapgcgslqditrd.wperelvsdtlapagvsiap..hleig 237
                                    gg ngysl + a++ lga+npYvyp++lPrvna+gGPgg+pgc  +q+itr+ wp+++lv+dt    g+s+ap  h+e+g
  gi|121636507|ref|YP_976730.1| 313 GG-NGYSL-AAAGTILGAPNPYVYPDNLPRVNAHGGPGGRPGC--WQTITRElWPAPYLVMDT----GASLAPynHVELG 384
                                    99.*****.6778888899************************..******************....99999999***** PP

                      Mce4_CUP1 238 vPawaeYvvgrqvgslligP 257
                                    +P+++eYv+grq+g+++i+P
  gi|121636507|ref|YP_976730.1| 385 QPMFTEYVWGRQYGENTINP 404
                                    *******************9 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   1.1e-17   9.9e-14       3      80 ..      44     124 ..      42     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.1e-17
                           MlaD   3 ytvtaqfdnang.LkvgapVryrGvtvGrVtsi.tldpdtrrv.tvtvdldkksetsipedsraqvstggllgekyiald 79 
                                     ++t+ +++a+  +++g++V+y+Gv++GrV si +++ d+r + ++ +d++++++++ip ++ a ++  +l+g+ky+al+
  gi|121636507|ref|YP_976730.1|  44 TELTMVASRAGLvMEAGSKVTYNGVEIGRVGSIsEIERDGRPAaKLVLDVNPRYISLIPVNVVADIEAATLFGNKYVALS 123
                                    689999***************************666777776669*********************************97 PP

                           MlaD  80 p 80 
                                     
  gi|121636507|ref|YP_976730.1| 124 A 124
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2669.24
//
Query:       gi|121636508|ref|YP_976731.1|  [L=343]
Description: mce-family protein mce2B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-16   58.3   1.2    2.9e-15   56.3   0.3    2.2  2  MlaD           MlaD protein
    4.9e-05   22.9   1.6      7e-05   22.4   1.6    1.1  1  Mce4_CUP1      Cholesterol uptake porter CUP1 of Mce4, putati
  ------ inclusion threshold ------
      0.041   13.9   1.4      0.059   13.4   1.4    1.2  1  EspB           Enterobacterial EspB protein
       0.19   10.1   0.0       0.25    9.7   0.0    1.1  1  Hemagglutinin  Haemagglutinin


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.3   6.4e-19   2.9e-15       5      78 ..      39     110 ..      35     113 .. 0.96
   2 ?   -0.2   0.0      0.28   1.3e+03      12      22 ..     318     328 ..     316     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.4e-19
                           MlaD   5 vtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyial 78 
                                    + a f++++gL +g+ Vr +Gv+vG+V+++tl + +++v v++++d   + s+++ ++a+++  +l+g++y++l
  gi|121636508|ref|YP_976731.1|  39 YSAVFTHVSGLRAGQFVRAAGVEVGKVAKVTLIDGDKQVLVDFTVD--RSLSLDQATTASIRYLNLIGDRYLEL 110
                                    7899******************************************..************************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                           MlaD  12 angLkvgapVr 22 
                                    +ngL++g pVr
  gi|121636508|ref|YP_976731.1| 318 VNGLQPGGPVR 328
                                    89********8 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.6   1.6e-08     7e-05       5     125 ..     145     265 ..     143     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-08
                      Mce4_CUP1   5 plleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavt 84 
                                    pl ++ dP k n++ s++ + ++G+G  + + l++  ++ ++l +r   + e +++l+++ ++  +   ++ +++d++ +
  gi|121636508|ref|YP_976731.1| 145 PLFQTLDPDKVNSIASSIITVFQGQGATINDILDQTASLTATLADRDHAIGEVVNNLNTVLATTVKHQTEFDRTVDKLEV 224
                                    7899**************************************************************************** PP

                      Mce4_CUP1  85 tsrTiveqqaeLdalllaavglsntgadllerngdnLirla 125
                                      + ++++++ L+a+ +++ +++ t+adll + ++ L + +
  gi|121636508|ref|YP_976731.1| 225 LITGLKNRADPLAAAAAHISSAAGTLADLLGADRPLLHSSF 265
                                    ********************************999987765 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   1.3e-05     0.059     120     201 ..     164     247 ..     153     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                           EspB 120 siadaagetvgklqqgiasvaaaaktrneqrakavedlqesnleeykkt..vresqDkiasvlqdlrstardlndlinrv 197
                                     + +  g t++++ + +as++a  + r+    ++v++l    + + k +   +++ Dk    +  l+++a+ l  + +++
  gi|121636508|ref|YP_976731.1| 164 TVFQGQGATINDILDQTASLTATLADRDHAIGEVVNNLNTVLATTVKHQteFDRTVDKLEVLITGLKNRADPLAAAAAHI 243
                                    5667789********************************99999988652268*************************** PP

                           EspB 198 aqSa 201
                                    +++a
  gi|121636508|ref|YP_976731.1| 244 SSAA 247
                                    *997 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   5.6e-05      0.25     358     418 ..     179     239 ..     167     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.6e-05
                                    TEEEEEEXHHHHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHH CS
                  Hemagglutinin 358 qGsavaadkkstqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvddgfld 418
                                    q ++++a +    +ai ++ +++n++    +k+ +   + +++le  i  l+++ d + + 
  gi|121636508|ref|YP_976731.1| 179 QTASLTATLADRDHAIGEVVNNLNTVLATTVKHQTEFDRTVDKLEVLITGLKNRADPLAAA 239
                                    55667777788899**************************************999977543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2287.27
//
Query:       gi|121636509|ref|YP_976732.1|  [L=481]
Description: mce-family protein mce2C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-11   42.6   0.1    1.1e-10   41.7   0.1    1.5  1  MlaD         MlaD protein
    3.4e-05   23.4   1.4       0.06   12.8   0.0    2.2  2  Mce4_CUP1    Cholesterol uptake porter CUP1 of Mce4, putative
    0.00075   19.7   1.7       0.21   11.9   0.1    2.6  3  DUF948       Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.023   15.2   0.9       0.04   14.4   0.9    1.3  1  FlgN         FlgN protein
      0.058   13.8   0.0       0.43   11.0   0.0    2.4  2  PLAC9        Placenta-specific protein 9
       0.16   10.8   0.2       0.23   10.3   0.2    1.2  1  Spc7         Spc7 kinetochore protein
       0.19   11.3   1.0       0.27   10.8   1.0    1.1  1  PspA_IM30    PspA/IM30 family
       0.19   11.7   1.8        4.8    7.3   0.1    2.8  2  MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndro
       0.19   11.7   0.4        5.1    7.2   0.0    2.4  3  DUF1664      Protein of unknown function (DUF1664)
        0.3   10.0   0.1       0.63    8.9   0.1    1.3  1  IFT57        Intra-flagellar transport protein 57
       0.36   11.0   2.5         11    6.1   1.7    2.3  2  DUF4107      Protein of unknown function (DUF4107)


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.1   6.6e-14   1.1e-10       2      80 ..      39     112 ..      38     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6.6e-14
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    + t++aqf + +g++ g++V+++Gv+vG V+s+ +   ++rv + ++l    ++ i  +sra ++t ++lg k ++++p
  gi|121636509|ref|YP_976732.1|  39 TPTYYAQFADMGGINTGDKVEIAGVNVGLVRSLAI--RGNRVLIGFSLP---GKTIGMQSRAAIRTDTILGRKNLEIEP 112
                                    579******************************99..***********9...*************************98 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.7e-05      0.06      59     108 ..     156     205 ..     150     209 .. 0.91
   2 !   10.6   0.6   0.00017      0.28      64     138 ..     203     276 ..     200     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                      Mce4_CUP1  59 reladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsn 108
                                    r+l+ l++++++ ap+l  aL+ +   s+T+  + +++++ll++a  +++
  gi|121636509|ref|YP_976732.1| 156 RSLNVLSETFDQTAPHLSAALEGVKAFSDTVGRRGEQIEQLLANANRIAR 205
                                    678899**************************************988876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                      Mce4_CUP1  64 ladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLakY 138
                                    +a v +d ++++   L na t  ++ ++++++L+ ll+++ ++s +++ l+++n +nL +++a+lr  +e L k 
  gi|121636509|ref|YP_976732.1| 203 IARVLGDRSEQVNGLLVNAKTLLAAFKQRSQALRILLTNVSEASAQVSGLITDN-PNLNHVLAQLRTVSEELVKR 276
                                    6788999999***************************************99987.89999999999888766665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0034       5.6      28      82 ..     151     205 ..     139     209 .. 0.87
   2 !   11.9   0.1   0.00013      0.21      42      87 ..     207     252 ..     201     254 .. 0.90
   3 ?   -3.0   0.0       5.5   8.9e+03      34      45 ..     265     276 ..     258     294 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                         DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                    +d++++++++l +  d++   + ++l+ v++  + v ++ e++++l ++++ +++
  gi|121636509|ref|YP_976732.1| 151 IDAVKRSLNVLSETFDQTAPHLSAALEGVKAFSDTVGRRGEQIEQLLANANRIAR 205
                                    6889999999999999999999999999999999999999999999999998876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                         DUF948  42 vdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    ++  +++v++ll ++++ll+  +++++++  l ++v +++++vs l
  gi|121636509|ref|YP_976732.1| 207 LGDRSEQVNGLLVNAKTLLAAFKQRSQALRILLTNVSEASAQVSGL 252
                                    566789*************************************976 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.5
                         DUF948  34 tieelekqvdpi 45 
                                    +++++ +++ + 
  gi|121636509|ref|YP_976732.1| 265 QLRTVSEELVKR 276
                                    233333333322 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9   2.5e-05      0.04       6     105 ..     181     275 ..     177     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTC CS
                           FlgN   6 eLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakee 85 
                                    ++ +++ ++ e++e+Ll+  ++ +++L ++  e+ ++ll + ++ll++ +q  q+++ ll+++++    a +s l+   +
  gi|121636509|ref|YP_976732.1| 181 AFSDTVGRRGEQIEQLLANANRIARVLGDRS-EQVNGLLVNAKTLLAAFKQRSQALRILLTNVSEA--SAQVSGLIT--D 255
                                    6677888899999*****************9.9*********************************..89******9..* PP

                                    CHHHHHHHHHHHHHHHHHHH CS
                           FlgN  86 deelkelwqelkelleelke 105
                                    ++ l+++ ++l+++ eel +
  gi|121636509|ref|YP_976732.1| 256 NPNLNHVLAQLRTVSEELVK 275
                                    ***********999997643 PP

>> PLAC9  Placenta-specific protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.43      20      48 ..     151     179 ..     138     186 .. 0.84
   2 ?   -1.3   0.0       1.9     3e+03      29      64 ..     269     303 ..     245     306 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                          PLAC9  20 hlavqsrldvieetvektvehleaevkGl 48 
                                      av++ l+v+ et ++t  hl a ++G+
  gi|121636509|ref|YP_976732.1| 151 IDAVKRSLNVLSETFDQTAPHLSAALEGV 179
                                    469*********************99986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                          PLAC9  29 vieetvektvehleaevkGllgqle.elawnlPpGPf 64 
                                    v ee+v +  e l a+v  llg+    l+  + +GPf
  gi|121636509|ref|YP_976732.1| 269 VSEELVKRKNE-L-ADVAVLLGRYTaALTEAVGSGPF 303
                                    55666655544.3.77888888764257777777777 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00014      0.23     136     226 ..     192     284 ..     170     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                           Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelaelka 213
                                     +e+L  +++++   l + +e+++    ++++ll +++++ ++l+  l++  ea+++++    d+ +L+ +  +l+++++
  gi|121636509|ref|YP_976732.1| 192 QIEQLLANANRIARVLGDRSEQVNGLLVNAKTLLAAFKQRSQALRILLTNVSEASAQVSGliTDNPNLNHVLAQLRTVSE 271
                                    57888888888888888888888888999999999999999999999999999999988876788999999999999999 PP

                           Spc7 214 eieekkkelaelq 226
                                    e+ ++k+ela++ 
  gi|121636509|ref|YP_976732.1| 272 ELVKRKNELADVA 284
                                    9999999988765 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00016      0.27      37     125 ..     184     274 ..     176     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                      PspA_IM30  37 selakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg..eeeLArealaeikslekqaealetqlaqqrsav 114
                                    +++++  ++++q++a++ + +r l + +eq++ l ++Ak +L +   + ++ r +l+   ++  q+ +l t   +++   
  gi|121636509|ref|YP_976732.1| 184 DTVGRRGEQIEQLLANANRIARVLGDRSEQVNGLLVNAKTLLAAFkqRSQALRILLTNVSEASAQVSGLITDNPNLNHVL 263
                                    56777789*******************************9998644499999**************************** PP

                      PspA_IM30 115 eqlrkqleale 125
                                    +qlr+  e+l 
  gi|121636509|ref|YP_976732.1| 264 AQLRTVSEELV 274
                                    ****9877665 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.083   1.4e+02       4      33 ..     191     220 ..     189     246 .. 0.89
   2 ?    7.3   0.1     0.003       4.8       6      47 ..     259     297 ..     256     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.083
                    MCC-bdg_PDZ   4 srIeeLkaqnelLsltleerkqqseeLsld 33 
                                    ++Ie+L a+ ++++++l  r++q ++L + 
  gi|121636509|ref|YP_976732.1| 191 EQIEQLLANANRIARVLGDRSEQVNGLLVN 220
                                    58********************99998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.003
                    MCC-bdg_PDZ   6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsnatALvlA 47 
                                    + ++ aq++ +s  l  rk++ +   ++lg++    +AL  A
  gi|121636509|ref|YP_976732.1| 259 LNHVLAQLRTVSEELVKRKNELADVAVLLGRYT---AALTEA 297
                                    67999***************************9...888766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0031       5.1      34     107 ..     142     215 ..     134     232 .. 0.66
   2 ?    3.4   0.0     0.044        72      38     110 ..     181     253 ..     178     256 .. 0.88
   3 ?    1.9   0.1      0.13   2.2e+02      44      65 ..     260     281 ..     256     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                        DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                    vTk      ++ v ++l+ +se+  +t  hLs+ ++ v +  d + +  ++i++ ++++++  + +g+ +e+v+
  gi|121636509|ref|YP_976732.1| 142 VTKAATGWDIDAVKRSLNVLSETFDQTAPHLSAALEGVKAFSDTVGRRGEQIEQLLANANRIARVLGDRSEQVN 215
                                    45555555566677777777777777777777777777777777766666666666666666666666666665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.044
                        DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                     +sd v + ++q+eq+ ++ ++  r L +r ++v+  l + k + ++ k+  +++r  l++++e + +v+ ++
  gi|121636509|ref|YP_976732.1| 181 AFSDTVGRRGEQIEQLLANANRIARVLGDRSEQVNGLLVNAKTLLAAFKQRSQALRILLTNVSEASAQVSGLI 253
                                    67899999999***************************99999999999999999999999988888887665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.13
                        DUF1664  44 esvskqleqvseslaatkrhLs 65 
                                    ++v  ql +vse+l + k++L+
  gi|121636509|ref|YP_976732.1| 260 NHVLAQLRTVSEELVKRKNELA 281
                                    77889*************9997 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00039      0.63     229     331 ..     175     283 ..     149     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00039
                          IFT57 229 mkkhkksieeslpetksqlkklhedisktlekiesrEkylnsql...eellqeyreaqeelsevkekykqlsegvseltr 305
                                      +  k++++++ +  +q+++l  + ++    +  r +++n  l   ++ll+ +++ ++ l  +  +++++s++vs l +
  gi|121636509|ref|YP_976732.1| 175 ALEGVKAFSDTVGRRGEQIEQLLANANRIARVLGDRSEQVNGLLvnaKTLLAAFKQRSQALRILLTNVSEASAQVSGLIT 254
                                    44455556666666667777777777777777777777777644222778888999999988888888888888777654 PP

                          IFT57 306 ...elaeiseelekvkqemeergssmtDg 331
                                       +l+ +  +l++v++e+ +r+++++D 
  gi|121636509|ref|YP_976732.1| 255 dnpNLNHVLAQLRTVSEELVKRKNELADV 283
                                    22258999999999999999999999996 PP

>> DUF4107  Protein of unknown function (DUF4107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.053        87      53      84 ..     191     222 ..     167     236 .. 0.83
   2 ?    6.1   1.7     0.007        11     115     139 ..     456     480 ..     444     481 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.053
                        DUF4107  53 desenllGdddeiaknlkdfsdqlkGeklnln 84 
                                    ++ e+ll + + ia+ l d s+q++G  +n  
  gi|121636509|ref|YP_976732.1| 191 EQIEQLLANANRIARVLGDRSEQVNGLLVNAK 222
                                    677999********************877655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.007
                        DUF4107 115 mppyagyGmynnpfepfdpkiGGsn 139
                                    +pp a+ G   +p epf   +GGsn
  gi|121636509|ref|YP_976732.1| 456 LPPNAPPGARTQPLEPFPDGTGGSN 480
                                    79**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 3367.14
//
Query:       gi|121636510|ref|YP_976733.1|  [L=516]
Description: mce-family protein mce2Da [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-12   46.5   0.0    5.7e-12   45.8   0.0    1.4  1  MlaD          MlaD protein
     0.0003   20.3   2.0    0.00056   19.4   2.0    1.4  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
     0.0074   15.9   0.1        0.6    9.6   0.2    2.1  2  Vps5          Vps5 C terminal like
  ------ inclusion threshold ------
      0.088   12.8   4.3        2.5    8.1   0.3    2.3  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.3e-15   5.7e-12       2      80 ..      46     120 ..      45     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.3e-15
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    + tv+a+f++a  L +g++V+++Gv+vG++++i  +p +++++vt+      +  +p+ ++a++ + +l+ ++ i+l+p
  gi|121636510|ref|YP_976733.1|  46 TTTVVAYFSEALALYPGDKVQIMGVRVGSIDKI--EPAGDKMRVTLHYS--NKYQVPATATASILNPSLVASRTIQLSP 120
                                    579******************************..88************..9999**********************98 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.0   1.3e-07   0.00056      20     128 ..     175     290 ..     171     309 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
                      Mce4_CUP1  20 sAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdna.......vttsrTiveq 92 
                                    +++a+ L+G+G++l e+l+ l + L++lN+   ++ +  r+la +  +  +  ++++   +n+       ++  + +++ 
  gi|121636510|ref|YP_976733.1| 175 ESAADNLAGKGRQLNETLNSLSQALTALNEGRGDFVAITRSLALFVSALYQNDQQFVALNENLaeftdwfTKSDHDLADT 254
                                    689999*************************9999999999998766555555555555555500000005555555555 PP

                      Mce4_CUP1  93 qaeLdalllaavglsntgadllerngdnLirlaadl 128
                                     +++d++l ++ ++ ++ +++l++  +nL++++++l
  gi|121636510|ref|YP_976733.1| 255 VERIDDVLGTVRKFVSDNRSVLAADVNNLADATTTL 290
                                    555555555555555555555555555555555554 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2   0.00013       0.6      35      89 ..     187     242 ..     182     257 .. 0.85
   2 !    5.3   0.0    0.0028        12      21      89 ..     239     308 ..     230     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                           Vps5  35 slesqLkkLykaiellvsqrkelasataelakslesLaslels.kslsralsqlae 89 
                                    +l+++L +L++a+ +l++ r +++++t  la  +++L + + +  +l + l+++++
  gi|121636510|ref|YP_976733.1| 187 QLNETLNSLSQALTALNEGRGDFVAITRSLALFVSALYQNDQQfVALNENLAEFTD 242
                                    799**********************************9988775666666666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0028
                           Vps5  21 EqDewFedkkqeldslesqLkkLykai.ellvsqrkelasataelakslesLaslelskslsralsqlae 89 
                                    E  +wF +  + l +  +++  +  ++ + ++++r+ la+ +++la + ++L + e   +l +al+ l +
  gi|121636510|ref|YP_976733.1| 239 EFTDWFTKSDHDLADTVERIDDVLGTVrKFVSDNRSVLAADVNNLADATTTLVQPEPRDGLETALHVLPT 308
                                    6667887777776665555555444441678999**********************99999999988765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4    0.0042        19      90     121 ..     174     205 ..     172     213 .. 0.79
   2 ?    8.1   0.3   0.00057       2.5      14      84 ..     229     303 ..     223     322 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0042
                   Baculo_PEP_C  90 lnsiltnLlssvtNinstLnnllqalnnldlg 121
                                    ++s   nL+ +   +n+tLn+l qal +l++g
  gi|121636510|ref|YP_976733.1| 174 IESAADNLAGKGRQLNETLNSLSQALTALNEG 205
                                    56666677777778899999999999999877 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00057
                   Baculo_PEP_C  14 qfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq........dtlr 84 
                                    qf+ L++ L+      ++   +la +++ i+ +L+++ + ++    + ++ l++ ++nL da  +l         +t  
  gi|121636510|ref|YP_976733.1| 229 QFVALNENLAEFTDWFTKSDHDLADTVERIDDVLGTVRKFVS----DNRSVLAADVNNLADATTTLVqpeprdglETAL 303
                                    677777777777666667777777777777777777555444....455566666666666666655444453333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3391.82
//
Query:       gi|121636511|ref|YP_976734.1|  [L=402]
Description: mce family lipoprotein LprL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-11   43.5   0.0    6.6e-11   42.4   0.0    1.6  1  MlaD          MlaD protein
  ------ inclusion threshold ------
       0.05   13.1   3.9      0.099   12.1   1.0    2.1  3  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
      0.082   13.0   7.1       0.18   11.8   3.4    2.5  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.1e-14   6.6e-11       4      79 ..      68     139 ..      65     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.1e-14
                           MlaD   4 tvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyiald 79 
                                    t+++q+++   L+ +++Vr++ v vG+V++i+l   +  +t+t++l+   ++++p++++a++ +++llg + ++l 
  gi|121636511|ref|YP_976734.1|  68 TIYVQMPDTLALNTNSRVRVADVWVGTVRDISL--RNWIATLTLELE--PTVRLPANATAKIGQTSLLGTQHVELA 139
                                    89*****************************99..666666666666..***********************9986 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   1.7e-05     0.099      41     124 ..     190     276 ..     166     285 .. 0.77
   2 ?   11.9   1.2   1.8e-05      0.11      26     140 ..     196     310 ..     194     318 .. 0.85
   3 ?   -2.7   0.0      0.54   3.2e+03      85     108 ..     340     363 ..     335     368 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                      Mce4_CUP1  41 nevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaa...vglsntgadllern 117
                                     e+L+ l+ +  q+re +++la++++  ++   dl +a+d++ +  + i+++++ Ld++l+++   ++   ++ +l+++ 
  gi|121636511|ref|YP_976734.1| 190 TEILNILDGHAGQIREFLERLATFTAELNNQRGDLTRAIDSTNQLLTIIANRNDTLDRVLTDVpplIEHFADTGQLFADA 269
                                    479999******************************************************99722222233344556666 PP

                      Mce4_CUP1 118 gdnLirl 124
                                     ++L r+
  gi|121636511|ref|YP_976734.1| 270 TESLGRF 276
                                    6666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.8e-05
                      Mce4_CUP1  26 LeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavg 105
                                    L+G   ++ e l++l ++ +elN++  +l++ i + ++l ++ a+  + l ++L+++    +  ++  +  +++  ++  
  gi|121636511|ref|YP_976734.1| 196 LDGHAGQIREFLERLATFTAELNNQRGDLTRAIDSTNQLLTIIANRNDTLDRVLTDVPPLIEHFADTGQLFADATESLGR 275
                                    56666777788899999999999999999999999999999999999999999999999999999999999999999999 PP

                      Mce4_CUP1 106 lsntgadllerngdnLirlaadlrptlelLakYsp 140
                                    +s+ +++ l++ ++nL +++++l+  l+ L++ sp
  gi|121636511|ref|YP_976734.1| 276 FSEVANRALAATRPNLHQTLQSLQRPLRQLERASP 310
                                    99999999999999999999999888888877776 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.54
                      Mce4_CUP1  85 tsrTiveqqaeLdalllaavglsn 108
                                     s+T     ++Ld++ll+ +g+s 
  gi|121636511|ref|YP_976734.1| 340 VSATFDVTLSALDNALLSGTGISG 363
                                    566666666777777777777665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.4     3e-05      0.18      47     118 ..     185     255 ..     168     274 .. 0.82
   2 ?    2.8   0.1     0.019   1.1e+02      45      79 ..     271     305 ..     257     359 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                   Baculo_PEP_C  47 LnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl 118
                                    L+ +++++ + l   + ++ ++l++L +  ++l+ + r +Lt      ++Ll+ ++N n tL  +l+++  l
  gi|121636511|ref|YP_976734.1| 185 LDVIQTEILNILDGHAGQIREFLERLATFTAELN-NQRGDLTRAIDSTNQLLTIIANRNDTLDRVLTDVPPL 255
                                    788999999999999999***********99999.457778777777789999999******9999999777 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.019
                   Baculo_PEP_C  45 tqLnalsedlksllaeldtrldtlltnLtdalnal 79 
                                    ++L+ +se  +++la+ + +l+++l+ L++ l +l
  gi|121636511|ref|YP_976734.1| 271 ESLGRFSEVANRALAATRPNLHQTLQSLQRPLRQL 305
                                    33333333334444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2518.74
//
Query:       gi|121636512|ref|YP_976735.1|  [L=516]
Description: mce-family protein mce2F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-16   58.4   0.2    1.2e-15   57.5   0.2    1.5  1  MlaD             MlaD protein
      3e-07   30.1   0.6    4.7e-07   29.5   0.6    1.2  1  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
    0.00011   22.4   0.2        0.2   11.9   0.0    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.026   14.6   1.4        3.6    7.6   0.8    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.085   13.0   0.0       0.15   12.2   0.0    1.3  1  BLOC1S3          Biogenesis of lysosome-related organelles co
       0.17   12.1   0.1         17    5.6   0.0    2.8  3  FAA_hydrolase_N  Fumarylacetoacetase N-terminal


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.2   4.2e-19   1.2e-15       3      79 ..      40     112 ..      38     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 4.2e-19
                           MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyiald 79 
                                    yt++a++++++gL   a+V+yrG+t+G+Vt +  +p++r++++t+++d   +  ip+d++a v++ + +ge++++l+
  gi|121636512|ref|YP_976735.1|  40 YTLYAELPRSGGLYRTANVTYRGITIGKVTGV--EPTERGARATMSID--NGYQIPTDASANVHSVSAVGEQFVDLV 112
                                    99******************************..88************..*************************97 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.6   1.6e-10   4.7e-07      14     140 ..     154     280 ..     147     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.6e-10
                      Mce4_CUP1  14 kLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqq 93 
                                      +++L+ ++eA+ G+G  l + +++ +++ +++  +l+++ + i++ a + d   ++ +++ +  +n+ t ++  ++  
  gi|121636512|ref|YP_976735.1| 154 RVASVLHEASEAVGGLGSSLNRLIEATQAIAHDVRGSLEDIDDIIERSAPIIDSQVNSGNEIARWAANLNTLAAQTAQTD 233
                                    4789**************************************************************************** PP

                      Mce4_CUP1  94 aeLdalllaavglsntgadllerngdnLirlaadlrptlelLakYsp 140
                                     +++++l++a+ ++++++  +++ +++L +++a+l+  +++L++Y++
  gi|121636512|ref|YP_976735.1| 234 PAVRSILANAAPTADQVNATFSDVRESLPQTLANLEVVIDMLKRYHN 280
                                    *********************************************86 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   6.7e-05       0.2      29      76 ..     153     200 ..     135     217 .. 0.78
   2 !    7.7   0.1    0.0014       4.3      21      64 ..     240     283 ..     215     300 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                         DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                    d++a+ ++e  + v+++   +++l++ +++++ dv++ le++d ++e 
  gi|121636512|ref|YP_976735.1| 153 DRVASVLHEASEAVGGLGSSLNRLIEATQAIAHDVRGSLEDIDDIIER 200
                                    456667777778888888888888888888888888888888887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                         DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvn 64 
                                    l +++ t+d+++at  ++++ + ++l ++e +++  ++  ++v+
  gi|121636512|ref|YP_976735.1| 240 LANAAPTADQVNATFSDVRESLPQTLANLEVVIDMLKRYHNGVE 283
                                    44555566666666666666666666666666666665555555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0071        21      29      94 ..     129     198 ..     124     202 .. 0.73
   2 ?    7.6   0.8    0.0012       3.6       9      80 ..     209     276 ..     203     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                   Baculo_PEP_C  29 nvqilaqlatlldaietqLnal.sedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                    ++++ +q+  +lda ++ L  l ++++ s+l e ++    l ++l++L +a +a++ ++r  L+ ++ i+
  gi|121636512|ref|YP_976735.1| 129 TTTVPSQIGPALDAANRGLAVLpKDRVASVLHEASEavgGLGSSLNRLIEATQAIAHDVRGSLEDIDDII 198
                                    5677788888888888888877345688888888885555666666666777777799999999998876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                   Baculo_PEP_C   9 ggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                    +++gn+       Ln++ +q++q+  ++ ++l++ + +    ++++++  +++++ l ++l+nL+  +  l+
  gi|121636512|ref|YP_976735.1| 209 VNSGNEIARWAANLNTLAAQTAQTDPAVRSILANAAPT----ADQVNATFSDVRESLPQTLANLEVVIDMLK 276
                                    67788877788889999999988888888888877664....445666666677777777777777776665 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05      0.15      98     166 ..     140     208 ..      92     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                        BLOC1S3  98 LrEsNarLrkdvkeavsqvysaaskelesvtsqLnksqsaiqnashsirlilddlkavsekldiitscs 166
                                    L+ +N+ L    k++v  v ++as+ +  + s Ln+   a q ++h +r  l+d++++ e+   i++++
  gi|121636512|ref|YP_976735.1| 140 LDAANRGLAVLPKDRVASVLHEASEAVGGLGSSLNRLIEATQAIAHDVRGSLEDIDDIIERSAPIIDSQ 208
                                    566677777777899*****************************************9998876666655 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   3.5e+03      15      36 ..      97     118 ..      90     142 .. 0.74
   2 ?    5.6   0.0    0.0058        17      46      78 ..     161     194 ..     126     204 .. 0.76
   3 ?    3.4   0.1     0.029        85      53      81 ..     218     246 ..     197     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                    SEEEEEEETTEEEEHHHHHHTT CS
                FAA_hydrolase_N  15 eprigvaIGdqvldLsalaeag 36 
                                    + +   a+G+q +dL   +++g
  gi|121636512|ref|YP_976735.1|  97 NVHSVSAVGEQFVDLVSTRTSG 118
                                    55677899*****998876655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0058
                                    .SSSGTT.SSSSSHHHHHT-HHHHHHHHHHHHHH CS
                FAA_hydrolase_N  46 eekesvf.sqptLnafaalgrevwravRaalqel 78 
                                    e+ e+v    ++Ln++++  +++ + vR  l ++
  gi|121636512|ref|YP_976735.1| 161 EASEAVGgLGSSLNRLIEATQAIAHDVRGSLEDI 194
                                    34444444569*****************999875 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.029
                                    SSSSSHHHHHT-HHHHHHHHHHHHHHHBT CS
                FAA_hydrolase_N  53 sqptLnafaalgrevwravRaalqelLsa 81 
                                     + +Ln +aa+ +++  avR+ l ++  +
  gi|121636512|ref|YP_976735.1| 218 WAANLNTLAAQTAQTDPAVRSILANAAPT 246
                                    4589*****************99988744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3270.43
//
Query:       gi|121636513|ref|YP_976736.1|  [L=130]
Description: hypothetical protein BCG_0641c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-15   55.2   0.0    1.1e-14   55.0   0.0    1.1  1  PIN       PIN domain
     0.0032   17.2   0.0     0.0054   16.5   0.0    1.4  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.2e-18   1.1e-14       3     119 ..       8     122 ..       6     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.2e-18
                                    E-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHH CS
                            PIN   3 lDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaa 82 
                                     DTsv+i +   + +     +++++ +e+ +s+++l El+ ++    s+ e+aa+++ +++l+ +++ l id+++ e +a
  gi|121636513|ref|YP_976736.1|   8 ADTSVFIGIEATRFDP----DRFAG-YEWGVSVVTLGELRLGVLQ-ASGPEAAARRLSTYQLAQRFEPLGIDEAVSEAWA 81 
                                    69*****777666666....45555.*******************.********************************** PP

                                    HHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  83 eialkyg.....llpnDaliaAtAkehgikliatfDedfrrv 119
                                     + +k++     + +nD +iaAtA +hgi+++ t D+d + +
  gi|121636513|ref|YP_976736.1|  82 LLVSKLRaaklrVPINDSWIAATAVAHGIAIL-TQDNDYAAM 122
                                    *****************************777.*****9876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     6e-07    0.0054      24      61 ..      84     122 ..      70     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-07
                        DUF5615  24 vlhvrelgleg.asDeeileyAkeedriivTkDkDFgel 61 
                                    v+ +r+++l+  ++D+ i + A +++ +i+T+D+D+  +
  gi|121636513|ref|YP_976736.1|  84 VSKLRAAKLRVpINDSWIAATAVAHGIAILTQDNDYAAM 122
                                    5566777777449**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 952.90
//
Query:       gi|121636514|ref|YP_976737.1|  [L=85]
Description: hypothetical protein BCG_0642c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-10   40.2   0.1    2.3e-10   40.1   0.1    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   1.3e-14   2.3e-10       2      52 ..       3      52 ..       2      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.3e-14
                                   EEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.H CS
                PhdYeFM_antitox  2 kivsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqelt 52
                                    ++++++++++ +e+l++v++gee + + + ++pva++v+l+  ++++ + 
  gi|121636514|ref|YP_976737.1|  3 ATIPARDLRNHTAEVLRRVAAGEE-IEVLKDNRPVARIVPLKRRRQWLPAA 52
                                   589*********************.****************9877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 631.98
//
Query:       gi|121636515|ref|YP_976738.1|  [L=411]
Description: hypothetical protein BCG_0643c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-25   89.8   0.0      2e-25   89.3   0.0    1.2  1  DUF4143   Domain of unknown function (DUF4143)
    1.4e-20   73.7   0.0    3.3e-20   72.5   0.0    1.6  2  AAA_14    AAA domain
  ------ inclusion threshold ------
      0.086   13.2   0.1        0.2   12.0   0.1    1.9  1  AAA_16    AAA ATPase domain
       0.12   12.8   0.0       0.49   10.8   0.0    1.9  2  DUF2746   Protein of unknown function (DUF2746)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   4.5e-29     2e-25       4     121 ..     202     358 ..     180     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 4.5e-29
                                    xxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143   4 irklagvrdpeelrk.......................................glverlppwsespnskkrlrkspKly 44 
                                    ir+++++++++e+++                                       +l++r+p+w  s+n++++++++pKl+
  gi|121636515|ref|YP_976738.1| 202 IREISPIERLAEMPRvlrlcaartgaelnvsalandlsiparttagylalleaaFLIHRVPAW--STNLSRKVIRRPKLV 279
                                    677888888888888999999999999999999999999999*********************..*************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  45 fvDtGLlvallgldkeelledsenkGallEnlVaqeLlky...sekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                    + D+GL+++llg++ ++l +    +G llE++Va+e++k+   s++ +++l+++rd+ gaEvD+v+e+ +g++++iEvK+
  gi|121636515|ref|YP_976738.1| 280 VSDSGLACHLLGVTGATLDRPGRPLGPLLETFVANEIRKQltwSTE-RPSLWHFRDRGGAEVDLVLEHPDGRVCGIEVKA 358
                                    *****************88888********************6555.9********99*********************8 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   7.3e-24   3.3e-20       3     129 ..      20     136 ..      18     138 .. 0.88
   2 ?   -2.6   0.0       1.2   5.2e+03      73      97 ..     258     280 ..     258     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 7.3e-24
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewek 81 
                                    +++v+ GaR+vGKTtl+ +l    +  + s   ++ldd  ++++a     ++++ ++ +       l++DE+q  p++++
  gi|121636515|ref|YP_976738.1|  20 PVVVVNGARQVGKTTLVARLD---Y--PGSSEVVSLDDVANRDAARD--DPRAFVSRpV-----DTLVIDEAQLEPGLFR 87 
                                    799*************98884...4..46788899999999877744..4799999834.....45************** PP

                         AAA_14  82 alkslvdeg.knldvivtGSnskllskeiatslagrvaeielyplsfaE 129
                                    a+k  vd++ + +++++tGS+ +l   ++a+ l+grv+ iel+p+s+ E
  gi|121636515|ref|YP_976738.1|  88 AIKAEVDRDrRPGRFLLTGSARLLSAPDMADALVGRVEIIELWPFSQGE 136
                                    *******88688**********************************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                         AAA_14  73 iqevpewekalkslvdegknldviv 97 
                                    i++vp w++ l + v ++++  ++v
  gi|121636515|ref|YP_976738.1| 258 IHRVPAWSTNLSRKVIRRPK--LVV 280
                                    7999*****99999988744..444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.5e-05       0.2      23      46 ..      18      41 ..       6     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellr 46
                                   ++++v++ G++ vGK++lv +l  
  gi|121636515|ref|YP_976738.1| 18 DTPVVVVNGARQVGKTTLVARLDY 41
                                   4589***************99984 PP

>> DUF2746  Protein of unknown function (DUF2746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   4.6e+03      61      83 ..      11      33 ..       6      40 .. 0.82
   2 ?   10.8   0.0   0.00011      0.49      10      35 ..     246     271 ..     240     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                        DUF2746 61 svkadisdlkeivlqgfhqvnes 83
                                   sv a ++d   +v++g +qv ++
  gi|121636515|ref|YP_976738.1| 11 SVLAALADTPVVVVNGARQVGKT 33
                                   78899999999******999876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                        DUF2746  10 gdyvtllgvafltfsvpawftgrark 35 
                                      y++ll  afl   vpaw t  +rk
  gi|121636515|ref|YP_976738.1| 246 AGYLALLEAAFLIHRVPAWSTNLSRK 271
                                    5799*****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3292.37
//
Query:       gi|121636516|ref|YP_976739.1|  [L=137]
Description: hypothetical protein BCG_0644c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-12   47.5   1.5    2.6e-12   47.3   1.5    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   1.5   1.5e-16   2.6e-12       3     120 ..       7     126 ..       5     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.5e-16
                                    E-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                            PIN   3 lDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                    +DTsv i ll r +  ++a+++++++  e +++ ++laE++ vl+r +++ +++a   +++ll  +    l ++++ +e+
  gi|121636516|ref|YP_976739.1|   7 VDTSVAIPLLvRTHTAHAAVVAWWAH-REAALCGHALAETYSVLTR-LPRDLRLAPMDAARLLtERFAAPLLLSSRTTEH 84 
                                    9************************9.*******************.777777777777777767777777788888888 PP

                                    HHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  81 aaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                      ++ ++ +     ++Dal+a  A eh+++l  t+D + +++ 
  gi|121636516|ref|YP_976739.1|  85 LPRVLAQFEitgGAVYDALVALAAAEHRAELA-TRDARAKDTY 126
                                    888888888888*****************999.****988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1018.31
//
Query:       gi|121636517|ref|YP_976740.1|  [L=78]
Description: hypothetical protein BCG_0645c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-07   31.4   0.0    1.8e-07   30.9   0.0    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    0.00098   19.1   0.0     0.0016   18.4   0.0    1.3  1  MraZ            MraZ protein, putative antitoxin-like
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.19   11.8   0.0    1.5  2  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     3e-11   1.8e-07       4      41 ..       6      43 ..       3      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3e-11
                                   TTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCC CS
                 MazE_antitoxin  4 GnsgavriPkevrfelgireGdevelevdgdkiilrpl 41
                                   +  g+++ Pk +r++lg+++G++ve+++ g ++ l+p 
  gi|121636517|ref|YP_976740.1|  6 DAAGRIVVPKPLREALGLQPGSTVEISRYGAGLHLIPT 43
                                   6679************************9998888886 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-07    0.0016      10      29 ..       5      24 ..       2      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-07
                                   B-TTSEEE--CHHHHHTTSC CS
                           MraZ 10 lDakGRlllPaklreeakle 29
                                   +Da+GR+ +P+ lre+++l+
  gi|121636517|ref|YP_976740.1|  5 VDAAGRIVVPKPLREALGLQ 24
                                   7****************998 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05      0.19      33      62 ..       3      32 ..       1      40 [. 0.89
   2 ?   -2.5   0.0      0.96   5.7e+03       6      12 ..      55      62 ..      51      77 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                      AbrB-like 33 vsVqknGnLliGsaYTkklgLkpGdefeIk 62
                                   + V   G++++ +   ++lgL+pG + eI+
  gi|121636517|ref|YP_976740.1|  3 AVVDAAGRIVVPKPLREALGLQPGSTVEIS 32
                                   679999**********************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.96
                      AbrB-like  6 lleAkG.i 12
                                   +l A G  
  gi|121636517|ref|YP_976740.1| 55 VLVATGeT 62
                                   45555533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 634.19
//
Query:       gi|121636518|ref|YP_976741.1|  [L=168]
Description: two component sensor kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-20   72.9   0.0    3.5e-20   72.6   0.0    1.1  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    0.00035   20.5   0.2    0.00053   20.0   0.2    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.053   13.3   0.0        6.3    6.6   0.0    2.2  2  HPTransfase  Histidine phosphotransferase C-terminal domain
      0.097   13.0   0.1       0.23   11.8   0.1    1.7  1  HalOD1       Halobacterial output domain 1
       0.13   12.2   0.0       0.41   10.6   0.0    1.8  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   9.8e-24   3.5e-20       2     110 ..      34     139 ..      33     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 9.8e-24
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                    d+++Lr+i+  ++dNa+ +   +gei v+ +a+++ + i v+D G+G     l+  f++f++ ++t+rgg g+GlGl+iv
  gi|121636518|ref|YP_976741.1|  34 DPDHLRRILTAVLDNAITH--GDGEIAVTAHARDGAVDIGVRDHGPGFADHFLPVAFDRFTR-ADTARGGRGSGLGLAIV 110
                                    899***************9..79********9889***************************.9**************** PP

                                    HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                     +l++++gG+ + ++ p++G + ++tlp 
  gi|121636518|ref|YP_976741.1| 111 AALTTTHGGHANATNHPDGGAELRITLPT 139
                                    **************************996 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   1.5e-07   0.00053      40     109 ..      46     114 ..      11     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.5e-07
                    HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGrGlalikglv 109
                                    + Na++h+      g++ v++  +++a+ + v+D+Gpgf  + lp           +  ++ +G+Gla++++l+
  gi|121636518|ref|YP_976741.1|  46 LDNAITHGD-----GEIAVTAHARDGAVDIGVRDHGPGFADHFLPVAFDRFTradtARGGRGSGLGLAIVAALT 114
                                    679999998.....578899999***************777755544332224456788888999999999886 PP

>> HPTransfase  Histidine phosphotransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0017       6.3      39      74 ..      42      78 ..      33      82 .. 0.88
   2 ?    4.6   0.0    0.0075        27      39      90 ..     107     157 ..     104     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0017
                                   HHHHHHHC-TT-.-EEEEEEEEETTCEEEEEEEESTT CS
                    HPTransfase 39 llliaedalprG.GtitvsaegeegageirvrakGer 74
                                   l  ++++a+ +G G+i+v+a++++ga  i vr +G+ 
  gi|121636518|ref|YP_976741.1| 42 LTAVLDNAITHGdGEIAVTAHARDGAVDIGVRDHGPG 78
                                   56788999999999***************99999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0075
                                    HHHHHHHC-TT--EEEEEEEEETTCEEEEEEEESTT----HHHHHHHTT--- CS
                    HPTransfase  39 llliaedalprGGtitvsaegeegageirvrakGerarldeelaeaLagaaa 90 
                                    l+++a+ +  +GG  + + +  +g +e+r++   +r  ++eel ++ + ++ 
  gi|121636518|ref|YP_976741.1| 107 LAIVAALTTTHGGHANATNH-PDGGAELRITLPTPRPPFHEELPRITSSDTK 157
                                    8899999999*******999.9*********************999888766 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.3e-05      0.23      15      58 ..      15      61 ..       7      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.3e-05
                         HalOD1 15 avegvdptel.ep.LydaiDpdALdaLfas.radgearadgsvsFty 58
                                   a++g d t   ep L+ +iDpd L ++++   ++  + +dg+++ t+
  gi|121636518|ref|YP_976741.1| 15 AATGADITTRaEPdLFVSIDPDHLRRILTAvLDNAITHGDGEIAVTA 61
                                   45667766655777*************99943444477777777665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.41       2      92 ..      34     129 ..      33     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                    HATPase_c_5   2 kdldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg........ekkkle..sskskkeehGiGl 71 
                                    ++ +l +il  +LdNAi         + +I +t++ +++++ i +  +  g          +++   ++ + ++  G+Gl
  gi|121636518|ref|YP_976741.1|  34 DPDHLRRILTAVLDNAITH------GDGEIAVTAHARDGAVDIGVRDHGPGfadhflpvAFDRFTraDTARGGRGSGLGL 107
                                    567789999999***9964......356899999999999999999997775555555422444434668889999**** PP

                    HATPase_c_5  72 ksireivkkykgnls.ieaedg 92 
                                      +  ++ +++g+++ +++ dg
  gi|121636518|ref|YP_976741.1| 108 AIVAALTTTHGGHANaTNHPDG 129
                                    ************9983444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1136.19
//
Query:       gi|121636519|ref|YP_976742.1|  [L=156]
Description: two component sensor kinase (first part) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-13   51.1   0.3    2.5e-13   50.2   0.3    1.5  1  HAMP            HAMP domain
    4.7e-06   26.5   0.6    4.6e-05   23.4   0.2    2.6  2  HisKA           His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
        1.1    9.6   5.4         11    6.3   5.4    2.3  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.3   4.2e-17   2.5e-13       1      53 []      61     117 ..      61     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4.2e-17
                                    HHHHTTHHHHHHHHHHHHHHTTT...BTSSTCCT.TSSSHHHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaaG...dldtrlpv.sgrDEiGeLarafNaMldrLre 53 
                                    ll+r+ lrP+ r+++aa+ +      d d++lpv  ++DEi+ La ++N+Ml+rL++
  gi|121636519|ref|YP_976742.1|  61 LLSRAALRPVDRIRAAAQTLTTTphpDTDAPLPVpPTDDEIAWLATTLNTMLTRLQR 117
                                    689******************85566*****************************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16   9.5e+02      16      31 ..      69      88 ..      67     120 .. 0.61
   2 !   23.4   0.2   7.7e-09   4.6e-05       3      26 ..     123     146 ..     121     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHHC...... CS
                          HisKA 16 PLsailgnaeaLkre....g 31
                                   P+  i+++a++L  +     
  gi|121636519|ref|YP_976742.1| 69 PVDRIRAAAQTLTTTphpdT 88
                                   66678888888866544330 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7.7e-09
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          HisKA   3 grflagvaHELrtPLsailgnaea 26 
                                    ++f+a+ +HELrtPL+ +   +e+
  gi|121636519|ref|YP_976742.1| 123 QQFVADASHELRTPLALLTTELEL 146
                                    79**************98877775 PP

>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.4    0.0019        11      52      78 ..      34      66 ..       1      67 [. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0019
                 PhaG_MnhG_YufB 52 a......slkllliilfllltaPvaahliaraa 78
                                          + +l+ i+ ++l+ a+vaa+l++raa
  gi|121636519|ref|YP_976742.1| 34 DditadlVRELVTILPIVLVIAAVAAYLLSRAA 66
                                   0455553446677778999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 998.03
//
Query:       gi|121636520|ref|YP_976743.1|  [L=253]
Description: two component DNA binding transcriptional regulatory protein tcrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-29  102.1   0.0    2.9e-29  101.5   0.0    1.3  1  Response_reg  Response regulator receiver domain
    1.2e-22   79.7   0.1    2.2e-22   78.9   0.1    1.4  1  Trans_reg_C   Transcriptional regulatory protein, C terminal


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.0   3.2e-33   2.9e-29       1     111 [.      25     134 ..      25     135 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 3.2e-33
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    +l+++D+p++ +ll+++l+eeg  +v++++dg+ a++ ++  ++d ++lD+++pg+dG+e++ ++r++   +pv++lta+
  gi|121636520|ref|YP_976743.1|  25 ILVIEDEPKMTALLARALTEEGH-TVDTVADGRHAVAAVDGGDYDAVVLDVMLPGIDGFEVCARLRRQRVWTPVLMLTAR 103
                                    89*********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++ +d++++l+ gadd+l+Kpf+ +eL ++l
  gi|121636520|ref|YP_976743.1| 104 GAVTDRIAGLDGGADDYLTKPFNLDELFARL 134
                                    ***************************9987 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.1   2.5e-26   2.2e-22       2      77 .]     168     242 ..     167     242 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2.5e-26
                                    EEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   2 eeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    +e++l++kef lLe+L+++pg v +r++Lle++w+  ++  ++ vdv+i++LR+k++  ++    +et+rg GYrl
  gi|121636520|ref|YP_976743.1| 168 TEIRLSHKEFTLLEALIRRPGIVHTRAQLLERCWDAAYEARSNIVDVYIRYLRDKIDR-PFGVTSLETIRGAGYRL 242
                                    789*******************************************************.88889**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1780.07
//
Query:       gi|121636521|ref|YP_976744.1|  [L=103]
Description: hypothetical protein BCG_0649 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-05   23.0   0.0    0.00015   22.2   0.0    1.3  1  PepSY     Peptidase propeptide and YPEB domain
     0.0034   17.3   1.2     0.0048   16.9   1.2    1.2  1  PepSY_2   Peptidase propeptide and YPEB domain
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.028   14.3   0.1    1.0  1  TrbI      Bacterial conjugation TrbI-like protein
      0.068   13.2   0.3       0.12   12.3   0.3    1.5  1  Rib       Rib/alpha-like repeat


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.4e-08   0.00015       4      53 ..      40      87 ..      39      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.4e-08
                                   HHHHHHHHHHHSTTE.EEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEE CS
                          PepSY  4 eeqAlaiAlaavpgk.iieielededdgrlvYevelstaepegpeyevfiD 53
                                   +++A+a+A +avpg  + e+e e + +g ++Y v +++  p+g+++ev  D
  gi|121636521|ref|YP_976744.1| 40 ADRARAAAVQAVPGGtAGEVETETG-EGAAAYGVLVTR--PDGTRVEVHLD 87
                                   689*********9888*********.*********999..99999887676 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.2   1.1e-06    0.0048       2      75 ..      13      88 ..      10      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                        PepSY_2  2 aalalalallaaaAlA..grrdtdspkadwlpreklvakleaqGykvkkievddggc...yEvegldkdGkkveikldp 75
                                   aa+a+ + + ++ A A  g+++ + p ad   r+++v+  +  G +  ++e + g+    y v ++  dG +ve+ ld 
  gi|121636521|ref|YP_976744.1| 13 AAAAIGIGAGSGIAAAfdGEDEVTGPDADRA-RAAAVQ--AVPGGTAGEVETETGEGaaaYGVLVTRPDGTRVEVHLDR 88
                                   3455555555566666778888888888865.444444..456778888888777666789999*************96 PP

>> TrbI  Bacterial conjugation TrbI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.1e-06     0.028     108     185 ..      15      90 ..       2      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.1e-06
                                    SS-SEEEEES---EEEE------------HHHHHHHHT-T.T-BHHHHHHHHHHHHTTS--EEEE-TT-EEEEEESSEE CS
                           TrbI 108 aalllsllsgagellnaassssttsstgtqslaaavgega.sqalsqvaqrilkraeniqptievpqGtkvtvvvnrdl 185
                                    aa+   ++++++ ++ a++ +++ ++   ++++aa+++++ + ++ +v +++ + a  +   ++ p Gt+v+v  +rd+
  gi|121636521|ref|YP_976744.1|  15 AAI---GIGAGSGIAAAFDGEDEVTGPDADRARAAAVQAVpGGTAGEVETETGEGAAAYGVLVTRPDGTRVEVHLDRDF 90 
                                    222...244455555677777777777778999999999867899********************************98 PP

>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   2.7e-05      0.12      33      58 ..      59      85 ..      31      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                            Rib 33 pdt.tksGekeavvvVtYPDGskdevp 58
                                   ++t t +G     v Vt PDG++ ev+
  gi|121636521|ref|YP_976744.1| 59 VETeTGEGAAAYGVLVTRPDGTRVEVH 85
                                   3331568999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 803.35
//
Query:       gi|121636522|ref|YP_976745.1|  [L=316]
Description: lipoprotein lpqO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-92  303.5   0.0    8.2e-46  154.8   0.0    2.1  2  DUF1529   Domain of Unknown Function (DUF1259)
  ------ inclusion threshold ------
        2.1    8.5   7.5       0.23   11.6   0.5    2.7  3  DUF3168   Protein of unknown function (DUF3168)
        6.2    6.9   6.2        7.7    6.6   2.8    2.8  2  PepSY_2   Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> DUF1529  Domain of Unknown Function (DUF1259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0   3.9e-47   2.3e-43       2     120 ..      52     171 ..      51     172 .. 0.98
   2 !  154.8   0.0   1.4e-49   8.2e-46       2     120 ..     194     311 ..     193     312 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 3.9e-47
                        DUF1529   2 aidkilgrkgtlkgg.vykvtipRndlkvtidgvelkpalglttwaaFqslgggkalvmGdlvlledEvnpvikalreng 80 
                                    ++++ilgr+g+l++g vyk+ ++R+dl+v+++gv+++pal+l++w+aF+++ +g++++mGdlv++edE+  v++a++++g
  gi|121636522|ref|YP_976745.1|  52 PVADILGRTGKLNDGsVYKIGFARSDLSVQTKGVTVAPALSLGSWVAFARTPDGQTMLMGDLVVTEDELASVTDAVQAGG 131
                                    699***************************************************************************** PP

                        DUF1529  81 ievtalHnhlleeqPrlfylHieavgdavklArklraald 120
                                    +++talH+hlle++P ++++Hi ++gda++lAr++r+ald
  gi|121636522|ref|YP_976745.1| 132 LQQTALHKHLLEQSPPIWWTHIAGHGDAADLARAVRSALD 171
                                    ***************************************8 PP

  == domain 2  score: 154.8 bits;  conditional E-value: 1.4e-49
                        DUF1529   2 aidkilgrkgtlkggvykvtipRndlkvtidgvelkpalglttwaaFqslgggkalvmGdlvlledEvnpvikalrengi 81 
                                    aid++lgr+gt++ggvyk+ i+R+d  vt++g+ ++p++gl+t+++Fq++g+g+a+++Gd+v++++Ev++v++alr +gi
  gi|121636522|ref|YP_976745.1| 194 AIDEALGRSGTIAGGVYKFFIARRDP-VTMSGMLIPPSMGLATALNFQPTGNGRAAINGDFVMTAAEVQDVVQALRGGGI 272
                                    79************************.***************************************************** PP

                        DUF1529  82 evtalHnhlleeqPrlfylHieavgdavklArklraald 120
                                    +++a+Hnh ++eqPrlfy+H++a++dav+lAr+lraa+d
  gi|121636522|ref|YP_976745.1| 273 DIVAIHNHGFDEQPRLFYMHFWAENDAVALARTLRAAVD 311
                                    *************************************98 PP

>> DUF3168  Protein of unknown function (DUF3168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.74   4.4e+03      73      83 ..      11      21 ..       4      49 .. 0.55
   2 ?   11.6   0.5   3.9e-05      0.23      60      89 ..     150     181 ..     149     205 .. 0.72
   3 ?   -0.1   0.1      0.17     1e+03      58      82 ..     292     312 ..     281     316 .] 0.60

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.74
                        DUF3168 73 aaavraaLdda 83
                                   a  + aaL+ +
  gi|121636522|ref|YP_976745.1| 11 ALLAAAALALT 21
                                   22222222222 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.9e-05
                        DUF3168  60 warepgraeakalaaavraaLddaala..lpg 89 
                                    w+   g+++a +la+avr+aLd+++ +  +p+
  gi|121636522|ref|YP_976745.1| 150 WTHIAGHGDAADLARAVRSALDATDTPppAPA 181
                                    6666899**************77766633333 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.17
                        DUF3168  58 dvwarepgraeakalaaavraaLdd 82 
                                    + wa+ +    a ala+  raa+d+
  gi|121636522|ref|YP_976745.1| 292 HFWAEND----AVALARTLRAAVDA 312
                                    6777333....44555555555533 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.8    0.0013       7.7       2      27 ..       9      34 ..       8      59 .. 0.86
   2 ?   -0.4   0.1       0.2   1.2e+03       3      28 ..      86     106 ..      85     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0013
                        PepSY_2  2 aalalalallaaaAlAgrrdtdspka 27
                                   +a++la+a+la +A Ag++d+ +p +
  gi|121636522|ref|YP_976745.1|  9 MAALLAAAALALTACAGSDDKGEPDD 34
                                   78999999999999998888877765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                        PepSY_2   3 alalalallaaaAlAgrrdtdspkad 28 
                                    ++a al+l + +A+A     ++p  +
  gi|121636522|ref|YP_976745.1|  86 TVAPALSLGSWVAFA-----RTPDGQ 106
                                    577799999******.....444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2304.54
//
Query:       gi|121636523|ref|YP_976746.1|  [L=202]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-15   56.5   1.3      5e-15   55.9   1.3    1.2  1  Resolvase  Resolvase, N terminal domain
     0.0066   16.6   0.0      0.017   15.3   0.0    1.7  1  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.3   0.5      0.061   13.1   0.1    1.9  2  HTH_23     Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   1.3   8.4e-19     5e-15       2     139 ..      61     193 ..      60     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 8.4e-19
                                    EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                      Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                    ++YaRvS+++q+ +l+rQ+++++ +a+++++ ++k++++   S  + +R+++ ++l++l+      +vve+ dR+ R  +
  gi|121636523|ref|YP_976746.1|  61 AVYARVSSADQKSDLDRQVARVTSWATAEQIPVDKVVTEV-GSVLNGHRRKFPAVLRDLSV---TRIVVEHRDRFCRFGS 136
                                    79***************************999999*****.9999999*************...689************* PP

                                    S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHH.HHHHHHCT-TTHHHH CS
                      Resolvase  82 dlltlleelrekgvslvsldegidtstpm.grlllqilaalaef.erelirertkeglaa 139
                                    ++++    l+++g +lv++d+  + +++    ++  + +++a++  ++  ++r k+++aa
  gi|121636523|ref|YP_976746.1| 137 EYVHA--ALAAQGRELVVVDS-AEVDDDLvWDMTEILTSMCARLyGKRAAQNRAKRAVAA 193
                                    ***99..99999999999996.44444443444444444445542333344444444444 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.8e-06     0.017      12      39 ..      19      48 ..      11      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-06
                         HTH_17 12 gvsrstvyrlirrgelpaa...kiGrrwrip 39
                                   gv r t+yr+ ++g l ++   k+Gr ++++
  gi|121636523|ref|YP_976746.1| 19 GVARVTAYRWFHAGLL-PVparKVGRLILVD 48
                                   99************99.55586799977776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     1e-05     0.061      14      39 ..       4      30 ..       1      32 [. 0.86
   2 ?   -3.5   0.1       1.7     1e+04       5      14 ..     187     196 ..     183     198 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                         HTH_23 14 lae.GlsvreIAreLgvsrrTvyrwlk 39
                                   +++ G++ ++ A++ gv r T yrw +
  gi|121636523|ref|YP_976746.1|  4 CRNrGMNLAAWAERNGVARVTAYRWFH 30
                                   4546999******************87 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                         HTH_23   5 reRlrillll 14 
                                     +R+ ++ ++
  gi|121636523|ref|YP_976746.1| 187 AKRAVAAAAV 196
                                    4566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1534.87
//
Query:       gi|121636524|ref|YP_976747.1|  [L=247]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-10   40.2   0.3    1.8e-10   40.2   0.3    2.2  3  HTH_OrfB_IS605  Helix-turn-helix domain
      6e-05   23.3   0.5    0.00016   21.9   0.0    2.0  2  OrfB_IS605      Probable transposase


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.3     2e-14   1.8e-10       4      41 ..      13      50 ..      12      57 .. 0.91
   2 ?   -3.3   0.1      0.73   6.5e+03      24      33 ..     104     113 ..     103     114 .. 0.78
   3 ?   -3.1   0.1      0.65   5.9e+03      24      28 ..     162     166 ..     161     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2e-14
                 HTH_OrfB_IS605  4 kaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkea 41
                                   +a+++ l PT eQ+ +lar+fG+ R +YN+  a+ k  
  gi|121636524|ref|YP_976747.1| 13 QAFRFTLDPTAEQAHALARHFGARRKAYNWTVAQLKAD 50
                                   69*****************************9998765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.73
                 HTH_OrfB_IS605  24 fGcvRfVYNk 33 
                                    +G+v   +N+
  gi|121636524|ref|YP_976747.1| 104 AGAVDAYWNW 113
                                    5777788**9 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.65
                 HTH_OrfB_IS605  24 fGcvR 28 
                                    +GcvR
  gi|121636524|ref|YP_976747.1| 162 IGCVR 166
                                    8***9 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.54   4.9e+03      71      87 ..     168     184 ..     165     189 .. 0.65
   2 !   21.9   0.0   1.8e-08   0.00016       4      37 ..     205     238 ..     200     247 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.54
                     OrfB_IS605  71 kkasrklarlhrkrsrr 87 
                                    ++ +r++ rl +k + r
  gi|121636524|ref|YP_976747.1| 168 HENTRRIERLIAKDRAR 184
                                    45677777777665554 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.8e-08
                     OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgt 37 
                                    v+ +++++++ +++++g+D+G+++Latv+t dg+
  gi|121636524|ref|YP_976747.1| 205 VQRPQQPNVELPESRIGVDVGVRRLATVATADGA 238
                                    44455699************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2035.61
//
Query:       gi|121636525|ref|YP_976748.1|  [L=128]
Description: hypothetical protein BCG_0653 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 979.43
//
Query:       gi|121636526|ref|YP_976749.1|  [L=81]
Description: hypothetical protein BCG_0654 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-23   82.6   1.7    2.8e-23   82.5   1.7    1.0  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   1.7   1.5e-27   2.8e-23       1      82 []       1      80 [.       1      80 [. 0.94

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.5e-27
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHT.S--SS-SSTTSTTTXXXXXX CS
                  PSK_trans_fac  1 MaLnIkdpeverlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaa.kaekedrspdekllyDeegl 81
                                   MaLnIkdp v++ ++++a++tges+ +Av +A+ erl+rl   r+++l++rlla+ ++ a  ++ +++r ++++llyDe+gl
  gi|121636526|ref|YP_976749.1|  1 MALNIKDPSVHQAVKQIAKITGESQARAVATAVNERLARL---RSDDLAARLLAIGHKTASrMSPEAKRLDHDALLYDERGL 79
                                   ****************************************...59***************96666677789999******** PP

                                   X CS
                  PSK_trans_fac 82 p 82
                                   p
  gi|121636526|ref|YP_976749.1| 80 P 80
                                   8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 586.54
//
Query:       gi|121636527|ref|YP_976750.1|  [L=133]
Description: hypothetical protein BCG_0655 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   54.8   0.1    1.3e-14   54.7   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   7.4e-19   1.3e-14       1     119 [.       1     124 [.       1     127 [. 0.92

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 7.4e-19
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    +++DTs++ia+lr+e++a+a++++l++++   +sa+++ E+ +vl +  ++     + +++l++ +++ + p+++++a+ 
  gi|121636527|ref|YP_976750.1|   1 MIVDTSAIIAILRDEDDAAAYADALANADVRRLSAASYLECGIVLDS--QRDPVISRALDELIEEAEFVVEPVTERQARL 78 
                                    68*********************************************..666666666666666**************** PP

                                    HHHHHHHHH........SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  81 aaeialkyg........llpnDaliaAtAkehgikliatfDedfrrv 119
                                    a++ ++  g        l+  D+l +A+A+ ++ +l+  + +df ++
  gi|121636527|ref|YP_976750.1|  79 ARAAYADFGrgsghpagLNFGDCLSYALAIDRREPLL-WKGNDFGHT 124
                                    *************************************.999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1041.72
//
Query:       gi|121636528|ref|YP_976751.1|  [L=75]
Description: hypothetical protein BCG_0656 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 550.23
//
Query:       gi|121636529|ref|YP_976752.1|  [L=385]
Description: hypothetical protein BCG_0657c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   18.9   1.2     0.0026   17.6   1.2    1.7  1  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.2   1.4e-07    0.0026      20      45 ..       2      27 ..       1      28 [. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-07
                           VbhA 20 saetvadleayvrGeIdadElvrrvr 45
                                   ++e++ +l++y+rGe++ad+++r ++
  gi|121636529|ref|YP_976752.1|  2 DDELRGLLARYARGELSADDARRAIL 27
                                   899********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2842.95
//
Query:       gi|121636530|ref|YP_976753.1|  [L=127]
Description: hypothetical protein BCG_0658c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-21   74.0   0.2    5.5e-21   73.7   0.2    1.1  1  DUF4926   Domain of unknown function (DUF4926)
  ------ inclusion threshold ------
       0.12   12.1   0.1       0.15   11.8   0.1    1.2  1  Phage_G   Major spike protein (G protein)
       0.22   11.4   0.0       0.29   11.0   0.0    1.2  1  SH3_13    ATP-dependent RecD-like DNA helicase SH3 domain


Domain annotation for each model (and alignments):
>> DUF4926  Domain of unknown function (DUF4926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.2   9.3e-25   5.5e-21       1      57 [.      58     113 ..      58     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9.3e-25
                        DUF4926   1 lldvVaLledlpekgLrrGqvGTvVevyeegeaYeVEFsdddGeTlalltLseeqle 57 
                                    ++dvV+L++d+p+k+L +G+vG+vV +y+ g +YeV+F+ ++G+T+a++tL+ ++++
  gi|121636530|ref|YP_976753.1|  58 EHDVVVLTRDVPDKSLIAGDVGAVVGRYAAG-GYEVDFTAANGCTVAVVTLAGDDIR 113
                                    8******************************.**********************997 PP

>> Phage_G  Major spike protein (G protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.6e-05      0.15      47     124 ..      17      93 ..       4     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                                    EEE-SEEEEEEEEEE--TTSS-SEEEEEEEEEEEESS----EEEEEEEEESS--SB--SS-EEE----EEETTEEEEE CS
                        Phage_G  47 ltvnagnggflhciqmdtsvnaanqvvsvgadiafdadpkffaclvrfesssvpttlptaydvyplngrhdggyytvk 124
                                    ++ n g  g+lhc+q  ++ n +  +      i   + p +    v + +  vp     a dv  + gr+  g y v 
  gi|121636530|ref|YP_976753.1|  17 VSWNHGAAGWLHCVQCGSATNPTACL-DWLPPIHARSGPMYAEHDVVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVD 93 
                                    56799***********9999987654.555678889999999999999999999999999999999999987777664 PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.9e-05      0.29      22      53 ..      52      83 ..      36      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                         SH3_13 22 ggrvfrvgDkVmqlkNnydkgvfNGDiGiike 53
                                   +g ++ + D V+ ++  +dk +  GD+G ++ 
  gi|121636530|ref|YP_976753.1| 52 SGPMYAEHDVVVLTRDVPDKSLIAGDVGAVVG 83
                                   56779***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 926.43
//
Query:       gi|121636531|ref|YP_976754.1|  [L=201]
Description: hypothetical protein BCG_0659 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1525.35
//
Query:       gi|121636532|ref|YP_976755.1|  [L=855]
Description: hypothetical protein BCG_0660c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-09   37.4   6.0    2.4e-09   36.9   6.0    1.2  1  SEC-C           SEC-C motif
     0.0014   18.6   0.4     0.0096   15.9   0.1    2.7  2  DUF2384         Protein of unknown function (DUF2384)
  ------ inclusion threshold ------
        7.5    6.9  11.0        2.3    8.5   0.6    4.2  4  Se-cys_synth_N  Selenocysteine synthase N terminal


Domain annotation for each model (and alignments):
>> SEC-C  SEC-C motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   6.0   4.1e-13   2.4e-09       1      17 [.     449     465 ..     449     467 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.1e-13
                          SEC-C   1 RNdpCPCGSGkKYKkCC 17 
                                    RN++C+CGSG+KYKkC+
  gi|121636532|ref|YP_976755.1| 449 RNEACWCGSGRKYKKCH 465
                                    9**************** PP

>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       0.7   4.2e+03      10      17 ..     363     370 ..     342     371 .. 0.73
   2 !   15.9   0.1   1.6e-06    0.0096      14      39 ..     800     825 ..     789     834 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.7
                        DUF2384  10 eraarWLr 17 
                                    + a+rWLr
  gi|121636532|ref|YP_976755.1| 363 RVAVRWLR 370
                                    45677998 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.6e-06
                        DUF2384  14 rWLrrPnpaLggrtPldlldteaGar 39 
                                     WL +P paL+g+tP + +d  +  +
  gi|121636532|ref|YP_976755.1| 800 SWLDQPIPALDGHTPRQAADDPTRRA 825
                                    5**************99998765555 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.24   1.4e+03       8      15 ..      39      52 ..      39      82 .. 0.81
   2 ?   -2.9   0.0       1.4   8.6e+03      20      31 ..     289     300 ..     285     306 .. 0.75
   3 ?    2.3   0.2     0.033   1.9e+02      17      32 ..     514     529 ..     496     529 .. 0.93
   4 ?    8.5   0.6   0.00039       2.3       5      24 ..     732     772 ..     732     774 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                 Se-cys_synth_N  8 DaLLtal......e 15
                                   Da+L+al      +
  gi|121636532|ref|YP_976755.1| 39 DAVLRALrletewP 52
                                   9*****96655554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                 Se-cys_synth_N  20 laalpRalvrda 31 
                                     ++lpR+++  a
  gi|121636532|ref|YP_976755.1| 289 PDELPRDVLATA 300
                                    568999998766 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.033
                 Se-cys_synth_N  17 rallaalpRalvrdav 32 
                                    +al+aal  +lv+dav
  gi|121636532|ref|YP_976755.1| 514 DALAAALADPLVLDAV 529
                                    699***********98 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.00039
                 Se-cys_synth_N   5 PsVDaLLtal.....................earallaalp 24 
                                    P++D++L++l                     ea+al++++p
  gi|121636532|ref|YP_976755.1| 732 PRMDRVLATLtrldpamtvldddrrplrntrEAAALAEQMP 772
                                    9**************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5957.39
//
Query:       gi|121636533|ref|YP_976756.1|  [L=330]
Description: hypothetical protein BCG_0661 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1724.08
//
Query:       gi|121636534|ref|YP_976757.1|  [L=80]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 529.66
//
Query:       gi|121636535|ref|YP_976758.1|  [L=88]
Description: hypothetical protein BCG_0663c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 674.93
//
Query:       gi|121636536|ref|YP_976759.1|  [L=75]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 589.51
//
Query:       gi|121636537|ref|YP_976760.1|  [L=133]
Description: hypothetical protein BCG_0664 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-10   39.9   0.0    6.4e-10   39.6   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   3.6e-14   6.4e-10       1     118 [.       3     120 ..       3     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.6e-14
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeia 78 
                                    ++lD++vlial+  ++++++aa+++l +     +t++ +   l+++l r  ++  +a+++v + +  s+++++p  +++ 
  gi|121636537|ref|YP_976760.1|   3 VLLDANVLIALVvAEHVHHDAAADWLMASdTGFATCPMTQGSLVRFLVRSGQSAAAARDVVSAVQCTSRHEFWP--DALS 80 
                                    68*************************99999*****************88899999999999999********..6666 PP

                                    HHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                            PIN  79 eeaaeialkyg.llpnDaliaAtAkehgikliatfDedfrr 118
                                        e+a   g + + Da++a +A++h+ +l  t D+ +++
  gi|121636537|ref|YP_976760.1|  81 FAGVEVAGVVGhRQVTDAYLAQLARSHDGQLA-TLDSGLAH 120
                                    66666666666799***************999.***98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1010.96
//
Query:       gi|121636538|ref|YP_976761.1|  [L=394]
Description: galactose-1-phosphate uridylyltransferase galT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-42  145.2   0.0    4.9e-42  144.4   0.0    1.3  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    2.8e-12   46.7   0.0    4.4e-12   46.0   0.0    1.2  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
  ------ inclusion threshold ------
      0.062   12.8   0.1       0.12   11.9   0.1    1.4  1  KNOX2            KNOX2 domain


Domain annotation for each model (and alignments):
>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4   0.0   8.1e-46   4.9e-42      12     184 .]      76     233 ..      67     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 8.1e-46
                GalP_UDP_transf  12 shrrfnpltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsra.ngefnpkykstfvftndFpalsedsn 90 
                                    s +rf++ tg+wv+v+++r++r++           +p+     c+LcPg++++ ++  +p+ ++++vf+n+Fp+l  +  
  gi|121636538|ref|YP_976761.1|  76 SRLRFDRATGQWVIVAAQRQDRTY-----------KPPA--ARCPLCPGPTGLsSEVPAPD-YDVVVFENRFPSLAGAGI 141
                                    667*********************...........3333..46**********66777888.8*************9988 PP

                GalP_UDP_transf  91 yikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifENkGaamgvsn 170
                                    ++  +   + + f ++p +Grcevi+fs++h++++a l+p++++ vv aW+++tael a  ++++v++fEN+G+++gv++
  gi|121636538|ref|YP_976761.1| 142 APIGA--PDGDGFVSAPGHGRCEVICFSADHTGSFAGLDPAHARLVVHAWRHRTAELTALPGVAQVFCFENRGEEIGVTL 219
                                    87773..45579******************************************************************** PP

                GalP_UDP_transf 171 phPHgqiwaeehlp 184
                                    +hPHgqi+a+++l+
  gi|121636538|ref|YP_976761.1| 220 THPHGQIYAYPYLT 233
                                    **********9985 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   7.3e-16   4.4e-12       8     123 ..     246     356 ..     239     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 7.3e-16
                                    HHHHH.SS-HHHHHHHHHHHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHH CS
                  GalP_UDP_tr_C   8 YfagsngsillhdyvqmelaekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkyd 87 
                                      + + g +l++  + +e+a+ +r+v+  + f a vp+ a WP+ev + +++ v++l+el+d e ++ a i  ++++++d
  gi|121636538|ref|YP_976761.1| 246 HRKRH-GDNLFASLLAREVADGSRIVVRGELFTAFVPFAARWPVEVHIYPNRLVRNLTELNDGELDEFARIYLDVLQRFD 324
                                    44455.999*********************************************************************** PP

                                    HHCTS---EEEEEE---SCCCTTTT--EEEEE--BC CS
                  GalP_UDP_tr_C  88 nlfetsfeysmGlhqaplnaeednswlHaHfevpll 123
                                     ++++  +y   lhq +    +   ++H  +e   +
  gi|121636538|ref|YP_976761.1| 325 RMYSSPLPYMSALHQFSEVQRD--GYFH--VELMSI 356
                                    *************997654443..3444..444444 PP

>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     2e-05      0.12       4      23 ..     305     324 ..     303     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                          KNOX2   4 adpELDqFMeaYcdvLvkYk 23 
                                    +d ELD+F   Y+dvL ++ 
  gi|121636538|ref|YP_976761.1| 305 NDGELDEFARIYLDVLQRFD 324
                                    589***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2867.38
//
Query:       gi|121636539|ref|YP_976762.1|  [L=363]
Description: galactokinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-15   56.5   0.1    4.2e-15   55.0   0.1    1.8  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
      2e-13   50.5   0.2    5.3e-13   49.1   0.2    1.7  1  GHMP_kinases_C   GHMP kinases C terminal
    3.1e-11   43.3   2.3    8.4e-11   42.0   2.3    1.8  1  GHMP_kinases_N   GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.1   7.1e-19   4.2e-15      15      47 ..       6      38 ..       3      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 7.1e-19
                                   EEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
                GalKase_gal_bdg 15 sAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                    APGRvnLiGEHtDYn Gf lp+A+++++++ +
  gi|121636539|ref|YP_976762.1|  6 GAPGRVNLIGEHTDYNLGFALPIALPRRTVVTF 38
                                   59****************************976 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   8.9e-17   5.3e-13       3      82 ..     262     339 ..     260     342 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 8.9e-17
                 GHMP_kinases_C   3 ealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                                    +al   d+ + g+ll+ s++s  +   ++i +++++ + e++ ++Galga+++G G+G++v+al+   d+a +va+ +r+
  gi|121636539|ref|YP_976762.1| 262 AALADSDFTAAGQLLTASHESmRE--DFAITTERIDLIAESAVRAGALGARMTGGGFGGAVIALV-PADRARDVADTVRR 338
                                    678889***************855..7**************************************.**********9977 PP

                 GHMP_kinases_C  82 e 82 
                                    +
  gi|121636539|ref|YP_976762.1| 339 A 339
                                    6 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   2.3   1.4e-14   8.4e-11       3      65 ..      95     160 ..      93     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.4e-14
                                    EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH...HHHHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                 GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglsl...eeaklaleaerlaqggngsggDvaasvyG 65 
                                    +i+s++ +g+GL+SSAAl+ a++ A+ a+ g ++   e a+la++ae+  +g+ ++  D  a+++G
  gi|121636539|ref|YP_976762.1|  95 SITSDVEIGSGLSSSAALIGAVLGAVGAATGTRIdrlERARLAQRAENDYVGAPTGLLDHLAALFG 160
                                    799****************************88532255***********99************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2679.42
//
Query:       gi|121636540|ref|YP_976763.1|  [L=385]
Description: hypothetical protein BCG_0667 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.041   13.5   0.1    1.4  1  zf_C2H2_13  Zinc finger domain
      0.032   14.5   2.0        2.3    8.5   0.0    2.5  2  DUF3040     Protein of unknown function (DUF3040)
      0.065   13.7   1.7       0.14   12.6   0.2    2.1  2  DUF3357     Domain of unknown function (DUF3357)


Domain annotation for each model (and alignments):
>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.8e-06     0.041      15      27 ..      39      51 ..      34      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-06
                     zf_C2H2_13 15 lnYRvCnkCGkPi 27
                                    +YR C+ CG Pi
  gi|121636540|ref|YP_976763.1| 39 WDYRFCERCGSPI 51
                                   68**********9 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00039       2.3      31      65 ..      62      97 ..      37     115 .. 0.82
   2 ?    4.9   0.4    0.0052        31      23      66 ..     220     267 ..     214     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                        DUF3040 31 ggaararrrslrrlavlavllfvaGllllvlG.vaa 65
                                   g++++a++rs   l+vla+ l+v+++++  +G +++
  gi|121636540|ref|YP_976763.1| 62 GTRQTAPARSFVPLVVLAATLLVVAVVVTAVGyAVT 97
                                   555668888888999999999999****99995544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0052
                        DUF3040  23 Pklaaalrggaar..arrrslrrlavlavllfva.GllllvlG.vaaa 66 
                                    P+laa+ +g++ r  ar +s+r+++v+a+ ++ a G +  v+G v+++
  gi|121636540|ref|YP_976763.1| 220 PALAATRKGRSDRsaARGGSARTTMVAAASAAPAyGSINAVAGaVLVE 267
                                    899999977777776888889998999988888889999999966655 PP

>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.4e-05      0.14      13      48 ..      62     103 ..      54     138 .. 0.69
   2 ?   -0.5   0.1      0.28   1.7e+03      13      45 ..     233     263 ..     217     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                        DUF3357  13 aaaaararrpllaavliasalvvlvvlvalagv......rla 48 
                                     + ++   r++ ++v++a+ l+v++v+v+++g+      r++
  gi|121636540|ref|YP_976763.1|  62 GTRQTAPARSFVPLVVLAATLLVVAVVVTAVGYavtrpaRND 103
                                    4556677889*********************99665444222 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.28
                        DUF3357  13 aaaaararrpllaavliasalvvlvvlvalagv 45 
                                    +aa++ + r   ++v++asa+ +  ++ a+ag+
  gi|121636540|ref|YP_976763.1| 233 SAARGGSAR--TTMVAAASAAPAYGSINAVAGA 263
                                    233333333..5666677777677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2968.26
//
Query:       gi|121636541|ref|YP_976764.1|  [L=315]
Description: hypothetical protein BCG_0668 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-07   31.1   1.0    9.1e-06   26.0   0.0    2.4  2  DUF732         Protein of unknown function (DUF732)
  ------ inclusion threshold ------
       0.03   14.4   0.6      0.065   13.3   0.6    1.5  1  DZR            Double zinc ribbon
      0.032   14.5   0.1      0.095   13.0   0.0    1.8  1  Big_6          Bacterial Ig domain
        3.7    7.4   5.2         64    3.5   5.2    2.5  1  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     2e-09   9.1e-06      20      64 ..     138     185 ..     111     188 .. 0.71
   2 ?    4.3   0.4     0.012        54      84      93 ..     187     196 ..     184     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2e-09
                         DUF732  20 saddaFlaalnqagi..aygspdaaialGkavCkkl.dsGksaeavva 64 
                                    s dd++laal+++g   +++s+++aia Gk+vC++l d G++++  v+
  gi|121636541|ref|YP_976764.1| 138 SIDDKYLAALRRSGLtgEFNSDANAIARGKQVCRQLqDGGEQQGMPVD 185
                                    789************8888899999***********633443333444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                         DUF732  84 aAvsayCPeq 93 
                                     Av++yCP+ 
  gi|121636541|ref|YP_976764.1| 187 VAVQYYCPQF 196
                                    79******96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.5e-05     0.065      14      36 ..       3      22 ..       1      29 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                            DZR 14 fCseCgtklkavaaedrCpsCge 36
                                   fC +Cg++l    +++rC +Cg+
  gi|121636541|ref|YP_976764.1|  3 FCVYCGAELA---DPTRCGACGA 22
                                   9********8...5*******97 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.095      23      75 ..     244     300 ..     219     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                          Big_6  23 agatVtvkdadgtvlgtg..tadadGeFsvtl..epaqangetlsvvatDaagntSd 75 
                                     g++Vtvk+ +g +l+t+  +a++ G+F  t+  + + ++ge+  vv +   g+ S 
  gi|121636541|ref|YP_976764.1| 244 RGTQVTVKNGQGDILATAflQAGQGGRFLCTFpfSFEITEGEDRYVVSVSRRGEMSY 300
                                    699***************8899******88882244559999999999998888875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   5.2     0.014        64       1       9 [.       3      11 ..       3      23 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                  zinc_ribbon_2  1 fCpnCGael 9 
                                   fC  CGael
  gi|121636541|ref|YP_976764.1|  3 FCVYCGAEL 11
                                   455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2004.56
//
Query:       gi|121636542|ref|YP_976765.1|  [L=84]
Description: hypothetical protein BCG_0669 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-27   95.7   3.1    2.3e-27   95.6   3.1    1.0  1  PSK_trans_fac  Rv0623-like transcription factor
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.16   12.2   0.0    1.1  1  MatP_C         MatP C-terminal ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   3.1   2.5e-31   2.3e-27       1      82 []       1      83 [.       1      83 [. 0.99

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 2.5e-31
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--HHHHHHHHHHHHHTS--SS-SSTTSTTTXXXXXX CS
                  PSK_trans_fac  1 MaLnIkdpeverlareLarltgeskteAvrrAleerlerlrre.raepllerllallrraaakaekedrspdekllyDeegl 81
                                   MaL+Ik pe++rlar La++tge++teAv +Al+erl+r+  + r  pl+++l+a+++r+aa ++ ++rs++ +l+yDe+gl
  gi|121636542|ref|YP_976765.1|  1 MALSIKHPEADRLARALAARTGETLTEAVVTALRERLARETGRaRVVPLRDELAAIRHRCAALPVVDNRSAEAILGYDERGL 82
                                   ****************************************9999************************************** PP

                                   X CS
                  PSK_trans_fac 82 p 82
                                   p
  gi|121636542|ref|YP_976765.1| 83 P 83
                                   8 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.8e-05      0.16      16      58 ..      12      55 ..      10      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                         MatP_C 16 rLs.klsqrrgsTLSetivqLieeaerkekyeeqvsslkedLke 58
                                   rL+ +l+ r g TL e++v+ + e+  +e+   +v  l+++L +
  gi|121636542|ref|YP_976765.1| 12 RLArALAARTGETLTEAVVTALRERLARETGRARVVPLRDELAA 55
                                   66635899*********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 639.29
//
Query:       gi|121636543|ref|YP_976766.1|  [L=131]
Description: hypothetical protein BCG_0670 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-15   55.2   0.0    1.1e-14   55.0   0.0    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0     6e-19   1.1e-14       1     120 [.       1     124 [.       1     126 [. 0.98

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 6e-19
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    +v+DTs+l+a+l++e++ae++++++e++   ++s +++ E++ v+++  +  e   ++++l+l ++a+ ++ + a++a+ 
  gi|121636543|ref|YP_976766.1|   1 MVIDTSALVAMLSDEPDAERFEAAVEADHIRLMSTASYLETALVIEA--RFGEPGGRELDLWLHRAAVDLVAVHADQADA 78 
                                    69*********************************************..******************************* PP

                                    HHHHHHHHH.......SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  81 aaeialkyg.......llpnDaliaAtAkehgikliatfDedfrrva 120
                                    a++ ++ yg       l+  D++ + +Ak +g +l+  + edf +++
  gi|121636543|ref|YP_976766.1|  79 ARAAYRTYGkgrhragLNYGDCFSYGLAKISGQPLL-FKGEDFQHTD 124
                                    ************************************.******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1019.24
//
Query:       gi|121636544|ref|YP_976767.1|  [L=246]
Description: hypothetical protein BCG_0671c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-21   76.2   8.4    2.9e-21   76.2   8.4    2.8  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
      0.012   15.7  12.9          1    9.5   2.5    3.7  3  FxsA         FxsA cytoplasmic membrane protein
       0.24   11.8   1.5       0.72   10.3   0.1    2.1  2  DUF5313      Family of unknown function (DUF5313)


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   5.8         3   1.8e+04       8      26 ..      21      35 ..      15      70 .. 0.62
   2 !   76.2   8.4   4.9e-25   2.9e-21       1     119 [.      71     188 ..      71     189 .. 0.98
   3 ?   -3.1   0.0       1.7     1e+04      22      28 ..     208     214 ..     197     228 .. 0.54

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                    SNARE_assoc  8 vaaGvlfglllgtlvtslg 26
                                   v+aG+l+g+++    ++++
  gi|121636544|ref|YP_976767.1| 21 VFAGFLVGMFY----LVAA 35
                                   44444444444....3333 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 4.9e-25
                    SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpiv 80 
                                    +P+++l++  G+lfg+l+g++vt+ +++  a++a l+gr++g +a  r+ll  +r+++ ++l+er g +a++  r++p++
  gi|121636544|ref|YP_976767.1|  71 VPGPILAASSGLLFGPLVGVFVTLGATVGTAVVASLVGRRAG-RASARALLGGERADRTDALIERCGLWAVVGQRFVPGI 149
                                    79****************************************.999999******************************* PP

                    SNARE_assoc  81 PrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                     +++++y++G+++v++++ ++++fiGs+p+a+ y+ lG+
  gi|121636544|ref|YP_976767.1| 150 SDAFASYAFGTFGVPLWQMAVGAFIGSAPRAFAYTALGA 188
                                    ************************************996 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.7
                    SNARE_assoc  22 vtslgal 28 
                                    ++++ga+
  gi|121636544|ref|YP_976767.1| 208 TAIIGAF 214
                                    2222222 PP

>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9   0.00082       4.9       4      41 ..      34      71 ..      29      80 .. 0.89
   2 ?    9.5   2.5   0.00017         1      15      52 ..      82     119 ..      69     154 .. 0.82
   3 ?    4.7   0.0    0.0054        32      26      58 ..     201     233 ..     183     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00082
                           FxsA  4 lllpvlEilllvlvasaiGvlatllllvltallGallv 41
                                    +  v++++++   +sa G  a l ++v++a+lGal+v
  gi|121636544|ref|YP_976767.1| 34 AATDVIDVAAVRGAVSATGPAAPLTYVVVSAVLGALFV 71
                                   466799999**************************987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                           FxsA  15 vlvasaiGvlatllllvltallGallvrrqgrralrrl 52 
                                    +l + ++Gv++tl  +v+ta++ +l+ rr+gr  +r+l
  gi|121636544|ref|YP_976767.1|  82 LLFGPLVGVFVTLGATVGTAVVASLVGRRAGRASARAL 119
                                    5678899*************************998876 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0054
                           FxsA  26 tllllvltallGallvrrqgrralrrlqeklaq 58 
                                    ++++  +ta++Ga+ +r+  r+   +++ + a 
  gi|121636544|ref|YP_976767.1| 201 AIAVWCVTAIIGAFAARHGYRQWRAHARGDGAD 233
                                    6889999*********98888776666666555 PP

>> DUF5313  Family of unknown function (DUF5313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00012      0.72      30      65 ..       7      42 ..       3      51 .. 0.84
   2 ?    0.2   0.2      0.16   9.7e+02      49      79 ..      65      94 ..      54     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                        DUF5313 30 agkgaaaRhviraavplvlilavllLlpgslyvrle 65
                                   + ++ ++Rh++r +v + +++ +++L+ ++ ++ ++
  gi|121636544|ref|YP_976767.1|  7 SAPTSRRRHIVRLVVFAGFLVGMFYLVAATDVIDVA 42
                                   457899*********************998777665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                        DUF5313 49 ilavllLlpgslyvrlemtllillvavlysl 79
                                   +l   l++pg+++   +  l + lv v+ +l
  gi|121636544|ref|YP_976767.1| 65 VL-GALFVPGPILAASSGLLFGPLVGVFVTL 94
                                   33.3489*****9999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2004.90
//
Query:       gi|121636545|ref|YP_976768.1|  [L=86]
Description: hypothetical protein BCG_0672 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-08   34.5   0.0    1.4e-08   34.4   0.0    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     8e-13   1.4e-08       1      48 [.       1      55 [.       1      76 [. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8e-13
                                   CEEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEH........HHHHHH CS
                PhdYeFM_antitox  1 mkivsiseakanlselldeveegeepviItrrGkpvaVlvsl........eeyerl 48
                                   m +v  +e++++ + +l++v++ge+ v+It  G+pvaVl ++        +++e l
  gi|121636545|ref|YP_976768.1|  1 MSEVASRELRNDTAGVLRRVRAGED-VTITVSGRPVAVLTPVrprrrrwlSKTEFL 55
                                   88999*******************8.***************966555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 640.33
//
Query:       gi|121636546|ref|YP_976769.1|  [L=135]
Description: hypothetical protein BCG_0673 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-16   58.8   1.7    8.2e-16   58.6   1.7    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.03   14.1   0.1      0.059   13.1   0.1    1.6  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   1.7   9.1e-20   8.2e-16       2     120 ..       9     125 ..       8     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 9.1e-20
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                    vlDTsv+ia  +g+      ++l+   ++++t++++laEl+ ++ +   + + +a+++++l+  ++++ lp+d+++a+++
  gi|121636546|ref|YP_976769.1|   9 VLDTSVFIATESGRQLD---EALIP--DRVATTVVTLAELRVGVLA-AATTDIRAQRLATLESVADMETLPVDDDAARMW 82 
                                    79******777777777...56665..9******************.99******************************* PP

                                    HHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  82 aeialkyg.....llpnDaliaAtAkehgikliatfDedfrrva 120
                                    a+++ ++      +++nD++iaA+A ++ +++i t D+df+ ++
  gi|121636546|ref|YP_976769.1|  83 ARLRIHLAesgrrVRINDLWIAAVAASRALPVI-TQDDDFAALD 125
                                    *********************************.******9987 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-06     0.059      26      61 ..      88     124 ..      74     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-06
                        DUF5615  26 hvrelgle.gasDeeileyAkeedriivTkDkDFgel 61 
                                    h+ e g + +++D  i ++A ++ + ++T+D DF  l
  gi|121636546|ref|YP_976769.1|  88 HLAESGRRvRINDLWIAAVAASRALPVITQDDDFAAL 124
                                    67777766469***********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1080.64
//
Query:       gi|121636547|ref|YP_976770.1|  [L=383]
Description: hypothetical protein BCG_0674c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-28   97.4   2.7      1e-26   94.0   0.1    2.5  2  FIST      FIST N domain
      1e-25   90.2   0.8    7.6e-25   87.4   0.1    2.1  2  FIST_C    FIST C domain


Domain annotation for each model (and alignments):
>> FIST  FIST N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.1   1.1e-30     1e-26       2     172 .]      35     219 ..      34     219 .. 0.82
   2 ?    2.9   0.1     0.011        97      19      44 ..     342     368 ..     321     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 1.1e-30
                           FIST   2 lvlvfas.aeasdleallealrealpgapliGcstageiasegleledgvvalalasa.................da..a 61 
                                    l++++ s ++ +++ +ll+a+++ +  a liGc++ g++a + +ele++ +a+a+++a                  a  +
  gi|121636547|ref|YP_976770.1|  35 LAVLLGSrSHTDQAVDLLAAVQASVEPAALIGCVAQGIVA-GRHELENE-PAVAVWLAsgppaetfhldfvrtgsGAliT 112
                                    667778878887888**********99************8.57889999.888887776677666666666654311454 PP

                           FIST  62 geelakalpkllllladglssneeellegldealaspdvpivGGlagdgtlafktyvlfnggvledgvvvvllsgeslev 141
                                    g ++ + +++l lll+d++s+  + l+e+l++ l  p++ +vGG+ ++g ++++t  + ++ vl++g+v+v l+g +   
  gi|121636547|ref|YP_976770.1| 113 GYRFDRTAHDLHLLLPDPYSFPSNLLIEHLNTDL--PGTTVVGGVVSGGRRRGDTRLFRDRDVLTSGLVGVRLPGAH--S 188
                                    555555447779*******************444..69******988886777688888999************995..4 PP

                           FIST 142 gtavsqgyrpigkpfvVTkaegnvileLdgk 172
                                     ++vsqg+rpig+p++VT a+g vi eL g+
  gi|121636547|ref|YP_976770.1| 189 VSVVSQGCRPIGEPYIVTGADGAVITELGGR 219
                                    57779***********************986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.011
                           FIST  19 ealrealpgapliGcstageiase.gl 44 
                                    +++++ l+g+pl+G  +agei++  g+
  gi|121636547|ref|YP_976770.1| 342 STIEDLLGGIPLAGFFAAGEIGPVaGH 368
                                    4588899**************553233 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.041   3.7e+02      86     126 ..      34      71 ..       6      86 .. 0.56
   2 !   87.4   0.1   8.4e-29   7.6e-25       2     130 .]     222     364 ..     221     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.041
                         FIST_C  86 allfsCigRglglgedadeelqavrealgdgvplaGfftyG 126
                                    al +   +R   + ++a + l+av+  + + + l+G+ + G
  gi|121636547|ref|YP_976770.1|  34 ALAVLLGSRS--HTDQAVDLLAAVQASVEP-AALIGCVAQG 71 
                                    4555545552..244444555555555555.6666666555 PP

  == domain 2  score: 87.4 bits;  conditional E-value: 8.4e-29
                         FIST_C   2 levylell...geedeelaqsalfplgleel.......ggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaeali 71 
                                    l  ++e++     +++el+++ l  +g++++       +gdfl+r llg+dp++g++ +++ ve+G ++q+++rda+a+ 
  gi|121636547|ref|YP_976770.1| 222 LHRLREIVlgmAPDEQELVSRGL-QIGIVVDehlavpgQGDFLIRGLLGADPTTGAIGIGEVVEVGATVQFQVRDAAAAD 300
                                    56677777887778899999999.99999889999999****************************************** PP

                         FIST_C  72 edlerlleeaak...e...gallfsCigRglgl.gedadeelqavrealgdgvplaGfftyGEigp 130
                                    +dl+ ++e+aa+       g+llf C gRg  + g    ++++++++ lg+ +plaGff+ GEigp
  gi|121636547|ref|YP_976770.1| 301 KDLRLAVERAAAelpGppvGGLLFTCNGRGRRMfGVTD-HDASTIEDLLGG-IPLAGFFAAGEIGP 364
                                    *9999999996644415659*********999976666.559******986.************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3134.14
//
Query:       gi|121636548|ref|YP_976771.1|  [L=575]
Description: exonuclease V (alpha chain) recD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-37  126.8   5.9    8.3e-37  126.8   5.9    2.3  2  AAA_30           AAA domain
      2e-29  102.8   0.5    1.2e-28  100.3   0.3    2.1  2  AAA_19           AAA domain
    4.2e-14   52.1   0.1      1e-13   50.9   0.1    1.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    1.7e-10   41.1   0.1    3.7e-07   30.2   0.0    2.2  2  AAA_11           AAA domain
    6.4e-10   39.2   0.1    1.2e-09   38.3   0.1    1.4  1  Helicase_RecD    Helicase
    1.1e-08   35.5   0.1    3.6e-08   33.8   0.1    1.9  1  AAA_22           AAA domain
      4e-08   33.3   0.1    0.00061   19.6   0.0    3.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    3.7e-06   26.7   0.3    0.00029   20.5   0.4    2.1  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    9.1e-05   22.2   0.0    0.00017   21.3   0.0    1.4  1  SH3_13           ATP-dependent RecD-like DNA helicase SH3 dom
     0.0002   21.8   1.8    0.00053   20.4   1.8    1.7  1  AAA_16           AAA ATPase domain
    0.00077   19.1   0.8    0.00077   19.1   0.8    2.3  2  AAA_25           AAA domain
     0.0022   16.0   0.1      0.082   10.8   0.1    2.3  3  Herpes_Helicase  Helicase
     0.0044   17.3   2.8      0.014   15.6   2.8    1.9  1  AAA_28           AAA domain
     0.0064   15.9   0.1      0.012   15.0   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.029   13.4   0.0    1.7  1  T2SSE            Type II/IV secretion system protein
      0.013   15.4   0.0      0.031   14.2   0.0    1.7  1  NTPase_1         NTPase
      0.026   14.3   0.0      0.073   12.8   0.0    1.8  1  AAA_29           P-loop containing region of AAA domain
      0.029   14.2   0.0      0.044   13.5   0.0    1.3  1  DEAD             DEAD/DEAH box helicase
      0.039   12.9   0.0      0.064   12.2   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.056   12.8   0.0       0.13   11.6   0.0    1.6  2  ATPase           KaiC
      0.077   13.5   0.0       0.12   12.9   0.0    1.2  1  AAA_23           AAA domain
      0.079   13.0   0.2       0.39   10.7   0.2    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
      0.096   12.3   0.7        0.2   11.3   0.7    1.5  1  SRP54            SRP54-type protein, GTPase domain
       0.15   11.9   0.1       0.26   11.1   0.1    1.3  1  MukB             MukB N-terminal
        0.2   10.9   0.0       0.32   10.2   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.22   11.1   0.5       0.45   10.1   0.5    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.24   12.0   2.2        4.7    7.9   0.1    2.6  2  SAF              SAF domain
       0.64    9.4   4.5       0.93    8.9   1.0    2.4  2  PhoH             PhoH-like protein


Domain annotation for each model (and alignments):
>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   5.9   1.3e-39   8.3e-37       4     184 ..     151     360 ..     149     369 .. 0.85
   2 ?    2.2   0.3      0.21   1.3e+02      61     126 ..     491     549 ..     464     565 .. 0.65

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1.3e-39
                         AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag.......grviglAptgkaAkvLae............ 64 
                                    +eQ++a+e +l++g  v+vltG++GtGKtt+++ l ++++++         r++++AptgkaA++Lae            
  gi|121636548|ref|YP_976771.1| 151 DEQRRAAEIALSQG--VTVLTGGPGTGKTTTVARLLALVAEQAelageprPRIALAAPTGKAAARLAEavrremakldat 228
                                    69*****9888888..9****************99777777745999***9****************7444444444444 PP

                         AAA_30  65 ...elg.ieastiakllkrlk......grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaG 134
                                        lg ++a t+++ll +        +r++  p+++++vDE++mv+ + +a+l++a++  ga++ilvGD +QlasVeaG
  gi|121636548|ref|YP_976771.1| 229 draRLGdLHAVTLHRLLGAKPgarfrqDRQNRLPHNVIVVDETSMVSLTLMARLAEAVRP-GARLILVGDADQLASVEAG 307
                                    333444469********8888****9976777888*************************.******************* PP

                         AAA_30 135 gvlrdlvea....agigtaeLtevvRqkeseeraaalalregdaeealealadr 184
                                    +vl+dlv+     +++ +a+L++ +R+  + + ++a+a+r gd +++l  l++ 
  gi|121636548|ref|YP_976771.1| 308 AVLADLVDGfsvrDDALVAQLRTSHRFG-KVIGTLAEAIRAGDGDAVLGLLRSG 360
                                    ******976777667899*********5.69*************9888877654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.21
                         AAA_30  61 vLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDer 126
                                    +L++   ++a+ti+k         ++++ t+l+  E + + t++l  l +a+++a+ kv++vG e+
  gi|121636548|ref|YP_976771.1| 491 RLGDVETMHAMTIHKSQ-----GSQVDEVTVLMPQEDSRLLTREL--LYTAVARAKRKVRVVGSEA 549
                                    44444445555555555.....23444556666666666555554..6677777889999999765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.3   1.8e-31   1.2e-28       1     144 [.     153     304 ..     153     306 .. 0.89
   2 ?   -0.3   0.0       1.9   1.2e+03      66      90 ..     497     516 ..     465     546 .. 0.65

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 1.8e-31
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaalgae........ 68 
                                    qr+a+e al+++v ++t+GpGtGKT+++   +al+ e+ +++     +i+l+a+tg+Aa +l+e+++   a+        
  gi|121636548|ref|YP_976771.1| 153 QRRAAEiALSQGVTVLTGGPGTGKTTTVARLLALVAEQAELAGeprPRIALAAPTGKAAARLAEAVRREMAKldatdrar 232
                                    899**99*********************99998888776654333389****************996655558899**** PP

                         AAA_19  69 .....atTiHrlalldfddlltealelleeaeeekklqeeellivDEfqdvd.elqyrLlkallgekkklllvGDpdQli 142
                                         a T+Hrl  l++++       +  ++++++ l  +++++vDE+++v+  l+ rL +a+  ++++l+lvGD+dQl 
  gi|121636548|ref|YP_976771.1| 233 lgdlhAVTLHRL--LGAKPGA----RF--RQDRQNRL-PHNVIVVDETSMVSlTLMARLAEAVR-PGARLILVGDADQLA 302
                                    ************..9999988....67..66889999.999***********************.8888**********9 PP

                         AAA_19 143 yv 144
                                    +v
  gi|121636548|ref|YP_976771.1| 303 SV 304
                                    86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                         AAA_19  66 gaeatTiHrlalldfddlltealel 90 
                                    +++a+TiH+    ++d+     +++
  gi|121636548|ref|YP_976771.1| 497 TMHAMTIHKSQGSQVDE-----VTV 516
                                    44577777763333333.....223 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   1.6e-16     1e-13       3      52 .]     499     545 ..     497     545 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.6e-16
                       UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                    +a+tihk+QGs+ + V v  p ++++    l+r+lLYtav RA++k+++v
  gi|121636548|ref|YP_976771.1| 499 HAMTIHKSQGSQVDEVTVLMPQEDSRL---LTRELLYTAVARAKRKVRVV 545
                                    79****************999999976...68***************998 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   5.8e-10   3.7e-07       4      76 ..     151     220 ..     150     248 .. 0.86
   2 !    8.8   0.0     0.002       1.3     219     256 ..     264     303 ..     250     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.8e-10
                         AAA_11   4 dsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                    d+qr+a + als+   t++ G PGtgKT+t++ ll+ ++++   e ++++ pri ++ap+ +A   l+e + r
  gi|121636548|ref|YP_976771.1| 151 DEQRRAAEIALSQGV-TVLTGGPGTGKTTTVARLLALVAEQ--AELAGEPRPRIALAAPTGKAAARLAEAVRR 220
                                    68***********96.*********************9554..57899***************9999998887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                         AAA_11 219 dvviIDEAaqavEpstliPlrlga...kkvvLvGDpkQLpa 256
                                     v+++DE ++   +  +  l +++   ++++LvGD  QL +
  gi|121636548|ref|YP_976771.1| 264 NVIVVDETSMV-SLTLMARLAEAVrpgARLILVGDADQLAS 303
                                    68999999885.344444454444666************86 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.1   1.8e-12   1.2e-09       1     113 [.     167     285 ..     167     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.8e-12
                  Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk......snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvr.. 72 
                                    vlt+++G+GK+++++ +la ++++++       +i ++ap+ +++++l e +++++ +l+ +++ +  + + + + +r  
  gi|121636548|ref|YP_976771.1| 167 VLTGGPGTGKTTTVARLLALVAEQAElageprPRIALAAPTGKAAARLAEAVRREMAKLDATDRARLGDLHAV-TLHRll 245
                                    79*******************999999999999***************************9996666665533.333356 PP

                  Helicase_RecD  73 ..kqrieyiapdellklkeqadllvvDEAAaiplpllkkllek 113
                                      k   ++ + ++    +  ++++vvDE +++ l+l+ +l e+
  gi|121636548|ref|YP_976771.1| 246 gaKPGARFRQDRQNRL-P--HNVIVVDETSMVSLTLMARLAEA 285
                                    6688888877666555.3..49****************99765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   5.6e-11   3.6e-08       4     131 ..     162     298 ..     159     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.6e-11
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell.eal 82 
                                    ++g++v+tG +GtGKTt+++rll    e+a+ + e+++ +   +p ++  + l++++ r++     + r+++ +l   +l
  gi|121636548|ref|YP_976771.1| 162 SQGVTVLTGGPGTGKTTTVARLLALVAEQAELAGEPRPRIALAAPTGKAAARLAEAVRREMAKLDATDRARLGDLHaVTL 241
                                    689***********************99999999888888888888888************9766665555555553334 PP

                         AAA_22  83 eqalrarav............ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp 131
                                    ++ l a+              + ++++DE   + s +++  L + +     g +liLvG  
  gi|121636548|ref|YP_976771.1| 242 HRLLGAKPGarfrqdrqnrlpHNVIVVDETSMV-SLTLMARLAEAVR---PGARLILVGDA 298
                                    4444333336667777788889********999.9888888855555...78888888865 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.014       8.7       2      28 ..     167     187 ..     166     227 .. 0.81
   2 ?    4.2   0.0      0.05        32      55     122 ..     258     321 ..     237     340 .. 0.70
   3 !   19.6   0.0   9.5e-07   0.00061     184     232 ..     499     544 ..     481     546 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvn 28 
                                    v  G pG GK+t + +ll        +
  gi|121636548|ref|YP_976771.1| 167 VLTGGPGTGKTTTVARLLAL------V 187
                                    789**********9999977......3 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.05
                Viral_helicase1  55 malvkstkgkililDEylllhaGyilllaal.skaklvilfGDplQipfhsrnasfllahlpsslshrv 122
                                    +++++    +++++DE  ++   ++  la        +il+GD  Q  + +  a + la+l+  +s r 
  gi|121636548|ref|YP_976771.1| 258 QNRLP---HNVIVVDETSMVSLTLMARLAEAvRPGARLILVGDADQLASVE--AGAVLADLVDGFSVRD 321
                                    44444...599*********977766654431333579********98885..5567777776666555 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 9.5e-07
                Viral_helicase1 184 evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvi 232
                                    +++t h  qG+++d+Vt++  +e +++ +  +re l++A  R+++++ +
  gi|121636548|ref|YP_976771.1| 499 HAMTIHKSQGSQVDEVTVLMPQEDSRL-L--TRELLYTAVARAKRKVRV 544
                                    59*******************997766.4..489***********9876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.4   4.6e-07   0.00029       4      73 ..     152     226 ..     150     247 .. 0.68
   2 ?    4.1   0.0     0.042        27     257     294 ..     263     300 ..     237     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.6e-07
                                    HHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS..STGGG....EEEEESSHHHHHHHHHHHHHHHHHCC CS
                  UvrD-helicase   4 eqreaias..lggpilveAsAGsGKTfvlaerilrlikeee..iepdr....ilvvTFTnkAaeElkeRieealkkae 73 
                                    eqr+a++   ++g +++  ++G+GKT+++a + +   +++e      +    i +   T kAa+ l e +++ + k  
  gi|121636548|ref|YP_976771.1| 152 EQRRAAEIalSQGVTVLTGGPGTGKTTTVARLLALVAEQAElaG---EprprIALAAPTGKAAARLAEAVRREMAKLD 226
                                    5666655554899999999*********8765554444444432...23446********************877754 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.042
                                    SSEEEESSGGG-BHHHHHHHHHHHTTTTT...EEEEE-GGG CS
                  UvrD-helicase 257 ykeiliDEyQDTnkiQyrilkllasghee...lfmvGDpkQ 294
                                     ++i +DE   T+ +  +++ +la++ +    l++vGD +Q
  gi|121636548|ref|YP_976771.1| 263 HNVIVVDE---TSMVSLTLMARLAEAVRPgarLILVGDADQ 300
                                    35799998...888888888888877655677********* PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.6e-07   0.00017       2      52 ..     423     468 ..     422     473 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                         SH3_13   2 NkelqealnpkskkkkevkvggrvfrvgDkVmqlkNnydkgvfNGDiGiik 52 
                                    N+++q++l +++ +++ ++     ++ g++ + + N+y + v+NGD+G++ 
  gi|121636548|ref|YP_976771.1| 423 NRRVQAWLAEET-GQPPWT----PWYAGRPLLVTANDYGLRVYNGDTGVVL 468
                                    778888887774.566554....69***********************996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.8   8.2e-07   0.00053      25     161 ..     164     316 ..     151     326 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.2e-07
                         AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipy.......sa.laqalareellrqlldeaesaele 95 
                                    ++++l+G +G+GK++ v +ll  + ++ +   l+g+ +     i++       +a la+a  r + +++l++ +++++ +
  gi|121636548|ref|YP_976771.1| 164 GVTVLTGGPGTGKTTTVARLLALVAEQaE---LAGEPRPR---IALaaptgkaAArLAEAV-R-REMAKLDATDRARLGD 235
                                    6789*****************65555531...55555555...333211133322266666.4.4444444444555555 PP

                         AAA_16  96 awrekleeala................avpelagaea........srllellkrllallsrderplvlvlDdlqwadeas 151
                                     ++ +l++ l+                                     l l++rl++  ++++r l+lv D  q a  + 
  gi|121636548|ref|YP_976771.1| 236 LHAVTLHRLLGakpgarfrqdrqnrlpH--------NvivvdetsMVSLTLMARLAEAVRPGAR-LILVGDADQLASVEA 306
                                    5555555555576665555544444432........0444444446777777777777777677.888888888888888 PP

                         AAA_16 152 lqllaaLlrl 161
                                     ++la L++ 
  gi|121636548|ref|YP_976771.1| 307 GAVLADLVDG 316
                                    8888888775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.8   1.2e-06   0.00077      33     107 ..     163     240 ..     148     304 .. 0.69
   2 ?   -1.5   0.1       2.4   1.5e+03      72      98 ..     362     391 ..     309     435 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                         AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds..edelrrRlravgeal.....rddarllv 105
                                    +++++l+G pgtGKtt +  l + va+  +++g    e+++ + ++a  +  +++l++ +r+ +++l     ++ ++l++
  gi|121636548|ref|YP_976771.1| 163 QGVTVLTGGPGTGKTTTVARLLALVAEQAELAG----EPRPRIALAAPTGkaAARLAEAVRREMAKLdatdrARLGDLHA 238
                                    789***********************9999999....5555555555444004444444444444444433322333333 PP

                         AAA_25 106 ld 107
                                    ++
  gi|121636548|ref|YP_976771.1| 239 VT 240
                                    33 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                         AAA_25  72 gkVlyvsaEdsedelrrRlravg..eal.....r 98 
                                     +  +v+ Ed++    +Rlrav+  +al     +
  gi|121636548|ref|YP_976771.1| 362 ERIEFVDDEDPA----PRLRAVLvpHALrlreaA 391
                                    444555555555....555555522222222220 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.04        25      35      80 ..     139     184 ..     122     188 .. 0.77
   2 ?   -3.5   0.0       2.8   1.8e+03     194     207 ..     263     276 ..     253     280 .. 0.77
   3 !   10.8   0.1   0.00013     0.082     731     771 ..     498     540 ..     481     557 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.04
                Herpes_Helicase  35 epe.lewfrseldleeeeeselslPFsaylitGtAGaGkstsiqala 80 
                                    +p+  ++f + +d ++ + + ++l   + ++tG  G+Gk+t+++ l 
  gi|121636548|ref|YP_976771.1| 139 VPDlRRLFPTGFDEQRRAAE-IALSQGVTVLTGGPGTGKTTTVARLL 184
                                    55535677788887777766.779999***************99875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                Herpes_Helicase 194 snviviDEaGllsr 207
                                     nviv+DE+ ++s 
  gi|121636548|ref|YP_976771.1| 263 HNVIVVDETSMVSL 276
                                    69******988775 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00013
                Herpes_Helicase 731 klamtiaksqGlslekvAicFgnh..knlklssvYvalsRatd 771
                                      amti ksqG  ++ v +   ++  + l ++ +Y a++Ra  
  gi|121636548|ref|YP_976771.1| 498 MHAMTIHKSQGSQVDEVTVLMPQEdsRLLTRELLYTAVARAKR 540
                                    579****************998766799999*********975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.8   2.3e-05     0.014       3      21 ..     167     185 ..     165     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                         AAA_28   3 vitGgestGKTtlleaLaa 21 
                                    v+tGg++tGKTt++++L a
  gi|121636548|ref|YP_976771.1| 167 VLTGGPGTGKTTTVARLLA 185
                                    9*************99874 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.9e-05     0.012       7      49 ..     149     190 ..     144     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                   Mg_chelatase   7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49 
                                    G +e++ra eia + g   +l+G pG+GKt   +rl +l+++ 
  gi|121636548|ref|YP_976771.1| 149 GFDEQRRAAEIALSQGVT-VLTGGPGTGKTTTVARLLALVAEQ 190
                                    66789*******997765.57999*************999875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.029     118     156 ..     155     190 ..     124     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                     a+ ++ +   +g+ +++Gg g+GKtt++  ll+ ++++
  gi|121636548|ref|YP_976771.1| 155 RAAEIALS---QGVTVLTGGPGTGKTTTVARLLALVAEQ 190
                                    44444555...9999******************999887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.8e-05     0.031       3      33 ..     167     196 ..     165     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-05
                                    EEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGf 33 
                                    ++TG pG+GKtT v ++l l+++ + +++G 
  gi|121636548|ref|YP_976771.1| 167 VLTGGPGTGKTTTVARLLALVAE-QAELAGE 196
                                    79****************99954.4677665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.073      17      50 ..     157     190 ..     149     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         AAA_29  17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50 
                                    +ei l++ +t+ltG  G+GK+T + A    Lv+++
  gi|121636548|ref|YP_976771.1| 157 AEIALSQgVTVLTGGPGTGKTTTV-ARLLALVAEQ 190
                                    45555555**************99.7777777765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.9e-05     0.044       2      75 ..     151     226 ..     150     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-05
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                    d Q++a +++l++g  ++ +  G+GKT+  +   l+ v+e+    g+++p++ + +Pt + a   ++ +++ + ++d
  gi|121636548|ref|YP_976771.1| 151 DEQRRAAEIALSQGVTVLTGGPGTGKTTTVARL-LALVAEQaelAGEPRPRIALAAPTGKAAARLAEAVRREMAKLD 226
                                    679***********************9874433.33455556669*************9999999999988887766 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001     0.064      17      44 ..     165     192 ..     157     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargd 44 
                                     ++++G+ G+GKt+++  ll+ + ++++
  gi|121636548|ref|YP_976771.1| 165 VTVLTGGPGTGKTTTVARLLALVAEQAE 192
                                    5899******************999983 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.13      19      68 ..     163     223 ..     137     242 .. 0.74
   2 ?   -3.4   0.1       7.7   4.9e+03     122     149 ..     508     536 ..     498     544 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                         ATPase  19 grvvlitGepGtGKtifalqFl...ikgaekygepgvfvtveepa........edlrenak 68 
                                    + v+ +tG+pGtGKt+ +++ l    ++ae  gep   +++  p         e++r++++
  gi|121636548|ref|YP_976771.1| 163 QGVTVLTGGPGTGKTTTVARLLalvAEQAELAGEPRPRIALAAPTgkaaarlaEAVRREMA 223
                                    568999***********99876222577888888877777777666555444444555444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.7
                         ATPase 122 rvviDsitgl.ayeekeavaReilrqlvr 149
                                       +D +t+l  +e++  ++Re l + v 
  gi|121636548|ref|YP_976771.1| 508 GSQVDEVTVLmPQEDSRLLTRELLYTAVA 536
                                    55689999996666666678887776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00019      0.12      13      36 ..     157     180 ..     148     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                         AAA_23  13 qeidFskgltlItGpNGaGKTTil 36 
                                     ei +s+g+t++tG  G+GKTT +
  gi|121636548|ref|YP_976771.1| 157 AEIALSQGVTVLTGGPGTGKTTTV 180
                                    5899******************75 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00061      0.39       3      24 ..     167     190 ..     166     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                                    EEE--SSSSHHHHHHHGGGGB..S CS
                          AAA_5   3 lLvGppGtgKselaerlaaal..n 24 
                                    +L G pGtgK++ + rl+a++  +
  gi|121636548|ref|YP_976771.1| 167 VLTGGPGTGKTTTVARLLALVaeQ 190
                                    79****************998433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00031       0.2       3      28 ..     165     190 ..     163     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                    EEEEEESTTSSHHHHHHHHHHHHHHT CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkke 28 
                                    v++l G  G+GKTtt+a+L al+ ++
  gi|121636548|ref|YP_976771.1| 165 VTVLTGGPGTGKTTTVARLLALVAEQ 190
                                    7899***************9988776 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0004      0.26      23      55 ..     160     191 ..     154     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                    -HHHHHHHHHS--SHHHHHHHHHHHHHHS--TT CS
                           MukB  23 dldelvttlsGgnGaGksttmaafvtaliPdls 55 
                                     l + vt l Gg G+Gk+tt+a ++ al+ +++
  gi|121636548|ref|YP_976771.1| 160 ALSQGVTVLTGGPGTGKTTTVARLL-ALVAEQA 191
                                    67899**************987654.6666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005      0.32       3      96 ..     165     270 ..     163     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                        DUF2075   3 vvlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef 77 
                                    v + tG++GtGKt    +lla +        e + + +++   ++  + l ea++++   k   ++ ++l  +   + + 
  gi|121636548|ref|YP_976771.1| 165 VTVLTGGPGTGKTTTVARLLALVaeqaeLAGEPRPRIALAAPTGKAAARLAEAVRREM-AKLDATDRARLGDLHAVTLHR 243
                                    6789*********999988887743332222233344455566666666666666666.444444444444444433333 PP

                        DUF2075  78 ........kkaeekkeepkedvvivDE 96 
                                            + +++++++ +++v++vDE
  gi|121636548|ref|YP_976771.1| 244 llgakpgaRFRQDRQNRLPHNVIVVDE 270
                                    355666655566666666777777777 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00071      0.45       2      22 ..     165     186 ..     164     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00071
                                    EEEEEESTTCCHHHHHHHHH.C CS
                           cobW   2 vtvltGflGsGKTtLlnhll.e 22 
                                    vtvltG +G+GKTt + +ll  
  gi|121636548|ref|YP_976771.1| 165 VTVLTGGPGTGKTTTVARLLaL 186
                                    89****************9952 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.23   1.5e+02       3      15 ..      51      63 ..      50      74 .. 0.90
   2 ?    7.9   0.1    0.0073       4.7      10      55 ..     304     349 ..     283     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                                   EEEESSTB-TT-B CS
                            SAF  3 VvvAardikaGev 15
                                   V+vA+r+++aG+v
  gi|121636548|ref|YP_976771.1| 51 VAVAVRALRAGSV 63
                                   9**********87 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0073
                                    B-TT-BE.BTTTEEEECECGGCCTSCCCGG.HHHHTTEEESS-B-TT- CS
                            SAF  10 ikaGevi.teddltlkrpiashkigllpia.ygeviGkratrdikaGe 55 
                                    ++aG v+ +  d   +r++a   ++l +++ +g viG +++ +i+aG+
  gi|121636548|ref|YP_976771.1| 304 VEAGAVLaDLVDGFSVRDDAL-VAQLRTSHrFGKVIG-TLAEAIRAGD 349
                                    667888887778888888765.889999999******.*********7 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       9.3     6e+03      34      49 ..      48      63 ..      46      64 .. 0.84
   2 ?    8.9   1.0    0.0014      0.93       8     158 ..     152     301 ..     148     332 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.3
                                   HHHHHHHHHHHHTTS- CS
                           PhoH 34 ylavalavealkkkkv 49
                                    lava+av+al++++v
  gi|121636548|ref|YP_976771.1| 48 ALAVAVAVRALRAGSV 63
                                   599*******998765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHH-SEEEEE--TTSSTT.....HHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHH CS
                           PhoH   8 eQkeylealkkndivfaiGpaGtGKt.....ylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrp 82 
                                    eQ++++e+  ++ +++ +G  GtGKt     +la+++  + l  +   ri l+ p+ +a  +l      +  k+d   r+
  gi|121636548|ref|YP_976771.1| 152 EQRRAAEIALSQGVTVLTGGPGTGKTttvarLLALVAEQAELAGEPRPRIALAAPTGKAAARLAEAVRREMAKLDATDRA 231
                                    789999998999*************9322222333333333444445567777776666666666666666666665555 PP

                                    HHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                           PhoH  83 lydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                        L+ ++    +++ll ++    a ++  R   l + ++++DE   ++ + m  +   +  +++++++Gd  q 
  gi|121636548|ref|YP_976771.1| 232 RLGDLHAVT----LHRLLGAK--PGARFRQDRQNRLPHNVIVVDETSMVSLTLMARLAEAVRPGARLILVGDADQL 301
                                    444444443....44444333..34555666666677777777777777777777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3463.44
//
Query:       gi|121636549|ref|YP_976772.1|  [L=897]
Description: exonuclease V subunit beta recBa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-60  202.8   0.0      2e-59  201.7   0.0    1.5  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    4.3e-23   82.3   0.0    1.6e-22   80.4   0.0    2.0  1  AAA_19           AAA domain
    2.6e-14   53.4   0.0    7.3e-07   28.9   0.0    2.6  2  UvrD_C           UvrD-like helicase C-terminal domain
    1.7e-07   31.1   6.6     0.0029   17.4   0.2    3.0  3  AAA_30           AAA domain
    4.2e-07   29.7   0.4       0.02   14.7   0.3    2.9  2  UvrD_C_2         UvrD-like helicase C-terminal domain
     0.0014   18.9   0.4       0.24   11.7   0.1    3.0  3  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.028   13.9   0.0        1.5    8.2   0.0    2.3  2  PhoH             PhoH-like protein
      0.029   14.1   0.0        1.7    8.4   0.0    2.2  2  AAA_11           AAA domain
      0.051   13.3   0.0        4.1    7.1   0.0    2.9  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        3.2    7.3   7.7        0.5    9.9   0.1    3.3  4  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.7   0.0   1.1e-62     2e-59      12     311 ..      13     310 ..       5     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 1.1e-62
                                    -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH......................HH CS
                  UvrD-helicase  12 lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee......................al 69 
                                     g+++++eAsAG+GKTf la ++ r ++e+  + d++l++TF ++A++El+eR++                       +l
  gi|121636549|ref|YP_976772.1|  13 EGTTTVLEASAGTGKTFALAGLVTRYLAETAATLDEMLLITFNRAASRELRERVRGqivealgalqgdappsgelvehLL 92 
                                    578899*****************************************************************999888866 PP

                                    HHCCHHCTT-H.HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSC...HSHT CS
                  UvrD-helicase  70 kkaeqessdde.rlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkellek...sadd 145
                                    + +  e++++  rlr+al+n++ a+i T H+fc  +lk      +   +++++++ +        l+ e++++   ++  
  gi|121636549|ref|YP_976772.1|  93 RGSDAERAQKRsRLRDALANFDAATIATTHEFCGSVLKSLGVAGDNAADVELKESLT-------DLVTEIVDDrylANFG 165
                                    666666665558******************************************999.......4555555421114555 PP

                                    TTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHH CS
                  UvrD-helicase 146 slnldkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkk 225
                                    ++++d + + ++                     a  l+ +v + +  ql+p + ++ + ka  + +++ae+l+e++++k 
  gi|121636549|ref|YP_976772.1| 166 RQETDPELTYAE---------------------ALALALAVVDDPCAQLRPPDPEPGS-KAAVRLRFAAEVLEELERRKG 223
                                    555555555544.....................678999999*************965.99******************* PP

                                    HHTCEEHHHHHHHHHHHHHH.CHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-T CS
                  UvrD-helicase 226 eenalDfsdllhallellee.neelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdi 304
                                    + +a+ f+dll++l ++le+ ++ +++++rer++++l+DE+QDT+++Q+r+l++ +s+h+ l+++GDpkQ+IYgFRg+di
  gi|121636549|ref|YP_976772.1| 224 RLRAQGFNDLLIRLATALEAaDSPARDRMRERWRIVLVDEFQDTDPMQWRVLERAFSRHSALILIGDPKQAIYGFRGGDI 303
                                    ********************999********************************************************* PP

                                    HHHHHHH CS
                  UvrD-helicase 305 elflkkk 311
                                    +++lk+ 
  gi|121636549|ref|YP_976772.1| 304 HTYLKAA 310
                                    ****986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   8.7e-26   1.6e-22      11     146 .]      15     299 ..      11     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 8.7e-26
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...................... 68 
                                    ++ ++ a +GtGKT  l + v+ +++++   ++e+ll++f++ A +elrer+++  +e                      
  gi|121636549|ref|YP_976772.1|  15 TTTVLEASAGTGKTFALAGLVTRYLAETAATLDEMLLITFNRAASRELRERVRGQIVEalgalqgdappsgelvehllrg 94 
                                    678999**********************************************887777999999**************** PP

                         AAA_19  69 .......................atTiHrlal................................................ 77 
                                                           + T H++                                                  
  gi|121636549|ref|YP_976772.1|  95 sdaeraqkrsrlrdalanfdaatIATTHEFCGsvlkslgvagdnaadvelkesltdlvteivddrylanfgrqetdpelt 174
                                    *****9999999999999998887788888669*********************************************** PP

                         AAA_19  78 .....................................................ldfddlltealelle..eaeeekklqe 102
                                                                                          +f+dll   +++le  ++  ++ ++e
  gi|121636549|ref|YP_976772.1| 175 yaealalalavvddpcaqlrppdpepgskaavrlrfaaevleelerrkgrlraQGFNDLLIRLATALEaaDSPARDRMRE 254
                                    ****************************************************9999999999999999886667888999 PP

                         AAA_19 103 ee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                    ++ +++vDEfqd+d++q+r+l++ + ++  l+l+GDp+Q+iy fr
  gi|121636549|ref|YP_976772.1| 255 RWrIVLVDEFQDTDPMQWRVLERAFSRHSALILIGDPKQAIYGFR 299
                                    *************************89988************997 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.1e-08   0.00013       3     129 ..     319     479 ..     317     488 .. 0.66
   2 !   28.9   0.0   4.1e-10   7.3e-07     280     343 ..     595     687 ..     530     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.1e-08
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx......................xxxxxxx......xxxxxxxxx RF
                         UvrD_C   3 LekNyRStksLlkaankflenilnrrale....kek......................ktvekge......kivvleaet 50 
                                    L  N+RS + L++ ++++l+ ++  +a+     + +                      k ++ g       +i+ l+   
  gi|121636549|ref|YP_976772.1| 319 LGVNWRSDRALVESLQTVLRDATLGHADIvvrgT-DahhaghrlasaprpapfrlrvvKRHTLGYdgtahvPIEALR--- 394
                                    5667777777777777777544443333332232.135566666666666666666553333333442333333333... PP

                                    xxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  51 eeeEaekiaatikall.......ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkll 123
                                     ++++++ aa + all       ++    +diav+v  +kda+   +aL + gip +  ++++ F  +  kd l++l+ +
  gi|121636549|ref|YP_976772.1| 395 -RHIPDDLAADVAALLasgatfaGRPVVAADIAVIVEHHKDARACRNALAEAGIPAIYTGDTDVFASQAAKDWLCLLEAF 473
                                    .33444444444444444447777777889************************************************99 PP

                                    xxxxxx RF
                         UvrD_C 124 ankqdk 129
                                    + +q++
  gi|121636549|ref|YP_976772.1| 474 DAPQRS 479
                                    988875 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 4.1e-10
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxx....xxxxxx RF
                         UvrD_C 280 eskkk.ekipiiTiHqAKGlEFdvVflagleegtfP............................syrskk....ekrleE 326
                                    +++++   ++i+T+  AKGl F++V+l  +++ ++                                  +     +  + 
  gi|121636549|ref|YP_976772.1| 595 RLDSDaAAVQIMTVFVAKGLQFPIVYLPFAFNRNVRsddillyhddgtrclyiggkdggaqrrtV----EglnrVEAAHD 670
                                    44555689*************************99988888888888888888887777644331....26556557778 PP

                                    xxxxxxxxxxxxxxxxx RF
                         UvrD_C 327 EkRlfYVaiTRAkkrLf 343
                                      Rl YVa+TRA+++++
  gi|121636549|ref|YP_976772.1| 671 NLRLTYVALTRAQSQVV 687
                                    99***********9976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.6e-06    0.0029      19      67 ..      15      67 ..      10     182 .. 0.80
   2 !   16.6   0.2   2.7e-06    0.0049      58     162 ..     204     330 ..     200     359 .. 0.66
   3 ?   -3.9   0.1       5.2   9.2e+03      57      82 ..     493     521 ..     487     535 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLaeelg 67
                                    ++vl++ AGtGKt+al++l+  + a+      ++++++ + +a+++L+e + 
  gi|121636549|ref|YP_976772.1| 15 TTTVLEASAGTGKTFALAGLVTRYLAETaatlDEMLLITFNRAASRELRERVR 67
                                   5789****************766666643688899999999999999*98654 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.7e-06
                         AAA_30  58 aAkvLaeelgi...........eastiakllkrlk.........grarlepg.tllivDEagmvdtkqlaallkaaekag 116
                                    aA +L+ ++++           +a+  + ll rl+         +r r++++ ++++vDE   +d  q++ l ++a +++
  gi|121636549|ref|YP_976772.1| 204 AAVRLRFAAEVleelerrkgrlRAQGFNDLLIRLAtaleaadspARDRMRERwRIVLVDEFQDTDPMQWRVL-ERAFSRH 282
                                    555555322222222222233388888888888889999999*9778999999********99998888655.5555559 PP

                         AAA_30 117 akvilvGDerQlasVeaGgvlrdlveaagi..gtaeLtevvRqkesee 162
                                      +il+GD++Q     +Gg +++ ++aag+     +L  ++R +++  
  gi|121636549|ref|YP_976772.1| 283 SALILIGDPKQAIYGFRGGDIHTYLKAAGTadARYTLGVNWRSDRALV 330
                                    9**********7665666666655566555224556666777655444 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.2
                         AAA_30  57 kaAkvLaeelgieastiakllkrlk...g 82 
                                    + A+ La+e ++ ++++a  l++++   +
  gi|121636549|ref|YP_976772.1| 493 ETAESLAAEGDALTDRVAGTLHEWAdhaR 521
                                    56777887777778888888887774330 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   8.6e-05      0.15       4      27 ..     605     626 ..     602     647 .. 0.81
   2 !   14.7   0.3   1.1e-05      0.02      14      50 ..     655     687 ..     653     688 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                       UvrD_C_2   4 altihkaQGsefpaVivfdpdlaa 27 
                                    ++t+  a+G++fp+V++  p + +
  gi|121636549|ref|YP_976772.1| 605 IMTVFVAKGLQFPIVYL--PFAFN 626
                                    79***************..65555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-05
                       UvrD_C_2  14 efpaVivfdpdlaaarmgelrrrlLYtavTRArekli 50 
                                    + ++V   + ++aa++    + rl Y+a+TRA+ +++
  gi|121636549|ref|YP_976772.1| 655 QRRTVEGLNRVEAAHD----NLRLTYVALTRAQSQVV 687
                                    6666666666777777....49***********9997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00013      0.24       7      90 ..      16      99 ..      12     112 .. 0.81
   2 ?    3.7   0.0     0.038        67      55     131 ..     209     291 ..     185     294 .. 0.64
   3 ?   -2.4   0.0       3.1   5.5e+03      56      86 ..     551     583 ..     505     588 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseellealeqalr 87
                                    +v+ + +GtGKT+ l+ l+ ++ +e +a+  +  +++++ ++s ++++  + ++++alg  + +    s el+e+l + ++
  gi|121636549|ref|YP_976772.1| 16 TTVLEASAGTGKTFALAGLVTRYLAETAATLDEMLLITFNRAASRELRERvRGQIVEALGALQGD-APPSGELVEHLLRGSD 96
                                   5788899****************988888889999999998888877666699999999987777.7778888888877776 PP

                         AAA_22 88 ara 90
                                   a +
  gi|121636549|ref|YP_976772.1| 97 AER 99
                                   655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.038
                         AAA_22  55 dllrellralglelka.erlsseellealeqalrarav............ielliiDEaqhlr..seealeeLrsllnls 119
                                     ++ e+l++l++++ + + +   +ll +l+ al+   +             +++++DE+q  +  + ++le     +   
  gi|121636549|ref|YP_976772.1| 209 RFAAEVLEELERRKGRlRAQGFNDLLIRLATALE---AadspardrmrerWRIVLVDEFQDTDpmQWRVLERA---FS-- 280
                                    4667777777776666433333333333333333...344477788889989********9954334444444...22.. PP

                         AAA_22 120 rkgvqliLvGtp 131
                                      + +liL+G p
  gi|121636549|ref|YP_976772.1| 281 -RHSALILIGDP 291
                                    .34477777776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                         AAA_22  56 l..lrellralglelkaerlsseellealeqal 86 
                                    l  l ++++ l++ +++erl +  l++ l++++
  gi|121636549|ref|YP_976772.1| 551 LtdLAHIAQLLHEAAHRERLGLPGLRDWLRRQA 583
                                    222455555555555555555555555555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.032        57      21      35 ..      16      30 ..       9      66 .. 0.82
   2 ?    8.2   0.0   0.00085       1.5     122     157 ..     258     293 ..     252     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                                   EEEEE--TTSSTTHH CS
                           PhoH 21 ivfaiGpaGtGKtyl 35
                                    ++  ++aGtGKt+ 
  gi|121636549|ref|YP_976772.1| 16 TTVLEASAGTGKTFA 30
                                   577889*******83 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00085
                                    EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE---- CS
                           PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtq 157
                                    +v++DE Q+t ++q +++   + ++s +++ Gd++q
  gi|121636549|ref|YP_976772.1| 258 IVLVDEFQDTDPMQWRVLERAFSRHSALILIGDPKQ 293
                                    799*************999999************99 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.031        55      19      58 ..      16      50 ..       6      80 .. 0.68
   2 ?    8.4   0.0   0.00096       1.7     176     253 ..     213     293 ..     203     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.031
                         AAA_11 19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriL 58
                                    t+++   GtgKT+++++l+ + l      e++++  ++L
  gi|121636549|ref|YP_976772.1| 16 TTVLEASAGTGKTFALAGLVTRYLA-----ETAATLDEML 50
                                   57788889************99953.....3334444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00096
                         AAA_11 176 elskeleeaeesleeevldeaeivltT.lsgagsklleklakkfdvviIDEAaqavEpstliPlrlga...kkvvLvGDp 251
                                    e+ +ele+++ +l+++  ++  i l+T l  a+s++ ++++++ ++v++DE  q + p  +  l ++    + ++L+GDp
  gi|121636549|ref|YP_976772.1| 213 EVLEELERRKGRLRAQGFNDLLIRLATaLEAADSPARDRMRERWRIVLVDEF-QDTDPMQWRVLERAFsrhSALILIGDP 291
                                    566788888888888888888887777356668888889999*********5.999*****9997777555889****** PP

                         AAA_11 252 kQ 253
                                    kQ
  gi|121636549|ref|YP_976772.1| 292 KQ 293
                                    *9 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.92   1.6e+03       2      21 ..      18      37 ..      17      67 .. 0.75
   2 ?    7.1   0.0    0.0023       4.1      63     107 ..     256     301 ..     239     353 .. 0.70
   3 ?    2.3   0.1     0.066   1.2e+02     213     230 ..     669     686 ..     662     688 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.92
                Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                   v  + +G GK+ ++  l+  
  gi|121636549|ref|YP_976772.1| 18 VLEASAGTGKTFALAGLVTR 37
                                   566789*****999877755 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0023
                Viral_helicase1  63 gkililDEylllhaGyillla.alskaklvilfGDplQipfhsrna 107
                                     +i+++DE++  ++ +  +l  a s+ + +il+GDp+Q  +  r +
  gi|121636549|ref|YP_976772.1| 256 WRIVLVDEFQDTDPMQWRVLErAFSRHSALILIGDPKQAIYGFRGG 301
                                    57999*****9998777774314466789*********98876655 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.066
                Viral_helicase1 213 sesrenllvAlTRhrksl 230
                                     ++    +vAlTR+ +++
  gi|121636549|ref|YP_976772.1| 669 HDNLRLTYVALTRAQSQV 686
                                    4567889*******9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00028       0.5      27      59 ..       8      40 ..       3     128 .. 0.76
   2 ?   -2.2   0.1       1.5   2.6e+03      92     153 ..     239     266 ..     206     297 .. 0.52
   3 ?   -1.8   0.0       1.1   1.9e+03      49      76 ..     401     429 ..     386     464 .. 0.75
   4 ?   -0.4   0.3      0.39     7e+02      78     139 ..     499     563 ..     483     585 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                         AAA_25 27 kgllpagelallaGapgtGKttlaldlalavat 59
                                   + l ++g++++l +  gtGKt+++  l+  ++ 
  gi|121636549|ref|YP_976772.1|  8 GPLPREGTTTVLEASAGTGKTFALAGLVTRYLA 40
                                   5566799******************99998874 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                         AAA_25  92 avgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr 153
                                     ++ea++ +ar +                                     ++r v +D ++ 
  gi|121636549|ref|YP_976772.1| 239 TALEAADSPARDRMRE----------------------------------RWRIVLVDEFQD 266
                                    3333332222222222..................................233333333333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                         AAA_25  49 laldlalavatGkpwlg.pvapeqgkVly 76 
                                    la d+a+ +a+G  ++g pv+   ++V++
  gi|121636549|ref|YP_976772.1| 401 LAADVAALLASGATFAGrPVVAADIAVIV 429
                                    45566666667777777666555555554 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.39
                         AAA_25  78 saEds..edelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                    +aE++   d+++  l+++  ++r+++  +v ++a+  +  + + ++rgg++   d++++++ + e
  gi|121636549|ref|YP_976772.1| 499 AAEGDalTDRVAGTLHEWADHARHRGVAAVFQAAQLaGMGRRVLSQRGGERDLTDLAHIAQLLHE 563
                                    56666334566666666666664444444444444444444455566666633455555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 5469.93
//
Query:       gi|121636550|ref|YP_976773.1|  [L=1097]
Description: exonuclease V (gamma chain) recC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.7e-201  669.4   0.0   8.6e-201  669.1   0.0    1.0  1  Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit
    3.2e-46  157.6   3.3    6.6e-45  153.4   0.2    2.9  2  RecC_C          RecC C-terminal domain


Domain annotation for each model (and alignments):
>> Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.1   0.0  9.6e-205  8.6e-201       2     755 ..       3     750 ..       2     766 .. 0.93

  Alignments for each domain:
  == domain 1  score: 669.1 bits;  conditional E-value: 9.6e-205
                                    EEEEEESSHHHHHHHHHHHHHHS--SSSS--EEEE-SSHHHHHHHHHHHH........HTTS-BESEB---HHHHHHHHH CS
                 Exonuc_V_gamma   2 ltlyqSnrlevLaellakllreeplanpfepeiilvqskgmarwLklelA........ekkGiaanlefplpasflwqll 73 
                                    l+l++++r+++La+ l +ll+ +p+++pf++e +lv  +g++rwL+++l+        +++G++a + f  p+s++ ++ 
  gi|121636550|ref|YP_976773.1|   3 LHLHRAERTDLLADGLGALLA-DPQPDPFAQELVLVAARGVERWLSQRLSlvlgcgpgRADGVCAGIAFRNPQSLIAEIT 81 
                                    99*******************.88889***************************************************** PP

                                    HHHSSS--SS-TT-HHHHHHHHHHHHHHHTSSSSTHHHHHHT........TSS-SS....HHHHHHHHHHHHHHHHHTTS CS
                 Exonuc_V_gamma  74 kavlpevpeespfskealtWrlmrlLpelleeeefaplrkyl........skdsdq....lklyqLaekiAdlFdqYlvy 141
                                     ++     +++p+s+eal+W l++++++ l+e+++++l+++l        +          ++y++a+++A lF  Y+  
  gi|121636550|ref|YP_976773.1|  82 GTL-----DDDPWSPEALAWPLLAVIDASLDEPWCRTLASHLghfattdaE----AelrrGRRYSVARRLAGLFASYARQ 152
                                    999.....678*******************************999865443....245559******************* PP

                                    SHHHHHHHCTT..---TT--TTHHHHHHHHHHHHHHHHHTT-----SHCCHHHHHHHHHSSTT--TS--SEEEEES---- CS
                 Exonuc_V_gamma 142 RpdwlaaWeageekklakleederWQaiLWralvaelkeekqeiqaranlheeflealakkekklkklPkrifvFgissl 221
                                    Rp +laaW  g   +l +l+ d +WQ+ LWralv+ + +++ +  +         +++a+ ++ +++lP+r+++Fg ++l
  gi|121636550|ref|YP_976773.1| 153 RPGLLAAWLDG---DLGELPGDLAWQPPLWRALVTTVGADPPHVRH--------DKTIARLRDGPADLPARLSLFGHTRL 221
                                    ***********...9**************************98887........78888889****************** PP

                                    -HHHHHHHHHHTTTSEEEEEEE-S-SS--S--S-TTTSTTHSSTT-SSSSBSS-SSHHHHHHTHHHHHHHHHHTT-.SSE CS
                 Exonuc_V_gamma 222 ppsylevLkalskhidVhlfllnPcreyWgdivdrkqllreqleeeeedelleegnpLLaslGkqgrdfldlleeleees 301
                                    + + +++L+al+ h d hl+l +P++e+W  ++  + +    l ++++ + +  ++pLL+ lG++ r++++ l      +
  gi|121636550|ref|YP_976773.1| 222 ACTDVQLLDALAVHHDLHLWLPHPSDELWRALAGFQGADG-LLPRRQDTSRRAAQHPLLETLGRDVRELQRALPAA--RA 298
                                    *********************************9777777.7789999999***********************99..56 PP

                                    EEEEE-----S-SHHHHHHHHHHHHHH--TTSEE--TT--SSEEEEESSHHHHHHHHHHHHHHHHHHSTT--GGGEEEEE CS
                 Exonuc_V_gamma 302 keidlfeeeeeeslLqqlqadilekaedeekklaleekDrSiqihsChsplREvevLhdqLlalleadptlqprDilVmv 381
                                     ++ l   +++++lL++lqadi   + +   +++l+ +DrS+q+h+Ch+p+R+++vL++ Ll lle+dptlqprDi+Vm+
  gi|121636550|ref|YP_976773.1| 299 TDEFLGATTKPDTLLGWLQADIAG-NAPRPAERSLSDADRSVQVHACHGPARQIDVLREVLLGLLEDDPTLQPRDIVVMC 377
                                    66666669****************.666667788********************************************** PP

                                    STHHHHHHHHHHHT......SCSTTTT---EEE-SEETGGGHHHHHHHHHHGGGGG----HHHHHHHTTSHHHHHHTT-- CS
                 Exonuc_V_gamma 382 pdieayaPyIeaVF......gaaederklpysiaDrsakeespllaaflelLeLpesrftasevldlLevpavarrfgld 455
                                    pdi++yaP+I a F      g+ + +++l++++aDr +++++pll+++ elL ++e+r tas++l+l + ++v+++fg++
  gi|121636550|ref|YP_976773.1| 378 PDIDTYAPLIVAGFglgevaGDCHPAHRLRVRLADRALTQTNPLLSVAAELLTIAETRATASQLLNLAQAAPVRAKFGFA 457
                                    **************7755544556******************************************************** PP

                                    HHHHHHHHHHHHHHT--S-SSHHHHHHTT----SSSSHHHHHHHHHHHHSS-S.TT--SSS----TTS-SCTHHHHHHHH CS
                 Exonuc_V_gamma 456 eedleqlrewlaeagirwGldaehreelglpadeqnswrfgLdRlllGyalge.engllegilpydevegseaellgkla 534
                                    ++dl++++ w++e++irwG+d  hr++ gl++  +n+wrfgLdR+l G+a++e ++++l+  lp+d+v ++++el+g+la
  gi|121636550|ref|YP_976773.1| 458 DDDLDTITTWVRESNIRWGFDPTHRRRYGLDTVVHNTWRFGLDRILTGVAMSEdSQAWLDTALPLDDVGSNRVELAGRLA 537
                                    *****************************************************777778899****************** PP

                                    HHHHHHHHHHHHSSS-B-HHHHTTHHHHHHHHH----SHHHHHHHHHHHHHHHHHHHHHHTT--S-B-HHHHHHHHHHHH CS
                 Exonuc_V_gamma 535 ellerLekwrqrlskprtleeWlerlselledffaedeeeeeelqelrealaelaeeaaaakfeqelslevvrelleerl 614
                                    e++erL++++  ls++r+l +Wl+ l + ++ + a   ++ ++ +++++++a++ + a + + +  l+l+ vr+ll ++l
  gi|121636550|ref|YP_976773.1| 538 EFVERLHHVVGGLSGARPLVAWLDALATGIDLLTAC--NDGWQRAQVQREFADVLARAGSRA-APLLRLPDVRALLDAQL 614
                                    *******************************99855..555666788899888855555444.245************** PP

                                    HH-EE-TTTTSSSEEEEE--TT----EEEEEEE--BTTTSS------SS-HHHHS--TT---HHHHHHHHHHHHHHHEEE CS
                 Exonuc_V_gamma 615 sqesasqrfltGkvtfctllpmrsiPfrvvclLGlndgdfPrqdepagfDlmakeprkgDrsrrdddrylfLeallsAre 694
                                    + ++++++f+tG++t+ct++pmrs+P+rvvcl+Gl+dg fPr  +p+g D++a+ep  g+r+ r +dr+l+L+a+ +A++
  gi|121636550|ref|YP_976773.1| 615 AGRPTRANFRTGTLTVCTMVPMRSVPHRVVCLVGLDDGVFPRLSHPDGDDVLAREPMTGERDIRSEDRQLLLDAIGAATQ 694
                                    ******************************************************************************** PP

                                    EEEEEEESBETTTTEB--B-HHHHHHHHHHHTTEE-SHHHHHHHHHHEEE--SSTTSGGGG CS
                 Exonuc_V_gamma 695 aLyiSYvgrsirdnserpPSvlvselldylaqnfalkgeealkalklvvehplqpfspknF 755
                                     L+i+Y+g ++r++++rpP+v++ elld+l+q++   ++  ++++  +v+hplqpf++kn 
  gi|121636550|ref|YP_976773.1| 695 TLVITYTGADERTGQPRPPAVPLAELLDALDQTT---SAPVRERI--LVTHPLQPFDRKNV 750
                                    *********************************9...78888887..799*********98 PP

>> RecC_C  RecC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.3    0.0051        46     111     160 ..     516     577 ..     499     617 .. 0.71
   2 !  153.4   0.2   7.3e-49   6.6e-45       2     198 ..     795    1020 ..     794    1021 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0051
                         RecC_C 111 levdldlggtg.....LtgtldglrergllrwrpsklkakdllraWlehLalca...........l 160
                                    l+  l+l+++g     L g+l +  e  +l+  ++ l++ + l aWl+ La               
  gi|121636550|ref|YP_976773.1| 516 LDTALPLDDVGsnrveLAGRLAEFVE--RLHHVVGGLSGARPLVAWLDALA--TgidlltacndgW 577
                                    445555555555568899***99994..58878******************..3335555555552 PP

  == domain 2  score: 153.4 bits;  conditional E-value: 7.3e-49
                         RecC_C    2 eelelddLirFlrnParaFlrqrLgvrleeeeeeleddepfeldgLeryqlkdrllealla..e..ellarlrargeL 75  
                                     ++++l+dL++F+++P++ F+r  L+  l+ + +++ed+ p+++d+L+++ +++r+l+++l+  +  ++++ +++rg+L
  gi|121636550|ref|YP_976773.1|  795 ADVTLADLLDFFKDPVKGFFRA-LDYTLPWDVDTVEDSIPVQVDALAEWTVGERMLRDMLRglHpdDAAHSEWRRGTL 871 
                                     689*****************98.**************************************772567*********** PP

                         RecC_C   76 PpgafGelaleelleqvealaealrallgeepleslevdldlggtg.LtgtldglrergllrwrpsklkakdllraWl 152 
                                     Ppg +G + ++e+++++++la+a+ a ++++  ++++vd+dlg+ + L+gt++ + + + + +++skl +k++l aW+
  gi|121636550|ref|YP_976773.1|  872 PPGRLGVRRAKEIRNRARDLAAAALAHRDGH-GQAHDVDVDLGDGRrLSGTVTPVFGGRTVSVTYSKLAPKHVLPAWI 948 
                                     ***************************9999.9**********7667******************************* PP

                         RecC_C  153 ehLalca..........................lpaeeArelLaellalyrqGlrqpLpffpktalayleal 198 
                                      ++ l+a                          +p+ ++ + L+el+ ly++G r+pLp+++kt++a+++a+
  gi|121636550|ref|YP_976773.1|  949 GLVTLAAqepgrewsalcigrsktrnhiarrlfVPPPDPVAVLRELVLLYDAGRREPLPLPLKTSCAWAQAR 1020
                                     ****999**************************99**********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1097 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 6869.61
//
Query:       gi|121636551|ref|YP_976774.1|  [L=231]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-27   96.1   1.5    2.4e-27   95.8   1.5    1.0  1  ECH_1            Enoyl-CoA hydratase/isomerase
    1.4e-13   51.1   0.9    1.6e-13   50.9   0.9    1.2  1  ECH_2            Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.012   15.5   1.7      0.058   13.3   0.6    2.1  2  CLP_protease     Clp protease
       0.64    9.9   3.2        5.2    7.0   0.0    3.0  3  Arg_repressor_C  Arginine repressor, C-terminal domain


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   1.5   5.4e-31   2.4e-27       2     203 ..       9     207 ..       8     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 5.4e-31
                                    EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHH CS
                          ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelw 81 
                                    +++++avi +++  +vNal +++ + l++a+ +++ d  v+a v+tG +++F+ G dlk ++ +e + + ++    +el 
  gi|121636551|ref|YP_976774.1|   9 RKDSIAVISMDDG-KVNALGPAMQQALNAAIDNADRD-DVGALVITGNGRVFSGGFDLKILTSGEVQPAIDMLRGGFELA 86 
                                    6789*********.***********************.9**************************9************** PP

                                    HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEH CS
                          ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisa 161
                                     +l++ pkpv+ a  G+ai+ G+ l ++ D ++aa   ++ +ne+ +G++ +  + +i+  ++ +s+ ++++ l+k + +
  gi|121636551|ref|YP_976774.1|  87 YRLLSYPKPVVMACTGHAIAMGAFLLSCGDHRVAAHAYNIQANEVAIGMTIPYAALEIMKLRLTRSAYQQATGLAKTFFG 166
                                    ******************************************************************************** PP

                                    HHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHH CS
                          ECH_1 162 qealkvGlvdkvvpeeqlleealelaeklaekspaalrqlke 203
                                    + al +G +d++   e +++ a e+a++ a   ++++ ++++
  gi|121636551|ref|YP_976774.1| 167 ETALAAGFIDEIALPEVMVSRAEEAAREFA-GLNQHAHAATK 207
                                    *************999************99.44444444443 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.9   3.5e-17   1.6e-13      10     137 ..      21     144 ..      13     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.5e-17
                                    GGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHHHC-SS- CS
                          ECH_2  10 kalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyliatypkp 89 
                                     ++NaL  +m +al++a+++  + d+v ++v++g+g + f+ G D++ l++ + + +    ++ r  ++l y++ +ypkp
  gi|121636551|ref|YP_976774.1|  21 GKVNALGPAMQQALNAAIDNA-DRDDVGALVITGNG-RVFSGGFDLKILTSGEVQPA---IDMLRGGFELAYRLLSYPKP 95 
                                    579*****************6.66779*******88.************99988866...459***************** PP

                                    EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT--.--TTHHH CS
                          ECH_2  90 vvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlf.PDvGgsy 137
                                    vv  + G ++  G+ l   g +rv+     +   E+aIG++ P  +   
  gi|121636551|ref|YP_976774.1|  96 VVMACTGHAIAMGAFLLSCGDHRVAAHAYNIQANEVAIGMTiPYAALEI 144
                                    ***************************************8514444444 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.3e-05     0.058      70      99 ..      90     118 ..      82     181 .. 0.79
   2 ?    1.8   0.1     0.042   1.9e+02      81     144 ..     157     217 ..     130     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                    HHHSSS-EEEEEEEEEETHHHHHHHTS-TT CS
                   CLP_protease  70 mqyikpdvsticlGlaaSmgslllaagekg 99 
                                    + y k +v++ c+G a  mg++ll++g++ 
  gi|121636551|ref|YP_976774.1|  90 LSYPK-PVVMACTGHAIAMGAFLLSCGDHR 118
                                    55544.4669*****************975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.042
                                    EEEEEET.HHHHHHHTS-TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHH CS
                   CLP_protease  81 clGlaaS.mgslllaagekgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneila 144
                                    ++Gla    g   laag  ++ +alp  ++m+ ++  +a+    +++++a+  +k+++r  +++a
  gi|121636551|ref|YP_976774.1| 157 ATGLAKTfFGETALAAGFIDE-IALP--EVMVSRAEEAARE-FAGLNQHAHAATKLRSRADALTA 217
                                    556666524777777777774.6666..4788887777666.78888888888888887776665 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5     0.046   2.1e+02      23      39 ..      30      46 ..       5      54 .. 0.63
   2 ?   -3.0   0.0       1.5   6.9e+03      17      33 ..      97     113 ..      96     119 .. 0.73
   3 ?    7.0   0.0    0.0012       5.2      10      40 ..     154     184 ..     148     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.046
                                   HHHHHHHHHHH-..TTE CS
                Arg_repressor_C 23 aAqavAaaiDslelpei 39
                                   + qa+ aaiD+++ +++
  gi|121636551|ref|YP_976774.1| 30 MQQALNAAIDNADRDDV 46
                                   33677777777776665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                    EE-STTHHHHHHHHHHH CS
                Arg_repressor_C  17 ikTlpGaAqavAaaiDs 33 
                                    +    G+A a++a++ s
  gi|121636551|ref|YP_976774.1|  97 VMACTGHAIAMGAFLLS 113
                                    55678999999988866 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0012
                                    EETTEEEEE-STTHHHHHHHHHHH-..TTEE CS
                Arg_repressor_C  10 saenlvvikTlpGaAqavAaaiDslelpeil 40 
                                    +++ +   kT  G   ++A +iD++ lpe++
  gi|121636551|ref|YP_976774.1| 154 YQQATGLAKTFFGETALAAGFIDEIALPEVM 184
                                    667777789********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1260.08
//
Query:       gi|121636552|ref|YP_976775.1|  [L=276]
Description: hypothetical protein BCG_0680c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   16.7   0.2     0.0046   16.7   0.2    1.8  2  DUF4748   Domain of unknown function (DUF4748)
  ------ inclusion threshold ------
        0.1   12.4   0.1       0.16   11.7   0.1    1.3  1  DUF4190   Domain of unknown function (DUF4190)


Domain annotation for each model (and alignments):
>> DUF4748  Domain of unknown function (DUF4748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.1e-07    0.0046       5      37 ..      22      53 ..      20      59 .. 0.88
   2 ?   -3.5   0.3         1   9.2e+03      31      41 ..     239     246 ..     233     254 .. 0.39

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-07
                        DUF4748  5 iwlgWgslcvaGigayyfAKrsidadRaaklea 37
                                   +wl+W++l   G+ a + +Kr+i ++R    e 
  gi|121636552|ref|YP_976775.1| 22 TWLAWAAL-GLGVVALVVTKRQIQRNRRLAAEQ 53
                                   7******9.88***************9866665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1
                        DUF4748  31 Raakleaerkr 41 
                                    Raa   ae + 
  gi|121636552|ref|YP_976775.1| 239 RAA---AETQD 246
                                    333...32222 PP

>> DUF4190  Domain of unknown function (DUF4190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.8e-05      0.16      17      45 ..      22      50 ..      12      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                        DUF4190 17 iitgivavilGhvAlrqirrsgerGkglA 45
                                   + ++ +a+ lG+vAl+  +r+ +r++ lA
  gi|121636552|ref|YP_976775.1| 22 TWLAWAALGLGVVALVVTKRQIQRNRRLA 50
                                   45788999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2001.84
//
Query:       gi|121636553|ref|YP_976776.1|  [L=237]
Description: glyoxalase II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-19   69.6   6.2    4.6e-19   69.2   6.2    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0019   17.7   2.0      0.003   17.1   2.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   6.2   5.1e-23   4.6e-19       7     197 .]      30     203 ..      24     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 5.1e-23
                                    EEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                    Lactamase_B   7 nsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                    ++yli   + g+++++D+ + +   + a     l+ ++ +++ v++TH+H+DH+Gg +   +  + +   +++  p++ +
  gi|121636553|ref|YP_976776.1|  30 FAYLIGdrTTGDCVVVDPAYAAGDLLDA-----LESDDMQLSGVLVTHHHPDHVGGSMMGFQLPGLAELLERASVPVHVN 104
                                    7999999999****************99.....7********************************************** PP

                                    HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.T CS
                    Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltl 164
                                     ++  + sr       v+ ++++  +  + g+  ++++  +   +++gh++g+ ++  ++ l++GD+l+ +  gr+d+  
  gi|121636553|ref|YP_976776.1| 105 THEALWVSR-------VTGIPVGDLITHEHGDKVSVGDIDIELLHTPGHTPGSQCFLLDGRLVAGDTLFLEGCGRTDF-- 175
                                    ***999998.......8999999999999999999999999999999999999999**********************.. PP

                                    TCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                    Lactamase_B 165 rgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                          +++d ++  +sl++la+l+ +  v+ gH
  gi|121636553|ref|YP_976776.1| 176 ------PGGDSDEMYRSLRQLAELPGDPTVFpGH 203
                                    ......9999999999*********999777799 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.0   3.4e-07     0.003      29     111 ..      63     146 ..      42     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-07
                                    .SEEEEE-SS--HHHHGGGGCCCCC--EE.EEEEEEHHHHHHCCTTCGHHHCHTT..TTEEEEEE-TTSEEEECSTTEEE CS
                  Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkk.lplyapkgvlavleanfvylaleee..pavnvheldwgesfelgdgglei 105
                                     ++ +Vl+th H DH+ g ++  +      ++l+  ++v  +++++    ++ +   p  ++ + + g+++++gd ++e+
  gi|121636553|ref|YP_976776.1|  63 MQLSGVLVTHHHPDHVGGSMMGFQ--LPGlAELLERASVPVHVNTHEALWVSRVTgiPVGDLITHEHGDKVSVGDIDIEL 140
                                    5899************88443333..222245555566666666664433333336666778888899999999877666 PP

                                    EEEEE- CS
                  Lactamase_B_2 106 tatpar 111
                                      tp +
  gi|121636553|ref|YP_976776.1| 141 LHTPGH 146
                                    666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1595.35
//
Query:       gi|121636554|ref|YP_976777.1|  [L=83]
Description: hypothetical protein BCG_0682 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-20   71.2   1.1    5.6e-20   71.0   1.1    1.1  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   1.1   3.1e-24   5.6e-20       1      47 []      16      68 ..      16      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.1e-24
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX------.-H.....H.... CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrk.re.....eldeL 47
                                   +r++Ie+DD+L++++ir++++k++rEaVnlALr+L+++++ +e     e+de+
  gi|121636554|ref|YP_976777.1| 16 KRVEIEVDDDLIQKVIRRYRVKGAREAVNLALRTLLGEADtAEhghddEYDEF 68
                                   8***************************************6447888999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 669.95
//
Query:       gi|121636555|ref|YP_976778.1|  [L=55]
Description: 50S ribosomal protein L33 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-23   82.1   5.9    3.1e-23   82.0   5.9    1.0  1  Ribosomal_L33   Ribosomal protein L33
     0.0056   16.1   1.4      0.021   14.3   0.2    2.0  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.015   15.2   1.5        1.6    8.7   0.4    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.016   15.3   2.6      0.034   14.3   2.6    1.5  1  Zn-ribbon_8     Zinc ribbon domain
       0.02   14.9   0.9      0.024   14.7   0.9    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.03   14.4   1.4       0.05   13.6   0.0    1.9  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
      0.049   13.2   2.0       0.11   12.0   2.1    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.054   13.2   1.5      0.054   13.2   1.5    2.0  2  zinc_ribbon_2   zinc-ribbon domain
       0.06   13.5   4.3       0.12   12.6   4.3    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.083   12.9   3.0       0.15   12.1   3.0    1.6  1  DZR             Double zinc ribbon
       0.11   12.3   3.4        3.1    7.7   0.5    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.14   12.1   4.1        0.2   11.6   0.6    2.2  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   5.9   2.1e-26   3.1e-23       2      47 .]      10      55 .]       9      55 .] 0.98

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.1e-26
                                   EEEEEET......EEEEETT..--S--EEEEEETTTTEEEEEEEE- CS
                  Ribosomal_L33  2 kvtLeCtecksrnYtttknkkntperLelkKYcprcrkhtlhkEtK 47
                                   k+tL+C+ ck+rnY+t+kn++n p+rLelkK+cp+c kh  h+Et+
  gi|121636555|ref|YP_976778.1| 10 KITLACEVCKHRNYITKKNRRNDPDRLELKKFCPNCGKHQAHRETR 55
                                   8*******************************************96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.19   2.9e+02       4      11 ..      14      22 ..      11      28 .. 0.72
   2 !   14.3   0.2   1.4e-05     0.021       2      11 ..      39      48 ..      38      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                    zf-ribbon_3  4 rCPnCGa.p 11
                                    C  C++ +
  gi|121636555|ref|YP_976778.1| 14 ACEVCKHrN 22
                                   577888766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.4e-05
                    zf-ribbon_3  2 tvrCPnCGap 11
                                   +++CPnCG++
  gi|121636555|ref|YP_976778.1| 39 KKFCPNCGKH 48
                                   5789999984 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0082        12      13      28 ..       3      19 ..       1      25 [. 0.83
   2 ?    8.7   0.4     0.001       1.6       2       9 ..      40      47 ..      40      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0082
                                   EEECSCCCE.EEESSSS CS
                 RNA_POL_M_15KD 13 pkedkegkn.feCrqCg 28
                                   + +d+  k+ ++C  C+
  gi|121636555|ref|YP_976778.1|  3 SSTDVRPKItLACEVCK 19
                                   6678888999******8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.001
                                   EBESTTTS CS
                 RNA_POL_M_15KD  2 kFCpkCgN 9 
                                   kFCp Cg 
  gi|121636555|ref|YP_976778.1| 40 KFCPNCGK 47
                                   7*****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.6   2.3e-05     0.034       7      38 ..      14      52 ..       9      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                    Zn-ribbon_8  7 rCeeCghefevlqsis.dap....lta.CPeCgs.evrr 38
                                    Ce C+h+  +  +    +p    l++ CP+Cg+ +++r
  gi|121636555|ref|YP_976778.1| 14 ACEVCKHRNYITKKNRrNDPdrleLKKfCPNCGKhQAHR 52
                                   6999999999777766544468889999******99887 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   1.6e-05     0.024      68      98 ..      10      51 ..       5      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                   --EEEETTTS-EEECHHHHH...........S-TTTSSS-EE CS
                           HypA 68 pvkvrCreCgkefeleekal...........rCpkCgsadve 98
                                   ++++ C++C+++  +++k+             Cp+Cg+++ +
  gi|121636555|ref|YP_976778.1| 10 KITLACEVCKHRNYITKKNRrndpdrlelkkFCPNCGKHQAH 51
                                   67899*****9998665422357889999999******9865 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-05      0.05      23      36 ..      12      25 ..       3      27 .. 0.84
   2 ?   -0.3   0.3      0.78   1.2e+03      26      30 ..      42      46 ..      39      50 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                 zf-Sec23_Sec24 23 rwiCnfCnhknevp 36
                                   +  C+ C+h+n+++
  gi|121636555|ref|YP_976778.1| 12 TLACEVCKHRNYIT 25
                                   568*********96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.78
                 zf-Sec23_Sec24 26 CnfCn 30
                                   C+ C+
  gi|121636555|ref|YP_976778.1| 42 CPNCG 46
                                   66665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   7.6e-05      0.11       3      26 ..      15      46 ..      13      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                                   ETTTTCEE.C.....HEETSTTCE..EESSSS CS
                   TF_Zn_Ribbon  3 CPnCgstn.l.....veDpergel..vCtdCG 26
                                   C +C+++n +      +Dp+r el  +C++CG
  gi|121636555|ref|YP_976778.1| 15 CEVCKHRNyItkknrRNDPDRLELkkFCPNCG 46
                                   999***996699999999*************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.6     9e+02      16      21 ..      15      20 ..      12      22 .. 0.72
   2 ?   13.2   1.5   3.6e-05     0.054      14      21 ..      40      47 ..      39      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.6
                  zinc_ribbon_2 16 CpyCGt 21
                                   C+ C +
  gi|121636555|ref|YP_976778.1| 15 CEVCKH 20
                                   888854 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.6e-05
                  zinc_ribbon_2 14 kFCpyCGt 21
                                   kFCp+CG 
  gi|121636555|ref|YP_976778.1| 40 KFCPNCGK 47
                                   78888886 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.3   7.8e-05      0.12       9      36 ..      13      52 ..       7      54 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                   NOB1_Zn_bind  9 lrChaCfk...vt.......kd..mtkkFCpkCGnktLkr 36
                                   l C  C +   +t       +d    kkFCp+CG+++ +r
  gi|121636555|ref|YP_976778.1| 13 LACEVCKHrnyITkknrrndPDrlELKKFCPNCGKHQAHR 52
                                   678888776653344443331144789*******987655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.0    0.0001      0.15      14      38 ..      14      50 ..       4      55 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                            DZR 14 fCseCgtk..lkavaa...........edrCpsCgek.v 38
                                    C+ C+++  + +  +           +++Cp+Cg+  +
  gi|121636555|ref|YP_976778.1| 14 ACEVCKHRnyITK--KnrrndpdrlelKKFCPNCGKHqA 50
                                   6888888854322..245788888888999999998734 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.008        12       2      11 ..      14      23 ..      11      32 .. 0.80
   2 ?    7.7   0.5    0.0021       3.1       2      12 ..      41      51 ..      40      55 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.008
                        TFIIS_C  2 kCpkCgsrea 11
                                    C+ C++r+ 
  gi|121636555|ref|YP_976778.1| 14 ACEVCKHRNY 23
                                   5999999886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                        TFIIS_C  2 kCpkCgsreay 12
                                    Cp+Cg+++a+
  gi|121636555|ref|YP_976778.1| 41 FCPNCGKHQAH 51
                                   6******9986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.17   2.5e+02      24      30 ..      14      20 ..      10      24 .. 0.75
   2 ?   11.6   0.6   0.00013       0.2       1      11 [.      40      50 ..      40      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
                                   EETTTTE CS
                      Nudix_N_2 24 vCpaCgt 30
                                    C+ C +
  gi|121636555|ref|YP_976778.1| 14 ACEVCKH 20
                                   6888876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                                   -B-TTT--B-E CS
                      Nudix_N_2  1 kFCsqCGtpve 11
                                   kFC++CG+  +
  gi|121636555|ref|YP_976778.1| 40 KFCPNCGKHQA 50
                                   9******8755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 426.59
//
Query:       gi|121636556|ref|YP_976779.1|  [L=158]
Description: (3R)-hydroxyacyl-ACP dehydratase subunit HadA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-27   94.9   0.3    4.6e-27   94.7   0.3    1.0  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.3   2.6e-31   4.6e-27       3     131 ..       8     137 ..       6     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.6e-31
                MaoC_dehydrat_N   3 iGaef.epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkap.ell..ealgidlsrllhg 78 
                                    +G+++  p+ +evere++re+a av++ +  y++e+ a++ gy++l aP tf  v+++ka+  ++    +    +++++ 
  gi|121636556|ref|YP_976779.1|   8 VGMHYrYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQaAFFkhANIATAEAQIVQV 87 
                                    7999978899************************************************99866774444455699***** PP

                MaoC_dehydrat_N  79 eqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                    +q +++++pi+aGD+l+++  +++v++  g   +++iv+++ vtn++G+ v +
  gi|121636556|ref|YP_976779.1|  88 DQVLKFEKPIVAGDKLYCDVYVDSVREAHG---TQIIVTKNIVTNEEGDLVQE 137
                                    ***************************875...***************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1133.20
//
Query:       gi|121636557|ref|YP_976780.1|  [L=142]
Description: (3R)-hydroxyacyl-ACP dehydratase subunit HadB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-29  100.0   0.0    8.4e-29   99.6   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    4.1e-05   23.7   0.0    5.2e-05   23.4   0.0    1.2  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   9.4e-33   8.4e-29      11     120 ..      15     125 ..       7     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 9.4e-33
                                    EEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--B CS
                MaoC_dehydratas  11 etekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVl 90 
                                      ek++++t++d ++ya+vsgDlnpiH+d+e+Ak++g++ +IahGmlt++i  ++v++++gd  +  v+e++vrFt++V+
  gi|121636557|ref|YP_976780.1|  15 LPEKTYPLTRQDLVNYAGVSGDLNPIHWDDEIAKVVGLDAAIAHGMLTMGIGGGYVTSWVGD--PGAVTEYNVRFTAVVP 92 
                                    45799*********************************************************..99************** PP

                                    TTCEEEEEEEEEE..EEEEE.EEEEEEEEEEEE CS
                MaoC_dehydratas  91 pgdtlkvelevvg..krdvr.ktkkvevtkevt 120
                                    ++++ k    v++  +++v+ ++k+v+   ++t
  gi|121636557|ref|YP_976780.1|  93 VPNDGKGAELVFNgrVKSVDpESKSVTIALTAT 125
                                    999999888877757777887888888777666 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.8e-09   5.2e-05       3      58 ..      11      66 ..       9      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.8e-09
                MaoC_dehydrat_N  3 iGaefepvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivla 58
                                   +G ++ +++++++r+++  +a   g+ np+++d+e a+  g ++ ia  ++++ ++
  gi|121636557|ref|YP_976780.1| 11 VGDQLPEKTYPLTRQDLVNYAGVSGDLNPIHWDDEIAKVVGLDAAIAHGMLTMGIG 66
                                   7999999**********************************999999877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 962.77
//
Query:       gi|121636558|ref|YP_976781.1|  [L=166]
Description: (3R)-hydroxyacyl-ACP dehydratase subunit HadC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-25   89.2   0.0    3.1e-25   88.8   0.0    1.1  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   1.7e-29   3.1e-25       9     131 ..      15     137 ..      11     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 1.7e-29
                MaoC_dehydrat_N   9 pvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkap.elleal..gidlsrllhgeqefeyh 85 
                                    p+ + v+re+ refa+av+  +pa+++eeaa++ gy++l+aP tf+++la   + ++++ +  g++  ++++ +q+f +h
  gi|121636558|ref|YP_976781.1|  15 PDYFIVGREQCREFARAVKCDHPAFFSEEAAADLGYDALVAPLTFVTILAKYVQlDFFRHVdvGMETMQIVQVDQRFVFH 94 
                                    67899****************************************99998755558996663377899************ PP

                MaoC_dehydrat_N  86 epiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                    +p+ aGD+l  +  i +v ++ g   ++++v+++ +tn +Ge v++
  gi|121636558|ref|YP_976781.1|  95 KPVLAGDKLWARMDIHSVDERFG---ADIVVTRNLCTNDDGELVME 137
                                    *********************75...9*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1179.85
//
Query:       gi|121636559|ref|YP_976782.1|  [L=161]
Description: preprotein translocase subunit SecE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   66.6   1.2    2.5e-18   65.8   1.2    1.4  1  SecE      SecE/Sec61-gamma subunits of protein translocation 
  ------ inclusion threshold ------
      0.042   13.5   0.0      0.047   13.3   0.0    1.1  1  SUR7      SUR7/PalI family
      0.055   13.6   0.0      0.082   13.1   0.0    1.2  1  DUF1510   Domain of unknown function (DUF1510)


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   1.2   4.1e-22   2.5e-18       2      55 .]     107     160 ..     106     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 4.1e-22
                                    HCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecE   2 kFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsklinlll 55 
                                    +++k+v+aE++KV+WP+rk++l++t vVl+f ++m +++++ Dl+++kl+ l++
  gi|121636559|ref|YP_976782.1| 107 NYLKQVVAEMRKVIWPNRKQMLTYTSVVLAFLAFMVALVAGADLGLTKLVMLVF 160
                                    79***********************************************98876 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.8e-06     0.047     116     166 ..      97     147 ..      54     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-06
                           SUR7 116 filhiialvlsfislvvgllaicvspdnsrllsflnlllsvlsflatllaa 166
                                      + +ia+v   +  vv+ +  +++p+ + +l+    +l++l+f+++l+a 
  gi|121636559|ref|YP_976782.1|  97 RSVNPIAFVYNYLKQVVAEMRKVIWPNRKQMLTYTSVVLAFLAFMVALVAG 147
                                    56889*************************9999999*******9999874 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.082      24      60 ..      55      91 ..      38      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                        DUF1510 24 gsvDwnEmekavskatglsednmivwwlgnggspqka 60
                                     vD +E   a+s+atg+ +d++++  +++   ++ka
  gi|121636559|ref|YP_976782.1| 55 ADVDVEEPSTAASEATGVAKDDSTTKAVSKAARAKKA 91
                                   67999***********************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1115.81
//
Query:       gi|121636560|ref|YP_976783.1|  [L=238]
Description: transcription antitermination protein NusG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   86.7   0.0    1.9e-24   86.0   0.0    1.4  1  NusG      Transcription termination factor nusG
     0.0034   17.3   0.0      0.015   15.2   0.0    2.1  2  KOW       KOW motif


Domain annotation for each model (and alignments):
>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   2.1e-28   1.9e-24       2      94 ..      48     150 ..      47     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.1e-28
                                    EEEEEEE-TTTHHHHHHHH...HHHCT-.....EEE-SCEEEEEEETTEEE....CSSTTEEEEEE---CHHHHHHHCST CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxx.....xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NusG   2 kWYvlqvepgkekkvkenL...leeegl.....evivPaeekveirqgkkk....klfpgyifikadmndkllmairktp 69 
                                    +WYv++ + g+e+kvk nL   +++ ++     +v vP+ee++ei++g++k    k++pgyi++++d++d++++a+r+tp
  gi|121636560|ref|YP_976783.1|  48 DWYVVHSYAGYENKVKANLetrVQNLDVgdyifQVEVPTEEVTEIKNGQRKqvnrKVLPGYILVRMDLTDDSWAAVRNTP 127
                                    7******************955555555999***************999999**************************** PP

                                    TEEEE-EETTSSCC-EB-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NusG  70 gVtgfvrvggeskpvplseeevqni 94 
                                    gVtgfv  g +s+p +l  ++v ++
  gi|121636560|ref|YP_976783.1| 128 GVTGFV--GATSRPSALALDDVVKF 150
                                    ******..8899**99987777665 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.18   1.6e+03      19      26 ..     180     187 ..     179     188 .. 0.86
   2 !   15.2   0.0   1.7e-06     0.015       1      31 [.     187     221 ..     187     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                                    EEEEETTT CS
                            KOW  19 Vvkvdqhk 26 
                                    Vv+vd+++
  gi|121636560|ref|YP_976783.1| 180 VVEVDYEV 187
                                    9****986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-06
                                    TTSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                            KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                    +G+ V V++Gp++   +++ +v+ +     v V +
  gi|121636560|ref|YP_976783.1| 187 VGESVTVMDGPFATLPATISEVNAEQqklkVLVSI 221
                                    799********************999887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1715.58
//
Query:       gi|121636561|ref|YP_976784.1|  [L=142]
Description: 50S ribosomal protein L11 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-31  108.5   0.2    1.9e-31  107.7   0.2    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    4.7e-28   97.5   1.9    4.7e-28   97.5   1.9    1.7  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.2   2.2e-35   1.9e-31       1      65 []       4      68 ..       3      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 2.2e-35
                Ribosomal_L11_N  1 akkvvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                                   +kkv++ +kl++ aG+A+paPp+GpaLG++G+ni++fck++n+aT+++ g  ipV+itvy+drsf
  gi|121636561|ref|YP_976784.1|  4 KKKVAGLIKLQIVAGQANPAPPVGPALGQHGVNIMEFCKAYNAATENQRGNVIPVEITVYEDRSF 68
                                   578*************************************************************9 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.59   5.3e+03      23      34 ..       4      15 ..       2      21 .. 0.55
   2 !   97.5   1.9   5.2e-32   4.7e-28       1      70 []      73     141 ..      73     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.59
                                   TTSXXEEEEHHH CS
                  Ribosomal_L11 23 gketvGtvslkq 34
                                   +k+++G ++l+ 
  gi|121636561|ref|YP_976784.1|  4 KKKVAGLIKLQI 15
                                   555556655543 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 5.2e-32
                                    ---SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                  Ribosomal_L11   1 ktPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                    ktPp++ lL+kaag+ kgs++p+k++v++v+++qv+eIA++Kk+dlna+ +++aa+k+i+gtArsmGi+V
  gi|121636561|ref|YP_976784.1|  73 KTPPAAKLLLKAAGVAKGSAEPHKTKVAKVTWDQVREIAETKKTDLNAN-DVDAAAKIIAGTARSMGITV 141
                                    8************************************************.******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1011.86
//
Query:       gi|121636562|ref|YP_976785.1|  [L=235]
Description: 50S ribosomal protein L1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-50  170.8   0.0    3.7e-50  170.5   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   0.0   2.1e-54   3.7e-50       2     204 .]      31     220 ..      29     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 2.1e-54
                                    HHHS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHH CS
                   Ribosomal_L1   2 lkhakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkky 81 
                                    ++++++k+d++ve+a++l +++p+kadq+++g+++Lph++gk++++++++ +++a+    a +ag  a+v+g ++l++++
  gi|121636562|ref|YP_976785.1|  31 KETSSTKQDATVEVAIRL-GVDPRKADQMVRGTVNLPHGTGKTARVAVFAVGEKAD---AAVAAG--ADVVGSDDLIERI 104
                                    567899************.*************************************...9*****..************* PP

                                    T-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEE CS
                   Ribosomal_L1  82 ksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkv 161
                                          + ++ efd ++a ++ m ++++ + +v+g+r++mP+p+  +gtv++dv+k+v +++++++ +r+dk+++l++ +
  gi|121636562|ref|YP_976785.1| 105 ------QGGWLEFDAAIAAPDQMAKVGR-IARVLGPRGLMPNPK--TGTVTADVAKAVADIKGGKINFRVDKQANLHFVI 175
                                    ......9*********************.***************..9********************************* PP

                                    EETTSSHHHHHHHHHHHHHHHHHTSTTT..SGSEEEEEEEETTS- CS
                   Ribosomal_L1 162 GklsftaeelaeNieavvkalvekvpkk..wkniksiylkttmsp 204
                                    Gk+sf+++ laeN  a+++++ + +p++  ++++k+i+++tt++p
  gi|121636562|ref|YP_976785.1| 176 GKASFDEKLLAENYGAAIDEVLRLKPSSskGRYLKKITVSTTTGP 220
                                    ************************999889*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1751.97
//
Query:       gi|121636563|ref|YP_976786.1|  [L=301]
Description: methoxy mycolic acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-119  398.6   0.0   1.4e-119  398.4   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    7.5e-09   35.6   0.0    1.1e-08   35.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    3.9e-08   33.9   0.0    7.4e-08   33.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    7.3e-07   29.7   0.0    1.5e-06   28.7   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.8e-06   28.6   0.0    3.3e-06   27.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   14.6   0.1      0.043   13.4   0.1    1.6  2  MetW             Methionine biosynthesis protein MetW
      0.021   14.6   0.0      0.035   13.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.024   14.4   0.0       0.04   13.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      0.082   12.4   0.0       0.12   11.8   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.11   11.4   0.0       0.23   10.4   0.0    1.5  1  Methyltransf_9   Protein of unknown function (DUF1698)


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.4   0.0  7.8e-123  1.4e-119       2     271 ..      13     290 ..      12     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 398.4 bits;  conditional E-value: 7.8e-123
                                    XSXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHH CS
                           CMAS   2 kkkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrav 81 
                                    k+++++e+i+ahYD+s+dffalf+dpt+tYsCAyfe ++ tLeeAq+aK+dl+l+kl+lkpGmtlLdiGcGWG+++rrav
  gi|121636563|ref|YP_976786.1|  13 KTRTRFEDIQAHYDVSDDFFALFQDPTRTYSCAYFEPPELTLEEAQYAKVDLNLDKLDLKPGMTLLDIGCGWGTTMRRAV 92 
                                    67899*************************************************************************** PP

                                    HHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-E CS
                           CMAS  82 erydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGl 161
                                    er dv+v+glTlSk+q+++++++++++d++r+++v+l+++ed++e+vdr+vs++afeh+g+enyd+ffk++++++++dG+
  gi|121636563|ref|YP_976786.1|  93 ERLDVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWEDFAEPVDRIVSIEAFEHFGHENYDDFFKRCFNIMPADGR 172
                                    ******************************************************************************** PP

                                    EEEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHH CS
                           CMAS 162 lllhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaeal 233
                                    +++++ +s+h+ e+a+rg+kl        kfi +eiFPgG+lps+e+++e+ ++agftv +  slr+hY+kTL++W ++l
  gi|121636563|ref|YP_976786.1| 173 MTVQSSVSYHPYEMAARGKKLsfetarfiKFIVTEIFPGGRLPSTEMMVEHGEKAGFTVPEPLSLRPHYIKTLRIWGDTL 252
                                    ******************999*********************************************************** PP

                                    HHTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEE CS
                           CMAS 234 qenkdeaialvseevarmyelYLagcaeaFrkgyidva 271
                                    q+nkd+ai+++seev+++y++YL+gc+++F+++++d+ 
  gi|121636563|ref|YP_976786.1| 253 QSNKDKAIEVTSEEVYNRYMKYLRGCEHYFTDEMLDCS 290
                                    ***********************************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   6.2e-12   1.1e-08      17     131 ..      66     189 ..      53     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.2e-12
                Methyltransf_23  17 lpk..lraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                    l+k  l++g+ +LdiGcG G++++ + ++  ++v+g  ls +++++ e    +++++++ q+  q +++ ++  d Iv++
  gi|121636563|ref|YP_976786.1|  66 LDKldLKPGMTLLDIGCGWGTTMRRAvERLDVNVIGLTLSKNQHARCEqvlaSIDTNRSRQVLLQGWEDFAEPVDRIVSI 145
                                    4443379999**********888877344466**************99******************************** PP

                Methyltransf_23  90 evlehvp..dppellrqiatllkpgGylllseplaslkedrlll 131
                                    e +eh+   ++   +++ ++++  +G++ ++ + ++++ +++++
  gi|121636563|ref|YP_976786.1| 146 EAFEHFGheNYDDFFKRCFNIMPADGRMTVQSSVSYHPYEMAAR 189
                                    ******9778********************99988886555544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   4.2e-11   7.4e-08       2      97 .]      78     171 ..      77     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.2e-11
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+GcG G++++++ +rl + +v+g+ +s+++ +++++ +++ +   + +q  ++ ++  ++ +D +vs+ a++h+ +e+
  gi|121636563|ref|YP_976786.1|  78 LDIGCGWGTTMRRAVERL-DVNVIGLTLSKNQHARCEQVLASID-TNRSRQVLLQGWEDFAEPVDRIVSIEAFEHFGHEN 155
                                    9****************9.7*******************96532.334455555777777789******999******** PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +++++k++++++  +G
  gi|121636563|ref|YP_976786.1| 156 YDDFFKRCFNIMPADG 171
                                    ********99876655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   8.4e-10   1.5e-06       1      94 [.      78     173 ..      78     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.4e-10
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    Ld+GcG G  ++   +r   +v+g+ lsk++++++++     +   + +++ +  e+  f++  +D +vs e+++h+  e
  gi|121636563|ref|YP_976786.1|  78 LDIGCGWGTTMRRAVERLdVNVIGLTLSKNQHARCEQVLASIDTnrSRQVLLQGWED--FAE-PVDRIVSIEAFEHFghE 154
                                    8***********9998888*************9997776665554322334444444..666.9**************99 PP

                                    CHHHHHHHHHHHEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGll 94 
                                    + ++++k +  ++  +G++
  gi|121636563|ref|YP_976786.1| 155 NYDDFFKRCFNIMPADGRM 173
                                    ***********99999986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.8e-09   3.3e-06       1      98 [.      78     172 ..      78     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.8e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L+iGcG G+++r+  e+  d++++g+ +s+++ ++ ++ la+++ n+  +v l+  +++ +     +D +v++++++h+ 
  gi|121636563|ref|YP_976786.1|  78 LDIGCGWGTTMRRAVER-LDVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWEDFAE----PVDRIVSIEAFEHFg 152
                                    8****************.9**************************9999999999998765....9************** PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     ++ +++++++ + +  +Gr
  gi|121636563|ref|YP_976786.1| 153 hENYDDFFKRCFNIMPADGR 172
                                    99999999999999888886 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.4e-05     0.043      11      54 ..      71     114 ..      61     135 .. 0.88
   2 ?   -3.1   0.0       2.8     5e+03     117     138 ..     162     184 ..     141     187 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                           MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecva 54 
                                    +kpg ++ld+GcG G+ ++   e+ +v+  Gl l+++  a+c +
  gi|121636563|ref|YP_976786.1|  71 LKPGMTLLDIGCGWGTTMRRAVERLDVNVIGLTLSKNQHARCEQ 114
                                    68999*******************************99999965 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                           MetW 117 vrlsll.skGrmPvtdalPyeWy 138
                                      ++++ + Grm v  ++ y+ y
  gi|121636563|ref|YP_976786.1| 162 RCFNIMpADGRMTVQSSVSYHPY 184
                                    33344325677777777777666 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.035      65     146 ..      65     142 ..      55     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                    HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-.SE CS
                           PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeeka.PY 143
                                     l+ l+lk+g+  L++G+G G    +   + + + +v+++  +k+  ++ ++ l   d+++   v     +G+e++a P 
  gi|121636563|ref|YP_976786.1|  65 NLDKLDLKPGMTLLDIGCGWGT--TMRRAVERLDVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLL---QGWEDFAePV 139
                                    578899***********99884..4444444557789999988888888888887777775444443...4555555466 PP

                                    EEE CS
                           PCMT 144 dai 146
                                    d+i
  gi|121636563|ref|YP_976786.1| 140 DRI 142
                                    766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05      0.04       2     112 ..      72     178 ..      71     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G+   ++ e+l  + +v+G+  s++   ++++ +++   +   ++  + +e++      e++D i+s
  gi|121636563|ref|YP_976786.1|  72 KPGMTLLDIGCGWGTTMRRAVERL--DVNVIGLTLSKNQHARCEQVLASIDTNrSRQVLLQGWEDFA-----EPVDRIVS 144
                                    6799*****************876..899***99999998888887666655545566667777755.....57888888 PP

                Methyltransf_31  81 nevlnala..dpdkileeiervlkpggilliedp 112
                                     e++ ++   + d+++++ ++ +  +g++ +++ 
  gi|121636563|ref|YP_976786.1| 145 IEAFEHFGheNYDDFFKRCFNIMPADGRMTVQSS 178
                                    8888555411445666666666666666666665 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.12      58     166 ..      76     182 ..      62     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                Methyltransf_PK  58 valdcGaGiGrvtknlLlkllskvDlvepvekflekakeelae.ekkkvgkvyvvglqeftPeegrYdliWiqWcvghLt 136
                                    + ld+G+G G   ++ + +l  +v  +   ++  ++ ++ la+ ++++ ++v   g ++f+   +r   i       h+ 
  gi|121636563|ref|YP_976786.1|  76 TLLDIGCGWGTTMRRAVERLDVNVIGLTLSKNQHARCEQVLASiDTNRSRQVLLQGWEDFAEPVDRIVSI---EAFEHFG 152
                                    67899999999988888888666666666677778888899989****************9888775544...4678999 PP

                Methyltransf_PK 137 DedlvaflkrckkalkpnGlivvkenvake 166
                                     e++ +f+krc + +  +G + v+  v+ +
  gi|121636563|ref|YP_976786.1| 153 HENYDDFFKRCFNIMPADGRMTVQSSVSYH 182
                                    99*******************999887765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.23     114     177 ..      71     135 ..      55     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                    -T.T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS CS
                 Methyltransf_9 114 lk.grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieql 177
                                    lk g t+ld+Gcg G  + r v +    v+G+  s+      e v   +++++  ++l  g e++
  gi|121636563|ref|YP_976786.1|  71 LKpGMTLLDIGCGWGTTMRRAVERLDVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWEDF 135
                                    4336799*************************988877776666666665555555554666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2001.85
//
Query:       gi|121636564|ref|YP_976787.1|  [L=293]
Description: methoxy mycolic acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-124  415.1   0.1   1.3e-124  414.9   0.1    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    8.1e-07   29.0   0.0    1.4e-06   28.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    5.3e-06   27.0   0.0    1.3e-05   25.7   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    2.4e-05   25.0   0.0    8.2e-05   23.2   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
     0.0022   18.7   0.0      0.006   17.3   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.046   13.5   0.0       0.17   11.7   0.0    1.9  2  Methyltransf_31  Methyltransferase domain
      0.051   13.4   0.0         11    5.8   0.0    2.3  2  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   0.1  5.2e-128  1.3e-124       2     273 .]      10     289 ..       9     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 5.2e-128
                                    XSXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHH CS
                           CMAS   2 kkkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrav 81 
                                    k++++v++++ahYDls++ffalf+dpt+tYsCAyferddmtL+eAq aKldl+l+kl+l+pGmtlLd+GcGWGs+++rav
  gi|121636564|ref|YP_976787.1|  10 KSRSNVDDVQAHYDLSDAFFALFQDPTRTYSCAYFERDDMTLHEAQVAKLDLTLGKLGLEPGMTLLDVGCGWGSVMKRAV 89 
                                    578899************************************************************************** PP

                                    HHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-E CS
                           CMAS  82 erydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGl 161
                                    erydv+vv lTlSk+q++++++++d++d++r+++v+l+d+ +++e+vdr+v+++a+eh+g+e+yd+ffk++++++++dG+
  gi|121636564|ref|YP_976787.1|  90 ERYDVNVVDLTLSKNQHAYCQQVLDKVDTNRSHRVLLSDWANFSEPVDRIVTIEAIEHFGFERYDDFFKFAYNAMPADGV 169
                                    ******************************************************************************** PP

                                    EEEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHH CS
                           CMAS 162 lllhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaeal 233
                                    +llh+it lh k++ erg++l        +fi ++iFPgG+lp+ie+iee++++agft++d++sl++h+a+TL++Waeal
  gi|121636564|ref|YP_976787.1| 170 MLLHSITGLHVKQVIERGIPLtmemakfiRFIVTDIFPGGRLPTIETIEEHVTKAGFTITDIQSLQPHFARTLDLWAEAL 249
                                    *******************9999********************************************************* PP

                                    HHTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 234 qenkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    q++kdeai+++s ev+++y++YL+gca+aFr+gyid++q+
  gi|121636564|ref|YP_976787.1| 250 QAHKDEAIEIQSAEVYERYMKYLTGCAKAFRMGYIDCNQF 289
                                    **************************************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.3e-10   1.4e-06      13     163 ..      59     229 ..      47     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.3e-10
                Methyltransf_23  13 lerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfd 84 
                                    l+ +l+k  l++g+ +Ld+GcG G++++ +  ++++v +vDl   +++ a       k ++++++ +  +++a+ ++  d
  gi|121636564|ref|YP_976787.1|  59 LDLTLGKlgLEPGMTLLDVGCGWGSVMKRA-VERYDVNVVDLTLSKNQHAYcqqvldKVDTNRSHRVLLSDWANFSEPVD 137
                                    4444545458999***********888844.346899999998776666668899999999999999999********** PP

                Methyltransf_23  85 lIvlrevlehvp..dppellrqiatllkpgGylllseplasl..........kedrllldwlylvpag.rhisffsarsl 151
                                     Iv +e +eh+    +   ++ +++ +  +G++ll+ ++  +             ++++ ++++v++    +++ + +++
  gi|121636564|ref|YP_976787.1| 138 RIVTIEAIEHFGfeRYDDFFKFAYNAMPADGVMLLHSITGLHvkqviergipLTMEMAKFIRFIVTDIfPGGRLPTIETI 217
                                    ***********95559*******************998765566566655533344444456666654556688888899 PP

                Methyltransf_23 152 kelleeaGlevv 163
                                    +e + +aG+++ 
  gi|121636564|ref|YP_976787.1| 218 EEHVTKAGFTIT 229
                                    999999998875 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.3e-09   1.3e-05       1      94 [.      75     170 ..      75     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.3e-09
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    LdvGcG G++++   +r+  +vv + lsk++++++++   + +   + +++ +d  +  f +  +D +v  e+++h+  e
  gi|121636564|ref|YP_976787.1|  75 LDVGCGWGSVMKRAVERYdVNVVDLTLSKNQHAYCQQVLDKVDTnrSHRVLLSDWAN--FSE-PVDRIVTIEAIEHFgfE 151
                                    8**************9999****************9999998876655667777776..766.9**************99 PP

                                    CHHHHHHHHHHHEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGll 94 
                                    + ++++k ++  +  +G++
  gi|121636564|ref|YP_976787.1| 152 RYDDFFKFAYNAMPADGVM 170
                                    9999999999988888876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.2e-08   8.2e-05       2      93 ..      75     164 ..      74     168 .. 0.80
   2 ?   -1.8   0.0       2.1   5.3e+03      50      58 ..     226     234 ..     192     266 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.2e-08
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    Ld+GcG G +++++ +r+ + +v+ + +s+++ +++++ +++ +   + +++  d  ++   ++ +D +v + a++h+  
  gi|121636564|ref|YP_976787.1|  75 LDVGCGWGSVMKRAVERY-DVNVVDLTLSKNQHAYCQQVLDKVDTnrSHRVLLSDWANF---SEPVDRIVTIEAIEHFGF 150
                                    9****************8.699999999*********9996633223555555555555...5789*****999****99 PP

                                    HHHHHHHHHHHHHE CS
                Methyltransf_25  80 edlekalkeiarvL 93 
                                    e++++++k +++++
  gi|121636564|ref|YP_976787.1| 151 ERYDDFFKFAYNAM 164
                                    99999999888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                                    EEESBCCGB CS
                Methyltransf_25  50 fvqgdaedl 58 
                                    f   d+++l
  gi|121636564|ref|YP_976787.1| 226 FTITDIQSL 234
                                    333333333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06     0.006       1      98 [.      75     169 ..      75     170 .. 0.85
   2 ?   -3.6   0.0         7   1.8e+04      13      30 ..     216     233 ..     212     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG Gs++++  e+  d++++ + +s+++ +  ++ l k + n+ ++v l +   +++     +D +v +++++h+ 
  gi|121636564|ref|YP_976787.1|  75 LDVGCGWGSVMKRAVER-YDVNVVDLTLSKNQHAYCQQVLDKVDTNRSHRVLLSDWANFSE----PVDRIVTIEAIEHFg 149
                                    8**************99.8999999999999998888888888888888888887776544....9*************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     +  +++++ +++++  +G+
  gi|121636564|ref|YP_976787.1| 150 fERYDDFFKFAYNAMPADGV 169
                                    98888888888888877775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7
                Methyltransf_12  13 alleklpdieytgvDisp 30 
                                     ++e+   + +t +Di++
  gi|121636564|ref|YP_976787.1| 216 TIEEHVTKAGFTITDIQS 233
                                    555666677777788765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.5e-05      0.17       2     101 ..      69     164 ..      68     205 .. 0.74
   2 ?   -1.1   0.0      0.55   1.4e+03      54      80 ..     222     247 ..     213     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G   +++ e+   + +vv +  s++   ++++ ++k   +   ++  +d+ +++     e++D i++
  gi|121636564|ref|YP_976787.1|  69 EPGMTLLDVGCGWGSVMKRAVER--YDVNVVDLTLSKNQHAYCQQVLDKVDTNrSHRVLLSDWANFS-----EPVDRIVT 141
                                    5789****************953..477888888888888888888888777766778888888877.....67888888 PP

                Methyltransf_31  81 nevl..naladpdkileeiervl 101
                                     e++    +   d++++ + +++
  gi|121636564|ref|YP_976787.1| 142 IEAIehFGFERYDDFFKFAYNAM 164
                                    88884434444455555555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.55
                Methyltransf_31  54 dnveFeqgdieeleklledekfDlils 80 
                                    + + F + di++l+ +++ ++ Dl+  
  gi|121636564|ref|YP_976787.1| 222 TKAGFTITDIQSLQPHFA-RTLDLWAE 247
                                    456688899999886777.78888544 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0046        12      74     112 ..      72     110 ..      24     141 .. 0.88
   2 ?    5.8   0.0    0.0042        11     162     217 ..     210     266 ..     200     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0046
                                    S-EEEES-TT-HHHHH--S-..EEEEESS-SSTTEEES- CS
                 Methyltransf_8  74 lvvadlGcGeakiaeavrekekvrsfdlvavnervvacd 112
                                    +++ d+GcG   + ++  e  +v+ +dl+  +++   c 
  gi|121636564|ref|YP_976787.1|  72 MTLLDVGCGWGSVMKRAVERYDVNVVDLTLSKNQHAYCQ 110
                                    5689**********999999********98877777775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0042
                                    G-S-HHHHHHHHHCTTEEEEEEE--STTEE.EEEEEE-SSS-TT---GG-------- CS
                 Methyltransf_8 162 rfesvklfaraltklGfevkskdlsnkqfv.lfefkkvekkgkkrelglklkpclyk 217
                                    r++ ++++++++tk Gf ++ ++  + +f   +++     +++k+e   + ++ +y 
  gi|121636564|ref|YP_976787.1| 210 RLPTIETIEEHVTKAGFTITDIQSLQPHFArTLDLWAEALQAHKDEAIEIQSAEVYE 266
                                    8999*******************9999996356776666666666665555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2011.83
//
Query:       gi|121636565|ref|YP_976788.1|  [L=287]
Description: methoxy mycolic acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-123  411.8   0.0   1.3e-123  411.6   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
      5e-11   42.7   0.0    6.2e-11   42.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    8.3e-10   39.2   0.0    1.8e-09   38.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    1.5e-09   38.3   0.0    3.4e-09   37.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.2e-07   31.0   0.0    6.2e-07   30.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0064   16.3   0.5      0.015   15.1   0.1    1.8  2  FliN_N           Flagellar motor switch protein FliN N-termin
  ------ inclusion threshold ------
      0.016   14.2   0.1      0.045   12.7   0.0    1.7  2  Methyltransf_9   Protein of unknown function (DUF1698)
      0.027   14.3   0.0      0.094   12.5   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
      0.051   13.1   0.0        0.1   12.1   0.0    1.5  1  MTS              Methyltransferase small domain
      0.068   12.5   0.0       0.11   11.8   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.094   12.4   0.1       0.26   11.0   0.0    1.6  2  Pilus_CpaD       Pilus biogenesis CpaD protein (pilus_cpaD)
       0.12   12.1   0.0       0.17   11.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.6   0.0  8.8e-127  1.3e-123       3     273 .]       5     283 ..       3     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 411.6 bits;  conditional E-value: 8.8e-127
                                    SXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                           CMAS   3 kkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrave 82 
                                     ++++e+++ahYDls+dff+lfldpt+tYsCA+fer+dmtLeeAq+aK+dl+l+kl+l+pGmtlLdiGcGWG+++rra++
  gi|121636565|ref|YP_976788.1|   5 LTPHFEDVQAHYDLSDDFFRLFLDPTQTYSCAHFEREDMTLEEAQIAKIDLALGKLGLQPGMTLLDIGCGWGATMRRAIA 84 
                                    6789**************************************************************************** PP

                                    HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EE CS
                           CMAS  83 rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGll 162
                                    +ydv+vvglTlSk+qa++++k++de+d+  +++v+l+++e+++e+vdr+vs+gafeh+g++++++ff++++k+l++dG+l
  gi|121636565|ref|YP_976788.1|  85 QYDVNVVGLTLSKNQAAHVQKSFDEMDTPLDRRVLLAGWEQFNEPVDRIVSIGAFEHFGHDRHADFFARAHKILPPDGVL 164
                                    ******************************************************************************** PP

                                    EEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHH CS
                           CMAS 163 llhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealq 234
                                    llhtit l++++++++gl+l        kfi++eiFPgG+ p+ie++ee+++++gft+++ +sl++hYa+TL++Waealq
  gi|121636565|ref|YP_976788.1| 165 LLHTITGLTRQQMVDHGLPLtlwlarflKFIATEIFPGGQPPTIEMVEEQSAKTGFTLTRRQSLQPHYARTLDLWAEALQ 244
                                    ******************999*********************************************************** PP

                                    HTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 235 enkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    e+k+eaia++seev+++y++YL+gca+ Fr gyidv+q+
  gi|121636565|ref|YP_976788.1| 245 EHKSEAIAIQSEEVYERYMKYLTGCAKLFRVGYIDVNQF 283
                                    *************************************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   4.1e-14   6.2e-11      11     121 ..      51     170 ..      37     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.1e-14
                Methyltransf_23  11 dklerllpk..lraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq...........ea 76 
                                    +k++ +l+k  l++g+ +LdiGcG G ++ + ++++ ++v+g  ls ++ +        ++++fde+            +
  gi|121636565|ref|YP_976788.1|  51 AKIDLALGKlgLQPGMTLLDIGCGWGaTMRRAIAQYDVNVVGLTLSKNQAAH-------VQKSFDEMdtpldrrvllaGW 123
                                    67777777767899************556667799999********987776.......577777777777777888888 PP

                Methyltransf_23  77 aepqgkfdlIvlrevlehvpd..ppellrqiatllkpgGylllsepl 121
                                    ++ ++  d Iv++  +eh+ +  ++  +++++++l p+G+lll++++
  gi|121636565|ref|YP_976788.1| 124 EQFNEPVDRIVSIGAFEHFGHdrHADFFARAHKILPPDGVLLLHTIT 170
                                    88999**************9558*********************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   1.2e-12   1.8e-09       2      97 .]      69     162 ..      68     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.2e-12
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    Ld+GcG G +++++ +++ + +v+g+ +s+++ +++++ ++e +   + +++ +  e++   ++ +D +vs+ga++h+ +
  gi|121636565|ref|YP_976788.1|  69 LDIGCGWGATMRRAIAQY-DVNVVGLTLSKNQAAHVQKSFDEMDTplDRRVLLAGWEQF---NEPVDRIVSIGAFEHFGH 144
                                    9************99998.7********************8854424556666666665...4689******99****** PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                    +++++++++++++L p+G
  gi|121636565|ref|YP_976788.1| 145 DRHADFFARAHKILPPDG 162
                                    ****************99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.3e-12   3.4e-09       1      95 [.      69     165 ..      69     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.3e-12
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    Ld+GcG G+ ++    ++  +vvg+ lsk++ + +++   e +     +++ a  e+  f++  +D +vs  +++h+  +
  gi|121636565|ref|YP_976788.1|  69 LDIGCGWGATMRRAIAQYdVNVVGLTLSKNQAAHVQKSFDEMDTplDRRVLLAGWEQ--FNE-PVDRIVSIGAFEHFghD 145
                                    8********9999998888*************9999888888876744567777776..776.9**************99 PP

                                    CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                    +++++++ ++++L p+G+l+
  gi|121636565|ref|YP_976788.1| 146 RHADFFARAHKILPPDGVLL 165
                                    99***************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.1e-10   6.2e-07       1      99 []      69     164 ..      69     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.1e-10
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L+iGcG G+++r+  ++  d++++g+ +s+++ ++ ++ + + +      ++ ++l ++ ++ ++ +D +v++++++h+ 
  gi|121636565|ref|YP_976788.1|  69 LDIGCGWGATMRRAIAQ-YDVNVVGLTLSKNQAAHVQKSFDEMDT----PLDRRVLLAGWEQFNEPVDRIVSIGAFEHFg 143
                                    8**********999999.9**************888888888886....5555555555555567*************** PP

                Methyltransf_12  80 kdir.evldnirklLkpgGrl 99 
                                     d++ +++++++k L p+G+l
  gi|121636565|ref|YP_976788.1| 144 HDRHaDFFARAHKILPPDGVL 164
                                    55555**************97 PP

>> FliN_N  Flagellar motor switch protein FliN N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       4.7     7e+03      34      47 ..      98     111 ..      96     112 .. 0.63
   2 !   15.1   0.1   9.9e-06     0.015      17      41 ..     237     260 ..     233     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.7
                         FliN_N  34 astegvFksLegqd 47 
                                    ++++ v ks++  d
  gi|121636565|ref|YP_976788.1|  98 NQAAHVQKSFDEMD 111
                                    46677777777655 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.9e-06
                         FliN_N  17 DLWAeAlneQaateksaastegvFk 41 
                                    DLWAeAl+e ++++ +  ++e+v++
  gi|121636565|ref|YP_976788.1| 237 DLWAEALQEHKSEAIAI-QSEEVYE 260
                                    9***********99876.9999987 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05     0.045     116     219 ..      65     168 ..      50     179 .. 0.73
   2 ?   -1.7   0.0       0.7   1.1e+03       9      42 ..     235     269 ..     229     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                    T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHH.HHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliq.feavrkllgedqrahllplgieqlpeleafdtvfsmGvlyh 194
                                    g t+ld+Gcg G  + r +++    vvG+  s+       ++  ++ +   r +ll  g eq++  e  d + s+G + h
  gi|121636565|ref|YP_976788.1|  65 GMTLLDIGCGWGATMRRAIAQYDVNVVGLTLSKNQAAHvQKSFDEMDTPLDRRVLL-AGWEQFN--EPVDRIVSIGAFEH 141
                                    6789************************9987655444045666666665666666.7888886..46788888888776 PP

                                    ..-S-HHHHHHHHHCTEEEEEEEEEEE CS
                 Methyltransf_9 195 ..rrsPldhllqlkdqlvkgGelvlet 219
                                           d + + ++ l  +G l+l t
  gi|121636565|ref|YP_976788.1| 142 fgHDRHADFFARAHKILPPDGVLLLHT 168
                                    333345667777777777777777766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.7
                                    TTHHHHHCHHHHHHHHH.HCTCCHHHCCHHHHHCS CS
                 Methyltransf_9   9 klsewletlpaqlkewq.ekehgdlkrwakalekl 42 
                                    +l  w e+l+++ +e    ++++ ++r++k l+  
  gi|121636565|ref|YP_976788.1| 235 TLDLWAEALQEHKSEAIaIQSEEVYERYMKYLTGC 269
                                    56779999998888776466777788888877654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.7   5.5e+03      55      77 ..      35      55 ..      31      58 .. 0.66
   2 ?   12.5   0.0   6.3e-05     0.094       2     113 ..      63     170 ..      62     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.7
                Methyltransf_31 55 nveFeqgdieeleklledekfDl 77
                                    ++Fe++d++  e   + +k+Dl
  gi|121636565|ref|YP_976788.1| 35 CAHFEREDMTLEE--AQIAKIDL 55
                                   5678888888866..34456776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.3e-05
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G+   ++      + +vvG+  s++   + ++  ++       ++  + +e+++     e++D i+s
  gi|121636565|ref|YP_976788.1|  63 QPGMTLLDIGCGWGATMRRAIA--QYDVNVVGLTLSKNQAAHVQKSFDEMDTPlDRRVLLAGWEQFN-----EPVDRIVS 135
                                    5789*************99993..3478899999998888777777666655556777778888877.....67899999 PP

                Methyltransf_31  81 nevlnalad..pdkileeiervlkpggilliedpr 113
                                     +++ ++ +   ++++ ++++ l p+g+ll+ ++ 
  gi|121636565|ref|YP_976788.1| 136 IGAFEHFGHdrHADFFARAHKILPPDGVLLLHTIT 170
                                    88887776622467788888888888888888877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.9e-05       0.1      32     137 ..      65     166 ..      54     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---STTT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPfhag 110
                                      ++lD+GcG+G+    + ++++  +v+ +  +++  +  ++ + + +    + v   + e+++ + +d ivs   f + 
  gi|121636565|ref|YP_976788.1|  65 GMTLLDIGCGWGATMRRAIAQYDV-NVVGLTLSKNQAAHVQKSFDEMDTPlDRRVLLAGWEQFN-EPVDRIVSIGAFEHF 142
                                    5678*******9755444444433.333333333333334444444444434444455566666.99*****98888665 PP

                                    CHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                            MTS 111 katelavaeeliaeAkeaLkegGeLli 137
                                     +   +   +++a A+++L ++G Ll+
  gi|121636565|ref|YP_976788.1| 143 GH---DRHADFFARAHKILPPDGVLLL 166
                                    55...67889*************9987 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.3e-05      0.11      43     176 ..      45     177 ..      30     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                                    HHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH....HHHHHHHHS-----TTEEEEES CS
                 Methyltransf_2  43 lqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe....VveaAkehlsageeervefvgG 118
                                    l+e +    + +l +  l++  +l+D+G G Ga+++ + ++y  ++v+ + l++     v++  + +++++++rv   g 
  gi|121636565|ref|YP_976788.1|  45 LEEAQIAKIDLALGKLGLQPGMTLLDIGCGWGATMRRAIAQYD-VNVVGLTLSKnqaaHVQKSFDEMDTPLDRRVLLAGW 123
                                    5556666677788888999999*******************95.445545444311113455555568889999999999 PP

                                    -TTTS-----SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS--- CS
                 Methyltransf_2 119 dffkdslPeaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsge 176
                                    + f++++   D i+       + +++ + + +r +k lp++G v++  ++ g  ++++
  gi|121636565|ref|YP_976788.1| 124 EQFNEPV---DRIVSIGAFEHFGHDRHADFFARAHKILPPDG-VLLLHTITGLTRQQM 177
                                    9997776...55555555555777778889999999999998.455556665555555 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   2.6e+03      38      68 ..      82     110 ..      77     120 .. 0.71
   2 ?   11.0   0.0   0.00018      0.26      34      82 ..     210     257 ..     205     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                     Pilus_CpaD  38 aeasldlkvasgdggLtaaqrarlealaeey 68 
                                    a a++d++v     +L+++q+a +++ ++e+
  gi|121636565|ref|YP_976788.1|  82 AIAQYDVNV--VGLTLSKNQAAHVQKSFDEM 110
                                    556666777..66778888888888887776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
                     Pilus_CpaD  34 vveeaeasldlkvasgdggLtaaqrarlealaeeyrregagaivisvps 82 
                                    +vee++a++ +++ +++++L++  +++l+ +ae+++++ ++ai+i+  +
  gi|121636565|ref|YP_976788.1| 210 MVEEQSAKTGFTL-TRRQSLQPHYARTLDLWAEALQEHKSEAIAIQSEE 257
                                    6999*********.*******************************9865 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.17      64     113 ..      55     102 ..      40     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHH CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelvee 113
                                    lal  l l++g+  L++G+G G  + +   + + + +vv++  +k+ +++
  gi|121636565|ref|YP_976788.1|  55 LALGKLGLQPGMTLLDIGCGWG--ATMRRAIAQYDVNVVGLTLSKNQAAH 102
                                    5666789***********9988..34445555666777777666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2283.04
//
Query:       gi|121636566|ref|YP_976789.1|  [L=286]
Description: methoxy mycolic acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-116  387.2   0.0     4e-116  387.1   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    8.3e-08   32.8   0.0    4.7e-07   30.4   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    1.1e-06   28.6   0.0    1.9e-06   27.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    3.9e-06   27.5   0.0      1e-05   26.2   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
    7.3e-06   26.5   0.0    2.6e-05   24.8   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
     0.0001   22.1   0.0    0.00023   21.0   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
     0.0022   17.8   0.0     0.0035   17.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0038   17.4   0.0     0.0068   16.5   0.0    1.4  1  Ku_PK_bind       Ku C terminal domain like
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.04   14.2   0.1    1.6  1  Arg_decarb_HB    Arginine decarboxylase helical bundle domain
      0.032   14.2   0.0       0.11   12.5   0.0    1.7  2  Methyltransf_32  Methyltransferase domain
      0.046   13.3   0.0       0.15   11.6   0.0    1.8  2  MetW             Methionine biosynthesis protein MetW
       0.06   12.9   0.0       0.12   11.9   0.0    1.5  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.1   0.0  2.7e-119    4e-116       3     273 .]       4     282 ..       2     282 .. 0.99

  Alignments for each domain:
  == domain 1  score: 387.1 bits;  conditional E-value: 2.7e-119
                                    SXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                           CMAS   3 kkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrave 82 
                                     ++ +e+ +++YD+s+dffalfldpt++Y+CAyferddmtLeeAqlaK+dl+l+kl+l+pGmtlLd+GcGWG+ ++rave
  gi|121636566|ref|YP_976789.1|   4 LRPYYEESQSAYDISDDFFALFLDPTWVYTCAYFERDDMTLEEAQLAKVDLALDKLNLEPGMTLLDVGCGWGGALVRAVE 83 
                                    678899************************************************************************** PP

                                    HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EE CS
                           CMAS  83 rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGll 162
                                    +ydv+v+glTlS+++++++k+r+++++++r++e +l+++e+++e+vdr+vs++af++++ke+y tff++ +++l++dG++
  gi|121636566|ref|YP_976789.1|  84 KYDVNVIGLTLSRNHYERSKDRLAAIGTQRRAEARLQGWEEFEENVDRIVSFEAFDAFKKERYLTFFERSYDILPDDGRM 163
                                    ******************************************************************************** PP

                                    EEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHH CS
                           CMAS 163 llhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealq 234
                                    llh+++++++++l+e+g++l        kf++++iFPgGelps  +i++++++agft+++v+ l++hYa+TL+aWa++lq
  gi|121636566|ref|YP_976789.1| 164 LLHSLFTYDRRWLHEQGIALtmsdlrflKFLRESIFPGGELPSEPDIVDNAQAAGFTIEHVQLLQQHYARTLDAWAANLQ 243
                                    ******************999*********************************************************** PP

                                    HTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 235 enkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    +++++aia++seev++++++YL+gcae+Fr+g i+vaq+
  gi|121636566|ref|YP_976789.1| 244 AARERAIAVQSEEVYNNFMHYLTGCAERFRRGLINVAQF 282
                                    *************************************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.2e-10   4.7e-07       2      97 .]      68     161 ..      67     161 .. 0.90
   2 ?   -0.3   0.0       1.2   1.7e+03      14      41 ..     223     249 ..     210     271 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.2e-10
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+GcG G  + ++ +++ + +v+g+ +s +  e+ + r+++ g   +  ++ ++ +++ ++ +D +vs+ a+  +++e+
  gi|121636566|ref|YP_976789.1|  68 LDVGCGWGGALVRAVEKY-DVNVIGLTLSRNHYERSKDRLAAIG-TQRRAEARLQGWEEFEENVDRIVSFEAFDAFKKER 145
                                    9**************998.7********************7655.666677778888888899******988******** PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    + +++++ +++L ++G
  gi|121636566|ref|YP_976789.1| 146 YLTFFERSYDILPDDG 161
                                    ********99998877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                    HHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                Methyltransf_25  14 alakrlgkakvtgvDiseemleaarera 41 
                                    +++   +++    +D  ++ l+aarera
  gi|121636566|ref|YP_976789.1| 223 HVQLL-QQHYARTLDAWAANLQAARERA 249
                                    44332.4566677888999999999887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.3e-09   1.9e-06      12     139 ..      51     185 ..      39     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                Methyltransf_23  12 klerllpk..lraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfd 84 
                                    k++ +l+k  l++g+ +Ld+GcG G  l +  +++ ++v+g  ls++  e+ +     + +++   ++ q ++e ++  d
  gi|121636566|ref|YP_976789.1|  51 KVDLALDKlnLEPGMTLLDVGCGWGgALVRAVEKYDVNVIGLTLSRNHYERSKdrlaAIGTQRRAEARLQGWEEFEENVD 130
                                    555555555479999********998999999*************9988887788888888888888889********** PP

                Methyltransf_23  85 lIvlrevlehvpd..ppellrqiatllkpgGylllseplaslkedrllldwlylvpa 139
                                     Iv++e +  ++   +   + + +++l ++G++ll+      + +r+l++ + + ++
  gi|121636566|ref|YP_976789.1| 131 RIVSFEAFDAFKKerYLTFFERSYDILPDDGRMLLHSLFT--YDRRWLHEQGIALTM 185
                                    ************6458888888899*********999754..455555553333222 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.9e-09     1e-05       1      98 [.      68     162 ..      68     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.9e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG G  l +  ek  d++++g+ +s++  e+ k +la+++ ++ ++ +l+  + +++     +D +v+++++ ++ 
  gi|121636566|ref|YP_976789.1|  68 LDVGCGWGGALVRAVEK-YDVNVIGLTLSRNHYERSKDRLAAIGTQRRAEARLQGWEEFEE----NVDRIVSFEAFDAFk 142
                                    8******9998888888.8**************************9999999999997765....9*************7 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     +    ++++ ++ L ++Gr
  gi|121636566|ref|YP_976789.1| 143 kERYLTFFERSYDILPDDGR 162
                                    55555999999999999887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.8e-08   2.6e-05       1      95 [.      68     164 ..      68     165 .. 0.78
   2 ?   -1.4   0.0       2.6   3.9e+03      20      39 ..     231     250 ..     216     271 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-08
                                    EEET-T.TSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEEEEEES-CCC-.. CS
                Methyltransf_11   1 LdvGcG.tGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDlvvssevlhhv.. 74 
                                    LdvGcG +G+l++a++k+  +v+g+ ls +  +++k++    g   +    +a+++    fe+  +D +vs+e+++ +  
  gi|121636566|ref|YP_976789.1|  68 LDVGCGwGGALVRAVEKYDVNVIGLTLSRNHYERSKDRLAAIGTqrR---AEARLQGWeEFEE-NVDRIVSFEAFDAFkk 143
                                    8*****5566666666666****************999999986333...5555555534655.9*************87 PP

                                    CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                    e+   +++  + +L  +G+++
  gi|121636566|ref|YP_976789.1| 144 ERYLTFFERSYDILPDDGRML 164
                                    778888999999998888875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.6
                                    EEEEEES-HHHHHHHHHHCC CS
                Methyltransf_11  20 rvvgvDlskemlklakekas 39 
                                       ++D +++ l++a+e+a 
  gi|121636566|ref|YP_976789.1| 231 YARTLDAWAANLQAARERAI 250
                                    45567888888888877764 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.1   1.1e+04      58      80 ..      37      57 ..      35      59 .. 0.69
   2 !   21.0   0.0   1.5e-07   0.00023       2      89 ..      62     143 ..      61     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.1
                Methyltransf_31 58 FeqgdieeleklledekfDlils 80
                                   Fe+ d++  e   + +k+Dl l+
  gi|121636566|ref|YP_976789.1| 37 FERDDMTLEE--AQLAKVDLALD 57
                                   7777777766..55678888776 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.5e-07
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                    + g+++lD+GCG G  + ++ e+   + +v+G+  s +  e+++ +++  g + ++e + + +ee+e     e++D i+s
  gi|121636566|ref|YP_976789.1|  62 EPGMTLLDVGCGWGGALVRAVEK--YDVNVIGLTLSRNHYERSKDRLAAIGTQrRAEARLQGWEEFE-----ENVDRIVS 134
                                    5789*****************54..3799************************9***********99.....66****** PP

                Methyltransf_31  81 nevlnalad 89 
                                    +e+++a++ 
  gi|121636566|ref|YP_976789.1| 135 FEAFDAFKK 143
                                    **9987764 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0035      62     125 ..      52     113 ..      41     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                                    HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCS CS
                           PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlen 125
                                    v lal+ l+l++g+  L+vG+G G   a++  + + + +v+++  +++ +e++k +l + ++++
  gi|121636566|ref|YP_976789.1|  52 VDLALDKLNLEPGMTLLDVGCGWG--GALVRAVEKYDVNVIGLTLSRNHYERSKDRLAAIGTQR 113
                                    5678999************99877..788888999999******************99888765 PP

>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.6e-06    0.0068      32      75 ..     225     267 ..     210     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                     Ku_PK_bind  32 qlvedslgdssydkaveclkalReeaieeeepelyNdFlrdlkk 75 
                                    ql++++++    d  +++l+a Re+ai  +  e+yN+F++ l  
  gi|121636566|ref|YP_976789.1| 225 QLLQQHYAR-TLDAWAANLQAARERAIAVQSEEVYNNFMHYLTG 267
                                    677777766.8888999**********************98765 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.7e-05      0.04      16      50 ..     247     281 ..     225     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                  Arg_decarb_HB  16 eelsqrnlqEiyhDavhyldearelFrlGllsLee 50 
                                    e +   +  E+y++ +hyl  + e Fr+Gl++ ++
  gi|121636566|ref|YP_976789.1| 247 ERAIAVQSEEVYNNFMHYLTGCAERFRRGLINVAQ 281
                                    333377889**********************9876 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-05      0.11      23      81 ..      61     116 ..      46     147 .. 0.74
   2 ?   -1.0   0.0         1   1.5e+03      49      76 ..     227     254 ..     205     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-05
                Methyltransf_32  23 esgaltvvDvGaGkg.YLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkr 81 
                                     ++ +t++DvG+G g  L ++++     y ++v+g+ +++++ e++++r +++g +  ++
  gi|121636566|ref|YP_976789.1|  61 LEPGMTLLDVGCGWGgALVRAVEK----YDVNVIGLTLSRNHYERSKDRLAAIGTQRRAE 116
                                    466789*******86145555555....9********************99999554332 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                Methyltransf_32  49 eyklkvvgidakeelvekaekraeklgk 76 
                                     ++++   +da +++ ++a++ra ++++
  gi|121636566|ref|YP_976789.1| 227 LQQHYARTLDAWAANLQAARERAIAVQS 254
                                    4577777888888888888888777664 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.15      10      56 ..      60     106 ..      51     147 .. 0.74
   2 ?   -1.2   0.0      0.85   1.3e+03      32      69 ..     225     262 ..     206     267 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                           MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakG 56 
                                     ++pg ++ld+GcG G  l    e+ +v+  Gl l+++   ++  + 
  gi|121636566|ref|YP_976789.1|  60 NLEPGMTLLDVGCGWGGALVRAVEKYDVNVIGLTLSRNHYERSKDRL 106
                                    478999********87766666689*********9998877766664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.85
                           MetW  32 keekqvdgrGleldeegvaecvakGlsviqgdldkdle 69 
                                    +  +q  +r l+  +++++++ ++ ++v  +++ +++ 
  gi|121636566|ref|YP_976789.1| 225 QLLQQHYARTLDAWAANLQAARERAIAVQSEEVYNNFM 262
                                    33344455666666666666666666666666655555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.2e-05      0.12      24     136 ..      56     164 ..      50     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                                    HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEE CS
                            MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdliv 102
                                    l++l+ e   ++lD+GcG+G   +  a e+ +++v  +  + +  e +k  l+a + +       ++ ee+e +++d iv
  gi|121636566|ref|YP_976789.1|  56 LDKLNLEPGMTLLDVGCGWGGALV-RAVEKYDVNVIGLTLSRNHYERSKDRLAAIGTQrRAEARLQGWEEFE-ENVDRIV 133
                                    67788888889********97433.34444455677777777788888888888887743333446677777.9999999 PP

                                    E---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 103 sNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                    s   f a  a +++   ++++ + ++L ++G++l
  gi|121636566|ref|YP_976789.1| 134 S---FEAFDAFKKERYLTFFERSYDILPDDGRML 164
                                    9...555555555788889999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2130.68
//
Query:       gi|121636567|ref|YP_976790.1|  [L=301]
Description: lipase/esterase lipG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-24   84.8   0.0    5.7e-17   62.2   0.0    2.0  2  Abhydrolase_1    alpha/beta hydrolase fold
    1.7e-13   50.4   0.0    6.8e-13   48.4   0.0    1.9  1  Hydrolase_4      Serine aminopeptidase, S33
    4.9e-12   46.9   7.7      6e-12   46.6   7.7    1.1  1  Abhydrolase_6    Alpha/beta hydrolase family
    0.00031   20.9   0.1    0.00051   20.2   0.1    1.3  1  Thioesterase     Thioesterase domain
     0.0093   15.8   0.0       0.02   14.7   0.0    1.6  1  Abhydrolase_3    alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.041   13.6   0.0    1.8  2  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
      0.019   13.7   0.0      0.027   13.2   0.0    1.1  1  Ndr              Ndr family
       0.02   14.5   0.0       0.06   13.0   0.0    1.7  1  FSH1             Serine hydrolase (FSH1)
        0.1   12.7   0.0       0.21   11.7   0.0    1.4  1  Abhydrolase_4    TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   2.9e-20   5.7e-17       1     106 [.      26     148 ..      26     167 .. 0.92
   2 !   20.8   0.0   1.3e-07   0.00025     190     251 ..     221     280 ..     195     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2.9e-20
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...................CHHSHHHHHHH CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin..................ddygtasvadd 62 
                                    p+++++ Gl++   +w+  + a+  ak g +vi +D r vg S++  + ++                    y++ ++a+d
  gi|121636567|ref|YP_976790.1|  26 PPVLLIMGLGAQMLLWRTDFCARLVAK-GLRVIRYDNRDVGLSTKTERHRPgqplatrlvrswlglpsqAAYTLEDMAAD 104
                                    89*************************.********************999******************99********* PP

                                    HHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  63 ldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                      ++ld+l++++ ++vG SmGGmia  +aa++ +r k l+ + +
  gi|121636567|ref|YP_976790.1| 105 AAALLDHLDVKHAHVVGASMGGMIAQIFAARFAQRTKTLAVIFS 148
                                    ********************************888777766544 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.3e-07
                                    HHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                  Abhydrolase_1 190 eqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                    +q+++ + + +llr+++   + apt+vi+g+ D+l+ p  ++  a++++++rlv i++ gH+
  gi|121636567|ref|YP_976790.1| 221 QQFSAILGSGSLLRYDR--RIVAPTVVIHGRADKLMRPFGGRAVARAINGARLVLIDGMGHD 280
                                    67888888889999999..7888**************************************8 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   3.4e-16   6.8e-13      21     234 ..      43     281 ..      26     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 3.4e-16
                    Hydrolase_4  21 aelaeaLaaqGfavyalDhrGhGrse......................gkrghvpsfddyvdDlaafvekvkeehpelpl 78 
                                     +++++L+a+G  v+ +D+r  G s                       + +     ++d+ +D+aa+++++  +h +   
  gi|121636567|ref|YP_976790.1|  43 TDFCARLVAKGLRVIRYDNRDVGLSTkterhrpgqplatrlvrswlglPSQ-AAYTLEDMAADAAALLDHLDVKHAH--- 118
                                    459*******************************************54333.47899***************88855... PP

                    Hydrolase_4  79 fllGhSmGGliallyllrypdkva..glilsaPalkikaklkappllklllkllgkllpklqv............snnlk 144
                                     ++G SmGG+ia+ +++r +++ +  ++i+s+ + +  +    pp+ ++ll ll    p+ +               ++ 
  gi|121636567|ref|YP_976790.1| 119 -VVGASMGGMIAQIFAARFAQRTKtlAVIFSSNNHRFLP----PPAPRALLALLTGPPPDSPRdvivdnavrvskIIGSP 193
                                    .69*************88888666558888888888774....4444444444444444444444578888855433344 PP

                    Hydrolase_4 145 adslsrdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdkt 223
                                    a  + +d+ + +a e+     h    ++ +  +l +  +l++ + +i +P+ ++hG aDk++ p + r+++++++    +
  gi|121636567|ref|YP_976790.1| 194 AYPIPEDQVRAEAAESYDRNfHPWGIAQQFSAIL-GSGSLLRYDRRIVAPTVVIHGRADKLMRPFGGRAVARAIN--GAR 270
                                    4555555555555554444435555555555444.5567888999999***************************..7** PP

                    Hydrolase_4 224 lklypglyHel 234
                                    l l++g+ H+l
  gi|121636567|ref|YP_976790.1| 271 LVLIDGMGHDL 281
                                    *********98 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   7.7     3e-15     6e-12       1     209 [.      28     282 ..      28     292 .. 0.58

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3e-15
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTST........................S-GGCS--HHH.CHHHHH CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhG........................rsdpppldled.ladlaa 55 
                                    vll+ G+g+    W++++ a+l a+g +v+ +D +  G                         ++ ++++led +ad aa
  gi|121636567|ref|YP_976790.1|  28 VLLIMGLGAQMLLWRTDFCARLVAKGLRVIRYDNRDVGlstkterhrpgqplatrlvrswlgLPSQAAYTLEDmAADAAA 107
                                    67888999999999767779999***999******9987777766655555555555444444466779999977888** PP

                                    HHCCTT..TTSEEEEEETCHHHHHHH.HHHCC..EE...EEES-........----TTTS----TTHHHHHHTT-C.... CS
                  Abhydrolase_6  56 lldelaagggpvvlvGHSlGGalala.aaplalvvg...vlldp......pptalpagllaaalelllallallrl.... 121
                                    lld+l+   + +++vG S+GG++a+  aa+ a++ +   v+ ++      p     ++ ++a+l+ll ++++  ++    
  gi|121636567|ref|YP_976790.1| 108 LLDHLD--VKHAHVVGASMGGMIAQIfAARFAQRTKtlaVIFSSnnhrflP-----PPAPRALLALLTGPPPDSPRdviv 180
                                    *****6..8888**************6666664444444555554444432.....333333333333333333331111 PP

                                    ............CCCHCCH.........S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE..CT CS
                  Abhydrolase_6 122 ............lawlsre.........plprlfladedadaawrarlarlaallaglgllpaaawadlpvpllvl..gg 178
                                                +a++  e         +++r f++        ++ +++ +      g  ++ ++ ++ v+  v+  g 
  gi|121636567|ref|YP_976790.1| 181 dnavrvskiigsPAYPIPEdqvraeaaeSYDRNFHP-----WGIAQQFSAIL------GSGSLLRYDRRIVAPTVVihGR 249
                                    111001111111333321112111112333333333.....33333333333......333333444444444333348* PP

                                    T-CHHHHCHHCCCH..STTEEETCE...SSS.-H CS
                  Abhydrolase_6 179 eDplvprllerlla..qagarlpvvlpgaGH.lp 209
                                    +D+l++++  r+ a  ++garl v++ g GH lp
  gi|121636567|ref|YP_976790.1| 250 ADKLMRPFGGRAVAraINGARL-VLIDGMGHdLP 282
                                    ********999999999*****.********544 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   2.6e-07   0.00051      41     100 ..      91     149 ..      72     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.6e-07
                                    HHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEE CS
                   Thioesterase  41 depplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslfli 100
                                    +++++ ++e++aa  a+ l    + +  +++G S+Gg++A+ +A++  ++  +++ +f +
  gi|121636567|ref|YP_976790.1|  91 PSQAAYTLEDMAADAAALLDHL-DVKHAHVVGASMGGMIAQIFAARFAQRTKTLAVIFSS 149
                                    6788999******987766655.55599**********************9999888765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05      0.02      53      98 ..     102     142 ..      90     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                    HHHHHHHHHTHH.HHTETTCEEEEEEETHHHHHHHHHHHHHHHTT-- CS
                  Abhydrolase_3  53 laalrwlaeqaw.elgadpsrivlaGdSaGGnlaaavalrardegep 98 
                                     a +       +   ++d ++  ++G S GG +a   a r++++ + 
  gi|121636567|ref|YP_976790.1| 102 AADAA------AlLDHLDVKHAHVVGASMGGMIAQIFAARFAQRTKT 142
                                    33333......334569************************999533 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.041      39      76 ..     113     150 ..      91     153 .. 0.74
   2 ?   -2.5   0.0       2.2   4.4e+03      12      22 ..     212     222 ..     206     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                    .-SEEEEESTSSHHHHHHHHHHHHSS--EEEEEE---- CS
                Eno-Rase_NADH_b  39 gpkkvLviGaStGYGLAsriaaafgagadtigVsfeke 76 
                                      k++ v+GaS G  +A   aa f+   +t+ V+f  +
  gi|121636567|ref|YP_976790.1| 113 DVKHAHVVGASMGGMIAQIFAARFAQRTKTLAVIFSSN 150
                                    479999*******555555568899**********865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                                    SS--HHHHHHH CS
                Eno-Rase_NADH_b  12 ltahPaGcakn 22 
                                    ++ hP G+a++
  gi|121636567|ref|YP_976790.1| 212 RNFHPWGIAQQ 222
                                    688****9987 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.027      79     130 ..      95     146 ..      88     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                    ---HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEE CS
                            Ndr  79 fpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLi 130
                                      +l+d+a +  a+ldh+++k++  +G+  G  i   fa+++ +r + l  i
  gi|121636567|ref|YP_976790.1|  95 AYTLEDMAADAAALLDHLDVKHAHVVGASMGGMIAQIFAARFAQRTKTLAVI 146
                                    469*****************************************99988766 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05      0.06     105     205 ..     118     284 ..      61     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                           FSH1 105 GiiGFSqGaalaallaslleellkea.................shpslkfailvsGfkleepk................. 150
                                     ++G S G+++a++ a+ + +  k+                  +      + l+ G  +++p+                 
  gi|121636567|ref|YP_976790.1| 118 HVVGASMGGMIAQIFAARFAQRTKTLavifssnnhrflpppapR----ALLALLTGPPPDSPRdvivdnavrvskiigsp 193
                                    57888888888888888888766644677766655554322220....22223445555444477777777777777777 PP

                           FSH1 151 ...........................yee...........yyeedkiqtptLhvlGelDtvvdeerseaLaeafknssk 192
                                                                 +            y +++i  pt+ ++G++D+++ +   +a a+a++  + 
  gi|121636567|ref|YP_976790.1| 194 aypipedqvraeaaesydrnfhpwgiaQ-QfsailgsgsllRY-DRRIVAPTVVIHGRADKLMRPFGGRAVARAINGARL 271
                                    7777778888888887666666666540.14445555655567.8999*****************************999 PP

                           FSH1 193 vlkHpggHfvPnk 205
                                    vl    gH +P++
  gi|121636567|ref|YP_976790.1| 272 VLIDGMGHDLPRQ 284
                                    999999*****87 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.21      35      74 ..     241     280 ..     231     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                  Abhydrolase_4  35 apvLllqnerDpaTPyegakklakalggavlvtvegeGHg 74 
                                    ap+ ++ ++ D    + g++++a+a++ga+lv  +g GH+
  gi|121636567|ref|YP_976790.1| 241 APTVVIHGRADKLMRPFGGRAVARAINGARLVLIDGMGHD 280
                                    6899***********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2146.23
//
Query:       gi|121636568|ref|YP_976791.1|  [L=488]
Description: hypothetical protein BCG_0696c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-36  123.5   0.1    8.9e-36  122.7   0.1    1.4  1  ABC1      ABC1 family
    9.7e-06   25.7   6.5    0.00061   19.8   6.5    3.4  1  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.56    9.8   0.0    1.8  2  RIO1      RIO1 family


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.1   1.5e-39   8.9e-36       1     119 []     150     271 ..     150     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.5e-39
                           ABC1   1 eelgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelrldleelv 80 
                                    eelg+++ ++Fa+f+eeP+A+ASiaqVh A+l+sgeeV+vK+qrpg+++r+++Dl++lk++a++++    + rl+ + +v
  gi|121636568|ref|YP_976791.1| 150 EELGDEPARLFASFEEEPFASASIAQVHYATLRSGEEVVVKIQRPGIRRRVAADLQILKRFAQTVELAKLGRRLSAQDVV 229
                                    689***************************************************************************** PP

                           ABC1  81 defskslleEldferEAknaekfrenfaklk...evkvPkvy 119
                                    ++f+++l+eEldf+ EA+++e + +++++ +   +++vP+v+
  gi|121636568|ref|YP_976791.1| 230 ADFADNLAEELDFRLEAQSMEAWVSHLHASPlgkNIRVPQVH 271
                                    ******************************99888*****95 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   6.5     1e-07   0.00061      91     201 ..     225     354 ..      43     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                                    HHHHHHHHHHHHCCHHCH..-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.HHHHHHHH........HHHHHHHH- CS
                            APH  91 lpellealgeflaalhqvd.paalpladflaqdlellrqlesatarllaselld.lleeleeq........vlaalaall 160
                                    ++++++++++ la+  +++  a+++ a+ ++  + +l +  +   ++++ ++   +++ +e+         +        
  gi|121636568|ref|YP_976791.1| 225 AQDVVADFADNLAEELDFRlEAQSMEAWVSHLHASPLGKNIRV--PQVHWDFTTeRVLTMERVhgiridntA-------- 294
                                    4555666666666555555555566666666666666666666..666666666555555552444444440........ PP

                                    -S......................SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEEC CS
                            APH 161 pg......................elptvllHgDlhpgNllvdpddgrvtGviDfedaglgpp 201
                                     +                       l+++l HgDlh gNl vd + gr+  ++Df+ +g  +p
  gi|121636568|ref|YP_976791.1| 295 -AirkagfdgvelvkallfsvfegGLRHGLFHGDLHAGNLYVD-EAGRI-VFFDFGIMGRIDP 354
                                    .344444444555555555588889******************.77887.7*****9998887 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.38   2.3e+03       2      22 ..     176     196 ..     175     213 .. 0.83
   2 ?    9.8   0.0   9.3e-05      0.56      69     150 ..     264     347 ..     255     364 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.38
                                    EEEEEETTTEEEEEEEE-S-- CS
                           RIO1   2 VyhavsedgkevaiKiyktst 22 
                                    V +a+ ++g+ev++Ki + ++
  gi|121636568|ref|YP_976791.1| 176 VHYATLRSGEEVVVKIQRPGI 196
                                    7889999999*****998776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.3e-05
                                    T--S--EEE..EETTEEEEE--EETTEEGGBHHHCG-.HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EE CS
                           RIO1  69 gvpvPkpie..lkrhvlvmefigedgvaapklkdvee.eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kv 144
                                    +++vP++      + vl me ++  g+++ +   +++   +  el++ +l ++     ++gl H+DL   N+ vde  ++
  gi|121636568|ref|YP_976791.1| 264 NIRVPQVHWdfTTERVLTMERVH--GIRIDNTAAIRKaGFDGVELVKALLFSVFEGGLRHGLFHGDLHAGNLYVDEAgRI 341
                                    57888886322567899999999..8888888888843556677778888877777779****************999** PP

                                    EE--GT CS
                           RIO1 145 viIDvs 150
                                    v++D++
  gi|121636568|ref|YP_976791.1| 342 VFFDFG 347
                                    ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3458.45
//
Query:       gi|121636569|ref|YP_976792.1|  [L=1398]
Description: alpha-mannosidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-70  236.1   0.0    6.9e-70  235.7   0.0    1.2  1  Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal dom
    7.6e-19   67.7   2.1    6.3e-17   61.6   0.1    3.5  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    1.7e-13   50.5   0.0    3.2e-13   49.6   0.0    1.5  1  Alpha-mann_mid   Alpha mannosidase middle domain
    0.00012   22.2   0.0     0.0002   21.5   0.0    1.3  1  Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   1.5e-73   6.9e-70       1     274 [.      95     379 ..      95     394 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 1.5e-73
                                    EEEEEEEEE--SSSSS-HHHH.........HCCTCHHHHHHH...HHHHHHSTT--EEES-CHHHHHHHCCS-CCCHHHH CS
                Glyco_hydro_38N   1 kvhvvpHsHiDvgWlktvdey.........qrrkvqrilssv...lellerdpdrkFilseaslferwweeapeekkelv 68 
                                    ++++++H+H+D++W++t+  y          r+++++ ++ v   le+++r+p++kF+l+e+++++ +w+++p+++++l 
  gi|121636569|ref|YP_976792.1|  95 TMFMISHFHYDPVWWNTQGAYtsqwredppGRARQANGFELVrahLEMARREPEYKFVLAEVDYLKPYWDTHPQDRADL- 173
                                    68****************************9999****9999888999*******************************. PP

                                    HHHHHCTSEEECTT-SS-B-SSSS-HHHHHHHHHCCCHHHHCCH--EESEEEESSSSSB-TCHHHHHHCTT--EEEESSS CS
                Glyco_hydro_38N  69 kklvaegrlevvgGgwvenDealpsgeslirqlleGqrflkeefgvrpkvaWliDpFGysatlPqllkkaGidsfltqrl 148
                                    ++++a+gr+ev+gG+++e++++l+s e++ir+l++G +f+++ +g++p++aW++D+FG+++++P l+++aG++s  ++r 
  gi|121636569|ref|YP_976792.1| 174 RRFLADGRIEVMGGTYNEPNTNLTSPETTIRNLVHGIGFQRDVLGAEPATAWQLDVFGHDPQFPGLAADAGLTSSSWARG 253
                                    ******************************************************************************** PP

                                    -HHCHCCHH.....HTT-SCEEEE-TTSTEEEEEE--TT.SSHCCCCCC.GGGTTTHHHCHHHHHHCHHHHHTTSSSSEE CS
                Glyco_hydro_38N 149 syndknkfa.....eqkhlefiWrgsdgteilthmlpadsydptygfqfdfkrdenvkeraekllaqvkklaektrtnev 223
                                     ++++ +++     +q ++ef W +++g+ +lth++pa+     y + + + +  +++ + ++++a +++l++++ t++v
  gi|121636569|ref|YP_976792.1| 254 PHHQWGPAQggvdrMQFCSEFEWIAPSGRGLLTHYMPAH-----YSAGWSMDSSTSLADAEAATYALFDQLKKVALTRNV 328
                                    *************************************97.....5556666778999*********************** PP

                                    EEEECEETHCCCCHHHHCCHHHHHHHHH.HCSSEEEEC--HHHHHHHHHHH....S CS
                Glyco_hydro_38N 224 llplGddfadgqggnteklleeinrsne.keslpkvqfgtpseYfdaleke....n 274
                                    llp+G+d     +++ +k++  i+r++  ++++p++ ++ p+e+f+a+++e     
  gi|121636569|ref|YP_976792.1| 329 LLPVGTD-----YTPPNKWVTAIHRDWGaRYTWPRFVCALPKEFFAAVRAElakrG 379
                                    *******.....*************999899*******************866432 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.1   1.4e-20   6.3e-17       2      78 ..    1191    1265 ..    1190    1266 .. 0.98
   2 ?   -3.7   0.0       3.3   1.5e+04      47      66 ..    1307    1324 ..    1304    1331 .. 0.63
   3 ?    3.7   0.2     0.017        75      41      69 ..    1346    1374 ..    1333    1382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.4e-20
                    NPCBM_assoc    2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakarl 78  
                                     +pG++v l+lt+++d+t+++ ++ +++ +P GW    ++pa+++ +l +G++++a++++++paga +G y+v+a++r+
  gi|121636569|ref|YP_976792.1| 1191 QPGDDVVLRLTAASDCTDSVLGGVVDVVCPLGWP---ATPARLPfTLGAGAHLQADIALSIPAGAPPGPYPVRAQLRV 1265
                                     69********************************...**************************************995 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.3
                    NPCBM_assoc   47 lapGetveatvkVtppagaa 66  
                                     la+G++++   +Vt++++a 
  gi|121636569|ref|YP_976792.1| 1307 LAAGDRARL--AVTIGSRAH 1324
                                     666666555..555555554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.017
                    NPCBM_assoc   41 pasaaslapGetveatvkVtppagaaaGd 69  
                                     pa +a l++   ++  ++Vtppa+ ++G+
  gi|121636569|ref|YP_976792.1| 1346 PALGAVLPARGMAKLAFDVTPPAWLEPGQ 1374
                                     6677889999999*************997 PP

>> Alpha-mann_mid  Alpha mannosidase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   7.2e-17   3.2e-13       9      96 .]     399     487 ..     392     487 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 7.2e-17
                                    SSCHHHHHHHHHHHHHHHHHHHCCTTT.-SCGC-HHHHHHHHHHHHHHHTCTTTTTT-S-HHHHHHCCHHHHHHHHHHHH CS
                 Alpha-mann_mid   9 SrarlKrlnrkleslLraaellssaaa.skgyeypkeeleelwkalllnqfHDilpGtsieeVyedaeerlaealkelek 87 
                                    S  ++K++nr +e+   +ae +++ aa  +g eyp+  l+++w +l+   +HD+++G++ ++Vy d  + +++a++ +++
  gi|121636569|ref|YP_976792.1| 399 SYIDTKQANRAAENAVLEAERFAVFAAlLTGAEYPQAALAKAWVQLAYGAHHDAITGSESDQVYLDLLTGWRDAWELGRA 478
                                    7789********************55569*************************************************** PP

                                    HCCCCCCCC CS
                 Alpha-mann_mid  88 llesalrkL 96 
                                      +++lr+L
  gi|121636569|ref|YP_976792.1| 479 ARDNSLRLL 487
                                    ****99986 PP

>> Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.5e-08    0.0002       1     126 [.     579     708 ..     579     729 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.5e-08
                                    XTTSS-EEEE.TTTSSEEEEESTTTS-EEE....EEEEEEEEEEECS....-S-SSS--BSTT-EEEE--.S-EEECEE- CS
                Glyco_hydro_38C   1 leNgflkveidaknGtlksiydkeakrevlke.qvgnqfaayedapd....ssdaydfkpdneekplevsekeveviesg 75 
                                    + N+++++ +d++ G   s + + ++r++++  +v n++a+ye++p+      + + + p     + ++  + +++ ++g
  gi|121636569|ref|YP_976792.1| 579 IANEHYRLAVDPERGGALSSLVQ-DGRQLIAAgRVANELALYEEYPShptqGEGPWHLLP-TGPVVCSSACPAQVQAYRG 656
                                    78*********988755454443.666666666**************999889******9.44444444449999***** PP

                                    SS-EEEEEEETTES...EEEEEEEEECCCCEEEEEEEE.-TTECEEEEEEEE CS
                Glyco_hydro_38C  76 plvaevtvkfkieaestisqeirLykgkkriefevkvd.weekevllkvafp 126
                                    pl ++++v+ +i    + +q+++L  g  r++ ++ +d + ++  ll++  p
  gi|121636569|ref|YP_976792.1| 657 PLGQRLVVRGRIGTLLRYTQTLTLWDGVDRVDCRTSIDeFTGEDRLLRLRWP 708
                                    ************98888********************999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 8925.83
//
Query:       gi|121636570|ref|YP_976793.1|  [L=224]
Description: malonyl CoA-ACP transacylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.5    7.4   7.2       0.44   10.7   1.1    2.3  2  PT-VENN   Pre-toxin domain with VENN motif


Domain annotation for each model (and alignments):
>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.6      0.12   2.2e+03      18      28 ..      24      34 ..      19      43 .. 0.64
   2 ?   10.7   1.1   2.5e-05      0.44      19      46 ..     109     136 ..     107     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.12
                        PT-VENN 18 laaGlaGgvvg 28
                                   ++a +aG +v 
  gi|121636570|ref|YP_976793.1| 24 VVATVAGVAVA 34
                                   56777776665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.5e-05
                        PT-VENN  19 aaGlaGgvvggtladavaGaeagenAVe 46 
                                    ++ +a++v  + la a  +a ++++AV 
  gi|121636570|ref|YP_976793.1| 109 IGSVAAAVLADPLARALFAAVTARVAVT 136
                                    6899***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1685.30
//
Query:       gi|121636571|ref|YP_976794.1|  [L=302]
Description: sugar kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-61  206.8   0.6      6e-61  206.5   0.6    1.0  1  ROK       ROK family


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.5   0.6   3.4e-65     6e-61       2     291 ..       4     299 ..       3     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 3.4e-65
                                    EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEE.EEEEEESSEEETTCCEBSSGGC CS
                            ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeli.avgigspGlisdksgkivstpn 80 
                                    +++diGgtkia+ l d +g+ +++ + +tp+   +e + +a+ae++++a   a+  + +vgi+s+G+i+ +sg +  +  
  gi|121636571|ref|YP_976794.1|   4 LCLDIGGTKIAAGLADPAGTLVHTAQRPTPAYGGAEQVWAAVAEMIADALGVAGGAVgGVGIASAGPIDLHSGRVSPINI 83 
                                    79***********************************************999887666**********888888777666 PP

                                    GCCCCTTHHHHHHHHH.TS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGGSB CS
                            ROK  81 itwenfdlvekleerl.nvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGHiq 159
                                      w  f+l + +++++ +vpv++  D  ++al+E+++ga  +++ ++ + v+tGvG+G +++g++  Gr+G+ag++GH+ 
  gi|121636571|ref|YP_976794.1|  84 GSWGGFPLRDRVAAAVpGVPVRLGGDGVCMALGEHWLGAGRGARFLLGLVVSTGVGGGLVLDGAPCLGRTGNAGHVGHVV 163
                                    778**********99868************************************************************** PP

                                    S-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC....CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                            ROK 160 ldpegekcgCGnqgClEtlasgralekraqq....kgekleakeiiklaekgdevaeevverlaeylakaiadlinlfdp 235
                                    +dp+g  c CG +gC+Et+asg++l+++a+     ++ ++ ake+ ++a  gd+va  + +r a +la++ia + ++ d 
  gi|121636571|ref|YP_976794.1| 164 VDPDGSPCPCGGRGCVETIASGPSLARWARAngwsAPPGAGAKELAEAAGAGDPVALRAFRRGAAALAAMIASVGAVCDL 243
                                    ******************************99999899999*************************************** PP

                                    SEEEEEHCCCTSTTHH.HHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHHHH CS
                            ROK 236 qaivlgGgvseadkll.eairklvkkylnkklevpvveivaaklgdkagllGaaaLa 291
                                    +  v+gGgv ++ +ll e++r++++ +++  + +   ++v+a+lg  agl+Gaa La
  gi|121636571|ref|YP_976794.1| 244 DLAVIGGGVAKSGRLLfEPLRAALADHARLDFLAGL-RVVPAELGGAAGLVGAARLA 299
                                    *****************************9999998.8****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2130.42
//
Query:       gi|121636572|ref|YP_976795.1|  [L=178]
Description: 50S ribosomal protein L10 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-26   90.7   0.1    9.2e-26   89.9   0.1    1.4  1  Ribosomal_L10  Ribosomal protein L10
     0.0046   16.0   0.1     0.0061   15.6   0.1    1.2  1  DUF3182        Protein of unknown function (DUF3182)


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.1     1e-29   9.2e-26       1     100 []       1      98 [.       1      98 [. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1e-29
                                    SSCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSSSEE CS
                  Ribosomal_L10   1 ktkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkgpva 80 
                                    +++++K+  v+++  ++k++++ ++++y+gltva+l elR++l ++ a++ v+Kntl++rA+ e+g+e  l+el++gp+a
  gi|121636572|ref|YP_976795.1|   1 MARADKATAVADIAAQFKESTATLITEYRGLTVANLAELRRSLTGS-ATYAVAKNTLIKRAASEAGIE-GLDELFVGPTA 78 
                                    6799*****************************************9.********************7.9********** PP

                                    EEEESS-TCHHHHCCCCCHH CS
                  Ribosomal_L10  81 lvftnedpvalakvleefak 100
                                    ++f++++pv++ak+++ fak
  gi|121636572|ref|YP_976795.1|  79 IAFVTGEPVDAAKAIKTFAK 98 
                                    ******************87 PP

>> DUF3182  Protein of unknown function (DUF3182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.8e-07    0.0061      21      84 ..      21      85 ..       4     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-07
                        DUF3182 21 laerlaellglefageleaatreea.klylvPaetlvgeeaaelGiegeedlfGGvvphafvatK 84
                                    a+ + e +gl++a+ +e  ++ ++  +y+v ++tl+++ a+e Gieg ++lf G    afv + 
  gi|121636572|ref|YP_976795.1| 21 TATLITEYRGLTVANLAELRRSLTGsATYAVAKNTLIKRAASEAGIEGLDELFVGPTAIAFVTGE 85
                                   4555555566655544444443333034***************************9999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1159.36
//
Query:       gi|121636573|ref|YP_976796.1|  [L=130]
Description: 50S ribosomal protein L7/L12 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-28   96.6   8.2    7.8e-28   96.6   8.2    2.1  2  Ribosomal_L12    Ribosomal protein L7/L12 C-terminal domain
    1.4e-19   69.5  10.4    2.4e-18   65.6   8.5    2.6  2  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain


Domain annotation for each model (and alignments):
>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.088   7.9e+02      24      40 ..      15      31 ..       9      57 .. 0.66
   2 !   96.6   8.2   8.7e-32   7.8e-28       1      67 []      63     130 .]      63     130 .] 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.088
                                   ---HHHHHHHHTTTTST CS
                  Ribosomal_L12 24 glgLkeaKdlVeaapkv 40
                                   ++ L e  d+V +  ++
  gi|121636573|ref|YP_976796.1| 15 EMTLLELSDFVKKFEET 31
                                   56777777777776554 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 8.7e-32
                                    EEEEEEE-TT-HHHHHHHHHHHH.---HHHHHHHHTTTTSTEEEEE-HHHHHHHHHHHHCTT-EEEEE CS
                  Ribosomal_L12   1 fdViLksagakKiaVIKaVreit.glgLkeaKdlVeaapkvvkegvskeeAeeikkkLeeaGAevelk 67 
                                    fdViL++ag+kKi VIK+Vrei+ glgLkeaKdlV++apk++ e+v+ke A+e+k+kLe+aGA+v++k
  gi|121636573|ref|YP_976796.1|  63 FDVILEAAGDKKIGVIKVVREIVsGLGLKEAKDLVDGAPKPLLEKVAKEAADEAKAKLEAAGATVTVK 130
                                    9*********************77******************************************98 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   8.5   2.7e-22   2.4e-18       2      48 .]       6      53 ..       5      57 .. 0.91
   2 !    3.0   0.0     0.009        80       9      22 ..      85      98 ..      78      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.7e-22
                                   HHHHHHHHHTSBHHHHHHHHHHHHHHTTHHHHHHHHHH.H.HHHHHHH CS
                Ribosomal_L12_N  2 ieeiieaikeltvLElseLvkalEekFGVsAAAPvavaaa.aaaaaaa 48
                                   ++e+++a+ke+t+LEls++vk++Ee+F V+AAAPvavaaa aa+a+aa
  gi|121636573|ref|YP_976796.1|  6 TDELLDAFKEMTLLELSDFVKKFEETFEVTAAAPVAVAAAgAAPAGAA 53
                                   79************************************7757777775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.009
                                   HHTSBHHHHHHHHH CS
                Ribosomal_L12_N  9 ikeltvLElseLvk 22
                                   +++l + E+++Lv+
  gi|121636573|ref|YP_976796.1| 85 VSGLGLKEAKDLVD 98
                                   78999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 848.22
//
Query:       gi|121636574|ref|YP_976797.1|  [L=231]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-17   63.6   3.6    2.3e-17   63.6   3.6    2.1  2  TetR_C_33  Tetracyclin repressor-like, C-terminal domain
    7.8e-12   44.8   0.1    1.6e-11   43.8   0.1    1.6  1  TetR_N     Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.068   6.1e+02      69     103 ..      29      64 ..       5      65 .. 0.68
   2 !   63.6   3.6   2.6e-21   2.3e-17       1     100 [.      81     198 ..      81     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.068
                                    HHHHHHHHHHHHHHHCTTT.TSSS-HHHHHHHHHHH CS
                      TetR_C_33  69 ralwaalhGlvsLelfghf.glpadpdalferlvda 103
                                    +   aa+ G  ++ +  hf g+   ++a +e+ +++
  gi|121636574|ref|YP_976797.1|  29 TRKVAAAAGTSTMAVYTHFgGMRGLIAAIAEEGLRQ 64 
                                    444678889999999999977777677888877765 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 2.6e-21
                                    HHHHHHHHHHHHHH-HHHHHHCCSS--T.T-S-H.......G.HHCCCCHHHHHHHHHHHGGG---TH........--CC CS
                      TetR_C_33   1 lralarayrrfAlahpaeYallfgspvp.gyaap.......d.elaaagarvlalllaalaalvaagl........ppad 63 
                                    l+a++ ayrr+A ++p++Y+l+fgs+   g + p       + +  +++++ +a++++a+++++ ag+        ++++
  gi|121636574|ref|YP_976797.1|  81 LLAIGTAYRRYAIERPHMYRLMFGSTSAhGINVPardvltlKvAEIEHQHPSFAHVVRAVHRCLLAGRfatalgadDDTA 160
                                    689********************777652333344445555358999999*************999999***99843555 PP

                                    HHHHHHHHHHHHHHHHHHHHCTTTTS.SS-HHHHHHHH CS
                      TetR_C_33  64 avaaaralwaalhGlvsLelfghfgl.padpdalferl 100
                                     va a+++w+++hG+v Lel+g +g  +a +++++ ++
  gi|121636574|ref|YP_976797.1| 161 IVATAAQFWSQIHGFVMLELAGFYGDrGAAVEPVLAAM 198
                                    99********************9965577777777766 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   1.8e-15   1.6e-11       1      47 []      11      57 ..      11      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.8e-15
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+a+++l+ ++G da+++r++A++AG+s  a+Y +F+++++L++a+
  gi|121636574|ref|YP_976797.1| 11 LLHAGVRLLDDHGPDALQTRKVAAAAGTSTMAVYTHFGGMRGLIAAI 57
                                   79******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1737.73
//
Query:       gi|121636575|ref|YP_976798.1|  [L=501]
Description: dioxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-113  379.0   0.0   4.9e-113  378.8   0.0    1.0  1  RPE65     Retinal pigment epithelial membrane protein


Domain annotation for each model (and alignments):
>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.8   0.0  2.7e-117  4.9e-113       2     463 .]      19     499 ..      18     499 .. 0.88

  Alignments for each domain:
  == domain 1  score: 378.8 bits;  conditional E-value: 2.7e-117
                                    S---S-EEEC--E..EEE---TT--EEEEEEEEE.ESCETTCCSSSGGGSEEEEEEEEECTTEE.EEEEEE---HHHHHH CS
                          RPE65   2 apvreevpeplevkvieGeiPawlkGtllRnGpgkpevgedgkvshwFDGdGmlhrfefkdgkv.tyrnRfvrtdaylae 80 
                                    apv++ev+++ +++v +G+iP++l+G +lRnGp+ p  + d +++hwF Gd+m+h+++++dgk+ +yrnR+vrt a+ a+
  gi|121636575|ref|YP_976798.1|  19 APVSTEVTAT-DLPV-TGRIPEHLDGRYLRNGPN-PVAEVDPATYHWFTGDAMVHGVALRDGKArWYRNRWVRTPAVCAA 95 
                                    7999***999.7777.6*****************.99999*********************9988************999 PP

                                    HHHTS--SBSTTTTSB-----SEEEEETTEEEEEETTCEEEEEETTTTEEEEE--CCC.TTS-B-SS-EEETTCEEEEEE CS
                          RPE65  81 rkagkslfdglpakkkknnantnvvyhggrllalteagkpyeidpetLetlgkvdldg.eseaftAHpkvdpetgelynf 159
                                      +  s  ++ ++   +   ntnv+ h+gr+lal eag +     ++L+t+g +d+dg  +  +tAHp++dp+tgel+++
  gi|121636575|ref|YP_976798.1|  96 LGEPISARPHPRTGIIEGGPNTNVLTHAGRTLALVEAGVVNYELTDELDTVGPCDFDGtLHGGYTAHPQRDPHTGELHAV 175
                                    7766665555556778889*****************998755555***********87744589**************** PP

                                    EECCTCECEEEEEEE-.T...T-.EEEEEEEECS.S..------EEE-SSEEEEEE--EECHC.H............... CS
                          RPE65 160 glslgkppsvtysvfdvaaaidk.srevkiklpgeklkpayiHdfalTenyvvlvelplklnlkk............... 223
                                    ++s+++   v+ysv+  +   ++ +r+v+i++ g      ++H+f lT+nyvv+++lp+++++ +               
  gi|121636575|ref|YP_976798.1| 176 SYSFARGHRVQYSVIGTD---GHaRRTVDIEVAG----SPMMHSFSLTDNYVVIYDLPVTFDPMQvvpasvprwlqrpar 248
                                    *****66669******77...5568999999988....9*********************9998899999999******* PP

                                    .......................CCCTCGGCEEE-TTS-EEEEEEETTT.T--GG...EEEEE--SEEEEEEEEEEET.. CS
                          RPE65 224 .......................gkksggdalewdpekptrfgvipRrg.ekegvakfrwfeteaffvfHtaNayeee.e 278
                                                           +++s   +++w+p++p+r+gv+pR+g + e v   rwf++e+++v+H +Nay e  +
  gi|121636575|ref|YP_976798.1| 249 lviqsvlgrvripdpiaalgnrmQGHSDRLPYAWNPSYPARVGVMPREGgN-EDV---RWFDIEPCYVYHPLNAYSECrN 324
                                    *********************77555677778****************623.322...8****************99976 PP

                                    TCE.EEEEEEEE.SS.--STTS-CT.T----.-...GGTGGG-EEEEEEEEETTTTTCEECE.EEEEESS-EEEEE--GG CS
                          RPE65 279 dge.vvvdlcryedaevldnlylenlrsrkgeakkeekaeesqsrlrryrldlktgsateekeeaalsdrslEfPrinpa 357
                                    + e +v+d++ry  + ++d+      r+  +         +s+++l r++++l+tg++t e      +dr+ EfPrin++
  gi|121636575|ref|YP_976798.1| 325 GAEvLVLDVVRY--SRMFDRD-----RR-GP-------GGDSRPSLDRWTINLATGAVTAE----CRDDRAQEFPRINET 385
                                    666778******..3355444.....21.11.......235789*********99999999....8************** PP

                                    GTTS--SEEEEEE-SSTTSS....-..-.-EEEEEET-TTTE..........EE--EEEEESTTTSSTT-EEEEEEEEET CS
                          RPE65 358 ysgrkyryvYgasasggsdk....askf.dglvkvDletkgrea.....eghypgEpiFVPragateEDdGvllsvvlde 427
                                     +g ++r++Y+++++gg +     a ++ + l+k D+ t ++ +     ++  +gE++FVP+++a++EDdG+l+ + +++
  gi|121636575|ref|YP_976798.1| 386 LVGGPHRFAYTVGIEGG-FLvgagA-ALsTPLYKQDCVTGSS-TvasldPDLLIGEMVFVPNPSARAEDDGILMGYGWHR 462
                                    **************887.4479954.556********99855.259999999**************************99 PP

                                    .TTEEEEEEEETTBCCCSEEEEESS---S--BEEEEE CS
                          RPE65 428 .eersellvldAktltevArvelpqrvpygfHGtfvp 463
                                     +++ +ll ldA+tl+++A+v+lpqrvp+gfHG+++p
  gi|121636575|ref|YP_976798.1| 463 gRDEGQLLLLDAQTLESIATVHLPQRVPMGFHGNWAP 499
                                    ***********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3720.12
//
Query:       gi|121636576|ref|YP_976799.1|  [L=359]
Description: ribonucleotide-transport ATP-binding protein ABC transporter mkl [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-27   95.1   0.0      9e-27   94.3   0.0    1.4  1  ABC_tran      ABC transporter
    5.6e-10   39.5   0.2      8e-06   25.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0032   17.2   0.0     0.0077   16.0   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0056   16.3   0.1      0.022   14.3   0.1    1.9  2  AAA_25        AAA domain
     0.0078   15.7   0.1        0.2   11.0   0.1    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.024   14.5   0.1    1.5  1  RsgA_GTPase   RsgA GTPase
      0.017   15.6   0.0       0.09   13.2   0.0    2.2  2  AAA           ATPase family associated with various cellular 
       0.02   14.3   0.0       0.25   10.7   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.027   14.4   0.2       0.46   10.4   0.1    2.4  2  NACHT         NACHT domain
      0.029   14.6   0.1       0.16   12.2   0.1    2.2  1  AAA_22        AAA domain
       0.05   12.4   0.1        0.1   11.4   0.0    1.5  2  PPV_E1_C      Papillomavirus helicase
       0.08   12.7   0.0       0.17   11.6   0.0    1.5  1  AAA_30        AAA domain
      0.088   13.2   0.1       0.28   11.6   0.0    1.8  2  AAA_16        AAA ATPase domain
        0.2   11.2   0.0        0.4   10.2   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
       0.21   13.2   0.0       0.33   12.5   0.0    1.3  1  DUF3729       Protein of unknown function (DUF3729)
       0.22   10.3   0.2        2.5    6.8   0.1    2.0  2  Adeno_IVa2    Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0     8e-30     9e-27       2     136 ..      44     191 ..      43     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 8e-30
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvre 78 
                                    ++v+l++ +ge+ +++G++G+GKS +lk l+gll+p+ G+i +dg+d+ e   +el + r  +gvl+q+  lf  +++++
  gi|121636576|ref|YP_976799.1|  44 EDVTLTIPAGEVSVLLGPSGTGKSVFLKSLIGLLRPERGSIIIDGTDIIEcsaKELYEIRTLFGVLFQDGALFGSMNLYD 123
                                    589*********************************************9999999************************* PP

                                    H..........HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    x..........xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n..........esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    n          ++++e  + +++kl l++l  +  k+ p ++SgG+++r  laral+ +p+++l+DEp 
  gi|121636576|ref|YP_976799.1| 124 NtafplrehtkKKESEiRDIVMEKLALVGLGGDE-KKFPGEISGGMRKRAGLARALVLDPQIILCDEPD 191
                                    *******998744444356678888888877777.5778****************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00017      0.19       1      26 [.      55      83 ..      55     147 .. 0.71
   2 !   25.9   0.0   7.2e-09     8e-06     235     301 ..     162     226 ..     156     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl...d 26
                                   + vl Gp g+GKS +L+ l +l r     
  gi|121636576|ref|YP_976799.1| 55 VSVLLGPSGTGKSVFLKSLIGLLRPergS 83
                                   579****************9997754431 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 7.2e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                     e+S G+++ ++l+ al  ++    ++l DEp++gL+P +++ l +l+ +++++ +a ++++TH+  +
  gi|121636576|ref|YP_976799.1| 162 GEISGGMRKRAGLARALVLDP---QIILCDEPDSGLDPVRTAYLSQLImDINAQIDATILIVTHNINI 226
                                    57899*****99999999999...9***********************95555559********9765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.8e-06    0.0077      16      50 ..      47      81 ..      42      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.8e-06
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   t++i   ++ +l GpsG+GKS +l +++ lL p++
  gi|121636576|ref|YP_976799.1| 47 TLTIPAGEVSVLLGPSGTGKSVFLKSLIGLLRPER 81
                                   5666644599*******************999986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     2e-05     0.022      29      53 ..      49      73 ..      41      75 .. 0.89
   2 ?   -1.6   0.0       1.5   1.7e+03     173     188 ..     207     222 ..     144     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                         AAA_25 29 llpagelallaGapgtGKttlaldl 53
                                    +page+++l G++gtGK++++ +l
  gi|121636576|ref|YP_976799.1| 49 TIPAGEVSVLLGPSGTGKSVFLKSL 73
                                   58******************98665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                         AAA_25 173 eriarrtgaavllvhH 188
                                     +i ++ +a++l+v H
  gi|121636576|ref|YP_976799.1| 207 MDINAQIDATILIVTH 222
                                    4677888999999988 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00018       0.2      25     213 ..      54     238 ..      28     244 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEE....EETTEESSSSSSCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitf....dnedkklkiekeevs 98 
                                    ++++++Gp G GKs +l ++   +G      lr e+ s +i      e ++ +  e+  +f    ++     +++  + +
  gi|121636576|ref|YP_976799.1|  54 EVSVLLGPSGTGKSVFLKSL---IG-----LLRPERGSIIIDGtdIIECSAKELYEIRTLFgvlfQDGALFGSMNLYDNT 125
                                    47788888888888888888...56.....35666666555552211222222233333333221333222222222222 PP

                                    EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                         +++++ e +i +  ++k  +  l  +++  + ++SgG ++ + la  + +   +p+ + l De d+ LD  +++ 
  gi|121636576|ref|YP_976799.1| 126 AFPLREHTKKKESEIRDIVMEKLALVGLGGDEKKFPGEISGGMRKRAGLARALVL---DPQ-IILCDEPDSGLDPVRTAY 201
                                    2222222222234566666666666666666666666899998888888765443...444.6788************** PP

                                    HHHHHH..HHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 179 vaellk..eksknaQfivislreemlekadklvgvtk 213
                                    +++l+   +++ +a +++++++ ++ + +  ++g+ +
  gi|121636576|ref|YP_976799.1| 202 LSQLIMdiNAQIDATILIVTHNINIARTVPDNMGMLF 238
                                    ****994445555899999999999998888888776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.1e-05     0.024      98     122 ..      52      76 ..      26      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                    TTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                    ++++svl+G+SG GKS ++++l++ 
  gi|121636576|ref|YP_976799.1|  52 AGEVSVLLGPSGTGKSVFLKSLIGL 76 
                                    459*************999999875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     8e-05      0.09       2      68 ..      57     191 ..      56     226 .. 0.67
   2 ?   -3.1   0.0       8.6   9.6e+03      38      65 ..     319     344 ..     314     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                                    EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS.................................. CS
                            AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk.................................. 37 
                                    +l Gp GtGK+ + k+++  l          g++++e s++el  +                                  
  gi|121636576|ref|YP_976799.1|  57 VLLGPSGTGKSVFLKSLIGLLrpergsiiidGTDIIECSAKELY-Eirtlfgvlfqdgalfgsmnlydntafplrehtkk 135
                                    589*****************955444444444556777766666.24677777777777777777777777777776666 PP

                                    ........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGG CS
                            AAA  38 ........................yvgesekkirelfkeakeka.kpsilfiDEid 68 
                                                            + ge +  +r+    a++   +p i++ DE d
  gi|121636576|ref|YP_976799.1| 136 keseirdivmeklalvglggdekkFPGEISGGMRKRAGLARALVlDPQIILCDEPD 191
                                    66666666666666666666555555555555555555555555556666666655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.6
                                    STTHHHHHHHHHHHHHHHTSTSEEEEEE CS
                            AAA  38 yvgesekkirelfkeakekakpsilfiD 65 
                                     v  +++++re++ ++ +ka     ++D
  gi|121636576|ref|YP_976799.1| 319 AVARRQARVREMLHTLPKKA--QAAILD 344
                                    56667788888888877776..344445 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.25      21      60 ..      53      91 ..      37     104 .. 0.78
   2 ?    1.1   0.0      0.19   2.2e+02      87     103 ..     147     165 ..     130     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                   Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlpsllpplseeealevaki 60
                                   G+ + +l+Gp+G+GK++  k l +ll p   + +++ + i
  gi|121636576|ref|YP_976799.1| 53 GEVS-VLLGPSGTGKSVFLKSLIGLLRPERGSIIIDGTDI 91
                                   4444.567******************98777666666655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                   Mg_chelatase  87 kaalvG..ggskpkpGeis 103
                                    k alvG  g +k  pGeis
  gi|121636576|ref|YP_976799.1| 147 KLALVGlgGDEKKFPGEIS 165
                                    67887642666999****9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00041      0.46       2      24 ..      55      77 ..      54      80 .. 0.88
   2 ?    1.8   0.0      0.18     2e+02      78     117 ..      77     114 ..      76     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                                   CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                   +++l G++G GK+++l++l+ ++
  gi|121636576|ref|YP_976799.1| 55 VSVLLGPSGTGKSVFLKSLIGLL 77
                                   789***************98765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                    CSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTT CS
                          NACHT  78 elperlLlilDglDelvtdlgqkekqpvrtlLselirkkl 117
                                     +per  +i+Dg D ++     ke  ++rtl++ l++   
  gi|121636576|ref|YP_976799.1|  77 LRPERGSIIIDGTDIIECSA--KELYEIRTLFGVLFQDGA 114
                                    5789999*******887644..447788888888777655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00015      0.16       8      60 ..      56     109 ..      52     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrel 60 
                                     v+ G+sGtGK++ l+ l   l  e         + +++++ ++++ + ++l+  l
  gi|121636576|ref|YP_976799.1|  56 SVLLGPSGTGKSVFLKSLIGLLRPERG--SiiiDGTDIIECSAKELYEIRTLFGVL 109
                                    6899*************9998843221..122433333333333333555555544 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     9e-05       0.1     259     287 ..      50      78 ..      44      86 .. 0.85
   2 ?   -3.5   0.0         3   3.4e+03     348     364 ..     212     228 ..     210     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                       PPV_E1_C 259 vPkknclvllGppntGkslfamslikfLk 287
                                    +P  ++ vllGp+ tGks+f +sli +L+
  gi|121636576|ref|YP_976799.1|  50 IPAGEVSVLLGPSGTGKSVFLKSLIGLLR 78 
                                    56777889*****************9996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                       PPV_E1_C 348 qlkcPPllitsnidvka 364
                                    q+ +  l++t ni++ +
  gi|121636576|ref|YP_976799.1| 212 QIDATILIVTHNINIAR 228
                                    77888899*****9975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.17      19      49 ..      54      84 ..      46      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                    v+vl Gp GtGK+  lk+l  +++ + g++
  gi|121636576|ref|YP_976799.1| 54 EVSVLLGPSGTGKSVFLKSLIGLLRPERGSI 84
                                   599****************998888775555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.28      25      52 ..      54      81 ..      41     189 .. 0.83
   2 ?   -1.2   0.0         2   2.3e+03     106     145 ..     292     347 ..     252     349 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                         AAA_16 25 elvllsGesGvGKsslvrellralekdg 52
                                   e+ +l G+sG+GKs  +++l   l+ ++
  gi|121636576|ref|YP_976799.1| 54 EVSVLLGPSGTGKSVFLKSLIGLLRPER 81
                                   66789************99987776664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                         AAA_16 106 a.................avpelagaea........srllellkrllallsrderplvlvlDdlq 145
                                    +                 a+       +         r  + ++++l  l+++++    +lDdl+
  gi|121636576|ref|YP_976799.1| 292 GhhaggveeiegvppqisAT-------PgmperkavARRQARVREMLHTLPKKAQ--AAILDDLE 347
                                    12333333333333333333.......1333444477777777888866666555..77777775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00036       0.4      32      60 ..      52      80 ..      43      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00036
                          AAA_7 32 nkkpvllvGptGtGKtviikdllkkldke 60
                                   ++   +l Gp+GtGK+v +k+l+  l +e
  gi|121636576|ref|YP_976799.1| 52 AGEVSVLLGPSGTGKSVFLKSLIGLLRPE 80
                                   55667899************998777655 PP

>> DUF3729  Protein of unknown function (DUF3729)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00029      0.33      72     113 .]     291     335 ..     264     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                        DUF3729  72 sdlvpsvakp...asppsplapkaparkvpappparrrrLLhtyP 113
                                    +   +++ +     +p+ +++p  p rk+ a  +ar r++Lht+P
  gi|121636576|ref|YP_976799.1| 291 AGHHAGGVEEiegVPPQISATPGMPERKAVARRQARVREMLHTLP 335
                                    444444333333378*****************************9 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0022       2.5      89     115 ..      55      79 ..      52     107 .. 0.78
   2 ?    1.3   0.0      0.11   1.2e+02     220     256 ..     199     235 ..     177     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                     Adeno_IVa2  89 iGviyGPtGsGksqllrnlissklisP 115
                                    + v+ GP G+Gks +l++li   l+ P
  gi|121636576|ref|YP_976799.1|  55 VSVLLGPSGTGKSVFLKSLIG--LLRP 79 
                                    56999**************96..5554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                     Adeno_IVa2 220 halPsklsakfkkctgfsvlvvlhnlnPrsdiagnia 256
                                     a+ s+l    +     ++l+v hn+n  + + +n+ 
  gi|121636576|ref|YP_976799.1| 199 TAYLSQLIMDINAQIDATILIVTHNINIARTVPDNMG 235
                                    566666666666667779*********9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2500.69
//
Query:       gi|121636577|ref|YP_976800.1|  [L=127]
Description: hypothetical protein BCG_0705c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.5   0.0      0.059   13.1   0.0    1.2  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.3e-06     0.059       6      61 ..      55     109 ..      51     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-06
                        DUF5615   6 DenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgel 61 
                                    D  ++ ++ +++ +a h      ++g  ++ D  i++ A +++++++  D+D+ el
  gi|121636577|ref|YP_976800.1|  55 DVPVPKSVWRWIDSAQHRLARAGAVGALSVVDLLICDTAAARGLVVLHDDADY-EL 109
                                    88899***********************************************9.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 866.43
//
Query:       gi|121636578|ref|YP_976801.1|  [L=51]
Description: hypothetical protein BCG_0706c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-16   59.1   1.9    3.2e-16   59.0   1.9    1.1  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   1.9   1.8e-20   3.2e-16       2      43 ..       3      44 ..       2      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.8e-20
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------HH CS
                 VapB_antitoxin  2 rtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkree 43
                                    t+I++DDe la+++r++ ++tK+EaVnlA+r++++r +r+e
  gi|121636578|ref|YP_976801.1|  3 VTQIDLDDEALADVMRIAAVHTKKEAVNLAMRDYVERFRRIE 44
                                   69*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 369.09
//
Query:       gi|121636579|ref|YP_976802.1|  [L=238]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   50.9   9.2    1.5e-13   50.9   9.2    2.4  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.016   14.8   1.2      0.027   14.0   1.2    1.5  1  DUF1295   Protein of unknown function (DUF1295)
        3.5    5.2   5.6        5.1    4.6   5.6    1.1  1  ACR_tran  AcrB/AcrD/AcrF family


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   3.3      0.84     5e+03      71      71 ..      67      67 ..      10     132 .. 0.55
   2 !   50.9   9.2   2.4e-17   1.5e-13       3      92 .]     134     222 ..     132     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.84
                                   H CS
                           CPBP 71 y 71
                                   +
  gi|121636579|ref|YP_976802.1| 67 I 67
                                   2 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 2.4e-17
                                    TTHHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-.HHHHHHHHHHHHHCSGGGHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                           CPBP   3 nlllvfllalllapllEEllfRglllqllqergss.tlailissilFglaHlpngpsvllaalaGlvlgylylktgslla 81 
                                    + l+vfl+++++apl+EE+++Rgll+ ++ +r +  ++a++++ ++F+laHl       l++++ + +++++ ++g lla
  gi|121636579|ref|YP_976802.1| 134 WALVVFLVVVFVAPLCEEIIYRGLLWGAVDRR-WGrWAALVVTTVVFALAHLEF-ARAPLLVVVAIPIALARFYSGGLLA 211
                                    6799****************************.4447**************987.5699999999999*******99*** PP

                                    HHHHHHHHHHH CS
                           CPBP  82 aillHallnll 92 
                                    +i++H ++nll
  gi|121636579|ref|YP_976802.1| 212 SIVTHQVTNLL 222
                                    *********85 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   4.5e-06     0.027      31     109 ..     125     203 ..      99     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                        DUF1295  31 llseaaklrrllvllLvvlWglRLalhllrrtlkkg.eDkryeelrkelgktiallsllvvfvlQavllylvalpvllaa 109
                                    + + +a++  +lv++Lvv+  + L   +++r l +g  D+r+ +  + + +t++  +l+ +  + a ll++va+p+ la 
  gi|121636579|ref|YP_976802.1| 125 FGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGaVDRRWGRWAALVVTTVV-FALAHLEFARAPLLVVVAIPIALAR 203
                                    33566889999*************************99*********9988844.4777777889999999999998876 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.6   0.00085       5.1     871     929 ..     171     232 ..     167     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.00085
                                    HHHHHHHHHH.HHHTSSSTCHHHHTTHHHHHH....HHHHHHHHTT--BSHHHHHHHHHHHHHH CS
                       ACR_tran 871 alllvflvLa.alyeslsepllilltvPlalv....GallalllrglelsviaqvGlilliGla 929
                                    al++  +v a a  e +++pll+++ +P+al+    G+lla +++++  ++    G++ll+Gl 
  gi|121636579|ref|YP_976802.1| 171 ALVVTTVVFAlAHLEFARAPLLVVVAIPIALArfysGGLLASIVTHQVTNLLP--GIVLLLGLT 232
                                    444444444423468899************854455***********999865..888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1759.90
//
Query:       gi|121636580|ref|YP_976803.1|  [L=102]
Description: hypothetical protein BCG_0708c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-11   43.1   0.0    5.2e-11   42.9   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   2.9e-15   5.2e-11       2     109 ..       3      98 ..       2     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.9e-15
                                    TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCH.SEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCCE CS
                     PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnek.ntvivvpltskdkdkkklpfhveleseildlngldkdswvkldqi 80 
                                    rGe++ +          g+ Rpv+V+++d   ++ ++v+vv+lt +++       + el++    +n  + d++v+ d i
  gi|121636580|ref|YP_976803.1|   3 RGELWFAAT-------PGGDRPVLVLTRDPVADRiGAVVVVALTRTRRGL---VSELELTA---VENRVPSDCVVNFDNI 69 
                                    677777777.......4689*********999888*********766322...45555553...23444578******** PP

                                    EEEEGGGEEEEEEE--HHHHHHHHHHHHH CS
                     PemK_toxin  81 rtvdkarlrkkigklsredlaevqralak 109
                                     t+++  +r++i++ls+++l e  ++l++
  gi|121636580|ref|YP_976803.1|  70 HTLPRTAFRRRITRLSPARLHEACQTLRA 98 
                                    **********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 750.12
//
Query:       gi|121636581|ref|YP_976804.1|  [L=81]
Description: hypothetical protein BCG_0709c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-05   23.0   1.3    0.00011   22.0   1.3    1.5  1  RHH_1          Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.014   16.1   1.1      0.016   16.0   1.1    1.1  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.3   1.2e-08   0.00011       2      37 ..       2      37 ..       2      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-08
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   +s+r d+ ++++ d+ arr++  rSel+R+Alr++l
  gi|121636581|ref|YP_976804.1|  2 LSFRADDHDVDLADAWARRLHIGRSELLRDALRRHL 37
                                   6899999999999********************998 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   1.1   1.7e-06     0.016      11      62 ..      11      68 ..       6      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XX--HHHHHHHHHHHHHTS CS
                  PSK_trans_fac 11 erlareLarltgeskteAvrrAleerlerlrre......raepllerllallrraaak 62
                                   ++la+  ar+ +    e  r+Al++ l+ l ++       ++pl+++  al++ a++ 
  gi|121636581|ref|YP_976804.1| 11 VDLADAWARRLHIGRSELLRDALRRHLAALAADqdvqayTERPLTDDENALAEIADWG 68
                                   579***************************9999888888888888888888877773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 532.80
//
Query:       gi|121636582|ref|YP_976805.1|  [L=145]
Description: hypothetical protein BCG_0710c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   46.6   0.3    4.9e-12   46.4   0.3    1.0  1  PIN       PIN domain
    0.00017   22.3   2.7    0.00029   21.6   2.7    1.4  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.3   5.5e-16   4.9e-12       1     120 [.       2     126 ..       2     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5.5e-16
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                    ivlDT vl+++   +++ ++ +r+l++++     +  t+a v++E+++v ar +++r  aa+l ++     + ++ p  +
  gi|121636582|ref|YP_976805.1|   2 IVLDTTVLVYAKgAEHPLRDPCRDLVAAIaderIAATTTAEVIQEFVHVRAR-RRDRSDAAALGRVTMPNCSRRYSPSIE 80 
                                    79*****************************999999***************.999*********************999 PP

                                    HHHHHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  76 eiaeeaaeialkyg.llpnDaliaAtAkehgikliatfDedfrrva 120
                                    +  ++ + +++    l + Da++aA+A + g+++++++D  f++++
  gi|121636582|ref|YP_976805.1|  81 ATSKRGLTLFETTPgLEACDAVLAAVAASAGATALVSADPAFADLS 126
                                    999999999999889**************************99876 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.7   3.2e-08   0.00029       2     114 ..       2     119 ..       1     121 [. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.2e-08
                          PIN_3   2 vvlDtnvlldallfdspaarkildal...etgaitlvvsprlldElervlarelaypqfklraadkaallakvalerkav 78 
                                    +vlDt+vl+ a   + p++ +++d++   ++++i + ++++++ E+  v ar+ ++ ++++   +     + ++   +  
  gi|121636582|ref|YP_976805.1|   2 IVLDTTVLVYAKGAEHPLRDPCRDLVaaiADERIAATTTAEVIQEFVHVRARRRDRSDAAALGRVT---MPNCS---RRY 75 
                                    7********99999999555555555555******************8888886655544444444...66665...666 PP

                          PIN_3  79 apdaelrpllkcr........DpdDqkvlelAlaaradvlVTkd 114
                                    +p+ e+++   +          + D+  +++A  a a +lV+ d
  gi|121636582|ref|YP_976805.1|  76 SPSIEATSKRGLTlfettpglEACDAVLAAVAASAGATALVSAD 119
                                    6666666655555666788999********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1034.84
//
Query:       gi|121636583|ref|YP_976806.1|  [L=122]
Description: hypothetical protein BCG_0711c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.2   3.9      0.056   13.4   0.4    2.3  2  RHH_1           Ribbon-helix-helix protein, copG family
      0.055   14.2   1.4      0.099   13.4   1.4    1.5  1  PSK_trans_fac   Rv0623-like transcription factor
       0.15   11.6   0.0       0.23   11.1   0.0    1.2  1  SMC_ScpB        Segregation and condensation complex subunit 
       0.16   12.4   0.0       0.21   12.0   0.0    1.3  1  Acetyltransf_7  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   1.3e-05     0.056       1      35 [.      46      80 ..      46      83 .. 0.93
   2 ?    2.8   0.2     0.027   1.2e+02       7      22 ..     107     122 .]     107     122 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                   r++i ld+e  +r+ + ar+rg+ +  ++ReA+ +
  gi|121636583|ref|YP_976806.1| 46 RLQILLDDECHRRITAVARERGVPVATVVREAIDR 80
                                   78999****************************76 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.027
                                    EHHHHHHHHHHHHHHT CS
                          RHH_1   7 deellerLdelarrrg 22 
                                    ++el+ +L++l++rrg
  gi|121636583|ref|YP_976806.1| 107 PRELKQELEALRARRG 122
                                    579999*******998 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   2.2e-05     0.099       7      61 ..      52     105 ..      46     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHT CS
                  PSK_trans_fac   7 dpeverlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaa 61 
                                    d+e +r ++ +ar +g+   ++vr+A+ + l      r+++  +rll+ ++  + 
  gi|121636583|ref|YP_976806.1|  52 DDECHRRITAVARERGVPVATVVREAIDRGLVSPAG-RRKSAGRRLLDAADMSVP 105
                                    8999*************************9987654.777777777776665444 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.2e-05      0.23     103     137 ..      62      96 ..      52      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.2e-05
                       SMC_ScpB 103 ieeiRGvnsdsvvrtLlerglieekgrkeepgrpi 137
                                    +++ RGv + +vvr+ ++rgl++ +gr+++ gr +
  gi|121636583|ref|YP_976806.1|  62 VARERGVPVATVVREAIDRGLVSPAGRRKSAGRRL 96 
                                    6777****************************975 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05      0.21       7      49 ..      62     103 ..      43     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                                    EEEETTEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHHH...T CS
                 Acetyltransf_7   7 VaeddgkivGfialslldaeitrlaVdpeyrgkGiGraLlea...a 49 
                                    Va++ g +v +++  +  + i r  V+p+ r+k  Gr+Ll+a    
  gi|121636583|ref|YP_976806.1|  62 VARERGVPVATVV--R--EAIDRGLVSPAGRRKSAGRRLLDAadmS 103
                                    6666666666443..2..2466777****************73330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 869.01
//
Query:       gi|121636584|ref|YP_976807.1|  [L=787]
Description: arylsulfatase atsD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-94  316.9   0.0    1.9e-94  316.5   0.0    1.1  1  Sulfatase    Sulfatase
    7.4e-06   26.2   0.0    2.1e-05   24.7   0.0    1.7  1  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.024   14.5   0.1    1.4  1  DUF4994      Domain of unknown function


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.5   0.0   3.2e-98   1.9e-94       1     308 [.      43     459 ..      43     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 316.5 bits;  conditional E-value: 3.2e-98
                                    EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT..... CS
                      Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg..... 75 
                                    pnv+lil+dd+g+g  +++gg+++ t + + la +glr+++f+++a lcsp+r+alltgr++h++g++ +te+++     
  gi|121636584|ref|YP_976807.1|  43 PNVLLILLDDVGFGASSAFGGPCR-TSTAELLAGNGLRYNRFHTTA-LCSPTRQALLTGRNHHSAGMGGITEIATgapgy 120
                                    9**********************9.8999999************98.********************************* PP

                                    .HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC........CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC CS
                      Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk........nrgfdrflgfptgsaalkdpekseyngevlrv 146
                                     + lp+t++ +++ lk +GYnta +gk+h  + +++s++         ++gf++f+gf++g+a++++p+ +e++++v+++
  gi|121636584|ref|YP_976807.1| 121 sSVLPNTMSPIARTLKLNGYNTAQFGKCHEVPVWQTSPVGpfdawpsgGGGFEYFYGFIGGEANQWYPSLYEGTTPVEVN 200
                                    *************************************7779***********************************9999 PP

                                    ..TTTTCSHHHHHHHHHHHHH...HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH............ CS
                      Sulfatase 147 ..ppeggysddrlldealefl...larn.dkpfflylatlapHappeapdeyakkyatffddgseaar............ 208
                                      p+eg++++++++d+al+++   +a + d+pff+y+a+ a+Hap+++p+e+a+ky+++fd g++a r            
  gi|121636584|ref|YP_976807.1| 201 rtPEEGYHFMADMTDKALGWIgqqKALApDRPFFVYFAPGATHAPHHVPREWADKYRGRFDVGWDALReetfarqkelgv 280
                                    99********************9955556*************************************9999999999**** PP

                                    .............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEE.ESSSSCCCG... CS
                      Sulfatase 209 .............................qlleaylnsveyvDdligrvlaaLeenglldntlvvft.SDhgaslee... 255
                                                                 +++e+y++++ey+D+++gr+++ L+++g+ld+tlv+++ +D+gas e+   
  gi|121636584|ref|YP_976807.1| 281 ipadcqltarhaeipawddmpedlkpvlcRQMEVYAGFLEYTDHHVGRLVDGLQRLGVLDDTLVFYIiGDNGASAEGtin 360
                                    ******************************************************************************** PP

                                    ............................................HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC..EE CS
                      Sulfatase 256 ............................................sngplrggkganayeggtrvPllvwwpgekap..rv 289
                                                                                +++p++++k++++++ggtr  ++v+wp+++a+  ++
  gi|121636584|ref|YP_976807.1| 361 gtynemlnfngladietprfmtdrldkfggpesynhysvgwahaMDTPYQWTKQVASHWGGTRNGTIVHWPNGIAAkgEM 440
                                    ******************************************************************************** PP

                                    ECSEEEGGGHHHHHHHHTT CS
                      Sulfatase 290 seelvshiDlfptildlag 308
                                    +++++++iD++ptil++ag
  gi|121636584|ref|YP_976807.1| 441 RWQFHHVIDVAPTILEAAG 459
                                    ******************9 PP

>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.5e-09   2.1e-05      13     139 ..     617     759 ..     605     762 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.5e-09
                    Laminin_G_3  13 slptssfTvsaWvkpdslpsaaqiiissssdgrgfelgldgsgrlrfsvnagngaeesvtsgasvpageWtHvavtyd.. 90 
                                    +l+++s Tv+a v + +++++  i+ +++s g g++l+ + +g+l   +n g+ + ++++s+ ++pag+ ++v + +   
  gi|121636584|ref|YP_976807.1| 617 NLKNKSHTVTAEVEVPETGAEGVIVAQGASIG-GWSLYAN-DGKLKYCYNLGGIKHFYAESADPLPAGA-HQVRMEFAya 693
                                    6789***************9766666355556.9***995.577777777778889***********99.8888888888 PP

                    Laminin_G_3  91 ......ggtlrlYvNGvevgsatltgg...llsatsgplviGrdp.........ggddpfdGlidev 139
                                          gg+++lYv+G++vg+ ++ ++   +   +++   +G d+         +g++ f+G i  v
  gi|121636584|ref|YP_976807.1| 694 ggglgkGGEVTLYVDGQQVGEGHVEATlaiV-FSADDGCDVGMDSgspvspdyaPGSNAFNGRIKGV 759
                                    999888888************9988886532.23333334444442334433333477777777666 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.1e-06     0.024      37      97 ..     504     564 ..     495     565 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                        DUF4994  37 svrkkkWkyiePskgpalikltkielGnskepqLydlkkdegekenvaekhpekvkelkel 97 
                                     +++k W  ++ +k p +   +++    +    Lyd +kd ++ +++a+++pek++el++l
  gi|121636584|ref|YP_976807.1| 504 GIYHKGWTAVTKHKTPWILVGEQTVAFDDDVWELYDTTKDWSQAKDLAKEMPEKLHELQRL 564
                                    577888999999999999999888888999999*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5432.65
//
Query:       gi|121636585|ref|YP_976808.1|  [L=90]
Description: hypothetical protein BCG_0713 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 533.61
//
Query:       gi|121636586|ref|YP_976809.1|  [L=112]
Description: hypothetical protein BCG_0714 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-05   25.3   0.5    2.9e-05   24.6   0.5    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.5   1.6e-09   2.9e-05       2     102 ..      10     109 ..      10     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-09
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    +lDTsv+i    +e        ++++l e++++s+ ++ El  +l +   ++  + ++ ++l l++    +p+++++   
  gi|121636586|ref|YP_976809.1|  10 LLDTSVFI---ARES-----GGAIADLpERVALSVMTIGELQLGLLN-AGDSATRSRRADTLALARTADQIPVSEAVMIS 80 
                                    58999999...3333.....446666679******************.44444444444444445555555666666666 PP

                                    HHHHHHHHH.......SBHHHHHHHHHHH CS
                            PIN  81 aaeialkyg.......llpnDaliaAtAk 102
                                     a++ +  +       +++ DaliaAtA+
  gi|121636586|ref|YP_976809.1|  81 LARLVADCRaagvrrsVKLTDALIAATAE 109
                                    6666666666777777************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 820.98
//
Query:       gi|121636587|ref|YP_976810.1|  [L=57]
Description: hypothetical protein BCG_0715 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 415.11
//
Query:       gi|121636588|ref|YP_976811.1|  [L=1172]
Description: DNA-directed RNA polymerase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-156  521.2   0.0   6.8e-156  519.2   0.0    1.8  2  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    1.6e-29  101.9   0.0    3.8e-29  100.6   0.0    1.7  1  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
    8.1e-29   99.7   2.4    1.1e-27   96.0   3.2    2.5  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
    5.8e-27   94.6   0.0    1.5e-26   93.2   0.0    1.7  1  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    2.5e-26   91.9   0.0    6.7e-26   90.5   0.0    1.8  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
      9e-22   77.6   0.0    2.6e-21   76.1   0.0    1.7  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
  ------ inclusion threshold ------
       0.17   12.1   0.5        1.1    9.6   0.0    2.5  3  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.26   6.6e+02       3      28 ..     586     611 ..     584     618 .. 0.87
   2 !  519.2   0.0  2.7e-159  6.8e-156       1     390 []     637    1056 ..     637    1056 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                                    HT-SS-TTB-HHHHHHHHHHGGGB-S CS
                 RNA_pol_Rpb2_6   3 klapvvehvqspriiiqaamekqalg 28 
                                    + +p+ eh +++r ++ a+m++qa+ 
  gi|121636588|ref|YP_976811.1| 586 AMIPFLEHDDANRALMGANMQRQAVP 611
                                    579*******************9975 PP

  == domain 2  score: 519.2 bits;  conditional E-value: 2.7e-159
                                     HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS.........GGGS-S CS
                 RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvl.dgpatekgelal 77  
                                     va+ ++v+e+v+++ i++ ++++    ++y+++kf rsn+ t   c nq P+v  gd+veagqv+ dgp+t+ ge+al
  gi|121636588|ref|YP_976811.1|  637 VAEESGVIEEVSADYITVMHDNGTR--RTYRMRKFARSNHGT---CANQCPIVDAGDRVEAGQVIaDGPCTDDGEMAL 709 
                                     68999***************55555..5**************...********************************* PP

                                     EEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..--SS-GGGS-TTSB--SS CS
                 RNA_pol_Rpb2_6   78 GqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnvseealkkLdedGivrvg 155 
                                     G+n++VA+m++eG+n+EDaiil++rlv++dv+tsihi+e+e++ardtklg+eeitrdipn s+e l++Lde+Givr+g
  gi|121636588|ref|YP_976811.1|  710 GKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIG 787 
                                     ****************************************************************************** PP

                                     -EEETT-EEE---...B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEE CS
                 RNA_pol_Rpb2_6  156 aevkegdilvgkvt.kgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkv 232 
                                     aev++gdilvgkvt kgeteltpee+llraifgekarev+dtsl+v++ge+g V+ ++vfsre++del+agvn+lv+v
  gi|121636588|ref|YP_976811.1|  788 AEVRDGDILVGKVTpKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRV 865 
                                     ****************************************************************************** PP

                                     EEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCS....... CS
                 RNA_pol_Rpb2_6  233 yvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaal....... 303 
                                     yvaqkRk++ GDK+a+rhG+KGv+++ilp+eDmPfl+dG++vDi+lN +gvP Rm+igq+lEt+lg+ a+        
  gi|121636588|ref|YP_976811.1|  866 YVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSgwkvdaa 943 
                                     ****************************************************************************** PP

                                     ..................SSS--B--TT-...-HHHHHHHHHTTS-T........T-EE-EEETTTS-B-SS-EEB-E CS
                 RNA_pol_Rpb2_6  304 ..................egkkvdatvFdgakeeeikelLeeaglea........sGkevlydGrtGekleaeifvGv 355 
                                                        +  v+++vFdga+e+e++ lL+ +  ++        +Gk +l+dGr+Ge++  +++vG+
  gi|121636588|ref|YP_976811.1|  944 kgvpdwaarlpdelleaqPNAIVSTPVFDGAQEAELQGLLSCTLPNRdgdvlvdaDGKAMLFDGRSGEPFPYPVTVGY 1021
                                     ***************99878899*****************965555566666666*********************** PP

                                     EEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                 RNA_pol_Rpb2_6  356 iYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 
                                     +Y++kL+hlv+dKihaRstGpys++tqQPlgGkaq
  gi|121636588|ref|YP_976811.1| 1022 MYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQ 1056
                                     *********************************97 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   1.5e-32   3.8e-29       1      68 []     432     500 ..     432     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 1.5e-32
                 RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvssl.rgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                    q++d+ npls l+h+rr+s+l +ggls+er++ evRd+hpsh+Gr+Cp+eTPEG+n+Gl+ sL+++arv
  gi|121636588|ref|YP_976811.1| 432 QFMDQNNPLSGLTHKRRLSALgPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARV 500
                                    89*****************************************************************98 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   3.2   4.3e-31   1.1e-27       1      65 []     510     576 ..     510     576 .. 0.97
   2 ?   -1.3   0.0         1   2.7e+03      37      55 ..    1029    1047 ..    1025    1050 .. 0.83

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 4.3e-31
                                    EEEEE.TEEEEEEEEEEHHHHTTSEEE-SSS-BETTSCBSSSEEEEECS.SCEEEEEGGG-SEEESS CS
                RNA_pol_Rpb2_45   1 YrkVe.gkvtdevvYLtAdeEekyviAqAnapldeegrfveerVlaRrk.gevelvepeeVdymDVS 65 
                                    YrkV+ g+v+de+vYLtAdeE+++v+AqAn+p+d++grfve+rVl+Rrk geve v+ +eVdymDVS
  gi|121636588|ref|YP_976811.1| 510 YRKVVdGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKaGEVEYVPSSEVDYMDVS 576
                                    9***99*****************************************6549***************9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                                     CBSSSEEEEECSSCEEEEE CS
                RNA_pol_Rpb2_45   37 rfveerVlaRrkgevelve 55  
                                     ++v+++++aR  g + +++
  gi|121636588|ref|YP_976811.1| 1029 HLVDDKIHARSTGPYSMIT 1047
                                     789*******999888876 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0   5.9e-30   1.5e-26       1     190 []     175     373 ..     175     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 5.9e-30
                                    -TSCEEEEE-SSSSSESSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTH CS
                 RNA_pol_Rpb2_2   1 rsngiyvekekdknkisatvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydseds 80 
                                    rs+g+y+    dk+  ++  +   i +rg++l+++ d+++ + +ri++kr+ p+ ++lkAlg +s + I+er        
  gi|121636588|ref|YP_976811.1| 175 RSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTS-EQIVERFG------ 247
                                    89***********999677777789*************************************987.89***999...... PP

                                    HHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHH......CHHHHHHHTTTTSSTTTTTSSSTC.H CS
                 RNA_pol_Rpb2_2  81 qlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilq......krydlgeigreklnkhlglsesle.n 153
                                        e++ ++ ek + + ++eal  i++  +lr+ge+++ +sa+ +l+      krydl ++gr+k+nk+lgl+     +
  gi|121636588|ref|YP_976811.1| 248 --FSEIMRSTLEKDNTVGTDEALLDIYR--KLRPGEPPTKESAQTLLEnlffkeKRYDLARVGRYKVNKKLGLHVGEPiT 323
                                    ..59999********************9..******************************************98654323 PP

                                    H...HHHHHHHHHHHHHHHHTTS............SSS--TTSGGGEEEE CS
                 RNA_pol_Rpb2_2 154 kr.lkaqdilymidrLlslklgr............revDDiDhlgnkRvr 190
                                     + l+ +d+++ i++L+ l+ g+             e+DDiDh+gn+R+r
  gi|121636588|ref|YP_976811.1| 324 SStLTEEDVVATIEYLVRLHEGQttmtvpggvevpVETDDIDHFGNRRLR 373
                                    335*****************997222222222222468**********97 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   2.6e-29   6.7e-26       1      85 [.    1058    1132 ..    1058    1134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.6e-29
                                     BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHT CS
                 RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLqsl 78  
                                     GG+rfGEME++a++ayGaa++L+e+ltikSD    d  gr+k+++a     ivk+e+ +e++ ipe+fk+Ll+eLqsl
  gi|121636588|ref|YP_976811.1| 1058 GGQRFGEMECWAMQAYGAAYTLQELLTIKSD----DTVGRVKVYEA-----IVKGENIPEPG-IPESFKVLLKELQSL 1125
                                     9******************************....***********.....***********.*************** PP

                                     TBEEEEE CS
                 RNA_pol_Rpb2_7   79 gialkll 85  
                                     ++++++l
  gi|121636588|ref|YP_976811.1| 1126 CLNVEVL 1132
                                     ***9986 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0     1e-24   2.6e-21      48     201 ..      99     417 ..      46     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1e-24
                                    EEEESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1  48 irlgkPvvdesdasereiyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeel 127
                                    ++ ++P +d+      +   +e++ +++tY apl+v  + + +   n+ eik++ v++G+ P+M++              
  gi|121636588|ref|YP_976811.1|  99 LSFSDPRFDD-----VKAPVDECKDKDMTYAAPLFVTAEFINN---NTGEIKSQTVFMGDFPMMTEK------------- 157
                                    4445555655.....344449******************9997...*********************............. PP

                                    HHTTS.TTS..SSEEETTCEEEEXEEEE.................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                 RNA_pol_Rpb2_1 128 velkEcpldqGGyFiinGtekvivaqek.................................................... 155
                                               G+FiinGte+v+v+q+                                                     
  gi|121636588|ref|YP_976811.1| 158 -----------GTFIINGTERVVVSQLVrspgvyfdetidkstdktlhsvkvipsrgawlefdvdkrdtvgvridrkrrq 226
                                    ...........********************************************************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                 RNA_pol_Rpb2_1 156 ................................................................................ 155
                                                                                                                    
  gi|121636588|ref|YP_976811.1| 227 pvtvllkalgwtseqiverfgfseimrstlekdntvgtdealldiyrklrpgepptkesaqtllenlffkekrydlarvg 306
                                    ******************************************************************************** PP

                                    ...................................................................XHHHHHHHHHHHH CS
                                    ...................................................................xxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1 156 ...................................................................laGeLlaslfrvl 168
                                                                                                       ++GeL++++ rv+
  gi|121636588|ref|YP_976811.1| 307 rykvnkklglhvgepitsstlteedvvatieylvrlhegqttmtvpggvevpvetddidhfgnrrlrTVGELIQNQIRVG 386
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1 169 lkklerdvkerlqksleklddlmlqllvnakpi 201
                                    + ++er v+er+  + ++ +++++q l+n +p+
  gi|121636588|ref|YP_976811.1| 387 MSRMERVVRERM--TTQDVEAITPQTLINIRPV 417
                                    ************..999***********99876 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00041       1.1       9      71 ..     629     698 ..     621     724 .. 0.66
   2 ?   -2.9   0.0       3.2   8.3e+03      50      76 ..     776     804 ..     771     811 .. 0.72
   3 ?   -2.2   0.1         2     5e+03      50      70 ..     860     880 ..     835     893 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00041
                                    EETTT-EEEESSSEEEEEEEEETTTEEEEEEEECTCEEEEEEE..ESEES..........S-TTEEE-TTCEEEE CS
                  Peptidase_M23   9 aapkgtpVlAaadGtVvfagkkegyGnvviidhgdgystlyah..lskis..........vkegqkVkaGqvIGt 71 
                                    a  +g+ V+A  +G++ +++ +     ++ + h++g+  +y      + +          v++g++V+aGqvI+ 
  gi|121636588|ref|YP_976811.1| 629 AIDAGDVVVAEESGVIEEVSAD-----YITVMHDNGTRRTYRMrkFARSNhgtcanqcpiVDAGDRVEAGQVIAD 698
                                    3346788888888888777663.....55555555544444432222222344566677799***********96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                    EEESEES.S-TTEEE-TTCE.EEEEBSTS CS
                  Peptidase_M23  50 ahlskis.vkegqkVkaGqv.IGtvgstg 76 
                                    a l++   v+ g +V+ G++ +G+v  +g
  gi|121636588|ref|YP_976811.1| 776 ADLDERGiVRIGAEVRDGDIlVGKVTPKG 804
                                    55666445999999***997358877666 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                    EEESEESS-TTEEE-TTCEEE CS
                  Peptidase_M23  50 ahlskisvkegqkVkaGqvIG 70 
                                      l ++ v ++ k++ G++++
  gi|121636588|ref|YP_976811.1| 860 NELVRVYVAQKRKISDGDKLA 880
                                    556678899999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 7751.82
//
Query:       gi|121636589|ref|YP_976812.1|  [L=1316]
Description: DNA-directed RNA polymerase subunit beta' [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-82  277.3   0.0    2.6e-82  276.7   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    3.7e-64  216.7   0.2      8e-64  215.6   0.2    1.6  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    2.6e-38  131.9   0.0    1.7e-35  122.7   0.0    2.5  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.8e-27   96.2   0.0    4.7e-27   94.9   0.0    1.8  2  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.3e-08   33.9   0.0    6.6e-08   32.5   0.0    1.7  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
  ------ inclusion threshold ------
      0.076   13.2   0.0        1.4    9.1   0.0    2.6  2  ApbA_C          Ketopantoate reductase PanE/ApbA C terminal


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.7   0.0   8.7e-86   2.6e-82       4     312 .]       7     417 ..       4     417 .. 0.79

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 8.7e-86
                                    --EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTT.........T---..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxx..... RF
                 RNA_pol_Rpb1_1   4 ikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkk.........eCeg..... 69 
                                    ++e+++g+a+ e+ir+wS++ev+k+eti++++lkPe+ Gl++e+++++++d+eC +Cgk+k          +C +     
  gi|121636589|ref|YP_976812.1|   7 FDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC-YCGKYKRvpfkgiiceRCGVevtra 85 
                                    7899**************************************************.*************999999999*** PP

                                    .....--EEEEEECEEE-HHHHHH...........HHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC....... CS
                                    .....xxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                 RNA_pol_Rpb1_1  70 .....hfGhieLakPvfhigffkl...........ilkilecvckecskllldeekkkllsklkkrekleelk....... 126
                                         ++GhieLa+Pv hi++fk              k+le+++++  +++ +  ++  +++l+  e+   ++       
  gi|121636589|ref|YP_976812.1|  86 kvrreRMGHIELAAPVTHIWYFKGvpsrlgylldlAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVErkavedq 165
                                    **********************************999**************99986644444443333222224445566 PP

                                    ...................................................CCHHHHHHHHCCS-BE-............ CS
                                    ...................................................xxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_1 127 ...................................................krlkaieelckkinlce............ 143
                                                                                       +rl+ i++                     
  gi|121636589|ref|YP_976812.1| 166 rdgelearaqkleadlaeleaegakadarrkvrdggeremrqirdraqrelDRLEDIWST-------Ftklapkqlivde 238
                                    677677666666666666666666666666666666555555554444444333333333.......0333333344444 PP

                                    .........SSSSB-EEE........EEETTEEEEEESSSST.....SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB CS
                                    .........xxxxxxxxx........xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 144 .........kCgavqpkl........eeegeklkaalkkske.....eekeklsaekvkkllkriededvevlgfkssgs 201
                                                               e+ +kl ++++ + e     +  ++ + +k ++ lkr++    +v  f++sg+
  gi|121636589|ref|YP_976812.1| 239 nlyrelvdrY-------GeyftgamgAESIQKLIENFDIDAEaeslrDVIRNGKGQKKLRALKRLK----VVAAFQQSGN 307
                                    4444433330.......0333333344444555554444444544432336667788889999999....9********* PP

                                    -GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 202 rPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneis 281
                                     P  ++l  +PV+Ppe+RP+vqldggr++++Dl++++r++i+rNnrLk+ ++ gape+i+++ek++LQe+v++lfdn  +
  gi|121636589|ref|YP_976812.1| 308 SPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRR 387
                                    ******************************************************************************** PP

                                    SSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 282 glkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                    g +p+t   +rplksls+ LkGK+GrfR+nL
  gi|121636589|ref|YP_976812.1| 388 G-RPVTGPGNRPLKSLSDLLKGKQGRFRQNL 417
                                    *.999*************************9 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.6   0.2   2.7e-67     8e-64       1     265 [.     843    1216 ..     843    1218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 2.7e-67
                                     B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS............ CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg............ 66  
                                     GL+v e+f+ t+g+R+GL+DtA++Ta+sGYl+Rrlv++ +dv+v+++d+ ++ g+ ++    + dg            
  gi|121636589|ref|YP_976812.1|  843 GLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGtlirdpyietsa 920 
                                     9***************************************************************************** PP

                                     ...................................................................B--TT-BHHHH CS
                                     ...................................................................xxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   67 ...................................................................lvepGeavGii 77  
                                                                                                        lv++GeavGi+
  gi|121636589|ref|YP_976812.1|  921 yartlgtdavdeagnvivergqdlgdpeidallaagitqvkvrsvltcatstgvcatcygrsmatgkLVDIGEAVGIV 998 
                                     ****************************************************************************** PP

                                     HHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSECBTTE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   78 aaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiekgikki 155 
                                     aaQSiGePgTQlt++TFH +Gv++  +t G+pr++e+ ++   +   ++ +  v  +++ le+   ++k ++    + 
  gi|121636589|ref|YP_976812.1|  999 AAQSIGEPGTQLTMRTFHQGGVGED-ITGGLPRVQELFEA--RVPRGKAPIADVTGRVR-LEDGERFYKITIVPDDGG 1072
                                     **********************986.69*********443..33333333333333323.333345666666666778 PP

                                     EEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEES...SHHHHHHHHCHHHHHHHHHHHHHHHHHHTT CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  156 krilvkeaekgkeeekelvletegvnlsevlkveevvdageilsn...diaeileilgieaarkallkeiqevykvqg 230 
                                     + ++  + +k ++      +  ++   ++vl+  ++v++g++l +   d++e+l++ g ++++ +l++e+qevy++qg
  gi|121636589|ref|YP_976812.1| 1073 EEVVYDKISKRQRL----RVFKHEDGSERVLSDGDHVEVGQQLMEgsaDPHEVLRVQGPREVQIHLVREVQEVYRAQG 1146
                                     88877755554444....455555667889999999******999999****************************** PP

                                     S---HHHHHHHHHHHTTTSS---SSTT...................................CHCCSSSH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxxxxxxx RF
                 RNA_pol_Rpb1_5  231 vsvndrHlelivdqmtkkgeivavnrs...................................Ginkaels 265 
                                     vs+ d+H+e+iv+qm+++++i++ + +                                   Gi+ka+l+
  gi|121636589|ref|YP_976812.1| 1147 VSIHDKHIEVIVRQMLRRVTIIDSGSTeflpgslidraefeaenrrvvaeggepaagrpvlmGITKASLA 1216
                                     ************************9998888888888888888888888888888888888888888765 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   5.8e-39   1.7e-35       1     165 [.     419     560 ..     419     561 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 5.8e-39
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk 80 
                                    Gkrvdys+Rsvi+++p+lkl++ g+P+ +a  l+ p ++++l      +l++            ++++ ++++++++   
  gi|121636589|ref|YP_976812.1| 419 GKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRL-----VDLNH-----------AQNIKSAKRMVERQ--- 479
                                    9********************************999876544.....33322...........23455667777777... PP

                                    HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHH CS
                 RNA_pol_Rpb1_2  81 lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEa 160
                                     + +++    v ++v+ +  vllNR+P+Lh+l+i+a++  ++e+k+++l+ +v++a+NaDFDGD+m++hlp s ea+aEa
  gi|121636589|ref|YP_976812.1| 480 -RPQVW---DVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEA 555
                                    .55677...68899****************************************************************** PP

                                    HHCSB CS
                 RNA_pol_Rpb1_2 161 eelll 165
                                    + l+l
  gi|121636589|ref|YP_976812.1| 556 RILML 560
                                    *9996 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   7.7e+03      48      83 ..     164     238 ..     133     270 .. 0.60
   2 !   94.9   0.0   1.6e-30   4.7e-27       1     157 []     564     736 ..     564     736 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                    C......................................SSSSSSSSSBESS.SEBEEHHHHHHCCCHCCCCEEE CS
                 RNA_pol_Rpb1_3  48 d......................................sktvtlrpailkp.kelwtgkqtfsrilpneinyer 83 
                                    d                                       +  ++r++  +  ++l  +  tf+++ p+++ +++
  gi|121636589|ref|YP_976812.1| 164 DqrdgelearaqkleadlaeleaegakadarrkvrdggeREMRQIRDRAQRElDRLEDIWSTFTKLAPKQLIVDE 238
                                    444555555555555555555555444444444443333244567777777777888888888888888777766 PP

  == domain 2  score: 94.9 bits;  conditional E-value: 1.6e-30
                                    CSEETTTTEESSS--THHHHHHHHHSSTT..................EEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS. CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTked..................vfidreeaqqllykgvgsdsktvtlrpailkp. 61 
                                    nilsp+sg+P++++  D+++G+y+lT+e                   v+++++ea+++ ++g      ++++r++i+++ 
  gi|121636589|ref|YP_976812.1| 564 NILSPASGRPLAMPRLDMVTGLYYLTTEVpgdtgeyqpasgdhpetgVYSSPAEAIMAADRG------VLSVRAKIKVRl 637
                                    9*************************************************************......899999999998 PP

                                    SE.....................BEEHHHHHHCCCHCCCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHH CS
                 RNA_pol_Rpb1_3  62 ke.....................lwtgkqtfsrilpneinyerkneekdgkvlikngelikGvidkkvvgkksqgslihv 120
                                    ++                      w+ ++t++r+++ne+++ +       + +++++++           kk q  +i+ 
  gi|121636589|ref|YP_976812.1| 638 TQlrppveieaelfghsgwqpgdAWMAETTLGRVMFNELLPLG-------YPFVNKQMH-----------KKVQAAIIND 699
                                    88999999**********************************9.......69*******...........9********* PP

                                    HHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
                 RNA_pol_Rpb1_3 121 lakeygiketvrfldslqrlgfkyllqsgftigigDt 157
                                    la++y +  +++++d+l++ gf+++++sg+t++++D+
  gi|121636589|ref|YP_976812.1| 700 LAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADV 736
                                    ************************************6 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   2.2e-11   6.6e-08       8      80 ..     754     828 ..     748     843 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.2e-11
                                    TCCHHHTTHCHHHHHH..HHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTT CS
                 RNA_pol_Rpb1_4   8 gkledlpgksleelfe..akinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnveg 80 
                                    +k+e++ ++   +  e  +   +i ++a+d++g++ +++++++N+i+++v+sGa G++++++ +ag+ G+ ++++
  gi|121636589|ref|YP_976812.1| 754 DKVEKQFQRGALNHDErnEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPK 828
                                    5555444443333333345555666779*************77***************************99883 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.22   6.5e+02      33      74 ..     919     960 ..     910     972 .. 0.83
   2 ?    9.1   0.0   0.00047       1.4      28      72 ..    1119    1163 ..    1114    1173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
                         ApbA_C  33 spelralvrallkEalavaeaegvelseerleeaveavlekt 74 
                                    s ++r l + +++Ea +v+ ++g+ l + ++++ ++a ++++
  gi|121636589|ref|YP_976812.1| 919 SAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQV 960
                                    67899999***************9988777888888777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00047
                         ApbA_C   28 gellespelralvrallkEalavaeaegvelseerleeaveavle 72  
                                     +e+l+ +  r++  +l++E+ +v++a+gv++ ++ +e +v++ l+
  gi|121636589|ref|YP_976812.1| 1119 HEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLR 1163
                                     567777777889999***************999977777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.98u 0.32s 00:00:01.30 Elapsed: 00:00:00.49
# Mc/sec: 8072.12
//
Query:       gi|121636590|ref|YP_976813.1|  [L=637]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-148  494.9   0.0   7.2e-147  490.1   0.0    2.0  1  Ceramidase_alk   Neutral/alkaline non-lysosomal ceramidase, N
    3.8e-37  127.8   0.0      7e-37  126.9   0.0    1.4  1  Ceramidse_alk_C  Neutral/alkaline non-lysosomal ceramidase, C


Domain annotation for each model (and alignments):
>> Ceramidase_alk  Neutral/alkaline non-lysosomal ceramidase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.1   0.0    8e-151  7.2e-147       3     507 .]       4     482 ..       2     482 .. 0.96

  Alignments for each domain:
  == domain 1  score: 490.1 bits;  conditional E-value: 8e-151
                                    EEEEEEE----SEEEEEESS--SS-EEEEESS--EEEEEEEEESS..S--EEEEEEESSS---HHHHHHHHHHHHHHSTT CS
                 Ceramidase_alk   3 vGvgkaDiTGpvaevnlmGYakleqkasGlhqRlysraFivadae..kkkrvvfvsldaamvsqavrlevlkkLkakygd 80 
                                    vG g+aDiTG++a+++++GY+k++q+++G+hqRl+sraF++ d +   + r++ +++++ + +q+v++evl++L+++ygd
  gi|121636590|ref|YP_976813.1|   4 VGRGIADITGEAADCGMLGYGKSDQRTAGIHQRLRSRAFVFRDDSqdGDARLLLIVAELPLPMQNVNEEVLRRLADLYGD 83 
                                    9*****************************************97653455****************************** PP

                                    T-SGGGEEEEE--BSBEE----SSHHHHGGGTB--HHHHHHHHHHHHHHHHHHHTT-EEEEEEEEEEE--SSEEETTHHH CS
                 Ceramidase_alk  81 lYteenvalsgtHtHsgpggylqyllyqitslGfvkqsfdaivdgivksikrAheslkpgklsvgkgelldaninRSpsa 160
                                    +Y+e+n ++++tHtH+gpggy  ylly++t+ Gf+  +f aivdgiv+s+++Ah++++p+++ +++gel +a+inRSpsa
  gi|121636590|ref|YP_976813.1|  84 TYSEQNTLITATHTHAGPGGYCGYLLYNLTTSGFRPATFAAIVDGIVESVEHAHADVAPAEVPLSHGELYGASINRSPSA 163
                                    ******************************************************************************** PP

                                    HTT-T..T-TT-TTS---EEEEEEEEE...T-EEEEEEE----B-SS-TT--SBB-HHHHHHHHHHHHTT--S......T CS
                 Ceramidase_alk 161 YlanPeeerakYksnvdkemtlLkledasdkkeiGvlnwfavHgtslnntntlisgDNkGvAayllekevekkek.sgke 239
                                    +++nP +++a +++ vd ++tl+++++  ++ ++Gv+ +fa+Hgts++n+n+lisgDNkG+Aay++e++v + ++ +g++
  gi|121636590|ref|YP_976813.1| 164 FDRNPPADKAFFPKRVDPHTTLVRIDR--GEATVGVIHFFATHGTSMTNRNHLISGDNKGFAAYHWERTVGGADYlAGQP 241
                                    ***************************..4568**************************************9988789** PP

                                    T-EEEEE-SS-TTEES-SS.....................SSS..TSSSTS-HHHHHHHHHHHHHHHHHHHHHHT-EEE- CS
                 Ceramidase_alk 240 kfvaafaqsnvGDvspnvlGalCedsgeeCdlekstCegksekcagrgpgkdefestkiigerqfekakellksakeevs 319
                                    +f+aafaq+n GD+spnv G+l                        ++p + ef++t+  g  qfe a + l+ a +++ 
  gi|121636590|ref|YP_976813.1| 242 DFIAAFAQTNPGDMSPNVDGPL----------------------SPEAPPDREFDNTRRTGLCQFEDAFTQLSGA-TPIG 298
                                    ******************9988......................345677669******************9987.6899 PP

                                    S-EEEEEEEEE-TT-EE-GG...TSS-EE-----EE----SS-SSSS-SS---SSS...-HHHHHHT-SS-S---HHHHH CS
                 Ceramidase_alk 320 gkvksrhqyvdmskvevklk...ngtevktckaalGysfaagttdgpgafdftqgeteknplwklvrklllakpskeqke 396
                                      +++r +yvd+ +v v+ +   +g+e +t ++++G+  +agt +gpg   f+qg+   np+w+ +++++ +   + + +
  gi|121636590|ref|YP_976813.1| 299 AGIDARFTYVDLGSVLVRGEytpDGEERRTGRPMFGAGAMAGTDEGPGFHGFRQGR---NPFWDRLSRAMYR-LARPTAA 374
                                    99***************9998788*******************************9...9********7776.9999*** PP

                                    HTTT--EEE--T..T-SS-SS-SEEEEEEEEETTEEEEE-SSEE-HHHHHHHHHHHHHHHGGGT..--EEEEE-SBSS-- CS
                 Ceramidase_alk 397 cqapkpilldtgelkkpyawapeivdvqilriGqlvivavpgEvttmaGrRlreavkealksegkkeeevvlaglaNtYs 476
                                    +qapk i+++    ++  ++++eiv+vq++riG l+++ +pgE t++aG Rlr+ v++ + +     ++v+  g++N+Y 
  gi|121636590|ref|YP_976813.1| 375 AQAPKGIVMPARLPNRIHPFVQEIVPVQLVRIGRLYLIGIPGEPTIVAGLRLRRMVASIVGAD---LADVLCVGYTNAYI 451
                                    *************************************************************98...69************ PP

                                    -EE--HHHHHH--HHHHT-TT-TTHHHHHHH CS
                 Ceramidase_alk 477 hYvtTeeEYqvQrYEgastlyGphtlsayiq 507
                                    hYvtT+eEY  QrYEg+stl+G+++l a +q
  gi|121636590|ref|YP_976813.1| 452 HYVTTPEEYLEQRYEGGSTLFGRWELCALMQ 482
                                    **************************99886 PP

>> Ceramidse_alk_C  Neutral/alkaline non-lysosomal ceramidase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   7.8e-41     7e-37       2     168 .]     485     636 ..     484     636 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 7.8e-41
                                    HHHHHHHHHT..-----------.-GG--B-S--------STT--TT-EEE---.SEETT-EEEEEEEE--GGG---TTS CS
                Ceramidse_alk_C   2 kklaralaagepeelkkgptPpdlsskqlslitgvvvDtaplgksFGdvltdveksyragdtvsvtFvganPrnnlrleg 81 
                                    ++la+a+++g+p +l  g  P+    ++ls + g  +D+     sFG+v+++++++yr+g+ v++ Fv+a P+n+lr++g
  gi|121636590|ref|YP_976813.1| 485 AELAEAMRDGRPVTL--GRRPRP--TRELSWVRGAPADA----GSFGAVIAEPSATYRPGQAVEAVFVSALPNNDLRRGG 556
                                    578999999965555..555554..33788888876665....58*********************************** PP

                                    -SEEEEEE...S-S--EEEEETTSTTEEEEEEEET..TTEEEEEEEEE-..-T--SEEEEEEEEEEEE-TTT--EEEEEE CS
                Ceramidse_alk_C  82 tFlaVerleeeegkkWetvrtDadwetrfeWkrtssllgtsevtieWeipeedakaGtYRiryfGdaksslggkitpfeG 161
                                    t+l+V r+   eg++W ++++D+dw+t f+W+r+    + s+v i+W++p  d+++G+YRi ++G a+   +g +t+f+ 
  gi|121636590|ref|YP_976813.1| 557 TYLEVVRR---EGASWVRIADDGDWATSFRWQRQG--RAGSHVSIRWDVPG-DTTPGQYRIVHHGTARD-RNGMLTAFSA 629
                                    *******8...4789******************95..899*********77.89**************8.5789****** PP

                                    E---EEE CS
                Ceramidse_alk_C 162 tSseFtv 168
                                    t++eFtv
  gi|121636590|ref|YP_976813.1| 630 TTREFTV 636
                                    *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 4271.74
//
Query:       gi|121636591|ref|YP_976814.1|  [L=252]
Description: endonuclease IV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-34  118.0   1.9    4.4e-34  117.8   1.9    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.057   12.7   0.2      0.086   12.1   0.2    1.3  1  BKACE         beta-keto acid cleavage enzyme


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   1.9   4.9e-38   4.4e-34       1     210 []      13     214 ..      13     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 4.9e-38
                                    HHHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHH CS
                   AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraiela 79 
                                    laaa++ G+d v++f+ +++++++    + r+ ++al+++ l i ++ ++  + ++  +    r r  s++ l++++ +a
  gi|121636591|ref|YP_976814.1|  13 LAAAEAEGADVVQIFLGNPQSWKA---PKPRDDAAALKAATLPIYVHAPYLINLASANN----RvRIPSRKILQETCAAA 85 
                                    6789999***************96...6***************************7764....246677*********** PP

                                    HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEE CS
                   AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvg 157
                                    a++Ga  +++h G  +  ++++++  ++r++++l++l  +     v ++lE++ag ++ + +  +++arl d ++++ +g
  gi|121636591|ref|YP_976814.1|  86 ADIGAAAVIVHGG--HVADDNDIDKGFQRWRKALDRLETE-----VPVYLENTAGGDHAMARrfDTIARLWDVIGDTGIG 158
                                    ***********99..99********************999.....*********************************** PP

                                    EEEEHHHHHHHTTTHHHHHHHHHGG...EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                   AP_endonuc_2 158 vclDtgHlliaeedvddalraladr...ikhvHikDakgdlgagrdrhvpigeGei 210
                                    +clDt+H+++a+e + da+++++     i +vH++D++++ g+grdrh+++g G+i
  gi|121636591|ref|YP_976814.1| 159 FCLDTCHTWAAGEALTDAVDRIKAItgrIDLVHCNDSRDEAGSGRDRHANLGSGQI 214
                                    ***********77777777777666666**************************87 PP

>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   9.6e-06     0.086      30      98 ..      80     146 ..      62     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-06
                                    HHHHHHHHHTESEEEE-EE-T.TTS-EE--HHHHHHHHHHHHHHHTTSEEEE-SSTTTTG-HHHHHTHHH CS
                          BKACE  30 eeaveaaeaGAaivHlHaRdp.edgrpsldpelyrevlarirekepdviinlttggastmsaeerlavle 98 
                                    e++++aa+ GAa+v +H     +d +  +  ++ r++l+r++  e+ v + +t gg++ m  ++r+++++
  gi|121636591|ref|YP_976814.1|  80 ETCAAAADIGAAAVIVHGGHVaDDNDIDKGFQRWRKALDRLET-EVPVYLENTAGGDHAM--ARRFDTIA 146
                                    5678999**********9998344555999*************.8**********99876..66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1652.27
//
Query:       gi|121636592|ref|YP_976815.1|  [L=280]
Description: lipoprotein lpqP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-18   66.0   0.3    5.3e-18   65.3   0.3    1.3  1  Esterase_phd   Esterase PHB depolymerase
     0.0049   16.7   0.1      0.014   15.2   0.1    1.7  2  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0049   16.4   0.4      0.012   15.2   0.2    1.7  2  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
        0.2   11.5   0.0        0.2   11.5   0.0    1.7  2  Abhydrolase_3  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.3   1.2e-21   5.3e-18       2     134 ..      45     175 ..      44     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.2e-21
                   Esterase_phd   2 ayrlylppGarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavv 81 
                                    +yrly p G +  + plvvmlhG   s+++  +    + lad   + v yp+   ra   +         r G  +   v
  gi|121636592|ref|YP_976815.1|  45 SYRLYKPVGLPS-SAPLVVMLHGGFGSAKQAERSYGWDELADSEKFLVAYPDGYHRAWNANGGGCCGRPAREGVDDIGFV 123
                                    6**********9.88*****************************************97777777788999********** PP

                   Esterase_phd  82 valvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhsGlalG 134
                                     a+v  ++++  +d+arvyv+G+s Ga ++  la +    faa+++ sG  l 
  gi|121636592|ref|YP_976815.1| 124 RAVVADIANNVSIDPARVYVTGMSNGAIMSYTLA-CNTSIFAAIGVVSGTQLD 175
                                    ***************************9999887.8899**********9875 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.68   3.1e+03      14      25 ..      58      70 ..      56     105 .. 0.79
   2 !   15.2   0.1   3.1e-06     0.014     100     172 ..     132     198 ..     121     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.68
                                   -EEEEEE--.TT- CS
                  Abhydrolase_2 14 qavviflHG.lGd 25
                                   +++v++lHG  G+
  gi|121636592|ref|YP_976815.1| 58 APLVVMLHGgFGS 70
                                   5789999962555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.1e-06
                                    TT..--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEE.ES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-H CS
                  Abhydrolase_2 100 kg..ipssriiigGFSqGaalalylaltlpkklggiva.fsgalplsqklessatavtkklpilqiHgeeDpvvpl 172
                                    +   i+  r+ + G S Ga+++  la  +++ ++ +++ +sg+ + + + +       + +++++iHg+ Dp+v +
  gi|121636592|ref|YP_976815.1| 132 NNvsIDPARVYVTGMSNGAIMSYTLA--CNTSIFAAIGvVSGTQLDPCQSP-------RPVSVIHIHGTADPLVRY 198
                                    4445999**************96544..44444444441567666555544.......5688***********987 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.6e-06     0.012      50      94 ..     125     168 ..      96     175 .. 0.80
   2 ?   -3.0   0.0      0.95   4.3e+03     144     159 ..     183     198 ..     176     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEE CS
                   Peptidase_S9  50 aaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaava 94 
                                    a++  +a++  +d+ r+++tG S+G  ++ +++  ++++F+a+  
  gi|121636592|ref|YP_976815.1| 125 AVVADIANNVSIDPARVYVTGMSNGAIMSYTLAC-NTSIFAAIGV 168
                                    3444445555*******************99999.9999999755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.95
                                    -EEEEEEETT-SSS-T CS
                   Peptidase_S9 144 pplLlihGlaDdrvpp 159
                                    ++++ ihG+aD  v +
  gi|121636592|ref|YP_976815.1| 183 VSVIHIHGTADPLVRY 198
                                    5677899999988866 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.6       2.6   1.2e+04      73      86 ..      13      26 ..      11      28 .. 0.86
   2 ?   11.5   0.0   4.4e-05       0.2      55      90 ..     123     158 ..     108     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.6
                                   EEEEEETHHHHHHH CS
                  Abhydrolase_3 73 ivlaGdSaGGnlaa 86
                                   +++aG S G  laa
  gi|121636592|ref|YP_976815.1| 13 LAFAGCSGGTRLAA 26
                                   6899*****99998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.4e-05
                                    HHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHH CS
                  Abhydrolase_3  55 alrwlaeqawelgadpsrivlaGdSaGGnlaaaval 90 
                                    +   +a+ a + ++dp+r+++ G S G+ +++ +a 
  gi|121636592|ref|YP_976815.1| 123 VRAVVADIANNVSIDPARVYVTGMSNGAIMSYTLAC 158
                                    444555555589******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2060.79
//
Query:       gi|121636593|ref|YP_976816.1|  [L=542]
Description: acyl-CoA dehydrogenase fadE8 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-51  174.5   2.8    1.9e-51  174.1   0.2    2.4  3  AidB_N         Adaptive response protein AidB N-terminal doma
    1.3e-28  100.1   4.7    2.4e-28   99.2   4.7    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.7e-15   57.0   0.0    3.4e-15   56.0   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    2.3e-09   37.6   2.7    4.5e-09   36.7   2.7    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   0.2   4.2e-55   1.9e-51       1     156 []       9     162 ..       9     162 .. 0.98
   2 ?   -0.4   0.1      0.21   9.5e+02      11     108 ..     292     334 ..     284     373 .. 0.52
   3 ?   -3.4   0.0       1.8   8.2e+03      52      70 ..     463     481 ..     444     484 .. 0.64

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 4.2e-55
                         AidB_N   1 NqpppledvnlfasdpaLqeavaregaaeaaeelaalGellgsaevlelarlanrnpPrlrthDrfGrRiDevefhpayh 80 
                                    Nq+pple++n  as p+L ea+ +eg ++  +e++++G++  s +++++++la+rn+P l+thD++G R+Deve++payh
  gi|121636593|ref|YP_976816.1|   9 NQVPPLENYNP-ASSPVLIEALIQEGGQWGLDEVNEVGAISASCQAQRWGELADRNRPILHTHDAYGYRVDEVEYDPAYH 87 
                                    9**********.67799*************************************************************** PP

                         AidB_N  81 almaaaveaglhasaweearegahvaraallyllaqveaGhlCPltmThAavpaLkaepalaeewlpkllsrdYdp 156
                                    +lm++a+++g+ha++w+++r+gahv+raa++ +++ ve+Gh+CP++mT+A vpaL+ +++la+ + p l+sr+Ydp
  gi|121636593|ref|YP_976816.1|  88 ELMRTAITHGMHAAPWADDRPGAHVVRAAKTSVWT-VEPGHICPISMTYAVVPALRYNSELAAVYEPLLTSREYDP 162
                                    *******************************9997.8**************************************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.21
                         AidB_N  11 lfasdpaLqeavaregaaea....aeelaalGellgsaevlelarlanrnpPrlrthDrfGrRiDevefhpayhalmaaa 86 
                                    l + d aL +a++     ++    a++ +a+G++l+ + ++                                       
  gi|121636593|ref|YP_976816.1| 292 LTRLDCALGSATSMRTGLTRavhhAQHRKAFGAYLIDQPLM--------------------------------------- 332
                                    55555555555544333222222345555555555554443....................................... PP

                         AidB_N  87 veaglhasaweearegahvara 108
                                                        r 
  gi|121636593|ref|YP_976816.1| 333 --------------------RN 334
                                    ....................33 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.8
                         AidB_N  52 lanrnpPrlrthDrfGrRi 70 
                                     ++r +P+l   D  G R+
  gi|121636593|ref|YP_976816.1| 463 HVERLRPQLGDLDTIGYRA 481
                                    4567778888888888775 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   4.7   5.3e-32   2.4e-28       1     149 [.     280     436 ..     280     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5.3e-32
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G+  ++e  n +Rl +a++++  +r  l +a+++a++rkafg  lid++l+r  la++a+e+eaa   ++r+a a d+
  gi|121636593|ref|YP_976816.1| 280 GRGVPTIIEMVNLTRLDCALGSATSMRTGLTRAVHHAQHRKAFGAYLIDQPLMRNVLADLAVEAEAATIVAMRMAGATDN 359
                                    689*************************************************************************9999 PP

                                    ----........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    +           r   ++aK+++++  +  a++a++ lGg+Gy e+ ++ rlyr+a ++ i+eG+ ++  ++  r++
  gi|121636593|ref|YP_976816.1| 360 AVRGneteallrRIGLAAAKYWVCKRSTAHAAEALECLGGNGYVEDSGMPRLYREAPLMGIWEGSGNVSALDTLRAM 436
                                    88888889************************************************************888777765 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   7.6e-19   3.4e-15       1      95 [.     176     269 ..     176     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 7.6e-19
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GG.....GEEE CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdap.....gvsv 75 
                                    ++ +TE+q+Gsdv++ +t+a+++++g+y l+G+K w t+a++++++lvla+     + +gls+fl+pr  p      + +
  gi|121636593|ref|YP_976816.1| 176 GMSMTEKQGGSDVRAGTTQATPNADGSYSLTGHK-WFTSAPMCDIFLVLAQ-----APDGLSCFLLPRVLPdgtrnRMFL 249
                                    589*******************************.678899**********.....466********8888655644555 PP

                                    -----BSS-TTS-EEEEEEE CS
                  Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfe 95 
                                    +r+++klG +  +++e++++
  gi|121636593|ref|YP_976816.1| 250 QRLKDKLGNHANASSEVEYD 269
                                    8888************9987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   2.7     1e-12   4.5e-09       7     128 ..     298     420 ..     296     424 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1e-12
                                    HHHHHHHH...HHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---.-HHHHHH CS
                  Acyl-CoA_dh_2   7 alGaAraa...laefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkev.tvedrae 82 
                                    alG A ++   l  +v++a++r+   +g+ l d+p +   la++a + +AA  +  r a + ++ a +g+e  +   r  
  gi|121636593|ref|YP_976816.1| 298 ALGSATSMrtgLTRAVHHAQHRKA--FGAYLIDQPLMRNVLADLAVEAEAATIVAMRMAGA-TDNAVRGNETeALLRRIG 374
                                    677777763335566777777777..*************************9999999988.555666666425555666 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                     ++a+ ++ ++++a++ ++ e  Gg+++ ++s + Rl+R+a  +++
  gi|121636593|ref|YP_976816.1| 375 LAAAKYWVCKRSTAHAAEALECLGGNGYVEDSGMPRLYREAPLMGI 420
                                    677799**********************************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 4126.65
//
Query:       gi|121636594|ref|YP_976817.1|  [L=312]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-31  107.0   0.0    4.1e-18   65.6   0.1    2.1  2  ECH_1          Enoyl-CoA hydratase/isomerase
    1.3e-16   61.0   0.0    5.9e-16   58.9   0.0    1.8  1  ECH_2          Enoyl-CoA hydratase/isomerase
     0.0051   15.8   0.1     0.0091   15.0   0.1    1.3  1  SDH_sah        Serine dehydrogenase proteinase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.068   13.3   0.0    2.1  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
       0.28   11.1   1.6       0.38   10.7   0.3    1.9  2  DUF3756        Protein of unknown function (DUF3756)


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.1e-13   3.9e-10       4      67 ..      22      85 ..      19     107 .. 0.86
   2 !   65.6   0.1   1.1e-21   4.1e-18      76     225 ..     124     270 ..     115     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.1e-13
                                   TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC CS
                          ECH_1  4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek 67
                                     +a i++nrPe+ Na+ a +  El +  e+++ d+ v ++ + G+++ F+aG dl + ae++ 
  gi|121636594|ref|YP_976817.1| 22 GRIARITFNRPEKGNAIIADTPLELSALVERADLDPGVHVILVSGRGEGFCAGFDLSAYAEGSS 85
                                   579******************************************************9999865 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 1.1e-21
                                    CHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                          ECH_1  76 evlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                     +   +  l++ +kp++  + G++++GG  +al +D viaa +a++g + +++  +p+ag    +a ++G ++A+++l +
  gi|121636594|ref|YP_976817.1| 124 RFVRGFASLMHADKPTVVKIHGYCVAGGTDIALHADQVIAAADAKIGYPPTRVWGVPAAG---LWAHRLGDQRAKRLLFT 200
                                    56667889999******************************************99**555...799************** PP

                                    T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfe 225
                                    g+ i+++ a+++Gl  ++   ++l e +  l++++a  + + l ++k aln +l ++ ++ + + +++f 
  gi|121636594|ref|YP_976817.1| 201 GDCITGAQAAEWGLAVEAPEPADLDERTERLVARIAALPVNQLIMVKLALNSALLQQGVATSRMVSTVFD 270
                                    *****************9888*******************************999998888887777776 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   1.7e-19   5.9e-16       2     187 ..      25     234 ..      24     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.7e-19
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS................ CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakeg................ 65 
                                    ++it+nrp++ Na+  +   +l++ +++ + d+ v++++++g g ++fCAG D+ a +e  +++                
  gi|121636594|ref|YP_976817.1|  25 ARITFNRPEKGNAIIADTPLELSALVERADLDPGVHVILVSGRG-EGFCAGFDLSAYAEGSSSTggggayqgtvldgktq 103
                                    689***************************************88.9*************9999899*********99888 PP

                                    ..........-THH...HHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT---- CS
                          ECH_2  66 ..........kkee...eeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPD 132
                                              +       +++++  +  + + +  kp+v  ++G+++ gG+ +++h+   ++  ++++  P t++  +P 
  gi|121636594|ref|YP_976817.1| 104 avnhlpnqpwD--PmidYQMMSRFVRGFASLMHADKPTVVKIHGYCVAGGTDIALHADQVIAAADAKIGYPPTRVWGVPA 181
                                    87776654331..12336778888888889999**********************************************8 PP

                                    TTHHHHHHCSSTTHHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT CS
                          ECH_2 133 vGgsyfLsrlpgelGlylalTGarlkgadalaaglathyvpseklealeeaLael 187
                                     G   +  rl  + ++ l  TG+ ++ga+a + gla    + ++l++ +e+L + 
  gi|121636594|ref|YP_976817.1| 182 AG--LWAHRLGDQRAKRLLFTGDCITGAQAAEWGLAVEAPEPADLDERTERLVAR 234
                                    77..5889*******************************9999999988888764 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.5e-06    0.0091     117     166 ..     134     183 ..     127     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-06
                        SDH_sah 117 ehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqypaas 166
                                    +   +t v +  y ++GGt ial ad++i   +a +G    ++  +paa 
  gi|121636594|ref|YP_976817.1| 134 HADKPTVVKIHGYCVAGGTDIALHADQVIAAADAKIGYPPTRVWGVPAAG 183
                                    334456667888************************98888888888875 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.068      38      83 ..      27      73 ..      15      77 .. 0.85
   2 ?   -1.4   0.0      0.74   2.6e+03      39      58 ..     138     157 ..     116     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                   B--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEE.EETTTEE CS
                  ACP_syn_III_C 38 vvvnldeyGntsaasiplaLdeaveegklkpgdlvllvg.fGaGltw 83
                                   ++ n  e Gn   a+ pl L+ +ve+ +l+pg +v+lv+  G G+  
  gi|121636594|ref|YP_976817.1| 27 ITFNRPEKGNAIIADTPLELSALVERADLDPGVHVILVSgRGEGFCA 73
                                   55666788************************998876548888765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.74
                                    --THHHH-B-GGGHHHHHHH CS
                  ACP_syn_III_C  39 vvnldeyGntsaasiplaLd 58 
                                    ++ ++ +G+++a +  +aL+
  gi|121636594|ref|YP_976817.1| 138 PTVVKIHGYCVAGGTDIALH 157
                                    45567789999999999988 PP

>> DUF3756  Protein of unknown function (DUF3756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00011      0.38      19      33 ..     205     219 ..     197     222 .. 0.87
   2 ?   -3.0   0.1         2   7.1e+03       6      19 ..     227     240 ..     227     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                        DUF3756  19 iGayaaEWALSTEpP 33 
                                     Ga aaEW L  E+P
  gi|121636594|ref|YP_976817.1| 205 TGAQAAEWGLAVEAP 219
                                    5************99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                        DUF3756   6 rTnAlvakqakisi 19 
                                    rT  lva+ a++++
  gi|121636594|ref|YP_976817.1| 227 RTERLVARIAALPV 240
                                    78889999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2305.75
//
Query:       gi|121636595|ref|YP_976818.1|  [L=240]
Description: hypothetical protein BCG_0723 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-17   61.2   0.3    1.7e-16   60.2   0.3    1.6  1  PaaX      PaaX-like protein
    1.6e-07   31.5   0.2    4.2e-07   30.2   0.2    1.8  1  PaaX_C    PaaX-like protein C-terminal domain
     0.0012   19.0   6.1     0.0012   19.0   6.1    2.2  2  MLTR_LBD  MmyB-like transcription regulator ligand binding do
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.019   15.0   0.0    1.2  1  DUF5457   Family of unknown function (DUF5457)


Domain annotation for each model (and alignments):
>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.3   3.7e-20   1.7e-16       2      69 ..       6      66 ..       5      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.7e-20
                           PaaX  2 arSlivtlygdyveprggaiwlgsLirllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69
                                   arS++++++   ++++++ + +++Li+l+a++Gi+e+++R+al+R++ aG+lvr+++g    YrLsd+
  gi|121636595|ref|YP_976818.1|  6 ARSVVLSVL---LGAHPAWATASELIQLTADFGIKETTLRVALTRMVGAGDLVRSADG----YRLSDR 66
                                   8********...**********************************************....*****8 PP

>> PaaX_C  PaaX-like protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.2   9.4e-11   4.2e-07      44      91 ..     186     229 ..     153     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 9.4e-11
                         PaaX_C  44 FlvrtlllheyrkllfrDPgLPeellpedWpGaaarelfrelyrelae 91 
                                    F+v   ++   r+ l++DP+LP+ellp+dWpGa  r+++++ + ++a+
  gi|121636595|ref|YP_976818.1| 186 FVVAAAMV---RH-LLTDPMLPAELLPADWPGAGLRAAYHDFATAMAK 229
                                    55555566...55.566********************99998887765 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9       0.2   8.8e+02      46      69 ..      64      87 ..      44     122 .. 0.70
   2 !   19.0   6.1   2.6e-07    0.0012       7      92 ..     143     237 ..     138     240 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                       MLTR_LBD 46 perNllrlvfldpglrpliedwee 69
                                    +r l+r+  +d+++rp+ + w+ 
  gi|121636595|ref|YP_976818.1| 64 SDRLLARQRRQDEAMRPRTRAWHG 87
                                   556677777778888888877764 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.6e-07
                       MLTR_LBD   7 rlLdalepvPAlVldrrwdvlaaNraaraLlgd......paalpeperNllrlvfldpglrpli..edweeva.ralvar 77 
                                    r+L+a +++PA   ++ wd+  + +a+++Llgd      ++ +    + ++r +++dp l + +  +dw  +  ra+ ++
  gi|121636595|ref|YP_976818.1| 143 RMLTARDEAPADLAGQLWDLSGWTEAGHRLLGDmaaatdMPGRFVVAAAMVRHLLTDPMLPAELlpADWPGAGlRAAYHD 222
                                    9********************************7764333333346799*********8865555699*76643888899 PP

                       MLTR_LBD  78 Lraeaarrpddpala 92 
                                    + +++a+r d  +l 
  gi|121636595|ref|YP_976818.1| 223 FATAMAKRRDATQLL 237
                                    999999998877775 PP

>> DUF5457  Family of unknown function (DUF5457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.3e-06     0.019      21      70 ..      18      67 ..       7      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                        DUF5457 21 kPleltkseifWkikdlkvtErqvrevLdwLVkkkkvleklgkYqldkvE 70
                                    P++ t+se++    d  + E  +r +L ++V    ++++++ Y l+ + 
  gi|121636595|ref|YP_976818.1| 18 HPAWATASELIQLTADFGIKETTLRVALTRMVGAGDLVRSADGYRLSDRL 67
                                   7********************************************98664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1567.42
//
Query:       gi|121636596|ref|YP_976819.1|  [L=263]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-42  144.4   0.0    4.5e-42  144.1   0.0    1.2  1  ECH_1          Enoyl-CoA hydratase/isomerase
    4.5e-20   72.4   0.1    2.3e-19   70.1   0.1    1.9  1  ECH_2          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.055   13.4   0.1          1    9.3   0.0    2.1  2  Peptidase_S49  Peptidase family S49


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   0.0   7.6e-46   4.5e-42       2     200 ..       9     205 ..       8     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 7.6e-46
                                    EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHH CS
                          ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelw 81 
                                    ++  v  + lnrP   Na++  + + l +a+e+++ d ++ ++vL G ++ F+aGadlk+      + + + +       
  gi|121636596|ref|YP_976819.1|   9 RKGRVTTVILNRPASRNAVNGPTAAALCAAFEQFDRDDAASVAVLWGAGGTFCAGADLKAFGTP--EANSVHRTGPGPMG 86 
                                    56779999*****************************************************996..56666666666666 PP

                                    HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEH CS
                          ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisa 161
                                       + + kpviaav+G+a++GGlelal cD+++a ++a+fg    + G+    ggt +l+r +G+s+A+ ++l+g+ + a
  gi|121636596|ref|YP_976819.1|  87 PSRMMLSKPVIAAVSGYAVAGGLELALWCDLRVAEEDAVFGVFCRRWGVPLIDGGTVRLPRLIGHSRAMDMILTGRGVPA 166
                                    6667789*****************************************98889*************************** PP

                                    HHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHH CS
                          ECH_1 162 qealkvGlvdkvvpeeqlleealelaeklaekspaalrq 200
                                    +eal +Gl ++vvp+ q  + a ela++la  +++ lr 
  gi|121636596|ref|YP_976819.1| 167 DEALAMGLANRVVPKGQARQAAEELAAQLAALPQQCLRS 205
                                    ******************************888777665 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   3.9e-23   2.3e-19       2     189 ..      14     196 ..      13     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.9e-23
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    ++++Lnrp++ Na++ + + al +a++++++dd++++ vl gag   fCAG D++a+ + + ++ ++     +    +  
  gi|121636596|ref|YP_976819.1|  14 TTVILNRPASRNAVNGPTAAALCAAFEQFDRDDAASVAVLWGAG-GTFCAGADLKAFGTPEANSVHR-----TGPGPMGP 87 
                                    6899**************************************99.89**********9998887555.....44556666 PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkga 160
                                        ++kpv+a + G+++ gG+ l++ + +rv+ e++vf +   + G+    Gg+  L+rl g + ++ + lTG+ + + 
  gi|121636596|ref|YP_976819.1|  88 SRMMLSKPVIAAVSGYAVAGGLELALWCDLRVAEEDAVFGVFCRRWGVPLIDGGTVRLPRLIGhSRAMDMILTGRGVPAD 167
                                    777799*****************************************988789*******976377999*********** PP

                                    HHHHTTS--EE--GGGHHHHHHHHHTT.. CS
                          ECH_2 161 dalaaglathyvpseklealeeaLaeles 189
                                    +ala+gla+ +vp+ +  + +e+La++  
  gi|121636596|ref|YP_976819.1| 168 EALAMGLANRVVPKGQARQAAEELAAQLA 196
                                    ***************99999999987533 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00017         1       6      41 ..      93     128 ..      90     130 .. 0.93
   2 ?    1.8   0.0     0.034     2e+02     114     152 ..     155     193 ..     150     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                                    T--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE- CS
                  Peptidase_S49   6 kkPvvasaenvaaSggYylasaadkivanpstivgs 41 
                                     kPv+a ++++a  gg  la  +d  va+  ++ g+
  gi|121636596|ref|YP_976819.1|  93 SKPVIAAVSGYAVAGGLELALWCDLRVAEEDAVFGV 128
                                    59***************************9999875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.034
                                    HHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCH CS
                  Peptidase_S49 114 vdkiAegrvltgqqAlklgLvdelgtvddavaeleelak 152
                                    +d i +gr   +++Al+ gL+ ++    +a + +eela+
  gi|121636596|ref|YP_976819.1| 155 MDMILTGRGVPADEALAMGLANRVVPKGQARQAAEELAA 193
                                    5666677888899*******************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1902.22
//
Query:       gi|121636597|ref|YP_976820.1|  [L=964]
Description: transmembrane transport protein mmpL5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.1e-223  739.7  38.0   4.8e-114  380.7  12.7    2.7  3  MMPL           MMPL family
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.092   12.2   0.0    1.6  1  LRR_9          Leucine-rich repeat
       0.65   10.0   6.0          4    7.5   0.3    2.6  2  DUF1664        Protein of unknown function (DUF1664)
        3.6    8.2   7.7        1.1    9.8   1.7    2.3  2  Hrs_helical    Hepatocyte growth factor-regulated tyrosine ki
        5.7    6.1   9.6        7.8    5.7   4.9    2.6  2  WBS28          Williams-Beuren syndrome chromosomal region 28
        7.1    6.4   8.5       0.74    9.6   1.7    2.1  2  Mer2           Mer2


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.7  12.7  1.6e-117  4.8e-114       1     333 []      63     393 ..      63     393 .. 0.99
   2 ?   -1.3   0.2      0.28   8.3e+02      81     118 ..     501     537 ..     420     571 .. 0.50
   3 !  369.1  11.9  5.7e-114  1.7e-110       7     332 ..     618     949 ..     612     950 .. 0.98

  Alignments for each domain:
  == domain 1  score: 380.7 bits;  conditional E-value: 1.6e-117
                           MMPL   1 slspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaaf 80 
                                    s+sp+ a+s+ +m+++++ f+e +dsd+++++vl eg++ lg+ aa+a++d+++ +l++dt+hv++++df++dp +a+++
  gi|121636597|ref|YP_976820.1|  63 SMSPDAAPSMISMKHIGKVFEE-GDSDSAAMIVL-EGQRPLGD-AAHAFYDQMIGRLQADTTHVQSLQDFWGDPLTATGA 139
                                    689*******************.***********.********.************************************ PP

                           MMPL  81 vSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviL 160
                                    +S+Dgkaa+++v+l+g++g+++a+esv+a++++ve++ p+ g+kv+vtG+aa++ad+++a+dr+l++ie+vt+ vi+v+L
  gi|121636597|ref|YP_976820.1| 140 QSSDGKAAYVQVKLAGNQGESLANESVEAVKTIVERLAPPPGVKVYVTGSAALVADQQQAGDRSLQVIEAVTFTVIIVML 219
                                    ******************************************************************************** PP

                           MMPL 161 livyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeav 240
                                    l+vyrS+++ +++l +vv++lla++g v++l ++ +++lstf+++llvvl+ia++tDYa++L++Ry+e+++ g+dre+a+
  gi|121636597|ref|YP_976820.1| 220 LLVYRSIITSAIMLTMVVLGLLATRGGVAFLGFHRIIGLSTFATNLLVVLAIAAATDYAIFLIGRYQEARGLGQDRESAY 299
                                    ******************************************************************************** PP

                           MMPL 241 iravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.lakprrkrkkrwW 319
                                    ++++++t++vv+++Glt+a+a+++L+++rlp+++++Gv++a+G++++v+++lTl PA++++++r++ l +p+r ++ r W
  gi|121636597|ref|YP_976820.1| 300 YTMFGGTAHVVLGSGLTIAGATFCLSFTRLPYFQTLGVPLAIGMVIVVAAALTLGPAIIAVTSRFGkLLEPKRMARVRGW 379
                                    ******************************************************************************** PP

                           MMPL 320 rrlgrlvvrrPlpv 333
                                    r++g+++vr+P p+
  gi|121636597|ref|YP_976820.1| 380 RKVGAAIVRWPGPI 393
                                    ***********985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.28
                           MMPL  81 vSkDgkaaralvtlegdpgsteadesvaairaaveear 118
                                    +S  g++  ++ +++ +  +    e+v++i++ +++ +
  gi|121636597|ref|YP_976820.1| 501 ISMQGTSQKLTEKYN-QDLTARMLEQVNDIQSNIDQME 537
                                    444444444444444.3334444444444444444444 PP

  == domain 3  score: 369.1 bits;  conditional E-value: 5.7e-114
                           MMPL   7 aesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.............ls 72 
                                    +++   m+rl++ +p+ +a ++++i++++++++++l +++++++++++++++++d++++ge++d+             ++
  gi|121636597|ref|YP_976820.1| 618 NNLLPLMQRLDTLMPQlTAMMPEMIQTMKSMKAQMLSMHSTQEGLQDQMAAMQEDSAAMGEAFDAsrnddsfylppevFD 697
                                    6667789**********************************************************999999999999999 PP

                           MMPL  73 dpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdasdrdlk 146
                                    +pd   + ++f+S+Dg+a+r+++++egdp s+++++++a+i++a++ea    pleg +++++G+aa+++dl+d+ ++dl+
  gi|121636597|ref|YP_976820.1| 698 NPDfqrGLEQFLSPDGHAVRFIISHEGDPMSQAGIARIAKIKTAAKEAIkgtPLEGSAIYLGGTAAMFKDLSDGNTYDLM 777
                                    **99999************************************************************************* PP

                           MMPL 147 lievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsR 225
                                    ++++ +l++i++i+li++rS+vaa+++++tvv+sl+a++gl vli++++lg+el++ vl+++v++l+avG+DY+llLv+R
  gi|121636597|ref|YP_976820.1| 778 IAGISALCLIFIIMLIITRSVVAAAVIVGTVVLSLGASFGLsVLIWQHILGIELHWLVLAMAVIILLAVGADYNLLLVAR 857
                                    ******************************************************************************** PP

                           MMPL 226 yreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGr 304
                                    ++ee++ag+++  ++ira++++g+vvtaaGl++a++m++++v++l+v+aqvG++i++G+l+d+liv++++ P++++llG+
  gi|121636597|ref|YP_976820.1| 858 LKEEIHAGINT--GIIRAMGGSGSVVTAAGLVFAFTMMSFAVSELTVMAQVGTTIGMGLLFDTLIVRSFMtPSIAALLGK 935
                                    ***********..******************************************************************* PP

                           MMPL 305 aalakprrkrkkrwWrrlgrlvvrrPlp 332
                                    +           +wW+++   v++rP+p
  gi|121636597|ref|YP_976820.1| 936 W-----------FWWPQV---VRQRPVP 949
                                    *...........***999...9999987 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05     0.092      15      97 ..     577     655 ..     564     671 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                          LRR_9  15 yinairer.eldlrgykipvienlGatldqfdtidlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleel 93 
                                    ++ +ir     + + y ipv   l +  d +d id+  +di++l  +Pl++rl tl+    +++ + +++ +++ ++++ 
  gi|121636597|ref|YP_976820.1| 577 FFRPIRSYfYWEKHCYDIPVCWSLRSVFDTLDGIDVMTEDINNL--LPLMQRLDTLMP---QLTAMMPEMIQTMKSMKAQ 651
                                    555666541346789***************************98..9********984...4555666666666666666 PP

                          LRR_9  94 vltn 97 
                                    +l+ 
  gi|121636597|ref|YP_976820.1| 652 MLSM 655
                                    6655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.0     0.012        37      57     104 ..     522     565 ..     501     582 .. 0.40
   2 ?    7.5   0.3    0.0013         4      47     103 ..     624     680 ..     613     685 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                        DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                                    + ++ ++++s+id+++     +  +++++++  +e+  +++ +  dve
  gi|121636597|ref|YP_976820.1| 522 MLEQVNDIQSNIDQME----RMHSLTQQMADVTHEMVIQMTGMVVDVE 565
                                    2222222222222222....2222222222222222222222333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0013
                        DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                     ++l++++ +l+a   ++ + ++++ +++ ++  +++ +++++++++ed +++ge +
  gi|121636597|ref|YP_976820.1| 624 MQRLDTLMPQLTAMMPEMIQTMKSMKAQMLSMHSTQEGLQDQMAAMQEDSAAMGEAF 680
                                    578899999999999999999999999999999999999999999999999988765 PP

>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       0.2     6e+02      66      87 ..     521     542 ..     501     575 .. 0.65
   2 ?    9.8   1.7   0.00038       1.1      33      79 ..     627     677 ..     624     687 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
                    Hrs_helical  66 dklaqikearealdalreehke 87 
                                      l+q+++ ++ +d++ + h+ 
  gi|121636597|ref|YP_976820.1| 521 RMLEQVNDIQSNIDQMERMHSL 542
                                    4455555555555555555542 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                    Hrs_helical  33 vqslFqkltamhsqllkriqeqeek....raeyeslqdklaqikeareald 79 
                                    +++l  +ltam +++++++++++ +     +++e+lqd++a ++e  +a+ 
  gi|121636597|ref|YP_976820.1| 627 LDTLMPQLTAMMPEMIQTMKSMKAQmlsmHSTQEGLQDQMAAMQEDSAAMG 677
                                    5788899******9999998877652222677899********99888774 PP

>> WBS28  Williams-Beuren syndrome chromosomal region 28 protein homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.035     1e+02      46     124 ..     280     356 ..     264     369 .. 0.80
   2 ?    5.7   4.9    0.0026       7.8      88     149 ..     788     844 ..     759     854 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.035
                          WBS28  46 WvsGLaqeaqGstskqahppaevaacplgralraglaLlevPvwLvlrgprLvlaavlgcaralglalklgaweqlGLs 124
                                    ++ G  qea+G  +++  +   +   +   +l +gl++     ++ l  +rL + + lg+  a+g+ + ++a  +lG +
  gi|121636597|ref|YP_976820.1| 280 FLIGRYQEARGLGQDRESAYYTMFGGTAHVVLGSGLTIAGA--TFCLSFTRLPYFQTLGVPLAIGMVIVVAAALTLGPA 356
                                    678999******88888887777778888889999998877..6667778999*9****99999999988888777754 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0026
                          WBS28  88 vwLvlrgprLvlaavlgcaralglalklgaweqlGLsvatwtdlllsclhsLmLvaLLllll 149
                                     +++l  +r    +v+ +a  +g ++ l+     GLsv +w+++l   lh L+L+  +++ll
  gi|121636597|ref|YP_976820.1| 788 FIIMLIITR----SVVAAAVIVG-TVVLSLGASFGLSVLIWQHILGIELHWLVLAMAVIILL 844
                                    333333333....3333333333.222555678*********************98888877 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.7   0.00025      0.74     113     173 ..     503     566 ..     488     568 .. 0.80
   2 ?    0.1   0.7       0.2   5.9e+02     157     188 ..     634     665 ..     603     682 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                           Mer2 113 lkvkkhksntdtksnLtellekkeakileeidkkqt...kleksvdttqelllnvnkQledvne 173
                                    ++  ++k   +++++Lt  + ++ + i ++id+ ++    +++  d+t+e+++ +   + dv+e
  gi|121636597|ref|YP_976820.1| 503 MQGTSQKLTEKYNQDLTARMLEQVNDIQSNIDQMERmhsLTQQMADVTHEMVIQMTGMVVDVEE 566
                                    55566777788999**************99997655444789999*********9988877776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                           Mer2 157 tqelllnvnkQledvnevllSlskdlenlstr 188
                                    +  ++  + + +++++  +lS+    e l+++
  gi|121636597|ref|YP_976820.1| 634 LTAMMPEMIQTMKSMKAQMLSMHSTQEGLQDQ 665
                                    33445555555555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (964 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1493  (0.0832729); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.95u 0.31s 00:00:01.26 Elapsed: 00:00:00.49
# Mc/sec: 5937.62
//
Query:       gi|121636598|ref|YP_976821.1|  [L=142]
Description: membrane protein mmpS5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-64  216.2   0.0    1.6e-64  216.0   0.0    1.0  1  Mycobact_memb  Mycobacterium membrane protein


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.0   8.8e-69   1.6e-64       1     139 []       5     142 .]       5     142 .] 0.99

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 8.8e-69
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEB-B----TT-----B---TTS------S CS
                  Mycobact_memb   1 lkrlWiplvivvvvvvggltvsrlhsifgsekrasvadklaedskpfnPkkvkyevfGpagtvadisyldadaepqridg 80 
                                    lkr+Wipl+i+vvv+++g+tv+r++++fgse   ++ +++a+d +pf+Pk v+yev+G+ g++++i+yld+da+pqridg
  gi|121636598|ref|YP_976821.1|   5 LKRAWIPLLILVVVAIAGFTVQRIRTFFGSEGILVTPKVFADDPEPFDPKVVEYEVSGS-GSYVNINYLDLDAKPQRIDG 83 
                                    69********************************************************9.******************** PP

                                    -SS--B--EE-SSS------B--SS-S------BBTTB---------S-TTSSS--S-- CS
                  Mycobact_memb  81 aalPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevnaltyClvksa 139
                                    aalPWslt+ktt++++++n++aqg+++si+Cri+vdg+vkder+++ v+altyC+vksa
  gi|121636598|ref|YP_976821.1|  84 AALPWSLTLKTTAPSAAPNILAQGDGTSITCRITVDGEVKDERTATGVDALTYCFVKSA 142
                                    *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1029.98
//
Query:       gi|121636599|ref|YP_976822.1|  [L=165]
Description: hypothetical protein BCG_0727 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   17.7   0.0     0.0045   16.9   0.0    1.5  1  MarR      MarR family
     0.0045   16.9   1.6      0.011   15.6   0.4    2.0  2  MarR_2    MarR family
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.026   14.7   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
      0.071   13.2   0.8       0.18   11.9   0.1    2.0  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-06    0.0045      18      58 ..      51      91 ..      31      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                           MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                   +s  eLa +l  s++ +++ ++ L++ G+ieR    +DrR 
  gi|121636599|ref|YP_976822.1| 51 QSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRT 91
                                   5566************************************6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   2.5e-06     0.011       3      61 ..      32      90 ..      30      91 .. 0.92
   2 ?   -0.2   0.0      0.21   9.3e+02      11      21 ..     122     135 ..     122     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   lt+   r+L++L   ++++ +  ela +l  s + +s   + L + G++er +  +D+R
  gi|121636599|ref|YP_976822.1| 32 LTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRR 90
                                   7888889****777777779********************************9999**9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                    HHHHHCTTTS...E CS
                         MarR_2  11 LaaLgrrpgr...d 21 
                                    L aLg++p++   +
  gi|121636599|ref|YP_976822.1| 122 LRALGDAPPQrsrR 135
                                    67888888864332 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.7e-06     0.026      13      47 ..      49      83 ..      38     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                         HTH_34 13 deadfvelkealeatdgnLsvhlkkLekagYievd 47
                                   ++ + +el +al a++g +s+++++L + g+ie+ 
  gi|121636599|ref|YP_976822.1| 49 ERQSSEELATALAASSGGISTNARMLIQFGFIERL 83
                                   55667899************************974 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     4e-05      0.18      14      56 ..      38      82 ..      33      85 .. 0.93
   2 ?   -1.2   0.1      0.48   2.1e+03      34      48 ..     125     139 ..     107     143 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                                   HHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 14 rilraL..araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   r+l +L  +++e ++ +ela +l  s   +s + r L + g++e+
  gi|121636599|ref|YP_976822.1| 38 RLLGWLlvCDPERQSSEELATALAASSGGISTNARMLIQFGFIER 82
                                   6788899999*********************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.48
                                    HTS-HHHHHHHHHHH CS
                         HTH_20  34 ldlskntlsyHLrvL 48 
                                    l+ ++ + s++Lr++
  gi|121636599|ref|YP_976822.1| 125 LGDAPPQRSRRLREM 139
                                    244555556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1245.07
//
Query:       gi|121636600|ref|YP_976823.1|  [L=165]
Description: hypothetical protein BCG_0728c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   76.1   5.2    2.1e-21   75.4   5.2    1.4  1  DUF3060   Protein of unknown function (DUF3060)
  ------ inclusion threshold ------
        3.1    7.9   7.2        6.2    6.9   7.2    1.5  1  DUF5061   17 kDa common-antigen outer membrane protein


Domain annotation for each model (and alignments):
>> DUF3060  Protein of unknown function (DUF3060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   5.2   2.3e-25   2.1e-21       1      58 []     101     159 ..     101     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.3e-25
                        DUF3060   1 vsGssNtvtltGeCeavtVsGssNtVtvdsvdk.itvsGldNtVtyksGePkvsdtGsn 58 
                                    v Gs+Nt+t++G+Ce+vtV G++N++ +d++d+ + v+GldNtVtyk+G+P++++ G +
  gi|121636600|ref|YP_976823.1| 101 VAGSDNTLTVNGTCETVTVGGANNKIAFDRIDErLVVVGLDNTVTYKNGDPTIDNLGAG 159
                                    89******************************************************976 PP

>> DUF5061  17 kDa common-antigen outer membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.2   0.00069       6.2       3      76 ..      22     117 ..      20     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00069
                        DUF5061   3 alval.llLaaCalkqeaasqeeegevvekp.......................leeflsqepagasavLddsefGksvr 58 
                                    al+a+ l+La+C+   ++++ +++++    +                       + ++l+  + g++a+Ld ++ Gks++
  gi|121636600|ref|YP_976823.1|  22 ALAAAaLPLAGCSSTANPPAATTTPATATTTtatsgptaaptvttgesttasiqIGDMLTYGSIGTTATLDCAD-GKSLN 100
                                    444444********88777766666644444779999****************99***************8665.99999 PP

                        DUF5061  59 vlveekftsAsGreCrrl 76 
                                    v   +  ++ +G  C   
  gi|121636600|ref|YP_976823.1| 101 VAGSDNTLTVNGT-CETV 117
                                    9877766666663.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1182.68
//
Query:       gi|121636601|ref|YP_976824.1|  [L=124]
Description: hypothetical protein BCG_0729c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-22   76.4   1.0    9.7e-22   76.4   1.0    1.6  2  DUF3060   Protein of unknown function (DUF3060)


Domain annotation for each model (and alignments):
>> DUF3060  Protein of unknown function (DUF3060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.26   4.6e+03      34      37 ..      37      40 ..      30      50 .. 0.52
   2 !   76.4   1.0   5.4e-26   9.7e-22       1      58 []      55     113 ..      55     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.26
                        DUF3060 34 itvs 37
                                   +t  
  gi|121636601|ref|YP_976824.1| 37 VTGQ 40
                                   2222 PP

  == domain 2  score: 76.4 bits;  conditional E-value: 5.4e-26
                        DUF3060   1 vsGssNtvtltGeCeavtVsGssNtVtvdsvdk.itvsGldNtVtyksGePkvsdtGsn 58 
                                    v+G++N vt+ G+C+avtV+GssNtV++d++ + itv+G+d tV++++G+P ++d+G++
  gi|121636601|ref|YP_976824.1|  55 VNGTQNIVTALGTCWAVTVMGSSNTVVADTIINdITVYGWDETVFFRNGDPFIWDRGRE 113
                                    89*******************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 942.15
//
Query:       gi|121636602|ref|YP_976825.1|  [L=196]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-18   66.5   2.7    4.6e-18   65.9   2.7    1.3  1  TetR_C_33  Tetracyclin repressor-like, C-terminal domain
    4.3e-05   23.2   0.0    7.8e-05   22.4   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.078   13.2   3.7       0.72   10.1   0.5    2.3  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   2.7   7.8e-22   4.6e-18       4     103 ..      86     179 ..      83     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 7.8e-22
                                    HHHHHHHHHHH-HHHHHHCCSS--T.T-S-HGHHCCCCHHHHHHHHHHHGGG---TH--CCHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_33   4 larayrrfAlahpaeYallfgspvp.gyaapdelaaagarvlalllaalaalvaaglppadavaaaralwaalhGlvsLe 82 
                                    +a ayr++A+ hp++Y +    ++p g ++p e++aa + + a ++a+l+ +   gl++++a +aa+ +w+alhG+v Le
  gi|121636602|ref|YP_976825.1|  86 MAGAYRSYAHHHPGRYSAFT--RMPlGGDDP-EYTAATRGAAAPVIAVLSSY---GLDGEQAFYAALEFWSALHGFVLLE 159
                                    789***************99..666599999.9*******************...**8777******************* PP

                                    HCTTTTSSS-HHHHHHHHHHH CS
                      TetR_C_33  83 lfghfglpadpdalferlvda 103
                                    + g +  + d+da+f  +v +
  gi|121636602|ref|YP_976825.1| 160 MTGVM-DDIDTDAVFTDMVLR 179
                                    ***77.4889999**999866 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-08   7.8e-05       1      47 []      12      58 ..      12      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-08
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   I+++A+  + ++G+d++t++++A ++G+  ++lY + +s e+L +a+
  gi|121636602|ref|YP_976825.1| 12 IVEGALTFLDREGWDSLTINALATQLGTKGPSLYNHVDSLEDLRRAV 58
                                   8899********************************99999998775 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.011        64      39      76 ..      50      87 ..      44      90 .. 0.77
   2 ?   10.1   0.5   0.00012      0.72      43     106 ..     115     182 ..     113     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHHH CS
                      TetR_C_31 39 eLraalarlrralrealaallaalGlpdpeeaarllva 76
                                    L ++ ++ r ++ + ++++l ++G+ ++++ a l++a
  gi|121636602|ref|YP_976825.1| 50 SLEDLRRAVRIRVIDDIITMLNRVGAGRARDDAVLVMA 87
                                   6777777778888999**********767767766665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHHHHHHHHHHCSS-HHH..HHHHHHHHHHHHHHHHHHSG..TS-HHHHHHHHHHHHT- CS
                      TetR_C_31  43 alarlrralrealaallaalGlpdpee..aarllvaaldGllldrLagp..aadpraevrellralld 106
                                     ++++ r+ ++ ++a+l   Gl++ ++  aa  +  al G +l  ++g   + d++a++++++ +l++
  gi|121636602|ref|YP_976825.1| 115 EYTAATRGAAAPVIAVLSSYGLDGEQAfyAALEFWSALHGFVLLEMTGVmdDIDTDAVFTDMVLRLAA 182
                                    6899999***************65553449999***************87666669999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1528.25
//
Query:       gi|121636603|ref|YP_976826.1|  [L=124]
Description: 30S ribosomal protein S12 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-42  143.4   3.1    2.3e-42  143.2   3.1    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   3.1   1.3e-46   2.3e-42       1     114 []      12     123 ..      12     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 1.3e-46
                                    --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.. CS
                Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk 80 
                                    r+ + +k k+ al+g+pq+rGv+++++t+++kkPnsAlRkv+rv+L+ ++ evta+ipgeg  ++l+Eh++vlvrG+r  
  gi|121636603|ref|YP_976826.1|  12 RRDKISKVKTAALKGSPQRRGVCTRVYTTTPKKPNSALRKVARVKLT-SQVEVTAYIPGEG--HNLQEHSMVLVRGGR-- 86 
                                    6788999****************************************.*************..***************.. PP

                                    ...BTTSTTEEEEBET....S---T..SSSTTTTT----T CS
                Ribosom_S12_S23  81 gkavkDlpGvrykvvk....vagvs..lkalskykkekpk 114
                                       vkDlpGvryk+++    ++gv+  ++a+s+y+++k+k
  gi|121636603|ref|YP_976826.1|  87 ---VKDLPGVRYKIIRgsldTQGVKnrKQARSRYGAKKEK 123
                                    ...*****************9***9999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 973.94
//
Query:       gi|121636604|ref|YP_976827.1|  [L=156]
Description: 30S ribosomal protein S7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-62  208.4   0.1      4e-62  208.3   0.1    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.057   14.5   0.0       0.21   12.6   0.0    1.8  2  Mak_N_cap     Maltokinase N-terminal cap domain


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.3   0.1   4.4e-66     4e-62       1     149 []       1     149 [.       1     149 [. 1.00

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 4.4e-66
                                    ..XSSSSCT------SSTTSBHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBS CS
                   Ribosomal_S7   1 msrrkkakkrevlpdpkynselveklinklmkdGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrv 80 
                                    m+r++ a+kr + +dp+y+s+lv++l+nk++ +GkkslAe+ivygal+  ++kt++dp+ +l++Al+nvkP +ev+srrv
  gi|121636604|ref|YP_976827.1|   1 MPRKGPAPKRPLVNDPVYGSQLVTQLVNKVLLKGKKSLAERIVYGALEQARDKTGTDPVITLKRALDNVKPALEVRSRRV 80 
                                    89****************************************************************************** PP

                                    SSSBEEEEEEE-HHHHHHHHHHHHHHHHSTSSSS-HHHHHHHHHHHHHTT-SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  81 GGatyqvpvevrpkRrqalAlrwiieaarkrkeksmaekLaeElidAaegegaavkkreethrmAeanr 149
                                    GGatyqvpvevrp+R+++lAlrw++ ++r+r+ek+m e+La+E++dA++g ga+vk+re+th+mAeanr
  gi|121636604|ref|YP_976827.1|  81 GGATYQVPVEVRPDRSTTLALRWLVGYSRQRREKTMIERLANEILDASNGLGASVKRREDTHKMAEANR 149
                                    ********************************************************************8 PP

>> Mak_N_cap  Maltokinase N-terminal cap domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.42   3.8e+03      74      85 ..      36      47 ..      20      48 .. 0.81
   2 ?   12.6   0.0   2.4e-05      0.21      36      76 ..      74     113 ..      50     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
                                   ETTCCEEEEEGG CS
                      Mak_N_cap 74 gplggrtvyDAl 85
                                   ++l++r+vy Al
  gi|121636604|ref|YP_976827.1| 36 KSLAERIVYGAL 47
                                   578999999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.4e-05
                                    EEEEEEEEETTEEEEEEEEECSS--CCGHC.CEEEEE.EETT CS
                      Mak_N_cap  36 ehllvrveeagdvYqvpLgyreappeglep.aligtaehgpl 76 
                                    e+   rv+   ++Yqvp+ +r++ ++ l+  +l+g +++ ++
  gi|121636604|ref|YP_976827.1|  74 EVRSRRVGG--ATYQVPVEVRPDRSTTLALrWLVGYSRQRRE 113
                                    333334444..69***************888***99876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1046.81
//
Query:       gi|121636605|ref|YP_976828.1|  [L=701]
Description: elongation factor G [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-68  228.1   0.0      1e-67  227.5   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.4e-45  153.9   0.1    2.8e-45  153.0   0.1    1.5  1  EFG_IV       Elongation factor G, domain IV
    6.6e-34  115.8   0.2    1.4e-33  114.8   0.2    1.6  1  EFG_II       Elongation Factor G, domain II
    1.7e-30  104.9   0.1    4.5e-30  103.5   0.1    1.8  1  EFG_C        Elongation factor G C-terminus
    4.2e-14   52.7   0.1    1.1e-13   51.4   0.1    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    5.1e-07   29.6   0.1    1.1e-06   28.4   0.1    1.5  1  RF3_C        Class II release factor RF3, C-terminal domain
    0.00042   20.4   0.0    0.00088   19.3   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.026   13.8   0.0    1.4  1  AIG1         AIG1 family
      0.037   13.9   0.0      0.098   12.6   0.0    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      0.098   12.3   0.1       0.28   10.7   0.1    1.9  1  ATP-grasp_4  ATP-grasp domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.5   0.0   5.7e-71     1e-67       2     194 .]      12     285 ..      11     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.5 bits;  conditional E-value: 5.7e-71
                                    CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG CS
                       GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv 81 
                                    r+rn+gi++h+D+GKtT+t+r+ly+tg+  k ge++++++++D++++E+ergiTi+saa++++  +k+ ++n+iDtPGHv
  gi|121636605|ref|YP_976828.1|  12 RVRNFGIMAHIDAGKTTTTERILYYTGINYKIGEVHDGAATMDWMEQEQERGITITSAATTTF--WKDNQLNIIDTPGHV 89 
                                    79***********************************9*************************..*************** PP

                                    GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH........ CS
                       GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk........ 153
                                    dF+ ev+r lrvlDgav v+d +eGvepq+e+v+r+a k++vp+i+f+NKmD+++a++  +v+++ ++l ++        
  gi|121636605|ref|YP_976828.1|  90 DFTVEVERNLRVLDGAVAVFDGKEGVEPQSEQVWRQADKYDVPRICFVNKMDKIGADFYFSVRTMGERLGANavpiqlpv 169
                                    *********************************************************************999******** PP

                                    ............................................................................HHHH CS
                       GTP_EFTU 154 ............................................................................eekl 157
                                                                                                                ++++
  gi|121636605|ref|YP_976828.1| 170 gaeadfegvvdlvemnakvwrgetklgetydtveipadlaeqaeeyrtkllevvaesdehllekylggeeltvdeiKGAI 249
                                    ********************************************999999999999988888877777777777777777 PP

                                    HHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSHH CS
                       GTP_EFTU 158 ekygekgekevpvvfgSalkgegvktllealvellps 194
                                    +k +  + +++pv++gSa+k++gv+++l+a+v++lps
  gi|121636605|ref|YP_976828.1| 250 RKLTIAS-EIYPVLCGSAFKNKGVQPMLDAVVDYLPS 285
                                    7776666.6**************************96 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.1   1.6e-48   2.8e-45       1     120 [.     483     604 ..     483     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 1.6e-48
                                    TCCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTT..TTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TT CS
                         EFG_IV   1 pqVayrEtirkpvkereeklkkqsggdgqyakvileiePle..egsgnefvdetkggqvpkeyieavekGfqealkeGpl 78 
                                    pqVay+Eti++ v+++e+++kkq+gg+gq+akvi+++eP +  eg+++ef+++++gg++p+eyi++v++G q+a++ G+l
  gi|121636605|ref|YP_976828.1| 483 PQVAYKETIKRLVQNVEYTHKKQTGGSGQFAKVIINLEPFTgeEGATYEFESKVTGGRIPREYIPSVDAGAQDAMQYGVL 562
                                    8**************************************99999************************************ PP

                                    TS--EESEEEEEEEEE--TTTC-HHHHHHHHCHHHHHHHHCC CS
                         EFG_IV  79 agepvtdvkvtLldgslhevdsseaafkpaarralkeallkA 120
                                    ag+p++++kvtLldg++hevdsse+afk+a++++lk+a++ A
  gi|121636605|ref|YP_976828.1| 563 AGYPLVNLKVTLLDGAYHEVDSSEMAFKIAGSQVLKKAAALA 604
                                    **************************************9877 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.2   7.9e-37   1.4e-33       1      75 []     408     482 ..     408     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 7.9e-37
                         EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelgk 75 
                                    fP+Pvi++aiepk+k+d++kls ++++l+eEDpt++v+ d+eT++t++ GmGelHl+i+v+r++re+kve+++gk
  gi|121636605|ref|YP_976828.1| 408 FPDPVIEVAIEPKTKSDQEKLSLSIQKLAEEDPTFKVHLDSETGQTVIGGMGELHLDILVDRMRREFKVEANVGK 482
                                    8***********************************************************************985 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.1   2.5e-33   4.5e-30       1      88 [.     607     693 ..     607     694 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 2.5e-33
                                    EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE CS
                          EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYee 80 
                                    v+lEPi+ ve+++pe+y+g+vi+dl+srrG+i+ me++  g  +++a++Pl+e++g+  +Lrs T+G++++sm f++Y+e
  gi|121636605|ref|YP_976828.1| 607 VILEPIMAVEVTTPEDYMGDVIGDLNSRRGQIQAMEER-AGARVVRAHVPLSEMFGYVGDLRSKTQGRANYSMVFDSYSE 685
                                    59************************************.9999************************************* PP

                                    --HHHHHH CS
                          EFG_C  81 vpgdklde 88 
                                    vp ++ +e
  gi|121636605|ref|YP_976828.1| 686 VPANVSKE 693
                                    **998765 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   5.9e-17   1.1e-13       1      73 [.     328     394 ..     328     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.9e-17
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    G ++++rvysGt++ G +v +   +++kk   +r ++l+ +h +++ +v+ a aG i a++gl+d+  +Gdtl
  gi|121636605|ref|YP_976828.1| 328 GKLTYIRVYSGTVESGSQVIN--ATKGKK---ERLGKLFQMHSNKENPVDRASAGHIYAVIGLKDT-TTGDTL 394
                                    7899*****************..*99999...*********************************7.*****9 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   6.3e-10   1.1e-06      15      94 ..     417     496 ..     408     516 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.3e-10
                                    EEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EEEEEE-SSH CS
                          RF3_C  15 vrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpyslarwvesede 94 
                                    ++ k  + + +l+  +++LaeE  +   + ++++ ++++g +G+L ++++ +R+++E++ve+++ + ++ +   +++  +
  gi|121636605|ref|YP_976828.1| 417 IEPKTKSDQEKLSLSIQKLAEEDPTFKVHLDSETGQTVIGGMGELHLDILVDRMRREFKVEANVGKPQVAYKETIKRLVQ 496
                                    66777888999***********9888777777899****************************99988887777755333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.9e-07   0.00088       7     114 .]      21     139 ..      15     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.9e-07
                                    STTSSHHHHHHHHH.........T.........STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHH CS
                       MMR_HSR1   7 rpNvGKStLinalt.........g.........ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgk 68 
                                    +  +GK+t   +++         g         +  + +++ g T++    +  +k+++++++DtpG ++       ++ 
  gi|121636605|ref|YP_976828.1|  21 HIDAGKTTTTERILyytginykiGevhdgaatmDWMEQEQERGITITSAATTTFWKDNQLNIIDTPGHVD-------FTV 93 
                                    566888888888875554444441343333222245667777888888777777999**********655.......666 PP

                                    HHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  69 aflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +++++ +  d ++ v+d  +e+++p+ e++ +  ++ + p i  +nk
  gi|121636605|ref|YP_976828.1|  94 EVERNLRvLDGAVAVFD-GKEGVEPQSEQVWRQADKYDVPRICFVNK 139
                                    666666646********.5588****999999988888888888887 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.026      31      67 ..      60      96 ..      25     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                   TTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHH CS
                           AIG1 31 saqsvtkkcqkksrtwdgkkinViDTPglfdlsvsad 67
                                   +++++t ++   ++ w+++++n+iDTPg +d  v+ +
  gi|121636605|ref|YP_976828.1| 60 QERGITITSAATTTFWKDNQLNIIDTPGHVDFTVEVE 96
                                   67899***********************999988765 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-05     0.098      23      76 ..     333     391 ..     329     398 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                                    EEEEEEEEETT-EEEET.TE...EEEEEEEEEETTE.EESEEETT-EEEE.EEESS-TT CS
                    GTP_EFTU_D4  23 vevlgGvikpgvklike.dGr..evGeilqiqdkgk.kleeakaGqevai.siegkivG 76 
                                    ++v +G++++g ++i++ +G+  ++G++ q++++++  ++ a+aG+  a+  +++++ G
  gi|121636605|ref|YP_976828.1| 333 IRVYSGTVESGSQVINAtKGKkeRLGKLFQMHSNKEnPVDRASAGHIYAViGLKDTTTG 391
                                    89************9853676336*******9876516*******98875145555555 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00016      0.28      29      69 ..     203     243 ..     157     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                    ATP-grasp_4  29 aavaaieeeleqakeeykeevveeesflvEeyieGeEfavd 69 
                                    +  a++ e++e+ +++  e v e+++ l+E+y+ GeE  vd
  gi|121636605|ref|YP_976828.1| 203 EIPADLAEQAEEYRTKLLEVVAESDEHLLEKYLGGEELTVD 243
                                    55577888999999999999999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5076.59
//
Query:       gi|121636606|ref|YP_976829.1|  [L=396]
Description: elongation factor Tu [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-58  197.3   0.4    2.4e-58  196.9   0.4    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.7e-32  112.0   0.0    3.7e-32  111.0   0.0    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    3.3e-17   62.6   6.0    1.1e-16   61.0   6.0    2.0  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.3e-06   26.3   1.1    2.2e-05   24.5   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
        0.1   12.5   0.0        0.3   11.0   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
       0.17   11.5   0.6       0.32   10.6   0.0    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.4     8e-62   2.4e-58       1     193 [.      10     202 ..      10     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 8e-62
                                    TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                       GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                    k+++nig+ighvDhGKtTLt ++++ +++   + +++++  ++D+++eEr+rgiTi++a+++++  t+k++++++D+PGH
  gi|121636606|ref|YP_976829.1|  10 KPHVNIGTIGHVDHGKTTLTAAITKVLHDKFPDLNETKAFDQIDNAPEERQRGITINIAHVEYQ--TDKRHYAHVDAPGH 87 
                                    579*****************************9888888888**********************..************** PP

                                    GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl.kaelkeiveevkqklsrkeekle 158
                                    +d++k++i+g++++Dga+lvv+a++G++pqt+e++ la+++gvp i v++NK+D + ++el e+ve+  ++l      l 
  gi|121636606|ref|YP_976829.1|  88 ADYIKNMITGAAQMDGAILVVAATDGPMPQTREHVLLARQVGVPyILVALNKADAVdDEELLELVEMEVREL------LA 161
                                    ********************************************999*********999*************......88 PP

                                    HHHHTTTTTEEEEEEBTTTTB........THHHHHHHHHHHSH CS
                       GTP_EFTU 159 kygekgekevpvvfgSalkge........gvktllealvellp 193
                                    ++++++  + pvv++Salk+          v++l++a++e +p
  gi|121636606|ref|YP_976829.1| 162 AQEFDE--DAPVVRVSALKALegdakwvaSVEELMNAVDESIP 202
                                    888886..69***********99999999999******99987 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   1.2e-35   3.7e-32       2     111 ..     301     394 ..     300     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 1.2e-35
                                    -EEECCEEEEEEESSS.....SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECC CS
                    GTP_EFTU_D3   2 ikphtkfeAqvyileke...rhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelik 78 
                                     +pht+fe qvyil+k+   rhtp++++Yrp++y+rt+dvtg vv+L       +e++     e+v+pGdn++++v+li+
  gi|121636606|ref|YP_976829.1| 301 TTPHTEFEGQVYILSKDeggRHTPFFNNYRPQFYFRTTDVTG-VVTL-------PEGT-----EMVMPGDNTNISVKLIQ 367
                                    589***************************************.****.......9999.....***************** PP

                                    EEEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                    GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvtei 111
                                    p+a+++g       rFaiReggrTv+aG vt+i
  gi|121636606|ref|YP_976829.1| 368 PVAMDEGL------RFAIREGGRTVGAGRVTKI 394
                                    ********......******************9 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   6.0   3.6e-20   1.1e-16       1      74 []     226     296 ..     226     296 .. 0.98
   2 ?   -2.8   0.0       2.9   8.8e+03      33      56 ..     338     361 ..     311     371 .. 0.66

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.6e-20
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                    Gtv++grv++G++++++ev+i+g  ++  k   t+++++e+f++ +d+  ag+n+G+++++++ ed +++G+++t
  gi|121636606|ref|YP_976829.1| 226 GTVVTGRVERGVINVNEEVEIVGiRPSTTK---TTVTGVEMFRKLLDQGQAGDNVGLLLRGVKRED-VERGQVVT 296
                                    9*************************9999...*********************************.*****986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                                    EEEEEEEEETEEESEEETTSEEEE CS
                    GTP_EFTU_D2  33 trissletfhededeavaganaGv 56 
                                    t+++++ t  e  + +++g+n  +
  gi|121636606|ref|YP_976829.1| 338 TDVTGVVTLPEGTEMVMPGDNTNI 361
                                    666666665555555555555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.3e-09   2.2e-05       2     113 ..      15     138 ..      14     139 .. 0.77
   2 ?   -0.3   0.2      0.37   1.1e+03      23      36 ..     291     304 ..     238     362 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.3e-09
                                    EEEEESTTSSHHHHHHHHHT..................STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg..................ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegasee 63 
                                    ++ +G+   GK+tL  a+t+                  ++a  +++ g T++i + +++++++++  vD pG  +     
  gi|121636606|ref|YP_976829.1|  15 IGTIGHVDHGKTTLTAAITKvlhdkfpdlnetkafdqiDNAPEERQRGITINIAHVEYQTDKRHYAHVDAPGHAD----- 89 
                                    889****************7777778888777777644478888999************999**********333..... PP

                                    HHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEE.EEE CS
                       MMR_HSR1  64 kglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplil.vln 113
                                      +++ +    ++d ++lvv a+ ++  p+ +e   l ++ + p+il +ln
  gi|121636606|ref|YP_976829.1|  90 -YIKNMITGAAQMDGAILVVAAT-DGPMPQTREHVLLARQVGVPYILvALN 138
                                    .4666666677899*99999977.545566566555556778887773555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                                    TEEESSSTTSSSSE CS
                       MMR_HSR1  23 kaivsdkpgtTrdi 36 
                                    + +v  kpgtT+  
  gi|121636606|ref|YP_976829.1| 291 RGQVVTKPGTTTPH 304
                                    34455555555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2   6.5e+03     106     121 ..      19      34 ..      15      46 .. 0.74
   2 ?   11.0   0.0    0.0001       0.3      13      74 ..      98     158 ..      74     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                                    CSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 106 GqSGvGKStLinallp 121
                                    G+   GK+tL  a++ 
  gi|121636606|ref|YP_976829.1|  19 GHVDHGKTTLTAAITK 34 
                                    6666799999888765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                                    EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelea 74 
                                    +a +d +++vv+++ +   +++ + +L++ +     ++++lnK+D +++ee le ++ e+++
  gi|121636606|ref|YP_976829.1|  98 AAQMDGAILVVAAT-DGPMPQTREHVLLARQVGVPYILVALNKADAVDDEELLELVEMEVRE 158
                                    89999999999999.6666777788887666655578899***********66655555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.3   3.8e+03       9      21 ..      21      33 ..      16      39 .. 0.72
   2 ?   10.6   0.0   0.00011      0.32     104     172 ..      93     162 ..      83     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                   TTCCHHHHHHHHH CS
                           cobW  9 lGsGKTtLlnhll 21
                                   +  GKTtL  +++
  gi|121636606|ref|YP_976829.1| 21 VDHGKTTLTAAIT 33
                                   5569***988776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                                    HHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCHC..HHHHHHHHHHHHTT CS
                           cobW 104 eelksdltldavvavvDaknleaeeekieekaedqlaaadllv.lnKtDlldeeallekleerlrqlnpe 172
                                    + ++ ++++d+ + vv a+     +++++ ++ +q+ +  +lv lnK+D +d+e+lle +e ++r+l ++
  gi|121636606|ref|YP_976829.1|  93 NMITGAAQMDGAILVVAATDGPMPQTREHVLLARQVGVPYILVaLNKADAVDDEELLELVEMEVRELLAA 162
                                    567778999*********99988999999999****999887769***************9999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2573.52
//
Query:       gi|121636607|ref|YP_976830.1|  [L=265]
Description: hypothetical protein BCG_0735 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-05   23.6   0.2    6.1e-05   22.6   0.2    1.5  1  SHOCT           Short C-terminal domain
  ------ inclusion threshold ------
       0.13   12.2   0.3        0.3   11.0   0.3    1.5  1  Epiglycanin_TR  Tandem-repeating region of mucin, epiglycanin
       0.22   11.9   4.4       0.42   11.0   4.4    1.4  1  DUF4133         Domain of unknown function (DUF4133)
        2.3    6.9   4.6        3.3    6.4   4.6    1.1  1  DUF2207         Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   1.4e-08   6.1e-05       1      27 [.     235     261 ..     235     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-08
                          SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                    ++L++L +L+a+G+ + +E+e k+a++
  gi|121636607|ref|YP_976830.1| 235 ERLAELESLRASGAVNAAEYESKRAQI 261
                                    68***********************98 PP

>> Epiglycanin_TR  Tandem-repeating region of mucin, epiglycanin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   6.7e-05       0.3      38      66 ..      58      86 ..      49      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                 Epiglycanin_TR 38 TsggtsTatNtaSsvtsggssttsstgts 66
                                   T+ g+ Ta++ta+++ sg  +++ stg s
  gi|121636607|ref|YP_976830.1| 58 TNYGAKTAAKTAALERSGVLALAQSTGLS 86
                                   999***********************987 PP

>> DUF4133  Domain of unknown function (DUF4133)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.4   9.4e-05      0.42      14      79 ..       6      71 ..       3      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.4e-05
                        DUF4133 14 LkaqylfilagglvallllvvilyiiGvsqliclalivvagsllvvlvfrl.nkkyGehGlmkklak 79
                                   +k q l++l+gglv+ ++lv + +++G+++l++ +++v++++ +  ++++l   +yG   ++k++a 
  gi|121636607|ref|YP_976830.1|  6 IKMQLLVLLCGGLVGPIFLV-VYFTLGLGSLMSWMFYVGLIITVADVLVALaLTNYGAKTAAKTAAL 71
                                   68899**********98876.67899********999999888776666651589999999998875 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.6   0.00073       3.3     381     453 ..       8      73 ..       3      74 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00073
                        DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGaellakwkgFkk 453
                                    + l +l+ g+++  ++l++++ l+l++l++++++++li+ ++ ++v+l        +t +Ga+ +ak+ ++++
  gi|121636607|ref|YP_976830.1|   8 MQLLVLLCGGLVGPIFLVVYFTLGLGSLMSWMFYVGLIITVADVLVALA-------LTNYGAKTAAKTAALER 73 
                                    5566666777777777777777777775666666666666666666655.......58888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2005.97
//
Query:       gi|121636608|ref|YP_976831.1|  [L=275]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-50  169.3   0.1    1.1e-48  165.9   0.1    1.9  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    9.8e-47  158.9   0.1    8.1e-46  155.9   0.1    1.9  1  adh_short     short chain dehydrogenase
    1.2e-15   57.9   0.1    1.6e-15   57.4   0.1    1.1  1  KR            KR domain
  ------ inclusion threshold ------
      0.019   14.4   0.1      0.076   12.5   0.1    2.0  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.1   2.4e-52   1.1e-48       1     232 [.      17     271 ..      17     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 2.4e-52
                                    TTTTSHHHHHHHHHHHTT-EEEEEES..............SGGHHHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHH CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdl..............neeakkrveelaeelgae.vlecDVtdeeqvealveevve 65 
                                    Gaa+  Gr  A +la+eGa++v+ d+              +e++ ++v+++++e+ +  + e+D++d++++++lv++ ve
  gi|121636608|ref|YP_976831.1|  17 GAARAQGRSHAVRLAREGADIVALDIcapvsgsvtyppatSEDLGETVRAVEAEGRKVlAREVDIRDDAELRRLVADGVE 96 
                                    899999****************99974444443333333234446777777777665544******************** PP

                                    HHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHH CS
                   adh_short_C2  66 kfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynayg 142
                                    +fg+lDi+v nag+     g++ e+++e++++++ vnl++++++++a +p ++ +g  gsiv +ss ++ +++p++ +y+
  gi|121636608|ref|YP_976831.1|  97 QFGRLDIVVANAGVLGW--GRLWELTDEQWETVIGVNLTGTWRTLRATVPaMIDAGngGSIVVVSSSAGLKATPGNGHYA 174
                                    *****************..*******************************54444478********************** PP

                                    HHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTG...GGGSTTHHHHHHHHHHHSTT....SS-B-HHHHHHHHHHHC CS
                   adh_short_C2 143 aaKaalealtrylAvelgpkgiRvNavspgpikTla...asgikgfdelleelearapl....grlgtpeevaeaalfLa 215
                                    a+K+al+alt +lA elg+ giRvN+++p  ++T++    + i+ f +   ++++  p+    + ++tp+e+ +++++La
  gi|121636608|ref|YP_976831.1| 175 ASKHALVALTNTLAIELGEFGIRVNSIHPYSVDTPMiepEAMIQTFAKHPGYVHSFPPMplqpKGFMTPDEISDVVVWLA 254
                                    ************************************6655668888887777777766533334477************* PP

                                    SGGGTT--SEEEEESTT CS
                   adh_short_C2 216 sdeasyitGqtlvvDgG 232
                                     d + + +G+++ vD G
  gi|121636608|ref|YP_976831.1| 255 GDGSGALSGNQIPVDKG 271
                                    ****************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.1   1.8e-49   8.1e-46       2     188 ..      12     212 ..      11     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 1.8e-49
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEES.............CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHH CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdr.............seekleevakelkeegakalaiqvDvtdreevealv 68 
                                    v++vtGa++  Gr  a +la+eGa++v++d+             ++e+l e++  +++eg+k+la +vD++d +e+++lv
  gi|121636608|ref|YP_976831.1|  12 VAFVTGAARAQGRSHAVRLAREGADIVALDIcapvsgsvtyppaTSEDLGETVRAVEAEGRKVLAREVDIRDDAELRRLV 91 
                                    89*************************9885334444444444468999999**************************** PP

                                    HHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBH CS
                      adh_short  69 ekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagva 147
                                    ++ v+++g+ld++v+NAG+ g g   el++e+we vi vNltg+  + ra +pam+ ++++G+Iv vsS ag+++ +g  
  gi|121636608|ref|YP_976831.1|  92 ADGVEQFGRLDIVVANAGVLGWGRLWELTDEQWETVIGVNLTGTWRTLRATVPAMIdAGNGGSIVVVSSSAGLKATPGNG 171
                                    ********************************************************89999******************* PP

                                    HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 148 aYsAsKaavagltrslakelaptgirvnavaPGlvdTdmak 188
                                     Y+AsK+a+++lt++la el + girvn+++P  vdT+m +
  gi|121636608|ref|YP_976831.1| 172 HYAASKHALVALTNTLAIELGEFGIRVNSIHPYSVDTPMIE 212
                                    **************************************976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   3.7e-19   1.6e-15       4     161 ..      14     185 ..      12     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.7e-19
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS...........--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHH CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsa.........aadedskaliaelealgaevevvaaDvsdkdaveallee 74 
                                    ++tG++ + G++ a  la++ga  ++l    +         a++ed  ++++++ea g +v ++++D+ d +++++l+++
  gi|121636608|ref|YP_976831.1|  14 FVTGAARAQGRSHAVRLAREGADIVALDICAPvsgsvtyppATSEDLGETVRAVEAEGRKVLAREVDIRDDAELRRLVAD 93 
                                    69*******************9877764333355788988877888889******************************* PP

                                    HHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHH CS
                             KR  75 ikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanY 149
                                      ++++++  v+  Agvl  + l e+t+e++e+v+   ++G+w   +++ +      +   +v++SS agl  ++g ++Y
  gi|121636608|ref|YP_976831.1|  94 GVEQFGRLDIVVANAGVLGWGRLWELTDEQWETVIGVNLTGTWRTLRATVPamidaGNGGSIVVVSSSAGLKATPGNGHY 173
                                    *******************************************987777773444455567******************* PP

                                    HHHHHHHHHHHH CS
                             KR 150 aaaNaflDalae 161
                                    aa  + l al +
  gi|121636608|ref|YP_976831.1| 174 AASKHALVALTN 185
                                    **9999888765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.7e-05     0.076       2     187 ..      14     218 ..      13     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEE.....S-STTTTCHHCHHC..............EEEE--TT-HHHHHHHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigld.....rlssasntarledl..............elveldltdrsalerlfke 62 
                                    +VtGa+   G+  + +l+++g ++++ld     + s + + a  edl                 e+d++d+++l+rl+++
  gi|121636608|ref|YP_976831.1|  14 FVTGAARAQGRSHAVRLAREGADIVALDicapvSGSVTYPPATSEDLgetvraveaegrkvLAREVDIRDDAELRRLVAD 93 
                                    79*******************88888872222244444444444444999********998788************9875 PP

                                    ....H.T-SEEEE--S---HHHHHHSHHHHHH....HHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTT CS
                      Epimerase  63 ....e.qpdavihlAavggvaassedpadfie....knlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettlt 133
                                        + + d+v+  A+v g+++ +e   + +e     nl gt++ l a   a +    + +S  v   +a     + t  
  gi|121636608|ref|YP_976831.1|  94 gveqFgRLDIVVANAGVLGWGRLWELTDEQWEtvigVNLTGTWRTLRATVPAMI-DAGNGGSIVVVSSSAG---LKAT-- 167
                                    333246899*****9999999877766665552222677777777777776555.4444444444444444...2223.. PP

                                    S----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHH CS
                      Epimerase 134 gplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvip 187
                                       + n  Yaa+K+a   l+  +a + g + i ++  + y+  +++ e++ +i 
  gi|121636608|ref|YP_976831.1| 168 ---PGNGHYAASKHALVALTNTLAIELGEFGIRVNSIHPYSVDTPMIEPEAMIQ 218
                                    ...557788888888887777777777777777777777776666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2153.33
//
Query:       gi|121636609|ref|YP_976832.1|  [L=406]
Description: ferredoxin reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-60  205.2   0.7    1.3e-60  205.2   0.7    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-19   69.1  15.2    4.4e-19   68.8   0.8    3.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.4e-13   48.5   0.0    2.6e-12   47.1   0.0    1.8  1  Reductase_C     Reductase C-terminal
    1.5e-05   24.3   0.1       0.18   10.9   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    1.7e-05   24.9   8.2      0.043   14.0   0.1    3.6  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.6e-05   22.8   0.0    0.00033   20.0   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00013   22.0  10.4       0.55   10.2   0.4    4.5  4  NAD_binding_9   FAD-NAD(P)-binding
    0.00027   21.4   6.1      0.036   14.5   0.0    3.0  3  NAD_binding_7   Putative NAD(P)-binding
    0.00033   20.1   3.6     0.0014   18.0   1.2    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0021   17.5   0.4      0.011   15.1   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0028   17.9   0.6       0.23   11.7   0.1    2.5  2  TrkA_N          TrkA-N domain
     0.0048   16.0  13.4      0.027   13.5   0.7    3.4  4  Lycopene_cycl   Lycopene cyclase protein
     0.0088   15.7   1.1     0.0088   15.7   1.1    4.1  4  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.027   14.3   0.2      0.027   14.3   0.2    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.03   13.4   0.6       0.03   13.4   0.6    4.1  4  GIDA            Glucose inhibited division protein A
      0.055   13.1   0.3       0.14   11.8   0.3    1.8  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.061   12.7   0.4      0.061   12.7   0.4    1.8  3  ThiF            ThiF family
      0.095   12.8   0.2        1.5    8.9   0.1    2.4  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
        1.5    9.1   5.6        3.6    7.9   2.0    2.5  2  FLgD_tudor      FlgD Tudor-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   0.7   1.4e-63   1.3e-60       3     293 ..      18     309 ..      16     310 .. 0.93
   2 ?   -1.0   0.3      0.87   8.2e+02       4      12 ..     374     382 ..     348     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 1.4e-63
                                    EEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHCCT CS
                                    xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllgee 74 
                                    +v++GgG A+ ++a++l++  ++++ t+v++e ++++++++lsk++l+++ d   ++      e      ++i l+lg+ 
  gi|121636609|ref|YP_976832.1|  18 IVIVGGGLAAARTAEQLRRagYSGRLTIVSDEVHLPYDRPPLSKEVLRSEVDDVALKprefydE------KDIALRLGSA 91 
                                    8******************777999*******************99999888866667765533......47******99 PP

                                    CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                    Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllp.krivvvGgGy 152
                                    +v++d+g+++v+l      d++ + yd+lv+AtG  pr++  +p +  ++++++r++d+  al+++    +++vvvG+G+
  gi|121636609|ref|YP_976832.1|  92 AVSLDTGEQTVTL-----ADGTVLGYDELVIATGLVPRRIpSLPDL--DGIRVLRSFDESMALRKHASAaRHAVVVGAGF 164
                                    *************.....7889************988888799999..888999**********9999999********* PP

                                    HHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                    Pyr_redox_2 153 iGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadl 230
                                    iG+E+Aa l+ lg++v+lve  + +l + l++++++ +++ +++eGv+v++g +v e++g+g+ ++ vvl+dg+e++adl
  gi|121636609|ref|YP_976832.1| 165 IGCEVAASLRGLGVDVVLVEPQPAPLaSVLGEQIGQLVTRLHRDEGVDVRTGVTVAEVRGKGH-VDaVVLTDGTELPADL 243
                                    **************************************************************8.666************* PP

                                    EEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC......TECCSS--HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 231 vvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva......ggkggpelaqaAvqq 293
                                    vvv++G +p te l e +g+e+  ++g+ +d+ +rt+ p+++a+GDva      g + ++e++ +  +q
  gi|121636609|ref|YP_976832.1| 244 VVVGIGSTPATEWL-EGSGVEV--DNGVICDKAGRTSAPNVWALGDVAswrdpmGHQARVEHWSNVADQ 309
                                    **************.*******..99999*******************988888888888888776665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.87
                                    EEE--SHHH CS
                                    xxxxxxxxx RF
                    Pyr_redox_2   4 vviGgGpAG 12 
                                     v+GgG+AG
  gi|121636609|ref|YP_976832.1| 374 GVVGGGMAG 382
                                    488888888 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00097      0.91       2      30 ..      18      48 ..      17     107 .. 0.74
   2 !   68.8   0.8   4.6e-22   4.4e-19       1      80 [.     156     235 ..     156     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00097
                                   EEEECSSHHHHHHHHHHHHTT..SEEEEEES CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvver 30
                                   +v+vGgG+ +   A+ l++ g   + t+v  
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGysGRLTIVSD 48
                                   8****************99994434454443 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 4.6e-22
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                    ++vvvG+G+ig+E+A+ l+ lg +V +ve ++ +l ++l+e++++++++ ++++g++v+++ +v+e++g++  v +v+l+
  gi|121636609|ref|YP_976832.1| 156 HAVVVGAGFIGCEVAASLRGLGVDVVLVEPQPAPLaSVLGEQIGQLVTRLHRDEGVDVRTGVTVAEVRGKGH-VDAVVLT 234
                                    78******************************************************************8887.9999998 PP

                                    T CS
                      Pyr_redox  80 d 80 
                                    d
  gi|121636609|ref|YP_976832.1| 235 D 235
                                    6 PP

>> Reductase_C  Reductase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   2.8e-15   2.6e-12       1      70 [.     330     398 ..     330     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.8e-15
                                    EEEEEETTEEEEEEE--TT--EEEEEEETTTTEEEEEEEETTEEEEEEEES-HHHHHHHHHHTTTT---- CS
                    Reductase_C   1 WfWSDqydlklQiaGlatgadevvvRgdpeerafsvfylrdgrlvaveavnrprdlmaarrliaagasvd 70 
                                    +fWSDqyd+k+Q +G +++ d v + +d++ r+f ++y rdg lv+v+  + + ++m +r  iaaga++ 
  gi|121636609|ref|YP_976832.1| 330 YFWSDQYDVKIQCLGEPHATDVVHLVEDDG-RKFLAYYERDGVLVGVVGGGMAGKVMKVRGKIAAGAPIA 398
                                    8******************99766666666.9**********************************9876 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00019      0.18     191     247 ..      15      70 ..       2      87 .. 0.83
   2 !   10.5   0.0   0.00026      0.24     151     210 ..     114     173 ..      94     184 .. 0.75
   3 ?   -2.4   0.1       2.1     2e+03     146     160 ..     238     252 ..     214     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                    K_oxygenase 191 kkriaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvneifsPeyvd 247
                                     + i++vG+G  aa  +e+l r   +  l++v+ +    p d  p+ +e++ +e  d
  gi|121636609|ref|YP_976832.1|  15 DDGIVIVGGGLAAARTAEQLRRAGYSGRLTIVSDEV-HLPYDRPPLSKEVLRSEVDD 70 
                                    678********************9999**9998765.56999999999999887655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                    K_oxygenase 151 nlvlgvGtep.kiPevleklegkervvHss.eylerkeellakkriaVvGsGqSaaeifedl 210
                                    +lv+++G  p  iP++ + l+g  rv+ s  e +  +++  a+++ +VvG+G  + e++  l
  gi|121636609|ref|YP_976832.1| 114 ELVIATGLVPrRIPSLPD-LDG-IRVLRSFdESMALRKHASAARHAVVVGAGFIGCEVAASL 173
                                    79*****77725776654.674.667666413333344588899999**********99876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                    K_oxygenase 146 elearnlvlgvGtep 160
                                    el a  +v+g+G++p
  gi|121636609|ref|YP_976832.1| 238 ELPADLVVVGIGSTP 252
                                    555666666666665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   0.00024      0.23       1      21 [.      20      40 ..      20      49 .. 0.87
   2 !   14.0   0.1   4.6e-05     0.043       1      30 [.     159     188 ..     159     213 .. 0.93
   3 ?    2.3   0.2      0.21     2e+02       1      10 [.     375     384 ..     375     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                   EE--SHHHHHHHHHHHCCTEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfd 21
                                   IvG+Gl+++ +A  L++ag++
  gi|121636609|ref|YP_976832.1| 20 IVGGGLAAARTAEQLRRAGYS 40
                                   9*****************994 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.6e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    +vGaG+ G+  A+ L+  g+dv+l+e ++ 
  gi|121636609|ref|YP_976832.1| 159 VVGAGFIGCEVAASLRGLGVDVVLVEPQPA 188
                                    8*************************9875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.21
                                    EE--SHHHHH CS
                  NAD_binding_8   1 IvGaGlsGlv 10 
                                    +vG+G++G v
  gi|121636609|ref|YP_976832.1| 375 VVGGGMAGKV 384
                                    8******965 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.1e+02     163     266 ..      14     120 ..       3     124 .. 0.52
   2 !   20.0   0.0   3.5e-07   0.00033     122     283 ..     109     266 ..      57     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                    Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke.......ekikvlfnaev 235
                                    +++ +v++Gg+  a+ +A +l r+g + ++ + ++e++   ++p    k + +++++++  +       + i +   + +
  gi|121636609|ref|YP_976832.1|  14 FDDGIVIVGGGLAAARTAEQLRRAGYSGRLTIVSDEVHLPYDRPPL-SKEVLRSEVDDVALKprefydeKDIALRLGSAA 92 
                                    4677899999999999999999998655544444433332222221.122233333333322333343244555555555 PP

                    Pyr_redox_3 236 keikekeeeykvktedgkkvevkddvvlatG 266
                                     ++++ e   +v+ +dg+ v  +d+ v+atG
  gi|121636609|ref|YP_976832.1|  93 VSLDTGE--QTVTLADGT-VLGYDELVIATG 120
                                    5555433..345556653.344666666666 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.5e-07
                    Pyr_redox_3 122 tyeAkkviiAtGef..dkPnklnipGeeklvk.hyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                    ++  ++++iAtG     +P +++  G   l     s     h  a ++ vV+G++  ++++A  l   g +V +v ++  
  gi|121636609|ref|YP_976832.1| 109 VLGYDELVIATGLVprRIPSLPDLDGIRVLRSfDESMALRKHASAARHAVVVGAGFIGCEVAASLRGLGVDVVLVEPQPA 188
                                    56668899****863368999*****99544313344447778999*******************************984 PP

                    Pyr_redox_3 199 iekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkksl 278
                                               l   i + + +l + e ++v +  +v e++ k +   v  +dg+++ + d vv+ +G +p ++ l+ s+
  gi|121636609|ref|YP_976832.1| 189 P------LASVLGEQIGQLVTRLHRDEGVDVRTGVTVAEVRGKGHVDAVVLTDGTELPA-DLVVVGIGSTPATEWLEGSG 261
                                    3......344577888888888888888***************9999999***999876.667777***********999 PP

                    Pyr_redox_3 279 felde 283
                                    +e d+
  gi|121636609|ref|YP_976832.1| 262 VEVDN 266
                                    98854 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.033        31       1      31 [.      19      46 ..      19      68 .. 0.81
   2 !    7.6   0.1    0.0038       3.6     130     154 ..      96     120 ..      82     122 .. 0.83
   3 ?    3.6   0.4     0.062        58       1      36 [.     158     188 ..     158     197 .. 0.84
   4 !   10.2   0.4   0.00059      0.55     103     155 ..     197     250 ..     194     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlf 31
                                   +ivG+G +++ ++e+L +    + + ++t++
  gi|121636609|ref|YP_976832.1| 19 VIVGGGLAAARTAEQLRRA---GYSGRLTIV 46
                                   7***************888...466666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0038
                  NAD_binding_9 130 radgqavlladgaslaadaVvLAlG 154
                                    + ++q+v+ladg+ l +d++v+A+G
  gi|121636609|ref|YP_976832.1|  96 DTGEQTVTLADGTVLGYDELVIATG 120
                                    4456789*****************9 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.062
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36 
                                    ++vGaG+ G  v++ L         +++ l++p+++
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASLRGL-----GVDVVLVEPQPA 188
                                    69***********999777.....599999999765 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00059
                  NAD_binding_9 103 lfeellarlpegvtvevhra.evvdleeradgqavlladgaslaadaVvLAlGh 155
                                    ++ +l+ rl+++  v+v ++ +v +++ ++   av+l+dg++l ad Vv+ +G 
  gi|121636609|ref|YP_976832.1| 197 QIGQLVTRLHRDEGVDVRTGvTVAEVRGKGHVDAVVLTDGTELPADLVVVGIGS 250
                                    667888888888888887665677777777778****************99985 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.8e-05     0.036      10      58 ..      18      83 ..      14     120 .. 0.72
   2 !    9.3   0.2    0.0016       1.5       7      46 ..     154     200 ..     150     311 .. 0.78
   3 ?   -2.1   0.8       5.6   5.3e+03      10      31 ..     373     395 ..     367     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                  NAD_binding_7 10 vlvvGgGevAarkvrklleag..akvtvvapevkeele.............elvklaeeel..ekd 58
                                   +++vGgG  Aar +++l +ag   ++t+v+ ev+   +             + v l+++e+  ekd
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGysGRLTIVSDEVHLPYDrpplskevlrsevDDVALKPREFydEKD 83
                                   79*****************997679*******9544445555555556655556677777755455 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele.......e 46 
                                     ++ +vvG+G ++ + + +l   g +v++v p+ ++ ++       +
  gi|121636609|ref|YP_976832.1| 154 ARHAVVVGAGFIGCEVAASLRGLGVDVVLVEPQPAPLASvlgeqigQ 200
                                    689*****************************953333344544443 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.6
                  NAD_binding_7  10 vlvvGgGevAa.rkvrklleaga 31 
                                    v vvGgG  +   kvr  ++aga
  gi|121636609|ref|YP_976832.1| 373 VGVVGGGMAGKvMKVRGKIAAGA 395
                                    679****9987567777777776 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.13   1.3e+02     226     262 ..      87     121 ..      74     144 .. 0.76
   2 !   18.0   1.2   1.5e-06    0.0014     209     261 ..     198     249 ..     190     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                                    ETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                  Amino_oxidase 226 rlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                    rl++     + + ++ tvtl dg+v+ +D  v+++ l
  gi|121636609|ref|YP_976832.1|  87 RLGSAAV--SLDTGEQTVTLADGTVLGYDELVIATGL 121
                                    4444444..445578899999***********99987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.5e-06
                                    THHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                  Amino_oxidase 209 lsqlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                    ++ql+ +l++   g+d+r++  V e++  g+  +v l+dg++++aD Vvv + 
  gi|121636609|ref|YP_976832.1| 198 IGQLVTRLHR-DEGVDVRTGVTVAEVRGKGHVDAVVLTDGTELPADLVVVGIG 249
                                    689*******.**************************************9876 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.011      28      71 ..     146     189 ..     136     209 .. 0.84
   2 ?   -0.5   0.2       0.7   6.7e+02      28      56 ..     362     390 ..     351     401 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                    CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                   2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71 
                                    al+ +  + +   ++G+G IG +va  l+++g++v+ +++++ +
  gi|121636609|ref|YP_976832.1| 146 ALRKHASAARHAVVVGAGFIGCEVAASLRGLGVDVVLVEPQPAP 189
                                    5666777788999*************************999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.7
                                    CGSBS-GTTSEEEEES-SHHHHHHHHHHH CS
                   2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlk 56 
                                     l  +e  g  vG++G G  G+ +  r k
  gi|121636609|ref|YP_976832.1| 362 FLAYYERDGVLVGVVGGGMAGKVMKVRGK 390
                                    56667888999********9998877766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.061        57       1      27 [.      18      46 ..      18      53 .. 0.79
   2 !   11.7   0.1   0.00025      0.23       2      38 ..     158     194 ..     157     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.061
                                   EEEES-SHHHHHHHHHHHH.TT..EEEEEE CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.gg..kdvvvi 27
                                   i+i+G G  + + ae+L++ g+  +  +++
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRaGYsgR-LTIV 46
                                   89*****************665643.5554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                                    EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelr 38 
                                    +++G+G +G ++a  L+  g  dvv+++ +++ ++++ 
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASLRGlGV-DVVLVEPQPAPLASVL 194
                                    8*****************666.7*******99887765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.004       3.8       2      36 ..      18      50 ..      17      57 .. 0.84
   2 !   13.5   0.7   2.8e-05     0.027       3      37 ..     158     190 ..     157     194 .. 0.94
   3 ?    4.3   0.1     0.018        17      96     141 ..     204     250 ..     191     269 .. 0.75
   4 ?   -4.3   0.6       7.7   7.3e+03       4      14 ..     375     385 ..     373     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.004
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   +v++G+G+A  + A++l +a +  +++++  s+++
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGYSGRLTIV--SDEV 50
                                   89***************999998888888..5555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.8e-05
                  Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                    vv+GaG  g+ +Aa l     g+ vvl+e+ p +l
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASL--RGLGVDVVLVEPQPAPL 190
                                    8***************..************99875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.018
                  Lycopene_cycl  96 rlv.engvkll.eakvesveeeeageslvvleggrkirarlvvdargl 141
                                    rl  ++gv  +   +v++v+ +      vvl +g +++a lvv++ g 
  gi|121636609|ref|YP_976832.1| 204 RLHrDEGVDVRtGVTVAEVRGKGH-VDAVVLTDGTELPADLVVVGIGS 250
                                    444456665440458899988877.68899**************9983 PP

  == domain 4  score: -4.3 bits;  conditional E-value: 7.7
                  Lycopene_cycl   4 viGaGpAglsl 14 
                                    v+G+G Ag  +
  gi|121636609|ref|YP_976832.1| 375 VVGGGMAGKVM 385
                                    9******9655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1     0.013        13       2      26 ..      18      46 ..      17      52 .. 0.84
   2 ?   -1.0   0.0       1.1     1e+03     163     207 ..      86     126 ..      80     152 .. 0.64
   3 !   15.7   1.1   9.3e-06    0.0088       1      30 [.     156     187 ..     156     195 .. 0.84
   4 ?    3.1   0.5     0.062        58     157     201 ..     207     249 ..     196     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                                   EEEECTSHHHHHHHHHHHHTT....EEEE CS
                            DAO  2 vviiGGGiiGlstAyeLarrg....Vtll 26
                                   +vi+GGG + + tA +L r+g     t++
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGysgrLTIV 46
                                   8****************777777786666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                    EEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH CS
                            DAO 163 ilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll 207
                                    +++g+ +++l+  +   ++v  t + g++  +d +V+a+G+  + +
  gi|121636609|ref|YP_976832.1|  86 LRLGSAAVSLDT-G--EQTV--TLAdGTVLGYDELVIATGLVPRRI 126
                                    677888888843.2..3455..223376644699*****9876655 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 9.3e-06
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                    + v++G+G iG+ +A  L   g  V+l+e ++
  gi|121636609|ref|YP_976832.1| 156 HAVVVGAGFIGCEVAASLRGLGvdVVLVEPQP 187
                                    679***************4446*******994 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.062
                                    HHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                            DAO 157 ealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                    ++ Gv++++g +v +++   g v  v + t+g++  ad vV+  G
  gi|121636609|ref|YP_976832.1| 207 RDEGVDVRTGVTVAEVR-GKGHVDAV-VLTDGTELPADLVVVGIG 249
                                    6789******9999994.34677777.667777745588888666 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.64   6.1e+02       2      30 ..      18      46 ..      17      56 .. 0.85
   2 ?   14.3   0.2   2.9e-05     0.027       3      50 ..     158     206 ..     156     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.64
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                   + ++G G+  a  a+++ +ag++ +l+ +
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGYSGRLTIV 46
                                   679******************98776655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                                    EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH.HHHHHHHCCT CS
                        3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekale.kieksleklv 50 
                                     v+GaG +G ++aa +   g++Vvlv+ +++ l+++l  +i + + +l+
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASLRGLGVDVVLVEPQPAPLASVLGeQIGQLVTRLH 206
                                    69***************************99998876514444444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.018        17       2      28 ..      18      44 ..      17      56 .. 0.88
   2 ?   -1.5   0.0       1.1   1.1e+03     129     149 ..     100     120 ..      62     124 .. 0.81
   3 ?   13.4   0.6   3.2e-05      0.03       3      33 ..     158     188 ..     156     203 .. 0.82
   4 ?    2.4   0.1     0.069        65     109     150 ..     209     250 ..     198     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                   ++++GgG+A    A ++ r+G++  L 
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGYSGRLT 44
                                   79*******************987775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                    EEEEETTS-EEEECEEEE--T CS
                           GIDA 129 kgvvtedgetikakavviatG 149
                                    + v+++dg+++  +  viatG
  gi|121636609|ref|YP_976832.1| 100 QTVTLADGTVLGYDELVIATG 120
                                    569999999999999999999 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 3.2e-05
                                    EEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkld 33 
                                    +V+G+G  Gce A+ +  lG++v+L+ ++  
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASLRGLGVDVVLVEPQPA 188
                                    8************************965544 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.069
                                    TTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 109 pnleiiee.eveeliveekkvkgvvtedgetikakavviatGt 150
                                    + ++++++ +v+e+   +++v +vv++dg+++ a+ vv+  G+
  gi|121636609|ref|YP_976832.1| 209 EGVDVRTGvTVAEV-RGKGHVDAVVLTDGTELPADLVVVGIGS 250
                                    55555555245556.44799*********************99 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00015      0.14       2      36 ..     158     193 ..     157     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                    EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHH CS
                           ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rleal 36 
                                    +++GaG iG+ +aa+L   g dv+l+  ++  l+++
  gi|121636609|ref|YP_976832.1| 158 VVVGAGFIGCEVAASLRGLGVDVVLVEPQPaPLASV 193
                                    69**************88********9988888874 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.6   3.4e+03      21      48 ..      18      46 ..      15      50 .. 0.84
   2 ?   12.7   0.4   6.4e-05     0.061      19      43 ..     155     179 ..     134     183 .. 0.82
   3 ?   -3.8   0.0         7   6.6e+03     190     207 ..     370     387 ..     366     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                                   EEEE--SHHHHHHHHHHHHHTT.TEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                           ThiF 21 vllvGaGglGsellknLalsGv.gkltlv 48
                                   +++vG G      +++L ++G  g+lt+v
  gi|121636609|ref|YP_976832.1| 18 IVIVGGGLAAARTAEQLRRAGYsGRLTIV 46
                                   78999999999999999999996799998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.4e-05
                                    SEEEEE--SHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  19 skvllvGaGglGsellknLalsGvg 43 
                                     + ++vGaG +G+e++  L ++Gv 
  gi|121636609|ref|YP_976832.1| 155 RHAVVVGAGFIGCEVAASLRGLGVD 179
                                    6889*******************95 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7
                                    HHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                           ThiF 190 atttavvaglaalellkl 207
                                    + +++vv+g +a +++k+
  gi|121636609|ref|YP_976832.1| 370 GVLVGVVGGGMAGKVMKV 387
                                    567899999999999997 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.44   4.1e+02      14      36 ..      17      39 ..       8      47 .. 0.83
   2 ?    8.9   0.1    0.0016       1.5      10      41 ..     152     183 ..     144     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                                   EEEEES-SHHHHHHHHHHHCCT- CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgv 36
                                    ++++G G  a ++a++L ++g+
  gi|121636609|ref|YP_976832.1| 17 GIVIVGGGLAAARTAEQLRRAGY 39
                                   689***************99876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                                    .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                   Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvv 41 
                                     + ++++++GaG ++ +va  L   gv+ v+v
  gi|121636609|ref|YP_976832.1| 152 SAARHAVVVGAGFIGCEVAASLRGLGVDVVLV 183
                                    457899********************998887 PP

>> FLgD_tudor  FlgD Tudor-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.34   3.3e+02      33      52 ..      92     109 ..      91     114 .. 0.82
   2 ?    7.9   2.0    0.0038       3.6       6      41 ..     161     237 ..     158     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.34
                                    EEEE.ETTEEEEEETTEE.E CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                     FLgD_tudor  33 sVslstggglmLnLglggtv 52 
                                    +Vsl ++g++++ L++g+ v
  gi|121636609|ref|YP_976832.1|  92 AVSL-DTGEQTVTLADGT-V 109
                                    7999.999999***9776.4 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0038
                                    TTCTTTSEEEEE.........................................TEEEE.E-EEEEEEEEEEEE.ETTE CS
                                    xxxxxxxxxxxx.........................................xxxxx.xxxxxxxxxxxxxxxxxxx RF
                     FLgD_tudor   6 AasLiGkeVlvp.........................................Gtsva.attlvygtVdsVslstggg 41 
                                    +a++iG eV ++                                          t v+ a++   g+Vd+V+l t+g+
  gi|121636609|ref|YP_976832.1| 161 GAGFIGCEVAASlrglgvdvvlvepqpaplasvlgeqigqlvtrlhrdegvdvRTGVTvAEVRGKGHVDAVVL-TDGT 237
                                    589999999999999999999999*************************99996778879*************.7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2671.45
//
Query:       gi|121636610|ref|YP_976833.1|  [L=84]
Description: hypothetical protein BCG_0738c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0075   17.1   0.7     0.0089   16.8   0.7    1.1  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.7     5e-07    0.0089      19     102 ..       1      77 [.       1      81 [. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-07
                   Glyoxalase_6  19 algwevereeaaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaevarlvalGArvlreprdgthgrvlaD 98 
                                    +lgw+v++ +   +   + +p   +   ++    p+pa  + + d+   d+da+var+ a+GA      + ++    +aD
  gi|121636610|ref|YP_976833.1|   1 MLGWTVKPGR---VADGWQAP---GVHLMARCSGPQPAS-ERRADMDGGDIDAAVARVRAAGALAEPSRQPDDMSAECAD 73 
                                    5899999999...33333333...222333333333433.57899999**************976655555544446888 PP

                   Glyoxalase_6  99 PeGn 102
                                     +G+
  gi|121636610|ref|YP_976833.1|  74 DQGA 77 
                                    7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 629.75
//
Query:       gi|121636611|ref|YP_976834.1|  [L=349]
Description: hypothetical protein BCG_0739c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-111  373.0   4.0   1.8e-111  372.8   4.0    1.0  1  DUF2332   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2332  Uncharacterized protein conserved in bacteria (DUF2332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.8   4.0    1e-115  1.8e-111       3     335 .]      10     348 ..       8     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.8 bits;  conditional E-value: 1e-115
                        DUF2332   3 rfrrfaeaeaagsSplyarlaravaddlealgllaa.......apagdavpllllaalhrlvlagraheLaayYpslggd 75 
                                    ++r++++ +++++Sp+y +l++ va+d e +g++a        ap+g+avpl+ll++lhr+vl+gra+ L+++Yps+gg+
  gi|121636611|ref|YP_976834.1|  10 TLRSQGRVCTSSGSPMYRELLELVAADVESGGVFASiladqkgAPEGQAVPLRLLGGLHRMVLDGRAPVLRRWYPSTGGT 89 
                                    799***************************************************************************** PP

                        DUF2332  76 aaaeelwaafrefllehedelrallatrpvQTNEvgRaavLlpalaavaeavarplallEvGaSAGLnLlldryayryeg 155
                                    ++ae++w+++ ++ +++ ++lra+l+++p QTNEvgR+a+L+++l+ +  +++ p++l+E+G+SAGLnL++dry+yry g
  gi|121636611|ref|YP_976834.1|  90 WQAEAAWPDIVRTATDQPESLRAALDRPP-QTNEVGRSAALIGGLLIACLQFDLPIRLFEIGSSAGLNLRPDRYRYRYLG 168
                                    *****************************.************************************************** PP

                        DUF2332 156 gelGdadspvvlaaawrgerppplpavevvsrvGlDlnpldltdeedalwLrAlvWpdqpeRlarleaAlalaredppel 235
                                    ge+G adspv+++ aw ge  pp+++v++v+r+G+D++p+d+t+++++l   +++Wpdq++Rl+rl+ A+a+ar+ p++l
  gi|121636611|ref|YP_976834.1| 169 GEWGLADSPVRIDNAWLGE-LPPTATVRIVERHGYDIAPIDVTSPDGELNALSYIWPDQTDRLERLRGAIAVARNIPADL 247
                                    *******************.466689****************************************************** PP

                        DUF2332 236 vrgdavdlLpaalaevpadallvVfhsivlqylpaeeraallaalaelga....erplawvslEadgva.gaaeeaelgl 310
                                    +r+ a ++++ +  +   dal+v++hsi++qylpa+eraa++a +++l+a    + p+++++lE++++  ga+ +  +++
  gi|121636611|ref|YP_976834.1| 248 HRQAAHAAVAGMTLTD--DALTVLWHSITWQYLPADERAAIRAGIDALAAqadaHCPFVHLTLEPAHQRpGAQIKYLVRM 325
                                    ************9996..8*********************************99************9999999999999* PP

                        DUF2332 311 rlwpggeereealaradpHGrwleW 335
                                    r+wpgg++r   l++++pHG +++W
  gi|121636611|ref|YP_976834.1| 326 RSWPGGHARV--LGECHPHGPPVTW 348
                                    ******9999..************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2100.97
//
Query:       gi|121636612|ref|YP_976835.1|  [L=198]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-43  146.8   0.9    3.4e-43  146.1   0.9    1.3  1  TetR_C_14    MftR C-terminal domain
    1.4e-13   50.4   0.5    2.4e-13   49.6   0.5    1.4  1  TetR_N       Bacterial regulatory proteins, tetR family
    0.00095   19.3   0.1     0.0035   17.5   0.0    1.9  3  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
     0.0075   16.0   0.6       0.14   12.0   0.0    2.8  3  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.067   13.3   0.1    2.0  2  HTH_7        Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> TetR_C_14  MftR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   0.9   9.5e-47   3.4e-43       3     111 ..      85     193 ..      83     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 9.5e-47
                                    HHHHHHHHHHHTT---GGGHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHH CS
                      TetR_C_14   3 lldalreAvlafnrvdeeeeeehrrRmrLiltvPaLqAhstlryaawrevvAefvAeRtgtdaddlvprtvaaavlaaal 82 
                                    l dalr+A+lafn++de+e+ +hr+Rmr+il++P+LqA+s+++ya wrev+A+fvA+R+g + +d++p+tva+++l++al
  gi|121636612|ref|YP_976835.1|  85 LRDALRAALLAFNTFDESETIRHRKRMRVILQTPELQAYSMTMYAGWREVIAKFVARRSGGKTTDFMPQTVAWTMLGVAL 164
                                    789***************************************************************************** PP

                                    HHHHHHHH-TTS-HHHHHHHHHHHHHH-S CS
                      TetR_C_14  83 aayeqwladedadlaelLdealdllaagl 111
                                    +aye+wl+de+ +l+e L +a+d + agl
  gi|121636612|ref|YP_976835.1| 165 SAYEHWLRDESVSLTEALGAAFDVVGAGL 193
                                    **************************998 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.5   6.8e-17   2.4e-13       2      43 ..      19      60 ..      18      60 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 6.8e-17
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeL 43
                                    d+A elfa +G+  ++v++IA++AG+++++l+ry++sK ++
  gi|121636612|ref|YP_976835.1| 19 SDVAIELFAAHGFTDVSVDDIARAAGIARRTLFRYYASKNAI 60
                                   589************************************985 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.7e-07    0.0035      15      51 ..      22      58 ..      17      69 .. 0.90
   2 ?   -2.2   0.0       1.2   4.3e+03      76      90 ..     111     124 ..      88     144 .. 0.58
   3 ?   -2.7   0.0       1.8   6.4e+03      35      50 ..     159     174 ..     146     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.7e-07
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHHH-HH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWkkkke 51
                                   a+el + + +  +++d+ia+  g++r+Tl+++   k+
  gi|121636612|ref|YP_976835.1| 22 AIELFAAHGFTDVSVDDIARAAGIARRTLFRYYASKN 58
                                   899****************************986655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                    HHHHHSSS--HHHHH CS
                    HTH_Tnp_1_2  76 lrkilkgrssvkAie 90 
                                    +r il+  ++++A +
  gi|121636612|ref|YP_976835.1| 111 MRVILQT-PELQAYS 124
                                    3334333.4444433 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.8
                                    HHTS-HHHHHHHHH-H CS
                    HTH_Tnp_1_2  35 evgvsrsTlykWkkkk 50 
                                     +gv+ s + +W++++
  gi|121636612|ref|YP_976835.1| 159 MLGVALSAYEHWLRDE 174
                                    5899999999999876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.8e-05      0.14      17      37 ..      33      53 ..      21      59 .. 0.79
   2 ?   -2.2   0.1       1.1   3.9e+03       3      12 ..     106     115 ..     104     120 .. 0.79
   3 ?    0.9   0.0      0.12   4.4e+02      26      39 ..     159     172 ..     152     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                         HTH_23 17 GlsvreIAreLgvsrrTvyrw 37
                                     sv +IAr+ g+ rrT+ r+
  gi|121636612|ref|YP_976835.1| 33 DVSVDDIARAAGIARRTLFRY 53
                                   6799***************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                         HTH_23   3 sereRlrill 12 
                                    + r+R+r++l
  gi|121636612|ref|YP_976835.1| 106 RHRKRMRVIL 115
                                    5689999987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                         HTH_23  26 eLgvsrrTvyrwlk 39 
                                    +Lgv  + + +wl+
  gi|121636612|ref|YP_976835.1| 159 MLGVALSAYEHWLR 172
                                    89**********98 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.42   1.5e+03       1      29 [.       8      23 ..       6      28 .. 0.57
   2 ?   13.3   0.1   1.9e-05     0.067      23      43 ..      35      55 ..      32      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.42
                                   S---SS-HHHHGGGGSSTTTT--STTTSS CS
                          HTH_7  1 GRpsklskndinrvvkLleeGisiskIAk 29
                                   GR+++ +++              is++A+
  gi|121636612|ref|YP_976835.1|  8 GRRRSTTPH-------------HISDVAI 23
                                   455555554.............4555554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.9e-05
                                   -STTTSSSS---SSSS--SS- CS
                          HTH_7 23 siskIAkevnisRsTvYRyla 43
                                   s+ +IA++ +i+R T+ Ry a
  gi|121636612|ref|YP_976835.1| 35 SVDDIARAAGIARRTLFRYYA 55
                                   6789***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1375.45
//
Query:       gi|121636613|ref|YP_976836.1|  [L=109]
Description: hypothetical protein BCG_0741 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 795.95
//
Query:       gi|121636614|ref|YP_976837.1|  [L=391]
Description: coenzyme PQQ synthesis protein E pqqE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-23   84.4   0.0    1.6e-23   83.9   0.0    1.2  1  Radical_SAM   Radical SAM superfamily
    1.9e-05   24.9   0.0    3.2e-05   24.2   0.0    1.3  1  Fer4_12       4Fe-4S single cluster domain
    2.4e-05   24.7   0.4    4.9e-05   23.8   0.4    1.5  1  SPASM         Iron-sulfur cluster-binding domain
    0.00014   22.0   0.0    0.00024   21.2   0.0    1.3  1  Fer4_14       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.076   12.9   0.2       0.82    9.6   0.1    2.5  3  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   4.5e-27   1.6e-23       3     165 ..      26     179 ..      24     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4.5e-27
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                     t +Cnl+C++C  ++     +++ +ls+++ +++++el ++++v +v +gggep+++pdf el++ + +     + + +
  gi|121636614|ref|YP_976837.1|  26 LTYACNLACVHCLSSS---GKRDPGELSTRQCKDIIDEL-ERMQVFYVNIGGGEPTVRPDFWELVDYATAH---HVGVKF 98 
                                    6889***********8...8*******************.9*****************************8...9***** PP

                                    EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                    +tng+++++e++ rl+      v+++l+ a+ e v + ++++++f+  ++al++l++ag+   v + v++   n ++l+e
  gi|121636614|ref|YP_976837.1|  99 STNGVRITPEVATRLAATDYVDVQISLDGATAE-VNDAIRGTGSFDMAVRALQNLAAAGFA-GVKISVVITRRNVAQLDE 176
                                    *********************************.***************************.999999999999999999 PP

                                    HHH CS
                                    xxx RF
                    Radical_SAM 163 lle 165
                                    ++ 
  gi|121636614|ref|YP_976837.1| 177 FAT 179
                                    875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   8.9e-09   3.2e-05      12     114 ..      27     122 ..      17     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.9e-09
                        Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                    +  Cnl+C  C   +  + + g+  t++  + ii++l+  +++ + + GGEP +   ++++ elv++  ++ + ++ +++
  gi|121636614|ref|YP_976837.1|  27 TYACNLACVHCLSSSG-KRDPGELSTRQC-KDIIDELERMQVFYVNIGGGEPTV---RPDFWELVDYATAHHV-GVKFST 100
                                    678*********6555.567777777766.6899********************...***************9.699999 PP

                        Fer4_12  92 tgytleelskkekeellkeidvl 114
                                    +g+ +    ++ +    +++dv 
  gi|121636614|ref|YP_976837.1| 101 NGVRITPEVAT-RLAATDYVDVQ 122
                                    99987655543.45555666653 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.4   1.4e-08   4.9e-05       1      67 [.     251     313 ..     251     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.4e-08
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGni.reesleeIw.nseeyqefrkskkfplielCrnC 67 
                                    C a++  + I++ GdV+ C +    +++ +  Gn+ ++  ++++w ns+ ++e+r   +++    C +C
  gi|121636614|ref|YP_976837.1| 251 CGAGRVVCLIDPVGDVYACPFA---IHDHFLAGNVlSDGGFQNVWkNSSLFRELR---EPQSAGACGSC 313
                                    666777789**********555...44449*****78888*****6667******...55556678888 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.7e-08   0.00024       7     113 ..      29     121 ..      26     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.7e-08
                        Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                     Cnl+C+ C+ ++  k + g+ +t++   +i+++l+  ++    + + GGeP      +++ +lv++   +   + +++ 
  gi|121636614|ref|YP_976837.1|  29 ACNLACVHCLSSS-GKRDPGELSTRQCK-DIIDELERMQV--FYVNIGGGEPTV---RPDFWELVDYATAHH--VGVKFS 99 
                                    6*********999.67778888887765.99988877777..679*******94...59********99988..9***** PP

                        Fer4_14  87 tngtleielektpdlkeklealskidl 113
                                    tng+       tp+   +l a +++d+
  gi|121636614|ref|YP_976837.1| 100 TNGVRI-----TPEVATRLAATDYVDV 121
                                    **9865.....3445555555555554 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.82   2.9e+03      11      30 ..      93     114 ..      89     115 .. 0.61
   2 ?    9.6   0.1   0.00023      0.82      17      44 ..     165     191 ..     153     192 .. 0.80
   3 ?   -0.8   0.0      0.38   1.4e+03      40      53 ..     205     218 ..     203     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.82
                   NIR_SIR_ferr  11 mvrlrvp.nG.ritaeqlrala 30 
                                    +v+++   nG rit+e +++la
  gi|121636614|ref|YP_976837.1|  93 HVGVKFStNGvRITPEVATRLA 114
                                    5555554444266888888887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00023
                   NIR_SIR_ferr  17 pnGritaeqlraladiaekygsgeirlT 44 
                                       r + +ql+++a +a +yg  ++r+T
  gi|121636614|ref|YP_976837.1| 165 VITRRNVAQLDEFATLASRYG-ATLRIT 191
                                    55556788*************.*****9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.38
                   NIR_SIR_ferr  40 eirlTtrQnlqlhg 53 
                                    +++ T++Q++ql +
  gi|121636614|ref|YP_976837.1| 205 DLHPTADQQVQLYD 218
                                    6899*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2934.67
//
Query:       gi|121636615|ref|YP_976838.1|  [L=396]
Description: L-lactate dehydrogenase (cytochrome) lldD1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     4e-108  361.5   0.1   4.7e-108  361.3   0.1    1.0  1  FMN_dh        FMN-dependent dehydrogenase
    2.7e-07   29.9   1.9    1.1e-06   27.9   1.3    2.0  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    3.5e-06   26.4   0.3    4.9e-06   25.9   0.3    1.2  1  Glu_synthase  Conserved region in glutamate synthase
     0.0092   15.3   0.8      0.024   14.0   0.8    1.7  1  ThiG          Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.012   15.1   1.0      0.094   12.2   0.2    2.3  2  His_biosynth  Histidine biosynthesis protein
      0.017   14.5   2.9      0.029   13.8   2.9    1.3  1  NMO           Nitronate monooxygenase
      0.025   13.7   0.3      0.043   12.9   0.3    1.3  1  Dus           Dihydrouridine synthase (Dus)
      0.051   12.8   0.5       0.12   11.6   0.3    1.6  1  DHO_dh        Dihydroorotate dehydrogenase
       0.12   11.8   0.0         12    5.3   0.0    2.6  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.99    9.5   8.0       0.14   12.2   0.4    3.0  3  PA            PA domain


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.3   0.1  2.6e-111  4.7e-108       1     344 [.      16     376 ..      16     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 361.3 bits;  conditional E-value: 2.6e-111
                                    HHCCS-HHHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHH CS
                         FMN_dh   1 ArkrlpkkafayvaggagdevtlrenraaferirlrprvlrdvskvdlsttllGqklslPvliaPvglaklahpdgelal 80 
                                    A++rlpk++++ +  ++++++t+++n aaf+++ + p+v+  + k+dlstt++Gq++slPv+i+P+g++  ++p ge+a+
  gi|121636615|ref|YP_976838.1|  16 AKRRLPKSVYSSLIAASEKGITVADNVAAFSELGFAPHVIGATDKRDLSTTVMGQEVSLPVIISPTGVQA-VDPGGEVAV 94 
                                    89*****************************************************************985.789****** PP

                                    HHHHHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHC.T CS
                         FMN_dh  81 araaakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerdlrn.g 159
                                    araaa+ g++++ls++as+++eev aa++ + +fq+y++  r+  +e ++ra++ag+  lv+t+D ++   R++   +  
  gi|121636615|ref|YP_976838.1|  95 ARAAAARGTVMGLSSFASKPIEEVIAANP-KTFFQVYWQGGRDALAERVERARQAGAVGLVVTTDWTFSHGRDWGSPKiP 173
                                    **************************766.*******************************************9888734 PP

                                    --BSTT-T.G.TTGGGSTSGSCCTTH......................THHHHHHCCCHB-TC--HHHHHHHHHHHSSEE CS
                         FMN_dh 160 fslppklklrnllqelakpewaaeal....................kkasaaaefvgkqldpsltwddikwlreqtklpl 219
                                     +++ k+ lr   ++ ++p+w ++++                          a++ + + +p  tw+di wlre + +p+
  gi|121636615|ref|YP_976838.1| 174 EEMNLKTILRLSPEAITRPRWLWKFAktlrppdlrvpnqgrrgepgP--PFFAAYGEWMATPPPTWEDIGWLRELWGGPF 251
                                    466666668889999*********************99877664321..222244444557999**************** PP

                                    EEEEE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                         FMN_dh 220 vvKGvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavll 299
                                    ++KGv++++dakrav+aGv++i vSNHGG +ldg+pa+i++Lp++ +avg+++evl+DgGirrGsDv+kA+alGA+av++
  gi|121636615|ref|YP_976838.1| 252 MLKGVMRVDDAKRAVDAGVSAISVSNHGGNNLDGTPASIRALPAVSAAVGDQVEVLLDGGIRRGSDVVKAVALGARAVMI 331
                                    ******************************************************************************** PP

                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                         FMN_dh 300 GRpflyglaagGeeGvervleilraelertmallGvksvaeldrs 344
                                    GR++l+glaa+G++Gve+vl+ilr  +++++  lG +sv++l+++
  gi|121636615|ref|YP_976838.1| 332 GRAYLWGLAANGQAGVENVLDILRGGIDSALMGLGHASVHDLSPA 376
                                    ******************************************987 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.3   6.2e-10   1.1e-06     200     238 ..     296     334 ..     284     345 .. 0.84
   2 ?   -0.2   0.0      0.22     4e+02     297     326 ..     345     374 ..     338     381 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.2e-10
                                    HHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 200 aeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                    ++aa   +v+v+ DGGi+   d+vkA+a+Ga avm+G+ 
  gi|121636615|ref|YP_976838.1| 296 VSAAVGDQVEVLLDGGIRRGSDVVKAVALGARAVMIGRA 334
                                    45566678*****************************85 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                    B-HHHHHHHHHHHHHHHHHHHT-SSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 297 gsvkevveqlvgglrsgmgylGaktieelk 326
                                    + v++v++ l gg+ s++  lG +++++l 
  gi|121636615|ref|YP_976838.1| 345 AGVENVLDILRGGIDSALMGLGHASVHDLS 374
                                    568999*******************99986 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   2.7e-09   4.9e-06     270     307 ..     299     336 ..     268     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.7e-09
                                    T-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                   Glu_synthase 270 glrdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                     + d+v++  dGg++ g dvvka+alGA av ig+a l
  gi|121636615|ref|YP_976838.1| 299 AVGDQVEVLLDGGIRRGSDVVKAVALGARAVMIGRAYL 336
                                    5789******************************9987 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.8   1.3e-05     0.024     165     206 ..     291     334 ..     255     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHH CS
                           ThiG 165 ealkiiieea..kvPvivDAGigspsdaaqamelGadavllnta 206
                                     al  + + +  +v v++D Gi++ sd+++a+ lGa av++  a
  gi|121636615|ref|YP_976838.1| 291 RALPAVSAAVgdQVEVLLDGGIRRGSDVVKAVALGARAVMIGRA 334
                                    344455555566899*************************9765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.16   2.8e+02      81     102 ..     255     276 ..     248     284 .. 0.86
   2 ?   12.2   0.2   5.2e-05     0.094      65     104 ..     296     334 ..     281     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
                                    SSSSHHHHHHHHHCT-SEEEES CS
                   His_biosynth  81 GIrsledveelleagadkviig 102
                                    G+ +++d++++++ag++ ++++
  gi|121636615|ref|YP_976838.1| 255 GVMRVDDAKRAVDAGVSAISVS 276
                                    8999999********9999987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.2e-05
                                    HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHH CS
                   His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigta 104
                                    v++ +   +++v ++GGIr+ +dv +++ +ga+ v+ig a
  gi|121636615|ref|YP_976838.1| 296 VSAAVGD-QVEVLLDGGIRRGSDVVKAVALGARAVMIGRA 334
                                    3332322.36667777777777777777777777777655 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.9   1.6e-05     0.029     178     227 ..     286     337 ..     248     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                            NMO 178 dkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                    +   ++ +p v  av   + v+  GGi ++ +v  a alGA +v ig ++L 
  gi|121636615|ref|YP_976838.1| 286 TPASIRALPAVSAAVGdqVEVLLDGGIRRGSDVVKAVALGARAVMIGRAYLW 337
                                    34467788999999978899*****************************996 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.4e-05     0.043     142     216 ..     260     335 ..     257     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
                            Dus 142 elakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrga 216
                                    + ak++ +aG+ a+ v     ++    +a ++a  +v  av   + v+  G+I+  +d+ ++++  Ga +vmigr+ 
  gi|121636615|ref|YP_976838.1| 260 DDAKRAVDAGVSAISVSNHGGNNLDGTPASIRALPAVSAAVGdqVEVLLDGGIRRGSDVVKAVAL-GARAVMIGRAY 335
                                    5688999999999999555455555559*************999********************9.*********86 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   6.5e-05      0.12     228     277 ..     287     336 ..     272     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                                    HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                         DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                    + +++ + ++++ + +++ ++  GGi  g D++  +  GA +v ++ a+ 
  gi|121636615|ref|YP_976838.1| 287 PASIRALPAVSAAVGDQVEVLLDGGIRRGSDVVKAVALGARAVMIGRAYL 336
                                    679999999************************************98864 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   4.5e+03     151     168 ..     139     156 ..     128     158 .. 0.77
   2 ?    3.7   0.0     0.021        38     149     170 ..     257     278 ..     237     279 .. 0.83
   3 ?    5.3   0.0    0.0066        12     139     173 .]     303     337 ..     285     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                                    HHHHHHHCTT.SSEEEE- CS
                   G3P_antiterm 151 kedveealkaGaiavsts 168
                                     e+ve+a +aGa++  ++
  gi|121636615|ref|YP_976838.1| 139 AERVERARQAGAVGLVVT 156
                                    578899999999886655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                                    -SHHHHHHHCTT.SSEEEE--H CS
                   G3P_antiterm 149 etkedveealkaGaiavstsnk 170
                                       +d ++a++aG++a+s+sn+
  gi|121636615|ref|YP_976838.1| 257 MRVDDAKRAVDAGVSAISVSNH 278
                                    4568999*************96 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0066
                                    ..EEEEESS--SHHHHHHHCTT.SSEEEE--HHHH CS
                   G3P_antiterm 139 kipiiaGGLietkedveealkaGaiavstsnkelW 173
                                    +++++  G i+  +dv +a++ Ga av+ ++  lW
  gi|121636615|ref|YP_976838.1| 303 QVEVLLDGGIRRGSDVVKAVALGARAVMIGRAYLW 337
                                    46677778899*********************999 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   7.8e-05      0.14      35      55 ..     126     158 ..      70     181 .. 0.68
   2 ?   -1.0   0.1       1.1   1.9e+03      37      87 ..     260     281 ..     255     305 .. 0.55
   3 ?    0.2   0.4      0.45     8e+02      39      54 ..     318     341 ..     306     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
                             PA  35 f............aeKarnAqaaGAagviivnd 55 
                                    f            ae+++ A++aGA+g+++ +d
  gi|121636615|ref|YP_976838.1| 126 FfqvywqggrdalAERVERARQAGAVGLVVTTD 158
                                    156666777777799***************943 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                             PA  37 eKarnAqaaGAagviivndgelgaatgasgnegepdgitiPavgvsredge 87 
                                    + a+ A +aG  ++ + n g+                             +
  gi|121636615|ref|YP_976838.1| 260 DDAKRAVDAGVSAISVSNHGG-----------------------------N 281
                                    556677777776655544332.............................2 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.45
                             PA  39 arnAqaaGAagviiv........n 54 
                                    +  A a GA +v i          
  gi|121636615|ref|YP_976838.1| 318 VVKAVALGARAVMIGraylwglaA 341
                                    567899999999998444433331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.20s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3112.18
//
Query:       gi|121636616|ref|YP_976839.1|  [L=251]
Description: hypothetical protein BCG_0744 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-59  200.4   0.4    3.6e-59  200.2   0.4    1.1  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.4     2e-63   3.6e-59      13     239 ..      25     237 ..      14     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 2e-63
                   Creatininase  13 keddvailPvGstEqHGphlplgtDtliaealaervaeklgak........alvlPtlpyGvseehlgfpGTislspetl 84 
                                     +++ +++P+GstEqHGphlpl tDt ia+a+a+ v ++l+a+        +l++P+++yG+s eh++f+GTis+++e l
  gi|121636616|ref|YP_976839.1|  25 STSPSIVIPLGSTEQHGPHLPLDTDTRIATAVARTVTARLHAEdlpiaqeeWLMAPAIAYGASGEHQRFAGTISIGTEAL 104
                                    567899*****************************99999777777777889**************************** PP

                   Creatininase  85 iavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeeeggg 164
                                    + +l ++++s+a + +rr+v+vngHggn+ al +a+  lrae ++a+++     +                      g+ 
  gi|121636616|ref|YP_976839.1| 105 TMLLVEYGRSAACW-ARRLVFVNGHGGNVGALTRAVGLLRAEGRDAGWC----PCTCPG------------------GDP 161
                                    **************.****************************888763....333333..................89* PP

                   Creatininase 165 HAgelEtSlmlalrpelVrmdraedpeeaklakeg.vstaedaeelspsGvlGdpskataekGealleaaveelae 239
                                    HAg++EtS++l+l p  Vr++r ++++ a+l+     +++ ++ ++s++GvlGdp+ ata++G+++++a+v+++++
  gi|121636616|ref|YP_976839.1| 162 HAGHTETSVLLHLSPADVRTERWRAGNRAPLPVLLpSMRRGGVAAVSETGVLGDPTTATAAEGRRIFAAMVDDCVR 237
                                    **************************9999998889999*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1726.15
//
Query:       gi|121636617|ref|YP_976840.1|  [L=470]
Description: membrane sugar transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-25   90.5   0.0    1.5e-25   89.9   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    8.7e-14   51.9   0.2    1.4e-13   51.3   0.2    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.8e-13   50.0   0.0    4.7e-13   49.2   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    4.2e-11   43.1   0.9    6.8e-11   42.4   0.9    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    6.5e-09   35.5   0.0    1.4e-08   34.4   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.056   13.1   0.0      0.099   12.3   0.0    1.3  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
       0.24   10.7   0.0       0.37   10.1   0.0    1.1  1  Glyco_transf_49  Glycosyl-transferase for dystroglycan


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0     6e-29   1.5e-25       1     165 [.      85     240 ..      85     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 6e-29
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-..SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgS..tDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                    +vvip+ N ++ l+++++sl+        ++ivvDDgS  + e+ +++ ++     ++ v+++++ +G+a+a+n+gl+a+
  gi|121636617|ref|YP_976840.1|  85 TVVIPVRNNASGLRRLVTSLRGL------RVIVVDDGSacPVESDDFVGAH----CDIEVLHHPHSKGPAAARNTGLAAC 154
                                    69********************8......*********5555555555555....59*********************** PP

                                    -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
                Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                    t+d+++flD+D++p ++wle l++++ ++ +++v++ ++    ++++  r +   + +   ++++   l++++  +++sa
  gi|121636617|ref|YP_976840.1| 155 TTDFVAFLDSDVTPRRGWLESLLGHFCDPTVALVAPRIVSLVEGENPVARYEAL-HSSLDLGQREAPVLPHSTVSYVPSA 233
                                    ****************************99988888888877777777776653.6666666666666666666666666 PP

                                    CEEEEHH CS
                Glycos_transf_2 159 allrrea 165
                                    a++ r++
  gi|121636617|ref|YP_976840.1| 234 AIVCRSS 240
                                    6666654 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.2   5.5e-17   1.4e-13       1     221 [.      81     291 ..      81     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 5.5e-17
                Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                    +rd++v++p+ n+++ l+++++sl       ++v+vv+d+s + + +  + ++ a+ d  + v++ ++  g+   + a n
  gi|121636617|ref|YP_976840.1|  81 HRDVTVVIPVRNNASGLRRLVTSLRG-----LRVIVVDDGSACPVES--DDFVGAHCD--IEVLHHPHSKGP---AAARN 148
                                    678*******************9876.....9************976..445556756..689999886666...55568 PP

                Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavg.tpvfllnrstlvsalgalefaerhlrfla.arralgvl 158
                                     +l a+++d+v+++D+D+    + l++ll  f +p v+ v    v l  +++ v+++ al+   +  ++ a +    +v 
  gi|121636617|ref|YP_976840.1| 149 TGLAACTTDFVAFLDSDVTPRRGWLESLLGHFCDPTVALVApRIVSLVEGENPVARYEALHSSLDLGQREApVLPHSTVS 228
                                    ********************************9********777777799999999988776666554433033344455 PP

                Glyco_tranf_2_3 159 tlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayi 221
                                    ++  +  + r +  ++ +g+d+  + ++D++l+ rl +ag r  y p a+v + +++ l + i
  gi|121636617|ref|YP_976840.1| 229 YVPSAAIVCRSSAIRDVGGFDETMHSGEDVDLCWRLIEAGARLRYEPIALVAHDHRTQLRDWI 291
                                    555699***********************************************9998877665 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.8e-16   4.7e-13       2     232 ..      86     297 ..      85     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.8e-16
                Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskae 81 
                                    vvip+r++     ++   ++ ++     +++ivvddgS+ +   e   ++ ++  + + + + ++ ++aaarN G   + 
  gi|121636617|ref|YP_976840.1|  86 VVIPVRNNASG--LR---RLVTSL--RGLRVIVVDDGSACP--VESDDFVGAHCDIEVLHHP-HSKGPAAARNTGLAACT 155
                                    66666666555..22...223333..458***********9..6667888888888555553.4579************* PP

                Glyco_tranf_2_2  82 sdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrv.ledllaakstlvkf 160
                                    +d+v FlD+D       +e +l      ++ +   a+v+  +v l++   + + ++e l  s ++ ++++ +   + v +
  gi|121636617|ref|YP_976840.1| 156 TDFVAFLDSDVTPRRGWLESLLG-----HFCDPTVALVAPRIVSLVE-GENPVARYEALHSSLDLgQREAPVLPHSTVSY 229
                                    **********************9.....7766666666666677765.56667899999999988577887755555544 PP

                Glyco_tranf_2_2 161 fapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykGfrrfl 232
                                     +p s  i+ +  a+  vGG+DE +  h+ ED dl  Rl  a   l   p  l  +++  +l+++   + f+
  gi|121636617|ref|YP_976840.1| 230 -VP-SAAIVCRSSAIRDVGGFDETM--HSGEDVDLCWRLIEAGARLRYEPIALVAHDHRTQLRDWIARKAFY 297
                                    .44.667899999************..**********************************99887666665 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.9   2.7e-14   6.8e-11       2     172 ..     159     326 ..     158     411 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.7e-14
                Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsv.Gsgafl 79 
                                    +++lD+D  + +  l+ ++ ++ +p va+v   ++   ++ n +++  al+ ++d g  +   + ++++v+ v  + ++ 
  gi|121636617|ref|YP_976840.1| 159 VAFLDSDVTPRRGWLESLLGHFCDPTVALVAPRIVSLvEGENPVARYEALHSSLDLGQ-REAPVLPHSTVSYVpSAAIVC 237
                                    789******************************998658999*********9988875.78889*******997888899 PP

                Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc........eleklil 151
                                    r sa+++vgg+d  + + +ED d++ rl ++G r+r+ p +lv   ++  lr+++++++ + + +               
  gi|121636617|ref|YP_976840.1| 238 RSSAIRDVGGFD-ETMHSGEDVDLCWRLIEAGARLRYEPIALVAHDHRTQLRDWIARKAFYGGSAaplavrhpD------ 310
                                    99**********.778*****************************************99777775332222110...... PP

                Glyco_trans_2_3 152 lvrllgylgsllwsalplhla 172
                                         + +++++  + + +++
  gi|121636617|ref|YP_976840.1| 311 -----KTAPLVISGGALMAWI 326
                                    .....2222222222222222 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   5.4e-12   1.4e-08      23     168 ..     148     294 ..     130     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5.4e-12
                Glyco_transf_21  23 lqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv.gsdakglaaaleaafl..ntlagvlqa.klsgl 98 
                                    +++l+a  +d++ ++Dsdv+ ++  Le+ll+++ dp+v+lV   +v  ++ ++  a+ ea++     +++ +     s +
  gi|121636617|ref|YP_976840.1| 148 NTGLAACTTDFVAFLDSDVTPRRGWLESLLGHFCDPTVALVAPRIVsLVEGENPVARYEALHSslDLGQREAPVlPHSTV 227
                                    6789999**********************************996664777778888888887643344444444556999 PP

                Glyco_transf_21  99 gfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRq 168
                                    + +  ++++ r +a++++GGf +   +  eD  l ++l +aG +++  p++++ ++   r+ lr++ aR 
  gi|121636617|ref|YP_976840.1| 228 SYVPSAAIVCRSSAIRDVGGFDE-TMHSGEDVDLCWRLIEAGARLRYEPIALVAHDH--RTQLRDWIARK 294
                                    9**********************.8888**********************9997765..56899999985 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05     0.099      24      64 ..     235     273 ..     227     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                Glyco_transf_7C  24 lalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleier 64 
                                    +++r++  ++++Gf++t++   gED +l+ Rl+++g ++  
  gi|121636617|ref|YP_976840.1| 235 IVCRSSAIRDVGGFDETMHS--GEDVDLCWRLIEAGARLRY 273
                                    56788999*********997..*************988765 PP

>> Glyco_transf_49  Glycosyl-transferase for dystroglycan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00015      0.37     120     152 ..     145     177 ..     142     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                Glyco_transf_49 120 vlRNvARkaaqtefvlvlDidlvpseglvekfl 152
                                    + RN +  a++t+fv  lD d+ p +g+ e++l
  gi|121636617|ref|YP_976840.1| 145 AARNTGLAACTTDFVAFLDSDVTPRRGWLESLL 177
                                    57**************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3352.19
//
Query:       gi|121636618|ref|YP_976841.1|  [L=479]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-55  186.3   0.0      1e-54  186.0   0.0    1.1  1  GMC_oxred_N    GMC oxidoreductase
    7.7e-30  104.3   0.7    8.2e-29  101.0   0.7    2.1  1  GMC_oxred_C    GMC oxidoreductase
    2.2e-06   27.5   3.9    6.2e-05   22.7   3.9    2.4  1  DAO            FAD dependent oxidoreductase
      0.002   18.3   0.7     0.0053   17.0   0.3    1.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0054   15.8   0.9     0.0081   15.3   0.9    1.2  1  Lycopene_cycl  Lycopene cyclase protein
     0.0074   15.6   0.3        0.2   10.8   0.1    2.5  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.08   12.2   0.3       0.15   11.3   0.3    1.4  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   0.0   3.9e-58     1e-54       2     296 .]       9     299 ..       8     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 3.9e-58
                    GMC_oxred_N   2 delveggGsagsvvAaRLsedpstsvlvleaggreknrl.imvlalalklidkklntayetepekalngrrlilp..aGk 78 
                                    d lv+g+GsagsvvA+RLs d s  v+vleag++  ++    + a+ l+l  +  +  +e++ ++ +++ +  lp  +G+
  gi|121636618|ref|YP_976841.1|   9 DVLVVGAGSAGSVVAERLSMDSSCVVTVLEAGPGLADPGlLAQTANGLQLPIGAGSPLVERYRTRLTDRPVRHLPivRGA 88 
                                    789**********************************9996666666666555554444444444444443333322*** PP

                    GMC_oxred_N  79 tlGGgsvvNwsayiRtpaadldeWeeeaglegwssdevlpafkkvetaqalesdlhgvdgrlgvtekgkeesplnkallk 158
                                    t+GG++++N++++ R+  +d+d+    a ++gw++ +vl+ f+ +et+ ++e+ +hg  g+++v ++  e  ++ + +++
  gi|121636618|ref|YP_976841.1|  89 TVGGSGAINGGYFCRGLPSDFDR----ASIPGWAWSDVLEHFRAIETDLDFETPVHGRSGPIPV-RRTHEMTGITESFMA 163
                                    *********************96....4578*********************************.8888999999***** PP

                    GMC_oxred_N 159 aaeelGlpvprdlngk...hqcGvcllgvtcrtgarqstarawLrpalerpnleiltgakaekiilegrkkravGVeasd 235
                                    aae++G++   dln+     ++Gv+ ++++  +g r s+a  +L+pal rpnl++l +++a ++ ++   + avGV+a  
  gi|121636618|ref|YP_976841.1| 164 AAEDAGFAWIADLNDVgpeMPSGVGAVPLNIVNGVRTSSAVGYLMPALGRPNLTLLARTRAVRLRFS--ATTAVGVDAIG 241
                                    ********555555444449********************************************887..*********** PP

                    GMC_oxred_N 236 kkgtvkrlvvaakevvvaaGalnsPqlLqrSGlGkaehLkevgvdvvvdlpvGknLqdHpv 296
                                     +g    ++ +a+ +v++aGa++s +lL++SG+G++e L++ gv+v + lpvG    dHp+
  gi|121636618|ref|YP_976841.1| 242 PGGP---VSLSADRIVLCAGAIQSAHLLMLSGVGEEEVLRSAGVKVLMALPVGMGCSDHPE 299
                                    *999...9***************************************************95 PP

>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.7   3.2e-32   8.2e-29       1     144 []     358     474 ..     358     474 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 3.2e-32
                                    ----EEEEESTT-TCCEEEEE--TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.HCHHCHHCHHCHH CS
                    GMC_oxred_C   1 PesrGrvtlsssdptgaplidpnylsdprdlaalvealkaarkilaaaaldvleeeltpgaaeetsdaavesdealekfv 80 
                                    P++rGr+tl ssdp+ + +i+ +y+s+p+d+aal+++ + a+++  aa        ++ g+       av+++       
  gi|121636618|ref|YP_976841.1| 358 PRARGRITLVSSDPQIPVRIEHRYDSEPADVAALRQGSALAHELCGAA--------TRIGP-------AVWATS------ 416
                                    89**********************************************........56666.......666666...... PP

                                    HHH-EE-S--B-TT-B-STCGC.BSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                    GMC_oxred_C  81 keavltsaHplGtcrMGadpkd.sVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                           +H +G+++MG+d+++ +VVD+++rv+g++nL+V+D+Sv+Ps+++  p +ti++l+++a
  gi|121636618|ref|YP_976841.1| 417 -------QHLCGSAPMGTDDDPrAVVDPRCRVRGIENLWVIDGSVLPSITSRGPHATIVMLGHRA 474
                                    .......6******************************************************997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   3.9   2.4e-08   6.2e-05       1     271 [.       9     377 ..       9     462 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.4e-08
                                    EEEEECTSHHHHHHHHHHHHTT...EEEEESSSS.........................................TTSSG CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdi.........................................agsga 36 
                                    dv+++G+G +G+ +A  L+      Vt+le+g+                                          + +ga
  gi|121636618|ref|YP_976841.1|   9 DVLVVGAGSAGSVVAERLSMDSscvVTVLEAGPGladpgllaqtanglqlpigagsplveryrtrltdrpvrhlpIVRGA 88 
                                    8*****************98767*********779999999999999999999999999998888888888888733588 PP

                                    GGSSEEEEESSS..STHHSTH...HHHHHHHHH.HHHHHHHHHHHSSTTS.EEEEEEEEEESSHHHHHHHHHHHHHH.HH CS
                            DAO  37 Sgrnsgllhsgl..rylpeas...elarlslea.leelreleeelgidid.yrrtGllslaadeeelealdkllall.le 108
                                    + + sg + +g+  r lp+      +  ++    le++r++e +l+++++ + r+G +++ +++ e+ ++ +++ ++ ++
  gi|121636618|ref|YP_976841.1|  89 TVGGSGAINGGYfcRGLPSDFdraSIPGWAWSDvLEHFRAIETDLDFETPvHGRSGPIPVRRTH-EMTGITESFMAAaED 167
                                    888888888888884444322443444666644246669999999999666999******8876.699975555544255 PP

                                    TTTTEEEEEHHHHHHHSTTST........TTSEEEEETTE.EEEEHHHHHHHHHHHHHHTT-EEEES.ECEEEEEEEETC CS
                            DAO 109 agldaelldaeevrelepalp........gllgalfypdt.gqvdpakltaalaraaealGveileg.tevtgleeedgk 178
                                    ag    ++    ++++ p  p        +++ ++ + ++ g + pa   + l   a++++v++++  t+++g+++  g 
  gi|121636618|ref|YP_976841.1| 168 AGF--AWIAD--LNDVGPEMPsgvgavplNIVNGVRTSSAvGYLMPALGRPNLTLLARTRAVRLRFSaTTAVGVDAI-GP 242
                                    555..59955..89999983345677889999999988877999999999999999******999983445555332.22 PP

                                    EEEEEEECTEEEEEEEEEEE--GGGHH..HHHTT...CTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE........ CS
                            DAO 179 vwgverttpgendaadavVnaaGawsd..llgll...keldlpispvrgqvlvlkplseklvspaailpvpe........ 245
                                    ++ v         +ad +V++aGa  +  ll +l   +e    +    g  + ++ +     s ++ + +p         
  gi|121636618|ref|YP_976841.1| 243 GGPV-----SL--SADRIVLCAGAIQSahLL-MLsgvGE--EEVLRSAGVKVLMALPVGMGCSDHPEWVMPTnwavavdr 312
                                    3444.....22..57********87444433.2222222..233333333322211112222222333333333444444 PP

                                    .....EEETTTTEEEEEETTSEEEEEESSE..................................E CS
                            DAO 246 .....tdddgrgvyvtprkdgrvlvGgtad..................................e 271
                                             ++g++++p+ +g v + g+++                                   
  gi|121636618|ref|YP_976841.1| 313 pvlevLLSTHDGIEIRPYTGGFVAMTGDGTaghrdwphigvalmqprargritlvssdpqipvrI 377
                                    44446566677777777776655555555466666666666666666666666666666665552 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   2.1e-06    0.0053       1      31 [.      12      43 ..      12      55 .. 0.91
   2 ?   -2.6   0.0       2.7   6.8e+03       8      40 ..     394     428 ..     394     438 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                                   EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31
                                   +vGaG +G+v A +L+ +  + v++le++++l
  gi|121636618|ref|YP_976841.1| 12 VVGAGSAGSVVAERLSMDsSCVVTVLEAGPGL 43
                                   8***************987999******9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                    HHHHHHHHHCC..TEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8   8 GlvaAylLaka..gfdvlllekrdrlGGraasyev 40 
                                    G+++A++L  a  ++   ++ ++++l+G a   ++
  gi|121636618|ref|YP_976841.1| 394 GSALAHELCGAatRIGPAVWATSQHLCGSAPMGTD 428
                                    66677776554345566777778888887766665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   3.2e-06    0.0081       1      37 [.       9      44 ..       9      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsll 37
                                   Dv+v+GaG Ag  +A+rl +      v+++ea+p+l 
  gi|121636618|ref|YP_976841.1|  9 DVLVVGAGSAGSVVAERL-SMDSSCVVTVLEAGPGLA 44
                                   9*****************.8889999********985 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1     8e-05       0.2       2      32 ..       9      40 ..       8      69 .. 0.79
   2 ?    1.6   0.0      0.05   1.3e+02      97     122 ..     247     274 ..     211     284 .. 0.73
   3 ?   -2.4   0.0      0.83   2.1e+03     247     274 ..     422     450 ..     411     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
                                   SEEEE--SHHHHHHHHHHHH.HTS-EEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq.agakvtlvele 32
                                   dv+v+G+G AG  +a++l+  +++ vt++e++
  gi|121636618|ref|YP_976841.1|  9 DVLVVGAGSAGSVVAERLSMdSSCVVTVLEAG 40
                                   89999999999999999999667777777533 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.05
                                    EEEESEEEE---E..EE-BCTCTTC.TT CS
                                    xxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                    Pyr_redox_2  97 kiaydklvlAtGs..sprdlgipGvaen 122
                                    ++ +d++vl+ G+  s+++l + Gv+e+
  gi|121636618|ref|YP_976841.1| 247 SLSADRIVLCAGAiqSAHLLMLSGVGEE 274
                                    6788999999998767777788888554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.83
                                    CCT-EEEETTEEE--TTSBES.STTEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                    Pyr_redox_2 247 klglelderggivvdeflrtn.vpgiyai 274
                                    ++ + +d++ + vvd+++r+  ++++++i
  gi|121636618|ref|YP_976841.1| 422 SAPMGTDDDPRAVVDPRCRVRgIENLWVI 450
                                    5556677888899*******88***9997 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   5.8e-05      0.15      17      49 ..       7      39 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                    sDv++vGaGs+G   a  l+ +    v++le+
  gi|121636618|ref|YP_976841.1|  7 HSDVLVVGAGSAGSVVAERLSMDSSCVVTVLEA 39
                                   79*******************999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3370.88
//
Query:       gi|121636619|ref|YP_976842.1|  [L=109]
Description: hypothetical protein BCG_0747 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 855.96
//
Query:       gi|121636620|ref|YP_976843.1|  [L=77]
Description: hypothetical protein BCG_0748 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 602.09
//
Query:       gi|121636621|ref|YP_976844.1|  [L=73]
Description: hypothetical protein BCG_0749 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 603.78
//
Query:       gi|121636622|ref|YP_976845.1|  [L=101]
Description: 30S ribosomal protein S10 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-34  117.3   0.1      3e-34  117.2   0.1    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.047   13.6   0.1      0.093   12.6   0.0    1.6  2  DUF384         Domain of unknown function (DUF384)


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.1   3.3e-38     3e-34       1      97 [.       7     100 ..       7     101 .] 0.99

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 3.3e-38
                                    EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--S--EEEEEEEEEEEEEEEE.E-HHHHHH CS
                  Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvdkksreqfeirthkRlidisdatketidt 80 
                                    rirlk+yd+++++ +++kiv+++ ++g+ v gpvplPt++  ++v++sph +k+sre+fe+rthkRlidi d+t++t+d+
  gi|121636622|ref|YP_976845.1|   7 RIRLKAYDHEAIDASARKIVETVVRTGASVVGPVPLPTEKNVYCVIRSPHKYKDSREHFEMRTHKRLIDIIDPTPKTVDA 86 
                                    8******************************************************************************* PP

                                    HS-...S---SS-EEEE CS
                  Ribosomal_S10  81 llkllqlnlpegVsvev 97 
                                    l++   ++lp+ V+v++
  gi|121636622|ref|YP_976845.1|  87 LMR---IDLPASVDVNI 100
                                    ***...*********98 PP

>> DUF384  Domain of unknown function (DUF384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.69   6.2e+03      33      43 ..      19      29 ..      10      32 .. 0.43
   2 ?   12.6   0.0     1e-05     0.093      17      37 ..      45      77 ..      44      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.69
                         DUF384 33 deeveeaierl 43
                                   d + ++ +e +
  gi|121636622|ref|YP_976845.1| 19 DASARKIVETV 29
                                   33333333333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1e-05
                         DUF384 17 skgvYpilRelhkaekdee............ve 37
                                   +k+vY ++R  hk+++  e            + 
  gi|121636622|ref|YP_976845.1| 45 EKNVYCVIRSPHKYKDSREhfemrthkrlidII 77
                                   69************7555555444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 772.10
//
Query:       gi|121636623|ref|YP_976846.1|  [L=217]
Description: 50S ribosomal protein L3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-19   70.1   6.7      9e-18   64.4   4.4    2.9  2  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.011     2e+02      53      90 ..      13      40 ..       2      63 .. 0.66
   2 !   64.4   4.4     5e-22     9e-18     198     290 ..      92     187 ..      85     217 .] 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.011
                                   EEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEEEEE CS
                   Ribosomal_L3 53 mthiVrevdkpgskldkkevveavtvvetppmvivgvv 90
                                   mt++  e           + v++vtvv+  p v+ +++
  gi|121636623|ref|YP_976846.1| 13 MTQVFDES----------NRVVPVTVVKAGPNVVTRIR 40
                                   55544444..........44566666666666666664 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 5e-22
                                    HHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSS..SSS-S-SS.-SSSSS--TTS--SEEES CS
                   Ribosomal_L3 198 arealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrg..lRkvaaig.awdparVsstvaraGqkG 274
                                    a+e    +   a++F++g ++Dv+g  kGkGf G++kR g++++ + ++ +  +R++++ig    parV  ++++aG++G
  gi|121636623|ref|YP_976846.1|  92 ATEYQVGQELTAEIFADGSYVDVTGTSKGKGFAGTMKRHGFRGQGASHGAQavHRRPGSIGgCATPARVFKGTRMAGRMG 171
                                    5555555888999***********************************9999********72568*************** PP

                                    CCEEEEEEEEEEEEET CS
                   Ribosomal_L3 275 yhhRtelnkkiyrigk 290
                                    + + t ln+ ++++++
  gi|121636623|ref|YP_976846.1| 172 NDRVTVLNLLVHKVDA 187
                                    ************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1663.14
//
Query:       gi|121636624|ref|YP_976847.1|  [L=223]
Description: 50S ribosomal protein L4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-65  218.1   0.2      1e-64  217.8   0.2    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.2   5.6e-69     1e-64       1     187 [.      24     208 ..      24     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 5.6e-69
                                    EEE-HHHHSS---HHHHHHHHHHHHHSS-EE------TTTSS---S-SS-SSSSSS---S-TTSTTSTT---SS---S.E CS
                   Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastkarsevsgsgrklwkQKGtGrARvgsirspiargGgvahgpkper 80 
                                    +eL++++F++p++  l+h++v+a++a++rqgt+stk+r+evsg+grk+++QKGtGrAR+gs+r+p++ gGgv+hgpkp r
  gi|121636624|ref|YP_976847.1|  24 IELPAELFDVPANIALMHQVVTAQRAAARQGTHSTKTRGEVSGGGRKPYRQKGTGRARQGSTRAPQFTGGGVVHGPKP-R 102
                                    79***************************************************************************9.* PP

                                    EHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-.-SS--HHHHHHHHHHTT-TTSSEEEEESSSSCHHHHHHTT-TT CS
                   Ribosomal_L4  81 dystklnkKvrrlAlrsaLsakakqglllvvdnl.epleesktkelvellkklglksksvLivvsekdenlvlaarnlpg 159
                                    dys++ +kK+  +Alr aLs +a++g+++++ +l e  ++++tk ++++l +l   +k+vL+v++++de  ++++rnlpg
  gi|121636624|ref|YP_976847.1| 103 DYSQRTPKKMIAAALRGALSDRARNGRIHAITELvE-GQNPSTKSARAFLASLTE-RKQVLVVIGRSDEAGAKSVRNLPG 180
                                    ********************************9966.99****************.************************ PP

                                    EEEEESTT--CHHHHHSSEEEEEHHHHH CS
                   Ribosomal_L4 160 vevieveslnvydllkadkvvitksave 187
                                    v+++  ++ln yd+l+ad+vv++ +a++
  gi|121636624|ref|YP_976847.1| 181 VHILAPDQLNTYDVLRADDVVFSVEALN 208
                                    **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1601.20
//
Query:       gi|121636625|ref|YP_976848.1|  [L=100]
Description: 50S ribosomal protein L23 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-31  106.9   0.1    5.7e-31  106.7   0.1    1.0  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.1   3.2e-35   5.7e-31       1      83 [.       9      91 ..       9      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 3.2e-35
                                   SSEEEE--SHHHHHHHTTE.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS- CS
                  Ribosomal_L23  1 dvilkPvitEkstklaeknkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkege 82
                                   d+il+Pvi+Eks+ l ++n y+F V++d+nK++ik avek+F VkV++Vnt+n++gk+kr+++ +g+rks+K+aiVtL++g+
  gi|121636625|ref|YP_976848.1|  9 DIILAPVISEKSYGLLDDNVYTFLVRPDSNKTQIKIAVEKIFAVKVASVNTANRQGKRKRTRTGYGKRKSTKRAIVTLAPGS 90
                                   79**********************************************************9888**************9986 PP

                                   S CS
                  Ribosomal_L23 83 k 83
                                   +
  gi|121636625|ref|YP_976848.1| 91 R 91
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 757.68
//
Query:       gi|121636626|ref|YP_976849.1|  [L=280]
Description: 50S ribosomal protein L2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-55  184.8   3.0    1.2e-54  183.9   3.0    1.5  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.2e-34  116.4   1.3    8.6e-34  115.3   1.3    1.6  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   3.0   1.3e-58   1.2e-54       1     126 []     126     251 ..     126     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.3e-58
                                    SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT-- CS
                 Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekk 80 
                                    k+Gn lpl+nip Gt++h++el+pg g+klarsaG++ q+++ke +++ +++pSge+r+v+ +crAt+G+v+n+e+ + +
  gi|121636626|ref|YP_976849.1| 126 KPGNNLPLRNIPAGTLIHAVELRPGGGAKLARSAGSSIQLLGKEASYASLRMPSGEIRRVDVRCRATVGEVGNAEQANIN 205
                                    68****************************************************************************** PP

                                    --STTHHHHTTBS----SSSS-TTTSSS--SSSS--SSSSTEETTC CS
                 Ribosomal_L2_C  81 lgkAgrkrwlgrrpkvrGvamnpvdHphGGGeGktksrkapvspwg 126
                                    +gkAgr rw+g+rp+vrGv+mnpvdHphGGGeGkt++ ++pvspwg
  gi|121636626|ref|YP_976849.1| 206 WGKAGRMRWKGKRPSVRGVVMNPVDHPHGGGEGKTSGGRHPVSPWG 251
                                    *************************************77******8 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   1.3   9.6e-38   8.6e-34       1      77 []      42     119 ..      42     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 9.6e-38
                                    TB-TT--BSSTT--------EE-B--S-.--SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE-- CS
                   Ribosomal_L2   1 GrnnsgritvrhrggGhkkkyrlidfkr.nkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvvs 77 
                                    Grn +grit+rh+ggGhk+ yr+idf+r +k++v++kV++ieyDp+R+A+iAl++y+dgekryiiap+gl+ Gd+v+s
  gi|121636626|ref|YP_976849.1|  42 GRNAHGRITTRHKGGGHKRAYRMIDFRRnDKDGVNAKVAHIEYDPNRTARIALLHYLDGEKRYIIAPNGLSQGDVVES 119
                                    9***************************88888******************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2192.66
//
Query:       gi|121636627|ref|YP_976850.1|  [L=93]
Description: 30S ribosomal protein S19 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-37  125.5   0.6    6.5e-37  125.3   0.6    1.0  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.6   3.6e-41   6.5e-37       1      81 []       3      83 ..       3      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 3.6e-41
                                   .HHHSSTTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
                  Ribosomal_S19  1 rslkkgpfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81
                                   rslkkgpfv+e+llkkv+ ++++++k+vikt+sR+stI+P+++g+t++V++G+++vpv ++e mvGhkLgEF+pTr++++h
  gi|121636627|ref|YP_976850.1|  3 RSLKKGPFVDEHLLKKVDVQNEKNTKQVIKTWSRRSTIIPDFIGHTFAVHDGRKHVPVFVTESMVGHKLGEFAPTRTFKGH 83
                                   89*******************999*******************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 688.37
//
Query:       gi|121636628|ref|YP_976851.1|  [L=197]
Description: 50S ribosomal protein L22 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-31  106.8   0.1    1.1e-30  105.9   0.1    1.5  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.1   6.1e-35   1.1e-30       1     102 [.      15     117 ..      15     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 6.1e-35
                                    EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT-SSTTHHHHHHHHHHHHHHHH..HT.-GGGEEEEEEEEEEEEEEEE CS
                  Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkfskkkaakfvlklLknaeanaelkgl.dvdslvIeeiqvnkgpklkr 79 
                                    ak++ +rvs++k+r+v++l+rg++v++Al++L+ +++ a+  v+k++ +a ana+++g+ d+ +lv++++++++gp+ kr
  gi|121636628|ref|YP_976851.1|  15 AKARFVRVSPRKARRVIDLVRGRSVSDALDILRWAPQAASGPVAKVIASAAANAQNNGGlDPATLVVATVYADQGPTAKR 94 
                                    7899***************************************************99889******************** PP

                                    EEEESTTEEEEEEEEEEEEEEEE CS
                  Ribosomal_L22  80 rtyrArGrinpirkspchievvl 102
                                    +++rA+Gr+ +ir++++hi+vv+
  gi|121636628|ref|YP_976851.1|  95 IRPRAQGRAFRIRRRTSHITVVV 117
                                    **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1417.08
//
Query:       gi|121636629|ref|YP_976852.1|  [L=274]
Description: 30S ribosomal protein S3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-37  126.1   0.2    1.2e-36  125.1   0.2    1.6  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    8.4e-19   67.2   0.6    1.4e-18   66.5   0.6    1.4  1  KH_2            KH domain
    0.00014   21.7   0.3    0.00032   20.5   0.3    1.6  1  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.2     2e-40   1.2e-36       1      83 []     119     202 ..     119     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2e-40
                                    HHHHHHTT--HHHHHHHHHHHHHHC.C-SEEEEEEEC-SS.TTT--EEEEEEC----TCHHHH-EEEEEEEEETTEEEEE CS
                 Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramka.gakGikiqvsGrLggaeiarsekykeGrvplhtlradidyavaeaktkyGiiGv 79 
                                    +aeql++rv+fRram+kai++am++ ++kGi++q+sGrLggae++rse y+eGrvplhtlradidy++ eakt+ G iGv
  gi|121636629|ref|YP_976852.1| 119 VAEQLSNRVAFRRAMRKAIQSAMRQpNVKGIRVQCSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGV 198
                                    699********************9989***************************************************** PP

                                    EEEE CS
                 Ribosomal_S3_C  80 kVwI 83 
                                    kVwI
  gi|121636629|ref|YP_976852.1| 199 KVWI 202
                                    ***9 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.6   2.4e-22   1.4e-18       2      77 ..      38     109 ..      37     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2.4e-22
                                    HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
                           KH_2   2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77 
                                    i+  l   ++ ag+++veIert++rv++ i++++pgivIG++G + ++i+++l+k +    gk+V+lni +Vk+pe
  gi|121636629|ref|YP_976852.1|  38 IRRLLSSGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLT----GKQVQLNILEVKNPE 109
                                    66677778899**********************************************....*************98 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   5.3e-08   0.00032      19      55 ..      53      87 ..      37      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.3e-08
                           KH_4 19 evteeeeeeeveielnvegedlGrvIGkrGrtldAlq 55
                                   +  +e+e++++++++++++   G+vIG+rG  +d ++
  gi|121636629|ref|YP_976852.1| 53 D--VEIERTRDRVRVDIHTARPGIVIGRRGTEADRIR 87
                                   4..4556889********************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1948.79
//
Query:       gi|121636630|ref|YP_976853.1|  [L=138]
Description: 50S ribosomal protein L16 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-46  158.0   0.3    1.3e-46  157.8   0.3    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.3   7.5e-51   1.3e-46       1     132 []       4     132 ..       4     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 7.5e-51
                                    HXSSXXBSSSXXSSTSXXXSXXXXXESXEEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXCEEXXSXXXXEEEEE-SS-T CS
                  Ribosomal_L16   1 pkrkkyrKsrkryirgvstkgtklefgdygLvalekgqltaealeaariainrylkkkrgkklwirvfphhpvtkkaged 80 
                                    p+++k+rK+++   rg ++ gt+++fgdyg++ale++++t++++e+ariainr++k  rg+k+wi++fp+ p+tkk++e+
  gi|121636630|ref|YP_976853.1|   4 PRKVKHRKQHHPRQRGIASGGTTVNFGDYGIQALEHAYVTNRQIESARIAINRHIK--RGGKVWINIFPDRPLTKKPAET 81 
                                    6799*******666******************************************..********************** PP

                                    TTSSSSXEEEEEEEEEXSSCEEEEETTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                  Ribosomal_L16  81 RmgkGkGkpegwvarvkigqiifeikagvneeiakealrraasKlpiktkiv 132
                                    Rmg+GkG+pe wva+vk+g+++fe+ +  ne +a+ al+ra +Klpik++i+
  gi|121636630|ref|YP_976853.1|  82 RMGSGKGSPEWWVANVKPGRVLFEL-SYPNEGVARAALTRAIHKLPIKARII 132
                                    *************************.7569*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1007.12
//
Query:       gi|121636631|ref|YP_976854.1|  [L=77]
Description: 50S ribosomal protein L29 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-24   85.4   5.8    2.2e-24   85.2   5.8    1.1  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.022   14.9   0.0    1.0  1  TRIF-NTD       TRIF N-terminal domain
      0.031   14.0   1.2      0.035   13.8   1.2    1.1  1  CCDC85         CCDC85 family
      0.054   13.6   0.2      0.082   13.1   0.2    1.3  1  Mrr_N          Mrr N-terminal domain
       0.13   11.9   1.1       0.13   11.9   1.1    2.0  3  LEM            LEM domain


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   5.8   6.2e-28   2.2e-24       2      57 .]       9      64 ..       8      64 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 6.2e-28
                                   HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHHH CS
                  Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlrer 57
                                   elrel+deeL e+l e k+eLfnLrfq atgql+n  r+r+vR +IARi+Tvlrer
  gi|121636631|ref|YP_976854.1|  9 ELRELTDEELAERLRESKEELFNLRFQMATGQLNNNRRLRTVRQEIARIYTVLRER 64
                                   9******************************************************8 PP

>> TRIF-NTD  TRIF N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.1e-06     0.022      60     115 ..       9      66 ..       7      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.1e-06
                       TRIF-NTD  60 kLdalrddrvanylaeklkgtagaaengahlql..eekdaevllsvAriyslLveekl 115
                                    +L +l d+++a++l e+++   + + ++a  ql  + +   v +++Ariy +L e +l
  gi|121636631|ref|YP_976854.1|   9 ELRELTDEELAERLRESKEELFNLRFQMATGQLnnNRRLRTVRQEIARIYTVLREREL 66 
                                    5889**************9966666655555553266778999***********9987 PP

>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   9.9e-06     0.035       7      62 ..       5      60 ..       2      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.9e-06
                         CCDC85  7 vsDeellklskeelvrrLRraeaekvsllvergrlikevnrrLqqhLleiRelkev 62
                                   vs  el++l+ eel++rLR++++e  +l  + +    + nrrL++  +ei  +  v
  gi|121636631|ref|YP_976854.1|  5 VSPGELRELTDEELAERLRESKEELFNLRFQMATGQLNNNRRLRTVRQEIARIYTV 60
                                   56789**************************99999999*****999999877655 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.3e-05     0.082      32      77 ..      12      57 ..       8      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                          Mrr_N 32 glseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwki 77
                                   +l++ee+ae l ++k+ +f+ r++ a  +L +   l + ++ + +i
  gi|121636631|ref|YP_976854.1| 12 ELTDEELAERLRESKEELFNLRFQMATGQLNNNRRLRTVRQEIARI 57
                                   79****************************9999999988877766 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         2   7.2e+03      17      22 ..       3       8 ..       2       8 .. 0.83
   2 ?   11.9   1.1   3.6e-05      0.13       2      16 ..      10      24 ..       9      27 .. 0.90
   3 ?   -1.8   0.0      0.66   2.4e+03      15      23 ..      64      72 ..      61      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                            LEM 17 yGvspG 22
                                    GvspG
  gi|121636631|ref|YP_976854.1|  3 VGVSPG 8 
                                   599999 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.6e-05
                            LEM  2 vasLsDeeLreeLkk 16
                                   + +L+DeeL e+L++
  gi|121636631|ref|YP_976854.1| 10 LRELTDEELAERLRE 24
                                   679**********97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.66
                            LEM 15 kkyGvspGP 23
                                   +++G+  GP
  gi|121636631|ref|YP_976854.1| 64 RELGLATGP 72
                                   579999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 601.13
//
Query:       gi|121636632|ref|YP_976855.1|  [L=136]
Description: 30S ribosomal protein S17 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-29   99.7   0.3      1e-28   99.2   0.3    1.2  1  Ribosomal_S17  Ribosomal protein S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.3   5.6e-33     1e-28       1      68 []      63     130 ..      63     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5.6e-33
                                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS--TT-EEEEEEECECSSSEEEEEEE CS
                  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdennsvkvGDiVrieecrPlSktkrfvvve 68 
                                    G Vvsdkm+kT+vV+ e + +hp+y+k+++ +kk++ahde+  + +GD+V  +e+rPlS tkr+++ve
  gi|121636632|ref|YP_976855.1|  63 GYVVSDKMQKTIVVELEDRMRHPLYGKIIRTTKKVKAHDEDSVAGIGDRVSLMETRPLSATKRWRLVE 130
                                    89****************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1135.65
//
Query:       gi|121636633|ref|YP_976856.1|  [L=787]
Description: arylsulfatase atsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-97  326.9   0.0    1.9e-97  326.4   0.0    1.2  1  Sulfatase     Sulfatase
     0.0058   16.3   0.0      0.076   12.6   0.0    2.1  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.022   15.3   0.0      0.045   14.3   0.0    1.5  1  Laminin_G_2   Laminin G domain
       0.11   11.0   0.0       0.16   10.5   0.0    1.1  1  DUF229        Protein of unknown function (DUF229)
       0.15   12.0   0.0       0.33   10.9   0.0    1.5  1  DUF4994       Domain of unknown function


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.4   0.0  5.3e-101   1.9e-97       1     309 []      37     466 ..      37     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 326.4 bits;  conditional E-value: 5.3e-101
                                    EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT..... CS
                      Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg..... 75 
                                    pn++++++dd+g++ ++++gg ++ +p+++r+ae+g+r+++f+++a lcsp+ra+lltgr+++++g+a+++e+++     
  gi|121636633|ref|YP_976856.1|  37 PNILYLVWDDVGIATWDCFGGLVE-MPAMTRVAERGVRLSQFHTTA-LCSPTRASLLTGRNATTAGMATIEEFTDgfpnc 114
                                    9**********************9.9******************98.********************************* PP

                                    .HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.......CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC. CS
                      Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.......nrgfdrflgfptgsaalkdpekseyngevlrv. 146
                                     g +p ++a Lpe+l e+GYnt+++gkwhl++ +++++++       +rgf+rf+gf +g++++++p+ + +n++v ++ 
  gi|121636633|ref|YP_976856.1| 115 nGRIPADTALLPEVLAEHGYNTYCVGKWHLTPLEESNMAStkrhwptSRGFERFYGFLGGETDQWYPDLVYDNHPVSPPg 194
                                    *************************************999************************************999* PP

                                    .TTTTCSHHHHHHHHHHHHH....HCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH............. CS
                      Sulfatase 147 .ppeggysddrlldealefl....larndkpfflylatlapHappeapdeyakkyatffddgseaar............. 208
                                     p+ g++++++++d+++ef+      ++dkp+f+y+++ a Hap+++++e+a++ya++fd+g+e++r             
  gi|121636633|ref|YP_976856.1| 195 tPEGGYHLSKDIADKTIEFIrdakVIAPDKPWFSYVCPGAGHAPHHVFKEWADRYAGRFDMGYERYReivlerqkalgiv 274
                                    *********************9976777**************************************9************* PP

                                    ............................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEE CS
                      Sulfatase 209 ............................................qlleaylnsveyvDdligrvlaaLeenglldntlvv 244
                                                                                +++e+++++++y+D +igr+l++Lee+g+ldnt++v
  gi|121636633|ref|YP_976856.1| 275 ppdtelspinpyldvpgpngetwplqdtvrpwdslsdeekklfcRMAEVFAGFLSYTDAQIGRILDYLEESGQLDNTIIV 354
                                    ******************************************************************************** PP

                                    EEESSSSCCCG.............................................HHTTSSSCTTCSSSHHHHBEEEEE CS
                      Sulfatase 245 ftSDhgaslee.............................................sngplrggkganayeggtrvPllv 279
                                    ++SD+gas e+                                              n+p+++ k+++++egg+ +P+++
  gi|121636633|ref|YP_976856.1| 355 VISDNGASGEGgpngsvnegkffngyidtvaesmklfdhlggpqtynhypigwamaFNTPYKLFKRYASHEGGIADPAII 434
                                    *********99********************************************************************* PP

                                    EETTTSHC..EEECSEEEGGGHHHHHHHHTTE CS
                      Sulfatase 280 wwpgekap..rvseelvshiDlfptildlagi 309
                                     wp+++a+  ++++++v+++D++pt++dl+g+
  gi|121636633|ref|YP_976856.1| 435 SWPNGIAAhgEIRDNYVNVSDITPTVYDLLGM 466
                                    ******************************96 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.067   2.4e+02      20      63 ..      60     101 ..      50     118 .. 0.85
   2 !   12.6   0.0   2.1e-05     0.076     197     239 ..     324     367 ..     301     421 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.067
                                    TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS- CS
                   Phosphodiest  20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGi 63 
                                    ++p + + a++gv+      +  +l  p  asl+TG++    G+
  gi|121636633|ref|YP_976856.1|  60 EMPAMTRVAERGVRLS--QFHTTALCSPTRASLLTGRNATTAGM 101
                                    7999999999999999..555667889**********9998887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH.T CS
                   Phosphodiest 197 vedalrrvDkaigdLlealderglsaetniilvSDHGmadvs.d 239
                                    ++  l++ D+ ig++l++l+e g  ++t i++ SD G++     
  gi|121636633|ref|YP_976856.1| 324 FAGFLSYTDAQIGRILDYLEESGQLDNTIIVVISDNGASGEGgP 367
                                    6778999***************9999999********9877544 PP

>> Laminin_G_2  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.045       2      51 ..     633     681 ..     632     697 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                    EE--SSEEEEEEEESTTEEEEEEEETTEEEEEEESSS-EEEEE-SSSS-E CS
                    Laminin_G_2   2 rTrqpdGlLlyagdeksdflalelkdgklvltynlgsgdtellssgkkln 51 
                                     T+ ++G+L+  g+  +    l ++dg+l+++yn+ +++++l+ss+ ++ 
  gi|121636633|ref|YP_976856.1| 633 DTTGAEGVLFKHGG-AHGGHVLFVRDGRLHYVYNFLGERQQLVSSSGPVP 681
                                    58999*********.899999**************999999988866664 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.4e-05      0.16     310     343 ..     327     360 ..     318     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                         DUF229 310 llealDedllkylkklekkgllentlvlllsDHG 343
                                    +l+ +D ++ ++l  le++g+l+nt+++++sD G
  gi|121636633|ref|YP_976856.1| 327 FLSYTDAQIGRILDYLEESGQLDNTIIVVISDNG 360
                                    78899***************************99 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.2e-05      0.33      67      97 ..     536     566 ..     524     567 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
                        DUF4994  67 epqLydlkkdegekenvaekhpekvkelkel 97 
                                    +  L+++++d+++ +++a++hp+k++elk+l
  gi|121636633|ref|YP_976856.1| 536 RWELFHIAADRSQCHDLAAEHPDKLEELKAL 566
                                    567*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4887.25
//
Query:       gi|121636634|ref|YP_976857.1|  [L=299]
Description: hypothetical protein BCG_0762 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-90  303.5   0.9    1.4e-90  303.4   0.9    1.0  1  FGE-sulfatase  Sulfatase-modifying factor enzyme 1


Domain annotation for each model (and alignments):
>> FGE-sulfatase  Sulfatase-modifying factor enzyme 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.4   0.9   8.1e-95   1.4e-90       2     260 .]       2     294 ..       1     294 [. 0.98

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 8.1e-95
                                    STTEEEE-SEEEEES-TSTTGGCCC-S-EEEEES-EEEESS--BHHHHHHHHHHH....H.................... CS
                  FGE-sulfatase   2 apemvlipgGsfemGseektandeeapahevtvraFaidkteVTnaqyaafveatgyete.................... 61 
                                    ++e+v +pgGsf+mGs  +++++eeap+h+vtvraFa+++++VTnaq+a+fv+atgy+t                     
  gi|121636634|ref|YP_976857.1|   2 LTELVDLPGGSFRMGS--TRFYPEEAPIHTVTVRAFAVERHPVTNAQFAEFVSATGYVTVaeqpldpglypgvdaadlcp 79 
                                    5899***********9..************************************************************** PP

                                    ...............SSETTEEEEETSCTTBCCTTC-SSTT-TTSB--S--HHHHHHHHHHHCHHHTS-EE---HHHHHH CS
                  FGE-sulfatase  62 ...............aasqwwaeveganvrhpegrksdikkradhPvvhVsweDavaYArwlgkktgegyrLPteaEwey 126
                                                   +++qww++v+ga++rhp gr+sdi++ra hPvv+V++ DavaYArw+g+      rLPteaEwey
  gi|121636634|ref|YP_976857.1|  80 gamvfcptagpvdlrDWRQWWDWVPGACWRHPFGRDSDIADRAGHPVVQVAYPDAVAYARWAGR------RLPTEAEWEY 153
                                    ****************************************************************......********** PP

                                    HHHTT-SSSSCTTBSTTSCCG....B...SSTTTTB--TTCGGS-SS.---TT-S-B-TTS-B-TTCSSEEEEEEE--.. CS
                  FGE-sulfatase 127 AArggkkgreypwgdelkpak....niwqGslakfekeaaaadsqngrtspvgsfppnalGlyDmaGNvwEWtsdwyk.. 200
                                    AArgg++ ++y+wgd++kp +    n+wqG   +f++++++a ++ g tspvg+fp+n +Gl+Dm+GNvwEWt++++   
  gi|121636634|ref|YP_976857.1| 154 AARGGTT-ATYAWGDQEKPGGmlmaNTWQG---RFPYRNDGALGWVG-TSPVGRFPANGFGLLDMIGNVWEWTTTEFYph 228
                                    ****996.66*********99*********...8*************.******************************** PP

                                    ......THCCH-SSCS----SS-SSEEEEC--TTS.T.TGGCTSTT-E.EEE-TT--BTTEEE--EE CS
                  FGE-sulfatase 201 ......kyalapaeelsqeaekgelrvvkGgswlkae.lssllraafrasaetpdtaasdvGfRlvr 260
                                          ++a+++  +l+++a+ +  + +kGgs+l+a+ +++++r+a+r s +++dta++++GfR+v+
  gi|121636634|ref|YP_976857.1| 229 hridppSTACCAPVKLATAADPTISQTLKGGSHLCAPeYCHRYRPAAR-SPQSQDTATTHIGFRCVA 294
                                    *****999999*************************************.9999************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1952.54
//
Query:       gi|121636635|ref|YP_976858.1|  [L=313]
Description: hypothetical protein BCG_0763 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.4e-105  350.6   3.4   4.4e-105  350.6   3.4    1.6  2  DUF4436   Domain of unknown function (DUF4436)


Domain annotation for each model (and alignments):
>> DUF4436  Domain of unknown function (DUF4436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.8      0.11     2e+03     228     246 ..      35      53 ..      34      55 .. 0.87
   2 !  350.6   3.4  2.4e-109  4.4e-105       2     254 ..      58     310 ..      57     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.11
                        DUF4436 228 wiDvavvlwvlvalvaslv 246
                                    ++Dv ++l vl+a v+sl 
  gi|121636635|ref|YP_976858.1|  35 VLDVCIILGVLIAYVFSLL 53 
                                    589999*******999985 PP

  == domain 2  score: 350.6 bits;  conditional E-value: 2.4e-109
                        DUF4436   2 laeskglgrpvdlsedadtpdrtsvtltvekldavanrLtvkvlvtpeealldekgevlkedlavrvsslaektdltypa 81 
                                    la++ g++++ d+ +    +d+t+v +++e+l++vanrL+vkvlv p+++++d++ +vl++d++vr+++++e +dl+yp 
  gi|121636635|ref|YP_976858.1|  58 LAHTPGPLPQPDVGT----TDDTVVLIRFEELHTVANRLDVKVLVLPDDSMIDHRLQVLTTDTSVRLYPENELGDLQYPV 133
                                    677888888887777....9************************************************************ PP

                        DUF4436  82 gklpaavevtveltGdiedwPFdrYrtgsltaevvvgagsdaapvpvrveltgrlegwdltvkrseea....dkaaavev 157
                                    gklpa+v++t+e++G++++wPFd+Y+t++++a+v+vgag+++++vp+rve+tg+legwd+++ r++e+    d+ ++v +
  gi|121636635|ref|YP_976858.1| 134 GKLPAQVATTIEAHGNPGAWPFDTYTTDTVQADVLVGAGDNRQYVPARVEVTGSLEGWDISAVRVGESsqtsDRPDNVII 213
                                    *****************************************************************999999999****** PP

                        DUF4436 158 tlaRskstlifalvivlvlialpvlalivaiqvlrgrrkleppaltwmAAmLFAvvplRnalPgsPPiGswiDvavvlwv 237
                                    tl+R+k++l+f+l+i+lvli+lp+lal+vaiq+++grrk++pp+ tw+AAmLFAvvplR++lPgsPP+G+wiD avv+wv
  gi|121636635|ref|YP_976858.1| 214 TLKRAKGPLVFDLGICLVLITLPTLALFVAIQMITGRRKFQPPFGTWYAAMLFAVVPLRTILPGSPPAGAWIDRAVVIWV 293
                                    ******************************************************************************** PP

                        DUF4436 238 lvalvaslvvyvvawvr 254
                                    l+al+a++vvy+vaw+r
  gi|121636635|ref|YP_976858.1| 294 LIALAAAMVVYIVAWYR 310
                                    ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1998.27
//
Query:       gi|121636636|ref|YP_976859.1|  [L=122]
Description: 50S ribosomal protein L14 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-55  184.6   0.3    6.5e-55  184.4   0.3    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
       0.14   12.2   0.2       0.56   10.2   0.1    1.9  2  DUF730         Protein of unknown function (DUF730)


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.3   7.3e-59   6.5e-55       1     122 []       1     122 []       1     122 [] 0.99

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 7.3e-59
                                    ..CSS-EEE--SSSSBSEEEEEEETT-.---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEES CS
                  Ribosomal_L14   1 miqlktrlkvaDNsgakevecikvlggkkrkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfd 80 
                                    miq+++rlkvaDN+gake+ ci+vlgg++r++a +Gd+iv++vk+a+p g+vk+gdvvkavvvrt ke rr+dGs+i+fd
  gi|121636636|ref|YP_976859.1|   1 MIQQESRLKVADNTGAKEILCIRVLGGSSRRYAGIGDVIVATVKDAIPGGNVKRGDVVKAVVVRTVKERRRPDGSYIKFD 80 
                                    9******************************************************************************* PP

                                    S-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                  Ribosomal_L14  81 dnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                    +naaV+++ +++p+Gtrifgpv relrek+f+ki+slApevl
  gi|121636636|ref|YP_976859.1|  81 ENAAVIIKPDNDPRGTRIFGPVGRELREKRFMKIISLAPEVL 122
                                    ****************************************96 PP

>> DUF730  Protein of unknown function (DUF730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.15   1.3e+03      28      41 ..      37      50 ..      30      53 .. 0.83
   2 ?   10.2   0.1   6.3e-05      0.56       8      38 ..      64      94 ..      58     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                         DUF730 28 kvvvatsrdpvtsg 41
                                    v+vat +d +  g
  gi|121636636|ref|YP_976859.1| 37 DVIVATVKDAIPGG 50
                                   699******99765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.3e-05
                         DUF730  8 rygenrrrdkgvpieldcnakvvvatsrdpv 38
                                   r  ++rrr  g  i+ d na+v++   +dp 
  gi|121636636|ref|YP_976859.1| 64 RTVKERRRPDGSYIKFDENAAVIIKPDNDPR 94
                                   55689********************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 863.69
//
Query:       gi|121636637|ref|YP_976860.1|  [L=105]
Description: 50S ribosomal protein L24 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-24   83.6   2.0    1.3e-23   83.1   2.0    1.2  1  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L
    3.7e-11   42.6   0.3    3.7e-11   42.6   0.3    2.4  3  KOW            KOW motif


Domain annotation for each model (and alignments):
>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   2.0   1.5e-27   1.3e-23       1      65 []      38     105 .]      38     105 .] 0.91

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.5e-27
                  ribosomal_L24   1 vnvvkkhvkp..sqqneq.GgiiekEapIhvSnVmlvdpkcgkptrvgfrlk.edgkkvRvskksgeei 65 
                                    vn +kkh+    +q++   Ggi+++EapIhvSnVm+vd+ +gkptr+g+r+  e gk+vR+sk++g++i
  gi|121636637|ref|YP_976860.1|  38 VNRIKKHTAIstTQRGARsGGIVTQEAPIHVSNVMVVDS-DGKPTRIGYRVDeETGKRVRISKRNGKDI 105
                                    8******987556788889*******************6.5********997678************97 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.3   4.1e-15   3.7e-11       1      32 []       5      36 ..       5      36 .. 0.98
   2 ?   -0.2   0.3      0.12   1.1e+03      18      26 ..      72      80 ..      70      98 .. 0.56
   3 ?   -1.3   0.0      0.27   2.4e+03      14      23 ..      92     101 ..      89     104 .. 0.61

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.1e-15
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                            KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                   +Gd+V V+sG++kG++GkV++ +++++rV+v+
  gi|121636637|ref|YP_976860.1|  5 KGDTVLVISGKDKGAKGKVLQAYPDRNRVLVE 36
                                   7*****************************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                                   EEEEEETTT CS
                            KOW 18 kVvkvdqhk 26
                                   +Vv+ d ++
  gi|121636637|ref|YP_976860.1| 72 MVVDSDGKP 80
                                   666666655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.27
                                    TCEEEEEEEE CS
                            KOW  14 GktGkVvkvd 23 
                                    Gk  ++ k++
  gi|121636637|ref|YP_976860.1|  92 GKRVRISKRN 101
                                    5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 722.84
//
Query:       gi|121636638|ref|YP_976861.1|  [L=187]
Description: 50S ribosomal protein L5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-38  128.3   0.0    1.4e-37  127.7   0.0    1.3  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.9e-26   92.1   0.7    3.3e-26   91.4   0.7    1.4  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
      0.014   15.0   0.1      0.018   14.6   0.1    1.1  1  DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase dom


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.0   2.4e-41   1.4e-37       1      94 []      91     184 ..      91     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 2.4e-41
                 Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttaktd 80 
                                    p+Gv+vtLrg++m+efld+l++++lpr+rdF+G+s+++fdg Gn++fG+ eq++f e+++dk+++++Gmdi++vt+a td
  gi|121636638|ref|YP_976861.1|  91 PVGVRVTLRGDRMWEFLDRLTSIALPRIRDFRGLSPKQFDGVGNYTFGLAEQAVFHEVDVDKIDRVRGMDINVVTSAATD 170
                                    79****************************************************************************** PP

                 Ribosomal_L5_C  81 eearallkelgipf 94 
                                    +e rall++lg+pf
  gi|121636638|ref|YP_976861.1| 171 DEGRALLRALGFPF 184
                                    *************9 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.7   5.5e-30   3.3e-26       1      57 []      31      87 ..      31      87 .. 1.00

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 5.5e-30
                                   SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                   Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                   NvMq+P ++K+v+nmgvGea++d+kl+++a+++La ItGQkP v++a+ksia+Fk+R
  gi|121636638|ref|YP_976861.1| 31 NVMQIPTVTKVVVNMGVGEAARDAKLINGAVNDLALITGQKPEVRRARKSIAQFKLR 87
                                   9*******************************************************9 PP

>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.1e-06     0.018     109     171 ..      12      74 ..      10      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                                    EGGGHHHHHHHHHHHH-TTTEEEEEEEEE--HHHHHHHHHHHH-GGHHHHHHHHHTS---SS- CS
                 DNA_pol3_alpha 109 ekerreevidyvkekyGkenvaqiitfgtlaakaairdvgralglplkevdklaklipkelgi 171
                                    ++++r e+ d++++++G  nv+qi t++++   + + +++r  +l + +v+ la  + +++++
  gi|121636638|ref|YP_976861.1|  12 KERYRSEIRDALRKQFGYGNVMQIPTVTKVVVNMGVGEAARDAKLINGAVNDLALITGQKPEV 74 
                                    6899***************************************99999999999888887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1300.10
//
Query:       gi|121636639|ref|YP_976862.1|  [L=61]
Description: 30S ribosomal protein S14 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-25   86.5   3.3    8.1e-25   86.4   3.3    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.015   14.8   2.1        2.4    7.8   0.4    2.3  2  Sgf11          Sgf11 (transcriptional regulation protein)
      0.042   13.9   0.6       0.05   13.6   0.6    1.2  1  Fer2_4         2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   3.3   1.3e-28   8.1e-25       3      54 .]      11      60 ..       9      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 1.3e-28
                                   -----SS..CTTT---SSS--SSSEE-GGG-EHHHHHHHTTT...TT-EE-- CS
                  Ribosomal_S14  3 aklprnssptrirnrCrvtGrprGvirkfgLsRicfRelAlkgelpGvkKaS 54
                                   a  pr++  +r ++rC  +Grpr+v+rkfgL+Ric+Re+A++gelpGv+K+S
  gi|121636639|ref|YP_976862.1| 11 AGKPRFA--VRAYTRCSKCGRPRAVYRKFGLCRICLREMAHAGELPGVQKSS 60
                                   668****..******************************************8 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4   0.00041       2.4       3      13 ..      20      30 ..      19      33 .. 0.89
   2 ?    6.6   0.1   0.00092       5.5       7      17 ..      40      50 ..      34      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00041
                                   -EEE-TTTSSE CS
                          Sgf11  3 eyvtCpnCgRq 13
                                   +y++C  CgR+
  gi|121636639|ref|YP_976862.1| 20 AYTRCSKCGRP 30
                                   799*******6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00092
                                   -TTTSSEEEGG CS
                          Sgf11  7 CpnCgRqiaas 17
                                   C +C R++a+ 
  gi|121636639|ref|YP_976862.1| 40 CRICLREMAHA 50
                                   ********985 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   8.4e-06      0.05      33      63 ..      21      52 ..       4      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                         Fer2_4 33 p.rsckygrprgelcaggeCrnClVevegepn 63
                                     r  k grpr+ +  +g Cr Cl e+   + 
  gi|121636639|ref|YP_976862.1| 21 YtRCSKCGRPRAVYRKFGLCRICLREMAHAGE 52
                                   43778899****************99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 452.05
//
Query:       gi|121636640|ref|YP_976863.1|  [L=132]
Description: 30S ribosomal protein S8 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-49  167.7   0.0    1.1e-49  167.6   0.0    1.0  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.6   0.0   6.2e-54   1.1e-49       1     127 []       5     132 .]       5     132 .] 0.97

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 6.2e-54
                                    -HHHHHHHHHHHHHHTT-SEEEEE--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE-SBTT CS
                   Ribosomal_S8   1 DpiadmltrirNaekakkeevevpasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrvskpg 79 
                                    Dpiad+ltr+rNa++a ++ev++p+sklk++i+++Lk+eGyi+df++e  +  k++ i+lky  ++++ i +l+rvskpg
  gi|121636640|ref|YP_976863.1|   5 DPIADFLTRLRNANSAYHDEVSLPHSKLKANIAQILKNEGYISDFRTEdARVGKSLVIQLKYGPSRERSIAGLRRVSKPG 84 
                                    9**********************************************85555677************************* PP

                                    C--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                   Ribosomal_S8  80 rrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                    +rvYak+++lp+vl+glG+ai+sTs+G++td++A +++vGGevlayvw
  gi|121636640|ref|YP_976863.1|  85 LRVYAKSTNLPRVLGGLGVAIISTSSGLLTDRQAARQGVGGEVLAYVW 132
                                    ************************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 984.06
//
Query:       gi|121636641|ref|YP_976864.1|  [L=179]
Description: 50S ribosomal protein L6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-41  138.4   1.6    7.9e-22   77.7   0.0    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.4   1.4e-20   2.5e-16       1      76 []      11      83 ..      11      83 .. 0.97
   2 !   77.7   0.0   4.4e-26   7.9e-22       1      75 [.      91     165 ..      91     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.4e-20
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                   Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                   +P+gv+v+i+g q ++v+Gpkg+l +++ e ++v+   +++ ++v+++++ ++ ++ l+g++r+l++n ++GVt+g
  gi|121636641|ref|YP_976864.1| 11 VPAGVDVTIEG-QSISVKGPKGTLGLTVAEPIKVAR-NDDGAIVVTRPDDERRNRS-LHGLSRTLVSNLVTGVTQG 83
                                   7*********8.***********************5.5999***************.*****************98 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 4.4e-26
                                    CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHT CS
                   Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVte 75 
                                    ++vg+rv++kg++l+  lG+++++ +e peg+t++v+     +t+ +vsgidk+kv    A+i+  r++ ++++kGV++
  gi|121636641|ref|YP_976864.1|  91 FGVGYRVQLKGSNLEFALGYSHPVVIEAPEGITFAVQ----APTKFTVSGIDKQKVgqiaANIRRLRRPDPYKGKGVRY 165
                                    79***********************************....************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1279.40
//
Query:       gi|121636642|ref|YP_976865.1|  [L=122]
Description: 50S ribosomal protein L18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-47  160.4   3.3    2.2e-47  160.2   3.3    1.0  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a
  ------ inclusion threshold ------
      0.064   13.0   0.1      0.093   12.5   0.1    1.3  1  LPD30           Large polyvalent protein associated domain 30


Domain annotation for each model (and alignments):
>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.2   3.3   2.5e-51   2.2e-47       2     116 .]       8     122 .]       7     122 .] 0.99

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 2.5e-51
                                    -CCHHHCHHHHHHTTT--TTSSS-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHH CS
                 Ribosomal_L18p   2 kkkearkrRhkRirkklsgtaerprlvvfrsnrhiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAera 81 
                                    +++ +r rRh+R+rkklsgtaerprlvv+rs+rhi++Q+++d +g+t+a+as++e+++++  +++k+++ +vg+liAera
  gi|121636642|ref|YP_976865.1|   8 TRRISRLRRHTRLRKKLSGTAERPRLVVHRSARHIHVQLVNDLNGTTVAAASSIEADVRGVPGDKKARSVRVGQLIAERA 87 
                                    7899**************************************************************************** PP

                                    CHHCHTC-EE--TTSSS-CHHHHHHHHHHCTSSB- CS
                 Ribosomal_L18p  82 kekgiekvvfDrggykYhGrvaalAdaaReaGlkf 116
                                    k++gi++vvfDrggy+Y Gr+aalAdaaRe+Gl+f
  gi|121636642|ref|YP_976865.1|  88 KAAGIDTVVFDRGGYTYGGRIAALADAARENGLSF 122
                                    *********************************98 PP

>> LPD30  Large polyvalent protein associated domain 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     1e-05     0.093      22      59 ..      65     103 ..      42     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                          LPD30  22 vyaihGeqspesvrvlggvistggsaefD.ivFdnGeks 59 
                                    v  + G+++  svrv +++++ +++a +D +vFd G  +
  gi|121636642|ref|YP_976865.1|  65 VRGVPGDKKARSVRVGQLIAERAKAAGIDtVVFDRGGYT 103
                                    566889***********************778*999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 919.56
//
Query:       gi|121636643|ref|YP_976866.1|  [L=220]
Description: 30S ribosomal protein S5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-28   98.4   2.3      3e-28   97.6   2.3    1.4  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    2.2e-28   97.5   0.6    3.3e-28   96.9   0.6    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   2.3   3.4e-32     3e-28       3      65 .]      44     106 ..      42     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 3.4e-32
                                    EEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                   Ribosomal_S5   3 ekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                    e+v++i+rv+kv+kgGrr+sf+alv+vGdgnG+vG+G+gkakev+ Ai k++e A+k++++vp
  gi|121636643|ref|YP_976866.1|  44 ERVVAINRVSKVVKGGRRFSFTALVIVGDGNGMVGVGYGKAKEVPAAIAKGVEEARKSFFRVP 106
                                    89**********************************************************997 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.6   3.7e-32   3.3e-28       2      72 .]     118     188 ..     117     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 3.7e-32
                                    EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS-SSHHHHHHHHHHHHHHTTTT-.-GGGG CS
                 Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslgsrnpinvvkAtfeALkklrspeevaalR 72 
                                    g+  a+ vll+pa++GtG+iagga+ravle+aG++D+lakslgs n invv+At+ ALk l+ peevaa+R
  gi|121636643|ref|YP_976866.1| 118 GEAAAGVVLLRPASPGTGVIAGGAARAVLECAGVHDILAKSLGSDNAINVVHATVAALKLLQRPEEVAARR 188
                                    788999**************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1664.42
//
Query:       gi|121636644|ref|YP_976867.1|  [L=65]
Description: 50S ribosomal protein L30 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-18   66.1   0.5    2.1e-18   65.9   0.5    1.0  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.5   1.2e-22   2.1e-18       1      51 []       4      54 ..       4      54 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.2e-22
                                   EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                   l++t++rs+ig  +k+r  L++LgLr+i ++v++++++++rG++  V+hlV
  gi|121636644|ref|YP_976867.1|  4 LKITQVRSTIGARWKQRESLRTLGLRRIRHSVIREDNAATRGLIAVVRHLV 54
                                   79************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 523.94
//
Query:       gi|121636645|ref|YP_976868.1|  [L=146]
Description: 50S ribosomal protein L15 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-33  114.3   2.4    7.4e-33  114.0   2.4    1.2  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.034   13.6   0.1    1.5  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   2.4   8.3e-37   7.4e-33       1     127 [.      28     144 ..      28     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 8.3e-37
                                    GGGGTSSTTTTTTTTT-S--......S--..........---GGG..---EEEEHHHHHHTTTTGTTS------EEEGGG CS
                 Ribosomal_L27A   1 kGktgGrGhkGqkkrsgvkkkpgfeGGqmplyrrlpk.rGfknskfkkeykvvnlkdLdelideerleladeaeeidlee 79 
                                    kGkt+GrG kG+++r++v     feGGqmp+++rlpk +Gf+n +f++ey++vn++d+++l++++          + +++
  gi|121636645|ref|YP_976868.1|  28 KGKTAGRGTKGTRARKQVP--VTFEGGQMPIHMRLPKlKGFRN-RFRTEYEIVNVGDINRLFPQGGA--------VGVDD 96 
                                    6**************8765..58**************99**98.78*************99999865........99*** PP

                                    TTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                 Ribosomal_L27A  80 laeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                    l+++g ++k+  vKvlg+g+lt+k++v a+kfS +A++kI aaGG+++
  gi|121636645|ref|YP_976868.1|  97 LVAKGAVRKNALVKVLGDGKLTAKVDVSAHKFSGSARAKITAAGGSAT 144
                                    *********************************************985 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.7e-06     0.034      89     119 ..     115     143 ..      99     146 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-06
                  Ribosomal_L18  89 vrllevPklsvaALrftetararilkaGGei 119
                                     +l+   k+ v A +f+ +ara+i++aGG  
  gi|121636645|ref|YP_976868.1| 115 GKLT--AKVDVSAHKFSGSARAKITAAGGSA 143
                                    5554..599********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1096.74
//
Query:       gi|121636646|ref|YP_976869.1|  [L=623]
Description: protease IV sppA (endopeptidase IV) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-101  336.7   0.1    1.8e-51  174.1   0.0    2.1  2  Peptidase_S49  Peptidase family S49
      1e-06   28.7   1.3     0.0013   18.6   0.2    3.2  3  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.032   14.4   3.6       0.12   12.6   3.6    2.1  1  PRODH          Proline utilization A proline dehydrogenase N-
      0.099   11.6   0.4       0.16   11.0   0.4    1.2  1  SDH_sah        Serine dehydrogenase proteinase
       0.19   11.0   2.0        2.7    7.3   0.4    3.1  4  ECH_1          Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   6.5e-51   2.3e-47       2     153 ..     129     282 ..     128     283 .. 0.98
   2 !  174.1   0.0     5e-55   1.8e-51       2     153 ..     403     554 ..     402     555 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 6.5e-51
                                    HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCC..CTTSS CS
                  Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksav..slrre 79 
                                    a +a kP +a+ae++  +++Yylasa+ +++++ps++vg++G++t++++l+++l+k+g+e+q+v++Geyksa+  ++++ 
  gi|121636646|ref|YP_976869.1| 129 AFSAVKPSLAWAETYPGTLSYYLASAFGEVWMQPSGSVGLVGFATNATFLRDALHKAGIEAQFVARGEYKSAAnlFTEDG 208
                                    56899********************************************************************999**** PP

                                    --HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                  Peptidase_S49  80 lteeereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                    +t+++re+++r+ld++++q++q+Vak+Rn+ v+++d++A+++ l++++A+++gL+d++g+ d+a+a+++el++v
  gi|121636646|ref|YP_976869.1| 209 FTDAHREAVTRMLDSLQDQVWQAVAKSRNIGVDALDELADRAPLLRDDAVTCGLIDRIGFRDQAYARMAELVGV 282
                                    ***********************************************************************998 PP

  == domain 2  score: 174.1 bits;  conditional E-value: 5e-55
                                    HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS-- CS
                  Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelt 81 
                                    a++++kPvvas+++vaaSggYy++++ad ivanp ti+gsiGvit +l +++l d+lgv  ++v+++++++a+s++ ++t
  gi|121636646|ref|YP_976869.1| 403 ARDRGKPVVASMGAVAASGGYYVSMGADAIVANPGTITGSIGVITGKLVVRDLKDRLGVGSDAVRTNANADAWSIDAPFT 482
                                    6899**************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                  Peptidase_S49  82 eeereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                    ++++++ +++ d +y++Fv+ Va++R++++++vd +A+grv+tg++Al++gLvdelg++++av++++ la++
  gi|121636646|ref|YP_976869.1| 483 PDQQAHREAEADLFYSDFVERVAEGRKMTTDAVDVVARGRVWTGADALDRGLVDELGGLRTAVRRAKVLAGL 554
                                    *******************************************************************99987 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0025         9     129     180 ..     218     268 ..     207     270 .. 0.88
   2 !   18.6   0.2   3.7e-07    0.0013      32      96 ..     362     429 ..     356     437 .. 0.80
   3 ?    0.5   0.0      0.13   4.7e+02     158     178 ..     518     538 ..     501     541 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-S CS
                   CLP_protease 129 aeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidevie 180
                                    ++ l+ +++++ + +ak+ +  ++ + +  dr   l  ++Av+ GLid++  
  gi|121636646|ref|YP_976869.1| 218 TRMLDSLQDQVWQAVAKSRNIGVDALDELADRAPLLR-DDAVTCGLIDRIGF 268
                                    57789999************************98875.89*********975 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.7e-07
                                    HHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEE.EETHHHHHHHTS CS
                   CLP_protease  32 kiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGl.aaSmgslllaag 96 
                                    +i a L  + a d+ + i+l ++spGGsvta+ +I+  ++    + + ++  +G  aaS g  + +++
  gi|121636646|ref|YP_976869.1| 362 TIAAALREVAADDSVSAIVLRVDSPGGSVTASETIWREVARArdRGKPVVASMGAvAASGGYYVSMGA 429
                                    566777788899999*********************99998856677888888852556666666665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.13
                                    HCSTEEEEHHHHHHHTSSSEE CS
                   CLP_protease 158 ldrdtflsaeeAveyGLidev 178
                                    + r ++ + ++A++ GL+de 
  gi|121636646|ref|YP_976869.1| 518 VARGRVWTGADALDRGLVDEL 538
                                    578889999**********96 PP

>> PRODH  Proline utilization A proline dehydrogenase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.6   3.4e-05      0.12       2      39 ..      86     123 ..      86     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                          PRODH   2 pLRqaItaayRrpEaecVapLleaArlpeaeraairal 39 
                                    +LR+a+ a +R+ E   Va L++  +lp++ + a+++l
  gi|121636646|ref|YP_976869.1|  86 ALRDAVAAIHRAAEDPRVAGLIARVQLPPSPAGAVQEL 123
                                    69******************************999987 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   4.4e-05      0.16      83     155 ..     365     443 ..     358     452 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.4e-05
                        SDH_sah  83 rairltpkd...kpidliihtpGGlvlaatqiakalkehkaktrviv...phyamsGGtlialaadeiildenavlGpv 155
                                     a+r    d     i l + +pGG v a++ i + +   + + + +v      a sGG  +++ ad i+ ++ ++ G +
  gi|121636646|ref|YP_976869.1| 365 AALREVAADdsvSAIVLRVDSPGGSVTASETIWREVARARDRGKPVVasmGAVAASGGYYVSMGADAIVANPGTITGSI 443
                                    55665554411145667789***********998877666665554411156899**************9999988876 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.78   2.8e+03      29      47 ..     364     382 ..     361     388 .. 0.85
   2 ?    7.3   0.4   0.00074       2.7      80     116 ..     399     435 ..     385     460 .. 0.85
   3 ?   -1.8   0.0      0.44   1.6e+03     205     237 ..     477     508 ..     469     513 .. 0.81
   4 ?    0.7   0.0     0.074   2.6e+02     149     173 ..     514     538 ..     510     552 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.78
                                    HHHHHHHHHSTTECEEEEE CS
                          ECH_1  29 iqalekleddksvravvLt 47 
                                    ++al ++  d sv a+vL 
  gi|121636646|ref|YP_976869.1| 364 AAALREVAADDSVSAIVLR 382
                                    68999999999******96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00074
                                    HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEE CS
                          ECH_1  80 lwtklytvpkpviaavnGaaigGGlelalacDiviaa 116
                                       ++++  kpv+a +   a+ GG  + + +D ++a 
  gi|121636646|ref|YP_976869.1| 399 EVARARDRGKPVVASMGAVAASGGYYVSMGADAIVAN 435
                                    556778889************************9986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHH CS
                          ECH_1 205 lnakledalaeqleaeaklfestfskddikeGl 237
                                    ++a+++  +++ +eaea+lf+s f +  + eG+
  gi|121636646|ref|YP_976869.1| 477 IDAPFTPDQQAHREAEADLFYSDFVE-RVAEGR 508
                                    67888999999*********998876.555665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.074
                                    HHHHHHHT-EEEHHHHHHCTSSSEE CS
                          ECH_1 149 AeeilllgkkisaqealkvGlvdkv 173
                                    A  ++  g+  ++++al++Glvd+ 
  gi|121636646|ref|YP_976869.1| 514 AVDVVARGRVWTGADALDRGLVDEL 538
                                    66788889999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.22s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4673.07
//
Query:       gi|121636647|ref|YP_976870.1|  [L=301]
Description: hypothetical protein BCG_0775c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-62  210.5   0.0    2.7e-62  210.1   0.0    1.1  1  LCM           Leucine carboxyl methyltransferase
  ------ inclusion threshold ------
      0.035   14.0   0.5      0.071   13.0   0.5    1.5  1  Phage_base_V  Type VI secretion system, phage-baseplate injec


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.0     3e-66   2.7e-62       1     178 [.      19     193 ..      19     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 3e-66
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    a++vaa+ral+++ + +gli+Dp+ae+lv+a+gl+++++  d+el+ +++ + +  +a+++ +giavRt++fdd+++ a+
  gi|121636647|ref|YP_976870.1|  19 ATMVAAGRALATKDP-RGLINDPFAEPLVRAVGLDFFTKLIDGELDIATTGNLSPGRAQAMIDGIAVRTKYFDDYFRTAT 97 
                                    79************9.********************************988999************************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     + g+rqvViL+AGlD+rayRlpw+ag++v+E+Dqp+v++fK++tl+ +ga+p+a +r+v +Dlr  dwp+aL+aag+d+
  gi|121636647|ref|YP_976870.1|  98 -DGGVRQVVILAAGLDARAYRLPWPAGTVVYEIDQPQVIDFKTTTLAGIGAKPTAIRRTVYIDLR-ADWPAALQAAGLDS 175
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HH CS
                            LCM 161 ekptawvaeGvlvYLtpe 178
                                    ++ptaw+aeG+l+YL+p+
  gi|121636647|ref|YP_976870.1| 176 TAPTAWLAEGMLIYLPPD 193
                                    ****************97 PP

>> Phage_base_V  Type VI secretion system, phage-baseplate injector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   7.9e-06     0.071       5      57 ..     211     265 ..     208     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-06
                                    HHHHHHEEEEEE.EEEETTTTEEEEEETTEEXXXEEEXX.SXBSSSBXXXXXXTT CS
                   Phage_base_V   5 RrlenlirlGvv.aevdlaaarvrvktgdlltdwlrwla.arAGktrswrapsvG 57 
                                    R l nl r   + +++ ++++r+r  +  ++++w rw+  a A ++ + +ap +G
  gi|121636647|ref|YP_976870.1| 211 RSLPNLSRALWIsTQAGYEKWRIRFASTAWTSTWRRWCIpANAATSSTTCAPRAG 265
                                    67777777766624567788*****************972457777888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2198.28
//
Query:       gi|121636648|ref|YP_976871.1|  [L=367]
Description: hypothetical protein BCG_0776c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-67  226.8   0.9    2.9e-67  226.2   0.9    1.3  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.2   0.9   1.6e-71   2.9e-67       1     187 [.      24     209 ..      24     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.2 bits;  conditional E-value: 1.6e-71
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHG.C.HCCCCT--HHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekek.e.eekkekkapelnrgiavRtrffddllka 78 
                                    a++vaaara+++r+a ++li+D++ae+lv+a+g+++l+r a +el++++ +  e+ ++++ ++++  avRt+ffd+++ +
  gi|121636648|ref|YP_976871.1|  24 ATMVAAARAMATRAA-NPLINDQFAEPLVRAVGVDVLTRLASGELTASDiDdPERPNASMVRMAEHHAVRTKFFDEFFMD 102
                                    79***********99.*******************************99874455567899******************* PP

                                    HHHCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT CS
                            LCM  79 alsaagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagf 158
                                    a+ +agirqvViL++GlD+rayRl+w+a+++v+E+Dqp+v+efK++tl+elga+p+a++r+v +Dlr  dwp+aL aagf
  gi|121636648|ref|YP_976871.1| 103 AT-RAGIRQVVILASGLDSRAYRLAWPAQTVVYEIDQPQVMEFKTRTLAELGATPTADRRVVTADLR-ADWPTALGAAGF 180
                                    **.7***************************************************************.************ PP

                                    -TTSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 159 dpekptawvaeGvlvYLtpeasdalleai 187
                                    dp++ptaw+aeG+l YL+pea+d+ll+++
  gi|121636648|ref|YP_976871.1| 181 DPTQPTAWSAEGLLRYLPPEAQDRLLDNV 209
                                    ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2530.34
//
Query:       gi|121636649|ref|YP_976872.1|  [L=218]
Description: L-fuculose phosphate aldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-45  154.3   0.3    3.8e-45  154.1   0.3    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.3   2.1e-49   3.8e-45       3     185 ..      11     186 ..       9     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 2.1e-49
                                    HHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHHH CS
                    Aldolase_II   3 laeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiyk 82 
                                    + +a++++ rrglvegt+GniS+r++ +++++itps vd++e+  +dlv+vd+  g v++  ++g++ps e+ lHla+y+
  gi|121636649|ref|YP_976872.1|  11 VLAAAKDMLRRGLVEGTAGNISARRS-DGNVVITPSSVDYAEMLLHDLVLVDAG-GAVLHA-KDGRSPSTELNLHLACYR 87 
                                    67999*******************99.99***********************86.899966.88999************* PP

                                    H-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEEE CS
                    Aldolase_II  83 arpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGll 162
                                    a+ d++ v+H+H+ +a++++ +a +e++p++  e a ++ g++v +++yaa gt+e+g+++++al+  + a+l++nHGl+
  gi|121636649|ref|YP_976872.1|  88 AFDDIGSVIHSHPVWATMFA-VA-HEPIPACIDEFAIYC-GGDVRCTEYAASGTPEVGRNAVRALE-GRAAALIANHGLV 163
                                    ********************.65.799**9888888856.666**********************8.779********** PP

                                    EEESSHHHHHHHHHHHHHHHHHH CS
                    Aldolase_II 163 tvGetleeAvalaetleeaaeiq 185
                                    +vG+  ++ ++ +  +e++a+i 
  gi|121636649|ref|YP_976872.1| 164 AVGPRPDQVLRVTALVERTAQIV 186
                                    ********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1627.72
//
Query:       gi|121636650|ref|YP_976873.1|  [L=326]
Description: D-3-phosphoglycerate dehydrogenase serA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-52  176.3   0.0    5.9e-52  175.6   0.0    1.3  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
    4.6e-11   42.5   0.0    5.6e-11   42.2   0.0    1.1  1  2-Hacid_dh    D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.0   6.5e-56   5.9e-52       1     178 []     115     288 ..     115     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 6.5e-56
                                    HHHHHHHHTTHHHHHHHHHTTCC.....HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregew.....ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75 
                                    +allla++r+l  ad++vr+g+         ++++g e++g t G++GlG++G+av  rl+++g++via+d++++  +  
  gi|121636650|ref|YP_976873.1| 115 VALLLAVARHLIPADADVRSGNIfrdgtIPYQRFRGAEIAGLTAGLVGLGAVGRAVRWRLSGLGLRVIAHDPYRD--D-- 190
                                    689******************998877777789****************************************77..3.. PP

                                    HHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                   2-Hacid_dh_C  76 eelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                       g   +sl+ellae+Divs+h+ +t++t ++i+a+++a+m++ga+++NtaR +l d++aL++aL+ gk+a+a+lD f 
  gi|121636650|ref|YP_976873.1| 191 --AG---HSLDELLAEADIVSMHAAVTDDTIGMIGAQQFAAMRDGAVFLNTARSQLHDTDALVDALRGGKLAAAGLDHFT 265
                                    ..23...49*********************************************************************** PP

                                    SSSSGTCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                     e lp+d+pl+++pnv+ltPHi+
  gi|121636650|ref|YP_976873.1| 266 GEWLPTDHPLVSMPNVVLTPHIG 288
                                    *********************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   6.2e-15   5.6e-11      30     134 .]      43     320 ..      20     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 6.2e-15
                                    HHHCHHHHTT..ESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH..... CS
                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                     2-Hacid_dh  30 teellekakd..adalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt..... 102
                                     e+l++++    ad+l+v s + v   v+e+  +L+v+a       nvD++ a++ Gi V ++p+ ++++vAE+t     
  gi|121636650|ref|YP_976873.1|  43 AEQLADRITAvaADVLVVESDS-VGGPVFER--GLRVVAATRGDPSNVDIPGATAAGIPVLHTPARNADAVAEMTvalll 119
                                    5666666666658888888887.99999999..8999999999999********************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|121636650|ref|YP_976873.1| 120 avarhlipadadvrsgnifrdgtipyqrfrgaeiagltaglvglgavgravrwrlsglglrviahdpyrddaghsldell 199
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|121636650|ref|YP_976873.1| 200 aeadivsmhaavtddtigmigaqqfaamrdgavflntarsqlhdtdalvdalrggklaaagldhftgewlptdhplvsmp 279
                                    ******************************************************************************** PP

                                    .........T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 .........aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                             +aT ++  + a+++a+ l a l+g++pa++vn
  gi|121636650|ref|YP_976873.1| 280 nvvltphigGATWNTEARQARMVADDLGALLSGNRPAHVVN 320
                                    *********999999999999*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2309.40
//
Query:       gi|121636651|ref|YP_976874.1|  [L=448]
Description: d-xylulose kinase xylB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-22   80.5   0.4    1.3e-22   80.5   0.4    1.7  2  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
    1.2e-10   41.4   0.0    1.5e-09   37.8   0.0    2.1  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
     0.0014   18.2   0.0     0.0022   17.5   0.0    1.4  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.23   12.0   1.1         13    6.4   0.0    3.5  3  RHS_repeat   RHS Repeat
        0.6   10.8   2.7         23    5.7   0.4    2.9  2  CtnDOT_TraJ  Homologues of TraJ from Bacteroides conjugative 


Domain annotation for each model (and alignments):
>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.8   6.4e+03     172     189 ..     180     197 ..     173     198 .. 0.79
   2 !   80.5   0.4   3.6e-26   1.3e-22      82     197 ..     291     402 ..     236     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                         FGGY_C 172 ilgvpVerpktaeatalG 189
                                     +gv+V+r++  e+  +G
  gi|121636651|ref|YP_976874.1| 180 DCGVTVDRMPRVETFGVG 197
                                    489******999998888 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 3.6e-26
                         FGGY_C  82 avadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgsk 161
                                    ++ + + +v +p+  g+r+p+ +pd+r+++ g++ s+++a++ rAa+ea  + +r+ +e      g+p++r+++ GGg++
  gi|121636651|ref|YP_976874.1| 291 LADPRRVPVWLPYIRGERTPFHEPDRRAVLDGVDLSQDAASVRRAAYEASGFVVRQLIELS----GAPVARIVAAGGGTR 366
                                    55667788999*********************************************99876....*************** PP

                         FGGY_C 162 ndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                     + +mq +Ad++g+pVe+ + ae++alGaA l+ +a
  gi|121636651|ref|YP_976874.1| 367 IQPWMQAIADATGRPVEVSRVAEGAALGAAFLGRLA 402
                                    *******************************99776 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   4.3e-13   1.5e-09       2     217 ..       7     202 ..       6     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 4.3e-13
                                    EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                     +g+D+Gtt +ka++ d +g+v a+ ++ ++l  p +++ e+d++e w +   a   +l+++     + +a+++++   +
  gi|121636651|ref|YP_976874.1|   7 TIGIDIGTTAVKAVAADDNGRVTARVRIGHQLAVPAPDRLEHDADEAWRRGPLA---ALDRL--VGPDTRALAVAAMVPS 81 
                                    69**********************************************986543...45555..56689*********** PP

                                    EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHHH CS
                         FGGY_N  82 lvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyLi 161
                                    l+++D  ++p+++ +l+ d r              ++  ++  +v s g t+  l+W + + p++      +       +
  gi|121636651|ref|YP_976874.1|  82 LTAVDPAGRPITPGLLYGDARGRVP----------NASVARAQSVPSVGETAEFLRWTAGQAPDASG----YWPAPAVAN 147
                                    *******************997644..........44455566777777788888888777777654....333444556 PP

                                    HHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEE CS
                         FGGY_N 162 wrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelk 217
                                    + L+g+ v d+  a ++  +      w+  ++a +g++ + +P++   +  +g+++
  gi|121636651|ref|YP_976874.1| 148 YALSGEAVIDYATAVTTLPL-FDGTGWNATACADCGVTVDRMPRVETFGVGVGQVR 202
                                    77788888887777666533.33456888888888888888887777666666666 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.1e-07    0.0022       1      28 [.       8      35 ..       8     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.1e-07
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE- CS
                    BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitn 28
                                   +GiD+G+T++kav  d++g v +r   +
  gi|121636651|ref|YP_976874.1|  8 IGIDIGTTAVKAVAADDNGRVTARVRIG 35
                                   7*******************99997655 PP

>> RHS_repeat  RHS Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.22   7.8e+02       2      10 ..      23      31 ..      23      38 .. 0.78
   2 ?    6.4   0.0    0.0036        13       7      28 ..      82     105 ..      82     114 .. 0.88
   3 ?    0.0   0.0      0.36   1.3e+03      23      31 ..     376     384 ..     373     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                     RHS_repeat  2 DaaGrLtev 10
                                   D++Gr+t+ 
  gi|121636651|ref|YP_976874.1| 23 DDNGRVTAR 31
                                   788888875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                     RHS_repeat   7 LtevtdpsGrvtt..YtY.DaqGrl 28 
                                    Lt+v dp+Gr  t  + Y Da+Gr+
  gi|121636651|ref|YP_976874.1|  82 LTAV-DPAGRPITpgLLYgDARGRV 105
                                    7888.******9888*********8 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.36
                     RHS_repeat  23 DaqGrlttl 31 
                                    Da Gr++++
  gi|121636651|ref|YP_976874.1| 376 DATGRPVEV 384
                                    566666554 PP

>> CtnDOT_TraJ  Homologues of TraJ from Bacteroides conjugative transposon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.022        80       8      21 ..     138     151 ..     136     193 .. 0.72
   2 ?    5.7   0.4    0.0063        23      19      59 ..     358     399 ..     355     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                    CtnDOT_TraJ   8 GyFtVPtvAnyivh 21 
                                    Gy+  P vAny   
  gi|121636651|ref|YP_976874.1| 138 GYWPAPAVANYALS 151
                                    9**********765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0063
                    CtnDOT_TraJ  19 ivhAgGGgallqkvnslassststalsaa.kagggmaadalg 59 
                                    iv AgGG  ++  +  +a  + + +     ++g++  a+ lg
  gi|121636651|ref|YP_976874.1| 358 IVAAGGGTRIQPWMQAIADATGRPVEVSRvAEGAALGAAFLG 399
                                    999****************99999855540555555555556 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2987.28
//
Query:       gi|121636652|ref|YP_976875.1|  [L=242]
Description: hypothetical protein BCG_0780 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-07   31.8   0.4      7e-07   30.0   0.0    2.0  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.6e-05   25.2   0.0    6.9e-05   23.2   0.0    1.9  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.3e-05   24.1   0.3    0.00015   22.0   0.0    2.0  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00068   18.6   0.3    0.00094   18.2   0.3    1.1  1  DNA_topoisoIV    DNA gyrase/topoisomerase IV, subunit A
     0.0035   17.3   0.3       0.19   11.7   0.0    2.6  3  Acetyltransf_13  ESCO1/2 acetyl-transferase
     0.0059   16.6   0.1      0.065   13.2   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.19   11.1   0.0    1.3  1  GNAT_acetyltr_2  GNAT acetyltransferase 2


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.69   1.8e+03      95      95 ..      63      63 ..      11     106 .. 0.60
   2 !   30.0   0.0   2.7e-10     7e-07       2     104 ..     114     212 ..     113     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.69
                 Acetyltransf_3 95 G 95
                                   G
  gi|121636652|ref|YP_976875.1| 63 G 63
                                   1 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 2.7e-10
                 Acetyltransf_3   2 LlLrpltee.Dlealfelrsdpevmry.....lpepltleeaeewlerawaeeseeegygwaivlkdtgv.iGsvglrdl 74 
                                    L Lrp++++ D  ++f+ r  +e+  +     +p   +++++ +  +++   ++  e+  w + + d+gv +G+v    +
  gi|121636652|ref|YP_976875.1| 114 LELRPFSPDeD-RDIFA-RRTEEMGAAgdgsgGP-AGSVDDEIRAAQKRV--DD--EEAAWFVAV-DSGVkVGMVFGELV 185
                                    78******955.99996.6667766556554333.344444444444333..22..444566643.55577****77777 PP

                 Acetyltransf_3  75 eeedeeaelgymlapsfwgkGyateavral 104
                                    ++e   +++ ++++p+++ kGy+t a+r  
  gi|121636652|ref|YP_976875.1| 186 HGE---VDVRIWIHPDHRKKGYGTAALRKS 212
                                    777...9********************984 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.93   2.4e+03      38      49 ..      24      38 ..      19      70 .. 0.58
   2 !   23.2   0.0   2.7e-08   6.9e-05       4      48 ..     166     211 ..     163     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.93
                                   TSSHHHHHHHH...T CS
                 Acetyltransf_7 38 gkGiGraLlea...a 49
                                   ++ i+ aLl+a   +
  gi|121636652|ref|YP_976875.1| 24 RREIADALLAAlerR 38
                                   667788888763220 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.7e-08
                                    EEEEEEETTEEEEEEEEEEES.TCTEEEEE-GGGTTSSHHHHHHHH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld.aeitrlaVdpeyrgkGiGraLlea 48 
                                      fVa d g  vG++  +l+  +   r++++p++r+kG+G+a l+ 
  gi|121636652|ref|YP_976875.1| 166 AWFVAVDSGVKVGMVFGELVHgEVDVRIWIHPDHRKKGYGTAALRK 211
                                    679999999999*98888876445555**************98874 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.52   1.3e+03      73      89 ..      23      39 ..      18      57 .. 0.66
   2 !   22.0   0.0   5.9e-08   0.00015      28      84 ..     159     211 ..     122     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.52
                                   TTSSHHHHHHHHHHHHH CS
                 Acetyltransf_1 73 rgkGlGsaLlealeera 89
                                    ++ ++ aLl ale+r 
  gi|121636652|ref|YP_976875.1| 23 ARREIADALLAALERRH 39
                                   57889999999999843 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 5.9e-08
                                    HHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                 Acetyltransf_1  28 fsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlea 84 
                                      +++e  ++va + g  +G++ +  +        +  +++++p++r+kG+G+a l++
  gi|121636652|ref|YP_976875.1| 159 RVDDEEaAWFVAVDSGVKVGMVFGELVHG-----EVDVRIWIHPDHRKKGYGTAALRK 211
                                    333444477779999*******8888777.....35559****************987 PP

>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   3.7e-07   0.00094     328     410 ..      18     102 ..      11     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                  DNA_topoisoIV 328 lekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeyllemrlrrLtkeeveklekeieelek 405
                                     ++  +r ei ++ll al+  +ev + i +  ++++a +++++    s+  ae++++m+  +Lt+  ++k+ +e+++l+k
  gi|121636652|ref|YP_976875.1|  18 HDQTAARREIADALLAALERRHEVADAIVEAANKAAAVEAIVNLlgTSHLAAEAVMSMSFDQLTQDARTKIIAELDDLNK 97 
                                    567788999**********************************955556789**************************** PP

                  DNA_topoisoIV 406 eikel 410
                                    +++  
  gi|121636652|ref|YP_976875.1|  98 QLSFT 102
                                    99765 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.15   3.8e+02      16      29 ..      36      49 ..      20      52 .. 0.59
   2 ?    2.9   0.1     0.042   1.1e+02      16      39 ..      36      59 ..      27      85 .. 0.84
   3 !   11.7   0.0   7.6e-05      0.19       9      33 ..     192     216 ..     191     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.15
                Acetyltransf_13 16 hRrkgiAtkLldaa 29
                                    Rr+ +A ++++aa
  gi|121636652|ref|YP_976875.1| 36 ERRHEVADAIVEAA 49
                                   46666666666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.042
                Acetyltransf_13 16 hRrkgiAtkLldaarenfiyglel 39
                                    Rr+ +A ++++aa +   +++++
  gi|121636652|ref|YP_976875.1| 36 ERRHEVADAIVEAANKAAAVEAIV 59
                                   79***********99988776655 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 7.6e-05
                Acetyltransf_13   9 riWvssshRrkgiAtkLldaarenf 33 
                                    riW++++hR+kg  t+ l   r+++
  gi|121636652|ref|YP_976875.1| 192 RIWIHPDHRKKGYGTAALRKSRSEM 216
                                    9***********9999888777766 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.17   4.4e+02      62      97 ..      21      52 ..      19      57 .. 0.69
   2 !   13.2   0.0   2.5e-05     0.065      21      75 ..     155     211 ..     147     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                Acetyltransf_10 62 eyrgqGigkaLleaveeeaekdgikleltvnaspya 97
                                    + ++ i+ aLl a+e++ e +    +  v+a+++a
  gi|121636652|ref|YP_976875.1| 21 TAARREIADALLAALERRHEVA----DAIVEAANKA 52
                                   5678999999999999986333....5566666654 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.5e-05
                Acetyltransf_10  21 alrerieegealllvaeeggkivGvi..elrdgshisllfVdpeyrgqGigkaLlea 75 
                                    a ++r++++ea  +va ++g  vG++  el  g+   ++ ++p++r++G+g+a l +
  gi|121636652|ref|YP_976875.1| 155 AAQKRVDDEEAAWFVAVDSGVKVGMVfgELVHGEVDVRIWIHPDHRKKGYGTAALRK 211
                                    6788999*******************98888888999**************986655 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.3e-05      0.19      98     120 ..     190     212 ..     178     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.3e-05
                GNAT_acetyltr_2  98 ivRiAvhpelqkmGYGsralell 120
                                     vRi +hp+ +k+GYG++al++ 
  gi|121636652|ref|YP_976875.1| 190 DVRIWIHPDHRKKGYGTAALRKS 212
                                    49*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1626.29
//
Query:       gi|121636653|ref|YP_976876.1|  [L=318]
Description: hypothetical protein BCG_0781c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-65  220.7   1.2      2e-65  220.3   1.2    1.2  1  LCM       Leucine carboxyl methyltransferase
  ------ inclusion threshold ------
      0.092   12.5   0.0       0.21   11.3   0.0    1.5  1  DUF2785   Protein of unknown function (DUF2785)


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.3   1.2   2.2e-69     2e-65       1     188 []      24     208 ..      24     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.3 bits;  conditional E-value: 2.2e-69
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    a++vaaara++ r++   l++D++ae+lv+a+g++++ r+a +el++++  e++++  +++++ +a+Rt++fd+++ +a+
  gi|121636653|ref|YP_976876.1|  24 ATMVAAARAVAGRAP-GALVNDQFAEPLVRAVGVDFFVRMASGELDPDELAEDEANGLRRFADAMAIRTHYFDNFFLDAT 102
                                    79************9.********************************977999************************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     +agirq+ViL++GlD+rayRl w+ag+ vfEvDqp+v++fK++tl+ lga p++++r+v+vDlr ddwp+aL++agfd+
  gi|121636653|ref|YP_976876.1| 103 -RAGIRQAVILASGLDSRAYRLRWPAGTIVFEVDQPQVIDFKTTTLAGLGAAPTTDRRTVAVDLR-DDWPTALQKAGFDN 180
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleaia 188
                                    +++taw+aeG+l YL++ea+d+ll++i+
  gi|121636653|ref|YP_976876.1| 181 AQRTAWIAEGLLGYLSAEAQDRLLDQIT 208
                                    *************************995 PP

>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05      0.21      51      80 ..     258     287 ..     252     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                        DUF2785  51 ylkleqDvRGyveekGWaHafahiadllde 80 
                                    y+   +D R y  ++GW  a a ++dll+e
  gi|121636653|ref|YP_976876.1| 258 YFGDRTDARTYLADHGWRTASASTTDLLAE 287
                                    777889**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2069.08
//
Query:       gi|121636654|ref|YP_976877.1|  [L=441]
Description: preprotein translocase subunit SecY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.3e-112  374.3  18.6   5.1e-112  374.1  18.6    1.1  1  SecY      SecY translocase


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.1  18.6  2.9e-116  5.1e-112       1     306 []      75     424 ..      75     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: 374.1 bits;  conditional E-value: 2.9e-116
                                    BTTSSTCHHHHHHHHHHHHHHHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHC.............. CS
                           SecY   1 sifaLGImPyitasIilqLltvvipkleelkkegeegrkkinqitryltvvlalvqalgia.lslg.............. 65 
                                    ++fa+G+mPyitasIi+qLltvvip++eel+keg++g+ k++q+tryl+++la++qa+ i+ l+                
  gi|121636654|ref|YP_976877.1|  75 TVFAVGVMPYITASIIVQLLTVVIPRFEELRKEGQAGQSKMTQYTRYLAIALAILQATSIVaLA-Anggllqgcsldiia 153
                                    89********************************************************988433.369************ PP

                                    ....HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS-HHHHSS..THHHHHHHHHHHHHHHH CS
                           SecY  66 ....lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkalsglielalegilallllllvtllvill 141
                                        ++l++ivl++t g++l+mw+gE+ite+GiGnG+sllif+gi+ar+p++ ++++e   +g + + ++++++l++i++
  gi|121636654|ref|YP_976877.1| 154 dqsiFTLVVIVLVMTGGAALVMWMGELITERGIGNGMSLLIFVGIAARIPAEGQSILES--RGGVVFTAVCAAALIIIVG 231
                                    ****889*******************************************999888766..46799999*********** PP

                                    HCHHHHBEEEECBBBSTT........S.S-EEEEETTCCCSCHHHHHHHHHHHHHCCCCS.................TCC CS
                           SecY 142 vvyveeaerripvqyakr..grk..ggqssylPlklnyagviPiIfassllalpstiaqfl................lal 201
                                    vv+ve+++rripvqyakr  gr+  gg+s+ylPlk+n+agviP+Ifassl+++p+ i+q++                   
  gi|121636654|ref|YP_976877.1| 232 VVFVEQGQRRIPVQYAKRmvGRRmyGGTSTYLPLKVNQAGVIPVIFASSLIYIPHLITQLIrsgsgvvgnswwdkfvG-- 309
                                    *******************99999999*******************************99999999998777666553.. PP

                                    CS.....THHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHCCHHTBSSSCTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecY 202 ls.....psvlyvvlyvlliifFayfyteitfnpkevaenlkksggfipgirpgketakyLekvlsritliGalflalia 276
                                     +     ++++y+ +y+ liifF+yfy++itfnp+e a+++kk ggfipgirpg++ta+yL++vlsritl+G+++l++ia
  gi|121636654|ref|YP_976877.1| 310 -TylsdpSNLVYIGIYFGLIIFFTYFYVSITFNPDERADEMKKFGGFIPGIRPGRPTADYLRYVLSRITLPGSIYLGVIA 388
                                    .0444677788********************************************************************* PP

                                    HHHHHHTT.....S..TT.TTHHHHHHHHHHHHHHH CS
                           SecY 277 vlpdllga.....sl.igafggtslLivVgvaletv 306
                                    vlp+l+ +     ++ ++ fggt++Li++gv l+tv
  gi|121636654|ref|YP_976877.1| 389 VLPNLFLQigaggTVqNLPFGGTAVLIMIGVGLDTV 424
                                    ******9999987224689**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2816.48
//
Query:       gi|121636655|ref|YP_976878.1|  [L=181]
Description: adenylate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-53  180.5   0.0    2.5e-53  180.2   0.0    1.0  1  ADK              Adenylate kinase
    7.7e-28   97.6   0.0    9.6e-28   97.3   0.0    1.1  1  AAA_17           AAA domain
    6.9e-10   39.2   0.0    8.9e-10   38.9   0.0    1.1  1  AAA_33           AAA domain
    6.8e-08   33.1   0.0      1e-07   32.5   0.0    1.3  1  AAA_18           AAA domain
    0.00022   21.0   0.2    0.00054   19.8   0.0    1.7  2  Cytidylate_kin   Cytidylate kinase
     0.0015   18.2   0.1        1.5    8.5   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
     0.0018   18.5   0.0     0.0038   17.5   0.0    1.9  1  AAA_28           AAA domain
     0.0085   16.5   0.0      0.016   15.6   0.0    1.5  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.043   13.2   0.0       0.32   10.3   0.0    2.2  2  IPT              Isopentenyl transferase
      0.055   13.2   0.0       0.13   12.0   0.0    1.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.056   13.7   0.0        3.5    7.9   0.0    2.2  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.11   12.5   0.0        0.2   11.6   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2   0.0   1.7e-56   2.5e-53       1     149 [.       5     158 ..       5     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 1.7e-56
                                    EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllD 80 
                                    llG+PgaGKGtqa kl++k+g++++stG+l+R ++++gt+lG eak+++d+g+lvp++++++lv+++l+++d+++gf+lD
  gi|121636655|ref|YP_976878.1|   5 LLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKLGVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILD 84 
                                    79****************************************************************************** PP

                                    SB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT.....GSHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  81 GfPRtveqaealeelleeekvkldlvleldvpeevlveRltg.....DneetvkkRletykkqtkplidyykkk 149
                                    G+PR+veqa+al+e+le++++++d+vle++v+eevl+eRl g     D+ + + +R+++y+++t+pl++yy+++
  gi|121636655|ref|YP_976878.1|  85 GYPRSVEQAKALHEMLERRGTDIDAVLEFRVSEEVLLERLKGrgradDTDDVILNRMKVYRDETAPLLEYYRDQ 158
                                    **********************************************999**********************976 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   6.4e-31   9.6e-28       1     135 [.       6     137 ..       6     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 6.4e-31
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                    lG+PG+GKgtq+ kl+ek+g++ +s+G+l+r ++++g +l ++a+ +++ ++l++ + + +++ +++++ ++ +g+++dg
  gi|121636655|ref|YP_976878.1|   6 LGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGtKLgVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDG 85 
                                    7*********************************999556799************************************* PP

                                    -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                         AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                    +pr  eqa++l ++ +   +++  da++ + +++e++ler++    rgr+dd+ ++i
  gi|121636655|ref|YP_976878.1|  86 YPRSVEQAKALHEMLERRGTDI--DAVLEFRVSEEVLLERLKG---RGRADDTDDVI 137
                                    ****************877777..***********99998865...89999988766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0     6e-13   8.9e-10       2     138 ..       3     146 ..       3     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 6e-13
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg....tdqqsktdytrvldr.lyqilnelarkal...sagrnv 73 
                                    vll G+pG+GK t a +l++klg   +s+ +l+rr  +     ++   ++y ++ d    + +nel++++l    a++++
  gi|121636655|ref|YP_976878.1|   3 VLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEegtkLGV-EAKRYLDAGDLvPSDLTNELVDDRLnnpDAANGF 81 
                                    7899*******************9999999988866652553223.334455555553233445555555522277899* PP

                         AAA_33  74 ildatnlsrrerarflklarrlgvpv.rivvvetdeetlkeRlakRaangddrsevpeealdrqka 138
                                    ild   +s ++ +++ ++++r g  + +++ ++++ee+l eRl+ R ++ d++ +v +  ++ +++
  gi|121636655|ref|YP_976878.1|  82 ILDGYPRSVEQAKALHEMLERRGTDIdAVLEFRVSEEVLLERLKGRGRADDTD-DVILNRMKVYRD 146
                                    ***********************99735689*****************97765.676666666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0     7e-11     1e-07       1     118 [.       3     132 ..       3     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7e-11
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleeg 74 
                                    +ll G+pG+GK t a  L+++lg+     g+  r ++ e g+ l+v+++  ld  + +  d +++l+d   +n++    +
  gi|121636655|ref|YP_976878.1|   3 VLLLGPPGAGKGTQAVKLAEKLGIpqistGELFRRNIEE-GTKLGVEAKrYLDAGDLVPSDLTNELVDDRLNNPD---AA 78 
                                    799**********************99999999998888.566666666699**************999999986...78 PP

                         AAA_18  75 knlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgyeea 118
                                    +  ++dg +   e+++a                  ++s+e+lleRl+ Rg+ ++
  gi|121636655|ref|YP_976878.1|  79 NGFILDGYPRSVEQAKALHEMLerrgtdidavLEFRVSEEVLLERLKGRGRADD 132
                                    999*********99988865559999****888889**************7665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.6e-07   0.00054       5      35 ..       7      37 ..       3      55 .. 0.94
   2 ?   -1.8   0.1       1.4   2.1e+03     145     176 ..     101     133 ..      95     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                                   -STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                 Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgalYRa 35
                                   GP g+GK++ a +laeklg+  ++tg+l+R 
  gi|121636655|ref|YP_976878.1|  7 GPPGAGKGTQAVKLAEKLGIPQISTGELFRR 37
                                   9****************************95 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                    HHHHHHHHHTT--.--HHHHHHHHHHHHHHHHC CS
                 Cytidylate_kin 145 kRRlkqlkakgts.vsleellaeikeRDklDke 176
                                    +RR ++ +a     vs e ll+++k R ++D +
  gi|121636655|ref|YP_976878.1| 101 ERRGTDIDAVLEFrVSEEVLLERLKGRGRADDT 133
                                    566666665543337788888889888888876 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0     0.001       1.5       3      47 ..       7      54 ..       7      72 .. 0.78
   2 !    8.1   0.0    0.0013         2     118     182 ..     107     172 ..      77     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                   ESTTSSHHHHHHHHHHHHHHTTE...EEEESS.STTSHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik..vvltre.pggteiGekirelll 47
                                   G  GaGK tqa +l+e+l    i+   +++r  ++gt++G  ++++l 
  gi|121636655|ref|YP_976878.1|  7 GPPGAGKGTQAVKLAEKLGIPQIStgELFRRNiEEGTKLGVEAKRYLD 54
                                   5669**************877777676666654778999999999887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                                    -SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHH CS
                Thymidylate_kin 118 PdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak.ederiliidasksieevh 182
                                     d+++ + v++ev l+Rl+ r+  d+++   l+  + +r     l++ ++++++++da   ++ev 
  gi|121636655|ref|YP_976878.1| 107 IDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYRDETAPLLEyYRDQLKTVDAVGTMDEVF 172
                                    577888899**************777777777777777777777777779*******988888775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.5e-06    0.0038       1      51 [.       2      54 ..       2     181 .] 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                         AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwved 51
                                   ++ ++G++++GK t + +La++ g+p +   E +r+ +ee+++ g +a ++  d
  gi|121636655|ref|YP_976878.1|  2 RVLLLGPPGAGKGTQAVKLAEKlGIPQIstGELFRRNIEEGTKLGVEAKRYL-D 54
                                   689*****************999***8879**********998887755543.3 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.016       1      30 [.       3      30 ..       3      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleis 30
                                   vll GppG GK + a  +a++lg++ +  s
  gi|121636655|ref|YP_976878.1|  3 VLLLGPPGAGKGTQAVKLAEKLGIPQI--S 30
                                   79*******************997633..3 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00021      0.32       5      31 ..       4      30 ..       1      99 [. 0.92
   2 ?   -1.9   0.0       1.2   1.8e+03     175     197 ..     107     129 ..      71     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                            IPT  5 lifGatttGKtaeaiklaketgapviv 31
                                   l+ G+ + GK  +a+kla++ g+p i+
  gi|121636655|ref|YP_976878.1|  4 LLLGPPGAGKGTQAVKLAEKLGIPQIS 30
                                   789********************9887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                            IPT 175 yryildyarkkkvtidklanlda 197
                                     + +l++   ++v +++l+ + +
  gi|121636655|ref|YP_976878.1| 107 IDAVLEFRVSEEVLLERLKGRGR 129
                                    45667777777777777766555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.7e-05      0.13      36      60 ..       3      27 ..       1      41 [. 0.85
   2 ?   -2.1   0.0         2   2.9e+03      51      59 ..     135     143 ..     102     173 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                                   vll GpPG Gk t a  +a++lg+ 
  gi|121636655|ref|YP_976878.1|  3 VLLLGPPGAGKGTQAVKLAEKLGIP 27
                                   9*******************99975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                         RuvB_N  51 kiiakelgv 59 
                                     +i + ++v
  gi|121636655|ref|YP_976878.1| 135 DVILNRMKV 143
                                    344444444 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0023       3.5       3      36 ..       4      37 ..       2      53 .. 0.78
   2 ?    3.9   0.0     0.037        56     171     197 ..      59      85 ..      54      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                      Hydin_ADK  3 ivhGaPlsGKtatavtLakkYeaAlltiDsvvle 36
                                   ++ G+P +GK + av+La k ++  ++  ++   
  gi|121636655|ref|YP_976878.1|  4 LLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRR 37
                                   5679***************999888877666555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.037
                      Hydin_ADK 171 LPedllveIlsERlqlndCyrGvvfDg 197
                                     P dl  e++ +Rl+  d   G ++Dg
  gi|121636655|ref|YP_976878.1|  59 VPSDLTNELVDDRLNNPDAANGFILDG 85 
                                    7*************************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014       0.2       2      24 ..       3      27 ..       2      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                   EEEE--SSSSHHHHHHHGGGGB..S CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal..n 24
                                   vlL+GppG gK + a +la+ l   
  gi|121636655|ref|YP_976878.1|  3 VLLLGPPGAGKGTQAVKLAEKLgiP 27
                                   8******************999553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1099.31
//
Query:       gi|121636656|ref|YP_976879.1|  [L=266]
Description: methionine aminopeptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-40  137.5   0.2    5.5e-40  137.3   0.2    1.0  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
      0.088   12.9   1.0      0.088   12.9   1.0    2.4  2  PT-VENN        Pre-toxin domain with VENN motif


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.2   6.2e-44   5.5e-40       2     209 .]      23     257 ..      22     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 6.2e-44
                                    HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTT.....TCEESSSSEEEEGGGGGSTTTBCS.SSB--TTE CS
                  Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhg.....arglafppivasgenaavlhytpn.drvlkegd 75 
                                    ++ +a+++++aal+a+ +a  pg+++  l++++e   +++ g      +++++p ++++++n+ v+h++p+  +vl +gd
  gi|121636656|ref|YP_976879.1|  23 AMAAAGAVVAAALRAIRAAAAPGTSSLSLDEIAESV-IRESGatpsfLGYHGYPASICASINDRVVHGIPStAEVLAPGD 101
                                    6999************999***************88.6777789999999********************75888***** PP

                                    EEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHT........TBCC CS
                  Peptidase_M24  76 lvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesa........glak 147
                                    lv id+ga++dg+++D + T+ vG  +++ + l ea++e ++a+i+a+  G++l+++ +a++   ++a        g   
  gi|121636656|ref|YP_976879.1| 102 LVSIDCGAVLDGWHGDAAITFGVGALSDADEALSEATRESLQAGIAAMVVGNRLTDVAHAIETGTRAAelrygrsfG--- 178
                                    ************************99998888**********************************86343333223... PP

                                    GBSSCSEEEESSSSSEEEEEESS..STTCSSB--TTBEEEEEE..............EEEEETTT........EEEEEBE CS
                  Peptidase_M24 148 ffphglGHgvGlevhdegpsvsr..esndgrkleeGmvftiEp..............giyfapge........ggvried 203
                                     +  + GHg+G+++h + p++++  ++++g  l++G v++iEp              +      +         ++++e+
  gi|121636656|ref|YP_976879.1| 179 IVAGYGGHGIGRQMHMD-PFLPNegAPGRGPLLAAGSVLAIEPmltlgttktvvlddK------WtvttadgsRAAHWEH 251
                                    3556899********98.**988666669**************555544432222220......2444444427****** PP

                                    EEEEES CS
                  Peptidase_M24 204 tvlvte 209
                                    tv vt+
  gi|121636656|ref|YP_976879.1| 252 TVAVTD 257
                                    ****96 PP

>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   2.4      0.58   5.2e+03      34      41 ..      25      32 ..      18      48 .. 0.65
   2 ?   12.9   1.0   9.8e-06     0.088      17      45 ..     141     169 ..     137     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.58
                        PT-VENN 34 avaGaeag 41
                                   a+aGa ++
  gi|121636656|ref|YP_976879.1| 25 AAAGAVVA 32
                                   44444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.8e-06
                        PT-VENN  17 tlaaGlaGgvvggtladavaGaeagenAV 45 
                                    +l aG+a+ vvg+ l+d++ + e+g +A 
  gi|121636656|ref|YP_976879.1| 141 SLQAGIAAMVVGNRLTDVAHAIETGTRAA 169
                                    578***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1815.71
//
Query:       gi|121636657|ref|YP_976880.1|  [L=177]
Description: RNA polymerase sigma factor SigL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-18   64.8   2.6    7.9e-18   64.0   2.6    1.4  1  Sigma70_r2       Sigma-70 region 2
    1.3e-14   53.4   0.2    3.5e-14   52.0   0.1    1.8  2  Sigma70_r4       Sigma-70, region 4
    7.8e-13   47.9   0.2    1.8e-12   46.7   0.2    1.7  1  Sigma70_r4_2     Sigma-70, region 4
    1.5e-05   25.0   1.0    2.7e-05   24.2   1.0    1.5  1  Sigma70_ECF      ECF sigma factor
    4.8e-05   23.0   0.1    0.00013   21.7   0.1    1.7  1  HTH_38           Helix-turn-helix domain
    0.00028   20.6   0.9    0.00028   20.6   0.9    2.5  2  HTH_23           Homeodomain-like domain
    0.00067   19.6   0.0     0.0012   18.7   0.0    1.5  2  Phage_antitermQ  Phage antitermination protein Q
     0.0014   18.1   0.0     0.0022   17.5   0.0    1.4  1  GerE             Bacterial regulatory proteins, luxR family
     0.0019   18.0   0.0     0.0044   16.9   0.0    1.6  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
  ------ inclusion threshold ------
      0.022   13.9   0.2      0.032   13.4   0.2    1.4  1  PaaA_PaaC        Phenylacetic acid catabolic protein


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   2.6   4.4e-21   7.9e-18       1      69 [.      18      85 ..      18      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 4.4e-21
                                   HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2  1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69
                                   l++++   ++r+a rl+g++a+aeD+vQe++lr+w++ e    ++++ ++awl+++arn +id+ R++r
  gi|121636657|ref|YP_976880.1| 18 LYDEHAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIG-DTARPARAWLFTVARNMIIDERRSAR 85
                                   799************************************999.8888*******************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1     2e-17   3.5e-14       1      49 [.     119     167 ..     119     168 .. 0.99
   2 ?   -1.7   0.0       1.2   2.2e+03      21      27 ..     168     174 ..     167     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2e-17
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    aLa+L++++r v++ ++++g++ ++I+  lgi +++V++++++A+r LR
  gi|121636657|ref|YP_976880.1| 119 ALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALR 167
                                    8***********************************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                    --HHHHH CS
                     Sigma70_r4  21 lTleEIg 27 
                                    lTl+E+g
  gi|121636657|ref|YP_976880.1| 168 LTLQELG 174
                                    8999998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2     1e-15   1.8e-12       2      54 .]     114     166 ..     113     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1e-15
                                    HHHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   2 qalrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    + + +ala+L+ + r+++  +y+ g+s+++IA  lgi egtVksrl+ A ++L
  gi|121636657|ref|YP_976880.1| 114 LLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRAL 166
                                    6799*******************************************998876 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.0   1.5e-08   2.7e-05      14     176 ..       6     163 ..       2     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-08
                    Sigma70_ECF  14 GdaeaaeqllelvydeLrrlagsklknerreetledtaLvfeaflrlvdkek.fpdlsgrdhlfalaaeamrrilidhaR 92 
                                    G a+a + l++++yde   +   + +    ++  ++   v e  lr+ ++ +   d   +    a + ++ r  +id+ R
  gi|121636657|ref|YP_976880.1|   6 GAAAAEAALMRALYDEHAAVLW-RYALRLTGDAAQAEDVVQETLLRAWQHPEvIGDTARPAR--AWLFTVARNMIIDERR 82 
                                    6666666677777766443322.222222333344444567777776663220233333333..4577899999999999 PP

                    Sigma70_ECF  93 rrkrqkRGGdvvraeldeeedsvdsdspdelleLdealerllsldpeqarlvelrkleGlsveEiAeklgvskrtverrl 172
                                    + + +   G + +    e+    +++++ ++l +++al +l   + e + +++  +  G+s + iA+ lg+++ tv+ rl
  gi|121636657|ref|YP_976880.1|  83 SARFRNVVGSTDQSGTPEQSTPDEVNAALDRLLIADALAQL---SAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRL 159
                                    99988888888777766666666778888888899988877...567888999*************************** PP

                    Sigma70_ECF 173 alaR 176
                                    ++a 
  gi|121636657|ref|YP_976880.1| 160 HYAV 163
                                    *984 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     7e-08   0.00013       4      37 ..     122     155 ..     120     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7e-08
                         HTH_38   4 hLsleeReeIerllaeGlslreIArrLgrspsTI 37 
                                    +Ls e R +I+r + +G+s ++IA  Lg + +T+
  gi|121636657|ref|YP_976880.1| 122 QLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTV 155
                                    89****************************9998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   2.8e+03       6      26 ..      21      40 ..      17      51 .. 0.61
   2 !   20.6   0.9   1.6e-07   0.00028       3      35 ..     124     156 ..     109     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                         HTH_23  6 eRlrillllaeGlsvreIAre 26
                                   e++ +l+ +a    + ++A++
  gi|121636657|ref|YP_976880.1| 21 EHAAVLWRYA-LRLTGDAAQA 40
                                   6777777777.4444455555 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.6e-07
                         HTH_23   3 sereRlrillllaeGlsvreIAreLgvsrrTvy 35 
                                    s+++R+ i + + +G+s+++IA+ Lg+ + Tv 
  gi|121636657|ref|YP_976880.1| 124 SAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVK 156
                                    7899***************************97 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   6.4e+03      66      81 ..      20      35 ..      12      50 .. 0.62
   2 !   18.7   0.0   6.8e-07    0.0012      42     115 ..     100     175 ..      73     177 .] 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                Phage_antitermQ 66 eelellvdyYvfgvsk 81
                                   +e+  ++ +Y+ +++ 
  gi|121636657|ref|YP_976880.1| 20 DEHAAVLWRYALRLTG 35
                                   5666666666666554 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.8e-07
                Phage_antitermQ  42 rpsCsDedgliidgcv..arLkkkrpeelellvdyYvfgvskraiarklkisekevrkklqkaegfiegclaaldv 115
                                     +s  De   ++d+ +  + L +  +e+  ++ + Y  g s+ +ia++l+i e++v+ +l+ a   +   l  l+v
  gi|121636657|ref|YP_976880.1| 100 EQSTPDEVNAALDRLLiaDALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGV 175
                                    45566776666666442245666667788899999**************************998888777777666 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.2e-06    0.0022      14      40 ..     135     161 ..     121     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                                    HCTTS-HHHHHHHHTS-HHHHHHHHHH CS
                           GerE  14 laeGksnkeIAeelniSekTVkvhksn 40 
                                     + G s+ +IA +l+i+e TVk+ +  
  gi|121636657|ref|YP_976880.1| 135 YYRGWSTAQIATDLGIAEGTVKSRLHY 161
                                    56899*****************98765 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0044      10      32 ..     135     157 ..     128     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                    Terminase_5  10 YwqGyrvaeIAeelglkeatVys 32 
                                    Y+ G++ a+IA+ lg+ e tV s
  gi|121636657|ref|YP_976880.1| 135 YYRGWSTAQIATDLGIAEGTVKS 157
                                    9*******************976 PP

>> PaaA_PaaC  Phenylacetic acid catabolic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.8e-05     0.032      56     130 ..      20      95 ..       9     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHHHHHHHTSS.-HHHHHHC--CCC----CGG...GS---SHHHHHHHHHHHHHHHHHHHHHHTT-SSH CS
                      PaaA_PaaC  56 DelGharllysaaeelegkgkdeddlaflrdegefknsllv...elpngdwadtivrqflvdaaaiilleaLkrssyg 130
                                    De  ha +l+++a  l+g+  +++d++++   +++++  ++    +p++ w  t++r++++d  + ++++++  s+++
  gi|121636657|ref|YP_976880.1|  20 DE--HAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIgdtARPARAWLFTVARNMIIDERRSARFRNVVGSTDQ 95 
                                    55..9***********************999999999988622268999*********************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1167.84
//
Query:       gi|121636658|ref|YP_976881.1|  [L=250]
Description: hypothetical protein BCG_0786 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-10   39.9   2.3    3.6e-10   39.9   2.3    1.8  2  zf-HC2    Putative zinc-finger


Domain annotation for each model (and alignments):
>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   2.3     2e-14   3.6e-10      10      35 .]      33      58 ..      32      58 .. 0.98
   2 ?   -3.6   0.1      0.78   1.4e+04      16      24 ..      71      79 ..      70      81 .. 0.64

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2e-14
                                   HHHCCT-SCCCHCCCHHHHCHTCHHC CS
                         zf-HC2 10 aYlDGeLspeerarveaHLaeCpdCr 35
                                   aY+ G+Ls+++r+++eaHLa+Cp+Cr
  gi|121636658|ref|YP_976881.1| 33 AYVLGALSAADRREFEAHLAGCPECR 58
                                   9************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.78
                                   -SCCCHCCC CS
                         zf-HC2 16 Lspeerarv 24
                                   Ls  +r++v
  gi|121636658|ref|YP_976881.1| 71 LSQLDRDEV 79
                                   566777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1709.59
//
Query:       gi|121636659|ref|YP_976882.1|  [L=165]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-09   36.5   0.0    5.9e-09   35.7   0.0    1.4  1  MarR            MarR family
    4.3e-08   32.9   0.3    8.1e-08   32.0   0.3    1.5  1  MarR_2          MarR family
    6.5e-08   33.0   0.1    1.5e-07   31.8   0.1    1.7  2  HTH_27          Winged helix DNA-binding domain
     0.0008   19.0   2.5     0.0018   17.9   0.0    2.5  3  GntR            Bacterial regulatory proteins, gntR family
     0.0017   18.5   0.0     0.0036   17.5   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0086   16.1   0.2      0.015   15.4   0.2    1.4  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.2   3.4       0.33   10.8   0.2    3.0  3  HTH_IclR        IclR helix-turn-helix domain
      0.032   14.2   0.2      0.071   13.1   0.2    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.034   14.0   0.0      0.051   13.4   0.0    1.3  1  HxlR            HxlR-like helix-turn-helix
       0.11   12.1   0.0       0.22   11.1   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.15   11.6   0.0        1.1    8.8   0.0    2.2  2  HTH_47          winged helix-turn-helix
       0.17   11.7   1.3       0.27   11.1   0.1    1.9  2  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   3.9e-12   5.9e-09       4      58 ..      57     113 ..      54     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.9e-12
                                    HHHHHHHHH..HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                           MarR   4 tqfviLril..yeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58 
                                    ++f++Lr+l  ++ g+l +++  ++l+v+ ++vt +++rLe +Gl++R ++p D R 
  gi|121636659|ref|YP_976882.1|  57 SRFELLRLLafSRIGALPITKASDRLQVHVTSVTHAIRRLEADGLVRRVPHPTDGRT 113
                                    567788887445899*****************************************6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.3   5.4e-11   8.1e-08       3      61 ..      54     112 ..      52     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.4e-11
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61 
                                    l+ + + +L  L+ +  + l ++   +rl++   +v+ +++rL+a GLv+r+p p+D+R
  gi|121636659|ref|YP_976882.1|  54 LSFSRFELLRLLAFSRIGALPITKASDRLQVHVTSVTHAIRRLEADGLVRRVPHPTDGR 112
                                    55566666666666554468999999********************************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1     1e-10   1.5e-07       5      68 .]      58     122 ..      54     122 .. 0.88
   2 ?   -2.3   0.0       4.4   6.6e+03      30      44 ..     146     160 ..     141     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1e-10
                         HTH_27   5 qalvLhlir.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +L+l++  r +   ++  ++rl+v  +++  ++++L++ GLv r + ++d+r+++v++T+ G
  gi|121636659|ref|YP_976882.1|  58 RFELLRLLAfSRIGALPITKASDRLQVHVTSVTHAIRRLEADGLVRRVPHPTDGRTTLVQITELG 122
                                    56677777777888888888899***************************************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                         HTH_27  30 vedshisyslkkLte 44 
                                     e+++ +++++ L +
  gi|121636659|ref|YP_976882.1| 146 EESQALVSAVETLRR 160
                                    455555588888876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         2   2.9e+03      36      48 ..      29      41 ..      28      44 .. 0.79
   2 !   17.9   0.0   1.2e-06    0.0018      31      58 ..      79     106 ..      69     108 .. 0.89
   3 ?   -0.1   0.0      0.49   7.3e+02      30      50 ..     115     135 ..     113     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                                   S-HHHHHHHHHHH CS
                           GntR 36 VsrttvReALrrL 48
                                   V  t+v++A++ L
  gi|121636659|ref|YP_976882.1| 29 VAVTSVMRAHQIL 41
                                   5678999999988 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                                    HHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           GntR  31 aaefgVsrttvReALrrLeaeglverrq 58 
                                    ++++ V  t+v  A+rrLea+glv r +
  gi|121636659|ref|YP_976882.1|  79 SDRLQVHVTSVTHAIRRLEADGLVRRVP 106
                                    57899*******************9976 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.49
                                    HHHHHTS-HHHHHHHHHHHHH CS
                           GntR  30 LaaefgVsrttvReALrrLea 50 
                                    L++  + +r+tv  A  +L +
  gi|121636659|ref|YP_976882.1| 115 LVQITELGRSTVEDATVTLNE 135
                                    66777889****999888865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0036      27      56 ..      77     106 ..      72     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                                    HHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress  27 dlaerLnvspssVsemlkkLekdGyveyek 56 
                                    + + rL+v+  sV+  +++Le dG+v  ++
  gi|121636659|ref|YP_976882.1|  77 KASDRLQVHVTSVTHAIRRLEADGLVRRVP 106
                                    5689**********************8665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   9.9e-06     0.015      12      59 ..      58     107 ..      54     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.9e-06
                                    HHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  12 RrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                    R ++lr+L  +r ++l  +   +rl+++ +++ + +r Le  gLv++v +
  gi|121636659|ref|YP_976882.1|  58 RFELLRLLafSRIGALPITKASDRLQVHVTSVTHAIRRLEADGLVRRVPH 107
                                    88999999999***********************************9976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.39   5.9e+02       1      10 [.      33      42 ..      33      43 .. 0.88
   2 ?   10.8   0.2   0.00022      0.33       7      52 .]      60     106 ..      59     106 .. 0.86
   3 ?    2.9   0.0     0.065        97      22      44 ..     113     135 ..     108     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.39
                                   HHHHHHHHHC CS
                       HTH_IclR  1 sldRalaiLd 10
                                   s++Ra +iL 
  gi|121636659|ref|YP_976882.1| 33 SVMRAHQILL 42
                                   89******95 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                                    HHHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                       HTH_IclR   7 aiLdalaeapqe.ltlselArrtglpkStvhRlLqtLvelGyveqdg 52 
                                    ++L++la  + + l ++  ++r+ ++ ++v + ++ L+  G+v++ +
  gi|121636659|ref|YP_976882.1|  60 ELLRLLAFSRIGaLPITKASDRLQVHVTSVTHAIRRLEADGLVRRVP 106
                                    67777777665538******************************975 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.065
                                    HHHHHHHTS-HHHHHHHHHHHHH CS
                       HTH_IclR  22 selArrtglpkStvhRlLqtLve 44 
                                    + l + t l +Stv   + tL e
  gi|121636659|ref|YP_976882.1| 113 TTLVQITELGRSTVEDATVTLNE 135
                                    568899********999999876 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   4.8e-05     0.071      16      40 ..      75      99 ..      64     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                   HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          HTH_1 16 ftrAAeeLglsqpavsrqikrLEee 40
                                   +t+A ++L +   +v+++i+rLE+ 
  gi|121636659|ref|YP_976882.1| 75 ITKASDRLQVHVTSVTHAIRRLEAD 99
                                   89*********************84 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05     0.051      36      72 ..      89     125 ..      75     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                           HxlR  36 LaqrLreLeqdglierevypevPpkveYsltekGrsl 72 
                                     ++ +r+Le+dgl+ r++ p+ +     ++te Grs 
  gi|121636659|ref|YP_976882.1|  89 VTHAIRRLEADGLVRRVPHPTDGRTTLVQITELGRST 125
                                    57889*****************************974 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.22      24      48 .]      79     103 ..      71     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                         HTH_24  24 AerlglSpstvnrrlkrLeeeGlIk 48 
                                    ++rl + ++ v+  ++rLe +Gl++
  gi|121636659|ref|YP_976882.1|  79 SDRLQVHVTSVTHAIRRLEADGLVR 103
                                    6777777899*************96 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00077       1.1      34      77 ..      59     103 ..      49     104 .. 0.87
   2 ?    0.1   0.0      0.39   5.8e+02      44      55 ..     110     121 ..     108     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00077
                                    HHHHHHHHH-E.EEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47  34 mallwvLnlaD.GkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                     +ll +L+++  G+  + + ++r+++ +  v++++r+L++ gl++
  gi|121636659|ref|YP_976882.1|  59 FELLRLLAFSRiGALPITKASDRLQVHVTSVTHAIRRLEADGLVR 103
                                    568888888855889999999**********************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.39
                                    EEEEEHHHHHHH CS
                         HTH_47  44 DGkrsLldiAer 55 
                                    DG+++L++i e 
  gi|121636659|ref|YP_976882.1| 110 DGRTTLVQITEL 121
                                    999***999874 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.2   4.8e+03       6      15 ..      35      44 ..      32      50 .. 0.69
   2 ?   11.1   0.1   0.00018      0.27       8      46 ..      59     101 ..      58     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.2
                         HTH_23  6 eRlrilllla 15
                                   +R++ +ll++
  gi|121636659|ref|YP_976882.1| 35 MRAHQILLAR 44
                                   6777666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00018
                         HTH_23   8 lrilllla..e..GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                    ++ l+lla  +   l++++++++L v+   v + ++r +++Gl
  gi|121636659|ref|YP_976882.1|  59 FELLRLLAfsRigALPITKASDRLQVHVTSVTHAIRRLEADGL 101
                                    55566666543466899********************977887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 959.14
//
Query:       gi|121636660|ref|YP_976883.1|  [L=182]
Description: hypothetical protein BCG_0788 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   48.9   9.5    1.4e-11   45.3   4.2    2.9  2  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
     0.0022   18.5   2.7     0.0071   16.9   2.7    1.9  1  DinB_2    DinB superfamily
  ------ inclusion threshold ------
       0.11   13.0   0.0         18    5.7   0.0    2.3  2  DUF664    Protein of unknown function (DUF664)


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   4.2   2.3e-15   1.4e-11       3     141 .]       9     121 ..       7     121 .. 0.91
   2 ?    0.9   0.2      0.12     7e+02      44      90 ..     140     177 ..     125     182 .] 0.47

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.3e-15
                        MDMPI_N   3 eewaalaalvagLtdeqwaapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaasla 82 
                                    ++ +a+aal+a ++ +q+  p+pc +Wt+ dl+ H+++ ++ + +++a +                         ++++ 
  gi|121636660|ref|YP_976883.1|   9 RAQDAFAALLANVRADQLGGPTPCSEWTINDLIEHVVGGNEQVGRWAASP------------------------IEPPAR 64 
                                    5779******************************************7664........................457889 PP

                        MDMPI_N  83 peallaafraavtrlaaalaalppdaiadrlgipggprslge.flrtrlvEavvHglDla 141
                                    p+ l+aa++aa++ + + +aa  p+   +++  p+g+ + g+ f+  r+ ++  H++Dla
  gi|121636660|ref|YP_976883.1|  65 PDGLVAAHQAAAAVAHEIFAA--PGGMSATFKLPLGEVP-GQvFIGLRTTDVLTHAWDLA 121
                                    999999999999999999997..9999999999999999.555***************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                        MDMPI_N  44 alaaalaaegaesalardaaaalvtaadaeavdlaaslapeallaaf 90 
                                    a+a+al ++ ++++       + +++a +e   ++ + ++++l+a +
  gi|121636660|ref|YP_976883.1| 140 AAARALVGP-QFRG-------PGKPFA-DEKPCPRERPPADQLAAFL 177
                                    333333332.2222.......333344.5555555555555555444 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.7   1.2e-06    0.0071       2      57 ..       7      82 ..       6     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                         DinB_2  2 lerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlrgeeap....................r 57
                                   ++ra++++ all+++ +++l  + +  +w+i  l++H++  +e + + +  + +p                    +
  gi|121636660|ref|YP_976883.1|  7 HQRAQDAFAALLANVRADQLGGPTPCSEWTINDLIEHVVGGNEQVGRWAASPIEPparpdglvaahqaaaavaheI 82
                                   689********************99999***************998888864333222233333333333333330 PP

>> DUF664  Protein of unknown function (DUF664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0031        18       7      47 ..       8      48 ..       4      61 .. 0.84
   2 ?    5.4   0.0    0.0038        23      77     114 ..      60      97 ..      48     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0031
                                   HHHHHHHHHHHTT--GGGTT--BTTB-S-HHHHHHHHHHHH CS
                         DUF664  7 drqretllakleGLsdeqarrravpsstsllgLvkHvaevE 47
                                   +r++++++a l+++  +q+  +++ s +++  L++Hv++  
  gi|121636660|ref|YP_976883.1|  8 QRAQDAFAALLANVRADQLGGPTPCSEWTINDLIEHVVGGN 48
                                   5677899999999999***999966666*********9755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0038
                                    SS---HHHHHHHHHHHHHHHHHHHTT--HHHHTSB-T- CS
                         DUF664  77 aedetladllaeyrravaradavvaaeldldetvrvpk 114
                                     + + +++l+a++++a+a a++++aa   +++t ++p 
  gi|121636660|ref|YP_976883.1|  60 EPPARPDGLVAAHQAAAAVAHEIFAAPGGMSATFKLPL 97 
                                    5667899******************9999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1105.49
//
Query:       gi|121636661|ref|YP_976884.1|  [L=282]
Description: hypothetical protein BCG_0789 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28   99.3   3.9    1.9e-28   98.9   3.9    1.2  1  DUF4226   Domain of unknown function (DUF4226)


Domain annotation for each model (and alignments):
>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   3.9   1.1e-32   1.9e-28       2     111 .]      12     122 ..      11     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.1e-32
                        DUF4226   2 rGsaadAarareaaLaqrlsataelDrqlaevlrsahakaaegrrrLdalqaeidqavatqa.laldTpaGarqfqrfLi 80 
                                     G  adAarare aL+q   ++ae+Dr+++  lr+a +  + grrrL a+ aei++ava+q+ l ldTpaGar+f rfL+
  gi|121636661|ref|YP_976884.1|  12 TGLGADAARAREVALTQHIGVSAETDRAVVPKLRQAYDSLVCGRRRLGAIGAEIENAVAHQRaLGLDTPAGARNFSRFLA 91 
                                    6889**************************************************************************** PP

                        DUF4226  81 aklreiakvVadasedsrskaalveaLtaqY 111
                                     k+++i++v a++++ s+++aa +++L + Y
  gi|121636661|ref|YP_976884.1|  92 TKAHDITRVLAATAAESQAGAARLRSLASSY 122
                                    ****************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1830.90
//
Query:       gi|121636662|ref|YP_976885.1|  [L=175]
Description: hypothetical protein BCG_0790 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1150.63
//
Query:       gi|121636663|ref|YP_976886.1|  [L=104]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-17   64.1   0.0    1.7e-17   64.0   0.0    1.0  1  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   9.4e-22   1.7e-17     164     238 ..       6      80 ..       1      82 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 9.4e-22
                   DDE_Tnp_ISL3 164 keearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayGfrnfenfrl 238
                                     ee+++al++wi++a+r++++ f +la  + +hr+ I +++d++l +g +E++N+ki++++r+a+Gfr++e++++
  gi|121636663|ref|YP_976886.1|   6 GEEGKQALDRWISWARRCRIPVFVELAGGIVRHRQAIDAALDHGLWQGLIESTNTKIRLLTRIAFGFRSPEALIA 80 
                                    68899*******************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 702.92
//
Query:       gi|121636664|ref|YP_976887.1|  [L=172]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-33  113.4  27.8    6.5e-33  112.9  27.8    1.2  1  PE             PE family
  ------ inclusion threshold ------
        3.5    8.1  18.6        4.5    7.8  18.6    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9  27.8   7.3e-37   6.5e-33       4      93 .]       1      90 [.       1      90 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 7.3e-37
                                   XXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  4 vvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaag 85
                                   +++aPea+aaaa+dla+igs++ aanaaaaa ttavlaa+aD+VS+aiAa+f+ah+q+yqalsaqaa+fh qfvqal+a+ag
  gi|121636664|ref|YP_976887.1|  1 MIAAPEAIAAAATDLASIGSTIGAANAAAAANTTAVLAAGADQVSVAIAAAFGAHGQAYQALSAQAATFHIQFVQALTAGAG 82
                                   689******************************************************************************* PP

                                   HHHS--XX CS
                             PE 86 sYaaaEaa 93
                                   sYaaaEaa
  gi|121636664|ref|YP_976887.1| 83 SYAAAEAA 90
                                   ******97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  18.6    0.0005       4.5       8      99 ..       4      96 ..       1      97 [. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0005
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaaagasaavldshGp..icaatndavaaaeaarraagealaaasteLadkLraAAaaY 87
                                    p+++ ++a+++ ++ ++i +a+aaaa +++avl   G+  +++a ++a+ a  +a +a  ++ a+ + ++ + L+a A+ Y
  gi|121636664|ref|YP_976887.1|  4 APEAIAAAATDLASIGSTIGAANAAAAANTTAVLAA-GAdqVSVAIAAAFGAHGQAYQALSAQAATFHIQFVQALTAGAGSY 84
                                   6999**********************7777777766.5333999999999999999999999999***************** PP

                  T7SS_ESX_EspC 88 eatDeeaagald 99
                                    a++ ++a ++ 
  gi|121636664|ref|YP_976887.1| 85 AAAEAASAASIT 96
                                   *******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 977.76
//
Query:       gi|121636665|ref|YP_976888.1|  [L=185]
Description: hypothetical protein BCG_0793c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 988.19
//
Query:       gi|121636666|ref|YP_976889.1|  [L=168]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-11   42.8   0.0    8.2e-11   41.9   0.0    1.5  1  HTH_17          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.4   0.1      0.051   13.4   0.1    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.077   13.2   0.0        0.2   11.9   0.0    1.6  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.4e-14   8.2e-11       1      45 [.       4      48 ..       4      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.4e-14
                         HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdlee 45
                                   ll+++EaA++Lgvsr++v ++++rge  ++ +G ++r+p s++e+
  gi|121636666|ref|YP_976889.1|  4 LLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVER 48
                                   799************************8889*************8 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.6e-06     0.051      15      55 ..      11      58 ..       3      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
                 YdaS_antitoxin 15 AealgvsqqaVsqWlkgkkq......vpaervp..eIekatnGeVtree 55
                                   A+ lgvs+q+V ++++ +++       + +rvp  e+e++t+ + tree
  gi|121636666|ref|YP_976889.1| 11 AQILGVSRQHVVNMCD-RGEmvcvhvGSHRRVPssEVERVTSRRLTREE 58
                                   999************7.34467988889999995559*********998 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.3e-05       0.2      14      43 ..       5      35 ..       4      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                        AbiEi_4 14 fttrelea.aGispsalrrLvrkGwLvrlrr 43
                                   + t+e+++ +G+s++++ +++++G+ v ++ 
  gi|121636666|ref|YP_976889.1|  5 LKTSEAAQiLGVSRQHVVNMCDRGEMVCVHV 35
                                   6799*********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 901.79
//
Query:       gi|121636667|ref|YP_976890.1|  [L=175]
Description: hypothetical protein BCG_0795 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1020.27
//
Query:       gi|121636668|ref|YP_976891.1|  [L=797]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-29  101.0  24.6    7.1e-29  100.0  24.6    1.6  1  PE               PE family
  ------ inclusion threshold ------
        4.5    6.7   4.9        6.9    6.1   4.9    1.1  1  Waikav_capsid_1  Waikavirus capsid protein 1


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0  24.6   7.9e-33   7.1e-29       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 7.9e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv + Pe+l +aa+dla++gs l aa+aaaaa+tt+++aa +DeVSaaiAalfsah+++yq +saqaaa+h+qfv+al+a
  gi|121636668|ref|YP_976891.1|  1 MSFVLAMPEVLGSAATDLAALGSVLGAADAAAAATTTGIVAAVQDEVSAAIAALFSAHGRAYQVASAQAAAVHAQFVEALSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEaa
  gi|121636668|ref|YP_976891.1| 83 GAGAYASAEAA 93
                                   *********97 PP

>> Waikav_capsid_1  Waikavirus capsid protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.9   0.00077       6.9      89     173 ..      22     107 ..      14     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00077
                Waikav_capsid_1  89 GtllaawdalgsatrrGiatavq..ltglpsilleasssslttltvkdpaiqsaiclsGsehsigrlGilkisvlnvlna 166
                                    G++l a da+++at  Gi++avq  +++    l+ a++ +  + + + +a+  +   + s ++ g   +   + + vl+ 
  gi|121636668|ref|YP_976891.1|  22 GSVLGAADAAAAATTTGIVAAVQdeVSAAIAALFSAHGRAYQVASAQAAAVHAQFVEALSAGA-GAYASAEAAGAAVLAN 100
                                    7788999***************9555677778899******9999999999998877766654.4556666777777777 PP

                Waikav_capsid_1 167 dkaatqe 173
                                    + ++ q+
  gi|121636668|ref|YP_976891.1| 101 PAQSVQQ 107
                                    7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.96u 0.31s 00:00:01.27 Elapsed: 00:00:00.57
# Mc/sec: 4221.94
//
Query:       gi|121636669|ref|YP_976892.1|  [L=893]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-32  111.4  21.6    3.1e-32  110.7  21.6    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7  21.6   1.7e-36   3.1e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.7e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms v+v+Pe++ aaaadlagigsa+s+anaaaa  tt++l a+aDeVS+aiAalf+a++q+yqa+saqaaaf +qfvqal+a
  gi|121636669|ref|YP_976892.1|  1 MSWVMVSPELVVAAAADLAGIGSAISSANAAAAVNTTGLLTAGADEVSTAIAALFGAQGQAYQAASAQAAAFYAQFVQALSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++g+YaaaEaa
  gi|121636669|ref|YP_976892.1| 83 GGGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      129  (0.00719505); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.02u 0.38s 00:00:01.40 Elapsed: 00:00:00.60
# Mc/sec: 4507.43
//
Query:       gi|121636670|ref|YP_976893.1|  [L=85]
Description: hypothetical protein BCG_0798 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-06   25.5   2.2    1.4e-05   24.8   2.2    1.4  1  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.013   15.4   0.3      0.029   14.3   0.3    1.6  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
      0.072   13.9   0.4       0.12   13.2   0.4    1.3  1  PSK_trans_fac   Rv0623-like transcription factor
       0.13   12.7   0.9       0.42   11.1   0.2    2.1  2  CcdA            Post-segregation antitoxin CcdA


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   2.2   3.2e-09   1.4e-05       1      35 [.       2      36 ..       2      39 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.2e-09
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                   r+++++++e+l++  ++ar+rg+S +++I++Alr+
  gi|121636670|ref|YP_976893.1|  2 RTTVSISDEILAAAKRRARERGQSLGAVIEDALRR 36
                                   89*******************************97 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   6.4e-06     0.029       1      33 [.       1      35 [.       1      37 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKr..EaVnlALr 33
                                   Mrt++ i De la A r+++ ++++  ++++ ALr
  gi|121636670|ref|YP_976893.1|  1 MRTTVSISDEILAAAKRRARERGQSlgAVIEDALR 35
                                   9*******************888876688888888 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   2.6e-05      0.12       9      41 ..      10      42 ..       7      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  PSK_trans_fac  9 everlareLarltgeskteAvrrAleerlerlr 41
                                   e  + a++ ar +g+s+ +++++Al+++ +  +
  gi|121636670|ref|YP_976893.1| 10 EILAAAKRRARERGQSLGAVIEDALRREFAAAH 42
                                   556789999******************998764 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.3e-05      0.42       3      36 ..       2      39 ..       1      44 [. 0.74
   2 ?   -1.5   0.0       0.8   3.6e+03      23      32 ..      71      80 ..      66      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
                           CcdA  3 avnlsldsdllaqA....ralgiNlSatleeaLaeevk 36
                                   ++++s++ ++la A    r+ g +l a++e+aL++e +
  gi|121636670|ref|YP_976893.1|  2 RTTVSISDEILAAAkrraRERGQSLGAVIEDALRREFA 39
                                   6899***9999876111156788888999999888866 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.8
                           CcdA 23 lSatleeaLa 32
                                   lS++l+e+L+
  gi|121636670|ref|YP_976893.1| 71 LSEVLDEGLE 80
                                   7888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 525.94
//
Query:       gi|121636671|ref|YP_976894.1|  [L=142]
Description: hypothetical protein BCG_0799 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-13   48.7   0.0    1.1e-12   48.6   0.0    1.0  1  PIN       PIN domain
     0.0066   16.2   0.1      0.016   15.0   0.0    1.7  2  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.2e-16   1.1e-12       2     120 ..       3     133 ..       2     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.2e-16
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkil 71 
                                    +lD++vl+a++  ++++++++r ++++l    +   +++lv+a +l+ +++      +s r +a ++ve+    + +   
  gi|121636671|ref|YP_976894.1|   3 LLDANVLLAAHrGDHPNHRTVRPWFDRLlaadDPFTVPNLVWASFLRLATNrrifeIPSPRAEAFAFVEAVTAQPHHLPT 82 
                                    79****************************************************************************** PP

                                    EBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  72 pidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                    + + +++   +++ ++++    l+ Da++aA A  h ++++ + D+df+r a
  gi|121636671|ref|YP_976894.1|  83 NPGPRHLVLLRKLCDEADasgDLIPDAVLAAIAVGHHCAVV-SLDRDFARFA 133
                                    **************************************999.*******987 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.88   7.9e+03       3       9 ..       2       8 ..       2      12 .. 0.82
   2 !   15.0   0.0   1.8e-06     0.016      32      65 ..     101     137 ..      87     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.88
                        DUF5615 3 lllDenl 9
                                  +llD+n+
  gi|121636671|ref|YP_976894.1| 2 FLLDANV 8
                                  7999997 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.8e-06
                        DUF5615  32 leg..asDeeileyAkeedriivTkDkDFgel.lllg 65 
                                     +g  ++D    ++A  + +++v+ D+DF +  + ++
  gi|121636671|ref|YP_976894.1| 101 ASGdlIPDAVLAAIAVGHHCAVVSLDRDFARFaSVRH 137
                                    4445699**********************99865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1008.07
//
Query:       gi|121636672|ref|YP_976895.1|  [L=45]
Description: hypothetical protein BCG_0800c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.6   0.0      0.073   13.6   0.0    1.1  1  MyTH4     MyTH4 domain


Domain annotation for each model (and alignments):
>> MyTH4  MyTH4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-06     0.073      34      58 ..      16      40 ..       4      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-06
                                   -HHHHHHHHHHHHHHHCC----CCC CS
                          MyTH4 34 nkesaergwqLlalclslfpPskkl 58
                                   + e +++ wqL +l l++f P+kk 
  gi|121636672|ref|YP_976895.1| 16 ELELLNQLWQLVSLRLNFFTPTKKA 40
                                   557899****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 287.01
//
Query:       gi|121636673|ref|YP_976896.1|  [L=81]
Description: hypothetical protein BCG_0801 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 514.39
//
Query:       gi|121636674|ref|YP_976897.1|  [L=294]
Description: 3-hydroxyisobutyrate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-46  158.5   0.8    2.4e-46  157.8   0.8    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    3.3e-35  121.0   0.6    6.7e-35  120.0   0.6    1.5  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
      1e-07   32.4   0.3    4.1e-07   30.5   0.1    2.0  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    7.6e-05   22.1   0.0    0.00011   21.6   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00043   19.9   0.4     0.0009   18.9   0.0    1.7  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00064   18.8   0.1    0.00091   18.3   0.1    1.2  1  PDH             Prephenate dehydrogenase
  ------ inclusion threshold ------
      0.019   14.9   1.3       0.34   10.8   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.8   9.2e-50   2.4e-46       1     158 []       3     159 ..       3     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 9.2e-50
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                    +i+f+GlG+MG++m  nl+ ag+ v +++  + ++  ++a+g+ ++ s+ e+va++dvvitm++ g+ v+ +++++l+a+
  gi|121636674|ref|YP_976897.1|   3 TIAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVAVFRSAPEAVAEADVVITMLPTGEVVRRCYTDVLAAA 82 
                                    59****************************************************************************** PP

                                    -TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEEE-E CS
                  NAD_binding_2  81 kkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvthviG 158
                                    ++ +++id+st+s++d+re+++ ++++g+  ldaPVSGG++gA+++tL++mvGG+e++++r++pvle ++ k++h+ G
  gi|121636674|ref|YP_976897.1|  83 RPATLFIDSSTISVTDAREVHALAESHGMLQLDAPVSGGVKGAAAATLAFMVGGDESTLRRARPVLEPMAGKIIHC-G 159
                                    **************************************************************************88.6 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.6   2.6e-38   6.7e-35       1     121 [.     162     287 ..     162     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 2.6e-38
                 NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenk......lpqrvlsrdfdpgFaldlm 74 
                                    GaGqa+K++nn++la++ +a++Ea+vlaek+Gl ++ +++vi++++g+++a++++      +p++++++df+pgF+++lm
  gi|121636674|ref|YP_976897.1| 162 GAGQAAKVCNNMVLAVQQIAIAEAFVLAEKLGLSAQSLFDVITGATGNCWAVHTNcpvpgpVPTSPANNDFKPGFSTALM 241
                                    9**************************************************7666666666******************* PP

                 NAD_binding_11  75 lKDlglalelareagaplpllalaeqlyaaaaaegggdaDhsaivrl 121
                                     KDlgla++++ + ga +p +++a+ +ya + a++++d D+sa+++ 
  gi|121636674|ref|YP_976897.1| 242 NKDLGLAMDAVAATGATAPRGSHAADIYAKF-AADHADLDFSAVIHT 287
                                    ******************************9.66699*******986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   1.6e-10   4.1e-07       1      74 [.       3      70 ..       3      93 .. 0.81
   2 ?   -0.8   0.0      0.94   2.4e+03      55      75 ..     163     183 ..     129     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.6e-10
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv 74
                                   +i+++G Gnmg+ +  +l+ ag   h ++ + ++ p  a  +a++ gv v+  ++ ea++eadvv+  +++  v
  gi|121636674|ref|YP_976897.1|  3 TIAFLGLGNMGAPMSANLVGAG---HVVR-GFDPAPTAASGAAAH-GVAVFR-SAPEAVAEADVVITMLPTGEV 70
                                   69********************...8888.999999977766665.899999.9************99987554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                                    HHHHHHH-SEEEE-S-HHHHH CS
                  F420_oxidored  55 neeaaeeadvvvlavkpedve 75 
                                    + +aa+ ++  vlav+  +++
  gi|121636674|ref|YP_976897.1| 163 AGQAAKVCNNMVLAVQQIAIA 183
                                    445666666666666655554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.3e-08   0.00011      38     136 ..       3     101 ..       1     114 [. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.3e-08
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHC CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlpltpetrhlinaeelak 116
                                    t++ +GlG++G  +   l + g  v ++d+ +++ + ++++gv  + s  e++ae+D+v+ +lp  +  r     + la+
  gi|121636674|ref|YP_976897.1|   3 TIAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVaVFRSAPEAVAEADVVITMLPTGEVVRRC-YTDVLAA 81 
                                    8999*****************************99988888984666*****************66665555.4577888 PP

                                    STTTEEEEESS-GGGB-HHH CS
                   2-Hacid_dh_C 117 mkkgailiNtaRGglvdeea 136
                                     ++  ++i  +  ++ d + 
  gi|121636674|ref|YP_976897.1|  82 ARPATLFIDSSTISVTDARE 101
                                    88888888777666666655 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.5e-07    0.0009       6      70 ..       3      67 ..       1      86 [. 0.86
   2 ?   -2.5   0.1       1.3   3.3e+03       9      28 ..     155     174 ..     154     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.5e-07
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE.HHHHHHT-SEEEE-S-H CS
                           IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt.vaeavkkadvvmiliPD 70
                                   +ia +G G+ G   + nl  +g +vv g     + ++ A ++g+ v + + eav++advv++++P 
  gi|121636674|ref|YP_976897.1|  3 TIAFLGLGNMGAPMSANLVGAG-HVVRGFDPAPTAASGAAAHGVAVFRsAPEAVAEADVVITMLPT 67
                                   89*****************999.6889*******************86156************995 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                    EES-SHHHHHHHHHHHHTT- CS
                           IlvN   9 viGyGsqGhaqalnlrdsgl 28 
                                    +i +G+ G  qa ++ ++ +
  gi|121636674|ref|YP_976897.1| 155 IIHCGAAGAGQAAKVCNNMV 174
                                    67777777777776655433 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.5e-07   0.00091      10     116 ..      23     128 ..      19     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-07
                                    --SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-G.GGHHHHHHHHHHHS-TT-EEEE--S--CHHHHH CS
                            PDH  10 fkvtvigydideekaeaalelglvdeatddieavkeadivvlavPv.evilevlkelaphlkedalitDvgsvKekvvre 88 
                                      + v g d  + +a+ a + g+   +  + eav ead+v+   P  ev++++  ++  + +++ l +D + + +  +re
  gi|121636674|ref|YP_976897.1|  23 AGHVVRGFDPAPTAASGAAAHGVAVFRSAP-EAVAEADVVITMLPTgEVVRRCYTDVLAAARPATLFIDSSTISVTDARE 101
                                    568999****************98888885.9*************867899***************************** PP

                                    HHHHCC..GCEEEEEES---S-SSGGG- CS
                            PDH  89 leellkegksfvgghPmaGteksGvdaa 116
                                    +++l +++  +   +P+ G+  +G +aa
  gi|121636674|ref|YP_976897.1| 102 VHALAESHGMLQLDAPVSGG-VKGAAAA 128
                                    ***99977777778999999.7777666 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013      0.34       1      39 [.       3      41 ..       3      49 .. 0.90
   2 ?    2.9   0.3     0.034        87      67     122 ..      45      99 ..      35     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekal 39
                                   ++a +G G mGa + a ++ ag+ V+ +d ++ a+  a+
  gi|121636674|ref|YP_976897.1|  3 TIAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAA 41
                                   5899**************************999887665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.034
                                    EEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHH CS
                        3HCDH_N  67 isfttdleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsisel 122
                                    + +  +  eav +ad+vi   +   e+ r+ ++++ ++a+p ++++ ++S++s+++ 
  gi|121636674|ref|YP_976897.1|  45 VAVFRSAPEAVaEADVVITMLP-TGEVVRRCYTDVLAAARPATLFI-DSSTISVTDA 99 
                                    5555555566669999998777.56777889999999999999887.5899999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1864.34
//
Query:       gi|121636675|ref|YP_976898.1|  [L=390]
Description: acyl-CoA dehydrogenase fadE9 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-47  160.8   1.4    2.7e-47  160.8   1.4    1.5  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.1e-26   91.8   0.0    8.9e-26   90.8   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.5e-24   86.0   0.0    2.8e-24   85.1   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.5e-18   67.4   2.7    5.4e-18   65.6   0.4    2.2  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.092   13.3   0.0       0.15   12.6   0.0    1.3  1  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
       0.13   11.9   0.1       0.33   10.6   0.1    1.6  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.4   7.2e+03      77     107 ..      19      49 ..       9      52 .. 0.61
   2 !  160.8   1.4   8.9e-51   2.7e-47       1     148 [.     233     381 ..     233     383 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                    --------HHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  77 aldagkpdraeasmaKlfaselaqevadlam 107
                                    a ++ +p+  e  +aK f  ++++e+a+l m
  gi|121636675|ref|YP_976898.1|  19 AGKRLAPHALEWDAAKHFPVDVLREAAELGM 49 
                                    4445555577777777777777777777766 PP

  == domain 2  score: 160.8 bits;  conditional E-value: 8.9e-51
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g Gf +am++ln +Rl++aa +lg a++a++ a +y+r+r+afg+ l+d + vr+ la+ma+ l+ +r+l++raa+ald+
  gi|121636675|ref|YP_976898.1| 233 GAGFGIAMSGLNGGRLNIAACSLGGAQAAFDKAGAYVRDRQAFGGSLLDEPTVRFTLADMATGLQTSRMLLWRAASALDD 312
                                    68****************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                    ++ d    ++maK ++++++ evad+a+ql+Gg+Gyl+ey++e+++rd rv ri+eGt+ei+r++i+r+
  gi|121636675|ref|YP_976898.1| 313 DDADkVELCAMAKRYVTDTCFEVADQALQLHGGYGYLREYGLEKIVRDLRVHRILEGTNEIMRLVIGRA 381
                                    ****5566789*******************************************************997 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0     3e-29   8.9e-26       2     111 ..       6     114 ..       5     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 3e-29
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                    ++++ + +t+++fa ++lapha ewd++++fp ++++++aelG+++i+  +++gG+gl  l+ a ++e+la ad ++a++
  gi|121636675|ref|YP_976898.1|   6 DDERVIVETAAAFAGKRLAPHALEWDAAKHFPVDVLREAAELGMAAIYCRDDVGGSGLRRLDGARIFEQLAIADPVTAAF 85 
                                    88999*************************************************************************** PP

                                    HHHHHHTTHHHHHHHS-HHHHHHHHHHHHT CS
                  Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklas 111
                                    l++h+ ++a++i  fGt+eq++ ++p+la+
  gi|121636675|ref|YP_976898.1|  86 LSIHN-MCAWMIDSFGTDEQRKDWIPRLAT 114
                                    ****9.5669******************97 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   9.4e-28   2.8e-24       1      97 []     120     218 ..     120     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9.4e-28
                                    EEE---SS-SS-GGG---EEEEETT.E...EEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdgge...yvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                    +++lTEp+aGsd+ +++t+a+++  g+   yvl+G K++i++aa +++++v+art+ +   rg+s f+v++++pg+s++ 
  gi|121636675|ref|YP_976898.1| 120 SYCLTEPGAGSDAGALSTRAVRHGSGKggdYVLDGVKQFISGAAASDVYVVMARTGAEG-PRGVSAFVVEKGTPGLSFGA 198
                                    589*****************6543333345************************77777.******************** PP

                                    ---BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                     e+k+G +  pt+++v++ v
  gi|121636675|ref|YP_976898.1| 199 PEAKMGWHAQPTAQVVLDGV 218
                                    ****************9976 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.11   3.2e+02      40      71 ..      19      50 ..      12      66 .. 0.78
   2 !   65.6   0.4   1.8e-21   5.4e-18       3     131 ..     250     369 ..     248     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl-CoA_dh_2 40 tqlalaeaaarldAAralleraaaraealaaa 71
                                   +  +la +a ++dAA+ +  ++ ++a +l  a
  gi|121636675|ref|YP_976898.1| 19 AGKRLAPHALEWDAAKHFPVDVLREAAELGMA 50
                                   66799**********99887777776665555 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 1.8e-21
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    iaa  lG A+aa++++ +++r+r+   +g +l d+p++ ++la++a+ l++ r+ll raa++     +++++   +++  
  gi|121636675|ref|YP_976898.1| 250 IAACSLGGAQAAFDKAGAYVRDRQA--FGGSLLDEPTVRFTLADMATGLQTSRMLLWRAASA----LDDDDA---DKVEL 320
                                    89***********************..***********************************....444444...56899 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                     ++a+ ++++++ +++d++ +++Gg++++ e+ l+ + RD+++ ++ ++
  gi|121636675|ref|YP_976898.1| 321 CAMAKRYVTDTCFEVADQALQLHGGYGYLREYGLEKIVRDLRVHRILEG 369
                                    9*****************************************9776555 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05      0.15      92     124 ..      86     117 ..      75     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                    THHHHHTHHHHHHHHS-HHHHHHHHHHHHTTSS CS
                  Acyl-CoA_ox_N  92 lglhfsMFlptlkgqgteeQqakWlpraenlei 124
                                    l++h +M    + + gt+eQ++ W+pr  ++ +
  gi|121636675|ref|YP_976898.1|  86 LSIH-NMCAWMIDSFGTDEQRKDWIPRLATMGV 117
                                    6677.78888999**************999866 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00011      0.33     180     268 ..     151     223 ..     148     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                    EEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE-------S..-TTT-TTTTT----EEEEE CS
                         HpaB_N 180 vVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfedkleesefdyplssrfdendalvv 259
                                    v  G+k +++gaa++d  +v+     +++e  +   af+v+  +pGl++ + e                    + +a vv
  gi|121636675|ref|YP_976898.1| 151 VLDGVKQFISGAAASDVYVVMAR---TGAEGPRGVSAFVVEKGTPGLSFGAPEAKMG-------------WHAQPTAQVV 214
                                    679******************99...3678899999***********9977665443.............1234566677 PP

                                    EEEEEEEGG CS
                         HpaB_N 260 fDdVfVPwe 268
                                    +D V VP e
  gi|121636675|ref|YP_976898.1| 215 LDGVRVPAE 223
                                    777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2712.38
//
Query:       gi|121636676|ref|YP_976899.1|  [L=510]
Description: methylmalonate-semialdehyde dehydrogenase mmsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.1e-137  456.9   0.0   8.6e-137  456.4   0.0    1.1  1  Aldedh    Aldehyde dehydrogenase family
    0.00033   19.8   0.0    0.00049   19.3   0.0    1.2  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.4   0.0  9.5e-141  8.6e-137       5     462 .]      17     490 ..      14     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 456.4 bits;  conditional E-value: 9.5e-141
                                    SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---H CS
                         Aldedh   5 es.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpl 83 
                                    +s ++ +v++P tg++ akvp a+++d+daava+A ea+k+wa++++++Ra++L+++ +l+++  +elael+++e Gk+l
  gi|121636676|ref|YP_976899.1|  17 QStRSADVFDPNTGQIQAKVPMAGKSDIDAAVASAVEAQKGWAAWNPQRRARVLMRFIELVNDTIDELAELLSREHGKTL 96 
                                    452559************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE- CS
                         Aldedh  84 aearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPa 162
                                    a+ar++v++ i+v++++ +  + l+ge ++   +g + ++ r+PlGvv+ ItP+NfP+++++wk+ pala+GN++vlKP+
  gi|121636676|ref|YP_976899.1|  97 ADARGDVQRGIEVIEFCLGIPHLLKGEYTEGaGPGIDVYSLRQPLGVVAGITPFNFPAMIPLWKAGPALACGNAFVLKPS 176
                                    ****************************99966*********************************************** PP

                                    TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEE CS
                         Aldedh 163 eetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpl 242
                                    e+ p + ++laelf eaglP+gv++vv+g ++e+ +a+++hp++++v f+Gs+++++ i++ aa++ kr +   G+kn++
  gi|121636676|ref|YP_976899.1| 177 ERDPSVPVRLAELFIEAGLPAGVFQVVHG-DKEAVDAILHHPDIKAVGFVGSSDIAQYIYAGAAATGKRAQCFGGAKNHM 255
                                    *****************************.899*********************************************** PP

                                    EE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEE.EEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHH CS
                         Aldedh 243 ivledaDldkaveaivkgafgnaGQvCiaasrll.vqesiydefveklveaakklkvgdpldedtdvGPliseaqlekve 321
                                    iv++daDld+av+a++ + +g+aG++C+a+s ++ v ++++++++++l+e++++l+vg++ld++ d+GPl++ a+l++v+
  gi|121636676|ref|YP_976899.1| 256 IVMPDADLDQAVDALIGAGYGSAGERCMAISVAVpVGDQTAERLRARLIERINNLRVGHSLDPKADYGPLVTGAALARVR 335
                                    *******************************97769999***************************************** PP

                                    HHHHHHHHTTSEEEE-TT............E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHH CS
                         Aldedh 322 kyveeakeegaklllGge............reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaiei 389
                                    +y+ +++++ga+l+++g+            + +a+le g+f+ Pt++++v  +m+i+++EiFGPVl++++++d eea+++
  gi|121636676|ref|YP_976899.1| 336 DYIGQGVAAGAELVVDGRdrasddltfglpEGDANLEGGFFIGPTLFDHVAAHMSIYTDEIFGPVLCMVRARDYEEALRL 415
                                    ***************999877766666554446677889***************************************** PP

                                    HHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES..-BSHHHHHHHTEEEEEE CS
                         Aldedh 390 aNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglG..reggkegleeytevktv 462
                                      + eyG++ ++ft+d + a+ +++r+++G+v++N ++ + +    fgG+k+Sg+G  +++g++++++yt+vktv
  gi|121636676|ref|YP_976899.1| 416 PSEHEYGNGVAIFTRDGDAARDFVSRVQVGMVGVNVPIPVPVAYHTFGGWKRSGFGdlNQHGPAAIQFYTKVKTV 490
                                    *************************************88888778***********99999************98 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.5e-08   0.00049      83     224 ..     134     269 ..     108     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-08
                           LuxC  83 syekaqprglvlhvlsgNvp.llpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksgdt 161
                                     y+ +qp g+v  +++ N p ++p++    +l ++n+ +lk+S  dp ++++l+  +++       a    vv  ++ ++
  gi|121636676|ref|YP_976899.1| 134 VYSLRQPLGVVAGITPFNFPaMIPLWKAGPALACGNAFVLKPSERDPSVPVRLAELFIEAGLP---AGVFQVV--HGDKE 208
                                    58999*************9945799*********************************99996...8888899..55555 PP

                           LuxC 162 kleeeivqnaD..vvvawGgeeaikaise.klkpgkqlikfGakvSfavvdkealeeealdkaaer 224
                                    ++ + i+++ D  +v   G+++  + i +  +++gk+   fG  +  ++v ++a    +ld+a+++
  gi|121636676|ref|YP_976899.1| 209 AV-DAILHHPDikAVGFVGSSDIAQYIYAgAAATGKRAQCFGGAKNHMIVMPDA----DLDQAVDA 269
                                    55.555566663367789999999999998999999999999888888888888....66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2804.60
//
Query:       gi|121636677|ref|YP_976900.1|  [L=584]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-29  102.4  26.5    1.2e-29  102.4  26.5    2.6  3  PE              PE family
    6.2e-19   68.5   0.2    2.3e-18   66.6   0.0    2.0  3  His_Phos_1      Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4  26.5   1.4e-33   1.2e-29       1      92 [.       1      92 [.       1      93 [. 0.99
   2 ?   -3.5   0.2       1.5   1.4e+04      73      80 ..     318     325 ..     310     333 .. 0.44
   3 ?    0.2   0.8      0.11   9.9e+02      39      60 ..     540     561 ..     531     567 .. 0.75

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.4e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+va +alaaaaadla+igsa++a n aaa pttav+aaaaDeVSaa Aalf+aha+eyqa++aqaaa heqfv+ l+a
  gi|121636677|ref|YP_976900.1|  1 MSFVIVARDALAAAAADLAQIGSAVNAGNLAAANPTTAVAAAAADEVSAALAALFGAHAREYQAAAAQAAAYHEQFVHRLSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   aa+sYa +E 
  gi|121636677|ref|YP_976900.1| 83 AATSYAVTEV 92
                                   *******996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                                    HHHHHHHH CS
                             PE  73 heqfvqal 80 
                                     + +++al
  gi|121636677|ref|YP_976900.1| 318 AQAIANAL 325
                                    22222222 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.11
                                    ---SSSSHHHHHHHHHHHHHHH CS
                             PE  39 vlaaaaDeVSaaiAalfsahaq 60 
                                     +  +aDeV aa+ ++  a a+
  gi|121636677|ref|YP_976900.1| 540 AVRDGADEVGAAVVQFPHAVAD 561
                                    45569******99988777766 PP

>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3      0.29   2.6e+03     142     177 ..      53      88 ..      36      97 .. 0.56
   2 !   66.6   0.0   2.6e-22   2.3e-18       3      89 ..     287     375 ..     285     381 .. 0.91
   3 ?   -3.2   0.0      0.64   5.7e+03     168     191 ..     469     493 ..     443     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.29
                                    EEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EE CS
                     His_Phos_1 142 vlvVsHggvirallarllglpleelrrleldnasls 177
                                    +l  +H+   +a++a++  ++ ++++rl  + +s+ 
  gi|121636677|ref|YP_976900.1|  53 ALFGAHAREYQAAAAQAAAYHEQFVHRLSAAATSYA 88 
                                    344455555555555555555555555555555544 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 2.6e-22
                                    EEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTT.S---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS-- CS
                     His_Phos_1   3 LvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlag.epidaiysSplkRarqTaeliaealglpveldegLrEi 80 
                                    +vRHG+t  na+         + Lt++G++qA+a+a++la+  p + i+ S+l R++qTa+++a+ lg+ +++ +gL+Ei
  gi|121636677|ref|YP_976900.1| 287 FVRHGQTPGNAAMLiDTAVPGPGLTALGQQQAQAIANALAAkGPYAGIFDSQLIRTQQTAAPLANLLGMAPQVLPGLNEI 366
                                    8***********88444567888*****************97888889******************************** PP

                                    --GGGTT-B CS
                     His_Phos_1  81 dfGdweglt 89 
                                    + G +e l+
  gi|121636677|ref|YP_976900.1| 367 HAGIFEDLP 375
                                    ******986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.64
                                    GB---TT-EEEEEE-SS-.EEEEEE CS
                     His_Phos_1 168 rleldnaslsvlefdegg.wrlvrl 191
                                     ++++n++ +v++ +++g w+lv++
  gi|121636677|ref|YP_976900.1| 469 THPVPNTGAVVVQGNPEGgWTLVSW 493
                                    4566899999998887544999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 3233.61
//
Query:       gi|121636678|ref|YP_976901.1|  [L=645]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-59  198.0 378.1    2.4e-09   36.9  27.1   13.4 13  Pentapeptide_2  Pentapeptide repeats (8 copies)
    4.4e-59  199.1  26.6    6.3e-59  198.6  26.6    1.2  1  PPE             PPE family
  ------ inclusion threshold ------
        1.1    9.6   8.1        1.4    9.2   3.9    2.5  2  WXG100          Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8  30.1   5.1e-09     3e-05       7      39 ..     177     209 ..     175     218 .. 0.66
   2 !    8.3  18.6   0.00035       2.1      15      32 ..     222     239 ..     211     248 .. 0.59
   3 !   26.2  32.5   9.2e-10   5.5e-06       2      39 ..     250     287 ..     249     288 .. 0.98
   4 !   13.5  31.2   8.3e-06      0.05       9      39 ..     299     329 ..     297     330 .. 0.82
   5 !   30.7  29.3   3.4e-11     2e-07       1      40 []     321     360 ..     321     360 .. 0.97
   6 !   31.6  32.1   1.8e-11   1.1e-07       3      39 ..     365     401 ..     363     402 .. 0.97
   7 !   36.9  27.1     4e-13   2.4e-09       1      39 [.     403     441 ..     403     442 .. 0.98
   8 !   29.9  28.2   6.4e-11   3.8e-07       1      39 [.     443     481 ..     443     482 .. 0.97
   9 !   36.8  26.9   4.4e-13   2.6e-09       1      39 [.     483     521 ..     483     522 .. 0.97
  10 !   25.5  18.2   1.5e-09   8.8e-06       2      31 ..     527     556 ..     526     558 .. 0.89
  11 !    6.3   8.7    0.0014       8.6       4      30 ..     560     586 ..     559     589 .. 0.67
  12 !    6.7   4.2    0.0011       6.5       8      22 ..     594     608 ..     590     609 .. 0.70
  13 !    4.8   4.1    0.0044        26      13      28 ..     620     635 ..     616     644 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.1e-09
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G gN+G++N+G+gNtG++NlG+gN G+ n+G
  gi|121636678|ref|YP_976901.1| 177 NLGVGNIGNLNVGNGNTGDYNLGNGNLGNANFG 209
                                    666666666666666666666666666666666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00035
                 Pentapeptide_2  15 ffNlGsgNtGsfNlGsgN 32 
                                    +fN+GsgN+G+fNlGsgN
  gi|121636678|ref|YP_976901.1| 222 SFNVGSGNIGNFNLGSGN 239
                                    455555555555554433 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 9.2e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+Gs+N+G++N+G +N+G  N+G++N+G++N+G+gn+G
  gi|121636678|ref|YP_976901.1| 250 NVGSGNIGNANVGGGNSGDNNFGFGNFGNANIGIGNAG 287
                                    9***********************************99 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 8.3e-06
                 Pentapeptide_2   9 GsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    G+gN+G +N G+gN+G +N+G++N+G gn+G
  gi|121636678|ref|YP_976901.1| 299 GNGNVGIGNGGNGNFGGGNTGNANIGLGNVG 329
                                    8888888888888888888888888888888 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 3.4e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +N+G +N+G gN+Gf+N+Gs N+G++N+G++N+G+g tGs
  gi|121636678|ref|YP_976901.1| 321 ANIGLGNVGDGNVGFGNSGSYNFGFGNTGNNNIGIGLTGS 360
                                    6*************************************96 PP

  == domain 6  score: 31.6 bits;  conditional E-value: 1.8e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G lNsGsgN+Gf+N+G+gN+G+fN+GsgN+G gn+G
  gi|121636678|ref|YP_976901.1| 365 FGGLNSGSGNIGFGNSGTGNIGFFNSGSGNFGVGNSG 401
                                    89**********************************9 PP

  == domain 7  score: 36.9 bits;  conditional E-value: 4e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +NtG++NsG+ NtGf+N+G+ NtG++N+ s+NtG+gn+G
  gi|121636678|ref|YP_976901.1| 403 TNTGVANSGNINTGFGNSGFINTGFGNALSVNTGFGNSG 441
                                    6*************************************9 PP

  == domain 8  score: 29.9 bits;  conditional E-value: 6.4e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +NtG++N+G +NtG+fN G  NtGsfN+G +N+Gs+n G
  gi|121636678|ref|YP_976901.1| 443 ANTGIGNAGDFNTGNFNGGIINTGSFNSGAFNSGSFNGG 481
                                    6************************************88 PP

  == domain 9  score: 36.8 bits;  conditional E-value: 4.4e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+G+lNsG +NtGf+N+G+ NtG fN+G+ NtG+gnt 
  gi|121636678|ref|YP_976901.1| 483 ANSGFLNSGLTNTGFANSGNINTGGFNAGNLNTGFGNTT 521
                                    6************************************95 PP

  == domain 10  score: 25.5 bits;  conditional E-value: 1.5e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsg 31 
                                    N+G++N+GsgN+Gf N+G gN G +N+G+ 
  gi|121636678|ref|YP_976901.1| 527 NSGFGNAGSGNSGFNNSGKGNSGAQNVGNL 556
                                    999999999999999999999999999986 PP

  == domain 11  score: 6.3 bits;  conditional E-value: 0.0014
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGs 30 
                                    G++NsG   tG  N+ s+  G++N G+
  gi|121636678|ref|YP_976901.1| 560 GFANSGQSVTGYNNSVSVTSGFGNKGT 586
                                    677777777777777777777777665 PP

  == domain 12  score: 6.7 bits;  conditional E-value: 0.0011
                 Pentapeptide_2   8 sGsgNtGffNlGsgN 22 
                                    sG gNtGf+ +G+gN
  gi|121636678|ref|YP_976901.1| 594 SGFGNTGFLQSGFGN 608
                                    577777777777777 PP

  == domain 13  score: 4.8 bits;  conditional E-value: 0.0044
                 Pentapeptide_2  13 tGffNlGsgNtGsfNl 28 
                                    +Gf+N+G    G fN+
  gi|121636678|ref|YP_976901.1| 620 SGFGNSGKQDSGGFNS 635
                                    5666666666666665 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6  26.6     1e-62   6.3e-59       1     158 []       6     163 ..       6     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 1e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE ns ++y G+gs+pllaAa aWdgLa+el++aa+++ sv++ela++aWqGp+saama+aa py++WL+aa+aqae
  gi|121636678|ref|YP_976901.1|   6 WLPPETNSLRMYLGAGSRPLLAAAGAWDGLAEELHAAASSFGSVTSELAGGAWQGPASAAMANAAGPYASWLTAAGAQAE 85 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     aA+qa+aaa a+e+Ala +v+pa++ anr ++  l+ +n+fGqn+paIaa+e  ye+mwaqd+a+ma+Y+aas+aaa
  gi|121636678|ref|YP_976901.1|  86 LAARQARAAAGAFEEALAGVVHPAVVQANRVRTWLLAVSNVFGQNAPAIAAMESTYEQMWAQDVAVMAGYHAASSAAA 163
                                    ***************************************************************************986 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.9   0.00024       1.4      10      83 ..      26     100 ..      23     102 .. 0.84
   2 ?    1.5   0.1     0.058   3.5e+02      44      71 ..     157     184 ..     122     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  10 rqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                     +aa + ++ aeel+++ ++  +  ++l +++W+G a+ a +++   +   ++   ++ e  +++ ++aa afe+
  gi|121636678|ref|YP_976901.1|  26 LAAAGAWDGLAEELHAAASSFGSVTSELaGGAWQGPASAAMANAAGPYASWLTAAGAQAELAARQARAAAGAFEE 100
                                    6899999*********************************99988777777777777777777777777777766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.058
                                    HHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  44 aaadafqaefeewkqaaqklvdaLeeis 71 
                                    aa++a +a+++ w++a+ +++ +  +i+
  gi|121636678|ref|YP_976901.1| 157 AASSAAAAQLASWQPALPNINLGVGNIG 184
                                    6999999********9988887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3542.21
//
Query:       gi|121636679|ref|YP_976902.1|  [L=61]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-14   51.9   0.2    4.8e-14   51.7   0.2    1.0  1  HTH_23          Homeodomain-like domain
    1.9e-13   50.3   0.2    2.3e-13   50.0   0.2    1.1  1  HTH_28          Helix-turn-helix domain
    4.9e-11   42.5   0.1    5.8e-11   42.3   0.1    1.1  1  HTH_29          Winged helix-turn helix
    2.3e-10   40.8   0.1    2.8e-10   40.6   0.1    1.1  1  LZ_Tnp_IS481    leucine-zipper of insertion element IS481
    4.1e-07   30.2   0.1    4.8e-07   30.0   0.1    1.0  1  HTH_Tnp_1       Transposase
    2.3e-06   27.6   0.0    2.8e-06   27.3   0.0    1.2  1  HTH_7           Helix-turn-helix domain of resolvase
    2.5e-05   24.4   0.1    2.6e-05   24.4   0.1    1.1  1  HTH_Tnp_1_2     Helix-turn-helix of insertion element transpo
    9.7e-05   22.2   0.0    0.00014   21.7   0.0    1.4  1  Terminase_5     Putative ATPase subunit of terminase (gpP-lik
    0.00014   21.2   0.2    0.00019   20.8   0.2    1.2  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
    0.00014   21.5   0.2     0.0005   19.8   0.2    1.9  1  MerR            MerR family regulatory protein
    0.00027   21.3   0.0    0.00031   21.1   0.0    1.1  1  HTH_40          Helix-turn-helix domain
    0.00029   20.3   0.0    0.00038   19.9   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00047   20.0   0.1    0.00057   19.7   0.1    1.1  1  MarR_2          MarR family
    0.00048   19.7   0.1    0.00065   19.3   0.1    1.2  1  Sigma70_r4_2    Sigma-70, region 4
    0.00069   19.7   0.1    0.00083   19.4   0.1    1.0  1  DUF1153         Protein of unknown function (DUF1153)
    0.00082   19.4   0.0     0.0012   18.9   0.0    1.3  1  HTH_3           Helix-turn-helix
    0.00094   18.9   0.1     0.0012   18.5   0.1    1.2  1  HTH_psq         helix-turn-helix, Psq domain
      0.001   19.6   0.3     0.0071   16.9   0.1    1.9  2  HTH_32          Homeodomain-like domain
     0.0016   18.5   0.0     0.0021   18.1   0.0    1.3  1  MerR_1          MerR HTH family regulatory protein
      0.002   18.3   0.0     0.0027   17.9   0.0    1.2  1  HTH_17          Helix-turn-helix domain
      0.002   17.6   0.0     0.0026   17.3   0.0    1.3  1  GerE            Bacterial regulatory proteins, luxR family
     0.0024   17.6   0.0      0.003   17.3   0.0    1.2  1  HTH_30          PucR C-terminal helix-turn-helix domain
      0.004   17.2   0.0     0.0046   17.0   0.0    1.1  1  DUF1804         Protein of unknown function (DUF1804)
     0.0045   17.1   0.0     0.0064   16.6   0.0    1.3  1  HTH_AraC        Bacterial regulatory helix-turn-helix protein
      0.005   17.2   0.3     0.0092   16.3   0.3    1.6  1  HTH_31          Helix-turn-helix domain
     0.0051   16.5   0.0     0.0068   16.2   0.0    1.3  1  HTH_38          Helix-turn-helix domain
     0.0051   16.6   0.0     0.0065   16.3   0.0    1.2  1  DUF746          Domain of Unknown Function (DUF746)
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.013   15.2   0.0    1.3  1  HTH_8           Bacterial regulatory protein, Fis family
       0.01   15.5   0.1      0.012   15.3   0.1    1.2  1  GntR            Bacterial regulatory proteins, gntR family
      0.011   15.6   0.1      0.014   15.2   0.1    1.3  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.015   15.3   0.1       0.02   14.9   0.1    1.2  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.017   15.1   0.0      0.021   14.8   0.0    1.2  1  HTH_11          HTH domain
      0.017   14.9   0.0      0.033   14.0   0.0    1.5  1  HTH_10          HTH DNA binding domain
      0.018   15.1   0.1      0.018   15.1   0.1    1.5  1  DUF2802         Protein of unknown function (DUF2802)
      0.022   14.4   0.0      0.025   14.3   0.0    1.1  1  UPF0175         Uncharacterised protein family (UPF0175)
      0.023   14.7   0.0      0.026   14.6   0.0    1.1  1  HTH_Tnp_IS630   Transposase
      0.024   14.8   0.0      0.026   14.7   0.0    1.1  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.033   14.0   0.0      0.053   13.3   0.0    1.3  1  TetR_N          Bacterial regulatory proteins, tetR family
      0.055   13.0   0.0      0.061   12.9   0.0    1.3  1  Sigma70_r4      Sigma-70, region 4
      0.063   13.1   0.0      0.095   12.5   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.08   13.4   0.1      0.083   13.3   0.1    1.1  1  GcrA            GcrA cell cycle regulator
      0.097   12.7   0.0        0.1   12.6   0.0    1.1  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.11   12.7   0.1       0.13   12.6   0.1    1.1  1  KORA            TrfB plasmid transcriptional repressor
       0.11   12.3   0.1       0.74    9.7   0.0    1.9  2  LacI            Bacterial regulatory proteins, lacI family
       0.12   12.3   0.1       0.14   12.1   0.1    1.1  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.13   12.4   0.0       0.21   11.7   0.0    1.3  1  HTH_22          HTH domain
       0.16   12.1   0.0       0.19   11.9   0.0    1.1  1  DUF1492         Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.2   1.3e-16   4.8e-14       4      50 .]       7      54 ..       5      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.3e-16
                         HTH_23  4 ereRlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGlegll 50
                                   +++R++++l++   Gls++++A++ gvsr+T+  wl ry++eGl+gl+
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVISdGLSISQVAEKVGVSRQTLHTWLARYEAEGLDGLR 54
                                   689*********88*************************88*****96 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.2   6.1e-16   2.3e-13       1      45 [.       9      54 ..       9      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 6.1e-16
                         HTH_28  1 qRleiikllaaGh.svreaArelgisrrtvyrWikryeegGiagLv 45
                                   qR+++++++++ + s++++A+++g+sr+t+  W+ rye++G++gL+
  gi|121636679|ref|YP_976902.1|  9 QRYQAVLAVISDGlSISQVAEKVGVSRQTLHTWLARYEAEGLDGLR 54
                                   8*********6666******************************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1   1.5e-13   5.8e-11       4      45 ..      13      54 ..      10      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.5e-13
                         HTH_29  4 alll.laeGvstvsqiAkllglsrrtvyrwlkrfeegGlaall 45
                                   a+l+ +++G+s +sq+A+ +g+sr+t  +wl r+e++Gl++l+
  gi|121636679|ref|YP_976902.1| 13 AVLAvISDGLS-ISQVAEKVGVSRQTLHTWLARYEAEGLDGLR 54
                                   44441688887.*****************************95 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   7.2e-13   2.8e-10      17      57 ..      13      53 ..       3      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 7.2e-13
                   LZ_Tnp_IS481 17 lvrrvvedrrtvaqvarelGvslrtaykwlarfraeGldGl 57
                                    v  v+ d  ++ qva+++Gvs++t + wlar+ aeGldGl
  gi|121636679|ref|YP_976902.1| 13 AVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEAEGLDGL 53
                                   577899**********************************9 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   1.2e-09   4.8e-07       9      51 ..       7      50 ..       6      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-09
                      HTH_Tnp_1  9 defKariVreslepgksvsevArrhgvspnqLykWrrqyr.ege 51
                                   +e++ ++V  + + g s+s+vA++ gvs+++L +W + y+ eg+
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEaEGL 50
                                   69*************************************95554 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   7.2e-09   2.8e-06       8      38 ..       8      38 ..       2      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7.2e-09
                                   HHHHGGGGSSTTTT--STTTSSSS---SSSS CS
                          HTH_7  8 kndinrvvkLleeGisiskIAkevnisRsTv 38
                                   + +++ v++ +++G sis++A+ v++sR+T+
  gi|121636679|ref|YP_976902.1|  8 EQRYQAVLAVISDGLSISQVAEKVGVSRQTL 38
                                   447999************************8 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   6.8e-08   2.6e-05      10      48 ..       7      43 ..       1      48 [. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.8e-08
                                   HHHHHHHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHHH CS
                    HTH_Tnp_1_2 10 akQkkaaellvendyekltldeiaeevgvsrsTlykWkk 48
                                   a+Q+  a l v  d   l+++++ae+vgvsr+Tl+ W+ 
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVISDG--LSISQVAEKVGVSRQTLHTWLA 43
                                   345555555555555..7*******************95 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.7e-07   0.00014      12      46 ..      20      54 ..       8      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.7e-07
                    Terminase_5 12 qGyrvaeIAeelglkeatVysWkkrdewddldpls 46
                                    G ++ ++Ae +g++++t + W  r+e ++ld+l 
  gi|121636679|ref|YP_976902.1| 20 DGLSISQVAEKVGVSRQTLHTWLARYEAEGLDGLR 54
                                   578999**************************985 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2     5e-07   0.00019      17      51 ..      10      45 ..      10      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5e-07
                   HTH_Tnp_ISL3 17 eayilellles.rsvkavArqlgvSwtTVwrildry 51
                                   +++++ +++++  s+++vA+ +gvS  T++ +l ry
  gi|121636679|ref|YP_976902.1| 10 RYQAVLAVISDgLSISQVAEKVGVSRQTLHTWLARY 45
                                   588999999999*********************998 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   1.3e-06    0.0005       1      20 [.      23      42 ..      23      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-06
                                   EHHHHHHHHTTTHHHHHHHH CS
                           MerR  1 tIgevAeltGvsprtLRyYE 20
                                   +I++vAe++Gvs +tL+ + 
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHTWL 42
                                   7****************985 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.2e-07   0.00031       3      40 ..      12      49 ..      10      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.2e-07
                         HTH_40  3 eetlelleeglsieeIAkerglkesTIegHLaelieeg 40
                                   ++ l  + +glsi ++A++ g++++T  + La++  eg
  gi|121636679|ref|YP_976902.1| 12 QAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEAEG 49
                                   66778899*************************99987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     1e-06   0.00038      17      46 ..      21      50 ..      13      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
                         HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGl 46
                                   ++s++++Ae++g+S++t+++ l r e eGl
  gi|121636679|ref|YP_976902.1| 21 GLSISQVAEKVGVSRQTLHTWLARYEAEGL 50
                                   89**********************999996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.5e-06   0.00057      10      50 ..      14      50 ..       7      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-06
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGL 50
                                   vLa++  ++g  l+++++a++ g+s+++++  l+r +a GL
  gi|121636679|ref|YP_976902.1| 14 VLAVI--SDG--LSISQVAEKVGVSRQTLHTWLARYEAEGL 50
                                   66666..455..9***************************8 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.7e-06   0.00065      16      49 ..      11      44 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVksrlsR 49
                                    +++l    +gls+ ++Ae+ g+s +t  ++l+R
  gi|121636679|ref|YP_976902.1| 11 YQAVLAVISDGLSISQVAEKVGVSRQTLHTWLAR 44
                                   4556666679**********************98 PP

>> DUF1153  Protein of unknown function (DUF1153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.2e-06   0.00083      32      80 ..       7      55 ..       3      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.2e-06
                                   HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHHCCT--TTSS-T CS
                        DUF1153 32 arRKaevvaavrggLlsleealerYklseeEfasWqkaverhGlagLra 80
                                   a  + + v av ++ ls +++ e+ ++s++ +++W + +e +Gl+gLr+
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEAEGLDGLRI 55
                                   5556666778888888********************************7 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     3e-06    0.0012       9      27 ..      21      39 ..      16      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3e-06
                                   THHHHHHHHHHTSSHHHHH CS
                          HTH_3  9 glsqeeLAeklGvsrstis 27
                                   gls+ ++Aek+Gvsr+t+ 
  gi|121636679|ref|YP_976902.1| 21 GLSISQVAEKVGVSRQTLH 39
                                   9****************96 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.2e-06    0.0012       8      34 ..      13      39 ..      11      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-06
                        HTH_psq  8 AleavvnGkmSirkAArkYgiPrsTLw 34
                                   A+ av++ ++Si++ A k g++r TL+
  gi|121636679|ref|YP_976902.1| 13 AVLAVISDGLSISQVAEKVGVSRQTLH 39
                                   999***999*****************8 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.45   1.7e+02      34      69 ..      11      38 ..       3      39 .. 0.74
   2 !   16.9   0.1   1.9e-05    0.0071       1      18 [.      37      54 ..      37      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.45
                         HTH_32 34 rariiallreeprWsprqlaarlaeregvkvShstv 69
                                    ++++a++ ++  +s +q+a+++       vS+ t 
  gi|121636679|ref|YP_976902.1| 11 YQAVLAVI-SD-GLSISQVAEKV------GVSRQTL 38
                                   56777888.66.78999999988......6888886 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.9e-05
                         HTH_32  1 TvsrwlkRyneeGlegLk 18
                                   T++ wl+Ry++eGl+gL+
  gi|121636679|ref|YP_976902.1| 37 TLHTWLARYEAEGLDGLR 54
                                   89**************97 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.6e-06    0.0021       2      24 ..      23      45 ..      22      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.6e-06
                                   EHHHHHHHHTS-HHHHHHHHHHT CS
                         MerR_1  2 sigevakilgvtthtlrywekeg 24
                                   si++va+++gv+  tl+ w  ++
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHTWLARY 45
                                   9******************9876 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     7e-06    0.0027       2      25 ..      22      45 ..      22      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7e-06
                         HTH_17  2 ltveEaAelLgvsrstvyrlirrg 25
                                   l+++++Ae  gvsr+t++ ++ r 
  gi|121636679|ref|YP_976902.1| 22 LSISQVAEKVGVSRQTLHTWLARY 45
                                   89****************998764 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.8e-06    0.0026       6      37 ..      10      41 ..       4      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.8e-06
                                   HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHH CS
                           GerE  6 RErevLrllaeGksnkeIAeelniSekTVkvh 37
                                   R + vL+ + +G+s  ++Ae+ ++S +T ++ 
  gi|121636679|ref|YP_976902.1| 10 RYQAVLAVISDGLSISQVAEKVGVSRQTLHTW 41
                                   6678************************8875 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.9e-06     0.003       6      37 ..      15      46 ..       7      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.9e-06
                                   HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHH CS
                         HTH_30  6 raylenggnisatAkaLhvHrnTlryRLrrie 37
                                    a +  g +is++A++ +v+r+Tl+  L r e
  gi|121636679|ref|YP_976902.1| 15 LAVISDGLSISQVAEKVGVSRQTLHTWLARYE 46
                                   57778899******************999976 PP

>> DUF1804  Protein of unknown function (DUF1804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.2e-05    0.0046       7      49 ..       9      51 ..       6      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-05
                        DUF1804  7 vrkavRsaYvferlsleeaAkkagvseaTarrwkreakekGdD 49
                                   +r ++  a +++ ls++++A+k+gvs++T + w +  +++G D
  gi|121636679|ref|YP_976902.1|  9 QRYQAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEAEGLD 51
                                   5666666779999********************9999999987 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-05    0.0064       6      27 ..      19      40 ..      17      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-05
                                   SCT--HHHHHHHTTSSHHHHHH CS
                       HTH_AraC  6 stnltiediAdelgfSrsyFsr 27
                                   s++l+i ++A+ +g+Sr+++++
  gi|121636679|ref|YP_976902.1| 19 SDGLSISQVAEKVGVSRQTLHT 40
                                   789****************985 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   2.4e-05    0.0092      14      35 ..      21      42 ..       6      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-05
                         HTH_31 14 GLsqeevAerlgvsestlsrlE 35
                                   GLs  +vAe +gvs+ tl+ + 
  gi|121636679|ref|YP_976902.1| 21 GLSISQVAEKVGVSRQTLHTWL 42
                                   9*************99887664 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-05    0.0068      14      42 ..      13      43 ..       1      44 [. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                         HTH_38 14 erl..laeGlslreIArrLgrspsTIsRElk 42
                                   + l  ++ Gls++++A ++g+s++T +  l 
  gi|121636679|ref|YP_976902.1| 13 AVLavISDGLSISQVAEKVGVSRQTLHTWLA 43
                                   44433689*****************987665 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.7e-05    0.0065       3      36 ..      12      45 ..      10      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                         DUF746  3 relIrlLsqplslaeaadllgtdegiiakwvreF 36
                                   +++ +  s  ls+ ++a+ +g++ ++ + w++++
  gi|121636679|ref|YP_976902.1| 12 QAVLAVISDGLSISQVAEKVGVSRQTLHTWLARY 45
                                   5677888999*********************987 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.5e-05     0.013      20      42 .]      23      45 ..      16      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-05
                                   -HHHHHHHHTS-HHHHHHHHHHT CS
                          HTH_8 20 nkskAArlLGisRrtLyrKLkkY 42
                                    +s++A+  G+sR+tL+  L++Y
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHTWLARY 45
                                   589*************9777776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     3e-05     0.012      23      62 ..      21      59 ..      11      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                                   B---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                           GntR 23 kLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                    L s +++a++ gVsr+t+   L r eaegl   r g Gt
  gi|121636679|ref|YP_976902.1| 21 GL-SISQVAEKVGVSRQTLHTWLARYEAEGLDGLRIGTGT 59
                                   57.899************************9777777776 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   3.7e-05     0.014      10      31 ..      23      44 ..      13      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-05
                 YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkg 31
                                   + +++Ae++gvs+q+ + Wl++
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHTWLAR 44
                                   66899**************975 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   5.2e-05      0.02       7      39 ..      14      47 ..       9      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_1  7 fvavaeeg.sftrAAeeLglsqpavsrqikrLEe 39
                                    +av   g s+++ Ae++g+s  ++   ++r E+
  gi|121636679|ref|YP_976902.1| 14 VLAVISDGlSISQVAEKVGVSRQTLHTWLARYEA 47
                                   445555555*****************99999887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.4e-05     0.021      15      43 ..      20      49 ..      10      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-05
                         HTH_11 15 p.isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   + +s+++ Ae+ +vSr+t +  +++ e+ g
  gi|121636679|ref|YP_976902.1| 20 DgLSISQVAEKVGVSRQTLHTWLARYEAEG 49
                                   3399***************98777766665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.7e-05     0.033      25      48 ..      23      46 ..      20      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.7e-05
                         HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                   +++++A++ G+s++tl+  L + e
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHTWLARYE 46
                                   6899*************9998865 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   4.8e-05     0.018      29      57 ..       7      35 ..       1      36 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-05
                        DUF2802 29 qsklYsqAiklvrqGasveelaeecgLsr 57
                                   ++++Y+  +  +  G+s++++ae++g sr
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVISDGLSISQVAEKVGVSR 35
                                   7899***********************98 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.5e-05     0.025      30      59 ..      18      47 ..       2      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
                        UPF0175 30 eegrlSlgkAaelaglsrveflelLarrgi 59
                                       lS++++ae +g+sr + +  Lar+++
  gi|121636679|ref|YP_976902.1| 18 ISDGLSISQVAEKVGVSRQTLHTWLARYEA 47
                                   56779**********************986 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.9e-05     0.026       9      44 ..      12      47 ..       6      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.9e-05
                  HTH_Tnp_IS630  9 lkvidyiesGggitkaskvfkvgratvyrWlkreel 44
                                   + v++ i  G +i ++ +  +v+r+t++ Wl r e 
  gi|121636679|ref|YP_976902.1| 12 QAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEA 47
                                   568999***************************886 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.9e-05     0.026      29      58 ..      17      46 ..       2      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-05
                        UPF0122 29 yyadDlSlsEiAeefnvsrqavydnikrte 58
                                    + d lS+s +Ae+  vsrq+++  + r e
  gi|121636679|ref|YP_976902.1| 17 VISDGLSISQVAEKVGVSRQTLHTWLARYE 46
                                   57899******************9988865 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00014     0.053      15      34 ..      20      39 ..      19      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                   TT--HHHHHHHHTSSHHHHH CS
                         TetR_N 15 dattvreIAkrAGvskgalY 34
                                   d+++++++A+++Gvs+ +l+
  gi|121636679|ref|YP_976902.1| 20 DGLSISQVAEKVGVSRQTLH 39
                                   689***************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016     0.061      16      36 ..      10      37 ..       2      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                   HH.......TTT--HHHHHHHHTS-HHH CS
                     Sigma70_r4 16 rf.......geglTleEIgerlgiSrer 36
                                   r+        +gl+ ++++e+ g+Sr +
  gi|121636679|ref|YP_976902.1| 10 RYqavlaviSDGLSISQVAEKVGVSRQT 37
                                   555555666789**************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00025     0.095      19      36 ..      23      40 ..      21      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                  HTH_AsnC-type 19 syaeLAervGlSestvlr 36
                                   s +++Ae+vG+S++t + 
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTLHT 40
                                   899************875 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00022     0.083       6      35 ..       9      37 ..       5      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00022
                           GcrA  6 ErvelLkklwleGlSasqiaaqlggvsRnA 35
                                    r ++     ++GlS+sq+a+++g vsR  
  gi|121636679|ref|YP_976902.1|  9 QRYQAVLAVISDGLSISQVAEKVG-VSRQT 37
                                   56667777889************9.**986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00026       0.1      21      50 ..      21      50 ..       3      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00026
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTS CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkregl 50
                                    l+  + A+ +G++r+t+   l++ + egl
  gi|121636679|ref|YP_976902.1| 21 GLSISQVAEKVGVSRQTLHTWLARYEAEGL 50
                                   578899*******************99998 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00033      0.13      11      48 ..       2      38 ..       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00033
                           KORA 11 kgleelaeqtveiargvLVegkkqadvatelgltkqav 48
                                   k l  +aeq  +++  v+ +g + ++va+++g+++q  
  gi|121636679|ref|YP_976902.1|  2 KEL-SVAEQRYQAVLAVISDGLSISQVAEKVGVSRQTL 38
                                   678.89*****************************986 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   4.7e+02      23      38 ..       3      18 ..       1      20 [. 0.77
   2 ?    9.7   0.0    0.0019      0.74       2      15 ..      24      37 ..      23      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                   SSSSTHHHHHHHHHHH CS
                           LacI 23 kerVseetrerVeaam 38
                                   + +V+e+  + V+a++
  gi|121636679|ref|YP_976902.1|  3 ELSVAEQRYQAVLAVI 18
                                   5678888889999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0019
                                   HHHHHHHCTS-HHH CS
                           LacI  2 ikDVArlAGVSkaT 15
                                   i  VA++ GVS +T
  gi|121636679|ref|YP_976902.1| 24 ISQVAEKVGVSRQT 37
                                   788*********99 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00036      0.14      14      50 ..      11      49 ..       3      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                                   CHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
                           TrmB 14 YlaLl..klgpatadeiaeelgvprskvYevLrsLedkG 50
                                   Y+a+l   ++ ++++++ae++gv+r++    L + e  G
  gi|121636679|ref|YP_976902.1| 11 YQAVLavISDGLSISQVAEKVGVSRQTLHTWLARYEAEG 49
                                   77777688999***************9988887766666 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00054      0.21      43      58 ..      23      38 ..      22      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00054
                         HTH_22 43 avekvAekLgiSraTv 58
                                   ++++vAek g+Sr+T+
  gi|121636679|ref|YP_976902.1| 23 SISQVAEKVGVSRQTL 38
                                   799************8 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00049      0.19      56      93 ..       7      43 ..       2      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00049
                        DUF1492 56 ensdsrsvLrmvyidkltvwqvidklnisrstyyrllr 93
                                    ++ +++vL ++  d l++ qv +k+++sr t +++l 
  gi|121636679|ref|YP_976902.1|  7 AEQRYQAVLAVI-SDGLSISQVAEKVGVSRQTLHTWLA 43
                                   577899999876.699*****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 362.67
//
Query:       gi|121636680|ref|YP_976903.1|  [L=241]
Description: hypothetical protein BCG_0808c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.015   15.2   0.3      0.099   12.5   0.1    2.2  2  BAT        GAF and HTH_10 associated domain
      0.016   15.6   0.0      0.031   14.7   0.0    1.5  1  DASH_Dad2  DASH complex subunit Dad2
       0.22   11.7   0.1       0.66   10.2   0.1    1.8  1  2C_adapt   2-cysteine adaptor domain


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15     9e+02      89     110 ..      97     118 ..      92     123 .. 0.83
   2 ?   12.5   0.1   1.7e-05     0.099      77     118 ..     135     176 ..     128     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                            BAT  89 lastlaehGgtvrsaeaedgra 110
                                    ++  l++ Gg + +++ae+g +
  gi|121636680|ref|YP_976903.1|  97 VVDLLTQPGGLLDRLTAEGGAM 118
                                    678899999********99976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.7e-05
                            BAT  77 gtlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPp 118
                                    + l+e  +s++ la +l + Gg + +++a dg  +  ++v++
  gi|121636680|ref|YP_976903.1| 135 DGLIERVLSEDGLADRLLAEGGLIDKITAKDGPLEQLADVAD 176
                                    479*****************************9999999986 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.1e-06     0.031       3      60 ..     160     217 ..     158     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                      DASH_Dad2   3 riaeKraELeaLkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlrais 60 
                                    +i +K   Le+L  + d  ++l+  +e+Le  ++tl+d   a   V++   ++ + i 
  gi|121636680|ref|YP_976903.1| 160 KITAKDGPLEQLADVADTLARLTPGMEALEPAIATLQDAVIALTMVVNPLSSIAERIP 217
                                    8999********************************************9999998875 PP

>> 2C_adapt  2-cysteine adaptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00011      0.66      16      30 ..      79      93 ..      79      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                       2C_adapt 16 gRkikpdGPtykkle 30
                                   gR+i+p+GP +++l+
  gi|121636680|ref|YP_976903.1| 79 GRAIAPNGPMDRMLR 93
                                   9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1425.34
//
Query:       gi|121636681|ref|YP_976904.1|  [L=247]
Description: two component system response transcriptional positive regulator phoP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-27   95.9   0.0    3.1e-27   95.0   0.0    1.5  1  Response_reg   Response regulator receiver domain
    1.7e-24   85.7   0.1    4.4e-23   81.2   0.0    2.2  2  Trans_reg_C    Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
      0.033   14.6   0.0      0.043   14.2   0.0    1.3  1  FleQ           Flagellar regulatory protein FleQ
      0.035   14.6   0.0      0.064   13.7   0.0    1.5  1  B12-binding_2  B12 binding domain
      0.043   13.9   0.0      0.079   13.0   0.0    1.4  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.0   8.6e-31   3.1e-27       1     111 [.      23     132 ..      23     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 8.6e-31
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl+vdD+  ++ell+  l+ +g+ ev +a++g++al+ ++e ++d ++lD++mpgmdG+ +l+++r++  + p ++lta+
  gi|121636681|ref|YP_976904.1|  23 VLVVDDEANIVELLSVSLKFQGF-EVYTATNGAQALDRARETRPDAVILDVMMPGMDGFGVLRRLRADGIDAPALFLTAR 101
                                    8**********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++ +d++++l +g dd+++Kpf+ ee++++l
  gi|121636681|ref|YP_976904.1| 102 DSLQDKIAGLTLGGDDYVTKPFSLEEVVARL 132
                                    **************************99987 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.048   1.7e+02      36      65 ..     115     144 ..     106     152 .. 0.78
   2 !   81.2   0.0   1.2e-26   4.4e-23       1      77 []     169     243 ..     169     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.048
                                    TTTSTSHTHHHHHHHHHHHHHHHTTTTSSS CS
                    Trans_reg_C  36 gededvddrtvdvhisrLRkkLeddekkpr 65 
                                    g+d+ +   +++  ++rLR  L+ ++k ++
  gi|121636681|ref|YP_976904.1| 115 GDDYVTKPFSLEEVVARLRVILRRAGKGNK 144
                                    6777778889999*********99865554 PP

  == domain 2  score: 81.2 bits;  conditional E-value: 1.2e-26
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    g++v+l+p+ef lL++++ n+g v+s+ ++l++vw++d+ +d ++v++++s+LR+k++  + ++rl++t+rgvGY+l
  gi|121636681|ref|YP_976904.1| 169 GQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT-G-EKRLLHTLRGVGYVL 243
                                    799********************************************************.4.688**********87 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05     0.043       1      49 [.      22      71 ..      22     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                           FleQ  1 kiLvidddaerrrdletiLeFlgee.veavsseelsaaleesssealavi 49
                                   ++Lv+dd+a+  + l++ L+F g e + a++ +++ + ++e++ +a+++ 
  gi|121636681|ref|YP_976904.1| 22 RVLVVDDEANIVELLSVSLKFQGFEvYTATNGAQALDRARETRPDAVILD 71
                                   69**********************94555666666788888888888775 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.064      19      48 ..      55      82 ..      28      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                  B12-binding_2 19 elidealaqgsaavdvlndvllpamkeVGd 48
                                   +++d+a+    ++++v+ dv++p+m+  G 
  gi|121636681|ref|YP_976904.1| 55 QALDRAR--ETRPDAVILDVMMPGMDGFGV 82
                                   4556666..345*************97775 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.079      20      80 ..      36      93 ..      31      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                    B12-binding 20 laaalrdagfeVqllganven.edivaairaekpdvvglSalltsqleavkelvel.lkrirp 80
                                   l   l+ +gfeV+      +n ++ ++++r+++pd+v l + +   ++++  l +l + +i++
  gi|121636681|ref|YP_976904.1| 36 LSVSLKFQGFEVYTA----TNgAQALDRARETRPDAVILDV-MMPGMDGFGVLRRLrADGIDA 93
                                   566789999999443....334899****************.999999999999887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1418.54
//
Query:       gi|121636682|ref|YP_976905.1|  [L=485]
Description: two component system response sensor kinase membrane associated phoR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-28   98.9   0.0    4.1e-28   98.1   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.8e-16   58.3   2.0    1.2e-15   57.2   0.9    2.2  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.7e-11   44.3   3.0    2.8e-11   43.6   0.6    2.5  2  HAMP         HAMP domain
    1.3e-05   25.1   0.0    2.2e-05   24.3   0.0    1.3  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    0.00088   19.3   0.2     0.0042   17.0   0.0    1.9  2  HrcA         HrcA protein C terminal domain
  ------ inclusion threshold ------
      0.013   15.7   1.0      0.033   14.5   1.0    1.6  1  Pelovaterin  Pelovaterin
      0.017   15.1   0.1      0.032   14.2   0.1    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.031   14.2   0.0      0.054   13.4   0.0    1.3  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   1.8e-31   4.1e-28       1     110 [.     358     468 ..     358     470 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 1.8e-31
                                    EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                      HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                    gde+rLrq+++nlv Na+++++++ +++v++ ++ dd  ++v D+G+G+++ed  ++fe+f++ d+s++r +ggtGlGls
  gi|121636682|ref|YP_976905.1| 358 GDESRLRQVLRNLVANAIQHTPESADVTVRVGTEGDDAILEVADDGPGMSQEDALRVFERFYRaDSSRARASGGTGLGLS 437
                                    79******************88999*****996669******************************************** PP

                                    HHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlpl 110
                                    iv++lv  +gG ++v++  g+G++f+++lp 
  gi|121636682|ref|YP_976905.1| 438 IVDSLVAAHGGAVTVTTALGEGCCFRVSLPR 468
                                    ****9999*******************9985 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.9   5.5e-19   1.2e-15       2      66 ..     250     312 ..     249     313 .. 0.94
   2 ?   -2.4   0.0       2.3   5.2e+03      26      46 ..     356     372 ..     352     377 .. 0.57

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 5.5e-19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                    +++f+ + +HELrtPL++i+g+ae+ +    +  ++  +l +iesea r+  lv+dlL l+r++a
  gi|121636682|ref|YP_976905.1| 250 MRQFITDASHELRTPLTTIRGFAELYRQ--GAARDVGMLLSRIESEASRMGLLVDDLLLLARLDA 312
                                    68***********************988..46788889*************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                                    HHHC..T-HSSCHHHHHHHHH CS
                          HisKA  26 aLkregklteelkeyleties 46 
                                    +L +e     +l++ l+ ++ 
  gi|121636682|ref|YP_976905.1| 356 VLGDE----SRLRQVLRNLVA 372
                                    56554....555555555544 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.6   1.2e-14   2.8e-11       2      53 .]     179     231 ..     178     231 .. 0.97
   2 ?   -0.5   0.1      0.72   1.6e+03      12      35 ..     362     394 ..     361     400 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.2e-14
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLre 53 
                                    ++rr lrPL + +++a++i+aG+ld r+p  ++r E+G+L  a+N Ml ++++
  gi|121636682|ref|YP_976905.1| 179 VVRRSLRPLAEFEQTAAAIGAGQLDRRVPQwHPRTEVGRLSLALNGMLAQIQR 231
                                    78***********************************************9985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.72
                                    HHHHHHHHHTTT.........BTSSTCCTTSSS CS
                           HAMP  12 rLaraarriaaG.........dldtrlpvsgrD 35 
                                    rL+++ r++ a+         d+++r+ ++g+D
  gi|121636682|ref|YP_976905.1| 362 RLRQVLRNLVANaiqhtpesaDVTVRVGTEGDD 394
                                    677777777776666668888999999998887 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   9.7e-09   2.2e-05       4     108 ..     364     469 ..     361     482 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.7e-09
                    HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknr.gktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklAs 81 
                                    +++l  lv N+++   e+ +++v     g+++ + + DdG Gms+e+  +++ r+ + + +    ++  G  G+Gl    
  gi|121636682|ref|YP_976905.1| 364 RQVLRNLVANAIQHTPESADVTVRVGTeGDDAILEVADDGPGMSQEDALRVFeRFYRADSS---RARASGGTGLGLSIVD 440
                                    678999*******888886666664332789999****************99456666666...6888899999965544 PP

                    HATPase_c_3  82 lslgkk..ltvitkkegesstltldvdki 108
                                      ++++  +  +t++ ge +++++++  +
  gi|121636682|ref|YP_976905.1| 441 SLVAAHggAVTVTTALGEGCCFRVSLPRV 469
                                    33444312233344556666666666555 PP

>> HrcA  HrcA protein C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.9e-06    0.0042      18     164 ..     141     300 ..     125     312 .. 0.78
   2 ?   -0.5   0.0      0.43   9.6e+02     161     182 ..     364     393 ..     355     399 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                           HrcA  18 vavvlapslskaklkhielvplsss.rllvvlvtdsgrvenrll....................elpeevseeelaklsn 76 
                                    ++v++     +++++++ l++++ +  +lvvl    + v +r l                    ++p+    +e+ +ls 
  gi|121636682|ref|YP_976905.1| 141 TTVAIDLADVRSTVRSLVLLQVGIGsAVLVVLGVAGYAVVRRSLrplaefeqtaaaigagqldrRVPQWHPRTEVGRLSL 220
                                    5555555666799*********98889*****************777766666665555544443777779999****** PP

                           HrcA  77 llneklagltlseiaerlreeklkeelseyeelleqllealeealerseelyvsGtsnllrqpefsddeklrellellee 156
                                     ln +la+ + + ++++ + ek     ++ e+ ++q+++ +++ l r+    ++G ++l rq     ++++  ll+ +e 
  gi|121636682|ref|YP_976905.1| 221 ALNGMLAQIQRAVASAESSAEK----ARDSEDRMRQFITDASHEL-RTPLTTIRGFAELYRQGA---ARDVGMLLSRIES 292
                                    ********99999999877776....3333467777777654444.445589***********5...5899********9 PP

                           HrcA 157 kvvllkll 164
                                    +++ + ll
  gi|121636682|ref|YP_976905.1| 293 EASRMGLL 300
                                    99988777 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.43
                           HrcA 161 lkllsels........daegvsvrIGsEne 182
                                     ++l++l         ++++v+vr+G+E +
  gi|121636682|ref|YP_976905.1| 364 RQVLRNLVanaiqhtpESADVTVRVGTEGD 393
                                    44443333434466555455******9975 PP

>> Pelovaterin  Pelovaterin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.0   1.5e-05     0.033       5      39 ..     423     461 ..     421     464 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                    S--T.TTSSB-S-EEGGG---SS-...B-SSS-TTEEB- CS
                    Pelovaterin   5 ssrC.GsGGWGPClPivdllCivh...vtvGCsGGfGCC 39 
                                    ssr   sGG G  l ivd l   h   vtv  + G GCC
  gi|121636682|ref|YP_976905.1| 423 SSRArASGGTGLGLSIVDSLVAAHggaVTVTTALGEGCC 461
                                    6665379****************99999*********** PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.032      31     108 ..     362     442 ..     330     454 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                    HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlal 104
                                    ++r ++  +++Na++h  +   +++v+vr+  +++   +evaD+Gpg   e++ +  e  +      +      G+Gl +
  gi|121636682|ref|YP_976905.1| 362 RLRQVLRNLVANAIQHTPE---SADVTVRVGTEGDDAILEVADDGPGMSQEDALRVFERFYradssrARASGGTGLGLSI 438
                                    5566677778899998887...477999999****************888776655443337777444444445555555 PP

                    HATPase_c_2 105 ikgl 108
                                    + +l
  gi|121636682|ref|YP_976905.1| 439 VDSL 442
                                    5554 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.054       6      90 ..     363     455 ..     359     466 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                    HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.........kklesskskkeehGiGlks 73 
                                    l  +l nl  NAi+   +       +++ v ++ ++ i+++     g   e          +   s+ + ++  G+Gl+ 
  gi|121636682|ref|YP_976905.1| 363 LRQVLRNLVANAIQHTPESA----DVTVRVGTEGDDAILEVADDGPGmsqEDalrvferfyRADSSRARASGGTGLGLSI 438
                                    66789999999998776655....59999************99966644422444453232333367889999******* PP

                    HATPase_c_5  74 ireivkkykgnlsieae 90 
                                    ++++v  ++g+++++++
  gi|121636682|ref|YP_976905.1| 439 VDSLVAAHGGAVTVTTA 455
                                    ***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2741.20
//
Query:       gi|121636683|ref|YP_976906.1|  [L=110]
Description: hypothetical protein BCG_0811c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   64.6   0.1    1.3e-17   64.3   0.1    1.1  1  HIT       HIT domain
    0.00041   20.8   0.0    0.00054   20.4   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.1   1.5e-21   1.3e-17      17      97 ..       2      77 ..       1      78 [. 0.96

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.5e-21
                                   EEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-T CS
                            HIT 17 afldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprre 97
                                   afl+i+p+++gh+Lv+p+++++++++++++ +++++s+++ + ka+++ f++++  ++i     ag +v+hlHiHv+p+r+
  gi|121636683|ref|YP_976906.1|  2 AFLTIEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFSTQRAGMII-----AGLEVPHLHIHVFPTRS 77
                                   9**************************************************99999999.....**************986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.1e-08   0.00054      29     104 ..       6      77 ..       1      84 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.1e-08
                                    SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT-.-S-S--EEEEE... CS
                         DcpS_C  29 ikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyqP.svyhlHlHvisldf 104
                                    i+p ++ h lv+p+++i++ ++++++    + ++ + + k++ + +++      r+g+ ++   v hlH+Hv  +++
  gi|121636683|ref|YP_976906.1|   6 IEPMTQGHTLVVPRAEIDHWQNVDPALFGRVMSVSQLIGKAVCRAFST-----QRAGMIIAGlEVPHLHIHVFPTRS 77 
                                    6788999***********************************999955.....4455555444788******87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 639.11
//
Query:       gi|121636684|ref|YP_976907.1|  [L=139]
Description: hypothetical protein BCG_0812c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   63.7   0.0    2.8e-17   63.4   0.0    1.1  1  NTF2      Nuclear transport factor 2 (NTF2) domain
    4.9e-10   40.0   0.0    6.5e-10   39.6   0.0    1.1  1  SnoaL_2   SnoaL-like domain
     0.0054   17.1   0.0     0.0084   16.5   0.0    1.3  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   4.7e-21   2.8e-17       5     119 ..      12     135 ..       9     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.7e-21
                                    HHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTE.......EEEESHHHHHHHHHHSSCSCEEEEEEEEEEEE....TSEG CS
                           NTF2   5 fvqqYYaaldagdregllalyaadaslltpegs.......spvkgreaIteffrslpftrielkittvdaqp....deas 73 
                                    + q+++++++a+dreg+lal+a+d ++++p g+       s +kg+ea+ +ff+++++++ +l++t+ ++ p    de +
  gi|121636684|ref|YP_976907.1|  12 ASQSSWRCVQAHDREGWLALMADDVVIEDPIGKsvtnpdgSGIKGKEAVGAFFDTHIAAN-RLTVTCEETFPssspDEIA 90 
                                    6799*******************************************************9.***************99** PP

                                    GGCEEEEEEEEEEEETTSCCE.EEEEEEEEEEEETTTEEEEEEEEEE CS
                           NTF2  74 lstgvlvmvtGelkvddfkkr.rkfsqtfilapqsnkgyfvlnDifr 119
                                    +   ++ ++ G ++ + ++   +++++++++++++  gy+ l+++++
  gi|121636684|ref|YP_976907.1|  91 HILVLHSEFDGGFTSEVRGVFtYRVNKAGLITNMR--GYWNLDMMTF 135
                                    ******************988*************9..*****99986 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.1e-13   6.5e-10       5     101 ..      17     123 ..      14     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.1e-13
                                    HHHHHTTCHHHHHHTEEEEEEEEETTSE.........EESHHHHHHHHHHHHHHEEEEEEEEEEE..EEETTEEEEEEEE CS
                        SnoaL_2   5 laalnagdldalaalfapdvvwedpgge.........lrGreairaffralfaafpdlrfeihdv..vadgdrvavewtv 73 
                                    +++++a+d ++++al+a+dvv edp g+         ++G+ea+ aff +  a   +l+++ ++     + d++a    +
  gi|121636684|ref|YP_976907.1|  17 WRCVQAHDREGWLALMADDVVIEDPIGKsvtnpdgsgIKGKEAVGAFFDTHIA-ANRLTVTCEETfpSSSPDEIAHILVL 95 
                                    56889******************9965669999999***************97.99999999999555555655444433 PP

                                    EEEEETTSSEEEEEEEEEEEE.ETTEEEE CS
                        SnoaL_2  74 tgtipatgrgvtvrgvdvfrv.rdGkive 101
                                    +  +   g + +vrgv ++rv + G+i+ 
  gi|121636684|ref|YP_976907.1|  96 HS-EFDGGFTSEVRGVFTYRVnKAGLITN 123
                                    32.4456889999********778***86 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-06    0.0084       8      95 ..      16     112 ..      12     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                    HHHHHHCT-HHHHHHCEEEEEEEE........-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEE..TT.EE.EEEE CS
                        DUF4440   8 leeafvagdaealaallapdavlv........gpsgtvldkeellealeagfaagrslelteeevrvl..gd.lA.vvtg 75 
                                     ++ + a+d+e + al+a+d+v+         +p+g+ + ++e + a+++ ++a  +l++t ee+ ++  +d +A +++ 
  gi|121636684|ref|YP_976907.1|  16 SWRCVQAHDREGWLALMADDVVIEdpigksvtNPDGSGIKGKEAVGAFFDTHIAANRLTVTCEETFPSssPDeIAhILVL 95 
                                    58999****************77766666666888999989999999999***********9999988775545545555 PP

                                    EEEEEECCTTEEEEEEEEEE CS
                        DUF4440  76 rytfegrgdgepvegrgrft 95 
                                    +  f+g   g + e+rg ft
  gi|121636684|ref|YP_976907.1|  96 HSEFDG---GFTSEVRGVFT 112
                                    555553...43344555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 810.06
//
Query:       gi|121636685|ref|YP_976908.1|  [L=375]
Description: zinc-containing alcohol dehydrogenaseAdhB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      9e-28   96.3   0.3      9e-28   96.3   0.3    1.7  2  ADH_N        Alcohol dehydrogenase GroES-like domain
    1.2e-18   67.3   0.9    2.7e-18   66.2   0.7    1.7  2  ADH_zinc_N   Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.015   14.6   0.7      0.088   12.1   0.1    2.0  2  PFK          Phosphofructokinase
      0.016   15.2   0.2      0.035   14.2   0.2    1.6  1  NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur bin


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.3     2e-31     9e-28       2     109 .]      28     155 ..      27     155 .. 0.97
   2 ?   -3.8   0.1       2.7   1.2e+04      46      61 ..     175     192 ..     169     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2e-31
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                    +ev i+++aag+C+sD h+++g + + + +p+  GHE +G+v evgp+v++++ Gd+Vv+ ++ scg+C++C+ g +nlC
  gi|121636685|ref|YP_976908.1|  28 DEVKIQMEAAGMCRSDHHLVTG-DIPMAGFPVLGGHEGAGIVTEVGPGVDDFAPGDHVVLAFIPSCGKCPSCQAGMRNLC 106
                                    89********************.8******************************************************** PP

                                    .....................TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                          ADH_N  82 .....................eeakllgvsldGgfaeyvvvpekklvkl 109
                                                         + ++++ ++l G+f+ y+vv+++++vk+
  gi|121636685|ref|YP_976908.1| 107 dlgagllagesvtdgsfriqaRGQNVYPMTLLGTFSPYMVVHRSSVVKI 155
                                    ****************99998889999999***************9986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                                    ESTT-CS..--TT-EEEE CS
                          ADH_N  46 vgpevkk..lkvGdrVvv 61 
                                     g++v++  ++ Gd V++
  gi|121636685|ref|YP_976908.1| 175 YGSAVRTadVRPGDDVAI 192
                                    566666555888999987 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.7     6e-22   2.7e-18       1     126 [.     197     329 ..     197     333 .. 0.91
   2 ?   -2.9   0.0       1.4   6.5e+03      99     116 ..     354     371 ..     341     374 .. 0.67

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 6e-22
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC..SHHHHHHHHH CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvG..sgatleaalk 77 
                                    gvG+aa+q A  +Ga  v+av + e k+++a k+Ga++v+   +      i+e t g  ++ v+ +vG  +ga ++++l+
  gi|121636685|ref|YP_976908.1| 197 GVGMAALQGAVSAGArYVFAVEPVEWKRDQALKFGATHVYPDIN-AALMGIAEVTYGLMAQKVIITVGklDGADVDSYLT 275
                                    9*****************************************66.89999******************999********* PP

                                    CEEEEEEEEECSC...TSSEEEEEHHHHHHTT-EEEEE-SSC..HHHHHHHHHH CS
                     ADH_zinc_N  78 llkpgGrlvvvGg...gkgeeefdlrnlllkeksilGsllgs..lreefkeald 126
                                    ++++gG++v+ ++   +  + +++l++l+l +k+i+G+++g+  ++ +++++l 
  gi|121636685|ref|YP_976908.1| 276 ITAKGGTCVLTAIgslVDTQVTLNLAMLTLLQKNIQGTIFGGgnPHYDIPKLLS 329
                                    *************865445555*******************9777777777665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                                    HHHHHHTT-EEEEE-SSC CS
                     ADH_zinc_N  99 lrnlllkeksilGsllgs 116
                                     ++ +l+ k+i+G+++++
  gi|121636685|ref|YP_976908.1| 354 GYQDMLNGKNIRGVIRYT 371
                                    444568899999998887 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.066     3e+02     177     199 ..     198     219 ..     189     230 .. 0.83
   2 ?   12.1   0.1     2e-05     0.088      30     115 ..     241     333 ..     227     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.066
                                    -THHHHHHHHHHT-SEEE-TTS- CS
                            PFK 177 cGwlAlmaglaggadvilipEep 199
                                     G  Al +++++ga +++  E p
  gi|121636685|ref|YP_976908.1| 198 VGMAALQGAVSAGARYVFAVE-P 219
                                    6999**************998.4 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2e-05
                                    -EEEEETTHHHHHHTT.......-EEEE-SGGGTT-TT--S-TT-----GGGGSHHHHHHHHHHHHHHT--EEEEEESHH CS
                            PFK  30 levygireGfeGliee.......eiekltledvsgilsegGtiLgsaRskefkeregrkkaaenlkklgidaLvviGGdg 102
                                    +  +gi e + Gl+ +       +++ ++ ++  +i+++gGt   +a     +++ +++ a+ +l +++i++ +  GG+ 
  gi|121636685|ref|YP_976908.1| 241 AALMGIAEVTYGLMAQkviitvgKLDGADVDSYLTITAKGGTCVLTAIGSLVDTQVTLNLAMLTLLQKNIQGTIFGGGNP 320
                                    557888888999977744442223333446677779***********9999988899**********************9 PP

                                    HHHHHHHHHHT.. CS
                            PFK 103 slkganklseerk 115
                                     +++ + ls ++ 
  gi|121636685|ref|YP_976908.1| 321 HYDIPKLLSMYKA 333
                                    9999998887655 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   7.8e-06     0.035      14      41 ..      91     118 ..      86     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-06
                                    --S--HHHHIIIIHHHHHHHHHTBT--- CS
                    NADH_4Fe-4S  14 sCGkCtpCreGtkrllelleriaagegt 41 
                                    sCGkC  C+ G++ l +l + + age+ 
  gi|121636685|ref|YP_976908.1|  91 SCGKCPSCQAGMRNLCDLGAGLLAGESV 118
                                    9***************999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2182.61
//
Query:       gi|121636686|ref|YP_976909.1|  [L=181]
Description: hypothetical protein BCG_0814c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-05   23.3   1.8    0.00011   22.8   1.8    1.2  1  SnoaL_2   SnoaL-like domain
    0.00075   19.8   0.7     0.0011   19.3   0.7    1.1  1  SnoaL_3   SnoaL-like domain
  ------ inclusion threshold ------
      0.075   13.2   1.1       0.11   12.7   1.0    1.4  1  SnoaL_4   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.8   1.8e-08   0.00011       7      98 ..      23     124 ..      13     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-08
                                    HHHTTCHHHHHHTEEEEEEEEETTSE.....EESHHHHHH.HHHHHHHHEEEEEEEEEEEEEETT..EEEEEEEEEEEEE CS
                        SnoaL_2   7 alnagdldalaalfapdvvwedpgge.....lrGreaira.ffralfaafpdlrfeihdvvadgd..rvavewtvtgtip 78 
                                    a  +gd+  la+++++d+++   +g+     ++G+++ir+ ++ +  +++ ++r+  ++vv d+   +v+  w   + + 
  gi|121636686|ref|YP_976909.1|  23 AERRGDWTLLADFYTDDATYGWNVGPnedvmCVGIDEIRDiALGQEMDGLQGWRYPYQRVVIDEKqgEVVGFWKQVA-TD 101
                                    6679****************8775566799**********877777779***********77654226666777776.66 PP

                                    TTSSEEEE..EEEEEEEEET.TE CS
                        SnoaL_2  79 atgrgvtv..rgvdvfrvrd.Gk 98 
                                    a+g++ +v   g ++fr ++ Gk
  gi|121636686|ref|YP_976909.1| 102 ANGAEQEVygIGGSWFRYAGgGK 124
                                    77777666444445555544234 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.7   1.8e-07    0.0011       4     111 ..      16     127 ..      13     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
                        SnoaL_3   4 lldafyeaaaegdfdalfalwaddivf...igtgadelltgreevrrs.lkqifakgegisfeltdvrvte.sgdvawvt 78 
                                     l+a  +a ++gd++ l ++++dd+++   +g+ +d +  g +e+r++ l q++++ +g+++  ++v + e  g+v+ + 
  gi|121636686|ref|YP_976909.1|  16 WLQANRTAERRGDWTLLADFYTDDATYgwnVGPNEDVMCVGIDEIRDIaLGQEMDGLQGWRYPYQRVVIDEkQGEVVGFW 95 
                                    5677788999************999884445666666777*******7369******************75389999999 PP

                        SnoaL_3  79 elldvtaaedgtegegqlrlTgvlrrtdg.gWki 111
                                     ++ ++  ++g+e e    +  ++r  +g +W +
  gi|121636686|ref|YP_976909.1|  96 KQVATD--ANGAEQEVYGIGGSWFRYAGGgKWNW 127
                                    987554..57777777779999999998856765 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   1.8e-05      0.11       6      59 ..       6      65 ..       5     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHHHHHT....T-HHHHHTTEEEEEEEEETTS.....--EESHHHHHHHHH CS
                        SnoaL_4  6 reaIrdlvarygyylDt....kdweeladlFtedavvdytgvg...egvlegrdairaalr 59
                                   r++  d+v+r+ ++  t    +dw +lad +t+da++ ++  g   +    g+d+ir+   
  gi|121636686|ref|YP_976909.1|  6 RDELEDVVHRWLQANRTaerrGDWTLLADFYTDDATYGWNV-GpneDVMCVGIDEIRDIAL 65
                                   6788999999998877667678***************9994.6687777899999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1046.28
//
Query:       gi|121636687|ref|YP_976910.1|  [L=68]
Description: ferredoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-10   39.6   0.2    8.3e-10   39.3   0.2    1.1  1  Fer4_15   4Fe-4S single cluster domain
    3.1e-07   30.8   0.1    3.8e-07   30.5   0.1    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.4e-06   28.3   0.1    1.6e-06   28.1   0.1    1.1  1  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.023   14.8   0.3        8.8    6.6   0.1    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.2   1.9e-13   8.3e-10       1      66 []       5      63 ..       5      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.9e-13
                        Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                   V+ Drd+C+g+++C  eape+f+  ++g  ++l       + e p++ +  ++ A+ aCP++A+++
  gi|121636687|ref|YP_976910.1|  5 VEADRDLCQGHAMCELEAPEYFRVPKRGQVEIL-------DPEPPEEARGVIKHAVWACPTQALSI 63
                                   778**************************9999.......5799*******************987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   8.6e-11   3.8e-07       2      57 ..       8      62 ..       7      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.6e-11
                        Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                   Drd C +++ C   aP+ F+  +  g++ + + + +ee +  ++ A+ aCP+++  
  gi|121636687|ref|YP_976910.1|  8 DRDLCQGHAMCELEAPEYFRVPKR-GQVEILDPEPPEEARGVIKHAVWACPTQALS 62
                                   99*****************98876.7899999999999***************975 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   3.6e-10   1.6e-06       7      63 ..       4      65 ..       2      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.6e-10
                        Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrkpwi.....kpdeasteeiievverCPSGALsyve 63
                                   ++e++r+lC++ + C  ++pe F++ +++ +     +p e+++  i+++v  CP  ALs+ e
  gi|121636687|ref|YP_976910.1|  4 RVEADRDLCQGHAMCELEAPEYFRVPKRGQVeildpEPPEEARGVIKHAVWACPTQALSIRE 65
                                   6999************************999988777788899999999**********976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.002       8.8       2      12 ..       5      18 ..       4      20 .. 0.75
   2 ?    6.5   0.0     0.002       9.1      16      24 .]      53      61 ..      53      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                         Fer4_6  2 veidpdkCig...C 12
                                   ve d+d+C g   C
  gi|121636687|ref|YP_976910.1|  5 VEADRDLCQGhamC 18
                                   899*****963336 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.002
                         Fer4_6 16 vrvCPegai 24
                                   v +CP++a+
  gi|121636687|ref|YP_976910.1| 53 VWACPTQAL 61
                                   679****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 415.16
//
Query:       gi|121636688|ref|YP_976911.1|  [L=451]
Description: cytochrome P450 51 cyp51 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-66  225.3   0.0    1.5e-66  225.1   0.0    1.0  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   8.4e-71   1.5e-66      11     458 ..      17     440 ..       7     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 8.4e-71
                                    HCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTC CS
                           p450  11 gnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfa 90 
                                    g+l ++++ + +   +++++ + g++ +++l +k+vv+lsg+ a +  + +++++  +       + +  p  g+gv+f+
  gi|121636688|ref|YP_976911.1|  17 GHLEEFRT-DPIGL-MQRVRDECGDVGTFQLAGKQVVLLSGSHANEFFFRAGDDDLDQA----KAYPFMTPIFGEGVVFD 90 
                                    66677773.55555.9*********************************9998555555....445555589******** PP

                                    GHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHTTTSSH CS
                           p450  91 ngekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdlledek 169
                                    ++++ +k   +l+++ + ++++    +++e++++++++ +    ge++e+d+ +++++ ++ +++ +l g++f    d+ 
  gi|121636688|ref|YP_976911.1|  91 ASPERRK--EMLHNAALRGEQMkGHAATIEDQVRRMIADW----GEAGEIDLLDFFAELTIYTSSACLIGKKFR---DQL 161
                                    *976554..4555555555255456666666666666666....5666799*********************88...555 PP

                                    HHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHC CS
                           p450 170 lselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdfldalllak 249
                                    + ++ k+ +el + +     ++l + +   ylp + +r+ +ea++ l  l+  +++ r ++  ++ ks+rd+ld+l+  k
  gi|121636688|ref|YP_976911.1| 162 DGRFAKLYHELERGT-----DPLAYVD--PYLPIESFRRRDEARNGLVALVADIMNGRIANPPTD-KSDRDMLDVLIAVK 233
                                    556777777773323.....3333333..589*********************************.89***********8 PP

                                    TTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHH CS
                           p450 250 kekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavik 329
                                     ++ g+  +s +e++   + ++faG++T+s t sw+L+eL+++ ++ +++  E+de  gd r++++  l ++p l++v+k
  gi|121636688|ref|YP_976911.1| 234 -AETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLK 312
                                    .7777779************************************************************************ PP

                                    HHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGG CS
                           p450 330 EtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGp 409
                                    EtLRlhp++   l+R+++ + +++g+ i +G+ v  ++   +r pe fp+P+ F p R+++ ++++  +   ++PFGaG+
  gi|121636688|ref|YP_976911.1| 313 ETLRLHPPLI-ILMRVAKGEFEVQGHRIHEGDLVAASPAISNRIPEDFPDPHDFVPARYEQPRQEDLLNRWTWIPFGAGR 391
                                    **********.899**************************************************999************* PP

                                    GS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEESSCSSEEESSS CS
                           p450 410 RnCiGerlArmelklflatlLqnFevelqpetdpppileksglllppkp 458
                                    + C+G  +A+m++k +++ lL+++e+e+ +  +   +++ +++++  +p
  gi|121636688|ref|YP_976911.1| 392 HRCVGAAFAIMQIKAIFSVLLREYEFEMAQPPESYRNDHSKMVVQLAQP 440
                                    ***************************9776666666665577776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2553.76
//
Query:       gi|121636689|ref|YP_976912.1|  [L=275]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-46  157.6   0.3      3e-46  157.4   0.3    1.1  1  adh_short     short chain dehydrogenase
    1.5e-39  135.9   0.2      2e-39  135.6   0.2    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    5.7e-11   42.7   0.9      8e-11   42.2   0.9    1.1  1  KR            KR domain
  ------ inclusion threshold ------
      0.079   12.5   0.0       0.14   11.6   0.0    1.3  1  DUF2460       Conserved hypothetical protein 2217 (DUF2460)
       0.14   11.6   0.1       0.99    8.8   0.1    2.5  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.3   8.4e-50     3e-46       2     193 ..      12     203 ..      11     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 8.4e-50
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    + +v GassGIG a+a ela +G+ v++ +r+ +kl+e++++++++g +a+a+++Dvtd e+v+ +v++ v+ lg++++L
  gi|121636689|ref|YP_976912.1|  12 TTVVAGASSGIGAATATELAGRGFPVALGARRMDKLAELVDKIRADGGEAVAFPLDVTDPESVKSFVAQTVEALGEVELL 91 
                                    679***************************************************************************** PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                    v  AG   +g+ +e+s e++ + +++ l+g+  l+ avlpam+++++G+ ++v+S +g+ + +++ aY+A+Ka++a+++ 
  gi|121636689|ref|YP_976912.1|  92 VSSAGDMLPGQLHEVSTEAFAEQVQIHLVGANRLATAVLPAMVARRRGDLIFVGSDVGLRQRPHMGAYGAAKAGLAAMVT 171
                                    ******************************************************************************** PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmakelrek 193
                                    +l++el+ tg+r ++v+PG++ T+m  +l+++
  gi|121636689|ref|YP_976912.1| 172 NLQMELEGTGVRASIVHPGPTLTGMGWQLSAE 203
                                    *************************9988766 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.2   5.5e-43     2e-39       1     216 [.      17     238 ..      17     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 5.5e-43
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIG+a+A +la +G  v+l  ++ ++ ++ v+++ +++g++v +++DVtd+e+v+++v+++ve +g++  lv +ag
  gi|121636689|ref|YP_976912.1|  17 GASSGIGAATATELAGRGFPVALGARRMDKlAELVDKIRADGGEAVaFPLDVTDPESVKSFVAQTVEALGEVELLVSSAG 96 
                                    899**********************999999************9966********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                     + +  g+++e+s e f++ +++ l ++ +la a+lp+m ++  g ++ + s  + r  p+  aygaaKa+l a++ +l 
  gi|121636689|ref|YP_976912.1|  97 DMLP--GQLHEVSTEAFAEQVQIHLVGANRLATAVLPAMVARrrGDLIFVGSDVGLRQRPHMGAYGAAKAGLAAMVTNLQ 174
                                    ****..*******************************5554447************************************ PP

                                    HHHGGGTEEEEEEEE--BHCTGGGGSTT..HHHHHHHHHHHSTTSS-B..-HHHHHHHHHHHCS CS
                   adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikg..fdelleelearaplgrlg..tpeevaeaalfLas 216
                                    +el   g+R   v+pgp+ T +  +++      +l+ ++++   +++   +p++ a+a++f a 
  gi|121636689|ref|YP_976912.1| 175 MELEGTGVRASIVHPGPTLTGMGWQLSAeqVGPMLADWAKWGQARHNYflRPSDLARAIAFVAE 238
                                    **********************77766533678*****999998885555***********986 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.9   2.2e-14     8e-11       3     164 ..      13     174 ..      12     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.2e-14
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     +++G+  g+G ++a+ la +g   ++l +R+    ++ ++l+++++a g e  ++++Dv+d+++v++ +++  +  +++
  gi|121636689|ref|YP_976912.1|  13 TVVAGASSGIGAATATELAGRGFP-VALGARR--M-DKLAELVDKIRADGGEAVAFPLDVTDPESVKSFVAQTVEALGEV 88 
                                    689*******************75.7777888..4.45566*************************************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDa 158
                                    +  + +Ag +  ++l e+++e++++ ++  + Ga  L +++ +    ++   ++++ S  gl   ++ ++Y aa a l a
  gi|121636689|ref|YP_976912.1|  89 ELLVSSAGDMLPGQLHEVSTEAFAEQVQIHLVGANRLATAVLPamvaRRRGDLIFVGSDVGLRQRPHMGAYGAAKAGLAA 168
                                    **************************************999887777666778999********************9999 PP

                                    HHHHHH CS
                             KR 159 laeyrr 164
                                    +++  +
  gi|121636689|ref|YP_976912.1| 169 MVTNLQ 174
                                    998765 PP

>> DUF2460  Conserved hypothetical protein 2217 (DUF2460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.9e-05      0.14      16      83 ..       7      73 ..       3      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                        DUF2460 16 gpefsTeivtlasGreeRnarwaqprrrydagfgvlseedlaellaffearrGrlygFrfkDpeDhks 83
                                    p ++T +v+ as     ++  + + r + ++ g+++ ++lael++  +a  G++ +F   D +D +s
  gi|121636689|ref|YP_976912.1|  7 HPARRTTVVAGASSGIGAATATELAGRGFPVALGARRMDKLAELVDKIRADGGEAVAFPL-DVTDPES 73
                                   589*******************************************************75.4444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00028      0.99       2      63 ..      14      81 ..      13     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00028
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkee 63
                                   +V+Ga+  iG+a++ +l+ +g  v   +r+ ++ +  +l d+            ld+td+++++ +++++
  gi|121636689|ref|YP_976912.1| 14 VVAGASSGIGAATATELAGRGFPVALGARRMDKLA--ELVDKiradggeaVAFPLDVTDPESVKSFVAQT 81
                                   69*******************99888888844333..33333579999998899**********999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1961.78
//
Query:       gi|121636690|ref|YP_976913.1|  [L=541]
Description: cytochrome P450 123 cyp123 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-21   74.4   0.0      1e-16   60.7   0.0    3.1  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0   0.00025       4.5      81     156 ..      80     152 ..      45     154 .. 0.88
   2 !   60.7   0.0   5.8e-21     1e-16     237     414 ..     206     352 ..     186     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00025
                                    TTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHH CS
                           p450  81 pfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldvigsi 156
                                    +++  ++l ++ + + ++R+++ + +t   +++le+ v e a+++++   ++ ++     ++e+  k ++dvi+++
  gi|121636690|ref|YP_976913.1|  80 AYRVMSMLAMDDPAHLRMRTLVSKGFTPRRIRELEPQVLELARIHLDSALQTESFD---FVAEFAGKLPMDVISEL 152
                                    566677888999999************99888*****************9999999...68999999999999876 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 5.8e-21
                                    SSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHH CS
                           p450 237 srrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyd 316
                                      +++++all a+   +g+  lsd+e++a ++ + +aG +Tt+  l+ a y+ a++P   +++  +      ++r     
  gi|121636690|ref|YP_976913.1| 206 PANNLTSALLAAE--LDGD-RLSDQEIMAFLFLMVIAGNETTTKLLANAVYWAAHHPGQLARVFAD------HSR----- 271
                                    4567888888885..8888.9*************************************99999887......333..... PP

                                    HCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTE CS
                           p450 317 dlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnsk 396
                                             + ++EtLR+ + +   l R v +d+++ + +ip+G + ++ +++ +rd+ vf++P+ ++++R   e g   
  gi|121636690|ref|YP_976913.1| 272 -------IPMWVEETLRYDTSSQ-ILARTVAHDLTLYDTTIPEGEVLLLLPGSANRDDRVFDDPDDYRIGR---EIG--- 337
                                    .......4578************.999******************************************99...544... PP

                                    SSCTT--TTEEGGGS-TT CS
                           p450 397 rksfaflPFGaGpRnCiG 414
                                       ++ + FG G++ C+G
  gi|121636690|ref|YP_976913.1| 338 ---CKLVSFGSGAHFCLG 352
                                    ...789***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 3120.16
//
Query:       gi|121636691|ref|YP_976914.1|  [L=213]
Description: hypothetical protein BCG_0819c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-12   45.9   3.5    3.1e-11   42.9   1.1    2.3  2  TetR_N     Bacterial regulatory proteins, tetR family
    1.3e-06   28.7   0.8     0.0001   22.6   0.0    2.2  2  TetR_C_20  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   1.1   3.4e-15   3.1e-11       2      47 .]      36      81 ..      35      81 .. 0.97
   2 !    3.1   0.1    0.0093        84      12      33 ..     179     200 ..     175     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.4e-15
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   l+aA++ + e+ y+ +tvr +A+rA+v++++ Y yF+sK  L++++
  gi|121636691|ref|YP_976914.1| 36 LAAAMATLREKSYADLTVRLVAARAKVAPATAYTYFSSKNHLIAEV 81
                                   99*****************************************996 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0093
                                    HHTTT--HHHHHHHHTSSHHHH CS
                         TetR_N  12 rGydattvreIAkrAGvskgal 33 
                                     G   +t  eIA+r+G+  g++
  gi|121636691|ref|YP_976914.1| 179 AGSGTFTYHEIADRLGYVVGLI 200
                                    566678889*******999987 PP

>> TetR_C_20  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.4    0.0053        47      34      63 ..      15      44 ..       7      62 .. 0.81
   2 !   22.6   0.0   1.1e-08    0.0001       7     104 ..     102     197 ..     101     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0053
                                   HH--TTT-GGGHHHHHHHHHHHHHHHT-SS CS
                      TetR_C_20 34 saadasaaaevdrvaavvealllralgeee 63
                                   + ++a+a++ ++r +a+++++l++a+++ +
  gi|121636691|ref|YP_976914.1| 15 TEPHAEAVSRNRRQQATFRKVLAAAMATLR 44
                                   56899*********************9766 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.1e-08
                                    HHHHHHHHHHHHHHTSHHHHHHHHHHHH..H--TTT-GGGHHHHHHHHHHHHHHHT-SS--HHHHHHHHHHHHHHHHHHH CS
                      TetR_C_20   7 rlaevLrratralqrePaLaeAmvrAls..aadasaaaevdrvaavvealllralgeeePteedadlarvlsdvwlglLv 84 
                                    r++  Lr+++   ++eP+   A + Al   +ad+++ a +dr++a +++ +++a+g   P++ d   +  l++  +g+Lv
  gi|121636691|ref|YP_976914.1| 102 RVTSSLRHLALVVADEPEIGAACTAALLdgGADPAVRAVRDRIGAEIHRRITSAIG---PGA-DPGTVFALEMAFFGALV 177
                                    688889999999**************96448999**********************...666.67778899********* PP

                                    HHHTTSS-HHHHHHHHHHHH CS
                      TetR_C_20  85 awlngrasitdveadlerav 104
                                    +  +g+ ++ +++++l   v
  gi|121636691|ref|YP_976914.1| 178 QAGSGTFTYHEIADRLGYVV 197
                                    ***************97766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1413.62
//
Query:       gi|121636692|ref|YP_976915.1|  [L=489]
Description: aldehyde dehydrogenase AldA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.1e-145  483.8   0.0   4.7e-145  483.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.072   13.1   0.0       0.18   11.9   0.0    1.7  1  PAS_8     PAS domain


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.6   0.0  5.2e-149  4.7e-145       5     461 ..      21     483 ..      17     484 .. 0.95

  Alignments for each domain:
  == domain 1  score: 483.6 bits;  conditional E-value: 5.2e-149
                                    SSSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH..HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH--- CS
                         Aldedh   5 esetievinPatgeviakvpaataedvdaavaaAkeafk..awaklpaeeRaeiLrkaadlleerkeelaeletletGkp 82 
                                    +++t++++nPat+ev++ +++a+aed+ +a++aA++af+   w++ + e R +++r+++d+++++ eel el   e+G p
  gi|121636692|ref|YP_976915.1|  21 RAGTFPTVNPATEEVLGVAADADAEDMGRAIEAARRAFDstDWSR-NTELRVRCVRQLRDAMQQHVEELRELTISEVGAP 99 
                                    45789**********************************766887.7899****************************** PP

                                    HHHHHH.HHHHHHHHHHHHHHHHHHHSE.EEEEE.C...TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-E CS
                         Aldedh  83 laeara.eveeaidvlryyaelaekleg.evlps.s...egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNt 156
                                       ++  ++e  +  l+++a+ ae +   + l   s     ++ +  re++GvvgaItPWNfP  + + kl palaaGNt
  gi|121636692|ref|YP_976915.1| 100 RMLTASaQLEGPVGDLSFAADTAESYPWkQDLGEaSplgIATRRTLAREAVGVVGAITPWNFPHQINLAKLGPALAAGNT 179
                                    9988888***************9996652333222345478889999********************************* PP

                                    EEEEE-TTSHHHHHHHHHHHHH.TTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEE CS
                         Aldedh 157 vvlKPaeetplsalllaelfee.aglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlE 235
                                    vvlKPa++tp++a++l e++ e  ++P+gv+n+vt s + +g+ l+++p+vd++sftGst++gr +++ aa+++k+v lE
  gi|121636692|ref|YP_976915.1| 180 VVLKPAPDTPWCAAALGEIIVEhTDFPPGVVNIVTSSSHALGALLAKDPRVDMISFTGSTATGRAVMADAAATIKKVFLE 259
                                    ******************987747******************************************************** PP

                                    E---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHH CS
                         Aldedh 236 lGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlisea 315
                                    lGGk++++vl+daDl +a +  +++a+++aGQ C  ++rl+v++  y+e v+  ++++++++ gdp d+ t  GPlis++
  gi|121636692|ref|YP_976915.1| 260 LGGKSAFVVLDDADLAAASAVSAFSACMHAGQGCAITTRLVVPRARYEEAVAIAAATMSSIRPGDPNDPGTVCGPLISAR 339
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSE CS
                         Aldedh 316 qlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdtey 395
                                    q+++v++y++ a++eg +  +Gg  + a++e g+++ePtv+a++t+d+r+a+eEiFGPVl+vi  + +++a++iaNd++y
  gi|121636692|ref|YP_976915.1| 340 QRDRVQGYLDLAVAEGGRFACGG-ARPADREVGFYIEPTVIAGLTNDARVAREEIFGPVLTVIAHDGDDDAVRIANDSPY 418
                                    ***********************.55899*************************************************** PP

                                    ESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                         Aldedh 396 GLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                    GL+++v+++d++ra r+a+rl++G+v++N    + a+a pfgG+kqSg+Gre+g  g+eey+e k 
  gi|121636692|ref|YP_976915.1| 419 GLSGTVYGADPQRAARIASRLRVGTVNVNGGVWYCADA-PFGGYKQSGIGREMGLLGFEEYLEAKL 483
                                    **************************************.************************996 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      25      57 ..      27      59 ..       6      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                          PAS_8 25 dvNqaalellGysadlkgellgqllpvlrplle 57
                                    vN+a++e lG+ ad ++e++g+ ++  r  ++
  gi|121636692|ref|YP_976915.1| 27 TVNPATEEVLGVAADADAEDMGRAIEAARRAFD 59
                                   59*******************988877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3020.76
//
Query:       gi|121636693|ref|YP_976916.1|  [L=248]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-67  225.0   3.0    1.1e-66  224.7   3.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.9e-50  170.4   3.7    3.4e-50  170.2   3.7    1.1  1  adh_short        short chain dehydrogenase
    7.4e-07   29.3   4.4    1.4e-06   28.4   2.1    1.9  2  KR               KR domain
     0.0001   22.6   0.6    0.00016   21.9   0.6    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0081   15.6   1.4      0.016   14.7   1.4    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.027   14.9   0.2       0.58   10.6   0.2    2.6  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.7   3.0   3.7e-70   1.1e-66       1     232 [.      11     243 ..      11     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 3.7e-70
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Gaa+gIG+a A+ala+eGa+vv++d+n ++ ++ ++++++++g+ + +++DV+de++ +a+v+++v  fg++D+lvnna+
  gi|121636693|ref|YP_976916.1|  11 GAAQGIGQAYAQALAREGASVVVADINADGaAAVAKQIVADGGTVIhVPVDVSDEDSAKAMVDRAVGAFGGIDYLVNNAA 90 
                                    9*****************************88888999999998878********************************* PP

                                    --EG.CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapk.lkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    i    +   +l+++ + +++ ++vn  +++ +++a+ ++m+++  g+ivn ss++a   +   n yg aK ++++lt++l
  gi|121636693|ref|YP_976916.1|  91 IYGGmKLDLLLTVPLDYYKKFMSVNHDGVLVCTRAVYKHMAKRggGAIVNQSSTAA---WLYSNFYGLAKVGVNGLTQQL 167
                                    ****666667778*************************7776659*********66...99999**************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    A+elg  +iR+Na++pgpi+T+a++ ++   el +++ + +pl r+gtpe+   ++lfL+sd as+itGq++ vDgG
  gi|121636693|ref|YP_976916.1| 168 ARELGGMKIRINAIAPGPIDTEATRTVT-PAELVKNMVQTIPLSRMGTPEDLVGMCLFLLSDSASWITGQIFNVDGG 243
                                    ***************************8.899********************************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   3.7   1.2e-53   3.4e-50       1     192 [.       5     196 ..       5     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.2e-53
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv++vtGa++GIG+a+a++la+eGa+vvv+d++++ +++vak++ ++g ++++++vDv+d+++++a+v++av  +g++d 
  gi|121636693|ref|YP_976916.1|   5 KVAIVTGAAQGIGQAYAQALAREGASVVVADINADGAAAVAKQIVADGGTVIHVPVDVSDEDSAKAMVDRAVGAFGGIDY 84 
                                    89****************************************************************************** PP

                                    EEE---S...S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
                      adh_short  81 LvnNAGi...tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                                    LvnNA+i    +      +  + +++ ++vN  gv+ +trav+++m k+ +G+Ivn sS+a+   +     Y+ +K +v+
  gi|121636693|ref|YP_976916.1|  85 LVNNAAIyggMKLDLLLTVPLDYYKKFMSVNHDGVLVCTRAVYKHMAKRGGGAIVNQSSTAA---WLYSNFYGLAKVGVN 161
                                    *******8766666677777888**************************************9...888999********* PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakelre 192
                                    glt++la+el   +ir+na+aPG++dT+ ++++++
  gi|121636693|ref|YP_976916.1| 162 GLTQQLARELGGMKIRINAIAPGPIDTEATRTVTP 196
                                    ****************************9998765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   2.1   4.6e-10   1.4e-06       4      93 ..       8      93 ..       6     121 .. 0.86
   2 ?    0.9   0.0      0.13   3.8e+02      14      58 ..     124     181 ..     117     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.6e-10
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EE CS
                             KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGv 85
                                   ++tG++ g+G++ a+ la++ga+ +v         + ++a  +++ a g +v  v++Dvsd+d+ +a+++++   ++ i   
  gi|121636693|ref|YP_976916.1|  8 IVTGAAQGIGQAYAQALAREGASVVVADINA----DGAAAVAKQIVADGGTVIHVPVDVSDEDSAKAMVDRAVGAFGGIDYL 85
                                   8*********************987764444....55667889999***************************999999999 PP

                                   EE------ CS
                             KR 86 ihaAgvlr 93
                                   ++ A +  
  gi|121636693|ref|YP_976916.1| 86 VNNAAIYG 93
                                   99888765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHS-EEEEE-SS...............--HHHHHHHHHHHHTT-EEEE- CS
                             KR  14 lelarwlaekgarhlvllsRsa.............aadedskaliaelealgaevevv 58 
                                    +++ +++a++g   +v  s +a              ++   ++l +el  + ++++++
  gi|121636693|ref|YP_976916.1| 124 RAVYKHMAKRGGGAIVNQSSTAawlysnfyglakvGVNGLTQQLARELGGMKIRINAI 181
                                    7889999999999999999988777777777776666666666677776666666655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.6   5.5e-08   0.00016       5      70 ..      11      75 ..       7      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                                   --.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTS CS
                Sacchrp_dh_NADP  5 Ga.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkeg 70
                                   Ga  ++Gqa a+ lar++     ++vad + ++++a+a+++   g +++ + +d++++++  +a++  +
  gi|121636693|ref|YP_976916.1| 11 GAaQGIGQAYAQALAREGAS---VVVADINADGAAAVAKQIvaDGGTVIHVPVDVSDEDS-AKAMVDRA 75
                                   66668************986...***************999*9*****************.99998766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.4   5.4e-06     0.016       2      79 ..       8      97 ..       7     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-06
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SEEEE-- CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpdavihlA 72
                                   +VtGa+  iG+a ++al+++g  v++ d + ++ +  +++ +        v +d+ d++     ++r++  + ++d+ ++ A
  gi|121636693|ref|YP_976916.1|  8 IVTGAAQGIGQAYAQALAREGASVVVADINADGAAAVAKQIVadggtvIHVPVDVSDEDsakaMVDRAVGAFgGIDYLVNNA 89
                                   8*************************999977776665555599**98888999999996665567777777799******9 PP

                                   S.---HHH CS
                      Epimerase 73 a.vggvaa 79
                                   a +gg + 
  gi|121636693|ref|YP_976916.1| 90 AiYGGMKL 97
                                   98887764 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2    0.0002      0.58       8      48 ..      18      61 ..      10      87 .. 0.77
   2 ?   -0.3   0.0      0.43   1.3e+03     129     149 ..     115     135 ..     104     139 .. 0.83
   3 ?    0.2   0.0      0.31   9.3e+02       6      31 ..     163     188 ..     159     230 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                Glyco_trans_4_4  8 aelaraLaarGheVtvlt...papapgapeleedgvrvhrlpvp 48
                                   ++ a+aLa++G++V+v     +++a++a ++++dg +v+++pv 
  gi|121636693|ref|YP_976916.1| 18 QAYAQALAREGASVVVADinaDGAAAVAKQIVADGGTVIHVPVD 61
                                   6789**********9963444888888999**********9975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                Glyco_trans_4_4 129 radavlvvseaeaeelralgv 149
                                    + d+vlv ++a+ ++++ +g+
  gi|121636693|ref|YP_976916.1| 115 NHDGVLVCTRAVYKHMAKRGG 135
                                    5699********999999886 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.31
                Glyco_trans_4_4   6 yvaelaraLaarGheVtvltpapapg 31 
                                     +++lar+L     ++  ++p+p   
  gi|121636693|ref|YP_976916.1| 163 LTQQLARELGGMKIRINAIAPGPIDT 188
                                    68999999999999999988665222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 1434.76
//
Query:       gi|121636694|ref|YP_976917.1|  [L=295]
Description: dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-37  127.7   0.5    6.8e-37  127.1   0.5    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.7e-10   41.2   1.5    1.5e-09   38.2   1.5    2.3  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.5   7.6e-41   6.8e-37       2     155 ..      10     165 ..       9     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 7.6e-41
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS...HCC CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg...lle 78 
                                    +g+iGlG+ G++ma++ll+    ++v++++ e++  +v+ ga+aa+s++++++ +d++ + v ++++v +vi+    l+ 
  gi|121636694|ref|YP_976917.1|  10 LGYIGLGNQGAPMAKRLLDWPGGLTVFDVRVEAMAPFVEGGATAAASVSDVAE-ADIISITVFDDAQVSSVITAdngLAT 88 
                                    79***********************************************9876.5******************9999*** PP

                                    C--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEE CS
                  NAD_binding_2  79 alkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvth 155
                                    ++k+g+i+  +st++ +++ +la++lk +g++++daPVSGG++ A+kG+L++mvG+++eaf+r+k+ ++++++ ++h
  gi|121636694|ref|YP_976917.1|  89 HAKPGTIVAIHSTIADTTAVDLAEKLKPQGIHIVDAPVSGGAAAAAKGELAVMVGADDEAFQRIKEPFSRWASLLIH 165
                                    ***********************************************************************997774 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.5   1.6e-13   1.5e-09       1     104 [.     170     280 ..     170     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.6e-13
                 NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinas...s..grsnalenk.lpqrvlsr.dfdpgFaldl 73 
                                    GaG+ +Kl+ n+l+ ++ aaa+Ea  lae++Gld+ ++ +v+++s   +  +++ +++n   p  +++  +   + + +l
  gi|121636694|ref|YP_976917.1| 170 GAGTRMKLARNMLTFVSYAAAAEAQRLAEACGLDLVALGKVVRHSdsfTggAGAIMFRNTtAPMEPADPlRPLLEHTRGL 249
                                    9*****************************************98733321133344443323333332202223556789 PP

                 NAD_binding_11  74 mlKDlglalelareagaplpllalaeqlyaa 104
                                      KDl+lal+l++ + ++lpl++la q +aa
  gi|121636694|ref|YP_976917.1| 250 GEKDLSLALALGEVVSVDLPLAQLALQRLAA 280
                                    9************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1909.56
//
Query:       gi|121636695|ref|YP_976918.1|  [L=144]
Description: 4-carboxymuconolactone decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-09   36.9   0.1    7.7e-09   35.5   0.0    1.8  2  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   4.3e-13   7.7e-09       2      74 ..      27     100 ..      26     110 .. 0.93
   2 ?   -1.6   0.0      0.17     3e+03      43      59 ..     112     128 ..     102     138 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.3e-13
                                    HHHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHH.HTT--HHHHHHHHHHHHHHHSHH CS
                            CMD   2 ellraltalrealla.reggLdpkereLialavsaangceyCvdaHtraAl.eaGvteeeiaevlaqaaayagwp 74 
                                    e++++++++ ++ ++ r+g L+ ++r ++ +av++a+g+ + + + ++a l ++ +t +e++e++     y g+p
  gi|121636695|ref|YP_976918.1|  27 EFFALTVDHLFGRIWtRPG-LSMRDRRMAVIAVLTAQGQSDLLEVQVNAVLhNDELTIDELRELAVFITHYVGFP 100
                                    789999*********9988.*********************66******99899**********99999999887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHTT--HHH CS
                            CMD  43 vdaHtraAleaGvteee 59 
                                    v+a  ++A e+G  ++ 
  gi|121636695|ref|YP_976918.1| 112 VAAKRKQAAENGSLPDT 128
                                    45555666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 943.14
//
Query:       gi|121636696|ref|YP_976919.1|  [L=422]
Description: phosphoribosylamine--glycine ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-61  204.9   0.0    1.3e-60  204.5   0.0    1.2  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
      1e-29  103.2   0.7    2.5e-29  101.9   0.7    1.7  1  GARS_N       Phosphoribosylglycinamide synthetase, N domain
    2.5e-24   85.4   0.4    2.5e-24   85.4   0.4    1.8  2  GARS_C       Phosphoribosylglycinamide synthetase, C domain
     0.0017   18.4   0.0     0.0044   17.1   0.0    1.7  2  ATP-grasp_3  ATP-grasp domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.5   0.0     3e-64   1.3e-60       1     194 []     101     292 ..     101     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 3e-64
                                    HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE....EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                         GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeataka....lVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                    +sK+fakd++++ag++ta+ e +++p+++++ +++++ +a    +VvK+d+laagKgv+v+++++ a ++ + +le    
  gi|121636696|ref|YP_976919.1| 101 GSKAFAKDVMAAAGVRTANSEIVDSPAHLDAALDRFGPPAgdpaWVVKDDRLAAGKGVVVTADRDVARAHGAALLE---- 176
                                    69*********************************988777777****************************9995.... PP

                                    CCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHH CS
                         GARS_A  77 GeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptve 156
                                      ag+ v++E++l+G Evsl+++vd + v+pl +aqd+krv+e D+g+nTGGmGay+p+p+++++++++++++i+ep++ 
  gi|121636696|ref|YP_976919.1| 177 --AGHPVLLESYLDGPEVSLFCVVDRTVVVPLLPAQDFKRVGEDDTGLNTGGMGAYAPLPWLPDNIYREVVSRIVEPVAA 254
                                    ..99**************************************************************************** PP

                                    HHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                         GARS_A 157 glkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                    +l ++g++f+G+Ly+gl +++ gp+v+efn+RfgDpet
  gi|121636696|ref|YP_976919.1| 255 ELVRRGSSFCGLLYVGLAITARGPAVVEFNCRFGDPET 292
                                    *************************************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.7   5.6e-33   2.5e-29       1      90 []       1     100 [.       1     100 [. 0.94

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 5.6e-33
                                    EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG...........TTHHHHHHHHHHCTESEEEE-SHHHHHTTHHH CS
                         GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvapgNagt...........edlealvefakeekidlvvvGpeapLvaGvad 69 
                                    m+vLv+GsG+Rehal  +l ++p+v+ ++vapgNagt           +++ea+v++a+e ++d+vv+Gpe pLv Gvad
  gi|121636696|ref|YP_976919.1|   1 MRVLVIGSGAREHALLLALGKDPQVSGLIVAPGNAGTariaeqhdvdiTSAEAVVALAREVGADMVVIGPEVPLVLGVAD 80 
                                    9************************************9999887766655568*************************** PP

                                    HHHHHHT-EEES--CCCCHHH CS
                         GARS_N  70 aleeekgikvfGpskeaAqlE 90 
                                    a++++ gi +fGp k+aA++E
  gi|121636696|ref|YP_976919.1|  81 AVRAA-GIVCFGPGKDAARIE 100
                                    **777.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   7.4e+03      36      56 ..      78      98 ..      37     117 .. 0.57
   2 !   85.4   0.4   5.5e-28   2.5e-24       1      80 []     328     414 ..     328     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                   EE-SSEEEEEEEEESSHHHHH CS
                         GARS_C 36 vtsGGRvlavvavgetleeAr 56
                                   v++  R  ++v  g   ++Ar
  gi|121636696|ref|YP_976919.1| 78 VADAVRAAGIVCFGPGKDAAR 98
                                   444555555555555555555 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 5.5e-28
                                    EEEEEEEETTTTSS--ST-EEBS.TTEEEEESSEE......EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE- CS
                         GARS_C   1 avgvvlaskGYPgsyekgkeitg.egvkvfhagtk......lvtsGGRvlavvavgetleeArakayeavkkikfeglfy 73 
                                    av+vvla+++YPg ++ g+++ g e   v+hagt+      +v+sGGRvl+vv++g++l++Ara+aye +++i+++g ++
  gi|121636696|ref|YP_976919.1| 328 AVTVVLAAENYPGRPRVGDVVVGsEAEGVLHAGTTrrddgaIVSSGGRVLSVVGTGADLSAARAHAYEILSSIRLPGGHF 407
                                    79*******************9995567******999***9*************************************** PP

                                    -STTTHH CS
                         GARS_C  74 RkDIGar 80 
                                    R+DIG r
  gi|121636696|ref|YP_976919.1| 408 RSDIGLR 414
                                    *****75 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5   6.9e+03     107     146 ..      33      69 ..      22      78 .. 0.60
   2 !   17.1   0.0   9.7e-07    0.0044      32     159 ..     143     288 ..     119     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                                    EEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS CS
                    ATP-grasp_3 107 GnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd 146
                                    Gn   ++  ++++v  +  e+v +l   a  vG D+v+  
  gi|121636696|ref|YP_976919.1|  33 GNAGTARIAEQHDVDITSAEAVVAL---AREVGADMVVIG 69 
                                    5555555555555555555555555...666777776554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.7e-07
                                    SSEEEEESS-------B--SS--TTE.............EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....... CS
                    ATP-grasp_3  32 kklvvKprdGaggesvrvveekeeaeaaieeve......lvqefieGkplSvsllsdgekvlvlavnrqliekaeke... 102
                                     ++vvK  + a+g++v+v  +++ a a  + +       l+  +++G ++S+ +++d   v++l   + +   +e++   
  gi|121636696|ref|YP_976919.1| 143 PAWVVKDDRLAAGKGVVVTADRDVARAHGAALLeaghpvLLESYLDGPEVSLFCVVDRTVVVPLLPAQDFKRVGEDDtgl 222
                                    579****************99998887777665788999*****************998888888777777666655866 PP

                                    .TEEEEEEES----HHHHHHHHHHHHHTTST........T--EEEEEEEEESS.SEEEEEEESS-- CS
                    ATP-grasp_3 103 .fvyaGnvtpietelkeevvelaeevvekle........glaGyvGvDlvlkdeepyviEvNPRlt 159
                                         G  +p +   ++  +e+++++ve +         +  G++ v l ++  +p v+E N R+ 
  gi|121636696|ref|YP_976919.1| 223 nTGGMGAYAPLPWLPDNIYREVVSRIVEPVAaelvrrgsSFCGLLYVGLAITARGPAVVEFNCRFG 288
                                    66666777777766666666666666555543221433355666667777999***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2893.16
//
Query:       gi|121636697|ref|YP_976920.1|  [L=512]
Description: bifunctional acylase ggtA: cephalosporin acylase + gamma-glutamyltranspeptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-168  560.8   0.0   3.4e-168  560.6   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.6   0.0  1.9e-172  3.4e-168       2     512 .]      22     507 ..      21     507 .. 0.98

  Alignments for each domain:
  == domain 1  score: 560.6 bits;  conditional E-value: 1.9e-172
                                    HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSGGG- CS
                G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktgalav 81 
                                    ++L +GGnAvDAavA+a++l+vvep s+GiG ++f +v+d ++ +   l+a++++P+a+t+++f   g + +++ g+++v
  gi|121636697|ref|YP_976920.1|  22 RMLADGGNAVDAAVATAITLTVVEPVSNGIGSDAFSIVWDGQKLHG--LNASGRSPSAWTPEYF---GGNAVPVLGWNSV 96 
                                    79*****************************************999..7***************...88999******** PP

                                    BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTSEE--HH CS
                G_glu_transpept  82 gVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkagellkqpa 161
                                    +VPG+v++++e+h+++G+lp+++l+epai + r+Gf vs+++a+++a++ + ++++p++a+ F+p g+++k+gel++ p+
  gi|121636697|ref|YP_976920.1|  97 TVPGAVSAWVELHARFGRLPFETLFEPAISYGRNGFLVSPTVAAQWAAQVPLFASQPGFADAFMPGGRAPKPGELFTFPD 176
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHHHHHHHHHHH CS
                G_glu_transpept 162 lAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssggivllqiLni 241
                                    +A+tLe++a ++ e+FY+GelA kl a+ +++gG+++a+DLa+++v+++++++ +y +gyt++++pp+++giv+l +L i
  gi|121636697|ref|YP_976920.1| 177 HAATLEKIAATNGEEFYRGELAAKLEAHSAANGGVMRADDLAAHRVDWVDTITGTY-RGYTIHQIPPNGQGIVALIALGI 255
                                    ********************************************************.99********************* PP

                                    HCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB..SGGGCSCGGC CS
                G_glu_transpept 242 legfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdkaatpsseyykaae 321
                                    le+fd++s+s +sae++h+++Ea+kla+ad++++++D d++++   + ++ll+key+++ra+lI++k+a+p       a+
  gi|121636697|ref|YP_976920.1| 256 LEHFDMSSWSVDSAESVHVQIEALKLAFADAQACVADIDYMPV---HPKRLLDKEYLRQRATLIDPKRAMP-------AA 325
                                    *****************************************95...5***********************9.......47 PP

                                    SCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B--- CS
                G_glu_transpept 322 aaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpspanaiePgkRplssma 401
                                    +  ++ggT++l+ +D+ g++VS++++++l+FGsgvvvpgtGi L+n+++df+        ++p ++n++ P+kRp+++++
  gi|121636697|ref|YP_976920.1| 326 TGIPRGGTVYLAAADAAGMMVSMIQSNYLGFGSGVVVPGTGISLHNRGSDFT--------VVPRHPNRVGPRKRPYHTII 397
                                    8899************************************************........******************** PP

                                    -EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEESSSSTEEEESTTS.HHHHHHHHHTTSEEE CS
                G_glu_transpept 402 PtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihhqllpdkvevEegfseevveeLearGhkvk 481
                                    P++v++dg pv+ +G++GG++++++++qvlv++ d+g+++q+a+d pr+ +    ++v++E+gf++++++eL++rGh++ 
  gi|121636697|ref|YP_976920.1| 398 PGFVTRDGAPVMSFGVMGGMMQPQGHVQVLVRIADYGQNPQAACDGPRFRWV-NGMRVSFENGFPDSTLDELRQRGHDLV 476
                                    ***************************************************5.578************************ PP

                                    ESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
                G_glu_transpept 482 evedsssvvaavavakekgvleaasDprkdg 512
                                     v+d s++++++a+++ ++ + aasDpr+dg
  gi|121636697|ref|YP_976920.1| 477 AVADYSQFGSCQAIWRLDDGYLAASDPRRDG 507
                                    *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3246.30
//
Query:       gi|121636698|ref|YP_976921.1|  [L=303]
Description: hypothetical protein BCG_0826c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-08   34.9   0.5    5.1e-08   32.9   0.5    1.9  1  Esterase       Putative esterase
     0.0051   16.5   0.7     0.0082   15.8   0.7    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.011   15.0   0.1      0.022   14.0   0.1    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
      0.022   13.7   0.0      0.027   13.4   0.0    1.1  1  Asp2           Accessory Sec system GspB-transporter
      0.037   13.8   0.4        5.1    6.8   0.0    2.2  2  Abhydrolase_2  Phospholipase/Carboxylesterase
        0.2   11.1   0.1       0.31   10.5   0.1    1.3  1  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.5   1.7e-11   5.1e-08       9     199 ..      87     260 ..      79     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.7e-11
                                    EEEEEE.CC.GGTTTEEEEEEE--T...THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEEE CS
                       Esterase   9 kvqvyLPedyspgrkypvvylldGl...tgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgarfyena 85 
                                    + ++  P++  +++ +  v++l+Gl    +   ++ ++++l +++  g +++ ++v v+ g  +     w++        
  gi|121636698|ref|YP_976921.1|  87 NWAIARPPG--QTQALRPVIALHGLggsASAVMDGGVEQGLAQAVNAG-LPPFAVVSVDGGSSY-----WHQR------- 151
                                    556666777..66667778899***999889999*******9999885.777777766666666.....8755....... PP

                                    TTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHC.STTTCCEEEEES--S-CCHCHHHC.TTCC CS
                       Esterase  86 tegpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalk.hpdrFgsvssfSpivnpsnamWgq.eeke 163
                                          e+    + +eL plld+++  +++  a +G SmGG+gAL+l+++  p r + + + Sp + +s+    + + ++
  gi|121636698|ref|YP_976921.1| 152 ---ASGEDAGAMVLNELIPLLDTQRLDTSR-VAFLGWSMGGYGALLLGSRlGPARTAAICAVSPALWLSAGAVAPgSFDG 227
                                    ...33344456899********99887777.9******************889***9******88777755555543333 PP

                                    HHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHT CS
                       Esterase 164 awqendpvllakelsaslkalriyldvGtseddlge 199
                                        +d  ++ +     l  + i +d G+s+++++ 
  gi|121636698|ref|YP_976921.1| 228 ---PDDWSANSVFGLPALGSIPIRVDCGNSDPFYAA 260
                                    ...344444445555678888999999999986653 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   2.8e-06    0.0082       2     125 ..     102     222 ..     101     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
                                    EEEEE-STTTCGGGGTTGHHHHHHHHT......TSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH.HHHCTTSS CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakd......gfdvillDlrGvgySspapacinddygtasvaddldri.ldalgddk 74 
                                    +++ lhGl+gs+   +  g+ ++La++       f v+ +D   + + ++a+    +d g + +++ +  +  ++l+  +
  gi|121636698|ref|YP_976921.1| 102 PVIALHGLGGSASAVMDGGVEQGLAQAvnaglpPFAVVSVDGGSSYWHQRASG---EDAGAMVLNELIPLLdTQRLDTSR 178
                                    79999*****8888777778888888888889999999999777777777777...7888888999999999******** PP

                                    EEEEEETHHHHHHHHHHHHH.GGGEEEEEEESECSSCCHHHHHHHHHHHHHH CS
                  Abhydrolase_1  75 ltlvGhSmGGmialayaaey.perVkalvllgaidpaaslieaqrqqaksfp 125
                                    ++ +G+SmGG  al + ++  p r +a+ ++++         +++ + +  p
  gi|121636698|ref|YP_976921.1| 179 VAFLGWSMGGYGALLLGSRLgPARTAAICAVSP--------ALWLSAGAVAP 222
                                    ****************************99999........44444444444 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.5e-06     0.022      74     116 ..     175     218 ..     155     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
                    Hydrolase_4  74 pelplfllGhSmGGliallyl.lrypdkvaglilsaPalkikak 116
                                     ++++  lG SmGG+ all++    p++ a++  ++Pal++ a 
  gi|121636698|ref|YP_976921.1| 175 DTSRVAFLGWSMGGYGALLLGsRLGPARTAAICAVSPALWLSAG 218
                                    3458899**************7677778889999*****99865 PP

>> Asp2  Accessory Sec system GspB-transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.1e-06     0.027     337     379 ..     159     201 ..     135     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                           Asp2 337 ekiikiikekleeLgfeeeqlilsGlSMGtfgalyYgaklnph 379
                                    + +++ +   l++ +++ + + + G SMG +gal  g++l p+
  gi|121636698|ref|YP_976921.1| 159 AMVLNELIPLLDTQRLDTSRVAFLGWSMGGYGALLLGSRLGPA 201
                                    446666667789999*************************985 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0043        13      15      54 ..     101     147 ..      86     155 .. 0.70
   2 ?    6.8   0.0    0.0017       5.1      86     142 ..     158     215 ..     136     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0043
                                    EEEEEE--TT--S.......HHHHHHHH.TT--TTEEEEEE---EEE CS
                  Abhydrolase_2  15 avviflHGlGdsg.......hawaeaakteaalpnikfifphgpelp 54 
                                      vi lHGlG s+         +++a++++a lp+++ ++  g + +
  gi|121636698|ref|YP_976921.1| 101 RPVIALHGLGGSAsavmdggVEQGLAQAVNAGLPPFAVVSVDGGSSY 147
                                    459*******9996666555556667777777888877777777666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                                    HHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-.SS--SEEEEES---TT CS
                  Abhydrolase_2  86 saekleelidaelkkgipssriiigGFSqGaalalylaltl.pkklggivafsgalpl 142
                                     a  l+eli    ++ ++ sr+++ G S+G+  al l+  l p + + i a+s al l
  gi|121636698|ref|YP_976921.1| 158 GAMVLNELIPLLDTQRLDTSRVAFLGWSMGGYGALLLGSRLgPARTAAICAVSPALWL 215
                                    55567777777778889**************999988766525578888888777665 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0001      0.31      56      83 ..     169     196 ..     139     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                    HHTTS--GGGEEEEEETHHHHHHHHHHH CS
                   Peptidase_S9  56 akegyvdserlaitGgSyGGyltgaaln 83 
                                     +++  d++r+a  G+S GGy ++ +  
  gi|121636698|ref|YP_976921.1| 169 LDTQRLDTSRVAFLGWSMGGYGALLLGS 196
                                    566788***************8876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1838.54
//
Query:       gi|121636699|ref|YP_976922.1|  [L=207]
Description: hypothetical protein BCG_0827 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-16   61.1   5.5      1e-16   61.1   5.5    2.2  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
    1.2e-08   34.6   0.6    2.2e-08   33.8   0.6    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.8      0.19   1.7e+03      62      62 ..      43      43 ..      13      86 .. 0.58
   2 !   61.1   5.5   1.1e-20     1e-16       1     106 [.      88     195 ..      88     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.19
                                   H CS
                      TetR_C_31 62 l 62
                                   +
  gi|121636699|ref|YP_976922.1| 43 A 43
                                   2 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 1.1e-20
                                    -TCCHHHHHHHHHCCCCCT...THHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHHHH CS
                      TetR_C_31   1 adreeladlladlldrala...drertlAryelfleaarrPeLraalarlrralrealaallaalGlpdpeeaarllvaa 77 
                                    +++e++a +l+dll + ++     e+++ rye++++++r P+Lr++++r+ r+ +ea+a++ +++G+ ++ e + +l+ a
  gi|121636699|ref|YP_976922.1|  88 RGPETTAVVLVDLLVGEMSspgLAEQLISRYERHIACTRLPDLRESMRRSLRQRAEAVAEAIERSGRSAQIELVCTLICA 167
                                    578999********8877779999*******************************************65656******** PP

                                    HHHHHHHHHHSGTS-HHHHHHHHHHHHT- CS
                      TetR_C_31  78 ldGllldrLagpaadpraevrellralld 106
                                    +dG ++++L+++ +dpra++ + + +l+d
  gi|121636699|ref|YP_976922.1| 168 VDGSVVSALVEG-RDPRAAALATVVDLID 195
                                    ***********8.8999999998888876 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.6   2.4e-12   2.2e-08       1      46 [.      18      63 ..      18      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.4e-12
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   +++aA+el++e G++a+  r++A+rAG+  ++  +yF+s ++L+++
  gi|121636699|ref|YP_976922.1| 18 LVSAAAELLGEGGFEAVRHRAVARRAGLPLASTTYYFSSLDDLIAR 63
                                   579************************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1375.96
//
Query:       gi|121636700|ref|YP_976923.1|  [L=259]
Description: hypothetical protein BCG_0828c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-32  110.6   8.6      1e-31  110.4   8.6    1.1  1  DUF429    Protein of unknown function (DUF429)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   8.6   5.8e-36     1e-31       1     198 [.       5     220 ..       5     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 5.8e-36
                         DUF429   1 GvDla..gcrtgwaavaledgrlrlvdv...eae.eivaalaallaaaeeaavvaiDaPiglperetggRaaDraarkll 74 
                                    GvDla  g++++++a++  d+++ lv v   +++  ++aal+ +     ++++va DaP+ +  ++tg+R+a++a+++++
  gi|121636700|ref|YP_976923.1|   5 GVDLAwaGRNPTGVAAV--DADGCLVGVgaaRDDaSVLAALRPY---VVGDCLVAFDAPLVVA-NRTGQRPAEAALNRDF 78 
                                    9******6665555555..6667777776433337888888888...799************9.**************** PP

                         DUF429  75 arrgasvfpvpar.aalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkkktaeg.. 151
                                    +++ a+++p+++  +++a+     +ra++l+++l+    ++d+ +++ +r++Ev+P++a+val+++ + +k+k  ++g  
  gi|121636700|ref|YP_976923.1|  79 RQFEAGAYPANTEkPEFADV----PRAARLARQLA---LDMDPLSSATRRAIEVYPHPATVALFRLPRALKYK-AKPGrs 150
                                    *************9898888....9**********...778999*****************************.567767 PP

                         DUF429 152 .raeRrellara......................iaellleseakkeklvaadDvlDAvacaltArraar 198
                                        + ell+++                        + +++ +++k+ l+aa+D +DAv+ca++A +a+r
  gi|121636700|ref|YP_976923.1| 151 vDLLKSELLRLMdgveglaqagvrmqvagqpdwvSLRRQVTVAQRKSDLRAAEDPIDAVVCAYVALYAQR 220
                                    788999999999********************7533445555559**********************944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1579.31
//
Query:       gi|121636701|ref|YP_976924.1|  [L=472]
Description: adenylosuccinate lyase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-24   85.6   0.0    5.6e-24   85.1   0.0    1.2  1  Lyase_1   Lyase
    3.7e-14   53.0   0.7    2.1e-13   50.6   0.7    2.4  1  ADSL_C    Adenylosuccinate lyase C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   6.3e-28   5.6e-24      29     307 ..      30     296 ..      12     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6.3e-28
                                    HCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT CS
                        Lyase_1  29 ikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtg 108
                                    ++   a+ +a a+++v +   a+++++  + v+++++l     +   ++   ++v+++++e+ +      ++  ++vh+g
  gi|121636701|ref|YP_976924.1|  30 RRLWLAVLRAQAELGVAV---ADSVLADYERVVDDVDLA---SISARERVLRHDVKARIEEFNA------LAGHEHVHKG 97 
                                    334556678999999999...999999999999977777...9*********************......7889****** PP

                                    --HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHH CS
                        Lyase_1 109 qSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlke 188
                                     +s D  +   +l+++++l e++ ++    +  l e+a+ ++d +++Gr h   A+++tlg+ ++++a+++   + rl+e
  gi|121636701|ref|YP_976924.1|  98 MTSRDLTENVEQLQIRRSL-EVIFAHGVAAVARLAERAVSYRDLIMAGRSHNVAAQATTLGKRFASAAQEMMIALRRLRE 176
                                    *******************.99********************************************************** PP

                                    HHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHH..HHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHH CS
                        Lyase_1 189 llkrllvellgggtavgtglnadpefaelvakela..kvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeD 265
                                    l +r+ +  ++g  ++g+ +      +++  + l+    + l+  +  ns+ +v +r    ++++al  l +  s +a  
  gi|121636701|ref|YP_976924.1| 177 LIDRYPLRGIKGPMGTGQDMLDLLGGDRAALADLErrVADFLGfATVFNSVGQVYPRSLDHDVVSALVQLGAGPSSLAHT 256
                                    *****9999998666666543333334445555554333455667789******************************** PP

                                    HHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHH CS
                        Lyase_1 266 lrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgva 307
                                    +rl++     l ++ +a ++ GSS MP+K N  ++E ++g  
  gi|121636701|ref|YP_976924.1| 257 IRLMAG--HELATEGFAPGQVGSSAMPHKMNTRSCERVNGLQ 296
                                    ******..67889999********************999875 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.7   2.4e-17   2.1e-13       1      73 []     366     449 ..     366     449 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.4e-17
                                    TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC.........HHHHHHT-HHHHCHHCHHHHHT.-GGGCCTTHHHH CS
                         ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee.........llelLaadpevkkseeeldalf.dpayylgsadei 69 
                                    +++++ +vl+a+v +g+gRe A++l+ e+a +++           ll++Laadp++ + +++l+a++ d +++ g+a+ +
  gi|121636701|ref|YP_976924.1| 366 PFLATTKVLMAAVrAGMGRESAHRLISEHAVATALAmrehgaepdLLDRLAADPRLPLGRDALEAALaDKKAFAGAAGDQ 445
                                    6899*********66*****************999999*******************84458998888************ PP

                                    HHHH CS
                         ADSL_C  70 vdrv 73 
                                    vd v
  gi|121636701|ref|YP_976924.1| 446 VDDV 449
                                    *986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2777.01
//
Query:       gi|121636702|ref|YP_976925.1|  [L=414]
Description: cytochrome P450 126 cyp126 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-24   84.6   0.0    8.9e-22   77.5   0.0    2.6  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0     0.064   1.2e+03      83     131 ..      91     139 ..      62     161 .. 0.75
   2 !   77.5   0.0     5e-26   8.9e-22     240     433 ..     220     384 ..     196     402 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.064
                                    TTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHC CS
                           p450  83 kgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrk 131
                                     g+ + +++ ++++++Rr++   lt   ++++e+ + + a+ l++ +++
  gi|121636702|ref|YP_976925.1|  91 AGQVLNMMDDPRHTRIRRLVSSGLTPRMIRRVEDDLRRRARGLLDGVEP 139
                                    5566667778999999999999999886667777777777777766665 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 5e-26
                                    SHHHHHHHHC.TTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHC CS
                           p450 240 dfldalllak.kekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddl 318
                                    d+l+++ +a+ ++ + +  lsd+el      l+ aG +Tt + ++ +L+ La+nP+  + lr +                
  gi|121636702|ref|YP_976925.1| 220 DMLSVVANATiDDPDAP-ALSDAELYLFFHLLFSAGAETTRNSIAGGLLALAENPDQLQTLRSD---------------- 282
                                    55555666655555666.9*************************************99999877................ PP

                                    CT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESS CS
                           p450 319 qklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrk 398
                                       ++l  +i+E+ R  +++p +  R +++ v+++g  i++G++v+v+ ++ +r p+vf++++eFd+ R          k
  gi|121636702|ref|YP_976925.1| 283 --FELLPTAIEEIVRWTSPSP-SKRRTASRAVSLGGQPIEAGQKVVVWEGSANRGPSVFDRADEFDITR----------K 349
                                    ..78*****************.889*****************************************986..........5 PP

                                    CTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHE CS
                           p450 399 sfaflPFGaGpRnCiGerlArmelklflatlLqnF 433
                                    +  +l+FG G++ C+G +lAr+el++++  lL++F
  gi|121636702|ref|YP_976925.1| 350 PNPHLGFGQGVHYCLGANLARLELRVLFEELLSRF 384
                                    6789******************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2482.87
//
Query:       gi|121636703|ref|YP_976926.1|  [L=206]
Description: hypothetical protein BCG_0831c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1434.76
//
Query:       gi|121636704|ref|YP_976927.1|  [L=297]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-95  319.8   0.0    1.5e-95  319.6   0.0    1.0  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.6   0.0  8.4e-100   1.5e-95       2     251 ..      11     260 ..      10     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.6 bits;  conditional E-value: 8.4e-100
                                    EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH--BSEEEE.........-SSSEE CS
                    SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklekipnhliksld....peqlegrsm 77 
                                    +++GKvr++Y++ dd++lllva+DrisA+d+vl+++ip+KG+vlt++saf+f +++  pnhl   +d    p+++ gr++
  gi|121636704|ref|YP_976927.1|  11 VASGKVREIYRV-DDEHLLLVASDRISAYDYVLDSTIPDKGRVLTAMSAFFFGLVDA-PNHLAGPPDdpriPDEVLGRAL 88 
                                    799********9.888*************************************9975.*****77668666559****** PP

                                    EEE-EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT-HH CS
                    SAICAR_synt  78 lvkklkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvealgtee 157
                                    +v++l+mlpvE+v+RgyltGs++ +y+++gkvcgi+lp+gl e++++ +p+ftp+tKa+ g+hDenis+++vve++g + 
  gi|121636704|ref|YP_976927.1|  89 VVRRLEMLPVECVARGYLTGSGLLDYQATGKVCGIALPPGLVEASRFATPLFTPATKAALGDHDENISFDRVVEMVG-AL 167
                                    *****************************************************************************.99 PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT CS
                    SAICAR_synt 158 eaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdw 237
                                     a+++++ +l+ y +aa++a +rgii++DtK+EFG+d+ +g+l+LaDe++tpDssR+w+a++y++g  q+s+DKqfvR+w
  gi|121636704|ref|YP_976927.1| 168 RANQLRDRTLQTYVQAADHALTRGIIIADTKFEFGIDR-HGNLLLADEIFTPDSSRYWPADDYRAGVVQTSFDKQFVRSW 246
                                    *************************************6.9**************************************** PP

                                    -STHHHHHHHHHHH CS
                    SAICAR_synt 238 leeveekwkekler 251
                                    l+  e++w++  +r
  gi|121636704|ref|YP_976927.1| 247 LTGSESGWDRGSDR 260
                                    ********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2422.90
//
Query:       gi|121636705|ref|YP_976928.1|  [L=719]
Description: protease II ptrB (oligopeptidase B) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.5e-119  398.8   0.0   3.1e-119  398.5   0.0    1.1  1  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
    8.8e-64  214.9   0.0    1.6e-63  214.0   0.0    1.4  1  Peptidase_S9    Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.044   13.6   0.0    1.4  1  Abhydrolase_3   alpha/beta hydrolase fold
      0.046   12.4   0.0      0.073   11.7   0.0    1.3  1  AXE1            Acetyl xylan esterase (AXE1)
      0.065   12.9   0.0       0.13   11.9   0.0    1.4  1  Abhydrolase_1   alpha/beta hydrolase fold
      0.099   12.3   0.0       0.24   11.0   0.0    1.5  1  Esterase        Putative esterase
       0.15   11.3   0.0       0.25   10.6   0.0    1.3  1  Hydrolase_4     Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.5   0.0  1.2e-122  3.1e-119       1     414 []      10     428 ..      10     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 398.5 bits;  conditional E-value: 1.2e-122
                                    ------TT.EEEETTEEEE-TTGGGGSTTSHHHHHHHHHHHHHHHHHHCTST.CHHHHHHHHHHHT-S-EE---EEETTE CS
                 Peptidase_S9_N   1 PetardesvvdelhgdkvsDpYrWLeDddspetkayleaenkyteevlaqlkelrekikeeitklikeddisapfrkgky 80 
                                    P++a++ ++ +e+hgd+++DpY+WL+D+dspe+ ayleaen+yte+ +a+l++lr+ki+ ei++++ke+d+s+p+r+g++
  gi|121636705|ref|YP_976928.1|  10 PPVAKRVQTRREHHGDVFVDPYEWLRDKDSPEVIAYLEAENDYTERTTAHLEPLRQKIFHEIKARTKETDLSVPTRRGNW 89 
                                    788899999*********************************************************************** PP

                                    EEEEEE-SS-SS-EEEEEC.STS-TT...........S-EEEEE-GGGGSTTS-.EEEEEEEE-TTSSEEEEEEEETTSS CS
                 Peptidase_S9_N  81 yyysrneggknqsvlyrqd.alskeg...........eeeevlLDpNtlsedgtfvalgefavsedgkllAyslsksGsd 148
                                    +yy r+ +gk++ v++r++ + ++++           + e++lLD+N  +++++f+alg+ +vs d +llAys++ +G++
  gi|121636705|ref|YP_976928.1|  90 WYYARTFEGKQYGVHCRCPvTDPDDWnppefderteiPGEQLLLDENVEADGHDFFALGAASVSLDDNLLAYSVDVVGDE 169
                                    ******************9988899999999999999******************************************* PP

                                    EEEEEEEETTTTEEEEEEEEEEESEEEEECTTSSEEEEEESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGT CS
                 Peptidase_S9_N 149 wytirvkdietgedlpdeledvkfsgivWaadekgffYtrydkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeep 228
                                    +yt+r+kd++tge++pde+ ++    ++Waad+++++Yt++d    r+d       +v+r +LG+++s+ e v++e++++
  gi|121636705|ref|YP_976928.1| 170 RYTLRFKDLRTGEQYPDEIAGIGAG-VTWAADNRTVYYTTVD-AAWRPD-------TVWRYRLGSGESS-ERVYHEADDR 239
                                    ***********************99.****************.99****.......*************.8899967777 PP

                                    TBEEEEEE-TTSSEEEEEEESSSS--EEEEEEGGGTSS--EEEEESSSSS.-EEEEEE...ETTEEEEEE-TT-TT-EEE CS
                 Peptidase_S9_N 229 kwllgaersedgkylfissasgtdtnelyvldlekeskkvlklvdnrfda.eysvehn...egdrfliltndgapnfrlv 304
                                     wl+ + r+++++yl+i+++s++ t+e++++ + +++ +++ +v +r+d+ eysveh     +drflil+ndga+nf+lv
  gi|121636705|ref|YP_976928.1| 240 FWLA-VGRTRSNAYLLIAAGSSI-TSEVRYAHAADPT-AQFSVVLPRRDGvEYSVEHAviaGQDRFLILHNDGAVNFTLV 316
                                    7777.******************.************9.7777777779999******976678***************** PP

                                    EEETTSSSGGGEEEEE--.SSCEEEEEEECTTEEEEEEEETTEEEEEEEETTTS-.......EEEEEB-SSSSEEEEEE- CS
                 Peptidase_S9_N 305 svdlndpspsewkelvperekvvleeitvfknylvvsyrkdvlsrvqvvdlkngkv......llfevplpgvgsvssasg 378
                                    +++++dp+  ++++l+++r++v l+ ++  +++lvvsyr+++l+rvq+++++++++      ++f+ +l  ++   + + 
  gi|121636705|ref|YP_976928.1| 317 EAPVEDPA--RQRTLIAHRDDVRLDAVDALAGHLVVSYRREALPRVQLWPIGPDGNygepeeISFDSEL--MSAGLGPNP 392
                                    *******9..89*******************************************99************..777789999 PP

                                    -TT-SEEEEEEEETTCEEEEEEEETTTTCEEEEEEE CS
                 Peptidase_S9_N 379 ekedselfysfsSfltPstiykldlatgelellker 414
                                    ++++++l++   Sf+tP +iy++dl tge++llke+
  gi|121636705|ref|YP_976928.1| 393 NWDSPKLRVGAGSFVTPVRIYDIDLVTGERTLLKEQ 428
                                    9********************************986 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.0   0.0   6.1e-67   1.6e-63       1     209 [.     484     700 ..     484     703 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 6.1e-67
                                    ----.HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                   Peptidase_S9   1 psfs.selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                    p+fs  +l+ll drG+v+vva++rG+g++G+ ++++gk   ++n+f+Dfia+a++l+++g++++++l++ GgS+GG+l+g
  gi|121636705|ref|YP_976928.1| 484 PRFSiARLSLL-DRGMVFVVAHVRGGGEMGRLWYENGKLLDKKNTFTDFIAVARHLVDTGLTSQQQLVALGGSAGGLLMG 562
                                    57898999999.******************************************************************** PP

                                    HHHHH-GGG-SEEEEESE---CCCHHCSTTS.THH.HCCCC--TTTCHHHHHHHHHH-CGGG--..---EEEEEEETT-S CS
                   Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsdtdl.lte.eymewgnpeeneegykelspyspldnvk..aypplLlihGlaDd 155
                                    a++n++pdlF++++a+vp+vd l++ +d++l lt  e++ewgnp ++ + y ++++ysp++nv+  +yp++L +++l+D+
  gi|121636705|ref|YP_976928.1| 563 AVANMAPDLFAGILAQVPFVDPLTTILDPSLpLTVtEWDEWGNPLNDSDVYAYVKSYSPYENVTaqKYPAILAMTSLNDT 642
                                    ********************************9999******************************************** PP

                                    SS-THHHHHHHHHHH..--S-S.EEEEEETTS-SSTTSSHHHH.HHHHHHHHHHHHHC CS
                   Peptidase_S9 156 rvppaealklvaaLq..kkgkn.vlllifpdegHgvgkprakv.eelarllaFlkeal 209
                                    rv + e++k+vaaL+  k++ n vll++ + +gHg+ ++r+++ +e+a  + +l+ + 
  gi|121636705|ref|YP_976928.1| 643 RVYYVEPAKWVAALRhaKTDGNsVLLKTQMHAGHGGISGRYERwKETAFQYGWLLATA 700
                                    ****************9777777*******************************9765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-05     0.044      49     154 ..     528     630 ..     525     657 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SST.SSTTSHHHHHCHHT. CS
                  Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdl.ertesesikkaeel. 126
                                    + d +a++r+l+++     + ++++v +G SaGG l+ ava +a d      ag++   P +d+ ++   +s  ++ ++ 
  gi|121636705|ref|YP_976928.1| 528 FTDFIAVARHLVDTG---LTSQQQLVALGGSAGGLLMGAVANMAPDL----FAGILAQVPFVDPlTTILDPSLPLTVTEw 600
                                    678899999999984...366789999999****************7....55555555544444333344443333331 PP

                                    .TTSSSSCHHHHHHHHHHHSS.GGGGGSTT CS
                  Abhydrolase_3 127 .adgplltraaldlfwrlylp.eadrddpl 154
                                     + g  l+ +++ ++++ y p e+  ++ +
  gi|121636705|ref|YP_976928.1| 601 dEWGNPLNDSDVYAYVKSYSPyENVTAQKY 630
                                    222334566777778888887433333444 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05     0.073     152     208 ..     525     582 ..     499     599 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-.SEEEEES-SS CS
                           AXE1 152 rrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekri.kavvadyPfL 208
                                    ++ f+D + +++ + +   + ++ +++lG+s GG l  ava + +++ + ++a++Pf+
  gi|121636705|ref|YP_976928.1| 525 KNTFTDFIAVARHLVDTGLTSQQQLVALGGSAGGLLMGAVANMAPDLfAGILAQVPFV 582
                                    689****************************************998636799*****7 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     5e-05      0.13      69     109 ..     543     584 ..     492     619 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                                    HCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.CSS CS
                  Abhydrolase_1  69 algddkltlvGhSmGGmialayaaeyperVkalvllga.idp 109
                                     + +++l+ +G+S GG+++ a+a ++p+  +++ +  + +dp
  gi|121636705|ref|YP_976928.1| 543 LTSQQQLVALGGSAGGLLMGAVANMAPDLFAGILAQVPfVDP 584
                                    57899*************************999998886443 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.3e-05      0.24      89     174 ..     523     606 ..     497     651 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.3e-05
                                    CCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHHHCTTCCHHHCC CS
                       Esterase  89 pgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamWgqeekeawqen 168
                                    +++  +++f++     l+d+ + ++++  +++G S GGl    +a  +pd+F+ ++++ p+v+p   + +++   +  e+
  gi|121636705|ref|YP_976928.1| 523 DKKNTFTDFIAVA-RHLVDTGLTSQQQ-LVALGGSAGGLLMGAVANMAPDLFAGILAQVPFVDPLTTILDPSLPLTVTEW 600
                                    5555555555432.3466666666666.99*********98888899*****************9777777444344444 PP

                                    -CCCCH CS
                       Esterase 169 dpvlla 174
                                    d++ + 
  gi|121636705|ref|YP_976928.1| 601 DEWGNP 606
                                    444444 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.8e-05      0.25      27     115 ..     493     586 ..     485     606 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.8e-05
                    Hydrolase_4  27 LaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpel..plfllGhSmGGliallyllrypdkv 101
                                    L ++G+ ++    rG G+ +    + g++ + +   +D+ a+ ++++++  ++  +l+ lG S GGl+  +++ + pd +
  gi|121636705|ref|YP_976928.1| 493 LLDRGMVFVVAHVRGGGEMGrlwYENGKLLDKKNTFTDFIAVARHLVDTGLTSqqQLVALGGSAGGLLMGAVANMAPDLF 572
                                    6778888889999999999888878888888999999*****9999977655445***********************99 PP

                    Hydrolase_4 102 aglilsaPalkika 115
                                    ag+    P++++ +
  gi|121636705|ref|YP_976928.1| 573 AGILAQVPFVDPLT 586
                                    99998888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4657.27
//
Query:       gi|121636706|ref|YP_976929.1|  [L=540]
Description: multidrug resistance integral membrane efflux protein emrB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-50  171.6  47.8    2.2e-50  171.6  47.8    2.4  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.086   12.7   0.5       0.19   11.6   0.5    1.5  1  DUF2826   Protein of unknown function (DUF2826)
       0.45   10.4   3.8       0.36   10.7   0.3    2.6  2  CAAD      CAAD domains of cyanobacterial aminoacyl-tRNA synth
        2.7    6.3  32.5       0.53    8.6  14.0    2.7  3  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.6  47.8     5e-54   2.2e-50       3     352 ..      50     443 ..      47     444 .. 0.86
   2 ?   -2.1   0.1      0.31   1.4e+03     150     179 ..     503     532 ..     492     536 .. 0.56

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 5e-54
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                    la ++++ + +++++a   +   d+g++ +++ + +t+y+l+ a  ++ +G+ +drfG rr+++ ++l+f lg+ll+++a
  gi|121636706|ref|YP_976929.1|  50 LASVMAHVDVTVVSVAQR-TFVADFGSTQAVVAWTMTGYMLALATVIPTAGWAADRFGTRRLFMGSVLAFTLGSLLCAVA 128
                                    556666666666666666.999***************************************************7777767 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    +++ ll+++rv+qG+g+g+l+p++ a++a+ + +++ gr+++++++ + lG++ gp+lgg+l+ ++gWr++f+++ +v+l
  gi|121636706|ref|YP_976929.1| 129 PNILLLIIFRVVQGFGGGMLTPVSFAILAREAGPKRLGRVMAVVGIPMLLGPVGGPILGGWLIGAYGWRWIFLVNLPVGL 208
                                    9999**************************************************************************** PP

                          MFS_1 163 lafvlfllllpeepperkrkspkeee..............................................kgtgpapl 196
                                     a+vl+++++p+++p+ + + +   +                                                + ++pl
  gi|121636706|ref|YP_976929.1| 209 SALVLAAIVFPRDRPAASENFDYMGLlllspglatflfgvssspargtmadrhvlipaitglaliaafvahsWYRTEHPL 288
                                    **********99999999998888889***************************99999999999999999888888888 PP

                          MFS_1 197 vpawkallkdpvlw.illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275
                                    ++  +++ ++ v    + +++l+  +g++g + llp+ylq+vl+ s  +++g+ +   +l+++ ++++ag+++dr g+ +
  gi|121636706|ref|YP_976929.1| 289 ID-MRLFQNRAVAQaNMTMTVLS--LGLFGSFLLLPSYLQQVLHQS-PMQSGVHIIPQGLGAMLAMPIAGAMMDRRGPAK 364
                                    88.66666666553333333333..38999****************.799995555555555555**********99977 PP

                          MFS_1 276 rlllallllllaalglallavtssavllll..vlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    + l+++ l+++++  +a+  + +   l +l  +l+++G+g+g+ + +l  +a++ + p++ ++ s l+++ +++gg++g
  gi|121636706|ref|YP_976929.1| 365 IVLVGIMLIAAGLGTFAFGVARQADYLPILptGLAIMGMGMGCSMMPLSGAAVQTLAPHQIARGSTLISVNQQVGGSIG 443
                                    77777776666666666666665555555578************88888888888878*******************99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.31
                          MFS_1 150 Wravfyilaivsllafvlfllllpeepper 179
                                      av +++a +++++ ++ +++lp  + ++
  gi|121636706|ref|YP_976929.1| 503 AYAVVFVIATALVVSTLIPAAFLPKQQASH 532
                                    445555555555555566666666666555 PP

>> DUF2826  Protein of unknown function (DUF2826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   4.2e-05      0.19      63     146 ..      28     115 ..      25     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                        DUF2826  63 ecsrhyfarllftalrqidasppesfaa.apcvvlpaqdsrvvlrladsqaplrwdmqgcglpl.tvlgtavwm..rrph 138
                                       r y  rl    lr        s  a   ++v+   + + v  +  +qa + w m g  l l tv+ ta w   r   
  gi|121636706|ref|YP_976929.1|  28 SGQRSYPDRLDVGLLRTAGVCVLASVMAhVDVTVVSVAQRTFVADFGSTQAVVAWTMTGYMLALaTVIPTAGWAadRFGT 107
                                    56788889999999999999988887651566778888888999******************98689******7324455 PP

                        DUF2826 139 ermycgti 146
                                     r++ g++
  gi|121636706|ref|YP_976929.1| 108 RRLFMGSV 115
                                    67777765 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   7.9e-05      0.36      13      54 ..     364     405 ..     352     408 .. 0.88
   2 ?   -1.6   0.3      0.57   2.5e+03      11      29 ..     501     519 ..     493     524 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.9e-05
                           CAAD  13 klkviglilaaivalklalavldaiddiPllpplleLvGlgy 54 
                                    k+ ++g++l+a     +a++v +  d +P+lp+ l + G+g 
  gi|121636706|ref|YP_976929.1| 364 KIVLVGIMLIAAGLGTFAFGVARQADYLPILPTGLAIMGMGM 405
                                    5678889999999999***********************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.57
                           CAAD  11 erklkviglilaaivalkl 29 
                                      +++v+++i++a+v+  l
  gi|121636706|ref|YP_976929.1| 501 SHAYAVVFVIATALVVSTL 519
                                    5566666777666666555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  14.0   0.00012      0.53      17     180 ..      50     208 ..      43     230 .. 0.86
   2 ?   -1.4   0.2      0.12   5.5e+02     255     302 ..     230     278 ..     207     285 .. 0.80
   3 ?    6.0   7.0   0.00075       3.4      34     164 ..     322     452 ..     297     465 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00012
                          MFS_3  17 iaslvsnlGtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvla 96 
                                    +as+++ +   + +va   +++d  ++++ vA       L +  +   aG  aD f  R++++   l   l+s+l +v  
  gi|121636706|ref|YP_976929.1|  50 LASVMAHVDVTVVSVAQRTFVADFGSTQAVVAWTMTGYMLALATVIPTAGWAADRFGTRRLFMGSVLAFTLGSLLCAVAP 129
                                    689999999999********************9999999999988889************99988888888887777654 PP

                          MFS_3  97 algllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna 176
                                         +  ll+++ ++ g G  + +P   A++      + +   +a+  + + +    GP lgG l+ a G  + f vn 
  gi|121636706|ref|YP_976929.1| 130 -----NILLLIIFRVVQGFGGGMLTPVSFAILAREAGPKRLGRVMAVVGIPMLLGPVGGPILGGWLIGAYGWRWIFLVNL 204
                                    .....56789***********************999999***************************************96 PP

                          MFS_3 177 lsyl 180
                                       l
  gi|121636706|ref|YP_976929.1| 205 PVGL 208
                                    3332 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.12
                          MFS_3 255 vy.GillgalGvGAilgalllsrLRerlsserlvllaavalAlvllsla 302
                                     y G+ll + G+  +l ++++s  R ++   +++  a  +lAl+++ +a
  gi|121636706|ref|YP_976929.1| 230 DYmGLLLLSPGLATFLFGVSSSPARGTMADRHVLIPAITGLALIAAFVA 278
                                    3449999999999999999999999999999999999999999887665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.00075
                          MFS_3  34 sWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgl.lspwlllaltll 112
                                    s+l   +++sp++  +  +   L  +l   +aGa+ D     k++l++ +l+a++  + +  +a +    p+l  +l+++
  gi|121636706|ref|YP_976929.1| 322 SYLQQVLHQSPMQSGVHIIPQGLGAMLAMPIAGAMMDRRGPAKIVLVGIMLIAAGLGTFAFGVARQAdYLPILPTGLAIM 401
                                    5566667788888777777888889998889*****************99999876555554444430334444444433 PP

                          MFS_3 113 .igiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlva 164
                                     +g+G + ++P   A+v+ l + +++    +L sv+  +  s+G Al  vl++
  gi|121636706|ref|YP_976929.1| 402 gMGMGCS-MMPLSGAAVQTLAP-HQIARGSTLISVNQQVGGSIGTALMSVLLT 452
                                    2455555.56888999987766.6799999*****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3865.50
//
Query:       gi|121636707|ref|YP_976930.1|  [L=228]
Description: hypothetical protein BCG_0835 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-18   64.7   0.0    1.1e-17   64.4   0.0    1.1  1  DUF2334   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   6.1e-22   1.1e-17      13     144 ..       9     132 ..       4     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 6.1e-22
                        DUF2334  13 edleklkeiadyldkegipfsvavIPrykdpktgskvnlsenpefvevLkylqakGgeialHGYtHqygtvksevsgegf 92 
                                    ++l+++ ++   +d++ +p+s++v Pr++d      ++l  +p +v++L  ++a G++++lHGY+   +    +++ ++f
  gi|121636707|ref|YP_976930.1|   9 STLADVDAFCAEMDARSVPVSLLVAPRMRDD-----YRLDRDPRTVDWLTGRRAAGDALVLHGYDEAAT----KRRRGEF 79 
                                    577888999999*******************.....*****************************9997....467999* PP

                        DUF2334  93 eflseseakeriekGieilkklgikpkgFeaPhyaaseetykalkky.fsiiy 144
                                     +l ++ea+ r+ ++ ++l++lg+++++F aP + +s+  + al  + f+++ 
  gi|121636707|ref|YP_976930.1|  80 AMLRAHEANLRLMAADRVLEHLGLRTRLFAAPGWLVSPGVRTALPANgFRLLA 132
                                    ********************************************998898876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1596.52
//
Query:       gi|121636708|ref|YP_976931.1|  [L=191]
Description: hypothetical protein BCG_0836 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-32  112.1   0.2    3.6e-32  112.0   0.2    1.0  1  FAD_binding_2   FAD binding domain
    3.1e-09   36.9   0.8    6.3e-09   35.9   0.8    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.6e-07   28.4   0.1    1.5e-06   27.8   0.1    1.2  1  FAD_binding_3   FAD binding domain
    3.7e-06   26.8   0.2    3.9e-06   26.7   0.2    1.2  1  DAO             FAD dependent oxidoreductase
    6.3e-06   25.6   0.2    8.7e-06   25.1   0.2    1.1  1  Thi4            Thi4 family
    1.2e-05   24.2   0.8    1.7e-05   23.8   0.8    1.1  1  HI0933_like     HI0933-like protein
    2.6e-05   23.5   0.3    3.3e-05   23.1   0.3    1.1  1  GIDA            Glucose inhibited division protein A
    4.1e-05   23.1   0.0    4.2e-05   23.1   0.0    1.1  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00011   21.6   0.1    0.00014   21.2   0.1    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00022   20.4   0.3    0.00033   19.8   0.3    1.2  1  Lycopene_cycl   Lycopene cyclase protein
    0.00094   18.5   0.0     0.0011   18.3   0.0    1.1  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0013   18.7   0.1     0.0017   18.3   0.1    1.2  1  NAD_binding_9   FAD-NAD(P)-binding
      0.008   16.7   0.3      0.012   16.1   0.3    1.3  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.017   14.4   0.1      0.028   13.7   0.1    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.031   13.6   0.2      0.039   13.2   0.2    1.1  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.11   12.0   0.0       0.16   11.5   0.0    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.23   11.3   0.2       0.32   10.9   0.2    1.2  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.2   3.4e-35   3.6e-32       1     122 [.      23     154 ..      23     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 3.4e-35
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS..GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHT....T CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg..atawsqGgidavlspeqkkagikdspelhrtdtlkal....d 74 
                                    D+iV+G+GlAGL+AA e+a++Gl+v+++++e++ +   +++ws+Gg+++v+speq+++gi+ds+el+++d+l+++    +
  gi|121636708|ref|YP_976931.1|  23 DAIVVGAGLAGLVAACELADRGLRVLILDQENRANVggQAFWSFGGLFLVNSPEQRRLGIRDSHELALQDWLGTAafdrP 102
                                    89****************************99766555*************************************9***9 PP

                                    T-S.-HHHHHHHHH.THHHHHHHHHHTT----BCCTS..SB-EEE-TT-SST CS
                  FAD_binding_2  75 ela.dqplveafve.aapeavdeLeelgvpfsrtedg..pvdvrelGglsat 122
                                    e++ ++++++a+v+ aa+e++++L++ g++++r   g  +v  +++G+ ++ 
  gi|121636708|ref|YP_976931.1| 103 EDYwPEQWAHAYVDfAAGEKRSWLRARGLKIFRWWAGpsVVVTTRRGTATRC 154
                                    9999**************************9995555656666666766554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.8     6e-12   6.3e-09       1      35 [.      26      62 ..      26      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6e-12
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS..SSGGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr..lGGra 35
                                   +vGaGl+GlvaA++La++g++vl+l++ +r  +GG+a
  gi|121636708|ref|YP_976931.1| 26 VVGAGLAGLVAACELADRGLRVLILDQENRanVGGQA 62
                                   8**************************8876689987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   1.4e-09   1.5e-06       2      42 ..      22      62 ..      21      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.4e-09
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS- CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpra 42
                                   +d ++VGaG+aGl++a +L+ +G rv+++++ +++ v ++a
  gi|121636708|ref|YP_976931.1| 22 ADAIVVGAGLAGLVAACELADRGLRVLILDQENRANVGGQA 62
                                   5889****************************999988887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   3.7e-09   3.9e-06       1      44 [.      23      69 ..      23     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT.SSGGGSSEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag.sgaSgrnsgll 44
                                   d +++G+G +Gl +A eLa rg  V++l+++++a   g+   + g l
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACELADRGlrVLILDQENRANvGGQAFWSFGGL 69
                                   789****************************8877435444444444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   8.3e-09   8.7e-06      17      64 ..      21      70 ..       7      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.3e-09
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEE..ESSSS--TTT.TTTSTTB CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvail..ersvspGGGa.wlGGqlf 64
                                    +D ++vGaG +GL aa  la + +l+v+il  e++  +GG a w  G lf
  gi|121636708|ref|YP_976931.1| 21 TADAIVVGAGLAGLVAACELADR-GLRVLILdqENRANVGGQAfWSFGGLF 70
                                   689********************.******943446677775437766666 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.8   1.6e-08   1.7e-05       2      34 ..      23      55 ..      22      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                   d iv+G+G AGl aA ++a+rg rVl+l+++++
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACELADRGLRVLILDQENR 55
                                   78***************************9986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   3.1e-08   3.3e-05       1      33 [.      23      56 ..      23      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.1e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GG CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkld 33
                                   d iV+G+G+AG+ AA ++a +G++vl++ +++  
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACELADRGLRVLILdQENRA 56
                                   579***********************99544444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     4e-08   4.2e-05       1      47 [.      23      71 ..      23     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve..ergvlGGlltsglvatdi 47
                                   D +VvG+g+aG++AA   a +G +vl+++  +r  +GG++    ++ ++
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACELADRGLRVLILDqeNRANVGGQAFWSFGGLFL 71
                                   779*************************833556799998666655555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.3e-07   0.00014       2      38 ..      23      58 ..      22      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclng 38
                                   d +v+G+G AGl aa +la  g++v++++ +++  n+
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACELADRGLRVLILD-QENRANV 58
                                   679*************************5.4444444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   3.1e-07   0.00033       1      46 [.      23      66 ..      23      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsd 46
                                   D +v+GaG+Agl  A +l  a  gl+v++++  +    +++  Ws+
  gi|121636708|ref|YP_976931.1| 23 DAIVVGAGLAGLVAACEL--ADRGLRVLILDQENRANVGGQAFWSF 66
                                   889***************..9***********99999999999997 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-06    0.0011       1      34 [.      25      57 ..      25      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                   i++GaG aGl aa+el + gl ++lil+++n  n
  gi|121636708|ref|YP_976931.1| 25 IVVGAGLAGLVAACELADRGL-RVLILDQENRAN 57
                                   89*******************.8*****997665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.7e-06    0.0017       2     100 ..      26     115 ..      25     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpas.emslftddpptfaeWlrergal 79 
                                    +vGaG +Gl ++ +L++r      l++ + d+ + +  g+ +  +    +l+N+p + ++ + + ++  +++Wl + + +
  gi|121636708|ref|YP_976931.1|  26 VVGAGLAGLVAACELADR-----GLRVLILDQeNRANVGGQAFWSFGGLFLVNSPEQrRLGIRDSHELALQDWLGTAA-F 99 
                                    8***************99.....5******9966664466666666789*****9872577777778*******9987.2 PP

                  NAD_binding_9  80 eeaeeldpddfvpRalyGrYl 100
                                    +     +p+d+ p +   +Y+
  gi|121636708|ref|YP_976931.1| 100 D-----RPEDYWPEQWAHAYV 115
                                    3.....366666666555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   1.2e-05     0.012       2      33 ..      24      55 ..      23      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                   ++vvG+G+ gl +A++la+ g +V +++ +++
  gi|121636708|ref|YP_976931.1| 24 AIVVGAGLAGLVAACELADRGLRVLILDQENR 55
                                   58**********************99988766 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.6e-05     0.028       1      26 [.      31      56 ..      31      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHTTEEEEEEESSSSS CS
                  Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrv 26
                                   laGL+aA +L+++G++V++l  ++r+
  gi|121636708|ref|YP_976931.1| 31 LAGLVAACELADRGLRVLILDQENRA 56
                                   79******************888773 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.7e-05     0.039      27      62 ..      20      55 ..       4      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                   ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                     a  +v+G+G aGl A+   +  g +V +lD + +
  gi|121636708|ref|YP_976931.1| 20 LTADAIVVGAGLAGLVAACELADRGLRVLILDQENR 55
                                   46899***************************8765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.16       5      33 ..      26      54 ..      22      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                   EE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                 UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDide 33
                                   v+G+G  Glv a  la +g  v+++D ++
  gi|121636708|ref|YP_976931.1| 26 VVGAGLAGLVAACELADRGLRVLILDQEN 54
                                   9*************************876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2    0.0003      0.32       4      34 ..      26      56 ..      23      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                   EE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseea 34
                                   v+GaG+ G   a  +a +gl+V ++d +++a
  gi|121636708|ref|YP_976931.1| 26 VVGAGLAGLVAACELADRGLRVLILDQENRA 56
                                   9*************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1363.48
//
Query:       gi|121636709|ref|YP_976932.1|  [L=368]
Description: hypothetical protein BCG_0837 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-61  206.4   0.1    8.7e-61  206.2   0.1    1.0  1  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   0.1   4.8e-65   8.7e-61     173     417 .]       3     349 ..       1     349 [. 0.96

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 4.8e-65
                                    EEEEEEEEET..........TTTCEEEEEESEEEE-----GG.................GSSSBSSGT.T-S-HHHHHHH CS
                  FAD_binding_2 173 rvtGavvenp..........esgrevrirakavvlatgGfgr.......allkellgaaaeaettnap.avtGdglalal 234
                                    +v+G v+e++          +s +++++ra av++a+gG+g+       +++ +++g+++++  +++p +v+G+++++a+
  gi|121636709|ref|YP_976932.1|   3 GVRGTVLEPSdeprgapssrKSVGKFEFRASAVIVASGGIGGnhelvrkNWP-RRMGRIPKQLLSGVPaHVDGRMIGIAQ 81 
                                    799****9999999999999999999**********************9999.6699999999999999*********** PP

                                    CTTSS.EES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH...................GGGS-HHH CS
                  FAD_binding_2 235 ragaa.lnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm...................nelasrdv 294
                                     agaa +n drm+++++++t+ +pi++++gi   ++++g++++++d+ G+r++                   ++ ++++v
  gi|121636709|ref|YP_976932.1|  82 KAGAAvINPDRMWHYTEGITNYDPIWPRHGI---RIIPGPSSLWLDAAGKRLPvplfpgfdtlgtleyitksGHDYTWFV 158
                                    *******************************...**************************************9999**** PP

                                    HHHHHH.HHHHTTTSCCBEEEE-TT................................................SSHHHHH CS
                  FAD_binding_2 295 vsrailekeiaeggseanvyldash...............................................gldaegle 327
                                    ++++i+eke+a +g+e+n++l+ +                                                 ld e+++
  gi|121636709|ref|YP_976932.1| 159 LNAKIIEKEFALSGQEQNPDLTGRRlgqllrsrahagppgpvqafidrgvdfvhanslrelvaamnelpdvvPLDYETVA 238
                                    ******************************************************************************** PP

                                    HHSHHHHHHHHHCCT......S-TTTS..................EEE.......EEEEEEEES-EEEBETTSBESTTEE CS
                  FAD_binding_2 328 atleaineeaangldkdfgrgidpadr..................pipgpfyavkvvpaqhytmgGvetdengrvldadg 389
                                    a + a+++e+ n+++kd + +  +a+r                  p+ gp++avk+++ +++t+gG+etd+++rvl+adg
  gi|121636709|ref|YP_976932.1| 239 AAVTARDREVVNKYSKDGQITAIRAARryrgdrfgrvvaphrltdPKAGPLIAVKLHILTRKTLGGIETDLDARVLKADG 318
                                    *******************888888877*******9987777655555******************************** PP

                                    ESSBTEEE-STCE...ESSSSTTS--TTHHH CS
                  FAD_binding_2 390 qpipGLYAaGeva...aggvhganrlgGnsl 417
                                    +p++GLYAaGeva   +ggvhg+++l+G++l
  gi|121636709|ref|YP_976932.1| 319 TPLAGLYAAGEVAgfgGGGVHGYRALEGTFL 349
                                    *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2821.43
//
Query:       gi|121636710|ref|YP_976933.1|  [L=129]
Description: hypothetical protein BCG_0838c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-06   28.2   0.1    1.9e-06   27.9   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.033   13.7   0.1      0.044   13.3   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   2.1e-10   1.9e-06      68     163 .]       4      94 ..       1      94 [. 0.92

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.1e-10
                  Lactamase_B_3  68 geslevggleiravatshdavggs.ergenngflleq..dgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgq 144
                                    g++l +++l +rav + h   +++ +  en+ +l+ +     +++h+G++            ++vDv+ tP   p +++ 
  gi|121636710|ref|YP_976933.1|   4 GDELPLAELTVRAVGGCHAVIHPEiPVIENISYLVGDskHRARLMHPGDALF-------VPGEQVDVLATPAAAP-WMKI 75 
                                    7889999***********99998889999******99555889******997.......67889***********.**** PP

                  Lactamase_B_3 145 eealelakrLkpklvlPmh 163
                                     ea+++++++ p   +P+h
  gi|121636710|ref|YP_976933.1|  76 SEAVDYLRAVAPARAVPIH 94 
                                    *****************99 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.9e-06     0.044     149     200 ..      43      94 ..       1      95 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-06
                                    HHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 149 eigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                    + ++++++ d l++++  ++     +    + ++eav+ ++++ ++r+v+iH
  gi|121636710|ref|YP_976933.1|  43 HRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIH 94 
                                    334578888888888888888776667888999******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 974.84
//
Query:       gi|121636711|ref|YP_976934.1|  [L=319]
Description: hypothetical protein BCG_0839 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2264.97
//
Query:       gi|121636712|ref|YP_976935.1|  [L=79]
Description: phosphoribosylformylglycinamidine synthase subunit PurS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-24   83.6   0.0    9.1e-24   83.4   0.0    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   5.1e-28   9.1e-24       2      75 ..       4      74 ..       3      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 5.1e-28
                                   EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                           PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75
                                   + v+V++K ++lDpqG+a+ +al +lg+ +++dvr+gk++ele++++ +   ++++ e++e+lLaN+vied++i
  gi|121636712|ref|YP_976935.1|  4 VVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVD---DTTLAEIAESLLANTVIEDWTI 74
                                   78*******************************************7643...469*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 602.62
//
Query:       gi|121636713|ref|YP_976936.1|  [L=224]
Description: phosphoribosylformylglycinamidine synthase I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-38  129.8   0.0    1.8e-37  128.9   0.0    1.4  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      1e-08   35.0   0.0    1.7e-08   34.3   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    4.3e-07   29.9   0.1    6.9e-07   29.2   0.1    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    6.7e-07   29.3   0.0    8.7e-07   28.9   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
     0.0011   18.7   0.4     0.0024   17.7   0.4    1.6  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.019   14.9   0.0    1.3  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0   5.9e-41   1.8e-37       3     235 ..       4     205 ..       2     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 5.9e-41
                       GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreal 82 
                                    ++ +++++G+  ++++a+a ++ G+e+v        + +++l+ +  +++pGGfsygD l +g+++   +   + + +++
  gi|121636713|ref|YP_976936.1|   4 RIGVVTFPGTLDDVDAARAARQVGAEVVSL-----WHADADLKGVDAVVVPGGFSYGDYLRAGAIAR--F---APVMDEV 73 
                                    7889**********************9765.....456669*********************98754..3...4789999 PP

                       GATase_5  83 ekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeglslpva 160
                                     +  +r +  +LGiCnGfq+L++ gl+pg          +ltrN    f++r v + v+s+++ +    +  + l +p +
  gi|121636713|ref|YP_976936.1|  74 VAAADR-GMPVLGICNGFQVLCEAGLLPG----------ALTRNVGLHFICRDVWLrVASTSTAWTSRfEPDADLLVPLK 142
                                    999999.**********************..........9************999977888899998756677******* PP

                       GATase_5 161 hGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavqk 235
                                     GeGr v+  e+vl+ele +g v++rY+d+            NgS ++iagi+s++GRv++lmpHpe ++ea+  
  gi|121636713|ref|YP_976936.1| 143 SGEGRYVA-PEKVLDELEGEGRVVFRYHDN-----------VNGSLRDIAGICSANGRVVGLMPHPEHAIEALTG 205
                                    ********.89*****************95...........9**************************9998765 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   5.8e-12   1.7e-08      16      90 ..      17      95 ..       4     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.8e-12
                       GATase_3 16 ldpLeaepevrvrfvpl..kdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                   +d+ +a+ +v  ++v+l   d +l + +d+v++pGg+++   +++ a++r   + +++ +aa +g+pvlgiC G+q+L+e
  gi|121636713|ref|YP_976936.1| 17 VDAARAARQVGAEVVSLwhADADL-KGVDAVVVPGGFSYgdyLRAGAIARFAPVMDEVVAAADRGMPVLGICNGFQVLCE 95
                                   555555555555555441156667.55*********97611166667888899999***********************8 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   2.3e-10   6.9e-07      55     115 ..      36     101 ..      14     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.3e-10
                                    GGCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                      DJ-1_PfpI  55 ddvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                     d++ +  Da+v+pGG +  ++lr+ +      v++ v  +a++g +v  IC g q+L +ag+l+g
  gi|121636713|ref|YP_976936.1|  36 ADADLKGVDAVVVPGGFSYGDYLRAGAiarfaPVMDEVVAAADRGMPVLGICNGFQVLCEAGLLPG 101
                                    47888899****************987554556788899999**********************98 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.9e-10   8.7e-07      15      87 ..      21      96 ..      18     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.9e-10
                                   HHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                         GATase 15 halvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaie 87
                                   +a++++g++v  +++          lk++d+++v+gG+ +               ++ +  a+++++P+LGIC G+Q+l+++
  gi|121636713|ref|YP_976936.1| 21 RAARQVGAEVVSLWHADA------DLKGVDAVVVPGGFSYGDylragaiarFAPVMDEVVAAADRGMPVLGICNGFQVLCEA 96
                                   667777777777775532......2578**********999989666654422223333334448**************986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   7.9e-07    0.0024      98     119 ..      73      94 ..      19     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.9e-07
                  Peptidase_C26  98 iraalergvPilgiCrGlqlln 119
                                    + aa +rg+P+lgiC G+q+l 
  gi|121636713|ref|YP_976936.1|  73 VVAAADRGMPVLGICNGFQVLC 94 
                                    56899***************95 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.2e-06     0.019      26      82 ..      35      94 ..      12     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.2e-06
                                   -SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
                            SNO 26 krkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlills 82
                                       dl++vda+++PGG s       + ++    +++++ + + ++  +vlG C G+ +l+
  gi|121636713|ref|YP_976936.1| 35 HADADLKGVDAVVVPGGFSYGdylrAGAIARFAPVMDEVVAAADRG-MPVLGICNGFQVLC 94
                                   45679************99752211445666666667766666666.89*******97775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1730.49
//
Query:       gi|121636714|ref|YP_976937.1|  [L=199]
Description: hypothetical protein BCG_0842c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00041   20.4   0.3     0.0006   19.9   0.3    1.3  1  YbjN      Putative bacterial sensory transduction regulator


Domain annotation for each model (and alignments):
>> YbjN  Putative bacterial sensory transduction regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   3.3e-08    0.0006       4     124 ..      55     180 ..      52     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-08
                                    HHHHHHHHH--S-EEEEETTEE.EEEEEETTEEEEEEE--SSTT-EEEEEEEEES-....-TTHHHHHHHHHHHTTTTTT CS
                           YbjN   4 lleevLeeagleyertedddgaivvvgtwggyrftiallgeseelllvlafvarvp....eedreallellnrwNrellf 79 
                                    l+e +L+++g +y r + d+    + ++++  r+ + l       + v+++ +       + d+  l+e +n wN +   
  gi|121636714|ref|YP_976937.1|  55 LIERYLRARGRRYFRGHHDAEF--FFVANAHLRLHVHLEISPAY-RDVFTIRVSPAyffpATDHTRLAEIVNAWNLQNHE 131
                                    6888888888888888888888..88888888888888776644.333333333335566******************** PP

                                    T-EEEEETTEEE...EEEEEE-..TT--HHHHHHHHHHHHHHHHHHHHH CS
                           YbjN  80 gkayldedgdvl...vehdldl.dagltpeqldrllalvleaadqffda 124
                                    + a ++ + d+    v   ++l ++ +  + + ++++++++aa ++f +
  gi|121636714|ref|YP_976937.1| 132 VTAIVHGSSDPHrigVAAERSLiRDRIRFDDFATFVDNAVSAATELFGQ 180
                                    *****9999999999999999999*******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1376.97
//
Query:       gi|121636715|ref|YP_976938.1|  [L=242]
Description: hypothetical protein BCG_0843c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-20   74.2   0.2    1.8e-20   73.4   0.2    1.4  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.2     1e-24   1.8e-20       2     112 .]      29     152 ..      28     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1e-24
                 Transglut_core   2 alaeeltagakdplekakaiyewvrknveys....aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtg 77 
                                    ++a+ l + a +++e++++iy++vr  v+y+      +  +g+++a++v+ +g + c++ as fval+Ra+G+paR++++
  gi|121636715|ref|YP_976938.1|  29 TTAATLIRDAVSDTERVRRIYYYVR-DVPYDvlasFRYLAQGHHRASDVIGHGVAFCMGKASSFVALCRAAGVPARIAFQ 107
                                    67888999999**************.8888888544455777888*********************************** PP

                 Transglut_core  78 ylsgeeekeq...........svasedaHawvevylegygWvplDp 112
                                    +++++++++            ++++  +H+  e+yl g++Wv+lD+
  gi|121636715|ref|YP_976938.1| 108 TIDAPDKEFLspqvralwggrTGRPFPWHSLGEAYL-GRRWVKLDA 152
                                    ****998888999999999999999999********.*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1662.06
//
Query:       gi|121636716|ref|YP_976939.1|  [L=347]
Description: hypothetical protein BCG_0844c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-57  195.9   1.1    1.1e-53  182.7   0.4    2.3  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.4   6.3e-58   1.1e-53      20     236 ..      23     277 ..       8     289 .. 0.91
   2 !   11.7   0.0   7.1e-06      0.13     292     313 ..     293     314 ..     279     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 6.3e-58
                 Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpgga..................................ldaftllaalaaa 65 
                                     s+r++v + ++aEe+Gfd+vw+ +h +  +                                    l+++t laal+  
  gi|121636716|ref|YP_976939.1|  23 GSYREMVVVSQTAEEYGFDSVWLCDHFLTISPGeyakvagiaadtgsatgtetggagqcapsrslplLECWTALAALSRD 102
                                    479************************96444489********************************************* PP

                 Bac_luciferase  66 TerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrge 142
                                    T+++rlgt+v++   rhP vlA++aatLd +s+GR++lglg+g++  e  ++G+   +  +r+  l+E ++v++++w++ 
  gi|121636716|ref|YP_976939.1| 103 TTKLRLGTSVLCNSYRHPSVLAKMAATLDVISQGRLDLGLGAGWFRRESQAYGIpfpPVGDRVSALAESLQVIKAVWTEP 182
                                    ********************************************************99*******************555 PP

                 Bac_luciferase 143 evdfeGeffsvkgalllprpgqgpiP.vyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadir 221
                                     ++++G+f++++ga+  p+p+q+p+P +++++ +++  ++aa+ha+gl +   +p+++ ++   l ++ ++agrdp+++r
  gi|121636716|ref|YP_976939.1| 183 NPTYAGRFYTLDGATCDPPPVQRPHPpLWIGGEGDRVQRIAAKHAQGLNVRWWSPQQVTQRRGFLTQASEAAGRDPDTLR 262
                                    55**********************666**************************************************999 PP

                 Bac_luciferase 222 vgisltvivadteee 236
                                    + + l ++ +++ ee
  gi|121636716|ref|YP_976939.1| 263 LSVTLLLAPTQSGEE 277
                                    999888877655544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.1e-06
                 Bac_luciferase 292 alvGtpeqvaerlaayaeagvd 313
                                    ++vGtp+ ++er+++y++ gv 
  gi|121636716|ref|YP_976939.1| 293 LIVGTPDRCVERIREYQDRGVG 314
                                    56*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2657.72
//
Query:       gi|121636717|ref|YP_976940.1|  [L=269]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-36  123.8   0.1    1.6e-35  122.1   0.0    1.8  2  UTRA       UTRA domain
    4.1e-17   61.6   1.3    8.7e-17   60.5   1.3    1.6  1  GntR       Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.011   15.4   0.4      0.061   13.0   0.1    2.3  2  HTH_41     Helix-turn-helix domain
      0.016   14.7   0.1      0.096   12.3   0.0    2.2  2  HTH_24     Winged helix-turn-helix DNA-binding
      0.019   14.7   1.1      0.073   12.9   0.2    2.4  3  HTH_IclR   IclR helix-turn-helix domain
      0.026   14.5   0.0      0.056   13.4   0.0    1.5  1  HTH_36     Helix-turn-helix domain
      0.037   13.9   0.5        0.2   11.6   0.4    2.4  2  MarR_2     MarR family
      0.046   13.7   0.1       0.11   12.5   0.1    1.7  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.053   13.8   0.3       0.11   12.8   0.3    1.5  1  PaaX       PaaX-like protein


Domain annotation for each model (and alignments):
>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.72   1.4e+03      11      27 ..      15      31 ..      14      34 .. 0.86
   2 !  122.1   0.0   7.8e-39   1.6e-35       2     141 .]     107     246 ..     106     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.72
                                   EEEEEEE--HHHHHHHT CS
                           UTRA 11 lsleevpasaeiaeaLg 27
                                   +s+  vpas ++aeaL+
  gi|121636717|ref|YP_976940.1| 15 ISRGSVPASTQLAEALK 31
                                   578899********997 PP

  == domain 2  score: 122.1 bits;  conditional E-value: 7.8e-39
                                    CCCSEEEEEEEEEEEE--HHHHHHHTS-TTSEEEEEEEEEEETTEEEEEEEEEEEGGGTTTCH...HHHHHCS-HHHHHH CS
                           UTRA   2 qglepktevlsleevpasaeiaeaLglpagepvlrieRlrladgepvaleesylpaslvpdll...eedleegslyayle 78 
                                     g +p++ vls+++ pa++ i+e+Lgl    +vl+i+R+ +++++p+al ++ylp+ + p ++   +  ++++++ya++e
  gi|121636717|ref|YP_976940.1| 107 CGVTPQVDVLSHQTGPAPQRISETLGL---VEVLCIRRRIRTGDQPLALVTAYLPPGVGPAVEpllSGSADTETTYAMWE 183
                                    699************************...***************************999888777666679******** PP

                                    HHHTTSEEEEEEEEEEEE--HHHHHHHTSTTT-EEEEEEEEEEETTSCEEEEEEEEEETTTEE CS
                           UTRA  79 erlgvpitraeetiearladaeeaelLgisagspvLviervtydadgrpveysrsyyrgdrfk 141
                                    +rlgv+i++a ++i+a  a++++a +Lg+++gspvLv++r++y++dg+p+e++++++r++r++
  gi|121636717|ref|YP_976940.1| 184 RRLGVRIAQATHEIHAAGASPDVADALGLAVGSPVLVVDRTSYTNDGKPLEVVVFHHRPERYQ 246
                                    *************************************************************96 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   1.3   4.4e-20   8.7e-17       3      64 .]      24      85 ..      22      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.4e-20
                                   HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR  3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                    q++e+L+++I++ +l  G +LPsereL ++ g sr tvR A  +L+++g+++rrqg GtfV
  gi|121636717|ref|YP_976940.1| 24 TQLAEALKAQIIQQRLPRGGRLPSERELIDRSGLSRVTVRAAVGMLQRQGWLVRRQGLGTFV 85
                                   799**********************************************************9 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.64   1.3e+03      14      34 ..      11      31 ..       7      38 .. 0.73
   2 ?   13.0   0.1   3.1e-05     0.061       3      48 .]      42      85 ..      41      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.64
                         HTH_41 14 keleLSvGlvQkALklLeddk 34
                                    +l +S+G v +  +l e+ k
  gi|121636717|ref|YP_976940.1| 11 ADLRISRGSVPASTQLAEALK 31
                                   57889***9977766666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                         HTH_41  3 GdRlktIeelakeleLSvGlvQkALklLeddkaislerrGrlGtfl 48
                                   G Rl++  el+  ++LS+ +v +A+ +L+ ++   + r+G lGtf+
  gi|121636717|ref|YP_976940.1| 42 GGRLPSERELIDRSGLSRVTVRAAVGMLQRQGWL-VRRQG-LGTFV 85
                                   88**************************999974.56666.88886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05     0.096      21      47 ..      49      75 ..      46      76 .. 0.94
   2 ?   -1.2   0.0      0.77   1.5e+03      22      32 ..     205     215 ..     204     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                   reL +r+glS+ tv++ +  L+++G++
  gi|121636717|ref|YP_976940.1| 49 RELIDRSGLSRVTVRAAVGMLQRQGWL 75
                                   8************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.77
                         HTH_24  22 eLAerlglSps 32 
                                    ++A++lgl ++
  gi|121636717|ref|YP_976940.1| 205 DVADALGLAVG 215
                                    79******987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.6e-05     0.073      22      50 ..      49      77 ..      37      79 .. 0.89
   2 ?   -1.7   0.0       1.3   2.7e+03      10      30 ..     114     133 ..     113     133 .. 0.81
   3 ?   -2.3   0.0         2   3.9e+03      23      31 ..     205     213 ..     198     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyveq 50
                                   +el +r+gl++ tv+  +  L+++G++ +
  gi|121636717|ref|YP_976940.1| 49 RELIDRSGLSRVTVRAAVGMLQRQGWLVR 77
                                   79************************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                    CT-CTTBSS-BHHHHHHHHTS CS
                       HTH_IclR  10 dalaeapqeltlselArrtgl 30 
                                    d l++++++   + +++ +gl
  gi|121636717|ref|YP_976940.1| 114 DVLSHQTGP-APQRISETLGL 133
                                    678888998.78999998887 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                                    HHHHHHTS- CS
                       HTH_IclR  23 elArrtglp 31 
                                    ++A+++gl+
  gi|121636717|ref|YP_976940.1| 205 DVADALGLA 213
                                    8999**997 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05     0.056      25      55 .]      45      75 ..      40      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                         HTH_36 25 fpsqetlakrlglsknTvsraikeLeqlGyi 55
                                    ps + l  r+gls+ Tv+ a+ +L + G++
  gi|121636717|ref|YP_976940.1| 45 LPSERELIDRSGLSRVTVRAAVGMLQRQGWL 75
                                   577788999*********************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   9.8e-05       0.2      23      57 ..      47      81 ..      21      83 .. 0.89
   2 ?   -3.0   0.0       3.4   6.9e+03      23      36 ..      99     112 ..      92     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                   EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                         MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                   + +el +r gls+ +v  ++  L+++G+++rr g+
  gi|121636717|ref|YP_976940.1| 47 SERELIDRSGLSRVTVRAAVGMLQRQGWLVRRQGL 81
                                   5579***************************9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                                    EHHHHHHHHTSSHH CS
                         MarR_2  23 tvgelarrlglsks 36 
                                    t++e+   +g++++
  gi|121636717|ref|YP_976940.1|  99 TITEVLLSCGVTPQ 112
                                    78888888999987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.7e-05      0.11      23      55 ..      47      79 ..      25      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgr 55
                                   + +el ++ Gl+r+tv  + + L+r+g++ r++
  gi|121636717|ref|YP_976940.1| 47 SERELIDRSGLSRVTVRAAVGMLQRQGWLVRRQ 79
                                   566777999********************9763 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   5.4e-05      0.11      28      56 ..      50      78 ..      39      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                           PaaX 28 rllaelGiseslvRaalsRlakaGwlvre 56
                                   +l+   G+s  +vRaa+  l+++Gwlvr 
  gi|121636717|ref|YP_976940.1| 50 ELIDRSGLSRVTVRAAVGMLQRQGWLVRR 78
                                   5677889999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 2265.80
//
Query:       gi|121636718|ref|YP_976941.1|  [L=101]
Description: hypothetical protein BCG_0846 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-17   62.1   0.0    4.6e-17   61.9   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   2.6e-21   4.6e-17       1      77 [.       4      78 ..       4      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.6e-21
                                   CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHHH CS
                            ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaahe 77
                                   +v via++ ++p+++ a+++++ +++ ++ ++e+Gc++y+l++ + d +e v++e+++s+ al++h+ sph+  +++
  gi|121636718|ref|YP_976941.1|  4 PVAVIARFMPRPDARSALRALLDAMITPT-RAEDGCRSYDLYE-SADGGELVLFERYRSRIALDEHRGSPHYLNYRA 78
                                   589**************************.6***********9.888888**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 853.39
//
Query:       gi|121636719|ref|YP_976942.1|  [L=203]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-20   73.6   0.0    2.1e-20   73.0   0.0    1.2  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,


Domain annotation for each model (and alignments):
>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   1.2e-24   2.1e-20       1     105 [.      81     187 ..      81     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 1.2e-24
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEE..CGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfk..angralayaetkgfvKlvadaktgkvlGahivGpgageliqe 78 
                                    +p+++ftdpe+a+vGlt ++A +ag++ik + +++    +g  l+ +   g +++v+d + g +lG+++vGpga+el++ 
  gi|121636719|ref|YP_976942.1|  81 VPQAFFTDPEAAAVGLTADQAAQAGHRIKAIDVEIGdvVMGAKLFADGYTGRARMVVDVDRGHLLGVTMVGPGAAELLHS 160
                                    799******************************998656788888888******************************** PP

                                    HHHHHHTTSBHHHHHTSBSSSSSTGGG CS
                  Pyr_redox_dim  79 lavaikagltvedladtihihPtlsea 105
                                    ++va+  ++ ++ l + +   Pt+se 
  gi|121636719|ref|YP_976942.1| 161 ATVAVAGQVPIDRLWHAVPCFPTISEL 187
                                    *************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1469.62
//
Query:       gi|121636720|ref|YP_976943.1|  [L=299]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-31  108.4   0.1    5.4e-31  107.9   0.1    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.9e-14   52.0   2.9    2.8e-10   40.6   0.1    2.3  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.1e-07   30.5   0.2    0.00031   20.1   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.8e-06   27.5   0.3      0.014   14.8   0.0    2.2  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00037   19.8   3.6       0.28   10.4   0.2    2.3  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00053   19.2   0.0     0.0015   17.7   0.0    1.6  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0021   18.6   0.3       0.82   10.2   0.0    2.4  2  XdhC_C         XdhC Rossmann domain
     0.0067   15.8   0.7       0.11   11.8   0.1    2.1  2  ThiF           ThiF family
  ------ inclusion threshold ------
      0.015   14.9   3.1        4.8    6.8   1.0    3.0  3  ApbA           Ketopantoate reductase PanE/ApbA
      0.016   14.5   0.2      0.016   14.5   0.2    1.7  2  Thi4           Thi4 family
      0.053   12.6   5.0        0.2   10.6   0.4    2.2  2  Lycopene_cycl  Lycopene cyclase protein
      0.069   12.2  12.9      0.056   12.5   0.6    3.1  3  FAD_binding_2  FAD binding domain
      0.074   12.1   7.6       0.78    8.7   0.4    2.3  2  GIDA           Glucose inhibited division protein A
      0.079   12.8   6.6        1.6    8.6   0.6    2.3  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.11   13.0   3.1        3.7    8.0   0.2    2.4  2  NAD_binding_7  Putative NAD(P)-binding
       0.12   12.5   1.7        7.1    6.7   0.5    2.3  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.16   12.3   3.8       0.23   11.7   0.3    2.3  2  TrkA_N         TrkA-N domain
       0.21   10.3   6.0       0.15   10.7   0.5    2.1  2  HI0933_like    HI0933-like protein
        0.3   11.1   0.3        3.9    7.5   0.1    2.2  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
        1.3    9.6   4.2         47    4.7   0.0    3.4  4  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
          2    8.7   5.0        6.6    7.0   0.2    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
        2.6    7.2   7.7        1.8    7.7   0.6    2.3  2  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.1   6.6e-34   5.4e-31       1     208 [.      22     257 ..      22     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 6.6e-34
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................... 57 
                                    +dvvv+G+Gp G ++a ++++ g++v++ve    +g+c ++ c++skall+   + + a+                    
  gi|121636720|ref|YP_976943.1|  22 YDVVVLGAGPVGQNVADRARAGGLRVAVVErelVGGECSYWACVPSKALLRPVIAISDARrvdgareavdgsintagvfg 101
                                    69***************************999*******************9999999999999**99999999999999 PP

                                    ...............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEE.SEEEE---EEE-BCTCTTC.T CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ...............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiay.dklvlAtGssprdlgipGvae 121
                                                   + v+ +++ +++  g    ++  g ++v+++k++ g+   +++ +++v++tGs+p ++++pG   
  gi|121636720|ref|YP_976943.1| 102 rrnryvahwddtgqaDWVSGIGATLIRGDG----RL-DGPRRVVVTKSS-GESVALTArHAVVICTGSRPALPDLPGI-- 173
                                    888888666655433222222222222222....33.344567776655.55555555699*****************.. PP

                                    TBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 122 nvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevk 201
                                      ++  r++++ +a     +p+r+++vG+G +GvE+A a+  lg+ vtl+ +++ ll+ +++ +++ + + l + Gv+v+
  gi|121636720|ref|YP_976943.1| 174 --TEA-RPWTNRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGRGLADAGVDVR 250
                                    ..333.9************************************************************************* PP

                                    ESCEEEE CS
                                    xxxxxxx RF
                    Pyr_redox_2 202 lgtsvke 208
                                    +g sv +
  gi|121636720|ref|YP_976943.1| 251 VGVSVRA 257
                                    ****965 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.4   0.00038      0.31       2      31 ..      24      53 ..      23      54 .. 0.96
   2 !   40.6   0.1   3.5e-13   2.8e-10       1      65 [.     193     257 ..     193     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                   vvv+G+G +g  +A  +++ g +V vver+
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVERE 53
                                   8***************************95 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 3.5e-13
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkvee 65 
                                    ++++vG+G +g+E+A+a++ lg++Vt++ r++ ll+ +++ +++++ + l + g++v+ + +v +
  gi|121636720|ref|YP_976943.1| 193 RLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGRGLADAGVDVRVGVSVRA 257
                                    689******************************************************99988776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0013       1.1       1      37 [.      25      60 ..      25      65 .. 0.88
   2 !   20.1   0.0   3.8e-07   0.00031     123     200 ..     151     227 ..     137     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiy 37
                                   ++ GaGP G ++a  ++  gl ++ ++E++ +g   +
  gi|121636720|ref|YP_976943.1| 25 VVLGAGPVGQNVADRARAGGL-RVAVVERELVGGECS 60
                                   689******************.8******98886655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.8e-07
                    Pyr_redox_3 123 yeA.kkviiAtGefdkPnklnipGeek.lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                    ++A + v+i tG   +P +++ pG ++  +  +++ ++   +  ++++++G++  +v++A+     ga+Vt++ rgs + 
  gi|121636720|ref|YP_976943.1| 151 LTArHAVVICTGS--RPALPDLPGITEaRPWTNRQATDN-STVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLL 227
                                    45514699****8..**********97345566666666.566899*****************************99765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.014      34      68 ..      19      53 ..       3      72 .. 0.86
   2 !   10.7   0.1   0.00031      0.25      23      66 ..     179     221 ..     172     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                   2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68
                                    +   v ++G+G +Gq+va+r++a g++v +++r 
  gi|121636720|ref|YP_976943.1| 19 GETYDVVVLGAGPVGQNVADRARAGGLRVAVVERE 53
                                   5566799***********************99886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00031
                                    CHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                   2-Hacid_dh_C  23 wksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                    w ++++ + ++    +++i+G+G +G ++a   +++g+ v+   
  gi|121636720|ref|YP_976943.1| 179 W-TNRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLA 221
                                    5.444555556666799**********************98765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.5   0.00037       0.3      22      60 ..      15      53 ..       2     104 .. 0.84
   2 !   10.4   0.2   0.00035      0.28      28      59 ..     191     222 ..     181     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                                   EETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C 22 gvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                   g+++ e   v+v+G+G +G++ +  a++ g +V v++ +
  gi|121636720|ref|YP_976943.1| 15 GCREGETYDVVVLGAGPVGQNVADRARAGGLRVAVVERE 53
                                   555556678***********************9999876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                    p +  ++G+G +G++ + + +glga+Vt+l  
  gi|121636720|ref|YP_976943.1| 191 PDRLAIVGAGGVGVEMATAWQGLGASVTLLAR 222
                                    57899***********************9865 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   1.2e+03       2      14 ..      21      33 ..      19      53 .. 0.69
   2 !   17.7   0.0   1.9e-06    0.0015     134     230 ..     138     228 ..     128     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                    K_oxygenase  2 ilDligiGiGpsn 14
                                   ++D++  G+Gp  
  gi|121636720|ref|YP_976943.1| 21 TYDVVVLGAGPVG 33
                                   6888888888864 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.9e-06
                    K_oxygenase 134 tveskdaegeeeelearn.lvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllr 212
                                    +v +++++ge+  l+ar+ +v+ +G++p++P++   +e  +r + + +++ +      ++r+a+vG+G  + e++     
  gi|121636720|ref|YP_976943.1| 138 RVVVTKSSGESVALTARHaVVICTGSRPALPDLPGITE--ARPWTNRQATDNS---TVPDRLAIVGAGGVGVEMATAWQG 212
                                    56667799********976899**********987554..7778777776665...799************998876544 PP

                    K_oxygenase 213 rqkkvelklvtrsealep 230
                                        ++++l++r+++l p
  gi|121636720|ref|YP_976943.1| 213 LG--ASVTLLARGSGLLP 228
                                    44..47888888887776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.001      0.82       1      29 [.      24      52 ..      24     115 .. 0.92
   2 ?    6.5   0.1     0.013        11       1      29 [.     194     222 ..     194     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdp 29
                                   +v++Gag+v+q +a+ a+a g+rv vv+ 
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVER 52
                                   689***********************986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                    EEEE--STTHHHHHHHHHHHTEEEEEEES CS
                         XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdp 29 
                                    l+i+Gag v+ ++a+  + lg +vt++  
  gi|121636720|ref|YP_976943.1| 194 LAIVGAGGVGVEMATAWQGLGASVTLLAR 222
                                    78***********************9865 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.11        90      19      36 ..      22      39 ..       7      55 .. 0.78
   2 !   11.8   0.1   0.00013      0.11      20      42 ..     193     215 ..     181     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                                   SEEEEE--SHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                           ThiF 19 skvllvGaGglGsellkn 36
                                     v+++GaG +G++++  
  gi|121636720|ref|YP_976943.1| 22 YDVVVLGAGPVGQNVADR 39
                                   679***********9975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                                    EEEEE--SHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  20 kvllvGaGglGsellknLalsGv 42 
                                    + ++vGaGg+G e+++++ ++G 
  gi|121636720|ref|YP_976943.1| 193 RLAIVGAGGVGVEMATAWQGLGA 215
                                    789**************999985 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.55   4.5e+02       1      29 [.      24      52 ..      24      54 .. 0.78
   2 ?    6.8   1.0    0.0059       4.8       2      31 ..     195     224 ..     194     231 .. 0.91
   3 ?    5.7   0.0     0.013        11       9      61 ..     234     292 ..     233     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.55
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilr 29
                                   +++lGaG +G+ +a +  + g  v ++ r
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVER 52
                                   689*******9999877667777766655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0059
                                    EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr 31 
                                    ai+GaG++G  +a   +  ga vtl++r+ 
  gi|121636720|ref|YP_976943.1| 195 AIVGAGGVGVEMATAWQGLGASVTLLARGS 224
                                    8***************99**********86 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHTHC......EEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH CS
                           ApbA   9 iGsllaakLakagad......vtlilrsrrlealkknGlrltseggeeilrppealsae 61 
                                    +G l++  La ag d      v  ++r + l+++++ + ++ s+g  ++ +pp++ +++
  gi|121636720|ref|YP_976943.1| 234 VGELIGRGLADAGVDvrvgvsVRALGRPNPLAQWSSSWTTVPSCGSTRYSSPPAEHREP 292
                                    899************9999999**********************977777777766554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2     2e-05     0.016      18      54 ..      22      57 ..      17      65 .. 0.85
   2 ?   -2.1   0.1       2.2   1.8e+03      20      33 ..     194     207 ..     183     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                    Dvv+ GaG+ G   a   a++ +l+va++er++  G
  gi|121636720|ref|YP_976943.1| 22 YDVVVLGAGPVGQNVADR-ARAGGLRVAVVERELVGG 57
                                   6*************9987.6677**********9755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                    EEEE--SHHHHHHH CS
                           Thi4  20 vvivGaGssGLtaa 33 
                                    ++ivGaG  G+  a
  gi|121636720|ref|YP_976943.1| 194 LAIVGAGGVGVEMA 207
                                    689****9998766 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00025       0.2       1      45 [.      23      63 ..      23      78 .. 0.79
   2 ?    3.9   0.5     0.028        23       2      36 ..     194     226 ..     193     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWs 45
                                   Dvvv GaGp g  +A r    + gl+v ++e     l +++   W 
  gi|121636720|ref|YP_976943.1| 23 DVVVLGAGPVGQNVADRA--RAGGLRVAVVE---RELVGGECsYWA 63
                                   9*****************..9999**99994...333455544555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.028
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                    ++++GaG  g+ +A     +  g +v+l+  + +l
  gi|121636720|ref|YP_976943.1| 194 LAIVGAGGVGVEMATAW--QGLGASVTLLARGSGL 226
                                    68**************9..********99777665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   6.9e-05     0.056       1      41 [.      23      63 ..      23      81 .. 0.92
   2 ?    5.5   0.0    0.0094       7.7     167     206 ..     126     167 ..     122     192 .. 0.71
   3 ?   -1.4   4.2       1.1   9.2e+02       3      31 ..     195     223 ..     193     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41
                                   Dv+V G+G  G   A +a+  Gl+vavve e + g  + w+
  gi|121636720|ref|YP_976943.1| 23 DVVVLGAGPVGQNVADRARAGGLRVAVVERELVGGECSYWA 63
                                   9*****************************99855588887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0094
                                    EEECTTEEEE...EEEEETTTTCEEEEEES.EEEE-----GG.. CS
                  FAD_binding_2 167 LivedgrvtG...avvenpesgrevrirak.avvlatgGfgral 206
                                    Li+ dgr  G   +vv  ++sg+ v+++a+ avv+ tg  ++ l
  gi|121636720|ref|YP_976943.1| 126 LIRGDGRLDGprrVVV-TKSSGESVALTARhAVVICTGSRPA-L 167
                                    6666664444331444.4899*****************9996.3 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                                    EEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                  FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavveke 31 
                                     ++G+G+ G   A++ +  G++v+++  +
  gi|121636720|ref|YP_976943.1| 195 AIVGAGGVGVEMATAWQGLGASVTLLARG 223
                                    79**********************99876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4   0.00096      0.78       1      61 [.      23      85 ..      23      94 .. 0.86
   2 ?    6.7   1.8    0.0041       3.4       3      32 ..     195     224 ..     193     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00096
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalgg 61
                                   dv+V+G+G  G   A  a   G++v+ +      +++   +C ps   +   +   + ++++g
  gi|121636720|ref|YP_976943.1| 23 DVVVLGAGPVGQNVADRARAGGLRVAVVerELVGGECSYWACVPSKALLRPVIAISDARRVDG 85
                                   79**************************76666799*********998877776666666665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0041
                                    EEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkl 32 
                                     ++G+G  G+e A a   lGa+v+L++   
  gi|121636720|ref|YP_976943.1| 195 AIVGAGGVGVEMATAWQGLGASVTLLARGS 224
                                    79***********************97654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6    0.0019       1.6       2      30 ..      24      52 ..      23      56 .. 0.94
   2 ?    7.4   0.8    0.0046       3.7       2      30 ..     194     222 ..     193     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                   v v+GaG +G+ +a  + + gl+V +v++
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVER 52
                                   89************************987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0046
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi 30 
                                    +a++GaG +G ++a++    g +V+l+ +
  gi|121636720|ref|YP_976943.1| 194 LAIVGAGGVGVEMATAWQGLGASVTLLAR 222
                                    69***********************9876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0046       3.7       9      41 ..      23      56 ..      19     166 .. 0.77
   2 ?    5.3   0.2     0.032        26       9      39 ..     193     223 ..     190     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev.k 41
                                    v+v G+G+v+++ + +  + g +v vv  e+  
  gi|121636720|ref|YP_976943.1| 23 DVVVLGAGPVGQNVADRARAGGLRVAVVERELvG 56
                                   69**************************999652 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.032
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvape 39 
                                    +  +vG+G v+ + +      ga vt++a  
  gi|121636720|ref|YP_976943.1| 193 RLAIVGAGGVGVEMATAWQGLGASVTLLARG 223
                                    578************************9976 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0088       7.1      26      53 ..      24      51 ..      19      61 .. 0.92
   2 ?    4.5   0.0     0.041        33      15      51 ..     183     219 ..     172     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0088
                                   EEEE--SHHHHHHHHHHHHCT-EEEEE- CS
                  AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarvivte 53
                                   +vv G G vG+  a+  ++ G rv v e
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVE 51
                                   89***********************998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.041
                                    HHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEE CS
                  AdoHcyase_NAD  15 ratdvllaGkvavvaGyGdvGkGcaaslkglGarviv 51 
                                    +atd         ++G G vG   a++ +glGa v++
  gi|121636720|ref|YP_976943.1| 183 QATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTL 219
                                    677777777788899******************9975 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00028      0.23       1      29 [.      24      52 ..      24      55 .. 0.90
   2 ?    1.1   0.3      0.57   4.6e+02       2      19 ..     195     212 ..     194     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEES CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidk 29
                                   ++++G+G vG+++a++ ++gg +v v+++
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGGLRVAVVER 52
                                   79*****************7756***997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.57
                                    EEES-SHHHHHHHHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLse 19 
                                    +i+G+G vG ++a   + 
  gi|121636720|ref|YP_976943.1| 195 AIVGAGGVGVEMATAWQG 212
                                    79**********988766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00019      0.15       1      32 [.      22      53 ..      22      58 .. 0.93
   2 ?    2.4   0.6     0.064        52       3      33 ..     194     224 ..     192     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +dv+v+G+G+ G   A +a++ g rV+++e++
  gi|121636720|ref|YP_976943.1| 22 YDVVVLGAGPVGQNVADRARAGGLRVAVVERE 53
                                   59***************************975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.064
                                    EEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekak 33 
                                    ++++G+G  G+  A + +  g++V+ll +++
  gi|121636720|ref|YP_976943.1| 194 LAIVGAGGVGVEMATAWQGLGASVTLLARGS 224
                                    68************************98765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0048       3.9      12      45 ..      21      53 ..      12      57 .. 0.89
   2 ?    1.2   0.0      0.42   3.4e+02      13      39 ..     192     217 ..     182     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0048
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45
                                   +  v+++GaG +++ va    a g++ v+v+ R+
  gi|121636720|ref|YP_976943.1| 21 TYDVVVLGAGPVGQNVADRARAGGLR-VAVVERE 53
                                   6689***************9999999.9999997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                                    -EEEEES-SHHHHHHHHHHHCCT-CEE CS
                   Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkv 39 
                                     +  ++GaG ++ ++a++    g+  v
  gi|121636720|ref|YP_976943.1| 192 DRLAIVGAGGVGVEMATAWQGLGAS-V 217
                                    5788********9999887766665.5 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.057        47       2      30 ..      24      49 ..      23      55 .. 0.80
   2 ?   -0.6   0.0       2.5     2e+03      10      50 ..     122     160 ..     121     167 .. 0.68
   3 ?    3.3   0.9      0.15   1.2e+02       1      28 [.     193     217 ..     193     225 .. 0.85
   4 ?   -1.5   0.0       4.7   3.8e+03      10      32 ..     234     253 ..     233     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.057
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivv 30
                                   + ++GaG +g+ +a ++ a g     + v
  gi|121636720|ref|YP_976943.1| 24 VVVLGAGPVGQNVADRARAGG---LRVAV 49
                                   6799***********999988...55554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                                    HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                  F420_oxidored  10 mgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50 
                                    +g++l++g  + +  p+ +vv+ +++ e+++ +a+++ v +
  gi|121636720|ref|YP_976943.1| 122 IGATLIRGDGRLD-GPRRVVVT-KSSGESVALTARHAVVIC 160
                                    5667777666666.78889955.777787877777765544 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCE CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqphei 28 
                                    +++i+GaG +g  +a  ++  g    ++
  gi|121636720|ref|YP_976943.1| 193 RLAIVGAGGVGVEMATAWQGLG---ASV 217
                                    689***************9999...555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.7
                                    HHHHHHHHHHHTTS-GGCEEEEE CS
                  F420_oxidored  10 mgealasgllaagaqpheivvan 32 
                                    +ge + +gl+ ag    +++v+ 
  gi|121636720|ref|YP_976943.1| 234 VGELIGRGLADAG---VDVRVGV 253
                                    6899999999999...7777664 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0081       6.6       1      36 [.      26      60 ..      26      69 .. 0.89
   2 ?    3.1   0.8      0.14   1.2e+02       1      29 [.     196     224 ..     196     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0081
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                   ++GaG  G   A +++  g++v ++e+   +GG ++
  gi|121636720|ref|YP_976943.1| 26 VLGAGPVGQNVADRARAGGLRVAVVERE-LVGGECS 60
                                   89***********************984.7777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                    IvGaG  G  +A + +  g++v+ll +++
  gi|121636720|ref|YP_976943.1| 196 IVGAGGVGVEMATAWQGLGASVTLLARGS 224
                                    9**********************997776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.6    0.0022       1.8       2      32 ..      22      52 ..      21      55 .. 0.94
   2 ?    2.9   1.4     0.066        54       5      34 ..     195     224 ..     192     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                   +dV++ GaGp+G   a   +  G rv +ve+
  gi|121636720|ref|YP_976943.1| 22 YDVVVLGAGPVGQNVADRARAGGLRVAVVER 52
                                   79****************************9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.066
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                    +IVGaG +G+  a+  +  G +v+l+ + s
  gi|121636720|ref|YP_976943.1| 195 AIVGAGGVGVEMATAWQGLGASVTLLARGS 224
                                    6**********************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1837.20
//
Query:       gi|121636721|ref|YP_976944.1|  [L=364]
Description: transposase for insertion sequence element IS1547 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-25   87.8   0.4    1.6e-24   86.5   0.4    1.7  1  DEDD_Tnp_IS110  Transposase
    1.8e-20   73.1   0.3    1.8e-20   73.1   0.3    1.9  2  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.4   1.8e-28   1.6e-24       1     152 [.       4     155 ..       4     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.8e-28
                 DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeegleallek.laakagevlvvveatghygallvaflleagitvvvvnpl 79 
                                    vG D +k++h+++++d+ g++l +++v+ + +g ++ + +  ++   e  +++e   + +a l   ll+ag++vv v+ +
  gi|121636721|ref|YP_976944.1|   4 VGTDAHKYSHTFVATDEVGRQLGEKTVKATTAGHATAIMWaREQFGLELIWGIEDCRNMSARLERDLLAAGQQVVRVPTK 83 
                                    8*********************************99999934455569******************************** PP

                 DEDD_Tnp_IS110  80 avkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdq 152
                                     + ++rk+ +++ K+D++DA   A++++ r++  pl+ +de+ +eL+ lt +r+ lv++rt+++nrlr l ++
  gi|121636721|ref|YP_976944.1|  84 LMAQTRKSARSRGKSDPIDALAVARAVL-RETDLPLATHDETSRELKLLTDRRDVLVAQRTSAINRLRWLVHE 155
                                    ****************************.99999*********************************987765 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.3     2e-24   1.8e-20       3      87 .]     222     307 ..     220     307 .. 0.97
   2 ?   -3.6   0.1       1.7   1.5e+04      54      71 ..     318     334 ..     311     342 .. 0.50

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2e-24
                 Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan.pe 81 
                                    +L +ipG+ ++taa ++ e+  ++rfks++++a+ a +ap++  SG+++++ r+s++Gnr+l++aL+++Al+ ir++ ++
  gi|121636721|ref|YP_976944.1| 222 ALLEIPGCAELTAAKIVGEAAGVTRFKSEAAFACHAAVAPIPVWSGNTAGQMRLSRSGNRQLNAALHRIALTQIRMTdSR 301
                                    6899**********************************************************************8877** PP

                 Transposase_20  82 lrayye 87 
                                     +ayy+
  gi|121636721|ref|YP_976944.1| 302 GQAYYQ 307
                                    ****97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                 Transposase_20  54 griskrGnrrlRraLyea 71 
                                      +++  +rrl r++++a
  gi|121636721|ref|YP_976944.1| 318 AALRC-LKRRLARTVFQA 334
                                    44444.334444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2330.72
//
Query:       gi|121636722|ref|YP_976945.1|  [L=265]
Description: 29 kDa antigen cfp29 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-95  318.6   0.0    2.8e-95  318.5   0.0    1.0  1  Linocin_M18  Encapsulating protein for peroxidase


Domain annotation for each model (and alignments):
>> Linocin_M18  Encapsulating protein for peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.5   0.0   1.5e-99   2.8e-95       1     255 []       1     251 [.       1     251 [. 1.00

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 1.5e-99
                                    --SS-GGGSS--HHHHHHHHHHHHHHHHHH-GGGGTSEEE----TT--EEEEEEEEE---TT-SSEEEEEEEEE-EEEEE CS
                    Linocin_M18   1 mnllkrelaPlteeaWeeideeavetakrqlagRrvvdvegPlGaglsavplgrlkeeeekeegvkakvrkvlplvelrk 80 
                                    mn+l r+laP+te+aW+ei+ ea++t+kr++agRrvvdv++P G+  +av++grl +++++++gv a+ r ++plv lr+
  gi|121636722|ref|YP_976945.1|   1 MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPVTAAVSTGRLIDVKAPTNGVIAHLRASKPLVRLRV 80 
                                    9******************************************************************************* PP

                                    EEEEEHHHHHHHHHT-SS---HHHHHHHHHHHHHHHHHHHT--TTTT---STT-GG.GBE---..SSHHHHHHHHHHHHH CS
                    Linocin_M18  81 dFtLsrrdleavergaedldlsavaeAArklAlaEdrlifeGlaeagieGlleakgkkklklsdwakagnileavleAle 160
                                    +FtLsr+++++verg++d+d+++v+eAA+klA++Edr+ifeG+++a+ieG+++a+++++l+l+  +++++i++ +++Al+
  gi|121636722|ref|YP_976945.1|  81 PFTLSRNEIDDVERGSKDSDWEPVKEAAKKLAFVEDRTIFEGYSAASIEGIRSASSNPALTLP--EDPREIPDVISQALS 158
                                    ***************************************************************..*************** PP

                                    HHHTT---SSEEEEEEHHHHHHHHHHSSS.SS-HHHHHHHHTS-EEEEESS-SS.EEEEETTSSSEEEEESS-SEEEEEE CS
                    Linocin_M18 161 kLreaGvegpyalvlspelYtklfrvsentgypeiehikelvdggvikapalkgdavlvstrggdfeLtvgqDlsigYls 240
                                    +Lr aGv+gpy+++ls++ Ytk++++s++ gyp++eh+++lvdg++i+apa++g a++++trggdf+L +g+D++igY s
  gi|121636722|ref|YP_976945.1| 159 ELRLAGVDGPYSVLLSADVYTKVSETSDH-GYPIREHLNRLVDGDIIWAPAIDG-AFVLTTRGGDFDLQLGTDVAIGYAS 236
                                    *****************************.************************.************************* PP

                                    E-SSEEEEEEEEEEE CS
                    Linocin_M18 241 heaenvelrltEslt 255
                                    h+ ++v+l+l+E+lt
  gi|121636722|ref|YP_976945.1| 237 HDTDTVRLYLQETLT 251
                                    *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1725.02
//
Query:       gi|121636723|ref|YP_976946.1|  [L=335]
Description: hypothetical protein BCG_0851c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-103  346.2   0.0   2.1e-103  345.8   0.0    1.2  1  Dyp_perox  Dyp-type peroxidase family


Domain annotation for each model (and alignments):
>> Dyp_perox  Dyp-type peroxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.8   0.0  1.2e-107  2.1e-103       2     326 ..       9     305 ..       8     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 345.8 bits;  conditional E-value: 1.2e-107
                                    SSSSS-C-SEEEEEEEEE-TTCHHHHHHHHHHHHHHHHHHHHCCCCSCSSHCTCCCTHSTTTT-EEEEEEEHHHHHHTTS CS
                      Dyp_perox   2 agiltplqaaaifvaldvkakdkakleallrkltarverLtagekappadtgealkarkpdsrLtvtvgiGsslfdrlgl 81 
                                    + il+pl++aaif+++++ a+ +a+++++l+k++  v++               +++r+p+++L+v+v+iGs+++drl++
  gi|121636723|ref|YP_976946.1|   9 QPILAPLTPAAIFLVATIGADGEATVHDALSKISGLVRA---------------IGFRDPTKHLSVVVSIGSDAWDRLFA 73 
                                    78*******************************999998...............67999********************* PP

                                    CGGS-TTCS----ETTTTEEGGGS--SEEEEEEESSHHHHHHHHHHHHHHHTTTEEEEEEEEEEEEHCTSTTCB-TTSSB CS
                      Dyp_perox  82 kekrpkeLkplpelkndkldapstdgDlliqiraeredvafealrailkafgdavevrdevkGFrsssgkvtarnLlGFv 161
                                    +  rp+eL+p+ el++++++ap+t+gDll++irae++dv+fe++ +ilk++gdav+v+dev+GFr+    +++r+LlGFv
  gi|121636723|ref|YP_976946.1|  74 G-PRPTELHPFVELTGPRHTAPATPGDLLFHIRAETMDVCFELAGRILKSMGDAVTVVDEVHGFRF----FDNRDLLGFV 148
                                    *.****************************************************************....********** PP

                                    SSTTS--TCHHHHHHHS-CSSSGGGTT-EEEEEEEEEE-HHHHTTS-HHHHHHHHTB-TTT--BTTTTSTTSTTTGSSS- CS
                      Dyp_perox 162 DGTeNpkgeeakeavvlikdedewaagGsYvvvrkirhdleaWdrlslkeQedviGRrKedgaeldddkeaddseekvip 241
                                    DGTeNp+g  a +a ++i+ded+++ag++Yv+v+k+ hd+ +W++ls++eQe+viGR+K d++eldd+         ++p
  gi|121636723|ref|YP_976946.1| 149 DGTENPSGPIAIKA-TTIGDEDRNFAGSCYVHVQKYVHDMASWESLSVTEQERVIGRTKLDDIELDDN---------AKP 218
                                    *************8.9*************************************************999.........*** PP

                                    TTSHHHHHSGE.STTTEC--EE--EEEEEEE-TTSSCEEEEEEEEEESSCHHCHHHHHHHH.....SCB-GGGGCEEEEE CS
                      Dyp_perox 242 kdsHvrlaklk.edgkglkilRralsygeGldkvgkldaGllFiaYqrtlenteqmlqrml.....gktdaLlefikavt 315
                                    ++sHv+l+ ++ +dg+++ki+R+++++ge    vgk+++G++Fi+Y+rt+++teqml++m+     g+td++l+f++avt
  gi|121636723|ref|YP_976946.1| 219 ANSHVALNVITdDDGTERKIVRHNMPFGE----VGKGEYGTYFIGYSRTPTVTEQMLRNMFlgdpaGNTDRVLDFSTAVT 294
                                    ***********8899**************....*********************************************** PP

                                    EEEEEE-BHHH CS
                      Dyp_perox 316 gglFfapsgvk 326
                                    gglFf+p+ ++
  gi|121636723|ref|YP_976946.1| 295 GGLFFSPTIDF 305
                                    *******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2310.71
//
Query:       gi|121636724|ref|YP_976947.1|  [L=433]
Description: aminopeptidase 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.1e-144  479.8   0.0   8.4e-144  479.5   0.0    1.0  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
    0.00061   18.9   0.1      0.055   12.5   0.0    2.3  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.5   0.0  9.4e-148  8.4e-144       1     431 [.      11     425 ..      11     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 479.5 bits;  conditional E-value: 9.4e-148
                                    HHHH--SHHHHHHHHHHHHHCTT-EESTTTS-STSTTCEEEEEEETTTEEEEEEEETTS-GGG--EEEEEE---SEEEEE CS
                  Peptidase_M18   1 finksptpyhvvaevaekllkagfkelsekekwkiepggkyfvtrngssliAFavgkkykaengfsiigaHtDsptlrvK 80 
                                    fi++sp+p+hv+a+va +ll ag++el+e ++w ++p g+yf++r+gs l+A++++++ + + +f+i+gaHtDsp+lrvK
  gi|121636724|ref|YP_976947.1|  11 FIDASPSPFHVCATVAGRLLGAGYRELREADRWPDKP-GRYFTVRAGS-LVAWNAEQSGHTQVPFRIVGAHTDSPNLRVK 88 
                                    9************************************.**********.******************************* PP

                                    CCEEEEETTEEEEEEEEESS.SS.GGGTT--EEEEEEEEECTT--EEEEEECCSTT---BBB----GGG-GG..GSS--T CS
                  Peptidase_M18  81 pkskkkaegylqvgvetYGggiw.etWldrdLsvaGrvlvkkkkeekleaklvnierPvlriPnlaiHLdrdineefkfn 159
                                    +++++ ++g+++v++++YGg +w ++WldrdL+++Gr++v++     ++++lv+i++P+lr+P+laiHL++d+ ++++++
  gi|121636724|ref|YP_976947.1|  89 QHPDRLVAGWHVVALQPYGG-VWlHSWLDRDLGISGRLSVRDG--TGVSHRLVRIDDPILRVPQLAIHLAEDR-KSLTLD 164
                                    ********************.999******************7..6899***********************8.****** PP

                                    TTTTSEEEEEEEE------TTCCCT.CCHHHHHHHHHHHHTS-CCCCCCCEEEEEE-S--EEETTT....T-EEEESSHH CS
                  Peptidase_M18 160 eetelepilglaeeeeeekedkekknkhkkalleliaeelgvevedivdlelilvdaqkakivGie....keflfaprlD 235
                                     ++++++++g+            +     +++++++a+++gv+ +d+++ +l+++d  +++++G+     + +l+aprlD
  gi|121636724|ref|YP_976947.1| 165 PQRHINAVWGVG-----------E---RVESFVGYVAQRAGVAAADVLAADLMTHDLTPSALIGASvngtASLLSAPRLD 230
                                    ***********2...........2...3578*********************************96333367******** PP

                                    HHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STTSGGCTHHHHHHHHHHHHHCSTT.-HCHHHHHC-EEEE CS
                  Peptidase_M18 236 nkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaqGadsnfleevlerisialkkse.afeeavlakSlliS 314
                                    n+ sc+a++eall+   d  + +  v ++a+fD+EEvGS s +Ga+s +l++vleri++a++ ++ +f +++ + S+l S
  gi|121636724|ref|YP_976947.1| 231 NQASCYAGMEALLAVDVD-SASSGFVPVLAIFDHEEVGSASGHGAQSDLLSSVLERIVLAAGGTReDFLRRL-TTSMLAS 308
                                    **************9777.566669***********************************999986777777.9****** PP

                                    E--EE---TTSGGGS-TTTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHH CS
                  Peptidase_M18 315 aDvahaihPnysskheenhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaak 394
                                    aD+aha+hPny+++he++h +++n+G+v+kv++n ryat+ ++aa++  ++q+a+v++Q++++r+d pcGstigp++aa+
  gi|121636724|ref|YP_976947.1| 309 ADMAHATHPNYPDRHEPSHPIEVNAGPVLKVHPNLRYATDGRTAAAFALACQRAGVPMQRYEHRADLPCGSTIGPLAAAR 388
                                    ******************************************************************************** PP

                                    HT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHHHHC CS
                  Peptidase_M18 395 tGirtiDlGaaqlsmHSireltgskdveeavklfkaF 431
                                    tGi t+D+Gaaql+mHS+rel+g++dv+ ++++++aF
  gi|121636724|ref|YP_976947.1| 389 TGIPTVDVGAAQLAMHSARELMGAHDVAAYSAALQAF 425
                                    ************************************9 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0026        24     128     172 ..     224     270 ..     214     293 .. 0.77
   2 !   12.5   0.0   6.1e-06     0.055     186     288 ..     307     417 ..     295     420 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0026
                                    EEETTHHHHHHHHHHHHHHHHHCTSS-S...SEEEEEEESTCTTTSHH CS
                  Peptidase_M42 128 ivskalDdragvavllellkelkeeele...atvylvatvqEEvGlrG 172
                                    +++  lD++a++++ +e+l ++   + +   + v l++  +EEvG   
  gi|121636724|ref|YP_976947.1| 224 LSAPRLDNQASCYAGMEALLAVDVDSASsgfVPV-LAIFDHEEVGSAS 270
                                    67889**************999888877443333.3333489999765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.1e-06
                                    EEEEEEEE-CSTTSTTTTSS.....TTS-CEEEEEETT.CCSHHHHHHHHHHHHHHTT--EEEEEES...SSSSTHHHHH CS
                  Peptidase_M42 186 iavDvtaagdtpgskekeak.....lgkGpvirvkDas.giyhpklrkkllelAkknnipyqlevls...gggtDAgaih 256
                                       D+++a++  +++++++      ++ Gpv++v  +  + ++ +    +  +++++++p+q +  +     g+  g + 
  gi|121636724|ref|YP_976947.1| 307 ASADMAHATHP-NYPDRHEPshpieVNAGPVLKVHPNLrYATDGRTAAAFALACQRAGVPMQRYEHRadlPCGSTIGPLA 385
                                    55677777443.33333322355779999999999665477788888888889999*****987443122478999999* PP

                                    TSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHH CS
                  Peptidase_M42 257 ltgegvptalisiptryiHspvevahlddlea 288
                                     +++g+pt+ ++ ++ ++Hs  e++  +d++a
  gi|121636724|ref|YP_976947.1| 386 AARTGIPTVDVGAAQLAMHSARELMGAHDVAA 417
                                    ****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2889.10
//
Query:       gi|121636725|ref|YP_976948.1|  [L=115]
Description: hypothetical protein BCG_0853 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-28   98.7   1.2    3.5e-28   98.5   1.2    1.0  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.088   12.0   0.0        0.1   11.8   0.0    1.1  1  MSP           Manganese-stabilising protein / photosystem II 


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   1.2   3.9e-32   3.5e-28       2     107 .]       8     113 ..       7     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 3.9e-32
                   Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe..paknrvHldlavedldaevarlval 79 
                                    v++d++dpa+la++wa+ ++++ ++      + e v  a +d+++l fq+vp+  p+knrvHld++++dldaev rlva+
  gi|121636725|ref|YP_976948.1|   8 VTFDCSDPAKLAGWWAEQFDGTTRELL----PGEFVVVARTDGPRLGFQKVPDpaPGKNRVHLDFTTKDLDAEVLRLVAA 83 
                                    89*****************77777766....4666777799999************************************ PP

                   Glyoxalase_6  80 GArvlreprdgthgr..vlaDPeGneFcvv 107
                                    GA+++++++ g+  r  vlaDPeGn Fcv+
  gi|121636725|ref|YP_976948.1|  84 GASEVGRHQVGESFRwvVLADPEGNAFCVA 113
                                    ***********9999*************96 PP

>> MSP  Manganese-stabilising protein / photosystem II polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05       0.1      97     160 ..      45     109 ..      25     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                                    EE..E-EEEEEEECTTS-EEEEEEE-EEEEEEE-SSSEESTT-EEEEEEEE.E-SS-TT-B-TTSBB CS
                            MSP  97 dG..idfqaitvqlpggeevpflFtvkelvaktepgesintstdfeGefkv.psYrgasFlDPkgRg 160
                                    dG  + fq +   +pg+++v + Ft k+l a+  +   + ++++  G+ +v  s+r     DP g +
  gi|121636725|ref|YP_976948.1|  45 DGprLGFQKVPDPAPGKNRVHLDFTTKDLDAEVLR--LVAAGASEVGRHQVgESFRWVVLADPEGNA 109
                                    5544789************************9987..677777778888884699999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 731.81
//
Query:       gi|121636726|ref|YP_976949.1|  [L=218]
Description: hypothetical protein BCG_0854c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-11   42.9   0.0    9.1e-11   42.6   0.0    1.2  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.25   11.6   0.0    1.4  1  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0     1e-14   9.1e-11       1     137 [.      16     163 ..      16     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1e-14
                 Acetyltransf_3   1 RLlLrpltee..D..lealfelrsdpevmry.lpepltleea.......eewlerawaeeseeegyg..waivlkdtgvi 66 
                                    RL L  +tee  D  +++++e + dp+ m + +p+++   e        + w++  +a   +++++   +a+ l d++++
  gi|121636726|ref|YP_976949.1|  16 RLQLQLPTEElcDqlIDTILEGVHDPDRMPFsVPWTRASREDlpfntlsHLWQQ--LAGF-KRDDWSlpLAV-LVDGRAV 91 
                                    556666665533333556667789***999989884433333244444433333..2222.23445544777.445547* PP

                 Acetyltransf_3  67 Gsvglrdleeedee.aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    G+  l + +   ++ ++ g +l+  ++g+Gy+te+ +a+l +af+el+++   ++   +N+aSi+v ++ G+
  gi|121636726|ref|YP_976949.1|  92 GVQALSSKDFPITRqVDSGSWLGLRYQGHGYGTEMRAAVLYFAFAELEAQVATSRSFVDNPASIAVSRRNGY 163
                                    ***999888887778*******************************************************97 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.7e-05      0.25      35     117 .]      81     163 ..      37     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                                    EEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHH CS
                 Acetyltransf_1  35 llvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYe 113
                                     l+++ dg+ +G   l+ +++    + +  + +    y+g+G+G+++  a++ +a+ e +++      ++dn a+i++ +
  gi|121636726|ref|YP_976949.1|  81 PLAVLVDGRAVGVQALSSKDF-PITRQVDSGSWLGLRYQGHGYGTEMRAAVLYFAFAElEAQVATSRSFVDNPASIAVSR 159
                                    444667777777777777777.233334446667778********************98886656688899*99999986 PP

                                    HTTE CS
                 Acetyltransf_1 114 klGF 117
                                    + G+
  gi|121636726|ref|YP_976949.1| 160 RNGY 163
                                    6776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1579.39
//
Query:       gi|121636727|ref|YP_976950.1|  [L=754]
Description: phosphoribosylformylglycinamidine synthase II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-59  198.1   4.3    2.6e-35  121.8   0.3    2.3  2  AIRS_C          AIR synthase related protein, C-terminal doma
    5.3e-49  164.8   7.6      4e-24   85.1   0.9    2.6  2  AIRS            AIR synthase related protein, N-terminal doma
    2.9e-17   62.9   0.0    6.6e-17   61.8   0.0    1.6  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.19   11.7   0.0    1.4  1  DUF5605         Domain of unknown function (DUF5605)


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.3   5.9e-39   2.6e-35       2     155 ..     212     368 ..     211     369 .. 0.97
   2 !   77.8   0.5   2.2e-25   9.7e-22       1     149 [.     588     725 ..     588     731 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 5.9e-39
                                    TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                         AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                    +G+++il g     +G+gg++++++++ ++e ++++  +vq+gd+++e+ li+ +++l a  glv +++D++g GL++a+
  gi|121636727|ref|YP_976950.1| 212 AGNKIILFGArtglDGIGGVSVLASDTFDAEGSRKKLpSVQVGDPFMEKVLIECCLELYAG-GLVIGIQDLGGAGLSCAT 290
                                    7*****************************9999988***********************5.****************** PP

                                    HHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEEE CS
                         AIRS_C  77 aemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsviv 155
                                    +e+a a++ g++i+ld vp++++ ++p+e+l+se+++r++ +v+p++ da+la++++++++ a+vIGevt++++l++++
  gi|121636727|ref|YP_976950.1| 291 SELASAGDGGMTIQLDSVPLRAKEMTPAEVLCSESQERMCAVVSPKNVDAFLAVCRKWEVL-ATVIGEVTDGDRLQITW 368
                                    ************************************************************7.************99886 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 2.2e-25
                                    STTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                         AIRS_C   1 kpGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                    +pG +l+l+g   + + g++ +++++ ++  gl+    +++d+++e+ l  v  ++ ++ glv+aahD+++GGL+ a+ e
  gi|121636727|ref|YP_976950.1| 588 EPGETLMLLGDtrDEFDGSV-WAQVTADHLGGLP----PVVDLAREKLLAAVLSSASRD-GLVSAAHDLSEGGLAQAIVE 661
                                    69******************.99***********....9*******8888888888887.******************** PP

                                    HHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                         AIRS_C  79 mapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                     a a++ g +i l+  +  d    p+ +l+se+ Gr+lvavp+ e+ +++ ++e++glp a +IG v  + 
  gi|121636727|ref|YP_976950.1| 662 SALAGETGCRIVLP--EGAD----PFVLLFSESAGRVLVAVPRTEESRFRGMCEARGLP-AVRIGVVDQGS 725
                                    **************..6665....59********************************7.*******9876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.9     9e-28     4e-24       4      93 ..      97     198 ..      81     199 .. 0.94
   2 !   82.8   0.9   4.8e-27   2.1e-23       5      94 .]     470     574 ..     452     574 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9e-28
                                    EEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEE CS
                           AIRS   4 avvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplv 74 
                                    av+++++shn+p++vep+++ +a++v+++++D++amGArP+a+++ l ++          l++vvrg++ +++ lg p +
  gi|121636727|ref|YP_976950.1|  97 AVTFKVESHNHPSYVEPYQG-AATGVGGIVRDIMAMGARPVAVMDQLRFGaadapdtrrVLDGVVRGIGGYGNSLGLPNI 175
                                    4799****************.*********************************************************** PP

                                    EEEEEEESS....EEEEEEEEEE CS
                           AIRS  75 gGdtsfsne....ptisvtavGl 93 
                                    gG+t f+++    p++++ +vG+
  gi|121636727|ref|YP_976950.1| 176 GGETVFDPCyagnPLVNALCVGV 198
                                    *******999************8 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 4.8e-27
                                    EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEE CS
                           AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplvg 75 
                                    ++v+td  +r++l++p+ + +++a+a++++++a++GA+P+a++++l+++         ++ ++vrgla++++ lg+p++g
  gi|121636727|ref|YP_976950.1| 470 IAVSTDASGRYTLLDPYAG-AQLALAEAYRNVAVTGATPVAVTNCLNFGspedpgvmwQFTQAVRGLADGCADLGIPVTG 548
                                    69*****************.************************************************************ PP

                                    EEEEEESS.......EEEEEEEEEEE CS
                           AIRS  76 Gdtsfsne.......ptisvtavGlv 94 
                                    G++sf+n+       pt++v+++G++
  gi|121636727|ref|YP_976950.1| 549 GNVSFYNQtgsaailPTPVVGVLGVI 574
                                    ******999***************86 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   1.5e-20   6.6e-17       6      50 .]      17      58 ..      14      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.5e-20
                 FGAR-AT_linker  6 kelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                    + +l+L+d+E+++++++   lgr Ptd+El m++++wSEHC++K
  gi|121636727|ref|YP_976950.1| 17 PYGELGLKDDEYRRIRQI---LGRRPTDTELAMYSVMWSEHCSYK 58
                                   5889**************...9**********************9 PP

>> DUF5605  Domain of unknown function (DUF5605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.2e-05      0.19       1      48 [.      51     101 ..      51     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                        DUF5605   1 WdvvlagaeeeyyliYfgferprerefelp...egsrykveviDtWnmtie 48 
                                    W ++++ +  ++ l+Yfg+  + e    +     +++  v++ D W++t +
  gi|121636727|ref|YP_976950.1|  51 WSEHCSYKSSKVHLRYFGETTSDEMRAAMLagiGENAGVVDIGDGWAVTFK 101
                                    9******************998876666654765557789999****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 5057.71
//
Query:       gi|121636728|ref|YP_976951.1|  [L=209]
Description: hypothetical protein BCG_0856 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-12   45.4   1.6    7.8e-12   45.4   1.6    2.4  2  CPBP       CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
        4.1    7.0   7.2       0.32   10.6   1.8    1.7  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.043   3.8e+02      56      82 ..      26      52 ..       5      74 .. 0.80
   2 !   45.4   1.6   8.7e-16   7.8e-12       6      90 ..      97     189 ..      90     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.043
                                   HHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                           CPBP 56 gpsvllaalaGlvlgylylktgsllaa 82
                                    + + l a +G vl ++++ t  l+++
  gi|121636728|ref|YP_976951.1| 26 PWRIPLQAGLGSVLVLVTRATMGLWPP 52
                                   455778888999999999999779987 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 8.7e-16
                                    HHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.......HHH.HHHHHHHHHHHHHHHHHTT CS
                           CPBP   6 lvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.......gps.vllaalaGlvlgylylktg 77 
                                    ++++ +   +  +EE+ fRg l +  ++ +++    ++++ +Fgl H++         +  vl++ +aG+++g+l+ ++g
  gi|121636728|ref|YP_976951.1|  97 WLVWHIPGGTVWAEEAAFRGALATIGARAFGRSGGRILQAGAFGLSHIADaratgepLVLtVLATGIAGWMFGWLADRSG 176
                                    5555555667789***********999997778999*******************9855569****************** PP

                                    -HHHHHHHHHHHH CS
                           CPBP  78 sllaaillHalln 90 
                                    sl+a++l+H+++n
  gi|121636728|ref|YP_976951.1| 177 SLAAPLLTHLAIN 189
                                    **********999 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   3.6e-05      0.32      98     192 ..       5      98 ..       2     102 .. 0.79
   2 ?   -1.2   0.3      0.15   1.3e+03     121     161 ..     157     198 ..     132     203 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.6e-05
                      CPP1-like  98 iraavflvlavltlvapaes.vpalllalglgasiyflnrKekklgravlltlvgLvvGlllGsllasllqvdvalsgls 176
                                    +++++ ++l++++lv+p      ++ l  glg+ +++++r  + l+   l++  gL +G+++G++ a+ +  + ++++ +
  gi|121636728|ref|YP_976951.1|   5 RALSLAAGLVGWSLVSPRLPaPWRIPLQAGLGSVLVLVTRATMGLWPPRLWA--GLRLGWAAGAAAATAIAATTPVPMVR 82 
                                    6788999**********998788999*************************6..89999999999999998884444333 PP

                      CPP1-like 177 seellvslvtlvllwl 192
                                           l++ v  wl
  gi|121636728|ref|YP_976951.1|  83 LSMSARELPASVPVWL 98 
                                    3333445555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.15
                      CPP1-like 121 lllalglg.asiyflnrKekklgravlltlvgLvvGlllGsl 161
                                     +la+g++   + +l +++++l   +l+ l+   +G++++ l
  gi|121636728|ref|YP_976951.1| 157 TVLATGIAgWMFGWLADRSGSLAAPLLTHLAINEAGAVAAVL 198
                                    344444431345566666666665555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1511.15
//
Query:       gi|121636729|ref|YP_976952.1|  [L=318]
Description: hypothetical protein BCG_0857 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-16   60.9   0.0    3.3e-16   60.4   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    5.3e-09   36.5   0.0      2e-08   34.6   0.0    1.8  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   3.6e-20   3.3e-16       3     203 ..      16     210 ..      14     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 3.6e-20
                                    EEEEESBTB.......TTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS......HHHHHHHHHHHHHHHH.TSEE CS
                    Metallophos   3 ilvigDlHl.......algggqlddllkllddllre.ekpdlvllaGDlvdrg......dlekellellaalvky.pipv 67 
                                    +l+i+D+Hl         ++   d+l +ll++l+++  +pd+++++GDl d g           l  l++++ ++ +  +
  gi|121636729|ref|YP_976952.1|  16 LLHISDTHLiggdrrlYGAVDADDRLGELLEQLNQSgLRPDAIVFTGDLADKGepaayrK----LRGLVEPFAAQlGAEL 91 
                                    69*******99988888888888888888888855559***************9753332....4444555555566699 PP

                                    EEEC-TTSCHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHC CS
                    Metallophos  68 ylllGNHegfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapep 146
                                    ++++GNH+  +  el  +  +++  s+   + +   ++l +++l         ++G+               ++ e+  +
  gi|121636729|ref|YP_976952.1|  92 VWVMGNHD--DRaELRKFLLDEAP-SMAPLDRVCMIDGLRIIVLD------TSVPGH---------------HHGEIRAS 147
                                    ********..33244444443333.33333334566777777733......344444...............22233333 PP

                                    CHHHHHH.HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 147 gdewlkd.lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                    +  wl++ l  ++++ ++++l+H p++          l ++ al ++l+  +v +++ GH H 
  gi|121636729|ref|YP_976952.1| 148 QLGWLAEeLATPAPDGTILALHHPPIPsvldmAVTVELRDQAALGRVLRGTDVRAILAGHLHY 210
                                    399****7777777777777777777777765555555555555599***************5 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.3e-12     2e-08       3     131 ..      16     212 ..      15     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.3e-12
                  Metallophos_2   3 laiiSDlH............snldaleavlealke..vgvdaiihaGDl.eeeep.......evleellela..pvlaVr 58 
                                    l++iSD+H            ++ d+l ++le+l++   ++dai+++GDl  ++ep         +e + +++  +++ V 
  gi|121636729|ref|YP_976952.1|  16 LLHISDTHliggdrrlygavDADDRLGELLEQLNQsgLRPDAIVFTGDLaDKGEPaayrklrGLVEPFAAQLgaELVWVM 95 
                                    689**************77777777777799988733569********997778833443323555555555******** PP

                  Metallophos_2  59 GNnD.................................eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl.. 102
                                    GN+D                                 ++    ++ ++  a   + l ee    +++ ++l +H+ p   
  gi|121636729|ref|YP_976952.1|  96 GNHDdraelrkflldeapsmapldrvcmidglriivlDTSvPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIps 175
                                    ****777777777776666666666666555554444222233333333333333345666777788899999999889* PP

                  Metallophos_2 103 ..........gvkdalaellkeaeegsdvvvcGHtHvpe 131
                                              ++++al ++l+    +++ +++GH H  +
  gi|121636729|ref|YP_976952.1| 176 vldmavtvelRDQAALGRVLRG--TDVRAILAGHLHYST 212
                                    9999999988888888888888..788899******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2402.98
//
Query:       gi|121636730|ref|YP_976953.1|  [L=532]
Description: udp-glucose-4-epimerase cpsY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-40  136.2   0.0    7.3e-40  135.5   0.0    1.4  1  Stealth_CR2  Stealth protein CR2, conserved region 2
    4.8e-19   68.0   0.6      1e-18   67.0   0.6    1.6  1  Stealth_CR3  Stealth protein CR3, conserved region 3
    5.1e-17   61.5   0.4    1.3e-16   60.2   0.2    1.8  2  Stealth_CR4  Stealth protein CR4, conserved region 4
    5.6e-10   38.8   0.0    1.1e-09   37.9   0.0    1.5  1  Stealth_CR1  Stealth protein CR1, conserved region 1
  ------ inclusion threshold ------
      0.033   14.5   0.0      0.088   13.2   0.0    1.7  1  N_NLPC_P60   NLPC_P60 stabilising domain, N term


Domain annotation for each model (and alignments):
>> Stealth_CR2  Stealth protein CR2, conserved region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0     2e-43   7.3e-40       1     105 [.     239     342 ..     239     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 2e-43
                    Stealth_CR2   1 rfrdldeLkYslrsvekyapwvrkiyivtdgqvpewlntenpkikvvkhkdilkeesklptfnsnaielnlhripglsek 80 
                                    r r++deLkY+lrsv+++apw+r+i+i td+  p wl  e+pki++v+ +d ++++s+lpt+ns+a+e++lh+ipglse+
  gi|121636730|ref|YP_976953.1| 239 RIRQIDELKYALRSVNMFAPWIRRIFIATDSTPPPWL-AEHPKITIVRAEDHFSDRSALPTYNSHAVESQLHHIPGLSEH 317
                                    7899*********************************.59**************************************** PP

                    Stealth_CR2  81 flylnDDvflgkpvkpedffkkegl 105
                                    fly nDD+f+g+p+k+++ff++ g+
  gi|121636730|ref|YP_976953.1| 318 FLYSNDDMFFGRPLKASMFFSPGGV 342
                                    ********************98776 PP

>> Stealth_CR3  Stealth protein CR3, conserved region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.6   2.8e-22     1e-18       2      48 ..     389     435 ..     388     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.8e-22
                    Stealth_CR3   2 HapktlsrsvlkelerrfpeelartashrFRsmnDlsmafsyhhyiv 48 
                                    H++ +l++svl e+er+fpee+arta+++FRs +D+s++ s++hy++
  gi|121636730|ref|YP_976953.1| 389 HTAVPLRKSVLIEMEREFPEEFARTAASPFRSDTDISVTNSFYHYYA 435
                                    **********************************************7 PP

>> Stealth_CR4  Stealth protein CR4, conserved region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.2   1.1e+04      38      47 ..     359     368 ..     359     372 .. 0.78
   2 !   60.2   0.2   3.5e-20   1.3e-16       2      53 ..     465     518 ..     464     520 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.2
                    Stealth_CR4  38 PvpSpFElpp 47 
                                    P +S FE ++
  gi|121636730|ref|YP_976953.1| 359 PARSGFENAA 368
                                    89999*9765 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 3.5e-20
                    Stealth_CR4   2 eirrrr.kkffCLNDdidhek.eeevkallrdfleslFPvpSpFElppgyrnrf 53 
                                    ++r++r ++ffCLND++++e+ ++++++ + +fle++FP+p+p+E+ +++ +r+
  gi|121636730|ref|YP_976953.1| 465 KLRKHRgYDFFCLNDGSFPEVpAAQRAERVVSFLERYFPIPAPWEKIAADVSRR 518
                                    79*******************8888*********************99998886 PP

>> Stealth_CR1  Stealth protein CR1, conserved region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.9e-13   1.1e-09       1      23 [.     201     223 ..     201     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.9e-13
                    Stealth_CR1   1 fpIDvVYTWVNGSDPewqakrak 23 
                                    f+ID V+ WV+GSDPe++a+r +
  gi|121636730|ref|YP_976953.1| 201 FDIDMVFSWVDGSDPEFRARRMA 223
                                    89*******************87 PP

>> N_NLPC_P60  NLPC_P60 stabilising domain, N term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.088      44      87 ..     477     522 ..     436     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                    HHH-TT--SS-HHHHHHHHHHHHHHHC...GGGG-SS--S-HHHHHG CS
                     N_NLPC_P60  44 eaasadrpllsaaeqaaldeefrrryF...aPWnqtklsvsaedaaw 87 
                                     ++ ++ p + aa++a++  +f +ryF   aPW++ +++vs++d+a 
  gi|121636730|ref|YP_976953.1| 477 LND-GSFPEVPAAQRAERVVSFLERYFpipAPWEKIAADVSRRDFAV 522
                                    555.66677889999****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3653.58
//
Query:       gi|121636731|ref|YP_976954.1|  [L=129]
Description: hypothetical protein BCG_0859 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  130.8   0.8    1.6e-38  130.4   0.8    1.2  1  SCP_3     Bacterial SCP ortholog


Domain annotation for each model (and alignments):
>> SCP_3  Bacterial SCP ortholog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.8   8.9e-43   1.6e-38       3      93 .]      34     125 ..      32     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 8.9e-43
                          SCP_3   3 aalaaavrltleelaekapGksvEvRvpPfaavqcveGprhtrgtPpnvvetdpetwlalatGlleweeavaagrvsasG 82 
                                    + laaavrlt+++la+ apG+svEvR+pPfaavqc++GprhtrgtPpnvv+tdp+twl +atGl  +++a  +g+++ sG
  gi|121636731|ref|YP_976954.1|  34 DVLAAAVRLTARTLAALAPGASVEVRIPPFAAVQCISGPRHTRGTPPNVVQTDPRTWLLVATGLSGVAQARGSGALQLSG 113
                                    5689**************************************************************************** PP

                          SCP_3  83 era.dlsalLPl 93 
                                    +ra +++a+LPl
  gi|121636731|ref|YP_976954.1| 114 SRAgEIEAWLPL 125
                                    ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 952.19
//
Query:       gi|121636732|ref|YP_976955.1|  [L=527]
Description: amidophosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-15   55.6   0.3    2.7e-14   53.5   0.1    2.0  2  GATase_6      Glutamine amidotransferase domain
    1.4e-12   47.6   0.0      9e-12   45.0   0.0    2.0  2  GATase_7      Glutamine amidotransferase domain
    1.6e-07   31.0   0.0      3e-07   30.1   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    8.7e-06   24.7   0.1      0.026   13.2   0.0    2.9  3  GATase_2      Glutamine amidotransferases class-II
    0.00067   18.6   0.0      0.001   18.0   0.0    1.3  1  GATase_4      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   7.6e-18   2.7e-14       5     134 .]      93     235 ..      86     235 .. 0.81
   2 ?   -1.0   0.0      0.51   1.8e+03     104     134 .]     442     471 ..     433     471 .. 0.70

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 7.6e-18
                       GATase_6   5 glaslvedevalaHvRlaivglaeeegaqPf...psedgrlllvhNGeiynykelreelpalkgla....frsrsDtevl 77 
                                    +l  +++++va++H R +++g ++ e aqP+   + +  +++l hNG   n+ +l++++++    a      +++D+ +l
  gi|121636732|ref|YP_976955.1|  93 TL-AAMQGHVAIGHCRYSTTGDTTWENAQPVfrnTAAGTGVALGHNGNLVNAAALAARARDAGLIAtrcpAPATTDSDIL 171
                                    33.566788**************88888***974445555*******************99444446666788******* PP

                       GATase_6  78 lall.........eelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                     all         e+++ ++l ++rG  af+++  +entl   rd  gv+pl+ +  ++g ++ase
  gi|121636732|ref|YP_976955.1| 172 GALLahgaadstlEQAALDLLPTVRG--AFCLTFMDENTLYACRDPYGVRPLSLGRLDRGWVVASE 235
                                    **885666665555555666779999..666666679***999**********************8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                       GATase_6 104 rentlilardrlgvkplyyavdesglafase 134
                                    + + l  +r+++g ++l y++  +g++ ase
  gi|121636732|ref|YP_976955.1| 442 EDEMLEAVRHAIGADTLGYIS-LRGMVAASE 471
                                    555666779999999999986.666777776 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   2.5e-15     9e-12       5     121 ..     109     239 ..     105     240 .. 0.85
   2 ?   -0.4   0.0      0.28     1e+03      85     118 ..     441     472 ..     435     474 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.5e-15
                       GATase_7   5 si..idseagaQPmvs..sedgrlvivfnGeiyNykelreeLeakg.....hrfrtksDtevllallea........ewg 67 
                                    s+  + + ++aQP+++  +++  +++ +nG ++N   l ++ +++g     +    ++D+ +l all++        +  
  gi|121636732|ref|YP_976955.1| 109 STtgDTTWENAQPVFRntAAGTGVALGHNGNLVNAAALAARARDAGliatrCPAPATTDSDILGALLAHgaadstleQAA 188
                                    55556677899****973345559999************998887743333566889**********99****9999899 PP

                       GATase_7  68 eealerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                     ++l  ++G f++  +de++  l+++RD++G++PL +g+ + +++++aSe  al
  gi|121636732|ref|YP_976955.1| 189 LDLLPTVRGAFCLTFMDENT--LYACRDPYGVRPLSLGRLD-RGWVVASETAAL 239
                                    99****************99..******************6.79******9998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                       GATase_7  85 eeekrlllaRDrlGikPLyygedkgdallfaSel 118
                                    +e++ l ++R  +G   L y   +  +++ aSe 
  gi|121636732|ref|YP_976955.1| 441 NEDEMLEAVRHAIGADTLGYISLR--GMVAASEQ 472
                                    555688899999999999999995..69999985 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   8.3e-11     3e-07      18     119 ..     306     410 ..     295     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 8.3e-11
                                    TTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE................EE----TTS CS
                   Pribosyltran  18 laaeileeyngkpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes........rlledpagk 88 
                                    la+e+      + d+v+g++  G p a  +a+e +vp+   + k  y + +  + ++++   +         l e ++gk
  gi|121636732|ref|YP_976955.1| 306 LARECPV----EADLVIGVPESGTPAAVGYAQESGVPYGqGLMKNAYVGRTFIQPSQTIR--QlgirlklnPLKEVIRGK 379
                                    4444444....48*********************99987677777777766666655443..14577888799999**** PP

                                    EEEEE-SEESSSHHHHHHHHHHHCC-BSEEE CS
                   Pribosyltran  89 kVliVDDildtGgTllaalelLkekgpeevr 119
                                    + ++VDD +  G+T +a ++ L+e+g+ e++
  gi|121636732|ref|YP_976955.1| 380 RLIVVDDSIVRGNTQRALVRMLREAGAVELH 410
                                    **************************98543 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.012        44      25      64 ..      55      94 ..      43      99 .. 0.84
   2 !   13.2   0.0   7.3e-06     0.026     190     284 ..      86     191 ..      73     197 .. 0.62
   3 !    7.1   0.0   0.00055         2     332     397 ..     199     261 ..     194     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.012
                                   HHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT- CS
                       GATase_2 25 lenleHRGavgadektGDGaGillqiPdeflrkeakekgi 64
                                   l  l+HRG  +a     DG+ +l+ +   +++++++e+ +
  gi|121636732|ref|YP_976955.1| 55 LYALQHRGQEAAGIAVADGSQVLVFKDLGLVSQVFDEQTL 94
                                   7789*******************99998888888877665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.3e-06
                                    HHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-.S........SEEEEE--TTHHHHHHHHHHHCTT--BT-HH.. CS
                       GATase_2 190 kefykdlkdeelesalalvHsRfstntfPsWelaqPl.R........llaHnGEintlrGnknwmkareaelksellg.. 258
                                    ++ + + + ++++ ++a+ H R+st    +We aqP+ R         l+HnG  n ++ +   ++ar+a l        
  gi|121636732|ref|YP_976955.1|  86 SQVFDEQTLAAMQGHVAIGHCRYSTTGDTTWENAQPVfRntaagtgvALGHNG--NLVNAAALAARARDAGLIATRCPap 163
                                    4556677778899***********************63533333332456777..3455555555666655544433211 PP

                                    ...HHHTC--S--TTS-HHHHHHHHHHH CS
                       GATase_2 259 ..delekllPivneegsDsasldnvlel 284
                                      ++ + l  ++ ++++Ds+  + +l+l
  gi|121636732|ref|YP_976955.1| 164 atTDSDILGALLAHGAADSTLEQAALDL 191
                                    1135555555666666666655555555 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00055
                                    EEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEEETT CS
                       GATase_2 332 alivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllvdle 397
                                     +++f+d +++ a+ D  G+RP      + +  v+asE+  ld+  ++ v+   ++PG++l++d +
  gi|121636732|ref|YP_976955.1| 199 FCLTFMDENTLYACRDPYGVRPLSLGRLD-RGWVVASETAALDIVGASFVR--DIEPGELLAIDAD 261
                                    5799******************9877765.55678*********9999987..589*******975 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-07     0.001      69     114 ..      97     143 ..      52     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-07
                       GATase_4  69 iksknvvaHiRkatqGevklenthpFvRel.wgrewifAHnGdlkey 114
                                    ++ ++++ H R  t+G+++ en++p  R+  +g    + HnG+l + 
  gi|121636732|ref|YP_976955.1|  97 MQGHVAIGHCRYSTTGDTTWENAQPVFRNTaAGTGVALGHNGNLVNA 143
                                    678999*******************888762688999*******764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3422.11
//
Query:       gi|121636733|ref|YP_976956.1|  [L=364]
Description: phosphoribosylaminoimidazole synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-34  120.0   0.1    1.7e-34  119.2   0.1    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.5e-16   60.8   0.7    3.4e-16   59.7   0.7    1.6  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.1   1.9e-38   1.7e-34       1     151 [.     186     351 ..     186     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1.9e-38
                                    STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.......TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHH CS
                         AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds.......avqlgdvlleptliyvkralaal.kglvkaahDvTgGGL 72 
                                    kpGdv+i +gs+Gl+++g+sl+rk+l e ++          ++ lg++llept+iy+k+ la++ + +v+ + +vTgGGL
  gi|121636733|ref|YP_976956.1| 186 KPGDVIIAMGSSGLHSNGYSLVRKVLLEIDRMNLaghveefGRTLGEELLEPTRIYAKDCLALAaETRVRTFCHVTGGGL 265
                                    79**************************9988779*****9999************************************ PP

                                    HHHHHHHHHTTTEEEEEECG...THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEE CS
                         AIRS_C  73 lgalaemapasgvgaeidld...kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIG 143
                                    +g+l++++p + + ae+d       p+f  ++      ++em +++n+G++++av+++e+  ++la+l++++l +++v+G
  gi|121636733|ref|YP_976956.1| 266 AGNLQRVIPHG-LIAEVDRGtwtPAPVFTMIAqrgrvRRTEMEKTFNMGVGMIAVVAPEDtTRALAVLTARHL-DCWVLG 343
                                    *********97.**********9999999999999**************************************.8***** PP

                                    EEEESSSE CS
                         AIRS_C 144 evtakeel 151
                                    +v ++++ 
  gi|121636733|ref|YP_976956.1| 344 TVCKGGKQ 351
                                    ***99876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.7   3.8e-20   3.4e-16       6      94 .]      71     174 ..      43     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.8e-20
                                    EEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEE CS
                           AIRS   6 vvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgG 76 
                                    +++ d++++++++    ++++++G  +va+++ Dl+++GA+Pl+ll+++a++      l+++v+g+a+++ ++g++l+gG
  gi|121636733|ref|YP_976956.1|  71 AASSDGVGTKLAIaqamDKHDTVGLDLVAMVVDDLVVCGAEPLFLLDYIAVGrivpeRLSAIVAGIADGCMRAGCALLGG 150
                                    6778888888887544466667********************************************************** PP

                                    EEEEESS......EEEEEEEEEEE CS
                           AIRS  77 dtsfsne......ptisvtavGlv 94 
                                    +t+++++      + is+t vG+v
  gi|121636733|ref|YP_976956.1| 151 ETAEHPGliepdhYDISATGVGVV 174
                                    *****9999*99999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2710.52
//
Query:       gi|121636734|ref|YP_976957.1|  [L=60]
Description: hypothetical protein BCG_0862c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-22   79.5   2.3    2.5e-22   79.3   2.3    1.0  1  DUF3073   Protein of unknown function (DUF3073)


Domain annotation for each model (and alignments):
>> DUF3073  Protein of unknown function (DUF3073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   2.3   1.4e-26   2.5e-22       1      59 [.       2      58 ..       2      60 .] 0.77

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.4e-26
                        DUF3073  1 GRGRqKAKqtKvAReLKYlspetDydaLerELsgkseesdsaddeesedddedddldeY 59
                                   GRGR+KAKqtKvAReLKY+sp+tD+++L+rELsg+ +++ + d  ++ dd+ +d +d++
  gi|121636734|ref|YP_976957.1|  2 GRGRAKAKQTKVARELKYSSPQTDFQRLQRELSGTGTDRLDGDGPSD-DDSWND-EDDW 58
                                   9*******************************998876655554443.444333.3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 459.02
//
Query:       gi|121636735|ref|YP_976958.1|  [L=368]
Description: hypothetical protein BCG_0863c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-22   78.5   0.0    7.3e-22   78.0   0.0    1.2  1  GCV_T     Aminomethyltransferase folate-binding domain
  ------ inclusion threshold ------
      0.067   13.1   0.1       0.16   11.9   0.1    1.7  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   8.1e-26   7.3e-22      23     254 ..      18     240 ..      15     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8.1e-26
                          GCV_T  23 qYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkatytlllnedGgvidDlivarlded 102
                                    +Y  +++  e++a + +a l+D Sh + + ++G d++ +L+++ t+++s+l++g +t+ l l+ +G+v+d+ i ++l+ +
  gi|121636735|ref|YP_976958.1|  18 HY--GDPLGEQRAGQADAVLVDRSHRAVLTLDGGDRQTWLHSISTQHVSDLPEGASTQNLSLDGQGRVEDHWIQTELG-G 94 
                                    46..88889*********************************************************************.7 PP

                          GCV_T 103 efllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkare..vlskllgadlselkffsfaevelaggkk 180
                                    + +l +++ + e +la+l+k      ++  v+ + +++a+l+l GP+ +e  vl +l    l+ l+  ++  v lagg  
  gi|121636735|ref|YP_976958.1|  95 TTYLDTEPWRGEPLLAYLRK-MV---FWSMVTPRAADMAVLSLLGPRLAEerVLDALG---LDVLP-AEWLAVPLAGGGI 166
                                    ********************.34...799999999***********977666787777...33332.3344445557888 PP

                          GCV_T 181 vlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRlE....aglrlyghdldeettPleagl 254
                                    v+ +  g  G+   ++++++ ++++  ++L    +++gv+paG+ A+++ R      a  +  g d+de+t P+e+g+
  gi|121636735|ref|YP_976958.1| 167 VRRMPDGLAGQIELDVVVKRGDRADWQRRL----TQAGVRPAGIWAYEAHRVAhrvpARRPRLGVDTDERTIPHEVGW 240
                                    ******************************....67789*********988771111556789************986 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.8e-05      0.16       1      53 [.     273     324 ..     273     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                        GCV_T_C   1 RrlvglelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkael 53 
                                    R lv l+ld+  + +  g+++l++g++vG++ ++     lg ++alA++k++l
  gi|121636735|ref|YP_976958.1| 273 RMLVLLHLDESVQRPSTGDAVLAGGRTVGRLGTVVEHVELG-PVALALLKRGL 324
                                    789*****9999999*******************9999998.69****99554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2659.42
//
Query:       gi|121636736|ref|YP_976959.1|  [L=289]
Description: 4-amino-4-deoxychorismate lyase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-40  137.7   0.0    5.9e-40  137.5   0.0    1.1  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.5   0.0   3.3e-44   5.9e-40       1     221 [.      29     261 ..      29     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 3.3e-44
                    Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsen...grlrllvsrgggglgaatsep 77 
                                    g+fEt++v++g+ ++ ++Hl+RL +sa+l+   +++d   +r+++e ++++   +    g lrl++srg     + +s+p
  gi|121636736|ref|YP_976959.1|  29 GVFETLLVRDGRACLVEAHLQRLTQSARLM-DLPEPDLPRWRRAVEVATQRWVASTadeGALRLIYSRGR----EGGSAP 103
                                    8**************************999.778889999999999877665555577788*********....7888** PP

                    Aminotran_4  78 svavyvsalppgpeseke.......lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtEg 150
                                    +++v+vs+ p     +++       l  ++ +d    +p+  + aKtl+y+ n+++ r+a+++ga +v++v++dg+v+Eg
  gi|121636736|ref|YP_976959.1| 104 TAYVMVSPVPARVIGARRdgvsaitLDRGLPADGGDAMPWLMASAKTLSYAVNMAVLRHAARQGAGDVIFVSTDGYVLEG 183
                                    ********************99999999999999999******************************************* PP

                    Aminotran_4 151 stsNvfivk.......ggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvr 221
                                     +s+v+i         + +l+tPp+   iL+G+t++al+e a+a+g  + +r+++++dl + ++++l++++    +v+
  gi|121636736|ref|YP_976959.1| 184 PRSTVVIATdgdqgggNPCLLTPPPWYPILRGTTQQALFEVARAKGYDCDYRALRVADLFDSQGIWLVSSMTLAARVH 261
                                    *****99999************************************************************99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2017.74
//
Query:       gi|121636737|ref|YP_976960.1|  [L=226]
Description: hypothetical protein BCG_0865c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-43  146.5   0.0    6.8e-43  146.2   0.0    1.1  1  DUF1794   Domain of unknown function (DUF1794)


Domain annotation for each model (and alignments):
>> DUF1794  Domain of unknown function (DUF1794)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.2   0.0   3.8e-47   6.8e-43       2     149 .]      65     223 ..      64     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 3.8e-47
                                    CGGGGGGBEEEEEEEEEEETTCEEEEEEEEEEEEESSSSEEEEEEEEEETT......TEEEEEEEEEE.......CTSCT CS
                        DUF1794   2 llpLawLvGtWrGeGeggyptieefafgqeiefshdggpylaYesrtwrld......eplhrEsGywr......ledgtd 69 
                                    ll+L++LvG+WrGeGeg  p+  +++fgq+i++shdgg+yl++esr+wrl+      ep  rE G+wr         +++
  gi|121636737|ref|YP_976960.1|  65 LLALLPLVGVWRGEGEGRGPDG-DYRFGQQIVVSHDGGDYLNWESRSWRLTatgdyqEPGLREAGFWRfvadpyDPSESQ 143
                                    789**************77766.9***************************888775599*************9778999 PP

                                    EEEEEEEETTTEEEEEEEEEETCCCEEEEECEEEEE.CTSSSEEEEEEEEEEE.CTCEEEEEEEEETTCECEEEEEEEEE CS
                        DUF1794  70 evelllahpsGvvelyeGevkngrksleLasdaiartstakevtaakrlyglv.dgdLeyveemaafgqelqshlsarLk 148
                                     +elllah++G+vel++G++++++ s+eL +da+ar+ ++  v +akrlyg+v  gdL+yvee+ ++++ l +hlsarL+
  gi|121636737|ref|YP_976960.1| 144 AIELLLAHSAGYVELFYGRPRTQS-SWELVTDALARSRSGVLVGGAKRLYGIVeGGDLAYVEERVDADGGLVPHLSARLS 222
                                    *********************776.9***************************9999**********************9 PP

                                    E CS
                        DUF1794 149 R 149
                                    R
  gi|121636737|ref|YP_976960.1| 223 R 223
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1637.07
//
Query:       gi|121636738|ref|YP_976961.1|  [L=100]
Description: hypothetical protein BCG_0866c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-42  142.6   0.2    2.9e-42  142.5   0.2    1.0  1  DUF1416          Protein of unknown function (DUF1416)
    5.7e-10   39.3   1.4    2.4e-09   37.3   1.2    1.8  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.014   15.0   0.4      0.072   12.7   0.2    1.8  2  DUF1069          Protein of unknown function (DUF1069)
       0.06   13.4   0.1      0.069   13.2   0.1    1.2  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.061   13.5   0.0      0.091   13.0   0.0    1.4  1  SdrD_B           SdrD B-like domain
      0.097   12.7   0.0       0.12   12.4   0.0    1.1  1  FixH             FixH


Domain annotation for each model (and alignments):
>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.2   9.8e-46   2.9e-42       1      97 []       2      99 ..       2      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 9.8e-46
                        DUF1416  1 CgapkqgaelpagvdvekeaviqGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRalarkgngda 81
                                   C+ pkqg +lpa+vd+eke+vi+G+v++ dg++vgga+vRLLdss+eFtaevv+sa+G+frFfaapG+Wt+Ral+++gngda
  gi|121636738|ref|YP_976961.1|  2 CSGPKQGLTLPASVDLEKETVITGRVVDgDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFFAAPGSWTLRALSAAGNGDA 83
                                   999*************************9***************************************************** PP

                        DUF1416 82 eveaesggvaevevav 97
                                    v+++++g++ev+v++
  gi|121636738|ref|YP_976961.1| 84 VVQPSGAGIHEVDVKI 99
                                   *************986 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.2   8.1e-13   2.4e-09       2      64 ..      23      85 ..      22      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.1e-13
                CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatr 64
                                   i+GrV+d +g+++ ga V++ +++++++a+++  a+G+fr+ + +pg+ ++++ sa+G   a +
  gi|121636738|ref|YP_976961.1| 23 ITGRVVDGDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRF-FAAPGSWTLRAlSAAGNGDAVV 85
                                   9****************************************.7999*******88888777665 PP

>> DUF1069  Protein of unknown function (DUF1069)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.4e-05     0.072     127     188 ..       7      72 ..       3      88 .. 0.76
   2 ?    1.8   0.0      0.05   1.5e+02     151     171 ..      76      96 ..      71      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                        DUF1069 127 sgvgvpagcrvsnevvvdgnlvr...qslagvavalvrssgigvdevty.asggdryhggpgmlec 188
                                     g+ +pa + + +e v+ g +v    q++ g  v l+ ss     ev   a+g  r+   pg    
  gi|121636738|ref|YP_976961.1|   7 QGLTLPASVDLEKETVITGRVVDgdgQAVGGAFVRLLDSSDEFTAEVVAsATGDFRFFAAPGSWTL 72 
                                    58899****************96444788888899998998777776650555569***9997544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.05
                        DUF1069 151 slagvavalvrssgigvdevt 171
                                    s ag   a+v+ sg g+ ev 
  gi|121636738|ref|YP_976961.1|  76 SAAGNGDAVVQPSGAGIHEVD 96 
                                    7899999**********9995 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05     0.069      24      82 ..      31      85 ..      18      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                           bMG3 24 sgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkdedlaf 82
                                   +g++v ga Vrlld ++e  ae  ++a+G  rf a      ++ + +++sA +++d  +
  gi|121636738|ref|YP_976961.1| 31 DGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFFAA----PGSWTLRALSAAGNGDAVV 85
                                   79******************************9877....3456666666666666554 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05     0.091      18      69 ..      29      79 ..      23     100 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                         SdrD_B 18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapag 69
                                   d + +++ g  V+L d+++e +a+++ +a+G ++F   +pG+++++  + ag
  gi|121636738|ref|YP_976961.1| 29 DGDGQAVGGAFVRLLDSSDEFTAEVVASATGDFRFF-AAPGSWTLRALSAAG 79
                                   666799*****************************7.578888887766544 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05      0.12      62     141 ..       9      81 ..       5      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                           FixH  62 lglsadvalde.geltitlrdaagkpveaaaltlslshptdagkDkklkLteaangvYrapleallkGrWyvqlaaeegg 140
                                    l l a+v+l++ + +t ++ d      +++a+ + + +  d+++ ++ + +++a g +r      ++G W ++  ++ g+
  gi|121636738|ref|YP_976961.1|   9 LTLPASVDLEKeTVITGRVVDG-----DGQAVGGAFVRLLDSSDEFTAEVVASATGDFRF---FAAPGSWTLRALSAAGN 80 
                                    4455555555533344444332.....457799999999*********************...5689******9555555 PP

                           FixH 141 e 141
                                    +
  gi|121636738|ref|YP_976961.1|  81 G 81 
                                    4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 730.90
//
Query:       gi|121636739|ref|YP_976962.1|  [L=277]
Description: thiosulfate sulfurtransferase cysA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-38  130.9   0.5    5.5e-20   71.9   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.2   8.7e-20   1.6e-15       1     106 [.       9     118 ..       9     119 .. 0.83
   2 !   71.9   0.0   3.1e-24   5.5e-20       3     105 ..     149     266 ..     147     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 8.7e-20
                      Rhodanese   1 sakelkellekgkvallDvR.ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdggg 77 
                                    sa++++ +l+++kv+++ v  +  +Y++ hI gA+ +  ++ l ++ k++  +++++ +ll++ gi n++tv++y+ +++
  gi|121636739|ref|YP_976962.1|   9 SADWAESNLHAPKVVFVEVDeDTSAYDRDHIAGAIKLdWRTDLQDPVKRDFVDAQQFSKLLSErGIANEDTVILYGGNNN 88 
                                    689*****************66666************43334445555555556666666666***************** PP

                      Rhodanese  78 r.aaaaaallkklGyknvsvldGGfkawke 106
                                      aa a++ +k +G+++v++ldGG k+w  
  gi|121636739|ref|YP_976962.1|  89 WfAAYAYWYFKLYGHEKVKLLDGGRKKWEL 118
                                    *9999999******766***********86 PP

  == domain 2  score: 71.9 bits;  conditional E-value: 3.1e-24
                      Rhodanese   3 kelkellekgkvallDvRppeeY...............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnk 66 
                                    +e+ + ++ ++  l+DvR+p+e+               ++ ghIpgA+nv++ ++ +++ + +++ el + +++ g+dn 
  gi|121636739|ref|YP_976962.1| 149 DEVLAAINVKN--LIDVRSPDEFsgkilapahlpqeqsQRpGHIPGAINVPWSRAANEDGTFKSDEELAKLYADAGLDNS 226
                                    67888888888..**********9999999999999987779************************************** PP

                      Rhodanese  67 ktvvvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                    k+ + yc+ g+r++ ++  l++ lG++nv+++dG+++++ 
  gi|121636739|ref|YP_976962.1| 227 KETIAYCRIGERSSHTWFVLRElLGHQNVKNYDGSWTEYG 266
                                    ************99999999988**888*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1843.31
//
Query:       gi|121636740|ref|YP_976963.1|  [L=140]
Description: thioredoxin thiX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-08   32.4   0.0    9.1e-08   32.0   0.0    1.1  1  Thioredoxin    Thioredoxin
    0.00082   19.4   0.0     0.0011   18.9   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
     0.0022   18.4   0.0      0.026   15.0   0.0    2.1  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.27   11.5   0.0    1.5  1  Glutaredoxin   Glutaredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0     2e-11   9.1e-08      19     101 ..      53     135 ..      46     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2e-11
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEE.TTEEEEEEESS-HHHHH CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfk.ngkevkkyegarekekl 97 
                                     + +v F Ap C++C ++   + +++ +l  +v  ++vd d+n++ a++++v ++Pt ++f  +g++  +++g  ++++l
  gi|121636740|ref|YP_976963.1|  53 GPTVVHFRAPGCAPCDRVRRGVGDVCADLG-DVAHIEVDLDSNPQAARRFSVLSLPTTLIFDvDGRQRYRTSGVPKAADL 131
                                    689**************************9.9************************977775277799999999999999 PP

                                    HHHH CS
                    Thioredoxin  98 aafl 101
                                    ++ l
  gi|121636740|ref|YP_976963.1| 132 RSAL 135
                                    8876 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.5e-07    0.0011       7      75 ..      61     135 ..      55     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                                    SSSSTTCHHHHHHHHHHCHCCT..CECEEECCTTHHHHHHCT-SSSSEE.ECT....TCEEEESS---CCHHHHHH CS
                  Thioredoxin_3   7 gpgCakCpklekavkeaaaekg..ikaevekvtdfeeiekygVmsvPal.vid....gkvvvsGkvpseeeirkll 75 
                                     pgCa C+++++ v  + a++g   ++ev+  ++++   ++ V s P++ + d     + ++sG vp+ +++r+ l
  gi|121636740|ref|YP_976963.1|  61 APGCAPCDRVRRGVGDVCADLGdvAHIEVDLDSNPQAARRFSVLSLPTTlIFDvdgrQRYRTSG-VPKAADLRSAL 135
                                    69*******************86455588888888888***********554566555678899.99999998766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.8e-06     0.026       6     107 ..      53     133 ..      49     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                     p++v+f +p+C  C++ ++ + ++  d+             + ++++++ + +++            ar++ v ++Pt+
  gi|121636740|ref|YP_976963.1|  53 GPTVVHFRAPGCAPCDRVRRGVGDVcADL------------GDVAHIEVDLDSNPQ-----------AARRFSVLSLPTT 109
                                    699*****************999993333............344566666666665...........6899999999998 PP

                  Thioredoxin_2  85 vfldgk.eivarlpGyvpaeelea 107
                                    +++d + +  +r  G  +a++l+ 
  gi|121636740|ref|YP_976963.1| 110 LIFDVDgRQRYRTSGVPKAADLRS 133
                                    888888766667777766677765 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05      0.27       1      39 [.      56      99 ..      56     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                   EEEEESTSSHHHHHHHHHH....HHTT.GGEEEEEGCCSHHHHH CS
                   Glutaredoxin  1 vvlftkptCpyCkkakrlL....kelg.vkfeeidvdkdeeire 39
                                   vv f  p+C  C +++r       +lg v++ e+d+d ++++  
  gi|121636740|ref|YP_976963.1| 56 VVHFRAPGCAPCDRVRRGVgdvcADLGdVAHIEVDLDSNPQAAR 99
                                   677899************99777666679999999999986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 823.34
//
Query:       gi|121636741|ref|YP_976964.1|  [L=270]
Description: hypothetical protein BCG_0869c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-23   84.8   0.4    1.2e-23   84.4   0.4    1.1  1  DUF2993   Protein of unknown function (DUF2993)


Domain annotation for each model (and alignments):
>> DUF2993  Protein of unknown function (DUF2993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.4   6.9e-28   1.2e-23       1     211 [.      26     255 ..      26     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 6.9e-28
                        DUF2993   1 vadrgaaavaeqriatelrsqlelaedpeVsiggfPfltqllaGeldsvsvaargvvvdgpglriesveltledvrldls 80 
                                    +ad+ga+ +ae+r++t +r +++l  dp V i  fPf +q+++ ++ + ++ a +v+  g g +  ++e+t++ ++l+  
  gi|121636741|ref|YP_976964.1|  26 GADFGASIYAEYRLSTTVRKAANLRSDPFVAILRFPFIPQAMREHYAELEIKAFAVEHAGSGTA--TLEATMHSIDLSYA 103
                                    59********************************************************655555..************** PP

                        DUF2993  81 dil.gkvrlvpvgrltatvtlteadlnralaspllitdlq...................dlsnggvkltgnn........ 132
                                    ++l  +++ +pvg+l+ +++++   l+r+l+  +l                                 +g++        
  gi|121636741|ref|YP_976964.1| 104 SWLiRPDAKLPVGELESRIIIDSMHLGRYLGISDL----MvaaprqesndatggttesgI--------SGSRglvfsgtp 171
                                    **9899*************************5544....335558888888555555553........333344444447 PP

                        DUF2993 133 ......lpvvveaglrlaagdg.qlrleltdleaglglpesavdlpaelldalleglselldlpglpfglrltevrvtdg 205
                                           +v+v ++l++a++d+ +l++++t++ +g++ ++  +++p++ +da+l  +   l+ ++lpfg+ +++v  +++
  gi|121636741|ref|YP_976964.1| 172 isanfaHRVSVLVDLSVASDDRaTLVITPTAVVTGPDTAD--QPVPDDKRDAVLHAFASKLPNQKLPFGVVPNTVGARGS 249
                                    88888889999999999888888********998877655..899**************999999*************** PP

                        DUF2993 206 glrltg 211
                                    +++++g
  gi|121636741|ref|YP_976964.1| 250 DVIIEG 255
                                    999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1769.76
//
Query:       gi|121636742|ref|YP_976965.1|  [L=255]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-28   97.8   0.0    4.2e-28   97.2   0.0    1.3  1  Trans_reg_C  Transcriptional regulatory protein, C terminal


Domain annotation for each model (and alignments):
>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.0   2.4e-32   4.2e-28       1      76 [.     145     218 ..     145     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.4e-32
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYr 76 
                                    g++++lt kef+lL++L++++grv++r++Ll evwg+d+++ +rtvdvh++rLR kL++  +++ lI tvr+vGY+
  gi|121636742|ref|YP_976965.1| 145 GRPLDLTYKEFELLKYLAQHAGRVFTRAQLLHEVWGYDFFGGTRTVDVHVRRLRAKLGP--EHEALIGTVRNVGYK 218
                                    6899*******************************************************..4567**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1652.08
//
Query:       gi|121636743|ref|YP_976966.1|  [L=315]
Description: hypothetical protein BCG_0871 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-17   64.1   0.0    1.1e-08   35.3   0.0    2.9  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.1e-12   46.8   0.0    7.9e-05   23.0   0.0    2.4  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.3e-09   37.8   1.1     0.0001   22.2   0.2    3.1  2  FR47             FR47-like protein
    1.7e-09   37.7   0.1     0.0025   17.8   0.0    3.0  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00015   22.4   0.0      0.028   15.1   0.0    2.4  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0078   16.3   0.1       0.28   11.3   0.0    2.6  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
       0.12   12.5   0.3       0.58   10.2   0.1    2.2  3  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     6e-09   1.5e-05      30      92 ..      45     106 ..      16     126 .. 0.74
   2 !   35.3   0.0   4.4e-12   1.1e-08      24     117 .]     194     299 ..     168     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6e-09
                                    STTCEEEE.EEET.TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                 Acetyltransf_1  30 leaegllv.aeed.geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                    + +e+llv +++  g +iG++ l++        +++ +l+V+p+ r++G+G+a+ +a++ +   +
  gi|121636743|ref|YP_976966.1|  45 QRTEHLLVaGSRPgGPIIGYLNLSPPRG---AGGAMAELVVHPQSRRRGIGTAMARAALAKTAGR 106
                                    3666777743333366*****9999999...89999*********************99755544 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 4.4e-12
                                    HHHHHHSTTCEEEEEEET......TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHH.......HHHHHHHHH CS
                 Acetyltransf_1  24 feesfsleaegllvaeed......geliGfisllkipdekggvayieslaVspeyrgkGlGsaL.......lealeerar 90 
                                     +++   +++gl++a  d      g+l+Gf   +  pd ++g ++++ l V+p+++++GlG++L       l      ar
  gi|121636743|ref|YP_976966.1| 194 EAWF---DPDGLILAFGDsprerpGRLLGFHWTKVHPD-HPGLGEVYVLGVDPAAQRRGLGQMLtsigivsL------AR 263
                                    3334...444455544445666779******9999999.9************************65554331......33 PP

                                    HTTESEEEE..........EEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  91 eegikkivl..........aveedndaairlYeklGF 117
                                    + g++k  l          +ve+dn+aa+r Y+ lGF
  gi|121636743|ref|YP_976966.1| 264 RLGGRK-TLdpavepavllYVESDNVAAVRTYQSLGF 299
                                    334422.222222333335*************88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.3e-08   0.00024       3      49 ..      48     101 ..      46     126 .. 0.68
   2 !   23.0   0.0   3.1e-08   7.9e-05      25      75 ..     233     300 ..     198     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                                    EEEEEEEET..TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..T CS
                 Acetyltransf_7   3 gevfVaedd..gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..a 49 
                                    ++++Va     g i+G++ ls+     +   +l+V+p+ r++GiG+a+ +a  a
  gi|121636743|ref|YP_976966.1|  48 EHLLVAGSRpgGPIIGYLNLSPPRgagGAMAELVVHPQSRRRGIGTAMARAalA 101
                                    566666555667788988888877654444449***************997331 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.1e-08
                                    TCTEEEEE-GGGTTSSHHHHHHHH.......TTSEEE.............EEEEEE...THH.HHHHHHHHTTEE CS
                 Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLlea.......aekgii.............leqlel...nae.kaikfYeklGFe 75 
                                    +e   l Vdp+++++G+G+ L  +       +                  +    l   +++ +a++ Y++lGF+
  gi|121636743|ref|YP_976966.1| 233 GEVYVLGVDPAAQRRGLGQMLTSIgivslarR----LggrktldpavepaV---LLyveSDNvAAVRTYQSLGFT 300
                                    3334488**************99755554431....023344556533431...33333223599*********7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.4e-05      0.14      21      49 ..      74     102 ..      70     112 .. 0.84
   2 !   22.2   0.2   3.9e-08    0.0001      20      80 ..     231     302 ..     225     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                    TSSEEEEEE-GGG-SSSHHHHHHHHHHHH CS
                           FR47  21 ggelgalqvlpehrrrGlgsrlvkalake 49 
                                    gg++  l v+p+ rrrG g+ +++a  ++
  gi|121636743|ref|YP_976966.1|  74 GGAMAELVVHPQSRRRGIGTAMARAALAK 102
                                    799********************986555 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.9e-08
                                    TTSSEEEEEE-GGG-SSSHHHHHHH....HHHHHHHHS.......-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  20 dggelgalqvlpehrrrGlgsrlvk....alakeiaer.......gktvllvvvasNtpsirlyeklGfeki 80 
                                      ge++ l v+p ++rrGlg+ l++    +la+++  r       +  vll+v  +N ++ r y++lGf+ +
  gi|121636743|ref|YP_976966.1| 231 GLGEVYVLGVDPAAQRRGLGQMLTSigivSLARRLGGRktldpavEPAVLLYVESDNVAAVRTYQSLGFTTY 302
                                    4599*******************9844446777776542222222456899******************988 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.6e-07    0.0025      28      79 ..      47     102 ..      23     118 .. 0.76
   2 !   14.8   0.1   8.1e-06     0.021      53     110 ..     234     303 ..     213     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.6e-07
                Acetyltransf_10  28 egealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveee 79 
                                    +++ l+ +   gg i+G+++l   ++    ++ l+V+p+ r++Gig+a+  a++++
  gi|121636743|ref|YP_976966.1|  47 TEHLLVAGSRPGGPIIGYLNLsPPRGaggAMAELVVHPQSRRRGIGTAMARAALAK 102
                                    44455555566799*****9965555899********************9999887 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.1e-06
                Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveee.aekdgikl..........eltvnasp.yavpfYeklGFkavg 110
                                    +++ l Vdp+++++G+g++L    +   a++ g+++           l v++++ +av+ Y++lGF++ +
  gi|121636743|ref|YP_976966.1| 234 EVYVLGVDPAAQRRGLGQMLTSIGIVSlARRLGGRKtldpavepavLLYVESDNvAAVRTYQSLGFTTYS 303
                                    677899**************98877663554444322211002234589*****************9875 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.028      51     107 ..      45     102 ..       5     130 .. 0.78
   2 ?    5.3   0.0     0.012        30      70     138 .]     219     300 ..     152     300 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                 Acetyltransf_3  51 eegygwaivl.kdtgv.iGsvglrdleeedeeaelgymlapsfwgkGyateavralley 107
                                    ++   +++   +++g  iG+ +l +  +  + a  +++++p+++++G++t ++ra+l  
  gi|121636743|ref|YP_976966.1|  45 QRTEHLLVAGsRPGGPiIGYLNLSPPRGAGG-AMAELVVHPQSRRRGIGTAMARAALAK 102
                                    44444555446888855*******9999998.***********************8865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                 Acetyltransf_3  70 glrdleeedeeaelg..ymla..psfwgkGyateavra.lleyafeel........gle.rlvavidkeNeaSirvlekl 135
                                    g+++ +  ++ + lg  y+l+  p+++++G+++  ++  ++ +a ++l         +e  +   ++ +N a +r +++l
  gi|121636743|ref|YP_976966.1| 219 GFHWTKVHPDHPGLGevYVLGvdPAAQRRGLGQMLTSIgIVSLA-RRLggrktldpAVEpAVLLYVESDNVAAVRTYQSL 297
                                    44444444444333333444432668888888887776455555.444344433432224699999************** PP

                 Acetyltransf_3 136 Gfe 138
                                    Gf+
  gi|121636743|ref|YP_976966.1| 298 GFT 300
                                    *96 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00011      0.28      29      54 ..      79     104 ..      62     109 .. 0.87
   2 ?    2.2   0.0      0.08   2.1e+02      28      46 ..     236     254 ..     218     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                Acetyltransf_CG  29 hTeVpeelrGkGiAkkLvkaalddar 54 
                                      +V+++ r++Gi+ ++++aal ++ 
  gi|121636743|ref|YP_976966.1|  79 ELVVHPQSRRRGIGTAMARAALAKTA 104
                                    679*******************8765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                Acetyltransf_CG  28 thTeVpeelrGkGiAkkLv 46 
                                    +   V+++ +++G+++ L+
  gi|121636743|ref|YP_976966.1| 236 YVLGVDPAAQRRGLGQMLT 254
                                    55679**********9996 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00023      0.58      76     107 ..      77     108 ..      72     114 .. 0.86
   2 ?   -3.2   0.0       3.3   8.4e+03      11      29 ..     164     183 ..     157     197 .. 0.67
   3 ?   -1.9   0.0       1.3   3.4e+03      76      94 ..     235     253 ..     226     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                    EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                 Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegq 107
                                     +   v+p+ r+rg+ +++ ++al++ + ++q
  gi|121636743|ref|YP_976966.1|  77 MAELVVHPQSRRRGIGTAMARAALAKTAGRNQ 108
                                    56788*******************99887776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHTT----H... CS
                 Acetyltransf_9  11 devlellkyaFqdeespl.e 29 
                                     e l++ ++aF+ ++++  +
  gi|121636743|ref|YP_976966.1| 164 AELLRVNNAAFAGHPEQGgW 183
                                    56788888899888888643 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                    EEEEEE-CCGTTS-HHHHH CS
                 Acetyltransf_9  76 vtgVavapehrgrgvlskL 94 
                                    v+  +v+p  ++rg+ + L
  gi|121636743|ref|YP_976966.1| 235 VYVLGVDPAAQRRGLGQML 253
                                    6778999999999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2239.35
//
Query:       gi|121636744|ref|YP_976967.1|  [L=170]
Description: phosphate-transport ATP-binding protein ABC transporter phoTa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-16   60.6   0.0    2.7e-16   60.3   0.0    1.1  1  ABC_tran     ABC transporter
    2.1e-05   24.8   0.0    2.9e-05   24.4   0.0    1.3  1  AAA_22       AAA domain
    2.3e-05   24.4   0.0    2.9e-05   24.0   0.0    1.1  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00067   19.6   0.0    0.00096   19.1   0.0    1.2  1  Rad17        Rad17 P-loop domain
    0.00085   19.1   0.0     0.0013   18.5   0.0    1.1  1  AAA_30       AAA domain
     0.0029   18.0   0.0      0.004   17.6   0.0    1.3  1  AAA_16       AAA ATPase domain
     0.0046   17.5   0.0     0.0073   16.9   0.0    1.3  1  AAA_18       AAA domain
     0.0061   16.7   0.0     0.0067   16.6   0.0    1.3  1  AAA_33       AAA domain
     0.0082   16.1   0.0      0.011   15.6   0.0    1.2  1  RsgA_GTPase  RsgA GTPase
      0.009   15.8   0.0      0.014   15.1   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.011   15.5   1.0      0.012   15.3   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
      0.014   15.7   0.0      0.022   15.0   0.0    1.3  1  AAA_28       AAA domain
      0.016   15.0   0.0       0.02   14.6   0.0    1.2  1  AAA_15       AAA ATPase domain
      0.029   14.7   0.1      0.043   14.1   0.1    1.2  1  AAA_19       AAA domain
      0.035   14.6   0.0      0.054   14.0   0.0    1.2  1  AAA_23       AAA domain
      0.045   13.7   0.0      0.068   13.2   0.0    1.2  1  AAA_5        AAA domain (dynein-related subfamily)
      0.066   12.9   0.0      0.092   12.5   0.0    1.2  1  AAA_24       AAA domain
       0.08   12.5   0.0       0.13   11.9   0.0    1.3  1  AAA_25       AAA domain
      0.081   13.3   0.0       0.11   13.0   0.0    1.2  1  AAA          ATPase family associated with various cellular a
       0.15   11.8   0.1        0.3   10.8   0.1    1.5  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.17   11.8   0.0       0.24   11.3   0.0    1.2  1  NACHT        NACHT domain
       0.18   11.0   0.0       0.28   10.3   0.0    1.2  1  NB-ARC       NB-ARC domain
       0.19   11.3   0.0       0.24   11.0   0.0    1.2  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.22   10.6   0.0        0.3   10.2   0.0    1.1  1  G-alpha      G-protein alpha subunit
       0.25   11.4   0.0       0.39   10.8   0.0    1.4  1  AAA_14       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   3.7e-19   2.7e-16       2     113 ..      21     153 ..      20     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.7e-19
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlfpel 74 
                                     +vsl + + +++a++G++G+GK+t+l++l ++++       eG +lld++d+    ++   +r+ ig+++q p+ fp +
  gi|121636744|ref|YP_976967.1|  21 ADVSLAILPRSVTALIGPSGCGKTTVLRTLNRMHEVipgarVEGAVLLDDQDIYApgIDPVGVRRAIGMVFQRPNPFPAM 100
                                    589*****************************9998889999*************9999999****************** PP

                                    BHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                    xxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  75 tvren..............esdeeiekalsklglkelkdtvvksspssLSgGq 113
                                    ++r+n                d+ +e  l+  +l +  ++++++ +  LSgG 
  gi|121636744|ref|YP_976967.1| 101 SIRNNvvaglklqgvrnrkVLDDTAESSLRGANLWDEVKDRLDKPGGGLSGGS 153
                                    *************99888777888******************9999******7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     4e-08   2.9e-05       5      70 ..      30     116 ..      28     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4e-08
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee......................erpevvfvtlpsstsskdllrellr 62 
                                    +++++++G+sG+GKTt+lr+l + ++  +  ++                      +r+  + ++ p++    +++++++ 
  gi|121636744|ref|YP_976967.1|  30 RSVTALIGPSGCGKTTVLRTLNRMHEV-IPGARvegavllddqdiyapgidpvgvRRAIGMVFQRPNPFPAMSIRNNVVA 108
                                    6789*******************9854.3333357777777777777777777665555557777777777777777777 PP

                         AAA_22  63 alglelka 70 
                                     l+l++ +
  gi|121636744|ref|YP_976967.1| 109 GLKLQGVR 116
                                    77777666 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.1e-08   2.9e-05       1     125 [.      32     152 ..      32     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.1e-08
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                    +++liGp g+GK+++L++l  ++ +   +r       +++++   ++i+    ++++ + f+   + f+  ++r +  + 
  gi|121636744|ref|YP_976967.1|  32 VTALIGPSGCGKTTVLRTLNRMHEVipgARVEGAVLLDDQDIYA-PGIDPVGVRRAIGMVFQRPNP-FPAMSIRNNVVAG 109
                                    69*********************998854444444444444444.444455556677777777777.8888888888888 PP

                         AAA_21  78 lersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvf 125
                                    l+ ++v     +++++l ++  +  r ++ +d++ ++ +   gg+s+ 
  gi|121636744|ref|YP_976967.1| 110 LKLQGV-----RNRKVLDDTAESSLRGANLWDEVKDRLDKPGGGLSGG 152
                                    888888.....8888888888888888888888888877777777665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06   0.00096      44      69 ..      29      54 ..      15      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                          Rad17 44 kkriLLisGPsGCgkstvvkvLskel 69
                                   ++ +  + GPsGCgk+tv++ L + +
  gi|121636744|ref|YP_976967.1| 29 PRSVTALIGPSGCGKTTVLRTLNRMH 54
                                   45577899**************9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-06    0.0013      17      51 ..      29      64 ..      21      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.ggrvig 51
                                   ++ v++l Gp G GKtt+l++l++++e   g rv g
  gi|121636744|ref|YP_976967.1| 29 PRSVTALIGPSGCGKTTVLRTLNRMHEVIpGARVEG 64
                                   56799**********************998888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.6e-06     0.004      25      46 ..      31      52 ..      18      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.6e-06
                         AAA_16 25 elvllsGesGvGKsslvrellr 46
                                   +++ l+G+sG+GK++++r+l r
  gi|121636744|ref|YP_976967.1| 31 SVTALIGPSGCGKTTVLRTLNR 52
                                   56789*************9985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-05    0.0073       3      25 ..      35      59 ..      34      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf..g 25
                                   l G++G+GKtt+ + L++++++  g
  gi|121636744|ref|YP_976967.1| 35 LIGPSGCGKTTVLRTLNRMHEVipG 59
                                   89**************999755552 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.4e-06    0.0067       1      30 [.      32      70 ..      32     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.4e-06
                         AAA_33  1 lvllvGlpGsGKstlaerl.........lkklgavllss 30
                                   ++ l+G++G+GK+t+++ l         ++ +gavll+ 
  gi|121636744|ref|YP_976967.1| 32 VTALIGPSGCGKTTVLRTLnrmhevipgARVEGAVLLDD 70
                                   5679**************944444333333333666654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.011      96     121 ..      27      52 ..       3      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                    HCTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                     l  ++++l+G+SG GK+t++ +l+ 
  gi|121636744|ref|YP_976967.1|  27 ILPRSVTALIGPSGCGKTTVLRTLNR 52 
                                    566799***************99976 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     2e-05     0.014       3      37 ..      34      66 ..      32      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                            PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegds 37
                                   ++ g+SG+Gkttv r+l+ + +   ++ a +eg +
  gi|121636744|ref|YP_976967.1| 34 ALIGPSGCGKTTVLRTLNRMHE--VIPGARVEGAV 66
                                   788*************998765..66666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.7e-05     0.012      15      39 ..      23      47 ..       9      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    ++ i ++++t l+GpsG GK+T+l
  gi|121636744|ref|YP_976967.1| 23 VSLAILPRSVTALIGPSGCGKTTVL 47
                                   4455667779*************97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     3e-05     0.022       3      22 ..      34      53 ..      32      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                         AAA_28  3 vitGgestGKTtlleaLaar 22
                                   +++G++++GKTt+l+ L+++
  gi|121636744|ref|YP_976967.1| 34 ALIGPSGCGKTTVLRTLNRM 53
                                   79***************975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.8e-05      0.02      23      47 ..      29      54 ..      14      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                         AAA_15 23 ee.ltvliGkNnsGKSsilealdlFl 47
                                   +  +t liG+ ++GK+++l+ l+ + 
  gi|121636744|ref|YP_976967.1| 29 PRsVTALIGPSGCGKTTVLRTLNRMH 54
                                   3359****************998775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.1e-05     0.043       8      35 ..      28      55 ..      23      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                         AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallv 35
                                   l+++v +++++ G+GKT+vl++  ++ +
  gi|121636744|ref|YP_976967.1| 28 LPRSVTALIGPSGCGKTTVLRTLNRMHE 55
                                   78899***************99876655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.5e-05     0.054      19      38 ..      30      49 ..      14      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                         AAA_23 19 kgltlItGpNGaGKTTildA 38
                                   + +t+++Gp G+GKTT+l+ 
  gi|121636744|ref|YP_976967.1| 30 RSVTALIGPSGCGKTTVLRT 49
                                   5699*************975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.5e-05     0.068       4      22 ..      35      53 ..      33      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-05
                                   EE--SSSSHHHHHHHGGGG CS
                          AAA_5  4 LvGppGtgKselaerlaaa 22
                                   L+Gp+G+gK+++ + l ++
  gi|121636744|ref|YP_976967.1| 35 LIGPSGCGKTTVLRTLNRM 53
                                   9*************99886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.092       5      25 ..      33      52 ..      30      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                         AAA_24  5 iliyGpsgiGKTtlakelgpk 25
                                    +++Gpsg GKTt++++l ++
  gi|121636744|ref|YP_976967.1| 33 TALIGPSGCGKTTVLRTL-NR 52
                                   589*************99.54 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.13      32      50 ..      29      47 ..      22      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                         AAA_25 32 agelallaGapgtGKttla 50
                                     ++++l+G++g+GKtt++
  gi|121636744|ref|YP_976967.1| 29 PRSVTALIGPSGCGKTTVL 47
                                   4799*************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015      0.11       3      20 ..      35      52 ..      33      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                   EESSTTSSHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavak 20
                                   l+Gp G+GKT++ + + +
  gi|121636744|ref|YP_976967.1| 35 LIGPSGCGKTTVLRTLNR 52
                                   89**********998765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00042       0.3       5      23 ..      34      52 ..      31      77 .. 0.89
   2 ?   -2.4   0.0       5.1   3.6e+03      77      98 ..      71      92 ..      65     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                      PduV-EutP  5 lliGkvgsGKttLtqalkg 23
                                    liG++g+GKtt+ ++l+ 
  gi|121636744|ref|YP_976967.1| 34 ALIGPSGCGKTTVLRTLNR 52
                                   59***********999985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                      PduV-EutP 77 esvfppgfasvfnkeviGiitk 98
                                   + +++pg+  v  +  iG++ +
  gi|121636744|ref|YP_976967.1| 71 QDIYAPGIDPVGVRRAIGMVFQ 92
                                   5678888888888888888754 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.24       2      20 ..      32      50 ..      31      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                   CEEEEC-TTTCHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                   + +l G++G+GKTt l+ l
  gi|121636744|ref|YP_976967.1| 32 VTALIGPSGCGKTTVLRTL 50
                                   6789************987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00039      0.28      22      46 ..      32      56 ..      27      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                                   EEEEEESTTSSHHHHHHHHCCSHCC CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnksde 46
                                   v al G  G+GKtt+++  ++ ++ 
  gi|121636744|ref|YP_976967.1| 32 VTALIGPSGCGKTTVLRTLNRMHEV 56
                                   7799************999988655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.24       2      23 ..      32      53 ..      31      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                   EEEEEESTTCCHHHHHHHHHCT CS
                           cobW  2 vtvltGflGsGKTtLlnhllen 23
                                   vt l G+ G GKTt+l++l + 
  gi|121636744|ref|YP_976967.1| 32 VTALIGPSGCGKTTVLRTLNRM 53
                                   7899*************98744 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042       0.3      28      48 ..      35      55 ..      30      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                                   EEESTTSSHHHHHHHHHHHCS CS
                        G-alpha 28 llGqseSGKsTilkqlkllyk 48
                                   l+G s++GK+T+l+ l ++++
  gi|121636744|ref|YP_976967.1| 35 LIGPSGCGKTTVLRTLNRMHE 55
                                   89*****************95 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00054      0.39       3      27 ..      31      55 ..      29      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                         AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                    + ++ G+  +GKTt+l++l + + 
  gi|121636744|ref|YP_976967.1| 31 SVTALIGPSGCGKTTVLRTLNRMHE 55
                                   57899************99976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1176.69
//
Query:       gi|121636745|ref|YP_976968.1|  [L=213]
Description: phosphate-transport system transcriptional regulatory protein phoY2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-25   87.2   5.3    4.8e-12   46.2   1.0    2.1  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.017   14.5   0.1      0.031   13.6   0.1    1.5  1  PhoU_div  Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   1.0   5.4e-16   4.8e-12       2      88 ..      17     103 ..      16     104 .. 0.97
   2 !   43.4   0.2   3.9e-15   3.5e-11       2      89 .]     122     204 ..     121     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 5.4e-16
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                     +m  ++  ++++a +al + d  la++vi++ ++i  l  + e+s++ +la + p+a dlr+++s+++++ d+ R+g  
  gi|121636745|ref|YP_976968.1|  17 GEMCGLAGIAMERATQALLQADLVLAEQVISDHEKIATLSARAEESAFVLLALQAPVAGDLRAIVSAIQMVADIDRMGAL 96 
                                    589999999*********************************************************************** PP

                                    HHHHHHH CS
                           PhoU  82 avniaer 88 
                                    a ++a++
  gi|121636745|ref|YP_976968.1|  97 ALHVAKI 103
                                    *****98 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 3.9e-15
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                     +m++++ e  + a e++ + d e a +++e+dd +d+l++ +   l+ +  k+      + +++++  ++r +ER +Dh
  gi|121636745|ref|YP_976968.1| 122 AEMGRVAVELGNSAQEVVLSHDPEKAAQIREEDDAMDDLHRHLFTVLMDREWKH-----GVAAAVDVTLLSRFYERFADH 196
                                    58***************************************9988866655333.....3566899************** PP

                                    HHHHHHHH CS
                           PhoU  82 avniaerv 89 
                                    av++a+rv
  gi|121636745|ref|YP_976968.1| 197 AVEVARRV 204
                                    *****986 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.5e-06     0.031      87     207 ..      90     203 ..      72     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-06
                       PhoU_div  87 lDeildvlediamlvtlr..kvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDql 164
                                    +D +   + ++a++ + r  + ++pee++  f ++  + ve  + ++ev+ + +        + +++ +i +  d +D+l
  gi|121636745|ref|YP_976968.1|  90 IDRMGALALHVAKIARRRhpQHALPEEVNGYFAEMGRVAVELGNSAQEVVLSHD--------P-EKAAQIREEDDAMDDL 160
                                    555555555666655544225679999999999999999999999999985544........3.456679999******* PP

                       PhoU_div 165 qrklikklfsredasnplevlllveiieklenvsdraedvadr 207
                                    +r+l ++l+ re   ++++ +++  + +  e  +d a +va r
  gi|121636745|ref|YP_976968.1| 161 HRHLFTVLMDREWKHGVAAAVDVTLLSRFYERFADHAVEVARR 203
                                    **********776666655555554444445566777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1386.98
//
Query:       gi|121636746|ref|YP_976969.1|  [L=684]
Description: hypothetical protein BCG_0875c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-47  159.6   0.0    1.1e-46  158.8   0.0    1.4  1  LytR_cpsA_psr  Cell envelope-related transcriptional attenuat
    4.5e-16   59.6   1.1    1.2e-15   58.3   1.1    1.8  1  LytR_C         LytR cell envelope-related transcriptional att


Domain annotation for each model (and alignments):
>> LytR_cpsA_psr  Cell envelope-related transcriptional attenuator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8   0.0   1.2e-50   1.1e-46       1     151 [.     254     428 ..     254     429 .. 0.92

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 1.2e-50
                                    --SEEEEEEEEGGGTEEEEEEE-TTBEE---....................--...--.......---EES-TTTTT-HH CS
                  LytR_cpsA_psr   1 rsDtimlvtvnakkkkvklvSipRDtlveip....................ggeskat.......gekkinsayalggae 53 
                                    rsDt+mlv+++a++++v++vS+pRD +++ +                    g     t       +e+k+nsa+++gg++
  gi|121636746|ref|YP_976969.1| 254 RSDTVMLVNIPASRERVVAVSFPRDLAITPIqceawnpetgkygpiydektG-----TmgprlvyTETKLNSAFSFGGPK 328
                                    8***************************9779*9**9999988777754431.....134556679************** PP

                                    HHHHHHHHHHTS---EEEEE-HHHHHHHHHHHT---B--------------------B---HHHHHH-----------.. CS
                  LytR_cpsA_psr  54 llvktvekllginidyYvevdfegfaklvdalgGvevdvkedvkdkeeselklkaGeqkldGeqalayvRfRkddeeg.. 131
                                    +lvk+++kl+g++i++++++df gfa++v+algGvev+++++++d+e +++  +aG+q +dG +al+yvR+R+ ++e+  
  gi|121636746|ref|YP_976969.1| 329 CLVKVIQKLSGLSINRFIAIDFVGFARMVEALGGVEVCSTTPLRDYELGTVLEHAGRQVIDGPTALNYVRARQVTTESng 408
                                    **********************************************9999***********************9876566 PP

                                    --SHHHHHHHHHHHHHHTT- CS
                  LytR_cpsA_psr 132 DlgRikrQqqvleallkklk 151
                                    D+gRikrQq +l++ll+++ 
  gi|121636746|ref|YP_976969.1| 409 DYGRIKRQQLFLSSLLRSMI 428
                                    *****************996 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   1.1   1.3e-19   1.2e-15       1      85 []     557     641 ..     557     641 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.3e-19
                         LytR_C   1 evkVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaalglgelqedsvkdasvtvv 80 
                                    ev+V+V N tg++GlA +++d+L+++Gf+v ++++++++   tt+++++++++aa ++aa +g ++++  +  ++ v+vv
  gi|121636746|ref|YP_976969.1| 557 EVTVQVSNSTGQAGLATTATDQLKRNGFNVMAPDDYPSSLLATTVFFSPGNEQAAATVAAVFGQSKIERVTGIGQLVQVV 636
                                    69******************************6666666666*****6655679********99996666666666**** PP

                         LytR_C  81 lGkdf 85 
                                    lG+df
  gi|121636746|ref|YP_976969.1| 637 LGQDF 641
                                    ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 5009.38
//
Query:       gi|121636747|ref|YP_976970.1|  [L=389]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.6e-111  369.8   0.0   1.1e-110  369.6   0.0    1.0  1  Dus       Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.6   0.0    6e-115  1.1e-110       1     299 [.      25     338 ..      25     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 369.6 bits;  conditional E-value: 6e-115
                                    EE---TTTS-HHHHHHHHHTT-S......SEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHH CS
                            Dus   1 llaPmagvtdlpfRelvrefgat......aLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAkl 74 
                                    +laPmagvt+++fR l+r++ +       +L+v+emvta+a+++++ v+++m++++ +e+p+++Ql++ dp+++++aA++
  gi|121636747|ref|YP_976970.1|  25 VLAPMAGVTNVAFRALCRQLEQSkvgtvsGLYVCEMVTARALIERHPVTMHMTTFSADESPRSLQLYTVDPDTTYAAARM 104
                                    59******************9999999999*************************************************9 PP

                                    HHH.TT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSS...S-EEEEEESESSTTTC.HHHHHHHHHHC CS
                            Dus  75 vad.lgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkave...iPvtvkirigiddeeenalelakiveaa 150
                                     a    ad+Id+N+GCP++kvt++g GaaL+ k++l+ qiv+a+v+a+e   iPvtvk+rigidd+++++l++++i+ea+
  gi|121636747|ref|YP_976970.1| 105 IAGeGLADHIDMNFGCPVPKVTKRGCGAALPFKRRLFGQIVAAAVRATEgtdIPVTVKFRIGIDDAHHTHLDAGRIAEAE 184
                                    887699******************************************9999**************************** PP

                                    T-SEEEEESSECCCTT-CG--CHHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHH CS
                            Dus 151 GaqaltvHgRtraqnyegtadweaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestav 229
                                    Ga+a+++H+Rt+aq+y+gtadwe+I+ +kq+v+ ipv++NGdI+da da a+++ tG+dgv+igrg+lg+Pwlfae  a+
  gi|121636747|ref|YP_976970.1| 185 GAAAVALHARTAAQRYSGTADWEQIARLKQHVRtIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLFAELSAA 264
                                    ****************************************************************************77** PP

                                    HHSC------.HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHHCC...HH CS
                            Dus 230 ktgeaepapp.laeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrreleevsdkeea...le 299
                                    +tg+++p+pp l e+a+i+++h + l++++gedkg+r+irkh+awyl+g+++ + lrr+l+ v++ +e    l+
  gi|121636747|ref|YP_976970.1| 265 FTGSPAPTPPtLGEVADIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHGFPAGSALRRALAMVKTLDELdclLD 338
                                    *****************************************************************999844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3081.50
//
Query:       gi|121636748|ref|YP_976971.1|  [L=338]
Description: acyl-ACP desaturase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-90  301.0   0.1    9.1e-90  300.8   0.1    1.0  1  FA_desaturase_2  Fatty acid desaturase
  ------ inclusion threshold ------
       0.13   12.8   0.4        1.1    9.9   0.0    2.5  2  AAA_18           AAA domain
       0.13   11.9   0.1       0.29   10.8   0.1    1.5  1  DUF1580          Protein of unknown function (DUF1580)


Domain annotation for each model (and alignments):
>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.8   0.1   1.5e-93   9.1e-90       2     320 ..       7     316 ..       6     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 300.8 bits;  conditional E-value: 1.5e-93
                FA_desaturase_2   2 klevlkslekvveenllellkPvekaWqpsdflPdsesee.faeevkelrerakelpddllvvlvgdmvTEeaLPtYesl 80 
                                    +l++l++le+vve++l+++l+ ++k W+p+d++P+s+ ++ +a   ++++  +++l+d ++v++v+++vTE++LP+Y+++
  gi|121636748|ref|YP_976971.1|   7 DLQLLHELEPVVEKYLNRHLS-MHKPWNPHDYIPWSDGKNyYALGGQDWDPDQSKLSDVAQVAMVQNLVTEDNLPSYHRE 85 
                                    6899*****************.***************999788899********************************** PP

                FA_desaturase_2  81 lntlegvrdetgasdtawakWvraWtaEEnrHgdlLnkYlylsgrvdmrevektvqelikaGfdikt.......ekdpyk 153
                                    +++ +g       +d aw++Wv++WtaEEnrHg +L++Yl++++ vd  e+ek + e++++Gf++++       +++  +
  gi|121636748|ref|YP_976971.1|  86 IAMNMG-------MDGAWGQWVNRWTAEENRHGIALRDYLVVTRSVDPVELEKLRLEVVNRGFSPGQnhqghyfAESLTD 158
                                    *****9.......899**************************************************9888888888999* PP

                FA_desaturase_2 154 gfvYtsfQErATkvsHrntaklakeagdellakicgaiaadEkrHeaaYtrvvekllevdpdeavlaladmmrkkitmPa 233
                                    +++Y+sfQE+AT++sHrnt+k+   ++d+++++++++i+adE+ H+++Y++v+e+++++ p++a+++l+ ++ + ++mP+
  gi|121636748|ref|YP_976971.1| 159 SVLYVSFQELATRISHRNTGKA---CNDPVADQLMAKISADENLHMIFYRDVSEAAFDLVPNQAMKSLHLILSH-FQMPG 234
                                    *********************9...9**********************************************99.***** PP

                FA_desaturase_2 234 allrdgkdeelFeefsavaqrlgvYtardyld.ileelikkWkieeleglsgegrrardyvcalperlrrvaeraeerak 312
                                      +      ++F++ + v++  gvY++r +ld +++ ++kkW+i e+e+++geg++ rd+++ + + l+ +++++e +++
  gi|121636748|ref|YP_976971.1| 235 FQV------PEFRRKAVVIAVGGVYDPRIHLDeVVMPVLKKWRIFEREDFTGEGAKLRDELALVIKDLELACDKFEVSKQ 308
                                    ***......9*********************99*******************************************9999 PP

                FA_desaturase_2 313 kkepeeev 320
                                    ++  +e++
  gi|121636748|ref|YP_976971.1| 309 RQLDREAR 316
                                    88777554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00018       1.1      28     117 ..      61     179 ..      17     183 .. 0.79
   2 ?   -0.6   0.1      0.31   1.9e+03      89     120 ..     288     320 ..     271     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
                         AAA_18  28 lrdvakenglllevdpe...aldeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikk........ 96 
                                    l+dva+  +    v+++    ++++  ++++++ ++ + ++++ + +e+ + + + + l+  +s + +++ k        
  gi|121636748|ref|YP_976971.1|  61 LSDVAQVAMVQNLVTEDnlpSYHREIAMNMGMDGAWGQWVNRWTA-EENRHGIALRDYLVVTRSVDPVELEKlrlevvnr 139
                                    556666666555555555568999999999999999999999997.7777888888888888888888877788888888 PP

                         AAA_18  97 ...................vvLtaspeelleRlekRgyee 117
                                                        vL++s +el+ R++ R++ +
  gi|121636748|ref|YP_976971.1| 140 gfspgqnhqghyfaesltdSVLYVSFQELATRISHRNTGK 179
                                    8888888999999999999*****************9765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                         AAA_18  89 eaakdikkvvLtasp.eelleRlekRgyeeaki 120
                                    e a  ik   L +++ e+ ++R  +R+ ++ k+
  gi|121636748|ref|YP_976971.1| 288 ELALVIKDLELACDKfEVSKQRQLDREARTGKK 320
                                    445555557789999899999999999888885 PP

>> DUF1580  Protein of unknown function (DUF1580)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   4.8e-05      0.29      19      41 ..     100     122 ..      97     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                        DUF1580  19 ilRWslkpnrHGvkLetwriGgr 41 
                                    + RW+ + nrHG+ L+ +++  r
  gi|121636748|ref|YP_976971.1| 100 VNRWTAEENRHGIALRDYLVVTR 122
                                    67*************99887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2266.15
//
Query:       gi|121636749|ref|YP_976972.1|  [L=213]
Description: hypothetical protein BCG_0878c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-05   24.5   0.1    2.8e-05   23.8   0.1    1.4  1  TetR_N          Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.047   13.3   0.0      0.069   12.7   0.0    1.2  1  Glyco_hydro_cc  Glycosyl hydrolase catalytic core
       0.13   12.4   0.0       0.28   11.3   0.0    1.6  1  HTH_AraC        Bacterial regulatory helix-turn-helix protein


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   4.8e-09   2.8e-05       1      47 []      26      72 ..      26      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.8e-09
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +++a+++l++  G  a+tvr++ ++AG++++ +Y  F+++e  ++a+
  gi|121636749|ref|YP_976972.1| 26 LVAAGVQLLGGAGGPALTVRAVCRHAGLTERYFYESFADREHFVRAV 72
                                   57899*************************************99986 PP

>> Glyco_hydro_cc  Glycosyl hydrolase catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.069      83     132 ..      86     136 ..      79     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                 Glyco_hydro_cc  83 snmspeeAaklwkqliqplr.ekgvklvsPavaatnseegleWldeFleac 132
                                    s+ +p+eA++ + +l+     ++ v l +Pav    + +g eW+ +F+e  
  gi|121636749|ref|YP_976972.1|  86 SAQTPREAVEQFVELMVDDPvRGRVLLLAPAVEPALTRSGAEWMPNFIELL 136
                                    7789************98444599********666669*********9865 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.7e-05      0.28       9      29 ..      42      62 ..      39      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.7e-05
                                   --HHHHHHHTTSSHHHHHHHH CS
                       HTH_AraC  9 ltiediAdelgfSrsyFsrlF 29
                                   lt++ ++ ++g+ ++yF+  F
  gi|121636749|ref|YP_976972.1| 42 LTVRAVCRHAGLTERYFYESF 62
                                   89****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1701.98
//
Query:       gi|121636750|ref|YP_976973.1|  [L=351]
Description: hypothetical protein BCG_0879 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-57  195.1  11.6    2.5e-57  194.7  11.6    1.1  1  DUF2236   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.7  11.6   1.4e-61   2.5e-57       1     224 [.      59     292 ..      59     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 194.7 bits;  conditional E-value: 1.4e-61
                        DUF2236   1 wryagdelilllgalaalllqaahplvltgvldhstf.adplrRllrTaqfiltvvygsgeeaeaaaarVrllHaavrgt 79 
                                    wry+gd++ +l g ++a+ +q++hp+++++v dhstf ++ + Rllr++  i +vv++ g++a  ++++Vr++H +++g+
  gi|121636750|ref|YP_976973.1|  59 WRYFGDWRGMLQG-PWAGSMQNMHPQLGAAVEDHSTFfRERWPRLLRSLYPIGGVVFD-GDRAPVTGVQVRDYHITIKGV 136
                                    9**********98.***********************555******************.99******************* PP

                        DUF2236  80 dasgerygainpedllwvhatfsasflraygrtvgpltaeeeeayyhewrrvgrllGvpdrllpatraafdayldemvla 159
                                    d +g+ry+a+np+ ++w+hatf+ + l++++r++g lt+++++++++e ++++r++G+++r +pat+++f++y+d+m+++
  gi|121636750|ref|YP_976973.1| 137 DGAGRRYHALNPDVFYWAHATFFVGTLHVAERFCGGLTEAQRRQLFDEHVQWYRMYGMSMRPVPATWEEFQDYWDHMCRN 216
                                    *99******************************999******************************************** PP

                        DUF2236 160 elevdeearel................gdarllparpalpllrvitrgllppalrellglpvpwssrdellvvalralvr 223
                                     le + +ar++                 +++  p+++++++ +++t+gl+ p++rel+g +  w +rde+l   +r++  
  gi|121636750|ref|YP_976973.1| 217 VLENNFAARAVldltelpkppfaqrvpDWLWAAPRKLLARFFVWLTVGLYDPPVRELMGYR--WLRRDEWL---HRRFGD 291
                                    ******9**999999998888888777666666****************************..********...888766 PP

                        DUF2236 224 l 224
                                    +
  gi|121636750|ref|YP_976973.1| 292 I 292
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2858.84
//
Query:       gi|121636751|ref|YP_976974.1|  [L=130]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-14   51.6   0.0    8.9e-14   51.1   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    1.3e-11   44.4   0.4    1.9e-11   43.8   0.4    1.3  1  HTH_20          Helix-turn-helix domain
    2.9e-07   30.3   0.3    4.9e-07   29.5   0.3    1.3  1  MarR_2          MarR family
    1.1e-05   25.1   1.4    1.4e-05   24.8   0.2    1.8  2  HTH_IclR        IclR helix-turn-helix domain
    3.8e-05   23.7   0.8      9e-05   22.5   0.8    1.7  1  DprA_WH         DprA winged helix domain
    0.00019   20.9   0.0    0.00032   20.2   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00024   21.4   0.0    0.00033   20.9   0.0    1.3  1  Rrf2            Transcriptional regulator
    0.00084   19.2   0.0     0.0013   18.6   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0077   16.1   0.0      0.011   15.6   0.0    1.3  1  TFIIE_alpha     TFIIE alpha subunit
     0.0089   16.0   0.1      0.013   15.5   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.049   13.8   0.0    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.044   13.7   0.1      0.092   12.7   0.1    1.5  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.048   13.2   0.0      0.072   12.7   0.0    1.3  1  HTH_47          winged helix-turn-helix
       0.16   12.4   0.0       0.28   11.7   0.0    1.4  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.16   11.6   0.0       0.21   11.2   0.0    1.1  1  ArsR            ArsR transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   7.5e-17   8.9e-14       1      46 [.      27      72 ..      27      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 7.5e-17
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   d tR+++L +La++e++v elae++g++ + vS+HL+kLr a+LV+
  gi|121636751|ref|YP_976974.1| 27 DATRVQVLWSLADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVR 72
                                   679******************************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.4   1.6e-14   1.9e-11       2      60 ..      20      77 ..      19      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.6e-14
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   ++++ La+ +R  +l  L  +++++++elae+++ +  ++s+HL++L+ a Lv+++r g
  gi|121636751|ref|YP_976974.1| 20 EVFRMLADATRVQVLWSL-ADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRDG 77
                                   6899**************.****************************99********87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.3   4.1e-10   4.9e-07       6      56 ..      29      76 ..      25      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.1e-10
                                   HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   +  +vL  L++r+   ++v+ela+  g + ++vs++l++L  a Lv++r++
  gi|121636751|ref|YP_976974.1| 29 TRVQVLWSLADRE---MSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRD 76
                                   7899********9...9********************************87 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.2   1.1e-08   1.4e-05      15      50 ..      38      73 ..      18      75 .. 0.83
   2 ?   -3.0   0.1       5.7   6.8e+03      15      28 ..     111     124 ..     109     125 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                   TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   a++e+++ elA++ g p ++v+ +L+ L   ++v++
  gi|121636751|ref|YP_976974.1| 38 ADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRT 73
                                   4566******************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.7
                                    TBSS-BHHHHHHHH CS
                       HTH_IclR  15 apqeltlselArrt 28 
                                    ++ + +l+ +A+++
  gi|121636751|ref|YP_976974.1| 111 HRAAGGLQSVAKAS 124
                                    55556777777665 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.8   7.5e-08     9e-05      11      59 ..      27      75 ..       4      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.5e-08
                        DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverlp 59
                                   d+++ +vL  L+   ++v +L++++g pa +vs +L  L +a lv+++ 
  gi|121636751|ref|YP_976974.1| 27 DATRVQVLWSLADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRR 75
                                   89999****************************************9875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.7e-07   0.00032      15      42 ..      39      66 ..      27      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                         HTH_24 15 nprisqreLAerlglSpstvnrrlkrLe 42
                                   +  +s +eLAe++g + + v+++l +L 
  gi|121636751|ref|YP_976974.1| 39 DREMSVNELAEQVGKPAPSVSQHLAKLR 66
                                   678***********************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.8e-07   0.00033      21      59 ..      38      75 ..      23      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-07
                                   STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   +++e +s++e+ae+++ +++ +++ lakLr a lv+++r
  gi|121636751|ref|YP_976974.1| 38 ADRE-MSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRR 75
                                   3444.9*******************************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0013      17      63 ..      37      83 ..      29      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEE CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYr 63
                                   L    +++++e+ae++g p ++v + L +L  + lV++++  ++ +Yr
  gi|121636751|ref|YP_976974.1| 37 LA-DREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRDGTTiFYR 83
                                   44.7799******************************99966552665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.1e-06     0.011       2      82 ..      17      90 ..      16      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.1e-06
                                   HHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHC CS
                    TFIIE_alpha  2 llkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklv 82
                                   l+ ev r  ++   v+vl +L+ + e++ ++la++++   + + + L++L+ arlv  +r    ++   + ++r++ e++ 
  gi|121636751|ref|YP_976974.1| 17 LVVEVFRMLADATRVQVLWSLA-DREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRD---GT---TIFYRLENEHVR 90
                                   788999999999**********.999*****************************988763...22...345555555555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.1e-05     0.013      20      58 ..      40      79 ..      20      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EE CS
                      HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrr.ir 58
                                     ++  elA+ +G    +vs+ l++L+ + l++++r+  +
  gi|121636751|ref|YP_976974.1| 40 REMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRDgTT 79
                                   46999****************************6543344 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.1e-05     0.049      23      56 ..      42      75 ..      31      78 .. 0.85
   2 ?   -0.6   0.0       1.4   1.6e+03      33      42 ..     119     128 ..      90     130 .] 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                    ++ +lae  +  ++sVs+ l kL+ + +v +  
  gi|121636751|ref|YP_976974.1| 42 MSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRR 75
                                   5789*********************999998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                    TS-HHHHHHH CS
                 Fe_dep_repress  33 nvspssVsem 42 
                                     v+++s+++ 
  gi|121636751|ref|YP_976974.1| 119 SVAKASATKD 128
                                    3889999985 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.7e-05     0.092       4      38 ..      31      66 ..      29      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_1  4 lrlfvavaeeg.sftrAAeeLglsqpavsrqikrLE 38
                                   ++++  +a+ + s+++ Ae++g   p+vs+++++L+
  gi|121636751|ref|YP_976974.1| 31 VQVLWSLADREmSVNELAEQVGKPAPSVSQHLAKLR 66
                                   566777777777**********************97 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     6e-05     0.072      36      77 ..      33      72 ..      21      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                   HHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 36 llwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   +lw  +laD ++s+ ++Ae++g p+  v + + +L+ a l++
  gi|121636751|ref|YP_976974.1| 33 VLW--SLADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVR 72
                                   444..789*****************************99986 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.28       6      32 ..      37      63 ..      36      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                         HTH_26  6 madrgitkseLargtgisaatlsrlvk 32
                                   +adr+++++eLa+++g  a+++s ++ 
  gi|121636751|ref|YP_976974.1| 37 LADREMSVNELAEQVGKPAPSVSQHLA 63
                                   79**************99999998765 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.21       7      59 ..      18      73 ..      12      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                           ArsR  7 LvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEs 59
                                   +v +++++ ++t  +v+ +l ++ ++ +el+e++g+    v++ l+ L+ ++l+ +
  gi|121636751|ref|YP_976974.1| 18 VVEVFRMLADATRVQVLWSLADREMSVNELAEQVGKPapsVSQHLAKLRMARLVRT 73
                                   5889*******************************975557777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 970.75
//
Query:       gi|121636752|ref|YP_976975.1|  [L=140]
Description: deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-11   41.6   0.1    1.3e-10   41.1   0.1    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.4e-08   34.6   0.0    1.9e-08   34.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.049   13.8   0.0      0.077   13.1   0.0    1.3  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   2.1e-14   1.3e-10      41     100 ..       8      68 ..       4      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.1e-14
                                    ESBHHCCTGTTB-HHHHHHHHHHHH.TSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                dCMP_cyt_deam_1  41 yngepaggsktiHAEvnAilkaakn.ggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                    + + ++ +++t+HAE +Ai++a+++ g+++l g+tl v   PC+mC   +  + +++vv++
  gi|121636752|ref|YP_976975.1|   8 FRRWAQTNDPTAHAESLAIRAACTKlGTEHLVGTTLNVLAHPCPMCYGSLYYCSPDEVVFL 68 
                                    556677899****************8999******************************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   3.2e-12   1.9e-08      44      91 ..      12      59 ..       4      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.2e-12
                    MafB19-deam 44 elnakataHaEiaalqqAakklkskrlddatlyvtlepCdmCagaivq 91
                                    + +++taHaE  a++ A+ kl++ +l ++tl v   pC+mC g + +
  gi|121636752|ref|YP_976975.1| 12 AQTNDPTAHAESLAIRAACTKLGTEHLVGTTLNVLAHPCPMCYGSLYY 59
                                   56789*************************************998766 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.077      15      61 ..      10      58 ..       4      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                          SNAD4 15 gvlknkke..haEllflekikseldpsqeyrvtwylswsPCaeCaekia 61
                                   +++++++   haE+l ++  + +l +++ +  t+ +   PC+ C  +++
  gi|121636752|ref|YP_976975.1| 10 RWAQTNDPtaHAESLAIRAACTKLGTEHLVGTTLNVLAHPCPMCYGSLY 58
                                   5655533347**********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1067.98
//
Query:       gi|121636753|ref|YP_976976.1|  [L=96]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-09   36.8   1.5    3.9e-09   36.3   1.5    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.009   15.9   0.6      0.015   15.2   0.6    1.3  1  ChW             Clostridial hydrophobic W


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   1.5   4.4e-13   3.9e-09      27      68 ..       4      44 ..       2      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.4e-13
                 OrfB_Zn_ribbon 27 TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68
                                   +SktC+ C ++++    +++++C+ C  +++rD nAaiN+++
  gi|121636753|ref|YP_976976.1|  4 SSKTCHACRHVQDI-GWDEKWQCDGCSITHQRDDNAAINLAR 44
                                   8*************.99***********************97 PP

>> ChW  Clostridial hydrophobic W
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   1.6e-06     0.015       1      14 [.      13      27 ..      13      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                            ChW  1 HVQniGW.qnwvkdG 14
                                   HVQ+iGW + w +dG
  gi|121636753|ref|YP_976976.1| 13 HVQDIGWdEKWQCDG 27
                                   *******55799999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 694.72
//
Query:       gi|121636754|ref|YP_976977.1|  [L=301]
Description: hypothetical protein BCG_0883 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-61  206.5   0.2    4.5e-61  206.1   0.2    1.2  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.1   0.2   2.5e-65   4.5e-61       1     188 []      19     200 ..      19     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.1 bits;  conditional E-value: 2.5e-65
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    a++vaa+ral++      lidDp+a++lv+a+g+++++r  d ++  e    ++e + ++++ g+a+Rtrffd+++ +a+
  gi|121636754|ref|YP_976977.1|  19 ATMVAAQRALAADPR-YALIDDPYAAPLVRAVGMDVYTRLVDWQIPVE---GDSEFDPQRMATGMACRTRFFDQFFLDAT 94 
                                    79*********8866.*******************9888877777775...578999*********************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     ++gi q+ViL++GlD+rayRl+w+ g+ v+EvD+pev+efK++tl +lgaep +e+r+v+vDlr ddw++aL++agfdp
  gi|121636754|ref|YP_976977.1|  95 -HSGIGQFVILASGLDARAYRLAWPVGSIVYEVDMPEVIEFKTATLSDLGAEPATERRTVAVDLR-DDWATALQTAGFDP 172
                                    .79**************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleaia 188
                                    ++p+aw+aeG+lvYL+ ea+dal+++i+
  gi|121636754|ref|YP_976977.1| 173 KVPAAWSAEGLLVYLPVEAQDALFDNIT 200
                                    *************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2442.77
//
Query:       gi|121636755|ref|YP_976978.1|  [L=271]
Description: hypothetical protein BCG_0884c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1990.96
//
Query:       gi|121636756|ref|YP_976979.1|  [L=910]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-29  100.5  23.4    4.9e-29  100.5  23.4    1.5  2  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5  23.4   2.7e-33   4.9e-29       1      92 [.       1      92 [.       1      93 [. 0.99
   2 ?   -4.3   0.4         1   1.8e+04      26      35 ..     517     526 ..     507     531 .. 0.48

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 2.7e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+v+v P +la+aa+++a+igsals a+a aaa t+av aaaaDeVSaaiAalfsah++++qalsa+aaafh++fvqalaa
  gi|121636756|ref|YP_976979.1|  1 MSYVSVLPATLATAATEVARIGSALSLASAVAAAQTSAVQAAAADEVSAAIAALFSAHGRDFQALSARAAAFHHEFVQALAA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +agsYa aE 
  gi|121636756|ref|YP_976979.1| 83 GAGSYAVAEI 92
                                   ********97 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1
                                    HHHHHHHHHH CS
                             PE  26 saanaaaaap 35 
                                    ++a aa+ ap
  gi|121636756|ref|YP_976979.1| 517 QQALAAVNAP 526
                                    3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (910 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.33u 0.39s 00:00:01.72 Elapsed: 00:00:00.63
# Mc/sec: 4364.81
//
Query:       gi|121636757|ref|YP_976980.1|  [L=882]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-33  114.5  22.6    4.1e-33  113.6  22.6    1.5  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6  22.6   2.3e-37   4.1e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 2.3e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aP+++a a++dlagig++l+aanaaaa pt+++laaa DeVSaaiAalfs+h+q+yqa+saqaaafh++fvqala+
  gi|121636757|ref|YP_976980.1|  1 MSFVIAAPDLVAMATEDLAGIGASLTAANAAAAVPTSGLLAAAGDEVSAAIAALFSSHGQQYQAMSAQAAAFHARFVQALAG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a g+YaaaEaa
  gi|121636757|ref|YP_976980.1| 83 AMGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.19u 0.31s 00:00:01.50 Elapsed: 00:00:00.57
# Mc/sec: 4631.04
//
Query:       gi|121636758|ref|YP_976981.1|  [L=214]
Description: lipoprotein lpqQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-27   95.6   0.0    4.3e-27   95.2   0.0    1.2  1  PknH_C    PknH-like extracellular domain


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.0   2.4e-31   4.3e-27       1     189 []      36     212 ..      36     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 2.4e-31
                                    --GGGGGGGS--HHHHHHHHT-S.--EE-S-B-S-B-S--EESSGG.......GHHHH-SSBHHHHTTS---EEEEEEEE CS
                         PknH_C   1 vpaaaldslLltpaelaailGtpeaasatesdttppdtaasvdppe.......ClgvasageesvYggsgvtavagqtlr 73 
                                    +p +++dsl+++ +++++i+       ++e+ +++++t+++ +p++       C++v+s++++  +g +++++++++ + 
  gi|121636758|ref|YP_976981.1|  36 PPTSRVDSLIVSIEDVRRIA-------NYEELAAHFQTDLREPPEAdtnvpgpCRVVGSSDRT--FG-TDWSEFRSAGYH 105
                                    6889****************.......78899999999999887778999999*****99888..33.456666666666 PP

                                    -SSTT-SEE.......EEEEEEE-SSHHHHHHHHHHHHHHHHTTTT-EEEEEETTEEEEEEE---B--TT-EEEEEE.ES CS
                         PknH_C  74 dsaddgasl.......vsqavvafptadaAqaffaalaaqwrrCagvttttdsggatetwtvgdvsdddgvltatvtvts 146
                                    +  dd ++        vsqa++++p++++A+ +f++l++++++Cag       +++ +++ +g ++++          t 
  gi|121636758|ref|YP_976981.1| 106 GVTDDLRPGgpvmvetVSQAIALYPDPSTARGVFHRLESSLAECAG------LHDPYFDFILGRPDAS----------TV 169
                                    6666666666666777******************************......9***************..........89 PP

                                    STT--EEEEEEEEETTEEEEEEEEE.SS-SSHHHHHHHHHHHH CS
                         PknH_C 147 ggdgarcqralavranvvvdvevcgfedggdaaaeiadaildk 189
                                    ++ +a+++++++++++v+++v v+g+e++++ a++i+++i d+
  gi|121636758|ref|YP_976981.1| 170 RIGAAGWSHVYRLKSSVFISVGVLGIEPAEPIANVILQTISDR 212
                                    999*************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1446.77
//
Query:       gi|121636759|ref|YP_976982.1|  [L=240]
Description: hypothetical protein BCG_0888c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0029   17.6   0.7      0.027   14.4   0.6    2.0  1  AbiEii         Nucleotidyl transferase AbiEii toxin, Type IV 
  ------ inclusion threshold ------
       0.26   10.7   0.0       0.46    9.9   0.0    1.5  2  Peptidase_C3G  Tungro spherical virus-type peptidase


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.6     3e-06     0.027      25     193 ..      15     180 ..      14     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-06
                         AbiEii  25 layglipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigege...dyeglrlrypaefggyarqk 101
                                     + g+ pR++ D D++ +  ++++ +ea+++ ++++ +   + ++ +++   +  ge    +++ r          +++ 
  gi|121636759|ref|YP_976982.1|  15 FCRGVPPRATNDTDIAGT-LNNWDHFEAIRATFRALGSTGHRFLIADRAVDALPFGEvesPTGTTRH---------PPGN 84 
                                    588999**********99.***********************9999988888877777443333333.........2223 PP

                         AbiEii 102 ikieigfreavppaerreippyleelggpafevpvysleellaeKllalldrgrdrsr...aRDlyDlalLle.aeldae 177
                                      +++      +   +  ++ ++  l  ++ +v    ++  +  Kl+a+l    drs    ++D  Dlal+      d +
  gi|121636759|ref|YP_976982.1|  85 QLMNV------HGCTDAYLRADVLPL-PGGLTVHLPQPPNYAVLKLHAWL----DRSAdhdYKDGPDLALVVHwYAGDLD 153
                                    34554......333444455555555.6788*******************....77776799999999999998777777 PP

                         AbiEii 178 alaeallaylasrgr...........p 193
                                    +l +  ++   +r++            
  gi|121636759|ref|YP_976982.1| 154 RLYAKPDQWALRRHDfdlrtaaaallG 180
                                    777777777777777333334433330 PP

>> Peptidase_C3G  Tungro spherical virus-type peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   5.2e-05      0.46      86     124 ..       7      46 ..       1      95 [. 0.85
   2 ?   -3.0   0.0      0.45     4e+03      99     131 ..     115     150 ..     114     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.2e-05
                  Peptidase_C3G  86 fqdlvvwdlGnsvpp.sidvldliatvedwdkfkdgsGal 124
                                     +dl+ w +   vpp + +  d+  t+++wd+f++   ++
  gi|121636759|ref|YP_976982.1|   7 CRDLLHWRFCRGVPPrATNDTDIAGTLNNWDHFEAIRATF 46 
                                    4799**********9567999************9866554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.45
                  Peptidase_C3G  99 ppsidvldliatvedw..dkfkdgsG.alavtkyna 131
                                    pp   vl+l a ++    +++kdg+  al+v  y+ 
  gi|121636759|ref|YP_976982.1| 115 PPNYAVLKLHAWLDRSadHDYKDGPDlALVVHWYAG 150
                                    677777777776654311469999865788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1716.05
//
Query:       gi|121636760|ref|YP_976983.1|  [L=342]
Description: hypothetical protein BCG_0889c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-42  143.3   0.0    8.6e-42  142.8   0.0    1.2  1  AbiEi_2   Transcriptional regulator, AbiEi antitoxin, Type IV


Domain annotation for each model (and alignments):
>> AbiEi_2  Transcriptional regulator, AbiEi antitoxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.8   0.0   4.8e-46   8.6e-42       1     140 [.     200     335 ..     200     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 4.8e-46
                        AbiEi_2   1 rlvkteeLldeWaaaYptrlrpklkllrfkgdeksweeekeleeagAalsGeaaaakliselrpqsatlYv..sdeklte 78 
                                    rlv+t+eLld WaaaYp +l++++kll+++gd ++w++++ l+    a+sGe+a++++i+  +p+s++lYv  ++++l++
  gi|121636760|ref|YP_976983.1| 200 RLVRTDELLDLWAAAYPGGLGRANKLLVASGDIHTWSAPDGLAV---AVSGEQALPDEIR--NPESLMLYVdtPAPGLPA 274
                                    89*****************************************9...67***********..**********99****** PP

                        AbiEi_2  79 elilelrlrrdpeGavelrraFwrakkavgdieivpplliYaDLlaigdpRlvevAqiiker 140
                                    +l++++r++rdp+G++++r+ Fwr+  ++++++++p++liYaDLla+++pR+vevA++++ +
  gi|121636760|ref|YP_976983.1| 275 DLLIHNRWHRDPHGSIVIRKLFWRNL-PDEQPGLAPTALIYADLLASREPRQVEVAHLMRRQ 335
                                    **************************.********************************943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2522.61
//
Query:       gi|121636761|ref|YP_976984.1|  [L=260]
Description: lipoprotein lpqR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-79  264.4   0.0    7.1e-79  264.2   0.0    1.0  1  Peptidase_M15  D-ala-D-ala dipeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M15  D-ala-D-ala dipeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.2   0.0     4e-83   7.1e-79       2     200 ..      63     259 ..      62     260 .] 0.98

  Alignments for each domain:
  == domain 1  score: 264.2 bits;  conditional E-value: 4e-83
                  Peptidase_M15   2 saglvdlaevladveidlkYatadnvtgk.alyqaariladkevalalaeaaavaaiagqqlvlwdayrpksaqdglllw 80 
                                    +aglvd+++v++d++idl+Yata+n+tg+ +++++ar+l+++++a++la+aaav++++gq+lv+wd+yrp+++q  ++++
  gi|121636761|ref|YP_976984.1|  63 AAGLVDVRGVVPDAAIDLRYATANNFTGTqLYPPGARCLVHESMAEGLAAAAAVLRPHGQVLVFWDCYRPHDVQ--VRMF 140
                                    789**************************9999*****************************************..**** PP

                  Peptidase_M15  81 avvPedklviekqvyqieaveninvatdsshsrgaaldltlr.ddegelvdmGsefDelseRslatakqtvepaaqrnRk 159
                                    +vvP++++v+++++y+++++++  +++d+++++++++++++r ++e++l+dmG++fD++s+R++a+a+q+v+++aq+nR+
  gi|121636761|ref|YP_976984.1| 141 DVVPNPAWVARPGKYAHSHEAG--RSVDVTFASAQRQCPSVRrSGELCLADMGTDFDDFSSRATAFATQGVSAEAQANRA 218
                                    **********************..******************************************************** PP

                  Peptidase_M15 160 lLraimesgGflsysgEWWHfelpdaasawlyddrylefav 200
                                    +Lra+m++gG+++ysgEWWHf++p+ +    +d+++le++v
  gi|121636761|ref|YP_976984.1| 219 HLRAAMQAGGLTVYSGEWWHFDGPGPGPGAGVDRPILEVPV 259
                                    *************************9999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2196.17
//
Query:       gi|121636762|ref|YP_976985.1|  [L=270]
Description: hypothetical protein BCG_0891 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-27   95.8   0.0    2.6e-27   95.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.9e-24   85.5   0.1    5.3e-24   84.7   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
      3e-23   82.3   0.1    5.3e-23   81.5   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    2.4e-19   69.8   0.0    3.7e-19   69.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.1e-16   60.5   0.0    3.3e-16   59.8   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    8.7e-15   54.7   0.0    1.2e-14   54.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.7e-07   30.3   0.0    4.2e-07   29.7   0.0    1.2  1  MTS              Methyltransferase small domain
    3.5e-07   30.0   0.0    5.5e-07   29.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    5.6e-07   29.4   0.0    8.2e-07   28.8   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    3.8e-05   22.8   0.0    7.1e-05   21.9   0.0    1.4  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0001   21.5   0.0    0.00014   21.0   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00027   20.8   0.0    0.00038   20.3   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00031   20.3   0.0     0.0005   19.6   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.005   16.3   0.0     0.0068   15.8   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0084   14.7   0.0      0.013   14.1   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
  ------ inclusion threshold ------
      0.023   14.1   0.0      0.034   13.6   0.0    1.1  1  TehB             Tellurite resistance protein TehB
      0.029   13.7   0.0       0.04   13.2   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
       0.04   13.0   0.0      0.062   12.4   0.0    1.2  1  DREV             DREV methyltransferase
       0.14   11.8   0.0       0.23   11.1   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   2.8e-30   2.6e-27       4     113 ..      40     146 ..      37     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 2.8e-30
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    gl+vlD+GCG G++t  la ++ p + v+G++ + +a++lAr++aq + l+n++F  +d+++l+  + d+ fD++++++v
  gi|121636762|ref|YP_976985.1|  40 GLSVLDVGCGPGTITVDLAARVVP-GSVTGVEPTDDALSLARAEAQLHRLSNISFTTSDVHKLD--FPDDAFDVVHAHQV 116
                                    789****************99998.99*************************************..************** PP

                Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr 113
                                    l+++adp  +l+e+ rv +pggi++++d++
  gi|121636762|ref|YP_976985.1| 117 LQHVADPVRALQEMRRVCTPGGIVAARDAD 146
                                    ***************************998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.1   5.7e-27   5.3e-24       1      95 [.      44     141 ..      44     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 5.7e-27
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                    LdvGcG G ++ +la r+  ++v+gv++++ +l la+++a+  +l +++f  +d++kl f+d+ fD+v +++vl+hv+dp
  gi|121636762|ref|YP_976985.1|  44 LDVGCGPGTITVDLAARVvpGSVTGVEPTDDALSLARAEAQLHRLsNISFTTSDVHKLDFPDDAFDVVHAHQVLQHVADP 123
                                    8**************8888************************99*********************************** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                     +al+e++Rv+ pgG+++
  gi|121636762|ref|YP_976985.1| 124 VRALQEMRRVCTPGGIVA 141
                                    ***************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.1   5.6e-26   5.3e-23       1      97 []      43     138 ..      43     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.6e-26
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    vLd+GcG+G++t +la+r+  ++vtgv++++++l  ar++a+ ++l n++f + d+++l+f+d+ fD+v++ ++l+h+  
  gi|121636762|ref|YP_976985.1|  43 VLDVGCGPGTITVDLAARVVPGSVTGVEPTDDALSLARAEAQLHRLsNISFTTSDVHKLDFPDDAFDVVHAHQVLQHVA- 121
                                    9*****************955********************999999************************877***98. PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                     d  +al+e++rv++pgG
  gi|121636762|ref|YP_976985.1| 122 -DPVRALQEMRRVCTPGG 138
                                    .5569************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0     4e-22   3.7e-19       5     164 ..      22     196 ..      17     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4e-22
                Methyltransf_23   5 reeelsdklerllpklraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae......kakkaqkdqfdeqea 76 
                                    r++ +      llp+l +g +vLd+GcG G i+ +++++ +  svtgv++ + a ++a+        ++  ++  d ++ 
  gi|121636762|ref|YP_976985.1|  22 RRRTAENSAGYLLPYLVPGLSVLDVGCGPGtITVDLAARVVPgSVTGVEPTDDALSLARaeaqlhRLSNISFTTSDVHKL 101
                                    44555555556789999999**********7777777777779**********************7777777777777** PP

                Methyltransf_23  77 aepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl........kedrllldwlylvpagrhisffsa 148
                                    ++p++ fd++++ +vl hv dp ++l+ +++ + pgG +  ++ + s         + dr+l+ ++ ++ a   +     
  gi|121636762|ref|YP_976985.1| 102 DFPDDAFDVVHAHQVLQHVADPVRALQEMRRVCTPGGIVAARDADYSGfiwfpklpALDRWLDLYERAARA-NGGEPDAG 180
                                    ********************************************988899997775566666665444444.45566777 PP

                Methyltransf_23 149 rslkelleeaGlevve 164
                                    r l  ++++aG+++v+
  gi|121636762|ref|YP_976985.1| 181 RRLLSWARAAGFDDVT 196
                                    8999999999999886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   3.5e-19   3.3e-16       1      98 [.      44     139 ..      44     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.5e-19
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsai..edakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                    L++GcG G+++  l+++  + ++tgv++  +a+  ++a+++l++ +n +++  ++ +ld  d    ++fD+v+a++vl+h
  gi|121636762|ref|YP_976985.1|  44 LDVGCGPGTITVDLAARVVPGSVTGVEPTDDALslARAEAQLHRLSNISFTTSDVHKLDFPD----DAFDVVHAHQVLQH 119
                                    8********************************55666666666665555555555555444....5************* PP

                Methyltransf_12  79 lkdirevldnirklLkpgGr 98 
                                    ++d+ ++l+++r++++pgG+
  gi|121636762|ref|YP_976985.1| 120 VADPVRALQEMRRVCTPGGI 139
                                    *******************7 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.3e-17   1.2e-14      47     150 ..      39     141 ..      20     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.3e-17
                                    -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                    +g +vlDv +G g ++++l+  v   g v++++  ++ L+ +++ ++ +  +ni f +++  +L+f dd+fDvv     l
  gi|121636762|ref|YP_976985.1|  39 PGLSVLDVGCGPGTITVDLAARVVP-GSVTGVEPTDDALSLARAEAQLHRLSNISFTTSDVHKLDFPDDAFDVVHAHQVL 117
                                    5889****************99975.89**************************************************** PP

                                    GG-S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlv 150
                                    + v+D  +aL+e++rv  pGG++ 
  gi|121636762|ref|YP_976985.1| 118 QHVADPVRALQEMRRVCTPGGIVA 141
                                    *********************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   4.5e-10   4.2e-07      23     101 ..      33     111 ..      23     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.5e-10
                                    HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS-EEE CS
                            MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle.eveekkfdl 100
                                    Ll +l      +vlD+GcG G +++ la++    +vt v+    Al +a++ ++ ++l+ +++++sdv + +++++ fd+
  gi|121636762|ref|YP_976985.1|  33 LLPYLVP--GLSVLDVGCGPGTITVDLAARVVPGSVTGVEPTDDALSLARAEAQLHRLSnISFTTSDVHKlDFPDDAFDV 110
                                    5555555..3359*****************9999************************99*******9874677888888 PP

                                    E CS
                            MTS 101 i 101
                                    +
  gi|121636762|ref|YP_976985.1| 111 V 111
                                    7 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.8e-10   5.5e-07      11     103 ..      37     135 ..      30     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.8e-10
                           MetW  11 ikpgsrvldlGcGdGellellkeekqvdg..rGleldeegvaecva.....kGlsviqgdldkdlenfedksfdyvvlsq 83 
                                    + pg  vld+GcG G++   l+  + v g   G+e  ++++  + a     +  ++     d     f+d++fd+v   q
  gi|121636762|ref|YP_976985.1|  37 LVPGLSVLDVGCGPGTITVDLAA-RVVPGsvTGVEPTDDALSLARAeaqlhRLSNISFTTSDVHKLDFPDDAFDVVHAHQ 115
                                    567889**********9888855.7776533799988877654433111113233444556666778************* PP

                           MetW  84 tlqatrnpkevldellrigr 103
                                     lq + +p + l+e+ r+  
  gi|121636762|ref|YP_976985.1| 116 VLQHVADPVRALQEMRRVCT 135
                                    *****************975 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.7e-10   8.2e-07      46     125 ..      42     126 ..      39     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.7e-10
                           NodS  46 dalevGcaaGalterlapyc..krltvvdvveeai..ararervkesshiswivsdvqqfs.tdekfdlivvaevlyyie 120
                                    ++l+vGc  G++t+ la      ++t v+  ++a+  ara  ++++ s+is+++sdv++++  d+ fd++   +vl ++ 
  gi|121636762|ref|YP_976985.1|  42 SVLDVGCGPGTITVDLAARVvpGSVTGVEPTDDALslARAEAQLHRLSNISFTTSDVHKLDfPDDAFDVVHAHQVLQHVA 121
                                    69**************97652278999999999863368889999***************955899***********999 PP

                           NodS 121 dvael 125
                                    d ++ 
  gi|121636762|ref|YP_976985.1| 122 DPVRA 126
                                    97653 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   7.5e-08   7.1e-05     116     214 ..      40     139 ..      31     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.5e-08
                                    T-EEEEET-TTSHHHHHHHHCT.-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GG CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvgeg.aklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvly 193
                                    g ++ldvGcg G     ++++  + +v G++P+   l   +a  +l    + +++    + +l+   +afd+v +  vl 
  gi|121636762|ref|YP_976985.1|  40 GLSVLDVGCGPGTITVDLAARVvPGSVTGVEPTDDALSLARAEAQLHRLSNISFTT-SDVHKLDFpDDAFDVVHAHQVLQ 118
                                    5689************999985268999******9999999998988777777666.67888887689************ PP

                                    G-S-HHHHHHHHHCTEEEEEE CS
                 Methyltransf_9 194 hrrsPldhllqlkdqlvkgGe 214
                                    h   P+  l++++   + gG 
  gi|121636762|ref|YP_976985.1| 119 HVADPVRALQEMRRVCTPGGI 139
                                    ***********9998888875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.5e-07   0.00014      30     108 ..      39     121 ..      32     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                                    TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEE CS
                         RrnaAD  30 ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpeevtekdsihqefl 105
                                    + l vl++g G+G  T+ La r+   +v+ +E   + + l +++ +    +++     D+ k ++p ++ +  + hq + 
  gi|121636762|ref|YP_976985.1|  39 PGLSVLDVGCGPGTITVDLAARVvpGSVTGVEPTDDALSLARAEAQlhRLSNISFTTSDVHKLDFPDDAFDVVHAHQVLQ 118
                                    7889***************99999********65555555554444238899999****************999999988 PP

                                    EEE CS
                         RrnaAD 106 vva 108
                                     va
  gi|121636762|ref|YP_976985.1| 119 HVA 121
                                    776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.1e-07   0.00038      69     147 ..      33     112 ..      19     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.1e-07
                                    TT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG.TTGGG-SEEE CS
                           PCMT  69 le..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk.GyeekaPYda 145
                                    l   l +g +vL+vG+G G  t+ la  v +   v ++e + +  + a+++ + + l+n++++++D +k  +++ a +d+
  gi|121636762|ref|YP_976985.1|  33 LLpyLVPGLSVLDVGCGPGTITVDLAARVVPGS-VTGVEPTDDALSLARAEAQLHRLSNISFTTSDVHKlDFPDDA-FDV 110
                                    333699*****************9998887755.9******************************97651344443.666 PP

                                    EE CS
                           PCMT 146 ih 147
                                    +h
  gi|121636762|ref|YP_976985.1| 111 VH 112
                                    66 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.2e-07    0.0005       4      64 ..      42     101 ..      40     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.2e-07
                                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                     vl++GcG G+++v+lA +    ++ G+E   + +  + ++++ ++l+N+  + +d  + l
  gi|121636762|ref|YP_976985.1|  42 SVLDVGCGPGTITVDLAARVVPGSVTGVEPTDDALSLARAEAQLHRLSNISFTTSDV-HKL 101
                                    589****************************************************97.433 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.2e-06    0.0068     160     254 ..      38     138 ..      24     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                           PrmA 160 kegeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkvea.kleva..lseellkeekadvivaN.I 234
                                     +g +vlDvG+G G +++  aa++   +v++v   + A++ a++ a+l ++++ ++++    + + ++   +dv+ a  +
  gi|121636762|ref|YP_976985.1|  38 VPGLSVLDVGCGPGTITVDlAARVVPGSVTGVEPTDDALSLARAEAQLHRLSNiSFTTSdvHKLDFPD-DAFDVVHAHqV 116
                                    56779************95488999**************************99655442113344445.899**988522 PP

                           PrmA 235 L...aevlielaedikklvkegg 254
                                    L   a+++  l +++ ++  +gg
  gi|121636762|ref|YP_976985.1| 117 LqhvADPVRAL-QEMRRVCTPGG 138
                                    21114444444.34555555555 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.3e-05     0.013     121     214 ..      43     139 ..      41     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                Methyltransf_29 121 vlDvGCgvasfgayllsrdvl..tlslapkDehe..aqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridwte 196
                                    vlDvGCg    +  l  r v      + p D+    a+    L R      +    ++l +P  +fd++h  +  +++ +
  gi|121636762|ref|YP_976985.1|  43 VLDVGCGPGTITVDLAARVVPgsVTGVEPTDDALslARAEAQLHRLSNISFTTSDVHKLDFPDDAFDVVHAHQV-LQHVA 121
                                    899999999999998888774113456677765411556667888777777888889*************8775.57778 PP

                Methyltransf_29 197 edgilllevdRvlRpgGy 214
                                    +    l e+ Rv  pgG 
  gi|121636762|ref|YP_976985.1| 122 DPVRALQEMRRVCTPGGI 139
                                    88899***********96 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05     0.034      33     138 ..      42     145 ..      32     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                                    EEEEES-TTSHHHHHHHHTT-..EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEEEESSGGGS- CS
                           TehB  33 kvldlgcgqgrnslylsllgy..dvtawdknensiafleeikekenlknistalydineakl.derydfilstvvlmfle 109
                                     vld+gcg g  ++ l++      vt ++  +++++  +  ++   l+nis ++ d+ ++++ d+ +d + +  vl  + 
  gi|121636762|ref|YP_976985.1|  42 SVLDVGCGPGTITVDLAARVVpgSVTGVEPTDDALSLARAEAQLHRLSNISFTTSDVHKLDFpDDAFDVVHAHQVLQHVA 121
                                    69*********9999987654228*************************************9667899999999998775 PP

                                    GGGHHHHHHHHHHTEEEEEEEEEEEEB-- CS
                           TehB 110 aeripsiienmqectkvggynlivaamst 138
                                       + + +++m++   +gg   ivaa ++
  gi|121636762|ref|YP_976985.1| 122 D-PV-RALQEMRRVCTPGG---IVAARDA 145
                                    4.34.45688999888998...6777665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05      0.04      60     140 ..      37     120 ..      32     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                    --TT-EEEEES-TTSHHHHHHHHH.H--EEEEEES-HHHHHHHHHHHHTS-SSS....-EEEEES-GGG-----SEEEEE CS
                           CMAS  60 lkpGmtlLdiGcGWGslvrraver.ydvkvvglTlSkeqaklakkrvdeldler....kvevklldyedldekvdrvvsv 134
                                    l pG  +Ld+GcG G++++  ++r    +v g+   ++   la+++ +   l++    + +v+ ld+ d  + +d v + 
  gi|121636762|ref|YP_976985.1|  37 LVPGLSVLDVGCGPGTITVDLAARvVPGSVTGVEPTDDALSLARAEAQLHRLSNisftTSDVHKLDFPD--DAFDVVHAH 114
                                    679*************99887666145678888666665555555544433332000022333333332..367777777 PP

                                    S-GGGT CS
                           CMAS 135 gafehv 140
                                    ++++hv
  gi|121636762|ref|YP_976985.1| 115 QVLQHV 120
                                    777776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05     0.062      97     183 ..      42     139 ..      39     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                           DREV  97 klldlGaGdGeitkrvaptfee...........vyatelsetmrdrlkkkkynvlsalelqetdvkldlilclnlldrcf 165
                                     +ld+G G G it  +a  +               +   +e   +rl+   +    + +l+  d  +d++ +  +l    
  gi|121636762|ref|YP_976985.1|  42 SVLDVGCGPGTITVDLAARVVPgsvtgveptddALSLARAEAQLHRLSNISFTTSDVHKLDFPDDAFDVVHAHQVLQHVA 121
                                    58***********99998887767777555544333344455566777777777666667777889************** PP

                           DREV 166 dplklledirsalepngr 183
                                    dp++ l+++r +  p g 
  gi|121636762|ref|YP_976985.1| 122 DPVRALQEMRRVCTPGGI 139
                                    ***********9998774 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.23      38     131 ..      37     130 ..      33     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                          GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDa. 116
                                    l pG  v++ G G g+++  +a  v P G +  +e  ++  + ar e + h+ls ++  t+ Dv k  f ++  ++v a 
  gi|121636762|ref|YP_976985.1|  37 LVPGLSVLDVGCGPGTITVDLAARVVP-GSVTGVEPTDDALSLARAEAQLHRLS-NISFTTSDVHKLDFPDDAFDVVHAh 114
                                    6799*********************99.99**********************97.6889999****99966655554432 PP

                          GCD14 117 .vfLDlPaPweaipha 131
                                     v+  +  P  a++++
  gi|121636762|ref|YP_976985.1| 115 qVLQHVADPVRALQEM 130
                                    2777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1673.23
//
Query:       gi|121636763|ref|YP_976986.1|  [L=286]
Description: proline iminopeptidase pip [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-18   65.6   0.0    1.4e-17   64.2   0.0    1.6  1  Abhydrolase_1  alpha/beta hydrolase fold
    3.6e-16   60.4   1.2    4.5e-16   60.1   1.2    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.8e-10   38.2   0.0    1.4e-06   27.8   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   2.4e-21   1.4e-17       2     257 .]      24     270 ..      23     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.4e-21
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH...HHHHHCTTSSEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld...rildalgddkltlv 78 
                                    +l+++hG+pg  +++ +    + L++ + +vi  D++G+g S  +     +d  ++++++++     + +al + ++++ 
  gi|121636763|ref|YP_976986.1|  24 PLLVVHGGPGLPHNYLA--PLRRLSD-EREVIFWDQLGCGNSACP-----SDVDLWTMNRSVAemaTVAEALALTRFHIF 95 
                                    89********9999999..8888888.***************444.....5689*********86555************ PP

                                    EETHHHHHHHHHHHHH.GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHH CS
                  Abhydrolase_1  79 GhSmGGmialayaaey.perVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrl 157
                                     hS+GGm+a +y ++  p+ V+  ++ ++   ++   +a + ++ks  d + + a+d  + ++ +++a ++aa++++ + 
  gi|121636763|ref|YP_976986.1|  96 SHSWGGMLAQQYVLDKaPDAVSLTIANST--ASIPEFSASLVSLKSCLDVATRSAIDRHEAAGTTHSAEYQAAIRTWNET 173
                                    *****************************..**********************************************442 PP

                                    HHHHHH.....HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC.........THHHHSEEEEEEETTCS CS
                  Abhydrolase_1 158 vdalkf.....pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre.........lknvlaptlvisgtsDp 223
                                       l+      +                + ++a    e ++t +  + ++  ++         l ++ +ptl++ g+ D 
  gi|121636763|ref|YP_976986.1| 174 --YLCRtrpwpR--------------ELTEAFANMGTEIFETMFGPSDFRIVGNvrdwdvvdrLADIAVPTLLVVGRFDE 237
                                    ..2333444443..............4444444444444444444433333333444445555777777*********** PP

                                    SSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 224 lvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                    + p ++++++++ + ++rl+ ++ + H+ f+e+p
  gi|121636763|ref|YP_976986.1| 238 CSP-EHMREMQGRIAGSRLEFFESSSHMPFIEEP 270
                                    **8.89999**********************997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   1.2   7.5e-20   4.5e-16       1     217 [.      25     273 ..      25     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 7.5e-20
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH......CHHHHHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled......ladlaalldelaagggpvvlvGHSl 74 
                                    +l++HG+++ ++ +  apL++l+ ++ +v+  D  G+G ++  p d++       +a+ a ++++la    +++++ HS+
  gi|121636763|ref|YP_976986.1|  25 LLVVHGGPGLPHNY-LAPLRRLSDER-EVIFWDQLGCG-NSACPSDVDLwtmnrsVAEMATVAEALA--LTRFHIFSHSW 99 
                                    6999**99988888.58*********.6699*******.3333333322222223677777777776..7789******* PP

                                    HHHHHHHHHHCC.......EE.EEES-..............----TTT.....S----TTHHHHHH.......TT-CCCC CS
                  Abhydrolase_6  75 GGalalaaapla.....lvvg.vlldp....pp........talpagl.....laaalelllalla.......llrllaw 124
                                    GG+la++   +      + v+  + ++    p+                     + a+  ++a+++       +++  +w
  gi|121636763|ref|YP_976986.1| 100 GGMLAQQ---YVldkapDAVSlTIANStasiPEfsaslvslK-----ScldvaTRSAIDRHEAAGTthsaeyqAAI-RTW 170
                                    *******...55444554344433333344311333332222.....02222333333333333332333222333.366 PP

                                    HCCH.S-HSCCCCHHH...C...CCCHCHCCCGHHHHCC..HHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH.S CS
                  Abhydrolase_6 125 lsre.plprlfladed...a...daawrarlarlaalla..glgllpaaawadlpvpllvl.ggeDplvprllerlla.q 193
                                      ++  ++r++ ++++   a    +++ +++ +         +++  ++++ad+ vp+l++ g  D+  p++++++   +
  gi|121636763|ref|YP_976986.1| 171 NETYlCRTRPWPRELTeafAnmgTEIFETMFGPSDFRIVgnVRDWDVVDRLADIAVPTLLVvGRFDECSPEHMREMQGrI 250
                                    6544544445555444222022323333333222222222233366799*********6665999**9999999999999 PP

                                    TTEEETCE...SSS-HHHHSHHHH CS
                  Abhydrolase_6 194 agarlpvvlpgaGHlphleepdev 217
                                    ag rl + ++ ++H+p++eep+++
  gi|121636763|ref|YP_976986.1| 251 AGSRL-EFFESSSHMPFIEEPARF 273
                                    *****.***************987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.3e-10   1.4e-06       8     164 ..      26     176 ..      21     199 .. 0.67
   2 !    8.5   0.0   0.00018       1.1     183     238 ..     217     269 ..     215     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-10
                    Hydrolase_4   8 vlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    ++vHG       y    ++L + + +v+ +D+ G G+s+ +  +++  +++ v+ +a++ e+++     +++ ++ hS+G
  gi|121636763|ref|YP_976986.1|  26 LVVHGGPGLPHNYLAPLRRLSD-EREVIFWDQLGCGNSAcPSDVDLWTMNRSVAEMATVAEALA----LTRFHIFSHSWG 100
                                    6788888888888888888876.589************999******************99998....557899****** PP

                    Hydrolase_4  87 Gliallyl.lrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplv 164
                                    G++a++y+ ++ pd v+  i  ++a +i++    + +l k +l ++ + + + +      ++   ++++ ++  ++  l+
  gi|121636763|ref|YP_976986.1| 101 GMLAQQYVlDKAPDAVSLTIANSTA-SIPEFSAsLVSL-KSCLDVATRSAIDRHE--AAGTTHSAEYQAAIRTWNETYLC 176
                                    ********55555555555555555.444321112222.2233333333333322..34455555555555555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00018
                    Hydrolase_4 183 leeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                    +++r a+i +P+ll+ G  D+  + e  re+  r++    +l+ ++   H+ + E+
  gi|121636763|ref|YP_976986.1| 217 VVDRLADIAVPTLLVVGRFDECSP-EHMREMQGRIA--GSRLEFFESSSHMPFIEE 269
                                    678999***************766.56666666666..469999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1894.33
//
Query:       gi|121636764|ref|YP_976987.1|  [L=80]
Description: hypothetical protein BCG_0893 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 670.50
//
Query:       gi|121636765|ref|YP_976988.1|  [L=430]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-20   73.8  59.1    1.7e-15   56.8  27.4    2.1  2  MFS_1       Major Facilitator Superfamily
    0.00053   19.0   0.0    0.00053   19.0   0.0    2.4  3  MFS_1_like  MFS_1 like family
      0.001   18.0   8.1      0.001   18.0   8.1    2.4  2  Sugar_tr    Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8  27.4   2.8e-19   1.7e-15      29     232 ..      54     254 ..      26     256 .. 0.78
   2 !   20.2  30.7   3.9e-08   0.00023       4     170 ..     237     403 ..     232     427 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.8e-19
                          MFS_1  29 ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpaga 107
                                      + ++g ++++y+lg av++l+ G+l+dr+G+r +l+ ++l+ a+ l+l++ + ++++ llv+ +++Gl + a  p+ +
  gi|121636765|ref|YP_976988.1|  54 HGAGAVGAVVAAYGLGWAVGQLLCGWLVDRVGARVTLVSTMLVAAAVLVLMAgL-HTVPGLLVGAMIAGLVCDAPRPVLG 132
                                    45778999***************************9999999999994444446.************************* PP

                          MFS_1 108 aliadwfpk.eergraigllsa.gfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspk 185
                                    a+ia+++++ ++r++  g+ ++   ++Ga+++ ++gg++a +l  +++++i++i +++++ l++  +p++  +r  +  +
  gi|121636765|ref|YP_976988.1| 133 AVIAELVADpQRRAQLDGWRYGwVLNIGAAITGGVGGVVAGWLDTPVLYWINGIGCAIFAGLAGRCIPADVCRRTESGLR 212
                                    ********97888888899877699**********************************998888886666555555433 PP

                          MFS_1 186 eeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllpl 232
                                             + v ++++ l+d+ l +l ++ l + + ++g+++ +p+
  gi|121636765|ref|YP_976988.1| 213 AC----TAMSKV-GYRQALSDKRLVLLAVSGLATLTTLMGFFAAVPM 254
                                    33....333444.4888888887742333333333344446666665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.9e-08
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdr.f..Grrr.vlllglllfalgllll 79 
                                    +++ + ++ + +++a+p +l+++ g+ + ++g++  + al+ ++ +++l ++  + +  G+r+ +l  + ++  l+ +++
  gi|121636765|ref|YP_976988.1| 237 SGLATLTTLMGFFAAVP-MLMSASGLGVGAYGWVQLINALAVVAVTPLLTPWLSKqLalGPRPdILAGAGVWVTLC-MAA 314
                                    55566666777889999.888888******************99999999998864466****6666666666666.333 PP

                          MFS_1  80 l.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyil 157
                                    + + +  +  + v+ + ++ g+ a f ++a ++ +++p+ + gr+ g++s++++++++ +p+l+++ ++++g  ++    
  gi|121636765|ref|YP_976988.1| 315 AgL-ARTTvGFSVAAAACSPGEIAWFVVAAGIVHRIAPPAHGGRYHGIWSMAVAASSVAAPILAAFNLANGGRLVLAATT 393
                                    346.555557**********************************************************888833333333 PP

                          MFS_1 158 aivsllafvlfll 170
                                      v+++++    l
  gi|121636765|ref|YP_976988.1| 394 VTVGFFGAA---L 403
                                    334443333...2 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.8e-08   0.00053      17      80 ..      40     103 ..      27     148 .. 0.89
   2 ?   -3.5   0.5      0.59   3.5e+03     262     293 ..     240     272 ..     234     288 .. 0.64
   3 ?    1.0   0.4     0.025   1.5e+02     330     358 ..     338     366 ..     303     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.8e-08
                     MFS_1_like  17 sllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80 
                                      +P+l  +   +g  a  +g ++++  l   +++++ g+l+Dr+g+r ++v+  l+++avl+l
  gi|121636765|ref|YP_976988.1|  40 FGYPFLAYHVAGRGHGAGAVGAVVAAYGLGWAVGQLLCGWLVDRVGARVTLVSTMLVAAAVLVL 103
                                    459******************************************************9999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.59
                     MFS_1_like 262 lGslvalgvvaeiplfffaekl.leklGhvkll 293
                                    +  ++ +g +a +p+++ a+ l +  +G v+l+
  gi|121636765|ref|YP_976988.1| 240 ATLTTLMGFFAAVPMLMSASGLgVGAYGWVQLI 272
                                    555666777777777777766655566666655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.025
                     MFS_1_like 330 lwaaaveyvskiapksleatgqgllsgly 358
                                     +++a+  v++iap+ + +++ g+ s++ 
  gi|121636765|ref|YP_976988.1| 338 WFVVAAGIVHRIAPPAHGGRYHGIWSMAV 366
                                    46788899999************999976 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   8.1   1.7e-07     0.001      48     150 ..      59     160 ..      43     194 .. 0.80
   2 ?   -6.4   7.0         3   1.8e+04     348     377 ..     314     343 ..     221     406 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-07
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                    +g++v+++ +G ++G+l+ g+l+dr+G + +l+ + +++ +  vl+a  +   +v  l+vg +++G+ + +   +    i
  gi|121636765|ref|YP_976988.1|  59 VGAVVAAYGLGWAVGQLLCGWLVDRVGARVTLVSTMLVAAAVLVLMAGLH---TVPGLLVGAMIAGLVCDAPRPVLGAVI 135
                                    699***************************99877777777677777767...9**************988888888888 PP

                                    HTT.S-SCCH.HHHHHHHHHHHHHH CS
                       Sugar_tr 128 sEi.ApkklR.galvslyqlaitfG 150
                                    +E+ A ++ R    +  y + + +G
  gi|121636765|ref|YP_976988.1| 136 AELvADPQRRaQLDGWRYGWVLNIG 160
                                    8852555555133344455555555 PP

  == domain 2  score: -6.4 bits;  conditional E-value: 3
                                    .CHHHHHHHHHHHHHHHTTTTHHHHHHHHH CS
                       Sugar_tr 348 asivaivfialfialfalgwgpvpwvlvsE 377
                                    a+++a + + + +a+ a+++g + w++v+ 
  gi|121636765|ref|YP_976988.1| 314 AAGLARTTVGFSVAAAACSPGEIAWFVVAA 343
                                    344444555555566666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3140.16
//
Query:       gi|121636766|ref|YP_976989.1|  [L=334]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-39  135.9   0.0    1.6e-39  135.7   0.0    1.0  1  E1_dh     Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.0   8.7e-44   1.6e-39      22     296 ..      42     312 ..      20     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 8.7e-44
                                    S-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTSSGTT-..-E..BTT..BEEE- CS
                          E1_dh  22 rigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgkggsrh.elmyaekesrilggn 100
                                    + g      gqea+ vg+aaal ++D+iit++R + + +  +++l  ++a + g+  g +++     ++a   +  l++ 
  gi|121636766|ref|YP_976989.1|  42 INGPLQGGFGQEAVSVGAAAALGEGDVIITTHRPHAQHVGTDAPLGPVIADMLGATAGDLEGADeDAHIAD-PRAGLPAA 120
                                    456666778***********************************************888888775555444.4467999* PP

                                    SSTTTHHHHHH.HHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEETTEEHHHH-S---GG CS
                          E1_dh 101 givgaqvplva.GialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkygisTeaekasaskela 179
                                    + v  q+pl+a G a+a   +++ +v+++++ D       + ea+ laa+w+lpv+  veN + ++s++  + ++ + ++
  gi|121636766|ref|YP_976989.1| 121 IRVVKQSPLLAiGHAYALWLRDTGRVTLCVTQDCDVDADAFNEAADLAAVWQLPVVILVENIRGALSVHLGRYTHEPRVY 200
                                    ******************************************************************************** PP

                                    G..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHH CS
                          E1_dh 180 drargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlk 259
                                     ra+++g+pg+ VdgnD++av+  v  A+ rar+g gp+l+ ++tYR +  s sD    yr   ++   ++  dp+   +
  gi|121636766|ref|YP_976989.1| 201 RRAVAYGMPGVSVDGNDVEAVRDCVANAVVRARAGGGPTLVQAITYRTTDFSGSD-RGGYR---DLAGSEQFLDPLIFAR 276
                                    *******************************************************.6689*...777777778******* PP

                                    HHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                          E1_dh 260 elLvkkgvvseeelkeiekevrkeveeavkkaeskke 296
                                    ++L+++g  ++  l+e e+ + ++v +av+ a++   
  gi|121636766|ref|YP_976989.1| 277 RRLIAAGT-TRGRLDEQERAACQQVADAVAFAKARAR 312
                                    *******7.5667788888889999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2650.55
//
Query:       gi|121636767|ref|YP_976990.1|  [L=216]
Description: nitrate/nitrite response transcriptional regulatory protein narL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-25   89.7   0.0      2e-25   89.1   0.0    1.3  1  Response_reg  Response regulator receiver domain
      9e-16   57.2   0.0    1.5e-15   56.5   0.0    1.4  1  GerE          Bacterial regulatory proteins, luxR family
    1.3e-05   24.8   0.0    3.3e-05   23.5   0.0    1.7  1  Sigma70_r4_2  Sigma-70, region 4
    0.00058   19.6   0.0     0.0012   18.6   0.0    1.5  1  HTH_30        PucR C-terminal helix-turn-helix domain
      0.002   18.2   0.2      0.023   14.8   0.0    2.6  2  HTH_28        Helix-turn-helix domain
     0.0035   17.2   0.1     0.0099   15.8   0.1    1.7  1  MarR_2        MarR family
     0.0053   16.5   0.0       0.01   15.6   0.0    1.5  1  HTH_38        Helix-turn-helix domain
     0.0091   15.5   0.0      0.019   14.5   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.054   13.3   0.0    1.9  1  HTH_23        Homeodomain-like domain
      0.023   15.1   0.0      0.065   13.7   0.0    1.8  1  HTH_40        Helix-turn-helix domain
       0.11   12.6   0.0       0.22   11.6   0.0    1.5  1  HTH_7         Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   1.2e-28     2e-25       1     111 [.      11     122 ..      11     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.2e-28
                                    EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEES CS
                   Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilta 79 
                                    v++ dD+pl+re++ ++l  +  +++v+ea+dg++alel+k++ +d+ llD +mpgmdG +++  +r  +  ++v++++a
  gi|121636767|ref|YP_976990.1|  11 VVVGDDHPLFREGVVRALSlSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISA 90 
                                    5677***************666678999**************************************************** PP

                                    STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    h+e + + +al+ ga +fl K+ +++e++ka+
  gi|121636767|ref|YP_976990.1|  91 HDEPAIVYQALQQGAAGFLLKDSTRTEIVKAV 122
                                    *****************************997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0     9e-19   1.5e-15       2      56 ..     154     208 ..     153     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 9e-19
                                    SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHH CS
                           GerE   2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrl 56 
                                    +Ls RErevL  +a G+s   IA+el +++ TVk+h++++++KL+v +r+++v  
  gi|121636767|ref|YP_976990.1| 154 VLSAREREVLNRIACGQSIPAIAAELYVAPSTVKTHVQRLYEKLGVSDRAAAVAE 208
                                    7**************************************************9975 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     2e-08   3.3e-05      11      54 .]     155     197 ..     153     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2e-08
                                    S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    L+ r+re++  +  +g s+  IA++l + ++tVk++++R  +kL
  gi|121636767|ref|YP_976990.1| 155 LSAREREVLNRI-ACGQSIPAIAAELYVAPSTVKTHVQRLYEKL 197
                                    99*********8.6*************************88887 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.5e-07    0.0012      10      43 ..     167     200 ..     165     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.5e-07
                                    HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS-- CS
                         HTH_30  10 enggnisatAkaLhvHrnTlryRLrrieellgld 43 
                                    ++g++i a A++L+v + T++  ++r+ e lg++
  gi|121636767|ref|YP_976990.1| 167 ACGQSIPAIAAELYVAPSTVKTHVQRLYEKLGVS 200
                                    79******************************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.56   9.1e+02       2      16 ..     115     130 ..     114     133 .. 0.74
   2 !   14.8   0.0   1.4e-05     0.023       4      40 ..     161     198 ..     160     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.56
                         HTH_28   2 RleiikllaaGh.svr 16 
                                    R ei+k+++++   ++
  gi|121636767|ref|YP_976990.1| 115 RTEIVKAVLDCAkGRD 130
                                    789*****99864554 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                         HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWikryee.gG 40 
                                    e++ ++a G s++++A+el + ++tv+  ++r+ e  G
  gi|121636767|ref|YP_976990.1| 161 EVLNRIACGQSIPAIAAELYVAPSTVKTHVQRLYEkLG 198
                                    78999999******************888777655355 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.1e-06    0.0099       3      47 ..     155     195 ..     154     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.1e-06
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLva 47 
                                    l+  ++ vL+ ++++     ++ ++a++l + +s+v  +++rL +
  gi|121636767|ref|YP_976990.1| 155 LSAREREVLNRIACGQ----SIPAIAAELYVAPSTVKTHVQRLYE 195
                                    5678999********7....9*********************965 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.3e-06      0.01       7      43 ..     157     192 ..     154     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                         HTH_38   7 leeReeIerllaeGlslreIArrLgrspsTIsRElkR 43 
                                      eR e    +a G s+ +IA +L ++psT+  +++R
  gi|121636767|ref|YP_976990.1| 157 ARER-EVLNRIACGQSIPAIAAELYVAPSTVKTHVQR 192
                                    5566.445567889******************99998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.1e-05     0.019      17      43 ..     169     195 ..     158     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                         HTH_24  17 risqreLAerlglSpstvnrrlkrLee 43 
                                    + s+  +A +l + pstv+++++rL e
  gi|121636767|ref|YP_976990.1| 169 GQSIPAIAAELYVAPSTVKTHVQRLYE 195
                                    678999******************965 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-05     0.054      10      47 ..     162     200 ..     155     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                         HTH_23  10 illllaeGlsvreIAreLgvsrrTvy.rwlkryreeGle 47 
                                    +l   a G+s+++IA+eL v ++Tv  ++ + y++ G++
  gi|121636767|ref|YP_976990.1| 162 VLNRIACGQSIPAIAAELYVAPSTVKtHVQRLYEKLGVS 200
                                    5555666*******************8888888767765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.065      11      39 ..     168     196 ..     159     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                         HTH_40  11 eglsieeIAkerglkesTIegHLaeliee 39 
                                     g+si +IA+e  +++sT+ +H+ +l+e+
  gi|121636767|ref|YP_976990.1| 168 CGQSIPAIAAELYVAPSTVKTHVQRLYEK 196
                                    699**********************9998 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.22      13      39 ..     161     187 ..     155     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                    GGGSSTTTT--STTTSSSS---SSSS- CS
                          HTH_7  13 rvvkLleeGisiskIAkevnisRsTvY 39 
                                    +v+ +++ G+si +IA e+ +++sTv+
  gi|121636767|ref|YP_976990.1| 161 EVLNRIACGQSIPAIAAELYVAPSTVK 187
                                    7999999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1519.00
//
Query:       gi|121636768|ref|YP_976991.1|  [L=425]
Description: two component sensor kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00029   21.3   0.0     0.0007   20.1   0.0    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0087   16.0   0.0      0.016   15.2   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.092   13.0   0.2       0.17   12.1   0.2    1.3  1  Gp5_OB       Gp5 N-terminal OB domain
       0.65    8.2  10.1          1    7.5  10.1    1.2  1  DUF2070      Predicted membrane protein (DUF2070)
        3.9    7.4  13.3       0.57   10.1   2.6    2.7  2  DUF5134      Domain of unknown function (DUF5134)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     2e-07    0.0007       9     111 ..     337     424 ..     331     425 .] 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2e-07
                                    HHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS.HHHHHHHHHHHH CS
                      HATPase_c   9 iisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtG.lGlsivkklvel 87 
                                    ++++l++N v++ + a++ +v++  ++++ v+ v D+G G++ + +        +      +  g+G +Gl+  ++ v+ 
  gi|121636768|ref|YP_976991.1| 337 VVRELLSNVVRH-SGATTASVRLGITDEKCVLDVADDGVGVTGDTMA-------R------RL-GEGhIGLASHRARVDA 401
                                    89**********.6666667776665679**************9998.......2......23.3343799999999998 PP

                                    TTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  88 mgGeiwvesepgrGttftftlple 111
                                     gG + +     rGt + ++lpl+
  gi|121636768|ref|YP_976991.1| 402 AGGVLVFL-ATPRGTHVCVELPLK 424
                                    88888884.445999999999986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.5e-06     0.016      35      86 ..     337     384 ..     303     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-06
                    HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdp 86 
                                    +v E+++N+v+h        + +vrl +++e++++ vaD+G g +  t +++
  gi|121636768|ref|YP_976991.1| 337 VVRELLSNVVRHSGA----TTASVRLGITDEKCVLDVADDGVGVTGDTMARR 384
                                    589**********98....455777889**************9777766554 PP

>> Gp5_OB  Gp5 N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.7e-05      0.17      18      70 ..      29      79 ..      14      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                         Gp5_OB 18 eeLlWmsvlqsitsaavsGigqsptGiveGthvyGfflDkfkqdgvilGtlpg 70
                                   + + W + l s   a+v  ig  ++G++  ++v+G  + ++ q+ v++G+++ 
  gi|121636768|ref|YP_976991.1| 29 DRVRWAHQLRSYRIASVLRIG--VVGLMVAAMVVGTSRSEWPQQIVLIGVYAV 79
                                   567899999999999998888..79**************************85 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  10.1   0.00029         1      11     189 ..      37     218 ..      30     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00029
                        DUF2070  11 lPswk.vsllliillalligllaflssk...lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivvii 85 
                                    l s++  s+l i +++l+++++++  s     ++i+l+g+ a++a+ ++l + + + +r + ++r   +  l  + + ++
  gi|121636768|ref|YP_976991.1|  37 LRSYRiASVLRIGVVGLMVAAMVVGTSRsewPQQIVLIGVYAVAALWALLLAYSAS-RRfFALRRFRSMGRLEPFAFTAV 115
                                    55666566666666666666665555557868888888888777777666666554.44366666544433333333333 PP

                        DUF2070  86 sllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.......fspesfllll 158
                                    ++l ++ +    +l++   +  l +++ l++lv + vs ++   + l +   +l++++++vl        +++  +++ +
  gi|121636768|ref|YP_976991.1| 116 DVLILTGF----QLLSTDGIYPLLIMILLPVLVGLDVSTRRAAVV-LAC---TLVGFAVAVLGdpvmlraIGWPETIFRF 187
                                    33333322....122222233344444444444444444443322.333...333333333334458999********** PP

                        DUF2070 159 llslifalavylfivvvdrplkrnlgvsald 189
                                    +l +++ + +++++++ +r +++ +g+sal+
  gi|121636768|ref|YP_976991.1| 188 ALYAFLCATALMVVRIEERHTRSVAGLSALR 218
                                    ***************************9985 PP

>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.6   0.00016      0.57      12      53 ..      51      93 ..      40     115 .. 0.73
   2 ?    2.1   2.6     0.044   1.6e+02      16      54 ..     137     180 ..     135     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                        DUF5134 12 MavgMaaMawpagvalpsagq...lavvfalaalwflvlavvrrr 53
                                   +++  aaM++ ++    +  q   l+ v+a+aalw+l+la  ++r
  gi|121636768|ref|YP_976991.1| 51 VGLMVAAMVVGTSRSEWP--QqivLIGVYAVAALWALLLAYSASR 93
                                   566667888876554333..2335899*************98776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                        DUF5134  16 MaaMawpagvalpsagqlavvfalaalwflvlavvrrr......a 54 
                                    M++  + +g++++++ + avv a++ + f+v+++ ++       +
  gi|121636768|ref|YP_976991.1| 137 MILLPVLVGLDVSTRRA-AVVLACTLVGFAVAVLGDPVmlraigW 180
                                    88888999999999997.999999999999999877766544331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3119.23
//
Query:       gi|121636769|ref|YP_976992.1|  [L=504]
Description: oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-36  124.0   3.0    4.6e-27   94.4   0.1    3.2  3  Cu-oxidase_3  Multicopper oxidase
    4.8e-35  120.3   5.4    1.1e-26   93.2   2.7    3.7  3  Cu-oxidase_2  Multicopper oxidase
    3.8e-32  111.6   0.0    1.6e-25   90.1   0.0    2.3  2  Cu-oxidase    Multicopper oxidase


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.1   7.7e-31   4.6e-27      15     118 ..      83     182 ..      72     183 .. 0.94
   2 !   13.2   0.0   1.1e-05     0.068      18      73 ..     250     307 ..     242     330 .. 0.82
   3 !   14.6   1.0   4.2e-06     0.025       9     110 ..     395     498 ..     388     500 .. 0.78

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 7.7e-31
                                    EEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEE CS
                   Cu-oxidase_3  15 revitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtl 94 
                                     +++t+ +++pgp i+++ gd++vv+vtN+l ++ts+hwhG+ +r++  mDG +  ++  i pg +ftyrf v +  gt+
  gi|121636769|ref|YP_976992.1|  83 VSTLTYGNTIPGPLIRATVGDEIVVSVTNRLGDPTSVHWHGIALRND--MDGTEP-ATANIGPGGDFTYRFSVPD-PGTY 158
                                    57899******************************************..*****9.7789***************.**** PP

                                    EEEE--TTHHHTT-EEEEEEE-HH CS
                   Cu-oxidase_3  95 wYhshlslqqaaGlaGaiiiedke 118
                                    w h+h+ lq  +Gl+ +++++d++
  gi|121636769|ref|YP_976992.1| 159 WAHPHVGLQGDHGLYLPVVVDDPT 182
                                    *********99*********9985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.1e-05
                                    EEECTSSBS-..EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG CS
                   Cu-oxidase_3  18 itvNgqfpgp..tievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqc 73 
                                     ++Ng++p     ++++ g++++++++N++ d  + i + G  +  t + DG p +++ 
  gi|121636769|ref|YP_976992.1| 250 YLINGRIPVAatSFKAKPGQRIRIRIINSAaDTAFRIALAGHSMTVT-HTDGYPVIPTE 307
                                    689999997622589999************89999****99999999.99***998864 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.2e-06
                                    CTTEESEEEEEECTS..SBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-..B-TT-EEEEE CS
                   Cu-oxidase_3   9 plggterevitvNgq..fpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcp..iqpgesftyr 84 
                                    + g++++  +t+Ng+       ++vr g++ ++ + N       ih+hG   +    +DG pg  ++   + p+++++  
  gi|121636769|ref|YP_976992.1| 395 LGGTMAKYDWTINGEpySTTNPLHVRLGQRPTLMFDNTTMMYHPIHLHGHTFQMI-KADGSPGARKDTviVLPKQKMRAV 473
                                    55666777899999832345669****************8888888888766555.68*****98875214678888877 PP

                                    EE--S-SEEEEEEE--TTHHHTT-EE CS
                   Cu-oxidase_3  85 ftvkqqagtlwYhshlslqqaaGlaG 110
                                    + +++  g    h h + +q+aG+a+
  gi|121636769|ref|YP_976992.1| 474 LVADN-PGVWVMHCHNNYHQVAGMAT 498
                                    77777.999999***********986 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   6.7e-09     4e-05      32     135 ..      94     180 ..      75     182 .. 0.85
   2 ?    0.8   0.0     0.064   3.8e+02      25      54 ..     254     283 ..     214     326 .. 0.65
   3 !   93.2   2.7   1.8e-30   1.1e-26      11     131 ..     394     500 ..     384     502 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.7e-09
                                    SEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-E CS
                   Cu-oxidase_2  32 tnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpG 111
                                     + i++  g+ + + ++n    p ++H+HG   +                    + ++  t+++ pgg +++rf++ +pG
  gi|121636769|ref|YP_976992.1|  94 GPLIRATVGDEIVVSVTNRLGDPTSVHWHGIALRNDM-----------------DGTEPATANIGPGGDFTYRFSVPDPG 156
                                    5677888899999999999999999999999544332.................234568******************** PP

                                    EEEEEESSHHHHHTT-EEEEEEEC CS
                   Cu-oxidase_2 112 vwllHCHilwHldqGmalqfvvrp 135
                                     +  H H+    d+G++l +vv++
  gi|121636769|ref|YP_976992.1| 157 TYWAHPHVGLQGDHGLYLPVVVDD 180
                                    *********************986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.064
                                    TCCTTTSSEEEEEETTEEEEEEEEE-SSS.- CS
                   Cu-oxidase_2  25 geefsentnvitlpkgevveiviqnntkl.p 54 
                                    g  ++  +  ++++ g++++i i n++    
  gi|121636769|ref|YP_976992.1| 254 G-RIPVAATSFKAKPGQRIRIRIINSAADtA 283
                                    3.35667788888889999999998877643 PP

  == domain 3  score: 93.2 bits;  conditional E-value: 1.8e-30
                                    CCEEEEEEEEEEE.ETCCTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSC CS
                   Cu-oxidase_2  11 qltsgneeaseit.ngeefsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvr 89 
                                    +l  g++ ++ +t nge++s +tn+++++ g++  ++++n+t++ HP+HlHGh+fq+++ ++++               r
  gi|121636769|ref|YP_976992.1| 394 TLG-GTMAKYDWTiNGEPYS-TTNPLHVRLGQRPTLMFDNTTMMYHPIHLHGHTFQMIKADGSP-------------GAR 458
                                    344.7888999999999999.*************************************999999.............89* PP

                                    BSEEEE-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEE CS
                   Cu-oxidase_2  90 rdtvqvppggwvairfkadnpGvwllHCHilwHldqGmalqf 131
                                    +dtv v p+++++    adnpGvw++HCH+ +H+ +Gma+++
  gi|121636769|ref|YP_976992.1| 459 KDTVIVLPKQKMRAVLVADNPGVWVMHCHNNYHQVAGMATRL 500
                                    **************************************9875 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   2.7e-29   1.6e-25       2     156 ..     190     349 ..     189     352 .. 0.89
   2 !   19.2   0.0   1.7e-07     0.001      58     144 ..     413     491 ..     383     500 .. 0.80

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.7e-29
                                    EEEEEEEEETCBCTTSCBC.HSSCHCHHHHHTT--SEEEETTBSS.......C...............TTTTSGGGEEEE CS
                     Cu-oxidase   2 eyvitlsDwyhkdakelekellasgkapadtppvpdavlingkggfnatladk...............dgaslatltvep 66 
                                    e++i+l Dw++   k++++ l+ + ++ ++ p++++++ + + +g++++l                   +++ ++++ +p
  gi|121636769|ref|YP_976992.1| 190 EWIIILDDWTDGIGKSPQQ-LYGELTD-PNKPTMQNTTGMPEGEGVDSNLLGGdggdiaypyylingrIPVAATSFKAKP 267
                                    5899*******99999999.8888776.55578899999999899998887746777788889999998899******** PP

                                    ETTEEEEEEEESSS-BEEEEETSB-EEEEEETCETTSEEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEEGSSSCHHHHT CS
                     Cu-oxidase  67 gktyrlriinvsaddslnfsIeGHkltVvevDgvyvepvevdsldIavGqrysvlvtanqapgnYwivasgrsnlieafe 146
                                    g+++r+riin +ad+++ ++++GH++tV ++Dg +v p+evd l I++++ry+v+vta    g + +va       ++++
  gi|121636769|ref|YP_976992.1| 268 GQRIRIRIINSAADTAFRIALAGHSMTVTHTDGYPVIPTEVDALLIGMAERYDVMVTAAG--GVFPLVA------LAEGK 339
                                    ***********************************************************8..*******......66777 PP

                                    TSEEEEEEEE CS
                     Cu-oxidase 147 ngtaaailry 156
                                    n  a+a+l++
  gi|121636769|ref|YP_976992.1| 340 NALARALLST 349
                                    8888887765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-07
                                    TSGGGEEEEETTEEEEEEEESSS-BEEEEETSB-EEEEEETCETTSEEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEEG CS
                     Cu-oxidase  58 slatltvepgktyrlriinvsaddslnfsIeGHkltVvevDgvyvepvevdsldIavGqrysvlvtanqapgnYwivasg 137
                                     +  l+v+ g++  l + n+++  ++++ ++GH+++ + +Dg++      d++ + + q + +++ a++ pg +++++  
  gi|121636769|ref|YP_976992.1| 413 TTNPLHVRLGQRPTLMFDNTTM-MYHPIHLHGHTFQMIKADGSPGAR--KDTVIVLPKQKMRAVLVADN-PGVWVMHC-- 486
                                    3567889999999998888775.59*******************875..799****************9.********.. PP

                                    SSSCHHH CS
                     Cu-oxidase 138 rsnliea 144
                                     +n + +
  gi|121636769|ref|YP_976992.1| 487 -HN-NYH 491
                                    .44.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3629.40
//
Query:       gi|121636770|ref|YP_976993.1|  [L=130]
Description: lipoprotein lpqS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.61   10.3   5.8        1.2    9.3   0.8    2.2  2  DUF4148   Domain of unknown function (DUF4148)


Domain annotation for each model (and alignments):
>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.8   6.8e-05       1.2       1      29 [.       4      41 ..       4      42 .. 0.69
   2 ?    3.6   0.4    0.0044        78       9      22 ..      86     110 ..      81     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6.8e-05
                        DUF4148  1 Mkstliaaalaaavaaaaala.........ahskspkT 29
                                   M s ++a al ++vaa+aa+          ah ++p+T
  gi|121636770|ref|YP_976993.1|  4 MRSAIVAVALGVTVAAVAAACwlpqlhrhvAHPNHPLT 41
                                   6664544444444444444449*************999 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0044
                        DUF4148   9 alaaavaaaaala...........a 22 
                                    ++aaa+ ++aal+           a
  gi|121636770|ref|YP_976993.1|  86 VVAAAPGMTAALTdpvapaargppA 110
                                    6899********9776665555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 881.33
//
Query:       gi|121636771|ref|YP_976994.1|  [L=372]
Description: cysteine synthase a cysK2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-45  155.8   0.1      2e-45  155.4   0.1    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.1   1.1e-49     2e-45       5     293 ..      31     314 ..      29     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 1.1e-49
                                    SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                           PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGl 79 
                                    +g+TP++ +p ls     +  +++KlE++np g++KdR a y+++ ++      ++  +ve++sG  g++lA+a++++  
  gi|121636771|ref|YP_976994.1|  31 VGNTPVLWIPELSGTSDPDrgFWAKLEGFNP-GGMKDRPALYMVECARARgdiAPGAAIVESTSGTLGLGLALAGKVYRH 109
                                    79***********88777788**********.89************77667999************************** PP

                                    EEEEEEETTS-HHHHHHHHHTT-EEEEE......CCHHHHHHHH.HHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHH CS
                           PALP  80 kvtivvpadaspekvallrllGaevvev......ggdydeavaa.aaelaaegegaylvsqfdnptviegygtiglEile 152
                                    +vt+v + +  p  +++l ++Ga v  v      gg +++a++  +a+l ae +ga + +q++np+++ +y +++lE+++
  gi|121636771|ref|YP_976994.1| 110 PVTLVTDPGLEPIIARMLTAYGAGVDMVtqphpvGG-WQQARKDrVAQLMAEYPGAWNPNQYGNPDNVGAYRSLALELVA 188
                                    ***********************8888877777355.55555555*********************************** PP

                                    HTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHH CS
                           PALP 153 qlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafe 231
                                    qlg ++d++v++vG+Gg  aG+a+ l+e +pd r+igv++ gs  +++ +          s+ ++ gl+ +  p + + +
  gi|121636771|ref|YP_976994.1| 189 QLG-RIDVLVCSVGTGGHSAGVARVLREFNPDMRLIGVDTIGSTIFGQPA----------SNRLMRGLGSSiYPRNVDYR 257
                                    **7.**********************************************..........9**********999999999 PP

                                    HHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE- CS
                           PALP 232 lldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvvilt 293
                                    ++d+       v   ea+ a+r la ++++  +  s  a+a +    a++l+++ ++ ++++
  gi|121636771|ref|YP_976994.1| 258 AFDEVHW----VAPPEAVWACRSLA-ATHYASGGWSVGAVALVAGWAARNLPADTTIAAVFP 314
                                    9988888....**************.777777774444444443478888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3140.58
//
Query:       gi|121636772|ref|YP_976995.1|  [L=419]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-25   88.9  50.6    3.6e-24   85.4  35.4    2.0  2  MFS_1           Major Facilitator Superfamily
    3.9e-06   25.7  29.6    2.3e-05   23.1  14.6    2.2  2  MFS_2           MFS/sugar transport protein
     0.0041   16.0   3.6     0.0041   16.0   3.6    2.2  2  MFS_1_like      MFS_1 like family
     0.0065   15.3   0.2      0.014   14.2   0.2    1.6  1  Folate_carrier  Reduced folate carrier
  ------ inclusion threshold ------
      0.053   13.0   0.0      0.091   12.3   0.0    1.3  1  DUF452          Protein of unknown function (DUF452)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4  35.4   9.9e-28   3.6e-24       2     309 ..      18     314 ..      17     318 .. 0.84
   2 !    7.6  11.4   0.00043       1.6      87     182 ..     313     409 ..     305     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 9.9e-28
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    ++ +f + +++++l+p l  +la  lg+++ ++gl++++  + +  + +++G l+drfG ++++++g l+   g++ll++
  gi|121636772|ref|YP_976995.1|  18 MINQFGINIGFYMLMPYLADYLAGPLGLAAWAVGLVMGVRNFSQQGMFFVGGTLADRFGYKPLIIAGCLIRTGGFALLVV 97 
                                    6788889999********99******************************************999999999999555555 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    a+sl+ +l++ + +G+++++++pa+  ++a+ + + ++  a+++++++++ G++lgpl+g +l+ +l +r + +++a+v+
  gi|121636772|ref|YP_976995.1|  98 AQSLPSVLIAAAATGFAGALFNPAVRGYLAAEAGE-RKIEAFAMFNVFYQSGILLGPLVGLVLL-ALDFRITVLAAAGVF 175
                                    577779***************************99.****************************.99************* PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevlgl 240
                                     l+ v  l+ lp+ + +++r+++           l + w+ ++++++++  l+a+ +++ ++s+ ++  lp+  q    +
  gi|121636772|ref|YP_976995.1| 176 GLLTVAQLVALPQHRADSEREKTS---------ILQD-WRVVVRNRPFL-TLAAAMTGCYALSFqIYLALPM--QASILM 242
                                    ***996557776666666666444.........4467.********994.4444444433333356666666..666666 PP

                          MFS_1 241 s..glllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllllvlvl 309
                                    +   +ll+++++a+++lv+++++l ++r+   r+g++r l+++  +l+++++ +a++++ +   ++++v++l
  gi|121636772|ref|YP_976995.1| 243 PrnQYLLIAAMFAVSGLVAVGGQLRITRWFaVRWGAERSLVVGATILAASFIPVAVIPNGQRFGVAVAVMAL 314
                                    6889999999************665555555*****************************777766666655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00043
                          MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllaf 165
                                    +l+++  l +++++alfp  + ++++++ ++  +  +g++s+ +++G+++g l+ g l+ ++       ++ +++ l+++
  gi|121636772|ref|YP_976995.1| 313 ALVLSASLLAVASAALFPFEMRAVVALSGDRLVATHYGFYSTIVGVGVLVGNLAIGSLMsAARRLNTDEIVWGGLILVGI 392
                                    5899999********************************************66555555155556666777777777777 PP

                          MFS_1 166 vlfllllpeepperkrk 182
                                    v ++ l + +  +++ +
  gi|121636772|ref|YP_976995.1| 393 VAVAGLRRLDTFTSGSQ 409
                                    77777777766666555 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   8.4   0.00039       1.4     238     336 ..      22     123 ..      11     165 .. 0.70
   2 !   23.1  14.6   6.5e-09   2.3e-05     178     384 ..     166     374 ..     145     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00039
                          MFS_2 238 lalgvl.nglllYyltyvlgngsaasvfllvvt.isal...lgiplwqplakrlgkkntyllgalltivllvlvlllqps 312
                                    ++++++ ++l+ Y ++y  g    a++  ++v+ + ++    ++++   la r+g k ++++g l+   +++l++++  +
  gi|121636772|ref|YP_976995.1|  22 FGINIGfYMLMPYLADYLAGPLGLAAWAVGLVMgVRNFsqqGMFFVGGTLADRFGYKPLIIAGCLIRTGGFALLVVA--Q 99 
                                    5555541478999999999966666666666651444477477777789*****************99999999988..* PP

                          MFS_2 313 nlllflvllviagfgvgvaallpw 336
                                    +l  +l++++++gf+ ++++ ++ 
  gi|121636772|ref|YP_976995.1| 100 SLPSVLIAAAATGFAGALFNPAVR 123
                                    **************9777765554 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 6.5e-09
                          MFS_2 178 ialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlgn 257
                                    i++L+++gv+ + l++ + v+  + +++ ++ek+s+l++++ v rnr+fl+l+++  +   al ++  l+l     +l  
  gi|121636772|ref|YP_976995.1| 166 ITVLAAAGVFGL-LTVAQLVALPQHRADSEREKTSILQDWRVVVRNRPFLTLAAAM-TGCYALSFQIYLALPMQASILMP 243
                                    445555555555.44444555566778899*********************98865.45555888888888888888889 PP

                          MFS_2 258 gsaasvfllvvtisal....lgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                    ++++ ++++++ +s+l      + +  ++a r+g  ++ ++ga+++++ ++ v +++ ++   + v++++  +++ ++a+
  gi|121636772|ref|YP_976995.1| 244 RNQYLLIAAMFAVSGLvavgGQLRITRWFAVRWGAERSLVVGATILAASFIPVAVIPNGQRFGVAVAVMALVLSASLLAV 323
                                    9999999999999999443334567889999999*******************999888888888888888999999*** PP

                          MFS_2 334 lpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsaf 384
                                    + +++++  + +    +G+r   + ++++s+i  +++ +g +++g l sa+
  gi|121636772|ref|YP_976995.1| 324 ASAALFPFEMRAVVALSGDRLVATHYGFYSTIVGVGVLVGNLAIGSLMSAA 374
                                    *******9999999**************************99999888776 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.6   1.1e-06    0.0041     244     358 ..      31     145 ..      15     162 .. 0.77
   2 ?    1.7   8.7     0.026        92     181     373 ..     170     370 ..     149     377 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                     MFS_1_like 244 ienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievL 322
                                    +  +l  YL   lg     +G ++ ++ +++  +ff++  l +++G   l+i++ l+ +  f l+ + +++  vl++ + 
  gi|121636772|ref|YP_976995.1|  31 LMPYLADYLaGPLGLAAWAVGLVMGVRNFSQQGMFFVGGTLADRFGYKPLIIAGCLIRTGGFALLVVAQSLPSVLIAAAA 110
                                    44568888877899999999999999999999999999999999999999999999999999999999999999999999 PP

                     MFS_1_like 323 hgisfgllwaaaveyvskiapks.leatgqgllsgly 358
                                     g++ +l+  a+  y +  a+++ +ea   ++++ +y
  gi|121636772|ref|YP_976995.1| 111 TGFAGALFNPAVRGYLAAEAGERkIEA--FAMFNVFY 145
                                    999999998888888887776541333..35555554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.026
                     MFS_1_like 181 allyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF............l 248
                                    a++ v+    +++++ +++l++ ++ s+ + t +lq+   +++n+  +++ ++++ +      ++ +             
  gi|121636772|ref|YP_976995.1| 170 AAAGVFG---LLTVAQLVALPQHRADSEREKTSILQDWRVVVRNRPFLTLAAAMTGCY--ALSFQIYlalpmqasilmpR 244
                                    3333333...344444446899999999999999998888888887766666655444..44444553346666665555 PP

                     MFS_1_like 249 flYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.........enawlvlpi 319
                                    + YL  l a  + ++ lva+g  + i+      +   + G+++ l+++ ++ ++ f+ +a+i           +  +++ 
  gi|121636772|ref|YP_976995.1| 245 NQYL--LIAAMFAVSGLVAVGGQLRIT-----RWFAVRWGAERSLVVGATILAASFIPVAVIpngqrfgvaVAVMALVLS 317
                                    5666..555566666666666555555.....455567799999******************999877764233333444 PP

                     MFS_1_like 320 evLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                                      L +++ ++l+   ++ v  + +++l at  g++s++ +g+G  +G+l+ G l
  gi|121636772|ref|YP_976995.1| 318 ASLLAVASAALFPFEMRAVVALSGDRLVATHYGFYSTI-VGVGVLVGNLAIGSL 370
                                    55667777777788888889999*************99.9********998876 PP

>> Folate_carrier  Reduced folate carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   3.8e-06     0.014      11     105 ..      20     112 ..      10     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                 Folate_carrier  11 clfGflaelrpsepFvtpyllgpdknlteeqvnnevyPvltYSylallvpvflltdylrYkpvivlqalalivvwllllf 90 
                                      fG+   +    p++++yl+gp  +l +  v   v+ v  +S+  + ++   l+d + Ykp+i++ +l     ++ll++
  gi|121636772|ref|YP_976995.1|  20 NQFGINIGFYMLMPYLADYLAGP-LGLAAWAVG-LVMGVRNFSQQGMFFVGGTLADRFGYKPLIIAGCLIRTGGFALLVV 97 
                                    55777777777789999999997.899988885.699******************************************* PP

                 Folate_carrier  91 tksllalqvlevfYg 105
                                    ++sl ++ ++  + g
  gi|121636772|ref|YP_976995.1|  98 AQSLPSVLIAAAATG 112
                                    ****98877765555 PP

>> DUF452  Protein of unknown function (DUF452)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05     0.091      58     168 ..     265     385 ..     236     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                         DUF452  58 hirlvawsmgvwvaervl.qgirlksatavngtglpcddqygipeavfkgtlen....ltedtrlkferr....icgdka 128
                                    ++r+  w    w aer l  g  +++a+ +  + +p  +++g+  av++  l++    ++  +   fe r    + gd+ 
  gi|121636772|ref|YP_976995.1| 265 QLRITRWFAVRWGAERSLvVGATILAASFIPVAVIPNGQRFGVAVAVMALVLSAsllaVASAALFPFEMRavvaLSGDRL 344
                                    689999**********87369*************************9987776422115566667788774443468888 PP

                         DUF452 129 lledyqqysarptlqeihaelialyallqqdrr..tdlirws 168
                                    +   y  ys+   ++ +  +l a+ +l++  rr  td i w 
  gi|121636772|ref|YP_976995.1| 345 VATHYGFYSTIVGVGVLVGNL-AIGSLMSAARRlnTDEIVWG 385
                                    888888888877777666655.55566666665446777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2842.77
//
Query:       gi|121636773|ref|YP_976996.1|  [L=110]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   17.9   0.3      0.012   16.2   0.3    1.9  2  zf-ISL3   zinc-finger of transposase IS204/IS1001/IS1096/IS11


Domain annotation for each model (and alignments):
>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   6.8e-07     0.012       6      45 ..       8      46 ..       5      50 .. 0.85
   2 ?   -1.7   0.0      0.27   4.9e+03       6      11 ..      48      53 ..      48      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-07
                        zf-ISL3  6 PnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCk 45
                                   P Cg+     +++ +r   +lp++g++++ r+  +RyrC 
  gi|121636773|ref|YP_976996.1|  8 PDCGREG-SYRDTITRPLTDLPVAGYPLVPRVASPRYRCT 46
                                   7899995.344456*************************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.27
                        zf-ISL3  6 PnCgsk 11
                                   P+Cg+ 
  gi|121636773|ref|YP_976996.1| 48 PQCGRA 53
                                   899985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 822.62
//
Query:       gi|121636774|ref|YP_976997.1|  [L=275]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-47  159.2   0.0    1.1e-46  158.8   0.0    1.1  1  adh_short     short chain dehydrogenase
    1.2e-37  129.7   0.0    1.8e-37  129.2   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    2.4e-16   60.2   0.0    3.4e-16   59.7   0.0    1.2  1  KR            KR domain
      0.002   18.1   1.6      0.068   13.2   0.8    2.9  2  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8   0.0   2.3e-50   1.1e-46       3     190 ..       9     197 ..       7     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 2.3e-50
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    +++tG++sGIG+a+  e+a++Ga+vv+ d  +  l++++++l++eg +++ + +Dv++reev  l ++a   lg++dv+ 
  gi|121636774|ref|YP_976997.1|   9 AVITGGASGIGLATGTEFARRGARVVLGDVDKPGLRQAVNHLRAEGFDVHGVMCDVRHREEVTHLADEAFRLLGHVDVVF 88 
                                    89****************************************************************************** PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                     NAGi   gp+ e++ ++w+ vi+v l g +++++a+lp +l ++ +G++v+++S ag+vp+ag+ aY+ +K +v+gl++
  gi|121636774|ref|YP_976997.1|  89 SNAGIVVGGPIVEMTHDDWRWVIDVDLWGSIHTVEAFLPRLLeQGTGGHVVFTASFAGLVPNAGLGAYGVAKYGVVGLAE 168
                                    ****************************************9978899********************************* PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmakel 190
                                    +la+e+  +gi v++++P +v+T++++++
  gi|121636774|ref|YP_976997.1| 169 TLAREVTADGIGVSVLCPMVVETNLVANS 197
                                    ************************99876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0   3.9e-41   1.8e-37       1     183 [.      13     198 ..      13     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 3.9e-41
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                    G asgIG a+  ++a++Ga+vvl d+++ + +++v+ l +e+  +v  + cDV+++e+v++l++e+ + +g++D+++ na
  gi|121636774|ref|YP_976997.1|  13 GGASGIGLATGTEFARRGARVVLGDVDKPGlRQAVNHLRAEGF-DVhgVMCDVRHREEVTHLADEAFRLLGHVDVVFSNA 91 
                                    669***************************9999999999854.4346******************************** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaaKaalealtry 154
                                    gi+    gp++e++ ++++ ++dv+l + +++++a+lp l+++g  g +v ++s+++ +  ++  ayg+aK ++++l+ +
  gi|121636774|ref|YP_976997.1|  92 GIVVG--GPIVEMTHDDWRWVIDVDLWGSIHTVEAFLPrLLEQGtgGHVVFTASFAGLVPNAGLGAYGVAKYGVVGLAET 169
                                    *****..*******************************98888899********************************** PP

                                    HHHHHGGGTEEEEEEEE--BHCTGGGGST CS
                   adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgik 183
                                    lA+e+ ++gi v + +p +++T+++++ +
  gi|121636774|ref|YP_976997.1| 170 LAREVTADGIGVSVLCPMVVETNLVANSE 198
                                    ***********************987655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   7.5e-20   3.4e-16       4     165 ..      10     172 ..       8     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 7.5e-20
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    +itGG+ g+Gl++ +  a++gar  v+l+     ++  ++ +++l+a g +v+ v +Dv ++++v++l +e+ +  + + 
  gi|121636774|ref|YP_976997.1|  10 VITGGASGIGLATGTEFARRGAR--VVLGDV--DKPGLRQAVNHLRAEGFDVHGVMCDVRHREEVTHLADEAFRLLGHVD 85 
                                    7*********************9..567777..67888889*************************************** PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaaNaflDa 158
                                     v+  Ag++  +++ emt +d++ v+   + G+ +  e++ +      +  ++v+++S agl+ +ag ++Y  a   + +
  gi|121636774|ref|YP_976997.1|  86 VVFSNAGIVVGGPIVEMTHDDWRWVIDVDLWGSIHTVEAFLPrlleqGTGGHVVFTASFAGLVPNAGLGAYGVAKYGVVG 165
                                    *********************************9877766663333367779********************99877777 PP

                                    HHHHHHH CS
                             KR 159 laeyrrs 165
                                    lae+ ++
  gi|121636774|ref|YP_976997.1| 166 LAETLAR 172
                                    7766655 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.8   1.5e-05     0.068      15      97 ..      18     106 ..       8     118 .. 0.74
   2 ?    1.5   0.0     0.066   2.9e+02      46      60 ..     170     184 ..     165     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                    B12-binding  15 lGlavlaaalrdagfeVqllganven.edivaairaekpdvvglSalltsqleavkelvel.......lkrirprvkvvv 86 
                                    +Gla   ++ r+ g +V+l +++ +   + v+ +rae +dv g+ +    + e+v++l+++       +  + +++ +vv
  gi|121636774|ref|YP_976997.1|  18 IGLATGTEFARR-GARVVLGDVDKPGlRQAVNHLRAEGFDVHGVMC-DVRHREEVTHLADEafrllghVDVVFSNAGIVV 95 
                                    566666666666.778877777777788888888888888888888.888888888888888888777777788888888 PP

                    B12-binding  87 GGahpsldpee 97 
                                    GG++++ ++++
  gi|121636774|ref|YP_976997.1|  96 GGPIVEMTHDD 106
                                    88888877776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.066
                    B12-binding  46 airaekpdvvglSal 60 
                                     +r+  +d +g+S+l
  gi|121636774|ref|YP_976997.1| 170 LAREVTADGIGVSVL 184
                                    578889*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1972.78
//
Query:       gi|121636775|ref|YP_976998.1|  [L=278]
Description: fatty-acid-CoA ligase fadD16 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.048   12.3   0.0      0.081   11.5   0.0    1.3  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-06     0.081     368     400 ..      17      48 ..      15      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-06
                                    EEEETTS-SEBTT-HHHHHHHEEETCCEEEEEE CS
                    AMP-binding 368 lvrgpgvmkgYlkkpeataeafdsegrwlrTGD 400
                                    l+r  +v +g l +p at ea+d +++w +TGD
  gi|121636775|ref|YP_976998.1|  17 LIRRCSVVQGCLDDPGATVEAID-DDGWPHTGD 48 
                                    68999*****************9.546****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1991.96
//
Query:       gi|121636776|ref|YP_976999.1|  [L=560]
Description: pyruvate or indole-3-pyruvate decarboxylase pdc [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-34  118.2   0.9    1.4e-31  109.4   0.0    2.5  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    3.8e-20   72.2   0.0    1.4e-19   70.4   0.0    2.0  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.2e-10   39.5   0.5    4.1e-09   36.3   0.2    2.2  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.039   12.7   0.0      0.058   12.2   0.0    1.2  1  XFP_N         XFP N-terminal domain
       0.19   10.7   0.0       0.29   10.1   0.0    1.2  1  E1_dh         Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0     4e-35   1.4e-31       2     171 ..      15     188 ..      14     189 .. 0.91
   2 !    6.7   0.3    0.0014       4.9      43     146 ..     231     338 ..     215     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 4e-35
                                    EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                   TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                    tv+++l+++L++lgv ++fgvpG+ +l++ld++ +++ ir+v + +E +a++aAdgy r+ g + +v++t g+G +++++
  gi|121636776|ref|YP_976999.1|  15 TVGDYLLDRLAELGVSEIFGVPGDYNLQFLDHIVAHPTIRWVGSANELNAGYAADGYGRLRG-MSAVVTTFGVGELSVTN 93 
                                    89**********************************************************87.9999999********** PP

                                    HHHHHHHHT--EEEEEEE--CCCHH.S..TC--T......-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                   TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg.qgvlqqel......dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                    a+a+ + +++P+++++g +  + +g + +l++ l      + l + r++t +a+    p+++ ++++r + +   ++++P
  gi|121636776|ref|YP_976999.1|  94 AIAGSYAEHVPVVHIVGGPTKDAQGtRRALHHSLgdgdfeHFLRISREIT-CAQANLMPATAGREIDRVLSEV-REQKRP 171
                                    **************************555555555552444555566999.8888889***************.****** PP

                                    EEEEEEHHHCC-EEEHH CS
                   TPP_enzyme_N 155 vylelpkdvlleevded 171
                                     y+ l+ dv +++++++
  gi|121636776|ref|YP_976999.1| 172 GYILLSSDVARFPTEPP 188
                                    ************99976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                                    EE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HHHHHHCHHHHHHHHH.....HT--EEEEEEE--CCCHHS..TC--T-C CS
                   TPP_enzyme_N  43 vlarhEqgaafaAdgyaratgkpgvvlvts.gpGatnaltalaeAkv.....driPllvlsgdrptslrgqgvlqqeldq 116
                                    ++a+ E  a  aAd +  at   g  l+    p+++ ++ ++a+A +     ++ P+lv +g ++t++++ g++ q +d 
  gi|121636776|ref|YP_976999.1| 231 LQAVKELEALLAADVVPHATLMWGKSLLDEsSPNFLGIYAGAASAERvraaiEGAPVLVTAGVVFTDMVS-GFFSQRIDP 309
                                    5677888888888888888877887777766888888888888765533333899***************.888878875 PP

                                    CHHHCCCSSEEEE-SSGGGHHHHHHHHHHH CS
                   TPP_enzyme_N 117 lalfrpvtkyaervtspeelpealrrAirt 146
                                    +    ++ +y+  v++   +p ++  A+++
  gi|121636776|ref|YP_976999.1| 310 ART-IDIGQYQSSVADQVFAPLEMSAALQA 338
                                    544.25666666666666666666666665 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.83     3e+03      54      74 ..     128     151 ..     117     181 .. 0.66
   2 !   70.4   0.0   3.9e-23   1.4e-19      12     153 .]     404     539 ..     393     539 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.83
                                    EHHHHHHT..GGGHHHHHHTT-.S CS
                   TPP_enzyme_C  54 GDGgflmi..lqelatavrrnl.p 74 
                                    GDG+f +   ++  +t+++ nl p
  gi|121636776|ref|YP_976999.1| 128 GDGDFEHFlrISREITCAQANLmP 151
                                    777776554456666666666544 PP

  == domain 2  score: 70.4 bits;  conditional E-value: 3.9e-23
                                    HHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHH CS
                   TPP_enzyme_C  12 llkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggq 91 
                                    + ++ +  +++ + ++g++Gy+lpaA+Ga++a+pdr+ v ++GDG+ + ++qel t+ r++l  ++vv+nN gy   +  
  gi|121636776|ref|YP_976999.1| 404 H-RLPQGVTFIGQPLWGSIGYTLPAAVGAAVAHPDRRTVLLIGDGAAQLTVQELGTFSREGLSPVIVVVNNDGYTVERAI 482
                                    4.445566788899************************************************************887774 PP

                                    HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EE..EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS
                   TPP_enzyme_C  92 qepfggkrksgpagkdlkpvdfaklaealGak.ga..rvekadveeleealkeal.ekkgpaliev 153
                                       +g+   ++p+ +d  + +  +l  alG++  +  r   ++  +l++al  a  ++++++l+ev
  gi|121636776|ref|YP_976999.1| 483 ---HGE---TAPY-NDIVSWNWTELPSALGVTnHLafR--AQTYGQLDDALTVAAaRRDRMVLVEV 539
                                    ...443...2223.2367889***********777555..5555********99889999999997 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.2   1.1e-12   4.1e-09       3     128 ..     210     334 ..     208     343 .. 0.83
   2 ?    0.9   0.0     0.098   3.5e+02      12     110 ..     438     472 ..     413     492 .. 0.53

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.1e-12
                                    HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHHHH-SEE CS
                   TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylg.mlglhgskaanealeeaDlv 81 
                                    +a+el++ ++   +l++  v+r +a +el++l+ +  +P +t + gk++++e++p++lg ++g ++++ +++a+e a ++
  gi|121636776|ref|YP_976999.1| 210 AAIELIADHQL-TVLADLLVHRLQAVKELEALLAADVVPHATLMWGKSLLDESSPNFLGiYAGAASAERVRAAIEGAPVL 288
                                    56777776655.5689999************************************************************* PP

                                    EEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEEC CS
                   TPP_enzyme_M  82 lalGarfddirttgsepefapeakiihididpaeigknyqvdlaivg 128
                                    +  G+ f+d  + g +++    a+ i i   ++++  ++ + l++ +
  gi|121636776|ref|YP_976999.1| 289 VTAGVVFTD-MVSGFFSQRIDPARTIDIGQYQSSVADQVFAPLEMSA 334
                                    *********.5777777444455899998888877777766555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.098
                                    SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTC CS
                   TPP_enzyme_M  12 krpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddi 91 
                                    +r v+l+G g+a + + +el  ++++   Pv                                                 
  gi|121636776|ref|YP_976999.1| 438 RRTVLLIGDGAA-QLTVQELGTFSREGLSPV------------------------------------------------- 467
                                    344555555555.444444444444433333................................................. PP

                                    CCTTTTTTTTTT-EEEEEE CS
                   TPP_enzyme_M  92 rttgsepefapeakiihid 110
                                                  i+ ++
  gi|121636776|ref|YP_976999.1| 468 --------------IVVVN 472
                                    ..............34444 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05     0.058     140     171 ..     419     450 ..     397     479 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                          XFP_N 140 GelGyalshayGavldnPdlivacvvGdGeae 171
                                    G +Gy+l  a+Ga++ +Pd  ++ ++GdG a+
  gi|121636776|ref|YP_976999.1| 419 GSIGYTLPAAVGAAVAHPDRRTVLLIGDGAAQ 450
                                    899**************************986 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     8e-05      0.29     113     164 ..     427     477 ..     385     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8e-05
                                    HHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEE CS
                          E1_dh 113 ialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkyg 164
                                    +a+ a ++  ++ ++lliGDgAa q +v e  +++     pvi vv+N +y 
  gi|121636776|ref|YP_976999.1| 427 AAVGAAVAHPDRRTVLLIGDGAA-QLTVQELGTFSREGLSPVIVVVNNDGYT 477
                                    35555577889999*******86.899*********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3953.11
//
Query:       gi|121636777|ref|YP_977000.1|  [L=147]
Description: hypothetical protein BCG_0906 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-20   71.4   0.3    1.1e-19   71.1   0.3    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.7e-15   56.7   0.1    3.2e-15   56.5   0.1    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.022   14.9   0.1      0.031   14.4   0.1    1.5  1  DUF2505          Protein of unknown function (DUF2505)
       0.14   12.2   0.0       0.19   11.7   0.0    1.3  1  DUF3849          Protein of unknown function (DUF3849)


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.3   2.4e-23   1.1e-19       5     141 ..       6     139 ..       2     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.4e-23
                                    EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS..SEEEEEEEEEETTTTEEEEEEE.. CS
                Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr..gtvreelvevdpegrllsyriv.. 80 
                                    ++ +vi+a+pe++ ++++dfe++ +W+p+ ++ve+ ++g++  g+ ++v+++ +  g + e++v+++ + r++++++v  
  gi|121636777|ref|YP_977000.1|   6 SRDIVIEASPEEILDVIADFEAMTEWSPAHQSVEILETGDD--GRPSKVKMKVKtaGITDEQVVAYSWTDRSVRWTLVss 83 
                                    6789******************************8886777..6666666555444559*******956********855 PP

                                    .SSS-TSEEEEEEEEECCETEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  81 kpvpvanyvatwtvtpdgggtrvtwtgefda.gplggpfekpaaakavkgdleagLerLkar 141
                                    ++++     + +++tp g++t v++++++d+  pl+g++    +++a+kg ++++ e+L+ +
  gi|121636777|ref|YP_977000.1|  84 TQQRSQ--DGKYELTPKGDNTLVQFEITVDPqVPLPGFV----LKRAIKGTIDTATEALRSQ 139
                                    555555..89********************866777777....9*************99876 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.1   7.2e-19   3.2e-15       1     130 []      11     137 ..      11     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 7.2e-19
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEE CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfkslegk 80 
                                    ++a+++++ +++ad+e ++e++p  +sve+le+ +     d++ +++ ++ +      +++ ++         + + + +
  gi|121636777|ref|YP_977000.1|  11 IEASPEEILDVIADFEAMTEWSPAHQSVEILETGD-----DGRPSKVKMKVKTAGITDEQVVAY--------SWTDRSVR 77 
                                    79*********************************.....999**********99999999999........99999*** PP

                                    EEECTECC...EEE.......CEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  81 Wtieslpp...nsg.......gtrtkvalevdfkfaspllgalvgqvaervldellaale 130
                                    Wt++s+ +   ++g       g+ t v++e+++++ +pl+g++++ +++ ++d+  +al+
  gi|121636777|ref|YP_977000.1|  78 WTLVSSTQqrsQDGkyeltpkGDNTLVQFEITVDPQVPLPGFVLKRAIKGTIDTATEALR 137
                                    ******996654448889999999********************************9986 PP

>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   6.9e-06     0.031      75     143 ..      62     129 ..      11     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.9e-06
                        DUF2505  75 trteswgplsdgratgtvsasvkgapvelsGtltLepegegtrlevegevkvkiPlvGgklEklvaenl 143
                                    t+++   ++s   ++ +++  ++ ++ + +G+++L+p+g+ t +++e++v+ ++Pl G  l +++   +
  gi|121636777|ref|YP_977000.1|  62 TDEQVV-AYSWTDRSVRWTLVSSTQQRSQDGKYELTPKGDNTLVQFEITVDPQVPLPGFVLKRAIKGTI 129
                                    444444.33325567888888888889999**************************9988888886665 PP

>> DUF3849  Protein of unknown function (DUF3849)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.19      53     121 ..      67     138 ..      52     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                        DUF3849  53 vleefgaeRvkyvLantvqekdwDgrfseenkewaktiavpedkd..ernlefvvd.shpalldlfieqare 121
                                    v+ ++  + v+++L ++ q++++Dg+++   k     ++++ + d       fv++ +  + +d  +e +r 
  gi|121636777|ref|YP_977000.1|  67 VAYSWTDRSVRWTLVSSTQQRSQDGKYELTPKGDNTLVQFEITVDpqVPLPGFVLKrAIKGTIDTATEALRS 138
                                    5556777889*****************999998887777666655435556677766666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1072.72
//
Query:       gi|121636778|ref|YP_977001.1|  [L=359]
Description: fatty-acid-CoA racemase far [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-75  252.5   0.1    8.9e-75  252.1   0.1    1.1  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.1   0.1   4.9e-79   8.9e-75       1     363 [.       7     349 ..       7     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 252.1 bits;  conditional E-value: 4.9e-79
                   CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellk 80 
                                    LaGv+V++l+ +  Gp a+++LAdlGA+V++v +p +g ++                 ++r+Kr v lD+k++   ++++
  gi|121636778|ref|YP_977001.1|   7 LAGVKVIELGGIGPGPHAGMVLADLGADVVRVRRP-GGLTMPS----------EDRDLLHRGKRIVDLDVKTQ--PQAML 73 
                                    89*********************************.6664443..........224799************88..789** PP

                   CoA_transf_3  81 rLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvg 160
                                    +L+akADV+++ frpg+ erlg+g+++++++nPrLi+a+++g+Gq+Gp a+++g+D+++ + +G ++  g +d+pP+ + 
  gi|121636778|ref|YP_977001.1|  74 ELAAKADVLLDCFRPGTCERLGIGPDDCASVNPRLIFARITGWGQDGPLASTAGHDINYLSQTGALAAFGYADRPPMPPL 153
                                    ******************************************************************************** PP

                   CoA_transf_3 161 vplgDivtg.llaavailaallarertGkGqvidvslleaalallapqlley.latgevperqgnrdpaaapygvyrtkd 238
                                    + ++D+ +g +l+ ++i+ al++rer G Gqv+d+++++++  l ++ ++++ + + + ++++   d +a++y++y+t+d
  gi|121636778|ref|YP_977001.1| 154 NLVADFGGGsMLVLLGIVVALYERERSGVGQVVDAAMVDGVSVLAQMMWTMKgIGSLRDQRESFLLDGGAPFYRCYETSD 233
                                    ******6662667789*************************9998888877765555555545677779999******** PP

                   CoA_transf_3 239 g.wvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntlee 317
                                    g ++a++a +++++aal+  lg  +  +     t+ + ++   ++ + +ae++a+rt++ew +++a  + +++pv  ++e
  gi|121636778|ref|YP_977001.1| 234 GkYMAVGAIEPQFFAALLSGLGLSAA-D---VPTQLD-VAGYPQMYDIFAERFASRTRDEWTRVFAGTDACVTPVLAWSE 308
                                    ***********************963.4...444444.45589************************************* PP

                   CoA_transf_3 318 vlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPk 363
                                    ++++++l+ar +v++       +v++ +  +r+s+tpa + r++P+
  gi|121636778|ref|YP_977001.1| 309 AANNDHLKARSTVITAH-----GVQQAAPAPRFSRTPAGPVRPPPA 349
                                    *************9433.....467999999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2531.82
//
Query:       gi|121636779|ref|YP_977002.1|  [L=134]
Description: hypothetical protein BCG_0908 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-08   34.8   0.0    1.8e-08   34.7   0.0    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    4.8e-07   30.1   0.0    5.7e-07   29.9   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0     2e-12   1.8e-08      10     125 ..       2     115 ..       1     120 [. 0.94

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2e-12
                                    HHHTTTGGCCSCCCCEEEEEE.SSSEE.......E...........EEECSTTSSCEEEEEEEEEEETTTEEECTTCCCC CS
                 Polyketide_cyc  10 alvadvesypeflphcssvevleeaes....glsa...........dlevgfggltesftarvtldppeeitfklvegdf 74 
                                    +++adv  +  ++p  + vev++  ++    +++a            le  +g+    ++a++t ++  +          
  gi|121636779|ref|YP_977002.1|   2 EALADVGVLASWSPLHKQVEVIDYYPDgrphHVRAtvkilglvdkeVLEYHWGPDWVCWDADQTFQQHGQ---------- 71 
                                    689***********************988887777999********999*********************.......... PP

                                    CEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  75 kslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldel 125
                                       +++ t+++ +     +r++v++++++++a+p++g++v+ + e vld  
  gi|121636779|ref|YP_977002.1|  72 ---HIEYTVKPEG----VDRARVRFDITVEPAGPIPGFIVKRASEHVLDAA 115
                                    ...**********....89************************99999876 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   6.4e-11   5.7e-07      20     141 ..       3     122 ..       1     124 [. 0.78

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.4e-11
                                    HHTTTTGGGGT-TTEEEEECSE..STSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSE..EEEEEEE CS
                Polyketide_cyc2  20 lvsdfenwprWhpevarveleg..gggpargvegtvrvggrgtvreelvevdpegrllsyrivkpvpvany..vatwtvt 95 
                                    +++d + +++W+p  ++ve+ +  ++g+   v+ tv+  g+  v  e++e+   +  + +++   + + ++    ++tv+
  gi|121636779|ref|YP_977002.1|   3 ALADVGVLASWSPLHKQVEVIDyyPDGRPHHVRATVKILGL--VDKEVLEYHWGPDWVCWDAD--QTFQQHgqHIEYTVK 78 
                                    7899999***********98766655555777799999996..********978999999994..33333323688**** PP

                                    ECC.ETEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  96 pdg.ggtrvtwtgefda.gplggpfekpaaakavkgdleagLerLkar 141
                                    p+g +  rv++++++++ gp++g++    +++a +  l+a+ ++L+++
  gi|121636779|ref|YP_977002.1|  79 PEGvDRARVRFDITVEPaGPIPGFI----VKRASEHVLDAAAKGLQKL 122
                                    ***999**********878888888....6777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 941.58
//
Query:       gi|121636780|ref|YP_977003.1|  [L=157]
Description: hypothetical protein BCG_0909 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-12   46.2   2.9    6.4e-12   46.0   2.9    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    4.7e-08   33.3   0.4    5.6e-08   33.1   0.4    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
     0.0016   18.7   0.6     0.0026   18.0   0.6    1.3  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   2.9   1.1e-15   6.4e-12       2     141 ..      10     147 ..       9     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.1e-15
                                    EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSE..STSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEE CS
                Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleg..gggpargvegtvrvggrgtvreelvevdpegrllsyri 79 
                                    ++++++vvi+appe + ++++d++++p+W++  +rve+++   +g+   v+ t++v+g   v  el+e+   +  + +++
  gi|121636780|ref|YP_977003.1|  10 IRASREVVIEAPPEVIVEALADMDAVPSWSSVHKRVEVVDtySDGRPHHVKVTIKVAGI--VDTELLEYHWGPDWVVWDA 87 
                                    57899*******************************98875655555777799999996..********978******** PP

                                    E...SSS-TSEEEEEEEEECC.ETEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  80 v..kpvpvanyvatwtvtpdg.ggtrvtwtgefda.gplggpfekpaaakavkgdleagLerLkar 141
                                       +++ +    +++ +  ++ + trv++t ++++ +pl++     ++  a k++l+a+ e+L+++
  gi|121636780|ref|YP_977003.1|  88 AktAQQHGQ--HGEYNLRREDnDKTRVRFTLTVEPsAPLPA----FWVNIARKKILHAATEGLRKQ 147
                                    555555555..4556666555457**********7444443....446666677777777777665 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.4   9.4e-12   5.6e-08       1     127 [.      18     142 ..      18     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 9.4e-12
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE.......E...........EEECSTTSSCEEEEEEEEEEETTTE CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes....glsa...........dlevgfggltesftarvtldppeei 65 
                                    ++ap++++ +++ad +  p +++  ++vev+++  +    ++++            le  +g+    ++a  t ++  + 
  gi|121636780|ref|YP_977003.1|  18 IEAPPEVIVEALADMDAVPSWSSVHKRVEVVDTYSDgrphHVKVtikvagivdteLLEYHWGPDWVVWDAAKTAQQHGQ- 96 
                                    79*********************************9766644448899*******999*********************. PP

                                    EECTTCCCCCEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  66 tfklvegdfkslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldella 127
                                                +g+ +++  +     ++t+v+++++++++ pl+++ v+ + +++l    +
  gi|121636780|ref|YP_977003.1|  97 ------------HGEYNLRRED----NDKTRVRFTLTVEPSAPLPAFWVNIARKKILHAATE 142
                                    ............**********....788******************999988888776665 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   4.3e-07    0.0026       2     102 ..      20     122 ..      19     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                                    S-HHHHHHHHH-HHHHHHHEEEEEEEE--STTEEEEEEETTTSEEEEEEEE..EEEEETTTEEEEEEEEE..TSET.... CS
                          AHSA1   2 apperVfraltdpellkrWftlteaemdlrpGgkfrlrdspdgkefgnege..ylevvpperlvytwrle..depe.... 73 
                                    appe + +al d +++ +W +  + ++++     +  ++  dg+ ++ +++  +  +v+ e l+y w+ +     +    
  gi|121636780|ref|YP_977003.1|  20 APPEVIVEALADMDAVPSW-SSVHKRVEV-----V--DTYSDGRPHHVKVTikVAGIVDTELLEYHWGPDwvV--Wdaak 89 
                                    89*****************.444444444.....1..222455555555555599************999553..25589 PP

                                    ...EEEEEEEEEEEE.ETTEEEEEEEEEEEEHC CS
                          AHSA1  74 ...eeestvtielee.egggTrltlthtglprk 102
                                       ++  + +++l    +++Tr+++t t +p+ 
  gi|121636780|ref|YP_977003.1|  90 taqQHGQHGEYNLRReDNDKTRVRFTLTVEPSA 122
                                    9999999*******988888******9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1008.64
//
Query:       gi|121636781|ref|YP_977004.1|  [L=397]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-61  206.9   0.0    5.8e-61  206.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.8e-08   32.1   0.0    8.6e-08   31.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    2.8e-06   26.1   0.0    4.2e-06   25.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00025   20.5   1.8    0.00039   19.9   1.8    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.024   13.9   0.0      0.043   13.1   0.0    1.7  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.7   0.0   1.6e-64   5.8e-61       4     363 .]      27     388 ..      24     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 1.6e-64
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    +nLg++ ++ d     +p+ ++a+++  +  g++n+y+p  g++ l+ a+a   +r+ ++++++e++v+v+ Ga+++i+a
  gi|121636781|ref|YP_977004.1|  27 VNLGQGFPDED----GPPKMLQAAQD--AIAGGVNQYPPGPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAA 100
                                    8**********....9**********..999********************9999999********************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyse.edfhldlealeealkeapegnkktkvilvesphNPtG 162
                                    +   l ++pg+e+l+ +p+y+sy++++ ++g+  v++pl +   +f ld++al +a++       +t+ ++++sphNPtG
  gi|121636781|ref|YP_977004.1| 101 AVLGL-VEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVPDgRGFALDADALRRAVTP------RTRALIINSPHNPTG 173
                                    *****.9*******************************999899**************9......*************** PP

                                    -B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 163 tvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvs 241
                                    +v++  el +++++a + nl+++ De+Y+++vf++ ++ + +a+++   + +++ +s +K f+++G+ +G+++g a+++ 
  gi|121636781|ref|YP_977004.1| 174 AVLSATELAAIAEIAVAANLVVITDEVYEHLVFDHARHLP-LAGFDGMAErTITISSAAKMFNCTGWKIGWACGPAELIA 252
                                    **********************************766666.67777766679**************************** PP

                                    HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH...C CS
                  Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae...t 316
                                     +r +++ + +   ++ q+ava al++++    ++ + r  l +rr++l ++L+e+g++v +s +++fl  d +++   +
  gi|121636781|ref|YP_977004.1| 253 GVRAAKQYLSYvgGAPFQPAVALALDTEDA---WVAALRNSLRARRDRLAAGLTEIGFAVHDSYGTYFLCADPRPLgydD 329
                                    ***9999887789**************997...**********************************************9 PP

                                    HHHHHHHHHHTCTEEEEEGGGGTS.............TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 317 akelskkLleevgvyvtpgtsftv.............pgrlRitvAglteeeleelveal 363
                                     +e++ +L e+vgv+ +p++ f                  +R+t+ +  +++l+e++++l
  gi|121636781|ref|YP_977004.1| 330 STEFCAALPEKVGVAAIPMSAFCDpaagqasqqadvwNHLVRFTF-CKRDDTLDEAIRRL 388
                                    9*****************99987788999999999999999****.99999999999986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   2.4e-11   8.6e-08      60     177 ..      84     200 ..      76     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.4e-11
                                    TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TT CS
                    Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnek 139
                                     e e+++t G+teai++++l+l   ++pg e+++ e  + +   p +++a ++ ++v  +p  ++  ld d+l+ +++++
  gi|121636781|ref|YP_977004.1|  84 PETEVLVTVGATEAIAAAVLGL---VEPGSEVLLIEPFYDSYS-PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPR 159
                                    4689******************...******************.9999999***********9999************** PP

                                    EEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE-T CS
                    Aminotran_5 140 tklvaithvsnvtGti...qpveeigklakkkgalvlvDaa 177
                                    t++++i+   n tG +    ++++i+++a +++ +v++D +
  gi|121636781|ref|YP_977004.1| 160 TRALIINSPHNPTGAVlsaTELAAIAEIAVAANLVVITDEV 200
                                    **************972224556666666777888888865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.2e-09   4.2e-06      72     176 ..      90     201 ..      83     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-09
                                    EESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS CS
                Cys_Met_Meta_PP  72 avssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtp 146
                                    ++   + Aiaaa+l l++ G+e+++ +  Y++ + ++  ++  + ++v  v        d+++l++a++++t+++ + +p
  gi|121636781|ref|YP_977004.1|  90 VTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVV-AMAGAHRVTVPLVPDgrgfaLDADALRRAVTPRTRALIINSP 168
                                    444445699*********************9766555.56677778888887657777899******************* PP

                                    -TTT...T----HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 147 tnpl...lkvvDiekiaklakkagvlvvvDntf 176
                                     np+   l+ + +++ia++a +a+++v+ D ++
  gi|121636781|ref|YP_977004.1| 169 HNPTgavLSATELAAIAEIAVAANLVVITDEVY 201
                                    ***83334557899999***********99876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.8   1.1e-07   0.00039      42     144 ..      89     198 ..      80     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                                    EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B..-TTTSSB-GGGCGGG--TTEEEEE... CS
                DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDv..dpdtynidpaaieaaitertkaIl... 116
                                    + +  +t+A++ a   l v+pg eV+     + +   +v+ +ga  v v    d   + +d++a+++a+t+rt+a +   
  gi|121636781|ref|YP_977004.1|  89 LVTVGATEAIAAAVLGL-VEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLvpDGRGFALDADALRRAVTPRTRALIins 167
                                    55556677766665443.679****99999888888899999998887776115668******************98333 PP

                                    EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 117 pVhlyGqva...dmdalkaiaakhglkvieD 144
                                    p +  G+v    +++a+ +ia + +l+vi D
  gi|121636781|ref|YP_977004.1| 168 PHNPTGAVLsatELAAIAEIAVAANLVVITD 198
                                    3345666533459****************99 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.043      89     167 ..     124     198 ..      37     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                    HHHHCC--EEEEE-EBTT...TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEE CS
                Beta_elim_lyase  89 aiaelagvklrdlknkea...GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplh 165
                                     ++++ag++ ++++   +     +d+++l++a+++      +++++++   +n   G v+s  el+++a+ia + ++ ++
  gi|121636781|ref|YP_977004.1| 124 PVVAMAGAHRVTVPLVPDgrgFALDADALRRAVTP------RTRALIINSPHNP-TGAVLSATELAAIAEIAVAANLVVI 196
                                    44556666666666555523246999999999999......5789999999995.9********************8888 PP

                                    EE CS
                Beta_elim_lyase 166 lD 167
                                     D
  gi|121636781|ref|YP_977004.1| 197 TD 198
                                    77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3045.28
//
Query:       gi|121636782|ref|YP_977005.1|  [L=403]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-49  168.6   0.0    2.1e-46  158.4   0.0    2.3  2  Thiolase_N     Thiolase, N-terminal domain
    1.7e-47  160.1   0.1      4e-47  158.9   0.1    1.7  1  Thiolase_C     Thiolase, C-terminal domain
    1.8e-05   24.4   0.2    3.8e-05   23.4   0.2    1.5  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    0.00019   21.6   0.0    0.00041   20.5   0.0    1.6  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.24   11.3   0.0    1.9  1  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.0   5.9e-50   2.1e-46       2     234 ..       6     226 ..       5     231 .. 0.93
   2 !    7.9   0.0    0.0005       1.8     240     258 ..     253     271 ..     238     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 5.9e-50
                                    EEEEEEEE--EE.TTSTTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEE CS
                     Thiolase_N   2 vivsaartpigk.fggslkdlsaeeLlaealkallekag.vdpeevdevivGnvlqa.gegqniarqaalkagipeevpa 78 
                                    +i +a rtp gk ++gsl++++   L   ++ +l ++ + +d++ +++vi+G+v     +g  iar+a+l++g+p +   
  gi|121636782|ref|YP_977005.1|   6 FIYEAIRTPRGKqKNGSLHEVKPLSLVVGLIDELRKRHPdLDENLISDVILGCVSPVgDQGGDIARAAVLASGMPVTSGG 85 
                                    5889********99************************9*****************9778888***************** PP

                                    EEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHH CS
                     Thiolase_N  79 vtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlt 158
                                    v +n++c+Sgl+av++aaq++++g  d v+agGvEsms++p+  +      + l+ ++  d++              G+ 
  gi|121636782|ref|YP_977005.1|  86 VQLNRFCASGLEAVNTAAQKVRSGWDDLVLAGGVESMSRVPMGSDG---GAMGLDPATNYDVMFVP----------QGIG 152
                                    *******************************************983...34555666666666444..........5*** PP

                                    HHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSS CS
                     Thiolase_N 159 aenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFk 234
                                    a+ +a   ++sRe+ d++A++s+qkaa+a++ g F++ +vPv+   ++g  ++d+de++r+++t e LaklkpaF+
  gi|121636782|ref|YP_977005.1| 153 ADLIATIEGFSREDVDAYALRSQQKAAEAWSGGYFAKSVVPVRD--QNGLLILDHDEHMRPDTTKEGLAKLKPAFE 226
                                    ***************************************99975..55789************************7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0005
                                    BTTSB--BEEEEEEEEEEE CS
                     Thiolase_N 240 tAgnasqisDGaaavllms 258
                                    t gn+s+i DGaa v++ s
  gi|121636782|ref|YP_977005.1| 253 TGGNSSGIVDGAALVMIGS 271
                                    89*************9966 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.1   1.1e-50     4e-47       2     123 .]     281     402 ..     280     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.1e-50
                                    --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                     Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                    +p a+i++ a++g dp i+ +gP++a++kvl++agltv+didlfE+nEAFa+++L+ +k+l++  ek+NvnGGaia+GHP
  gi|121636782|ref|YP_977005.1| 281 TPRARIVATATSGADPVIMLTGPTPATRKVLDRAGLTVDDIDLFELNEAFASVVLKFQKDLNIPDEKLNVNGGAIAMGHP 360
                                    799***************************************************************************** PP

                                    TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                     Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                    lGa+Ga i+ t++ el++++++ ++++lCiggg+gva++ie+
  gi|121636782|ref|YP_977005.1| 361 LGATGAMILGTMVDELERRNARRALITLCIGGGMGVATIIER 402
                                    ****************************************96 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   1.1e-08   3.8e-05     175     206 ..      92     123 ..      76     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.1e-08
                                    GGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                  ketoacyl-synt 175 CsSslvavhaavqslrsgeadvalaGGvelll 206
                                    C+S+l av+ a q++rsg  d++laGGve + 
  gi|121636782|ref|YP_977005.1|  92 CASGLEAVNTAAQKVRSGWDDLVLAGGVESMS 123
                                    *****************************875 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.1e-07   0.00041       1      86 [.     311     399 ..     311     403 .] 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                    HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEE.EEE CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvll.vgf 77 
                                    L++aglt++did++ ++ a ++++ +  k l++p+ek  vn     +G+   a+  + L ++v+e + ++  ++l+ + +
  gi|121636782|ref|YP_977005.1| 311 LDRAGLTVDDIDLFELNEAFASVVLKFQKDLNIPDEKLNVNGgaIAMGHPLGATGAMILGTMVDELERRNARRALItLCI 390
                                    799***********************************999855678999999999999999998766666665551458 PP

                                    ETTTEEEEE CS
                  ACP_syn_III_C  78 GaGltwgaa 86 
                                    G+G+ ++ +
  gi|121636782|ref|YP_977005.1| 391 GGGMGVATI 399
                                    888876655 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.8e-05      0.24       3      40 ..      88     125 ..      86     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlski 40 
                                    ln  C++ + a+++A++ ++sg    vL  g e +s++
  gi|121636782|ref|YP_977005.1|  88 LNRFCASGLEAVNTAAQKVRSGWDDLVLAGGVESMSRV 125
                                    7899*******************9****999***9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2954.68
//
Query:       gi|121636783|ref|YP_977006.1|  [L=720]
Description: fatty oxidation protein fadB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-62  211.0   0.1    2.2e-62  210.1   0.1    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
    3.5e-32  111.7   0.8    6.2e-32  110.9   0.8    1.3  1  ECH_1          Enoyl-CoA hydratase/isomerase
    4.9e-21   75.2   0.3    2.6e-20   72.8   0.0    2.4  3  3HCDH          3-hydroxyacyl-CoA dehydrogenase, C-terminal do
      9e-20   71.4   0.3    1.5e-19   70.6   0.3    1.3  1  ECH_2          Enoyl-CoA hydratase/isomerase
     0.0014   18.8   0.8     0.0055   16.9   0.8    2.1  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0067   17.0   0.1       0.02   15.5   0.1    1.9  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.02   14.8   0.2          2    8.4   0.0    3.0  3  Peptidase_S49  Peptidase family S49
      0.022   14.3   0.2       0.43   10.1   0.1    2.6  2  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
      0.097   12.9   0.6        0.3   11.3   0.6    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.1   1.1e-65   2.2e-62       2     179 ..     328     505 ..     327     506 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 1.1e-65
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SE CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadl 81 
                                    ++v+GaG+mGagia+v a+ag+eVvl d+s ea++k++   ek  +k+ e+g++++e  +a+lari++t+d ++++++d+
  gi|121636783|ref|YP_977006.1| 328 IGVLGAGMMGAGIAYVSAKAGYEVVLKDVSLEAAAKGKGYSEKLEAKALERGRTTQERSDALLARITPTADAADFKGVDF 407
                                    89*****************************************999********************************** PP

                                    EEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                        3HCDH_N  82 viEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetva 161
                                    viEav+En elK+kvf e+e i++p+ail snTS+l+i+ la+ +kr+e +ig+HFf+P+++m+LvE+++gekTs+e++a
  gi|121636783|ref|YP_977006.1| 408 VIEAVFENQELKHKVFGEIEDIVEPNAILGSNTSTLPITGLATGVKRQEDFIGIHFFSPVDKMPLVEIIKGEKTSDEALA 487
                                    ******************************************************************************** PP

                                    HHHHHHHHTT-EEEEECS CS
                        3HCDH_N 162 tvvelakkigktpvvvkd 179
                                    +v++++ +igktp+vv+d
  gi|121636783|ref|YP_977006.1| 488 RVFDYTLAIGKTPIVVND 505
                                    ****************98 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.8   3.1e-35   6.2e-32       4     195 ..      13     213 ..      10     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.1e-35
                                    TTEEEEEE--CG.CTTEE-HHHHHHHHHHHHHH..HHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHH...CCH CS
                          ECH_1   4 agvaviklnrPe.avNalsaelltEliqalekl..eddksvravvLtGgdkaFaaGadlkemaeeekakqallk...eev 77 
                                    +g++ +++++P    N ++++ ++ + +a  +l  e+d s+++vv+++  k F aG+d+k m +  ++++ ++    e++
  gi|121636783|ref|YP_977006.1|  13 DGIVTLTMDDPSgSTNVMNEAYIESMGKAVDRLvaEKD-SITGVVVASAKKTFFAGGDVKTMIQARPEDAGDVFntvETI 91 
                                    699********7468***************98622555.9*************************997777665011555 PP

                                    HHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETT..TEEE-GGGGGTS--CTTCHHHHHHHHHHHHHH.HHHH CS
                          ECH_1  78 lelwtklytvpkpviaavnGaaigGGlelalacDiviaadn..asfglnelklGlipgaggtqilarkvGkskAe.eill 154
                                    +  ++ l t+ kpv+aa+nGaa+gGGle+alac  +iaad   ++ gl+e+ lGl+pg gg+ + +r  G + A   +l 
  gi|121636783|ref|YP_977006.1|  92 KRQLRTLETLGKPVVAAINGAALGGGLEIALACHHRIAADVkgSQLGLPEVTLGLLPGGGGVTRTVRMFGIQNAFvSVLA 171
                                    66777788888****************************953367***************************99626788 PP

                                    HT-EEEHHHHHHCTSSSEEESG.GGHHHHHHHHHHHHHHSCH CS
                          ECH_1 155 lgkkisaqealkvGlvdkvvpe.eqlleealelaeklaeksp 195
                                     g++++++ a+++Glvd+ v+  e+l+  a +++++ +++ p
  gi|121636783|ref|YP_977006.1| 172 QGTRFKPAKAKEIGLVDELVATvEELVPAAKAWIKEELKANP 213
                                    9********************9999**999999988776655 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.2   1.6e+04      41      86 ..     338     381 ..     327     386 .. 0.57
   2 !   72.8   0.0   1.3e-23   2.6e-20       1      97 []     508     607 ..     508     607 .. 0.89
   3 ?   -1.9   0.0       2.7   5.4e+03       5      25 ..     637     657 ..     635     671 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.2
                                    SCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT-- CS
                          3HCDH  41 mGpfelldlvgldvakkilevlaeelgerayapsplleklveagrl 86 
                                     G+  ++  +g +v++k  + l+++ + + y   +l  k +e gr 
  gi|121636783|ref|YP_977006.1| 338 AGIAYVSAKAGYEVVLKDVS-LEAAAKGKGYS-EKLEAKALERGRT 381
                                    55566666666666666554.44444444444.4666666666655 PP

  == domain 2  score: 72.8 bits;  conditional E-value: 1.3e-23
                                    TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTH.....GGHH-H CS
                          3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelger.....ayapsp 75 
                                    GF+++Rv+++++nea++++ eg ++p++i++a ++ +G+p  p++l+d+++l++++ki+ + +++ ++       + +  
  gi|121636783|ref|YP_977006.1| 508 GFFTSRVIGTFVNEALAMLGEG-VEPASIEQAGSQ-AGYPAPPLQLSDELNLELMHKIAVATRKGVEDAggtyqPHPAEA 585
                                    9*********************.************.************************66666666666334333357 PP

                                    HHHHHHHTT--BGGGTBSSSBC CS
                          3HCDH  76 lleklveagrlgrktgkgfyky 97 
                                    ++ek++e gr gr +g+gfy+y
  gi|121636783|ref|YP_977006.1| 586 VVEKMIELGRSGRLKGAGFYEY 607
                                    9*******************98 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHHHHHTTSS- CS
                          3HCDH   5 nRvlapllneavrlveegvas 25 
                                    +R+l++   e+ ++++egv++
  gi|121636783|ref|YP_977006.1| 637 DRMLFAEALETQKCLDEGVLT 657
                                    799999999*********765 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.3   7.8e-23   1.5e-19       4     174 ..      18     193 ..      15     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 7.8e-23
                                    EEE--GG.GTT-B-HHHHHHHHHHHHHH.CC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   4 itLnrpk.alNaLslemvralkealkew.ekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    +t++ p+ + N+++ + ++++ +a+++  +++d+++ vv+ +a+ k f AGgDv+++ +a+ e++ +  + +++  +   
  gi|121636783|ref|YP_977006.1|  18 LTMDDPSgSTNVMNEAYIESMGKAVDRLvAEKDSITGVVVASAK-KTFFAGGDVKTMIQARPEDAGDVFNTVETIKRQLR 96 
                                    6666665368***************9963788999999999976.99****************98886667777777788 PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-T..T-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHH..H---B CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvte..rtvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylal..TGarl 157
                                    +++t+ kpvva ++G ++GgG+ +++ +++r++ +   +++  PE+++Gl P  Gg     r+ g    ++ +   G+r+
  gi|121636783|ref|YP_977006.1|  97 TLETLGKPVVAAINGAALGGGLEIALACHHRIAADvkGSQLGLPEVTLGLLPGGGGVTRTVRMFGIQNAFVSVlaQGTRF 176
                                    89999****************************973257************************997777776533699** PP

                                    -HHHHHHTTS--EE--G CS
                          ECH_2 158 kgadalaaglathyvps 174
                                    k a a ++gl + +v +
  gi|121636783|ref|YP_977006.1| 177 KPAKAKEIGLVDELVAT 193
                                    ************99875 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   2.8e-06    0.0055       1      84 [.     327     434 ..     327     456 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHHHC CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelvasl 56 
                                    +ig++G G+MG+ +a   +kagy+v++ +++ e++ +                             ++++++++++ +++
  gi|121636783|ref|YP_977006.1| 327 RIGVLGAGMMGAGIAYVSAKAGYEVVLKDVSLEAAAKGKGYSekleakalergrttqersdallarITPTADAADF-KGV 405
                                    59***************************99888877665545566666666666666666655443344433332.455 PP

                                    SEEEE-SSSHHHHHHHHHS.HCCC--TT- CS
                  NAD_binding_2  57 dvvitmvkagkavdevieg.llealkkgd 84 
                                    d+vi  v ++++ ++ ++g + + +++++
  gi|121636783|ref|YP_977006.1| 406 DFVIEAVFENQELKHKVFGeIEDIVEPNA 434
                                    77777776666666666665555555555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     1e-05      0.02       1      41 [.     327     363 ..     327     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaee 41 
                                    +ig++GaG mg+++a   ++ag   +e+v+  + + e a++
  gi|121636783|ref|YP_977006.1| 327 RIGVLGAGMMGAGIAYVSAKAG---YEVVLK-DVSLEAAAK 363
                                    79********************...999943.555554443 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   2.9e+03      25      52 ..      39      66 ..      30      95 .. 0.75
   2 ?    2.7   0.0     0.054   1.1e+02       6      34 ..     102     130 ..      97     134 .. 0.89
   3 ?    8.4   0.0     0.001         2     114     144 ..     167     198 ..     158     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                   HTTSSEEEE-TT-EEE---EEEEEEE-H CS
                  Peptidase_S49 25 asaadkivanpstivgsiGvitqllnle 52
                                   + a d+ va++ +i+g++   ++++++ 
  gi|121636783|ref|YP_977006.1| 39 GKAVDRLVAEKDSITGVVVASAKKTFFA 66
                                   5678999999999999986666666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.054
                                    T--EEEEEEEEEETHHHHHHTTSSEEEE- CS
                  Peptidase_S49   6 kkPvvasaenvaaSggYylasaadkivan 34 
                                    +kPvva +++ a  gg  +a a+ + +a+
  gi|121636783|ref|YP_977006.1| 102 GKPVVAAINGAALGGGLEIALACHHRIAA 130
                                    8*********************9988775 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.001
                                    HHCHHCCHEEEHHHHHHTTSSSEET.SHHHHH CS
                  Peptidase_S49 114 vdkiAegrvltgqqAlklgLvdelg.tvddav 144
                                    v  +A+g  ++ ++A++ gLvdel  tv+++v
  gi|121636783|ref|YP_977006.1| 167 VSVLAQGTRFKPAKAKEIGLVDELVaTVEELV 198
                                    7789*******************862455555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00022      0.43       6      71 ..     336     401 ..     329     448 .. 0.84
   2 ?    1.4   0.0     0.099     2e+02     137     162 ..     685     711 ..     662     713 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEE CS
                   adh_short_C2   6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklD 71 
                                    +G++iA   a++G+evvl d++ ea+++ +   e+l+a++le   t +e  +al ++++ + +  D
  gi|121636783|ref|YP_977006.1| 336 MGAGIAYVSAKAGYEVVLKDVSLEAAAKGKGYSEKLEAKALERGRTTQERSDALLARITPTADAAD 401
                                    799*************************************99999999999999998865443333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.099
                                    TTT.HHHHHHHHHHHHHHHHHHHHGGG CS
                   adh_short_C2 137 nyn.aygaaKaalealtrylAvelgpk 162
                                    +y+   g+ Kaa +a tr lA+ +g++
  gi|121636783|ref|YP_977006.1| 685 GYSgPAGTGKAAFVARTRELAAAYGDR 711
                                    444477889***************986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00015       0.3       1      26 [.     330     355 ..     330     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                    EE--SHHHHHHHHHHHCCTEEEEEE- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvllle 26 
                                    ++GaG+ G+ +Ay  akag++v+l +
  gi|121636783|ref|YP_977006.1| 330 VLGAGMMGAGIAYVSAKAGYEVVLKD 355
                                    89********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 5378.60
//
Query:       gi|121636784|ref|YP_977007.1|  [L=542]
Description: DNA helicase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-44  151.6   1.8      2e-44  150.8   0.7    2.0  2  Helicase_C_3   Helicase conserved C-terminal domain
    5.8e-42  143.6   0.0      8e-42  143.2   0.0    1.1  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.9e-13   50.8   0.0    2.8e-13   50.2   0.0    1.2  1  ResIII         Type III restriction enzyme, res subunit
    9.8e-10   38.8   0.0    1.9e-09   37.8   0.0    1.5  1  Helicase_C     Helicase conserved C-terminal domain
     0.0008   18.2   0.0     0.0034   16.2   0.0    1.7  1  SNF2_N         SNF2 family N-terminal domain
     0.0076   16.0   0.0      0.013   15.2   0.0    1.4  1  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.095   12.5   0.1       0.17   11.7   0.1    1.4  1  DUF3767        Protein of unknown function (DUF3767)


Domain annotation for each model (and alignments):
>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.8   0.7   7.9e-48     2e-44       4     127 .]       2     127 ..       1     127 [. 0.98
   2 ?   -2.4   0.0       1.9     5e+03      19      34 ..     364     379 ..     357     387 .. 0.77

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 7.9e-48
                   Helicase_C_3   4 qaDltillegdsplaeearaaLaafAelesrpehahtyrltplSlrrAldaGltaeeiiefLerlskypvPqaleylird 83 
                                    q+D+t+lle+d++la +araa+a+fAele++peh+htyr+tpl+l++A++aG++ae+++++L ++s+y+vPq+l ++i d
  gi|121636784|ref|YP_977007.1|   2 QSDKTVLLEVDHELAGAARAAIAPFAELERAPEHVHTYRITPLALWNARAAGHDAEQVVDALVSYSRYAVPQPLLVDIVD 81 
                                    9******************************************************************************* PP

                   Helicase_C_3  84 varryGklrlgl..easlvlrsddpalleelladkkiaklllrria 127
                                    +++ryG+l+l++  +  l l s d+a+lee+l++kkia++l++ri+
  gi|121636784|ref|YP_977007.1|  82 TMARYGRLQLVKnpAHGLTLVSLDRAVLEEVLRNKKIAPMLGARID 127
                                    *************9999*************************9985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                   Helicase_C_3  19 eearaaLaafAelesr 34 
                                    ++ ++++ a+Ae+e r
  gi|121636784|ref|YP_977007.1| 364 TDSERMMYATAEPEER 379
                                    567899999****998 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   3.1e-45     8e-42       2     193 ..     346     530 ..     345     537 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 3.1e-45
                  ERCC3_RAD25_C   2 qekgylakvqcaevWcpmtaefykeylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklk 81 
                                    +++g++a ++c+ev   mt +    y +a+ +++  ++ +  +k+ +++ ++  h    ++ +v    +  L e++ +l 
  gi|121636784|ref|YP_977007.1| 346 EAQGWIAPAECVEVRVTMTDSERMMYATAEPEERYRICSTVHTKIAVVKSILAKHPD--EQTLVIGAYLDQLDELGAELG 423
                                    579*************************************************99975..567888999999********* PP

                  ERCC3_RAD25_C  82 kpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefn 161
                                     p i+G+t+++er +++++f++  +v t+++skv++ siDlPea v +q+s  fgsr+ eaqrlGriLr+k++    +  
  gi|121636784|ref|YP_977007.1| 424 APVIQGSTRTSEREALFDAFRRG-EVATLVVSKVANFSIDLPEAAVAVQVSGTFGSRQEEAQRLGRILRPKAD----GGG 498
                                    ********************987.899********************************************99....899 PP

                  ERCC3_RAD25_C 162 affYsLvskDtkemaystkrqqflvdqGYafk 193
                                    a fYs+v++D  + +y+++rq+fl +qGY + 
  gi|121636784|ref|YP_977007.1| 499 AIFYSVVARDSLDAEYAAHRQRFLAEQGYGYI 530
                                    *****************************995 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.1e-16   2.8e-13       3     170 ..     174     320 ..     172     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.1e-16
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    +lr+yQ  a +++ +         g++++++G+GKTlv a+++++         +l+lv ++    q+++e+   +s + 
  gi|121636784|ref|YP_977007.1| 174 QLRDYQRLAADSFWAG------GSGVVVLPCGAGKTLVGAAAMAKAGA-----TTLILVTNIVAARQWKRELVARTSLTE 242
                                    5777777777777744......4699*****************99988.....7******************99999988 PP

                                    ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEE CS
                         ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavl 162
                                    +eig++  ++k+++          +++t+q+++++ + e ++ e +++    +ii DE+H l a   +r  ++  +++ +
  gi|121636784|ref|YP_977007.1| 243 NEIGEFSGERKEIR--------PATISTYQMITRRTKGEYRHLELFDSRDWGLIIYDEVHLLPA-PVFRMTADL-QSKRR 312
                                    86776666666666........9*************9999999999999999************.999886565.88*** PP

                                    EEEESS-S CS
                         ResIII 163 lglTATpe 170
                                    lglTAT+ 
  gi|121636784|ref|YP_977007.1| 313 LGLTATLI 320
                                    ******85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   7.6e-13   1.9e-09       2     109 ..     389     491 ..     388     493 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 7.6e-13
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                    k++ ++ +l  ++ ++++l++  + d+l+    l    ++ + v++g++ ++ere+ +++f++ge+  L+ ++va  +id
  gi|121636784|ref|YP_977007.1| 389 KIAVVKSIL-AKHPDEQTLVIGAYLDQLD---EL--GAELGAPVIQGSTRTSEREALFDAFRRGEVATLVVSKVANFSID 462
                                    677888888.899***************5...55..35688999************************************ PP

                                    STTESEEEESSSS.SSHHHHHHHHTTSSS CS
                     Helicase_C  82 ipkvnlVinfdlp.rnvtsyiqriGRtgR 109
                                    +p++ + ++++    + ++  qr GR+ R
  gi|121636784|ref|YP_977007.1| 463 LPEAAVAVQVSGTfGSRQEEAQRLGRILR 491
                                    ********99988455899********99 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-06    0.0034     151     230 ..     257     333 ..     199     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                                    -EEEE-HHHHHHHT.......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 151 dvvittYdvlsreaelq.kkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledlygLlkf 229
                                       i tY+++ r+++ +  + + + +++w  ++ DE h l      +  +  +L++++r+ lt+T i ++ ++    +++
  gi|121636784|ref|YP_977007.1| 257 PATISTYQMITRRTKGEyRHLELFDSRDWGLIIYDEVHLLPA---PVFRMTADLQSKRRLGLTATLIREDGRE-GDVFSL 332
                                    55699******99988889999******************75...57777778************99885554.233344 PP

                                    H CS
                                    x RF
                         SNF2_N 230 L 230
                                    +
  gi|121636784|ref|YP_977007.1| 333 I 333
                                    4 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.3e-06     0.013       2     144 ..     177     302 ..     176     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-06
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    d+Q+ a + +  gg+ +v  + G+GKTl+ + ++         k g  +li++     a+q  ++l  +++ ++ ++   
  gi|121636784|ref|YP_977007.1| 177 DYQRLAADSFWAGGSGVVVLPCGAGKTLVGAAAMA--------KAGATTLILVTNIVAARQWKRELVARTSLTE-NEIGE 247
                                    78999999999******************999999........78899***********************665.55566 PP

                                    ETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                    ++g++++   +++ ++   i+  t g   + l+   ++ ++  +++ DE++ l    f     r
  gi|121636784|ref|YP_977007.1| 248 FSGERKEIRPATI-STyQMITRRTKGEYRH-LE--LFDSRDWGLIIYDEVHLLPAPVF-----R 302
                                    7888888999999.5515555556666555.54..677999**********9977643.....3 PP

>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.8e-05      0.17      19      70 ..     193     244 ..     182     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                        DUF3767  19 lvsiPCaRdslltGigagavvGglrfvlkknvakaaNWavgafllgsivaye 70 
                                    +v  PC    +l+G +a+a +G+ +++l +n+  a  W    ++ +s+ + e
  gi|121636784|ref|YP_977007.1| 193 VVVLPCGAGKTLVGAAAMAKAGATTLILVTNIVAARQWKRELVARTSLTENE 244
                                    5678**********************************87777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3449.00
//
Query:       gi|121636785|ref|YP_977008.1|  [L=756]
Description: hypothetical protein BCG_0914c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-38  130.7   0.1    7.3e-38  129.6   0.1    1.7  1  Helicase_C_3  Helicase conserved C-terminal domain
     0.0079   16.3   0.0      0.014   15.4   0.0    1.4  1  WYL           WYL domain


Domain annotation for each model (and alignments):
>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.1   8.1e-42   7.3e-38       1     127 []     479     601 ..     479     601 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 8.1e-42
                   Helicase_C_3   1 livqaDltillegdsplaeearaaLaafAelesrpehahtyrltplSlrrAldaGltaeeiiefLerlskypvPqaleyl 80 
                                    ++vqaDlt++++g  pl++e+++ L+++A +es+ + a++yr++++S+r+Ald+G + + + ef+++ sk+pvPq+l+yl
  gi|121636785|ref|YP_977008.1| 479 FLVQADLTVVVPG--PLQRELADDLTTVATVESA-GTAMVYRVSEQSIRHALDVGKSRDWLQEFFANRSKTPVPQGLTYL 555
                                    58***********..*******************.**********************************99********* PP

                   Helicase_C_3  81 irdvarryGklrlgleaslvlrsddpalleelladkkiaklllrria 127
                                    i+dvarr+G+lr+g  a++++r++dp+ll++++a+++++ l+lr++a
  gi|121636785|ref|YP_977008.1| 556 IDDVARRHGQLRIG-MAASFVRCEDPTLLAQVVAAPEADGLALRALA 601
                                    **************.****************************9875 PP

>> WYL  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-06     0.014       3      68 ..     690     751 ..     688     756 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                            WYL   3 letlaeAieerrrvefrYrspagegeertvePyglvlkngrwYLvaydekrdeirtfrldRisele 68 
                                    +  l++A +++ ++ ++Y+++ag +++r v P+ l+   g+  Lva+d +++++r f+++Ri+++ 
  gi|121636785|ref|YP_977008.1| 690 MSLLQRAAKDQATLVISYLDAAGVATQRVVAPITLR--GGQ--LVAFDSSSGRLRDFAIHRITSVV 751
                                    5679****************888888******9987..555..9*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 4795.26
//
Query:       gi|121636786|ref|YP_977009.1|  [L=93]
Description: hypothetical protein BCG_0915 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 655.47
//
Query:       gi|121636787|ref|YP_977010.1|  [L=142]
Description: molybdenum cofactor biosynthesis protein MoaC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-54  181.4   2.9    9.1e-54  181.2   2.9    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.2   2.9   5.1e-58   9.1e-54       1     136 []       1     134 [.       1     134 [. 0.99

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 5.1e-58
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvd++ek++tkrtAvA+g++++s+++++li+++ l+kGd+la+ar+agimaaK+ts+liplcH+l+lt v+v++++   +
  gi|121636787|ref|YP_977010.1|   1 MVDITEKATTKRTAVAAGILRTSAQVVALISTGGLPKGDALATARVAGIMAAKRTSDLIPLCHQLALTGVDVDFTVG--Q 78 
                                    9*************************************************************************986..8 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT-EEEEEEEEEEESS CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdkemvieevrlveKsgG 136
                                      +ei+atv+ +++tGvemEALtavsvaalt+yDm+Kavd ++ i+++r+++K+gG
  gi|121636787|ref|YP_977010.1|  79 LDIEITATVRSTDRTGVEMEALTAVSVAALTLYDMIKAVDPGALIDDIRVLHKEGG 134
                                    9******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1029.13
//
Query:       gi|121636788|ref|YP_977011.1|  [L=160]
Description: molybdopterin biosynthesis mog protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-25   87.2   0.2    9.1e-25   87.0   0.2    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.2   5.1e-29   9.1e-25       2     143 ..       8     147 ..       7     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 5.1e-29
                                    EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHHHHHH CS
                  MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpealak 80 
                                    +++v+++ ++g ++D  gp++a +l+++g++  + +vv+D  + + eal++a+++  dviit+GGtG++p D tpe + +
  gi|121636788|ref|YP_977011.1|   8 IVVVSSRAAAGVYTDDCGPIIAGWLEQHGFSSVQPQVVADG-NPVGEALHDAVNAGvDVIITSGGTGISPTDTTPEHTVA 86 
                                    89*************************************98.789999988877767*********************** PP

                                    HHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  81 lfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillpale 143
                                    +++  ++g++ a+rr +l        +p+ +lsr+v    g+t ii+LPGsp++v+++l ++  ++l+
  gi|121636788|ref|YP_977011.1|  87 VLDYVIPGLADAIRRSGLP------KVPTSVLSRGVcgvaGRTlIINLPGSPGGVRDGLGVLA-DVLD 147
                                    *****************99......688889999999999778799************99987.7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1268.37
//
Query:       gi|121636789|ref|YP_977012.1|  [L=141]
Description: molybdenum cofactor biosynthesis protein e2 moaE2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-30  105.8   1.6    1.7e-30  105.6   1.6    1.0  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   1.6   9.4e-35   1.7e-30       1     113 []       9     121 ..       9     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 9.4e-35
                                    EESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCC.TTSEEEEEEE-EE CS
                           MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerw.elervavvHrlGe 79 
                                    lt++p+ +ae+e+lv++++aGA+v FvG++Rd+  g+ v +Ley+a+ p+a ++l+++++e++e+  ++++va+ Hr+G 
  gi|121636789|ref|YP_977012.1|   9 LTDQPIFLAEHEELVSHRSAGAIVGFVGMIRDRDGGRGVLRLEYSAH-PSAAQVLADLVAEVAEESsGVRAVAASHRIGV 87 
                                    6899***************************9988************.99*********999988868************ PP

                                    EETTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                           MoaE  80 levgeasvvvavssahRkeafeaceylidelKkr 113
                                    l+vgea++v+av+++hR++af  c++l++++K+r
  gi|121636789|ref|YP_977012.1|  88 LQVGEAALVAAVAADHRRAAFGTCAHLVETIKAR 121
                                    ********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1064.55
//
Query:       gi|121636790|ref|YP_977013.1|  [L=407]
Description: resuscitation-promoting factor rpfA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-35  120.9   7.2    5.8e-35  119.8   7.2    1.6  1  Transglycosylas  Transglycosylase-like domain


Domain annotation for each model (and alignments):
>> Transglycosylas  Transglycosylase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   7.2   3.2e-39   5.8e-35       1      77 []      38     114 ..      38     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 3.2e-39
                                    .XTHHHHHHHHHHHHSS-TT-TTSSSEBTTTTBEHHHHHHTTCCST.SCGGGS-HHHHHHHHHHHHHHHCGGGSTTC CS
                Transglycosylas   1 aadesnwdaiAqcEsggnwaintgnGyyGglqfsqstWeavggekyapsaaqAsreqQiavAekvlatqGagaWptc 77 
                                    aa++ +wd++A+cEsggnw+intgnGy Gglqf+qstW+a+gg ++apsa+ AsreqQiav e+vlatqG gaWp+c
  gi|121636790|ref|YP_977013.1|  38 AATDGEWDQVARCESGGNWSINTGNGYLGGLQFTQSTWAAHGGGEFAPSAQLASREQQIAVGERVLATQGRGAWPVC 114
                                    578899**********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2932.02
//
Query:       gi|121636791|ref|YP_977014.1|  [L=92]
Description: molybdenum cofactor biosynthesis protein D 2 moaD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   51.2   0.0    1.7e-13   51.0   0.0    1.1  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   9.6e-18   1.7e-13       1      77 []      15      92 .]      15      92 .] 0.98

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.6e-18
                                   EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG.TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela.lerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   v++fa +r +ag  +e++ l +g+tvael++ L+ r+ +la    r+  +++g +v++  +  +l++gD++++lpp+aGG
  gi|121636791|ref|YP_977014.1| 15 VRYFAAARAAAGagSEKVTLRSGATVAELIDGLSVRDVRLAtVLSRCSYLRDGIVVRD--DAVALSAGDTIDVLPPFAGG 92
                                   89****************************************88**************..999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 717.14
//
Query:       gi|121636792|ref|YP_977015.1|  [L=360]
Description: molybdenum cofactor biosynthesis protein A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-36  124.3   0.0    3.9e-36  123.8   0.0    1.2  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    4.7e-26   92.1   0.0    6.9e-26   91.6   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    4.6e-05   23.7   0.0    6.8e-05   23.2   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
    9.3e-05   22.5   0.0    0.00017   21.7   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   8.7e-40   3.9e-36       1     127 [.     211     342 ..     211     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 8.7e-40
                                    -EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SS.T-SSEEEEE....TTT--EEEEE-TTTS--GGG- CS
                    Mob_synth_C   1 ielrfIElmpvgegeewrekkvvsadeilerieerlalleakket.kgpakryki....kdgkgeiglIapvsepFCasC 75 
                                    ++lr+IE+mp++ g++wr++  +sad++l+ ++ +++l+++++++ ++pa+ + +    +  +g++g+Ia+vs++FC++C
  gi|121636792|ref|YP_977015.1| 211 YQLRVIEQMPLDAGHSWRRNIALSADDVLAALRPHFRLRPDPAPRgSAPAELWLVdagpNTPRGRFGVIASVSHAFCSTC 290
                                    58****************************************7777*********88844455***************** PP

                                    -EEEE-TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT----HH CS
                    Mob_synth_C  76 nRlRltadGklktCLfaeeeidlrdllregaseeeLkelikealarkkekhk 127
                                    +R+RltadG++++CLf++ee+dlr+llr ga+++++++++++a+++k+++h 
  gi|121636792|ref|YP_977015.1| 291 DRTRLTADGQIRSCLFSTEETDLRRLLRGGADDDAIEAAWRAAMWSKPAGHG 342
                                    ************************************************9995 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   1.5e-29   6.9e-26       2     166 ..      44     205 ..      43     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.5e-29
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                    + t  CnlrCs+C   +  r+ + ++ l ++e+++++ ++  + gv  v ++ggepll  ++ e +++ a+l+ p  +i+
  gi|121636792|ref|YP_977015.1|  44 SLTDRCNLRCSYCMPERGLRWLPGEQLLRPDELARLIHIAVTRLGVTSVRFTGGEPLLAHHLDEVVAATARLR-PRPEIS 122
                                    6799************************************9*********************99999999997.****** PP

                                    EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeele 161
                                    ++tng+ +  + + +l+e+g+drv+++l+++d   +  ++ r++ + +vl++l ++++ag+ +v+++ v+ p   +e+++
  gi|121636792|ref|YP_977015.1| 123 LTTNGVGL-ARRAGALAEAGLDRVNVSLDSIDRAHFAAIT-RRDRLAHVLAGLAAAKAAGLTPVKVNAVLDPTTGREDVV 200
                                    ********.*************************999999.88************************************* PP

                                    HHHHH CS
                                    xxxxx RF
                    Radical_SAM 162 ellel 166
                                    +ll++
  gi|121636792|ref|YP_977015.1| 201 DLLRF 205
                                    ***98 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.5e-08   6.8e-05      12      90 ..      46     123 ..      36     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.5e-08
                        Fer4_12  12 vsgCnlsCkgCfnketwsfksgkef..tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                    + +Cnl+C++C+ +   +   g++   ++el++ i   +    ++ + ++GGEPll   a  l e+v    +  p ++i 
  gi|121636792|ref|YP_977015.1|  46 TDRCNLRCSYCMPERGLRWLPGEQLlrPDELARLIHIAVTRLGVTSVRFTGGEPLL---AHHLDEVVAATARLRPRPEIS 122
                                    679**********9987766666653357777666666667788************...666777776666666654444 PP

                        Fer4_12  90 l 90 
                                    l
  gi|121636792|ref|YP_977015.1| 123 L 123
                                    4 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.8e-08   0.00017       5      90 ..      46     128 ..      43     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.8e-08
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    + +Cnl C  C  +   +   g++  + ++ ++l +   ++     + +tGGePL+ +  +e++    rl+ +    +i 
  gi|121636792|ref|YP_977015.1|  46 TDRCNLRCSYCMPERGLRWLPGEQLLRPDELARLIHIAVTRLGVTSVRFTGGEPLLAHHLDEVVAATARLRPRP---EIS 122
                                    579*********8887777666666665555555588888888999*********8866666666666666555...999 PP

                        Fer4_14  85 letngt 90 
                                    l tng+
  gi|121636792|ref|YP_977015.1| 123 LTTNGV 128
                                    999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2368.79
//
Query:       gi|121636793|ref|YP_977016.1|  [L=129]
Description: hypothetical protein BCG_0922c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-34  118.9  30.1      8e-18   64.9  14.7    2.1  2  YccF          Inner membrane component domain


Domain annotation for each model (and alignments):
>> YccF  Inner membrane component domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9  14.7   4.4e-22     8e-18       1      51 []       4      54 ..       4      54 .. 0.98
   2 !   60.3   7.4   1.2e-20   2.1e-16       1      51 []      68     118 ..      68     118 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 4.4e-22
                           YccF  1 lgNilWlllfGwwlaliyllaglllfitiigipygrvlfklakyllwPFGk 51
                                   ++N++Wl+++G+wlal+ylla+l++f++ii+ip+g + +++a y+lwPFG+
  gi|121636793|ref|YP_977016.1|  4 ILNVIWLVFGGLWLALGYLLASLVCFLLIITIPFGFAALRIASYALWPFGR 54
                                   69************************************************6 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 1.2e-20
                           YccF   1 lgNilWlllfGwwlaliyllaglllfitiigipygrvlfklakyllwPFGk 51 
                                    +gN++W+llfG+wlal++l++++++++tiigip +++ +kl+ ++l+P Gk
  gi|121636793|ref|YP_977016.1|  68 IGNVIWVLLFGIWLALGHLVSAAAMAVTIIGIPLALANLKLIPVSLVPLGK 118
                                    79************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 835.40
//
Query:       gi|121636794|ref|YP_977017.1|  [L=135]
Description: cold shock-like protein B cspB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-15   56.0   0.0    3.6e-15   55.6   0.0    1.2  1  CSD       'Cold-shock' DNA-binding domain
     0.0018   17.9   0.0     0.0032   17.1   0.0    1.4  1  OB_RNB    Ribonuclease B OB domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0     4e-19   3.6e-15       2      63 ..       3      62 ..       2      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4e-19
                                   EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEE CS
                            CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanV 63
                                   tG+Vkw++ +kgfGF ++e g+ dv+v  sa+ +   + L++gq+VeF + +g +gp+A ++
  gi|121636794|ref|YP_977017.1|  3 TGKVKWYDPDKGFGFLSQEGGE-DVYVRSSALPTGV-EALKAGQRVEFGIASGRRGPQALSL 62
                                   8*****************9999.*********9887.**********************876 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.5e-07    0.0032       7      28 ..      12      32 ..       4      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-07
                                   SSS-EEEEECT.TEEEEE-HHH CS
                         OB_RNB  7 kkGFGFlipdegkeDifippeq 28
                                   +kGFGFl++++ +eD++++++ 
  gi|121636794|ref|YP_977017.1| 12 DKGFGFLSQEG-GEDVYVRSSA 32
                                   59********5.******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 992.99
//
Query:       gi|121636795|ref|YP_977018.1|  [L=609]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-35  120.0  19.5      7e-35  119.2  19.5    1.4  1  PE              PE family
  ------ inclusion threshold ------
      0.093   13.2  11.4       0.17   12.4  11.4    1.4  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2  19.5   7.8e-39     7e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 7.8e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+v ++Pe++aaaa++la+igs+lsaanaaa aptt+vlaa+aDeVSaa+A+lfs haq+yq+l++qaaafhe+f+qal++
  gi|121636795|ref|YP_977018.1|  1 MSYVLATPEMVAAAANNLAQIGSTLSAANAAALAPTTGVLAAGADEVSAAVASLFSGHAQAYQTLGTQAAAFHERFIQALST 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aag+Y +aEaa
  gi|121636795|ref|YP_977018.1| 83 AAGAYGSAEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  11.4   1.9e-05      0.17       8      99 ..       7      99 ..       2     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYe 88
                                   +p+ + ++a  + ++ +++++a+aaa a+++  ++     ++aa+++ ++   +a ++ g++ aa ++ + + L +AA+aY 
  gi|121636795|ref|YP_977018.1|  7 TPEMVAAAANNLAQIGSTLSAANAAAlAPTTGVLAAGADEVSAAVASLFSGHAQAYQTLGTQAAAFHERFIQALSTAAGAYG 88
                                   7999**********************444444445555579***************************************** PP

                  T7SS_ESX_EspC 89 atDeeaagald 99
                                    ++ ++a+ l+
  gi|121636795|ref|YP_977018.1| 89 SAEAANASPLQ 99
                                   *******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.95u 0.32s 00:00:01.27 Elapsed: 00:00:00.50
# Mc/sec: 3699.95
//
Query:       gi|121636796|ref|YP_977019.1|  [L=650]
Description: acyl-CoA dehydrogenase fadE10 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-32  111.2   2.7    9.3e-32  110.3   2.7    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.5e-21   74.2   0.0    1.6e-20   73.1   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.8e-20   72.3   0.1    6.6e-19   68.6   0.0    2.6  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    0.00012   22.4   1.5    0.00012   22.4   1.5    2.4  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
     0.0027   17.3   0.1     0.0046   16.6   0.1    1.3  1  DUF1974        Domain of unknown function (DUF1974)
     0.0037   17.0   0.0      0.008   15.9   0.0    1.5  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   2.7   3.1e-35   9.3e-32       1     148 [.     277     435 ..     277     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 3.1e-35
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G+++a++tln +Rl++ a a g+a++al  a+e++ +r + gkp+++h++v+ k+  +aa   a+ + v+   +++d+
  gi|121636796|ref|YP_977019.1| 277 GDGLKIALTTLNAGRLSLPAIATGVAKQALKIAREWSVERVQWGKPVGQHEAVASKISFIAATNYALDAVVELSSQMADE 356
                                    79****************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT..........SGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGy..........leeypverlyrdarvlrigeGtseiqrniiarr 148
                                    g++d r ea++aKl+ se+a+ v d+ +q+ Gg+Gy          ++  pve+++rd r++ri+eG+sei+r++iar 
  gi|121636796|ref|YP_977019.1| 357 GRNDiRIEAALAKLWSSEMACLVGDELLQIRGGRGYetaeslaargERAVPVEQMVRDLRINRIFEGSSEIMRLLIARE 435
                                    **************************************9999977667777**************************97 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   5.4e-24   1.6e-20       1      96 [.     167     264 ..     167     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 5.4e-24
                                    EEE---SS-SS-GGG---EEEEETT.E.EEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE--- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdgge.yvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrri 78 
                                    af lTEp++Gsd a++++ta++ d+g+ y l+G K w tn+  a+l++v+ar  + + +++g+s f+v++d+pg++v+r 
  gi|121636796|ref|YP_977019.1| 167 AFLLTEPDVGSDPARMASTATPIDDGQaYELEGVKLWTTNGVVADLLVVMARVPRSEgHRGGISAFVVEADSPGITVERR 246
                                    799*****************66665545************************44444579*****************999 PP

                                    --BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  79 eeklGlrglptgelvfed 96 
                                     + +Glrg+++g  ++++
  gi|121636796|ref|YP_977019.1| 247 NKFMGLRGIENGVTRLHR 264
                                    9*********99888765 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   2.2e-22   6.6e-19       5     112 ..      58     163 ..      54     164 .. 0.92
   2 ?    0.3   0.0      0.37   1.1e+03     101     113 .]     467     479 ..     423     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.2e-22
                                    HHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHH CS
                  Acyl-CoA_dh_N   5 ealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgv 84 
                                    ea+  ++ref+++        +++++++p+e +k laelG +g+ +p eygG++++ +++  v+  ++ + ++l++ll++
  gi|121636796|ref|YP_977019.1|  58 EAFLVKLREFLDTVD---GSVIERAAQIPDEYVKGLAELGCFGLKIPSEYGGLNMSQVAYNRVLMMVTTVHSSLGALLSA 134
                                    677788889988854...566777789***************************************************** PP

                                    HHHTTH.HHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  85 hsslva.pailrfGteeqkrryLpklasg 112
                                    h+s+++ +++   Gt+eqkrr+Lp++a+g
  gi|121636796|ref|YP_977019.1| 135 HQSIGVpEPLKLAGTAEQKRRFLPRCAAG 163
                                    *****988*******************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N 101 qkrryLpklasge 113
                                      +++Lpkl+ ge
  gi|121636796|ref|YP_977019.1| 467 FYAKWLPKLVFGE 479
                                    5579999999987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.5   3.9e-08   0.00012       4     114 ..     295     396 ..     292     426 .. 0.80
   2 ?   -2.1   0.1       1.4   4.3e+03      81      89 ..     452     460 ..     429     478 .. 0.49

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.9e-08
                                    HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                  Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                     a+a+G+A+ al+ + e+  erv+   g+++ +++a+  ++  +aa   A+ a++e   +     a++g++   + r ea
  gi|121636796|ref|YP_977019.1| 295 PAIATGVAKQALKIAREWSVERVQ--WGKPVGQHEAVASKISFIAATNYALDAVVELSSQM----ADEGRN---DIRIEA 365
                                    689*********************..77777777777777777777777766666655555....444444...56**** PP

                                    HHHHHHHHHHHHHHHHHHHHHCGGGGGBTT- CS
                  Acyl-CoA_dh_2  84 rraaalavelaiaavdalfeaaGgsalrkes 114
                                    ++a+++ +e+a  + d+l ++ Gg+++ +++
  gi|121636796|ref|YP_977019.1| 366 ALAKLWSSEMACLVGDELLQIRGGRGYETAE 396
                                    **************************98765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                    HHHHHHHHH CS
                  Acyl-CoA_dh_2  81 aearraaal 89 
                                    a+ r +aa+
  gi|121636796|ref|YP_977019.1| 452 ADLRQKAAA 460
                                    223333333 PP

>> DUF1974  Domain of unknown function (DUF1974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.5e-06    0.0046      62     156 ..     491     590 ..     476     601 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                        DUF1974  62 etkryyrqlnrlSaafAllaDlallvLGGeLKrkerlsaRlgDvlSqLYlasavLkrfede.....grqeedlplvhwal 136
                                    +++++ r ++r S ++A  +   ++   ++L +k+ + +R+ D+ ++L+ +sa+  r e++      + e+   l++  +
  gi|121636796|ref|YP_977019.1| 491 ALATHLRFVERSSRKLARNTFYGMARWQASLEKKQGFLGRIVDIGAELFAISAACVRAEAQrtadpVEGEQAYELAEAFC 570
                                    67889999*********************************************99999888443333456788899999* PP

                        DUF1974 137 qdalaqaeealdellaNfpn 156
                                    q+a  ++e  +d+l +N ++
  gi|121636796|ref|YP_977019.1| 571 QQATLRVEALFDALWSNTDS 590
                                    *********99999999765 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06     0.008     182     236 ..     198     251 ..     197     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                    EEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE------ CS
                         HpaB_N 182 rGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfed 236
                                    +G+k+ +T++++ad ++v+    +++e+ +    af+v++d+pG+++  r++f  
  gi|121636796|ref|YP_977019.1| 198 EGVKLWTTNGVVADLLVVMARV-PRSEGHRGGISAFVVEADSPGITVERRNKFMG 251
                                    69*****************995.5599*******************988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4678.72
//
Query:       gi|121636797|ref|YP_977020.1|  [L=386]
Description: hypothetical protein BCG_0926c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-25   87.3   1.0    1.3e-24   86.7   0.2    1.7  2  FIST_C           FIST C domain
    7.1e-24   84.7   0.2    5.4e-22   78.6   0.0    2.2  2  FIST             FIST N domain
  ------ inclusion threshold ------
      0.096   12.9   0.1       0.26   11.5   0.1    1.7  1  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.52   3.1e+03      71     121 ..      18      66 ..       9      71 .. 0.47
   2 !   86.7   0.2   2.1e-28   1.3e-24       2     130 .]     222     364 ..     221     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.52
                         FIST_C  71 iedlerlleeaakeg.allfsCigRglglgedadeelqavrealgdgvplaG 121
                                    +e++ ++  e a+e+  l +   +R  ++ ++a+++l+av + + +   l+G
  gi|121636797|ref|YP_977020.1|  18 VEAAGQARDELAGEApSLAVLLGSR--AHTDRAADVLSAVLQMIDP-PALVG 66 
                                    3333333322222222444444455..3356666666666666443.45555 PP

  == domain 2  score: 86.7 bits;  conditional E-value: 2.1e-28
                         FIST_C   2 levylell...geedeelaqsalfplgleel.......ggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaeali 71 
                                    l+ ++e++   + +++ l+++ l  +g++++       +gdf++r llg+dp +gs+ + + v++G ++q+++rda+ + 
  gi|121636797|ref|YP_977020.1| 222 LQRLREIVeglSPDERALVSHGL-QIGIVVDehlaapgQGDFVIRGLLGADPSTGSIEIDEVVQVGATMQFQVRDAAGAD 300
                                    788999999999999********.99999889************************************************ PP

                         FIST_C  72 edlerlleeaak......egallfsCigRglgl.gedadeelqavrealgdgvplaGfftyGEigp 130
                                    +dl+  +e+aa+      +gallf C gRg  + g    +++++++e lg+ +plaGff+ GEigp
  gi|121636797|ref|YP_977020.1| 301 KDLRLTVERAAArlpgraAGALLFTCNGRGRRMfGVAD-HDASTIEELLGG-IPLAGFFAAGEIGP 364
                                    *7777766664444445458*********999975555.559******986.************97 PP

>> FIST  FIST N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0     9e-26   5.4e-22       2     172 .]      35     219 ..      34     219 .. 0.78
   2 !    4.2   0.0    0.0067        40      19      44 ..     342     368 ..     321     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 9e-26
                           FIST   2 lvlvfas.aeasdleallealrealpgapliGcstageiasegleledgvvalalasa...............daageel 65 
                                    l++++ s a+ + ++++l+a+ +      l+Gc++ +++a + +e+ed+ +a+++++a                      
  gi|121636797|ref|YP_977020.1|  35 LAVLLGSrAHTDRAADVLSAVLQMIDPPALVGCIAQAIVA-GRHEIEDE-PAVVVWLAsglaaetfqldfvrtG------ 106
                                    66777888999999***********99************8.57889999.677776663343444444443331...... PP

                           FIST  66 akal.............pkllllladglssneeellegldealaspdvpivGGlagdgtlafktyvlfnggvledgvvvv 132
                                                      +l lll+d++++  + l+e+ ++ l  p++ +vGG+ ++g ++++t  + ++ vl++gvv+v
  gi|121636797|ref|YP_977020.1| 107 ---SgalitgyrfdrtaRDLHLLLPDPYTFPSNLLIEHPNTDL--PGTAVVGGVVSGGRRRGDTRLFRDHDVLTSGVVGV 181
                                    ...0333444444444455699999***************444..69******988886677688888999********* PP

                           FIST 133 llsgeslevgtavsqgyrpigkpfvVTkaegnvileLdgk 172
                                     l+g+      +vsqg+rpig+p++VT a+g  i eL g+
  gi|121636797|ref|YP_977020.1| 182 RLPGMR--GVPVVSQGCRPIGYPYIVTGADGILITELGGR 219
                                    ****96..447789***************9877****986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0067
                           FIST  19 ealrealpgapliGcstageiase.gl 44 
                                    ++++e l+g+pl+G  +agei++  g 
  gi|121636797|ref|YP_977020.1| 342 STIEELLGGIPLAGFFAAGEIGPIaGR 368
                                    4689999**************552233 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.4e-05      0.26      35      90 ..      16      79 ..       6      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHHHHHHHHHHHHHH........T-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHT--H CS
                PEP-utilisers_N 35 rleeAlekvreelealaeka........lgeeeaaifeahlmlleDpelleeveerIregglna 90
                                      eA  ++r+el+  a ++          +++a++++a l++++ p+l++ + ++I +g++  
  gi|121636797|ref|YP_977020.1| 16 AAVEAAGQARDELAGEAPSLavllgsraHTDRAADVLSAVLQMIDPPALVGCIAQAIVAGRHEI 79
                                   33455556666665533333566454422223488**********************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2745.35
//
Query:       gi|121636798|ref|YP_977021.1|  [L=162]
Description: hypothetical protein BCG_0927c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-51  172.5   0.1    6.7e-51  172.3   0.1    1.0  1  DUF2771     Protein of unknown function (DUF2771)


Domain annotation for each model (and alignments):
>> DUF2771  Protein of unknown function (DUF2771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.3   0.1   3.7e-55   6.7e-51       3     152 ..       7     159 ..       5     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 3.7e-55
                        DUF2771   3 alvavvvvvvaavvavqvwalareeaepedpeitayshgeetevaPysyCelgk.ddCee.gepaelevepdeevqlslP 80 
                                    +l +++v+++++++++  w l+r  + p++pei+ayshg+ t+v+Py yC++++ ddC++ ++++el v+++++vqls+P
  gi|121636798|ref|YP_977021.1|   7 TLPVILVILLSVAAGAGAWLLVRG-HGPQQPEISAYSHGHLTRVGPYLYCNVVDlDDCQTpQAQGELPVSERYPVQLSVP 85 
                                    456777888889999999*****9.***************************999************************* PP

                        DUF2771  81 keiadapWsllkiYedpaaneeslhkpnerravtiptedeerlrLvvveiqllllvvDeegee..vphatWsis 152
                                    + i++apW+ll++Y+dpa+++++l++p++r avtipt+d++r+rL+++++qll+lvvD++ge   vpha+Ws++
  gi|121636798|ref|YP_977021.1|  86 EVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTIPTVDPQRGRLTGIVVQLLTLVVDHSGELrdVPHAEWSVR 159
                                    **************************************************************999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1086.30
//
Query:       gi|121636799|ref|YP_977022.1|  [L=548]
Description: hypothetical protein BCG_0928c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-11   42.9  31.1    4.6e-11   42.2  31.1    1.3  1  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2  31.1   2.6e-15   4.6e-11      13     352 ..     122     484 ..     108     485 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.6e-15
                          MFS_1  13 silgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrf..Grrrvlllglllfalglllllf....a... 82 
                                    +++ +++   + a + g s+s + l l +  + +av ++++G+  dr+  Grr  l l++ l  + +++l++    a   
  gi|121636799|ref|YP_977022.1| 122 AMAVALANTlFFAAASGESKSRVALYLLITIAPFAVIAPLIGPALDRLqhGRRVALALSFGLRTALAVVLIMnydgAtgs 201
                                    2322222223667777889999999999999999*************666****99999999888856666544653445 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGa.ilgpllgg...lla.sslgWravfyi 156
                                     ++w+l+ + + + +++ ++  +  a++ ++ p+  +  r+++ l+++  lG  i g ++++   +++ +++  +++ ++
  gi|121636799|ref|YP_977022.1| 202 FPSWVLYPCALAMMVFSKSFSVLRSAVTPRVMPPtIDLVRVNSRLTVFGLLGGtIAGGAIAAgveFVCtHLFQLPGALFV 281
                                    55888999**************************6699*********999999455555555577555355555555444 PP

                          MFS_1 157 laivsllafvlfllll.........peepperkrkspkeee.............kgtgpaplvp...awkallkdpvlwi 211
                                    + ++++ ++ l                            e               ++ p ++++    +++ l ++    
  gi|121636799|ref|YP_977022.1| 282 VVAITIAGASL--SMRiprwvevtsG-------------EVpatlsyhrdrgrlRRRWPEEVKNlggTLRQPLGRN---- 342
                                    44444444332..1113332232221.............2122333545545543333444444444555555555.... PP

                          MFS_1 212 llialllfffgfsg..lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaal 289
                                    ++++l +++++  +  +l+l p ++ + +  +g++++g +l+l+++++a++ + + + s rl+  r+ +l + +++l+++
  gi|121636799|ref|YP_977022.1| 343 IITSLWGNCTIKVMvgFLFLYPAFVAKAHEANGWVQLG-MLGLIGAAAAVGNFAGNFTSARLQLGRPAVLVVRCTVLVTV 421
                                    66666666544333449999999989999999*99999.89999999999998888999**7776677777766666666 PP

                          MFS_1 290 glallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    + + +av+ s ++++++ ++    ++++ +sl a +++ +p+e +++ +g   ++ +l+++lg
  gi|121636799|ref|YP_977022.1| 422 LAIAAAVAGSLAATAIATLITAGSSAIAKASLDASLQHDLPEESRASGFGRSESTLQLAWVLG 484
                                    6666666655555555555555599999*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3999.03
//
Query:       gi|121636800|ref|YP_977023.1|  [L=262]
Description: hypothetical protein BCG_0929 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-80  270.4   0.3    1.2e-80  270.1   0.3    1.1  1  DUF3027   Protein of unknown function (DUF3027)


Domain annotation for each model (and alignments):
>> DUF3027  Protein of unknown function (DUF3027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.1   0.3   6.9e-85   1.2e-80       1     192 [.      45     234 ..      45     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.1 bits;  conditional E-value: 6.9e-85
                        DUF3027   1 GehlgveaegervvthrfeaklpgYrGWewavtlarasrakkvtvsevvLlpgedallapewvPwkeRlrpgDlgpgdll 80 
                                    G++lgv+ e+ +++thrf a+lpgY+GW+wav++a+ s+a+++t+sevvL+pg+ allap+wvPw++R+rpgDl+pgdll
  gi|121636800|ref|YP_977023.1|  45 GDYLGVSYEDGNAATHRFIAHLPGYQGWQWAVVVASYSGADHATISEVVLVPGPTALLAPDWVPWEQRVRPGDLSPGDLL 124
                                    89****************************************************************************** PP

                        DUF3027  81 pteedDerlepgyeasedeeeeeevaeelglgrkrvlsregreeaaeRWyegeagpkselakaakaaCstCgflvplags 160
                                    ++++dD+rl+pgy+as+d++ ++e+a+e+glgr+ v+s+ gr+++a+RW++g++gp s++a+++k+ C+ Cgf++plags
  gi|121636800|ref|YP_977023.1| 125 APAKDDPRLVPGYTASGDAQ-VDETAAEIGLGRRWVMSAWGRAQSAQRWHDGDYGPGSAMARSTKRVCRDCGFFLPLAGS 203
                                    ***************99999.7999******************************************************* PP

                        DUF3027 161 lgqafGvCaNelspaDgrvvsldygCGaHsev 192
                                    lg++fGvC+Nels aDg+vv+ +ygCGaHs++
  gi|121636800|ref|YP_977023.1| 204 LGAMFGVCGNELS-ADGHVVDRQYGCGAHSDT 234
                                    *************.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1589.48
//
Query:       gi|121636801|ref|YP_977024.1|  [L=442]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-57  192.2  28.4    8.5e-57  191.7  28.4    1.2  1  PPE             PPE family
    4.4e-28   96.9 146.7      2e-08   34.0  22.0    6.2  6  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7  28.4   9.4e-61   8.5e-57       1     157 [.       5     164 ..       5     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 9.4e-61
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT....TTS-SHHHHHHHHHTHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaela...aeaWqGpssaamaaaaapylaWLsaaaa 77 
                                    +lpPEvnsa++yaG+g++p+laAa aWdgLaael +aaa+++ ++++l+   ++aWqGp++aamaaaaapyl+WL+aa+a
  gi|121636801|ref|YP_977024.1|   5 VLPPEVNSARIYAGAGPAPMLAAAVAWDGLAAELGMAAASFSLLISGLTagpGSAWQGPAAAAMAAAAAPYLSWLNAATA 84 
                                    59**********************************************9555679************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  78 qaeeaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +ae aAa a+aaaa+YeaA+aa+ +pa++aanr++l +lv +n+fGqn paIaatea+ye++waqd+aam +Y+  ++++
  gi|121636801|ref|YP_977024.1|  85 RAEGAAAGAKAAAAVYEAARAATAHPALVAANRNQLLSLVLSNLFGQNLPAIAATEASYEQLWAQDVAAMVGYHGGASTV 164
                                    ***************************************************************************99886 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  31.8   1.4e-08   0.00013       2      40 .]     205     244 ..     200     244 .. 0.95
   2 !   29.7  36.3   4.8e-11   4.3e-07       1      40 []     235     274 ..     235     274 .. 0.98
   3 !   27.5  25.7   2.4e-10   2.2e-06       1      37 [.     265     301 ..     265     301 .. 0.95
   4 !   34.0  22.0   2.2e-12     2e-08       1      37 [.     290     326 ..     290     327 .. 0.97
   5 !   26.2  27.4   5.9e-10   5.3e-06       1      39 [.     333     371 ..     333     372 .. 0.97
   6 !    5.7   1.9    0.0015        13      14      30 ..     366     382 ..     366     385 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-08
                 Pentapeptide_2   2 NtGslNs.GsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+ G gN+G+ N+GsgNtG++N+G gN+G+ n+G+
  gi|121636801|ref|YP_977024.1| 205 NIGVGNFlGIGNIGNNNVGSGNTGDYNFGIGNIGNANLGN 244
                                    9*****55******************************96 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 4.8e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+G+gN+G++NlGsgN G+fN+G+gN G++n+Gs
  gi|121636801|ref|YP_977024.1| 235 GNIGNANLGNGNIGNANLGSGNAGFFNFGNGNDGNTNFGS 274
                                    8**************************************6 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 2.4e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    gN G++N+GsgN Gf+N+GsgN Gs+NlG+gN G+ n
  gi|121636801|ref|YP_977024.1| 265 GNDGNTNFGSGNAGFLNIGSGNEGSGNLGFGNAGDDN 301
                                    89********************************876 PP

  == domain 4  score: 34.0 bits;  conditional E-value: 2.2e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    gN G++N+G  NtG++N+G +NtG fN+G+ NtG+g 
  gi|121636801|ref|YP_977024.1| 290 GNLGFGNAGDDNTGWGNSGDTNTGGFNSGDLNTGIGS 326
                                    8*********************************986 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 5.9e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+G++N+G+g++GffN+G+   G++NlG+g +G+gn++
  gi|121636801|ref|YP_977024.1| 333 ANSGFGNTGTGHSGFFNSGNSGSGFQNLGNGSSGFGNAS 371
                                    6************************************86 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.0015
                 Pentapeptide_2  14 GffNlGsgNtGsfNlGs 30 
                                    Gf+N   ++ G++N+G+
  gi|121636801|ref|YP_977024.1| 366 GFGNASDTSSGFQNAGT 382
                                    56666666666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3044.12
//
Query:       gi|121636802|ref|YP_977025.1|  [L=91]
Description: hypothetical protein BCG_0931c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-29  102.6  10.7    1.1e-29  102.4  10.7    1.0  1  DUF2530   Protein of unknown function (DUF2530)
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.016   15.4   0.1    1.7  2  DUF3493   Low psii accumulation1 / Rep27


Domain annotation for each model (and alignments):
>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4  10.7   1.3e-33   1.1e-29       2      77 .]      10      84 ..       9      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.3e-33
                        DUF2530  2 qpPeLprrLtdprpvivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGlaiflwQRrAaRrGsrgAqqGL 77
                                   +pP+Lp++L++++pvi+vg+l+Wlva+v+++vv + l+sw+pv++aGl++GllG++if+wQ +AaRrG+rgAq GL
  gi|121636802|ref|YP_977025.1| 10 EPPPLPPVLLEVWPVIAVGALAWLVAAVAAFVV-PGLASWRPVTVAGLATGLLGTTIFVWQLAAARRGARGAQAGL 84
                                   79*****************************99.*****************************************8 PP

>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3      0.29   2.6e+03      36      36 ..      34      34 ..      23      43 .. 0.46
   2 ?   15.4   0.1   1.7e-06     0.016      25      56 ..      54      85 ..      50      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                        DUF3493 36 i 36
                                   +
  gi|121636802|ref|YP_977025.1| 34 V 34
                                   1 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-06
                        DUF3493 25 afaaSaliGalifllrllaaragaesapelee 56
                                   a  a +l+G+ if+ +l+aar+ga++a+   e
  gi|121636802|ref|YP_977025.1| 54 AGLATGLLGTTIFVWQLAAARRGARGAQAGLE 85
                                   67899********************9965444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 632.74
//
Query:       gi|121636803|ref|YP_977026.1|  [L=143]
Description: MarR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-14   52.4   0.0      1e-13   51.0   0.0    1.8  2  MarR            MarR family
    6.5e-07   29.1   1.0    2.1e-06   27.5   0.1    2.3  2  MarR_2          MarR family
     0.0024   18.4   0.0     0.0052   17.2   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   15.1   0.6      0.073   13.1   0.0    2.2  2  HTH_20          Helix-turn-helix domain
      0.022   14.6   0.0      0.037   13.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.023   14.9   0.0       0.16   12.2   0.0    2.2  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         2   6.1e+03      23      38 ..       8      23 ..       7      24 .. 0.72
   2 !   51.0   0.0   3.4e-17     1e-13       2      59 .]      33      90 ..      32      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                                   HHHHHTS-HHHHHHHH CS
                           MarR 23 Lakklgvskstvtrvl 38
                                   La+ l++  + ++r+l
  gi|121636803|ref|YP_977026.1|  8 LASDLSLAVMRLSRQL 23
                                   6777788878788776 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 3.4e-17
                                   -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                           MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                   +l+q+++L++l+++g+++   La +  v ++++trv+  L + G+++R ++p D R+v
  gi|121636803|ref|YP_977026.1| 33 SLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQV 90
                                   799*****************************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   7.1e-10   2.1e-06       2      62 .]      31      89 ..      30      89 .. 0.96
   2 ?   -1.1   0.1      0.61   1.8e+03      18      31 ..     105     117 ..      90     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.1e-10
                                   T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                         MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                    ++++q+ +L  L++++   +t+g+la r ++ +++++r+++ L + G+v r p p D+R+
  gi|121636803|ref|YP_977026.1| 31 PVSLSQLSALTTLANEGA--MTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQ 89
                                   5789*************9..**************************************995 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.61
                                    TTSEEEHHHHHHHH CS
                         MarR_2  18 pgrdltvgelarrl 31 
                                     + + ++  la+rl
  gi|121636803|ref|YP_977026.1| 105 AR-RARQEWLAERL 117
                                    32.46888888887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0052      35      68 .]      65      98 ..      36      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                         HTH_27 35 isyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   +  ++  L  +G+v r + + d+r+++v+++++G
  gi|121636803|ref|YP_977026.1| 65 MTRVIASLADMGFVDRAPHPIDGRQVLVSVSESG 98
                                   6789****************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.4e-05     0.073       9      57 ..      30      81 ..      28      84 .. 0.88
   2 ?   -0.7   0.1      0.51   1.5e+03       6      17 ..     118     129 ..      99     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                   -HHHHHHHHHH...STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  9 hPvRrrilraL...araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   +Pv +  l+aL   a ++++t+++la r ++++ ++ + ++ L++ g+v++ 
  gi|121636803|ref|YP_977026.1| 30 SPVSLSQLSALttlANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRA 81
                                   56666667778888***********************************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
                                    HHS-HHHHHHHH CS
                         HTH_20   6 ALahPvRrrilr 17 
                                    A+++++ r+ilr
  gi|121636803|ref|YP_977026.1| 118 ATLNRSERDILR 129
                                    455555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.037      11      56 ..      37      82 ..      33      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                   CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                    ++ ++L ++g +t   +a +  v  ++  +v+ sL d+G+V+r +
  gi|121636803|ref|YP_977026.1| 37 LSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAP 82
                                   578899************************************9976 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.36   1.1e+03      25      47 ..      16      38 ..      10      41 .. 0.82
   2 ?   12.2   0.0   5.2e-05      0.16      21      56 ..      47      82 ..      37      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.36
                                   HHHHHHHHTS-HHHHHHHHHHHH CS
                 Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLe 47
                                   +++l++ L  + +s   +l+ L+
  gi|121636803|ref|YP_977026.1| 16 VMRLSRQLRFRNPSSPVSLSQLS 38
                                   68999999999999877777775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.2e-05
                                   SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                   +  ++  la r  v+p+s +  +  L+++G+v+ ++
  gi|121636803|ref|YP_977026.1| 47 GAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAP 82
                                   5567778888889*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1030.58
//
Query:       gi|121636804|ref|YP_977027.1|  [L=288]
Description: rRNA methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-30  103.7   0.0    1.2e-29  103.3   0.0    1.1  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.038   14.3   0.0    1.3  1  PHP             PHP domain


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   1.4e-33   1.2e-29       3     142 .]     132     275 ..     130     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.4e-33
                                    EEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEES CS
                 SpoU_methylase   3 ivvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvats 82 
                                    + vl++++d++NlG+i+R a+ + ++++v+ ++ +ad+l ++a+r+++g++ ++++++++++   l  lke+gf+l+a++
  gi|121636804|ref|YP_977027.1| 132 VAVLEGVNDHENLGSIFRNAAGLSVDAVVF-GTGCADPLYRRAVRVSMGHALLVPYARAADWPTELMTLKESGFRLLAMT 210
                                    679**********************99999.66*********************************************** PP

                                    TT-SEGC.....CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  83 lkgksls.....eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                    ++g+ ++      +  +e++al++G E+ Gl+  +l+  d  v+Ipms  ++SLNva+A+a+++y
  gi|121636804|ref|YP_977027.1| 211 PHGNACKlpeaiAAVSHERIALLVGAEGPGLTAAALRISDVRVRIPMSRGTDSLNVATAAALAFY 275
                                    *8887776643333666*********************************************987 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.3e-06     0.038      24      65 ..     199     237 ..     195     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-06
                                    HHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  24 akelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGle 65 
                                     ke g+  +a+T hgn+ + +e++ a+     ++i +++G+e
  gi|121636804|ref|YP_977027.1| 199 LKESGFRLLAMTPHGNACKLPEAIAAV---SHERIALLVGAE 237
                                    6899***********************...5567*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2065.70
//
Query:       gi|121636805|ref|YP_977028.1|  [L=94]
Description: hypothetical protein BCG_0934 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-30  103.3  24.1      7e-30  103.1  24.1    1.0  1  DUF2537   Protein of unknown function (DUF2537)


Domain annotation for each model (and alignments):
>> DUF2537  Protein of unknown function (DUF2537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1  24.1   3.9e-34     7e-30       2      79 ..      10      87 ..       9      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 3.9e-34
                        DUF2537  2 pWatGltvavfvavvvavavvalslalaevhpllavvvnvvvvaGlaPtvwllrrvpvlRWvvlGvaaGvlvgwiall 79
                                   pWatGl+va fva+v+avavv+lsl+l++vhpllav++n+v+v+GlaPt+w +rr+pvlRW+vlG+a+Gv+ +w+all
  gi|121636805|ref|YP_977028.1| 10 PWATGLAVAGFVAAVIAVAVVVLSLGLIRVHPLLAVGLNIVAVSGLAPTLWGWRRTPVLRWFVLGAAVGVAGAWLALL 87
                                   9***************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 733.61
//
Query:       gi|121636806|ref|YP_977029.1|  [L=253]
Description: hypothetical protein BCG_0935c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-59  201.2   0.9    1.4e-59  200.9   0.9    1.1  1  DUF3071   Protein of unknown function (DUF3071)


Domain annotation for each model (and alignments):
>> DUF3071  Protein of unknown function (DUF3071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.9   0.9   7.7e-64   1.4e-59       1     166 []       1     171 [.       1     171 [. 0.96

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 7.7e-64
                        DUF3071   1 MreLrlvglesdgeslvleae.egeefflavddeLraalreeser....qaeaeeesslrpreIQariRaGasveevaee 75 
                                    MreL++vgl+ dg++++++ +  +e+f l+vdd+Lraalr++s +    q ++e ++ l+p+eIQariRaGasve+va++
  gi|121636806|ref|YP_977029.1|   1 MRELKVVGLDADGKNIICQGAiPSEQFKLPVDDRLRAALRDDSVQpeqaQLDIEVTNVLSPKEIQARIRAGASVEQVAAA 80 
                                    9*******************879******************54444457899999999********************** PP

                        DUF3071  76 agvsververyahPvlaERariaelarkahvvredgpakltLgevlaealaargvdleeveWdAwreeseqWvvtvswka 155
                                    +g +++r++r+ahPvl+ER+r+aela++ah+v +dgpa lt++e++a+al arg ++++++WdAwr+e+++W+v+++wka
  gi|121636806|ref|YP_977029.1|  81 SGSDIARIRRFAHPVLLERSRAAELATAAHPVLADGPAVLTMQETVAAALVARGLNPDSLTWDAWRNEDSRWTVQLAWKA 160
                                    ******************************************************************************** PP

                        DUF3071 156 geseneAewsf 166
                                    g+s+n A+++f
  gi|121636806|ref|YP_977029.1| 161 GRSDNLAHFRF 171
                                    *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1949.95
//
Query:       gi|121636807|ref|YP_977030.1|  [L=376]
Description: phosphoserine aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   59.6   0.0      4e-16   59.0   0.0    1.2  1  Aminotran_5  Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   2.2e-20     4e-16      28     333 ..      41     335 ..      23     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.2e-20
                                    CSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHH.HHHHHHCCCC-TTTSEEEEETTSHGGGTHHHH CS
                    Aminotran_5  28 anvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteai.nlvalslarslkpgdeivvteaehhanlvpwq 106
                                    a++  +++h+++ +++ v  +r+ +ael+  ++ +e+i   G+++a+  ++a +l     ++++  +t  e  a++  ++
  gi|121636807|ref|YP_977030.1|  41 AAALFGTSHRQAPVKNLVGRVRSGLAELFSLPDGYEVILGNGGATAFwDAAAFGL----IDKRSLHLTYGEFSAKFASAV 116
                                    33334899**********************************9997724555555....789**************8888 PP

                                    HHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS--- CS
                    Aminotran_5 107 elakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipid 186
                                      + + g  + +i+ d++   ++++     ++ ++++a +h++++tG+   v +        +alv++Da++++g  p+d
  gi|121636807|ref|YP_977030.1| 117 SKNPFVGEPI-IITSDPGSAPEPQT-----DPSVDVIAWAHNETSTGVAVAVRRPE---GSDDALVVIDATSGAGGLPVD 187
                                    8888889888.88998888888766.....699***************99888877...678****************** PP

                                    HHHHTESEEEEETTTTTSST.T-EEEEEEHHHHHTS..SS.STTSE.EEEET.TEEEEHCTTGGGS.SS--HHHHHHHHH CS
                    Aminotran_5 187 vkklgvDflafsghKllgPt.GiGvlyvrkellekleplllggemv.eevsl.eettfaeapskfeaGTpnvagiiglga 263
                                    ++++++  ++f  +K+++ + G+ + ++++++l ++e +   g  v +  sl      + + + ++  Tp +a +  l++
  gi|121636807|ref|YP_977030.1| 188 IAETDA--YYFAPQKNFASDgGLWLAIMSPAALSRIEAIAATGRWVpDFLSLpIAVENSLKNQTYN--TPAIATLALLAE 263
                                    ***999..*******77765279999************9999998746677755555555667788..************ PP

                                    HHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE.TTCSHHHHHHHHHHTTE CS
                    Aminotran_5 264 aleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf.kgvhaedvatlLdeegI 333
                                     +++l  ++gl+ + k+ +  +++l++  ++ p ++ +++d+  r++ + ++ f ++v+a  va++L+ +gI
  gi|121636807|ref|YP_977030.1| 264 QIDWLvGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLRSQVVGTIDFvDDVDAGTVAKILRANGI 335
                                    ****************************************************999**************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2667.15
//
Query:       gi|121636808|ref|YP_977031.1|  [L=340]
Description: hypothetical protein BCG_0937 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.8e-108  360.5   0.0   6.9e-108  360.2   0.0    1.0  1  AurF      P-aminobenzoate N-oxygenase AurF


Domain annotation for each model (and alignments):
>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.2   0.0  3.8e-112  6.9e-108       1     283 []      19     303 ..      19     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 360.2 bits;  conditional E-value: 3.8e-112
                                    XXXX-HHHHHHHHHHHHH-T---........-.-.---TTS-SS-GGGSGGGGSCHHHHS-HHHHHHHHHHHHHHHHHHH CS
                           AurF   1 dedreevlerllessarrsfdplvdiDwdapl.a.qedddrwdlppellpLygtplwqrlteeqriellrwelaniakvg 78 
                                    d+++ e+l++l+e+s+rr+f+p++diDw++p+ a + +d+rw+l p ++pL+++p++q++++e++ie+++w++an+akvg
  gi|121636808|ref|YP_977031.1|  19 DAEYVEMLATLSEGSVRRNFNPYTDIDWESPEfAvTDNDPRWIL-PATDPLGRHPWYQAQSRERQIEIGMWRQANVAKVG 97 
                                    57899***************************************.999******************************** PP

                                    HHHHHHTHHHHHCT-STT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--S---HHHHHHHHHHHH--SHHHHHHHHH CS
                           AurF  79 iwfEsiliqlllrdaypldntspevryalteiaDEcrHslMfaeaverigadvpgmyrvrrllrelakllktiarglvff 158
                                    ++fEsili++l++++++ +n+spe+ry+l+e ++Ec+H++Mf+e+v+r+gadvpg +r+ r++++l++l+++   +++ff
  gi|121636808|ref|YP_977031.1|  98 LHFESILIRGLMNYTFWMPNGSPEYRYCLHESVEECNHTMMFQEMVNRVGADVPGLPRRLRWVSPLVPLVAGPL-PVAFF 176
                                    **************************************************************************.***** PP

                                    HHHHHHHHHHHHHHHHHHT-SS.S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHS-- CS
                           AurF 159 aavlvgEeiidalqrelmrdee.lqPlvrrvmriHvaEEarHisfareelrrrvprlsraerallrlllalalrafassl 237
                                    ++vl+gEe+id++q++++r+++ l+P+++rvm iHvaEEarHisfa+e+lr+r+prl r +r++++l+++l++r +++++
  gi|121636808|ref|YP_977031.1| 177 IGVLAGEEPIDHTQKNVLREGKsLHPIMERVMSIHVAEEARHISFAHEYLRKRLPRLIRMQRFWISLYFPLTMRSLCNAI 256
                                    ******************************************************************************** PP

                                    HHHHHHHHHT-TTHHHHHHHH.HHHHTT--S----.HHHHHHHHHTT CS
                           AurF 238 vnppvyalagldpaeavrael.ianphsretlrdaaaklrklldelG 283
                                    v pp+++++++d++++v++el + +p+sr+ l d++a+ r+l++++G
  gi|121636808|ref|YP_977031.1| 257 VVPPKAFWEEFDIPREVKKELfFGSPESRKWLCDMFADARMLAHDTG 303
                                    ********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2421.71
//
Query:       gi|121636809|ref|YP_977032.1|  [L=575]
Description: NADPH:adrenodoxin oxidoreductase fprB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-11   41.8   0.1    2.8e-08   33.3   0.1    2.4  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.9e-07   29.0  19.8    4.2e-06   26.4   6.1    2.3  2  Fer4           4Fe-4S binding domain
    1.2e-05   25.1   5.0    1.2e-05   25.1   5.0    2.4  2  Fer4_6         4Fe-4S binding domain
    2.2e-05   24.9  14.2    4.1e-05   24.1  14.2    1.4  1  Fer4_7         4Fe-4S dicluster domain
    6.4e-05   23.8   9.1    0.00043   21.2   0.5    2.4  2  Fer4_16        4Fe-4S double cluster binding domain
    0.00012   22.2   0.0    0.00034   20.8   0.0    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00024   20.4   0.0    0.00044   19.6   0.0    1.4  1  FAD_binding_3  FAD binding domain
    0.00033   20.8  11.4    0.00062   19.9  11.4    1.4  1  Fer4_9         4Fe-4S dicluster domain
    0.00053   19.9   4.0    0.00053   19.9   4.0    2.5  2  Fer4_2         4Fe-4S binding domain
    0.00078   19.5   2.4    0.00078   19.5   2.4    2.2  2  Fer4_10        4Fe-4S dicluster domain
    0.00079   19.9   0.2       0.72   10.5   0.1    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.007   16.8   0.3       0.54   10.7   0.0    2.8  2  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.013   15.9   2.7      0.013   15.9   2.7    2.3  1  Fer4_4         4Fe-4S binding domain
      0.022   15.2   0.2      0.022   15.2   0.2    2.3  2  Fer4_8         4Fe-4S dicluster domain
      0.032   14.2   0.2       0.37   10.8   0.0    2.4  3  NAD_binding_9  FAD-NAD(P)-binding
      0.033   12.9   0.0      0.051   12.3   0.0    1.2  1  HI0933_like    HI0933-like protein
      0.035   13.4   0.1        4.7    6.4   0.0    2.3  2  Thi4           Thi4 family
      0.064   13.3   0.3          3    7.9   0.0    2.9  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.074   12.9   0.1       0.22   11.4   0.1    1.8  1  UPF0146        Uncharacterised protein family (UPF0146)
       0.17   11.1   0.0        3.9    6.6   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.18   12.0  16.6    1.5e+02    2.6   6.7    2.2  1  Fer4_21        4Fe-4S dicluster domain
        0.2   11.5   0.2        2.5    8.0   0.0    2.2  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
        1.9    9.1  11.0       0.35   11.5   0.3    2.4  2  Fer4_17        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   3.6e-11   2.8e-08       3     164 ..     115     272 ..     113     303 .. 0.67
   2 !    6.0   0.0    0.0076       5.9     218     276 ..     395     456 ..     370     479 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.6e-11
                                    EEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHCCTC CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaq.agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllgeev 75 
                                    v+v+G+GpA++ aa +l   +g++v ++ ++  +++g  + s ++   +  +++ +       +       ++++l+   
  gi|121636809|ref|YP_977032.1| 115 VAVVGSGPAAMYAADELLVqQGVQVNVF-EKLPTPYG-LVRSGVAPDHQNTKRVTRlfdriaGH-----RRFRFYLN--- 184
                                    99************9986648*******.44445555.55555555555555544433333322.....23666666... PP

                                    EEEEESCEEEEETEEECTCEEE.EEESEEEE---E.EE-BCTCTTC........TTBEECCSECHHHHHHCCSS-TSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  76 vkidpgkkkvklekkkegdeek.iaydklvlAtGs.sprdlgipGv.......aenvgklvrtldsaealklkllpkriv 146
                                    v+i  gk   +l     g+ e     ++++ A G+   r+l+i+G+       a++ +  +    + + l  +l  +r+v
  gi|121636809|ref|YP_977032.1| 185 VEI--GK---HL-----GHAELlAHHHAVLYAVGApDDRRLTIDGMglpgtgtATELVAWLNGHPDFNDLPVDLSHERVV 254
                                    333..44...22.....22222034589999***9888999***99989877744444444777777777777777**** PP

                                    EES-SHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 147 vvGgGyiGvElAaalakl 164
                                    ++G+G++++++A +la  
  gi|121636809|ref|YP_977032.1| 255 IIGNGNVALDVARVLAAD 272
                                    *************98654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                                    EEETTSCE.EEESEEEE-S-EEES-HHCS...HCCT-EEEETTEEE--TTSBESSTTEEE-GG CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 218 vvledgee.idadlvvvavGvrpstelle...eklglelderggivvdeflrtnvpgiyaiGD 276
                                    v+ +d+ + +da lv++++G+r ++       e++ l + ++gg v+d+     vpg y++G 
  gi|121636809|ref|YP_977032.1| 395 VTGTDELRqLDAGLVLTSIGYRGKPIPDLpfdEQAAL-VPNDGGRVIDPGTGEPVPGAYVAGW 456
                                    555555445************9886432246444444.5678888999999888999999995 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   5.7    0.0023       1.8       3      23 ..       4      24 ..       2      25 .. 0.87
   2 !   26.4   6.1   5.3e-09   4.2e-06       2      23 ..      40      61 ..      39      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                                   EETTTSSS-THHHHHSTTTEE CS
                           Fer4  3 ideekCigCGaCvevCPvgAI 23
                                   +++  C +   Cv +CPv++I
  gi|121636809|ref|YP_977032.1|  4 VITQSCCNDASCVFACPVNCI 24
                                   6777899999**********9 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.3e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   +id+  C+ CGaCv +CPv AI
  gi|121636809|ref|YP_977032.1| 40 YIDPVACVDCGACVTACPVSAI 61
                                   89*******************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   5.8      0.64     5e+02      12      24 .]      10      24 ..       2      24 .. 0.82
   2 !   25.1   5.0   1.6e-08   1.2e-05       4      24 .]      41      61 ..      39      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.64
                         Fer4_6 12 Cgd..CvrvCPegai 24
                                   C+d  Cv +CP + i
  gi|121636809|ref|YP_977032.1| 10 CNDasCVFACPVNCI 24
                                   67777******9876 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.6e-08
                         Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                   idp +C++Cg+Cv++CP  ai
  gi|121636809|ref|YP_977032.1| 41 IDPVACVDCGACVTACPVSAI 61
                                   9*****************998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1  14.2   5.2e-08   4.1e-05       6      52 .]      13      60 ..       8      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.2e-08
                         Fer4_7  6 gaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52
                                     Cv aCpv++i  +++e  +g+   e ++idp  C++CgaCv++CP+ a
  gi|121636809|ref|YP_977032.1| 13 ASCVFACPVNCIHPTPDE--PGFatsEMLYIDPVACVDCGACVTACPVSA 60
                                   59************9984..44433355699****************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.7     0.026        20       3      20 ..      10      27 ..       8      40 .. 0.75
   2 !   21.2   0.5   5.5e-07   0.00043       2      23 ..      46      67 ..      45      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                        Fer4_16  3 gtCgkCaevCPtnaikek 20
                                    +   C+ +CP+n+i+ +
  gi|121636809|ref|YP_977032.1| 10 CNDASCVFACPVNCIHPT 27
                                   44457**********976 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 5.5e-07
                        Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                   C++Cg+C+ +CP++ai  +++ 
  gi|121636809|ref|YP_977032.1| 46 CVDCGACVTACPVSAIAPNTRL 67
                                   ****************998544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-07   0.00034       1      42 [.     117     159 ..     117     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                                    EE--SHHHHHHH.HHHHCCTEEEEEE-SSSSSSGGG-EECETT CS
                  NAD_binding_8   1 IvGaGlsGlvaA.ylLakagfdvlllekrdrlGGraasyevpg 42 
                                    +vG+G ++++aA  lL ++g++v ++ek + + G ++s   p+
  gi|121636809|ref|YP_977032.1| 117 VVGSGPAAMYAAdELLVQQGVQVNVFEKLPTPYGLVRSGVAPD 159
                                    8***********5567999***********9999999988865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.7e-07   0.00044       3      44 ..     114     156 ..     112     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.7e-07
                                    EEEEE--SHHHHHHHH.HHHHTTHHEEEEESSSSSCCSSS--E CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlal.lLseaGvrvvlvekrsttvvlpradg 44 
                                    +V++VG+Gpa + +a  lL ++Gv+v + ek  t + l r+++
  gi|121636809|ref|YP_977032.1| 114 TVAVVGSGPAAMYAADeLLVQQGVQVNVFEKLPTPYGLVRSGV 156
                                    79************9626789****************999987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9  11.4     8e-07   0.00062       2      51 .]       9      61 ..       8      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8e-07
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51
                                   C++  +Cv aCp + + +   e   +  +  +    aC++CgaCv aCp  ai
  gi|121636809|ref|YP_977032.1|  9 CCNDASCVFACPVNCIHPTPDEPGFATSEMLYidpVACVDCGACVTACPVSAI 61
                                   444467**********999988888876555589999************9887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.1     0.088        69       3      21 ..       2      20 ..       1      21 [. 0.77
   2 !   19.9   4.0   6.8e-07   0.00053       3      21 ..      39      57 ..      37      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.088
                         Fer4_2  3 vvvdtdrCigCg..aCvsaCP 21
                                   ++v t++C  C+  +Cv aCP
  gi|121636809|ref|YP_977032.1|  2 PHVITQSC--CNdaSCVFACP 20
                                   67777777..76668****** PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.8e-07
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                    ++d+ +C+ CgaCv+aCP
  gi|121636809|ref|YP_977032.1| 39 LYIDPVACVDCGACVTACP 57
                                   5789999************ PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0  17.1   0.00046      0.36       6      56 .]       6      57 ..       1      57 [. 0.84
   2 !   19.5   2.4     1e-06   0.00078       2      23 ..      39      60 ..      38      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                        Fer4_10  6 ddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +++C + + Cv aCP++  +    ++    +e+  +++ +C +cgaCv aCP
  gi|121636809|ref|YP_977032.1|  6 TQSCCNDASCVFACPVNCiHPTPDEPGFATSEMLYIDPVACVDCGACVTACP 57
                                   6799999*********88666666666667788888***************9 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                   ++id+  C+ Cg+Cv+aCP+++
  gi|121636809|ref|YP_977032.1| 39 LYIDPVACVDCGACVTACPVSA 60
                                   589****************944 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       8.6       2      34 ..     115     148 ..     114     154 .. 0.88
   2 !   10.5   0.1   0.00092      0.72       1      20 [.     252     271 ..     252     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                                    EEEECSSHHHHHHHHHH.HHTTSEEEEEESSSSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgal.aelgkkVtvversdkl 34 
                                    v+vvG+G  ++ +A +l  + g +V v+e  +++
  gi|121636809|ref|YP_977032.1| 115 VAVVGSGPAAMYAADELlVQQGVQVNVFEKLPTP 148
                                    89*************9956699******998775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00092
                                    EEEEECSSHHHHHHHHHHHH CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalae 20 
                                    +vv++G G+++l++A +la+
  gi|121636809|ref|YP_977032.1| 252 RVVIIGNGNVALDVARVLAA 271
                                    79***************975 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.16   1.2e+02       8      36 ..     113     142 ..     107     212 .. 0.79
   2 !   10.7   0.0    0.0007      0.54       3      28 ..     246     271 ..     244     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklle.agakvtvv 36 
                                     +v vvG G+ A+  +  ll  +g +v v 
  gi|121636809|ref|YP_977032.1| 113 LTVAVVGSGPAAMYAADELLVqQGVQVNVF 142
                                    6899*********99998875266888884 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0007
                  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklle 28 
                                    +dl+ ++v+++G G+vA+  +r l++
  gi|121636809|ref|YP_977032.1| 246 VDLSHERVVIIGNGNVALDVARVLAA 271
                                    7999*************988877765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   2.7   1.7e-05     0.013       4      16 ..      46      58 ..      43      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                         Fer4_4  4 CigCgsCvaaCPq 16
                                   C++Cg+Cv aCP+
  gi|121636809|ref|YP_977032.1| 46 CVDCGACVTACPV 58
                                   ************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   6.2       9.3   7.3e+03      49      64 ..       7      22 ..       3      23 .. 0.85
   2 ?   15.2   0.2   2.8e-05     0.022       4      18 ..      45      59 ..      42      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.3
                         Fer4_8 49 wsCttcgaCtevCpvg 64
                                   +sC +  +C+ +Cpv+
  gi|121636809|ref|YP_977032.1|  7 QSCCNDASCVFACPVN 22
                                   78999999******97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.8e-05
                         Fer4_8  4 kCieCgaCqsaCpvl 18
                                   +C+ CgaC +aCpv 
  gi|121636809|ref|YP_977032.1| 45 ACVDCGACVTACPVS 59
                                   688888888888865 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00047      0.37       1      36 [.     116     147 ..     116     166 .. 0.80
   2 ?    0.3   0.1       0.8   6.3e+02       4      22 ..     219     240 ..     216     266 .. 0.75
   3 ?   -2.5   0.0       5.9   4.6e+03       1      20 [.     254     273 ..     254     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36 
                                    a+vG Gp++++++++Ll +    + +++ +f++ ++
  gi|121636809|ref|YP_977032.1| 116 AVVGSGPAAMYAADELLVQ----QGVQVNVFEKLPT 147
                                    89****************9....5999****99443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.8
                  NAD_binding_9   4 GaGprGlavlerLlara...kk 22 
                                    G+G  G+ ++++L+a+    ++
  gi|121636809|ref|YP_977032.1| 219 GMGLPGTGTATELVAWLnghPD 240
                                    9999999999999999855434 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.9
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    +i+G G  +l v++ L+a  
  gi|121636809|ref|YP_977032.1| 254 VIIGNGNVALDVARVLAADP 273
                                    69999999999999999885 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-05     0.051       2      33 ..     114     146 ..     113     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                    SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisa.akrgkrVlllekak 33 
                                    +v+v+G G+A ++aA ++  ++g +V ++ek +
  gi|121636809|ref|YP_977032.1| 114 TVAVVGSGPAAMYAADELlVQQGVQVNVFEKLP 146
                                    699************99989**********965 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.006       4.7      20      50 ..     115     145 ..     108     156 .. 0.87
   2 ?    4.4   0.0     0.024        19      14      40 ..     247     273 ..     240     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.006
                                    EEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                           Thi4  20 vvivGaGssGLtaayylakkpdlkvailers 50 
                                    v++vG+G++ + aa  l  + +++v ++e+ 
  gi|121636809|ref|YP_977032.1| 115 VAVVGSGPAAMYAADELLVQQGVQVNVFEKL 145
                                    89************9999888*******985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                                    HHTEEEEEEE--SHHHHHHHHHHHHCT CS
                           Thi4  14 kyaesDvvivGaGssGLtaayylakkp 40 
                                    ++    vvi+G G   L  a++la +p
  gi|121636809|ref|YP_977032.1| 247 DLSHERVVIIGNGNVALDVARVLAADP 273
                                    566678******************986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.54   4.2e+02      14      42 ..     114     142 ..     104     154 .. 0.85
   2 ?    7.9   0.0    0.0039         3       9      33 ..     247     271 ..     241     279 .. 0.88
   3 ?   -0.1   0.0       1.1   8.9e+02      23      45 ..     281     303 ..     276     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.54
                                    EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                   Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvva 42 
                                    +v ++G G  a  +a  Ll ++  +v v+
  gi|121636809|ref|YP_977032.1| 114 TVAVVGSGPAAMYAADELLVQQGVQVNVF 142
                                    799************99887766668776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0039
                                    ..TT-EEEEES-SHHHHHHHHHHHC CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLla 33 
                                    +l++++v++iG+G++a  va+ L+a
  gi|121636809|ref|YP_977032.1| 247 DLSHERVVIIGNGNVALDVARVLAA 271
                                    6899*****************9987 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH  23 maelvakhLlakgvkkvvvaNRt 45 
                                    +a  ++++L ++ v++vvva R 
  gi|121636809|ref|YP_977032.1| 281 IADHALSALRNSAVREVVVAARR 303
                                    67788999************995 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00028      0.22      13      55 ..     249     293 ..     242     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                    -SSEEEEET-TT.--HHHHHHHHHS-EEEEE-SS-S.....STTE CS
                        UPF0146  13 argkvvEvGiGr.kldvaealakrgvdlvatDikekkak.egvri 55 
                                     +++vv +G G   ldva+ la    +l atDi ++    +   +
  gi|121636809|ref|YP_977032.1| 249 SHERVVIIGNGNvALDVARVLAADPHELAATDIADHALSaLRNSA 293
                                    578********7368******************998444344444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.13     1e+02     166     195 ..     114     144 ..     105     163 .. 0.86
   2 ?    6.6   0.0     0.005       3.9     160     185 ..     246     271 ..     235     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.13
                    Pyr_redox_3 166 kvvViGgknSavDaAlel.vrkgaeVtvvtr 195
                                     v+V+G +  a+ aA el v++g +V+v+ +
  gi|121636809|ref|YP_977032.1| 114 TVAVVGSGPAAMYAADELlVQQGVQVNVFEK 144
                                    5899***********9963678999998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.005
                    Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvr 185
                                     ++++++vv+iG +n a D+A  l++
  gi|121636809|ref|YP_977032.1| 246 VDLSHERVVIIGNGNVALDVARVLAA 271
                                    57889****************87765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   6.7      0.19   1.5e+02      35      58 ..       3      25 ..       1      26 [. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.19
                        Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                   +v++++C   + C+  CPv +ci+
  gi|121636809|ref|YP_977032.1|  3 HVITQSCCNDASCVFACPV-NCIH 25
                                   578999999999******9.9996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.36   2.8e+02       1      30 [.     114     144 ..     114     174 .. 0.83
   2 ?    8.0   0.0    0.0032       2.5       2      48 ..     253     299 ..     252     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                                    EEEEE--SCCHHHHH.HHHHHTT-EEEEE-S CS
                        3HCDH_N   1 kvaviGaGtmGagia.avfasagleVvlvdi 30 
                                    +vav+G+G      a ++++++g++V++++ 
  gi|121636809|ref|YP_977032.1| 114 TVAVVGSGPAAMYAAdELLVQQGVQVNVFEK 144
                                    69******99988884578899****99876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHC CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiekslek 48 
                                    v +iG G +   +a v+a+  +e   +di+++al + ++++ +++  
  gi|121636809|ref|YP_977032.1| 253 VVIIGNGNVALDVARVLAADPHELAATDIADHALSALRNSAVREVVV 299
                                    89********************************9999887766555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   5.4       1.3     1e+03      44      58 ..       7      21 ..       3      23 .. 0.88
   2 ?   11.5   0.3   0.00045      0.35       2      15 ..      46      59 ..      43      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.3
                        Fer4_17 44 slCieCgeCerkCPq 58
                                   ++C++   C+ +CP 
  gi|121636809|ref|YP_977032.1|  7 QSCCNDASCVFACPV 21
                                   79************6 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                        Fer4_17  2 CiqCgyClpeCpsy 15
                                   C  Cg+C+ +Cp  
  gi|121636809|ref|YP_977032.1| 46 CVDCGACVTACPVS 59
                                   55566666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 4460.50
//
Query:       gi|121636810|ref|YP_977033.1|  [L=152]
Description: hypothetical protein BCG_0939c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-10   41.9   0.0    2.4e-10   41.1   0.0    1.3  1  Glyoxalase_6  Glyoxalase-like domain
      2e-10   41.0   0.0      4e-10   40.0   0.0    1.4  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
       0.02   15.2   0.0       0.07   13.4   0.0    1.9  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.1e-14   2.4e-10       6     105 ..      15     129 ..      12     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.1e-14
                   Glyoxalase_6   6 aadpaalaaFwaaal.gweveree........aaledpegvgpaaedaatllfqrvpe...........paknrvHldla 65 
                                    ++d+a +++F+ +a+  +e+ r +        aal+         ++ + +l   vp+            + ++v ++l+
  gi|121636810|ref|YP_977033.1|  15 VDDAASAIDFYVKAFdAVELGRVPgpdgklihAALRI--------NGFTVMLNDDVPQmcggksmtptsLGGTPVTIHLT 86 
                                    56999999******95556666555554444311111........12223333344446666666676634447999*** PP

                   Glyoxalase_6  66 vedldaevarlvalGArvlreprdgthgr...vlaDPeGneFc 105
                                    v+d+da+ +r++++GA+v+++ +d+ +g+   v+aDP G+ + 
  gi|121636810|ref|YP_977033.1|  87 VTDVDAKFQRALNAGATVVTALEDQLWGDrygVVADPFGHHWS 129
                                    ***************************99***********876 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   6.7e-14     4e-10       7     127 ..      13     129 ..       8     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 6.7e-14
                                    EEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC...TSEEEEEEEEE CS
                     Glyoxalase   7 llvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee...tvhhvafiald 83 
                                    l+v+d++ ++dFY k++++  + +++  +++++l +a+++++g  ++l +  +   + k+     +    +     i l+
  gi|121636810|ref|YP_977033.1|  13 LVVDDAASAIDFYVKAFDAVELGRVP--GPDGKLIHAALRINGFTVMLNDDVPQMCGGKSM----TptsLGGTPVTIHLT 86 
                                    78************************..**********************99999999998....444456777889999 PP

                                    HCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEE CS
                     Glyoxalase  84 vedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGille 127
                                    v dv++ ++r+  ag  vv+ ++++ +g++y++ + Dp+G+ + 
  gi|121636810|ref|YP_977033.1|  87 VTDVDAKFQRALNAGATVVTALEDQLWGDRYGV-VADPFGHHWS 129
                                    ********************************9.******9985 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05      0.07       5      96 ..      13     107 ..      12     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                    EE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT.....-THHHTS-EEEEEEEEES-H CS
                   Glyoxalase_4   5 ivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp.....eflaehgeglhhlaywvddl 79 
                                    +vV+D   a++++ ++++  +  r++ ++ +   a ++ ++  + + L   +++       +    g+    + + v+d+
  gi|121636810|ref|YP_977033.1|  13 LVVDDAASAIDFYVKAFDAVELGRVPGPDGKLIHAALRING--FTVMLNDDVPQMcggksMTPTSLGGTPVTIHLTVTDV 90 
                                    69*************************99999888888888..56666665553344544555667777777888999** PP

                                    HHHHHHHCTTTEEEEEE CS
                   Glyoxalase_4  80 daavarleeqGfevvqk 96 
                                    da+ +r+ ++G++vv +
  gi|121636810|ref|YP_977033.1|  91 DAKFQRALNAGATVVTA 107
                                    *************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1161.69
//
Query:       gi|121636811|ref|YP_977034.1|  [L=490]
Description: hypothetical protein BCG_0940 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-13   50.4   1.2    2.8e-13   50.4   1.2    2.4  2  Big_9            Bacterial Ig domain
    4.6e-13   49.2   0.1    6.8e-13   48.7   0.1    1.3  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.016   15.8   0.0      0.016   15.8   0.0    2.7  3  Cadherin_4       Bacterial cadherin-like domain
      0.055   13.4   1.2      0.094   12.7   0.1    1.9  2  Cadherin_5       Cadherin-like domain
      0.098   12.5   0.0        0.2   11.5   0.0    1.6  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.2   7.7e-17   2.8e-13      11      89 ..     103     186 ..      94     187 .. 0.88
   2 ?   -1.6   0.3       1.3   4.6e+03      41      41 ..     364     364 ..     326     420 .. 0.61

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.7e-17
                          Big_9  11 vndaPvavddsvtvtedsvla....ndtdpdgdaltvtsltvtlvtapanGtvtin.adgtltytpnagfsgtdsftYtv 85 
                                    +n+ Pva++++v+v+e++++      + dpdg+ +t++     +  +p++G vt++  + ++ yt+++gf gtd+f++ v
  gi|121636811|ref|YP_977034.1| 103 ENRTPVANPQQVSVPEGGTVGpvrfDACDPDGNRMTFAVRERGAPGGPQHGIVTVDqRTASFIYTADPGFVGTDTFSVNV 182
                                    79***************995555579*********988766666667*********77888******************* PP

                          Big_9  86 sDgs 89 
                                    sD++
  gi|121636811|ref|YP_977034.1| 183 SDDT 186
                                    **86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                          Big_9  41 l 41 
                                     
  gi|121636811|ref|YP_977034.1| 364 A 364
                                    1 PP

>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   1.9e-16   6.8e-13       1     233 []     228     473 ..     228     473 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.9e-16
                                    EEEEESTG....CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH...................TTCE CS
                                    xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxx RF
                  Exo_endo_phos   1 ltwNvngq....aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal...................ggfl 57 
                                    lt+N+ g     +s +l +   ++ + + l ay  +v  +QE   +++++i+   +                        
  gi|121636811|ref|YP_977034.1| 228 LTYNIAGLpfplSSAILPRFFYTKEIGKRLNAY--YVANVQEDFAYHQFLIKKSKMPsqtppepptllwpigvpfsD--- 302
                                    79*****99999888888888888899999999..9999***99999888888886666666666666555444440... PP

                                    EEEECCH...................ECSSSTTSSEEEEEECSTE..EEEEEEEEEETSSSSGCEEEEEEEEEEEEEEEC CS
                                    xxxxxxx...................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Exo_endo_phos  58 gasstsp...................tgggggggnggavlsrfpl..tslfrrtfiefndlvaalrreplaakleqlnia 116
                                                              +   ++ + +g ++s+++l     +  +  ++n  + ++ +             
  gi|121636811|ref|YP_977034.1| 303 ------GlntlsefkvqrldrqtwyeCTSDNCLTLKGFTYSQMRLpgGDTVDVYNLHTNTGGGPTTN------------- 363
                                    ......0444555666666666677777788999999999999998844434444444444444444............. PP

                                    CCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHH...SSCESCETTTTTTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                  Exo_endo_phos 117 shrdhdlvrdlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapv...glyllgggptptyvtr 193
                                                + + + ++ + ++  g+ viv+GDfNar sdd+s +l+ ++     +++   ++ ++++  +pt++  
  gi|121636811|ref|YP_977034.1| 364 ------------ANLAQVANYIQQNSAGRAVIVTGDFNARYSDDQSALLQFAQVNGLTDAWvqvEHGPTTPPFAPTCMVG 431
                                    ............445555666779*******************************999997789**************** PP

                                    TTEB-BEEEEEEC.HHHCCEEEEEEECCHHEEC........TSSCSSSB CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx........xxxxxxxx RF
                  Exo_endo_phos 194 aggsrlDrilasp.alalfrsgvlppplalvrr........ealtlSDH 233
                                    + +  lD i++++ +  +  + ++        +         ++ lSDH
  gi|121636811|ref|YP_977034.1| 432 NECELLDKIFYRSgQGVTLQAVSYG-------NeapkffnsKGEPLSDH 473
                                    ************7433333333333.......23666666899999999 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   4.5e-06     0.016      10      72 .]     103     166 ..     100     166 .. 0.79
   2 ?   -1.9   0.8       1.6   5.6e+03      22      32 ..     181     191 ..     168     231 .. 0.57
   3 ?   -2.2   0.3       1.8   6.6e+03      23      23 ..     369     369 ..     342     418 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                     Cadherin_4  10 vndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavt....vagtyGtltlna.dGsftY 72 
                                     n  Pva+++ ++v+e++++      v  ++ D+dg+ +t++       + +++G +t+++ + sf Y
  gi|121636811|ref|YP_977034.1| 103 ENRTPVANPQQVSVPEGGTVGP----VRFDACDPDGNRMTFAVRErgapGGPQHGIVTVDQrTASFIY 166
                                    5999*************99976....8899********77754333344567******9985666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                     Cadherin_4  22 tvtedtpltit 32 
                                    +v +dt+l + 
  gi|121636811|ref|YP_977034.1| 181 NVSDDTSLHVH 191
                                    44556666553 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                     Cadherin_4  23 v 23 
                                    v
  gi|121636811|ref|YP_977034.1| 369 V 369
                                    2 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.6e-05     0.094      50      89 ..     150     190 ..     127     195 .. 0.74
   2 ?   -2.5   0.1       1.4   5.1e+03      38      57 ..     344     363 ..     342     383 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                     Cadherin_5  50 aenGtvv.dngdGtftftpeanynGevtlsYtvsDgeggtt 89 
                                     ++G v+ d+   +f +t +  + G+ t+s +vsD+++  +
  gi|121636811|ref|YP_977034.1| 150 PQHGIVTvDQRTASFIYTADPGFVGTDTFSVNVSDDTSLHV 190
                                    4678877588899**********************987665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                     Cadherin_5  38 gdtLsvssltadaenGtvvd 57 
                                    gdt+ v +l+++++ G +++
  gi|121636811|ref|YP_977034.1| 344 GDTVDVYNLHTNTGGGPTTN 363
                                    78999999976665555544 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.7e-05       0.2       6      43 ..     349     392 ..     345     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                Exo_endo_phos_2   6 vYippsd.....elenlestlekllselksp.kiiilGDfNakh 43 
                                    vY+  ++     +++  ++++ ++++++++   +i++GDfNa+ 
  gi|121636811|ref|YP_977034.1| 349 VYNLHTNtgggpTTNANLAQVANYIQQNSAGrAVIVTGDFNARY 392
                                    66666666777777888889999999999889*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3171.38
//
Query:       gi|121636812|ref|YP_977035.1|  [L=373]
Description: citrate synthase 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-83  281.4   0.3    2.2e-82  277.1   0.3    2.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.1   0.3   1.2e-86   2.2e-82       1     360 [.      11     348 ..      11     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 277.1 bits;  conditional E-value: 1.2e-86
                                    GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HH.HHHHHHHHHHCTTS--HHHHHHHH CS
                   Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtke.elkefkeelaearklpekvleale 79 
                                    gl gv+a +tei+e d++ g lrYRG+die+L++++ +f +v++lL+ g+  +    ++ f   +++   +  +v    +
  gi|121636812|ref|YP_977035.1|  11 GLDGVVAFTTEIAEPDKDGGALRYRGVDIEDLVSQRVTFGDVWALLVDGNFGSGLpPAEPFPLPIHSG-DVRVDV----Q 85 
                                    799***********************************************665431478888888886.333333....3 PP

                                    CSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHH CS
                   Citrate_synt  80 alpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflyml 159
                                    a  +++ p+     +  +l  dd      ++ +++ +r +++ ++ ++  a  iy+  + + ++  d+  +++++f+  +
  gi|121636812|ref|YP_977035.1|  86 AGLAMLAPIW---GYAPLLDIDD------ATARQQLARASVMALSYVAQSARGIYQPAVPQ-RI-IDECSTVTARFMTRW 154
                                    2222334444...3444444443......44556777867777777777777777777754.44.345579********* PP

                                    HSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHH CS
                   Citrate_synt 160 rgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleeigsaeveve 239
                                    +g +pd+++++++d+++v  a+H++naSTf+arv+aSt+ad+ +a++++iga++Gplhgga  +vl ml+e+++a  +++
  gi|121636812|ref|YP_977035.1| 155 QG-EPDPRHIEAIDAYWVSAAEHGMNASTFTARVIASTGADVAAALSGAIGAMSGPLHGGAPARVLPMLDEVERAG-DAR 232
                                    99.*********************************************************************7776.*** PP

                                    HHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHH.GCT-EB-THHHH CS
                   Citrate_synt 240 eylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkeke.eknlypNvDfys 318
                                    ++++ +l+++ e+l+GfGHrvy+ +DpRa++l+ +ae+l +     p +++a ++e++a + l+e++ ++ + +Nv+f++
  gi|121636812|ref|YP_977035.1| 233 SVVKGILDRG-EKLMGFGHRVYRAEDPRARVLRAAAERLGA-----PRYEVAVAVEQAALSELRERRpDRAIETNVEFWA 306
                                    ********86.***************************976.....9*****************999************* PP

                                    HHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------ CS
                   Citrate_synt 319 gvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRP 360
                                    +v+++   +p ++++++f ++R+aGw+Ahileq++ +k++RP
  gi|121636812|ref|YP_977035.1| 307 AVVLDFARVPANMMPAMFTCGRTAGWCAHILEQKRLGKLVRP 348
                                    *********************************999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2279.56
//
Query:       gi|121636813|ref|YP_977036.1|  [L=882]
Description: LuxR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-19   67.8   0.0    7.9e-19   67.0   0.0    1.5  1  GerE          Bacterial regulatory proteins, luxR family
    4.1e-07   29.6   0.0      1e-06   28.3   0.0    1.7  1  Sigma70_r4_2  Sigma-70, region 4
    0.00014   21.5   0.0    0.00063   19.5   0.0    2.2  1  HTH_23        Homeodomain-like domain
    0.00033   20.4   0.0    0.00087   19.0   0.0    1.7  1  HTH_38        Helix-turn-helix domain
    0.00057   20.2   0.1     0.0023   18.2   0.0    2.0  1  AAA_22        AAA domain
     0.0014   18.6   0.0     0.0046   16.9   0.0    2.0  1  HTH_29        Winged helix-turn helix
     0.0026   17.0   0.0     0.0058   15.8   0.0    1.5  1  NB-ARC        NB-ARC domain
     0.0045   16.5   0.0      0.013   15.1   0.0    1.8  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0084   15.5   0.0      0.041   13.3   0.0    2.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.032   14.7   0.0    1.7  1  HTH_40        Helix-turn-helix domain
      0.039   13.5   0.0        0.1   12.2   0.0    1.7  1  Sigma70_r4    Sigma-70, region 4
      0.054   13.6   0.0       0.21   11.7   0.0    2.0  1  HTH_7         Helix-turn-helix domain of resolvase
      0.056   13.1   0.0      0.056   13.1   0.0    2.5  2  DUF4807       Domain of unknown function (DUF4807)
      0.088   12.5   0.0        0.2   11.3   0.0    1.5  1  CENP-B_N      CENP-B N-terminal DNA-binding domain
       0.12   12.3   6.0        0.6   10.1   0.2    4.2  4  MarR_2        MarR family
          8    6.7  12.3       0.55   10.4   5.2    2.7  2  HemY_N        HemY protein N-terminus


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0     7e-22   7.9e-19       2      56 ..     820     874 ..     819     875 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 7e-22
                                    SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHH CS
                           GerE   2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrl 56 
                                    sL++ Er+v rl+ eG+snk+IA++l++S++TV++h+++++ KL++ srv+lv+ 
  gi|121636813|ref|YP_977036.1| 820 SLTPTERDVVRLVSEGLSNKDIAKRLFVSPRTVQTHLTHVYAKLGLASRVQLVDE 874
                                    7***************************************************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   8.9e-10     1e-06      10      54 .]     820     863 ..     819     863 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.9e-10
                                    TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    +L++ +r ++ l   egls k+IA++l +s++tV+++l    +kL
  gi|121636813|ref|YP_977036.1| 820 SLTPTERDVVRL-VSEGLSNKDIAKRLFVSPRTVQTHLTHVYAKL 863
                                    79**********.67***********************9888776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.6e-07   0.00063      10      35 ..     828     853 ..     826     868 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.6e-07
                         HTH_23  10 illllaeGlsvreIAreLgvsrrTvy 35 
                                    +++l+ eGls ++IA++L vs+rTv+
  gi|121636813|ref|YP_977036.1| 828 VVRLVSEGLSNKDIAKRLFVSPRTVQ 853
                                    799**********************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.8e-07   0.00087       5      42 ..     821     857 ..     820     858 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-07
                         HTH_38   5 LsleeReeIerllaeGlslreIArrLgrspsTIsRElk 42 
                                    L+++eR    rl +eGls+++IA+rL +sp T++ +l 
  gi|121636813|ref|YP_977036.1| 821 LTPTER-DVVRLVSEGLSNKDIAKRLFVSPRTVQTHLT 857
                                    788888.6779**********************99886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-06    0.0023       5     104 ..       8      94 ..       5     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                     ++++++G  G+GKT+l+ ++++  +        r+++ fv+l+  t+s  ++   +ra+gl+        +  ++ l++
  gi|121636813|ref|YP_977036.1|   8 NRLVTLCGTGGVGKTRLAIQIASASEL-------RDGLCFVDLAPITESGIVAATAARAVGLPDQP----GRSTMDSLRR 76 
                                    57899******************9864.......9**************************86555....788889**** PP

                         AAA_22  85 alraravielliiDEaqhlr 104
                                     + +r++  l+++D+ +hl 
  gi|121636813|ref|YP_977036.1|  77 FIGNRRM--LMVLDNCEHLL 94 
                                    *******..*********72 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-06    0.0046       4      51 ..     828     879 ..     826     882 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                         HTH_29   4 allllaeGvstvsqiAkllglsrrtvyrwl.krfeegGlaa...lld.rrrsg 51 
                                    +++l++eG+s  ++iAk+l +s+rtv+++l + + + Gla+   l d   r+g
  gi|121636813|ref|YP_977036.1| 828 VVRLVSEGLS-NKDIAKRLFVSPRTVQTHLtHVYAKLGLASrvqLVDeAARRG 879
                                    89*******8.****************99833466666666666555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.2e-06    0.0058      20     113 ..       8      91 ..       3     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                                    SEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHH CS
                         NB-ARC  20 slvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeveslkrklvrl 99 
                                      +v+l G gGvGKt la qi +  +e++   d++ +v ++   +s  +  t ++ ++l    +  ++ +    + l+r+
  gi|121636813|ref|YP_977036.1|   8 NRLVTLCGTGGVGKTRLAIQIASA-SELR---DGLCFVDLAPITESGIVAATAARAVGLP---D--QPGRS-TMDSLRRF 77 
                                    4589*******************9.6766...7888999999999999999999999887...2..22222.56899999 PP

                                    CCCTTEEEEEEEE- CS
                         NB-ARC 100 LltkrfllvlDDVw 113
                                    + ++r+l+vlD   
  gi|121636813|ref|YP_977036.1|  78 IGNRRMLMVLDNCE 91 
                                    99999999999764 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.013      14      38 ..     834     856 ..     821     857 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                         HTH_24  14 knprisqreLAerlglSpstvnrrl 38 
                                    +  ++s++++A+rl +Sp tv ++l
  gi|121636813|ref|YP_977036.1| 834 E--GLSNKDIAKRLFVSPRTVQTHL 856
                                    4..9******************997 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.6e-05     0.041      17      48 ..     825     856 ..     822     860 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                   HTH_Tnp_ISL3  17 eayilelllesrsvkavArqlgvSwtTVwril 48 
                                    e+ +++l+ e+ s k++A++l vS++TV+  l
  gi|121636813|ref|YP_977036.1| 825 ERDVVRLVSEGLSNKDIAKRLFVSPRTVQTHL 856
                                    7889************************9755 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.8e-05     0.032       6      39 ..     829     862 ..     824     877 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                         HTH_40   6 lelleeglsieeIAkerglkesTIegHLaeliee 39 
                                     +l+ egls ++IAk+  +++ T+++HL++ + +
  gi|121636813|ref|YP_977036.1| 829 VRLVSEGLSNKDIAKRLFVSPRTVQTHLTHVYAK 862
                                    6899************************997665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-05       0.1       4      48 ..     820     863 ..     819     864 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                                    HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    sL++ er+v++l+  egl+ ++I++rl +S  +V  +++    kL
  gi|121636813|ref|YP_977036.1| 820 SLTPTERDVVRLVS-EGLSNKDIAKRLFVSPRTVQTHLTHVYAKL 863
                                    7***********96.899****************99888777776 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.21      14      38 ..     828     852 ..     824     853 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                    GGSSTTTT--STTTSSSS---SSSS CS
                          HTH_7  14 vvkLleeGisiskIAkevnisRsTv 38 
                                    vv+L++eG s ++IAk++ +s+ Tv
  gi|121636813|ref|YP_977036.1| 828 VVRLVSEGLSNKDIAKRLFVSPRTV 852
                                    9**********************98 PP

>> DUF4807  Domain of unknown function (DUF4807)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.96   1.1e+03      55      72 ..     439     456 ..     430     463 .. 0.83
   2 ?   13.1   0.0     5e-05     0.056      59     105 ..     521     567 ..     517     593 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.96
                        DUF4807  55 qQlklAlklgdPlllarc 72 
                                    q l++A+++gdP  l+r+
  gi|121636813|ref|YP_977036.1| 439 QALAMAREVGDPAALVRA 456
                                    55899*******998886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5e-05
                        DUF4807  59 lAlklgdPlllarcklylalsliQrgklkkakrlirriyrfakskke 105
                                    lA  +gd ++   c l+l+l+ +  g+l++a +l r+i   a+ ++ 
  gi|121636813|ref|YP_977036.1| 521 LADTIGDRFVSRHCSLWLSLAQMWAGNLTEALELSREITAEAEASND 567
                                    8999********************************99988874333 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018       0.2       6      44 ..     820     857 ..     815     859 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                    S--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHH CS
                       CENP-B_N   6 sLTlreKievIqrleegeSkaelarrfnvpestlsdilk 44 
                                    sLT+ e  +v++++ eg S +++a+r+ v + t+ + l 
  gi|121636813|ref|YP_977036.1| 820 SLTPTER-DVVRLVSEGLSNKDIAKRLFVSPRTVQTHLT 857
                                    7999996.9************************998665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.25   2.8e+02      13      31 ..     156     172 ..     155     173 .. 0.82
   2 ?   -0.3   0.1      0.89     1e+03      22      54 ..     250     283 ..     237     299 .. 0.81
   3 ?   -1.5   0.0       2.2   2.4e+03       6      20 ..     577     591 ..     576     635 .. 0.74
   4 ?   10.1   0.2   0.00053       0.6       3      44 ..     821     858 ..     820     879 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.25
                                    HHHCTTTSEEEHHHHHHHH CS
                         MarR_2  13 aLgrrpgrdltvgelarrl 31 
                                     ++++     +vge++rrl
  gi|121636813|ref|YP_977036.1| 156 TIANHNA--AAVGEICRRL 172
                                    5777877..8********9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.89
                                    E.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  22 l.tvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    l +v+++a+  +l++ +v   l  Lv++ Lv+  
  gi|121636813|ref|YP_977036.1| 250 LaAVRAVAAGSDLDPFSVLDQLTLLVDKSLVVAD 283
                                    448999999999***99999********999644 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHCTTTS CS
                         MarR_2   6 aqarvLaaLgrrpgr 20 
                                    +qa+vLa+ g++   
  gi|121636813|ref|YP_977036.1| 577 TQAQVLAYCGASAAH 591
                                    799999999888754 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00053
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkr 44 
                                    ltp++++v   +  +    l+ +++a+rl +s+ +v+ +l  
  gi|121636813|ref|YP_977036.1| 821 LTPTERDVVRLVSEG----LSNKDIAKRLFVSPRTVQTHLTH 858
                                    899*******99666....9****************998864 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.2    0.0005      0.55      37     107 .]     626     698 ..     610     698 .. 0.87
   2 ?   -1.2   0.7       2.1   2.4e+03      35      80 ..     745     790 ..     726     802 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                         HemY_N  37 lrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAekaaakaaklsea..pllayllaAqAaqaqg 107
                                    +++ l+++ ++r   r++  +   ++++ + +ala+Gd+ +A++ a++a +  +   +++a+ + A+ a a+g
  gi|121636813|ref|YP_977036.1| 626 VTAALEASDAARPILRAQPDQVTMHQVLMAQLALAGGDAIAARQFANDAVDATNGwhRMVALTIRARVATARG 698
                                    6678888999999999*********************************9999778999*********99876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                         HemY_N  35 rllrlllrlparvrrwrrrrrerkarealseGli.alaeGdfarAek 80 
                                    rll++  +l +++r+  r +  +++++a  ++l  a++ +df rA  
  gi|121636813|ref|YP_977036.1| 745 RLLGAAAALRQQTRQV-RFKIWDAGYQASVTALReAMGDEDFDRAWA 790
                                    6777777777777766.556677888888888873577778888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 6086.25
//
Query:       gi|121636814|ref|YP_977037.1|  [L=285]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-12   47.2   0.0    2.3e-11   43.7   0.0    2.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.3e-15   2.3e-11       5     172 ..      87     237 ..      84     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.3e-15
                  Guanylate_cyc   5 sydevtilFadIvgftalssahspievvklLnelyarfdelldekk.vykvk.tiGdaymvvsglpeekaahaaklaela 82 
                                    ++ +vt+l ad++++t+l++ + p+++ ++++ l   + e +++++ v+ vk + Gd++++++          +++a +a
  gi|121636814|ref|YP_977037.1|  87 PTGTVTLLLADVEESTHLWQMC-PEDMATAIAHLDHTVSEAITNHGgVQPVKrYEGDSFVAAFTRA-------SDAAACA 158
                                    7899******************.**********************9888898579******99776.......6666777 PP

                  Guanylate_cyc  83 LdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellk...eeq 159
                                    Ld+          s   +++r+G+htG+v ++          + G t+n ++r+  ++++g++ +s++t +l +     +
  gi|121636814|ref|YP_977037.1| 159 LDLQR-------TSLAPIRLRIGLHTGEVQLRDE-------LYVGPTINRTARLRDLAHGGQVVLSAATGDLVTgrlPAD 224
                                    77643.......345689**********988765.......689*************************99888666566 PP

                  Guanylate_cyc 160 feltergevevkG 172
                                      l ++g+ +++G
  gi|121636814|ref|YP_977037.1| 225 AWLVDLGRHPLRG 237
                                    6666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1796.68
//
Query:       gi|121636815|ref|YP_977038.1|  [L=495]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-21   76.3   0.0    7.2e-21   74.2   0.0    1.9  1  FMO-like        Flavin-binding monooxygenase-like
      3e-17   62.9   0.0    4.5e-14   52.4   0.0    2.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-13   50.5   0.0    9.4e-12   44.7   0.0    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-12   47.5   0.3    4.9e-12   45.9   0.0    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.6e-09   36.1   7.5    3.2e-05   23.7   0.4    3.6  3  DAO             FAD dependent oxidoreductase
    1.8e-08   33.9   0.1    8.7e-06   25.1   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    9.3e-07   29.0   5.1     0.0021   18.1   0.0    4.4  4  NAD_binding_9   FAD-NAD(P)-binding
    7.8e-06   25.4   0.1    0.00087   18.7   0.0    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
    3.5e-05   24.3   0.2       0.11   13.0   0.0    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00028   20.1   0.9    0.00055   19.1   0.6    1.6  2  FAD_binding_2   FAD binding domain
     0.0034   17.5   0.6       0.76    9.8   0.0    2.9  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.014   14.6   0.1       0.03   13.6   0.1    1.5  1  FAD_binding_3   FAD binding domain
       0.15   12.0   2.4        9.9    6.1   0.2    2.3  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.16   11.0   3.8          1    8.3   0.2    2.5  3  GIDA            Glucose inhibited division protein A
       0.22   10.9   0.1        3.5    6.9   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.31    9.7   4.6       0.12   11.1   0.7    2.1  3  HI0933_like     HI0933-like protein
        1.8    8.4   5.7        1.2    9.0   0.5    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        3.4    7.3   4.6         19    4.9   0.9    2.4  2  ApbA            Ketopantoate reductase PanE/ApbA
        4.1    6.7   4.5         33    3.7   0.0    2.6  3  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   7.6e-24   7.2e-21       4     331 ..       8     337 ..       5     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 7.6e-24
                       FMO-like   4 vaviGaGvsGlasikccleegleptc.fersddiGGlwrfkenveeGrasiyksvvsnsskemscfsdfplpedypnflh 82 
                                    vav+GaG+sG+    + l  g+  +c +e++dd+GG wr  +n        y  +  ++   +  +s    p+    f +
  gi|121636815|ref|YP_977038.1|   8 VAVVGAGMSGMCVAITLLSAGITDVCiYEKADDVGGTWR--DN-------TYPGLTCDVPSRLYQYSFAKNPNWTQMFSR 78 
                                    9************************977**********8..33.......477777888888888987777777788999 PP

                       FMO-like  83 nsklleylklfakefdllkyiqfkttvcsvkkrpdfstsGqwevvtekegkkesavfdavmvctGhhvnphlplesfpGi 162
                                      ++++yl+  a++++l   i+f +tv+s +        G+w + t  +  +es+v d ++  tG + +p +p     G+
  gi|121636815|ref|YP_977038.1|  79 GGEIQDYLRGIAERYGLRHRIRFGATVVSARF-----DDGRWVLRT--DSGTESTV-DFLISATGVLHHPRIPP--IAGL 148
                                    99*************************98653.....469**6655..45556654.9999***********95..78** PP

                       FMO-like 163 ekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvl..........srvsdsGypwdm 232
                                    + f+G +fhs  + +   + g+r+ viG G +g ++ + l+  a +v +  r+  wvl          +rv+++ +p   
  gi|121636815|ref|YP_977038.1| 149 DDFRGTVFHSARWDHTVPLLGRRIAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQWVLpwpnprysklARVFHRAFPCLG 228
                                    *********************************************************64444444333799999999755 PP

                       FMO-like 233 llvtrfksllkni.........lptalsnwlvekklnkrfn.henyglkpkkralakepvlndelparilaGavkvkssv 302
                                     l+ +  sl  ++         l ++l+ ++    l +  +     +l+p  + + k+ v+   +  +i    v++ +  
  gi|121636815|ref|YP_977038.1| 229 SLAYKAYSLSFETfavalsnpgLHRKLVGAVCRASLRRVRDpRLRRALTPDYEPMCKRLVMSGGFYRAIQRDDVELVTAG 308
                                    5554444444444000000001556666666666665544413467899*************************999998 PP

                       FMO-like 303 keltetsaifedgtveedidvvifatGyt 331
                                    ++  e   i  d  v +++dv+++atG+ 
  gi|121636815|ref|YP_977038.1| 309 IDHVEHRGIVTDDGVLHEVDVIVLATGFD 337
                                    888899889888899999*********95 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   4.8e-17   4.5e-14       2     200 ..      10     205 ..       9     219 .. 0.83
   2 !    7.4   0.0    0.0024       2.3     189     272 ..     255     341 ..     245     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 4.8e-17
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeeklsr 80 
                                    ++GaG  G+ +ai+l  ag++d++i Ek+  +g ++++      + +   +s+   +      s  ++p++   +   ++
  gi|121636815|ref|YP_977038.1|  10 VVGAGMSGMCVAITLLSAGITDVCIYEKAdDVGGTWRDNTYPGLTCD--VPSR---LY---QYSFAKNPNW--TQMFSRG 79 
                                    8****************************99**99997444444433..3333...22...2223344543..4567799 PP

                    Pyr_redox_3  81 kealeYlrevaksfelp..iklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhys 154
                                     e+ +Ylr +a+++ l+  i+   +V s   +d+  +++t+++ + + +++i AtG  ++P+ + i G ++   +v h++
  gi|121636815|ref|YP_977038.1|  80 GEIQDYLRGIAERYGLRhrIRFGATVVSARFDDGRWVLRTDSGtESTVDFLISATGVLHHPRIPPIAGLDDfrgTVFHSA 159
                                    ***************95448899999999999**********9678889********************98656678888 PP

                    Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                      ++  ++ g++++ViG + ++v   + l+    +Vt++ r++++ 
  gi|121636815|ref|YP_977038.1| 160 RWDHTVPLLGRRIAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQWV 205
                                    889999999*********************************9875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0024
                    Pyr_redox_3 189 eVtvvtrgseiekeesdpsyslkpdienrleelvke.ekikvlfnaevkeikekeeeykvk...tedgkkvevkddvvla 264
                                     V  v r s ++ ++ +    l pd+e+  ++lv + + ++++++ +v+ ++    +++ +   t+dg  +++ d +vla
  gi|121636815|ref|YP_977038.1| 255 LVGAVCRASLRRVRDPRLRRALTPDYEPMCKRLVMSgGFYRAIQRDDVELVTAGIDHVEHRgivTDDG-VLHEVDVIVLA 333
                                    57778888888889999999**************9986678888888887775444333222226665.67777999999 PP

                    Pyr_redox_3 265 tGykpdls 272
                                    tG+++++ 
  gi|121636815|ref|YP_977038.1| 334 TGFDSHAF 341
                                    ***98764 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0     1e-14   9.4e-12       2     176 ..       7     203 ..       6     222 .. 0.78
   2 ?    3.7   0.0     0.031        29     210     261 ..     313     356 ..     277     364 .. 0.67

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1e-14
                                    SEEEE--SHHHHHHHHHHHHHTS.-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqaga.kvtlve.........legtclnggcllskallgvaedaeias.............. 57 
                                     v+v+G+G+ G+ +a+tl  ag+ +v ++e         +++t ++ +c +++ l +++ +++                 
  gi|121636815|ref|YP_977038.1|   7 TVAVVGAGMSGMCVAITLLSAGItDVCIYEkaddvggtwRDNTYPGLTCDVPSRLYQYSFAKNPNWtqmfsrggeiqdyl 86 
                                    69******************8761566665667788899**********9988888888887755567888887777777 PP

                                    .HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E..EE-BCTCTTC.TTBEECCSECHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs..sprdlgipGvaenvgklvrtldsae 134
                                        ++++   + + g++vv+  ++ ++ +l+   ++++++ + d l+ AtG   +pr+++i G+ +  g++   ++sa+
  gi|121636815|ref|YP_977038.1|  87 rGIAERYGLRHRIRFGATVVSARFDDGRWVLR---TDSGTESTVDFLISATGVlhHPRIPPIAGLDDFRGTV---FHSAR 160
                                    74455555555556667899999999999994...4678899**********777**********6666544...55554 PP

                                    HHC.CSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSS CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 135 alk.lkllpkrivvvGgGyiGvElAaalaklgkevtlveardr 176
                                      +   ll +ri+v+G G +Gv l + la ++ +vt+ ++  +
  gi|121636815|ref|YP_977038.1| 161 WDHtVPLLGRRIAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQ 203
                                    3330344559***************************998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                                    EETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE-- CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 210 dgngekle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvd 261
                                    +     ++  v++dg   ++d +v+a+G+     +  + ++l+   r+gi +d
  gi|121636815|ref|YP_977038.1| 313 E-----HRgIVTDDGVLHEVDVIVLATGFDSHAFF--RPMQLT--GRDGIRID 356
                                    2.....33467778888888888888888776544..344443..36666666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   5.1e-15   4.9e-12       1      66 [.      10      77 ..      10      78 .. 0.94
   2 ?   -2.7   0.2       7.5     7e+03       1      16 [.     174     189 ..     174     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 5.1e-15
                                   EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG-EECETTCEECTS---E.EETTHHHHCHHHHC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraasyevpgvrvdygahif.hgsgyypnvrrllr 66
                                   +vGaG+sG++ A +L  ag+ dv ++ek+d++GG ++++++pg ++d++ + +  ++ ++pn+++++ 
  gi|121636815|ref|YP_977038.1| 10 VVGAGMSGMCVAITLLSAGItDVCIYEKADDVGGTWRDNTYPGLTCDVPSRLYqYSFAKNPNWTQMFS 77
                                   8*****************9989*******************************6667899*****997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                                    EE--SHHHHHHHHHHH CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                                    ++G+G +G  + + La
  gi|121636815|ref|YP_977038.1| 174 VIGTGSTGVQLVCGLA 189
                                    7899988876666555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.4   3.4e-08   3.2e-05       2      41 ..       8      49 ..       7      74 .. 0.91
   2 !    7.2   0.5    0.0036       3.4     161     232 ..      97     163 ..      80     236 .. 0.71
   3 !    7.1   0.0    0.0038       3.6     152     211 ..     293     343 ..     241     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.4e-08
                                   EEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSE CS
                            DAO  2 vviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrns 41
                                   v+++G+G+ G+++A  L  +g   V+++ek+d++g g+   n+
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGitdVCIYEKADDVG-GTWRDNT 49
                                   99***************9999**************.9876665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0036
                                    -EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEE...EEEEEEEEEECCT CS
                            DAO 161 veilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpisp...vrgqvlvlkplse 232
                                     +i++g++v++ + +dg+ w +   t+ g+++++d ++ a+G+     +       +pi +   +rg+v++ ++++ 
  gi|121636815|ref|YP_977038.1|  97 HRIRFGATVVSARFDDGR-WVL--RTDsGTESTVDFLISATGVLHHpRI-------PPIAGlddFRGTVFHSARWDH 163
                                    489********9888888.999..66669987889*******7633333.......344444449999999877765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0038
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTC CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllk 211
                                    ++ra+++  ve+++   + ++e+      g+  +t+ g  +++d +V+a+G  s  ++   +
  gi|121636815|ref|YP_977038.1| 293 FYRAIQRDDVELVTA-GIDHVEH-----RGI--VTDdGVLHEVDVIVLATGFDSHaFF---R 343
                                    677888888888887.6666643.....456..4555977899********9987655...2 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.084        79     193     213 ..       7      27 ..       3      38 .. 0.85
   2 !   25.1   0.0   9.2e-09   8.7e-06      81     219 ..      60     195 ..      55     214 .. 0.75
   3 ?    2.7   0.0     0.059        56     324     341 ..     320     337 ..     294     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.084
                    K_oxygenase 193 riaVvGsGqSaaeifedllrr 213
                                    ++aVvG+G S+  ++  ll+ 
  gi|121636815|ref|YP_977038.1|   7 TVAVVGAGMSGMCVAITLLSA 27 
                                    69*********9999988865 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 9.2e-09
                    K_oxygenase  81 rLykFlnlet....flpsR.kefedYlrWvasq..leeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlv 153
                                    rLy++ ++++    ++ sR  e +dYlr +a++  l +++rfg++v + ++d+ +   +l+ +s    g+  e +   l+
  gi|121636815|ref|YP_977038.1|  60 RLYQYSFAKNpnwtQMFSRgGEIQDYLRGIAERygLRHRIRFGATVVSARFDDGR--WVLRTDS----GT--ESTVDFLI 131
                                    666666666411113333325999*******97447799*************975..4555554....54..55555666 PP

                    K_oxygenase 154 lgvG..tepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvel 219
                                     ++G   +p iP+++   + + +v+Hs++  ++    l ++riaV+G G ++ +++  l+  +   ++
  gi|121636815|ref|YP_977038.1| 132 SATGvlHHPRIPPIAGLDDFRGTVFHSARWDHTV--PLLGRRIAVIGTGSTGVQLVCGLAGVAG--KV 195
                                    6777559*******98777789***********9..6999*************99999887655..34 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.059
                    K_oxygenase 324 geeetlevdavvlATGYr 341
                                    ++   +evd++vlATG++
  gi|121636815|ref|YP_977038.1| 320 DDGVLHEVDVIVLATGFD 337
                                    5566789*********96 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.2e-06    0.0021       1     154 [.       9     135 ..       9     137 .. 0.66
   2 ?    0.1   0.1      0.75     7e+02       1      17 [.     173     189 ..     173     209 .. 0.82
   3 ?    3.5   0.1     0.068        65     132     154 ..     313     335 ..     285     337 .. 0.81
   4 ?   -2.6   0.0       5.2   4.9e+03      13      36 ..     400     423 ..     391     438 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftddpptfaeWlrergale 80 
                                    a+vGaG++G++v+  Ll+       +++ +++++    g+ wr++  + l   vp++  ++            ++ +   
  gi|121636815|ref|YP_977038.1|   9 AVVGAGMSGMCVAITLLSA----GITDVCIYEKADDV-GGTWRDNTYPGLTCDVPSRLYQYSFA---------KNPN--- 71 
                                    89****************9....699*******9999.9*******999999999876664322.........2222... PP

                  NAD_binding_9  81 eaeeldpddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                        +  + f +   +++Ylr ++e+   r     +++ + a+vv+ + +++++ +++++g++ ++d ++ A+G
  gi|121636815|ref|YP_977038.1|  72 ----W-TQMFSRGGEIQDYLRGIAERYGLRH----RIR-FGATVVSARFDDGRWVLRTDSGTESTVDFLISATG 135
                                    ....1.2234444455566666666555444....233.35556666666666666666666666666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.75
                  NAD_binding_9   1 aivGaGprGlavlerLl 17 
                                    a++G G +G+ ++  L+
  gi|121636815|ref|YP_977038.1| 173 AVIGTGSTGVQLVCGLA 189
                                    89********9998886 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.068
                  NAD_binding_9 132 dgqavlladgaslaadaVvLAlG 154
                                    +++ ++++dg  +++d +vLA+G
  gi|121636815|ref|YP_977038.1| 313 EHRGIVTDDGVLHEVDVIVLATG 335
                                    34568999**************9 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.2
                  NAD_binding_9  13 lerLlarakkkspleitlfdpsep 36 
                                    +e+++++ k+ ++ e + ++p+++
  gi|121636815|ref|YP_977038.1| 400 AEHIVQWIKRWRHGEFDTMEPKSA 423
                                    334444433333444444444333 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   9.2e-07   0.00087       1      41 [.      15      56 ..      15      73 .. 0.86
   2 ?    4.0   0.0     0.026        25     203     261 ..      75     135 ..      59     144 .. 0.87
   3 ?   -2.7   0.0       2.8   2.7e+03     375     416 ..     393     434 ..     389     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.2e-07
                                   HHHHHHHHHHHHTT.EEEEEEESSSSSBTTS-EEEET...TEEEE CS
                  Amino_oxidase  1 laGLaaArqLlsaG.fdVtvlEardrvGGRirtvrsd...Gylie 41
                                   ++G+++A +LlsaG  dV ++E  d vGG   t+r++   G +++
  gi|121636815|ref|YP_977038.1| 15 MSGMCVAITLLSAGiTDVCIYEKADDVGG---TWRDNtypGLTCD 56
                                   8****************************...5555544577776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                                    CEETTH.THHHHHHHHH.TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                  Amino_oxidase 203 llprgG.lsqlpealae.elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                    ++ rgG ++   + +ae + ++ +ir+++ V + + +++   +++ +g++ ++D  ++++ 
  gi|121636815|ref|YP_977038.1|  75 MFSRGGeIQDYLRGIAErYGLRHRIRFGATVVSARFDDGRWVLRTDSGTESTVDFLISATG 135
                                    55577778888999999888899*************9999******************986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.8
                                    GTSSTCSEEEEEECCTETTTSSSEEE.BTTH.HHHHHHHHHCH CS
                  Amino_oxidase 375 eevpepkatlvtrWhtdplargsysyvsvgp.ghedydplakp 416
                                    ++v e++a ++++W  +++++g + ++ + +  +e+y  + + 
  gi|121636815|ref|YP_977038.1| 393 TAVAESQAEHIVQWI-KRWRHGEFDTMEPKSaATEAYNTVLRA 434
                                    567788888899998.999999999998887555555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2    0.0023       2.2       2      34 ..       8      41 ..       7      49 .. 0.85
   2 !   13.0   0.0   0.00012      0.11       1      33 [.     171     203 ..     171     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                                   EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkl 34
                                   v+vvG+G +g+ +A +l   g  +V + e +d +
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGiTDVCIYEKADDV 41
                                   89***************99996788888887766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdk 33 
                                    +++v+G G +g+ l + la  + kVt+++r  +
  gi|121636815|ref|YP_977038.1| 171 RIAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQ 203
                                    79**************************99876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   5.8e-07   0.00055       2      37 ..       8      44 ..       7      46 .. 0.95
   2 ?   -3.5   0.0       4.2     4e+03     135     182 ..     214     263 ..     173     279 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.8e-07
                                   EEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl.kvavvekeqefgga 37
                                   v V+G+G++G++ A+++  aG  +v++ ek++ +gg+
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGItDVCIYEKADDVGGT 44
                                   89*****************************999986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                                    ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT...EEEEEEEEET CS
                  FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedg...rvtGavvenp 182
                                     +l+  ++ + + + s+   +  + ++t+a++L    g   + +Gav++ +
  gi|121636815|ref|YP_977038.1| 214 SKLARVFHRAFPCLGSLAYKAYSLSFETFAVALSN-PGlhrKLVGAVCRAS 263
                                    44444444555555555444477778888888844.555667778777744 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00081      0.76      14      43 ..       7      36 ..       3      46 .. 0.91
   2 ?    4.1   0.1     0.049        46      12      47 ..     169     203 ..     162     206 .. 0.83
   3 ?   -0.8   0.0       1.5   1.5e+03      72      85 ..     323     336 ..     312     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                                   EEEEES-SHHHHHHHHHHHCCT-CEEEEEE CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaN 43
                                   +v ++GaG+ +  va  Ll++g+++v++  
  gi|121636815|ref|YP_977038.1|  7 TVAVVGAGMSGMCVAITLLSAGITDVCIYE 36
                                   799***********************9975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.049
                                    T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                   Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                    ++++ +iG+G ++ +++  L+     kv+ + Rt +
  gi|121636815|ref|YP_977038.1| 169 GRRIAVIGTGSTGVQLVCGLAGVA-GKVTMFQRTAQ 203
                                    789**************9999654.55999999975 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                                    HHHT-SEEEE-SSS CS
                   Shikimate_DH  72 llaeadvvisatas 85 
                                    +l+e+dv++ at+ 
  gi|121636815|ref|YP_977038.1| 323 VLHEVDVIVLATGF 336
                                    799********985 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.2e-05      0.03       3      35 ..       7      39 ..       5      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   +V++VGaG +G+  a  L +aG+  v++   ++
  gi|121636815|ref|YP_977038.1|  7 TVAVVGAGMSGMCVAITLLSAGITDVCIYEKAD 39
                                   599********************9777755554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.014        13       2      30 ..       8      37 ..       7      48 .. 0.85
   2 ?    6.1   0.2      0.01       9.9       2      33 ..     172     203 ..     171     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                   EEEE--SHHHHHHHHHHHTTT.--EEEE-S CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaeng.hevrlwvr 30
                                   +av+GaG+ G  +A++l ++g  +v+++ +
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGiTDVCIYEK 37
                                   9***************99998677887765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-HH CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreee 33 
                                    iav+G+Gs G  l + la  + +v++++r ++
  gi|121636815|ref|YP_977038.1| 172 IAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQ 203
                                    9**************************99875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0011         1       2      36 ..       8      42 ..       7      51 .. 0.89
   2 ?   -2.7   0.3       2.5   2.4e+03       2      28 ..     172     198 ..     171     208 .. 0.78
   3 ?    3.4   0.0     0.036        34     109     150 ..     300     336 ..     285     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtia 36
                                   v V+G+G++G+  A+++  +G+  + i +k d+++
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGITDVCIYEKADDVG 42
                                   89*******************98888878888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                    EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                    + ViG G  G+     +a    kv+++
  gi|121636815|ref|YP_977038.1| 172 IAVIGTGSTGVQLVCGLAGVAGKVTMF 198
                                    7899***99998888888777777777 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.036
                                    TTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 109 pnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    +++e++++ +++++      +g+vt+dg   + +++v+atG 
  gi|121636815|ref|YP_977038.1| 300 DDVELVTAGIDHVEH-----RGIVTDDGVLHEVDVIVLATGF 336
                                    667777777777766.....9********************5 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.23   2.2e+02      38      67 ..       7      37 ..       4      49 .. 0.84
   2 ?    6.9   0.0    0.0038       3.5      29      70 ..     162     203 ..     148     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                                   EEEEES-SHHHHHHHHHHHHTT-.EEEEESS CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgm.kviaydr 67
                                   tv+++G+G  G  va +l + g+ +v +y++
  gi|121636815|ref|YP_977038.1|  7 TVAVVGAGMSGMCVAITLLSAGItDVCIYEK 37
                                   89*************9999888867777765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                                    GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                     +   l g+++++iG+G+ G ++   l+++  kv++++r+ +
  gi|121636815|ref|YP_977038.1| 162 DHTVPLLGRRIAVIGTGSTGVQLVCGLAGVAGKVTMFQRTAQ 203
                                    55667889****************************999865 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00012      0.12       2      36 ..       7      42 ..       6      44 .. 0.87
   2 ?   -1.3   0.0      0.71   6.7e+02     124     169 ..      97     141 ..      72     142 .. 0.73
   3 ?   -4.5   0.5       6.5   6.1e+03       3      16 ..     172     185 ..     171     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                   SEEEE--SHHHHHHHHHHHHTT.--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrg.krVlllekakklg 36
                                   +v+v+G+G +G+  Ai++ ++g  +V ++eka+ +g
  gi|121636815|ref|YP_977038.1|  7 TVAVVGAGMSGMCVAITLLSAGiTDVCIYEKADDVG 42
                                   699***************6666378******99887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.71
                                    -EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                    HI0933_like 124 vklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                     ++r   +v s++  +dg+  ++t+s++e + d l+ AtG l  P+
  gi|121636815|ref|YP_977038.1|  97 HRIRFGATVVSARF-DDGRWVLRTDSGTESTVDFLISATGVLHHPR 141
                                    35667777888755.6666999**9***************887776 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 6.5
                                    EEEE--SHHHHHHH CS
                    HI0933_like   3 viviGgGaAGlmaA 16 
                                    ++viG G  G+   
  gi|121636815|ref|YP_977038.1| 172 IAVIGTGSTGVQLV 185
                                    789****9997554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0013       1.2       1      31 [.       7      38 ..       7      49 .. 0.82
   2 ?    1.8   0.6       0.2   1.9e+02       2      32 ..     172     202 ..     171     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                   EEEEE--SCCHHHHHHHHHHTT-E.EEEE-S- CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagle.Vvlvdis 31
                                   +vav+GaG+ G  +a  ++sag++ V +++ +
  gi|121636815|ref|YP_977038.1|  7 TVAVVGAGMSGMCVAITLLSAGITdVCIYEKA 38
                                   69********************8526666555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdise 32 
                                    +aviG+G  G ++   +a    +V+++++++
  gi|121636815|ref|YP_977038.1| 172 IAVIGTGSTGVQLVCGLAGVAGKVTMFQRTA 202
                                    9************999999999999988765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.054        51       1      23 [.       8      30 ..       8      47 .. 0.86
   2 ?    4.9   0.9      0.02        19       1      31 [.     172     202 ..     172     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.054
                                   EEEES-SHHHHHHHHHHHHHTHC CS
                           ApbA  1 iailGaGaiGsllaakLakagad 23
                                   +a++GaG  G ++a +L  ag +
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGIT 30
                                   69***************998865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr 31 
                                    ia++G+G+ G  l + La  + +vt+  r++
  gi|121636815|ref|YP_977038.1| 172 IAVIGTGSTGVQLVCGLAGVAGKVTMFQRTA 202
                                    89***************986668**999987 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.037        35      21      45 ..       8      32 ..       5      38 .. 0.89
   2 ?   -2.6   0.7         3   2.8e+03      19      39 ..     170     190 ..     162     197 .. 0.82
   3 ?    3.7   0.0     0.035        33     109     218 ..     301     421 ..     283     444 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.037
                                   EEEE--SHHHHHHHHHHHHHTTTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 21 vllvGaGglGsellknLalsGvgkl 45
                                   v++vGaG  G  ++ +L  +G+  +
  gi|121636815|ref|YP_977038.1|  8 VAVVGAGMSGMCVAITLLSAGITDV 32
                                   89*******************9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                                    SEEEEE--SHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  19 skvllvGaGglGsellknLal 39 
                                     +++++G G  G  l+  La+
  gi|121636815|ref|YP_977038.1| 170 RRIAVIGTGSTGVQLVCGLAG 190
                                    6899*******9998877765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.035
                                    T-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE.EE..CCS-ECTSS-TGGS.EECCCCEEHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 109 svDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi.ip..gktgcyeCldpsstedptekkvplctsiagn 185
                                    +v lV  ++D +e r +v +  v +++ +i   + gf+++++++ ++  g++g+  +     ++d + +  +++ +i g 
  gi|121636815|ref|YP_977038.1| 301 DVELVTAGIDHVEHRGIVTDDGVLHEVDVIV-LATGFDSHAFFRpMQltGRDGIRIDDV---WQDGPHAH-QTV-AIPGF 374
                                    6789999**************9999999999.999*****9999643655555544443...22222222.222.23443 PP

                                    ..........E-B-HHHHHHHHHHHHHHHHHHH....TTBCGGGCCE CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                           ThiF 186 ..........ipaiatttavvaglaalellkll....sgkeklensl 218
                                              +p+  + ++ va  +a ++++++    +g+ ++++ +
  gi|121636815|ref|YP_977038.1| 375 pnffmmlgphSPVGNFPLTAVAESQAEHIVQWIkrwrHGEFDTMEPK 421
                                    44444444588888888999999999999999976664444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 3672.80
//
Query:       gi|121636816|ref|YP_977039.1|  [L=325]
Description: hypothetical protein BCG_0945c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-56  191.3   0.1    2.3e-56  190.7   0.1    1.3  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.1   1.3e-60   2.3e-56       2     185 ..      19     196 ..      18     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 1.3e-60
                                    HHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   2 lgvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaals 81 
                                    l vaaarale+++a d+l  Dp+ae +++aag e+  +  d++l ++     +    +++ +++ +Rtr+fd+++ +a+ 
  gi|121636816|ref|YP_977039.1|  19 LLVAAARALETQKA-DPLAIDPYAEVFCRAAGGEW-ADVLDGKLPDHY--LTTGDFGEHFVNFQGARTRYFDEYFSRAT- 93 
                                    579**********9.******************97.888888888876..34667899*********************. PP

                                    CTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-TT CS
                            LCM  82 aagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdpe 161
                                    aag++qvViL+AGlD+ra+Rl+w+ g+++fE+D+p+vl+fK+++l++ +++p+a++r v+vDlr d+w+ aL ++gfd++
  gi|121636816|ref|YP_977039.1|  94 AAGMKQVVILAAGLDSRAFRLQWPIGTTIFELDRPQVLDFKNAVLADYHIRPRAQRRSVAVDLR-DEWQIALCNNGFDAN 172
                                    7***************************************************************.*************** PP

                                    SEEEEEEESSGGGS-HHHHHHHHH CS
                            LCM 162 kptawvaeGvlvYLtpeasdalle 185
                                    +p+aw+aeG+lvYL++ea+++l+ 
  gi|121636816|ref|YP_977039.1| 173 RPSAWIAEGLLVYLSAEAQQRLFI 196
                                    **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2165.29
//
Query:       gi|121636817|ref|YP_977040.1|  [L=393]
Description: LuxR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-07   30.9   1.0    3.4e-06   27.6   1.0    2.3  1  AAA_16       AAA ATPase domain
     0.0056   16.3   0.0      0.013   15.1   0.0    1.6  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.028   14.3   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
      0.019   14.9   1.5       0.22   11.4   1.7    2.4  2  NACHT        NACHT domain
      0.024   14.9   0.0      0.061   13.6   0.0    1.7  1  AAA_22       AAA domain
      0.072   12.8   0.0       0.13   11.9   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
       0.11   12.0   0.0       0.16   11.4   0.0    1.2  1  PhoH         PhoH-like protein
       0.13   11.4   0.0       0.22   10.7   0.0    1.4  1  NB-ARC       NB-ARC domain
       0.16   11.9   0.0       0.34   10.8   0.0    1.5  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   1.0   1.7e-09   3.4e-06       2     127 ..      43     155 ..      42     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.7e-09
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81 
                                    +vGR++el+ ++++l++      +lv l+G+ G+GKs+l+ ++  ++  +   f++g++d          la++ +r + 
  gi|121636817|ref|YP_977040.1|  43 FVGRKAELNDVRRLLSD-----KRLVTLTGPDGMGKSRLALQIGAQIAHE---FTYGRWDCD--------LATVTDR-DC 105
                                    9*************994.....49************************99...999999988........6666644.44 PP

                         AAA_16  82 lrqlldeaesaeleawrekleeala....avpelagaea.....srllellkrll 127
                                    +     +a    +++   ++++ ++    a              ++ll+++++++
  gi|121636817|ref|YP_977040.1| 106 VSISMLNALGLPVQPGLSAIDTLVGvindARVL-----LvldhcEHLLDACAAII 155
                                    444444444445555555555555522222222.....12444466666666666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.5e-06     0.013      26      59 ..      53      86 ..      41     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.5e-06
                         AAA_25 26 vkgllpagelallaGapgtGKttlaldlalavat 59
                                   v++ll  + l+ l+G+ g GK+ lal++++ +a 
  gi|121636817|ref|YP_977040.1| 53 VRRLLSDKRLVTLTGPDGMGKSRLALQIGAQIAH 86
                                   567888999**********************994 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.028       1      40 [.      43      80 ..      43      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                       ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkei 40
                                   F+ R++el++++++l+   ++ + ++Gp g GK++L  +i
  gi|121636817|ref|YP_977040.1| 43 FVGRKAELNDVRRLLSD--KRLVTLTGPDGMGKSRLALQI 80
                                   999************99..89999************9998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   0.00011      0.22       1     130 [.      61     174 ..      61     199 .. 0.78
   2 ?   -2.2   0.0       1.7   3.4e+03     131     131 ..     341     341 ..     268     371 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                    SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                          NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavllel 79 
                                    rlv l+G+ G+GK+ L+ ++  ++a++  ++          l++++++  +  s+ + l  + ++  +++++   v + +
  gi|121636817|ref|YP_977040.1|  61 RLVTLTGPDGMGKSRLALQIGAQIAHEFTYGRW-----DCDLATVTDRDCVsISMLNALGLPVQPGLSAIDT--LVGVIN 133
                                    7899*********************99999953.....3444454444322357777777777777788888..344557 PP

                                    CCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECC CS
                          NACHT  80 perlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpr 130
                                      r+Ll+lD  + l +   +         + +l+r   +p+ ++l t++  
  gi|121636817|ref|YP_977040.1| 134 DARVLLVLDHCEHLLDACAA--------IIDSLLRS--CPRLTILTTSTEA 174
                                    899******99999987666........99999999..9999999888765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                    C CS
                          NACHT 131 a 131
                                    +
  gi|121636817|ref|YP_977040.1| 341 R 341
                                    1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-05     0.061       3     103 ..      58     147 ..      54     174 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                         AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst..sskdllrellralglelkaerlsseell 79 
                                    ++++++++tG+ G+GK++l+ ++  q          +  ++ + ++   t  +++ +   +l+algl+           +
  gi|121636817|ref|YP_977040.1|  58 SDKRLVTLTGPDGMGKSRLALQIGAQIA--------HEFTYgRWDCDLATvtDRDCVSISMLNALGLPVQP----GLSAI 125
                                    578999*****************99984........44555555555555413333466777777765555....33333 PP

                         AAA_22  80 ealeqalraravielliiDEaqhl 103
                                    ++l   +++++v  ll++D  +hl
  gi|121636817|ref|YP_977040.1| 126 DTLVGVINDARV--LLVLDHCEHL 147
                                    444444444444..5555555553 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.7e-05      0.13      44      71 ..      57      84 ..      38      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialgvea 71
                                   +++k  + l+Gp G+GKs la  +g + 
  gi|121636817|ref|YP_977040.1| 57 LSDKRLVTLTGPDGMGKSRLALQIGAQI 84
                                   56777899****************9885 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05      0.16      12      47 ..      53      88 ..      44      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
                                   HHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                           PhoH 12 ylealkkndivfaiGpaGtGKtylavalavealkkk 47
                                   + + l+++ +v+ +Gp G GK+ la+++++++ ++ 
  gi|121636817|ref|YP_977040.1| 53 VRRLLSDKRLVTLTGPDGMGKSRLALQIGAQIAHEF 88
                                   556788999********************9988765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.22      19     112 ..      59     144 ..      46     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                    CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEE.EEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHH CS
                         NB-ARC  19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvaw.vvvsktdkseeiletilkeLslseddleekeeveslkrklv 97 
                                    ++ +v+l G  G+GK+ la qi  +   + ++F    w + ++   +   +  ++l+ L+l        + + s+ + lv
  gi|121636817|ref|YP_977040.1|  59 DKRLVTLTGPDGMGKSRLALQIGAQ---IAHEFTYGRWdCDLATVTDRDCVSISMLNALGLP------VQPGLSAIDTLV 129
                                    34489*****************888...9999996666477777777777888888888777......223334668888 PP

                                    HHCCCTTEEEEEEEE CS
                         NB-ARC  98 rlLltkrfllvlDDV 112
                                     ++++ r+llvlD  
  gi|121636817|ref|YP_977040.1| 130 GVINDARVLLVLDHC 144
                                    888888888888864 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.34      85     119 ..      45      80 ..      29      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                    TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                     +k++l+++++ll+d ++++l G+ G+GKS L  ++
  gi|121636817|ref|YP_977040.1|  45 GRKAELNDVRRLLSDkRLVTLTGPDGMGKSRLALQI 80 
                                    5678999*******989999**********997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2689.77
//
Query:       gi|121636818|ref|YP_977041.1|  [L=505]
Description: hypothetical protein BCG_0947 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-94  314.1   6.4    1.3e-93  313.6   6.4    1.3  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    1.2e-30  106.4   0.0    2.5e-30  105.4   0.0    1.5  1  DUF1298         Protein of unknown function (DUF1298)
     0.0017   17.1   0.0      0.065   11.9   0.0    2.1  2  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.6   6.4   2.2e-97   1.3e-93       1     264 []      32     296 ..      32     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 313.6 bits;  conditional E-value: 2.2e-97
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    ++++Dalfl++e++++p+hvgalavl++p++g+g+ +lr++++a+ +r+++ap++r++++++ ++l++++W++++++Dld
  gi|121636818|ref|YP_977041.1|  32 MAAADALFLWAETPTRPLHVGALAVLSQPDNGTGR-YLRKVFSAAVARQQVAPWWRRRPHRSLTSLGQWSWRTETEVDLD 110
                                    6899*******************************.9******************************************* PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yHvR +alp +++++el++lvs+L++ +LDrsrPlW+v +iEGl ggr+A+++kvHHAl+DGv++++ll+r++++dp+++
  gi|121636818|ref|YP_977041.1| 111 YHVRLSALPPRAGTAELWALVSELHAGMLDRSRPLWQVDLIEGLPGGRCAVYVKVHHALADGVSVMRLLQRIVTADPHQR 190
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdr..srtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRr 238
                                    ++p+ ++vp++++  ++t++r s++  +l++g+ +++++v+g+v+++++++++a+++rs++l++aap+tpln+p+++aR+
  gi|121636818|ref|YP_977041.1| 191 QMPTLWEVPAQASvaKHTAPRGSSRPLTLAKGVLGQARGVPGMVRVVADTTWRAAQCRSGPLTLAAPHTPLNEPIAGARS 270
                                    **************9***************************************************************** PP

                 WES_acyltransf 239 faaaslpLadvkavakalgvtiNDvv 264
                                    +a++s+p++++++va+++++tiNDvv
  gi|121636818|ref|YP_977041.1| 271 VAGCSFPIERLRQVAEHADATINDVV 296
                                    *************************7 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   4.1e-34   2.5e-30       2     144 ..     341     486 ..     340     487 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 4.1e-34
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaal.ikrl...lsnttlviSNvp 77 
                                    GN+ig+++++L+++la P+erl++++++m++ K   +  + +++l++ ++l  a++a a+ + r+   l+  +++iSNvp
  gi|121636818|ref|YP_977041.1| 341 GNKIGTLMCSLATHLASPVERLSAIRASMRDGKAAIAGRSRNQALAM-SALGAAPLALAMaLGRVpapLRPPNVTISNVP 419
                                    9**********************************************.999999998888444448889*********** PP

                        DUF1298  78 GPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    GPq  ly++Ga+l+a+y ++  ++g alnit+   ++++++gl++++++vp ++ l+d+l+++le l
  gi|121636818|ref|YP_977041.1| 420 GPQGALYWNGARLDALYLLSAPVDGAALNITCSGTNEQITFGLTGCRRAVPALSILTDQLAHELELL 486
                                    ****************************************************************976 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.1e-05     0.065     115     155 ..     142     183 ..     115     204 .. 0.84
   2 !    3.0   0.0    0.0054        32     238     266 ..     279     307 ..     249     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                                    CS-SEEEEEEE.SSTTEEEEEEEEECCT--TTTHHHHHHHHH CS
                   Condensation 115 kgpLfraalfk.iaenrlllllsvHHiivDGvSlgillrdla 155
                                    + pL+++ l++ +   r  ++++vHH ++DGvS+  ll+ + 
  gi|121636818|ref|YP_977041.1| 142 SRPLWQVDLIEgLPGGRCAVYVKVHHALADGVSVMRLLQRIV 183
                                    44999999997345678899*************988888765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0054
                                    HHHHHHHHSTSS-HHHHHHHHHHHHHHHH CS
                   Condensation 238 eklrklakeqgvtlndvllaalgllLsky 266
                                    e+lr++a+  ++t+ndv la+ g +L  y
  gi|121636818|ref|YP_977041.1| 279 ERLRQVAEHADATINDVVLAMCGGALRAY 307
                                    689*******************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3645.98
//
Query:       gi|121636819|ref|YP_977042.1|  [L=431]
Description: type II citrate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-133  445.5   0.0   1.6e-133  445.3   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.3   0.0  8.7e-138  1.6e-133       1     361 []      48     414 ..      48     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 445.3 bits;  conditional E-value: 8.7e-138
                                    GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHC CS
                   Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealea 80 
                                    g+ ++aa++++i+++dg++g+lrYRGy+i++La eks+f ev+ylL++gelP++++l++f+ +++++++l+e++++ ++ 
  gi|121636819|ref|YP_977042.1|  48 GFANTAAAKSSITYIDGDAGILRYRGYPIDQLA-EKSTFIEVCYLLIYGELPDTDQLAQFTGRIQRHTMLHEDLKRFFDG 126
                                    7889*****************************.8********************************************* PP

                                    SSTTS-HHHHHHHHHHHHHHHSTT.CTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.--.---TTSSHHHHHHHH CS
                   Citrate_synt  81 lpkdahpmavlraavsalsaddee.seakeeseeaalrdalkliAklptiaaaiyrarlgrepl.epddklsyaenflym 158
                                    +p++ahpm vl+++v+alsa++++   +  + + ++  ++++l+Aklptiaa++y+ ++g+ p+ +pd++l+++enfl++
  gi|121636819|ref|YP_977042.1| 127 FPRNAHPMPVLSSVVNALSAYYQDaL-DPMD-NGQVELSTIRLLAKLPTIAAYAYKKSVGQ-PFlYPDNSLTLVENFLRL 203
                                    **********************9742.3333.3445555677*****************97.777***99********** PP

                                    HHS.....S---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSS CS
                   Citrate_synt 159 lrg.....kkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleeigs 233
                                    ++g     +++d+e++++ld++++lhaDHe+n+ST ++r+v+S++a+l+++i++gi+al+Gplhggan+avl+mle i++
  gi|121636819|ref|YP_977042.1| 204 TFGfpaepYQADPEVVRALDMLFILHADHEQNCSTSTVRLVGSSRANLFTSISGGINALWGPLHGGANQAVLEMLEGIRD 283
                                    **9999**99********************************************************************65 PP

                                    GG..GHHHHHHHHHHTTT.S--TTBC-SSSSS--HHHHHHHHHHHHHHTC.HTHHHHHHHHHHHHHHHHHHHHCHHGCT- CS
                   Citrate_synt 234 aev.eveeylekvlakek.erlpGfGHrvykksDpRakilkelaeelaee.kgkdpllklaeeleevapevlkekeeknl 310
                                    +   +v+e+++kv+++e   +l+GfGHrvyk++DpRa+i+ke a+++ ++ +g+d ll +a+elee+a  + ++ e ++l
  gi|121636819|ref|YP_977042.1| 284 S-GdDVSEFVRKVKNREAgVKLMGFGHRVYKNYDPRARIVKEQADKILAKlGGDDSLLGIAKELEEAALTDDYFIE-RKL 361
                                    5.34***********98459**************************99999*************************.*** PP

                                    EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH..HT------E CS
                   Citrate_synt 311 ypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql..adnkiiRPr 361
                                    ypNvDfy+g++yralg+p+++ftvlfa++R+ Gw+Ah++e     d+ki RPr
  gi|121636819|ref|YP_977042.1| 362 YPNVDFYTGLIYRALGFPTRMFTVLFALGRLPGWIAHWREMHdeGDSKIGRPR 414
                                    ****************************************75555699****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2974.11
//
Query:       gi|121636820|ref|YP_977043.1|  [L=535]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-09   35.5   0.8    8.8e-09   35.5   0.8    2.7  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-06   27.6   0.9    6.4e-06   25.6   1.0    1.8  2  FAD_binding_3   FAD binding domain
    1.6e-06   27.5   0.2      3e-06   26.7   0.2    1.3  1  Thi4            Thi4 family
    3.1e-06   26.5   0.6    4.8e-06   25.9   0.6    1.2  1  GIDA            Glucose inhibited division protein A
    3.1e-06   27.0   8.4    0.00069   19.3   3.4    3.0  3  DAO             FAD dependent oxidoreductase
    5.9e-06   25.7   2.2    0.00034   19.9   1.3    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-05   24.5   3.4    1.6e-05   24.5   3.4    1.8  2  FAD_oxidored    FAD dependent oxidoreductase
    1.9e-05   23.9   4.0    1.9e-05   23.9   4.0    1.9  2  FAD_binding_2   FAD binding domain
    3.6e-05   23.2   1.6      0.039   13.2   0.6    2.3  2  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00058   18.7   0.7    0.00085   18.1   0.7    1.2  1  HI0933_like     HI0933-like protein
    0.00078   20.0   0.8     0.0043   17.6   1.2    2.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.012   14.5   0.8      0.018   13.9   0.8    1.2  1  Trp_halogenase  Tryptophan halogenase
      0.044   12.8   1.1       0.12   11.4   0.7    1.8  2  Lycopene_cycl   Lycopene cyclase protein
      0.062   13.0   0.0       0.11   12.1   0.0    1.4  1  CHASE2          CHASE2 domain
        9.9    6.0   6.3        1.8    8.4   0.6    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.8   7.3e-12   8.8e-09       1      44 [.      12      56 ..      12      72 .. 0.89
   2 ?   -2.2   0.2       4.4   5.2e+03       9      22 ..     244     257 ..     237     264 .. 0.55
   3 ?   -3.3   0.0       9.6   1.2e+04      32      51 ..     464     489 ..     449     497 .. 0.60

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.3e-12
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TTCE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pgvr 44
                                   +vG+G  GlvaA++La+ag++v lle+  ++GG a s++  +gv 
  gi|121636820|ref|YP_977043.1| 12 VVGGGHNGLVAAAYLARAGLRVRLLERLAQTGGAAVSIQAfDGVE 56
                                   8***********************************998767743 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                                    HHHHHHHHCCTEEE CS
                  NAD_binding_8   9 lvaAylLakagfdv 22 
                                    +++A ++a++g+++
  gi|121636820|ref|YP_977043.1| 244 SALATAAARHGAEI 257
                                    23344455667665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.6
                                    SGGG-EECE......TTCEECTS--- CS
                  NAD_binding_8  32 GGraasyev......pgvrvdygahi 51 
                                    GG++    +      ++ ++d++a+ 
  gi|121636820|ref|YP_977043.1| 464 GGNIFHGALswpfadNDDPLDTPARQ 489
                                    34444443333334334666666665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.0   5.4e-09   6.4e-06       2      36 ..       8      42 ..       7      47 .. 0.94
   2 ?   -1.4   0.0      0.88     1e+03     107     158 ..     242     291 ..     237     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.4e-09
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                    dV++VG+G  Gl++a  L++aG rv+l+e+ ++t
  gi|121636820|ref|YP_977043.1|  8 FDVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQT 42
                                   69*****************************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.88
                                    HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEE CS
                  FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYl 158
                                    ++ +L+ +a+++g+++  +++v +l  d +g      d ++g+e  vr +++
  gi|121636820|ref|YP_977043.1| 242 VTSALATAAARHGAEIVTGADVFAL--DPDGTVRYHSDGSDGAEHLVRGRFV 291
                                    6778999999999999999999855..5555334555777788877877776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   2.5e-09     3e-06      18      64 ..       8      52 ..       2      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.5e-09
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64
                                    Dvv+vG+G  GL aa yla++ +l+v +ler ++  GGa    q f
  gi|121636820|ref|YP_977043.1|  8 FDVVVVGGGHNGLVAAAYLARA-GLRVRLLER-LAQTGGAAVSIQAF 52
                                   6*********************.********7.66666666666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.6     4e-09   4.8e-06       1      46 [.       9      54 ..       9      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4e-09
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsigg 46
                                   dv+V+GgGh G+ AA+ +ar+G++v L+    +t +  +   ++ g
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQTGGAAVSIQAFDG 54
                                   79**************************777777777776666666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.4   5.8e-07   0.00069       1      36 [.       9      45 ..       9      51 .. 0.90
   2 ?    0.6   0.0      0.28   3.4e+02     237     296 ..      75     139 ..      45     166 .. 0.64
   3 !    7.7   0.1     0.002       2.4     146     180 ..     240     273 ..     223     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.8e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                   dvv++GGG  Gl +A +Lar+g  V lle+  + g ga
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYLARAGlrVRLLERLAQTG-GA 45
                                   9****************************987666.54 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                    SGCSEEEEEEEETTTTEEEEEETTSE..EEEEESSEEETTCSS...TSCSHHHHHHHHHHHHHHS CS
                            DAO 237 paailpvpetdddgrgvyvtprkdgr..vlvGgtadeesgddd...pevdeedidellealrklf 296
                                    +++++pv+  ++++ ++   p   gr  +l+G+t++++++      +++d++ ++++++++r + 
  gi|121636820|ref|YP_977043.1|  75 ADLGAPVRLARRPFSSYTPAPATAGRsgLLIGPTGEPRAAHLAaigAAPDAHGFAAFYRRCRLVT 139
                                    34777777677777776666653343339999999643333336667888888888888887555 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.002
                                    HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEE CS
                            DAO 146 akltaalaraaealGveilegtevtgleeedgkvw 180
                                      +t ala aa+++G+ei++g+ v +l ++dg v 
  gi|121636820|ref|YP_977043.1| 240 GSVTSALATAAARHGAEIVTGADVFAL-DPDGTVR 273
                                    57899********************99.5555543 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.3   2.8e-07   0.00034       1      30 [.       8      37 ..       8      58 .. 0.82
   2 ?    4.2   0.0     0.017        21     186     241 ..     243     299 ..     238     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve 30
                                   +dvvv+GgG+ Gl aa +la+ag++v l+e
  gi|121636820|ref|YP_977043.1|  8 FDVVVVGGGHNGLVAAAYLARAGLRVRLLE 37
                                   589999999999999999999999999996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHTTEEEEESCEEEEEEETTE.EEEEEETTSCEEEESEEEE-S-EEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 186 saaleealekeGvevklgtsvkeidgnge.klevvledgeeidadlvvvavGvrpst 241
                                    + al+ a  ++G e+++g+ v ++d++g+ +++   +dg e  ++  +v vGv+p  
  gi|121636820|ref|YP_977043.1| 243 TSALATAAARHGAEIVTGADVFALDPDGTvRYHSDGSDGAEHLVRGRFVLVGVTPAV 299
                                    56778889999*****************96666899999999***********9975 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   3.4   1.3e-08   1.6e-05       1      40 [.       9      48 ..       9      62 .. 0.95
   2 ?   -3.9   1.7       5.3   6.3e+03       5      25 ..     237     257 ..     234     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.3e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                   DvvVvGGg  G++AA   araG +v L+e+    GG + s
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQTGGAAVS 48
                                   9***********************************9865 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.3
                   FAD_oxidored   5 vGGgpaGvaAAiaAaraGakv 25 
                                     G g+   a A aAar+Ga+ 
  gi|121636820|ref|YP_977043.1| 237 GGMGSVTSALATAAARHGAEI 257
                                    4667777777889*****976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.0   1.6e-08   1.9e-05       1      39 [.       9      47 ..       9      60 .. 0.94
   2 ?   -1.9   0.1       1.1   1.3e+03     106     151 ..     153     192 ..     117     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                   Dv+V+G+G  GL+AA+ +a+aGl+v ++e   ++gga++
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQTGGAAV 47
                                   9**********************************9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    CCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHH CS
                  FAD_binding_2 106 tedgpvdvrelGglsatartlhdaadarretlvtghallarlvesa 151
                                    +e+ + d+ e Gg+ a    +  + d+       gha++ ++++ +
  gi|121636820|ref|YP_977043.1| 153 REQARRDIVEYGGHEAA-AAWQAMVDE-----PIGHAIAGAVANDL 192
                                    33336666677777777.344435554.....46666666666555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.6   3.3e-05     0.039       3      33 ..      19      49 ..      19      82 .. 0.90
   2 !    8.8   0.0   0.00075      0.89     199     276 ..     228     306 ..     172     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHHTTEEEEEEESSSSSBTTS-EE CS
                  Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvGGRirtv 33
                                   GL+aA +L++aG++V +lE   ++GG + ++
  gi|121636820|ref|YP_977043.1| 19 GLVAAAYLARAGLRVRLLERLAQTGGAAVSI 49
                                   9*************************88776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00075
                                    TSCCCEE.TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE.....EESEEEE-S-HHHHHSSEE CS
                  Amino_oxidase 199 ggslllp.rgGlsqlpealae..elrgldirlntrVkeikregdgvtvtledgevv.....eaDaVvvTvplgvlkailf 270
                                    g +++ +  gG++++  ala    ++g +i +++ V  ++  +++v+ +  dg++      +++ V+v v ++vl+    
  gi|121636820|ref|YP_977043.1| 228 GTGVWHVpIGGMGSVTSALATaaARHGAEIVTGADVFALDP-DGTVRYHS-DGSDGaehlvRGRFVLVGVTPAVLA---- 301
                                    4444433589******************************9.55566664.455555779****************.... PP

                                    ESCC.SH CS
                  Amino_oxidase 271 sPpl.pd 276
                                      +l  +
  gi|121636820|ref|YP_977043.1| 302 --SLlGE 306
                                    ..33332 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.7   7.1e-07   0.00085       1      36 [.       8      43 ..       8      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.1e-07
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +dv+v+GgG  Gl aA+ +a++g rV lle+  ++g
  gi|121636820|ref|YP_977043.1|  8 FDVVVVGGGHNGLVAAAYLARAGLRVRLLERLAQTG 43
                                   59****************************988776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.2   3.6e-06    0.0043       2      33 ..      10      41 ..       9      49 .. 0.92
   2 ?   -2.0   0.0       4.8   5.7e+03      44      70 ..     244     270 ..     238     275 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                   vvvvGgG  gl +A++la+ g +V ++er  +
  gi|121636820|ref|YP_977043.1| 10 VVVVGGGHNGLVAAAYLARAGLRVRLLERLAQ 41
                                   8***************************9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                    HHHHHHHHHTTEEEECSEEEEEEEEET CS
                      Pyr_redox  44 kilqeklekngievllntkveeiegse 70 
                                    ++l++   ++g e+++++ v +++ ++
  gi|121636820|ref|YP_977043.1| 244 SALATAAARHGAEIVTGADVFALDPDG 270
                                    556666777888888888887777554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   1.5e-05     0.018       1      32 [.       9      37 ..       9      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                   ++v+vGGG  G +aAa+la+a+   l+v l+e
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYLARAG---LRVRLLE 37
                                   69*******************9...8999988 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7    0.0001      0.12       1      31 [.       9      37 ..       9      43 .. 0.93
   2 ?   -2.3   0.0       1.5   1.7e+03     146     166 ..      43      63 ..      39      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                   Dvvv+G+G  gl  Aa l  a++gl+v l+e
  gi|121636820|ref|YP_977043.1|  9 DVVVVGGGHNGLVAAAYL--ARAGLRVRLLE 37
                                   9*****************..9******9997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                  Lycopene_cycl 146 karrlglQtfyGvevevdnpp 166
                                    ++ ++++Q f Gvev +++  
  gi|121636820|ref|YP_977043.1|  43 GGAAVSIQAFDGVEVALSRYS 63 
                                    677899*********988765 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.5e-05      0.11     100     222 ..     112     326 ..      28     352 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                         CHASE2 100 aaaglGfvnvvpDaDg...vvRr.pll.veselipsla....................lalalrylkae........... 143
                                     aa+l+ + ++pDa g   ++Rr  l+ ++   +p+l                      a+a      +           
  gi|121636820|ref|YP_977043.1| 112 RAAHLAAIGAAPDAHGfaaFYRRcRLVtARL--WPTLIeplrtreqarrdiveyggheAAAAW-----Qamvdepighai 184
                                    4466666666777777555577755553333..333331211222222222222222212222.....022222333444 PP

                         CHASE2 144 ...............................................klrlpvdesgg...lllnyrgg.sktf.ptvsl 171
                                                                                     ++p    g+   +l     + +++  + v+ 
  gi|121636820|ref|YP_977043.1| 185 agavandllrgviatdaligtfarmhepslmqnicflyhlvgggtgvW-HVPIGGMGSvtsALAT---AaARHGaEIVTG 260
                                    444444444444444444444444443433333333333333322110.2222222223321111...111122255777 PP

                         CHASE2 172 advle........vpp.......e.efkdkiVliGatatglkdlfstPfssempgveihAnalsnll 222
                                    adv++                  e  ++++ Vl+G+t + l+ l   P++   pg ++  n++   l
  gi|121636820|ref|YP_977043.1| 261 ADVFAldpdgtvrY-HsdgsdgaEhLVRGRFVLVGVTPAVLASLLGEPVAALAPGAQVKVNMVVRRL 326
                                    89988555554441.034444442356**********************999*********997766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6    0.0015       1.8       2      31 ..      10      39 ..       9      53 .. 0.89
   2 ?   -0.1   0.6       0.6   7.1e+02       2      26 ..     234     258 ..     233     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                   v v+G G  G   aa +a+agl+V+l+++ 
  gi|121636820|ref|YP_977043.1| 10 VVVVGGGHNGLVAAAYLARAGLRVRLLERL 39
                                   89************************9975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.6
                                    EEEE--SCCHHHHHHHHHHTT-EEE CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVv 26 
                                    v + G G + + +a+++a++g e+v
  gi|121636820|ref|YP_977043.1| 234 VPIGGMGSVTSALATAAARHGAEIV 258
                                    556699***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 3063.36
//
Query:       gi|121636821|ref|YP_977044.1|  [L=87]
Description: hypothetical protein BCG_0950c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-32  112.3   2.5    1.2e-32  112.2   2.5    1.0  1  DUF2630   Protein of unknown function (DUF2630)
  ------ inclusion threshold ------
      0.048   13.6   2.7      0.088   12.7   2.7    1.4  1  CHASE3    CHASE3 domain


Domain annotation for each model (and alignments):
>> DUF2630  Protein of unknown function (DUF2630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   2.5   1.3e-36   1.2e-32       1      79 [.       8      86 ..       8      87 .] 0.98

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.3e-36
                        DUF2630  1 ddkeilarikeLveeEheLrekleagelseeeErarLkeleeeLDqcWDLLrqRrAkreagedpdeaevrpaseVegYr 79
                                   +d+e la+i++Lv+eE++Lr++l +g++se+eE+++L+++e eLDqcWDLLrqRrA r++g dp+ea vrpa++VegY 
  gi|121636821|ref|YP_977044.1|  8 TDSETLAHIRDLVAEEKALRAQLRHGGISESEEQQQLRRIEIELDQCWDLLRQRRALRQTGGDPREAVVRPADQVEGYT 86
                                   58999*************************************************************************6 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.7   9.8e-06     0.088      37     102 ..       9      74 ..       7      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-06
                         CHASE3  37 deefLepyeqaraeiqealeelreltadnpeqqerldrlealieqklaeleetialrreggleaal 102
                                    d+e L+  ++ +ae ++  ++lr+   ++ e+q++l r+e   +q +++l++  alr++gg++ ++
  gi|121636821|ref|YP_977044.1|   9 DSETLAHIRDLVAEEKALRAQLRHGGISESEEQQQLRRIEIELDQCWDLLRQRRALRQTGGDPREA 74 
                                    56677777777777777778888777799999999************************7776433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 620.48
//
Query:       gi|121636822|ref|YP_977045.1|  [L=326]
Description: outer membrane protein A ompA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.7e-21   74.5   0.0    1.7e-20   73.2   0.0    1.7  2  OmpA       OmpA family
    2.4e-10   40.6   0.0    4.8e-06   26.8   0.0    2.7  2  BON        BON domain
  ------ inclusion threshold ------
       0.21   10.7   0.0       0.28   10.2   0.0    1.1  1  Parvo_NS1  Parvovirus non-structural protein NS1


Domain annotation for each model (and alignments):
>> OmpA  OmpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3   1.4e+04      12      35 ..     170     196 ..     164     198 .. 0.56
   2 !   73.2   0.0   2.8e-24   1.7e-20       2      95 .]     225     319 ..     224     319 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                                    GGHHHHHHHHHHHHS-S--....EEEEE CS
                           OmpA  12 kaksaldkiaellkkpeqk....itveG 35 
                                    ++k+a++++a     p++k    i+v+G
  gi|121636822|ref|YP_977045.1| 170 EHKDAVKRAATSTW-PDMKivnnIEVTG 196
                                    56666666655544.4444344466655 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 2.8e-24
                                    B-TTS--B-GGGHHHHHHHHHHHH.S-S--EEEEE---S---HHHHHHHHHHHHHHHHHHHHHTTSSGGGEEEEE-TT-- CS
                           OmpA   2 FapgsseLtpkaksaldkiaellk.kpeqkitveGhtdaagseernweLSqkRAeaVanylqnegvppsrisvsgyGaer 80 
                                    F  + ++L p+ ++ l+++a+ lk  p+ ++t++G+td++gse  n  LS++RA+ Va+yl+++gv  + i ++g G+++
  gi|121636822|ref|YP_977045.1| 225 FGNDGASLIPADYEILNRVADKLKaCPDARVTINGYTDNTGSEGINIPLSAQRAKIVADYLVARGVAGDHIATVGLGSVN 304
                                    677788999*********************************************************************** PP

                                    ------------EE. CS
                           OmpA  81 pitanntaekkarnr 95 
                                    pi++n+t+e++a+nr
  gi|121636822|ref|YP_977045.1| 305 PIASNATPEGRAKNR 319
                                    *************98 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   6.9e-05      0.41      29      68 ..      86     127 ..      82     128 .. 0.90
   2 !   26.8   0.0     8e-10   4.8e-06      20      68 ..     147     195 ..     141     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.9e-05
                                    ETTC.EEEECEEECHHHHHHHHHHHHC.CTTEEEEEEEEEEE CS
                            BON  29 enGv.VtLsGtVdseaekekAveiarn.vaGVkkVvnelkvr 68 
                                     +G+ VtL G  ++ea+k + + + ++ +a   +V+++++v 
  gi|121636822|ref|YP_977045.1|  86 RSGNtVTLIGDFPDEAAKAALMTALNGlLAPGVNVIDQIHVD 127
                                    45888**********************999888******996 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 8e-10
                                    TGCCCEEEEETTCEEEECEEECHHHHHHHHHHHHCCTTEEEEEEEEEEE CS
                            BON  20 daadinVevenGvVtLsGtVdseaekekAveiarnvaGVkkVvnelkvr 68 
                                    + +d   +ve+  VtL+Gt++s ++k+++ ++a ++    k+vn+++v+
  gi|121636822|ref|YP_977045.1| 147 PIPDFGLKVERDTVTLTGTAPSSEHKDAVKRAATSTWPDMKIVNNIEVT 195
                                    5566667899999**********************************97 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   4.7e-05      0.28      63     146 ..     107     191 ..      83     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.7e-05
                      Parvo_NS1  63 kaaldilakkevtadfdieenriykllslngynpvevgqvllawlskqlgkrntvwfyGpa..ntGktnlaeaIakavpl 140
                                    ++al+ l+ + v+  ++i+  ++++ l  ++++pv +++v ++ +  + + r+tv ++G+a  +  k  + +a + + p+
  gi|121636822|ref|YP_977045.1| 107 MTALNGLLAPGVNVIDQIHVDPVVRSLDFSSAEPVFTASVPIPDFGLK-VERDTVTLTGTApsSEHKDAVKRAATSTWPD 185
                                    5666667777777799*******************************9.9*********984356788888899999999 PP

                      Parvo_NS1 141 ygcvnw 146
                                    +++vn+
  gi|121636822|ref|YP_977045.1| 186 MKIVNN 191
                                    988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2665.34
//
Query:       gi|121636823|ref|YP_977046.1|  [L=50]
Description: hypothetical protein BCG_0952 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 439.13
//
Query:       gi|121636824|ref|YP_977047.1|  [L=175]
Description: hypothetical protein BCG_0953 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1372.95
//
Query:       gi|121636825|ref|YP_977048.1|  [L=446]
Description: two component sensor histidine kinase prrB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-17   63.5   0.0    4.2e-17   62.7   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-10   41.1   1.1    3.4e-10   39.8   1.1    1.7  1  HisKA        His Kinase A (phospho-acceptor) domain
    2.2e-08   34.4   1.3      8e-07   29.3   0.2    2.7  2  HAMP         HAMP domain
    8.2e-05   22.6   0.0    0.00017   21.5   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.015   15.1   0.2        0.4   10.5   0.0    2.4  2  LapA_dom     Lipopolysaccharide assembly protein A domain
      0.057   13.2   0.0       0.11   12.4   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.16   11.4   0.3       0.27   10.6   0.3    1.3  1  Med14        Mediator complex subunit MED14


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   1.6e-20   4.2e-17       3     109 ..     340     443 ..     338     446 .] 0.88

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.6e-20
                                    HHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                      HATPase_c   3 ekrLrqiisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                    + +Lr +++n++ Navk+ +  g   v+++a  s   ++i + DnG G+p+ +++ +fe+fs+  +++ +++g+GlGl++
  gi|121636825|ref|YP_977048.1| 340 PAGLRLAVDNAIANAVKH-G--GATLVQLSAvsSRAGVEIAIDDNGSGVPEGERQVVFERFSR--GSTASHSGSGLGLAL 414
                                    57899************9.5..55556666543558***************************..6778889******** PP

                                    HHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                      HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlp 109
                                    v + ++l+gG+ ++e++p +G + +++lp
  gi|121636825|ref|YP_977048.1| 415 VAQQAQLHGGTASLENSPLGGARLVLRLP 443
                                    ***********************999998 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   1.1   1.3e-13   3.4e-10       3      63 ..     232     292 ..     230     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.3e-13
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsr 63 
                                    ++f+a  +HELrtPL+a++ n+e+L+  +  +++ ke l+++++   r+++ ++ l +l++
  gi|121636825|ref|YP_977048.1| 232 RDFAAVSSHELRTPLTAMRTNLEVLSTLDLPDDQRKEVLNDVIRTQSRIEATLSALERLAQ 292
                                    89***********************666567788888***************999988886 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.2   3.1e-10     8e-07       2      51 ..     168     217 ..     167     219 .. 0.95
   2 ?    3.2   0.1     0.047   1.2e+02      10      29 ..     280     302 ..     275     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.1e-10
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                    la   +rP ++La+++r+i+aGd  +r++v+g  E  e+a+a++ Ml+r+
  gi|121636825|ref|YP_977048.1| 168 LAAFAVRPFKQLAEQTRSIDAGDEAPRVEVHGASEAIEIAEAMRGMLQRI 217
                                    77889*******************************************98 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.047
                                    HHHHHHHHHHHTTTBTSST...C CS
                           HAMP  10 LrrLaraarriaaGdldtr...l 29 
                                    ++   +a +r+a+G+l+t+   +
  gi|121636825|ref|YP_977048.1| 280 IEATLSALERLAQGELSTSddhV 302
                                    55556899******999984444 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.8e-08   0.00017      32     107 ..     343     417 ..     311     420 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.8e-08
                    HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.....keslkegGrGlalik 106
                                    +rlav+ a++Nav+h+        v++++ s+   +++ + D+G g +  +++   + e      ++s   +G+Glal++
  gi|121636825|ref|YP_977048.1| 343 LRLAVDNAIANAVKHGGA----TLVQLSAVSSRAGVEIAIDDNGSGVPEGERQV--VFERfsrgsTASHSGSGLGLALVA 416
                                    89***************8....899***999**************955543322..22223345599***********98 PP

                    HATPase_c_2 107 g 107
                                    +
  gi|121636825|ref|YP_977048.1| 417 Q 417
                                    6 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.078     2e+02      23      55 ..      18      52 ..       3      57 .. 0.66
   2 ?   10.5   0.0   0.00016       0.4      21      56 ..     150     186 ..     142     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.078
                       LapA_dom 23 llvafgiGallgwllslwsyl..rlrrelrrlkkk 55
                                   ++va +iGa + +l+    ++   ++ +  rl+++
  gi|121636825|ref|YP_977048.1| 18 VVVATAIGAAIPVLIVGTVVWvgITNDRKERLDRR 52
                                   78999****98888887544444233333344444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                       LapA_dom  21 llllvafgiGa..llgwllslwsylrlrrelrrlkkki 56 
                                    +ll+ +f+iGa  +++wll+++  +r  ++l ++++ i
  gi|121636825|ref|YP_977048.1| 150 VLLICTFAIGAaaVFAWLLAAF-AVRPFKQLAEQTRSI 186
                                    689999999998899****995.667777777777666 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.2e-05      0.11       6      62 ..     346     403 ..     342     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                    HATPase_c_3   6 AlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsske 62 
                                    A+   + N++  + a+ v++++   r +  ei i D+G+G++e e + ++ r+ + s+ 
  gi|121636825|ref|YP_977048.1| 346 AVDNAIANAVKhGGATLVQLSAVSSR-AGVEIAIDDNGSGVPEGERQVVFeRFSRGSTA 403
                                    55556677776677888******998.799*************9877776345555444 PP

>> Med14  Mediator complex subunit MED14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00011      0.27      72     163 ..     214     304 ..     200     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHHCHHCHCTTCHCHCCCCCCSCSH--S--.-SHHHHHHHHHHHHH CS
                          Med14  72 llaflrqqneafedaadalkelkeslanaklpnpdlktAleVLstGrysrlpslikeeyppkpl.takeilktlkdlnel 150
                                    l+   ++qn++ e++a a   +  s ++ ++p   + t leVLst    +lp+ +++e+ ++ + t+++i+ tl+ l++l
  gi|121636825|ref|YP_977048.1| 214 LQRIWNEQNRTKEALASARDFAAVSSHELRTPLTAMRTNLEVLSTL---DLPDDQRKEVLNDVIrTQSRIEATLSALERL 290
                                    4555677888888888888889999999****************98...6688887776666665999************ PP

                                    HHHHHHH.BS---C CS
                          Med14 151 irlrLal.hekiPk 163
                                     +  L++  +++P 
  gi|121636825|ref|YP_977048.1| 291 AQGELSTsDDHVPV 304
                                    *****996666776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3341.03
//
Query:       gi|121636826|ref|YP_977049.1|  [L=236]
Description: two component response transcriptional regulatory protein prrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-29  101.3   0.1    4.8e-29  100.8   0.1    1.3  1  Response_reg  Response regulator receiver domain
    1.1e-25   89.5   0.0    2.5e-25   88.3   0.0    1.6  1  Trans_reg_C   Transcriptional regulatory protein, C terminal
     0.0032   17.3   0.0      0.012   15.5   0.0    1.9  1  DUF1869       Domain of unknown function (DUF1869)
  ------ inclusion threshold ------
      0.031   14.6   0.0      0.053   13.8   0.0    1.3  1  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.1   1.1e-32   4.8e-29       1     112 []      13     123 ..      13     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.1e-32
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl+vdDd +v++ l++ l+ +g+ eva+a dg+eal+ + e+++d i+lDinmp +dG+ +++ +r+ d+++pv +l+a+
  gi|121636826|ref|YP_977049.1|  13 VLVVDDDSDVLASLERGLRLSGF-EVATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSAR 91 
                                    8**********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkale 112
                                    s+ +d+v++l+agadd+l+Kpf  +eL+++++
  gi|121636826|ref|YP_977049.1|  92 SSVDDRVAGLEAGADDYLVKPFVLAELVARVK 123
                                    ****************************9985 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0   5.6e-29   2.5e-25       3      77 .]     160     233 ..     158     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 5.6e-29
                                    EEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   3 eveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    +v+lt++ef+lL++L+e++  v+sr++Lle vwg+d++ d+++vdv i +LR+kLe+ +  prl++tvrgvG++l
  gi|121636826|ref|YP_977049.1| 160 DVDLTKREFDLLAVLAEHKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA-GGGPRLLHTVRGVGFVL 233
                                    799******************************************************.6699**********986 PP

>> DUF1869  Domain of unknown function (DUF1869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-06     0.012      13      56 ..     156     202 ..     154     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                                    TT--EEE...EEE--SCGGC-HHHHHHHHHHHHHHHHHTTSSSSS-S CS
                        DUF1869  13 nNGVSVD...kefeslaeLkdpevaaevvKdLiNivRgYdsdeetnv 56 
                                     NGV VD   +ef+ la L++ ++a  +  +L+ +v gYd   +tnv
  gi|121636826|ref|YP_977049.1| 156 VNGVDVDltkREFDLLAVLAEHKTAVLSRAQLLELVWGYDFAADTNV 202
                                    59*****77679**********************************9 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.053       6      73 ..      23      92 ..      19     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                     OKR_DC_1_N  6 irelaealekegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetr 73
                                   +++l++ l+  gfev ++ +  ++l  + + +r +a+vl+++    +   ++ ++r+  +d+Pv +l+ ++
  gi|121636826|ref|YP_977049.1| 23 LASLERGLRLSGFEVATAVDGAEALRSATE-NRPDAIVLDINmpvLDGVSVVTALRAMDNDVPVCVLSARS 92
                                   67889999999*********9999998887.799*********9988889***************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1557.50
//
Query:       gi|121636827|ref|YP_977050.1|  [L=495]
Description: acetyl-coenzyme A carboxylase carboxyl transferase (subunit beta) accD3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-94  317.4   0.0    1.9e-94  317.1   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    5.8e-05   22.5   0.3     0.0024   17.2   0.2    3.0  2  ECH_1           Enoyl-CoA hydratase/isomerase
    7.5e-05   22.6   0.0    0.00026   20.9   0.0    1.8  2  ACCA            Acetyl co-enzyme A carboxylase carboxyltransf
  ------ inclusion threshold ------
       0.11   11.9   9.4       0.26   10.7   2.2    2.7  3  MdcE            Malonate decarboxylase gamma subunit (MdcE)
        3.7    6.5   6.7        1.2    8.1   0.4    2.1  2  DEC-1_N         DEC-1 protein, N-terminal region


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.1   0.0   5.3e-98   1.9e-94       3     491 ..      14     479 ..      12     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 317.1 bits;  conditional E-value: 5.3e-98
                                    CTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEE CS
                 Carboxyl_trans   3 hprGkltareridllldpgsFgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekl 82 
                                     +rG++++++++ l++   +  +++++++++++++g     ++++v+tg G+v+Gr+v+vva+++++lggs+g a++e++
  gi|121636827|ref|YP_977050.1|  14 LDRGSFVSWDSEPLAVPVAD--SYARELAAARAATG-----ADESVQTGEGRVFGRRVAVVACEFDFLGGSIGVAAAERI 86 
                                    57999***********9999..89999999999999.....79************************************* PP

                                    CHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHH.CS-EEEEESSEEETHHHHHHHHTSEEEEET CS
                 Carboxyl_trans  83 lkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasg.eIpqislvtgrcaGggaYlpalgdrvimve 161
                                    ++a+e+a+++++pl++  +sgG+  r+qeg++++ +++ki+++ +++++ ++p+++++ ++++G g+++++ +  +++v+
  gi|121636827|ref|YP_977050.1|  87 TAAVERATAERLPLLASPSSGGT--RMQEGTVAFLQMVKIAAAIQLHNQaRLPYLVYLRHPTTG-GVFASWGSLGHLTVA 163
                                    ***********************..**************************************9.9************** PP

                                    T.EEEEESSTHHHHHHHHS.SCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECS CS
                 Carboxyl_trans 162 e.tskifltGpdvikkvlg.reevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPiveta 239
                                    e  + i++ Gp+v++ ++g +  +  +++++ ++h  ++Gv++l + +++ + +l++ + +  P +a+++++++P v+t+
  gi|121636827|ref|YP_977050.1| 164 EpGALIGFLGPRVYELLYGdPFPSGVQTAENLRRHGIIDGVVALDRLRPMLDRALTVLIDAPEPLPAPQTPAPVPDVPTW 243
                                    *99****************8899********************************************************* PP

                                    SGSSSH..HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHH CS
                 Carboxyl_trans 240 depdrdlieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavKa 319
                                    d++ +   + +Pd   +p   + + ++++d+  ++++++g A+t+++++Ar+gG+p++v++++++v++G++++  +a+++
  gi|121636827|ref|YP_977050.1| 244 DSVVA---SRRPD---RPGVRQLLRHGATDRVLLSGTDQGEAATTLLALARFGGQPTVVLGQQRAVGGGGSTVGPAALRE 317
                                    ***99...8****...9*************************************************************** PP

                                    HHHHHHHHH.TT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEE CS
                 Carboxyl_trans 320 arfirlcda.enlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlva 398
                                    ar+ ++++a  +lPlv+++d++G ++++++e+gg+++++a+++++l+++++P+++++l++++GG+ ++m ++++  ++++
  gi|121636827|ref|YP_977050.1| 318 ARRGMALAAeLCLPLVLVIDAAGPALSAAAEQGGLAGQIAHCLAELVTLDTPTVSILLGQGSGGPALAMLPADRVLAALH 397
                                    ********989********************************************************************* PP

                                    ETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEE CS
                 Carboxyl_trans 399 awptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvialel 478
                                    +w    +a l+pega++i+fr++++aae     laa  ++ +++++  ++ ++++++ ++ Da+++p e++ +l++a ++
  gi|121636827|ref|YP_977050.1| 398 GW----LAPLPPEGASAIVFRDTAHAAE-----LAA--AQGIRSADLLKSGIVDTIVPEYPDAADEPIEFALRLSNAIAA 466
                                    **....*****************99998.....666..8***************************************** PP

                                    HGGGHHHHHHHHH CS
                 Carboxyl_trans 479 ewkkarklparkr 491
                                    e+++ rk+pa++r
  gi|121636827|ref|YP_977050.1| 467 EVHALRKIPAPER 479
                                    ******9999876 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.083     3e+02     160     180 ..     191     211 ..     187     226 .. 0.82
   2 !   17.2   0.2   6.7e-07    0.0024      69     204 ..     348     474 ..     338     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.083
                                    EHHHHHHCTSSSEEESGGGHH CS
                          ECH_1 160 saqealkvGlvdkvvpeeqll 180
                                    +a+++ ++G++d vv+ + l 
  gi|121636827|ref|YP_977050.1| 191 TAENLRRHGIIDGVVALDRLR 211
                                    688999**********99875 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.7e-07
                                    HHHHHHCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHH CS
                          ECH_1  69 kqallkeevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGksk 148
                                    +q  l  ++ + + +l t++ p+++ + G++ gG ++  l +D v aa +            +p+ g++ i+ r   ++ 
  gi|121636827|ref|YP_977050.1| 348 EQGGLAGQIAHCLAELVTLDTPTVSILLGQGSGGPALAMLPADRVLAALHGWL-------APLPPEGASAIVFRDTAHA- 419
                                    56667777788889999999999999999999988888888998888765443.......3468899999999987664. PP

                                    HHHHHHHT-EEEHHHHHHCTSSSEEESG.GGHHHHHHHHHHHHHHSCHHHHHHHHHH CS
                          ECH_1 149 AeeilllgkkisaqealkvGlvdkvvpe.eqlleealelaeklaekspaalrqlkea 204
                                      e l  ++ i+ +++lk G+vd++vpe  +  +e +e a +l +++ a + +l+++
  gi|121636827|ref|YP_977050.1| 420 -AE-LAAAQGIRSADLLKSGIVDTIVPEyPDAADEPIEFALRLSNAIAAEVHALRKI 474
                                    .33.456888******************99******************999999875 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.63   2.3e+03      88     110 ..      46      68 ..      37      70 .. 0.85
   2 !   20.9   0.0   7.2e-08   0.00026      52     114 ..     241     302 ..     235     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                           ACCA  88 fadDkAivgglarlegqpvmvig 110
                                     + D+++ +g +r+ g+ v v++
  gi|121636827|ref|YP_977050.1|  46 TGADESVQTGEGRVFGRRVAVVA 68 
                                    5789***************9996 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 7.2e-08
                           ACCA  52 tpwqkvqlaRhpeRpktldyiealfedfvelhGDrafadDkAivgglarlegqpvmvigqqKG 114
                                      w+ v  +R+p+Rp +++ +++  +d v l+G ++ +  ++ + +lar+ gqp +v+gqq++
  gi|121636827|ref|YP_977050.1| 241 PTWDSVVASRRPDRPGVRQLLRHGATDRVLLSGTDQGEA-ATTLLALARFGGQPTVVLGQQRA 302
                                    57*******************************988665.556668***************96 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0048        17       5      78 ..      38     111 ..      35     138 .. 0.79
   2 ?   -2.0   0.0      0.57     2e+03      96     119 ..     282     305 ..     277     317 .. 0.78
   3 ?   10.7   2.2   7.2e-05      0.26      66     136 ..     331     398 ..     321     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0048
                                    HHHS--TTS-TTEEEEEEEETTEEEEEEEE---TT...SS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B-- CS
                           MdcE   5 aLfpdgsgiaaslkvldgsltlesvrfvaVigdan...kgevGvdealaLaaaVleaieraekrpilvlvDvasQrl 78 
                                    +L++ + +  a+++v +g+     +r vaV++      +g +Gv  a +++aaV+ a+  ae+ p+l+   + + r+
  gi|121636827|ref|YP_977050.1|  38 ELAAARAATGADESVQTGEGRV-FGRRVAVVACEFdflGGSIGVAAAERITAAVERAT--AERLPLLASPSSGGTRM 111
                                    6788888888999999999877.8999999997656889****************998..77888887655555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.57
                                    HHHHHHHHHT--EEEEEEEEEEHH CS
                           MdcE  96 kalarArlaGhpvigllvGkavsG 119
                                      la+Ar  G+p++ l   +av G
  gi|121636827|ref|YP_977050.1| 282 TLLALARFGGQPTVVLGQQRAVGG 305
                                    45899*******998877667666 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 7.2e-05
                                    EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTTTT-SEEEEEET CS
                           MdcE  66 pilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahglqanrlialpg 136
                                    p+++++D+a+ +l+   E  G+ + +ah    l+  +    p++++l G+   G  la+  + ++l al+g
  gi|121636827|ref|YP_977050.1| 331 PLVLVIDAAGPALSAAAEQGGLAGQIAHCLAELVTLD---TPTVSILLGQGSGGPALAMLPADRVLAALHG 398
                                    99**************************988887655...7******************999999999998 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00034       1.2     127     148 ..     224     245 ..     192     266 .. 0.77
   2 ?    1.3   1.1     0.038   1.4e+02      92     144 ..     352     407 ..     333     473 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00034
                        DEC-1_N 127 ppapapvpddpapapaapqaaa 148
                                     p p p+p++pap+p+ p+  +
  gi|121636827|ref|YP_977050.1| 224 APEPLPAPQTPAPVPDVPTWDS 245
                                    3677778899******997554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.038
                        DEC-1_N  92 lgpqvGaalqsl..lplqsldgllGaaapapalaaapp.papapvpddpapapaap 144
                                    l  q+ + l++l  l  ++++ llG+ +  pala  p     a      ap p   
  gi|121636827|ref|YP_977050.1| 352 LAGQIAHCLAELvtLDTPTVSILLGQGSGGPALAMLPAdRVLAALHGWLAPLPPEG 407
                                    55788888898833444678889999999999888877333444444446665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3441.44
//
Query:       gi|121636828|ref|YP_977051.1|  [L=243]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-44  150.0   0.1    8.1e-44  149.8   0.1    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.8e-21   77.0   0.0    2.6e-21   76.5   0.0    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.1     9e-48   8.1e-44       3     250 ..       7     242 ..       5     243 .] 0.95

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 9e-48
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                     ++v+ i l+rPe  Nal+ +l++El+qa+ k+ d  s+ra+vLtG + aF+aGadl        a++a++   + el +
  gi|121636828|ref|YP_977051.1|   7 AEAVLTIELQRPERRNALNSQLVEELTQAIRKAGDG-SARAIVLTGQGTAFCAGADLSGD-----AFAADYPDRLIELHK 80 
                                    689*****************************9888.*******************9864.....6789*********** PP

                                    HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                          ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                    ++  +p+pv+ a+nG aig+Gl+la+ cD++++a +a f  + +k+Gl  + +   +l   vG+ +A+ +ll ++k++a+
  gi|121636828|ref|YP_977051.1|  81 AMDASPMPVVGAINGPAIGAGLQLAMQCDLRVVAPDAFFQFPTSKYGLALDNWSIRRLSSLVGHGRARAMLLSAEKLTAE 160
                                    ******************************************************************************** PP

                                    HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHT CS
                          ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflE 242
                                     al+ G+ +++   +     a ++a+++a+ +p+a++ +k  ln +   a +e+  a ++lf +   ++d+ e   a +E
  gi|121636828|ref|YP_977051.1| 161 IALHTGMANRIGTLA----DAQAWAAEIARLAPLAIQHAKRVLNDD--GAIEEAWPAHKELFDKAWGSQDVIEAQVARME 234
                                    ***********8765....5778999999999***********987..5678889999*******9999999999999** PP

                                    CSH----- CS
                          ECH_1 243 krkpefed 250
                                    kr+p+f++
  gi|121636828|ref|YP_977051.1| 235 KRPPKFQG 242
                                    ******86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   2.9e-25   2.6e-21       3     238 ..      12     233 ..      10     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 2.9e-25
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                    +i+L+rp+  NaL+ ++v++l++a+++ + d +++++vl+g+g  afCAG D+   + aa+        +  +  +l ++
  gi|121636828|ref|YP_977051.1|  12 TIELQRPERRNALNSQLVEELTQAIRK-AGDGSARAIVLTGQG-TAFCAGADLSGDAFAAD--------YPDRLIELHKA 81 
                                    89************************9.6999*********88.9*******976544444........4557789**** PP

                                    HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHH CS
                          ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgad 161
                                    +   p pvv  ++G ++G G+ l++++ +rvv  ++ f  P  + Gl  D      Ls l g   ++ + l++++l+++ 
  gi|121636828|ref|YP_977051.1|  82 MDASPMPVVGAINGPAIGAGLQLAMQCDLRVVAPDAFFQFPTSKYGLALDNWSIRRLSSLVGhGRARAMLLSAEKLTAEI 161
                                    **************************************************999999999866478999************ PP

                                    HHHTTS--EE--GGGHHHHHHHHHTT........--------......----SHHHHHHHHHHHT.-S.-TTTHHHHH CS
                          ECH_2 162 alaaglathyvpseklealeeaLaelessdeeaveevleelaeeaeeeeeeselaekreaidrlfsad.sveeiveaL 238
                                    al++g+a+ +   ++ +a ++++a+l   + ++ ++vl++  +       e+++ +++e  d++ +++  +e+ v+++
  gi|121636828|ref|YP_977051.1| 162 ALHTGMANRIGTLADAQAWAAEIARLAPLAIQHAKRVLNDDGAI------EEAWPAHKELFDKAWGSQdVIEAQVARM 233
                                    ********************999999777666666666663321......2344445666666664442355555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1849.38
//
Query:       gi|121636829|ref|YP_977052.1|  [L=372]
Description: hypothetical protein BCG_0958 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-49  167.7   1.4    3.5e-49  167.1   1.4    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.9e-16   59.1   0.1    8.1e-16   58.3   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.17   11.3   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
        0.2   12.0   0.3        2.1    8.7   0.0    2.3  2  DUF58          Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   1.4   7.7e-53   3.5e-49       2     201 .]     123     321 ..     122     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 7.7e-53
                                    EEEES--TT.......HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEEHHHHHHCC CS
                  Lactamase_B_2   2 riLiDagpd.......lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlre..lrpkklplyapkgvlavle 71 
                                    r+L+D++++       ++++ +r++ P + +++ lp++daV+++h+HyDHl +++t+ +  +++ ++p+++p+gv+a+l+
  gi|121636829|ref|YP_977052.1| 123 RVLTDPVWSdrcspsdVVGP-QRLH-PPPvQLAALPAVDAVVISHDHYDHL-DIDTVVAlvGMQ-RAPFLVPLGVGAHLR 198
                                    9**************99999.8887.44557999*****************.*******75443.49************* PP

                                    TTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..HH CS
                  Lactamase_B_2  72 anfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip..ee 149
                                    +++v+       + +++eldw++s +++  +l++ ++parh+sgr l rn+++++++++ g+++r+y++gDtgy++   +
  gi|121636829|ref|YP_977052.1| 199 SWGVP-------QDRIVELDWNQSAQVD--ELTVVCVPARHFSGRFLSRNTTLWASWAFVGPNHRAYFGGDTGYTKsfTQ 269
                                    **985.......456777*********9..699*******************************************999* PP

                                    HHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSS...SSEEEEESB CS
                  Lactamase_B_2 150 igerlggadllllditayeddemirhmgHltpeeaveaaadlg...akrlvliHi 201
                                    ig+ +g++dl+ll+i+ay+  +    ++H++peeav+a+ d+     + lv++H+
  gi|121636829|ref|YP_977052.1| 270 IGADHGPFDLTLLPIGAYNTAW---PDIHMNPEEAVRAHLDVTdsgSGMLVPVHW 321
                                    **********************...79*************99866678******9 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   1.8e-19   8.1e-16       2     149 ..     107     303 ..     106     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.8e-19
                  Lactamase_B_3   2 ltwlghnsflletagarilvDPf............kanlgyeppa...........eeaDlvlisqaledHahletlkql 58 
                                    ++w+gh++ lle++g r+l+DP+                    ++           + +D+v+is+++ dH +++t+ +l
  gi|121636829|ref|YP_977052.1| 107 VSWFGHSTALLEIDGYRVLTDPVwsdrcspsdvvgP-------QRlhpppvqlaalPAVDAVVISHDHYDHLDIDTVVAL 179
                                    79********************98877755443320.......2255556899999************************ PP

                  Lactamase_B_3  59 ........................aenvkvleegeslevggleiravatshdavggserge..nngflleqdgltiyhlG 112
                                                            ++++  l+  +s++v++l +  v++ h ++    r++     + +   +++ y+ G
  gi|121636829|ref|YP_977052.1| 180 vgmqrapflvplgvgahlrswgvpQDRIVELDWNQSAQVDELTVVCVPARHFSGRFLSRNTtlWASWAFVGPNHRAYFGG 259
                                    **8888888888888888888876666666666899***************665544444422445667778******** PP

                  Lactamase_B_3 113 hlahelsseel.kelgrvDvvltPvgg......pltlgqeeale 149
                                    +++++ s++++ + +g+ D+ l+P+g        + +++eea++
  gi|121636829|ref|YP_977052.1| 260 DTGYTKSFTQIgADHGPFDLTLLPIGAyntawpDIHMNPEEAVR 303
                                    *********997899***********988888777888888775 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.7e-05      0.17       1      49 [.     116     171 ..     116     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                  Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelek........viptvdliLLshatlehl 49 
                                    lLe+d+ ++L D+ w++  +s ++++ + +         ++p vd++++sh   +hl
  gi|121636829|ref|YP_977052.1| 116 LLEIDGYRVLTDPVWSDR-CSPSDVVGPQRLhpppvqlaALPAVDAVVISHDHYDHL 171
                                    79**************96.7666666655552333333346**********999997 PP

>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.15   6.8e+02      14      27 ..      68      81 ..      66      85 .. 0.86
   2 ?    8.7   0.0   0.00047       2.1      11      33 ..     202     224 ..     195     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                          DUF58 14 DplrrIdWkatARt 27
                                   ++lr I W  +AR+
  gi|121636829|ref|YP_977052.1| 68 EELRLIVWELVARH 81
                                   57999********8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00047
                          DUF58  11 vpgDplrrIdWkatARtgelyvr 33 
                                    vp D++  +dW+++A  +el v 
  gi|121636829|ref|YP_977052.1| 202 VPQDRIVELDWNQSAQVDELTVV 224
                                    799****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2759.81
//
Query:       gi|121636830|ref|YP_977053.1|  [L=526]
Description: hypothetical protein BCG_0959 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-60  205.0   5.4    2.1e-60  204.7   5.4    1.1  1  Beta-lactamase  Beta-lactamase
    3.4e-13   50.0   0.0    6.8e-13   49.0   0.0    1.5  1  DUF3471         Domain of unknown function (DUF3471)


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.7   5.4   2.4e-64   2.1e-60       1     321 [.      57     393 ..      57     402 .. 0.90

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 2.4e-64
                                    HHHHHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTE....EESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTT CS
                 Beta-lactamase   1 ldrlvrelmaqggipGvavavvrdgkvvldkggGvadleggr....pvtadtlfriaSvtKtftaaavlqlveeGkldLd 76 
                                    +d lv elm+++gipG+ava+v++gk++++kg+Gv+d+++g     +v+adt+f++aSv+K++ a++v+  v ++ +++d
  gi|121636830|ref|YP_977053.1|  57 VDGLVGELMQNTGIPGMAVAIVHGGKTLYAKGFGVRDVGKGGgpdnKVDADTVFQLASVSKSVGATVVAHAVTDNVVTWD 136
                                    578999**********************************998999********************************** PP

                                    SBGGGTST....TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHHHH CS
                 Beta-lactamase  77 dpVskylP....efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgygll 152
                                    +pV   lP    +++   +g++T++dL +H+sGlpd+ a dlle+  +d++++l++l+ lp++  ++  ++Y n g + +
  gi|121636830|ref|YP_977053.1| 137 TPVVSKLPwfalRDPYV-TGQVTIADLYSHRSGLPDH-AGDLLEDLGYDRRQVLQRLKYLPLAP-FRISYAYTNFGVTAA 213
                                    ***88899888554444.555****************.*************************6.*************** PP

                                    HHHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC.TTTBEEEEHHHHHHH CS
                 Beta-lactamase 153 gellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae.gagglistardlarf 231
                                    +e++++++g+s+e+l +e ++rpLgm +t+    +  +++ +a+ + +++++++++ + +++a+ +agg+ s+++d+ ++
  gi|121636830|ref|YP_977053.1| 214 AEAVAAAAGQSWEDLSDEVLYRPLGMGSTSSRFTDFLARPNHAVNHVKVADRWEARYQRDPDAQsPAGGVSSSLNDMTHW 293
                                    ******************************************************************************** PP

                                    H......HHHHHCCSSSSHHHHHHH.HHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE...STEEEEEEEECGG CS
                 Beta-lactamase 232 l......glalegglllsaetlaql.taklssgttrpagiraglglGwvladktgapgtfghtG...ggygtyvfvdpea 301
                                    l      g+ +++++++ ++ l     +  s+++++p   +  +g+G++++ ++++++ ++h+G   +g+ ++++v p +
  gi|121636830|ref|YP_977053.1| 294 LamvladGVYNGRRITSPEALLLVYtPQVISRHPVSPRARASFYGYGFNVGVTSSGRTEYSHSGafgLGAAANFVVLPSE 373
                                    *8888876655555554444443332666677777777777777************************************ PP

                                    TEEEEEEESBCSSHHHHHHH CS
                 Beta-lactamase 302 nlvvavltnrdppnedaaed 321
                                    +l+++ ltn  p   ++   
  gi|121636830|ref|YP_977053.1| 374 DLAIIALTNAGPIGVPETLT 393
                                    *********98865555555 PP

>> DUF3471  Domain of unknown function (DUF3471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   7.6e-17   6.8e-13       3      75 ..     433     506 ..     431     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 7.6e-17
                        DUF3471   3 kanttpslpleaYvGtYedpgygtvtvslegdrLflrfdrtprlqgeLehyhgdfFlarwddrs..seadakveF 75 
                                    +an++ps+pl++YvG+Y ++  g +tv+ ++++L l +  ++ +++ L h++gd+F++++++++       k++F
  gi|121636830|ref|YP_977053.1| 433 PANPAPSRPLNDYVGVYANDYWGPATVTYHDGQLRLSLGPKN-QTFDLTHWDGDTFTFTLSTENalPGSISKATF 506
                                    7899**********************************5555.5577************9998877333455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3811.71
//
Query:       gi|121636831|ref|YP_977054.1|  [L=797]
Description: metal cation transporter atpase P-type ctpE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-40  138.7   0.6    1.5e-40  138.7   0.6    3.5  5  E1-E2_ATPase     E1-E2 ATPase
    1.6e-19   71.1   2.4    2.9e-19   70.2   2.4    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.5e-05   23.7   0.0    6.3e-05   22.8   0.0    1.3  1  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.14   11.8   0.0    2.1  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
       0.17   11.6  19.4      0.012   15.3   9.3    3.3  4  Cation_ATPase_C  Cation transporting ATPase, C-terminus
        1.7    9.1   4.9          2    8.9   1.8    2.6  2  HRG              Haem-transporter, endosomal/lysosomal, haem-


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.9       2.7   8.1e+03     115     143 ..      42      70 ..      33      83 .. 0.62
   2 !  138.7   0.6   4.9e-44   1.5e-40       7     179 ..     103     277 ..      98     279 .. 0.96
   3 ?   -2.1   2.4      0.79   2.4e+03     152     163 ..     638     649 ..     561     689 .. 0.57
   4 ?   -0.4   1.0      0.24   7.1e+02     115     146 ..     664     702 ..     649     740 .. 0.69
   5 ?   -2.9   0.1       1.4   4.2e+03     124     158 ..     735     772 ..     730     776 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHHHHHHHHHHS-STTTSS CS
                   E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgks 143
                                    ++ ++++ +++++l++++++   l++g +
  gi|121636831|ref|YP_977054.1|  42 ANVFTRINAILGVLLLIVLATGSLINGMF 70 
                                    55666666666666666666655555544 PP

  == domain 2  score: 138.7 bits;  conditional E-value: 4.9e-44
                                    EEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEE CS
                   E1-E2_ATPase   7 akvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmvfsGtvvvsgeakavV 85 
                                      v+r   +++  ++e+v +Di++l +gd+v++Dg++ve+++ e+des+LTGE+ p+ k++gd+v+sG++vvsg   +++
  gi|121636831|ref|YP_977054.1| 103 PLVRRQSGTRTRSTNEVVLDDIIELGPGDQVVVDGEVVEEENlEIDESLLTGEADPIAKDAGDTVMSGSFVVSGAGAYRA 182
                                    5688999999********************************************************************** PP

                                    EE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHHHHS-TTHH CS
                   E1-E2_ATPase  86 tatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallvaaiPcaLp 164
                                    t++g++ + +k+a+ +++ +  k++l + ++++ ++++ + + ++ll++ ++l++++  + e++lr+++ lv ++P++L+
  gi|121636831|ref|YP_977054.1| 183 TKVGSEAYAAKLAAEASKFTLVKSELRNGINRILQFITYLLVPAGLLTIYTQLFTTHVGWrESVLRMVGALVPMVPEGLV 262
                                    ****************************************************999998777******************* PP

                                    HHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 165 lavplalalgarrla 179
                                    l++++a+a+g+ rl 
  gi|121636831|ref|YP_977054.1| 263 LMTSIAFAVGVVRLG 277
                                    ***********9985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.79
                                    HHHHHHHS-TTH CS
                   E1-E2_ATPase 152 lallvaaiPcaL 163
                                     a +++ iP  +
  gi|121636831|ref|YP_977054.1| 638 AAWFTIGIPAFI 649
                                    333333333332 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.......H CS
                   E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgksla.......e 146
                                    +++++   vp++l+i++++f++ l   ++         +
  gi|121636831|ref|YP_977054.1| 664 VRRVMTSAVPFGLVIGVATFVTYLAAYQGRYaswqeqeQ 702
                                    567777888888888888888877644333334455553 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHH CS
                   E1-E2_ATPase 124 pvvlliallvflialllgksla...eallralallvaa 158
                                    +++ l+++++f + l ++k+l    +  + ++al+v++
  gi|121636831|ref|YP_977054.1| 735 LASGLAYVVIFSLPLAREKFLLdasNLATTSIALAVGV 772
                                    45555566666666666666667665555566666654 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   2.4   9.7e-23   2.9e-19       1     210 []     295     548 ..     295     548 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 9.7e-23
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHH..HHCHHHHHHHHHHHHH.HHHHHHHHH........ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxxxx........ RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.......alalaaaletg..sehpigkalvaaakar.sgaltgfat........ 62 
                                    +++v+ Dk+GTLt++ ++v +v +           +  aal+ +   +    +a+++a++   ++ ++ +a         
  gi|121636831|ref|YP_977054.1| 295 VDVVCADKTGTLTESGMRVCEVEELDgagrqesVADVLAALAAAdaRPNASMQAIAEAFHSPpGWVVAANAPfksatkws 374
                                    5899***************9998888777766633333444444567777777887777777533334555433344444 PP

                                    ...ETTTEHHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..............TTHHHHHHHHHHTHHBHTTHHH CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  63 ...figrgayaigkpewltaldippdlgaaigsaqsqgrtvall..............qaralavftiadplkvkpeaae 125
                                       f ++g   ig p+ l +    +    + +   +qg  v ll              q   +a++ ++++  v+p+a+e
  gi|121636831|ref|YP_977054.1| 375 gvsFRDHGNWVIGAPDVLLDP--ASVAARQAERIGAQGLRVLLLaagsvavdhaqapgQVTPVALVVLEQK--VRPDARE 450
                                    555666668888888888888..666666666777777777777899999999988888899999999999..******* PP

                                    HHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.......GGGESEEEEHHCES..........STTTSHHHHHHHHHHHTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxx RF
                      Hydrolase 126 avasLkaagievvlltgdnpetaeraanqlG.......ddyfdaviasdiet..........vakpspegkvaaireLqg 188
                                    ++ ++  +++ v +++gdn   + ++a++lG       +      + +  e+          ++ + p++k+a++  Lq 
  gi|121636831|ref|YP_977054.1| 451 TLDYFAVQNVSVKVISGDNAVSVGAVADRLGlhgeamdA----RALPTGREEladtldsytsFGRVRPDQKRAIVHALQS 526
                                    *******************************99555431....2222222224566777889****************** PP

                                    TGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 189 kpeevamVGDgvnDaaalaaAg 210
                                     ++ vam GDgvnD+ al+ A+
  gi|121636831|ref|YP_977054.1| 527 HGHTVAMTGDGVNDVLALKDAD 548
                                    *******************998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.1e-08   6.3e-05     195     246 ..     520     571 ..     517     579 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.1e-08
                                    HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--G CS
                    Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksn 246
                                    +++ l+ +   v+  GDg ND+  L+ a++gvAmg++s+   ++A+ v  +n
  gi|121636831|ref|YP_977054.1| 520 IVHALQSHGHTVAMTGDGVNDVLALKDADIGVAMGSGSPASRAVAQIVLLNN 571
                                    677888888999999*******************************999887 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.14      16      66 ..       6      56 ..       2      59 .. 0.88
   2 ?   -4.3   2.1       5.1   1.5e+04      56      69 .]     710     723 ..     706     723 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                Cation_ATPase_N 16 dlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaa 66
                                   + + GLt+ae+a+r ++  +N ++e+  +++ +++  ++   +  +L v+ 
  gi|121636831|ref|YP_977054.1|  6 SATAGLTDAEVAQRVAEGKSNDIPERVTRTVGQIVRANVFTRINAILGVLL 56
                                   5689***************************99999998888888887765 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 5.1
                Cation_ATPase_N  56 nplvilLlvaalvs 69 
                                     +l+  L+v+a+++
  gi|121636831|ref|YP_977054.1| 710 TLLMTALWVLAVIA 723
                                    678999*****985 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17     5e+02      27      66 ..      22      61 ..      20     104 .. 0.83
   2 ?   -2.1   0.4      0.87   2.6e+03     123     173 ..     218     272 ..     196     277 .. 0.64
   3 ?    1.1   0.1      0.09   2.7e+02      89     140 ..     601     647 ..     562     654 .. 0.73
   4 ?   15.3   9.3     4e-06     0.012      40     177 ..     657     779 ..     629     784 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                Cation_ATPase_C 27 eppekdimkrpPrkkkepliskkmlrri.liqgllqalvtl 66
                                   e ++ di +r  r +  +++  ++++ri +i g+l+++v  
  gi|121636831|ref|YP_977054.1| 22 EGKSNDIPERVTR-TVGQIVRANVFTRInAILGVLLLIVLA 61
                                   6778888888888.888999999999999999999888764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.87
                Cation_ATPase_C 123 fsnkllllaillslllqvlivyvpglnavfgta....plsleewlialllalvvl 173
                                    f  +ll+ a ll++  q++ + v + ++v++++    p+ +e ++++  +a++v 
  gi|121636831|ref|YP_977054.1| 218 FITYLLVPAGLLTIYTQLFTTHVGWRESVLRMVgalvPMVPEGLVLMTSIAFAVG 272
                                    3567788888888888888888865444555443333777777777766666654 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.09
                Cation_ATPase_C  89 yaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqv 140
                                       ++ +  lv ++++ a+ lr+ +  lf+f+ ++    +++     +++ +
  gi|121636831|ref|YP_977054.1| 601 TVYSVLLALLVGIECLIAIPLRR-DPLLFPFQPIHVTIAAWFT----IGIPA 647
                                    45677888899999999999999.7789998888755444433....33333 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 4e-06
                Cation_ATPase_C  40 kkkepliskkmlrriliqgllqalvtllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkf 119
                                    ++ +p + +++++ ++  gl+++++t++++++++++  +s +e    +++a+t+a+itl ++ ++ + ++ +      + 
  gi|121636831|ref|YP_977054.1| 657 ERAYPGFVRRVMTSAVPFGLVIGVATFVTYLAAYQGRYASWQE----QEQASTAALITLLMTALWVLAVIAR------P- 725
                                    556666888999999********************88555555....357****************888888......3. PP

                Cation_ATPase_C 120 sglfsnkllllaillslllqvlivyv.pglnavfgtaplsleewlialllalvvllvde 177
                                         +++  la++l+ +l+ ++++  p  ++ f +   +l    ial++++v  +  e
  gi|121636831|ref|YP_977054.1| 726 ----YQWW-RLALVLASGLAYVVIFSlPLAREKFLLDASNLATTSIALAVGVVGAATIE 779
                                    ....3344.45555555555555555488888888877777777777777776665555 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.8   0.00068         2      10      47 ..     674     719 ..     666     729 .. 0.79
   2 ?   -0.4   0.1      0.54   1.6e+03       6      31 ..     762     787 ..     760     794 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00068
                            HRG  10 fgsilglsaflvylvlaivnkq................gvslptSfylsavWsl 47 
                                    fg+++g++ f++yl++  ++ +                +++      ++a+W+l
  gi|121636831|ref|YP_977054.1| 674 FGLVIGVATFVTYLAA--YQGRyaswqeqeqastaaliTLL------MTALWVL 719
                                    9***************..88778888888988888655444......8899987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                            HRG   6 aygifgsilglsaflvylvlaivnkq 31 
                                    a + +++++g++++++  +++ ++ +
  gi|121636831|ref|YP_977054.1| 762 ATTSIALAVGVVGAATIEAMWWIRSR 787
                                    567888999*****999999988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 4959.70
//
Query:       gi|121636832|ref|YP_977055.1|  [L=59]
Description: hypothetical protein BCG_0961 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-17   62.4   0.5    4.1e-17   62.2   0.5    1.1  1  MT0933_antitox  MT0933-like antitoxin protein
  ------ inclusion threshold ------
      0.096   13.1   0.1       0.11   13.0   0.1    1.1  1  Phage_Gp19      Phage protein Gp19/Gp15/Gp42


Domain annotation for each model (and alignments):
>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.5   4.6e-21   4.1e-17       1      46 [.       4      49 ..       4      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.6e-21
                 MT0933_antitox  1 fDKakdlaekhedkvdqgiDKAgdavddktGgKysdkIdkgqdaak 46
                                   +DK+k l++++ dkv+ +i KAg++vd++t+g ysd+I+k qdaa 
  gi|121636832|ref|YP_977055.1|  4 LDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLQDAAS 49
                                   6*******************************************97 PP

>> Phage_Gp19  Phage protein Gp19/Gp15/Gp42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.2e-05      0.11      11      44 ..       5      38 ..       2      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                     Phage_Gp19 11 draeaLlevasdelereikkvgkdldkmiaasae 44
                                   d++++Ll +  d++e+ i+k g  +d++ + + +
  gi|121636832|ref|YP_977055.1|  5 DKVKNLLSQNADKVETVINKAGEFVDEQTQGNYS 38
                                   89*********************99998765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 392.28
//
Query:       gi|121636833|ref|YP_977056.1|  [L=144]
Description: hypothetical protein BCG_0962 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-21   77.2   0.1    1.7e-21   77.0   0.1    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
       0.04   14.1   0.2       0.53   10.5   0.2    2.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
        0.2   11.6   0.0       0.24   11.4   0.0    1.1  1  IMS              impB/mucB/samB family


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.1   2.8e-25   1.7e-21       1     142 [.       1     142 [.       1     143 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.8e-25
                                    EEEEEEEEEESS-HHHHHHHHTTTTGGGGT..-TTEEEEECSE..STSSSTTTEEEEECCCS.SEEEEEEEEEET.TTTE CS
                Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprW..hpevarveleg..gggpargvegtvrvggr.gtvreelvevdp.egrl 74 
                                    m+k++ s++++ ppe++w ++sd++ +++W  ++ v r++l++  ++g+  +ve+ v v+g+ +++++++v++ p eg++
  gi|121636833|ref|YP_977056.1|   1 MAKLSGSIDVPLPPEEAWMHASDLTRYREWltIHKVWRSKLPEvlEKGT--VVESYVEVKGMpNRIKWTIVRYKPpEGMT 78 
                                    7899**************************8888999999998677888..999*********99*********659999 PP

                                    EEEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  75 lsyrivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarl 142
                                    l  ++   v++ +++   +v+p ++g+ v++++++ +++l gp+ +  +a+a+++d++++L+++ +++
  gi|121636833|ref|YP_977056.1|  79 LNGDG---VGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPI-GMIVAAALRADIRESLQNFVTVF 142
                                    99999...79999***********************88898998.7889**************99875 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   8.9e-05      0.53       1     128 [.      10     137 ..      10     139 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.9e-05
                                    ESS-HHHHHHHHTTTGGCCSCCCCEE.....EEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcs.....svevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfk 75 
                                    vp p+++++   +d  +y e+l   +       evle+ +  ++  +ev+  + +                         
  gi|121636833|ref|YP_977056.1|  10 VPLPPEEAWMHASDLTRYREWLTIHKvwrskLPEVLEKGT-VVESYVEVKGMPNR------------------------- 63 
                                    5677777777777777777777755533222244444444.22233333333333......................... PP

                                    EEEEEEEECTECCEEE......................CEEEEEEEEEEE..E-SSCHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  76 slegkWtieslppnsg......................gtrtkvalevdf..kfaspllgalvgqvaervldellaa 128
                                       +kWti+ ++p +g                      + + +v+++v++      +++g++v  +++ +++e l++
  gi|121636833|ref|YP_977056.1|  64 ---IKWTIVRYKPPEGmtlngdgvggvkvkliakvapkEHGSVVSFDVHLggPALLGPIGMIVAAALRADIRESLQN 137
                                    ...44555554442222222333333444444444444555566666666223334444555555556666655555 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.24      63     131 ..      17     136 ..      10     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                                    -EEEEEE-HHHHHHHHHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-S............................ CS
                            IMS  63 livvkvdlekyrraskkileilkrfispkvekasiDEayldltgleelaese............................ 114
                                    + +  +dl++yr+    i+++ ++  ++ +ek  + E y++++g+ ++ + +                            
  gi|121636833|ref|YP_977056.1|  17 AWMHASDLTRYREW-LTIHKVWRSKLPEVLEKGTVVESYVEVKGMPNRIKWTivrykppegmtlngdgvggvkvkliakv 95 
                                    66778999999987.5799******9*99***************99999999999************************* PP

                                    ........................HHHHHHHHHHHHHHHH- CS
                            IMS 115 ........................gaalakelrkaikeelg 131
                                                            g  +a++lr++i e l+
  gi|121636833|ref|YP_977056.1|  96 apkehgsvvsfdvhlggpallgpiGMIVAAALRADIRESLQ 136
                                    ************************99999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1012.82
//
Query:       gi|121636834|ref|YP_977057.1|  [L=257]
Description: hypothetical protein BCG_0963 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-18   64.9   0.4    4.2e-08   33.9   0.0    2.1  2  Glyoxalase_6  Glyoxalase-like domain
    7.2e-13   48.9   0.1    2.7e-06   27.6   0.0    3.0  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0086   16.3   0.2        9.6    6.5   0.1    3.1  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.8e-10   1.1e-06       4     105 ..      17     121 ..      14     123 .. 0.78
   2 !   33.9   0.0   7.1e-12   4.2e-08       4     106 ..     145     252 ..     142     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.8e-10
                   Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree....aaledpegvgpaaedaatllfqrvpe.paknrvHldlavedldaevarlva 78 
                                    l ++d++++ +F+ +++gw  e+        +  ++g++p     +  l+ ++pe +  + + + +++ d+ a+va+l a
  gi|121636834|ref|YP_977057.1|  17 LTTSDVDRAQDFYGTVFGWAFESAGpdygGYINAAKGGHP-----VAGLMANRPEfQSPDGWATYFHTVDIGATVAKLAA 91 
                                    5689*******************99666634444444444.....3334455555555567******************* PP

                   Glyoxalase_6  79 lGArvlreprdgthgr...vlaDPeGneFc 105
                                    +G++   +p +  +++      DP+G+ F 
  gi|121636834|ref|YP_977057.1|  92 AGGSSCLDPMEVPGKGfmsLAVDPSGAAFG 121
                                    ****999998888777899999*****995 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 7.1e-12
                   Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree.........aaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaeva 74 
                                    l ++d + +++F+++++gw+ e+ +         a+ +d++  g    d+ + l + vp      + + + +ed+d++ +
  gi|121636834|ref|YP_977057.1| 145 LTTRDYRSVIDFYRQVFGWRTEQISdtdefcyttAWFDDQQLLGV--MDGSSCLPEGVPS----NWTIFFGAEDVDETLR 218
                                    568999****************99966777766555555544444..5666666666666....6*************** PP

                   Glyoxalase_6  75 rlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                     + + G++v+r+ +    gr    aDP G +F +
  gi|121636834|ref|YP_977057.1| 219 VICDNGGSVVRAAENTPYGRlaAAADPMGVVFNL 252
                                    *****************999************86 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-07    0.0025       5     126 ..      15     120 ..      13     149 .. 0.89
   2 !   27.6   0.0   4.5e-10   2.7e-06       7     127 ..     145     251 ..     134     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                                    EEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEH CS
                     Glyoxalase   5 vallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdv 84 
                                    + l ++d++++ dFY  v+G+      +    + g  i +   g  +++l+ n+++  ++ ++            +++ +
  gi|121636834|ref|YP_977057.1|  15 IDLTTSDVDRAQDFYGTVFGWAFESAGP----DYGGYINAAKGGHPVAGLMANRPEFQSPDGW-----------ATYFHT 79 
                                    56889*****************999999....99999999999999****************9...........888889 PP

                                    CHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEE CS
                     Glyoxalase  85 edvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGill 126
                                     d+g+++ +l++ag++    p   + ++ +s  + Dp+G  +
  gi|121636834|ref|YP_977057.1|  80 VDIGATVAKLAAAGGSSCLDPMEVPGKGFMSL-AVDPSGAAF 120
                                    99999999999999988888888888888877.888888665 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 4.5e-10
                                    EEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCH CS
                     Glyoxalase   7 llvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdved 86 
                                    l ++d+   +dFY++v+G++    +d    +e+   ++  ++++ +++++ ++  ++ ++           + i++  ed
  gi|121636834|ref|YP_977057.1| 145 LTTRDYRSVIDFYRQVFGWRTEQISD---TDEFCYTTAWFDDQQLLGVMDGSSCLPEGVPS---------NWTIFFGAED 212
                                    7899**********************...56888888888999999999999999988888.........599******* PP

                                    HHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEE CS
                     Glyoxalase  87 vgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGille 127
                                    v+++l+ + ++g++vv+  + +++g+l    + Dp G+ + 
  gi|121636834|ref|YP_977057.1| 213 VDETLRVICDNGGSVVRAAENTPYGRLAA--AADPMGVVFN 251
                                    ****************************6..9*****9885 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1    0.0016       9.6       5      31 ..      17      43 ..      15     141 .. 0.61
   2 !    6.3   0.0    0.0018        11       6      97 ..     146     231 ..     143     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0016
                                   EE-S-HHHHHHHHHH.TT-EESS--E. CS
                   Glyoxalase_4  5 ivVeDleaavarfsallGvgpwqryrd 31
                                   + + D+++a +++++++G+ ++   +d
  gi|121636834|ref|YP_977057.1| 17 LTTSDVDRAQDFYGTVFGWAFESAGPD 43
                                   5689**************887755544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0018
                                    E-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES-HHHHHHH CS
                   Glyoxalase_4   6 vVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvddldaavar 85 
                                     ++D    ++++ +++G++ +q+   ++  +++a+++ ++      L    +g++ l e+ +  + + +  +d+d++++ 
  gi|121636834|ref|YP_977057.1| 146 TTRDYRSVIDFYRQVFGWRTEQISDTDEFCYTTAWFDDQQ------LLGVMDGSSCLPEGVPSNWTIFFGAEDVDETLRV 219
                                    678999999********99999988888888888888877......889999999999999999999999********** PP

                                    HCTTTEEEEEEE CS
                   Glyoxalase_4  86 leeqGfevvqkg 97 
                                      ++G +vv ++
  gi|121636834|ref|YP_977057.1| 220 ICDNGGSVVRAA 231
                                    999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1687.46
//
Query:       gi|121636835|ref|YP_977058.1|  [L=149]
Description: hypothetical protein BCG_0964 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        6.8    6.5   6.5        0.3   10.8   0.6    1.9  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
          8    6.1   7.2        1.1    8.9   1.0    2.1  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.8       0.9     8e+03      17      25 ..      31      39 ..      28      46 .. 0.52
   2 ?   10.8   0.6   3.4e-05       0.3      22      65 ..      69     113 ..      63     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.9
                Phage_holin_2_4 17 tggGavvsf 25
                                    ggG+ v  
  gi|121636835|ref|YP_977058.1| 31 VGGGGWVNA 39
                                   344444544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.4e-05
                Phage_holin_2_4  22 vvsfaGflasselialvGlavAl.iGlLvnWyYkreanRRaaaeh 65 
                                    v+++aG  +s +l ++  l+v l i +L  WyYk + n    ae+
  gi|121636835|ref|YP_977058.1|  69 VGAMAGRGLSVKLSSIAALVVSLlIVALTVWYYKLNVNPPVSAEY 113
                                    57889999999999999999985378999*****99886666665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.6     0.041   3.7e+02       5      24 ..       8      27 ..       3      80 .. 0.51
   2 ?    8.9   1.0   0.00012       1.1       3      56 ..      81     141 ..      78     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
                        DUF4131  5 lalvllalllllllllllll 24
                                    +lv+l ++++++ +   +l
  gi|121636835|ref|YP_977058.1|  8 GWLVALSAAVIAASTWMPWL 27
                                   44444444444444443332 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00012
                        DUF4131   3 lplalvllalllllllllllllrr.......rprrrvllllllllllallgfalrapqpna 56 
                                    l++ + l+++ll+++l+ ++++++        +   + ++ +++++ ++l++a++a++p++
  gi|121636835|ref|YP_977058.1|  81 LSSIAALVVSLLIVALTVWYYKLNvnppvsaEYGLYFGAAGGVCAVGCSLWAAVSAASPGR 141
                                    5666788888888888888888888888885555555666666666666777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 1020.77
//
Query:       gi|121636836|ref|YP_977059.1|  [L=502]
Description: dioxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.1e-103  346.5   0.0   3.5e-103  346.3   0.0    1.0  1  RPE65     Retinal pigment epithelial membrane protein


Domain annotation for each model (and alignments):
>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.3   0.0    2e-107  3.5e-103       2     463 .]      27     483 ..      26     483 .. 0.88

  Alignments for each domain:
  == domain 1  score: 346.3 bits;  conditional E-value: 2e-107
                                    S---S-EEEC--E..EEE---TT--EEEEEEEEE.ESCETTCCSSSGGGSEEEEEEEEECTTEEEEEEEE---HHHHHHH CS
                          RPE65   2 apvreevpeplevkvieGeiPawlkGtllRnGpgkpevgedgkvshwFDGdGmlhrfefkdgkvtyrnRfvrtdaylaer 81 
                                    +p+++e+++  +++ ++Ge+Pa+l+G +lRn  + p ++  ++++h+FDGdGm+h + f+dgk++yrnRf+rtd++lae+
  gi|121636836|ref|YP_977059.1|  27 RPQTTEWDAD-DLTTVTGEVPADLDGIYLRNTEN-PLHP-AFATYHPFDGDGMIHVVGFRDGKAFYRNRFIRTDGFLAEN 103
                                    7899999999.555568*****************.****.**************************************** PP

                                    HHTS--SBSTT..............TTSB-----SEEEEETTEEEEEE.TTCEEEEEETTTTEEEEE--CCC.....TTS CS
                          RPE65  82 kagkslfdglp..............akkkknnantnvvyhggrllalt.eagkpyeidpetLetlgkvdldg.....ese 141
                                    +ag++l++gl               +   k+ ++t v+ h+g +l++  + g +y+idp +  tlgk +++g     +  
  gi|121636836|ref|YP_977059.1| 104 EAGGPLWPGLAepvqlakrehgwgaRGLMKDASSTDVIVHRGIALTSFyQCGDLYRIDPYSANTLGKESWHGrfpfdW-- 181
                                    *******99989999999999**999999*************9999888*********************87777433.. PP

                                    -B-SS-EEETTCEEEEEEEECCTCECEEEEEEE-.T...T-.EEEEEEEECS.S..------EEE-SSEEEEEE--EECH CS
                          RPE65 142 aftAHpkvdpetgelynfglslgkppsvtysvfdvaaaidk.srevkiklpgeklkpayiHdfalTenyvvlvelplkln 220
                                     ++AHpkvd++tgel++f++s + +p+++y v+d +   ++  + v+++lpg    p + Hd+a+Tenyv+l ++pl ++
  gi|121636836|ref|YP_977059.1| 182 GVSAHPKVDNKTGELLFFNYSKQ-EPYMRYGVVDQN---NElVHYVDVPLPG----PRLPHDMAFTENYVILNDFPLFWD 253
                                    77******************987.5559******77...4456788899998....************************ PP

                                    C.HCCCTCGGCEEE-TTS-EEEEEEETTTT--GG...EEEEE--SEEEEEEEEEEET.TCEEEEEEEEE.SS.--STTS- CS
                          RPE65 221 lkkgkksggdalewdpekptrfgvipRrgekegvakfrwfeteaffvfHtaNayeeeedgevvvdlcryedaevldnlyl 300
                                    ++   +   +  ++ pe p+rf v+ Rrg++      rwfe+++ fv+H++Naye+  ++e+v+d     d++ ld+   
  gi|121636836|ref|YP_977059.1| 254 PRLL-ERDVHLPRFYPEIPSRFAVVARRGND-----IRWFEADPTFVLHFTNAYEQ--GDEIVLDGFYEGDPQPLDTGGT 325
                                    9433.4455666****************932.....39****************99..7778899765544434433322 PP

                                    CT.T----.-...GG.....TGGG-EEEEEEEEETTTTTCEECE.EEEEESS-EEEEE--GGGTTS--SEEEEEE-SSTT CS
                          RPE65 301 enlrsrkgeakkeek.....aeesqsrlrryrldlktgsateekeeaalsdrslEfPrinpaysgrkyryvYgasasggs 375
                                    +          +e+       ++ qsrl+r+rl++ tg+++ee    +ls+  +Ef +in +y+   yry+Y+a+ + ++
  gi|121636836|ref|YP_977059.1| 326 K----------WEKLfrflaLDRLQSRLHRWRLNMVTGAVHEE----QLSESITEFGTINADYAASSYRYTYAATGKPSW 391
                                    2..........222233444237899*********99999998....9****************************7764 PP

                                    SS-..--EEEEEET-TTTE.........EE--EEEEESTTTSSTT-EEEEEEEEET.TTEEEEEEEETTBCCC..SEEEE CS
                          RPE65 376 dkaskfdglvkvDletkgrea....eghypgEpiFVPragateEDdGvllsvvlde.eersellvldAktlte..vArve 448
                                         fdglvk+Dl t ++e     +g+y +E    Pr g+++EDdG+l+++  d  ++ s++lv+dA++  +  ++++ 
  gi|121636836|ref|YP_977059.1| 392 ---FLFDGLVKHDLLTGNHECysfgDGVYGSETAMAPRVGSSAEDDGYLVTLTTDMnDDASYCLVFDAARPGDgpICKLA 468
                                    ...367********9997766999999***************************88************************ PP

                                    ESS---S--BEEEEE CS
                          RPE65 449 lpqrvpygfHGtfvp 463
                                    lp r+  g H  +vp
  gi|121636836|ref|YP_977059.1| 469 LPERISSGTHSAWVP 483
                                    *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3411.21
//
Query:       gi|121636837|ref|YP_977060.1|  [L=412]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-10   38.5   0.5    7.4e-09   35.4   0.5    2.1  1  Thiolase_N     Thiolase, N-terminal domain
    5.4e-08   32.5   0.0    1.1e-07   31.5   0.0    1.5  1  Thiolase_C     Thiolase, C-terminal domain
    0.00065   19.4   0.6     0.0016   18.1   0.6    1.6  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.5   1.2e-12   7.4e-09       3     258 ..       7     235 ..       5     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                                    EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHT.......TS-TT CS
                     Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalka.......gipee 75 
                                    i +++ + + + + s ++    +L +e++ + l+ a+vd++++    v  v++a+ g++ arq +l a       ++ ++
  gi|121636837|ref|YP_977060.1|   7 ILGGYQSDFAR-NLSKENRDFADLTREVVDGTLTAAKVDAADLAAAGVVHVANAF-GEMFARQGHLGAmpatvcdDL-WD 83 
                                    55666666666.5667778889*********************999998888885.556666655543222222155.89 PP

                                    SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSS.SSEE.EEEHHHHHHTEETTTTS CS
                     Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglkl.gdek.akdllipdgladafnee 153
                                    +pa++ + +c+Sg  a  +a+  +++g++ v++++G E   ++p +++++  s +   g+e      l p+         
  gi|121636837|ref|YP_977060.1|  84 TPATRHEAACASGSVATLAAMADLRSGAYRVALVVGLELEKTVPGDTAAEHLSAAAWtGHEGaEARYLWPS--------- 154
                                    9**************************************99999988866554333202222023334444......... PP

                                    EHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSS CS
                     Thiolase_N 154 hmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaF 233
                                    + +  a+++ ++y+++ +++ + A  + ++a+ +++a+     i P    +      ++ d+a ++ +t  +L++     
  gi|121636837|ref|YP_977060.1| 155 MFAQVADEYDRRYGLDDTHLRAIAQLNFANARRNPNAQTRGWTI-P----D-----PITDDDATNP-LTEGRLRRF---- 219
                                    78999********************************9555544.3....2.....3344555544.888888888.... PP

                                    STTSS-BTTSB--BEEEEEEEEEEE CS
                     Thiolase_N 234 kkeGtvtAgnasqisDGaaavllms 258
                                             ++sq++DG a ++l+s
  gi|121636837|ref|YP_977060.1| 220 ---------DCSQMTDGGAGLVLVS 235
                                    .........8888888888888876 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.9e-11   1.1e-07      28     102 ..     287     379 ..     266     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.9e-11
                                    HHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHH CS
                     Thiolase_C  28 ikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRi 89 
                                    +  +l +a +t++d+d +E+++ F+     ++ +++l                      +N  GG i  GHP+GasG+R+
  gi|121636837|ref|YP_977060.1| 287 VLDALRRARVTLDDLDGIEVHDCFTPSEYLAIDHIGLTGpgeswkaiengeieiggrLPINPSGGLIGGGHPVGASGVRM 366
                                    45799********************999999999**99999**************98889******************** PP

                                    HHHHHHHHHHCTT CS
                     Thiolase_C  90 vvtllselkkegg 102
                                    +  +++++    g
  gi|121636837|ref|YP_977060.1| 367 LLDAAKQVSGIAG 379
                                    *999988766555 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.6   2.7e-07    0.0016     167     205 ..      85     123 ..      81     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-07
                                    SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE-- CS
                  ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvell 205
                                    p+   ++AC+S+ va  aa+  lrsg   val+ G el 
  gi|121636837|ref|YP_977060.1|  85 PATRHEAACASGSVATLAAMADLRSGAYRVALVVGLELE 123
                                    667779******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2851.17
//
Query:       gi|121636838|ref|YP_977061.1|  [L=423]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-60  201.9  30.2    5.9e-60  201.9  30.2    2.2  2  PPE       PPE family
    3.8e-14   53.3  14.3    3.8e-14   53.3  14.3    4.8  2  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.9  30.2   6.6e-64   5.9e-60       2     157 ..       6     161 ..       5     162 .. 0.99
   2 ?    0.0   1.7      0.09     8e+02      75     102 ..     180     206 ..     173     232 .. 0.60

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 6.6e-64
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPEvns ++y+Gpg++++laAaaaWdg+aael+saa ++ sv+++l  e W Gp++aamaaaa+py+ WL+a+aa a+e
  gi|121636838|ref|YP_977061.1|   6 LPPEVNSSRMYSGPGPESMLAAAAAWDGVAAELTSAAVSYGSVVSTLIVEPWMGPAAAAMAAAATPYVGWLAATAALAKE 85 
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +A+qa+aaa+a+ +A+a++vpp ++aanr +l++lva+n++Gqn++aIaat aey+emwaqdaa+m++Ye asaaa
  gi|121636838|ref|YP_977061.1|  86 TATQARAAAEAFGTAFAMTVPPSLVAANRSRLMSLVAANILGQNSAAIAATQAEYAEMWAQDAAVMYSYEGASAAA 161
                                    *************************************************************************997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.09
                                    HHHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                            PPE  75 aaaqaeeaAaqaeaaaaaYeaAlaamvp 102
                                    aaa a+++Aa a a+a a +a+la+ +p
  gi|121636838|ref|YP_977061.1| 180 AAAAAATQAAGAGAVADA-QATLAQLPP 206
                                    455555555555555555.445555555 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -36.9  49.5         2   1.8e+04      54      54 ..     107     107 ..      17     249 .. 0.67
   2 !   53.3  14.3   4.3e-18   3.8e-14       1      71 [.     319     395 ..     319     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -36.9 bits;  conditional E-value: 2
                       PE_PPE_C  54 l 54 
                                     
  gi|121636838|ref|YP_977061.1| 107 P 107
                                    2 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 4.3e-18
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal......sgttaaaaaaaagaalggmPlaaagaggaaggaapryg 71 
                                    sAg+G+Aa+vGaLSVP+sW++aap+++ a++a+       g+ ++a  ++++++l+gm+la+++a+g++gg+++r g
  gi|121636838|ref|YP_977061.1| 319 SAGVGHAALVGALSVPHSWTTAAPEIQLAVQATptfsssAGADPTALNGMPAGLLSGMALASLAARGTTGGGGTRSG 395
                                    8*******************************977776666666777777777777*****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2934.16
//
Query:       gi|121636839|ref|YP_977062.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-26   92.1   6.1    2.3e-26   91.9   6.1    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   6.1   1.3e-30   2.3e-26       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.3e-30
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++P +laaa++dl +ig+a+sa n+a+ aptt+vl++aa +VS+ +Aa f+ah ++y+ +s+ aa +h +fv+  aa
  gi|121636839|ref|YP_977062.1|  1 MSFVTIQPVVLAAATGDLPTIGTAVSARNTAVCAPTTGVLPPAANDVSVLTAARFTAHTKHYRVVSKPAALVHGMFVALPAA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                    a++Ya++Ea
  gi|121636839|ref|YP_977062.1| 83 TADAYATTEA 92
                                   *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 735.87
//
Query:       gi|121636840|ref|YP_977063.1|  [L=593]
Description: glycine betaine transport integral membrane protein betP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-181  601.5  41.7     1e-180  601.3  41.7    1.0  1  BCCT      BCCT, betaine/carnitine/choline family transporter
  ------ inclusion threshold ------
       0.45   10.4   5.9          8    6.4   0.3    2.7  2  ODV-E18   Occlusion-derived virus envelope protein ODV-E18


Domain annotation for each model (and alignments):
>> BCCT  BCCT, betaine/carnitine/choline family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.3  41.7  1.2e-184    1e-180       1     482 [.      23     508 ..      23     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 601.3 bits;  conditional E-value: 1.2e-184
                           BCCT   1 vflvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefstlsW 80 
                                    vf+ + ++iv+++++ +v ++ +e+++ +lns+i+  +gw+y+l++++f+vf+l+  +s++g+i+LG+dde pefs++ W
  gi|121636840|ref|YP_977063.1|  23 VFIPASVVIVAMIVVSVVYSSVAENAFVRLNSAITGGVGWWYILVATGFVVFALYCGISRIGTIRLGRDDELPEFSFWAW 102
                                    89999*************************************************************************** PP

                           BCCT  81 famlfaaglgigllfwgvaEplahylspppga..eagteeaaqeAlaytffhwGlhaWaiyalvalalayfayrkglplt 158
                                    +amlf+ag+gigl+f+gvaEpl+hyl+pp +    a t++aa++A+a+t+fhwGlhaWaiy++v+l +ay++yr+g+pl+
  gi|121636840|ref|YP_977063.1| 103 LAMLFSAGMGIGLVFYGVAEPLSHYLRPPRSRgvPALTDAAANQAMALTVFHWGLHAWAIYVVVGLGMAYMTYRRGRPLS 182
                                    ***************************995555589999999************************************** PP

                           BCCT 159 issalypllge.ringllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvitalatvsavsG 237
                                    ++ +l p++g+ r++g+lg++vDv+a+++t+fGvatslG+g++qi++gl++l  i+  +++ + +i++ita+at+s+vsG
  gi|121636840|ref|YP_977063.1| 183 VRWLLEPVVGRgRVEGALGHAVDVIAIVGTLFGVATSLGFGITQIASGLEYLGWIRVDNWWMVGMIAAITATATASVVSG 262
                                    **********989******************************************************************* PP

                           BCCT 238 ldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaaeeaeewlasWTvFyWawwiawap 317
                                    ++kG+k+lSn+n++la++l+lfvll+Gptlf+l+++vq+lg y+q+l++++l+t+++++++ wl +WT+FyW+wwi+wap
  gi|121636840|ref|YP_977063.1| 263 VSKGLKWLSNINMALAAALALFVLLLGPTLFLLQSWVQNLGGYVQSLPQFMLRTAPFSHDG-WLGDWTIFYWGWWISWAP 341
                                    **********************************************************999.****************** PP

                           BCCT 318 fvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaeaaeasveaalfalleqlplgsilsvl 397
                                    fvG+FiAriSrGRtiRefi +vllvpt++  lwft++G +a+  ++++   l++  + +++++lf+ll+ lp+g+i+svl
  gi|121636840|ref|YP_977063.1| 342 FVGMFIARISRGRTIREFIGAVLLVPTVIASLWFTIFGDSALLRQRNNGDMLVN-GAVDTNTSLFRLLDGLPIGAITSVL 420
                                    ******************************************999998888888.899********************** PP

                           BCCT 398 avvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllagg...lealqsasiiaalPftlvlllm 474
                                    av++i++ffvTs+DS++lv++ l++gg+ +pp+ +rv+W+vl+g+ aavlll+gg   l+al++a+i++alPf++v++++
  gi|121636840|ref|YP_977063.1| 421 AVLVIVFFFVTSSDSGSLVIDILSAGGELDPPKLTRVYWAVLEGVAAAVLLLIGGagsLTALRTAAIATALPFSIVMVVA 500
                                    *****************************************************88888********************** PP

                           BCCT 475 vvsllkal 482
                                    +++++ka+
  gi|121636840|ref|YP_977063.1| 501 CYAMTKAF 508
                                    *****997 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3   0.00089         8      15      52 ..      12      47 ..       4      60 .. 0.77
   2 ?    5.4   1.1    0.0018        16       8      50 ..     397     436 ..     391     446 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00089
                        ODV-E18 15 strrlarlePsllltilvvlviiillvllvqssstGsd 52
                                   +   l  ++P++++   + +vi++++v+ v  ss+ ++
  gi|121636840|ref|YP_977063.1| 12 VVDALRSIQPAVFI--PASVVIVAMIVVSVVYSSVAEN 47
                                   55667778888885..5788899999999999997766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0018
                        ODV-E18   8 ttstdagstrrlarlePsllltilvvlviiillvllvqssstG 50 
                                    ++ t+++  r l++l    +  +l+vlvi+ ++v    ss +G
  gi|121636840|ref|YP_977063.1| 397 AVDTNTSLFRLLDGLPIGAITSVLAVLVIVFFFV---TSSDSG 436
                                    5678888999999999999999999999876554...344333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3889.27
//
Query:       gi|121636841|ref|YP_977064.1|  [L=158]
Description: hypothetical protein BCG_0970 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-24   85.6   3.8    1.7e-24   85.6   3.8    1.4  2  DUF1778   Protein of unknown function (DUF1778)


Domain annotation for each model (and alignments):
>> DUF1778  Protein of unknown function (DUF1778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.61   1.1e+04      64      75 ..      28      39 ..      28      42 .. 0.67
   2 !   85.6   3.8   9.3e-29   1.7e-24       1      77 [.      74     150 ..      74     152 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.61
                        DUF1778 64 ppkpnprLlkaa 75
                                   p++ ++rL++ a
  gi|121636841|ref|YP_977064.1| 28 PVATQQRLRRQA 39
                                   567778888766 PP

  == domain 2  score: 85.6 bits;  conditional E-value: 9.3e-29
                        DUF1778   1 RLelRispeakeliqrAAalsgktltdFvleaaleaAekviedherieLseedfqafvaaLdeppkpnprLlkaarr 77 
                                    RL +R++pe+ +li+rAA+++g++lt+F ++aal++A++v++d++ + L+++++++f+aaLd+p++++prL+k++++
  gi|121636841|ref|YP_977064.1|  74 RLAARLTPEQDALIRRAAEAEGTDLTNFTVTAALAHARDVLADRRLFVLTDAAWTEFLAALDRPVSHKPRLEKLFAA 150
                                    99************************************************************************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1125.23
//
Query:       gi|121636842|ref|YP_977065.1|  [L=166]
Description: hypothetical protein BCG_0971 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-10   40.3   0.0    3.9e-10   40.0   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.2e-09   35.9   0.0    3.2e-08   33.5   0.0    1.8  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.8e-08   33.6   0.0    5.9e-08   33.0   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.096   12.8   0.0       0.47   10.5   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   8.7e-14   3.9e-10      28     117 .]      38     143 ..       9     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 8.7e-14
                                    HHSTTCEEEEEEETTEEEEEEEEEEEET..............TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT. CS
                 Acetyltransf_1  28 fsleaegllvaeedgeliGfisllkipd..............ekggvayieslaVspeyrgkGlGsaLlealeeraree. 92 
                                    + +  ++++v ++dg+++Gf  l                      +v+ + +laV+++ +g+GlGs+Ll++++ r+ +  
  gi|121636842|ref|YP_977065.1|  38 HVQGGSRCFVTCRDGRVVGFYALASGSVahadapgrvrrnmpDPVPVILLSRLAVDRKEQGRGLGSHLLRDAIGRCVQAa 117
                                    3334448999***********66666666666666666667677899999***********************6666664 PP

                                    ...TESEEEEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  93 ...gikkivlaveedndaairlYeklGF 117
                                       g+++  l v++ +d a+++Y  + F
  gi|121636842|ref|YP_977065.1| 118 dsiGLRA-IL-VHALHDEARAFYVHFDF 143
                                    3236666.44.6677999*****77766 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   7.2e-12   3.2e-08      14     107 ..      27     144 ..      15     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 7.2e-12
                Acetyltransf_10  14 kefispealrerieegealllvaeeggkivGvielrdgs.....................hisllfVdpeyrgqGigkaL 72 
                                    ++++ + al++++ +g   ++v  ++g++vG+ +l +gs                      +s+l+Vd++ +g+G+g+ L
  gi|121636842|ref|YP_977065.1|  27 DDYLRKRALANHV-QGGSRCFVTCRDGRVVGFYALASGSvahadapgrvrrnmpdpvpviLLSRLAVDRKEQGRGLGSHL 105
                                    5778888899999.8888899999999999999998888899999999999999**99999******************* PP

                Acetyltransf_10  73 leaveeeaekdgikl...eltvnasp.yavpfYeklGFk 107
                                    l +++ ++ ++  ++   ++ v+a + +a++fY ++ F+
  gi|121636842|ref|YP_977065.1| 106 LRDAIGRCVQAADSIglrAILVHALHdEARAFYVHFDFE 144
                                    *******99888877779******999***********8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.3e-11   5.9e-08       3      75 ..      43     144 ..      41     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.3e-11
                                    EEEEEEEETTEEEEEEEEEEES....................TCTEEEEE-GGGTTSSHHHHHHH.H......TT..SEE CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld....................aeitrlaVdpeyrgkGiGraLle.a......ae..kgi 53 
                                    +++fV  +dg++vGf+al+  +                      + rlaVd + +g+G+G+ Ll+ a      a+   g+
  gi|121636842|ref|YP_977065.1|  43 SRCFVTCRDGRVVGFYALASGSvahadapgrvrrnmpdpvpvILLSRLAVDRKEQGRGLGSHLLRdAigrcvqAAdsIGL 122
                                    689************99999989999999888888887775555555*****************9665555431133332 PP

                                    E..EEEEEETHHHHHHHHHHTTEE CS
                 Acetyltransf_7  54 i..leqlelnaekaikfYeklGFe 75 
                                    +  l+   l++ +a++fY ++ Fe
  gi|121636842|ref|YP_977065.1| 123 RaiLV-HALHD-EARAFYVHFDFE 144
                                    22222.23333.7999******98 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001      0.47      70     109 ..      81     120 ..      17     146 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                    EEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--E CS
                 Acetyltransf_9  70 tlkaagvtgVavapehrgrgvlskLlaraleemreegqpl 109
                                     +++  ++  av+ +++grg+ s+Ll+ a++++ +  +++
  gi|121636842|ref|YP_977065.1|  81 PVPVILLSRLAVDRKEQGRGLGSHLLRDAIGRCVQAADSI 120
                                    578899999*********************9998765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1228.09
//
Query:       gi|121636843|ref|YP_977066.1|  [L=439]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-145  484.5   0.0   2.6e-145  484.0   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
    0.00012   21.7   0.0       0.39   10.1   0.0    2.5  2  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
       0.03   14.6   0.0      0.084   13.1   0.0    1.8  1  DDE_Tnp_IS240    DDE domain
      0.059   13.0   0.0        6.1    6.6   0.0    2.6  2  Sigma70_r4_2     Sigma-70, region 4
      0.065   13.3   0.0       0.24   11.5   0.0    2.0  1  EutK_C           Ethanolamine utilization protein EutK C-term
       0.11   13.1   0.0       0.51   11.0   0.0    2.2  2  HTH_32           Homeodomain-like domain
       0.17   12.3   0.0       0.57   10.6   0.0    1.9  2  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.0   0.0    1e-148  2.6e-145       6     375 ..      33     405 ..      29     407 .. 0.97

  Alignments for each domain:
  == domain 1  score: 484.0 bits;  conditional E-value: 1e-148
                Transposase_mut   6 lllelealkaie..easgkddllkellktvleelleaeldealgaeryerseers.nqRnGsrerklsTrag.tlelriP 81 
                                    l+ +l++++++e  +++g d+llk+l+ktvle++l++e++e+lg++r++++++ s n+RnGsr++k++T+a+ ++e+++P
  gi|121636843|ref|YP_977066.1|  33 LVGDLVRQARAEgvALTGPDGLLKALTKTVLEAALQEEMTEHLGYDRHAAAGRGSgNSRNGSRNKKVITDACgQVEIAVP 112
                                    56677777777666899*****************************************************998******* PP

                Transposase_mut  82 rdRsGsFspallerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeeke 161
                                    rdR+G+F+p+++ ++kRr +++++vv++ly+kG++t++++++++++yg +svSk+++S+it+++ e+++a+++R+Le++ 
  gi|121636843|ref|YP_977066.1| 113 RDRNGTFEPVIVGKRKRRVTDVDRVVLSLYAKGLTTGEIAAHFADVYG-VSVSKDTISRITDRVIEEMQAWWSRPLEKV- 190
                                    ************************************************.99****************************. PP

                Transposase_mut 162 ypllflDalylkvReegrvvskavliaigvdadGsreiLgleva..dsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                    y+++f+Da+++k+R +g+v++++v++aigvd dG+++iLg++++  d+Es+kfWlavl++L+nrG+k++ ++v+D++kGL
  gi|121636843|ref|YP_977066.1| 191 YAAVFIDAIMVKIR-DGQVRNRPVYAAIGVDLDGHKDILGMWAGegDGESAKFWLAVLTELRNRGVKDIFFLVCDGLKGL 269
                                    **************.9***************************98899******************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    ++++sa+fp a+vQ+C++Hl+rn+++++++k++dk++ +lk iy+a++a+ear ++eef+ek+gk yp++++l+d+a+e+
  gi|121636843|ref|YP_977066.1| 270 PDSVSAAFPLATVQTCIIHLIRNTFRYASRKYWDKISVDLKPIYTAASAAEARLRYEEFAEKWGKPYPAITRLWDSAWEE 349
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeah 375
                                    +++fl+++ +irr  +stN++E+LN+++rR++r++g+FPne+s+l+++++v+++++
  gi|121636843|ref|YP_977066.1| 350 FIPFLDYDVEIRRVPCSTNAIESLNARYRRAVRARGHFPNEQSALKTLYLVTRSLD 405
                                    ***************************************************99876 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00015      0.39      11      64 ..     136     190 ..     134     198 .. 0.87
   2 !    8.9   0.0   0.00037      0.95     127     189 ..     260     322 ..     245     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                   DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarl.Gvelsrgtlanwvkraaelleplvealkaal 64 
                                    +++++ ya++l    +++++a++ Gv +s+ t+++ + r+ e+++    +  +++
  gi|121636843|ref|YP_977066.1| 136 RVVLSLYAKGLTTGEIAAHFADVyGVSVSKDTISRITDRVIEEMQAWWSRPLEKV 190
                                    589999************************************9998776655555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00037
                   DDE_Tnp_IS66 127 vlvsDgyagYnklae...eqvthalCwaHlrRkfvdaeeakkksqaaaealarigklyaierear.e 189
                                    +lv+Dg +g     +   + +t + C  Hl R+ ++   +    +++++   +++ +y+++ +a+ +
  gi|121636843|ref|YP_977066.1| 260 FLVCDGLKGLPDSVSaafPLATVQTCIIHLIRNTFRYASR----KYWDKISVDLKPIYTAASAAEaR 322
                                    799*******98655689999**************99975....689999999*****988887432 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.3e-05     0.084      85     127 ..     356     398 ..     286     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                  DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktla 127
                                     +v+ + v+   n iEs ++++++ +r+ + f + +sa ktl 
  gi|121636843|ref|YP_977066.1| 356 YDVEIRRVPCSTNAIESLNARYRRAVRARGHFPNEQSALKTLY 398
                                    67899999******************************99986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0024       6.1      14      41 ..     134     164 ..     124     165 .. 0.82
   2 ?    3.5   0.0     0.022        57       6      21 ..     368     383 ..     367     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                                    HHHHHHHHHHTS---HHHHHHHH....T--HH CS
                   Sigma70_r4_2  14 rqreifllryleglsykEIAell....giseg 41 
                                     +r ++ l y +gl++ EIA+ +    g+s++
  gi|121636843|ref|YP_977066.1| 134 VDRVVLSL-YAKGLTTGEIAAHFadvyGVSVS 164
                                    57888888.99*********999888887775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.022
                                    HHHTTS-HHHHHHHHH CS
                   Sigma70_r4_2   6 ealaeLperqreifll 21 
                                    +a+++L  r+r+++  
  gi|121636843|ref|YP_977066.1| 368 NAIESLNARYRRAVRA 383
                                    69***********975 PP

>> EutK_C  Ethanolamine utilization protein EutK C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-05      0.24      15      28 ..     143     156 ..     136     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                         EutK_C  15 rqGmtaGevaahfa 28 
                                     +G+t Ge+aahfa
  gi|121636843|ref|YP_977066.1| 143 AKGLTTGEIAAHFA 156
                                    47***********8 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.2   1.1e+04      29      44 ..      26      41 ..      20      70 .. 0.64
   2 ?   11.0   0.0    0.0002      0.51      25      72 ..     127     171 ..     105     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                         HTH_32 29 lsdevrariiallree 44
                                   ls ++ra + +l+r++
  gi|121636843|ref|YP_977066.1| 26 LSGAERALVGDLVRQA 41
                                   5666666666666433 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                         HTH_32  25 rprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                    r+r+++d  r  +   +  +  +++ ++aa+ a+ +gv+vS+ t+ ri
  gi|121636843|ref|YP_977066.1| 127 RKRRVTDVDRVVLSLYA--K-GLTTGEIAAHFADVYGVSVSKDTISRI 171
                                    44455554444444444..3.689***********************8 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.3   1.1e+04      66      76 ..     171     181 ..     148     203 .. 0.59
   2 ?   10.6   0.0   0.00022      0.57      38      96 .]     236     292 ..     209     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.3
                           MULE  66 itDkekallna 76 
                                    itD+  + ++a
  gi|121636843|ref|YP_977066.1| 171 ITDRVIEEMQA 181
                                    34433333333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                           MULE  38 eseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                    + e+ + +  +l+el+++ +  +    +++D  k+l   +++ fp a ++ C+ H+ +n
  gi|121636843|ref|YP_977066.1| 236 DGESAKFWLAVLTELRNRGV--KDIFFLVCDGLKGLPDSVSAAFPLATVQTCIIHLIRN 292
                                    67888888888889888644..588899***************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3130.52
//
Query:       gi|121636844|ref|YP_977067.1|  [L=193]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-20   72.5   0.2    4.7e-20   72.2   0.2    1.1  1  Resolvase  Resolvase, N terminal domain
    0.00063   19.9   0.0     0.0016   18.6   0.0    1.7  1  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.035   13.9   0.0    1.7  1  HTH_23     Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.2   7.8e-24   4.7e-20       1     143 [.      52     189 ..      52     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 7.8e-24
                                    EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S.. CS
                      Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsv 80 
                                    +++YaRvS+++ + +l+rQ+++l+a+a+e++l + +++ +   SG + +Rp+l+r l++  +   +v+vve+ dRLaR  
  gi|121636844|ref|YP_977067.1|  52 VVLYARVSSHDRRSDLDRQVARLTAWATERDLGVGQVVCEV-GSGLNGKRPKLRRILSDPDA---RVIVVEHRDRLARFG 127
                                    689********8888***************9999999****.****************9999...7*************8 PP

                                    .S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHH.HHHHHHCT-TTHHHHHHHH CS
                      Resolvase  81 rdlltlleelrekgvslvsldegidtstpm.grlllqilaalaef.erelirertkeglaaakak 143
                                     + l+    l+++g ++v++d   +t+++    ++  + +++a++  r+  r+r ++++ +ak++
  gi|121636844|ref|YP_977067.1| 128 VEHLEA--ALSAQGRRIVVADP-GETTDDLvCDMIEVLTGMCARLyGRRGARNRAMRAVTEAKRE 189
                                    888877..8************5.455555548889999999999867899999999999999876 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.6e-07    0.0016       5      38 ..       4      39 ..       1      43 [. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-07
                         HTH_17  5 eEaAelLgvsrstvyrlirrgelpaa...kiGrrwri 38
                                   ++ Ae  gv r+t+yr+ r+g l ++   ++Gr +++
  gi|121636844|ref|YP_977067.1|  4 ADWAESVGVNRHTAYRWFREGTL-PVpaeRVGRLILV 39
                                   5668888****************.5547778887766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-06     0.035      21      39 ..       4      22 ..       1      27 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                         HTH_23 21 reIAreLgvsrrTvyrwlk 39
                                   ++ A+  gv+r+T yrw +
  gi|121636844|ref|YP_977067.1|  4 ADWAESVGVNRHTAYRWFR 22
                                   678999***********55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1370.27
//
Query:       gi|121636845|ref|YP_977068.1|  [L=550]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-30  104.5   0.0    6.9e-30  103.7   0.0    1.3  1  OrfB_IS605      Probable transposase
    1.9e-05   24.5   0.0    4.8e-05   23.2   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0012   18.3   0.5      0.072   12.6   0.0    2.4  2  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   1.2e-33   6.9e-30       3     117 ..     271     394 ..     269     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.2e-33
                     OrfB_IS605   3 pveveve...lpkpkgnkaagiDlGinnLatvvtedgtw......flykgrrlksdykylakeiaelqsklkksknykka 73 
                                    +++++++   +p ++++ +ag+DlG+++Latv+t d+++      +++++++lk+++ + +++ +el++++++s+ ++++
  gi|121636845|ref|YP_977068.1| 271 CYALRTPttrSPLTQPTVRAGMDLGVRTLATVATLDTATgeqtiiEYPNPAPLKATLVARRRAGRELSRRIPGSHGHRAV 350
                                    6666666667999***********************999***************************************** PP

                     OrfB_IS605  74 srklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                    ++klarl+r++ + r++++h+l+t+l+ t+ +v++e+L+v++mk
  gi|121636845|ref|YP_977068.1| 351 KAKLARLDRRCVHLRREAAHQLTTELAGTYGQVVIEDLDVAAMK 394
                                    *******************************************9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     8e-09   4.8e-05       7      67 ..     417     485 ..     413     486 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8e-09
                 OrfB_Zn_ribbon   7 qleykakeyGikveevnpay.TSktCseCgsknke.......alsgrtfkCpnCgfeadrDvnAaiNil 67 
                                    ql+yk  +    ++++++++ +S+  + C s + +        + ++ + Cp  g + drD nAa+N+ 
  gi|121636845|ref|YP_977068.1| 417 QLAYKTAKCSGVLTVADRWFaSSQIHHGCTSPDGTpcrlqgkGRIDKHLLCPVTGEVVDRDRNAALNLR 485
                                    7999999999999999***99***********9999999888888999*******************96 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   1.2e-05     0.072      15      38 ..      99     122 ..      84     127 .. 0.80
   2 ?    3.2   0.3      0.01        62      28      46 ..     146     164 ..     143     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                 HTH_OrfB_IS605  15 eQeeklartfGcvRfVYNkaLaer 38 
                                    + + + + +fG+ R ++N++La+ 
  gi|121636845|ref|YP_977068.1|  99 QRAGLVRSHFGARRKAFNWGLAQV 122
                                    555566789*************86 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.01
                 HTH_OrfB_IS605  28 RfVYNkaLaerkeayeeeg 46 
                                    R+++N+a ++   +++e+ 
  gi|121636845|ref|YP_977068.1| 146 RWAWNRAKDDVAPWWAENS 164
                                    *******999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 4240.98
//
Query:       gi|121636846|ref|YP_977069.1|  [L=354]
Description: hypothetical protein BCG_0975c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-42  145.1   0.0    2.2e-42  144.7   0.0    1.1  1  Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase
    3.4e-14   53.0   0.0    6.5e-14   52.1   0.0    1.4  1  AIG2_2           AIG2-like family
    1.5e-12   48.1   0.0    3.8e-12   46.9   0.0    1.7  2  GGACT            Gamma-glutamyl cyclotransferase, AIG2-like


Domain annotation for each model (and alignments):
>> Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   3.6e-46   2.2e-42      16     166 ..     168     322 ..     160     329 .. 0.92

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 3.6e-46
                Gamma_PGA_hydro  16 dyrieeeekkksrllvlaiHGGgiEpgtseiaeaiae.adysvYlfeglkksgnkelHitStrFdeplalklak...eae 91 
                                    ++ + e+++ +sr+++laiHGGg+E++t+ iae+ ae a +svYl++++++   +++H++S+rFd +++++la+   +++
  gi|121636846|ref|YP_977069.1| 168 QPGVIETSQLRSRFGFLAIHGGGLEQVTDLIAERSAEaAGASVYLLRHPDN---YPHHLPSARFDPAESARLAEfldHVD 244
                                    5678888999***************************9**********998...******************99999*** PP

                Gamma_PGA_hydro  92 vvvslHGyeeee..ehvlvGGtdrelaekiveaLeeaGfsv....elapekeelagtspeNivNrtktgegvqLElsral 165
                                    v+vslHGy++ +  +++l+GG++r+la++++++++ +G++v    +++p  eel+g +p+N+vNr+++g g+qLEls ++
  gi|121636846|ref|YP_977069.1| 245 VAVSLHGYDRIGrsTQLLAGGRNRALAAHLARHIQLPGYRVvtdlAAIP--EELRGLHPDNPVNRVRDG-GTQLELSIRV 321
                                    *********9998899*************************87544455..5***************99.********** PP

                Gamma_PGA_hydro 166 R 166
                                    R
  gi|121636846|ref|YP_977069.1| 322 R 322
                                    9 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   1.1e-17   6.5e-14       1      83 []      57     137 ..      57     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                         AIG2_2   1 eVfGvlweidlenlkdLDkqEgvedgiyrpievrVstatgeevlaraYvlsnqpetkPsetYlkvlvkGAeesglPedYv 80 
                                    +V Gvlw++++++l +LD+ Egv+   yr+ +++V+t +++ + a++Y+      ++P+  Yl  +++GA+++glP+ ++
  gi|121636846|ref|YP_977069.1|  57 KVHGVLWQLSERDLVRLDSAEGVPV-RYRRERLTVHT-DDTALPAWVYIDHRVMPGRPRPGYLPRVIDGARHHGLPQRWI 134
                                    699*********************9.9*********9.6679************************************99 PP

                         AIG2_2  81 krL 83 
                                    + L
  gi|121636846|ref|YP_977069.1| 135 DYL 137
                                    887 PP

>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   6.4e-16   3.8e-12       1     103 [.       8     104 ..       8     120 .. 0.85
   2 ?   -3.4   0.0       2.5   1.5e+04      30     107 ..     204     216 ..     193     229 .. 0.46

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6.4e-16
                                    EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TTTTSE CS
                          GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelEpeepseY 80 
                                    +F+YG+     ++ ++  +   + + +pa+l ++     ++++  + p +g+kV+G+l+++++++l rLD  E + p  Y
  gi|121636846|ref|YP_977069.1|   8 YFAYGSNL--CAHQMASRCP-DAGAPRPAVLSDHNWLINQRGVATVEPFAGNKVHGVLWQLSERDLVRLDSAE-GVPVRY 83 
                                    6*******..4444434444.78889*******99777556899999**************************.9***** PP

                                    EEEEEEEEC.TTS-EEEEEEEEE CS
                          GGACT  81 ereevkvevledgeqveawvYvy 103
                                    +re+++v++  d+++++awvY+ 
  gi|121636846|ref|YP_977069.1|  84 RRERLTVHT--DDTALPAWVYID 104
                                    ***888877..**********85 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
                                    ECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TTTTSEEEEEEEEEC.TTS-EEEEEEEEETT.. CS
                          GGACT  30 tlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelEpeepseYereevkvevledgeqveawvYvyagee 107
                                                                                                        a vY+ ++ +
  gi|121636846|ref|YP_977069.1| 204 EAA----------------------------------------------------------------GASVYLLRH-P 216
                                    333................................................................344444422.1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2633.54
//
Query:       gi|121636847|ref|YP_977070.1|  [L=428]
Description: manganese transport protein MntH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.4e-113  377.0  16.2   1.3e-112  376.3  16.2    1.3  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.3  16.2  7.4e-117  1.3e-112       1     357 [.      52     400 ..      52     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 376.3 bits;  conditional E-value: 7.4e-117
                          Nramp   1 iatdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaA 80 
                                    +a+++++GaqfGy Llwv++ ++++a+l+q+lsa+LGlvTg++l+e+i +r+++++++++w++ae++++atd+aeviG+A
  gi|121636847|ref|YP_977070.1|  52 VAANVSSGAQFGYLLLWVIVAANVMAALVQYLSAKLGLVTGRSLPEAIGKRMGRPARLAYWAQAEIVAMATDVAEVIGGA 131
                                    699***************************************************************************** PP

                          Nramp  81 ialnllfgipllvgvlitavlvllllfle.kggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpgkes 159
                                    ial+++f++pl +g++it+v++llll+++ ++g r +E++i al+lvia+ F+a++f+v p+ ++vl gl  P+++g+es
  gi|121636847|ref|YP_977070.1| 132 IALRIMFNLPLPIGGIITGVVSLLLLTIQdRRGQRLFERVITALLLVIAIGFTASFFVVTPPPNAVLGGLA-PRFQGTES 210
                                    *****************************9***************************************99.******** PP

                          Nramp 160 lllavgilGatvmphnlflhsslvqerkitidrseke.ealkyeriDtiialivaflinlailivaAavlysggkdvesl 238
                                    +lla+ i+Gatvmph+++lhs l ++r+ ++d   ++ + l+++r+D+ +a+++a+ +n+a+l+vaA  +  g++d++s+
  gi|121636847|ref|YP_977070.1| 211 VLLAAPIMGATVMPHAVYLHSGLARDRHGHPDPGPQRrRLLRVTRWDVGLAMLIAGGVNAAMLLVAALNMR-GRGDTASI 289
                                    ****************************88877666679****************************8888.88899*** PP

                          Nramp 239 edaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpalivilligaele 318
                                    e+a++a    lG +  +vlFa+gLla+Gl S+++g++ag+++m+g+l++++++  rrlit    + pal++++l+ ++++
  gi|121636847|ref|YP_977070.1| 290 EGAYHAVHDTLG-ATIAVLFAVGLLASGLASSSVGAYAGAMIMQGLLHWSVPMLVRRLIT----LGPALAILTLGFDPTR 364
                                    ************.7***************************************9999888....**************** PP

                          Nramp 319 lvkllvlsqvllslllPfaliplllltsskklMGefkns 357
                                        lvlsqv+ls+++Pfa++pl+ lt s ++MG  +n+
  gi|121636847|ref|YP_977070.1| 365 ---TLVLSQVVLSFGIPFAVLPLVKLTGSPAVMGGDTNH 400
                                    ...*******************************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2805.79
//
Query:       gi|121636848|ref|YP_977071.1|  [L=245]
Description: divalent cation-transport integral membrane protein mntH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-11   43.2   0.0    4.2e-11   42.8   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.22   11.4   0.0    1.6  2  GCSF          Granulocyte colony-stimulating factor
        0.2   11.3   0.0       0.28   10.8   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0     7e-15   4.2e-11       2     147 ..      19     171 ..      18     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 7e-15
                                    EEEEEES--STT...-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                        FMN_red   2 kilvisGSlrkg...sntrklaewaaealkeagaevelidladl.ilpcalcdkdlesegqtsddvaellekiaaadali 77 
                                    + l i+++l++    s t+ l+e+    ++e+g++v+ ++  d+ i+    ++ d +++g   d+  +l++++ +a++l+
  gi|121636848|ref|YP_977071.1|  19 RALFINATLKRSpelSHTDGLIERSSGIMREHGVQVDTLRAVDHdIAT--GVWPDMTEHGWATDEWPALYRRVLDAHILV 96 
                                    567889998855566*****************************8888..444455445569****************** PP

                                    EEEEECTTCE-HHHHHHHHCHT-.......SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSE CS
                        FMN_red  78 ivtPeYngsysgllKnalDrlsr......trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraa 147
                                    ++ P++ g  s+++K++++rl +      ++g+ +  g++++++ +g +++g  +++      l +lg +++p+a+
  gi|121636848|ref|YP_977071.1|  97 LCGPIWLGDNSSVMKRVIERLYAcssllnEDGQYAYYGRAGGCLITG-NEDGVKHCAMNVLYSLQHLGYTIPPQAD 171
                                    *********************88*****9999************776.89******99999999999988888765 PP

>> GCSF  Granulocyte colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.22      65     108 ..      36      79 ..      23      86 .. 0.90
   2 ?   -2.5   0.0      0.71   4.2e+03     123     138 ..     131     146 ..     129     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                    HHHHHHHTTTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHCT-S- CS
                           GCSF  65 yqgllqalegispelaptldtlqldvadfattiwqqmeelgvap 108
                                     +gl++  +gi  e +  +dtl+    d+at +w +m e g a 
  gi|121636848|ref|YP_977071.1|  36 TDGLIERSSGIMREHGVQVDTLRAVDHDIATGVWPDMTEHGWAT 79 
                                    57999******************999*************99886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHHHHHHH CS
                           GCSF 123 afqrraggvlvasqlq 138
                                    a+  ragg l++ + +
  gi|121636848|ref|YP_977071.1| 131 AYYGRAGGCLITGNED 146
                                    678899*999987655 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.7e-05      0.28      34     104 ..      50     118 ..      19     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                                    TEEEEEEHHCCT-----CCCCHCC.HHHHTT.CHHHHHHH.HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS CS
                   Flavodoxin_2  34 hevtvrdLyadflpvlttrdlaak.layeek.padveseq.iekllaadaivlqfPlwwfgvPailKgwiDrvl 104
                                    h v+v  L a     ++++ +++   ++ e+  a  e  +   ++l+a+++vl  P+w    ++++K  i+r +
  gi|121636848|ref|YP_977071.1|  50 HGVQVDTLRA-----VDHDIATGVwPDMTEHgWATDEWPAlYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLY 118
                                    4455555555.....23333333132333332233444444589**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1814.55
//
Query:       gi|121636849|ref|YP_977072.1|  [L=358]
Description: hypothetical protein BCG_0978c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   19.0   0.0     0.0019   18.3   0.0    1.3  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.054   13.9   0.0    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-07    0.0019       4      67 ..       6      68 ..       3     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-07
                                   EEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH CS
                         DapB_N  4 avvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlek 67
                                   + +G  G +G + ++a+ +++++el+++  +++ +  gkda el+gl  ++gv  ++dl++vl+ 
  gi|121636849|ref|YP_977072.1|  6 VQLGT-GNVGVHSLRALIADPEFELTGVWVSSD-AKAGKDAAELAGLAdSTGVRASTDLNAVLAT 68
                                   55675.9************************98.99************9*************987 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     6e-06     0.054       6      46 ..       9      49 ..       5      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-06
                                   TTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSG CS
                 Semialdhyde_dh  6 GatGyvGqellrlLeehpevelvvllsssr.saGkklaeavk 46
                                   G tG+vG   lr L  +pe+el+ +  ss  +aGk  ae+++
  gi|121636849|ref|YP_977072.1|  9 G-TGNVGVHSLRALIADPEFELTGVWVSSDaKAGKDAAELAG 49
                                   6.*********************998888879****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2460.74
//
Query:       gi|121636850|ref|YP_977073.1|  [L=263]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-56  190.9   6.4      3e-56  190.6   6.4    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      6e-45  153.1   4.7    7.3e-45  152.8   4.7    1.1  1  adh_short        short chain dehydrogenase
    6.7e-10   39.2   4.2    9.4e-10   38.7   4.2    1.1  1  KR               KR domain
     0.0045   16.9   1.0     0.0073   16.2   1.0    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.019   15.4   0.2      0.035   14.5   0.2    1.4  1  NAD_binding_7    Putative NAD(P)-binding
      0.025   14.9   0.1       0.05   13.9   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.11   12.5   0.1       0.32   11.1   0.1    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   6.4   1.2e-59     3e-56       4     234 .]      20     252 ..      15     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 1.2e-59
                                    TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----E CS
                   adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiap 81 
                                    +g+G+aiA a+a++Ga+v+++ +  ++ ++v+e  ++ g+++  +++D +++e  ++l+ ++v  fgklDi+vnn+g + 
  gi|121636850|ref|YP_977073.1|  20 RGLGAAIALAFAQAGADVLIASRTSSELDAVAEQIRAAGRRAhtVAADLAHPEVTAQLAGQAVGAFGKLDIVVNNVGGTM 99 
                                    8**************************66666666666655335************************************ PP

                                    GCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  82 klkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    +  + +l+ts +++++a++ n+  +++l+ aa+plm e+   gs++n+ss+ ++ +  + +ayg+aKaal + tr +A +
  gi|121636850|ref|YP_977073.1| 100 P--NTLLSTSTKDLADAFAFNVGTAHALTVAAVPLMLEHsggGSVINISSTMGRLAARGFAAYGTAKAALAHYTRLAALD 177
                                    *..*******************************77766689************************************** PP

                                    HGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                    l p ++RvNa++pg i T a + ++ +del++ +e+ +pl+rlg+p ++a+aa++Las++ s+ tG+tl vDgGlt
  gi|121636850|ref|YP_977073.1| 178 LCP-RVRVNAIAPGSILTSALEVVAANDELRAPMEQATPLRRLGDPVDIAAAAVYLASPAGSFLTGKTLEVDGGLT 252
                                    ***.9*********************************************************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   4.7   2.8e-48   7.3e-45       1     188 [.      11     198 ..      11     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 2.8e-48
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv+++tG+++G+G aia ++a++Ga+v++++r++++l +va++++++g++a+++++D+++ e + +l  +av  +gkld+
  gi|121636850|ref|YP_977073.1|  11 KVAVITGGGRGLGAAIALAFAQAGADVLIASRTSSELDAVAEQIRAAGRRAHTVAADLAHPEVTAQLAGQAVGAFGKLDI 90 
                                    89****************************************************************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                    +vnN+G t +++  ++s ++  + ++ N+  +  lt a++p ml  + +G+++n+sS+ g+ +  g+aaY+++Kaa+a++
  gi|121636850|ref|YP_977073.1|  91 VVNNVGGTMPNTLLSTSTKDLADAFAFNVGTAHALTVAAVPLMLeHSGGGSVINISSTMGRLAARGFAAYGTAKAALAHY 170
                                    ********************************************677889****************************** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdmak 188
                                    tr +a +l p+ +rvna+aPG + T   +
  gi|121636850|ref|YP_977073.1| 171 TRLAALDLCPR-VRVNAIAPGSILTSALE 198
                                    **********8.************98765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   4.2   3.7e-13   9.4e-10       4     157 ..      14     168 ..      12     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.7e-13
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    +itGG  gLG ++a   a+ ga  l + sR+   +++ +a  ++++a g + ++vaaD+++++  ++l  ++   ++++ 
  gi|121636850|ref|YP_977073.1|  14 VITGGGRGLGAAIALAFAQAGADVL-IASRT---SSELDAVAEQIRAAGRRAHTVAADLAHPEVTAQLAGQAVGAFGKLD 89 
                                    8********************9866.57898...344456789999********************************** PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SE.....EEEEEEHHHHH--TT-HHHHHHHHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldf.....fvlfSSiagllgsagqanYaaaNaflD 157
                                     v++  g ++ ++l +++++dl+ ++a  v  a+ L  +  +  l++     ++ +SS  g l ++g a+Y +a a l 
  gi|121636850|ref|YP_977073.1|  90 IVVNNVGGTMPNTLLSTSTKDLADAFAFNVGTAHALTVAAVPLMLEHsgggsVINISSTMGRLAARGFAAYGTAKAALA 168
                                    *************************************999887776544444899999999999999999999988654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.0   2.9e-06    0.0073       1      49 [.      11      61 ..      11     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                   EEEEE.--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                        3HCDH_N  1 kvavi.GaGt.mGagiaavfasagleVvlvdiseealekalekiekslekl 49
                                   kvavi G G  +Ga ia +fa+ag +V +  ++++ l++++e+i++  +++
  gi|121636850|ref|YP_977073.1| 11 KVAVItGGGRgLGAAIALAFAQAGADVLIASRTSSELDAVAEQIRAAGRRA 61
                                   578774555459********************************9844433 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.4e-05     0.035       2      82 ..       5      81 ..       5     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                  NAD_binding_7  2 fldlkgkkvlvvGgGe.vAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneriaeaa 82
                                   +++l++k  ++ GgG+ ++a  +  +++aga+v + + +     ++ +++  e++++   +a++v a   ++e+ +++a +a
  gi|121636850|ref|YP_977073.1|  5 MFRLDDKVAVITGGGRgLGAAIALAFAQAGADVLIASRT-----SSELDAVAEQIRAAGRRAHTVAADLAHPEVTAQLAGQA 81
                                   57899**********769****************99999.....34467788888888889999999999999998888876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.9e-05      0.05       8      86 ..      21     104 ..      13     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEEE-SS CS
                Sacchrp_dh_NADP   8 svGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkeg.......dlvvnlsp 78 
                                    + G a+a   a+ +    ++ +a+r+ ++l+a+a+++  +g r++++a d + +e  +a+l  ++       d+vvn ++
  gi|121636850|ref|YP_977073.1|  21 GLGAAIALAFAQAGA---DVLIASRTSSELDAVAEQIraAGRRAHTVAADLAHPEV-TAQLAGQAvgafgklDIVVNNVG 96 
                                    456666666666665...6*****************99999999999999999887.88888887888899999999988 PP

                                    GGGHHHHH CS
                Sacchrp_dh_NADP  79 pissldvl 86 
                                     +  +++l
  gi|121636850|ref|YP_977073.1|  97 GTMPNTLL 104
                                    87666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00013      0.32       9      60 ..       7      58 ..       2      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                   ..TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET CS
                   Shikimate_DH  9 slkekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkgee 60
                                   +l++k +++ G G+ ++  +a +++++g++ v++a Rt +  +++ae+++++ 
  gi|121636850|ref|YP_977073.1|  7 RLDDKVAVITGGGRgLGAAIALAFAQAGAD-VLIASRTSSELDAVAEQIRAAG 58
                                   477888888899975788888888888888.*****************97764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1453.33
//
Query:       gi|121636851|ref|YP_977074.1|  [L=370]
Description: periplasmic phosphate-binding lipoprotein pstS3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-55  186.4   8.7    1.1e-54  186.0   8.7    1.1  1  PBP_like_2  PBP superfamily domain
      3e-11   43.8   1.7    3.7e-11   43.5   1.7    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.1e-05   24.6   0.1    5.8e-05   22.3   0.1    2.0  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   8.7   1.9e-58   1.1e-54      10     276 ..      49     336 ..      29     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 1.9e-58
                     PBP_like_2  10 geifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaang.aggliqv 88 
                                    ++++++Gst++a+a++ +   fe+a+pg+++ny++ GSgagi ++ ++++df+gsd pl+++e a  +a+++ + ++++ 
  gi|121636851|ref|YP_977074.1|  49 KTLKASGSTAQANAMTRFVNVFEQACPGQTLNYTANGSGAGISEFNGNQTDFGGSDVPLSKDEAA--AAQRRcGSPAWNL 126
                                    459***************999*****************************************883..556669******* PP

                     PBP_like_2  89 pvaigaialvvnkd..nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttflfstalaeq. 157
                                    pv++g+ia+ +n +  + lnl+  +LakIf g It+Wn+         ++lp ++ I+vv+rsd+sgtt++f+++l  + 
  gi|121636851|ref|YP_977074.1| 127 PVVFGPIAVTYNLNsvSSLNLDGPTLAKIFNGSITQWNNpaiqalnrDFTLP-GERIHVVFRSDESGTTDNFQRYLQAAs 205
                                    ************7769******************************977777.***********************9999 PP

                     PBP_like_2 158 ..........gpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaata...asalkv 223
                                                ++  g ga g++g + a+ +++g i+y ++++++a+ ++++a +   ag+   +   t+    + +  
  gi|121636851|ref|YP_977074.1| 206 ngawgkgagkSFQGGVGEGARGNDGTSAAAkNTPGSITYNEWSFAQAQ-HLTMANIVTSAGGDPVAI--TIdsvGQTIAG 282
                                    988887774444445555577799999999566*************99.*****9988888754444..33224777888 PP

                     PBP_like_2 224 akias..nplawslqpveeniadgayPlsrftyiivyqpyayh.gnnaalakaFld 276
                                    a+i++  n+l  ++++ + +  +g+yP++ +ty iv++  +y+ ++  +++kaFl+
  gi|121636851|ref|YP_977074.1| 283 ATISGvgNDLVLDTDSFYRPKRPGSYPIVLATYEIVCS--KYPdSQVGTAVKAFLQ 336
                                    99999*9999999999998877****************..6784555*******96 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   1.7   6.2e-15   3.7e-11       4     230 ..      51     272 ..      48     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 6.2e-15
                                    HHH.HHHHHHHHHHH....HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE.CGGHHH..HHHHT..TS CS
                      SBP_bac_1   4 lte.gaalqalvaka....fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav.dndwia..rlaka..gl 70 
                                    l++ g++ qa ++++    fe+++pg + +++  gsg+++      +++++++d p     + d +  a  r  +   +l
  gi|121636851|ref|YP_977074.1|  51 LKAsGSTAQANAMTRfvnvFEQACPGQTLNYTANGSGAGISefnGNQTDFGGSDVP----LSkDEAAAAqrRCGSPawNL 126
                                    55559999999999988889*********************998999999999977....444333333445555589** PP

                                    BECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCT CS
                      SBP_bac_1  71 llpldpyvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgk 150
                                    +  ++p+++ y+ + v    ++l++ +l+ki++            g i+               W+ +++ a + +   +
  gi|121636851|ref|YP_977074.1| 127 PVVFGPIAVTYNLNSVS--SLNLDGPTLAKIFN------------GSIT--------------QWNNPAIQALNRDFTLP 178
                                    ************99998..89999*********............6677..............***************** PP

                                    CT.HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..............HHCSHHHHS..HHHHHHHHHHHHHHHHHH CS
                      SBP_bac_1 151 kp.iggarggsasgtayyfalalakslggkvfdkdgg..............gldnpegvt..aatylvklyavanltkel 213
                                    ++ i ++++++ sgt++ f  +l + ++g ++++ g+              g+++ +  t  ++ty ++++a+a     l
  gi|121636851|ref|YP_977074.1| 179 GErIHVVFRSDESGTTDNFQRYLQAASNGAWGKGAGKsfqggvgegargndGTSAAAKNTpgSITYNEWSFAQAQ---HL 255
                                    ************************************************999888888888999999999997765...44 PP

                                    HTTEEECSSHHHHHHHH CS
                      SBP_bac_1 214 kgkgaenkdgaaalalf 230
                                    ++++  ++ g + +a+ 
  gi|121636851|ref|YP_977074.1| 256 TMANIVTSAGGDPVAIT 272
                                    44444444444444333 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   9.7e-09   5.8e-05       4     121 ..      70     242 ..      67     304 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.7e-09
                                    HHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH........................HCCCCCEEE.EEE CS
                       PBP_like   4 laeknpgvrvavanvGsggGlkalrageadiagshlldketee........................ynapalrka.ldg 58 
                                    ++++ pg +++++  Gsg+G++ ++ +++d +gs+++ +++e+                        yn++ +  + ldg
  gi|121636851|ref|YP_977074.1|  70 FEQACPGQTLNYTANGSGAGISEFNGNQTDFGGSDVPLSKDEAaaaqrrcgspawnlpvvfgpiavtYNLNSVSSLnLDG 149
                                    889999*******************************8877774444444444433333333333334444443331222 PP

                                    EEEEEE-CC-HCHCCCCHCCHHHS--BGG...GC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT............... CS
                       PBP_like  59 ievvlvnlarreqglvvakgnpkkitnwk...dladaplrlvnRetGSGtrdlfdellkkegisk............... 120
                                          +la+   g +++ +np +i+ ++    l+ +++ +v R   SGt d f++ l+ +  s+               
  gi|121636851|ref|YP_977074.1| 150 -----PTLAKIFNGSITQWNNP-AIQALNrdfTLPGERIHVVFRSDESGTTDNFQRYLQAA--SNgawgkgagksfqggv 221
                                    .....35555555666666655.3433331114588********************99765..22234445555555444 PP

                                    ....................E CS
                       PBP_like 121 ....................s 121
                                                         
  gi|121636851|ref|YP_977074.1| 222 gegargndgtsaaakntpgsI 242
                                    444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1997.55
//
Query:       gi|121636852|ref|YP_977075.1|  [L=324]
Description: phosphate-transport integral membrane ABC transporter pstC2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-16   60.2  16.3    2.2e-16   60.2  16.3    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.8     0.022     4e+02     155     174 ..      33      52 ..      12      56 .. 0.70
   2 !   60.2  16.3   1.2e-20   2.2e-16       2     179 ..     104     317 ..      99     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.022
                   BPD_transp_1 155 nggvlalviavlllnlvadi 174
                                    +g++++++i+++++ l++++
  gi|121636852|ref|YP_977075.1|  33 AGSTIVIAILLIAIFLLVRA 52 
                                    57777777777777777765 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.2e-20
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlilp.vi 57 
                                    +++++++  +  ++l++ +  ++++l ++Ps+++++  ++v+                        + s +g + +  + 
  gi|121636852|ref|YP_977075.1| 104 VGIAVFLTHYAPRRLSRPFGAMVDLLAAVPSIIFGLWGIFVLapklepiarflnrnlgwlflfkqGNVSLAGGGTIFtAG 183
                                    678888889999*********************999988888899********************8888888666666** PP

                   BPD_transp_1  58 illllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGl 137
                                    i+l ++++p+v+ i r+++r+ p  ++eaa+alGa++w+++r  vlP   + +++  +l +g++lg++v+++ ++ +   
  gi|121636852|ref|YP_977075.1| 184 IVLSVMILPIVTSISREVFRQTPLIQIEAALALGATKWEVVRMTVLPYGRSGVVAASMLGLGRALGETVAVLVILRS--A 261
                                    ***************************************************************************88..5 PP

                   BPD_transp_1 138 gtllleailgydyseis..............nggvlalviavlllnlvadilqrll 179
                                     ++ + ++    y+++s               g+++ +++a+++l++++++ +r++
  gi|121636852|ref|YP_977075.1| 262 ARPGTWSLFDGGYTFASkiasaasefseplpTGAYISAGFALFVLTFLVNAAARAI 317
                                    66666666666666666779999999999999******************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2245.84
//
Query:       gi|121636853|ref|YP_977076.1|  [L=304]
Description: phosphate-transport integral membrane ABC transporter pstA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-22   79.6  17.0    2.3e-22   79.6  17.0    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
          1    9.4   0.0          1    9.4   0.0    3.2  4  DUF5316       Family of unknown function (DUF5316)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7     0.013   1.2e+02      13      44 ..      29      64 ..      20     101 .. 0.61
   2 !   79.6  17.0   2.6e-26   2.3e-22       1     179 [.     103     300 ..     103     304 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.013
                   BPD_transp_1 13 nkkldkllrpliivllslPsfvlaillvlvf......v 44
                                   ++ +   + + ++v+  +P ++l+ +++  +       
  gi|121636853|ref|YP_977076.1| 29 KNSVATTFFFTSFVVALIPLVWLLWVVI--ArgwfavT 64
                                   4555555555666666777777444444..24344542 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 2.6e-26
                   BPD_transp_1   1 gillGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                    +++lG+++a     +  ++ +++ ++ ++vl ++Ps+v a++++ + +   ++++++++v+++l+l ++p+v++  +++l
  gi|121636853|ref|YP_977076.1| 103 AVPLGLMTAvylvEYGTGRMSRVTTFTVDVLAGVPSIVAALFVFSLWIATLGFQQSAFAVALALVLLMLPVVVRAGEEML 182
                                    589999999998888889999*****************7777666556777999************************** PP

                   BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..........lgtllleail 146
                                    r +p++l+ea++alG+++w++++++v P a+p i++g++l++++++g+++ ++ l +++           + +l l +  
  gi|121636853|ref|YP_977076.1| 183 RLVPDELREASYALGVPKWKTIVRIVAPIAMPGIVSGILLSIARVVGETAPVLVLVGYSHsinldvfhgnMASLPLLI-- 260
                                    ********************************************************9998966666644444444444.. PP

                   BPD_transp_1 147 gydyseis..............nggvlalviavlllnlvadilqrll 179
                                           +              +g++l+l+i+v+ +nl+a  +  + 
  gi|121636853|ref|YP_977076.1| 261 -------YteltnpehagflrvWGAALTLIIVVATINLAAAMIRFVA 300
                                    .......2444445666********************9998776655 PP

>> DUF5316  Family of unknown function (DUF5316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.46   4.1e+03       8      19 ..      42      53 ..      27      62 .. 0.51
   2 ?    9.4   0.0   0.00012         1      42      71 ..     118     147 ..     109     150 .. 0.83
   3 ?   -0.1   0.1      0.11   9.8e+02      17      30 ..     211     224 ..     203     231 .. 0.76
   4 ?   -2.2   0.9      0.47   4.2e+03      55      71 ..     283     299 ..     279     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.46
                        DUF5316  8 isGfvglvfili 19
                                   +   + lv +l+
  gi|121636853|ref|YP_977076.1| 42 VVALIPLVWLLW 53
                                   222333344444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
                        DUF5316  42 kedrrkrfklsknllliglPNllaalllyl 71 
                                     + r +r+++ +  +l g+P+++aal+++ 
  gi|121636853|ref|YP_977076.1| 118 GTGRMSRVTTFTVDVLAGVPSIVAALFVFS 147
                                    566789999999**************9985 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.11
                        DUF5316  17 iliagllsGafvsg 30 
                                    i++ g++sG++ s 
  gi|121636853|ref|YP_977076.1| 211 IAMPGIVSGILLSI 224
                                    77888888888765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.47
                        DUF5316  55 llliglPNllaalllyl 71 
                                    +++++ +Nl aa++ ++
  gi|121636853|ref|YP_977076.1| 283 IIVVATINLAAAMIRFV 299
                                    57889999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1920.63
//
Query:       gi|121636854|ref|YP_977077.1|  [L=369]
Description: Ser/Thr protein kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-41  136.9  17.2    2.1e-08   33.8   0.0    6.5  6  NHL             NHL repeat
    4.5e-14   52.2  17.3    0.00081   19.3   0.1    6.8  7  SBBP            Beta-propeller repeat
    8.8e-13   48.4   5.4    3.6e-08   33.3   3.6    5.0  4  SGL             SMP-30/Gluconolactonase/LRE-like region
    7.6e-07   28.6   4.3        1.3    8.2   0.0    5.1  5  SdiA-regulated  SdiA-regulated
      2e-06   28.1   8.3        1.8    8.9   0.0    5.9  6  US22            US22 like
     0.0008   19.8   1.0        1.3    9.5   0.1    3.7  4  DUF4140         N-terminal domain of unknown function (DUF414
     0.0015   19.0   0.3         34    4.9   0.0    4.4  5  SUKH-3          SUKH-3 immunity protein
     0.0021   18.1   0.1          1    9.3   0.0    3.6  5  Phytase-like    Esterase-like activity of phytase
     0.0037   17.7   1.2         94    3.6   0.0    5.2  6  Ldl_recept_b    Low-density lipoprotein receptor repeat class
     0.0043   18.3   0.0         13    7.1   0.0    4.0  3  RNR_inhib       Ribonucleotide reductase inhibitor
  ------ inclusion threshold ------
      0.024   14.8   7.1         45    4.3   0.0    5.4  5  RbcS            Ribulose-1,5-bisphosphate carboxylase small s
       0.26   11.9  30.5        2.2    8.9   0.1    6.7  6  PQQ_3           PQQ-like domain


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.027       3      18 ..     132     147 ..     131     147 .. 0.94
   2 !   21.3   0.0   1.3e-07   0.00019       1      22 [.     173     194 ..     173     195 .. 0.95
   3 !   33.8   0.0   1.4e-11   2.1e-08       1      27 [.     214     240 ..     214     241 .. 0.96
   4 !   32.3   0.9   4.1e-11   6.2e-08       1      27 [.     256     282 ..     256     283 .. 0.95
   5 !   21.5   0.0   1.1e-07   0.00016       4      27 ..     301     324 ..     299     325 .. 0.95
   6 !   21.1   0.1   1.5e-07   0.00022       1      27 [.     340     366 ..     340     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                    SEEEEEEETTTEEEEE CS
                            NHL   3 yPhGvavdsnGdiyVa 18 
                                    +P+Gvavds G++yV+
  gi|121636854|ref|YP_977077.1| 132 SPSGVAVDSAGNVYVT 147
                                    6**************8 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.3e-07
                                    BSSEEEEEEETTTEEEEEECCC CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsen 22 
                                    +++P+G+avd  G +yV+D++n
  gi|121636854|ref|YP_977077.1| 173 LYQPQGLAVDGAGTVYVTDFNN 194
                                    78*****************998 PP

  == domain 3  score: 33.8 bits;  conditional E-value: 1.4e-11
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +nyP+G+avd++G +yVaD++n+rv++
  gi|121636854|ref|YP_977077.1| 214 LNYPEGLAVDTQGAVYVADRGNNRVVK 240
                                    79***********************97 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 4.1e-11
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +n+P Gvavd++G++yV+D+ n+rv++
  gi|121636854|ref|YP_977077.1| 256 LNDPDGVAVDNSGNVYVTDTDNNRVVK 282
                                    799**********************97 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.1e-07
                                    EEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   4 PhGvavdsnGdiyVaDsenhrvqv 27 
                                    P+G+avd  G +yV++ ++++v++
  gi|121636854|ref|YP_977077.1| 301 PWGIAVDEAGTVYVTEHNTNQVVK 324
                                    9*********************87 PP

  == domain 6  score: 21.1 bits;  conditional E-value: 1.5e-07
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +n P  vavds+  +yVaD++n rv++
  gi|121636854|ref|YP_977077.1| 340 LNTPLAVAVDSDRTVYVADRGNDRVVK 366
                                    68899******************9987 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.5e-07   0.00081      13      30 ..     131     148 ..     126     150 .. 0.89
   2 !    9.6   0.0   0.00061      0.92      12      29 ..     173     190 ..     170     190 .. 0.91
   3 !    8.3   0.1    0.0015       2.3      14      29 ..     216     231 ..     210     236 .. 0.90
   4 !   14.2   0.2   2.2e-05     0.033      15      29 ..     259     273 ..     251     273 .. 0.91
   5 !    6.8   0.1    0.0046       6.9      17      29 ..     303     315 ..     296     315 .. 0.91
   6 ?   -2.5   0.0       3.5   5.2e+03      29      37 ..     327     335 ..     326     336 .. 0.77
   7 ?    0.6   0.0      0.39   5.8e+02      18      29 ..     346     357 ..     342     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-07
                           SBBP  13 tygngIavDsnGNiYvtG 30 
                                    ++++g+avDs GN+Yvt 
  gi|121636854|ref|YP_977077.1| 131 LSPSGVAVDSAGNVYVTS 148
                                    579*************95 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
                           SBBP  12 stygngIavDsnGNiYvt 29 
                                     ++++g+avD  G +Yvt
  gi|121636854|ref|YP_977077.1| 173 LYQPQGLAVDGAGTVYVT 190
                                    589**************8 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0015
                           SBBP  14 ygngIavDsnGNiYvt 29 
                                    y+ g+avD+ G +Yv+
  gi|121636854|ref|YP_977077.1| 216 YPEGLAVDTQGAVYVA 231
                                    89************97 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 2.2e-05
                           SBBP  15 gngIavDsnGNiYvt 29 
                                    + g+avD +GN+Yvt
  gi|121636854|ref|YP_977077.1| 259 PDGVAVDNSGNVYVT 273
                                    569***********9 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0046
                           SBBP  17 gIavDsnGNiYvt 29 
                                    gIavD+ G +Yvt
  gi|121636854|ref|YP_977077.1| 303 GIAVDEAGTVYVT 315
                                    9***********8 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 3.5
                           SBBP  29 tGsTngnnf 37 
                                    +GsT+++ +
  gi|121636854|ref|YP_977077.1| 327 AGSTTSTVL 335
                                    89**99765 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.39
                           SBBP  18 IavDsnGNiYvt 29 
                                    +avDs+  +Yv+
  gi|121636854|ref|YP_977077.1| 346 VAVDSDRTVYVA 357
                                    89********97 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   6.7e-08    0.0001      85     213 ..     130     244 ..      73     253 .. 0.75
   2 !   33.3   3.6   2.4e-11   3.6e-08      44     243 ..     135     315 ..     133     316 .. 0.83
   3 !    7.1   0.1    0.0024       3.5     172     212 ..     288     327 ..     285     358 .. 0.72
   4 ?    0.7   0.0      0.22   3.2e+02     188     210 ..     345     367 ..     329     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.7e-08
                            SGL  85 llrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldpd..gklervlddltipNGlawspdgktlYlaDsltrkiwayd 162
                                    +l++  ++vd++G++++++ g+     +  g +++l ++  g++++  ++l  p Gla++ +g t+Y++D  +r ++   
  gi|121636854|ref|YP_977077.1| 130 RLSPSGVAVDSAGNVYVTSEGM-----Y--GRVVKLATGstGTTVLPFNGLYQPQGLAVDGAG-TVYVTDFNNRVVTLAA 201
                                    6667778999999999998654.....4..777778777667888999***********9987.7999997777665444 PP

                            SGL 163 vdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpd 213
                                            sn ++++ ++  + +p GlavD +G v+vA  g+++vv+++  
  gi|121636854|ref|YP_977077.1| 202 G-------SNNQTVLPFDGLN-YPEGLAVDTQGAVYVADRGNNRVVKLAAG 244
                                    3.......4556677777777.7**********************998765 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 2.4e-11
                            SGL  44 Gaiaprkdgrlvvasksglall.dlasgeletladeeedekpllrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldp 122
                                    G++++  +g+++v+s++   ++ +la+g+  t + +++    l ++  ++vd +G +++++ +++ ++            
  gi|121636854|ref|YP_977077.1| 135 GVAVD-SAGNVYVTSEGMYGRVvKLATGSTGTTVLPFN---GLYQPQGLAVDGAGTVYVTDFNNRVVTLA-------AGS 203
                                    77777.889*******99999999***********984...4699999*************998886655.......334 PP

                            SGL 123 dgklervlddltipNGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvw 202
                                    ++++++  d+l+ p Gla++ +g  +Y+aD  ++++++    ++++      +++ ++  +  pDG+avD++Gnv+v+  
  gi|121636854|ref|YP_977077.1| 204 NNQTVLPFDGLNYPEGLAVDTQGA-VYVADRGNNRVVKLAAGSKTQ------TVLPFTGLN-DPDGVAVDNSGNVYVTDT 275
                                    4899999*************9985.8***********999965555......667777777.5***************** PP

                            SGL 203 gggkvvrfdpdGklieeiklpakrvtscaF.gGpdlrtLyit 243
                                    ++++vv+++ + +  +++ lp + +t++   +  +  t+y+t
  gi|121636854|ref|YP_977077.1| 276 DNNRVVKLEAESN--NQVVLPFTDITAPWGiAVDEAGTVYVT 315
                                    *******999975..889999888887753255555666665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0024
                            SGL 172 nrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdp 212
                                    n +v++ +++ + +p G+avD+ G v+v+  ++++vv++  
  gi|121636854|ref|YP_977077.1| 288 NNQVVLPFTDIT-APWGIAVDEAGTVYVTEHNTNQVVKLLA 327
                                    667777777776.699*************999999998754 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.22
                            SGL 188 GlavDaeGnvwvAvwgggkvvrf 210
                                     +avD++  v+vA  g+++vv++
  gi|121636854|ref|YP_977077.1| 345 AVAVDSDRTVYVADRGNDRVVKL 367
                                    579999999***99999999876 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0026       3.8     225     241 ..     133     149 ..     131     152 .. 0.92
   2 ?    3.6   0.0     0.022        33     222     239 ..     173     190 ..     151     200 .. 0.83
   3 ?    4.3   0.0     0.014        20     223     239 ..     215     231 ..     196     238 .. 0.88
   4 !    8.2   0.0   0.00089       1.3      46      99 ..     237     290 ..     230     298 .. 0.73
   5 ?    3.9   0.0     0.018        27     221     239 ..     297     315 ..     294     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
                 SdiA-regulated 225 aEGvamDeegnlYivsE 241
                                    + Gva+D++gn+Y+ sE
  gi|121636854|ref|YP_977077.1| 133 PSGVAVDSAGNVYVTSE 149
                                    57**************9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.022
                 SdiA-regulated 222 ipqaEGvamDeegnlYiv 239
                                    + q+ G+a+D +g++Y+ 
  gi|121636854|ref|YP_977077.1| 173 LYQPQGLAVDGAGTVYVT 190
                                    579*************97 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.014
                 SdiA-regulated 223 pqaEGvamDeegnlYiv 239
                                    + +EG+a+D +g +Y+ 
  gi|121636854|ref|YP_977077.1| 215 NYPEGLAVDTQGAVYVA 231
                                    569************96 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00089
                 SdiA-regulated  46 elveLskeGevlrriplkgfkdpEaveylgdgrlaivdEreqalvvvkvdadtk 99 
                                    ++v+L    +    +p +g++dp++v++ + g++ ++d  ++++v+++ +++++
  gi|121636854|ref|YP_977077.1| 237 RVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQ 290
                                    566666666666777888888888888888888888888888888877766655 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.018
                 SdiA-regulated 221 dipqaEGvamDeegnlYiv 239
                                    di  + G+a+De+g++Y+ 
  gi|121636854|ref|YP_977077.1| 297 DITAPWGIAVDEAGTVYVT 315
                                    678889***********95 PP

>> US22  US22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.34   5.1e+02      65     107 ..      86     159 ..      66     163 .. 0.61
   2 ?    3.4   0.1      0.06        90      85     107 ..     179     201 ..     153     206 .. 0.83
   3 !    8.9   0.0    0.0012       1.8      85     108 ..     220     243 ..     211     246 .. 0.91
   4 ?    4.4   0.0     0.028        42      85     106 ..     262     283 ..     259     290 .. 0.90
   5 ?    4.6   0.0     0.025        37      83     106 ..     302     325 ..     285     332 .. 0.80
   6 ?    5.6   0.0     0.012        18      79     106 ..     342     367 ..     327     369 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.34
                           US22  65 avvGtva..................vgptamagpaa.................lvvlldelgaVygyd.plddevyrlA 107
                                    avvG+ a                    pt+     a                   v +d  g+Vy+      + v++lA
  gi|121636854|ref|YP_977077.1|  86 AVVGAAAivlvaivaaagylvlrpsWSPTQ-----AsgqtvlpftgidfrlspSGVAVDSAGNVYVTSeGMYGRVVKLA 159
                                    566666666665655666664333322222.....22333466666677766566999999999998523344666665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.06
                           US22  85 vlldelgaVygydplddevyrlA 107
                                    + +d  g+Vy+ d  ++ v + A
  gi|121636854|ref|YP_977077.1| 179 LAVDGAGTVYVTDFNNRVVTLAA 201
                                    6799*********7777776666 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0012
                           US22  85 vlldelgaVygydplddevyrlAa 108
                                    + +d  gaVy+ d+ ++ v++lAa
  gi|121636854|ref|YP_977077.1| 220 LAVDTQGAVYVADRGNNRVVKLAA 243
                                    679********************7 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.028
                           US22  85 vlldelgaVygydplddevyrl 106
                                    v +d +g+Vy+ d +++ v++l
  gi|121636854|ref|YP_977077.1| 262 VAVDNSGNVYVTDTDNNRVVKL 283
                                    789***********99999987 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.025
                           US22  83 lvvlldelgaVygydplddevyrl 106
                                    + + +de g+Vy+ +  +++v++l
  gi|121636854|ref|YP_977077.1| 302 WGIAVDEAGTVYVTEHNTNQVVKL 325
                                    5589**********9777776654 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.012
                           US22  79 gpaalvvlldelgaVygydplddevyrl 106
                                    +p  l v +d + +Vy+ d+ +d v++l
  gi|121636854|ref|YP_977077.1| 342 TP--LAVAVDSDRTVYVADRGNDRVVKL 367
                                    34..89******************9987 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.65   9.7e+02      19      50 ..     116     147 ..     110     150 .. 0.88
   2 ?    5.1   0.0     0.021        31      16      57 ..     155     197 ..     152     205 .. 0.86
   3 ?    0.2   0.0      0.68     1e+03      16      49 ..     197     230 ..     193     233 .. 0.82
   4 !    9.5   0.1   0.00088       1.3      16      65 ..     239     288 ..     232     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.65
                        DUF4140  19 kaGtnevtiegLpptldedSlrVegagaatil 50 
                                    + G++ + ++g++  l ++ + V++ag++ ++
  gi|121636854|ref|YP_977077.1| 116 ASGQTVLPFTGIDFRLSPSGVAVDSAGNVYVT 147
                                    568888999******************98877 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                        DUF4140  16 v.elkaGtnevtiegLpptldedSlrVegagaatildvqverv 57 
                                    v +l+ G++  t+  + +  +++ l V+gag++ ++d + + v
  gi|121636854|ref|YP_977077.1| 155 VvKLATGSTGTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVV 197
                                    448999*999***************************986655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.68
                        DUF4140  16 velkaGtnevtiegLpptldedSlrVegagaati 49 
                                    v+l+aG+n  t+  +++   ++ l V+ +ga+ +
  gi|121636854|ref|YP_977077.1| 197 VTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYV 230
                                    489********99999999999999988888766 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00088
                        DUF4140  16 velkaGtnevtiegLpptldedSlrVegagaatildvqvervpnreaeee 65 
                                    v+l+aG+ + t+  +++  d+d + V+ +g++ ++d +  rv   eae++
  gi|121636854|ref|YP_977077.1| 239 VKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESN 288
                                    4899********************************99998887777765 PP

>> SUKH-3  SUKH-3 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.1   1.7e+03     109     130 ..     135     153 ..     115     163 .. 0.81
   2 ?    4.1   0.0     0.039        59     107     134 ..     176     206 ..     163     210 .. 0.75
   3 ?    1.2   0.0      0.32   4.7e+02     110     126 ..     220     240 ..     214     252 .. 0.74
   4 ?    1.6   0.0      0.23   3.5e+02     107     125 ..     259     277 ..     248     292 .. 0.79
   5 ?    4.9   0.0     0.023        34     109     136 ..     303     334 ..     273     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                         SUKH-3 109 tlaidedGrvfaldhtgewflG 130
                                     +a+d+ G v++    +e++ G
  gi|121636854|ref|YP_977077.1| 135 GVAVDSAGNVYVT---SEGMYG 153
                                    589********99...555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                         SUKH-3 107 eatlaidedGrvfaldhtg...ewflGedid 134
                                     + la+d+ G v++ d+ +       G++ +
  gi|121636854|ref|YP_977077.1| 176 PQGLAVDGAGTVYVTDFNNrvvTLAAGSNNQ 206
                                    5679*************99766555666655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.32
                         SUKH-3 110 laidedGrvfaldhtg....e 126
                                    la+d++G v++ d  +    +
  gi|121636854|ref|YP_977077.1| 220 LAVDTQGAVYVADRGNnrvvK 240
                                    99*********9887766444 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.23
                         SUKH-3 107 eatlaidedGrvfaldhtg 125
                                     + +a+d +G v++ d+ +
  gi|121636854|ref|YP_977077.1| 259 PDGVAVDNSGNVYVTDTDN 277
                                    56699*********98776 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.023
                         SUKH-3 109 tlaidedGrvfal.dhtg...ewflGedidea 136
                                     +a+de G v++  ++t+   + + G++ +++
  gi|121636854|ref|YP_977077.1| 303 GIAVDEAGTVYVTeHNTNqvvKLLAGSTTSTV 334
                                    589**********4555577766777776665 PP

>> Phytase-like  Esterase-like activity of phytase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.24   3.5e+02      70      89 ..     133     153 ..     112     187 .. 0.75
   2 !    9.3   0.0   0.00067         1      66     104 ..     212     251 ..     134     256 .. 0.76
   3 ?    3.6   0.0     0.035        52      66     100 ..     254     289 ..     246     311 .. 0.80
   4 ?   -2.1   0.0       1.9   2.9e+03      72      94 ..     303     325 ..     298     339 .. 0.80
   5 ?   -2.7   0.0         3   4.4e+03      73      93 ..     346     366 ..     343     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.24
                   Phytase-like  70 pEgiavapdgtfwvssEgg.p 89 
                                    p g+av++ g+++v+sEg   
  gi|121636854|ref|YP_977077.1| 133 PSGVAVDSAGNVYVTSEGMyG 153
                                    56999************9754 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00067
                   Phytase-like  66 kgl.DpEgiavapdgtfwvssEggpfilefdadGkllrel 104
                                    +gl  pEg+av+ +g ++v++ g++++++  a  k ++ l
  gi|121636854|ref|YP_977077.1| 212 DGLnYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVL 251
                                    444349**********************998877766665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.035
                   Phytase-like  66 kgl.DpEgiavapdgtfwvssEggpfilefdadGkl 100
                                     gl Dp g+av++ g+++v++  ++++++ +a+ + 
  gi|121636854|ref|YP_977077.1| 254 TGLnDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNN 289
                                    55669**********************999887544 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.9
                   Phytase-like  72 giavapdgtfwvssEggpfilef 94 
                                    giav++ gt++v++   +++++ 
  gi|121636854|ref|YP_977077.1| 303 GIAVDEAGTVYVTEHNTNQVVKL 325
                                    89999999999998888877765 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3
                   Phytase-like  73 iavapdgtfwvssEggpfile 93 
                                    +av++d+t++v++ g+ ++++
  gi|121636854|ref|YP_977077.1| 346 VAVDSDRTVYVADRGNDRVVK 366
                                    677888888888888877765 PP

>> Ldl_recept_b  Low-density lipoprotein receptor repeat class B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.5   1.3e+04      35      41 ..     133     139 ..     132     139 .. 0.89
   2 ?    3.1   0.0     0.091   1.4e+02      32      41 ..     173     182 ..     157     182 .. 0.82
   3 ?    3.6   0.0     0.063        94      21      41 ..     202     223 ..     185     224 .. 0.76
   4 ?    2.5   0.0      0.14     2e+02      32      41 ..     256     265 ..     238     266 .. 0.86
   5 ?    1.2   0.0      0.35   5.2e+02      31      42 .]     297     308 ..     286     308 .. 0.87
   6 ?   -0.1   0.0      0.91   1.4e+03      32      41 ..     340     349 ..     322     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                                    EEEEEEE CS
                   Ldl_recept_b  35 PrgiAvD 41 
                                    P g+AvD
  gi|121636854|ref|YP_977077.1| 133 PSGVAVD 139
                                    99****9 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.091
                                    -S-EEEEEEE CS
                   Ldl_recept_b  32 lqnPrgiAvD 41 
                                    l+ P+g+AvD
  gi|121636854|ref|YP_977077.1| 173 LYQPQGLAVD 182
                                    899******9 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.063
                                    S---EEEE-SS.-S-EEEEEEE CS
                   Ldl_recept_b  21 Gshrktlfqed.lqnPrgiAvD 41 
                                    Gs+  t++  d l+ P+g+AvD
  gi|121636854|ref|YP_977077.1| 202 GSNNQTVLPFDgLNYPEGLAVD 223
                                    555556666667999******9 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.14
                                    -S-EEEEEEE CS
                   Ldl_recept_b  32 lqnPrgiAvD 41 
                                    l++P+g+AvD
  gi|121636854|ref|YP_977077.1| 256 LNDPDGVAVD 265
                                    899******9 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.35
                                    S-S-EEEEEEET CS
                   Ldl_recept_b  31 dlqnPrgiAvDp 42 
                                    d+ +P giAvD+
  gi|121636854|ref|YP_977077.1| 297 DITAPWGIAVDE 308
                                    6889*******5 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.91
                                    -S-EEEEEEE CS
                   Ldl_recept_b  32 lqnPrgiAvD 41 
                                    l++P ++AvD
  gi|121636854|ref|YP_977077.1| 340 LNTPLAVAVD 349
                                    899******9 PP

>> RNR_inhib  Ribonucleotide reductase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.049        73      48      72 ..     201     225 ..     108     244 .. 0.80
   2 !    7.1   0.0    0.0089        13      48      92 ..     243     286 ..     230     298 .. 0.69
   3 ?    0.5   0.0         1   1.6e+03      47      63 ..     321     342 ..     304     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.049
                      RNR_inhib  48 aasanrellpfcGinkvgglavqse 72 
                                    a s+n+++lpf G+n   glav ++
  gi|121636854|ref|YP_977077.1| 201 AGSNNQTVLPFDGLNYPEGLAVDTQ 225
                                    6677888888888888888888744 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0089
                      RNR_inhib  48 aasanrellpfcGinkvgglavqseeeaspateeenaavddadae 92 
                                    a s+++++lpf G+n  +g+av +  +  + t+++n++v + +ae
  gi|121636854|ref|YP_977077.1| 243 AGSKTQTVLPFTGLNDPDGVAVDNSGN-VYVTDTDNNRVVKLEAE 286
                                    678899****************94443.33444444444444444 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1
                      RNR_inhib  47 s.....aasanrellpfcGink 63 
                                    +     a s+++++lpf G+n 
  gi|121636854|ref|YP_977077.1| 321 QvvkllAGSTTSTVLPFTGLNT 342
                                    1234568899999******986 PP

>> RbcS  Ribulose-1,5-bisphosphate carboxylase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.094   1.4e+02      17      30 ..     112     127 ..      90     129 .. 0.74
   2 ?    0.6   0.0      0.45   6.7e+02      17      30 ..     160     173 ..     153     176 .. 0.79
   3 ?    1.0   0.0      0.34   5.1e+02      12      30 ..     198     214 ..     193     217 .. 0.71
   4 ?    4.3   0.0      0.03        45      16      30 ..     242     256 ..     236     261 .. 0.78
   5 ?    4.1   0.1     0.036        54      18      31 ..     328     341 ..     321     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.094
                           RbcS  17 apaQas..mvAPFtGL 30 
                                    +p+Qas   v PFtG+
  gi|121636854|ref|YP_977077.1| 112 SPTQASgqTVLPFTGI 127
                                    68888755899****6 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.45
                           RbcS  17 apaQasmvAPFtGL 30 
                                    +++  + v PF+GL
  gi|121636854|ref|YP_977077.1| 160 TGSTGTTVLPFNGL 173
                                    555667899****9 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.34
                           RbcS  12 tinRaapaQasmvAPFtGL 30 
                                    t+  aa++  + v PF GL
  gi|121636854|ref|YP_977077.1| 198 TL--AAGSNNQTVLPFDGL 214
                                    43..44555559******9 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.03
                           RbcS  16 aapaQasmvAPFtGL 30 
                                    aa++  + v PFtGL
  gi|121636854|ref|YP_977077.1| 242 AAGSKTQTVLPFTGL 256
                                    45566669******9 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.036
                           RbcS  18 paQasmvAPFtGLK 31 
                                    ++  s v PFtGL 
  gi|121636854|ref|YP_977077.1| 328 GSTTSTVLPFTGLN 341
                                    456799******95 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       8.8   1.3e+04      14      22 ..      31      43 ..      25      47 .. 0.47
   2 ?    1.3   8.2      0.36   5.4e+02      17      38 ..     176     201 ..     126     203 .. 0.85
   3 ?    4.1   0.2     0.048        72      15      38 ..     218     243 ..     208     245 .. 0.80
   4 ?    8.9   0.1    0.0015       2.2      16      40 .]     261     287 ..     251     287 .. 0.86
   5 ?    1.1   0.0       0.4     6e+02      16      27 ..     303     315 ..     294     320 .. 0.73
   6 ?    5.5   0.2     0.017        25      17      33 ..     344     364 ..     326     367 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.8
                          PQQ_3 14 nssp....avdgg 22
                                     sp    +v+g 
  gi|121636854|ref|YP_977077.1| 31 RWSPgdsaTVAGP 43
                                   4444444445544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                          PQQ_3  17 p...avdg.glvyvgtgdGtlyAlDa 38 
                                    p   avdg g+vyv++ +++++ l a
  gi|121636854|ref|YP_977077.1| 176 PqglAVDGaGTVYVTDFNNRVVTLAA 201
                                    24449**99********999987766 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.048
                          PQQ_3  15 sspavdg.glvyvgtg.dGtlyAlDa 38 
                                     ++avd  g vyv++  +++++ l a
  gi|121636854|ref|YP_977077.1| 218 EGLAVDTqGAVYVADRgNNRVVKLAA 243
                                    578999779*******9999998877 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0015
                          PQQ_3  16 spavdg.glvyvgtg.dGtlyAlDaet 40 
                                    ++avd+ g vyv+++ +++++ l+ae+
  gi|121636854|ref|YP_977077.1| 261 GVAVDNsGNVYVTDTdNNRVVKLEAES 287
                                    6799988****************9986 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.4
                          PQQ_3  16 spavdg.glvyvg 27 
                                    + avd+ g+vyv+
  gi|121636854|ref|YP_977077.1| 303 GIAVDEaGTVYVT 315
                                    46999889***97 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.017
                          PQQ_3  17 p..avd.gglvyvgtg.dGtl 33 
                                    +  avd +++vyv++  + ++
  gi|121636854|ref|YP_977077.1| 344 LavAVDsDRTVYVADRgNDRV 364
                                    343553599*****9865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2578.29
//
Query:       gi|121636855|ref|YP_977078.1|  [L=291]
Description: Ser/Thr protein kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-44  151.8   0.0    2.5e-44  151.6   0.0    1.0  1  Pkinase         Protein kinase domain
    5.3e-29  101.3   0.0    6.5e-29  101.0   0.0    1.0  1  Pkinase_Tyr     Protein tyrosine kinase
    5.8e-07   29.7   1.6    5.4e-05   23.2   0.1    2.7  3  APH             Phosphotransferase enzyme family
    1.3e-05   24.7   0.0    2.1e-05   24.0   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.001   17.9   0.0     0.0015   17.3   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0021   17.7   0.0      0.025   14.2   0.0    2.0  2  FTA2            Kinetochore Sim4 complex subunit FTA2
     0.0054   15.7   0.0     0.0092   15.0   0.0    1.3  1  Haspin_kinase   Haspin like kinase domain


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.0   9.8e-48   2.5e-44       1     254 [.      15     263 ..      15     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 9.8e-48
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    y+ l+ lG+G++G+Vy+a ++++++ vA+K i+ +  ++     +++rE     +l  p+iv + ++ e + ++++ + +
  gi|121636855|ref|YP_977078.1|  15 YQLLRLLGRGGMGEVYEAEDTRKHRVVALKLISPQYSDNAVFrARMQREADTAGRLTEPHIVPIHDYGEINGQFFVEMRM 94 
                                    778999*************************9987666554459************************************ PP

                                    -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS..BCTT CS
                        Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk..ltsf 157
                                    ++g++l  ll++ g l++++a  i++qi+++l+  H++g+ HrD+KpeNiL+  ++   ++DFG+a+ ++      + + 
  gi|121636855|ref|YP_977078.1|  95 IDGTSLRALLKQYGPLTPARAVAIVRQIAAALDAAHANGVTHRDVKPENILVTASDFAYLVDFGIARAASDPGLtqTGTA 174
                                    *****************************************************9999*************9887668899 PP

                                    TSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHH CS
                        Pkinase 158 vgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseea 237
                                    vgt +Y+APE  ++ e++  +D+++l+++l e ltg pp+++++ +  ++++l++           + +  ++  +++ +
  gi|121636855|ref|YP_977078.1| 175 VGTYNYMAPERFTGDEVTYRADIYALACVLGECLTGAPPYRADSVERLIAAHLMD--------PAPQPSQLRPGRVPPAL 246
                                    *****************************************66665544444444........13345556667779999 PP

                                    HHHHHHHT-SSGCCSTT CS
                        Pkinase 238 kdllkkllkkdpkkRlt 254
                                     +++ k ++k+p +R+ 
  gi|121636855|ref|YP_977078.1| 247 DQVIAKGMAKNPAERFM 263
                                    99999999999999975 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   2.5e-32   6.5e-29       3     249 ..      17     261 ..      15     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 2.5e-32
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeepllivt 80 
                                    l + lG+G  G+V+e++ +    +k+  Va+K ++ +++++   ++++ +ea++  +l  p+iv ++     +++ ++ +
  gi|121636855|ref|YP_977078.1|  17 LLRLLGRGGMGEVYEAEDT----RKHRVVALKLISPQYSDNAvfRARMQREADTAGRLTEPHIVPIHDYGEINGQFFVEM 92 
                                    6789************988....88999******999999988899999**********************9******** PP

                                    E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEE CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyv 160
                                     +++g +L+  L++    +lt  + + ++ q+A++++  +++ + Hrd+   N+L++ ++++ + DfG+ar+  +d   +
  gi|121636855|ref|YP_977078.1|  93 RMIDGTSLRALLKQY--GPLTPARAVAIVRQIAAALDAAHANGVTHRDVKPENILVTASDFAYLVDFGIARAA-SDPGLT 169
                                    *************98..9*****************************************************99.99999* PP

                                    ETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHH.HHHTTEE...S-BBTTSBHHHHH CS
                    Pkinase_Tyr 161 kkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevle.klkegkr...lekpekcpeelye 236
                                    ++++a   +++mapE ++  ++t ++D+++ + +l E +t g+ py+  + e++++ +l +        +p  +p++l +
  gi|121636855|ref|YP_977078.1| 170 QTGTAVGTYNYMAPERFTGDEVTYRADIYALACVLGECLT-GAPPYRADSVERLIAaHLMDPAPqpsQLRPGRVPPALDQ 248
                                    ****************************************.*****9987777654144333221115578999****** PP

                                    HHHHHT-SSGGGS CS
                    Pkinase_Tyr 237 lmkkcweedpeeR 249
                                    ++ k ++++p+eR
  gi|121636855|ref|YP_977078.1| 249 VIAKGMAKNPAER 261
                                    **********999 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   0.00016      0.41      12     106 ..      28     130 ..      18     133 .. 0.74
   2 !   23.2   0.1   2.1e-08   5.4e-05     146     198 ..     113     162 ..     103     165 .. 0.78
   3 ?   -0.9   0.0      0.49   1.3e+03     119     143 ..     224     248 ..     175     287 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                    EEEEEEETT..--EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS... CS
                            APH  12 rtylvttpa..gryvlrrnppa..raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr... 84 
                                     +y+ ++++  + ++l++++p+  ++a + +r++++ +   ++  p  ++++    +e +g  f+ +  ++g+sl+    
  gi|121636855|ref|YP_977078.1|  28 EVYEAEDTRkhRVVALKLISPQysDNAVFRARMQREADTAGRLTEPHIVPIH--DYGEINGQFFVEMRMIDGTSLRAllk 105
                                    5788888885345669*****9776777777777777776666555556666..899999999************99997 PP

                                    ...HHHHHHHHHHHHHHHHHHCCHH CS
                            APH  85 ...klsaaqlpellealgeflaalh 106
                                       +l++a + +++++++++l a h
  gi|121636855|ref|YP_977078.1| 106 qygPLTPARAVAIVRQIAAALDAAH 130
                                    7777777777777777777777766 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.1e-08
                                    HHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 146 eeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    +++ + + +++aa l+++ + +++H+D +p N+lv++ d    +++Df+ a++
  gi|121636855|ref|YP_977078.1| 113 ARAVA-IVRQIAAALDAAHANGVTHRDVKPENILVTASDFA--YLVDFGIARA 162
                                    45555.77777888888889****************55555..6*****9876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.49
                                    HCHTCCHHHHHHCHHHCCCGCCTCC CS
                            APH 119 laqdlellrqlesatarllaselld 143
                                    +a+ +++++q  + ++++++++l++
  gi|121636855|ref|YP_977078.1| 224 AAHLMDPAPQPSQLRPGRVPPALDQ 248
                                    2233333333333333444444444 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   8.3e-09   2.1e-05     101     167 ..      96     158 ..      83     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.3e-09
                            Kdo 101 gaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    +  +L +ll+++  l  ++  a++++++++    h+ gv H+d+ + nil+ + +     ++l+D+ 
  gi|121636855|ref|YP_977078.1|  96 DGTSLRALLKQYGPLTPARAVAIVRQIAAALDAAHANGVTHRDVKPENILVTASD----FAYLVDFG 158
                                    4468999***998999*************************************99....89999995 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     6e-07    0.0015     318     397 ..     125     197 ..     110     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6e-07
                 Pkinase_fungal 318 ghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgeeHsyrhDL 397
                                    ++   +   g+ HrD+  +Nil+t     +++   L+D+ +a   sd     + ++ +GT ++ma e   g e +yr D+
  gi|121636855|ref|YP_977078.1| 125 ALDAAH-ANGVTHRDVKPENILVT-----ASDFAYLVDFGIARAASD-PGLTQTGTAVGTYNYMAPERFTGDEVTYRADI 197
                                    555555.78999************.....78999************8.5666779***************9999999997 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.085   2.2e+02      24      62 ..      15      55 ..       7      78 .. 0.72
   2 !   14.2   0.0   9.9e-06     0.025     153     205 ..      96     146 ..      70     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.085
                           FTA2 24 iefleyLgkglhsiVlkvkirgk..eYALKlFrfleaeele 62
                                   +++l +Lg+g  + V++++  +k  + ALKl   ++ ++  
  gi|121636855|ref|YP_977078.1| 15 YQLLRLLGRGGMGEVYEAEDTRKhrVVALKLISPQYSDNAV 55
                                   689999************9655545999**98877665544 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.9e-06
                           FTA2 153 kkrpiraIVKelellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyid 205
                                      + +ra+ K+  +      + v++++++   l+ +h+ g+ +rD+k+en++ 
  gi|121636855|ref|YP_977078.1|  96 DGTSLRALLKQ--YGPLTPARAVAIVRQIAAALDAAHANGVTHRDVKPENILV 146
                                    56778899999..667888999****************************974 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.6e-06    0.0092     208     286 ..     115     199 ..      96     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                  Haspin_kinase 208 alsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRle.....ssegkvl..ytrlddpllFqGggDy 280
                                    a  i  qi++ L +a ++    HRd + +niLv ++    l+d+ ++R+      +++g+++  y+ +  + +   +  y
  gi|121636855|ref|YP_977078.1| 115 AVAIVRQIAAALDAAHAN-GVTHRDVKPENILVTASDFAYLVDFGIARAAsdpglTQTGTAVgtYNYMAPERFTGDEVTY 193
                                    566777888888877765.789***************************9888884544443226666555554455689 PP

                  Haspin_kinase 281 qfeiYr 286
                                    + +iY 
  gi|121636855|ref|YP_977078.1| 194 RADIYA 199
                                    999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1951.61
//
Query:       gi|121636856|ref|YP_977079.1|  [L=370]
Description: periplasmic phosphate-binding lipoprotein pstS2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-46  159.1   7.8    2.4e-46  158.7   7.8    1.1  1  PBP_like_2     PBP superfamily domain
      7e-15   55.8   2.2    9.2e-15   55.4   2.2    1.1  1  SBP_bac_1      Bacterial extracellular solute-binding protein
    1.7e-05   24.1   0.0    3.3e-05   23.1   0.0    1.5  1  PBP_like       PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   7.8   3.9e-50   2.4e-46       9     276 ..      46     336 ..      27     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 3.9e-50
                     PBP_like_2   9 vgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangaggliq 87 
                                     +e++ +Gst++++a++++  a+ +++pg+++ y + GSgag  +++n+++dfagsd pl  s+   +++a + + +++ 
  gi|121636856|ref|YP_977079.1|  46 KKELHSSGSTAQENAMEQFVYAYVRSCPGYTLDYNANGSGAGVTQFLNNETDFAGSDVPLNPSTGQpDRAAERCGSPAWD 125
                                    345****************99******************************************88755444444****** PP

                     PBP_like_2  88 vpvaigaialvvnkd..nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttflfstalaeq 157
                                     p ++g+ia+ +n +  + lnl+  + akIf g+It Wnd        +  lp  +pI+v++rsd+sgt ++f+++l  +
  gi|121636856|ref|YP_977079.1| 126 LPTVFGPIAITYNIKgvSTLNLDGPTTAKIFNGTITVWNDpqiqalnsGTDLP-PTPISVIFRSDKSGTSDNFQKYLDGA 204
                                    *************66699999**************************988888.9**********************999 PP

                     PBP_like_2 158 ...........gpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagk.fvlptaataasalkva 224
                                                  +  g+gasg+ g +  + +++g i+y +++++  + ++ +a++   ag   v+ t++++ + +  a
  gi|121636856|ref|YP_977079.1| 205 sngawgkgaseTFNGGVGVGASGNNGTSALLqTTDGSITYNEWSFAVGK-QLNMAQIITSAGPdPVAITTESVGKTIAGA 283
                                    9966555554433336677788888888887688**********99977.99999998888852688899999******* PP

                     PBP_like_2 225 kias..nplawslqpveeniadgayPlsrftyiivyqpyayh.gnnaalakaFld 276
                                    ki +  n+l  ++ + + + ++g+yP++ +ty iv++  +y+  ++ ++++aF++
  gi|121636856|ref|YP_977079.1| 284 KIMGqgNDLVLDTSSFYRPTQPGSYPIVLATYEIVCS--KYPdATTGTAVRAFMQ 336
                                    *****7777776777776666****************..7786777*******86 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   2.2   1.5e-18   9.2e-15       7     313 ..      53     343 ..      47     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.5e-18
                                    HHHHHHHHHHH....HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEECGGHHHHHHHT......TSBEC CS
                      SBP_bac_1   7 gaalqalvaka....fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviavdndwiarlaka......glllp 73 
                                    g++ q+ ++++    + + +pg++  ++  gsg++ +   +  +++a++d p      ++++ +r a+       +l++ 
  gi|121636856|ref|YP_977079.1|  53 GSTAQENAMEQfvyaYVRSCPGYTLDYNANGSGAGVTqflNNETDFAGSDVPLNP---STGQPDRAAERcgspawDLPTV 129
                                    5566666655544446899*******************************88333...44444444444455599***** PP

                                    CHHHHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT. CS
                      SBP_bac_1  74 ldpyvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkp. 152
                                    ++p+++ y+++gv   +++l++ +++ki++            g i+               W+++ + a + + + + + 
  gi|121636856|ref|YP_977079.1| 130 FGPIAITYNIKGVS--TLNLDGPTTAKIFN------------GTIT--------------VWNDPQIQALNSGTDLPPTp 181
                                    ************98..9*************............9999..............*****************999 PP

                                    HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..............HHCSHHHHS..HHHHHHHHHHHHHHHHHHHTT CS
                      SBP_bac_1 153 iggarggsasgtayyfalalakslggkvfdkdgg..............gldnpegvt..aatylvklyavanltkelkgk 216
                                    i ++++++ sgt + f  +l + ++g ++++                 g+++  + t  ++ty ++++a   + k+l ++
  gi|121636856|ref|YP_977079.1| 182 ISVIFRSDKSGTSDNFQKYLDGASNGAWGKGASEtfnggvgvgasgnnGTSALLQTTdgSITYNEWSFA---VGKQLNMA 258
                                    *******************************999***********999999999999999999999995...556***** PP

                                    EEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCS CS
                      SBP_bac_1 217 gaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsk 296
                                    +  ++ g++ +a+  +  ++ +i+g +     m +++   +++++ + +   g  p           ++  ++ i+++ k
  gi|121636856|ref|YP_977079.1| 259 QIITSAGPDPVAIT-TESVGKTIAGAKI----MGQGNDLVLDTSSFYRPTQPGSYP-----------IVLATYEIVCS-K 321
                                    *********99988.7999999999776....445555555555555544444444...........25666777764.4 PP

                                    THHH.....HHHHHHHHTSHHH CS
                      SBP_bac_1 297 npea.....AkkFldfllspea 313
                                    +p+a     +++F++ + +p++
  gi|121636856|ref|YP_977079.1| 322 YPDAttgtaVRAFMQAAIGPGQ 343
                                    4455577888888888888876 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.5e-09   3.3e-05       8     119 ..      72     205 ..      67     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.5e-09
                                    -TTCEEEEEES-HHHHHHHHHTTS-SEEEESS-..........................--CCCHHCCCCCEEE.EEEEE CS
                       PBP_like   8 npgvrvavanvGsggGlkalrageadiagshll..........................dketeeynapalrka.ldgie 60 
                                     pg+++ +   Gsg+G++++ ++e+d ags+++                           +   +yn++ + ++ ldg +
  gi|121636856|ref|YP_977079.1|  72 CPGYTLDYNANGSGAGVTQFLNNETDFAGSDVPlnpstgqpdraaercgspawdlptvfGPIAITYNIKGVSTLnLDG-P 150
                                    69999***************************9777777777776666666666666663334449999998763455.4 PP

                                    EEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEEC CS
                       PBP_like  61 vvlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfdellkkegis 119
                                     + ++ ++  + + + ++ + ++++  dl+  p+ ++ R   SGt d f++ l ++  s
  gi|121636856|ref|YP_977079.1| 151 -TTAKIFNGTITVWNDPQIQ-ALNSGTDLPPTPISVIFRSDKSGTSDNFQKYLDGA--S 205
                                    .8999999999999999966.99999*************************99664..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2522.10
//
Query:       gi|121636857|ref|YP_977080.1|  [L=71]
Description: hypothetical protein BCG_0986 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.8   0.0     0.0003   21.3   0.0    1.2  1  ABC_tran  ABC transporter
     0.0021   17.5   0.1     0.0026   17.2   0.1    1.1  1  ATPase    KaiC
     0.0026   17.5   0.1     0.0048   16.6   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0048   16.5   0.2     0.0057   16.3   0.1    1.3  1  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.021   15.3   0.1      0.024   15.2   0.1    1.1  1  AAA_23    AAA domain
       0.11   11.5   0.1       0.11   11.5   0.1    1.1  1  T2SSE     Type II/IV secretion system protein
       0.15   12.5   0.0       0.21   11.9   0.0    1.2  1  AAA_16    AAA ATPase domain
       0.19   11.8   0.3       0.31   11.0   0.3    1.6  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
        0.2   11.4   0.1       0.21   11.3   0.1    1.2  1  DEAD      DEAD/DEAH box helicase
       0.21   11.2   0.1       0.37   10.4   0.1    1.4  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.29   10.3   0.0       0.36   10.0   0.0    1.2  1  NB-ARC    NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.9e-07    0.0003       1      28 [.      37      64 ..      37      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.9e-07
                                   EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                   l++vs+ + +  ++ ++G++G+GK+t++
  gi|121636857|ref|YP_977080.1| 37 LDQVSMGFPARAVTSLMGPTGSGKTTFF 64
                                   799***********************87 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.6e-06    0.0026       8      36 ..      37      64 ..      32      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                         ATPase  8 lDeilkgGipegrvvlitGepGtGKtifa 36
                                   lD++   G+p ++v+ ++G +G+GKt+f 
  gi|121636857|ref|YP_977080.1| 37 LDQVS-MGFPARAVTSLMGPTGSGKTTFF 64
                                   78885.9*******************995 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.9e-06    0.0048      13      39 ..      38      64 ..      32      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                   d+ ++ +  + +t l+Gp+GsGK+T++
  gi|121636857|ref|YP_977080.1| 38 DQVSMGFPARAVTSLMGPTGSGKTTFF 64
                                   556677776779*************86 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.5e-06    0.0057      22      50 ..      37      64 ..      17      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                         AAA_25 22 rrwlvkgllpagelallaGapgtGKttla 50
                                   ++++ +g+ pa +++ l+G++g+GKtt+ 
  gi|121636857|ref|YP_977080.1| 37 LDQVSMGF-PARAVTSLMGPTGSGKTTFF 64
                                   56666788.9*****************95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.5e-05     0.024      20      36 ..      48      64 ..      30      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                         AAA_23 20 gltlItGpNGaGKTTil 36
                                    +t + Gp+G+GKTT++
  gi|121636857|ref|YP_977080.1| 48 AVTSLMGPTGSGKTTFF 64
                                   578999*********98 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.7e-05      0.11     131     145 ..      49      63 ..      15      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.7e-05
                          T2SSE 131 lilvsGgTgsGKttl 145
                                    +  + G+TgsGKtt+
  gi|121636857|ref|YP_977080.1|  49 VTSLMGPTGSGKTTF 63 
                                    55578*********8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.21      14      39 ..      35      62 ..      34      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         AAA_16 14 salervrsgrp..elvllsGesGvGKss 39
                                   ++l++v++g p   ++ l G+ G+GK++
  gi|121636857|ref|YP_977080.1| 35 TVLDQVSMGFParAVTSLMGPTGSGKTT 62
                                   5799999**9999999***********9 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00019      0.31      19      36 ..      47      64 ..       8      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                   TEEEEEEESTTSSHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlv 36
                                   ++v  L G+ G+GKTt+ 
  gi|121636857|ref|YP_977080.1| 47 RAVTSLMGPTGSGKTTFF 64
                                   45689***********96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00013      0.21      19      34 ..      52      67 ..      21      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                   EEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                           DEAD 19 vaaeTGsGKTlaflip 34
                                   + ++TGsGKT+ f+ p
  gi|121636857|ref|YP_977080.1| 52 LMGPTGSGKTTFFAHP 67
                                   789********99876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.37       2      19 ..      49      66 ..      48      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                                   EEEEEESTTCCHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnh 19
                                   vt l G+ GsGKTt+  h
  gi|121636857|ref|YP_977080.1| 49 VTSLMGPTGSGKTTFFAH 66
                                   7899**********8765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00022      0.36      15      38 ..      42      65 ..      32      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                                   TTTSCSEEEEEEESTTSSHHHHHH CS
                         NB-ARC 15 kdelqslvvalvGmgGvGKttlak 38
                                   ++ + + v +l+G  G+GKtt ++
  gi|121636857|ref|YP_977080.1| 42 MGFPARAVTSLMGPTGSGKTTFFA 65
                                   666778899************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 521.12
//
Query:       gi|121636858|ref|YP_977081.1|  [L=213]
Description: phosphate-transport protein ABC transporter pstBb [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   64.6   0.0    1.8e-17   64.2   0.0    1.2  1  ABC_tran  ABC transporter
    2.3e-09   37.5   0.0      3e-09   37.1   0.0    1.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.4e-06   27.9   0.0    2.1e-06   27.3   0.0    1.3  1  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.095   13.0   0.0        1.8    8.8   0.0    2.3  1  SbcCD_C   Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   3.9e-21   1.8e-17      38     137 .]      16     129 ..       2     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 3.9e-21
                                    SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGE CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  38 teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren..............esdeeiekalsklglkelkdtvv 102
                                     +G++ll g+++ + ++  ++r+++g+l+q p+ fp + + +n              e +  +++ l+++gl +  ++++
  gi|121636858|ref|YP_977081.1|  16 YSGDVLLGGRSIFNyRDVLEFRRRVGMLFQRPNPFPMS-IMDNvlagvrahklvprkEFRGVAQARLTEVGLWDAVKDRL 94 
                                    68999999999877799999******************.88888***9999998876666669999************** PP

                                    STTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 103 ksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    ++sp  LSgGq+q ++lar+l+ +p++lllDEpt+
  gi|121636858|ref|YP_977081.1|  95 SDSPFRLSGGQQQLLCLARTLAVNPEVLLLDEPTS 129
                                    *********************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   6.7e-13     3e-09     233     299 ..      97     159 ..      61     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.7e-13
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    +++ lS G+++ll+l+  l+  +    +ll+DEp + L+P  ++++ e++++l++ +  vi++TH+ 
  gi|121636858|ref|YP_977081.1|  97 SPFRLSGGQQQLLCLARTLAVNP---EVLLLDEPTSALDPTTTEKIEEFIRSLAD-RLTVIIVTHNL 159
                                    57889*******99999999988...9**************************99.*********95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.7e-10   2.1e-06     136     203 ..     100     163 ..      27     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.7e-10
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                     LSgG+++L+ la  +A++   p+ + llDe  +aLD + ++k+ e++++  ++  +i+++++  + +
  gi|121636858|ref|YP_977081.1| 100 RLSGGQQQLLCLARTLAVN---PE-VLLLDEPTSALDPTTTEKIEEFIRSLADRLTVIIVTHNLAQAA 163
                                    69***********999975...65.5689*********************************876655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00041       1.8      61      88 ..     116     143 ..      82     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00041
                        SbcCD_C  61 epalrlvfLDEAFsklDeesiatllell 88 
                                      ++++++LDE  s lD+++++++ e++
  gi|121636858|ref|YP_977081.1| 116 AVNPEVLLLDEPTSALDPTTTEKIEEFI 143
                                    3468999***********9999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1656.28
//
Query:       gi|121636859|ref|YP_977082.1|  [L=374]
Description: periplasmic phosphate-binding lipoprotein pstS1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-41  140.9   4.8    7.9e-41  140.6   4.8    1.1  1  PBP_like_2  PBP superfamily domain
      9e-28   98.1   3.3    1.1e-27   97.8   3.3    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.4e-07   30.8   0.0      9e-07   28.2   0.1    2.1  2  PBP_like    PBP superfamily domain
  ------ inclusion threshold ------
      0.088   12.8   0.1        2.2    8.2   0.1    2.2  2  GrlR        T3SS negative regulator,GrlR


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   4.8   1.8e-44   7.9e-41       4     281 ..      47     342 ..      36     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 1.8e-44
                     PBP_like_2   4 aeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangag 83 
                                    a++++   +  +Gst ++p+++ +  af + +p+++++ ++tGSgagi++ ++g+v +++sd+ l+e + aa       +
  gi|121636859|ref|YP_977082.1|  47 ASSPVT--LAETGSTLLYPLFNLWGPAFHERYPNVTITAQGTGSGAGIAQAAAGTVNIGASDAYLSEGDMAA------HK 118
                                    455555..8889*************99*****************************************8854......46 PP

                     PBP_like_2  84 gliqvpvaigaialvvnkd...nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttflfst 152
                                    gl+++  ai+a  + +n +     l+l  ++La+ ++g+I++W+d        +++lp ++++ + hrsdgsg tflf++
  gi|121636859|ref|YP_977082.1| 119 GLMNIALAISAQQVNYNLPgvsEHLKLNGKVLAAMYQGTIKTWDDpqiaalnpGVNLP-GTAVVPLHRSDGSGDTFLFTQ 197
                                    7****************996777777***************************99999.********************* PP

                     PBP_like_2 153 alaeqgpwt................asgigasgsegvasav.snngaigyvsvaywlavk..gysladvtngagkfvlpt 213
                                    +l++q p +                 +++g +g++g+++    ++g  +y+ +++  +    g+ +a++ n  g+f lp 
  gi|121636859|ref|YP_977082.1| 198 YLSKQDPEGwgkspgfgttvdfpavPGALGENGNGGMVTGCaETPGCVAYIGISFLDQASqrGLGEAQLGNSSGNFLLPD 277
                                    *****7766445555455555544455666888*******9577*********986655456****************** PP

                     PBP_like_2 214 aataasalkvakias.nplawslqpveeniadgayPlsrftyiivyqpyayh.gnnaalakaFldyllsd 281
                                    a+++++a+  +  ++    +   +++ + +a++ yP+ ++ y+iv++  +++  ++a+ ++aFl+++++d
  gi|121636859|ref|YP_977082.1| 278 AQSIQAAAAGFASKTpA--N-QAISMIDGPAPDGYPIINYEYAIVNN--RQKdAATAQTLQAFLHWAITD 342
                                    99999988876665542..3.4667889*******************..6666889**********9986 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   3.3   2.5e-31   1.1e-27      10     314 ..      65     345 ..      52     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 2.5e-31
                                    HHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTS...SSCSEEEECGGHHHHHHHT..TSBECCHHHHHHT CS
                      SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGd...gpaDviavdndwiarlaka..glllpldpyvkay 81 
                                    ++     af +++p+++++ + +gsg+++    ++t+ i+a+d    + D++a+         k+  + +l +++  ++y
  gi|121636859|ref|YP_977082.1|  65 FNLWG-PAFHERYPNVTITAQGTGSGAGIAqaaAGTVNIGASDaylSEGDMAAH---------KGlmNIALAISAQQVNY 134
                                    44455.679999******************666666666666666655566666.........4466************* PP

                                    TECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT.HCCHCCEE CS
                      SBP_bac_1  82 lapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkp.iggarggs 160
                                    + pgv + ++kl+++vl+++++            g i               tWd++ +aa +++ + +++ ++ +++++
  gi|121636859|ref|YP_977082.1| 135 NLPGVSE-HLKLNGKVLAAMYQ------------GTIK--------------TWDDPQIAALNPGVNLPGTaVVPLHRSD 187
                                    ****887.**********9988............8999..............**************************** PP

                                    HHHHHHHHHHHHHHHHTGGGEECCCT...................HHCSHHHHS..HHHHHHHHHHHHHHHHHHHTTEEE CS
                      SBP_bac_1 161 asgtayyfalalakslggkvfdkdgg...................gldnpegvt..aatylvklyavanltkelkgkgae 219
                                    +sg++++f+++l+k+ +  ++++ g                    g+++++++t   ++y+  +++ +  +++l+ ++  
  gi|121636859|ref|YP_977082.1| 188 GSGDTFLFTQYLSKQDPEGWGKSPGFgttvdfpavpgalgengngGMVTGCAETpgCVAYIGISFLDQASQRGLGEAQLG 267
                                    ******************************************************************************** PP

                                    CSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHH CS
                      SBP_bac_1 220 nkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpe 299
                                    n++g+++l++ ++ +aa+a +          +++ ++ a+++ + +  +g+++            ++y +ai+++ ++ +
  gi|121636859|ref|YP_977082.1| 268 NSSGNFLLPDAQSIQAAAAGFA---------SKTPANQAISMIDGPAPDGYPI------------INYEYAIVNNRQKDA 326
                                    ******************7666.........467*******************............*************99 PP

                                    H....HHHHHHHHTSHHHH CS
                      SBP_bac_1 300 a....AkkFldfllspeaq 314
                                    a     ++Fl ++ +++++
  gi|121636859|ref|YP_977082.1| 327 AtaqtLQAFLHWAITDGNK 345
                                    9999***********9987 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1     2e-10     9e-07       4     116 ..      72     202 ..      70     218 .. 0.64
   2 ?   -1.8   0.0      0.31   1.4e+03      95     113 ..     318     336 ..     312     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2e-10
                                    HHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS-...................--CCCHHCCCCCEEEEEEEEEEEE CS
                       PBP_like   4 laeknpgvrvavanvGsggGlkalrageadiagshll...................dketeeynapalrkaldgievvlv 64 
                                    ++e+ p+v+++ +++Gsg+G+++ +ag++ i++s+ +                   + ++ +yn+p + ++l        
  gi|121636859|ref|YP_977082.1|  72 FHERYPNVTITAQGTGSGAGIAQAAAGTVNIGASDAYlsegdmaahkglmnialaiSAQQVNYNLPGVSEHL-------- 143
                                    88999********************************44444444444444444443333344444444443........ PP

                                    -CC-HCHCCCCHCCHHHS--BGGGC...........-S-B-EEEEE-TTSHHHHHHHHHHC-C CS
                       PBP_like  65 nlarreqglvvakgnpkkitnwkdl...........adaplrlvnRetGSGtrdlfdellkke 116
                                        +  g v+a++ +  i++w d            +   ++   R  GSG   lf++ l+k+
  gi|121636859|ref|YP_977082.1| 144 ----KLNGKVLAAMYQGTIKTWDDPqiaalnpgvnlPGTAVVPLHRSDGSGDTFLFTQYLSKQ 202
                                    ....33444555555555555554333333333322557777789999999999999999665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.31
                                    EEEEE-TTSHHHHHHHHHH CS
                       PBP_like  95 rlvnRetGSGtrdlfdell 113
                                     + nR++++ t + ++  l
  gi|121636859|ref|YP_977082.1| 318 IVNNRQKDAATAQTLQAFL 336
                                    5669999999999888776 PP

>> GrlR  T3SS negative regulator,GrlR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0005       2.2      13      56 ..      84     128 ..      78     137 .. 0.81
   2 ?    2.2   0.0     0.038   1.7e+02      25      49 ..     141     165 ..     128     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                           GrlR  13 ndrdlgeGvivlregkvnGG.dfgyyyqGelkivdgavkallkvt 56 
                                    + ++ g+G++    g vn G   +y+  G++++++g +++ l + 
  gi|121636859|ref|YP_977082.1|  84 QGTGSGAGIAQAAAGTVNIGaSDAYLSEGDMAAHKGLMNIALAIS 128
                                    5567799***********6615678899***********999875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.038
                           GrlR  25 regkvnGGdfgyyyqGelkivdgav 49 
                                    ++ k+nG   + +yqG++k  d  +
  gi|121636859|ref|YP_977082.1| 141 EHLKLNGKVLAAMYQGTIKTWDDPQ 165
                                    67799*************9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3060.00
//
Query:       gi|121636860|ref|YP_977083.1|  [L=338]
Description: phosphate ABC transporter transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-14   52.1   8.7    6.4e-14   52.1   8.7    2.2  2  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
        6.5    6.4   7.9       0.84    9.3   3.1    2.0  2  Keratin_assoc  Keratinocyte-associated protein 2


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.4     0.012   1.1e+02      26      68 ..      21      99 ..       5     112 .. 0.66
   2 !   52.1   8.7   7.2e-18   6.4e-14       4     180 ..     104     328 ..     101     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.012
                   BPD_transp_1 26 vllslPsfvlaillvlvf...................................vilsilghlilp.viillllsaapyv 68
                                   ++  +P ++l+++lv+++                                   ++  ++++++lp ++ +l++sa++++
  gi|121636860|ref|YP_977083.1| 21 IGAVIPLLALVLVLVVLVieamgairlnglhfftatewnpgntygetvvtdgvAHPVGAYYGALPlIVGTLATSAIALI 99
                                   6677888888888776667888888888888888888888888888888888844444444444433333333333332 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 7.2e-18
                   BPD_transp_1   4 lGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf.........................vilsilghlil 54 
                                    +++ aa     +  k+l +++ ++ ++l ++Ps+v+++   + f                           + + g ++l
  gi|121636860|ref|YP_977083.1| 104 VSVGAAlvivERLPKRLAEAVGIVLELLAGIPSVVVGLWGAMTFgpfiahhiapviahnapdvpvlnylRGDPGNGEGML 183
                                    555555556678899********************999999999999********************7766667789999 PP

                   BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                       ++l+++ +p++  ++ + +r++p   +e a alG+s w+ +r+v+lP + + i+  ++l +g++lg+++++ ++ + 
  gi|121636860|ref|YP_977083.1| 184 VSGLVLAVMVVPIIATTTHDLFRQVPVLPREGAIALGMSNWECVRRVTLPWVSSGIVGAVVLGLGRALGETMAVAMVSGA 263
                                    99***************************************************************************955 PP

                   BPD_transp_1 135 pGlgtllleailgydyseis....................nggvlalviavlllnlvadilqrlld 180
                                      lg +  +++  + + +++                    + + l+l +++ll n++a+ ++r ++
  gi|121636860|ref|YP_977083.1| 264 V-LGAMPANIYATMTTIAATivsqldsamtdstnfavktlAEVGLVLMVITLLTNVAARGMVRRVS 328
                                    4.887777777777766666888888888******9777777777777777777777776666655 PP

>> Keratin_assoc  Keratinocyte-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.58   5.2e+03       9      26 ..      28      45 ..      25      54 .. 0.61
   2 ?    9.3   3.1   9.4e-05      0.84      10      93 ..     237     330 ..     231     332 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.58
                  Keratin_assoc  9 lssllavlvfalmqlyks 26
                                   l+++l+++v+ +  + + 
  gi|121636860|ref|YP_977083.1| 28 LALVLVLVVLVIEAMGAI 45
                                   566666666666555544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 9.4e-05
                  Keratin_assoc  10 ssllavlvfalmqlyksklasselltilgGflgsllF....vllLTavgnl.etllfgkgfqakllpEv.....llclvl 79 
                                    s ++  +v++l +   +++a + +   + G++ + ++    ++  T+v+ l  +++ +++f +k l+Ev     +++l++
  gi|121636860|ref|YP_977083.1| 237 SGIVGAVVLGLGRALGETMAVAMVSGAVLGAMPANIYatmtTIAATIVSQLdSAMTDSTNFAVKTLAEVglvlmVITLLT 316
                                    556666666666666665555555554445444444411116677899999555556789********954444456667 PP

                  Keratin_assoc  80 aliasglvHrvciT 93 
                                     ++a g+v rv+ T
  gi|121636860|ref|YP_977083.1| 317 NVAARGMVRRVSRT 330
                                    78899******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2397.47
//
Query:       gi|121636861|ref|YP_977084.1|  [L=301]
Description: phosphate ABC transporter transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-26   91.1  12.5      7e-26   91.1  12.5    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.0      0.01   1.9e+02      19      68 ..      49      94 ..      22     102 .. 0.49
   2 !   91.1  12.5   3.9e-30     7e-26       2     182 ..     102     297 ..      99     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.01
                   BPD_transp_1 19 llrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyv 68
                                   l + +  v +++P+f + +l++     +++ g +   +ii +++ a++++
  gi|121636861|ref|YP_977084.1| 49 LWMLIGVVSRAVPVFHWSVLVQ----DSQGNGGGLRNAIIGTAVLAIGVI 94
                                   2333334444444444444444....333333333334444443333333 PP

  == domain 2  score: 91.1 bits;  conditional E-value: 3.9e-30
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                    +l+Gi++  +  +k++ +lr+ ++vl+++Ps+vl+ + +l++v+  ++g++  +++++l ++++py+   +++al ++p+
  gi|121636861|ref|YP_977084.1| 102 VLTGIYLSEFATGKTRSILRGAYEVLSGIPSIVLGYVGYLALVVYFDWGFSLAAGVLVLSVMSIPYIAKATESALAQVPT 181
                                    678999999999*************************9999999999********************************* PP

                   BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyseis.... 154
                                    +++eaa+alG++    +rk+vl+ a+p i+tg+++a+++++g+++ l+++++w+     g+l+ ++  +  y+ ++    
  gi|121636861|ref|YP_977084.1| 182 SYREAAEALGLPAGWALRKIVLKTAMPGIVTGMLVALALAIGETAPLLYTAGWSNsppTGQLTDSPVGYLTYPIWTfynq 261
                                    *****************************************************988887777777777777777778888 PP

                   BPD_transp_1 155 .........nggvlalviavlllnlvadilqrlldpr 182
                                             + ++l l+ ++lll++++  l  +l++r
  gi|121636861|ref|YP_977084.1| 262 psksaqdlsYDAALLLI-VFLLLLIFIGRLINWLSRR 297
                                    88888888544444444.4444444444444455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2013.86
//
Query:       gi|121636862|ref|YP_977085.1|  [L=273]
Description: hypothetical protein BCG_0991c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-41  142.9   0.0    1.3e-41  142.5   0.0    1.1  1  Ku            Ku70/Ku80 beta-barrel domain
  ------ inclusion threshold ------
      0.039   14.2   0.0      0.083   13.1   0.0    1.5  1  MmoB_DmpM     MmoB/DmpM family
      0.039   13.5   0.3       0.13   11.8   0.0    1.9  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Ku  Ku70/Ku80 beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.0   2.2e-45   1.3e-41       2     202 ..      11     192 ..      10     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 2.2e-45
                             Ku   2 gggvsipVklykateeakkpkfkkldketnepvkvetkyvcsdtge.vdeedivkgyey.Ggevvpltkeelekiksfds 79 
                                    +g+v++pVk+y+at + ++++f+++++++n   ++++k+vc+ +ge vd+ d+ ++ye  +g++v +t+++++++++  s
  gi|121636862|ref|YP_977085.1|  11 FGLVNVPVKVYSATAD-HDIRFHQVHAKDNG--RIRYKRVCEACGEvVDYRDLARAYESgDGQMVAITDDDIASLPEERS 87 
                                    789************9.**************..***********888************8667**************66* PP

                             Ku  80 kglkllgFvplseilkeylsikssyfiyPddkdekgstkafsaLveamleskkvaivrfvlrskskprlvaLvPqeeels 159
                                    + +++l+Fvp++ +++  +  ++syf+ P   d+k+s+  + +L +++ e++++aiv f+lr+k++  l+aL++    + 
  gi|121636862|ref|YP_977085.1|  88 REIEVLEFVPAADVDPMMF--DRSYFLEP---DSKSSK-SYVLLAKTLAETDRMAIVHFTLRNKTR--LAALRVK---DF 156
                                    *******************..********...888666.9**************************..*******...33 PP

                             Ku 160 seeekeglvlvtLpfaddiRslkfpsldeeeeekknkpteeql 202
                                     +  +e+++++tL ++d+iR ++fp ld     +k +++ ++l
  gi|121636862|ref|YP_977085.1| 157 GK--REVMMVHTLLWPDEIRDPDFPVLD-----QKVEIKPAEL 192
                                    32..46********************92.....4445555555 PP

>> MmoB_DmpM  MmoB/DmpM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.083      28      82 ..      24      79 ..      17      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                   EEEE-SSEEEEEEESEEEEEHHHHHHHHTST--HHHHTTSEEEEESEEE.ESSSEE CS
                      MmoB_DmpM 28 tvedrpayvridaegrleirreeieealGrefdlqelevnlssfaGrid.tdddei 82
                                   t ++   +  ++a+++ +ir++ + ea G+ +d ++l  +  s  G+++ ++dd i
  gi|121636862|ref|YP_977085.1| 24 TADHDIRFHQVHAKDNGRIRYKRVCEACGEVVDYRDLARAYESGDGQMVaITDDDI 79
                                   5667777899***************************************9999877 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.2e-05      0.13      19      33 ..      45      59 ..      41      63 .. 0.86
   2 ?   -2.2   0.1      0.53   3.2e+03      30      41 ..      75      86 ..      74      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                                   CEEESSSSBEEEECC CS
                   TF_Zn_Ribbon 19 elvCtdCGlVledns 33
                                     vC++CG+V+++++
  gi|121636862|ref|YP_977085.1| 45 KRVCEACGEVVDYRD 59
                                   569*********987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.53
                                   EECCCCCCCHHH CS
                   TF_Zn_Ribbon 30 ednsidegpewr 41
                                    d++i + pe+r
  gi|121636862|ref|YP_977085.1| 75 TDDDIASLPEER 86
                                   69999999*998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1826.75
//
Query:       gi|121636863|ref|YP_977086.1|  [L=759]
Description: ATP-dependent DNA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-38  130.1   0.1    6.4e-38  129.3   0.1    1.5  1  LigD_N          DNA polymerase Ligase (LigD)
    2.7e-27   95.7   0.0    5.5e-27   94.7   0.0    1.5  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
      6e-23   81.3   0.0    1.5e-22   80.1   0.0    1.7  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    1.4e-06   28.7   0.0    2.5e-06   27.9   0.0    1.4  1  RNA_ligase      RNA ligase
      0.001   19.1   0.0      0.011   15.8   0.0    2.2  1  DNA_primase_S   DNA primase small subunit


Domain annotation for each model (and alignments):
>> LigD_N  DNA polymerase Ligase (LigD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.1   1.8e-41   6.4e-38       1     105 []     329     432 ..     329     432 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 1.8e-41
                                    EEEESSSEEEEEEEEETTEEEEEEETT---SSTTSEEEEEEEEEE-GGGGGEEEEE-TTSTT-EEEEEEEEEEEEE..-H CS
                         LigD_N   1 qeHdaprlHYDlrLeidevlsswavpkglpedpnskrlAvetedhpleyadfegliekgeygaGsvliwDtGtyeveekl 80 
                                    qeH+a+r HYD+rLe+d+vl+swavpk+lp +++ ++lA++tedhpleya+feg i++geygaG+v+iwD+Gty++ ek+
  gi|121636863|ref|YP_977086.1| 329 QEHHARRPHYDFRLERDGVLVSWAVPKNLPDNTSVNHLAIHTEDHPLEYATFEGAIPSGEYGAGKVIIWDSGTYDT-EKF 407
                                    89**************************************************************************.7** PP

                                    HHHHHHTEEEEEEECSSSEEEEEEE CS
                         LigD_N  81 aealkkrkiklrLhGeklkgkyvlv 105
                                    +++ +++++ ++LhG +++g+y+l+
  gi|121636863|ref|YP_977086.1| 408 HDDPHTGEVIVNLHGGRISGRYALI 432
                                    **********************995 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   1.5e-30   5.5e-27       2     204 .]     461     637 ..     458     637 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.5e-30
                                    EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEE CS
                 DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElv 81 
                                    mLA   +     +  l+++++ +E K+DG+R+ v+ + + v+l SR+++d+ta++p+l   ++ +++++   v+lDGE+v
  gi|121636863|ref|YP_977086.1| 461 MLATHGT-----VAGLKASQWAFEGKWDGYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHH---VVLDGEAV 532
                                    5544444.....4556678999************************************77666666665...9******* PP

                                    EEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEE CS
                 DNA_ligase_A_M  82 avdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslev 161
                                    ++d     +  f ++++r  ++         +++ + +FD+Lyldg  l+ + +++RrklLe++   + + + + e l +
  gi|121636863|ref|YP_977086.1| 533 VLDSS--GVPSFSQMQNR-GRD---------TRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLA--NATSLTVPELLPG 598
                                    *9877..55566666666.233.........468899**************************99..6777777777777 PP

                                    SSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 162 kdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                    +     +++++ + ++g EG+++K  ds+Y+pg+r + w+K K
  gi|121636863|ref|YP_977086.1| 599 DG----AQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDK 637
                                    66....788999*****************************88 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   4.1e-26   1.5e-22       2      99 .]     657     751 ..     656     751 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 4.1e-26
                                    GGSEEEEEEEEEETTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTT.EEE-TT-EEEEEESEEECT CS
                 DNA_ligase_A_C   2 gglvgslllgvyddgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrd.vWvePelvveVkfaeitas 80 
                                    +++vgsll+g+   g l+++g+vgtG+s++el++l+++l +l+++++pf  + p+++++  ++v+P+lv+eV+++e+t++
  gi|121636863|ref|YP_977086.1| 657 SSGVGSLLMGIPGPGGLQFAGRVGTGLSERELANLKEMLAPLHTDESPFDVPLPARDAKGiTYVKPALVAEVRYSEWTPE 736
                                    6899*********************************************99999999988******************** PP

                                    SSSTTEECT-EEEEE-TTS CS
                 DNA_ligase_A_C  81 gkykaslRfPrfkrlReDk 99 
                                    g    +lR+ ++++lR+Dk
  gi|121636863|ref|YP_977086.1| 737 G----RLRQSSWRGLRPDK 751
                                    *....*************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     7e-10   2.5e-06       3     159 ..     476     635 ..     474     637 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7e-10
                                    EEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.......SS.. CS
                     RNA_ligase   3 vvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig......hsi.. 72 
                                    +  + K DG+++ +  +++ v++ sRs+   +++++++            +l+e+la ++++l GE +       +s   
  gi|121636863|ref|YP_977086.1| 476 WAFEGKWDGYRLLVEADHGaVRLRSRSGRDvTAEYPQL-----------RALAEDLADHHVVLDGEAVVldssgvPSFsq 544
                                    66666777777777776445777777766632233333...........37888888889*********98755533353 PP

                                    ....TTSS....EEEEEEEEEEE..CTTBECE--HHHH.HHHHHCCT.B..EEEEE.SSHHHHHCCC.HHHHTC--EEEE CS
                     RNA_ligase  73 ..kygglpk...efyvFdifdir..dkeeqrylspdev.ealakglg.tvpvlyegkflaaeellelllskgnkrEGlVi 143
                                       +g+  +   ef++Fd++ ++       ry +++++ e la+ +  tvp l  g+  +a ++     s ++  EG++ 
  gi|121636863|ref|YP_977086.1| 545 mqNRGR--DtrvEFWAFDLLYLDgrALLGTRYQDRRKLlETLANATSlTVPELLPGDGAQAFAC-----SRKHGWEGVIA 617
                                    332222..1456*********99665559***************9989*****66555433333.....466899***** PP

                                    EESSSSBE.TTE.BSEEE CS
                     RNA_ligase 144 kpeselyk.nkg.raifK 159
                                    k  +++y+   +   ++K
  gi|121636863|ref|YP_977086.1| 618 KRRDSRYQpGRRcASWVK 635
                                    *****9998877877777 PP

>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.011       1     174 [.     136     254 ..     136     257 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                                    EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH... CS
                  DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnl 80 
                                    FD+D+ +  +           + + ++++ ++ ll  d+g   +++v+sg++G+H+++++++ +++  +   a ++    
  gi|121636863|ref|YP_977086.1| 136 FDLDPGEGVM----------MAQLAEVARAVRDLL-ADIGLV-TFPVTSGSKGLHLYTPLDEPVSSRGATVLA-KR---- 198
                                    6666666666..........455677888888999.9***96.******************988554332222.32.... PP

                                    ...............................HCHHHHCT--------..................--------------- CS
                  DNA_primase_S  81 yrplhpflsrsmlkivkpvveeiileeqdpfeikkllrllpdkslrekkkweakedivlvllyprldeqvtkgikhllka 160
                                       ++  l++                     ++  l ++ ++kslr              + ++++ ++   + ++++ a
  gi|121636863|ref|YP_977086.1| 199 ---VAQRLEQ---------------------AMPALVTSTMTKSLRA------------GKVFVDWSQN---SGSKTTIA 239
                                    ...2222222.....................2333333333333333............4444444444...34444445 PP

                                    --....---.----- CS
                  DNA_primase_S 161 pfcihgktg.nvcvp 174
                                    p++++g+t   v++p
  gi|121636863|ref|YP_977086.1| 240 PYSLRGRTHpTVAAP 254
                                    555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 4238.05
//
Query:       gi|121636864|ref|YP_977087.1|  [L=644]
Description: bifunctional enzyme: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase + cyclase/dehydrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-48  165.0   0.0    4.5e-48  163.8   0.0    1.6  2  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
    4.6e-22   79.0   7.5    1.4e-21   77.4   3.1    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily
    9.5e-06   25.3   0.1      2e-05   24.2   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
      0.007   17.2   1.5      0.018   15.9   0.2    2.5  2  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0     1e-51   4.5e-48       4     218 .]      75     300 ..      73     300 .. 0.87
   2 ?   -3.0   0.0         1   4.7e+03     160     184 ..     500     524 ..     497     543 .. 0.76

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 1e-51
                                    EEEEE--SHHHHHTTT......-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--H CS
                  FAA_hydrolase   4 cdglnyaehvreagka.....aeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsv 78 
                                     d l++ +h+r++++a          ++ ip    f+++ +s++ gp d+ +   gs   d+E+E+a+vig+  +++ +v
  gi|121636864|ref|YP_977087.1|  75 RDSLCFLDHMRNCQEAmgggrVLMDTWYRIPA---FYFACPSTVLGPYDDAPTAPGSAWQDFELEIAAVIGTSGKDL-TV 150
                                    678999*******9999999755566777777...***************9877777777*****************.89 PP

                                    HHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT--...-S..S-EEEEEETTEEEEEEEG CS
                  FAA_hydrolase  79 eeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeled...pe..dlelrlrvngeevqdsnt 153
                                    e+Ae  i Gyt++nD+saRdlq+ e  +l   ++k+ d+  ++Gp +vtpdele+    +  +l++ + vng+++++++t
  gi|121636864|ref|YP_977087.1| 151 EQAERSIIGYTIFNDWSARDLQMLEG-QLRIGQAKGKDSGITLGPYLVTPDELEPycrGGklSLRVIALVNGTVIGSGST 229
                                    **************************.888888999999***************9854332244444445********** PP

                                    GGTTTSHHHHHHHHHHHH-B-TT-EEEEEES...............S--EE--TT-EEEEEETTTEEEEEEE. CS
                  FAA_hydrolase 154 kdmifspaeliahlsagltLepGdliltGTpsgvga........eeeslkflkdgDeveveieglGelrnrVa 218
                                    ++m +s+ e+ia++s+g+tL pGd++++GT++   +         e+ + +l+dgD+v++++eglGe r++V+
  gi|121636864|ref|YP_977087.1| 230 AQMDWSFGEVIAYASRGVTLTPGDVFGSGTVPT--CtlvehlrpPESFPGWLHDGDVVTLQVEGLGETRQTVR 300
                                    *******************************75..223445555566799*********************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1
                                    HHHHHHHHHHHH-B-TT-EEEEEES CS
                  FAA_hydrolase 160 paeliahlsagltLepGdliltGTp 184
                                     a+ + h++    L +Gdl++ G  
  gi|121636864|ref|YP_977087.1| 500 TADSVVHVADAGVLFAGDLLFIGCT 524
                                    5677888888888999999999954 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.015        68     139     194 ..       9      58 ..       4      61 .. 0.86
   2 !   77.4   3.1   3.2e-25   1.4e-21       3     197 .]     353     554 ..     351     554 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.015
                                    EETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEE CS
                    Lactamase_B 139 eygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlv 194
                                    + g+++ +++GDa++a +     l      ++ + +a+ ++ + +++++++a+v++
  gi|121636864|ref|YP_977087.1|   9 DHGERTGVLSGDAIYAMPPDVSLL------DLVGRGADGLRTAGERAVRSPAAVVA 58 
                                    6788999********999999999......99999999999999999999999986 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 3.2e-25
                                    CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                    Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                     +++n+ l+ gdg  +L+Dt+++ + +r++l+  +   +  ++++ ++TH+  DH+ g   l +   +  ++   e+ ++
  gi|121636864|ref|YP_977087.1| 353 YGFSNAGLVAGDGASLLVDTLFDLALTREMLAAMKPVTERAPITDALITHSNGDHTHGTQLLDRSVRIIAAKGTSEEIEH 432
                                    5789************************************************************9998888888777777 PP

                                    HCHHHHHHHHHCCHH.................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCE CS
                    Lactamase_B  83 fmeeaddaasrkgll.................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkv 145
                                     +  ++ a+    +l                   +  ++++ +++ +l++++ggrr      gp+h+  + vv+  +++v
  gi|121636864|ref|YP_977087.1| 433 GPAPEMLARIQTADLgpvatrylrdrfghfdfSGIKLRNADLTFDRDLAIELGGRRVDLLNLGPAHTTADSVVHVADAGV 512
                                    7777777777766667799*************9*********************************************** PP

                                    EEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 146 lftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                    lf+GD+l++g+t+ +            ++ +++ ++ + +++l+a ++vpgH
  gi|121636864|ref|YP_977087.1| 513 LFAGDLLFIGCTPIVWA----------GPIANWVAACDAMIALDAPTVVPGH 554
                                    *****************..........************************* PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   4.5e-09     2e-05       3      80 ..     368     440 ..     367     473 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.5e-09
                                    EEES--TTHHHH..HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCH CS
                  Lactamase_B_2   3 iLiDagpdlrqq..alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylale 80 
                                    +L+D+ +dl+    +l a++Pv+   e +pi   l+th+  DH++g   l +    +++++a kg+++++e++  +++l 
  gi|121636864|ref|YP_977087.1| 368 LLVDTLFDLALTreMLAAMKPVT---ERAPITDALITHSNGDHTHGTQLLDR----SVRIIAAKGTSEEIEHGPAPEMLA 440
                                    69******666655666667775...4469999*************999999....388*************98776655 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   3.9e-06     0.018       1      50 []       1      67 [.       1      67 [. 0.88
   2 ?   -2.8   0.1       2.9   1.3e+04      31      42 ..     297     308 ..     277     310 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                   -EEEEEEETTEEEEEEEE.EEEEEESS.....-TT....SS-EEEEEEE........EGGGSEEE-S CS
                        DUF2437  1 MriaRFshgggpryGvlegdtvvvlag.....dpf....gavqpTGerv........pLadVrLLAP 50
                                   M+++ ++ ++g r Gvl gd + +        d +    +++++ Ger         +L++V+L AP
  gi|121636864|ref|YP_977087.1|  1 MKWVTYRSDHGERTGVLSGDAIYAMPPdvsllDLVgrgaDGLRTAGERAvrspaavvALDEVTLAAP 67
                                   ***************************555553337776799999999999****99*********9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                                    SS-EEEEEEEEG CS
                        DUF2437  31 gavqpTGervpL 42 
                                    ++v+++G  +pL
  gi|121636864|ref|YP_977087.1| 297 QTVRTSGTPFPL 308
                                    456666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 3514.79
//
Query:       gi|121636865|ref|YP_977088.1|  [L=288]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-46  158.2   0.1    4.4e-46  157.7   0.1    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.1   2.5e-50   4.4e-46      19     218 ..      10     226 ..       2     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 2.5e-50
                 Bac_luciferase  19 saslrylvelaraaEelGfdavwvaehhggpgga....................ldaftllaalaaaTerirlgtavtpl 78 
                                    + ++  ++ la+aaE++G+ ++ ++++   p+ +                     ++f+l aal a+T+r+r+   v+ l
  gi|121636865|ref|YP_977088.1|  10 T-DFTFYIPLAKAAEAAGYSSMTIPDSIAYPFESdskypytpdgnrefmdgkpfIETFVLTAALGAVTTRLRFNFFVLKL 88 
                                    3.7888999*********************9999********************************************** PP

                 Bac_luciferase  79 ytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgall 158
                                    + r Pa++A+qa +L  l g R+glg+gt+ ++++++ +Gv++++r +r +E +e++r+l +g+  +f+Gef+ + ++  
  gi|121636865|ref|YP_977088.1|  89 PIRPPALVAKQAGSLAALIGNRVGLGVGTSPWPEDYELMGVPFAKRGKRIDECIEIVRGLTTGDYFEFHGEFYDIPKTKM 168
                                    *************************************************************99999************** PP

                 Bac_luciferase 159 lprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpa 218
                                    +p p q+ iP++v+++ +a+l+ aar adg+++ g +p+e+ +li+r++   +eag++++
  gi|121636865|ref|YP_977088.1| 169 TPAPTQP-IPILVGGHADAALRRAAR-ADGWMHGGGDPDELDRLIARVKRLREEAGKTSP 226
                                    ****998.***************997.9****************************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1926.78
//
Query:       gi|121636866|ref|YP_977089.1|  [L=257]
Description: hypothetical protein BCG_0995c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-11   42.2   0.0    9.7e-11   41.3   0.0    1.5  1  STAS      STAS domain
  ------ inclusion threshold ------
       0.37   11.2   3.6          8    6.9   1.7    2.5  2  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.1e-14   9.7e-11       2     117 .]      16     120 ..      15     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.1e-14
                                    EEEEECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHH.HTT CS
                           STAS   2 idaeeiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelk.rig 80 
                                    i ++++++++il+ dg +d  ++  ++++l+ra+ e+p         + +i++ +++++   s+++++++++ +   r +
  gi|121636866|ref|YP_977089.1|  16 IAVRTQDSVVILTADGALDSSSSALLRDSLTRATLEQP---------SAVIVNVTELQVAEESAWSVFISARWQADfRAD 86 
                                    578999*******************************7.........*****************************9*** PP

                                    -EEEEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  81 vevvlvnikpevreklektgffdeveeeklfltvhdA 117
                                    v v+lv+ + + r  +++tg+++++   ++++t + A
  gi|121636866|ref|YP_977089.1|  87 VPVLLVCGHRAGRAAVTRTGVARFM---PVYPTEKAA 120
                                    *************************...****99876 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.7   0.00089         8       1      55 [.      27      82 ..      27     106 .. 0.89
   2 ?    3.6   0.0    0.0093        83      39      56 ..     221     238 ..     202     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00089
                         STAS_2  1 LsLsGeldldtaaelreqlleal.aagaevvvDlsgvervDsaalalLlalartar 55
                                   L+  G+ld ++ a lr+ l +a   ++++v v +++++ +  +a +++++++ +a+
  gi|121636866|ref|YP_977089.1| 27 LTADGALDSSSSALLRDSLTRATlEQPSAVIVNVTELQVAEESAWSVFISARWQAD 82
                                   5678*****************9965558*******************999987775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0093
                         STAS_2  39 vDsaalalLlalartara 56 
                                    +D+++la ++al r++++
  gi|121636866|ref|YP_977089.1| 221 IDVSGLAIVAALSRAWGS 238
                                    8*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1749.14
//
Query:       gi|121636867|ref|YP_977090.1|  [L=92]
Description: hypothetical protein BCG_0996 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 617.58
//
Query:       gi|121636868|ref|YP_977091.1|  [L=346]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-29  102.2   0.2    3.3e-29  100.9   0.2    1.7  1  DUF4873        Domain of unknown function (DUF4873)
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.051   14.0   0.0    1.9  2  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> DUF4873  Domain of unknown function (DUF4873)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.2   3.7e-33   3.3e-29       1      90 [.     250     337 ..     250     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 3.7e-33
                        DUF4873   1 eeeYrGpatlvvggeeveveveLrghfePidGryrWyGrvaaeeelkealekkrrevtirvpegsaaarlserdlwgryr 80 
                                    +++Y+G+atl+++g++++v+v+L+gh++PidG+y+W+G+v   ++l+e+  +++r++t++++ +sa+ar++e+++wg+++
  gi|121636868|ref|YP_977091.1| 250 DQTYDGAATLTLAGARFRVRVRLTGHLDPIDGNYHWQGTV--FDSLPETSLTHARAATLTIGGRSAPARITEQTPWGTHS 327
                                    579*************************************..9************************************* PP

                        DUF4873  81 vaGvgaPPfa 90 
                                    vaGvg PP+a
  gi|121636868|ref|YP_977091.1| 328 VAGVGPPPYA 337
                                    *********6 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.7e-06     0.051       4      40 ..      39      75 ..      38     133 .. 0.79
   2 ?   -1.4   0.0      0.35   3.2e+03      46      73 ..     224     251 ..     184     262 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-06
                  NAD_binding_7  4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                   d  gk++ vvG    Aa+ +++l e+ a vtv +++ 
  gi|121636868|ref|YP_977091.1| 39 DPAGKRIAVVGTDAAAAHYISRLSESAASVTVFTQAP 75
                                   6789****************************98874 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.35
                  NAD_binding_7  46 elvklaeeelekdlegadlviaatddre 73 
                                    +l  +++    + le +dl  aat+d++
  gi|121636868|ref|YP_977091.1| 224 QLKPAQPHRQTGGLEAFDLSSAATEDDQ 251
                                    2222222223344778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2261.63
//
Query:       gi|121636869|ref|YP_977092.1|  [L=158]
Description: formamidopyrimidine-DNA glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-18   65.7   0.0    3.8e-18   65.3   0.0    1.1  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
    4.5e-08   32.8   1.3    8.3e-08   32.0   1.3    1.5  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
     0.0018   17.6   2.6      0.003   16.9   2.6    1.4  1  zf-TFIIB        Transcription factor zinc-finger
     0.0093   16.4   0.0      0.012   16.0   0.0    1.2  1  Ribosomal_S13   Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.065   12.0   0.0       0.07   11.9   0.0    1.0  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
       0.12   12.3   0.3         14    5.7   0.0    2.3  2  zf_CopZ         Zinc binding domain
       0.15   12.0   0.4       0.28   11.1   0.4    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.34   11.0   3.9       0.34   11.0   0.2    2.2  2  DUF2752         Protein of unknown function (DUF2752)
       0.39   10.9   3.1        4.8    7.4   3.5    2.1  2  Zn-ribbon_8     Zinc ribbon domain
        0.8    9.4   4.2        3.2    7.5   4.2    1.9  1  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


Domain annotation for each model (and alignments):
>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   2.1e-21   3.8e-18       2      84 ..      11      91 ..       9      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.1e-21
                                   --BTTSTTS-HHHHHHHHHT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHHHHH CS
                           H2TH  2 gpeplseaftvdalaerlkkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqeikevlkeaie 83
                                   gp++l  ++++d la  l+ ++  ikt++ Dqk++aG+GN y dE+L+ aki+P  +a +ls ++l  lh+++++vl  a++
  gi|121636869|ref|YP_977092.1| 11 GPDAL--DVSTDDLAGLLAGNTGRIKTVITDQKVIAGIGNAYSDEILHVAKISPFATAGKLSGAQLTCLHEAMASVLSDAVR 90
                                   55555..4566778999999999**********************************************************8 PP

                                   T CS
                           H2TH 84 l 84
                                   +
  gi|121636869|ref|YP_977092.1| 91 R 91
                                   5 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   1.3   4.6e-11   8.3e-08       1      28 [.     115     142 ..     115     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.6e-11
                                    TSB-TTT--BBEEEECTTEEEEE-TTTT CS
                   zf-FPG_IleRS   1 GepCpRCwryiervgqagrstyfCprCq 28 
                                    G pCp+C+ ++++v++a  s  +Cp+Cq
  gi|121636869|ref|YP_977092.1| 115 GLPCPVCGDTVREVSFADKSFQYCPTCQ 142
                                    89************************** PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.6   1.7e-06     0.003       2      26 ..     118     142 ..     117     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                       zf-TFIIB   2 CPkCqdeleeserggveidyCpqCr 26 
                                    CP+C+d+ +e+ + +  ++yCp C+
  gi|121636869|ref|YP_977092.1| 118 CPVCGDTVREVSFADKSFQYCPTCQ 142
                                    ************************6 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06     0.012      18      72 ..      41      95 ..      26     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                  Ribosomal_S13 18 taikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinr 72
                                   + i GiG+ ++ +il+ a+++  + +g+l+  ++  ++e ++   ++ +   + +
  gi|121636869|ref|YP_977092.1| 41 KVIAGIGNAYSDEILHVAKISPFATAGKLSGAQLTCLHEAMASVLSDAVRRSVGQ 95
                                   579**************************************99887777666555 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.07     168     245 ..      13      91 ..       4     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                                    XTTSXXH.HHHHHHHHHS.XXXHHHHH..HHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX.. CS
                           FbpA 168 nPleaeeleefkellskkekdlvkaLv..kafqGlspllaeelleragldketsakelseedlerlyealqelleeleee 245
                                    + l++++ +++  ll  ++++++  +   k + G++++++ e+l+ a++ +  +a +ls  +l+ l+ea+ ++l++  + 
  gi|121636869|ref|YP_977092.1|  13 DALDVST-DDLAGLLAGNTGRIKTVITdqKVIAGIGNAYSDEILHVAKISPFATAGKLSGAQLTCLHEAMASVLSDAVRR 91 
                                    5556666.666777666778888888522679****************************************99987653 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.017        30       3      15 ..     117     129 ..     115     132 .. 0.85
   2 ?    5.7   0.0     0.008        14       3      23 ..     137     157 ..     136     158 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                                    B-TTT--B-EEE- CS
                        zf_CopZ   3 kCPvCgkkGkkVk 15 
                                     CPvCg   ++V+
  gi|121636869|ref|YP_977092.1| 117 PCPVCGDTVREVS 129
                                    6*****9998886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.008
                                    B-TTT--B-EEE-HHHHHHHB CS
                        zf_CopZ   3 kCPvCgkkGkkVkliTvkhll 23 
                                     CP C++ Gk         ll
  gi|121636869|ref|YP_977092.1| 137 YCPTCQTGGKALADRRMSRLL 157
                                    5*********98877666655 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00016      0.28      25      54 ..     112     143 ..     104     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                 OrfB_Zn_ribbon  25 ayTSktCseCgsknke.alsgrtf.kCpnCgf 54 
                                    a T   C++Cg +++e + +++ f +Cp C++
  gi|121636869|ref|YP_977092.1| 112 ARTGLPCPVCGDTVREvSFADKSFqYCPTCQT 143
                                    568888***********666666537*99975 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00019      0.34       4      15 ..     111     122 ..     110     125 .. 0.86
   2 ?    0.6   0.4      0.34   6.1e+02      10      14 ..     137     141 ..     135     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                        DUF2752   4 kaltGipCPGCG 15 
                                    +a tG+pCP CG
  gi|121636869|ref|YP_977092.1| 111 HARTGLPCPVCG 122
                                    677********* PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                        DUF2752  10 pCPGC 14 
                                    +CP+C
  gi|121636869|ref|YP_977092.1| 137 YCPTC 141
                                    8**** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0039         7      28      39 ..     117     128 ..     108     129 .. 0.80
   2 ?    7.4   3.5    0.0027       4.8       8      33 ..     118     142 ..     117     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                    Zn-ribbon_8  28 aCPeCgsevrrv 39 
                                    +CP Cg +vr v
  gi|121636869|ref|YP_977092.1| 117 PCPVCGDTVREV 128
                                    6*****999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                    Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCg 33 
                                    C  Cg +  ++  ++d++ + CP+C+
  gi|121636869|ref|YP_977092.1| 118 CPVCGDTVREVS-FADKSFQYCPTCQ 142
                                    999997777765.78899999****7 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.2    0.0018       3.2       2      27 ..     113     141 ..     112     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                        zf-RRN7   2 ekgppCgvCgc..rsftl.ddGfyyCrrC 27 
                                    ++g pC+vCg   r++ + d  f yC  C
  gi|121636869|ref|YP_977092.1| 113 RTGLPCPVCGDtvREVSFaDKSFQYCPTC 141
                                    6799******9887777766556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1240.29
//
Query:       gi|121636870|ref|YP_977093.1|  [L=253]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-43  147.2   0.2    4.8e-43  146.9   0.2    1.1  1  adh_short        short chain dehydrogenase
    2.7e-29  102.4   1.2    3.3e-29  102.1   1.2    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    5.3e-12   46.0   0.3    8.8e-12   45.3   0.3    1.3  1  KR               KR domain
    0.00021   20.8   0.1    0.00059   19.4   0.1    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.072   13.2   0.1    2.0  2  MLTR_LBD         MmyB-like transcription regulator ligand bin
      0.017   14.2   0.0      0.025   13.7   0.0    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.07   12.2   0.0        0.1   11.6   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
       0.19   11.6   0.0       0.19   11.6   0.0    2.3  3  TruB_C           tRNA Pseudouridine synthase II, C terminal


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.2   2.1e-46   4.8e-43       2     192 ..       9     202 ..       8     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 2.1e-46
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79 
                                     +l+tGassG+G  +a+ +a++G ++++++r+ ++l e+++el +     k+ ++++Dv+d+e+v +++++  +++g++d
  gi|121636870|ref|YP_977093.1|   9 KILITGASSGLGAGMARSFAAQGRDLALCARRTDRLTELKAELSQRypDIKIAVAELDVNDHERVPKVFAELSDEIGGID 88 
                                    69*******************************************999999***************************** PP

                                    EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTB.HHHHHHHHHHHH CS
                      adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagv.aaYsAsKaavag 158
                                     ++ NAGi + +   + +  + +++ie+Nl++++  ++++l+++ ++ sG+ v +sSv g ++v+gv aaY+AsKa+v++
  gi|121636870|ref|YP_977093.1|  89 RVIVNAGIGKGARLGSGKLWANKATIETNLVAALVQIETALDMFNQRGSGHLVLISSVLGVKGVPGVkAAYAASKAGVRS 168
                                    ********99999999999999*******************************************87479********** PP

                                    HHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 159 ltrslakelaptgirvnavaPGlvdTdmakelre 192
                                    l +sl+ e+a+  irv+++ PG+++++m++++ +
  gi|121636870|ref|YP_977093.1| 169 LGESLRAEYAQGPIRVTVLEPGYIESEMTAKSAS 202
                                    *****************************99876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   1.2   1.5e-32   3.3e-29       1     185 [.      14     203 ..      14     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.5e-32
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE...EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae...vlecDVtdeeqvealveevvekfgklDilvnn 76 
                                    Ga sg+G+++A+++a++G +++l+ ++ ++  +  +el ++++     v e+DV+d e v ++++e+ +++g++D ++ n
  gi|121636870|ref|YP_977093.1|  14 GASSGLGAGMARSFAAQGRDLALCARRTDRlTELKAELSQRYPDIkiaVAELDVNDHERVPKVFAELSDEIGGIDRVIVN 93 
                                    899***********************99997888888888887434435******************************* PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTT.HHHHHHHHHHHHHH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnyn.aygaaKaalealtr 153
                                    agi +   +++ + +    + ++++nl +++  ++ al +++++  g +v +ssv + ++vp+ + ay+a+Ka++ +l  
  gi|121636870|ref|YP_977093.1|  94 AGIGKG--ARLGSGKLWANKATIETNLVAALVQIETALDMFNQRgsGHLVLISSVLGVKGVPGVKaAYAASKAGVRSLGE 171
                                    *****9..9*999**************************999886889****************99************** PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTTH CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikgf 185
                                    +l +e+++  iRv +  pg+i+ +++++ +++
  gi|121636870|ref|YP_977093.1| 172 SLRAEYAQGPIRVTVLEPGYIESEMTAKSAST 203
                                    *************************8877654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.3   3.9e-15   8.8e-12       4     161 ..      11     171 ..       9     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.9e-15
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT..T-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal..gaevevvaaDvsdkdavealleeikaeepp 81 
                                    litG+  gLG  +ar  a++g r l+l++R+   +++ ++l ael+++  ++++ v+++Dv d++ v ++++e+++e + 
  gi|121636870|ref|YP_977093.1|  11 LITGASSGLGAGMARSFAAQG-RDLALCARR---TDRLTELKAELSQRypDIKIAVAELDVNDHERVPKVFAELSDEIGG 86 
                                    9*******************9.68*******...344455788888887799**************************** PP

                                    --EEEE---------TTT--HHHHHHH.....HTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT.-HHHHHHHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqv.....lapKvkGawnLhelledesldffvlfSSiagllgsag.qanYaaaNaf 155
                                    i  vi  Ag+ + + l + +  + ++      +a+ v+    L+ +++++   ++vl+SS+ g+ g +g +a+Yaa  a 
  gi|121636870|ref|YP_977093.1|  87 IDRVIVNAGIGKGARLGSGKLWANKATietnlVAALVQIETALD-MFNQRGSGHLVLISSVLGVKGVPGvKAAYAASKAG 165
                                    **********9999887765544444300000344444444444.44558999**************9956788887776 PP

                                    HHHHHH CS
                             KR 156 lDalae 161
                                    + +l e
  gi|121636870|ref|YP_977093.1| 166 VRSLGE 171
                                    666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.6e-07   0.00059       1     169 [.      10     189 ..      10     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-07
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHH....H.T-S CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.........elveldltdrsalerlfke....e.qpd 66 
                                    il+tGa+  +G+ +++ ++++g ++   +r++++  t+++++l          + eld+ d++++ ++f+e      ++d
  gi|121636870|ref|YP_977093.1|  10 ILITGASSGLGAGMARSFAAQGRDLALCARRTDR-LTELKAELsqrypdikiAVAELDVNDHERVPKVFAElsdeIgGID 88 
                                    8************************999999544.44555555799*****************99888876222235799 PP

                                    EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHH..........HHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS-- CS
                      Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaar..........kagvkrllflsSsevYGkdaeqpkeettltgpl 136
                                     vi  A++g  a+      +++ + + + +nl+ a+           ++g   l+ +sS  v G +   p          
  gi|121636870|ref|YP_977093.1|  89 RVIVNAGIGKGAR--LGSGKLWANKATIETNLVAALVqietaldmfnQRGSGHLVLISS--VLGVKGV-P---------- 153
                                    9999999777776..44456777777777777777774433333333334445555555..4442222.2.......... PP

                                    --SSHHHHHHHHHHHHHHHHHHHHT...-EEEEEEE CS
                      Epimerase 137 kpnspYaaaKlageklveayaaqyg...lnaiilrl 169
                                        +Yaa+K+ + +l e+++a+y    +++++l +
  gi|121636870|ref|YP_977093.1| 154 GVKAAYAASKAGVRSLGESLRAEYAqgpIRVTVLEP 189
                                    445567888877777777777777434555555555 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.2e-05     0.072      70     124 ..      23      77 ..      20      81 .. 0.87
   2 ?   -1.6   0.0       1.1   2.5e+03      58      82 ..     153     177 ..     131     183 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                       MLTR_LBD  70 varalvarLraeaarrpddpalaalvaeLsaaspefarlwarhdvaarrsgrkrl 124
                                    +ar++ a+ r  a    + ++l++l aeLs+++p+ +   a+ dv ++++ +k +
  gi|121636870|ref|YP_977093.1|  23 MARSFAAQGRDLALCARRTDRLTELKAELSQRYPDIKIAVAELDVNDHERVPKVF 77 
                                    6777777777777777789******************************999987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                       MLTR_LBD  58 pglrpliedweevaralvarLraea 82 
                                    pg+++ ++  ++  r+l + Lrae+
  gi|121636870|ref|YP_977093.1| 153 PGVKAAYAASKAGVRSLGESLRAEY 177
                                    4444444444455555555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.025       1      76 [.      10      80 ..      10     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76
                                   +l+tGa+  +G  + r ++++  + + l  r   +l e++ el++++ + k+     +   dv+d+er+ k++ el
  gi|121636870|ref|YP_977093.1| 10 ILITGASSGLGAGMARSFAAQ-GRDLALCARRTDRLTELKAELSQRYPDIKIA----VAELDVNDHERVPKVFAEL 80
                                   89*************998875.688999***************9999985553....4467**********99876 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05       0.1       2      52 ..       9      82 ..       8      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHHHHHHHH-- CS
                  RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeavaellkeakp 52
                                   kil+tGa+  lG  +a+++a++g ++  + r+                       eld++d e+v ++++e + 
  gi|121636870|ref|YP_977093.1|  9 KILITGASSGLGAGMARSFAAQGRDLALCARRtdrltelkaelsqrypdikiavaELDVNDHERVPKVFAELSD 82
                                   89*********************999999888899999999999999999999999999999999999988664 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.3e-05      0.19      26      49 ..      21      44 ..      16      48 .. 0.88
   2 ?   -3.0   0.1       2.9   6.5e+03      24      34 ..     151     161 ..     147     162 .. 0.76
   3 ?   -3.3   0.1       3.7   8.3e+03      38      49 ..     216     227 ..     215     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                                   -S-EEEE-TTS-EEEEEEEETTEE CS
                         TruB_C 26 kgvvAaiaPdGrliALleerggra 49
                                   +g+++ +a++Gr +AL+++r +r+
  gi|121636870|ref|YP_977093.1| 21 AGMARSFAAQGRDLALCARRTDRL 44
                                   79999************9998876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                                    ---S-EEEE-T CS
                         TruB_C  24 gikgvvAaiaP 34 
                                    g +gv Aa a+
  gi|121636870|ref|YP_977093.1| 151 GVPGVKAAYAA 161
                                    67899999886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.7
                                    EEEEEEEETTEE CS
                         TruB_C  38 liALleerggra 49 
                                    l+A +e++ gra
  gi|121636870|ref|YP_977093.1| 216 LVAAIEREPGRA 227
                                    788887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1962.80
//
Query:       gi|121636871|ref|YP_977094.1|  [L=553]
Description: glucose-6-phosphate isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.3e-201  668.0   0.0   8.3e-201  667.8   0.0    1.0  1  PGI       Phosphoglucose isomerase


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.8   0.0  4.6e-205  8.3e-201       1     486 []      54     542 ..      54     542 .. 0.97

  Alignments for each domain:
  == domain 1  score: 667.8 bits;  conditional E-value: 4.6e-205
                                    E-TTSS--HHHHHHHHHHHHHTTHHHHHHHHHTT---BTTTTB---HHHHT-TT----EETTEESHHHHHHHHHHHHHHH CS
                            PGI   1 dysknkvddeilealvklaeeaklkaarealfaGekinstenravlhvalrnrsnkpilvdGkdvvpevkevldkmkefs 80 
                                    dysk++v+ e+l  l++la+ a+l+++r+++faG +in+ e+ravlh+alr +++  ++vdG+dvv++v++vld m  f+
  gi|121636871|ref|YP_977094.1|  54 DYSKHRVTRETLALLIDLARTAHLEERRDQMFAGVHINTSEDRAVLHTALRLPRDAELVVDGQDVVTDVHAVLDAMGAFT 133
                                    9******************************************************************************* PP

                                    HHHHTT-SB-TTS-B--EEEEE--GGGTHHHHHHHHHTGGG-TT.-EEEEE--SSHHHHHHHHTT--GGGEEEEEE-SSS CS
                            PGI  81 ekvrsGewkGatgkaitdvvniGiGGsdlGPvlvtealkkeser.lkvafvsnvdgthiaevlkkldpettlfivasktf 159
                                    +++rsGew Gatgk i+ vvniGiGGsdlGPv+v +al++++++ ++ +fvsnvd+ ++  +l++ldp ttlfivasktf
  gi|121636871|ref|YP_977094.1| 134 DRLRSGEWTGATGKRISTVVNIGIGGSDLGPVMVYQALRHYADAgISARFVSNVDPADLIATLADLDPATTLFIVASKTF 213
                                    ******************************************99999********************************* PP

                                    --HHHHHHHHHHHHHHHHHH--GGGGGGTEEEESS-HHHHHHHT--GGGEEE--TTS-GGG-TTSGGGHHHHHHH-HHHH CS
                            PGI 160 ttaetllnaesakewllkalkedsavakhfvalstnaekveefGideknmfefwdwvGGryslwsaiGlsvalsiGfenf 239
                                     t etl+na++a++wl +al+ d av++hfva+stn++ v++fGi+++nmf fwdwvGGrys+ saiGls++  iG + f
  gi|121636871|ref|YP_977094.1| 214 STLETLTNATAARRWLTDALG-DAAVSRHFVAVSTNKRLVDDFGINTDNMFGFWDWVGGRYSVDSAIGLSLMTVIGRDAF 292
                                    ********************9.788******************************************************* PP

                                    HHHHHHHHHHHHHHHHS-GGG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH---BBTTS-B-SS CS
                            PGI 240 eelleGaaaidkhfleaplekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGksvtkdgvlvdv 319
                                     ++l G + id+hf++aple n+Pvll+l+g+wy+nf+ga+++++lpy++ l r++aylqql mesnGks   dg+ v+ 
  gi|121636871|ref|YP_977094.1| 293 ADFLAGFHIIDRHFATAPLESNAPVLLGLIGLWYSNFFGAQSRTVLPYSNDLSRFPAYLQQLTMESNGKSTRADGSPVSA 372
                                    ******************************************************************************** PP

                                    --S-EEE---TTTGGGTSHHHHHHSSS---EEEEEEEE-S-.....GGGGHHHHHHHHHHHHHHHHHHH-B-HHHHHHHH CS
                            PGI 320 etgeiifGeagtngqhafyqlihqGtkliPcdfiaavksqn.....ieiadhhkillsnffaqtealmvGkseeevkkel 394
                                    +tgei +Ge+gtngqhafyql+hqGt+l+P+dfi+ ++  +       +++ h+ l+snffaqt+ l++Gk++ee+ ++ 
  gi|121636871|ref|YP_977094.1| 373 DTGEIFWGEPGTNGQHAFYQLLHQGTRLVPADFIGFAQPLDdlptaEGTGSMHDLLMSNFFAQTQVLAFGKTAEEIAADG 452
                                    **************************************87778865567899************************9977 PP

                                    HHTHHHHHGGGG-B-----EEEEEEEE--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHHHHHHHHHHSSS-- CS
                            PGI 395 akakveklvphktfeGnrPsnsillekltpaelGalialyehkilvqGviwginsfdqwGvelGkelakkilkeleasek 474
                                       ++ ++v+hk+  GnrPs+sil+++ltp  lG+lialyeh+++++Gv+wgi+sfdqwGvelGk+ ak++l+ ++    
  gi|121636871|ref|YP_977094.1| 453 ---TPAHVVAHKVMPGNRPSTSILASRLTPSVLGQLIALYEHQVFTEGVVWGIDSFDQWGVELGKTQAKALLPVITGAGS 529
                                    ...567*******************************************************************9987644 PP

                                    .--SS-HHHHHHH CS
                            PGI 475 .vsdfdsstngli 486
                                       + dsst+gl+
  gi|121636871|ref|YP_977094.1| 530 pPPQSDSSTDGLV 542
                                    15599****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3959.33
//
Query:       gi|121636872|ref|YP_977095.1|  [L=76]
Description: mycolyl transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 593.59
//
Query:       gi|121636873|ref|YP_977096.1|  [L=105]
Description: hypothetical protein BCG_1002c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-11   42.2   0.5      1e-10   41.8   0.5    1.2  1  CM_2         Chorismate mutase type II
  ------ inclusion threshold ------
       0.19   11.9   0.3       0.19   11.9   0.3    1.8  2  GreA_GreB_N  Transcription elongation factor, N-terminal


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.5   1.2e-14     1e-10       1      52 [.      33      85 ..      33      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.2e-14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH.H CS
                           CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee.g 52
                                   R+eId++D+eil+L ++Rae++k++g+++ ++g + +  +Re +v+er +e g
  gi|121636873|ref|YP_977096.1| 33 REEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERYSElG 85
                                   9***********************************************99954 PP

>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.37   3.3e+03      41      47 ..       9      15 ..       7      24 .. 0.75
   2 ?   11.9   0.3   2.1e-05      0.19       5      35 ..      33      62 ..      31      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.37
                                   SSHHHHH CS
                    GreA_GreB_N 41 ENaeYda 47
                                   ENae+ a
  gi|121636873|ref|YP_977096.1|  9 ENAELAA 15
                                   8998866 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHHHHHHHHHHXHHHHHHHHHHHHHH CS
                    GreA_GreB_N  5 kegyekleeeLeelktverpeiaeaikeare 35
                                   +e +++l +e+  l + +r e+++ai +ar 
  gi|121636873|ref|YP_977096.1| 33 REEIDRLDAEILALVK-RRAEVSKAIGKARM 62
                                   6899************.************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 574.70
//
Query:       gi|121636874|ref|YP_977097.1|  [L=771]
Description: ATP dependent DNA helicase uvrD1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-76  256.9   0.0    3.5e-75  253.5   0.0    2.0  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    3.1e-68  230.7   0.0      8e-68  229.4   0.0    1.6  1  UvrD_C           UvrD-like helicase C-terminal domain
      7e-34  117.3   0.0    1.2e-33  116.4   0.0    1.4  1  AAA_19           AAA domain
      1e-11   44.5   0.0    3.8e-11   42.6   0.0    2.1  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.9e-07   30.0   3.0    1.2e-05   25.1   0.4    2.3  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.056   14.1   0.2       0.34   11.6   0.1    2.4  2  CarD_CdnL_TRCF   CarD-like/TRCF domain
      0.086   12.6   0.2        4.1    7.1   0.0    3.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0   1.4e-78   3.5e-75       1     314 [.      23     296 ..      23     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 1.4e-78
                                    SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-H CS
                  UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdde 80 
                                    lnp+qr+a+++ g+p+l++A+AGsGKT+vl+ ri++l++++++ + +il++TFTnkAa+E++eR+  +++++        
  gi|121636874|ref|YP_977097.1|  23 LNPQQRQAVVHEGSPLLIVAGAGSGKTAVLTRRIAYLMAARGVGVGQILAITFTNKAAAEMRERVVGLVGEK-------- 94 
                                    79********************************************************************98........ PP

                                    HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT.SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHH CS
                  UvrD-helicase  81 rlrlalqnlseanisTlHsfcqkilkkeanrig.ldpnfrildeedeedlkqqellkelleksaddslnldkkkleklik 159
                                            ++ +++sT+Hs c +il+++a  i+ l++nf+i+d +d     +++ll+ +       +l ld k ++++  
  gi|121636874|ref|YP_977097.1|  95 --------ARYMWVSTFHSTCVRILRNQAALIEgLNSNFSIYDADD-----SRRLLQMVGR-----DLGLDIKRYSPR-- 154
                                    ........79**********************88************.....7888877764.....589999999866.. PP

                                    HHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS.TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHH CS
                  UvrD-helicase 160 elsksrnikkeelslskskaeelrelvskakekqlspkelkkaf.ekasdlqkkiaeflkeyqeqkkeenalDfsdllha 238
                                                          l++++s++k+++++p++  +   e ++dl +++a ++ eyq+++++ nalDf+dl+ +
  gi|121636874|ref|YP_977097.1| 155 ---------------------LLANAISNLKNELIDPHQALAGLtEDSDDLARAVASVYDEYQRRLRAANALDFDDLIGE 213
                                    .....................8*****************99887899********************************* PP

                                    HHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT.......EEEEE-GGG--GGGGTB-THHHHHHH CS
                  UvrD-helicase 239 llelleeneelaealrerykeiliDEyQDTnkiQyrilkllasghee.......lfmvGDpkQsIYgFRgAdielflkkk 311
                                    ++++l++ +++a+++r+r++++l+DEyQDTn++Qy +++ l+ + ++       l++vGD +QsIY+FRgA i+++  ++
  gi|121636874|ref|YP_977097.1| 214 TVAVLQAFPQIAQYYRRRFRHVLVDEYQDTNHAQYVLVRELVGRDSNdgippgeLCVVGDADQSIYAFRGATIRNIEDFE 293
                                    ******************************************************************************** PP

                                    HHS CS
                  UvrD-helicase 312 kdf 314
                                    +d+
  gi|121636874|ref|YP_977097.1| 294 RDY 296
                                    998 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.4   0.0   3.1e-71     8e-68       1     345 [.     302     652 ..     302     655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 3.1e-71
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         UvrD_C   1 ivLekNyRStksLlkaankflenilnrralekek...ktvekgekivvleaeteeeEaekiaatikall.eknekledia 76 
                                    i Le+NyRSt+++l aan++++++ +r     ek   +++  ge iv + a++e +Ea+++a++i al+ + ++ ++d+a
  gi|121636874|ref|YP_977097.1| 302 ILLEQNYRSTQNILSAANSVIARNAGR----REKrlwTDAGAGELIVGYVADNEHDEARFVAEEIDALAeGSEITYNDVA 377
                                    679******************999999....333457999*****************************9999******* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  77 vLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatveriseelk 156
                                    v +R+n+ ++++++ L + gip++vv++ +f++r+ei+di ayl++l+n+ d ++l+ril+++ +gig+++ + +    +
  gi|121636874|ref|YP_977097.1| 378 VFYRTNNSSRSLEEVLIRAGIPYKVVGGVRFYERKEIRDIVAYLRVLDNPGDAVSLRRILNTPRRGIGDRAEACVAVYAE 457
                                    **********************************************************************9999977888 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 157 klglsltDfikedtleygeeFieliraleeknlelllkk.iektaeerqalvskyadlfkelaeklaelkekseskrkke 235
                                    + g+   D +  + +         +  l+ ++++ ++   +e   e r +l    ++l +++ e     +e   s +++e
  gi|121636874|ref|YP_977097.1| 458 NTGVGFGDALVAAAQG-------KVPMLNTRAEK-AIAGfVEMFDELRGRLDDDLGELVEAVLERTGYRRELEASTDPQE 529
                                    8888888887777644.......23333444433.566668888888888888888888888888777777777777655 PP

                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                         UvrD_C 236 e.klenlreLysllkelekkeeeeeveek.............lneileiatLseseleeskkk.ekipiiTiHqAKGlEF 300
                                      +l+nl+eL+s++ e++ + e+     +             l+++le  +L ++ +e  ++    ++++T+H AKGlEF
  gi|121636874|ref|YP_977097.1| 530 LaRLDNLNELVSVAHEFSTDRENAA---AlgpddedvpdtgvLADFLERVSLVADADEIPEHGaGVVTLMTLHTAKGLEF 606
                                    58****************9666544...2345888**********************8888889**************** PP

                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 301 dvVflagleegtfPsyrskk.ekrleEEkRlfYVaiTRAkkrLfis 345
                                    +vVf+ g e+g fP++r+ +   +l+EE+Rl YV+iTRA++rL++s
  gi|121636874|ref|YP_977097.1| 607 PVVFVTGWEDGMFPHMRALDnPTELSEERRLAYVGITRARQRLYVS 652
                                    ******************998789*********************9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   4.9e-37   1.2e-33       1     146 []      27     282 ..      27     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 4.9e-37
                         AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......atTiHr 74 
                                    qr+av  ++ ++ll++aG+G+GKT vl+ ++a+l +++gv + +il+++ft++Aa e+rer+ +l +e       +T+H+
  gi|121636874|ref|YP_977097.1|  27 QRQAV-VHEGSPLLIVAGAGSGKTAVLTRRIAYLMAARGVGVGQILAITFTNKAAAEMRERVVGLVGEkarymwVSTFHS 105
                                    899**.9*******************************************************9998889**********9 PP

                         AAA_19  75 lal............................................................................. 77 
                                      +                                                                             
  gi|121636874|ref|YP_977097.1| 106 TCVrilrnqaalieglnsnfsiydaddsrrllqmvgrdlgldikrysprllanaisnlknelidphqalagltedsddla 185
                                    988***************************************************************************** PP

                         AAA_19  78 ...................ldfddlltealelle.eaeeekklqeee.llivDEfqdvdelqyrLlkallgekkk..... 131
                                                       ldfddl+ e++++l+   +  +  ++++ +++vDE+qd++  qy L+++l+g++ +     
  gi|121636874|ref|YP_977097.1| 186 ravasvydeyqrrlraanaLDFDDLIGETVAVLQaFPQIAQYYRRRFrHVLVDEYQDTNHAQYVLVRELVGRDSNdgipp 265
                                    **********************************84456777788889**********************9995559*** PP

                         AAA_19 132 ..lllvGDpdQliyvfr 146
                                      l++vGD+dQ+iy+fr
  gi|121636874|ref|YP_977097.1| 266 geLCVVGDADQSIYAFR 282
                                    ***************97 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.5e-14   3.8e-11       2      51 ..     593     651 ..     592     652 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.5e-14
                       UvrD_C_2   2 ayaltihkaQGsefpaVivfdpd.laaarmgel........rrrlLYtavTRAreklil 51 
                                    ++ +t h a+G+efp+V+v+  +  + + m +l         rrl+Y+++TRAr++l++
  gi|121636874|ref|YP_977097.1| 593 VTLMTLHTAKGLEFPVVFVTGWEdGMFPHMRALdnptelseERRLAYVGITRARQRLYV 651
                                    5789***************8755466655555689999*******************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.4   4.8e-09   1.2e-05       2      66 ..      23      87 ..      22     120 .. 0.80
   2 !    5.0   0.1     0.007        18      85     171 ..     227     324 ..     171     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.8e-09
                         AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaag...grviglAptgkaAkvLaeel 66
                                   ln++Q++av   ++++    +++++AG+GKt +l+   + +++a+g   g++++++ t+kaA++++e +
  gi|121636874|ref|YP_977097.1| 23 LNPQQRQAVV--HEGS--PLLIVAGAGSGKTAVLTRRiAYLMAARGvgvGQILAITFTNKAAAEMRERV 87
                                   8999*99994..3333..5899***********987626666666899******************864 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.007
                         AAA_30  85 rlepg.tllivDEagmvdtkqlaallkaaeka......gakvilvGDerQlasVeaGgvlrdlvea.....agigtaeLt 152
                                     ++++ + ++vDE   ++ +q   + + + ++        ++ +vGD +Q     +G+++r +  +      +++t+ L+
  gi|121636874|ref|YP_977097.1| 227 YYRRRfRHVLVDEYQDTNHAQYVLVRELVGRDsndgipPGELCVVGDADQSIYAFRGATIRNIE-DferdyPDTRTILLE 305
                                    3445558888888887766665554454444333333337899*******999999******94.3565555779***** PP

                         AAA_30 153 evvRqkeseeraaalalre 171
                                    +++R +++   aa   +++
  gi|121636874|ref|YP_977097.1| 306 QNYRSTQNILSAANSVIAR 324
                                    ****987655555554444 PP

>> CarD_CdnL_TRCF  CarD-like/TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.8   9.7e+03      13      21 ..      66      81 ..      63     117 .. 0.66
   2 ?   11.6   0.1   0.00013      0.34       1      21 [.     721     741 ..     721     765 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.8
                 CarD_CdnL_TRCF 13 GiGriegi.......e 21
                                   G+G+i +i        
  gi|121636874|ref|YP_977097.1| 66 GVGQILAItftnkaaA 81
                                   9999999965433220 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                 CarD_CdnL_TRCF   1 lkvGDyVvhedhGiGriegie 21 
                                    l+vGD V h ++G Gr+e++ 
  gi|121636874|ref|YP_977097.1| 721 LQVGDRVTHDKYGLGRVEEVS 741
                                    79****************993 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.081   2.1e+02       3      20 ..      40      57 ..      38     114 .. 0.66
   2 ?   -3.1   0.0         2   5.2e+03      62      75 ..     231     244 ..     212     255 .. 0.76
   3 ?    7.1   0.0    0.0016       4.1     185     231 ..     595     650 ..     574     652 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                Viral_helicase1  3 vhGvpGcGKStlirkllr 20
                                   + + +G+GK+ ++ + + 
  gi|121636874|ref|YP_977097.1| 40 IVAGAGSGKTAVLTRRIA 57
                                   55679*****99988764 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                Viral_helicase1  62 kgkililDEylllh 75 
                                    +++ +++DEy+  +
  gi|121636874|ref|YP_977097.1| 231 RFRHVLVDEYQDTN 244
                                    47789999998654 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0016
                Viral_helicase1 185 vttvhevqGltfdkVtlv............llketdlelisesrenllvAlTRhrkslv 231
                                     +t h + Gl+f++V +             l+++t+   +se+r   +v++TR+r++l+
  gi|121636874|ref|YP_977097.1| 595 LMTLHTAKGLEFPVVFVTgwedgmfphmraLDNPTE---LSEERRLAYVGITRARQRLY 650
                                    567777777777776663222222222221454543...33679************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4693.56
//
Query:       gi|121636875|ref|YP_977098.1|  [L=332]
Description: hypothetical protein BCG_1004c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-30  104.1   0.2    6.7e-30  103.2   0.2    1.5  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.2   3.7e-34   6.7e-30       3      96 .]     222     316 ..     220     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.7e-34
                                    ESSEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEEEEBSTSSCSSSE CS
                  Peptidase_M23   3 hkGidiaapkgtpVlAaadGtVvfagkkegyGnvviidhgdgystlyahlskisvkegqkVkaGqvIGtvgstgrstgph 82 
                                    h Gid+a + gtp++A++dG+V+ ag++ gyG +v + h+dg++tly+h++++ v++g++V aG++I+t+gs+g stgph
  gi|121636875|ref|YP_977098.1| 222 HAGIDLANAIGTPIYAVSDGVVIDAGPTAGYGMWVKLLHADGTVTLYGHVNTTLVSVGERVMAGDQIATMGSRGFSTGPH 301
                                    99**************************9*************************************************** PP

                                    EEEEEEE.TTEEE-C CS
                  Peptidase_M23  83 Lhfeirk.ngkavdp 96 
                                    Lhfe+     ++vdp
  gi|121636875|ref|YP_977098.1| 302 LHFEVLLgGTERVDP 316
                                    *****8515567776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2399.21
//
Query:       gi|121636876|ref|YP_977099.1|  [L=387]
Description: succinyl-CoA synthetase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-70  234.2   0.2    1.7e-69  233.4   0.2    1.4  1  ATP-grasp_2  ATP-grasp domain
      3e-13   49.9   2.0    5.5e-13   49.0   2.0    1.4  1  Ligase_CoA   CoA-ligase
    2.7e-08   33.5   1.4      3e-07   30.1   1.4    2.1  1  ATP-grasp_5  ATP-grasp domain
    4.6e-06   26.3   0.2    1.1e-05   25.1   0.2    1.6  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
     0.0014   18.4   0.0     0.0026   17.5   0.0    1.4  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.28   11.0   0.0    1.2  1  Baculo_E25   Occlusion-derived virus envelope protein E25


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.4   0.2   5.8e-73   1.7e-69       1     201 [.       2     194 ..       2     195 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.4 bits;  conditional E-value: 5.8e-73
                                    BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEE CS
                    ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkel 80 
                                    +l+Eyqake++ak++v+++ g+v+++ae a+++a+++g+ + +vKaQv++GGRGKagGvk+++++++a+e+ak++lg ++
  gi|121636876|ref|YP_977099.1|   2 DLFEYQAKELFAKHNVPSTPGRVTDTAEGAKAIATEIGRPV-MVKAQVKIGGRGKAGGVKYAATPQDAYEHAKNILGLDI 80 
                                    599***********************************999.9************************************* PP

                                    E-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHH CS
                    ATP-grasp_2  81 vtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqar 160
                                    +       G++v+k+lv+ea+di++E+Yls++lDra++++++++S eGG++iEevaa+kPe+++kv+++++kg++ + ar
  gi|121636876|ref|YP_977099.1|  81 K-------GHIVKKLLVAEASDIAEEYYLSFLLDRANRTYLAMCSVEGGMEIEEVAATKPERLAKVPVNAVKGVDLDFAR 153
                                    *.......************************************************************************ PP

                                    HHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                    ATP-grasp_2 161 eiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                    +ia++ +l++e++++aa +i+kl++lfv++datlvE+NPLv
  gi|121636876|ref|YP_977099.1| 154 SIAEQGHLPAEVLDTAAVTIAKLWELFVAEDATLVEVNPLV 194
                                    ****************************************8 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   2.0   1.8e-16   5.5e-13       3     150 ..     256     378 ..     254     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.8e-16
                                    SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEE CS
                     Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldiv 82 
                                    nG++La+ ++d++  a          ++  g ++++++d+G++a            + +   l  ++ d++vk ++++++
  gi|121636876|ref|YP_977099.1| 256 NGAGLAMSTLDVVAYA---------GEKHGGVKPANFLDIGGGAS----------AEVMAAGLDVVLGDQQVKSVFVNVF 316
                                    8**************9.........5566799*************..........7************************ PP

                                    ESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                     Ligase_CoA  83 lGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                    +G+ +++ +a +++ka+  +  +  ++p+v+r+ G++++     e++++l+ea   +++  a +++aa
  gi|121636876|ref|YP_977099.1| 317 GGITSCDAVATGIVKALGMLG-DEANKPLVVRLDGNNVE-----EGRRILTEANHPLVTLVATMDEAA 378
                                    ********************9.88899************.....999999999988887777776665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   1.4     1e-10     3e-07      10     222 .]       3     210 ..       2     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1e-10
                    ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervk 89 
                                    L e++akel++  ++p ++ r+ ++ae a ++a eig pv +K +++ i  + ++gGv+    ++   ++a+e+ ++ + 
  gi|121636876|ref|YP_977099.1|   3 LFEYQAKELFAKHNVPSTPGRVTDTAEGAKAIATEIGRPVMVKAQVK-IGGRGKAGGVKY-AATP---QDAYEHAKNILG 77 
                                    6699***************************************9975.************.4455...555555555555 PP

                    ATP-grasp_5  90 ekspeariegvlVqemakrggrElivgvteDpvFGpvilfG..lGGtavevlkdvavalpplnstlareliertkaskll 167
                                       +++ ++++lV e  +  + E  ++   D      +++   +GG+++e ++ ++ +       +a + ++ +  ++ +
  gi|121636876|ref|YP_977099.1|  78 LDIKGHIVKKLLVAEASD-IAEEYYLSFLLDRANRTYLAMCsvEGGMEIEEVAATKPERLAKVPVNAVKGVD-LDFARSI 155
                                    567899999****99999.78888888888887776655541279999998887764433333333333333.3333333 PP

                    ATP-grasp_5 168 kgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllvee.egvvalDarirl 222
                                     +  + ++  l+  + ++ +l +L v     + +++nPl+ ++ ++++alDa+i+l
  gi|121636876|ref|YP_977099.1| 156 AEQGHLPAEVLDTAAVTIAKLWELFVA-EDATLVEVNPLVRTPdHKILALDAKITL 210
                                    333333234455555577777777776.67999**********555********87 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   3.5e-09   1.1e-05       4      54 ..       7      55 ..       5      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.5e-09
                                   HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE CS
                    CPSase_L_D2  4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm 54
                                   +ake+ +k nvp  p+  +  +t+e a aia eig Pv++ka + +GG+G 
  gi|121636876|ref|YP_977099.1|  7 QAKELFAKHNVPSTPGRVT--DTAEGAKAIATEIGRPVMVKAQVKIGGRGK 55
                                   6788999999999999988..****************************96 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.8e-07    0.0026       6      89 ..       8      94 ..       5     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-07
                                   HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCCCSSE CS
                         GARS_A  6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGeagekv 83
                                   ak+l++k+++p++  ++++ +e ak++ +e + ++  vKa+   +g+    gv+ a++ ++a +++k+il     G+  +k+
  gi|121636876|ref|YP_977099.1|  8 AKELFAKHNVPSTPGRVTDTAEGAKAIATEIGRPV-MVKAQVKIGGRgkagGVKYAATPQDAYEHAKNILGLDIKGHIVKKL 88
                                   79*********************************.6666544444311338999****************9999*999999 PP

                                   EEEE-- CS
                         GARS_A 84 viEell 89
                                   ++ e  
  gi|121636876|ref|YP_977099.1| 89 LVAEAS 94
                                   887765 PP

>> Baculo_E25  Occlusion-derived virus envelope protein E25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.3e-05      0.28      97     165 ..     306     380 ..     285     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.3e-05
                     Baculo_E25  97 kkfkslfi.vfkGvey.....skivednlmlrfevdkmvvalidastatlselelrelrksicvlvytrnaaaql 165
                                    ++ ks+f+ vf G++      + iv+  +ml  e++k +v+ +d ++     + l e +++  +lv t + aa +
  gi|121636876|ref|YP_977099.1| 306 QQVKSVFVnVFGGITScdavaTGIVKALGMLGDEANKPLVVRLDGNNVEEGRRILTEANHPLVTLVATMDEAADK 380
                                    57899998799999972222255788899***************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2903.12
//
Query:       gi|121636877|ref|YP_977100.1|  [L=303]
Description: succinyl-CoA synthetase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-27   95.1   4.5      3e-26   91.9   1.8    2.5  2  CoA_binding    CoA binding domain
    8.2e-14   51.7   0.5    1.8e-13   50.6   0.5    1.6  1  Ligase_CoA     CoA-ligase
    3.2e-11   43.2   0.1    6.4e-11   42.2   0.1    1.5  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
     0.0003   21.3   0.2    0.00074   20.0   0.0    1.8  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   1.8   6.6e-30     3e-26       2      96 .]      10     111 ..       9     111 .. 0.98
   2 ?    3.2   0.0     0.031   1.4e+02      16      68 ..     169     216 ..     161     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 6.6e-30
                                    TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET.........TEEEESCHHHHHHHCTTTEEEEES-H CS
                    CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl.........glpvyksvdeleektevdvavitvPa 72 
                                    +d+kviv+G++g+  + ++h++++l+ g+++v+gvn rk+gt+v           lpv+ sv+e++ekt++dv++i+vP+
  gi|121636877|ref|YP_977100.1|  10 RDNKVIVQGITGS--EATVHTARMLRAGTQIVGGVNARKAGTTVThedkggrliKLPVFGSVAEAMEKTGADVSIIFVPP 87 
                                    589**********..999************************************************************** PP

                                    HHHHHHHHHHHHTT-SEEEEESST CS
                    CoA_binding  73 esaqeavdelveagikgiviiteg 96 
                                    ++a++a++e+++a+i++ v+iteg
  gi|121636877|ref|YP_977100.1|  88 TFAKDAIIEAIDAEIPLLVVITEG 111
                                    **********************97 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.031
                                    HHHH.HHHHHHHHECEEEEEEC-TT.TTTCEETTEEEESCHHHHHHHCTTTEEEE CS
                    CoA_binding  16 iagl.yhfkeklkygikavfgvnpr.kvgtevlglpvyksvdeleektevdvavi 68 
                                    + ++   ++e ++ g++ ++g++++  +gt++    + ++++  e++  +d+++i
  gi|121636877|ref|YP_977100.1| 169 GTLTyQMMFELRDLGFSTAIGIGGDpVIGTTH----I-DAIEAFEKD--PDTKLI 216
                                    45553456677889999999999885555433....2.244444444..555555 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.5     4e-17   1.8e-13      33     152 ..     181     283 ..     165     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4e-17
                                    T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EE CS
                     Ligase_CoA  33 gseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvv 112
                                    + + ++ i++G+d            +t++i+a++ + +dp +k i++ +++G g +e+ aa+++k+ +        +pvv
  gi|121636877|ref|YP_977100.1| 181 DLGFSTAIGIGGDPVI---------GTTHIDAIEAFEKDPDTKLIVMIGEIG-GDAEERAADFIKT-NVS------KPVV 243
                                    4577899********8.........9**************************.**********986.334......5*** PP

                                    EEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                     Ligase_CoA 113 arvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                     +vaG +a+ ++ +++a+a+ +++  +a++k++al+aa++
  gi|121636877|ref|YP_977100.1| 244 GYVAGFTAPEGKTMGHAGAIVSGSSGTAAAKQEALEAAGV 283
                                    ************************************9985 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   1.4e-14   6.4e-11       1     125 [.     159     286 ..     159     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.4e-14
                   Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkflsaarra 78 
                                    pG+i+l+s+SG+l  +++  +++  lgfs+++ +G    + ++  d +e++++dp+tk+i++  E  +d+++ ++   ++
  gi|121636877|ref|YP_977100.1| 159 PGPIGLVSKSGTLTYQMMFELRD--LGFSTAIGIGGdpVIGTTHIDAIEAFEKDPDTKLIVMIGEIGGDAEERAADFIKT 236
                                    79***************999987..7*********93345566779***********************98777777777 PP

                   Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgala....gsdavvdaafrqaGvlrv 125
                                    + +kpvv + +G ++   ++ + h ga++    g  a+ ++a++ aGv + 
  gi|121636877|ref|YP_977100.1| 237 NVSKPVVGYVAGFTAPEGKT-MGHAGAIVsgssGTAAAKQEALEAAGVKVG 286
                                    779*********87665554.577777652211455666677777777655 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-07   0.00074      37     114 ..      57     142 ..      25     144 .. 0.82
   2 ?   -2.6   0.0       1.7   7.6e+03      91     105 ..     271     285 ..     250     298 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                    -SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT..---HHHHHHHHH....TT-EEE.E CS
                  CoA_binding_2  37 eeeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg..sedeeaaelaee....agirvvgd 108
                                    ++++   +v+ s+ae+  ++  d+  +f+pp+ + + + ea++++++ +++  +   ++++a+++a +    ++ r++g+
  gi|121636877|ref|YP_977100.1|  57 GGRLIKLPVFGSVAEAmeKTGADVSIIFVPPTFAKDAIIEAIDAEIPLLVVITEgiPVQDTAYAWAYNleagHKTRIIGP 136
                                    466667799999998457999********************99998877777776877888888888788889******* PP

                                    S-HHHH CS
                  CoA_binding_2 109 rCilve 114
                                    +C++++
  gi|121636877|ref|YP_977100.1| 137 NCPGII 142
                                    ***997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                    -HHHHHHHHHTT-EE CS
                  CoA_binding_2  91 deeaaelaeeagirv 105
                                     ++  e++e+ag++v
  gi|121636877|ref|YP_977100.1| 271 AAAKQEALEAAGVKV 285
                                    333334445566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1953.76
//
Query:       gi|121636878|ref|YP_977101.1|  [L=282]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-51  173.9   5.5    7.4e-51  173.4   5.5    1.2  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   5.5   4.1e-55   7.4e-51      27     217 ..      18     228 ..      15     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 4.1e-55
                 Bac_luciferase  27 elaraaEelGfdavwvaehhggpgga....................ldaftllaalaaaTerirlgtavtplytrhPavl 86 
                                    + ar+aE++Gf ++ v+eh ++p ++                    ld+++ l+a++a+T+rirl tav  +  ++P++l
  gi|121636878|ref|YP_977101.1|  18 AAARLAESHGFRTFYVPEHTHIPVKRqaahptagdaslpddrymrtLDPWVSLGAASAVTSRIRLATAVALPVEHDPITL 97 
                                    679*******************9999****************************************************** PP

                 Bac_luciferase  87 AqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgp 166
                                    A+++atLdhls+GR+++g+g g+++ e   +Gv+  +r  +lrE++e++r+lw++ee  ++Gef++    + +p+p+q+ 
  gi|121636878|ref|YP_977101.1|  98 AKSIATLDHLSHGRVSVGVGFGWNTDELVDHGVPPGRRRTMLREYLEAMRALWTQEEACYDGEFVKFGPSWAWPKPVQPH 177
                                    *****************************************************99999********************99 PP

                 Bac_luciferase 167 iPvyvaaas.paglelaarhadglllageppeeaaelierlragaaeagrdp 217
                                    iPv+v+aa+ +++ ++ ar adg+++++ +  ++ e ++ l+  +a+agrd 
  gi|121636878|ref|YP_977101.1| 178 IPVLVGAAGtEKNFKWIARSADGWITTPRDV-DIDEPVKLLQDIWAAAGRDG 228
                                    ****************************555.46677888888889999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2035.60
//
Query:       gi|121636879|ref|YP_977102.1|  [L=303]
Description: hypothetical protein BCG_1008 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-57  192.9  13.4    3.1e-57  192.9  13.4    2.6  2  DUF5336          Family of unknown function (DUF5336)
  ------ inclusion threshold ------
      0.031   15.0   1.8      0.031   15.0   1.8    2.6  2  GRP              Glycine rich protein family
        0.5   10.8  10.8        1.1    9.8  10.6    1.6  1  MerC             MerC mercury resistance protein
          2    8.0  22.0        6.3    6.3  22.0    1.8  1  DUF998           Protein of unknown function (DUF998)
        2.9    8.3  14.4       0.64   10.4  10.9    1.8  2  DUF4233          Protein of unknown function (DUF4233)
        3.1    7.6  11.1        7.3    6.4  10.8    1.8  2  DUF2157          Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9  13.4     1e-60   3.1e-57       1     169 [.       8     169 ..       8     170 .. 0.98
   2 ?  -13.0  14.9         6   1.8e+04       3       4 ..     234     235 ..     178     268 .. 0.66

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 1e-60
                        DUF5336   1 pGyppaqqgqqyggptqsfakqeeaqaaagpskLplyLsiavaaLGliayllgFgplltvsassadleeasatsgglgla 80 
                                    pGyp+aq++++ygg t+sfa+++e     g+skLp+yL+iava+LGl+ay+++Fgp++t+s++    +   a+sg++gl+
  gi|121636879|ref|YP_977102.1|   8 PGYPQAQPAGSYGGVTPSFAHADE-----GASKLPMYLNIAVAVLGLAAYFASFGPMFTLSTEL--GGGDGAVSGDTGLP 80 
                                    8**********************9.....99*********************************..889999******** PP

                        DUF5336  81 vvllLlagLlAgvslLPkqksktavaAvlsvlgfLlvlaevinapegvsiawglwvvlvlallqaaaAvaaLLfeagvit 160
                                    v ++Lla+LlAgv+l+Pk+ks+++v+Avl vlg++l++++++n+p+++s++w+lwvvl+++++qa+aAv aLL+e+g it
  gi|121636879|ref|YP_977102.1|  81 VGVALLAALLAGVALVPKAKSHVTVVAVLGVLGVFLMVSATFNKPSAYSTGWALWVVLAFIVFQAVAAVLALLVETGAIT 160
                                    ******************************************************************************** PP

                        DUF5336 161 pPapkpkae 169
                                    +Pap+pk++
  gi|121636879|ref|YP_977102.1| 161 APAPRPKFD 169
                                    *******87 PP

  == domain 2  score: -13.0 bits;  conditional E-value: 6
                        DUF5336   3 yp 4  
                                    y 
  gi|121636879|ref|YP_977102.1| 234 YT 235
                                    22 PP

>> GRP  Glycine rich protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.5       1.8   5.3e+03       8      25 ..      85     102 ..      83     124 .. 0.75
   2 ?   15.0   1.8     1e-05     0.031      50      92 ..     171     235 ..     133     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                            GRP   8 lLglllaavlLissevaa 25 
                                    lL+ lla v L+ ++ ++
  gi|121636879|ref|YP_977102.1|  85 LLAALLAGVALVPKAKSH 102
                                    777888888888766554 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-05
                            GRP  50 khggGgygggggggngGGGykgggGgygg...............gggggeggy.......GgGyg 92 
                                    ++++G yg  g++g + GGy+g++G  +                g g ++ggy       G+Gy 
  gi|121636879|ref|YP_977102.1| 171 YGQYGRYGQYGQYGVQPGGYYGQQGAQQAaglqspgpqqspqppGYGSQYGGYssspsqsGSGYT 235
                                    33689999999999999********9999999999999999999555555555555566799986 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  10.6   0.00036       1.1      19     106 ..      58     146 ..      41     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                           MerC  19 Pvllallpllglsflasel........lhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeet 90 
                                    P+++++  l g                l + +++l+++++++alv+ +++h  t v vlg+lG+++++ a+f + +a++t
  gi|121636879|ref|YP_977102.1|  58 PMFTLSTELGGG------DgavsgdtgLPVGVALLAALLAGVALVPKAKSHV-TVVAVLGVLGVFLMVSATFNKPSAYST 130
                                    444444444443......1333334458899999*************99885.7899*************9999666666 PP

                           MerC  91 llfgslwqvltvlGaa 106
                                     ++ +++  ++v+ a+
  gi|121636879|ref|YP_977102.1| 131 GWALWVVLAFIVFQAV 146
                                    6555555544444444 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  22.0    0.0021       6.3      14     124 ..      50     148 ..      37     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
                         DUF998  14 aallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavaglglvlagvfptdp 93 
                                    aa+    + p+     eLg+  g+g+   ++gl +  +l++al++g++ ++++++   ++++l+v g++l++++ f+++ 
  gi|121636879|ref|YP_977102.1|  50 AAYF-ASFGPMFTLSTELGG--GDGAVSGDTGLPVGVALLAALLAGVALVPKAKSHVTVVAVLGVLGVFLMVSATFNKPS 126
                                    3333.666777777779999..*********************************************************8 PP

                         DUF998  94 gggspslsglvHglasavaflalavavllla 124
                                    + +            +++++la++v  +++a
  gi|121636879|ref|YP_977102.1| 127 AYSTG---------WALWVVLAFIVFQAVAA 148
                                    86432.........22222333322222222 PP

>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.6   7.8e+03      59      72 ..      40      53 ..      32      63 .. 0.54
   2 ?   10.4  10.9   0.00021      0.64      16      80 ..      85     149 ..      74     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                        DUF4233 59 lglvlQvlliaagf 72
                                   l++++ vl +aa f
  gi|121636879|ref|YP_977102.1| 40 LNIAVAVLGLAAYF 53
                                   44444444443333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00021
                        DUF4233  16 lLallv...aiglrdtepatvlsvggvlavallllagllrrpwglalglvlQvlliaagfvvpamfvv 80 
                                    lLa+l    a    +++ ++++++++++  ++l+++++ ++p ++  g++l v+l    +v++a+++v
  gi|121636879|ref|YP_977102.1|  85 LLAALLagvALVP-KAKSHVTVVAVLGVLGVFLMVSATFNKPSAYSTGWALWVVLA--FIVFQAVAAV 149
                                    4444442212122.2233344444445555667778899************88776..4444444333 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.89   2.6e+03     101     120 ..      44      63 ..      37      69 .. 0.59
   2 ?    6.4  10.8    0.0024       7.3      72     138 ..      83     143 ..      44     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.89
                        DUF2157 101 laalllgaaialvgqifqls 120
                                    +a+l l a +a +g +f ls
  gi|121636879|ref|YP_977102.1|  44 VAVLGLAAYFASFGPMFTLS 63 
                                    34444555555566666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0024
                        DUF2157  72 vllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifqlsgdaysllllwalllllma 138
                                    v+ll++ll+g a++       p+    + ++a+l +++ + +v+ +f+  +  +++ +lw++l++++ 
  gi|121636879|ref|YP_977102.1|  83 VALLAALLAGvALV-------PKAKSHVTVVAVLGVLGVFLMVSATFNKPSAYSTGWALWVVLAFIVF 143
                                    34444444442333.......44667889999*******************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1995.14
//
Query:       gi|121636880|ref|YP_977103.1|  [L=455]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3230.56
//
Query:       gi|121636881|ref|YP_977104.1|  [L=215]
Description: phosphoribosylglycinamide formyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-41  140.9   0.0    4.3e-41  140.6   0.0    1.1  1  Formyl_trans_N  Formyl transferase
  ------ inclusion threshold ------
      0.095   12.6   0.0        0.3   11.0   0.0    1.8  2  DUF2000         Protein of unknown function (DUF2000)


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   0.0   4.8e-45   4.3e-41       2     181 .]      14     191 ..      13     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 4.8e-45
                                    EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-S CS
                 Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkad 81 
                                    ++vvl+sgtgs l+ llda+  g+  a vv+v  +  +++ +e a++as p++++  ++  +r + + +++++ +++++d
  gi|121636881|ref|YP_977104.1|  14 RLVVLASGTGSLLRSLLDAAV-GDYPARVVAVGVD-RECRAAEIAAEASVPVFTVRLADHPSRDAWDVAITAATAAHEPD 91 
                                    89****************986.5666888887555.567889************************************** PP

                                    EEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT-- CS
                 Formyl_trans_N  82 livlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedt 161
                                    l+v ag+m++l++++++++ ++ ln Hp+LLP+f+G++ +  al  G+k+tG+t+h vd + DtG+ilaq+ v+++  d+
  gi|121636881|ref|YP_977104.1|  92 LVVSAGFMRILGPQFLSRFYGRTLNTHPALLPAFPGTHGVADALAYGVKVTGATVHLVDAGTDTGPILAQQPVPVLDGDD 171
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                 Formyl_trans_N 162 keeleqrvadaehkalveal 181
                                    +e+l +r++  e ++lv a+
  gi|121636881|ref|YP_977104.1| 172 EETLHERIKVTERRLLVAAV 191
                                    ****************9886 PP

>> DUF2000  Protein of unknown function (DUF2000)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.35   3.2e+03      78      97 ..      32      51 ..      15      69 .. 0.55
   2 ?   11.0   0.0   3.3e-05       0.3      38      84 ..     147     192 ..     131     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.35
                                   ---EEEEGGGGG---HHHHH CS
                        DUF2000 78 ltvvdFtdaaqstksyeeyr 97
                                    +v d+++   + + ++e r
  gi|121636881|ref|YP_977104.1| 32 AAVGDYPARVVAVGVDRECR 51
                                   33444444444444444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.3e-05
                                    -EE-TTS-EE---BSS-EEEEEE.-HHHHHHHHHHHHHT.T---EEEE CS
                        DUF2000  38 dyaDadgeahagiselPvpvlka.ssekLrelrekaleregltvvdFt 84 
                                     ++Da   + + + ++Pvpvl + ++e+L+e ++   er +l+v+   
  gi|121636881|ref|YP_977104.1| 147 HLVDAGTDTGPILAQQPVPVLDGdDEETLHERIKV-TER-RLLVAAVA 192
                                    567999999999***********778888875544.555.56666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1711.17
//
Query:       gi|121636882|ref|YP_977105.1|  [L=523]
Description: bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-108  361.8   0.0   3.7e-108  361.5   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    4.9e-25   87.6   0.0    9.4e-25   86.6   0.0    1.5  1  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.5   0.0  4.1e-112  3.7e-108       1     296 []     141     457 ..     141     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: 361.5 bits;  conditional E-value: 4.1e-112
                                    HHHTTTT-EEE-SGGGHHHHHHHHHCT.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........CSE...EEEEEE CS
                AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkkgevsletrkklaakaFahtaaYDaaiaeylskq.........lpetlklslekk 71 
                                    AAKNh s +vv+dp  Y+ vl++l++g ++l++rk+la  aF+h a+YD a+a++++++         +p+ +  s++++
  gi|121636882|ref|YP_977105.1| 141 AAKNHPSAAVVTDPLGYHGVLAALRAGGFTLAERKRLASLAFQHIAEYDIAVASWMQQTlapehpvaaFPQWFGRSWRRV 220
                                    9*******************************************************8889999998888899999***** PP

                                    EEESSSSSTTS-EEEEE-TT.STTHHH-EEEESS---HHHHHHHHHHHHHHCTS..EEEEEEETTEEEEEEEES.SHHHH CS
                AICARFT_IMPCHas  72 qkLrYGeNphQkaalyeeee.eeglakaeqlqGkelsynNllDadaalelvkef..aavaivKHanpcGvAvge.tlaeA 147
                                    + LrYGeNphQ+aaly + +   gla+aeql+Gk++synN++Dadaa++++ ++  ++vai+KHanpcG+A+++ ++a+A
  gi|121636882|ref|YP_977105.1| 221 AMLRYGENPHQQAALYGDPTaWPGLAQAEQLHGKDMSYNNFTDADAAWRAAFDHeqTCVAIIKHANPCGIAISSvSVADA 300
                                    ****************98888789****************************88767***************99679*** PP

                                    HHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-SS-.....EEEEETTEE CS
                AICARFT_IMPCHas 148 yekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelkee.....elrsvsggl 222
                                    ++kA+++Dp+Sa+Gg+ia+n+ev +e+ae ++++f+evi+Ap++ + al++l++kkn+rvl + e      elr +sggl
  gi|121636882|ref|YP_977105.1| 301 HRKAHECDPLSAYGGVIAANTEVSVEMAEYVSTIFTEVIVAPGYAPGALDVLARKKNIRVLVAAEPlaggsELRPISGGL 380
                                    *************************************************************9988345667********* PP

                                    EEEE--G..TTCC...CSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHHHHHHHH CS
                AICARFT_IMPCHas 223 Lvqerdeakieee...elkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsarlAvek 296
                                    L+q++d+ + + +   +++++t + +++++l+dl faw+++++vkSNaiv+a+dg+tvg+G+Gq++Rvd+arlAve+
  gi|121636882|ref|YP_977105.1| 381 LIQQSDQLDAHGDnpaNWTLATGSPADPATLTDLVFAWRACRAVKSNAIVIAADGATVGVGMGQVNRVDAARLAVER 457
                                    ******77766666679*********************************************************986 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   1.1e-28   9.4e-25       1      94 [.      22     135 ..      22     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.1e-28
                                    THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH..................HHHHHHHTTSCC CS
                            MGS   1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv..................eildaikngeid 62 
                                    glv+la+ l+++g+e+++Tg Tak+++++gipvt v+++tg++e l+grv                  e+ +a+++ +i+
  gi|121636882|ref|YP_977105.1|  22 GLVDLAQGLSAAGVEIISTGSTAKTIADTGIPVTPVEQLTGFPEVLDGRVktlhprvhaglladlrksEHAAALEQLGIE 101
                                    689***************************************************************************** PP

                                    ...EEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                            MGS  63 ...lvintlypfkatvakdgykirraaenidIplp 94 
                                       lv+++lypf++tv+ +g+++++++e+idI++p
  gi|121636882|ref|YP_977105.1| 102 afeLVVVNLYPFSQTVE-SGASVDDCVEQIDIGGP 135
                                    ****************8.9**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3879.72
//
Query:       gi|121636883|ref|YP_977106.1|  [L=459]
Description: magnesium chelatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-08   33.2   0.0    0.00078   18.9   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.6e-07   29.2   0.0    4.5e-05   23.2   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      1e-06   28.8   0.0      0.021   14.8   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    1.6e-05   24.8   0.0    0.00013   21.8   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
    0.00017   20.6   0.0    0.00076   18.5   0.0    1.8  2  AAA_PrkA         PrkA AAA domain
    0.00061   18.9   0.0     0.0057   15.8   0.0    2.1  2  MCM              MCM P-loop domain
     0.0035   17.8   0.5      0.014   15.8   0.5    2.3  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.038   14.5   0.0    1.8  2  ABC_tran         ABC transporter
      0.048   13.6   0.0      0.097   12.6   0.0    1.5  1  NACHT            NACHT domain
       0.07   12.0   0.0       0.18   10.6   0.0    1.6  2  DLIC             Dynein light intermediate chain (DLIC)


Domain annotation for each model (and alignments):
>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   7.3e-05      0.13      16      49 ..      57      90 ..      50      95 .. 0.88
   2 !   18.9   0.0   4.3e-07   0.00078      92     159 ..     163     228 ..     129     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                   Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                   e a + gH+++l+G  G GKt l ++l++ll + 
  gi|121636883|ref|YP_977106.1| 57 ERALIAGHDFVLLGERGQGKTRLLRALAGLLDEW 90
                                   5577889***********************9775 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.3e-07
                   Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                    G  +++  G i +ah+G++ ++Elp++ +++  ++ + +e++ ++++   ++++ p ++ +va++Np 
  gi|121636883|ref|YP_977106.1| 163 GDPETIAYGLIPRAHRGIVAVNELPDLAERIQVSMLNVMEERDIQVR--GYTLRLPLDVLVVASANPE 228
                                    556678889**********************************9996..578899***********95 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.029        52      11      42 ..      52      83 ..      49      95 .. 0.85
   2 !   23.2   0.0   2.5e-08   4.5e-05      86     143 ..     170     227 ..     161     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.029
                                   HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellarai 42
                                   ++ q++++     + +++Ge G GK+ l ra+
  gi|121636883|ref|YP_977106.1| 52 VIPQVERALIAGHDFVLLGERGQGKTRLLRAL 83
                                   6778888888999999*********9987776 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.5e-08
                                    EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS CS
                Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatne 143
                                     Gl+ +a+ G++ ++e+ +l  ++Q+ +l+v++e+ ++  G +   ++dv ++a++n 
  gi|121636883|ref|YP_977106.1| 170 YGLIPRAHRGIVAVNELPDLAERIQVSMLNVMEERDIQVRGYTLRLPLDVLVVASANP 227
                                    599**************************************************99874 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00015      0.26       1      24 [.      65      89 ..      65      98 .. 0.85
   2 !   14.8   0.0   1.2e-05     0.021      26     138 .]     132     244 ..     125     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                   EEEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaal.n 24
                                   d++L+G+ G gK++l + la +l +
  gi|121636883|ref|YP_977106.1| 65 DFVLLGERGQGKTRLLRALAGLLdE 89
                                   589*****************99954 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.2e-05
                                    -EEEEE--TT--HHHHH--B--...........--------.....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
                          AAA_5  26 eveyvqltrdtteedlkgrreik..ngttslvdsplvraar.....egeilvlDEveraesevlnsLlslleerrlllee 98 
                                    ++++++ t dt+ +dl+g +++    +++sl d +           +  i+ ++E+  +   ++ s+l+++eer ++   
  gi|121636883|ref|YP_977106.1| 132 RYTEKLATPDTSVADLVGDVDPIkvAEGRSLGDPETIAY-GlipraHRGIVAVNELPDLAERIQVSMLNVMEERDIQ-VR 209
                                    6889999**************996755566666555533.25899988999**************************.45 PP

                                    SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  99 ggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    g +l   + d     + v+a+anp d   + ++  ++++Rf
  gi|121636883|ref|YP_977106.1| 210 GYTLRL-PLD-----VLVVASANPEDyTNRGRIITPIKDRF 244
                                    555554.443.....9**********877778888888887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.49   8.8e+02       4      24 ..      68      88 ..      65      93 .. 0.84
   2 !   21.8   0.0   7.1e-08   0.00013      65     117 ..     180     232 ..     138     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.49
                          AAA_3  4 legvPGlaktllvkalakald 24
                                   l g  G +kt+l +ala  ld
  gi|121636883|ref|YP_977106.1| 68 LLGERGQGKTRLLRALAGLLD 88
                                   557789***********9886 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 7.1e-08
                          AAA_3  65 llladeinrappktqsalleameerqvtvegethklpepflvlatqnPieqeG 117
                                    ++ ++e+   + ++q ++l++meer++ v+g t +lp   lv+a  nP +++ 
  gi|121636883|ref|YP_977106.1| 180 IVAVNELPDLAERIQVSMLNVMEERDIQVRGYTLRLPLDVLVVASANPEDYTN 232
                                    6667788888899***********************************88765 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.25   4.5e+02      92     139 ..      67     114 ..      64     130 .. 0.82
   2 !   18.5   0.0   4.3e-07   0.00076     199     348 ..     143     287 ..     128     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                       AAA_PrkA  92 yllGPvggGksslverlkklleaa.piyalegsPvfeePlhli.peelrk 139
                                     llG  g Gk+ l  +l  ll++  p  ++ g+ + e+P++ i pe++r+
  gi|121636883|ref|YP_977106.1|  67 VLLGERGQGKTRLLRALAGLLDEWtP--VIAGAELGEHPYTPItPESIRR 114
                                    699****************9988745..5779999999999887887765 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.3e-07
                       AAA_PrkA 199 disalvGkvdirkleey.sendpdaysysGalnranrGllefvemfkadikvlhplltatqegnyksteklslipfdgii 277
                                     +++lvG vd  k++e  s  dp+  +y G + ra rG++   e+    +++  ++l +  e+ ++  + +  +p d ++
  gi|121636883|ref|YP_977106.1| 143 SVADLVGDVDPIKVAEGrSLGDPETIAY-GLIPRAHRGIVAVNELPDLAERIQVSMLNVMEERDIQVRGYTLRLPLDVLV 221
                                    5899******8887776599*****999.99************************************************* PP

                       AAA_PrkA 278 lahsnesewkkfksnkknealldri.vvvkvPyclrvseekkiyekllkeseladahiaPetlevlarfsil 348
                                    +a +n  ++++    +    + dr    ++  y l+++ e  +   +++e++l +a++    ++vlarf+  
  gi|121636883|ref|YP_977106.1| 222 VASANPEDYTN--RGRIITPIKDRFgAEIRTHYPLELEAEMGV---IVQEAHL-SAQVPDYLMQVLARFARY 287
                                    ******99986..456777899998457999999999999876...8899999.888888899999999855 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   2.7e+02      59      79 ..      65      85 ..      52      94 .. 0.82
   2 !   15.8   0.0   3.2e-06    0.0057     113     175 ..     169     229 ..     157     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                                   EEEEEESSTSTHHHHHHHHHH CS
                            MCM 59 nvllvgdpgtaKsqlLkyvek 79
                                   + +l+g+ g +K++lL++++ 
  gi|121636883|ref|YP_977106.1| 65 DFVLLGERGQGKTRLLRALAG 85
                                   56899***********99875 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.2e-06
                                    EETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                            MCM 113 eaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                      G +  a++G++++ e+    e+ +++++++mE+  i++   G +  L+  + v+a+anp+ 
  gi|121636883|ref|YP_977106.1| 169 AYGLIPRAHRGIVAVNELPDLAERIQVSMLNVMEERDIQVR--GYTLRLPLDVLVVASANPED 229
                                    56777789******************************997..778999999*********85 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5     8e-06     0.014      27     107 ..      66     150 ..      55     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                         AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeal 105
                                     +l Ge+G GK++l+r+l+  l +   + + ++  ++    py +   + +   +  +ql+d+    ++ aw+++ e+ +
  gi|121636883|ref|YP_977106.1|  66 FVLLGERGQGKTRLLRALAGLLDEWTPVIAGAELGEH----PYTPiTPESI---RRAAQLGDD----LPVAWKHRSERYT 134
                                    5799***************888887666677777777....8888677777...467778877....6667777776666 PP

                         AAA_16 106 a..............a 107
                                    +              +
  gi|121636883|ref|YP_977106.1| 135 EklatpdtsvadlvgD 150
                                    6555666655554441 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.1e-05     0.038       8      37 ..      60      89 ..      54     126 .. 0.85
   2 ?   -3.2   0.0       6.1   1.1e+04      57      73 ..     256     272 ..     243     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkp 37
                                   l +g+  +++Ge G GK+ Ll++lagll+ 
  gi|121636883|ref|YP_977106.1| 60 LIAGHDFVLLGERGQGKTRLLRALAGLLDE 89
                                   66788999******************9875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.1
                                    CCHCEEEE-SS--S-TT CS
                                    xxxxxxxxxxxxxxxxx RF
                       ABC_tran  57 lrkeigvlpqepqlfpe 73 
                                    l++e+gv+ qe++l  +
  gi|121636883|ref|YP_977106.1| 256 LEAEMGVIVQEAHLSAQ 272
                                    56778888888777654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05     0.097       4      28 ..      67      91 ..      64      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                   EEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  4 ilqGeaGsGKTtLlqklalawaegk 28
                                   +l Ge G+GKT Ll+ la ++ e++
  gi|121636883|ref|YP_977106.1| 67 VLLGERGQGKTRLLRALAGLLDEWT 91
                                   799***************9999887 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.18       2      49 ..      37      87 ..      36      92 .. 0.86
   2 ?   -1.9   0.0      0.62   1.1e+03     384     459 ..     340     422 ..     287     431 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                           DLIC  2 egqnlwsail...sevstrsssklPsgksvlvlGedgsGkttliaklqGve 49
                                   +g+n+w  il   + v  + +  l +g + ++lGe g Gkt l+  l G+ 
  gi|121636883|ref|YP_977106.1| 37 DGDNVWPGILgfdDTVIPQVERALIAGHDFVLLGERGQGKTRLLRALAGLL 87
                                   799******9443367779999**********************9999975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.62
                           DLIC 384 kkidpklkaaaaseGvlanffnsllskksGsPgsagagggaaagrgsnvq.dsvkksgkkavltdvqae......ldrls 456
                                      + +kl+  + +eG     ++ ll + +   +s   gg  +++  + v+ +s+ ++g++    dv a       +dr++
  gi|121636883|ref|YP_977106.1| 340 DVLRGKLEFESGEEGREQAVLEHLLRRATADTASRVLGGIDVGSLVTAVEgGSAVTTGERVSAKDVLAAvpglpvVDRIA 419
                                    44556777777788888888888888888888888887776666555443145666666666666654312222257777 PP

                           DLIC 457 rkv 459
                                    rk 
  gi|121636883|ref|YP_977106.1| 420 RKL 422
                                    775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2908.20
//
Query:       gi|121636884|ref|YP_977107.1|  [L=672]
Description: hypothetical protein BCG_1013 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-06   26.6   0.0    0.00016   22.3   0.0    3.2  1  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.19   11.7   2.4        2.4    8.2   0.3    3.7  3  DUF1932   Domain of unknown function (DUF1932)
        1.6    9.5   8.4       0.14   12.9   1.7    2.9  3  LTXXQ     LTXXQ motif family protein
        7.1    7.5   8.6        1.3    9.9   2.7    2.4  2  PAPA-1    PAPA-1-like conserved region


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.6e-08   0.00016       1     107 []     484     581 ..     484     581 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.6e-08
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk....slpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggt 76 
                                    + +++DtS Sm  ++    r+  +k+ + al +    +++ d + +++f+  +++++  +      l+ l ++   ++gt
  gi|121636884|ref|YP_977107.1| 484 VALLVDTSFSMVMEN----RWLPMKRTALALHHlvctRFRSDALQIIAFGRYARTVTAAE------LTGLAGVY--EQGT 551
                                    579********7773....666666666655554443779***********998876443......34566777..48** PP

                          VWA_2  77 nlaaaLqlarkalkkrrkgekrvivlitDge 107
                                    nl+ aL la  +l++   g++ v++++tDge
  gi|121636884|ref|YP_977107.1| 552 NLHHALALAGRHLRRHA-GAQPVVLVVTDGE 581
                                    **************886.***********96 PP

>> DUF1932  Domain of unknown function (DUF1932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.19   8.6e+02      26      43 ..     183     200 ..     164     214 .. 0.77
   2 ?   -1.2   0.1      0.47   2.1e+03       8      23 ..     240     255 ..     239     275 .. 0.67
   3 ?    8.2   0.3   0.00055       2.4       4      54 ..     360     414 ..     358     464 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHH CS
                        DUF1932  26 ergltgmppkAyRwveEM 43 
                                    +++l+g +   +R+v EM
  gi|121636884|ref|YP_977107.1| 183 KQALAGATDDDRRRVTEM 200
                                    555666666668999999 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
                                    HHHHHHHHHHSSTHHH CS
                        DUF1932   8 delldeleeslpalla 23 
                                    +elld+l+++  a+++
  gi|121636884|ref|YP_977107.1| 240 EELLDSLAKRAAAAQR 255
                                    6777777777755443 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00055
                                    TT-HHHHHHHHHHHS..STHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHCTT CS
                        DUF1932   4 lGVldelldeleesl..pallaraergltgmppkAyRwveE..Meeiaetlaeeg 54 
                                    + V+ + l+ele+ l  +++l+r + g  +  pkA R+  E  ++ +a+ l+  +
  gi|121636884|ref|YP_977107.1| 360 AAVDARTLAELERALvnQGFLDRGSDGQWRLSPKAMRRLGEtaLRDVAQQLSGRH 414
                                    66888999****99999***********************966678887777766 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.4   6.2e+03      30      89 ..      54     106 ..      43     112 .. 0.52
   2 ?   -2.4   0.1       1.9   8.3e+03      29      62 ..     112     147 ..     102     168 .. 0.50
   3 ?   12.9   1.7     3e-05      0.14      71     103 ..     239     271 ..     174     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                    HHHHS---..-HHHHHHHHHHHTSSS--HHHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                          LTXXQ  30 araeakplkakkeemramrkkvlaanfdetaperlarmeamlearleavkkraealkqfy 89 
                                     +a a+p        ra+ + + + +  +t ++rla+  +++++ l ++   + +l+++ 
  gi|121636884|ref|YP_977107.1|  54 VMAGASPR-------RALSELLRRGTRNLTGADRLAAEVNRRRRELLRRNNLDGTLQEIK 106
                                    44444444.......444444445566788888888665555555555555555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                    HHHHHS---..-HHHHHHHHHHH...TSSS--HHHHH CS
                          LTXXQ  29 aaraeakplkakkeemramrkkv...laanfdetape 62 
                                    a  ae+k+l  +  +++ + + +   + ++ +++a++
  gi|121636884|ref|YP_977107.1| 112 AVLAERKELARALDDDARFAE-LqldALPASPAKAVQ 147
                                    444555555222222222222.223333334444444 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                          LTXXQ  71 learleavkkraealkqfyavLtpEQkakldal 103
                                    +e+ l ++ kra+a + f+++L+ EQ+ +ldal
  gi|121636884|ref|YP_977107.1| 239 VEELLDSLAKRAAAAQRFRNSLSQEQRDELDAL 271
                                    456778899**********************98 PP

>> PAPA-1  PAPA-1-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.7   0.00029       1.3       7      46 ..      83     125 ..      82     165 .. 0.75
   2 ?    0.1   0.3      0.31   1.4e+03       4      24 ..     247     267 ..     244     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00029
                                    HHHHHHHHHHHHHHHHHHHHXHHHHHHXXXXXXXXXX.....X CS
                         PAPA-1   7 aEmarrRknqsekrleeekaeTInkLLkkqagkkkkkkk...a 46 
                                    aE  rrR+++  + + +   + I+kLL +++  ++k+ +   +
  gi|121636884|ref|YP_977107.1|  83 AEVNRRRRELLRRNNLDGTLQEIKKLLDEAVLAERKELAralD 125
                                    7999***************************999999654441 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                                    XHHHHHHHHHHHHHHHHHHHH CS
                         PAPA-1   4 lrraEmarrRknqsekrleee 24 
                                     +ra +a+r +n   + +++e
  gi|121636884|ref|YP_977107.1| 247 AKRAAAAQRFRNSLSQEQRDE 267
                                    79*******999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.42
# Mc/sec: 4748.49
//
Query:       gi|121636885|ref|YP_977108.1|  [L=73]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.6   0.6      0.013   15.4   0.4    1.8  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.012   15.4   0.4      0.016   15.0   0.4    1.2  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
       0.12   12.3   0.0       0.16   12.0   0.0    1.1  1  DUF2761   Protein of unknown function (DUF2761)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   2.2e-06     0.013       6      28 ..       9      31 ..       8      39 .. 0.92
   2 ?   -1.4   0.0      0.44   2.6e+03      14      22 ..      33      41 ..      30      43 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                                   EEHHHHHHHHHHHHHHTSSHHHH CS
                          RHH_1  6 ldeellerLdelarrrgrSrSel 28
                                   ++++++erL++la+  + S+S++
  gi|121636885|ref|YP_977108.1|  9 VPDDVVERLERLAELAKTSVSAV 31
                                   79******************985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.44
                                   HHHHHHHHT CS
                          RHH_1 14 Ldelarrrg 22
                                   ++el ++++
  gi|121636885|ref|YP_977108.1| 33 VRELTEASR 41
                                   556655554 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.7e-06     0.016       8      32 ..       9      33 ..       8      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                          RHH_5  8 LPeelleeLeewAdeegRsvSnlaa 32
                                   +P+++ e+Le++A+    svS +a 
  gi|121636885|ref|YP_977108.1|  9 VPDDVVERLERLAELAKTSVSAVAV 33
                                   8*************99999998886 PP

>> DUF2761  Protein of unknown function (DUF2761)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.16      11      59 ..      26      72 ..      22      73 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                        DUF2761 11 tgrvavlvkdyaasdlngdapayfyseeaeglgldpwrlvegvdahtag 59
                                   t   av v++++++    d pa +   +  ++g+d   l+ g+da  ag
  gi|121636885|ref|YP_977108.1| 26 TSVSAVAVRELTEASRRADNPALL--GDLPDIGIDTTELIGGIDAERAG 72
                                   67789*****************87..56789**************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 522.67
//
Query:       gi|121636886|ref|YP_977109.1|  [L=127]
Description: hypothetical protein BCG_1014 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-15   56.8   0.4    3.4e-15   56.6   0.4    1.0  1  PIN             PIN domain
    0.00098   19.4   0.1     0.0025   18.0   0.1    1.6  1  PIN_2           PIN domain
  ------ inclusion threshold ------
       0.18   10.5   0.0       0.27   10.0   0.0    1.2  1  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.4   5.7e-19   3.4e-15       1     119 [.       2     115 ..       2     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.7e-19
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEE.BCHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilp.idaeia 78 
                                    iv+D+s+ +a+l ++ +a   r+l+++ e+l+++ lv +E++ +l+r  +++r+ aa+ +++l+ +++l +      +++
  gi|121636886|ref|YP_977109.1|   2 IVVDASAALAALLNDGQA---RQLIAA-ERLHVPHLVDSEIASGLRRlAQRDRLGAADGRRALQTWRRLAVTRyPVVGLF 77 
                                    79**************99...9***98.*********************************************8899*** PP

                                    HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                    e+++ei+++  l+++Da  +A+A++ +++l+ t+D +++++
  gi|121636886|ref|YP_977109.1|  78 ERIWEIRAN--LSAYDASYVALAEALNCALV-TADLRLSDT 115
                                    ********8..8****************999.***999876 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.3e-07    0.0025       1     119 [.       3     116 ..       3     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                          PIN_2   1 VvdaNivvsallksrikkrlilvekaleliapeeaveeiekhkealvkksklseeeleellellet.kikiveeslyesk 79 
                                    Vvda + ++all+ + + r+++++++l+  +p+ + +ei+     l+++ +l ++    +l++ ++ +++ ++   + + 
  gi|121636886|ref|YP_977109.1|   3 VVDASAALAALLN-DGQARQLIAAERLH--VPHLVDSEIASGLRRLAQRDRLGAADGRRALQTWRRlAVTRYPVVGLFER 79 
                                    9***********6.88888888888777..9999999*********************9999776514455555444466 PP

                          PIN_2  80 ikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdligaG 119
                                    i e +  +      D+ +vAla +l++++ T D  l  +G
  gi|121636886|ref|YP_977109.1|  80 IWEIRANLSA---YDASYVALAEALNCALVTADLRLSDTG 116
                                    6665555555...899*****************9999888 PP

>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.5e-05      0.27     173     205 ..      80     112 ..      77     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.5e-05
                                    TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT CS
                 Glyco_hydro_15 173 lWEenqgeselnassvgmakAlleaideadlfg 205
                                    +WE++   s + as v+ a Al +a+  adl  
  gi|121636886|ref|YP_977109.1|  80 IWEIRANLSAYDASYVALAEALNCALVTADLRL 112
                                    9****************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 944.07
//
Query:       gi|121636887|ref|YP_977110.1|  [L=115]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   13.1   0.3      0.082   13.1   0.3    2.4  3  DIM       DIM protein


Domain annotation for each model (and alignments):
>> DIM  DIM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5      0.25   4.5e+03       3       3 ..      37      37 ..      20      45 .. 0.61
   2 ?   13.1   0.3   4.6e-06     0.082       2      28 ..      67      93 ..      66      94 .. 0.94
   3 ?   -1.8   0.3      0.21   3.7e+03       9      14 ..     101     106 ..      97     112 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.25
                            DIM  3 c 3 
                                   +
  gi|121636887|ref|YP_977110.1| 37 W 37
                                   3 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.6e-06
                            DIM  2 kcLsLlaflllllalaaanalpGkViI 28
                                   +++ + a+lll l++ + n++ G+V+I
  gi|121636887|ref|YP_977110.1| 67 MWIGVGAVLLLTLVVMVRNSSRGNVVI 93
                                   699999********************9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.21
                            DIM   9 flllll 14 
                                    ++l+l+
  gi|121636887|ref|YP_977110.1| 101 LALGLV 106
                                    444533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 869.44
//
Query:       gi|121636888|ref|YP_977111.1|  [L=224]
Description: lipoprotein lprP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-32  112.5   0.1    7.9e-32  110.3   0.0    2.0  3  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   4.4e-36   7.9e-32       2     148 ..      28     170 ..      27     171 .. 0.96
   2 ?   -2.0   0.0      0.16     3e+03     145     153 .]     180     188 ..     176     188 .. 0.83
   3 ?   -1.8   0.0      0.15   2.7e+03     115     132 ..     202     219 ..     200     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.4e-36
                                    -HHHHHH.HHHHHHHHHHHGGG--HHHHHHHHHHHHHHHHHHHHHHSTT--EEE---HH..HH-EESSS-TTTEEE-B-- CS
                           LppA   2 gepealtskeevaeaedelrqkPslEeaeeqleallariadaisalvpgltWktdedrs..rngCedpyeetdgrrvale 79 
                                     +p+a+++++e++++++ ++++P+lE++++ql++l a+i+++i+++ p+++++t    s  +ngC+dp+++t+gr++a+e
  gi|121636888|ref|YP_977111.1|  28 FDPYANPGRGELDRRQKIVNGRPDLETVQQQLANLDATIRAMIAKYSPQTRFSTGVTVShlTNGCNDPFTRTIGRQEASE 107
                                    689*****************************************************666567****************** PP

                                    -EEESS---HHHHHHHHHHHHHHHHTTT--EEE-S-BSSS-EEEEEEET.TEEEEEEESSSEEEEEE-- CS
                           LppA  80 svvsagpipddqWpqaleiVrelAakygatevevfkDepgdhdvrftgpeGgeiklgtakaavltittg 148
                                     ++++++ +++qW   l+iV+elA+ ++a++++ +++ pgd+++ + +p+   +++++++++++++++g
  gi|121636888|ref|YP_977111.1| 108 LFFGRPAPTPQQW---LQIVTELAPVFKAAGFRPNNSVPGDPPQPLGAPN---YSQIRDDGVTINLVNG 170
                                    *************...*********************************7...************9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.16
                                    EE---EE-H CS
                           LppA 145 ittgCrLpe 153
                                     +tgC+Lp+
  gi|121636888|ref|YP_977111.1| 180 YNTGCHLPA 188
                                    689****85 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.15
                                    -BSSS-EEEEEEET.TEE CS
                           LppA 115 kDepgdhdvrftgpeGge 132
                                    ++ p+ h+ +++g+ Gg+
  gi|121636888|ref|YP_977111.1| 202 ANDPDVHYPYLYGSPGGR 219
                                    578**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1661.59
//
Query:       gi|121636889|ref|YP_977112.1|  [L=266]
Description: hypothetical protein BCG_1017c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-72  242.7   2.5    2.3e-72  242.3   2.5    1.1  1  Abhydrolase_8  Alpha/beta hydrolase
  ------ inclusion threshold ------
      0.083   12.5   0.0       0.15   11.6   0.0    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   2.5   2.6e-76   2.3e-72       1     177 [.      53     230 ..      53     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 2.6e-76
                  Abhydrolase_8   1 DpagkvlaavavGdldrAerVsVtvpGvdttlrrtlatmvaearglraeaaaaeeaagkpe..svAviAWlgYeaPagas 78 
                                    Dp +kvlaav+vGd+d+AerV+Vt++G++t++++++++mv+ea+++ra+aa+++e+ag+p+  +vA+iAWlgY+aP + +
  gi|121636889|ref|YP_977112.1|  53 DP-RKVLAAVGVGDVDNAERVGVTMGGLNTRVSSSVGDMVKEAGIQRAKAAELRERAGWPNydAVASIAWLGYDAP-DGL 130
                                    78.89*******************************************************999*************.9** PP

                  Abhydrolase_8  79 kevatddrAaagAaeLnallrdlrats.vpgqhlallgHSYGSlvaslAlddaaseVsdvvlyGSPGleaesaakLgled 157
                                    k+v++d++A+++A++Ln+++++l+at+ v++qh++++gHSYGSlv+slAl++ +++VsdvvlyGSPG+e+++a++Lg+e+
  gi|121636889|ref|YP_977112.1| 131 KDVMHDWSARDAAGPLNRFDKGLAATTnVSDQHITAFGHSYGSLVTSLALQQ-GAPVSDVVLYGSPGTELTHASQLGVEP 209
                                    ***************************99***********************.*************************** PP

                  Abhydrolase_8 158 arvfvmrgadDlienv.pela 177
                                    +++f+m+g++D+++n+ pe++
  gi|121636889|ref|YP_977112.1| 210 GHAFYMIGVNDHVANTiPEFG 230
                                    ***************999986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.7e-05      0.15      71     116 ..     160     202 ..     131     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                    TTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHH CS
                  Abhydrolase_1  71 gddkltlvGhSmGGmialayaaeyperVkalvllgaidpaasliea 116
                                     d+++t  GhS+G+++ + ++++   +V+ +vl g+  p  +l +a
  gi|121636889|ref|YP_977112.1| 160 SDQHITAFGHSYGSLVTSLALQQ-GAPVSDVVLYGS--PGTELTHA 202
                                    699***********999988887.788999999999..66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1905.41
//
Query:       gi|121636890|ref|YP_977113.1|  [L=160]
Description: hypothetical protein BCG_1018c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.3   1.0      0.052   13.6   1.0    1.3  1  MurB_C    UDP-N-acetylenolpyruvoylglucosamine reductase, C-te
       0.34   11.2   1.7       0.59   10.4   1.7    1.4  1  DUF1328   Protein of unknown function (DUF1328)


Domain annotation for each model (and alignments):
>> MurB_C  UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   5.8e-06     0.052      63     106 ..       4      47 ..       3      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-06
                                    TT-TTSEETTEEEESSSTTEEEESSS--HHHHHHHHHHHHHHHH CS
                         MurB_C  63 aglkGlrvggaqvsekhalflvNgggataadilalarevrkkVk 106
                                    +g+ G   ++aqv ++h+ +l+ +++  ++ +++ a++  ++V+
  gi|121636890|ref|YP_977113.1|   4 LGFGGAAAEAAQVATHHTTVLLDHHAGACEAVARAAEKAAEEVA 47 
                                    5999*******************888899999999999999986 PP

>> DUF1328  Protein of unknown function (DUF1328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.7   6.5e-05      0.59      11      26 ..       2      17 ..       1      19 [. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.5e-05
                        DUF1328 11 gvLGFgGiagaaagiA 26
                                   g+LGFgG a+ aa++A
  gi|121636890|ref|YP_977113.1|  2 GLLGFGGAAAEAAQVA 17
                                   89************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1033.09
//
Query:       gi|121636891|ref|YP_977114.1|  [L=139]
Description: hypothetical protein BCG_1019c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   18.0   4.7      0.013   16.1   1.5    2.4  2  DUF2563   Protein of unknown function (DUF2563)


Domain annotation for each model (and alignments):
>> DUF2563  Protein of unknown function (DUF2563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.9    0.0096   1.7e+02      22      57 ..      61      99 ..      49     103 .. 0.65
   2 !   16.1   1.5     7e-07     0.013      77     101 ..     102     126 ..      90     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0096
                        DUF2563 22 areGadql...arGpllsGmfGdfaaadafhdavvaaha 57
                                   a eGa      +    lsG++ ++a a + h a    h+
  gi|121636891|ref|YP_977114.1| 61 AAEGARPGwvgSSAGALSGLLDSWAEASTAHAAHIGDHS 99
                                   445544320112334579************999877775 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7e-07
                        DUF2563  77 arhaakGftdmdeqnaeelkavrls 101
                                     ++aa Gf++m+e+na++l av ++
  gi|121636891|ref|YP_977114.1| 102 MHLAAVGFAEMEEHNAAALAAVYPT 126
                                    699******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1041.36
//
Query:       gi|121636892|ref|YP_977115.1|  [L=200]
Description: hypothetical protein BCG_1020c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-16   58.1   8.9    9.7e-16   57.6   7.9    1.7  2  DUF1707   Domain of unknown function (DUF1707)
    4.6e-05   23.3   0.0    8.1e-05   22.5   0.0    1.4  1  DUF2154   Cell wall-active antibiotics response 4TMS YvqF


Domain annotation for each model (and alignments):
>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   7.9   1.1e-19   9.7e-16       2      53 .]      18      69 ..      17      69 .. 0.99
   2 ?   -1.8   0.0      0.38   3.4e+03      25      41 ..     127     143 ..     125     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.1e-19
                        DUF1707  2 RasdadReravelLrealaeGrLtldEfdeRleaalaArtrgeLaalvaDLP 53
                                   Rasd+dR ++++lL+ a+++GrL l+++++Rl++a+aA+t++eL++l aDLP
  gi|121636892|ref|YP_977115.1| 18 RASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQELDRLRADLP 69
                                   9**************************************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.38
                        DUF1707  25 tldEfdeRleaalaArt 41 
                                    t +E d R   ++ A+t
  gi|121636892|ref|YP_977115.1| 127 TSTEVDIRAYSIMGAQT 143
                                    77899999999999998 PP

>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   9.1e-09   8.1e-05      14      72 ..     104     163 ..      96     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.1e-09
                        DUF2154  14 l.edinissiiGdttiDLtkavlpegetvivirkliGdvkilVPedvevsveasvifGdv 72 
                                    + +++ + ++ G+ ++DL++a+ +  e  i   +++G  +il+P +v+v+++   ++G  
  gi|121636892|ref|YP_977115.1| 104 VpKKLTTFTLWGSGVLDLRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGF 163
                                    54668889999*****************************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1622.60
//
Query:       gi|121636893|ref|YP_977116.1|  [L=119]
Description: hypothetical protein BCG_1021 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   86.4   0.9    1.6e-24   86.0   0.9    1.1  1  Trns_repr_metal  Metal-sensitive transcriptional repressor
  ------ inclusion threshold ------
      0.091   12.2   0.0      0.091   12.2   0.0    1.1  1  Rogdi_lz         Rogdi leucine zipper containing protein


Domain annotation for each model (and alignments):
>> Trns_repr_metal  Metal-sensitive transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.9   1.8e-28   1.6e-24       2      76 ..       9      87 ..       8      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.8e-28
                                   HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHH CS
                Trns_repr_metal  2 kkkllnrLkrieGQvrgiqrmieedryCidiltQlaAvrsalnkvglelledhlkhcvaeaiee....ekieeliellk 76
                                   k+++lnrLk+++G+++gi rm+e d+yC+d+++Q++Av+s l+++++ +l++hl++c++ a+ +    ++ieeli+++k
  gi|121636893|ref|YP_977116.1|  9 KRAALNRLKTVRGHLDGIVRMLESDAYCVDVMKQISAVQSSLERANRVMLHNHLETCFSTAVLDghgqAAIEELIDAVK 87
                                   7899*******************************************************9995567889******9985 PP

>> Rogdi_lz  Rogdi leucine zipper containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     1e-05     0.091      77     152 ..       5      78 ..       1     111 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                       Rogdi_lz  77 lnptkpivleqLtdlrtlltqaldlLdltlktgdelsksaqflssqLrllleslseAkalLkgppepelafpang..... 151
                                    l+ +k   l+ L+++r +l+ ++ +L+   + ++ +      +++q+ ++++sl++A +++  ++  e  f++ +     
  gi|121636893|ref|YP_977116.1|   5 LTAKKRAALNRLKTVRGHLDGIVRMLE---SDAYCV-----DVMKQISAVQSSLERANRVMLHNHL-ETCFSTAVldghg 75 
                                    66788899*******************...433344.....589**************99988888.5577776555555 PP

                       Rogdi_lz 152 ..w 152
                                      +
  gi|121636893|ref|YP_977116.1|  76 qaA 78 
                                    553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 874.75
//
Query:       gi|121636894|ref|YP_977117.1|  [L=98]
Description: hypothetical protein BCG_1022 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-38  129.6   8.0    4.1e-38  129.3   8.0    1.0  1  DUF1490     Protein of unknown function (DUF1490)
  ------ inclusion threshold ------
        6.8    6.1   7.5         14    5.1   3.1    2.3  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   8.0   4.6e-42   4.1e-38       1      86 [.       1      90 [.       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 4.6e-42
                        DUF1490  1 mvvqgllakaattvvtGvvGvaayevlrkavakaplreaaVaatalglrgaRkae....eaaEsarLkvaDvvaeAreriGe 78
                                   mv++g+laka++tvvtG+vGvaaye+lrk+v+kaplr a+V+++a+g+r aR+ae    e+aE+arL++aDv+aeA+er+Ge
  gi|121636894|ref|YP_977117.1|  1 MVWHGFLAKAVPTVVTGAVGVAAYEALRKMVVKAPLRAATVSVAAWGIRLAREAErkagESAEQARLMFADVLAEASERAGE 82
                                   9******************************************************9999*********************** PP

                        DUF1490 79 eapppava 86
                                   e+pp+ava
  gi|121636894|ref|YP_977117.1| 83 EVPPLAVA 90
                                   *****997 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.1    0.0016        14      19      29 ..      13      23 ..       6      24 .. 0.86
   2 ?    2.9   0.1    0.0076        68      16      26 ..      37      47 ..      36      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0016
                     UCR_Fe-S_N 19 TgavgaVGaaa 29
                                   T+++gaVG+aa
  gi|121636894|ref|YP_977117.1| 13 TVVTGAVGVAA 23
                                   99********8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0076
                     UCR_Fe-S_N 16 yiATgavgaVG 26
                                    +AT++v+a G
  gi|121636894|ref|YP_977117.1| 37 RAATVSVAAWG 47
                                   689*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 746.69
//
Query:       gi|121636895|ref|YP_977118.1|  [L=770]
Description: metal cation transporter P-type atpase ctpV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-55  186.0   5.7    1.1e-54  184.8   5.7    1.7  1  E1-E2_ATPase  E1-E2 ATPase
    1.3e-52  179.2  10.4    2.3e-52  178.3  10.4    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.5e-05   24.9   0.5     0.0002   21.2   0.1    2.1  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
     0.0087   16.5   0.5      0.054   13.9   0.5    2.2  1  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.018   15.1   0.1       0.13   12.4   0.0    2.4  2  Hydrolase_6   Haloacid dehalogenase-like hydrolase
      0.051   13.5   0.8       0.11   12.4   0.8    1.5  1  APH           Phosphotransferase enzyme family
       0.07   13.2   0.0       0.15   12.1   0.0    1.5  1  HAD_2         Haloacid dehalogenase-like hydrolase
       0.42   10.2   3.5       0.49    9.9   0.0    2.8  3  DUF4225       Protein of unknown function (DUF4225)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   5.7   4.7e-58   1.1e-54       3     179 ..     260     436 ..     258     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 4.7e-58
                                    S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEE CS
                   E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeak 82 
                                     +++a+++ dg+e  ++++++++GD+v +++g+++p+Dg++ +g a vdes+LTGEs+pvek++gd+v + tv+++g ++
  gi|121636895|ref|YP_977118.1| 260 GAKEATLLVDGQELLVPVDQVQVGDLVRVRPGEKIPVDGEVTDGRAAVDESMLTGESVPVEKTAGDRVAGATVNLDGLLT 339
                                    57899*************************************************************************** PP

                                    EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TT CS
                   E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPca 162
                                    +++ta+g dt l++i+rlve+a+ +k+p+q+ +d++++v+vp+v+ +a+++f+ + l+  +++  ++ a+a+l++a+Pca
  gi|121636895|ref|YP_977118.1| 340 VRATAVGADTALAQIVRLVEQAQGDKAPVQRLADRVSAVFVPAVIGVAVATFAGWTLIAANPVAGMTAAVAVLIIACPCA 419
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 163 Lplavplalalgarrla 179
                                    L+la+p+a+++g++r a
  gi|121636895|ref|YP_977118.1| 420 LGLATPTAIMVGTGRGA 436
                                    **************988 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3  10.4     1e-55   2.3e-52       1     210 []     454     672 ..     454     672 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 1e-55
                                    SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg.... 67 
                                    i+tvvfDk+GTLt+ +++v+dvi+         l laaa e gsehpig+a+vaaa++r    +a   f++++g+g    
  gi|121636895|ref|YP_977118.1| 454 IDTVVFDKTGTLTRARMRVTDVIAGQrrqpnqVLRLAAAVESGSEHPIGAAIVAAAHERglaIPAANAFTAVAGHGvraq 533
                                    79************************999999999************************6655555************** PP

                                    ....HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEE CS
                                    ....xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 ....ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvl 139
                                         + +g++++++++    p++l aa  + +++grt++++  ++++++v+++ad+  vk++aa++v +L+a+g++v++
  gi|121636895|ref|YP_977118.1| 534 vnggPVVVGRRKLVDEQhlVLPDHLAAAAVEQEERGRTAVFVgqDGQVVGVLAVADT--VKDDAADVVGRLHAMGLQVAM 611
                                    ******************************************9999***********..********************* PP

                                    EESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 140 ltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    +tgdn +ta ++a+q+G           ie+  a+++p++kva +r+Lq +++ vamVGDgvnDa+al +A+
  gi|121636895|ref|YP_977118.1| 612 ITGDNARTAAAIAKQVG-----------IEKvLAEVLPQDKVAEVRRLQDQGRVVAMVGDGVNDAPALVQAD 672
                                    *****************...........7777**************************************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.078   1.8e+02      15      56 ..     590     631 ..     584     636 .. 0.88
   2 !   21.2   0.1   9.1e-08    0.0002     206     255 .]     655     704 ..     644     704 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.078
                                    ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                    Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                    ++++ +++++ +l++ g +v+  TG + r++  +++++g++ 
  gi|121636895|ref|YP_977118.1| 590 TVKDDAADVVGRLHAMGLQVAMITGDNARTAAAIAKQVGIEK 631
                                    6888999999*****************************985 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 9.1e-08
                                    EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                    v+ +GDg ND + L +a+lg+A+g +++ +++a+d +  s   dGV++a+
  gi|121636895|ref|YP_977118.1| 655 VAMVGDGVNDAPALVQADLGIAIGTGTDVAIEASDITLMSGRLDGVVRAI 704
                                    7789******************************************9997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   2.4e-05     0.054      86     187 ..     591     668 ..     544     668 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                            HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaae 165
                                     + +a +++ + +a G +v++++g + + + ++++++g++ vla+      +              ++kva++r+     
  gi|121636895|ref|YP_977118.1| 591 VKDDAADVVGRLHAMGLQVAMITGDNARTAAAIAKQVGIEKVLAE------V------------LPQDKVAEVRR----- 647
                                    4568899999999*************************8888888......2............22335555555..... PP

                            HAD 166 gegidleevvayGDspsDlpll 187
                                       ++   v  +GD+++D p+l
  gi|121636895|ref|YP_977118.1| 648 -LQDQGRVVAMVGDGVNDAPAL 668
                                    .34455556666******9987 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.97   2.2e+03      58      90 ..     547     579 ..     545     582 .. 0.85
   2 ?   12.4   0.0   5.8e-05      0.13       6      51 ..     582     627 ..     580     664 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.97
                                    --GGGEEEHHHHHHHHHHHHSXXXEEEEESXHH CS
                    Hydrolase_6  58 iteeqvvtsataaaeylkkrkadkkvlvigeeg 90 
                                    ++e+++v +   aa+ +++++++++ + +g++g
  gi|121636895|ref|YP_977118.1| 547 VDEQHLVLPDHLAAAAVEQEERGRTAVFVGQDG 579
                                    578999999999999999999988888888876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.8e-05
                                    TTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                    Hydrolase_6   6 dGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                     GvL   d++ + aa+++ +l+a+g +v+++T  + ++  ++ak++
  gi|121636895|ref|YP_977118.1| 582 VGVLAVADTVKDDAADVVGRLHAMGLQVAMITGDNARTAAAIAKQV 627
                                    69************************************98888876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   4.9e-05      0.11      54     153 ..     554     646 ..     504     673 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                                    --B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHH CS
                            APH  54 vPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesat 133
                                     P  la    ++e++ + a++ +++g+++      a+++ + ++++++ ++lh+++ + ++ +++ a++++  ++ +   
  gi|121636895|ref|YP_977118.1| 554 LPDHLAAAAVEQEERGRTAVFVGQDGQVVGV---LAVADTVKDDAADVVGRLHAMGLQVAMITGDNARTAAAIAKQVGI- 629
                                    444444444555555599*************...**********************999*****999999999999999. PP

                                    HCCCGCCTCCHHHHHHHHHH CS
                            APH 134 arllaselldlleeleeqvl 153
                                      ++ +e+l+ + +++e v+
  gi|121636895|ref|YP_977118.1| 630 -EKVLAEVLP-QDKVAE-VR 646
                                    .778878777.445444.33 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.8e-05      0.15      81     133 ..     592     644 ..     588     673 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                          HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvek 133
                                     d++ +++  L+++g++++ +T  +++++    +q+gie+++  ++ +++v +
  gi|121636895|ref|YP_977118.1| 592 KDDAADVVGRLHAMGLQVAMITGDNARTAAAIAKQVGIEKVLAEVLPQDKVAE 644
                                    6899999**************************************99999876 PP

>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00022      0.49      45      93 ..     209     259 ..     196     272 .. 0.86
   2 ?   -2.9   1.5         2   4.4e+03      46      72 ..     383     407 ..     379     415 .. 0.61
   3 ?   -1.7   0.0      0.84   1.9e+03     100     116 ..     710     726 ..     704     730 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                        DUF4225  45 gvVagglqivaGvalv.skasetvvgavaGalLilhGannvvenisyll.g 93 
                                    ++V +  q++aG  l   +++  ++++v+G +L +  ++  +e+is+ll  
  gi|121636895|ref|YP_977118.1| 209 AFVYSTYQLFAGGPLFfDTSALIIAFVVLGRHLEARATGKASEAISKLLeL 259
                                    79**************7777889999**********************943 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                        DUF4225  46 vVagglqivaGvalvskasetvvgava 72 
                                    v+  +++++aG +l+  a++ v+g+ a
  gi|121636895|ref|YP_977118.1| 383 VIGVAVATFAGWTLI--AANPVAGMTA 407
                                    66678899******9..3333333333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.84
                        DUF4225 100 lvrdvYreaaeklGysk 116
                                    ++r +Y++ + ++Gy++
  gi|121636895|ref|YP_977118.1| 710 TLRTIYQNLGWAFGYNT 726
                                    79*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 5631.01
//
Query:       gi|121636896|ref|YP_977119.1|  [L=210]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-37  126.9  31.5    5.7e-37  126.9  31.5    1.4  2  DUF5134   Domain of unknown function (DUF5134)


Domain annotation for each model (and alignments):
>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       0.3   5.4e+03     105     119 ..       8      22 ..       6      31 .. 0.65
   2 !  126.9  31.5   3.2e-41   5.7e-37       3     151 .]      36     206 ..      34     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.3
                        DUF5134 105 tgvlavyFaaaalvw 119
                                     +v++ +F++ a+  
  gi|121636896|ref|YP_977119.1|   8 RWVVTGLFVLTAAEC 22 
                                    677777777777644 PP

  == domain 2  score: 126.9 bits;  conditional E-value: 3.2e-41
                        DUF5134   3 rvsavlhllMavgMaaMawpagvalpsagqlavvfalaalwflvlavvrrrataarrlahlyhavmmlAMvyMaaam... 79 
                                     v+++lh++Mav+Ma+Mawp+g+++p++g+ av+f+laa+wf ++avv+  +++a+r+ ++yh +mmlA ++M+aam   
  gi|121636896|ref|YP_977119.1|  36 IVNHGLHFAMAVAMAVMAWPWGARVPTTGP-AVFFLLAAVWFGATAVVAV-RGTATRGLYGYHGLMMLATAWMYAAMnpr 113
                                    589***************************.****************998.8999************************9 PP

                        DUF5134  80 alaaggghsghaaagasmpgg................vplvtgvlavyFaaaalvwlarllp.....apapa...elara 135
                                     l+ ++ ++ ++++  smp++                +++v+++ +v+Fa+aa++w++r++      a   +     +++
  gi|121636896|ref|YP_977119.1| 114 LLPVRSCTEYATEPDGSMPAMdmtamnmppnsgspiwFSAVNWIGTVGFAVAAVFWACRFVMerrqeA---TqsrLPGSI 190
                                    6777777777777777777777777788888*******************************776542...14446789* PP

                        DUF5134 136 crlvMalGMaaMllal 151
                                    ++++Ma+GMa++++a+
  gi|121636896|ref|YP_977119.1| 191 GQAMMAAGMAMLFFAM 206
                                    **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1533.41
//
Query:       gi|121636897|ref|YP_977120.1|  [L=269]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-43  146.7   0.0    9.1e-43  146.4   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
      1e-26   94.3   0.1    1.2e-26   94.0   0.1    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.0     1e-46   9.1e-43       7     250 ..      18     261 ..      15     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 1e-46
                                    EEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC...HHHHHHHCCHHHHHHH CS
                          ECH_1   7 aviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek...akqallkeevlelwtk 83 
                                    a ++ln P++ Nals +l+  l q l  +e d++vr vvL   ++ F+aGadl e+ +++    + +     e+ +l+++
  gi|121636897|ref|YP_977120.1|  18 ARLTLNSPHNRNALSSTLVSQLHQGLSAAEADPAVRLVVLGHTGGTFCAGADLSEAGGGGGdpyRMAVARAREMTALLRA 97 
                                    678*************************************99**************9987644455555678899***** PP

                                    HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHH CS
                          ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqe 163
                                    + ++p+pv+ a+nG++ +GG+ l+ acD+v+a+ ++ f+l+e+++G+ p a ++ +l  k+  ++A +  l+g+k++a e
  gi|121636897|ref|YP_977120.1|  98 IVESPLPVVGAINGHVRAGGFGLVGACDMVVAGPESTFALTEARIGVAP-AIISLTLLPKLSPRAAARYYLTGEKFGARE 176
                                    *************************************************.66666666677888888899********** PP

                                    HHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                          ECH_1 164 alkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                    a+++Gl+   ++++++     +l++ + + sp+ l++ k+   a++ +   +  e   +    +f +d+ +eG+ afl k
  gi|121636897|ref|YP_977120.1| 177 AADIGLIT--MAADDVDAAVAALVADVGRGSPQGLAASKALTTAAVLEGFDRDAERLTEESARLFVSDEAREGMLAFLQK 254
                                    *******7..6789999999999999999999999988887777766555555555555566677778889********* PP

                                    SH----- CS
                          ECH_1 244 rkpefed 250
                                    r+p++ +
  gi|121636897|ref|YP_977120.1| 255 RPPRWVQ 261
                                    *****76 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.1   1.3e-30   1.2e-26       3     186 ..      19     199 ..      17     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 1.3e-30
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                    ++tLn p++ NaLs ++v++l++ l++ e+d++v+lvvl  +g   fCAG D+ +      +  + + +  re  +l  +
  gi|121636897|ref|YP_977120.1|  19 RLTLNSPHNRNALSSTLVSQLHQGLSAAEADPAVRLVVLGHTG-GTFCAGADLSEAGGGGGDPYRMAVARAREMTALLRA 97 
                                    79*************************************8876.89*********99999998777788899999***** PP

                                    HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHHH CS
                          ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgada 162
                                    i + p pvv  ++G v  gG Gl   + + v+  +++fA  E +IG+ P +    +L++l+ + +    lTG+++++++a
  gi|121636897|ref|YP_977120.1|  98 IVESPLPVVGAINGHVRAGGFGLVGACDMVVAGPESTFALTEARIGVAPAIISLTLLPKLSPRAAARYYLTGEKFGAREA 177
                                    ************************************************************888888888*********** PP

                                    HHTTS--EE--GGGHHHHHHHHHT CS
                          ECH_2 163 laaglathyvpseklealeeaLae 186
                                      +gl t   ++  ++a  +aL +
  gi|121636897|ref|YP_977120.1| 178 ADIGLITMAADD--VDAAVAALVA 199
                                    *****9987764..3444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1941.31
//
Query:       gi|121636898|ref|YP_977121.1|  [L=388]
Description: acyl-CoA dehydrogenase fadE12 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-30  104.1   4.3    1.2e-29  103.4   4.3    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.1e-28   98.7   1.5    1.2e-27   96.8   0.2    2.2  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    7.8e-19   67.7   0.0    1.6e-18   66.7   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.2e-09   38.6   4.7    2.2e-09   37.7   4.7    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   4.3   2.8e-33   1.2e-29      10     147 ..     240     379 ..     235     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 2.8e-33
                                    TT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------..HHH CS
                  Acyl-CoA_dh_1  10 tlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd..rae 87 
                                    +ln eR++ aa a+g+ r al +a++y+++rk   +p+++hq +++ la++++e+e a+l++ +aa ++d+g++     +
  gi|121636898|ref|YP_977121.1| 240 GLNPERIMGAASAVGMGRFALGRAVDYVKTRKVWSTPIGAHQGLAHPLAQCHIEVELAKLMTQKAATLYDHGDDFgaAEA 319
                                    69*************************************************************************98889 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                  Acyl-CoA_dh_1  88 asmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    a+maK+ a+e+  +++d+a+q +Gg+G+++ey+v++++  ar+ ri+  + e+ +n +a+
  gi|121636898|ref|YP_977121.1| 320 ANMAKYAAAEASSRAVDQAVQSMGGNGLTKEYGVAAMMTSARLARIAPISREMVLNFVAQ 379
                                    99********************************************98777777777776 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.2   2.7e-31   1.2e-27       1     112 [.       9     119 ..       9     120 .. 0.93
   2 ?    0.6   0.1      0.19   8.7e+02      15      55 ..     315     352 ..     295     380 .. 0.55

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2.7e-31
                                    THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                    +ee +alr++v++++++   ++  +  +++e+  elw ++++lG+lg+++peeygG g+++ e  +v+ee+a+a+++l l
  gi|121636898|ref|YP_977121.1|   9 SEERQALRKAVASWVANYGHEYYLDKARKHEHTSELWAEAGKLGFLGVNLPEEYGGGGAGMYELSLVMEEMAAAGSAL-L 87 
                                    699**************998877777777888899**************************************99996.4 PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasg 112
                                    l+ v+ ++++ +i++fGt++qk+r+Lp +a+g
  gi|121636898|ref|YP_977121.1|  88 LMVVSPAINGTIIAKFGTDDQKKRWLPGIADG 119
                                    6889999***********************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                    HHHHTHHHHHHHHHHTSGH...HHHHHHHHHTTCTSTTS-GGGT CS
                  Acyl-CoA_dh_N  15 aeeelaphaaewdeegefp...relwkklaelGllgitvpeeyg 55 
                                     + e+a  a+ + ++++     +++++ ++ +Gl+     +eyg
  gi|121636898|ref|YP_977121.1| 315 GAAEAANMAKYA-AAEASSravDQAVQSMGGNGLT-----KEYG 352
                                    444444322222.2222120012345555555553.....4444 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   3.6e-22   1.6e-18       1      81 [.     124     204 ..     124     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3.6e-22
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    afa+TEp+aGs+  +++t +a+rdg +++++G+K++i++  +a+ +lv++r+e+++ ++ +  lf+vp+dapg+s ++ie
  gi|121636898|ref|YP_977121.1| 124 AFAITEPDAGSNSHKITT-TARRDGSDWIIKGQKVFISGIDQAQAVLVVGRSEEAKtGKLRPALFVVPTDAPGFSYTPIE 202
                                    79***************9.99999999************************555555588899*************9998 PP

                                    -B CS
                  Acyl-CoA_dh_M  80 ek 81 
                                     +
  gi|121636898|ref|YP_977121.1| 203 ME 204
                                    65 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   4.7     5e-13   2.2e-09       3     114 ..     248     351 ..     246     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5e-13
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                     aa a+G+ r al  +v+++++r+     +++  ++ + + la++  +++ A++++++aa+      + g+ +       
  gi|121636898|ref|YP_977121.1| 248 GAASAVGMGRFALGRAVDYVKTRKV--WSTPIGAHQGLAHPLAQCHIEVELAKLMTQKAATL----YDHGDDF--GAAEA 319
                                    5899*******************99..99*********************************....7888887..44567 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT- CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkes 114
                                    a +a+ +a+e + +avd++++++Gg++l+ke+
  gi|121636898|ref|YP_977121.1| 320 ANMAKYAAAEASSRAVDQAVQSMGGNGLTKEY 351
                                    7899************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2913.41
//
Query:       gi|121636899|ref|YP_977122.1|  [L=667]
Description: acetyl-/propionyl-coenzyme A carboxylase alpha chain subunit alpha accA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-56  191.7   0.0      2e-56  190.9   0.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.6e-39  134.9   0.1    2.7e-39  134.1   0.1    1.4  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    8.7e-28   96.6   0.0    4.9e-27   94.1   0.0    2.2  2  Biotin_carb_C    Biotin carboxylase C-terminal domain
    3.6e-18   65.2   0.3    9.8e-18   63.8   0.3    1.8  1  Biotin_lipoyl    Biotin-requiring enzyme
      1e-07   31.6   0.5    0.00014   21.6   0.3    2.9  2  Biotin_lipoyl_2  Biotin-lipoyl like
    3.6e-07   29.9   0.0    6.6e-07   29.1   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    7.3e-05   23.4   1.3      0.049   14.3   0.2    3.5  3  HlyD_3           HlyD family secretion protein
    0.00094   18.5   0.3       0.13   11.4   0.1    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.022   14.8   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
      0.024   14.9   0.3       0.11   12.7   0.1    2.2  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   0.0   1.1e-59     2e-56      30     209 ..     133     317 ..     107     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 1.1e-59
                                    HHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEE CS
                    CPSase_L_D2  30 alaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgnvit 109
                                      +++ +   Pv++ka++g+GG+Gmrv+++ + l + v++a++ea++afg+++v+ e++l   +++Ev+v++D++g+v  
  gi|121636899|ref|YP_977122.1| 133 DPDAVTTAQLPVLVKASAGGGGRGMRVVHELSALPAEVEAARREAQSAFGDPTVFCERYLPTGHHVEVQVMADTHGTVWA 212
                                    3356677789********************************************************************** PP

                                    EEEEEECCECTCCCCEEEES-SS--H..HHHHHHHHHHHHHHHHHT-EEEEEEEEEEET...TTTEEEEEEEESS--CCH CS
                    CPSase_L_D2 110 vcerenslqlrtqkvievAPsqtLtd..eerqalreaavkvvrevgvvgagtveflldp...kskeyyviEvNtRlsves 184
                                    v+ere+s q+r+qk+ie+APs+ +++    r +l  aa  +++++g++gagtvefl d    +++e+y++E+NtRl+ve+
  gi|121636899|ref|YP_977122.1| 213 VGERECSFQRRHQKIIEEAPSPLVERvpGMRAKLFDAARLAASAIGYTGAGTVEFLADDspgREGEFYFLEMNTRLQVEH 292
                                    ************************9733689**************************985566899************** PP

                                    HHHHHHHS--HHHHHHHHHTT--GC CS
                    CPSase_L_D2 185 alaekaTGldlvkeaakialgekLe 209
                                    +++e++TGldlv+ ++ ia   +L+
  gi|121636899|ref|YP_977122.1| 293 PVTEETTGLDLVELQLMIADCGRLD 317
                                    *******************988776 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.1   1.5e-42   2.7e-39       2     109 ..       3     107 ..       2     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 1.5e-42
                                    --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE-- CS
                  Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpG 81 
                                    i++vl+anrGeiA r++ ++r+lg+ tvavy+++da+++hv ead+ v+l+   +++ Yln+e+i++aa+++gadavhpG
  gi|121636899|ref|YP_977122.1|   3 ITRVLVANRGEIARRVFATCRRLGLGTVAVYTDPDAAAPHVAEADARVRLP---QTTDYLNAEAIIAAAQAAGADAVHPG 79 
                                    789***********************************************7...7789********************** PP

                                    SSTTTT-HHHHHHHHHTT-EESSS-HHH CS
                  Biotin_carb_N  82 yGflsEnaefaeaveeagivfiGPsaea 109
                                    yGflsEnaefa+av+eag++++GP+ +a
  gi|121636899|ref|YP_977122.1|  80 YGFLSENAEFAAAVQEAGLTWVGPPVDA 107
                                    ************************9876 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.0   2.8e-30   4.9e-27       1     107 [.     329     445 ..     329     446 .. 0.99
   2 ?   -1.0   0.0       1.1   1.9e+03      14      33 ..     628     647 ..     621     654 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 2.8e-30
                                    EEEEESEETTTTTEE--CE-SEEE--..........-STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHH CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelp..........egpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrr 70 
                                    eaR++aEdp+++ +p++G ++++e+p          +++g+R+dsg+  gs+vs +yD++laK++ +g+tr++a   l++
  gi|121636899|ref|YP_977122.1| 329 EARLYAEDPAHGWQPQAGVMHTIEVPgvraqfdslgQRTGIRLDSGIVDGSTVSIHYDPMLAKVVSYGATRRQAALVLAD 408
                                    89****************************************************************************** PP

                                    HHHT-EEESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                  Biotin_carb_C  71 aLaelrieGvktnieflrailedeefakgeldtkfle 107
                                    aL + r++G++tn e+l ++l++++f +g++dt+f +
  gi|121636899|ref|YP_977122.1| 409 ALVRARLHGLRTNRELLVNVLRHPAFLDGATDTGFFD 445
                                    **********************************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                    EE--CE-SEEE---STTEEE CS
                  Biotin_carb_C  14 lpssGkvtelelpegpgvRv 33 
                                    +p+ G +t++++++g++v v
  gi|121636899|ref|YP_977122.1| 628 APADGVLTHVSVNTGQQVEV 647
                                    7999*********9999977 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.3   5.4e-21   9.8e-18       4      72 ..     590     653 ..     587     654 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 5.4e-21
                                    EESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                  Biotin_lipoyl   4 ksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72 
                                     +Pm+G++++     +  +vGd+V+agq+l+ +eamKme++i ap++Gv++ + v+ G++vevg +la+
  gi|121636899|ref|YP_977122.1| 590 VAPMPGNVIR-----IGAEVGDTVTAGQPLIWLEAMKMEHTIAAPADGVLTHVSVNTGQQVEVGAILAR 653
                                    68********.....****************************************************97 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0025       4.6       7      34 ..     591     618 ..     585     624 .. 0.86
   2 !   21.6   0.3     8e-08   0.00014       4      36 ..     625     657 ..     623     659 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                Biotin_lipoyl_2   7 apvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                    ap +G V ++  + G+ V aG+ L+ l+
  gi|121636899|ref|YP_977122.1| 591 APMPGNVIRIGAEVGDTVTAGQPLIWLE 618
                                    78899999****************9876 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 8e-08
                Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsr 36 
                                    +Iaap +G+++ + V  Gq+V+ G +La+ + +
  gi|121636899|ref|YP_977122.1| 625 TIAAPADGVLTHVSVNTGQQVEVGAILARVEAP 657
                                    7***************************98865 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.7e-10   6.6e-07      31     174 ..     136     286 ..     124     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.7e-10
                                    HHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEE CS
                Dala_Dala_lig_C  31 veeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevsevge 103
                                     +++ ++pv+VK++  G   G+  v+  + l + +e+a +       d +v+ E+++  g+ +ev v+ + + +v  vge
  gi|121636899|ref|YP_977122.1| 136 AVTTAQLPVLVKASAGGGGRGMRVVHELSALPAEVEAARREaqsafgDPTVFCERYLpTGHHVEVQVMADTHGTVWAVGE 215
                                    567889**************************999999875444455899*****************************9 PP

                                    EE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEE....TTTEEEEEEEES CS
                Dala_Dala_lig_C 104 ivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflt....eegeivlnEvNt 174
                                    +    +f + ++k ++ +a   +  ++ + +++k+ ++a  a +a++ +G + v f+ +    +ege+++ E+Nt
  gi|121636899|ref|YP_977122.1| 216 REC--SFQRRHQKIIE-EAPSPLVERV-PGMRAKLFDAARLAASAIGYTGAGTVEFLADdspgREGEFYFLEMNT 286
                                    876..68899999984.4444444444.5678899999*******************963333589********9 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.9   1.1e+04      66      94 ..     258     291 ..     236     299 .. 0.65
   2 ?    5.8   0.0     0.012        22       2      28 ..     589     615 ..     588     619 .. 0.93
   3 !   14.3   0.2   2.8e-05     0.049       1      35 [.     625     659 ..     625     665 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                         HlyD_3  66 dytlkgkierisptvdaktgaykv.....evsle 94 
                                    +yt  g++e +++++  ++g +++     ++++e
  gi|121636899|ref|YP_977122.1| 258 GYTGAGTVEFLADDSPGREGEFYFlemntRLQVE 291
                                    5677899999988775556666654444444444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdell 28 
                                    l Ap  G v  + +e+g+ v+ag++l 
  gi|121636899|ref|YP_977122.1| 589 LVAPMPGNVIRIGAEVGDTVTAGQPLI 615
                                    78**********************985 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.8e-05
                         HlyD_3   1 tlrApvdGvvvelnveegevvqagdelleiippdt 35 
                                    t+ Ap dGv++ ++v+ g+ v+ g+ l+++  p++
  gi|121636899|ref|YP_977122.1| 625 TIAAPADGVLTHVSVNTGQQVEVGAILARVEAPQN 659
                                    689**************************998865 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0076        14     111     138 ..     589     616 ..     579     622 .. 0.64
   2 !   11.4   0.1   7.3e-05      0.13     108     140 ..     623     655 ..     617     659 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0076
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 111 vkapisGvVteknvreGqyvqpgdtlft 138
                                    + ap+ G V++  +  G++v++g++l+ 
  gi|121636899|ref|YP_977122.1| 589 LVAPMPGNVIRIGAEVGDTVTAGQPLIW 616
                                    4566666666666666666666666654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.3e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlftia 140
                                    + t+ ap++Gv t+ +v++Gq v+ g  l+++ 
  gi|121636899|ref|YP_977122.1| 623 EHTIAAPADGVLTHVSVNTGQQVEVGAILARVE 655
                                    556777777777777777777777777776664 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.022       4     159 ..     114     289 ..     111     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE--- CS
                    ATP-grasp_3   4 KlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie 71 
                                    K+++ k + +agv+v ++l  + ++ ++ ++ vK + G+gg ++rvv+e  ++ a +e                  ++++
  gi|121636899|ref|YP_977122.1| 114 KIESKKLMAAAGVPVLEELDPDAVTTAQLPVLVKASAGGGGRGMRVVHELSALPAEVEAARreaqsafgdptvFCERYLP 193
                                    6666666666677777**********************************999999988779999*******76777885 PP

                                    .SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEESS. CS
                    ATP-grasp_3  72 .GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel...keevvelaeevvekleglaGyvGvDlvlkd. 146
                                     G+++ v++++d++  +  +  r+   +++++ +     +p   +    + +++++a+ + +++ g  G   v+++  d 
  gi|121636899|ref|YP_977122.1| 194 tGHHVEVQVMADTHGTVWAVGERECSFQRRHQKIIEEAPSPLVERVpgmRAKLFDAARLAASAI-GYTGAGTVEFLADDs 272
                                    499********99777666666666555455555555555554333455999999999999999.999999999998887 PP

                                    .....SEEEEEEESS-- CS
                    ATP-grasp_3 147 ....eepyviEvNPRlt 159
                                        +e y++E N Rl+
  gi|121636899|ref|YP_977122.1| 273 pgreGEFYFLEMNTRLQ 289
                                    777799*********97 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8     5e+03      15      30 ..     201     216 ..     194     227 .. 0.79
   2 ?   12.7   0.1   6.1e-05      0.11      15      76 ..     588     658 ..     581     665 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                    EEEESSSEEEEEEEEE CS
                  Peptidase_M23  15 pVlAaadGtVvfagkk 30 
                                    +V+A ++GtV  +g++
  gi|121636899|ref|YP_977122.1| 201 QVMADTHGTVWAVGER 216
                                    7999999999988874 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.1e-05
                                    EEEESSSEEEEEEEEET....TT.EEEEEEEECTCEEEEEEE....ESEESS-TTEEE-TTCEEEEEBSTS CS
                  Peptidase_M23  15 pVlAaadGtVvfagkke....gy.Gnvviidhgdgystlyah....lskisvkegqkVkaGqvIGtvgstg 76 
                                    + +A++ G V+ +g +     ++   ++++++ +  +t+ a     l ++sv++gq+V+ G+++++v + +
  gi|121636899|ref|YP_977122.1| 588 SLVAPMPGNVIRIGAEVgdtvTAgQPLIWLEAMKMEHTIAAPadgvLTHVSVNTGQQVEVGAILARVEAPQ 658
                                    4789******99988323455552456666665555666655555577777***************98554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4641.60
//
Query:       gi|121636900|ref|YP_977123.1|  [L=529]
Description: acetyl-/propionyl-coa carboxylase subunit beta accD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.1e-145  484.6   0.0   3.5e-145  484.4   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
  ------ inclusion threshold ------
       0.11   11.8   0.2        0.4   10.0   0.0    1.9  2  ECH_1           Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   0.0  3.9e-149  3.5e-145       2     484 ..      46     518 ..      45     527 .. 0.96

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 3.9e-149
                                    SCTTCEEEEEEEEHTTSGGGE.BEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCE CS
                 Carboxyl_trans   2 ehprGkltareridllldpgs.FgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakge 80 
                                    +h+rGklt reri+ll+dp+s F+el+ l+++  +++      ++ ++vtg+Gav+G+++++va+d tv+gg+++p++ +
  gi|121636900|ref|YP_977123.1|  46 HHARGKLTPRERIELLVDPDSpFLELSPLAAY-GSNFQ-----IGASLVTGIGAVCGVECMIVANDPTVKGGTSNPWTLR 119
                                    89****************************99.77788.....89*********************************** PP

                                    EECHHHHHHHHHTEEEEEEEEE-ESSS.GHHSSHHHHHHHHHHHHHHHHHHH.CS-EEEEESSEEETHHHHHHHHTSEEE CS
                 Carboxyl_trans  81 kllkaqeeaikagepligindsgGaeg.riqegveslrgsGkifgenskasg.eIpqislvtgrcaGggaYlpalgdrvi 158
                                    k+l+a+++a+++++p+i +++sgGa++ +++e++      G++f++ +++s  +Ip+i+lv+g++++ggaY+p ++d+v+
  gi|121636900|ref|YP_977123.1| 120 KILRANQIAFENRLPVISLVESGGADLpTQKEIFIPG---GQMFRDLTRLSAaGIPTIALVFGNSTAGGAYVPGMSDHVV 196
                                    *************************777999999887...**************************************** PP

                                    EETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----EC CS
                 Carboxyl_trans 159 mveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivet 238
                                    m++e+sk+fl+Gp+++k+++g ee+++e+lgGa++h+++sG+a+++a d+++a+++ r++++ l+ + ++++++aP+ e+
  gi|121636900|ref|YP_977123.1| 197 MIKERSKVFLAGPPLVKMATG-EESDDESLGGAEMHARISGLADYFALDELDAIRIGRRIVARLN-WIKQGPAPAPVTEP 274
                                    *********************.*******************************************.99999******887 PP

                                    SSGSSSH..HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHH CS
                 Carboxyl_trans 239 adepdrdlieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavK 318
                                      + +  li ivP++ + p+D+reviar+vd +eF+E+k+ y++++V+G+Arl+G+p+G++An +    G vlf+++++K
  gi|121636900|ref|YP_977123.1| 275 LFDAEE-LIGIVPPDLRIPFDPREVIARIVDGSEFDEFKPLYGSSLVTGWARLHGYPLGILANAR----G-VLFSEESQK 348
                                    655555.7********************************************************8....9.********* PP

                                    HHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEE CS
                 Carboxyl_trans 319 aarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlva 398
                                    a++fi+l ++ + Pl++l++++G++vG++ e+gg++khG+++++a+++++vP+i+++++++yG+++++m+++++++++++
  gi|121636900|ref|YP_977123.1| 349 ATQFIQLANRADTPLLFLHNTTGYMVGKDYEEGGMIKHGSMMINAVSNSTVPHISLLIGASYGAGHYGMCGRAYDPRFLF 428
                                    ******************************************************************************** PP

                                    ETTT-EEESS-HHHHHHHHSHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTS CS
                 Carboxyl_trans 399 awptariaVlgpegaveilfrkekaaaemer.....kdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklv 473
                                    awp+a+ aV+g+++++++l   ++aaae+++     + +aa+r++ + ++e e + p v + + ++D vidp++tr++l 
  gi|121636900|ref|YP_977123.1| 429 AWPSAKSAVMGGAQLSGVLSIVARAAAEARGqqvdeAADAAMRAAVEGQIEAE-SLPLVLSGMLYDDGVIDPRDTRTVLG 507
                                    ****************************9998877766777799999999999.99************************ PP

                                    SSEEEHGGGHH CS
                 Carboxyl_trans 474 ialelewkkar 484
                                    ++l++ ++ + 
  gi|121636900|ref|YP_977123.1| 508 MCLSAIANGPI 518
                                    ****9998877 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.4e-05       0.4      76     117 ..     158     199 ..     145     214 .. 0.87
   2 ?   -1.6   0.1      0.15   1.4e+03      80     104 ..     390     414 ..     373     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.4e-05
                                    CHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEET CS
                          ECH_1  76 evlelwtklytvpkpviaavnGaaigGGlelalacDiviaad 117
                                    +++  +t+l+   +p+ia v G + +GG+ +  + D v++ +
  gi|121636900|ref|YP_977123.1| 158 QMFRDLTRLSAAGIPTIALVFGNSTAGGAYVPGMSDHVVMIK 199
                                    5667789999**************************998754 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.15
                                    HHHHHHHSSSEEEEEE-SEEETHHH CS
                          ECH_1  80 lwtklytvpkpviaavnGaaigGGl 104
                                      ++++++ +p i+ + Ga+ g+G+
  gi|121636900|ref|YP_977123.1| 390 MINAVSNSTVPHISLLIGASYGAGH 414
                                    567899999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3691.72
//
Query:       gi|121636901|ref|YP_977124.1|  [L=382]
Description: acyl-coa dehydrogenase fadE13 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-42  144.7   5.3    3.2e-42  144.3   5.3    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    9.1e-25   86.7   0.1    1.5e-24   86.0   0.1    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.2e-23   81.1   1.2    2.8e-22   79.5   0.1    2.4  3  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.6e-14   54.4   4.0    2.8e-14   53.5   4.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.099   12.9   0.0        0.3   11.4   0.0    1.8  2  Hpt            Hpt domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.3   5.3     9e-46   3.2e-42       1     148 [.     229     377 ..     229     379 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 9e-46
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++Gf+++ +++  eR+++aa+a+  a+r+l+ +++++r+r++fg+pli+ q+v+  laema ++++ar ++ +++e++ a
  gi|121636901|ref|YP_977124.1| 229 NSGFTQIARAFVSERIGLAAQAYSSAQRCLDLTAQWCRDRETFGRPLISRQSVQNTLAEMARRIDVARVYAHHVVERQLA 308
                                    78****************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                    g+ d  a++  aK+ a ++ ++va++a+ql+Gg+Gy++e +ver yrd+r+l ig+Gt+ei+  + a+ 
  gi|121636901|ref|YP_977124.1| 309 GETDlIAQVCFAKNTAVQAGEWVANQAVQLFGGMGYMAESEVERQYRDMRILGIGGGTTEILTALAAKT 377
                                    **************************************************************9998886 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.1   4.1e-28   1.5e-24       1      97 []     123     217 ..     123     217 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 4.1e-28
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE----- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrriee 80 
                                    a+a+TEp++Gsdv  ++t  a rdg++yv+nG+K++it++  a+++++ +rt++p  a g+sl++v++d+pg++v+r+ +
  gi|121636901|ref|YP_977124.1| 123 ALAITEPGGGSDVGHLRT-SAVRDGDHYVINGAKTYITSGVRADYVVTAVRTGGPG-AAGVSLLVVEKDTPGFEVTRKLD 200
                                    79****************.77778888************************99999.******************9999* PP

                                    BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  81 klGlrglptgelvfedv 97 
                                    k+G r+ +t+el+++dv
  gi|121636901|ref|YP_977124.1| 201 KMGWRSSDTAELCYTDV 217
                                    *************9987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.1   7.7e-26   2.8e-22       1     113 []       6     119 ..       6     119 .. 0.94
   2 ?   -2.1   0.0       1.6   5.8e+03       7      26 ..     232     251 ..     227     266 .. 0.66
   3 ?   -1.8   0.0       1.4   4.9e+03      41      42 ..     309     310 ..     278     348 .. 0.50

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 7.7e-26
                                    THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                    t+e ++lr+tvr+fae+e+ ph++ew++ ge pr l++ ++++Gllg  +pe++gG g+d  + +i++ee+ +a+a++++
  gi|121636901|ref|YP_977124.1|   6 TPERQQLRKTVRAFAEREILPHVDEWERIGELPRGLHRLAGAAGLLGAGFPEAVGGGGGDGADPVIICEEMHQAGAPGGV 85 
                                    799***************************************************************************** PP

                                    HHHH.HHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  81 llgv.hsslvapailrfGteeqkrryLpklasge 113
                                    + ++   ++++p +++ G e   + y+++ ++ge
  gi|121636901|ref|YP_977124.1|  86 YASLfTCGIAVPHMVASGDERLIATYVRPTLAGE 119
                                    66662666666********************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHTHHHHHHH CS
                  Acyl-CoA_dh_N   7 lrdtvrefaeeelaphaaew 26 
                                    + + +r+f++e++   a+ +
  gi|121636901|ref|YP_977124.1| 232 FTQIARAFVSERIGLAAQAY 251
                                    56678999999985434333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.4
                                    HH CS
                  Acyl-CoA_dh_N  41 ae 42 
                                    +e
  gi|121636901|ref|YP_977124.1| 309 GE 310
                                    33 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   4.0   7.9e-18   2.8e-14       2     127 ..     245     361 ..     244     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 7.9e-18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                    g+aa+a   A+++l+ ++++ r+r +  +g++l  ++ +q +lae+a r+d Ar   +++++r      ag+    ++ a
  gi|121636901|ref|YP_977124.1| 245 GLAAQAYSSAQRCLDLTAQWCRDRET--FGRPLISRQSVQNTLAEMARRIDVARVYAHHVVER----QLAGET---DLIA 315
                                    678888889*****************..***********************************....455554...5689 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                    +   a+ +av+    +++++++++Gg+++ +es+++R++RD+++++
  gi|121636901|ref|YP_977124.1| 316 QVCFAKNTAVQAGEWVANQAVQLFGGMGYMAESEVERQYRDMRILG 361
                                    9999**************************************9875 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.4e-05       0.3      21      45 ..      24      53 ..       7      58 .. 0.75
   2 ?   -4.3   0.0         5   1.8e+04       4      15 ..     282     293 ..     279     298 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                                   H.....SCCHHHHHHHHHHHHHHHHHHTTB CS
                            Hpt 21 l.....dqedlqelaraaHtLKGsagmlGl 45
                                   +     + e + el r +H+L+G+ag lG+
  gi|121636901|ref|YP_977124.1| 24 IlphvdEWERIGELPRGLHRLAGAAGLLGA 53
                                   146555667889999*************97 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 5
                                    HHHHHHHHHHHH CS
                            Hpt   4 elfleeaeelle 15 
                                    +  l+e++ +++
  gi|121636901|ref|YP_977124.1| 282 QNTLAEMARRID 293
                                    566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2840.36
//
Query:       gi|121636902|ref|YP_977125.1|  [L=560]
Description: hypothetical protein BCG_1030c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   7.1e-130  432.8   0.0   9.2e-130  432.4   0.0    1.1  1  AtuA        Acyclic terpene utilisation family protein AtuA
  ------ inclusion threshold ------
      0.019   15.1   0.1       0.05   13.7   0.1    1.7  1  sCache_3_2  Single cache domain 3


Domain annotation for each model (and alignments):
>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.4   0.0    1e-133  9.2e-130       1     338 [.       3     329 ..       3     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 432.4 bits;  conditional E-value: 1e-133
                           AtuA   1 ignasGfagDrveaalelaekgeldvlvgdylaEltialaakrkkkdpekgyeptllealekllpelaekgikvvtnaGa 80 
                                    ign+sGf+gDr++a++e+++ geld+l+gdylaElt+ +  ++++k+p++gy++t+l++le++l  ++++g+++vtnaG+
  gi|121636902|ref|YP_977125.1|   3 IGNCSGFYGDRLSAMREMLTGGELDYLTGDYLAELTMLILGRDRMKNPDRGYAKTFLAQLEDCLGLAHDRGVRIVTNAGG 82 
                                    9******************************************************************************* PP

                           AtuA  81 lnpkalaekvaelakelglkkelkvavveGDdvlekveelleegelleegeelvsanaYlGaegIveALeagAdiVitGR 160
                                    lnp++la++v++la++lg+    +va+veGDd+++++ el           ++++anaYlGa+gIv+++e+gAd+V+tGR
  gi|121636902|ref|YP_977125.1|  83 LNPAGLANAVRALAARLGIP--AQVAHVEGDDLQPRAAELGLG--------TPLTANAYLGAWGIVDCFERGADVVVTGR 152
                                    *******************4..8**********9999995554........699************************** PP

                           AtuA 161 vaDaslvlapaawefgWkeddydelAgalvaGhllECgaqvtGGnfagfkevedlanlgfPiaeisadGevvitkeegtg 240
                                    v+Das+v+++aa +fgW ++dy++lAga+vaGh++ECg q+tGGn+a+f+e+ dl++ gfP+aei+adG+ vitk++gtg
  gi|121636902|ref|YP_977125.1| 153 VTDASVVVGAAAAHFGWGRTDYHRLAGAVVAGHVIECGVQATGGNYAFFTEIGDLTHAGFPLAEIAADGSSVITKHHGTG 232
                                    ******************************************************************************** PP

                           AtuA 241 GlvtvdtvkeqllYEiqgpalYlnpDvvadlseveleqvgedrVrvsgvkgepppptlkvavtykggyqaeaelslaGld 320
                                    Glv+vdt+++qllYEi+g  +Y npDv+a++++vel+  g+drVr+sgv geppppt+kv+++  gg+++ ++++l+Gld
  gi|121636902|ref|YP_977125.1| 233 GLVSVDTITAQLLYEITGA-RYANPDVTARMDSVELSPDGPDRVRISGVIGEPPPPTYKVSLNSIGGFRNAMTFVLTGLD 311
                                    *******************.************************************************************ PP

                           AtuA 321 aeekaelaeeqvrerlek 338
                                    +++ka+l+++q++++l+ 
  gi|121636902|ref|YP_977125.1| 312 IDAKADLVRRQLEAALTV 329
                                    *************99973 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.5e-06      0.05      68     119 ..     358     413 ..     311     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-06
                     sCache_3_2  68 h....pdpaevgrklsgpataaalkagrayvgtvtgtlgpslrvklPvfdadgrvi 119
                                         pdpa+vgr++s+ a + al++ + ++ t+ +++g+++ v++P   + g+v+
  gi|121636902|ref|YP_977125.1| 358 CvardPDPANVGRQFSSAAVELALASYPGFTATAPPGDGQVYGVFTPGYVDAGKVA 413
                                    144469*********9999999*************************777788875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4174.30
//
Query:       gi|121636903|ref|YP_977126.1|  [L=923]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-29  100.2  12.6    9.4e-29   99.6  12.6    1.3  1  PE              PE family
  ------ inclusion threshold ------
       0.12   12.9   3.3        0.2   12.1   3.3    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6  12.6   1.1e-32   9.4e-29       1      91 [.       1      91 [.       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.1e-32
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv+aP +la+aa+dl gi+s +s+ana aa  tta+++aaaDeVSaaiAalfs++a++yq+ls q++afh qf+q+l++
  gi|121636903|ref|YP_977126.1|  1 MSFVVTAPPVLASAASDLGGIASMISEANAMAAVRTTALAPAAADEVSAAIAALFSSYARDYQTLSVQVTAFHVQFAQTLTN 82
                                   9********************************************************************************* PP

                                   HHHHHHS-- CS
                             PE 83 aagsYaaaE 91
                                   a++ Ya  +
  gi|121636903|ref|YP_977126.1| 83 AGQLYAVVD 91
                                   *****9887 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.3   2.3e-05       0.2       9      95 ..       8      95 ..       2     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                  T7SS_ESX_EspC  9 pdhlrelaakhdevaaeiasavaaaagasaavlds.hGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYea 89
                                   p +l ++a++++++a+ i+ a+a+aa +++a+++     ++aa ++ ++++ ++ ++   ++ a + ++a+ L+ A ++Y  
  gi|121636903|ref|YP_977126.1|  8 PPVLASAASDLGGIASMISEANAMAAVRTTALAPAaADEVSAAIAALFSSYARDYQTLSVQVTAFHVQFAQTLTNAGQLYAV 89
                                   557999*******************777777766515579999*************************************** PP

                  T7SS_ESX_EspC 90 tDeeaa 95
                                   +D  ++
  gi|121636903|ref|YP_977126.1| 90 VDVGNG 95
                                   **9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.50
# Mc/sec: 5516.82
//
Query:       gi|121636904|ref|YP_977127.1|  [L=335]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-30  102.8  19.7    2.3e-29  101.5  19.7    1.7  1  PE        PE family
    1.1e-13   50.4  11.2    9.3e-07   28.6   0.8    3.4  3  NHL       NHL repeat
    0.00054   19.6   0.9        0.1   12.2   0.0    2.7  2  SGL       SMP-30/Gluconolactonase/LRE-like region
  ------ inclusion threshold ------
      0.016   15.5   4.8        4.3    7.7   0.4    3.8  3  Kelch_3   Galactose oxidase, central domain
       0.14   11.6   0.2       0.21   11.1   0.2    1.2  1  DUF2884   Protein of unknown function (DUF2884)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5  19.7   6.5e-33   2.3e-29       1      93 []       1      92 [.       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 6.5e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+vaP+++++aaad a+igsa+++an+aaaa+t+ vl aa+DeVS+aiAalf++h+q+yqa+saq+aa +e+fv al++
  gi|121636904|ref|YP_977127.1|  1 MSFVNVAPQLVSTAAADAARIGSAINTANTAAAATTQ-VLVAAQDEVSTAIAALFGSHGQHYQAISAQVAAYQERFVLALSQ 81
                                   9******************************998666.******************************************** PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a+++Ya aEaa
  gi|121636904|ref|YP_977127.1| 82 AGSTYAVAEAA 92
                                   *********97 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.8   2.6e-10   9.3e-07       1      27 [.     221     247 ..     221     248 .. 0.95
   2 !   15.1   0.3   4.8e-06     0.017       2      27 ..     264     290 ..     264     291 .. 0.94
   3 !   12.7   0.3   2.9e-05       0.1       4      19 ..     309     325 ..     308     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.6e-10
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    fn+PhGvav+++G++yV+++++ +v v
  gi|121636904|ref|YP_977127.1| 221 FNDPHGVAVNPGGNVYVTNFGSGTVSV 247
                                    9********************999987 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.8e-06
                                    SSEEEEEEE.TTTEEEEEECCCTEEEE CS
                            NHL   2 nyPhGvavd.snGdiyVaDsenhrvqv 27 
                                    n P+Gvav+  +G ++V+++ +++v v
  gi|121636904|ref|YP_977127.1| 264 NGPSGVAVSpVTGLVFVTNFDSNTVSV 290
                                    68********************99987 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2.9e-05
                                    EEEEEEE.TTTEEEEEE CS
                            NHL   4 PhGvavd.snGdiyVaD 19 
                                    P+Gvav+  +G++yV++
  gi|121636904|ref|YP_977127.1| 309 PTGVAVNpVTGEVYVTN 325
                                    9***************8 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.8e-05       0.1     176     215 ..     216     254 ..     203     261 .. 0.77
   2 !    5.1   0.1    0.0041        15     183     243 ..     264     324 ..     255     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                            SGL 176 fadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpd.Gk 215
                                    + + + ++  p G+av   Gnv+v+ +g+g+v++++p+  +
  gi|121636904|ref|YP_977127.1| 216 ITHASFND--PHGVAVNPGGNVYVTNFGSGTVSVINPAtNT 254
                                    44444443..99*************************9444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0041
                            SGL 183 egepDGlavDa.eGnvwvAvwgggkvvrfdpd.Gkliee.iklpakrvtscaFgGpdlrtLyit 243
                                    +g p G+av   +G v+v+ +++++v+++dp   ++++  i++  + +t +a   p   ++y+t
  gi|121636904|ref|YP_977127.1| 264 NG-PSGVAVSPvTGLVFVTNFDSNTVSVIDPTtNTVTGSpITV-GTAPTGVAV-NPVTGEVYVT 324
                                    44.8899***99*******************966666541333.467777774.5666666666 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0031        11      13      40 ..     237     268 ..     232     273 .. 0.80
   2 ?    7.7   0.4    0.0012       4.3       8      39 ..     275     310 ..     274     315 .. 0.78
   3 ?    0.6   0.1      0.21   7.4e+02      15      31 ..     315     331 ..     306     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0031
                        Kelch_3  13 dgqdrlndvyvydldtntWa....eiaslppa 40 
                                     ++ ++++v v++++tnt++    +i++ p++
  gi|121636904|ref|YP_977127.1| 237 VTNFGSGTVSVINPATNTVTgspiTIGNGPSG 268
                                    578999**************776666888885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                        Kelch_3   8 GGlgddgqdrlndvyvydldtntWa....eiaslpp 39 
                                    +Gl + ++  +n+v v+d+ tnt++    ++++ p+
  gi|121636904|ref|YP_977127.1| 275 TGLVFVTNFDSNTVSVIDPTTNTVTgspiTVGTAPT 310
                                    678888999***************955433366665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                        Kelch_3  15 qdrlndvyvydldtntW 31 
                                    ++++++vyv +++ +t+
  gi|121636904|ref|YP_977127.1| 315 NPVTGEVYVTNFAGDTV 331
                                    7899*****99988875 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.7e-05      0.21      67     136 ..      33     102 ..      29     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                        DUF2884  67 elasdgvdlAsdaldevltellgedsevaeklktkldelkarvkekfykdgdklvlgaqslesldeafdk 136
                                    + ++ ++  A+d ++++++ l+g+  + ++ ++++++ +++r    ++++g+++ ++++++++  +++++
  gi|121636904|ref|YP_977127.1|  33 AATTQVLVAAQDEVSTAIAALFGSHGQHYQAISAQVAAYQERFVLALSQAGSTYAVAEAASATPLQQIEQ 102
                                    556778899*********************************************9999888764444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2108.05
//
Query:       gi|121636905|ref|YP_977128.1|  [L=64]
Description: hypothetical protein BCG_1033c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 476.59
//
Query:       gi|121636906|ref|YP_977129.1|  [L=57]
Description: 50S ribosomal protein L32 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.0   3.9    2.3e-11   43.8   3.9    1.0  1  Ribosomal_L32p  Ribosomal L32p protein family
      0.002   17.9   0.7     0.0033   17.2   0.7    1.5  1  N36             36-mer N-terminal peptide of the N protein (N


Domain annotation for each model (and alignments):
>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   3.9   2.6e-15   2.3e-11       1      44 [.       2      46 ..       2      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.6e-15
                                   S--SS---HHHHHHHGGGT------EEEETTTC.CEECTTC-BTT CS
                 Ribosomal_L32p  1 AVPKrKtSksrrrkRrahwklkapnlvecpncg.elklpHrvcps 44
                                   AVPKr++S+s++r+Rr++wk+    lv  ++ g ++k+p+r++++
  gi|121636906|ref|YP_977129.1|  2 AVPKRRKSRSNTRSRRSQWKAAKTELVGVTVAGhAHKVPRRLLKA 46
                                   9******************************998999****9876 PP

>> N36  36-mer N-terminal peptide of the N protein (N36)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.7   3.7e-07    0.0033       6      28 ..       6      31 ..       2      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-07
                                   HHHHTHH...HHHHHHCTSCCGCCSS CS
                            N36  6 RRERRAE...KqAqWKAAnPLLvGvs 28
                                   RR  R +   +  qWKAA   LvGv 
  gi|121636906|ref|YP_977129.1|  6 RRKSRSNtrsRRSQWKAAKTELVGVT 31
                                   4444443122679***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 441.11
//
Query:       gi|121636907|ref|YP_977130.1|  [L=457]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-30  103.0  21.3    1.6e-29  102.1  21.3    1.5  1  PE              PE family
    1.8e-15   56.1  16.6    2.4e-06   27.3   0.6    4.4  4  NHL             NHL repeat
    5.1e-05   23.4   6.5        2.2    8.7   0.1    4.6  3  Kelch_3         Galactose oxidase, central domain
    0.00074   19.0   0.6          8    6.1   0.0    4.0  3  Kelch_1         Kelch motif
  ------ inclusion threshold ------
      0.079   13.2   0.3        9.1    6.6   0.0    3.0  4  Arylesterase    Arylesterase
        0.2   11.1   0.2       0.32   10.5   0.2    1.2  1  DUF2884         Protein of unknown function (DUF2884)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1  21.3   5.3e-33   1.6e-29       1      93 []       1      92 [.       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 5.3e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+vaP+++++aaad a+igsa+++an+aaaa+t+ vlaaa+DeVS+aiAalf++h+q+yqa+saq+aa +e+fv al++
  gi|121636907|ref|YP_977130.1|  1 MSFVNVAPQLVSTAAADAARIGSAINTANTAAAATTQ-VLAAAQDEVSTAIAALFGSHGQHYQAISAQVAAYQERFVLALSQ 81
                                   9******************************998666.******************************************** PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a+++Ya aEaa
  gi|121636907|ref|YP_977130.1| 82 ASSTYAVAEAA 92
                                   *********97 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.6   8.1e-10   2.4e-06       1      27 [.     291     317 ..     291     318 .. 0.92
   2 !   14.6   0.3   8.5e-06     0.025       2      27 ..     333     359 ..     333     360 .. 0.94
   3 !   12.9   0.2   2.9e-05     0.087       6      20 ..     379     394 ..     378     400 .. 0.86
   4 !   10.8   0.6   0.00013       0.4       3      20 ..     418     436 ..     417     436 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.1e-10
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    fn+PhGvav+++G+iyV++ ++++v v
  gi|121636907|ref|YP_977130.1| 291 FNDPHGVAVNPGGNIYVTNQGSNTVSV 317
                                    9******************99888876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.5e-06
                                    SSEEEEEEE.TTTEEEEEECCCTEEEE CS
                            NHL   2 nyPhGvavd.snGdiyVaDsenhrvqv 27 
                                    n P+Gvav+  +G ++V+++ +++v v
  gi|121636907|ref|YP_977130.1| 333 NGPSGVAVSpVTGLVFVTNFDSNTVSV 359
                                    68********************99987 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 2.9e-05
                                    EEEEETTTEEEEEE.C CS
                            NHL   6 GvavdsnGdiyVaD.s 20 
                                    Gvav+++G+iyV++ +
  gi|121636907|ref|YP_977130.1| 379 GVAVNPGGNIYVTNqF 394
                                    9************974 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00013
                                    SEEEEEEE.TTTEEEEEEC CS
                            NHL   3 yPhGvavd.snGdiyVaDs 20 
                                    +P+Gvav+  +G +yV++s
  gi|121636907|ref|YP_977130.1| 418 DPTGVAVNpVTGVVYVTNS 436
                                    6***************985 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00074       2.2      14      40 ..     308     337 ..     302     342 .. 0.80
   2 !    7.8   0.2    0.0013         4       8      34 ..     344     370 ..     343     383 .. 0.82
   3 !    7.2   0.2    0.0021       6.3      14      34 ..     391     411 ..     384     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00074
                        Kelch_3  14 gqdrlndvyvydldtntWaei...aslppa 40 
                                    +++++n+v v+d++tnt++ +   ++ p++
  gi|121636907|ref|YP_977130.1| 308 TNQGSNTVSVIDPVTNTVTGSitdGNGPSG 337
                                    6899***************44355887775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                        Kelch_3   8 GGlgddgqdrlndvyvydldtntWaei 34 
                                    +Gl + ++  +n+v v+d++tnt++ +
  gi|121636907|ref|YP_977130.1| 344 TGLVFVTNFDSNTVSVIDPNTNTVTGS 370
                                    678888999**************9954 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0021
                        Kelch_3  14 gqdrlndvyvydldtntWaei 34 
                                    +++++n+v v+d++tnt++ +
  gi|121636907|ref|YP_977130.1| 391 TNQFSNTVSVIDPATNTVTGS 411
                                    699**************9965 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0032       9.5      23      38 ..     309     324 ..     295     326 .. 0.85
   2 ?    2.3   0.1     0.041   1.2e+02      26      38 ..     354     366 ..     345     368 .. 0.89
   3 !    6.1   0.0    0.0027         8      23      38 ..     392     407 ..     377     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0032
                                    SSBEEEEEEEETTTTE CS
                        Kelch_1  23 gnalssvevyDpetnt 38 
                                    ++ +++v v+Dp+tnt
  gi|121636907|ref|YP_977130.1| 309 NQGSNTVSVIDPVTNT 324
                                    7899***********8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.041
                                    EEEEEEEETTTTE CS
                        Kelch_1  26 lssvevyDpetnt 38 
                                    +++v v+Dp tnt
  gi|121636907|ref|YP_977130.1| 354 SNTVSVIDPNTNT 366
                                    79**********8 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0027
                                    SSBEEEEEEEETTTTE CS
                        Kelch_1  23 gnalssvevyDpetnt 38 
                                    ++++++v v+Dp tnt
  gi|121636907|ref|YP_977130.1| 392 NQFSNTVSVIDPATNT 407
                                    89*************8 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   3.4e+03      51      78 ..     289     315 ..     284     323 .. 0.74
   2 ?    2.8   0.0     0.046   1.4e+02      54      80 ..     333     359 ..     321     365 .. 0.80
   3 ?   -3.2   0.0       3.5     1e+04      67      80 ..     387     400 ..     377     406 .. 0.65
   4 ?    6.6   0.0     0.003       9.1      56      79 ..     419     442 ..     414     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                   Arylesterase  51 sglssanGInidadkkyiyvadilresi 78 
                                    ++++ + G+ +++    iyv++   + +
  gi|121636907|ref|YP_977130.1| 289 ASFNDPHGVAVNPGG-NIYVTNQGSNTV 315
                                    578888999998876.479987666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                   Arylesterase  54 ssanGInidadkkyiyvadilresihv 80 
                                    + + G+ ++++   ++v++   + + v
  gi|121636907|ref|YP_977130.1| 333 NGPSGVAVSPVTGLVFVTNFDSNTVSV 359
                                    5699**************988887766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                   Arylesterase  67 yiyvadilresihv 80 
                                     iyv++   + + v
  gi|121636907|ref|YP_977130.1| 387 NIYVTNQFSNTVSV 400
                                    47888777776655 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.003
                   Arylesterase  56 anGInidadkkyiyvadilresih 79 
                                    ++G+ ++++  ++yv+++l++ + 
  gi|121636907|ref|YP_977130.1| 419 PTGVAVNPVTGVVYVTNSLDDTVS 442
                                    9******************99875 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00011      0.32      67     132 ..      33      98 ..      29     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                        DUF2884  67 elasdgvdlAsdaldevltellgedsevaeklktkldelkarvkekfykdgdklvlgaqsleslde 132
                                    + ++ +++ A+d ++++++ l+g+  + ++ ++++++ +++r    ++++++++ ++++++++  +
  gi|121636907|ref|YP_977130.1|  33 AATTQVLAAAQDEVSTAIAALFGSHGQHYQAISAQVAAYQERFVLALSQASSTYAVAEAASATPLQ 98 
                                    56678899*********************************************9999888876444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2526.30
//
Query:       gi|121636908|ref|YP_977131.1|  [L=230]
Description: two component response transcriptional regulatory protein MprA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-31  108.8   0.0    2.1e-31  108.4   0.0    1.2  1  Response_reg  Response regulator receiver domain
    6.4e-26   90.2   0.1    2.2e-25   88.5   0.1    1.9  2  Trans_reg_C   Transcriptional regulatory protein, C terminal
     0.0014   19.0   0.0     0.0019   18.6   0.0    1.2  1  FleQ          Flagellar regulatory protein FleQ
      0.004   17.4   0.0     0.0068   16.7   0.0    1.3  1  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.0   4.7e-35   2.1e-31       1     111 [.       5     114 ..       5     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 4.7e-35
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    +l+vdDd++vre lr+ l  +gy +v+ a dg eal+++ ++++d ++lD++mp++dGle+++++r + ++lp+++lta+
  gi|121636908|ref|YP_977131.1|   5 ILVVDDDRAVRESLRRSLSFNGY-SVELAHDGVEALDMIASDRPDALVLDVMMPRLDGLEVCRQLRSTGDDLPILVLTAR 83 
                                    8**********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++ +++v++l+agadd+l Kpf+ eeLl+++
  gi|121636908|ref|YP_977131.1|  84 DSVSERVAGLDAGADDYLPKPFALEELLARM 114
                                    ***************************9986 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.85   3.8e+03      45      60 ..     106     121 ..      94     126 .. 0.71
   2 !   88.5   0.1     5e-29   2.2e-25       2      77 .]     151     225 ..     149     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.85
                                    HHHHHHHHHHHHHHTT CS
                    Trans_reg_C  45 tvdvhisrLRkkLedd 60 
                                    +++   +r+R  L+ +
  gi|121636908|ref|YP_977131.1| 106 ALEELLARMRALLRRT 121
                                    5666778888888774 PP

  == domain 2  score: 88.5 bits;  conditional E-value: 5e-29
                                    EEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   2 eeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    ++++lt++ef+lLe+L++np+rv++r ++leevwg d+ ++ ++++v++ +LR+k e+d+ +prlI+tvrgvGY+l
  gi|121636908|ref|YP_977131.1| 151 RRISLTRTEFALLEMLIANPRRVLTRSRILEEVWGFDFPTSGNALEVYVGYLRRKTEADG-EPRLIHTVRGVGYVL 225
                                    569*******************************************************87.99***********87 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.2e-07    0.0019       1      82 [.       4      88 ..       4     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-07
                           FleQ  1 kiLvidddaerrrdletiLeFlgeeveavsseel.saaleesssealavilgsvs.sleealealaekdphlPvlllgesde 80
                                   +iLv+ddd + r+ l   L+F g +ve+  +     +  ++++ +al++          e +++l ++   lP+l+l+ +d+
  gi|121636908|ref|YP_977131.1|  4 RILVVDDDRAVRESLRRSLSFNGYSVELAHDGVEaLDMIASDRPDALVLDVMMPRlDGLEVCRQLRSTGDDLPILVLTARDS 85
                                   69***********************99988764436667777777777766666666899******************9998 PP

                           FleQ 81 a.e 82
                                     e
  gi|121636908|ref|YP_977131.1| 86 VsE 88
                                   844 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0068       7      74 ..      16      86 ..      11      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                     OKR_DC_1_N  7 relaealekegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetr.t 74
                                   ++l ++l+ +g++v  +++  ++l +i +  r +a+vl+v     +  e+++++r ++ dlP+ +l+ ++  
  gi|121636908|ref|YP_977131.1| 16 ESLRRSLSFNGYSVELAHDGVEALDMIAS-DRPDALVLDVMmprLDGLEVCRQLRSTGDDLPILVLTARDsV 86
                                   5788899999*****************99.799********9999999******************997744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1508.37
//
Query:       gi|121636909|ref|YP_977132.1|  [L=504]
Description: two component sensor kinase mprB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-20   73.3   0.0    3.6e-20   72.5   0.0    1.4  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A
    9.2e-13   48.4   1.7    2.4e-12   47.0   1.7    1.8  1  HAMP       HAMP domain
    1.8e-11   43.9   0.2    4.6e-11   42.6   0.2    1.7  1  HisKA      His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   6.1e-24   3.6e-20       1     109 [.     351     463 ..     351     466 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 6.1e-24
                                    EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHH CS
                      HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGls 79 
                                    gd  +L ++  nl+dNa+k ++++g++ v++++ +  + ++ v+D G+Gip++++ ++fe+f++ ++++r   g+GlGl+
  gi|121636909|ref|YP_977132.1| 351 GDTAGLSRMALNLMDNAAKWSPPGGHVGVRLSQlDASHAELVVSDRGPGIPVQERRLVFERFYR-SASARALPGSGLGLA 429
                                    68899***************99**********75338***************************.99************* PP

                                    HHHHHHHHTTTEEEEEEET.TT...EEEEEEEEE CS
                      HATPase_c  80 ivkklvelmgGeiwvesep.gr...Gttftftlp 109
                                    ivk++v  +gG +++e+++ g+   Gt++++ lp
  gi|121636909|ref|YP_977132.1| 430 IVKQVVLNHGGLLRIEDTDpGGqppGTSIYVLLP 463
                                    ****8888*******7777522466999999887 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   1.7     4e-16   2.4e-12       2      52 ..     184     234 ..     183     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 4e-16
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    ++r+ lrP+ rL++aa+r+a+ d   ++pv g DE+++L +afN Ml++L 
  gi|121636909|ref|YP_977132.1| 184 VTRAGLRPVGRLTEAAERVARTDDLRPIPVFGSDELARLTEAFNLMLRALA 234
                                    79*******************998888*********************995 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.2   7.7e-15   4.6e-11       2      67 .]     240     311 ..     239     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 7.7e-15
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC..........T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre........gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                    + r++ +  HELrtPL++++ n+e+L+ +        +k  +e  ++ +++  +++ l+ lv dl dlsr +ag
  gi|121636909|ref|YP_977132.1| 240 QARLVTDAGHELRTPLTSLRTNVELLMASmapgaprlPK--QEMVDLRADVLAQIEELSTLVGDLVDLSRGDAG 311
                                    579***********************9999888754333..555569***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3137.81
//
Query:       gi|121636910|ref|YP_977133.1|  [L=464]
Description: serine protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-34  119.2   3.7    2.7e-34  119.2   3.7    2.5  3  Trypsin_2      Trypsin-like peptidase domain
    1.4e-15   57.3   1.2      3e-15   56.3   1.2    1.6  1  PDZ_2          PDZ domain
    1.7e-13   50.9   0.1    1.7e-13   50.9   0.1    1.8  2  Trypsin        Trypsin
    4.3e-06   26.5   1.1    1.3e-05   25.0   1.1    1.9  1  PDZ_6          PDZ domain
    5.3e-06   26.7   0.3    1.5e-05   25.3   0.3    1.8  1  PDZ            PDZ domain
    0.00062   18.6   1.3       0.66    8.5   0.0    2.1  2  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
      0.025   14.6   0.3      0.084   12.9   0.3    2.0  1  Tricorn_PDZ    Tricorn protease PDZ domain
        0.1   12.6   0.0       0.23   11.5   0.0    1.6  1  PDZ_1          PDZ-like domain


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   2.7         8   1.8e+04     131     140 ..     131     138 ..      19     143 .. 0.68
   2 !  119.2   3.7   1.2e-37   2.7e-34       1     150 []     181     331 ..     181     331 .. 0.94
   3 ?   -1.3   0.2       1.6   3.7e+03      55     105 ..     410     460 ..     369     463 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8
                      Trypsin_2 131 tspGsSGGpl 140
                                       G SGGp+
  gi|121636910|ref|YP_977133.1| 131 A--GPSGGPV 138
                                    2..6677777 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 1.2e-37
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsea 80 
                                    GsG++++++glilTn+Hv++ a++ +  ++  k +++++dgr+ p +vv+adp +D+A+++v  +  +gl p+ lg+s++
  gi|121636910|ref|YP_977133.1| 181 GSGIILSAEGLILTNNHVIAAAAKPPLGSPPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRV--QGVSGLTPISLGSSSD 258
                                    9**************************99*********************************..**************** PP

                      Trypsin_2  81 lkggepvyvvGyplggeksgsvssGivsgvve.....sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                    l++g+pv ++G plg e+  +v++Givs++++     +e  ++++  + +qtdaa++pG+SGG+l++ + ++vG+
  gi|121636910|ref|YP_977133.1| 259 LRVGQPVLAIGSPLGLEG--TVTTGIVSALNRpvsttGEAGNQNTVLDAIQTDAAINPGNSGGALVNMNAQLVGV 331
                                    ******************..9*************5555555555555555************************8 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.6
                      Trypsin_2  55 lDlAllkvssderaglpplplgpsealkggepvyvvGyplggeksgsvssG 105
                                    + + + kv++++ ++ ++l ++ +++++g + +  ++ p+gg +  +v+ G
  gi|121636910|ref|YP_977133.1| 410 KGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLG 460
                                    366677775555555555555555555555555555667777776666666 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   1.2   1.3e-18     3e-15       2      82 .]     378     459 ..     377     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.3e-18
                                    ...XX------..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEE.TTEEEEEEE CS
                          PDZ_2   2 ylGvsvsdeedtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlR.dgkkktvev 80 
                                     lGv+v++++dt g+ +v+V  gg aa+ag+ +g v++kvd+++++s + l  ++++k pG tV lt++   g  +tv+v
  gi|121636910|ref|YP_977133.1| 378 SLGVQVTNDKDTPGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDpSGGSRTVQV 457
                                    79*******************************************************************97788888888 PP

                                    E- CS
                          PDZ_2  81 kl 82 
                                    +l
  gi|121636910|ref|YP_977133.1| 458 TL 459
                                    86 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.3   5.1e+03     177     188 ..     130     141 ..     121     143 .. 0.79
   2 !   50.9   0.1   7.4e-17   1.7e-13      24     216 ..     179     360 ..     155     365 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.3
                                    TTTTTTSEEEET CS
                        Trypsin 177 cqGDSGGPlvcs 188
                                     +G SGGP+ +s
  gi|121636910|ref|YP_977133.1| 130 PAGPSGGPVAAS 141
                                    5799****9876 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 7.4e-17
                                    EEEEEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBS CS
                        Trypsin  24 khlCgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgd 102
                                    ++  +G+++s++  +lT++H++    + k+ lg+   k + +   ++ ++ ++v  + +p     Dia+++++      +
  gi|121636910|ref|YP_977133.1| 179 EE-GSGIILSAEgLILTNNHVIAA--AAKPPLGSPPPKTTVTF-SDGRTAPFTV-VGADPT---SDIAVVRVQGV----S 246
                                    33.4455665555**********8..77777888444444443.2333333222.245555...5*********8....9 PP

                                    SBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHH.HHHHH.TTTTSTTTEEEEESTTSSSBCTTTT CS
                        Trypsin 103 tvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsre.tcksa.ykgkvtenmlcagakeggkdacqGD 180
                                       pi+l + ss+l vg+ +l++G +    +g   t++++ v++++r  + + +  ++++  + ++++a     ++++G+
  gi|121636910|ref|YP_977133.1| 247 GLTPISLGS-SSDLRVGQPVLAIGSPLG-LEG---TVTTGIVSALNRPvSTTGEaGNQNTVLDAIQTDA-----AINPGN 316
                                    9********.888*************96.444...6888888888887333333344445566688888.....****** PP

                                    TTSEEEETTTEEEEEEEEE..SSSSCTTS......EEEEEEGGG CS
                        Trypsin 181 SGGPlvcsdgelvGivswg..kgcakgnr......pgvytkvss 216
                                    SGG+lv+++ +lvG++s+    g ++++        g++++v++
  gi|121636910|ref|YP_977133.1| 317 SGGALVNMNAQLVGVNSAIatLGADSADAqsgsigLGFAIPVDQ 360
                                    *****************775433333322334556666666665 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   1.1   5.6e-09   1.3e-05       2      54 ..     394     445 ..     393     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.6e-09
                          PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlvv 54 
                                    + +V++g+ A++AG+  G ++++v+++p+   s + ++a++r  ++g  v l++
  gi|121636910|ref|YP_977133.1| 394 IVEVVAGGAAANAGVPKGVVVTKVDDRPI--NSADALVAAVRsKAPGATVALTF 445
                                    678**************************..***********666666666666 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   6.5e-09   1.5e-05       6      80 ..     373     444 ..     368     446 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.5e-09
                                    TSTTSESSEEEEEETTSSSSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEE CS
                            PDZ   6 kegrgglGfslkggsdqrgdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLt 80 
                                    k ++ +lG+++  ++d    +g+ + ev++ggaa+ +g+ +G ++++v+++++++   + a+   k ++ +v+Lt
  gi|121636910|ref|YP_977133.1| 373 KASHASLGVQVTNDKDT---PGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALT 444
                                    55899*******99997...7**********9999999******************7777777777777799887 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0003      0.66      49      68 ..     181     200 ..     175     204 .. 0.87
   2 !    8.5   0.7   0.00031       0.7     627     651 ..     308     332 ..     286     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0003
                                    EE-EE-STT-EEEE-HHHHH CS
                  Peptidase_S46  49 CtasfVSpeGLvlTNHHCay 68 
                                     ++ + S+eGL+lTN H++ 
  gi|121636910|ref|YP_977133.1| 181 GSGIILSAEGLILTNNHVIA 200
                                    699**************976 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00031
                                    ES----TT-TT-EEE-TTS-EEEEE CS
                  Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGla 651
                                    +++ i  GNSG +++n +++lvG++
  gi|121636910|ref|YP_977133.1| 308 TDAAINPGNSGGALVNMNAQLVGVN 332
                                    6788899****************97 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.7e-05     0.084      34      88 .]     404     457 ..     386     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                    GGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE-STT-EEEEEE CS
                    Tricorn_PDZ  34 aepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvkrkdgkarrvvv 88 
                                    a+ Gv   +G ++++vd++p+++ + +  +  +ka g++v Lt+++ +g++r+v v
  gi|121636910|ref|YP_977133.1| 404 ANAGVP--KGVVVTKVDDRPINSADALVAAVRSKApGATVALTFQDPSGGSRTVQV 457
                                    667777..9*************999988888777747***************9987 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.23      37      72 ..     397     432 ..     375     435 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                          PDZ_1  37 easgsfklsskekkgviitsinnqptpnLdefievv 72 
                                      +g+ + + ++ kgv++t+++++p+ + d+++ +v
  gi|121636910|ref|YP_977133.1| 397 VVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAV 432
                                    445666666679*******************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3090.85
//
Query:       gi|121636911|ref|YP_977134.1|  [L=181]
Description: pterin-4-alpha-carbinolamine dehydratase moaB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   84.9   1.9    5.9e-24   84.4   1.9    1.2  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.75   10.0   4.4        1.1    9.4   0.3    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   1.9   6.6e-28   5.9e-24       2     140 ..      30     167 ..      29     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 6.6e-28
                                    EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHHHHHH CS
                  MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpealak 80 
                                    v++v d+ ++g+ eD++gpl+ ell+e+g+ v  +  v  de ei++al +a+ +  d++++ GGtG+tp+Dvtpea+++
  gi|121636911|ref|YP_977134.1|  30 VVVVDDRTAHGD-EDHSGPLVTELLTEAGFVVDGVVAVSADEVEIRNALNTAVIGGvDLVVSVGGTGVTPRDVTPEATRD 108
                                    789999999996.************************************55555555*********************** PP

                                    HHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHG CS
                  MoCF_biosynth  81 lfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillp 140
                                    ++++e+ g++ea+r+ +l      g++ +  lsr+     g+t +++L Gs  av++++ ++  p
  gi|121636911|ref|YP_977134.1| 109 ILDREILGIAEAIRASGLSA----GIVDA-GLSRGLagvsGSTlVVNLAGSRYAVRDGMATLN-P 167
                                    *******************6....34444.6899889999888899************99886.5 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.02   1.8e+02      44     122 ..      15      95 ..       2     102 .. 0.75
   2 ?    9.4   0.3   0.00013       1.1     103     154 ..     120     173 ..     115     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                                    EE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS..HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHH CS
                  NAD_binding_2  44 kaaesieelvasldvvitmvkagkavdevieg..llealkkgdilidgstsspedtrelakelkekglkfldaPVSGGee 121
                                     ++e+ +elv +  +v+++   +++ de  +g  + e l +  +++dg  +  +d  e+ ++l+ + +  +d  VS G  
  gi|121636911|ref|YP_977134.1|  15 APMEQRAELVVGRALVVVVDDRTAHGDEDHSGplVTELLTEAGFVVDGVVAVSADEVEIRNALNTAVIGGVDLVVSVGGT 94 
                                    45555556666655555555556666777777878888999999999999999999*********999999999997765 PP

                                    H CS
                  NAD_binding_2 122 g 122
                                    g
  gi|121636911|ref|YP_977134.1|  95 G 95 
                                    5 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00013
                                    HHHHTT..-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEE CS
                  NAD_binding_2 103 elkekg..lkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvt 154
                                    +++++g  + ++da+ S G +g +  tL + ++Gs+ a+++    l+ ++a+++
  gi|121636911|ref|YP_977134.1| 120 AIRASGlsAGIVDAGLSRGLAGVSGSTLVVNLAGSRYAVRDGMATLNPLAAQII 173
                                    55555533568******************************9999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1345.14
//
Query:       gi|121636912|ref|YP_977135.1|  [L=151]
Description: large-conductance mechanosensitive channel [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-33  114.8   1.9    3.1e-33  114.6   1.9    1.0  1  MscL      Large-conductance mechanosensitive channel, MscL


Domain annotation for each model (and alignments):
>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   1.9   1.8e-37   3.1e-33       1     120 [.       1     121 [.       1     122 [. 0.85

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.8e-37
                           MscL   1 llkeFkefilrGnvidLAvgviiGaaftkiVtslvkdiimpliglllgg..vdfselkiklkaeaavlkygafiqavinF 78 
                                    +lk+Fkef++rGn++dLAv+v+iG+aft++Vt+++++ii+pli+ +  +   d+  l+i +  + ++++++ +++a inF
  gi|121636912|ref|YP_977135.1|   1 MLKGFKEFLARGNIVDLAVAVVIGTAFTALVTKFTDSIITPLINRIGVNaqSDVGILRIGIG-GGQTIDLNVLLSAAINF 79 
                                    99******************************************998442234555555554.789************** PP

                           MscL  79 liiafvi.Flivkainkkkkeeeeeeeaeekeeellteirdll 120
                                    ++iaf++ Fl+v ++n+ +k+ e  e++ ++++ llteirdll
  gi|121636912|ref|YP_977135.1|  80 FLIAFAVyFLVVLPYNTLRKKGEV-EQPGDTQVVLLTEIRDLL 121
                                    *******9********95444333.34667899********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1155.44
//
Query:       gi|121636913|ref|YP_977136.1|  [L=248]
Description: adhesion component transport atp-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-35  121.8   0.0    5.3e-35  120.9   0.0    1.5  1  ABC_tran     ABC transporter
    1.7e-06   28.0   0.0    2.8e-06   27.4   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
    1.5e-05   24.5   0.0      0.011   15.2   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    2.4e-05   24.3   0.9      0.029   14.2   0.5    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    5.1e-05   22.9   0.1     0.0001   22.0   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00016   22.1   0.1    0.00028   21.3   0.1    1.5  1  AAA_16       AAA ATPase domain
     0.0015   19.1   0.2     0.0023   18.5   0.2    1.4  1  AAA_23       AAA domain
     0.0045   17.1   0.0     0.0074   16.4   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0059   16.2   0.0      0.057   13.0   0.0    2.1  2  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.014   14.6   0.0    1.1  1  G-alpha      G-protein alpha subunit
      0.013   15.6   0.0      0.014   15.4   0.0    1.3  1  Dynamin_N    Dynamin family
      0.038   13.9   0.2       0.17   11.8   0.1    1.9  2  NACHT        NACHT domain
      0.039   13.7   0.0        0.2   11.4   0.0    2.0  3  AAA_30       AAA domain
      0.054   12.8   0.0       0.41    9.9   0.0    2.0  2  Zeta_toxin   Zeta toxin
       0.12   12.6   0.1       0.38   11.0   0.0    1.8  2  AAA_22       AAA domain
       0.13   11.7   0.0       0.24   10.9   0.0    1.4  1  FeoB_N       Ferrous iron transport protein B
       0.15   10.8   0.0       0.21   10.3   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
       0.15   11.2   0.0       0.28   10.3   0.0    1.4  1  NB-ARC       NB-ARC domain
       0.17   10.5   0.0       0.26    9.9   0.0    1.2  1  AAA_13       AAA domain
       0.21   11.3   0.1        4.2    7.0   0.1    2.0  2  AAA_15       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   5.9e-38   5.3e-35       1     136 [.      26     174 ..      26     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 5.9e-38
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltv 76 
                                    l+++++++++ge va++G++G+GKStLl+l++g +kpt G+++++g  +++    +++ + r +ig+++q  +l p+ltv
  gi|121636913|ref|YP_977136.1|  26 LDHITFDFEPGEFVALLGQSGSGKSTLLNLISGIEKPTTGDVTINGFAITQkterDRTLFRRDQIGIVFQFFNLIPTLTV 105
                                    789*******************************************99999888777778899***************** PP

                                    HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     en             ++ + + ++l+k+g+ + + t       +LSgG++qrva+ ral+ +p l+l+DEpt
  gi|121636913|ref|YP_977136.1| 106 LENitlpqelagvsqrKAAVVARDLLEKVGMADRERTFP----DKLSGGEQQRVAISRALAHNPMLVLADEPT 174
                                    ***********9876666666999******999555555....*****************************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.1e-09   2.8e-06      86     153 ..      22      91 ..       6      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.1e-09
                                    THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-----.---------SEEEEEETTTE CS
                    RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevsek.lgrGkhTTtavellelaegg 153
                                    +++ l++++  ++  ++++l+GqSG GKStL+n + + ++  tg+v  +     + T + ++l++ ++ g
  gi|121636913|ref|YP_977136.1|  22 RRQVLDHITFDFEPgEFVALLGQSGSGKSTLLNLISGIEKPTTGDVTINgFAITQKTERDRTLFRRDQIG 91 
                                    4577889999999889*********************999999999754145667777777777666555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.011     126     211 ..     130     219 ..      23     223 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                    HHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                    xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          SMC_N 126 llesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivisl 197
                                    lle++g+          LSgGe++ va++  +A +      l+l De   +LD     kv ++l   + +    +i+ ++
  gi|121636913|ref|YP_977136.1| 130 LLEKVGMADRertfpdKLSGGEQQRVAISRALAHNP----MLVLADEPTGNLDSDTGDKVLDVLLDLTRQagKTLIMATH 205
                                    33333332224445559*******999998877542....36777**************999998766663367899999 PP

                                    SHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxx RF
                          SMC_N 198 reemlekadklvgv 211
                                    +  m+++ad++v +
  gi|121636913|ref|YP_977136.1| 206 SPSMTQHADRVVNL 219
                                    99******999876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.5   3.3e-05     0.029       1      49 [.      38      83 ..      38     101 .. 0.66
   2 !    8.3   0.0     0.002       1.7     250     301 ..     160     209 ..     138     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                   + +l G  gsGKS+LL +++++    +  +g+ ++++   + +  + + 
  gi|121636913|ref|YP_977136.1| 38 FVALLGQSGSGKSTLLNLISGI---EKPTTGDVTINGFAITQKTERDRT 83
                                   6799***************999...555555555554444444444444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                         AAA_21 250 allralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    al+  +    l+l DEp  +L+     ++l++l +l+r  g  +i++THSp+ 
  gi|121636913|ref|YP_977136.1| 160 ALAHNP---MLVLADEPTGNLDSDTGDKVLDVLLDLTRqAGKTLIMATHSPSM 209
                                    444444...46777888889999777777777744444378899*******85 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.1e-07    0.0001      13      40 ..      27      54 ..      23      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllD 40
                                   d+ t+++++ +++ l G+sGsGKSTll 
  gi|121636913|ref|YP_977136.1| 27 DHITFDFEPGEFVALLGQSGSGKSTLLN 54
                                   56689999999***************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   3.1e-07   0.00028      10      84 ..      23     102 ..      14     203 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.1e-07
                         AAA_16  10 eqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.......ggiflrgkcdql....esa......ipysa 71 
                                    +q+l+ +      +p e v l G+sG+GKs+l++ +   +ek        +g+++++k+++     +++           
  gi|121636913|ref|YP_977136.1|  23 RQVLDHITFDF--EPgEFVALLGQSGSGKSTLLNLIS-GIEKPttgdvtiNGFAITQKTERDrtlfRRDqigivfQ---- 95 
                                    44455554333..34499******************9.67777788888766667777777722221112222220.... PP

                         AAA_16  72 laqalareellrq 84 
                                    + +      l+  
  gi|121636913|ref|YP_977136.1|  96 FFN------LIPT 102
                                    222......2222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   2.6e-06    0.0023      11      40 ..      27      57 ..      23      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-06
                         AAA_23 11 rdqeidFskg.ltlItGpNGaGKTTildAik 40
                                   ++ ++dF++g ++++ G+ G+GK+T+l+ i 
  gi|121636913|ref|YP_977136.1| 27 DHITFDFEPGeFVALLGQSGSGKSTLLNLIS 57
                                   56789**9963889*************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.3e-06    0.0074       2      28 ..      39      66 ..      38     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.3e-06
                                   EEEEESTTSSHHHHHHHHHTS.TEEESS CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsd 28
                                   va++G++ +GKStL+n ++g  k  ++d
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLISGIeKPTTGD 66
                                   89****************9843444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   6.4e-05     0.057       9      50 ..      13      53 ..       3      59 .. 0.82
   2 ?    0.8   0.0      0.35   3.1e+02     160     189 ..     176     206 ..     166     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                         AAA_25  9 avsvadlaapppprrwlvkgllpagelallaGapgtGKttla 50
                                   ++++++ +++ + ++++  ++   ge+++l G++g+GK+tl+
  gi|121636913|ref|YP_977136.1| 13 SWTFREGETRRQVLDHITFDF-EPGEFVALLGQSGSGKSTLL 53
                                   467777888888888888889.67****************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                         AAA_25 160 nsnsdv.galvealeriarrtgaavllvhHv 189
                                    n +sd+ +++++ l ++ r+ g ++++  H+
  gi|121636913|ref|YP_977136.1| 176 NLDSDTgDKVLDVLLDLTRQAGKTLIMATHS 206
                                    6677877999******************997 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.014      26      51 ..      39      64 ..      22     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                   EEEEESTTSSHHHHHHHHHHHCS--- CS
                        G-alpha 26 llllGqseSGKsTilkqlkllykkgf 51
                                   + llGqs+SGKsT+l+ +  ++k++ 
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLISGIEKPTT 64
                                   579***************99999983 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.6e-05     0.014       1      32 [.      39      68 ..      39     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                   +a++G+  sGKS++ln + g +   +g    T
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLISGIEKPTTGDV--T 68
                                   7999****************994434443..3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00018      0.17       3      20 ..      39      56 ..      37      76 .. 0.88
   2 ?   -0.4   0.0       1.1   9.4e+02      95     138 ..     175     216 ..     147     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                   v+l G++GsGK+tLl  +
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLI 56
                                   899***********9755 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                    S-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTT CS
                          NACHT  95 tdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeq 138
                                      l+ ++  +v ++L +l r+    ++ +++t +p+  +++ + 
  gi|121636913|ref|YP_977136.1| 175 GNLDSDTGDKVLDVLLDLTRQ--AGKTLIMATHSPSMTQHADRV 216
                                    444445556788888899988..888889999999888776655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022       0.2      19      58 ..      37      78 ..      23      90 .. 0.83
   2 ?   -1.9   0.1       2.5   2.2e+03      93      93 ..     169     169 ..     115     204 .. 0.56
   3 ?   -1.5   0.0         2   1.8e+03      29      50 ..     196     217 ..     193     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grviglAptgka 58
                                    +++l G  G+GK+t+l+ +  + +   g  ++ g+A t+k 
  gi|121636913|ref|YP_977136.1| 37 EFVALLGQSGSGKSTLLNLISGIEKPTtGdVTINGFAITQKT 78
                                   578999**************8888777444777799988875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                         AAA_30  93 i 93 
                                    +
  gi|121636913|ref|YP_977136.1| 169 L 169
                                    3 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2
                         AAA_30  29 tGKttalkalreaweaaggrvi 50 
                                    +GKt ++++    ++++  rv+
  gi|121636913|ref|YP_977136.1| 196 AGKTLIMATHSPSMTQHADRVV 217
                                    7999999998888888776776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00045      0.41      19      38 ..      39      58 ..      27      71 .. 0.79
   2 ?    0.3   0.0      0.41   3.6e+02      30     160 ..     199     231 ..     179     241 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                     Zeta_toxin 19 illgGqpGAGKselaellkd 38
                                   + l Gq+G+GKs+l++l+  
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLISG 58
                                   5677***********99875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.41
                     Zeta_toxin  30 selaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengyniivegtlrspdv 109
                                    + +++                                                                           
  gi|121636913|ref|YP_977136.1| 199 TLIMATH------------------------------------------------------------------------- 205
                                    4444444......................................................................... PP

                     Zeta_toxin 110 vkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaegRlvpkeehd 160
                                                              S ++ +dR+ +  ++gRl+p  + +
  gi|121636913|ref|YP_977136.1| 206 ------------------------SPSMTQHADRVVNL-QGGRLIPALNRE 231
                                    ........................44555555555555.444666555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00043      0.38       6      24 ..      37      55 ..      33      87 .. 0.89
   2 ?   -1.5   0.0       3.1   2.8e+03      80      99 ..     155     172 ..     115     207 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                         AAA_22  6 gilvvtGesGtGKTtllrr 24
                                    ++++ G+sG+GK+tll+ 
  gi|121636913|ref|YP_977136.1| 37 EFVALLGQSGSGKSTLLNL 55
                                   58899***********986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                         AAA_22  80 ealeqalraravielliiDE 99 
                                     a+ +al +  +  l++ DE
  gi|121636913|ref|YP_977136.1| 155 VAISRALAHNPM--LVLADE 172
                                    444444444444..555555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00026      0.24       3      25 ..      39      61 ..      37      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                                   EEEEESTTSSHHHHHHHHHTTSE CS
                         FeoB_N  3 valvGnpnvGkttlfnaltgakq 25
                                   val+G+  +Gk+tl+n ++g ++
  gi|121636913|ref|YP_977136.1| 39 VALLGQSGSGKSTLLNLISGIEK 61
                                   89*****************9875 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00024      0.21      26      55 ..      37      66 ..      31      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                           DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGr 55
                                     v +lG++gsGk+tl+  + G+e++  G 
  gi|121636913|ref|YP_977136.1| 37 EFVALLGQSGSGKSTLLNLISGIEKPTTGD 66
                                   56899********************99885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00032      0.28       8      40 ..      25      56 ..      19      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                                   HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqi 40
                                   v ++     e++  +val G  G+GK+tl++ i
  gi|121636913|ref|YP_977136.1| 25 VLDHITFDFEPG-EFVALLGQSGSGKSTLLNLI 56
                                   555665566777.79**************9765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00029      0.26      23      76 ..      43      95 ..      34     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00029
                         AAA_13 23 GwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVfNrdFveenls 76
                                   G+ G+GK+tL +l++ +e+     + +   ++it+++e d   f rd +   ++
  gi|121636913|ref|YP_977136.1| 43 GQSGSGKSTLLNLISGIEKPT-TGDVTINGFAITQKTERDRTLFRRDQIGIVFQ 95
                                   899**************8755.557788889999*****999999998776665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0047       4.2      16      44 ..      28      57 ..      24      98 .. 0.83
   2 ?    2.6   0.0     0.097        87     327     368 ..     168     209 ..      96     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0047
                         AAA_15 16 dveidlsee.ltvliGkNnsGKSsileald 44
                                   +++ d+++  +  l G  +sGKS++l+++ 
  gi|121636913|ref|YP_977136.1| 28 HITFDFEPGeFVALLGQSGSGKSTLLNLIS 57
                                   5555666667999**************995 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.097
                         AAA_15 327 lliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    +l +EP  +L  +    + + l++l ++  + +i+ THSp +
  gi|121636913|ref|YP_977136.1| 168 VLADEPTGNLDSDTGDKVLDVLLDLTRQAGKTLIMATHSPSM 209
                                    55566666666666667788999999999999********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 1945.98
//
Query:       gi|121636914|ref|YP_977137.1|  [L=855]
Description: adhesion component transport transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-20   71.9  18.0    4.4e-12   46.3   4.9    6.3  7  FtsX      FtsX-like permease family
    1.6e-15   58.0  11.3      9e-13   49.0   0.8    2.9  3  MacB_PCD  MacB-like periplasmic core domain


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.27   2.5e+03      70      84 ..      29      43 ..      24      64 .. 0.50
   2 ?    0.6   0.4     0.091   8.2e+02      15      38 ..     251     274 ..     249     285 .. 0.72
   3 !   40.3   5.1   3.6e-14   3.2e-10       3      94 ..     290     386 ..     288     388 .. 0.88
   4 ?   -1.1   6.7      0.31   2.7e+03      24      87 ..     428     503 ..     420     512 .. 0.55
   5 ?    1.4   0.4     0.049   4.4e+02      14      49 ..     475     510 ..     465     533 .. 0.78
   6 ?   -0.5   0.9      0.19   1.7e+03      63      88 ..     719     744 ..     674     750 .. 0.53
   7 !   46.3   4.9   4.9e-16   4.4e-12       3      95 ..     755     847 ..     753     848 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                           FtsX 70 liiivlllllallag 84
                                   l++++++l +a++++
  gi|121636914|ref|YP_977137.1| 29 LLVLGIALGVAMIVA 43
                                   333333333333332 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.091
                           FtsX  15 kqvlllllteillitlvalviGlg 38 
                                    kq+   +++ + +++l+al++G+ 
  gi|121636914|ref|YP_977137.1| 251 KQMTDAFTVNLTALSLIALLVGIF 274
                                    666777888888888999988833 PP

  == domain 3  score: 40.3 bits;  conditional E-value: 3.6e-14
                           FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.....selkisidlitvliiivlll 77 
                                     ++ilr+lG+++ q+++l++te+l+ +l+++ +Gl++g+++ + l  ++ +  +          +s++ +++l ++++++
  gi|121636914|ref|YP_977137.1| 290 FFAILRCLGVTREQLFWLIMTESLVAGLIGTGLGLLIGIWLGEGLIGLVTQTINDfyfviNVRNVSVSAESLLKGLIIGI 369
                                    589**********************************99999996666666654444448999***************** PP

                           FtsX  78 llallagllsiskilkk 94 
                                    + a+la+l +++ ++++
  gi|121636914|ref|YP_977137.1| 370 FAAMLATLPPAIEAMRT 386
                                    **********9999886 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.31
                           FtsX  24 eillitlvalviGlglgllaaqllsdvllssvf..........s..selkisidlitvliiivlllllallaglls 87 
                                     +l++++v+l++ l++++l+a +l  ++   +           +      i  +l+   i+i+ l++ ++l++ +s
  gi|121636914|ref|YP_977137.1| 428 NNLVVAFVGLFSVLIALALIAPPLTRFVMLRLApglgrllgpiGrmAPRNIVRSLSRTSIAIAALMMAVSLMVGVS 503
                                    6789999999999999999999977776555333333333333133233333333333333333333333333333 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.049
                           FtsX  14 kkqvlllllteillitlvalviGlglgllaaqllsd 49 
                                     + +++ l   +++i+++ ++++l +g+ ++  ++ 
  gi|121636914|ref|YP_977137.1| 475 PRNIVRSLSRTSIAIAALMMAVSLMVGVSISVGSFR 510
                                    677888889999999999999999998877766555 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 0.19
                           FtsX  63 sidlitvliiivlllllallagllsi 88 
                                    +   +t+ i++ l+  ++ ++g+ls+
  gi|121636914|ref|YP_977137.1| 719 FDRSFTITIALQLVATVVAFIGVLSA 744
                                    33333333333333333333344443 PP

  == domain 7  score: 46.3 bits;  conditional E-value: 4.9e-16
                           FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                    e+g++ra+Gm+++q+++l+++e+ l +  a +++l  g+++a++l   ++   f+  l++ +   ++l +++++++ al+
  gi|121636914|ref|YP_977137.1| 755 ELGVFRAIGMTTRQLWKLMFIETGLMGGMAGLMALPTGCILAWILVRIINVRSFGWTLQMHFESAHFLRALLVAVVAALA 834
                                    89****************************************************************************** PP

                           FtsX  83 agllsiskilkke 95 
                                    ag+++++++ +++
  gi|121636914|ref|YP_977137.1| 835 AGMYPAWRLGRMT 847
                                    ********99886 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.8     1e-16     9e-13       2     192 ..      28     234 ..      27     236 .. 0.68
   2 ?   -4.9   1.3         2   1.8e+04       1      15 [.     262     276 ..     262     284 .. 0.71
   3 !   16.0   0.0   1.3e-06     0.012      10     194 ..     487     695 ..     485     697 .. 0.58

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1e-16
                       MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdl..gnlvtvtpgkgsgeslsdpdvealrrevpveavapvv....tv 75 
                                    +l vLGia+Gva ++ai +  +++q++++ + ++     + ++  g+   ++++++++ +lrr+ + +  apv+    ++
  gi|121636914|ref|YP_977137.1|  28 ILLVLGIALGVAMIVAIDVSSNSAQRAFDLSAAAItgKSTHRLVSGP---AGVDQQLYVDLRRH-GYDFSAPVIegyvLA 103
                                    588***************************98866632344455544...33444444345542.233335555443222 PP

                       MacB_PCD  76 rgggsgeeevtvvgvdp...dyfk.....vfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl......k 140
                                    rg g  +++ +  g+dp   + f+     + ++  + G f+      ++pn+vv+++++a+++  +vGd+i l       
  gi|121636914|ref|YP_977137.1| 104 RGLG--NRAMQFMGTDPfaeSAFRsplwsNQNIA-ELGGFL------TRPNGVVLSRQVAQKYGlAVGDRIALqvkgapT 174
                                    4555..6668999999644444443333333331.223333......59*************88*******9999**999 PP

                       MacB_PCD 141 pftVvGvledppgsgsalg.ddavylplttlqrrs........itvrlkdgadleaaaael 192
                                    ++t vG l++   + s++   d ++ +++t+q+ +        i + +kd a+++ ++++l
  gi|121636914|ref|YP_977137.1| 175 TVTLVGLLTPA-DEVSNQKlSDLIIADISTAQELFhmpgrlshIDLIIKDEATATRIQQRL 234
                                    9******9542.22333333467888899886544668888889999*********99987 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 2
                       MacB_PCD   1 slltvLGiaiGvaav 15 
                                    ++l+++++ +G++ +
  gi|121636914|ref|YP_977137.1| 262 TALSLIALLVGIFLI 276
                                    688888888888766 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.3e-06
                       MacB_PCD  10 iGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk............gsgeslsdpdvealrr..evp.ve.avapvv 73 
                                    i++aa+++ vsl+ g++ sv s  + l+n + vt ++            + +++l+ +   a+r   + p v+ av +++
  gi|121636914|ref|YP_977137.1| 487 IAIAALMMAVSLMVGVSISVGSFRQTLANWLEVTLKSdvyvspptltsgRPSGNLPVD---AVRNisKWPgVRdAVMARY 563
                                    7888888888888888888877666667766676665555333445442222223332...3322224666663343333 PP

                       MacB_PCD  74 ....tvrgggsg.eeevtvvgvdpdyfkv.fglklaeGrffteadlrg.....gpnvvvigeelaerlf....pvGdtir 138
                                        +     ++ ++ev + +v+ d  +  + +++  G   t           + ++v+++e +  r      p  + i+
  gi|121636914|ref|YP_977137.1| 564 ssvfA-----PDwGREVELMAVSGDISDGkRPYRWIDGNKDT-----LwprflAGKGVMLSEPMVSRQHlqmpP--RPIT 631
                                    22211.....22323355555555555531344445574332.....1222347888********995568743..9999 PP

                       MacB_PCD 139 l......kpftVvGvledppgsgsalgddavylp.......lttlqrrsitvrlkdgadleaaaaelek 194
                                    l      ++f V +v++d++     +++  ++++       +++ +++++++ l++ga+  a+ ++l++
  gi|121636914|ref|YP_977137.1| 632 LmtdsgpQTFPVLAVFSDYT-----SDQGVILMDrasyrahWQDDDVTTMFLFLASGANSGALIDQLQA 695
                                    9***************8863.....24457888866644344443556688889999988888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 6224.39
//
Query:       gi|121636915|ref|YP_977138.1|  [L=386]
Description: hypothetical protein BCG_1043 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-53  182.3   1.0    6.4e-53  179.8   0.8    1.9  2  CrtC         CrtC N-terminal lipocalin domain
    6.9e-41  139.6   0.3    1.6e-40  138.4   0.1    1.7  2  Lipocalin_9  Lipocalin-like domain


Domain annotation for each model (and alignments):
>> CrtC  CrtC N-terminal lipocalin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.8   7.1e-57   6.4e-53       1     164 [.      71     246 ..      71     248 .. 0.96
   2 ?    0.4   0.0      0.11   9.4e+02      53     107 ..     284     338 ..     253     369 .. 0.69

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 7.1e-57
                                    EEEEEEEEEEE-TT--EEEEEEEEEEE----..........S.SS--EEEEEEEEEE-TTTSS-EEEEEEEEESS-TTTE CS
                           CrtC   1 iEwWYltGnLedeegreyGfqltffrsalep..........aawateqlymahaavtdveagkflseervargglglaga 70 
                                    +EwWY+tGnLe+++gr +G+qltffr al+p          ++w+t+q+ymah+a++d++++ f  +e+++r++lglaga
  gi|121636915|ref|YP_977138.1|  71 TEWWYYTGNLETADGRLFGYQLTFFRRALAPpgegvaiadaSSWRTTQVYMAHFAISDISNRGFDPAEKFSRQALGLAGA 150
                                    7****************************99999998876438************************************* PP

                                    EE-SSEEEETTEEEEETS...-EEEEEE-SSEEEEEEEE--S--EE-TBTTEEE-SSSTT-EEEEEEEEEEEEEEEEEE. CS
                           CrtC  71 eekpfkvrlddWqlksssellparlrasaegfsldLtlsstkppvlqgdnGysrkgaepeqasyYySqprlavkGtltl. 149
                                    +++p+ v+lddW +++s +  +++l a++++  ldLtl++t pp+lqg++G+s+kga+p++as YyS+ r + +Gt+++ 
  gi|121636915|ref|YP_977138.1| 151 SSEPYAVWLDDWYARES-NNNSVQLFARTQNTVLDLTLTQTLPPILQGNAGLSVKGAQPGNASNYYSLVRQESRGTVSVn 229
                                    **************874.57899999*****************************************************9 PP

                                    ..EEEEEEEEEEEEEEE CS
                           CrtC 150 ..kvsVtGeaWlDhews 164
                                      ++ V+G +W Dhe+ 
  gi|121636915|ref|YP_977138.1| 230 gdTFMVSGLSWKDHEYM 246
                                    99999**********95 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                                    S-EEEEEEEEESS-TTTEEE-SSEEE.ETTEEEEETS...-EEEEEE-SSEEEEEE CS
                           CrtC  53 kflseervargglglagaeekpfkvr.lddWqlksssellparlrasaegfsldLt 107
                                    +f+s   va    g    e+++f+++  d+W+  +s+++ p+  +++ e++ l+L+
  gi|121636915|ref|YP_977138.1| 284 RFSSGTFVAGD-GGVIPLESSDFRIKtTDRWTSDQSGATYPIAWEIEIERIGLTLR 338
                                    44443333333.56777788999998456677777777777777777777777553 PP

>> Lipocalin_9  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.79     7e+03      30      48 ..      68      86 ..      61      90 .. 0.81
   2 !  138.4   0.1   1.8e-44   1.6e-40       1     130 []     250     381 ..     250     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.79
                                   TS-EEEEE..EEEE-TTS- CS
                    Lipocalin_9 30 dgsaeeastsgtliaadge 48
                                   d+++e+ +++g+l +adg+
  gi|121636915|ref|YP_977138.1| 68 DYQTEWWYYTGNLETADGR 86
                                   6777888888998888886 PP

  == domain 2  score: 138.4 bits;  conditional E-value: 1.8e-44
                                    S-TTEEEEEEEEEEETTS-EEEEEEEEETTS-EEEEE..EEEE-TTS-EEEE-GGGEEEEEEEEEE-TTT--EEEE.... CS
                    Lipocalin_9   1 laksqvGWdwfslqlddgsalmlfrlrkkdgsaeeastsgtliaadgeatalskediklepletwtspktgakyPvkwqv 80 
                                    la+++vGWdwf+lq+ +g+almlf++r++dgs ++ s sgt++a dg ++ l+++d++++++++wts+++ga+yP++w++
  gi|121636915|ref|YP_977138.1| 250 LAPEDVGWDWFGLQFYNGTALMLFQIRQADGSVTRFS-SGTFVAGDGGVIPLESSDFRIKTTDRWTSDQSGATYPIAWEI 328
                                    67899***************************77666.7***************************************** PP

                                    EEEETTEEEEEEES-S--EEET--EEEEEEEEETT......EEEEEEEEEE-- CS
                    Lipocalin_9  81 elpseeldltvepllkdqeldttipYWEGavkvegsgs...vnGrGYlEltGY 130
                                    e+++ +l+l+ ++l+++qel+++ +YWEGav +eg+ +    +GrGY+E+tGY
  gi|121636915|ref|YP_977138.1| 329 EIERIGLTLRGAALMANQELRLSRTYWEGAVALEGRYQgmpISGRGYVEMTGY 381
                                    *********************************65555679***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3026.08
//
Query:       gi|121636916|ref|YP_977139.1|  [L=325]
Description: polyprenyl-diphosphate synthase grcC2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-40  139.3   0.0    1.4e-40  139.0   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   0.0   7.5e-45   1.4e-40       3     253 ..      37     274 ..      35     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 7.5e-45
                                    HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHH CS
                polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnkl 82 
                                     +++ + +lv+agG  +Rpl+++laa++ ++++    ++ v+++++el+h  +L hD ++D+s++ R  p+ + ++ n+ 
  gi|121636916|ref|YP_977139.1|  37 VMRDTVAHLVDAGGTPFRPLFTVLAAQLGSDPD--GWEVTVAGAAIELMHLGTLCHDRVVDESDMSRKTPSDNTRWTNNF 114
                                    5778899***********************444..4679***************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHH CS
                polyprenyl_synt  83 AindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvala 162
                                    Ai++gd+ +a+a++l ++l   ++e++++++e+ ++++ Gq+  ++    ++++  ++e+yl++v+ KT++l+a++ +l+
  gi|121636916|ref|YP_977139.1| 115 AILAGDYRFATASQLASRL---DPEAFAVVAEAFAELITGQMRATRGP-ASHID--TIEHYLRVVHEKTGSLIAASGQLG 188
                                    *******************...77*******************99444.46666..8*********************** PP

                                    HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTTSS CS
                polyprenyl_synt 163 allagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilgkk 242
                                    a+l+ga++e++++++++g+ +G aF i  D++ ++gd+++l    g+D+ +   tlp+l+al++++p+   +l+e+l   
  gi|121636916|ref|YP_977139.1| 189 AALSGAAEEQIRRVARLGRMIGAAFEISRDIIAISGDSATLS---GADLGQAVHTLPMLYALREQTPDTS-RLRELLA-G 263
                                    ******99*******************************974...78****************9999965.9999998.4 PP

                                    HHHHHHHHHHH CS
                polyprenyl_synt 243 aekeedvkeal 253
                                    + ++++v+eal
  gi|121636916|ref|YP_977139.1| 264 PIHDDHVAEAL 274
                                    44666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2680.78
//
Query:       gi|121636917|ref|YP_977140.1|  [L=218]
Description: hypothetical protein BCG_1045c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-10   41.2   0.2    4.8e-10   39.9   0.2    1.6  1  SAF       SAF domain
    1.3e-07   31.7   0.1    4.1e-07   30.1   0.0    1.9  2  ChapFlgA  Chaperone for flagella basal body P-ring formation


Domain annotation for each model (and alignments):
>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   5.3e-14   4.8e-10       2      58 ..      55     111 ..      54     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 5.3e-14
                                    EEEEESSTB-TT-BEBTTTEEEECECGG.CCTSCCCGGHHHHTTEEESS-B-TT-B-B CS
                            SAF   2 nVvvAardikaGeviteddltlkrpias.hkigllpiaygeviGkratrdikaGepvh 58 
                                    +VvvAa+d+++G+ +t+ d++l++  a  ++ g  ++ +++v+G++++++ ++Ge+++
  gi|121636917|ref|YP_977140.1|  55 EVVVAAHDLRPGTALTPGDVRLEKRSATtLPDGSQAD-LDAVVGSTLASPTRRGEVLT 111
                                    7************************************.9*****************98 PP

>> ChapFlgA  Chaperone for flagella basal body P-ring formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.5e-11   4.1e-07       2      59 ..      55     114 ..      54     120 .. 0.90
   2 ?   -2.9   0.0      0.75   6.7e+03      63      76 ..     142     155 ..     135     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.5e-11
                       ChapFlgA   2 evvvaarpLkrgevitasdlalkkrdlsrlrggvl.t.deaigkkvkrsiragqpirqnm 59 
                                    evvvaa++L++g+ +t++d++l+kr+ ++l++g   + d+++g+++ ++ r+g++++   
  gi|121636917|ref|YP_977140.1|  55 EVVVAAHDLRPGTALTPGDVRLEKRSATTLPDGSQaDlDAVVGSTLASPTRRGEVLTDVR 114
                                    8******************************66552689****************99765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.75
                       ChapFlgA  63 pplVkkgqkVtiia 76 
                                    ++lV+ g+ V ++a
  gi|121636917|ref|YP_977140.1| 142 VDLVRVGDVVDVLA 155
                                    57888899888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1623.36
//
Query:       gi|121636918|ref|YP_977141.1|  [L=110]
Description: hypothetical protein BCG_1046c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-14   52.5   0.7    5.8e-14   51.9   0.7    1.3  1  Zn-ribbon_8  Zinc ribbon domain
  ------ inclusion threshold ------
        1.9    7.2   7.2        2.1    7.1   7.2    1.0  1  Apt1         Golgi-body localisation protein domain
          2    6.6   9.9        1.6    6.9   9.9    1.1  1  RAP1         Rhoptry-associated protein 1 (RAP-1)


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.7   9.7e-18   5.8e-14       1      40 []       1      40 [.       1      40 [. 0.97

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 9.7e-18
                    Zn-ribbon_8  1 MPiYeYrCeeCghefevlqsisdapltaCPeCgsevrrvi 40
                                   MP+Y Y+C++C ++f+v+q+++d++lt+C +C +++r+++
  gi|121636918|ref|YP_977141.1|  1 MPTYSYECTQCANRFDVVQAFTDDALTTCERCSGRLRKLF 40
                                   ********************99**********99****86 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.2   0.00036       2.1     318     370 ..      58     103 ..      32     109 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00036
                           Apt1 318 desdeesessssssssssssassssssssrssslelrlkptsstssssssess 370
                                     es ++s+s+   ++ ss+s+s++ss ss+ss ++++    + ++s+++s+ss
  gi|121636918|ref|YP_977141.1|  58 RESGKKSKSQ---TNGSSTSESTKSSGSSGSSGSSES----KASGSTEKSTSS 103
                                    2222222221...122222222222222222222222....111111111111 PP

>> RAP1  Rhoptry-associated protein 1 (RAP-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.9   0.00027       1.6     140     185 ..      60     104 ..       6     110 .] 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00027
                           RAP1 140 eslksssdskskasaksnvksaskyGesssseesatdsskasasva 185
                                    +++ks s+++ +++++s  ks+   G s sse  a  s+++s+s +
  gi|121636918|ref|YP_977141.1|  60 SGKKSKSQTNGSSTSEST-KSSGSSGSSGSSESKASGSTEKSTSST 104
                                    233333333333333332.333333444444444444444443322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1300  (0.0725082); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 866.16
//
Query:       gi|121636919|ref|YP_977142.1|  [L=197]
Description: hypothetical protein BCG_1047c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-44  152.1   0.0    1.7e-44  151.9   0.0    1.0  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.0   9.5e-49   1.7e-44       1     187 []       6     186 ..       6     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 9.5e-49
                                    HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-SEEEE----TTS---HHHHHHHHHTTEEEEEEEECSSCTE CS
                 5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqeakrvalyvsvkgeidtkelikklleegkevllPrvrlesgs 80 
                                    K++lR+qllaa+r+++++ +aae+++l +++e++++s+  ++v++yv+v+ge+   e+++ ll++  +vllP++r+  g+
  gi|121636919|ref|YP_977142.1|   6 KSALRDQLLAARRRVADDVRAAEARMLRGHLERMVTSD--STVCAYVPVGGEPGSIEMLDVLLRRAGRVLLPVARTAGGD 83 
                                    899**********************************8..9*************************************** PP

                                    ECEEEEEECCCCCCCCCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTST-SS--EEE CS
                 5-FTHF_cyc-lig  81 lkvvrlttlkeedslesgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkggagdkpltv 160
                                    l +   + ++++  l++ ++gl+eP+e++  e al+++ lvlvP++A+d++ +RlG+G+G+yDr+l++ +     +  +v
  gi|121636919|ref|YP_977142.1|  84 LPLPLRWGEYRAGGLARARWGLLEPPEPWLPEAALAQASLVLVPALAVDRQSVRLGRGRGFYDRSLRCRDP----HARLV 159
                                    ***********************************************************************....***** PP

                                    EE--GGGEES-----ST----SEEE-S CS
                 5-FTHF_cyc-lig 161 glaldeqlverlPleehDvpvdevvte 187
                                    +++ + +lv+ lP+e+hDvp+++ +t+
  gi|121636919|ref|YP_977142.1| 160 AVVRTVELVDVLPSEPHDVPMTHALTP 186
                                    ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1369.80
//
Query:       gi|121636920|ref|YP_977143.1|  [L=306]
Description: UTP--glucose-1-phosphate uridylyltransferase galU [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-26   92.5   0.0    3.8e-26   92.2   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
      9e-07   29.4   3.4    1.8e-06   28.4   3.4    1.7  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.051   13.8   0.0        0.1   12.9   0.0    1.4  1  Imm75            Putative Immunity protein 75


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   6.4e-30   3.8e-26       2     243 ..      12     280 ..      11     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 6.4e-30
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT......... CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg......... 72 
                                    a++ a G GtR+ P t+t++k l+pv+++ + i+ ++ ++a++g e+ +v++t+e +  v  ++ e   ++         
  gi|121636920|ref|YP_977143.1|  12 AIVPAAGLGTRFLPATKTVPKELLPVVDT-PGIELVAAEAAAAGAER-LVIVTSEGKDGVVAHFVEDLVLEgtleargki 89 
                                    68889************************.*****************.777777777777777777766778999***** PP

                                    ............SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEE. CS
                NTP_transferase  73 ............vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgi. 139
                                                ++v+ +++ e+ g+ +A+  ++  l  ++ d++++ L++D +    + e++ k ++++  gtv+++i 
  gi|121636920|ref|YP_977143.1|  90 amlakvrrapalIKVESVVQAEPLGLGHAIGCVEPTLSPDE-DAVAVLLPDDLVLPTGVLETMSKVRASRG-GTVLCAIe 167
                                    **********************************9999888.79*************99999999999999.66666552 PP

                                    EESS-CTTSEEEEEC...........TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHH CS
                NTP_transferase 140 vpveeateyGviead...........eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdi 207
                                    v +ee ++yGv  ++           +  +v+ +vEKPk+++a s +a++G Yv ++ +++ l + +++ + ge ++td+
  gi|121636920|ref|YP_977143.1| 168 VAREEISAYGVFDVEpvpdgdytddpNVLKVRGMVEKPKAETApSRYAAAGRYVLDRAIFDAL-RRIDRGAGGEVQLTDA 246
                                    788899********999988776554444**************999****************9.77************** PP

                                    HHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
                NTP_transferase 208 lpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                    +  +++eg++   ++ ++++   D+G++  +l+a+ 
  gi|121636920|ref|YP_977143.1| 247 IALLIAEGHPVHVVVHQGSR--HDLGNPGGYLKAAV 280
                                    ******************87..******99999875 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   3.4     3e-10   1.8e-06       1     144 [.      12     233 ..      12     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3e-10
                                    EEEEEESS-TTT....TT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH.................... CS
                   NTP_transf_3   1 aviLAGGrSsRm....gg.dKallplggkpllervldalraagvdevvvvggd..eevla.................... 53 
                                    a++ A+G ++R+    ++ +K llp+ ++p +e v++ ++aag++++v+v+ +  + v a                    
  gi|121636920|ref|YP_977143.1|  12 AIVPAAGLGTRFlpatKTvPKELLPVVDTPGIELVAAEAAAAGAERLVIVTSEgkDGVVAhfvedlvlegtleargkiam 91 
                                    6788********6654348*******************************977544444445556666666666666555 PP

                                    ..HHTTC....TS-EEE-TTSS-SHHHHHHHHHHH.H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                   NTP_transf_3  54 ..alarl....gvrvvededpgkgplaslaaalra.aadadavlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                       ++r     +v+ v++++   g ++++ +     ++d+dav+vl+ D   l++ ++e++ +  a++g+ v+++    +
  gi|121636920|ref|YP_977143.1|  92 laKVRRApaliKVESVVQAE-PLGLGHAIGCVEPTlSPDEDAVAVLLPDDLVLPTGVLETMSKVRASRGGTVLCAIEVAR 170
                                    55223332233566666664.47888888888888445********************************9999988877 PP

                                    E..............................................EECCEEEGGGHHHHHHH CS
                   NTP_transf_3 127 r..............................................ghpllfrarllsalaal 144
                                    +                                              g   ++ +++++al+++
  gi|121636920|ref|YP_977143.1| 171 EeisaygvfdvepvpdgdytddpnvlkvrgmvekpkaetapsryaaaG-RYVLDRAIFDALRRI 233
                                    777777777777777777777777777777777777777766544431.224444455555554 PP

>> Imm75  Putative Immunity protein 75
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05       0.1       7      56 ..      30      80 ..      24      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                          Imm75  7 lkrellpgvti.fidsvrleaiddkadrlmvttsvgeearlvyfnpdfagt 56
                                   + +ellp v +  i+ v  ea    a+rl++ ts g++  + +f  d+   
  gi|121636920|ref|YP_977143.1| 30 VPKELLPVVDTpGIELVAAEAAAAGAERLVIVTSEGKDGVVAHFVEDLVLE 80
                                   568*****96637**************************999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2125.52
//
Query:       gi|121636921|ref|YP_977144.1|  [L=426]
Description: molybdopterin biosynthesis protein moeA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-38  130.3   5.9    5.2e-38  130.3   5.9    1.6  2  MoeA_N         MoeA N-terminal region (domain I and II)
    3.8e-20   71.8   0.1    2.2e-19   69.4   0.1    2.3  2  MoeA_C         MoeA C-terminal region (domain IV)
    1.6e-19   70.0   0.2    3.1e-19   69.0   0.2    1.5  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.18   11.8   0.6       0.39   10.7   0.0    1.9  2  V_ATPase_prox  Vacuolar ATPase Subunit I N-terminal proximal 


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   5.9   1.2e-41   5.2e-38       2     157 .]       3     181 ..       2     181 .. 0.87
   2 ?   -3.6   0.0       1.9   8.6e+03      73      90 ..     398     415 ..     383     417 .. 0.63

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 1.2e-41
                                    -HHHHHHHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--................. CS
                         MoeA_N   2 sveealaiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep............ 68 
                                    svee++a+i+aa+ ++++  v++ aea+g ++ae+vv ++++P+fd++a+DGYAvr+ + +g   +              
  gi|121636921|ref|YP_977144.1|   3 SVEEQQARISAAAVAPRPIrVAI-AEAQGLMCAEEVVTERPMPGFDQAAIDGYAVRSVDVAGVGDTGGvqvfadhgdldg 81 
                                    8***********95556655***.99*****************************8888888766666778888888888 PP

                                    ..................-S---TT-EEEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TT CS
                         MoeA_N  69 ............saageeperllpggavrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaG 135
                                                +a++++ +rl+p++avr++TGaplP+ adaV+p+ +t+     ++v+v + + +g+ vrraG+d++ G
  gi|121636921|ref|YP_977144.1|  82 rdvltlpvmgtiEAGARTLSRLQPRQAVRVQTGAPLPTLADAVLPLRWTD--GGMSRVRVlRGAPSGAYVRRAGDDVQPG 159
                                    88999999999666666677777777**********************94..3334445568999999************ PP

                                    SEEE-TTBB--CCCHHHHHHCT CS
                         MoeA_N 136 evllragtrltpaeigllasvG 157
                                    +v++ragt++++a++glla+vG
  gi|121636921|ref|YP_977144.1| 160 DVAVRAGTIIGAAQVGLLAAVG 181
                                    *********************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.9
                                    ..-S---TT-EEEE-TTS CS
                         MoeA_N  73 eeperllpggavrimTGa 90 
                                    +++  ++p ga +i TG 
  gi|121636921|ref|YP_977144.1| 398 ANCLVVVPTGAEQIRTGE 415
                                    444555566677777775 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.78   3.5e+03       7      24 ..     276     295 ..     271     300 .. 0.70
   2 !   69.4   0.1   4.9e-23   2.2e-19       2      72 .]     347     422 ..     346     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.78
                                    -EE--SSS-EEEEEEEE..S CS
                         MoeA_C   7 dlksdpgrreflRvilt..e 24 
                                    ++ s+ g +e +Rv ++  +
  gi|121636921|ref|YP_977144.1| 276 SVLSELGEMEVVRVAMHpgS 295
                                    55567788899999988444 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 4.9e-23
                                    EEESS-EE--SSS-EEEEEEEE..S-S-EEEEEE-S...---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                         MoeA_C   2 arlaedlksdpgrreflRvilt..eedgeyvaeptg...kqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                    ar+ ++++s +gr+ +lR++l+  +++gey ++ +g     +S+lL++laeAn+l+v+p g+e++++Ge V+v +l
  gi|121636921|ref|YP_977144.1| 347 ARTLSPITSVAGRKGYLRGQLMrdQDSGEYLVQALGgapGASSHLLATLAEANCLVVVPTGAEQIRTGEIVDVAFL 422
                                    8999******************98888*********9999*********************************876 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.2     7e-23   3.1e-19       2     143 ..     195     332 ..     194     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 7e-23
                                    EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                  MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                    v++vG el+       +g+++D n++ la++ +++g+ev ++++v  d++e+ e ++ +l++a+v+++ GG+G ++   +
  gi|121636921|ref|YP_977144.1| 195 VMAVGGELVdisrtpgNGQVYDVNSYALAAAGRDAGAEVNRVGIVSNDPTELGEIVEGQLNRAEVVVIAGGVGGAAAEAV 274
                                    7889999999999999****************************************9999******************** PP

                                    HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                    + +l++l+e+        + rv+++pg+ +g++++   +r  g + + LP +p+++ +++e++++p ++
  gi|121636921|ref|YP_977144.1| 275 RSVLSELGEM-------EVVRVAMHPGSVQGFGQL---GRD-GVPTFLLPANPVSALVVFEVMVRPLIR 332
                                    *********5.......778899999998888888...665.778*******************99875 PP

>> V_ATPase_prox  Vacuolar ATPase Subunit I N-terminal proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.6e-05      0.39      14      38 ..     227     251 ..     223     259 .. 0.82
   2 ?   -4.0   0.2       3.3   1.5e+04      14      27 ..     275     288 ..     272     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.6e-05
                  V_ATPase_prox  14 reLLaeLqrvGvvhLdPLeveeLsa 38 
                                    r+  ae+ rvG+v  dP e  e+  
  gi|121636921|ref|YP_977144.1| 227 RDAGAEVNRVGIVSNDPTELGEIVE 251
                                    66679**************999865 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.3
                  V_ATPase_prox  14 reLLaeLqrvGvvh 27 
                                    r +L+eL  + vv 
  gi|121636921|ref|YP_977144.1| 275 RSVLSELGEMEVVR 288
                                    77888988887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3232.66
//
Query:       gi|121636922|ref|YP_977145.1|  [L=203]
Description: ribosomal-protein-alanine acetyltransferase rimJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-12   46.6   0.0      7e-12   46.2   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    6.1e-05   23.2   0.0    8.7e-05   22.7   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00032   20.9   0.0    0.00037   20.6   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
        2.1    8.5   6.3        3.8    7.7   6.3    1.4  1  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.6e-15     7e-12       3     138 .]      14     158 ..      13     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.6e-15
                 Acetyltransf_3   3 lLrplteeDlealf..el.rsdpevmrylpepltleeaeewlera.........waeeseeeg..ygwaivlkdtgviGs 68 
                                     Lrp++ +D  +++  ++ ++d++     p++++ + +++   ++         +++e +++g  + ++i+l ++ + G 
  gi|121636922|ref|YP_977145.1|  14 RLRPVRMRD--GVHwsRIrLADRAH--LEPWEPSADGEWTVRHTVaawpavcsgLRSE-ARNGrmLPYVIELDGQ-FCGQ 87 
                                    688888877..44411332333332..2688777788877777667777777774432.22333377***55555.8999 PP

                 Acetyltransf_3  69 vglrdleeedee.aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                      + ++ +   + a +gy++ +++ g G+at a++  l+++f    l+r++a++ +eN aS++vl k+Gf+
  gi|121636922|ref|YP_977145.1|  88 LTIGNVTHGALRsAWIGYWVPSAATGGGVATGALALGLDHCFGPVMLHRVEATVRPENAASRAVLAKVGFR 158
                                    9998887776667*****************************9999************************6 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.9e-08   8.7e-05      34     117 .]      74     157 ..      33     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-08
                                    EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHH CS
                 Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaairlY 112
                                      +v+e dg+  G +++  +++    + + ++++V +++ g G+++  l   +++++    +++++++v++ n a+++++
  gi|121636922|ref|YP_977145.1|  74 LPYVIELDGQFCGQLTIGNVTH-GALRSAWIGYWVPSAATGGGVATGALALGLDHCFGPvMLHRVEATVRPENAASRAVL 152
                                    6788******************.67778888****************************888****************** PP

                                    HHTTE CS
                 Acetyltransf_1 113 eklGF 117
                                     k+GF
  gi|121636922|ref|YP_977145.1| 153 AKVGF 157
                                    ****9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.3e-08   0.00037      49     154 ..      73     177 ..      27     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.3e-08
                 Acetyltransf_4  49 eyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgre.lidaleqvlkeqnienllaeiaspnensiq 127
                                      ++ ++ +++  G++++g++   +   +a++ +++   ++   g++   l   l  ++    +++ +a +  +n++s +
  gi|121636922|ref|YP_977145.1|  73 MLPYVIELDGQFCGQLTIGNVTH-GALRSAWIGYWVP-SAATGGGVATGaLALGLDHCFGPVMLHRVEATVRPENAASRA 150
                                    45676666**************9.9***********7.678888887764777788************************ PP

                 Acetyltransf_4 128 fhkalGFelvgifkkcikkngrwiDmi 154
                                    +++++GF+ +g ++++ ++   w D++
  gi|121636922|ref|YP_977145.1| 151 VLAKVGFREEGLLRRYLEVDRAWRDHL 177
                                    ***********************9997 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.3   0.00085       3.8      16      58 ..      81     122 ..      78     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00085
                Bacteriocin_IIc  16 eGGkcaqgtvggivggalaGaatGaatlgilgaavGavvGavv 58 
                                    +G+ c q t+g++  gal  a +G++  + +++++G ++Ga++
  gi|121636922|ref|YP_977145.1|  81 DGQFCGQLTIGNVTHGALRSAWIGYW-VPSAATGGGVATGALA 122
                                    67889999******************.9999999****99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1362.95
//
Query:       gi|121636923|ref|YP_977146.1|  [L=358]
Description: hypothetical protein BCG_1051 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2582.38
//
Query:       gi|121636924|ref|YP_977147.1|  [L=76]
Description: hypothetical protein BCG_1052 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 512.56
//
Query:       gi|121636925|ref|YP_977148.1|  [L=83]
Description: hypothetical protein BCG_1053 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 593.42
//
Query:       gi|121636926|ref|YP_977149.1|  [L=143]
Description: hypothetical protein BCG_1054 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 968.53
//
Query:       gi|121636927|ref|YP_977150.1|  [L=333]
Description: hypothetical protein BCG_1055 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   53.5   0.0    4.2e-14   52.4   0.0    1.6  1  cNMP_binding     Cyclic nucleotide-binding domain
    2.8e-06   28.0   0.0    4.4e-06   27.4   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00034   21.0   0.0     0.0019   18.6   0.0    2.2  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00068   19.9   0.1     0.0015   18.7   0.0    1.7  2  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.048   13.6   0.0       0.13   12.2   0.0    1.8  2  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   1.2e-17   4.2e-14       3      82 ..      40     118 ..      38     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.2e-17
                                    EE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHHH CS
                   cNMP_binding   3 sfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprddf 82 
                                    + +ag+v++rqG+pa s+ ++ sG+++v+++ +dg   ++a+  pG ++Ge+all+++pr+atv+++++ + +   r +f
  gi|121636927|ref|YP_977150.1|  40 RAAAGQVLLRQGEPAVSFLLISSGSAEVSHVGDDGVA-IIARALPGMIVGEIALLRDSPRSATVTTIEPLTGWTGGRGAF 118
                                    6789*******************************76.*****************************9988777666666 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.2e-09   4.4e-06       2     137 ..     156     289 ..     155     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                 Acetyltransf_3   2 LlLrplteeDleal.f.el.rsdpe.vmrylpe.pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdlee 76 
                                    L+Lrp+ + D e++ + ++ +s ++  +r+++   ++  +  ++l+    e +  + + w++++ +++ + ++++ + e 
  gi|121636927|ref|YP_977150.1| 156 LMLRPVLPGDRERTvHgHIqFSGETlYRRFMSArVPS-PALMHYLS----EVDYVDHFVWVVTD-GSDPVADARFVRDET 229
                                    6788888888888866443355555455664442222.22233333....334457899***54.4437********999 PP

                 Acetyltransf_3  77 edeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    +++ ae+ +++a++++g+G+++    al  +a +  g+er+ a++  +N  +++++ + G 
  gi|121636927|ref|YP_977150.1| 230 DPTVAEIAFTVADAYQGRGIGSFLIGALSVAA-RVDGVERFAARMLSDNVPMRTIMDRYGA 289
                                    9999*****************97666665555.8888********************9996 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.81   2.9e+03      40      49 ..     126     135 ..     125     184 .. 0.75
   2 !   18.6   0.0   5.2e-07    0.0019       3      48 ..     207     256 ..     205     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.81
                                    SHHHHHHHHT CS
                 Acetyltransf_7  40 GiGraLleaa 49 
                                    G+G +Ll+ a
  gi|121636927|ref|YP_977150.1| 126 GVGERLLRTA 135
                                    8999999852 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.2e-07
                                    EEEEEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea 48 
                                    + v+V+ d+  +v  +++++++      ++ + V+ +y+g+GiG+ L+ a
  gi|121636927|ref|YP_977150.1| 207 HFVWVVTDGSDPVADARFVRDEtdptVAEIAFTVADAYQGRGIGSFLIGA 256
                                    569******99*999999998876544444488**************976 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.4   8.4e+03      76      89 ..     126     139 ..     126     141 .. 0.86
   2 !   18.7   0.0   4.3e-07    0.0015      44     109 ..     218     281 ..     179     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.4
                                    SHHHHHHHHHHHHH CS
                 Acetyltransf_1  76 GlGsaLlealeera 89 
                                    G+G +Ll+++ +r+
  gi|121636927|ref|YP_977150.1| 126 GVGERLLRTARQRL 139
                                    899****9998876 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.3e-07
                                    EEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHH CS
                 Acetyltransf_1  44 liGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaai 109
                                    +++ +++  +   ++ va+i  + V+ +y+g+G+Gs L+ al   ar  g+++  +   +dn++++
  gi|121636927|ref|YP_977150.1| 218 PVADARFVRDET-DPTVAEI-AFTVADAYQGRGIGSFLIGALSVAARVDGVERFAARMLSDNVPMR 281
                                    555554444444.5556666.9*********************99999999996667777788776 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2     7e+03      67      80 ..     126     139 ..     123     141 .. 0.85
   2 ?   12.2   0.0   3.6e-05      0.13      30      86 ..     206     267 ..     179     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                Acetyltransf_10  67 GigkaLleaveeea 80 
                                    G+g++Ll ++++++
  gi|121636927|ref|YP_977150.1| 126 GVGERLLRTARQRL 139
                                    99*****9999875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.6e-05
                Acetyltransf_10  30 ealllvaeeggkivGviel.rdgs..hisll..fVdpeyrgqGigkaLleaveeeaekdgik 86 
                                    +++++v+++g  +v  ++  rd+    ++ +   V+++y+g+Gig+ L+ a+  +a+ dg +
  gi|121636927|ref|YP_977150.1| 206 DHFVWVVTDGSDPVADARFvRDETdpTVAEIafTVADAYQGRGIGSFLIGALSVAARVDGVE 267
                                    7899999999999999999898888955444338***************9998888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2058.83
//
Query:       gi|121636928|ref|YP_977151.1|  [L=252]
Description: hypothetical protein BCG_1056 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-74  247.9   4.3      8e-70  234.4   1.4    2.0  2  DUF5642   Domain of unknown function (DUF5642)


Domain annotation for each model (and alignments):
>> DUF5642  Domain of unknown function (DUF5642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.1e-06      0.02     165     185 .]       2      22 ..       1      22 [. 0.94
   2 !  234.4   1.4   4.5e-74     8e-70       1     185 []      63     251 ..      63     251 .. 1.00

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
                        DUF5642 165 vppldtefAadLLvktVsalr 185
                                     ppl ++fAadLLvktVs+lr
  gi|121636928|ref|YP_977151.1|   2 RPPLAPQFAADLLVKTVSTLR 22 
                                    689****************98 PP

  == domain 2  score: 234.4 bits;  conditional E-value: 4.5e-74
                        DUF5642   1 dparvkrvrselppgyevtevlptgidPkllwg..lppgltadPaeCaklA.ekalppgakgnaagvsasGeGgiviavv 77 
                                    d+a+v++v+s ++p+y+vt+v p++idP ++ +  lp+gl++dPa+Ca++A +++lp+g++gn+a+vsa+G+G+++++++
  gi|121636928|ref|YP_977151.1|  63 DIAKVAEVKSGFGPEYTVTDVTPRAIDPGFFSArkLPDGLSFDPANCAQVAaGPQLPTGLQGNMAAVSAEGNGNRFVVIA 142
                                    89****************************************************************************** PP

                        DUF5642  78 vetsepvpdnavadeCkkvslsggkttglVevvdaPaidgaqtvgmhrvlqtvveggtetgelaytfvAylgdyvvivtv 157
                                    vets+p+p ++++++C kv++sg +++g +evvd P+idg qt+g+hrvlq+vv g  +tgel y+++A++gdy+viv++
  gi|121636928|ref|YP_977151.1| 143 VETSQPLPAPSPGKDCSKVTFSGTQLRGGIEVVDVPHIDGTQTLGVHRVLQAVVGGSARTGEL-YDYSARFGDYQVIVIA 221
                                    ***************************************************************.**************** PP

                        DUF5642 158 ..ltdpgspvppldtefAadLLvktVsalr 185
                                      l+ pg pv+++dt++A+dLLv++V+a+r
  gi|121636928|ref|YP_977151.1| 222 npLVIPGRPVARVDTQRARDLLVQAVAAVR 251
                                    *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1845.98
//
Query:       gi|121636929|ref|YP_977152.1|  [L=205]
Description: hypothetical protein BCG_1057c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-15   56.7   0.0    5.5e-15   56.1   0.0    1.4  1  2OG-FeII_Oxy_2  2OG-Fe(II) oxygenase superfamily
     0.0096   16.4   0.0      0.015   15.7   0.0    1.3  1  2OG-FeII_Oxy    2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> 2OG-FeII_Oxy_2  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   6.2e-19   5.5e-15      91     192 ..     102     196 ..      42     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.2e-19
                 2OG-FeII_Oxy_2  91 egwspnaalvnfYrdga.riglHqDkees..aleapivSlSLGasatfrfgkesreeeiiailLesGdllvmggesrkay 167
                                     g  +++a   +Yrdg+ ++++H D   +  + + +++ +SLGa+++f +++ + + +  +++L +Gdllvmgg  ++++
  gi|121636929|ref|YP_977152.1| 102 LGEPFTTAGLCYYRDGSdSVAWHGDTIGRgsTEDTMVAIVSLGATRVFALRP-RGRGPSLRLPLAHGDLLVMGGSCQRTF 180
                                    45677788889**************98444477899999************9.57789********************** PP

                 2OG-FeII_Oxy_2 168 .HgvprikkdtapeleleelrtrRin 192
                                     H+vp+    t+           R++
  gi|121636929|ref|YP_977152.1| 181 eHAVPKTSAPTG----------PRVS 196
                                    *****9988654..........4444 PP

>> 2OG-FeII_Oxy  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06     0.015       8      98 ..     112     200 ..     107     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                                    EEE-S------....---EEEEEESSSEEE.EEEE-.TT---EEEETE.EEE----TTEEEEEE-HHHHHHTTS-S---- CS
                   2OG-FeII_Oxy   8 nyypphpdpev....ilglgahtdasllti.llqdd.vgglevfkdgk.wlrvppvdnslivniGdallflsngryksvl 80 
                                    +yy    d       ++g +++t++++++i  l+ + v+ l+  +  + +lr+p          Gd ll++ +  +++++
  gi|121636929|ref|YP_977152.1| 112 CYYRDGSDSVAwhgdTIG-RGSTEDTMVAIvSLGATrVFALRP-RGRGpSLRLPL-------AHGD-LLVMGGSCQRTFE 181
                                    666555444335555788.889999999997777778999987.44445999985.......7788.78888888999** PP

                                    EEE-.---GTGSEEEEEEE CS
                   2OG-FeII_Oxy  81 HrVl.pvnegerRvsiayf 98 
                                    H+V   + ++  Rvsi ++
  gi|121636929|ref|YP_977152.1| 182 HAVPkTSAPTGPRVSIQFR 200
                                    ***977777777****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1496.24
//
Query:       gi|121636930|ref|YP_977153.1|  [L=402]
Description: arginine deiminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-103  346.6   0.0   1.6e-103  346.4   0.0    1.0  1  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.4   0.0  8.8e-108  1.6e-103       1     340 []      19     399 ..      19     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 346.4 bits;  conditional E-value: 8.8e-108
                                    E----HHHHT--TTTTTTTT-SS---HHHHHHHHHHHHHHHHTTT-EEEEHHHHHHHHCTSHHHHHHHHHHHSSTTTTIT CS
                  Amidinotransf   1 mvrPgrflenltetasdnllqddeiilekaqkEHdafvqvLrekGveVlvledllaealeaeearkekldeklleselgi 80 
                                    ++rPg++l++lt++++d+ll+d  +++++aq+EHd+f+++L ++G+eVl+l dll+eal+++ a++++ +++++++ +  
  gi|121636930|ref|YP_977153.1|  19 LHRPGAELRRLTPRNTDQLLFDGLPWVSRAQDEHDEFAELLASRGAEVLLLSDLLTEALHHSGAARMQGIAAAVDAPRLG 98 
                                    79**********************************************************************99998776 PP

                                    TT.........................GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEBSEEEE---S CS
                  Amidinotransf  81 kl.........................gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstigggvvlnpma 135
                                                               ++++++++++++ +l+ ++++  +f+i+plpnlvFtrd++++ig  vv+ ++a
  gi|121636930|ref|YP_977153.1|  99 LPlaqelsaylrsldpgrlahvltagmTFNELPSDTRTDVSLVLRMHHGGDFVIEPLPNLVFTRDSSIWIGPRVVIPSLA 178
                                    6679**************************************************************************** PP

                                    SGGGHHHHHHHHHHHHHSHTSB-EEEEE-T.TS--TT----GGGEEEEETTEEEEEESSSS-HHHHHHHHHHHHHTTS-S CS
                  Amidinotransf 136 apnRrrErllaeliykkhpgvkvakvldis.gkeeesktlEGGdfvvlskgvvaigvssRtdeegieelakklfyktvaf 214
                                     ++R rE +l+ liy++hp++      +++ ++e++++ +EGGd+++l +gvva+gv++Rt+++g+e+la++lf +  a+
  gi|121636930|ref|YP_977153.1| 179 LRARVREASLTDLIYAHHPRF-----TGVRrAYESRTAPVEGGDVLLLAPGVVAVGVGERTTPAGAEALARSLFDDDLAH 253
                                    *******************44.....555546899********************************************* PP

                                    EEEEEE--GGSSTS-GGGTEEEEETTEEEE-HHHH.TT-E..............SS-HHHHHHHHTT-SS-EEEE-C... CS
                  Amidinotransf 215 kviaieipkgraimHldtvftvvdddavvclpsildaegv..............kakereavaqaLkekgleiIeig... 277
                                    +v+a+ i+++ra mHldtv+t+vd+d++v++ +++d+ ++              +a++ ea a+a++ ++l++I++g   
  gi|121636930|ref|YP_977153.1| 254 TVLAVPIAQQRAQMHLDTVCTMVDTDTMVMYANVVDTLEAftiqrtpdgvtigdAAPFAEAAAKAMGIDKLRVIHTGmdp 333
                                    ************************************9988**************************************** PP

                                    ...S-SS-B---S-EEEETTEEEEETTGHHHHHHHHHTT-EEEEE-HTTTGGGS--TTTT-EEEEE CS
                  Amidinotransf 278 ...eeeqwnfggNvLelkpgvvvaydrntvtnekleeagievievpiselerGgGgarCmsaplfr 340
                                       e+eqw++g+N+L+l+pgvvvay+rn +tn+ l++agiev+++++sel+ G+Gg+rCms+p  r
  gi|121636930|ref|YP_977153.1| 334 vvaEREQWDDGNNTLALAPGVVVAYERNVQTNARLQDAGIEVLTIAGSELGTGRGGPRCMSCPAAR 399
                                    ***************************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2732.25
//
Query:       gi|121636931|ref|YP_977154.1|  [L=503]
Description: hypothetical protein BCG_1059c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-18   65.3  25.4    2.9e-17   62.9  11.5    3.5  3  PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltra
    2.5e-17   63.3  14.6    9.6e-13   48.3  15.3    3.6  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer
    5.9e-08   33.1   2.0    5.9e-08   33.1   2.0    3.3  4  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       0.3   1.8e+03      62      83 ..     107     128 ..      98     170 .. 0.58
   2 !    9.6   1.1   0.00011      0.64      58     115 ..     218     283 ..     200     288 .. 0.80
   3 !   62.9  11.5   4.8e-21   2.9e-17       4     199 .]     311     502 ..     309     502 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.3
                       PMT_4TMC  62 lstiallvfvllllalllrrqr 83 
                                    ++ ++l v+++ l++ ++rr  
  gi|121636931|ref|YP_977154.1| 107 FTGALLGVLLVALVVRIVRRIS 128
                                    4444444444444444444332 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                       PMT_4TMC  58 vlwwlstiallvfvllllalllrrqrgvkdl........eeeetr...llnsglflllgwalhylPffl 115
                                    ++ w+++ ++l+f ++ la  ++ +r+++ +        +   ++    +  gl+++  +++ y+P+f 
  gi|121636931|ref|YP_977154.1| 218 ATKWSGVYFVLFFGAMALAFDVAARRQYQVQrpwlgtvrR---DVlpsGYALGLIPFAVYLATYAPWFA 283
                                    56799******99999999999999999988888875432...22344666777*************97 PP

  == domain 3  score: 62.9 bits;  conditional E-value: 4.8e-21
                       PMT_4TMC   4 kflelqkamltsnnaltes....hpyaSepyeWplllrgisywtkneekkq.........iyllGNpvlwwlstiallvf 70 
                                     ++++ ++ ++++++lt+s    hp++S+p++Wp+ lr++ y  ++++ +            l+G p++wwl++ +l+ +
  gi|121636931|ref|YP_977154.1| 311 SLWHYTAKAFHFHAGLTNSagnyHPWESKPWTWPMSLRPVLYAIDQQDVAGcgaqscvkaEMLVGTPAMWWLAVPVLA-Y 389
                                    7899*************978************************976655589999999899***********99999.4 PP

                       PMT_4TMC  71 vllllalllrrqrgvkdleeeetrllnsglflllgwalhylPffl.mgRvlflhhYlpAllfailllaalldfllkslkk 149
                                    +++   +++rr ++              + ++l+g+++ +lP+f  ++R+++++       f ++ ++ +l  +l ++  
  gi|121636931|ref|YP_977154.1| 390 AGWR--MFVRRDWR--------------YAVVLVGYCAGWLPWFAdIDRQMYFFYAATMAPFLVMGISLVLGDIL-YHPG 452
                                    4444..23333332..............35789**********9879*****99777777788888888887777.4555 PP

                       PMT_4TMC 150 slkkkklvklivvvvllvlviavFiffspltyGlpgtseevkklkwlssW 199
                                    + +++++++livv+ +++lv+  F ++ p+  Glp+++++++   wl+sW
  gi|121636931|ref|YP_977154.1| 453 QGSERRTLGLIVVCCYVALVVTNFAWLYPVLTGLPISQQTWNLEIWLPSW 502
                                    555779******************************************** PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0     2e-05      0.12       3      64 ..      31     102 ..      29     105 .. 0.78
   2 !   48.3  15.3   1.6e-16   9.6e-13      80     239 ..     100     280 ..      98     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                            PMT   3 ltllallirlwrlslpnsv...vfdevhfgkfasdYlehs.......ffmdvhpplgkmllalggyLagkdg 64 
                                    +tlla ++r+++l+   +    +fde h+   a++ l++        + + vhpp gk+l+a g +++g++g
  gi|121636931|ref|YP_977154.1|  31 ITLLATVTRFLNLGSLTDAgtpIFDEKHYAPQAWQVLNNHgvednpgYGLVVHPPVGKQLIAIGEAIFGYNG 102
                                    79999999999998776543448*************99872222222445579*****************98 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 1.6e-16
                            PMT  80 vpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkfe.... 155
                                     + ++ R+  allg+l+v+lv+ +++++ +s l++++a +l++ +   ++ +r +lld +L+ff ++++  l+       
  gi|121636931|ref|YP_977154.1| 100 YNGFGWRFTGALLGVLLVALVVRIVRRISRSTLVGAIAGVLLICDGVSFVTARTALLDGFLTFFVVAAFGALIVDRdqvr 179
                                    6899*****************************************************************99998778899 PP

                            PMT 156 ..........rkapf....srswwlwllltgvalglavsvKwvglftvllvgllliw..elwqllgdkslllksi.vkhl 218
                                              r+a +    + + ++w + +gv lgla+ +Kw g+++vl +g +++    + +++++  +++       +
  gi|121636931|ref|YP_977154.1| 180 ermhiallagRSAATvwgpRVGVRWWRFGAGVLLGLACATKWSGVYFVLFFGAMALAfdVAARRQYQVQRPWLGTvRRDV 259
                                    999*****99444441222556789********************99987776554321555666666666655534556 PP

                            PMT 219 laralaliviPvtlylavftv 239
                                    l    al +iP+++yla++++
  gi|121636931|ref|YP_977154.1| 260 LPSGYALGLIPFAVYLATYAP 280
                                    777788999999999998776 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.5   1.5e+04      97     115 ..      21      39 ..      20      41 .. 0.69
   2 !   33.1   2.0   9.9e-12   5.9e-08       2      88 ..      83     170 ..      82     194 .. 0.92
   3 !   11.9   1.0   3.3e-05       0.2      99     145 ..     203     253 ..     198     256 .. 0.84
   4 ?   -2.3   0.8      0.76   4.5e+03     122     151 ..     383     410 ..     369     417 .. 0.56

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.5
                          PMT_2  97 klkywllagvlfGlgflsK 115
                                    +l+ w+++g++  l++ ++
  gi|121636931|ref|YP_977154.1|  21 RLRGWIVTGLITLLATVTR 39 
                                    5677888888777777776 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 9.9e-12
                          PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdaplvl 80 
                                    hPP+   l+a++ ++fg + ++ r+  al+gvl ++l+ +++rr+   + ++++a +ll +  + ++++++  +d +l++
  gi|121636931|ref|YP_977154.1|  83 HPPVGKQLIAIGEAIFGYNGFGWRFTGALLGVLLVALVVRIVRRISRsTLVGAIAGVLLICDGVSFVTARTALLDGFLTF 162
                                    9********************************************997889**********999999999********** PP

                          PMT_2  81 lwalalyl 88 
                                    ++++a  +
  gi|121636931|ref|YP_977154.1| 163 FVVAAFGA 170
                                    **998655 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 3.3e-05
                          PMT_2  99 kyw.llagvlfGlgflsKytaallliaall.yllis..arrilkekkpyla 145
                                    ++w + agvl+Gl++ +K   +++++ + + +l ++  arr  + ++p+l+
  gi|121636931|ref|YP_977154.1| 203 RWWrFGAGVLLGLACATKWSGVYFVLFFGAmALAFDvaARRQYQVQRPWLG 253
                                    788899*******************95545788888977779999999995 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.76
                          PMT_2 122 liaallyllisarrilkekkpylalllall 151
                                    ++++l+y+ ++    ++ ++ y+++l++ +
  gi|121636931|ref|YP_977154.1| 383 AVPVLAYAGWR--MFVRRDWRYAVVLVGYC 410
                                    33344444443..46666777775555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3743.23
//
Query:       gi|121636932|ref|YP_977155.1|  [L=285]
Description: hypothetical protein BCG_1060 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-24   86.5   2.9    3.5e-24   85.9   2.9    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.062   13.3   0.7        1.3    9.0   0.1    2.3  2  DUF4245       Protein of unknown function (DUF4245)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   2.9   3.9e-28   3.5e-24       7     213 .]      11     208 ..       6     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.9e-28
                   TP_methylase   7 vGpGdpellTvrAlralktadvvlgddsr.aleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvll 85 
                                    +++G p + ++r ++al+tadvv+++d+r + +++++l+       +  g+ ++  +++ +  + al +a ++g +V+++
  gi|121636932|ref|YP_977155.1|  11 TPLGQPSDASPRLAAALATADVVAAEDTRrVRKLAKALDI------RIGGRVVSLFDRVEALRVTALLDAINNGATVLVV 84 
                                    678************************8866666665553......345555666666677777777************* PP

                   TP_methylase  86 v.sGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtl 164
                                    + +G P ++++g +lv a+ +  ag++v  +PG+s++++a   +g+p +++  + +    ++++ +++ l++l+++++t 
  gi|121636932|ref|YP_977155.1|  85 SdAGTPVISDPGYRLVAACID--AGVSVTCLPGPSAVTTALVMSGLPAEKFCFEGFAP--RKGAARRAWLAELAEERRTC 160
                                    ****************99999..*************************9666665555..66778*************** PP

                   TP_methylase 165 vllkaprklaelaelLkealyddttpvavveragtedervvrgtleela 213
                                    v++++pr+la  + +  e+l++  +p+a+++++++ +e+vvrg+l ela
  gi|121636932|ref|YP_977155.1| 161 VFFESPRRLAACLNDAVEQLGG-ARPAAICRELTKVHEEVVRGSLDELA 208
                                    ********99999999999777.56*********************986 PP

>> DUF4245  Protein of unknown function (DUF4245)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.014   1.2e+02     104     156 ..      30      89 ..      17      94 .. 0.77
   2 ?    9.0   0.1   0.00015       1.3     142     166 .]     215     239 ..     196     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.014
                        DUF4245 104 ddlvasvlgga....eetgtvevgGrtWqvy..aedkwetalvr.eegdvtvvvtGtase 156
                                    +d+va+++  +     +   +++gGr   ++  +e+ ++tal +  ++++tv+v  +a +
  gi|121636932|ref|YP_977155.1|  30 ADVVAAEDTRRvrklAKALDIRIGGRVVSLFdrVEALRVTALLDaINNGATVLVVSDAGT 89 
                                    55566666555666555557999***9999999999999999876678889999888865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00015
                        DUF4245 142 eegdvtvvvtGtaseeeletlAaal 166
                                      g+ tvvv G+a+ +el  l+a++
  gi|121636932|ref|YP_977155.1| 215 VLGEITVVVAGAAPHAELSSLIAQV 239
                                    45999****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2104.21
//
Query:       gi|121636933|ref|YP_977156.1|  [L=419]
Description: hypothetical protein BCG_1061c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.1    9.9   0.0        1.1    9.9   0.0    3.6  3  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.52   9.3e+03       7       7 ..     146     146 ..     140     151 .. 0.50
   2 ?   -0.4   0.1       0.1   1.9e+03       7      21 ..     248     262 ..     245     268 .. 0.82
   3 ?    9.9   0.0   6.4e-05       1.1       6      40 ..     272     308 ..     271     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.52
                                    S CS
                          HHH_5   7 v 7  
                                    +
  gi|121636933|ref|YP_977156.1| 146 I 146
                                    3 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.1
                                    STT--HHHHHHHHTT CS
                          HHH_5   7 vsGiGpktAlallsa 21 
                                    ++G+ p+  la++ a
  gi|121636933|ref|YP_977156.1| 248 LPGVTPASLLAMAAA 262
                                    79*****99999877 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 6.4e-05
                                    TSTT--HHHHHHHHTT.T.--SHHHHHHS-HHHHHTS CS
                          HHH_5   6 svsGiGpktAlallsa.G.iesvedlaaadveeLaki 40 
                                    s++G+ p + +a++ a G  +s+  la ++++eL+++
  gi|121636933|ref|YP_977156.1| 272 SLPGVSPTDLMAMAAAaGlPTSLPGLAGMSPAELTAL 308
                                    79*************9997889************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2759.95
//
Query:       gi|121636934|ref|YP_977157.1|  [L=478]
Description: aminodeoxychorismate synthase component I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-67  226.3   0.0    5.8e-67  226.0   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.0   0.0   3.3e-71   5.8e-67       2     258 .]     208     455 ..     207     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 3.3e-71
                                    HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTS CS
                Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggr 81 
                                    r+++++ v ++ e+i ag++y++++++++  +     +pl+++ +   r+  + s+++  +   + + SPEl+l+++g+ 
  gi|121636934|ref|YP_977157.1| 208 RAAHRDGVLACLEAIGAGEVYQACVCTQFAGT--VTGSPLDFFIDGFGRTAPSRSAFVAGPWGAVASLSPELFLRRRGS- 284
                                    678899999***********************..7789********************999999*************77. PP

                                    EEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEE CS
                Chorismate_bind  82 rietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstieg 161
                                     ++++pi+GT +  + p        +l++++Ke aE+ mivdl+rndLg+va +g+v+vpel  v+  + v+hlvst+++
  gi|121636934|ref|YP_977157.1| 285 VVTSSPIKGTLPLDAPP-------SALRASAKEVAENIMIVDLVRNDLGRVAVTGTVTVPELLVVRPAPGVWHLVSTVSA 357
                                    ***********886666.......689***************************************************** PP

                                    EESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEE.ETTEEEEEEEE CS
                Chorismate_bind 162 elkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavv.kdkelrlgaGa 240
                                    +++ +  +  ll+a fP+++vtG+Pk ra ++i + E +rRg+Y+G+vg++++ + +el+v+IRt+++ +++++ lg+G+
  gi|121636934|ref|YP_977157.1| 358 RVPLEEPMSALLDAAFPPASVTGTPKLRARQLISQWERYRRGIYCGTVGLASPVAGCELNVAIRTVEFdTAGNAVLGVGG 437
                                    *****************************************************99*************77799******* PP

                                    EEETT--HHHHHHHHHHH CS
                Chorismate_bind 241 GIvadSdpeaEyeEtlaK 258
                                    GI+adSdp+aE++E+l+K
  gi|121636934|ref|YP_977157.1| 438 GITADSDPDAEWAECLHK 455
                                    ****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 3202.23
//
Query:       gi|121636935|ref|YP_977158.1|  [L=567]
Description: hypothetical protein BCG_1063 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-06   25.8   0.0    1.4e-05   25.1   0.0    1.3  1  DUF4832         Domain of unknown function (DUF4832)
  ------ inclusion threshold ------
       0.13   11.6   0.0       0.25   10.6   0.0    1.4  1  Glyco_hydro_42  Beta-galactosidase


Domain annotation for each model (and alignments):
>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.5e-09   1.4e-05      58     193 ..     370     514 ..     344     526 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.5e-09
                        DUF4832  58 lekalkelakmhvsyLnsdy..deavldkwksqgvegrsvydyirkhLGYRfvlessslskkvkaggtlsleltlkNeGf 135
                                    +ek l+++ ++hvs+ +s    d++ +     + +    v+ + ++  GYR+ +e    s++  ag+ +++++t++N+G 
  gi|121636935|ref|YP_977158.1| 370 YEKGLRDVIRYHVSMTSSVNfpDQTATSPMDPALY---LVWAQANAAAGYRYSVEAQPGSQAL-AGKVATISVTWTNYGA 445
                                    55666666666666665555332222233333333...5666777788*******99998777.5*************** PP

                        DUF4832 136 Aalynerkvelvlrdeegeekyklkldadprkwlpgtttt..........itiklklp.selakGkykv 193
                                    Aa+ +++     l+d +g++ ++l++ +d++++ ++++ +          +  ++ ++ s+l++G y++
  gi|121636935|ref|YP_977158.1| 446 AAATEKWVPGYRLVDSTGQVVRTLPAAVDLKTLVSDQRGDrssdqptpasVAETVRVDlSGLPAGHYTL 514
                                    ********************999************7665544455656544444777777777777766 PP

>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.8e-05      0.25      39     130 ..     109     215 ..     105     224 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.8e-05
                                    SBTTB---HHHHHHHHHHHCTT-EEEEE-S..............TTS--HHHHHH-GGGS-B-TTS-B--SSSS---.-T CS
                 Glyco_hydro_42  39 PeegkydFewLdevldllekagikviLatp..............taapPaWlvkkyPeilavdadgskrkfgsrqhi.cl 103
                                    P++ kydF+++d++l +l+++g++  L+                + a+P W               + ++ g  q +  +
  gi|121636935|ref|YP_977158.1| 109 PDDRKYDFSVIDNALTRLADRGMRLTLRVYaysscckasypdgtNIAIPDWERAIASTNTSYPGPATDPSTGVVQVVpNF 188
                                    9999***********************97767778844444444444444432222222222222222233333322246 PP

                                    T-HHHHHHHHHHHHHHHHHHTT-TTEE CS
                 Glyco_hydro_42 104 sspvyrekvakivealaerYkdhpavi 130
                                    + ++y +  a++  al +rY  ++++ 
  gi|121636935|ref|YP_977158.1| 189 NDSTYLNDFAQLLAALGRRYDGDERLS 215
                                    667777777777777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3884.35
//
Query:       gi|121636936|ref|YP_977159.1|  [L=519]
Description: methionyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.6e-106  355.7   0.0    6.9e-63  212.7   0.0    2.0  2  tRNA-synt_1g  tRNA synthetases class I (M)
    1.2e-26   93.2   0.0    3.5e-14   52.0   0.0    3.3  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    6.8e-12   45.3   0.0      9e-06   25.2   0.0    2.1  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00043   20.3   0.0     0.0008   19.4   0.0    1.4  1  Anticodon_1   Anticodon-binding domain of tRNA
     0.0021   17.1   0.0       0.27   10.1   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   0.1   9.2e-45   3.3e-41       1     134 [.       4     137 ..       4     145 .. 0.97
   2 !  212.7   0.0   1.9e-66   6.9e-63     173     390 ..     150     362 ..     137     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 9.2e-45
                                    EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                    ++vtta++Y+n+++H+Gh++e+i++D++aR+krl g++v f++gtDehG +++++A+++gv  ++l++++++ ++++ + 
  gi|121636936|ref|YP_977159.1|   4 YYVTTAIAYPNAAPHVGHAYEYIATDAIARFKRLDGYDVRFLTGTDEHGLKVAQAAAAAGVPTAALARRNSDVFQRMQEA 83 
                                    69****************************************************************************** PP

                                    TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG CS
                   tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdry 134
                                    lnisfd ++rtt+ +h+e+++e+++++ + g iy  +++++y+++derf+ +++
  gi|121636936|ref|YP_977159.1|  84 LNISFDRFIRTTDADHHEASKELWRRMSAAGDIYLDNYSGWYSVRDERFFVESE 137
                                    *************************************************98876 PP

  == domain 2  score: 212.7 bits;  conditional E-value: 1.9e-66
                                    .....EEE.EEEEEE-GGGGHHHHHHHH.HH-TT..SHHHHHHHH.HHHHT----EE-E.SS-SSS-EETTECCEEE-HH CS
                   tRNA-synt_1g 173 gskp.evketehlffklskfekklkewieeeeke..leenvkkivkewlkegLkdlais.rdldwGipvPgaekkvlYVW 248
                                      +p ++ e++ +ff+ls++++kl +++ + +++   +e  ++ v ++++ gL dl+is + +dwG++vP+++++v+YVW
  gi|121636936|ref|YP_977159.1| 150 TGTPvTWTEEQTYFFRLSAYTDKLLAHY-HANPDfiAPETRRNEVISFVSGGLDDLSISrTSFDWGVQVPEHPDHVMYVW 228
                                    44443678899**************999.55556689999999999*************6679***************** PP

                                    HHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE--EEE----- CS
                   tRNA-synt_1g 249 ldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvaheyltvegkKl 328
                                    +dAl +Y++  +      +++e +++yW +       h+igkdii+FH+++wPa+l++a+++lp++++ah++l  +g+K+
  gi|121636936|ref|YP_977159.1| 229 VDALTNYLTGAGFPD---TDSELFRRYWPA-----DLHMIGKDIIRFHAVYWPAFLMSAGIELPRRIFAHGFLHNRGEKM 300
                                    *********999987...7789******44.....49******************************************* PP

                                    ---------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH CS
                   tRNA-synt_1g 329 SkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRv 390
                                    SkS g++v++  ++e l +d++RY+l++e p+ +D ++s e +v r+N++La++lgnl++R+
  gi|121636936|ref|YP_977159.1| 301 SKSVGNIVDPVALAEALGVDQVRYFLLREVPFGQDGSYSDEAIVTRINTDLANELGNLAQRS 362
                                    *************************************************************7 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     4e-12   1.4e-08      27      80 ..       6      59 ..       1     122 [. 0.67
   2 !    4.4   0.0    0.0026       9.3     367     432 ..     149     218 ..     128     222 .. 0.85
   3 !   52.0   0.0   9.9e-18   3.5e-14     484     598 ..     222     335 ..     219     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4e-12
                    tRNA-synt_1 27 lvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80
                                   ++    y + ++H+Gha++ +  d + r+kr++G++v++++G+D +Gl + ++ 
  gi|121636936|ref|YP_977159.1|  6 VTTAIAYPNAAPHVGHAYEYIATDAIARFKRLDGYDVRFLTGTDEHGLKVAQAA 59
                                   55555677889*************************************998764 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0026
                    tRNA-synt_1 367 rskkpiiyrateqWfvrvkeladaalkave.kvqf.vpkskekryaswle.niqdWciSRqr.wWGhrip 432
                                     +++p+     +++f r+++ +d++l++ + +  f  p++++++  s++     d  iSR    WG+++p
  gi|121636936|ref|YP_977159.1| 149 ETGTPVTWTEEQTYFFRLSAYTDKLLAHYHaNPDFiAPETRRNEVISFVSgGLDDLSISRTSfDWGVQVP 218
                                    5789999*******************99997555516999999999999735899*****7527****99 PP

  == domain 3  score: 52.0 bits;  conditional E-value: 9.9e-18
                    tRNA-synt_1 484 edvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrK 563
                                    + v+ vW +      +  g+p++d+e +++++pad+ + G Diir+       + +    + P ++++ hg++  + G K
  gi|121636936|ref|YP_977159.1| 222 DHVMYVWVDALTNYLTGAGFPDTDSELFRRYWPADLHMIGKDIIRFHAVYWPAFLMSAGIELP-RRIFAHGFLH-NRGEK 299
                                    569999***99999999*****************************87777666666666677.88******76.68*** PP

                    tRNA-synt_1 564 mSKslgNvidpldvikkygadalRltli.lsdvgrd 598
                                    mSKs+gN++dp+ +++++g+d +R++l+ + + g+d
  gi|121636936|ref|YP_977159.1| 300 MSKSVGNIVDPVALAEALGVDQVRYFLLrEVPFGQD 335
                                    ***************************977777776 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.5e-09     9e-06      22     122 ..      16     117 ..       3     153 .. 0.78
   2 !   18.0   0.0   4.1e-07    0.0015     235     283 ..     281     329 ..     253     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-09
                                    --BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB.--B CS
                   tRNA-synt_1e  22 ashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptl.epr 100
                                    a h+Gha +++a+D ++r+ +  gYdv+f+    +   k+ + a++++  +++la +  + f++  eaLn+    + ++ 
  gi|121636936|ref|YP_977159.1|  16 APHVGHAYEYIATDAIARFKRLDGYDVRFLTGTDEHGLKVAQAAAAAGVPTAALARRNSDVFQRMQEALNISFDRFiRTT 95 
                                    67****************************99999999********************************9864431344 PP

                                    GGGGHHHHHHHHHHHHHTTSEE CS
                   tRNA-synt_1e 101 vsekvdeiielvekliekgyaY 122
                                     +++ ++  el  ++ + g  Y
  gi|121636936|ref|YP_977159.1|  96 DADHHEASKELWRRMSAAGDIY 117
                                    4455555566666666666555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.1e-07
                                    S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                   tRNA-synt_1e 235 kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                     +l +  + +g+l+  gekmsks++n++   ++ +     q+R++ll +
  gi|121636936|ref|YP_977159.1| 281 IELPRRIFAHGFLHNRGEKMSKSVGNIVDPVALAEALGVDQVRYFLLRE 329
                                    4455555666**********************************99864 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.2e-07    0.0008       1      97 [.     384     479 ..     384     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.2e-07
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.....raaqevllevletllr 75 
                                    d  +l+  + l+++v+ +++   ++ a+ a++  ++ d  + y+ + +p+   +s++++     r++ +v  ev++    
  gi|121636936|ref|YP_977159.1| 384 DAALLATADGLLERVRGHFDAQAMHLALEAIWL-MLGDA-NKYFSVQQPWVLRKSESEAdqarfRTTLYVTCEVVRIAAL 461
                                    5678999999**********************7.78888.***********999988887555333559999******** PP

                    Anticodon_1  76 llaPfmPfitEelwqreeeelg 97 
                                    l++P+mP  + ++     ++lg
  gi|121636936|ref|YP_977159.1| 462 LIQPVMPESAGKIL----DLLG 479
                                    *******8888877....5555 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0035        12      33      70 ..      13      50 ..       2      56 .. 0.87
   2 !   10.1   0.0   7.4e-05      0.27     262     313 ..     280     331 ..     255     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0035
                   tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                   p   +H+G + e + +d++ar  r  g +vr+++  D+
  gi|121636936|ref|YP_977159.1| 13 PNAAPHVGHAYEYIATDAIARFKRLDGYDVRFLTGTDE 50
                                   55679***************************998886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.4e-05
                   tRNA-synt_1f 262 ggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkP 313
                                    g+e P  +    +l + gekms+S Gn++ +  + e +  + +r+++lr+ P
  gi|121636936|ref|YP_977159.1| 280 GIELPRRIFAHGFLHNRGEKMSKSVGNIVDPVALAEALGVDQVRYFLLREVP 331
                                    5667777777778899999*****************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3180.72
//
Query:       gi|121636937|ref|YP_977160.1|  [L=264]
Description: deoxyribonuclease TatD (YjjV protein) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-70  235.6   0.0    6.6e-70  235.4   0.0    1.0  1  TatD_DNase    TatD related DNase
    0.00031   20.2   0.5    0.00088   18.7   0.3    1.9  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.059   12.8   1.6        2.1    7.7   0.1    2.3  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.4   0.0   1.1e-73   6.6e-70       1     254 [.       2     257 ..       2     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.4 bits;  conditional E-value: 1.1e-73
                                    EEEEE-TTS.CCCTTTHHHHH.HHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHH CS
                     TatD_DNase   1 iDaHcHlds.kefeedreeil.eraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelk 78 
                                    +DaH+Hld     ++d  + l era++agv+avv+v  ++++ + v++ a+  + +vya++ +HP+++d  ++   +el+
  gi|121636937|ref|YP_977160.1|   2 VDAHTHLDAcGARDADTVRSLvERAAAAGVTAVVTVADDLESARWVTRAAE-WDRRVYAAVALHPTRADALTDAARAELE 80 
                                    7********7666778777777******************98888887776.5777*************9999999**** PP

                                    HHHHCCCTSEEEEEEEEEET-....CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEE CS
                     TatD_DNase  79 elanvkhskvvaiGeiGLDyy....sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvl 154
                                    +l  v+h++vva+Ge+G+D+y     +  +++++q+e+F ++++lAk++++pl+iH+r+a++d+l++l+++++++ +v+l
  gi|121636937|ref|YP_977160.1|  81 RL--VAHPRVVAVGETGIDMYwpgrLDGCAEPHVQREAFAWHIDLAKRTGKPLMIHNRQADRDVLDVLRAEGAPD-TVIL 157
                                    **..****************644443445778***************************************9999.9*** PP

                                    TT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHH CS
                     TatD_DNase 155 HsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklael 234
                                    H+fs++a +a+ +++ g+ +slsg++ f+na+elre+v  +p ++lL+ETDaPyltp+p+rg +nep +++y+v++lael
  gi|121636937|ref|YP_977160.1| 158 HCFSSDAAMARTCVDAGWLLSLSGTVSFRNARELREAVPLMPVEQLLVETDAPYLTPHPHRGLANEPYCLPYTVRALAEL 237
                                    ******************************************************************************** PP

                                    HTS-HHHHHHHHHHHHHHHH CS
                     TatD_DNase 235 kaltleelaeitaeNakrlf 254
                                     +  +ee+a it++Na+r++
  gi|121636937|ref|YP_977160.1| 238 VNRRPEEVALITTSNARRAY 257
                                    ******************98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.5e-07   0.00088       6     207 ..       1     192 [.       1     220 [. 0.70
   2 ?   -1.5   0.0       0.2   1.2e+03     280     299 ..     240     259 ..     228     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-07
                                    EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSE CS
                   Amidohydro_1   6 lIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvs 85 
                                    ++DaH+Hl              +++   a +++s +++a  +G+t v  +   + ++++++ +aae+   + r++++   
  gi|121636937|ref|YP_977160.1|   1 MVDAHTHLD-------------ACGARDADTVRSLVERAAAAGVTAVVTVAD-DLESARWVTRAAEW---DRRVYAAVA- 62 
                                    59******7.............9*************************9999.677***********...778877732. PP

                                    GGS......GCCCSHHHHHHHHHHHHHHHH.HHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCH CS
                   Amidohydro_1  86 ldr......gsaetskasreklkagaaeti.kgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHaletkg 157
                                               ++  +a+ e+l+a ++ +   +++ ++     l+  + p++++e+ ++ +++ak+ ++p++iH    + 
  gi|121636937|ref|YP_977160.1|  63 --LhptradALTDAARAELERLVAHPRVVAvGETGIDMYWpGRLDGCAEPHVQREAFAWHIDLAKRTGKPLMIHNRQADR 140
                                    ..2445788344444555555555543333033333445556678888999************************77777 PP

                                    HHHHHHHHHTT...TEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HH....HHHHHH CS
                   Amidohydro_1 158 evedaeaafge...tiehgthlevaeslglldeiklilahgvhlt..pt....eaellk 207
                                    +v d+++a g     i h++  + a+        ++++  g++l+   t    +a+ l+
  gi|121636937|ref|YP_977160.1| 141 DVLDVLRAEGApdtVILHCFSSDAAMA-------RTCVDAGWLLSlsGTvsfrNARELR 192
                                    777777777631113555566666555.......8888888888855223333444444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.2
                                    CHHHHHHHHHTHHHHHHTT- CS
                   Amidohydro_1 280 lslkealrmaTingAkalgl 299
                                     +++e+  ++T n+ +a+gl
  gi|121636937|ref|YP_977160.1| 240 RRPEEVALITTSNARRAYGL 259
                                    578999999*********98 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3    0.0044        26      61     107 ..      12      54 ..       2      59 .. 0.69
   2 ?    7.7   0.1   0.00035       2.1       9      88 ..      58     133 ..      47     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0044
                                    TTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHH CS
                   AP_endonuc_2  61 rearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawe 107
                                    ++++     d +++ +e+aaa G+  +v+ + +  +    ++++ w+
  gi|121636937|ref|YP_977160.1|  12 GARD----ADTVRSLVERAAAAGVTAVVTVADDLESARWVTRAAEWD 54 
                                    4455....8999*****************977544444444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00035
                                    -SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEE CS
                   AP_endonuc_2   9 fdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllv 88 
                                    + +v l++  ++  +    +++r+  ++l ++   +a+ ++ ++ ++p+   ++a+   +++a+  +i+la++ G pl++
  gi|121636937|ref|YP_977160.1|  58 YAAVALHPTRADALT----DAARAELERLVAHPRVVAVGETGIDMYWPGRLDGCAEPHVQREAFAWHIDLAKRTGKPLMI 133
                                    667788888888887....35666666777777777999********99997777745569****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1742.09
//
Query:       gi|121636938|ref|YP_977161.1|  [L=362]
Description: resuscitation-promoting factor rpfB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-35  120.4   5.0    7.4e-35  119.4   5.0    1.5  1  Transglycosylas  Transglycosylase-like domain
    3.6e-23   81.0   7.5    1.7e-07   30.9   1.4    3.5  3  DUF348           G5-linked-Ubiquitin-like domain
      8e-17   61.4   1.4    1.7e-16   60.4   1.4    1.6  1  G5               G5 domain


Domain annotation for each model (and alignments):
>> Transglycosylas  Transglycosylase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   5.0   1.2e-38   7.4e-35       3      77 .]     281     355 ..     279     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 1.2e-38
                                    THHHHHHHHHHHHSS-TT-TTSSSEBTTTTBEHHHHHHTTCCST.SCGGGS-HHHHHHHHHHHHHHHCGGGSTTC CS
                Transglycosylas   3 desnwdaiAqcEsggnwaintgnGyyGglqfsqstWeavggekyapsaaqAsreqQiavAekvlatqGagaWptc 77 
                                    des wdaiA cE+ggnwaintgnGyyGg+qf+q tWea+gg +yap+a+ A+re+QiavAe +  +qG+gaWp+c
  gi|121636938|ref|YP_977161.1| 281 DESIWDAIAGCEAGGNWAINTGNGYYGGVQFDQGTWEANGGLRYAPRADLATREEQIAVAEVTRLRQGWGAWPVC 355
                                    5789**********************************************************************9 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   1.4   2.8e-11   1.7e-07       1      39 [.      27      65 ..      27      75 .. 0.98
   2 !   26.5   0.1   6.7e-10     4e-06       2      30 ..      85     114 ..      84     118 .. 0.93
   3 !   25.9   0.0     1e-09   6.2e-06       1      40 [.     141     180 ..     141     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.8e-11
                                   EEEEETTEEEEE----SSHHHHHHHTT----TT-EEES- CS
                         DUF348  1 VtltvDGktvtvrTaadTVgdlLeeagitlgeqDkVsPs 39
                                   VtltvDG  + v+T+++ V d+ ee+g +++++D ++P+
  gi|121636938|ref|YP_977161.1| 27 VTLTVDGTAMRVTTMKSRVIDIVEENGFSVDDRDDLYPA 65
                                   9*************************************8 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 6.7e-10
                                    EEEETTE.EEEE----SSHHHHHHHTT--- CS
                         DUF348   2 tltvDGk.tvtvrTaadTVgdlLeeagitl 30 
                                    +++ DG   ++v+T+a+TV ++L+++ +t+
  gi|121636938|ref|YP_977161.1|  85 QISLDGHdAKQVWTTASTVDEALAQLAMTD 114
                                    7999**********************9995 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 1e-09
                                    EEEEETTEEEEE----SSHHHHHHHTT----TT-EEES-T CS
                         DUF348   1 VtltvDGktvtvrTaadTVgdlLeeagitlgeqDkVsPsL 40 
                                    V+l+++G  +tv+ +a++V++lL++ag++l + D V P+ 
  gi|121636938|ref|YP_977161.1| 141 VQLNDGGLVRTVHLPAPNVAGLLSAAGVPLLQSDHVVPAA 180
                                    899*9999******************************95 PP

>> G5  G5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   1.4   2.9e-20   1.7e-16       2      75 .]     198     271 ..     197     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.9e-20
                                    EEEEEE.EE---EEEEE-TTS-TT-EEEEE--B-EEEEEEEEEEEETTEEEEE---EEEEEE--B-EEEEE--E CS
                             G5   2 kevteeeeipfetetkeDpslpkgeekVvqeGknGvkevtyrvtyenGkevsrevvseevvkepvpevvkvGtk 75 
                                    k+vte  ++p++  ++eDp+++   e+V+ +G++G+++vt+ v  +nG+e++r  v++ vv+++ ++vv+vGtk
  gi|121636938|ref|YP_977161.1| 198 KKVTERLPLPPNARRVEDPEMNMSREVVEDPGVPGTQDVTFAVAEVNGVETGRLPVANVVVTPAHEAVVRVGTK 271
                                    789****************************************99****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2364.53
//
Query:       gi|121636939|ref|YP_977162.1|  [L=317]
Description: dimethyladenosine transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-39  133.7   0.0    7.5e-39  133.4   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    8.5e-05   23.2   0.0    0.00017   22.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0013   19.4   0.0     0.0022   18.7   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0043   17.7   0.0     0.0095   16.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0045   16.8   0.0      0.011   15.6   0.0    1.7  2  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.15   11.8   0.1       0.21   11.3   0.1    1.2  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.4   0.0   2.5e-42   7.5e-39       4     258 ..      30     287 ..      27     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 2.5e-42
                                    CXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.....TCCCE CS
                         RrnaAD   4 lrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.....kdekl 78 
                                     rks+gqnf+++ +++ +++ ++ ++ ++ vle+gpG G lT  L++r   v+++E+d+ La +lq+++      + ++l
  gi|121636939|ref|YP_977162.1|  30 PRKSLGQNFVHDANTVRRVVAASGVSRSDLVLEVGPGLGSLTLALLDRGATVTAVEIDPLLASRLQQTVAehshsEVHRL 109
                                    699****************************************************************9998877777899 PP

                                    EEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHH CS
                         RrnaAD  79 kvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrls 158
                                    +vv++D+l       +        + +vvanlPy++  +   +ll  + + ++ +++++q e+a+rl+a+pgsk+++  s
  gi|121636939|ref|YP_977162.1| 110 TVVNRDVLALRREDLA------AAPTAVVANLPYNVAVPALLHLLV-EFPSIRVVTVMVQAEVAERLAAEPGSKEYGVPS 182
                                    *******999988855......7**********************5.77779**************************** PP

                                    HHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S.--S-H..HHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHH CS
                         RrnaAD 159 vlreaftdvklvakveksifsPppkvdsalvelerkdedl.pqkdl..kkyesvvrkllnrkrktlstslksllpggelq 235
                                    v + +f  v+    v +++f+P p+v s lv+++r ++++ p  d   ++   +v ++++++rkt ++++ +    g   
  gi|121636939|ref|YP_977162.1| 183 VKLRFFGRVRRCGMVSPTVFWPIPRVYSGLVRIDRYETSPwPTDDAfrRRVFELVDIAFAQRRKTSRNAFVQWAGSGSES 262
                                    *************************************99886555422778899***************99877666544 PP

                                    HCTT...T--TTTCCCCSGHHHHHH CS
                         RrnaAD 236 alsst..gindnalvkklsaeqtld 258
                                    a+      i+   + + ls++++++
  gi|121636939|ref|YP_977162.1| 263 ANRLLaaSIDPARRGETLSIDDFVR 287
                                    4322233666666666666666665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.5e-08   0.00017       1      62 [.      60     123 ..      60     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.5e-08
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGBSSST CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedlpfed 62 
                                    vL++G G G ltlal++r+  a+vt+v+i++ +  + ++ ++e++     ++++v+ d+ +l  ed
  gi|121636939|ref|YP_977162.1|  60 VLEVGPGLGSLTLALLDRG--ATVTAVEIDPLLASRLQQTVAEHSHsevhRLTVVNRDVLALRRED 123
                                    9*****************5..************999999998844445589********9998665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.5e-07    0.0022       1      64 [.      61     122 ..      61     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-07
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg 64 
                                    Le+G G Gsl+ all++  ++++t+v+i+p    + ++  a+++   ++++++ ++d+l l  +
  gi|121636939|ref|YP_977162.1|  61 LEVGPGLGSLTLALLDR--GATVTAVEIDPLLASRLQQTVAEHSHSEVHRLTVVNRDVLALRRE 122
                                    8****************..************************************999877655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.2e-06    0.0095       1      52 [.      61     116 ..      61     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.2e-06
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEEC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl....kvefvvada 52 
                                    L+vG G G+l+ al +rga+v++v++++ +  + ++ + e  +    ++++v  d+
  gi|121636939|ref|YP_977162.1|  61 LEVGPGLGSLTLALLDRGATVTAVEIDPLLASRLQQTVAEHSHsevhRLTVVNRDV 116
                                    89**************************9997777766666555555666666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.5e-06     0.011      25      68 ..      59     102 ..      11     158 .. 0.80
   2 ?   -2.4   0.0       1.2   3.7e+03     129     159 ..     265     293 ..     235     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqk 68 
                                     vL++G+G G+l+  l ++g++vt+v+++p + ++++++   ++
  gi|121636939|ref|YP_977162.1|  59 LVLEVGPGLGSLTLALLDRGATVTAVEIDPLLASRLQQTVAEHS 102
                                    69****************************98888763333333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                Methyltransf_23 129 llldwlylvpagrhisffsarslkelleeaG 159
                                    +ll  + ++pa r +   s +++ +ll+++G
  gi|121636939|ref|YP_977162.1| 265 RLLA-ASIDPA-RRGETLSIDDFVRLLRRSG 293
                                    3332.345666.7778888888888888877 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     7e-05      0.21      93     177 ..      48     136 ..      37     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                                    HHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC..EEEEES-GGG---TT-E CS
                         Met_10  93 rlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv..vkpileDgrevireqla 169
                                     +a+  v+  ++V++v  G G +++++    ++ +v a++++P     l++ ++    ++v  +++++ D+  + re+la
  gi|121636939|ref|YP_977162.1|  48 VVAASgVSRSDLVLEVGPGLGSLTLALLD--RGATVTAVEIDPLLASRLQQTVAEHSHSEVhrLTVVNRDVLALRREDLA 125
                                    3333359999***********99999987..99***********999999999876554431156777777777766555 PP

                                    E...EEEE--T CS
                         Met_10 170 d...rvvmnlp 177
                                         vv nlp
  gi|121636939|ref|YP_977162.1| 126 AaptAVVANLP 136
                                    44444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2408.63
//
Query:       gi|121636940|ref|YP_977163.1|  [L=306]
Description: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-08   35.4   1.1    2.9e-08   34.0   1.1    1.8  1  GHMP_kinases_C  GHMP kinases C terminal
      2e-08   34.3   0.3      2e-08   34.3   0.3    2.2  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   1.1   3.2e-12   2.9e-08       2      80 ..     207     279 ..     206     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.2e-12
                 GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                    l+al +gd + l+ ll     +e  a + +l p+l ++l+a  e+Gal++ +sG+  Gpt++ l+++ + a +v  +l+
  gi|121636940|ref|YP_977163.1| 207 LAALAAGDPDQLAPLLG----NEMQAAAVSLDPALARALRAGVEAGALAGIVSGS--GPTCAFLCTSASSAIDVGAQLS 279
                                    679999**********9....53334*****************************..********99999998887775 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.3   2.2e-12     2e-08       2      66 .]      91     148 ..      90     148 .. 0.89
   2 ?   -2.6   0.8      0.75   6.7e+03      56      56 ..     258     258 ..     227     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.2e-12
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                    i i++ iPv+ G+++++A+a+a+++A+++l+       +l +    l  ++   g Dv+++++Gg
  gi|121636940|ref|YP_977163.1|  91 IMIDKSIPVAGGMAGGSADAAAVLVAMNSLW-------ELNVPRRDLRMLAARLGSDVPFALHGG 148
                                    89*****************************.......677777766666788********9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.75
                                    S CS
                 GHMP_kinases_N  56 g 56 
                                    g
  gi|121636940|ref|YP_977163.1| 258 G 258
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2075.98
//
Query:       gi|121636941|ref|YP_977164.1|  [L=104]
Description: hypothetical protein BCG_1069 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 763.28
//
Query:       gi|121636942|ref|YP_977165.1|  [L=544]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-66  222.3   0.1    1.1e-65  221.9   0.1    1.1  1  AMP-binding      AMP-binding enzyme
    1.8e-06   28.1   0.0    3.2e-06   27.4   0.0    1.3  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9   0.1   1.2e-69   1.1e-65      20     422 ..      27     442 ..       9     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 1.2e-69
                                    TEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE CS
                    AMP-binding  20 gqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvli 99 
                                      + T++e++er++ +A gL ++Gv+ gd+V++l+   +e   +++a+++ Ga + +l   +++ +la   ed+   + +
  gi|121636942|ref|YP_977165.1|  27 PVRHTWGEVHERARCIAGGLAAAGVGLGDVVGVLAGFPVEIAPTAQALWMRGASLTMLHQPTPRTDLAVWAEDTMTVIGM 106
                                    6789*****************99**************************************************9999999 PP

                                    ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEE CS
                    AMP-binding 100 atvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVml 179
                                      ++++++     + ++ +   ++ +l++++++  + ++  + s+     p  + e+ +ddla+++ TSG+TG PK+V++
  gi|121636942|ref|YP_977165.1| 107 --IEAKAV-----IVSE-PFLVAIPILEQKGMQVLTVADLLA-SD-----PIGPIEVGEDDLALMQLTSGSTGSPKAVQI 172
                                    ..554442.....2222.333445667776666553333333.22.....3344479*********************** PP

                                    EHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEE CS
                    AMP-binding 180 shrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtvia 258
                                    +hrn+ +n+ ++ +  + ++ ++dv++s+lp++h++g++ +l ++++ Ga++v +++ ++ +d  l+++li+k++ t ++
  gi|121636942|ref|YP_977165.1| 173 THRNIYSNAEAMFVGAQYDV-DKDVMVSWLPCFHDMGMVGFLTIPMFFGAELVKVTPMDFlRDTLLWAKLIDKYQGT-MT 250
                                    ***********984444434.79*************************************88899************.66 PP

                                    EEHHHHHHHHHCCCHHCHHHHC....CGTT-SEEEEESS-EBHHHHHHHHHHHTC......EEEEEEEEGGGSSECEE.. CS
                    AMP-binding 259 gvPrvleallesgalkaakkak....dlsslrlvllggeplspellrffralfge......evlegYGlTEttgvvtv.. 326
                                    ++P ++ all+++ +++a   k    dls lr++l+g+ep++p+ ++ + + +++      ++l +YG++Ett +v++  
  gi|121636942|ref|YP_977165.1| 251 AAPNFAYALLAKRLRRQA---KpgdfDLSTLRFALSGAEPVEPADVEDLLDAGKPfglrpsAILPAYGMAETTLAVSFse 327
                                    777777777665434322...12335**************************999*****99**************7777 PP

                                    ......................CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHH CS
                    AMP-binding 327 ......................lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpea 384
                                                          + +++++++l + G+ l + e++i+De+ g  +p   +G + +rg+++++gYl     
  gi|121636942|ref|YP_977165.1| 328 cnaglvvdevdadllaalrravPATKGNTRRLATLGPLLQDLEARIIDEQ-GDVMPARGVGVIELRGESLTPGYLTM--- 403
                                    889999****************5558888899****************98.9***********************66... PP

                                    HHHHEEE...TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 385 taeafds...egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        f++   e +w+ TGDlg+l+e+G++ ++gR kd+i++
  gi|121636942|ref|YP_977165.1| 404 --GGFIPaqdEHGWYDTGDLGYLTEEGHVVVCGRVKDVIIM 442
                                    ..45554332546**************************86 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.5e-10   3.2e-06       1      91 [.     444     536 ..     444     538 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.5e-10
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET..TEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--.EEEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg..elDelevkvEvkegfsdelkelealekkiakklksklgvsv.kvelv 77 
                                    G n++P+ ie++  ++++v p   + v+ +   ++++++v vE +   +++ +e +++e+++a+++ +++ v++ +v ++
  gi|121636942|ref|YP_977165.1| 444 GRNIYPTDIERAAGRVDGVRPGCAVAVRLDAghSRESFAVAVESNA--FEDPAEVRRIEHQVAHEVVAEVDVRPrNVVVL 521
                                    78*********************99998875125777777777665..56679********************85799** PP

                                    -TT-S----.----- CS
                AMP-binding_C_2  78 epgtlprse.gKakr 91 
                                     pgt+p++  gK++r
  gi|121636942|ref|YP_977165.1| 522 GPGTIPKTPsGKLRR 536
                                    *******85259888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4200.79
//
Query:       gi|121636943|ref|YP_977166.1|  [L=191]
Description: peptidyl-tRNA hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-58  196.5   0.0    3.6e-58  196.3   0.0    1.0  1  Pept_tRNA_hydro  Peptidyl-tRNA hydrolase


Domain annotation for each model (and alignments):
>> Pept_tRNA_hydro  Peptidyl-tRNA hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.3   0.0     2e-62   3.6e-58       1     170 [.       6     187 ..       6     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 2e-62
                                    EEEE---SSTCCTTCGGGHHHHHHHHHHHH............TCEEEEEETTEEEEEEEESS-GGGHHHHHHHHHHHCT- CS
                Pept_tRNA_hydro   1 livGLGNpgkeYektRHNvGflvvdelakk............aevaegkiegekvlllkPqtymNlsGeavkellkfyki 68 
                                    l+vGLGNpg++Y++tRHN+Gf v+d la +            aeva+g+ +g++++l+kP+ ymN+sG+ +  l+kfy++
  gi|121636943|ref|YP_977166.1|   6 LVVGLGNPGANYARTRHNLGFVVADLLAARlgakfkahkrsgAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSV 85 
                                    89*************************988888888888888888888******************************** PP

                                    -..GEEEEEEETTSSTTEEEEEESS--TT-HHHHHHHHHHT-S-SEEEEEEE---ST-CGGHHHHCTSB-HHHHHC.HHH CS
                Pept_tRNA_hydro  69 eseeilvvhDdldlplgkirlkkkgssgghnGlksiikklgtekfvRlriGIgrpekakkkvadyVLskfskeeek.lee 147
                                    ++ +i+v+hDdldl++g+irlk +g++gghnGl+s++++lgt++f+R+riGIgrp+  +k+ a +VL++f+ +e++ + +
  gi|121636943|ref|YP_977166.1|  86 APANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPG-RKDPAAFVLENFTPAERAeVPT 164
                                    99*****************************************************98.768**********999666*** PP

                                    HHHHHHHCHHHHHHHTSCCHCCC CS
                Pept_tRNA_hydro 148 vlekaaealeellkeeleaamnk 170
                                    ++e+aa+a+e l+++++e a+n+
  gi|121636943|ref|YP_977166.1| 165 ICEQAADATELLIEQGMEPAQNR 187
                                    *************9889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1282.14
//
Query:       gi|121636944|ref|YP_977167.1|  [L=215]
Description: 50S ribosomal protein L25 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-23   81.9   0.1    7.1e-23   80.9   0.1    1.5  1  Ribosomal_L25p   Ribosomal L25p family
    3.9e-16   59.2   3.6    7.2e-16   58.3   3.6    1.4  1  Ribosomal_TL5_C  Ribosomal protein TL5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L25p  Ribosomal L25p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.1   7.9e-27   7.1e-23       1      81 []       9      95 ..       9      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 7.9e-27
                                   EEEEECTS.SCCCHHHHHHTTEEEEEEEESSSCEEEEEEEHHHHHHHCH....CSEEEEEETT..CEEEEEEEEEETTTTCE CS
                 Ribosomal_L25p  1 LkaekRte.gkgaarrlRregkvPavlyGggkepisisvdakelrkllkt...stlieLevdg..ekvllkdvqrhpvkdki 76
                                   L +++Rte gkga+rr Rr+gk+PavlyG+g ep++++++ ++   +l++   +++++L++ g  + +l k+++ hp++++i
  gi|121636944|ref|YP_977167.1|  9 LRVTVRTEtGKGASRRARRAGKIPAVLYGHGAEPQHLELPGHDYAAVLRHsgtNAVLTLDIAGkeQLALTKALHIHPIRRTI 90
                                   67899*988***************************************889**********98778**************** PP

                                   EEEEE CS
                 Ribosomal_L25p 77 lHvDF 81
                                    H+D+
  gi|121636944|ref|YP_977167.1| 91 QHADL 95
                                   ****7 PP

>> Ribosomal_TL5_C  Ribosomal protein TL5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   3.6     8e-20   7.2e-16       1      84 [.     103     181 ..     103     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 8e-20
                                    -SEEEEEEEEES..--TTTTTTSEEEESSSEEEEESSTTS--SSEEEE-TT--SSBEEETTTS--SSS-EESS-TTSEEE CS
                Ribosomal_TL5_C   1 kvtveVpvhfvgeeespgvkkggvleqvlreveveclpkdlPeeievDvsgleigdsihvsdlklpegvelltdpdevvv 80 
                                    kv veV v+++g  + +g     +++q+ +++e+e+++ ++Pe+++v+++g e g++++++++ lp+gv+l++dpd +vv
  gi|121636944|ref|YP_977167.1| 103 KVVVEVSVVVEG--Q-AG--PDTLVTQETNSIEIEAEALSIPEQLTVSIEGAEPGTQLTAGQIALPAGVSLISDPDLLVV 177
                                    799*********..3.44..467********************************************************* PP

                                    EEE- CS
                Ribosomal_TL5_C  81 svva 84 
                                    +vv+
  gi|121636944|ref|YP_977167.1| 178 NVVK 181
                                    **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1609.52
//
Query:       gi|121636945|ref|YP_977168.1|  [L=252]
Description: lipoprotein lpqT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-48  163.5   0.0    4.6e-48  163.0   0.0    1.2  1  Lpp-LpqN  Probable lipoprotein LpqN
  ------ inclusion threshold ------
       0.13   11.1   1.9       0.18   10.6   1.9    1.2  1  EP400_N   E1A-binding protein p400, N-terminal


Domain annotation for each model (and alignments):
>> Lpp-LpqN  Probable lipoprotein LpqN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.0   5.1e-52   4.6e-48       2     139 ..      57     189 ..      56     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 5.1e-52
                                    SS-HHHHHHHTT-EEEE--STT--SEEEE----TT-EE-SS---TTEEEEEEETT.SSSSS-EEEEEEEEEEES---HHH CS
                       Lpp-LpqN   2 svtladYleengvteepvaagdlgaltvdlplPegWedagdpnledayaviaktqpesgedtptavllvskLtGdvDpae 81 
                                    +v+l++Yle+ gvt+epva+++l++ltv++p+P+gW+++++pn+++++++iak     ge++pta+l+v+kL++d+D ae
  gi|121636945|ref|YP_977168.1|  57 PVPLWKYLESVGVTGEPVAPSSLTDLTVSIPTPPGWAPMKNPNITPNTEMIAK-----GESYPTAMLMVFKLHRDFDIAE 131
                                    589*************************************************9.....9********************* PP

                                    HHCCTTHHHHTSTT-EEEEEE---BTTB-EEEEEEEEECTTEEEEEEEEEEEEEETT. CS
                       Lpp-LpqN  82 alehapvdaqnlpgfkatdgstadlsGfpssqieGtYdkdgkrlavaqrtViitgapp 139
                                    al+h+++da+ +++f+++d+stad++Gfpss+i+G+Yd++g+rl++++r+V+ tga +
  gi|121636945|ref|YP_977168.1| 132 ALKHGTADARLSTNFTELDSSTADFNGFPSSMIQGSYDLHGRRLHTWNRIVFPTGAGQ 189
                                    ******************************************************9764 PP

>> EP400_N  E1A-binding protein p400, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.9     2e-05      0.18      41     105 ..      18      91 ..       4      98 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2e-05
                        EP400_N  41 spvasfasaaspsapqspnyqiimsrspvtGqnvnit.........lqnvGqvvagnqqitltplplqnpaspg 105
                                      va++a +a    p+sp++q i+s sp t      t         l++vG         +lt l +  p+ pg
  gi|121636945|ref|YP_977168.1|  18 VAVATLAMSAVACGPKSPDFQSILSTSPTTSAVSTTTevpvplwkyLESVGVTGEPVAPSSLTDLTVSIPTPPG 91 
                                    56899***********************9865332221112222224555522222333456666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1757.40
//
Query:       gi|121636946|ref|YP_977169.1|  [L=326]
Description: ribose-phosphate pyrophosphokinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-46  155.2   0.0    1.4e-45  153.9   0.0    1.6  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    5.3e-21   75.5   0.2    2.3e-20   73.4   0.1    2.0  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.4e-18   67.0   0.2    5.1e-18   65.1   0.1    2.0  2  Pribosyltran    Phosphoribosyl transferase domain
    2.2e-05   24.0   0.0    3.6e-05   23.3   0.0    1.2  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.18   11.3   0.1       0.51    9.8   0.0    1.8  2  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.0     4e-49   1.4e-45       1     116 []      12     128 ..      12     128 .. 0.99
   2 ?   -2.3   0.0       1.2   4.2e+03      29      56 ..     205     232 ..     183     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 4e-49
                 Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasak 80 
                                    l++fag++++eLae++ak+l+v++++ + ++fa+gEi v+++esvrg+d f++qs+ +pvn  lme l+midal+r+sak
  gi|121636946|ref|YP_977169.1|  12 LMLFAGRAHPELAEQVAKELDVHVTSQDAREFANGEIFVRFHESVRGCDAFVLQSCPAPVNRWLMEQLIMIDALKRGSAK 91 
                                    589***************************************************************************** PP

                 Pribosyltran_N  81 ritaViPylgysrqdrk.ksrepisaklvaklLeaaG 116
                                    ritaV+P+++y+rqd+k + repisa+l+a+lL++aG
  gi|121636946|ref|YP_977169.1|  92 RITAVMPFYPYARQDKKhRGREPISARLIADLLKTAG 128
                                    *****************889***************99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                 Pribosyltran_N  29 vsrfadgEikveieesvrgkdvfiiqsl 56 
                                     +r +++ ++ ++  +v g+++++i ++
  gi|121636946|ref|YP_977169.1| 205 DPRVPNQVVSNRVVGDVAGRTCVLIDDM 232
                                    5566777777788888999999998876 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   5.7e+03     103     120 ..     121     138 ..     119     140 .. 0.81
   2 ?   -1.3   0.0      0.52   1.8e+03       4      34 ..     171     202 ..     170     215 .. 0.84
   3 !   73.4   0.1   6.4e-24   2.3e-20      76     183 ..     216     322 ..     200     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                    HHHHHHTT--EEEEEEEE CS
                 Pribosyl_synth 103 aevlkerGaykiyvlath 120
                                    a++lk  Ga +i+ +  h
  gi|121636946|ref|YP_977169.1| 121 ADLLKTAGADRIVTVDLH 138
                                    789999999999887666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                                    GEEEEESSGGGHHHHHHHHHHTT.-EEEEE-- CS
                 Pribosyl_synth   4 navivakspgsakkatsyaerlr.lglavihG 34 
                                    n v+v+ + g ++ a+ +a+ l  + la ih 
  gi|121636946|ref|YP_977169.1| 171 NMVVVSPDSGRVRIAEKWADALGgVPLAFIHK 202
                                    78999999999999******995378899985 PP

  == domain 3  score: 73.4 bits;  conditional E-value: 6.4e-24
                                    -EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-T CS
                 Pribosyl_synth  76 tvvGdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcs 155
                                     vvGdv+Gr  +++dd+id   ++  a  +l++ Ga  +++ athG+ls+ a+++l +    ev+vtnt+p      r  
  gi|121636946|ref|YP_977169.1| 216 RVVGDVAGRTCVLIDDMIDTGGTIAGAVALLHNDGAGDVIIAATHGVLSDPAAQRLASCGAREVIVTNTLPIGE-DKRFP 294
                                    69*********************************************************************987.56899 PP

                                    TEEEE--HHHHHHHHHHHHHT---TT-S CS
                 Pribosyl_synth 156 kiktvdislllaeairrihngesmsylf 183
                                    ++  + i+ lla +ir ++++ s++ lf
  gi|121636946|ref|YP_977169.1| 295 QLTVLSIAPLLASTIRAVFENGSVTGLF 322
                                    ***********************99998 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.44   1.6e+03     107     133 ..      82     108 ..      80     132 .. 0.73
   2 !   65.1   0.1   1.4e-21   5.1e-18      22     130 ..     163     269 ..     145     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.44
                                    HHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                   Pribosyltran 107 lelLkekgpeevriavlvdkpateeev 133
                                    +++Lk+  ++++ ++ ++++ a++ ++
  gi|121636946|ref|YP_977169.1|  82 IDALKRGSAKRITAVMPFYPYARQDKK 108
                                    678888889988888888554444433 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 1.4e-21
                                    EEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSS CS
                   Pribosyltran  22 ileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtG 100
                                    i+++y+  + vvv +++g v +a + ad+L +vpla++ k++    +++++++         +d+ag++++++DD++dtG
  gi|121636946|ref|YP_977169.1| 163 IRDNYPDGNMVVVSPDSGRVRIAEKWADALgGVPLAFIHKTRDPRVPNQVVSNR------VVGDVAGRTCVLIDDMIDTG 236
                                    44559*************************************999999999874......789***************** PP

                                    HHHHHHHHHHHCC-BSEEEEEEEE...E-HHHH CS
                   Pribosyltran 101 gTllaalelLkekgpeevriavlv...dkpate 130
                                    gT+  a+ lL++ g+  v+ia+ +     pa +
  gi|121636946|ref|YP_977169.1| 237 GTIAGAVALLHNDGAGDVIIAATHgvlSDPAAQ 269
                                    *********************998666444444 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     1e-08   3.6e-05      88     174 ..     191     276 ..     182     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1e-08
                        UPRTase  88 llpearvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvk 167
                                    +l ++++  +   r++     + + n++  ++a rt +l+D +i TGg++a a+ lL + g+g   I     + s  +++
  gi|121636946|ref|YP_977169.1| 191 ALGGVPLAFIHKTRDPR-VPNQVVSNRVVGDVAGRTCVLIDDMIDTGGTIAGAVALLHNDGAGDVIIAATHGVLSDPAAQ 269
                                    55566666666667774.4557888999999*********************************9999999********9 PP

                        UPRTase 168 rlaeefp 174
                                    rla+   
  gi|121636946|ref|YP_977169.1| 270 RLASCGA 276
                                    9997655 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   4.2e+03      30      63 ..      22      55 ..      18      68 .. 0.55
   2 ?    9.8   0.0   0.00014      0.51     122     158 ..     224     259 ..     209     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                       PRTase_2 30 stvreagaaLaellaeakkeelpepvlvigfAEt 63
                                   + +++++++L  ++++++++e+++  +++ f E 
  gi|121636946|ref|YP_977169.1| 22 ELAEQVAKELDVHVTSQDAREFANGEIFVRFHES 55
                                   4444444444444444444556666666666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
                       PRTase_2 122 kelvLvDDEistGktalnliralqeklprkryvvvsl 158
                                    ++ vL+DD i tG t++  +  l+++   + + +++ 
  gi|121636946|ref|YP_977169.1| 224 RTCVLIDDMIDTGGTIAGAVALLHNDGAGDVI-IAAT 259
                                    789*****************999998766544.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2224.62
//
Query:       gi|121636947|ref|YP_977170.1|  [L=495]
Description: bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-22   75.8   6.7    3.6e-05   23.3   0.1    5.0  5  Hexapep          Bacterial transferase hexapeptide (six repea
    2.3e-20   73.6   7.1    3.9e-20   72.8   4.8    2.3  2  NTP_transf_3     MobA-like NTP transferase domain
    5.4e-17   62.2   0.0    7.4e-17   61.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    3.5e-11   43.3   3.6    3.5e-11   43.3   3.6    2.2  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    7.1e-09   35.3   6.8      0.045   13.5   0.1    5.7  6  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.052   13.5   0.0       0.12   12.2   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   1.2e-08   3.6e-05       1      35 [.     277     311 ..     277     312 .. 0.94
   2 !    9.9   0.1    0.0002       0.6       2      28 ..     296     321 ..     295     323 .. 0.90
   3 !   19.7   0.0   1.7e-07    0.0005       1      35 [.     328     362 ..     328     363 .. 0.94
   4 !   10.9   0.1   9.7e-05      0.29       1      33 [.     363     394 ..     363     397 .. 0.93
   5 !   22.5   0.1   2.1e-08   6.4e-05       2      35 ..     406     439 ..     405     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    +++IG +++I+p+++++g ++IG ++++g+ ++++
  gi|121636947|ref|YP_977170.1| 277 DVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLT 311
                                    589***************************99986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0002
                                    EEEETTEEE-TTEEEETTEEE-TTEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                    t+IG  +++gp +++  +V +Gd++ +
  gi|121636947|ref|YP_977170.1| 296 TQIGGRCVVGPDTTL-TDVAVGDGASV 321
                                    79*************.*******9976 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 1.7e-07
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    s+ IG+++ +gpf+++++++ +G + k+ga+v ++
  gi|121636947|ref|YP_977170.1| 328 SSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVK 362
                                    578*****************************997 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 9.7e-05
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                    +++IG ++++ + +++ g++ IG+++ Iga +v
  gi|121636947|ref|YP_977170.1| 363 NSTIGTGTKVPHLTYV-GDADIGEYSNIGASSV 394
                                    579*************.*************998 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 2.1e-08
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    t++Gs+v  g+ +++ ++V+IGd+++ gag+v++
  gi|121636947|ref|YP_977170.1| 406 TTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVR 439
                                    79******************************97 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   4.8   1.3e-23   3.9e-20       1     124 [.       9     143 ..       9     262 .. 0.80
   2 ?    0.3   0.0      0.26   7.8e+02      21      77 ..     280     336 ..     277     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.3e-23
                                    EEEEEESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC.........HHHHHHTTCTS-EEE-TTSS CS
                   NTP_transf_3   1 aviLAGGrSsRmgg..dKallplggkpllervldalraagvdevvvvggde.........evlaalarlgvrvvededpg 69 
                                    +++LA+G ++Rm +  +K l  l+g+++l +vl a++++  ++++vv g++         e++ +  ++ ++v+ ++   
  gi|121636947|ref|YP_977170.1|   9 VLVLAAGPGTRMRSdtPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDhqriaplvgELA-DTLGRTIDVALQD-RP 86 
                                    58**********9888***********************99******9995343333222221.2234457777776.46 PP

                                    -SHHHHHHHHHHHH...SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                   NTP_transf_3  70 kgplaslaaalraaa..dadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                     g++++++++l+a++   a  v+v+++D+Pll++++++ l+a ++a +a+v+v+t+ 
  gi|121636947|ref|YP_977170.1|  87 LGTGHAVLCGLSALPddYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTT 143
                                    9************88668999***********************9999999887765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                    CCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                   NTP_transf_3  21 lggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplasla 77 
                                    +g  ++++   + l + +++  +vvg+d  +++ + + g++vv+   ++  ++ + a
  gi|121636947|ref|YP_977170.1| 280 IGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAA 336
                                    56667777777888888899999*****9999999999******9877766666665 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.5e-20   7.4e-17       3     225 ..      10     231 ..       8     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.5e-20
                                    EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
                NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                    ++La G GtR++    +  +k ++ l + +++ ++l+++a+   +++ivvl ++h+ ++    + ++ +g ++ +al++ 
  gi|121636947|ref|YP_977170.1|  10 LVLAAGPGTRMR----SDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDR 85 
                                    79********95....7789999999999*****************99999888876655444445557789******** PP

                                    --BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEE CS
                NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrve 160
                                    + gt +Av+ ++  l d++   +v+v +gD    d  ++ ++++ +++ +a   vt++++  +++ +yG i + ++++v 
  gi|121636947|ref|YP_977170.1|  86 PLGTGHAVLCGLSALPDDY-AGNVVVTSGDTPLLDadTLADLIATHRAVSA--AVTVLTTTLDDPFGYGRILRTQDHEVM 162
                                    *******************.69********97766689*************..9************************** PP

                                    EEECS....-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTT CS
                NTP_transferase 161 rfvEK....PkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkd 225
                                     +vE     P++ +    +++G+Y f+  +l  +++   ++ +++e  +td++  + ++g+   a   +d
  gi|121636947|ref|YP_977170.1| 163 AIVEQtdatPSQRE-IREVNAGVYAFDIAALRSALSrLSSNNAQQELYLTDVIAILRSDGQTVHASHVDD 231
                                    ****8444455555.789******************89999999*********99999998776655555 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   3.6   1.2e-14   3.5e-11       2     195 ..       8     225 ..       7     250 .. 0.68
   2 ?   -1.9   0.2      0.75   2.3e+03     178     200 ..     313     335 ..     307     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.2e-14
                                    EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG........CCEEEEE- CS
                           IspD   2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld........ksiqlvaG 73 
                                    +v++ AAG G+Rm++++pK + +l+g+++l+h ++a+++  a ++++vv+ +d+ ++++ l ++         ++ l + 
  gi|121636947|ref|YP_977170.1|   8 AVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKL-APQRLIVVLGHDH-QRIAPLVGEladtlgrtIDVALQDR 85 
                                    58999********************************995.5566666666555.6888888777777885445666666 PP

                                    -SSHHHHHHHHHHTTSSTT.SEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEE..E-SS.....EEEEEETTT...B CS
                           IspD  74 GdeRaesVlnglkalegea.kfVLvHDaARpllkaadiaellaaaeqstqgailal..pvkD.....tikrveadg...l 142
                                         ++Vl gl al+++    V+v  +  pll a+++a+l+a+ +   ++a+ +l   + D      i r++ ++   +
  gi|121636947|ref|YP_977170.1|  86 PLGTGHAVLCGLSALPDDYaGNVVVTSGDTPLLDADTLADLIATHRA-VSAAVTVLttTLDDpfgygRILRTQDHEvmaI 164
                                    67778**********9987699**********************997.66666555114555222222444443333322 PP

                                    EEE...EETGTTEEEEEEE.EEEEHHHHHHHHHHH....HHCT---SSHHHHHHHTT--EE CS
                           IspD 143 vae...tedRegLwaaqtP.qgFrvdlllaahakg....eqegaeitDdaslvekiGlsvk 195
                                    v +   t+   +++++     +F+++ l++a+++      q+    tD +++++  G++v+
  gi|121636947|ref|YP_977170.1| 165 VEQtdaTPSQREIREVNAGvYAFDIAALRSALSRLssnnAQQELYLTDVIAILRSDGQTVH 225
                                    2221114445555555543246777777776665433333444556677777777676666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.75
                                    ---SSHHHHHHHTT--EEEEE-- CS
                           IspD 178 aeitDdaslvekiGlsvkvVeGe 200
                                    + + D as+v++ G s  + +G 
  gi|121636947|ref|YP_977170.1| 313 VAVGDGASVVRTHGSSSSIGDGA 335
                                    567899**********9999986 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.5e-05     0.045       2      28 ..     278     306 ..     277     312 .. 0.88
   2 !   11.8   0.4     5e-05      0.15       2      25 ..     296     320 ..     295     321 .. 0.88
   3 !    6.5   0.0    0.0024       7.1       3      28 ..     330     357 ..     329     357 .. 0.90
   4 ?   -3.5   0.0       3.2   9.5e+03      13      17 ..     363     367 ..     362     370 .. 0.50
   5 ?    2.5   0.0     0.043   1.3e+02       4      16 ..     383     396 ..     381     402 .. 0.79
   6 !    9.8   0.0   0.00022      0.66       2      32 ..     406     438 ..     405     440 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                    EEE-TT-EE-TT-EE.S.EEE-TT-EE-T CS
                      Hexapep_2   2 viIGdnCliGanagi.G.vslGdncvvga 28 
                                    v+IG +++i++     G +++G +cvvg+
  gi|121636947|ref|YP_977170.1| 278 VTIGRDTVIHPGTQLlGrTQIGGRCVVGP 306
                                    89************55***********98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5e-05
                                    EEE-TT-EE-TT-E.ESEEE-TT-E CS
                      Hexapep_2   2 viIGdnCliGanag.iGvslGdncv 25 
                                    + IG +C++G++ + + v +Gd++ 
  gi|121636947|ref|YP_977170.1| 296 TQIGGRCVVGPDTTlTDVAVGDGAS 320
                                    57**********9967******986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0024
                                    EE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                      Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvga 28 
                                    +IGd   +G++ +   G+ lG + ++ga
  gi|121636947|ref|YP_977170.1| 330 SIGDGAAVGPFTYLrpGTALGADGKLGA 357
                                    7************889*****9877776 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 3.2
                                    T-EES CS
                      Hexapep_2  13 nagiG 17 
                                    n++iG
  gi|121636947|ref|YP_977170.1| 363 NSTIG 367
                                    45554 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.043
                                    E-TT-EE-TT-E.E CS
                      Hexapep_2   4 IGdnCliGanag.i 16 
                                    IG+ ++iGa+++ +
  gi|121636947|ref|YP_977170.1| 383 IGEYSNIGASSVfV 396
                                    9999******9955 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00022
                                    EEE-TT-EE-TT-E.E.SEEE-TT-EE-TT-EE CS
                      Hexapep_2   2 viIGdnCliGanag.i.GvslGdncvvgaGvvi 32 
                                    +++G  +  G++   + +v++Gd++  gaG v+
  gi|121636947|ref|YP_977170.1| 406 TTVGSHVRTGSDTMfVaPVTIGDGAYTGAGTVV 438
                                    567777788888887579*************98 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.12      16     120 ..      26     135 ..       8     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                                    GGGSEETTEEHHHHHHHHHHHTTTTSE..EEEEES-HHHHHHHHHTT......SEEEE--TTCSSHHHHHHHHHHHHTTT CS
                   CTP_transf_3  16 Knlldlggkpliayvleaalkskafek..vivaTDseeiknvakefg......asvlvtrsslesdterflevvkaflms 87 
                                    K+l  l+g+ ++ +vl+a+ k +  ++  v++  D+++i+ ++ e+       + v + + +l ++ + ++    a+  +
  gi|121636947|ref|YP_977170.1|  26 KVLHTLAGRSMLSHVLHAIAKLAP-QRliVVLGHDHQRIAPLVGELAdtlgrtIDVALQDRPLGTGHAVLCGLS-ALPDD 103
                                    9*****************999555.66789999*****997776665544477888888888888866665544.44444 PP

                                    .TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
                   CTP_transf_3  88 eneeiivnlqGdnPllqeevikkaietlkenqe 120
                                      +  +v + Gd Pll+  +++ +i t++    
  gi|121636947|ref|YP_977170.1| 104 -YAGNVVVTSGDTPLLDADTLADLIATHRAVSA 135
                                    .355788899*************9999987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2954.61
//
Query:       gi|121636948|ref|YP_977171.1|  [L=197]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-17   62.1   0.1    5.1e-17   61.4   0.1    1.4  1  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.033   14.6   0.0        0.5   10.9   0.0    2.2  2  HTH_40    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   5.7e-21   5.1e-17       4      45 ..      13      54 ..      10      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 5.7e-21
                                   HHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  4 aArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                    Ar lfaerGyd+t+++eIA+rA+vsk+ +Y +F++Ke+L++
  gi|121636948|ref|YP_977171.1| 13 IARSLFAERGYDGTSIEEIAQRANVSKPVVYEHFGGKEGLYA 54
                                   69**************************************86 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.5e-05       0.5      11      33 ..      24      46 ..      20      73 .. 0.93
   2 ?    1.3   0.0     0.053   4.8e+02      22      40 ..     166     184 ..     159     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.5e-05
                         HTH_40 11 eglsieeIAkerglkesTIegHL 33
                                   +g sieeIA++ ++++  +++H+
  gi|121636948|ref|YP_977171.1| 24 DGTSIEEIAQRANVSKPVVYEHF 46
                                   699*******************7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.053
                         HTH_40  22 rglkesTIegHLaelieeg 40 
                                    r+ k+  ++ HL++l+ +g
  gi|121636948|ref|YP_977171.1| 166 REPKKEVVAAHLVNLVWNG 184
                                    7778999********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1257.99
//
Query:       gi|121636949|ref|YP_977172.1|  [L=1234]
Description: transcription-repair coupling factor mfd [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-28   98.4   0.0    6.6e-28   97.3   0.0    1.7  1  CarD_CdnL_TRCF  CarD-like/TRCF domain
    6.6e-23   80.9   0.0    3.1e-21   75.5   0.0    3.0  3  TRCF            TRCF domain
    2.5e-19   69.3   0.0    5.9e-19   68.0   0.0    1.7  1  UvrB_inter      UvrB interaction domain
    4.3e-16   59.2   0.1    9.1e-16   58.1   0.1    1.6  1  DEAD            DEAD/DEAH box helicase
    5.6e-16   58.9   0.4    4.1e-14   52.9   0.1    2.6  3  Helicase_C      Helicase conserved C-terminal domain
    0.00023   21.2   0.0    0.00081   19.4   0.0    1.8  1  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.022   14.0   0.1       0.73    9.0   0.0    3.1  3  LSDAT_prok      SLOG in TRPM, prokaryote
       0.11   12.8   0.1        1.6    9.0   0.1    2.7  2  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> CarD_CdnL_TRCF  CarD-like/TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0     3e-31   6.6e-28       1      96 []     518     620 ..     518     620 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3e-31
                 CarD_CdnL_TRCF   1 lkvGDyVvhedhGiGriegiekrevegaekeylvleyad.k......kgdklyvPvdqldlirkyiskeepkldklggkr 73 
                                    l+ GD+Vvh +hGiGr++++++r+v ga++eylvleya+ k      + dklyvP+d+ld++++y++ ++p l++lgg++
  gi|121636949|ref|YP_977172.1| 518 LTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASaKrgggakNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSD 597
                                    578***********************************95488999977*****************999*********** PP

                 CarD_CdnL_TRCF  74 wektkekakkgvkeeaaelvkly 96 
                                    w++tk+ka+++v+e+a elv ly
  gi|121636949|ref|YP_977172.1| 598 WANTKTKARRAVREIAGELVSLY 620
                                    ********************998 PP

>> TRCF  TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.5   7.8e+03      31      47 ..      69      85 ..      66      87 .. 0.86
   2 ?    1.4   0.0      0.19   4.2e+02      38      65 ..     638     664 ..     636     668 .. 0.87
   3 !   75.5   0.0   1.4e-24   3.1e-21       1      77 [.    1060    1136 ..    1060    1152 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                           TRCF 31 eeeldeleeeLiDrFGk 47
                                    +e d+l++eL+  FG+
  gi|121636949|ref|YP_977172.1| 69 GREADDLAAELRGVFGD 85
                                   5789***********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                           TRCF  38 eeeLiDrFGklpeevenLlevarlklla 65 
                                    ++eL+D FG ++e v++L ++ ++k+ +
  gi|121636949|ref|YP_977172.1| 638 QAELEDAFG-FTETVDQLTAIEEVKADM 664
                                    78*******.7899*******9999866 PP

  == domain 3  score: 75.5 bits;  conditional E-value: 1.4e-24
                           TRCF    1 ldvdalipeeYipdeserlelYkriasieteeeldeleeeLiDrFGklpeevenLlevarlkllakklgiekikekk 77  
                                     l+vda++p++Yi+++++rle Y+r+a++++++e+ ++ +eL+Dr+G lpe++++L +varl+ll++  gi+++++ +
  gi|121636949|ref|YP_977172.1| 1060 LPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAAS 1136
                                     79***********************************************************************9743 PP

>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   2.6e-22   5.9e-19       1      84 [.     154     236 ..     154     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.6e-22
                     UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgkslekl 80 
                                    l+l+vg++ + + ++++Lvel Y+r d++ +rG+F+vrG +++if+++  e+++r+ef+gdei ++r +  ++++s+ ++
  gi|121636949|ref|YP_977172.1| 154 LTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPT-AEHPVRVEFWGDEITEMRMFSVADQRSIPEI 232
                                    789*********************************************.5**************************9998 PP

                     UvrB_inter  81 eeit 84 
                                    +  t
  gi|121636949|ref|YP_977172.1| 233 DIHT 236
                                    7555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   4.1e-19   9.1e-16      15     173 ..     670     811 ..     650     814 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.1e-19
                                    CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT..STSEEE.EEETTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky..idlrvl.liiggvaardql 91 
                                     d ++++++G+GKT++++ +++++v     ++g+++ +++Pt+ La q+l+++ ++++   ++++ l  ++   + r  +
  gi|121636949|ref|YP_977172.1| 670 MDRVICGDVGYGKTEIAVRAAFKAV-----QDGKQVAVLVPTTLLADQHLQTFGERMSGfpVTIKGLsRFTDAAESRAVI 744
                                    57789*****************999.....7899************************7334455442334455557777 PP

                                    HHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  92 skldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                    + l  g vdiv+gt+  l+  +     + +++ ++V+DE +r+  +  +++i+++ +++            v+ +SAT+ 
  gi|121636949|ref|YP_977172.1| 745 DGLADGsVDIVIGTHRLLQTGV-----RWKDLGLVVVDEEQRFGVE-HKEHIKSLRTHV-------D----VLTMSATPI 807
                                    7776557********7777644.....499***************9.9******99999.......2....*******98 PP

                                    .HHH CS
                                    .xxx RF
                           DEAD 171 .kdv 173
                                     +++
  gi|121636949|ref|YP_977172.1| 808 pRTL 811
                                    6665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.6   1.7e+04      79      93 ..     476     490 ..     473     496 .. 0.82
   2 ?    3.3   0.0     0.046     1e+02      10      89 ..     691     775 ..     682     786 .. 0.75
   3 !   52.9   0.1   1.8e-17   4.1e-14      12     110 ..     853     954 ..     843     955 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.6
                                    SSTSTTESEEEESSS CS
                     Helicase_C  79 GidipkvnlVinfdl 93 
                                    G+ ip++nlV++ + 
  gi|121636949|ref|YP_977172.1| 476 GVIIPGANLVVITET 490
                                    8889******99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.046
                                    HHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES.GGGTSSSTSTT CS
                     Helicase_C  10 lkleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiat.dvaerGidipk 84 
                                    +k  ++g+++ + v+t+  +++ ++ + e+     +++  l   + + e +++++   +g++d++i t + +++G+  ++
  gi|121636949|ref|YP_977172.1| 691 FKAVQDGKQVAVLVPTTLLADQhLQTFGERMsgfPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGThRLLQTGVRWKD 770
                                    4788999999999999998886767775555633455555666699*****************88877256777777777 PP

                                    ESEEE CS
                     Helicase_C  85 vnlVi 89 
                                    + lV+
  gi|121636949|ref|YP_977172.1| 771 LGLVV 775
                                    66665 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 1.8e-17
                                    HTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESE CS
                     Helicase_C  12 leeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnl 87 
                                    +  ++g++  + n++++++  +  ++  +   + +v+v hg++p +  e ++++f + e+d+L++t+++e+G+di ++n+
  gi|121636949|ref|YP_977172.1| 853 ELLRDGQAFYVHNRVSSIDAaAARVR--ElvpEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANT 930
                                    34688999999999998886633332..233599********************************************** PP

                                    EEESSSS.SSHHHHHHHHTTSSST CS
                     Helicase_C  88 Vinfdlp.rnvtsyiqriGRtgRa 110
                                    +i   ++ +++++++q +GR+gR 
  gi|121636949|ref|YP_977172.1| 931 LIVERADtFGLSQLHQLRGRVGRS 954
                                    *******888*************6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.6e-07   0.00081       8     169 ..     653     806 ..     647     808 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.6e-07
                                    HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEE CS
                         ResIII   8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigk 87 
                                    Q +aie++++ +++      +i    G GKT +a++++ +  + gk  ++ +lvp++ l +q l++f + +s        
  gi|121636949|ref|YP_977172.1| 653 QLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGK--QVAVLVPTTLLADQHLQTFGERMSGF----PV 726
                                    8889999999998877788899999******************977..9******************6666542....22 PP

                                    EESSS-B--................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-- CS
                         ResIII  88 kvsgdkkka.........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfk 158
                                     ++g ++              ++ + +i++ t   l+             + +   ++++DE  r+g  ++ ++i+    
  gi|121636949|ref|YP_977172.1| 727 TIKGLSRFTdaaesraviDGLADGSVDIVIGTHRLLQTGV----------RWKDLGLVVVDEEQRFGV-EHKEHIKSLRT 795
                                    3333333330011122323333444555555544444444..........344444888888888888.66777777777 PP

                                    -SEEEEEESS- CS
                         ResIII 159 eavllglTATp 169
                                    +  +l ++ATp
  gi|121636949|ref|YP_977172.1| 796 HVDVLTMSATP 806
                                    77788888888 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00033      0.73     137     169 ..      49      81 ..      22      98 .. 0.82
   2 ?    0.1   0.0      0.18   4.1e+02     106     152 ..     271     316 ..     253     359 .. 0.83
   3 ?   -1.4   0.0      0.51   1.1e+03     133     165 ..     683     715 ..     674     739 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00033
                     LSDAT_prok 137 lkdiresvkagrpilvvaGsgrladeiaaalrg 169
                                    +  ++ +++++ p+lvv+ +gr ad++aa+lrg
  gi|121636949|ref|YP_977172.1|  49 RLLVASALARQGPLLVVTATGREADDLAAELRG 81 
                                    5558899********************999876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                     LSDAT_prok 106 GdEspwlarlatala.ekkpsvt.vlvnGgeitlkdiresvkagrpilv 152
                                    G+ s++la+la+ +a ++ ++v  vl  +g+  l    +++  g p+lv
  gi|121636949|ref|YP_977172.1| 271 GSASDMLAKLAEGIAvDGMEAVLpVLWSDGHALLT---DQLPDGTPVLV 316
                                    8899***********87778888899999996554...45555555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.51
                     LSDAT_prok 133 geitlkdiresvkagrpilvvaGsgrladeiaa 165
                                     ei+++ + ++v+ g+++ v+  +  lad+ ++
  gi|121636949|ref|YP_977172.1| 683 TEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQ 715
                                    579999999******************998554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.1   6.9e+03      22      70 ..     242     290 ..     240     318 .. 0.61
   2 ?    9.0   0.1   0.00071       1.6       9     121 ..     673     805 ..     672     824 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                         AAA_22  22 lrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka 70 
                                    +r+ll + d +a a++  +r +    + ++ +s +d+l +l++ + +++ +
  gi|121636949|ref|YP_977172.1| 242 CRELLLSEDVRARAAQlaARHP--AAESTVTGSASDMLAKLAEGIAVDGME 290
                                    7777778777777777444444..444444455588888888877776655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00071
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdl..lrellralglelk 69 
                                    v++G +G GKT  + r + +++++ k+                   er + + vt+++++  +d    r++   l +   
  gi|121636949|ref|YP_977172.1| 673 VICGDVGYGKTEIAVRAAFKAVQDGKQVAvlvpttlladqhlqtfgERMSGFPVTIKGLSRFTDAaeSRAVIDGLAD--G 750
                                    79999999999999999988877655555777667666655555555555555555555533333112222222222..1 PP

                         AAA_22  70 aerlsseellealeqalraravielliiDEaqhlr..seealeeLrsllnl...srk 121
                                        +     ++l q   + ++ +l+++DE q++   ++e+++ Lr+ +++   s +
  gi|121636949|ref|YP_977172.1| 751 --SVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGveHKEHIKSLRTHVDVltmSAT 805
                                    ..2345555544444444444469*********965448888888887776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 8045.14
//
Query:       gi|121636950|ref|YP_977173.1|  [L=325]
Description: nucleoside triphosphate pyrophosphohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-24   85.1   0.0    5.4e-24   84.2   0.0    1.5  1  MazG      MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
      0.015   15.8   0.1      0.032   14.7   0.1    1.6  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0     6e-28   5.4e-24       1      73 [.     107     181 ..     107     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 6e-28
                                    --HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH..HH---HHHHHHHHHHHHHHH-GGG CS
                           MazG   1 qtpetllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaee..eggidledvaetileKlerRhphv 73 
                                    qt+++l +ylleE++E+++a++++  d+l+eELGD+Llqvlf+a+iae+  ++ ++++dva+t+++Kl +R p v
  gi|121636950|ref|YP_977173.1| 107 QTHDSLRRYLLEETYELLDAVRSGSVDQLREELGDLLLQVLFHARIAEDasQSPFTIDDVADTLMRKLGNRAPGV 181
                                    89**********************************************98899******************9976 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.5e-06     0.032      20      60 ..     105     145 ..      90     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                                    -HHHHHHHHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHH CS
                         PRA-PH  20 taelaslraaligEEavElleaasegdlaeladelaDllYv 60 
                                    ++++ + ++ ++ EE  Ell+a+  g+  +l +el Dll +
  gi|121636950|ref|YP_977173.1| 105 SEQTHDSLRRYLLEETYELLDAVRSGSVDQLREELGDLLLQ 145
                                    4455555999****************************754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2362.66
//
Query:       gi|121636951|ref|YP_977174.1|  [L=243]
Description: lipoprotein lpqU [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.0   5.3    1.6e-05   24.3   0.5    2.6  2  SLT_2     Transglycosylase SLT domain
    0.00067   19.3   0.0     0.0017   18.0   0.0    1.7  1  SLT       Transglycosylase SLT domain


Domain annotation for each model (and alignments):
>> SLT_2  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.8e-09   1.6e-05     151     197 ..     156     201 ..      97     215 .. 0.85
   2 !    5.3   0.4    0.0011        10     272     290 ..     216     234 ..     213     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-09
                          SLT_2 151 SwaGamGltQFmPssylkyAvDfdgdgrrDlwnspaDalaSvAnyLk 197
                                    ++  amG +QF+ ++++ y+v   +dg +++ n  +Da  S+A yL 
  gi|121636951|ref|YP_977174.1| 156 AVERAMGPMQFISETWRLYGVAARNDGIANVDN-IDDAALSAAGYLC 201
                                    55669************************9976.***********95 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0011
                          SLT_2 272 vitrYNrStlYalaVaela 290
                                    +++ YN+S +Ya aV   a
  gi|121636951|ref|YP_977174.1| 216 ALRAYNNSVIYARAVRDWA 234
                                    7899***********8766 PP

>> SLT  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-07    0.0017      12      96 ..      96     222 ..      86     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-07
                                    S-HHHHHHHHHHHHTT-TT-B-...TTS....................................EBTTTTBETTTHHHHH CS
                            SLT  12 vepsllaaiaqvESgfnpkAvs...ksg....................................avGLmQimpstakrlg 52 
                                    +++++la i +vES+   +      ++g                                    a+G mQ++++t + +g
  gi|121636951|ref|YP_977174.1|  96 LAWTTLAGIGRVESHHGTYRGAtiaPNGdvsppirgvrldgtggtlrivdrdgggldgdaaverAMGPMQFISETWRLYG 175
                                    5566666666666664433222222444566666666666666777777777777777778888**************** PP

                                    HHHT.-SHHHHCSHHHHHHHHHHHHHHHHHTTTT..HHHHHHHHHHH CS
                            SLT  53 lrvk.lsedelldPeknisagakyLkslykqyng..slllalaAYNa 96 
                                       + +++ ++ +  +++  +a yL ++ k + +   ++ al AYN+
  gi|121636951|ref|YP_977174.1| 176 VAARnDGIANVDNIDDAALSAAGYLCWRGKDLATprGWITALRAYNN 222
                                    9988899*************************99999*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1890.00
//
Query:       gi|121636952|ref|YP_977175.1|  [L=429]
Description: phosphopyruvate hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.3e-124  415.3   0.0   1.7e-124  414.9   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.8e-56  188.9   0.0    6.1e-56  188.2   0.0    1.3  1  Enolase_N  Enolase, N-terminal domain
    1.1e-10   41.4   0.1    1.8e-10   40.8   0.1    1.4  1  MR_MLE_C   Enolase C-terminal domain-like
     0.0076   15.4   0.0      0.012   14.8   0.0    1.3  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   0.0  3.7e-128  1.7e-124       2     290 ..     139     418 ..     138     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 3.7e-128
                                    -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHH CS
                      Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnke 81 
                                    ++lPvP++n++nGG ha+ ++++qefm++P+ga+sf ealr+Gaevyh lksvlkk++   +t +GdeGGfaP++  +  
  gi|121636952|ref|YP_977175.1| 139 HILPVPMMNILNGGAHADTAVDIQEFMVAPIGAPSFVEALRWGAEVYHALKSVLKKEG--LSTGLGDEGGFAPDVAGTTA 216
                                    79*******************************************************9..99****************** PP

                                    HHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S- CS
                      Enolase_C  82 aldliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpld 159
                                    aldli+ aie aG ++  +v +ald+a++ef+++    y +++ +         t++q++++y  l   yP+vsiedpl 
  gi|121636952|ref|YP_977175.1| 217 ALDLISRAIESAGLRPgaDVALALDAAATEFFTDG-TGYVFEGTT--------RTADQMTEFYAGLLGAYPLVSIEDPLS 287
                                    ***************999**************666.678877666........799************************ PP

                                    TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC- CS
                      Enolase_C 160 eddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGe 239
                                    eddw++w+ lt+++gd+vqivGdd++vtnp+rl+e+ie+++anall+kvnqiG+lte+l+av la++ gy +++shrsGe
  gi|121636952|ref|YP_977175.1| 288 EDDWDGWAALTASIGDRVQIVGDDIFVTNPERLEEGIERGVANALLVKVNQIGTLTETLDAVTLAHHGGYRTMISHRSGE 367
                                    ******************************************************************************** PP

                                    -S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GG CS
                      Enolase_C 240 tedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGk 290
                                    tedt+iadlav++ +GqiktGaparser+akynqllriee+lg++a+yaG 
  gi|121636952|ref|YP_977175.1| 368 TEDTMIADLAVAIGSGQIKTGAPARSERVAKYNQLLRIEEALGDAARYAGD 418
                                    *************************************************96 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.2   0.0   1.4e-59   6.1e-56       1     131 []       4     133 ..       4     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 1.4e-59
                                    EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSB CS
                      Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligld 80 
                                    I++v areildSrGnpTvevev + dg+++raavpsGaStge+ea+elrDg  +ry+gkgv+kav++v ++i pa+igl+
  gi|121636952|ref|YP_977175.1|   4 IEQVGAREILDSRGNPTVEVEVALIDGTFARAAVPSGASTGEHEAVELRDG-GDRYGGKGVQKAVQAVLDEIGPAVIGLN 82 
                                    899***********************************************9.89************************** PP

                                    TT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                      Enolase_N  81 vtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                    + dq+ +D++l++lDgt++ks+lG+Nail+vSlAvakaaA+++elpl+ry+
  gi|121636952|ref|YP_977175.1|  83 ADDQRLVDQALVDLDGTPDKSRLGGNAILGVSLAVAKAAADSAELPLFRYV 133
                                    **************************************************7 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1     4e-14   1.8e-10      41     171 ..     230     380 ..     175     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4e-14
                                    HTTTSTSEEEEE-TTT.S..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH.HH.SSEEE CS
                       MR_MLE_C  41 vgpgddvdlmvDanqa.w..............dlatAirvarelee.ldllwlEEPvppeddleglaelra.ra.sipia 102
                                    + pg dv l++Da +  +              ++++  ++   l   + l  +E+P++  dd++g a+l+a +  +++i+
  gi|121636952|ref|YP_977175.1| 230 LRPGADVALALDAAATeFftdgtgyvfegttrTADQMTEFYAGLLGaYPLVSIEDPLSE-DDWDGWAALTAsIGdRVQIV 308
                                    3468888888888877525777777888877777777777766645599*********9.78********986689**** PP

                                    ESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSS..HHHHHHHHHHHH CS
                       MR_MLE_C 103 agEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsg..glglaaslhlaa 171
                                    ++    + +++++e +e+g++ ++ ++v+++g +te+++ + la++ g++ ++ + sg    +++a l +a+
  gi|121636952|ref|YP_977175.1| 309 GDDIFVTnPERLEEGIERGVANALLVKVNQIGTLTETLDAVTLAHHGGYRTMISHRSGetEDTMIADLAVAI 380
                                    ***87766******************************************7776643412444444444444 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-06     0.012     109     219 ..     281     383 ..     237     389 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-06
                         MAAL_C 109 liegPldagskeeqierlaelreklkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyck 187
                                     ie+Pl +++     +  a+l++++   g +v++v D+ +  + e ++e ++++ a+++ +k+  +G++++t++av  ++
  gi|121636952|ref|YP_977175.1| 281 SIEDPLSEDDW----DGWAALTASI---GDRVQIVGDDiFVTNPERLEEGIERGVANALLVKVNQIGTLTETLDAVTLAH 353
                                    56666654433....3344444444...6679***99835677899********************************** PP

                         MAAL_C 188 ekgvgaylGGscnetdvsarvsvhvalatrpa 219
                                    + g ++++   + et+ +  +++++a+a+++ 
  gi|121636952|ref|YP_977175.1| 354 HGGYRTMISHRSGETEDT--MIADLAVAIGSG 383
                                    *********999999975..556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2981.91
//
Query:       gi|121636953|ref|YP_977176.1|  [L=228]
Description: hypothetical protein BCG_1081 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-19   67.7   0.0      8e-19   67.2   0.0    1.3  1  DivIC     Septum formation initiator


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   4.5e-23     8e-19       1      77 [.      86     161 ..      86     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 4.5e-23
                                    XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          DivIC   1 llllfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARselglvkpgEtvyrv 77 
                                    l++++++l+ ++++++++y+++++e+++l a+ a l+ ++++Le++  +L  d++yi+++AR++lg+v+pg++ ++v
  gi|121636953|ref|YP_977176.1|  86 LAAVVCVLTLTIARPVRTYFAQRAEMEQLAATEAMLRRQIADLEEQQVKL-ADPAYIAAQARERLGFVMPGDIPFQV 161
                                    67899*********************************************.7***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1636.75
//
Query:       gi|121636954|ref|YP_977177.1|  [L=155]
Description: hypothetical protein BCG_1082 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-35  120.3   0.0    2.3e-33  114.9   0.0    2.0  1  DUF501    Protein of unknown function (DUF501)
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.23   11.5   0.0    1.3  1  Imm2      Immunity protein Imm2


Domain annotation for each model (and alignments):
>> DUF501  Protein of unknown function (DUF501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   2.6e-37   2.3e-33       2     139 ..      17     136 ..      16     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 2.6e-37
                         DUF501   2 aarcadgvPvvlltaplrkklsrgkpfptlywLtcpelvkavsrLEaeglvkaleeklaedeelaqalekahaeyaakRe 81 
                                    a+rc++g P v++tap+   l++g+pfptly+Lt+p l++a srLE  gl+++++++l +d+ela+a+++ah++y+++R+
  gi|121636954|ref|YP_977177.1|  17 AYRCPNGEPGVVKTAPR---LPDGTPFPTLYYLTHPVLTAAASRLETTGLMREMNRRLGQDAELAAAYRRAHESYLSERD 93 
                                    78***************...**********************************************************98 PP

                         DUF501  82 ellteeerselekseesselkdlgvgGianvtrVKCLHahvAhyLat.egkNpvGelvl 139
                                     l ++ +             + +++gG++  +rVKCLH+++Ah+La+ +g Np+G+ +l
  gi|121636954|ref|YP_977177.1|  94 AL-EPLG-------------TTVSAGGMP--DRVKCLHVLIAHSLAKgPGLNPFGDEAL 136
                                    87.2222.............5689*****..************************9875 PP

>> Imm2  Immunity protein Imm2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05      0.23       2      33 ..      95     126 ..      94     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                           Imm2   2 levlalilsaGrssdkvkryhldiihGllkei 33 
                                    le l   +saG   d+vk  h+ i h l k  
  gi|121636954|ref|YP_977177.1|  95 LEPLGTTVSAGGMPDRVKCLHVLIAHSLAKGP 126
                                    77888899********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1227.04
//
Query:       gi|121636955|ref|YP_977178.1|  [L=319]
Description: hypothetical protein BCG_1083 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-91  307.0   0.1    1.5e-91  306.8   0.1    1.0  1  Ppx-GppA  Ppx/GppA phosphatase family
     0.0025   16.8   2.9     0.0055   15.7   2.4    1.7  2  DDR       Diol dehydratase reactivase ATPase-like domain
      0.005   17.2   0.1        1.3    9.4   0.0    2.5  2  FtsA      Cell division protein FtsA
  ------ inclusion threshold ------
       0.17   10.6   0.0       0.22   10.2   0.0    1.1  1  MSP1_C    Merozoite surface protein 1 (MSP1) C-terminus


Domain annotation for each model (and alignments):
>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.8   0.1   3.3e-95   1.5e-91       2     284 ..      20     316 ..      19     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 306.8 bits;  conditional E-value: 3.3e-95
                                    EEEECTTE....EEEEEEEEEE--CCCCCHCCSSC-HHHHHHHHHHHHHHHHHCCCTTGCCEEEEEEHHHHHSTTHHHHH CS
                       Ppx-GppA   2 iarkaagl....lqivarekrkvrLaeglnesgrlqeeaiertisaLkefaellqkfkvenvrvVATsalRdavNadeFl 77 
                                    ia++ agl    l++v+re+r+vrL++g++++gr+++eai+rt++aL+++aell+++++e+vr+VATsa+Rd+vN+d+F+
  gi|121636955|ref|YP_977178.1|  20 IADVGAGLargeLHDVHRETRIVRLGQGVDATGRFAPEAIARTRTALTDYAELLTFHHAERVRMVATSAARDVVNRDVFF 99 
                                    677777777777******************************************************************** PP

                                    HHHCCCCS.....S-EEEE-HHHHHHHHHHHHHHHT.---SSEEEEEEETTEEEEEEEETTEEEEEEEES--CCHHHHHH CS
                       Ppx-GppA  78 arvkkevg.....lkveiisgeeEarliylgvvssl.lekgrglviDiGGGStElvlgeekevsklvSlplGavrlterf 151
                                    a++++++g     +++e+i+g+eEa+l+++g+v +l ++ ++++v+D+GGGStE+vlg e+ev++++S+++G+vrlter+
  gi|121636955|ref|YP_977178.1| 100 AMTADVLGaalpgSAAEVITGAEEAELSFRGAVGELgSAGAPFVVVDLGGGSTEIVLG-EHEVVASYSADIGCVRLTERC 178
                                    ********999999********************************************.9******************** PP

                                    SGCCC--HHHHHHHHHHHHHHCTTTHHHHCCCE..HHCCCCCCCHCCHHCHHHHHHCT.S...SCEEEHHHHHHHHHHHC CS
                       Ppx-GppA 152 ltddpltkeeveaarkavekeleevkdevkkeg..ewtrlvgtsgtisalaeltelhgek...gyeitaeeleeliekll 226
                                    l++dp+t +ev++ar++v+++le++ ++v+ e+  +w+ l+gt++t+sala+++++++++    ++++ ++l e++++l+
  gi|121636955|ref|YP_977178.1| 179 LHSDPPTLQEVSTARRLVRERLEPALRTVPLELarTWVGLAGTMTTLSALAQSMTAYDAAaihLSRVPGADLLEVCQRLI 258
                                    **********************************************************999******************* PP

                                    TSSCHHHHHSTTS-CCHHCTHHHHHHHHHHHHHHCT-SEEEEES--HHHHHHHHHHHH CS
                       Ppx-GppA 227 qlkkeeelklagvsdeRadvivagalilsavlealeieaviisegalrEGvlyslllk 284
                                    +++++++++la+++++Radvi +ga+++++++++l+++a i + +++++++l++++l+
  gi|121636955|ref|YP_977178.1| 259 GMTRKQRAALAPMHPGRADVIGGGAIVVEELARELRERAGIDQLTVSEHDILDGIALS 316
                                    ****************************************************998875 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.12   5.2e+02     216     263 ..      55     101 ..      25     109 .. 0.75
   2 !   15.7   2.4   1.2e-06    0.0055     100     158 ..     103     163 ..      77     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.12
                            DDR 216 dpevfarvvllkedelvpleedlslekirsvRreaKekvfvtnalRal 263
                                    +pe++ar+ +  +d ++ l + +++e++r v ++a ++v+ ++++ a+
  gi|121636955|ref|YP_977178.1|  55 APEAIARTRTALTD-YAELLTFHHAERVRMVATSAARDVVNRDVFFAM 101
                                    57777777665544.455666788999999999999999988777766 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-06
                            DDR 100 aeeleeel...gvkvevggvEaemAilGalttPGte.kplailDlGaGstDaalieeegevka 158
                                    a+ l + l     +v +g+ Eae   +Ga    G+  +p++++DlG+Gst+  ++  e+ev a
  gi|121636955|ref|YP_977178.1| 103 ADVLGAALpgsAAEVITGAEEAELSFRGAVGELGSAgAPFVVVDLGGGSTE--IVLGEHEVVA 163
                                    55555555433567888999***********9997538************9..4444455544 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0047        21       1      28 [.       7      44 ..       7     124 .. 0.68
   2 !    9.4   0.0    0.0003       1.3       1      28 [.     143     169 ..     143     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0047
                                   EEEEE-SSSEEEEEEETTE.EEE..........EEEES- CS
                                   xxxxxxxxxxxxxxxxxxx.xxx..........xxxxxx RF
                           FtsA  1 alvDiGagktdvavaedga.lvh..........lrvigv 28
                                   a++D G++++ +++a+ ga l +          +r++ +
  gi|121636955|ref|YP_977178.1|  7 AAIDCGTNSIRLLIADVGAgL-ArgelhdvhreTRIVRL 44
                                   79***************9852.23444455566777766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0003
                                    EEEEE-SSSEEEEEEETTEEEEEEEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           FtsA   1 alvDiGagktdvavaedgalvhlrvigv 28 
                                    ++vD+G+g+t+++++e++ +v++ +  +
  gi|121636955|ref|YP_977178.1| 143 VVVDLGGGSTEIVLGEHE-VVASYSADI 169
                                    79**************96.444444444 PP

>> MSP1_C  Merozoite surface protein 1 (MSP1) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   4.9e-05      0.22     233     304 ..      48     121 ..      27     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.9e-05
                         MSP1_C 233 knytGkknsdnvkevkealeaykellPkvstsea.avttavtadaavpdatPe.glsvrgagvsGavkeetpep 304
                                     + tG+  ++ +++ + al  y ell    ++ +  v+t+++ d+ ++d+    +  v ga+ +G+++e +  +
  gi|121636955|ref|YP_977178.1|  48 VDATGRFAPEAIARTRTALTDYAELLTFHHAERVrMVATSAARDVVNRDVFFAmTADVLGAALPGSAAEVITGA 121
                                    5789***********************87666651578999999999998755145689999****99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2113.70
//
Query:       gi|121636956|ref|YP_977179.1|  [L=226]
Description: transcriptional regulatory protein kdpE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-26   93.1   0.0    1.7e-26   92.6   0.0    1.3  1  Response_reg   Response regulator receiver domain
      1e-22   80.0   0.0    3.4e-22   78.3   0.0    1.8  2  Trans_reg_C    Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.041   14.3   0.0    1.5  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0   2.9e-30   1.7e-26       1     111 [.       4     112 ..       4     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 2.9e-30
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl++dD+p ++++lr  l+ +gy +v +a++g+ al+ + e+ +d+++lD+ +p+m+G+++l  +r    + pvi+l+a+
  gi|121636956|ref|YP_977179.1|   4 VLVIDDEPQILRALRINLTVRGY-QVITASTGAGALRAAAEHPPDVVILDLGLPDMSGIDVLGGLRGWL-TAPVIVLSAR 81 
                                    89*********************.9999***************************************77.********** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++++d+v+al+agadd+++Kpf ++e l++l
  gi|121636956|ref|YP_977179.1|  82 TDSSDKVQALDAGADDYVTKPFGMDEFLARL 112
                                    **************************99987 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.61   3.6e+03      49      62 ..     108     121 ..     102     132 .. 0.71
   2 !   78.3   0.0   5.7e-26   3.4e-22       1      77 []     148     224 ..     148     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.61
                                    HHHHHHHHHHTTTT CS
                    Trans_reg_C  49 hisrLRkkLeddek 62 
                                      +rLR  ++ +++
  gi|121636956|ref|YP_977179.1| 108 FLARLRAAVRRNTA 121
                                    67899998888643 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 5.7e-26
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    g ev+ltp+e+ +Le+L++n+g+ v r eLl+evwg  ++++++ ++v+ ++LR+kLedd+++p+++ t  g+GYr+
  gi|121636956|ref|YP_977179.1| 148 GAEVHLTPTEWGMLEMLARNRGKLVGRGELLKEVWGPAYATETHYLRVYLAQLRRKLEDDPSHPKHLLTESGMGYRF 224
                                    578************************************************************************97 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.9e-06     0.041      36     100 ..      19     115 ..      11     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-06
                                    EE.EEHCCH-H...HHHHHHHHCTGGG-TSEEEEE--CCC.....................CCTT--HHHHHHH...... CS
                  Lipase_GDSL_2  36 vnnlgvsGatt.allrllerlrdllrlkpdlvtiliGtND.....................lgrgvpaaaaaand..... 88 
                                    + nl v G+ +  +   ++ lr+++++ pd+v++ +G  D                                  +     
  gi|121636956|ref|YP_977179.1|  19 I-NLTVRGYQViTASTGAGALRAAAEHPPDVVILDLGLPDmsgidvlgglrgwltapvivlS------------Artdss 85 
                                    4.49999998876788888899999***************6666666666555555555431............022223 PP

                                    ...................HHHHHHHHCCC CS
                  Lipase_GDSL_2  89 ..................nleelidalraa 100
                                                      +++e++++lraa
  gi|121636956|ref|YP_977179.1|  86 dkvqaldagaddyvtkpfGMDEFLARLRAA 115
                                    333333566677777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1670.35
//
Query:       gi|121636957|ref|YP_977180.1|  [L=860]
Description: sensor protein kdpD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-98  326.7   0.6    1.1e-97  325.6   0.6    1.6  1  KdpD             Osmosensitive K+ channel His kinase sensor d
    7.5e-24   83.6   9.0    1.6e-23   82.5   9.0    1.6  1  DUF4118          Domain of unknown function (DUF4118)
    2.7e-19   69.7   0.0    6.5e-19   68.5   0.0    1.6  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    2.8e-13   49.7   0.9    1.2e-12   47.6   0.9    2.3  1  HisKA            His Kinase A (phospho-acceptor) domain
    3.5e-11   43.8   5.1    4.2e-11   43.5   0.5    3.4  2  Usp              Universal stress protein family
  ------ inclusion threshold ------
       0.02   15.0   1.0      0.037   14.1   1.0    1.3  1  Thia_YuaJ        Thiamine transporter protein (Thia_YuaJ)
      0.037   13.9   0.1        0.1   12.5   0.1    1.8  1  DUF2631          Protein of unknown function (DUF2631)
      0.043   14.0   0.8       0.13   12.5   0.8    1.8  1  Antimicrobial_1  Frog antimicrobial peptide
        8.2    6.7   6.6       0.39   11.0   1.1    1.7  2  GtrA             GtrA-like protein


Domain annotation for each model (and alignments):
>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.6   0.6  5.5e-101   1.1e-97       1     210 []      25     234 ..      25     234 .. 1.00

  Alignments for each domain:
  == domain 1  score: 325.6 bits;  conditional E-value: 5.5e-101
                           KdpD   1 krGrlkiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveykgkeleeldldaila 80 
                                    krG+l+i+lGaapGvGktyamL ea+++ e+g+dvv ++vethgr++t++lleg+e+i ++ vey+g+++ eld++a+l+
  gi|121636957|ref|YP_977180.1|  25 KRGQLRIYLGAAPGVGKTYAMLGEAHRRLERGTDVVAAVVETHGRNKTAKLLEGIEMISPRYVEYRGARFPELDVEAVLR 104
                                    69****************************************************************************** PP

                           KdpD  81 rkpevvlvDelahtnapgsrhekryqdveelLeagidVittvnvqhleslndvvekitgvrvretvPdevleeAdevelv 160
                                    r+p+vvlvDelahtn+pgs+++kr+qdv+e+L+agi Vi+tvn+qhle lndvve+itg++++e++Pde++++Ad+velv
  gi|121636957|ref|YP_977180.1| 105 RHPQVVLVDELAHTNTPGSKNPKRWQDVQEILDAGITVISTVNIQHLEGLNDVVEQITGIEQKEKIPDEIVRAADQVELV 184
                                    ******************************************************************************** PP

                           KdpD 161 DltpeeLlerLkegkvykkekaeralknffrkgnLtaLRelaLrrvAdrv 210
                                    D+tpe+L++rL++g+vy++e++++al+n+fr+gnLtaLRe+aL ++Ad+v
  gi|121636957|ref|YP_977180.1| 185 DITPEALRRRLAHGNVYAAERVDAALSNYFRTGNLTALREIALLWLADQV 234
                                    ************************************************97 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   9.0     8e-27   1.6e-23       1     107 []     400     507 ..     400     507 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 8e-27
                        DUF4118   1 yllavlllalatllalll.dkllslanivllfllavllvallgglgpgllaallsvllfnyfftpPyftltiadpeyllt 79 
                                    +l+a++++ +++++++++ d++++    ++lf+++vl+vallgg++p++l+alls +l+nyf+t+P++t tia+p+  +t
  gi|121636957|ref|YP_977180.1| 400 WLAALVVPSVICAITVAWlDRFMGIGGESALFFIGVLIVALLGGVAPAALSALLSGMLLNYFLTEPRYTWTIAEPDAAVT 479
                                    8999999999999988885777888******************************************************* PP

                        DUF4118  80 lvvflvvallvstlvararrqarqarer 107
                                     +v+l++a++v++lv+ a+ ++r+ar++
  gi|121636957|ref|YP_977180.1| 480 EFVLLAMAVAVAVLVDGAASRTREARRA 507
                                    *************************985 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   3.2e-22   6.5e-19       2     108 ..     749     853 ..     748     857 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.2e-22
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE...EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika...seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGl 78 
                                    d   L++++ nl+dNa+++   a+++ v+++a   + +++ i v D G+G+p+   ++lf++f++  ++ +++ g+GlG+
  gi|121636957|ref|YP_977180.1| 749 DAGLLERVLANLIDNALRY---APDCVVRVDAgrvR-ERVLINVIDEGPGVPRGTEEQLFAPFQR-PGDHDNTTGVGLGM 823
                                    667899************7...56888999975443.6***************************.99999********* PP

                                    HHHHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                      HATPase_c  79 sivkklvelmgGeiwvesepgrGttftftl 108
                                    s+++ +ve mgG+i+ +++pg+G t+++ l
  gi|121636957|ref|YP_977180.1| 824 SVARGFVEAMGGTISATDTPGGGLTVVIDL 853
                                    *************************99866 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.9   6.2e-16   1.2e-12       2      67 .]     633     700 ..     632     700 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.2e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                    ++ +l+ v+H+LrtPL+a + +++ L+ e  +  +e+ +e+l+tie+++++l++lv +lLd sr+ ag
  gi|121636957|ref|YP_977180.1| 633 RRSLLSAVSHDLRTPLAAAKVAVSSLRTEdvAFSPEDTAELLATIEESIDQLTALVANLLDSSRLAAG 700
                                    6789**********************888996667*****************************9876 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.5   2.1e-14   4.2e-11       3     129 ..     255     364 ..     253     376 .. 0.91
   2 ?   -1.1   0.4       1.3   2.5e+03      70     100 ..     595     630 ..     534     688 .. 0.59

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.1e-14
                                    SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                            Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                    +r++Vav g +es+ ++++A + a ++ ael+++hvi  ++ + vs++     +e + + +a                 +
  gi|121636957|ref|YP_977180.1| 255 ERVVVAVTGGPESETLVRRASRIASKSSAELMVVHVIRGDDLAGVSAPQLGRVRELATSLGA-----------------T 317
                                    79*****************************************************9999998.................5 PP

                                    EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHH CS
                            Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyv 129
                                    +++v++ d+ +++l++a+e +a  +VvG+++rs+ +rl+      + 
  gi|121636957|ref|YP_977180.1| 318 MHTVVGDDVPTALLDFAREMNATQLVVGTSRRSRWARLFDEGIGART 364
                                    68***********************************9865555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                    H.....HHHHHHCTTCEEEEEEEESSHHHHHHHHHH CS
                            Usp  70 a.....akaaaeaggvkvevvveegdpaeeilevae 100
                                          ++ a++a+g + + ++ e  +  e +  a+
  gi|121636957|ref|YP_977180.1| 595 RdrrvlTAVATQAAGLVKQRELAEEAGQAEAIARAD 630
                                    233444223333333333333333333333333333 PP

>> Thia_YuaJ  Thiamine transporter protein (Thia_YuaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.0   1.8e-05     0.037      22     118 ..     422     521 ..     403     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                      Thia_YuaJ  22 lpqggsislsmiPilllalrrGlkagllaGllwGll..qlilgkay...iltplqvlldYpiafllvglaGlfakkvqka 96 
                                    +  gg+ +l +i +l++al  G+++++l+ ll G+l   +++++ y   i+ p +++ ++++  ++v++a l+  + +++
  gi|121636957|ref|YP_977180.1| 422 MGIGGESALFFIGVLIVALLGGVAPAALSALLSGMLlnYFLTEPRYtwtIAEPDAAVTEFVLLAMAVAVAVLVDGAASRT 501
                                    5668888999************************98444778999877789999******************99854433 PP

                      Thia_YuaJ  97 lkenkkkkalaliilgvliasf 118
                                     ++++   +  + +l+ + +s+
  gi|121636957|ref|YP_977180.1| 502 REARR--ASQEAELLALFAGSV 521
                                    32222..222333444555554 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.1e-05       0.1      19      45 ..     381     407 ..     362     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                        DUF2631  19 PSaaWGWsgespkttriaGlisvlall 45 
                                     S a GWs++sp+  +ia ++++l++ 
  gi|121636957|ref|YP_977180.1| 381 ASRASGWSRVSPRERHIASWLAALVVP 407
                                    47788******************9975 PP

>> Antimicrobial_1  Frog antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   6.4e-05      0.13       8      21 ..     401     414 ..     397     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                Antimicrobial_1   8 vAAKvlPkifCaIt 21 
                                    +AA v+P+++CaIt
  gi|121636957|ref|YP_977180.1| 401 LAALVVPSVICAIT 414
                                    799**********9 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.4       8.7   1.7e+04      33      45 ..     406     418 ..     398     418 .. 0.69
   2 ?   11.0   1.1   0.00019      0.39       1      81 [.     420     498 ..     420     523 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8.7
                           GtrA  33 aiafivailfnFi 45 
                                    + ++i+ai+++++
  gi|121636957|ref|YP_977180.1| 406 VPSVICAITVAWL 418
                                    4478888888885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00019
                           GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnr.rwtFkdrekakllkqflkFvlvsllglllnl 79 
                                    rF+ +G+ ++l  +++l++ l l   +++ A + a + ++l n++l + r+t+  +e+  ++ +f+  +++ ++++l++ 
  gi|121636957|ref|YP_977180.1| 420 RFMGIGGESALFFIGVLIVAL-L--GGVAPAALSALLSGMLLNYFLTEpRYTWTIAEPDAAVTEFVLLAMAVAVAVLVDG 496
                                    677788888888888877777.4..6899999***********9886559*********99**********999999987 PP

                           GtrA  80 li 81 
                                    + 
  gi|121636957|ref|YP_977180.1| 497 AA 498
                                    76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (860 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 5446.55
//
Query:       gi|121636958|ref|YP_977181.1|  [L=30]
Description: membrane protein kdpF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-09   36.4   5.0    3.7e-09   36.3   5.0    1.0  1  Potass_KdpF  F subunit of K+-transporting ATPase (Potass_KdpF


Domain annotation for each model (and alignments):
>> Potass_KdpF  F subunit of K+-transporting ATPase (Potass_KdpF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   5.0   2.1e-13   3.7e-09       1      24 []       7      30 .]       7      30 .] 0.98

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.1e-13
                                   HHHHHHHHHHHHHHHHHHHS--XX CS
                    Potass_KdpF  1 illllvavaLlvYLfyALlrPErF 24
                                   i++l++avaL++ Lf+ALl+PE+F
  gi|121636958|ref|YP_977181.1|  7 IVGLVIAVALMAFLFAALLFPEKF 30
                                   79*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 245.03
//
Query:       gi|121636959|ref|YP_977182.1|  [L=571]
Description: potassium-transporting ATPase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-237  789.2  23.8   1.7e-237  789.0  23.8    1.0  1  KdpA      Potassium-transporting ATPase A subunit


Domain annotation for each model (and alignments):
>> KdpA  Potassium-transporting ATPase A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.0  23.8  9.4e-242  1.7e-237       2     547 .]      11     568 ..      10     568 .. 0.99

  Alignments for each domain:
  == domain 1  score: 789.0 bits;  conditional E-value: 9.4e-242
                                    HHHHHHHHHHHHHHHHHHHHHTT-....--SS-SHHHHHHHHHHT---.----HHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                           KdpA   2 lllllllllalplgkylakvfege.ktlldkllkpverllyrllgvdeeeemtwkeYalalllfnlvlllllylllrlqg 80 
                                    +l+++lll+a  lg ylak++ +e k+  d+++ p+er++y++++vd+ +e++w++Yal++l+f+++++llly + r+qg
  gi|121636959|ref|YP_977182.1|  11 ALIAVLLLTAPALGGYLAKIYGDEaKKPGDRVFGPIERVIYQVCRVDPGSEQRWSTYALSVLAFSVMSFLLLYGIARFQG 90 
                                    578999***************77625679*************************************************** PP

                                    TSS--SS------HHHHHHHHHHHHTT-----S-HHHH--HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS-S-S---- CS
                           KdpA  81 vlplnpeglealspdlafntavSFvtntnlQhYsgestlsylsqmlgltvlnFvsaatGlavavalirglarketkelGn 160
                                    vlp+np++ +a++ ++afn+avSF+tntn+Q+Ysge+t+s+++qm+gl+v+nFvsa++G++v++alirglark++++lGn
  gi|121636959|ref|YP_977182.1|  91 VLPFNPTDKPAVTDHVAFNAAVSFMTNTNWQSYSGEATMSHFTQMTGLAVQNFVSASAGMCVLAALIRGLARKRASTLGN 170
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHTHHHHHHHHHHHHHHHT--------EEEE-SSS-EEEE--SSHHHHHHHHHHTT----SSSSTTTSTTT CS
                           KdpA 161 fyvdlvrailrvLLPlslvvalllvaqGvpqtlsgkaevttlegakqtialGpvAsleaIkqlGtnGGGffgaNsahpfe 240
                                    f+vdl r++lr+++Pls+vva+llv+qGv+q+l+g   ++tlega q i+ GpvAs++aIkqlGtnGGGff++Nsahpfe
  gi|121636959|ref|YP_977182.1| 171 FWVDLARTVLRIMFPLSFVVAILLVSQGVIQNLHGFIVANTLEGAPQLIPGGPVASQVAIKQLGTNGGGFFNVNSAHPFE 250
                                    ******************************************************************************** PP

                                    S-SHHHHHHHHHHHHHHHHHHHHHHHHHTS-THHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH...........--- CS
                           KdpA 241 nptaltnlleilaillipaalvftfGrmvkdkrqglailavmlvlflvllvvvvvaeaagnpalae.........eqagg 311
                                    n t++ n++e +ail+ip+al+f+fG+mv+d+rqg+a+la+m ++++ + v+++ +ea+gnp l++         +q+gg
  gi|121636959|ref|YP_977182.1| 251 NYTPIGNFVENWAILIIPFALCFAFGKMVHDRRQGWAVLAIMGIIWIGMSVAAMSFEAKGNPRLDAlgvtqqttvDQSGG 330
                                    ****************************************************************999**999999999** PP

                                    --TTB-SSS-HHHHHHHHHHHHHTT----SS-GGGS-HHHHHHHHHHHHT.S-TT-TTTHHHHHHHHHHHHHHHHHHHHH CS
                           KdpA 312 nmeGkEvrfGiaasalfavvttatstGavnamhdsltplgglvpllnmml.evvfGGvGvGllnllvfvilavFiagLmv 390
                                    n+eGkEvrfG+ as l+a++tt ts+G+vn+mhds+tplgg+vpl++mml ev +GG+GvGl +llv++ilavFiagLmv
  gi|121636959|ref|YP_977182.1| 331 NLEGKEVRFGVGASGLWAASTTGTSNGSVNSMHDSYTPLGGMVPLAHMMLgEVSPGGTGVGLNGLLVMAILAVFIAGLMV 410
                                    ******************************************************************************** PP

                                    TS--EETTEE--HHHHHHHHHHHHHHHHHHHHHHHHHTTSH.HHTT--S-THHHHHHHHHHHHHHHTT-----S-S---S CS
                           KdpA 391 GrtPeylgkkiearevklaalaiLvhpllilvgtalalalp.alaslsnpgahglsevLYeftSaaanNGSafeGlgdnt 469
                                    GrtPeylgkki+a+e+kl++l+iL++p+++l ++a +++++ alas +npg+hglse+LY++tS a+nNGSaf+Gl+++t
  gi|121636959|ref|YP_977182.1| 411 GRTPEYLGKKIQATEMKLVTLYILAMPIALLSFAAASVLISsALASRNNPGPHGLSEILYAYTSGANNNGSAFAGLTAST 490
                                    ****************************************978889********************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS------TT---SSHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHH CS
                           KdpA 470 vfwnltlglamllgRflpiiavlaiAgslaakkkvpesagtlktdtplFvvllvgvilivgaLtFlPalaLGPiaehl 547
                                      +++t+g+aml+gRf+ ii+vlaiAgsla+k ++p +a t++t++plFv+l++gv+livg LtF+PalaLGPi+e+l
  gi|121636959|ref|YP_977182.1| 491 WSYDTTIGVAMLIGRFFLIIPVLAIAGSLARKGTTPVTAATFPTHKPLFVGLVIGVVLIVGGLTFFPALALGPIVEQL 568
                                    ****************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3828.93
//
Query:       gi|121636960|ref|YP_977183.1|  [L=709]
Description: potassium-transporting ATPase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-35  122.6   4.2    1.2e-35  122.6   4.2    2.4  2  E1-E2_ATPase  E1-E2 ATPase
    3.6e-31  109.1   3.0    3.6e-31  109.1   3.0    1.6  2  Hydrolase     haloacid dehalogenase-like hydrolase
     0.0021   17.9   0.4     0.0046   16.7   0.4    1.5  1  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.036   14.5   0.0       0.28   11.6   0.0    2.4  1  HAD           haloacid dehalogenase-like hydrolase
       0.15   10.9   0.0       0.28   10.0   0.0    1.3  1  DUF759        Borrelia burgdorferi protein of unknown functio


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   4.2   3.5e-39   1.2e-35       7     180 ..     126     301 ..     121     302 .. 0.94
   2 ?   -0.3   0.8      0.19   6.7e+02     118     164 ..     614     664 ..     592     669 .. 0.61

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 3.5e-39
                                    EEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G...-TTEE-TT-EEEE-EEE CS
                   E1-E2_ATPase   7 akvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpveke...kgdmvfsGtvvvsgeak 82 
                                    a+++  +g++e+++++ l  +D+v++ ag+++p Dg+i+eg a+vdesa+TGEs pv +e    ++ v++Gtvv+s++++
  gi|121636960|ref|YP_977183.1| 126 ANRRtAAGNIESVPSSRLDLDDVVEVSAGETIPSDGEIIEGIASVDESAITGESAPVIREsggDRSAVTGGTVVLSDRIV 205
                                    44445899***************************************************64447899************* PP

                                    EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TT CS
                   E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPca 162
                                    +++ta   +t+++++++lve a++++tp +  l+ l + l+++ ll+++++  +a++ g++  + ++  +allv+ iP  
  gi|121636960|ref|YP_977183.1| 206 VRITAKQGQTFIDRMIALVEGAARQQTPNEIALNILLAGLTIIFLLAVVTLQPFAIYSGGG--QRVVVLVALLVCLIPTT 283
                                    *******************************************************999998..89*************** PP

                                    HHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 163 Lplavplalalgarrlak 180
                                    ++++++ + ++g+ rl +
  gi|121636960|ref|YP_977183.1| 284 IGALLSAIGIAGMDRLVQ 301
                                    *************99965 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHHS-STTTSSTT....HHHHHHHHHHHHHS-TTHH CS
                   E1-E2_ATPase 118 lgkvlvpvvlliallvflialllgksla....eallralallvaaiPcaLp 164
                                    +++++ ++ + ++ ++  ++++  +s++     a+++   ++va iP aL 
  gi|121636960|ref|YP_977183.1| 614 YFAIIPAMFVGLYPVLDKLNVMALHSPRsailSAVIFNALVIVALIPLALR 664
                                    333333334444444444566667777755554455555578999999986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.7   9.8e+03      44      79 ..      85     115 ..      59     157 .. 0.57
   2 !  109.1   3.0     1e-34   3.6e-31       1     210 []     318     557 ..     318     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  44 kalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                    + lvaa+   +   ++fa+     a a+g+ +  +a
  gi|121636960|ref|YP_977183.1|  85 NGLVAAFLWFTVLFANFAE-----AMAEGRGKAQAA 115
                                    4444444444444455555.....333333332222 PP

  == domain 2  score: 109.1 bits;  conditional E-value: 1e-34
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHH.HHCHHHHHHHHHHHHH.........HHHHHHHHHETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.....alalaaaletg.sehpigkalvaaakar.........sgaltgfatfig 65 
                                    ++t+++Dk+GT+t g+++ +++++ +     a+a aa+l     e+p g+ +v  ak++           + ++f  f+ 
  gi|121636960|ref|YP_977183.1| 318 VNTLLLDKTGTITLGNRQATEFVPINgvsaeAVADAAQLSSLaDETPEGRSIVVLAKDEfglrardegVMSHARFVPFTA 397
                                    69********************999988866666666666669*********9999999887776544222233333333 PP

                                    TE..................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH.......TTHHHHHHHHHHTHH CS
                                    xx..................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF
                      Hydrolase  66 rg..................ayaigkpewltal..dippdlgaaigsaqsqgrtvall.......qaralavftiadplk 118
                                    +                    +a    +w++++  + ++++ga ++   s g t  ++       +ara +v+ ++d   
  gi|121636960|ref|YP_977183.1| 398 ETrmsgvdlaevsgirrirkGAAAAVMKWVRDHggHPTEEVGAIVDGISSGGGTPLVVaewtdnsSARAIGVVHLKDI-- 475
                                    3377778888888888777777777777*******99**************************9999***********.. PP

                                    BHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 119 vkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVG 197
                                    vk +++e + + +++ i++v++tgdnp+ta+++a+++G           ++   a++ pe+k+a+i++ q  ++ vam G
  gi|121636960|ref|YP_977183.1| 476 VKVGIRERFDEMRRMSIRTVMITGDNPATAKAIAQEAG-----------VDDfLAEATPEDKLALIKREQQGGRLVAMTG 544
                                    **************************************...........6667*****************88888***** PP

                                    SSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxx RF
                      Hydrolase 198 DgvnDaaalaaAg 210
                                    Dg nDa+ala+A+
  gi|121636960|ref|YP_977183.1| 545 DGTNDAPALAQAD 557
                                    ************8 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.3e-06    0.0046     206     242 ..     540     576 ..     528     581 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                                    EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                    Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                    v+  GDg ND + L +a++gvAm+ +++ + +a ++v
  gi|121636960|ref|YP_977183.1| 540 VAMTGDGTNDAPALAQADVGVAMNTGTQAAREAGNMV 576
                                    6778************************999887665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.8e-05      0.28      85     186 ..     475     552 ..     456     554 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                            HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                    + + g++e++++ r+  +r+v+++g +   ++++++e g+d++la+        t e           +k+a +++    
  gi|121636960|ref|YP_977183.1| 475 IVKVGIRERFDEMRRMSIRTVMITGDNPATAKAIAQEAGVDDFLAE-------ATPE-----------DKLALIKR---- 532
                                    45559999***9***************************8888888.......2222...........34444455.... PP

                            HAD 165 egegidleevvay.GDspsDlpl 186
                                    e +     ++va  GD+ +D p+
  gi|121636960|ref|YP_977183.1| 533 EQQ---GGRLVAMtGDGTNDAPA 552
                                    222...22344444666666666 PP

>> DUF759  Borrelia burgdorferi protein of unknown function (DUF759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   7.7e-05      0.28     270     347 ..     542     619 ..     538     654 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.7e-05
                         DUF759 270 lggdgselfdllkksgvgdkyiedakmawqsgaqvdldsritkmmemfkdfksfgltkkvnnaesiqsnlasaeqtls 347
                                    + gdg++    l ++ vg      ++ a ++g  vdlds  tk++e+ +  k + +t+    + si  ++a     + 
  gi|121636960|ref|YP_977183.1| 542 MTGDGTNDAPALAQADVGVAMNTGTQAAREAGNMVDLDSDPTKLIEVVEIGKQLLITRGALTTFSIANDVAKYFAIIP 619
                                    679999999999******************************************999999999999888886655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4687.71
//
Query:       gi|121636961|ref|YP_977184.1|  [L=189]
Description: potassium-transporting ATPase subunit C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-73  246.9   0.0    1.3e-73  246.8   0.0    1.0  1  KdpC      K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   0.0   7.1e-78   1.3e-73       2     182 .]       6     188 ..       5     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 7.1e-78
                                    HHHHHHHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE.ETEEEEETTT------SSS--------S..T-TTT---- CS
                           KdpC   2 rkalrlllvltvllgliYplavtgiaqllfpeqAnGslieadgkvvGseligqeftsdkYfhgRpsavn..ynaaasggs 79 
                                    ++al++llv+tv++g++Yplavtg++ql+f +qAnG l+e+dg+v+Gs+ igq+ft++kYfh+Rps+++  y+aaas+gs
  gi|121636961|ref|YP_977184.1|   6 LPALTMLLVFTVITGIVYPLAVTGVGQLFFGDQANGALLERDGQVIGSAHIGQQFTAAKYFHPRPSSAGdgYDAAASSGS 85 
                                    689*****************************************************************99********** PP

                                    ---SS-HHHHHHHHHHHHHHHHH-TTS..-SB-HHHHS-BSSS---EE-HHHHHHTHHHHHHHHT--HHHHHHHHHHTEE CS
                           KdpC  80 nlgpsnpellerveervaalraenpekkkeevPadlvtaSgSGLDPhIspeaAelQvarvakarglseeeveklvaente 159
                                    nlgp+n++ll++v+erv+a+r+en+  +++ vP+d+vt SgSGLDP Is+ +A+lQ++rva+ar++s ++ve+l++++t+
  gi|121636961|ref|YP_977184.1|  86 NLGPTNEKLLAAVAERVTAYRKENNLPADTLVPVDAVTGSGSGLDPAISVVNAKLQAPRVAQARNISIRQVERLIEDHTD 165
                                    ******************************************************************************** PP

                                    --SSTTT---EEEHHHHHHHHHH CS
                           KdpC 160 grllgilGeprVnVlklNlaLdk 182
                                     r lg+lGe+ VnVl+lNlaLd+
  gi|121636961|ref|YP_977184.1| 166 ARGLGFLGERAVNVLRLNLALDR 188
                                    *********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1474.80
//
Query:       gi|121636962|ref|YP_977185.1|  [L=509]
Description: two component sensor histidine kinase trcS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-23   81.1   0.0      3e-22   79.2   0.0    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.9e-17   61.7   2.5    8.6e-17   60.9   0.8    2.3  3  HisKA        His Kinase A (phospho-acceptor) domain
      3e-08   33.9   0.1      1e-07   32.2   0.1    2.0  1  HAMP         HAMP domain
    0.00023   21.1   0.0    0.00098   19.1   0.0    2.1  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0038   17.1   0.0     0.0097   15.8   0.0    1.7  1  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.053   13.2   0.3          3    7.5   0.1    2.3  2  Neurensin    Neurensin
       0.12   12.4   0.0       0.29   11.1   0.0    1.7  1  FixQ         Cbb3-type cytochrome oxidase component FixQ
       0.39   11.0  10.7       0.29   11.4   0.5    3.0  2  DUF3040      Protein of unknown function (DUF3040)
        4.2    7.2   8.3        2.1    8.2   0.7    2.4  2  DUF4307      Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         3     6e+03      73      85 ..     168     181 ..     132     198 .. 0.70
   2 !   79.2   0.0   1.5e-25     3e-22       1     110 [.     387     500 ..     387     502 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3
                                    SSSHHHHHHHH.HH CS
                      HATPase_c  73 gtGlGlsivkk.lv 85 
                                     +G++ls++++ ++
  gi|121636962|ref|YP_977185.1| 168 FVGVSLSLANQiIA 181
                                    46889999998444 PP

  == domain 2  score: 79.2 bits;  conditional E-value: 1.5e-25
                                    EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.....EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                      HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika.....seddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                    gd  rL+q++snl++Na  +++++ ++++ i+      +   +++sv+D+G+ i++e+l++lf++f+++++++++g+g+G
  gi|121636962|ref|YP_977185.1| 387 GDHARLHQLVSNLLTNAWVHTQPGVTVTIGITChrtgpNAPCVELSVTDDGPDIDPEILPHLFDRFVRASKSRSNGSGHG 466
                                    6889****************6666666666665435442279**************************77778889**** PP

                                    HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                    lGl+iv ++v+ ++G+++ es   + t f+++lp+
  gi|121636962|ref|YP_977185.1| 467 LGLAIVSSIVKAHRGSVTAESGN-GQTVFRVRLPM 500
                                    *******************7777.56669999986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.1   6.2e+03      20      45 ..      47      67 ..      46      80 .. 0.58
   2 !   60.9   0.8   4.3e-20   8.6e-17       2      67 .]     278     344 ..     277     344 .. 0.93
   3 ?   -1.9   0.0       1.8   3.5e+03      49      60 ..     390     401 ..     385     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                   HHHHHHHHHC..T-HSSCHHHHHHHH CS
                          HisKA 20 ilgnaeaLkregklteelkeyletie 45
                                   ++g++ a+ +      el e l+ + 
  gi|121636962|ref|YP_977185.1| 47 LSGYVTAMND-----AELVESLHALN 67
                                   6788888877.....44444444443 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 4.3e-20
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                    +++f+ + +HELrtPL+ai+g+ae+ + +  +l++  + +l++iesearr++ lv++lL lsr+ +g
  gi|121636962|ref|YP_977185.1| 278 MRQFITDASHELRTPLAAIQGYAELTRQDsSDLPPTTEYALARIESEARRMTLLVDELLLLSRLSEG 344
                                    68***********************955459999*****************************9876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHH CS
                          HisKA  49 rrldhlvedlLd 60 
                                     rl +lv++lL+
  gi|121636962|ref|YP_977185.1| 390 ARLHQLVSNLLT 401
                                    5999*****996 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   5.1e-11     1e-07       1      51 [.     204     264 ..     204     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.1e-11
                                    HHHHTTHHHHHHHHHHHHHHTT.T........BTSST..CCT.TSSSHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaa.G........dldtr..lpv.sgrDEiGeLarafNaMldrL 51 
                                    +++++ lrPLrr+a++a+++a            +  r  + + ++++E+G +++++N++ld++
  gi|121636962|ref|YP_977185.1| 204 WVVGYALRPLRRVAATAAEVATmPltdddhqiSV--RvrPGDtDPDNEVGIVGHTLNRLLDNV 264
                                    788999***************8634545554444..2556666999***************97 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   4.2e+03      65      77 ..     132     144 ..     130     150 .. 0.83
   2 !   19.1   0.0   4.9e-07   0.00098      31     114 ..     391     483 ..     360     497 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                    HATPase_c_2  65 ealtvevaDsGpg 77 
                                    +a++++v+D Gp+
  gi|121636962|ref|YP_977185.1| 132 RAIEAQVWDGGPP 144
                                    57899******99 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.9e-07
                    HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeea...ltvevaDsGpgfdpetlpdpteeep......keslkegGrG 101
                                    +++  v+ ++tNa+ h +++ +  ++ +++ +++     ++++v+D+Gp  dpe lp+              ++  +G+G
  gi|121636962|ref|YP_977185.1| 391 RLHQLVSNLLTNAWVHTQPGVT-VTIGITCHRTGPNapcVELSVTDDGPDIDPEILPHLFDR-FvrasksRSNGSGHGLG 468
                                    6666788899*********988.5555554444444678999***********988765432.25777889999****** PP

                    HATPase_c_2 102 lalikglvDev..ey 114
                                    la++ ++v     ++
  gi|121636962|ref|YP_977185.1| 469 LAIVSSIVKAHrgSV 483
                                    ******998874444 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.8e-06    0.0097      57      97 ..     455     495 ..     388     499 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                    HATPase_c_5  57 lesskskkeehGiGlksireivkkykgnlsieaedglFtls 97 
                                      +s s+++ hG+Gl  +++ivk + g+++ e  +g     
  gi|121636962|ref|YP_977185.1| 455 ASKSRSNGSGHGLGLAIVSSIVKAHRGSVTAESGNGQTVFR 495
                                    335678999*********************99988754444 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.029        57      30      83 ..      15      68 ..       3      93 .. 0.67
   2 ?    7.5   0.1    0.0015         3      34      70 ..     178     217 ..     153     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                      Neurensin 30 qrakqksesllwkvslvvgtlvlllGvtall..vGylvpr.rlelvksegelvvvDk 83
                                    r+++ ++ ll  v  vv ++++++Gv+ +l   Gy++     elv   ++l  + +
  gi|121636962|ref|YP_977185.1| 15 WRPRSLRQQLLLGVLAVVTVVLVAVGVVSVLslSGYVTAMnDAELV---ESLHALNH 68
                                   5566667888889999999*******99764225998876234555...44444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                      Neurensin  34 qk.sesllwkvslvvgtlvlllGvtallvGylvpr..rle 70 
                                    q      +  v+lv + lv+++ +t+ +vGy++ +  r++
  gi|121636962|ref|YP_977185.1| 178 QIiARKKVTTVALVGAALVVTAALTVWVVGYALRPlrRVA 217
                                    44456677889*********************98743333 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.29      15      49 .]     195     231 ..     186     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                           FixQ  15 llflvllfygvviyafrpgnr..kdfedaAnlpLkdD 49 
                                    l++ ++l + vv ya+rp +r  ++ ++ A +pL dD
  gi|121636962|ref|YP_977185.1| 195 LVVTAALTVWVVGYALRPLRRvaATAAEVATMPLTDD 231
                                    7778899999**********5559**********998 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00014      0.29      30      79 ..       8      54 ..       4      57 .. 0.71
   2 ?    2.4   3.9     0.093   1.9e+02      36      69 ..     180     213 ..     167     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                        DUF3040 30 rggaar.arrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvml 79
                                   r+++a  +r rslr++ +l  +l+v+ ++l+ +Gv+    vl++ G v+++
  gi|121636962|ref|YP_977185.1|  8 RSRKAPcWRPRSLRQQ-LLLGVLAVVTVVLVAVGVVS---VLSLSGYVTAM 54
                                   4455556889999995.5555577889*******663...57888877765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.093
                        DUF3040  36 arrrslrrlavlavllfva.GllllvlGvaaaavv 69 
                                    ++r+++ ++a+++++l+v+ +l++ v+G a++  +
  gi|121636962|ref|YP_977185.1| 180 IARKKVTTVALVGAALVVTaALTVWVVGYALRP-L 213
                                    5566667778888888888799999**977664.3 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.6      0.07   1.4e+02       4      26 ..      24      46 ..      21      61 .. 0.61
   2 ?    8.2   0.7    0.0011       2.1       5      57 ..     190     243 ..     185     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.07
                        DUF4307  4 llvillvvlvvvalalvawigys 26
                                   ll+ +l+v++vv++a+ ++ ++s
  gi|121636962|ref|YP_977185.1| 24 LLLGVLAVVTVVLVAVGVVSVLS 46
                                   55555666666655555555544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                        DUF4307   5 lvillvvlvvvalalvawigysq.gsadvsaevvgfevvddstvevtfeVtrdd 57 
                                    lv +++v++++++++v+ ++++  ++   +a +v+    +d+  +++++V+  d
  gi|121636962|ref|YP_977185.1| 190 LVGAALVVTAALTVWVVGYALRPlRRVAATAAEVATMPLTDDDHQISVRVRPGD 243
                                    334444444455555555555558677777777777777888889999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3343.32
//
Query:       gi|121636963|ref|YP_977186.1|  [L=257]
Description: two component transcriptional regulator trcR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-27   94.9   0.1    4.8e-27   94.4   0.1    1.2  1  Response_reg  Response regulator receiver domain
    7.8e-27   93.2   0.1      1e-25   89.6   0.0    2.2  2  Trans_reg_C   Transcriptional regulatory protein, C terminal


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.1   5.3e-31   4.8e-27       1     111 [.      34     143 ..      34     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 5.3e-31
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl+vdD+p++ +l++ +l  eg  +v++a dg+ea++++++  +d+++lDi++p++dGle+l+++re d  +p ++lta+
  gi|121636963|ref|YP_977186.1|  34 VLLVDDEPALTNLVKMALHYEGW-DVEVAHDGQEAIAKFDKVGPDVLVLDIMLPDVDGLEILRRVRESDVYTPTLFLTAR 112
                                    89*********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++  d+v +l  gadd+++Kpf+ eeL+++l
  gi|121636963|ref|YP_977186.1| 113 DSVMDRVTGLTSGADDYMTKPFSLEELVARL 143
                                    ****************************997 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.041   3.7e+02      39      61 ..     129     151 ..     110     156 .. 0.76
   2 !   89.6   0.0   1.2e-29     1e-25       1      77 []     179     253 ..     179     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.041
                                    STSHTHHHHHHHHHHHHHHHTTT CS
                    Trans_reg_C  39 edvddrtvdvhisrLRkkLedde 61 
                                    + +   +++  ++rLR  L+ ++
  gi|121636963|ref|YP_977186.1| 129 YMTKPFSLEELVARLRGLLRRSS 151
                                    45666689999*****9999854 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 1.2e-29
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    g++++l+++ef+lL++L++np+r +sr+e+l++vw++d+++ ++ vd +is+LRkk++   ++p +I+tvrg+GY+l
  gi|121636963|ref|YP_977186.1| 179 GTPISLSSTEFELLRFLMRNPRRALSRTEILDRVWNYDFAGRTSIVDLYISYLRKKIDS-DREP-MIHTVRGIGYML 253
                                    689********************************************************.4466.**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1706.50
//
Query:       gi|121636964|ref|YP_977187.1|  [L=129]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-07   29.2   0.1      2e-06   27.6   0.1    1.7  1  DDE_Tnp_1    Transposase DDE domain
    3.4e-06   27.3   0.0    5.2e-06   26.7   0.0    1.2  1  DDE_Tnp_1_6  Transposase DDE domain
     0.0044   17.4   0.5     0.0067   16.8   0.5    1.2  1  DDE_Tnp_1_2  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.4e-10     2e-06      56     214 .]       3     121 ..       1     121 [. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.4e-10
                      DDE_Tnp_1  56 pgnvhdskglkqlldelrpr...kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnk 132
                                    +gn  d ++l + +  +++r   ++++v+aD+GY+ a++ ++l e gv+ ++++                   rk    +
  gi|121636964|ref|YP_977187.1|   3 QGNPPDAPQLAPAVAWVKKRagrTPRTVTADRGYGEAAVDQQLTEVGVKNVLIP-------------------RKGKPSQ 63 
                                    69999*******999999999***************************999988...................5555555 PP

                      DDE_Tnp_1 133 iltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                     ++ +++r+ +                         +  + R ++E  ++ lkr +g+dr r  gl+++++++    +a+
  gi|121636964|ref|YP_977187.1|  64 DRRAEEHRKAF------------------------RRTIKWRTGCEGRISHLKRGYGWDRGRIGGLEGTRTWVGHGVFAH 119
                                    55555554444........................467899999******************999999999998888888 PP

                      DDE_Tnp_1 213 nl 214
                                    nl
  gi|121636964|ref|YP_977187.1| 120 NL 121
                                    86 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   8.6e-10   5.2e-06      56     122 ..      57     122 ..      44     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.6e-10
                    DDE_Tnp_1_6  56 elselaekarerikseegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlk 122
                                    +  +  +  r++ + +++++  k R  ++Eg ++ +kr +g +r r+ Gl+ +++++   ++a+Nl 
  gi|121636964|ref|YP_977187.1|  57 RKGKPSQDRRAEEHRKAFRRTIKWRT-GCEGRISHLKRGYGWDRGRIGGLEGTRTWVGHGVFAHNLV 122
                                    45677788888889999999998887.**************************************96 PP

>> DDE_Tnp_1_2  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   1.1e-06    0.0067       1      64 [.      30      96 ..      30      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-06
                    DDE_Tnp_1_2  1 vlaDrgYrsralrealkergI.rasipplgrpakn..kaapkkqarederarnvvErsfgwlkrrrs 64
                                   v aDrgY   a+ + l+e g+ ++ ip +g+p+++   ++ +k  r+  + r   E++++ lkr ++
  gi|121636964|ref|YP_977187.1| 30 VTADRGYGEAAVDQQLTEVGVkNVLIPRKGKPSQDrrAEEHRKAFRRTIKWRTGCEGRISHLKRGYG 96
                                   789******************88889999****9973333333334445567778999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 900.87
//
Query:       gi|121636965|ref|YP_977188.1|  [L=228]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.065   13.1   0.2      0.065   13.1   0.2    2.6  4  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
       0.25   10.4   1.7       0.41    9.7   1.7    1.2  1  APG17            Autophagy protein Apg17
        1.1    9.1  15.6        2.8    7.8  15.7    1.7  1  Apolipoprotein   Apolipoprotein A1/A4/E domain


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.54   3.2e+03      45      58 ..      20      33 ..      17      35 .. 0.82
   2 ?   -2.9   0.1       1.1   6.4e+03      55      61 ..      61      67 ..      60      68 .. 0.85
   3 ?   13.1   0.2   1.1e-05     0.065       5      37 ..     102     134 ..      99     135 .. 0.95
   4 ?   -2.8   0.1      0.98   5.9e+03      39      48 ..     155     164 ..     153     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.54
                                   H---HHHHHHHHHH CS
                Glycos_trans_3N 45 kGetaeEiaalaeA 58
                                    G++++ +a++aeA
  gi|121636965|ref|YP_977188.1| 20 DGLNEALLAKAAEA 33
                                   68899999999998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                   HHHHHHH CS
                Glycos_trans_3N 55 laeAmre 61
                                   la+Amr+
  gi|121636965|ref|YP_977188.1| 61 LAKAMRR 67
                                   799**95 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.1e-05
                                    HHHHTT.---HHHHHHHHHHHHTTSS-HHHHHH CS
                Glycos_trans_3N   5 kklrdgeeLtaeeirfaihgilkgevtdaqiaA 37 
                                    +klr+++eL ++e+r+a+  ++   ++ aq+aA
  gi|121636965|ref|YP_977188.1| 102 AKLRSRAELGRDEARAAVLRFTGELAELAQAAA 134
                                    799*****************************8 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.98
                                    HHHHHHH--- CS
                Glycos_trans_3N  39 LmAlrlkGet 48 
                                    ++Al ++Ge 
  gi|121636965|ref|YP_977188.1| 155 AAALAARGER 164
                                    5788899886 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.7   6.9e-05      0.41       4      69 ..     135     200 ..     134     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.9e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIII CS
                          APG17   4 laAkksLseaqtlcqrAnelltsarqeleeavkllakteflrdglkqQlkllekirkslerklekg 69 
                                    ++A++ L +a++ + rA+  +++   + e+ ++   +++ l++++++  +ll++ r+ + ++++++
  gi|121636965|ref|YP_977188.1| 135 QEAQQLLDNAKQAVLRAKAKAAALAARGERDAVAGRRCGGLVRAVNDLTELLNATRQIVAQTRQRV 200
                                    68*******************************************************999999876 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  15.7   0.00048       2.8      60     162 ..      60     161 ..      22     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00048
                                    HHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                 Apolipoprotein  60 vqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelke 139
                                    + ++ + ++ +  +r++++  ++r r+  +++++ ++  ++a++lr+r+e + ++ +a +  ++ el +  ++ ++e ++
  gi|121636965|ref|YP_977188.1|  60 LLAKAMRRIAATGKRIQAAGGAVRTRVGDRSRAAGRRAHAVAAKLRSRAELGRDEARAAVLRFTGELAELAQAAAQEAQQ 139
                                    44555566666677888888888888888888888888888888888888888888888888888888888888888888 PP

                                    -----..-----SSSHHHHHHHT CS
                 Apolipoprotein 140 slaphaeeveerlssrveelrek 162
                                     l++++++v  r+  ++ +l ++
  gi|121636965|ref|YP_977188.1| 140 LLDNAKQAVL-RAKAKAAALAAR 161
                                    8888888776.444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1677.49
//
Query:       gi|121636966|ref|YP_977189.1|  [L=112]
Description: IS1560 transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.002   18.1   0.0     0.0038   17.2   0.0    1.5  1  DUF772    Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-07    0.0038       1      35 [.      77     111 ..      77     112 .] 0.97

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-07
                         DUF772   1 GrpayppelmlkllllqylyglSdreleealrenl 35 
                                    Grp+ p e+ l l+++++ y+l  + l++++ +++
  gi|121636966|ref|YP_977189.1|  77 GRPSTPMEVYLQLMFVKFRYRLGYESLCREVADSI 111
                                    9*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 771.86
//
Query:       gi|121636967|ref|YP_977190.1|  [L=94]
Description: ESAT-6 like protein 1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   50.6   1.2    1.9e-13   50.4   1.2    1.0  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.12   12.8   0.1    1.1  1  HrpB7     Bacterial type III secretion protein (HrpB7)


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.2   2.2e-17   1.9e-13       2      86 .]       3      87 ..       2      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.2e-17
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83
                                   i++++ +++++ a +++ a++le+e+q++ ++v   ++ W Ga + a+q++++++ +++q ++++ + +++++++a+n++++
  gi|121636967|ref|YP_977190.1|  3 INYQFGDVDAHGAMIRALAGSLEAEHQAIISDVLTASDFWGGAGSAACQGFITQLGRNFQVIYEQANAHGQKVQAAGNNMAQ 84
                                   89******************************************************************************** PP

                                   HHC CS
                         WXG100 84 aDe 86
                                   +D+
  gi|121636967|ref|YP_977190.1| 85 TDS 87
                                   *95 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.3e-05      0.12      52     118 ..      25      91 ..       9      94 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                          HrpB7  52 vraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaarqaldaaedavaatarkiaR 118
                                    +++h++ + d++t+s   + a  +ac+ ++++l  + ++  ++  a  q+++aa +++a+t+ ++++
  gi|121636967|ref|YP_977190.1|  25 EAEHQAIISDVLTASDFWGGAGSAACQGFITQLGRNFQVIYEQANAHGQKVQAAGNNMAQTDSAVGS 91 
                                    56799999*******98899999***************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 628.76
//
Query:       gi|121636968|ref|YP_977191.1|  [L=98]
Description: ESAT-6 like protein 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-19   70.2   3.1    1.4e-19   70.1   3.1    1.0  1  WXG100         Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.087   13.3   2.7        0.1   13.1   2.7    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   3.1   1.6e-23   1.4e-19       2      86 .]       5      90 ..       4      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.6e-23
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82
                                   +++dp ++r++a rf  +a+++ede +r+ a+ +++ ++gWsG a  +  +++++++qa++++v++L+++++ l + an++e
  gi|121636968|ref|YP_977191.1|  5 FMTDPHAMRDMAGRFEVHAQTVEDEARRMWASAQNIsGAGWSGMAEATSLDTMTQMNQAFRNIVNMLHGVRDGLVRDANNYE 86
                                   689******************************************************************************* PP

                                   HHHC CS
                         WXG100 83 daDe 86
                                   ++++
  gi|121636968|ref|YP_977191.1| 87 QQEQ 90
                                   **97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.7   1.1e-05       0.1       4      98 ..       4      96 ..       1      98 [] 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                  T7SS_ESX_EspC  4 nLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAa 85
                                   +   dp ++r +a +++  a+++++ ++ +  asa++ +  G  ++a +++++ + +  ++a + +  ++ +++d L   A 
  gi|121636968|ref|YP_977191.1|  4 RFMTDPHAMRDMAGRFEVHAQTVEDEARRM-WASAQNISGAGWSGMAEATSLDTM-TQMNQAFRNIVNMLHGVRDGLVRDAN 83
                                   55668999***************9999999.566666666688888888888776.55689999999*************** PP

                  T7SS_ESX_EspC 86 aYeatDeeaagal 98
                                   +Ye+ ++++ + l
  gi|121636968|ref|YP_977191.1| 84 NYEQQEQASQQIL 96
                                   ****999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 690.68
//
Query:       gi|121636969|ref|YP_977192.1|  [L=391]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-59  200.5  34.7    1.7e-59  200.5  34.7    2.9  2  PPE       PPE family
    2.2e-21   76.5  17.8    2.2e-21   76.5  17.8    5.5  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5  34.7   1.9e-63   1.7e-59       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -5.4   5.9         2   1.8e+04      57     101 ..     253     303 ..     243     318 .. 0.57

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 1.9e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+nsa++yaG+g+gp++aA aaW+gLaael ++aa++esv++ l++e+W Gp+s+am+aaa+pylaWL+ +a+ a+
  gi|121636969|ref|YP_977192.1|   5 ALPPEINSARMYAGAGAGPMMAAGAAWNGLAAELGTTAASYESVITRLTTESWMGPASMAMVAAAQPYLAWLTYTAEAAA 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a++qa a aaaYeaA+a++vpp+++aanra laalvatn++G+ntpaI+atea y+emwaqda am++Y+aas aa
  gi|121636969|ref|YP_977192.1|  85 HAGSQAMASAAAYEAAYAMTVPPEVVAANRALLAALVATNVLGINTPAIMATEALYAEMWAQDALAMYGYAAASGAA 161
                                    *************************************************************************9876 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 2
                                    HHHHHHHHTHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHS- CS
                            PPE  57 ssaamaaaaapylaWLsaaaaq......aeeaAaqaeaaaaaYeaAlaamv 101
                                    ++a++++aa p + +L++a ++      ae a + ae aa+a  a la  v
  gi|121636969|ref|YP_977192.1| 253 TAAWYVNAAIPTAIFLANALNSgapvaiAEGAIEAAEGAASAAAAGLADSV 303
                                    567777777777777765533300111123333334444444444455555 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   2.4      0.14   1.3e+03      43      62 ..      16      32 ..       4      52 .. 0.44
   2 ?  -25.0  37.4         2   1.8e+04      18      62 ..      56     101 ..      54     220 .. 0.82
   3 ?   -1.9   8.6      0.72   6.5e+03      18      61 ..     255     300 ..     253     307 .. 0.75
   4 !   76.5  17.8   2.5e-25   2.2e-21       2      79 ..     310     387 ..     309     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                       PE_PPE_C 43 aaagaalggmPlaaagagga 62
                                    a ++   + P++aaga+ +
  gi|121636969|ref|YP_977192.1| 16 YAGAG---AGPMMAAGAAWN 32
                                   22222...333333333322 PP

  == domain 2  score: -25.0 bits;  conditional E-value: 2
                       PE_PPE_C  18 sWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagagga 62 
                                    sW ++a+ a+ aaa+   ++ + +a+aaa+a+ ++m+ aaa +++ 
  gi|121636969|ref|YP_977192.1|  56 SWMGPASMAMVAAAQPyLAWLTYTAEAAAHAGSQAMASAAAYEAAY 101
                                    8977776666555555255555555555555555777777766665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.72
                       PE_PPE_C  18 sW..aaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagagg 61 
                                    +W   aa+p+a  +a+al + +++a a++a +a+ g++ aaa++ +
  gi|121636969|ref|YP_977192.1| 255 AWyvNAAIPTAIFLANALNSGAPVAIAEGAIEAAEGAASAAAAGLA 300
                                    5755677788888999998888888888888888888887777654 PP

  == domain 4  score: 76.5 bits;  conditional E-value: 2.5e-25
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    A+lG+A++vG+LSVP++W++aapa++a a+al g++++ aa++ag + g+mP++a++a+g++++a+prygf+ptvmp+
  gi|121636969|ref|YP_977192.1| 310 ASLGEATLVGRLSVPAAWSTAAPATTAGATALEGSGWTVAAEEAGPVTGMMPGMASAAKGTGAYAGPRYGFKPTVMPK 387
                                    9*******************************99999999999999999************9***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2809.11
//
Query:       gi|121636970|ref|YP_977193.1|  [L=275]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-28   98.7  13.9    1.8e-28   98.7  13.9    2.9  3  PE        PE family
    2.1e-18   67.0  18.1    2.1e-18   67.0  18.1    4.1  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7  13.9     2e-32   1.8e-28       1      91 [.       1      91 [.       1      93 [. 0.99
   2 ?   -2.2   0.1       0.6   5.4e+03      13      33 ..      97     113 ..      95     122 .. 0.47
   3 ?   -6.4   6.3         2   1.8e+04      25      25 ..     195     195 ..     156     240 .. 0.60

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2e-32
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msf+ ++Pe+l+aaaa+l +ig+a++a+naaaaaptta+++aa DeVSa +Aalf+a+++ yq++sa+a+a+h++fv++l  
  gi|121636970|ref|YP_977193.1|  1 MSFLKTVPEELTAAAAQLGTIGAAMAAQNAAAAAPTTAIAPAALDEVSALQAALFTAYGTFYQQVSAEAQAMHDMFVNTLGI 82
                                   9********************************************************************************* PP

                                   HHHHHHS-- CS
                             PE 83 aagsYaaaE 91
                                   +ag+Y  +E
  gi|121636970|ref|YP_977193.1| 83 SAGTYGVTE 91
                                   *****9988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.6
                                    HHHHHHHHHHHHHHHHHHHHH CS
                             PE  13 aaaadlagigsalsaanaaaa 33 
                                    aaa+ l gi+ + sa      
  gi|121636970|ref|YP_977193.1|  97 AAASPLSGITGEASAI----I 113
                                    4555555554444433....3 PP

  == domain 3  score: -6.4 bits;  conditional E-value: 2
                                    H CS
                             PE  25 l 25 
                                    l
  gi|121636970|ref|YP_977193.1| 195 L 195
                                    1 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.3  17.2         2   1.8e+04      26      61 ..      11      43 ..       5     130 .. 0.76
   2 ?   -1.5   7.7      0.54   4.9e+03      19      62 ..     139     181 ..     135     191 .. 0.41
   3 !   67.0  18.1   2.3e-22   2.1e-18       1      80 []     192     272 ..     192     272 .. 0.96

  Alignments for each domain:
  == domain 1  score: -8.3 bits;  conditional E-value: 2
                       PE_PPE_C 26 asaaaaalsgttaaaaaaaagaalggmPlaaagagg 61
                                   ++aaaa+l+ ++aa aa+ a+aa++   ++a + ++
  gi|121636970|ref|YP_977193.1| 11 LTAAAAQLGTIGAAMAAQNAAAAAP---TTAIAPAA 43
                                   5555555544444444444444433...33333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.54
                       PE_PPE_C  19 Waaaapaasaaaaal..sgttaaaaaaaagaalggmPlaaagagga 62 
                                    Wa+a++++  +a     ++     aa+aa+a++g ++l+ +ga ga
  gi|121636970|ref|YP_977193.1| 139 WASATSTLIGLAGGGllPAE---EAAEAASALGGEAALGELGALGA 181
                                    65555544443332211333...23333334444444444444444 PP

  == domain 3  score: 67.0 bits;  conditional E-value: 2.3e-22
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    +AglG+A+++G LSVPp+Wa++a  +s++++    g+taaa +aaag+ ++gmP+ a++a+++ag++apryg++p vmp+
  gi|121636970|ref|YP_977193.1| 192 AAGLGSASAIGMLSVPPAWAGQATLVSTTSTLPgAGWTAAAPQAAAGTFIPGMPGVASAARNSAGFGAPRYGVKPIVMPK 271
                                    6**************************99999988999999999999********************************9 PP

                       PE_PPE_C  80 p 80 
                                    p
  gi|121636970|ref|YP_977193.1| 272 P 272
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1588.98
//
Query:       gi|121636971|ref|YP_977194.1|  [L=135]
Description: IS like-2 transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-27   95.0   1.8    3.1e-27   94.6   1.8    1.2  1  DUF4096   Putative transposase of IS4/5 family (DUF4096)


Domain annotation for each model (and alignments):
>> DUF4096  Putative transposase of IS4/5 family (DUF4096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   1.8   1.8e-31   3.1e-27       1      75 []       7      80 ..       7      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.8e-31
                        DUF4096  1 LtDeqWellepllpepkkrrGrprkvdlrevlngIlyvlrtGcpWrdLPedfgswstvyrrfrrWskagvwerif 75
                                   ++De W+++epl+p+++ ++Gr+ + d+r +l+gI +++rtG pWrdLP++fg+w+tv++r++rWs +g+ +++f
  gi|121636971|ref|YP_977194.1|  7 ISDEFWAVVEPLMPSHEGKPGRRFS-DHRLILEGIAWRFRTGSPWRDLPAEFGPWQTVWKRHHRWSLDGTCDEVF 80
                                   69************98888799997.*********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 942.85
//
Query:       gi|121636972|ref|YP_977195.1|  [L=341]
Description: hypothetical protein BCG_1101c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-18   65.9   0.4    1.1e-17   65.3   0.4    1.3  1  Trypsin_2  Trypsin-like peptidase domain
    1.6e-07   31.4   0.0    2.7e-07   30.6   0.0    1.3  1  Trypsin    Trypsin
  ------ inclusion threshold ------
       0.38   10.4   0.8         54    3.5   0.0    3.0  3  DUF2292    Uncharacterized small protein (DUF2292)


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.4   1.8e-21   1.1e-17       1     150 []     145     293 ..     145     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.8e-21
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadp......elDlAllkvssderaglpplp 74 
                                    G+G +v+ ++ ++Tn Hvv++ +g+++        ++ ++ +  +a++v ++        lD+A++k+  + + g   ++
  gi|121636972|ref|YP_977195.1| 145 GTGLVVDHNH-VITNKHVVTGLAGTSA------GLSVYPSSNHAEAELVNFSGtahphpTLDVAVIKF--EMPEGKYIPR 215
                                    9*********.********99999888......2334444444444433333222222277*******..5555656666 PP

                      Trypsin_2  75 lgp...sealkggepvyvvGyp...lggeksgsvssGivsgvvesesaasgegesfl.qtdaatspGsSGGplfdsdGrv 147
                                    lg+   +++   + +vyv+Gyp   +  e+  +v++G+v          +++g+  +  ++a   pG+SGGp++ +dGrv
  gi|121636972|ref|YP_977195.1| 216 LGGmafRDPDWAD-EVYVFGYPrvpMTAEMAITVQRGEVVNPAA----TTIPGRQKIfLYSAIARPGNSGGPIVAQDGRV 290
                                    5553326666666.*******54448888888************....555555555788888888************** PP

                      Trypsin_2 148 vGl 150
                                    +Gl
  gi|121636972|ref|YP_977195.1| 291 IGL 293
                                    **8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   4.6e-11   2.7e-07      26     199 ..     144     297 ..     125     311 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.6e-11
                                    EEEEEEEETTEEEEEGGGTTT.GGGEEEEESE.SBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSS CS
                        Trypsin  26 lCgGslisenwvlTAaHCvsn.asdvkvvlge.hnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdt 103
                                    + +G +++ n v+T++H+v++ a       g+   l+ + ++ ++++ e v + ++  +   + D+a++k + p   g++
  gi|121636972|ref|YP_977195.1| 144 WGTGLVVDHNHVITNKHVVTGlA-------GTsAGLSVYPSS-NHAEAELVNF-SGTAHPHPTLDVAVIKFEMP--EGKY 212
                                    669*****************931.......221223333332.3333333222.2222222247**********..7777 PP

                                    BHCCBBCSTTHTTSTTTEEEEEESSB.SSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTT CS
                        Trypsin 104 vrpiclpaassslpvgttclvsGwgr.tkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSG 182
                                    +  +   a  +++   ++++v G++r + + +   t+q +ev +    t+  +      ++ +   a      a +G+SG
  gi|121636972|ref|YP_977195.1| 213 IPRLGGMA-FRDPDWADEVYVFGYPRvPMTAEMAITVQRGEVVNPAATTIPGR------QKIFLYSA-----IARPGNSG 280
                                    77777777.444578889********644444667888777777666666663......44444444.....6899**** PP

                                    SEEEETTTEEEEEEEEE CS
                        Trypsin 183 GPlvcsdgelvGivswg 199
                                    GP+v++dg ++G+v   
  gi|121636972|ref|YP_977195.1| 281 GPIVAQDGRVIGLVVED 297
                                    ************99765 PP

>> DUF2292  Uncharacterized small protein (DUF2292)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.087   5.2e+02      19      27 ..     246     254 ..     243     255 .. 0.89
   2 ?    3.0   0.1     0.014        81      19      27 ..     283     291 ..     282     293 .. 0.92
   3 ?    3.5   0.0     0.009        54       4      17 ..     321     334 ..     319     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.087
                        DUF2292  19 ivvqdGrvv 27 
                                    i+vq G vv
  gi|121636972|ref|YP_977195.1| 246 ITVQRGEVV 254
                                    9*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                        DUF2292  19 ivvqdGrvv 27 
                                    iv qdGrv+
  gi|121636972|ref|YP_977195.1| 283 IVAQDGRVI 291
                                    899*****8 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.009
                        DUF2292   4 kIlealeelkyGsv 17 
                                    ++++al+el +G +
  gi|121636972|ref|YP_977195.1| 321 EVIRALDELDFGGI 334
                                    799*********77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2491.44
//
Query:       gi|121636973|ref|YP_977196.1|  [L=207]
Description: hypothetical protein BCG_1102 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-13   49.9   1.3    2.6e-13   49.9   1.3    2.7  3  AbiEi_4   Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.3   1.5e-17   2.6e-13       1      49 []      18      66 ..      18      66 .. 0.97
   2 ?   -2.9   0.1      0.45   8.1e+03      36      43 ..     123     130 ..     123     130 .. 0.90
   3 ?    2.0   0.1     0.013   2.3e+02      15      38 ..     152     179 ..     152     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.5e-17
                        AbiEi_4  1 erlpelasrqvGlfttreleaaGispsalrrLvrkGwLvrlrrGvYali 49
                                   +rl+e a++q+G++ttr+++  G++p +lr L  +G+L+r++rGvY+++
  gi|121636973|ref|YP_977196.1| 18 DRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGRGVYRVP 66
                                   69********************************************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.45
                        AbiEi_4  36 GwLvrlrr 43 
                                    G+L r++r
  gi|121636973|ref|YP_977196.1| 123 GELYRVHR 130
                                    899**998 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.013
                        AbiEi_4  15 ttreleaaGispsa....lrrLvrkGwL 38 
                                    t +++ + G +p++    + r+  +G L
  gi|121636973|ref|YP_977196.1| 152 TIKDCVKTGTDPYQlraaIERAEAEGTL 179
                                    67899999999*9955566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1418.22
//
Query:       gi|121636974|ref|YP_977197.1|  [L=293]
Description: hypothetical protein BCG_1103 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   60.0   0.1    3.9e-16   59.7   0.1    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   2.2e-20   3.9e-16       6     215 ..      49     278 ..      44     293 .] 0.79

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.2e-20
                         AbiEii   6 lslsaladklvFkGGTaLslayg.lipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigegedye 84 
                                    l +++ a+ l  kGG +L l+ g +++R S+D D +      ++++e + e l+++ +  +e  + ++ a+++    d +
  gi|121636974|ref|YP_977197.1|  49 LTDDTGAPLLLVKGGSSLELRRGiPDSRTSKDFDTV-----ARRDIELIHEQLADAGETGWEGFTAIFTAPEEI---DVP 120
                                    6678889999*************99*********76.....588999999999999999999888888888888...566 PP

                         AbiEii  85 glrl...rypaef..ggyarqkikieigfreavppaerreippyleel..ggpafevpvysleellaeKllall...drg 154
                                    g+ +   r++a++   g+a  ++ ie+++ ea    +  ++++++ +l     a+ vp+++++  +a Kl+a+    +++
  gi|121636974|ref|YP_977197.1| 121 GMPVkprRFTAKLsyRGRAFATVPIEVSSVEAGNADQFDTLTSDALGLvgVPAAVAVPCMTIPWQIAQKLHAVTavlEEP 200
                                    666655555666666999*******************************99***************************** PP

                         AbiEii 155 rdrsraRDlyDlalLle..aeldaealaeallaylasrgr...............pgelrlaplellreaeadealra 215
                                    + + ra Dl+Dl+lL     ++d    + a+ a ++ r +               +    l+ l+ l+ a+  +a ++
  gi|121636974|ref|YP_977197.1| 201 KVNDRAHDLVDLQLLEGllLDADLMPTRSACIAIFEARAQhpwpprvatlphwplIYAGALEGLDHLELARTVDAAAQ 278
                                    *****************77666666688**********9966655555554444433333333333333333333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2118.79
//
Query:       gi|121636975|ref|YP_977198.1|  [L=197]
Description: hypothetical protein BCG_1104c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1474.50
//
Query:       gi|121636976|ref|YP_977199.1|  [L=415]
Description: IS1081 transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-154  514.6   0.0   1.6e-154  514.4   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      2e-05   24.9   0.0    5.2e-05   23.6   0.0    1.7  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.4   0.0  1.7e-158  1.6e-154       1     380 [.       1     379 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 514.4 bits;  conditional E-value: 1.7e-158
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l+++e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121636976|ref|YP_977199.1|   1 MTSSH-LIDTEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.89999********************************************************************* PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121636976|ref|YP_977199.1|  80 PKLRQGSYFPdWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **********9***************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121636976|ref|YP_977199.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    v+ai+a++p+aa+QrCr+H+++nl+a++pk ++ +v++ l+siy+++dae+++++++++l++l++k+p+vae+ld+a++d
  gi|121636976|ref|YP_977199.1| 239 VAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTD 318
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    +laf+afp+qi+r+i+s+N++ErLN+e+rRrt+vvgiFP+++si+rlvgavlae+hdew+e
  gi|121636976|ref|YP_977199.1| 319 LLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIE 379
                                    ***********************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.8e-09   5.2e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.8e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121636976|ref|YP_977199.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3191.42
//
Query:       gi|121636977|ref|YP_977200.1|  [L=371]
Description: hypothetical protein BCG_1106c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2806.65
//
Query:       gi|121636978|ref|YP_977201.1|  [L=148]
Description: transcriptional repressor protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-12   45.4   0.5      1e-11   44.5   0.5    1.4  1  MarR_2          MarR family
    1.2e-06   28.4   0.3    1.8e-06   27.9   0.3    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    3.4e-05   24.1   0.1    5.5e-05   23.4   0.1    1.3  1  Rrf2            Transcriptional regulator
    4.6e-05   23.3   0.3    0.00011   22.0   0.3    1.7  1  MarR            MarR family
    0.00017   21.1   0.1    0.00035   20.1   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00028   20.9   0.2    0.00077   19.5   0.2    1.7  1  HTH_20          Helix-turn-helix domain
    0.00051   20.5   0.3    0.00074   20.0   0.3    1.3  1  HTH_27          Winged helix DNA-binding domain
    0.00085   18.9   0.3     0.0017   18.0   0.3    1.5  1  GntR            Bacterial regulatory proteins, gntR family
     0.0023   17.7   0.2     0.0051   16.6   0.2    1.5  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.2   0.2      0.078   12.9   0.1    2.0  2  HTH_11          HTH domain
      0.023   14.6   0.0      0.034   14.0   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.03   14.2   0.0      0.051   13.4   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.038   14.2   0.1      0.062   13.5   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.052   13.5   0.1      0.069   13.1   0.1    1.2  1  Pertussis_S2S3  Pertussis toxin, subunit 2 and 3, C-terminal 
      0.086   12.7   0.0       0.18   11.6   0.0    1.6  1  TetR_N          Bacterial regulatory proteins, tetR family
       0.11   12.3   0.0       0.19   11.5   0.0    1.4  1  LexA_DNA_bind   LexA DNA binding domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.5     9e-15     1e-11       1      61 [.      33      95 ..      33      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 9e-15
                                   TT--HHHHHHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2  1 lgltpaqarvLaaLgrrpgr...dltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   +glt +q+  La++  ++g    dlt++ela+r g+++ +++r l+ + + GLv+  +g +D+R
  gi|121636978|ref|YP_977201.1| 33 SGLTNTQFSTLAVISLSEGSagiDLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAG-ADAR 95
                                   79****************************************************87765.6665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.3   1.6e-09   1.8e-06      19      52 ..      54      87 ..      17     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.6e-09
                                   EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                      HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis 52
                                    ++lt+ elA+++G+ r t++r l  ++r+gl++
  gi|121636978|ref|YP_977201.1| 54 GIDLTMSELAARIGVERTTLTRNLEVMRRDGLVR 87
                                   4899****************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   4.9e-08   5.5e-05       6      62 ..      37      93 ..      35      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.9e-08
                                   HHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                           Rrf2  6 kteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                    t++++ a++ L++ + +  ++++e+a+r +++++ l + l+ +r+ glv++  G+ 
  gi|121636978|ref|YP_977201.1| 37 NTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAGAD 93
                                   56778889999999999999**********************************985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3     1e-07   0.00011       1      52 [.      35      91 ..      35      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1e-07
                                   --HHHHHHHHHHHHSTT.....EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR  1 ltltqfviLrilyeqgp.....lsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                   lt tqf++L+ ++ +++     l++seLa ++gv+++t+tr l  + ++Gl++ +  
  gi|121636978|ref|YP_977201.1| 35 LTNTQFSTLAVISLSEGsagidLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAG 91
                                   79999999999986654322115666**************************98776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.1e-07   0.00035      18      48 .]      57      87 ..      56      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.1e-07
                         HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++++eLA r+g+ ++t++r l+ + ++Gl++
  gi|121636978|ref|YP_977201.1| 57 LTMSELAARIGVERTTLTRNLEVMRRDGLVR 87
                                   8****************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   6.9e-07   0.00077      25      56 ..      57      88 ..      56      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-07
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLvev 56
                                   lt sela+r+++ ++tl ++L+v+++ gLv+v
  gi|121636978|ref|YP_977201.1| 57 LTMSELAARIGVERTTLTRNLEVMRRDGLVRV 88
                                   688***************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   6.6e-07   0.00074       3      68 .]      37     105 ..      35     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.6e-07
                         HTH_27   3 rqqalvLhlir...hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    + q  +L +i    +  + +   ++l+ r  ve ++   +l+ + + GLv  ++  ad r kr++lT+kG
  gi|121636978|ref|YP_977201.1|  37 NTQFSTLAVISlseGSAGIDLTmSELAARIGVERTTLTRNLEVMRRDGLVRVMAG-ADARCKRIELTAKG 105
                                    555566666666655555555559**************************66666.8************9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   1.5e-06    0.0017      19      57 ..      52      89 ..      44      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                                   -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           GntR 19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                   ++G  L + +eLaa++gV rtt+ + L    ++glv + 
  gi|121636978|ref|YP_977201.1| 52 SAGIDL-TMSELAARIGVERTTLTRNLEVMRRDGLVRVM 89
                                   577789.99***************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.5e-06    0.0051      18      49 ..      56      87 ..      45      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                                   S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyve 49
                                   +lt selA+r+g+ ++t  R L  + + G+v+
  gi|121636978|ref|YP_977201.1| 56 DLTMSELAARIGVERTTLTRNLEVMRRDGLVR 87
                                   499***************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     7e-05     0.078      16      47 ..      57      89 ..      52     104 .. 0.89
   2 ?   -0.3   0.0      0.97   1.1e+03      32      39 ..     133     140 ..     133     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                         HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg.vpIe 47
                                   ++ +eLA +++v r+t  r ++ ++  g v++ 
  gi|121636978|ref|YP_977201.1| 57 LTMSELAARIGVERTTLTRNLEVMRRDGlVRVM 89
                                   899*********************999976665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.97
                         HTH_11  32 vrrdIkaL 39 
                                    vrrdI+ L
  gi|121636978|ref|YP_977201.1| 133 VRRDIANL 140
                                    89***998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.1e-05     0.034      23      56 ..      57      90 ..      34     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   +t++e+a ++gv+r++  + L+ + + GlV++  
  gi|121636978|ref|YP_977201.1| 57 LTMSELAARIGVERTTLTRNLEVMRRDGLVRVMA 90
                                   699***************************9865 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.6e-05     0.051      16      46 ..      57      87 ..      47      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   l+ +ela+ +g+ + t+ + L ++r  GLV+
  gi|121636978|ref|YP_977201.1| 57 LTMSELAARIGVERTTLTRNLEVMRRDGLVR 87
                                   799***************************7 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.6e-05     0.062      24      54 ..      58      88 ..      43      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                 Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyvey 54
                                   + ++la r++v+  + +  l+ +++dG+v +
  gi|121636978|ref|YP_977201.1| 58 TMSELAARIGVERTTLTRNLEVMRRDGLVRV 88
                                   4579************************975 PP

>> Pertussis_S2S3  Pertussis toxin, subunit 2 and 3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.2e-05     0.069       9      86 ..      22      98 ..      13     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
                                   --EEEEEEEEEEEEEEETTS-EEEEEEETTEEEEEEEE-SSSSTTCCCHHHHHHHHHHHHHCT-EEEEEEEEEEEE-- CS
                 Pertussis_S2S3  9 atdhyysnvtatrlldstnsrlcavfvrdGqpvigacisPyeGryresyaalrrllellyvaGlavrvyvskeeryyd 86
                                     + y   ++ + l ++ +s l  +   +G + i+  +s  + r     ++l r le+++++Gl vrv    + r + 
  gi|121636978|ref|YP_977201.1| 22 LGQAYDRALRPSGLTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGL-VRVMAGADARCKR 98
                                   4456666778889999****************************99999**************9.8999888877665 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.18      13      35 ..      54      75 ..      51      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   HTTT--HHHHHHHHTSSHHHHHH CS
                         TetR_N 13 GydattvreIAkrAGvskgalYr 35
                                   G+d +t++e+A+r Gv + +l r
  gi|121636978|ref|YP_977201.1| 54 GID-LTMSELAARIGVERTTLTR 75
                                   667.89*************9965 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.19       2      62 ..      33      92 ..      32      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                   X---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                  LexA_DNA_bind  2 kkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgk 62
                                   ++LT+ Q   l +i  s  + g   ++ e+a ++g++   +    L+ ++r G+++++ g+
  gi|121636978|ref|YP_977201.1| 33 SGLTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVE-RTTLTRNLEVMRRDGLVRVMAGA 92
                                   589**********************************.8899**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1154.03
//
Query:       gi|121636979|ref|YP_977202.1|  [L=301]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-52  176.0   0.7    7.8e-52  175.6   0.7    1.1  1  adh_short     short chain dehydrogenase
    9.4e-38  130.1   0.4    1.2e-37  129.7   0.4    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      2e-12   47.4   1.3    3.4e-12   46.7   1.3    1.4  1  KR            KR domain
     0.0021   17.6   0.1     0.0031   17.0   0.1    1.2  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.075   12.5   4.6       0.14   11.6   2.1    2.1  2  Herpes_UL56   Herpesvirus UL56 protein
        0.1   12.4   1.7       0.22   11.3   1.7    1.6  1  DFP           DNA / pantothenate metabolism flavoprotein
       0.81   10.0   5.4        7.3    7.0   0.0    2.5  2  EccE          Putative type VII ESX secretion system transloc


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.7     3e-55   7.8e-52       1     191 [.       9     200 ..       9     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 3e-55
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    +vvl+tGassGIG a+ak++a+eGa v++++r+e +l++va e++++g +a+++++Dv+++e+v+a+v+++v ++g++dv
  gi|121636979|ref|YP_977202.1|   9 QVVLITGASSGIGEATAKAFAREGAVVALAARREGALRRVAREIEAAGGRAMVAPLDVSSSESVRAMVADVVGEFGRIDV 88 
                                    69****************************************************************************** PP

                                    EEE---SS--SSGG.GCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfs.elseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                    + nNAG++ +gp+  e+  +++++++e+ + g++ ++r+vlp m++q+sGrI n+sSv+g++++a +a Ys++ +a+ag+
  gi|121636979|ref|YP_977202.1|  89 VFNNAGVSLVGPVDaETFLDDTREMLEIDYLGTVRVVREVLPIMKQQRSGRIMNMSSVVGRKAFARFAGYSSAMHAIAGF 168
                                    *******88887751555566*********************************************************** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdmakelr 191
                                    +++l++el+ +gi v++++P+l++T++ +++ 
  gi|121636979|ref|YP_977202.1| 169 SDALRQELRGSGIAVSVIHPALTQTPLLANVD 200
                                    **************************998875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.4   4.6e-41   1.2e-37       1     183 [.      15     200 ..      15     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 4.6e-41
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIG+a+Aka+a+eGa v+l+ ++e a ++ ++e+++++g++ v ++DV++ e+v+a+v++vv +fg++D+++nnag
  gi|121636979|ref|YP_977202.1|  15 GASSGIGEATAKAFAREGAVVALAARREGAlRRVAREIEAAGGRAmVAPLDVSSSESVRAMVADVVGEFGRIDVVFNNAG 94 
                                    899***************************77888888888887767********************************* PP

                                    --EGCSS-G.GGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpf.letsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    ++    gp+ +et  ++ +++l+++  +++++++++lp+mk++  g+i+n+ssv ++++++  + y+ a +a+ +++ +l
  gi|121636979|ref|YP_977202.1|  95 VSLV--GPVdAETFLDDTREMLEIDYLGTVRVVREVLPIMKQQrsGRIMNMSSVVGRKAFARFAGYSSAMHAIAGFSDAL 172
                                    ***9..77625689**************************99999*********************************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGST CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgik 183
                                      el   gi v +++p +++T++ ++++
  gi|121636979|ref|YP_977202.1| 173 RQELRGSGIAVSVIHPALTQTPLLANVD 200
                                    **********************998886 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   1.3   1.3e-15   3.4e-12       2     173 ..      10     186 ..       9     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.3e-15
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeepp 81 
                                    ++litG+  g+G ++a+  a++ga  ++l +R++    + ++  +e+ea g + +v+++Dvs++++v+a+++++  e+++
  gi|121636979|ref|YP_977202.1|  10 VVLITGASSGIGEATAKAFAREGAV-VALAARRE---GALRRVAREIEAAGGRAMVAPLDVSSSESVRAMVADVVGEFGR 85 
                                    579********************96.78888883...34455779*********************************** PP

                                    --EEEE---------TTT--.HHHHHHHHTTTTHHHHHHHH....HTTTS--SEEEEEEEHHHHH--TT-HHHHHHHH.. CS
                             KR  82 ikGvihaAgvlrdklleemt.aedleqvlapKvkGawnLhe....lledesldffvlfSSiagllgsagqanYaaaNa.. 154
                                    i  v++ Agv+  ++++  t  +d +++l+    G+  + +    ++++++   ++ +SS+ g    a  a Y++a +  
  gi|121636979|ref|YP_977202.1|  86 IDVVFNNAGVSLVGPVDAETfLDDTREMLEIDYLGTVRVVRevlpIMKQQRSGRIMNMSSVVGRKAFARFAGYSSAMHai 165
                                    **********99999987773588888988888887654431111556688999999******99999999999997622 PP

                                    ..HHHHHHHHHHHHHHTEEEE CS
                             KR 155 ..flDalaeyrrsqglpavsi 173
                                      f Dal ++ r +g ++ +i
  gi|121636979|ref|YP_977202.1| 166 agFSDALRQELRGSGIAVSVI 186
                                    225566666666666655555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.2e-06    0.0031       1     115 [.      11     145 ..      11     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH....H.T-SEE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke....e.qpdav 68 
                                    +l+tGa+  iG a++ka++++g  v   +r++ a ++   +++        +  ld+  ++++++++++    + ++d+v
  gi|121636979|ref|YP_977202.1|  11 VLITGASSGIGEATAKAFAREGAVVALAARREGALRRV-AREIeaaggraMVAPLDVSSSESVRAMVADvvgeFgRIDVV 89 
                                    79********************8877777773333332.3333689***988899999999777665542222679**** PP

                                    EE--S---HH.....HHHHSHHHHHHHHTHHHHHHHHHHH....HHTCTEEEEEEE CS
                      Epimerase  69 ihlAavggva.....assedpadfieknlqgtlnlleaar....kagvkrllflsS 115
                                    ++ A+v+ v+     +  +d  +++e++  gt++++ ++     ++   r++++sS
  gi|121636979|ref|YP_977202.1|  90 FNNAGVSLVGpvdaeTFLDDTREMLEIDYLGTVRVVREVLpimkQQRSGRIMNMSS 145
                                    ***99887642222144567778888888888888877664443334446666666 PP

>> Herpes_UL56  Herpesvirus UL56 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.1   5.6e-05      0.14      58     115 ..       9      66 ..       6      83 .. 0.85
   2 ?    0.9   0.0       0.1   2.6e+02      45      76 ..     201     232 ..     191     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                    Herpes_UL56  58 lvvlvspassgegevsergrsrraaqraarrarrraerrarrrsfgpggllvetplfl 115
                                     vvl++ assg ge++ +  +r+ a  a    r  a rr  r     gg  + +pl +
  gi|121636979|ref|YP_977202.1|   9 QVVLITGASSGIGEATAKAFAREGAVVALAARREGALRRVAREIEAAGGRAMVAPLDV 66 
                                    5899*********************998877777899999999999999877788865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                    Herpes_UL56  45 ptdspppysagtllvvlvspassgegevserg 76 
                                    p+d ppp+ + t + v    a+  +g +  r 
  gi|121636979|ref|YP_977202.1| 201 PADMPPPFRSLTPIPVHWVAAAVLDGVARRRA 232
                                    88888888655444444444555666665555 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.7   8.6e-05      0.22      18      93 ..       8      96 ..       4     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                                   CTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS--..........-TT-EEEE-...-SHHHHHHHHHHHHTT-SE CS
                            DFP 18 DpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.slet..........pegvevvkv...esaeemleaveealkeadi 85
                                   D+V +i+  SSG  G a A+a+a++Ga V l +    +l+            + v  ++v   es++ m + v  ++ + d+
  gi|121636979|ref|YP_977202.1|  8 DQVVLITGASSG-IGEATAKAFAREGAVVALAARREgALRRvareieaaggRAMVAPLDVsssESVRAMVADVVGEFGRIDV 88
                                   9999********.6*****************987743554333344444442334444450004555555555556666799 PP

                                   EEE---S- CS
                            DFP 86 vimaAAva 93
                                   v+  A v+
  gi|121636979|ref|YP_977202.1| 89 VFNNAGVS 96
                                   99999887 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.6     0.044   1.1e+02      23      57 ..      28      62 ..      21      82 .. 0.81
   2 ?    7.0   0.0    0.0029       7.3      24      76 ..     153     205 ..     147     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.044
                           EccE 23 saRgggtegaaraaaaaarRlakaLreqGirarvl 57
                                    aR+g++  +a+    a rR+a++++ +G ra v+
  gi|121636979|ref|YP_977202.1| 28 FAREGAVVALAARREGALRRVAREIEAAGGRAMVA 62
                                   4788999999999999*************999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0029
                           EccE  24 aRgggtegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaa 76 
                                    aR +g  +a  a+a  ++ l ++Lr+ Gi+++v + +  ++ l a ++ ++++
  gi|121636979|ref|YP_977202.1| 153 ARFAGYSSAMHAIAGFSDALRQELRGSGIAVSVIHPALTQTPLLANVDPADMP 205
                                    5667889999*********************9998776666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2321.99
//
Query:       gi|121636980|ref|YP_977203.1|  [L=251]
Description: hypothetical protein BCG_1109c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-13   50.2   0.0      4e-13   49.9   0.0    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy
    1.1e-07   31.9   0.0      2e-07   31.1   0.0    1.5  1  HTH_17    Helix-turn-helix domain
     0.0058   16.7   0.0      0.015   15.4   0.0    1.6  1  MerR_1    MerR HTH family regulatory protein
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.035   13.9   0.0    1.7  1  MerR      MerR family regulatory protein


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0     9e-17     4e-13      51     197 ..       8     152 ..       3     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 9e-17
                         AbiEii  51 ealkealeeiaaalaeeglkvklaasigege....dyeglrlrypaefggyarqkikieigfreav.ppaerreippyle 125
                                    e l +++++ia +  ++g+ + l+ s+ ++     dy+glr+r+     g  ++    +++++e++ p + r++i  +l 
  gi|121636980|ref|YP_977203.1|   8 EHLTQVVRDIAVIDIDDGVAFNLDTSSVQEIreraDYPGLRVRVAMS-VGPWQGIAAWDVSTGEPIaPWPTRVTIDRILG 86 
                                    56677777777777888888777777766668888*******99999.999999999*********87777888888887 PP

                         AbiEii 126 elggpafevpvysleellaeKllalldrgrdrsraRDlyDlalLleaeldaealaeallaylasrgrpgelr 197
                                    e+    +++  y +e+++aeK +++l+rg  ++r RD++D+++L ++++d+++l +  +a+ ++rg   +l+
  gi|121636980|ref|YP_977203.1|  87 EP----ITLLGYAPETIIAEKGVTILERGITSTRWRDYVDIVQLDRRGIDDDELLRSARAVAQYRGA--TLE 152
                                    77....***********************************************99999999999988..332 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.5e-11     2e-07       1      50 [.     195     245 ..     195     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.5e-11
                         HTH_17   1 lltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewlekr 50 
                                    ll+ ++++e+ gv + t++ ++++   pa   +Grr+ ++r+++ +w+ kr
  gi|121636980|ref|YP_977203.1| 195 LLDAKQVSEMIGVPVGTLRHWRHSDIGPASFtLGRRVVYRRDEVSRWISKR 245
                                    6999***********************99955****************987 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-06     0.015       4      44 ..     199     239 ..     197     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                                    HHHHHHHTS-HHHHHHHHHHTT-S-EE.-TTS-EEEEHHHHH CS
                         MerR_1   4 gevakilgvtthtlrywekegllkpkr.teggrryYtdedie 44 
                                    ++v++++gv++ tlr+w++   + p+  t g r  Y+++++ 
  gi|121636980|ref|YP_977203.1| 199 KQVSEMIGVPVGTLRHWRHS-DIGPASfTLGRRVVYRRDEVS 239
                                    79***************875.566666577777888888875 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.7e-06     0.035       3      19 ..     199     215 ..     198     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-06
                                    HHHHHHHTTTHHHHHHH CS
                           MerR   3 gevAeltGvsprtLRyY 19 
                                    ++v+e+ Gv++ tLR++
  gi|121636980|ref|YP_977203.1| 199 KQVSEMIGVPVGTLRHW 215
                                    79**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1712.33
//
Query:       gi|121636981|ref|YP_977204.1|  [L=129]
Description: hypothetical protein BCG_1110 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 971.31
//
Query:       gi|121636982|ref|YP_977205.1|  [L=91]
Description: hypothetical protein BCG_1111c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 708.54
//
Query:       gi|121636983|ref|YP_977206.1|  [L=104]
Description: integrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 782.41
//
Query:       gi|121636984|ref|YP_977207.1|  [L=44]
Description: integrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 340.21
//
Query:       gi|121636985|ref|YP_977208.1|  [L=254]
Description: hypothetical protein BCG_1114 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-41  137.7   0.1    7.8e-30  102.6   0.0    2.2  2  NTP_transf_9  Domain of unknown function (DUF427)


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.9e-12   3.4e-08       4      76 ..      25      96 ..      22     111 .. 0.84
   2 !  102.6   0.0   4.3e-34   7.8e-30       1      93 []     142     235 ..     142     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-12
                                   E-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEEESS CS
                   NTP_transf_9  4 klngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslavdgkevkdaaWsYpe 76
                                    l+ ++v +t++a +v+e  ++p+yY+p +dv++e+l+++++ +     G  + +sl+ +g++++ aa +++ 
  gi|121636985|ref|YP_977208.1| 25 YLGHVLVFDTSAARYVWEVPYYPQYYIPLADVRMEFLRDENHPQ-RVQLGPSRLHSLVSAGQTHRSAARVFDV 96
                                   567899*********************************99855.5567999*****9999999999998874 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 4.3e-34
                                    EEEE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTE.EEEEEEEEETTEEEEEEEEEESS--T CS
                   NTP_transf_9   1 vrvklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKG.easyyslavdgkevkdaaWsYpeptp 79 
                                    vrv+l+g v+a+t+++v+++etg p+ryY+ p+d+++e+l+p++t+t Cp+KG +  y+s++v++ +++d aW+Y  p p
  gi|121636985|ref|YP_977208.1| 142 VRVELDGIVLADTRSPVLLFETGIPTRYYIDPADIAFEHLEPTSTQTLCPYKGtTSGYWSVRVGDAVHRDLAWTYHYPLP 221
                                    799**************************************************4456*********************** PP

                                    T-GGGTT-BEE-TT CS
                   NTP_transf_9  80 eaaeikgyvaFyae 93 
                                    ++a+i+g+vaFy+e
  gi|121636985|ref|YP_977208.1| 222 AVAPIAGLVAFYNE 235
                                    ************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1740.37
//
Query:       gi|121636986|ref|YP_977209.1|  [L=393]
Description: hypothetical protein BCG_1115 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-09   36.0   0.5      0.034   13.4   0.0    4.1  4  Lactonase     Lactonase, 7-bladed beta-propeller
    1.2e-06   28.3   0.6        4.1    7.5   0.0    5.3  5  PD40          WD40-like Beta Propeller Repeat
    4.8e-05   22.0   1.3     0.0063   15.1   0.1    3.3  3  Cytochrom_D1  Cytochrome D1 heme domain
    0.00067   18.6   0.1      0.038   12.8   0.0    2.8  3  SBP56         56kDa selenium binding protein (SBP56)
     0.0049   17.7   6.1         12    6.9   0.1    5.7  5  WD40          WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0014       5.1     296     331 ..      42      75 ..      31      86 .. 0.66
   2 !   13.4   0.0   9.4e-06     0.034     243     309 ..     123     190 ..      94     210 .. 0.74
   3 !   11.3   0.0   4.2e-05      0.15     197     264 ..     130     192 ..     128     295 .. 0.63
   4 !   10.5   0.0   7.4e-05      0.27      21     114 ..     275     358 ..     257     380 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                                    EEE-TTSSEEEEEETTTTEEEEEEEETTTTEEEEES CS
                      Lactonase 296 faldpsgklllvanqksdnvtvferdaetGkLtelg 331
                                    +a++++g+ll+v n  +d+v+v+  d  t ++t+++
  gi|121636986|ref|YP_977209.1|  42 IAISRDGSLLVVTNNGTDTVSVVGTD--TCRVTQTV 75 
                                    56677777777777777777776654..44444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.4e-06
                                    ---EEEEEE-TTSSEEEEEETS..STEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEE CS
                      Lactonase 243 knsaaeIrlspdgkflyvSnRg..adsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvan 309
                                    + s +++ lspd+k+lyvS  g     +av++    +  +  v+  ++ g++     ++p+g++l+v+ 
  gi|121636986|ref|YP_977209.1| 123 ALSVSDLTLSPDDKYLYVSRNGtrGADVAVLDT-TTGALIDVVDVSQAPGTTTQCVRMSPDGSVLYVGA 190
                                    357899999999999999987766556888887.66667788888888899999999999999999875 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 4.2e-05
                                    EE-TTSSEEEEEETTTTEEEEEEEE-TTTEEEEEEEEESS-TSS-S---EEEEEE-TTSSEEEEEETS CS
                      Lactonase 197 aFhpdgkiaYvvnELsstvsvfsydeatgaleelqtvstlpegftgknsaaeIrlspdgkflyvSnRg 264
                                    +++pd k++Yv    ++  +v  +d++tgal ++ +vs  p++ t+      +r+spdg+ lyv   g
  gi|121636986|ref|YP_977209.1| 130 TLSPDDKYLYVSRNGTRGADVAVLDTTTGALIDVVDVSQAPGTTTQC-----VRMSPDGSVLYVGANG 192
                                    45566666666665555555555555566666666666666555555.....6666666666665555 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 7.4e-05
                                    ETTTS-EEEEEE.EEESS---SEEE-TTSSEEEEEET.STTTEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSSE CS
                      Lactonase  21 dtetgkltplel.vaelenPsyLalspdgktlYavnetgeeggvsafaidkdsgeltllnkvssegaspchlsvdedgkl 99 
                                    dt+t ++t+     + ++ ++ + +s d+++ Y v+e+  + +v   + +       ++++ +  g+++c+++ ++dgk+
  gi|121636986|ref|YP_977209.1| 275 DTRTHQITSSRAiSEIGGLVTRVSVSGDADRAYLVSED--RVTVLCTRTH------DVIGTIR-TGQPSCVVE-SPDGKY 344
                                    44666666666645556677777888888888888874..5555555544......3678777.788888888.599999 PP

                                    EEEEETTTTEEEEEE CS
                      Lactonase 100 lavAnYsggsvsvfp 114
                                    l++A+Ys g+++  +
  gi|121636986|ref|YP_977209.1| 345 LYIADYS-GTITRTA 358
                                    9999995.4454444 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.042   1.5e+02       8      24 ..      36      52 ..      35      59 .. 0.85
   2 !    7.3   0.0    0.0013       4.5      15      33 ..     130     147 ..     128     152 .. 0.85
   3 ?    1.7   0.0     0.076   2.7e+02      17      24 ..     180     187 ..     176     196 .. 0.89
   4 ?    1.8   0.0      0.07   2.5e+02      15      26 ..     250     260 ..     247     263 .. 0.78
   5 !    7.5   0.0    0.0011       4.1      17      26 ..     339     348 ..     335     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.042
                                   SS.EEEEEE-TTSSEEE CS
                           PD40  8 pgnegaPsfSPDGkrla 24
                                    g++g++++S DG+ l+
  gi|121636986|ref|YP_977209.1| 36 GGPIGGIAISRDGSLLV 52
                                   5789*********9997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0013
                                    EE-TTSSEEEEEEECT.TC CS
                           PD40  15 sfSPDGkrlaFsSdRgsGk 33 
                                    ++SPD k+l+ s++++  +
  gi|121636986|ref|YP_977209.1| 130 TLSPDDKYLYVSRNGT-RG 147
                                    78************98.43 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.076
                                    -TTSSEEE CS
                           PD40  17 SPDGkrla 24 
                                    SPDG+ l+
  gi|121636986|ref|YP_977209.1| 180 SPDGSVLY 187
                                    9***9998 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.07
                                    EE-TTSSEEEEE CS
                           PD40  15 sfSPDGkrlaFs 26 
                                    ++SPDG  +a++
  gi|121636986|ref|YP_977209.1| 250 ALSPDG-AIAYV 260
                                    79****.77765 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0011
                                    -TTSSEEEEE CS
                           PD40  17 SPDGkrlaFs 26 
                                    SPDGk+l+++
  gi|121636986|ref|YP_977209.1| 339 SPDGKYLYIA 348
                                    9*******86 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.8e-06    0.0063      74     215 ..      34     170 ..       1     188 [. 0.54
   2 ?    1.7   0.0     0.021        76      68      95 ..     235     262 ..     231     288 .. 0.67
   3 ?   -0.0   0.0      0.07   2.5e+02      40      60 ..     335     355 ..     308     361 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-06
                                    E-SSEEEEEEE--TTSEEEEEEEETTEEEEEETTT--EEEEEE--EE-SSSS---EEEEEE-SSSSEEEEEETTTTEEE. CS
                   Cytochrom_D1  74 kiGlnarsvavSqddryvivgnYlPgqlvildaetLelvkvisargltvderesRVaaivasperpefvvnlkdtgeil. 152
                                    ++G+   ++a+S d+ +++v n    +++++ ++t    +++ +++      e+   a+ ++   + +v  +  + +++ 
  gi|121636986|ref|YP_977209.1|  34 VQGGPIGGIAISRDGSLLVVTNNGTDTVSVVGTDTCRVTQTVTSVN------EPFAIAMGNAEANRAYVSTVSSAYDAIa 107
                                    4555555666666666666666666666666666666555554433......3445566666666666666655543330 PP

                                    EEE-SSSSSEEEEEEE--SSEEEEEE-TTSSEEEEEEGGGT..EEEEEETTTTEEEEEEE-SSSB CS
                   Cytochrom_D1 153 lvdysdlknlktrtieaakflhDggldpdkRYflaaanaed..kvavvdtkegklvilldvgktp 215
                                    ++d +  + l t     a  + D +l+pd +Y+ ++ n+     vav+dt +g l   +dv+++p
  gi|121636986|ref|YP_977209.1| 108 VIDVATNTVLGT--HPLALSVSDLTLSPDDKYLYVSRNGTRgaDVAVLDTTTGALIDVVDVSQAP 170
                                    334433333333..334445566666666666666666655556666666666666666665554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.021
                                    SEEEEEE-SSEEEEEEE--TTSEEEEEE CS
                   Cytochrom_D1  68 eivaevkiGlnarsvavSqddryvivgn 95 
                                    ++va++ iG+  r va S d+  + v++
  gi|121636986|ref|YP_977209.1| 235 RVVATIDIGSSVRDVALSPDGAIAYVAS 262
                                    6899999999999999999987554433 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.07
                                    EEE-TT.SSEEEEEETTSEEE CS
                   Cytochrom_D1  40 srvfasdgRyvyvigRDgkvt 60 
                                     +v ++dg+y+y++   g++t
  gi|121636986|ref|YP_977209.1| 335 CVVESPDGKYLYIADYSGTIT 355
                                    456677888888877666665 PP

>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.19   6.8e+02     362     385 ..      31      55 ..      14      59 .. 0.81
   2 !   12.8   0.0     1e-05     0.038     279     325 ..     100     144 ..      82     190 .. 0.85
   3 ?    2.7   0.0     0.012        44     304     384 ..     243     348 ..     143     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.19
                          SBP56 362 grkleggPq.mvelslDGkrlYvtn 385
                                    +  ++ggP   + +s+DG  l vtn
  gi|121636986|ref|YP_977209.1|  31 KIPVQGGPIgGIAISRDGSLLVVTN 55 
                                    457899995369*******999998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1e-05
                          SBP56 279 dekweaekvieipakkvegeelpelpglvtDillslDDrflyvsnWl 325
                                     ++++a  vi++ +++v g+   +l+  v+D++ls DD++lyvs  +
  gi|121636986|ref|YP_977209.1| 100 SSAYDAIAVIDVATNTVLGT--HPLALSVSDLTLSPDDKYLYVSRNG 144
                                    56788999999999999886..677888***************9765 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.012
                          SBP56 304 pglvtDillslDDrflyvsnWltGdlrqydisdpkkPkltgq...vrlGGiirka......................ehp 358
                                     + v D++ls D    yv++ ++      d+ d+++ + t++     +GG++++                       +++
  gi|121636986|ref|YP_977209.1| 243 GSSVRDVALSPDGAIAYVASCGSDFGAVVDVIDTRTHQITSSraiSEIGGLVTRVsvsgdadraylvsedrvtvlctRTH 322
                                    66678888888888888888777666677888877777776522135788888888888888888888888888887555 PP

                          SBP56 359 avkgrkleggPqmvelslDGkrlYvt 384
                                     v g+  +g P  v  s DGk lY++
  gi|121636986|ref|YP_977209.1| 323 DVIGTIRTGQPSCVVESPDGKYLYIA 348
                                    66677778888888888888888876 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.25   8.9e+02      12      27 ..      38      53 ..      29      68 .. 0.77
   2 ?    3.1   0.0     0.057   2.1e+02       6      32 ..     116     144 ..     112     148 .. 0.75
   3 ?    0.9   0.0      0.27   9.7e+02      15      29 ..     176     190 ..     166     194 .. 0.86
   4 !    6.9   0.1    0.0034        12      11      31 ..     244     266 ..     235     269 .. 0.82
   5 ?    2.6   0.1     0.082   2.9e+02      14      34 ..     334     354 ..     277     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                                   SEEEEEEETTSSEEEE CS
                           WD40 12 svtslafspdgawlas 27
                                   ++ ++a s+dg++l+ 
  gi|121636986|ref|YP_977209.1| 38 PIGGIAISRDGSLLVV 53
                                   5889999******975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.057
                                    EEESSSS....EEEEEEETTSSEEEEEETTS CS
                           WD40   6 tltGHss....vtslafspdgawlasGsdDg 32 
                                    +l +H +    v++l  spd ++l  + ++g
  gi|121636986|ref|YP_977209.1| 116 VLGTH-PlalsVSDLTLSPDDKYLYVS-RNG 144
                                    56778.44456999*********9854.355 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.27
                                    EEEEETTSSEEEEEE CS
                           WD40  15 slafspdgawlasGs 29 
                                    +++ spdg+ l  G 
  gi|121636986|ref|YP_977209.1| 176 CVRMSPDGSVLYVGA 190
                                    8999*****998886 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0034
                                    SSEEEEEEETTSSE..EEEEETT CS
                           WD40  11 ssvtslafspdgaw..lasGsdD 31 
                                    ssv+++a spdga   +as++ D
  gi|121636986|ref|YP_977209.1| 244 SSVRDVALSPDGAIayVASCGSD 266
                                    379***********777776546 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.082
                                    EEEEEETTSSEEEEEETTSEE CS
                           WD40  14 tslafspdgawlasGsdDgtv 34 
                                    +++  spdg++l  +++ gt+
  gi|121636986|ref|YP_977209.1| 334 SCVVESPDGKYLYIADYSGTI 354
                                    488899999999777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2366.77
//
Query:       gi|121636987|ref|YP_977210.1|  [L=543]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-97  324.9   0.0    7.6e-97  324.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.7e-18   65.9   0.1    1.1e-17   64.8   0.1    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
     0.0079   16.1   0.3      0.021   14.7   0.3    1.7  1  DUF3659        Protein of unknown function (DUF3659)
  ------ inclusion threshold ------
       0.24   11.5   1.4          7    6.8   0.0    3.0  3  DUF3701        Phage integrase protein


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.6   0.0  1.7e-100   7.6e-97      12     422 ..      27     437 ..      17     438 .. 0.89

  Alignments for each domain:
  == domain 1  score: 324.6 bits;  conditional E-value: 1.7e-100
                                    EEEEE.CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHH CS
                    AMP-binding  12 valvd.sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayil 90 
                                    ++ +  ++++++ +Yr++ +r+ +lA++Lr+lGv+ ++rVa +++n  e++v+++a+ ++Gav+ +ln +l +e++ay+ 
  gi|121636987|ref|YP_977210.1|  27 TVTTAtGEGYRHSSYRDVGQRAGQLANALRRLGVTGDQRVATFMWNNTEHLVTYFAVPSMGAVLHTLNIRLFPEQIAYVT 106
                                    444335678*********************************************************************** PP

                                    HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEEEE CS
                    AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddlayi 164
                                    +++e +v++  vd  l+  l+++ +kl++v +vi + +++    +e+ ++     ++       +    +++++++ a +
  gi|121636987|ref|YP_977210.1| 107 NEAEDRVIL--VDLSLARLLAPVLPKLDTVHTVIAVGEGDTTPLREAGKTVLRF-AELidaespDF-GWPQIDENSAAAM 182
                                    *********..99999999999********999999988877766655555333.33145667533.55689******** PP

                                    EEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHH CS
                    AMP-binding 165 iYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldp 242
                                    +YTSGTTG+PKGV++sh  ++++++a++  +t   +++++d+vl i+p++h+ g+    ++al++Ga +vl++   +ld+
  gi|121636987|ref|YP_977210.1| 183 CYTSGTTGNPKGVVYSHrSSFLHTMAAC--TTNgIGVGSSDKVLPIVPMFHANGW-GLPYAALMAGADLVLPD--RHLDA 257
                                    *****************88889999996..444467899****************.***************77..55788 PP

                                    HHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGS CS
                    AMP-binding 243 klllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEtt 321
                                    + l++++e+lk+t+  +vP++++ +++  ++      ++d+sslrlv +gg++++++l+r f+++   ++ +++G+TEt+
  gi|121636987|ref|YP_977210.1| 258 RSLIHMVETLKPTLAGAVPTIWNDVMHyLEKD----PDHDMSSLRLVACGGSAVPESLMRTFEDKHDVQIRQLWGMTETS 333
                                    89***********************9955333....467**************************999************ PP

                                    SECEE......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETC CS
                    AMP-binding 322 gvvtv......lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpeataeafdseg 393
                                    + +t+       p++++++ + ++G+p++gve +ivD++ g+ +p dg+  Ge+ vrgp+++  Y++   + +++fd + 
  gi|121636987|ref|YP_977210.1| 334 PLATMawpppgTPDDQHWAFRITQGQPVCGVETRIVDDD-GQVLPnDGNAvGEVEVRGPWIAGSYYGG--RDESKFD-S- 408
                                    ***8889****88899999999****************9.66666477668***************97..67789*9.6. PP

                                    CEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 394 rwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +wlrTGD+gr+de+G + +++R+kd+ik+
  gi|121636987|ref|YP_977210.1| 409 GWLRTGDVGRIDEQGFITLTDRAKDVIKS 437
                                    6**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   2.4e-21   1.1e-17       1      76 []     446     521 ..     446     521 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.4e-21
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E++l++hp+V eaaVvGvpde++ e+++a+Vv ++g +  + +L+a++++++  ++ p++  fvde+p+t  GK
  gi|121636987|ref|YP_977210.1| 446 ELENCLIAHPDVLEAAVVGVPDERWQERPLAVVVVREGATVSAGDLRAFLADKVVRWWLPERWAFVDEIPRTSVGK 521
                                    89*********************************98943468********************************9 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   4.7e-06     0.021      36      57 ..     367     388 ..     354     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-06
                        DUF3659  36 kkvdedGnivdedGnviGkael 57 
                                    + vd+dG+++ +dGn +G++e+
  gi|121636987|ref|YP_977210.1| 367 RIVDDDGQVLPNDGNAVGEVEV 388
                                    448*****************96 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.055   2.5e+02      49      74 ..      50      75 ..      42      83 .. 0.80
   2 ?    6.8   0.0    0.0016         7      17      54 ..     408     445 ..     404     447 .. 0.93
   3 ?   -1.1   0.2      0.46   2.1e+03      17      51 ..     468     503 ..     456     505 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.055
                        DUF3701 49 rWwravprlGaakArrieafLaahae 74
                                   +  +a++rlG ++ +r++ f+ ++ e
  gi|121636987|ref|YP_977210.1| 50 QLANALRRLGVTGDQRVATFMWNNTE 75
                                   566889*************9977654 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                        DUF3701  17 arWlsprvarrLaaagvktLaeLiarinrrgkrWwrav 54 
                                    + Wl+   + r+ ++g+ tL +  + + + g++W ++v
  gi|121636987|ref|YP_977210.1| 408 SGWLRTGDVGRIDEQGFITLTDRAKDVIKSGGEWISSV 445
                                    57***********************9999999**9988 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.46
                        DUF3701  17 arWlsprvarrLaaagvk.tLaeLiarinrrgkrWw 51 
                                    +rW +  +a    ++g +   ++L+a+   +  rWw
  gi|121636987|ref|YP_977210.1| 468 ERWQERPLAVVVVREGATvSAGDLRAFLADKVVRWW 503
                                    578887888877777776467899999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3775.43
//
Query:       gi|121636988|ref|YP_977211.1|  [L=354]
Description: hypothetical protein BCG_1117 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-06   27.8   0.0    3.6e-06   27.1   0.0    1.3  1  DapB_N    Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     2e-10   3.6e-06       8      95 ..      11      97 ..       7     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2e-10
                                   TTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEEEE-S-HHHHHHHHHHHH CS
                         DapB_N  8 asGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek.advliDFTtpeavlenlklal 88
                                   a+G +G + +k v ++++lelv+   ++  + +gkd+ge++g+ +lgv  t+++++vl+  ad +i      +v + ++++l
  gi|121636988|ref|YP_977211.1| 11 ATGSVGVAAIKGVLQHPELELVGCWVHSA-AKSGKDVGEIIGSPPLGVIATNSIDDVLALdADAVIYAPLLPSV-DEVAALL 90
                                   79*************************97.9****************************999*99966644444.4445555 PP

                                   HTT-EEE CS
                         DapB_N 89 ekgvklV 95
                                   ++g+++V
  gi|121636988|ref|YP_977211.1| 91 RSGKNVV 97
                                   6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2335.66
//
Query:       gi|121636989|ref|YP_977212.1|  [L=157]
Description: hypothetical protein BCG_1118 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-17   64.1   0.9    1.9e-17   63.8   0.9    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.023   14.9   0.1    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.9   2.2e-21   1.9e-17      25     142 ..      34     155 ..       4     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.2e-21
                                    TGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE......SSS-TSEEEEEEEEECCE CS
                Polyketide_cyc2  25 enwprWhpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyriv.....kpvpvanyvatwtvtpdgg 99 
                                    ++w   +p++++v+ ++g ++++g +++++++g g+vreel+ vdp +r+++y+++         va +++ w+++p+++
  gi|121636989|ref|YP_977212.1|  34 SHWYGLIPPIKEVRDQTGAWDSVGQARVITMVGGGRVREELTSVDP-PRSFGYTLTdikgpLAPLVALVEGKWSFAPADT 112
                                    5566669****99777778888777799995555************.********54677533333346999******** PP

                                    TEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2 100 gtrvtwtgefda.gplggpfekpaaakavkgdleagLerLkarl 142
                                    gt+vtw++++++ ++l++p+  p++a++++g+ +  Le+L a+l
  gi|121636989|ref|YP_977212.1| 113 GTTVTWQWTIHPrSALAAPV-LPVFARMWRGYARGVLEKLSALL 155
                                    ***********978888887.7999***************9875 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.5e-06     0.023      59     117 ..      91     136 ..      33     149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                                    EEETTTEEECTTCCCCCEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHH CS
                 Polyketide_cyc  59 ldppeeitfklvegdfkslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqv 117
                                     +p +         ++   egkW++++ ++   gt ++++ +  + ++s+l ++++  +
  gi|121636989|ref|YP_977212.1|  91 KGPLAP--------LVALVEGKWSFAPADT---GTTVTWQWT--IHPRSALAAPVLPVF 136
                                    444444........778899*****99985...555555555..666777777665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1142.53
//
Query:       gi|121636990|ref|YP_977213.1|  [L=287]
Description: hypothetical protein BCG_1119 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-22   79.4   0.0    2.4e-22   79.1   0.0    1.1  1  GATase_4  Glutamine amidotransferases class-II
    1.3e-08   35.1   0.1    2.3e-08   34.3   0.1    1.4  1  GATase_6  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   2.7e-26   2.4e-22       1     249 [.       1     251 [.       1     269 [. 0.77

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.7e-26
                       GATase_4   1 mceLLgmssnvp..tdisfsftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreyp.iksknvvaH 77 
                                    mc+L+g+ s +   t+    +++  + + ++    dG G++ ++++    ++ ++p a  + a +  e   +  + +vaH
  gi|121636990|ref|YP_977213.1|   1 MCRLFGLHSGTDavTATFWLLNASDSLAEQSRRNPDGTGLGVFDEHHQPRLH-KQPIAAWQDADFATEAHeLTGTTFVAH 79 
                                    9******9865410444444555555666777899*********87665554.445555556666655444********* PP

                       GATase_4  78 iRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl...egrfePvGsTDsElafCelleelasrfekaeps 151
                                    +R at+G+   +nthpF      +  ifAHnG +++   ++++l         +G+TDsE++f  +  ++++r +   ++
  gi|121636990|ref|YP_977213.1|  80 VRYATTGSLDIRNTHPFLQ----DGRIFAHNGVVEGldvLDERLrevGADDLVLGQTDSERVFALITASIRARDG---NE 152
                                    *****************86....456******99874434555555323345679******************95...56 PP

                       GATase_4 152 aeeleralaelakeiaelGvfnlllsdgralfahas...trLvyilRkaPfgeaelkdedlevdfeevttkedrvavvat 228
                                     + l +al+ la+++  +  +n+lls + +++a +    ++L+++ R+   g  e+     +++ ++++ +e+  +v at
  gi|121636990|ref|YP_977213.1| 153 SAGLIDALRWLAANVPIY-AVNVLLSTATDVWALRYpesHELYILDRRG-DGAPEFHLRSKRIRAHSTHLRERSSVVFAT 230
                                    788999999999999877.57************8764435677776654.4556666667788889999999999***** PP

                       GATase_4 229 epLtrdetWkklepGellvfr 249
                                    ep+ ++ +W+ l+ Gel+ + 
  gi|121636990|ref|YP_977213.1| 231 EPMDDNPRWRLLDAGELVHVD 251
                                    ****************98764 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   2.6e-12   2.3e-08       6      82 ..      67     147 ..      56     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.6e-12
                       GATase_6   6 laslvedevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkgla..frsrsDtevllall. 81 
                                     a+  ++++ +aHvR a++g   + ++ +Pf   +++ +++hNG ++  + l e+l++  g++  + +++D+e ++al+ 
  gi|121636990|ref|YP_977213.1|  67 EAHELTGTTFVAHVRYATTGSL-DIRNtHPF--LQDGRIFAHNGVVEGLDVLDERLRE-VGADdlVLGQTDSERVFALIt 142
                                    4444577899***********6.99999***..777789******************9.777778889*********985 PP

                       GATase_6  82 ....e 82 
                                        +
  gi|121636990|ref|YP_977213.1| 143 asirA 147
                                    44431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2147.23
//
Query:       gi|121636991|ref|YP_977214.1|  [L=285]
Description: hypothetical protein BCG_1120 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-18   66.1   6.0    2.3e-17   63.8   6.0    1.9  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   6.0   1.3e-21   2.3e-17       1     203 [.       7     203 ..       7     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.3e-21
                        Patatin   1 LvlsGGGsr.gafslgalkaL......kkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllir 73 
                                    Lvl+GGG    a++ g+l+ +      + +l+ + d+++GtSaGA +a+ +++g + + l++   + +++ i        
  gi|121636991|ref|YP_977214.1|   7 LVLAGGGLAgIAWETGVLRGIadespaAARLLLDSDVLVGTSAGATVAAQISSGCPLDTLYERQLAETSAEIDPGV---- 82 
                                    8********77*********778888899*******************9999995555544444444444444444.... PP

                        Patatin  74 elaanlaarlsgllgkgglfdaealrellr....kvladktlkrlsarlgklpllkslftanqavpaittataatastan 149
                                         +    + l+ +    +  + r++l+     +la +t+ + ++r  ++        ++  +  + + + + ++ + 
  gi|121636991|ref|YP_977214.1|  83 -----DIDAITDLFLTAVTEPHISTRRRLQrigaVALAVDTVPESVRRQVIA--------QRLPSHDWPDRVLRVTAIDI 149
                                    .....44445555544444444455555552222558888888888888888........678899************** PP

                        Patatin 150 ranglytedddddvdladavraSsafPglfppvsldgelyvDGGilsNvPilaa 203
                                     +  l   +++ +v l+dav+aS+++Pg+ ppv++ g++y+DGG++s v++ +a
  gi|121636991|ref|YP_977214.1| 150 ATGELVVFHRESNVALVDAVAASCSVPGAWPPVTIAGRRYMDGGVASSVNLGVA 203
                                    ***********************************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2185.35
//
Query:       gi|121636992|ref|YP_977215.1|  [L=360]
Description: hypothetical protein BCG_1121c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-16   60.5  10.4      1e-14   55.2   8.4    3.0  2  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   8.4   5.7e-19     1e-14       1     200 [.      19     175 ..      19     178 .. 0.85
   2 ?    1.8   0.0     0.013   2.3e+02      81     120 ..     210     249 ..     185     325 .. 0.65

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 5.7e-19
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanla 80 
                                    L+l+ GG+rg++++g+++aL  e+g+++  i+G+S GA+++   a+gr      d++  + ++++ +             
  gi|121636992|ref|YP_977215.1|  19 LALGSGGARGYAHIGVIQAL-RERGYDIVGIAGSSMGAVVGGVHAAGRL-----DEFAHWAKSLTQRTI----------L 82 
                                    899*****************.********************66666633.....444444444444444..........5 PP

                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglyteddd 160
                                    ++l+  +   g++ ae + + +r ++++++++ l ++  ++                            ++  +      
  gi|121636992|ref|YP_977215.1|  83 RLLDPSISAAGILRAEKILDAVRDIVGPVAIEQLPIPYTAV---------------------------ATDLLAGKSVWF 135
                                    557**************************************...........................556666666666 PP

                        Patatin 161 ddvdladavraSsafPglfppvsldgelyvDGGilsNvPi 200
                                      ++l  a+raS a+Pg++ p+++dg+l++DGGil+ +P 
  gi|121636992|ref|YP_977215.1| 136 QRGPLDAAIRASIAIPGVIAPHEVDGRLLADGGILDPLPM 175
                                    6888999999**************************9996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.013
                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgk 120
                                    ++++  + +++lfd+ a+r+ll++  a+  l+r+ a+++ 
  gi|121636992|ref|YP_977215.1| 210 WLNRMVRSTSALFDVSAARSLLDRPTARAVLSRFGAAAAE 249
                                    4444455566677777777777766555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2463.06
//
Query:       gi|121636993|ref|YP_977216.1|  [L=139]
Description: lipoprotein lpqV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-48  162.4   4.0    4.9e-48  162.1   4.0    1.1  1  LpqV      Putative lipoprotein LpqV


Domain annotation for each model (and alignments):
>> LpqV  Putative lipoprotein LpqV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   4.0   2.8e-52   4.9e-48      10     115 .]      34     139 .]      26     139 .] 0.93

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 2.8e-52
                           LpqV  10 taaaestaasaapgavevsPgGvttavdvpaesteeeYfqaCraAkewmdeqggdpksqiEpYLaslqssdsagpgtfnt 89 
                                      +++s a ++++g v+vsP+Gvtt+vd+paesteeeY+qaC+aA+ wmd+q+g+ +s+iEpYLa++q+s+s+++g+++ 
  gi|121636993|ref|YP_977216.1|  34 AGRSSSVAGTLPAGVVGVSPAGVTTRVDAPAESTEEEYYQACHAARLWMDAQPGSGESLIEPYLAVVQASPSGVAGSWHI 113
                                    3345556999********************************************************************** PP

                           LpqV  90 pWaeLtparqaavivAveaAadeeCg 115
                                    +Wa+LtparqaavivA++aAa++eCg
  gi|121636993|ref|YP_977216.1| 114 RWAALTPARQAAVIVAARAAANAECG 139
                                    *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1026.52
//
Query:       gi|121636994|ref|YP_977217.1|  [L=188]
Description: hypothetical protein BCG_1123 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   54.8   1.8    1.3e-11   44.1   0.1    2.0  2  CDO_I     Cysteine dioxygenase type I
     0.0093   15.7   0.0      0.016   14.9   0.0    1.4  1  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.029   14.0   0.0       0.04   13.6   0.0    1.2  1  Auxin_BP  Auxin binding protein


Domain annotation for each model (and alignments):
>> CDO_I  Cysteine dioxygenase type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   2.2e-15   1.3e-11      58     117 ..      55     114 ..      50     131 .. 0.86
   2 !   10.4   0.2   4.9e-05      0.29     149     167 ..     148     166 ..     140     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.2e-15
                                    -EEEEE-GGGT-EEEEEEE-TT-B--EE--TT-EEEEEEEES-EEEEEE----SS----- CS
                          CDO_I  58 ytrnlvagngksellllcWgpGtassvHDHtdsvgalkllaGeLkEtkfAwalkrleesd 117
                                    +   ++ g  + +++l++W pG+ +++HDH++s gal +l+G L+E ++  ++ r   +d
  gi|121636994|ref|YP_977217.1|  55 RWYTRIHGDEELDIWLISWVPGQPTELHDHGGSLGALTVLSGSLNEYRWDGRRLRRRRLD 114
                                    5556899**************************************988877766665555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.9e-05
                                    -EEEEEEEES--SEEEEE- CS
                          CDO_I 149 gAVSlHlYaPPldtirayd 167
                                    +  S+H+Y+PPl  +  y+
  gi|121636994|ref|YP_977217.1| 148 PTLSVHAYSPPLTAMSYYE 166
                                    568************9986 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.7e-06     0.016       3      58 ..      71     130 ..      69     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-06
                                    EEEETTEEEEEECSSSEEEEEEEEESE.EEEEECTE...EEEEETTEEEEE-TT-EEEEE CS
                        Cupin_2   3 velppGesapshrHpgedeffyVleGe.geltvdge...eveleaGdsvyfpagtpHrfr 58 
                                    ++  pG+ ++ h H g+   + Vl+G   e++ dg+   + +l aGd + fp g  H+++
  gi|121636994|ref|YP_977217.1|  71 ISWVPGQPTELHDHGGSLGALTVLSGSlNEYRWDGRrlrRRRLDAGDQAGFPLGWVHDVV 130
                                    5667999999*****************556669*99999******************986 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.7e-06      0.04      38      74 ..      60      97 ..      49     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-06
                                   HH--SSEEEEEEEE-TT-B--EEEESS-.EEEEEEE-- CS
                       Auxin_BP 38 lhgmkevevwlqtlapgsrtpihrhsce.evfvvlkgk 74
                                    hg  e+++wl +  pg+ t +h h      ++vl g+
  gi|121636994|ref|YP_977217.1| 60 IHGDEELDIWLISWVPGQPTELHDHGGSlGALTVLSGS 97
                                   69***********************7542567777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1353.76
//
Query:       gi|121636995|ref|YP_977218.1|  [L=131]
Description: hypothetical protein BCG_1124 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-07   29.6   0.0    1.1e-06   29.1   0.0    1.2  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   6.1e-11   1.1e-06       8     104 ..      26     116 ..      19     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.1e-11
                      Rhodanese   8 llekgkvallDvRppeeYek.ghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaa 84 
                                       +g+ +l+D+Rp+++ ++ g +pgA+ +      r+  + + +   p+++++l   +d++ + v++c++g  ++ aaa
  gi|121636995|ref|YP_977218.1|  26 AARRGA-VLVDIRPQAQRAReGEVPGALVI-----ERNVLEWRCD---PTSDARLpqAVDDDVEWVILCSEGYTSSLAAA 96 
                                    454554.5**********999*********.....2222333333...33333335568899************777777 PP

                      Rhodanese  85 llkklGyknvsvldGGfkaw 104
                                     l  lG+++   + GG++a 
  gi|121636995|ref|YP_977218.1|  97 SLLDLGLHRATDVVGGYRAL 116
                                    6666*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 985.74
//
Query:       gi|121636996|ref|YP_977219.1|  [L=671]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-32  110.3  22.0    6.9e-32  109.6  22.0    1.3  1  PE              PE family
  ------ inclusion threshold ------
        2.3    8.7  11.8        4.1    7.9  11.8    1.4  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6  22.0   7.7e-36   6.9e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 7.7e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv v+P +l aaaad+agigsa+saanaaa apt+ ++aa+aDeVSaa+Aalfsaha +yq+l+a+aa fheqfvqal++
  gi|121636996|ref|YP_977219.1|  1 MSFVLVSPSQLMAAAADVAGIGSAISAANAAALAPTSVLAAAGADEVSAAVAALFSAHAGQYQQLGARAALFHEQFVQALTG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aa++Ya+aEa+
  gi|121636996|ref|YP_977219.1| 83 AASAYASAEAT 93
                                   *********95 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  11.8   0.00046       4.1       6      94 ..       5      94 ..       1      97 [. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00046
                  T7SS_ESX_EspC  6 sVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp..icaatndavaaaeaarraagealaaasteLadkLraAAa 85
                                    V p++l ++aa++ ++ + i++a+aaa  a+++vl   G+  ++aa+++ ++a     ++ g++ a  ++++ + L+ AA 
  gi|121636996|ref|YP_977219.1|  5 LVSPSQLMAAAADVAGIGSAISAANAAA-LAPTSVLAAAGAdeVSAAVAALFSAHAGQYQQLGARAALFHEQFVQALTGAAS 85
                                   699*************************.999******99733555555555555555555555566667899999****** PP

                  T7SS_ESX_EspC 86 aYeatDeea 94
                                   aY  ++ ++
  gi|121636996|ref|YP_977219.1| 86 AYASAEATN 94
                                   ***999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.98u 0.30s 00:00:01.28 Elapsed: 00:00:00.51
# Mc/sec: 3943.43
//
Query:       gi|121636997|ref|YP_977220.1|  [L=730]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-33  112.9  13.6    9.3e-33  112.4  13.6    1.2  1  PE              PE family
  ------ inclusion threshold ------
        3.2    8.3   7.6        5.2    7.6   7.6    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4  13.6     1e-36   9.3e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 1e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+++++P++l++aa+dla+igs+++a + aaaa+tt +l+aaaDeVSa iAalfs h++ yqa+++q+aafh+qf  al++
  gi|121636997|ref|YP_977220.1|  1 MSYMIAVPDMLSSAAGDLASIGSSINASTRAAAAATTRLLPAAADEVSAHIAALFSGHGEGYQAIARQMAAFHDQFTLALTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEa+
  gi|121636997|ref|YP_977220.1| 83 SAGAYASAEAT 93
                                   *********95 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.6   0.00058       5.2       5      94 ..       4      94 ..       1      97 [. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00058
                  T7SS_ESX_EspC  5 LsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp.icaatndavaaaeaarraagealaaasteLadkLraAAa 85
                                   +  +pd l ++a ++ ++ + i+++++aaa a++++l+     ++a  ++ ++   +  +a ++++aa ++++   L+++A+
  gi|121636997|ref|YP_977220.1|  4 MIAVPDMLSSAAGDLASIGSSINASTRAAAAATTRLLPAAADeVSAHIAALFSGHGEGYQAIARQMAAFHDQFTLALTSSAG 85
                                   5679*************************9999999998776155555666777777788888999999************* PP

                  T7SS_ESX_EspC 86 aYeatDeea 94
                                   aY  ++ ++
  gi|121636997|ref|YP_977220.1| 86 AYASAEATN 94
                                   ***999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.08u 0.34s 00:00:01.42 Elapsed: 00:00:00.56
# Mc/sec: 3932.25
//
Query:       gi|121636998|ref|YP_977221.1|  [L=587]
Description: hypothetical protein BCG_1127c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.7e-131  435.1   1.1   1.2e-130  434.7   1.1    1.1  1  Abhydrolase_9    Alpha/beta-hydrolase family
    6.2e-73  245.2   8.1    1.7e-72  243.8   8.1    1.8  1  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus


Domain annotation for each model (and alignments):
>> Abhydrolase_9  Alpha/beta-hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.7   1.1  1.4e-134  1.2e-130       1     288 []     287     574 ..     287     574 .. 1.00

  Alignments for each domain:
  == domain 1  score: 434.7 bits;  conditional E-value: 1.4e-134
                  Abhydrolase_9   1 iRvyvGlesaedaeeraelvvaeleRtgafdRkvlvvvtttGtGwvneaaaealeyltnGdtAivamQYsylpSwlsflv 80 
                                    iR+y+Gl+sa+ + ++ael+++el Rtg+++R+v++v+t+tGtGw+nea+a+aley++nGdtAiv+mQYs+lpSwlsflv
  gi|121636998|ref|YP_977221.1| 287 IRTYAGLNSADGIMATAELAARELARTGGLRRAVVAVATSTGTGWINEAEASALEYMYNGDTAIVSMQYSFLPSWLSFLV 366
                                    8******************************************************************************* PP

                  Abhydrolase_9  81 dkekareagraLfeavyerwkelpedeRPkllvfGeSLGalgseaafseledllarvdgalwvGppnaselwrelteeRd 160
                                    dke+ar+ag+aLfeav++ +++lpe +RPkl+vfGeSLG++g+ea f +l+++lar+dgal++Gp++++++w++lt++Rd
  gi|121636998|ref|YP_977221.1| 367 DKENARHAGEALFEAVDKLIRQLPESQRPKLVVFGESLGSFGGEAPFMNLNNILARTDGALFSGPTFNNTVWNSLTANRD 446
                                    ******************************************************************************** PP

                  Abhydrolase_9 161 pgspevlPvyddgrvvrfaaeaeeleeeeaeWeeprvvylqhasDpvvwwspdlllrrPdWlkeprgadvspelrwvPvv 240
                                    +gsp++lP+yddgr+vrf+a+a++l++++a+W++ rvvylqhasDp++ww+p+ll+r+PdWl+e+rg dv+p++rw+Pvv
  gi|121636998|ref|YP_977221.1| 447 AGSPQWLPIYDDGRNVRFVARARDLQRPDAPWGRLRVVYLQHASDPIAWWTPRLLFREPDWLREQRGYDVLPQTRWIPVV 526
                                    ******************************************************************************** PP

                  Abhydrolase_9 241 tflqvalDlavatkvpeghGHnYaeevvdawaavlepegwteedterl 288
                                    tf+qv++D+avat+vp+ghGH+Y ++v+d+waavl+p+gwt+++terl
  gi|121636998|ref|YP_977221.1| 527 TFVQVSADMAVATHVPDGHGHRYVATVADGWAAVLSPPGWTQQKTERL 574
                                    *********************************************997 PP

>> Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.8   8.1     2e-76   1.7e-72       1     209 []      63     270 ..      63     270 .. 1.00

  Alignments for each domain:
  == domain 1  score: 243.8 bits;  conditional E-value: 2e-76
                Abhydrolase_9_N   1 LtPSLLPRtwlfqgvvsGlsaaiGYglGvllawlvrrllrlpepsrrvrrrlrlalavvalvvllvalvlaarwQrelra 80 
                                    +tPSLLPR++lfqg+vsG++ a+GYglGv++ wlvr+++ +++ s++ +r+++  l++v++v+++ ++v+++ wQ+++r+
  gi|121636998|ref|YP_977221.1|  63 MTPSLLPRGPLFQGLVSGICGAFGYGLGVFAVWLVRYMR-SHNSSPPPPRWAWPPLIAVGAVGMVGMAVQFHVWQDDVRD 141
                                    7*************************************9.99************************************** PP

                Abhydrolase_9_N  81 lmgaeplgaaeyllvllvallvfalllllgrllralvrllarllgrvlprrvaavlgvlvvvvlvvllvdgvvvrgvlaa 160
                                    lmg+e+l++++y+l+++++l+v++ l+++g+++r+l+r+l  +++r++p rv+a++ v+++vvl+++l++gvv++ +++ 
  gi|121636998|ref|YP_977221.1| 142 LMGVEHLRWYDYPLAAALSLVVLFTLVEIGQFIRWLFRFLVGQVDRIAPFRVSAAIVVVLLVVLTITLLNGVVLKFAMNS 221
                                    ******************************************************************************** PP

                Abhydrolase_9_N 161 anrsfaaanaetdpgveqPtsperSGSpaSlvsWesLGrqGrrfvsgGP 209
                                    +n++faa+n+e++p+ ++P++p+rSG+p+SlvsWesLG+qGr fv +GP
  gi|121636998|ref|YP_977221.1| 222 MNSTFAAVNNEMNPDSAPPKTPLRSGGPGSLVSWESLGHQGRIFVHSGP 270
                                    ************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3783.11
//
Query:       gi|121636999|ref|YP_977222.1|  [L=257]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-81  272.2   1.1    3.8e-81  272.1   1.1    1.0  1  ECH_1      Enoyl-CoA hydratase/isomerase
    4.6e-40  138.1   4.5    2.9e-35  122.3   1.1    2.0  2  ECH_2      Enoyl-CoA hydratase/isomerase
     0.0013   18.8   0.2     0.0028   17.7   0.1    1.6  2  DUF218     DUF218 domain
  ------ inclusion threshold ------
       0.17   12.1   0.9       0.28   11.3   0.3    1.7  2  TetR_C_21  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.1   1.1   8.5e-85   3.8e-81       2     250 ..      10     256 ..       9     257 .] 0.98

  Alignments for each domain:
  == domain 1  score: 272.1 bits;  conditional E-value: 8.5e-85
                                    EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHH CS
                          ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelw 81 
                                    + + v  i+lnrP+a+Nal+ ++++E++ a  +l+dd+ ++a+++tG+ kaFaaGad+kema     +++ +   +++ w
  gi|121636999|ref|YP_977222.1|  10 RDQRVGIITLNRPQALNALNSQVMNEVTSAATELDDDPDIGAIIITGSAKAFAAGADIKEMADL--TFADAFTADFFATW 87 
                                    5678999********************************************************7..8************* PP

                                    HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEH CS
                          ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisa 161
                                     kl  v  p+iaav G+a+gGG+ela++cD+ iaad+a+fg++e+klG++pg+gg+q+l+r++Gk+kA+ ++l+g+ + a
  gi|121636999|ref|YP_977222.1|  88 GKLAAVRTPTIAAVAGYALGGGCELAMMCDVLIAADTAKFGQPEIKLGVLPGMGGSQRLTRAIGKAKAMDLILTGRTMDA 167
                                    ******************************************************************************** PP

                                    HHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHH CS
                          ECH_1 162 qealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqafl 241
                                    +ea++ Glv++vvp+++ll ea++ a+ + + s  a+r++kea+n+++e+ l e+l  e++lf+s f+++d  eG+ af+
  gi|121636999|ref|YP_977222.1| 168 AEAERSGLVSRVVPADDLLTEARATATTISQMSASAARMAKEAVNRAFESSLSEGLLYERRLFHSAFATEDQSEGMAAFI 247
                                    ******************************************************************************** PP

                                    TCSH----- CS
                          ECH_1 242 Ekrkpefed 250
                                    Ekr p+f+ 
  gi|121636999|ref|YP_977222.1| 248 EKRAPQFTH 256
                                    *******86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   1.1   6.5e-39   2.9e-35       1     177 [.      14     185 ..      14     189 .. 0.95
   2 !   17.5   0.1   5.2e-07    0.0023     249     319 ..     189     256 ..     186     257 .] 0.91

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 6.5e-39
                                    .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHH CS
                          ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYkln 80 
                                    vg+itLnrp+alNaL+ ++++++++a +e ++d+++ +++++g+  kaf AG D++++++   +++     f ++ ++  
  gi|121636999|ref|YP_977222.1|  14 VGIITLNRPQALNALNSQVMNEVTSAATELDDDPDIGAIIITGSA-KAFAAGADIKEMADLTFADA-----FTADFFATW 87 
                                    689****************************************65.**************999954.....888888889 PP

                                    HHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-H CS
                          ECH_2  81 yliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkg 159
                                      +a +++p++a + G+++GgG+ l++ + + ++ ++++f  PE+++G+ P  Ggs  L+r+ g + ++ l lTG+++++
  gi|121636999|ref|YP_977222.1|  88 GKLAAVRTPTIAAVAGYALGGGCELAMMCDVLIAADTAKFGQPEIKLGVLPGMGGSQRLTRAIGkAKAMDLILTGRTMDA 167
                                    999**********************************************************977367999********** PP

                                    HHHHHTTS--EE--GGGH CS
                          ECH_2 160 adalaaglathyvpsekl 177
                                    a+a   gl + +vp+++l
  gi|121636999|ref|YP_977222.1| 168 AEAERSGLVSRVVPADDL 185
                                    **************9986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.2e-07
                                    HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------SS CS
                          ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWkp 319
                                    a++t++t++++s  +++++ e+++r+ + s l+e l  E rl ++++a++D  eG  a +++k ++P++++
  gi|121636999|ref|YP_977222.1| 189 ARATATTISQMSASAARMAKEAVNRAFESS-LSEGLLYERRLFHSAFATEDQSEGMAA-FIEK-RAPQFTH 256
                                    7899*************************5.************************966.5777.7899875 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3     6e+03      28      35 ..      51      59 ..      28      76 .. 0.56
   2 !   17.7   0.1   6.3e-07    0.0028      13      80 ..     142     206 ..     109     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                         DUF218 28 kiivsGg.g 35
                                    ii++G  +
  gi|121636999|ref|YP_977222.1| 51 AIIITGSaK 59
                                   377777541 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.3e-07
                         DUF218  13 laeRldeaaelyragkiivsGggadedvseaeamaeylrelgvpeeailledrsr.nTeenarfskell 80 
                                      +Rl++a+  ++a  +i++G     ++  aea +  l+++ vp++++l+e r++ +T + + +s++ +
  gi|121636999|ref|YP_977222.1| 142 GSQRLTRAIGKAKAMDLILTGR----TMDAAEAERSGLVSRVVPADDLLTEARATaTTISQMSASAARM 206
                                    458*****************95....58899*************99********967788888887766 PP

>> TetR_C_21  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.9   8.5e+03      52      70 ..       8      25 ..       7      45 .. 0.60
   2 ?   11.3   0.3   6.3e-05      0.28      52      95 ..     167     210 ..     145     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                      TetR_C_21 52 iraaQraGtvdaswkpedl 70
                                   +++ Qr G ++ + +p+ l
  gi|121636999|ref|YP_977222.1|  8 VERDQRVGIITLN-RPQAL 25
                                   5667777777765.44444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.3e-05
                      TetR_C_21  52 iraaQraGtvdaswkpedlltlvlalasawaaaparaaaaaada 95 
                                     ++a r+G v++ ++++dllt   a+a++ ++ +a+aa++a++a
  gi|121636999|ref|YP_977222.1| 167 AAEAERSGLVSRVVPADDLLTEARATATTISQMSASAARMAKEA 210
                                    57899*************************99999444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1658.86
//
Query:       gi|121637000|ref|YP_977223.1|  [L=345]
Description: 3-hydroxyisobutyryl-CoA hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-118  395.5   0.0   2.6e-118  395.3   0.0    1.0  1  ECH_2     Enoyl-CoA hydratase/isomerase
    2.9e-30  105.4   0.1    5.5e-29  101.2   0.2    2.0  2  ECH_1     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.3   0.0  2.9e-122  2.6e-118       1     334 []      16     336 ..      16     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.3 bits;  conditional E-value: 2.9e-122
                                    .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHH CS
                          ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYkln 80 
                                    vg++tLnrpka+N+L+++mv+ l+  l +we++d+v++vvl+gage+++CAGgDv+a+y++a+++  e+++f+r+eY ln
  gi|121637000|ref|YP_977223.1|  16 VGFVTLNRPKAINSLNQTMVDLLATVLMSWEHEDAVHAVVLSGAGERGLCAGGDVVAVYHSARKDGVEARRFWRHEYLLN 95 
                                    589**************************************************************9999*********** PP

                                    HHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HH CS
                          ECH_2  81 yliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkga 160
                                    +li ++ kp+valmdGivmGgGvG+s+h++ rvvt+++++AmPE++IG++PDvGg y+Lsr+pg+lGl+ alTGa ++ga
  gi|121637000|ref|YP_977223.1|  96 ALIGRFAKPYVALMDGIVMGGGVGVSAHANTRVVTDTSKVAMPEVGIGFIPDVGGVYLLSRAPGALGLHAALTGAPFSGA 175
                                    ******************************************************************************** PP

                                    HHHHTTS--EE--GGGHHHHHHHHHTT........--------......----SHHHHHHHHHHHT.-S-TTTHHHHHH. CS
                          ECH_2 161 dalaaglathyvpseklealeeaLaelessdeeaveevleelaeeaeeeeeeselaekreaidrlfsadsveeiveaLek 240
                                    da+a+g+a+h+vp+ +l+a+++++ +        ve++l+++a e++    +s+la++r++id+++++dsv++iv+aL+ 
  gi|121637000|ref|YP_977223.1| 176 DAIALGFADHFVPHGDLDAFTQKIVTG------GVESALAAHAVEPP----PSTLAAQRDWIDECYAGDSVADIVAALR- 244
                                    ************************995......8999*999886665....499************************9. PP

                                    T..--SHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------SSS CS
                          ECH_2 241 aeaeedewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWkpa 320
                                      +++ e a ++ + +++rsP++l vtl+++rr++kl++l++vl +++r++++ l+++D+veG+ra+l+dkd++P+W+pa
  gi|121637000|ref|YP_977223.1| 245 --KQGGEPAVNASDLIASRSPIALSVTLQAVRRAAKLDTLEDVLIQDYRVSSASLRSHDLVEGIRAQLIDKDRNPNWSPA 322
                                    ..457899************************************************************************ PP

                                    SGGG--HHHHHHH. CS
                          ECH_2 321 tleevtdeavealf 334
                                    tl+ +t++++ea+f
  gi|121637000|ref|YP_977223.1| 323 TLDAITAADIEAYF 336
                                    ************99 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.2   6.1e-33   5.5e-29       3     181 ..      13     194 ..      11     213 .. 0.91
   2 ?    2.1   0.0     0.011        96     182     239 ..     250     308 ..     236     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 6.1e-33
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC...HHHHHHHCCHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek...akqallkeevl 78 
                                    e gv  ++lnrP+a N+l++++++ l+ +l   e + +v avvL G g++  +aG+d+ ++++       ++  ++ + +
  gi|121637000|ref|YP_977223.1|  13 EGGVGFVTLNRPKAINSLNQTMVDLLATVLMSWEHEDAVHAVVLSGaGERGLCAGGDVVAVYHSARkdgVEARRFWRHEY 92 
                                    6799**********************************************************987655556778999999 PP

                                    HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-E CS
                          ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkk 158
                                     l  ++    kp +a + G ++gGG+ +   +  +++ d+++ + +e+ +G+ip++gg+  l r+ G ++  +++l+g +
  gi|121637000|ref|YP_977223.1|  93 LLNALIGRFAKPYVALMDGIVMGGGVGVSAHANTRVVTDTSKVAMPEVGIGFIPDVGGVYLLSRAPG-ALGLHAALTGAP 171
                                    99999******************************************************99999876.67778899**** PP

                                    EEHHHHHHCTSSSEEESGGGHHH CS
                          ECH_1 159 isaqealkvGlvdkvvpeeqlle 181
                                    +s+++a   G  d++vp+ +l  
  gi|121637000|ref|YP_977223.1| 172 FSGADAIALGFADHFVPHGDLDA 194
                                    *****************988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHCTSHHHHHHHHH CS
                          ECH_1 182 ealelaeklaekspaalrqlkealnakle.dalaeqleaeaklfestfskddikeGlqa 239
                                     a+++   +a+ sp al    +a++++++ d+l+ +l ++ ++ ++   ++d  eG+ a
  gi|121637000|ref|YP_977223.1| 250 PAVNASDLIASRSPIALSVTLQAVRRAAKlDTLEDVLIQDYRVSSASLRSHDLVEGIRA 308
                                    567777889999********************************999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2382.72
//
Query:       gi|121637001|ref|YP_977224.1|  [L=278]
Description: hypothetical protein BCG_1130 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-85  284.5  13.0    6.7e-85  284.3  13.0    1.0  1  BaxI_1     Bax inhibitor 1 like
      2e-19   70.2  23.5    2.6e-19   69.9  23.5    1.1  1  Bax1-I     Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.3  13.0   7.5e-89   6.7e-85      20     232 .]      25     277 ..       6     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 284.3 bits;  conditional E-value: 7.5e-89
                         BaxI_1  20 a.......................mtvddvvvktaillgvlvvtavvtwflvlaaaaa...lllvgalvglvlalvasf. 72 
                                                            +t+ddvv+kt+++l++l+ tavv++flv ++ a    l+lvgal+gl+l+lva+f 
  gi|121637001|ref|YP_977224.1|  25 GtaqqgfpadpylapyreakatrpLTIDDVVTKTGLTLAMLAGTAVVSYFLVVSNVALampLTLVGALGGLALVLVATFg 104
                                    155555666666666666666677***************************997766699*******************9 PP

                         BaxI_1  73 kkkvspalvllYAvleGlflGgislvfea........pgivvqAvlgTlgvfavmlvlYktgairvtpkftkivvaalig 144
                                    +k+ +pa+vl YA+leGlflG+is+v+++          ++ +A+lgT+gvf++mlv+Yktgairvtpkft++vvaal+g
  gi|121637001|ref|YP_977224.1| 105 RKQDNPAIVLSYAALEGLFLGAISFVLANftvasanaGVLIGEAILGTMGVFFGMLVVYKTGAIRVTPKFTRMVVAALFG 184
                                    9**********************************988899*************************************** PP

                         BaxI_1 145 illlylvnlvlslfgvge....glrdgg.lgilfslvvivlAalsLllDFdqieqgvragaPkkyeWyaAfGLlvTLVWL 219
                                    +l+l+l nlvl++f vg     glr+ g lgi+fslv+i++Aa+s+l+DFd+++q++ragaP+k++W +A+GL+vTLVWL
  gi|121637001|ref|YP_977224.1| 185 VLVLMLGNLVLAMFNVGGgeglGLRSPGpLGIIFSLVCIGIAAFSFLIDFDAADQMIRAGAPEKAAWGVALGLTVTLVWL 264
                                    **************555543345999988*************************************************** PP

                         BaxI_1 220 YleiLrLLsylrs 232
                                    Y+eiLrLLsyl++
  gi|121637001|ref|YP_977224.1| 265 YIEILRLLSYLQN 277
                                    **********986 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9  23.5   2.9e-23   2.6e-19      11     207 .]      58     272 ..      51     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.9e-23
                         Bax1-I  11 lalgllltalvaavvlsspaqlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlslspillv 90 
                                    ++l+l++ a++a+v +++   +++ l ++l lv+ l++lalv+++  + r++  +++   a++l +++leGl+l+ i +v
  gi|121637001|ref|YP_977224.1|  58 TGLTLAMLAGTAVVSYFLV-VSNVALAMPLTLVGALGGLALVLVA-TFGRKQ--DNP---AIVLSYAALEGLFLGAISFV 130
                                    4555555555555555555.55688899**************845.443443..333...69****************99 PP

                         Bax1-I  91 yt.........gaiilqaflltaaifgglslyalttkrdls.glggflfagligliiaslvnlF.............lp. 146
                                     +         g +i +a+l+t+++f+g+ ++  t   +++ +++ +++a+l+g+++++l+nl              l+ 
  gi|121637001|ref|YP_977224.1| 131 LAnftvasanaGVLIGEAILGTMGVFFGMLVVYKTGAIRVTpKFTRMVVAALFGVLVLMLGNLVlamfnvgggeglgLRs 210
                                    999*****************************9999999999********************985666666666644337 PP

                         Bax1-I 147 ssalelais..ylgvllfsglilyDtq.kiierageygeedailaalsLyldfinlFlslLril 207
                                     + l +++s  ++g+  fs li +D   ++i+ ag+++   a+  al L +++++l++ +Lr+l
  gi|121637001|ref|YP_977224.1| 211 PGPLGIIFSlvCIGIAAFSFLIDFDAAdQMIR-AGAPEKA-AWGVALGLTVTLVWLYIEILRLL 272
                                    7778988877899************9657775.7776555.9********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2026.04
//
Query:       gi|121637002|ref|YP_977225.1|  [L=283]
Description: hypothetical protein BCG_1131 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-07   31.7   0.0    2.2e-07   30.9   0.0    1.4  1  MTES_1575  REase_MTES_1575
    0.00098   19.0   0.1     0.0017   18.2   0.1    1.3  1  DUF559     Protein of unknown function (DUF559)


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.5e-11   2.2e-07      20      77 ..     207     261 ..     189     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.5e-11
                      MTES_1575  20 vgvggfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiws 77 
                                    +g  ++ +D+ +ed    +la+e dg+++  s+++  +d+er e+++r+GW+ +R+  
  gi|121637002|ref|YP_977225.1| 207 YGHPKYFLDMGWEDI---MLAVEYDGEQHRLSRDQFVKDVERLEYIRRAGWTHIRVLA 261
                                    5566899*****999...*************************************976 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.9e-07    0.0017      43      91 ..     211     262 ..     206     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-07
                                    TEEEEEEETTTTEEEEEE-------...----HHHHHHHHHTT-EEEEEEHH CS
                         DUF559  43 sYivDfvclkaklivelDGaqhdee...eeyDaeRtelLeslGftvlRfknd 91 
                                    +Y++D   +   l ve DG qh  +     +D eR e++ + G+t +R   d
  gi|121637002|ref|YP_977225.1| 211 KYFLDMGWEDIMLAVEYDGEQHRLSrdqFVKDVERLEYIRRAGWTHIRVLAD 262
                                    79999999**************977333568****************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2119.54
//
Query:       gi|121637003|ref|YP_977226.1|  [L=405]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-63  212.4   0.0    1.3e-62  211.5   0.0    1.4  1  Thiolase_N     Thiolase, N-terminal domain
    1.4e-48  163.6   0.4    2.8e-48  162.6   0.4    1.5  1  Thiolase_C     Thiolase, C-terminal domain
    0.00089   18.9   1.4       0.02   14.5   0.1    2.9  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
     0.0038   17.0   0.1        2.9    7.8   0.0    2.5  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.5   0.0   2.9e-66   1.3e-62       2     258 ..       5     272 ..       4     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 2.9e-66
                                    EEEEEEEE--EE.TTSTTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEE CS
                     Thiolase_N   2 vivsaartpigk.fggslkdlsaeeLlaealkallekag.vdpeevdevivGnvlqa.gegqniarqaalkagipeevpa 78 
                                    vivs+ar+pig+ ++gsl  ++ ++L+ ++++a+l+k++ ++p+++d++++G+ l + ++g niar +a+++g  +  p 
  gi|121637003|ref|YP_977226.1|   5 VIVSTARSPIGRaMKGSLVGMRPDDLAVQMVRAALDKVPaLNPHQIDDLMMGCGLPGgESGFNIARVVAVALGY-DFLPG 83 
                                    9*******************************************************9899**************.***** PP

                                    EEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT...............TGGSSSSEEEEEHHHH CS
                     Thiolase_N  79 vtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr...............sglklgdekakdllip 143
                                    +tvn+ csS+l++  +a  +i+age d+++  GvE+ s+  + +s d+                + +  g+++ +d    
  gi|121637003|ref|YP_977226.1|  84 TTVNRYCSSSLQTTRMAFHAIKAGEGDAFISAGVETVSRFAKGNS-DSWpdtknplfdgaqersAAAAAGADEWHDPRTD 162
                                    *****************************************9998.5556999*******99987888888888998888 PP

                                    HHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--H CS
                     Thiolase_N 144 dgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevta 223
                                    + l d++  + mG taen+a +++isReeqd++ v+s+++a++a+k+g F++ei Pv++++     tv++d+++r+++t 
  gi|121637003|ref|YP_977226.1| 163 QKLPDIY--IAMGQTAENVAIMTGISREEQDRWGVRSQNRAEEAIKNGFFEREITPVTLPDGT---TVSTDDGPRPGTTY 237
                                    8888887..68*************************************************966...************** PP

                                    HHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                     Thiolase_N 224 ekLaklkpaFkkeGtvtAgnasqisDGaaavllms 258
                                    ek+++lkpaF+ +GtvtAgna++++DGaaav+++s
  gi|121637003|ref|YP_977226.1| 238 EKVSELKPAFRPNGTVTAGNACPLNDGAAAVVITS 272
                                    ********************************987 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.4   6.3e-52   2.8e-48       1     123 []     281     403 ..     281     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 6.3e-52
                                    ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B CS
                     Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGH 80 
                                    l+pla+i+s  ++g  pei+glgP+ a+kk+l++ag+ + didl+EinEAFa+q+L +a++l++d++k+N+ GGaialGH
  gi|121637003|ref|YP_977226.1| 281 LTPLARIVSTGVSGLSPEIMGLGPIEASKKALERAGMAITDIDLVEINEAFAVQVLGSARELGIDEDKLNISGGAIALGH 360
                                    589***************************************************************************** PP

                                    -TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                     Thiolase_C  81 PlGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                    P+G++GaRi++tll++l+  ++++g+ ++C gggqg+a+vie+
  gi|121637003|ref|YP_977226.1| 361 PFGMTGARITTTLLNNLQTYDKTFGLETMCVGGGQGMAMVIER 403
                                    *****************************************96 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.5e-06      0.02     170     205 ..      85     120 ..      69     131 .. 0.91
   2 ?    1.8   0.0     0.032   1.4e+02       3      37 ..     286     323 ..     285     350 .. 0.69
   3 ?   -2.1   0.0       0.5   2.2e+03     198     247 ..     351     400 ..     335     404 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                                    EEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE-- CS
                  ketoacyl-synt 170 tvdtACsSslvavhaavqslrsgeadvalaGGvell 205
                                    tv   CsSsl    +a +++++ge d+ +  Gve+ 
  gi|121637003|ref|YP_977226.1|  85 TVNRYCSSSLQTTRMAFHAIKAGEGDAFISAGVETV 120
                                    66677****************************975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.032
                                    -EEEEEEEEEBTTBSS...HHHHHHHHHTT---EEES- CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd...veefwelLlegrdaiselp 37 
                                    +++ +G++++ P+  +    e+  ++L + + ai++++
  gi|121637003|ref|YP_977226.1| 286 RIVSTGVSGLSPEIMGlgpIEASKKALERAGMAITDID 323
                                    67777777777777777777777777777777777666 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.5
                                    EEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB..-SB-BB-EEEEEEE CS
                  ketoacyl-synt 198 laGGvellltpeavagfsaagllspdgrckafdpka..dGfvlGEGvGavvL 247
                                    + GG+ +l +p ++ g   +  l ++   +++d+      +++G G G+ ++
  gi|121637003|ref|YP_977226.1| 351 ISGGAIALGHPFGMTGARITTTLLNN--LQTYDKTFglETMCVGGGQGMAMV 400
                                    66777777777777766655533333..455554444566777777776655 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00064       2.9       3      41 ..      86     124 ..      85     142 .. 0.90
   2 !    6.4   0.1    0.0018       7.9      52      67 ..     261     276 ..     253     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00064
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskil 41 
                                    +n  Cs+ ++   +A ++i++g+    +  g et+s++ 
  gi|121637003|ref|YP_977226.1|  86 VNRYCSSSLQTTRMAFHAIKAGEGDAFISAGVETVSRFA 124
                                    6788********************************986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                                    B-EEEEEEEEEEESSS CS
                    ACP_syn_III  52 fGDGAgAvvleaseee 67 
                                    + DGA+Avv++ +++ 
  gi|121637003|ref|YP_977226.1| 261 LNDGAAAVVITSDTKA 276
                                    67*********98543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2932.33
//
Query:       gi|121637004|ref|YP_977227.1|  [L=314]
Description: hypothetical protein BCG_1133c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-14   54.6   0.0    2.3e-14   54.2   0.0    1.2  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    0.00022   21.3   0.0     0.0019   18.2   0.0    2.3  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   2.6e-18   2.3e-14       1     179 []      76     255 ..      76     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 2.6e-18
                                    EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT-EEEEE..EEHCCH-H..HHHHHHHH..CTGGG-TSEEEEE--CCCCCT CS
                  Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarlgldvvnn.lgvsGattallrllerlr..dllrlkpdlvtiliGtNDlgr 77 
                                    ++GDS + Gyg  ++++    ++ar la+++g + +    ++ Gat+    + ++++   +    pd+ +i+iG+ND+ +
  gi|121637004|ref|YP_977227.1|  76 IFGDSTATGYGCASAEEVPGVLIARGLAEQTGKRIRLStKAIVGATS--KGVCGQVDamFVVGPPPDAAVIMIGANDITA 153
                                    59**********98888888899********77777777********..77777777554555567***********999 PP

                                    T--HHHHHHH..HHHHHHHHCCC...GEEE..CEEEEE-TTT-TTSTCC.HHHHHHHHHHHHHHHHHHCT-EEE-HHHHH CS
                  Lipase_GDSL_2  78 gvpaaaaaandnleelidalraaapgaril..vlgplpptpeaaadare.lnaviaaynealrevaaeegvpfvDlhdal 154
                                     +  +  a++  l+  +++lr++  ga ++  +++ l++ +  +++ r  ++ +  ++++a+ ++ ++ g + v+l ++l
  gi|121637004|ref|YP_977227.1| 154 LNGIGPSAQR--LADCVRRLRTR--GAVVVvgTCPDLGVITAIPQPLRAlAHTRGVRLARAQTAAVKAAGGVPVPLGHLL 229
                                    9999999999..***********..9988878444445555555555554566667777777777777666668998888 PP

                                    HHCCCCCGGBBTTS..SSB-HHHHHH CS
                  Lipase_GDSL_2 155 adsgerladlladdg.lHPnaaGyrl 179
                                    a+  +  ++l+   +  HP+a  y+l
  gi|121637004|ref|YP_977227.1| 230 APKFRAMPELMFSADrYHPSAPAYAL 255
                                    8888777766555555*****99975 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-07    0.0019       2     131 ..      75     195 ..      74     260 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-07
                                    EEEESHHHHTT.................THHHHHHHCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHH CS
                                    xxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL   2 vafGDSltdGd.................gaatlntiqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseq 64 
                                    + fGDS   G+                 +  t+  i+l t             i  ++ kg          +++  ++  
  gi|121637004|ref|YP_977227.1|  75 MIFGDSTATGYgcasaeevpgvliarglAEQTGKRIRLSTKA-----------IVGATSKGVC--------GQVDAMF-- 133
                                    578999988887774444444433222222222222222211...........1222222222........2333334.. PP

                                    HHHCTTSEEEEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCH......C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                    Lipase_GDSL  65 lkalhpdlviislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgp......q 131
                                      +  pd  +i++G+ND+        +a + +    ++l + +++l+    ++a+vv+ + p+lg        
  gi|121637004|ref|YP_977227.1| 134 VVGPPPDAAVIMIGANDI--------TALNGIGPSAQRLADCVRRLR---TRGAVVVVGTCPDLGVitaipqP 195
                                    4455689***********........******************999...577***********983333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2233.52
//
Query:       gi|121637005|ref|YP_977228.1|  [L=297]
Description: lipase lipU [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-43  148.5   0.6    2.9e-43  148.2   0.6    1.1  1  Abhydrolase_3    alpha/beta hydrolase fold
      9e-09   34.7   0.0    1.2e-08   34.3   0.0    1.1  1  Say1_Mug180      Steryl acetyl hydrolase
    5.1e-05   23.5   0.5    7.7e-05   22.9   0.5    1.4  1  Thioesterase     Thioesterase domain
    0.00086   18.3   0.0     0.0013   17.7   0.0    1.2  1  Chlorophyllase2  Chlorophyllase enzyme
      0.001   18.6   0.0     0.0084   15.6   0.0    2.0  1  Peptidase_S9     Prolyl oligopeptidase family
     0.0011   18.3   0.0     0.0017   17.7   0.0    1.5  1  Hydrolase_4      Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.042   13.2   0.0       0.05   13.0   0.0    1.1  1  DUF2235          Uncharacterized alpha/beta hydrolase domain 
      0.058   13.3   0.0       0.11   12.4   0.0    1.6  1  UPF0227          Uncharacterised protein family (UPF0227)
      0.098   12.6   0.0       0.15   12.0   0.0    1.3  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
       0.13   11.8   0.0          7    6.1   0.0    2.2  2  DLH              Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.2   0.6   1.6e-46   2.9e-43       1     210 [.      66     272 ..      66     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 148.2 bits;  conditional E-value: 1.6e-46
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    ++y+HGG+f+++++++h +l++ l+k ++  v+ vdYrl P+h + +a++d+ + +rwl+      g++p++ivlaGdSa
  gi|121637005|ref|YP_977228.1|  66 VLYLHGGAFLTCGANSHGRLVELLSKFADSPVLVVDYRLIPKHSIGMALDDCHDGYRWLRLL----GYEPEQIVLAGDSA 141
                                    79**********************************************************97....8************* PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHT.TTSSSSCHHHHHHHHHHHSSGGGGGST...... CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeel.adgplltraaldlfwrlylpeadrddp...... 153
                                    GG la+a+a+r+++  + ++a++v i+P+++l ++e+++    + + +++++++++a+d++  l+++ a r++       
  gi|121637005|ref|YP_977228.1| 142 GGYLALALAQRLQEV-GEEPAALVAISPLLQL-AKEHKQA---HPNiKTDAMFPARAFDALDALVASAAARNQVdgepee 216
                                    **************8.679*********9988.4444444...3344788999999999888888765555555444566 PP

                                    TTSGGGCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 154 laspllaedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                    l++pl +    glp+tl+ v + ++l ++++  a++l+aagv++e+++++g+vH+f+
  gi|121637005|ref|YP_977228.1| 217 LYEPLEH-ITPGLPRTLIHVSGSEVLLHDAQLAAAKLAAAGVPAEVRVWPGQVHDFQ 272
                                    8888855.7999*******************************************96 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   6.6e-12   1.2e-08     124     249 ..      65     184 ..      51     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 6.6e-12
                    Say1_Mug180 124 vllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvkskgf..knvvvlG 201
                                     +lylHGG f l     +   L  l  +f d ++lv+DY ++   ++s+   l   ++   y +l   +g+   ++v+ G
  gi|121637005|ref|YP_977228.1|  65 AVLYLHGGAF-LTCGANSHGRLVELLSKFADSPVLVVDYRLIP--KHSIGMALD--DCHDGYRWLR-LLGYepEQIVLAG 138
                                    689*****99.6788889999*********************9..788888877..9*******98.67763369***** PP

                    Say1_Mug180 202 dSaGGnlvLslllklsklnkvvlPkkaiaiSPWlnltildekekeylk 249
                                    dSaGG l L l  +l++++    P   +aiSP l+l+  +++    +k
  gi|121637005|ref|YP_977228.1| 139 DSAGGYLALALAQRLQEVGE--EPAALVAISPLLQLAKEHKQAHPNIK 184
                                    *****************999..7*************988777766666 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.5   4.3e-08   7.7e-05      68     117 ..     134     182 ..     125     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                                    EEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHT CS
                   Thioesterase  68 yalfGhSlGgllAfevArqLesqGlavkslflidssapseteaqeasrra 117
                                     +l+G S+Gg+lA ++A++L++ G+++++l+ i        +++++ + +
  gi|121637005|ref|YP_977228.1| 134 IVLAGDSAGGYLALALAQRLQEVGEEPAALVAISPLLQ-LAKEHKQAHPN 182
                                    689******************************84444.33555555554 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.5e-07    0.0013      90     142 ..     132     185 ..     128     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.5e-07
                Chlorophyllase2  90 sklalsgHSrGgktafalalgkaktslkfsaligvdPvag.askskqtepkiLt 142
                                    ++++l+g S+Gg+ a+ala   +++  + +al+++ P+   a+++kq +p+i t
  gi|121637005|ref|YP_977228.1| 132 EQIVLAGDSAGGYLALALAQRLQEVGEEPAALVAISPLLQlAKEHKQAHPNIKT 185
                                    5799*********************************98857778899999976 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.7e-06    0.0084      45      87 ..     114     155 ..     107     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                                    HHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GG CS
                   Peptidase_S9  45 fdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpd 87 
                                    +dD+ ++ ++l   gy ++e++++ G S+GGyl++a++ + ++
  gi|121637005|ref|YP_977228.1| 114 LDDCHDGYRWLRLLGY-EPEQIVLAGDSAGGYLALALAQRLQE 155
                                    7899999999988887.5*****************99885544 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.6e-07    0.0017      72     138 ..     128     198 ..     108     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.6e-07
                    Hydrolase_4  72 ehpelplfllGhSmGGliallyllrypd...kvaglilsaPalkikaklk.appllklllkllgkllpklq 138
                                     ++ ++++l G S GG++al++++r ++   + a+l+ ++P+l+++++ k a+p  k  + + ++++  l 
  gi|121637005|ref|YP_977228.1| 128 GYEPEQIVLAGDSAGGYLALALAQRLQEvgeEPAALVAISPLLQLAKEHKqAHPNIKTDAMFPARAFDALD 198
                                    4556689****************55555555999************9998899988887777777766655 PP

>> DUF2235  Uncharacterized alpha/beta hydrolase domain (DUF2235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.8e-05      0.05      76     136 ..     113     171 ..      48     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                        DUF2235  76 gldehvveaYefl.mrnyepgDeIylfGFSRGAytaRalagmlekvGllskgneeqvpfayk 136
                                     l +++ ++Y++l +  yep ++I+l G S G y a ala+ l++vG  ++     ++ + +
  gi|121637005|ref|YP_977228.1| 113 AL-DDCHDGYRWLrLLGYEP-EQIVLAGDSAGGYLALALAQRLQEVGE-EPAALVAISPLLQ 171
                                    44.4699******5567888.8*************************8.4444445555555 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.2e-05      0.11       3     174 ..      67     273 ..      65     285 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                        UPF0227   3 lYlHG..FdS.SPlshka..qllsqfiaedvlaielsvlklkedpqqalkelek.....lvaelgddnillvGssLGGyy 72 
                                    lYlHG  F     +sh    +lls+f ++ vl ++++ l +k++   al   +       +  + +++i+l G s GGy+
  gi|121637005|ref|YP_977228.1|  67 LYLHGgaFLTcGANSHGRlvELLSKFADSPVLVVDYR-LIPKHSIGMALDDCHDgyrwlRLLGYEPEQIVLAGDSAGGYL 145
                                    6666645444344455432245666666666666665.446666666666666422221244567788************ PP

                        UPF0227  73 atrlgerfglrq....vllnPalkplenlagklgeeavqstqetyvleeyhiielkalelsr.................. 130
                                    a  l++r + +     +l+  a+ pl +la+   + a ++ + + ++++++ ++l al  s+                  
  gi|121637005|ref|YP_977228.1| 146 ALALAQRLQEVGeepaALV--AISPLLQLAKEHKQ-AHPNIKTDAMFPARAFDALDALVASAaarnqvdgepeelyeple 222
                                    *****99765433432333..56677777666544.66666777777777777777777766666666666666666665 PP

                        UPF0227 131 .lkrperilvllskqDevl..dyrravaefr....aaaeiveddgdHafkd 174
                                     ++   +  +++  + evl  d + a+a+++    +a  +v+ ++ H f+ 
  gi|121637005|ref|YP_977228.1| 223 hITPGLPRTLIHVSGSEVLlhDAQLAAAKLAaagvPAEVRVWPGQVHDFQV 273
                                    555445555555556665433445555555511112345666666666665 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.3e-05      0.15       9      69 ..     120     183 ..     117     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-05
                                    HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS....SEEEEEEES--SB--SSEEEETTE. CS
                         BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflk....kisavvlingsavvvegklvykdes 69 
                                    ++++l+     + ++i l G S Gg lal+la +l+    ++ a+v+i++     ++++ ++ ++
  gi|121637005|ref|YP_977228.1| 120 GYRWLRLL-GYEPEQIVLAGDSAGGYLALALAQRLQevgeEPAALVAISPLLQLAKEHKQAHPNI 183
                                    56677666.66779*********************966666789999999877777777666664 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.023        41      79     122 ..     114     156 ..     103     210 .. 0.78
   2 ?    6.1   0.0    0.0039         7     162     192 ..     244     274 ..     231     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.023
                            DLH  79 lddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpev 122
                                    ldd ++  ++l+  + ++++++++ G   GG lal+la++ +ev
  gi|121637005|ref|YP_977228.1| 114 LDDCHDGYRWLRLLG-YEPEQIVLAGDSAGGYLALALAQRLQEV 156
                                    667777777888888.8889******************998766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                            DLH 162 evekleealkaanvdlelkvYpgagHaFand 192
                                    +++  + +l+aa+v++e+ v+pg +H F  +
  gi|121637005|ref|YP_977228.1| 244 DAQLAAAKLAAAGVPAEVRVWPGQVHDFQVA 274
                                    457778899*******************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2223.28
//
Query:       gi|121637006|ref|YP_977229.1|  [L=464]
Description: cystathionine beta-synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-61  208.6   0.6    1.9e-61  208.1   0.6    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme
    5.3e-16   58.8   0.1      2e-06   28.2   0.0    2.7  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.6   2.1e-65   1.9e-61       2     294 .]       8     296 ..       7     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 2.1e-65
                                    GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT CS
                           PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallG 78 
                                    +  ig+TPlvrl+++  +  + + +K E+lnp+gS KdR a+ ++++++     +++ t+ve +sGN+g++lA++a++ G
  gi|121637006|ref|YP_977229.1|   8 SELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASgqlKPGGTIVEPTSGNTGVGLALVAQRRG 87 
                                    6789***********9776667*************************7766799************************** PP

                                    -EEEEEEETTS-HHHHHHHHHTT-EEEEE.....CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHH CS
                           PALP  79 lkvtivvpadaspekvallrllGaevvev.....ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEile 152
                                    +k++ v+p+++s++k+  l ++Gaevv++     + d+ +  ++  +l ++++ga   +q+ np + +  y t+g+Ei++
  gi|121637006|ref|YP_977229.1|  88 YKCVFVCPDKVSEDKRNVLIAYGAEVVVCptavpPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPAShYVTTGPEIWA 167
                                    *****************************88777666777777788********************************** PP

                                    HTTTTEEEEEEE-SSSHHHHHHHHHHHH.HSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCH CS
                           PALP 153 qlggkpdavvvpvGgGgliaGiaaglke.rrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselaf 230
                                    ++ gk++++v+++G+Gg+i+G +++lke +++ vr++g++pegs   +++            + +++g++ +  p++++ 
  gi|121637006|ref|YP_977229.1| 168 DTEGKVTHFVAGIGTGGTITGAGRYLKEvSGGRVRIVGADPEGSVYSGGAG----------RPYLVEGVGEDfWPAAYDP 237
                                    ****************************99999*********777666665..........69********966666666 PP

                                    HHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                           PALP 231 elldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                    ++     dei++vsd + +++ r+lar+e ++v+ s+++a+ a+ l+ a+e ++++ +vv+l++
  gi|121637006|ref|YP_977229.1| 238 SVP----DEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAA-LKVAEEAGPDALIVVLLPD 296
                                    555....68888********************************.**************99975 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.2e-10     2e-06       8      55 ..     343     395 ..     329     397 .. 0.80
   2 !   27.9   0.0   2.6e-10   2.3e-06       3      56 ..     408     458 ..     403     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.2e-10
                                    SCEEEETTSBHHHHHHHHHHHTSSEEEEE.....ETTTBEEEEEEHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekgvsrlPVV.....dedgklvGivtlrDllral 55 
                                     +v  +p++t+++a+ ++re+gvs++PVV        g++ G v++r ll+a+
  gi|121637006|ref|YP_977229.1| 343 ALVHTHPSETVRDAIGILREYGVSQMPVVgaeppVMAGEVAGSVSERELLSAV 395
                                    55999************************8877733669***********997 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.6e-10
                                    HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    + m++++ ++   + ++ a + +r+   ++l+VV e+gk+vG++t+ Dll +l+
  gi|121637006|ref|YP_977229.1| 408 AHMSPPLRMIGAGELVSAAGKALRD--WDALMVV-EEGKPVGVITRYDLLGFLS 458
                                    4499999999999**********77..*******.9***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3579.28
//
Query:       gi|121637007|ref|YP_977230.1|  [L=240]
Description: hypothetical protein BCG_1136 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.4   3.7    1.7e-22   80.1   3.7    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   3.7   9.6e-27   1.7e-22       2     140 ..      89     233 ..      88     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 9.6e-27
                            RDD   2 aslgrRllAfliDlvllliislllallivall..............nakasaneavagslllllllvlllvllvyqllll 67 
                                      +  R+lA++iD+   ++++++ ++++ + +              + ++s+ + +  ++++ll++  l++l++ +++  
  gi|121637007|ref|YP_977230.1|  89 TPWITRVLAAFIDWAPYVVLVGIGWVIMLVTQtsscvtsiseydvgQFCVSQPSMIGQLVQWLLSVGGLAYLVWNYGYRQ 168
                                    56889**********9999999999999998799***********988899999999999******************** PP

                            RDD  68 skkgqTlGklllglkvvd.edgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDkla 140
                                     ++g+++Gk +l+ kvv+ ++g+++g++ +++R+l          +++ ++++++gflf+l++ krq+l Dk++
  gi|121637007|ref|YP_977230.1| 169 GTTGSSIGKSVLKFKVVSeTTGQPIGFGMSVVRQL---------AHFIDAIICFVGFLFPLWDAKRQTLADKIM 233
                                    ***********************************.........9***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2017.43
//
Query:       gi|121637008|ref|YP_977231.1|  [L=388]
Description: cystathionine gamma-synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-145  484.3   0.0   2.1e-145  484.1   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    9.7e-10   38.3   0.1    1.9e-09   37.3   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.4e-07   28.2   0.0    1.1e-06   27.5   0.0    1.3  1  Met_gamma_lyase  Methionine gamma-lyase
    0.00011   21.2   0.0    0.00016   20.8   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.043   13.1   0.0       0.14   11.5   0.0    1.7  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.1   0.0  5.8e-149  2.1e-145       2     381 ..      16     387 ..      15     388 .] 0.98

  Alignments for each domain:
  == domain 1  score: 484.1 bits;  conditional E-value: 5.8e-149
                                    HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHH CS
                Cys_Met_Meta_PP   2 TllvhagqekdeqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAia 81 
                                    T ++hag ++d++tgav+vpiy++st+ ++    + +g + g+eY+R+gnptr +le+++aa+e+g+ a a+ssGmaA++
  gi|121637008|ref|YP_977231.1|  16 TRAIHAGYRPDPATGAVNVPIYASSTFAQD----GVGGLRGGFEYARTGNPTRAALEASLAAVEEGAFARAFSSGMAATD 91 
                                    899***************************....77778888************************************** PP

                                    HHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHH CS
                Cys_Met_Meta_PP  82 aailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiak 161
                                    +a++a+l+ Gd++v+ dd+Yggt+rl++kv++++ ++++ v  +dl+++ +ai+++t+l+++Etptnpll+++Di++ia+
  gi|121637008|ref|YP_977231.1|  92 CALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQYTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAE 171
                                    ******************************************************************************** PP

                                    HHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHH CS
                Cys_Met_Meta_PP 162 lakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawl 241
                                    l  ++++ v+vDntfasp+lq+pl+lgaD+v+hS+TKy+gGhsdvv+G++v+++ eel++e++flqn +Gav  pfda+l
  gi|121637008|ref|YP_977231.1| 172 LGTDRSAKVLVDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTND-EELDEEFAFLQNGAGAVPGPFDAYL 250
                                    ******************************************************.************************* PP

                                    HHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SS CS
                Cys_Met_Meta_PP 242 llrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlkl 321
                                    ++rGlkTL lR++rh+enA +vAefL+ hp+v++v Ypglpshp+he+a++q++g+gg++s +++ ++++a++++ ++++
  gi|121637008|ref|YP_977231.1| 251 TMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMRGFGGMVSVRMRAGRRAAQDLCAKTRV 330
                                    ******************************************************************************** PP

                                    SEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                Cys_Met_Meta_PP 322 fslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                    f+laeslGgveslie+p  mthas+  ++     v ddl+RlsvGiEd+ Dl+ Dl+qal
  gi|121637008|ref|YP_977231.1| 331 FILAESLGGVESLIEHPSAMTHASTAGSQ---LEVPDDLVRLSVGIEDIADLLGDLEQAL 387
                                    ***********************998765...5688***********************8 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   5.3e-13   1.9e-09      21     200 ..      59     238 ..      47     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5.3e-13
                                    S.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB CS
                DegT_DnrJ_EryC1  21 s.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyni 99 
                                    + +p+ +++E+ +aa  + ++a a+ssG aA   aLra+ + pgd V++p   + +t   + ++    + v  +p     
  gi|121637008|ref|YP_977231.1|  59 TgNPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAM-LRPGDHVVIPDDAYGGTFRLIDKVFT-RWDVQYTPVR-LA 135
                                    34788999******************************7.789*****************998854.4555555444.45 PP

                                    -GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS. CS
                DegT_DnrJ_EryC1 100 dpaaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnl. 175
                                    d +a+ aait+rt+ I   +p + +  +ad+ a+ ++ ++   kv+ D   A  a  +  ++Ga  d+   S   tK + 
  gi|121637008|ref|YP_977231.1| 136 DLDAVGAAITPRTRLIwveTPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQQPLRLGA--DVVLHS--TTKYIg 211
                                    9*************994444677777889**************************999999996..444444..577776 PP

                                    -SSS..-EEEEESTHHHHHHHHHHHBT CS
                DegT_DnrJ_EryC1 176 ttGe..GGavvtndeelaekarvlrnh 200
                                       +  GGa+vtndeel+e+   l+n 
  gi|121637008|ref|YP_977231.1| 212 GHSDvvGGALVTNDEELDEEFAFLQNG 238
                                    5554559*************9999884 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     3e-10   1.1e-06      49     244 ..      53     229 ..      45     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3e-10
                Met_gamma_lyase  49 GyGyddlGrdtldkvyaevfgaeaalvrpqlvsGthaiatalfgvlrpgdellaitGkPydtleeviGlrgegqgslkdf 128
                                    G+ y   G  t  ++ a++   e+++    + sG  a  +al ++lrpgd+++ i    y     +i         +  +
  gi|121637008|ref|YP_977231.1|  53 GFEYARTGNPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVV-IPDDAYGGTFRLI------DKVFTRW 125
                                    777888888888888888888888888889********************986.5555555444444......457899* PP

                Met_gamma_lyase 129 gikykevdlleegkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveeke 208
                                    +++y  v l +     ++av +ai+++t+li +       + + lsi++i+ i +l  + +    v+vdn +      ++
  gi|121637008|ref|YP_977231.1| 126 DVQYTPVRLAD-----LDAVGAAITPRTRLIWVETP----TNPLLSIADITAIAELGTDRS--AKVLVDNTFASP-ALQQ 193
                                    *********87.....889**************976....5799*******9999866555..55679****986.5789 PP

                Met_gamma_lyase 209 PtevGadliaGsliknpGGgiaktGGyiaGkeelve 244
                                    P ++Gad++  s  k +GG    +GG ++ ++e ++
  gi|121637008|ref|YP_977231.1| 194 PLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELD 229
                                    **************************9998877655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-08   0.00016      80     204 ..      92     211 ..      73     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-08
                                    HCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--H CS
                    Aminotran_5  80 slars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpv 158
                                    +++r+ l+pgd++v+ +  + +++  + ++   t  +v++ p+    + dld++ ++++++t+l+ +    n +  i ++
  gi|121637008|ref|YP_977231.1|  92 CALRAmLRPGDHVVIPDDAYGGTFRLIDKVF--TRWDVQYTPV---RLADLDAVGAAITPRTRLIWVETPTNPLLSIADI 166
                                    333444******************9999995..7799999999...99******************************** PP

                                    HHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTS CS
                    Aminotran_5 159 eeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllg 204
                                     +i++l  ++ a vlvD + a +  +  + +lg+D++  s+ K++g
  gi|121637008|ref|YP_977231.1| 167 TAIAELGTDRSAKVLVDNTFASPALQQPL-RLGADVVLHSTTKYIG 211
                                    *********************99999888.69***********988 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.14      30     273 ..      60     279 ..      52     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                    --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTTTB CS
                Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiael.agvklrdlknkeaGk 108
                                    +++t  +Le+ +a++ + + a  + +G aA   +l+++l++g+ v++ ++a + +      ++   +v+ ++++ ++   
  gi|121637008|ref|YP_977231.1|  60 GNPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTrWDVQYTPVRLAD--- 136
                                    67888899999999998888888999*****************9999999987776664444443666666666655... PP

                                    E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTT CS
                Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsy 188
                                      l+++ aai++      +++li +++ +n      +s++ + ++a++  ++  ++++D +    a   l+++   +  +
  gi|121637008|ref|YP_977231.1| 137 --LDAVGAAITP------RTRLIWVETPTNP----LLSIADITAIAELGTDRSAKVLVDNTFASPA---LQQP---LRLG 198
                                    ..8889999988......699*********5....9**********************97733333...3333...3357 PP

                                    SSEEEEESSS..TT--S.S-EEEEE-HH....HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHH CS
                Beta_elim_lyase 189 vDsvtmslkK..dllan.vGgvlafrddeledylaerveqrkylggglrqagvlaaleagiraleeglaslerdhktaeq 265
                                    +D+v  s +K  +++   vGg l+++d+     l+e  ++ +  +g      + a     +r l+  + +++r+ ++a  
  gi|121637008|ref|YP_977231.1| 199 ADVVLHSTTKyiGGHSDvVGGALVTNDE----ELDEEFAFLQNGAGAVP-GPFDAY--LTMRGLKTLVLRMQRHSENACA 271
                                    8888888888443443337889999888....56666666666666665.335555..6666666666666666666666 PP

                                    HHHHHHHC CS
                Beta_elim_lyase 266 laeklelv 273
                                     ae l+++
  gi|121637008|ref|YP_977231.1| 272 VAEFLADH 279
                                    66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3045.94
//
Query:       gi|121637009|ref|YP_977232.1|  [L=164]
Description: transcription elongation factor GreA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-25   87.6   3.3    6.4e-25   87.1   3.3    1.3  1  GreA_GreB_N  Transcription elongation factor, N-terminal
    5.2e-14   51.9   0.2    8.3e-14   51.3   0.2    1.3  1  GreA_GreB    Transcription elongation factor, GreA/GreB, C-te
  ------ inclusion threshold ------
       0.11   12.9   0.7       0.17   12.2   0.7    1.3  1  SbcD_C       Type 5 capsule protein repressor C-terminal doma


Domain annotation for each model (and alignments):
>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   3.3   1.1e-28   6.4e-25       2      71 .]       8      76 ..       7      76 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.1e-28
                                   EE-HHHHHHHHHHHHHHHHXHHHHHHHHHHHHHHHSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHTEEE CS
                    GreA_GreB_N  2 ylTkegyekleeeLeelktverpeiaeaikeareeGDlsENaeYdaAkeeqaeiearIreLedkLanaev 71
                                   +lT+e +++l++eL++l    rp ia++i++ reeGDl+EN +Y+aA+eeq++ earIr+L+d L+na+v
  gi|121637009|ref|YP_977232.1|  8 WLTQESHDRLKAELDQLIA-NRPVIAAEINDRREEGDLRENGGYHAAREEQGQQEARIRQLQDLLSNAKV 76
                                   89*****************.************************************************98 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.2   1.4e-17   8.3e-14       2      76 ..      82     160 ..      80     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.4e-17
                                    ..SS--TT-EEEEE-.SS--EEEE----TTT-BS-SS...B--TTSHHHHHHTT--TT-EE---BTTB.---EEEEEEX CS
                      GreA_GreB   2 pkdvVtfGstVtledldtgeeetytiVgpdeadpskg...kiSveSPlGkaLlgkkvGdevevkapsg.kikveIlkie 76 
                                    +++v+ +Gs+V++++  ++++ +++++ +++  +s g   ++S++SPlG aL+ +kvG++ ++++p+g +++v+ ++ e
  gi|121637009|ref|YP_977232.1|  82 QSGVALPGSVVKVYYNGDKSDSETFLIATRQEGVSDGkleVYSPNSPLGGALIDAKVGETRSYTVPNGsTVSVTLVSAE 160
                                    5688899********9***************9998887889***************************99999998876 PP

>> SbcD_C  Type 5 capsule protein repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   2.8e-05      0.17      30      81 ..       6      70 ..       4      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                         SbcD_C 30 vevtdedplpdlrerlrellegipvevlrlrrtr.............ekasaeleqeaeetlael 81
                                   v+  +++    l+++l +l++++pv   +++++r               +++++++++ ++l++l
  gi|121637009|ref|YP_977232.1|  6 VTWLTQESHDRLKAELDQLIANRPVIAAEINDRReegdlrenggyhaAREEQGQQEARIRQLQDL 70
                                   56667888999**************99***77778888877666554223566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1214.69
//
Query:       gi|121637010|ref|YP_977233.1|  [L=144]
Description: hypothetical protein BCG_1139c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-34  118.4   6.5    1.5e-34  118.1   6.5    1.0  1  DUF4307    Domain of unknown function (DUF4307)
     0.0074   16.5   0.0     0.0088   16.2   0.0    1.2  1  DUF2371    Uncharacterised conserved protein (DUF2371)
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.016   14.9   0.0    1.2  1  Neurensin  Neurensin
      0.012   15.9   1.1      0.017   15.4   1.1    1.2  1  RskA       Anti-sigma-K factor rskA
      0.018   15.3   1.1      0.032   14.5   1.1    1.4  1  DUF3040    Protein of unknown function (DUF3040)
      0.085   12.7   0.2       0.12   12.3   0.2    1.2  1  TraD       Conjugal transfer protein TraD
       0.09   12.9   0.2       0.14   12.2   0.2    1.3  1  DUF2275    Predicted integral membrane protein (DUF2275)


Domain annotation for each model (and alignments):
>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   6.5   5.8e-38   1.5e-34       2     110 .]      23     133 ..      22     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 5.8e-38
                        DUF4307   2 rrllvillvvlvvvalalvawigysq.gsadvsaevvgfevvddstvevtfeVtrddgs.pavCiVrAldedgaevGrre 79 
                                    rr+++i+l+vlv++a++++a+igy++ +++ v++++vg++ vdd+t++vt++Vtr+d+s p+ CiVr+++ +g+e+Grre
  gi|121637010|ref|YP_977233.1|  23 RRRVAIALGVLVAAAGIVIAVIGYQRiSTSAVTGSLVGYRLVDDETASVTISVTRSDPSrPVACIVRVRATNGSETGRRE 102
                                    899***************************************************************************** PP

                        DUF4307  80 vlvpagdertvrvtvtvrTtaravtgevygC 110
                                     lvp+++++tv+vt+tv++++++v+++vygC
  gi|121637010|ref|YP_977233.1| 103 LLVPPSEATTVQVTTTVKSSQPPVMADVYGC 133
                                    ******************************* PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.4e-06    0.0088      41      67 ..      25      55 ..      14     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                        DUF2371 41 glvlllGllvllvGiamavlgywpkk....a 67
                                    + ++lG+lv + Gi++av+gy   +    +
  gi|121637010|ref|YP_977233.1| 25 RVAIALGVLVAAAGIVIAVIGYQRIStsavT 55
                                   56789*****************987744440 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.4e-06     0.016      39      86 ..      22      69 ..       8      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.4e-06
                      Neurensin 39 llwkvslvvgtlvlllGvtallvGylvprrlelvksegelvvvDkqai 86
                                   +  +v++++g+lv ++G+++ ++Gy   + +++  s   +++vD++ +
  gi|121637010|ref|YP_977233.1| 22 ARRRVAIALGVLVAAAGIVIAVIGYQRISTSAVTGSLVGYRLVDDETA 69
                                   55689*********************9999999999999999998765 PP

>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.1   6.5e-06     0.017      26     106 ..      11     115 ..       2     133 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-06
                                    .......................XXXXXXXXXXXXXX.............................XXXXXXXXXXXXXX CS
                           RskA  26 aaaapppaaapaararr......laaaaAaalllvlg...................qlavasaaldplrqsaaqaeavva 80 
                                    a+  +p+  ++a  +rr      +++aaA ++++v+g                    + +as ++   r +++++ a ++
  gi|121637010|ref|YP_977233.1|  11 ARYGRPRLSRRA--RRRvaialgVLVAAAGIVIAVIGyqristsavtgslvgyrlvDDETASVTISVTRSDPSRPVACIV 88 
                                    222222222222..222568777888888888899999999998888888888777666666666666666666665555 PP

                                    XXXXX.XXXX.XXXXXXXXXXXXXXXX CS
                           RskA  81 vlaap.daagatatvvdsasggalvld 106
                                     ++a+ +++ +   +++ +s+   v +
  gi|121637010|ref|YP_977233.1|  89 RVRATnGSETGRRELLVPPSEATTVQV 115
                                    555444333333344444444333333 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.1   1.2e-05     0.032      32      77 ..      14      59 ..       7      64 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                        DUF3040 32 gaar.arrrslrrlavlavllfvaGllllvlG.vaaaavvlgvvGfvv 77
                                   g++r +rr ++r ++ l+vl+++aG+++ v+G    +  + +v+G +v
  gi|121637010|ref|YP_977233.1| 14 GRPRlSRRARRRVAIALGVLVAAAGIVIAVIGyQRIS--TSAVTGSLV 59
                                   566744444456666677777777********43333..455555444 PP

>> TraD  Conjugal transfer protein TraD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   4.5e-05      0.12       3      23 ..      19      39 ..      17      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                           TraD  3 aRkertRelielGgLVvkAGl 23
                                    R++r R  i lG LV++AG+
  gi|121637010|ref|YP_977233.1| 19 SRRARRRVAIALGVLVAAAGI 39
                                   6*******************3 PP

>> DUF2275  Predicted integral membrane protein (DUF2275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   5.6e-05      0.14      25      65 ..      14      54 ..       5      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                        DUF2275 25 llvrlflrlkrklalaglivlilAavgfgvvsyatiskmdv 65
                                   +  rl +r +r++a+a+ +++++A +++ v+ y +is+  v
  gi|121637010|ref|YP_977233.1| 14 GRPRLSRRARRRVAIALGVLVAAAGIVIAVIGYQRISTSAV 54
                                   55689999*******999999999999**********9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1106.21
//
Query:       gi|121637011|ref|YP_977234.1|  [L=288]
Description: Mycothiol conjugate amidase Mca [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-26   92.1   0.1    6.4e-26   91.5   0.1    1.3  1  PIG-L     GlcNAc-PI de-N-acetylase


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.1   3.6e-30   6.4e-26       1     130 [.       7     152 ..       7     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 3.6e-30
                                    EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH....-HHHHHHHHHHHHHHHHCTE..EEEEEC CS
                          PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleek....eelaeiRekEaraaakhlgvadedvffl 76 
                                    ++v+AHpDDe+   ++t+a+++++g++v +v+lt G+ g+ l    +     +++aeiR++E  +aa++lgv   ++++l
  gi|121637011|ref|YP_977234.1|   7 MAVHAHPDDESSKGAATLARYADEGHRVLVVTLTGGERGEILNPAMDLpdvhGRIAEIRRDEMTKAAEILGV---EHTWL 83 
                                    79*************************************7766655558999********************...88888 PP

                                    CCBTT-STT..............S-CHHHHHHHHHHHHHH--SEEEEE-TTTT.H-HHHHHHHHHHHHH CS
                          PIG-L  77 dfpDgsles..............ydedellddlaklieryrPdvvltldpegd.dhpDHtavasaavaa 130
                                    +f D++l +              ++ +  +++l+++++++rP+v+ t+d++g+ +hpDH  ++++ vaa
  gi|121637011|ref|YP_977234.1|  84 GFVDSGLPKgdlppplpddcfarVPLEVSTEALVRVVREFRPHVMTTYDENGGyPHPDHIRCHQVSVAA 152
                                    88888888888888888888888*****************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2302.32
//
Query:       gi|121637012|ref|YP_977235.1|  [L=88]
Description: hypothetical protein BCG_1141 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.3   1.7      0.061   12.7   1.7    1.3  1  SKG6      Transmembrane alpha-helix domain
       0.06   13.3   0.0      0.069   13.0   0.0    1.1  1  DUF3504   Domain of unknown function (DUF3504)


Domain annotation for each model (and alignments):
>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.7   6.8e-06     0.061      18      35 ..      27      44 ..      26      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-06
                           SKG6 18 VPVaViiivLlailifvr 35
                                   V++ Vi+++++a l++vr
  gi|121637012|ref|YP_977235.1| 27 VGLLVIVLLVIATLFLVR 44
                                   8999*************9 PP

>> DUF3504  Domain of unknown function (DUF3504)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.7e-06     0.069      16      56 ..      21      61 ..      18      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-06
                        DUF3504 16 LGaqsPivLLntllyfntkyfglrtveeHlkLsfsnverqt 56
                                   +G+ sP+ LL  +l +++  f +r+++++lk   ++++r +
  gi|121637012|ref|YP_977235.1| 21 FGKASPVGLLVIVLLVIATLFLVRSMNQQLKKVPKSFDRDH 61
                                   89***************************998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 569.14
//
Query:       gi|121637013|ref|YP_977236.1|  [L=673]
Description: hypothetical protein BCG_1142 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-67  226.0   0.0    3.4e-67  225.5   0.0    1.2  1  Thioredox_DsbH  Protein of unknown function, DUF255
    2.8e-11   43.4   0.1    7.1e-11   42.1   0.1    1.7  1  Thioredoxin_7   Thioredoxin-like
    2.3e-05   23.8   0.5       0.11   11.7   0.1    2.6  2  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.0   5.7e-71   3.4e-67       1     162 [.       9     164 ..       9     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 5.7e-71
                 Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDr 80 
                                    +n+la ++spYl+qha+npv+W++w+ +al++a ++  pills+Gy+achWChvm++esf+d+evaa +n+ fv++kvDr
  gi|121637013|ref|YP_977236.1|   9 TNTLALATSPYLRQHADNPVHWQQWTPQALAEAAARAVPILLSVGYAACHWCHVMAHESFDDDEVAAAMNAGFVCIKVDR 88 
                                    59999*************************************************************************** PP

                 Thioredox_DsbH  81 eerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeelle 160
                                    eerPd+d++ym+a+ altg+ggWP+++fltp+++pff+gtY+pk        fl++l++i+e+w+e+r e+e++++++++
  gi|121637013|ref|YP_977236.1|  89 EERPDIDAVYMNATVALTGQGGWPMTCFLTPNGRPFFCGTYYPK------AAFLQLLSAISETWRERRAEVEQASDHIAA 162
                                    *******************************************9......58************************9998 PP

                 Thioredox_DsbH 161 al 162
                                    +l
  gi|121637013|ref|YP_977236.1| 163 EL 164
                                    87 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   1.2e-14   7.1e-11       1      83 []      29     119 ..      29     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-14
                                    ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.........-TT- CS
                  Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani........lelde 72 
                                    +w+++ ++ala+aa+r  p+l+ +g + c+ C++++ +  +d+ev+aa++  fv+ +vd +er + i        ++l++
  gi|121637013|ref|YP_977236.1|  29 HWQQWTPQALAEAAARAVPILLSVGYAACHWCHVMAHESFDDDEVAAAMNAGFVCIKVDREERPD-IdavymnatVALTG 107
                                    6**********************************9999999999999************99987.54555555544444 PP

                                    --.SSEEEEE-T CS
                  Thioredoxin_7  73 qg.vPvvafldp 83 
                                    qg  P+ +fl+p
  gi|121637013|ref|YP_977236.1| 108 QGgWPMTCFLTP 119
                                    446999999987 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   1.8e-05      0.11      44     118 ..     232     309 ..     219     327 .. 0.78
   2 !    9.6   0.0     8e-05      0.48     148     326 ..     476     519 ..     402     529 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHTTTTTB-TTTSSB-SEEETTEEEE-..-EEHHHHHHHHHHHHH.HHTTT-TTHHHHHHHHHHHHHHHTEE CS
                  GlcNAc_2-epim  44 lvehGlkflekvlrdaehggyfsalrdggvlda..skdaYdhaFvllalas.alaageeeakdlldetlavlekhlwe 118
                                    +++ G ++ ++   d+  gg+++   dg  + +  +k +Yd a  l a+a+ a  +g++ a++++++t ++l  +l +
  gi|121637013|ref|YP_977236.1| 232 VARTGNAMARGGIYDQLGGGFARYSVDGAWVVPhfEKMLYDNALLLRAYAHwARRTGDPLARRVAAQTARFLLDELGS 309
                                    444454555555569999999999999997766225679*******************************99777655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8e-05
                                    HHHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGTT----EE-TT--B-TTTTTT-STT-SSB-HHHHHHHHHHHHHHHHHT CS
                  GlcNAc_2-epim 148 mLalaeatgdkeyleraeeiaelvisefadaesglvrEhfdedWnvapdyngedlfrpygvePGHqiEwawLlldlallk 227
                                    +                                                                               
  gi|121637013|ref|YP_977236.1| 476 L------------------------------------------------------------------------------- 476
                                    4............................................................................... PP

                                    T----THHHHHHHHHHHHHHHHBS-SSSSB-S-B-TTS-BSS--EEHHHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHH CS
                  GlcNAc_2-epim 228 reraakllekArkLfetalakgwdkdrgglvytldaagkpvddakllWpqtEalkaaaalaeltgearylewyarvaeyl 307
                                                                                             +al++lt e   l+ +  ++++ 
  gi|121637013|ref|YP_977236.1| 477 ---------------------------------------------------------LALYQLTSEGAWLTAATGLLDTA 499
                                    .........................................................55566666666666666666666 PP

                                    HHHTB-TT.TSSB-SEE-TT CS
                  GlcNAc_2-epim 308 erhlidpe.kGlWfdkldad 326
                                     +h+ dp+  G Wfd  d  
  gi|121637013|ref|YP_977236.1| 500 VAHFGDPQrPGRWFDTADDA 519
                                    66666664355666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4432.88
//
Query:       gi|121637014|ref|YP_977237.1|  [L=242]
Description: hemolysin-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-42  144.5  16.5    4.6e-42  144.2  16.5    1.0  1  HlyIII    Haemolysin-III related


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2  16.5   2.6e-46   4.6e-42       4     224 .]      32     234 ..      30     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 2.6e-46
                         HlyIII   4 hnEtlniwtHllgailfivlailllslaevkensklakvvvlvfllgallcllcSalyHtlsihseeklrkffaklDysg 83 
                                    +++ +++w+H++ a+ ++++   l++++ + + s++a +  l + ++ ++++++Sa+yH ++++s   +r+++++ D+s+
  gi|121637014|ref|YP_977237.1|  32 TKPRFRGWIHVYSAGTAVLAGASLVAVSWAVG-SAKAGLTTLAYTAATITMFTVSATYHRVNWKSA-TARNWMKRADHSM 109
                                    67899***********************9999.89*******************************.9************ PP

                         HlyIII  84 Islliagsylplilyalakapkagllylslilalgvlgiisklvplfsrpearplravlfillgllgvipllhlllvltq 163
                                    I+++iagsy+p++l+al+   + g ++ls+++  +++gi++k+++    +++r + + l++llg+++v++++++l++ + 
  gi|121637014|ref|YP_977237.1| 110 IFVFIAGSYTPFALLALPA--HDGRVVLSIVWGGAIAGILLKMCWP---AAPRSVGVPLYLLLGWVAVWYTATILHNAGV 184
                                    *****************66..67***********************...************************6666663 PP

                         HlyIII 164 lgeaaelalvllvlggvlylvGavfYalrvPErlkpgkfdivghsHqiFHvfvvlgalfhy 224
                                          +alvll++gg+ly +G+++Ya+r     +p+++++++++H++FH ++ ++a++hy
  gi|121637014|ref|YP_977237.1| 185 ------TALVLLFVGGALYSIGGILYAVR-----WPDPWPTTFGYHEFFHACTAVAAICHY 234
                                    ......46*********************.....9*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1605.49
//
Query:       gi|121637015|ref|YP_977238.1|  [L=262]
Description: Short (C15) chain Z-isoprenyl diphosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-66  223.7   0.0    2.4e-66  223.5   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.5   0.0   1.3e-70   2.4e-66       2     224 .]      39     261 ..      38     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 223.5 bits;  conditional E-value: 1.3e-70
                                    E--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prenyltransf   2 mDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkeelkellk 81 
                                    +DGNrRwA++ g  ++++G+++Ga +++e+l++c e+g++  tvY +SteN++R+++e+ al+e+++ ++++e       
  gi|121637015|ref|YP_977238.1|  39 CDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIIT-DVVEEI--CAPA 115
                                    6*****************************************************************5.588776..5778 PP

                                    TTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.....GGHSHHHH CS
                   Prenyltransf  82 egvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.....eeideetl 156
                                    ++++vr++Gdl l+ e+ +++l+ a+e+t +  + +++n+av Yg+r+eiv+avr+l++++ ++  +     ++++ e +
  gi|121637015|ref|YP_977238.1| 116 NHWSVRTVGDLGLIGEEPARRLRGAVESTPEVAS-FHVNVAVGYGGRREIVDAVRALLSKELANGATaeelvDAVTVEGI 194
                                    8*****************************6655.**********************8777644444332333445688* PP

                                    HCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                   Prenyltransf 157 ekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                    +++lyt+ + pdpDl+iRtsGe+RlS+Fllwq+ayse++f+++ WP f++ d+l+al++y++r+rr+g
  gi|121637015|ref|YP_977238.1| 195 SENLYTSGQ-PDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSARHRRYG 261
                                    *****9777.********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1940.97
//
Query:       gi|121637016|ref|YP_977239.1|  [L=809]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-36  123.6  21.8    4.8e-36  123.0  21.8    1.3  1  PE              PE family
  ------ inclusion threshold ------
       0.23   10.9   0.1       0.32   10.5   0.1    1.1  1  DUF2884         Protein of unknown function (DUF2884)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0  21.8   5.3e-40   4.8e-36       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 5.3e-40
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   MsfvvvaPe+laaaa+dlagigs+l++anaaa apttavlaa+aDeVSaaiA+lf+ah+q+yqa+saq++afh+qf+qal++
  gi|121637016|ref|YP_977239.1|  1 MSFVVVAPEVLAAAASDLAGIGSTLAQANAAALAPTTAVLAAGADEVSAAIASLFGAHGQAYQAVSAQMSAFHAQFMQALTG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   a+g+YaaaEa
  gi|121637016|ref|YP_977239.1| 83 AGGAYAAAEA 92
                                   *********9 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   3.5e-05      0.32      71     149 ..      38     116 ..      29     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.5e-05
                        DUF2884  71 dgvdlAsdaldevltellgedsevaeklktkldelkarvkekfykdgdklvlgaqsles.ldeafdkefeqeieelvees 149
                                     +++ + d ++ ++++l+g   ++++ ++++++ + a+ ++ +  +g+ +  +a++++    +++++++ ++i+   e  
  gi|121637016|ref|YP_977239.1|  38 AVLAAGADEVSAAIASLFGAHGQAYQAVSAQMSAFHAQFMQALTGAGGAYA-AAEAVNVsAAQSVEQDLLAAINARFERI 116
                                    567778899*************************************99666.5555553367777777766666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.06u 0.35s 00:00:01.41 Elapsed: 00:00:00.54
# Mc/sec: 4485.27
//
Query:       gi|121637017|ref|YP_977240.1|  [L=106]
Description: hypothetical protein BCG_1146 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-07   30.2   0.0    1.1e-06   28.3   0.0    1.9  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   6.2e-11   1.1e-06     152     183 ..      17      47 ..       2      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.2e-11
                                    SHHHHHCTSTT..TSSS-SEEEEESS--S-TT CS
                   Prenyltransf 152 deetlekhlytakalpdpDlliRtsGeeRlSn 183
                                    + e++ ++l t+ + pdpDl+iRtsGe+RlS+
  gi|121637017|ref|YP_977240.1|  17 AVEAICENLNTSGQ-PDPDLVIRTSGEQRLSG 47 
                                    34778899999766.****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 750.02
//
Query:       gi|121637018|ref|YP_977241.1|  [L=144]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-28   97.8   8.6    5.6e-28   97.1   8.6    1.3  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   8.6   3.1e-32   5.6e-28       1      87 [.       1      87 [.       1      90 [. 0.97

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 3.1e-32
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+++++P al+aaa+d++gigsa+s anaaa a+tt+vlaa+ DeV aaiA+lf+a+a+ey+alsaq+aaf++ fv++l++
  gi|121637018|ref|YP_977241.1|  1 MSYMIATPAALTAAATDIDGIGSAVSVANAAAVAATTGVLAAGGDEVLAAIARLFNANAEEYHALSAQVAAFQTLFVRTLTG 82
                                   9********************************************************************************9 PP

                                   HHHHH CS
                             PE 83 aagsY 87
                                   + g +
  gi|121637018|ref|YP_977241.1| 83 GCGVF 87
                                   98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1097.58
//
Query:       gi|121637019|ref|YP_977242.1|  [L=101]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.018   15.3   0.0    2.1  2  CBM_2          Cellulose binding domain


Domain annotation for each model (and alignments):
>> CBM_2  Cellulose binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.8      0.11     2e+03      66      66 ..      32      32 ..       6      62 .. 0.46
   2 ?   15.3   0.0     1e-06     0.018       2      24 ..      64      86 ..      63      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.11
                                   T CS
                          CBM_2 66 w 66
                                    
  gi|121637019|ref|YP_977242.1| 32 S 32
                                   1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1e-06
                                   EEEEEEEEE-SSEEEEEEEEEE- CS
                          CBM_2  2 eatyavtseWetGftasvtvkNs 24
                                   +atyav s+W++G+ a+ t++  
  gi|121637019|ref|YP_977242.1| 64 AATYAVASQWDGGYVANYTINQF 86
                                   589****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 755.76
//
Query:       gi|121637020|ref|YP_977243.1|  [L=34]
Description: cellulase celA2a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        97  (0.00541023); expected 358.6 (0.02)
Passed bias filter:                       81  (0.00451782); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 264.49
//
Query:       gi|121637021|ref|YP_977244.1|  [L=151]
Description: cellulase celA2b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-37  130.0   2.5    1.3e-37  129.9   2.5    1.0  1  Glyco_hydro_12  Glycosyl hydrolase family 12


Domain annotation for each model (and alignments):
>> Glyco_hydro_12  Glycosyl hydrolase family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   2.5   7.3e-42   1.3e-37      61     214 .]       2     151 .]       1     151 [] 0.96

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 7.3e-42
                                    T----EEGGGEEEEEEEEEEEEE-TT--EEEEEEEEEESSTT-S--TT-EEEEEEEE.EES---SSEEEEEEEETTEEEE CS
                 Glyco_hydro_12  61 gvalpvkvssvssiptevsfsiddtnvkanvaydlflaaeknqvtsigdvElmiWlarygniqPiGekietavvgGetWe 140
                                    g++lp++v ++ s+pt++++++  t v  +++yd+ l++++++ t++++ E+miW+++ g+iqP+G++++  +++G+ + 
  gi|121637021|ref|YP_977244.1|   2 GTNLPTEVGQILSAPTSIDYNYPTTGVW-DASYDICLDSTPKT-TGVNQQEIMIWFNHQGSIQPVGSPVGNTTIEGKNFV 79 
                                    789************************9.***********998.9*********************************** PP

                                    EEE.EESSSEEEEEEESS--EEEEEEHHHHHHHHH-SS---GGGSEE-EEEEE--B..--TT-EEEEEEEEEEE CS
                 Glyco_hydro_12 141 lwlGaeaeqdvlsFvakspikgysfDvkdFldaltsargldaedlylislqiGtEpftgspetlkvenfsasve 214
                                    +w G ++ ++ +++va++pi+ +sfDv+ F+d  t      ++++yl+s+++G Ep+ ++ + l v++fsa+v+
  gi|121637021|ref|YP_977244.1|  80 VWDGSNGMNNAMAYVATEPIEVWSFDVMSFVDH-TATMEPITDSWYLTSIRAGLEPWSDGVG-LGVDSFSAKVN 151
                                    *********************************.6666666789****************99.********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1071.11
//
Query:       gi|121637022|ref|YP_977245.1|  [L=850]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-35  121.1  21.4    3.1e-35  120.4  21.4    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4  21.4   1.7e-39   3.1e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.7e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPeal a+a+dlagigsal++anaaa aptta+laa+aDeVSaaiAalf+ah+q+yq++saqa+afh+qfvqal++
  gi|121637022|ref|YP_977245.1|  1 MSFVIAAPEALVAVASDLAGIGSALAEANAAALAPTTALLAAGADEVSAAIAALFGAHGQAYQTVSAQASAFHAQFVQALTG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++g+YaaaEaa
  gi|121637022|ref|YP_977245.1| 83 GGGAYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.23u 0.32s 00:00:01.55 Elapsed: 00:00:00.55
# Mc/sec: 4656.40
//
Query:       gi|121637023|ref|YP_977246.1|  [L=312]
Description: pantothenate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.4   0.0    2.4e-11   43.8   0.0    1.3  1  PRK       Phosphoribulokinase / Uridine kinase family
     0.0049   17.4   0.0      0.008   16.7   0.0    1.5  1  AAA_18    AAA domain
  ------ inclusion threshold ------
      0.024   14.3   0.0        0.2   11.3   0.0    2.2  2  CoaE      Dephospho-CoA kinase


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0     4e-15   2.4e-11       1     141 [.      92     229 ..      92     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4e-15
                            PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekd.leleerkrakekevsflspeandfdllyevlk 79 
                                    +Igvags + Gk+t+ar l+ +++r   +      + ++++d ++   +el++r+  + k +    pe  +   l + + 
  gi|121637023|ref|YP_977246.1|  92 IIGVAGSVAVGKSTTARVLQALLARWDHH----PRVDLVTTDGFLYPnAELQRRNLMHRKGF----PESYNRRALMRFVT 163
                                    8***********************87777....45666777777554044444444554444....99999999****** PP

                            PRK  80 elkegkkvd.kpiYsheteeaapdkeeliegadvlviEGlhalyder...vaelldlkiyvdisid 141
                                    + k+g      p+Ysh + ++ p  e+++  +d+l++EGl  l       v +l d++ yvd+ i+
  gi|121637023|ref|YP_977246.1| 164 SVKSGSDYAcAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPtlmVSDLFDFSLYVDARIE 229
                                    ****9876538*****************************9999888999************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06     0.008       1      44 [.      93     138 ..      93     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpe 44 
                                    I+++G  +vGK+t a+ L+ +l+   +    d+++ +g l+++ + 
  gi|121637023|ref|YP_977246.1|  93 IGVAGSVAVGKSTTARVLQALLARwdHHPRVDLVTTDGFLYPNAEL 138
                                    89*******************9667*9************9999988 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.3e-05       0.2       2      23 ..      92     113 ..      91     125 .. 0.91
   2 ?    0.1   0.0     0.092   5.5e+02     108     140 ..     276     308 ..     257     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                                    EEEEEESTTSSHHHHHHHHHHT CS
                           CoaE   2 ivgltGgiasGKstvanlfadl 23 
                                    i+g++G +a GKst a+++++l
  gi|121637023|ref|YP_977246.1|  92 IIGVAGSVAVGKSTTARVLQAL 113
                                    8*****************9985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.092
                                    EE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHH CS
                           CoaE 108 ldvPLLvEkqlekliervlvvdvelelqveRlv 140
                                    ++ P LvE+ l ++ + +lv+  + ++ ++Rl 
  gi|121637023|ref|YP_977246.1| 276 INRPNLVENILPTRPRATLVLRKDADHSINRLR 308
                                    566999999999999999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2188.67
//
Query:       gi|121637024|ref|YP_977247.1|  [L=426]
Description: serine hydroxymethyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-157  524.0   0.0   2.2e-157  523.8   0.0    1.1  1  SHMT             Serine hydroxymethyltransferase
    1.6e-05   24.4   0.1    2.6e-05   23.7   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0078   15.2   0.0      0.014   14.4   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.013   14.8   0.3        1.1    8.4   0.0    2.2  2  Beta_elim_lyase  Beta-eliminating lyase
      0.097   12.9   0.4        1.5    9.1   0.1    2.5  2  DUF4157          Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.8   0.0  6.2e-161  2.2e-157       1     399 []       5     386 ..       5     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 523.8 bits;  conditional E-value: 6.2e-161
                                    HHHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT CS
                           SHMT   1 leesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfk 80 
                                    l+e+dp++ae++ ke  rq++++e+iasenf+ +avl+a+GsvltnkyaeG+PG+ryyGGce+vd+ve+la+drak lf+
  gi|121637024|ref|YP_977247.1|   5 LAEVDPDIAELLAKELGRQRDTLEMIASENFAPRAVLQAQGSVLTNKYAEGLPGRRYYGGCEHVDVVENLARDRAKALFG 84 
                                    5789**************************************************************************** PP

                                    -STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHH CS
                           SHMT  81 ldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidyde 160
                                    ++    ++nvqp+sG+qan+av +al++pg+r+lgldla+GGhlthG+++++     s+kl+e   y+vd++t+lid+d+
  gi|121637024|ref|YP_977247.1|  85 AE----FANVQPHSGAQANAAVLHALMSPGERLLGLDLANGGHLTHGMRLNF-----SGKLYENGFYGVDPATHLIDMDA 155
                                    **....********************************************99.....*********************** PP

                                    HHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-E CS
                           SHMT 161 lekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprgg 240
                                    ++ +a ef+Pk+i+aG say+r++d+a +r iadevga llvdmah+aGlvaag++psP+++advv+tt hktl G r+g
  gi|121637024|ref|YP_977247.1| 156 VRATALEFRPKVIIAGWSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLHPSPVPHADVVSTTVHKTLGGGRSG 235
                                    ******************************************************************************** PP

                                    EEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHH... CS
                           SHMT 241 lillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealk... 317
                                    li+ +              ++++k insavfPg+qGGPl+hvia+kavalk a++pef   q++ l+ a+ +a+ l+   
  gi|121637024|ref|YP_977247.1| 236 LIVGK--------------QQYAKAINSAVFPGQQGGPLMHVIAGKAVALKIAATPEFADRQRRTLSGARIIADRLMapd 301
                                    **988..............6899***********************************************9998875333 PP

                                    ..HTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT--HHHHHH CS
                           SHMT 318 ..ekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrgfkeedlek 394
                                      + g ++vsgGtd hlvlvdlr+  ldG++ae +l++v it+n+n+vP+d + ++vtsGlr+Gtpal++rgf++ ++++
  gi|121637024|ref|YP_977247.1| 302 vaKAGVSVVSGGTDVHLVLVDLRDSPLDGQAAEDLLHEVGITVNRNAVPNDpRPPMVTSGLRIGTPALATRGFGDTEFTE 381
                                    33799*************************************************************************** PP

                                    HHHHH CS
                           SHMT 395 vakfi 399
                                    va++i
  gi|121637024|ref|YP_977247.1| 382 VADII 386
                                    **986 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   7.1e-09   2.6e-05      89     188 ..     141     242 ..     137     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.1e-09
                                    EE-B-TTTSSB-GGGCGG.G--TTEEEEEEB.-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEE CS
                DegT_DnrJ_EryC1  89 fvDvdpdtynidpaaiea.aitertkaIlpV.hlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaav 166
                                    f  vdp+t+ id +a++a a++ r k I++   +y +v d++a + ia++ g k++ D Ah  G   +g +   +  a v
  gi|121637024|ref|YP_977247.1| 141 FYGVDPATHLIDMDAVRAtALEFRPKVIIAGwSAYPRVLDFAAFRSIADEVGAKLLVDMAHFAGLVAAGLHPSPVPHADV 220
                                    6789************98355556688776438999*********************************999999***** PP

                                    EE-BTTSSS-SSS-EEEEESTH CS
                DegT_DnrJ_EryC1 167 fSFyptKnlttGeGGavvtnde 188
                                    +S    K+l  G  G++v + +
  gi|121637024|ref|YP_977247.1| 221 VSTTVHKTLGGGRSGLIVGKQQ 242
                                    *****************97754 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.8e-06     0.014     176     235 ..     190     249 ..     182     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                                    EEES-B-S-GGGGT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHH CS
                           SelA 176 DlGsGllvdlseyglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkk 235
                                    ++G+ llvd++++       ++ +    +d+vs +  k lGg ++G+ivGk+++ + +++
  gi|121637024|ref|YP_977247.1| 190 EVGAKLLVDMAHFAGLVAAGLHPSPVPHADVVSTTVHKTLGGGRSGLIVGKQQYAKAINS 249
                                    56777777777764444444444444459*************************998875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00032       1.1      26      89 ..      60     128 ..      46     160 .. 0.79
   2 ?    4.5   0.0    0.0049        18     151     279 ..     182     346 ..     174     352 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
                                    CCCT--HHHHHHHHHHHH....HTT-S.EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTH CS
                Beta_elim_lyase  26 esYgedktvnrLedavae....lfgke.aalfvpqGtaAnsillkillqrgeevivtepahihfdetga 89 
                                      Yg+ + v ++e+ +++    lfg+e a +  ++G +An+  l +l+ +ge  +  + a++   + g 
  gi|121637024|ref|YP_977247.1|  60 RYYGGCEHVDVVENLARDrakaLFGAEfANVQPHSGAQANAAVLHALMSPGERLLGLDLANGGHLTHGM 128
                                    5677766666666555544444*****6678899****************9999888888876666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0049
                                    HHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH................. CS
                Beta_elim_lyase 151 revaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel............... 215
                                    ++ + ia++ g +l++D A fa  + + g +++  + ++D+v+  + K l+    g+++++++ +               
  gi|121637024|ref|YP_977247.1| 182 AAFRSIADEVGAKLLVDMAHFAGLV-AAGLHPSP-VPHADVVSTTVHKTLGGGRSGLIVGKQQYAkainsavfpgqqggp 259
                                    5678999************999755.66777765.5799*************999******9944666666666666666 PP

                                    ..........................HHH.HHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHH CS
                Beta_elim_lyase 216 ........................edyla.erveqrkylggglrqagvlaaleagiraleeglaslerdhktaeqlaekl 270
                                                               l+  r+   + ++    +agv ++   g   +++ l  l++++  ++   + l
  gi|121637024|ref|YP_977247.1| 260 lmhviagkavalkiaatpefadrqRRTLSgARIIADRLMAPDVAKAGVSVV--SGGTDVHLVLVDLRDSPLDGQAAEDLL 337
                                    666666666666666665555555333320233334444555555555555..555555555666666666666666666 PP

                                    HHCT--EEE CS
                Beta_elim_lyase 271 elvrlaipr 279
                                     +v ++++r
  gi|121637024|ref|YP_977247.1| 338 HEVGITVNR 346
                                    666666555 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00043       1.5       6      33 ..      75     102 ..      71     106 .. 0.87
   2 ?    1.1   0.0      0.13   4.7e+02      11      68 ..     280     339 ..     271     345 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                        DUF4157   6 vraemerafgadlsdVrvhtgsaaaraa 33 
                                     r ++++ fga++ +V+ h+g++a++a 
  gi|121637024|ref|YP_977247.1|  75 ARDRAKALFGAEFANVQPHSGAQANAAV 102
                                    6889999**************9998875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                        DUF4157  11 erafgadlsdVrvhtgsaaaraaralgAqAfTlgndivf..aageyqpesaagrellaHE 68 
                                    + +    ls +r+  ++  a   ++ g++ +  g+d+++   + +++p   + +e l HE
  gi|121637024|ref|YP_977247.1| 280 ADRQRRTLSGARIIADRLMAPDVAKAGVSVVSGGTDVHLvlVDLRDSPLDGQAAEDLLHE 339
                                    55666779999*****99999999999999999999998444445555555555555565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3070.39
//
Query:       gi|121637025|ref|YP_977248.1|  [L=275]
Description: acyl-ACP desaturase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-35  121.1   0.1    5.7e-35  120.7   0.1    1.1  1  FA_desaturase_2  Fatty acid desaturase
    0.00055   20.3   1.1      0.063   13.7   0.0    1.7  2  Rubrerythrin     Rubrerythrin
  ------ inclusion threshold ------
      0.093   12.2   0.0       0.14   11.6   0.0    1.2  1  Ribonuc_red_sm   Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.1   9.5e-39   5.7e-35       8     277 ..      13     264 ..       7     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 9.5e-39
                FA_desaturase_2   8 slekvveenllellkPvekaWqpsdflPdsesee.faeevkelrerakelpddllvvlvgdmvTEeaLPtYesllntleg 86 
                                    +le+vve+n++++l  +e++W+++d++P ++ e+ ++   ++++ ++++lp +++ +    ++  ++L  ++++l ++  
  gi|121637025|ref|YP_977248.1|  13 ELEPVVEANMTRHLD-TEDIWFAHDYVPFDQGENfAFLGGRDWDPSQSTLPRTITDACEILLILKDNLAGHHRELVEHFI 91 
                                    89*************.***************99956799***************99999999**************9998 PP

                FA_desaturase_2  87 vrdetgasdtawakWvraWtaEEnrHgdlLnkYlylsgrvdmrevektvqelikaGfdiktekdpykgfvYtsfQErATk 166
                                            ++ w++W+ +WtaEE+ H+ +L++Yl++++ vd  + e ++ +++ +G + + + ++ +++vY +f Er  +
  gi|121637025|ref|YP_977248.1|  92 -------LEDWWGRWLGRWTAEEHLHAIALREYLVVTREVDPVANEDVRVQHVMKGYRAE-KYTQVETLVYMAFYERCGA 163
                                    .......5667***********************************************98.667889************* PP

                FA_desaturase_2 167 vsHrntaklakeagdellakicgaiaadEkrHeaaYtrvvekllevdpdeavlaladmmrkkitmPaallrdgkdeelFe 246
                                    v  rn a +    ++++la ++ +ia dE rHe +++++v+++l+   de+++a+a+   + ++  +a +      e+++
  gi|121637025|ref|YP_977248.1| 164 VFCRNLAAQ---IEEPILAGLIDRIARDEVRHEEFFANLVTHCLDYTRDETIAAIAARAAD-LDVLGADI------EAYR 233
                                    ****98877...788****************************************987777.55555555......9999 PP

                FA_desaturase_2 247 efsavaqrlgvYtardyldileelikkWkie 277
                                    +  + ++ +g++   +  +++ + i+ W ++
  gi|121637025|ref|YP_977248.1| 234 DKLQNVADAGIFGKPQLRQLISDRITAWGLA 264
                                    9999999999999999999999999999876 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   2.1e-05      0.12      10     136 ..     159     199 ..      98     200 .. 0.57
   2 !   13.7   0.0   1.1e-05     0.063      10      55 ..     159     202 ..     150     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHH CS
                   Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeai 89 
                                    E  +  + ++la +++   p +a l+ ++A++E +H++++++                                      
  gi|121637025|ref|YP_977248.1| 159 ERCGAVFCRNLAAQIE--EPILAGLIDRIARDEVRHEEFFAN-------------------------------------- 198
                                    3334444455555555..555555555555555555555554...................................... PP

                                    HHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  90 egayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                                                                  l
  gi|121637025|ref|YP_977248.1| 199 ----------------------------------------------L 199
                                    ..............................................3 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllek 55 
                                    E  +  + ++la +++   p +a l+ ++A++E +H++++++l+  
  gi|121637025|ref|YP_977248.1| 159 ERCGAVFCRNLAAQIE--EPILAGLIDRIARDEVRHEEFFANLVTH 202
                                    6666777789999999..8999*****************9998765 PP

>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.14     130     208 ..     134     206 ..     117     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHCTTTSCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                 Ribonuc_red_sm 130 aewikkwyeskkdeekfaerlvafallegilfysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkee 208
                                    ++ ++k y+ +k  ++ +e+lv +a+ e+    +g ++  +l+ +   p la  i+ i+rDe  H +f+++l+++ ++ 
  gi|121637025|ref|YP_977248.1| 134 VQHVMKGYRAEK--YTQVETLVYMAFYER----CGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLVTHCLDY 206
                                    566667776555..346888999988888....78888888998888999999*********************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1837.93
//
Query:       gi|121637026|ref|YP_977249.1|  [L=433]
Description: phoH-like protein phoH2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-52  176.8   0.0    4.7e-52  176.4   0.0    1.1  1  PhoH      PhoH-like protein
    2.1e-29  102.5   0.0    3.3e-29  101.8   0.0    1.3  1  PIN_4     PIN domain
    3.1e-07   30.3   0.1    6.1e-07   29.3   0.1    1.5  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.7      0.079   13.2   0.7    2.0  1  AAA_22    AAA domain
      0.021   15.2   0.8      0.054   13.9   0.8    1.7  1  AAA_16    AAA ATPase domain
      0.046   14.1   0.0      0.081   13.3   0.0    1.3  1  Histone   Core histone H2A/H2B/H3/H4
      0.072   12.9   0.0       0.62    9.8   0.0    2.1  2  DEAD      DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   1.8e-55   4.7e-52       3     204 ..     222     426 ..     220     427 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 1.8e-55
                                    ---SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEEEEEE-S--T.T----SS---------T CS
                           PhoH   3 kpktkeQkeylealk..kndivfaiGpaGtGKtylavalavealkk.kkvkriiltrpavea.geelGflpgdleekvdp 78 
                                    + +++eQ+ +l+ l   +  iv   G+aGtGK+ la+++++ea+ + ++ ++++++rp   + g+elG+lpg ++ek+ p
  gi|121637026|ref|YP_977249.1| 222 RGRSAEQRVALDLLLdeSVGIVSLGGKAGTGKSALALCAGLEAVLErRTHRKVVVFRPLYAVgGQELGYLPGSESEKMGP 301
                                    67999*********9555569*********************9887366789********9989**************** PP

                                    TTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                           PhoH  79 ylrplydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                    + +++ d+L+ l + + +e++l++g++ev+pl+++RGr+l+d+fvi+DEAQ+++++ + ++l+RlG +s+vv+t+d++q 
  gi|121637026|ref|YP_977249.1| 302 WAQAVFDTLEGLASPAVLEEVLSRGMLEVLPLTHIRGRSLHDSFVIVDEAQSLERNVLLTVLSRLGTGSRVVLTHDIAQR 381
                                    ******************************************************************************** PP

                                    ---.------THHHHHHTTT-TTEEEEE--GGG----HHHHHHHHHH CS
                           PhoH 159 dlp.kgkksGlaealevlknvegieivelkkkdvvRhplvkkivkay 204
                                    d+  +g+++G+a ++e+lk++  +++++l   +  R+p+++ +++++
  gi|121637026|ref|YP_977249.1| 382 DNLrVGRHDGVAAVIEKLKGHPLFAHITL--LRSERSPIAALVTEML 426
                                    **9777**************999999888..7788999999888775 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   1.3e-32   3.3e-29       1     131 []       7     145 ..       7     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.3e-32
                          PIN_4   1 fVlDTnvlLhdpealksfkeehdvviPitVleELdklKkgsserelarlarqanrlldelleke.......sgrlkvqts 73 
                                    +VlDT+vlL+dp+a+ +f  ehdvv+P++V++EL+++++++   el+  arqa+rl+d+l  ++           ++ t+
  gi|121637026|ref|YP_977249.1|   7 YVLDTSVLLSDPWACSRF-AEHDVVVPLVVISELEAKRHHH---ELGWFARQALRLFDDLRLEHgrldqpiPVGTQGGTL 82 
                                    8*****************.***************9888887...5************99966655664444222255555 PP

                          PIN_4  74 aeelpee.e......seseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgieaedye 131
                                    + el+++ +      ++ ++nD+rIl++a +l+ e   ++v+LvskDi lr+kA a g++a +y+
  gi|121637026|ref|YP_977249.1|  83 HVELNHTdPavlpagFRTDSNDSRILSCAANLAAEG--KRVTLVSKDIPLRVKAAAVGLAADEYH 145
                                    7777776447777764468***************97..9**********************9996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   2.4e-10   6.1e-07       3     134 ..     225     387 ..     223     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.4e-10
                         AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKtta..lkalreaweaa.ggrviglAptgkaAkv.La.......eelgieas 71 
                                    +aeQ+ a++ ll ++  ++ l G AGtGK+ +   ++l++++e++  ++v+++ p  ++  + L+       e++g  a+
  gi|121637026|ref|YP_977249.1| 225 SAEQRVALDLLLDESVGIVSLGGKAGTGKSALalCAGLEAVLERRtHRKVVVFRPLYAVGGQeLGylpgsesEKMGPWAQ 304
                                    689***************************85226889*****99889***99998777544499555554444444444 PP

                         AAA_30  72 tiakllkrlk.......................grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQl 128
                                     +   l+ l+                       g  r  +++ +ivDEa  +  + l ++l+++ + g +v+l  D +Q 
  gi|121637026|ref|YP_977249.1| 305 AVFDTLEGLAspavleevlsrgmlevlplthirG--RSLHDSFVIVDEAQSLERNVLLTVLSRLGT-GSRVVLTHDIAQR 381
                                    44444444448999999999*********96542..334459**********************99.************8 PP

                         AAA_30 129 asVeaG 134
                                    +    G
  gi|121637026|ref|YP_977249.1| 382 DNLRVG 387
                                    866555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   3.1e-05     0.079       6     115 ..     241     365 ..     237     384 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee........erpevv.....fvtlpsst..sskdllrellralglelka 70 
                                    gi+ + G +GtGK+ l+     +++ e    +             +     + +lp+s+  +    +++++  l+  ++ 
  gi|121637026|ref|YP_977249.1| 241 GIVSLGGKAGTGKSALALCAGLEAVLERRTHRkvvvfrplY----AvggqeLGYLPGSEseKMGPWAQAVFDTLEGLASP 316
                                    677788999*****999998888765444333567744430....25555555555555334444456666666543333 PP

                         AAA_22  71 ...erlsseell.ealeqalrarav......ielliiDEaqhlrseealeeLrsl 115
                                       e     e+l + + + l  ++        +++i+DEaq l + ++l ++ s+
  gi|121637026|ref|YP_977249.1| 317 avlE-----EVLsRGMLEVLPLTHIrgrslhDSFVIVDEAQSL-ERNVLLTVLSR 365
                                    4432.....333333333333333333355889**********.75555554333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   2.1e-05     0.054       2      88 ..     221     316 ..     220     383 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslv.....rellralekd....ggif...lrgkcdql...... 63 
                                    l GR +e+   + al+ + + + ++v l G +G+GKs+l+     +++l+    +    ++++   l++   q       
  gi|121637026|ref|YP_977249.1| 221 LRGRSAEQ---RVALDLLLDESVGIVSLGGKAGTGKSALAlcaglEAVLE----RrthrKVVVfrpLYAVGGQElgylpg 293
                                    56899988...677777778888****************95433333333....22333322223322222222122332 PP

                         AAA_16  64 esaipysalaqalareellrqllde 88 
                                    +++  + ++aqa  + + l+ l+++
  gi|121637026|ref|YP_977249.1| 294 SESEKMGPWAQAV-F-DTLEGLASP 316
                                    2222234466666.4.444444444 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.081     102     126 ..     106     130 ..     105     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHTTXSEEXHHHHHH CS
                        Histone 102 elfeeAnllakhaKRvTitpkDiql 126
                                    ++++ A++la + KRvT+ +kDi l
  gi|121637026|ref|YP_977249.1| 106 RILSCAANLAAEGKRVTLVSKDIPL 130
                                    8999*******************87 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00024      0.62       4      57 ..     228     281 ..     225     289 .. 0.83
   2 ?    0.5   0.0      0.17   4.5e+02     123     136 ..     344     357 ..     314     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHTT..CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSH CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 Qaeaiplilgg..gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtr 57 
                                    Q+ a++l+l++  g v + ++ G+GK++ +l + l++v+e  ++t+ k+++  P+ 
  gi|121637026|ref|YP_977249.1| 228 QRVALDLLLDEsvGIVSLGGKAGTGKSALALCAGLEAVLE--RRTHRKVVVFRPLY 281
                                    77788888854236777899******************98..999999**999975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                    EEEEEETHHHHHHT CS
                                    xxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldq 136
                                    +f+++DEa+ l  +
  gi|121637026|ref|YP_977249.1| 344 SFVIVDEAQSLERN 357
                                    79******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2737.30
//
Query:       gi|121637027|ref|YP_977250.1|  [L=291]
Description: glycosyl hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-35  119.1   0.0    7.6e-34  116.3   0.0    2.0  2  Polysacc_deac_1  Polysaccharide deacetylase
     0.0087   15.3   0.0      0.011   14.9   0.0    1.2  1  Polysacc_deac_2  Divergent polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   8.5e-38   7.6e-34       7     121 ..      47     161 ..      44     164 .. 0.98
   2 ?    0.3   0.0     0.067     6e+02       8      34 ..     194     222 ..     189     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 8.5e-38
                                    TEEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHH CS
                Polysacc_deac_1   7 ksvalTfDdgprdntteilpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreiera 86 
                                    k+valTfDdgp  +t+++l +L ++++katff+ig++v+ +p  +r++a++G+eig+Ht+ h+n+++  +e++  ++ ra
  gi|121637027|ref|YP_977250.1|  47 KCVALTFDDGPGPYTDRLLHILTDNDAKATFFLIGNKVAANPAGARRIADAGMEIGSHTWEHPNMTTIPPEDIPGQFSRA 126
                                    89****************************************************************************** PP

                                    HHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT. CS
                Polysacc_deac_1  87 kdalrkalgreprlfryPygsasatvlevarelgf 121
                                    +d++ +a+gr+p+l+r+ +g  ++ v+++a+++g 
  gi|121637027|ref|YP_977250.1| 127 NDVIAAATGRTPTLYRPAGGLSNDAVRQAAAKVGQ 161
                                    ********************************996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.067
                                    EEEEEEEESS..CSCHHHHHHHHHHCT-- CS
                Polysacc_deac_1   8 svalTfDdgp..rdntteilpvLkkykvk 34 
                                    sv+l  D+ +   d++ +++pvLk+++ +
  gi|121637027|ref|YP_977250.1| 194 SVVLFHDTYSstVDVVYQFIPVLKANGYR 222
                                    566655655577899999******99865 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-06     0.011     169     213 .]     186     230 ..     148     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
                                    HHHHHCCSEEEEEEE-SCCHHHHHHHHHHHHHHCTEEE--HHHH- CS
                Polysacc_deac_2 169 aklakkkGsaiaighprpetieaLkewlpeleaegielvpvsall 213
                                    + +  k Gs+++    ++ t++++ + +p l+a+g++lv+vs+ll
  gi|121637027|ref|YP_977250.1| 186 LMTQIKPGSVVLFHDTYSSTVDVVYQFIPVLKANGYRLVTVSELL 230
                                    5556689************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2102.78
//
Query:       gi|121637028|ref|YP_977251.1|  [L=293]
Description: membrane glycine and proline rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   13.8   0.1       0.11   12.4   0.1    1.7  1  ODV-E18   Occlusion-derived virus envelope protein ODV-E18


Domain annotation for each model (and alignments):
>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.9e-06      0.11      23      60 ..      65     101 ..      62     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-06
                        ODV-E18  23 ePsllltilvvlviiillvllvqssstGsdssssnann 60 
                                    +P l+l+ l+vl +i+l+v+lv     G++ s++ ++ 
  gi|121637028|ref|YP_977251.1|  65 TPWLILAGLAVLGVILLVVILVIGLR-GDNKSTTATSP 101
                                    799******************98887.66666555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1998.96
//
Query:       gi|121637029|ref|YP_977252.1|  [L=474]
Description: fumarate hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.2e-101  340.3   0.0   1.7e-101  339.7   0.0    1.2  1  Lyase_1      Lyase
    1.9e-18   66.6   0.6    6.5e-18   64.9   0.1    2.3  2  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.7   0.0  1.9e-105  1.7e-101       1     312 []      18     342 ..      18     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 339.7 bits;  conditional E-value: 1.9e-105
                                    CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHH CS
                        Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegklddqfv 71 
                                    g++ v+a +l+ ++t+r+ enf +s+   +     al++lk a+a++n dl     e+a+aii+a+ e+++ g++ddqf+
  gi|121637029|ref|YP_977252.1|  18 GEVRVPAKALWRAQTQRAVENFPISGRGLErtqirALGLLKGACAQVNSDLgllaPEKADAIIAAAAEIAD-GQHDDQFP 96 
                                    78999*******************98766567778************************************.******** PP

                                    HBSSSSSHHHHHHHHHHHHHHHHTT...HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH CS
                        Lyase_1  72 lkviqegsgtavnmnlnevigellg...ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekake 148
                                    ++v+q+gsgt++nmn+nevi+++ +    +++pnd+v+++qSsnD++pTa ++a+++a  ++L+pal+qL+dal +ka  
  gi|121637029|ref|YP_977252.1|  97 IDVFQTGSGTSSNMNTNEVIASIAAkggVTLHPNDDVNMSQSSNDTFPTATHIAATEAAVAHLIPALQQLHDALAAKALD 176
                                    *********************666666799****************************99******************** PP

                                    TTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCS CS
                        Lyase_1 149 fkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtgl 228
                                       vvk GrThl dA+Pvtlgqe+s+ya+++e  +er++  l   l el+ ggtavgtglna   f  +v++ l + tgl
  gi|121637029|ref|YP_977252.1| 177 WHTVVKSGRTHLMDAVPVTLGQEFSGYARQIEAGIERVRACL-PRLGELAIGGTAVGTGLNAPDDFGVRVVAVLVAQTGL 255
                                    ******************************************.7777888888*********************999999 PP

                                    T..EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHH CS
                        Lyase_1 229 p..vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltg 305
                                        +a+nsfea ++rD +ve++gal+++a+sL k+a+D+r++ sg+ +gl e++l+  +pGSSiMPgKvNPv  E++t+
  gi|121637029|ref|YP_977252.1| 256 SelRTAANSFEAQAARDGLVEASGALRTIAVSLTKIANDIRWMGSGPlTGLAEIQLPDLQPGSSIMPGKVNPVLPEAVTQ 335
                                    88899*************************************************************************** PP

                                    HHHHHHH CS
                        Lyase_1 306 vagrvvG 312
                                    va++v+G
  gi|121637029|ref|YP_977252.1| 336 VAAQVIG 342
                                    *****98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.7   6.2e+03      34      47 ..      67      80 ..      62      88 .. 0.67
   2 !   64.9   0.1   7.2e-22   6.5e-18       1      53 [.     408     464 ..     408     465 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.7
                                   HTT-.-HHHHHHHT CS
                    FumaraseC_C 34 elgllteeeldell 47
                                   +lgll  e+ d+++
  gi|121637029|ref|YP_977252.1| 67 DLGLLAPEKADAII 80
                                   56777777777665 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 7.2e-22
                                    GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.....-HHHHHHHT-HHHHH CS
                    FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgl....lteeeldelldpekMt 53 
                                    +VT+Ln  IGYe+Aa++Ak+Alke+kt+r+ v+++gl    l+ e+ld+ ld+++M+
  gi|121637029|ref|YP_977252.1| 408 IVTPLNSAIGYEEAAAVAKQALKERKTIRQTVIDRGLigdrLSIEDLDRRLDVLAMA 464
                                    8*******************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3304.80
//
Query:       gi|121637030|ref|YP_977253.1|  [L=328]
Description: fructose 1,6-bisphosphatase II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   6.1e-139  462.1   5.9   6.9e-139  462.0   5.9    1.0  1  FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-enco


Domain annotation for each model (and alignments):
>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.0   5.9  3.8e-143  6.9e-139       5     308 .]       1     304 [.       1     304 [. 1.00

  Alignments for each domain:
  == domain 1  score: 462.0 bits;  conditional E-value: 3.8e-143
                    FBPase_glpX   5 lelvrvteaAAlaaarlvGrgdkeaadqaAveamrkalneleikgevviGegekdeapmLyiGekvGsgegpevdiavdp 84 
                                    +elvrvtea A+aa r+vGrgdke  d aAv+amr+ +n+++++g+vviGegekd+apmLy+Ge+vG+g+gpe+d avdp
  gi|121637030|ref|YP_977253.1|   1 MELVRVTEAGAMAAGRWVGRGDKEGGDGAAVDAMRELVNSVSMRGVVVIGEGEKDHAPMLYNGEEVGNGDGPECDFAVDP 80 
                                    79****************************************************************************** PP

                    FBPase_glpX  85 leGttlvAkglpnaisviAvaekgsllk.apdvYmeKlvvgpeakgvidldapveenlkavakalgkevedltvvvLdrp 163
                                    ++Gttl++kg++naisv+Ava++g++++ ++ +Ym+K++vgp+a++v+d++ap++en++avak+++ +v+d+tv++Ldrp
  gi|121637030|ref|YP_977253.1|  81 IDGTTLMSKGMTNAISVLAVADRGTMFDpSAVFYMNKIAVGPDAAHVLDITAPISENIRAVAKVKDLSVRDMTVCILDRP 160
                                    ****************************999************************************************* PP

                    FBPase_glpX 164 RheelieeireagarvklisdGDvaaaiaaaleesgvdvllGiGgapEGvlaAaalkclgGemqarlvprkeeereraek 243
                                    Rh++li+++r++gar++li+dGDva+ai+a+ ++sg+d+l GiGg+pEG++aAaa++c+gG++qa+l+pr+++er++a +
  gi|121637030|ref|YP_977253.1| 161 RHAQLIHDVRATGARIRLITDGDVAGAISACRPHSGTDLLAGIGGTPEGIIAAAAIRCMGGAIQAQLAPRDDAERRKALE 240
                                    ******************************************************************************** PP

                    FBPase_glpX 244 mgiedldkvltledLvkgddvifaatgvTdgelLkgvrfkgggarteslvmrsksgtvrfiesih 308
                                    +g+ dl++vlt+edLv+g++v+f+atgvTdg+lLkgvr+  gg +t+s+vmrsksgtvr+ie++h
  gi|121637030|ref|YP_977253.1| 241 AGY-DLNQVLTTEDLVSGENVFFCATGVTDGDLLKGVRYYPGGCTTHSIVMRSKSGTVRMIEAYH 304
                                    ***.**********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2410.38
//
Query:       gi|121637031|ref|YP_977254.1|  [L=233]
Description: hypothetical protein BCG_1160 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-52  177.8   0.0    1.9e-52  177.6   0.0    1.1  1  DUF4245   Protein of unknown function (DUF4245)


Domain annotation for each model (and alignments):
>> DUF4245  Protein of unknown function (DUF4245)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.6   0.0   1.1e-56   1.9e-52       1     166 []      34     224 ..      34     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.6 bits;  conditional E-value: 1.1e-56
                        DUF4245   1 RinqslrdmvlSlavlvavvlvlvgltgrcsfnp.....gqvpevDvaaaletaaraapfpvraPglpegWkansarrta 75 
                                    R++q++rdm++Sla+lv+++++l+gl+g+csf+      g++p++D+a+al+++a++++fp+r+P+lp gW++ns+ r +
  gi|121637031|ref|YP_977254.1|  34 RLLQDGRDMFWSLAPLVVGCILLAGLVGMCSFQLggtkrGPIPSYDAAQALRADAKTLGFPIRLPQLPGGWTPNSGGRGG 113
                                    899*****************************9999*9999*************************************** PP

                        DUF4245  76 vdg............epawtvGyvtpegqyisltqsdadeddlvasvlggaeetgtvevgGrtWqvy........aedkw 135
                                    +++            ++++ vG+++p g+y+sltqs+aded+lv s++++ ++tgtv+vgG++W+vy        +e+ w
  gi|121637031|ref|YP_977254.1| 114 IENgradpatgqrrnAATSIVGFISPTGRYLSLTQSNADEDKLVGSIHPSMYPTGTVDVGGTRWVVYegsdengaVEPVW 193
                                    ******************************************************************************** PP

                        DUF4245 136 etalvreegdvtvvvtGtaseeeletlAaal 166
                                    +t+l+ + g++++++tG++s ++++tlA+a+
  gi|121637031|ref|YP_977254.1| 194 TTRLTGPGGATQLAITGAGSIDQFRTLASAT 224
                                    ****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1694.22
//
Query:       gi|121637032|ref|YP_977255.1|  [L=342]
Description: hypothetical protein BCG_1161c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-65  221.0  25.5    2.5e-65  220.8  25.5    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.8  25.5   1.4e-69   2.5e-65      34     326 ..       1     302 [.       1     303 [. 0.97

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 1.4e-69
                AI-2E_transport  34 llnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvkslp.........ayidslqnilnelpsll 104
                                    +++p++k++ ++++++ l+++++ll++l+++v++v++lv l+i+q++++v+s+          ++ d++++++n l++++
  gi|121637032|ref|YP_977255.1|   1 MFTPLFKWF-TKRFNTGLSAACTLLSALAAVVVPVGALVGLAIVQIARMVDSVAdwvrttdlsTLGDKILQFVNGLFDRV 79 
                                    589******.********************************************************************** PP

                AI-2E_transport 105 eele.n.liqalkqslskilsnilssilnsllsllasllglilslvlvllllffllldgeklrqgilkllpervrervka 182
                                    ++l+ + +++al+++++++++n+ +++l++l+++++sl+g+i+s+++++++++ ll+++eklr+ i +l p + ++ ++ 
  gi|121637032|ref|YP_977255.1|  80 PFLHiTvTADALRKAMISVAQNVGEWLLHFLRDAAGSLAGVITSAIIFVYVFVALLVNREKLRTLIGQLNPLG-EDVTDL 158
                                    ****88*******************************************************************.****** PP

                AI-2E_transport 183 ilrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglan.liPyiGavivlipiaiialltggikevli 261
                                    +l+++ ++++g+++gq+++a+++gv+++++++i+g++++++++ +v +a  +iP++G+++++ +  i ++++g+i+ +++
  gi|121637032|ref|YP_977255.1| 159 YLQKMGSMVRGTVNGQFVIAACQGVAGAASIYIAGFHHGFFIFAIVLTALsIIPLGGGIVTIPF-GIGMIFYGNIAGGIF 237
                                    ***************************************977666666554***9999998888.7************** PP

                AI-2E_transport 262 vlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavikaileay 326
                                    vl+++llv++ ++n+l+P+l+ ++++l+ +++lls++ag+++fG++G+i++++l+++i +++++y
  gi|121637032|ref|YP_977255.1| 238 VLLWHLLVVTNIDNVLRPILVPRDARLNSALMLLSVFAGITMFGPWGIIIGPVLMILIVTTIDVY 302
                                    **************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2551.96
//
Query:       gi|121637033|ref|YP_977256.1|  [L=103]
Description: hypothetical protein BCG_1162c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-11   43.3   0.1    4.4e-11   43.2   0.1    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   2.4e-15   4.4e-11      18     100 ..       9      85 ..       3      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.4e-15
                                    --SEEEEEE-S-HHHHCH.SEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCCEEEEEGGGEEEEEEE-- CS
                     PemK_toxin  18 qgkrRpvvVvsndafnek.ntvivvpltskdkdkkklpfhveleseildlngldkdswvkldqirtvdkarlrkkigkls 96 
                                     +k Rpv+++++++ + +   v+v+p+t++ +      ++v+++    ++ngl+++s+v +d i+t++   l+++ig l 
  gi|121637033|ref|YP_977256.1|   9 LDKARPVLILTREVVRPHlTNVTVAPITTTVRGL---ATEVPVD----AVNGLNQPSVVSCDNIQTIPVCDLGRQIGYLL 81 
                                    6799*********9998879***********544...7888887....6788889**************99*99999865 PP

                                    HHHH CS
                     PemK_toxin  97 redl 100
                                    + + 
  gi|121637033|ref|YP_977256.1|  82 ASQE 85 
                                    5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 664.07
//
Query:       gi|121637034|ref|YP_977257.1|  [L=106]
Description: hypothetical protein BCG_1163c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   14.3   0.3      0.061   13.9   0.3    1.2  1  UreF      UreF


Domain annotation for each model (and alignments):
>> UreF  UreF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   3.4e-06     0.061       5      56 ..      39      87 ..      35      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-06
                                   HHHHHHHHHHHTTHHHHTHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--SH CS
                           UreF  5 aslaawledqLllglarldlavlarayraaragdaaalrelddwllatreta 56
                                   +++ a++ d+++ + ar+ +av++ra+   +++   +l+e d+++lat ++a
  gi|121637034|ref|YP_977257.1| 39 DEIVAFIDDEVRGQHARSRAAVVLRAL---ERERRRRLAERDAEILATNTSA 87
                                   67789**********************...6667889999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 696.50
//
Query:       gi|121637035|ref|YP_977258.1|  [L=229]
Description: para-nitrobenzyl esterase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-69  235.4   0.0    1.7e-69  235.1   0.0    1.0  1  COesterase     Carboxylesterase family
    3.6e-11   43.3   0.6    1.8e-05   24.7   0.2    2.1  2  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.072   11.9   0.0      0.076   11.9   0.0    1.1  1  Say1_Mug180    Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.1   0.0   2.8e-73   1.7e-69       4     194 ..       7     196 ..       4     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 2.8e-73
                                    EEEETTEEEEEEEEEESTCSEEEEEEEEESSB---GGGTTS--BE----SSEEECBS---BESEECSSSSSCGHHCHHHB CS
                     COesterase   4 vvetslGkvrGkrvklksekevdaFlGiPYAepPvgelRFkkPepaepwtgvrdAtkfspaCpqnaeksekeekeleawv 83 
                                    v e ++G+vrG +        v++++Gi+YA+pP+g+lRF+ Pep+e+wt+v dAt+f+paCpq a +  +    l a +
  gi|121637035|ref|YP_977258.1|   7 VAESRYGPVRGADDG-----RVKVWKGIRYAAPPLGDLRFRTPEPPERWTEVADATTFGPACPQPAIPNMPLD--LGASQ 79 
                                    556789*****9999.....9********************************************96555544..4455* PP

                                    ES---EEEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-.....SSTT CS
                     COesterase  84 sEDCLyLnvytPkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlst.....gdee 156
                                    sEDC  Ln+++P+++ e   + PV+Vw+hGg++  gs+s+  y+g+ Laa+g+v+vVt+nYRlG+lGFl +     + + 
  gi|121637035|ref|YP_977258.1|  80 SEDCWSLNIWAPADT-EPGDGKPVMVWLHGGAYILGSGSQplYNGRRLAASGDVVVVTVNYRLGALGFLDLssfntSRRR 158
                                    ************996.666666***********************************************98555434499 PP

                                    SBS-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETH CS
                     COesterase 157 apGNvGllDqvlALrWVkenIasFGGdpervtlfGesA 194
                                    ++ N+Gl D+ + LrWV +nIa FGGdpe+vtlfGesA
  gi|121637035|ref|YP_977258.1| 159 FDSNIGLRDVLAVLRWVADNIAVFGGDPEKVTLFGESA 196
                                    *************************************8 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.2   3.1e-09   1.8e-05       1      40 [.     103     142 ..     103     143 .. 0.96
   2 !   16.9   0.0   7.4e-07    0.0044      49      80 ..     165     196 ..     159     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.1e-09
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---T CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlA 40 
                                    +v++HGG+++lgs +++    r+la+  ++vvv v+Yrl 
  gi|121637035|ref|YP_977258.1| 103 MVWLHGGAYILGSGSQPLYNGRRLAASGDVVVVTVNYRLG 142
                                    79************************************95 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.4e-07
                                    HHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    + d+la+lrw+a++ + +g dp++++l+G+Sa
  gi|121637035|ref|YP_977258.1| 165 LRDVLAVLRWVADNIAVFGGDPEKVTLFGESA 196
                                    689***********99***************8 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05     0.076     103     136 ..      78     114 ..      72     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                    Say1_Mug180 103 ikskfvwlrkv..petfdPkvD.pvllylHGGgfalk 136
                                     +s+  w  ++  p + +P+   pv+++lHGG ++l+
  gi|121637035|ref|YP_977258.1|  78 SQSEDCWSLNIwaPADTEPGDGkPVMVWLHGGAYILG 114
                                    5788999999888******9878***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1653.38
//
Query:       gi|121637036|ref|YP_977259.1|  [L=171]
Description: para-nitrobenzyl esterase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-17   62.8   0.0      3e-17   62.7   0.0    1.0  1  COesterase  Carboxylesterase family


Domain annotation for each model (and alignments):
>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   1.7e-21     3e-17     373     498 ..      25     154 ..      13     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.7e-21
                                    CHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTT-SEEEEEEE--STTSSST....TTGSSBTTTTHHHHTTGGGTSGCS. CS
                     COesterase 373 daeksrkallelltdvlfkapvlrtaklhasrgspvYlYsfdyrnssskkp....kwmgvvhgdeleyvfglpllekee. 447
                                    + ++++ + l+++tdv f++p++++a+ h s  +pvYlY+fdy++     p      + ++h++el+yv+g+   +++  
  gi|121637036|ref|YP_977259.1|  25 SRWRRKARSLSMATDVGFRMPSVWLAEGH-SGVAPVYLYRFDYST-----PllklLLVRAAHATELPYVWGNLGGSQDPa 98 
                                    56778889999******************.*************99.....54445899**************99988888 PP

                                    ....S-HHHHHHHHHHHHHHHHHHHHSSTTS.TTSS----B.TTTBEEEEESSSSS CS
                     COesterase 448 ....ftkedeklsrkmmtywtnFaktgnPnk.eeeekWpkytkeeekylkinlkpk 498
                                        + k+   +sr++ t w nFa+ g+P++ ++e+ Wp y++ ++  l i+++  
  gi|121637036|ref|YP_977259.1|  99 lklgDAKAAIAVSRRVRTRWINFATRGKPTGpDGEPDWPCYEEAHRACLIIGRRDA 154
                                    88766666888********************9*****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1322.67
//
Query:       gi|121637037|ref|YP_977260.1|  [L=370]
Description: cholesterol dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-58  197.2   0.0    3.5e-58  196.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      2e-29  102.8   0.0    2.5e-29  102.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-16   60.8   0.0    2.8e-16   59.8   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.8e-16   60.5   0.1    2.5e-16   60.1   0.1    1.3  1  NAD_binding_10   NAD(P)H-binding
    1.4e-13   50.7   0.4    3.7e-10   39.4   0.4    2.3  1  NAD_binding_4    Male sterility protein
    1.5e-12   47.2   0.0      2e-12   46.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.1e-08   34.6   0.1      4e-07   29.5   0.4    2.6  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.3e-08   32.7   1.9    1.9e-06   27.9   1.9    2.2  1  KR               KR domain
    2.6e-07   30.4   0.2    5.1e-07   29.5   0.2    1.4  1  NmrA             NmrA-like family
    0.00076   19.0   0.1     0.0013   18.3   0.1    1.3  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.8   0.0   1.9e-61   3.5e-58       1     274 [.      18     277 ..      18     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 196.8 bits;  conditional E-value: 1.9e-61
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +vtGgaGF+G++lv +L+++++   vr++D +  p+ll    +++   v++gD+td+d   +a++g+d ++h+a++++++
  gi|121637037|ref|YP_977260.1|  18 LVTGGAGFVGANLVTTLLDRGH--WVRSFDRA--PSLLPAHPQLE---VLQGDITDADVCAAAVDGIDTIFHTAAIIELM 90 
                                    69*******************5..8****965..55544444444...67****************************99 PP

                      3Beta_HSD  81 g.....kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEk 155
                                    g       ++++   vnv GT+n+l a  +agv+++vYtSs +vv +   g++i  gdE+l+y   ++d y+e+K +aE+
  gi|121637037|ref|YP_977260.1|  91 GgasvtDEYRQRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVMG---GQNIAGGDETLPYTDRFNDLYTETKVVAER 167
                                    863222234566778********************************...****************************** PP

                      3Beta_HSD 156 lvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAaralqdp 235
                                    +vl+ Ng    +g  ++Tca+Rp+gi+G+gd+++++ l +++ +g+ ++ +g +++  d  Yv N+ +  ilAa +l  +
  gi|121637037|ref|YP_977260.1| 168 FVLAQNG---VDG--MLTCAIRPSGIWGNGDQTMFRKLFESVLKGHVKVLVGRKSARLDNSYVHNLIHGFILAAAHLVPD 242
                                    *******...788..*************************9999*9*******************************988 PP

                      3Beta_HSD 236 kkkssvagqayfisddsPvesyddfnltllkelglelks 274
                                        ++ gqayfi d +P + +++f++++l++ g + ++
  gi|121637037|ref|YP_977260.1| 243 ---GTAPGQAYFINDAEPIN-MFEFARPVLEACGQRWPK 277
                                    ...7899*************.99*********9988766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   1.4e-32   2.5e-29       1     229 [.      17     239 ..      17     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 1.4e-32
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.-...-- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.v...gg 76 
                                    +lVtG++Gf+G++lv  ll++g+ v  +dr +s     ++++le+ ++d+td++ ++++++  ++d+++h Aa +   gg
  gi|121637037|ref|YP_977260.1|  17 VLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPS--LLPAHPQLEVLQGDITDADVCAAAVD--GIDTIFHTAAiIelmGG 92 
                                    79*****************************44..33445566******************..*********96555567 PP

                                    HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--..--SSHHHHHHHHHHHHH CS
                      Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgpl..kpnspYaaaKlageklv 153
                                     +++ e++++ +  n+ gt nll+a ++agv+r+++ sS +v   ++++   +et+   p+  + n  Y  +K+ +e+ v
  gi|121637037|ref|YP_977260.1|  93 ASVTDEYRQRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVMGGQNIAgGDETL---PYtdRFNDLYTETKVVAERFV 169
                                    778889999******************************99998899875488888...998899*************** PP

                                    HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHH CS
                      Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehv 229
                                     a +   g+ ++++r++ + G +     ++ ++ +l +++l+g+   +l+g  +a+ d  yv  ++ +++l+++h 
  gi|121637037|ref|YP_977260.1| 170 LAQNGVDGMLTCAIRPSGIWGNG-----DQTMFRKLFESVLKGH-VKVLVGRKSARLDNSYVHNLIHGFILAAAHL 239
                                    ***********************.....88888999999999*9.999************************9994 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   1.6e-19   2.8e-16       1     330 [.      18     342 ..      18     344 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.6e-19
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGf+G++l+  Ll++g+ v  ++r  s++               ++++l++ +gD+tD++    +++ +  d+++
  gi|121637037|ref|YP_977260.1|  18 LVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLLP--------------AHPQLEVLQGDITDADVCAAAVDGI--DTIF 81 
                                    9***********************99998888744..............2356899*********999999997..8888 PP

                                    E--S---H..HHHTTS..HHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEE.GGGG-S-SSSSB-TTS----..-SHH CS
                  GDP_Man_Dehyd  81 nLAAqshV..dvsfek..PeytaevnvlGtlrLLeairalglekkvrfyqaSt.sEvYGkvqevpqtEttpfyP..rsPY 153
                                    + AA      + s+++   ++ + vnv Gt +LL a +++g++   rf+ +S+ s v G ++ +  +Et p++   +  Y
  gi|121637037|ref|YP_977260.1|  82 HTAAIIELmgGASVTDeyRQRSFAVNVGGTENLLHAGQRAGVQ---RFVYTSSnSVVMGGQNIAGGDETLPYTDrfNDLY 158
                                    8888765422344433113467899****************96...665555527789**99999*******9734689* PP

                                    HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHH CS
                  GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveam 233
                                      +K++a+ +v + +   g+ ++  + +   +     + + rk+ + v    +g+ +vl +G  +a+ d  +v+  ++++
  gi|121637037|ref|YP_977260.1| 159 TETKVVAERFVLAQNGVDGMLTCAIRPSGIWGNGD--QTMFRKLFESVL---KGHVKVL-VGRKSARLDNSYVHNLIHGF 232
                                    **************************999999874..556677776665...6776666.8******************9 PP

                                    HHHHHCSS-......--EEE-TT-EEECHHCHHCCHHCCCHHHH.HH..............TTGGCCCEECGG--SS--S CS
                  GDP_Man_Dehyd 234 wlmlqqdkp......edyviatgethsvrefvelaflelgktie.wegkgeeevgrak..esgkvvvevdpkyfrpgevd 304
                                     l+  +  p      + y i++ e  ++ ef++  ++++g++   ++ +g   + +++  +  + +  +      p  v+
  gi|121637037|ref|YP_977260.1| 233 ILAAAHLVPdgtapgQAYFINDAEPINMFEFARPVLEACGQRWPkMRISGPAVRWVMTgwQRLHFRFGFPAPLLEPLAVE 312
                                    99998855511112345778888888888888877777776432022222222222221133334444555678889999 PP

                                    B--B-....THHHHHHH----SS-HHHHHH CS
                  GDP_Man_Dehyd 305 lllgd....askakeeLgWkpkvsfeelvr 330
                                    +l+ d    ++ka+++Lg++p ++ ++ ++
  gi|121637037|ref|YP_977260.1| 313 RLYLDnyfsIAKARRDLGYEPLFTTQQALT 342
                                    998763333589999999999988888766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.4e-19   2.5e-16       1     137 [.      21     176 ..      21     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.4e-19
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.......--TCC CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal.......ggggk 73 
                                    G+ G vG  lv+ ll+rg h v+ + R p+ l+   a+++lev++gd+td++  a+a++g+d+++ ++       g  ++
  gi|121637037|ref|YP_977260.1|  21 GGAGFVGANLVTTLLDRG-HWVRSFDRAPSLLP---AHPQLEVLQGDITDADVCAAAVDGIDTIFHTAaiielmgG--AS 94 
                                    99***************5.************99...699***************************9999999642..33 PP

                                    ....HHHH..........HHHHHHHHHHCT--EEEEEEETTT...TSGCGCH..HHHHHHHCCHHHHHHHHHHHHH.HHH CS
                 NAD_binding_10  74 ....deeg..........aknivdaakeagvkRfvlvsaigv...gdevpge..fgewnkellkaylaakraaeel.lra 133
                                                      ++n++ a ++agv+Rfv+ s+  v   g++++g   + ++++++   y + k  ae+  l +
  gi|121637037|ref|YP_977260.1|  95 vtdeY--RqrsfavnvggTENLLHAGQRAGVQRFVYTSSNSVvmgGQNIAGGdeTLPYTDRFNDLYTETKVVAERFvLAQ 172
                                    34431..25668888999********************976633223333321133334444455556677788752455 PP

                                    SSSE CS
                 NAD_binding_10 134 sgld 137
                                     g+d
  gi|121637037|ref|YP_977260.1| 173 NGVD 176
                                    5555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.4   2.1e-13   3.7e-10      58     246 ..      53     221 ..      19     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.1e-13
                                    HTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.ST......TSSE.EHHHHHHHHHHHHHHHTSSS--.- CS
                  NAD_binding_4  58 laerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfde......pyke.llrvNveGtrevlelakklkklkv 130
                                    +  +++v++GD+++ ++          ++ +d i+h aA +++++      +y++  ++vNv Gt+++l   ++   +  
  gi|121637037|ref|YP_977260.1|  53 AHPQLEVLQGDITDADV------CAAAVDGIDTIFHTAAIIELMGgasvtdEYRQrSFAVNVGGTENLLHAGQRAGVQ-R 125
                                    45677778888877664......45567788888888888887764443335654599************88866555.* PP

                                    EEEEEE.GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
                  NAD_binding_4 131 llhvST.ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitge 209
                                    +++ S+ ++v g ++ +                ++++   + +++ Y+ +K++aE+ v +++  +g+ ++ +Rps i   
  gi|121637037|ref|YP_977260.1| 126 FVYTSSnSVVMGGQNIA--------------GGDETLPYTDRFNDLYTETKVVAERFVLAQNGVDGMLTCAIRPSGI--- 188
                                    ******99998888843..............577788899999*****************99999************... PP

                                    SSST---TTSHHHHHHHHHHHH-EEES-SB---TT-- CS
                  NAD_binding_4 210 sktGwingsdlgirgllgliakgvlpeilgdkeavld 246
                                        w ng+++++r l+ ++ kg+++ ++g+k+a+ld
  gi|121637037|ref|YP_977260.1| 189 ----WGNGDQTMFRKLFESVLKGHVKVLVGRKSARLD 221
                                    ....778888899999999999999999988888776 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.1e-15     2e-12       2     234 ..      16     274 ..      15     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.1e-15
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------HHH.. CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytavDk.. 66 
                                    ++lvtG+ G +G +L+  l  +g+ v +++r+             + d+tda+  a++++    d + ++AA  +     
  gi|121637037|ref|YP_977260.1|  16 RVLVTGGAGFVGANLVTTLLDRGHWVRSFDRApsllpahpqlevlQGDITDADVCAAAVDG--IDTIFHTAAIIELMGga 93 
                                    79**********************************************************9..677******99875411 PP

                                    ..HHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SS.....HHHHHHHHHHHHHHH CS
                  RmlD_sub_bind  67 ..aEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPln.....vYGrtKlaGEqavla 138
                                        + +++++avn+ ++e+l +a +++g++ +++ S+  V  G   ++ +  det P +     +Y +tK+  E+ vla
  gi|121637037|ref|YP_977260.1|  94 svTDEYRQRSFAVNVGGTENLLHAGQRAGVQrFVYTSSNSVVMGG--QNIAGGDETLPYTdrfndLYTETKVVAERFVLA 171
                                    1134448999*******************955*******998887..4457788888864333449*************9 PP

                                    ....H-SSEEEEEE-SEESSSSS-HHHHHHHHH.HH-SEEEEESS-.EE--EEHHHHHHHHHHHHHHCHH.GGG.-EEEE CS
                  RmlD_sub_bind 139 ....agkkalivRtswvygekgknfvktmlrla.kereelkvvaDq.lgsPTsardlAevllqllekaaeekel.agvyH 211
                                        +g  ++ +R s ++g+ ++ + +++++ + k + ++ v         +++++l +  + ++++ + + ++  + y 
  gi|121637037|ref|YP_977260.1| 172 qngvDGMLTCAIRPSGIWGNGDQTMFRKLFESVlKGHVKVLVGRKSaRLDNSYVHNLIHGFILAAAHLVPDGTApGQAYF 251
                                    554444567789********988888887777636666666655441345678888777766666666665555478888 PP

                                    ---BS-EEHHHHHHHHHHHHCHT CS
                  RmlD_sub_bind 212 lanegetswlefArailkeagad 234
                                    +  ++ ++ +efAr +l+++g++
  gi|121637037|ref|YP_977260.1| 252 INDAEPINMFEFARPVLEACGQR 274
                                    88888899999999999998865 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.4   2.2e-10     4e-07       1     133 [.      17     136 ..      17     169 .. 0.81
   2 ?   -1.6   0.0      0.66   1.2e+03     221     250 ..     246     274 ..     232     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.2e-10
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    vlvtG++G +G +lv+++l++  + ++ ++r+   l   + +l         +    ++ gd++d++ ++ a++  ++d+
  gi|121637037|ref|YP_977260.1|  17 VLVTGGAGFVGANLVTTLLDRG-HWVRSFDRAPSLLP-AHPQL---------E----VLQGDITDADVCAAAVD--GIDT 79 
                                    7899999999999999888865.56788887654433.23333.........2....2359*************..**** PP

                                    EEE------H....HHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS CS
                Polysacc_synt_2  81 vfhaAAlKhV....PlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvn 133
                                    +fh+AA+ ++     + +e+    +  Nv gten+++a ++agv+++v+ S+   v 
  gi|121637037|ref|YP_977260.1|  80 IFHTAAIIELmggaSVTDEYRQRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVM 136
                                    ******8775333378999999*****************************987764 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                                    -SS-EEEE--.-EEEHHHHHHHH....... CS
                Polysacc_synt_2 221 kggeifvldmGepvkivdlakalielsgle 250
                                     g   f+ d+ ep+++ + a+ ++e +g +
  gi|121637037|ref|YP_977260.1| 246 PGQAYFINDA-EPINMFEFARPVLEACGQR 274
                                    4556899999.**********999988854 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.9   1.1e-09   1.9e-06       1     144 [.      15     139 ..      15     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                                    SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                             KR   1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                    g +l+tGG+G +G  l+++l+++g        Rs        ++  +l     + ev++ D++d+d  +a+++ i+    
  gi|121637037|ref|YP_977260.1|  15 GRVLVTGGAGFVGANLVTTLLDRGHW-----VRS-------FDRAPSLLPAHPQLEVLQGDITDADVCAAAVDGID---- 78 
                                    6789*******************963.....466.......12345566778899**************9999887.... PP

                                    ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                             KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                        ++h+A +++    +++t+e  ++ +a  v G++nL ++ ++  +  fv++SS + ++g +
  gi|121637037|ref|YP_977260.1|  79 ---TIFHTAAIIELMGGASVTDEYRQRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVMGGQ 139
                                    ...8********************************************************9975 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   2.8e-10   5.1e-07       1     102 [.      17     131 ..      17     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.8e-10
                                    EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG..... CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy..... 75 
                                    +lv+G++G  G+ +v  ll++gh vr   R ++   a+       e+++gd+ d ++ ++a++g d++f + ++      
  gi|121637037|ref|YP_977260.1|  17 VLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLLPAH----PQLEVLQGDITDADVCAAAVDGIDTIFHTAAIIelmgg 92 
                                    79************************999988654433....235788*********************999988999** PP

                                    ............S-HHHHHHHHHHHHHHHS-SEEEEEE- CS
                           NmrA  76 ............skeiedgkklvdAakeaGvkhfiySsl 102
                                                  ++    +l +A  +aGv++f+y s 
  gi|121637037|ref|YP_977260.1|  93 asvtdeyrqrsfAVNVGGTENLLHAGQRAGVQRFVYTSS 131
                                    ***999998866666667789***************875 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   7.1e-07    0.0013       3     118 ..      17     117 ..      15     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.1e-07
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    vlvtG+++ +G +++ +l+ +G  v  +dr ++ l    ++      ++ ++q+D+td++ + a+v+ +       d + 
  gi|121637037|ref|YP_977260.1|  17 VLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLL---PAH-----PQLEVLQGDITDADVCAAAVDGI-------DTIF 81 
                                    8************************9999998876...333.....33779***********9999877.......8888 PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltra 118
                                    + A+i +    +++++e  +r+++vN+ g+ +l +a
  gi|121637037|ref|YP_977260.1|  82 HTAAIIELMGGASVTDEYRQRSFAVNVGGTENLLHA 117
                                    888887777778889999999999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2448.67
//
Query:       gi|121637038|ref|YP_977261.1|  [L=85]
Description: exodeoxyribonuclease VII small subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-15   57.0   0.4    1.8e-15   56.7   0.4    1.1  1  Exonuc_VII_S  Exonuclease VII small subunit


Domain annotation for each model (and alignments):
>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.4   9.9e-20   1.8e-15       1      50 [.      24      73 ..      24      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 9.9e-20
                   Exonuc_VII_S  1 FEealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkv 50
                                   +E+  +eL e+v+ LE+g l+L+ sl l+e+G++L+k+Ce+ L  a+q+v
  gi|121637038|ref|YP_977261.1| 24 YEACRDELMEVVRLLEQGGLDLDASLRLWERGEQLAKRCEEHLAGARQRV 73
                                   89999********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 612.53
//
Query:       gi|121637039|ref|YP_977262.1|  [L=415]
Description: exodeoxyribonuclease VII large subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-69  232.9   0.1    1.4e-60  205.4   0.2    2.1  2  Exonuc_VII_L     Exonuclease VII, large subunit
    3.4e-13   49.6   0.0    6.3e-13   48.7   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    0.00043   20.2   0.0    0.00089   19.2   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0052   16.9   0.1       0.79    9.9   0.1    2.5  2  Death            Death domain
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.087   12.9   0.0    1.6  1  Peptidase_S66    LD-carboxypeptidase N-terminal domain


Domain annotation for each model (and alignments):
>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.2     4e-64   1.4e-60       1     207 [.     128     336 ..     128     342 .. 0.96
   2 !   29.1   0.0     2e-10     7e-07     235     302 ..     328     405 ..     319     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 4e-64
                   Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvliiaR 80 
                                    lfd+  k+p+p lp+ ig++t + +aa rD+ ++++ r+p++++ + +++vQG +a+ +i++al+++++  ++Dv+++aR
  gi|121637039|ref|YP_977262.1| 128 LFDPRLKRPIPYLPNMIGLITGRASAAERDVTTVASARWPAARFAVRNVAVQGPNAVGQIVEALRELDRDPDVDVIVLAR 207
                                    79****************************************************************************** PP

                   Exonuc_VII_L  81 GGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleelerrlekai 160
                                    GGGS+eDL +F de+l+raiaa+++Pv+savGHE D  ++D+v dlra+TPt aA++vvpd a  ++ +++l+rr  +a+
  gi|121637039|ref|YP_977262.1| 208 GGGSVEDLLPFSDETLCRAIAACRTPVVSAVGHEPDNPLCDLVVDLRAATPTDAAKKVVPDTAAEQRLIDDLRRRSAQAL 287
                                    ******************************************************************************** PP

                   Exonuc_VII_L 161 krlleekkqrleklasrl..kspeellerkrqrldeleerleralkkql 207
                                    ++ ++++++ + +l+sr   ++p ++++ ++++++++++ l+r+l+  +
  gi|121637039|ref|YP_977262.1| 288 RNWVSREQRAVAQLRSRPvlADPMTMVSVRAEEVHRARSTLRRNLTLMV 336
                                    **************9887657******************9999776555 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 2e-10
                   Exonuc_VII_L 235 lkerle.lleekkerleeleeklealsplkvLkrGyaivrk.e........dgkvvtsakdlkkgdeleirladgevk 302
                                    l+++l+ ++++++er+ +l+++l++l+p ++L+rGyaiv++ +        + +v++s++d+ +g++l++r+adg ++
  gi|121637039|ref|YP_977262.1| 328 LRRNLTlMVAAETERIGHLAARLATLGPAATLARGYAIVQTvAqtgpeggsEPQVLRSVHDAPEGTKLRVRVADGALA 405
                                    333444679999***************************997545555554569*********************986 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   1.8e-16   6.3e-13       3      94 ..      12     104 ..      10     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.8e-16
                    tRNA_anti_2   3 VseltraikelleaelkkavwvrGeisnlk.rkasghvYftLkD..ekakisavifrsraaklkftledGmkVlvkgrls 79 
                                    V++++ ++   ++ +l +avwv+G++++++ r++ ++v++ L+D  +++++ +++ r  + +  ++l +G +V+v g++s
  gi|121637039|ref|YP_977262.1|  12 VRAVAIRVAGWID-KL-GAVWVEGQLAQITmRPDAKTVFMVLRDpaADMSLTVTCSRDLVLSAPVKLAEGVQVVVCGKPS 89 
                                    6666666766774.56.67**********9667799********9888999999**99998888**************** PP

                    tRNA_anti_2  80 vYeprGsyqlivedi 94 
                                    +Y+ rG+++l+ ++i
  gi|121637039|ref|YP_977262.1|  90 FYTGRGTFSLRLSEI 104
                                    ***********9998 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.5e-07   0.00089       1      74 [.      29     105 ..      17     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-07
                                    EEEEEEEEEEEEEEETTEEEEEEEETTE..EEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS.SEEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtg..riqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg.elelkveeie 74 
                                    V+v+G + +i +r  +k +f++lrD  +  +++v++ r+ + +   +l eG  v v G+++++ g+  ++l  +ei+
  gi|121637039|ref|YP_977262.1|  29 VWVEGQLAQITMRPDAKTVFMVLRDPAAdmSLTVTCSRDLVLSAPVKLAEGVQVVVCGKPSFYTGRgTFSLRLSEIR 105
                                    78888888888****************7225555555588888888888**************44446999998886 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.014        51      57      77 ..     179     198 ..     174     204 .. 0.81
   2 !    9.9   0.1   0.00022      0.79      36      66 ..     272     301 ..     267     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                                    HTTTCSHHHHHHHHHHTTHHH CS
                          Death  57 egenatvgtLleaLrklgrdd 77 
                                    +g+na vg+ +eaLr+l+rd 
  gi|121637039|ref|YP_977262.1| 179 QGPNA-VGQIVEALRELDRDP 198
                                    56776.9************96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                    HHSS.STHHHHHHHHHHHHHHHHTTTCSHHHH CS
                          Death  36 eken.nslrsqsyalLqlWedregenatvgtL 66 
                                    e++  ++lr +s + L++W++r  e+ +v++L
  gi|121637039|ref|YP_977262.1| 272 EQRLiDDLRRRSAQALRNWVSR--EQRAVAQL 301
                                    344489****************..78888777 PP

>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.087      54      91 ..     188     225 ..     177     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHC-TTECEEEES--SS-CHHCHHHH-HCCHH CS
                  Peptidase_S66  54 aadLnealadpeikaiicarGGygaarllpyldfdaik 91 
                                    +++L e+ +dp++++i+ arGG  +  llp+ d ++ +
  gi|121637039|ref|YP_977262.1| 188 VEALRELDRDPDVDVIVLARGGGSVEDLLPFSDETLCR 225
                                    57899999**********************99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2998.96
//
Query:       gi|121637040|ref|YP_977263.1|  [L=212]
Description: hypothetical protein BCG_1169c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1707.69
//
Query:       gi|121637041|ref|YP_977264.1|  [L=335]
Description: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-88  296.9   0.1    1.3e-88  296.7   0.1    1.0  1  LYTB      LytB protein


Domain annotation for each model (and alignments):
>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.7   0.1   7.1e-93   1.3e-88       1     263 [.      28     305 ..      28     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 296.7 bits;  conditional E-value: 7.1e-93
                                    EEE-TT-SS-HHHHHHHHHHHHHHCCC-S.EEECS-SSS-HHHHHHHHHCTEEEESSSST.....EEEE-TT---HHHHH CS
                           LYTB   1 illaksaGfCfGVerAieiaeealeekke.vyvlgeivHNeqvverLeekgvkfieelee.....vviirAhGvskevee 74 
                                    +lla+++G+C+GV+rA+e++e+al++++  vyv++eivHN++vv++L++ g+ f+ee+e+     +v+++AhGv++ v+ 
  gi|121637041|ref|YP_977264.1|  28 VLLAEPRGYCAGVDRAVETVERALQKHGPpVYVRHEIVHNRHVVDTLAKAGAVFVEETEQvpegaIVVFSAHGVAPTVHV 107
                                    689***********************999**************************88664334567************** PP

                                    HHHHTTEEEEE---HHHHHHHHHHHHHHHCT-EEEEES-TT-HHHHHHHCCT--TEEEESSCHHHHHG......CEEEEE CS
                           LYTB  75 elkekglevvDatCplVkkvqkevkklakegyeiviiGkkkHpEvegilgqaeekvvvveeseevekl......kvalvs 148
                                     ++e++l+v+DatCplV+kv++e++++a+++y+i++iG+++H+Ev+g++g+a+++v +v+  ++v+++      kv+++s
  gi|121637041|ref|YP_977264.1| 108 SASERNLQVIDATCPLVTKVHNEARRFARDDYDILLIGHEGHEEVVGTAGEAPDHVQLVDGVDAVDQVtvrdedKVVWLS 187
                                    ***********************************************************655557777889999****** PP

                                    -TTS-HHHHHHHHHHHHHHSTCEEE..C-S--CHHHHHHHHHHHHHGHSSEEEEES-TT-HHHHHHHHHHHHC.SCTEEE CS
                           LYTB 149 QTTlsveefeeivealkkklkelev..kdtiCkatqeRqeavkelakevdlvivvGgknSsNtkkLveiakek.nkktyl 225
                                    QTTlsv+e+ eiv  l++++++l+   +d+iC+atq+Rq avk++a e++lvivvG++nSsN+ +Lve+a  +  + ++l
  gi|121637041|ref|YP_977264.1| 188 QTTLSVDETMEIVGRLRRRFPKLQDppSDDICYATQNRQVAVKAMAPECELVIVVGSRNSSNSVRLVEVALGAgARAAHL 267
                                    ************************999********************************************996678899 PP

                                    ESSGGG--HHHHTT-SEEEEEE-TTS-HHHHHHHHHHH CS
                           LYTB 226 iesaeeldeewlegvkkvgitaGaStpeelieeviekl 263
                                    ++ a+++d++wl+gv++vg+t+GaS pe l++ v+e+l
  gi|121637041|ref|YP_977264.1| 268 VDWADDIDSAWLDGVTTVGVTSGASVPEVLVRGVLERL 305
                                    **********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2313.44
//
Query:       gi|121637042|ref|YP_977265.1|  [L=327]
Description: hypothetical protein BCG_1171c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   10.9  12.7       0.17   11.6   2.5    2.0  2  Yip1      Yip1 domain


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   9.8   7.9e-05       1.4      19     121 ..      22     133 ..       5     134 .. 0.78
   2 ?   11.6   2.5   9.7e-06      0.17      25      90 ..      84     152 ..      72     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 7.9e-05
                           Yip1  19 lrapdlallllalltlllgllas....lnlgqtlasg...............eevqgltlssllgaiiggylglllglll 79 
                                       p++a +l+a+++ + g+++                              ++v   ++s l++a++  +l+l+ ++  
  gi|121637042|ref|YP_977265.1|  22 PGVPWWAAILIAVTATAIGYAIDagsgH--------KaltlvftgcyiagcvGAVLAVRQSDLFTALVQPPLILFCAVPG 93 
                                    4456666666666666666666635542........033334556888889999999999******************** PP

                           Yip1  80 lalllhliakllggkgsfkqtlsvvgya...llPlilgaliaill 121
                                      +l+h      g+ g fk++l   gy+    +Pl+lg  +++ll
  gi|121637042|ref|YP_977265.1|  94 AYWLFHG-----GTIGKFKDLLINCGYSlieRFPLMLGTAAGVLL 133
                                    *******.....99999***********99999999999988775 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.7e-06
                           Yip1  25 allllalltlllgllaslnlgqtlasg...eevqgltlssllgaiiggylglllgllllalllhliakl 90 
                                    +l+l+++++ +++l+ ++++g++ +     +++   ++  +lg+++g +l++l+ ++l ++l++ ia+ 
  gi|121637042|ref|YP_977265.1|  84 PLILFCAVPGAYWLFHGGTIGKFKDLLincGYSLIERFPLMLGTAAGVLLIGLVRWYLGTALFDSIARK 152
                                    7899999999999999988877777778889999999999999********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1838.87
//
Query:       gi|121637043|ref|YP_977266.1|  [L=357]
Description: GTP-dependent nucleic acid-binding protein EngD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-39  133.3   0.1    4.3e-39  132.6   0.1    1.4  1  YchF-GTPase_C  Protein of unknown function (DUF933)
    1.2e-23   83.4   0.0    2.2e-23   82.5   0.0    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
    6.4e-09   35.5   0.0    1.2e-08   34.7   0.0    1.4  1  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.044   13.8   0.0        3.9    7.5   0.0    2.3  2  Dynamin_N      Dynamin family
      0.066   13.3   1.0       0.31   11.1   0.6    2.2  2  TGS            TGS domain
       0.19   12.3   0.0       0.57   10.7   0.0    1.8  2  AAA_18         AAA domain


Domain annotation for each model (and alignments):
>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6   0.1   1.4e-42   4.3e-39       1      84 []     273     356 ..     273     356 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 1.4e-42
                  YchF-GTPase_C   1 LitffTaGekevraWtikkgttapqaAgviHsDfekgFiraevikyedlvelgseaaakeagklrlegkdyvvqdgDiil 80 
                                    L+tf+TaG+ke+raWti++g tap+aAgviHsDfekgFi+ae+++y+dlv++gs+aaak+agk+r+egkdyv+ dgD+++
  gi|121637043|ref|YP_977266.1| 273 LQTFLTAGPKEARAWTIHQGDTAPKAAGVIHSDFEKGFIKAEIVSYDDLVAAGSMAAAKAAGKVRIEGKDYVMADGDVVE 352
                                    89****************************************************************************** PP

                  YchF-GTPase_C  81 fkfN 84 
                                    f+fN
  gi|121637043|ref|YP_977266.1| 353 FRFN 356
                                    ***9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   7.5e-27   2.2e-23       2      87 ..       5     116 ..       4     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 7.5e-27
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.................EEEEECGGCSSHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.................ielvDtpGliegaseek 64 
                                     +ivG pNvGKStL+nalt++++ ++++p++T+++neg v+l +++                 +++vD++Gli+gase+ 
  gi|121637043|ref|YP_977266.1|   5 LGIVGLPNVGKSTLFNALTRNNVVAANYPFATIEPNEGVVSLPDPRldklaelfgsqrvvpapVTFVDIAGLIKGASEGA 84 
                                    58**************************************95432355566666666677777***************** PP

                                    HHHHHHHHHHC.TSEEEEEEETT........T CS
                       MMR_HSR1  65 glgkaflalee.adlillvvdas........e 87 
                                    glg++fla+++ +d+i+ vv++         +
  gi|121637043|ref|YP_977266.1|  85 GLGNKFLAHIReCDAICQVVRVFvdddvthvT 116
                                    ********99889*******976644443331 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.9e-12   1.2e-08       4      46 ..       6      48 ..       3      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.9e-12
                                   EEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT CS
                         FeoB_N  4 alvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg 46
                                    +vG pnvGk+tlfnalt  +   +N+p  t+e +eg ++l +
  gi|121637043|ref|YP_977266.1|  6 GIVGLPNVGKSTLFNALTRNNVVAANYPFATIEPNEGVVSLPD 48
                                   689**********************************998655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0013       3.9       2      25 ..       6      29 ..       5      41 .. 0.82
   2 ?    3.9   0.0     0.017        50     101     138 ..      66     106 ..      49     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                                   EEEEBTTTTHHHHHHHHHTS--S- CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilp 25
                                    +vG  + GKS++ naL++ ++  
  gi|121637043|ref|YP_977266.1|  6 GIVGLPNVGKSTLFNALTRNNVVA 29
                                   58999999**********999865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.017
                                    -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEET CS
                      Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsa 138
                                      +t+vD  Gl++ + +     +    +i+++d+i  v+  
  gi|121637043|ref|YP_977266.1|  66 APVTFVDIAGLIKGASEGAglgNKFLAHIRECDAICQVVRV 106
                                    679***********999998888889999999999999865 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.3     1e+04       9      26 ..      60      77 ..      59      79 .. 0.76
   2 ?   11.1   0.6   0.00011      0.31      13      57 ..     289     352 ..     279     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                                   SEEEEETTB-HHHHHHHH CS
                            TGS  9 kvpdlprgatveDfAykI 26
                                   ++  +p   t +D+A  I
  gi|121637043|ref|YP_977266.1| 60 SQRVVPAPVTFVDIAGLI 77
                                   566688889999999776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                    EETTB-HHHHHHHHSTTHHHHEEEEEECS...................EEEETTSBB-SSEEEE CS
                            TGS  13 lprgatveDfAykIhrslakkfiyAlVnG...................qrvgldhvLedgdvve 57 
                                    +++g t+  +A  Ih+++ k fi A +                     ++ g d+v+ dgdvve
  gi|121637043|ref|YP_977266.1| 289 IHQGDTAPKAAGVIHSDFEKGFIKAEIVSyddlvaagsmaaakaagkvRIEGKDYVMADGDVVE 352
                                    7889999999999************9999999*************999999************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.57       2      22 ..       6      26 ..       5      60 .. 0.80
   2 ?   -2.4   0.1       2.2   6.6e+03      99     120 ..     132     153 ..     115     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                         AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                   ++ G p vGK+tl ++L + +
  gi|121637043|ref|YP_977266.1|  6 GIVGLPNVGKSTLFNALTRNN 26
                                   589**************8764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                         AAA_18  99 LtaspeelleRlekRgyeeaki 120
                                    L + + + leR   R ++ea++
  gi|121637043|ref|YP_977266.1| 132 LILADLQTLERATGRLEKEART 153
                                    6667777888999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2309.19
//
Query:       gi|121637044|ref|YP_977267.1|  [L=65]
Description: hypothetical protein BCG_1173 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-12   47.0   2.2    2.1e-12   46.7   2.2    1.1  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   2.2   1.2e-16   2.1e-12       1      42 [.       1      42 [.       1      47 [. 0.94

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-16
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------H CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkre 42
                                   Mrt++++DD+Lla+A +ltg+k+K+ + +++L++L++ ++++
  gi|121637044|ref|YP_977267.1|  1 MRTTVTVDDALLAKAAELTGVKEKSTLLREGLQTLVRVESAR 42
                                   9************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 411.66
//
Query:       gi|121637045|ref|YP_977268.1|  [L=124]
Description: hypothetical protein BCG_1174 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-08   34.3   0.0    3.2e-08   34.1   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.8e-12   3.2e-08       1     119 [.       2     111 ..       2     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.8e-12
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiae 79 
                                    i++DTsv+i++lr  + +  +++ll + +e    +lv++El+ +  +       ++++v++ll  l ++ ++  d+ +++
  gi|121637045|ref|YP_977268.1|   2 ILVDTSVWIEHLRAADAR--LVELLGD-DEAGCHPLVIEELALGSIK-------QRDVVLDLLAnLYQFPVVTHDEVLRL 71 
                                    79**********888855..6888876.*******************.......89999999999*************** PP

                                    HHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  80 eaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                      ++  + +gl++ Da ++      g + ++t+D++++ +
  gi|121637045|ref|YP_977268.1|  72 VGRRRLWGRGLGAVDANLLGSVALVGGARLWTRDKRLKAA 111
                                    ****************988888777777888*****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 995.44
//
Query:       gi|121637046|ref|YP_977269.1|  [L=232]
Description: hypothetical protein BCG_1175 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1713.93
//
Query:       gi|121637047|ref|YP_977270.1|  [L=61]
Description: hypothetical protein BCG_1176 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 503.04
//
Query:       gi|121637048|ref|YP_977271.1|  [L=91]
Description: hypothetical protein BCG_1177c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 665.88
//
Query:       gi|121637049|ref|YP_977272.1|  [L=107]
Description: hypothetical protein BCG_1178 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-17   61.5   0.6    7.4e-17   61.2   0.6    1.1  1  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.6   4.1e-21   7.4e-17       1      77 [.       1      76 [.       1      77 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 4.1e-21
                                   CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHHH CS
                            ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaahe 77
                                   m+++++++++kp+  e + d++a++  ++ ++e+G+l +e+ rs +dp e+v++e +++ +a   h++s+hf++a++
  gi|121637049|ref|YP_977272.1|  1 MIFIVVKFETKPEWTERWPDLVASFTAAT-RAEEGNLWFEWSRSLDDPAEYVLVESFRDGEAGGVHVNSDHFRQAMR 76
                                   99*************************99.6*******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 925.71
//
Query:       gi|121637050|ref|YP_977273.1|  [L=286]
Description: hypothetical protein BCG_1179c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0058   16.7   0.0      0.099   12.7   0.0    2.3  2  Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX


Domain annotation for each model (and alignments):
>> Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.5e-06     0.099       2      96 ..      69     180 ..      68     186 .. 0.62
   2 ?    1.0   0.0     0.022     4e+02     108     125 ..     232     248 ..     227     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-06
                  Peptidase_C92   2 lekGdiifqtsraslseainpatasefkHvgivvgeegderlvveaaake............gvrvtpLseflar..... 64 
                                    +++Gd+ + + r++  +ai++ t+   +Hvg+ v   +  +l+ +a                gv+++  ++ +++     
  gi|121637050|ref|YP_977273.1|  69 TRTGDLWLFRGRSRPDRAIQTLTNAPVNHVGMTVAIDDLPPLIWHAELGDklldvwtgtnhrGVQLNDARQVVQQwagry 148
                                    579******************************99888555555553222333333333333555544444444444445 PP

                  Peptidase_C92  65 rssiavyrlkealtaeqrqkaaeaalrrlgkp 96 
                                    r+++ ++ l+  ++++q  k+     r+ g+p
  gi|121637050|ref|YP_977273.1| 149 RQRCWLRQLTPHANRDQEDKLLRVIARMNGTP 180
                                    55555555555555555555555555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.022
                  Peptidase_C92 108 lYCsklVakaykealgik 125
                                     YC + Va  y e++g+ 
  gi|121637050|ref|YP_977273.1| 232 AYCAETVAITY-EEMGLL 248
                                    6**********.666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2091.11
//
Query:       gi|121637051|ref|YP_977274.1|  [L=49]
Description: hypothetical protein BCG_1180c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 360.39
//
Query:       gi|121637052|ref|YP_977275.1|  [L=164]
Description: hypothetical protein BCG_1181c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-10   38.5   0.0    1.2e-09   38.1   0.0    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   6.6e-14   1.2e-09       7     110 ..      53     150 ..      48     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.6e-14
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                     +v ilF+dI+++tal ++      vkl+  + + + el+++  +  v   Gd +m+++          ++++++++d+ 
  gi|121637052|ref|YP_977275.1|  53 GRVVILFSDIEESTALDERIGDRTWVKLIGAHDKLVHELVRRWSGHMVTSQGDGFMIAFARA-------EQAVRCGIDIQ 125
                                    6899****************99***********************************98665.......78888899999 PP

                  Guanylate_cyc  87 ealeevaves.keglkvrvGihtGp 110
                                    +al++ a+++ ++g++vr+G   G 
  gi|121637052|ref|YP_977275.1| 126 DALRNSAKRKrNQGIRVRIGTTWGA 150
                                    99955555554899******98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1275.15
//
Query:       gi|121637053|ref|YP_977276.1|  [L=466]
Description: glucose-6-phosphate 1-dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-86  290.3   0.0    1.8e-86  289.9   0.0    1.1  1  G6PD_C    Glucose-6-phosphate dehydrogenase, C-terminal domai
    2.7e-41  142.1   0.0    4.8e-41  141.3   0.0    1.4  1  G6PD_N    Glucose-6-phosphate dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> G6PD_C  Glucose-6-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.9   0.0     2e-90   1.8e-86       2     285 ..     183     452 ..     182     457 .. 0.94

  Alignments for each domain:
  == domain 1  score: 289.9 bits;  conditional E-value: 2e-90
                                    HHHHS-STTSTTSSTTTEEEEEEEEEESS--TTTHHHHTTTHHHHHTTTTHHHHHHHHHH----SSSSHHHHHHHHHHHH CS
                         G6PD_C   2 vlRfaNalfeplwnrnyidhvqitvketlgvegrggYydeaGalrDvvqnHllqllalvamepPasldaedirdekvkvL 81 
                                     lRfaN+ + +lw+rn+i++++it++e++gve+rg++yd +GalrDvvqnHllq+lalv+mepP+  +a+d++d+k++v+
  gi|121637053|ref|YP_977276.1| 183 YLRFANQALAELWDRNSISEIHITMAEDFGVEDRGKFYDAVGALRDVVQNHLLQVLALVTMEPPVGSSADDLNDKKAEVF 262
                                    59****************************************************************************** PP

                                    TTB----G...GG.EEEEEE.....E--TGS-STTSTTS-TT----SEEEEEEEB-STTTTT-EEEEEEESSBSS-EEEE CS
                         G6PD_C  82 kslrplkleevekkvvrGqYaagavkgkevkgYreeegvakdSkteTfvalkleidnerwagVPfylrtGKrLnekktei 161
                                    ++++pl++   + ++vrGqY           gY+e  gva+dS teT+val+ eidn+rwagVP+++r+GK+L+ k+te+
  gi|121637053|ref|YP_977276.1| 263 RAMAPLDP---D-RCVRGQY----------LGYTEVAGVASDSATETYVALRTEIDNWRWAGVPIFVRAGKELPAKVTEV 328
                                    *******9...4.59*****..........9************************************************* PP

                                    EEEE---SS-SS..---....--EEEEEEESS-EEEEEEEEE-SSSE.....EEEEEEHHHHTT.---HHHHHHHHHHHT CS
                         G6PD_C 162 riqfkkvpsdlf..kkke...rneLviriqpdeaislklnakkpgleleleeveldlsykerfk.lpeaYerLlldvlkg 235
                                    r+ +++vp   f  + ++   +n++v+ri+pd +++l+++a +  +    ++++ld s++       + YerLl+  l g
  gi|121637053|ref|YP_977276.1| 329 RLFLRRVPALAFlpN-RRpaePNQIVLRIDPDPGMRLQISAHTDDSW---RDIHLDSSFAVDLGePIRPYERLLYAGLVG 404
                                    ************752.22578*******************9998774...8999***99977776778************ PP

                                    -GTTSB-HHHHHHHHHHHHHHHHHHHH---EEEETTSSS-HHHHHHHHHH CS
                         G6PD_C 236 dqtlFvrsdeveaaWkivdpileaweeeklekYeagsrgPeeadellekd 285
                                    d++lF+r+d++e++W+iv+p+l++    +++ Y+ gs+gPe+a++ll+ +
  gi|121637053|ref|YP_977276.1| 405 DHQLFAREDSIEQTWRIVQPLLDNP--GEIHRYDRGSWGPEAAQSLLRGH 452
                                    *************************..4589***************9876 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   0.0   5.4e-45   4.8e-41       1     175 [.      13     178 ..      13     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 5.4e-45
                         G6PD_N   1 vifGasGdLakrkllPaLyelaregllpeevrivgvarsklsdeefrekvkealkkekekeeldeekleeflkrleyvsg 80 
                                    vifG +GdLa++ ++ aLy+l r++ll  ++ i+gva +++s  ++ ++++e++    ++e++d++++++++ rl+y++g
  gi|121637053|ref|YP_977276.1|  13 VIFGITGDLARKMTFRALYRLERHQLL--DCPILGVASDDMSVGQLVKWARESIG---RTEKIDDAVFDRLAGRLSYLHG 87 
                                    8**************************..789**********************4...455689**************** PP

                         G6PD_N  81 dleeeeeyekLkekleeleanrlfYlavppslfeevaeklkkaglakeeewkrvvvEKPfGkdlesarelneelkkvfke 160
                                    d+++++ y++L+e + +   + l+Yl +pp+lf++++e+l++ +l +    +rv vEKPfG+dl+sa eln++l++v+ e
  gi|121637053|ref|YP_977276.1|  88 DVTDSQLYDSLAELIGS-ACRPLYYLEMPPALFAPIVENLANVRLLE---RARVAVEKPFGHDLASALELNARLRAVLGE 163
                                    ***************99.8899*********************9996...79**************************** PP

                         G6PD_N 161 eqiyrIDhYLGketv 175
                                    +qi r+Dh+LGk+ v
  gi|121637053|ref|YP_977276.1| 164 DQILRVDHFLGKQPV 178
                                    ************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3143.97
//
Query:       gi|121637054|ref|YP_977277.1|  [L=340]
Description: 6-phosphogluconate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-39  135.3   0.0    2.9e-39  134.8   0.0    1.2  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.7e-21   76.2   1.0    1.3e-09   37.8   0.4    3.1  3  6PGD             6-phosphogluconate dehydrogenase, C-terminal
      4e-06   27.3   0.1    8.6e-06   26.2   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.6e-05   23.2   0.0    5.2e-05   22.7   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    9.7e-05   22.6   0.1    0.00032   20.9   0.0    1.8  2  TrkA_N           TrkA-N domain
    0.00092   19.1   0.1     0.0013   18.6   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0061   17.4   0.0      0.012   16.5   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.021   14.4   0.0    1.5  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.03   14.4   0.0       0.11   12.5   0.0    1.9  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.041   14.1   0.1       0.35   11.1   0.1    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.049   13.9   0.1       0.12   12.6   0.1    1.7  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
      0.063   13.1   0.1       0.12   12.2   0.1    1.5  1  Rossmann-like    Rossmann-like domain
       0.12   11.3   0.0       0.19   10.7   0.0    1.3  1  PDH              Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   2.1e-42   2.9e-39       1     152 [.       2     156 ..       2     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 2.1e-42
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHSH CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.akaaesieelvasl...dvvitmvkagkavdeviegl 76 
                                    ++g+iGlG MG+n++++l+k g++ +vy++++++v++++ e   ++++s++el ++l   +vv++mv+ag+ + +vie+l
  gi|121637054|ref|YP_977277.1|   2 QLGMIGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKAMAGEDrTTGVASLRELSQRLsapRVVWVMVPAGNITTAVIEEL 81 
                                    58*************************************99669999******9999999******************** PP

                                    CCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEE CS
                  NAD_binding_2  77 lealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigak 152
                                    +++l++gdi+idg+++ ++d  + +k l +kg+++ld++ SGG++g e+G   +m+GG+ +af+r++p++ +++  
  gi|121637054|ref|YP_977277.1|  82 ANTLEAGDIVIDGGNTYYRDDLRHEKLLFKKGIHLLDCGTSGGVWGRERGY-CLMIGGDGDAFARAEPIFATVAPG 156
                                    ***************************************************.*******************99975 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.4   9.8e-13   1.3e-09       1      29 [.     186     214 ..     186     223 .. 0.94
   2 !   14.4   0.0   1.4e-05     0.019     169     208 ..     235     274 ..     232     280 .. 0.90
   3 !   21.0   0.0   1.3e-07   0.00018      82     118 ..     282     318 ..     277     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 9.8e-13
                           6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkv 29 
                                    Gh+VKmvHNGieyg+m  +aE  ++l+++
  gi|121637054|ref|YP_977277.1| 186 GHFVKMVHNGIEYGMMASLAEGLNILRNA 214
                                    9*************************985 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.4e-05
                           6PGD 169 eygwnlnlaeiariWrgGCiIrakfldkikeafeknpele 208
                                     y++++++ e+a++Wr G++I + +ld  + a++++p+l+
  gi|121637054|ref|YP_977277.1| 235 CYQYDFDIPEVAEVWRRGSVIGSWLLDLTAIALRESPDLA 274
                                    589************************9999999988876 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 1.3e-07
                           6PGD  82 qkGTgkwtvqealelgvpvptiaeavfaRllSslkee 118
                                      G g+wt+++a++ gvp+p++++a+++R++S + ++
  gi|121637054|ref|YP_977277.1| 282 DSGEGRWTAIAAIDEGVPAPVLTTALQSRFASRDLDD 318
                                    5799****************************87654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.3e-09   8.6e-06       2      94 ..       3      94 ..       2      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.3e-09
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHHH-SEEEE-S-HHHHH.HHHH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdneeaaeeadvvvlavkpedve.evls 79
                                   +g iG G+mg+ ++++l++ g   h+ vv  + +p+ ++++a e     v    ++ ++ ++   vv + v+  +++ +v++
  gi|121637054|ref|YP_977277.1|  3 LGMIGLGRMGANIVRRLAKGG---HDCVVY-DHDPDAVKAMAGEDRttgVASL-RELSQRLSAPRVVWVMVPAGNITtAVIE 79
                                   799******************...****55.***********77764332222.35666667899*******9887527899 PP

                                   HCGHHHHTTSEEEEE CS
                  F420_oxidored 80 elakdalkgklvisv 94
                                   ela+ + +g +vi+ 
  gi|121637054|ref|YP_977277.1| 80 ELANTLEAGDIVIDG 94
                                   999**********95 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.8e-08   5.2e-05      38     111 ..       2      80 ..       1      95 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH....CHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSH CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee....eeeelgv.elvsleellaesDivslhlpltpetrhlina 111
                                    ++G+iGlGr+G ++ +rl++ g + ++yd+ +++ +    e++++gv +l +l + l+   +v +++p+ + t+ +i++
  gi|121637054|ref|YP_977277.1|   2 QLGMIGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKamagEDRTTGVaSLRELSQRLSAPRVVWVMVPAGNITTAVIEE 80 
                                    79**************************99999877777777777775677999999999*********9999998865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.3e-07   0.00032       4      41 ..       6      43 ..       5      78 .. 0.86
   2 ?   -1.7   0.0       2.4   3.4e+03       6      19 ..      70      83 ..      65     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                                   ES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                         TrkA_N  4 iGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41
                                   iGlGr+G +++++L +gg+d+vv d+d+++v+ ++ e 
  gi|121637054|ref|YP_977277.1|  6 IGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKAMAGED 43
                                   8***************6668************998776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                                   -SHHHHHHHHHHHH CS
                         TrkA_N  6 lGrvGrslaeeLse 19
                                   +G+++++++eeL +
  gi|121637054|ref|YP_977277.1| 70 AGNITTAVIEELAN 83
                                   78999999999987 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   9.5e-07    0.0013       2      40 ..       3      41 ..       2      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.5e-07
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                   ++ iG G mGa i   +a+ g++ v++d +++a+++ + 
  gi|121637054|ref|YP_977277.1|  3 LGMIGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKAMAG 41
                                   689******************************998655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.4e-06     0.012       2      75 ..       2      73 ..       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT.TESEEEE-S-GGGH CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp.eidavivatpngth 75
                                   + ++iG+G++g + +r l +   +++ v ++d d+ + +a+a + +   +++l+el++   ++++v+v++p+g  
  gi|121637054|ref|YP_977277.1|  2 QLGMIGLGRMGANIVRRLAKG--GHDCV-VYDHDPDAVKAMAGEDRTTGVASLRELSQRLsAPRVVWVMVPAGNI 73
                                   679************888777..55555.89**********888888888888888887679*********9653 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.021       1      46 [.       1      46 [.       1      63 [. 0.85
   2 ?   -3.8   0.0         6   8.3e+03     101     118 ..      75      92 ..      73      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi 46
                                   m++ +iGlG +G+     la+ gh+ ++ D d  +v+++  ++   
  gi|121637054|ref|YP_977277.1|  1 MQLGMIGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKAMAGEDRTT 46
                                   67899********************************998776655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6
                                    HHHHHHHHHHHHCEEEEE CS
                 UDPG_MGDP_dh_N 101 esaarsiaealkkgkvvv 118
                                    +++++++a++l+ g++v+
  gi|121637054|ref|YP_977277.1|  75 TAVIEELANTLEAGDIVI 92 
                                    578999999999999997 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.3e-05      0.11      16      81 ..       4      66 ..       1      93 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                                   EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                   Shikimate_DH 16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                                    +iG G+m+  +++ L++ g +  vv   + + +k++a e +++   + +l el+++l++  vv +
  gi|121637054|ref|YP_977277.1|  4 GMIGLGRMGANIVRRLAKGGHD-CVVYDHDPDAVKAMAGEDRTT--GVASLRELSQRLSAPRVVWV 66
                                   68**************976666.9**************999666..999*******9998888765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.35       2      98 ..       4     118 ..       3     132 .. 0.81
   2 ?   -2.9   0.0       5.6   7.7e+03      43      67 ..     305     328 ..     280     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                    EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....................TTTCEEEEE--TTTHHH CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka....................lgvrfeaialdaenyea 61 
                                     +iG G++G  +++ la+ ++     +v d + + ++a+a +                       v + a  ++ + +e+
  gi|121637054|ref|YP_977277.1|   4 GMIGLGRMGANIVRRLAKGGHD---CVVYDHDPDAVKAMAGEDrttgvaslrelsqrlsaprvVWVMVPAGNITTAVIEE 80 
                                    69****************9985...9*********999998779999999999999995555544455555666666777 PP

                                    HHHHHHTTSSEEEE-SSGG..GHHHHHHHHHHHT-EEEE CS
                Sacchrp_dh_NADP  62 vLaallkegdlvvnlsppi..ssldvlkaCietgvhyvd 98 
                                     La  l+ gd+v++    +   +l   k+  ++g+h +d
  gi|121637054|ref|YP_977277.1|  81 -LANTLEAGDIVIDGGNTYyrDDLRHEKLLFKKGIHLLD 118
                                    .99999999999999877766777888999999999998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                    HHTTTCEEEEE--TTTHHHHHHHHH CS
                Sacchrp_dh_NADP  43 kalgvrfeaialdaenyeavLaall 67 
                                    +al++rf ++ ld    +a L+a+ 
  gi|121637054|ref|YP_977277.1| 305 TALQSRFASRDLDDFANKA-LSAMR 328
                                    3367777777777777777.77765 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.8e-05      0.12       1      33 [.     184     216 ..     184     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                 NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGl 33 
                                    G+G+ vK+v+n +    +a ++E+l +++ a++
  gi|121637054|ref|YP_977277.1| 184 GSGHFVKMVHNGIEYGMMASLAEGLNILRNADV 216
                                    9**************************999988 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     9e-05      0.12      12     102 ..       2      93 ..       1      98 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                  Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasrera.errlPdvpvl.evedvaaraellllavPdaelp.glvkgl 88 
                                    ++G+i+ Gr+G+ +   l++ gh  v      +a +  a e r  +v+ l e+ +      ++ + vP  +++  ++++l
  gi|121637054|ref|YP_977277.1|   2 QLGMIGLGRMGANIVRRLAKGGHDCVVYDHDPDAVKAMAgEDRTTGVASLrELSQRLSAPRVVWVMVPAGNITtAVIEEL 81 
                                    68***********************9999999999998846788888776357777788889999****9997257899* PP

                  Rossmann-like  89 aatgavraGtivah 102
                                    a+t  + aG iv+ 
  gi|121637054|ref|YP_977277.1|  82 ANT--LEAGDIVID 93 
                                    *99..999*99975 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.19       3      79 ..      17      95 ..      15     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                   HHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-.GGGGCCGSEEEE-S-G.GGHHHHHHHHHHHS-TT-EEEE-- CS
                            PDH  3 ralrrkgfkvtvigydideekaeaalelglvdeatdd.ieavkeadivvlavPv.evilevlkelaphlkedalitDvg 79
                                   r l + g +  v+  d d+ ka a++++  + +   +  + ++   +v + vP  + +  v++ela++l+ + +++D g
  gi|121637054|ref|YP_977277.1| 17 RRLAKGGHDCVVYDHDPDAVKAMAGEDRTTGVASLRElSQRLSAPRVVWVMVPAgNITTAVIEELANTLEAGDIVIDGG 95
                                   667788999999999********9999888888888734556666********9456789*****************77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2060.93
//
Query:       gi|121637055|ref|YP_977278.1|  [L=302]
Description: peroxidase bpoB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-14   54.0   4.2    4.2e-14   53.7   4.2    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    4.7e-14   52.6   0.0    4.2e-13   49.5   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    8.1e-13   48.2   0.1    1.3e-09   37.6   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.054   13.6   0.0    1.9  2  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   4.2   9.3e-18   4.2e-14       1     218 [.      52     291 ..      52     293 .. 0.66

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.3e-18
                                    EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS...--HHH.CHHHHHHHCCTT..TTSEEEEEETCH CS
                  Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdppp...ldled.ladlaalldelaagggpvvlvGHSlG 75 
                                    +l+lHG+g ++ sW  ++++  l+ +g+hv+a+D +G G+sd++p   +++e    d++++++++   g++vv+v  S+G
  gi|121637055|ref|YP_977278.1|  52 ILMLHGGGQNRFSWKnTGQI--LADEGHHVVALDTRGPGDSDRAPgadYAVETpTTDVLHVVEAI---GRRVVVVEASMG 126
                                    79************658899..55666777*********7766665324444445899*******...8*********** PP

                                    HHHHHHHHHCC.....EE.EEES-.....----TTT...S----TTHHHHHHTT-C....CCCHCCH..S-HS.CCCCHH CS
                  Abhydrolase_6  76 Galalaaapla...lvvg.vlldppp...talpagl...laaalelllallallrl....lawlsre..plpr.lflade 138
                                    G+ + ++a  a    v g vl+d  p        g+   +++ l  ++++++l+ +    +++l  +  p+++ ++ +++
  gi|121637055|ref|YP_977278.1| 127 GLTGILVAERAgpqTVNGlVLVDVVPryeK---EGNariRDFMLGNIDGFGSLEEAadavAEYLPHRdkPRSPeGLKRNL 203
                                    *97777555556765577799999773332...33333344444444444443333333434443334544444666655 PP

                                    H.CCCCHCHCCCGHHHHCCHHC.HTTCCHHTT-TTGC....EEE.C.TT-CHHHHCHHCCCH.STTEEETCE...SSS-H CS
                  Abhydrolase_6 139 d.adaawrarlarlaallaglg.llpaaawadlpvpl....lvl.g.geDplvprllerlla.qagarlpvvlpgaGHlp 209
                                       d +w + ++++  +++g + +l+ ++++++ + l    l++ g  +D +  + ++++la ++ a++ v+l +aG   
  gi|121637055|ref|YP_977278.1| 204 RlRDGRWHWHWDPAMMTAPGHDpQLRTENFERAAMGLtipvLLIrGkLSDVVSSDGARDFLAkVPNAEF-VELSNAGRTA 282
                                    544799999999998777755533344444444444444437777745555666779999999999999.*******866 PP

                                    HHHSHHHHH CS
                  Abhydrolase_6 210 hleepdeva 218
                                      +++d++ 
  gi|121637055|ref|YP_977278.1| 283 AGDDNDAFT 291
                                    666777765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   9.3e-17   4.2e-13       1     106 [.      50     150 ..      50     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 9.3e-17
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p++++lhG++ +  +w +   ++ La++g++v++lD rG+g S++ap     dy   +   d+  +++a g + + +v  
  gi|121637055|ref|YP_977278.1|  50 PTILMLHGGGQNRFSWKN--TGQILADEGHHVVALDTRGPGDSDRAPG---ADYAVETPTTDVLHVVEAIGRRVV-VVEA 123
                                    789***************..9999************************...9******************97655.9999 PP

                                    THHHHHHHHHHHHH.GGGEEEEEEESE CS
                  Abhydrolase_1  81 SmGGmialayaaey.perVkalvllga 106
                                    SmGG+++  +a+++ p+ V++lvl++ 
  gi|121637055|ref|YP_977278.1| 124 SMGGLTGILVAERAgPQTVNGLVLVDV 150
                                    *************************98 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1     3e-13   1.3e-09       4     107 ..      49     148 ..      46     167 .. 0.92
   2 !    8.6   0.0   0.00022      0.98     180     220 ..     230     270 ..     217     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3e-13
                    Hydrolase_4   4 kavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                    + +++++HG ++     +++++ La++G +v+alD rG G s+ + g    +++ ++D+  +ve++      ++++++  
  gi|121637055|ref|YP_977278.1|  49 RPTILMLHGGGQNRFSWKNTGQILADEGHHVVALDTRGPGDSDRAPGADYAVETPTTDVLHVVEAIG-----RRVVVVEA 123
                                    789********************************************999*********99999888.....7899**** PP

                    Hydrolase_4  84 SmGGliallyl.lrypdkvaglils 107
                                    SmGGl+ +l++    p+ v+gl+l+
  gi|121637055|ref|YP_977278.1| 124 SMGGLTGILVAeRAGPQTVNGLVLV 148
                                    ***********666677899***97 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00022
                    Hydrolase_4 180 mkrleeraakitlPllllhGeaDkvvdpeasrelyerlgsk 220
                                    +++ e+ a  +t+P+ll+ G+   vv+ +++r+++++++ +
  gi|121637055|ref|YP_977278.1| 230 TENFERAAMGLTIPVLLIRGKLSDVVSSDGARDFLAKVPNA 270
                                    566778888899*************************9964 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.2   9.9e+03      48      71 ..     102     125 ..     100     143 .. 0.65
   2 ?   13.6   0.0   1.2e-05     0.054      28      92 ..     234     299 ..     211     302 .] 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.2
                  Abhydrolase_4  48 TPyegakklakalggavlvtvege 71 
                                    TP+    ++ +a+g+ v+v++ + 
  gi|121637055|ref|YP_977278.1| 102 TPTTDVLHVVEAIGRRVVVVEASM 125
                                    677777777777777555555444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                  Abhydrolase_4  28 estakg.aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                    e  a g ++pvLl+ ++   ++   ga+ +  + ++a+ v   ++G +a  + n++  + v ++++
  gi|121637055|ref|YP_977278.1| 234 ERAAMGlTIPVLLIRGKLSDVVSSDGARDFLAKVPNAEFVELSNAGRTAAGDDNDAFTDVVVDFVR 299
                                    333334579****************************************99**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2098.48
//
Query:       gi|121637056|ref|YP_977279.1|  [L=316]
Description: epoxide hydrolase ephC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-16   62.0  18.9    1.5e-16   61.7  18.9    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.5e-16   58.4   0.3    2.4e-13   50.3   0.2    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    8.6e-08   31.7   0.2    7.4e-07   28.7   0.2    1.9  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7  18.9   2.6e-20   1.5e-16       2     219 ..      45     306 ..      44     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.6e-20
                                    EEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTS.TS-GGCS--HHHCHHH.HHHHCCTT...TTSE.EEEEETCHH CS
                  Abhydrolase_6   2 lllHGagssassWlvapLaallaag.vhvlapDlpGh.Grsdpppldledladl.aalldelaa.gggpv.vlvGHSlGG 76 
                                    l+lHG++ +a++W+   +a++la+  +hv+ap  +G+  +s p++ ++    +l +++l+   a gg +  v++GH++G+
  gi|121637056|ref|YP_977279.1|  45 LCLHGFPDTAYGWR--KVAPRLAESgWHVVAPFMRGYaPSSIPADGSYHV-GALmHDALRVRSAaGGTERdVIIGHDWGA 121
                                    89***********8..9988888888999********4356666666644.33333333333224455556********* PP

                                    HHHHHHHHCC....EE.EEES-.........----TTT................S----TTHHHHHHTT-CCCCHCCH.. CS
                  Abhydrolase_6  77 alalaaapla..lvvg.vlldppp.......talpagl................laaalelllallallrllawlsre.. 128
                                    + a+ +a+ +  + ++ v+++ pp       +                      +++++ +++ ++ ++r++ w++    
  gi|121637056|ref|YP_977279.1| 122 IAATGLAAMPdsPFAKaVIMSVPPsaafrplG-----RvpergrllrelphqllRSWYILYFQLPWLPERSASWVVPLlw 196
                                    *9999666668944556777777766554331.....2344534433333333333333333333334444444422243 PP

                                    .S-HSCCCCHHH......C..........CCCHCHCCCGHHHHCCHHCHTT.CCHHTT-TTGCEEECTT-C.....HHHH CS
                  Abhydrolase_6 129 .plprlfladed......a..........daawrarlarlaallaglgllp.aaawadlpvpllvlggeDp.....lvpr 185
                                       +++++a+ed      a            ++ra+ +  +a +++ +l++ +++ + lpv++ + +g D+     +  +
  gi|121637056|ref|YP_977279.1| 197 rRWSPGYHAEEDlrhvdaAigtpegrraaLGPYRATMRNTRAPADYADLNRlWTEAPKLPVLY-L-HGHDDgcatsAFTH 274
                                    323349999999776554133333442233333333333333333333333255555555555.5.46666577666668 PP

                                    CHHCCCHSTTEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 186 llerllaqagarlpvvlpgaGHlphleepdevae 219
                                    + +r l  ag ++  v+++aGH+++le+pd++ae
  gi|121637056|ref|YP_977279.1| 275 WTARVLP-AGSEV-AVVEHAGHFLQLEQPDKIAE 306
                                    8888888.99999.******************98 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.2     4e-17   2.4e-13       4     110 ..      45     146 ..      42     161 .. 0.92
   2 !    6.4   0.0     0.001       6.1     212     256 ..     254     300 ..     193     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4e-17
                                    EEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEE.EEEETH CS
                  Abhydrolase_1   4 vilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddklt.lvGhSm 82 
                                    ++lhG+p++++ w++  +ap La++g++v+++ +rG++ Ss + +     y+  ++  d  r++ a g  +   ++Gh++
  gi|121637056|ref|YP_977279.1|  45 LCLHGFPDTAYGWRK--VAPRLAESGWHVVAPFMRGYAPSSIPAD---GSYHVGALMHDALRVRSAAGGTERDvIIGHDW 119
                                    89*************..****************************...99*************99999999998****** PP

                                    HHHHHHHHHHHHGGGEEEEEEESECSSC CS
                  Abhydrolase_1  83 GGmialayaaeyperVkalvllgaidpa 110
                                    G   a+ +aa+ +++ ++ v ++  +p+
  gi|121637056|ref|YP_977279.1| 120 GAIAATGLAAMPDSPFAKAVIMSV-PPS 146
                                    ********************9999.333 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                                    S.EEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 212 a.ptlvisgtsDplvpp.kaledlaqllpkkrlvvisdagHlafleg 256
                                    + p+l+++g +D++++     +  + l  ++++ v+++agH+++le 
  gi|121637056|ref|YP_977279.1| 254 KlPVLYLHGHDDGCATSaFTHWTARVLPAGSEVAVVEHAGHFLQLEQ 300
                                    23*************9777777777666669*************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   1.2e-10   7.4e-07       8     238 ..      45     300 ..      40     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.2e-10
                    Hydrolase_4   8 vlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    + +HG+ +++    ++a +La+ G++v+a   rG+  s  ++ g   ++  ++ D+  + +++    ++++ +++Gh +G
  gi|121637056|ref|YP_977279.1|  45 LCLHGFPDTAYGWRKVAPRLAESGWHVVAPFMRGYAPSSiPADG-SYHVGALMHDALRVRSAAG---GTERDVIIGHDWG 120
                                    578***********************************977777.8889999999977744443...444668******* PP

                    Hydrolase_4  87 Gliallyllrypdkva.glilsaPalkikaklk.appllklllkllgkllpklqv.....................snnl 143
                                    ++ a+ ++++  + +a ++i+s P  +   +l  +p+  +ll++l  +ll+++++                      + +
  gi|121637056|ref|YP_977279.1| 121 AIAATGLAAMPDSPFAkAVIMSVPPSAAFRPLGrVPERGRLLRELPHQLLRSWYIlyfqlpwlpersaswvvpllwRRWS 200
                                    ********999999996777777666655566559999999**********************99999999776663333 PP

                    Hydrolase_4 144 kadslsrdpevvaayeadplv..hgkitvrlllelldamkrleeraakit..........lPllllhGeaDkvvdpeasr 211
                                          +d ++v+a    p          r  +  ++a ++        +          lP+l lhG +D     + ++
  gi|121637056|ref|YP_977279.1| 201 PGYHAEEDLRHVDAAIGTPEGrrAALGPYRATMRNTRAPADYA------DlnrlwteapkLPVLYLHGHDDGCATSAFTH 274
                                    3333333333333333333321111122333333333333333......233444477778***********99999999 PP

                    Hydrolase_4 212 elyerlgskdktlklypglyHellnEp 238
                                     +++ l++   ++++ +++ H l  E+
  gi|121637056|ref|YP_977279.1| 275 WTARVLPA-GSEVAVVEHAGHFLQLEQ 300
                                    99999996.999*******99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2083.23
//
Query:       gi|121637057|ref|YP_977280.1|  [L=414]
Description: hypothetical protein BCG_1186 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-09   36.7   0.0    6.1e-09   36.0   0.0    1.4  1  DUF1298         Protein of unknown function (DUF1298)
     0.0015   18.3   1.8      0.004   17.0   1.8    1.8  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer


Domain annotation for each model (and alignments):
>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   6.9e-13   6.1e-09       3     141 ..     270     413 ..     269     414 .] 0.94

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.9e-13
                        DUF1298   3 NqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl.......lsnttlviSN 75 
                                    N++g v++ L   l +P er+r++   +++++r++e+  + ++ ++ ++ +pa+++++ ++++       +   ++v+S+
  gi|121637057|ref|YP_977280.1| 270 NHFGNVVVGLYPRL-EPDERVRRIATDLANARRRFEHPAMLSADRA-FAAVPAALLRWGVSQFdaevrpvRVAGNTVVSS 347
                                    88999999999888.8***************************999.9***********88888888887888999**** PP

                        DUF1298  76 vpGPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleeal 141
                                    v      l++ +ap++  ++   ++p+++l+  v    +++ i++ + +++v+d++++++ l  al
  gi|121637057|ref|YP_977280.1| 348 VYRGAADLSFGDAPVVLTAGYPALSPAMGLTHGVHGIGDTVAISVHAAESAVSDIDAYMRLLDAAL 413
                                    *999999****************************************************9999888 PP

>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.8   4.4e-07     0.004      28     161 ..      32     162 ..       6     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-07
                 WES_acyltransf  28 ppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDldyHvRrvalpaPGterellelvsrLass 107
                                         ++  +l+r++ ++ +r++ +p l ++v+++ ++la p Wv  + ++ d  v    l+++  +  l ++v  La +
  gi|121637057|ref|YP_977280.1|  32 G----EPT-DLERAVAQVYRRARGCPGLGMRVQDR-GALAYPQWVPTP-VQRDQLVC-HDLADRSWQGCL-AAVVGLAGK 102
                                    3....344.78899999999999999999987765.789999999999.88888887.678888875555.55556**** PP

                 WES_acyltransf 108 pLDrsrPlWevhv......iEGleg.griAillkvHHAliDGvgglkllarlldldpddpp 161
                                    +LD++r +W +hv      ++G+ g g++A ++++ HAl DG ++ +++a l  +    p+
  gi|121637057|ref|YP_977280.1| 103 QLDMRRMPWRLHVftpvhdVPGVSGlGTVA-VMQFAHALGDGARASAMAAWLFGRPAAVPE 162
                                    ***********9988888899*99945555.579**************9977665444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2673.25
//
Query:       gi|121637058|ref|YP_977281.1|  [L=201]
Description: hypothetical protein BCG_1187c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00095   19.6   0.1     0.0021   18.5   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0012   18.9   0.0      0.002   18.1   0.0    1.4  1  HemN_C          HemN C-terminal domain
  ------ inclusion threshold ------
      0.012   15.4   0.5      0.024   14.5   0.5    1.6  1  MarR_2          MarR family
      0.017   15.3   0.0      0.028   14.6   0.0    1.4  1  Polyketide_cyc  Polyketide cyclase / dehydrase and lipid tran


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.8e-07    0.0021       5      53 ..       3      47 ..       2      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.8e-07
                         HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                   +  vL  +r   +r++ +dl+++l  + + ++  +++Lt++GL+    d
  gi|121637058|ref|YP_977281.1|  3 ELTVLQAVR-LKGRVITTDLAQTLGEDLADVAATVDRLTAAGLL---VD 47
                                   567889999.9*********************************...33 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.5e-07     0.002      16      66 .]      11      59 ..       5      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.5e-07
                         HemN_C 16 RlreGldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprGrl 66
                                   Rl   +   +++q  g+dl+++ aa++++l+++GLL  d++ lr +p Gr+
  gi|121637058|ref|YP_977281.1| 11 RLKGRVITTDLAQTLGEDLADV-AATVDRLTAAGLL-VDATPLRISPSGRM 59
                                   55556666799*******9998.999**********.788*********95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   5.2e-06     0.024       7      52 ..       3      46 ..       1      74 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   ++ vL a++  ++  +  ++la++lg + + v  +++rL aaGL++
  gi|121637058|ref|YP_977281.1|  3 ELTVLQAVRLKGR--VITTDLAQTLGEDLADVAATVDRLTAAGLLV 46
                                   7789999999998..9****************************95 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.3e-06     0.028      64      92 ..      74     114 ..      45     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.3e-06
                                    T.......EEECTTCCCCCEEEEEEEECTECCEEE.....C CS
                 Polyketide_cyc  64 e.......itfklvegdfkslegkWtieslppnsg.....g 92 
                                    +        +f  v+ dfk+l++ W+++  +pn++     +
  gi|121637058|ref|YP_977281.1|  74 StvlaaayRDFRSVNADFKRLVTDWQLKGEKPNTHddaeyD 114
                                    1444444478999******************9877433322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1393.12
//
Query:       gi|121637059|ref|YP_977282.1|  [L=490]
Description: pyruvate phosphate dikinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-39  134.3   0.0    7.9e-29  101.0   0.0    3.1  2  PPDK_N         Pyruvate phosphate dikinase, PEP/pyruvate bind
    8.2e-22   76.7   2.4    2.3e-21   75.3   2.4    1.8  1  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   8.8e-33   7.9e-29       2     219 ..      31     257 ..      30     269 .. 0.91
   2 !   23.7   0.1   2.9e-09   2.6e-05     270     323 ..     269     320 ..     255     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 8.8e-33
                         PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeel 81 
                                    e++G Kg ++  + ++ ++pvPp f+it+++  ++l++   e++i ++ +                            ++
  gi|121637059|ref|YP_977282.1|  31 EILGNKGHGIDMM-RRHHLPVPPAFCITTEVGVRYLAAP--ESTIAAIWD----------------------------DV 79 
                                    689*******999.88*********************99..888877666............................69 PP

                         PPDK_N  82 eeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle...................... 137
                                     ++++ ++ e++ +fg    +l+v+VRS+      +++s++G++dt+L vg  ++v +                      
  gi|121637059|ref|YP_977282.1|  80 LDRMSWLETETSCTFGRGpnPLLVSVRSG------ATQSMPGMMDTILDVGMTDAVERvlarpgaadfahdtrrrftsmy 153
                                    999999999999999998889********......99*************999988889********************* PP

                         PPDK_N 138 ....................aikavfaSlfnerAilYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetGf 194
                                                        +i+avfaS++++rA++Yr ++gld ++ ++avvvq+mv+++l     +GV  s++p tG 
  gi|121637059|ref|YP_977282.1| 154 rrivgsagpitddpyaqlraSIEAVFASWNSPRAVAYRDHHGLD-DQGGTAVVVQAMVFGNLTansGAGVLSSRNPITG- 231
                                    ********************************************.9***************999999************. PP

                         PPDK_N 195 kdevlinasyG.lGeaVVaGrvtpde 219
                                    ++e + +   G +G +VV+G v    
  gi|121637059|ref|YP_977282.1| 232 ANEPFGEWLPGgQGDDVVSGLVAVAP 257
                                    666666665544********776544 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.9e-09
                         PPDK_N 270 veeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaet 323
                                     ++L   a+ +e+  g+ ++iEf+++  + +l+llQ+R  +r  +++++ a + 
  gi|121637059|ref|YP_977282.1| 269 YDQLMAAARSLERMAGDVQEIEFTVE--DSQLWLLQTRGAERSAQAAVRLALQL 320
                                    579999********************..**************999998766655 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   2.4   2.5e-25   2.3e-21       4      73 .]     389     458 ..     386     458 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.5e-25
                                    S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    e+vILv+++t p+d+ g+ +a+Givte GG+ SHaA+v+relg  aVvg+g     +  g++itvDg++G
  gi|121637059|ref|YP_977282.1| 389 EPVILVRDHTRPEDVMGMLAAQGIVTEVGGAASHAAVVSRELGRVAVVGCGPGVAAALAGKEITVDGYEG 458
                                    56****************************************************999999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3016.55
//
Query:       gi|121637060|ref|YP_977283.1|  [L=451]
Description: hypothetical protein BCG_1189c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.6e-108  362.1  10.0   3.1e-108  361.8  10.0    1.1  1  DUF222    Domain of unknown function (DUF222)
  ------ inclusion threshold ------
       0.12   12.6   0.2       0.27   11.4   0.2    1.6  1  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.8  10.0  3.5e-112  3.1e-108       3     301 .]      37     360 ..      35     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 361.8 bits;  conditional E-value: 3.5e-112
                         DUF222   3 aaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lpa 71 
                                    a le++e+a+r+l++ve++l+++++e+ ++ee g++ +  ++a+rlri+r+eA+rrv++A++l++r           L+a
  gi|121637060|ref|YP_977283.1|  37 ALLEHCETARRQLPSVEHTLINQIGEQSTEEELGGK-LGLTLADRLRITRSEAKRRVAEAADLGQRraltgeplpplLTA 115
                                    789*********************************.******************************************* PP

                         DUF222  72 vaaalraGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrre 151
                                    +a+a+r+G i+  +v+vI+a++++lp++vdl+t++kae++l+++a++++p++Lakl+ r++++l+pDg+++de++arrr+
  gi|121637060|ref|YP_977283.1| 116 TAKAQRHGLIGDGHVEVIRAFVHRLPSWVDLKTLEKAERDLAKQATQYRPDQLAKLAARIMDCLNPDGDYTDEDRARRRG 195
                                    ******************************************************************************** PP

                         DUF222 152 ltltk.dedGmsrisgeldaeaaaaldavLdslaap.vcap..............dgtkDpRspaqrraDALlallrlal 215
                                    ltl+k d+dGmsr+sg++++e +a+++av+++laap +c+p              ++++D+Rs+ qr++DAL+a+lr +l
  gi|121637060|ref|YP_977283.1| 196 LTLGKqDVDGMSRLSGYVTPELRATIEAVWAKLAAPgMCNPeqkapcvngapskeQARRDTRSCPQRNHDALNAGLRSLL 275
                                    ******************************************************************************** PP

                         DUF222 216 aagaldchagvpatvvvhvtaeeltaaaggaaltgggglLpasdvrrLAkdAt..laifdepagrpldlgrtkrtasaal 293
                                    ++g+l++h+g+pa+++v++t+++l+aaag+ +ltggg++Lp+sdv+rLA++A+  laifd+  g++l+l++tkr+as+a+
  gi|121637060|ref|YP_977283.1| 276 TSGNLGQHNGLPASIIVTTTLKDLEAAAGA-GLTGGGTILPISDVIRLARHANhyLAIFDR--GKALALYHTKRLASPAQ 352
                                    *****************************9.***********************99*****..***************** PP

                         DUF222 294 rralraRD 301
                                    r++l+a+D
  gi|121637060|ref|YP_977283.1| 353 RIMLYAKD 360
                                    *******9 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2     3e-05      0.27       4      37 ..     363     398 ..     361     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllC 37 
                                    C  ++ ++  +++ev+H+ p++q   +d ++l+l C
  gi|121637060|ref|YP_977283.1| 363 CSAPGCDVpgYYCEVHHVTPYAQCRNTDVNDLTLGC 398
                                    555555555699***********9999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3390.18
//
Query:       gi|121637061|ref|YP_977284.1|  [L=486]
Description: transcriptional regulator protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-65  218.4   0.0    6.5e-65  217.8   0.0    1.3  1  DUF2083         Predicted transcriptional regulator (DUF2083)
    2.1e-20   72.9   0.3    1.3e-19   70.4   0.0    2.3  3  Peptidase_M78   IrrE N-terminal-like domain
    8.3e-13   48.2   0.1    1.9e-12   47.0   0.1    1.6  1  HTH_3           Helix-turn-helix
      2e-10   40.9   0.6    7.1e-10   39.1   0.6    1.9  1  HTH_31          Helix-turn-helix domain
    1.4e-09   37.9   0.0    3.1e-09   36.7   0.0    1.6  1  HTH_19          Helix-turn-helix domain
    7.6e-05   22.5   1.1    0.00016   21.5   1.1    1.5  1  HTH_25          Helix-turn-helix domain
     0.0033   16.9   0.1       0.02   14.4   0.1    2.3  2  Sigma70_r4      Sigma-70, region 4
     0.0036   16.8   0.4      0.024   14.2   0.1    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.01   16.3   0.1      0.026   15.0   0.1    1.7  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.033   14.1   0.0      0.073   13.0   0.0    1.5  1  HTH_37          Helix-turn-helix domain
       0.12   12.2   0.0       0.56   10.1   0.0    2.1  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> DUF2083  Predicted transcriptional regulator (DUF2083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.0     4e-68   6.5e-65       1     157 []     323     479 ..     323     479 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 4e-68
                        DUF2083   1 tLqrpgargvPfffvrvDrAGniskrasatgfqfarfggaCPlwnvheafetpgrilvqlaelpdgeryltiartvekes 80 
                                    tLqrp +rg+Pf+fvr+D+AGniskr+sat+f+f+r+gg+CPlw vh+af++p+ri++q+a++pdg++y+++a+t+++ +
  gi|121637061|ref|YP_977284.1| 323 TLQRPRQRGIPFIFVRTDKAGNISKRQSATAFHFSRVGGSCPLWVVHDAFAQPERIVRQVAQMPDGRSYFWVAKTTAADG 402
                                    8******************************************************************************* PP

                        DUF2083  81 gafgepekrfaialgceikhaeklvyadgldleekaaatpiGvgCrlCeredCaqRafpplgrelevdenerglspy 157
                                     ++  p+k+fa++lgc+++ha+klvy++g+ l+++++ +piG+gC++C+r++CaqRafp lg +++vden+ + +py
  gi|121637061|ref|YP_977284.1| 403 LGYLGPHKNFAVGLGCDLAHAHKLVYSTGVVLDDPSTEVPIGAGCKICNRTSCAQRAFPYLGGRVAVDENAGSSLPY 479
                                    **********************************************************************9999888 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.76   1.2e+03      72     116 ..      27      74 ..      15      77 .. 0.79
   2 ?   -2.7   0.1       3.3   5.3e+03      49     105 ..     115     171 ..     113     178 .. 0.69
   3 !   70.4   0.0   7.8e-23   1.3e-19       2     123 .]     200     322 ..     199     322 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.76
                  Peptidase_M78  72 erlereanafAaelllPeeaflalaatqrkdlee...rlaeyfgVSke 116
                                    +++     a+A +l l++  + +l ++qr +       l e+f+ S +
  gi|121637061|ref|YP_977284.1|  27 QERGLTQVALAKALDLSTSYVNQLENDQRPITVPvllLLTERFDLSAQ 74 
                                    555566677899999999999999888888877788888888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                  Peptidase_M78  49 ElgHlllhherdkfreegdskaqerlereanafAaelllPeeaflalaatqrkdlee 105
                                    E gH l    r  + ++   + ++ +  + +++ ++  +P e++++++ ++++++++
  gi|121637061|ref|YP_977284.1| 115 EVGHSLVAVHRRLRAATEELEGYRSRATAETELPPARPMPFEEVRDFFYDRNNYIHD 171
                                    566666666666666666677777777777778888888888888888877777665 PP

  == domain 3  score: 70.4 bits;  conditional E-value: 7.8e-23
                  Peptidase_M78   2 erlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlere.... 77 
                                    +r+gi v+  d +  d++++r+++  tkv+ +   + p +++f++a +l+ +   + +    ++ d+ ++e++  +    
  gi|121637061|ref|YP_977284.1| 200 DRFGISVV-IDDNLPDTAKRRYHPD-TKVLRVAHWLMPGQRAFQIATQLALVGQSDLISSIVATDDQLSTEARGVArigl 277
                                    78999999.999999*******998.********************************999***************9999 PP

                  Peptidase_M78  78 anafAaelllPeeaflalaatqrkdleerlaeyfgVSkeavavrls 123
                                    an+fA+++llP+++f+ +a++ r+d+++ l ++fgV +e+v++rls
  gi|121637061|ref|YP_977284.1| 278 ANYFAGAFLLPYREFHRAAEQLRYDIDL-LGRRFGVGFETVCHRLS 322
                                    ***************************9.***************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   1.2e-15   1.9e-12       1      55 []      22      76 ..      22      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.2e-15
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                   l++lR+++gl+q  LA++l++s s+++++En++r +++ +l++l + +++s +++
  gi|121637061|ref|YP_977284.1| 22 LRRLRQERGLTQVALAKALDLSTSYVNQLENDQRPITVPVLLLLTERFDLSAQYF 76
                                   89************************************************99986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.6   4.4e-13   7.1e-10       3      55 ..      19      70 ..      19      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.4e-13
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                   Ga+Lr+lR+++GL+q ++A++l +s s++++lE+ +r+  +  vl  l + ++
  gi|121637061|ref|YP_977284.1| 19 GARLRRLRQERGLTQVALAKALDLSTSYVNQLENDQRP-ITVPVLLLLTERFD 70
                                   89***********************************7.99999887766555 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.9e-12   3.1e-09       1      59 [.      19      76 ..      19      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.9e-12
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyl 59
                                   G rL+++R e+gltq +la+ l+ s s+ +++En+++  ++ ++ll + e ++++++y+
  gi|121637061|ref|YP_977284.1| 19 GARLRRLRQERGLTQVALAKALDLSTSYVNQLENDQR-PITVPVLLLLTERFDLSAQYF 76
                                   89***********************************.999***************997 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.1   9.7e-08   0.00016       1      34 [.      21      54 ..      21      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.7e-08
                                   HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                         HTH_25  1 rLraaRearglsleevaketkIrkdylealEedd 34
                                   rLr+ R++rgl+  ++ak + ++++y+ +lE+d+
  gi|121637061|ref|YP_977284.1| 21 RLRRLRQERGLTQVALAKALDLSTSYVNQLENDQ 54
                                   7*******************************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.2e-05      0.02      14      42 ..      24      52 ..      21      53 .. 0.92
   2 ?   -1.6   0.0       1.2     2e+03      26      41 ..     306     321 ..     305     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                   HHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                     Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrqiek 42
                                   +lr ++glT+  +++ l++S + V q+e+
  gi|121637061|ref|YP_977284.1| 24 RLRQERGLTQVALAKALDLSTSYVNQLEN 52
                                   5788***********************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                    HHHHHTS-HHHHHHHH CS
                     Sigma70_r4  26 IgerlgiSrerVrqie 41 
                                    +g+r+g+  e+V  ++
  gi|121637061|ref|YP_977284.1| 306 LGRRFGVGFETVCHRL 321
                                    599********98775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.5e-05     0.024       9      36 ..      22      49 ..      22      50 .. 0.94
   2 ?    0.2   0.0      0.34   5.5e+02      26      43 ..     115     132 ..     115     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                         HTH_24  9 LelLqknprisqreLAerlglSpstvnr 36
                                   L+ L+++ +++q  LA++l+lS s vn+
  gi|121637061|ref|YP_977284.1| 22 LRRLRQERGLTQVALAKALDLSTSYVNQ 49
                                   78899********************996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.34
                         HTH_24  26 rlglSpstvnrrlkrLee 43 
                                    ++g S+ +v+rrl+  +e
  gi|121637061|ref|YP_977284.1| 115 EVGHSLVAVHRRLRAATE 132
                                    5899999******98776 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.6e-05     0.026       1      43 [.      21      62 ..      21      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                         HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtL 43
                                   +Lr+l ++rg+t+  La+++++s + ++ l +++ + ++  +L
  gi|121637061|ref|YP_977284.1| 21 RLRRLRQERGLTQVALAKALDLSTSYVNQLENDQ-RPITVPVL 62
                                   79******************************98.56666655 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05     0.073      22      61 ..      21      59 ..      11      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                   HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--H CS
                         HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsl 61
                                   ++++l+++r+l+q  +a++l  + + v++l++ +++ +++
  gi|121637061|ref|YP_977284.1| 21 RLRRLRQERGLTQVALAKALDLSTSYVNQLEN-DQRPITV 59
                                   699****************************8.6666665 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034      0.56      10      37 ..      32      59 ..      30      67 .. 0.85
   2 ?   -2.4   0.0       2.8   4.5e+03       9      31 ..     407     429 ..     405     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                 YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpa 37
                                   +q+aLA+al+ s + V+q+ ++++++++
  gi|121637061|ref|YP_977284.1| 32 TQVALAKALDLSTSYVNQLENDQRPITV 59
                                   599****************998888543 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                 YdaS_antitoxin   9 GgqkaLAealgvsqqaVsqWlkg 31 
                                    G  k +A  lg+  ++ +++++ 
  gi|121637061|ref|YP_977284.1| 407 GPHKNFAVGLGCDLAHAHKLVYS 429
                                    667889999***99999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3247.80
//
Query:       gi|121637062|ref|YP_977285.1|  [L=526]
Description: hypothetical protein BCG_1191 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-125  419.2   7.7   1.7e-125  419.0   7.7    1.0  1  MmgE_PrpD  MmgE/PrpD family


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.0   7.7  9.5e-130  1.7e-125       1     437 [.      43     496 ..      43     498 .. 0.97

  Alignments for each domain:
  == domain 1  score: 419.0 bits;  conditional E-value: 9.5e-130
                                    HHHHHHHHHH-----H....HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHHH CS
                      MmgE_PrpD   1 teqlaefvaelryddlpe..evverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfvn 78 
                                    te++a  +a++++d ++   ev +++ ++i+D+++v +a++ +++v+ a+++++++++++ga+v+g +  +s+ +AA++n
  gi|121637062|ref|YP_977285.1|  43 TEHMAYKIAQVAADPVDVdpEVADMVCNRIIDNAAVSAASMVRRPVTVARHQALAHPVRHGAKVFGVEGSYSADWAAWAN 122
                                    68899999999999765555************************************************************ PP

                                    HHHHHCTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHHHH CS
                      MmgE_PrpD  79 GaaihalDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfgaaa 158
                                    G+a+++lDf+Dt+laa+++hp+d++p+++AvA++lg  g++l++++v++yE++++l + +++++++ +d+v+++++++aa
  gi|121637062|ref|YP_977285.1| 123 GVAARELDFHDTFLAADYSHPADNIPPLVAVAQQLGVCGAELIRGLVTAYEIHIDLTRGICLHEHK-IDHVAHLGPAVAA 201
                                    ******************************************************************.************* PP

                                    HHHHHTT--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHHHHST CS
                      MmgE_PrpD 159 aaakLlgLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGflavlsg 238
                                    +++++l+Ld+e+i++A+g+a++ ++++rq+r+++++s+k++a+++A++ G+ea+++A+rG+ +p +i+ege+G++a+l+ 
  gi|121637062|ref|YP_977285.1| 202 GIGTMLRLDQETIYHAIGQALHLTTSTRQSRKGAISSWKAFAPAHAGKVGIEAVDRAMRGEGSPAPIWEGEDGVIAWLLA 281
                                    ******************************************************************************** PP

                                    T-----S.S-SS....SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC---S...... CS
                      MmgE_PrpD 239 gkdlelevkplge.gesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkkg...... 311
                                    g++ +++v+ +++ +++ +i++ ++K ++ae++++a id+a +lr+++++ +d+I+si+++ts++++ +ig+++      
  gi|121637062|ref|YP_977285.1| 282 GPEHTYRVPLPAPgEPKRAILDSYTKQHSAEYQSQAPIDLACRLRERIGD-LDQIASIVLHTSHHTHVVIGTGSgdpqkf 360
                                    *******99999999**********************************8.*********************999***** PP

                                    .---SHHHHCT-CCHHHHHHHHCS---CCC.CSCCCCTSCHHCCHHCCEEEEE-HHHHHHH....TTT---...EEEEET CS
                      MmgE_PrpD 312 .ppenradadhSlqyvvAvalldgrvtled.federladpevqaLrekvevvedpeltady....pekrsi...vvvvlk 382
                                     p ++r++ dhSl+y++Aval+dg +++e  + +er+++++++aL++k+++vedpe+t++y    p+k+++   ++v+l 
  gi|121637062|ref|YP_977285.1| 361 dPDASRETLDHSLPYIFAVALQDGCWHHERsYAPERARRSDTVALWHKISTVEDPEWTRRYhcadPAKKAFgarAEVTLH 440
                                    ****************************76377888*****************************9999999******** PP

                                    TS-B---EEESS-TTS.GGHHHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHSH CS
                      MmgE_PrpD 383 dggrtleerveypkGh.prnplsreeleeKfrrlaegvlseeeaereeileevlel 437
                                     g+++++e +++++++   +p++r++++eKf++la+gv+++ e++r+++++e+l++
  gi|121637062|ref|YP_977285.1| 441 SGEVIVDELAVADAHPlGTRPFERKQYVEKFTELADGVVEPVEQQRFLAVVESLAD 496
                                    ****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3711.62
//
Query:       gi|121637063|ref|YP_977286.1|  [L=393]
Description: citrate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.3e-114  382.3   0.1   2.6e-114  382.1   0.1    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.1   0.1  1.5e-118  2.6e-114       1     360 [.      31     377 ..      31     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.1 bits;  conditional E-value: 1.5e-118
                                    GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHC CS
                   Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealea 80 
                                    gl gv++ +t+is+v +++  l+YRGy++++La +++sfe+va+lL+ gelPt +el+ f+++ +++r++++++l+ l +
  gi|121637063|ref|YP_977286.1|  31 GLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLA-ARCSFEQVAFLLWRGELPTDAELALFSQRERASRRVDRSMLSLLAK 109
                                    799************999988************.7********************************************* PP

                                    SSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHHH CS
                   Citrate_synt  81 lpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflymlr 160
                                    lp+++hpm+v+r+a+s l+a+d+++++++  + +a+r    ++A lpti+a   r+r+g +p++p+++l ya+nfl+m++
  gi|121637063|ref|YP_977286.1| 110 LPDNCHPMDVVRTAISYLGAEDPDEDDAAANRAKAMR----MMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCF 185
                                    **********************965555555555555....*******************9*****99************ PP

                                    SS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHH CS
                   Citrate_synt 161 gkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleeigsaevevee 240
                                    g+ p+  ++ ++++ ++l+a+H++naSTfaarvv+St++d+ysa++++igalkG lhgganeav++ + eig+++ +++e
  gi|121637063|ref|YP_977286.1| 186 GEVPETAVVSAFEQSMILYAEHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEIGDPA-NARE 264
                                    *99999********************************************************************9.**** PP

                                    HHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHGCT-EB-THHHHHH CS
                   Citrate_synt 241 ylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekeeknlypNvDfysgv 320
                                    +l+++la+ ke+++GfGHrvy+++D R+  +k+++e++    + +++l++++ l + + +       +++ pN+Df +g 
  gi|121637063|ref|YP_977286.1| 265 WLRAKLAR-KEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDGQRWLDIYQVLAAEMAS-----A-TGILPNLDFPTGP 337
                                    *******8.6*******************************99999******99999988.....6.89*********** PP

                                    HHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------ CS
                   Citrate_synt 321 lyralgipeelftvlfaisRvaGwlAhileqladnkiiRP 360
                                     y+ +g++   ft++f++sR++Gw+Ahi+eq++ n +iRP
  gi|121637063|ref|YP_977286.1| 338 AYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRP 377
                                    *******************************9999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2819.72
//
Query:       gi|121637064|ref|YP_977287.1|  [L=576]
Description: hypothetical protein BCG_1193 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-284  945.3  10.0   1.2e-284  945.1  10.0    1.0  1  DUF3556   Transmembrane protein of unknown function (DUF3556)
  ------ inclusion threshold ------
        6.7    6.6  10.5       0.05   13.5   0.9    2.3  3  TMEM239   Transmembrane protein 239 family


Domain annotation for each model (and alignments):
>> DUF3556  Transmembrane protein of unknown function (DUF3556)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  945.1  10.0  1.4e-288  1.2e-284       1     572 [.       1     573 [.       1     574 [. 1.00

  Alignments for each domain:
  == domain 1  score: 945.1 bits;  conditional E-value: 1.4e-288
                        DUF3556   1 mGflkpdlpdvdlaefskkplaerlrllarhwvevGfgtpkvvhllYvlkillyvlggvlvvlltsGldgltdvgeWwse 80 
                                    mGfl+p+lpd+dlae+s+ ++++++r++a+hw+evGfgtp+ +hl+Yv+killyvl+g+l+vl+t+G+dg+td ++W++e
  gi|121637064|ref|YP_977287.1|   1 MGFLQPRLPDIDLAEWSQGSRSQKIRPMAQHWAEVGFGTPVLLHLFYVAKILLYVLVGWLIVLTTKGIDGFTDAAAWYAE 80 
                                    9******************************************************************************* PP

                        DUF3556  81 pivyqkvvlytllfevvglgcsfGPLaakfkPplggilywlrpgtiRLppwPdkvPltkGdkRtvvDvalYaallvslvv 160
                                    piv++kvvlyt+lfev+glgc+fGPL+++f+Pp+g+ilyw+r gtiRLppwPd+vP+t+G+kR++vDvalYa l+++l+ 
  gi|121637064|ref|YP_977287.1|  81 PIVFEKVVLYTMLFEVIGLGCGFGPLNNRFFPPMGSILYWMRFGTIRLPPWPDRVPWTRGTKRKPVDVALYALLVMMLLS 160
                                    ******************************************************************************** PP

                        DUF3556 161 alvspGvgeaaaaetevgllpavqvvaliallvvlgLRDkviflaaRgeqYlllllvflvla..fvdmivalklvilviW 238
                                    al+++G+g++++++t+vgllpa+q+v ++ ll vlgLRDkviflaaRge+Y++l+++fl+ +   +dmiva+klv+lviW
  gi|121637064|ref|YP_977287.1| 161 ALFTDGAGPIPELGTTVGLLPAWQIVLILLLLGVLGLRDKVIFLAARGEVYATLTVTFLFGRlnGIDMIVAAKLVFLVIW 240
                                    ***********************************************************987779*************** PP

                        DUF3556 239 lGaavsklnkhfplvvstmlsnspllrskslkralyrnfpdDlrPsklaklvahvagtvvellvPlvLlfstnktltlva 318
                                    +Gaa+skln+hfp+v+stm+sn+pl+r++ +kr+++++fp DlrP+ l+++vahv +tv+e++vP+vL+++++++ t+va
  gi|121637064|ref|YP_977287.1| 241 IGAATSKLNRHFPFVISTMMSNNPLFRPRFIKRMFFKKFPGDLRPGLLSRIVAHV-STVIEMCVPVVLFVAHGGWPTVVA 319
                                    *******************************************************.************************ PP

                        DUF3556 319 avlmvvfhlfilstlplavPleWnvffifavlflflgfagvgvadlssplllalllavlvvvpvlGnlrPdkvsfLpsmR 398
                                    a++mv+fhl il+++p++vPleWnvf+if+vl lf+g+a +g+ad+++p++la+l+av++ ++++Gn++P+k+sfL++mR
  gi|121637064|ref|YP_977287.1| 320 ATIMVCFHLGILTAIPMGVPLEWNVFMIFGVLSLFVGHACLGLADVKNPVPLAILIAVVAGIVIAGNVFPRKISFLAAMR 399
                                    ******************************************************************************** PP

                        DUF3556 399 yYaGnWatalwafkpgaeeklekeivksaklqadqleklyekeaaeivlqkvlafRalhshgrallslllrald..dede 476
                                    yYaGnW+t+lw++kp+ae+k+++ iv++a+++a+qle++y+k++a+i ++ ++afRa++shgral++l++ra++  ded+
  gi|121637064|ref|YP_977287.1| 400 YYAGNWDTTLWCIKPSAEDKINRGIVAIASMPAAQLERFYGKDRAQIPMYLGYAFRAMNSHGRALFTLAHRAMAghDEDD 479
                                    *************************************************************************999**** PP

                        DUF3556 477 ytlregelvcstlvgwnfGdghlhneqliaavqkrcefepGelvvvllesqpihrqtqeyrvvDaalGvierGyvkvada 556
                                    y++++ge+vcst+vgwnfGdghlhneqliaa+q+rc+f+pGe++vvll++qpihrqtqeyr+vDaa+G++erGyv+vad+
  gi|121637064|ref|YP_977287.1| 480 YVITDGERVCSTAVGWNFGDGHLHNEQLIAAMQQRCGFQPGEVRVVLLDAQPIHRQTQEYRLVDAATGEFERGYVRVADM 559
                                    ******************************************************************************** PP

                        DUF3556 557 vaeqPWlpddeipvev 572
                                    v++qPW  dd++pv+v
  gi|121637064|ref|YP_977287.1| 560 VNRQPW--DDDVPVHV 573
                                    ******..******98 PP

>> TMEM239  Transmembrane protein 239 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.49   4.4e+03      44      74 ..      26      57 ..      14      70 .. 0.54
   2 ?   13.5   0.9   5.5e-06      0.05      65     133 ..     145     215 ..     112     229 .. 0.78
   3 ?   -2.4   0.5      0.44     4e+03      89     124 ..     287     322 ..     285     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.49
                        TMEM239 44 rrwitwcsssnwrvplqrllwllesi.lylll 74
                                   r   + ++   +  p+   l+ +  i ly+l+
  gi|121637064|ref|YP_977287.1| 26 RPMAQHWAEVGFGTPVLLHLFYVAKIlLYVLV 57
                                   34556666667777766555555444145444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.5e-06
                        TMEM239  65 llesilylllalglchalfttgshllrslwpvvaa..vwkhllpallllvlsalpallfaasfllllstll 133
                                     ++ +ly ll ++l  alft g+  +  l   v     w+ +l  lll vl     ++f a+   +++tl 
  gi|121637064|ref|YP_977287.1| 145 PVDVALYALLVMMLLSALFTDGAGPIPELGTTVGLlpAWQIVLILLLLGVLGLRDKVIFLAARGEVYATLT 215
                                    46889************************999875226*****9999999999999999988777777664 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.44
                        TMEM239  89 llrslwpvvaavwkhllpallllvlsalpallfaas 124
                                    ll+ +   v++v    +p +l+++    p+++ a+ 
  gi|121637064|ref|YP_977287.1| 287 LLSRIVAHVSTVIEMCVPVVLFVAHGGWPTVVAATI 322
                                    566777778888888888888888888887765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3930.65
//
Query:       gi|121637065|ref|YP_977288.1|  [L=759]
Description: 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   6.9e-158  525.1   0.3   2.8e-154  513.2   0.1    2.1  2  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   8.4e-115  383.6   0.0   1.1e-109  366.8   0.0    2.2  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
     0.0087   15.9   3.4      0.038   13.9   0.5    3.3  3  VbhA         Antitoxin VbhA
  ------ inclusion threshold ------
      0.028   14.2   1.2      0.051   13.3   0.1    2.1  2  SHOCT        Short C-terminal domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   8.1e-05      0.36     126     183 ..     161     219 ..     145     296 .. 0.73
   2 !  513.2   0.1  6.2e-158  2.8e-154       1     323 [.     432     754 ..     432     755 .. 1.00

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 8.1e-05
                                    EEE-HHHHHHTSEE-TTS.-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEE-TTSSTT-- CS
                    Meth_synt_2 126 lltGpvtilnwsfvrddv.draeaaaqialalrdevkdLeaaGikviQiDepalreGlp 183
                                    ++ Gp+t l  s   d      e + +++ +  + +  L ++G++ +Q+Depal + l 
  gi|121637065|ref|YP_977288.1| 161 VIIGPITFLLLSKAVDGAgAPIERLEELVPVYSELLSLLADGGAQWVQFDEPALVTDLS 219
                                    57788888888876644413456788899999999999***************987654 PP

  == domain 2  score: 513.2 bits;  conditional E-value: 6.2e-158
                                    S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--S CS
                    Meth_synt_2   1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftk 80 
                                    lpTttiGS+Pqt+++r ara++++ge++e+ey +++r+ei++v++ qe+lg+DvlvhgepeR+dmv+yf+e+l+gf++t+
  gi|121637065|ref|YP_977288.1| 432 LPTTTIGSYPQTSAIRVARAALRAGEIDEAEYVRRMRQEITEVIALQERLGLDVLVHGEPERNDMVQYFAEQLAGFFATQ 511
                                    79****************************************************************************** PP

                                    S--EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHH CS
                    Meth_synt_2  81 ngwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrdev 160
                                    ngwvqsygsrcvrppi++gdvsrp+amtv+++++aqsltdkpvkg+ltGpvtil+wsfvrdd+++a++a+q+ala+rde+
  gi|121637065|ref|YP_977288.1| 512 NGWVQSYGSRCVRPPILYGDVSRPRAMTVEWITYAQSLTDKPVKGMLTGPVTILAWSFVRDDQPLADTANQVALAIRDET 591
                                    ******************************************************************************** PP

                                    HHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEEES CS
                    Meth_synt_2 161 kdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvitie 240
                                     dL++aGi+viQ+Depalre lpl++ad+a+yl+wav afrl+t++++d tq+htHlCyse+ +++ aia+ld+Dv++ie
  gi|121637065|ref|YP_977288.1| 592 VDLQSAGIAVIQVDEPALRELLPLRRADQAEYLRWAVGAFRLATSGVSDATQIHTHLCYSEFGEVIGAIADLDADVTSIE 671
                                    ******************************************************************************** PP

                                    BSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHHHHHHHHHH CS
                    Meth_synt_2 241 asrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCGLktrkreearaalknmvd 320
                                    a+rs++e+l+ l+++++++gvg+Gvydihsprvps+ee+a+++++al+++p+erlwvnPdCGLktr+++e++a+l+nmv+
  gi|121637065|ref|YP_977288.1| 672 AARSHMEVLDDLNAIGFANGVGPGVYDIHSPRVPSAEEMADSLRAALRAVPAERLWVNPDCGLKTRNVDEVTASLHNMVA 751
                                    ******************************************************************************** PP

                                    HHH CS
                    Meth_synt_2 321 aAk 323
                                    aA+
  gi|121637065|ref|YP_977288.1| 752 AAR 754
                                    *97 PP

>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.8   0.0  2.5e-113  1.1e-109       2     309 ..      12     315 ..      11     319 .. 0.97
   2 !   14.8   0.0   3.4e-06     0.015     148     210 ..     552     613 ..     533     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 366.8 bits;  conditional E-value: 2.5e-113
                                    EB-S---SSTTTTHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHCTT-SBEEES---SS-HHHHHHHHTT---GGG CS
                    Meth_synt_1   2 ssilGfPriGekRelkkalesywkgkiseeeLektakeLrakhwkkqkeagidlipvndfslYDhvLdtavllgaiPerf 81 
                                    ++i G PriG++Relk+a+e yw+g++s++eLe++a++Lr+++w+ +++ag+d++pvn+fs+YD++Ldtavllga+P r 
  gi|121637065|ref|YP_977288.1|  12 ATITGSPRIGPRRELKRATEGYWAGRTSRSELEAVAATLRRDTWSALAAAGLDSVPVNTFSYYDQMLDTAVLLGALPPRV 91 
                                    5799***************************************************************************8 PP

                                    TT.SSSSSHHHHHHHHHSCTTCT--EEEESTTSS-EEEE-BE-SS.----S-THHHHHHHHHHHTTGGEEEEEE-HHHHH CS
                    Meth_synt_1  82 kleekkeeldtyFalaRGkkdvaalemtkwFntnYHYlvPelekdtefklaseklleevkeakalgieakpvllGpltfl 161
                                    +    ++ ld+yFa aRG++++a+lemtkwF+tnYHYlvPe+ ++t+f+l+  k+l+e+kea  +gi a+pv++Gp+tfl
  gi|121637065|ref|YP_977288.1|  92 SP--VSDGLDRYFAAARGTDQIAPLEMTKWFDTNYHYLVPEIGPSTTFTLHPGKVLAELKEALGQGIPARPVIIGPITFL 169
                                    75..89************************************************************************** PP

                                    HT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHHHHHHHHHHHHTCCTTTSEEEEE--SS CS
                    Meth_synt_1 162 kLskakeekveklellekLlpvYkelleeLkeagvewvqidEPalvldlekeelealkeaYeelakekkelklllatyFd 241
                                     Lska +++ +++e le+L+pvY+ell+ L++ g++wvq+dEPalv+dl+++  ++++++Y++l + ++++ +++atyF+
  gi|121637065|ref|YP_977288.1| 170 LLSKAVDGAGAPIERLEELVPVYSELLSLLADGGAQWVQFDEPALVTDLSPDAPALAEAVYTALCSVSNRPAIYVATYFG 249
                                    ******************************************************************************** PP

                                    -.CCHHHHHTTSSTSEEEEETSS.HCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHH CS
                    Meth_synt_1 242 svaealellaelpveglglDlvr.aeenlealkkaglpedkvLsaGvidGrniWradlekalelleela 309
                                    +  +al +la++pve++g+Dlv+ a+++++ + +    ++k+L+aGv+dGrn+Wr+dle+al +l++l 
  gi|121637065|ref|YP_977288.1| 250 DPGAALPALARTPVEAIGVDLVAgADTSVAGVPE---LAGKTLVAGVVDGRNVWRTDLEAALGTLATLL 315
                                    ***********************88888888888...599*************************9986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-06
                                    GGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSG CS
                    Meth_synt_1 148 ieakpvllGpltflkLskakeekveklellekLlpvYkelleeLkeagvewvqidEPalvldl 210
                                      +k +l Gp+t l+ s  ++++   +++ +++  + ++   +L++ag+ ++q+dEPal   l
  gi|121637065|ref|YP_977288.1| 552 KPVKGMLTGPVTILAWSFVRDDQ-PLADTANQVALAIRDETVDLQSAGIAVIQVDEPALRELL 613
                                    457899**************999.888899999999999999****************97544 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   5.2e+03      21      40 ..      24      43 ..      22      46 .. 0.82
   2 ?    0.2   0.0      0.16     7e+02       2      20 ..      51      69 ..      51      72 .. 0.85
   3 !   13.9   0.5   8.4e-06     0.038      24      46 ..     447     469 ..     440     469 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                           VbhA 21 aetvadleayvrGeIdadEl 40
                                   +e+++++e y +G+ +  El
  gi|121637065|ref|YP_977288.1| 24 RELKRATEGYWAGRTSRSEL 43
                                   78999999999999887665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                           VbhA  2 rraVrqAlAsnelEGleps 20
                                   rr +++AlA++ l+ ++++
  gi|121637065|ref|YP_977288.1| 51 RRDTWSALAAAGLDSVPVN 69
                                   7999*******99987776 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 8.4e-06
                           VbhA  24 vadleayvrGeIdadElvrrvra 46 
                                    + + +a+ +GeId +E+vrr+r+
  gi|121637065|ref|YP_977288.1| 447 RVARAALRAGEIDEAEYVRRMRQ 469
                                    55668899*************96 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.1   9.2e+03       2       9 ..     181     188 ..     180     188 .. 0.80
   2 ?   13.3   0.1   1.1e-05     0.051       2      25 ..     445     468 ..     444     469 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                          SHOCT   2 aLekLkeL 9  
                                    ++e+L eL
  gi|121637065|ref|YP_977288.1| 181 PIERLEEL 188
                                    78999987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
                          SHOCT   2 aLekLkeLyarGeIteEEFeakKa 25 
                                    a++  ++ + +GeI+e+E+ ++ +
  gi|121637065|ref|YP_977288.1| 445 AIRVARAALRAGEIDEAEYVRRMR 468
                                    8999999************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 5377.01
//
Query:       gi|121637066|ref|YP_977289.1|  [L=78]
Description: hypothetical protein BCG_1195 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 601.91
//
Query:       gi|121637067|ref|YP_977290.1|  [L=618]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-68  226.6 331.8      5e-11   42.3  28.4   12.3 13  Pentapeptide_2  Pentapeptide repeats (8 copies)
    1.9e-56  190.6  35.3    2.7e-56  190.0  35.3    1.2  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  18.3   3.2e-06     0.028       1      27 [.     198     225 ..     194     225 .. 0.51
   2 !   42.3  28.4   5.6e-15     5e-11       1      40 []     209     248 ..     209     248 .. 0.98
   3 !   29.1  30.7   7.3e-11   6.5e-07       1      40 []     249     288 ..     249     288 .. 0.98
   4 !   36.4  21.5   3.8e-13   3.4e-09       1      39 [.     279     317 ..     279     317 .. 0.99
   5 !   36.8  23.6     3e-13   2.7e-09       1      39 [.     289     327 ..     289     327 .. 0.99
   6 !   28.5  25.9   1.2e-10     1e-06       2      39 ..     315     352 ..     314     353 .. 0.98
   7 !   31.1  30.1   1.7e-11   1.5e-07       3      39 ..     358     394 ..     356     395 .. 0.96
   8 !   36.4  31.9   3.8e-13   3.4e-09       2      40 .]     397     435 ..     396     435 .. 0.98
   9 !   32.5  31.4   6.4e-12   5.7e-08       1      39 [.     426     464 ..     426     465 .. 0.98
  10 !   36.0  12.1   5.3e-13   4.8e-09       2      37 ..     467     502 ..     466     504 .. 0.97
  11 !   19.0  22.4     1e-07   0.00094       2      39 ..     510     544 ..     509     545 .. 0.80
  12 !    9.0  24.1   0.00014       1.2       3      38 ..     546     583 ..     544     585 .. 0.89
  13 !    7.4   7.5   0.00043       3.9      13      36 ..     593     616 ..     589     617 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                 Pentapeptide_2   1 gNtGslNs.GsgNtGffNlGsgNtGsfN 27 
                                    gNtG++N+ + gN+G++NlG+gNtG++N
  gi|121637067|ref|YP_977290.1| 198 GNTGIGNIfSIGNIGDYNLGNGNTGNAN 225
                                    4555555324555555555555555555 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 5.6e-15
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+G+gNtG++NlGsgNtG +NlGsgNtG++n+Gs
  gi|121637067|ref|YP_977290.1| 209 GNIGDYNLGNGNTGNANLGSGNTGQANLGSGNTGFFNFGS 248
                                    8**************************************6 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 7.3e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gNt ++N+GsgN+G++NlGsgN G++N+G gN+G+gn Gs
  gi|121637067|ref|YP_977290.1| 249 GNTANTNFGSGNLGNLNLGSGNDGNGNFGLGNIGDGNRGS 288
                                    8************************************996 PP

  == domain 4  score: 36.4 bits;  conditional E-value: 3.8e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N GsgN+G+fN G++N GsfN+Gs+N+Gs n+G
  gi|121637067|ref|YP_977290.1| 279 GNIGDGNRGSGNVGSFNFGTANAGSFNVGSANHGSPNVG 317
                                    8************************************98 PP

  == domain 5  score: 36.8 bits;  conditional E-value: 3e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+Gs+N+G++N G+fN+Gs+N+Gs N+G++N G++n+G
  gi|121637067|ref|YP_977290.1| 289 GNVGSFNFGTANAGSFNVGSANHGSPNVGFANLGNNNLG 327
                                    8************************************99 PP

  == domain 6  score: 28.5 bits;  conditional E-value: 1.2e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G++N+G+ N+G +NlG+ N G +NlG++N+G+g tG
  gi|121637067|ref|YP_977290.1| 315 NVGFANLGNNNLGIANLGNNNLGIANLGNNNIGIGLTG 352
                                    9***********************************99 PP

  == domain 7  score: 31.1 bits;  conditional E-value: 1.7e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G lNsG gN+Gf+N+G+ N+G fN+G++N+G++n+G
  gi|121637067|ref|YP_977290.1| 358 IGALNSGIGNLGFGNSGNNNIGLFNSGNNNIGFFNSG 394
                                    8***********************************9 PP

  == domain 8  score: 36.4 bits;  conditional E-value: 3.8e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++NsG +NtGf+N G++NtG++N+GsgN+G+gn+G+
  gi|121637067|ref|YP_977290.1| 397 NFGFFNSGDTNTGFGNAGFTNTGFGNAGSGNFGFGNAGN 435
                                    *************************************96 PP

  == domain 9  score: 32.5 bits;  conditional E-value: 6.4e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+G+ N+Gf+N+G+ N+G +N+G +NtGs+n+G
  gi|121637067|ref|YP_977290.1| 426 GNFGFGNAGNNNFGFGNSGFENMGVGNSGAYNTGSFNSG 464
                                    8*************************************9 PP

  == domain 10  score: 36.0 bits;  conditional E-value: 5.3e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    NtG+lNsG +NtG++N+G  NtG f +G+ NtG+g 
  gi|121637067|ref|YP_977290.1| 467 NTGDLNSGDFNTGWANSGDINTGGFHSGDLNTGFGS 502
                                    **********************************96 PP

  == domain 11  score: 19.0 bits;  conditional E-value: 1e-07
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G++N+G+gN+Gf N+G +N G++N+   NtG++ +G
  gi|121637067|ref|YP_977290.1| 510 NSGFGNIGTGNSGFNNSGDANSGFQNT---NTGAFFIG 544
                                    899999999999999999999999986...77777665 PP

  == domain 12  score: 9.0 bits;  conditional E-value: 0.00014
                 Pentapeptide_2   3 tGslNsGsg.NtGffNlGsg.NtGsfNlGsgNtGsgnt 38 
                                    +G lNsG g ++G  N+G+g NtG fN+G++NtG+gn+
  gi|121637067|ref|YP_977290.1| 546 SGLLNSGGGqHVGISNSGTGfNTGLFNTGFNNTGIGNS 583
                                    699999877479******988***************97 PP

  == domain 13  score: 7.4 bits;  conditional E-value: 0.00043
                 Pentapeptide_2  13 tGffNlGsgNtGsfNlGsgNtGsg 36 
                                    +G +N+G  + G fN+G+  +G++
  gi|121637067|ref|YP_977290.1| 593 SGVANSGDNSSGGFNAGNDQSGFF 616
                                    588888888888888888888876 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0  35.3     3e-60   2.7e-56       1     157 [.       5     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 3e-60
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPEvnsal++aG+gsgp laAaaaWdgLaael +aa++++s +a+la++aWqGp+++amaaaaapy++WLs+aa++a 
  gi|121637067|ref|YP_977290.1|   5 VLPPEVNSALMFAGAGSGPTLAAAAAWDGLAAELGQAANSFSSATAALADTAWQGPAATAMAAAAAPYASWLSTAATRAL 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aAaqa+aaaa+YeaA+aa+v+p ++aanr +l++lv +n+fGqn+paIaatea+ye++wa+d+aam +Y++ ++a+
  gi|121637067|ref|YP_977290.1|  85 SAAAQAKAAAAVYEAARAATVDPLLVAANRHQLVSLVLSNLFGQNAPAIAATEAAYEQLWAADVAAMVSYHSGASAV 161
                                    *************************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4628.52
//
Query:       gi|121637068|ref|YP_977291.1|  [L=80]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-16   59.3   0.0      3e-16   59.2   0.0    1.1  1  Thiolase_C  Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   1.7e-20     3e-16      74     122 ..      30      78 ..      16      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.7e-20
                                    -HHHH-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                     Thiolase_C  74 GaialGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                     aialGHP+G sGaR+++t+l+++  +g ++g+ ++C g gq++a+++e
  gi|121637068|ref|YP_977291.1|  30 SAIALGHPFGGSGARLMTTVLHHMPDKGIRYGLQTMCEGRGQANATIVE 78 
                                    59*********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 554.31
//
Query:       gi|121637069|ref|YP_977292.1|  [L=113]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-20   72.5   0.0    3.7e-20   72.3   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    3.5e-13   49.8   0.0    3.5e-13   49.8   0.0    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   4.1e-24   3.7e-20       8     118 ..       2     112 ..       1     113 [] 0.90

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4.1e-24
                                    EEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHH CS
                          ECH_1   8 viklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlelwtklyt 86 
                                    vi++nrPea Na++ +++  + +ale++ d++ vravv+tG gdk  +aGadlk++a++e+  +    e   + +++   
  gi|121637069|ref|YP_977292.1|   2 VITINRPEARNAVNGAVSIVVGDALEEAHDNPDVRAVVITGaGDKSLCAGADLKAIARRENPYHPHHGEWGIAGYRH-HF 80 
                                    8*********************************************************9855555555666666666.56 PP

                                    SSSEEEEEE-SEEETHHHHHHHHSSEEEEETT CS
                          ECH_1  87 vpkpviaavnGaaigGGlelalacDiviaadn 118
                                    ++kp+ aav+G a+  G+e ala D+v+a+++
  gi|121637069|ref|YP_977292.1|  81 IDKPTSAAVSGTALDDGAEPALASDLVVADEH 112
                                    9****************************985 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   3.9e-17   3.5e-13       3      66 ..       2      65 ..       1     113 [] 0.86

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.9e-17
                                   EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS- CS
                          ECH_2  3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegk 66
                                   vit+nrp+a Na++ ++   + +al+e +++++v++vv++gag+k++CAG D++a+++ ++  +
  gi|121637069|ref|YP_977292.1|  2 VITINRPEARNAVNGAVSIVVGDALEEAHDNPDVRAVVITGAGDKSLCAGADLKAIARRENPYH 65
                                   89******************************************************99877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 876.05
//
Query:       gi|121637070|ref|YP_977293.1|  [L=122]
Description: hypothetical protein BCG_1199c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 935.60
//
Query:       gi|121637071|ref|YP_977294.1|  [L=338]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-15   56.3   7.4    4.5e-10   39.3   4.0    3.1  2  FAD_binding_3  FAD binding domain
    3.1e-05   23.5   0.2    6.5e-05   22.5   0.2    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
      6e-05   22.3   0.9      6e-05   22.3   0.9    2.3  3  FAD_binding_2  FAD binding domain
    0.00016   21.0   0.4    0.00027   20.3   0.4    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00018   20.7   7.4      0.049   12.7   0.3    2.9  3  Lycopene_cycl  Lycopene cyclase protein
    0.00024   20.8   3.7    0.00083   19.0   0.2    2.2  2  DAO            FAD dependent oxidoreductase
     0.0011   17.7   0.3     0.0017   17.1   0.3    1.2  1  HI0933_like    HI0933-like protein
     0.0022   18.2   0.1     0.0065   16.7   0.1    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0075   15.6   0.2      0.011   15.0   0.2    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
        0.1   11.8   0.1       0.26   10.5   0.1    1.7  2  Thi4           Thi4 family
       0.12   13.0   0.1       0.25   11.9   0.1    1.6  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   4.0   2.8e-13   4.5e-10       1     187 [.       5     168 ..       5     219 .. 0.83
   2 !   11.9   0.1   5.9e-05     0.096     276     316 ..     237     277 ..     228     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.8e-13
                                    EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEEC CS
                  FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynel 80 
                                    +td l+VG+Gp Gl +al  + +G +v++ e r++ +++  ++gl +  +  l +lG++      g p +++  a  +e 
  gi|121637071|ref|YP_977294.1|   5 DTDLLVVGGGPGGLATALHARARGLSVIVAEPRENPIDKACGEGLMPGGLAELTSLGVD----PVGLPFHGI--AYVGE- 77 
                                    6899*****************************************************97....567666654..44444. PP

                                    CCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE CS
                  FAD_binding_3  81 sdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvG 160
                                        ++r++    ++      +  t l  +L+++a+e+ ++  ++ +v +++qd  gvta            vrak+lv+
  gi|121637071|ref|YP_977294.1|  78 ----HRRVQAR--FRTGPGRGVRRTTLHAALAARAKEQDTEWIRS-RVATIQQDAHGVTAA----------GVRAKWLVA 140
                                    ....3344444..5566677999**************99998876.5666*******9984..........589****** PP

                                    --GTT-HHHHHHTGG.EEEEEEEEEEEE CS
                  FAD_binding_3 161 aDGgrStvrktlgie.fegeetvyeagv 187
                                    aDG +S+vr+++gi+   g+ + y +++
  gi|121637071|ref|YP_977294.1| 141 ADGLHSAVRRAVGIKaTAGTPRRYGVRW 168
                                    **************97778777766655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.9e-05
                                    EEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHH CS
                  FAD_binding_3 276 rvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLaw 316
                                    +v+++   grv+l+GDAa      +G G+ +a++ a   ++
  gi|121637071|ref|YP_977294.1| 237 QVVSRRVAGRVLLVGDAAGYEDALTGEGISLAVKQAAAAVS 277
                                    67777889*************************99987665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2     4e-08   6.5e-05       1      31 [.       7      37 ..       7      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                   D++VvGGgp+G+a A+ A  +G +v++ e+r
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHARARGLSVIVAEPR 37
                                   99*************************9997 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.9   3.7e-08     6e-05       1      32 [.       7      38 ..       7      50 .. 0.90
   2 ?   -0.1   1.1      0.24   3.9e+02      95     185 ..      56     143 ..      48     174 .. 0.56
   3 ?   -3.2   0.1       2.1   3.4e+03     224     240 ..     259     276 ..     251     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.7e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   D++V+G+G +GLa Al a+ +Gl+v+v e  +
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHARARGLSVIVAEPRE 38
                                   89*************************98655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                                    HHHHT.....T----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEE CS
                  FAD_binding_2  95 eLeel.....gvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLiv 169
                                    eL++l     g+pf++      +v e   ++a+ rt+++++++         +l a+l+++a++ + + + r +++++ +
  gi|121637071|ref|YP_977294.1|  56 ELTSLgvdpvGLPFHG----IAYVGEHRRVQARFRTGPGRGVR-------RTTLHAALAARAKE-QDTEWIRSRVATIQQ 123
                                    5555544444555555....33333333334445666666665.......44455555555533.356688888888888 PP

                                    CTTEEEEEEEEET....TTT CS
                  FAD_binding_2 170 edgrvtGavvenp....esg 185
                                    +  +vt a v+ +    ++g
  gi|121637071|ref|YP_977294.1| 124 DAHGVTAAGVRAKwlvaADG 143
                                    77788888877666664333 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.1
                                    T-S-HHHHHHHCTTSS.E CS
                  FAD_binding_2 224 avtGdglalalragaa.l 240
                                    a tG+g++la+ ++aa +
  gi|121637071|ref|YP_977294.1| 259 ALTGEGISLAVKQAAAaV 276
                                    779999999999998844 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   1.7e-07   0.00027       2      33 ..       7      38 ..       6     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   d++v+GgGp+Gla+al++++ g+ v++ e ++
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHARARGLSVIVAEPRE 38
                                   789************************97333 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3     3e-05     0.049       1      36 [.       7      40 ..       7      46 .. 0.92
   2 !   10.2   0.1   0.00017      0.28      82     150 ..      91     152 ..      69     183 .. 0.78
   3 ?    0.9   0.3      0.12   1.9e+02     253     316 ..     242     303 ..     231     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   D++v+G+Gp gl+ A +    + gl+v++ e+ +++
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHA--RARGLSVIVAEPRENP 40
                                   99***************9..999*******998876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                  Lycopene_cycl  82 grvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrl 150
                                    + v+++ l++ l+ r  e+  +  +++v+ ++++       v+++g  +ra++ v a gl s+   r++
  gi|121637071|ref|YP_977294.1|  91 RGVRRTTLHAALAARAKEQDTEWIRSRVATIQQDAH----GVTAAG--VRAKWLVAADGLHSAV-RRAV 152
                                    569*****************************9998....355555..8999*****9977766.2333 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                  Lycopene_cycl 253 rleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlwprerkrqr 316
                                    r++ +vl +G aag     TG  +  ++++a    sai++       ++ aw++  +  r   r
  gi|121637071|ref|YP_977294.1| 242 RVAGRVLLVGDAAGYEDALTGEGISLAVKQAAAAVSAIVDDTP--ASYEAAWHRITRDYRLVTR 303
                                    445569999******9999*99999999999844444444433..4556666666666555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   5.1e-07   0.00083       1      30 [.       7      38 ..       7      48 .. 0.91
   2 ?    3.1   0.3     0.036        59     148     208 ..      98     149 ..      76     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.1e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                   d++++GGG  Gl+tA+++ +rg  V++ e ++
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHARARGlsVIVAEPRE 38
                                   789***************9999*****99985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHHH CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdllg 208
                                    l aala++a+++  e ++  +v  ++++   ++gv  t++g +  a+ +V a G++s  ++
  gi|121637071|ref|YP_977294.1|  98 LHAALAARAKEQDTEWIRS-RVATIQQD---AHGV--TAAGVR--AKWLVAADGLHSA-VR 149
                                    5578888999999999997.88889664...7788..444875..6889999999985.22 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3     1e-06    0.0017       2      38 ..       7      43 ..       6      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                   d++v+GgG+ Gl +A++a++rg +V++ e  +++  K
  gi|121637071|ref|YP_977294.1|  7 DLLVVGGGPGGLATALHARARGLSVIVAEPRENPIDK 43
                                   789**************************99988777 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     4e-06    0.0065       1      29 [.      10      38 ..      10      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                   +vG+G +Gl++A +++ +g++v + e r+
  gi|121637071|ref|YP_977294.1| 10 VVGGGPGGLATALHARARGLSVIVAEPRE 38
                                   8*********************9999876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   6.8e-06     0.011       1      28 [.       9      35 ..       9      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilE 28
                                   +++G+GP Gla+a++++  gl ++++ E
  gi|121637071|ref|YP_977294.1|  9 LVVGGGPGGLATALHARARGL-SVIVAE 35
                                   69*******************.677766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.26      17      50 ..       5      37 ..       1      55 [. 0.77
   2 ?   -2.6   0.0       1.6   2.5e+03     173     218 ..     265     308 ..     245     314 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                                   ++D+++vG+G+ GL++a     + +l v++ e +
  gi|121637071|ref|YP_977294.1|  5 DTDLLVVGGGPGGLATALHARAR-GLSVIVAEPR 37
                                   68************999875555.9****99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                                    TTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE- CS
                           Thi4 173 vavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyva 218
                                    ++++vk+ + +  ++ + +  ++  e a + i ++ r v  +l++a
  gi|121637071|ref|YP_977294.1| 265 ISLAVKQAAAA--VSAIVDDTPASYEAAWHRITRDYRLVTRGLVLA 308
                                    44444444433..366777777777777777777777777776655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00015      0.25       2      40 ..       8      47 ..       7      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDe 40
                                   ++vvGgG  gl  A  +++ g +V v e ++++  ++++e
  gi|121637071|ref|YP_977294.1|  8 LLVVGGGPGGLATALHARARGLSVIVAEPRENPIdKACGE 47
                                   69******************************99555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2386.44
//
Query:       gi|121637072|ref|YP_977295.1|  [L=166]
Description: hypothetical protein BCG_1201c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-27   93.4   1.1    8.7e-27   93.4   1.1    2.0  2  ICMT      Isoprenylcysteine carboxyl methyltransferase (ICMT)
    1.1e-08   35.4   0.7    1.1e-08   35.4   0.7    1.6  2  PEMT      Phospholipid methyltransferase
     0.0082   15.7   0.7     0.0082   15.7   0.7    2.1  2  DUF1295   Protein of unknown function (DUF1295)


Domain annotation for each model (and alignments):
>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       0.3   1.8e+03      47      58 ..      38      49 ..      33      62 .. 0.63
   2 !   93.4   1.1   1.5e-30   8.7e-27       1      92 [.      73     163 ..      73     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                           ICMT 47 PnYllfvilela 58
                                   P Y++ vil  a
  gi|121637072|ref|YP_977295.1| 38 PHYVVMVILHTA 49
                                   788886655433 PP

  == domain 2  score: 93.4 bits;  conditional E-value: 1.5e-30
                           ICMT   1 llllvllaqalrlvvmatlGeiwttrvailpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvall 80 
                                    +l++v+++q lr++++++lG+ w+trv++lp ++lv++g+y+++rHPnY++ v+ e  +l+L++ a+ltalv+++++a l
  gi|121637072|ref|YP_977295.1|  73 MLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPNYVA-VVAEGFALPLVHTAWLTALVFTLANATL 151
                                    57889**********************************************.99************************** PP

                           ICMT  81 lfvRikeEekaL 92 
                                    l+vR++ E++ L
  gi|121637072|ref|YP_977295.1| 152 LTVRLRVENSVL 163
                                    *********987 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.98   5.9e+03      54      68 ..      38      52 ..      36      61 .. 0.63
   2 !   35.4   0.7   1.8e-12   1.1e-08       8      98 ..      75     163 ..      68     166 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.98
                           PEMT 54 PeyvgstlgflGlaL 68
                                   P yv +++   +l L
  gi|121637072|ref|YP_977295.1| 38 PHYVVMVILHTALLL 52
                                   666666665555544 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.8e-12
                           PEMT   8 llialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvyl 87 
                                    +++++ + l+++ +++lg+  + +  + l+   +lv++G+Yr++++P yv++++  ++l L++  +++ l+ +l+ ++ l
  gi|121637072|ref|YP_977295.1|  75 AVVVASQGLRWWCVKSLGK-RWNTRVIVLP-HATLVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLL 152
                                    5667788899999999997.4666777664.558*********************************9888888888888 PP

                           PEMT  88 ialkfvEephl 98 
                                     ++ +vE+ +l
  gi|121637072|ref|YP_977295.1| 153 TVRLRVENSVL 163
                                    88888**9876 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.6     0.075   4.5e+02     175     197 ..      67      90 ..      63     103 .. 0.79
   2 !   15.7   0.7   1.4e-06    0.0082     155     206 ..     107     158 ..     101     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.075
                        DUF1295 175 iWwglflialea.leglealaiag 197
                                     W+g  ++a+ + ++gl ++++ +
  gi|121637072|ref|YP_977295.1|  67 PWLGWPMLAVVVaSQGLRWWCVKS 90 
                                    699998888766478999999976 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-06
                        DUF1295 155 vldsGLwrysRHPNYfgealiWwglflialealeglealaiagpllltlllv 206
                                    ++++G +r+ RHPNY + +   ++l l+ +  l+ l + +  + ll++ l v
  gi|121637072|ref|YP_977295.1| 107 LVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRV 158
                                    67899*********************99998888876655556555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1161.81
//
Query:       gi|121637073|ref|YP_977296.1|  [L=282]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-09   36.1   5.0    6.1e-09   36.1   5.0    2.2  2  CPBP       CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.084   12.2   0.1       0.18   11.1   0.0    1.5  2  OST3_OST6  OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.1      0.17   1.5e+03      61      66 ..     111     116 ..      58     167 .. 0.57
   2 !   36.1   5.0   6.8e-13   6.1e-09       5      90 ..     186     269 ..     182     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                                    HHHHHH CS
                           CPBP  61 laalaG 66 
                                    ++ala 
  gi|121637073|ref|YP_977296.1| 111 TLALAA 116
                                    222222 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 6.8e-13
                                    HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.HHH.HHHHHHHHHHHHHHHHHTT-HHHH CS
                           CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.gps.vllaalaGlvlgylylktgsllaa 82 
                                    ll +ll++l+++++EE++fRg l+++l +r+     + is +l++ a ++  ++   ++a+++G v+++ ++ +g +la+
  gi|121637073|ref|YP_977296.1| 186 LLPILLITLINGIAEEMFFRGALYTALGRRYP----VTISTVLYVGATMASaNLMlGFAAIFVGTVCALERRASGGVLAP 261
                                    77899*************************44....4455555544444442222359999******************* PP

                                    HHHHHHHH CS
                           CPBP  83 illHalln 90 
                                    il+H+++ 
  gi|121637073|ref|YP_977296.1| 262 ILTHFVWG 269
                                    *****985 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     2e-05      0.18     109     193 ..      33     119 ..      18     127 .. 0.83
   2 ?   -3.3   0.5      0.49   4.4e+03     157     189 ..     239     274 ..     219     276 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2e-05
                      OST3_OST6 109 k..eskkkdtydfsrggfdaealakfisertgvkirikrppnyskiiitallvlllvlllklrrklllkilksktlwavl 186
                                    +  + +++  +  s++ ++   la+f    t+v ++ ++pp + +   +++ v+l+++++ l  +l  +   s + w++l
  gi|121637073|ref|YP_977296.1|  33 DhsNRESPACMSQSTTPYRSSVLAEFRRAITNVAVPHHEPPGIVRRRRVVVGVTLVIGAVMLGFSLRRTPGESSFYWLTL 112
                                    222333777788888888999***************************************99999998888********* PP

                      OST3_OST6 187 slliill 193
                                    +l+++++
  gi|121637073|ref|YP_977296.1| 113 ALAAVWI 119
                                    *999876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.49
                      OST3_OST6 157 llvlllvlllklrrkll...lkilksktlwavlsll 189
                                    +++++++++  l r+     l  +   ++w++++++
  gi|121637073|ref|YP_977296.1| 239 FAAIFVGTVCALERRASggvLAPILTHFVWGLIMVF 274
                                    223333332222222221112224555666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2008.23
//
Query:       gi|121637074|ref|YP_977297.1|  [L=268]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-44  150.8   0.0    4.6e-44  150.6   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.8e-23   83.0   0.1    4.2e-20   72.5   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
       0.24   10.7   3.0        0.2   11.0   0.2    2.0  2  YdjM      LexA-binding, inner membrane-associated putative hy
       0.96    9.4   3.3         36    4.3   0.0    3.9  4  PT-TG     Pre-toxin TG


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0     1e-47   4.6e-44       5     250 ..      22     267 ..      18     268 .] 0.97

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 1e-47
                                    TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHH CS
                          ECH_1   5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtkl 84 
                                     v+ +++nrP  +N+l+  +lt +++ le++  d+ v++v L G ++ F++G  +      +    + + ee +   +++
  gi|121637074|ref|YP_977297.1|  22 RVLSVRINRPSSLNSLTVPILTGIADTLERAAADPVVKVVRLGGVGRGFSSGVSMSVDDVWGGGPPTAIVEEANRAVRAV 101
                                    6899************************************************999876666668999999999******* PP

                                    HHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHH CS
                          ECH_1  85 ytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqea 164
                                      +p pv+a v+G a+g  + lalacD++ a+d+a f+l+ +k+ l+p+ g++  +a + G+ +A++++ll++++ a ea
  gi|121637074|ref|YP_977297.1| 102 AALPHPVVAVVQGPAVGVAVSLALACDFILASDSAFFMLANTKVALMPDGGASALVAAATGRIRAMRLALLAEQLPAREA 181
                                    ******************************************************************************** PP

                                    HHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCS CS
                          ECH_1 165 lkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkr 244
                                    l +Gl+++v p+ +++ e  +++ +l+  + +a++q+k+a+na++  +l+  ++ e + +e +  ++d+ eG  afl +r
  gi|121637074|ref|YP_977297.1| 182 LAWGLISAVYPDSDFEAEVDKVISRLLAGPALAFAQAKNAINAAALTELEPTFARELDGQEVLLRTHDFAEGAAAFLQRR 261
                                    ******************************************************************************** PP

                                    H----- CS
                          ECH_1 245 kpefed 250
                                     p+f++
  gi|121637074|ref|YP_977297.1| 262 TPNFTG 267
                                    ****86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   9.3e-24   4.2e-20       4     182 ..      26     201 ..      23     214 .. 0.92
   2 !    9.2   0.0   0.00017      0.75     257     311 ..     208     261 ..     198     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 9.3e-24
                                    EEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHH CS
                          ECH_2   4 itLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyli 83 
                                    + +nrp++lN+L+ ++++ ++++l++ ++d+ vk+v l g g ++f++G  v + +++   g    +++++e  +   ++
  gi|121637074|ref|YP_977297.1|  26 VRINRPSSLNSLTVPILTGIADTLERAAADPVVKVVRLGGVG-RGFSSG--VSMSVDDVWGGGPP-TAIVEEANRAVRAV 101
                                    789*************************************88.******..56667777776655.68************ PP

                                    HC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTH.HHHHHHH---B-HHHH CS
                          ECH_2  84 atypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgel.GlylalTGarlkgada 162
                                    a +p pvva+++G ++G  v+l++ + f  +++++ f    t++ l+PD G+s + + + g++ ++ lal +++l +++a
  gi|121637074|ref|YP_977297.1| 102 AALPHPVVAVVQGPAVGVAVSLALACDFILASDSAFFMLANTKVALMPDGGASALVAAATGRIrAMRLALLAEQLPAREA 181
                                    *************************************************************987999************* PP

                                    HHTTS--EE--GGGHHHHHH CS
                          ECH_2 163 laaglathyvpseklealee 182
                                    la gl + + p++++ea  +
  gi|121637074|ref|YP_977297.1| 182 LAWGLISAVYPDSDFEAEVD 201
                                    ***********999976544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                                    HHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS- CS
                          ECH_2 257 kkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdk 311
                                     +   ++ + + ++++ ++ + +l+ ++++El+  + ll+++Df+eG  a l  +
  gi|121637074|ref|YP_977297.1| 208 LAGPALAFAQAKNAINAAALT-ELEPTFARELDGQEVLLRTHDFAEGAAAFLQRR 261
                                    555555666666677777777.6************************99988554 PP

>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.13   5.8e+02       8      41 ..     116     150 ..     111     153 .. 0.72
   2 ?   11.0   0.2   4.4e-05       0.2       7      47 ..     155     198 ..     148     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                           YdjM   8 llGaalglalaallgaakeavllavavlg....AllPD 41 
                                    ++G+a++lala     a +    a+ +l+    Al+PD
  gi|121637074|ref|YP_977297.1| 116 AVGVAVSLALACDFILASD---SAFFMLAntkvALMPD 150
                                    6899999999988888754...3444444446799998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.4e-05
                           YdjM   7 allGaalglalaallgaake....avllavavlgAllPDiDhpss 47 
                                    al++aa+g + a +l+  +e     ++la++++ A+ PD D + +
  gi|121637074|ref|YP_977297.1| 155 ALVAAATGRIRAMRLALLAEqlpaREALAWGLISAVYPDSD-FEA 198
                                    6777777777777777776688888****************.444 PP

>> PT-TG  Pre-toxin TG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.008        36      30      45 ..      11      26 ..      10      28 .. 0.93
   2 ?   -0.5   0.0      0.25   1.1e+03      10      23 ..      37      50 ..      29      70 .. 0.81
   3 ?    1.8   0.2     0.049   2.2e+02      36      57 ..      91     112 ..      89     124 .. 0.79
   4 ?   -0.3   0.0      0.23     1e+03      16      28 ..     151     163 ..     147     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.008
                          PT-TG 30 piTGeklsdwdRllaa 45
                                   p+TG  ++ +dR+l++
  gi|121637074|ref|YP_977297.1| 11 PVTGLNVTLTDRVLSV 26
                                   89***********986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                          PT-TG 10 dfvpevggvkdaie 23
                                    +vp+++g+ d +e
  gi|121637074|ref|YP_977297.1| 37 LTVPILTGIADTLE 50
                                   57899999988776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.049
                          PT-TG  36 lsdwdRllaavalvpggvgkvg 57 
                                    +++  R+++ava++p +v+ v+
  gi|121637074|ref|YP_977297.1|  91 VEEANRAVRAVAALPHPVVAVV 112
                                    67788*********99766654 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.23
                          PT-TG  16 ggvkdaieaitGr 28 
                                    gg+ +++ a+tGr
  gi|121637074|ref|YP_977297.1| 151 GGASALVAAATGR 163
                                    89999*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1734.21
//
Query:       gi|121637075|ref|YP_977298.1|  [L=268]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-49  167.4   0.0    3.9e-49  167.2   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.3e-27   96.4   0.1    1.1e-25   90.8   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.2   0.0   4.3e-53   3.9e-49       4     250 ..      21     267 ..      18     268 .] 0.97

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 4.3e-53
                                    TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                          ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                    +gv+ ++++rPe +N+l++ +l+ +++a+e + +d+ v++v L G ++ F++G+ +           +++  e +   ++
  gi|121637075|ref|YP_977298.1|  21 DGVLSVTIDRPESLNSLTKPVLAGMADAIEGAATDPRVKVVRLGGAGRGFSSGGAISVDDVWASGPPTDTVAEANRTVRA 100
                                    79****************************************************999877776789999999999***** PP

                                    HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHH CS
                          ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqe 163
                                    +  +p pv+a v+G  +g G+ lalacD+v a+dna f+l+ +++Gl+p+ g++  ++ ++G+ +A++++ll +++ a+e
  gi|121637075|ref|YP_977298.1| 101 IVALPQPVVAVVQGPTVGCGVSLALACDLVLASDNAFFMLAHTNVGLMPDGGASALVQAAIGRIRAMHMALLPDRVPAAE 180
                                    ******************************************************************************** PP

                                    HHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                          ECH_1 164 alkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                    al +Glv++v p++++  e  +l+ +l+  + +a++  k+a+na++  +la  l  e + +  +  +dd+ eG +af  +
  gi|121637075|ref|YP_977298.1| 181 ALSWGLVSAVYPAADFDAEVDKLISRLLAGPALAIAKTKNAINAATLTELAPTLLRELDGQALLLRTDDFAEGATAFQQR 260
                                    ******************************************************************************** PP

                                    SH----- CS
                          ECH_1 244 rkpefed 250
                                    r p f++
  gi|121637075|ref|YP_977298.1| 261 RTPMFTG 267
                                    ****987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   1.3e-29   1.1e-25       3     185 ..      25     204 ..      23     209 .. 0.92
   2 !    4.3   0.0    0.0026        23     256     306 ..     207     256 ..     200     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.3e-29
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                     +t++rp++lN+L+ +++  +++a++  ++d++vk+v l gag ++f++Gg +    +   +g    ++ ++e  +   +
  gi|121637075|ref|YP_977298.1|  25 SVTIDRPESLNSLTKPVLAGMADAIEGAATDPRVKVVRLGGAG-RGFSSGGAISV-DDVWASGP-P-TDTVAEANRTVRA 100
                                    589**************************************99.*******9964.33334433.3.4699********* PP

                                    HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTH.HHHHHHH---B-HHH CS
                          ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgel.GlylalTGarlkgad 161
                                    i  +p+pvva+++G ++G Gv+l++ + +  +++++ f    t++Gl+PD G+s + + + g++ ++++al  +r+ +a+
  gi|121637075|ref|YP_977298.1| 101 IVALPQPVVAVVQGPTVGCGVSLALACDLVLASDNAFFMLAHTNVGLMPDGGASALVQAAIGRIrAMHMALLPDRVPAAE 180
                                    ************************************************************998879************** PP

                                    HHHTTS--EE--GGGHHHHHHHHH CS
                          ECH_2 162 alaaglathyvpseklealeeaLa 185
                                    al  gl + + p+++++a  ++L 
  gi|121637075|ref|YP_977298.1| 181 ALSWGLVSAVYPAADFDAEVDKLI 204
                                    ***************998887776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0026
                                    HHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHH CS
                          ECH_2 256 lkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvra 306
                                    l +   ++++ t ++++ +  + +la +l +El+  + ll+++Df+eG +a
  gi|121637075|ref|YP_977298.1| 207 LLAGPALAIAKTKNAINAATLT-ELAPTLLRELDGQALLLRTDDFAEGATA 256
                                    5555566677777777777777.6************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1697.65
//
Query:       gi|121637076|ref|YP_977299.1|  [L=360]
Description: alpha-methylacyl-CoA racemase mcr [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-80  270.4   0.1    3.7e-80  269.8   0.1    1.2  1  CoA_transf_3  CoA-transferase family III
     0.0054   17.4   0.4       0.24   12.1   0.0    2.4  2  SnoaL_2       SnoaL-like domain


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.8   0.1   4.1e-84   3.7e-80       1     355 [.       5     343 ..       5     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 269.8 bits;  conditional E-value: 4.1e-84
                   CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellk 80 
                                    L+G+rV++l+ +  Gp a+++L+dlGA+V+++++p++ D +                a+ rn+r v+ Dlks++g el++
  gi|121637076|ref|YP_977299.1|   5 LSGLRVVELAGIGPGPHAAMILGDLGADVVRIDRPSSVDGI-------------SRDAMLRNRRIVTADLKSDQGLELAL 71 
                                    89*********************************999943.............346899******************** PP

                   CoA_transf_3  81 rLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvg 160
                                    +L+akADV+ie +rpgv erlglg+ee++++n rLiya+++g+Gq+Gp+++++g+D+++ +  G+++  g  d++Pv + 
  gi|121637076|ref|YP_977299.1|  72 KLIAKADVLIEGYRPGVTERLGLGPEECAKVNDRLIYARMTGWGQTGPRSQQAGHDINYISLNGILHAIGRGDERPVPPL 151
                                    ******************************************************************************** PP

                   CoA_transf_3 161 vplgDi.vtgllaavailaallarertGkGqvidvslleaalallapqlley...latgevperqgnrdpaaapygvyrt 236
                                    + +gD+  + +++ v+ilaal +r++ GkGqv+d+++++++  l+++ +++    ++t +  +  +  d +a+ y++y++
  gi|121637076|ref|YP_977299.1| 152 NLVGDFgGGSMFLLVGILAALWERQSSGKGQVVDAAMVDGSSVLIQMMWAMRatgMWTDTRGA--NMLDGGAPYYDTYEC 229
                                    ******55558899***************************9999888766433333333333..455558888****** PP

                   CoA_transf_3 237 kdg.wvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntl 315
                                    +dg +va++a +++++aa+++ lg ++ ae p  +++a       el+a+l+e++a++++++w +++a+ + +++pv   
  gi|121637076|ref|YP_977299.1| 230 ADGrYVAVGAIEPQFYAAMLAGLGLDA-AELPPQNDRAR----WPELRALLTEAFASHDRDHWGAVFANSDACVTPVLAF 304
                                    *************************96.46666666666....6************************************ PP

                   CoA_transf_3 316 eevlddpqlaarglvvevddpdygevpvvglpvrlsetpa 355
                                     ev ++p++ +r+++ e + +  +++p++++  + s++p 
  gi|121637076|ref|YP_977299.1| 305 GEVHNEPHIIERNTFYEANGGW-QPMPAPRFSRTASSQPR 343
                                    ****************999986.88999998877777654 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   2.7e-05      0.24      45     101 ..     171     236 ..     165     237 .. 0.71
   2 ?    3.2   0.1     0.015   1.3e+02       6      41 ..     277     315 ..     271     348 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                                    HHHH.HEEEEEEEEEEEEEETTEEEEEEEEEEE...EETTSSEEEE.....EEEEEEEEETTEEEE CS
                        SnoaL_2  45 alfa.afpdlrfeihdvvadgdrvavewtvtgt...ipatgrgvtv.....rgvdvfrvrdGkive 101
                                    al++ ++++    +++ ++dg  v++++ + ++   + ++ rg ++     +++d+++ +dG+ v+
  gi|121637076|ref|YP_977299.1| 171 ALWErQSSGKGQVVDAAMVDGSSVLIQMMWAMRatgMWTDTRGANMldggaPYYDTYECADGRYVA 236
                                    33332246666677777*********96666544465555555555999*************9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                                    HHHHTTCHHHHHHTEE.EEEEEEET..TSEEESHHHHHH CS
                        SnoaL_2   6 aalnagdldalaalfa.pdvvwedp..ggelrGreaira 41 
                                    +a++++d d + a+fa  d+ ++ +  +ge++    i +
  gi|121637076|ref|YP_977299.1| 277 EAFASHDRDHWGAVFAnSDACVTPVlaFGEVHNEPHIIE 315
                                    5*************9845555555556666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2426.00
//
Query:       gi|121637077|ref|YP_977300.1|  [L=250]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-41  141.5   0.6    2.6e-41  141.2   0.6    1.1  1  adh_short       short chain dehydrogenase
    7.8e-33  114.0   0.1    9.7e-33  113.7   0.1    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    5.5e-07   29.7   6.3    7.1e-06   26.1   6.2    2.5  1  KR              KR domain
    1.2e-05   24.9   0.4    1.7e-05   24.4   0.4    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
    0.00067   18.7   0.5     0.0013   17.8   0.5    1.4  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
  ------ inclusion threshold ------
      0.039   13.9   1.7      0.055   13.4   1.7    1.3  1  NAD_binding_10  NAD(P)H-binding
       0.22   10.6   0.5        0.4    9.7   0.5    1.3  1  RmlD_sub_bind   RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.6     1e-44   2.6e-41       2     191 ..       7     198 ..       6     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 1e-44
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    v++vtG++sG+G+a+ k+l+ +Ga+vvvvd + +++      ++ +g++a ++q+Dvtd+++v++++e a + lg++ v+
  gi|121637077|ref|YP_977300.1|   7 VAVVTGGASGLGLATTKRLLDAGAQVVVVDLRGDDV------VGGLGDRARFAQADVTDEAAVSNALELA-DSLGPVRVV 79 
                                    89******************************9988......5555678******************998.99******* PP

                                    EE---S....S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.....HCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short  82 vnNAGi....tgsgpfselseeewervievNltgvflltravlpaml.....kqssGrIvnvsSvagkvpvagvaaYsAs 152
                                    vn+AG        +    +  +++++++++Nl+g+f++ r+ ++ +       +++G I+n++Sva++ + +g+aaYsAs
  gi|121637077|ref|YP_977300.1|  80 VNCAGTgnaiRVLSRDGVFPLAAFRKIVDINLVGTFNVLRLGAERIAktepiGEERGVIINTASVAAFDGQIGQAAYSAS 159
                                    ******88776666677789999*********************9888888899************************** PP

                                    HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                      adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                    K++v+g+t  +a++la++ irv+++aPGl+dT++ ++l 
  gi|121637077|ref|YP_977300.1| 160 KGGVVGMTLPIARDLASKLIRVVTIAPGLFDTPLLASLP 198
                                    *********************************998876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.1   3.8e-36   9.7e-33       1     231 [.      12     243 ..      12     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 3.8e-36
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    G asg+G a+ k+l ++Ga+vv++dl+ ++   v  l +   a++ ++DVtde++v ++ e  ++++g + ++vn+ag  
  gi|121637077|ref|YP_977300.1|  12 GGASGLGLATTKRLLDAGAQVVVVDLRGDD--VVGGLGD--RARFAQADVTDEAAVSNALEL-ADSLGPVRVVVNCAGTG 86 
                                    669************************998..5666655..3668*************9975.6789************* PP

                                    EG..CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC......CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHH CS
                   adh_short_C2  81 pk..lkgpfletsreefdraldvnlyslfllakaalp.lmkeg......gsivnlssvgaervvpnynaygaaKaaleal 151
                                    ++  + ++   ++ + f++++d+nl ++f++++  ++ ++k +      g i+n++sv+a  +  +++ay+a+K++++++
  gi|121637077|ref|YP_977300.1|  87 NAirVLSRDGVFPLAAFRKIVDINLVGTFNVLRLGAErIAKTEpigeerGVIINTASVAAFDGQIGQAAYSASKGGVVGM 166
                                    **66444445579********************9988544433677778******************************* PP

                                    HHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTT.SS-B-HHHHHHHHHHHCSGGGTT--SEEEEES CS
                   adh_short_C2 152 trylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearapl.grlgtpeevaeaalfLasdeasyitGqtlvvD 230
                                    t  +A++l++k iRv +++pg+ +T++ ++++   e ++ l ++ p   rlg+p+e ++++l ++   + + +G+++  D
  gi|121637077|ref|YP_977300.1| 167 TLPIARDLASKLIRVVTIAPGLFDTPLLASLP--AEAKASLGQQVPHpSRLGNPDEYGALVLHIIE--NPMLNGEVIRLD 242
                                    *******************************9..677788888888625799*******9999987..569999999999 PP

                                    T CS
                   adh_short_C2 231 g 231
                                    g
  gi|121637077|ref|YP_977300.1| 243 G 243
                                    7 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   6.2   2.8e-09   7.1e-06       2     152 ..       7     159 ..       6     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.8e-09
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeepp 81 
                                    + ++tGG+ gLGl++++ l++ ga+ +v+  R        ++    +  lg + ++++aDv+d++av+++le ++ + +p
  gi|121637077|ref|YP_977300.1|   7 VAVVTGGASGLGLATTKRLLDAGAQVVVVDLRG-------DDV---VGGLGDRARFAQADVTDEAAVSNALELAD-SLGP 75 
                                    679**********************99999998.......223...4567889*******************998.667* PP

                                    --EEEE---------TTT--....HHHHHHHHTTTTHHHHHHHHHTTT.........S--SEEEEEEEHHHHH--TT-HH CS
                             KR  82 ikGvihaAgvlrdklleemt....aedleqvlapKvkGawnLhelled.........esldffvlfSSiagllgsagqan 148
                                    ++ v+++Ag+ +   + + +     +++++++   + G+ n+ +l ++         e+  +++ ++S+a++ g+ gqa+
  gi|121637077|ref|YP_977300.1|  76 VRVVVNCAGTGNAIRVLSRDgvfpLAAFRKIVDINLVGTFNVLRLGAEriaktepigEERGVIINTASVAAFDGQIGQAA 155
                                    **********9987777765333368999999999999999988877767667777778889999999999999999999 PP

                                    HHHH CS
                             KR 149 Yaaa 152
                                    Y+a 
  gi|121637077|ref|YP_977300.1| 156 YSAS 159
                                    9985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.4   6.8e-09   1.7e-05       2      76 ..       9      87 ..       8     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.8e-09
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHH...HH.T-SEEEE--S--- CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfk...ee.qpdavihlAavgg 76
                                   +VtG++  +G a++k+ll++g +v+++d + ++   ++ +++++ ++d+td++a+ ++++   +   + +v+++A+ g+
  gi|121637077|ref|YP_977300.1|  9 VVTGGASGLGLATTKRLLDAGAQVVVVDLRGDDVVGGLGDRARFAQADVTDEAAVSNALEladSLgPVRVVVNCAGTGN 87
                                   8*****************************999999999999***********99877651114456789999998544 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   5.2e-07    0.0013       1     101 [.       9     119 ..       9     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.2e-07
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvd......vvihla 74 
                                    vvtGga  lG a  k+L++++   +v v+Dlr ++ +       +++ + ++Dvtd++ +++ale +d      vv+  a
  gi|121637077|ref|YP_977300.1|   9 VVTGGASGLGLATTKRLLDAG--AQVVVVDLRGDDVVGGLG---DRARFAQADVTDEAAVSNALELADslgpvrVVVNCA 83 
                                    8********************..59********99993333...333478*************98654222322788888 PP

                      3Beta_HSD  75 slvdvagklted.........eimkvnvkGTrnvle 101
                                    +  +   +l++d         +i ++n+ GT nvl 
  gi|121637077|ref|YP_977300.1|  84 GTGNAIRVLSRDgvfplaafrKIVDINLVGTFNVLR 119
                                    776665555544222222222678888888888875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7   2.1e-05     0.055       1      73 [.      12      88 ..      12     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                   TTTSHHHHHHHHHHHHC-T-EEEEE.ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT......T-SEEEES---TCC CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtal.vRnpeklaeleaeeglevvegdvtdvedlaealk......gadaVvsalggggk 73
                                   G+  + G + +k+ll++g  +v+++  R  + +  l   ++++  ++dvtd++++ +al+       + +Vv ++g+g+ 
  gi|121637077|ref|YP_977300.1| 12 GGASGLGLATTKRLLDAG-AQVVVVdLRGDDVVGGLG--DRARFAQADVTDEAAVSNALEladslgPVRVVVNCAGTGNA 88
                                   666679***********6.888888789999999886..79******************944444344477777776654 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00016       0.4       4      59 ..       9      83 ..       7      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                                   EEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH-...-.SEEEE-- CS
                  RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeak...p.dvvvnaA 59
                                   +vtG+   lG + +k+l  +g++v+ ++ +               ++d+td++av ++l+ a+   p +vvvn+A
  gi|121637077|ref|YP_977300.1|  9 VVTGGASGLGLATTKRLLDAGAQVVVVDLRgddvvgglgdrarfaQADVTDEAAVSNALELADslgPvRVVVNCA 83
                                   79*************************8888**************************9965441113269****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1798.06
//
Query:       gi|121637078|ref|YP_977301.1|  [L=781]
Description: transmembrane transport protein mmpL13 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-75  251.5  42.4    2.1e-50  171.5  12.1    2.8  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.5  12.1   1.2e-54   2.1e-50       3     329 ..      44     375 ..      42     394 .. 0.91
   2 !   84.9  22.1   2.6e-28   4.7e-24     116     311 ..     514     733 ..     487     752 .. 0.85

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 1.2e-54
                           MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpd.vaaafv 81 
                                    +++  es++a++ l+ +f +  +++k+ +vv+   + a+ +  a+++ +++v+ l ++++ v +v ++++ p  +aa ++
  gi|121637078|ref|YP_977301.1|  44 QDPRSESARAIEVLTDKFGQ--SGQKMLIVVT-AAAGADSP-PAREVGTDIVEVL-RRSPLVYNVTSPWTVPPtAAADLL 118
                                    567899**************..6689999999.66666666.7888888888888.6666788888888888879999** PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    S Dgk+  ++v+++g  g+++a+++++ + + v++ r  +g++v+ +G+a+ +a ++   + dl ++e++++ + +++L+
  gi|121637078|ref|YP_977301.1| 119 STDGKSGLIVVNVKG--GENDAQNHAQTLSDEVAHDR--DGVTVRAGGSAMEYAQINRQNKDDLLVMELIAIPLSFLVLI 194
                                    **************9..899999**************..***************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                     v++ l+aa+lp++ +v+ ++ ++++  +   + + e+stf+l+l+++l++a ++DY+ll+vsRyr+ela+g+dr+ea+i
  gi|121637078|ref|YP_977301.1| 195 WVFGGLLAAGLPMAQAVLAVVGSMAV--LRLVTFATEVSTFALNLSTALGLALAIDYTLLIVSRYRDELAEGSDRDEALI 272
                                    ***********************999..55566789******************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.lakprrkrkk.... 316
                                    r++a++g++v+++++tva++m + ++  + +l++++ a   +v++++ +++ ++PA +vllG +    + rr +++    
  gi|121637078|ref|YP_977301.1| 273 RTMATSGRTVLFSAVTVALSMSATALFPMYFLKSFAYAGVATVAFVATASIVITPAAIVLLGPRLdALDVRRLVRRllgr 352
                                    **************************************9999999999999999**********8777888888888888 PP

                           MMPL 317 ..........rwWrrlgrlvvrr 329
                                               +W r++++v rr
  gi|121637078|ref|YP_977301.1| 353 pdpvhkpvkqLFWYRSSKFVMRR 375
                                    99999999996666777888776 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 2.6e-28
                           MMPL 116 earpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilall 194
                                    +   ++g  v  +G+a +++d  da++  l ++  +++++  v+L+++++S+v ++  l+  v+sl aa+g  v i++  
  gi|121637078|ref|YP_977301.1| 514 QVAGPAGRSVVMAGVAQVNRDSVDAVTDRLPMVLGLIAAITYVLLFLLTGSVVLPAKALVCNVLSLTAAFGAlVWIFQEG 593
                                    344578999*********************************************************************99 PP

                           MMPL 195 lglelstf........vlgllvvlliavGtDYallLvsRyreelaa.gedree.............aviravastgkvvt 252
                                    ++ +l t+        ++ ll+ ++++ + DY ++LvsR+re+  + g  r +             +v+  va+tg+v+t
  gi|121637078|ref|YP_977301.1| 594 HFGALGTTpsgtlvanMPVLLFCIAFGLSMDYEVFLVSRIREYWLEsGAARPArrsvaevhaandeSVALGVARTGRVIT 673
                                    98877664333333337789**********************854413333224556667777777************** PP

                           MMPL 253 aaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraalakpr 311
                                    aa+l++ +++++L +a +++++ +G+ + l+v+ d+ +v+ ++ PA++ ++Gr+++ +pr
  gi|121637078|ref|YP_977301.1| 674 AAALVMSMSFAALIAAHVSFMRMFGLGLTLAVAADATLVRMVVvPAFMHVTGRWNWWAPR 733
                                    ***********************************999999999**********755553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4876.56
//
Query:       gi|121637079|ref|YP_977302.1|  [L=216]
Description: hypothetical protein BCG_1208 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.8   0.0    1.4e-15   57.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      9e-12   45.5   0.0    1.5e-11   44.8   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.4e-09   37.7   0.0    3.9e-09   37.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      1e-08   35.8   0.0    1.6e-08   35.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    7.9e-05   22.5   0.0    0.00014   21.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.021   14.5   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      0.048   13.0   0.0       0.06   12.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.17   10.8   0.0       0.23   10.4   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.19   11.5   0.0       0.26   11.0   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   6.9e-19   1.4e-15       3     160 ..      26     186 ..      24     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 6.9e-19
                Methyltransf_23   3 aqreeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqe 75 
                                    a+++e++++++ + l     +grvL++G+G+G++  ++   + +v+++++ p++ ++a+        ++   ++ +   e
  gi|121637079|ref|YP_977302.1|  26 AHEAEAIRALRRENL--AGLSGRVLEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARiaaadapVPIVVTDKTV---E 100
                                    666777888887766..47899**************9988888***************999987773333333333...4 PP

                Methyltransf_23  76 aaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllld....wlylvpagrhisffsarsl 151
                                    +  + ++fd +v++ vl++v dp ++l+++++ll+ gG l  +e+ as+ ++ +++       +++ a +    ++ r+ 
  gi|121637079|ref|YP_977302.1| 101 EFRDTETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEHVASAGARGRVQRfvdaTFWPRLA-GN--CHTHRHT 177
                                    555688****************************************9996555555544442445555.22..2223355 PP

                Methyltransf_23 152 kelleeaGl 160
                                    +++  +aG+
  gi|121637079|ref|YP_977302.1| 178 ERAILDAGF 186
                                    555555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   7.3e-15   1.5e-11       1      94 [.      48     140 ..      48     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7.3e-15
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T.T-EEEEEEES-CCC-CCHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed.nsfDlvvssevlhhvedpek 79 
                                    L+vG+G G +++++  ++++v+++++ +++ + a+ +a +++  v +vv d +   f+d ++fD+vv+s vl+ v dp +
  gi|121637079|ref|YP_977302.1|  48 LEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARIAAADAP--VPIVVTDKTVEEFRDtETFDAVVCSLVLCSVSDPGA 125
                                    89*************888********************9999..778888877558***88******************* PP

                                    HHHHHHHHEEEEEEE CS
                Methyltransf_11  80 alkeiaRvLkpgGll 94 
                                    +l+ ++ +L+ gG l
  gi|121637079|ref|YP_977302.1| 126 VLAHLRSLLRRGGEL 140
                                    *************76 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0     2e-12   3.9e-09       1      97 []      47     138 ..      47     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2e-12
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vL++G+G G++ ++   ++  ++v+++++ +++ ++ar  a+++ + + +  + +e++    ++fD+vv+s +l+ +s  
  gi|121637079|ref|YP_977302.1|  47 VLEVGAGVGTNFAYYPVAV--EQVIAMEPEPRLAAKARIAAADAPVPIVVTDKTVEEFRDT-ETFDAVVCSLVLCSVS-- 121
                                    9*************99998..9*******************99988999999999999855.6*******86666666.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    d  ++l++++++L+ gG
  gi|121637079|ref|YP_977302.1| 122 DPGAVLAHLRSLLRRGG 138
                                    6679************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   7.9e-12   1.6e-08       1      99 []      48     140 ..      48     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 7.9e-12
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le+G+G+G++ ++   +    +++++++ p+    ak+++a+ ++     + ++++ +++  + ++fD+vv+s vl+ + 
  gi|121637079|ref|YP_977302.1|  48 LEVGAGVGTNFAYYPVA--VEQVIAMEPEPRLA--AKARIAAADAPV--PIVVTDKTVEEFRDTETFDAVVCSLVLCSVS 121
                                    8*************999..88899*********..888888877633..3333333333333336*************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d+ +vl+++r+lL+ gG l
  gi|121637079|ref|YP_977302.1| 122 DPGAVLAHLRSLLRRGGEL 140
                                    *****************76 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.2e-08   0.00014      59     113 ..      95     146 ..      44     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.2e-08
                Methyltransf_31  59 eqgdieeleklled.ekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                        +ee+     d e+fD +++  vl+ ++dp ++l  + ++l+ gg+l   ++ 
  gi|121637079|ref|YP_977302.1|  95 TDKTVEEFR----DtETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEHV 146
                                    444555544....3389*********************************988887 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     1e-05     0.021      42     133 ..      42     134 ..      21     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                           NodS  42 gsiadalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfstdekfdlivvaevlyyie 120
                                    g  + +levG   G+      +  +++  ++  ++  a+ar    +++  i  + + v++f  +e fd +v++ vl  ++
  gi|121637079|ref|YP_977302.1|  42 GLSGRVLEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARIAAADAPvPIVVTDKTVEEFRDTETFDAVVCSLVLCSVS 121
                                    556789****99999999999999999999999999999999888866246666778**********************9 PP

                           NodS 121 dvaelraavrnlv 133
                                    d  ++ a +r l+
  gi|121637079|ref|YP_977302.1| 122 DPGAVLAHLRSLL 134
                                    9888877777654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05      0.06     100     154 ..      90     145 ..      50     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                    EEEEE--TTT-TTS-.T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                Ubie_methyltran 100 ieflqanaeeLpfed.dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                    +  ++++    +f d ++fD v  s  l  v+D   +L +++  l+ GG+l  le 
  gi|121637079|ref|YP_977302.1|  90 VPIVVTDKTVEEFRDtETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEH 145
                                    55666666777899989**********************************99996 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.23     119     216 ..      47     141 ..      36     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                    EEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSE..EEE---GGGS-T---EEEEEEES-GGG-S CS
                 Methyltransf_9 119 ildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqra..hllplgieqlpeleafdtvfsmGvlyhrr 196
                                    +l+vG g G   +       ++v+ ++P+        a  ++ + d ++  ++   ++e++  +e+fd+v    vl   +
  gi|121637079|ref|YP_977302.1|  47 VLEVGAGVGTN-FAYYPVAVEQVIAMEPEPRL----AAKARIAAADAPVpiVVTDKTVEEFRDTETFDAVVCSLVLCSVS 121
                                    56666666643.33333344556666666543....3334444444443114445689********************** PP

                                    -HHHHHHHHHCTEEEEEEEE CS
                 Methyltransf_9 197 sPldhllqlkdqlvkgGelv 216
                                     P   l  l+  l++gGel 
  gi|121637079|ref|YP_977302.1| 122 DPGAVLAHLRSLLRRGGELR 141
                                    ******************94 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.26       9      88 ..      27      97 ..      21     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                         DUF938  9 rnrepilevLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtae 88
                                   +  e+i +  ++ la  + rvLE+++G G   +++  a++++  ++ +++++l        +++ ++   +P+ + vt++
  gi|121637079|ref|YP_977302.1| 27 HEAEAIRALRRENLAGLSGRVLEVGAGVGTNFAYYPVAVEQV--IAMEPEPRLA-------AKARIAAADAPVPIVVTDK 97
                                   56678888889999999899**************99998876..5666666663.......2222333344555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1515.06
//
Query:       gi|121637080|ref|YP_977303.1|  [L=482]
Description: hypothetical protein BCG_1209c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-99  333.0  14.2    2.5e-99  332.6  14.2    1.2  1  DUF222     Domain of unknown function (DUF222)
    9.7e-05   22.5   0.3    0.00023   21.2   0.3    1.6  1  HNH        HNH endonuclease
  ------ inclusion threshold ------
      0.039   14.2   1.3        5.5    7.3   0.1    3.2  3  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
       0.16   11.9   2.2       0.52   10.3   0.0    2.9  3  MarR_2     MarR family


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.6  14.2  5.6e-103   2.5e-99       2     301 .]      65     389 ..      64     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 332.6 bits;  conditional E-value: 5.6e-103
                         DUF222   2 laaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lp 70 
                                    la+l++le  +rr+ a+e++l+++la+++++ee g++ +++++a+rl+i+++eAsrr+++A++l+er           L+
  gi|121637080|ref|YP_977303.1|  65 LACLQRLEVERRRQGAAEHALINQLAGQACEEELGGT-LRTALANRLHITPGEASRRIAEAEDLGERraltgeplpaqLT 143
                                    6899*********************************.****************************************** PP

                         DUF222  71 avaaalraGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrr 150
                                    a+aaa+r+G+i+ ++++ I+a++++l++avdl  +++aea+l++ a++ +p++L+ l+++l+++l+pDg+++d+e+ar+r
  gi|121637080|ref|YP_977303.1| 144 ATAAAQREGKIGREHIKEIQAFFKELSAAVDLGIREAAEAQLAELATSRRPDHLHGLATQLMDWLHPDGNFSDQERARKR 223
                                    ******************************************************************************** PP

                         DUF222 151 eltltk.dedGmsrisgeldaeaaaaldavLdslaap.vcap..............dgtkDpRspaqrraDALlallrla 214
                                    ++t++k + dGmsrisg l++e +a+++avL++laap  c+p              + ++D+Rs+aqr++DA+la+lr +
  gi|121637080|ref|YP_977303.1| 224 GITMGKqEFDGMSRISGLLTPELRATIEAVLAKLAAPgACNPddqtplvddtpdadAVRRDTRSQAQRNHDAFLAALRGL 303
                                    ******9************************************************999********************** PP

                         DUF222 215 laagaldchagvpatvvvhvtaeeltaaaggaaltgggglLpasdvrrLAkdAt..laifdepagrpldlgrtkrtasaa 292
                                    la+g+l++h+g+p+t+vv++t++el+aa+g+ ++tggg+++p+sd +r+A++A+  la+fd   ++pl+l++tkr+as+a
  gi|121637080|ref|YP_977303.1| 304 LASGELGQHKGLPVTIVVSTTLKELEAATGK-GVTGGGSRVPMSDLIRMASNANhyLALFDG--AKPLALYHTKRLASPA 380
                                    *******************************.**********************99999999..**************** PP

                         DUF222 293 lrralraRD 301
                                    +r++l+a+D
  gi|121637080|ref|YP_977303.1| 381 QRIMLYAKD 389
                                    ********9 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   5.2e-08   0.00023       4      42 ..     392     432 ..     390     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.2e-08
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHn 42 
                                    C r++ +   + +ev+H+ p+    ++di++l+l+C   ++
  gi|121637080|ref|YP_977303.1| 392 CSRPGCDApaYHSEVHHVTPWTTTHRTDINDLTLACGPDNR 432
                                    7777777677899***********************88886 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        67      26      60 ..      19      53 ..      12      58 .. 0.91
   2 ?    7.3   0.1    0.0012       5.5      30     104 ..     148     221 ..     139     223 .. 0.82
   3 ?   -1.6   0.0       0.7   3.1e+03      36      62 ..     281     307 ..     277     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                                   HHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_24 26 aavllrelraLspehreeiralrreyerllrdlie 60
                                     v+lr +r +  + reei a  ++y++ l+++++
  gi|121637080|ref|YP_977303.1| 19 LSVVLRRIRGMRSDTREEISAALDAYHASLSRVLD 53
                                   578999***********************999985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0012
                                    HHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHCHHHC--TTSSS-HHHHHH CS
                      TetR_C_24  30 lrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmlnwvyrWyrpdGplspeeiad 104
                                     +       eh +ei+a  +e+ + ++  i+e+++a+  ++l ++     + g+ +++  W +pdG  s +e a+
  gi|121637080|ref|YP_977303.1| 148 AQREGKIGREHIKEIQAFFKELSAAVDLGIREAAEAQL-AELATSRRPDHLHGLATQLMDWLHPDGNFSDQERAR 221
                                    44457788999999999999999999999999988885.5777777788899*****************999776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.7
                                    S-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_24  36 LspehreeiralrreyerllrdlieeG 62 
                                    +  + r++ ++ ++++ + lr l++ G
  gi|121637080|ref|YP_977303.1| 281 VRRDTRSQAQRNHDAFLAALRGLLASG 307
                                    556777888888888888888888877 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.32   1.4e+03       6      43 ..      14      53 ..      12      54 .. 0.75
   2 ?   10.3   0.0   0.00011      0.52      26      49 ..     105     128 ..      94     129 .. 0.92
   3 ?   -3.3   0.0         2   9.1e+03      38      48 ..     321     331 ..     320     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHH CS
                         MarR_2  6 aqarvLaaLgrrpgr...dltvgelarrlglsksavsrilk 43
                                   + ar L ++ rr ++   d t  e+ ++l+  ++++sr+l+
  gi|121637080|ref|YP_977303.1| 14 MTARFLSVVLRRIRGmrsD-TREEISAALDAYHASLSRVLD 53
                                   5666666666666556545.999999999999999999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                                    HHHHHHTSSHHHHHHHHHHHHHTT CS
                         MarR_2  26 elarrlglsksavsrilkrLvaaG 49 
                                    +la rl+++++ +sr+++++++ G
  gi|121637080|ref|YP_977303.1| 105 ALANRLHITPGEASRRIAEAEDLG 128
                                    79******************9987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2
                                    HHHHHHHHHHT CS
                         MarR_2  38 vsrilkrLvaa 48 
                                    vs +lk+L+aa
  gi|121637080|ref|YP_977303.1| 321 VSTTLKELEAA 331
                                    8999****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3307.61
//
Query:       gi|121637081|ref|YP_977304.1|  [L=135]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-27   95.0   1.8    3.1e-27   94.6   1.8    1.2  1  DUF4096   Putative transposase of IS4/5 family (DUF4096)


Domain annotation for each model (and alignments):
>> DUF4096  Putative transposase of IS4/5 family (DUF4096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   1.8   1.8e-31   3.1e-27       1      75 []       7      80 ..       7      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.8e-31
                        DUF4096  1 LtDeqWellepllpepkkrrGrprkvdlrevlngIlyvlrtGcpWrdLPedfgswstvyrrfrrWskagvwerif 75
                                   ++De W+++epl+p+++ ++Gr+ + d+r +l+gI +++rtG pWrdLP++fg+w+tv++r++rWs +g+ +++f
  gi|121637081|ref|YP_977304.1|  7 ISDEFWAVVEPLMPSHEGKPGRRFS-DHRLILEGIAWRFRTGSPWRDLPAEFGPWQTVWKRHHRWSLDGTCDEVF 80
                                   69************98888799997.*********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 993.53
//
Query:       gi|121637082|ref|YP_977305.1|  [L=237]
Description: NAD-dependent deacetylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-54  184.6   0.0    1.8e-54  184.4   0.0    1.0  1  SIR2      Sir2 family


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.0     1e-58   1.8e-54       1     177 []       8     184 ..       8     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 1e-58
                                    -GGGGGGGT---SSS.TTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEE CS
                           SIR2   1 GAGiStesGipdfRs.keGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllrli 79 
                                    GAGiS+esG+p+fR+ k+Gl+a+++++el+s++ + +++++v+  +y +++ l+a ++epn  H+a++ +++++  +++i
  gi|121637082|ref|YP_977305.1|   8 GAGISAESGVPTFRDdKNGLWARFDPYELSSTQGWLRNPERVWG-WYLWRHYLVA-NVEPNDGHRAIAAWQDHA-EVSVI 84 
                                    9**************9****************************.*******999.7***************99.889** PP

                                    ES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHC..HHHCCTT.B-TTTCCBEEEEE--CTSB-S.HHHHHH CS
                           SIR2  80 TQNiDgLekkaGskkvvelHGslakakcvkcekkldkeelqe..eieaekvpecekcgkllkpdvvfFGealp.dklkkl 156
                                    TQN+D+L+++aGs +v++lHGsl +++c++c+  ++  +l e  e   e +p +++cg+l++pd+v+FGe lp + ++++
  gi|121637082|ref|YP_977305.1|  85 TQNVDDLHERAGSGAVHHLHGSLFEFRCARCGVPYTD-ALPEmpEPAIEVEPPVCDCGGLIRPDIVWFGEPLPeEPWRSA 163
                                    *********************************9987.44440144567788999******************999**** PP

                                    HHHHHH-SEEEEES--STSTT CS
                           SIR2 157 iekveeadlllviGtSlkVap 177
                                    +e++ +ad+++v+GtS+ V+p
  gi|121637082|ref|YP_977305.1| 164 VEATGSADVMVVVGTSAIVYP 184
                                    *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1650.27
//
Query:       gi|121637083|ref|YP_977306.1|  [L=121]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-14   53.2   0.1    2.7e-14   52.5   0.1    1.3  1  GntR           Bacterial regulatory proteins, gntR family
    8.8e-05   22.1   0.0    0.00014   21.5   0.0    1.3  1  HTH_41         Helix-turn-helix domain
    0.00033   20.4   0.5       0.01   15.6   0.1    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00033   20.4   0.9       0.78    9.6   0.1    2.2  2  HTH_IclR       IclR helix-turn-helix domain
    0.00043   20.1   1.8     0.0074   16.1   0.3    2.3  3  MarR_2         MarR family
    0.00052   19.9   0.1     0.0012   18.8   0.0    1.6  2  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0019   18.1   0.0      0.015   15.2   0.0    2.0  2  HTH_36         Helix-turn-helix domain
     0.0021   17.6   0.0     0.0052   16.3   0.0    1.6  2  HTH_CodY       CodY helix-turn-helix domain
     0.0024   17.2   0.0      0.094   12.1   0.0    2.3  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
     0.0029   17.1   0.0      0.017   14.7   0.0    1.9  2  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.022   14.6   0.0       0.75    9.6   0.0    2.2  2  HTH_10         HTH DNA binding domain
      0.025   14.7   0.1      0.081   13.0   0.0    1.8  2  HTH_20         Helix-turn-helix domain
       0.07   13.0   0.0        1.6    8.7   0.0    2.1  2  TrmB           Sugar-specific transcriptional regulator TrmB
       0.11   12.3   0.1       0.96    9.3   0.0    2.1  2  HTH_23         Homeodomain-like domain
       0.15   11.7   0.2        3.7    7.2   0.0    2.3  2  HTH_50         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1   2.3e-17   2.7e-14       5      64 .]      21      80 ..      17      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.3e-17
                                   HHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                           GntR  5 vyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                   +  ++ + +++g l pG++LP++r+La ++gV ++tv +A+r+Le++ +ve r + Gtf+
  gi|121637083|ref|YP_977306.1| 21 LRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARAYRELESAAIVETRGRFGTFI 80
                                   55666777899***********************************************97 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.1e-07   0.00014       3      48 .]      37      80 ..      36      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                         HTH_41  3 GdRlktIeelakeleLSvGlvQkALklLeddkaislerrGrlGtfl 48
                                   G Rl+t+ +la +l++   +v  A   Le++ ++  e rGr Gtf+
  gi|121637083|ref|YP_977306.1| 37 GTRLPTVRDLAGQLGVAANTVARAYRELESAAIV--ETRGRFGTFI 80
                                   89***************************98876..77*******7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   8.6e-06      0.01      19      42 .]      42      65 ..      41      65 .. 0.95
   2 ?    3.0   0.0     0.079        95      23      35 ..     100     112 ..      90     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.6e-06
                  HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrLe 42
                                   ++++LA ++G++++tv+r +r Le
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELE 65
                                   589******************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.079
                  HTH_AsnC-type  23 LAervGlSestvl 35 
                                    +A+++Gl+ s ++
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDAM 112
                                    8*******99776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00066      0.79      19      50 ..      41      72 ..      31      74 .. 0.83
   2 !    9.6   0.1   0.00065      0.78      24      40 ..     100     116 ..      90     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00066
                                   -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                    t+++lA ++g++  tv R  + L+   +ve+
  gi|121637083|ref|YP_977306.1| 41 PTVRDLAGQLGVAANTVARAYRELESAAIVET 72
                                   49*****************9999998877776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00065
                                    HHHHHTS-HHHHHHHHH CS
                       HTH_IclR  24 lArrtglpkStvhRlLq 40 
                                    +Ar++gl+kS + R+L 
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDAMRYLT 116
                                    7**************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   6.2e-06    0.0074      20      54 ..      37      73 ..      23      75 .. 0.88
   2 ?   -3.3   0.0       7.4   8.8e+03      14      28 ..      80      94 ..      79      96 .. 0.59
   3 ?    3.1   0.0     0.076        91      27      42 ..     100     115 ..      98     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.2e-06
                                   S.EE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 20 r.dl.tvgelarrlglsksavsrilkrLvaaGLverr 54
                                   + +l tv++la  lg+   +v r+ ++L++a  ve+r
  gi|121637083|ref|YP_977306.1| 37 GtRLpTVRDLAGQLGVAANTVARAYRELESAAIVETR 73
                                   24667******************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.4
                                   HHCTTTSEEEHHHHH CS
                         MarR_2 14 Lgrrpgrdltvgela 28
                                   + r ++ d ++++ a
  gi|121637083|ref|YP_977306.1| 80 ISRFDPTDAAMAAAA 94
                                   667777666665555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.076
                                    HHHHHTSSHHHHHHHH CS
                         MarR_2  27 larrlglsksavsril 42 
                                    +ar+lgl+ks + r l
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDAMRYL 115
                                    59********998865 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-06    0.0012      23      55 ..      42      75 ..      22      84 .. 0.88
   2 ?   -2.2   0.0       3.7   4.4e+03      28      42 ..     101     115 ..     100     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.rgr 55
                                   t ++lA  lG+   tv r+ +eL+ + +++ rgr
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELESAAIVEtRGR 75
                                   779***************************5554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                                    HHHTTSSHHHHHHHH CS
                      HTH_Crp_2  28 AsmlGltretvsril 42 
                                    A+ lGlt +   r l
  gi|121637083|ref|YP_977306.1| 101 ARALGLTKSDAMRYL 115
                                    778888887766666 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05     0.015      26      52 ..      41      67 ..      36      70 .. 0.92
   2 ?    0.5   0.0       0.5     6e+02      32      46 ..     101     115 ..      97     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                         HTH_36 26 psqetlakrlglsknTvsraikeLeql 52
                                   p++++la +lg+  nTv ra +eLe +
  gi|121637083|ref|YP_977306.1| 41 PTVRDLAGQLGVAANTVARAYRELESA 67
                                   99**********************976 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                         HTH_36  32 akrlglsknTvsrai 46 
                                    a++lgl k+ ++r++
  gi|121637083|ref|YP_977306.1| 101 ARALGLTKSDAMRYL 115
                                    7899*********98 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.3e-06    0.0052       9      45 ..      45      79 ..      39      84 .. 0.85
   2 ?   -2.2   0.0       2.6   3.1e+03      11      18 ..     101     108 ..      91     115 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                       HTH_CodY  9 kiaDriGitrsvivnaLrkLesaGiiesrsLGmkGtY 45
                                    +a ++G++   +  a r Lesa i+e r  G  Gt+
  gi|121637083|ref|YP_977306.1| 45 DLAGQLGVAANTVARAYRELESAAIVETR--GRFGTF 79
                                   678999**********************9..556666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                       HTH_CodY  11 aDriGitr 18 
                                    a  +G+t+
  gi|121637083|ref|YP_977306.1| 101 ARALGLTK 108
                                    44445555 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.9e-05     0.094      29      50 ..      42      63 ..      38      65 .. 0.90
   2 ?    2.7   0.0     0.068        82      32      50 ..      99     117 ..      97     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                   HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrildr 50
                                   +v++ A qlgv ++TV r++++
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRE 63
                                   99****************9986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.068
                   HTH_Tnp_ISL3  32 avArqlgvSwtTVwrildr 50 
                                     vAr lg++ +  +r+l +
  gi|121637083|ref|YP_977306.1|  99 GVARALGLTKSDAMRYLTH 117
                                    59********999999987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.4e-05     0.017      19      44 ..      42      67 ..      41      71 .. 0.93
   2 ?    0.2   0.0      0.48   5.7e+02      23      37 ..     100     114 ..      97     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                         HTH_24 19 sqreLAerlglSpstvnrrlkrLeee 44
                                   + r+LA +lg+  +tv r  ++Le++
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELESA 67
                                   789********************985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                         HTH_24  23 LAerlglSpstvnrr 37 
                                    +A++lgl++s   r+
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDAMRY 114
                                    699****99866666 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00063      0.75      25      48 ..      42      65 ..      38      69 .. 0.83
   2 ?    2.9   0.0     0.083        99      29      45 ..     100     116 ..      94     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                         HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                   t+++LA +lG++++t+    r+ e
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELE 65
                                   789************987766655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.083
                         HTH_10  29 LAkelGIskstlsehLr 45 
                                    +A +lG++ks+++ +L 
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDAMRYLT 116
                                    7999********99996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.8e-05     0.081      26      58 ..      42      74 ..      24      76 .. 0.93
   2 ?   -1.2   0.0       1.8   2.2e+03      30      42 ..     100     113 ..      90     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 26 taselaerldlskntlsyHLrvLeeagLvevvr 58
                                   t+ +la +l+++ nt+ +  r+Le+a +ve+++
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELESAAIVETRG 74
                                   77899**************************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                    HHHHHTS-HHH.HH CS
                         HTH_20  30 laerldlsknt.ls 42 
                                    +a++l+l+k+  ++
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSDaMR 113
                                    68899999987444 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0013       1.6      24      55 ..      42      73 ..      40      88 .. 0.91
   2 ?    2.3   0.0      0.13   1.5e+02       3      16 ..     103     116 ..     100     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                                   HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                           TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVere 55
                                   t++++a +lgv  ++v ++ r+Le++ +Ve++
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYRELESAAIVETR 73
                                   89**************************9987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                                    HCHHHHHCCCHCHH CS
                           TrmB   3 klGLseyEakvYla 16 
                                    +lGL++ +a  Yl+
  gi|121637083|ref|YP_977306.1| 103 ALGLTKSDAMRYLT 116
                                    79*******99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00081      0.96      19      41 ..      42      64 ..      42      70 .. 0.84
   2 ?    0.6   0.0      0.45   5.4e+02      19      32 ..      96     109 ..      88     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                         HTH_23 19 svreIAreLgvsrrTvyrwlkry 41
                                   +vr+ A +Lgv  +Tv r  +  
  gi|121637083|ref|YP_977306.1| 42 TVRDLAGQLGVAANTVARAYREL 64
                                   7899*************987664 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.45
                         HTH_23  19 svreIAreLgvsrr 32 
                                     +  +Ar+Lg +++
  gi|121637083|ref|YP_977306.1|  96 EYVGVARALGLTKS 109
                                    55568899998875 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0031       3.7      24      42 ..      41      59 ..      38      64 .. 0.87
   2 ?    2.4   0.0       0.1   1.2e+02      29      39 ..     100     110 ..      92     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                         HTH_50 24 pStRklAkrLGvShtaian 42
                                   p +R lA +LGv   ++a+
  gi|121637083|ref|YP_977306.1| 41 PTVRDLAGQLGVAANTVAR 59
                                   668**************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                         HTH_50  29 lAkrLGvShta 39 
                                    +A++LG++++ 
  gi|121637083|ref|YP_977306.1| 100 VARALGLTKSD 110
                                    8******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 857.75
//
Query:       gi|121637084|ref|YP_977307.1|  [L=282]
Description: O-methyltransferase omt [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-13   49.8   0.2      6e-12   45.9   0.2    2.5  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.2   3.4e-16     6e-12       1     187 [.      20     179 ..      20     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.4e-16
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    al + +ara+e+rr  d +idDp+a +lv++  + +                   +k+    +g+a+R+r+fd + ++ l
  gi|121637084|ref|YP_977307.1|  20 ALLTLNARAAEARRR-DTIIDDPMAVALVESIDFGF-------------------AKFGPTGQGFALRARAFDMAAQHYL 79 
                                    677899********9.****************7775...................35888999***************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTT...TEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHT CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwla...glkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaag 157
                                    +++ ++ vV L+ Gl t ++Rl+      + ++  vD p ++++++++l  ++  + + +   ++D     w + +    
  gi|121637084|ref|YP_977307.1|  80 DQHPAATVVALAEGLQTSFWRLDVAIpggQFRWLTVDLPPIVDLRTRLLPSSPRVSVCAQS--ALDYS---WMDSV---- 150
                                    668899****************9988899********************877766665444..55655...88876.... PP

                                    T-TTSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 158 fdpekptawvaeGvlvYLtpeasdalleai 187
                                     dp+   ++ aeG+l+YL+pe++  l+++ 
  gi|121637084|ref|YP_977307.1| 151 -DPAGGVFITAEGLLMYLQPEQALGLIAQC 179
                                    .555667****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2129.30
//
Query:       gi|121637085|ref|YP_977308.1|  [L=213]
Description: hypothetical protein BCG_1215c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-34  116.8   0.0    1.4e-33  116.2   0.0    1.2  1  DUF1697   Protein of unknown function (DUF1697)


Domain annotation for each model (and alignments):
>> DUF1697  Protein of unknown function (DUF1697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   7.8e-38   1.4e-33       1     128 [.      38     163 ..      38     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 7.8e-38
                        DUF1697   1 MttyiaLLRGiNvggknkvkmaeLralleelGfedVkTyiqSGNvvfeseedaaeleakiekaleeefgfevpvlvrtae 80 
                                    M +++a+LRG+Nvgg n +kmae+ ++l+++Gf +V+T+++SGNv++es+  aae+++k e++l+e+fg++++ l+++ +
  gi|121637085|ref|YP_977308.1|  38 MAKFAAFLRGVNVGGVN-LKMAEVATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVD 116
                                    99*************88.************************************************************** PP

                        DUF1697  81 eleaivaanPfeeeeeeekklyviflkeepsaealeelealaeederv 128
                                    ++++ivaa+Pfe e  e++++yv+f++++   ++l +l++ a  de++
  gi|121637085|ref|YP_977308.1| 117 TVRTIVAAYPFECE-LEGYQSYVTFVADAAILDELSALADTAGPDENI 163
                                    **************.*************99999999999888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1751.11
//
Query:       gi|121637086|ref|YP_977309.1|  [L=147]
Description: hypothetical protein BCG_1216 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-16   59.6   0.0    3.4e-16   59.2   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   1.9e-20   3.4e-16       1      85 [.       6      90 ..       6      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.9e-20
                                   HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEE CS
                 Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtae 82
                                   +d++l++++++ +++vlAT+++dGrP++s v + +++++ +i +++++ ++k+rnl+++pr+++l++ d+   +   eGta+
  gi|121637086|ref|YP_977309.1|  6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQ 87
                                   699*******************************************************************9999999****9 PP

                                   EES CS
                 Putative_PNPOx 83 lvs 85
                                   l  
  gi|121637086|ref|YP_977309.1| 88 LTP 90
                                   976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1210.85
//
Query:       gi|121637087|ref|YP_977310.1|  [L=195]
Description: hypothetical protein BCG_1217 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-25   90.2   0.0    1.4e-25   89.9   0.0    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   7.6e-30   1.4e-25       1     105 [.      25     191 ..      25     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 7.6e-30
                                    HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTT....STTHHHHHHHHHHHHHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx.......... RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelire....lGfyrrKakyikelArilv.......... 66 
                                    v+++l+qq+++e+a++ ++++++r+g++++ d+ad+d++k+++l++e    ++f++++ak+i++lA+i+v          
  gi|121637087|ref|YP_977310.1|  25 VGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADYDPDKFVALCSErpaiHRFPGSMAKRIQALAQIIVdrydgdaaal 104
                                    79****************************************************************************** PP

                                    ...................................................S-SS.S--TTSHHHHHHHHHHTTSSSSTT CS
                                    ...................................................xxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ...................................................gkpd.vlivvDvhvrrilkrlrsikekkt 94 
                                                                                       g+p+ +l+v+D++++++l+++rs+k++  
  gi|121637087|ref|YP_977310.1| 105 wtagepdgnellrrlkglpgfgeqkariflallgkqygvtpkgwqvaagefGQPGtYLSVADIVDAGSLGQVRSHKRQ-- 182
                                    ***************************************************99999*********************9.. PP

                                    HHHHHHHHHHH CS
                                    xxxxxxxxxxx RF
                        HhH-GPD  95 kkkvekkleel 105
                                     +k+++k+ e+
  gi|121637087|ref|YP_977310.1| 183 -RKAAAKA-EG 191
                                    .6666666.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1521.74
//
Query:       gi|121637088|ref|YP_977311.1|  [L=347]
Description: hypothetical protein BCG_1218c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2529.31
//
Query:       gi|121637089|ref|YP_977312.1|  [L=227]
Description: hypothetical protein BCG_1219c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      129  (0.00719505); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1578.60
//
Query:       gi|121637090|ref|YP_977313.1|  [L=431]
Description: mannosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-52  178.5  32.2    1.7e-52  178.5  32.2    3.1  3  GT87      Glycosyltransferase family 87


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.7     0.051   9.2e+02     198     224 ..      43      69 ..      10      81 .. 0.56
   2 !  178.5  32.2   9.5e-57   1.7e-52       1     239 []     103     334 ..     103     334 .. 0.91
   3 ?   -5.3   8.9         1   1.8e+04      22      65 ..     365     409 ..     343     419 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.051
                           GT87 198 lvlvllvvalaavaawrlrrrerllal 224
                                    ++++llv+ ++a +aw +++++ + ++
  gi|121637090|ref|YP_977313.1|  43 AAVLLLVLSVGARLAWTYLAPNGANFV 69 
                                    334455566666666666655544444 PP

  == domain 2  score: 178.5 bits;  conditional E-value: 9.5e-57
                           GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgral.....asavalalllaalalepvlstlgfGq 75 
                                    FtYPPfaa++f+pl+l+p+gl ++lw ++++aal++a+r+  r++g+++     a+++++a   +a+++ep++st+++Gq
  gi|121637090|ref|YP_977313.1| 103 FTYPPFAAVVFYPLHLVPFGLIALLWQVVTMAALYGAVRISQRLMGGTAetghfAAMLWTA---IAIWIEPLRSTFDYGQ 179
                                    9********************************************9999**6655555555...5*************** PP

                           GT87  76 inllllllvlldllllrrrrpllaGlliGlaaaiKltPalfllylllrrrwralaaaaatalvltalpllllppssleyf 155
                                    in+ll+l++l+++ + r    +l+Gll+G+a ++KltPa+ ++yl+  rr++a+a +++++l++++++ll+++ ++++yf
  gi|121637090|ref|YP_977313.1| 180 INVLLMLAALWAVYTPR---WWLSGLLVGVASGVKLTPAITAVYLVGVRRLHAAAFSVVVFLATVGVSLLVVGDEARYYF 256
                                    ************88888...478********************************************************* PP

                           GT87 156 letlfdtseri..aedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlrrrerllalaaallvall 233
                                    +++l d+ +r+  +++ +nqs   ++g+++r+l+  + + + l l++++ +++la +a+++l r +rl  l    +v l+
  gi|121637090|ref|YP_977313.1| 257 TDLLGDA-GRVgpIATSFNQS---WRGAISRILGHDA-GFGPLVLAAIASTAVLAILAWRALDRSDRLGKLL---VVELF 328
                                    *******.9999*9999****...9999999776666.5666666666666777777777777999999999...***** PP

                           GT87 234 alLvsP 239
                                    +lL+sP
  gi|121637090|ref|YP_977313.1| 329 GLLLSP 334
                                    *****9 PP

  == domain 3  score: -5.3 bits;  conditional E-value: 1
                           GT87  22 alalwallnlaalllalrlllrrlgral.asavalalllaalale 65 
                                    +++ w++l+++ + ++l  +   ++       +a+a l++++a+ 
  gi|121637090|ref|YP_977313.1| 365 LGWGWLVLTIVGVPWLLSFAQPSIWQIGrPWYLAWAGLVYVVATL 409
                                    567777788887777777777765432232222222222333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3409.75
//
Query:       gi|121637091|ref|YP_977314.1|  [L=94]
Description: pterin-4-alpha-carbinolamine dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-27   93.4   0.1    7.8e-27   93.3   0.1    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
      0.079   13.1   0.1       0.15   12.2   0.1    1.4  1  IF-2       Translation-initiation factor 2


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.1   8.7e-31   7.8e-27       3      90 ..       4      90 ..       2      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 8.7e-31
                      Pterin_4a  3 lseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenDfkl 84
                                   l++e+++++l++l+gW++  +  l+r++kf +f ++i+ v rva+ aee nHhpdi +++++vt+ l Th++gg+tenD+++
  gi|121637091|ref|YP_977314.1|  4 LTDEQVDAALHDLNGWQR-AGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDIRWRTVTFALVTHAVGGITENDIAM 84
                                   89********999****9.7789*********************************************************** PP

                      Pterin_4a 85 Aakide 90
                                   A+ id+
  gi|121637091|ref|YP_977314.1| 85 AHDIDA 90
                                   ****97 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.7e-05      0.15      41      67 ..      64      90 ..      57      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                   STEEEECEEEESSB-HHHHHHHHHSTE CS
                           IF-2 41 evkvkvihsgvGaitesDvelasasna 67
                                    v++  + ++vG ite+D+ +a+  +a
  gi|121637091|ref|YP_977314.1| 64 TVTFALVTHAVGGITENDIAMAHDIDA 90
                                   68889999*************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 752.33
//
Query:       gi|121637092|ref|YP_977315.1|  [L=141]
Description: mutator protein mutT2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-15   56.5   0.5    3.6e-15   56.2   0.5    1.1  1  NUDIX          NUDIX domain
    1.6e-05   24.9   0.2    3.6e-05   23.7   0.2    1.6  1  NUDIX_4        NUDIX domain
  ------ inclusion threshold ------
      0.063   12.9   0.0       0.08   12.5   0.0    1.1  1  NUDIX_2        Nucleotide hydrolase
      0.077   12.8   1.0          4    7.3   0.0    2.7  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.5     8e-19   3.6e-15       5     129 ..       7     124 ..       3     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 8e-19
                                    EEEEEEEETTSEEEEEEESSSSTTT...EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   5 avgvvllnekgevLlvrrskkpfpg...WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygde 81 
                                     +g++++     vL+++r  +p+     WelPgGkv +gEt ++A++REl+EE+Gle+ +l + +r+     +d++  + 
  gi|121637092|ref|YP_977315.1|   7 VAGAIVRGCT--VLVAQRV-RPPELagrWELPGGKVAAGETERAALARELAEELGLEVADLAVGDRV-----GDDIALNG 78 
                                    5677777777..*******.4443358*****************************99999999855.....56666667 PP

                                    EEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                          NUDIX  82 heilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                    +  l  ++ + + ge++ +   ++++++wv+ +el + + ++++r +++
  gi|121637092|ref|YP_977315.1|  79 TTTLRAYRvHLLGGEPRAR---DHRALCWVTAAELHDVDWVPADRGWIA 124
                                    7778888878888998888...778999999999977777777777766 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2     8e-09   3.6e-05       4      99 ..      10     114 ..       7     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8e-09
                                    EEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEEEEEEEEEEEEETTE....EEEEEEEEE CS
                        NUDIX_4   4 lirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgieveelepgtvkHvftHf....rltltvylv 75 
                                    +i+++  vl+ +R     l+g we+Pgg+  +ge++++ala   +eelg+ev  l+ g+   v  ++    + tl+ y+v
  gi|121637092|ref|YP_977315.1|  10 AIVRGCTVLVAQRVRPPELAGRWELPGGKvAAGETERAALArelAEELGLEVADLAVGD--RVGDDIalngTTTLRAYRV 87 
                                    566666788888888788***********988999777776677789999777554443..3444441112445555555 PP

                                    EEE.S..---....EEEEEEGGGGGGS- CS
                        NUDIX_4  76 rveegeeapa....elrwvtpeeleeya 99 
                                    ++  g e+ a    +l wvt++el+++ 
  gi|121637092|ref|YP_977315.1|  88 HLL-GGEPRArdhrALCWVTAAELHDVD 114
                                    433.2222223567899**999998765 PP

>> NUDIX_2  Nucleotide hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05      0.08      69     111 ..      31      70 ..      12      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                        NUDIX_2  69 efkLpggklksgedeiegLkrkLakklskekeveeeievgell 111
                                     ++Lpggk+ +ge+e+ +L r La+ l  e    +++ vg+ +
  gi|121637092|ref|YP_977315.1|  31 RWELPGGKVAAGETERAALARELAEELGLE---VADLAVGDRV 70 
                                    689***********************9977...4555555555 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.013        59      21      30 ..      51      60 ..      47      71 .. 0.87
   2 ?    7.3   0.0    0.0009         4      21      37 ..     124     140 ..     122     141 .] 0.95

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                  HTH_AsnC-type 21 aeLAervGlS 30
                                   +eLAe++Gl 
  gi|121637092|ref|YP_977315.1| 51 RELAEELGLE 60
                                   89******95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0009
                  HTH_AsnC-type  21 aeLAervGlSestvlrR 37 
                                    a+LA+ ++ S++ v+rR
  gi|121637092|ref|YP_977315.1| 124 ADLARTLNGSAADVHRR 140
                                    89**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1101.99
//
Query:       gi|121637093|ref|YP_977316.1|  [L=1232]
Description: respiratory nitrate reductase (alpha chain) narG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.2e-132  440.9   0.0   6.4e-132  440.6   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.5e-21   75.8   0.1    7.1e-21   74.3   0.1    1.8  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.057   13.4   0.1    1.7  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.6   0.0  1.1e-135  6.4e-132       1     431 [.     118     828 ..     118     829 .. 0.99

  Alignments for each domain:
  == domain 1  score: 440.6 bits;  conditional E-value: 1.1e-135
                                    B--S-EEEC..................................TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEE CS
                  Molybdopterin   1 RlkyPmvRk..................................qargeGkFvrvsWdeAleliaaslkytikkygpdrva 46 
                                    R++yP+ R+                                  qarg+G++vrvsW eA e++aa+++ tik+ygpdrva
  gi|121637093|ref|YP_977316.1| 118 RVRYPYARGvlvemyreaktrlgdpvlawadiqadperrrryqQARGKGGLVRVSWAEASEMVAAAHVHTIKTYGPDRVA 197
                                    9******************************************************************************* PP

                                    EEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHS CS
                  Molybdopterin  47 gfssgplmsmeslaslkkllsllggknlsfydwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreer 126
                                    gfs++p+msm+s+a+++++++l+gg ++sfydwyadlp as+  ++ +d+++++es+    d+ ++++ ++wGsNv+ +r
  gi|121637093|ref|YP_977316.1| 198 GFSPIPAMSMVSHAAGSRFVELIGGVMTSFYDWYADLPVASP--QVFGDQTDVPESG----DWWDASYLVMWGSNVPITR 271
                                    ******************************************..56688999*****....******************* PP

                                    HHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCC CS
                  Molybdopterin 127 pilnarirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpll 206
                                    +++ a+ +++a++++akv+v++p+ya+ +kfadew+   +gtd ala+amghvil+e +v ++   + +y++++td p+l
  gi|121637093|ref|YP_977316.1| 272 TPD-AHWMAEARYRGAKVVVVSPDYADNTKFADEWVRCAAGTDTALAMAMGHVILSECYVRNQVPFFVDYVRRYTDLPFL 350
                                    ***.***********************99*************************************************** PP

                                    CEECCS.......................................................................... CS
                  Molybdopterin 207 vtleee.......................................................................... 212
                                      le++                                                                          
  gi|121637093|ref|YP_977316.1| 351 IKLEKRgdllvpgkfltaadigeesenaafkpalldeltntvvvpqgslgfrfgedgvgkwnldlgsvvpalsvemdkav 430
                                    ******************************************************************************** PP

                                    ...............................................................................H CS
                  Molybdopterin 213 ...............................................................................t 213
                                                                                                                   t
  gi|121637093|ref|YP_977316.1| 431 ngdrsaelvtlpsfdtidghgetvsrglpvrragkhlvctvfdlmlahygvaraglpgewptgyhdrtqqntpawqesiT 510
                                    ******************************************************************************** PP

                                    HHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESS............ CS
                  Molybdopterin 214 gkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnG............ 281
                                    g+  ++ +r a+e+arna +  g+smii+G g+ h++++d +yr v+ L++l+g +g++gGgwah++G            
  gi|121637093|ref|YP_977316.1| 511 GVPAAQAIRFAKEFARNATESGGRSMIIMGGGICHWFHSDVMYRSVLALLMLTGSMGRNGGGWAHYVGqekvrpltgwqt 590
                                    ******************************************************************************** PP

                                    .........................................................................CTTHHHC CS
                  Molybdopterin 282 .........................................................................qlilaga 288
                                                                                                             +l +a++
  gi|121637093|ref|YP_977316.1| 591 mamatdwsrpprqvpgasywyahtdqwrydgygadklaspvgrgrfagkhtmdlltsatamgwspfypqfdrsSLDVADE 670
                                    ******************************************************************************** PP

                                    HHHHTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH..............HHHHSTT CS
                  Molybdopterin 289 aekvgalpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgn.............npevdhad 355
                                    a+ +g+   ++ +++l ++k+k+ + +p+n +n pr l v+r+nl++ssgk+ +y+l++              + v++ d
  gi|121637093|ref|YP_977316.1| 671 ARAAGRDVGDYVAEQLAQHKLKLSITDPDNPVNWPRVLTVWRANLIGSSGKGGEYFLRHllgtdsnvqsdppTDGVHPRD 750
                                    **********************************************************************99999***** PP

                                    SCCCHCHHH.CSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEE.EEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 356 enevekale.kldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqh.lkqavsppgeaksdwkIlkaLak 431
                                     ++ ++ +e kldl++ +d+r+tst l +D++LPaatwyEk+dl+++d+++  h +++a++pp+e +sd+  + a+a+
  gi|121637093|ref|YP_977316.1| 751 VVWDSDIPEgKLDLIMSIDFRMTSTTLVSDVVLPAATWYEKSDLSSTDMHPYVHsFSPAIDPPWETRSDFGAFAAIAR 828
                                    ****999999*****************************************************************996 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   1.2e-24   7.1e-21       2     102 ..    1086    1195 ..    1085    1205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.2e-24
                                     EEEEE-BTTBSTTTT.TCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEES CS
                Molydop_binding    2 rLitgrsldqlhsqt.rtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpf 78  
                                     r+ t++s++++hs++ ++  +l+l++ +p + +++p dAa+ +++d+d+Ve  +++G  ++ra v++r+++Gvvf+++
  gi|121637093|ref|YP_977316.1| 1086 RYLTPHSKWSFHSTYqDNLYMLSLSRGGP-TMWMSPGDAAKINVRDNDWVEAVNANGIYVCRAIVSHRMPEGVVFVYH 1162
                                     678************99999999999999.************************************************ PP

                                     SHCC..............S-GHCTS--SCSTTT CS
                Molydop_binding   79 gwwe.........agekggnaNaltddatdpls 102 
                                      +++         +g++ggn Nalt+ +++p +
  gi|121637093|ref|YP_977316.1| 1163 VQERtvdtprtetNGKRGGNHNALTRVRIKPSH 1195
                                     **99*********************99999976 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.5e-06     0.057       4      49 ..      56     109 ..      53     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-06
                                    EEEE-S.SBTT--EEEEEEETTEEEEEEE-TTSTTTT.......T---HHHHTC CS
                 Molybdop_Fe4S4   4 vktaCp.yCgvgCglevhvkdgkivkvegdpdhpvne.......grlCvKGrtl 49 
                                    v+++   +C+ +C+ +++vkdg i++  +++d+p+          r C++G++ 
  gi|121637093|ref|YP_977316.1|  56 VRSTHGvNCTGSCSWKIYVKDGIITWETQQTDYPSVGpdrpeyePRGCPRGASF 109
                                    55555559*****************6666666666666666666*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 7477.74
//
Query:       gi|121637094|ref|YP_977317.1|  [L=558]
Description: respiratory nitrate reductase subunit beta narH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-36  123.3   6.3    3.5e-36  123.3   6.3    1.8  2  Fer4_11         4Fe-4S dicluster domain
    5.1e-28   96.6   0.0    9.6e-28   95.7   0.0    1.5  1  Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal
    2.4e-08   34.0  15.6    7.1e-06   26.0   3.4    3.3  3  Fer4_10         4Fe-4S dicluster domain
    1.2e-06   29.0  20.4     0.0017   18.9   7.1    3.6  4  Fer4_7          4Fe-4S dicluster domain
    3.1e-06   27.0  18.7     0.0044   17.0   0.2    4.4  4  Fer4_6          4Fe-4S binding domain
     0.0006   19.7  24.0       0.01   15.8   1.5    4.5  4  Fer4_2          4Fe-4S binding domain
     0.0012   19.0  21.0     0.0049   17.0   5.0    3.1  3  Fer4_9          4Fe-4S dicluster domain
     0.0098   16.3  24.6      0.034   14.7   1.1    4.1  4  Fer4_4          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.3  18.3      0.036   13.9   2.2    4.5  4  Fer4            4Fe-4S binding domain
       0.04   14.7   8.4       0.33   11.7   0.3    2.8  2  Fer4_15         4Fe-4S single cluster domain
      0.063   13.8   6.0       0.42   11.2   0.2    3.0  3  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
       0.11   12.6  22.0      0.068   13.3   1.5    3.0  3  Fer4_21         4Fe-4S dicluster domain
       0.26   11.8   0.1       0.26   11.8   0.1    3.7  1  Fer4_8          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       2.6   3.5e+03       8      23 ..      14      27 ..       5      48 .. 0.54
   2 !  123.3   6.3   2.5e-39   3.5e-36       2      98 ..     177     272 ..     176     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                        Fer4_11  8 eqCrhCleppCvasap 23
                                   ++C  C    C  +++
  gi|121637094|ref|YP_977317.1| 14 DKCIGCH--TCSVTCK 27
                                   4444443..3444444 PP

  == domain 2  score: 123.3 bits;  conditional E-value: 2.5e-39
                        Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaG 81 
                                    ++++lp++C+hCl+p+Cvas+ps+a++k+ e+G+Vl+d+++++ ++r++v++cPyk+v+ n++tgk+ekC++c++r+e G
  gi|121637094|ref|YP_977317.1| 177 FMFYLPRICEHCLNPSCVASCPSGAMYKRTEDGIVLVDQDRCR-GWRMCVSGCPYKKVYFNHKTGKAEKCTLCYPRIEVG 255
                                    699***************************************9.************************************ PP

                        Fer4_11  82 llpacvescptgalnfg 98 
                                    l+++c+e+c+++++++g
  gi|121637094|ref|YP_977317.1| 256 LPTVCSETCVGRLRYLG 272
                                    **************998 PP

>> Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   6.9e-31   9.6e-28       1      81 []     360     441 ..     360     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 6.9e-31
                 Nitr_red_bet_C   1 LsPvvsaveagkld.eeadgllpaveslRiPveYLAnLltAGdeepvekaLkrllamRaymRaknvegeadeavleevgl 79 
                                    LsPvv+av++ ++d e+  +l++a+++lRiP+ YLA+L+tAGd+e+v+ +L+rl+amR ymR+ n+++e++ ++ e+vg+
  gi|121637094|ref|YP_977317.1| 360 LSPVVDAVSRDGHDgEDLGNLFGALDALRIPIAYLAELFTAGDTEVVAGVLRRLAAMRCYMRDINLGRETQPHIPESVGM 439
                                    9*************999999************************************************************ PP

                 Nitr_red_bet_C  80 te 81 
                                    te
  gi|121637094|ref|YP_977317.1| 440 TE 441
                                    96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   6.8e-05     0.094       2      19 ..       9      26 ..       8      62 .. 0.79
   2 !   26.0   3.4   5.2e-09   7.1e-06       5      56 .]     181     229 ..     177     229 .. 0.94
   3 ?    2.8   0.7     0.097   1.3e+02      37      55 ..     237     264 ..     230     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                        Fer4_10  2 vvidddtCirCgkCvkaC 19
                                   +v + d+Ci+C +C   C
  gi|121637094|ref|YP_977317.1|  9 MVMNLDKCIGCHTCSVTC 26
                                   78899************* PP

  == domain 2  score: 26.0 bits;  conditional E-value: 5.2e-09
                        Fer4_10   5 dddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +  C +C    Cv++CP+     ga ++++e++ v ++ ++C g+ +Cv+ CP
  gi|121637094|ref|YP_977317.1| 181 LPRICEHCLnpSCVASCPS-----GAMYKRTEDGIVLVDQDRCRGWRMCVSGCP 229
                                    5789****9899*******.....*****************************9 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.097
                        Fer4_10  37 avrkkvekCtgc.........gaCveaC 55 
                                    ++ +k ekCt c         + C e C
  gi|121637094|ref|YP_977317.1| 237 HKTGKAEKCTLCyprievglpTVCSETC 264
                                    5667999*****7777776666999988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   2.2e-05      0.03       1      19 [.      15      33 ..      10      63 .. 0.79
   2 !    9.9   1.9   0.00082       1.1      33      52 .]     180     201 ..     159     201 .. 0.76
   3 !   18.9   7.1   1.2e-06    0.0017       2      50 ..     185     230 ..     184     232 .. 0.88
   4 !    8.4   7.6    0.0024       3.3       1      48 [.     217     264 ..     217     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                         Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                   +CigC+ C ++C++ + + 
  gi|121637094|ref|YP_977317.1| 15 KCIGCHTCSVTCKQAWTNR 33
                                   7***********9888764 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00082
                         Fer4_7  33 idpekClgCga..CvavCPtga 52 
                                    + p+ C +C +  Cva CP+ga
  gi|121637094|ref|YP_977317.1| 180 YLPRICEHCLNpsCVASCPSGA 201
                                    45778****9999*******97 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.2e-06
                         Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                    C +C    Cva Cp++a++ + e   +    v +d+++C g ++Cv+ CP+
  gi|121637094|ref|YP_977317.1| 185 CEHCLnpSCVASCPSGAMYKRTE---D--GIVLVDQDRCRGWRMCVSGCPY 230
                                    99995559***********9876...3..48999****************8 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0024
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgC.........gaCvavC 48 
                                    rC g + Cv+ Cp+k ++++ +         ++++ekC+ C         ++C ++C
  gi|121637094|ref|YP_977317.1| 217 RCRGWRMCVSGCPYKKVYFNHK---------TGKAEKCTLCyprievglpTVCSETC 264
                                    799999*************887.........57889999996655555555788888 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.2   0.00034      0.47       3      19 ..      10      26 ..       8      32 .. 0.89
   2 !    7.6   1.6    0.0031       4.3       8      23 ..     184     201 ..     178     202 .. 0.85
   3 !   17.0   0.2   3.2e-06    0.0044       1      21 [.     210     230 ..     210     234 .. 0.91
   4 ?    1.5   0.1      0.27   3.7e+02       6      14 ..     242     250 ..     241     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                         Fer4_6  3 eidpdkCigCgdCvrvC 19
                                   + + dkCigC  C + C
  gi|121637094|ref|YP_977317.1| 10 VMNLDKCIGCHTCSVTC 26
                                   6789************9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0031
                         Fer4_6   8 kCigC.gd.CvrvCPega 23 
                                     C +C ++ Cv+ CP ga
  gi|121637094|ref|YP_977317.1| 184 ICEHClNPsCVASCPSGA 201
                                    799**666*******998 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.2e-06
                         Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                    +v +d+d+C g + Cv+ CP+
  gi|121637094|ref|YP_977317.1| 210 IVLVDQDRCRGWRMCVSGCPY 230
                                    5889****************8 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.27
                         Fer4_6   6 pdkCigCgd 14 
                                    ++kC+ C++
  gi|121637094|ref|YP_977317.1| 242 AEKCTLCYP 250
                                    689****85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.5   7.6e-06      0.01       3      21 ..       9      27 ..       7      28 .. 0.87
   2 !    9.5   1.6   0.00081       1.1       4      21 ..     179     198 ..     177     199 .. 0.88
   3 !    8.1   0.2    0.0022       3.1       3      22 .]     211     230 ..     209     230 .. 0.89
   4 ?   -0.3   1.4       1.1   1.5e+03       7      14 ..     242     249 ..     241     265 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.6e-06
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   +v + d+CigC +C   C 
  gi|121637094|ref|YP_977317.1|  9 MVMNLDKCIGCHTCSVTCK 27
                                   67899*********88895 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00081
                         Fer4_2   4 vvdtdrCigCg..aCvsaCP 21 
                                    ++ +++C +C   +Cv +CP
  gi|121637094|ref|YP_977317.1| 179 FYLPRICEHCLnpSCVASCP 198
                                    78899*****889******* PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0022
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    v vd drC g + Cvs CP+
  gi|121637094|ref|YP_977317.1| 211 VLVDQDRCRGWRMCVSGCPY 230
                                    7899****9999*******5 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.1
                         Fer4_2   7 tdrCigCg 14 
                                    +++C+ C 
  gi|121637094|ref|YP_977317.1| 242 AEKCTLCY 249
                                    58999996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.8   9.2e-05      0.13       1      21 [.      15      35 ..       6      46 .. 0.77
   2 !   17.0   5.0   3.6e-06    0.0049       2      49 ..     185     231 ..     184     233 .. 0.90
   3 ?   -0.1   7.9      0.78   1.1e+03       2      46 ..     218     264 ..     217     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                         Fer4_9  1 kCtgCgaCveaCpagvvveda 21
                                   kC+gC++C   C++  ++++ 
  gi|121637094|ref|YP_977317.1| 15 KCIGCHTCSVTCKQAWTNRSG 35
                                   688999998888776666655 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                         Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    C  C +  Cv++Cp+g++ ++   +++ ++++   +C g + Cv  Cp +
  gi|121637094|ref|YP_977317.1| 185 CEHCLNpsCVASCPSGAMYKRTEDGIVLVDQD---RCRGWRMCVSGCPYK 231
                                    99998666*******************99875...7************85 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.78
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaC 46 
                                    C g + Cv+ Cp++ v   ++++ka+       +C+ C           C e C
  gi|121637094|ref|YP_977317.1| 218 CRGWRMCVSGCPYKKVYFNHKTGKAE-------KCTLCYPrievglptvCSETC 264
                                    777789********999999999998.......499998766777777766666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.2    0.0018       2.5       2      16 ..      14      28 ..      13      32 .. 0.91
   2 ?    5.9   2.5     0.016        22       8      17 .]     191     200 ..     183     202 .. 0.78
   3 !   14.7   1.1   2.5e-05     0.034       1      16 [.     215     230 ..     215     231 .. 0.94
   4 ?   -1.5   0.1       3.5   4.9e+03       2       7 ..     243     248 ..     242     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   ++CigC  C  +C+q
  gi|121637094|ref|YP_977317.1| 14 DKCIGCHTCSVTCKQ 28
                                   99********99986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                         Fer4_4   8 gsCvaaCPqg 17 
                                    +sCva+CP+g
  gi|121637094|ref|YP_977317.1| 191 PSCVASCPSG 200
                                    49******75 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.5e-05
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    q+rC g + Cv+ CP+
  gi|121637094|ref|YP_977317.1| 215 QDRCRGWRMCVSGCPY 230
                                    79*************8 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.5
                         Fer4_4   2 erCigC 7  
                                    e+C+ C
  gi|121637094|ref|YP_977317.1| 243 EKCTLC 248
                                    899999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.2   2.6e-05     0.036       3      18 ..      11      26 ..       9      28 .. 0.88
   2 ?    5.7   0.2    0.0099        14      14      23 ..     193     202 ..     192     203 .. 0.89
   3 ?    4.4   0.3     0.026        36       3      20 ..     213     230 ..     211     231 .. 0.88
   4 ?    0.5   0.2      0.43   5.9e+02       6      11 ..     243     248 ..     241     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                   EETTTSSS-THHHHHS CS
                           Fer4  3 ideekCigCGaCvevC 18
                                    + +kCigC +C   C
  gi|121637094|ref|YP_977317.1| 11 MNLDKCIGCHTCSVTC 26
                                   689*********9999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0099
                                    HHHHSTTTEE CS
                           Fer4  14 CvevCPvgAI 23 
                                    Cv  CP gA 
  gi|121637094|ref|YP_977317.1| 193 CVASCPSGAM 202
                                    ********96 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.026
                                    EETTTSSS-THHHHHSTT CS
                           Fer4   3 ideekCigCGaCvevCPv 20 
                                    +d+++C g   Cv+ CP+
  gi|121637094|ref|YP_977317.1| 213 VDQDRCRGWRMCVSGCPY 230
                                    8999999999*******7 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.43
                                    TTSSS- CS
                           Fer4   6 ekCigC 11 
                                    ekC+ C
  gi|121637094|ref|YP_977317.1| 243 EKCTLC 248
                                    9***** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0038       5.3       4      30 ..      12      37 ..       9      60 .. 0.78
   2 ?   11.7   0.3   0.00024      0.33       1      30 [.     211     242 ..     211     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0038
                        Fer4_15  4 DrdaCigcglCvaeapevfeldedgla 30
                                   + d+Cigc  C   +++  ++   g  
  gi|121637094|ref|YP_977317.1| 12 NLDKCIGCHTCSVTCKQAWTNR-SGTE 37
                                   579************9887776.5555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00024
                        Fer4_15   1 VvvDrdaCigcglCvaea..pevfeldedgla 30 
                                    V vD+d+C g  +Cv  +  ++v  +++ g+a
  gi|121637094|ref|YP_977317.1| 211 VLVDQDRCRGWRMCVSGCpyKKVYFNHKTGKA 242
                                    78***************966566666667777 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00031      0.42       3      25 ..      13      35 ..      11      60 .. 0.79
   2 ?   -2.5   0.2       5.9   8.2e+03      12      18 ..     193     199 ..     188     210 .. 0.68
   3 ?    4.8   0.1      0.03        41       1      17 [.     213     229 ..     213     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                        Fer4_13  3 rdtCiacgaCvelaPdvFeedde 25
                                    d+Ci+c++C  ++ +       
  gi|121637094|ref|YP_977317.1| 13 LDKCIGCHTCSVTCKQAWTNRSG 35
                                   69************987776654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.9
                        Fer4_13  12 CvelaPd 18 
                                    Cv+ +P 
  gi|121637094|ref|YP_977317.1| 193 CVASCPS 199
                                    6666664 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.03
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD+d+C +   Cv+ +P
  gi|121637094|ref|YP_977317.1| 213 VDQDRCRGWRMCVSGCP 229
                                    9***************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   4.9e-05     0.068       4      20 ..      12      28 ..       4      34 .. 0.75
   2 ?   11.9   4.1   0.00014      0.19       9      53 ..     186     230 ..     182     234 .. 0.74
   3 ?   -3.5   1.6       8.6   1.2e+04      11      14 ..     245     248 ..     236     265 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                        Fer4_21  4 dedkCigCgkCliaCed 20
                                   + dkCigC  C ++C++
  gi|121637094|ref|YP_977317.1| 12 NLDKCIGCHTCSVTCKQ 28
                                   55788888888888875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                        Fer4_21   9 igC..gkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                     +C   +C+ +C+       + +++ ++ v +d+C G  +C+s CP 
  gi|121637094|ref|YP_977317.1| 186 EHClnPSCVASCPS--GAMYKRTEDGIVLVDQDRCRGWRMCVSGCPY 230
                                    4442247******5..333466677788889***************6 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.6
                        Fer4_21  11 CgkC 14 
                                    C++C
  gi|121637094|ref|YP_977317.1| 245 CTLC 248
                                    3333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00019      0.26       2      16 ..      13      27 ..       8      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                         Fer4_8  2 lekCieCgaCqsaCp 16
                                   l+kCi+C  C  +C 
  gi|121637094|ref|YP_977317.1| 13 LDKCIGCHTCSVTCK 27
                                   578888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3841.08
//
Query:       gi|121637095|ref|YP_977318.1|  [L=201]
Description: respiratory nitrate reductase (delta chain) narJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-07   31.4   0.1    2.4e-07   30.8   0.1    1.3  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   1.4e-11   2.4e-07      17     105 ..      43     124 ..      21     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.4e-11
                Nitrate_red_del  17 ealaa.ededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrqaglevaeefneppDHlaveLe 95 
                                    +   + ++ +  + aa+Y+++F+   rr+   y +++++++  + +g++ l+++ +yr+ag++ +++   + D+l+v+Le
  gi|121637095|ref|YP_977318.1|  43 A---ElRALAPMAAAAQYVETFD--MRRRSTMYLTYWTAGDT-RNRGREMLAFATAYRDAGVKPPRTE--ALDYLPVVLE 114
                                    3...2478888999*********..7999999*******777.7888888************966553..79******** PP

                Nitrate_red_del  96 flahLaerea 105
                                    f a+   ++ 
  gi|121637095|ref|YP_977318.1| 115 FAATVDPEAG 124
                                    **97654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1361.38
//
Query:       gi|121637096|ref|YP_977319.1|  [L=246]
Description: respiratory nitrate reductase (gamma chain) narI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-84  280.5  13.1    9.5e-84  280.3  13.1    1.0  1  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
       0.35   11.3   3.4        0.4   11.1   0.1    2.8  3  COX7a            Cytochrome c oxidase subunit VII


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.3  13.1   1.1e-87   9.5e-84       3     219 .]       9     228 ..       7     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 280.3 bits;  conditional E-value: 1.1e-87
                Nitrate_red_gam   3 llfvvlPYvalavlvvgsllryrydqftwtskSsqllekklLrlgsplFHvGilvvllgHlvGlliPksvtealgvseel 82 
                                    +++ + PYv++a++vvg+++ryryd+f+wt++Ssql+e++lL++gsp+FH+G l+v++gH++Gl+iP+s+t+a+g+s++l
  gi|121637096|ref|YP_977319.1|   9 IFWDAAPYVVVAIAVVGTWWRYRYDKFGWTTRSSQLYESRLLSIGSPMFHFGSLLVIMGHVMGLFIPDSWTRAFGMSDHL 88 
                                    79****************************************************************************** PP

                Nitrate_red_gam  83 yqllalvaGliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldygse...retispwl 159
                                    y+l+al++G+ ag+++l+G+ lL++RR+ ++ v  at+++Dk+++l+L+++i++Gl++tl+ a++ g +   r ++s w+
  gi|121637096|ref|YP_977319.1|  89 YHLQALLLGAPAGFATLLGIGLLIYRRRIQTPVWLATTRNDKLMYLVLVCAIVAGLACTLMGATHEGDMhdyRRSVSVWF 168
                                    **************************************************************9965433345******** PP

                Nitrate_red_gam 160 rslltlqpdaellaevplifklHvllglllfalfPFtrLvHvlsapleYllrpyqvvrsr 219
                                    rs+++l p+ +l+a++ l++++Hvl++l+lf+l+PFtrLvH++sap++Yl+rpy+v+rsr
  gi|121637096|ref|YP_977319.1| 169 RSIWMLAPRGDLMAQATLYYQVHVLIALALFVLWPFTRLVHAFSAPIAYLFRPYIVYRSR 228
                                    **********************************************************97 PP

>> COX7a  Cytochrome c oxidase subunit VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.31   2.8e+03      18      27 ..      26      35 ..      16      36 .. 0.78
   2 ?   11.1   0.1   4.4e-05       0.4      13      46 ..     116     150 ..     112     153 .. 0.75
   3 ?   -2.4   0.1      0.76   6.8e+03      19      31 ..     172     184 ..     170     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                          COX7a 18 lwlrgprskl 27
                                   +w+r +++k+
  gi|121637096|ref|YP_977319.1| 26 TWWRYRYDKF 35
                                   7888888876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.4e-05
                          COX7a  13 sdkkplwlrgprsklylypyyalfavg.llgslyg 46 
                                    + ++p+wl + r   ++y  +++++v+ l+++l g
  gi|121637096|ref|YP_977319.1| 116 RIQTPVWLATTRNDKLMYLVLVCAIVAgLACTLMG 150
                                    5678****************888877505555555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.76
                          COX7a  19 wlrgprsklylyp 31 
                                    w+  pr  l+  +
  gi|121637096|ref|YP_977319.1| 172 WMLAPRGDLMAQA 184
                                    6666666665433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1829.30
//
Query:       gi|121637097|ref|YP_977320.1|  [L=628]
Description: GTP-binding translation elongation factor typA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-50  169.1   0.0    1.2e-49  168.5   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.2e-21   75.1   0.0      7e-21   74.1   0.0    1.6  1  EFG_C        Elongation factor G C-terminus
    1.5e-12   47.8   0.5    3.8e-12   46.4   0.5    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.3e-06   27.6   0.0    5.2e-06   26.5   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.019   14.3   0.0       0.03   13.6   0.0    1.2  1  Septin       Septin


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0   3.4e-53   1.2e-49       3     193 ..       3     212 ..       1     213 [. 0.88

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 3.4e-53
                                    EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..T.TCSSEEEEEEEESS CS
                       GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..k.etkkylinliDtPG 79 
                                     rn++i++hvDhGKtTL+d++l ++ga +++ge +e  rv+Dt + Ere+giTi ++++ ++  + +++ + in+iDtPG
  gi|121637097|ref|YP_977320.1|   3 FRNVAIVAHVDHGKTTLVDAMLRQSGALRERGELQE--RVMDTGDLEREKGITILAKNTAVHrhHpDGTVTVINVIDTPG 80 
                                    79****************************999987..99**********************75369999********** PP

                                    SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  80 HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklek 159
                                    H+dF  ev+rgl+++Dg++l+vda+eG+ pqt+ vlr al+ ++p+i+++NK Dr++a++ e+v++ ++ l ++ ++l++
  gi|121637097|ref|YP_977320.1|  81 HADFGGEVERGLSMVDGVLLLVDASEGPLPQTRFVLRKALAAHLPVILVVNKTDRPDARIAEVVDASHDLLLDVASDLDD 160
                                    ********************************************************************999777555554 PP

                                    HHHTTT...TTEEEEEEBTTTTB...............THHHHHHHHHHHSH CS
                       GTP_EFTU 160 ygekge...kevpvvfgSalkge...............gvktllealvellp 193
                                     ++ +       p +++S+  g                ++++l+e+l +++p
  gi|121637097|ref|YP_977320.1| 161 EAAAAAehaLGLPTLYASGRAGVasttappdgqvpdgtNLDPLFEVLEKHVP 212
                                    4333323446789999999999866666666666666666688888888887 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   1.9e-24     7e-21       2      86 ..     417     501 ..     416     504 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.9e-24
                                    EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                          EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                    l+EP++++++++peey+g+v++++++r+G++ +m ++++g+v++ + +P+++lig +t++ + T+G g+ +  f+gY+++
  gi|121637097|ref|YP_977320.1| 417 LHEPFESMTVDCPEEYIGAVTQLMAARKGRMVEMANHTTGWVRMDFVVPSRGLIGWRTDFLTETRGSGVGHAVFDGYRPW 496
                                    89****************************************************************************** PP

                                    -HHHH CS
                          EFG_C  82 pgdkl 86 
                                     g++ 
  gi|121637097|ref|YP_977320.1| 497 AGEIR 501
                                    99875 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.5     1e-15   3.8e-12       1      74 []     236     309 ..     236     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1e-15
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                    G++al+r+y+G ++kG++v  ++ +d +++  + +i+ l++ ++ e+ + + a+aG+iva+ gl + i++Gdtl+
  gi|121637097|ref|YP_977320.1| 236 GRLALIRIYNGRIRKGQQVAWIRqVDGQQTVTTAKITELLATEGVERKPTDAAVAGDIVAVAGLPE-IMIGDTLA 309
                                    899******************9988777777***********************************.******95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.5e-09   5.2e-06       1     114 []       5     132 ..       5     132 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                                    EEEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEEETTEE.........EEEEECGG CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvklkgke.........ielvDtpG 55 
                                    +vaiv +   GK+tL+ a+++                ++   ++++g T+  +   v+    +         i+++DtpG
  gi|121637097|ref|YP_977320.1|   5 NVAIVAHVDHGKTTLVDAMLRqsgalrergelqervmDTGDLEREKGITILAKNTAVH----RhhpdgtvtvINVIDTPG 80 
                                    5899999*************76666654444443222234555555666666555555....0233455666******** PP

                                    CSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  56 liegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                             ++g ++++  + +d +ll+vdas e+  p+ + + +    a+ p+ilv+nk
  gi|121637097|ref|YP_977320.1|  81 -H------ADFGGEVERGLSmVDGVLLLVDAS-EGPLPQTRFVLRKALAAHLPVILVVNK 132
                                    .2......24555555544437********99.5466666777777678999*******8 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.3e-06      0.03       6      75 ..       5      84 ..       3      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                                   EEEEEEBTTSSCCCCCCTTSSSS----.......--------------S-EEEEEEEEE...TTCEEEEEEEE---BSSS CS
                         Septin  6 tlmvvGesglGkttlintlfetdliee.......ekleeasekkkktveikkkkvviee...dgvklnltviDtpgfGda 75
                                   ++ +v +   Gkttl++++++++   +       + +++   + +k ++i +k++ ++    dg+   ++viDtpg+ d+
  gi|121637097|ref|YP_977320.1|  5 NVAIVAHVDHGKTTLVDAMLRQSGALRergelqeRVMDTGDLEREKGITILAKNTAVHRhhpDGTVTVINVIDTPGHADF 84
                                   677899999**********98875544467777444444455788888888776666541226888999*******8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.21s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4689.29
//
Query:       gi|121637098|ref|YP_977321.1|  [L=635]
Description: lipoprotein lpqW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-32  112.0   0.1    5.3e-32  111.2   0.1    1.3  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.1     3e-36   5.3e-32       4     355 ..     108     483 ..     105     500 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 3e-36
                                    ESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEES CS
                      SBP_bac_5   4 paLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlk 83 
                                    p L  s+  ++    t+t+k+R++++++D +p+ A+D+++ ++ ++ +++   +a ++   +++++ e  +  +v+f   
  gi|121637098|ref|YP_977321.1| 108 PTLLVSADVTNNHPFTVTYKIRPEAQWTDNAPIAADDFWYLWQQMVTQPGVVDPAGYHL-ITSVQSLEGGKQAVVTFA-- 184
                                    666666667788889**************************************999996.778888888888888887.. PP

                                    SETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSSEEEEEE-.S CS
                      SBP_bac_5  84 kpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkldriefkvipd 162
                                    +p++   +l++++ ++   +++   + +++  ++ pv+ G +++++++p++ +i + rn+ Yw g + k+  i f+    
  gi|121637098|ref|YP_977321.1| 185 QPYPAWRELFTDILPAHI-VKDIPGGFASGLARALPVTGGQFRVENIDPQRdEILIARNDRYW-GPPSKPGIILFRRAGA 262
                                    777744444444444333.344468999999******************778***********.888999******9955 PP

                                    HHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE.EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCT CS
                      SBP_bac_5 163 sdaraaalqsGeiddvaepppsdieqlkeakglkv.lyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavl 241
                                    ++a a+++++G+   va+++ ++++  + +   +v +++  +++v  +++  + p+++d+ vR+A+   +D + ++ +  
  gi|121637098|ref|YP_977321.1| 263 PAALADSVRNGDT-QVAQVHGGSAAFAQLSAIPDVrTARIVTPRVMQFTLRANVPKLADTQVRKAILGLLDVDLLAAVGA 341
                                    66666666*****.6667888888877777777773355555555555555569*******************9999998 PP

                                    TTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC.......................... CS
                      SBP_bac_5 242 egyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek.......................... 295
                                    + + t++    +  sp+ +++ ++a++a   ++A  lL++ G++ + ++ ++++                          
  gi|121637098|ref|YP_977321.1| 342 GTDNTVTLDQAQIRSPSDPGYVPTAPPAMSSAAALGLLEASGFQVDTNTSVSPApsvpdstttsvstgppevirgriskd 421
                                    7766666655666666666666666667789********************999************************** PP

                                    ..EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEE CS
                      SBP_bac_5 296 ..klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgw 355
                                      +l+l++ +a+++p++ a+a+  ++ql+++Gi ++v ++d+ + y ++ +d+ +d+i+++ 
  gi|121637098|ref|YP_977321.1| 422 geQLTLVIGVAANDPTSVAVANTAADQLRDVGIAATVLALDPVTLYHDALNDNRVDAIVGWR 483
                                    ****************************************998999999*******999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 4097.27
//
Query:       gi|121637099|ref|YP_977322.1|  [L=201]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-14   53.9   0.2      2e-14   53.9   0.2    2.0  2  TetR_C_11    Tetracyclin repressor-like, C-terminal domain
    5.6e-12   45.3   1.1    9.7e-12   44.5   1.1    1.4  1  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.095   12.7   0.0    1.8  1  TetR_C_7     AefR-like transcriptional repressor, C-terminal 
      0.077   13.0   0.0       0.13   12.2   0.0    1.4  1  TetR_C_36    Tetracyclin repressor-like, C-terminal domain
      0.093   12.6   0.1       0.15   11.9   0.1    1.3  1  Sigma70_ECF  ECF sigma factor


Domain annotation for each model (and alignments):
>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.23   8.3e+02      13      62 ..      22      68 ..      15      74 .. 0.52
   2 !   53.9   0.2   5.5e-18     2e-14       6     112 ..      85     190 ..      80     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                      TetR_C_11 13 allralaealaspra.gallrallaeaqrdpelaealrerlleprraalra 62
                                   al +a+ ++l+s    g ++ +++a aq+     +al +  ++  r+ + a
  gi|121637099|ref|YP_977322.1| 22 ALYDATLAELESAGYgGLTMEGIAARAQT---GKAALYR-RWAGKRELVLA 68
                                   56666666666644404444554444433...3344444.25555554444 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 5.5e-18
                      TetR_C_11   6 slrgDLrallralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldl 85 
                                    s r+ L+a+ +a +e la+ +++     +++++ ++pel++ +   +++pr + ++ +l+ +v+ Ge+++ + +++ + +
  gi|121637099|ref|YP_977322.1|  85 SARENLLAVFTANCEILAG-KTALPSMEIVSQLLHEPELRAIFINSVWAPRLRIVESILQAGVRSGEIDPATLTPMTARI 163
                                    7899***************.57888888899999********************************************** PP

                      TetR_C_11  86 llgpllyrllltgeplddafaerlvda 112
                                     ++++++++l+tg+p+d++ + r++da
  gi|121637099|ref|YP_977322.1| 164 GPALIHQHVLFTGSPPDREQLTRIIDA 190
                                    *************************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   1.1   2.7e-15   9.7e-12       2      47 .]      24      69 ..      23      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.7e-15
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                    da+++ ++  Gy ++t++ IA+rA+++k+alYr++++K+eL++a+
  gi|121637099|ref|YP_977322.1| 24 YDATLAELESAGYGGLTMEGIAARAQTGKAALYRRWAGKRELVLAA 69
                                   79*****************************************996 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05     0.095      26     108 ..     112     190 ..      88     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                    HHHHHHT-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB-SS.-HHHHHHHHHHHHHHHHTHHHHHH------HHHHHH CS
                       TetR_C_7  26 viaeaerfPelarafyeagpgrveealaayLeaavaaGrLrid.DpelAAeqflgllkgelfwprlfgveeppseeeier 104
                                    +++++ ++Pel   f +++ +++ + ++++L+a v++G+++ +  + ++A+   +l+++     +lf + +pp++e++ r
  gi|121637099|ref|YP_977322.1| 112 IVSQLLHEPELRAIFINSVWAPRLRIVESILQAGVRSGEIDPAtLTPMTARIGPALIHQ----HVLFTG-SPPDREQLTR 186
                                    468999*********************************98762345666666665544....344554.5567777766 PP

                                    HHHH CS
                       TetR_C_7 105 vves 108
                                    ++++
  gi|121637099|ref|YP_977322.1| 187 IIDA 190
                                    6665 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.8e-05      0.13      51     110 ..     136     192 ..     110     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                      TetR_C_36  51 aavaelleeevaageleppldlddlAyllvRiaEsflYadli.ageepdidkaetavraLL 110
                                    ++v+++l++ v++g    ++d+++l+ +  Ri+ + ++++++ +g +pd ++ +++++a++
  gi|121637099|ref|YP_977322.1| 136 RIVESILQAGVRSG----EIDPATLTPMTARIGPALIHQHVLfTGSPPDREQLTRIIDAMI 192
                                    57788888888888....68899*****************7659*************9986 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.3e-05      0.15     135     178 ..      21      65 ..      16      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                    Sigma70_ECF 135 s.ldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRaw 178
                                    + l ++ + ++e +   Gl++e iA++ + +k++ +rr+a  R+ 
  gi|121637099|ref|YP_977322.1|  21 RaLYDATLAELESAGYGGLTMEGIAARAQTGKAALYRRWAGKREL 65 
                                    446788899999***************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1284.54
//
Query:       gi|121637100|ref|YP_977323.1|  [L=180]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-46  156.3  10.2    7.3e-46  156.1  10.2    1.0  1  PPE        PPE family
      0.008   16.1   0.2      0.012   15.5   0.2    1.3  1  VIT1       VIT family
  ------ inclusion threshold ------
      0.092   12.9   0.1       0.15   12.2   0.1    1.3  1  GxGYxYP_N  GxGYxY sequence motif in domain of unknown functio


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1  10.2   1.2e-49   7.3e-46       2     158 .]       6     159 ..       5     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 1.2e-49
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    +pPE+ns +++    ++p+l Aa+aW++L++el+ aa+ +es +++l  ++W+Gpss+ maaa+ap+ aW+ ++a  ae 
  gi|121637100|ref|YP_977323.1|   6 FPPEFNSLNIQGS--ARPFLVAANAWKNLSNELSYAASRFESEINGLI-TSWRGPSSTIMAAAVAPFRAWIVTTASLAEL 82 
                                    7********9977..789******************************.******************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                    +A +++++a aYeaA+aa vp+++i +nr ++ al++tn+fG++tpaI a++a y+++w qd +am+ Y++++aaaa
  gi|121637100|ref|YP_977323.1|  83 VADHISVVAGAYEAAHAAHVPLPVIETNRLTRLALATTNIFGIHTPAIFALDALYAQYWSQDGEAMNLYATMAAAAA 159
                                    ************************************************************************99985 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2     2e-06     0.012      20      59 ..      62     100 ..      56     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                           VIT1  20 aGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkse 59 
                                    +  ++a   ++++v +a lael+A+ iS  +G+Y ++++ 
  gi|121637100|ref|YP_977323.1|  62 MAAAVAP-FRAWIVTTASLAELVADHISVVAGAYEAAHAA 100
                                    3444345.4889**********************999875 PP

>> GxGYxYP_N  GxGYxY sequence motif in domain of unknown function N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.5e-05      0.15      45      99 ..      33      86 ..      22      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                   ESSHHHHHHHHHH---EEEEETTTT--HHHHHHHHHHHHTEEEEEGGGHHHHHHT CS
                      GxGYxYP_N 45 lkdlasllkkfkneidgyVlydpakdeslnvAltiAalenaivvtesllelakel 99
                                    ++l+ + ++f++ei+g++      + s+ +A+ +A    +iv t+sl el++++
  gi|121637100|ref|YP_977323.1| 33 SNELSYAASRFESEINGLITSWR-GPSSTIMAAAVAPFRAWIVTTASLAELVADH 86
                                   57888999**********99875.89*********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1448.27
//
Query:       gi|121637101|ref|YP_977324.1|  [L=100]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-23   81.9   0.0    3.6e-23   81.7   0.0    1.0  1  PE        PE family
  ------ inclusion threshold ------
      0.086   12.7   0.0       0.11   12.4   0.0    1.1  1  Sec7_N    Guanine nucleotide exchange factor in Golgi transpo
       0.18   11.1   0.0        6.5    6.2   0.0    2.2  2  SeqA_N    SeqA protein N-terminal domain


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0     6e-27   3.6e-23       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 6e-27
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++ P+ + ++aa+l++ig ++sa +  +++ +t+v ++a D VS+ ++ lfs h++ y+a+++qa+  he fvq+l++
  gi|121637101|ref|YP_977324.1|  1 MSFVTTRPDSIGETAANLHEIGVTMSAHDDGVTPLITNVESPAHDLVSIVTSMLFSMHGELYKAIARQAHVIHESFVQTLQT 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   + +sY  +E 
  gi|121637101|ref|YP_977324.1| 83 SKTSYWLTEL 92
                                   ******9996 PP

>> Sec7_N  Guanine nucleotide exchange factor in Golgi transport N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11      69     128 ..      35      93 ..      27      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                         Sec7_N  69 LlknlsespsfpvferslrivllLlkkfrseLktEievflsllilillesdsslwqrvla 128
                                    L++n+ esp+  ++++++++++ +  ++++ + ++ +v+ + +++ l +s++s+w  +la
  gi|121637101|ref|YP_977324.1|  35 LITNV-ESPAHDLVSIVTSMLFSMHGELYKAIARQAHVIHESFVQTLQTSKTSYWLTELA 93 
                                    89999.*****************************************8889999987765 PP

>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.011        66      14      26 ..       4      16 ..       2      22 .. 0.78
   2 ?    6.2   0.0    0.0011       6.5       9      24 ..      60      75 ..      56      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.011
                         SeqA_N 14 IasntqaiGESaS 26
                                   +  +  +iGE+a 
  gi|121637101|ref|YP_977324.1|  4 VTTRPDSIGETAA 16
                                   5566679****97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0011
                         SeqA_N  9 eLYrYIasntqaiGES 24
                                   eLY+ Ia +   i ES
  gi|121637101|ref|YP_977324.1| 60 ELYKAIARQAHVIHES 75
                                   9************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 779.85
//
Query:       gi|121637102|ref|YP_977325.1|  [L=303]
Description: N-Acetyl-1-D-myo-Inosityl-2-amino-2-deoxy-alpha- D-glucopyranoside deacetylase mshB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-28   97.9   0.7    1.1e-27   97.3   0.3    1.5  2  PIG-L           GlcNAc-PI de-N-acetylase
  ------ inclusion threshold ------
      0.012   15.6   0.8       0.07   13.1   0.1    2.2  2  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.3   1.2e-31   1.1e-27       1     130 [.       8     157 ..       8     158 .. 0.96
   2 ?   -3.6   0.0       1.8   1.6e+04      55      68 ..     228     241 ..     215     253 .. 0.61

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 1.2e-31
                                    EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH......-HHHHHHHHHHHHHHHHCTE..EEEE CS
                          PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleek......eelaeiRekEaraaakhlgvadedvf 74 
                                    l+v+AHpDDe+l+ g+tia+++++g++v++v++t G++g+     +++      ++l+ +R  E+ aa+++lgv  +  +
  gi|121637102|ref|YP_977325.1|   8 LFVHAHPDDESLSNGATIAHYTSRGAQVHVVTCTLGEEGEVIGDRWAQltadhaDQLGGYRIGELTAALRALGV--SAPI 85 
                                    79******************************************9*99***99999******************..9999 PP

                                    ECC....CBTT-STT...........S-CHHHHHHHHHHHHHH--SEEEEE-TTTT.H-HHHHHHHHHHHHH CS
                          PIG-L  75 fld....fpDgsles...........ydedellddlaklieryrPdvvltldpegd.dhpDHtavasaavaa 130
                                     l+    ++D++++             d +++  +l+++i+++rP+vv+t+dp+g+ +hpDH+ ++ +++aa
  gi|121637102|ref|YP_977325.1|  86 YLGgagrWRDSGMAGtdqrsqrrfvdADPRQTVGALVAIIRELRPHVVVTYDPNGGyGHPDHVHTHTVTTAA 157
                                    999999988888888999999999999999**************************************9998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHCTE CS
                          PIG-L  55 RekEaraaakhlgv 68 
                                     ++E  +aak+  +
  gi|121637102|ref|YP_977325.1| 228 EADEQARAAKVAAL 241
                                    44555555555444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.061   5.5e+02      13      31 ..      26      44 ..      23      59 .. 0.78
   2 ?   13.1   0.1   7.8e-06      0.07       8      89 ..      69     161 ..      65     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.061
                 Glyco_transf_4 13 raLarrGheVtvvtpgddg 31
                                    +   rG +V+vvt + ++
  gi|121637102|ref|YP_977325.1| 26 AHYTSRGAQVHVVTCTLGE 44
                                   577889*******765544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.8e-06
                 Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkre............kpDv 75 
                                    + eL+ aL+++G+   ++  g ++  +     +++ ++ +++ ++++++++ +l ++ r l+ +            +pD 
  gi|121637102|ref|YP_977325.1|  69 IGELTAALRALGVSAPIYLGGAGRWRDSG-MAGTDQRSQRRFVDADPRQTVGALVAIIRELRPHvvvtydpnggygHPDH 147
                                    66899999999999999965555555555.7899********************************************** PP

                 Glyco_transf_4  76 vHahspaalgaall 89 
                                    vH+h+  ++ +a++
  gi|121637102|ref|YP_977325.1| 148 VHTHTVTTAAVAAA 161
                                    *****888765543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2282.03
//
Query:       gi|121637103|ref|YP_977326.1|  [L=146]
Description: hypothetical protein BCG_1234 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   12.6   1.4        0.2   11.7   1.4    1.4  1  HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 co


Domain annotation for each model (and alignments):
>> HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   1.1e-05       0.2      20      32 ..     102     114 ..     101     114 .. 0.40

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                HemolysinCabind  20 GgaGnDtlyGGaG 32 
                                    Gg G+D++ GG+G
  gi|121637103|ref|YP_977326.1| 102 GGPGDDVILGGQG 114
                                    4444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1098.77
//
Query:       gi|121637104|ref|YP_977327.1|  [L=308]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-33  113.9  20.6    3.3e-33  113.9  20.6    2.7  2  PE              PE family
  ------ inclusion threshold ------
       0.28   11.4   2.3       0.45   10.7   0.0    2.5  3  FeS_assembly_P  Iron-sulfur cluster assembly protein
        1.1    9.6   3.9        1.2    9.5   2.1    2.0  2  MHB             Haemophore, haem-binding
        1.3    9.8  10.2         17    6.2   5.9    2.9  3  TetR_C_15       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9  20.6   7.4e-37   3.3e-33       1      92 [.       1      93 [.       1      94 [. 0.97
   2 ?    1.9   5.2     0.061   2.7e+02      26      81 ..     149     204 ..     141     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 7.4e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaa.afheqfvqala 81
                                   Msfv +aPealaaaaad+agigs+l+aan  aa ptt+vlaaaaDeVS+++Aal+sahaq yq+ls+q+  afh+qfvqal+
  gi|121637104|ref|YP_977327.1|  1 MSFVFAAPEALAAAAADMAGIGSTLNAANVVAAVPTTGVLAAAADEVSTQVAALLSAHAQGYQQLSRQMMtAFHDQFVQALR 82
                                   9******************************************************************97526********** PP

                                   HHHHHHHS--X CS
                             PE 82 aaagsYaaaEa 92
                                   a+a++Ya+aEa
  gi|121637104|ref|YP_977327.1| 83 ASADAYATAEA 93
                                   **********8 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.061
                                    HHHHHHHHHHHH----S.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  26 saanaaaaapttavlaa.aaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqala 81 
                                    +aanaaa+++++ + +  +a   Sa  A l  a a++  al a aa+ + ++++ l 
  gi|121637104|ref|YP_977327.1| 149 AAANAAASGALQ-LQPTgGASGLSAVGALLPRAGAAAAAALPALAAESIGNAIKNLY 204
                                    578888888887.77775788888888888888888888888888888888777765 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1         1   4.5e+03      45      45 ..      91      91 ..      68     112 .. 0.53
   2 ?   -2.8   0.1       1.6   7.3e+03      55      64 ..     182     191 ..     171     201 .. 0.52
   3 ?   10.7   0.0    0.0001      0.45      16      55 ..     241     280 ..     240     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                   T CS
                 FeS_assembly_P 45 p 45
                                   +
  gi|121637104|ref|YP_977327.1| 91 A 91
                                   2 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                    HHHHHHHC.S CS
                 FeS_assembly_P  55 adaeaalral 64 
                                    a+a aal al
  gi|121637104|ref|YP_977327.1| 182 AAAAAALPAL 191
                                    3333333333 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0001
                                    TSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHH CS
                 FeS_assembly_P  16 lgvdlvslglvreidieggkVsvditltypacslaeaira 55 
                                    lg ++v++ l  +id  +g+V+++ +lt+++ + a+ i +
  gi|121637104|ref|YP_977327.1| 241 LGEPIVQAVLFNAIDFVDGTVTFSQALTNIETATAASINQ 280
                                    799****************************999988866 PP

>> MHB  Haemophore, haem-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.1   0.00026       1.2       8      71 ..      40     109 ..      36     113 .. 0.80
   2 ?   -2.0   0.0      0.99   4.4e+03      30      44 ..     264     278 ..     245     285 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00026
                            MHB   8 larvvsgVaastsaYLdthPd.....vnqaltslkgqprdqaraavkaYfdanPqvaadL.rgIrqPltd 71 
                                    la  + +V+++++a L++h +       q++t+ ++q  ++ ra+ +aY +a+  +a+ + +++++P++ 
  gi|121637104|ref|YP_977327.1|  40 LAAAADEVSTQVAALLSAHAQgyqqlSRQMMTAFHDQFVQALRASADAYATAEASAAQTMvNAVNAPARA 109
                                    577788999999999999987333334678899999999**************99998874678888875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.99
                            MHB  30 nqaltslkgqprdqa 44 
                                     qalt++++ ++  +
  gi|121637104|ref|YP_977327.1| 264 SQALTNIETATAASI 278
                                    445555544444333 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.091   4.1e+02      34      60 ..      34      60 ..      28      64 .. 0.75
   2 ?    6.2   5.9    0.0037        17      23      95 ..      51     120 ..      40     130 .. 0.73
   3 ?    3.8   0.1     0.022        99      44      84 ..     166     206 ..     150     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.091
                      TetR_C_15 34 lgelelvealeqriaealaalLarrrp 60
                                   +++    +a+ +++ +++aalL ++++
  gi|121637104|ref|YP_977327.1| 34 VPTTGVLAAAADEVSTQVAALLSAHAQ 60
                                   555556678888999999999998875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0037
                      TetR_C_15  23 lrrvlleeapslgel..elvealeqriaealaalLarrrpelppedlelaafvaveaveallhlaleedpadrea 95 
                                    + ++l++ a  +++l  ++ +a+++++++al+a  ++++++ +      aa+++v+av+a  +++l ++ ++++a
  gi|121637104|ref|YP_977327.1|  51 VAALLSAHAQGYQQLsrQMMTAFHDQFVQALRASADAYATAEA-----SAAQTMVNAVNAPARALLGHPLISADA 120
                                    5566666666666554455666777777777777766666666.....9*****************999866665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.022
                      TetR_C_15  44 eqriaealaalLarrrpelppedlelaafvaveaveallhl 84 
                                     +   +a+ alL r+ ++ +++ ++laa+ + +a+++l  +
  gi|121637104|ref|YP_977327.1| 166 GASGLSAVGALLPRAGAAAAAALPALAAESIGNAIKNLYNA 206
                                    5566789999**************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1862.24
//
Query:       gi|121637105|ref|YP_977328.1|  [L=856]
Description: FO synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-27   95.7   0.0    2.1e-12   47.8   0.0    2.7  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   7.2e-16   1.3e-11       1     165 [.      92     275 ..      92     277 .. 0.90
   2 !   47.8   0.0   1.1e-16   2.1e-12       1     165 [.     552     724 ..     552     726 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 7.2e-16
                                    EEEESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.. CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.. 74 
                                    ++vtr C+ +C++C++ +     r  g + ++ ++eil+ ++++ ae g ++ ++ +g+ p ++++ +++++ ++  +  
  gi|121637105|ref|YP_977328.1|  92 IPVTRLCRDNCHYCTFVTVpgkLRAQGSSTYMEPDEILDVARRG-AEFGcKEALFTLGDRPEARWRQAREWLGERGYDst 170
                                    689**************99*************************.899999999999*******8888888888888888 PP

                                    ...........CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHT.CTSHHHHHHHHHHHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx.xxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 ...........vpgiritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmn.rghtfeevlealeklr 138
                                                +   +    n+++ ++  + rl++     + + le+++ +    k l + + + +++  +l++l  + 
  gi|121637105|ref|YP_977328.1| 171 lsyvramairvLEQTGLLPHLNPGVMSWSEMSRLKPVA-PSMGMMLETTSRRlfetKGLAHYGsPDKDPAVRLRVLTDAG 249
                                    8887777755666666666666666669999*****87.*****************99999999**************** PP

                                    HTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 139 eagikrvvdrivglpGendeeleelle 165
                                    ++ i+  +++++++ Ge+ +e+ ++l+
  gi|121637105|ref|YP_977328.1| 250 RLSIP-FTTGLLVGIGETLSERADTLH 275
                                    *****.***************999986 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 1.1e-16
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla..... 74 
                                    +++t+ C  +C+fCa+ +  +   +++slsv e+++ + e++   g ++++++gg +p l    + +l r++k +     
  gi|121637105|ref|YP_977328.1| 552 INFTNICYTGCRFCAFAQR-KGDADAYSLSVGEVADRAWEAH-VAGaTEVCMQGGIDPELPVTGYADLVRAVKARvpsmh 629
                                    689***************6.9999*****************6.5566**************************9966666 PP

                                    .....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEE.EEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 .....vpgiritvetngtlpdeeklerllelgvdrv.slgleaaddekvlklmn.rghtfeevlealeklreagikrvvd 147
                                           +i + v+ +g+ + +e+l  l+e+g+d++    +e++dde v+  +  ++   + ++e + +++e+g++ +++
  gi|121637105|ref|YP_977328.1| 630 vhafsPMEIANGVTKSGLSI-REWLIGLREAGLDTIpGTAAEILDDE-VRWVLTkGKLPTSLWIEIVTTAHEVGLR-SSS 706
                                    55555555555555555555.***********666615667777777.888887788999****************.788 PP

                                    EEEEBTTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 148 rivglpGendeeleelle 165
                                    +++ ++  + ++++++l+
  gi|121637105|ref|YP_977328.1| 707 TMMYGHVDSPRHWVAHLN 724
                                    888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (856 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5601.44
//
Query:       gi|121637106|ref|YP_977329.1|  [L=110]
Description: hypothetical protein BCG_1237c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 794.19
//
Query:       gi|121637107|ref|YP_977330.1|  [L=674]
Description: NADPH dependent 2,4-dienoyl-CoA reductase fadH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-77  260.4   0.0    3.4e-77  260.0   0.0    1.1  1  Oxidored_FMN    NADH:flavin oxidoreductase / NADH oxidase fam
    1.3e-23   83.7   0.2    2.1e-23   83.0   0.2    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-10   41.1   0.2    7.2e-10   39.0   0.1    2.3  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.2e-08   33.3   3.7    7.1e-06   26.5   0.2    4.0  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.9e-08   32.5   0.3    9.4e-08   31.8   0.3    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    1.5e-07   30.5   0.1    2.8e-07   29.6   0.1    1.4  1  HI0933_like     HI0933-like protein
    1.9e-06   27.7   0.2    1.9e-06   27.7   0.2    3.6  3  DAO             FAD dependent oxidoreductase
    3.8e-06   26.2   0.5    8.4e-06   25.1   0.5    1.6  1  FAD_binding_2   FAD binding domain
    1.4e-05   24.5   1.3       0.06   12.6   0.1    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00014   21.1   0.1    0.00025   20.3   0.1    1.4  1  GIDA            Glucose inhibited division protein A
     0.0003   20.7   0.6      0.018   14.9   0.2    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00043   19.7   0.0    0.00081   18.8   0.0    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0086   16.1   3.0      0.032   14.2   0.1    3.0  3  NAD_binding_9   FAD-NAD(P)-binding
      0.009   15.3   0.5      0.021   14.1   0.0    1.8  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.012   14.7   0.1       0.52    9.4   0.0    2.2  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.012   14.8   2.7       0.02   14.2   0.1    2.3  3  FAD_binding_3   FAD binding domain
      0.014   14.7   1.8       0.02   14.2   0.0    2.0  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.016   14.3   0.5      0.039   13.0   0.2    1.8  2  Lycopene_cycl   Lycopene cyclase protein
      0.017   14.5   0.3        1.7    8.0   0.1    2.5  2  PALP            Pyridoxal-phosphate dependent enzyme
      0.047   13.1   0.3        5.5    6.3   0.1    2.5  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.15   12.0   0.2       0.58   10.1   0.0    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.28   10.8   1.1       0.45   10.1   0.0    1.9  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.32   10.0   1.8       0.75    8.8   0.1    2.4  3  Dus             Dihydrouridine synthase (Dus)
       0.32   11.4   1.6        1.8    9.0   0.1    2.4  2  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.0   0.0   4.6e-80   3.4e-77       2     341 ..       8     332 ..       7     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: 260.0 bits;  conditional E-value: 4.6e-80
                                    CCS-EEETTEEESSSEEE---.-S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHH CS
                   Oxidored_FMN   2 LFkPikignmtLknRivmapm.trlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdeeqie 80 
                                    L  P+++g++tL+nR+vm++m t l+       + d++a+y+++ra+++v+liit++ ++n ++   + a  + +  q++
  gi|121637107|ref|YP_977330.1|   8 LLSPLDLGFTTLRNRVVMGSMhTGLEDRARH--I-DRLADYFAERARGGVGLIITGGYAPNRTGWLLPFASELVTSAQAR 84 
                                    889******************8888877776..4.59******************************************* PP

                                    HHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHHHHHHH CS
                   Oxidored_FMN  81 ewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefveAAkr 160
                                     +r +  avh+ g+k+ +q++h+Gr+a   y++ + + sp+     +a+++    +  +++l+++ ++ +i +f+++A++
  gi|121637107|ref|YP_977330.1|  85 RHRRINRAVHDSGAKILLQILHAGRYA---YHPLAVSASPI-----KAPIT----PFRPRALSARGVEATIADFARCAQL 152
                                    ***************************...88888844555.....66644....44489******************** PP

                                    HHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE--STTS--HHH CS
                   Oxidored_FMN 161 aieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedvvekgldfae 239
                                    a++Ag+DgVei+g++GYLlnqFl p++nkrtD +gG   nR rF++e+++  + avg+++ + yRlS+ d+v +g+   e
  gi|121637107|ref|YP_977330.1| 153 ARDAGYDGVEIMGSEGYLLNQFLAPRTNKRTDSWGGTPANRRRFPVEIIRRSRAAVGSDFiICYRLSMADYVAEGQSWDE 232
                                    ************************************************************99***************999 PP

                                    H...HHHHHHHCHCCEEEEEEETT-SS.SSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS CS
                   Oxidored_FMN 240 t...aqkivllkelekrlkdgkklalv.haaeprkrgagsvrteqekntefvkevwkkplitvgriadeekaaeivaege 315
                                        a +++ +++++ +   g+++a+v ++++ ++ ga+    +       v e++  p+++ +ri+ ++ a+ i+ae +
  gi|121637107|ref|YP_977330.1| 233 IvalATEVEGAGATIINSGFGWHEARVpTIVTSVPGGAFVDISS------AVAEHVTIPVVASNRINMPQAAERILAETQ 306
                                    99889999999****************88888777777766655......9***************************** PP

                                    -SEEEESTHHHH-TTHHHHHHCCTCG CS
                   Oxidored_FMN 316 adLvamgRefladpdlveklkkglpl 341
                                      L++m+R++l+dpd+v k+++++ +
  gi|121637107|ref|YP_977330.1| 307 VRLISMARPMLSDPDWVLKAQSNRVD 332
                                    **********************9976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.2   2.8e-26   2.1e-23       2     244 ..     378     636 ..     377     658 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.8e-26
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpg 81 
                                    +v+v+G+GpAGla+a ++aq g++vtl+ + + + +g+  ++  + g +e+ e+++         + ++l++++v++  g
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQRGHRVTLF-EANDFIGGQFDMARRIPGKEEFSETIRY--------FSTILAKHGVEVRLG 448
                                    79**************************.9999*******************97773........567777788999888 PP

                                    CEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T..SEEEEES-SHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  82 kkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp..krivvvGgGyiGvElAa 159
                                      +v  +++         yd++vlAtG  pr++ ipG  ++       l+ aea+    +p  + ++vvG+G iG +++ 
  gi|121637107|ref|YP_977330.1| 449 T-RVAAQEL-------TGYDEVVLATGVAPRIPAIPGI-DHPM----VLTYAEAIT-GVRPvgRTVAVVGAGGIGFDVTE 514
                                    8.7777444.......47********************.5553....345555543.22223468*************** PP

                                    HH..............HHHT-.......................EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEE CS
                                    xx..............xxxxx.......................xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 160 al..............aklgk.......................evtlveardrll.raldkelsaaleealekeGvevk 201
                                     l              a   +                       ev+l+++ + +  + l+k  +   ++ l+++Gv+  
  gi|121637107|ref|YP_977330.1| 515 LLvtdssptlnlkewkA---EwgvadpreargalttplpapparEVYLLQRTKGPQgKRLGKTTGWVHRASLKAKGVHQL 591
                                    *9777777655555443...0555889999999999*******99************9********************** PP

                                    ESCEEEEEEETTEEEE..EEETTSCEEEESEEEE-S-EEES-HHC CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 202 lgtsvkeidgngekle..vvledgeeidadlvvvavGvrpstell 244
                                     g + ++i+++g +++   +    + +++d vvv++G +p ++l 
  gi|121637107|ref|YP_977330.1| 592 SGVNYEQINDDGLHISfgPKRRRPQLLAVDNVVVCAGQEPVRDLE 636
                                    *********99974445577777777**************99884 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   9.6e-13   7.2e-10       1      54 [.     381     436 ..     381     445 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 9.6e-13
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TT.CEECTS---EEE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pg.vrvdygahifhg 54 
                                    +vGaG +Gl++A+ +a++g++v+l+e++d +GG+   +++ pg   +    ++f +
  gi|121637107|ref|YP_977330.1| 381 VVGAGPAGLATAANAAQRGHRVTLFEANDFIGGQFDMARRiPGkEEFSETIRYFST 436
                                    8*********************************9999887665666666666655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   9.5e-09   7.1e-06       1      69 [.     378     457 ..     378     467 .. 0.81
   2 ?    3.3   0.5      0.17   1.3e+02       2      17 ..     500     515 ..     499     520 .. 0.86
   3 ?   -1.2   0.0       4.2   3.1e+03      24      69 ..     556     602 ..     554     607 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9.5e-09
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSS...........HHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllD...........eeaskilqeklekngievllntkveeiegs 69 
                                    +v+vvG+G  gl  A+++a+ g++Vt++e++d +  ++D            e+ +++ + l k+g+ev+l+t+v++ e +
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQRGHRVTLFEANDFIGGQFDmarripgkeefSETIRYFSTILAKHGVEVRLGTRVAAQELT 457
                                    699***********************************96655555533334555668999999*********9988744 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                                    EEEECSSHHHHHHHHH CS
                      Pyr_redox   2 vvvvGgGyiglElAga 17 
                                    v+vvG+G ig ++ + 
  gi|121637107|ref|YP_977330.1| 500 VAVVGAGGIGFDVTEL 515
                                    89********998765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.2
                                    EEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                      Pyr_redox  24 kVtvversdkll.rllDeeaskilqeklekngievllntkveeiegs 69 
                                    +V++++r + +  + l+++++ + + +l+++g++ l + + e+i+ +
  gi|121637107|ref|YP_977330.1| 556 EVYLLQRTKGPQgKRLGKTTGWVHRASLKAKGVHQLSGVNYEQINDD 602
                                    7888899999988999999999999999****999999888888855 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.3   1.3e-10   9.4e-08       2      38 ..     379     415 ..     378     462 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.3e-10
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                    v VvG+gpaG+a A  Aa++G +v L e ++++GG++
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGHRVTLFEANDFIGGQF 415
                                    89*********************************97 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   3.8e-10   2.8e-07       2      41 ..     378     417 ..     377     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.8e-10
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHH CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKili 41 
                                    +v+v+G+G+AGl +A++aa+rg+rV+l+e+++ +g  + +
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQRGHRVTLFEANDFIGGQFDM 417
                                    699****************************999988776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   2.6e-09   1.9e-06       2      35 ..     379     413 ..     378     416 .. 0.94
   2 ?   -0.2   4.2      0.79   5.9e+02     156     226 ..     438     491 ..     429     509 .. 0.70
   3 ?   -0.4   0.0      0.93   6.9e+02     151     202 ..     577     629 ..     568     658 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                    v+++G+G +Gl+tA  +a+rg  Vtl+e++d++g g
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGhrVTLFEANDFIG-G 413
                                    99******************99********9999.6 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.79
                                    HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH..HHHTTCTTTSEEEEEEEEEEE CS
                            DAO 156 aealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd..llgllkeldlpispvrgqvlv 226
                                    ++++Gve+++gt+v + e     ++       g    +d vV+a+G+  +   +   + +d+p++ + ++ ++
  gi|121637107|ref|YP_977330.1| 438 LAKHGVEVRLGTRVAAQE-----LT-------G----YDEVVLATGVAPRipAI---PGIDHPMVLTYAEAIT 491
                                    577888888888887631.....33.......3....488******88665444...6668887777777665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.93
                                    HHHHH.HHHTT-EEEESECEEEEEEEETCEEEEE....EECTEEEE.....EEEEEEE--GG CS
                            DAO 151 alara.aealGveilegtevtgleeedgkvwgve....rttpgend.....aadavVnaaGa 202
                                    ++ ra ++a+Gv+ l g + + +++ d  + ++     r      +     a+d vV++aG 
  gi|121637107|ref|YP_977330.1| 577 WVHRAsLKAKGVHQLSGVNYEQIND-D--GLHISfgpkR------RrpqllAVDNVVVCAGQ 629
                                    5555557888899999988888843.3..3333234432......1223447899****994 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.5   1.1e-08   8.4e-06       2      41 ..     379     418 ..     378     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41 
                                    v V+G+G AGLa A++aa++G++v++ e  +  gg+  ++
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGHRVTLFEANDFIGGQFDMA 418
                                    89****************************9999987766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1     8e-05      0.06       2      30 ..     381     408 ..     380     427 .. 0.87
   2 !   10.7   0.1   0.00031      0.23     126     180 ..     460     513 ..     429     532 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                    ++GaGPaGla+a ++ + g  +++  E +
  gi|121637107|ref|YP_977330.1| 381 VVGAGPAGLATAANAAQRGH-RVTLFEAN 408
                                    8****************998.67777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00031
                    Pyr_redox_3 126 kkviiAtGefdkPnklnipGeeklvkhyskvkefhkya..gqkvvViGgknSavDaA 180
                                    ++v++AtG    P+ + ipG + ++++  + ++++ ++  g+ v+V+G++  ++D+ 
  gi|121637107|ref|YP_977330.1| 460 DEVVLATGV--APRIPAIPGID-HPMVLTYAEAITGVRpvGRTVAVVGAGGIGFDVT 513
                                    579******..**********9.999999999888777669********99999975 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.3e-07   0.00025       2      29 ..     379     406 ..     378     441 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-07
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                    v V+G+G AG++ A++aa++G++v+L+ 
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGHRVTLFE 406
                                    89************************93 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.5e-05     0.018       2      31 ..     379     408 ..     378     419 .. 0.93
   2 ?    3.8   0.0     0.064        48       1      20 [.     499     518 ..     499     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdis 31 
                                    vav+GaG  G   aa +a++g++V+l++ +
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGHRVTLFEAN 408
                                    9*************************9987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.064
                                    EEEEE--SCCHHHHHHHHHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfas 20 
                                    +vav+GaG +G  ++++++ 
  gi|121637107|ref|YP_977330.1| 499 TVAVVGAGGIGFDVTELLVT 518
                                    69**********99999876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06   0.00081       2      28 ..     387     413 ..     386     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                  Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                    aGLa+A   +++G++Vt++Ea+d +GG
  gi|121637107|ref|YP_977330.1| 387 AGLATAANAAQRGHRVTLFEANDFIGG 413
                                    9*************************9 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.3e-05     0.032       1      40 [.     380     413 ..     380     420 .. 0.87
   2 ?    0.2   0.1      0.89   6.7e+02     140     155 ..     453     468 ..     438     469 .. 0.72
   3 ?   -1.5   0.0       2.9   2.2e+03       1      20 [.     501     520 ..     501     544 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40 
                                    a+vGaGp+Gla++++ ++r      +++tlf+ + +  g+
  gi|121637107|ref|YP_977330.1| 380 AVVGAGPAGLATAANAAQR-----GHRVTLFEANDFI-GG 413
                                    89************99999.....59*******9995.44 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.89
                  NAD_binding_9 140 dgaslaadaVvLAlGh 155
                                     ++ + +d+VvLA+G 
  gi|121637107|ref|YP_977330.1| 453 AQELTGYDEVVLATGV 468
                                    4445689*******95 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.9
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    a+vGaG  G  v+e L+  +
  gi|121637107|ref|YP_977330.1| 501 AVVGAGGIGFDVTELLVTDS 520
                                    79*******99999999876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.8e-05     0.021      19      55 ..     378     413 ..     373     418 .. 0.91
   2 ?   -2.5   0.1       3.3   2.5e+03      19      37 ..     499     517 ..     486     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                    EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                     v++vGaG++GL++a   a++ + +v+++e++  +GG
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQR-GHRVTLFEANDFIGG 413
                                    599******************.********9988887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                                    EEEEE--SHHHHHHHHHHH CS
                           Thi4  19 DvvivGaGssGLtaayyla 37 
                                     v++vGaG  G   +  l 
  gi|121637107|ref|YP_977330.1| 499 TVAVVGAGGIGFDVTELLV 517
                                    5899****99998777665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.062        46     189     217 ..     374     402 ..     361     410 .. 0.69
   2 ?    9.4   0.0   0.00069      0.52     150     214 ..     460     520 ..     417     535 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.062
                    K_oxygenase 189 lakkriaVvGsGqSaaeifedllrrqkkv 217
                                    ++++++aVvG+G  +   + ++++r ++v
  gi|121637107|ref|YP_977330.1| 374 RRARSVAVVGAGPAGLATAANAAQRGHRV 402
                                    56677777777777776666666665543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00069
                    K_oxygenase 150 rnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrq 214
                                     ++vl++G  p iP++   ++ ++ v+  +e+ +    +  ++++aVvG+G  + +++e l++++
  gi|121637107|ref|YP_977330.1| 460 DEVVLATGVAPRIPAIPG-ID-HPMVLTYAEAITGV--RPVGRTVAVVGAGGIGFDVTELLVTDS 520
                                    689***********9876.66.48999999988888..7899**********9999999888773 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.6e-05      0.02       3      32 ..     378     407 ..     376     409 .. 0.91
   2 ?   -3.5   0.0         6   4.5e+03      17      34 ..     435     452 ..     431     458 .. 0.76
   3 ?   -0.2   0.2      0.62   4.6e+02       3      21 ..     499     517 ..     498     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                    +V++VGaGpaGl +a   +++G rv+l e 
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQRGHRVTLFEA 407
                                    699*********************999875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                                    HHHHHHTTHHEEEEESSS CS
                  FAD_binding_3  17 allLseaGvrvvlvekrs 34 
                                    +++L+++Gv+v+l ++ +
  gi|121637107|ref|YP_977330.1| 435 STILAKHGVEVRLGTRVA 452
                                    578999999998866655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.62
                                    EEEEE--SHHHHHHHHHHH CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLs 21 
                                    +V++VGaG  G+  + lL 
  gi|121637107|ref|YP_977330.1| 499 TVAVVGAGGIGFDVTELLV 517
                                    699********99998886 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05      0.02      27      61 ..     375     409 ..     356     441 .. 0.85
   2 ?   -1.7   0.8         2   1.5e+03      14      40 ..     481     509 ..     478     514 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                    ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                    ++  v v+G+G aGl+ +a+a++ g +Vt+++ + 
  gi|121637107|ref|YP_977330.1| 375 RARSVAVVGAGPAGLATAANAAQRGHRVTLFEAND 409
                                    355799*************************9886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                    TSEEETTCEETCB---..EEEEESTSHHH CS
                    AlaDh_PNT_C  14 ggkgtlaGgvpgvepa..kvlviGgGvaG 40 
                                    ++  t a  ++gv+p   +v v+G+G  G
  gi|121637107|ref|YP_977330.1| 481 PMVLTYAEAITGVRPVgrTVAVVGAGGIG 509
                                    677888888999988533799****9877 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         3   2.2e+03      96     160 ..      76     141 ..      73     144 .. 0.75
   2 ?   13.0   0.2   5.3e-05     0.039       2      34 ..     379     409 ..     378     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3
                  Lycopene_cycl  96 rlvengvklleakvesveeeeageslv.vleggrkirarlvvdarglaslkkarrlglQtfyGvev 160
                                    +lv+++  +++ +++++++++ ++ l  +l++gr  + +l+v a+++ ++  + r     ++Gve+
  gi|121637107|ref|YP_977330.1|  76 ELVTSAQARRHRRINRAVHDSGAKILLqILHAGRYAYHPLAVSASPIKAPITPFRPRALSARGVEA 141
                                    677777788888899999999866554278999999999999999977777777777777777765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.3e-05
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasp 34 
                                    v+v+GaGpAgl+ Aa+   a+ g +v+l ea +
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANA--AQRGHRVTLFEAND 409
                                    89***************..9999*****99876 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0023       1.7      51      84 ..     372     405 ..     350     430 .. 0.80
   2 ?    4.0   0.0     0.038        28     237     285 ..     620     667 ..     582     672 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                                    TTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE CS
                           PALP  51 egtgaktvveassGNhgralAaaaallGlkvtiv 84 
                                    ++++a+ v++ ++G +g+a+Aa aa  G +vt++
  gi|121637107|ref|YP_977330.1| 372 PTRRARSVAVVGAGPAGLATAANAAQRGHRVTLF 405
                                    337899**************************98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.038
                                    EEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC CS
                           PALP 237 vdeivtvsdeealeamrllarregivvepssaaalaalklreagelkeg 285
                                    vd +v    +e ++ ++   rr+gi +  s++aa+aa  l  ++++k+g
  gi|121637107|ref|YP_977330.1| 620 VDNVVVCAGQEPVRDLESELRRHGINPHISGGAAVAAE-LDAKRAIKQG 667
                                    666777777777777777788****************9.8888888887 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.039        29      29      66 ..     369     406 ..     347     416 .. 0.82
   2 ?    6.3   0.1    0.0074       5.5      28      55 ..     489     516 ..     483     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                                    GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                   2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                    +l+ + + + v+++G+G  G a+a  +++ g +v+ ++
  gi|121637107|ref|YP_977330.1| 369 VLSPTRRARSVAVVGAGPAGLATAANAAQRGHRVTLFE 406
                                    5555677899*******************999998775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0074
                                    CGSBS-GTTSEEEEES-SHHHHHHHHHH CS
                   2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrl 55 
                                    a++g +  g+tv+++G+G IG  v ++l
  gi|121637107|ref|YP_977330.1| 489 AITGVRPVGRTVAVVGAGGIGFDVTELL 516
                                    566777889************9999876 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00077      0.58       1      33 [.     378     416 ..     378     455 .. 0.82
   2 ?   -1.7   0.0       3.4   2.5e+03       2      19 ..     500     517 ..     499     531 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00077
                                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H......H CS
                 NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree......e 33 
                                    ++av+GaG  G a A+  a++gh+v+l+  ++      +
  gi|121637107|ref|YP_977330.1| 378 SVAVVGAGPAGLATAANAAQRGHRVTLFEANDfiggqfD 416
                                    59**************************98875554444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                                    EEEE--SHHHHHHHHHHH CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvla 19 
                                    +av+GaG  G  +  +l 
  gi|121637107|ref|YP_977330.1| 500 VAVVGAGGIGFDVTELLV 517
                                    9*******9998887765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.2   5.4e+03      59     107 ..     287     334 ..     279     341 .. 0.69
   2 ?   10.1   0.0    0.0006      0.45       3      32 ..     379     408 ..     377     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                                    CHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB-THHHHHHHHHH CS
                 UDPG_MGDP_dh_N  59 vesgrlsfttdvekaveeadvifiaVgTPskkkgkaaDlkyvesaarsi 107
                                    v+s+r++  + +e+ ++e++v +i+   P+ + +    lk+  + +++i
  gi|121637107|ref|YP_977330.1| 287 VASNRINMPQAAERILAETQVRLISMARPMLS-DPDWVLKAQSNRVDEI 334
                                    55667777778888888999999999888887.4444555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                                    EEEE--STTHHHHHHHHHHCTSEEEEE-S- CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDid 32 
                                    ++v+G+G  Gl taa  a++gh v++   +
  gi|121637107|ref|YP_977330.1| 379 VAVVGAGPAGLATAANAAQRGHRVTLFEAN 408
                                    89**********************987665 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.5   1.1e+03      66      85 ..     144     163 ..     139     164 .. 0.88
   2 ?    8.8   0.1     0.001      0.75     176     231 ..     276     333 ..     228     368 .. 0.79
   3 ?   -1.4   0.0       1.3   9.5e+02      37      77 ..     358     398 ..     349     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHTT-SCEEE CS
                            Dus  66 allaeaAklvadlgadeIdl 85 
                                    a  a +A+l+ d g+d++++
  gi|121637107|ref|YP_977330.1| 144 ADFARCAQLARDAGYDGVEI 163
                                    67899************987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                                    HHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCST.THHHH.HHHHHH CS
                            Dus 176 kevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnP.wlfae.stavkt 231
                                    ++v ++v+ipv+a   I  +++a++il+et +  + ++r  l++P w++++ s++v++
  gi|121637107|ref|YP_977330.1| 276 SAVAEHVTIPVVASNRINMPQAAERILAETQVRLISMARPMLSDPdWVLKAqSNRVDE 333
                                    579999***************************************5555544555544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                                    ---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHH CS
                            Dus  37 vreekvrirmlseeeeetplavQlggsdpallaeaAklvad 77 
                                    +++++ r  +l  +++++ ++v ++g+ pa la+aA+ ++ 
  gi|121637107|ref|YP_977330.1| 358 LNPRAGRETQLVLSPTRRARSVAVVGAGPAGLATAANAAQR 398
                                    56666677777777888889****************98875 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0024       1.8       7      53 ..     376     420 ..     373     469 .. 0.60
   2 ?    0.5   0.2       1.1   8.2e+02       6      20 ..     496     510 ..     493     521 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaee 53 
                                     ++v vvG+G+ ++  + + ++ g +vt+   +  +++ +++++a++
  gi|121637107|ref|YP_977330.1| 376 ARSVAVVGAGPAGLATAANAAQRGHRVTLFEAN--DFIGGQFDMARR 420
                                    6899*************************8666..455555554432 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                  NAD_binding_7   6 kgkkvlvvGgGevAa 20 
                                     g++v vvG+G ++ 
  gi|121637107|ref|YP_977330.1| 496 VGRTVAVVGAGGIGF 510
                                    589********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4320.89
//
Query:       gi|121637108|ref|YP_977331.1|  [L=189]
Description: hypothetical protein BCG_1239c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-18   66.1   0.3    9.4e-18   64.7   0.1    1.8  3  Vir_act_alpha_C  Virulence activator alpha C-term
    7.5e-13   48.2   0.0    1.8e-12   47.0   0.0    1.6  2  PadR             Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   1.8e+04      31      44 ..      37      50 ..      34      62 .. 0.55
   2 ?   -2.5   0.0      0.98   8.8e+03       8      22 ..      67      81 ..      67      85 .. 0.77
   3 !   64.7   0.1   1.1e-21   9.4e-18       4      77 .]     105     186 ..     104     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                Vir_act_alpha_C 31 heekLaeyeeieer 44
                                   h++  ++++ +e++
  gi|121637108|ref|YP_977331.1| 37 HQQIYRTLRVMENN 50
                                   55555555555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.98
                Vir_act_alpha_C  8 Klfaaavldpealie 22
                                   K++a++  ++++l++
  gi|121637108|ref|YP_977331.1| 67 KVYAISDSGRAELAR 81
                                   889999999888876 PP

  == domain 3  score: 64.7 bits;  conditional E-value: 1.1e-21
                Vir_act_alpha_C   4 elllKlfaaavldpealieeLerrreeheekLaeyeeieerl........eeargqylvLrrgiryeeawieWcdealel 75 
                                    ++++Kl++a+++d +al +++++ r+e+ + L++y+ ie+r         ++a++qylvLr+gir ee+ i+W+de+ e+
  gi|121637108|ref|YP_977331.1| 105 DIAVKLRGAGYGDVAALYTQVTALRAERVKSLDTYRGIEKRTfadpsaldGAALHQYLVLRGGIRAEESAIDWLDEVAEA 184
                                    689*********************************************9888***************************9 PP

                Vir_act_alpha_C  76 Le 77 
                                    L+
  gi|121637108|ref|YP_977331.1| 185 LQ 186
                                    95 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0     2e-16   1.8e-12       1      74 [.       7      80 ..       7      81 .. 0.97
   2 ?   -2.6   0.0       0.6   5.4e+03      32      44 ..     119     131 ..     108     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2e-16
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                   iL  l eq s Gye++++++++++ ++++ + ++Y++L+ +e++++v ++ + +  +p +k+Y++ d Gr+ela
  gi|121637108|ref|YP_977331.1|  7 ILVSLCEQASSGYELARRFDRSIGYFWTATHQQIYRTLRVMENNNWVRATTVLQHGRPDKKVYAISDSGRAELA 80
                                   7889999*****************************************************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.6
                                    HHHHHHHHHHHHT CS
                           PadR  32 GslYpaLkrLeke 44 
                                    + lY++ + L++e
  gi|121637108|ref|YP_977331.1| 119 AALYTQVTALRAE 131
                                    5789999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1338.21
//
Query:       gi|121637109|ref|YP_977332.1|  [L=108]
Description: ferredoxin fdxC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-11   43.0  14.4    1.4e-08   34.2   5.2    2.4  2  Fer4      4Fe-4S binding domain
      3e-06   28.1   4.3    0.00029   21.7   0.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    7.1e-06   26.1   4.7    0.00013   22.0   0.1    2.2  2  Fer4_10   4Fe-4S dicluster domain
    1.7e-05   25.3  12.8    0.00037   21.0  13.3    2.2  2  Fer4_7    4Fe-4S dicluster domain
    0.00015   21.7   4.9    0.00015   21.7   4.9    2.3  2  Fer4_6    4Fe-4S binding domain
    0.00029   21.1   2.1    0.00029   21.1   2.1    2.5  2  Fer4_4    4Fe-4S binding domain
    0.00033   20.8  10.2    0.00081   19.5  10.3    1.6  1  Fer4_9    4Fe-4S dicluster domain
     0.0005   20.5   4.5     0.0021   18.5   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
    0.00079   19.9   9.7      0.012   16.1   1.2    2.2  4  Fer4_17   4Fe-4S dicluster domain
     0.0012   18.8   3.7     0.0012   18.8   3.7    2.4  2  Fer4_2    4Fe-4S binding domain
     0.0016   18.5  14.9     0.0082   16.3  15.0    1.9  1  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.8   7.8      0.067   13.7   1.3    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.13   13.3  15.4       0.25   12.4   7.1    2.6  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.7   2.2e-05      0.03      12      24 .]      15      27 ..      12      27 .. 0.87
   2 !   34.2   5.2     1e-11   1.4e-08       2      23 ..      34      55 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                   THHHHHSTTTEEE CS
                           Fer4 12 GaCvevCPvgAIt 24
                                   +aC+e CPv++I+
  gi|121637109|ref|YP_977332.1| 15 KACIEECPVDCIY 27
                                   79*********96 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1e-11
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   +i+++ C+ CGaC+ vCPv+AI
  gi|121637109|ref|YP_977332.1| 34 YIHPDECVDCGACEPVCPVEAI 55
                                   89*******************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.9     0.004       5.5       6      20 ..      15      29 ..       9      37 .. 0.84
   2 !   21.7   0.1   2.1e-07   0.00029       2      20 ..      40      58 ..      39     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                        Fer4_16  6 gkCaevCPtnaikek 20
                                   ++C+e CP+++i e 
  gi|121637109|ref|YP_977332.1| 15 KACIEECPVDCIYEG 29
                                   68*********9887 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-07
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C++Cg+C  vCP++ai  +
  gi|121637109|ref|YP_977332.1| 40 CVDCGACEPVCPVEAIFYE 58
                                   ***************9755 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.3     0.012        17      44      56 .]       8      22 ..       2      31 .. 0.68
   2 !   22.0   0.1   9.2e-08   0.00013       2      24 ..      33      63 ..      32     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                        Fer4_10 44 kCtgcg..aCveaCP 56
                                    C ++   aC+e+CP
  gi|121637109|ref|YP_977332.1|  8 PCVDIKdkACIEECP 22
                                   566654447777776 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 9.2e-08
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl........t 24
                                   ++i +d C+ Cg+C  +CP+ +        +
  gi|121637109|ref|YP_977332.1| 33 LYIHPDECVDCGACEPVCPVEAifyeddvpE 63
                                   5799****************66555444440 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.3     0.019        26      36      51 ..       7      24 ..       2      25 .. 0.70
   2 !   21.0  13.3   2.7e-07   0.00037       6      52 .]      15      54 ..       9      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                         Fer4_7 36 ekClgCga..CvavCPtg 51
                                   e C++ +   C+++CP++
  gi|121637109|ref|YP_977332.1|  7 EPCVDIKDkaCIEECPVD 24
                                   6677654334******97 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.7e-07
                         Fer4_7  6 gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   +aC + Cpv++i+   +        ++i+p++C++CgaC+ vCP++a
  gi|121637109|ref|YP_977332.1| 15 KACIEECPVDCIYEGAR-------MLYIHPDECVDCGACEPVCPVEA 54
                                   69**********98554.......59******************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.1     0.043        59       7      24 .]       7      26 ..       5      30 .. 0.72
   2 !   21.7   4.9   1.1e-07   0.00015       4      24 .]      35      55 ..      33      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.043
                         Fer4_6  7 dkCig..CgdCvrvCPegai 24
                                   ++C++    +C+  CP + i
  gi|121637109|ref|YP_977332.1|  7 EPCVDikDKACIEECPVDCI 26
                                   7888622455******8654 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.1e-07
                         Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                   i pd C++Cg+C+ vCP  ai
  gi|121637109|ref|YP_977332.1| 35 IHPDECVDCGACEPVCPVEAI 55
                                   77999*************998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.0      0.48   6.6e+02       9      16 ..      16      23 ..       7      27 .. 0.72
   2 !   21.1   2.1   2.1e-07   0.00029       1      16 [.      37      52 ..      37      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                         Fer4_4  9 sCvaaCPq 16
                                   +C+  CP+
  gi|121637109|ref|YP_977332.1| 16 ACIEECPV 23
                                   56666664 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.1e-07
                         Fer4_4  1 qerCigCgsCvaaCPq 16
                                   ++ C++Cg+C+ +CP+
  gi|121637109|ref|YP_977332.1| 37 PDECVDCGACEPVCPV 52
                                   689************6 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  10.3   5.9e-07   0.00081       6      51 .]      15      55 ..       8      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.9e-07
                         Fer4_9  6 gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   +aC+e Cp + + e a   ++  +     +C++CgaC+ +Cp +ai
  gi|121637109|ref|YP_977332.1| 15 KACIEECPVDCIYEGARMLYIHPD-----ECVDCGACEPVCPVEAI 55
                                   68**********999998888864.....5************9987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.7     0.092   1.3e+02      54      64 ..      14      24 ..       2      25 .. 0.74
   2 !   18.5   0.1   1.5e-06    0.0021       4      17 ..      39      52 ..      31     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.092
                         Fer4_8 54 cgaCtevCpvg 64
                                    +aC e+Cpv+
  gi|121637109|ref|YP_977332.1| 14 DKACIEECPVD 24
                                   46799999986 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-06
                         Fer4_8  4 kCieCgaCqsaCpv 17
                                   +C+ CgaC+  Cpv
  gi|121637109|ref|YP_977332.1| 39 ECVDCGACEPVCPV 52
                                   57777777777773 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.7      0.43   5.9e+02      50      58 ..      15      23 ..       4      28 .. 0.65
   2 ?    2.5   0.7      0.16   2.2e+02       7      18 ..      16      27 ..      12      37 .. 0.66
   3 !   14.4   1.8   2.9e-05     0.041      44      58 ..      38      52 ..      29      55 .. 0.81
   4 !   16.1   1.2   8.8e-06     0.012       1      25 [.      39      65 ..      39      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.43
                        Fer4_17 50 geCerkCPq 58
                                   + C ++CP 
  gi|121637109|ref|YP_977332.1| 15 KACIEECPV 23
                                   456666653 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                        Fer4_17  7 yClpeCpsyeay 18
                                   +C++eCp   +y
  gi|121637109|ref|YP_977332.1| 16 ACIEECPVDCIY 27
                                   577777765555 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.9e-05
                        Fer4_17 44 slCieCgeCerkCPq 58
                                   ++C+ Cg Ce +CP 
  gi|121637109|ref|YP_977332.1| 38 DECVDCGACEPVCPV 52
                                   679999999999985 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 8.8e-06
                        Fer4_17  1 rCiqCgyClpeCpsyea..ydnepkkl 25
                                   +C  Cg+C+p+Cp  ++   d+ p+++
  gi|121637109|ref|YP_977332.1| 39 ECVDCGACEPVCPVEAIfyEDDVPEQW 65
                                   588888888888887664322335544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.054        74       9      21 ..       8      22 ..       3      23 .. 0.74
   2 !   18.8   3.7   8.9e-07    0.0012       3      21 ..      33      51 ..      30      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.054
                         Fer4_2  9 rCigCg..aCvsaCP 21
                                    C+  +  aC+  CP
  gi|121637109|ref|YP_977332.1|  8 PCVDIKdkACIEECP 22
                                   577775559*****9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.9e-07
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                    ++ +d C+ CgaC  +CP
  gi|121637109|ref|YP_977332.1| 33 LYIHPDECVDCGACEPVCP 51
                                   57889************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  15.0   5.9e-06    0.0082      10      57 ..      13      55 ..       5      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.9e-06
                        Fer4_21 10 gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                   + + C+  C+   +++i  +++++l +  deCv C  C  vCPv ++i
  gi|121637109|ref|YP_977332.1| 13 KDKACIEECP---VDCIY-EGARMLYIHPDECVDCGACEPVCPV-EAI 55
                                   4467999999...8***6.6899999*****************9.655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.016        23      47      56 ..      17      26 ..      10      27 .. 0.83
   2 ?   13.7   1.3   4.9e-05     0.067       4      24 ..      38      60 ..      35      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                        Fer4_13 47 AadaCPvesI 56
                                    +++CPv++I
  gi|121637109|ref|YP_977332.1| 17 CIEECPVDCI 26
                                   4789***999 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.9e-05
                        Fer4_13  4 dtCiacgaCvelaP..dvFeedd 24
                                   d+C++cgaC  ++P   +F edd
  gi|121637109|ref|YP_977332.1| 38 DECVDCGACEPVCPveAIFYEDD 60
                                   8*************666787776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.1     0.029        40       6      14 ..      16      24 ..       7      25 .. 0.82
   2 ?   12.4   7.1   0.00018      0.25       1      15 []      40      54 ..      40      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                         Fer4_3  6 aCvevCPvg 14
                                   aC e CPv+
  gi|121637109|ref|YP_977332.1| 16 ACIEECPVD 24
                                   8******97 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+ CgaC+ vCPv A
  gi|121637109|ref|YP_977332.1| 40 CVDCGACEPVCPVEA 54
                                   999*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 853.80
//
Query:       gi|121637110|ref|YP_977333.1|  [L=362]
Description: N-succinyldiaminopimelate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-41  142.0   0.0    4.5e-41  141.2   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.12   10.9   0.0       0.17   10.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.0     5e-45   4.5e-41       5     363 .]      29     360 ..      25     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 5e-45
                                    ESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHH CS
                  Aminotran_1_2   5 nLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalieal 84 
                                    +L+++ + +      +   ++++   ++a + +  y+ + g + l+e +   l r+++++  +eaav+   G+++li+ l
  gi|121637110|ref|YP_977333.1|  29 DLSVGTPVDP-----VAPLIQEA---LAAASAAPGYPATAGTARLRESVVAALARRYGITRLTEAAVLPVIGTKELIAWL 100
                                    5555555443.....33333444...57889999****************99999************************* PP

                                    HHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B CS
                  Aminotran_1_2  85 ifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtv 164
                                    ++ll l   d ++vp++ y+ y+ ++rl+g  v r              a    l+++ ++++   +++++sp+NPtG v
  gi|121637110|ref|YP_977333.1| 101 PTLLGLGGADLVVVPELAYPTYDVGARLAGTRVLRAD------------A----LTQLGPQSP--ALLYLNSPSNPTGRV 162
                                    ********************************99999............3....333444555..9************** PP

                                    --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavat.ranveeepn..llivgslsKafGlaGeRvGyilgnaavvs 241
                                    +  ++l+k+++ a+ +++l+++De Y g+ ++++ +v++ ++ v ++++  ll v slsK+ +laG R G+++g+ ++v 
  gi|121637110|ref|YP_977333.1| 163 LGVDHLRKVVEWARGRGVLVVSDECYLGLGWDAE-PVSVlHPSVCDGDHtgLLAVHSLSKSSSLAGYRAGFVVGDLEIVA 241
                                    *******************************965.44446******9999************************999888 PP

                                    HHHHHHHH..HTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHH CS
                  Aminotran_1_2 242 qlrklsrp..flsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetake 319
                                     l  +  +  + +++++qaa +aal+d+     +  + r+r+++rr  l  +L ++g++v  s++g++l+    +    +
  gi|121637110|ref|YP_977333.1| 242 ELLAVRKHagMMVPAPVQAAMVAALDDDA----HERQQRERYAQRRAALLPALGSAGFAVDYSDAGLYLWATRGEP-CRD 316
                                    8887765411666**************99....89***********************************544444.555 PP

                                    HHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 320 lskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                        L+++ g++v pg  ++    +++R+ + + t+e +  +v +l
  gi|121637110|ref|YP_977333.1| 317 SVAWLAQR-GILVAPGDFYGPggAQHVRVAL-TATDERVAAAVGRL 360
                                    5666****.******99999999999*****.999*9999999876 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   1.9e-05      0.17     136     176 ..     145     188 ..     124     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.9e-05
                                    TTEEEEEEESS-TTTT----...HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 136 entklvylEtptnpllkvvD...iekiaklakkagvlvvvDntf 176
                                    +   l+yl +p+np+ +v+    ++k+++ a+ +gvlvv D ++
  gi|121637110|ref|YP_977333.1| 145 QSPALLYLNSPSNPTGRVLGvdhLRKVVEWARGRGVLVVSDECY 188
                                    567899********98886411267899999*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2585.18
//
Query:       gi|121637111|ref|YP_977334.1|  [L=939]
Description: hypothetical protein BCG_1242c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-17   62.6   0.0    6.5e-17   62.1   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.026   14.9   0.0    1.5  1  Helicase_C  Helicase conserved C-terminal domain
       0.62    9.4   7.2        1.2    8.4   7.2    1.4  1  ThrE        Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   1.1e-20   6.5e-17       3     170 ..      15     196 ..      13     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.1e-20
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    ++r yQ++a++++ + +   +d+r++++++ G+GKT++ +++++rl +     + l+lvp++++  q+  ++ + +++ +
  gi|121637111|ref|YP_977334.1|  15 NWRVYQQQALDAFDADVA-AGDNRAYLVLPPGAGKTMIGLEAARRLGR-----RSLVLVPNTAVQAQWAAAWDNSFPSSD 88 
                                    6899*************9.***************************99.....89************************9 PP

                                    ..GEEEESSS-B--.......-SEEEEEHHHHHHTH..................HHHTTT-S.................. CS
                         ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseee..........eeeseellrdrfd.................. 134
                                     +++k  ++++  +         + v t+qsl  +  e+          +++++ ll    d                  
  gi|121637111|ref|YP_977334.1|  89 RSASKCGTERGLAS--------AMNVLTYQSLAVIDAETdstvrrevlrNRDQQALL----Dllhpngravieraatlgp 156
                                    88888888888888........999********999777877777666533333333....14445889999******** PP

                                    .EEEEETGGGTTS.TTTHHHHHT---.....SEEEEEESS-S CS
                         ResIII 135 .viiiDEaHrlgakkswreilekfke.....avllglTATpe 170
                                      ++ DE+H+l a  +w +++ ++ +       l+glTATp 
  gi|121637111|ref|YP_977334.1| 157 wTLVLDECHHLLA--TWGALVSALASvlgaqTALIGLTATPA 196
                                    *************..777765555333444499*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.3e-06     0.026      60     110 ..     528     579 ..     483     580 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                                    HHHHTTSSSEEEESG.GGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  60 eqfnkgesdvLiatd.vaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    e f +g+ +vL+ t+  +++G d   vn+ i++   ++ + + q++GR++R 
  gi|121637111|ref|YP_977334.1| 528 EYFLAGRARVLVGTRsLLGEGWDCAAVNVNIDLTSATTQAAITQMRGRAIRN 579
                                    56779999****996268********************************95 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.2    0.0002       1.2     113     176 ..     730     793 ..     722     805 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0002
                           ThrE 113 laaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallav 176
                                     a ++a+a +++l+g++   ++va+ +gl++ ++    ++  + +++le +aa++a +l+++ +
  gi|121637111|ref|YP_977334.1| 730 TATAVASANLGMLAGAGTAGAIVAAGVGLVATAAAAESRRLDHAPNALEQLAAVVADALYAAGG 793
                                    6899*****************************************************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (939 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 6127.59
//
Query:       gi|121637112|ref|YP_977335.1|  [L=2085]
Description: polyketide beta-ketoacyl synthase pks3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-93  313.4   1.1    3.6e-93  312.6   1.1    1.5  1  Acyl_transf_1    Acyl transferase domain
    1.2e-87  293.7   2.9    1.9e-87  293.0   0.1    2.7  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.1e-59  201.3   0.9    1.1e-59  201.3   0.9    3.2  4  KR               KR domain
    6.8e-50  170.0   6.7    1.3e-49  169.0   6.7    1.5  1  PS-DH            Polyketide synthase dehydratase
    9.3e-38  128.9   1.5    9.3e-38  128.9   1.5    2.4  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.6e-21   76.6   0.0    7.5e-21   74.5   0.0    2.2  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.8e-17   64.6   0.5    1.1e-16   62.1   0.1    2.8  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    2.1e-11   44.3   0.2    1.4e-10   41.6   0.0    2.5  3  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.2e-09   38.4   0.0    4.1e-09   36.6   0.0    2.0  1  PP-binding       Phosphopantetheine attachment site
    6.7e-09   35.5   1.3    1.4e-08   34.5   0.0    2.1  2  adh_short        short chain dehydrogenase
    1.9e-06   27.7   0.0    8.2e-06   25.7   0.0    2.2  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    3.2e-06   26.7   3.2    4.5e-06   26.2   0.1    2.9  4  Thiolase_N       Thiolase, N-terminal domain
     0.0093   15.4   0.0       0.27   10.6   0.0    2.3  2  NMT1_3           NMT1-like family
  ------ inclusion threshold ------
       0.12   12.0   0.0         21    4.8   0.0    2.6  2  LEM              LEM domain


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.6   1.1   2.8e-96   3.6e-93       1     317 [.     538     853 ..     538     855 .. 0.98

  Alignments for each domain:
  == domain 1  score: 312.6 bits;  conditional E-value: 2.8e-96
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    v+vfsGqGsQw GMG+eLl  +++faa++a+++++++ ++gfsv++++ + +  ++++i+ vqp ++avq+ala+ lks+
  gi|121637112|ref|YP_977335.1| 538 VWVFSGQGSQWPGMGTELLVAEPVFAATVAAMEPVIARESGFSVTEAMSAPQ--TVSGIDRVQPTIFAVQVALAAALKSY 615
                                    7***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.....HHHHHHH..TT.EEEEEEECC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel....aeeeeklrcqddvvgavanspr 156
                                    Gvrp+a++GHSlGE Aaavvagals+ ++l+++++rsrlm ++ag g+ma+vel    + +e+++r + dvv++v++sp 
  gi|121637112|ref|YP_977335.1| 616 GVRPGAIIGHSLGEAAAAVVAGALSLHDGLRVICRRSRLMSRIAGSGAMASVELpgqqVLSELAIRGISDVVLSVVASPT 695
                                    *******************************************************99888999***************** PP

                                    CCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHH CS
                  Acyl_transf_1 157 rvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaey 236
                                    ++v++g ++++r+lv+ +++++v a++++v+va+h pqvd+i d+l++ la++ p  p+++++s+t  d+++ + + +ey
  gi|121637112|ref|YP_977335.1| 696 STVVGGATQSIRDLVAAWEQQDVLAREVAVDVASHTPQVDPILDELLEVLAEVDPTAPEIPYYSATLWDPRERPSFTGEY 775
                                    ******************************************************************************** PP

                                    HHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT CS
                  Acyl_transf_1 237 wvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltg 316
                                    wv+nlr +vrfa+av++a++++++vf e++pH+ll+ a+e+   s  d++ atl+  ++r+ +     ++ + a +h +g
  gi|121637112|ref|YP_977335.1| 776 WVENLRYTVRFAAAVQAALKDGYRVFGELAPHPLLTYAVEQNAAS-LDMPIATLAA-MRRGEQL-PFGLRGFVADVHNAG 852
                                    ********************************************6.********99.9*99999.888888888888887 PP

                                    - CS
                  Acyl_transf_1 317 s 317
                                    +
  gi|121637112|ref|YP_977335.1| 853 A 853
                                    6 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.0   0.1   1.5e-90   1.9e-87       3     253 .]       8     256 ..       6     256 .. 0.95
   2 ?   -0.9   0.4      0.79     1e+03     177     203 ..    1057    1083 ..    1057    1092 .. 0.89

  Alignments for each domain:
  == domain 1  score: 293.0 bits;  conditional E-value: 1.5e-90
                                    -EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispr 80 
                                    +va++Gm++r+Pgg d ++ +we+Ll+g d ++e+padrwda+ +ydp++ ++g++ +++g+fld v  fd  ffg ++r
  gi|121637112|ref|YP_977335.1|   8 SVAVIGMACRLPGGIDsPQRLWEALLRGDDLVGEIPADRWDANVYYDPEPGVPGRSVSRWGAFLDdVGGFDCDFFGLTER 87 
                                    7***************9*************************************************************** PP

                                    HHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTT.GGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  81 eaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgs.evkaspkavgavlanviagris 159
                                    ea+a+dpq+rllle++wea+e+ag++p++l +s++gvf+G+++gdy+    l+ d +  +  +  ++g+ ++++++gr++
  gi|121637112|ref|YP_977335.1|  88 EATAIDPQHRLLLEVSWEAIEHAGVDPATLAESQTGVFVGLTHGDYEL---LSADCGaAEGPYG-FTGT-SNSFASGRVA 162
                                    ********************************************9953...3333331455666.9999.********** PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlG 239
                                    y+lgl+Gp+vtvdtACsS+l+avh+a++sl +ge+d+alaGGv ++l+p++ ++ s +g+lsp+grc+afd++adGfv G
  gi|121637112|ref|YP_977335.1| 163 YTLGLHGPAVTVDTACSSGLTAVHQACRSLDDGESDLALAGGVVVTLEPRKSVSGSLQGMLSPTGRCHAFDEAADGFVSG 242
                                    ******************************************************************************** PP

                                    -EEEEEEEEECHHH CS
                  ketoacyl-synt 240 EGvGavvLkrleda 253
                                    EG+ +++Lkrl da
  gi|121637112|ref|YP_977335.1| 243 EGCVVLLLKRLPDA 256
                                    ***********887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.79
                                     HHHHHHHHHHHHHHTTS-SEEEEEEEE CS
                  ketoacyl-synt  177 SslvavhaavqslrsgeadvalaGGve 203 
                                     S+lvavh a  ++ +  a+val G+  
  gi|121637112|ref|YP_977335.1| 1057 SGLVAVHTARGAVTTVLAEVALPGAIR 1083
                                     89********************99876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.76   9.7e+02      13      66 ..     671     731 ..     668     748 .. 0.71
   2 ?   -2.9   0.0       4.2   5.4e+03      42      85 ..    1221    1261 ..    1213    1266 .. 0.63
   3 ?   -3.1   0.0         5   6.4e+03      27      72 ..    1299    1354 ..    1269    1360 .. 0.46
   4 !  201.3   0.9   8.9e-63   1.1e-59       1     180 []    1745    1923 ..    1745    1923 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHHS-EEEEE-SS.........--HHHHHHHHHHHHTT-EEEE----TT-HH CS
                             KR  13 GlelarwlaekgarhlvllsRsa.......aadedskaliaelealgaevevvaaDvsdkd 66 
                                    G+++   la +g + +vl    +        a+++ ++l+a++e++++  + va+Dv++++
  gi|121637112|ref|YP_977335.1| 671 GQQVLSELAIRGISDVVLSVVASptstvvgGATQSIRDLVAAWEQQDVLAREVAVDVASHT 731
                                    5666667777776666654333334466666677788899****************99764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.2
                                     HHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EE CS
                             KR   42 kaliaelealgaevevvaaDvsdkdavealleeikaeeppikGv 85  
                                     + l+a+l++    v + +  v+++++v++l + +    ++++Gv
  gi|121637112|ref|YP_977335.1| 1221 DPLTAQLADALNAVGAQSTSVASASDVAQLRSLLG---GRLTGV 1261
                                     34566677777777777777888888877776664...455555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5
                                     EEEEE-SS.......--HHHHHHHHHHHHTT-............EEEE----TT-HHHHHHHH CS
                             KR   27 hlvllsRsa.....aadedskaliaelealga............evevvaaDvsdkdaveall 72  
                                     +l +++Rsa     +        +a+le+ g             +  + a+Dv + + v+al+
  gi|121637112|ref|YP_977335.1| 1299 RLFVVTRSAasvlpS-------DLANLEQAGLrglmrvidsehpHLGATAIDVDNDETVAALV 1354
                                     555555553222220.......23333333332222222222225555666666666666655 PP

  == domain 4  score: 201.3 bits;  conditional E-value: 8.9e-63
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     g+yl+tGGlGgLGl la  la+ g  ++vl sRs ++++++++ i++l+a ga+++v   D++d++  +++++ ++a+
  gi|121637112|ref|YP_977335.1| 1745 GAYLVTGGLGGLGLFLAGELAAAGCGRIVLNSRS-TPSPHATRVIERLRAAGADIQVECGDIADAATAHRVVAVATAS 1821
                                     89********************************.88999999*********************************** PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     + p++Gv+haA v++d++l+++t+e ++++ apKv+Gawn+h++++ ++l++f lfSS+a+l+gs+gq++YaaaN++l
  gi|121637112|ref|YP_977335.1| 1822 GLPVRGVLHAAAVVEDATLANVTDELIDRCWAPKVHGAWNIHRATAAQPLEWFCLFSSAAALVGSPGQGAYAAANSWL 1899
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BTT CS
                             KR  157 Dalaeyrrsqglpavsinwglwae 180 
                                     Da+a++rr+qglpa+si+wg+wae
  gi|121637112|ref|YP_977335.1| 1900 DAFAHWRRAQGLPATSIAWGAWAE 1923
                                     **********************86 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   6.7     1e-52   1.3e-49       1     290 [.     898    1175 ..     898    1183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 1e-52
                                     BTTB.-EE--..-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B CS
                          PS-DH    1 hpllGsrvrsa.sdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvl 77  
                                     hpllG++v+   +++++v+++ + +  +pwL DHr+++ + +Pga+y emal+Aar + ge    e+rd+ +++ l l
  gi|121637112|ref|YP_977335.1|  898 HPLLGAHVHLLeEPERHVWQAGVGTGAHPWLGDHRIHNVAAFPGAAYCEMALAAARTTLGEL--SEVRDIKFEQTLLL 973 
                                     9****99998879**********************************************877..9************* PP

                                     --SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-----.--B--HHHHHHHS-SEE....E-H CS
                          PS-DH   78 pedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaa.aaavdlealqarcaepaslrsvss 154 
                                     +e++ v    ++ +      +  ++f + S+++g+   ++ a++ +++ e+ + ++  d +al     + a+ +s+s+
  gi|121637112|ref|YP_977335.1|  974 DEQTVVSSAATIAA------PGILQFAVESHQEGEP--ARRASAMLHALEEMPqPPGYDTNAL-----TAAHESSMSG 1038
                                     *7653333333333......3346***********7..8********9998885556666666.....4445556999 PP

                                     HHHHHHHHHHSEEE-GGG--EEEEEEETT...EEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG--------- CS
                          PS-DH  155 aefYerlaargleyGpsFqglralwrgdg...ealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekada 229 
                                     +e+ +++ + g++yGp+F gl a+++ +g    +lae++lp ++++++say+ hPallDa++Q++++  + ++   + 
  gi|121637112|ref|YP_977335.1| 1039 EELRKMFNSLGIQYGPAFSGLVAVHTARGavtTVLAEVALPGAIRSQQSAYASHPALLDACFQSVLVHPEVQKATVGG 1116
                                     9999999999****************96644589*****************************776666667889999 PP

                                     -EEEEEEEEEEE-S...-BTS--EEEEEE.----SS-EEEEEEEE-SS-BEEEEEESEEEEE CS
                          PS-DH  230 aylPvaierlrvyrpssaageelwvharl.eeegarsivadltlvdedGrvvaeieglrlrr 290 
                                     ++lPv++ rlr y  s   ++  ++ ar+ ++++a + +adl+++d++G+v++++eglrl +
  gi|121637112|ref|YP_977335.1| 1117 LMLPVGVRRLRNYH-S--TRSAHYCLARVtSSSRAGECEADLDVFDQAGTVLLTVEGLRLAA 1175
                                     *************5.4..4566777777766667789**********************976 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   1.5   7.3e-41   9.3e-38       1     117 [.     264     377 ..     264     378 .. 0.99
   2 ?   -2.7   0.4       4.5   5.8e+03      86     101 ..     622     637 ..     603     645 .. 0.72

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 7.3e-41
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a+++g+a+n+dg++  + ap+++aq +++++ala agv++++v++veahgtgtp+gDp+E+++l++v+g+++   p+a+
  gi|121637112|ref|YP_977335.1| 264 LAIVRGTAANQDGRTVNIAAPSAQAQIAVYQQALAAAGVEASTVGMVEAHGTGTPVGDPVEYASLAAVYGTEG---PCAL 340
                                    699********************************************************************98...9*** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    +SvK+n GHl++A+G ++l+k++lal+hgv+p++l++
  gi|121637112|ref|YP_977335.1| 341 TSVKTNFGHLQSASGPLGLMKTILALRHGVVPQNLHF 377
                                    ************************************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                                    HH-B-GGGHHHHHHHH CS
                Ketoacyl-synt_C  86 niGHleaAaGvaelik 101
                                     iGH+++ a++a ++ 
  gi|121637112|ref|YP_977335.1| 622 IIGHSLGEAAAAVVAG 637
                                    5899888776654443 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   5.8e-24   7.5e-21       1     110 [.    1550    1659 ..    1550    1680 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 5.8e-24
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHC CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkl 78  
                                     gvG+aa+++A+a+G+e++a+++s+++++l+ ++G+++v++++++++ e+i+  t+g gvdvv++ +  ga+ +a ++l
  gi|121637112|ref|YP_977335.1| 1550 GVGQAAIAIARAAGCEIFATAGSAQRRQLLHDMGVEHVYDSRSTEFAEQIRGDTDGYGVDVVLNSLP-GAAQRAGIEL 1626
                                     9****************************************555***********************.********** PP

                                     EEEEEEEEECSC..TSSEEEEEHHHHHHTT-EEE CS
                     ADH_zinc_N   79 lkpgGrlvvvGg..gkgeeefdlrnlllkeksil 110 
                                     l+ gGr+v +G    +g++ + l++ +++++s++
  gi|121637112|ref|YP_977335.1| 1627 LAFGGRFVEIGKrdIYGDTRLGLFP-FRRNLSLY 1659
                                     ***********99999999866666.35555555 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   8.8e-20   1.1e-16       2     133 .]    1583    1721 ..    1582    1721 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 8.8e-20
                                     T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--....S-EEE-CHHHCTTT- CS
                   ADH_zinc_N_2    2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp...lsaallkpakkrkgr 71  
                                     G+++v+d+r+++f+     +t+g gvDvvl+++ g+a  +a +++l+ gGr+v+ig +++   ++ +l + +++ +  
  gi|121637112|ref|YP_977335.1| 1583 GVEHVYDSRSTEFAeqirGDTDGYGVDVVLNSLPGAAQ-RAGIELLAFGGRFVEIGkRDIygdTRLGLFPFRRNLSLY 1659
                                     99*******99999999999999*************99.*******888*******6666866666666666666666 PP

                                     EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   72 svkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                     +v++ +l+  +++  +++l+++ +   eG+l ++ + ++p+++aa A+r++  + ++GK+Vl
  gi|121637112|ref|YP_977335.1| 1660 AVDLALLTHSHPHTVRRLLKTVYQHTVEGTLPVPQTTHYPIHDAAVAIRLVGGAGHTGKVVL 1721
                                     666666665555566666*************9999999***********************8 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   1.1e-13   1.4e-10      10      88 ..     388     475 ..     383     503 .. 0.85
   2 ?   -2.9   0.0       7.5   9.6e+03      13      39 ..    1608    1634 ..    1605    1636 .. 0.85
   3 ?   -1.9   0.0       3.5   4.4e+03      11      47 ..    1688    1725 ..    1684    1740 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.1e-13
                 KAsynt_C_assoc  10 egrlkVvteptpwpggi.....vgvNsfGfGGsnvHviLksnkkekrkeesk....eeslprLlvlsgrteeaveallek 80 
                                    +++l V++ +t+wp+++     ++v+s+G++G+nvH+iL++++  +++ + +    e+    L+++s+ ++e ++ ++++
  gi|121637112|ref|YP_977335.1| 388 DTELFVPQANTSWPDNTgqprrAAVSSYGMSGTNVHAILEQAPVSEPAASGPeltpEAGGLALFPVSATSAEQLHVTAAR 467
                                    56899***********999************************7777777777888999********************* PP

                 KAsynt_C_assoc  81 leehllda 88 
                                    l+++ +++
  gi|121637112|ref|YP_977335.1| 468 LADWVDQN 475
                                    ***96654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.5
                 KAsynt_C_assoc   13 lkVvteptpwpggivgvNsfGfGGsnv 39  
                                     + Vv + +p   +++g+    fGG +v
  gi|121637112|ref|YP_977335.1| 1608 VDVVLNSLPGAAQRAGIELLAFGGRFV 1634
                                     56888999999999**********887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.5
                 KAsynt_C_assoc   11 grlkVv.teptpwpggivgvNsfGfGGsnvHviLksnk 47  
                                     g+l V+ t++ p+++ +v++  +G  G  + v+L+ ++
  gi|121637112|ref|YP_977335.1| 1688 GTLPVPqTTHYPIHDAAVAIRLVGGAGHTGKVVLDVPR 1725
                                     55666514567888889*****************9765 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   3.2e-12   4.1e-09       2      67 .]    2010    2073 ..    2009    2073 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.2e-12
                     PP-binding    2 klrelvaevlgvplee.idpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     ++r+lv++++ + l + idpd +l+d+GlDSl  +el  ++e e g++++++ +   +t++ la+++
  gi|121637112|ref|YP_977335.1| 2010 TVRRLVSDQISLLLRRtIDPDRPLSDYGLDSLGNLELRTRIETETGIRVSPTKI---TTVRGLAEHV 2073
                                     6899999999995555589*********************************88...9******997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4       1.9   2.5e+03       3      37 ..    1542    1576 ..    1540    1586 .. 0.85
   2 !   34.5   0.0   1.1e-11   1.4e-08       4     160 ..    1748    1903 ..    1746    1915 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                     EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHH CS
                      adh_short    3 vlvtGassGIGraiakelakeGakvvvvdrseekl 37  
                                     vl+  +++G+G+a      ++G+++++++ s+++ 
  gi|121637112|ref|YP_977335.1| 1542 VLIHSGTGGVGQAAIAIARAAGCEIFATAGSAQRR 1576
                                     899999*******9999999******998887766 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.1e-11
                                     EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH...HHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvvvdrseek...leevakelkeegakalaiqvDvtdreevealvekavkklgkl 78  
                                     lvtG+ +G+G+ +a ela++G+  +v+++++ +   + +v++ l+++ga++ +  +D++d++ + ++v+ a +   ++
  gi|121637112|ref|YP_977335.1| 1748 LVTGGLGGLGLFLAGELAAAGCGRIVLNSRSTPsphATRVIERLRAAGADIQVECGDIADAATAHRVVAVATASGLPV 1825
                                     8*********************8888555444311256678888888******************************* PP

                                     SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                      adh_short   79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156 
                                       + + A++ ++++ +++++e ++r+ +  ++g+ ++ ra + + l          sS a++v+++g+ aY+A+   +
  gi|121637112|ref|YP_977335.1| 1826 RGVLHAAAVVEDATLANVTDELIDRCWAPKVHGAWNIHRATAAQPL----EWFCLFSSAAALVGSPGQGAYAAANSWL 1899
                                     *************************************999888733....467889*****************97777 PP

                                     HHHH CS
                      adh_short  157 aglt 160 
                                     ++++
  gi|121637112|ref|YP_977335.1| 1900 DAFA 1903
                                     7766 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.4e-09   8.2e-06       1      69 [.    1426    1494 ..    1426    1557 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.4e-09
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SS CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscge 69  
                                     pge+ + v+a++++  D+ ++ g+  +   + + lG +++G+v +vgp+v++ ++Gd+V    +  c +
  gi|121637112|ref|YP_977335.1| 1426 PGEIEVAVTASSVNFADVLVAFGRYPTFEGYRQQLGIDFAGVVTAVGPDVTEHRIGDHVGGMSANGCWS 1494
                                     589********************999999999***************************9999998854 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   2.1e+03      24      51 ..      96     123 ..      89     132 .. 0.85
   2 !   26.2   0.1   3.5e-09   4.5e-06      67     112 ..     162     205 ..     150     216 .. 0.90
   3 ?   -3.4   0.0       3.8   4.8e+03     175     190 ..     992    1007 ..     992    1012 .. 0.86
   4 ?   -3.1   0.0         3   3.9e+03      87     110 ..    1057    1080 ..    1055    1116 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHHTS-GGGCCEEEEE CS
                     Thiolase_N  24 eeLlaealkallekagvdpeevdevivG 51 
                                    + Ll e+ ++++e+agvdp+++ e   G
  gi|121637112|ref|YP_977335.1|  96 HRLLLEVSWEAIEHAGVDPATLAESQTG 123
                                    789999*************999886665 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 3.5e-09
                                    HHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  67 alkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                    a  +g+  + pavtv+ +csSgl+av++a++s+  ge+d ++agGv
  gi|121637112|ref|YP_977335.1| 162 AYTLGL--HGPAVTVDTACSSGLTAVHQACRSLDDGESDLALAGGV 205
                                    555666..889**********************************7 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.8
                                     HHHHHHHHHHHHHHHT CS
                     Thiolase_N  175 efAvkshqkaaaaqka 190 
                                     +fAv+shq ++ a  a
  gi|121637112|ref|YP_977335.1|  992 QFAVESHQEGEPARRA 1007
                                     69********999876 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3
                                     HHHHHHHHHHHHHHTTSHSEEEEE CS
                     Thiolase_N   87 Sglkavalaaqsiaageadvvvag 110 
                                     Sgl av++a +++ +  a+v++ g
  gi|121637112|ref|YP_977335.1| 1057 SGLVAVHTARGAVTTVLAEVALPG 1080
                                     999999999999999988888765 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.093   1.2e+02     131     192 ..    1231    1289 ..    1221    1301 .. 0.74
   2 !   10.6   0.0   0.00021      0.27     130     197 ..    1787    1851 ..    1776    1867 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.093
                         NMT1_3  131 lealglsekdlklleelgygesadalkdgqldgaalvaGvPvsavtqlaasediklipldde 192 
                                     l+a+g +++ ++     +   + + l  g+l g+++v+G+P++  tq       +l+++  e
  gi|121637112|ref|YP_977335.1| 1231 LNAVGAQSTSVAS---ASDVAQLRSLLGGRLTGVVVVTGPPTGGLTQCGRDYVSQLVGIARE 1289
                                     4555555444443...333466778999******************9888777777777655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                         NMT1_3  130 ilealglsekdlklleelgygesadalkdgqldgaalvaGvPvsavtqlaas.edikliplddeqldkl 197 
                                     ++e l    +d++    ++ g+ ada +  ++ ++a+++G+Pv  v  +aa  ed++l +++de +d+ 
  gi|121637112|ref|YP_977335.1| 1787 VIERLRAAGADIQ----VECGDIADAATAHRVVAVATASGLPVRGVLHAAAVvEDATLANVTDELIDRC 1851
                                     5555555556665....5789******************************7479*********99986 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.016        21      10      26 ..     608     624 ..     606     625 .. 0.89
   2 ?    4.3   0.0     0.023        30       4      23 ..    1035    1054 ..    1034    1056 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                            LEM  10 LreeLkkyGvspGPIta 26 
                                    L + Lk+yGv pG I +
  gi|121637112|ref|YP_977335.1| 608 LAAALKSYGVRPGAIIG 624
                                    8999*********9975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                            LEM    4 sLsDeeLreeLkkyGvspGP 23  
                                     s+s eeLr+   ++G++ GP
  gi|121637112|ref|YP_977335.1| 1035 SMSGEELRKMFNSLGIQYGP 1054
                                     7999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2085 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 1.05u 0.31s 00:00:01.36 Elapsed: 00:00:00.51
# Mc/sec: 12386.32
//
Query:       gi|121637113|ref|YP_977336.1|  [L=472]
Description: polyketide synthase associated protein papA3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-18   67.0   0.0    1.6e-18   66.6   0.0    1.1  1  Condensation  Condensation domain


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0     9e-23   1.6e-18      14     440 ..      55     468 ..      41     471 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 9e-23
                                    HHHHHHHSSSSSTTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSS CS
                   Condensation  14 mwflekleeessaynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdlees 93 
                                     +  +k ++  ++  m ++ +  g+ d+ + + ++++ ++rhd+ R  f+ + ng+++ +   ++++++e++ + + e +
  gi|121637113|ref|YP_977336.1|  55 GYCEQKAKGLDYSRLMVVSCQQPGQCDIRAANYVINAHLRRHDTYRSWFQYNGNGQIIRRT-IQDPADIEFVPVHHGELT 133
                                    566666666667777788888899999**********************988777665544.567788888888864444 PP

                                    SHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT-.------S CS
                   Condensation  94 eeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekge.elplpqk 172
                                        +i e++q+    p  L +  +fr+++++   +++++++sv H+ vD++ +g+ l +++ +Y++l  g+ +l+lp+ 
  gi|121637113|ref|YP_977336.1| 134 L--PQIREIVQN---TPDPL-QWGCFRFGIVQ-GCDHFTFFASVDHVHVDAMIVGVTLMEFHLMYAALVGGHaPLELPPA 206
                                    3..469999995...44444.4579*******.***********************************999836788888 PP

                                    --HHHHHHHHHHHHCSHHHHH.HHHHHHHHHH......S.---BSS---SS---S-EEEEEE.EE-S-HHHHHHHHSTSS CS
                   Condensation 173 tpYkdyaeweqqyleskdlek.eeaYWseqlegelpvlq.Lpkdkarpakrsfkadrlsikl.deeteeklrklakeqgv 249
                                     +Y d+  ++  ++    +e+ + + W++  eg+  +   +p      +++  +ad +++ + dee ++++++++ + g+
  gi|121637113|ref|YP_977336.1| 207 GSYDDFCRRQHTFSSTLTVESpQVRAWTKFAEGTNGSFPdFPLP-LGDPSKPSDADIVTVMMlDEEQTAQFESVCTAAGA 285
                                    88***********9999999845689******977766556666.333333344455555546***************** PP

                                    -HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHHHHHHHHHHHCCT CS
                   Condensation 250 tlndvllaalgllLskytgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfselikrvkedllkaephq 329
                                          la+ gl+ +++tg++ +   t+   R  +  +   + G+F+  +P+ + + ++ +f ++ ++ ++   +  +  
  gi|121637113|ref|YP_977336.1| 286 RFIGGVLACCGLAEHELTGTTTYYGLTPRDTRRTP--ADAMTQGWFTGLIPITVPI-AGSAFGDAARAAQTSFDSGVKLA 362
                                    ***********************************..778899*************.5566******************* PP

                                    TS-HHHHHHCSS.SS-SSSS-S-SEEEEESSS-HH....CCCEEECCCCSEEECEE...E.....SSEEEEEEETTSSEE CS
                   Condensation 330 gypleeLvkdlelqrkesrspLfdpvfsfenylgq....eseeeesqlselklsvssveaeeeskydlsleasetngklt 405
                                    ++p+ ++v+ + +           p f   n+l       s   + +l++ +++  +++     +y ls+ +  ++++  
  gi|121637113|ref|YP_977336.1| 363 EVPYDRVVELSSTLTM--PR----PNFPVVNFLDAgaapLSVLLTAELTGTNIG--VYS-DGRYSYQLSIYVIRVEQGTA 433
                                    *******998875543..22....333333334444445555555555555555..333.66778888888888888888 PP

                                    EEEEEETTTS-HHHHHHHHHHHHHHHHHHHHSTTS CS
                   Condensation 406 ikieYntslFdeetierflerlkelleqviehpeq 440
                                    + + +  +   +e++ r l +lk + ++v+e  +q
  gi|121637113|ref|YP_977336.1| 434 VAVMFPDNPIARESVARYLATLKSVFQRVAESGQQ 468
                                    88888888888888888888888888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3142.60
//
Query:       gi|121637114|ref|YP_977337.1|  [L=1002]
Description: transmembrane transport protein mmpL10 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   8.9e-194  642.8  37.6   1.4e-105  352.9  17.6    2.3  2  MMPL            MMPL family
  ------ inclusion threshold ------
      0.039   13.4   0.9      0.095   12.1   0.2    2.0  2  HEPN_SAV2148    SAV2148-like HEPN
      0.045   13.6   8.5      0.022   14.6   2.4    2.7  2  PhageMin_Tail   Phage-related minor tail protein
       0.48   10.4   0.0       0.48   10.4   0.0    4.0  5  T2SSF           Type II secretion system (T2SS), protein F
        5.9    6.7  14.1       0.11   12.3   2.3    2.5  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.9  17.6    4e-109  1.4e-105       2     332 ..      30     357 ..      29     358 .. 0.99
   2 !  295.7  12.1   9.7e-92   3.5e-88       4     308 ..     635     967 ..     632     991 .. 0.94

  Alignments for each domain:
  == domain 1  score: 352.9 bits;  conditional E-value: 4e-109
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    ++pada+s++a++++++af+e ++s++i vv+l ++++ lg+ a+e+++++lvd+l++d+k+v +++dfl++p +++++ 
  gi|121637114|ref|YP_977337.1|  30 VLPADAPSSVAVRQMAEAFHE-SGSENILVVLL-TDEKGLGA-ADENVYHTLVDRLRNDAKDVVMLQDFLTTPPLREVLG 106
                                    689******************.9999*999999.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    SkDgka+++++ l+gd g++++++++++++++v+++++ + l+++vtGpaat+adl+da++rd++ ie++++v++lviL+
  gi|121637114|ref|YP_977337.1| 107 SKDGKAWILPIGLAGDLGTPKSYHAYTDVERIVKRTVAGTTLTANVTGPAATVADLTDAGARDRASIELAIAVMLLVILM 186
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                    ++yr++v++llpl+t++ sl++a++lv+ ++l+ gl++s++++ ll++++ ++GtDYa++L+sRy+e+++ ge+ e+av+
  gi|121637114|ref|YP_977337.1| 187 VIYRNPVTMLLPLVTIGASLMTAQALVAGVSLVGGLAVSNQAIVLLSAMIAGAGTDYAVFLISRYHEYVRLGEHPERAVQ 266
                                    ******************************************************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrr 321
                                    ra++s+gkv++a+++tv i++lg+ +a+l+v+++vG+a+a+G++v++l+++TllPA+lvl++ +++++pr +r  ++Wrr
  gi|121637114|ref|YP_977337.1| 267 RAMMSVGKVIAASAATVGITFLGMRFAKLGVFSTVGPALAIGIAVSFLAAVTLLPAILVLASPRGWVAPRGERMATFWRR 346
                                    ******************************************************************************** PP

                           MMPL 322 lgrlvvrrPlp 332
                                     g+++vrrP++
  gi|121637114|ref|YP_977337.1| 347 AGTRIVRRPKA 357
                                    *********86 PP

  == domain 2  score: 295.7 bits;  conditional E-value: 9.7e-92
                           MMPL   4 padaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf............. 70 
                                     +++++v+++++l+ + p+ a  + +i +  + +d a   ++ + +v+ lvd+ k+++ +++++s+f             
  gi|121637114|ref|YP_977337.1| 635 RSLNSVVRSLKSLGLDNPD-AARARLISMQNGANDLASAGRQVADGVQMLVDQTKNMGIGLNQASAFlmamgndasqpsm 713
                                    56788999***********.8889*******************************************8888888888888 PP

                           MMPL  71 .........lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatla 135
                                             l+ ++   va+af+S+Dg+++r+ ++++++p+st+a+++v+ i ++++ a+    l+++ ++ +G +++l+
  gi|121637114|ref|YP_977337.1| 714 agfnvppqvLKSEEfkkVAQAFISPDGHTVRYFIQTDLNPFSTAAMDQVNTIIDTAKGAQpntSLADASISMSGYPVMLR 793
                                    88777777644444667*******************************************998999************** PP

                           MMPL 136 dlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliav 214
                                    d+rd+++rd++li++vt+vv+++iL+ ++r++va+l+++++vv+s++ a+gl v++++ +lg+el+++v+gl++v+l+av
  gi|121637114|ref|YP_977337.1| 794 DIRDYYERDMRLIVAVTVVVVILILMALLRAIVAPLYLVGSVVISYMSAIGLgVVVFQVFLGQELHWSVPGLAFVVLVAV 873
                                    ******************************************************************************** PP

                           MMPL 215 GtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTl 294
                                    G+DY++lL sR+r+e+a g ++  +vir+v+ tg+v+taaGl++a++m gL++++++++ q G+ i++G+l+d+++v+T+
  gi|121637114|ref|YP_977337.1| 874 GADYNMLLASRLRDESALGVRS--SVIRTVRCTGGVITAAGLIFAASMSGLLFSSIGTVVQGGFIIGVGILIDTFVVRTI 951
                                    **********************..******************************************************** PP

                           MMPL 295 l.PAllvllGraa.la 308
                                    + PA+++llGra  ++
  gi|121637114|ref|YP_977337.1| 952 TvPAMATLLGRASwWP 967
                                    ************6444 PP

>> HEPN_SAV2148  SAV2148-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   7.6e+03     105     117 ..      93     105 ..      83     106 .. 0.70
   2 ?   12.1   0.2   2.6e-05     0.095     144     196 ..     634     686 ..     624     702 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                   HEPN_SAV2148 105 lsfltlpqlrelv 117
                                      flt p lre++
  gi|121637114|ref|YP_977337.1|  93 QDFLTTPPLREVL 105
                                    36********975 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.6e-05
                   HEPN_SAV2148 144 arsvvsrnralsravldqaeraaarllellgageeaaaaarlpvdavedlvgd 196
                                     rs  s  r+l+   ld+ + a arl+++ +++++ a+a r  +d v+ lv +
  gi|121637114|ref|YP_977337.1| 634 GRSLNSVVRSLKSLGLDNPDAARARLISMQNGANDLASAGRQVADGVQMLVDQ 686
                                    5777788899**************************************99976 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4     0.067   2.4e+02      45     100 ..     508     566 ..     457     579 .. 0.75
   2 ?   14.6   2.4     6e-06     0.022      45     135 ..     626     715 ..     614     780 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.067
                  PhageMin_Tail  45 lataggaddleeaaeilstalnafglsaa.....daeeaaDvlaaaanngatsvedlaeal 100
                                    ++ a+    + +++++l+ + n+fg ++      +a+++++ + a++++ +++++++a+++
  gi|121637114|ref|YP_977337.1| 508 VSRAVA-G-VRSLVDALAYIQNQFGGNKTfneidNAARLVSNIHALGDALQVNFDGIANSF 566
                                    455555.5.7788888888888888884245566888888888888888888888888554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6e-06
                  PhageMin_Tail  45 lataggaddleeaaeilstalnafglsaadaeea.aDvlaaaanngatsvedlaealkevgavakaaGlsfeetaaalal 123
                                    ++++++ d l+ + ++++  l+ +gl++ da++a +  +  +an  a+ +++ a++ + +  + k++G+ +++++a+l +
  gi|121637114|ref|YP_977337.1| 626 VSAVVN-D-LGRSLNSVVRSLKSLGLDNPDAARArLISMQNGANDLASAGRQVADGVQMLVDQTKNMGIGLNQASAFLMA 703
                                    556666.6.99999*************6666655366788899999********************************** PP

                  PhageMin_Tail 124 laaagikgseAg 135
                                    + +   ++s+Ag
  gi|121637114|ref|YP_977337.1| 704 MGNDASQPSMAG 715
                                    ***888999998 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.0      0.72   2.6e+03     107     123 ..     173     189 ..     169     189 .. 0.71
   2 ?   -3.3   0.1       2.3   8.1e+03      98     115 ..     266     283 ..     231     290 .. 0.50
   3 ?   10.4   0.0   0.00013      0.48       4      53 ..     507     556 ..     506     576 .. 0.86
   4 ?   -3.5   0.1       2.6   9.5e+03       8      28 ..     669     689 ..     660     704 .. 0.76
   5 ?   -1.0   1.8      0.44   1.6e+03     100     119 ..     803     822 ..     788     832 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                                    XXXXXXXXXXXXXXXXX CS
                          T2SSF 107 lllvvallvllillail 123
                                    ++l++a+++l+il++i+
  gi|121637114|ref|YP_977337.1| 173 IELAIAVMLLVILMVIY 189
                                    56777777777777765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                    HHHHHHTTXXXXXXXXXX CS
                          T2SSF  98 llaallepllllvvallv 115
                                     +a++   +++++ a+ v
  gi|121637114|ref|YP_977337.1| 266 QRAMMSVGKVIAASAATV 283
                                    233333334444444444 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00013
                                    HHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC CS
                          T2SSF   4 qlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale 53 
                                    q+++++++  +lv+aL +++++ +  +   e++++ar +++ ++l +al+
  gi|121637114|ref|YP_977337.1| 507 QVSRAVAGVRSLVDALAYIQNQFGGNKTFNEIDNAARLVSNIHALGDALQ 556
                                    678999999***************99999999****************98 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.6
                                    HHHTT--HHHHHHHHHHHHSS CS
                          T2SSF   8 llsaGvplveaLellaeeaen 28 
                                    l saG  +++ +++l ++++n
  gi|121637114|ref|YP_977337.1| 669 LASAGRQVADGVQMLVDQTKN 689
                                    557788888888888777764 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.44
                                    HHHHTTXXXXXXXXXXXXXX CS
                          T2SSF 100 aallepllllvvallvllil 119
                                     +l+  + ++vv+l+++++l
  gi|121637114|ref|YP_977337.1| 803 MRLIVAVTVVVVILILMALL 822
                                    44443444444444444444 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.3   3.2e-05      0.11       8     137 ..     200     328 ..     194     340 .. 0.76
   2 ?   -0.7   4.2      0.33   1.2e+03      14      91 ..     833     914 ..     822     962 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHC.CHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCH CS
                 Sterol-sensing   8 LglagviivllsvasslgllaylgltltliilevlPflvlavgvdn.ifvlvkavqrtsrsldeseriaealgevgpsil 86 
                                    +++++ ++++ ++++ ++l+  l ++ + i+l  l  ++   g+d  +f++ + ++ +   ++ +  +++a+ +vg  i 
  gi|121637114|ref|YP_977337.1| 200 VTIGASLMTAQALVAGVSLVGGLAVSNQAIVL--LSAMIAGAGTDYaVFLISRYHEYVRLGEHPERAVQRAMMSVGKVIA 277
                                    56667777777777777777766666666655..88899999**972566666666666667778899***********9 PP

                                    HCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                 Sterol-sensing  87 ltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldi 137
                                    ++++t  +++l   + ++ + ++     a++++v+Fl  +t+  a+L l  
  gi|121637114|ref|YP_977337.1| 278 ASAATVGITFLGMRFAKLGVFSTVGPALAIGIAVSFLAAVTLLPAILVLAS 328
                                    9999988887633355555555566678*******************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.33
                                    HHHHCCHHHHCCH.HHHHHHHH...HHHHHHHHHHHHH.HHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHC CS
                 Sterol-sensing  14 iivllsvasslgl.laylgltl...tliilevlPflvl.avgvdnifvlvkavqrtsrsldeseriaealgevgpsillt 88 
                                      v++s++s++gl + ++++ l    ++++  l f+vl avg d   +l+ +  r ++ l + + + ++++ +g  i++ 
  gi|121637114|ref|YP_977337.1| 833 GSVVISYMSAIGLgVVVFQVFLgqeLHWSVPGLAFVVLvAVGADYN-MLLASRLRDESALGVRSSVIRTVRCTGGVITAA 911
                                    4566777777776323455554111455555688988636888754.455566677888888888888888877777766 PP

                                    CCH CS
                 Sterol-sensing  89 slt 91 
                                     l 
  gi|121637114|ref|YP_977337.1| 912 GLI 914
                                    554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1002 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.94u 0.36s 00:00:01.29 Elapsed: 00:00:00.55
# Mc/sec: 5489.60
//
Query:       gi|121637115|ref|YP_977338.1|  [L=359]
Description: hypothetical protein BCG_1246c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-74  250.4   2.6    2.2e-74  249.8   2.6    1.2  1  PE-PPE    PE-PPE domain


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.8   2.6   1.2e-78   2.2e-74       1     226 [.      79     316 ..      79     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 249.8 bits;  conditional E-value: 1.2e-78
                         PE-PPE   1 PgadaelvsyPa.........sflpvtg.lksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarla 70 
                                    P+a+++l++yPa         ++lp+ +  +++tv+++v++Gt++L++ai++    +++++++G+Sqg+lv+++e+arla
  gi|121637115|ref|YP_977338.1|  79 PNAKHDLIDYPAgaafswwptMLLPPGShQDNMTVGVAVKDGTNSLDNAIHH---GTDPAAAVGLSQGSLVLDQEQARLA 155
                                    8899************99998777777789**********************...89*********************** PP

                         PE-PPE  71 alsepaa..pdqlsfvlvgnpnrp....nggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplN 144
                                    +  +p+a  pd+l+f+++g+p+++     ++l+++fp+g++ipi  i++t+++++dsqydT++vv++YDg++dfPd+p+N
  gi|121637115|ref|YP_977338.1| 156 N--DPTApaPDKLQFTTFGDPTGRhafgASFLARIFPPGSHIPIPFIEYTMPQQVDSQYDTNHVVTAYDGFSDFPDRPDN 233
                                    *..777777***************99999*************************************************** PP

                         PE-PPE 145 llAdvNailGialvHt..nyetevaeqlpanirttvnsrgakttyylipteelPLlqplrslgvpeplvdaldavLrvlv 222
                                    llA++Na +G+a+ Ht  ++ t + +++p+nirttvnsrga+tt+yl+p ++lPL++plr+lg++++ vd++d+vL++ +
  gi|121637115|ref|YP_977338.1| 234 LLAVANAAIGAAIAHTpiGF-TGPGDVPPQNIRTTVNSRGATTTTYLVPVNHLPLTLPLRYLGMSDAEVDQIDSVLQPQI 312
                                    ****************9888.999******************************************************** PP

                         PE-PPE 223 dlgY 226
                                    d++Y
  gi|121637115|ref|YP_977338.1| 313 DAAY 316
                                    **** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1889.51
//
Query:       gi|121637116|ref|YP_977339.1|  [L=578]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-72  241.9   0.0    1.1e-71  241.6   0.0    1.1  1  AMP-binding      AMP-binding enzyme
     0.0056   17.0   0.0      0.027   14.8   0.0    2.0  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.6   0.0   1.3e-75   1.1e-71       2     422 ..      11     466 ..      10     467 .. 0.86

  Alignments for each domain:
  == domain 1  score: 241.6 bits;  conditional E-value: 1.3e-75
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                    +e+a  +pd+ a+++        g  +tlT++e+ +r++ +A+  r+  ++ gdr +il+p+++ +++a+l+ ++aGa++
  gi|121637116|ref|YP_977339.1|  11 RERAGLQPDDAAFTYidyeqdwAGITETLTWSEVFRRTRIVAHEVRR-HCTTGDRAVILAPQGLAYIAAFLGSMQAGAIA 89 
                                    6788899******999999999999*********************8.8******************************* PP

                                    EEEET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                    AMP-binding  75 vplnp...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                    vpl+    ++  e+++ +l+d+ ++v++  + s+ +e+++e+ +++ +  +  +++ d+l+ +    ++++s        
  gi|121637116|ref|YP_977339.1|  90 VPLSVpqiGSHDERVSAVLADASPSVIL--TTSAVAEAVAEHIHRPNTNNVGPIIEIDSLDLT----GNSPSF------- 156
                                    ****9999999*****************..766668889898888877777777776665433....333222....... PP

                                    CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTT.....T-EEEESS-TTSCHHHHHHHHHHHH CS
                    AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklke.....ddvvlsilplahifglilelllall 226
                                      +  +  + ay++YTSG+T  P GVm+shrnl an ++l ++++f+ ++     d +++s+lp++h++gl+l++++++l
  gi|121637116|ref|YP_977339.1| 157 --RVKDLPSAAYLQYTSGSTRAPAGVMISHRNLQANFQQL-MSNYFGDRNgvappDTTIVSWLPFYHDMGLVLGIIAPIL 233
                                    ..22456689**************************9998.55553322234457999********************** PP

                                    TT-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHH CS
                    AMP-binding 227 sGatvvllpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffra 305
                                     G +  l ++ a+l+ p+++l+ +++ +++  a+++ ++e  +++ + + + +  dl+ +  + +g+e++ p++l +f +
  gi|121637116|ref|YP_977339.1| 234 GGYRSELTSPLAFLQrPARWLHSLANGSPSWSAAPNFAFELAVRKTTDA-DIEGLDLGNVLGITSGAERVHPNTLSRFCN 312
                                    *************666**************99999999**999964443.677789999777789*************** PP

                                    HHTC......EEEEEEEEGGGSSECEE........................CHCTTTCTSTTS-BEE-......TTEEEE CS
                    AMP-binding 306 lfge......evlegYGlTEttgvvtv........................lpleedkkklgsvGkpl......pgvevk 349
                                    +f +       +  +YGl+E+t  v+                         +         +++G+pl          v+
  gi|121637116|ref|YP_977339.1| 313 RFAPynfredMIRPSYGLAEATLYVASrnsgdkpevvyfepdklstgsanrC--------EPKTGTPLlsygmpTSPTVR 384
                                    **99****988**************666788999999999999766554432........344454444444424889** PP

                                    EE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.........TCC.EEEEEEEEEEETTSEEEEEEECCCE CS
                    AMP-binding 350 ivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds.........egr.wlrTGDlgrldedGyleivgRkkdl 419
                                    ivD++t  ++p g+ Ge++v+g +v++gY++kp++t+++f +         +++ wlrTGDlg+l  + +++ivgR kd+
  gi|121637116|ref|YP_977339.1| 385 IVDPDTCIECPAGTIGEIWVKGDNVAEGYWNKPDETRHTFGAmlvhpsagtPDGsWLRTGDLGFLS-EDEMFIVGRMKDM 463
                                    ****************************************989999999975455*********99.56*********** PP

                                    EEE CS
                    AMP-binding 420 ikl 422
                                    +++
  gi|121637116|ref|YP_977339.1| 464 LIV 466
                                    986 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.33     3e+03      64      85 ..     289     310 ..     273     313 .. 0.87
   2 !   14.8   0.0     3e-06     0.027       1      91 [.     468     561 ..     468     563 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.33
                                    HHHHHSS--EEEEE-TT-S--- CS
                AMP-binding_C_2  64 lksklgvsvkvelvepgtlprs 85 
                                    l ++lg++   e v+p+tl r 
  gi|121637116|ref|YP_977339.1| 289 LGNVLGITSGAERVHPNTLSRF 310
                                    67899*************9985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-06
                                    TEEE-HHHHHHHHHT-TTEE.EEEEEEEEEETT.EEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--.EEEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieeve.peYqivvtrege.lDelevkvEvkegfsdelkelealekkiakklksklgvsv.kvelv 77 
                                    G n +P  ie+ ++ei +   +   + v+++++   ++e+k   + ++ + ++el+ +++++++++ ++ g++v ++ lv
  gi|121637116|ref|YP_977339.1| 468 GRNHYPEDIESTVQEITGGRvAAISVPVDHTEKlVTVIELKLLGD-SAGEAMDELDVIKNNVTAAISRSHGLNVaDLVLV 546
                                    7799***********987652455566665543134445554333.45577899******************9659**** PP

                                    -TT-S----.----- CS
                AMP-binding_C_2  78 epgtlprse.gKakr 91 
                                    +pg++p ++ gK +r
  gi|121637116|ref|YP_977339.1| 547 PPGSIPTTTsGKIRR 561
                                    ******975269988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3437.90
//
Query:       gi|121637117|ref|YP_977340.1|  [L=538]
Description: hypothetical protein BCG_1248c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-21   75.3   0.2    8.3e-21   73.6   0.2    2.0  1  HTH_30    PucR C-terminal helix-turn-helix domain
     0.0016   18.3   0.0      0.016   15.1   0.0    2.4  2  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
     0.0039   16.9   0.1      0.015   15.0   0.0    2.1  2  HTH_8     Bacterial regulatory protein, Fis family
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.21   11.7   0.0    1.3  1  DUF3479   Domain of unknown function (DUF3479)


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.2   1.8e-24   8.3e-21       1      59 []     475     533 ..     475     533 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.8e-24
                                    ...HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHH CS
                         HTH_30   1 LleTLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddpddrlaLylAlrl 59 
                                    L +TLrayl++ g+i a+A++L vH+nT+ryR+rrie+ll  +l dpd rl ++l lr+
  gi|121637117|ref|YP_977340.1| 475 LAQTLRAYLDAFGDIGAAARSLQVHPNTVRYRIRRIEQLLSTSLGDPDVRLLFSLGLRA 533
                                    689****************************************************9996 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.27   1.2e+03      33      45 ..     386     398 ..     381     401 .. 0.88
   2 !   15.1   0.0   3.6e-06     0.016      14      45 ..     487     518 ..     478     525 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                                    HHHHHHHHHTS-S CS
                          HTH_1  33 qikrLEeelgvpL 45 
                                     i++L++elgv L
  gi|121637117|ref|YP_977340.1| 386 TISALRAELGVAL 398
                                    699*******998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.6e-06
                                    SSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-S CS
                          HTH_1  14 gsftrAAeeLglsqpavsrqikrLEeelgvpL 45 
                                    g + +AA+ L + + +v  +i+r E++l + L
  gi|121637117|ref|YP_977340.1| 487 GDIGAAARSLQVHPNTVRYRIRRIEQLLSTSL 518
                                    7899************************9887 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.5   1.1e+04      24      30 ..     310     316 ..     307     316 .. 0.78
   2 !   15.0   0.0   3.4e-06     0.015      10      41 ..     479     509 ..     476     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                                    HHHHHTS CS
                          HTH_8  24 AArlLGi 30 
                                     Ar+LG+
  gi|121637117|ref|YP_977340.1| 310 IARELGV 316
                                    69***96 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.4e-06
                                    HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH CS
                          HTH_8  10 IeaALertgGnkskAArlLGisRrtLyrKLkk 41 
                                    + a L+++g  + +AAr L ++++t+++++++
  gi|121637117|ref|YP_977340.1| 479 LRAYLDAFG-DIGAAARSLQVHPNTVRYRIRR 509
                                    677888888.********************97 PP

>> DUF3479  Domain of unknown function (DUF3479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.8e-05      0.21      28     103 ..      28     101 ..      10     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                        DUF3479  28 elelsvfadeelrekpealeelaaavaeAdifiasllfdedqvealrealeaarekldavlvfeSapelmrltkvG 103
                                    +l+l v +++ ++++ +    laaa  +Ad+f+   + d++ v+++ ++ ++++  + +++  +S + +    + G
  gi|121637117|ref|YP_977340.1|  28 GLDLPVASTALIDSD-DVRLGLAAAAGSADVFFLIGVTDDEAVRWVDDQARQRAP-VAIFVKHPSDSVVAGAVRAG 101
                                    677777777777777.4455789999***********************999555.77777777776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3881.39
//
Query:       gi|121637118|ref|YP_977341.1|  [L=543]
Description: pyrroline-5-carboxylate dehydrogenase rocA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-93  311.4   0.0    9.6e-93  311.2   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.2   0.0   5.3e-97   9.6e-93       4     460 ..      53     523 ..      50     525 .. 0.93

  Alignments for each domain:
  == domain 1  score: 311.2 bits;  conditional E-value: 5.3e-97
                                    -SSSEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHH.HTHHHHHHHHHHHH-- CS
                         Aldedh   4 sesetievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlle.erkeelaeletletGk 81 
                                    +++e+i+v++P+ +   +++ ++at +d+ aav+aA +a++ wa+lp+ eRa+++ +aadll+   +e++a++ +l + k
  gi|121637118|ref|YP_977341.1|  53 GDGERIDVVQPHrHAARLGTLTNATHADAAAAVEAAMSAKSDWAALPFDERAAVFLRAADLLAgPWREKIAAATMLGQSK 132
                                    56689*******9999***********************************************778************** PP

                                    -HHHHHH.HHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-.SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEE CS
                         Aldedh  82 plaeara.eveeaidvlryyaelaeklegevlps.segklalvrrePl.GvvgaItPWNfPlllaawklapalaaGNtvv 158
                                    ++ +a+   v e id+ r+ ++ a+++ ++  p+  +g+ + + ++Pl G+v aItP+Nf  +     +apal+ GNtv+
  gi|121637118|ref|YP_977341.1| 133 SVYQAEIdAVCELIDFWRFNVAFARQILEQQ-PIsGPGEWNRIDYRPLdGFVYAITPFNFTSIAGNLPTAPALM-GNTVI 210
                                    *******9999***************77655.44249************************************9.***** PP

                                    EEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT......SEE CS
                         Aldedh 159 lKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl......krv 232
                                    +KP+ + +l a+l ++l+e+aglP+gv+n+vtg+g  v++  +++p+++ ++ftGst++  ++ +  ++n+       r+
  gi|121637118|ref|YP_977341.1| 211 WKPSITQTLAAYLTMQLLEAAGLPPGVINLVTGDGFAVSDVALADPRLAGIHFTGSTATFGHLWQWVGTNIgryhsyPRL 290
                                    ******************************************************************9988544444499* PP

                                    EEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---S CS
                         Aldedh 233 tlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPli 312
                                    + E+GGk+ ++ +++a  d   +a+++gaf ++GQ+C+a+sr+++ +s+++++ ++l+++a++l+ gd  d ++  G+li
  gi|121637118|ref|YP_977341.1| 291 VGETGGKDFVVAHASARPDVLRTALIRGAFDYQGQKCSAVSRAFIAHSVWQRMGDELLAKAAELRYGDITDLSNYGGALI 370
                                    ******************************************************************************** PP

                                    SHHHHHHHHHHHHHHHHTTSEEEE.-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESS..HHHHHHH CS
                         Aldedh 313 seaqlekvekyveeakeegaklll.GgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkd..eeeaiei 389
                                    +++++ k  + +e+ak + a  +  Gg   e ++++gyfv+Ptvl   +p ++ +  E+FGP+lsv  + d   e+++++
  gi|121637118|ref|YP_977341.1| 371 DQRAFVKNVDAIERAKGAAAVTVAvGG---EYDDSEGYFVRPTVLLSDDPTDESFVIEYFGPLLSVHVYPDerYEQILDV 447
                                    ****************99887666599...7799*********************************9997336899988 PP

                                    HH.SSSEESEEEEE-SBHHHHHHHHHHS..-SSEEEESSSST--TTT.SEB--CGGGEES-BSH.HHHHHHTEEEE CS
                         Aldedh 390 aN.dteyGLaagvftkdleraervaerl..eaGnvyiNdsttgaaea.lpfgGvkqSglGregg.kegleeytevk 460
                                        ++y+L+++v+++d + ++++ +rl   aGn y+Nd+ tga+   +pfgG + Sg+++++g +  l ++t  +
  gi|121637118|ref|YP_977341.1| 448 IDtGSRYALTGAVIADDRQAVLTALDRLrfAAGNFYVNDKPTGAVVGrQPFGGARGSGTNDKAGsPLNLLRWTSAR 523
                                    76369**********************96679****************************8777577777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3513.27
//
Query:       gi|121637119|ref|YP_977342.1|  [L=329]
Description: proline dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-27   97.4   0.0    1.4e-27   97.1   0.0    1.1  1  Pro_dh    Proline dehydrogenase


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   7.6e-32   1.4e-27       6     293 ..      53     312 ..      48     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 7.6e-32
                                    HHHHHTTEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-S.EEE-GGG.TT-SGGGHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxx RF
                         Pro_dh   6 eklkkrgvrlsldllgeavlteedadryleayleaiksiekaskalkvleapg.vsvklsa.prletaeeeevmeelver 83 
                                    ++l+++g  ls+d+lge+v++++da++ ++ayl +++ +++  +   +  +p  vs+klsa  +    +     + ++++
  gi|121637119|ref|YP_977342.1|  53 TALRDSGRYLSIDYLGENVTDADDAAAAVRAYLGLLDVLGRRGDIACDGVRPLeVSLKLSAlGQALDRD---GQKIALDN 129
                                    677867888******************************999883333555557******963333333...34568999 PP

                                    HHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCTTT---EEEEEETTBTTHHHHHHHHHHHHHHTTS-EEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Pro_dh  84 lrtlakeakelgvrlliDaEeaklqeltlelfrklnkepelkdwevvgntyQaYlkdalevlqkllelAeregfrlgvkL 163
                                     r+++++a++ g+ +++DaE+++  + tl++   l  +        +g ++QaYl+++l+++ +l++          v+L
  gi|121637119|ref|YP_977342.1| 130 ARAICERAERVGAWVTVDAEDHTTTDSTLSISGDLRVDFPW-----LGTVVQAYLRRTLADCAELAAVG------ARVRL 198
                                    ***********************************976666.....************99998887765......569** PP

                                    E--S-HHHHHHHHHHTT-S-SB-SSHHHHHHHHHHHHHHHHHTTTTEEEEEE-S-HHHHHHHHHHHHHT..T--GGGEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Pro_dh 164 VrGAYldsErkraqelgyespifdtkeeTDanYdavaelllenrdeiypavAsHNaesvakalalaeelgqekeksevef 243
                                     +GAY   E++        s+ + + ++   +Y ++++ l +   + yp+vA+H    +a++  + +e   ++ + ++e+
  gi|121637119|ref|YP_977342.1| 199 CKGAY--DEPA--------SVAYRDAAQVTDSYLRCLRVLTAG--RGYPMVATHDPVIIAAVPGITRES--GRSQGDFEY 264
                                    *****..5777........678999999999********9876..579*********************..********* PP

                                    EEETTSSHHHHHHHHHTTS-EEEEEEECEHHHHHHHHHHHHHHHH-TT-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Pro_dh 244 qqLlGMadnlsfalakagynvrkYlPvGpveevlpYLvRRleENtanssf 293
                                    q+L+G  d+ ++ l+ ag +vr+Y+P+G+      Y +RRl E  an+ f
  gi|121637119|ref|YP_977342.1| 265 QMLYGVRDDEQRRLTGAGNHVRVYVPFGT--RWYGYFLRRLAERPANLAF 312
                                    ****************************7..6899********9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2397.81
//
Query:       gi|121637120|ref|YP_977343.1|  [L=401]
Description: RNA polymerase sigma factor SigI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-11   43.5   0.1      5e-11   42.1   0.2    1.7  2  Sigma70_r4_2   Sigma-70, region 4
    1.4e-08   34.4   0.2    2.9e-08   33.3   0.2    1.6  1  Sigma70_r2     Sigma-70 region 2
    0.00042   19.8   0.1     0.0009   18.7   0.1    1.6  1  Sigma70_r4     Sigma-70, region 4
     0.0023   17.6   0.0     0.0031   17.2   0.0    1.2  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.018   14.3   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   1.4e-14     5e-11       2      54 .]     110     162 ..     109     162 .. 0.95
   2 ?   -3.8   0.0       3.1   1.1e+04      12      28 ..     172     188 ..     169     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.4e-14
                                    HHHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   2 qalrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    +al+ +l++L + +r +f+l++++gl+y++IA  +g   +t+++  +RAr+k+
  gi|121637120|ref|YP_977343.1| 110 LALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKI 162
                                    577779*********************************************96 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.1
                                    -HHHHHHHHHHHTS--- CS
                   Sigma70_r4_2  12 perqreifllrylegls 28 
                                     + q ++++  ++e +s
  gi|121637120|ref|YP_977343.1| 172 EPAQHRVVTRAFIEACS 188
                                    68899999999988877 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   8.1e-12   2.9e-08       3      69 ..      12      74 ..      10      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8.1e-12
                                   HHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHH.GGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2  3 erylplvkrlarrllgsgadaeDlvQeaflrlwra.verfdpergvsfsawllriarnaaidrlRkrr 69
                                   ++++  ++ la r++g+   aeD+vQeaf rl+ra v + d+erg     wl+ ++ ++++d++++++
  gi|121637120|ref|YP_977343.1| 12 RAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRApVGDIDDERG-----WLIVVTSRLCLDHIKSAS 74
                                   79999*****************************94455555555.....**************9876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.5e-07    0.0009       2      48 ..     116     162 ..     115     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                                    HHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   2 LasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    L++L + er v++l    gl++++I+ + g   ++ rq+ +rA+rk+
  gi|121637120|ref|YP_977343.1| 116 LERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKI 162
                                    899******************************************97 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.7e-07    0.0031     206     252 ..     326     379 ..     265     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.7e-07
                                    C.......THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSH CS
                  Abhydrolase_1 206 e.......lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHla 252
                                            l++v++p+ +++g++D++vp +++e   + lp+++l++++++ Hla
  gi|121637120|ref|YP_977343.1| 326 FardwgfrLDEVKVPVRWWHGDHDHIVPFSHGEHVVSRLPDAKLLHLPGESHLA 379
                                    04444666778*****************************************98 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.9e-06     0.018     150     232 ..     296     377 ..     225     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                    Hydrolase_4 150 rdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                      pe+ a + +d l  ++k  +  +++++  + +   r +++++P+   hG++D++v+ +  ++++ rl+  d +l   p
  gi|121637120|ref|YP_977343.1| 296 ARPEFKAMFLDDLLNgSRKQLAAPFADVIAFARDWGFRLDEVKVPVRWWHGDHDHIVPFSHGEHVVSRLP--DAKLLHLP 373
                                    45677777777777777788888889999999999999*******************************9..67777666 PP

                    Hydrolase_4 229 glyH 232
                                    g  H
  gi|121637120|ref|YP_977343.1| 374 GESH 377
                                    6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2738.20
//
Query:       gi|121637121|ref|YP_977344.1|  [L=275]
Description: hypothetical protein BCG_1252 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-05   24.5   0.0    2.1e-05   24.5   0.0    1.1  1  Palm_thioest   Palmitoyl protein thioesterase
    5.4e-05   23.0   0.0    0.00012   21.8   0.0    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00036   20.3   0.0    0.00086   19.1   0.0    1.6  2  PGAP1          PGAP1-like protein
     0.0012   18.2   0.0     0.0017   17.7   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0083   16.8  10.0      0.016   15.8  10.0    1.5  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.086   12.5   0.0       0.16   11.6   0.0    1.4  1  Abhydrolase_8  Alpha/beta hydrolase
      0.091   12.9   0.0       0.11   12.5   0.0    1.2  1  Thioesterase   Thioesterase domain
       0.18   11.4   0.0       0.26   10.9   0.0    1.2  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   9.3e-09   2.1e-05      55     103 ..     103     147 ..      52     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.3e-09
                   Palm_thioest  55 veavckk..lelangfhaiGfSQGglflRaliercddkknvrnlislggpq 103
                                    ++    k  +++ + + +iG S Gg+f+R+l+  + +   vr++i+lg+p 
  gi|121637121|ref|YP_977344.1| 103 LD----KlhSRYHTPVSLIGWSLGGIFARGLARDH-PSA-VRQVITLGSPF 147
                                    33....244568899*******************9.454.*********96 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.3e-08   0.00012      75     127 ..     113     164 ..      99     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.3e-08
                                    EE.EEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCH CS
                  Abhydrolase_1  75 lt.lvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdf 127
                                    ++ l+G+S+GG +a+ +a ++p+ V+ +++lg+  p+ + + ++ ++a+sf ++
  gi|121637121|ref|YP_977344.1| 113 PVsLIGWSLGGIFARGLARDHPSAVRQVITLGS--PFGMRDTCETRSAWSFNRY 164
                                    4449*****************************..7766666666666666544 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   2.8e+03       3      13 ..      49      59 ..      48      67 .. 0.85
   2 !   19.1   0.0   3.9e-07   0.00086      84     131 ..     105     149 ..      78     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                          PGAP1  3 sGipVlFvpGn 13
                                   +G pVl +pG+
  gi|121637121|ref|YP_977344.1| 49 DGHPVLVLPGL 59
                                   699*******7 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.9e-07
                          PGAP1  84 sssekeptsviliGHSmGGivaraaltlknyikqsvntiltlasPhal 131
                                    + +++  t v liG S+GGi ar ++      +++v++++tl+sP  +
  gi|121637121|ref|YP_977344.1| 105 KLHSRYHTPVSLIGWSLGGIFARGLARD---HPSAVRQVITLGSPFGM 149
                                    446778899*************976544...3789**********866 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.5e-07    0.0017      54     117 ..      91     153 ..      71     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.5e-07
                    Hydrolase_4  54 sfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikakl 117
                                    ++ + v  ++ +++k+ +++ ++p+ l+G S+GG+ a  ++ ++p+ v+ +i  ++ ++++   
  gi|121637121|ref|YP_977344.1|  91 PTAKAVSGMRDLLDKLHSRY-HTPVSLIGWSLGGIFARGLARDHPSAVRQVITLGSPFGMRDTC 153
                                    55667777888888888766.568******************************9999988765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  10.0     7e-06     0.016       1     160 [.      53     247 ..      53     272 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7e-06
                                    EEEE--.GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT...TTSEEEEEETCHHHH CS
                  Abhydrolase_6   1 vlllHG.agssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa.gggpvvlvGHSlGGal 78 
                                    vl+l+G + +++s W  +++  l++ g+   a+ + G Gr+ +p      +   ++lld+l +  + pv l+G+SlGG+ 
  gi|121637121|ref|YP_977344.1|  53 VLVLPGlLAGDGSTWILRRI--LRRLGY--AAYGW-GLGRNIGPTAKA--VSGMRDLLDKLHSrYHTPVSLIGWSLGGIF 125
                                    67788853444788954555..333367..78999.999775555555..6666888888877668999**********9 PP

                                    HHHHHHCC.....EE..EEES-..----TTT...S----TTHHHHHH................TT-C............C CS
                  Abhydrolase_6  79 alaaapla...lvvg..vlldppptalpagl...laaalelllalla................llrl............l 122
                                    a  +a+     +  +  + l +p    ++++    + a+++ + +                  +                
  gi|121637121|ref|YP_977344.1| 126 ARGLARDHpsaV--RqvITLGSPF---GMRDtceTRSAWSFNRYAHLhterhelplemeseplP--VpttaiysrcdgmV 198
                                    999444445653..2447777733...2222233333333333222211111111111111111..01111111121222 PP

                                    CCHCCH................S-HS.CCCCHHHCCCCHCHCCCGHHHHCCHHCH CS
                  Abhydrolase_6 123 awlsre................plpr.lfladedadaawrarlarlaallaglgl 160
                                    aw                    +  + ++ ++++  + w+ +++ ++++ a+  +
  gi|121637121|ref|YP_977344.1| 199 AWQ--TcmnspseraeniavrsS--HiGYGHNPP--VVWAIADRLAQPQGAWAPF 247
                                    222..011222222233222111..125555555..5555555555555554443 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-05      0.16      92     146 ..      97     150 ..      88     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                  Abhydrolase_8  92 aeLnallrdlratsvpgqhlallgHSYGSlva.slAlddaaseVsdvvlyGSP.Gle 146
                                    + ++ ll +l+++    ++++l+g S G + a +lA d+ +s V +v+  GSP G++
  gi|121637121|ref|YP_977344.1|  97 SGMRDLLDKLHSRY--HTPVSLIGWSLGGIFArGLARDH-PSAVRQVITLGSPfGMR 150
                                    55667777777777..899**********9884677666.*************6665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-05      0.11      65      86 ..     111     132 ..      94     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                    SSSEEEEEETHHHHHHHHHHHH CS
                   Thioesterase  65 egPyalfGhSlGgllAfevArq 86 
                                    + P+ l+G+SlGg++A  +Ar 
  gi|121637121|ref|YP_977344.1| 111 HTPVSLIGWSLGGIFARGLARD 132
                                    34**************999985 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.26     104     166 ..     101     160 ..      97     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                    HHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHHHC....TTCCHHH CS
                       Esterase 104 plldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamWgq....eekeawq 166
                                    +lld+  + + +  +++G S+GG +A  la +hp    +v+ +        ++ g     e+++aw 
  gi|121637121|ref|YP_977344.1| 101 DLLDKLHSRYHTPVSLIGWSLGGIFARGLARDHPSAVRQVITLG-------SPFGMrdtcETRSAWS 160
                                    566777777777799**********************9999875.......3333333355555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1953.39
//
Query:       gi|121637122|ref|YP_977345.1|  [L=473]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-65  220.8   0.9    2.2e-64  217.6   0.9    1.9  1  AMP-binding    AMP-binding enzyme
    3.7e-20   72.7   0.3    3.7e-20   72.7   0.3    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.6   0.9   2.5e-68   2.2e-64      47     416 ..      46     374 ..      25     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 2.5e-68
                                    T-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEE CS
                    AMP-binding  47 gdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvliatvdselleklleaaakleavklvivl 126
                                      rVa+l+ +++  v+a+ ++l aG+ vvp+ ++ +  e +++l+ds++++ +          l ++ a l  + + + +
  gi|121637122|ref|YP_977345.1|  46 AHRVAVLATPTASTVLAITGCLIAGVPVVPVPADVGVTERRHMLTDSGVQAWL-G-------PLPDDPAGL--PHIPVRT 115
                                    679**************************************************.2.......222222222..1122211 PP

                                    SCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEE CS
                    AMP-binding 127 dadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvl 206
                                    +             +  +++      + e++p  +a+++YTSGTTG PKGV+ls r+++a + +l   + ++ +++dv++
  gi|121637122|ref|YP_977345.1| 116 H-------------A--RSWH--R-YP-EPSPGAIAMVVYTSGTTGPPKGVQLSRRAIAADLDAL--AEAWQWTAEDVLV 174
                                    1.............2..2221..2.23.589******************************9997..45677679***** PP

                                    ESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT- CS
                    AMP-binding 207 silplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlssl 285
                                    + lpl+h+ gl+l+ll++l  G + v   k ++   +  ++++ + + t+++gvP+v+ ++++ + a         l+  
  gi|121637122|ref|YP_977345.1| 175 HGLPLYHVHGLVLGLLGSLRFGNRFVHTGKPTP---AGYAQACYEAHGTLFFGVPTVWSRVAAdQAAA------GALKPA 245
                                    *************************99775544...456789999999*************9945433......38999* PP

                                    SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE. CS
                    AMP-binding 286 rlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgee. 364
                                    rl+++g ++l+  + +++ +l+g++ +e YG +E ++ ++  +  + ++++g vG pl+gv+ ++vD+++ge  +dge+ 
  gi|121637122|ref|YP_977345.1| 246 RLLVSGSAALPVPVFDKLVQLTGHRPVERYGASESLITLS-TR-ADGERRPGWVGLPLAGVQTRLVDDDGGEVPHDGETv 323
                                    ************************88999*********98.44.3333689******************9999999999* PP

                                    EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEEC CS
                    AMP-binding 365 GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRk 416
                                    G+l vrgp+++ gYl++p+ata afd  + w+rTGD++++d  G  +ivgR 
  gi|121637122|ref|YP_977345.1| 324 GKLQVRGPTLFDGYLNQPDATAAAFD-ADSWYRTGDVAVVDGSGMHRIVGRE 374
                                    *************************9.645*********************7 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1         2   1.8e+04       9      23 ..      43      57 ..      31      68 .. 0.61
   2 !   72.7   0.3   4.1e-24   3.7e-20       1      76 []     390     463 ..     390     463 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2
                                   STTEEEEEEE----- CS
                  AMP-binding_C  9 hpaVaeaaVvGvpde 23
                                   + +   +aV + p++
  gi|121637122|ref|YP_977345.1| 43 VAGAHRVAVLATPTA 57
                                   444445566665555 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 4.1e-24
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E +l+ hp+VaeaaVvGvpd+  G+++va+Vv +++++  ++ L+ +v+++l  +++p++v++vd+lp+++ GK
  gi|121637122|ref|YP_977345.1| 390 EIETVLLGHPDVAEAAVVGVPDDDLGQRIVAYVVGSANVD--ADGLINFVAQQLSVHKRPREVRIVDALPRNALGK 463
                                    8*********************************855653..6******************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3385.70
//
Query:       gi|121637123|ref|YP_977346.1|  [L=421]
Description: hypothetical protein BCG_1254c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   44.8   1.7    3.3e-11   43.5   0.8    2.2  2  GGDEF_2   GGDEF-like domain
    8.4e-11   41.5   2.7    8.4e-11   41.5   2.7    2.5  4  HTH_30    PucR C-terminal helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.3   0.3       0.08   12.9   0.3    1.7  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.8   5.5e-15   3.3e-11      11     115 ..     187     294 ..     181     295 .. 0.81
   2 ?   -1.2   0.0      0.39   2.3e+03      60      75 ..     312     330 ..     291     396 .. 0.59

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 5.5e-15
                        GGDEF_2  11 ra.rrlgldldgpyvvvvielee..daerllraleealral..gpdalvavrgd.rlvlllpaedeedaeallerlarrl 84 
                                    ra + lg++l++ +++++i+ +e   +++ l++ ++++ ++  + ++l++v g  + +++++ +d  d +++++++ ++ 
  gi|121637123|ref|YP_977346.1| 187 RAeAKLGYPLSRAHTAAIIWSDEldGDHSYLDRAADLFCHAvgSTRPLTVVAGAaSRWAWVTDADGLDIDTVQAAVDNAP 266
                                    44157****************999644446666666664444877777776665599********999999999999988 PP

                        GGDEF_2  85 gglsvriGiGspveglaglrrSyreArrAlr 115
                                    g+   ri+iG++++g++g+rrS+ eA+ + r
  gi|121637123|ref|YP_977346.1| 267 GA---RIAIGTTANGVEGFRRSHLEALITQR 294
                                    87...*********************98876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                        GGDEF_2  60 rlvlllpaedeedae...a 75 
                                    + v+l++ +++++ e    
  gi|121637123|ref|YP_977346.1| 312 KMVALISQNPDAASEfitS 330
                                    5666666655554443332 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.73   4.4e+03      36      51 ..     129     144 ..     127     148 .. 0.78
   2 ?   -3.4   0.0       1.5   9.1e+03      34      50 ..     186     202 ..     186     204 .. 0.76
   3 ?   -3.8   0.1       1.9   1.1e+04      19      25 ..     220     226 ..     213     227 .. 0.76
   4 !   41.5   2.7   1.4e-14   8.4e-11       4      54 ..     345     395 ..     342     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.73
                                    HHHHHS--TTSHHHHH CS
                         HTH_30  36 ieellgldlddpddrl 51 
                                    ++ell+++ ++ +d  
  gi|121637123|ref|YP_977346.1| 129 LRELLDVSARSVNDFI 144
                                    7899999999988765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                    HHHHHHHS--TTSHHHH CS
                         HTH_30  34 rrieellgldlddpddr 50 
                                    +r+e  lg++l+++ ++
  gi|121637123|ref|YP_977346.1| 186 ERAEAKLGYPLSRAHTA 202
                                    58888899999887665 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.9
                                    HHHHTS- CS
                         HTH_30  19 AkaLhvH 25 
                                    A+ L++H
  gi|121637123|ref|YP_977346.1| 220 AADLFCH 226
                                    8889998 PP

  == domain 4  score: 41.5 bits;  conditional E-value: 1.4e-14
                                    HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSHHHHHHHH CS
                         HTH_30   4 TLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddpddrlaLy 54 
                                     L +++++++n+s++Ak+Lh HrnT+  RL+ +++ll ++ld ++  +a+ 
  gi|121637123|ref|YP_977346.1| 345 ALLTFINEQCNASRAAKRLHTHRNTFLRRLESAQRLLPRPLDHTSVHVAVA 395
                                    699***************************************887555544 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.3e-05      0.08       7      45 ..     347     385 ..     343     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-S CS
                          HTH_1   7 fvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpL 45 
                                    +  + e+ + +rAA++L++   +  r++ +  ++l  pL
  gi|121637123|ref|YP_977346.1| 347 LTFINEQCNASRAAKRLHTHRNTFLRRLESAQRLLPRPL 385
                                    55678999*************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2935.52
//
Query:       gi|121637124|ref|YP_977347.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-31  108.5  23.3      2e-31  108.2  23.3    1.1  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2  23.3   1.1e-35     2e-31       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 1.1e-35
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++ Pe+laaaa+ l++ig++  a naaaaaptt+v+++aaDeVSa +Aa+f+aha+ yq++sa+aaa h+qfv++la+
  gi|121637124|ref|YP_977347.1|  1 MSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAAHAAMYQSVSARAAAIHDQFVATLAS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a+sYaa+E a
  gi|121637124|ref|YP_977347.1| 83 SASSYAATEVA 93
                                   *********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 723.81
//
Query:       gi|121637125|ref|YP_977348.1|  [L=390]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-59  198.9  29.4    7.2e-59  198.4  23.2    2.5  2  PPE       PPE family
    1.3e-17   64.5  15.4    1.3e-17   64.5  15.4    5.0  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
       0.16   11.2   0.0       0.32   10.3   0.0    1.4  1  DegV      Uncharacterised protein, DegV family COG1307


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4  23.2   1.2e-62   7.2e-59       1     157 [.       6     162 ..       6     163 .. 0.99
   2 ?    3.6   0.4     0.011        63      41      90 ..     238     287 ..     221     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 1.2e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+nsa++yaGpgs++l+aAa+ Wd++a++l saa++++sv+ +l+ ++W G+s+  m+aaa py+aW+s +a qae
  gi|121637125|ref|YP_977348.1|   6 ALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGSWIGSSAGLMVAAASPYVAWMSVTAGQAE 85 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     +Aaq+++aaaaYe+A+  +vpp++ia+nrael+ l+atn++GqntpaIa++eaey emwaqdaaam +Y+aa+a+a
  gi|121637125|ref|YP_977348.1|  86 LTAAQVRVAAAAYETAYGLTVPPPVIAENRAELMILTATNLLGQNTPAIAVNEAEYGEMWAQDAAAMFGYAAATATA 162
                                    **************************************************************************987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.011
                                    HHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  41 lesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaeeaAaqaeaaa 90 
                                    l+++++ l++     +s  +ma+    +l+  + aaaqa e+Aaq  + a
  gi|121637125|ref|YP_977348.1| 238 LSNIVSMLNNHVSMTNSGVSMASTLSSMLKGFAPAAAQAVETAAQNGVRA 287
                                    56667777777777889999************************987766 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.0   9.4         3   1.8e+04      25      48 ..      78     101 ..      17     125 .. 0.63
   2 ?   -4.0   8.1         3   1.8e+04      23      62 ..     157     196 ..     122     214 .. 0.59
   3 ?    2.7   0.9      0.04   2.4e+02      43      73 ..     260     286 ..     226     303 .. 0.47
   4 !   64.5  15.4   2.1e-21   1.3e-17       1      79 [.     305     385 ..     305     386 .. 0.89

  Alignments for each domain:
  == domain 1  score: -6.0 bits;  conditional E-value: 3
                       PE_PPE_C  25 aasaaaaalsgttaaaaaaaagaa 48 
                                    +++a  a l+++++  aaaa ++a
  gi|121637125|ref|YP_977348.1|  78 SVTAGQAELTAAQVRVAAAAYETA 101
                                    223333333333343444443333 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                       PE_PPE_C  23 apaasaaaaalsgttaaaaaaaagaalg.gmPlaaagagga 62 
                                    a++a+a+a+ l+  +a+ +++a g +   ++++  a+ ++a
  gi|121637125|ref|YP_977348.1| 157 AATATATATLLPFEEAPEMTSAGGLL-EqAVAVEEASDTAA 196
                                    23333333333333333333333322.23555555544444 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.04
                       PE_PPE_C  43 aaagaalggmPlaaagaggaaggaaprygfr 73 
                                    ++ +++l g + aaa+a  +a+ ++     r
  gi|121637125|ref|YP_977348.1| 260 STLSSMLKGFAPAAAQAVETAAQNGV----R 286
                                    22222223444444444444222222....2 PP

  == domain 4  score: 64.5 bits;  conditional E-value: 2.1e-21
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaa.aaaaaagaalggmPlaaagagga.aggaaprygfrptvmp 78 
                                    +A lG+Aa+vG+LSVPp+Waaa++a+++aa+al+ t  + aa+ ++g++lgg+P++++ga+++ + ++++r+ +rp vmp
  gi|121637125|ref|YP_977348.1| 305 AANLGRAASVGSLSVPPAWAAANQAVTPAARALPLTSLTsAAERGPGQMLGGLPVGQMGARAGgGLSGVLRVPPRPYVMP 384
                                    69*******************************887765155667888999********999966789************ PP

                       PE_PPE_C  79 r 79 
                                    +
  gi|121637125|ref|YP_977348.1| 385 H 385
                                    7 PP

>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.3e-05      0.32     122     168 ..     183     229 ..     177     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTEEEEEEES-THHHHH CS
                           DegV 122 glgllvleaarlakqGksfeeilkkleeikektklyfvvddLdyLvk 168
                                    +++++v+ea + a++++ ++ + ++l+++++ tk++  +d+L  L+k
  gi|121637125|ref|YP_977348.1| 183 EQAVAVEEASDTAAANQLMNNVPQALQQLAQPTKSIWPFDQLSELWK 229
                                    7899*****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2951.75
//
Query:       gi|121637126|ref|YP_977349.1|  [L=98]
Description: ESAT-6 like protein 3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.0   3.4    1.7e-19   69.8   3.4    1.0  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   3.4   9.4e-24   1.7e-19       2      86 .]       5      90 ..       4      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 9.4e-24
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82
                                   +++dp ++r++a rf  +a+++ede +r+ a+ +++ ++gWsG a  +  +++++++qa++++v++L+++++ l + an++e
  gi|121637126|ref|YP_977349.1|  5 FMTDPHAMRDMAGRFEVHAQTVEDEARRMWASAQNIsGAGWSGMAEATSLDTMAQMNQAFRNIVNMLHGVRDGLVRDANNYE 86
                                   689******************************************************************************* PP

                                   HHHC CS
                         WXG100 83 daDe 86
                                   ++++
  gi|121637126|ref|YP_977349.1| 87 QQEQ 90
                                   **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 624.80
//
Query:       gi|121637127|ref|YP_977350.1|  [L=94]
Description: ESAT-6 like protein 4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-13   48.6   1.5    8.2e-13   48.4   1.5    1.0  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   1.5   4.6e-17   8.2e-13       2      86 .]       3      87 ..       2      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 4.6e-17
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83
                                   i++++ +++++ a +++qa+ le+e+q++ ++v   ++ W Ga + a+q++++++ +++q ++++ + +++++++a+n++++
  gi|121637127|ref|YP_977350.1|  3 INYQFGDVDDHGAMIRAQAGLLEAEHQAIIRDVLTASDFWGGAGSAACQGFITQLGRNFQVIYEQANAHGQKVQAAGNNMAQ 84
                                   89******************************************************************************** PP

                                   HHC CS
                         WXG100 84 aDe 86
                                   +D+
  gi|121637127|ref|YP_977350.1| 85 TDS 87
                                   *95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 667.83
//
Query:       gi|121637128|ref|YP_977351.1|  [L=415]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-154  514.6   0.0   1.6e-154  514.4   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      2e-05   24.9   0.0    5.2e-05   23.6   0.0    1.7  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.4   0.0  1.8e-158  1.6e-154       1     380 [.       1     379 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 514.4 bits;  conditional E-value: 1.8e-158
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l+++e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121637128|ref|YP_977351.1|   1 MTSSH-LIDTEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.89999********************************************************************* PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121637128|ref|YP_977351.1|  80 PKLRQGSYFPgWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **************************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121637128|ref|YP_977351.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    v+ai+a++p+aa+QrCr+H+++nl+a++pk ++ +v++ l+siy+++dae+++++++++l++l++k+p+vae+ld+a++d
  gi|121637128|ref|YP_977351.1| 239 VAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTD 318
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    +laf+afp+qi+r+i+s+N++ErLN+e+rRrt+vvgiFP+++si+rlvgavlae+hdew+e
  gi|121637128|ref|YP_977351.1| 319 LLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIE 379
                                    ***********************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.8e-09   5.2e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.8e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121637128|ref|YP_977351.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3019.81
//
Query:       gi|121637129|ref|YP_977352.1|  [L=425]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-34  118.5  25.2    5.7e-31  107.9  25.2    2.0  1  Sugar_tr  Sugar (and other) transporter
    1.6e-24   86.5  43.0    1.6e-24   86.5  43.0    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        3.9    7.1  11.3         11    5.7   3.8    2.8  2  DUF21     Cyclin M transmembrane N-terminal domain


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9  25.2   9.5e-35   5.7e-31       2     445 ..       5     422 ..       4     424 .. 0.81

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 9.5e-35
                                    HHHHHHHHHHHHHHHHCGGGTHHHHH.HHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHH CS
                       Sugar_tr   2 alvaalggllfgYdtgvigafltllk.faknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksll 80 
                                    al   +g+ ++ Yd+ ++g++++l   ++++ +l+ ++++ +     s  +++++++ + +G+ ++g++gdr+GRkk+l+
  gi|121637129|ref|YP_977352.1|   5 ALACLVGSAIEFYDFLIYGTAAALVFpTVFFPHLDPTVAAVA-----SMGTFAVAFLSRPFGAAVFGYFGDRLGRKKTLV 79 
                                    55566788***********98887651455555666666555.....588999999**********************99 PP

                                    HHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  81 iaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaa 155
                                    ++ +++  ++v  ++ + +      +  +l+++R+l G++vG++ + + ++ +E+Ap+++Rg  ++++ ++  +  ++++
  gi|121637129|ref|YP_977352.1|  80 ATLLIMGLATVTVGLVPTTvaigaAAPLILTTMRLLQGFAVGGEWAGSALLSAEYAPASKRGWYGMFTVVGGGIALVLTS 159
                                    9999888777777777766666669999999************************************************* PP

                                    HHHHHHHTSS-.......TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHH CS
                       Sugar_tr 156 ifglglnktsn.......adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeek 228
                                     + lg+n+t +       ++gwri++ +++++  + l++++ ++E+P +  e+                 d++ +l    
  gi|121637129|ref|YP_977352.1| 160 LTFLGVNYTIGessptfmQWGWRIPFLVSAALIAVALYVRFNIDETPVFARERA----------------DEKTRLGPAE 223
                                    ******988888********************99*************9977666................2223333333 PP

                                    HHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHH CS
                       Sugar_tr 229 dsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfv 306
                                    + + +            l++  +r+ ++++++ +++ +   + a +y++++    lg+s    l  +++ g + +v+t  
  gi|121637129|ref|YP_977352.1| 224 TPIAQV-----------LRR--QRREIVLAAGSAVCCFGFVYLASTYLASYAQTRLGYSRGsiLFDSVLGGLLCIVFTAL 290
                                    333333...........333..366788888888888888889*****************99777788888999****** PP

                                    HHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHH CS
                       Sugar_tr 307 aiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRsk 386
                                    +  l d++GRR++ll G a+++   +++   + l+ ++s     ++ v+++ + a+ ++g+gp+  ++ +Elf +s R++
  gi|121637129|ref|YP_977352.1| 291 SSALCDQLGRRRVLLAGWAVALPWSLLV---MPLIDSGS---PSLFAVAVVGMYAIGGFGFGPTASFI-PELFATSYRYT 363
                                    ********************99888888...45555665...789999999999***********887.*********** PP

                                    HHHHHHHHHHHHHH.HHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--C CS
                       Sugar_tr 387 alaiavavnwlanf.lisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtl 445
                                    ++a+a+++  +a   l  ++   ++ ++g + ++++ a+la++  +++   +pet+g+ l
  gi|121637129|ref|YP_977352.1| 364 GSALAANLAGVAGGaLPPVIAGALVATYGSWAIGVMLAILALI-SLVCTYRLPETAGSAL 422
                                    *****98665554303344444455555555555555555444.45555679***99876 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5  43.0   2.6e-28   1.6e-24      26     346 ..      37     373 ..       9     380 .. 0.70
   2 !    4.3   7.4    0.0027        16     128     175 ..     371     415 ..     368     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.6e-28
                          MFS_1  26 dlgispseigl..lltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllf..a....sslw.lllvlrvlq 95 
                                    +l  +++++     +++ +l   +++ ++G+++dr+Gr+++l+++ll+++l+ ++++l+  +    +  + +l  +r+lq
  gi|121637129|ref|YP_977352.1|  37 HLDPTVAAVASmgTFAVAFLSRPFGAAVFGYFGDRLGRKKTLVATLLIMGLAtVTVGLVptTvaigAAAPlILTTMRLLQ 116
                                    33444444444233555777779*****************************66666644414567667879******** PP

                          MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg................Wravfyilai 159
                                    G++ g+ ++++a l a+++p ++rg    ++++++ +G  ++ +l +l    lg                Wr +f++ a+
  gi|121637129|ref|YP_977352.1| 117 GFAVGGEWAGSALLSAEYAPASKRG----WYGMFTVVGGGIALVLTSLTF--LGvnytigessptfmqwgWRIPFLVSAA 190
                                    *********************9996....666666666666666666333..222233557788888888********** PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeee.kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevl 238
                                    + ++a  l + +  +e p  +r++  e+   g++++p++++++  ++  vl  +  ++++ f ++++++t+l +y+q++l
  gi|121637129|ref|YP_977352.1| 191 LIAVA--LYVRFNIDETPVFARERADEKTrLGPAETPIAQVLRRQRREIVL--AAGSAVCCFGFVYLASTYLASYAQTRL 266
                                    ****9..43344444444444444433324777777777766666666666..55555555558888************* PP

                          MFS_1 239 gls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll....vlvliGfg 313
                                    g+s g  ++++ + l++l+++++  l+++l d lgrrr ll + +++l ++l++++l  + s++l+++    ++++ Gfg
  gi|121637129|ref|YP_977352.1| 267 GYSrG--SILFDSVLGGLLCIVFTALSSALCDQLGRRRVLLAGWAVALPWSLLVMPLIDSGSPSLFAVavvgMYAIGGFG 344
                                    ***63..6666677888888888*************************************88888888555444445556 PP

                          MFS_1 314 lgfvfpsllalasdlappeeagtasglfntags 346
                                    +g + + +  l + ++  +++g+a++++    +
  gi|121637129|ref|YP_977352.1| 345 FGPTASFIPELFATSY--RYTGSALAANLA--G 373
                                    6666666666666666..666666555443..3 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0027
                          MFS_1 128 agfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpee 175
                                    ++  +G +l p+++g+l+ ++++W a+ ++lai++l+++v+    ++ +
  gi|121637129|ref|YP_977352.1| 371 LAGVAGGALPPVIAGALVaTYGSW-AIGVMLAILALISLVC---TYRLP 415
                                    5677899999********555556.8999999999999985...44444 PP

>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.8    0.0018        11      64     127 ..      50     118 ..      40     120 .. 0.74
   2 ?    4.9   0.9    0.0031        19      58     107 ..     367     417 ..     349     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0018
                          DUF21  64 nillsalatalfvellae..............galavviatvivtllilvfgEilPkslalkyaekialalapplrvl 127
                                    +++ + l                         g+   ++at+++  l  v   ++P ++a+  a ++ l ++++l+ +
  gi|121637129|ref|YP_977352.1|  50 TFAVAFLS---------RpfgaavfgyfgdrlGRKKTLVATLLIMGLATVTVGLVPTTVAIGAAAPLILTTMRLLQGF 118
                                    22333333.........23444555569999988899******************************99999999877 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0031
                          DUF21  58 igntlvnillsalatalfvellae.galavviatvivtllilvfgEilPks 107
                                    ++ +l+ ++ +al  ++++ l+a+ g++a+ + ++i+ l+ lv++  lP +
  gi|121637129|ref|YP_977352.1| 367 LAANLAGVAGGALPPVIAGALVATyGSWAIGVMLAILALISLVCTYRLPET 417
                                    677999999999999999999999999****************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2630.48
//
Query:       gi|121637130|ref|YP_977353.1|  [L=317]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-20   73.1   0.1    2.8e-20   72.1   0.1    1.6  1  THDPS_M    Tetrahydrodipicolinate N-succinyltransferase middl
    2.6e-16   59.1  11.4    1.2e-15   56.9   2.3    2.8  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase
    0.00013   21.6   6.3     0.0095   15.6   0.1    3.2  3  Hexapep    Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> THDPS_M  Tetrahydrodipicolinate N-succinyltransferase middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.1   4.6e-24   2.8e-20       1      41 []     111     150 ..     111     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.6e-24
                                    S--EEEETTEEE-HHHHHHHHHHHHHTT------EEESS-B CS
                        THDPS_M   1 LpNVaWTnygPvavedfeerrlrlraagrsvtVlsVDKFPR 41 
                                    L+NV+WTn+gP+a+++fe++r+rlr++g +vtV++VDKFPR
  gi|121637130|ref|YP_977353.1| 111 LTNVVWTNHGPCAIDGFEAVRARLRRRG-PVTVYGVDKFPR 150
                                    9***************************.***********9 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   1.8    0.0011       6.8      16      32 ..     202     220 ..     192     221 .. 0.76
   2 !   56.9   2.3   2.1e-19   1.2e-15       2      34 .]     232     264 ..     231     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                                    E..SEEE-TT-EE-TT-EE CS
                      Hexapep_2  16 i..GvslGdncvvgaGvvi 32 
                                    i  Gv +Gd++ vg G  i
  gi|121637130|ref|YP_977353.1| 202 IsaGVVVGDGSDVGGGASI 220
                                    5669**********99876 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 2.1e-19
                                    EEE-TT-EE-TT-EESEEE-TT-EE-TT-EE-S CS
                      Hexapep_2   2 viIGdnCliGanagiGvslGdncvvgaGvvita 34 
                                    ++IG++Cl+Gan+g G+slGd+cvv+aG+++ta
  gi|121637130|ref|YP_977353.1| 232 ISIGKRCLLGANSGLGISLGDDCVVEAGLYVTA 264
                                    79******************************7 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.4   2.4e+03      13      22 ..     171     180 ..     159     182 .. 0.68
   2 !    7.0   1.4   0.00082       4.9      16      34 ..     202     220 ..     201     222 .. 0.85
   3 !   15.6   0.1   1.6e-06    0.0095       3      35 ..     233     263 ..     232     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.4
                                    TEEEETTEEE CS
                        Hexapep  13 faviggnVkI 22 
                                    +a++++++++
  gi|121637130|ref|YP_977353.1| 171 GAHLAPGTTV 180
                                    5666666665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00082
                                    EETTEEE-TTEEEETTEEE CS
                        Hexapep  16 iggnVkIGdnvkIgagvvi 34 
                                    i ++V++Gd++ +g g+ i
  gi|121637130|ref|YP_977353.1| 202 ISAGVVVGDGSDVGGGASI 220
                                    56899*********99977 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.6e-06
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                     IG+ +l+g+++ +  ++ +Gd+++++ag +++
  gi|121637130|ref|YP_977353.1| 233 SIGKRCLLGANSGL--GISLGDDCVVEAGLYVT 263
                                    6*************..************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2439.61
//
Query:       gi|121637131|ref|YP_977354.1|  [L=354]
Description: succinyl-diaminopimelate desuccinylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-20   73.6   0.2    2.4e-20   73.1   0.2    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
      4e-11   42.8   0.0    1.6e-10   40.9   0.0    2.0  1  M20_dimer      Peptidase dimerisation domain
    8.5e-09   35.4   0.0    4.9e-07   29.6   0.0    2.1  2  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
       0.02   15.1   0.0       0.31   11.3   0.0    2.4  2  Cyclase        Putative cyclase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.2   5.4e-24   2.4e-20       1     205 [.      65     352 ..      65     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 5.4e-24
                                    EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHH CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGak 79 
                                    ll++HlD+Vp +++      p  ++ e++ l+G+Ga+dmk g + +l+++++l++      ++++l+f   EE+   +a+
  gi|121637131|ref|YP_977354.1|  65 LLAGHLDTVPvAGNL-----P--SRRENDQLHGCGAADMKSGDAVFLHLAATLAEP----THDLTLVFYDCEEID--SAA 131
                                    699*******77777.....4..445699***********************9999....79***********94..454 PP

                                    HHHHHHHTTTCESEEE..EEEEESSSBTCHSTETEEEE.......................................... CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.......................................... RF
                  Peptidase_M20  80 allegleerekvdavf..elhieepgileagklaigvv.......................................... 115
                                    + l+ ++ re +d++    ++++ep+      + +g                                            
  gi|121637131|ref|YP_977354.1| 132 NGLGRIQ-RELPDWLSadVAILGEPTAGC---IEAGCQgtlrvvlsvtgtrahsarswlgdnaihklgavldrlavyrar 207
                                    4444333.344444332224466666555...333444667777888899****************************** PP

                                    ...........................................................EEEEEEEEEESHEEEC.CHHH CS
                                    ...........................................................xxxxxxxxxxxxxxxx.xxxx RF
                  Peptidase_M20 116 ...........................................................kvevelleggapvtln.dspl 135
                                                                                               +v++e+  ++a +    ++p 
  gi|121637131|ref|YP_977354.1| 208 svdidgctyreglsavrvaggvagnvipdaasvtinyrfapdrsvaaalqhvhdvfdglDVQIEQTDAAAGALPGlSEPA 287
                                    *********************************************************99888886655555554477999 PP

                                    HHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 136 vkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgikvlarll 205
                                    +kal eaa  +    v   ++  g+td + f  +gip+v  +gpg+  laH  +E+v + ++ +++++l r+l
  gi|121637131|ref|YP_977354.1| 288 AKALVEAAGGQ----V--RAKY-GWTDVSRFaaLGIPAV-NYGPGDpNLAHCRDERVPVGNITAAVDLLRRYL 352
                                    99999997553....2..2344.9999999988888988.69999889*********************9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   3.5e-14   1.6e-10       5     101 ..     166     263 ..     163     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.5e-14
                                    EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......TCCTCCCCCEECCE-CCCCEESSEEEEEEEEE CS
                      M20_dimer   5 GlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.eerslprttlnvtgiegGsaknvipdeaeakidiR 83 
                                    G + + ++v+g+ +Hs+    g+NAi+kl  +l++l   + +    +  + r+ l+   + gG a nvipd a+++i+ R
  gi|121637131|ref|YP_977354.1| 166 GTLRVVLSVTGTRAHSARSWLGDNAIHKLGAVLDRLAVYRARSVdIDGCTYREGLSAVRVAGGVAGNVIPDAASVTINYR 245
                                    67788899******************************987755544555677788899999****************** PP

                                    HHHHHHHHHHHHHHHHHH CS
                      M20_dimer  84 llpgedpeevleeieeil 101
                                    + p  +++++l+ + +++
  gi|121637131|ref|YP_977354.1| 246 FAPDRSVAAALQHVHDVF 263
                                    ********9999998876 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.1e-10   4.9e-07       2      73 ..      52     127 ..      51     157 .. 0.88
   2 ?    3.6   0.0      0.01        46     132     167 ..     289     324 ..     260     340 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-10
                                    EEEEESTTCESEEEEEEEE--B-TTT.......TCC...T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSC CS
                  Peptidase_M28   2 viatlegkatdevlllgAHyDsvgvg.......rgp...ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaE 71 
                                    v+a+++ +  + ++ll++H+D+v+v+       + +      GA D  sg a+ L la +la+    p++++ ++f+d+E
  gi|121637131|ref|YP_977354.1|  52 VLARTKLNR-SSRVLLAGHLDTVPVAgnlpsrrE-NdqlHGCGAADMKSGDAVFLHLAATLAE----PTHDLTLVFYDCE 125
                                    667777777.889************999999862.2456677********************6....9************ PP

                                    SG CS
                  Peptidase_M28  72 Ea 73 
                                    E 
  gi|121637131|ref|YP_977354.1| 126 EI 127
                                    *5 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.01
                                    -TTSC.CEEEEESSTT-STTHHHHTTT--EEEECTSS CS
                  Peptidase_M28 132 raaae.dpfdersgrgrsDhspflkagvpvldlaetg 167
                                    +a  e    + r  +g +D s f++ g+p++++   g
  gi|121637131|ref|YP_977354.1| 289 KALVEaAGGQVRAKYGWTDVSRFAALGIPAVNY-GPG 324
                                    33333245566778889*************998.444 PP

>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.31      50      99 ..      12      61 ..       3     116 .. 0.79
   2 ?    1.3   0.0     0.081   3.6e+02     108     122 ..     273     294 ..     175     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
                        Cyclase 50 pavvldvsakaaaedyeiitaedleaalakqg...veikpgdivlirTgwskr 99
                                    a+++d+ +++ +++ +i  a+++eaal++q      i++g++vl rT  ++ 
  gi|121637131|ref|YP_977354.1| 12 TAALIDIPSES-RKEARI--ADEVEAALRAQAsgfEIIRNGNAVLARTKLNRS 61
                                   689****6653.234545..999****999984444499*********88765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.081
                        Cyclase 108 n.......pglseeaaewlaek 122
                                            pglse aa+ l+e 
  gi|121637131|ref|YP_977354.1| 273 TdaaagalPGLSEPAAKALVEA 294
                                    033333459********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2445.88
//
Query:       gi|121637132|ref|YP_977355.1|  [L=194]
Description: hypothetical protein BCG_1263c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          3    8.6  26.9      0.092   13.4  11.6    3.7  4  TPR_16    Tetratricopeptide repeat
        5.6    8.1  26.1        5.3    8.1   0.3    4.4  4  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.056     5e+02       3      24 ..       3      24 ..       1      33 [. 0.75
   2 ?   13.4  11.6     1e-05     0.092       3      64 ..      42     105 ..      40     112 .. 0.91
   3 ?    1.4   0.5     0.057   5.1e+02       4      27 ..     102     125 ..     101     129 .. 0.86
   4 ?    0.9   3.3     0.081   7.3e+02      32      66 ..     156     192 ..     146     194 .] 0.68

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.056
                         TPR_16  3 laraalragdyddAaaaleaal 24
                                   la+ ++  g++ +Aa +le a 
  gi|121637132|ref|YP_977355.1|  3 LAYVLITKGEFGAAASMLEPAA 24
                                   6777777788888888777665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1e-05
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                    la+a +++g+ ++ a+ l++a +r++  ++  a+e  l++++ +++++++++A+a+ r+a+r a
  gi|121637132|ref|YP_977355.1|  42 LATAIAQQGHIAESAKTLQRAEARHGTKSAlfAPELGLARAWTRAAAQDMTGAIAAAREAARTA 105
                                    677889*********************999999999999999999***************9765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.057
                         TPR_16   4 araalragdyddAaaaleaalkrd 27 
                                    ar a rag+ + A+ a++ a++++
  gi|121637132|ref|YP_977355.1| 102 ARTAERAGQAAVALCAWHNAVRLG 125
                                    889999999999999999999876 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.081
                         TPR_16  32 daaeAllllgdaalrq..grlaeAaalyraalraapd 66 
                                    ++ +A+ l ++a   +  g  a+Aa++ +aa+r +p+
  gi|121637132|ref|YP_977355.1| 156 ADGDAAELTAVAEELAgiGMAAAAADATKAAARLGPQ 192
                                    5666777777777666555566677888888899887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0018        16       6      30 ..       2      26 ..       1      31 [. 0.89
   2 ?    8.1   0.3   0.00059       5.3       4      32 ..      39      67 ..      36      78 .. 0.81
   3 ?    4.2   6.8     0.011        95       2      41 ..      76     115 ..      75     118 .. 0.82
   4 ?    1.2   1.9       0.1   9.2e+02       8      34 ..     167     193 ..     158     194 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                         TPR_14  6 alaeallalGdpdeAiallrralal 30
                                   +la +l + G++ +A+ +l+ a a+
  gi|121637132|ref|YP_977355.1|  2 LLAYVLITKGEFGAAASMLEPAAAT 26
                                   69******************99775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00059
                         TPR_14  4 llalaeallalGdpdeAiallrralalaP 32
                                   l++la a +++G  +e+++ l+ra a++ 
  gi|121637132|ref|YP_977355.1| 39 LMLLATAIAQQGHIAESAKTLQRAEARHG 67
                                   567889999***************99875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.011
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                    e+ la+a+  +a++d  +Aia++r+a ++a    +a  +l
  gi|121637132|ref|YP_977355.1|  76 ELGLARAWTRAAAQDMTGAIAAAREAARTAERAGQAAVAL 115
                                    677899999*****************99887766555554 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.1
                         TPR_14   8 aeallalGdpdeAiallrralalaPdd 34 
                                    ae l+  G  ++A+++ ++a +l+P++
  gi|121637132|ref|YP_977355.1| 167 AEELAGIGMAAAAADATKAAARLGPQQ 193
                                    555566689999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1350.09
//
Query:       gi|121637133|ref|YP_977356.1|  [L=562]
Description: hypothetical protein BCG_1264c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-06   27.2   1.9     0.0026   18.2   0.0    4.0  5  AAA_16        AAA ATPase domain
    4.1e-05   23.9   0.0    0.00014   22.1   0.0    1.9  1  AAA_22        AAA domain
     0.0022   17.9   0.0     0.0047   16.9   0.0    1.5  1  NACHT         NACHT domain
      0.008   16.2   0.1      0.062   13.3   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0087   16.5   0.0      0.017   15.6   0.0    1.5  1  AAA           ATPase family associated with various cellular 
     0.0091   15.7   0.1      0.026   14.2   0.1    1.8  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.049   12.8   0.0       0.16   11.1   0.0    1.8  2  NB-ARC        NB-ARC domain
       0.12   11.7   6.2        1.2    8.5   0.7    2.3  2  DUF2014       Domain of unknown function (DUF2014)
       0.39   10.6   2.7       0.78    9.6   0.2    3.0  3  Tnp_DNA_bind  Transposase DNA-binding


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.3e-06    0.0026      19      69 ..      11      64 ..       2      75 .. 0.65
   2 !   16.6   0.5     4e-06    0.0079     115     164 ..      79     128 ..      65     135 .. 0.78
   3 ?   -1.9   0.0       1.9   3.7e+03      86     122 ..     137     173 ..     127     188 .. 0.59
   4 ?   -2.0   2.2       2.1   4.2e+03      73      89 ..     308     326 ..     236     389 .. 0.54
   5 ?   -2.9   0.0         4     8e+03       2      24 ..     394     416 ..     393     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd.....ggiflrgkcdql...esaipy 69
                                   v s++ + v+l+G+ GvGK+ l++ +++++  +     +     ++++     ++aip+
  gi|121637133|ref|YP_977356.1| 11 VDSPDRCGVVLVGPHGVGKTLLAQLAAEQVMSEdgrsgR-----ARWVVGtapGRAIPF 64
                                   44566699*******************988877444442.....333333222334555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4e-06
                         AAA_16 115 easrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrlles 164
                                    +  r ++ll+++ + l+ d+  l+lv+Dd++ +d+ s++l ++L+r++ +
  gi|121637133|ref|YP_977356.1|  79 DIGRPAALLRAARSSLTGDAGDLLLVVDDAHNLDPLSATLVYQLARAGAA 128
                                    4467777777777666666777************************9876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                         AAA_16  86 ldeaesaeleawrekleealaavpelagaea.srllel 122
                                    ++e+ +a ++ w++ l++++a + +l++a+    +  +
  gi|121637133|ref|YP_977356.1| 137 EAEPPDAIAALWSDDLLTRVA-IEPLDRAQTaAFVESA 173
                                    445666688889999999988.4444444441333333 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.1
                         AAA_16  73 aqalareellrqllde...a 89 
                                    a al r +l++ql+ +   +
  gi|121637133|ref|YP_977356.1| 308 AHAL-RVSLVAQLAKHpsdH 326
                                    3444.445555555552221 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 4
                         AAA_16   2 lvGReeeleqLlsalervrsgrp 24 
                                    + GR++e +++l+a++++   ++
  gi|121637133|ref|YP_977356.1| 394 WQGRGREADAVLAAVNPAELTET 416
                                    679********999998766555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     7e-08   0.00014       8     112 ..      19     122 ..      14     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7e-08
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                    +v++G+ G+GKT+l++  +eq   e    +    r++ v  t+p+   +   +r+l +   ++++   ++  +ll+a + 
  gi|121637133|ref|YP_977356.1|  19 VVLVGPHGVGKTLLAQLAAEQVMSE----DgrsGRARWVVGTAPGRAIPFGAFRHLISLPASGADI--GRPAALLRAARS 92 
                                    589******************8543....2334688888888888886666666666666666666..899999999999 PP

                         AAA_22  85 alraravielliiDEaqhlr..seealeeL 112
                                     l   a   ll++D+a++l+  s++++ +L
  gi|121637133|ref|YP_977356.1|  93 SLTGDAGDLLLVVDDAHNLDplSATLVYQL 122
                                    99888888***********87666666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0047       3     162 ..      19     173 ..      18     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCC..CCTS--SSS-CCHHHHCCSC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfs..qlpepaapvsevwavllelp 80 
                                    v+l G+ G+GKT L+q  a++  +++  +g+ + v     ++    g++r+l+ l +s  +   paa  +  ++ l+  +
  gi|121637133|ref|YP_977356.1|  19 VVLVGPHGVGKTLLAQLAAEQVMSEDGRSGRARWVVGTAPGRAIPFGAFRHLISLPASgaDIGRPAALLRAARSSLTGDA 98 
                                    799***************************99999999999999999999999998763367789999999********* PP

                                    CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH..HCTTSSCE....EEEE--TCCHHH CS
                          NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd..leeqleea..ivlevegfsesrrk 156
                                      lLl++D++  l   l++       tl  +l r+     a+l++tv ++a +   ++ + ++   +++++e++ + +++
  gi|121637133|ref|YP_977356.1|  99 GDLLLVVDDAHNLDP-LSA-------TLVYQLARA---GAARLVVTVASEAEPPdaIAALWSDDllTRVAIEPLDRAQTA 167
                                    *************98.666.......688888888...9999*******9998777777777769999************ PP

                                    HHHHHC CS
                          NACHT 157 qlvrky 162
                                    ++v+  
  gi|121637133|ref|YP_977356.1| 168 AFVESA 173
                                    999865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.1e-05     0.062       1      22 [.      18      39 ..      18      52 .. 0.88
   2 ?   -0.5   0.0      0.57   1.1e+03      37      79 ..     323     370 ..     299     377 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                   EEEEE--SSSSHHHHHHHGGGG CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaa 22
                                   +v+LvGp G+gK+ la+  a+ 
  gi|121637133|ref|YP_977356.1| 18 GVVLVGPHGVGKTLLAQLAAEQ 39
                                   599**************99986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                                    -HHHHH--B--.............--------.G-SEEEEESGGG--H CS
                          AAA_5  37 teedlkgrreik....ngttslvdsplvraar.egeilvlDEveraes 79 
                                    +++++  +++++    +  +s ++ ++++aa+  g+ l+l++v  ae+
  gi|121637133|ref|YP_977356.1| 323 PSDHVSDQLRLSslaiDVPASATPAAVTDAATaAGQALRLGDVRLAER 370
                                    445555555555555588889999999999999999999999987765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.3e-06     0.017       1      22 [.      19      40 ..      19     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.3e-06
                                   EEEESSTTSSHHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel 22
                                   v+l+Gp G+GKTlla+  a+++
  gi|121637133|ref|YP_977356.1| 19 VVLVGPHGVGKTLLAQLAAEQV 40
                                   689**************99986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.3e-05     0.026      10     121 ..       7     132 ..       4     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                         AAA_30  10 vealltsgdrv.avltGpAGtGKttalkalreaweaa.g.....grviglAptgkaAkv.Lae.....elgieastiakl 76 
                                    vea++ s+dr+ +vl+Gp G GKt + + ++e + ++ g     + v+g Ap  +      ++     ++g++  + a l
  gi|121637133|ref|YP_977356.1|   7 VEAAVDSPDRCgVVLVGPHGVGKTLLAQLAAEQVMSEdGrsgraRWVVGTAPGRAIPFGaFRHlislpASGADIGRPAAL 86 
                                    677777877763679*************998877777579999999******9887554234333333445555555666 PP

                         AAA_30  77 lkrlkgrarlepg.tllivDEagmvdtkqlaallkaaekagakvil 121
                                    l++ ++  + ++g  ll+vD a  +d  +++ + + a++  a++++
  gi|121637133|ref|YP_977356.1|  87 LRAARSSLTGDAGdLLLVVDDAHNLDPLSATLVYQLARAGAARLVV 132
                                    6666644555667578899999999999999999988887677765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     8e-05      0.16       8      58 ..       3      54 ..       1      71 [. 0.83
   2 ?   -1.9   0.0      0.78   1.5e+03     175     229 ..     450     508 ..     433     519 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8e-05
                                   HHHHHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEE CS
                         NB-ARC  8 viekLle.kdelqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvv 58
                                   v+++     d++++  v lvG  GvGKt la+ + ++  + +gr  +  wvv
  gi|121637133|ref|YP_977356.1|  3 VWKHVEAaVDSPDRCGVVLVGPHGVGKTLLAQLAAEQVMSEDGRSGRARWVV 54
                                   5666555467889999****************99999777777777777775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.78
                                    -GGCHH...CHHHHHHHHHHCTT-HHHHHHHHHHHC-T...CSCCHHHHHHHHHHCTGC CS
                         NB-ARC 175 kkleekes.leevakeivekckGlPlalkvlggllstk...ktveewkkvlekleskll 229
                                     +  + +s l ++a   + +++ lP a+ +  ++ls     ++   w+  +  l+s ++
  gi|121637133|ref|YP_977356.1| 450 VTEPTARStLDALAATFAMNSGNLPRAITLATEVLSGPaadDMAVAWAASAAALSSARM 508
                                    33333332499999999999999999999999998742223667777777776766665 PP

>> DUF2014  Domain of unknown function (DUF2014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7   0.00059       1.2     184     229 ..     139     181 ..     102     186 .. 0.82
   2 ?    5.9   0.6    0.0036       7.2     146     196 ..     419     469 ..     403     506 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00059
                                    -SHHHHHHHHHHHHHHHHHHHHH.......HS---CHHHHHHHHHS CS
                        DUF2014 184 spldavAaWyssqllqrvLlesLeeekeeeakkeveselelalkva 229
                                     p da+Aa +s +ll+rv +e L   +++++++ ves l+  l+va
  gi|121637133|ref|YP_977356.1| 139 EPPDAIAALWSDDLLTRVAIEPL---DRAQTAAFVESALDATLDVA 181
                                    588********************...77777888888888888887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                                    GGGXXXXXXXGG..GGGHHHH.HXXXXXXSGGGGGSS--SHHHHHHHHHHH CS
                        DUF2014 146 sddvvqraynLafnrpttenveeedegldsvveDvavrspldavAaWyssq 196
                                      + + ra n  +  +  e++++  ++  s v  +  rs lda+Aa ++ +
  gi|121637133|ref|YP_977356.1| 419 MAWAIPRAANRFWMLNEPERATAFLQTTRSRVTEPTARSTLDALAATFAMN 469
                                    566788999999999999999999999*******************99865 PP

>> Tnp_DNA_bind  Transposase DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.6   3.2e+03      22      34 ..     313     325 ..     312     330 .. 0.84
   2 ?    9.6   0.2   0.00039      0.78       8      41 ..     358     391 ..     341     396 .. 0.88
   3 ?   -3.4   0.1       4.5   9.1e+03      20      34 ..     475     489 ..     475     502 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                   Tnp_DNA_bind  22 vklaeslaekpga 34 
                                    v+l+ +la++p+ 
  gi|121637133|ref|YP_977356.1| 313 VSLVAQLAKHPSD 325
                                    68999*****986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00039
                   Tnp_DNA_bind   8 gsadLgDkRltkRlvklaeslaekpgasiPqacq 41 
                                    ++++LgD Rl +Rl++ a + +    a++P a  
  gi|121637133|ref|YP_977356.1| 358 QALRLGDVRLAERLARAALDRSDALAARLPLAYA 391
                                    6789**************9999999999998876 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.5
                   Tnp_DNA_bind  20 Rlvklaeslaekpga 34 
                                    R+++la++ ++ p a
  gi|121637133|ref|YP_977356.1| 475 RAITLATEVLSGPAA 489
                                    788888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3964.74
//
Query:       gi|121637134|ref|YP_977357.1|  [L=187]
Description: hypothetical protein BCG_1265 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-39  133.9   0.0    4.4e-39  133.6   0.0    1.1  1  Lysine_decarbox  Possible lysine decarboxylase
    8.1e-20   71.0   0.0    9.9e-20   70.7   0.0    1.1  1  LDcluster4       SLOG cluster4 family


Domain annotation for each model (and alignments):
>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   4.9e-43   4.4e-39       1     131 [.      54     183 ..      54     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 4.9e-43
                                    HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHHHHHTTS CS
                Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleElleiltliqlgk 80 
                                    m+ava++a  +gg ++G+ipk+l+ +e ++++++el+++++m+eRk+ + +++daf++lPGG+GTl+El++++t  +lg+
  gi|121637134|ref|YP_977357.1|  54 MGAVASAARACGGWTVGVIPKMLVYRELADHDADELIVTDTMWERKQIMEDRSDAFIVLPGGVGTLDELFDAWTDGYLGT 133
                                    9******************************************************************************* PP

                                    S-S.EEEEEEGGGCCHHHHHHHHHHHHTTSS-GGGGGCEEEESSHHHHHHH CS
                Lysine_decarbox  81 hqkvPiillnpkgyydkllefletlveegtisekareliivvddpeevlek 131
                                    h+k Pi++++p+g++d l ++l+ l+++g++s++a+e ++vvd+++++l++
  gi|121637134|ref|YP_977357.1| 134 HDK-PIVMVDPWGHFDGLRAWLNGLLDTGYVSPTAMERLVVVDNVKDALRA 183
                                    ***.*******************************************9986 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   1.1e-23   9.9e-20       4     120 ..      13     129 ..      10     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.1e-23
                     LDcluster4   4 igVmGsaeteakeealelaeelGrliAkegavlltGgrt.GvmeaaskGakeagGltvGilpassekehsnk.yvdiiiy 81 
                                    ++V  +a+  ++ e lela e+G +iA +g++l+ Gg + + m a++ +a+  gG tvG++p+    ++ ++   d +i+
  gi|121637134|ref|YP_977357.1|  13 VAVYCAASP-THAELLELAAEVGAAIAGRGWTLVWGGGHvSAMGAVASAARACGGWTVGVIPKMLVYRELADhDADELIV 91 
                                    677777774.56678**********************999***********************54444433325799*** PP

                     LDcluster4  82 TGlglagRnlilvlssdvviaiggrsGTlsEialaleeg 120
                                    T++  + R  i+   sd+ i+++g++GTl E+  a+++g
  gi|121637134|ref|YP_977357.1|  92 TDTMWE-RKQIMEDRSDAFIVLPGGVGTLDELFDAWTDG 129
                                    ****99.*************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1369.92
//
Query:       gi|121637135|ref|YP_977358.1|  [L=597]
Description: long-chain-acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-67  226.9   0.0    4.1e-67  226.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.2e-09   37.3   0.0    9.1e-09   36.2   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.6   0.0   4.6e-71   4.1e-67       1     422 [.      53     464 ..      53     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 4.6e-71
                                    HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                    ++++aa++ d+v+l +  ++q+lTYr+ ++ +nr+Aa+L ++Gv++gd+V+i+l+nsp  v+a+la++k Ga++ +ln +
  gi|121637135|ref|YP_977358.1|  53 FQDRAARYGDRVFLKF--GDQQLTYRDANATANRYAAVLAARGVGPGDVVGIMLRNSPSTVLAMLATVKCGAIAGMLNYH 130
                                    799***********99..9*********************99************************************** PP

                                    S-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTS CS
                    AMP-binding  81 ltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpdd 160
                                     + e la+ l   +akvli   +s+l+++++e+ a++ +v+  +++ +d  ++++++++++        p  +++++++d
  gi|121637135|ref|YP_977358.1| 131 QRGEVLAHSLGLLDAKVLI--AESDLVSAVAECGASRGRVAGDVLTVEDVERFATTAPATN--------PASASAVQAKD 200
                                    *******************..8888899999999998888777766665555554433333........3355679**** PP

                                    EEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC CS
                    AMP-binding 161 layiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa 239
                                    +a+ i+TSGTTG PK+ +++h  ++ ++a +  +    +lk +d+++s+lpl+h  +l++++  ++ sGat+ l + ++a
  gi|121637135|ref|YP_977358.1| 201 TAFYIFTSGTTGFPKASVMTHHRWLRALAVFGgMG--LRLKGSDTLYSCLPLYHNNALTVAVSSVINSGATLALGKSFSA 278
                                    *********************99999988876665..445579*******************************999988 PP

                                    CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEE CS
                    AMP-binding 240 ldpklllelieklkvtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffralfge.evlegYGl 317
                                      ++++ + + + ++t ++++ +++++ll+++a+      +d  + +r+  ++g+ l+pe++++f  +fg  +v e Y  
  gi|121637135|ref|YP_977358.1| 279 --SRFW-DEVIANRATAFVYIGEICRYLLNQPAKP-----TDRAHqVRV--ICGNGLRPEIWDEFTTRFGVaRVCEFYAA 348
                                    ..5566.66666******************87666.....255555787..79******************9******** PP

                                    GGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE..........TTSEEEEEEEET..TS-SEBTT-HHH CS
                    AMP-binding 318 TEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvp..........dgeeGellvrgp..gvmkgYlkkpea 384
                                    +E   ++++ ++   +  ++g    pl+ ve+ +   +tg p++          dge+G ll r +  + + gY  +p a
  gi|121637135|ref|YP_977358.1| 349 SEGNSAFINiFN-VPR--TAGVSPMPLAFVEYDL---DTGDPLRdasgrvrrvpDGEPGLLLSRVNrlQPFDGYT-DPVA 421
                                    ******975333.223..2343346777777776...45566655555555666********7766559******.8899 PP

                                    HHHHEEE....TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 385 taeafds....egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                     +++++     +g+ w++TGD+   +  G+  +v+R+ d++ +
  gi|121637135|ref|YP_977358.1| 422 SEKKLVRnafrDGDcWFNTGDVMSPQGMGHAAFVDRLGDTFRW 464
                                    999999777754788*********9989************987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0     1e-12   9.1e-09       2      76 .]     474     549 ..     473     549 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1e-12
                                    HHHHHHSSTTEEEEEEE-----TTS.---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkG.ealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    vE+al+s + V+e+ V+Gv+ +++G +a +a ++l++g e   ++L + v  +l+ ya p  v++v +l  t++ K
  gi|121637135|ref|YP_977358.1| 474 VEAALASDQTVEECTVYGVQIPRTGgRAGMAAITLRAGAEFDGQALARTVYGHLPGYALPLFVRVVGSLAHTTTFK 549
                                    9*********************7777*********98843356*****************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4178.14
//
Query:       gi|121637136|ref|YP_977359.1|  [L=318]
Description: dihydropteroate synthase 2 folP2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-72  244.5   0.1    1.6e-72  244.1   0.1    1.1  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.29   11.0   0.0    1.6  1  PspC         PspC domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.1   0.1   1.8e-76   1.6e-72       1     244 []      45     289 ..      45     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 1.8e-76
                                    EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TSEEEEE CS
                    Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dvpisiD 79 
                                    m+i+N tpdsf+d+g +++ ++a +++++ v++GAd++D+gg ++ Pg ervd+++e++r+vp++e+lr+ + d++is+D
  gi|121637136|ref|YP_977359.1|  45 MAIVNRTPDSFYDKGATFSDAAARDAVHRAVADGADVIDVGGVKAGPG-ERVDVDTEITRLVPFIEWLRGAYpDQLISVD 123
                                    89**********************************************.9****************************** PP

                                    -S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESEC.....SSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                    Pterin_bind  80 ttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmr.....gtpktmqeeegqyedvveeveaflearv 154
                                    t++a+va+aA++agad++Nd++g+  dp+m+e++ae+ga +v+ h+      ++p+++++ + +++ vv+ v ++++a++
  gi|121637136|ref|YP_977359.1| 124 TWRAQVAKAACAAGADLINDTWGGV-DPAMPEVAAEFGAGLVCAHTGgalprTRPFRVSYGT-TTRGVVDAVISQVTAAA 201
                                    *************************.********************9888888999999999.***************** PP

                                    HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHH CS
                    Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaaflalaa 234
                                    e+a++aGva+e++l+Dp + fgk++ h l llr++ +l +++++pvl+++S+k+++g++l ++  +eR +gt+a++alaa
  gi|121637136|ref|YP_977359.1| 202 ERAVAAGVAREKVLIDPAHDFGKNTFHGLLLLRHVADL-VMTGWPVLMALSNKDVVGETLGVD-LTERLEGTLAATALAA 279
                                    **************************************.*******************99444.68************** PP

                                    HTT-SEEEES CS
                    Pterin_bind 235 aaGadivrVh 244
                                    aaGa+++rVh
  gi|121637136|ref|YP_977359.1| 280 AAGARMFRVH 289
                                    *********9 PP

>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.29      12      36 ..      84     108 ..      82     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                           PspC  12 lgGVcaGlAeyfgvdptlvRlifvl 36 
                                    +gGV aG +e+ +vd+ ++Rl++++
  gi|121637136|ref|YP_977359.1|  84 VGGVKAGPGERVDVDTEITRLVPFI 108
                                    79*******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2184.40
//
Query:       gi|121637137|ref|YP_977360.1|  [L=324]
Description: glucosyl-3-phosphoglycerate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.6   0.0    2.2e-10   40.6   0.0    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    2.1e-07   31.1   0.0    3.1e-07   30.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00075   18.3   0.0        0.3    9.7   0.0    2.9  3  Osmo_MPGsynth    Mannosyl-3-phosphoglycerate synthase (osmo_M
  ------ inclusion threshold ------
      0.035   13.6   0.0      0.047   13.2   0.0    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0     5e-14   2.2e-10       1     109 [.      46     156 ..      46     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5e-14
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCH..HHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDet..veileelak.edprvrvirreenvGkagalnaglra 77 
                                    svv p+ Nee+t++ +++s+    + + +e+iv+D gStD+t  ++i+  ++  ++++        + Gk+ al + l+a
  gi|121637137|ref|YP_977360.1|  46 SVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTeiRAIASGARVvSREQALPEVPV-RPGKGEALWRSLAA 124
                                    8***************************************9955566666654433333333333.33************ PP

                                    --SSEEEEEESSEEE-TT.HHHHHHHHHHH.TT CS
                Glycos_transf_2  78 atgdyilflDaDdepdpd.wleklvealekdga 109
                                    ++gd+++f+D+D++ +   +++ lv++l   g+
  gi|121637137|ref|YP_977360.1| 125 TSGDIVVFIDSDLINPHPlFVPWLVGPLLT-GE 156
                                    *************98888788888888877.55 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   6.8e-11   3.1e-07       3     113 ..      44     153 ..      42     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6.8e-11
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaq.eyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn....arnlgstgksr 77 
                                    +++v+ p++nee+++++v++s++   +   +e++v + +s+++t  +a +     +++  rvv +    ++ + + gk +
  gi|121637137|ref|YP_977360.1|  44 TISVVLPALNEEATIESVIDSISPLvDGLVDELIVLDSGSTDDTEIRAIA-----SGA--RVVSReqalPEVPVRPGKGE 116
                                    699********************6625677*******9998887543333.....233..34444223335664459*** PP

                Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvv.ePdtlkrllqffl 113
                                    al + l a+++d+v+++D+D +  +P ++++l+  +l
  gi|121637137|ref|YP_977360.1| 117 ALWRSLAATSGDIVVFIDSDLINpHPLFVPWLVGPLL 153
                                    *********************999****999998773 PP

>> Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.038   1.7e+02      48      74 ..      40      65 ..      27      90 .. 0.79
   2 !    4.0   0.0    0.0037        16     141     175 ..     109     140 ..      90     143 .. 0.74
   3 !    9.7   0.0   6.8e-05       0.3     256     290 ..     210     244 ..     185     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.038
                  Osmo_MPGsynth 48 evesklaivvpiknEelkvlegvlsgi 74
                                   +  + +++v+p  nEe  ++e+v+ +i
  gi|121637137|ref|YP_977360.1| 40 KAGRTISVVLPALNEEA-TIESVIDSI 65
                                   555788999****9986.789999988 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0037
                  Osmo_MPGsynth 141 lirnGKgEgmllgillakllgkkyvgFiDaDnyvp 175
                                     +r GKgE++  ++  a++   + v FiD+D ++p
  gi|121637137|ref|YP_977360.1| 109 PVRPGKGEALWRSL--AAT-SGDIVVFIDSDLINP 140
                                    599******98765..444.568999*****9887 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 6.8e-05
                  Osmo_MPGsynth 256 aGEhAmtleLalklrfatGyaiEpfelidllekfe 290
                                    +GE A + eL ++l fa Gy +E   lid +++++
  gi|121637137|ref|YP_977360.1| 210 SGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLG 244
                                    8****************************999983 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05     0.047       1      92 [.      46     137 ..      46     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeei.elivvddgSsekfleevssiidlnllvylkde.ddk..ayslaaarNrG 76 
                                    svv+p  ++e +  ie  +  +    d  + eliv+d gS+++   e+++i      v+ +++ ++     +++ a  r 
  gi|121637137|ref|YP_977360.1|  46 SVVLPALNEEAT--IESVIDSISPLVDGLVdELIVLDSGSTDD--TEIRAIASGARVVSREQAlPEVpvRPGKGEALWRS 121
                                    788888888888..888888888888875548***********..9*****99888886554425553345777788888 PP

                Glyco_tranf_2_2  77 askaesdlvlFlDaDc 92 
                                       + +d+v+F+D+D 
  gi|121637137|ref|YP_977360.1| 122 LAATSGDIVVFIDSDL 137
                                    888999*******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2404.11
//
Query:       gi|121637138|ref|YP_977361.1|  [L=122]
Description: hypothetical protein BCG_1269 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.3   0.0    0.00026   21.1   0.0    1.1  1  DivIVA    DivIVA protein


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-08   0.00026       2      47 ..      50      95 ..      49     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-08
                                   -HHHHHH----EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIVA  2 tplDIknkeFkkklrGYdedeVdeFLdqvakdyeallkeneelkek 47
                                   t  D+   +F++ lrGY++ eVd  L+ + +++eal ++  ++ + 
  gi|121637138|ref|YP_977361.1| 50 TRADVDAVKFTQVLRGYKTSEVDWVLERLGRELEALRSQLGAIHAS 95
                                   899********************************98776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      891  (0.049696); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 800.61
//
Query:       gi|121637139|ref|YP_977362.1|  [L=204]
Description: DNA-3-methyladenine glycosylase i tagA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-66  222.3   0.0    4.6e-66  221.9   0.0    1.0  1  Adenine_glyco  Methyladenine glycosylase


Domain annotation for each model (and alignments):
>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9   0.0   2.6e-70   4.6e-66       5     175 ..      20     187 ..      17     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 2.6e-70
                  Adenine_glyco   5 dplyvaYhDeeWGvpvtddkklFelLvLegfqaglswetilkkreafreafdgFdlekvakydeekveelladegiirnr 84 
                                    ++ly++YhD+eWG+p +   +lFe+++Le+fq+glsw +il+kre+fr+af+gFd++k+a+y++++v++llad+gi+rnr
  gi|121637139|ref|YP_977362.1|  20 AQLYRDYHDNEWGRPLYGRVALFERMSLEAFQSGLSWLIILRKRENFRRAFSGFDIDKIARYTDTDVRRLLADDGIVRNR 99 
                                    689***************************************************************************** PP

                  Adenine_glyco  85 lKieavisnAravlalqeefgsfseylwsfvdgkpiveelksaeevpattelsealskdLkkrGfkfvGptivysflqav 164
                                    +Kiea+i+nAra+ +l ++ +++se+lwsf+   p  ++  + +e+p+ +++s+a+s++Lk+rGf+fvGpt++y+++qa+
  gi|121637139|ref|YP_977362.1| 100 AKIEATIANARAAADLGSS-EDLSELLWSFAP-PPRPRP-VDGSEIPSVSTESKAMSRELKRRGFRFVGPTTAYALMQAT 176
                                    ****************776.9**********8.344555.5589************************************ PP

                  Adenine_glyco 165 GlvndhleeCf 175
                                    G+v+dh++ C+
  gi|121637139|ref|YP_977362.1| 177 GMVDDHIQACW 187
                                    **********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1365.86
//
Query:       gi|121637140|ref|YP_977363.1|  [L=75]
Description: hypothetical protein BCG_1271 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-28   97.5   4.2    3.5e-28   97.1   4.2    1.1  1  DUF3117   Protein of unknown function (DUF3117)


Domain annotation for each model (and alignments):
>> DUF3117  Protein of unknown function (DUF3117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   4.2     2e-32   3.5e-28       1      50 []      24      73 ..      24      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 2e-32
                        DUF3117  1 mKPRtgdGplEvvkegrgivlRvPleGGGRLVvelnkeEaaeLgealkev 50
                                   mKPRtgdGplE++kegrgiv+RvPleGGGRLVvel+++Eaa+Lg++lk+v
  gi|121637140|ref|YP_977363.1| 24 MKPRTGDGPLEATKEGRGIVMRVPLEGGGRLVVELTPDEAAALGDELKGV 73
                                   9**********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 561.11
//
Query:       gi|121637141|ref|YP_977364.1|  [L=387]
Description: glycosyl transferase family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-28   98.9   0.0    3.4e-28   98.3   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    6.3e-28   97.9   1.5    6.3e-28   97.9   1.5    2.0  3  Glyco_transf_4   Glycosyltransferase Family 4
    4.6e-23   82.1   1.0    8.8e-23   81.2   1.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.9e-15   56.6   8.5    3.9e-15   56.6   8.5    3.0  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.7e-11   44.3   0.0    6.3e-11   42.5   0.0    2.0  1  Glyco_trans_1_2  Glycosyl transferases group 1
    7.8e-07   29.0   3.3    4.1e-05   23.4   0.9    2.3  2  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   1.2e-31   3.4e-28       9     172 .]     193     364 ..     190     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.2e-31
                                    TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.......STTHHHHHHHHHHHCTTCGGGEEECCH CS
                Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG......ngeeekelkklaeelelsdnviflgevs 82 
                                    lg + +++++++vgr++++Kgv +l++a++++    +++v+lv++       ++++ +   + ae + ++  v++++   
  gi|121637141|ref|YP_977364.1| 193 LGVDPNRPMAVFVGRITRQKGVVHLVTAAHRF----RSDVQLVLCAgaadtpEVAD-EVRVAVAELARNRTGVFWIQDRL 267
                                    5678899************************9....57888888765997533333.33345566677888899999887 PP

                                    .SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT......-HHHHHHHHHHH CS
                Glycos_transf_1  83 .redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn......naealaeairkl 155
                                       +l e+l++a +fv+ps +E++Giv lEAma+ ++v+as++gg++evv+dg tG lv+         ++ +aea++ l
  gi|121637141|ref|YP_977364.1| 268 tIGQLREILSAATVFVCPSVYEPLGIVNLEAMACATAVVASDVGGIPEVVADGITGSLVHYDaddatgYQARWAEAVNAL 347
                                    799*******************************************************976642111345679******* PP

                                    HHSHHHHHHHHHHHHHH CS
                Glycos_transf_1 156 ledeelrerlgenarkr 172
                                    + d+ ++er+g ++r+r
  gi|121637141|ref|YP_977364.1| 348 VADPATAERYGHAGRQR 364
                                    *************9986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   1.5   2.1e-31   6.3e-28       1     169 [.      15     176 ..      15     177 .. 0.85
   2 ?   -2.4   0.1       1.3     4e+03       9      36 ..     215     243 ..     211     281 .. 0.49
   3 ?   -1.4   0.0      0.67     2e+03     117     141 ..     262     286 ..     253     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 2.1e-31
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                    +GG+++hv eL+ +L+r+ + V+v + g ++p + +       p ++l + + +l +l++ + +++++      vvH+h+
  gi|121637141|ref|YP_977364.1|  15 YGGAGVHVTELVAYLRRL-CAVDVHCMGAPRPGAFA-----YRPDPRLGSANAALSTLSADLVMANAAS--AATVVHSHT 86 
                                    7*****************.*******9999998888.....2344444444555555555555555555..9******** PP

                 Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllk.arlkplsrllralerrllrradrviavSeatadelreryg.vppek 158
                                    +++++a++la+ + ++ip++lt+H+l++ r++k   l+ ++++  ++e+ ++ +a++viavS a+++++++ y+ ++p+ 
  gi|121637141|ref|YP_977364.1|  87 WYTALAGHLAAIL-YDIPHILTAHSLEPLRPWKkEQLGGGYQVSTWVEQTAVLAANAVIAVSSAMRNDMLRVYPsLDPNL 165
                                    ************9.**************66665056688999************************************** PP

                 Glyco_transf_4 159 itVipnGvDle 169
                                    ++Vi nG+D+e
  gi|121637141|ref|YP_977364.1| 166 VHVIRNGIDTE 176
                                    **********8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                 Glyco_transf_4   9 leLaraLarrGheVtvv.tpgddgpleee 36 
                                    ++L+ a  r   +V++v + g  + +e +
  gi|121637141|ref|YP_977364.1| 215 VHLVTAAHRFRSDVQLVlCAGAADTPEVA 243
                                    45555555555556555522222222222 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.67
                 Glyco_transf_4 117 kplsrllralerrllrradrviavS 141
                                    + ++rl    +r +l++a  ++++S
  gi|121637141|ref|YP_977364.1| 262 WIQDRLTIGQLREILSAATVFVCPS 286
                                    67778888889999**********9 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   1.0   2.9e-26   8.8e-23       2     134 .]     200     350 ..     199     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2.9e-26
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT....T-T....TEEEE---...THHHHHH CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa....gle...erveftGfv...edlaell 70 
                                    p  +fvGr+  ++kgv  l+ a+++ r +dv+lv++ +    p e+ ++++    +l+    +v +   +    +l+e+l
  gi|121637141|ref|YP_977364.1| 200 PMAVFVGRI-TRQKGVVHLVTAAHRFR-SDVQLVLCAGAAdTP-EVADEVRvavaELArnrTGVFWIQDRltiGQLREIL 276
                                    788******.567**************.669988877443333.4443332223333322156999988877778***** PP

                                    HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT..-HH....HHHHHHHHHHH- CS
                Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppg..dpe....alaeailrLled 134
                                    +aa+vfv+Ps  e +g++ lEama++++vVa+dvggi+evv  g +g lv  +  d+      +aea+ +L++d
  gi|121637141|ref|YP_977364.1| 277 SAATVFVCPSvyEPLGIVNLEAMACATAVVASDVGGIPEVVadGITGSLVHYDadDATgyqaRWAEAVNALVAD 350
                                    ***********************************************999543223224555889999988876 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   8.5   1.3e-18   3.9e-15       1     160 []      16     172 ..      16     172 .. 0.80
   2 ?    1.6   1.6      0.11   3.4e+02       9      67 ..     216     276 ..     211     317 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.3e-18
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt.papapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvh 78 
                                    gG+g++v el++ L+++ + V+v +  ap+pga+         +r p pr   + a++a ++  ++l+ + ++    vvh
  gi|121637141|ref|YP_977364.1|  16 GGAGVHVTELVAYLRRL-CAVDVHCmGAPRPGAF--------AYR-PDPRL--GSANAALSTLSADLVmANAASAATVVH 83 
                                    8****************.8899999444444455........333.33333..235555555556667777899999*** PP

                Glyco_trans_4_4  79 ahsptaglaarlarrrrgiplvvtlhglllrrg.....sgavrrlyralerrllrradavlvvseaeaeelralg..vpa 151
                                    +h+++++la+ la+   +ip+++t+h+l++ r+      g  +++ +++e++++  a av++vs a++ ++ + +  +++
  gi|121637141|ref|YP_977364.1|  84 SHTWYTALAGHLAAILYDIPHILTAHSLEPLRPwkkeqLGGGYQVSTWVEQTAVLAANAVIAVSSAMRNDMLRVYpsLDP 163
                                    **************************86644333344578888899***************************55599** PP

                Glyco_trans_4_4 152 drvvvvpng 160
                                    + v+v++ng
  gi|121637141|ref|YP_977364.1| 164 NLVHVIRNG 172
                                    ********8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                Glyco_trans_4_4   9 elaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladla...alralrrll 67 
                                    +l+ a  +   +V+++  a+a++ p +++d vrv    + r++ ++ + +    + +lr++l
  gi|121637141|ref|YP_977364.1| 216 HLVTAAHRFRSDVQLVLCAGAADTP-EVADEVRVAVAELARNRTGVFWIQdrlTIGQLREIL 276
                                    5555555555678888777777777.788888888888777776555533211445666555 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   2.1e-14   6.3e-11       2      91 ..     282     379 ..     280     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.1e-14
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dlee.......laekiryllanpeerraiaeaa 73 
                                    ++ ps +e +  +++Ea+ac + ++++d  g++e + +g ++ l++ d ++       +ae++++l+a+p+ +++ ++a+
  gi|121637141|ref|YP_977364.1| 282 FVCPSVYEPLGIVNLEAMACATAVVASDVGGIPEVVADGITGSLVHyDADDatgyqarWAEAVNALVADPATAERYGHAG 361
                                    56689999999*****************************88888776655333333389******************** PP

                Glyco_trans_1_2  74 rervlaehtydhraeqll 91 
                                    r+r+ +e++++  aeq l
  gi|121637141|ref|YP_977364.1| 362 RQRCIQEFSWAYIAEQTL 379
                                    ***************987 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0039        12       1      36 [.       2      35 ..       2      43 .. 0.87
   2 !   23.4   0.9   1.4e-08   4.1e-05     121     231 ..      66     156 ..      43     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                 Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdv 36
                                   ++ +++ E++p    GG + +v++L   L++l + v
  gi|121637141|ref|YP_977364.1|  2 RVAMLTREYPP-EVYGGAGVHVTELVAYLRRL-CAV 35
                                   799********.*****************987.444 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.4e-08
                 Glyco_transf_5 121 aalellekl.gwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdel.aalglpaedfekldg 198
                                      ++l+         v+h h W+tal++ l++ ly       +i+ ++t H+l+  + ++k++l    ++          
  gi|121637141|ref|YP_977364.1|  66 LSADLVMANaASAATVVHSHTWYTALAGHLAAILY-------DIPHILTAHSLEPLRPWKKEQLgGGYQV---------- 128
                                    333333331122599************99999999.......6*************99999998443333.......... PP

                 Glyco_transf_5 199 lefygkvnflk.agivyadavttVSptyakEilt 231
                                            +++ +++++a+av++VS  + ++ l+
  gi|121637141|ref|YP_977364.1| 129 ------STWVEqTAVLAANAVIAVSSAMRNDMLR 156
                                    ......3566669*************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2814.51
//
Query:       gi|121637142|ref|YP_977365.1|  [L=404]
Description: glucose-1-phosphate adenylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-72  242.7   0.0    5.7e-72  242.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    9.9e-07   29.3   0.0    1.5e-06   28.7   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00066   18.7   0.0     0.0013   17.8   0.0    1.4  1  Fucokinase       L-fucokinase
     0.0054   16.4   8.7        1.1    9.0   3.0    3.4  3  Hexapep          Bacterial transferase hexapeptide (six repea


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.0   1.3e-75   5.7e-72       2     245 ..       9     276 ..       8     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 1.3e-75
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT......SEE CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg......vev 75 
                                    +++LaGG+G+RL+PLt ++ak++vp++g +rli+++ls+l+n+++ + i+vltq++s++++++++++++++      ++ 
  gi|121637142|ref|YP_977365.1|   9 GIVLAGGEGKRLYPLTADRAKPAVPFGGAYRLIDFVLSNLVNARYLR-ICVLTQYKSHSLDRHISQNWRLSglageyITP 87 
                                    79*********************************************.*********************99********* PP

                                    EEEEESS--....BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEE CS
                NTP_transferase  76 lialepegk....gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvi 151
                                     +a+++ g     g+AdA++++++l+ de+ +++++v+g+Dh+++++ e++v+++i+++a  tv+ + vp+e+at++G+i
  gi|121637142|ref|YP_977365.1|  88 VPAQQRLGPrwytGSADAIYQSLNLIYDED-PDYIVVFGADHVYRMDPEQMVRFHIDSGAGATVAGIRVPRENATAFGCI 166
                                    ********9*********************.6****************************77****************** PP

                                    EECTTSBEEEEECS-SSHSH......CSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECST CS
                NTP_transferase 152 eadeegrverfvEKPkeaka......selassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfk 224
                                     ad++gr+++fvEKP e++       ++++s+G+Y+f+++vl  +++ d+++ ++ +d+++di+p+++++g +a++ +f+
  gi|121637142|ref|YP_977365.1| 167 DADDSGRIRSFVEKPLEPPGtpddpdTTFVSMGNYIFTTKVLIDAIRaDADDDHSDHDMGGDIVPRLVADGMAAVY-DFS 245
                                    ***********************************************************************99987.999 PP

                                    TEE..........-EEEXSSHHHHHHHHHHH CS
                NTP_transferase 225 dae..........yWsDvGtldslleanekl 245
                                    d+e          yW+DvGtld++++a+++l
  gi|121637142|ref|YP_977365.1| 246 DNEvpgatdrdraYWRDVGTLDAFYDAHMDL 276
                                    999*************************986 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.4e-10   1.5e-06       1     117 [.       9     147 ..       9     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.4e-10
                                    EEEEEESS-TTT.....TTTHHHHCCCCC.CHHHHHHHHHCTT.-CEEEEECSH..CHHHH..............HHTTC CS
                   NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggk.pllervldalraagvdevvvvggd..eevla..............alarl 58 
                                    +++LAGG+++R+      + K+ +p+gg  +l++ vl +l  a   +++v +++  +++ +              ++ + 
  gi|121637142|ref|YP_977365.1|   9 GIVLAGGEGKRLypltaDRAKPAVPFGGAyRLIDFVLSNLVNARYLRICVLTQYksHSLDRhisqnwrlsglageYITPV 88 
                                    79**********7776557*******77549************999******9953344445555555555544455555 PP

                                    TS-EEE-TTSS-SHHHHHHHHHHH..H.SSSCEEEEETT-TT.--HHHHHHHHHCHHHHTSS CS
                   NTP_transf_3  59 gvrvvededpgkgplaslaaalra..aadadavlvlacDmPl.ltpelverllaaaaasgad 117
                                    +++    + +++g + +++  l+    +d d+++v+ +D+++ ++pe   ++++ + +sga 
  gi|121637142|ref|YP_977365.1|  89 PAQQRLGPRWYTGSADAIYQSLNLiyDEDPDYIVVFGADHVYrMDPE---QMVRFHIDSGAG 147
                                    8888999***************98545599*********99844443...333333334444 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.8e-07    0.0013     270     324 ..     330     390 ..     289     397 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-07
                     Fucokinase 270 k.......kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslel 324
                                            +++a+v  Sv+ ++ +vg+g+v+ h  l++nv +g + +v g++le++ e++ +
  gi|121637142|ref|YP_977365.1| 330 VlssnvvvDDGAIVEGSVIMPGTRVGRGAVVRHAILDKNVVVGPGEMV-GVDLEKDRERFAI 390
                                    012222347777777788888888888888888888888888888777.7777777766666 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   3.0   0.00026       1.1       2      31 ..     313     346 ..     312     348 .. 0.90
   2 !    8.9   0.1   0.00029       1.3      13      29 ..     345     361 ..     344     362 .. 0.82
   3 !    4.4   1.0    0.0074        33       2      30 ..     352     373 ..     351     374 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                                    EEEETTEEE-T....TEEEETTEEE-TTEEEETT CS
                        Hexapep   2 tvIGsnvlIgp....faviggnVkIGdnvkIgag 31 
                                    +v+G +++I +    ++v+ +nV++ d+++++  
  gi|121637142|ref|YP_977365.1| 313 SVVGAGSIISAasvrNSVLSSNVVVDDGAIVEGS 346
                                    6899999999*********************874 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00029
                                    TEEEETTEEE-TTEEEE CS
                        Hexapep  13 faviggnVkIGdnvkIg 29 
                                    ++vi++++ +G+++++ 
  gi|121637142|ref|YP_977365.1| 345 GSVIMPGTRVGRGAVVR 361
                                    68999999999999886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0074
                                    EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                    t++G +++++  a++  nV++G      +
  gi|121637142|ref|YP_977365.1| 352 TRVGRGAVVR-HAILDKNVVVG------P 373
                                    4555555555.44444455444......4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 2463.23
//
Query:       gi|121637143|ref|YP_977366.1|  [L=110]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-30  103.4  22.6      1e-29  102.7  22.6    1.3  1  PE        PE family
  ------ inclusion threshold ------
       0.99    8.7   8.0        1.2    8.4   8.0    1.1  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7  22.6   1.1e-33     1e-29      10      92 ..       1      83 [.       1      84 [. 0.99

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 1.1e-33
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                             PE 10 alaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaagsYaaaE 91
                                   +la+aa+dlagigsalsaanaaaaaptta+laa aDeVSa +A+lf+ haq+yqals qa+afh+qfvqal++a+g+YaaaE
  gi|121637143|ref|YP_977366.1|  1 MLASAATDLAGIGSALSAANAAAAAPTTAMLAACADEVSAVVASLFARHAQAYQALSLQATAFHQQFVQALTGAGGAYAAAE 82
                                   79******************************************************************************** PP

                                   X CS
                             PE 92 a 92
                                   a
  gi|121637143|ref|YP_977366.1| 83 A 83
                                   9 PP

>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.0   0.00014       1.2       4      74 ..      22      94 ..      19     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00014
                           MtrE  4 lalmgalatiagaaedlesdvgsqsnpnsqv..qLapqmgylhrifnkaisGePvaygllaavagavalvlls 74
                                   +a++ ++a++a +a+++ + v+s     +q    L+ q + +h+ f +a++G   ay++  av +ava  + +
  gi|121637143|ref|YP_977366.1| 22 AAAAPTTAMLAACADEVSAVVASLFARHAQAyqALSLQATAFHQQFVQALTGAGGAYAAAEAVNAAVAQSVQQ 94
                                   466778999**************988888763258899******************************98763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 812.87
//
Query:       gi|121637144|ref|YP_977367.1|  [L=561]
Description: hypothetical protein BCG_1275c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-41  141.7   0.0    8.7e-39  133.7   0.0    2.1  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    7.1e-22   78.5   0.1    3.4e-21   76.2   0.0    2.1  2  PepX_C         X-Pro dipeptidyl-peptidase C-terminal non-cata
    2.4e-05   23.9   0.0    3.9e-05   23.2   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
     0.0067   15.7   0.0       0.17   11.1   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   0.0   1.9e-42   8.7e-39       1     252 [.      55     293 ..      55     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 1.9e-42
                                    TS-EEEEEEEEE..TTSSSEEEEEEEESS-.....CCT.CCCCHTTCHHCCHGGGHH....................... CS
                  Peptidase_S15   1 DGvrLavdiyrPetkskeklPvlltrtPYg.....kndelasdkalaleelelqdkv....................... 52 
                                    DG++L ++++r   ++++  Pv+    PYg     +++ +++   +  ++                              
  gi|121637144|ref|YP_977367.1|  55 DGTLLRINVFRS--AEGGARPVIASIHPYGkdalpRRRGNRW---TFSPQ------Yrmlrqpkpltfsaltgweapdpa 123
                                    9***********..****************554332222222...22222......1223455789999*********** PP

                                    .HHHTT-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEE CS
                  Peptidase_S15  53 .fvarGYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivp 131
                                     + a+G++vV +d+rG g S+G  +  + +eaed++d + Wla q+ws+G+V m+G+SYl++ q+++aa ++pal+ai+p
  gi|121637144|ref|YP_977367.1| 124 wWTAQGFVVVNADSRGCGRSDGTGDLLSHQEAEDTYDLVGWLADQSWSDGRVVMLGVSYLAISQYAVAALQPPALRAICP 203
                                    ******************************************************************************** PP

                                    ECE-S-TCCCCSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHHTHHHHCCCC--SS CS
                  Peptidase_S15 132 eaaisdlyddyyregGlvrapgglswedldllaealtsrradegdalkaaaryeaasdellaeldrqtpveselletgdy 211
                                      + +d y+d +++gG+ ++ ++  w           +rr   +++++            +++++++         ++ +
  gi|121637144|ref|YP_977367.1| 204 WEGFTDAYRDLAFPGGIRESGFTRLW-------SRGVRRR--TRQTYD------------MEQMQEA---------HPLR 253
                                    ***********************999.......2222222..222222............4455566.........999* PP

                                    SHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHH CS
                  Peptidase_S15 212 dafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyea 252
                                    d+fW++r ++  ++++k+p+l+ g++ D+n   +g+i+++ +
  gi|121637144|ref|YP_977367.1| 254 DDFWRSRVPD--LSAIKVPMLVCGSFSDNNLHsRGSIRAFTR 293
                                    ********88..8*****************999*****9976 PP

>> PepX_C  X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.32   1.4e+03       1      73 [.      92     169 ..      92     216 .. 0.65
   2 !   76.2   0.0   7.6e-25   3.4e-21       9     222 ..     338     551 ..     333     555 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.32
                         PepX_C   1 ngvertppvrlqvldggsgs...........twrtedawpspntkattlyls....qrgag.stgdgtlsaasplsdeaa 64 
                                    n+++ +p++r+ ++  + ++           +w t + +                 +rg+g s+g+g+l  +++++d+ +
  gi|121637144|ref|YP_977367.1|  92 NRWTFSPQYRMLRQPKPLTFsaltgweapdpAWWTAQGFV-----------VvnadSRGCGrSDGTGDLLSHQEAEDTYD 160
                                    6777788888888888877555553222222222222222...........13333444432678888888888888888 PP

                         PepX_C  65 aseedlydp 73 
                                    ++++ + ++
  gi|121637144|ref|YP_977367.1| 161 LVGWLADQS 169
                                    766655555 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 7.6e-25
                         PepX_C   9 vrlqvldggsgs.twrtedawpspntkattlylsqrgagstgdgtlsaasplsdeaaaseedlydptnpldqdqreerad 87 
                                    vrl+v+ + ++  + r+e++wp ++t+ + +yl         + +l a++p ++  ++                  ++ +
  gi|121637144|ref|YP_977367.1| 338 VRLEVREDRDTItAVREETQWPLAGTRWRPMYLA--------GPGLLATEPPPTAGSI------RF----------QTRS 393
                                    566666555544569*******************........6666777777777773......44..........5578 PP

                         PepX_C  88 slafttaplaedtelvGapkakLrvssdapda.dlsvtLvdvdpdGea..........tlitkGwlrlsnRasdeep... 153
                                    ++a ++++ +ed+el+G++ a+L+v  d+ d+ +l+v + + +   +            ++t+Gw r+s R++d+e    
  gi|121637144|ref|YP_977367.1| 394 RAAAFNWTIPEDIELTGPMAARLWVQLDGCDDaNLFVGVEKWRDGQFVafegsygwgrDRVTTGWQRVSLRELDPELsqp 473
                                    *****************************9888******99976633344455677779********************* PP

                         PepX_C 154 ..........eplePGevydleieLqptayrfpkGhrlrlsvsssdfpmilpnpetdtltldlakl.kakntvhtgaerp 222
                                              +p+++Gev+ ++++L p+a  f +G++lrl+v +    ++++np t++ +    ++ +++ t+h g++++
  gi|121637144|ref|YP_977367.1| 474 wepvpacarpRPVTAGEVVAVDVALGPSATLFRAGEQLRLVVGGR--WLSPRNPLTGQFPAAYPRPpRGRVTLHWGPRYD 551
                                    *****************************************9663..344555555554444444445555555555555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.7e-09   3.9e-05       7     167 ..     122     292 ..     118     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.7e-09
                                    HHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-G CS
                   Peptidase_S9   7 lqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrp 86 
                                    +++++++G+vvv a+ rG g +++   d     l  +e++D  + + +la++++ d  r+++ G Sy      a+++ +p
  gi|121637144|ref|YP_977367.1| 122 PAWWTAQGFVVVNADSRGCG-RSDGTGD----LLSHQEAEDTYDLVGWLADQSWSD-GRVVMLGVSYLAISQYAVAALQP 195
                                    6899**************99.4444444....5678899**************986.69********************* PP

                                    GG-SEEEEESE---CCCHHCSTTS.....THH.HCCCC--TTTCHHHHHHHHHH-CGGG--..........---EEEEEE CS
                   Peptidase_S9  87 dlFkaavaevpvvdvlrydsdtdl.....lte.eymewgnpeeneegykelspyspldnvk..........aypplLlih 150
                                       +a+    +++d  r+  ++       +t+ +  +    +++  +++++++++pl+  +          +++p+L++ 
  gi|121637144|ref|YP_977367.1| 196 PALRAICPWEGFTDAYRDLAFPGGiresgFTRlWSRGVRRRTRQTYDMEQMQEAHPLRDDFwrsrvpdlsaIKVPMLVCG 275
                                    ******************99975556679999777776666556666666666666666559****************** PP

                                    ETT-SSS-THHHHHHHH CS
                   Peptidase_S9 151 GlaDdrvppaealklva 167
                                    +  D++ +   +++ ++
  gi|121637144|ref|YP_977367.1| 276 SFSDNNLHSRGSIRAFT 292
                                    *******9988887765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   3.8e-05      0.17      26      85 ..     124     182 ..     121     202 .. 0.65
   2 ?    2.1   0.0     0.021        96     186     229 ..     263     306 ..     257     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                    Hydrolase_4  26 aLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvk.eehpelplfllGhSm 85 
                                    +++aqGf v+  D rG Grs+g  g++ s ++  +D   +v  ++ + +++ ++++lG S 
  gi|121637144|ref|YP_977367.1| 124 WWTAQGFVVVNADSRGCGRSDGT-GDLLSHQEA-EDTYDLVGWLAdQSWSDGRVVMLGVSY 182
                                    799*****************854.334443332.344444433332666666777777775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                    Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypg 229
                                    + ++i++P+l+  + +D+  + ++s +++ r g  + +l +  g
  gi|121637144|ref|YP_977367.1| 263 DLSAIKVPMLVCGSFSDNNLHSRGSIRAFTRSGCGHARLYTHRG 306
                                    56799************************999988887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3657.54
//
Query:       gi|121637145|ref|YP_977368.1|  [L=224]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-12   45.7   1.1    6.9e-12   45.7   1.1    1.9  2  PEMT        Phospholipid methyltransferase
      1e-08   35.5   0.1    2.5e-08   34.2   0.1    1.7  1  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
    1.4e-05   24.7   0.5    1.9e-05   24.3   0.2    1.4  1  DUF1295     Protein of unknown function (DUF1295)
    1.5e-05   23.9   0.0    2.2e-05   23.4   0.0    1.2  1  ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
     0.0053   16.3   0.7     0.0053   16.3   0.7    1.8  2  NnrU        NnrU protein
  ------ inclusion threshold ------
          1    9.9   6.9         24    5.5   5.4    3.0  2  DUF3899     Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       1.6   4.8e+03      70      80 ..      31      41 ..       9      51 .. 0.58
   2 !   45.7   1.1   2.3e-15   6.9e-12       4     100 ..     111     203 ..     109     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                           PEMT 70 tgsaaglllal 80
                                   +++a+++l+a+
  gi|121637145|ref|YP_977368.1| 31 YWQAWVFLAAF 41
                                   33344444444 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2.3e-15
                           PEMT   4 ilGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvl 83 
                                    ++G +l+++gl +++ ++ + +++  ++     e  + l ++G+Y+++++P+y g ++++ G+ L+ gs++++++++  +
  gi|121637145|ref|YP_977368.1| 111 VIGDVLVMTGLGIAMLVVIQNRYAASTVRV---EAGQILASDGLYKIVRHPMYAGNVVMMTGIPLALGSYWAMFILVPGT 187
                                    569*********************999886...7889**********************************666666666 PP

                           PEMT  84 lvylialkfvEephlak 100
                                    lv  + +   Ee+ l +
  gi|121637145|ref|YP_977368.1| 188 LVLVFRIL-DEEKLLTQ 203
                                    66555555.78777765 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   8.2e-12   2.5e-08      22      93 ..     133     202 ..     108     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.2e-12
                           ICMT  22 iwttrvailpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvalllfvRikeEekaLa 93 
                                    +    v ++ ++ l  +glyk++rHP Y+++v++ + +++L++   + a+++l+  +l+l+ Ri +Eek L 
  gi|121637145|ref|YP_977368.1| 133 YAASTVRVEAGQILASDGLYKIVRHPMYAGNVVM-MTGIPLALGS-YWAMFILVPGTLVLVFRILDEEKLLT 202
                                    4445566678888999**************8876.7889999999.7788877779999999*******997 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.2   6.3e-09   1.9e-05     116     228 ..     105     217 ..      58     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.3e-09
                        DUF1295 116 alkaldviglalwlvgivlealaDqQlsafkkdpa.nkgk.vldsGLwrysRHPNYfgealiWwglflialealegleal 193
                                    + +a+ vig +l+++g+++++l   Q     ++ +  +g+ +  +GL++  RHP Y g++++  g+ l+  +   ++ ++
  gi|121637145|ref|YP_977368.1| 105 VPAAVCVIGDVLVMTGLGIAMLVVIQNRYAASTVRvEAGQiLASDGLYKIVRHPMYAGNVVMMTGIPLALGSY--WAMFI 182
                                    44778899**************99998765555442567768889*********************9854444..45579 PP

                        DUF1295 194 aiagpllltlllvfvsgipllEkkalkkykdkeey 228
                                    ++ g l+l++ +++     + E +  ++y++  +y
  gi|121637145|ref|YP_977368.1| 183 LVPGTLVLVFRILDEEKLLTQELSGYREYRQLVRY 217
                                    99998888777777666666666666666555555 PP

>> ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   7.3e-09   2.2e-05     342     432 .]     137     224 .]     128     224 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.3e-09
                     ERG4_ERG24 342 yiqtktGskLlvsGWyglarkinYlgDwlqslswsLatgfqsvlpyfyvlyFlvlLvhRelRDeekCkkkYGedweeYkk 421
                                     ++ + G+ L  +G y+++r++ Y g++++     La g  s  + f  +   ++Lv R l Deek   +  + + eY++
  gi|121637145|ref|YP_977368.1| 137 TVRVEAGQILASDGLYKIVRHPMYAGNVVMMTGIPLALG--SYWAMFILVPGTLVLVFRIL-DEEKLLTQELSGYREYRQ 213
                                    678899*********************998654444433..44555555555679999965.89999999999******* PP

                     ERG4_ERG24 422 kvpykiipyvy 432
                                     v+y+++pyv+
  gi|121637145|ref|YP_977368.1| 214 LVRYRLVPYVW 224
                                    *********96 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.38   1.1e+03      46      71 ..      13      40 ..       4      71 .. 0.60
   2 !   16.3   0.7   1.8e-06    0.0053      41     120 ..      83     164 ..      58     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.38
                           NnrU 46 lvlliigfgaarye..vllWeppawlrh 71
                                   l+l+++g++   ++  +++W+  ++l++
  gi|121637145|ref|YP_977368.1| 13 LGLVVFGALLFGPAgtFDYWQAWVFLAA 40
                                   5555555555555544444444433333 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.8e-06
                           NnrU  41 vsllglvlliigfgaaryevllWepp.....awlrhlalllmlvafillaaallpgnplsvglkadlaetgivritrHPm 115
                                    + l  ++++++ + ++ry    W+       ++   l+++   +a+++++   +++ ++ v + + la+ g+++i+rHPm
  gi|121637145|ref|YP_977368.1|  83 AFLGFFAMMVLSACDHRYG---WSSVpaavcVIGDVLVMTGLGIAMLVVIQNRYAASTVRVEAGQILASDGLYKIVRHPM 159
                                    5566788999999999999...4433123345556677777889999999999999998888889*************** PP

                           NnrU 116 llgva 120
                                     +g +
  gi|121637145|ref|YP_977368.1| 160 YAGNV 164
                                    99965 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.4    0.0079        24       4      32 ..       7      35 ..       6      94 .. 0.89
   2 ?    2.6   0.0     0.066     2e+02       6      22 ..     177     193 ..     174     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0079
                        DUF3899  4 lFllglllliigillivlnsGfFdgfsyg 32
                                   +F++g+l l++ ++l+   +G+Fd ++ +
  gi|121637145|ref|YP_977368.1|  7 IFIWGVLGLVVFGALLFGPAGTFDYWQAW 35
                                   6***********************99865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.066
                        DUF3899   6 llglllliigillivln 22 
                                    ++++++l+ g l++v++
  gi|121637145|ref|YP_977368.1| 177 YWAMFILVPGTLVLVFR 193
                                    77888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1606.36
//
Query:       gi|121637146|ref|YP_977369.1|  [L=548]
Description: tetronasin-transport integral membrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.5    7.8  15.9       0.21   10.7   3.4    2.4  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   4.7    0.0034        61     219     343 ..     106     270 ..      97     272 .. 0.57
   2 ?   10.7   3.4   1.2e-05      0.21     159     252 ..     360     493 ..     339     534 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0034
                ABC2_membrane_3 219 lqlllilllafgl...................gipfg.nlglllllfllfglayialgyllsslfknsetaqil.ifivi 277
                                    + +l+++++++ +                    +  + nl  +lll++  ++a+ a+g+l   +++ + +++++  +++ 
  gi|121637146|ref|YP_977369.1| 106 FHTLIAVAVILTVirhtradeesgraelidstVVGRYaNLTGALLLSFGASIATGAIGALGLLATDVAPAGSVAfGVALA 185
                                    55555555444444555666666666666554333336888899999999999999999999999988776553244444 PP

                ABC2_membrane_3 278 lllsgffgglfpledlpsalkw....ifsiiPffapglgllrlitgdplwe..................illsliilalf 335
                                     + ++f ++  +  +l+ +++     +f ++ +     ++ + ++g+                       ++ l++ +++
  gi|121637146|ref|YP_977369.1| 186 ASGMVFTAVAAVAAQLSPSARFtravAFAVLGTAFALRAIGDAGSGT---LswcsplgwslqvrpyageRWWVLLLSLAT 262
                                    45555555555544444333322222444555555555555555444...033357777777777766666666666666 PP

                ABC2_membrane_3 336 avvyllla 343
                                    a+v+++la
  gi|121637146|ref|YP_977369.1| 263 AAVLTVLA 270
                                    66666666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 1.2e-05
                ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl....... 231
                                    +   ++++i ++++ + +s +++  +++ e++++   l++g    ++wl++ l+++l++  ++ li ++a gl       
  gi|121637146|ref|YP_977369.1| 360 FLALAFTMIGMVAAAFAVSLTLR--LHQEETGLRAETLLAGAVSRTHWLASHLAMALAGSAVATLISGVAAGLaygmtvg 437
                                    23333446666666666665554..7777999*999999*********************99999988655554544777 PP

                ABC2_membrane_3 232 ...................................gipfgnlglllllfllfglay 252
                                                                        ++   +g+l+ ++ l++l +
  gi|121637146|ref|YP_977369.1| 438 dvggklptvvgtaavqlpavwllsavtvglfglapRFTPVAWGVLVGFIALYLLGS 493
                                    77777777776666666666666666666666666444444444443333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3615.35
//
Query:       gi|121637147|ref|YP_977370.1|  [L=311]
Description: tetronasin-transport atp-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-26   91.7   0.0    9.8e-26   90.9   0.0    1.4  1  ABC_tran  ABC transporter
      5e-12   46.2   0.5    2.9e-06   27.3   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.1e-06   29.2   0.0      2e-06   28.4   0.0    1.5  1  DUF4162   Domain of unknown function (DUF4162)
      0.004   16.9   0.1      0.015   15.0   0.1    2.0  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.027   14.9   0.0      0.051   14.0   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.028   14.0   0.0       0.05   13.2   0.0    1.4  1  AAA_27    AAA domain
      0.037   14.5   0.0      0.067   13.7   0.0    1.3  1  AAA_23    AAA domain
      0.048   13.4   0.0       0.13   12.0   0.0    1.7  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   4.4e-29   9.8e-26       1     136 [.      25     163 ..      25     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.4e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                    l+ ++l+++ege+++++G+nGaGKSt l++l+gl+k + G+++l  g+++++     l+++i+++p + +l+p lt +e+
  gi|121637147|ref|YP_977370.1|  25 LDGLDLTVREGEVHGFLGPNGAGKSTTLRILLGLVKADGGSVRLLgGDPWTD--AVDLHRHIAYVPGDVTLWPSLTGGET 102
                                    6899**************************************9996777877..9**********************9*9 PP

                                    ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               ++++ +++++++gl+   ++++    +++S+G +q+v+l  al ++++llllDEp+
  gi|121637147|ref|YP_977370.1| 103 idllarmrggIDNARRAELIERFGLDP--TKKA----RTYSKGNRQKVSLISALSSHATLLLLDEPS 163
                                    *****9999999999999******999..5555....78***************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.7e-06    0.0037       3      22 ..      39      58 ..      37      78 .. 0.78
   2 !   27.3   0.0   1.3e-09   2.9e-06     235     297 ..     134     193 ..     102     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++ GpNg+GKS+ L++l +l
  gi|121637147|ref|YP_977370.1| 39 GFLGPNGAGKSTTLRILLGL 58
                                   789**************887 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.3e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                    r  S G ++   l++al + +   +lll+DEp +gL+P l++ ++ + + e++++g+ v+l++H
  gi|121637147|ref|YP_977370.1| 134 RTYSKGNRQKVSLISALSSHA---TLLLLDEPSSGLDP-LMENVFqQCIGEARQRGVTVLLSSH 193
                                    445999************999...**************.8888888****************** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   9.1e-10     2e-06       1      79 [.     217     294 ..     217     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.1e-10
                                    E-HHHHHTTS-SSEEEEE..-------..---EEEE-TTS-EEEEE-----------------EEEEEEEE---HHHHHH CS
                        DUF4162   1 GtleeiKrsygknrieve..adaeelleepgveeveeeggelelkledeeaanellkaltsgveirsFeeeePsLndIFi 78 
                                    G+l+ +++   ++ i+ e  +d+++l +++gve+++ eg++++ ++++ e+ +el++ l  ++ +rs+  ++P+L++ F+
  gi|121637147|ref|YP_977370.1| 217 GSLDALRHL-SRTSIKAEmiGDPGDLSRIKGVEDISIEGTTVRAQVDS-ESLRELIQVL-GHAGVRSLVSQPPTLEELFL 293
                                    566666655.555666667799*****************99*****98.7*********.8899***************9 PP

                                    H CS
                        DUF4162  79 e 79 
                                    +
  gi|121637147|ref|YP_977370.1| 294 R 294
                                    8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   6.7e-06     0.015      18      53 ..      35      70 ..      28     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.7e-06
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglA 53
                                     v+   Gp G+GK+t+l+ l  +++a+gg+v +l 
  gi|121637147|ref|YP_977370.1| 35 GEVHGFLGPNGAGKSTTLRILLGLVKADGGSVRLLG 70
                                   4588899**********************9999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.051      29     143 ..      40     161 ..      22     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                         AAA_16  29 lsGesGvGKsslvrellralekdggif......lrgkcdqlesaipy....salaqalareellrqlldeaesaeleawr 98 
                                    + G+ G GKs+ +r ll  +++dgg +       ++++++l++ i+y    ++l+  l+  e +  l+++ +    +a r
  gi|121637147|ref|YP_977370.1|  40 FLGPNGAGKSTTLRILLGLVKADGGSVrllggdPWTDAVDLHRHIAYvpgdVTLWPSLTGGETIDLLARM-RGGIDNARR 118
                                    57***************99999977776666667777777799999999955599999998888888888.555899999 PP

                         AAA_16  99 ekleealaavpelagaea....srllellkrllallsrderplvlvlDd 143
                                    ++l e+++    l++ ++    s  +++  +l++ ls+  + ++l+lD+
  gi|121637147|ref|YP_977370.1| 119 AELIERFG----LDPTKKartySKGNRQKVSLISALSS--HATLLLLDE 161
                                    99999999....33333334456777777777755554..346777775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05      0.05      18      47 ..      27      56 ..      15      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                    ld+   e ++h  +GpN AGKst+lr + 
  gi|121637147|ref|YP_977370.1| 27 GLDLTVREGEVHGFLGPNGAGKSTTLRILL 56
                                   5888889999****************9765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     3e-05     0.067       6      38 ..      18      54 ..      15      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                         AAA_23  6 nfrsfrdqe.idF...skgltlItGpNGaGKTTildA 38
                                   +f+s r  + +d+   +  +  + GpNGaGK+T l+ 
  gi|121637147|ref|YP_977370.1| 18 HFGSVRALDgLDLtvrEGEVHGFLGPNGAGKSTTLRI 54
                                   67777666666776677778899**********9975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.8e-05      0.13      15      39 ..      28      52 ..      23      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    ++++++ +++ + Gp+G+GKST l
  gi|121637147|ref|YP_977370.1| 28 LDLTVREGEVHGFLGPNGAGKSTTL 52
                                   5566665558899**********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1852.10
//
Query:       gi|121637148|ref|YP_977371.1|  [L=212]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-46  156.8   0.3    3.2e-46  156.0   0.3    1.4  1  TetR_C_25  Tetracyclin repressor-like, C-terminal domain
    2.8e-14   52.6   0.6      6e-14   51.6   0.6    1.6  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.044   13.7   0.2       0.21   11.5   0.1    2.0  2  T2SSF      Type II secretion system (T2SS), protein F
      0.061   13.6   5.1       0.39   11.0   0.0    3.1  3  TetR_C_11  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_25  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.3     7e-50   3.2e-46       1     106 []      89     192 ..      89     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 7e-50
                      TetR_C_25   1 eeyaplvaYlvrslqaGgdlakallehmvedaeayleegvaaGtirpsrdpkarArylalsslGalllelqlheeedptd 80 
                                    e+yapl+aYlvrs+q+Gg+lak+l ++m+++ae+yl+egv+aGt++psrdp+arAr+la++++G++ll+lq+he  +ptd
  gi|121637148|ref|YP_977371.1|  89 ESYAPLMAYLVRSMQSGGELAKMLCQKMIDNAEEYLDEGVRAGTVKPSRDPRARARFLAITGGGGFLLYLQMHE--NPTD 166
                                    89************************************************************************..**** PP

                      TetR_C_25  81 lravlreylermvlPalElyteGllt 106
                                    lra+lr+y+++mvlP+lE+yteGll+
  gi|121637148|ref|YP_977371.1| 167 LRAALRDYAHDMVLPSLEVYTEGLLA 192
                                    ************************96 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.6   1.3e-17     6e-14       1      47 []      12      57 ..      12      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.3e-17
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   I +aA e f+++G+  +++r+IA++AGvs++++ ++F+sKe+L +a+
  gi|121637148|ref|YP_977371.1| 12 IREAAIEQFGRHGFG-VGLRAIAEAAGVSAALVIHHFGSKEGLRKAC 57
                                   779************.***************************9885 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.7e-05      0.21      11      81 ..      36     112 ..      30     126 .. 0.81
   2 ?   -0.4   0.0      0.24   1.1e+03      67      88 ..     157     178 ..     153     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                                    TT--HHHHHHHHHHHHS.....SHHHHHHHHHHHHHHHTTSSHHHHHCT-TT.TS.-HHHHHHHHHHHHHT-HHHHH CS
                          T2SSF  11 aGvplveaLellaeeae.....ngplaeelkriarrlraGgslsealertpssef.pelvvqlirageeggnLaevL 81 
                                    aGv+ + +++++++  +     +  +aee+++ ++      ++ + l+++ + e  ++l++ l+r+ ++gg La++L
  gi|121637148|ref|YP_977371.1|  36 AGVSAALVIHHFGSKEGlrkacDDFVAEEIRSSKAAALKSNDPTTWLAQMAEIESyAPLMAYLVRSMQSGGELAKML 112
                                    67777777777776666777778889999999999999999999999988885555********************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                                    HHHHHHHHT-HHHHHHHHHHHH CS
                          T2SSF  67 lirageeggnLaevLerlaeyl 88 
                                    ++++ e   +L ++L+++a+++
  gi|121637148|ref|YP_977371.1| 157 YLQMHENPTDLRAALRDYAHDM 178
                                    6789999999*******99987 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.28   1.2e+03      24      57 ..      34      65 ..      26      74 .. 0.66
   2 ?   11.0   0.0   8.7e-05      0.39      14      84 ..      81     144 ..      76     149 .. 0.80
   3 ?    2.6   0.4     0.035   1.6e+02       9      46 ..     165     202 ..     164     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                      TetR_C_11 24 spragallrallaeaqrdpelaealrerlleprr 57
                                   + +ag   + ++++  +++ l++a+ + +++++ 
  gi|121637148|ref|YP_977371.1| 34 E-AAGVSAALVIHHFGSKEGLRKACDD-FVAEEI 65
                                   4.4555666777778888888888888.666554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.7e-05
                      TetR_C_11  14 llralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvld 84 
                                    +l ++ae ++s   + l++ l+  +q+  ela+ l ++++    + +++ l+ +v+ G +++  d+++ + 
  gi|121637148|ref|YP_977371.1|  81 WLAQMAE-IES--YAPLMAYLVRSMQSGGELAKMLCQKMI----DNAEEYLDEGVRAGTVKPSRDPRARAR 144
                                    5555544.444..7899***************99999666....678899999999******999987665 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.035
                      TetR_C_11   9 gDLrallralaealaspragallrallaeaqrdpelae 46 
                                    +DLra lr++a  +  p  +    +lla+ +  +++ +
  gi|121637148|ref|YP_977371.1| 165 TDLRAALRDYAHDMVLPSLEVYTEGLLADRAMYEAFLA 202
                                    69999999999999999999888999888776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1580.60
//
Query:       gi|121637149|ref|YP_977372.1|  [L=215]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-25   89.1   0.0    2.5e-25   88.9   0.0    1.0  1  Methyltransf_3   O-methyltransferase
    3.9e-14   53.6   0.1    6.3e-14   52.9   0.1    1.3  1  Methyltransf_24  Methyltransferase domain
    6.2e-09   35.8   0.0      8e-09   35.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.7e-08   35.0   0.0    3.1e-08   34.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.2e-07   31.4   0.0    5.2e-07   30.2   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00059   19.4   0.0    0.00099   18.7   0.0    1.5  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.026   14.3   0.1      0.037   13.8   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.029   13.7   0.0      0.041   13.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.03   13.7   0.2        1.1    8.6   0.0    2.1  2  GidB             rRNA small subunit methyltransferase G
       0.17   11.5   0.0       0.21   11.3   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   1.4e-28   2.5e-25      24     209 ..      35     212 ..      20     215 .] 0.93

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 1.4e-28
                                    T.TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-G.GGEE CS
                 Methyltransf_3  24 tdlsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagva.ekie 102
                                    td+    v+++ g +L lL kl++ k v e+G+  G s L +  ++ +DG +++idi++e+  +a++ +  ag++  +  
  gi|121637149|ref|YP_977372.1|  35 TDIGAGAVTPAVGALLCLLAKLSGGKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIGpSRTR 114
                                    455566789999**************************************************************846899 PP

                                    EEES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG-SS--SHHHHH.....H CS
                 Methyltransf_3 103 liegdalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvveeddeeakalreyravl 182
                                    li g a++vL +l + +    +D++f+DaD  + + y  ++++L++ Gg+i++  +   G   ++ +  a++++     +
  gi|121637149|ref|YP_977372.1| 115 LISGRAQEVLTRLADAS----YDLVFIDADPIDQPDYVAEGVRLLRSGGVIVVHRAALGGRAGDPGARDAEVIA-----V 185
                                    *************9877....9****************************************999999999999.....8 PP

                                    HHHHHHHTT-TTEEEEEE-SBT-EEEE CS
                 Methyltransf_3 183 lelnkklaeDprveisllsvgDGitLv 209
                                     e  + +aeD+r+  +l+++gDG+  +
  gi|121637149|ref|YP_977372.1| 186 REAARLIAEDERLTPALVPLGDGVLAA 212
                                    8999*******************9866 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   3.5e-17   6.3e-14       2     104 ..      64     164 ..      63     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.5e-17
                Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare.....aglddrvrlikadseealaslaagsiDllfiD 76 
                                    E+G+ +Gvs lwll+ +r+ g   l+++d +p   e+ +lar+         +r rli+++++e+l++la+ s+Dl+fiD
  gi|121637149|ref|YP_977372.1|  64 EVGTGAGVSGLWLLSGMRDDG--VLTTIDIEP---EHLRLARQafaeaGIGPSRTRLISGRAQEVLTRLADASYDLVFID 138
                                    9******************99..5********...5444444433332445568************************** PP

                Methyltransf_24  77 gghaaeavledleallprlapggvvlfd 104
                                    +++   +  +++    ++l++ggv++++
  gi|121637149|ref|YP_977372.1| 139 ADP--IDQPDYVAEGVRLLRSGGVIVVH 164
                                    995..45555678889***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   4.4e-12     8e-09       3     113 ..      58     167 ..      56     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.4e-12
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee.leklledekfDlil 79 
                                     g+ v ++G+G+G  ++ l + +++++ ++ iDi++e ++lAr+  ++ g+   + ++  g ++e l   l+d+++Dl++
  gi|121637149|ref|YP_977372.1|  58 GGKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIGpsRTRLISGRAQEvLTR-LADASYDLVF 136
                                    68899********************************************999889**********6665.89******** PP

                Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr 113
                                     +   + +  pd + e+  r+l++gg++++  + 
  gi|121637149|ref|YP_977372.1| 137 ID--ADPIDQPDYVAEG-VRLLRSGGVIVVHRAA 167
                                    *9..3445555555555.89********998776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.7e-11   3.1e-08       1      97 []      62     159 ..      62     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.7e-11
                                    EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCG..BSSSTTTEEEEEEESTG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl...nvefvqgdaed..lpfedgsfDlvvssgal 74 
                                    v ++G+G G   l+l+  +  ++ +t +Di +e l+ ar+ ++e+g+   + +++ g a++    ++d+s+Dlv++  a 
  gi|121637149|ref|YP_977372.1|  62 VAEVGTGAGVSGLWLLSGMrDDGVLTTIDIEPEHLRLARQAFAEAGIgpsRTRLISGRAQEvlTRLADASYDLVFID-A- 139
                                    789*************99954999********************99999**********9953358**********4.4. PP

                                    GGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       ++ d++++++e  r+L+ gG
  gi|121637149|ref|YP_977372.1| 140 ---DPIDQPDYVAEGVRLLRSGG 159
                                    ...455678899*********99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.9e-10   5.2e-07       2      96 .]      64     163 ..      63     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.9e-10
                                    EET-TTSHHHHHHH...HTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCC.T.SS-TT-EEEEEEES-CCC CS
                Methyltransf_11   2 dvGcGtGrlaeala...krgarvvgvDlskemlklakekaseegl...kvefvvadaek.l.pfednsfDlvvssevlhh 73 
                                    +vG+G+G    +l    +  + ++++D+ +e l+la+++  e+g+   + +++ ++a++ l  ++d+s+Dlv++    + 
  gi|121637149|ref|YP_977372.1|  64 EVGTGAGVSGLWLLsgmRDDGVLTTIDIEPEHLRLARQAFAEAGIgpsRTRLISGRAQEvLtRLADASYDLVFIDA--DP 141
                                    799999999999995543338***************************999*******96458**********996..55 PP

                                    -CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                    + d+ ++++e +R+L+ gG++v+
  gi|121637149|ref|YP_977372.1| 142 I-DQPDYVAEGVRLLRSGGVIVV 163
                                    5.899***************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.5e-07   0.00099      25     102 ..      51     136 ..      33     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.5e-07
                                    HHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTSTTS CS
                            MTS  25 etlpke.lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle......vevvasdvleeveek 96 
                                      l k    + v+ +G+GaGv g++l++   +   +t +d++ + l++a++ +++ ++       ++ +a++vl  ++++
  gi|121637149|ref|YP_977372.1|  51 CLLAKLsGGKAVAEVGTGAGVSGLWLLSGMRDDGvLTTIDIEPEHLRLARQAFAEAGIGpsrtrlISGRAQEVLTRLADA 130
                                    444444235669*************99877666559*******************99988888888889999******** PP

                                    -EEEEE CS
                            MTS  97 kfdliv 102
                                    ++dl+ 
  gi|121637149|ref|YP_977372.1| 131 SYDLVF 136
                                    ***985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.1e-05     0.037      58     171 ..      43     163 ..      30     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                                    -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC....SEEEEES-G CS
                           PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle....nvivvvgDG 133
                                     p + al++ l +l+ g+ v evG+G+G     l   ++++g + +i+  +e  + a++   + ++     ++i   +  
  gi|121637149|ref|YP_977372.1|  43 TPAVGALLCLLAKLSGGKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIGpsrtRLISGRAQE 122
                                    5777788888888*****************************999*******9999999999998876644444444444 PP

                                    GGTTGGG-SEEEEEESSBBSS--HHH...HHTEEEEEEEEE CS
                           PCMT 134 rkGyeekaPYdaihvgaaapeiPeal...idQLkeGGrlvv 171
                                         + a Yd +++ a + + P+     ++ L +GG +vv
  gi|121637149|ref|YP_977372.1| 123 VLTRLADASYDLVFIDADPIDQPDYVaegVRLLRSGGVIVV 163
                                    45555678888888888877777655222456777777765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.3e-05     0.041      48     151 ..      59     163 ..      50     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                    TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS..TEEEEE--TTT-..TTS-T-EEEEEEE CS
                Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki..nieflqanaeeL..pfeddsfDvvtvs 123
                                    g+ v +v +G+g   + l++ +++ g ++ +Di+++ L+ +++   e g    + +++ + a+e+     d s+D+v + 
  gi|121637149|ref|YP_977372.1|  59 GKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIGpsRTRLISGRAQEVltRLADASYDLVFID 138
                                    567889999*************************************99887669********997334678999999998 PP

                                    S-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                           D++  + e  r l+ GG +vv
  gi|121637149|ref|YP_977372.1| 139 AD---PIDQPDYVAEGVRLLRSGGVIVV 163
                                    65...55666667899999999999887 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.02        36      38      64 ..      20      46 ..       7      57 .. 0.75
   2 ?    8.6   0.0   0.00059       1.1      46     123 ..      57     139 ..      48     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.02
                                   HHHHGGCS-CCC-.EEEETSTTTTTHH CS
                           GidB 38 slsvlellkekrdkviDvGsGaGlPGi 64
                                   s+s   +l  +r++  D+G+Ga  P++
  gi|121637149|ref|YP_977372.1| 20 SISEDVILAGARERATDIGAGAVTPAV 46
                                   566666677778789*******99987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00059
                                    -CCC-.EEEETSTTTTTHHH.HHHH-TTSEEEEEES-HHHHHHHHHHHHH..CT-SSEEEEES-CCC...TTTTT-EEEE CS
                           GidB  46 kekrdkviDvGsGaGlPGip.LaiarpelkltLleslekkiaFLeevkee..lklenveivearaee...kqeeekydvv 119
                                    +  + +v+ vG+GaG+ G+  L+ +r +  lt ++ +    +  +++ +e  ++ + ++ +  ra+e   +    +yd+v
  gi|121637149|ref|YP_977372.1|  57 SGGK-AVAEVGTGAGVSGLWlLSGMRDDGVLTTIDIEPEHLRLARQAFAEagIGPSRTRLISGRAQEvltRLADASYDLV 135
                                    4455.69***********96156777777788776666555555555555114456788888888887666667778877 PP

                                    EEC- CS
                           GidB 120 tsRA 123
                                     + A
  gi|121637149|ref|YP_977372.1| 136 FIDA 139
                                    7766 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.21      35      91 ..      53     111 ..      43     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                          GCD14  35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel..s 91 
                                      +l  G  v e GtG+g     ++  +   G l t++   +  + ar+ f e ++  s
  gi|121637149|ref|YP_977372.1|  53 LAKLSGGKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIgpS 111
                                    55788999***********99********************************999541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1524.34
//
Query:       gi|121637150|ref|YP_977373.1|  [L=257]
Description: RNA polymerase sigma factor SigE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-22   78.2   0.9    5.1e-22   77.4   0.9    1.4  1  Sigma70_r2     Sigma-70 region 2
    1.8e-17   62.7   0.1    4.9e-17   61.3   0.0    1.7  2  Sigma70_r4_2   Sigma-70, region 4
    3.9e-14   51.9   0.0    7.9e-14   50.9   0.0    1.5  1  Sigma70_r4     Sigma-70, region 4
    0.00084   19.3   0.0     0.0015   18.5   0.0    1.4  1  Sigma70_ECF    ECF sigma factor
     0.0028   17.4   0.1     0.0081   15.9   0.1    1.8  1  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
      0.051   13.4   0.0       0.12   12.2   0.0    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
        1.1    8.9   3.8       0.64    9.6   0.2    2.5  3  UBM            Ubiquitin binding region


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.9     2e-25   5.1e-22       1      70 [.      87     153 ..      87     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2e-25
                                    HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 
                                    lv+++ ++v+rla+rl g+++daeDl+Qe+f+r++r+v++++  +g  f+ wl+ri++n+++d +R+r+r
  gi|121637150|ref|YP_977373.1|  87 LVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQ--PG-TFEGWLHRITTNLFLDMVRRRAR 153
                                    799************************************999..99.9********************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         2   5.2e+03       8      15 ..     156     163 ..     155     166 .. 0.80
   2 !   61.3   0.0   1.9e-20   4.9e-17       4      54 .]     186     236 ..     185     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                                    HTTS-HHH CS
                   Sigma70_r4_2   8 laeLperq 15 
                                    +++Lpe++
  gi|121637150|ref|YP_977373.1| 156 MEALPEDY 163
                                    789***98 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 1.9e-20
                                    HHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   4 lrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    l++ala+Lp++ r++++l+++eglsy+EI + lg++ gtV+sr++R+r++L
  gi|121637150|ref|YP_977373.1| 186 LQAALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQAL 236
                                    899*********************************************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   3.1e-17   7.9e-14       1      50 []     189     238 ..     189     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.1e-17
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                                    aLasLp++ r  ++l+  egl++eEIg++lg+ +++Vr++++r+++ LR+
  gi|121637150|ref|YP_977373.1| 189 ALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRD 238
                                    8***********************************************95 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.7e-07    0.0015      52     180 ..     112     237 ..      75     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.7e-07
                    Sigma70_ECF  52 LvfeaflrlvdkekfpdlsgrdhlfalaaeamrrilidhaRrrkrqkRGGdvvraeldeeeds..vdsdspdelle...L 126
                                    L  e f+r+ +   + +  +++ + + + +++     d  Rrr r +       ++l e+ d    d+++p+++ +   L
  gi|121637150|ref|YP_977373.1| 112 LTQETFIRVFR---SVQNYQPGTFEGWLHRITTNLFLDMVRRRARIR------MEALPEDYDRvpADEPNPEQIYHdarL 182
                                    56666777666...333344677777777777777777777776644......445555555544556666666431224 PP

                    Sigma70_ECF 127 d.ealerllsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawle 180
                                      +    l+sl+pe +  v l  +eGls eEi+++lgv   tv+ r +  R+ l+
  gi|121637150|ref|YP_977373.1| 183 GpDLQAALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALR 237
                                    4133456788**********************************99998887666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.2e-06    0.0081      10      39 ..     200     231 ..     198     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.2e-06
                         HTH_23  10 illllae.GlsvreIAreLgvsrrTvy.rwlk 39 
                                    ++ l++  Gls++eI + Lgv   Tv+ r+++
  gi|121637150|ref|YP_977373.1| 200 AVVLCDIeGLSYEEIGATLGVKLGTVRsRIHR 231
                                    78899966*******************55543 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.7e-05      0.12      18      40 ..     209     231 ..     208     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                  HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                    +sy+e+++ +G+   tv+ R++r
  gi|121637150|ref|YP_977373.1| 209 LSYEEIGATLGVKLGTVRSRIHR 231
                                    59*******************98 PP

>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.61   1.6e+03      14      20 ..     156     162 ..     156     162 .. 0.86
   2 ?   -3.3   0.0       2.8   7.3e+03      17      23 ..     182     188 ..     182     189 .. 0.81
   3 ?    9.6   0.2   0.00025      0.64      14      26 ..     190     202 ..     190     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.61
                            UBM  14 LaaLPpd 20 
                                    ++aLP+d
  gi|121637150|ref|YP_977373.1| 156 MEALPED 162
                                    58***98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                            UBM  17 LPpdLRe 23 
                                    L pdL++
  gi|121637150|ref|YP_977373.1| 182 LGPDLQA 188
                                    789*996 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00025
                            UBM  14 LaaLPpdLReEVL 26 
                                    La+LPp+ R++V 
  gi|121637150|ref|YP_977373.1| 190 LASLPPEFRAAVV 202
                                    9*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1955.38
//
Query:       gi|121637151|ref|YP_977374.1|  [L=154]
Description: hypothetical protein BCG_1282 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.0   1.2       0.05   13.9   1.2    1.6  1  zf-HC2    Putative zinc-finger


Domain annotation for each model (and alignments):
>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   2.8e-06      0.05       5      35 .]      44      74 ..      42      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-06
                                   HHHHHHHHCCT-SCCCHCCCHHHHCHTCHHC CS
                         zf-HC2  5 relLsaYlDGeLspeerarveaHLaeCpdCr 35
                                    e++ a++DGeL    + r  +HL+ C+ C+
  gi|121637151|ref|YP_977374.1| 44 IEAIAAFVDGELRMNAHLRAAHHLSLCAQCA 74
                                   58999*************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1033.46
//
Query:       gi|121637152|ref|YP_977375.1|  [L=528]
Description: serine protease htrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-35  123.2   3.5    3.7e-35  122.0   3.5    1.7  1  Trypsin_2      Trypsin-like peptidase domain
    1.9e-15   57.3   0.5    1.9e-15   57.3   0.5    1.6  2  Trypsin        Trypsin
    3.7e-13   49.6   1.1    3.7e-13   49.6   1.1    2.8  3  PDZ_2          PDZ domain
    3.3e-07   30.0   3.8    3.1e-06   26.9   1.4    3.2  3  PDZ_6          PDZ domain
    6.6e-07   29.6   1.6    3.2e-06   27.4   0.9    2.5  2  PDZ            PDZ domain
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.056   13.8   0.0    1.9  2  GRASP55_65     GRASP55/65 PDZ-like domain
      0.029   13.0   1.4       0.75    8.4   0.4    2.1  2  Peptidase_S46  Peptidase S46
       0.11   12.3   0.0       0.18   11.6   0.0    1.3  1  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
       0.12   12.2   0.0       0.41   10.5   0.0    1.8  2  PIG-H          GPI-GlcNAc transferase complex, PIG-H componen
        0.3   10.6   0.4        8.3    5.8   0.0    2.1  2  DUF31          Putative peptidase (DUF31)
        1.2    9.3  11.6         23    5.2   0.1    3.2  2  DUF4330        Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   3.5   2.3e-38   3.7e-35       1     150 []     254     401 ..     254     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 2.3e-38
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsea 80 
                                    GsG++v+++g+i+Tn+Hv+++a++ +    ++k +++ +dg+evpa++v++dp +DlA+lkv  d  ++l +++lg+s++
  gi|121637152|ref|YP_977375.1| 254 GSGVIVDGRGYIVTNNHVISEAANNPS---QFKTTVVLNDGKEVPANLVGRDPKTDLAVLKV--DNVDNLTVARLGDSSK 328
                                    9**************************...9*********************999*******..**************** PP

                      Trypsin_2  81 lkggepvyvvGyplggeksgsvssGivsgvve.....sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                    +++g++v +vG plg  +  +v++Givs++ +     +e++++ +  + +qtda++++G+SGGpl+d d +v+G+
  gi|121637152|ref|YP_977375.1| 329 VRVGDEVLAVGAPLGLRS--TVTQGIVSALHRpvplsGEGSDTDTVIDAIQTDASINHGNSGGPLIDMDAQVIGI 401
                                    ******************..9*************9999999999999999************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       4.3     7e+03     171     184 ..      22      35 ..      14      35 .. 0.76
   2 !   57.3   0.5   1.1e-18   1.9e-15      25     217 ..     252     424 ..     234     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.3
                                    TSSSBCTTTTTTSE CS
                        Trypsin 171 eggkdacqGDSGGP 184
                                    e+++ + qG+ GGP
  gi|121637152|ref|YP_977375.1|  22 EDEVTSDQGNNGGP 35 
                                    4568899******9 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.1e-18
                                    EEEEEEEEETT.EEEEEGGGTTT....GGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSST CS
                        Trypsin  25 hlCgGslisen.wvlTAaHCvsn....asdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvk 99 
                                       +G++++ + +++T++H++s+    +s++     +++++ ++gke  +++         +p+t   D+a+lk+++   
  gi|121637152|ref|YP_977375.1| 252 MQGSGVIVDGRgYIVTNNHVISEaannPSQF-----KTTVVLNDGKEVPANLVG------RDPKT---DLAVLKVDNV-- 315
                                    556899999999**********964333333.....358999999744444444......78888...*********9.. PP

                                    SBSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTT CS
                        Trypsin 100 lgdtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqG 179
                                      d+   ++l + ss++ vg+++l++G +     +  +t++++ v+++ r    s  +g  t++ + a    +++++++G
  gi|121637152|ref|YP_977375.1| 316 --DNLTVARLGD-SSKVRVGDEVLAVGAPLG--LR--STVTQGIVSALHRPVPLS-GEGSDTDTVIDAIQ--TDASINHG 385
                                    ..999999***9.777889988888888885..44..679999999999984444.34445666655555..667***** PP

                                    TTTSEEEETTTEEEEEEEEESSSSCTTS.EEEEEEGGGG CS
                        Trypsin 180 DSGGPlvcsdgelvGivswgkgcakgnr.pgvytkvssy 217
                                    +SGGPl+ +d +++Gi+++gk+ ++     g++++v+++
  gi|121637152|ref|YP_977375.1| 386 NSGGPLIDMDAQVIGINTAGKSLSDSASgLGFAIPVNEM 424
                                    ********************5544444449****99976 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3   4.8e+03      23      40 ..       9      27 ..       5      31 .. 0.73
   2 ?   -0.5   0.1      0.94   1.5e+03      30      42 ..     327     339 ..     296     341 .. 0.71
   3 !   49.6   1.1   2.3e-16   3.7e-13       1      81 [.     440     522 ..     440     522 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                                   TTSGGGGT..--TT-EEEE CS
                          PDZ_2 23 eggPaakag.lkagDvilk 40
                                   +++Pa  +  ++ +D++++
  gi|121637152|ref|YP_977375.1|  9 NAMPARFSAqIQNEDEVTS 27
                                   6678765444999**9997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.94
                                    T.--TT-EEEEET CS
                          PDZ_2  30 aglkagDvilkvd 42 
                                    ++++ gD++l+v+
  gi|121637152|ref|YP_977375.1| 327 SKVRVGDEVLAVG 339
                                    4567788888885 PP

  == domain 3  score: 49.6 bits;  conditional E-value: 2.3e-16
                                    ....XX------....-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEE CS
                          PDZ_2   1 pylGvsvsdeed..tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktv 78 
                                    p lG+ ++++++  ++g+ v++Vk g+Pa+k g+  +Dvi+kv++++v +++++  ++++  +G++  ++v R+g+  t+
  gi|121637152|ref|YP_977375.1| 440 PTLGINTRSVSNaiASGAQVANVKAGSPAQKGGILENDVIVKVGNRAVADSDEFVVAVRQLAIGQDAPIEVVREGRHVTL 519
                                    679*******99999***************************************************************** PP

                                    EEE CS
                          PDZ_2  79 evk 81 
                                    +vk
  gi|121637152|ref|YP_977375.1| 520 TVK 522
                                    997 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   5.2e+03      30      43 ..     197     210 ..     194     216 .. 0.81
   2 ?    1.3   0.0      0.19   3.1e+02      16      26 ..     329     339 ..     323     340 .. 0.84
   3 !   26.9   1.4   1.9e-09   3.1e-06       2      43 ..     459     498 ..     458     512 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                          PDZ_6  30 veglsladvaallr 43 
                                    v+g+++a+v+++  
  gi|121637152|ref|YP_977375.1| 197 VIGRKTAEVVDAFT 210
                                    78999*****9987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.19
                          PDZ_6  16 lrvGDiilsvN 26 
                                    +rvGD +l+v+
  gi|121637152|ref|YP_977375.1| 329 VRVGDEVLAVG 339
                                    8********96 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 1.9e-09
                          PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr 43 
                                    V  V++gsPA ++G+  +D+i++v+++ v   + ++++ ++r
  gi|121637152|ref|YP_977375.1| 459 VANVKAGSPAQKGGILENDVIVKVGNRAV--ADSDEFVVAVR 498
                                    789**************************..99888877766 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.7e+03      42      54 ..     327     339 ..     323     341 .. 0.82
   2 !   27.4   0.9   1.9e-09   3.2e-06      11      60 ..     441     489 ..     431     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                    HTSSTTEEEEEET CS
                            PDZ  42 dglkvGDkIlsvN 54 
                                    ++++vGD++l+v+
  gi|121637152|ref|YP_977375.1| 327 SKVRVGDEVLAVG 339
                                    4489******996 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.9e-09
                                    ESSEEEEEETTSSSSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTT CS
                            PDZ  11 glGfslkggsdqrgdkgifvsevlpggaaeadglkvGDkIlsvNgvdven 60 
                                     lG++ ++ s++  + g+ v++v +g++a+++g+ ++D+I++v+++ v++
  gi|121637152|ref|YP_977375.1| 441 TLGINTRSVSNAI-ASGAQVANVKAGSPAQKGGILENDVIVKVGNRAVAD 489
                                    6899999999985.99*****************************98876 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2     2e+03      39      87 ..     235     287 ..     214     317 .. 0.73
   2 ?   13.8   0.0   3.4e-05     0.056      27      88 ..     441     499 ..     420     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                    TTTTS-EEEEEEBTTSHHHHHT.--TTTEEEEEEE....SSSSSTSCSHHHHT CS
                     GRASP55_65  39 kaaeevwhvldvlegsPaakag.LvpksDYiiGldk...gllkgeedlselve 87 
                                    ++a++v+ +  v ++   + +g +v+ + Yi+  ++   +  ++ +++ ++v 
  gi|121637152|ref|YP_977375.1| 235 AVADSVVTIESVSDQEGMQGSGvIVDGRGYIVTNNHvisEAANNPSQFKTTVV 287
                                    35677888888888888888887888999999888733333335555665555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.4e-05
                                    SSSEEEEEEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTT CS
                     GRASP55_65  27 llGlslrlaslekaaeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselvea 88 
                                    +lG+     s+++a  +  +v +v+ gsPa+k g+++ +D i+ + +  ++++++++  v++
  gi|121637152|ref|YP_977375.1| 441 TLGIN--TRSVSNAIASGAQVANVKAGSPAQKGGILE-NDVIVKVGNRAVADSDEFVVAVRQ 499
                                    45554..5566778999*****************987.69*************999998876 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.013        22      48      76 ..     253     281 ..     225     291 .. 0.84
   2 ?    8.4   0.4   0.00046      0.75     627     652 ..     378     403 ..     367     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.013
                                    TEE-EE-STT-EEEE-HHHHHHHHHHT-- CS
                  Peptidase_S46  48 gCtasfVSpeGLvlTNHHCaygaiqqhss 76 
                                      ++ +V  +G ++TN H++ +a ++ s+
  gi|121637152|ref|YP_977375.1| 253 QGSGVIVDGRGYIVTNNHVISEAANNPSQ 281
                                    479******************99998886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00046
                                    ES----TT-TT-EEE-TTS-EEEEEE CS
                  Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGlaF 652
                                    +++ i  GNSG P+++ +++++G++ 
  gi|121637152|ref|YP_977375.1| 378 TDASINHGNSGGPLIDMDAQVIGINT 403
                                    6778899****************985 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.18      57     166 ..     208     318 ..     190     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                         CLP1_P  57 gfsldaplvyffG.dtspsdnpslylalvkelareveekleenkkakasgliIntpGwvkglgaellleliealepdvvv 135
                                     f + + +    G  + p +  +++ a+v++ + ++e+ ++ ++ ++ sg+i++  G++   ++ + +++ +  + +  v
  gi|121637152|ref|YP_977375.1| 208 AFTTSKVTLSTTGnAQEPAGRFTKVAAAVADSVVTIES-VSDQEGMQGSGVIVDGRGYIVTNNHVISEAANNPSQFKTTV 286
                                    55544444444441467999999999999999999995.66668********************9*99999999999999 PP

                         CLP1_P 136 vldq.eellnelkrdlplskvkvvklpkspgv 166
                                    vl + +e  ++l    p++++ v+k++ ++ +
  gi|121637152|ref|YP_977375.1| 287 VLNDgKEVPANLVGRDPKTDLAVLKVDNVDNL 318
                                    99998888899999999999999999988765 PP

>> PIG-H  GPI-GlcNAc transferase complex, PIG-H component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.41       9      48 ..      64     103 ..      60     107 .. 0.82
   2 ?   -2.9   0.0       3.8   6.2e+03       4      15 ..     438     449 ..     437     461 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                          PIG-H   9 GvQlsssylsrllpfsggtsrrFiplekirdvvInEaf.kg 48 
                                    GvQ s    +r +p++ + ++ F p +++ d v+ Eaf + 
  gi|121637152|ref|YP_977375.1|  64 GVQGSFV-AERVRPQKYQDQSDFTPNDQLADPVLQEAFgRP 103
                                    6666554.47889999**********************665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                          PIG-H   4 vlrglGvQlsss 15 
                                    v + lG+ ++s 
  gi|121637152|ref|YP_977375.1| 438 VHPTLGINTRSV 449
                                    77899**99998 PP

>> DUF31  Putative peptidase (DUF31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.041        68      58      75 ..     264     281 ..     262     331 .. 0.74
   2 ?    5.8   0.0    0.0051       8.3     348     373 .]     379     404 ..     373     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.041
                          DUF31  58 YlATNlHVaaalrnandk 75 
                                    Y+ TN HV+++  n+ ++
  gi|121637152|ref|YP_977375.1| 264 YIVTNNHVISEAANNPSQ 281
                                    999*******77776663 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0051
                          DUF31 348 ssalagGaSGSlvrnkdnklvGIyfa 373
                                    + ++ +G SG ++++ d +++GI+ a
  gi|121637152|ref|YP_977375.1| 379 DASINHGNSGGPLIDMDAQVIGINTA 404
                                    66899******************975 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   7.9     0.056        91      12      56 ..     174     217 ..     169     356 .. 0.64
   2 ?    5.2   0.1     0.014        23     119     153 ..     475     509 ..     445     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.056
                        DUF4330  12 gkvnilDllailvilavivgiflkpgts.gsvaqaeaaatkpvevd 56 
                                    gkv+ l l+++++i +vi gi  ++g++ ++v  a   +t++v+ +
  gi|121637152|ref|YP_977375.1| 174 GKVSYLALGILVAIALVIGGIGGVIGRKtAEVVDA--FTTSKVTLS 217
                                    8*************************994333222..234444432 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                        DUF4330 119 lkdllvtlegkakitedglvlggqkvkvGkevele 153
                                     +d++v +  +a++++d++v++ +++ +G++  +e
  gi|121637152|ref|YP_977375.1| 475 ENDVIVKVGNRAVADSDEFVVAVRQLAIGQDAPIE 509
                                    579**************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3545.90
//
Query:       gi|121637153|ref|YP_977376.1|  [L=131]
Description: sec-independent translocase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00012   21.4   0.8    0.00012   21.3   0.0    1.5  2  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     7e-09   0.00012       1      44 [.       5      48 ..       5      71 .. 0.89
   2 ?   -2.8   0.2      0.22     4e+03      23      30 ..     105     112 ..     102     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7e-09
                                   S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHH CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkele 44
                                   +g+ e+l++++V l++ Gp++LP + r + ++Lr+ +  +++ +
  gi|121637153|ref|YP_977376.1|  5 IGWGEMLVLVMVGLVVLGPERLPGAIRWAASALRQARDYLSGVT 48
                                   79***********************9999999998776666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.22
                                    HHHHHHHH CS
                    MttA_Hcf106  23 PEvaraLG 30 
                                    P++a ++G
  gi|121637153|ref|YP_977376.1| 105 PDAAGSAG 112
                                    99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 902.89
//
Query:       gi|121637154|ref|YP_977377.1|  [L=276]
Description: hypothetical protein BCG_1285c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-22   77.8   0.0      1e-21   76.9   0.0    1.5  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    5.9e-19   67.9   0.1    2.1e-18   66.1   0.2    2.0  2  Hydrolase_like   HAD-hyrolase-like
    8.4e-12   45.8   6.5    5.7e-06   26.8   0.3    3.0  2  Hydrolase        haloacid dehalogenase-like hydrolase
    1.9e-10   41.1   1.7    7.5e-07   29.4   0.0    3.0  3  HAD_2            Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.039   13.6   0.1    1.4  1  PGP_phosphatase  Mitochondrial PGP phosphatase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   2.9e-25     1e-21       1      95 [.      11     105 ..      11     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.9e-25
                                    EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHSXX CS
                    Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkrkad 80 
                                    +lfDidGvL+   +aipgaae++++l+ +g+ +++lTN ++++++++a+ l + g+++++++v+t+++ +aeyl+ ++++
  gi|121637154|ref|YP_977377.1|  11 VLFDIDGVLVLSWRAIPGAAETVRQLTHRGIACAYLTNTTTRTRRQIAEALGAAGIPVAADDVITAGVLTAEYLHGAYPG 90 
                                    69****************************************************************************** PP

                                    XEEEEESXHHHHHHH CS
                    Hydrolase_6  81 kkvlvigeeglreel 95 
                                     +++++ + ++ e l
  gi|121637154|ref|YP_977377.1|  91 ARCFLVNNGDITEDL 105
                                    *****9998888765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.2   1.5e+04      42      51 ..      90      99 ..      89     105 .. 0.78
   2 !   66.1   0.2     6e-22   2.1e-18       2      73 ..     192     268 ..     191     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.2
                                   T-EEEEESSS CS
                 Hydrolase_like 42 GwksvLVltG 51
                                   G+++ LV  G
  gi|121637154|ref|YP_977377.1| 90 GARCFLVNNG 99
                                   8899999888 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 6e-22
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHH.....HHHHHT---SEEE CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedlee.....pehkptyvaddla 73 
                                    +gKP++e + +a+ ++g+dp++++miGD+l+ D+++A+++G+++vLV+tG++r++ l +      + +p++v+d++a
  gi|121637154|ref|YP_977377.1| 192 IGKPAAEGFLAAADRVGVDPQQMVMIGDDLHNDVLAAQAVGMTGVLVRTGKFRQQTLDRwlagaSATRPHHVIDSVA 268
                                    6*****************************************************9988888886668*******997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.4   2.7e-07   0.00095     107     173 ..      15      77 ..       8      87 .. 0.77
   2 !   26.8   0.3   1.6e-09   5.7e-06     167     210 .]     187     232 ..     166     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                    HHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 107 alavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvak 173
                                    +++v+ ++      p+aae+v++L  +gi  + lt+   +t + +a+ lG  +  + +a+d++  a+
  gi|121637154|ref|YP_977377.1|  15 IDGVLVLSWR--AIPGAAETVRQLTHRGIACAYLTNTTTRTRRQIAEALG--AAGIPVAADDVITAG 77 
                                    6778888877..99************************************..333334444433444 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.6e-09
                                    HCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                    xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 167 diet.vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                     + t ++kp  eg++aa+++ +++p++++m+GD +  D+ a++a+g
  gi|121637154|ref|YP_977377.1| 187 KTATaIGKPAAEGFLAAADRVGVDPQQMVMIGDDLHnDVLAAQAVG 232
                                    333369*****************************99******987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       0.1   3.6e+02       1      10 [.      11      20 ..      11      25 .. 0.88
   2 !    8.2   0.0   0.00067       2.4      80     117 ..      25      62 ..      21      66 .. 0.90
   3 !   29.4   0.0   2.1e-10   7.5e-07     123     176 ..     182     236 ..     171     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                          HAD_2  1 iiFDlDgTll 10
                                   ++FD+Dg+l+
  gi|121637154|ref|YP_977377.1| 11 VLFDIDGVLV 20
                                   79******97 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00067
                          HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlg 117
                                     ++g+ e++ +L+++g+ ++  T+ ++++ ++  e+lg
  gi|121637154|ref|YP_977377.1|  25 AIPGAAETVRQLTHRGIACAYLTNTTTRTRRQIAEALG 62 
                                    689***********************999999888887 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 2.1e-10
                          HAD_2 123 dvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                    ++ ++++ +   KP++e +++a ++ ++++++++++GD   +D+ aa+++g++ +
  gi|121637154|ref|YP_977377.1| 182 EQACGKTATAIGKPAAEGFLAAADRVGVDPQQMVMIGDDLhNDVLAAQAVGMTGV 236
                                    566777888889****************************9***********865 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.039     135     166 ..     210     241 ..     197     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                PGP_phosphatase 135 eadeiavvgDRllTdvllanmmGslgvwlrdg 166
                                    ++++++++gD l  dvl+a+ +G +gv++r g
  gi|121637154|ref|YP_977377.1| 210 DPQQMVMIGDDLHNDVLAAQAVGMTGVLVRTG 241
                                    799*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1898.74
//
Query:       gi|121637155|ref|YP_977378.1|  [L=487]
Description: hypothetical protein BCG_1286c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-26   89.9   2.4    1.6e-14   53.8   0.3    3.3  3  bPH_2          Bacterial PH domain
  ------ inclusion threshold ------
        5.9    6.6  15.8        2.7    7.8   1.7    2.8  3  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.3   1.8e-18   1.6e-14       1      74 [.      62     135 ..      62     143 .. 0.87
   2 !   11.9   0.0   2.2e-05       0.2      12      57 ..     255     300 ..     252     324 .. 0.87
   3 !   22.5   0.1   1.1e-08   9.9e-05       7      60 ..     401     454 ..     395     466 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.8e-18
                          bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdae 74 
                                    +++tty+i+d+ v++r+Gil+r+ + +p++rI++v++e+ ll+r+lgl+ +++ t++++r e+ ++l  v+ a+
  gi|121637155|ref|YP_977378.1|  62 WFFTTYRIDDENVSLRTGILSRRAVSVPRNRIRSVQTEARLLHRLLGLTVLRVGTGQEARGEAAFELDAVDSAR 135
                                    899*********************************************************99555555444443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.2e-05
                          bPH_2  12 rvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietag 57 
                                     +++r+G+l+ ++++  ++r + ++l+++ll r+l+ + +    +g
  gi|121637155|ref|YP_977378.1| 255 VLHLRHGLLRVREHTYDMRRLRGATLREPLLVRLLRGARLDAVMTG 300
                                    589********************************99888766655 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.1e-08
                          bPH_2   7 titdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsr 60 
                                    ++ d  +v r G l+r++ +i  + I   +++q+l+qrr g++t+v  ta g +
  gi|121637155|ref|YP_977378.1| 401 RVADGWLVARAGSLQRRRDCIACTGIIGWTVRQTLFQRRAGVATLVAATAAGRK 454
                                    666677899******************************************997 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       0.4   3.6e+03       4     178 ..      47      62 ..      22      83 .. 0.59
   2 ?    7.8   1.7    0.0003       2.7      90     167 ..     163     239 ..     146     288 .. 0.64
   3 ?    7.4   2.6   0.00038       3.4     118     175 ..     334     390 ..     316     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.4
                  FA_desaturase   4 lallla..lllglfllgitgslaHeaaHgalfkkrklnrwlndllgallglplgisysawrisHlrHHaytngpdeDpdl 81 
                                    ++++l+  +++g+                                                                   
  gi|121637155|ref|YP_977378.1|  47 PLAALGvtVVFGV------------------------------------------------------------------- 59 
                                    2222221222222................................................................... PP

                  FA_desaturase  82 aplalsrfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllgla 161
                                                                                                                    
  gi|121637155|ref|YP_977378.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                  FA_desaturase 162 lllwlvplllllfllal 178
                                                  l++
  gi|121637155|ref|YP_977378.1|  60 --------------LRW 62 
                                    ..............222 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0003
                  FA_desaturase  90 eglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrk...wrllawlllllawlglwlalllllglalllwl 166
                                    +++ ry++  ++gl+++g +++l    + ++la+r   s  +r     ++  +++l++++ ++l++++++ll++++  wl
  gi|121637155|ref|YP_977378.1| 163 SSWLRYAPLSFSGLVMIGAVIGLG---YQTGLAVRLPESGFARSAvdaAQRAGVVLVVAVTVLLVVGVSALLAVLF-SWL 238
                                    567788888888888888444444...8888888888777777766653333333333333444444444333333.443 PP

                  FA_desaturase 167 v 167
                                     
  gi|121637155|ref|YP_977378.1| 239 T 239
                                    3 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00038
                  FA_desaturase 118 lrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfl 175
                                    + +l+r +  +++rr+++ ll   l+  ++l++++++l+++g+a+ lw+v  + ++ l
  gi|121637155|ref|YP_977378.1| 334 AGPLRRHGPAAARRRWTRALLVPTLAG-VALIAAAPILGVPGWAWTLWAVLTAGCAGL 390
                                    556777777777777754443333333.349*************99999987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3508.12
//
Query:       gi|121637156|ref|YP_977379.1|  [L=177]
Description: hypothetical protein BCG_1287c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-16   59.1   0.3    5.1e-16   58.6   0.3    1.2  1  bPH_2     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.3   2.8e-20   5.1e-16       1      80 []      87     165 ..      87     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.8e-20
                          bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeelaell 80 
                                    yr ++++i+ + v  r+G+l +++++ p++r+q+v++ +++++r++gl+++ ++ta++++ +v++++++ + a+++ ++l
  gi|121637156|ref|YP_977379.1|  87 YRVHRWEISPQAVFTRTGWLVQERRITPISRVQTVDTYRGPMDRLFGLANVTVTTASSAG-AVHIEALDTDVADRVVAQL 165
                                    8999*******************************************************7.9*************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1184.11
//
Query:       gi|121637157|ref|YP_977380.1|  [L=185]
Description: lipoprotein lpqX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1378.17
//
Query:       gi|121637158|ref|YP_977381.1|  [L=390]
Description: MRP-related protein mrp [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-86  287.9   0.2    7.5e-86  287.6   0.2    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    6.8e-18   64.6   0.2      2e-17   63.1   0.2    1.9  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
    6.8e-14   52.0   0.0    1.5e-13   50.9   0.0    1.6  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    2.2e-08   34.2   0.7    3.3e-07   30.4   0.7    2.1  1  AAA_31          AAA domain
    7.5e-08   32.0   0.0    1.5e-07   31.0   0.0    1.5  1  MipZ            ATPase MipZ
    0.00014   21.4   0.0     0.0003   20.3   0.0    1.5  1  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
     0.0019   17.8   1.7     0.0032   17.1   0.7    1.8  2  AAA_25          AAA domain
     0.0027   16.9   0.4     0.0045   16.2   0.2    1.5  2  ArsA_ATPase     Anion-transporting ATPase
  ------ inclusion threshold ------
      0.075   12.8   1.9        6.8    6.5   0.1    2.4  2  AAA_26          AAA domain
      0.082   12.2   1.0      0.094   12.0   0.1    1.5  2  VirC1           VirC1 protein
       0.14   11.9   0.0       0.25   11.1   0.0    1.4  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
       0.15   11.9   0.0       0.34   10.8   0.0    1.5  1  APS_kinase      Adenylylsulphate kinase
       0.17   10.6   0.0       0.42    9.3   0.0    1.5  2  DUF1073         Protein of unknown function (DUF1073)
       0.25   10.8   0.9        6.4    6.2   0.5    2.3  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
       0.49   10.3   4.4       0.32   10.9   0.4    2.3  2  BAT             GAF and HTH_10 associated domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.6   0.2   6.3e-89   7.5e-86       3     244 ..     126     370 ..     124     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 287.6 bits;  conditional E-value: 6.3e-89
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfll 82 
                                    ++v+av+SgKGGVGKStv+vnlA+a+a +gl++g+lDaDi+G+sipr++g++++ p+q e++++P  a+++kv+Si+ ++
  gi|121637158|ref|YP_977381.1| 126 TRVYAVASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHSIPRMMGTTDR-PTQVESMILPPIAHQVKVISIAQFT 204
                                    6899*************************************************6.8888889****************** PP

                           ParA  83 esedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkk 162
                                    +  +++vvwrGpm+++a++q+l+dv+wg+lD+L++DlPPGtgD++++vaq +p a+ ++Vttpq +a++++++a +++ +
  gi|121637158|ref|YP_977381.1| 205 Q-GNTPVVWRGPMLHRALQQFLADVYWGDLDVLLLDLPPGTGDVAISVAQLIPNAELLVVTTPQLAAAEVAERAGSIALQ 283
                                    9.****************************************************************************** PP

                           ParA 163 vkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgv......pllgeipldpeireasdegkplvlkepeseaak 236
                                    ++++++GvveNmsg++ p+ g+++++fg+ggg+ +ae+l+       pllg+ipldp+++ a+d+g plvl++p+s++ k
  gi|121637158|ref|YP_977381.1| 284 TRQRIVGVVENMSGLTLPD-GTTMQVFGEGGGRLVAERLSRavgadvPLLGQIPLDPALVAAGDSGVPLVLSSPDSAIGK 362
                                    ******************8.8999**********9999654445555********************************* PP

                           ParA 237 aleeiaek 244
                                    +l++ia+ 
  gi|121637158|ref|YP_977381.1| 363 ELHSIADG 370
                                    ****9986 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.2   1.7e-20     2e-17       2      73 ..      20      92 ..      19      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.7e-20
                                   HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
                 FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveVe 73
                                   +a+++aL +V+DPel +++++lg+v++id    g+V+v i lt+++c+ +++i +++ +a++ +pg+  v+V+
  gi|121637158|ref|YP_977381.1| 20 AAIRTALGKVIDPELRRPITELGMVKSIDTGPdGSVHVEIYLTIAGCPKKSEITERVTRAVADVPGTSAVRVS 92
                                   79***************************9989*********************************8888887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   1.2e-16   1.5e-13       2     127 ..     130     350 ..     129     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.2e-16
                                    EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                    a+as+kGGvGK+t+++nLa+a+a rgl + ++DaD  + +    +g+  +  +                           
  gi|121637158|ref|YP_977381.1| 130 AVASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHSIPRMMGTTDRPTQvesmilppiahqvkvisiaqftqgntp 209
                                    89***********************************999887777777777799************************* PP

                                    ..........................................................................CCHCCC CS
                                    ..........................................................................xxxxxx RF
                           CbiA  55 ..........................................................................dlkrll 60 
                                                                                                              +++r++
  gi|121637158|ref|YP_977381.1| 210 vvwrgpmlhralqqfladvywgdldvllldlppgtgdvaisvaqlipnaellvvttpqlaaaevaeragsialqTRQRIV 289
                                    ******************************************************************************** PP

                                    HHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  61 ellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                    +++e++++      ++ g     +++    +l  e l +      vp+lg ip d a++ a  +g p
  gi|121637158|ref|YP_977381.1| 290 GVVENMSGL----TLPDGTTMQVFGEG-GGRLVAERLSRAV-GADVPLLGQIPLDPALVAAGDSGVP 350
                                    *******88....67888888887776.4666666666644.349**************99999977 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.7   2.7e-10   3.3e-07       2      44 ..     127     169 ..     126     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.7e-10
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQana 44 
                                    +v a+a  KGGvGK+T +vnlaaa+a +g  + + D+D  + +
  gi|121637158|ref|YP_977381.1| 127 RVYAVASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHS 169
                                    7899**********************************87654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.3e-10   1.5e-07       4     113 ..     130     247 ..     127     266 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.3e-10
                                    EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EE..E-SSS-HHHHTTS- CS
                           MipZ   4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpea..lalseaeeaeveee 81 
                                     ++  kGG Gkst++v +a a++ +G++++++d d+  +++ r ++     ++ + + Lp   +   ++s a+ ++ + +
  gi|121637158|ref|YP_977381.1| 130 AVASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHSIPRMMGTTDRPTQVESMILPPIAHqvKVISIAQFTQGNTP 209
                                    68899****************************************99888888888888754440133443333333322 PP

                                    HH....HHHHHHHHHHHHHH.HH-SEEEEE--.SS--H CS
                           MipZ  82 ee....aevaeleelvadle.aeldfividtP.Gsdsa 113
                                          +  ++l++ +ad+   +ld++++d P G+ + 
  gi|121637158|ref|YP_977381.1| 210 VVwrgpMLHRALQQFLADVYwGDLDVLLLDLPpGTGDV 247
                                    22000022344555555543145788888865255444 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.5e-07    0.0003       6      69 ..     133     196 ..     128     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                      Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvk 69 
                                     GkGG+Gkst + nl+aa+a +g  + ++  D    s   ++g+   +t ++ +     + +vk
  gi|121637158|ref|YP_977381.1| 133 SGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHSIPRMMGTTDRPTQVESMILPPIAHQVK 196
                                    59**************************999999999999999999999888776655555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.7   2.7e-06    0.0032      36      62 ..     130     157 ..     112     185 .. 0.86
   2 ?   -2.9   0.0       3.5   4.2e+03      72      93 ..     303     324 ..     268     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                         AAA_25  36 allaGapgtGKttlaldlalava.tGkp 62 
                                    a+  G +g+GK+t++++la+a+a +G +
  gi|121637158|ref|YP_977381.1| 130 AVASGKGGVGKSTVTVNLAAAMAvRGLS 157
                                    6778*******************98876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                         AAA_25  72 gkVlyvsaEdsedelrrRlrav 93 
                                    g+++ v +E++   +++Rl+++
  gi|121637158|ref|YP_977381.1| 303 GTTMQVFGEGGGRLVAERLSRA 324
                                    4444455566666666666653 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   3.8e-06    0.0045       5      38 ..     131     164 ..     127     188 .. 0.82
   2 ?   -3.8   0.0       4.8   5.7e+03     115     136 ..     223     245 ..     220     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                                    EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                    + +GKGGVGK+tv   +a+ ++  g ++ ++  D
  gi|121637158|ref|YP_977381.1| 131 VASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDAD 164
                                    569******************9999888877776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.8
                                    HHHHHHHCSSSSEEEEESBS.CC CS
                    ArsA_ATPase 115 ellkyvkeeeydvvvlDtaP.TG 136
                                    ++l  v   + dv++lD +P TG
  gi|121637158|ref|YP_977381.1| 223 QFLADVYWGDLDVLLLDLPPgTG 245
                                    55556666789*******99555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.013        16       5      34 ..     131     160 ..     127     162 .. 0.85
   2 ?    6.5   0.1    0.0057       6.8     124     196 ..     252     343 ..     240     344 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                         AAA_26   5 vtgtdtgvGKTvvslgLvralkrkgvkvgy 34 
                                    v++   gvGK++v+  L++a+  +g ++g+
  gi|121637158|ref|YP_977381.1| 131 VASGKGGVGKSTVTVNLAAAMAVRGLSIGV 160
                                    7778889**************988888876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                         AAA_26 124 aknl.gapvilVargglgtinqllltiealrqknvrvlGvilNk..vrnpe..............nvetlekksg..ipv 184
                                    a+ + +a+ ++V++++l + + +  + +++ q+  r++Gv+ N   ++ p+                e l+ + g  +p+
  gi|121637158|ref|YP_977381.1| 252 AQLIpNAELLVVTTPQLAAAEVAERAGSIALQTRQRIVGVVENMsgLTLPDgttmqvfgegggrlVAERLSRAVGadVPL 331
                                    55444677777777777766665555566678899******8874444443534444444544444444444433779** PP

                         AAA_26 185 lGvvPylpdlea 196
                                    lG++P +p l a
  gi|121637158|ref|YP_977381.1| 332 LGQIPLDPALVA 343
                                    *******99976 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.9e-05     0.094       5      39 ..     130     164 ..     126     168 .. 0.93
   2 ?   -3.7   0.1       5.1   6.1e+03     132     161 ..     259     288 ..     248     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                          VirC1   5 tfcslkGGaGkttalmglcsalasdgkrvalfead 39 
                                    +++s kGG Gk+t  + l +a+a +g  +++++ad
  gi|121637158|ref|YP_977381.1| 130 AVASGKGGVGKSTVTVNLAAAMAVRGLSIGVLDAD 164
                                    67999*****************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.1
                          VirC1 132 elllaeelaipvailrqrvPvrrltssqrl 161
                                    ell+  ++++ +a + +r  +  l++ qr+
  gi|121637158|ref|YP_977381.1| 259 ELLVVTTPQLAAAEVAERAGSIALQTRQRI 288
                                    666666677777766666666666666654 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.25       1      43 [.     134     174 ..     134     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                         CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgti 43 
                                    G+  +GKST++ +L+  ++ +g ++ ++D+D+   +  +P ++
  gi|121637158|ref|YP_977381.1| 134 GKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHS--IPRMM 174
                                    66789**************************96544..55555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.34       8      53 ..     133     178 ..     127     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                                    ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                     APS_kinase   8 tGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53 
                                    +G  g GKst++++l+ ++  +g s+ +Ld d   h + + +g ++
  gi|121637158|ref|YP_977381.1| 133 SGKGGVGKSTVTVNLAAAMAVRGLSIGVLDADIHGHSIPRMMGTTD 178
                                    7899****************************98888888887665 PP

>> DUF1073  Protein of unknown function (DUF1073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   1.7e+03     335     350 ..      92     107 ..      77     109 .. 0.81
   2 ?    9.3   0.0   0.00035      0.42     184     239 ..     247     303 ..     244     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                        DUF1073 335 pLwqlsekekAeirkk 350
                                    +L+ +s++++ e+rk+
  gi|121637158|ref|YP_977381.1|  92 SLDVMSDEQRTELRKQ 107
                                    7888999999888886 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00035
                        DUF1073 184 aaasvaqlleranllviktdgla.dalaagdeedeleerleliklarsnegmlvidk 239
                                    +a svaql+ +a llv+ t++la + +a+  ++ +l+ r++++  ++++ g+++ d 
  gi|121637158|ref|YP_977381.1| 247 VAISVAQLIPNAELLVVTTPQLAaAEVAERAGSIALQTRQRIVGVVENMSGLTLPDG 303
                                    6789*******************7678888888999999999999999999988775 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5    0.0054       6.4      10      38 ..     135     163 ..     127     168 .. 0.87
   2 ?    2.3   0.0     0.083        99     105     146 ..     221     264 ..     208     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0054
                       CBP_BcsQ  10 RGGvGttsllaaLawalhelgesvlviDl 38 
                                    +GGvG++++++ La a+   g s+ v+D+
  gi|121637158|ref|YP_977381.1| 135 KGGVGKSTVTVNLAAAMAVRGLSIGVLDA 163
                                    7****************999999888886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.083
                       CBP_BcsQ 105 llaalkelk.eqyrwillDlpagasaltrellal.adlvllvve 146
                                    l+++l+ +  ++ + +llDlp g+ +++ ++ +l  + +llvv+
  gi|121637158|ref|YP_977381.1| 221 LQQFLADVYwGDLDVLLLDLPPGTGDVAISVAQLiPNAELLVVT 264
                                    555555555688899*******9999987766642355555544 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00027      0.32      90     141 ..      57     107 ..       8     115 .. 0.83
   2 ?    0.4   0.1      0.44   5.2e+02      25      80 ..     246     298 ..     231     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                            BAT  90 astlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvar 141
                                    ++ + +  g +++ e+++  +r v++vP + +vR  ++ ++++  ++eL+ +
  gi|121637158|ref|YP_977381.1|  57 VEIYLTIAGCPKKSEITERVTRAVADVPGTSAVRVSLDVMSDEQ-RTELRKQ 107
                                    5555666678889999*************************997.9999987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                            BAT  25 dcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtll 80 
                                    d ++++ +l+p  +   l+ +t+ + +++ev++ a ++   +  r+v+  ++ + l
  gi|121637158|ref|YP_977381.1| 246 DVAISVAQLIPNAE---LLVVTTPQLAAAEVAERAGSIALQTRQRIVGVVENMSGL 298
                                    55677777777655...788999999999999999999999999998888874443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2331.87
//
Query:       gi|121637159|ref|YP_977382.1|  [L=411]
Description: hypothetical protein BCG_1290c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-09   37.1   3.1    2.4e-08   33.5   0.3    2.1  2  SLT_2     Transglycosylase SLT domain
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.094   12.4   0.0    1.6  1  SLT       Transglycosylase SLT domain


Domain annotation for each model (and alignments):
>> SLT_2  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.3   2.7e-12   2.4e-08     152     207 ..     194     248 ..     188     254 .. 0.88
   2 !    4.7   0.2    0.0017        15     271     289 ..     252     270 ..     247     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.7e-12
                          SLT_2 152 waGamGltQFmPssylkyAvDfdgdgrrDlwnspaDalaSvAnyLkkhgWqagepw 207
                                    +a amG +QF+P ++ +yA D+d+dg +D  n   D+   +A+yL + g +  +p 
  gi|121637159|ref|YP_977382.1| 194 YARAMGPMQFLPGTWARYATDGDDDGVADPQN-LFDSTLAAARYLCSGGLNLRDPA 248
                                    788***************************87.9***********98887666555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0017
                          SLT_2 271 kvitrYNrStlYalaVael 289
                                     ++ rYN+S  Ya+ V+  
  gi|121637159|ref|YP_977382.1| 252 AALLRYNNSMPYAQNVLGW 270
                                    6899**********99865 PP

>> SLT  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     1e-05     0.094      11      96 ..     136     259 ..     127     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                                    TS-HHHHHHHHHHHHTT.-TT-B-TTS..................................EBTTTTBETTTHHHHHHHH CS
                            SLT  11 gvepsllaaiaqvESgf.npkAvsksg..................................avGLmQimpstakrlglrv 55 
                                    gv+++lla i + ES+  n  A+   g                                  a+G mQ+ p t  r++  +
  gi|121637159|ref|YP_977382.1| 136 GVSWNLLAGIGRIESMHaNGGATDARGtaiqpiygptldgtlpgneiiiqssvgnrvtyarAMGPMQFLPGTWARYATDG 215
                                    6778888888888886514556654445567777777777888888888888888888888**************99986 PP

                                    T.-SHHHHCSHHHHHHHHHHHHHHHHHTTTT..HHHHHHHHHHH CS
                            SLT  56 k.lsedelldPeknisagakyLkslykqyng..slllalaAYNa 96 
                                      +++ + ++  +++ a+a+yL s   ++++  ++ +al  YN+
  gi|121637159|ref|YP_977382.1| 216 DdDGVADPQNLFDSTLAAARYLCSGGLNLRDpaQVMAALLRYNN 259
                                    6666666666678999*****98765555545556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2618.91
//
Query:       gi|121637160|ref|YP_977383.1|  [L=180]
Description: hypothetical protein BCG_1291c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-36  123.0   0.0    8.9e-36  122.1   0.0    1.5  1  DUF1003   Protein of unknown function (DUF1003)


Domain annotation for each model (and alignments):
>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.0   4.9e-40   8.9e-36       1     104 []      39     140 ..      39     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 4.9e-40
                        DUF1003   1 mGsakFlvlftaivilWialnllvlpglkpfDpypFillnlvlslqaalaaplIllsqnRqadrdrvraeedrqvnlkae 80 
                                    +G+ ++l+++t++v++Wi+lnl++     ++DpypFillnl++s+qa++aaplIll+qnRq++rdr   eedr+++++++
  gi|121637160|ref|YP_977383.1|  39 FGTGRYLLVQTLLVLTWIVLNLFA--VGLRWDPYPFILLNLAFSTQASYAAPLILLAQNRQEKRDRAVFEEDRRRAAQTK 116
                                    69*********************8..79**************************************************** PP

                        DUF1003  81 aeiekLtrevaalrealgevatrd 104
                                    a++e+ +re+aalr a+gev trd
  gi|121637160|ref|YP_977383.1| 117 ADTEYNARELAALRLAIGEVPTRD 140
                                    *******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1269.32
//
Query:       gi|121637161|ref|YP_977384.1|  [L=435]
Description: hypothetical protein BCG_1292c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-23   83.5   1.2      3e-23   82.4   1.2    1.6  1  MgtE_N    MgtE intracellular N domain
    1.9e-13   50.7   0.3    1.8e-06   28.3   0.1    3.1  2  CBS       CBS domain
    0.00095   19.3   0.7      0.049   13.8   0.4    3.0  3  FliG_M    FliG middle domain
     0.0085   16.6   0.2       0.33   11.5   0.1    2.8  2  FliG_N    FliG N-terminal domain
  ------ inclusion threshold ------
      0.073   13.3   0.2       0.66   10.2   0.2    2.4  2  FliG_C    FliG C-terminal domain
       0.11   12.5   0.0       0.48   10.5   0.0    2.0  2  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   1.2   9.9e-27     3e-23       3     102 .]     186     285 ..     184     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 9.9e-27
                                    HHHHHHCHCCS-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHH CS
                         MgtE_N   3 padiaelleelpeeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeekveell 82 
                                    ++d+a+++  lp+++r+++++ l ++++a+vl+el+e +q+e++++l  e++a++lee+d+Ddaadll  l ++++e ll
  gi|121637161|ref|YP_977384.1| 186 AVDVADAIRGLPPKRRHEVFKALHDKRLADVLQELPELDQAEVLSQLGTERAADVLEEMDPDDAADLLAVLNPTEAELLL 265
                                    68****************************************************************************** PP

                                    HCS-HHHHHHHHHHCTS-TT CS
                         MgtE_N  83 saldeeereeieellsYped 102
                                    +++d+ ++ ++++ll++++d
  gi|121637161|ref|YP_977384.1| 266 TRMDPGDSGQVRRLLTHSPD 285
                                    ***************99876 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.6e-07    0.0014       2      53 ..     288     349 ..     287     350 .. 0.73
   2 !   28.3   0.1   5.9e-10   1.8e-06       1      56 [.     356     411 ..     356     412 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-07
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHT....SSEEEE.E......ETTTBEEEEEEHHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekg....vsrlPV.V......dedgklvGivtlrDllr 53 
                                    g +mt+d+v+++pdt+++eal + r+ +    + ++ V V         g+++G v+l  llr
  gi|121637161|ref|YP_977384.1| 288 GGLMTSDPVVLTPDTSIAEALARVRDPDltpaLASM-VfVarpptaTPTGHYLGCVHLQRLLR 349
                                    669*********************986653334344.43367777755667777777777765 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 5.9e-10
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllrall 56 
                                    Vg +  +d++t++p+t+l+ + + ++ +++    PVVd++++l+G vt  Dll+ ll
  gi|121637161|ref|YP_977384.1| 356 VGGVVDTDLLTLTPETPLAAVTRYFAAYNL-VCgPVVDDENHLLGAVTVDDLLDHLL 411
                                    56677899*****************99884.444***999*************9886 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.25   7.6e+02      29      46 ..     190     207 ..     174     212 .. 0.82
   2 !    7.1   0.1    0.0021       6.3      23      47 ..     208     232 ..     204     237 .. 0.83
   3 !   13.8   0.4   1.7e-05     0.049      16      44 ..     225     253 ..     211     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.25
                                    HHHHHTS-HHHHHHHHHH CS
                         FliG_M  29 AevLseLpeelraevirr 46 
                                    A+ +  Lp+++r ev + 
  gi|121637161|ref|YP_977384.1| 190 ADAIRGLPPKRRHEVFKA 207
                                    778899999999999876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                                    S-HHHHHHHHHTS-HHHHHHHHHHH CS
                         FliG_M  23 LdpeqAAevLseLpeelraevirri 47 
                                    L+ ++ A+vL+eLpe  +aev+ ++
  gi|121637161|ref|YP_977384.1| 208 LHDKRLADVLQELPELDQAEVLSQL 232
                                    5566779**************9876 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.7e-05
                                    HHHHHHTS-HHHHHHHHHTS-HHHHHHHH CS
                         FliG_M  16 iAliLsyLdpeqAAevLseLpeelraevi 44 
                                    +A +Ls+L  e+AA+vL+e++++ +a+++
  gi|121637161|ref|YP_977384.1| 225 QAEVLSQLGTERAADVLEEMDPDDAADLL 253
                                    789*******************9999976 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.1   3.1e+02      15      44 ..     196     225 ..     187     228 .. 0.83
   2 !   11.5   0.1   0.00011      0.33      11      37 ..     228     254 ..     224     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                                    CXHHHHHHHHTTSXHHHHHHHHHHHHCHTT CS
                         FliG_N  15 LgeeeaaevlkhLdeeeiekltkeiaslks 44 
                                    L +++  ev+k L+++ ++++ +e+ +l++
  gi|121637161|ref|YP_977384.1| 196 LPPKRRHEVFKALHDKRLADVLQELPELDQ 225
                                    677888999999999999999999877765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                                    HHHHCXHHHHHHHHTTSXHHHHHHHHH CS
                         FliG_N  11 lllaLgeeeaaevlkhLdeeeiekltk 37 
                                    +l +Lg e+aa vl+++d+++ ++l +
  gi|121637161|ref|YP_977384.1| 228 VLSQLGTERAADVLEEMDPDDAADLLA 254
                                    677788888888888888887776654 PP

>> FliG_C  FliG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00022      0.66      22      76 ..     191     245 ..     185     268 .. 0.93
   2 ?   -0.2   0.0      0.37   1.1e+03      20      49 ..     292     321 ..     287     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                    GGGGGS-HHHHHHHHTTS-HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHH CS
                         FliG_C  22 edlvrlddraiqrllrevdkedLalaLkgaseelrekilsnmSkraaemlreele 76 
                                    + +  l+++   ++++ +++++La  L+  +e  ++ +ls++ +++a+ + ee++
  gi|121637161|ref|YP_977384.1| 191 DAIRGLPPKRRHEVFKALHDKRLADVLQELPELDQAEVLSQLGTERAADVLEEMD 245
                                    678999************************************9999999999996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.37
                                    -GGGGGGS-HHHHHHHHTTS-HHHHHHHHC CS
                         FliG_C  20 tfedlvrlddraiqrllrevdkedLalaLk 49 
                                    t + +v  +d++i + l  v + dL+ aL+
  gi|121637161|ref|YP_977384.1| 292 TSDPVVLTPDTSIAEALARVRDPDLTPALA 321
                                    5566788899****************9997 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.48       4      63 ..       7      64 ..       5      78 .. 0.81
   2 ?   -2.0   0.0       1.3     4e+03       4      26 ..     380     402 ..     378     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                   CCS---TT-EEEETTSSEEEEEEEEEEET....TTTEEEEEEEEETTT.....-EEEEEGG.CE CS
                            PRC  4 frasdliGkeVytedGeklGkVkDvvide....kegrvralvvsvggflgigekevliPfdlav 63
                                   +++++l  ++V    Ge  G+V Dvvi +    ++ rv++lvv+   +     ++++iP+  +v
  gi|121637161|ref|YP_977384.1|  7 VYLARLSRMSVLGPLGESFGRVRDVVISIsivrQQPRVLGLVVDLATR-----RKIFIPIL-RV 64
                                   78999999****999***********9973333599999999999976.....9****998.44 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                    CCS---TT-EEEETTSSEEEEEE CS
                            PRC   4 frasdliGkeVytedGeklGkVk 26 
                                    f+a +l+  +V+++++  lG V+
  gi|121637161|ref|YP_977384.1| 380 FAAYNLVCGPVVDDENHLLGAVT 402
                                    66777777789999999999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2844.78
//
Query:       gi|121637162|ref|YP_977385.1|  [L=198]
Description: hypothetical protein BCG_1293c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   63.4  13.2    1.6e-17   63.0  13.2    1.2  1  DUF4190          Domain of unknown function (DUF4190)


Domain annotation for each model (and alignments):
>> DUF4190  Domain of unknown function (DUF4190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0  13.2   8.8e-22   1.6e-17       1      62 []     132     192 ..     132     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 8.8e-22
                        DUF4190   1 lAiasLvlgilgllfliitgivavilGhvAlrqirrsgerGkglAiaGivlGwigllllvll 62 
                                    +A++sL+ +++g+l+ +i++iv++++G +A +qi++++e+G+glA+aGiv+G+++ll+++++
  gi|121637162|ref|YP_977385.1| 132 MALVSLISALVGVLC-CIGSIVGIVFGAIAINQIKQTREEGYGLAVAGIVIGIATLLVYMIA 192
                                    79***********99.5*****************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1487.12
//
Query:       gi|121637163|ref|YP_977386.1|  [L=175]
Description: hypothetical protein BCG_1294 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0067   16.4   1.5      0.013   15.4   1.5    1.5  1  Phage_holin_2_1  Bacteriophage P21 holin S
  ------ inclusion threshold ------
      0.014   14.4   2.1      0.019   14.0   2.1    1.1  1  FecCD            FecCD transport family
        1.5    9.2   6.1        5.9    7.3   0.8    2.3  2  Romo1            Reactive mitochondrial oxygen species modula


Domain annotation for each model (and alignments):
>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.5   2.2e-06     0.013      20      50 ..     100     132 ..      87     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                Phage_holin_2_1  20 lkqlldklspeeWsai..gvlgglvigllTylt 50 
                                    +  +l  +sp+ Wsa+  g+++g+++gl+T ++
  gi|121637163|ref|YP_977386.1| 100 IGLVLGFFSPNPWSALvtGLVAGVFFGLITSAV 132
                                    55678899******96669***********876 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   3.2e-06     0.019      74     137 ..      83     152 ..      76     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-06
                          FecCD  74 Psil..Gissgaalgavlallll....lgslslfalplaaflgallalllvlllarkrkgasplkliLaG 137
                                    P++l  G+ sga+lg++++l+l+     +++ l++ ++a ++++l+++++ +++ar+++ +s+++ ++aG
  gi|121637163|ref|YP_977386.1|  83 PKVLggGVLSGAWLGLFIGLVLGffspNPWSALVTGLVAGVFFGLITSAVPYAMARGTRDFSSTMQLVAG 152
                                    666633699**************55543344444445556688888899999999999999998888877 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.8   0.00099       5.9       8      28 ..      88     108 ..      81     109 .. 0.81
   2 ?    4.5   0.5    0.0076        45      11      43 ..     116     147 ..     113     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00099
                          Romo1   8 mGalmGaaVGlaiGllfGtfs 28 
                                     G+l Ga +Gl iGl++G+fs
  gi|121637163|ref|YP_977386.1|  88 GGVLSGAWLGLFIGLVLGFFS 108
                                    588899999999999999885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0076
                          Romo1  11 lmGaaVGlaiGllfGtfsalryglrgrgllrtl 43 
                                    + G + G+ +Gl++  +   +++ ++r++++t+
  gi|121637163|ref|YP_977386.1| 116 VTGLVAGVFFGLITSAVPYAMAR-GTRDFSSTM 147
                                    56888888888888888877777.777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1207.44
//
Query:       gi|121637164|ref|YP_977387.1|  [L=468]
Description: sugar-binding lipoprotein lpqY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-31  108.8   1.1    6.6e-31  108.4   0.3    1.5  2  SBP_bac_1  Bacterial extracellular solute-binding protein
    6.6e-15   55.7   0.0    1.6e-14   54.4   0.0    1.6  1  SBP_bac_8  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.3   7.4e-35   6.6e-31       5     307 ..      42     372 ..      38     379 .. 0.89
   2 ?   -2.5   0.0      0.43   3.8e+03     128     146 ..     443     461 ..     440     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 7.4e-35
                                    HHHHHHHHHHHHH....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHH CS
                      SBP_bac_1   5 tegaalqalvaka....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvka 80 
                                    t+ga++ a++ ++    f  + +  +V +  ++  +   +l+ ++ ++d   Dv+a d  w+a++a+ag++lpl+++ + 
  gi|121637164|ref|YP_977387.1|  42 TDGATFTAIA-QRcnqqFGGRFTIAQVSLPRSPNEQRL-QLARRLTGNDRTLDVMALDVVWTAEFAEAGWALPLSDDPAG 119
                                    5677888888.884444333334444444444444444.699**********************************8888 PP

                                    TTECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHC CS
                      SBP_bac_1  81 ylapgvkdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpig 154
                                     +       + ++  ++lp+ l++ ++   ly  P+ + +++l+Y++dl+     +pp+ W+  ++ a +l ++g+   +
  gi|121637164|ref|YP_977387.1| 120 LA-------ENDAVADTLPGPLATaGWnhkLYaAPVTTnTQLLWYRPDLVN----SPPTDWNAMIAEAARLHAAGEPS-W 187
                                    75.......444566799*****87779*********99************....7889*****************98.* PP

                                    CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHT CS
                      SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfea 232
                                    +a ++ ++  + +++++l+ s+gg v ++dg+  +l+++++  aat     +++  +t   ++++ + + + +a+ +fe+
  gi|121637164|ref|YP_977387.1| 188 IAVQANQGEGLVVWFNTLLVSAGGSVLSEDGRhvTLTDTPAHRAATVSALQILKSVATTPGADPSITRTEEGSARLAFEQ 267
                                    **********************************9999999999999999999999************************ PP

                                    TSCSEEEEEHHHHHHHHCEEEEE............................CHHCHHHHTTSTEEEECEEBETTTTSEE. CS
                      SBP_bac_1 233 Geaamaivglwaalaamkvapkv............................afaadkekpkeelgvaplPagkggkpgi. 283
                                    G+aa+ +++++   +++  a k+                            +f ++++     +g+ap Pa+ +g p+  
  gi|121637164|ref|YP_977387.1| 268 GKAALEVNWPFVFASMLENAVKGgvpflplnripqlagsindigtftpsdeQFRIAYDASQQVFGFAPYPAVAPGQPAKv 347
                                    ***********988888888888****************************9999999999999**************** PP

                                    .EEEEEEEEBTTCSTHHHHHHHHHH CS
                      SBP_bac_1 284 .lgayglaipkgsknpeaAkkFldf 307
                                     +g+ +la+ k++ ++++A++ ++ 
  gi|121637164|ref|YP_977387.1| 348 tIGGLNLAVAKTTRHRAEAFEAVRC 372
                                    *******************998865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.43
                                    TGGGSHBHHHHHHHHHHHH CS
                      SBP_bac_1 128 gldppwtWdelveaakklk 146
                                    ++dp+ t del++ a+k++
  gi|121637164|ref|YP_977387.1| 443 EIDPESTADELAAQAQKAI 461
                                    68899999********986 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   1.8e-18   1.6e-14      34     277 ..      85     404 ..      49     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.8e-18
                                    TT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH.......-HHHHHTT--TS.----EEEEEEE-EEEEEHHHHH CS
                      SBP_bac_8  34 agtapdidvvwanedalatlaeeglladlsdl.dnldd.......ltdalaavgydgklygvPyasetpyvliynkdlle 105
                                    +g+  ++dv   +  + a++ae+g+  +lsd    l++       l+  la++g++ kly+ P++++t ++l y+ dl+ 
  gi|121637164|ref|YP_977387.1|  85 TGNDRTLDVMALDVVWTAEFAEAGWALPLSDDpAGLAEndavadtLPGPLATAGWNHKLYAAPVTTNT-QLLWYRPDLVN 163
                                    455557999999999***************6535666644443333445555599999*********8.8********** PP

                                    HS.---BHHHHHHHHHHH..HHH-......SEGG---G...GGGGGTHHETTEE---H............HHH.HHHHHH CS
                      SBP_bac_8 106 kaedpktwdellaaakkl..kgkf......glpdpasg...wlqaallakdgksldddg..........gkdglkealel 164
                                       +p++w ++ a a+ l             ++++++g   w+ ++l+ ++g  l++dg           +++++ al++
  gi|121637164|ref|YP_977387.1| 164 -S-PPTDWNAMIAEAARLhaA--GepswiaVQANQGEGlvvWFNTLLVSAGGSVLSEDGrhvtltdtpaHRAATVSALQI 239
                                    .4.********9944544442..244443355889999887888888885555558888888776644444444555555 PP

                                    HHHHHHTT-EE.......-S...--SSTTTTTSBSEEEE-TTHHHHHH................................ CS
                      SBP_bac_8 165 lkklkdngkty.......dtg.adavsefanGevaftingswdiaaaq................................ 204
                                    lk+     +t+        t   +a  +f +G++a  +n++  +a+                                  
  gi|121637164|ref|YP_977387.1| 240 LKSVA---TTPgadpsitRTEeGSARLAFEQGKAALEVNWPFVFASMLenavkggvpflplnripqlagsindigtftps 316
                                    55555...3224445444443256777************99555544434448999999999999988888888888877 PP

                                    ........-TTT.SEEEE.--......S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-T CS
                      SBP_bac_8 205 ........kagk.klgai.vp......kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksa 268
                                            +a++  +g++ +p      + ++ +gg +lav k + ++++ A + +++l +  nq+  +  +g++ v+ s+
  gi|121637164|ref|YP_977387.1| 317 deqfriayDASQqVFGFApYPavapgqPAKVTIGGLNLAVAKTTRHRAE-AFEAVRCLRDQHNQRYVSLEGGLPAVRASL 395
                                    666655554433134444434664443235******************7.****************************** PP

                                    TTHHHHHH- CS
                      SBP_bac_8 269 alspevkkd 277
                                    + +p+++++
  gi|121637164|ref|YP_977387.1| 396 YSDPQFQAK 404
                                    *****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3284.32
//
Query:       gi|121637165|ref|YP_977388.1|  [L=307]
Description: sugar-transport integral membrane protein ABC transporter sugA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-12   45.3  13.4    7.6e-12   45.3  13.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   6.3     0.014   2.6e+02     115     175 ..      24     101 ..      20     109 .. 0.88
   2 !   45.3  13.4   4.2e-16   7.6e-12       3     179 ..     101     295 ..      99     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.014
                   BPD_transp_1 115 ilafggllggavlleflgswpGlgtllleailgydyseis..................nggvlalviavlllnlvadil 175
                                    +laf+++  +a+l+  ++++p +g+ l+ +++ ++++  +                  ++++la+++a+ ++++ + ++
  gi|121637165|ref|YP_977388.1|  24 RLAFMLVAPAAMLMVAVTAYP-IGYALWLSLQRNNLATPNdtafiglgnyhtilidryWWTALAVTLAITAVSVTIEFV 101
                                    589999999***********9.*************9977799****************888888888888888776665 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 4.2e-16
                   BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf................vilsilghlilp.viilllls 63 
                                    +lG+ +a  ++r  +++ l+r+ + +++++ ++v    ++++                       +   l+ v+i+ ++ 
  gi|121637165|ref|YP_977388.1| 101 VLGLALAlvMHRTLIGKGLVRTAVLIPYGIVTVVASYSWYYAWtpgtgylanllpydsaP--LTQQIPSLGiVVIAEVWK 178
                                    677777777777777788888888888888777733333333355555555555554331..222233455589999*** PP

                   BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllle 143
                                    ++p++ l+  a+l  +p+dl +aa ++Gas w+++ kv+lP+++p i+  l+++   ++  +  ++ l++  G +++   
  gi|121637165|ref|YP_977388.1| 179 TTPFMSLLLLAGLALVPEDLLRAAQVDGASAWRRLTKVILPMIKPAIVVALLFRTLDAFRIFDNIYVLTG--GSNNTGSV 256
                                    *********************************************************************5..56888888 PP

                   BPD_transp_1 144 ailgydyseis...nggvlalviavlllnlvadilqrll 179
                                    +ilgyd  +       g+++ v+++  + ++a+i+ +l+
  gi|121637165|ref|YP_977388.1| 257 SILGYDNLFKGfnvGLGSAISVLIFGCVAVIAFIFIKLF 295
                                    888888776666766677777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.20s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2220.86
//
Query:       gi|121637166|ref|YP_977389.1|  [L=274]
Description: sugar-transport integral membrane protein ABC transporter sugB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-21   77.2  19.8    1.3e-21   77.2  19.8    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.37    9.2   0.0       0.49    8.8   0.0    1.1  1  Borrelia_P83  Borrelia P83/100 protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.2     0.019   1.7e+02      30      69 ..      22      90 ..       5      96 .. 0.56
   2 !   77.2  19.8   1.4e-25   1.3e-21       1     182 [.      80     266 ..      80     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.019
                   BPD_transp_1 30 lPsfvlaillvlvf.............................vilsilghlilpviillllsaapyvr 69
                                   lP+++++ l +                                ++++++g + +  +i+++l+a++   
  gi|121637166|ref|YP_977389.1| 22 LPVLWIFSLSLKPTstvkdgklipstvtfdnyrgifrgdlfssALINSIGIGLITTVIAVVLGAMAAYA 90
                                   566665555553335555666666666666666666666666655555665555544444444444333 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 1.4e-25
                   BPD_transp_1   1 gillGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilp.viillllsaapyvrlirraa 75 
                                    +++lG++aa    +  +++++ll +   ++ ++Ps+ l+ +l+    i  ++g +  +p +i+ ++++a+p+++++ +a+
  gi|121637166|ref|YP_977389.1|  80 AVVLGAMAAyavARLEFPGKRLLIGAALLITMFPSISLVTPLF---NIERAIGlFDTWPgLILPYITFALPLAIYTLSAF 156
                                    5899*****9999****************************99...566666665555559******************* PP

                   BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyse 152
                                    +r++p dl++aa+++Ga++ q frkv++P+a+p ++t +il+f++++++ +l++ l++ ++       + +++ ++++ e
  gi|121637166|ref|YP_977389.1| 157 FREIPWDLEKAAKMDGATPGQAFRKVIVPLAAPGLVTAAILVFIFAWNDLLLALSLTATKAaitAPVAIANFTGSSQFEE 236
                                    *******************************************************9977766443333444444455555 PP

                   BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldpr 182
                                     +  +++ ++++++++++++ i+qr +   
  gi|121637166|ref|YP_977389.1| 237 PTGSIAAGAIVITIPIIVFVLIFQRRIVAG 266
                                    557788888888899999999999888765 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   5.5e-05      0.49       9      56 ..      46      94 ..      39     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 5.5e-05
                   Borrelia_P83  9 ktlefvnykGpyd.svdsaeqirgiGefLaralkagnagdsarYavira 56
                                    t+ f ny+G +  +  s + i  iG +L ++++a + g +a Yav r 
  gi|121637166|ref|YP_977389.1| 46 STVTFDNYRGIFRgDLFSSALINSIGIGLITTVIAVVLGAMAAYAVARL 94
                                   799*******995378999***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2035.71
//
Query:       gi|121637167|ref|YP_977390.1|  [L=393]
Description: sugar-transport ATP-binding protein ABC transporter sugC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-30  104.3   0.0    1.2e-29  103.6   0.0    1.3  1  ABC_tran         ABC transporter
    4.1e-12   46.8   0.6    2.2e-11   44.4   0.2    2.5  2  OB_MalK          MalK OB fold domain
    5.9e-06   26.4   1.6      0.027   14.6   0.2    3.3  2  TOBE_2           TOBE domain
    0.00041   20.3   0.0     0.0011   19.0   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
    0.00048   20.0   0.0       0.25   11.1   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00078   19.4   0.0     0.0015   18.5   0.0    1.5  1  Rad17            Rad17 P-loop domain
     0.0017   17.8   0.0     0.0038   16.7   0.0    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0033   17.7   0.1     0.0056   16.9   0.1    1.6  1  AAA_22           AAA domain
      0.006   17.0   0.1      0.012   16.0   0.1    1.7  1  AAA_16           AAA ATPase domain
     0.0094   16.4   0.0      0.018   15.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.022   15.3   0.4       0.15   12.7   0.1    2.6  2  CysA_C_terminal  CysA C-terminal regulatory domain
      0.037   14.3   1.8          1    9.7   0.4    3.2  3  TOBE             TOBE domain
      0.037   13.6   0.1       0.16   11.5   0.1    2.0  2  AAA_25           AAA domain
      0.046   13.4   0.0      0.097   12.4   0.0    1.5  1  AAA_30           AAA domain
      0.052   12.9   0.0      0.091   12.1   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.061   12.4   0.0       0.12   11.5   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
      0.088   13.0   0.0       0.26   11.5   0.0    1.8  2  AAA_28           AAA domain
      0.095   12.4   0.0       0.12   12.1   0.0    1.1  1  AAA_15           AAA ATPase domain
       0.12   12.3   0.2       0.41   10.6   0.0    1.9  3  Mur_ligase_M     Mur ligase middle domain
       0.13   12.7   0.1       0.23   11.9   0.1    1.4  1  AAA_23           AAA domain
       0.22   11.3   0.2       0.59    9.9   0.1    1.8  1  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.4e-32   1.2e-29       2     136 ..      21     162 ..      20     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.4e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++++l++  ge + +vG++G+GK+t l+++agl++  +Ge+++ g+ ++e  +   ++ i++++q   l p++tvr+n  
  gi|121637167|ref|YP_977390.1|  21 RDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRIAGERVNE--KAPKDRDIAMVFQSYALYPHMTVRQNia 98 
                                    689**********************************************9..8888999********************* PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             + + ++k+ ++ ++ +  ++ ++++ps+LSgGq+qrva+ ra++++pk +l+DEp 
  gi|121637167|ref|YP_977390.1|  99 fpltlakmRKADIAQKVSETAKILD-LTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPL 162
                                    ****987433333555555555555.788889999*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.2   2.6e-14   2.2e-11       1      53 []     236     287 ..     236     287 .. 0.91
   2 ?   -1.3   0.0         5   4.2e+03      13      44 ..     341     367 ..     338     387 .. 0.62

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.6e-14
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                    GSPaMNf+pa++++ g+++ +g+vtl+ pe q + +++ + ++vi+G+RPEhi
  gi|121637167|ref|YP_977390.1| 236 GSPAMNFFPARLTAIGLTLPFGEVTLA-PEVQGVIAAHPKPENVIVGVRPEHI 287
                                    9***************9999**99999.455558999999************9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5
                        OB_MalK  13 eedgvlvegggvtlplpeeqklalklyagkev 44 
                                    e++  ++ ++++  ++p+e     k + g+ v
  gi|121637167|ref|YP_977390.1| 341 EGES-ALHENQFVARVPAES----KVAIGQSV 367
                                    5444.555566666666655....44444444 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.91   7.8e+02      41      66 ..     186     207 ..     170     209 .. 0.59
   2 !   14.6   0.2   3.2e-05     0.027       1      76 []     280     379 ..     280     379 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.91
                         TOBE_2  41 ggqlvvvrqpnadrdsalapGdtVel 66 
                                      +   v  + +   +a++ Gd+V +
  gi|121637167|ref|YP_977390.1| 186 TTTV-YVTHDQT---EAMTLGDRVVV 207
                                    3332.3444444...49999999987 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-05
                         TOBE_2   1 laiRPEklrla....aagg.an.glsGtVedveylGsstryvvelaggqlvvv.....................rqpnad 53 
                                    +++RPE+++ a    a ++ +  +++ +V  ve lG++  ++ ++++ +   v                     r+p   
  gi|121637167|ref|YP_977390.1| 280 VGVRPEHIQDAalidAYQRiRAlTFQVKVNLVESLGADKYLYFTTESPAVHSVqldelaevegesalhenqfvaRVP--- 356
                                    68999999998887522333356999999999999999999999998888777666666666666666533221222... PP

                         TOBE_2  54 rd.salapGdtVelswdpddavvl 76 
                                     + s +a+G+ Vel++d++++ v+
  gi|121637167|ref|YP_977390.1| 357 -AeSKVAIGQSVELAFDTARLAVF 379
                                    .22467777777777777777766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-06    0.0011      88     131 ..      18      62 ..       7      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                                    TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                    +++++l+  ++d ++ +lvG+SG GK+t +n++++ ++++ ge++
  gi|121637167|ref|YP_977390.1|  18 TAVRDLNLTIADgEFLILVGPSGCGKTTTLNMIAGLEDISSGELR 62 
                                    56677888888879********************99898888876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0003      0.25       2      48 ..      33      67 ..      32      79 .. 0.69
   2 !    6.8   0.0    0.0062       5.3     230     298 ..     128     194 ..      91     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48
                                    +l+Gp g+GK++ L  + +l             + ++g++r+   +
  gi|121637167|ref|YP_977390.1| 33 LILVGPSGCGKTTTLNMIAGLE------------DISSGELRIAGER 67
                                   69****************9994............4444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0062
                         AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                     ++ +++lS G+++  a+  a+ r +   + +l DEp ++L+ kl     + + +l+r  g+  + +TH+
  gi|121637167|ref|YP_977390.1| 128 LDRKPSQLSGGQRQRVAMGRAIVRHP---KAFLMDEPLSNLDAKLRVQMRGEIAQLQRrLGTTTVYVTHD 194
                                    45567788999998888888888877...67*******************99988888677778*****8 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-06    0.0015      43      72 ..      28      57 ..      15     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                          Rad17 43 rkkriLLisGPsGCgkstvvkvLskelgik 72
                                   +  + L++ GPsGCgk+t++++++    i+
  gi|121637167|ref|YP_977390.1| 28 ADGEFLILVGPSGCGKTTTLNMIAGLEDIS 57
                                   5556899*************9998765555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.5e-06    0.0038      24     208 ..      30     205 ..      11     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                     +f ++vGp G+GK+  l+ i   L + s+ +lr +   + +++ k+ +  + a v   +    + ++ ++  + ++  +
  gi|121637167|ref|YP_977390.1|  30 GEFLILVGPSGCGKTTTLNMIA-GLEDISSGELRIA--GERVNE-KAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAK 105
                                    57899*************9993.3333344455543..333444.45555555555555544444444444445555554 PP

                                    ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                    +r    +  i +k  + +++ +l +  + ++++LSgG+++ va+    Ai +  p+  +l+De  ++LD+k + ++   +
  gi|121637167|ref|YP_977390.1| 106 MR----KADIAQKVSETAKILDLTNLLDRKPSQLSGGQRQRVAMG--RAIVRH-PK-AFLMDEPLSNLDAKLRVQMRGEI 177
                                    44....555999999999999999999999*********977765..455543.44.36899988888887666665555 PP

                                    HHHCTT...SEEEEE-SSHHHCCC-SCE CS
                                    xxxxxx...xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 184 kekskn...aQfivislreemlekadkl 208
                                     + + +   + + v+  ++e ++  d++
  gi|121637167|ref|YP_977390.1| 178 AQLQRRlgtTTVYVTHDQTEAMTLGDRV 205
                                    5554441113333333334444444555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.6e-06    0.0056       5      29 ..      30      54 ..      27     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                     +l+++G+sG+GKTt+l++++   
  gi|121637167|ref|YP_977390.1| 30 GEFLILVGPSGCGKTTTLNMIAGLE 54
                                   5799**************9987665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.4e-05     0.012      23      45 ..      29      51 ..      18     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                   ++e ++l+G+sG+GK++ +++++
  gi|121637167|ref|YP_977390.1| 29 DGEFLILVGPSGCGKTTTLNMIA 51
                                   3489***************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.1e-05     0.018       1      35 [.      33      69 ..      33      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                                   EEEESSTTSSHHHHHHHHHHH..HTHEEEEEETTTCS CS
                            AAA  1 vllyGppGtGKTllakavake..lgvefleisgsell 35
                                   ++l+Gp G+GKT++ + +a    +++  l+i g ++ 
  gi|121637167|ref|YP_977390.1| 33 LILVGPSGCGKTTTLNMIAGLedISSGELRIAGERVN 69
                                   589***************9862233444555555555 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00017      0.15       1      41 [.     241     287 ..     241     288 .. 0.69
   2 ?   -2.4   0.0       8.7   7.4e+03       1      20 [.     349     370 ..     349     382 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                CysA_C_terminal   1 NlFhGrve.dG.klriGglalpvP......elagadgqevvayVRPhDl 41 
                                    N+F++r+   G +l +G+++l+ +      +++    ++v+++VRP+++
  gi|121637167|ref|YP_977390.1| 241 NFFPARLTaIGlTLPFGEVTLAPEvqgviaAHP--KPENVIVGVRPEHI 287
                                    788888863554566688888877667533333..5599*********9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.7
                CysA_C_terminal   1 NlFhGrv.edGklriGg.lalp 20 
                                    N F +rv  + k+ iG+ ++l+
  gi|121637167|ref|YP_977390.1| 349 NQFVARVpAESKVAIGQsVELA 370
                                    7777888556688887755554 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.5   2.1e+03      35      54 ..     189     206 ..     170     208 .. 0.64
   2 ?    1.6   0.0       0.4   3.4e+02       6      27 ..     303     324 ..     302     327 .. 0.87
   3 ?    9.7   0.4    0.0012         1      18      63 ..     336     377 ..     328     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                           TOBE  35 ArvtrrsaeeLgLapGeeVf 54 
                                    + vt ++ e+  ++ G++V+
  gi|121637167|ref|YP_977390.1| 189 VYVTHDQTEA--MTLGDRVV 206
                                    4566666777..77777776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.4
                           TOBE   6 qlpgtVvvveplgseveVrvdl 27 
                                    +++++V+ ve lg++ +++ ++
  gi|121637167|ref|YP_977390.1| 303 TFQVKVNLVESLGADKYLYFTT 324
                                    6999*********999988765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0012
                           TOBE  18 g.seveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                    + +eve + +l   +  +Arv+ +s ++    +G+ V ++++ a+++
  gi|121637167|ref|YP_977390.1| 336 ElAEVEGESALHENQ-FVARVPAESKVA----IGQSVELAFDTARLA 377
                                    357777777888888.************....**********99886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.16      30      50 ..      27      47 ..      18      52 .. 0.88
   2 ?   -1.7   0.0       2.1   1.8e+03     171     188 ..     176     193 ..     162     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                         AAA_25 30 lpagelallaGapgtGKttla 50
                                   ++ ge+ +l+G++g+GKtt +
  gi|121637167|ref|YP_977390.1| 27 IADGEFLILVGPSGCGKTTTL 47
                                   6789**************965 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                         AAA_25 171 aleriarrtgaavllvhH 188
                                     +++++rr+g +++ v H
  gi|121637167|ref|YP_977390.1| 176 EIAQLQRRLGTTTVYVTH 193
                                    578899999999999999 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.097      16      43 ..      29      55 ..      19      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreawe 43
                                   +g  + +l+Gp G GKtt+l+ ++ + +
  gi|121637167|ref|YP_977390.1| 29 DG-EFLILVGPSGCGKTTTLNMIAGLED 55
                                   44.489***************9987655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.091      10      45 ..      18      53 ..      14      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                   Mg_chelatase 10 eakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                   +a r l++++a g  l+lvGp+G+GKt   + +++l
  gi|121637167|ref|YP_977390.1| 18 TAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGL 53
                                   67789999*******************988777665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.12     122     150 ..      23      51 ..       3     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          T2SSE 122 lrkavrerglilvsGgTgsGKttllyall 150
                                    l+  ++    +++ G+ g GKtt+l+++ 
  gi|121637167|ref|YP_977390.1|  23 LNLTIADGEFLILVGPSGCGKTTTLNMIA 51 
                                    56667777889999***********9764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.26       3      22 ..      34      53 ..      32     126 .. 0.71
   2 ?   -2.3   0.0       5.4   4.6e+03     117     145 ..     273     296 ..     262     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                         AAA_28  3 vitGgestGKTtlleaLaar 22
                                   +++G++++GKTt+l+ +a  
  gi|121637167|ref|YP_977390.1| 34 ILVGPSGCGKTTTLNMIAGL 53
                                   799************99953 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
                         AAA_28 117 papeidddgeRredleereaiderlreal 145
                                    p pe +  g+R+e+ ++++ id+     +
  gi|121637167|ref|YP_977390.1| 273 PKPENVIVGVRPEHIQDAALIDA-----Y 296
                                    55555566778877777665543.....3 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.12      24      76 ..      30      79 ..      19     142 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskd 76
                                     + +l+G+ ++GK++ l+++  + + +    + ++ i+ e ++++  +++++ 
  gi|121637167|ref|YP_977390.1| 30 GeFLILVGPSGCGKTTTLNMIAGLEDIS----SGELRIAGERVNEKAPKDRDIA 79
                                   3399*****************8777766....5555555555555544444433 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.41       6      57 ..      42     119 ..      40     129 .. 0.94
   2 ?   -3.2   0.0       8.1   6.9e+03       8      42 ..     186     223 ..     186     227 .. 0.77
   3 ?   -2.5   0.0       5.1   4.4e+03      86     115 ..     294     324 ..     278     338 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                    -HHHHHHHHHHHHHCTEEEEETTC..........................SS-THHHHHHHHHHHHHTT-SEEEEE-- CS
                   Mur_ligase_M   6 GKTTtteliaailekagkvigtvg..........................ttnneiglpktlaemekkeaeyavlEvs 57 
                                    GKTTt  +ia + + + + + ++g                          t  ++i +p+tla+m+k+++   v E++
  gi|121637167|ref|YP_977390.1|  42 GKTTTLNMIAGLEDISSGELRIAGervnekapkdrdiamvfqsyalyphmTVRQNIAFPLTLAKMRKADIAQKVSETA 119
                                    9***********9999999999999******************************************99999998875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.1
                                    HHHHHHHHHHHHCT...EEEEETTCSS-THHHHHHHHH CS
                   Mur_ligase_M   8 TTtteliaaileka...gkvigtvgttnneiglpktla 42 
                                    TTt ++++   e++     v+ + g   ++ig+p+ l+
  gi|121637167|ref|YP_977390.1| 186 TTTVYVTHDQTEAMtlgDRVVVMYGGIAQQIGTPEELY 223
                                    78888888888888776668888888888888888776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.1
                                    HHHSSHHH.HHHHHHHHHHTSETTCEEEEET CS
                   Mur_ligase_M  86 dfhgtlen.yaeaKaelferlkeegiavina 115
                                    d ++ + +  ++ K +l+e+l++++++    
  gi|121637167|ref|YP_977390.1| 294 DAYQRIRAlTFQVKVNLVESLGADKYLYFTT 324
                                    3444444423567777777777777665555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00027      0.23      20      39 ..      31      50 ..      11      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                         AAA_23 20 gltlItGpNGaGKTTildAi 39
                                    + +++Gp G+GKTT l+ i
  gi|121637167|ref|YP_977390.1| 31 EFLILVGPSGCGKTTTLNMI 50
                                   455789***********988 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00069      0.59      18      39 ..      26      47 ..      16      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00069
                         AAA_29 18 eidlkg.atlltGpsGsGKSTll 39
                                   +i   g + +l+GpsG GK+T l
  gi|121637167|ref|YP_977390.1| 26 TIAD-GeFLILVGPSGCGKTTTL 47
                                   4553.448999**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2642.44
//
Query:       gi|121637168|ref|YP_977391.1|  [L=366]
Description: magnesium and cobalt transport transmembrane protein corA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-65  219.9   0.0    5.2e-65  219.6   0.0    1.0  1  CorA      CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.096   12.7   0.2       0.22   11.5   0.2    1.6  1  Phasin    Poly(hydroxyalcanoate) granule associated protein (


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.6   0.0   5.8e-69   5.2e-65       2     291 ..      68     361 ..      67     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.6 bits;  conditional E-value: 5.8e-69
                           CorA   2 agfvWldlsspteeeleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeev......plsill 75 
                                    + fvW+ l  p+e  ++ +a+ +gl++la ed++  ++rp++e yd++l+lvl+ v++   e            ++ i++
  gi|121637168|ref|YP_977391.1|  68 EAFVWIGLHEPDENQMQDVADVFGLHPLAVEDAVHAHQRPKLERYDETLFLVLKTVNYVPHESVVLAReivetgEIMIFV 147
                                    679******************************************************9888776544456899******* PP

                           CorA  76 gdnflitvrreplealdevikrlk.deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrela 154
                                    g++f++tvr+++   l ev+kr++ d ++ +  p+ +++++ d +vd+++e++  +e+++d +e+  +   +k +++ ++
  gi|121637168|ref|YP_977391.1| 148 GKDFVVTVRHGEHGGLSEVRKRMDaDPEHLRLGPYAVMHAIADYVVDHYLEVTNLMETDIDSIEEVAFAPGRKLDIEPIY 227
                                    *************************999**************************************************** PP

                           CorA 155 qlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvm 234
                                     l+r++v+lrr+++p+ +++ ++++++ ++l+++e ++ylrd+ d+ + +++++ ++ ++l+sl ++  +++  ++N  m
  gi|121637168|ref|YP_977391.1| 228 LLKREVVELRRCVNPLSTAF-QRMQTESKDLISKEVRRYLRDVADHQTEAADQIASYDDMLNSLVQAALARVGMQQNMDM 306
                                    ********************.88888****************************************************** PP

                           CorA 235 kvLTvltaif.lPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfk 291
                                    ++++ ++ i+ +P T+i+GiyGmNf ++Pel++ +gyp v  +g m+l++++l+ +f+
  gi|121637168|ref|YP_977391.1| 307 RKISAWAGIIaVP-TMIAGIYGMNFHFMPELDSRWGYPTV--IGGMVLICLFLYHVFR 361
                                    *************.**************************..************9997 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   2.4e-05      0.22      55     111 ..     258     310 ..     231     316 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                         Phasin  55 aeekleevresvkskveevkekaeeqwdklekafdervakaLsrlgvpsredveaLs 111
                                    + +   evr+    +v + +++a++q  + + ++++ v++aL r+g++++ d++++s
  gi|121637168|ref|YP_977391.1| 258 ISK---EVRR-YLRDVADHQTEAADQIASYDDMLNSLVQAALARVGMQQNMDMRKIS 310
                                    222...2332.224456667777788888999********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2690.46
//
Query:       gi|121637169|ref|YP_977392.1|  [L=329]
Description: malate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-33  113.8   0.0      1e-32  113.4   0.0    1.2  1  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal
    1.4e-30  106.2   0.0    2.5e-30  105.4   0.0    1.4  1  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   1.2e-36     1e-32       1     163 [.     157     323 ..     157     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.2e-36
                                    THHHHHHHHHHHHHHHTS.-GGGEE--EEBSSST........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHH CS
                        Ldh_1_C   1 TtLDivRaktflaekagv.tprsvkvtViGgHsg........vtiipllsqvkellklsekqleeliervqnggdevvka 71 
                                    T+LD++Ra  +la k+g   ++ +k+t++G+Hs            +   + + e ++++ + ++e+i++v ++g++++ a
  gi|121637169|ref|YP_977392.1| 157 TRLDHNRAISQLAAKTGAaVTDIKKMTIWGNHSAtqypdlfhA--EVAGKNAAEVVNDQAWIEDEFIPTVAKRGAAIIDA 234
                                    9*****************888899**********999999653..3333477888999********************** PP

                                    HTTSSSS-HHHHHHHHHHHHHHHTTH..TEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHH CS
                        Ldh_1_C  72 kkGagsatlsmAvAgakfveallrdt..keilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekl 149
                                    +   +s+++s+A A +++++++l +t   +++s++v++dg +g+++    + s+Pv+ +  G + ++++l++++f++ ++
  gi|121637169|ref|YP_977392.1| 235 RG--ASSAASAASATIDAARDWLLGTpaDDWVSMAVVSDGSYGVPEG--LISSFPVTTK-GGNWTIVSGLEIDEFSRGRI 309
                                    *5..8999*******************9******************8..9999*****9.******************** PP

                                    HHHHHHHHHHHHHH CS
                        Ldh_1_C 150 eksvkeLkkeiekg 163
                                    +ks +eL +e   +
  gi|121637169|ref|YP_977392.1| 310 DKSTAELADERSAV 323
                                    *******9998766 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   2.7e-34   2.5e-30       2     137 ..       7     150 ..       6     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.7e-34
                                    EEEEETTTSHHHHHHHHHHHHT.TSSSE....EEEE-SSHH..HHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEE CS
                        Ldh_1_N   2 kvavvGaaGgiGqslalllank.klade....laLlDiake..kleGvaldlshistflsvkvkvsekeeealkdadvvv 74 
                                    kvav+GaaG+iG+sl++ la++  l+ +    l+Ll+i+++  +leGv+++l +++++l++ v++++++++++ ++++++
  gi|121637169|ref|YP_977392.1|   7 KVAVTGAAGQIGYSLLFRLASGsLLGPDrpieLRLLEIEPAlqALEGVVMELDDCAFPLLSGVEIGSDPQKIFDGVSLAL 86 
                                    9*********************7777779999*******9999************************************* PP

                                    E--S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHT.TTSEEEE-SSSHHHHHHHHHHHHTS-GG CS
                        Ldh_1_N  75 itagvprkpGetRddLlkvNakIvkeiveaiakva.pnaivlvvsNPvdiltevlkkasglpkk 137
                                    ++++ pr  G++R+dLl++N +I++++++a+++va +++ v v +NP+++++ ++  +++ +++
  gi|121637169|ref|YP_977392.1|  87 LVGARPRGAGMERSDLLEANGAIFTAQGKALNAVAaDDVRVGVTGNPANTNALIAMTNAPDIPR 150
                                    **********************************9999***************99998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2461.67
//
Query:       gi|121637170|ref|YP_977393.1|  [L=86]
Description: hypothetical protein BCG_1301 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0079   16.1   0.7     0.0079   16.1   0.7    1.9  3  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
        0.8    9.7   8.1       0.48   10.4   2.5    3.0  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.7   8.8e-07    0.0079       1      37 [.       2      38 ..       2      39 .. 0.97
   2 ?   -1.7   0.0      0.36   3.2e+03      12      21 ..      64      73 ..      62      76 .. 0.68
   3 ?   -1.5   0.3      0.32   2.9e+03      10      18 ..      75      83 ..      67      86 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-07
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   r++++ld++++++++  + r++r + ++I +Alr++l
  gi|121637170|ref|YP_977393.1|  2 RTTLTLDDDVVRLVEDAVHRERRPMKQVINDALRRAL 38
                                   89********************************988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                                   HHHHHHHHHH CS
                          RHH_1 12 erLdelarrr 21
                                   + +++la+++
  gi|121637170|ref|YP_977393.1| 64 AGFNKLADEL 73
                                   6677787765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.32
                                   HHHHHHHHH CS
                          RHH_1 10 llerLdela 18
                                   + ++Ld+ +
  gi|121637170|ref|YP_977393.1| 75 DEALLDATR 83
                                   445555555 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.5   5.3e-05      0.48       1      13 [.       1      13 [.       1      50 [. 0.70
   2 ?    0.7   0.3     0.057   5.1e+02       6      19 ..      72      85 ..      72      86 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.3e-05
                                   XXXXXXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLla 13
                                   Mrt++++DD+ ++
  gi|121637170|ref|YP_977393.1|  1 MRTTLTLDDDVVR 13
                                   9********9764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.057
                                   XXXXXXXXXXXXXX CS
                 VapB_antitoxin  6 eiDDeLlaeAirlt 19
                                   e++De l +A r++
  gi|121637170|ref|YP_977393.1| 72 ELEDEALLDATRRA 85
                                   68999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 645.16
//
Query:       gi|121637171|ref|YP_977394.1|  [L=143]
Description: hypothetical protein BCG_1302 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.9   0.0      3e-06   27.7   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.7e-10     3e-06       2     121 ..       3     134 ..       2     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-10
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkil 71 
                                    + D + l++++  g +++++a++++++      ++ ++  +l  +l+++++      ++    a++ v+++l  +++ +l
  gi|121637171|ref|YP_977394.1|   3 IPDINLLLYAViTGFPQHRRAHAWWQDTvnghTRIGLTYPALFGFLRIATSarvlaAPLPTADAIAYVREWLSQPNVDLL 82 
                                    567788999989999999999999999999999999999999999999999999999*********************** PP

                                    EBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  72 pidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvak 121
                                      + +++++a+ + +k+g    l+ D  +aA  +e+++  i++ D+df+r a 
  gi|121637171|ref|YP_977394.1|  83 TAGPRHLDIALGLLDKLGtasHLTTDVQLAAYGIEYDA-EIHSSDTDFARFAD 134
                                    **************************************.788********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1139.29
//
Query:       gi|121637172|ref|YP_977395.1|  [L=562]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-33  112.7  22.4    7.5e-33  112.7  22.4    1.6  2  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7  22.4   4.2e-37   7.5e-33       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -3.4   0.5       0.7   1.2e+04      38      53 ..     231     246 ..     223     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 4.2e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   M ++++a ++l aaaadl+gigsal+aan aa+aptt++laa+aDeVSaaiA+lfs +aq+yqalsaqaaafh+qfv+al++
  gi|121637172|ref|YP_977395.1|  1 MEYLIAAQDVLVAAAADLEGIGSALAAANRAAEAPTTGLLAAGADEVSAAIASLFSGNAQAYQALSAQAAAFHQQFVRALSS 82
                                   99******************************************************************************** PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aagsYaaaEaa
  gi|121637172|ref|YP_977395.1| 83 AAGSYAAAEAA 93
                                   *********97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.7
                                    ----SSSSHHHHHHHH CS
                             PE  38 avlaaaaDeVSaaiAa 53 
                                    a  a ++  VS ++ +
  gi|121637172|ref|YP_977395.1| 231 AAGANGQNPVSHQVTH 246
                                    3446788888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 3765.57
//
Query:       gi|121637173|ref|YP_977396.1|  [L=286]
Description: lipoprotein lpqZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-29  101.2   2.3    2.5e-28   99.4   2.3    1.7  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   2.3   1.4e-32   2.5e-28       2     257 .]      33     281 ..      32     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.4e-32
                                    EEEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH................HHH CS
                          OpuAC   2 tivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgta................yea 65 
                                    ++v+gs++ +e+++la+i+ ++l++ G++++  +++     +a+l+sG ++v+p ++tg++                y+a
  gi|121637173|ref|YP_977396.1|  33 ELVVGSTPDSEAMLLAAIYVAALRSYGFAAHAETAAD---PVAKLDSGAFTVVP-AFTGQMlqtlqpdasvrsdaqvYRA 108
                                    79**************************666666666...379***********.*******************999999 PP

                                    HHHHHHHHHEEEEEE.EESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT CS
                          OpuAC  66 ykkaveekkglevlg.plgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYg 144
                                    + +a++  +g+++ + +++a+++ +l+v++ +a+++g  ++s+L  p++       g ++gr +g+     t +++    
  gi|121637173|ref|YP_977396.1| 109 IVSALP--EGIAAGDyTTAAEDKPALVVTQSTAKAWGGGDLSEL--PSH-----CRGLLVGRVAGAH----TPAAVGPCR 175
                                    999999..77777788****************************..444.....789********99....445555555 PP

                                    -TTCEEEGSCEEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHH CS
                          OpuAC 145 ldkvelvegseaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPevaafLe 224
                                    l      +  e   da++ aa+++g+ v+++++t+d+ i++  l +L+d+k +++ a+n+vp++r+++++++     +++
  gi|121637173|ref|YP_977396.1| 176 L-----PAPREFRNDATMFAALRAGQLVAAWTTTADPDIPAD-LIMLTDGKPALIRAENIVPLYRRNALTER--KLLAVN 247
                                    5.....3677788899************************96.****************************9..677889 PP

                                    HHC..--HHHHHHHHHHHHTTTT-HHHHHHHHHHH CS
                          OpuAC 225 kls..ldtetlnelnaqvdvegkdpeevAkawlae 257
                                    +++  ldt +l  +++qv+  g+dp++vA+ wlae
  gi|121637173|ref|YP_977396.1| 248 EVAgvLDTTALIGMRRQVAA-GADPAAVAAGWLAE 281
                                    9999***************9.************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2035.18
//
Query:       gi|121637174|ref|YP_977397.1|  [L=276]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-50  169.9   1.2    5.7e-50  169.5   1.2    1.1  1  adh_short      short chain dehydrogenase
    8.6e-35  120.4   3.4      1e-34  120.2   3.4    1.1  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    2.3e-13   50.5   0.3    4.1e-13   49.6   0.3    1.3  1  KR             KR domain
    0.00022   21.2   1.6     0.0086   16.0   0.2    2.1  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.015   14.6   0.0      0.036   13.4   0.0    1.6  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.017   15.2   0.0      0.025   14.6   0.0    1.2  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.035   14.2   0.8       0.12   12.5   0.8    1.8  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.11   11.9   0.1       0.26   10.7   0.1    1.6  2  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   1.2   2.5e-53   5.7e-50       1     193 [.       7     201 ..       7     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 2.5e-53
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv++vtGa+sGIG+a+a ela++Gakv++ d   + l+ +   lk+ ++ + + ++Dvt+re+  a+ +++ +++g+++ 
  gi|121637174|ref|YP_977397.1|   7 KVAVVTGAGSGIGQALAIELARSGAKVAISDVDTDGLADTEHRLKAISTPVKTDRLDVTEREAFLAYADAVNEHFGTVNQ 86 
                                    89****************************************************************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    ++nNAGi+ +g+++  + +++erv++v + gv++ t+a+lp+++++  G+++n+sSv g+ + +g+aaY ++K+av+g+t
  gi|121637174|ref|YP_977397.1|  87 IYNNAGIAFTGDIEVSQFKDIERVMDVDFWGVVNGTKAFLPHLIASGDGHVINISSVFGLFSAPGQAAYNSAKFAVRGFT 166
                                    ********99****9***************************************************************** PP

                                    HHHHHHHGGGT..EEEEEEEESSBSSHHHHHHCTH CS
                      adh_short 161 rslakelaptg..irvnavaPGlvdTdmakelrek 193
                                    ++l++e+a  g  ++v++v+PG+v+T++a++++++
  gi|121637174|ref|YP_977397.1| 167 EALRQEMALAGhpVKVTTVHPGGVKTAIARNATAA 201
                                    ******9998888***************9998775 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   3.4   4.5e-38     1e-34       1     212 [.      13     230 ..      13     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 4.5e-38
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIG+a+A +la+ Ga+v+++d++ ++ +++e   +++++ v   ++DVt++e+  a +++v e+fg+++ + nnag
  gi|121637174|ref|YP_977397.1|  13 GAGSGIGQALAIELARSGAKVAISDVDTDGLADTEHRLKAISTPVktDRLDVTEREAFLAYADAVNEHFGTVNQIYNNAG 92 
                                    889***************************778888888888887669******************************** PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                    ia +  g+++  + ++++r++dv++ ++++ +ka+lp l+++g g ++n+ssv +  + p+++ay+ aK a+ ++t +l 
  gi|121637174|ref|YP_977397.1|  93 IAFT--GDIEVSQFKDIERVMDVDFWGVVNGTKAFLPhLIASGdGHVINISSVFGLFSAPGQAAYNSAKFAVRGFTEALR 170
                                    ****..*******************************9778888***********************************9 PP

                                    HHHGG..GTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B..-HHHHHHHHH CS
                   adh_short_C2 157 velgp..kgiRvNavspgpikTlaasgikgfdelleelearaplgrlg..tpeevaeaal 212
                                     e++   + ++v +v+pg +kT +a++++ ++ l ++  a++  +r++  +p+  a+++l
  gi|121637174|ref|YP_977397.1| 171 QEMALagHPVKVTTVHPGGVKTAIARNATAAEGLDQAELAETFDKRVAhlSPQRAAQIIL 230
                                    886542288********************9999999999999999977445666665554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.3   1.8e-16   4.1e-13       4     166 ..      10     172 ..       8     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.8e-16
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    ++tG+  g+G++la  la++ga+  v +s     ++  +++ ++l+a  + v++ ++Dv++++a  a+ +++++++++++
  gi|121637174|ref|YP_977397.1|  10 VVTGAGSGIGQALAIELARSGAK--VAISDV--DTDGLADTEHRLKAISTPVKTDRLDVTEREAFLAYADAVNEHFGTVN 85 
                                    89*******************99..455555..3445555678899999******************************* PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--S.EEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esld.ffvlfSSiagllgsagqanYaaaNaflDal 159
                                     +++ Ag++ ++ +e  + +d+e+v+   + G+ n  +++ +    s d +++ +SS+ gl+ ++gqa+Y +a   + ++
  gi|121637174|ref|YP_977397.1|  86 QIYNNAGIAFTGDIEVSQFKDIERVMDVDFWGVVNGTKAFLPhliASGDgHVINISSVFGLFSAPGQAAYNSAKFAVRGF 165
                                    *********************************999999988677444438999*******************9999888 PP

                                    HHHHHHH CS
                             KR 160 aeyrrsq 166
                                     e  r++
  gi|121637174|ref|YP_977397.1| 166 TEALRQE 172
                                    8765543 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   3.9e-06    0.0086       2      66 ..       8      73 ..       7      87 .. 0.82
   2 ?    4.5   0.1     0.012        28      16      70 ..     171     223 ..     166     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                   EEEE.--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHC CS
                        3HCDH_N  2 vavi.GaGt.mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalar 66
                                   vav+ GaG  +G+ +a  +a++g +V + d++++ l++ ++++++ ++  v+  +l+  e+ea la 
  gi|121637174|ref|YP_977397.1|  8 VAVVtGAGSgIGQALAIELARSGAKVAISDVDTDGLADTEHRLKA-ISTPVKTDRLDVTEREAFLAY 73
                                   56544999769********************************97.777778888877777766655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                    HHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEE CS
                        3HCDH_N  16 avfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisft 70 
                                    + +a ag++V+++ +++  +++a ++ ++  e l +++ ++  ++++++a +s++
  gi|121637174|ref|YP_977397.1| 171 QEMALAGHPVKVTTVHPGGVKTAIARNATAAEGLDQAELAE--TFDKRVAHLSPQ 223
                                    56899********************9999888887766644..777777766655 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.6e-05     0.036      35      76 ..       5      46 ..       2      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                   TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                  THF_DHG_CYH_C 35 egkkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76
                                   +gk +vv G+++ +g++la+ L++++a V + +  t+ la++
  gi|121637174|ref|YP_977397.1|  5 AGKVAVVTGAGSGIGQALAIELARSGAKVAISDVDTDGLADT 46
                                   799*********************************988875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.025      18      88 ..      21     237 ..      17     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                           CbiA  18 nLaralarrglrVllvDaDpqannlaileglendiep........................................... 54 
                                    +La+ lar g +V+  D+D+++ +++  e   + i +                                           
  gi|121637174|ref|YP_977397.1|  21 ALAIELARSGAKVAISDVDTDGLADT--EHRLKAISTpvktdrldvtereaflayadavnehfgtvnqiynnagiaftgd 98 
                                    699******************99987..222222222577899999999******************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121637174|ref|YP_977397.1|  99 ievsqfkdiervmdvdfwgvvngtkaflphliasgdghvinissvfglfsapgqaaynsakfavrgftealrqemalagh 178
                                    *********************************************************99999999999999999999999 PP

                                    ........................CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS.. CS
                                    ........................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                           CbiA  55 ........................dlkrllellealgkkkall..lkiagvvlnrvdgen 88 
                                                            +l++  el+e+++k++a+l   + a ++l+ v +++
  gi|121637174|ref|YP_977397.1| 179 pvkvttvhpggvktaiarnataaeGLDQ-AELAETFDKRVAHLspQRAAQIILTGVAKNK 237
                                    9999999999999999999999999988.9999999999999899888999999888873 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   5.2e-05      0.12      21      55 ..       4      39 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                                   -TTSEEEEE--SH.HHHHHHHHHHHCT-EEEEE-S- CS
                  AdoHcyase_NAD 21 laGkvavvaGyGd.vGkGcaaslkglGarvivtevd 55
                                   +aGkvavv+G G  +G+  a  l   Ga+v +++vd
  gi|121637174|ref|YP_977397.1|  4 FAGKVAVVTGAGSgIGQALAIELARSGAKVAISDVD 39
                                   69*********96599999999*************9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00012      0.26       2      61 ..      10      75 ..       9     126 .. 0.75
   2 ?   -1.5   0.0      0.63   1.4e+03     140     164 ..     153     177 ..     129     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHH CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfk 61
                                   +VtGa   iG+al+ +l++ g +v   d ++++ +  +++ l       +  +ld+t+r+a+ ++ +
  gi|121637174|ref|YP_977397.1| 10 VVTGAGSGIGQALAIELARSGAKVAISDVDTDGLADTEHR-LkaistpvKTDRLDVTEREAFLAYAD 75
                                   8********************9999999996655544333.24779777777777777774443333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.63
                                    SHHHHHHHHHHHHHHHHHHHHT-EE CS
                      Epimerase 140 spYaaaKlageklveayaaqyglna 164
                                     +Y  aK a+   +ea++++  l  
  gi|121637174|ref|YP_977397.1| 153 AAYNSAKFAVRGFTEALRQEMALAG 177
                                    5677777777777777777765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1952.45
//
Query:       gi|121637175|ref|YP_977398.1|  [L=97]
Description: hypothetical protein BCG_1306c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-10   39.9   0.2    5.7e-10   39.7   0.2    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.051   13.6   0.0    1.2  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
      0.088   12.9   0.1       0.15   12.1   0.1    1.3  1  YoeB_toxin       YoeB-like toxin of bacterial type II toxin-a


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   9.5e-14   5.7e-10       1      89 [.       9      88 ..       9      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.5e-14
                                   EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEE CS
                     ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilr 82
                                   v +t +A +dl+++ + i      a    + +e  +  l++np++  ++ + +l+gl ++r+gdyr++Y idd++  v i++
  gi|121637175|ref|YP_977398.1|  9 VAITATAARDLQRLPEKI------A---AACVEFVFGPLLNNPHRLGKPLRNDLEGLHSARRGDYRVVYAIDDGHHRVEIIH 81
                                   56899**********877......5...67777779*******999997777789****************88888888*** PP

                                   EEEHHHH CS
                     ParE_toxin 83 vlhrsed 89
                                   + +rs  
  gi|121637175|ref|YP_977398.1| 82 IARRSAS 88
                                   *999865 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.5e-06     0.051       2      84 ..      10      90 ..       9      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-06
                ParE-like_toxin  2 lqtrrfkkalkklkek.lkadldkavkeiiedPe.lGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGtheN 81
                                     t ++++ l++l ek  +a ++     ++++P+ lG++   DL+g+ +     +   +++ Y +d+ ++ ++++ +  +  
  gi|121637175|ref|YP_977398.1| 10 AITATAARDLQRLPEKiAAACVEFVFGPLLNNPHrLGKPLRNDLEGLHS----ARRGDYRVVYAIDDGHHRVEIIHIARRSA 87
                                   568899**********455555555699*****757***********86....57899**********9999***9999887 PP

                ParE-like_toxin 82 fYr 84
                                    Yr
  gi|121637175|ref|YP_977398.1| 88 SYR 90
                                   776 PP

>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.6e-05      0.15      42      74 ..      47      80 ..      41      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                                   EE-SGGGTTEEEEESSSSEEEEEEEESSE..EEEE CS
                     YoeB_toxin 42 epLkedlsglwsRRideehRlvYlvedde..ltil 74
                                   +pL++dl+gl+s R   + R+vY+++d++  ++i+
  gi|121637175|ref|YP_977398.1| 47 KPLRNDLEGLHSARR-GDYRVVYAIDDGHhrVEII 80
                                   47**********995.579*******875125555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 797.02
//
Query:       gi|121637176|ref|YP_977399.1|  [L=89]
Description: hypothetical protein BCG_1307c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-21   76.3   0.1    1.4e-21   76.0   0.1    1.1  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.1     8e-26   1.4e-21       1      74 [.       1      73 [.       1      74 [. 0.97

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 8e-26
                                   CEEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHHHHHHHC CS
                PhdYeFM_antitox  1 mkivsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslplnaerlaesgaever 74
                                   m +v++ e +++lse++ eve ++e+++Itr+G+p+aVl+s++++ +++e t+ +l+ p+++e ++e+ a+v +
  gi|121637176|ref|YP_977399.1|  1 MAVVPLGEVRNRLSEYVAEVELTHERITITRHGHPAAVLISADDLASIEE-TLEVLRTPGASEAIREGLADVAA 73
                                   899***********************************************.****************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 621.70
//
Query:       gi|121637177|ref|YP_977400.1|  [L=1214]
Description: alpha-ketoglutarate decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-57  194.6   0.0    3.8e-57  193.5   0.0    1.5  2  E1_dh            Dehydrogenase E1 component
    2.6e-55  187.4   0.0    3.9e-55  186.8   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    1.1e-53  181.6   0.0    1.7e-53  181.0   0.0    1.3  1  Transket_pyr     Transketolase, pyrimidine binding domain
    7.9e-41  139.3   0.0    1.2e-40  138.6   0.0    1.3  1  OxoGdeHyase_C    2-oxoglutarate dehydrogenase C-terminal
    3.5e-05   23.3   0.6    3.5e-05   23.3   0.6    1.9  2  2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.3   4.5e+03     224     235 ..     361     372 ..     357     377 .. 0.70
   2 !  193.5   0.0   1.1e-60   3.8e-57       4     297 ..     472     800 ..     469     803 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.3
                                    E--SS-SSTTSH CS
                          E1_dh 224 tYRyggHsesDd 235
                                     YR  gH + D 
  gi|121637177|ref|YP_977400.1| 361 AYRNRGHLMADT 372
                                    577777777773 PP

  == domain 2  score: 193.5 bits;  conditional E-value: 1.1e-60
                                    HHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TT..SEEEES.S--HHHHHHTT--..HHHHHHHHTT-T. CS
                          E1_dh   4 vllrrvedaldalykrkkrigfyhlsagqealkvgiaaaleke..Dliite.YReagvllargls..leeilaeltgkv. 77 
                                     +   +e +l+ +y  +kr++++  +  ++ +  +i++  e++  +++i + +R++ ++la+ +     +i+ e+ g+  
  gi|121637177|ref|YP_977400.1| 472 NAAEAFETFLQTKYVGQKRFSLEGAESVIPMMDAAIDQCAEHGldEVVIGMpHRGRLNVLANIVGkpYSQIFTEFEGNLn 551
                                    56678999*********************************99955666668*********9776669************ PP

                                    ..........TTSSGTT-...-E..BTT..BEEE-SSTTTH..HHHHHHHHHHHH............HHTS---EEEEEE CS
                          E1_dh  78 ..........kgkggsrh..elmyaekesrilggngivgaq..vplvaGialaak............iegkkevailliG 131
                                              k+++g+      m++ +  ++  + ++++++   p+++G+++a++            ++   +v ++l+G
  gi|121637177|ref|YP_977400.1| 552 psqahgsgdvKYHLGATGlyLQMFGDNDIQVSLTANPSHLEavDPVLEGLVRAKQdlldhgsidsdgQRAFSVVPLMLHG 631
                                    ****55555555555554322344455556666667776666689999****************888888899999**** PP

                                    GGG.TT-HHHHHHHHHHHHTT--E...EEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHH CS
                          E1_dh 132 DgA.anqGdvyealnlaalwklpv...ifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfA 207
                                    D+A a+qG v+e+lnla+l+++ v   i++++NN++g++T++e++++s++ +d+a+  g+p+++V+g+Dp+a+  +++ A
  gi|121637177|ref|YP_977400.1| 632 DAAfAGQGVVAETLNLANLPGYRVggtIHIIVNNQIGFTTAPEYSRSSEYCTDVAKMIGAPIFHVNGDDPEACVWVARLA 711
                                    ******************************************************************************** PP

                                    HHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHH CS
                          E1_dh 208 aeraregkgpllielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveea 287
                                    +++++++k++++i++++YR+ gH+e Ddps +  + +++ v+ k+   + + e+L+ +g +s +e ++  + ++ + e  
  gi|121637177|ref|YP_977400.1| 712 VDFRQRFKKDVVIDMLCYRRRGHNEGDDPSMTN-PYMYDVVDTKRGARKSYTEALIGRGDISMKEAEDALRDYQGQLERV 790
                                    *********************************.*****************************************99999 PP

                                    HHHHHHS--- CS
                          E1_dh 288 vkkaeskkel 297
                                    ++++ + +++
  gi|121637177|ref|YP_977400.1| 791 FNEVRELEKH 800
                                    9999877665 PP

>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.0   1.1e-58   3.9e-55       5     225 ..      86     318 ..      82     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 1.1e-58
                                    XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE CS
                   2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasv 84 
                                    e   l+g  +a++k++++s+ e+p++t ++ v ++ l++ r  +++++++++  k++++++l +a+++A+k+fP++n ++
  gi|121637177|ref|YP_977400.1|  86 EVAVLRGAAAAVVKNMSASL-EVPTATSVRAVPAKLLIDNRIVINNQLKRTRGGKISFTHLLGYALVQAVKKFPNMNRHY 164
                                    566789999***********.***************************98888*************************** PP

                                    .EES..EEEE--SS--EEEE----.....----EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE--- CS
                   2-oxoacid_dh  85 deee..keivvkkhvniGvAvatp.....rGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlG 157
                                    +e +  ++ v+++h+n+G+A++++     r+L+v+ ik++++++++++ +++++++++ar+gkl+ ed+ g t++++N G
  gi|121637177|ref|YP_977400.1| 165 TEVDgkPTAVTPAHTNLGLAIDLQgkdgkRSLVVAGIKRCETMRFAQFVTAYEDIVRRARDGKLTTEDFAGVTISLTNPG 244
                                    65554579***************99988888************************************************* PP

                                    ------------TT-SEEEEE---.B--TTSTT-.......HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT CS
                   2-oxoacid_dh 158 mlGvtsftPiinppqvaIlgvgrikerpvvkege.......lvvrkvmtlslsaDHRvidGaeaarFlntlkkll 225
                                    ++G+ ++ P ++p+q aI+gvg++ e p+  +g+       l ++k++tl+ ++DHR+i+Gae  +Fl+t+++ll
  gi|121637177|ref|YP_977400.1| 245 TIGTVHSVPRLMPGQGAIIGVGAM-EYPAEFQGAseeriaeLGIGKLITLTSTYDHRIIQGAESGDFLRTIHELL 318
                                    ************************.999998888899***********************************998 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   4.6e-57   1.7e-53       2     178 .]     862    1063 ..     861    1063 .. 0.99

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 4.6e-57
                                     EEEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT......................TEGEEE--S-H CS
                   Transket_pyr    2 kiawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg......................egrvidsgisE 57  
                                     ki+w+ +e +al++l++e++ v+l+g+D+++gtfs+r+++l d++                      ++ v+ds++sE
  gi|121637177|ref|YP_977400.1|  862 KIDWAFGELLALGSLVAEGKLVRLSGQDSRRGTFSQRHSVLIDRHtgeeftplqllatnsdgsptggKFLVYDSPLSE 939 
                                     79**************************************************************************** PP

                                     HHHHHHHHHHHHHCT.TEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHH CS
                   Transket_pyr   58 qavlgfavGaalagp.llviveaqFgdFangAqiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflr 134 
                                     +a++gf++G+ + +p + v++eaqFgdF+ngAq ++d++i+sgeak+++ ++vv++lp+g +++Gp h sa++e+fl+
  gi|121637177|ref|YP_977400.1|  940 YAAVGFEYGYTVGNPdAVVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSNVVLLLPHGHEGQGPDHTSARIERFLQ 1017
                                     ****************************************************************************** PP

                                     TSTT..EEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC.T CS
                   Transket_pyr  135 lipg..lkvvrPsdpaetkhllrrairredrkPvvlrlpksllrhk 178 
                                     l ++  +++++Ps+p++++hllrr +    ++P+++++pks lrhk
  gi|121637177|ref|YP_977400.1| 1018 LWAEgsMTIAMPSTPSNYFHLLRRHALDGIQRPLIVFTPKSMLRHK 1063
                                     ***************************9889*************85 PP

>> OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.0   3.5e-44   1.2e-40       2     152 .]    1067    1213 ..    1066    1213 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 3.5e-44
                  OxoGdeHyase_C    2 SsleelaegtsFqrvledeeeea.lkepekvkrvvlcsGkvyydLlkerekkekekdvaivriEqlyPfpfeelkeel 78  
                                     S++++++e  +F++vle+++ e+ + +++kv+r++l+sGk+yy+L+++++k+++ +d+aivr+Eql+P+p ++l+e+l
  gi|121637177|ref|YP_977400.1| 1067 SEIKDFTEI-KFRSVLEEPTYEDgIGDRNKVSRILLTSGKLYYELAARKAKDNR-NDLAIVRLEQLAPLPRRRLRETL 1142
                                     999****99.*********99878899*******************99998766.*********************** PP

                  OxoGdeHyase_C   79 ekYpnakelvWvQeEpkNqGawsfveprletvlkekkkkkkklryvgreasaspAtGskkvhkkeqealleeaf 152 
                                     ++Y+n+ke++WvQeEp+NqGaw  +  +l ++l +k      +++++r+a+++p+ Gs+kvh+ eq+++l+eaf
  gi|121637177|ref|YP_977400.1| 1143 DRYENVKEFFWVQEEPANQGAWPRFGLELPELLPDK---LAGIKRISRRAMSAPSSGSSKVHAVEQQEILDEAF 1213
                                     *********************************855...678******************************98 PP

>> 2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.6   9.9e-09   3.5e-05      15      34 ..       1      20 [.       1      27 [. 0.89
   2 ?   -2.4   0.1       1.1   3.9e+03      30      37 ..     324     331 ..     323     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.9e-09
                2-oxogl_dehyd_N 15 lYeayleDPsSVdesWrayF 34
                                   +Y+++++DPsSVd+sW+++ 
  gi|121637177|ref|YP_977400.1|  1 MYRKFRDDPSSVDPSWHEFL 20
                                   9****************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                2-oxogl_dehyd_N  30 WrayFknl 37 
                                    W+++F++l
  gi|121637177|ref|YP_977400.1| 324 WDEVFREL 331
                                    ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.26s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 8212.58
//
Query:       gi|121637178|ref|YP_977401.1|  [L=262]
Description: hypothetical protein BCG_1309c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0094   15.6   0.2      0.017   14.8   0.0    1.6  2  EcsC        EcsC protein family
  ------ inclusion threshold ------
      0.013   16.1   0.7       0.29   11.8   0.7    2.5  1  HTH_32      Homeodomain-like domain
      0.029   14.6   0.1      0.064   13.5   0.1    1.7  1  TetR_C_30   Tetracyclin repressor-like, C-terminal domain
       0.22   10.9   3.3       0.24   10.8   0.7    2.3  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> EcsC  EcsC protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       0.8   3.6e+03      89     108 ..      77      96 ..      58     107 .. 0.70
   2 !   14.8   0.0   3.7e-06     0.017     190     240 ..     190     241 ..     120     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.8
                           EcsC  89 klakkrklaaaaeGagtGag 108
                                    kl k+   +++a+Ga+ G+ 
  gi|121637178|ref|YP_977401.1|  77 KLEKRFLSVVTASGAAVGTA 96 
                                    45555556666777776654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.7e-06
                           EcsC 190 eelikeiakelrdqvdkkkllqliPv.iGavvGalaNysfikdvaeaAkmly 240
                                    ++++k ++k+++ + +   + +l+P+ iGa++Ga+ N+ + k+++++A+ ++
  gi|121637178|ref|YP_977401.1| 190 SRMLKYVVKRFALKRGALMFGKLVPMgIGAIIGAIGNRLVGKKLVRNARSAF 241
                                    4789*********************55*********************9887 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   6.5e-05      0.29      28      62 ..      50      85 ..       5      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                         HTH_32 28 klsdevrariiallreeprWsprqlaarlaere.gv 62
                                      ++ +a++ +l+r +p  sp +++a+l++r+  v
  gi|121637178|ref|YP_977401.1| 50 IQGPAAQAYVARLRRAHPGASPAKIVAKLEKRFlSV 85
                                   35567777777777667899*********9999333 PP

>> TetR_C_30  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.4e-05     0.064      43      71 ..      50      78 ..      37     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                      TetR_C_30 43 eydpvarrfiaalrralPdlpeeelfwrl 71
                                     +p a++++a lrra+P++++++++ +l
  gi|121637178|ref|YP_977401.1| 50 IQGPAAQAYVARLRRAHPGASPAKIVAKL 78
                                   5789*******************999877 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   5.4e-05      0.24      13      30 ..      81      98 ..      80     100 .. 0.93
   2 ?   -1.5   0.1      0.36   1.6e+03       8      18 ..     139     149 ..     135     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.4e-05
                     UCR_Fe-S_N 13 DFLyiATgavgaVGaaaa 30
                                   +FL + T++ +aVG+aa+
  gi|121637178|ref|YP_977401.1| 81 RFLSVVTASGAAVGTAAT 98
                                   7***************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.36
                     UCR_Fe-S_N   8 eptRRDFLyiA 18 
                                    + +RR+ L++A
  gi|121637178|ref|YP_977401.1| 139 HRERRRALVLA 149
                                    56899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2021.32
//
Query:       gi|121637179|ref|YP_977402.1|  [L=579]
Description: drug-transport integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-52  176.7  59.2    2.1e-51  175.0  56.8    2.6  2  MFS_1      Major Facilitator Superfamily
    2.8e-08   33.0  16.1    2.8e-08   33.0  16.1    2.5  2  Sugar_tr   Sugar (and other) transporter
    3.6e-06   25.7  17.2    7.8e-06   24.6  17.2    1.4  1  TRI12      Fungal trichothecene efflux pump (TRI12)
    4.9e-06   25.8  11.9    4.9e-06   25.8  11.9    3.4  4  PUCC       PUCC protein
    0.00072   18.4   5.4     0.0014   17.5   1.5    2.2  2  LacY_symp  LacY proton/sugar symporter
  ------ inclusion threshold ------
       0.42   10.1   4.1          2    7.9   4.1    2.3  1  SKG6       Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0  56.8   6.9e-55   2.1e-51       2     352 ..      25     415 ..      24     416 .. 0.89
   2 ?    0.6   0.0     0.068     2e+02     237     263 ..     458     483 ..     437     507 .. 0.54

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 6.9e-55
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    ++++f+++l+++++++a p +++ +l i  +++ +++++y l++av +l++Grl+drfG++ ++l+gl +f +++l + +
  gi|121637179|ref|YP_977402.1|  25 MVGFFMIMLDSTVVAIANP-TIMAQLRIGYATVVWVTSAYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGVFTVASLGCGL 103
                                    67999**************.999***************************************************788888 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    +s+  +l+++rv+qG+gag+l+p  ++ i+++fp  +rg a+g +++ +s+++++gpl+gg+l++s gW+++f+++ +v+
  gi|121637179|ref|YP_977402.1| 104 SSGAGMLIAARVVQGVGAGLLTPQTLSTITRIFPAHRRGVALGAWGTVASVASLVGPLAGGALVDSMGWEWIFFVNVPVG 183
                                    67777*************************************************************************** PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeee...........................................kgtgpaplvp 198
                                    +++++l++ l+p+ p+ ++r+     +                                           ++ ++ pl+p
  gi|121637179|ref|YP_977402.1| 184 VIGLILAAYLIPALPHHPHRFDWFGVGlsgagmflivfglqqgqsanwqpwiwavivggigfmslfvywqARNAREPLIP 263
                                    *****99999988888888885444449**************************************99999999999999 PP

                          MFS_1 199 awkallkdpvlwillialllfffgfsglltllpl..ylqevlglsglllaglllallalvgailallagrlsdrlgrrrr 276
                                       ++++d+ +   l  l ++ ++f+g+ ++lp+  y+q v gls    +++l+a +a+vg +la+++g ++dr  + + 
  gi|121637179|ref|YP_977402.1| 264 --LEVFNDRNF--SLSNLGIAIIAFAGTGMMLPVtfYAQAVCGLS-PTHTAVLFAPTAIVGGVLAPFVGMIIDRSHPLCV 338
                                    ..777777777..666666666677777777777779********.7999999*********************666555 PP

                          MFS_1 277 lllallllllaalglallavtssavllllvlvl.iGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    l +++++l++a   l+   ++ ++++ l++ ++ +G++++fv+++l++ a++++ p+ ag+ sg+fn +++lg++lg
  gi|121637179|ref|YP_977402.1| 339 LGFGFSVLAIAMTWLLCEMAPGTPIWRLVLPFIaLGVAGAFVWSPLTVTATRNLRPHLAGASSGVFNAVRQLGAVLG 415
                                    5555555554444444444449999999966666*****************************************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.068
                          MFS_1 237 vlglsglllaglllallalvgailall 263
                                     +  +   ++ ll+a++al+g+++al+
  gi|121637179|ref|YP_977402.1| 458 PFAAA-MSQSMLLPAFVALFGIVAALF 483
                                    44444.233333333333333333222 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  16.1   9.5e-12   2.8e-08      48     188 ..      56     190 ..      21     199 .. 0.92
   2 ?   -1.1   9.0      0.21   6.3e+02      55     164 ..     312     425 ..     278     438 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.5e-12
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                    + +++s++l+  ++  l+ag lgdrfG k+ +li+  +f ++++ ++++       +li++Rv+ G+g+Gl +  +  +i
  gi|121637179|ref|YP_977402.1|  56 VVWVTSAYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGVFTVASLGCGLSS---GAGMLIAARVVQGVGAGLLTPQTLSTI 132
                                    679***********************************************...88************************* PP

                                    HTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                       Sugar_tr 128 sEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                      i p++ Rg   + + +  ++  lv+   g +l ++ +   w + +++++   ++ lil 
  gi|121637179|ref|YP_977402.1| 133 TRIFPAHRRGVALGAWGTVASVASLVGPLAGGALVDSMG---WEWIFFVNVPVGVIGLILA 190
                                    ********************************9999999...*******999999988775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS. CS
                       Sugar_tr  55 flvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGigvGlasvlvPmyisEiA. 131
                                    f   ai+G+++a ++g +++R   l + ++ f++ a+ + +   +    + +  +   ++ +gv +a v +P+++     
  gi|121637179|ref|YP_977402.1| 312 FAPTAIVGGVLAPFVGMIIDRSHPLCVLGFGFSVLAIAMTWLLCEmaPGTPIWRLVLPFIALGVAGAFVWSPLTVTATRn 391
                                    555689**************************999999988653322333333333345788889999999988765444 PP

                                    .-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                       Sugar_tr 132 .pkklRgalvslyqlaitfGilvaaifglglnkt 164
                                      ++l+ga  ++++   ++G ++++ +++++ ++
  gi|121637179|ref|YP_977402.1| 392 lRPHLAGASSGVFNAVRQLGAVLGSASMAAFMTS 425
                                    499999******************9999988765 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6  17.2   2.6e-09   7.8e-06      64     337 ..      39     300 ..       9     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-09
                          TRI12  64 asalpnilqdvgqsensslfst.lwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctat.kfntllaamtll 141
                                    a a p i+ ++     + ++ t  + +  av +lv grl drfg + + ++   +  v a +gc  +     l+aa  + 
  gi|121637179|ref|YP_977402.1|  39 AIANPTIMAQLRIGYATVVWVTsAYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGVFTV-ASLGCGLSsGAGMLIAARVVQ 117
                                    44556677665555555544431578899***************99987776544444.5678876515677889999** PP

                          TRI12 142 gvaagpagaspl.fvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavllivvwyypp 220
                                    gv ag      l  +  ++  + + + l      + v s ++p  g  l     w wif++ + +  i   li+  y  p
  gi|121637179|ref|YP_977402.1| 118 GVGAGLLTPQTLsTITRIFPAHRRGVALGAWGTVASVASLVGPLAGGALVDSMGWEWIFFVNVPVGVIG--LILAAYLIP 195
                                    *****988877735889999999988888888777788889********************99988776..677889999 PP

                          TRI12 221 sfaqlhgkkvrkreelakldwigiilvivgvslfllgvswggkpn.spwnsakviglissglgslvvfalyevygkpvrp 299
                                    ++   h           + dw g+ l  +g+ l+++g+  g   n +pw  a ++g    g+g + +f  ++   +  +p
  gi|121637179|ref|YP_977402.1| 196 ALPH-H---------PHRFDWFGVGLSGAGMFLIVFGLQQGQSANwQPWIWAVIVG----GIGFMSLFVYWQA-RNAREP 260
                                    8754.3.........3469*********************9988857997776665....8899999976665.67889* PP

                          TRI12 300 ivppalfkdtrgfvc...illissimgamnlslviiypqqv 337
                                    ++p  +f+d    +    i +i+     m l  v +y q v
  gi|121637179|ref|YP_977402.1| 261 LIPLEVFNDRNFSLSnlgIAIIAFAGTGMMLP-VTFYAQAV 300
                                    ********976544411134443333334443.44566666 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.0      0.29   8.6e+02      96     163 ..      24      93 ..      19      99 .. 0.79
   2 !   25.8  11.9   1.6e-09   4.9e-06     285     363 ..      91     170 ..      51     198 .. 0.83
   3 ?   -5.6  10.8       5.5   1.7e+04     233     355 ..     296     418 ..     267     440 .. 0.75
   4 ?   -1.6   0.2      0.34     1e+03     293     322 ..     459     488 ..     443     495 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                           PUCC  96 llvGlgvslsqTallALladlaeeeerpkvvgllyvm..lligivvsaivvgallkdytearLirvvqgv 163
                                    ++vG+ + +   +++A++  +   + r   +++++v    l++ +v  +v g+l + + +++L  +  gv
  gi|121637179|ref|YP_977402.1|  24 MMVGFFMIMLDSTVVAIANPTIMAQLRIGYATVVWVTsaYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGV 93 
                                    6889999999999999999999999999999999985337888889999999998888888887665555 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.6e-09
                           PUCC 285 llsflll.ilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQaiaaglavllggalrdll 363
                                    l+ f++  +  +l +   +l+a+ ++ G+++Gl++  +l+ + ++ ++ r g+alGaWG + ++a  ++ l+ggal d +
  gi|121637179|ref|YP_977402.1|  91 LGVFTVAsLGCGLSSGAGMLIAARVVQGVGAGLLTPQTLSTITRIFPAHRRGVALGAWGTVASVASLVGPLAGGALVDSM 170
                                    444443303344444478999*******************************************************9976 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 5.5
                           PUCC 233 YgGevlgLtvgeTTkLtalfal..GtlvGlllaglvlsrglkkarlaslgvllgllsflllilaallen.vallvagvll 309
                                    Y+  v gL  ++T  L a  a+  G+l+ +  +g+++  + ++  + ++g  + +++++ l++ ++ +  ++ lv+  ++
  gi|121637179|ref|YP_977402.1| 296 YAQAVCGLSPTHTAVLFAPTAIvgGVLAPF--VGMIID-RSHPLCVLGFGFSVLAIAMTWLLCEMAPGTpIWRLVLPFIA 372
                                    888999999999999988766422566555..566655.789999999999999999999999888887799******** PP

                           PUCC 310 lGlasGlf.avaaltlmldlaaeeraglalGaWGaaQaiaaglavll 355
                                    lG+a+ ++ +  ++t++ +l  +  ag   G+  a+  + a l+ + 
  gi|121637179|ref|YP_977402.1| 373 LGVAGAFVwSPLTVTATRNLR-PHLAGASSGVFNAVRQLGAVLGSAS 418
                                    **9855431334555555554.5678889999999988888887664 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.34
                           PUCC 293 laallenvallvagvlllGlasGlfavaal 322
                                    +aa++++++ll a v+l+G+ + lf v  +
  gi|121637179|ref|YP_977402.1| 459 FAAAMSQSMLLPAFVALFGIVAALFLVDFT 488
                                    688899999999999999999988866555 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.5   4.8e-07    0.0014     256     396 ..      51     190 ..      19     200 .. 0.87
   2 ?    2.3   0.1     0.019        56      32      69 ..     295     332 ..     266     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-07
                      LacY_symp 256 aGtrvfGyvttagellnalimfiaplivnriGaknalliagvimsvrilgsafattalevvilkllhalevplllvgvfk 335
                                     G     +vt+a  l  a+ m++a  + +r G+kn  li+  + +v  lg+ ++  a  ++  +++  +   ll   ++ 
  gi|121637179|ref|YP_977402.1|  51 IGYATVVWVTSAYLLAYAVPMLVAGRLGDRFGPKNLYLIGLGVFTVASLGCGLSSGAGMLIAARVVQGVGAGLLTPQTLS 130
                                    5666677899999999**************************************************************** PP

                      LacY_symp 336 yitsafdkrlsatifligfqlskqlaivllstlaGklydkvGfqtaylvlgiivlsltlis 396
                                     it  f ++    + l ++  + ++a+++     G l d++G++ +++v   + +  ++++
  gi|121637179|ref|YP_977402.1| 131 TITRIFPAHR-RGVALGAWGTVASVASLVGPLAGGALVDSMGWEWIFFVNVPVGVIGLILA 190
                                    ******9875.56889999999*******999****************9655555545544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.019
                      LacY_symp  32 vwlkevlglsktetGivfsvislfsilfqplfGlisdk 69 
                                     + + v gls t+t ++f+   ++  ++ p+ G+i d+
  gi|121637179|ref|YP_977402.1| 295 FYAQAVCGLSPTHTAVLFAPTAIVGGVLAPFVGMIIDR 332
                                    4567899****************************998 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.1   0.00066         2      16      32 ..     178     194 ..     178     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00066
                           SKG6  16 VaVPVaViiivLlaili 32 
                                    V VPV+Vi ++L+a+li
  gi|121637179|ref|YP_977402.1| 178 VNVPVGVIGLILAAYLI 194
                                    56*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3662.59
//
Query:       gi|121637180|ref|YP_977403.1|  [L=1139]
Description: hypothetical protein BCG_1311c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-24   85.2   0.0    3.7e-23   82.2   0.0    2.3  2  AAA_12           AAA domain
    1.2e-17   64.4   0.0    1.8e-17   63.8   0.0    1.3  1  RNase_H_2        RNase_H superfamily
      2e-13   50.5   0.1    6.8e-13   48.8   0.1    1.9  1  AAA_30           AAA domain
    9.3e-13   48.6   0.0    3.7e-05   23.6   0.0    2.9  3  AAA_11           AAA domain
    1.4e-07   32.0   0.0    3.9e-07   30.5   0.0    1.8  1  AAA_19           AAA domain
    2.1e-06   27.4   0.0    5.6e-06   26.1   0.0    1.8  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    5.8e-06   26.3   0.0    1.1e-05   25.3   0.0    1.5  1  Helicase_RecD    Helicase
    3.2e-05   23.8   0.0      0.033   13.9   0.0    3.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00071   19.9   0.0     0.0027   18.0   0.0    2.0  1  AAA_22           AAA domain
     0.0028   18.1   0.0     0.0078   16.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
     0.0035   17.3   0.0     0.0073   16.2   0.0    1.6  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
     0.0066   16.9   0.0      0.025   15.0   0.0    2.0  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.027   14.5   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
      0.048   13.8   0.0       0.13   12.5   0.0    1.7  1  AAA_33           AAA domain
      0.048   12.9   0.0       0.14   11.3   0.0    1.8  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.061   13.6   0.4       0.15   12.4   0.4    1.6  1  DUF4226          Domain of unknown function (DUF4226)
       0.24   10.8   0.0       0.46    9.9   0.0    1.3  1  PhoH             PhoH-like protein


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.1   3.2e+03     117     135 ..     182     200 ..     175     207 .. 0.82
   2 !   82.2   0.0   3.5e-26   3.7e-23      15     195 ..     933    1110 ..     916    1113 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.1
                         AAA_12 117 itpYraqvellkkklkeke 135
                                    i  Yr+q  ll++ l+ + 
  gi|121637180|ref|YP_977403.1| 182 IPVYRSQRALLQRLLDGHY 200
                                    778*********9998665 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 3.5e-26
                         AAA_12   15 ekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekkeksyiNeeEa 92  
                                     e+  +Ld  YRmhp+++  +s l Y+g+L ++++ +  +        + + p v  ++ + +++     +s+  +eEa
  gi|121637180|ref|YP_977403.1|  933 ERGYFLDRSYRMHPAVCAAVSALSYEGRLCSHTERTAVRRL------DGYPPGV--HTRGVHHKG----NSIESPEEA 998 
                                     56689************************998876666655......4455533..333333332....68999**** PP

                         AAA_12   93 elvvklvekllkk.gsee......erkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdviilsl 163 
                                     e+++  +++ll + +++e      + +++ v++pY+aqv l++++l+++     +  ++v+tvd+fQG +  v+++s+
  gi|121637180|ref|YP_977403.1|  999 EAILAELRQLLGSpWTDEhgtrplAASDVLVLAPYNAQVALVRRRLASAGLG-GADGVRVGTVDKFQGGQAPVVFISM 1075
                                     ***9999998866255559999**99*********************76666.4667********************* PP

                         AAA_12  164 VRsn...ekkeigflkderrlNValTRAkskliiv 195 
                                       s+     + i+fl +++rlNVa++RA+++ +iv
  gi|121637180|ref|YP_977403.1| 1076 TASSaddVPRGISFLLNRNRLNVAVSRAQYAAVIV 1110
                                     ***94434447********************9998 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.7e-20   1.8e-17       1     165 [.     312     501 ..     312     502 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.7e-20
                      RNase_H_2   1 lffDiEttGl....spkknliyliGvldvdekeiekltqllaeepeeekailelf....lellekkkalvtfngksFDvp 72 
                                    lffD+E ++l     ++ +l yl+Gvl+  +   + ++ l a+++++e+++l  f    + + ++++++++++++ ++ +
  gi|121637180|ref|YP_977403.1| 312 LFFDFEGDPLwtadGKQWGLEYLFGVLEAGRAG-V-FRPLWAHDRTAERQALTDFlaivARRRRRHPNMHIYHYAPYEKT 389
                                    7*********77533444789******755444.4.89999999999999998884555555666699************ PP

                      RNase_H_2  73 flkrlfkkyklde.......eefrhiDLlkelrkkkl...esysLksveke.lgierreed.lsGsqavklyqeylrtgd 140
                                     l rl+ +y + e       ++   +DL+  +rk+     +s+sLk++e   lg + r+ d +  +++++ y +y++ + 
  gi|121637180|ref|YP_977403.1| 390 ALLRLVGRYGIGEddvddllRNGVLVDLYPLVRKSIRvgtDSFSLKALEPLyLGTQPRSGDvTTAADSINSYARYCELRA 469
                                    ******9999999888888777799*****9999877788999*******9899999765537899**********8776 PP

                      RNase_H_2 141 ee.......llekilaYNedDvralatlyekl 165
                                              l++i  YN+ D+r++ +l+++l
  gi|121637180|ref|YP_977403.1| 470 AGrideaatVLKEIEGYNHYDCRSTRALRDWL 501
                                    4445555669*********************8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   6.4e-16   6.8e-13      14     135 ..     755     910 ..     748     959 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.4e-16
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLae...elgieastiakllkrlk........ 81 
                                    l  +  + +++Gp+GtGKt++ + + +e+++++  r+ ++A +++  ++L e   ++g++   +ak  + ++        
  gi|121637180|ref|YP_977403.1| 755 LDLDSSYLAVHGPPGTGKTYTAARViAELVTEHAWRIGVVAQSHATVENLLEgviSAGLDPGQVAKKPHDHTagrwqsid 834
                                    444455889**********7765554***********************9986666777777777777777778888999 PP

                         AAA_30  82 ..........................grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaG 134
                                                              +r+  + + +ll++DEag    +++ a++ aa++    ++l+GD++Ql+ V++G
  gi|121637180|ref|YP_977403.1| 835 gsqytefirdtagcviggtawdfangNRVPKA-SlDLLVIDEAGQFCLANTIAVAPAATN----LLLLGDPQQLPQVSQG 909
                                    999999999999************86433344.35***********99999999888877....***************9 PP

                         AAA_30 135 g 135
                                     
  gi|121637180|ref|YP_977403.1| 910 T 910
                                    6 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.5e-08   3.7e-05      19      79 ..     761     814 ..     748     824 .. 0.85
   2 !   20.7   0.1   2.8e-07   0.00029     217     255 ..     867     904 ..     849     908 .. 0.84
   3 ?   -0.4   0.0      0.75   7.9e+02      47      94 ..    1017    1058 ..     995    1078 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.5e-08
                         AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr.gll 79 
                                       ++GPPGtgKT t + ++++l          ++  ri v a+S+a v +lle +++ gl 
  gi|121637180|ref|YP_977403.1| 761 YLAVHGPPGTGKTYTAARVIAEL--------VTEHAWRIGVVAQSHATVENLLEGVISaGLD 814
                                    4689*******************........57899******************99996554 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.8e-07
                         AAA_11 217 kfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLp 255
                                      d+++IDEA+q + + t i+   +a +++L+GDp+QLp
  gi|121637180|ref|YP_977403.1| 867 SLDLLVIDEAGQFCLANT-IAVAPAATNLLLLGDPQQLP 904
                                    689*********875555.6777777************9 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.75
                         AAA_11   47 seeeksakpriLvCapSNaAvDellerllrglldsegekykpkivRvg 94  
                                       ++  a   +Lv ap Na v  +  rl++          + + vRvg
  gi|121637180|ref|YP_977403.1| 1017 HGTRPLAASDVLVLAPYNAQVALVRRRLAS------AGLGGADGVRVG 1058
                                     4667778899*****************999......445555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.7e-10   3.9e-07       5     144 ..     753     906 ..     749     908 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.7e-10
                         AAA_19   5 ve.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....atTiHrlal.. 77 
                                    ++ +l ++ l+v ++pGtGKT++   ++a+lv ++ +   +i +va  +  +++l e + ++g++    a+  H  +   
  gi|121637180|ref|YP_977403.1| 753 AAlDLDSSYLAVHGPPGTGKTYTAARVIAELVTEHAW---RIGVVAQSHATVENLLEGVISAGLDpgqvAKKPHDHTAgr 829
                                    44489999***************************66...9****************99888877899955555443322 PP

                         AAA_19  78 .ldfddlltealelle..............eaeeekklqeee..llivDEfqdvdelqyrLlkallgekkklllvGDpdQ 140
                                       +d+   +  e+++                 + + + ++   ll++DE+ +   l++++  a+++ +++lll+GDp+Q
  gi|121637180|ref|YP_977403.1| 830 wQSIDGS--QYTEFIRdtagcviggtawdfA--NGNRVPKASldLLVIDEAGQFC-LANTI--AVAPAATNLLLLGDPQQ 902
                                    2333332..3556666777777789999652..33333333225******98765.23333..34445677********* PP

                         AAA_19 141 liyv 144
                                    l+ v
  gi|121637180|ref|YP_977403.1| 903 LPQV 906
                                    *987 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   5.3e-09   5.6e-06       2      52 .]    1055    1110 ..    1054    1110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.3e-09
                       UvrD_C_2    2 ayaltihkaQGsefpaVivfdpdlaaarmgel........rrrlLYtavTRAreklilv 52  
                                     + + t+ k+QG+++p+V++     +a +   +        +r+ L +av+RA+   ++v
  gi|121637180|ref|YP_977403.1| 1055 VRVGTVDKFQGGQAPVVFISMTASSADD---VprgisfllNRNRLNVAVSRAQYAAVIV 1110
                                     5788***************444444444...4567*****************9888876 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.1e-08   1.1e-05       2     101 ..     764     878 ..     763     895 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-08
                  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfefla.kglealglkeeekkkkaekaelrvrkqrieyia 80 
                                    + + +G+GK+ +++ ++a+l+ e+  +i v+a s+++v++l+e ++ +gl+  ++ +++++++a + +    +q  e+i+
  gi|121637180|ref|YP_977403.1| 764 VHGPPGTGKTYTAARVIAELVTEHAWRIGVVAQSHATVENLLEGVIsAGLDPGQVAKKPHDHTAGRWQSIDGSQYTEFIR 843
                                    67889*************************************97651678888888866666665555555566666666 PP

                  Helicase_RecD  81 pdellklkeqa..............dllvvDEAAa 101
                                     ++ +    +a              dllv+DEA +
  gi|121637180|ref|YP_977403.1| 844 DTAGCVIGGTAwdfangnrvpkaslDLLVIDEAGQ 878
                                    6666666666666666677777777********76 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.093        98       2      20 ..     763     781 ..     762     811 .. 0.80
   2 !   13.9   0.0   3.1e-05     0.033      59     106 ..     864     909 ..     853     941 .. 0.82
   3 ?    3.3   0.0     0.055        58     180     232 ..    1053    1109 ..    1040    1111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.093
                Viral_helicase1   2 vvhGvpGcGKStlirkllr 20 
                                     vhG pG GK+    +++ 
  gi|121637180|ref|YP_977403.1| 763 AVHGPPGTGKTYTAARVIA 781
                                    69*********86655554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.1e-05
                Viral_helicase1  59 kstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrn 106
                                    ++ + ++l++DE+++   ++ + +a  + a +++l+GDp+Q p+ s+ 
  gi|121637180|ref|YP_977403.1| 864 PKASLDLLVIDEAGQ--FCLANTIAVAPAATNLLLLGDPQQLPQVSQG 909
                                    4456799******87..578999********************99754 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.055
                Viral_helicase1  180 lgvrevttvhevqGltfdkVtlvllketdlelis.....esrenllvAlTRhrkslvi 232 
                                      gvr v tv   qG ++++V +  + ++ +++ +      +r+ l vA +R+  + vi
  gi|121637180|ref|YP_977403.1| 1053 DGVR-VGTVDKFQGGQAPVVFISMTASSADDVPRgisflLNRNRLNVAVSRAQYAAVI 1109
                                     5778.99*********************999998999996699********9866665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0027       7      60 ..     761     808 ..     757     910 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60 
                                     l+v+G++GtGKT++++r+  +l+ e      ++  + v ++s  + ++ll+ +
  gi|121637180|ref|YP_977403.1| 761 YLAVHGPPGTGKTYTAARVIAELVTE------HAWRIGVVAQSHATVENLLEGV 808
                                    589*******************9765......5555566666666666665555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.4e-06    0.0078       3      22 ..     764     783 ..     762     845 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.4e-06
                                    EESSTTSSHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakel 22 
                                    ++GppGtGKT++a  v+ el
  gi|121637180|ref|YP_977403.1| 764 VHGPPGTGKTYTAARVIAEL 783
                                    89***********9999997 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     7e-06    0.0073     115     181 ..     100     157 ..      11     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                       PDDEXK_1 115 rpvale.lefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaege 181
                                     pv ++ + f+    r++G+ D + ++++++r+ D K  ++p        +   lQl++Y++al +  
  gi|121637180|ref|YP_977403.1| 100 APVVYQaAMFD---GRFVGFADFLIRDGHRYRVADTKLARSP----T---VTALLQLAAYADALVHSG 157
                                    34444433444...48*********88889*******76633....3...44568**********982 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.025      23      63 ..     758     798 ..     745     866 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    +++++ ++G++G+GK+  + ++  +l +++++ +   ++++
  gi|121637180|ref|YP_977403.1| 758 DSSYLAVHGPPGTGKTYTAARVIAELVTEHAWRIGVVAQSH 798
                                    55899**************9999899998655444444333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.027      27      72 ..     761     806 ..     734     876 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                    EE.EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHH CS
                         ResIII  27 gl.ikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtle 72 
                                    +l ++ + GtGKT++aa++i++l ++ +  ++ +++++ + +e +le
  gi|121637180|ref|YP_977403.1| 761 YLaVHGPPGTGKTYTAARVIAELVTE-HAWRIGVVAQSHATVENLLE 806
                                    44478899****************97.55699999998888877765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.13       4      33 ..     764     789 ..     762     832 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                         AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtl 33 
                                    ++G+pG+GK++ a r+++    +l+++ ++
  gi|121637180|ref|YP_977403.1| 764 VHGPPGTGKTYTAARVIA----ELVTEHAW 789
                                    89**************95....55555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.14       4      97 ..     762     876 ..     759     960 .. 0.76
   2 ?   -2.0   0.0       1.6   1.7e+03     341     360 ..    1091    1110 ..    1079    1112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                        DUF2075   4 vlVtGvaGtGKtvvllnllael..............eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklss 69 
                                    + V+G +GtGKt+ + +++ael              + + e+  + ++s   +  +v ++  + ++ ++  + + +++++
  gi|121637180|ref|YP_977403.1| 762 LAVHGPPGTGKTYTAARVIAELvtehawrigvvaqsHATVENLLEGVISAGLDPGQVAKKPHDHTA-GRWQSIDGSQYTE 840
                                    679*******************66555555554443333355556666666666666666666666.6666666677777 PP

                        DUF2075  70 finnlsef........kkaeekkeepkedvvivDEA 97 
                                    fi ++             + ++ ++  +d++++DEA
  gi|121637180|ref|YP_977403.1| 841 FIRDTAGCviggtawdFANGNRVPKASLDLLVIDEA 876
                                    777777557777777666677777777888888887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                        DUF2075  341 llkNayrVLLtRGrkGlyiy 360 
                                     l +N+++V  +R+++  +i+
  gi|121637180|ref|YP_977403.1| 1091 LNRNRLNVAVSRAQYAAVIV 1110
                                     569***********999986 PP

>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00014      0.15      35      72 ..      48      85 ..      13      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                        DUF4226 35 rsahakaaegrrrLdalqaeidqavatqalaldTpaGa 72
                                   r a+  +a++ rrLd+l +e  +ava ++  ++TpaG 
  gi|121637180|ref|YP_977403.1| 48 RAAVLGSAHEGRRLDQLRHEFGDAVAIIGRPAYTPAGL 85
                                   66777888899******************99******5 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00043      0.46      18      50 ..     758     790 ..     749     821 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                                    H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                           PhoH  18 kndivfaiGpaGtGKtylavalavealkkkkvk 50 
                                    +++ + + Gp GtGKty a  + +e+++++  +
  gi|121637180|ref|YP_977403.1| 758 DSSYLAVHGPPGTGKTYTAARVIAELVTEHAWR 790
                                    55667889***********99999888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 6681.87
//
Query:       gi|121637181|ref|YP_977404.1|  [L=202]
Description: lipoprotein lprE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-14   52.4   0.3    2.3e-13   50.1   0.3    2.1  1  Lipoprotein_21  LppP/LprE lipoprotein
  ------ inclusion threshold ------
        1.3    9.0  16.3        1.4    8.9  15.0    1.7  2  DUF3558         Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Lipoprotein_21  LppP/LprE lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.3   2.5e-17   2.3e-13       2      86 ..     113     190 ..     112     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.5e-17
                 Lipoprotein_21   2 gydpcaaLswvvistegatasspqqallFhdgeflGtatpepyasip.rvlrsdddtVtVeYrwykpddplccpsgtatv 80 
                                    +y++ca+Ls+vvi+ ++ ++++ ++a++Fh g+++ ++ p++y+++  + ++ ++dtV+++Y+              ++v
  gi|121637181|ref|YP_977404.1| 113 NYNECAQLSAVVIKANTNAGNPTTRAVMFHLGKYIPQGVPDTYGFTGiDTSQCTGDTVALTYA--------SGIGLNNVV 184
                                    8***************9989999**********************999**************9........455566777 PP

                 Lipoprotein_21  81 tFrwdg 86 
                                    +Frw+g
  gi|121637181|ref|YP_977404.1| 185 KFRWNG 190
                                    777776 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  15.0   0.00016       1.4       1      49 [.      24      81 ..      24     106 .. 0.68
   2 ?   -1.1   0.0      0.18   1.6e+03      37      57 ..     107     127 ..      84     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                        DUF3558  1 lllaGCssttdGt..apaasssassssttsssaapav.......pldtsgvlfdpCgl 49
                                   ++l+GC+s +++   +p+a++s s++ ++++s++p++       p++ s++++dpC++
  gi|121637181|ref|YP_977404.1| 24 ATLTGCGSGDSTVakTPEATPSLSTAHPAPPSSEPSPpsataapPSNHSAAPVDPCAV 81
                                   589****555555774444444444444444444444446788899**********75 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.18
                        DUF3558  37 ldtsgvlfdpCglltddqlae 57 
                                     ++ +  +++C++l++ ++++
  gi|121637181|ref|YP_977404.1| 107 PEPLAGNYNECAQLSAVVIKA 127
                                    455666789999998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1458.34
//
Query:       gi|121637182|ref|YP_977405.1|  [L=563]
Description: cold-shock dead-box protein a deaD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-50  170.0   0.1    9.2e-49  165.6   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
    1.2e-28   99.7   0.0    4.5e-28   97.8   0.1    2.0  2  Helicase_C       Helicase conserved C-terminal domain
    6.2e-20   71.0   0.0    1.9e-19   69.4   0.0    1.9  1  DbpA             DbpA RNA binding domain
     0.0004   20.4   0.0    0.00096   19.2   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.064   13.0   0.0    1.3  1  FtsK_4TM         4TM region of DNA translocase FtsK/SpoIIIE
       0.04   13.3   1.4       0.12   11.7   0.3    2.0  2  HEM4             Uroporphyrinogen-III synthase HemD
       0.22   11.8   0.0       0.49   10.7   0.0    1.5  1  B_solenoid_dext  Beta solenoid repeat from Dextranase


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   0.0   3.6e-52   9.2e-49       1     175 [.      37     203 ..      37     204 .. 0.95
   2 ?    2.3   0.0      0.05   1.3e+02      51     105 ..     254     308 ..     219     324 .. 0.60

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 3.6e-52
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvl 79 
                                    t+iQa++ip+++ g dv++ a+TG+GKT+af+ip+l+++    +++ p+al+++PtreLa q+++ + +++ y  +l+vl
  gi|121637182|ref|YP_977405.1|  37 TAIQAATIPALMAGSDVVGLAQTGTGKTAAFAIPMLSKID--ITSKVPQALVLVPTRELALQVAEAFGRYGAYlSQLNVL 114
                                    79**********************************9994..59999**************************566**** PP

                                    EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                     i+gg+++  ql+ l++g+++vvgtpgr++d+l++ +l+ls+v flVlDEad++l +gf d+++ril+++p       + 
  gi|121637182|ref|YP_977405.1| 115 PIYGGSSYAVQLAGLRRGAQVVVGTPGRVIDHLERATLDLSRVDFLVLDEADEMLTMGFADDVERILSETP-------EY 187
                                    **********************************************************************4.......44 PP

                                    SEEEEEESSBSHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                           DEAD 160 rqvivlSATlpkdvkk 175
                                    +qv ++SAT+p  ++k
  gi|121637182|ref|YP_977405.1| 188 KQVALFSATMPPAIRK 203
                                    57*********88776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.05
                                    EEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET...TSSHHHHHHHHHTT.CSEEEEEH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxx RF
                           DEAD  51 livePtreLaeqtlnnlkkfkkyidlrvlliig...gvaardqlskldng.vdivvgtp 105
                                    ++ + t++ +e+++++l+ ++     ++ +i g   + ++++ +++l+ g +di+v+t 
  gi|121637182|ref|YP_977405.1| 254 IVFVRTKQATEEIAEKLRARGF----SAAAISGdvpQAQRERTITALRDGdIDILVATD 308
                                    3334444444444444444444....5555656222455556666666667*****996 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   9.3e+03      15      49 ..      80     119 ..      72     131 .. 0.59
   2 !   97.8   0.1   1.7e-31   4.5e-28       2     111 .]     237     345 ..     236     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                                    TTSEEEEEESSHH.HHHHHHHHHHHT....TSTEEEESTT CS
                     Helicase_C  15 eggkilifvntid.rlekvklllekk....gikvavlhge 49 
                                    +  ++l+ v+t++  l+ ++ + +      +++v++++g 
  gi|121637182|ref|YP_977405.1|  80 KVPQALVLVPTRElALQVAEAFGRYGaylsQLNVLPIYGG 119
                                    5568889999998633323444222233335666666665 PP

  == domain 2  score: 97.8 bits;  conditional E-value: 1.7e-31
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                    k++al++ l + e  + +++fv+t++  e+ ++ l + +g+++a++ g+ pq +re+++++ ++g++d+L+atdva+rG+
  gi|121637182|ref|YP_977405.1| 237 KMDALTRVL-EVEPFEAMIVFVRTKQATEEiAEKL-RARGFSAAAISGDVPQAQRERTITALRDGDIDILVATDVAARGL 314
                                    788899999.89999***********997655555.4559**************************************** PP

                                    TSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                    d++++++V n+d+p +++sy++riGRtgRag
  gi|121637182|ref|YP_977405.1| 315 DVERISHVLNYDIPHDTESYVHRIGRTGRAG 345
                                    *****************************97 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   7.5e-23   1.9e-19       1      68 [.     471     538 ..     471     542 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 7.5e-23
                                    EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT-HHHHHHHHTT--SSS--- CS
                           DbpA   1 rlfinvGkkdklrpgdivgaiakeaglsgkdIGkIdildkfSfvevpkekaeevlkalkkkkikGrkv 68 
                                    +++++vGk++k+ pg ivgaia+e+gl ++d G+I+i ++fS+ve+p++ ++ +lk+l++++i G  +
  gi|121637182|ref|YP_977405.1| 471 TYRVAVGKRHKIGPGAIVGAIANEGGLHRSDFGQIRIGPDFSLVELPAKLPRATLKKLAQTRISGVLI 538
                                    79*************************************************************99766 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.7e-07   0.00096      32     169 ..      58     197 ..      53     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.7e-07
                                    STTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--........-SEE CS
                         ResIII  32 aTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke..igkkvsgdkkka.kekdstnkkil 107
                                     TGtGKT    + +  ++    k  ++l+lvp+++l  q  e+f ++      +  +  ++ g ++    ++ +  ++++
  gi|121637182|ref|YP_977405.1|  58 QTGTGKTAAFaIPMLSKIDITSKVPQALVLVPTRELALQVAEAFGRYGAYLS-QlnVLPIYGGSSYAVqLAGLRRGAQVV 136
                                    6******999455556666666667*******************98876443.33544444444444455667789999* PP

                                    EEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---SEEEE.EESS- CS
                         ResIII 108 vttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfkeavllg.lTATp 169
                                    v t  ++  ++     e+ +l+ +r d+++ DEa  +  +   + +++il   +e+++++ ++AT+
  gi|121637182|ref|YP_977405.1| 137 VGTPGRVIDHL-----ERATLDLSRVDFLVLDEADEMLTMgfaDDVERILSETPEYKQVAlFSATM 197
                                    ***99999999.....88889999999999999999999877669999999988888887468886 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.5e-05     0.064      40      83 ..      94     138 ..      83     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                       FtsK_4TM  40 aaavhNwgGrvGAwladlll.slfGlsawllvvlllawglrllrr 83 
                                    a +v+ ++Gr GA+l+ l +  + G s++++ ++ l+ g++++ +
  gi|121637182|ref|YP_977405.1|  94 ALQVAEAFGRYGAYLSQLNVlPIYGGSSYAVQLAGLRRGAQVVVG 138
                                    568999************9967*****************999887 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.8e-05      0.12     105     176 ..     239     307 ..     215     309 .. 0.79
   2 ?   -0.2   0.0      0.21   5.3e+02      77     117 ..     362     402 ..     341     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                                    HHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHHTT--SEEEES CS
                           HEM4 105 egLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealkagevdavvft 176
                                    ++L  +l+ +  +  ++++r ++a +++ae+L++rg++  ++      +++ ++e++ +al++g++d++v+t
  gi|121637182|ref|YP_977405.1| 239 DALTRVLEVEPFEAMIVFVRTKQATEEIAEKLRARGFSAAAISG---DVPQAQRERTITALRDGDIDILVAT 307
                                    555555553333345899*******************9999875...467999***************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                    E.ESSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---E CS
                           HEM4  77 a.avGpaTaraLeelglrvdlvpseegtaegLaeelaeslag 117
                                      a+ +aT++ L+e+ l  +    +++ ++++a+++ ++l+g
  gi|121637182|ref|YP_977405.1| 362 LkAIEKATRQTLTEAQLPTV-EDVNTQRVAKFADSITNALGG 402
                                    44777899999999999886.777799999999999987776 PP

>> B_solenoid_dext  Beta solenoid repeat from Dextranase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.49       4      27 ..     170     193 ..     170     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                B_solenoid_dext   4 sMDfyGdsdnisvevaDYKQVGaF 27 
                                    +M+f  d ++i +e  +YKQV+ F
  gi|121637182|ref|YP_977405.1| 170 TMGFADDVERILSETPEYKQVALF 193
                                    8********************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3898.75
//
Query:       gi|121637183|ref|YP_977406.1|  [L=383]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-28   97.7  39.7    7.8e-28   97.5  39.7    1.0  1  Acyl_transf_3  Acyltransferase family
  ------ inclusion threshold ------
       0.29   10.9   0.1       0.29   10.9   0.1    2.9  4  Gemini_mov     Geminivirus putative movement protein


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5  39.7   8.7e-32   7.8e-28       2     339 ..      23     372 ..      22     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 8.7e-32
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                  Acyl_transf_3   2 aylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla.......amlyrrrglskl 74 
                                    a+l ++R++A+llVv  Ha++  + ++++ ++              +gvp+FF+lSGf+l+       a++ ++++ls++
  gi|121637183|ref|YP_977406.1|  23 ASLTGIRAVAALLVVGTHAAYTTGKYTHGYWGLMS-------SRMEIGVPIFFVLSGFLLFrpwvksaATGGPPPSLSRY 95 
                                    6899*****************99999999998754.......678*********************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  75 ikrRilrlliplliwllliillialvaghiqanasanvtlfdet......kglmfllfefpatghlWfLwalfvlylllp 148
                                     ++R++r++ ++ ++ ll +l+ ++   ++++   ++v lf+++      ++ +   f  ++  ++W+L++++ +yl+lp
  gi|121637183|ref|YP_977406.1|  96 AWHRVRRIMPAYTVTVLLAYLVYHFRTAGPNP-GHTWVGLFRNLtltqiyTDGYLGAFLHQGLTQMWSLAVEVAFYLALP 174
                                    **************999999999998888887.666666666667*********************************** PP

                                    xx......xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 149 ll......lrllrkvrkshlllllilllllslvf.irhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrg 221
                                     l      l + r++ ++ ll++ ++l+++s  + i+ +++++ +    l lp +  l+ f+ G++la +   + +    
  gi|121637183|ref|YP_977406.1| 175 ALaylllvLVCRRRWQPRLLLATMAGLTMISPAWlILVHNTHWMPDGARLWLPTY--LAWFVGGMMLAVLAAMGVRCYAF 252
                                    ****998777777777777777777787776555055555555555555555555..9************9999877666 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 222 lkislllsllllalillalfgqtdg....gglvasvliqsasll.lvslgimllllllfalpsrsafkllrylgkiSygi 296
                                      i l++ +  ++ + +a + +t +      lv++ ++   ++l +  l++     ++ +l+sr     +++lg+iSy i
  gi|121637183|ref|YP_977406.1| 253 VAIPLAVICYFIVSTPIAGAPTTSPtalaEALVKTAFYAVIAVLaVAPLALGDQGWYAQLLASR----PMVFLGEISYEI 328
                                    6666666666666666666666644333333333322222222202222223333444444444....6*********** PP

                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 297 YliHlpllmllqkllrdwgln.lgevlllvlllvvsvivsvvll 339
                                    +liHl+ + + +  +  +     ++v l ++ lv+++ ++++l 
  gi|121637183|ref|YP_977406.1| 329 FLIHLVTMEIAMVDVLGYRVYtSSMVNLCLVTLVLTIPLAWLLH 372
                                    ****7777777777777744455889999999999999999985 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.3e-05      0.29      25      56 ..      88     119 ..      75     121 .. 0.89
   2 ?   -0.7   0.4      0.14   1.2e+03      33      60 ..     160     186 ..     155     188 .. 0.68
   3 ?   -2.2   0.2      0.41   3.7e+03      23      50 ..     273     297 ..     257     302 .. 0.57
   4 ?   -4.1   0.3       1.6   1.4e+04      42      57 ..     358     371 ..     351     372 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                     Gemini_mov  25 aapssselpwsrvgeiailtlvavlvlYLlyt 56 
                                    + ps s ++w rv  i+    v+vl  YL+y 
  gi|121637183|ref|YP_977406.1|  88 PPPSLSRYAWHRVRRIMPAYTVTVLLAYLVYH 119
                                    67899**************************6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.14
                     Gemini_mov  33 pwsrvgeiailtlvavlvlYLlytlvlk 60 
                                     ws  +e+a+ + +     YLl +lv +
  gi|121637183|ref|YP_977406.1| 160 MWSLAVEVAFYLALPA-LAYLLLVLVCR 186
                                    6888888877655543.35888888765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.41
                     Gemini_mov  23 ptaapssselpwsrvgeiailtlvavlv 50 
                                    pt +p++ +     ++  a+   +avl+
  gi|121637183|ref|YP_977406.1| 273 PTTSPTALAE---ALVKTAFYAVIAVLA 297
                                    3344443333...345555555555554 PP

  == domain 4  score: -4.1 bits;  conditional E-value: 1.6
                     Gemini_mov  42 iltlvavlvlYLlytl 57 
                                    ++tl  vl + L+++l
  gi|121637183|ref|YP_977406.1| 358 LVTL--VLTIPLAWLL 371
                                    2222..4555566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2765.39
//
Query:       gi|121637184|ref|YP_977407.1|  [L=99]
Description: hypothetical protein BCG_1315c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.8   0.0      0.086   13.4   0.0    1.3  1  TORC_C    Transducer of regulated CREB activity, C terminus


Domain annotation for each model (and alignments):
>> TORC_C  Transducer of regulated CREB activity, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-06     0.086      58      74 ..      16      32 ..       1      33 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-06
                         TORC_C 58 dmvlaDpavEdtFRlDR 74
                                    mv++Dpav d +R+DR
  gi|121637184|ref|YP_977407.1| 16 GMVVTDPAVTDGYRQDR 32
                                   599*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 722.69
//
Query:       gi|121637185|ref|YP_977408.1|  [L=419]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-35  120.7  70.6    2.1e-26   92.7  45.6    1.9  2  MFS_1     Major Facilitator Superfamily
    4.9e-19   68.1  33.3    6.5e-19   67.7  33.3    1.0  1  MFS_3     Transmembrane secretion effector
    0.00022   20.2  20.3      0.034   13.0   0.8    3.0  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
      0.044   13.6   0.6       0.32   10.8   0.6    2.5  1  CAAD      CAAD domains of cyanobacterial aminoacyl-tRNA synth


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7  45.6   4.7e-30   2.1e-26       1     352 [.      12     363 ..      12     364 .. 0.86
   2 !   41.8  17.0   1.4e-14   6.1e-11      25     173 ..     252     396 ..     244     416 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4.7e-30
                          MFS_1   1 lllaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lll 78 
                                    +l+a++++a++ ++ ++a+p+  l+++   s+ ++++++++ +l  ++a+l++G  +d fGrrrv +++ +l++++ + +
  gi|121637185|ref|YP_977408.1|  12 ILFATLMAAAGDGVSIVAFPWlVLQRE--GSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAvAGV 89 
                                    689*****************7666666..7**********************************9999999999884444 PP

                          MFS_1  79 ll..fa.....sslwlllvlrvlqGlgagalfpagaaliadwfpk..eergraigllsagfslGailgpllggllasslg 149
                                    +l  ++      ++ +l+vl +l+++++ a+++a  +++ + +++      r +g + a  +l++i+gp++ggl+++ +g
  gi|121637185|ref|YP_977408.1|  90 PLvaWGyggdaVNVLVLAVLAALAAAFGPAGMTARDSMLPEAAARagWSLDRINGAYEAILNLAFIVGPAIGGLMIATVG 169
                                    4444425566577889***************************99445999*************************9999 PP

                          MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsgllt 228
                                       +++i a ++ l+++ +++l +e + +++  s  +       ++++++++ +++ +vl  + +i l ++++ + + ++
  gi|121637185|ref|YP_977408.1| 170 GITTMWITATAFGLSILAIAALQLEGAGKPHHTSRPQG----LVSGIAEGLRFVWNLRVLRtLGMIDLTVTALYLPMESV 245
                                    99999999999999988544444444444444444444....68888889999999999965677777777777778999 PP

                          MFS_1 229 llplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                    l+p y  +++  +  +++g++l+++a +g+++al  + l+ r++rr ++  a+l l la++ +a+l++    ++++++++
  gi|121637185|ref|YP_977408.1| 246 LFPKY-FTDHQQP--VQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPL---PVIMVLCA 319
                                    ****9.8888888..999999999999999999899999999***************************...99999*** PP

                          MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    ++G+ +g ++p+++++++  a ++ +g+++g+++++ +++g lg
  gi|121637185|ref|YP_977408.1| 320 VVGLVYGPIQPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLG 363
                                    **********************************9999998887 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 1.4e-14
                          MFS_1  25 edlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfp 104
                                    +d++ +p ++g++l + a g +v++l +++l+ r+ rr ++ +++l+++l++++++f ++l++++vl ++ Gl +g + p
  gi|121637185|ref|YP_977408.1| 252 TDHQ-QPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPIQP 330
                                    4434.8999**************************8888************66666559********************* PP

                          MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                    + +++i   +++  rgr++g++++ + ++  lg ll+g l++++g +a+f++la+  +  +++    ++
  gi|121637185|ref|YP_977408.1| 331 IYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIVCTGLV---AIR 396
                                    *******************************************************99999884...333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7  33.3   1.5e-22   6.5e-19      15     412 ..      12     414 ..       6     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.5e-22
                          MFS_3  15 iWiaslvsnlGtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltv 94 
                                    i  a+l++  G  +  va  Wl+ + + s  +  +v  a+ LP+++ +++aG   D f rR+v +++ +l  ++ + + +
  gi|121637185|ref|YP_977408.1|  12 ILFATLMAAAGDGVSIVAFPWLVLQREGSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVAGVPL 91 
                                    56799**********************************************************99998876554444444 PP

                          MFS_3  95 laalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvg......iniaRsvGPAlgGvlvaavGa 168
                                    +a     + + +l+l++l+++ aa+  Pa   + + +++    +a   L  ++      +n+a  vGPA+gG+++a+vG 
  gi|121637185|ref|YP_977408.1|  92 VAWGYGGDAVNVLVLAVLAALAAAF-GPAGMTARDSMLPEAAARAGWSLDRINgayeaiLNLAFIVGPAIGGLMIATVGG 170
                                    4433335778899999999998887.799999999************9999876666667******************** PP

                          MFS_3 169 alafavnalsylalivallrwkre...vrksslprEkllealraglRftaasreikav.lvRaalFglsasavlaLLPlv 244
                                    +++  ++a ++   i+a+++ + e   +++++     l++++ +glRf+   r +++  ++  ++  l       L P  
  gi|121637185|ref|YP_977408.1| 171 ITTMWITATAFGLSILAIAALQLEgagKPHHTSRPQGLVSGIAEGLRFVWNLRVLRTLgMIDLTVTALYLPMESVLFPKY 250
                                    *********9988888888877652225666777899************9888887642544444444444444578877 PP

                          MFS_3 245 ardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWita 324
                                      d  + +++  G  l a+  G ++gal  + L  r+     +++a+++l l  +++a+ ++l v+++  ++ G  +   
  gi|121637185|ref|YP_977408.1| 251 FTD--HQQPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPI 328
                                    776..5679*********************************************************************** PP

                          MFS_3 325 lstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklpeleasdla 404
                                       +n  +q+   + ++gR++ v   + + +  +G ll G +++a++++ + la a+ ++   + l+ ++lp+l++ dla
  gi|121637185|ref|YP_977408.1| 329 QPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIV--CTGLVAIRLPALRELDLA 406
                                    ***************************************************997665555..5555678999******** PP

                          MFS_3 405 psnrfeep 412
                                    p+++++ p
  gi|121637185|ref|YP_977408.1| 407 PQADIDRP 414
                                    *9988877 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.8   7.7e-06     0.034      44      91 ..      40      87 ..      16     118 .. 0.83
   2 !   10.8  12.5   3.6e-05      0.16      16     152 ..     233     362 ..     150     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-06
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigav 91
                                   s+ + ++++s++++  ++  l+ag+++d+fGR+ + ++a +l+ ++ +
  gi|121637185|ref|YP_977408.1| 40 SAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVA 87
                                   44578999*****************************99999765544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.6e-05
                                    HHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                       Sugar_tr  16 tgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                    + v + +l + ++++  +++ ++     + v++g+ + +   G+++G+l    l+ r+ R+ ++ +a++ +  +++++a+
  gi|121637185|ref|YP_977408.1| 233 LTVTALYLPMESVLFPKYFTDHQ-----QPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAF 307
                                    44445555555544444444444.....45678*********************************88888888888888 PP

                                    TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHH.HHHHHHHHHHHH CS
                       Sugar_tr  96 akgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalv.slyqlaitfGil 152
                                     +    + v++v   +vG+  G ++ +    i+  A ++lRg++v +++ la+++G l
  gi|121637185|ref|YP_977408.1| 308 LP---PLPVIMVLCAVVGLVYGPIQPIYNYVIQTRAAQHLRGRVVgVMTSLAYAAGPL 362
                                    87...79**********************************98761667788887755 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   7.2e-05      0.32      20      74 ..     291     346 ..     287     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                           CAAD  20 ilaaivalklalavldaiddiPllpplleLvGlgyt.gwFvyryLlkaekRqelle 74 
                                    + +a+++l la+ v+  +  +P++  l+ +vGl+y  +  +y+y+++  + q l  
  gi|121637185|ref|YP_977408.1| 291 MSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGpIQPIYNYVIQTRAAQHLRG 346
                                    567999*****************************746778999988887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2984.53
//
Query:       gi|121637186|ref|YP_977409.1|  [L=299]
Description: hypothetical protein BCG_1317 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-29  102.1   0.0    3.9e-29  101.6   0.0    1.2  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   2.2e-33   3.9e-29       1     153 [.     120     291 ..     120     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.2e-33
                                    HHC-CTT-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG........CTEEEEESSS....SECG CS
                            UDG   1 pgegppdakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese........qgvyitnvvkcrppgnrd 70 
                                    pg+g + ++++i+G aP a+  ++tg++F+g r+g++l ++l++agl + + s+        +++ it  v+c+ppgn+ 
  gi|121637186|ref|YP_977409.1| 120 PGWGSKRPRLLILGLAPAAHgANRTGRMFTGdRSGDQLYAALHRAGLVNSPVSVdaadglraNRIRITAPVRCAPPGNS- 198
                                    7899****************99***************************99888***********************99. PP

                                    CTTCCCCTCCHHHHHHHHHHHH..SSEEEEESHHHHHH........HH.HHSCESCCCSCT...SEEEEES-SSTTTTTT CS
                            UDG  71 tptsaeikacaplleeeiellk..prlivllGktaakall......ge.klgklrgklleak..irvlplphPsplnrnf 139
                                     pt+ae   c+p+l++e++l++   r+iv+lG  a++  l      g  k ++ +g + e    +r+l ++hPs +n+ +
  gi|121637186|ref|YP_977409.1| 199 -PTPAERLTCSPWLNAEWRLVSdhIRAIVALGGFAWQVALrlagasGTpKPRFGHGVVTELGagVRLLGCYHPSQQNMFT 277
                                    .*****99**************88888***********87778665333445666888777689**************** PP

                                    TTSHHHHHHHHHHH CS
                            UDG 140 fksnpelkaeawed 153
                                    ++ +p+++++++++
  gi|121637186|ref|YP_977409.1| 278 GRLTPTMLDDIFRE 291
                                    ********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1931.74
//
Query:       gi|121637187|ref|YP_977410.1|  [L=274]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-13   48.1   0.0    1.3e-12   47.6   0.0    1.1  1  FAD_binding_3  FAD binding domain
    7.6e-05   22.2   0.2    0.00014   21.4   0.0    1.5  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00012   21.4   0.1    0.00076   18.8   0.1    2.0  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00016   21.8   0.7    0.00042   20.5   0.2    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0045   16.6   1.4      0.021   14.4   0.4    2.1  2  DAO            FAD dependent oxidoreductase
     0.0086   16.6   0.1       0.02   15.4   0.1    1.7  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.029   13.6   0.1      0.041   13.1   0.1    1.2  1  Thi4           Thi4 family
      0.078   12.2   0.0        2.9    7.1   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.25   10.4   0.4       0.36    9.9   0.4    1.2  1  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   6.8e-16   1.3e-12       3     245 ..       3     239 ..       2     263 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.8e-16
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                    +V++ Ga+ aG  +a  L ++G +v++ve++    + ++a  +    +++l+ +Gl + ++++ ++  + +++ +     
  gi|121637187|ref|YP_977410.1|   3 TVVVSGASVAGTAAAYWLGRHGYSVTMVERHPGLRPGGQAIDVRGPALDVLERMGLLAAAQEHKTRIRGASFVDRDG--- 79 
                                    58999***********************************************************7777655554444... PP

                                    CCEEEEEHH.....CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEE CS
                  FAD_binding_3  83 tpkaradle.....lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakY 157
                                     ++   d e        + ++++++  + l  +L+  a++  ++  f+  + +l++d+++v+ ++   ++ e      + 
  gi|121637187|ref|YP_977410.1|  80 -NELFRDTEstptgGPVNSPDIELLRDD-LVELLY-GATQPSVEYLFDDSISTLQDDGDSVRVTFERAAAREF-----DL 151
                                    .444444441111112344444444333.333444.447777**********9****9999888877765555.....9* PP

                                    EEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC...CEEEEECCTTEEEEEECCE..TEEEEEEEEE CS
                  FAD_binding_3 158 lvGaDGgrStvrktlgiefegeetvyeagvldvlfda.dlsdivep...lvlilsaesrgvmviPlen..tlerfyvqve 231
                                    ++GaDG +S vr+ +  +  +e+ v ++g   ++f++ ++    e    +++ + + s++  v + +n  + ++++ +++
  gi|121637187|ref|YP_977410.1| 152 VIGADGLHSNVRRLVFGP--EEQFVKRLGTHAAIFTVpNFL---ELdywQTWHYGD-STMAGVYSARNntEARAALAFMD 225
                                    ************988644..444444567777777665555...332323344333.33345555555233333344444 PP

                                    CCE-GGGSCCCHHH CS
                  FAD_binding_3 232 araekeersekfte 245
                                    ++ +++ r+++ + 
  gi|121637187|ref|YP_977410.1| 226 TELRIDYRDTEAQF 239
                                    44444444444444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.8e-08   0.00014       2     127 ..       4     143 ..       3     155 .. 0.67
   2 ?   -2.3   0.0       1.1   2.1e+03     248     284 ..     190     224 ..     171     258 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.8e-08
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvl..GGlltsglvatdignkaeeqvvtgiareflerlrq.....rgga. 73 
                                    vvV G+ +aG+aAA+   r+G +v +ve+++ l  GG++    +++++  +  +      a+e   r+r      r+g  
  gi|121637187|ref|YP_977410.1|   4 VVVSGASVAGTAAAYWLGRHGYSVTMVERHPGLrpGGQAIDVRGPALDVLERMG--LLAAAQEHKTRIRGasfvdRDGNe 81 
                                    9***************************8886555****999998888866444..444555555555433222222222 PP

                   FAD_oxidored  74 ....rlkkrskwn.........tfepevakavleeml...aeagvtvllntrlvevekegkriesvtves 127
                                                +         + + e ++  l e+l   +++ v+ l++  ++  + +g +   vt+e+
  gi|121637187|ref|YP_977410.1|  82 lfrdT-------EstptggpvnSPDIELLRDDLVELLygaTQPSVEYLFDDSISTLQDDG-DSVRVTFER 143
                                    23211.......011223333377777777777777788878888888888888887776.556666654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                   FAD_oxidored 248 vstdlienldlpeaeyegreqireeareltqgllkyl 284
                                     ++d+++ + + +++++g   +r   +  +++ l ++
  gi|121637187|ref|YP_977410.1| 190 LELDYWQTWHYGDSTMAGVYSAR--NNTEARAALAFM 224
                                    45666666666666666654444..222222222222 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.8e-07   0.00076       2      31 ..       3      33 ..       2      82 .. 0.85
   2 ?    0.3   0.0      0.17   3.3e+02     197     241 ..     118     162 ..     113     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE.T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.l 31
                                    vvv G+ +AG+aaa  l+++g+ vt+ve  
  gi|121637187|ref|YP_977410.1|  3 TVVVSGASVAGTAAAYWLGRHGYSVTMVErH 33
                                   69999***********************642 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                    TEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 197 GvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                                     ve  +  s+ +++++g++++v+ e     + dlv+ a G+  + 
  gi|121637187|ref|YP_977410.1| 118 SVEYLFDDSISTLQDDGDSVRVTFERAAAREFDLVIGADGLHSNV 162
                                    588889999999*****999999999999*******999998775 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   2.1e-07   0.00042       3      39 ..       8      46 ..       6      67 .. 0.88
   2 ?   -2.3   0.0       2.8   5.5e+03      30      47 ..     176     194 ..     175     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                                   --SHHHHHHHHHHHCCTEEEEEE-SSSS..SSGGG-EEC CS
                  NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllekrdr..lGGraasye 39
                                   Ga ++G +aAy L ++g++v+ +e++++  +GG+a +++
  gi|121637187|ref|YP_977410.1|  8 GASVAGTAAAYWLGRHGYSVTMVERHPGlrPGGQAIDVR 46
                                   999***********************9756899987765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                    SSSGGG-EECETT.CEECT CS
                  NAD_binding_8  30 rlGGraasyevpg.vrvdy 47 
                                    rlG +aa ++vp+   +dy
  gi|121637187|ref|YP_977410.1| 176 RLGTHAAIFTVPNfLELDY 194
                                    6777777777777533333 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.4   1.1e-05     0.021       2      31 ..       4      35 ..       3      44 .. 0.89
   2 ?    1.4   0.0     0.096   1.9e+02     156     225 ..     114     181 ..      42     261 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                   vv+ G+ ++G ++Ay+L r+g  Vt +e+++ 
  gi|121637187|ref|YP_977410.1|  4 VVVSGASVAGTAAAYWLGRHGysVTMVERHPG 35
                                   8999*************************965 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.096
                                    HHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEEEEE--GGGHHHH.HTT..CTTTSEEEEEEEEEE CS
                            DAO 156 aealGveilegtevtgleeedgkvwgve..rttpgendaadavVnaaGawsdll.gll..keldlpispvrgqvl 225
                                    a +  ve l+   +  l++ dg+ ++v   r+++   +++d v+ a G++s+ + +l+  +e   +++ + g++ 
  gi|121637187|ref|YP_977410.1| 114 ATQPSVEYLFDDSISTLQD-DGDSVRVTfeRAAA---REFDLVIGADGLHSN-VrRLVfgPEE--QFVKRLGTHA 181
                                    4444455555555555533.33333332322221...235667777777775.2133332222..3333333333 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05      0.02       2      36 ..       4      39 ..       3      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.T CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.r 36
                                   vvv G+++ g  +A  l ++g +Vt+ver++ l+  
  gi|121637187|ref|YP_977410.1|  4 VVVSGASVAGTAAAYWLGRHGYSVTMVERHPGLRpG 39
                                   8******************************99954 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-05     0.041      19      82 ..       3      58 ..       1      75 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT- CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgi 82
                                    vv+ Ga  +G +aay l+++ +  v+++er+     G   GGq   ai vr pa ++L+ +g+
  gi|121637187|ref|YP_977410.1|  3 TVVVSGASVAGTAAAYWLGRH-GYSVTMVERHP----GLRPGGQ---AIDVRGPALDVLERMGL 58
                                   599******************.*********83....5556665...34466666666666665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0015       2.9     165     200 ..       2      37 ..       1      58 [. 0.89
   2 ?    3.1   0.0     0.023        47     222     274 ..     114     165 ..      88     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                    Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                    + vvV G++  +  aA+ l r+g +Vt+v r+  ++
  gi|121637187|ref|YP_977410.1|   2 KTVVVSGASVAGTAAAYWLGRHGYSVTMVERHPGLR 37 
                                    578999*************************98765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.023
                    Pyr_redox_3 222 vkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsfl 274
                                     ++ +++ lf+ ++  ++++  +++v++e++   ++ d v+ a G +++++ l
  gi|121637187|ref|YP_977410.1| 114 ATQPSVEYLFDDSISTLQDDGDSVRVTFERA-AAREFDLVIGADGLHSNVRRL 165
                                    44567999**********************5.668889999999*99998765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00018      0.36       2      30 ..       4      32 ..       3      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLith 30
                                   v+V G+  AG++AA+ + r G++v+++  
  gi|121637187|ref|YP_977410.1|  4 VVVSGASVAGTAAAYWLGRHGYSVTMVER 32
                                   8999**********************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2122.89
//
Query:       gi|121637188|ref|YP_977411.1|  [L=102]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-06   26.2   0.1    6.4e-06   25.6   0.1    1.3  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.037   13.3   0.0      0.041   13.2   0.0    1.1  1  Aldose_epim    Aldose 1-epimerase
       0.22   10.5   0.0       0.25   10.4   0.0    1.1  1  SE             Squalene epoxidase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   1.1e-09   6.4e-06     274     341 ..       2      67 ..       1      73 [. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-09
                                    EEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHHHHHH CS
                  FAD_binding_3 274 aqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtYeeerrav 341
                                    +q +++++++grv l+GDA  + +P  GqG  +a+  a+ La  L a+  G+  +     Y++e + +
  gi|121637188|ref|YP_977411.1|   2 SQILMDRWSRGRVALVGDAGYCCSPLSGQGTSVALLGAYILAGELKAA--GDDYQLGFANYHAEFHGF 67 
                                    677899***********************************9999875..445555566666666555 PP

>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.9e-06     0.041      65     102 ..      44      80 ..      30      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-06
                                    TEEEETTEEEECCCCBTTTCEETBSGGGSB-EEEEEEE CS
                    Aldose_epim  65 GeFeldGkpyqlpqneegknplHGgargreWeveevke 102
                                    Ge +  G +yql   + ++++ HG++   +W v+++ +
  gi|121637188|ref|YP_977411.1|  44 GELKAAGDDYQLGFAN-YHAEFHGFVERNQWLVSDNIP 80 
                                    899999**********.****************99865 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.2e-05      0.25     132     169 ..      14      51 ..       4      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.2e-05
                             SE 132 lillGDalnmRHPltggGmtvalnDivllskllkpled 169
                                    + l+GDa     Pl g G  val  +++l+  lk   d
  gi|121637188|ref|YP_977411.1|  14 VALVGDAGYCCSPLSGQGTSVALLGAYILAGELKAAGD 51 
                                    679***************************99998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 705.93
//
Query:       gi|121637189|ref|YP_977412.1|  [L=149]
Description: hypothetical protein BCG_1320c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-56  188.2   0.1    6.6e-56  188.0   0.1    1.0  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   0.1   3.7e-60   6.6e-56       2     129 ..      16     147 ..      15     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 3.7e-60
                                    XXXXXXXXXXXXXXXTTXTTS--.-EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEE CS
                F420H2_quin_red   2 lReqvaiyrrtegkvgrrlegvp.vllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevq 80 
                                    lR+++aiyr t+g++g+r++g+p +llL+ttG+kt++pr+t+l+++rdgd+yl+vaskgG+p++p+wy+NlkanP+ve++
  gi|121637189|ref|YP_977412.1|  16 LRLHDAIYRGTNGRIGHRIPGAPpSLLLHTTGAKTSQPRTTSLTYARDGDAYLIVASKGGDPRSPGWYHNLKANPDVEIN 95 
                                    699******************998******************************************************** PP

                                    ETTEEEEEEEEE--..HHHHHHHHHHHHHH-TH.HHHHHHHHSSTS-EEEEE CS
                F420H2_quin_red  81 vgakkldvtAreve..ddekarlwklvvensps.YadyqsktdreipvvVle 129
                                    vg+k++ vtA++v+  d+++arlw++v+en+++ Y++yqs+t+r+ipvvVl+
  gi|121637189|ref|YP_977412.1|  96 VGPKRFGVTAKPVQphDPDYARLWQIVNENNANrYTNYQSRTSRPIPVVVLT 147
                                    ***************9**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1077.07
//
Query:       gi|121637190|ref|YP_977413.1|  [L=144]
Description: HIT family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   95.9   0.0    2.3e-27   95.6   0.0    1.1  1  HIT       HIT domain
    5.2e-11   43.0   0.0    6.6e-11   42.7   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
       0.21   11.5   0.0        0.3   11.0   0.0    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   3.8e-31   2.3e-27       2      97 ..      11     106 ..      10     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 3.8e-31
                                    GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGG CS
                            HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngaha 81 
                                    +e+p+  +yed  +la+ldi+p ++gh+Lv+pk+h+ +l+d+++e+la+++++ +++a+a +++  +++++++in+g++a
  gi|121637190|ref|YP_977413.1|  11 GEAPAIRIYEDGGYLAILDIRPFTRGHTLVLPKRHTVDLTDTPPEALADMVAIGQRIARAARATKLADATHIAINDGRAA 90 
                                    6899**************************************************************************** PP

                                    T-SSSS-EEEEEEC-T CS
                            HIT  82 gqsvahlHiHviprre 97 
                                     q+v+h+H+Hv+prr+
  gi|121637190|ref|YP_977413.1|  91 FQTVFHVHLHVLPRRN 106
                                    **************97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.1e-14   6.6e-11       2     101 ..       3     103 ..       2     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.1e-14
                                    -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEE CS
                         DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdae 80 
                                    +vf+ ++ g+ p+  +yed +++++ Di+p ++ h lv+pkr+  +l+d  +e l  + ++ + +  +++  + +     
  gi|121637190|ref|YP_977413.1|   3 CVFCAIIAGEAPAIRIYEDGGYLAILDIRPFTRGHTLVLPKRHTVDLTDTPPEALADMVAIGQRIARAARATKLAdATHI 82 
                                    9*****************************************99888888777666666666666665555443245555 PP

                                    EE--SCCCT--S-S--EEEEE CS
                         DcpS_C  81 elrvgvhyqPsvyhlHlHvis 101
                                     ++ g  + ++v+h+HlHv+ 
  gi|121637190|ref|YP_977413.1|  83 AINDGRAAFQTVFHVHLHVLP 103
                                    5667999999*********86 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     5e-05       0.3      35      84 ..      23      73 ..       2     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                                   EEEE---.S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHHH CS
                       CwfJ_C_1 35 vYlalpk.gpLssgHvliipieHisallsldeevldeirkfrkalvkmykk 84
                                    Yla+    p + gH l++p  H+  l+ ++ e+l ++ +  + +++   +
  gi|121637190|ref|YP_977413.1| 23 GYLAILDiRPFTRGHTLVLPKRHTVDLTDTPPEALADMVAIGQRIARAARA 73
                                   599999999*********************999999998777766666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1074.22
//
Query:       gi|121637191|ref|YP_977414.1|  [L=462]
Description: amidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-98  330.5   0.0    3.2e-98  329.6   0.0    1.4  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.6   0.0  1.8e-102   3.2e-98       2     451 .]      28     442 ..      27     442 .. 0.91

  Alignments for each domain:
  == domain 1  score: 329.6 bits;  conditional E-value: 1.8e-102
                                    HHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS- CS
                        Amidase   2 lveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekD 81 
                                    l+e +l+rie++++ l a+  v ++ a+a+A++++++     e+ pL GvPi++KD +d++g  tt+Gs       a+ D
  gi|121637191|ref|YP_977414.1|  28 LLEVYLQRIERLDSHLRAYRVVQFDRARAEAEAAQQRLD-AGERLPLLGVPIAIKDDVDIAGEVTTYGSAGHGP-AATSD 105
                                    6899*******************************9986.9****************************88766.9999* PP

                                    -HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHH CS
                        Amidase  82 atvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAs 161
                                    a+vv+rL++aGavi+gkTn++e++    te+ +fg+trNPw ++rtpGGSSGGsAAavAagl+p+a+G+D+GGSiRiP+ 
  gi|121637191|ref|YP_977414.1| 106 AEVVRRLRAAGAVIIGKTNVPELMIMPFTESLAFGATRNPWCLNRTPGGSSGGSAAAVAAGLAPVALGSDGGGSIRIPCT 185
                                    ******************************************************************************** PP

                                    HCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEE CS
                        Amidase 162 fcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriG 241
                                    +cgl+GlKP++ r+S ++  +  ++l+v+Gp+arsv d+alll+++         + +   +++++ ++++ ++  lri+
  gi|121637191|ref|YP_977414.1| 186 WCGLFGLKPQRDRISLEPHDGAWQGLSVNGPIARSVMDAALLLDATT--------TVP--GPEGEFVAAAARQPGRLRIA 255
                                    ********************************************987........333..357899999*********** PP

                                    EEGGGC...SS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCC CS
                        Amidase 242 vvkedg...vasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkvls 318
                                    + +  +    ++  ++  +av +a + L+++Gh vv  ++ ++++ ++ y+   +   s                     
  gi|121637191|ref|YP_977414.1| 256 LSTRVPtplPVRCGKQELAAVHQAGALLRDLGHDVVVRDPDYPASTYANYLPRFFRGIS--------------------- 314
                                    ***999888788999999*******************9999999988888777775554..................... PP

                                    CCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCS CS
                        Amidase 319 ellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktids 398
                                    +   +    + +e  +r i + +  +s++     +   ++++ +l  +++ +f ++Dv+++P a+t + r+g+ ++ +  
  gi|121637191|ref|YP_977414.1| 315 DDADAQAHPDRLEARTRAIARLGSFFSDRR----MAALRAAEVVLSSRIQSIFDDVDVVVTPGAATGPSRIGAYQRRGAV 390
                                    556667777777777777777777787774....77777778899*****************************988744 PP

                                    HHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                        Amidase 399 ytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                     t l  +  ++    ++nl+g+pa  vp+ ++ dglP +vq++g++++e+tlL
  gi|121637191|ref|YP_977414.1| 391 STLLLVVQRVP-YFQVWNLTGQPAAVVPWDFDGDGLPMSVQLVGRPYDEATLL 442
                                    44444444444.7899***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3374.86
//
Query:       gi|121637192|ref|YP_977415.1|  [L=397]
Description: adenylyl cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-82  275.4   6.1    2.9e-82  275.0   6.1    1.2  1  Ad_Cy_reg      Adenylate cyclase regulatory domain
    2.4e-14   53.4   0.0    5.8e-14   52.1   0.0    1.6  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
      0.032   14.5   0.3        0.2   12.0   0.1    2.5  2  FeoA           FeoA domain


Domain annotation for each model (and alignments):
>> Ad_Cy_reg  Adenylate cyclase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.0   6.1   4.8e-86   2.9e-82       2     186 .]      10     194 ..       9     194 .. 0.99

  Alignments for each domain:
  == domain 1  score: 275.0 bits;  conditional E-value: 4.8e-86
                      Ad_Cy_reg   2 dveasgLLdgLegkaRaeRaeliewLlerGvsieeiraaaepmLLaaervlgddgtyvsareisektGidlellqrlqrA 81 
                                    d ++++LL +L g+aRaeRa+l+ewLle+G++ +eira++ p+LLa+++++gddgtyvsareise++G+dlellqr+qrA
  gi|121637192|ref|YP_977415.1|  10 DANIDDLLGDLGGTARAERAKLVEWLLEQGITPDEIRATNPPLLLATRHLVGDDGTYVSAREISENYGVDLELLQRVQRA 89 
                                    7899**************************************************************************** PP

                      Ad_Cy_reg  82 vGLprvddpDaavllraDaeaaarakrfldlGldedqivavarvLaegLsraaevlReaalkallepgaselelakaaea 161
                                    vGL+rvddpDa v++raD eaaara+rf++lGl++dq+v v+rvLaegLs+aae++R++al+a+++pga+el++ak ++a
  gi|121637192|ref|YP_977415.1|  90 VGLARVDDPDAVVHMRADGEAAARAQRFVELGLNPDQVVLVVRVLAEGLSHAAEAMRYTALEAIMRPGATELDIAKGSQA 169
                                    ******************************************************************************** PP

                      Ad_Cy_reg 162 lvaeiapllgpmiqellalqlRhql 186
                                    lv++i pllgpmiq++l++qlRh++
  gi|121637192|ref|YP_977415.1| 170 LVSQIVPLLGPMIQDMLFMQLRHMM 194
                                    ***********************98 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   9.7e-18   5.8e-14       6     177 ..     213     370 ..     209     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.7e-18
                  Guanylate_cyc   6 ydevtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdm 85 
                                     ++vt+ Fad+vgft+l +  s++e+ +l     a + + l++  v  +ktiGda m v+  p       a l++  L++
  gi|121637192|ref|YP_977415.1| 213 ARQVTVAFADLVGFTQLGEVVSAEELGHLAGR-LAGLARDLTAPPVWFIKTIGDAVMLVCPDP-------APLLDTVLKL 284
                                    579******************99998765555.555566667788999*************99.......6788888999 PP

                  Guanylate_cyc  86 leal.eevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellk....eeqf 160
                                    +e + + ++       ++r G+ +G  v++         d +G  vn+Asr+  ++ +g + v ++++e l      ++f
  gi|121637192|ref|YP_977415.1| 285 VEVVdTDNNFP-----RLRAGVASGMAVSRAG-------DWFGSPVNVASRVTGVARPGAVLVADSVREALGdapeADGF 352
                                    99884444444.....7***********9998.......********************************9999999** PP

                  Guanylate_cyc 161 eltergevevkG.kgkle 177
                                    +++  g+  ++G +g++ 
  gi|121637192|ref|YP_977415.1| 353 QWSFAGPRRLRGiRGDVR 370
                                    **********99777766 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.65   3.9e+03      22      37 ..      29      44 ..      13      45 .. 0.80
   2 ?   12.0   0.1   3.3e-05       0.2      18      43 ..     105     132 ..      80     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.65
                                   SSHHHHHHHHT--TT- CS
                           FeoA 22 pellrrLremGlvpGa 37
                                   ++l   L+e G++p++
  gi|121637192|ref|YP_977415.1| 29 AKLVEWLLEQGITPDE 44
                                   566677999***9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.3e-05
                                    -T..T.SSHHHHHHHHT--TT-EEEEEE CS
                           FeoA  18 sd..edpellrrLremGlvpGarievva 43 
                                    ++  e ++ ++r+ e+Gl+p++++ vv+
  gi|121637192|ref|YP_977415.1| 105 RAdgEAAARAQRFVELGLNPDQVVLVVR 132
                                    3344667778***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2878.19
//
Query:       gi|121637193|ref|YP_977416.1|  [L=226]
Description: hypothetical protein BCG_1324 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1550.59
//
Query:       gi|121637194|ref|YP_977417.1|  [L=596]
Description: transmembrane serine/threonine-protein kinase H pknH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-54  185.2   5.5    2.3e-54  184.2   5.5    1.6  1  PknH_C          PknH-like extracellular domain
    8.3e-45  153.2   0.0    1.1e-44  152.8   0.0    1.1  1  Pkinase         Protein kinase domain
    9.4e-31  107.0   0.0    1.3e-30  106.6   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    1.4e-05   25.2   0.3    0.00011   22.3   0.2    2.2  2  APH             Phosphotransferase enzyme family
    7.3e-05   21.7   0.0    0.00011   21.1   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
    0.00014   21.2   0.0     0.0003   20.2   0.0    1.5  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.38   10.3   0.0    1.7  2  FTA2            Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   5.5   8.9e-58   2.3e-54       1     189 []     407     592 ..     407     592 .. 0.99

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 8.9e-58
                                    --GGGGGGGS--HHHHHHHHT-S.--EE-S-B-S-B-S--EESSGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT-S CS
                         PknH_C   1 vpaaaldslLltpaelaailGtpeaasatesdttppdtaasvdppeClgvasageesvYggsgvtavagqtlrdsaddga 80 
                                    v++++l++lLl ++e++a++G+  +++  ++ t++ ++ ++v+ p+C+g++++++++vY+g+g+ta++g   ++++d+ +
  gi|121637194|ref|YP_977417.1| 407 VAEERLSALLLNSSEVNAVMGSS-SMQPGKPITSMDSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYE 485
                                    6799*******************.******************************************************** PP

                                    EEEEEEEEE-SSHHHHHHHHHHHHHHHHTTTT-EEEEEETTEEEEEEE---B--TT-EEEEEE.ESSTT--EEEEEEEEE CS
                         PknH_C  81 slvsqavvafptadaAqaffaalaaqwrrCagvttttdsggatetwtvgdvsdddgvltatvtvtsggdgarcqralavr 160
                                    ++v+qavvafptad+A+af++++a++w++Cag+t+t +++ +t++wt+ dv+ +  ++t++ t ++g++g++cqra++v+
  gi|121637194|ref|YP_977417.1| 486 HWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVTNKAKTYRWTFADVKGSPPTITVIDT-QEGAEGWECQRAMSVA 564
                                    ***************************************************************.**************** PP

                                    TTEEEEEEEEE.SS-SSHHHHHHHHHHHH CS
                         PknH_C 161 anvvvdvevcgfedggdaaaeiadaildk 189
                                    +nvvvdv++cg ++++++a +ia +i+dk
  gi|121637194|ref|YP_977417.1| 565 NNVVVDVNACG-YQITNQAGQIAAKIVDK 592
                                    ***********.***************98 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   0.0   4.3e-48   1.1e-44       1     252 [.      16     261 ..      16     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 4.3e-48
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    y+ ++ lG+G++G+Vy+a ++ ++ +vAvK +  e  k+    +++ rE +i  +l+ p++v + ++ e + +++l + +
  gi|121637194|ref|YP_977417.1|  16 YHLKRLLGRGGMGEVYEAEHTVKEWTVAVKLMTAEFSKDPVFrERMKREARIAGRLQEPHVVPIHDYGEVDGQMFLEMRL 95 
                                    78999***************************99977765445************************************* PP

                                    -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS..BCTT CS
                        Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk..ltsf 157
                                    veg++l+++l+r g l++ +a  i++qi+++l+  H+ g++HrD+Kp+NiLi +++   ++DFG+a+  + ++   l + 
  gi|121637194|ref|YP_977417.1|  96 VEGTDLDSVLKRFGPLTPPRAVAIITQIASALDAAHADGVMHRDVKPQNILITRDDFAYLVDFGIASATTDEKLtqLGTA 175
                                    *****************************************************999************9998877799** PP

                                    TSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHH CS
                        Pkinase 158 vgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseea 237
                                    vgt +Y+APE  ++ e++  +D+++l+++l e ltg pp+++++  + v+++l+          +  + ++ +  i++ +
  gi|121637194|ref|YP_977417.1| 176 VGTWKYMAPERFSNDEVTYRADIYALACVLHECLTGAPPYRADSAGTLVSSHLMG---------PIPQPSAIRPGIPKAF 246
                                    *****************************************66666555544444.........3334444444455555 PP

                                    HHHHHHHT-SSGCCS CS
                        Pkinase 238 kdllkkllkkdpkkR 252
                                      ++ + ++k+p++R
  gi|121637194|ref|YP_977417.1| 247 DAVVARGMAKKPEDR 261
                                    555555555555555 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0     5e-34   1.3e-30       2     249 ..      17     261 ..      16     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 5e-34
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeeplliv 79 
                                    +l++ lG+G  G+V+e++ +     ke +VavK +++e +++   +e++ +ea+i  +l+ p++v ++     ++++++ 
  gi|121637194|ref|YP_977417.1|  17 HLKRLLGRGGMGEVYEAEHT----VKEWTVAVKLMTAEFSKDPvfRERMKREARIAGRLQEPHVVPIHDYGEVDGQMFLE 92 
                                    57899************999....999********99888877679999******************************* PP

                                    EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEE CS
                    Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddey 159
                                    + +v+g dL++ L++    +lt  + + +++q+A++++  ++  ++Hrd+  +N+L+++++++ + DfG+a+++ +d++ 
  gi|121637194|ref|YP_977417.1|  93 MRLVEGTDLDSVLKRF--GPLTPPRAVAIITQIASALDAAHADGVMHRDVKPQNILITRDDFAYLVDFGIASAT-TDEKL 169
                                    ***************8..9*****************************************************99.89999 PP

                                    EETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTT...EES-BBTTSBHHHHH CS
                    Pkinase_Tyr 160 vkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkeg...krlekpekcpeelye 236
                                    ++ ++a    k+mapE +++ ++t ++D+++ + +l+E +t g+ py+  ++ ++++    g   +  +    +p+++  
  gi|121637194|ref|YP_977417.1| 170 TQLGTAVGTWKYMAPERFSNDEVTYRADIYALACVLHECLT-GAPPYRADSAGTLVSSHLMGpipQPSAIRPGIPKAFDA 248
                                    99***************************************.*****877555544433222011222233345555556 PP

                                    HHHHHT-SSGGGS CS
                    Pkinase_Tyr 237 lmkkcweedpeeR 249
                                    ++ + ++++pe+R
  gi|121637194|ref|YP_977417.1| 249 VVARGMAKKPEDR 261
                                    6666666666665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0051        13      22     106 ..      41     131 ..      22     133 .. 0.69
   2 !   22.3   0.2   4.1e-08   0.00011     135     198 ..     102     163 ..      66     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0051
                                    -EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHH CS
                            APH  22 ryvlrrnppa..raaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpell 95 
                                    ++++++  ++  + + + +r+ ++ r   ++   +v  ++++++ d++  l+++l+e+ +  s+l    +l+++ + +++
  gi|121637194|ref|YP_977417.1|  41 TVAVKLMTAEfsKDPVFRERMKREARIAGRLQEpHVVPIHDYGEVDGQMFLEMRLVEGTDLDSVLKrfgPLTPPRAVAII 120
                                    5555665555545555556666666666655554565667777777777777888877777777779**99********* PP

                                    HHHHHHHCCHH CS
                            APH  96 ealgeflaalh 106
                                     +++++l a h
  gi|121637194|ref|YP_977417.1| 121 TQIASALDAAH 131
                                    ****9998887 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 4.1e-08
                                    CCCGCCTCC.HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 135 rllaselld.lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    +++  ++++    ++ + ++ ++a  l+++ + +++H+D +p+N+l++   + + +++Df+ a++
  gi|121637194|ref|YP_977417.1| 102 DSVLKRFGPlTPPRAVA-IITQIASALDAAHADGVMHRDVKPQNILIT--RDDFAYLVDFGIASA 163
                                    55666666655667777.8899999999999*****************..444458*****9875 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.4e-08   0.00011     325     397 ..     132     198 ..     115     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.4e-08
                 Pkinase_fungal 325 kagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgeeHsyrhDL 397
                                      g++HrD+  +Nilit     +++   L+D+ +a+ + d ++  + ++ +GT ++ma e  ++ e +yr D+
  gi|121637194|ref|YP_977417.1| 132 ADGVMHRDVKPQNILIT-----RDDFAYLVDFGIASATTD-EKLTQLGTAVGTWKYMAPERFSNDEVTYRADI 198
                                    5699*************.....999*************97.6666789*************999999999997 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-07    0.0003      98     167 ..      94     159 ..      23     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                            Kdo  98 rlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    rl +  dL+ +l+++  l   +  a++ +++ +    h+ gv+H+d+ ++nil+  ++     ++l+D+ 
  gi|121637194|ref|YP_977417.1|  94 RLVEGTDLDSVLKRFGPLTPPRAVAIITQIASALDAAHADGVMHRDVKPQNILITRDD----FAYLVDFG 159
                                    444456999999998889999999*******************************998....88999995 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.87   2.2e+03      31      57 ..      23      51 ..      17      92 .. 0.55
   2 ?   10.3   0.0   0.00015      0.38     172     205 ..     114     147 ..     104     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.87
                           FTA2 31 gkglhsiVlkvkirgkeY..ALKlFrfle 57
                                   g+g  + V++++   ke+  A+Kl +   
  gi|121637194|ref|YP_977417.1| 23 GRGGMGEVYEAEHTVKEWtvAVKLMTAEF 51
                                   56666666666655554322444433222 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                           FTA2 172 elevsqlpkllrdlkklhklgIvvrDlkeenyid 205
                                    ++ v+++ ++ + l+ +h+ g+++rD+k++n++ 
  gi|121637194|ref|YP_977417.1| 114 PRAVAIITQIASALDAAHADGVMHRDVKPQNILI 147
                                    678999*************************873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3766.96
//
Query:       gi|121637195|ref|YP_977418.1|  [L=388]
Description: transcriptional regulatory protein embR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-48  163.1   2.9    9.7e-48  162.3   2.9    1.4  1  BTAD          Bacterial transcriptional activator domain
    6.8e-16   58.4   4.1    1.2e-15   57.6   4.1    1.4  1  FHA           FHA domain
    1.6e-12   47.6   0.1    3.1e-12   46.6   0.1    1.4  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
    1.4e-11   44.3   0.0    3.1e-11   43.2   0.0    1.6  2  Trans_reg_C   Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
          1   10.4   8.6        9.3    7.4   0.4    3.7  4  TPR_14        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3   2.9   2.7e-51   9.7e-48       1     146 []     110     255 ..     110     255 .. 1.00

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 2.7e-51
                                    BHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                           BTAD   1 vDlarfealvaagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraee 80 
                                    +Dl rf a+++ag +a+aag++e+a ++l+aAl++wrGp+l+dl++++++e+++++l e+++ a++a aeae+++Gra++
  gi|121637195|ref|YP_977418.1| 110 CDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASA 189
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHHHHHH CS
                           BTAD  81 alaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpelralheeil 146
                                    ++aeleal+ ehP+rE l+ ql++A++ s+rq++AL++Y+r++ +La++Lg++pgp+lral+e+il
  gi|121637195|ref|YP_977418.1| 190 VIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNERIL 255
                                    ****************************************************************98 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   4.1   3.4e-19   1.2e-15       2      68 ..     309     371 ..     308     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3.4e-19
                                    EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEE CS
                            FHA   2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdviel 68 
                                    +iGR +d+divld++ +Sr+Ha+i+ +++  ++ + Dl+S+nG+ v ++ri++   v L++gd i++
  gi|121637195|ref|YP_977418.1| 309 RIGRLHDNDIVLDSANVSRHHAVIVDTGT--NYVINDLRSSNGVHVQHERIRS--AVTLNDGDHIRI 371
                                    7*************************999..*********************9..**********97 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   8.8e-16   3.1e-12       8      89 ..     297     379 ..     292     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 8.8e-16
                                    TT-EEEETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-S.ECC--TTSEEEETTEEE CS
                   Yop-YscD_cpl   8 kGaeveLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerve.elelrpgdvlelGttel 86 
                                    +G+ ++L+  + +iG+ +d+DivL+  +vsr+h+++  + ++++++dl+s ng+ v +er+    +l++gd++ +   e+
  gi|121637195|ref|YP_977418.1| 297 SGRGYPLQAAATRIGRLHDNDIVLDSANVSRHHAVIVDTGTNYVINDLRSSNGVHVQHERIRsAVTLNDGDHIRICDHEF 376
                                    7999*********************************************************94555*******9998888 PP

                                    EEE CS
                   Yop-YscD_cpl  87 alv 89 
                                    +++
  gi|121637195|ref|YP_977418.1| 377 TFQ 379
                                    875 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   8.6e-15   3.1e-11       6      77 .]      31     103 ..      25     103 .. 0.96
   2 ?   -3.7   0.1       3.7   1.3e+04      42      58 ..     346     362 ..     342     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.6e-15
                                    -SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTS.TSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   6 ltpkefklLelLlenpgrvvsreeLleevwgede.dvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                     tpk++++L++L+ n++r+v  + L+ ++w+e +  ++  ++++++s+LRk L+ ++ +pr++      GYrl
  gi|121637195|ref|YP_977418.1|  31 GTPKQRAVLAMLVINRNRPVGVDALITALWEEWPpSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRL 103
                                    59******************************999999*********************************97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.7
                                    HTHHHHHHHHHHHHHHH CS
                    Trans_reg_C  42 ddrtvdvhisrLRkkLe 58 
                                    +++ v+v+  r+R  + 
  gi|121637195|ref|YP_977418.1| 346 SSNGVHVQHERIRSAVT 362
                                    67777787788887665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0026       9.3      11      31 ..     125     145 ..     117     154 .. 0.81
   2 ?    5.9   0.2    0.0078        28       4      42 ..     174     212 ..     171     214 .. 0.90
   3 ?    3.3   0.1     0.053   1.9e+02       3      27 ..     207     231 ..     205     241 .. 0.85
   4 ?   -3.5   0.0         5   1.8e+04      19      29 ..     287     297 ..     285     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                         TPR_14  11 llalGdpdeAiallrralala 31 
                                     +a+G++++A ++l +al+ +
  gi|121637195|ref|YP_977418.1| 125 AAAAGRFEQASRHLSAALREW 145
                                    4789**************964 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0078
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    + a aea+ a G+  + ia l+++   +P  + +w++l 
  gi|121637195|ref|YP_977418.1| 174 HTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLI 212
                                    567899*****************************9986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.053
                         TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                    ++ +l  a++ +++  +A+ ++rr+
  gi|121637195|ref|YP_977418.1| 207 LWTQLITAYYLSDRQSDALGAYRRV 231
                                    68999******************98 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 5
                         TPR_14  19 eAiallrrala 29 
                                    +A+a+l+++ +
  gi|121637195|ref|YP_977418.1| 287 QAVAYLHDIAS 297
                                    67888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2647.06
//
Query:       gi|121637196|ref|YP_977419.1|  [L=232]
Description: hypothetical protein BCG_1327c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-08   35.8   0.3    1.5e-08   35.3   0.3    1.2  1  Peptidase_C39_2  Peptidase_C39 like family
  ------ inclusion threshold ------
      0.093   13.0   0.4       0.43   10.8   0.3    1.9  1  BtrH_N           Butirosin biosynthesis protein H, N-terminal
       0.64    9.4   4.0          7    6.0   0.2    2.1  2  EII-Sor          PTS system sorbose-specific iic component


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.3   2.5e-12   1.5e-08       5     143 ..      47     202 ..      43     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.5e-12
                Peptidase_C39_2   5 lynQldelpngCeptslamvlsyl.gkkvtqnelakelktns....sgdpntgfvgnit.dksglgvynepivklaekyg 78 
                                    + +Q  ++ + C   s+a v+    g++++   + k +++++    +g+  t  + +    +sg+g++ + i +l ++yg
  gi|121637196|ref|YP_977419.1|  47 YWRQ--QTYDDCVLMSAADVIGQVtGREPSERAIIKVAQSTPsvvhPGSIYTKPA-DAEhPNSGMGTSVADIPTLLAHYG 123
                                    5566..6777899999999996666*****************9887666666554.444589****************** PP

                Peptidase_C39_2  79 l..kvsdtrgssi..........eevkkeidagkPvvvsvttfkpl.......ndgeikftssgHlvvitGYdekgkrvy 139
                                           +++++           + +++++ +g++v+vs+++  ++       ++++++   s H+vv+tG d ++  v 
  gi|121637196|ref|YP_977419.1| 124 VdaV---ITDEDHatatgvatgmAALEQYLGSGHAVIVSINA--EMiwgqpveETDSAGNPRSDHAVVVTGVDTENGIVH 198
                                    9441...3333334556677788*****************84..44467999988889****************9999** PP

                Peptidase_C39_2 140 vnDP 143
                                    +nD+
  gi|121637196|ref|YP_977419.1| 199 LNDS 202
                                    **97 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   7.2e-05      0.43      70     133 ..     134     201 ..     124     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                         BtrH_N  70 ketkdpeeawkalkeeLdaGrpvivqvdvyyL..pYlpke.srlh.fnaHnvvvyGyddeegealvsD 133
                                     + +  +++++al++ L +G+ viv ++   +  + +++  s     ++H vvv+G d e+g +++ D
  gi|121637196|ref|YP_977419.1| 134 ATATGVATGMAALEQYLGSGHAVIVSINAEMIwgQPVEETdSAGNpRSDHAVVVTGVDTENGIVHLND 201
                                    5666677788888888888888888655444311323222022224578***************9988 PP

>> EII-Sor  PTS system sorbose-specific iic component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5    0.0027        16      56      83 ..      18      45 ..      10      66 .. 0.87
   2 ?    6.0   0.2    0.0012         7      71     122 ..     117     167 ..     105     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0027
                        EII-Sor 56 ylGvvtiGgavppdaalagiigtalail 83
                                   + G v++G a+p+daa++++ g + a +
  gi|121637196|ref|YP_977419.1| 18 AAGAVALGLASPADAAAGTMYGDPAAAA 45
                                   6799****************99887765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0012
                        EII-Sor  71 alagiigtalailsgasaeaavalavpvallgqllttlvrtinsvfvhkadk 122
                                    +l +  g+  +i+ +++ ++a+++a+ +a+l q+l    ++i s+ +++++ 
  gi|121637196|ref|YP_977419.1| 117 TLLAHYGVDAVIT-DEDHATATGVATGMAALEQYLGSGHAVIVSINAEMIWG 167
                                    5555556555555.88889*********************999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1594.53
//
Query:       gi|121637197|ref|YP_977420.1|  [L=124]
Description: hypothetical protein BCG_1328c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.5   5.0    1.1e-18   67.5   5.0    1.4  2  DUF4189   Domain of unknown function (DUF4189)


Domain annotation for each model (and alignments):
>> DUF4189  Domain of unknown function (DUF4189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.45   8.1e+03      59      59 ..      20      20 ..       5      36 .. 0.50
   2 !   67.5   5.0   6.2e-23   1.1e-18       1      84 [.      39     115 ..      39     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.45
                        DUF4189 59 k 59
                                   +
  gi|121637197|ref|YP_977420.1| 20 T 20
                                   1 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 6.2e-23
                        DUF4189   1 ygaiavspstgkvgasvnyssreeAeaaAlkeCakkggsdCkvvvsfknacgAvaeskkkaaagvgsgasleeaeeaAlk 80 
                                    ygaia+s +++ +g s++y++r++Aea+A+k+C   g sdCkv++sf +acgAva++++  a++ g g++l++a ++Al 
  gi|121637197|ref|YP_977420.1|  39 YGAIAYSGNGS-WGRSWDYPTRAAAEATAVKSC---GYSDCKVLTSF-TACGAVAANDR--AYQGGVGPTLAAAMKDALT 111
                                    9******9996.*********************...***********.**********9..8****************** PP

                        DUF4189  81 kCkk 84 
                                    k++ 
  gi|121637197|ref|YP_977420.1| 112 KLGG 115
                                    9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 929.41
//
Query:       gi|121637198|ref|YP_977421.1|  [L=244]
Description: lipoprotein lprA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-67  225.5   6.2    5.9e-67  225.2   6.2    1.1  1  LppX_LprAFG  LppX_LprAFG lipoprotein
  ------ inclusion threshold ------
      0.062   12.6   0.2        1.1    8.6   0.0    2.1  2  DUF2092      Predicted periplasmic protein (DUF2092)


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.2   6.2   6.6e-71   5.9e-67       1     191 [.      45     239 ..      45     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 6.6e-71
                                    .HHHHHHHHHHHHHT-SEEEEEEEEEC--TTSTEEEEEEEEETTTT.EEEEEEEEEETTCEEEEEEEEETTEEEEEECT. CS
                    LppX_LprAFG   1 daakllaesakatkslksvhlaltvngkvdglpvesvegdltnqpagaakgnakvtlagqavdvkfvvvdgklyaklpp. 79 
                                    daa+ll+++++a+++++++h++l+v+g+v++l+v+++egd++n+p+++a+g+a++ +++++ d+kfv+vdg+ly +l++ 
  gi|121637198|ref|YP_977421.1|  45 DAAMLLKQATDAMRKVTGMHVRLAVTGDVPNLRVTKLEGDISNTPQTVATGSATLLVGNKSEDAKFVYVDGHLYSDLGQp 124
                                    89*****************************************************************************9 PP

                                    TEEEEEEEHGHCHHHHCGG-TTTSHHHHCCTEEEEEEEEEEEETTEEEEEEEEEE-HHHHHHH-CC..G-SS.S.EEEEE CS
                    LppX_LprAFG  80 etwsdlgpaekiydpavlLdpdkGlanvLagvtdakaegreeidGtatvkitGtvdadvvsaivps..lked.gtvpitl 156
                                    +t++d+g++++iy+++vlLdp+kGlan+La+++da+++g+++ dG+at+kitG+ +ad ++++++s  ++ed +tvp+t+
  gi|121637198|ref|YP_977421.1| 125 GTYTDFGNGASIYNVSVLLDPNKGLANLLANLKDASVAGSQQADGVATTKITGNSSADDIATLAGSrlTSEDvKTVPTTV 204
                                    *****************************************************************99888889******* PP

                                    EEESSTT--EEEEEEEECTCEEEEEEEESTT---T CS
                    LppX_LprAFG 157 Wiaedgelrlvrvvvdkesgesveltlskwgkpvt 191
                                    Wia+dg+++lv++++++++++sv+lt+s+wgk+vt
  gi|121637198|ref|YP_977421.1| 205 WIASDGSSHLVQIQIAPTKDTSVTLTMSDWGKQVT 239
                                    **********************************8 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.011        97       2      36 ..      47      81 ..      46     121 .. 0.86
   2 ?    8.6   0.0   0.00012       1.1     119     187 ..     151     234 ..     141     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.011
                        DUF2092  2 eeiLkamsdylkalksfsvtadttydsvlasgqkl 36
                                     +Lk+++d ++++  + v++ +t d++     kl
  gi|121637198|ref|YP_977421.1| 47 AMLLKQATDAMRKVTGMHVRLAVTGDVPNLRVTKL 81
                                   678***********************987766665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00012
                        DUF2092 119 dlteevksakyvgtskvngqecehl..................afrnkdvdwqlWIsqgdkpLprkivityktdpgapqy 180
                                    +l +++k+a++ g+++ +g++++++                    + k+v+  +WI++++   + +i i+ ++d+     
  gi|121637198|ref|YP_977421.1| 151 NLLANLKDASVAGSQQADGVATTKItgnssaddiatlagsrltSEDVKTVPTTVWIASDGSSHLVQIQIAPTKDT---SV 227
                                    6778999999999999999999999999999999***999866556677899*******9999999999988877...56 PP

                        DUF2092 181 taefsdW 187
                                    t+++sdW
  gi|121637198|ref|YP_977421.1| 228 TLTMSDW 234
                                    6777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1807.86
//
Query:       gi|121637199|ref|YP_977422.1|  [L=113]
Description: hypothetical protein BCG_1330c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-23   81.8   6.2    4.3e-23   81.5   6.2    1.1  1  DUF732    Protein of unknown function (DUF732)
  ------ inclusion threshold ------
      0.028   14.8   0.8      0.045   14.2   0.8    1.3  1  DUF5455   Family of unknown function (DUF5455)
      0.069   13.0   0.5       0.16   11.9   0.0    1.9  2  DUF4907   Domain of unknown function (DUF4907)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   6.2   7.3e-27   4.3e-23       3      94 ..      19     109 ..      17     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 7.3e-27
                         DUF732   3 aallaaalllaapAaAdsaddaFlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaaqfv 82 
                                    aa++++a+++a++A A+++d+aF+a++++ g++++sp+ a + ++ vCkkl+sG++ +++++ev + +++l+++qaa+fv
  gi|121637199|ref|YP_977422.1|  19 AAAIGLAVATAGTAGANTKDEAFIAQMESIGVTFSSPQVATQQAQLVCKKLASGETGTEIAEEVLS-QTNLTTKQAAYFV 97 
                                    8999*************************************************************9.************* PP

                         DUF732  83 gaAvsayCPeql 94 
                                    ++A++ayCP+++
  gi|121637199|ref|YP_977422.1|  98 VDATKAYCPQYA 109
                                    **********97 PP

>> DUF5455  Family of unknown function (DUF5455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   7.5e-06     0.045      17      73 ..       8      66 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                        DUF5455 17 ylatfltkklAvaivalgliialivgllvvllaalsglssi..aetlpselsqgislvv 73
                                   ++++ +t+ ++ a++ l++  a ++g+++   a++ +++si   +++p+++ q ++lv 
  gi|121637199|ref|YP_977422.1|  8 RIIAAFTTAVGAAAIGLAVATAGTAGANTKDEAFIAQMESIgvTFSSPQVATQQAQLVC 66
                                   68999***********************9777777776665224899999999999985 PP

>> DUF4907  Domain of unknown function (DUF4907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.42   2.5e+03      34      49 ..      12      27 ..      10      29 .. 0.84
   2 ?   11.9   0.0   2.7e-05      0.16      33      61 ..      50      79 ..      35      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.42
                        DUF4907 34 pFkteedArkvgklVv 49
                                   +F+t   A+ +g  V+
  gi|121637199|ref|YP_977422.1| 12 AFTTAVGAAAIGLAVA 27
                                   8999999999998875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.7e-05
                        DUF4907 33 kpFkteedArkvgklVvekLkkge.npsvt 61
                                    +F++ + A++ ++lV++kL++ge    + 
  gi|121637199|ref|YP_977422.1| 50 VTFSSPQVATQQAQLVCKKLASGEtGTEIA 79
                                   58********************99445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 719.84
//
Query:       gi|121637200|ref|YP_977423.1|  [L=631]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-66  223.1   4.3    6.7e-66  222.7   4.3    1.1  1  ABC_membrane    ABC transporter transmembrane region
    1.2e-29  103.5   0.0    2.4e-29  102.6   0.0    1.5  1  ABC_tran        ABC transporter
    6.4e-05   22.5   5.2    0.00014   21.4   5.2    1.5  1  ABC_membrane_2  ABC transporter transmembrane region 2
    0.00044   19.8   0.2      0.045   13.2   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00049   20.5   0.1     0.0017   18.7   0.1    1.9  1  AAA_16          AAA ATPase domain
    0.00051   19.8   0.1     0.0016   18.2   0.1    1.8  1  AAA_30          AAA domain
    0.00056   20.2   2.1     0.0049   17.1   0.6    2.8  2  AAA_22          AAA domain
     0.0049   16.8   0.0       0.01   15.7   0.0    1.5  1  RsgA_GTPase     RsgA GTPase
     0.0077   16.8   0.0      0.014   15.9   0.0    1.4  1  AAA_23          AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.057   13.8   0.0    2.1  1  AAA             ATPase family associated with various cellula
      0.013   15.8   0.2        0.5   10.6   0.2    2.5  2  AAA_28          AAA domain
      0.013   15.6   0.0      0.034   14.2   0.0    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
      0.041   14.0   0.1        0.1   12.7   0.1    1.6  1  DUF87           Helicase HerA, central domain
      0.059   13.1   0.0       0.15   11.8   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
      0.067   12.4   0.2        3.5    6.8   0.1    2.8  3  PRTase_1        Phosphoribosyl transferase (PRTase)
      0.067   12.5   0.1       0.17   11.2   0.0    1.6  2  FtsK_SpoIIIE    FtsK/SpoIIIE family
      0.078   12.6   0.1       0.17   11.4   0.1    1.6  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.081   13.5   0.0       0.16   12.6   0.0    1.5  1  AAA_18          AAA domain
      0.093   12.7   0.0       0.19   11.7   0.0    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
       0.12   12.2   0.0        7.4    6.3   0.0    2.4  2  DEAD            DEAD/DEAH box helicase
       0.15   12.2   2.1        0.7   10.0   0.4    2.7  2  AAA_33          AAA domain
       0.18   11.3   0.0       0.36   10.3   0.0    1.4  1  AAA_7           P-loop containing dynein motor region
        0.2   11.5   1.4        3.3    7.4   0.2    2.3  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.7   4.3   8.6e-69   6.7e-66       3     274 .]      55     353 ..      53     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 222.7 bits;  conditional E-value: 8.6e-69
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH...........................HHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   3 liillailagvlsplfplvlgrildtlldkgdpet...........................ealnvysllllllglaqf 55 
                                     +i+  il++++++lf+ v+gr l+  ++k+++                             +a+ +++ l l+l+la +
  gi|121637200|ref|YP_977423.1|  55 GVIVPRILGHATDLLFNGVIGRGLPGGITKAQAVAsarargdntfadllsgmnvvpgqgvdfAAVERTLALALALYLAAA 134
                                    579999***********************9777777888999999*********************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  56 ilallqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvggliv 135
                                    ++ ++q +lln t +++++rlr+++ +k++r+p+s+fd ++ Gellsr+tnd+++l+++l+++++++++s+lt+v++l++
  gi|121637200|ref|YP_977423.1| 135 LMIWAQARLLNLTVQKTMVRLRTDVEDKVHRLPLSYFDGQQRGELLSRVTNDIDNLQSSLSMTISQLVTSILTMVAVLAM 214
                                    ******************************************************************************** PP

                                    HHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 136 mfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakk 215
                                    m+ ++  l+l++l ++pl +lv+  i++++++l+  ++++++++++++eE+ sg+ +Vk fg++++ +e+f++ ++++++
  gi|121637200|ref|YP_977423.1| 215 MVSISGLLALITLLTVPLSLLVTRAITRRSQPLFVAHWTSTGRLNAHLEETYSGFTVVKTFGHQAAARERFHELNDDVYQ 294
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 216 agikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslfailfgal 274
                                    ag+ +++++gl++++t ++g+l y+++++ G+ +v +g++++g++ +f++++ +++++l
  gi|121637200|ref|YP_977423.1| 295 AGFGAQFLSGLVQPATAFIGNLGYVAVAVAGGLQVATGQITLGSIQAFIQYIRQFNMPL 353
                                    ********************************************************996 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0     3e-32   2.4e-29       2     137 .]     414     562 ..     413     562 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 3e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    +++sl  ++g++vaivG++GaGK+tL++ll++ ++  +G+il+dg d+ + +++slr++ig++ q++ l +++ ++en  
  gi|121637200|ref|YP_977423.1| 414 RDLSLVAEPGSTVAIVGPTGAGKTTLVNLLMRFYEIGSGRILIDGVDIASVSRQSLRSRIGMVLQDTWLYDGT-IAENia 492
                                    6899999***********************************************************9999998.99**9* PP

                                    ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  ++ +++++++++l   +  +t+v+ ++ s+S G+kq + +ara+l +p+ll+lDE+t+
  gi|121637200|ref|YP_977423.1| 493 ygrpeattdeiveaARAAHVDRFVNTLPAGY--QTRVSGDGGSISVGEKQLITIARAFLARPQLLILDEATS 562
                                    **99988888876666666888888888888..88888888*****************************96 PP

>> ABC_membrane_2  ABC transporter transmembrane region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   5.2   1.8e-07   0.00014      51     195 ..     121     261 ..     107     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                 ABC_membrane_2  51 raFvlsllkfallavpasfvnsalkYltqkLalafRkrLtkhllseYlknrtyYkvsnlderidnpDqritqDvekFtss 130
                                    r+  l+l+ ++++a+++ + + +l+ + qk  ++ R+ + + +++  l+   y++ ++ +e       r+t+D+++  ss
  gi|121637200|ref|YP_977423.1| 121 RTLALALALYLAAALMIWAQARLLNLTVQKTMVRLRTDVEDKVHRLPLS---YFDGQQRGEL----LSRVTNDIDNLQSS 193
                                    6677889999999999999999999999999999999999999998775...8887777774....569*********** PP

                 ABC_membrane_2 131 lssLlsglvkpildvilftfiLwslsgtlgl...lllllyvllatvilriigpplgklvaeeeklege 195
                                    ls  +s+lv++il+++ + + ++s+sg l+l   l++ l +l++ +i+r+ +p ++       +l+++
  gi|121637200|ref|YP_977423.1| 194 LSMTISQLVTSILTMVAVLAMMVSISGLLALitlLTVPLSLLVTRAITRRSQPLFVAHWTSTGRLNAH 261
                                    *****************************994444445556777777777777777776666666665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.027        21      26      42 ..     425     441 ..     414     451 .. 0.84
   2 !   13.2   0.0   5.8e-05     0.045     136     213 ..     533     606 ..     448     611 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                                    EEEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlld 42 
                                      aivGp G+GK+ l++
  gi|121637200|ref|YP_977423.1| 425 TVAIVGPTGAGKTTLVN 441
                                    579**********9986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.8e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                    ++S Gek+L+ +a  f      +  l +lDe  +  D +    + + ++e + +   ++i++r  ++++ad+++ v++
  gi|121637200|ref|YP_977423.1| 533 SISVGEKQLITIARAF----LARPQLLILDEATSSVDTRTELLIQRAMRELRRDRTSFIIAHRLSTIRDADHILVVQT 606
                                    6799999999998775....33445899*******************************************9988865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.2e-06    0.0017      25     164 ..     424     581 ..     414     589 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalareellrqllde...........aesa 92 
                                    + v ++G+ G GK++lv+ l+r +e   g i++ g    +        + ++  r + +  +l++               
  gi|121637200|ref|YP_977423.1| 424 STVAIVGPTGAGKTTLVNLLMRFYEIGsGRILIDGVDIAS--------VSRQSLR-SRIGMVLQDtwlydgtiaenI--- 491
                                    789******************8666552233333333333........2333324.555555555444444333321... PP

                         AAA_16  93 eleawrekleeala.................................avpelagaea...srllellkrllallsrderp 136
                                                 a                                  v+ + g+++   ++l    +++l      +rp
  gi|121637200|ref|YP_977423.1| 492 -------------AygrpeattdeiveaaraahvdrfvntlpagyqtRVSGDGGSISvgeKQLITIARAFL------ARP 552
                                    .............1122222222222222344444444555566544444444444455444444444444......457 PP

                         AAA_16 137 lvlvlDdlqwadeaslql.laaLlrlles 164
                                     +l+lD++    ++  +l ++  +r+l +
  gi|121637200|ref|YP_977423.1| 553 QLLILDEATSSVDTRTELlIQRAMRELRR 581
                                    78888888844444444447777777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     2e-06    0.0016      14     110 ..     419     573 ..     416     587 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaa.g.........grviglAptgkaAkvLa.................... 63 
                                    ++++  +++++Gp G+GKtt+++ l + +e   g                  +   + L+                    
  gi|121637200|ref|YP_977423.1| 419 VAEPGSTVAIVGPTGAGKTTLVNLLMRFYEIGsGrilidgvdiA--------SVSRQSLRsrigmvlqdtwlydgtiaen 490
                                    556667899*********************99554444333333........3333335522333333444444444433 PP

                         AAA_30  64 ...........eelgi....eastiakllkrlk........................grarlepgtllivDEagm.vdtk 103
                                               e   i    +a+ +++++++l                         +ra l++ +lli DEa   vdt+
  gi|121637200|ref|YP_977423.1| 491 iaygrpeattdE---IveaaRAAHVDRFVNTLPagyqtrvsgdggsisvgekqlitiARAFLARPQLLILDEATSsVDTR 567
                                    333333222111...022225555555555555999999***********999999977788888*******96514555 PP

                         AAA_30 104 qlaallk 110
                                    + + l++
  gi|121637200|ref|YP_977423.1| 568 T-ELLIQ 573
                                    4.44444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.9   7.7e+03      46      90 ..     145     191 ..     139     198 .. 0.68
   2 !   17.1   0.6   6.3e-06    0.0049       6      38 ..     424     479 ..     420     609 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.9
                         AAA_22  46 tlpsstsskdllrellralglelka..erlsseellealeqalrara 90 
                                    +l+++++   l++++  ++++   +   ++++ ell+++++ +++ +
  gi|121637200|ref|YP_977423.1| 145 NLTVQKTMVRLRTDVEDKVHRLPLSyfDGQQRGELLSRVTNDIDNLQ 191
                                    55666666667777777776666556777888888888877776655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.3e-06
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.......................e 38 
                                    + ++++G++G+GKTtl++ l++ +++ +                            
  gi|121637200|ref|YP_977423.1| 424 STVAIVGPTGAGKTTLVNLLMRFYEIGSGRILidgvdiasvsrqslrsrigmvlqD 479
                                    5679*******************987644333444444444444444444444440 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05      0.01      99     121 ..     423     445 ..     408     468 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                    TSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                    ++t+++vG++G+GK+tL+n l+ 
  gi|121637200|ref|YP_977423.1| 423 GSTVAIVGPTGAGKTTLVNLLMR 445
                                    38999**************9975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05     0.014      22      38 ..     426     442 ..     401     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                         AAA_23  22 tlItGpNGaGKTTildA 38 
                                    ++I+Gp+GaGKTT+++ 
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNL 442
                                    58************986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.3e-05     0.057       2      74 ..     427     567 ..     426     612 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
                                    EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS.................................. CS
                            AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk.................................. 37 
                                     ++Gp G GKT+l++ +++            gv++ ++s  +l+s                                   
  gi|121637200|ref|YP_977423.1| 427 AIVGPTGAGKTTLVNLLMRFYeigsgrilidGVDIASVSRQSLRSRigmvlqdtwlydgtiaeniaygrpeattdeivea 506
                                    589***************99644444444555778888888888778888888998888888888888888888888888 PP

                                    ..........................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA  38 ..........................yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                                               ++ +ek++  + ++    + p  l++DE+ + + +r
  gi|121637200|ref|YP_977423.1| 507 araahvdrfvntlpagyqtrvsgdggSISVGEKQLITIARA-FLAR-PQLLILDEATSSVDTR 567
                                    88888888888888888888888887777777777777654.3333.7888888888888777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00064       0.5       2      20 ..     426     444 ..     425     452 .. 0.90
   2 ?    2.4   0.0      0.21   1.6e+02      74     120 ..     479     523 ..     462     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00064
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    ++i+G+ ++GKTtl++ L 
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNLLM 444
                                    89*************9985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                         AAA_28  74 kvlfcDrglldtlaYarayggeaeaeleaaarekrydlvfllppape 120
                                    ++ ++D  + +++aY r +  +   e+++aar+ + d+++ + pa++
  gi|121637200|ref|YP_977423.1| 479 DTWLYDGTIAENIAYGRPEATT--DEIVEAARAAHVDRFVNTLPAGY 523
                                    4567888888888888877777..78888999999**9999888774 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-05     0.034       2      21 ..     426     445 ..     425     480 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                    vaivG + +GK+tL+n l++
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNLLMR 445
                                    9***************9986 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00013       0.1      26      45 ..     426     445 ..     422     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                          DUF87  26 lAilgsTGsGKSntvavLle 45 
                                    +Ai+g TG+GK+++v +L++
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNLLMR 445
                                    7***************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.15      23      39 ..     423     440 ..     414     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                         AAA_29  23 g.atlltGpsGsGKSTll 39 
                                    g ++ ++Gp+G+GK+Tl+
  gi|121637200|ref|YP_977423.1| 423 GsTVAIVGPTGAGKTTLV 440
                                    34899************8 PP

>> PRTase_1  Phosphoribosyl transferase (PRTase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0045       3.5      72     110 ..      28      66 ..      19      72 .. 0.86
   2 ?    2.3   0.0       0.1        81     140     168 ..     242     270 ..     229     299 .. 0.79
   3 ?   -3.4   0.0         6   4.7e+03     129     161 ..     458     492 ..     456     502 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0045
                       PRTase_1  72 avlaeailaekgkeivlvSLaRAGtpiGvllkralkekl 110
                                    a+l ++++ +++ +i+++ L  AGt iGv++ r+l +++
  gi|121637200|ref|YP_977423.1|  28 ARLVKRLAPQRRLSIAVITLGIAGTTIGVIVPRILGHAT 66 
                                    5677888889999********************997755 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                       PRTase_1 140 eeasivFvDgWtgKGaitreLkkaleefe 168
                                    ++++ +Fv  Wt+ G ++ +L+++ + f+
  gi|121637200|ref|YP_977423.1| 242 RRSQPLFVAHWTSTGRLNAHLEETYSGFT 270
                                    456668*****************998886 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6
                       PRTase_1 129 enAleyilar..heeasivFvDgWtgKGaitreLk 161
                                     + ++ + ++  +++  +v  D W   G+i+++++
  gi|121637200|ref|YP_977423.1| 458 GVDIASVSRQslRSRIGMVLQDTWLYDGTIAENIA 492
                                    55555566662233445567799999999998875 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021      0.17      28      60 ..     409     444 ..     399     445 .. 0.90
   2 ?   -3.1   0.0       5.3   4.1e+03     110     134 ..     558     584 ..     554     627 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                    S-EEEEEGGGS-....SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE  28 gnplvldlkkma...shllvaGatgsGKStalntLi 60 
                                    g p++ dl+ +a   s + ++G tg GK+t +n L+
  gi|121637200|ref|YP_977423.1| 409 GTPVIRDLSLVAepgSTVAIVGPTGAGKTTLVNLLM 444
                                    78999999999999999****************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                                    HHHHHHHHHHHHHHHHTT-SSHHH..H CS
                   FtsK_SpoIIIE 110 eeLvkemeeryalfreagvrsiaa..y 134
                                    +e ++ ++ r +l+ ++ +r++++   
  gi|121637200|ref|YP_977423.1| 558 DEATSSVDTRTELLIQRAMRELRRdrT 584
                                    555666666666666666666666431 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00022      0.17       3      21 ..     426     444 ..     424     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    + ++G+ G+GKTtL+n l+
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNLLM 444
                                    679************9887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002      0.16       1      44 [.     426     493 ..     426     545 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf........................gvnlrdvakenglllevdpe 44 
                                    +++ G+ G+GKttl + L +  ++                        g +l+d++  +g+  e+ ++
  gi|121637200|ref|YP_977423.1| 426 VAIVGPTGAGKTTLVNLLMRFYEIgsgrilidgvdiasvsrqslrsriGMVLQDTWLYDGTIAENIAY 493
                                    689***************66434466555555555555555555555555555555555555555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.19      19      44 ..     423     448 ..     410     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    g+++++ G+ GaGKTtlv  l++ ++
  gi|121637200|ref|YP_977423.1| 423 GSTVAIVGPTGAGKTTLVNLLMRFYE 448
                                    6789***************9998765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0095       7.4      13      33 ..     422     442 ..     412     473 .. 0.84
   2 ?    3.3   0.0     0.077        60     119     151 ..     549     581 ..     486     590 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0095
                                    TTCEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlafli 33 
                                     g  v + ++TG+GKT+   +
  gi|121637200|ref|YP_977423.1| 422 PGSTVAIVGPTGAGKTTLVNL 442
                                    577899**********97554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.077
                                    CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                    l + ++l+lDEa    d   +  i+r +++l++
  gi|121637200|ref|YP_977423.1| 549 LARPQLLILDEATSSVDTRTELLIQRAMRELRR 581
                                    677899************999999999999965 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.97   7.6e+02      20      59 ..     147     191 ..     138     210 .. 0.69
   2 ?   10.0   0.4    0.0009       0.7       3      21 ..     427     445 ..     426     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.97
                         AAA_33  20 lkklgavllssdtlrrrlfg.....tdqqsktdytrvldrlyqil 59 
                                      + ++v+l++d++ + ++      ++qq+ + ++rv++++ + +
  gi|121637200|ref|YP_977423.1| 147 TVQKTMVRLRTDVEDKVHRLplsyfDGQQRGELLSRVTNDIDNLQ 191
                                    445669*****9976644334567788888888888887777654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0009
                         AAA_33   3 llvGlpGsGKstlaerllk 21 
                                     +vG+ G+GK+tl+  l++
  gi|121637200|ref|YP_977423.1| 427 AIVGPTGAGKTTLVNLLMR 445
                                    689***********98885 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.36      28      55 ..     418     445 ..     414     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                          AAA_7  28 lllknkkpvllvGptGtGKtviikdllk 55 
                                    l+ + +  v +vGptG GKt++++ l++
  gi|121637200|ref|YP_977423.1| 418 LVAEPGSTVAIVGPTGAGKTTLVNLLMR 445
                                    566778899**************98876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0042       3.3       3      19 ..     427     443 ..     426     471 .. 0.72
   2 ?    2.4   0.1      0.14   1.1e+02     236     293 ..     533     587 ..     484     590 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                         AAA_21   3 vliGpNgsGKSnLLdal 19 
                                    +++Gp g+GK++L  +l
  gi|121637200|ref|YP_977423.1| 427 AIVGPTGAGKTTLVNLL 443
                                    79***********9888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQvi 293
                                    ++S G k+l+ ++ a+l+++    ll++DE  ++ +  +++ l+ + ++el+r ++ +i
  gi|121637200|ref|YP_977423.1| 533 SISVGEKQLITIARAFLARP---QLLILDEATSSVDT-RTELLIqRAMRELRRDRTSFI 587
                                    3499*****99999999988...99*****9999998.666666666677777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 3920.35
//
Query:       gi|121637201|ref|YP_977424.1|  [L=582]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-52  177.8  11.7    4.6e-52  177.4  11.7    1.1  1  ABC_membrane  ABC transporter transmembrane region
    4.6e-30  104.9   0.0    3.9e-29  101.9   0.0    2.1  2  ABC_tran      ABC transporter
    1.7e-08   34.2   0.1    3.5e-05   23.3   0.0    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00021   21.5   0.2    0.00034   20.8   0.2    1.2  1  DUF87         Helicase HerA, central domain
     0.0018   17.6   0.3     0.0048   16.2   0.0    1.8  2  Zeta_toxin    Zeta toxin
     0.0022   17.7   1.5     0.0044   16.7   0.2    2.1  2  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.017   15.7   0.1      0.027   15.0   0.1    1.2  1  AAA_23        AAA domain
      0.044   13.7   0.0      0.092   12.6   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.055   13.1   0.4       0.11   12.0   0.0    1.6  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.066   12.6   0.0       0.13   11.6   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.14   12.3   0.0        0.4   10.8   0.0    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
        0.2   12.0   0.7       0.46   10.9   0.7    1.7  1  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4  11.7   3.1e-55   4.6e-52       2     274 .]      18     288 ..      17     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 3.1e-55
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                     ++++l+++++++s+  p v + i+d+ + kgd+ t  ++++  ++l+++ +q+++a++ +yl + tg    ++lr+ +f
  gi|121637201|ref|YP_977424.1|  18 AMLMMLQLVSTLASLYLPTVNAAIVDDGVAKGDTAT--IVRLGAVMLGVTGLQVLCAIGAVYLGSRTGAGFGRDLRSAMF 95 
                                    57899*******************************..****************************************** PP

                                    HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsavi 161
                                    ++i+  + +   +  + +ll+r tndv+++  +++++  +++++ +++vgg+i+++ +   lt++ll+ +p++++ +++i
  gi|121637201|ref|YP_977424.1|  96 EHIITFSERETARFGAPTLLTRSTNDVRQILFLVQMTATVLVTAPIMCVGGIIMAIHQEAALTWLLLVSVPILAVANYWI 175
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 162 akilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyal 241
                                     +++ +l++++q+ ++ +++v++++lsg+r+V+af+re y+++kf +a++   +a++++ ++++l+ ++t+l +++s ++
  gi|121637201|ref|YP_977424.1| 176 ISHMLPLFRRMQSLIDGINRVMRDQLSGVRVVRAFTREGYERDKFAQANTALSNAALSAGNWQALMLPVTTLTINASSVA 255
                                    ******************************************************************************** PP

                                    HHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 242 alwfGttlvisgelsvgdlvvflslfailfgal 274
                                     +wfG+  ++sg+++vg+l++fls+fa++++a+
  gi|121637201|ref|YP_977424.1| 256 LIWFGGLRIDSGQMQVGSLIAFLSYFAQILMAV 288
                                    ***************************999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.55   8.3e+02      96     122 ..     219     245 ..     182     255 .. 0.73
   2 !  101.9   0.0   2.6e-32   3.9e-29       1     136 [.     352     501 ..     352     502 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                                    GTTCBGESTTSGGS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  96 elkdtvvksspssLSgGqkqrvalara 122
                                    ++++ +   s + LS G +q ++l  +
  gi|121637201|ref|YP_977424.1| 219 KFAQANTALSNAALSAGNWQALMLPVT 245
                                    3444444456699*******9998655 PP

  == domain 2  score: 101.9 bits;  conditional E-value: 2.6e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+++sl+ ++g+++aivG++G+GKStL++l+++l++ t+G +l+dg d++e  +e+l + ig +pq + lf+++ v++n 
  gi|121637201|ref|YP_977424.1| 352 LQDISLTARPGTTTAIVGSTGSGKSTLVSLICRLYDVTAGAVLVDGIDVREYHTERLWSAIGLVPQRSYLFSGT-VADNl 430
                                    789***********************************************************************.9**** PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   ++  ++++a   ++ +   +t+v +++ ++SgGq+qr+a+ara++++p ++++D+++
  gi|121637201|ref|YP_977424.1| 431 rygggpdqvvteqemWEALRVAAADGFVQTD-GLQTRVAQGGVNFSGGQRQRLAIARAVIRRPAIYVFDDAF 501
                                    ******9997754333333344444444444.5667777999***************************996 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2   0.00088       1.3      25      44 ..     363     382 ..     353     390 .. 0.84
   2 !   23.3   0.0   2.3e-08   3.5e-05     136     211 ..     473     544 ..     387     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00088
                                    SEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                      taivG+ GSGKs l+  i
  gi|121637201|ref|YP_977424.1| 363 TTTAIVGSTGSGKSTLVSLI 382
                                    4699**********998765 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.3e-08
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                    ++SgG+++ +a+    A   +++ ++y++D+  +aLD +  +kv   l++ s +a +iv++ r    ++ad+++ v
  gi|121637201|ref|YP_977424.1| 473 NFSGGQRQRLAI----ARAVIRRPAIYVFDDAFSALDVHTDAKVHASLRQVSGDATIIVVTQRISNAAQADQVIVV 544
                                    799999986655....455788999**********************************************99877 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   2.3e-07   0.00034      26      47 ..     365     385 ..     362     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                          DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                    +Ai+gsTGsGKS++v+++++ l
  gi|121637201|ref|YP_977424.1| 365 TAIVGSTGSGKSTLVSLICR-L 385
                                    69*************99886.4 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.2e-06    0.0048      20      58 ..     366     404 ..     353     409 .. 0.92
   2 ?   -2.6   0.2       1.8   2.7e+03     170     189 ..     529     548 ..     525     550 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.2e-06
                     Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelh 58 
                                     ++G++G+GKs+l +l+ +  + + ++v +d+ d+Re+h
  gi|121637201|ref|YP_977424.1| 366 AIVGSTGSGKSTLVSLICRLYDVTAGAVLVDGIDVREYH 404
                                    589************************************ PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                     Zeta_toxin 170 vealeeekqldrvkikdrdg 189
                                    ++++ ++ q+d+v+++d+++
  gi|121637201|ref|YP_977424.1| 529 TQRISNAAQADQVIVVDNGK 548
                                    68899999******999876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.7   2.6e+03      43      58 ..     238     253 ..     236     255 .. 0.88
   2 !   16.7   0.2   2.9e-06    0.0044      21      39 ..     361     379 ..     352     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                         AAA_29  43 qalLvpakkvrfNkaa 58 
                                    qal++p ++++ N+++
  gi|121637201|ref|YP_977424.1| 238 QALMLPVTTLTINASS 253
                                    799*****99999998 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.9e-06
                         AAA_29  21 lkg.atlltGpsGsGKSTll 39 
                                    + g +t ++G +GsGKSTl+
  gi|121637201|ref|YP_977424.1| 361 P-GtTTAIVGSTGSGKSTLV 379
                                    3.449**************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.8e-05     0.027      21      40 ..     364     383 ..     353     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                         AAA_23  21 ltlItGpNGaGKTTildAik 40 
                                     t+I+G +G+GK+T++  i+
  gi|121637201|ref|YP_977424.1| 364 TTAIVGSTGSGKSTLVSLIC 383
                                    69*************99998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.1e-05     0.092      99     122 ..     362     385 ..     347     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                                    TSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                    + t+++vG++G GKStL+  +   
  gi|121637201|ref|YP_977424.1| 362 GTTTAIVGSTGSGKSTLVSLICRL 385
                                    4899**************988765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.11       2      35 ..     364     397 ..     363     410 .. 0.87
   2 ?   -2.8   0.0       2.7   4.1e+03      47      61 ..     535     549 ..     515     562 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                    EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS CS
                           cobW   2 vtvltGflGsGKTtLlnhllenraglklavivNe 35 
                                    +t ++G+ GsGK+tL++ +++  +    av+v  
  gi|121637201|ref|YP_977424.1| 364 TTAIVGSTGSGKSTLVSLICRLYDVTAGAVLVDG 397
                                    5889****************99999999998865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                    HCCCT.EEEETTTTE CS
                           cobW  47 retgveivelenGci 61 
                                    ++++++++ + nG+i
  gi|121637201|ref|YP_977424.1| 535 AAQADQVIVVDNGKI 549
                                    122333555566655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.9e-05      0.13      40      63 ..     363     385 ..     341     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                                    .SEEEE--TTSSHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  40 shllvaGatgsGKStalntLilSl 63 
                                      + ++G+tgsGKSt + +Li+ l
  gi|121637201|ref|YP_977424.1| 363 TTTAIVGSTGSGKSTLV-SLICRL 385
                                    4689**********966.688765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027       0.4       2      21 ..     365     384 ..     364     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                     aivG + +GKStL++ +++
  gi|121637201|ref|YP_977424.1| 365 TAIVGSTGSGKSTLVSLICR 384
                                    59*************99987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7    0.0003      0.46      24      54 ..     361     392 ..     352     546 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                         AAA_16  24 p.elvllsGesGvGKsslvrellralekdggi 54 
                                    p   + ++G  G+GKs+lv  + r +  + g 
  gi|121637201|ref|YP_977424.1| 361 PgTTTAIVGSTGSGKSTLVSLICRLYDVTAGA 392
                                    3467899*************999865555333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.25s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4060.81
//
Query:       gi|121637202|ref|YP_977425.1|  [L=185]
Description: lipoprotein lprB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-37  129.1   0.1    1.9e-37  129.0   0.1    1.0  1  DUF3558   Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.1     1e-41   1.9e-37       2     174 .]      21     183 ..      20     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 1e-41
                        DUF3558   2 llaGCssttdGtapaasssassssttsssaapavpldtsgvlfdpCglltddqlaelggdkekeeaastgangpgCsWqa 81 
                                    ++aGCs          s++  + +t +s++a+a+  +++g++f +Cg+++d++++el+     ++ ++t++n++gC+W a
  gi|121637202|ref|YP_977425.1|  21 AVAGCS---------DSGDNKPGATIPSTPANAE--GRHGPFFPQCGGVSDQTVTELTRV---TGLVNTAKNSVGCQWLA 86 
                                    79****.........6778999999999999999..************************...***************** PP

                        DUF3558  82 adsagygvsvsfswyegspirrerateerl.....ditieGrpaviardpgd..eas.Cevavgvadgqvvvvsvsesrg 153
                                     + +  g+++sfswy+gspi+rer+tee++     di+i+G++++ia  ++   ++s Cev+++++d+ ++++svs    
  gi|121637202|ref|YP_977425.1|  87 GG-GILGPHFSFSWYRGSPIGRERKTEELSrasveDINIDGHSGFIAIGNEPslGDSlCEVGIQFSDD-FIEWSVS--FS 162
                                    *9.*********************************************6666556668**********.*******..88 PP

                        DUF3558 154 kaagadpCeaarklaelvvpn 174
                                    +++++ pC++a++l++++++n
  gi|121637202|ref|YP_977425.1| 163 QKPFPPPCDIAKELTRQSIAN 183
                                    8999************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1412.87
//
Query:       gi|121637203|ref|YP_977426.1|  [L=180]
Description: lipoprotein lprC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-29  102.1   0.3    3.7e-29  101.9   0.3    1.0  1  DUF3558   Protein of unknown function (DUF3558)
  ------ inclusion threshold ------
      0.087   13.4   2.8        0.4   11.3   2.8    2.1  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.3   4.2e-33   3.7e-29       1     173 [.      16     177 ..      16     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 4.2e-33
                        DUF3558   1 lllaGCssttdGtapaasssassssttsssaapavpldtsgvlfdpCglltddqlaelggdkekeeaastgangpgCsWq 80 
                                    l+l+GC+++++Gta +a++++ + +  s        ++++++l ++C++lt+d la++ g+  ++ + ++++ g++C+Wq
  gi|121637203|ref|YP_977426.1|  16 LVLTGCTKSISGTAVKAGGAGVPRNNNS--------QERYPNLLKECEVLTTDILAKTVGA--DPLDIQSTFVGAICRWQ 85 
                                    69***********333333333333322........2568899******************..9**************** PP

                        DUF3558  81 aadsagygvsvsfswyegspirrerateerl.....ditieGrpaviardpgdeasCevavgvadgqvvvvsvsesrgka 155
                                    aa+ + + ++++  w+e++++ +er+++e l     ++ i+G + +++r+ + +++C+va ++a g vv ++v+   ++a
  gi|121637203|ref|YP_977426.1|  86 AAN-PAGLIDITRFWFEQGSLSNERKVAEGLkyqveTRAIQGVDSIVMRTGDPNGACGVASDAA-G-VVGWWVN---PQA 159
                                    ***.*********************************************9999999*******9.4.9******...99* PP

                        DUF3558 156 agadpCeaarklaelvvp 173
                                    +g d+C++a kl+el+++
  gi|121637203|ref|YP_977426.1| 160 PGIDACGQAIKLMELTLA 177
                                    ***************986 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.8   4.5e-05       0.4       1      18 []       1      22 [.       1      22 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                         LPAM_1  1 MKKi....llalgalllLsGCs 18
                                   M++       +++all+L+GC+
  gi|121637203|ref|YP_977426.1|  1 MRRVlvgaAALITALLVLTGCT 22
                                   555544445689*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1281.16
//
Query:       gi|121637204|ref|YP_977427.1|  [L=158]
Description: hypothetical protein BCG_1335c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-07   29.2   1.0    1.8e-06   27.8   0.3    1.8  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.3     1e-10   1.8e-06       4      81 ..       1      71 [.       1      87 [. 0.79
   2 ?    0.5   0.0     0.023   4.1e+02     129     158 ..      79     109 ..      76     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1e-10
                                   EE---BTTB--....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                     His_Phos_1  4 vRHGetewnaegrlqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealglpveldegLrEid 81
                                   +RH+++++         +d pL ++G+++A  ++ +l++    +da+++S+  RarqT ++ +   + p     +  E+ 
  gi|121637204|ref|YP_977427.1|  1 MRHAKSAYPDG---IADHDRPLAPRGIREAGLAGGWLRAnlPAVDAVLCSTATRARQTLAHTG--IDAPA----RYAERL 71
                                   69******988...89***********************76677888***********98765..23444....444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.023
                                    HHHHHHHHTTTSE.EEEEE-HHHHHHHHHHH CS
                     His_Phos_1 129 aleelaarheget.vlvVsHggvirallarl 158
                                    ++ee+ +  ++ t +lvV H  +  al+  l
  gi|121637204|ref|YP_977427.1|  79 VIEEINRVGDNVTsLLVVGHEPTTSALAIVL 109
                                    5677777777766799999987666554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1243.74
//
Query:       gi|121637205|ref|YP_977428.1|  [L=417]
Description: hypothetical protein BCG_1336 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-12   47.0   0.0    5.9e-12   46.5   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    0.00027   21.2   0.1    0.00059   20.1   0.0    1.7  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.082   13.0   0.4      0.082   13.0   0.4    2.3  3  baeRF_family2  Bacterial archaeo-eukaryotic release factor fa


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   9.8e-16   5.9e-12       1     126 [.      35     203 ..      35     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 9.8e-16
                                    EEEEEEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEE CS
                    Metallophos   1 lrilvigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipv 67 
                                    +r+l+++D++l             +  +  +d+++ l+ l+++ ++ +v++aGD++++++l   ++ + l+a+   + pv
  gi|121637205|ref|YP_977428.1|  35 MRFLHTADWQLgmtrhflagdaqPRYSAARRDAVAGLKALAADVGAEFVVVAGDVFEHNQLAPQIVGQsLEAMRVIGLPV 114
                                    89***************999888666677777777778888888***************99998999989999999**** PP

                                    EEEC-TTS......................CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEE CS
                    Metallophos  68 ylllGNHe......................gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgs...lkvlllh 121
                                    yll+GNH+                       ++  ++ + ++   i ++pwrs+a + + +  +  g  +   +++l++h
  gi|121637205|ref|YP_977428.1| 115 YLLPGNHDpldassvytstlfraerpdnvvVLDRaGVHEVRPGVQIVAAPWRSKAPTTDPVAEVLAGLPTdaaIRLLVAH 194
                                    ******************************66666899999999999999*99977776666666555556688****** PP

                                    SE....CEE CS
                    Metallophos 122 Gg....spe 126
                                    Gg    +p+
  gi|121637205|ref|YP_977428.1| 195 GGvdalDPD 203
                                    **4444222 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.8e-08   0.00059      12     103 ..      64     209 ..      35     273 .. 0.61
   2 ?   -2.2   0.1      0.71   4.2e+03      84     103 ..     281     306 ..     254     328 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.8e-08
                  Metallophos_2  12 nldaleavlealkevgvdaiihaGDl...eeeepevleellela.....pvlaVrGNnD..................... 62 
                                    ++da++ + + +++vg++ +++aGD+   ++ +p+++ + le       pv+  +GN+D                     
  gi|121637205|ref|YP_977428.1|  64 RRDAVAGLKALAADVGAEFVVVAGDVfehNQLAPQIVGQSLEAMrviglPVYLLPGNHDpldassvytstlfraerpdnv 143
                                    44555555666777888********98766777764444444334777***********999999998888888888877 PP

                  Metallophos_2  63 ......eev.veedvlreaaelgtdlp.eeaelel.......agekvlliHgdpl..........g 103
                                          + + v+  v+  aa+++ + p ++ + e+       a  ++l+ Hg  +           
  gi|121637205|ref|YP_977428.1| 144 vvldraGVHeVRPGVQIVAAPWRSKAPtTDPVAEVlaglptdAAIRLLVAHGGVDaldpdhdkpsL 209
                                    777654222566667777777777777555555545444444444488888875577666444331 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.71
                  Metallophos_2  84 eaelelagekvlliHgdpl......g 103
                                     +   ++++++  +H++ +       
  gi|121637205|ref|YP_977428.1| 281 VDARRIGRWRFVTLHHQVDtsrdiaD 306
                                    34444688888888886334444442 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.4e-05     0.082      64      94 ..      68      98 ..      54     110 .. 0.83
   2 ?   -2.7   0.1       0.9   5.4e+03      61      87 ..     173     199 ..     167     201 .. 0.82
   3 ?   -2.8   0.3      0.99   5.9e+03     101     119 ..     385     398 ..     379     414 .. 0.43

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                  baeRF_family2 64 AeevdrlvresgaelVvlaGDvrarsllrde 94
                                    + +++l++++gae+Vv+aGDv + + l+ +
  gi|121637205|ref|YP_977428.1| 68 VAGLKALAADVGAEFVVVAGDVFEHNQLAPQ 98
                                   456899****************999988766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.9
                  baeRF_family2  61 eavAeevdrlvresgaelVvlaGDvra 87 
                                    + vAe ++ l ++ + +l+v  G v a
  gi|121637205|ref|YP_977428.1| 173 DPVAEVLAGLPTDAAIRLLVAHGGVDA 199
                                    668999999999999999998888876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.99
                  baeRF_family2 101 elvvevegggraagadrea 119
                                    elv +  gg      d+ a
  gi|121637205|ref|YP_977428.1| 385 ELVATARGGD-----DESA 398
                                    2222222222.....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3106.10
//
Query:       gi|121637206|ref|YP_977429.1|  [L=875]
Description: hypothetical protein BCG_1337 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-09   37.9   0.0    2.4e-09   37.4   0.0    1.1  1  AAA_15    AAA ATPase domain
    2.7e-08   33.6   0.0    2.7e-08   33.6   0.0    3.4  3  AAA_27    AAA domain
      8e-07   29.8   0.0    1.9e-06   28.5   0.0    1.6  1  AAA_23    AAA domain
    8.9e-06   25.3   0.0     0.0088   15.5   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00048   19.8   0.0    0.00099   18.8   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
    0.00053   19.4   0.0     0.0012   18.2   0.0    1.6  1  DUF2813   Protein of unknown function (DUF2813)
  ------ inclusion threshold ------
      0.037   13.9   0.0       0.09   12.6   0.0    1.6  1  HxlR      HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   9.3e-13   2.4e-09       1      58 [.       1      59 [.       1      80 [. 0.84

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 9.3e-13
                         AAA_15  1 MkIkkikikNFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvi 58
                                   Mk++++ + N+R + + ++++ +  + v++G+N +GKSs +ealdl+l+ k++  kk++
  gi|121637206|ref|YP_977429.1|  1 MKLHRLALTNYRGIAHRDVEFPDHgVVVVCGANEIGKSSMVEALDLLLEYKDRSTKKEV 59
                                   ***********************99************************8844443222 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-11   2.7e-08       1     198 [.       1     210 [.       1     219 [. 0.61
   2 ?   -1.9   0.2       0.8   2.1e+03     147     172 ..     301     326 ..     253     355 .. 0.56
   3 ?   -2.8   0.7       1.6     4e+03     155     180 ..     606     631 ..     576     690 .. 0.54

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                         AAA_27   1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnflhdak..kLrigavleead 78 
                                    M+l+rL L+ y  ++ r ++f+  ++++ ++ G+NE GKs++++A+ dll   + r++++ + + k  +  +g  + ++ 
  gi|121637206|ref|YP_977429.1|   1 MKLHRLALTNYRGIAHRDVEFP--DHGVVVVCGANEIGKSSMVEAL-DLLLEYKDRSTKKEVKQVKptNADVGSEVIAEI 77 
                                    9********************9..9********************8.788888888888777655412556666544322 PP

                         AAA_27  79 g.......eelefaRrkgrkktlldaddqalp.....eevlaallggldretFealFgLdher...LreGGealleaege 143
                                             + +f++r +++ t+l+++ ++l+     e+v + l + +d e ++a   L++++   +   G + l+   +
  gi|121637206|ref|YP_977429.1|  78 SsgpyrfvYRKRFHKRCETELTVLAPRREQLTgdeahERVRTMLAETVDTELWHAQRVLQAAStaaVDLSGCDALSRALD 157
                                    22233333333344444455566666666555222213333333344555555555444433201133334444444444 PP

                         AAA_27 144 lgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                    l+    +a +G++sl  ++e++eae  ++f+p+++ + ++ +a ++l++a++++ 
  gi|121637206|ref|YP_977429.1| 158 LAAGDDAALSGTESL--LIERIEAEYARYFTPTGRPTGEWSAAVSRLAAAEAAVA 210
                                    444444444444443..56888888888888888888888888888888877765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.8
                         AAA_27 147 lLfeasaGlaslrevleaLeaeadel 172
                                    ++++a+a  ++ ++ +++ +aea++ 
  gi|121637206|ref|YP_977429.1| 301 AVVAAEAKARQAADEQATARAEAEAC 326
                                    33333333333333333333333332 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                         AAA_27 155 laslrevleaLeaeadelfkprkskk 180
                                     a+l + +++L  e+ ++ +++ ++k
  gi|121637206|ref|YP_977429.1| 606 SAELGAAMTRLACERASVGDDELAAK 631
                                    44455555555544444443333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   7.5e-10   1.9e-06       1      66 [.       5      72 ..       5     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.5e-10
                         AAA_23  1 kLkienfrsfrdqeidF.skgltlItGpNGaGKTTildAiklaL.ygetprlsrksgrgfeksdveie 66
                                   +L + n+r + + +++F ++g+++++G N+ GK++ ++A+ l L y + ++ +  ++ +  ++dv  e
  gi|121637206|ref|YP_977429.1|  5 RLALTNYRGIAHRDVEFpDHGVVVVCGANEIGKSSMVEALDLLLeYKDRSTKKEVKQVKPTNADVGSE 72
                                   68899***************************************888777766666556666665544 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.4e-06    0.0088       2      52 ..       3      52 ..       2      80 .. 0.84
   2 !    8.0   0.0   0.00067       1.7     135     199 ..     392     857 ..     166     870 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
                                   EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGers 52
                                   l+rl ++n++ +a ++ +   ++++ ++ G+N  GKs++++A+  +L  ++
  gi|121637206|ref|YP_977429.1|  3 LHRLALTNYRGIA-HRDVEFPDHGVVVVCGANEIGKSSMVEALDLLLEYKD 52
                                   799*********9.5555666788*******************98887654 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00067
                                    T............................................................................... CS
                                    x............................................................................... RF
                          SMC_N 135 e............................................................................... 135
                                    e                                                                               
  gi|121637206|ref|YP_977429.1| 392 Ellsrieraaaavdrggaqlasisaaveftaavdielgvgdqrvslsagqswsvtatgptevkvpgvltarivpgatald 471
                                    15555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637206|ref|YP_977429.1| 472 fqakyaaaqqeladalaagevadlaaarsadlcrrellsrrdqltatlaglcgdeqvdqlrsrleqlcagqpaeldlvst 551
                                    55555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637206|ref|YP_977429.1| 552 dtataraeldaveaariaaekdcetrrqiaagaarrlaetstratvlqnaaaaesaelgaamtrlacerasvgddelaak 631
                                    55555555555566666666666666666666666666666666666666666666666666666666667777777777 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637206|ref|YP_977429.1| 632 aeadlrvlqtaeqrvidladelaatapdavaaelaeaadavellrerhdeairalhevgvelsvfgtqgrkgkldaaete 711
                                    77777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ...............................................................................C CS
                                    ...............................................................................x RF
                          SMC_N 136 ...............................................................................l 136
                                                                                                                    
  gi|121637206|ref|YP_977429.1| 712 rehaashharvgrraraarllrsvmarhrdttrlryvepyraelhrlgrpvfgpsfevevdtdlrirsrtlddrtvpyeC 791
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777* PP

                                    S-HHHHHHHHHHHHHH...HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfA...iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                    LSgG k  + +  ++A   + + + a  +l+D+     D ++ +k+ e++++   + Q+iv + + 
  gi|121637206|ref|YP_977429.1| 792 LSGGAKEQLGILARLAgaaLVAKEDAVPVLIDDALGFTDPERLAKMGEVFDTIGADGQVIVLTCSP 857
                                    ******9888888888788555556666789******************************99875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.9e-07   0.00099       1      46 [.       3      48 ..       3      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.9e-07
                         AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   L+rl l N   + ++++e+  +g++++ G+++ GKS+++ A+  lL
  gi|121637206|ref|YP_977429.1|  3 LHRLALTNYRGIAHRDVEFPDHGVVVVCGANEIGKSSMVEALDLLL 48
                                   7899**************************************9998 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.8e-07    0.0012       1      51 [.       1      53 [.       1      63 [. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                        DUF2813  1 myLerieisGFRGinrLSlsleentvLi..GENaWGKSSLldALslilnveke 51
                                   m L+r+ ++ +RGi +  +++ ++ v++  G N  GKSS+++AL l+l+ +++
  gi|121637206|ref|YP_977429.1|  1 MKLHRLALTNYRGIAHRDVEFPDHGVVVvcGANEIGKSSMVEALDLLLEYKDR 53
                                   899******************988654334******************98765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05      0.09      12      47 ..     217     251 ..     213     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                    HHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTT CS
                           HxlR  12 vellkgkkRfselkralpkisqkmLaqrLreLeqdg 47 
                                     e+ +g +R +el++++ ++sq++La++Lr Le+ +
  gi|121637206|ref|YP_977429.1| 217 AEVDDGVRRHTELTEQVAELSQQLLAHQLR-LEAAR 251
                                    67789************************8.66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (875 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.44
# Mc/sec: 5938.41
//
Query:       gi|121637207|ref|YP_977430.1|  [L=528]
Description: dehydrogenase FAD flavoprotein GMC oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   8.6e-103  343.8   0.0   1.1e-102  343.5   0.0    1.1  1  GMC_oxred_N    GMC oxidoreductase
      1e-37  129.8   0.1    2.2e-37  128.8   0.1    1.6  1  GMC_oxred_C    GMC oxidoreductase
     0.0017   18.0   4.3     0.0069   16.0   4.3    1.9  1  DAO            FAD dependent oxidoreductase
     0.0021   17.3   0.0       0.62    9.2   0.0    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0026   16.9   0.9       0.48    9.4   0.1    2.3  2  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.027   13.5   0.0      0.042   12.9   0.0    1.3  1  Lycopene_cycl  Lycopene cyclase protein
      0.073   13.3   0.1       0.23   11.7   0.1    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.17   11.1   0.1       0.35   10.1   0.1    1.4  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.5   0.0  4.8e-106  1.1e-102       2     296 .]       6     298 ..       5     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 343.5 bits;  conditional E-value: 4.8e-106
                    GMC_oxred_N   2 delveggGsagsvvAaRLsedpstsvlvleaggreknrlimvlalalklidkklntayetepekalngrrlilpaGktlG 81 
                                    d++v+g+Gsag+vvA+RLs+dp+t+v++leag+r+knr+i v a+++kl++++++++y+tep+++l+gr +++p+Gk+lG
  gi|121637207|ref|YP_977430.1|   6 DYVVVGTGSAGAVVASRLSTDPATTVVALEAGPRDKNRFIGVPAAFSKLFRSEIDWDYLTEPQPELDGREIYWPRGKVLG 85 
                                    89****************************************************************************** PP

                    GMC_oxred_N  82 GgsvvNwsayiRtpaadldeWeeeaglegwssdevlpafkkvetaqale....sdlhgvdgrlgvtekgkeespln..ka 155
                                    G+s++N+++++R+ a+d+deW+++ag + ws+++vl +f+++e+ +a++     d +gv+g+l++ +  +++sp++  +a
  gi|121637207|ref|YP_977430.1|  86 GSSSMNAMMWVRGFASDYDEWAARAGPR-WSYADVLGYFRRIENVTAAWhfvsGDDSGVTGPLHI-S--RQRSPRSvtAA 161
                                    ****************************.*******************9***99***********.4..4445544449* PP

                    GMC_oxred_N 156 llkaaeelGlpvprdlngkhqcGvcllgvtcrtgarqstarawLrpalerpnleiltgakaekiilegrkkravGVeasd 235
                                    +l+aa+e+G++   + n+ +++G+c + vt+r+gar+sta+a+L+pa++r+nl++ltga+a++++++  ++ravGVe+++
  gi|121637207|ref|YP_977430.1| 162 WLAAARECGFA-AARPNSPRPEGFCETVVTQRRGARFSTADAYLKPAMRRKNLRVLTGATATRVVID--GDRAVGVEYQS 238
                                    ***********.999****************************************************..*********** PP

                    GMC_oxred_N 236 kkgtvkrlvvaakevvvaaGalnsPqlLqrSGlGkaehLkevgvdvvvdlp.vGknLqdHpv 296
                                    +++t  r+v+a++evv++aGa+nsPqlL++SG+G+++hL+e+++d+v+++p vG+nL dH+v
  gi|121637207|ref|YP_977430.1| 239 DGQT--RIVYARREVVLCAGAVNSPQLLMLSGIGDRDHLAEHDIDTVYHAPeVGCNLLDHLV 298
                                    ****..******************************************************96 PP

>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.1   9.8e-41   2.2e-37       1     144 []     383     522 ..     383     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 9.8e-41
                                    ----EEEEESTT-TCCEEEEE--TT-SHH..HHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.HCHHCHHCHHC CS
                    GMC_oxred_C   1 PesrGrvtlsssdptgaplidpnylsdpr..dlaalvealkaarkilaaaaldvleeeltpgaaeetsdaavesdealek 78 
                                    P+srG++tl+s+dp+++p+i+p+ylsd    d+aa++++l+ +++i++a +l         g   +++++++ +++ le 
  gi|121637207|ref|YP_977430.1| 383 PQSRGQITLRSADPHAKPVIEPRYLSDLGgvDRAAMMAGLRICARIAQARPL-----RDLLGSIARPRNSTELDEATLEL 457
                                    99************************97666*******************74.....34444444444445555554455 PP

                                    HHHHH-EE-S--B-TT-B-STCGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                    GMC_oxred_C  79 fvkeavltsaHplGtcrMGadpkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                    ++ + ++t +Hp+GtcrMG+d++ sVVD++lrv+gvd+LrV+DaSv+Ps + +++ ++ ++++eka
  gi|121637207|ref|YP_977430.1| 458 ALATCSHTLYHPMGTCRMGSDEA-SVVDPQLRVRGVDGLRVADASVMPSTVRGHTHAPSVLIGEKA 522
                                    5555555************7777.****************************************97 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.3   3.1e-06    0.0069       1     204 [.       6     259 ..       6     277 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                                    EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT...SSGGGSSEEEEESSS..STHHSTH................. CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag...sgaSgrnsgllhsgl..rylpeas................. 55 
                                    d v++G G +G+ +A  L++ +   V+ le+g++      g   + s+l++s +  +yl e +                 
  gi|121637207|ref|YP_977430.1|   6 DYVVVGTGSAGAVVASRLSTDPattVVALEAGPRDKnrfIGVPAAFSKLFRSEIdwDYLTEPQpeldgreiywprgkvlg 85 
                                    89*****************998999*******774455338999999999998887444433367889999999999999 PP

                                    .......HHHHHHHHHHHHHHHHHHHHSSTTSEEE.......EEEEEEES.....SHHHHHH.HHHHHHHHHHTTTTEEE CS
                            DAO  56 .......elarlslealeelreleeelgididyrr.......tGllslaa.....deeelea.ldkllallleagldael 115
                                               +++     ++e++++ g+ + y            +  a+     d++   + l +  +++++  + a +
  gi|121637207|ref|YP_977430.1|  86 gsssmnaM--MWVRGFASDYDEWAARAGPRWSYADvlgyfrrIENVTAAWhfvsgDDSGVTGpLHI-SRQRSPRSVTAAW 162
                                    99987641..34443345555555555665555431000000333333322333222233332322.2222555565678 PP

                                    EEH.HH..HHHHSTTST...TTSEEEEETTEEEEEHHHHHHHHHHH.HHHTT-EEEESECEEEEEEEETCEEEEE.EECT CS
                            DAO 116 lda.ee..vrelepalp...gllgalfypdtgqvdpakltaalara.aealGveilegtevtgleeedgkvwgve.rttp 187
                                    l a +e   ++  p++p   g++  +++   g    +  + a+++  ++++  ++l+g+++t++  ++++++gve +   
  gi|121637207|ref|YP_977430.1| 163 LAAaREcgFAAARPNSPrpeGFCETVVTQRRGA--RFSTADAYLKPaMRRKNLRVLTGATATRVVIDGDRAVGVEyQSD- 239
                                    888433333355565334578888777666443..455556666663788889**********98888999***87332. PP

                                    EEEE...EEEE.EEE--GGGH CS
                            DAO 188 gend...aada.vVnaaGaws 204
                                    g+++   a +  vV++aGa  
  gi|121637207|ref|YP_977430.1| 240 GQTRivyA-RReVVLCAGAVN 259
                                    54432333.446******864 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00027      0.62       2      35 ..       6      44 ..       5      62 .. 0.71
   2 !    5.9   0.0    0.0029       6.6     185     244 ..     200     264 ..     181     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00027
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEE.E....TTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x....xxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlv.e....legtc 35
                                   d+vv+G G AG  +a +l++  a +++  e    +++ +
  gi|121637207|ref|YP_977430.1|  6 DYVVVGTGSAGAVVASRLSTDPATTVVAlEagprDKNRF 44
                                   89******************7666555424455455545 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                                    HHHHHHHHHHHTTEEEEESCEEEEEEETTE...EEEEEETTSCE..EEESEEEE-S-EEES-HHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgnge...klevvledgee..idadlvvvavGvrpstell 244
                                    + a+l+ a+++++ +v +g++++++  +g+    +e++ + +++  ++ + vv+++G   s++ll
  gi|121637207|ref|YP_977430.1| 200 ADAYLKPAMRRKNLRVLTGATATRVVIDGDravGVEYQSDGQTRivYARREVVLCAGAVNSPQLL 264
                                    55677888999999999999999999999876655544444444555556799999998888876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0023       5.1       1      31 [.       6      37 ..       6      42 .. 0.83
   2 !    9.4   0.1   0.00021      0.48     130     204 ..     189     260 ..      92     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0023
                                   SEEEE--SHHHHHHHHHHHHTTT.-EEEEESS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavveke 31
                                   D +V+G+G AG + A +++   + +v+ +e +
  gi|121637207|ref|YP_977430.1|  6 DYVVVGTGSAGAVVASRLSTDPAtTVVALEAG 37
                                   88******************999566666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                                    TT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES.EEEE-----GG CS
                  FAD_binding_2 130 adarr.etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirak.avvlatgGfgr 204
                                     ++rr  ++ t  a l++ +++    ++++++ + a++++++++r++G++ +  ++g+++ + a+  vvl +g+++ 
  gi|121637207|ref|YP_977430.1| 189 VTQRRgARFSTADAYLKPAMRRK---NLRVLTGATATRVVIDGDRAVGVEYQ--SDGQTRIVYARrEVVLCAGAVNS 260
                                    45555566677777777776666...79*************999********..888888888988*******9987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.042       1      35 [.       6      39 ..       6      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                   D vv+G G Ag  +A rl +  p+  vv +ea+p 
  gi|121637207|ref|YP_977430.1|  6 DYVVVGTGSAGAVVASRL-STDPATTVVALEAGPR 39
                                   789***************.999**********996 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001      0.23       1      30 [.       9      39 ..       9      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                   EE--SHHHHHHHHHHHCCTE.EEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdr 30
                                   +vG+G +G+v A++L+ + +  v+ le+++r
  gi|121637207|ref|YP_977430.1|  9 VVGTGSAGAVVASRLSTDPAtTVVALEAGPR 39
                                   8****************96648999999875 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00016      0.35      17      49 ..       4      36 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                   +sD v+vG+Gs+G   a  l+++p   v+ le+
  gi|121637207|ref|YP_977430.1|  4 QSDYVVVGTGSAGAVVASRLSTDPATTVVALEA 36
                                   69*************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3669.39
//
Query:       gi|121637208|ref|YP_977431.1|  [L=591]
Description: periplasmic oligopeptide-binding lipoprotein oppA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-51  173.3   0.5      1e-50  172.8   0.5    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.5   5.7e-55     1e-50      16     375 ..     150     511 ..     138     513 .. 0.86

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 5.7e-55
                                    TTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEESSETT........ CS
                      SBP_bac_5  16 DgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlkkpna........ 87 
                                      +++t+++++++ +sDGtp+t  D++  +  + + d a   as+            vdd++ ++t++kp+a        
  gi|121637208|ref|YP_977431.1| 150 APQVVTYTINPEAVWSDGTPITWRDIASQIHAISGADKAFEIASSSGAERVASVTRGVDDRQAVVTFAKPYAewrgmfag 229
                                    56899****************************************9865555566679**************88876654 PP

                                    TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEET.TTEEEEEE-TTSTTTSCSSSSEEEEEE-.SHHHH CS
                      SBP_bac_5  88 lfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkp.gqkivlernpdYwgggkpkldriefkvipdsdar 166
                                    + + l a + a++       e+ ++++ + +  + GP+++ + ++  q+ivl+rnp +w g +p+ld+i++ v  d++ar
  gi|121637208|ref|YP_977431.1| 230 NGMLLPASMTATP-------EAFNKGQLDGPGPSAGPFVVSALDRtAQRIVLTRNPRWW-GARPRLDSITYLVL-DDAAR 300
                                    3333333333333.......456677777777789*******888567***********.**************.***** PP

                                    HHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT.STGGGSHHHHHHHHHHS-HHHHHHHCTTTSS CS
                      SBP_bac_5 167 aaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtk.kppfddkrvRqAlsyAiDreeivkavlegya 245
                                    + alq++ id     +++++     +kg+ + +++pg++++++++N +   +++dk++R A++  iDr +i++++ +g+ 
  gi|121637208|ref|YP_977431.1| 301 LPALQNNTIDATGVGTLDQLTIAARTKGISI-RRAPGPSWYHFTLNGApGSILADKALRLAIAKGIDRYTIARVAQYGLT 379
                                    *********99999999999999********.****************988************************77777 PP

                                    EEESSSSTTTSTTCCSCHCCCSHH..SHHHHHHHHHHHTT-BCSSTSCEETC..EEEEEEEEETTSHHHHHHHHHHHHHH CS
                      SBP_bac_5 246 tpansllppsspgadeeykpayka..ydpekAkklLkeaGykdgdggglrek..klkltlllasgspaekaiaeliqqql 321
                                         l  +++ + ++ y++++    y+pe+Ak+ L++ G+  +++  +rek  +++++  l ++ +  ++ a++ q +l
  gi|121637208|ref|YP_977431.1| 380 SDPVPLNNHVFVAGQDGYQDNSGVvaYNPEQAKRELDALGWRRSGA--FREKdgRQLVIRDLFYDAQSTRQFAQIAQHTL 457
                                    66666666777777777766554488*****************975..5555687777778888888889********** PP

                                    HHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCT CS
                      SBP_bac_5 322 kkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssga 375
                                    ++iG+k+e+++ + +  + ++v+ g fd++++gw +d ++ ++ ++ + s++++
  gi|121637208|ref|YP_977431.1| 458 AQIGVKLELQAKSGSGFFSDYVNVGAFDIAQFGWVGDAFPLSSLTQIYASDGES 511
                                    ************98899999******************9999999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4693.01
//
Query:       gi|121637209|ref|YP_977432.1|  [L=612]
Description: oligopeptide-transport ATP-binding protein ABC transporter oppD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-58  194.7   0.0    6.6e-30  104.4   0.0    2.2  2  ABC_tran         ABC transporter
    2.9e-23   82.1   0.0    1.4e-14   54.3   0.0    2.4  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    3.9e-13   49.9   2.5    0.00013   21.9   0.0    4.0  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.6e-08   34.3   0.4     0.0013   18.2   0.0    3.5  2  SMC_N            RecF/RecN/SMC N terminal domain
    3.9e-07   30.4   0.1     0.0054   17.0   0.0    3.0  2  AAA_22           AAA domain
    1.2e-06   28.2   0.1      0.019   14.7   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    6.1e-06   26.7   2.1     0.0063   16.9   0.0    2.9  3  AAA_16           AAA ATPase domain
    9.3e-05   22.6   0.2       0.59   10.3   0.2    2.7  2  AAA_33           AAA domain
    0.00027   20.9   0.0       0.24   11.3   0.0    2.4  2  NACHT            NACHT domain
    0.00095   19.1   0.2       0.31   10.9   0.1    2.3  2  RsgA_GTPase      RsgA GTPase
    0.00099   18.9   0.0      0.044   13.5   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0013   18.8   0.2       0.58   10.3   0.0    3.2  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0037   16.6   0.6        2.4    7.4   0.1    2.3  2  Zeta_toxin       Zeta toxin
     0.0063   16.1   0.1        1.7    8.1   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
     0.0065   15.6   0.1      0.065   12.3   0.1    2.1  2  T2SSE            Type II/IV secretion system protein
     0.0091   15.4   0.2        0.3   10.4   0.1    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.01   15.6   5.0       0.16   11.7   0.0    2.9  2  AAA_30           AAA domain
      0.011   15.1   0.1       0.54    9.6   0.0    2.7  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.014   15.8   0.1         13    6.2   0.1    3.6  2  AAA              ATPase family associated with various cellul
      0.016   14.8   1.0          2    7.9   0.0    3.2  3  AAA_25           AAA domain
      0.017   15.2   2.5      0.085   12.9   0.2    2.2  2  DUF87            Helicase HerA, central domain
      0.025   14.6   0.6          9    6.3   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
      0.048   12.7   0.3        4.6    6.1   0.1    2.4  2  DUF3987          Protein of unknown function (DUF3987)
      0.051   12.9   1.1        2.5    7.4   0.1    2.2  2  AIG1             AIG1 family
      0.059   13.9   0.0        2.3    8.6   0.0    2.1  2  AAA_23           AAA domain
      0.072   12.8   1.5         20    4.8   0.0    3.4  4  Sigma54_activat  Sigma-54 interaction domain
       0.11   12.2   0.2        2.3    7.9   0.0    2.2  2  AAA_24           AAA domain
       0.11   11.6   0.2        4.4    6.4   0.0    2.1  2  NB-ARC           NB-ARC domain
       0.13   12.6   0.1         13    6.2   0.0    2.4  2  RNA_helicase     RNA helicase
       0.13   12.6   0.2        4.6    7.6   0.0    2.5  2  AAA_19           AAA domain
       0.18   10.7   0.3       0.72    8.7   0.1    1.9  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0   1.1e-27   6.1e-25       2     136 ..      25     182 ..      24     183 .. 0.92
   2 !  104.4   0.0   1.1e-32   6.6e-30       2     136 ..     378     527 ..     377     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.1e-27
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pqlfp 72 
                                    + +s  +++ge+va+vGe+G+GKS  ++++ gll       G+++l+g++l         ++  k ig+++q+  + l p
  gi|121637209|ref|YP_977432.1|  25 RGISYRVEPGEVVAMVGESGSGKSAAAMAVVGLLPEyaqVRGSVRLQGTELLGladnAMSRFRGKAIGTVFQDpmSALTP 104
                                    57999**************************9987766699**********99999788888999********9999*** PP

                                    TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +tv+++               ++++++ ++l+ +g+++ ++++ +  p++LSgG++qrv++a a++++p+ll++DEpt
  gi|121637209|ref|YP_977432.1| 105 VYTVGDQiaeaievhqprvgkkAARRRAVELLDLVGISQ-PQRRSRAFPHELSGGERQRVVIAIAIANDPDLLICDEPT 182
                                    *******************98888888999999999999.777878999*****************************9 PP

  == domain 2  score: 104.4 bits;  conditional E-value: 1.1e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                    + +sl+l++g++++ivGe+G+GKSt l  +++l  p++G+i++ g+d+ +    e++slr+ i+v++q+  ++l+p+l v
  gi|121637209|ref|YP_977432.1| 378 DGISLELRQGRTLGIVGESGSGKSTTLHEILELAAPQSGSIEVLGTDVATlgtAERRSLRRDIQVVFQDpvASLDPRLPV 457
                                    789*************************************************9****************9999******* PP

                                    HHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +            ++e  +++++ l++++l++  +++ p+++SgGqkqr+ +aral+ +pk+l lDEp 
  gi|121637209|ref|YP_977432.1| 458 FDLiaeplqangfGKNETHARVAELLDIVGLRHGDASRYPAEFSGGQKQRIGIARALALQPKILALDEPV 527
                                    *99**********555555555666666666666666779*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   2.4e-17   1.4e-14       1      65 []     234     299 ..     234     299 .. 0.98
   2 !   25.6   0.0   2.3e-08   1.3e-05       1      33 [.     579     611 ..     579     612 .] 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.4e-17
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE + +++l ++ + PYT +Ll svprld+ +  +l+ i+g +psl  l  GCpFapRCp + +eC
  gi|121637209|ref|YP_977432.1| 234 VESAGVNDLYRDRRMPYTVGLLGSVPRLDAAQGtRLVPIPGAPPSLAGLAPGCPFAPRCPLVIDEC 299
                                    8999***************************999******************************** PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.3e-08
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd 33 
                                    vE+g+s+++f +p+H YT+ Ll +vp++d+ ++
  gi|121637209|ref|YP_977432.1| 579 VEQGDSEEVFGNPKHEYTRRLLGAVPQPDPARR 611
                                    8***************************99876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.4   2.3e+02       2      22 ..      37      57 ..      36      82 .. 0.84
   2 !   21.9   0.0   2.3e-07   0.00013     235     302 ..     153     218 ..     114     219 .. 0.88
   3 ?    2.6   0.1      0.17        99       3      16 ..     391     404 ..     390     430 .. 0.86
   4 !   20.7   0.1   5.2e-07    0.0003     228     302 ..     491     563 ..     473     564 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.4
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    +++G  gsGKS    a  +l
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAMAVVGL 57
                                   679*********988877766 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.3e-07
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    +elS G ++   ++ a++ a+++ +ll+ DEp + L+  +++ +l++lk++++ +ga v++ TH+  ++
  gi|121637209|ref|YP_977432.1| 153 HELSGGERQR--VVIAIAIANDP-DLLICDEPTTALDVTVQAQILDVLKAARDvTGAGVLIITHDLGVV 218
                                    4667777776..77788888888.*****************************************8876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                         AAA_21   3 vliGpNgsGKSnLL 16 
                                    +++G  gsGKS+ L
  gi|121637209|ref|YP_977432.1| 391 GIVGESGSGKSTTL 404
                                    69*********976 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 5.2e-07
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                    ++  + ++e+S G+k+ ++++ al+ ++   ++l++DEp + L+ ++++ ++ ll ++ ++ g   ++++H+ +++
  gi|121637209|ref|YP_977432.1| 491 GDASRYPAEFSGGQKQRIGIARALALQP---KILALDEPVSALDVSIQAGIINLLlDLQEQFGLSYLFVSHDLSVV 563
                                    666778899********99999999988...9********************9995666669*********98875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-06    0.0013      26     208 ..      36     225 ..      27     235 .. 0.76
   2 !   10.8   0.1   0.00042      0.24      28     211 ..     391     572 ..     375     580 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TT..TTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersa..kklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                    + a+vG+ GSGKs    A+  +L e ++   ++r + + +l+    ++ ++     +  +f+++ ++    ++ +++  +
  gi|121637209|ref|YP_977432.1|  36 VVAMVGESGSGKSAAAMAVVGLLPEYAQvrGSVRLQGT-ELLGLaDNAMSRFRGKAIGTVFQDPMSA---LTPVYTVGDQ 111
                                    67899**************9999864331113333333.3333324455555555677778888777...6778899999 PP

                                    EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                    + +  e +    gk++ ++   ell  +gis+          +LSgGe++ v +a+ +A    +   l + De   aLD 
  gi|121637209|ref|YP_977432.1| 112 IAEAIEVHQPRVGKKAARRRAVELLDLVGISQPqrrsrafphELSGGERQRVVIAIAIA----NDPDLLICDEPTTALDV 187
                                    99988877777888888889999*******998899999999*******9877776554....55669999********* PP

                                    HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxx RF
                          SMC_N 174 knvkkvaellkekskn..aQfivislreemleka.dkl 208
                                    +  +++ ++lk++++   a +++i+++ +++++  d+ 
  gi|121637209|ref|YP_977432.1| 188 TVQAQILDVLKAARDVtgAGVLIITHDLGVVAEFaDRA 225
                                    ***********887654589******998876642554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                                    EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkg 107
                                     ivG+ GSGKs  l  i   L   ++ ++    ++       +++++ + +++++f+++ ++l  + + + +  +  + +
  gi|121637209|ref|YP_977432.1| 391 GIVGESGSGKSTTLHEI-LELAAPQSGSIEVLGTDVATL-GTAERRSLRRDIQVVFQDPVASLDPRLPVFDLIAEPLQAN 468
                                    69999999999999999.455555555666655444444.4778888899999999999998555555555444444444 PP

                                    EEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 108 eseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                       +   gk+ t + v+ell  +g+          ++SgG+k+ + +a  +A+q      +  lDe  +aLD +  + + 
  gi|121637209|ref|YP_977432.1| 469 G--F---GKNETHARVAELLDIVGLRHGdasrypaEFSGGQKQRIGIARALALQPK----ILALDEPVSALDVSIQAGII 539
                                    4..3...55666666666666666665556666669**************999854....7899*********9999999 PP

                                    HHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 181 ellkekskn..aQfivislreemlekadklvgv 211
                                    +ll   +++    ++ +s++  ++++  + v v
  gi|121637209|ref|YP_977432.1| 540 NLLLDLQEQfgLSYLFVSHDLSVVKHLAHQVAV 572
                                    999888877445678888887777777666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0014      0.78       7      38 ..      36      82 ..      31     215 .. 0.69
   2 !   17.0   0.0   9.4e-06    0.0054       7      70 ..     389     450 ..     384     562 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee...............e 38
                                   +++ +GesG+GK+  +  ++  l+e+a+ +                +
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGLLPEYAQVRGsvrlqgtellgladnA 82
                                   67789***************999999887776666555555555550 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 9.4e-06
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka 70 
                                     l ++GesG+GK+t+l ++le +  ++     + ev+  +++ ++  ++++l+r++   ++++  +
  gi|121637209|ref|YP_977432.1| 389 TLGIVGESGSGKSTTLHEILELAAPQS----GSIEVLGTDVATLGtaERRSLRRDIQVVFQDPVAS 450
                                    56699****************985433....46666666666555567777777777777766666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00052       0.3      17      38 ..      29      50 ..      23      63 .. 0.79
   2 !   14.7   0.1   3.2e-05     0.019      17      49 ..     382     414 ..     375     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                         AAA_29 17 ieidlkgatlltGpsGsGKSTl 38
                                   +++++ +++ ++G+sGsGKS+ 
  gi|121637209|ref|YP_977432.1| 29 YRVEPGEVVAMVGESGSGKSAA 50
                                   567777899***********86 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-05
                         AAA_29  17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                    +e++ +g +  ++G+sGsGKST l  i  l  p+
  gi|121637209|ref|YP_977432.1| 382 LELR-QGrTLGIVGESGSGKSTTLHEILELAAPQ 414
                                    5565.454667***********987766666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.4    0.0049       2.8      22      51 ..      34      60 ..      21     211 .. 0.68
   2 ?   -1.3   0.0       4.3   2.5e+03      84     116 ..     176     208 ..     145     230 .. 0.73
   3 !   16.9   0.0   1.1e-05    0.0063      20      52 ..     385     422 ..     369     542 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0049
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                   g  e+v  +GesG+GKs+ + ++   l  +
  gi|121637209|ref|YP_977432.1| 34 G--EVVAMVGESGSGKSAAAMAVV-GLLPE 60
                                   3..78999**********998776.34444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.3
                         AAA_16  84 qlldeaesaeleawrekleealaavpelagaea 116
                                     ++de+++a+    +++++++l+a+++++ga+ 
  gi|121637209|ref|YP_977432.1| 176 LICDEPTTALDVTVQAQILDVLKAARDVTGAGV 208
                                    577788888888888888888888888888765 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.1e-05
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd.......g 52 
                                    r+g  + + ++GesG+GKs+ + e+l+ +  +       g
  gi|121637209|ref|YP_977432.1| 385 RQG--RTLGIVGESGSGKSTTLHEILELAAPQsgsievlG 422
                                    444..66889****************86666633332220 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2     0.001      0.59       1      28 [.      36      64 ..      36     164 .. 0.84
   2 !    9.7   0.0    0.0016       0.9       4      33 ..     392     426 ..     390     466 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg.avll 28
                                   +v +vG +GsGKs  a  ++  l+ +  +
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGLLPeYAQV 64
                                   799*************9998777765444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                         AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdtl 33 
                                    +vG +GsGKst ++++l+  +      ++l +d++
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILELAApqsgsIEVLGTDVA 426
                                    59*************97443366789999999984 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0074       4.3       2      23 ..      36      57 ..      35      68 .. 0.85
   2 !   11.3   0.0   0.00041      0.24       1      25 [.     388     412 ..     388     462 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0074
                                   CEEEEC-TTTCHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                   +v++ Ge+GsGK++ +  ++ +
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGL 57
                                   799***********99988765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00041
                                    SCEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   1 rlvilqGeaGsGKTtLlqklalawa 25 
                                    r++ + Ge+GsGK+t l+++ +++a
  gi|121637209|ref|YP_977432.1| 388 RTLGIVGESGSGKSTTLHEILELAA 412
                                    67889***************98776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.021        12      99     114 ..      33      49 ..       9      69 .. 0.81
   2 !   10.9   0.1   0.00054      0.31      84     121 ..     371     409 ..     345     422 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                                    T.SEEEEECSTTSSHHH CS
                    RsgA_GTPase  99 d.ktsvlvGqSGvGKSt 114
                                      +++++vG+SG GKS+
  gi|121637209|ref|YP_977432.1|  33 PgEVVAMVGESGSGKSA 49 
                                    44899***********7 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00054
                                    TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                      + ++++ ++ +l++ +t  +vG+SG GKSt + ++l+
  gi|121637209|ref|YP_977432.1| 371 IGEVRAVDGISLELRQgRTLGIVGESGSGKSTTLHEILE 409
                                    55566777888888887999************9988876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.11        66       1      23 [.      36      58 ..      36      84 .. 0.83
   2 !   13.5   0.0   7.6e-05     0.044       2      84 ..     390     471 ..     389     478 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                            PRK  1 vIgvagsSGaGkttvarklekif 23
                                   v+++ g+SG+Gk++ a +++ ++
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGLL 58
                                   68999********9998877666 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-05
                            PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlkel 81 
                                    +g+ g+SG+Gk+t+ +++ ++ +  +  + e+ g+ + +l  ae +   ++ +  ++  v  l+p+   fdl+ e l++ 
  gi|121637209|ref|YP_977432.1| 390 LGIVGESGSGKSTTLHEILELAA-PQSGSIEVLGTDVATLGTAERRSLRRDIQVVFQDPVASLDPRLPVFDLIAEPLQAN 468
                                    59****************99888.7777799999999**********************************999888776 PP

                            PRK  82 keg 84 
                                    + g
  gi|121637209|ref|YP_977432.1| 469 GFG 471
                                    655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.064        37       2      55 ..      37     140 ..      36     210 .. 0.55
   2 !   10.3   0.0     0.001      0.58       2      56 ..     390     488 ..     389     548 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.064
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.................................. 47 
                                    va vG + +GKS    a +g   + ++  g  r   ++ + l ++                                   
  gi|121637209|ref|YP_977432.1|  37 VAMVGESGSGKSAAAMAVVGLLPEYAQVRGSVRLQGTELLGLADNAmsrfrgkaigtvfqdpmsaltpvytvgdqiaeai 116
                                    78888888888888777776444444444433333333333222112233333333333333334444444444444444 PP

                                    ................EEEEECGG CS
                       MMR_HSR1  48 ................ielvDtpG 55 
                                                    +el+D++G
  gi|121637209|ref|YP_977432.1| 117 evhqprvgkkaarrraVELLDLVG 140
                                    444444444444444466666666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                                    EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEEETTEE............................ CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvklkgke............................ 47 
                                     +ivG + +GKSt +  +++     +   +v  +  +T+ + e+r   ++ +                            
  gi|121637209|ref|YP_977432.1| 390 LGIVGESGSGKSTTLHEILElaapqSgSIEVLGTDVATLGTAERRSLRRDIQvvfqdpvasldprlpvfdliaeplqang 469
                                    68****************98443322234555555555555555443232334555555555556666666666666666 PP

                                    ..........EEEEECGGC CS
                       MMR_HSR1  48 ..........ielvDtpGl 56 
                                               el+D++Gl
  gi|121637209|ref|YP_977432.1| 470 fgknetharvAELLDIVGL 488
                                    6666666666666666665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0045       2.6      18      53 ..      36      74 ..      27     103 .. 0.79
   2 !    7.4   0.1    0.0042       2.4      21      53 ..     392     424 ..     386     428 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                     Zeta_toxin 18 lillgGqpGAGKselaellkdele...rqgnvvrldpDd 53
                                   ++ ++G +G+GKs++a ++   l    + ++ vrl++++
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGLLPeyaQVRGSVRLQGTE 74
                                   789*************99887766444556667766665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0042
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                    ++G +G+GKs++++++ +  ++q++ +++ ++d
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILELAAPQSGSIEVLGTD 424
                                    689************999988888888876655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.017        10      33      58 ..      34      59 ..      26      89 .. 0.84
   2 !    8.1   0.0     0.003       1.7      29      57 ..     383     411 ..     372     427 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                          AAA_7 33 kkpvllvGptGtGKtviikdllkkld 58
                                   +  v +vG++G+GK++ ++ ++  l+
  gi|121637209|ref|YP_977432.1| 34 GEVVAMVGESGSGKSAAAMAVVGLLP 59
                                   667899**********9988776666 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                          AAA_7  29 llknkkpvllvGptGtGKtviikdllkkl 57 
                                     l++++ + +vG++G+GK+++++++l+  
  gi|121637209|ref|YP_977432.1| 383 ELRQGRTLGIVGESGSGKSTTLHEILELA 411
                                    578889999**************988755 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.38   2.2e+02     131     156 ..      36      61 ..       7      65 .. 0.84
   2 !   12.3   0.1   0.00011     0.065      69     156 ..     323     414 ..     308     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.38
                          T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                    ++ + G  gsGK+  + a++  ++++
  gi|121637209|ref|YP_977432.1|  36 VVAMVGESGSGKSAAAMAVVGLLPEY 61 
                                    55677999************999987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                          T2SSE  69 qdarlpekgvrlrvvllPvvag.ealviR.kksakeltlddlgaeealkekiaev..lrkavrerglilvsGgTgsGKtt 144
                                    + +r   + +r++  + P++ g  ++v+R ++ +k ++l++ ++ ++   ++++v  ++  +r+  ++ + G  gsGK+t
  gi|121637209|ref|YP_977432.1| 323 VTGRSAADIYRVKTEARPAALGdASVVVRvRHLVKTYRLAKGVVLRRAIGEVRAVdgISLELRQGRTLGIVGESGSGKST 402
                                    5555557889***********9889****888888999998877777766666544488888888999999********* PP

                          T2SSE 145 llyallkeinks 156
                                    +l  +l+  + +
  gi|121637209|ref|YP_977432.1| 403 TLHEILELAAPQ 414
                                    ***999887665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.12        71      42      59 ..      37      54 ..      24      62 .. 0.83
   2 !   10.4   0.1   0.00052       0.3      42      64 ..     390     412 ..     354     431 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                                   EEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE 42 llvaGatgsGKStalntL 59
                                   +  +G +gsGKS a ++ 
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAMAV 54
                                   5679********998875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00052
                                    EEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  42 llvaGatgsGKStalntLilSla 64 
                                    l ++G +gsGKSt+l+ ++  +a
  gi|121637209|ref|YP_977432.1| 390 LGIVGESGSGKSTTLHEILELAA 412
                                    459*************9875555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.8      0.18     1e+02      18      45 ..      34      61 ..      27     214 .. 0.78
   2 ?   11.7   0.0   0.00028      0.16      19      52 ..     388     421 ..     381     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.18
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                     v++++G  G+GK+ a  a++ ++ + 
  gi|121637209|ref|YP_977432.1| 34 GEVVAMVGESGSGKSAAAMAVVGLLPEY 61
                                   468999*********9988888776655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00028
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvigl 52 
                                    r+  ++G  G+GK+t+l ++ e+++ + g++ +l
  gi|121637209|ref|YP_977432.1| 388 RTLGIVGESGSGKSTTLHEILELAAPQSGSIEVL 421
                                    46789***************99998885555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00094      0.54      25      51 ..      37      63 ..      24     109 .. 0.91
   2 ?   -2.5   0.0       4.8   2.8e+03       4      33 ..     154     183 ..     153     197 .. 0.82
   3 ?    2.3   0.0      0.16        92      22      51 ..     387     416 ..     367     448 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplse 51
                                   + +vG +GsGK+  a ++ +llp+  +
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAMAVVGLLPEYAQ 63
                                   679********************9765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.8
                   Mg_chelatase   4 dvkGqeeakraleiaaaGgHnlllvGppGs 33 
                                    ++ G e+++ ++ ia+a   +ll++  p +
  gi|121637209|ref|YP_977432.1| 154 ELSGGERQRVVIAIAIANDPDLLICDEPTT 183
                                    5679999999999**999999999887765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.16
                   Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplse 51 
                                    g  l +vG +GsGK+   + + +l +p s 
  gi|121637209|ref|YP_977432.1| 387 GRTLGIVGESGSGKSTTLHEILELAAPQSG 416
                                    5667799*******9988888877766553 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.022        13       2      35 ..      38      76 ..      37     184 .. 0.60
   2 ?    4.3   0.0     0.088        51       3      37 ..     392     431 ..     390     531 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                                   EEESSTTSSHHHHHHHHHHHH....T.HEEEEEETTTCS CS
                            AAA  2 llyGppGtGKTllakavakel....g.vefleisgsell 35
                                    ++G  G GK+++a av+  l    + +  ++++g+ell
  gi|121637209|ref|YP_977432.1| 38 AMVGESGSGKSAAAMAVVGLLpeyaQvRGSVRLQGTELL 76
                                   57899************9997443322335777777776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.088
                                    EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS CS
                            AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk 37 
                                    ++G  G GK+++ + + + +     ++e+l +++++l   
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILELAapqsgSIEVLGTDVATLGTA 431
                                    6899***********9998755333344444444444433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0035         2      17      53 ..      19      54 ..       3      59 .. 0.77
   2 ?    0.9   0.1      0.49   2.8e+02      95     188 ..     125     213 ..      83     214 .. 0.65
   3 ?    2.3   0.0      0.19   1.1e+02      33      58 ..     387     411 ..     376     490 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                         AAA_25 17 apppprrwlvkgllpagelallaGapgtGKttlaldl 53
                                    p + +r +  ++   ge+++ +G +g+GK+++a+ +
  gi|121637209|ref|YP_977432.1| 19 DPVTAVRGISYRV-EPGEVVAMVGESGSGKSAAAMAV 54
                                   5556666666666.67****************99865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.49
                         AAA_25  95 ealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalveale 173
                                    +++++++ + +ldl+g  ++ + ++  + ++l  ++ +++  ai  +++++l++ D  + al+   +     +++++ l+
  gi|121637209|ref|YP_977432.1| 125 KKAARRRAVELLDLVGIsQPQR-RSRAFPHELSGGERQRVVIAIAIANDPDLLICDEPTTALDVTVQ-----AQILDVLK 198
                                    5555555555666655533333.34455555555555555555555577788887777777766655.....56666666 PP

                         AAA_25 174 riarrtgaavllvhH 188
                                      ++ tga vl++ H
  gi|121637209|ref|YP_977432.1| 199 AARDVTGAGVLIITH 213
                                    666668888888888 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                         AAA_25  33 gelallaGapgtGKttlaldlalava 58 
                                    g +  ++G +g+GK+t + ++ l++a
  gi|121637209|ref|YP_977432.1| 387 GRTLGIVGESGSGKSTTL-HEILELA 411
                                    5566689********954.4444444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.37   2.2e+02      26      40 ..      37      51 ..      35      58 .. 0.86
   2 ?   12.9   0.2   0.00015     0.085      24      48 ..     388     412 ..     370     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.37
                          DUF87 26 lAilgsTGsGKSntv 40
                                   +A +g++GsGKS  +
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAA 51
                                   6889********865 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                          DUF87  24 rHlAilgsTGsGKSntvavLleell 48 
                                    r l+i+g++GsGKS+t   +le ++
  gi|121637209|ref|YP_977432.1| 388 RTLGIVGESGSGKSTTLHEILELAA 412
                                    779**************99998766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.026        15       2      23 ..      37      58 ..      36      78 .. 0.85
   2 ?    6.3   0.0     0.016         9       4      24 ..     392     414 ..     390     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   v +vG++G+gKs  a+ +  +l
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAMAVVGLL 58
                                   569************9988777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                                    EE--SSSSHHHHHHHGGGGB..S CS
                          AAA_5   4 LvGppGtgKselaerlaaal..n 24 
                                    +vG++G+gKs+   +++++   +
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILELAapQ 414
                                    69**************9997744 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.008       4.6      38      64 ..      36      62 ..      22      66 .. 0.82
   2 ?    4.0   0.0     0.037        21      41      60 ..     392     411 ..     389     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.008
                        DUF3987 38 ytlvvapsGerKSpvdklvlrpleeie 64
                                    ++ v++sG++KS+++ +v+ +l e+ 
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAVVGLLPEYA 62
                                   5789************99998887765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.037
                        DUF3987  41 vvapsGerKSpvdklvlrpl 60 
                                    +v++sG++KS+++  +l+++
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILELA 411
                                    8***********99998876 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.039        23       4      22 ..      38      56 ..      35      58 .. 0.85
   2 ?    7.4   0.1    0.0044       2.5       3      29 ..     390     416 ..     388     443 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                                   EEESSTTSSHHHHHHHHHT CS
                           AIG1  4 vlvGktgnGkSaTgNsilg 22
                                    +vG +g+GkSa++ +++g
  gi|121637209|ref|YP_977432.1| 38 AMVGESGSGKSAAAMAVVG 56
                                   58**********9987766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0044
                                    EEEESSTTSSHHHHHHHHHTS--SS-- CS
                           AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesk 29 
                                    + +vG +g+GkS+T   il+  a +s 
  gi|121637209|ref|YP_977432.1| 390 LGIVGESGSGKSTTLHEILELAAPQSG 416
                                    568***************998776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.24   1.4e+02      22      39 ..      37      54 ..      32      72 .. 0.85
   2 ?    8.6   0.0     0.004       2.3      22      36 ..     390     404 ..     371     412 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.24
                         AAA_23 22 tlItGpNGaGKTTildAi 39
                                   ++ +G+ G+GK++   A+
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAMAV 54
                                   6789********987775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.004
                         AAA_23  22 tlItGpNGaGKTTil 36 
                                      I+G+ G+GK+T l
  gi|121637209|ref|YP_977432.1| 390 LGIVGESGSGKSTTL 404
                                    36***********88 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.035        20      24      42 ..      36      54 ..      21      65 .. 0.82
   2 ?   -3.1   0.0       9.3   5.4e+03     103     119 ..     183     199 ..     169     202 .. 0.78
   3 ?    4.0   0.0     0.062        36      24      47 ..     389     412 ..     373     426 .. 0.78
   4 ?    0.1   0.0      0.96   5.5e+02      78     117 ..     500     542 ..     496     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.035
                                   -EEEECSTTSSHHHHHHHH CS
                Sigma54_activat 24 svlitGesGtGKellarai 42
                                    v ++GesG+GK+  a a+
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAAMAV 54
                                   57899********999876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.3
                                    GGS-HHHHHHHHHHHHH CS
                Sigma54_activat 103 gelplelQekLlrvlqe 119
                                    + l++++Q+++l vl+ 
  gi|121637209|ref|YP_977432.1| 183 TALDVTVQAQILDVLKA 199
                                    578999******99975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.062
                                    -EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  24 svlitGesGtGKellaraiheask 47 
                                    ++ i+GesG+GK++  + i e   
  gi|121637209|ref|YP_977432.1| 389 TLGIVGESGSGKSTTLHEILELAA 412
                                    56699********99888877655 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.96
                                    STTTSS-BEHHHHH..TTTSEEEEET.GGGS-HHHHHHHHHHH CS
                Sigma54_activat  78 FtGAekekkGlfek..adgGtlfLDe.igelplelQekLlrvl 117
                                    F+G +k++ G  ++   +  +l LDe ++ l++++Q+ ++++l
  gi|121637209|ref|YP_977432.1| 500 FSGGQKQRIGIARAlaLQPKILALDEpVSALDVSIQAGIINLL 542
                                    8999999999877521467899***99999******9888766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.25   1.4e+02       4      19 ..      36      51 ..      34      61 .. 0.85
   2 ?    7.9   0.0    0.0039       2.3       4      22 ..     389     407 ..     386     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                         AAA_24  4 kiliyGpsgiGKTtla 19
                                    ++++G+sg+GK+  a
  gi|121637209|ref|YP_977432.1| 36 VVAMVGESGSGKSAAA 51
                                   57899********876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0039
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     + i+G+sg+GK+t++ e+
  gi|121637209|ref|YP_977432.1| 389 TLGIVGESGSGKSTTLHEI 407
                                    6789***********9987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.089        51      18      40 ..      33      54 ..      23      63 .. 0.84
   2 ?    6.4   0.0    0.0076       4.4      22      42 ..     389     409 ..     375     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.089
                                   SCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 18 lqslvvalvGmgGvGKttlakqi 40
                                   ++  vva+vG  G+GK+  a  +
  gi|121637209|ref|YP_977432.1| 33 PG-EVVAMVGESGSGKSAAAMAV 54
                                   55.69************877665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0076
                                    EEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqiln 42 
                                     +++vG  G+GK+t +++il+
  gi|121637209|ref|YP_977432.1| 389 TLGIVGESGSGKSTTLHEILE 409
                                    689***********9999975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.11        62       2      17 ..      38      53 ..      37      68 .. 0.85
   2 ?    6.2   0.0     0.023        13       3      20 ..     392     409 ..     390     425 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                   RNA_helicase  2 wlyGpsgeGKStlake 17
                                    ++G+sg GKS +a  
  gi|121637209|ref|YP_977432.1| 38 AMVGESGSGKSAAAMA 53
                                   589*********9987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.023
                   RNA_helicase   3 lyGpsgeGKStlakeLak 20 
                                    ++G+sg GKSt+ +e+ +
  gi|121637209|ref|YP_977432.1| 392 IVGESGSGKSTTLHEILE 409
                                    78**********999654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.32   1.8e+02      10      41 ..      34      65 ..      28     204 .. 0.77
   2 ?    7.6   0.0    0.0079       4.6       9      36 ..     386     413 ..     380     485 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.32
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvk 41
                                    +v+++++  G+GK+   +++v ll e  +v 
  gi|121637209|ref|YP_977432.1| 34 GEVVAMVGESGSGKSAAAMAVVGLLPEYAQVR 65
                                   578999999******99999998887776664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0079
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallve 36 
                                    + ++l +++  G+GK+++l++i++l+  
  gi|121637209|ref|YP_977432.1| 386 QGRTLGIVGESGSGKSTTLHEILELAAP 413
                                    5678999***************998764 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.83   4.8e+02      18      33 ..      37      52 ..      22      60 .. 0.77
   2 ?    8.7   0.1    0.0012      0.72       4      40 ..     377     412 ..     374     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.83
                  TrwB_AAD_bind 18 ilivGttGsGKtqale 33
                                   +++vG  GsGK+ a+ 
  gi|121637209|ref|YP_977432.1| 37 VAMVGESGSGKSAAAM 52
                                   689*********9875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                  TrwB_AAD_bind   4 iagvplpkeretqhilivGttGsGKtqalekllrair 40 
                                    ++g++l+ ++  + + ivG  GsGK+++l+++l+ + 
  gi|121637209|ref|YP_977432.1| 377 VDGISLELRQ-GRTLGIVGESGSGKSTTLHEILELAA 412
                                    6677776654.56789****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 4311.47
//
Query:       gi|121637210|ref|YP_977433.1|  [L=291]
Description: oligopeptide-transport integral membrane protein ABC transporter oppC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-23   81.2  13.3    7.6e-23   81.2  13.3    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
    9.1e-09   35.2   1.8    9.1e-09   35.2   1.8    3.4  4  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
      0.034   13.1  19.6      0.027   13.4  11.3    2.6  2  MFS_1         Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.5       0.3   1.8e+03     133     168 ..      56      94 ..      15      98 .. 0.48
   2 !   81.2  13.3   1.3e-26   7.6e-23       3     182 ..     101     282 ..      99     285 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                   BPD_transp_1 133 swpGlgtllleailgydyseis...nggvlalviavlll 168
                                    + pG   +l +  lg+d+ + +   +  +  ++++v+++
  gi|121637210|ref|YP_977433.1|  56 QPPGTKHWLGTNALGQDLLAQTlrgMQKSMLIGVCVAVI 94 
                                    233333333333333333333355545555555555554 PP

  == domain 2  score: 81.2 bits;  conditional E-value: 1.3e-26
                   BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                    ++G++++ +++++ d+ l++++++ll +Psf+l+ +++      +   + ++ v++l+ +++++  r++r + ++ ++++
  gi|121637210|ref|YP_977433.1| 101 TVGAISG-YFGGWRDRTLMWVVDLLLVVPSFILIAIVT---PRTKNSANIMFLVLLLAGFGWMISSRMVRGMTMSLRERE 176
                                    78*****.************************999999...444555555566*************************** PP

                   BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis........ 154
                                    +++aar +G+s ++i++ +v+Pn+++ +i  ++l++++++ + + l+flg    +g +  +++lg  ++ ++        
  gi|121637210|ref|YP_977433.1| 177 FIRAARYMGVSSRRIIVGHVVPNVASILIIDAALNVAAAILAETGLSFLG----FGIQPPDVSLGTLIADGTasatafpw 252
                                    **************************************************....***************9999*****99 PP

                   BPD_transp_1 155 ..nggvlalviavlllnlvadilqrlldpr 182
                                       +++ +lv++++  nl  d l ++ldp 
  gi|121637210|ref|YP_977433.1| 253 vfLFPASILVLILVCANLTGDGLRDALDPA 282
                                    99**************************97 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   1.8   1.5e-12   9.1e-09       6      51 .]      11      58 ..       6      58 .. 0.85
   2 ?   -3.8   0.3       2.2   1.3e+04      15      24 ..      91     100 ..      86     108 .. 0.59
   3 ?   -2.5   2.4      0.88   5.3e+03      27      36 ..     131     140 ..     123     162 .. 0.66
   4 ?   -1.8   0.2      0.52   3.1e+03      22      30 ..     260     268 ..     258     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.5e-12
                         OppC_N  6 awrrFkrNklAvvglvilllllliaifaPliaPydpqdliqn..llpP 51
                                   + rrF+rN++Av++l+ llll++ a   P + Py++ dl+ n  l+pP
  gi|121637210|ref|YP_977433.1| 11 VVRRFLRNRAAVASLAALLLLFVSAYALPPLLPYSYDDLDFNalLQPP 58
                                   78********************9998889999***9677634469999 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                         OppC_N  15 lAvvglvill 24 
                                    +Av++  i +
  gi|121637210|ref|YP_977433.1|  91 VAVISTGIAA 100
                                    3555555544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.88
                         OppC_N  27 lliaifaPli 36 
                                    +liai+ P  
  gi|121637210|ref|YP_977433.1| 131 ILIAIVTPRT 140
                                    5666665544 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.52
                         OppC_N  22 illllllia 30 
                                    il+l+l++a
  gi|121637210|ref|YP_977433.1| 260 ILVLILVCA 268
                                    666676665 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  11.3   4.5e-06     0.027     203     329 ..      15     173 ..       3     188 .. 0.67
   2 ?    4.2   1.2    0.0028        17     136     167 ..     236     267 ..     203     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-06
                          MFS_1 203 llkdpvlwillialllfffgfsglltllplylqevlgls...................................glllag 247
                                    +l+++   + l+alll f+  ++l  llp    ++l+++                                   g+  a+
  gi|121637210|ref|YP_977433.1|  15 FLRNRAAVASLAALLLLFVSAYALPPLLPYS-YDDLDFNallqppgtkhwlgtnalgqdllaqtlrgmqksmliGVCVAV 93 
                                    3333433346777777777777788888874.677777777777777777777777777777777766676666566666 PP

                          MFS_1 248 lllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll..vlvliGfglgfvfpsllala 325
                                    +  +++a vgai++ ++g+      r  ++++ lll++ +++++a++ + +++++ ++  vl+l+Gfg+ + + ++  ++
  gi|121637210|ref|YP_977433.1|  94 ISTGIAATVGAISGYFGGW----RDRTLMWVVDLLLVVPSFILIAIVTPRTKNSANIMflVLLLAGFGWMISSRMVRGMT 169
                                    6666666666655544444....555999999999999999999999999888888884355558888888866666666 PP

                          MFS_1 326 sdla 329
                                    ++l 
  gi|121637210|ref|YP_977433.1| 170 MSLR 173
                                    6654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0028
                          MFS_1 136 lgpllggllasslgWravfyilaivsllafvl 167
                                    lg l++   as+  +++vf++ a +++l +v+
  gi|121637210|ref|YP_977433.1| 236 LGTLIADGTASATAFPWVFLFPASILVLILVC 267
                                    56666666677777*************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2014.70
//
Query:       gi|121637211|ref|YP_977434.1|  [L=325]
Description: oligopeptide-transport integral membrane protein ABC transporter oppB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-36  124.9  10.4    5.1e-36  124.2  10.4    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2  10.4   2.8e-40   5.1e-36       1     184 [.     113     323 ..     109     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 2.8e-40
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf............................vilsilghl 52 
                                    g+++G++ a ++ +  d+++++l  ++ls+P+fv+a ll+l +                             + + l+hl
  gi|121637211|ref|YP_977434.1| 113 GVVIGAWGAIRQYRLSDRVMTTLALLVLSTPTFVVANLLILGAlrvnwavgiqlfdytgetspgvaggvwdRLGDRLQHL 192
                                    789999999*******************************888*************************99977789**** PP

                   BPD_transp_1  53 ilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                    ilp ++l+l  aa++ r+ r+a+l++l +d++++ara+G++r++ + k+ l+ al+p++t++++ ++gl++gav++e ++
  gi|121637211|ref|YP_977434.1| 193 ILPSLTLALAAAAGFSRYQRNAMLDVLGQDFIRTARAKGLTRRRALLKHGLRTALIPMATLFAYGVAGLVTGAVFVEKIF 272
                                    ******************************************************************************** PP

                   BPD_transp_1 133 swpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                    +w+G+g ++++ i+ +d++  + +++++ +++vll  l++d+++++ldprvr
  gi|121637211|ref|YP_977434.1| 273 GWHGMGEWMVRGISTQDTNIVA-AITVFSGAVVLLAGLLSDVIYAALDPRVR 323
                                    *******************999.****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2088.32
//
Query:       gi|121637212|ref|YP_977435.1|  [L=163]
Description: beta-carbonic anhydrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-13   50.4   0.4    4.6e-12   46.5   0.4    2.0  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.4   2.6e-16   4.6e-12       2      74 ..      31     102 ..      30     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.6e-16
                                    EEEEETTTTS-HHHHTTS-TTSEEEEEETTG---TT-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHS..H CS
                         Pro_CA   2 lvigCsDSRvppelitdagpGdlFvvrnvgnlvppadssvlaaleyAvevlkvkhivVlGHskCGavkaalk..a 74 
                                    ++++C+D+R++   +++ + G+  v+rn+g +v    ++v+ +l  + + l++++i+ l H++CG+ + + +  +
  gi|121637212|ref|YP_977435.1|  31 AIVACMDARLDVYRMLGIKEGEAHVIRNAGCVV---TDDVIRSLAISQRLLGTREIILLHHTDCGMLTFTDDdfK 102
                                    689******************************...999***************************995543432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 924.75
//
Query:       gi|121637213|ref|YP_977436.1|  [L=332]
Description: sulfate adenylyltransferase subunit 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-50  170.3   0.0    4.7e-50  170.0   0.0    1.1  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.015   15.0   0.0    1.3  1  ATP_bind_3       PP-loop family
       0.01   15.9   0.0       0.59   10.2   0.0    2.2  2  DpaA_N           Dipicolinate synthase subunit A N-terminal d
      0.065   12.7   0.0      0.096   12.2   0.0    1.3  1  Diphthami_syn_2  Diphthamide synthase
        0.1   12.1   0.0       0.16   11.5   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0   1.3e-53   4.7e-50       2     173 ..      63     285 ..      62     286 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 1.3e-53
                                    EEEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                    PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv....pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                    +v+++sgGkds+V+lhLalkaf+p+    pv++vdtgh+f+e+i+++del+   g+rl v++ +++++++ + e+++s++
  gi|121637213|ref|YP_977436.1|  63 PVLLFSGGKDSIVMLHLALKAFRPGrlpfPVMHVDTGHNFDEVIATRDELVAAAGVRLVVASVQDDIDAGRVVETIPSRN 142
                                    89**********************66777***********************************************9987 PP

                                    HHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S......................CEEE-C CS
                    PAPS_reduct  78 yeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek......................slrvfP 135
                                            +++++l +a++++++da+++GaRrde+k+rak+++++++++f +                      ++rvfP
  gi|121637213|ref|YP_977436.1| 143 -------PIQTVTLLRAIRENQFDAAFGGARRDEEKARAKERVFSFRDEFGQwdpkaqrpelwnlyngrhhkgeHIRVFP 215
                                    .......899********************************************************************** PP

                                    CCT--HHHHHHHHHHCT--B-CCCCTT................................-SS--BCTTB- CS
                    PAPS_reduct 136 llnWteedvwqyilrenipynpLydqg................................frsiGcvpctg 173
                                    l+nWte d+w+yi +e++++ ++y+++                                fr++G+v+ctg
  gi|121637213|ref|YP_977436.1| 216 LSNWTEFDIWSYIGAEQVRLPSIYFAHrrkvfqrdgmllavhrhmqpradepvfeatvrFRTVGDVTCTG 285
                                    *********************************************************************7 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.3e-06     0.015       5      67 ..      66     126 ..      62     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                                    E--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE..-SSSTCHHHHHHHHHHHHHHTT-EEEEEE-- CS
                     ATP_bind_3   5 AvSgGlDSmaLllllaklkkklgiklvaihvd..hglreeskeeaelvkelckklnikleiekvd 67 
                                     +SgG DS+++l+l+ k  +   + + ++hvd  h++ e  +       el++  +++l++++v+
  gi|121637213|ref|YP_977436.1|  66 LFSGGKDSIVMLHLALKAFRPGRLPFPVMHVDtgHNFDEVIATR----DELVAAAGVRLVVASVQ 126
                                    59******************999999999999334444433333....44444444444444444 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.59      37      98 ..      11      72 ..       3      83 .. 0.88
   2 ?    3.4   0.0     0.021        75      33     108 ..      99     177 ..      90     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                                   TTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BSS-SS-EE-.HHHHHTS-TT-EEEESS-- CS
                         DpaA_N 37 egvekaesleealedadviilPvpgtkdggeintpfseeklsl.eelleklkkgqllfgGiip 98
                                   +g+ ++e++e++  ++dv ++P pg  +  +++  +++e +++ +e++++ ++  llf+G  +
  gi|121637213|ref|YP_977436.1| 11 TGFIRYEDVEQEAMTSDVTVGPAPGQYQLSHLRL-LEAEAIHViREVAAEFERPVLLFSGGKD 72
                                   67788999999999********************.888888888**************99765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                                    SS-BTTEEEE-GGGS-GGG-SEEE--TT.-BETTTEE-BSS-SS-EE-HHHHHTS-TT-E..EEESS--HHHHHHHHHC CS
                         DpaA_N  33 eekiegvekaesleealedadviilPvp.gtkdggeintpfseeklsleelleklkkgql..lfgGiippelkelaeek 108
                                     +++++v  + +   a + +++++  v+  ++ g+ ++t  s ++++  +ll++++++q    fgG  ++e k+ a+e+
  gi|121637213|ref|YP_977436.1|  99 GHNFDEVIATRDELVAAAGVRLVVASVQdDIDAGRVVETIPSRNPIQTVTLLRAIRENQFdaAFGGARRDEEKARAKER 177
                                    5667777777777777789999999999889999***********************9987788888888877777765 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05     0.096       4      28 ..      64      88 ..      61     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                Diphthami_syn_2  4 avlysGGkDsilaLykalkeseves 28
                                   + l+sGGkDsi+ L+ alk +    
  gi|121637213|ref|YP_977436.1| 64 VLLFSGGKDSIVMLHLALKAFRPGR 88
                                   789***************9876555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.4e-05      0.16       3      53 ..      64     118 ..      62     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                    EEE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-TTSHHHHHHHHHHHHT-- CS
                           QueC   3 vvllSGGlDSttvlalakkeg....kevealtfdYgqrhkkeleaakkiakelgv 53 
                                    v+l+SGG DS ++l la+k++        ++++d g++ ++ + +++++++++gv
  gi|121637213|ref|YP_977436.1|  64 VLLFSGGKDSIVMLHLALKAFrpgrLPFPVMHVDTGHNFDEVIATRDELVAAAGV 118
                                    89*****************993322235577888888877777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2386.99
//
Query:       gi|121637214|ref|YP_977437.1|  [L=614]
Description: bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-68  227.2   0.0    1.7e-67  226.3   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
    2.3e-39  134.9   0.1    3.3e-39  134.5   0.1    1.3  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    5.1e-07   29.8   0.1    2.4e-05   24.4   0.0    3.1  2  MMR_HSR1         50S ribosome-binding GTPase
      3e-06   27.4   0.0    2.8e-05   24.3   0.0    2.5  3  AAA_33           AAA domain
    1.5e-05   25.3   0.0    7.8e-05   23.0   0.0    2.3  2  GTP_EFTU_D2      Elongation factor Tu domain 2
    0.00038   20.9   0.0     0.0013   19.2   0.0    1.9  2  AAA_16           AAA ATPase domain
     0.0035   17.3   0.1        6.7    6.6   0.0    3.6  3  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.038   13.7   0.3          1    9.2   0.0    2.6  2  AAA_29           P-loop containing region of AAA domain
      0.065   12.5   0.0       0.15   11.3   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.069   12.6   0.0       0.14   11.6   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.089   13.3   0.0       0.25   11.9   0.0    1.8  1  AAA_18           AAA domain
      0.095   13.2   0.0       0.52   10.8   0.0    2.2  2  ABC_tran         ABC transporter
       0.11   12.1   0.0        0.2   11.3   0.0    1.3  1  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   0.0   1.2e-70   1.7e-67       1     153 [.     442     595 ..     442     599 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.2e-70
                                    S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                     APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlva 80 
                                    rg +vw+tGlsgsGKs++a+ +e+kL ekgis+y+LdGdn+RhgLn dLgfs++dR+en+rr+++va+llad+g++vlv 
  gi|121637214|ref|YP_977437.1| 442 RGKTVWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLRHGLNADLGFSMADRAENLRRLSHVATLLADCGHLVLVP 521
                                    689***************************************************************************** PP

                                    ----SHHHHHHHHHHHHCH.TEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEET CS
                     APS_kinase  81 fisPyreeReaarelleea.lkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdt 153
                                    +isP +e+R  ar+++++a ++f+evf+dtpl+ ce+rDpkglY+kar+Gei++ftGidspY++P+np+l+++ 
  gi|121637214|ref|YP_977437.1| 522 AISPLAEHRALARKVHADAgIDFFEVFCDTPLQDCERRDPKGLYAKARAGEITHFTGIDSPYQRPKNPDLRLTP 595
                                    *****************999**************************************************9975 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.1   2.4e-42   3.3e-39       4     182 ..       5     188 ..       2     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 2.4e-42
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST.............HCHSHHHHHHTSCSSCEEEEEETTCSS CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv.............lDtlkeErergiTiksaaisleketkk 69 
                                    + ++++g vD GK+TL++rLly+++a+ +++    e ++              +D l +Ere+giTi++a  ++   t k
  gi|121637214|ref|YP_977437.1|   5 LRLATAGSVDDGKSTLIGRLLYDSKAVMEDQWASvE-QTSkdrghdytdlalvTDGLRAEREQGITIDVAYRYFA--TPK 81 
                                    67899**********************998876642.22246789999***************************..*** PP

                                    EEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHHHHHH CS
                       GTP_EFTU  70 ylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...kaelkeivee 145
                                    +++ + DtPGH+++++++ +g++++ +++++vda++G  +q+++++ la+ +g++ +++++NKmD l   +++++ i +e
  gi|121637214|ref|YP_977437.1|  82 RKFIIADTPGHIQYTRNMVTGASTAQLVIVLVDARHGLLEQSRRHAFLASLLGIRhLVLAVNKMDLLgwdQEKFDAIRDE 161
                                    *******************************************************************9988999999999 PP

                                    HHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                       GTP_EFTU 146 vkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                     +  +         +  +  ++v+ +++Sal+g++v 
  gi|121637214|ref|YP_977437.1| 162 FH-AF------A--ARLDV-QDVTSIPISALHGDNVV 188
                                    88.66......2..33333.36899*********986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.7e-08   2.4e-05       3      94 ..       8     124 ..       6     144 .. 0.67
   2 ?    0.4   0.0      0.48   6.6e+02       2      15 ..     446     459 ..     445     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                                    EEEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEEEEEE CS
                       MMR_HSR1   3 aivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgkeielv 51 
                                    a +G    GKStLi +l+                    +           +  ++++++g T+d+ ++ +++ +++++++
  gi|121637214|ref|YP_977437.1|   8 ATAGSVDDGKSTLIGRLLydskavmedqwasveqtskdRghdytdlalvtDGLRAEREQGITIDVAYRYFATPKRKFIIA 87 
                                    67899999*********977777766666666655555055555554443467899999******9999998889***** PP

                                    ECGGCSSHHHHHHHHHHHHHH.HHCTSEEEEEEETTTTCSHHHH CS
                       MMR_HSR1  52 DtpGliegaseekglgkafla.leeadlillvvdaseeklkpld 94 
                                    DtpG i+        ++++      a+l++++vda+++ l++ +
  gi|121637214|ref|YP_977437.1|  88 DTPGHIQ-------YTRNMVTgASTAQLVIVLVDARHGLLEQSR 124
                                    ****776.......444444414458********9954443332 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.48
                                    EEEEESTTSSHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStL 15 
                                    v + G + +GKS++
  gi|121637214|ref|YP_977437.1| 446 VWFTGLSGSGKSSV 459
                                    7799********97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   1.9e+03      11      27 ..      16      32 ..      11     142 .. 0.74
   2 ?   -2.1   0.0       2.8   3.9e+03      55      85 ..     318     346 ..     262     358 .. 0.63
   3 !   24.3   0.0     2e-08   2.8e-05       2     115 ..     446     560 ..     446     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                         AAA_33 11 GKstlaerllkklgavl 27
                                   GKstl+ rll   +av 
  gi|121637214|ref|YP_977437.1| 16 GKSTLIGRLLYDSKAVM 32
                                   88888888875555443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                         AAA_33  55 lyqilnelarkalsagrnvildatnlsrrer 85 
                                    +  ++++ a  +l+ gr++++  t ++ r+r
  gi|121637214|ref|YP_977437.1| 318 TVCWMADNA--VLEPGRDYVVKHTTRTVRAR 346
                                    333343433..46778888888888877766 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2e-08
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil. 75 
                                    v++ Gl+GsGKs +a  + +kl      a++l+ d+lr  l ++   s  d+++    l ++l+ +a+  +  g  v++ 
  gi|121637214|ref|YP_977437.1| 446 VWFTGLSGSGKSSVAMLVERKLLekgisAYVLDGDNLRHGLNADLGFSMADRAEN---L-RRLSHVATLLADCGHLVLVp 521
                                    7899***********999888877889****************999999875554...3.45557776555566666663 PP

                         AAA_33  76 .datnlsrrerarflklarrlgvpvrivvvetdeetlkeRl 115
                                      ++++  ++ra  +k+  ++g  +  v+++t+ + +++R 
  gi|121637214|ref|YP_977437.1| 522 aISPLA--EHRALARKVHADAGIDFFEVFCDTPLQDCERRD 560
                                    334455..55555556666669999*************995 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.7e-08   7.8e-05       6      72 ..     243     301 ..     241     303 .. 0.81
   2 ?   -2.9   0.0       6.6   9.2e+03      10      26 ..     406     422 ..     405     436 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.7e-08
                                    EEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                    GTP_EFTU_D2   6 grvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                    g+v sG+++ Gdev++l+     k+   tri+++  +++++ ea +  ++ v +a  ++ d i +Gd 
  gi|121637214|ref|YP_977437.1| 243 GTVASGVMRSGDEVVVLPiG---KT---TRITAIDGPNGPVAEAFPPMAVSVRLAD-DI-D-ISRGDM 301
                                    7899************7744...66...****************998888888873.33.3.667765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                                    ESEEETTEEEEEECTCT CS
                    GTP_EFTU_D2  10 sGtlkkGdevrilgndt 26 
                                    +Gt+  G+ +r ++ +t
  gi|121637214|ref|YP_977437.1| 406 NGTVAAGMVLRDVSART 422
                                    78888898888766555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.1   9.7e+03      36      45 ..      16      25 ..      16      58 .. 0.73
   2 !   19.2   0.0   9.1e-07    0.0013      17      67 ..     438     492 ..     429     611 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.1
                         AAA_16 36 GKsslvrell 45
                                   GKs+l+ +ll
  gi|121637214|ref|YP_977437.1| 16 GKSTLIGRLL 25
                                   8999997776 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.1e-07
                         AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdg..giflrgkcdqlesa....i 67 
                                    +r    r+  v ++G sG+GKss++  + r l ++g  +++l g++ +++ +     
  gi|121637214|ref|YP_977437.1| 438 DRPP--RGKTVWFTGLSGSGKSSVAMLVERKLLEKGisAYVLDGDNLRHGLNadlgF 492
                                    3343..4489*************************5448889999999844422331 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.046        63     108     160 ..      13      91 ..       6      98 .. 0.77
   2 ?    2.7   0.0     0.075     1e+02      32      74 ..     120     164 ..      94     187 .. 0.66
   3 !    6.6   0.0    0.0049       6.7      98     116 ..     442     460 ..     427     479 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.046
                                    TTSSHHHHHHHHCTT.........................-----S--------------SEEEEEETT.TEEEESS-S CS
                    RsgA_GTPase 108 SGvGKStLinallpe.........................lelktgevseklgrGkhTTtavellelae.gglliDtPG 160
                                       GKStLi +ll +                         l l t  ++++ ++G     a + ++ ++ + +++DtPG
  gi|121637214|ref|YP_977437.1|  13 VDDGKSTLIGRLLYDskavmedqwasveqtskdrghdytdLALVTDGLRAEREQGITIDVAYRYFATPKrKFIIADTPG 91 
                                    55699****9999877888888888888888888888877788888888888888888888888888773556778888 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.075
                                    HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHH CS
                    RsgA_GTPase  32 lnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeelea 74 
                                    l++  r  +la   gi ++v+++nK+Dll  ++ +++++++e++a
  gi|121637214|ref|YP_977437.1| 120 LEQSRRHAFLASLLGIrHLVLAVNKMDLLGWDQeKFDAIRDEFHA 164
                                    444455556666677768999*******97655456666665554 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0049
                                    TTSEEEEECSTTSSHHHHH CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLi 116
                                    ++kt+ + G SG GKS++ 
  gi|121637214|ref|YP_977437.1| 442 RGKTVWFTGLSGSGKSSVA 460
                                    5799*************75 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.19   2.7e+02      28      39 ..      10      21 ..       6      29 .. 0.85
   2 ?    9.2   0.0   0.00074         1      21      38 ..     441     459 ..     434     461 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.19
                         AAA_29 28 tGpsGsGKSTll 39
                                   +G    GKSTl+
  gi|121637214|ref|YP_977437.1| 10 AGSVDDGKSTLI 21
                                   578889*****8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                         AAA_29  21 lkg.atlltGpsGsGKSTl 38 
                                    ++g ++ +tG sGsGKS++
  gi|121637214|ref|YP_977437.1| 441 PRGkTVWFTGLSGSGKSSV 459
                                    4566889**********85 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.15      14      56 ..     441     484 ..     429     487 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                     r k +   G +G+GKs++a l++++l  ++ ++ +ld+D+lR 
  gi|121637214|ref|YP_977437.1| 441 PRGKTVWFTGLSGSGKSSVAMLVERKLLeKGISAYVLDGDNLRH 484
                                    55578888999***************986788999******995 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.8e-05      0.14       4      41 ..     446     483 ..     445     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                    v +tGl  sGKs++a  ++++l e+++s +v+d + l+
  gi|121637214|ref|YP_977437.1| 446 VWFTGLSGSGKSSVAMLVERKLLEKGISAYVLDGDNLR 483
                                    669******************************88876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.25       1      29 [.     446     483 ..     446     538 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........gvnlr 29 
                                    ++ tG +G+GK+++a  ++++l +         g+nlr
  gi|121637214|ref|YP_977437.1| 446 VWFTGLSGSGKSSVAMLVERKLlEKgisayvldGDNLR 483
                                    689***************99863324455444444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         3   4.2e+03      23      33 ..      16      26 ..       7      53 .. 0.74
   2 ?   10.8   0.0   0.00037      0.52      10      35 ..     442     467 ..     440     509 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3
                                   SHHHHHHHHTT CS
                                   xxxxxxxxxxx RF
                       ABC_tran 23 GKStLlkllag 33
                                   GKStL+  l+ 
  gi|121637214|ref|YP_977437.1| 16 GKSTLIGRLLY 26
                                   99999965554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00037
                                    TTSEEEEEESTTSSHHHHHHHHTTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  10 egekvaivGenGaGKStLlkllagll 35 
                                    +g++v ++G +G+GKS++++l+ ++l
  gi|121637214|ref|YP_977437.1| 442 RGKTVWFTGLSGSGKSSVAMLVERKL 467
                                    799***************99988765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015       0.2       2      28 ..     449     476 ..     448     483 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                    EESTTSSHHHHHHHHHHHHHHTTE..EE CS
                Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegik.vv 28 
                                     Gl G+GK+++a+l+ ++l e+gi+ +v
  gi|121637214|ref|YP_977437.1| 449 TGLSGSGKSSVAMLVERKLLEKGISaYV 476
                                    599*********************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4226.35
//
Query:       gi|121637215|ref|YP_977438.1|  [L=161]
Description: hypothetical protein BCG_1346 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-25   88.8   0.0    3.7e-25   88.1   0.0    1.4  1  Rrf2          Transcriptional regulator
     0.0056   16.5   0.0     0.0084   16.0   0.0    1.3  1  TFIIE_alpha   TFIIE alpha subunit
     0.0085   15.7   0.0      0.015   15.0   0.0    1.4  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   6.2e-29   3.7e-25       1      83 []       1      83 [.       1      83 [. 0.99

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 6.2e-29
                                   X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBHHHHHHH CS
                           Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlldvvra 82
                                   M++s+k eya++a++ La+ ++++ v+++++a+ q+i+p++l  il++Lr   lv+s rG++GGy La+p  eI+++dv+r+
  gi|121637215|ref|YP_977438.1|  1 MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYELARPGTEISIADVLRC 82
                                   9*******************************************************************************98 PP

                                   H CS
                           Rrf2 83 v 83
                                   +
  gi|121637215|ref|YP_977438.1| 83 I 83
                                   6 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0084      23      66 ..      21      64 ..       5      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                   HCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETT CS
                    TFIIE_alpha 23 lekgevteedlakelkidlnelrklLnrLyearlvkykrrrdee 66
                                   ++  +v+ +dla   +i ++ l  +L +L+ +rlv  +r r+ +
  gi|121637215|ref|YP_977438.1| 21 ASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGG 64
                                   4567899*********************************9954 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-06     0.015      10      64 ..      11      66 ..       3      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-06
                   HrcA_DNA-bdg 10 lqaLielyrkk.kravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYk 64
                                   ++a+++l +   ++ vK+ ++A++ +  +  +  +l+ L++  Lv +  G +GGY 
  gi|121637215|ref|YP_977438.1| 11 VRAMVQLATAAsGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYE 66
                                   578888887765899****************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1137.22
//
Query:       gi|121637216|ref|YP_977439.1|  [L=405]
Description: hypothetical protein BCG_1347 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-68  229.2   0.0    1.3e-67  228.1   0.0    1.5  2  Esterase       Putative esterase
    5.5e-18   64.8   0.0    9.7e-10   38.4   0.0    2.4  2  LysM           LysM domain
    2.8e-07   30.1   7.0    0.00017   21.2   0.1    3.2  4  Phage_tail_X   Phage Tail Protein X
  ------ inclusion threshold ------
      0.016   14.8   0.1      0.027   14.1   0.1    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
      0.024   14.3   0.2        4.6    6.9   0.0    3.8  5  Phage_gp53     Base plate wedge protein 53
       0.03   13.6   0.0      0.044   13.1   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
       0.21   10.5   1.4       0.29   10.0   1.4    1.1  1  Asp2           Accessory Sec system GspB-transporter


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   2.9e+03     137     154 ..      24      41 ..      13      69 .. 0.71
   2 !  228.1   0.0     5e-71   1.3e-67       2     251 .]     131     392 ..     130     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                    TTTCCEEEEES--S-CCH CS
                       Esterase 137 pdrFgsvssfSpivnpsn 154
                                     +++  +++ S+i++p  
  gi|121637216|ref|YP_977439.1|  24 AELYRLIAAASGIADPDV 41 
                                    578889999999998864 PP

  == domain 2  score: 228.1 bits;  conditional E-value: 5e-71
                                    TTTTEEEEEEEEE.CC..GGTTTEEEEEEE--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB. CS
                       Esterase   2 ealgreikvqvyLPedy.spgrkypvvylldGltgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgar 80 
                                    +a+g++ +v+v+LP+dy ++gr+ypv+yl++G  g+dq+fr++++l+  +r+ ++ ++ii+v+p+gg++         ++
  gi|121637216|ref|YP_977439.1| 131 SAIGWNPGVNVLLPDDYrTSGRTYPVLYLFHG-GGTDQDFRTFDFLG--IRDLTAGKPIIIVMPDGGHA---------GW 198
                                    689*****************************.*************8..********************.........89 PP

                                    TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCC..EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC..... CS
                       Esterase  81 fyenategpgaeayetfltqeLlplldanfrtapdg..ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps..... 153
                                    ++++++++ g +++etf+ ++Llp+++anfrt++++  ravaG+SmGG+gAL +a+k++++F+s+ss+S++++++     
  gi|121637216|ref|YP_977439.1| 199 YSNPVSSFVGPRNWETFHIAQLLPWIEANFRTYAEYdgRAVAGFSMGGFGALKYAAKYYGHFASASSHSGPASLRrdfgl 278
                                    9******************************************************************************* PP

                                    .....................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHH CS
                       Esterase 154 .....................namWgqeekeawqendpvllakelsaslkalriyldvGtseddlgeqlsveilevlarn 212
                                                         +++W+q       +++++++ +e+++s++++ri+l++Gts+d++++++sv++++vla++
  gi|121637216|ref|YP_977439.1| 279 vvhwanlssavldlgggtvygAPLWDQ-------ARVSADNPVERIDSYRNKRIFLVAGTSPDPANWFDSVNETQVLAGQ 351
                                    ********************9999998.......9********************************************* PP

                                    CCHHHHCCCCCCTT-SCCCC--SSHHH..HHHHHHHCHHHH CS
                       Esterase 213 relkeqlaargvegedheydGghswey..WraqLiaaladl 251
                                    re++e+l+++g+++e+he++Ggh +++  +r +L +++a+l
  gi|121637216|ref|YP_977439.1| 352 REFRERLSNAGIPHESHEVPGGHVFRPdmFRLDLDGIVARL 392
                                    **************************999******999875 PP

>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.8e-09   2.5e-05       2      44 .]       6      51 ..       5      51 .. 0.87
   2 !   38.4   0.0   3.8e-13   9.7e-10       1      43 [.      56     101 ..      56     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.8e-09
                                   EE-TT--HHHHHHHC....TCHHHHHHHHCTCSSCGG--TTEEEEEE CS
                           LysM  2 tVkkGDTLwsIAkry....gitveklleaNnlsspdkifpGqkLkiP 44
                                    V  G+TL+++A r+     +  + +++a ++ +pd + +Gq+L+ P
  gi|121637216|ref|YP_977439.1|  6 AVVAGETLSALALRFygdaELY-RLIAAASGIADPDVVNVGQRLIMP 51
                                   599**************74444.7777777**************988 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 3.8e-13
                                    EEE-TT--HHHHHHHC....TCHHHHHHHHCTCSSCGG--TTEEEEE CS
                           LysM   1 YtVkkGDTLwsIAkry....gitveklleaNnlsspdkifpGqkLki 43 
                                    YtV  GDTL+++A+r+    ++    +++ N++ +p+ i +Gq+L+i
  gi|121637216|ref|YP_977439.1|  56 YTVVAGDTLSALAARFygdaSLY-PLIAAVNGIADPGVIDVGQVLVI 101
                                    9******************6555.9********************99 PP

>> Phage_tail_X  Phage Tail Protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   6.7e-08   0.00017       6      56 ..       7      55 ..       2      59 .. 0.90
   2 !   12.6   0.2   3.3e-05     0.084       6      43 ..      58      99 ..      54     103 .. 0.73
   3 ?   -3.4   0.0       3.1     8e+03      46      53 ..     138     145 ..     137     149 .. 0.86
   4 ?   -2.4   0.2       1.6     4e+03      15      23 ..     253     261 ..     252     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.7e-08
                                   -.TT-SHHHHHHHTTS--TTTHHHHHHHSTTTTTT-S---TTEEEE-TT--S CS
                   Phage_tail_X  6 t.qgdtlDalcwryYGrtlgvveavleaNPgLAelgpvLphGtavelPdist 56
                                      g+tl al++r+YG+++ +  + ++a  g+A+   v   G ++++Pd + 
  gi|121637216|ref|YP_977439.1|  7 VvAGETLSALALRFYGDAELY--RLIAAASGIADP-DVVNVGQRLIMPDFTR 55
                                   447****************99..************.*************875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.3e-05
                                   -.TT-SHHHHHHHTTS--..TTTHHHHHH.HSTTTTTT-S-- CS
                   Phage_tail_X  6 t.qgdtlDalcwryYGrt..lgvveavle.aNPgLAelgpvL 43
                                      gdtl al+ r+YG++    ++ av   a Pg+ ++g+vL
  gi|121637216|ref|YP_977439.1| 58 VvAGDTLSALAARFYGDAslYPLIAAVNGiADPGVIDVGQVL 99
                                   447**************9544566666533678888888887 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.1
                                    TEEEE-TT CS
                   Phage_tail_X  46 GtavelPd 53 
                                    G++v lPd
  gi|121637216|ref|YP_977439.1| 138 GVNVLLPD 145
                                    899****8 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.6
                                    HHHTTS--T CS
                   Phage_tail_X  15 cwryYGrtl 23 
                                    + +yYG+ +
  gi|121637216|ref|YP_977439.1| 253 AAKYYGHFA 261
                                    579***976 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     1e-05     0.027      52     106 ..     213     268 ..     155     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                    CHHSHHHHHHHHH.HHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  52 ddygtasvaddld.rildalgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                    +++++a +  +++  ++     d  ++ G+SmGG+ al yaa+y  + ++  + ++
  gi|121637216|ref|YP_977439.1| 213 ETFHIAQLLPWIEaNFRTYAEYDGRAVAGFSMGGFGALKYAAKYYGHFASASSHSG 268
                                    77888888888886669999999999******************777776666655 PP

>> Phage_gp53  Base plate wedge protein 53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.059   1.5e+02      49      73 ..      15      39 ..       4      63 .. 0.76
   2 ?    6.9   0.0    0.0018       4.6      39      73 ..      56      90 ..      43      97 .. 0.77
   3 ?   -1.5   0.0      0.65   1.7e+03     118     131 ..     117     130 ..     107     136 .. 0.75
   4 ?   -2.6   0.0       1.4   3.7e+03      20      36 ..     228     244 ..     223     247 .. 0.86
   5 ?   -0.2   0.0      0.26   6.6e+02     115     149 ..     328     360 ..     304     368 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.059
                                   --TTTSS--SS---SSHHHHT-S-T CS
                     Phage_gp53 49 elayelygdtslywlllllnervdp 73
                                    la  +ygd++ly l+       dp
  gi|121637216|ref|YP_977439.1| 15 ALALRFYGDAELYRLIAAASGIADP 39
                                   589999*********9988888777 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0018
                                   -----S---S--TTTSS--SS---SSHHHHT-S-T CS
                     Phage_gp53 39 ykikgdyrpeelayelygdtslywlllllnervdp 73
                                   y +        la  +ygd+sly l+  +n   dp
  gi|121637216|ref|YP_977439.1| 56 YTVVAGDTLSALAARFYGDASLYPLIAAVNGIADP 90
                                   444444445689******************99998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.65
                                    -TTS-S-BEESS-T CS
                     Phage_gp53 118 ddenprvwydkfdk 131
                                    ++++pr wy +f+ 
  gi|121637216|ref|YP_977439.1| 117 NENDPRLWYYRFQT 130
                                    34569****99875 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.4
                                    -S-HHHHHHHHTTTS-- CS
                     Phage_gp53  20 fknlkdyfkrilasyrl 36 
                                    f+ + +y  r++a++ +
  gi|121637216|ref|YP_977439.1| 228 FRTYAEYDGRAVAGFSM 244
                                    999**********9975 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.26
                                    EE--TTS-S-BEESS-TT----B..........-S CS
                     Phage_gp53 115 lveddenprvwydkfdkerkapeegqedyrellye 149
                                    +     +p +w+d  +  +     gq ++re l +
  gi|121637216|ref|YP_977439.1| 328 VAGTSPDPANWFDSVNETQVL--AGQREFRERLSN 360
                                    555667899***998766544..379999997755 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05     0.044      77     123 ..     236     283 ..     224     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                    Hydrolase_4  77 plfllGhSmGGliallyllrypdkva.glilsaPalkikaklk.appll 123
                                     + + G SmGG+ al+y+++y  ++a +   s+Pa  ++ ++  +  ++
  gi|121637216|ref|YP_977439.1| 236 GRAVAGFSMGGFGALKYAAKYYGHFAsASSHSGPAS-LRRDFGlVVHWA 283
                                    56899*****************99998888888884.454554455555 PP

>> Asp2  Accessory Sec system GspB-transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.4   0.00011      0.29     359     377 ..     239     257 ..     234     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                           Asp2 359 lsGlSMGtfgalyYgakln 377
                                    + G SMG fgal+Y+ak+ 
  gi|121637216|ref|YP_977439.1| 239 VAGFSMGGFGALKYAAKYY 257
                                    68**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3067.14
//
Query:       gi|121637217|ref|YP_977440.1|  [L=210]
Description: hypothetical protein BCG_1348 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1674.44
//
Query:       gi|121637218|ref|YP_977441.1|  [L=521]
Description: hypothetical protein BCG_1349c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-103  345.3   0.2   4.4e-103  344.9   0.2    1.2  1  DUF2254   Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.9   0.2  2.5e-107  4.4e-103       3     365 ..      69     438 ..      67     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 344.9 bits;  conditional E-value: 2.5e-107
                        DUF2254   3 slwfipllivllavllalllllldealslsldleelkegaeaaralLstiagsmltvagfvfSitvvalqlassqfsPRl 82 
                                     +w++p++ v+++++ +++l +++ + ++ +d+ +++ ++ +ar +L ++++ m+t +g+vfS+tv++lq+assqfs Rl
  gi|121637218|ref|YP_977441.1|  69 AVWVLPTFGVAIGLGSGAVLSMIPVKSGTLIDKLMFQGTPGDARGVLIVVSATMITTIGIVFSLTVLSLQIASSQFSVRL 148
                                    68*********************999899998888888****************************************** PP

                        DUF2254  83 lrnfmrdrvtqvvLGtfigtfvYsllvlrairteee....vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarv 158
                                    lr+f+rd ++qvvL++f +tf+Ys  +l+++++ ++    +p+++v+ +l+la+vs+++LiyF+hhl++siq+++++++v
  gi|121637218|ref|YP_977441.1| 149 LRTFLRDVPNQVVLAIFACTFAYSTGGLHTVGEHRDggafIPKVAVTGSLALAFVSIAALIYFLHHLMHSIQIDTIMDKV 228
                                    ********************************8888******************************************** PP

                        DUF2254 159 eeelrkailearedeeeeeeeeakdeeeseeeeatpiraersGylqaidveaLvklaeehdlvielevrpGdfvvkgepl 238
                                      ++   +  ++   e+++++++ ++ +s++++a p+ a++sGylq++dv+++ +la +++ +  l++ +Gd+v++g  l
  gi|121637218|ref|YP_977441.1| 229 RLRTLGLV--DQLYPESDTADRQVETPPSPPADAVPLLAPHSGYLQTVDVDDIAELAAASRYTALLVTFVGDYVTAGGLL 306
                                    ********..455555566666777778999************************************************* PP

                        DUF2254 239 akvwgee.....ddeelaeklreafligrertfeqDpefglrqLvEIAlRALSPGiNDpgTAiecidrlssllarlaere 313
                                    +++w++        +++ +++ ++++ig ert +qD++fglrq+v+IAlRALSP+ NDp+TAi+++++ls++ + la+r 
  gi|121637218|ref|YP_977441.1| 307 GWCWRRGtapgaPGSDFPQRCLRHVHIGFERTLQQDIRFGLRQMVDIALRALSPALNDPYTAIQVVHHLSAVESVLASRA 386
                                    ****999*****6678**************************************************************** PP

                        DUF2254 314 lpspylrdedgelrvilpelsfedlldlafdqirrygagdvaVlirlleala 365
                                    lp++++rd+ gel  +lp +sf+++l+ +++qirryg++++ Vl++ll++l+
  gi|121637218|ref|YP_977441.1| 387 LPDDVRRDRAGELLFWLPYPSFATYLHVGCAQIRRYGSREPLVLTALLQLLS 438
                                    *************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3520.09
//
Query:       gi|121637219|ref|YP_977442.1|  [L=104]
Description: hypothetical protein BCG_1350 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 805.54
//
Query:       gi|121637220|ref|YP_977443.1|  [L=111]
Description: hypothetical protein BCG_1351c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.0   9.3    1.8e-23   82.7   9.3    1.1  1  DUF732    Protein of unknown function (DUF732)
  ------ inclusion threshold ------
          7    7.1   8.6          2    8.8   2.0    2.1  2  HOASN     Haem-oxygenase-associated N-terminal helices


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   9.3     2e-27   1.8e-23       2      94 ..      17     108 ..      16     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 2e-27
                         DUF732   2 aaallaaalllaapAaAdsaddaFlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaaqf 81 
                                    aa l++aal++a++A+A+s+d+aFla+l++ gi+ +s+++ai+ ++avC++ld+G+sa+av+++v++  +gls++ a++f
  gi|121637220|ref|YP_977443.1|  17 AATLGLAALGFAGTASASSTDEAFLAQLQADGITPPSAARAIKDAHAVCDALDEGHSAKAVIKAVAK-ATGLSAKGAKTF 95 
                                    78999*************************************************************9.************ PP

                         DUF732  82 vgaAvsayCPeql 94 
                                    +++A+sayCP+++
  gi|121637220|ref|YP_977443.1|  96 AVDAASAYCPQYV 108
                                    ***********96 PP

>> HOASN  Haem-oxygenase-associated N-terminal helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7     0.022     2e+02      40      68 ..      17      45 ..       5      56 .. 0.77
   2 ?    8.8   2.0   0.00023         2      13      53 ..      55      95 ..      47     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          HOASN 40 ekllalaekGlkGdasayaayqalllvls 68
                                    + l la+ G+ G asa ++  a+l +l+
  gi|121637220|ref|YP_977443.1| 17 AATLGLAALGFAGTASASSTDEAFLAQLQ 45
                                   45678999999999999999888888775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00023
                                   T--SHHHHHHHHHTSTT--HHHHHHHHHHHHHHHHHHHTT- CS
                          HOASN 13 nlpieeaalladalkvgasldqidlalekllalaekGlkGd 53
                                      i++a  + dal  g s + +  a+ k   l++kG k  
  gi|121637220|ref|YP_977443.1| 55 ARAIKDAHAVCDALDEGHSAKAVIKAVAKATGLSAKGAKTF 95
                                   55799999999****99999999999999999999998863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 896.97
//
Query:       gi|121637221|ref|YP_977444.1|  [L=550]
Description: arginyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-40  136.7   0.0    7.3e-40  135.9   0.0    1.5  1  DALR_1           DALR anticodon binding domain
    3.9e-23   81.8   0.0    1.5e-22   80.0   0.0    2.1  2  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    3.1e-18   65.8   0.0    5.2e-17   61.8   0.0    2.0  1  tRNA-synt_1d     tRNA synthetases class I (R)
    4.3e-07   29.0   0.4       0.31    9.7   0.0    3.9  4  tRNA-synt_1g     tRNA synthetases class I (M)
    5.3e-07   28.3   0.0    4.3e-05   22.0   0.0    2.3  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
     0.0062   15.5   0.0       0.36    9.7   0.0    2.5  3  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0065   16.2   0.1      0.012   15.3   0.1    1.4  1  Peripla_BP_6     Periplasmic binding protein


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9   0.0   2.8e-43   7.3e-40       1     119 []     429     550 .]     429     550 .] 0.97

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 2.8e-43
                                    HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCT CS
                         DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnker 80 
                                    vqyahaR++ ++r+a+e     ++++l ll++++e  Ll++l +fp+vle+aa+ +eph++++yl++La ++h+fY+++r
  gi|121637221|ref|YP_977444.1| 429 VQYAHARLSALARNAAELALIPDTNHLELLNHDKEGTLLRTLGEFPRVLETAASLREPHRVCRYLEDLAGDYHRFYDSCR 508
                                    8******************************************************************************* PP

                                    STTSCTHHH....HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                         DALR_1  81 vlkeeeeel...aaaRLaLvkavrqvLangLdlLGieapekm 119
                                    vl++ +e+    ++aRLaL++a+rqv+angL+++G++ape+m
  gi|121637221|ref|YP_977444.1| 509 VLPQGDEQPtdlHTARLALCQATRQVIANGLAIIGVTAPERM 550
                                    ***888876777*****************************9 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   5.9e-26   1.5e-22      13      85 .]      16      93 ..       4      93 .. 0.85
   2 ?   -3.2   0.0         5   1.3e+04      52      68 ..     305     321 ..     300     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 5.9e-26
                                   HHH.....SS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTTEEEEEEETT.EEEEEE CS
                Arg_tRNA_synt_N 13 kaa.....gadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaeklekseiiekvevagpGFiNffL 85
                                   ++      +a + ++ + +e+p+ p++GDya+n+amqlakk+++nPre+A  +ae+l k ++i+++evagpGFiN++L
  gi|121637221|ref|YP_977444.1| 16 AVLaerglDASALPQMVTVERPRIPEHGDYASNLAMQLAKKVGTNPRELAGWLAEALTKVDGIASAEVAGPGFINMRL 93
                                   333455576667778899**********************************************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5
                                    -HHHHHHHHHHT---TT CS
                Arg_tRNA_synt_N  52 nPreiAeeiaeklekse 68 
                                    +P  iA ++a +l+k++
  gi|121637221|ref|YP_977444.1| 305 KPAYIAGDLAYYLDKRQ 321
                                    79999****99999875 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0     2e-20   5.2e-17      19     296 ..     120     390 ..     102     409 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2e-20
                                    T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-----SCC CS
                   tRNA-synt_1d  19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelqdLe 98 
                                     +kv ++f s n   ++h+G  r + +Gda+ rll   G dv+r  +  D G q   ++  l    + + +   +    +
  gi|121637221|ref|YP_977444.1| 120 GRKVNLEFVSANPTGPIHIGGTRWAAVGDALGRLLTTQGADVVREYYFNDHGAQIDRFANSLIAAAKGEPT---P----Q 192
                                    58999*************************************************99988888776665533...3....4 PP

                                    CHHHHHHHHCCCSHCCCHHHHHHHHHHHCT.-HHHHHHHHH.HHHHHHHHHHHHHHHCT---EC--CC.CCCCCHHHHHH CS
                   tRNA-synt_1d  99 afykeakkdydeeeifaerarnyvvkLqsg.dedirklwkl.lvditrtelqklydrldvtlierGes.lykeslneivk 175
                                    + y  +      e+ + ++a + +   +++  e +r +    + d +++ l++  + +dv      +s     +++++++
  gi|121637221|ref|YP_977444.1| 193 DGYAGSYITNIAEQ-VLQKAPDALSLPDAElRETFRAIGVDlMFDHIKQSLHEFGTDFDVYT--HEDSmHTGGRVENAIA 269
                                    55666655544455.556677666655544155677765443899***************99..5677345679****** PP

                                    HHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHC CS
                   tRNA-synt_1d 176 elkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkk 255
                                     l++ g + e+dGa+ +  + fg+   +vv ksDG   y + D+a   ++ ++  +d  +y++ +  + ++ ++ +++  
  gi|121637221|ref|YP_977444.1| 270 RLRETGNIYEKDGATWLRTSAFGDDKDRVVIKSDGKPAYIAGDLAYYLDK-RQRGFDLCIYMLGADHHGYIARLKAAAAA 348
                                    ********************************************988775.5678************************* PP

                                    TTSSTTTSE.EEEEEE--EE-TTSSB..SBCSSSTC-BHHHHHH CS
                   tRNA-synt_1d 256 igyvpeskd.lehanfGmvlgkdkkk..fktrkGetvkLadlLd 296
                                     g +p +++ l  ++  +v  +d+++  ++ r+G +  L+dl++
  gi|121637221|ref|YP_977444.1| 349 FGDDPATVEvLIGQMVNLV--RDGQPvrMSKRAGTVLTLDDLVE 390
                                    *****96551566777777..8888644889**********986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.069   1.8e+02      11      56 ..     133     178 ..     129     193 .. 0.87
   2 !    9.3   0.0   0.00017      0.43      71     123 ..     235     287 ..     223     300 .. 0.89
   3 !    3.9   0.0    0.0071        18      23      59 ..     309     347 ..     306     367 .. 0.80
   4 !    9.7   0.0   0.00012      0.31     327     366 ..     374     414 ..     366     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.069
                                    SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHH CS
                   tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkA 56 
                                    +g++H+G  + +  +D++ R    +g +v+       hG +i   A
  gi|121637221|ref|YP_977444.1| 133 TGPIHIGGTRWAAVGDALGRLLTTQGADVVREYYFNDHGAQIDRFA 178
                                    699*******9999**************998888888998887666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEE CS
                   tRNA-synt_1g  71 heeikelfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlyc 123
                                     ++ik+ +++++  fd y++ +s++    v++ + +l e g iyek+ + +  
  gi|121637221|ref|YP_977444.1| 235 FDHIKQSLHEFGTDFDVYTHEDSMHTGGRVENAIARLRETGNIYEKDGATWLR 287
                                    5678999***************************************9888765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0071
                                    HHHH.HHHHHHHHTT-E.EEEEEEE---SHHHHHHHHHT CS
                   tRNA-synt_1g  23 isaD.ifaRykrlrgee.vlfvcgtDehGtpielkAeke 59 
                                    i++D +++  kr+rg + ++++ g D+hG    lkA+++
  gi|121637221|ref|YP_977444.1| 309 IAGDlAYYLDKRQRGFDlCIYMLGADHHGYIARLKAAAA 347
                                    55562355568999**9899**********999998765 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00012
                                    -----------HHHHHHHH-HHHHHHHHHH.HS-TTS-EEE CS
                   tRNA-synt_1g 327 KlSkSrgvvvkakealerldadllRYylaa.eapekkDldf 366
                                    ++Sk  g+v + ++++e + +d+ RY l++ + ++  D+d+
  gi|121637221|ref|YP_977444.1| 374 RMSKRAGTVLTLDDLVEAIGVDAARYSLIRsSVDTAIDIDL 414
                                    7****************************945555567766 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0054        14      33      88 ..     131     186 ..     122     237 .. 0.86
   2 !   22.0   0.0   1.7e-08   4.3e-05     519     601 ..     328     412 ..     316     413 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0054
                    tRNA-synt_1  33 yvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgake 88 
                                    + tG +HiG     ++ d + r  + +G +v +   +  +G  i+   +  ++a +
  gi|121637221|ref|YP_977444.1| 131 NPTGPIHIGGTRWAAVGDALGRLLTTQGADVVREYYFNDHGAQIDRFANSLIAAAK 186
                                    669**************************************999887777766655 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.7e-08
                    tRNA-synt_1 519 mlleGlDiirgWvarlillslaltgsePfkevlv...hglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdv 595
                                    +++ G D + g++arl   + a+ ++    evl+     lvrd++  +mSK+ g v+  +d++++ g+da R+ li s+v
  gi|121637221|ref|YP_977444.1| 328 IYMLGAD-HHGYIARLKAAAAAFGDDPATVEVLIgqmVNLVRDGQPVRMSKRAGTVLTLDDLVEAIGVDAARYSLIRSSV 406
                                    6667777.4588888888888877777777888622256899**********************************9999 PP

                    tRNA-synt_1 596 grdinl 601
                                      +i++
  gi|121637221|ref|YP_977444.1| 407 DTAIDI 412
                                    888876 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.02        51      32      69 ..     131     169 ..     127     179 .. 0.87
   2 ?   -2.2   0.0      0.56   1.4e+03     113     146 ..     236     270 ..     230     278 .. 0.73
   3 !    9.7   0.0   0.00014      0.36     273     322 ..     366     415 ..     331     443 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.02
                   tRNA-synt_1f  32 spSGliHiGnlrevltadlvaralrkrgee.vrlilisD 69 
                                     p G+iHiG  r  + +d++ r l+ +g + vr  ++ D
  gi|121637221|ref|YP_977444.1| 131 NPTGPIHIGGTRWAAVGDALGRLLTTQGADvVREYYFND 169
                                    589***********************9999677766666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.56
                   tRNA-synt_1f 113 aelvesLdelgievefisate.lYksglydeaike 146
                                     ++++sL+e+g ++++++ ++ + + g+ ++ai +
  gi|121637221|ref|YP_977444.1| 236 DHIKQSLHEFGTDFDVYTHEDsMHTGGRVENAIAR 270
                                    5678999*******998766526677777776654 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00014
                   tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                    l+ + +   ms+  G+vltl+d++e +  +  r+ ++r+   +a+++dl 
  gi|121637221|ref|YP_977444.1| 366 LVRDGQPVRMSKRAGTVLTLDDLVEAIGVDAARYSLIRSSVDTAIDIDLA 415
                                    455555559************************************99986 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   4.6e-06     0.012     229     322 ..     144     240 ..      79     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                                    HHHHHHHHH.HHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCT...HCCHHHH CS
                   Peripla_BP_6 229 eedlkalgg.eaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaag...sltreav 304
                                    ++   alg     +g+ +v  y+ +  +++ ++f++++ aa++g+p p+  +ag yi+  +  ++l++a    sl  +++
  gi|121637221|ref|YP_977444.1| 144 AAVGDALGRlLTTQGADVVREYYFNDHGAQIDRFANSLIAAAKGEPTPQDGYAGSYIT-NIAEQVLQKAPdalSLPDAEL 222
                                    444455555334678888888666557999***************8888888888875.556*******5466899**** PP

                                    HHHHHHS-BECCCTCCBE CS
                   Peripla_BP_6 305 raaleslgfdgllgplkf 322
                                    r++++++g+d ++  +k 
  gi|121637221|ref|YP_977444.1| 223 RETFRAIGVDLMFDHIKQ 240
                                    **********99877553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3548.06
//
Query:       gi|121637222|ref|YP_977445.1|  [L=447]
Description: diaminopimelate decarboxylase lysA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-56  192.0   0.0    1.4e-56  191.6   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    1.2e-14   54.3   0.0    1.6e-14   53.9   0.0    1.4  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    0.00029   20.5   0.3    0.00052   19.7   0.3    1.4  1  Ala_racemase_N   Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0   2.3e-60   1.4e-56       2     246 ..      48     306 ..      47     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 2.3e-60
                                    HHHHHHHHHHHHHCT.CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHH CS
                  Orn_Arg_deC_N   2 asierklkrwkkalp.rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryal 80 
                                    +++++++++ + a++  ++v+Ya Ka+   +v ++++e+Gl ld+   +El+ +l a ++peri+ ++++k+++el +a+
  gi|121637222|ref|YP_977445.1|  48 DDFRSRCRETAAAFGsGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAV 127
                                    578999*********999************************************************************** PP

                                    HCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHC..HHHHHHHHHHHHTTEEE CS
                  Orn_Arg_deC_N  81 ekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaale..eavealleaakeenlql 154
                                    + gv +++vd++ e+e+l+ +a e    ++vl+R +++v+a+t+e+ist++e++KFG +++   a++a++++   ++l l
  gi|121637222|ref|YP_977445.1| 128 KAGVGHIVVDSMTEIERLDAIAGEagivQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVAsgAAMAAVRRVFATDHLRL 207
                                    *********************************************************999988999************** PP

                                    EEEE---BSSC-SCHHHHHHHHHHHHHHHHHH.HHT....---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHH CS
                  Orn_Arg_deC_N 155 vGvsfHvGSgvsdleafvkavekalklfdela.elG....vklkiLdvGGGfgveyeeeeeplkleeiaekirealeeaf 229
                                    vG++ H+GS+++d+ +f  a++++++l+  ++ e+G     ++ ++d+GGG+g+ y   ++p +++e a k+ + + +  
  gi|121637222|ref|YP_977445.1| 208 VGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVgEFGpektAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDES 287
                                    **************************9998888888333358999*****************************998877 PP

                                    H..TSSS-EEEE--SHHHH CS
                  Orn_Arg_deC_N 230 p..gdkevtiiaEpGRalv 246
                                       g + +++++EpGRa++
  gi|121637222|ref|YP_977445.1| 288 TavGLPTPKLVVEPGRAIA 306
                                    678**************97 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   2.7e-18   1.6e-14      11      98 .]     313     403 ..     135     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.7e-18
                                    EEEEEEEEEET.C....EEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEE CS
                                    xxxxxxxxxxx.x....xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Orn_DAP_Arg_deC  11 vtrViavkese.k....kkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdrelp 84 
                                    + +V +vk+++ +    +++v vd+Gm+d++r alyg+ +++  v++     ++++  ++++vG+ CesgD++++d  +p
  gi|121637222|ref|YP_977445.1| 313 LYEVGTVKDVDvSatahRRYVSVDGGMSDNIRTALYGAQYDVrLVSR----VSDAPPVPARLVGKHCESGDIIVRDTWVP 388
                                    5566667766533667799***********************77753....34557799********************* PP

                                    E.--TT-EEEESS-S CS
                                    x.xxxxxxxxxxxxx RF
                Orn_DAP_Arg_deC  85 e.levGdllafedaG 98 
                                    + +++Gdl+a+  +G
  gi|121637222|ref|YP_977445.1| 389 DdIRPGDLVAVAATG 403
                                    ***********9887 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   8.7e-08   0.00052       1     159 [.      45     217 ..      45     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.7e-08
                                    EEHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHH.HHHHHHTTSCSEEEEESC.ST CS
                 Ala_racemase_N   1 idldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleE.alelreagitapilvleg.fs 78 
                                    id d +r+++r  +a++g+ga++    Ka        evar   e+   ++ v+t  E a++l ++   ++i + +   s
  gi|121637222|ref|YP_977445.1|  45 IDEDDFRSRCRETAAAFGSGANVHYAAKA----FLCSEVARWISEE-GLCLDVCTGGElAVALHASFPPERITLHGNnKS 119
                                    66777777777777777666777777777....6666777766666.344555555552568999988999988888889 PP

                                    GGGHHHHHHT.TEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSS..............SSSBSC..HHHHHHHHHH CS
                 Ala_racemase_N  79 peelaalaey.dltvtvdsleqlealaaaareagkplrvhlkidtgmg..............RlGftp..eeleelleal 141
                                     +el a++++   +++vds+ ++e+l+a+a eag  ++v++ + +g +              + G++    ++ ++++++
  gi|121637222|ref|YP_977445.1| 120 VSELTAAVKAgVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEahthefistahedqKFGLSVasGAAMAAVRRV 199
                                    *********9455899******************************999999*************6665377899***** PP

                                    HHTTTEEEEEEE-S-SST CS
                 Ala_racemase_N 142 aalpglrleglmtHfasa 159
                                     a ++lrl+gl +H +s 
  gi|121637222|ref|YP_977445.1| 200 FATDHLRLVGLHSHIGSQ 217
                                    **************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3309.48
//
Query:       gi|121637223|ref|YP_977446.1|  [L=441]
Description: homoserine dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-66  221.7   0.3    1.2e-65  220.7   0.3    1.5  1  Homoserine_dh  Homoserine dehydrogenase
    2.2e-22   79.9   1.5    3.2e-22   79.4   0.6    1.8  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
    1.8e-10   40.4   2.3    1.9e-10   40.3   0.4    2.0  2  ACT            ACT domain


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.7   0.3     2e-69   1.2e-65       1     173 []     139     322 ..     139     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 2e-69
                                    --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTT CS
                  Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgl 80 
                                    P+i++l+++l+gd++ r+ Gi+ngt+nyil++m+++ga+++++l++a +lGyaeaDpt+DveG+Daa+K+aila++af++
  gi|121637223|ref|YP_977446.1| 139 PVIRPLTQSLAGDTVLRVAGIVNGTTNYILSAMDSTGADYASALADASALGYAEADPTADVEGYDAAAKAAILASIAFHT 218
                                    9******************************************************************************* PP

                                    T--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE...........CEEEEEEEEEETTSGGGHSSST-EEEEEEESSS CS
                  Homoserine_dh  81 eveledvevegiskltaedikeakeegkvlklvasa...........vearVkpelvpkshplasvkgsenavlvetdrl 149
                                    +v+ +dv++egi+k+t++d+  a++ g+++kl+ ++           v+arV p+lvp shpla v+g++nav+ve++++
  gi|121637223|ref|YP_977446.1| 219 RVTADDVYREGITKVTPADFGSAHALGCTIKLLSICerittdegsqrVSARVYPALVPLSHPLAAVNGAFNAVVVEAEAA 298
                                    **************************************9999999988******************************** PP

                                    EEEEEEES-SSHHHHHHHHHHHHH CS
                  Homoserine_dh 150 gelviqGpgaGaepTAsavlsDll 173
                                    g+l+++G+gaG++pTAsav +Dl+
  gi|121637223|ref|YP_977446.1| 299 GRLMFYGQGAGGAPTASAVTGDLV 322
                                    **********************96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.6   5.4e-26   3.2e-22       1     117 []      14     131 ..      14     131 .. 0.98
   2 ?   -3.5   0.0       2.6   1.6e+04      59      66 ..     287     295 ..     246     299 .. 0.60

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 5.4e-26
                                    --SHHHHHHHHHHHH---S......SEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-.S--HHHH CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrdsllskdrkallasealtldlddliahldpdvvVEc.asseava 73 
                                    GlG++Gs+v++++++++++      ++l l+++ +r+      + + ++ e lt+d+++l+a++d+d+vVE+ +++e  +
  gi|121637223|ref|YP_977446.1|  14 GLGNVGSEVVRIIENSAEDlaarvgAPLVLRGIGVRR----VTTDRGVPIELLTDDIEELVAREDVDIVVEVmGPVEPSR 89 
                                    9*****************9******************....777889********************************* PP

                                    TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                  NAD_binding_3  74 elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                    + +l aL++gk+vvtank++la  + + eL++aae++++++y+e
  gi|121637223|ref|YP_977446.1|  90 KAILGALERGKSVVTANKALLA--TSTGELAQAAESAHVDLYFE 131
                                    **********************..******************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                    S.-EEEEE- CS
                  NAD_binding_3  59 d.pdvvVEc 66 
                                    + + vvVE+
  gi|121637223|ref|YP_977446.1| 287 AfNAVVVEA 295
                                    336777776 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.51     3e+03      14      50 ..      34      66 ..      33      80 .. 0.63
   2 !   40.3   0.4   3.2e-14   1.9e-10       1      65 [.     355     424 ..     355     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEE CS
                            ACT 14 LarvfgaladrgiNidsieqrssedkvagivfvvivv 50
                                   +arv++ l  rgi ++++++ +      +i  +++ +
  gi|121637223|ref|YP_977446.1| 34 AARVGAPLVLRGIGVRRVTTDRGV----PIELLTDDI 66
                                   678888888888877777766553....344444444 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 3.2e-14
                                    EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.....ECEEEEEEEEEEHHHHHHHHHHHHTT CS
                            ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk.....vagivfvvivvdeedleevlealkkl 65 
                                    +++++ v+D+PG+L++v++ +a+r ++i+ + q  + d+     +a+iv+v++++ ++ l+e+++al +l
  gi|121637223|ref|YP_977446.1| 355 YYVSMNVADKPGVLSAVAAEFAKREVSIAEVRQEGVVDEggrrvGARIVVVTHLATDAALSETVDALDDL 424
                                    7899***************************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3328.20
//
Query:       gi|121637224|ref|YP_977447.1|  [L=360]
Description: threonine synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-71  239.8   6.8    4.6e-71  239.6   6.8    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.6   6.8   2.6e-75   4.6e-71       2     294 .]      33     327 ..      32     327 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.6 bits;  conditional E-value: 2.6e-75
                                    GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                           PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                    tl +g+TPl+++ +lsk++g+ + lK E+lnptgSfKdRg++ +++++  + g++ v++as+GN+ +++Aa+aa++G+ +
  gi|121637224|ref|YP_977447.1|  33 TLLEGGTPLIAATNLSKQTGCTIHLKVEGLNPTGSFKDRGMTMAVTDALAH-GQRAVLCASTGNTSASAAAYAARAGITC 111
                                    7899*******************************************9999.9*************************** PP

                                    EEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEE CS
                           PALP  82 tivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpda 160
                                     +++p+++ + +k+a+  ++Ga++++++g++d+++++a+++aa+ + + lv++  np +ieg++t+++Ei++ lg++pd+
  gi|121637224|ref|YP_977447.1| 112 AVLIPQGKIAmGKLAQAVMHGAKIIQIDGNFDDCLELARKMAADFPTISLVNSV-NPVRIEGQKTAAFEIVDVLGTAPDV 190
                                    *********87*******************************************.9************************ PP

                                    EEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHH. CS
                           PALP 161 vvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafell. 233
                                      +pvG++g+i++ ++g+ e    +  d  +r++g +++g+++l  +       +v++++tia+++++gsp++ + ++  
  gi|121637224|ref|YP_977447.1| 191 HALPVGNAGNITAYWKGYTEyhqlGLIDklPRMLGTQAAGAAPLVLGE------PVSHPETIATAIRIGSPASWTSAVEa 264
                                    ********************8876333368******************......99999**********77777776665 PP

                                    .SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                           PALP 234 .drlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                     +++ +++ + sdee+l+a  l+ar eg++vep+saa++a+l k+ ++g +++g++vv+ +tg
  gi|121637224|ref|YP_977447.1| 265 qQQSKGRFLAASDEEILAAYHLVARVEGVFVEPASAASIAGLlKAIDDGWVARGSTVVCTVTG 327
                                    588889*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2614.22
//
Query:       gi|121637225|ref|YP_977448.1|  [L=316]
Description: homoserine kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-10   40.9   3.1    1.8e-10   40.9   3.1    2.5  2  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00018   21.8   0.9     0.0014   19.0   0.0    2.6  3  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.18   1.6e+03      21      36 ..      13      28 ..       9      62 .. 0.53
   2 !   40.9   3.1     2e-14   1.8e-10       2      66 .]      90     154 ..      89     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHTTEHH CS
                 GHMP_kinases_N 21 avalvaAllallglsl 36
                                   a a+vaA  a lg  +
  gi|121637225|ref|YP_977448.1| 13 ASAVVAASSANLGPGF 28
                                   3344444333334333 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 2e-14
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.eeaklaleaerlaqggngsggDvaasvyGg 66 
                                    +++++ iP+++GLGSSAA++v+++aA++ l  ++  + +   +e  +la   +g+++++aa+v+Gg
  gi|121637225|ref|YP_977448.1|  90 VRCRNAIPHSRGLGSSAAAVVGGLAAVNGLV-VQTdSSPSSDAELIQLASEFEGHPDNAAAAVLGG 154
                                    6799**************************9.5532333333333344444669***********8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.2   1.8e+03      29      53 ..      64      88 ..      56      90 .. 0.80
   2 ?   -1.1   0.0      0.28   2.5e+03      28      56 ..     122     155 ..     102     163 .. 0.75
   3 !   19.0   0.0   1.6e-07    0.0014      23      74 ..     236     285 ..     220     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.2
                 GHMP_kinases_C 29 vgilppeleellealselGalgakl 53
                                   +g+++ +++++   l+++G+ +a+l
  gi|121637225|ref|YP_977448.1| 64 LGPEHLVVRAVQHGLQAAGVSAAGL 88
                                   6777888899999999999888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.28
                 GHMP_kinases_C  28 vvgilppeleellealselG.....algaklsGa 56 
                                    +++++p +  el++++se       a +a+l Ga
  gi|121637225|ref|YP_977448.1| 122 QTDSSPSSDAELIQLASEFEghpdnAAAAVLGGA 155
                                    5566777777888888777767777666666666 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.6e-07
                 GHMP_kinases_C  23 s...elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeq 74 
                                    +   ++  +++  + +  e l++l+++   +a lsGa  Gp+++al +d +   +
  gi|121637225|ref|YP_977448.1| 236 DllhQP--QRAAAMTASAEYLRLLRRHN-VAAALSGA--GPSLIALSTDSELPTD 285
                                    245678..9999999*********9999.9*******..********77665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2319.24
//
Query:       gi|121637226|ref|YP_977449.1|  [L=602]
Description: transcription termination factor Rho [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-28   96.8   0.1    1.4e-27   95.4   0.1    1.8  1  Rho_RNA_bind  Rho termination factor, RNA-binding domain
    2.9e-25   89.2   0.0      5e-25   88.4   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
    1.1e-10   41.2   0.0    1.3e-09   37.8   0.1    2.5  2  Rho_N         Rho termination factor, N-terminal domain
    4.3e-05   23.2   0.1    0.00026   20.6   0.0    2.3  2  AAA_25        AAA domain
     0.0042   17.0   0.0     0.0084   16.0   0.0    1.4  1  NACHT         NACHT domain
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.55   10.7   0.0    2.2  2  AAA           ATPase family associated with various cellular 
       0.46   11.1   4.4       0.87   10.2   4.4    1.4  1  HNF-1_N       Hepatocyte nuclear factor 1 (HNF-1), N terminus


Domain annotation for each model (and alignments):
>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.1   5.3e-31   1.4e-27       1      73 []     226     303 ..     226     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 5.3e-31
                                    EEEEEEE-TTS-EEEE-GTT---TT-EEE-CCCCCCTT--TT-EEEEEEE--......-SSS-SEEECEECEETTEEXX CS
                   Rho_RNA_bind   1 veGiLeilpdgygFlRtsnylpgpedvYVsasqirkfgLrtGDaveGkvrpp......kerekynaLlrvesvngeepe 73 
                                    v+GiL++l d+y+F+Rts+ylpgp+dvYVs++++rk g+r+GDav+G+vr p      ++r+k+n+L+r++s+ng ++e
  gi|121637226|ref|YP_977449.1| 226 VAGILDVL-DNYAFVRTSGYLPGPHDVYVSMNMVRKNGMRRGDAVTGAVRVPkegeqpNQRQKFNPLVRLDSINGGSVE 303
                                    58******.*******************************************99999888***************8875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   1.9e-28     5e-25       2     211 ..     334     538 ..     333     540 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1.9e-28
                                    SHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   2 irvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd..d.aiiyvgiGergnevaevleefpegtimkrtvlvant 78 
                                     rv+D+++pi++Gqr li++  + Gkt+i+q +++  + +  +    +v++ er +ev+++ ++++ +       ++a+t
  gi|121637226|ref|YP_977449.1| 334 TRVIDLIMPIGKGQRALIVSPPKAGKTTILQDIANAITRNnpEcHLMVVLVDERPEEVTDMQRSVKGE-------VIAST 406
                                    59********************************998777555688999***********99888764.......79*** PP

                                    TTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  79 snepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdr 158
                                     ++p+     ++ ++i  A  + +qgk+v++++ds++r  +A+++ s + g++ +  g  ++  +   +++  a ++ ++
  gi|121637226|ref|YP_977449.1| 407 FDRPPSDHTSVAELAIERAKRLVEQGKDVVVLLDSITRLGRAYNNASPASGRILS-GGVDSTALYPPKRFLGAARNI-EE 484
                                    ****************************************************976.799999999************.67 PP

                                    EEEEEEEEEEE-GGCSTTSHH.HHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTE CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 159 tGsvtivaavspaggDfsdpv.ttatlgitdgfivLdkklaqrkhfPainvlvS 211
                                     Gs+ti+a+  ++ g   d v  ++  g  ++ + Ld+k+a+r++fPa++v  S
  gi|121637226|ref|YP_977449.1| 485 GGSLTIIATAMVETGSTGDTViFEEFKGTGNAELKLDRKIAERRVFPAVDVNPS 538
                                    8****************88761577888889********************988 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   5.2e-13   1.3e-09       2      36 ..      37      71 ..      36      78 .. 0.91
   2 ?    0.1   0.0       0.3   7.7e+02      21      31 ..     536     546 ..     524     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.2e-13
                                   HHHS-HHHHHHHHHHTT-TTGGGS-HHHHHHHHHH CS
                          Rho_N  2 LkektlseLraiAkelgienysrlRKqdLIfaIlk 36
                                   L ++ l+eLra+A+  g++++s++RK++LI aI +
  gi|121637226|ref|YP_977449.1| 37 LATMVLPELRALANRAGVKGTSGMRKNELIAAIEE 71
                                   889******************************87 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                                    TGGGS-HHHHH CS
                          Rho_N  21 nysrlRKqdLI 31 
                                    n+s+ RK +L 
  gi|121637226|ref|YP_977449.1| 536 NPSGTRKDELL 546
                                    89*******96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.94   2.4e+03     163     182 ..      58      79 ..      29      82 .. 0.68
   2 !   20.6   0.0     1e-07   0.00026      25     169 ..     339     460 ..     321     466 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.94
                         AAA_25 163 sdv..galvealeriarrtgaa 182
                                    s +  ++l++a+e+i+r+ + a
  gi|121637226|ref|YP_977449.1|  58 SGMrkNELIAAIEEIRRQANGA 79 
                                    4444467888888888887765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1e-07
                         AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarll 104
                                    l++ +  +g  al++ +p++GKtt++ d+a a+++  p  +        V++v+ E +e e+    r v  +        
  gi|121637226|ref|YP_977449.1| 339 LIMPI-GKGQRALIVSPPKAGKTTILQDIANAITRNNPECH------LMVVLVD-ERPE-EVTDMQRSVKGE-------V 402
                                    55555.799**************************997533......3455554.8888.444443333333.......3 PP

                         AAA_25 105 vldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalv 169
                                    + +     ++p   + ++ ++++ ++++  + +e+  + ++v +D+++r+ ++ +n++ + g+++
  gi|121637226|ref|YP_977449.1| 403 IAST---FDRP---PSDHTSVAELAIERAKRLVEQ-GKDVVVLLDSITRLGRAYNNASPASGRIL 460
                                    3332...1222...234555678899999999999.8899999********99999999888876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.3e-06    0.0084      12     104 ..     358     456 ..     355     469 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                                    CHHHHHHHHHHHHCTS-SCCCC-SEEEEE..ETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE..... CS
                          NACHT  12 GKTtLlqklalawaegklpqgafklvFfl..slrelsrsgnarsladllfsqlpepaapvsevwavllelperlL..... 84 
                                    GKTt lq +a a+ ++++++    +v ++  +  e+++ +++    ++++s ++ p ++++ v ++ +e+++rl+     
  gi|121637226|ref|YP_977449.1| 358 GKTTILQDIANAITRNNPECH--LMVVLVdeRPEEVTDMQRS-VKGEVIASTFDRPPSDHTSVAELAIERAKRLVeqgkd 434
                                    *****************8884..3333331134455555544.6679***************999999999999999999 PP

                                    ..EEEE-STT-SS-TCH..... CS
                          NACHT  85 ..lilDglDelvtdlgqkekqp 104
                                       +lD++ +l +  +++ +++
  gi|121637226|ref|YP_977449.1| 435 vvVLLDSITRLGRAYNNASPAS 456
                                    99******99998887745444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.1   1.1e+04      63      98 ..      41      74 ..      32      79 .. 0.68
   2 ?   10.7   0.0   0.00021      0.55       2      79 ..     350     453 ..     349     462 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                                   EEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                            AAA 63 fiDEidalaksrsgseseeeervvnqLlteldgvkk 98
                                   ++ E+ ala++   + ++ +    n+L++++++ ++
  gi|121637226|ref|YP_977449.1| 41 VLPELRALANRA--GVKGTSGMRKNELIAAIEEIRR 74
                                   566777777666..5555666667888888877765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                                    EEESSTTSSHHHHHHHHHHHHTHE...................EEEEETTTCSSS...........STTHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgve...................fleisgsellsk...........yvgesekkirelfk 51 
                                    l++ pp  GKT++ + +a+ + ++                              +           ++   +++   + +
  gi|121637226|ref|YP_977449.1| 350 LIVSPPKAGKTTILQDIANAITRNnpechlmvvlvderpeevtD----------MqrsvkgeviasTFDRPPSDHTSVAE 419
                                    7899****************976633444444333333333330..........14444444444444444444444443 PP

                                    HHHHTS.......TSEEEEEETGGGHHHHHTTCCC CS
                            AAA  52 eakeka.......kpsilfiDEidalaksrsgses 79 
                                     a e a       k +++++D i +l+++  +++s
  gi|121637226|ref|YP_977449.1| 420 LAIERAkrlveqgKDVVVLLDSITRLGRAY-NNAS 453
                                    332222334455346999999999987776.4444 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.4   0.00034      0.87      11      82 ..      57     130 ..      55     192 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                        HNF-1_N  11 esGltkeelihALedldrldrehgek.leklrlaegeea.dskggittlangagkssknasssttksklsqtqr 82 
                                     sG+ k+eli+A+e++ r  +   +   ++ ++ +g+++ +s++ +t+ +++ +++ +++s+ +   + s t +
  gi|121637226|ref|YP_977449.1|  57 TSGMRKNELIAAIEEIRRQANGAPAVdRSAQEHDKGDRPpSSEAPATQGEQTPTEQIDSQSQQVRPERRSATRE 130
                                    59***************996444322023333444555533333333333333333333333333222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4253.46
//
Query:       gi|121637227|ref|YP_977450.1|  [L=80]
Description: 50S ribosomal protein L31 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-32  111.3   0.2    2.2e-32  111.1   0.2    1.1  1  Ribosomal_L31  Ribosomal protein L31
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.015   15.1   0.1    1.1  1  DUF1364        Protein of unknown function (DUF1364)


Domain annotation for each model (and alignments):
>> Ribosomal_L31  Ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.2   2.4e-36   2.2e-32       1      67 []       1      66 [.       1      66 [. 0.99

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 2.4e-36
                  Ribosomal_L31  1 mKkgiHPeyrevvvkcacgeefltrStlkekpeikvdvcsksHPfYtGkqklvdtaGrvekFkkryg 67
                                   mK++iHP y+e++v+c cg++f+trSt k    i v+vcs++HPfYtGkqk++d++Grv++F+kryg
  gi|121637227|ref|YP_977450.1|  1 MKSDIHPAYEETTVVCGCGNTFQTRST-KPGGRIVVEVCSQCHPFYTGKQKILDSGGRVARFEKRYG 66
                                   9**************************.9999**********************************7 PP

>> DUF1364  Protein of unknown function (DUF1364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.7e-06     0.015      25      70 ..      11      55 ..       7      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-06
                                   GG-EEEE--------------SSSEEEE-HHHHHHHTTSS-SS-HH CS
                        DUF1364 25 eTtvlahyrlaglagvglksddllaafaCsachdaidrRtrildae 70
                                   eTtv++    ++    ++k+ + + +  Cs+ch    ++++ild +
  gi|121637227|ref|YP_977450.1| 11 ETTVVCGC-GNTFQTRSTKPGGRIVVEVCSQCHPFYTGKQKILDSG 55
                                   9*****98.67777889************************99943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 575.31
//
Query:       gi|121637228|ref|YP_977451.1|  [L=357]
Description: peptide chain release factor 1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-61  208.1   0.3    1.1e-60  204.9   0.0    2.0  2  PCRF          PCRF domain
    4.3e-39  133.0   1.4    7.1e-39  132.3   1.4    1.3  1  RF-1          RF-1 domain
    0.00046   20.4   4.5       0.09   13.0   0.0    3.4  3  ABC_tran_CTD  ABC transporter C-terminal domain
  ------ inclusion threshold ------
      0.084   12.8   7.2       0.29   11.0   0.4    2.4  2  CHASE3        CHASE3 domain


Domain annotation for each model (and alignments):
>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.0   2.3e-64   1.1e-60       3     193 .]      13     204 ..      11     204 .. 0.97
   2 ?    1.3   0.1      0.06   2.7e+02      28      63 ..     259     292 ..     253     323 .. 0.65

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 2.3e-64
                                    HHHTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH CS
                           PCRF   3 eeleelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleelekeleel 82 
                                    +e++ele +l+dp++++++++a+++ +++a+l++iv++ ++l++a++dle+a+el+++de++a    +e+++le+++ el
  gi|121637228|ref|YP_977451.1|  13 AEHAELELALADPALHSNPAEARRVGRRFARLAPIVATHRKLTSARDDLETARELVASDESFA----AEVAALEARVGEL 88 
                                    799*****************************************************8998888....69*********** PP

                                    ..HHHHHT-..SSSTTSEEEEEEEE-SSTHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEESSS.SEEEEEEEEEST... CS
                           PCRF  83 eeelkklLlpkdendeknaileiraGaGGdeaalfaedLlrmYtryaerkgwkvevldaseeeagGikevtleiege... 159
                                    +++l+++L p+d++d+ +++le+++G+GG+e+alfa+dL+rmY ryaer+gw v+vld++++++gG+k++tl+i  +   
  gi|121637228|ref|YP_977451.1|  89 DAQLTDMLAPRDPHDADDIVLEVKSGEGGEESALFAADLARMYIRYAERHGWAVTVLDETTSDLGGYKDATLAIASKadt 168
                                    ***************************************************************************88555 PP

                                    ..THHHHHGGG-EEEEEEEE-TTSSS--EEEEEEEE CS
                           PCRF 160 ..gaYgkLkfEsGvHRvqRvpetesqgrihTStatV 193
                                      g+++++kfE GvHRvqRvp+tesqgr+hTS+a V
  gi|121637228|ref|YP_977451.1| 169 pdGVWSRMKFEGGVHRVQRVPVTESQGRVHTSAAGV 204
                                    557*******************************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.06
                                    THHHHHTHHHHHHHHHHHHHTTTHHH...HT....- CS
                           PCRF  28 skelaeleeivealeeleealedleeakelleedee 63 
                                    ++e ++l++ ++al+ l ++l+ ++e ++l+  d++
  gi|121637228|ref|YP_977451.1| 259 QNERSQLQNKTRALQVLAARLQAMAEEQALA--DAS 292
                                    5677777777777777777777777755555..222 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   1.4   1.6e-42   7.1e-39       4     116 .]     215     322 ..     211     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1.6e-42
                                    CCE--GGGEEEEEE---SSSSSSGCSSSCEEEEEETTTTEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCHT CS
                           RF-1   4 eieidekdleidtfrssGaGGQnVNktesaVrlthlptgvivvecqeeRsqekNrekAlerLkaklkekeleeekeeekk 83 
                                    +++ide+dl+id+frssG+GGQ VN+t+saVr+thlptg ivv+cq+eRsq +N+ +Al++L+a+l+++  e+  +++++
  gi|121637228|ref|YP_977451.1| 215 QVQIDESDLRIDVFRSSGKGGQGVNTTDSAVRITHLPTG-IVVTCQNERSQLQNKTRALQVLAARLQAMAEEQALADASA 293
                                    499************************************.8*************************65533333333333 PP

                                    TTTT-.S.-S---S.--ECEEEECGCTTEEEETT CS
                           RF-1  84 rrvkkekkkigtgs.sekiRtynkkpqsrvkdhr 116
                                    +r     ++i+t + se+iRtyn+ p++r++dhr
  gi|121637228|ref|YP_977451.1| 294 DR----ASQIRTVDrSERIRTYNF-PENRITDHR 322
                                    33....358999999*********.********9 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     2e-05      0.09      16      53 ..       7      44 ..       5      67 .. 0.88
   2 !    6.7   0.1    0.0019       8.4      15      34 ..      76      95 ..      65     108 .. 0.84
   3 ?   -0.3   0.5       0.3   1.4e+03      41      56 ..     270     285 ..     258     299 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                   ABC_tran_CTD 16 eIeaLEeeiaeleaeladpelysdpeklaelsaeleel 53
                                   +I+ L +e aele +ladp+l s+p++  ++ ++ ++l
  gi|121637228|ref|YP_977451.1|  7 TIDVLLAEHAELELALADPALHSNPAEARRVGRRFARL 44
                                   7888999******************9999888887665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0019
                   ABC_tran_CTD 15 aeIeaLEeeiaeleaeladp 34
                                   ae +aLE++  el+a+l d 
  gi|121637228|ref|YP_977451.1| 76 AEVAALEARVGELDAQLTDM 95
                                   78999**********99985 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.3
                   ABC_tran_CTD  41 eklaelsaeleeleae 56 
                                     +l+ l a+l++  +e
  gi|121637228|ref|YP_977451.1| 270 RALQVLAARLQAMAEE 285
                                    2233333333333333 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   6.5e-05      0.29      49     124 ..      55     130 ..      47     138 .. 0.89
   2 ?    4.7   1.5     0.006        27      63     111 ..     259     306 ..     247     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                         CHASE3  49 aeiqealeelreltadnpeqqerldrlealieqklaeleetialrreggleaalalvrsdegkelmdeiraliaem 124
                                    ++ +++le++rel+a++++ ++ +++lea++ +  a+l  ++a r   + ++ +  v+s+eg e    + a +a+m
  gi|121637228|ref|YP_977451.1|  55 TSARDDLETARELVASDESFAAEVAALEARVGELDAQLTDMLAPRDPHDADDIVLEVKSGEGGEESALFAADLARM 130
                                    567889********************************************************88776666666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.006
                         CHASE3  63 adnpeqqerldrlealieqklaeleetialrreggleaalalvrsdegk 111
                                    +++ +q+++ +r+ +  +++l+ ++e+ al+ + + + a ++   d++ 
  gi|121637228|ref|YP_977451.1| 259 QNERSQLQNKTRALQVLAARLQAMAEEQALADA-SADRASQIRTVDRSE 306
                                    6778999999*********************99.888888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2563.90
//
Query:       gi|121637229|ref|YP_977452.1|  [L=325]
Description: hemk protein hemK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-13   49.2   0.1    1.3e-12   48.1   0.1    1.6  1  PrmC_N           PrmC N-terminal domain
    1.4e-09   38.5   0.4    5.6e-09   36.6   0.0    2.2  3  Methyltransf_25  Methyltransferase domain
    1.3e-08   34.8   0.0      2e-08   34.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.9e-07   29.8   0.0    9.1e-07   28.6   0.0    1.5  1  MTS              Methyltransferase small domain
    1.2e-06   29.1   0.6    2.3e-05   24.9   0.2    2.8  2  Methyltransf_11  Methyltransferase domain
    0.00016   21.4   0.0    0.00034   20.4   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
    0.00043   19.8   0.0    0.00063   19.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.092   12.7   0.0       0.14   12.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   5.9e-16   1.3e-12       1      71 []      26      94 ..      26      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 5.9e-16
                         PrmC_N  1 eaLreaearLkaagieeaeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaarePlqyIlG 71
                                   +a+  a+a L++ag+++a+ dAe L+ah+ g++r +l l       +e + r++ +++ Ra+r+Plq+++G
  gi|121637229|ref|YP_977452.1| 26 QAIDLAAALLAEAGVDSARCDAEQLAAHLAGTDRGRLPLFEP--PGDEFFGRYRDIVTARARRVPLQHLIG 94
                                   688899*****************************9999875..599999********************9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.8   1.1e+04      34      58 ..      28      50 ..      25      58 .. 0.50
   2 !   36.6   0.0   2.5e-12   5.6e-09       1      71 [.     134     209 ..     134     222 .. 0.89
   3 ?   -2.3   0.0       3.4   7.5e+03      85      97 .]     245     257 ..     240     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHTTTTEEEEESBCCGB CS
                Methyltransf_25 34 leaareraeeeglnvefvqgdaedl 58
                                   ++ a++ ++e+   v+  ++dae+l
  gi|121637229|ref|YP_977452.1| 28 IDLAAALLAEA--GVDSARCDAEQL 50
                                   44444444333..344444555544 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 2.5e-12
                                    EEEET-TTSHHHHHHHCTS...T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG...BSSSTTTEEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl...g.kakvtgvDiseemleaareraeeeglnvefvqgdaed...lpfedgsfDlvvss 71 
                                    ++d+++G+G l+ ala++    g ka+++g+D s+ +l++ar++a  +g  ve+v++d+++   lp+ dg++Dl+vs+
  gi|121637229|ref|YP_977452.1| 134 IVDACTGSGALAVALAQHRanlGlKARIIGIDDSDCALDYARRNA--AGTPVELVRADVTTpclLPELDGQVDLMVSN 209
                                    79***************96655589********************..688*********998889***********95 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.4
                                    HHHHHHHHEEEEE CS
                Methyltransf_25  85 alkeiarvLkpgG 97 
                                    ++  + r+L+pgG
  gi|121637229|ref|YP_977452.1| 245 VVGLAGRWLRPGG 257
                                    5666789*****9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.9e-12     2e-08       7     113 ..     134     265 ..     132     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.9e-12
                Methyltransf_31   7 vlDlGCGtGeltfelae...elgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee...leklledekfDlils 80 
                                    ++D+ +G+G+l+ +la+   +lg ka+++GiD s  a+ +Ar na+    + ve+ ++d+++   l++   d ++Dl++s
  gi|121637229|ref|YP_977452.1| 134 IVDACTGSGALAVALAQhraNLGLKARIIGIDDSDCALDYARRNAAG---TPVELVRADVTTpclLPE--LDGQVDLMVS 208
                                    6899**************999999********************994...456777777777421454..37******** PP

                Methyltransf_31  81 n....................evl....naladpdkileeiervlkpggilliedpr 113
                                    n                     +l    + ++   ++ + + r l+pgg +++e+ +
  gi|121637229|ref|YP_977452.1| 209 NppyipdaavlepevaqhdphHALfggpDGMTVISAVVGLAGRWLRPGGLFAVEHDD 265
                                    *99888886666644444444222566666666666666999*******99999876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     4e-10   9.1e-07      34     110 ..     133     215 ..     120     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4e-10
                                    EEEEET-TTSHHHHHHHHHTTC.....EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTSTTS-EEEEEE--- CS
                            MTS  34 kvlDlGcGaGvlgaalakespe....aevtlvdvdarAlesakenleankle...vevvasdvleeveekkfdlivsNPP 106
                                     ++D ++G G+l++ala++  +    a++  +d +  Al+ a++n++ + +e   ++v++  +l e++ +++dl+vsNPP
  gi|121637229|ref|YP_977452.1| 133 LIVDACTGSGALAVALAQHRANlglkARIIGIDDSDCALDYARRNAAGTPVElvrADVTTPCLLPELD-GQVDLMVSNPP 211
                                    499**************999872211457789***************999988767777777777777.*********** PP

                                    STTT CS
                            MTS 107 fhag 110
                                    +  +
  gi|121637229|ref|YP_977452.1| 212 YIPD 215
                                    8655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2     1e-08   2.3e-05       2      69 ..     136     210 ..     135     261 .. 0.77
   2 ?   -1.9   0.0       2.4   5.4e+03      59      78 ..     269     288 ..     266     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1e-08
                                    EET-TTSHHHHHHH....HTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC...TSS-TT-EEEEEEES CS
                Methyltransf_11   2 dvGcGtGrlaeala....krg..arvvgvDlskemlklakekaseeglkvefvvadaek...lpfednsfDlvvsse 69 
                                    d+ +G+G+la ala    + g  ar++g+D s+ +l++a+++a + +  ve+v+ad+++   lp  d+++Dl vs+ 
  gi|121637229|ref|YP_977452.1| 136 DACTGSGALAVALAqhraNLGlkARIIGIDDSDCALDYARRNAAGTP--VELVRADVTTpclLPELDGQVDLMVSNP 210
                                    666799*******965443349************************9..9********99967***********985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                    TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11  59 dnsfDlvvssevlhhvedpe 78 
                                    ++++Dlv s+  +  v+ ++
  gi|121637229|ref|YP_977452.1| 269 SSTVDLVSSTKLFVDVQARK 288
                                    5789****999998886655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.5e-07   0.00034      69     131 ..     149     212 ..     118     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                    HHHHHH..HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
                        UPF0020  69 aeeear..aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
                                    a+++a+   +++++g+D    +++ ar+Na  + v+ l+ + +   + L++ +g+vd++v+npPY
  gi|121637229|ref|YP_977452.1| 149 AQHRANlgLKARIIGIDDSDCALDYARRNAAGTPVE-LVRADVTTPCLLPELDGQVDLMVSNPPY 212
                                    344444435667******************987775.67788888899***************** PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.8e-07   0.00063     164     233 ..     133     209 ..     114     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.8e-07
                           PrmA 164 evlDvGtGSGiLaiaaak....Lgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadvivaN 233
                                     ++D  tGSG La+a a+    Lg k +++++D  + A++ a++Na+   ve  + +v+++  l++ ++++d++v+N
  gi|121637229|ref|YP_977452.1| 133 LIVDACTGSGALAVALAQhranLGLKaRIIGIDDSDCALDYARRNAAGTPVELvRADVTTPCLLPElDGQVDLMVSN 209
                                    578***********97652222665438***********************9999999888888877799***9999 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.14      26      70 ..     131     177 ..     121     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                Methyltransf_32  26 altvvDvGaGkgYLsfvlal..kekeyklkvvgidakeelvekaekr 70 
                                    +  +vD++ G g L+ +la+   +  +k +++gid ++   + a++ 
  gi|121637229|ref|YP_977452.1| 131 RPLIVDACTGSGALAVALAQhrANLGLKARIIGIDDSDCALDYARRN 177
                                    5679****************7444469********888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2161.80
//
Query:       gi|121637230|ref|YP_977453.1|  [L=217]
Description: hypothetical protein BCG_1361 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-45  153.0   0.0    6.5e-45  152.8   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   0.0   3.6e-49   6.5e-45       2     179 .]      23     197 ..      22     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 3.6e-49
                                    HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                 Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                    a+++G++v++pt+tvYg+++da +++av+ l  +Kgr +d p+ vlv s+ +++ l+  + ++ a +l+++fwPG + l+
  gi|121637230|ref|YP_977453.1|  23 AIKAGQLVVMPTDTVYGIGADAFDSSAVAALLSAKGRGRDMPVGVLVGSWHTIEGLVY-SMPDGARELIRAFWPGALSLV 101
                                    799******************************************************9.********************* PP

                                    EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS- CS
                 Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgv 161
                                    + + + +l+ ++   ++tv +r+P +p+a +Ll+++g p++++San+sg+p++ dae+++++lg+ v ++ld+g+ ++++
  gi|121637230|ref|YP_977453.1| 102 VVQ-APSLQWDLGDAHGTVMLRMPLHPVAIELLREVG-PMAVSSANISGHPPPVDAEQARSQLGDHVAVYLDAGPSEQQA 179
                                    **6.445*****************************9.****************************************** PP

                                    --EEEETTSSTSSECEXX CS
                 Sua5_yciO_yrdC 162 dstVvdltegkpkilRrG 179
                                     st+vdlt+ +p++lR+G
  gi|121637230|ref|YP_977453.1| 180 GSTIVDLTGATPRVLRQG 197
                                    ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1528.26
//
Query:       gi|121637231|ref|YP_977454.1|  [L=404]
Description: undecapaprenyl-phosphate alpha-n-acetylglucosaminyltransferase rfe [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-34  117.4  17.2    5.7e-34  117.4  17.2    2.2  2  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4  17.2   3.2e-38   5.7e-34       2     158 ..     110     274 ..     109     276 .. 0.87
   2 ?   -1.3   0.2      0.11     2e+03      38      55 ..     347     364 ..     291     390 .. 0.51

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3.2e-38
                Glycos_transf_4   2 llllltillilllGflDDvlglkarlKlilqilaalililtldlslttlglllt.qvlielglilavlltllvivgvtNa 80 
                                    +++l++ ++i+ +G++DD +gl+a++K+++qi+aa +l+ ++  +++ l+++++  ++i l    ++lltl + v+++Na
  gi|121637231|ref|YP_977454.1| 110 PAVLVAGAVIMGIGLIDDRWGLDALTKFAGQITAASVLVTMGV-AWSVLYIPVGgVGTIVLDQASSILLTLALTVSIVNA 188
                                    679999*****************************99866665.8899999888568899999***************** PP

                Glycos_transf_4  81 vNliDGldGlaagvsiiialalvvla...avd.....grsellllalallgallGfllfNrypAkvFmGDsgslflGlvl 152
                                    +N++DGldGlaag+ +i+ala+++++   ++d       +  ++++++l+ga+lGfl++N+++Ak+FmGDsgs+++Gl+l
  gi|121637231|ref|YP_977454.1| 189 MNFVDGLDGLAAGLGLITALAICMFSvglLRDhggdvLYYPPAVISVVLAGACLGFLPHNFHRAKIFMGDSGSMLIGLML 268
                                    ************************997773333222233444555889999***************************** PP

                Glycos_transf_4 153 avlail 158
                                    a+++ +
  gi|121637231|ref|YP_977454.1| 269 AAASTT 274
                                    *99876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.11
                Glycos_transf_4  38 ililtldlslttlglllt 55 
                                    +li++l +++  +g  ++
  gi|121637231|ref|YP_977454.1| 347 VLIIYLWVGIGAFGAASS 364
                                    222222233333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2968.22
//
Query:       gi|121637232|ref|YP_977455.1|  [L=161]
Description: hypothetical protein BCG_1363 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-10   41.1  10.7    2.7e-10   40.5  10.7    1.3  1  ATP-synt_I  ATP synthase I chain
  ------ inclusion threshold ------
        1.2    7.4   8.3        1.4    7.1   8.3    1.0  1  DUF2070     Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> ATP-synt_I  ATP synthase I chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5  10.7     3e-14   2.7e-10       1      99 [.      21     114 ..      21     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3e-14
                     ATP-synt_I   1 rivliqlvllavlalgwlltgsasvalsallGglisvlpfalfalrvfrfsgalarkkkkivrslylgeairlaltiall 80 
                                    r+++i++ l+av++l+++++g+++v++ + lG+l+++l+++l+++++    +++++k+++  rs++l  a rla++ +l 
  gi|121637232|ref|YP_977455.1|  21 RLFFINVGLAAVAMLVAGVFGHLTVGMFLGLGLLLGLLNALLVRRSA----ESITAKEHPLKRSMALNSASRLAIITILG 96 
                                    6899*******************************************....7788889***************9988888 PP

                     ATP-synt_I  81 ilalklvkelsllallvGl 99 
                                    ++++++  + + l++++Gl
  gi|121637232|ref|YP_977455.1|  97 LIIAYI-FRPAGLGVVFGL 114
                                    888888.789999999998 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.3   0.00015       1.4      19     124 ..      24     124 ..      11     144 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00015
                        DUF2070  19 lliillalligllaflssklfgillfglp....alvaflltlpvlrilggrltykrslflalltelivviisllaillsa 94 
                                    ++ + la+++ l+a  +++l+  +++gl     +l a+l+   + +i+ +  ++krs+ l+ ++ l  +ii++l++++++
  gi|121637232|ref|YP_977455.1|  24 FINVGLAAVAMLVAGVFGHLTVGMFLGLGlllgLLNALLVRRSAESITAKEHPLKRSMALNSASRL--AIITILGLIIAY 101
                                    444556666666665555533333333331131333333333333333333777777766666665..566678888887 PP

                        DUF2070  95 ll.qalvllalvlslalvfalrllvlvavsd 124
                                    ++ +a        +l +vf+l ++ +++v+ 
  gi|121637232|ref|YP_977455.1| 102 IFrPA--------GLGVVFGLAFFQVLLVAT 124
                                    67422........222333333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1177.73
//
Query:       gi|121637233|ref|YP_977456.1|  [L=250]
Description: F0F1 ATP synthase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-49  166.2  16.5    1.1e-48  166.0  16.5    1.0  1  ATP-synt_A    ATP synthase A chain
  ------ inclusion threshold ------
       0.25   11.6   0.0       0.25   11.6   0.0    3.8  3  DUF2304       Uncharacterized conserved protein (DUF2304)
        5.7    6.6  10.2       0.22   11.1   1.1    3.0  3  SPW           SPW repeat


Domain annotation for each model (and alignments):
>> ATP-synt_A  ATP synthase A chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0  16.5   1.9e-52   1.1e-48       2     211 .]      31     240 ..      30     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 1.9e-52
                                    HHHHHHHHHHHCCC.CCSS.T..TTTSHHHHHHHHHHHHHHHHHHHHCTSSSTXHHHHHHHHHHHHHHHHHCCHCCSST. CS
                     ATP-synt_A   2 lttlivllilllllllatrkkk.kklpgklqnlvealvefvdnlvksvigkkkkkkffpliltlflfilvsNllgliPg. 79 
                                    l+t i+ li++ l+++++ k + +++pg++q ++ea+   ++n+v+s ig + +  ++pl++t+f+fil+sN+l ++P+ 
  gi|121637233|ref|YP_977456.1|  31 LSTAIAGLIVIALAFYLRAKVTsTDVPGGVQLFFEAITIQMRNQVESAIGMRIAPFVLPLAVTIFVFILISNWLAVLPVq 110
                                    7899999****888888877774666***********************95477999******************99999 PP

                                    ...........TTTTTCHHHHHHHHHHHHHHHHHHHHHHHHGG..GGCHHHSSSCCCCHHHHHHHHHH.HHHHHHHHHHH CS
                     ATP-synt_A  80 ...........lraatadinvtlalAlivfllvlilgikkkglkgyfkklfvpplllvplllpielisefarpvsLalRL 148
                                               l +a adin  lalAl+vf++++ +gi ++g++g+  kl+      v ll+pi+l++e+a+p+sL+lRL
  gi|121637233|ref|YP_977456.1| 111 ytdkhghttelLKSAAADINYVLALALFVFVCYHTAGIWRRGIVGHPIKLLK---GHVTLLAPINLVEEVAKPISLSLRL 187
                                    999999999999*********************************9999983...346799******************* PP

                                    HHHHHHHHHHHHHHHHHHCCCTGCCCTTCHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_A 149 fgNifAGelllallagllllllllavllsvli.lllavlllllelfvgfiQAfvFtlLtlvYis 211
                                    fgNifAG +l+al+a++            ++i ++ ++++ +++lfvg+iQAf+F+lLt++Y+s
  gi|121637233|ref|YP_977456.1| 188 FGNIFAGGILVALIALF-----------PPYImWAPNAIWKAFDLFVGAIQAFIFALLTILYFS 240
                                    **************944...........2333245789************************86 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.1e-05      0.25      54      91 ..      17      54 ..       5      57 .. 0.91
   2 ?   -2.4   5.0       0.9   5.4e+03      32      46 ..      92     106 ..      60     151 .. 0.57
   3 ?    3.5   1.5     0.014        82      34      86 ..     191     243 ..     164     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                        DUF2304 54 lanllGvgrgtnllfllgivfllvilfslslklsklee 91
                                    a++lG   +t+ ++  +i+ l+vi++ ++l+ +  ++
  gi|121637233|ref|YP_977456.1| 17 TATWLGMTVNTDTVLSTAIAGLIVIALAFYLRAKVTST 54
                                   589****************************9987766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.9
                        DUF2304  32 llwlllalilivlsl 46 
                                    +++++++li  +l++
  gi|121637233|ref|YP_977456.1|  92 VTIFVFILISNWLAV 106
                                    333333333333333 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.014
                        DUF2304  34 wlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfslslkl 86 
                                    +++ ++++++++lfp  +++  n++   + + +  + +++f l++++++s ++
  gi|121637233|ref|YP_977456.1| 191 IFAGGILVALIALFPPYIMWAPNAIWKAFDLFVGAIQAFIFALLTILYFSQAM 243
                                    4566788889999**99999999877666665555666666666666666554 PP

>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   3.7e-05      0.22      18      44 ..      21      47 ..      18      50 .. 0.90
   2 ?   -3.1   0.4         1   6.3e+03       4      13 ..     132     141 ..     131     142 .. 0.59
   3 ?    0.6   0.1     0.071   4.2e+02      34      42 ..     195     203 ..     190     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                            SPW 18 lGfsattgaawnnvivGavvavLalaf 44
                                   lG + +t+++++  i+G++v++La++ 
  gi|121637233|ref|YP_977456.1| 21 LGMTVNTDTVLSTAIAGLIVIALAFYL 47
                                   69999*******************985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1
                            SPW   4 nlllGlwliv 13 
                                    +l+l+l+++v
  gi|121637233|ref|YP_977456.1| 132 VLALALFVFV 141
                                    4566666665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.071
                            SPW  34 GavvavLal 42 
                                    G++va++al
  gi|121637233|ref|YP_977456.1| 195 GILVALIAL 203
                                    99****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1959.31
//
Query:       gi|121637234|ref|YP_977457.1|  [L=81]
Description: F0F1 ATP synthase subunit C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.5e-09   36.2   9.7    8.6e-09   35.6   9.7    1.3  1  ATP-synt_C  ATP synthase subunit C
  ------ inclusion threshold ------
       0.47   10.0   1.6        0.6    9.7   1.6    1.1  1  Dip         gp37/Dip protein


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   9.7   9.6e-13   8.6e-09       1      56 [.      11      70 ..      11      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 9.6e-13
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSG....HHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnp....klftksliilafaeaialygLiv 56
                                   +g gl ++ +a+g+Gig G+ag+a i++var+p    +lft ++i ++++ea   + L +
  gi|121637234|ref|YP_977457.1| 11 IGGGLIMAGGAIGAGIGDGVAGNALISGVARQPeaqgRLFTPFFITVGLVEAAYFINLAF 70
                                   799******************************999999999*********987777665 PP

>> Dip  gp37/Dip protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.6   6.7e-05       0.6      91     127 ..       5      39 ..       2      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.7e-05
                                    HHHHHHHHTSTTEEEESSEEEEEEEESSTT-EEEEEE CS
                            Dip  91 laagavicgndeyisdgnvvgihiadgvggnklilpv 127
                                    +aaga+i g    i  g  +g  i dgv gn li  v
  gi|121637234|ref|YP_977457.1|   5 IAAGALIGGG--LIMAGGAIGAGIGDGVAGNALISGV 39 
                                    799**99985..79999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 653.34
//
Query:       gi|121637235|ref|YP_977458.1|  [L=171]
Description: F0F1 ATP synthase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-33  113.3   6.0    1.1e-32  112.9   6.0    1.2  1  ATP-synt_B  ATP synthase B/B' CF(0)
     0.0019   17.7   7.4      0.039   13.4   3.8    2.1  2  DUF3552     Domain of unknown function (DUF3552)
  ------ inclusion threshold ------
      0.035   14.0   7.1      0.051   13.4   7.1    1.3  1  HrpE        HrpE/YscL/FliH and V-type ATPase subunit E
      0.079   13.4   2.1        2.1    8.8   0.0    2.2  2  DUF2681     Protein of unknown function (DUF2681)
      0.098   12.3   0.1       0.13   11.9   0.1    1.1  1  PepSY_TM    PepSY-associated TM region
       0.11   13.3   0.0       0.21   12.4   0.0    1.4  1  YMF19       Plant ATP synthase F0
       0.11   13.5   0.0       0.18   12.8   0.0    1.5  1  DUF4834     Domain of unknown function (DUF4834)
        2.5    8.2  10.2       0.67   10.0   7.5    1.4  2  DivIVA      DivIVA protein
        7.2    6.8  10.2        7.1    6.8   1.5    2.2  2  Caudo_TAP   Caudovirales tail fibre assembly protein, lambda 


Domain annotation for each model (and alignments):
>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   6.0   5.5e-36   1.1e-32       1     131 [.      30     160 ..      30     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 5.5e-36
                     ATP-synt_B   1 tlvvnliallilvgllikfawkplkkvLdkReekIadeiaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaek 80 
                                    t++v+l+++l++++++ +f+++p++kvL +R++++a+++a+ +++ +++aa++a++ +++ eAr +A+ +++nA+++++k
  gi|121637235|ref|YP_977458.1|  30 TFFVVLAIFLVVLAVIGTFVVPPILKVLRERDAMVAKTLADNKKSDEQFAAAQADYDEAMTEARVQASSLRDNARADGRK 109
                                    799***************************************************************************** PP

                     ATP-synt_B  81 lkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvvalavqiaekll 131
                                    + e+++ +ae++++++ ++A++++++e+d+++ +Lr+ v+ ++   a+++l
  gi|121637235|ref|YP_977458.1| 110 VIEDARVRAEQQVASTLQTAHEQLKRERDAVELDLRAHVGTMSATLASRIL 160
                                    *************************************************98 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3   0.00081       1.6       3      68 ..      36     102 ..      31     103 .. 0.79
   2 !   13.4   3.8     2e-05     0.039      27      75 ..      98     146 ..      89     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00081
                        DUF3552   3 iilaivalvvglvvgylvrkkiaekkiaeAeeeAkkiieeAk.keAeakkkealleakeeihklree 68 
                                     i+++v +v+g++v   + k   e+ +  A++ A++  ++ +   A+a  +ea++ea+ ++  lr++
  gi|121637235|ref|YP_977458.1|  36 AIFLVVLAVIGTFVVPPILKVLRERDAMVAKTLADNKKSDEQfAAAQADYDEAMTEARVQASSLRDN 102
                                    4556677777777777779***************99877766256788899******9999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2e-05
                        DUF3552  27 kkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelke 75 
                                    +  ++A+++ +k+ie+A+  Ae++    l  a e++++ r+ +e +l+ 
  gi|121637235|ref|YP_977458.1|  98 SLRDNARADGRKVIEDARVRAEQQVASTLQTAHEQLKRERDAVELDLRA 146
                                    55679***************************************99986 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   7.1   2.6e-05     0.051      29     107 ..      82     160 ..      57     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                           HrpE  29 slrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqlltaveqLLsdalarlL 107
                                    +   +e + eAr+qA +l ++ar   ++++e a   Ae+q  +  +   ++l++eR a+e +l ++v+ +     +r+L
  gi|121637235|ref|YP_977458.1|  82 QADYDEAMTEARVQASSLRDNARADGRKVIEDARVRAEQQVASTLQTAHEQLKRERDAVELDLRAHVGTMSATLASRIL 160
                                    3445789********************************************************9999988766666666 PP

>> DUF2681  Protein of unknown function (DUF2681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       2.1       4      66 ..      35     102 ..      32     114 .. 0.77
   2 ?    3.7   1.0     0.042        84      25      50 ..     116     141 ..     113     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                        DUF2681   4 lallvgliaavlllvaylswqlkkar.....kknaklqaekqqlkvekavaeaevknakvkqkneent 66 
                                    la+ + ++a++  +v    +++ ++r     k +a  ++  +q ++ +a  ++ +  a+v+       
  gi|121637235|ref|YP_977458.1|  35 LAIFLVVLAVIGTFVVPPILKVLRERdamvaKTLADNKKSDEQFAAAQADYDEAMTEARVQASSLRDN 102
                                    56677778888888888899999999999999999999******999999999999999987654443 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.042
                        DUF2681  25 lkkarkknaklqaekqqlkvekavae 50 
                                    ++ +++ +++lq+  +qlk e  + e
  gi|121637235|ref|YP_977458.1| 116 VRAEQQVASTLQTAHEQLKRERDAVE 141
                                    566778899**********9988765 PP

>> PepSY_TM  PepSY-associated TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.5e-05      0.13      10     118 ..      34     134 ..      33     167 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x RF
                       PepSY_TM  10 ivglfllvlalTGallvfkpeieawlnpellvvapaaaaallaaeaaaaaaaaaaaaaaaaatavvrtaa.........g 80 
                                    ++++fl+vla+ G++ v  p+i ++l++  + va++ a  ++   ++++ aaa+a+ + a+ +a+v+ ++         +
  gi|121637235|ref|YP_977458.1|  34 VLAIFLVVLAVIGTFVV--PPILKVLRERDAMVAKTLADNKK---SDEQFAAAQADYDEAMTEARVQASSlrdnaradgR 108
                                    799***********977..44444444444444443333332...22333333333333333333311112222221110 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       PepSY_TM  81 ekrsvfvdpytgevlgersgesasafaeflrrlHrgll 118
                                                +v+++ + ++++++a++l+  H +l 
  gi|121637235|ref|YP_977458.1| 109 ------------KVIEDARVRAEQQVASTLQTAHEQLK 134
                                    ............23333333333455556666666443 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.21      12      80 ..      31      97 ..      29     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          YMF19 12 ffWlclfFitlYivllknilpkiarilklrkkllsslssevsklkkeqknlivskdsalanvslsteas 80
                                   ff ++ +F+++  v+ ++++p i+++l+ r +++ +     +k +++    +  +d+a++++++  +as
  gi|121637235|ref|YP_977458.1| 31 FFVVLAIFLVVLAVIGTFVVPPILKVLRERDAMVAKTLADNKKSDEQFAAAQADYDEAMTEARV--QAS 97
                                   4444445666666666**********************99999999999999999999999866..444 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     9e-05      0.18       3      75 ..      31     102 ..      29     140 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                        DUF4834   3 fLlfilifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksq....srsetkeegeiieeers 75 
                                    f  ++ if+++++vig  ++  il+ +    + + ++  a+    n+++++q++      ++  t++  ++ + +++
  gi|121637235|ref|YP_977458.1|  31 FFVVLAIFLVVLAVIGTFVVPPILKVL----RERDAM-VAKTLADNKKSDEQFAAAqadyDEAMTEARVQASSLRDN 102
                                    666777888888888888888888887....333333.222222233333333322111122222223333333333 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       7.3   1.5e+04      69      78 ..       8      17 ..       4      21 .. 0.66
   2 ?   10.0   7.5   0.00033      0.67      55     124 ..      68     138 ..      54     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.3
                                   XXXXXXXXXX CS
                         DivIVA 69 lvvaqetaee 78
                                   +++a ++aee
  gi|121637235|ref|YP_977458.1|  8 VLAASQAAEE 17
                                   5666777765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXX CS
                         DivIVA  55 lkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakk.....iaeeieelkrqar 124
                                    l++ k+ +e+      +aq   +e+ ++a+ +a+ + ++A+++ +k++e+a+ +a++     +++ +e+lkr+++
  gi|121637235|ref|YP_977458.1|  68 LADNKKSDEQ----FAAAQADYDEAMTEARVQASSLRDNARADGRKVIEDARVRAEQqvastLQTAHEQLKRERD 138
                                    4444444444....7789999999999999999999999999999999988777654111113444455555544 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.4     0.019        37      48      91 ..      61     105 ..      52     115 .. 0.82
   2 ?    6.8   1.5    0.0035       7.1      62      93 ..     113     144 ..     106     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                      Caudo_TAP  48 dgeglpawvedk.keeqiqqAeqekqqllaqAseqiaplqdavdl 91 
                                    d  ++++++++k ++eq ++A++  ++ +++A+ q ++l+d+++ 
  gi|121637235|ref|YP_977458.1|  61 DAMVAKTLADNKkSDEQFAAAQADYDEAMTEARVQASSLRDNARA 105
                                    445555666655689999**********************98875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0035
                      Caudo_TAP  62 eqiqqAeqekqqllaqAseqiaplqdavdlgi 93 
                                    + +  Aeq+ ++ l++A eq +  +dav+l+ 
  gi|121637235|ref|YP_977458.1| 113 DARVRAEQQVASTLQTAHEQLKRERDAVELDL 144
                                    67788************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1234.71
//
Query:       gi|121637236|ref|YP_977459.1|  [L=446]
Description: F0F1 ATP synthase subunit delta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-29  100.9   6.2    4.4e-28   98.6   0.2    3.1  3  OSCP          ATP synthase delta (OSCP) subunit
      1e-19   70.9  15.8    1.1e-19   70.8  13.6    2.2  2  ATP-synt_B    ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
       0.28   11.0   5.0        4.3    7.3   0.1    3.6  4  RACo_linker   RACo linker region
       0.77    8.9   2.0        1.2    8.3   2.0    1.2  1  TMPIT         TMPIT-like protein


Domain annotation for each model (and alignments):
>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.7      0.81   3.6e+03      19      38 ..      73      92 ..      34     153 .. 0.56
   2 !    4.1   0.0    0.0098        44      19      80 ..     199     260 ..     189     273 .. 0.89
   3 !   98.6   0.2   9.8e-32   4.4e-28       7     170 ..     277     442 ..     276     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.81
                           OSCP 19 leeveeelealeavlaedkk 38
                                   +ee  ++ e ++++l+++++
  gi|121637236|ref|YP_977459.1| 73 VEEARTDAERIAEQLEAQAD 92
                                   23333333333333333332 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0098
                           OSCP  19 leeveeelealeavlaedkklaellsnpavsaeekkdlleelfkeklseavknflkllaenk 80 
                                    l + + el +++++l++++ + ++l+ pa +a+ +  l+e+l+++k+   + ++l++ + ++
  gi|121637236|ref|YP_977459.1| 199 LTTLAGELVSVARLLDREAVVTRYLTVPAEDATPRIRLIERLVSGKVGAPTLEVLRTAVSKR 260
                                    777888999999*************************************9999999887765 PP

  == domain 3  score: 98.6 bits;  conditional E-value: 9.8e-32
                           OSCP   7 kAlfelAkekgaleeveeelealeavlaedkklaellsnpavsaeekkdlleelfke...klseavknflkllaenkRla 83 
                                    +Al+elA+++g+++eve++l+ ++++l+ +++la ll + av+ae ++ ll+++++     ++++v  +l+  +e  R +
  gi|121637236|ref|YP_977459.1| 277 QALLELAERAGQVDEVEDQLFRFSRILDVQPRLAILLGDCAVPAEGRVRLLRKVLERadsTVNPVVVALLSHTVELLRGQ 356
                                    69*****************************************************999999******************* PP

                           OSCP  84 lLpeiaeefeellaeargiveaeVtsavpLtdeqlekleaalakklgkkkvkleekvdpsliGGvvvkvgdkviDgSvkg 163
                                     ++e +    e++ ++rg++ a+V  a++L+d+q+++l++ l++ +g   v+++ ++d+ l+GG+ + vgd+viDg++++
  gi|121637236|ref|YP_977459.1| 357 AVEEAVLFLAEVAVARRGEIVAQVGAAAELSDAQRTRLTEVLSRIYGH-PVTVQLHIDAALLGGLSIAVGDEVIDGTLSS 435
                                    ************************************************.8****************************** PP

                           OSCP 164 kLeklke 170
                                    +L+  ++
  gi|121637236|ref|YP_977459.1| 436 RLAAAEA 442
                                    **97665 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8  13.6   2.5e-23   1.1e-19       1     130 [.       3     132 ..       3     134 .. 0.98
   2 ?    1.2   0.1     0.081   3.6e+02     109     127 ..     127     145 ..     119     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.5e-23
                     ATP-synt_B   1 tlvvnliallilvgllikfawkplkkvLdkReekIadeiaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaek 80 
                                    t++ +l+ ++++v l+ +f+++ ++++++ R++ +++++a+A ++++ +a++ ++ +++l++A++eA++++++A+ +ae+
  gi|121637236|ref|YP_977459.1|   3 TFIGQLFGFAVIVYLVWRFIVPLVGRLMSARQDTVRQQLADAAAAADRLAEASQAHTKALEDAKSEAHRVVEEARTDAER 82 
                                    6899**************************************************************************** PP

                     ATP-synt_B  81 lkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvvalavqiaekl 130
                                    ++e++ea+a  eaer+k ++a +++  ++++ ++Lr + +  +v  a++l
  gi|121637236|ref|YP_977459.1|  83 IAEQLEAQADVEAERIKMQGARQVDLIRAQLTRQLRLELGHESVRQAREL 132
                                    **************************************999999999876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.081
                     ATP-synt_B 109 dralaeLreqvvalavqia 127
                                     +a++ +r+ v+++a q a
  gi|121637236|ref|YP_977459.1| 127 RQARELVRNHVADQAQQSA 145
                                    4788888999999988876 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1   0.00096       4.3      24      47 ..      73      96 ..      69     118 .. 0.87
   2 ?    3.9   0.1     0.011        48      23      60 ..     139     178 ..     132     181 .. 0.86
   3 ?   -3.0   0.0       1.5   6.8e+03      31      59 ..     250     276 ..     248     280 .. 0.68
   4 ?   -1.9   0.0      0.72   3.2e+03      32      51 ..     392     417 ..     385     422 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00096
                    RACo_linker 24 ledpsgDleRLkeaLekqwdleid 47
                                   +e+ + D eR+ e+Le+q d+e++
  gi|121637236|ref|YP_977459.1| 73 VEEARTDAERIAEQLEAQADVEAE 96
                                   58899*************986654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.011
                    RACo_linker  23 tledpsgDleRLkeaLekqwd..leidlsvLrkLpevLrk 60 
                                    +  ++s+ ++R+ ++L +      ++d+++L+k+ ++ r+
  gi|121637236|ref|YP_977459.1| 139 DQAQQSATVDRFLDQLDAMAPatADVDYPLLAKMRSASRR 178
                                    667889999*******99995569**********999886 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.5
                    RACo_linker  31 leRLkeaLekqwdleidlsvLrkLpevLr 59 
                                    le L++a++k+w  +++  ++  + +v r
  gi|121637236|ref|YP_977459.1| 250 LEVLRTAVSKRW--SANSDLIDAIEHVSR 276
                                    567888999999..566666666666555 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.72
                    RACo_linker  32 eRLkeaLekqwd......leidlsvL 51 
                                    +RL+e L++ ++      l+id ++L
  gi|121637236|ref|YP_977459.1| 392 TRLTEVLSRIYGhpvtvqLHIDAALL 417
                                    58888898888555334455555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.0   0.00027       1.2      17     111 ..      33     131 ..      28     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                          TMPIT  17 takeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk....evesllpkk 92 
                                    ++++++q+l++ ++  ++++++ + ++k l++ ks+ +++ ++++++ e+++e+l+++ + + + +k    +  +l+ ++
  gi|121637236|ref|YP_977459.1|  33 RQDTVRQQLADAAAAADRLAEASQAHTKALEDAKSEAHRVVEEARTDAERIAEQLEAQADVEAERIKmqgaRQVDLIRAQ 112
                                    567899*************************************9999999999999988776666664443333444455 PP

                          TMPIT  93 nglylklvlGnvnvsllnk 111
                                      + l+l lG+ +v+  ++
  gi|121637236|ref|YP_977459.1| 113 LTRQLRLELGHESVRQARE 131
                                    6777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1405  (0.0783647); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.24s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 3215.45
//
Query:       gi|121637237|ref|YP_977460.1|  [L=549]
Description: F0F1 ATP synthase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-69  234.5   0.0    1.6e-69  233.8   0.0    1.3  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    6.5e-50  168.7   0.4    1.2e-49  167.9   0.4    1.4  1  ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal doma
    2.5e-17   63.1   2.0    7.3e-17   61.7   2.0    1.8  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.11   12.1   0.3       0.36   10.4   0.0    1.9  2  AAA_25         AAA domain
       0.13   11.6   0.0       0.41   10.0   0.0    1.9  1  TniB           Bacterial TniB protein
       0.27   10.5   1.9       0.41    9.9   0.1    2.0  2  ATPase         KaiC


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.8   0.0   5.2e-73   1.6e-69       1     213 []     152     375 ..     152     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 5.2e-73
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHH.HHHHHHSSTS.......S.EEEEEEESEEHHHHHHHHHHCHHSSGGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.......x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvis.qslskqsnsd.......d.aiiyvgiGergnevaevleefpegtimkr 71 
                                    Gi+++Da++pi++Gqr+li+g++++Gkt+++ +++++q ++        +  ++yv+iG++g ++a v ++++eg++m++
  gi|121637237|ref|YP_977460.1| 152 GIKAIDAMTPIGRGQRQLIIGDRKTGKTAVCvDTILNQRQNWesgdpkkQvRCVYVAIGQKGTTIAAVRRTLEEGGAMDY 231
                                    99***************************99999999965448999998689**************************** PP

                                    EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  72 tvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyER 151
                                    t++va+ ++e++  + +++ytg ++A +++++gk+vl+i+d+l+++aeA+r isl+l+++p++++yp+++++ +++l+ER
  gi|121637237|ref|YP_977460.1| 232 TTIVAAAASESAGFKWLAPYTGSAIAQHWMYEGKHVLIIFDDLTKQAEAYRAISLLLRRPPGREAYPGDVFYLHSRLLER 311
                                    ******************************************************************************** PP

                                    SEEETSS..EEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 152 agkapdr..tGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++k++d+   Gs+t +++++++++D+s++++t++++itdg+ +L+++l++++++Painv+vSvS
  gi|121637237|ref|YP_977460.1| 312 CAKLSDDlgGGSLTGLPIIETKANDISAYIPTNVISITDGQCFLETDLFNQGVRPAINVGVSVS 375
                                    ****666679*****************************************************9 PP

>> ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.4   3.9e-53   1.2e-49       1     126 []     382     507 ..     382     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 3.9e-53
                  ATP-synt_ab_C   1 QtkamkkvagsLklelaqYrEleaFaqFgsdLDeatkkqLerGerlvelLkQkqysplsveeqviilyaatngllddipv 80 
                                    Q+kamk+vagsL+l+l+qYrEleaFa F+sdLD+a+k+qLerG+rlvelLkQ+q +p++veeqv++++++t g+ld++pv
  gi|121637237|ref|YP_977460.1| 382 QIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQLERGARLVELLKQPQSQPMPVEEQVVSIFLGTGGHLDSVPV 461
                                    9******************************************************************************* PP

                  ATP-synt_ab_C  81 ekvkefekelleyleeekkeileeieekkklsdeleeklkeaikef 126
                                    e+v++fe+ell++++++++eil+ei++++kl++e+++kl+e+ik+f
  gi|121637237|ref|YP_977460.1| 462 EDVRRFETELLDHMRASEEEILTEIRDSQKLTEEAADKLTEVIKNF 507
                                    *******************************************987 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   2.0   2.4e-20   7.3e-17       3      69 .]      29      95 ..      28      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.4e-20
                                   EEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  3 qviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   +++G+vvd+++gi+++ g+  +++ el ef+ ++lgvalnl+e++V+++++g+++++++G+ VkrTG
  gi|121637237|ref|YP_977460.1| 29 EEVGTVVDAGDGIAHVEGLPSVMTQELLEFPGGILGVALNLDEHSVGAVILGDFENIEEGQQVKRTG 95
                                   589***************************************************************9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.36      31      87 ..     163     217 ..     154     278 .. 0.80
   2 ?   -1.9   0.0       0.7   2.1e+03     106     139 ..     472     506 ..     460     511 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                         AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelr 87 
                                     +g   l++G+++tGKt++++d  l   + ++  g p   +q++++yv+  ++  +++
  gi|121637237|ref|YP_977460.1| 163 GRGQRQLIIGDRKTGKTAVCVDTILNQRQNWES-GdP--KKQVRCVYVAIGQKGTTIA 217
                                    6788999******************99998865.534..69******99877775554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.7
                         AAA_25 106 ldlagv.eslpLfakdrggtl.ltadvdaleaaiee 139
                                    ld ++  e+  L++ +r++++ ++++ d+l ++i+ 
  gi|121637237|ref|YP_977460.1| 472 LDHMRAsEEEILTE-IRDSQKlTEEAADKLTEVIKN 506
                                    33344434444544.455555377888888888876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00014      0.41      24      82 ..     154     214 ..     130     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                           TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppe.kd.edaekvpvlvvqappkpd 82 
                                    +++ ++ +  r +  l++Gd ++GKt+++     +++++ ++   +++v+ ++v + +k +
  gi|121637237|ref|YP_977460.1| 154 KAIDAMTPIGRGQRQLIIGDRKTGKTAVCVDTILNQRQNwESgDPKKQVRCVYVAIGQKGT 214
                                    555556677888999************9987765555442441447789999999888765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00014      0.41       2      46 ..     150     192 ..     149     230 .. 0.75
   2 ?   -1.0   0.3      0.31   9.4e+02      73     119 ..     463     508 ..     462     513 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek 46 
                                    +tgI+ +D ++   i +g+  li G+  tGKt ++   ++++ ++
  gi|121637237|ref|YP_977460.1| 150 QTGIKAIDAMT--PIGRGQRQLIIGDRKTGKTAVCVDTILNQRQN 192
                                    8*********8..7889999***************9999998664 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.31
                         ATPase  73 dlekleeegklaiidasesaeesaeekdkedleelieelaeaikeik 119
                                    d++++e e +l  + ase+++ ++ +++++ +ee +++l+e+ik++k
  gi|121637237|ref|YP_977460.1| 463 DVRRFETE-LLDHMRASEEEILTEIRDSQKLTEEAADKLTEVIKNFK 508
                                    56666666.67777777887777777888888999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3923.35
//
Query:       gi|121637238|ref|YP_977461.1|  [L=305]
Description: F0F1 ATP synthase subunit gamma [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-90  303.6   0.1    1.8e-90  303.4   0.1    1.0  1  ATP-synt     ATP synthase
  ------ inclusion threshold ------
       0.15   11.3   0.3       0.28   10.3   0.0    1.6  2  IF-2B        Initiation factor 2 subunit family
       0.16   12.1   5.7        0.8    9.8   2.1    2.2  2  Flagellin_N  Bacterial flagellin N-terminal helical region


Domain annotation for each model (and alignments):
>> ATP-synt  ATP synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.4   0.1   3.1e-94   1.8e-90       1     279 []       4     301 ..       4     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 3.1e-94
                                    THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHHHCEHHHHTTT..SSG.S...SSEEEEEEE CS
                       ATP-synt   1 slkeikrRiksvkstkkItkAmkmVaaaklrkaqealeaarpyaekleevlealakreeeekhpllke..eekkvllivi 78 
                                    +l+e++ Ri+s  s+kkItkA +++a++++++aq++le+arpya +++++l++la+ e+  +hpll e  e k+++++v+
  gi|121637238|ref|YP_977461.1|   4 TLRELRGRIRSAGSIKKITKAQELIATSRIARAQARLESARPYAFEITRMLTTLAA-EAALDHPLLVErpEPKRAGVLVV 82 
                                    69****************************************************66.45578888555455999****** PP

                                    --SSSSSTTHHHHHHHHHHHHHHHHHTTT.ETEEEEESHHHHHHH.HHSS.EHHTTCE-TSS--HHHHHHHHHHHHSHH. CS
                       ATP-synt  79 tSDrGLcGgfNsnvikkaeklieelkkeg.evklvvvGkkgreyf.krkvevqleftgvskkptfeeaseiaeeildly. 155
                                    +SDrGLcG++N+n++++ e+l + l++ g +  l+vvG+k+++y+ +r+ ++++++ g+s++pt+e+a+eia++++d++ 
  gi|121637238|ref|YP_977461.1|  83 SSDRGLCGAYNANIFRRSEELFSLLREAGkQPVLYVVGRKAQNYYsFRNWNITESWMGFSEQPTYENAAEIASTLVDAFl 162
                                    ******************55544344566478********************999************************8 PP

                                    ............HTTSBSEEEEEEEEECCTSEEEEEEEEESST...HC...S..SSTSEESS.HCCCHHHHHHHHHHHHH CS
                       ATP-synt 156 ............eegeideveivynkfksaisqeptvekllplekeee...kkekseyefepdeeevleellpeylasli 220
                                                + + +de++ivy++fks++sq  +++++ p+  e       +++ y+fepd++ ++e+llp+yl++++
  gi|121637238|ref|YP_977461.1| 163 lgtdngedqrsdSGEGVDELHIVYTEFKSMLSQSAEAHRIAPMVVEYVeedIGPRTLYSFEPDATMLFESLLPRYLTTRV 242
                                    88776665555333489*************************5443334456789999*****9**************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       ATP-synt 221 yrallesaasEqaaRmtaMdnAtknakelidkltleyNraRQaaITqELieIvsGaeAL 279
                                    y allesaasE a+R+ aM++At+na++li+ ltl  Nr RQa+ITqE++eIv+Ga+AL
  gi|121637238|ref|YP_977461.1| 243 YAALLESAASELASRQRAMKSATDNADDLIKALTLMANRERQAQITQEISEIVGGANAL 301
                                    **********************************************************8 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.8e-05      0.28      23      65 ..      19      63 ..       3      91 .. 0.87
   2 ?   -2.9   0.1       0.5     3e+03      77      89 ..     262     274 ..     237     295 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.8e-05
                                   CCCSTHHHH..HHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHC CS
                          IF-2B 23 aktskvaeL..keelrkaidlLkkarPtavslgnairrllkeise 65
                                   +k +k++eL  ++++ +a ++L++arP a+++  ++  l +e + 
  gi|121637238|ref|YP_977461.1| 19 KKITKAQELiaTSRIARAQARLESARPYAFEITRMLTTLAAEAAL 63
                                   4577999**999************************999997554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.5
                                    HHHHHHHHHHHHH CS
                          IF-2B  77 ksliekikelike 89 
                                    ks+ +++++lik 
  gi|121637238|ref|YP_977461.1| 262 KSATDNADDLIKA 274
                                    2222222222222 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.013        77      65      97 ..      27      60 ..       5      65 .. 0.77
   2 ?    9.8   2.1   0.00013       0.8      66     120 ..     249     299 ..     240     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHT- CS
                    Flagellin_N 65 slgisrlqtaqgalselsdilqr.lkelavaasn 97
                                    +++sr+++aq +l++ +  + +  + l++ a++
  gi|121637238|ref|YP_977461.1| 27 LIATSRIARAQARLESARPYAFEiTRMLTTLAAE 60
                                   3699************999999978888888776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHH CS
                    Flagellin_N  66 lgisrlqtaqgalselsdilqr.lkelavaasndsnsdedrqslqaelqqLtdeln 120
                                     ++s l++ q a+++ +d++++ +k+l+  a+ +++ ++     ++e+++ ++ +n
  gi|121637238|ref|YP_977461.1| 249 SAASELASRQRAMKSATDNADDlIKALTLMANRERQAQI-----TQEISEIVGGAN 299
                                    68899*****************9*****99999888555.....555655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2117.41
//
Query:       gi|121637239|ref|YP_977462.1|  [L=486]
Description: F0F1 ATP synthase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-62  210.6   0.0    3.1e-62  210.0   0.0    1.3  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    6.5e-22   77.8   0.2    1.5e-21   76.7   0.2    1.7  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
     0.0028   17.5   1.4      0.015   15.1   1.4    2.1  1  T3SS_ATPase_C  T3SS EscN ATPase C-terminal domain
     0.0052   17.1   0.6       0.15   12.4   0.2    2.3  2  AAA_19         AAA domain
     0.0054   16.7   0.0      0.012   15.5   0.0    1.5  1  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.014   15.8   0.7       0.14   12.6   0.7    2.5  1  AAA_16         AAA ATPase domain
      0.017   15.6   0.0       0.36   11.2   0.0    2.6  2  AAA            ATPase family associated with various cellular
      0.026   14.1   0.1      0.067   12.8   0.1    1.7  1  AAA_25         AAA domain
      0.053   12.7   0.1       0.11   11.6   0.1    1.5  1  NB-ARC         NB-ARC domain
      0.062   13.2   0.2       0.32   10.9   0.0    2.3  2  NACHT          NACHT domain
      0.066   13.1   0.0       0.13   12.2   0.0    1.4  1  ATPase_2       ATPase domain predominantly from Archaea
      0.081   13.2   0.1       0.38   11.0   0.0    2.2  2  AAA_22         AAA domain
       0.09   12.1   0.1       0.34   10.2   0.1    1.9  2  ATPase         KaiC
        0.1   13.0   0.0       0.31   11.4   0.0    1.8  1  RNA_helicase   RNA helicase
       0.15   12.0   0.1       0.38   10.8   0.1    1.6  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
       0.22   11.0   0.0       0.47   10.0   0.0    1.5  1  AAA_7          P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.0   2.8e-65   3.1e-62       1     213 []     151     364 ..     151     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 2.8e-65
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS.S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd.d.aiiyvgiGergnevaevleefpegtimkrtvlvant 78 
                                    G++v+D+l+p+v+G++++++g++gvGktv++q++++    +   +++++g+Ger++e ++++ e+ e++++k t lv+ +
  gi|121637239|ref|YP_977462.1| 151 GLKVVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNfGgTSVFAGVGERTREGNDLWVELAEANVLKDTALVFGQ 230
                                    89*****************************9999998777636************************************ PP

                                    TTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  79 snepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapd 157
                                    ++ep+ +r+++++ ++t+AE+frd qg++vll++d+++r+++A  e+s++lg+mp++ gy+++l+ ++ +l+ER++++  
  gi|121637239|ref|YP_977462.1| 231 MDEPPGTRMRVALSALTMAEWFRDeQGQDVLLFIDNIFRFTQAGSEVSTLLGRMPSAVGYQPTLADEMGELQERITST-- 308
                                    ******************************************************************************.. PP

                                    SEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 158 rtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    r  s+t+++av+++++D++dp + +t++++d+++ L+++++++++fPa+++l+S S
  gi|121637239|ref|YP_977462.1| 309 RGRSITSMQAVYVPADDYTDPAPATTFAHLDATTELSRAVFSKGIFPAVDPLASSS 364
                                    788***************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.2   1.3e-24   1.5e-21       1      69 []      23      94 ..      23      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 1.3e-24
                                   EEEEETTEEEEESSTSCETCTTEEEEECCET...CSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelve...fgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   +v+v+Gpvvdvef++g +p++ nal+ e++     +tl+l+va++lg++ Vr+i + +tdGl+rG eV++TG
  gi|121637239|ref|YP_977462.1| 23 VVRVTGPVVDVEFPRGSIPELFNALHAEITFeslAKTLTLEVAQHLGDNLVRTISLQPTDGLVRGVEVIDTG 94
                                   79**************************8879999************************************9 PP

>> T3SS_ATPase_C  T3SS EscN ATPase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.4   1.3e-05     0.015       2      62 ..     373     432 ..     372     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                  T3SS_ATPase_C   2 spehlqaarklrellatyqenedLiniGaYkkGsdpelDeAiakrpainafLkQgvdekvs 62 
                                     +eh++ a+++ ++l++y++ +d+i i    + s ++  + +++  +i++fL Q++  + +
  gi|121637239|ref|YP_977462.1| 373 GDEHYRVAQEVIRILQRYKDLQDIIAILGIDELSEED-KQLVNRARRIERFLSQNMMAAEQ 432
                                    68*************************8888766544.36789999999999999987655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   0.00014      0.15       9      37 ..     163     191 ..     157     200 .. 0.85
   2 ?    2.6   0.0      0.14   1.5e+02      68     116 ..     322     411 ..     293     424 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvel 37 
                                    + + +++ +G+G GKT +++++++ + ++
  gi|121637239|ref|YP_977462.1| 163 RGGKIALFGGAGVGKTVLIQEMINRIARN 191
                                    667899****************9988765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                         AAA_19  68 e.........atTiHrlal..............................ldfddlltealelleeaeeekklqeee.lli 107
                                    +         atT+ +l                                +  d+    a e+++  ++ k+lq+   +l 
  gi|121637239|ref|YP_977462.1| 322 PaddytdpapATTFAHLDAttelsravfskgifpavdplassstildpsVVGDEHYRVAQEVIRILQRYKDLQDIIaILG 401
                                    14455555557777777556777777777777777777777777777773344444455666665566777777777888 PP

                         AAA_19 108 vDEfqdvd.e 116
                                    +DE ++ d +
  gi|121637239|ref|YP_977462.1| 402 IDELSEEDkQ 411
                                    9999988744 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05     0.012      89     157 ..     154     223 ..     136     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                    THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEE.EEETTTEEEES CS
                    RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavel.lelaegglliD 157
                                     ++ l++++++  ++l G  GvGK+ Li +++++   + g +s   g G  T     l +elae  +l D
  gi|121637239|ref|YP_977462.1| 154 VVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERTREGNDLwVELAEANVLKD 223
                                    567789999999999**********************************999776665245555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   0.00012      0.14      26      63 ..     166     205 ..     153     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                         AAA_16  26 lvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63 
                                     + l G +GvGK+ l++e  +++ ++  g  +++g  ++ 
  gi|121637239|ref|YP_977462.1| 166 KIALFGGAGVGKTVLIQEMINRIARNfgGTSVFAGVGERT 205
                                    478999******************9975333344444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.36       2      74 ..     168     274 ..     167     287 .. 0.59
   2 ?    0.9   0.1       0.5   5.6e+02      80     123 ..     374     418 ..     354     432 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS....................................STTHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk....................................yvgesekk 45 
                                     l+G  G+GKT l++ +++ + ++f  +s+   + +                                     v  s+  
  gi|121637239|ref|YP_977462.1| 168 ALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGErtregndlwvelaeanvlkdtalvfgqmdeppgtrmRVALSALT 247
                                    699*****************866643333333332222223344333444444444566666666666555566666666 PP

                                    HHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA  46 irelfkeakekakpsilfiDEidalaksr 74 
                                    ++e f++ ++ +  + lfiD+i +++++ 
  gi|121637239|ref|YP_977462.1| 248 MAEWFRD-EQGQ-DVLLFIDNIFRFTQAG 274
                                    7777766.3333.4777777776666555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.5
                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH.S.TT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpall.r.gR 123
                                    +e+ rv+++ ++ l+++k+ ++ +i i+   + ++ d++l+ r +R
  gi|121637239|ref|YP_977462.1| 374 DEHYRVAQEVIRILQRYKDLQD-IIAILGIDELSEEDKQLVnRaRR 418
                                    4555666666666666666544.55555555555555555523333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     6e-05     0.067      31      97 ..     162     231 ..     140     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                         AAA_25  31 pagelallaGapgtGKttlaldlalava...tGkpwlg...pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                    ++g+ ++l+G  g+GKt+l  ++   +a    G +++    + +++ g+ l+v + +++  l+  +  v+ ++
  gi|121637239|ref|YP_977462.1| 162 VRGGKIALFGGAGVGKTVLIQEMINRIArnfGGTSVFAgvgE-RTREGNDLWVELAEAN-VLKDTAL-VFGQM 231
                                    48999***********************88877777767854.5788888888877776.5655555.33333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001      0.11      23      51 ..     167     192 ..     154     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                    EEEEESTTSSHHHHHHHHCCSHCCCCCCB CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksdevegrF 51 
                                    +al G +GvGKt+l+++++n    + ++F
  gi|121637239|ref|YP_977462.1| 167 IALFGGAGVGKTVLIQEMINR---IARNF 192
                                    799**************9998...55555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.32       3      27 ..     167     191 ..     166     282 .. 0.89
   2 ?   -0.7   0.1       1.1   1.2e+03      79      93 ..     461     475 ..     384     481 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                    EEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                    ++l G aG+GKT+L+q+++  +a++
  gi|121637239|ref|YP_977462.1| 167 IALFGGAGVGKTVLIQEMINRIARN 191
                                    5788**************9999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                    SCCCEEEEEE-STT- CS
                          NACHT  79 lperlLlilDglDel 93 
                                    +pe++ +++ glD+l
  gi|121637239|ref|YP_977462.1| 461 VPEQAFFLIGGLDDL 475
                                    344444666666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.13      25     136 ..     169     276 ..     164     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                       ATPase_2  25 iYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvf 103
                                    ++G  g+GKt L++e+i++  ++ +   ++    ++ ++ +      e  e++ l++++  ++++  ++e   ++ + + 
  gi|121637239|ref|YP_977462.1| 169 LFGGAGVGKTVLIQEMINRIaRNFGGTSVFAGVGERTREGNDLWV--ELAEANVLKDTA-LVFGQ--MDEPPGTRMRVAL 243
                                    79*****************97777778888776666655543333..555555555555.22222..2222234557777 PP

                       ATPase_2 104 kaielllekikkkgkkiiiiiDelqklidlgln 136
                                    +a++ +     ++g+ + ++iD +++  + g++
  gi|121637239|ref|YP_977462.1| 244 SALTMAEWFRDEQGQDVLLFIDNIFRFTQAGSE 276
                                    888888888888888888888888888866655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.38       6      29 ..     165     188 ..     162     280 .. 0.84
   2 ?   -1.5   0.0       2.5   2.8e+03      80     115 ..     381     419 ..     335     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                         AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                    g ++++G +G+GKT+l++++ ++ 
  gi|121637239|ref|YP_977462.1| 165 GKIALFGGAGVGKTVLIQEMINRI 188
                                    5589***************99886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                         AAA_22  80 ealeqalrarav....ielliiDEaqhlrseealeeLrsl 115
                                    + + + l+++++    i++l iDE      +++++  r++
  gi|121637239|ref|YP_977462.1| 381 QEVIRILQRYKDlqdiIAILGIDELSEE-DKQLVNRARRI 419
                                    4555566666666445666666665443.35555555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0003      0.34       3      60 ..     150     205 ..     148     217 .. 0.84
   2 ?   -1.7   0.0       1.3   1.5e+03       2      32 ..     444     477 ..     443     478 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                         ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa 60 
                                    tg +  D ++   + +g  + + G++G GKt++ ++ + + a+++g   vf  v e+ 
  gi|121637239|ref|YP_977462.1| 150 TGLKVVDLLT--PYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERT 205
                                    5555555554..578889999******************************9999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                         ATPase   2 ktgIeglDeilkgGi...pegrvvlitGepGtGK 32 
                                    k  Ie +D+++kg +   pe++  li G  + +K
  gi|121637239|ref|YP_977462.1| 444 KETIEAFDRLCKGDFdhvPEQAFFLIGGLDDLAK 477
                                    6789*******96553337888888888766655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.31       1      26 [.     167     192 ..     167     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    i l+G +g+GK++l++e+++++++++
  gi|121637239|ref|YP_977462.1| 167 IALFGGAGVGKTVLIQEMINRIARNF 192
                                    5699******************9887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00033      0.38       9      43 ..     149     188 ..     141     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                                    HHHHHHHHCH.....TEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE   9 algkklakal.....gdvilLeGdLGaGKTtlvrglakal 43 
                                    + g k+ + l     g  i+L G  G+GKT+l++++++ +
  gi|121637239|ref|YP_977462.1| 149 ETGLKVVDLLtpyvrGGKIALFGGAGVGKTVLIQEMINRI 188
                                    4555555544444444559****************99876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00042      0.47      35      58 ..     166     189 ..     154     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00042
                          AAA_7  35 pvllvGptGtGKtviikdllkkld 58 
                                    ++ l G +G+GKtv+i+++++++ 
  gi|121637239|ref|YP_977462.1| 166 KIALFGGAGVGKTVLIQEMINRIA 189
                                    57789*************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3339.99
//
Query:       gi|121637240|ref|YP_977463.1|  [L=121]
Description: F0F1 ATP synthase subunit epsilon [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-23   81.6   0.2    3.4e-23   81.3   0.2    1.1  1  ATP-synt_DE_N  ATP synthase, Delta/Epsilon chain, beta-sandwi


Domain annotation for each model (and alignments):
>> ATP-synt_DE_N  ATP synthase, Delta/Epsilon chain, beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   1.9e-27   3.4e-23       1      80 []       4      84 ..       4      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.9e-27
                                   EEEEEEESSSEEEEEEEEEEEEEESSSEEEE-TT--SEEEEEES.EEEEEEEGGGEEEEEEESSEEEEEETTEEEEEESSS CS
                  ATP-synt_DE_N  1 lkleivtpervvfsgeveevvaptteGelgilpgHaplitaLkp.gelriktedgeeesiavsgGflevqdnkvtiladta 80
                                   l++eiv  +r ++sg+++++  +tt Ge+gilp+H+pl+++L    ++r+++e++++ +iav+gGfl+v+++ v+ila++a
  gi|121637240|ref|YP_977463.1|  4 LNVEIVAVDRNIWSGTAKFLFTRTTVGEIGILPRHIPLVAQLVDdAMVRVEREGEKDLRIAVDGGFLSVTEEGVSILAESA 84
                                   68****************************************976999*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 903.40
//
Query:       gi|121637241|ref|YP_977464.1|  [L=144]
Description: hypothetical protein BCG_1372 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-41  138.8   0.6    1.1e-40  138.5   0.6    1.0  1  DUF2550   Protein of unknown function (DUF2550)
  ------ inclusion threshold ------
        0.4   10.6   1.8       0.44   10.5   0.4    1.7  2  DUF3377   Domain of unknown function (DUF3377)


Domain annotation for each model (and alignments):
>> DUF2550  Protein of unknown function (DUF2550)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.6   1.3e-44   1.1e-40       1     126 [.      11     139 ..      10     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 1.3e-44
                        DUF2550   1 lvlvvllvlallarrrlllrrrGafevalRelpaeggrgWrlGvarYsgeelewyrllslrprPsrvlsRrglevegrre 80 
                                    lv+v+ l++++l++r++ lr++G ++ ++R  pa gg+gWr+Gv+rY+g e  +yrl+slr++P+r+lsRrg+e+ +rr+
  gi|121637241|ref|YP_977464.1|  11 LVVVLGLAVLALSYRLWKLRQGG-TAGIMRDIPAVGGHGWRHGVIRYRGGEAAFYRLSSLRLWPDRRLSRRGVEIISRRA 89 
                                    6788889999999*******955.99****************************************************** PP

                        DUF2550  81 pegeeaaalaedlvvvelreegee....lelamdeealtgllsWlEsaPp 126
                                    p+g+e +++++++vvvel +++++    +e+a+d++alt++lsWlEs+P+
  gi|121637241|ref|YP_977464.1|  90 PRGDEFDIMTDEIVVVELCDSTQDrrvgYEIALDRGALTAFLSWLESRPS 139
                                    *****************96654444677*********************7 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   4.9e-05      0.44      31      57 ..       8      34 ..       2      37 .. 0.91
   2 ?   -1.8   0.0      0.33     3e+03      10      24 ..      99     113 ..      91     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                        DUF3377 31 aVvvPlvLllciLvliyailqfrrkgt 57
                                   +Vv+ +vL l +L+l y + ++r+ gt
  gi|121637241|ref|YP_977464.1|  8 MVVLVVVLGLAVLALSYRLWKLRQGGT 34
                                   9999*******************9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                        DUF3377  10 eeevdvvvkiddees 24 
                                    ++e+ vv+ +d ++ 
  gi|121637241|ref|YP_977464.1|  99 TDEIVVVELCDSTQD 113
                                    456666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1043.74
//
Query:       gi|121637242|ref|YP_977465.1|  [L=243]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-56  190.7   0.0    3.7e-56  190.5   0.0    1.0  1  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.0   2.1e-60   3.7e-56      43     238 ..       2     219 ..       1     221 [. 0.97

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 2.1e-60
                   DDE_Tnp_ISL3  43 fleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvklanealdevRrreqkelre............... 107
                                    f+++l++++++++++v++D + +++++v e++P+A  ++D+FHvv++a+eald  Rrr ++++r+               
  gi|121637242|ref|YP_977465.1|   2 FFDALGAERAAQITHVSADAADWIADVVTERCPDAIQCADPFHVVAWATEALDVERRRAWNDARAiartepkwgrgrpgk 81 
                                    89999**********************************************************7777788999999**** PP

                   DDE_Tnp_ISL3 108 ........ekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelkeelrevfrkkdkeearkalkewiekae 179
                                            e++++lk++r++l+knpe+lte+q ++l ++++++p+l +aY lke+lr+vf   + ee+++al++wi++a+
  gi|121637242|ref|YP_977465.1|  82 naaprpgrERARRLKGARYALWKNPEDLTERQSAKLAWIAKTDPRLYRAYLLKESLRHVFS-VKGEEGKQALDRWISWAQ 160
                                    *******999999***********************************************9.78**************** PP

                   DDE_Tnp_ISL3 180 rsglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayGfrnfenfrl 238
                                    r++++ f +la+ +k+hr  I +++d++ls+g +E++N+ki++++r+a+Gfr+++++++
  gi|121637242|ref|YP_977465.1| 161 RCRIPVFVELAARIKRHRVAIDAALDHGLSQGLIESTNTKIRLLTRIAFGFRSPQALIA 219
                                    *******************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1755.54
//
Query:       gi|121637243|ref|YP_977466.1|  [L=205]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-13   48.5   3.9    1.6e-12   46.6   3.3    2.2  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    9.7e-10   39.0   1.1    1.7e-09   38.1   0.4    1.8  2  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/
    5.5e-06   26.3   0.0    8.3e-06   25.7   0.0    1.2  1  DDE_Tnp_ISL3  Transposase
  ------ inclusion threshold ------
      0.055   13.1   0.0       0.11   12.1   0.0    1.5  1  ThiP_synth    Thiamine-phosphate synthase


Domain annotation for each model (and alignments):
>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.21   9.5e+02      29      45 ..       3      19 ..       1      20 [. 0.78
   2 !   46.6   3.3   3.7e-16   1.6e-12       2      52 .]      98     147 ..      97     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                   HTH_Tnp_ISL3 29 svkavArqlgvSwtTVw 45
                                   +v+   ++lgv+ +TV+
  gi|121637243|ref|YP_977466.1|  3 NVRLFRALLGVDKRTVI 19
                                   666667899******96 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 3.7e-16
                   HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                    ++Pwar+++++T ++++ +++l+  + s +av++++++ w+TV  i+ r++
  gi|121637243|ref|YP_977466.1|  98 AVPWARHHAGHTYAFDDTVAWLAVAC-SKTAVCELMRIAWRTVGAIVARVW 147
                                    79************************.*******************99875 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.4   3.9e-13   1.7e-09       3      47 .]      47      92 ..      46      92 .. 0.96
   2 ?   -3.8   0.0         4   1.8e+04      12      21 ..     179     188 ..     178     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.9e-13
                        zf-ISL3  3 hrCPnCgsk.tvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                   +rC +Cg+k +++++g   r++r l++g  +v+L+++ +R+ C+++
  gi|121637243|ref|YP_977466.1| 47 RRCGRCGRKaSWYDRGAGLRQWRSLDWGTVEVFLEAEAPRVNCPTH 92
                                   69*******999*******************************986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                        zf-ISL3  12 tvvkhgkker 21 
                                    +vv+h++ + 
  gi|121637243|ref|YP_977466.1| 179 VVVDHDSGRL 188
                                    5788987655 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.9e-09   8.3e-06       1      34 [.     163     194 ..     163     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                   DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpg 34 
                                    +giDEis+k++h+y+tvvvd+  d grl++++p 
  gi|121637243|ref|YP_977466.1| 163 IGIDEISYKRHHRYLTVVVDH--DSGRLVWAAPS 194
                                    8********************..*******9986 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.11      80     136 ..      32      87 ..      25      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                                    T--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECE CS
                     ThiP_synth  80 evraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdv 136
                                     +r+ + +r  +++l+++ + g k++++dr +  ++  ++++wg+ e++ e+e p+v
  gi|121637243|ref|YP_977466.1|  32 GARVIARVRPRSAVLRRCGRCGRKASWYDRGAGLRQ-WRSLDWGTVEVFLEAEAPRV 87 
                                    6799999999**************************.6**********999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1635.26
//
Query:       gi|121637244|ref|YP_977467.1|  [L=193]
Description: hypothetical protein BCG_1375c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-57  193.4   0.0    3.1e-57  193.3   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.3   0.0   1.7e-61   3.1e-57       1     163 [.       8     175 ..       8     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 1.7e-61
                                    XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT....-BT CS
                Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp...ekk 77 
                                    iyTrtGD+GtT+l +++rv+K+d+r+ ay+++De+n+aig a+a l +++++++++L++iqn+Lfd+ga+l+tp   + k
  gi|121637244|ref|YP_977467.1|   8 IYTRTGDDGTTGLSDMSRVAKTDARLVAYADCDEANAAIGAALA-LGHPDTQITDVLRQIQNDLFDAGADLSTPiveNPK 86 
                                    9******************************************5.568899*************************9889 PP

                                    CCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS....HHHHHHHHHHHH CS
                Cob_adeno_trans  78 kekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee...veeevlkylNRLS 154
                                    + + +i ++ +++le ++d+++a lp lksf+lpggsp++a lhvaRtv+RraER+++++ +++   v+    kylNRLS
  gi|121637244|ref|YP_977467.1|  87 HPPLRIAQSYIDRLEGWCDAYNAGLPALKSFVLPGGSPLSALLHVARTVVRRAERSAWAAVDAHpegVSVLPAKYLNRLS 166
                                    9999********************************************************9977877788889******* PP

                                    HHHHHHHHH CS
                Cob_adeno_trans 155 DlLfvlarv 163
                                    DlLf+l+rv
  gi|121637244|ref|YP_977467.1| 167 DLLFILSRV 175
                                    *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1398.75
//
Query:       gi|121637245|ref|YP_977468.1|  [L=418]
Description: UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.2e-116  388.1   0.1   4.8e-116  387.9   0.1    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.9   0.1  2.7e-120  4.8e-116       1     417 []       7     406 ..       7     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: 387.9 bits;  conditional E-value: 2.7e-120
                                    EECSS--EEEEE--B-HHHHHHHHHHHGGGBSS.EEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--E CS
                  EPSP_synthase   1 vekgkrlegevkvpGsksisnralllAaLaege.stitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfe 79 
                                    v++g+rl+gev v G +++s+++l++A+L+++  stitn++d+ Dv  m+e+lr Lga +++ld  + + i+++++ +++
  gi|121637245|ref|YP_977468.1|   7 VTGGNRLSGEVAVGG-AKNSVLKLMAATLLAEGtSTITNCPDILDVPLMAEVLRGLGA-TVELD-GDVARITAPDEPKYD 83 
                                    57899**********.************987776***********************6.66885.5778888888***** PP

                                    E-HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEETSS-BEEEE CS
                  EPSP_synthase  80 apeelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkglklkgvei 159
                                    a+ ++v+++++s+++l++L++++++a  +v+L+G+++i++RP+d++  +LrqlGa++++e+g++ a ++    +l+g+ei
  gi|121637245|ref|YP_977468.1|  84 ADFAAVRQFRASVCVLGPLVGRCKRA--RVALPGGDAIGSRPLDMHQAGLRQLGAHCNIEHGCVVARAE----TLRGAEI 157
                                    **99********************98..9**********************************999998....9****** PP

                                    ETSSTTHHHHHHHHHHHTTSBSEEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHH CS
                  EPSP_synthase 160 kaevsSqqvtsllllaallaegtteleelasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassA 239
                                    ++e++S+++t+++l+aa++aeg t+++++a+ep+++d+++ml+++g+++e++g+++ +t++G+++l+ te++v+gD++ A
  gi|121637245|ref|YP_977468.1| 158 QLEFPSVGATENILMAAVVAEGVTTIHNAAREPDVVDLCTMLNQMGAQVEGAGSPT-MTITGVPRLHPTEHRVIGDRIVA 236
                                    ***************************************************99998.*********************** PP

                                    HHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGGGHHHH CS
                  EPSP_synthase 240 ayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptlavlaaf 319
                                    a++ +aAa+t+g++ v +v++ +lq    ++ ++l+++ga++tq++ as++v++  +++k+v+++tlp ++++++++ + 
  gi|121637245|ref|YP_977468.1| 237 ATWGIAAAMTRGDISVAGVDPAHLQ----LVLHKLHDAGATVTQTD-ASFRVTQ-YERPKAVNVATLPFPGFPTDLQPMA 310
                                    *************************....9999*************.8999999.7************************ PP

                                    HHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEE CS
                  EPSP_synthase 320 aegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegeve 399
                                    +++ ++++g++++++++++ ++ +++e+ +lGa+++++ +    + +  ql++a v++  D+R+++ l+laglva+g++e
  gi|121637245|ref|YP_977468.1| 311 IALASIADGTSMITENVFEARFRFVEEMIRLGADARTDGHHAV-VRGLPQLSSAPVWCS-DIRAGAGLVLAGLVADGDTE 388
                                    *************************************988865.666679*********.******************** PP

                                    EETTHHHHHHSSSHHHHH CS
                  EPSP_synthase 400 iddiectdksfpefeekL 417
                                    + d+ ++d+++p f+e+L
  gi|121637245|ref|YP_977468.1| 389 VHDVFHIDRGYPLFVENL 406
                                    ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3089.84
//
Query:       gi|121637246|ref|YP_977469.1|  [L=165]
Description: methylated-DNA--protein-cysteine methyltransferase ogt [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-35  121.4   0.0    1.6e-35  121.1   0.0    1.2  1  DNA_binding_1    6-O-methylguanine DNA methyltransferase, DNA
    2.2e-15   57.2   0.0    3.7e-15   56.5   0.0    1.4  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   1.8e-39   1.6e-35       1      80 [.      75     154 ..      75     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 1.8e-39
                                    HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
                  DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80 
                                    +fqqrVw++l +IpyG++ +YgeiA+++g+p+aaraVg a+++np+ai+vPcHRV+ga+gkl+gy gg++rkralLe E+
  gi|121637246|ref|YP_977469.1|  75 DFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEK 154
                                    59****************************************************************************96 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   4.2e-19   3.7e-15       1      77 []       1      71 [.       1      71 [. 0.97

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.2e-19
                                   --EEEEEEETTEEEEEEEETTCEEEEEEEC-HHHCCHHHCCCTTTSCCHCCHHHHHHHHHHHHHHHHS--B-SHCHH CS
                Methyltransf_1N  1 alyytlidsplgrlllagdEkgllaidlldkdtselkelpkllkqdeelpalaelkqaleeYfageekpaltlPldl 77
                                   +++y++idsp+g+l lag++++l+++++l++++    e+++ ++ ++   a+ +++++l +Yfage++ ++ ++ldl
  gi|121637246|ref|YP_977469.1|  1 MIHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTY----EPSRTHWTPD-PGAFSGAVDQLNAYFAGELT-EFDVELDL 71
                                   78*******************************....6*********.********************.**999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1239.09
//
Query:       gi|121637247|ref|YP_977470.1|  [L=496]
Description: ada regulatory protein alkA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-29  102.4   0.0    5.4e-29  100.8   0.0    1.9  1  AlkA_N          AlkA N-terminal domain
    5.2e-28   96.9   6.7      1e-27   96.0   6.7    1.5  1  Ada_Zn_binding  Metal binding domain of Ada
    8.2e-15   54.8   0.2      2e-14   53.6   0.2    1.7  1  HTH_18          Helix-turn-helix domain
    2.2e-07   30.8   0.0    0.00034   20.6   0.0    2.5  2  HTH_AraC        Bacterial regulatory helix-turn-helix protein
    2.5e-07   31.1   0.0    9.8e-07   29.2   0.0    2.0  2  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
     0.0052   16.6   0.2      0.021   14.7   0.1    2.1  2  HHH             Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   1.8e-32   5.4e-29       2     116 .]     202     316 ..     201     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.8e-32
                         AlkA_N   2 lrLayrpPydwaallaFlaaraiegvEavdedsygRtlrldgakGvvevrhepeksalkvrlslsdlraleaviarvrrl 81 
                                    lrL++r P++++ ++++laa a++g+E+v++++y+Rtlrl+ ++G+v+++++p  +++++ l l+d+r+l +++ar+rrl
  gi|121637247|ref|YP_977470.1| 202 LRLPVRAPFAFEGVFGHLAATAVPGCEEVRDGAYRRTLRLPWGNGIVSLTPAP--DHVRCLLVLDDFRDLMTATARCRRL 279
                                    89*************************************************99..89*********************** PP

                         AlkA_N  82 lDLdadpeaieaaL..dpllapevaarpGlRvPgavd 116
                                    lDLdadpeai +aL  dp l++ v ++pG R+P++vd
  gi|121637247|ref|YP_977470.1| 280 LDLDADPEAIVEALgaDPDLRAVVGKAPGQRIPRTVD 316
                                    **********************************987 PP

>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   6.7   3.3e-31     1e-27       2      65 .]       8      71 ..       7      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 3.3e-31
                                   HHHHHHHTSTTCCTTBEEEETTTTEEE-TT-SSS-S-SCCEEEESSHHHHHHTT-EEETTTTTS CS
                 Ada_Zn_binding  2 rwqavlardaradgsFvyavkttgiyCrpsCparlPkrenveFfdtaaeAeaagfrpCkrcrPd 65
                                   +++av+++dar+dg Fv+av ttg+yCrpsCp+r P   nv+F +taa+A+ +gfr+CkrcrPd
  gi|121637247|ref|YP_977470.1|  8 CYRAVQSKDARFDGWFVVAVLTTGVYCRPSCPVRPPFARNVRFLPTAAAAQGEGFRACKRCRPD 71
                                   9**************************************************************7 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.2   6.8e-18     2e-14       1      81 []     106     185 ..     106     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 6.8e-18
                                    HHHHHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHHHH CS
                         HTH_18   1 laaalgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPseyrr 80 
                                    laa+lg++ r+L+rl+++v+g  p +++r+ R++ Ar  L+e+t+l+  ++A+a+GFs+ ++F++  r +   tP++ r+
  gi|121637247|ref|YP_977470.1| 106 LAAQLGYTIRQLERLLQAVVGAGPLALARAQRMQTARV-LIETTNLPFGDVAFAAGFSSIRQFNDTVRLACDGTPTALRA 184
                                    89************************************.5599*********************************9998 PP

                                    H CS
                         HTH_18  81 r 81 
                                    r
  gi|121637247|ref|YP_977470.1| 185 R 185
                                    6 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0014       4.2      14      38 ..     106     130 ..     104     132 .. 0.92
   2 !   20.6   0.0   1.1e-07   0.00034       1      41 [.     145     183 ..     145     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                    HHHHTTSSHHHHHHHHHHHSSS-HH CS
                       HTH_AraC  14 iAdelgfSrsyFsrlFkketGmtPs 38 
                                    +A++lg+  +++ rl+++++G  P 
  gi|121637247|ref|YP_977470.1| 106 LAAQLGYTIRQLERLLQAVVGAGPL 130
                                    69*******************9996 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.1e-07
                                    HHCCCSCT--HHHHHHHTTS.SHHHHHHHHHHHSSS-HHHHH CS
                       HTH_AraC   1 LrenlstnltiediAdelgf.SrsyFsrlFkketGmtPsqyr 41 
                                    ++   +tnl  +d+A ++gf S ++F  + + +++ tP++ r
  gi|121637247|ref|YP_977470.1| 145 IE---TTNLPFGDVAFAAGFsSIRQFNDTVRLACDGTPTALR 183
                                    56...9*********************************987 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   4.3e+03      60      90 ..     139     168 ..     102     173 .. 0.72
   2 !   29.2   0.0   3.3e-10   9.8e-07       1     106 [.     322     470 ..     322     472 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                    HHHHHHHS-SSS--TTSHHHHHHHHHHTTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  60 elArilvgkpdvlivvDvhvrrilkrlrsik 90 
                                    ++Ar l+   ++l+  Dv ++ +++ +r+ +
  gi|121637247|ref|YP_977470.1| 139 QTARVLIET-TNLPFGDVAFAAGFSSIRQFN 168
                                    345555554.458999999988888887765 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 3.3e-10
                                    HHHHHHTTS-HHHHHHHHHHHHHHHS.............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfg.............fptpedladadeekLrelirelGfyrrKakyikelArilv. 66 
                                    v+a+l qq+s+++a +   rl++++g             fp+ e+la++d+ +L+         + + + i +l   l+ 
  gi|121637247|ref|YP_977470.1| 322 VRAVLAQQVSTKAASTHAGRLVAAYGrpvhdrhgalthtFPSIEQLAEIDPGHLAVP-------KARQRTINALVASLAd 394
                                    789**************************************************9765.......899*******99999* PP

                                    .....................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                                    .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 .....................................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                                                                         g pd++++ D+++r ++k+l++  ++  +  v  ++++++
  gi|121637247|ref|YP_977470.1| 395 kslvldagcdwqrargqllalpgvgpwtaeviamrglGDPDAFPASDLGLRLAAKKLGLPAQR-RALTVHSARWRPW 470
                                    *************************************99******************998774.6666666666666 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.8   1.1e+04       8      16 ..     362     370 ..     361     370 .. 0.80
   2 !   14.7   0.1   7.2e-06     0.021      12      27 ..     411     426 ..     408     427 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.8
                                    SSHHHHHTS CS
                            HHH   8 asreeLlal 16 
                                     s+e+L+++
  gi|121637247|ref|YP_977470.1| 362 PSIEQLAEI 370
                                    599**9875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.2e-06
                                    HHHTSTT-SHHHHHHH CS
                            HHH  12 eLlalPGVGpktAeaI 27 
                                    +LlalPGVGp tAe+I
  gi|121637247|ref|YP_977470.1| 411 QLLALPGVGPWTAEVI 426
                                    79************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3087.27
//
Query:       gi|121637248|ref|YP_977471.1|  [L=541]
Description: adenylate cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-21   75.0   0.0    8.9e-21   74.3   0.0    1.3  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    2.1e-08   34.4   0.7    5.6e-08   33.0   0.7    1.8  1  HAMP           HAMP domain
  ------ inclusion threshold ------
       0.21   11.2   2.3       0.27   10.9   1.4    1.6  1  TMEM240        TMEM240 family
       0.64    9.7   3.6        1.7    8.3   3.6    1.8  1  DUF2937        Protein of unknown function (DUF2937)
        1.6    8.4  10.2        1.3    8.6   1.8    2.4  2  Wzy_C          O-Antigen ligase
          5    6.5   8.4         12    5.3   1.4    2.8  3  DUF1129        Protein of unknown function (DUF1129)
        8.1    6.0   9.6       0.43   10.2   0.5    2.4  2  DUF1449        Protein of unknown function (DUF1449)


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   3.5e-24   8.9e-21       7     176 ..     358     527 ..     355     531 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 3.5e-24
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                    ++v+++F+dIvg+t+l++   p +vvklLn+ +a + + +d++++   k+ Gda ++++g+p    + + +  + aL+  
  gi|121637248|ref|YP_977471.1| 358 RHVAVVFIDIVGSTQLVTSRPPADVVKLLNKFFAIVVDEVDRHHGLVNKFEGDASLTIFGAP----NRLPCPEDKALAAA 433
                                    68************************************************************....8999999******* PP

                  Guanylate_cyc  87 ealeevaveskeglkvrvGihtGpvvagviG.akkprydvwGntvnlAsrmestgk..agkiqvseetyellk.eeqfel 162
                                     a+    v++ ++ + ++G+  G+v+ag +G +++++y+v+G+ vn A+r+  ++k  +gk   s+++++ ++ ee  ++
  gi|121637248|ref|YP_977471.1| 434 RAIADRLVNEMPECQAGIGVAAGQVIAGNVGaRERFEYTVIGEPVNEAARLCELAKsrPGKLLASAQAVDAASeEERARW 513
                                    ***77777778********************8889****************98877225788889999998887888999 PP

                  Guanylate_cyc 163 tergevevkGkgkl 176
                                    +   +v+++G ++ 
  gi|121637248|ref|YP_977471.1| 514 SLGRHVKLRGHDQP 527
                                    99999999997765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.7   2.2e-11   5.6e-08       2      52 ..     275     325 ..     274     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.2e-11
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    la+ +  P+r +++a rr+ +G+l+t l v  + E+GeL r fNaM+  Lr
  gi|121637248|ref|YP_977471.1| 275 LAWLTATPVRVVRAALRRVERGELRTNLVVFDGTELGELQRGFNAMVAGLR 325
                                    789999*****************************************9998 PP

>> TMEM240  TMEM240 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.4    0.0001      0.27      90     118 ..     261     289 ..     247     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                        TMEM240  90 lvlglllgfiiswlllwldgvlhlavraw 118
                                     ++ l++gfi+ w+l wl     ++vra 
  gi|121637248|ref|YP_977471.1| 261 SMVTLVFGFILMWILAWLTATPVRVVRAA 289
                                    5889****************999999984 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.6   0.00068       1.7     108     162 .]     237     292 ..     233     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00068
                        DUF2937 108 llraadaeileetlenfspavp.ltpeglafglvgalllallvelllallarlvrr 162
                                    l+  +++ +l+ t  +f  +v+ +++ +l+fg++++ +la+l   +++++++++rr
  gi|121637248|ref|YP_977471.1| 237 LMAMFEMVLLNLTRMQFATGVLiISMVTLVFGFILMWILAWLTATPVRVVRAALRR 292
                                    667788889999999****99835899************************99886 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8   0.00052       1.3      17     110 ..      61     155 ..      50     185 .. 0.78
   2 ?    4.6   1.5    0.0091        23       8      59 ..     221     279 ..     215     397 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00052
                          Wzy_C  17 sgiigllvalivlliifykrripfllllgilvgvilliilfvlstnletlknitkafgkldkkkgkdksgssRlyiwkra 96 
                                    + ++g++val+++ i+ +++ i++     +  gv+ +++l++l    ++l+++t +  +++++  k +   +R ++    
  gi|121637248|ref|YP_977471.1|  61 ANLLGIGVALLLVTIAIPEPSIVRDTPRWLTFGVVPGYVLLALALGSYALTRQTVQALRWAIEGRKPTREEERRTFLAPW 140
                                    5689******************4444444555667777777777777888888888888888799999999999999988 PP

                          Wzy_C  97 lplikdspilGtG.v 110
                                      ++ + +++G+G  
  gi|121637248|ref|YP_977471.1| 141 RVAVGHLMFWGVGtA 155
                                    889999999999941 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0091
                          Wzy_C   8 lalflstsRsgiigllvalivlliifykrri..pfllllgilvgvilliilfv.....l 59 
                                    +++ l +s ++++g++++ ++ ++++   r+  +  +l++ +v +++++il++      
  gi|121637248|ref|YP_977471.1| 221 MVVWLLGSGVPVVGIALMAMFEMVLLNLTRMqfATGVLIISMVTLVFGFILMWilawlT 279
                                    45556666667777755555555555555553344555557777777777777444440 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.48   1.2e+03     140     174 ..      41      75 ..      33      85 .. 0.66
   2 ?    4.3   0.1    0.0095        24     138     187 ..     128     177 ..      99     196 .. 0.79
   3 ?    5.3   1.4    0.0047        12      92     137 ..     237     281 ..     221     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.48
                        DUF1129 140 kkkrpplwkrllilllllvvwlvlftlvallpavi 174
                                    +++r+  +++ ++l++l+v   +l + vall  +i
  gi|121637248|ref|YP_977471.1|  41 ESQRRRRVRIQVMLTALVVTANLLGIGVALLLVTI 75 
                                    56666666666666666666666666666666555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0095
                        DUF1129 138 kkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvliiig 187
                                     ++++r+ ++  + ++++ l++w v ++l++ l   iN    p  l+++ 
  gi|121637248|ref|YP_977471.1| 128 TREEERRTFLAPWRVAVGHLMFWGVGTALLTTLYGLINNAFIPRFLFAVS 177
                                    67899*********************************998877666653 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0047
                        DUF1129  92 fallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltre 137
                                    ++++f ++  ++   ++ ++G++ + +v+lv+G++++ +  +lt +
  gi|121637248|ref|YP_977471.1| 237 LMAMFEMVL-LNLTRMQFATGVLIISMVTLVFGFILMWILAWLTAT 281
                                    334444333.3333444446*******************9999864 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00017      0.43      52      94 ..      80     122 ..      50     128 .. 0.84
   2 ?   -0.9   3.1      0.41     1e+03      72     110 ..     245     282 ..     210     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                        DUF1449  52 dgalsklLgWLrvgrvPvLilLvlfLtlFglvGlvlqslvasl 94 
                                     +++ ++  WL +g vP  +lL l L  ++l+  ++q+l  ++
  gi|121637248|ref|YP_977471.1|  80 PSIVRDTPRWLTFGVVPGYVLLALALGSYALTRQTVQALRWAI 122
                                    467777889***********************99999886665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                        DUF1449  72 lLvlfLtlFglvGlvlqslvasllgallpallaaaiall 110
                                    lL l  + F+ +G+++ s+v+ ++g++l ++la + a  
  gi|121637248|ref|YP_977471.1| 245 LLNLTRMQFA-TGVLIISMVTLVFGFILMWILAWLTATP 282
                                    3333333444.7888999999999999999998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3325.98
//
Query:       gi|121637249|ref|YP_977472.1|  [L=535]
Description: adenylate cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-20   73.1   0.0    3.3e-20   72.5   0.0    1.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    7.3e-09   35.9   0.7    3.8e-08   33.6   0.2    2.4  2  HAMP           HAMP domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   3.6e-24   3.3e-20       8     176 ..     360     528 ..     356     533 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.6e-24
                  Guanylate_cyc   8 evtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdmle 87 
                                    + +++F dIvg+t+l+ ++ + +vvklLn  +a + + +d++++   k+ Gda ++++g+p    + + +  + aL+   
  gi|121637249|ref|YP_977472.1| 360 HAAVVFVDIVGSTQLVDNQPAAHVVKLLNRFFAIVVNEVDRHHGLINKFAGDAALAIFGAP----NRLDRPEDAALAAAR 435
                                    5789*********************************************************....8889999999**999 PP

                  Guanylate_cyc  88 al.eevaveskeglkvrvGihtGpvvagviG.akkprydvwGntvnlAsrmestgkagkiqv..seetyellk.eeqfel 162
                                    a+ +  a+e  ++++ ++G+  G++vag +G +++++y+v G+ vn A+r+  ++k+    +  s++t + ++ +e  ++
  gi|121637249|ref|YP_977472.1| 436 AIaDRLANE-MPEVQAGIGVAAGQIVAGNVGaKQRFEYTVVGKPVNQAARLCELAKSHPARLlaSSDTLHAASeTERAHW 514
                                    995666666.5********************8899*****************9998876666558888888877899999 PP

                  Guanylate_cyc 163 tergevevkGkgkl 176
                                    +  + v ++G ++ 
  gi|121637249|ref|YP_977472.1| 515 SLGETVTLRGHEQP 528
                                    99999999996654 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.23   2.1e+03      39      50 ..      10      21 ..       9      24 .. 0.85
   2 !   33.6   0.2   4.2e-12   3.8e-08       2      53 .]     276     327 ..     275     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHH CS
                           HAMP 39 eLarafNaMldr 50
                                   +L++a+++M ++
  gi|121637249|ref|YP_977472.1| 10 RLGQALETMTRQ 21
                                   79*******876 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 4.2e-12
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                    la+ + +P+r +++a +r+ +Gdl+ +l v  + E+GeL r fNaM++ Lre
  gi|121637249|ref|YP_977472.1| 276 LAWLTAAPVRVVRAALKRVEQGDLRGDLVVFDGTELGELQRGFNAMVNGLRE 327
                                    79999******************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3098.01
//
Query:       gi|121637250|ref|YP_977473.1|  [L=567]
Description: adenylate cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-20   71.1   0.0    1.4e-19   70.5   0.0    1.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    4.8e-09   36.5   0.2    1.3e-08   35.1   0.2    1.8  1  HAMP           HAMP domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   1.5e-23   1.4e-19       7     175 ..     358     526 ..     355     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 1.5e-23
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                    ++v+++F dIvg+t+l++   + evv lLn  ++ + + ++++++   k+ Gda ++v+g+p    + ++   + aL+  
  gi|121637250|ref|YP_977473.1| 358 RHVAVVFVDIVGSTQLVTSRPAAEVVMLLNRFFTVIVDEVNHHRGLVNKFQGDASLAVFGAP----NRLSHPEDAALATA 433
                                    68******************9*****************************************....55666667899999 PP

                  Guanylate_cyc  87 ealeevaveskeglkvrvGihtGpvvagviG.akkprydvwGntvnlAsrmestgkag..kiqvseetyellk.eeqfel 162
                                     a+    +++ ++ + ++G+  G+vvag +G  ++++y+v+G+ vn A+r+  ++k++  +   s++t + ++ +e  ++
  gi|121637250|ref|YP_977473.1| 434 RAIADRLASEMPECQAGIGVAAGQVVAGNVGaHERFEYTVIGEPVNEAARLCELAKSYpsRLLASSQTLRGASeNECARW 513
                                    9995555555699******************999*****************99998751155558888888885566667 PP

                  Guanylate_cyc 163 tergevevkGkgk 175
                                    +  + v ++G ++
  gi|121637250|ref|YP_977473.1| 514 SLGETVTLRGHDQ 526
                                    7777888888766 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   1.4e-12   1.3e-08       2      53 .]     275     326 ..     274     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.4e-12
                                    HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                           HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                    la+ +  P+r +++a +r+ +Gdl+ +l v  + E+GeL r fN+M++ Lre
  gi|121637250|ref|YP_977473.1| 275 LAWLTATPVRVVREALNRVEQGDLSGDLVVFDGTELGELQRGFNRMVEGLRE 326
                                    789999******************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3521.82
//
Query:       gi|121637251|ref|YP_977474.1|  [L=226]
Description: hypothetical protein BCG_1382 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.8e-105  349.3   0.0   8.7e-105  349.1   0.0    1.0  1  NucS      Endonuclease NucS
     0.0086   16.3   0.0      0.016   15.4   0.0    1.4  1  UPF0102   Uncharacterised protein family UPF0102


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.1   0.0  9.7e-109  8.7e-105       1     229 []       1     226 []       1     226 [] 0.99

  Alignments for each domain:
  == domain 1  score: 349.1 bits;  conditional E-value: 9.7e-109
                           NucS   1 ksavlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkd.rkvePvnWqppkssltaevedgslilksirrkpeee 79 
                                    +s+v++v+a+C+v+y+Gr++++L++++rl+++k+dG+++vh+d r+++P+nW++p+++lt e+++g+++++++++k++e+
  gi|121637251|ref|YP_977474.1|   1 MSRVRLVIAQCTVDYIGRLTAHLPSARRLLLFKADGSVSVHADdRAYKPLNWMSPPCWLT-EESGGQAPVWVVENKAGEQ 79 
                                    689***************************************99****************.******************* PP

                           NucS  80 LkveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrk 159
                                    L+++ie++eh+s++el+++++lv+dG+ea+l++l++eh++L++eG+++v+rey++aiG+vd+L++de+g++v+ve+krr 
  gi|121637251|ref|YP_977474.1|  80 LRITIEGIEHDSSHELGVDPGLVKDGVEAHLQALLAEHIQLLGEGYTLVRREYMTAIGPVDLLCRDERGGSVAVEIKRR- 158
                                    ******************************************************************************9. PP

                           NucS 160 aevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldppkdskrnidskklrvl 229
                                    +e+d+veqL+ry+ell++dsvl++v+Gv++a++i+++a++l++++g+++++ld  +d++r++ds+++r++
  gi|121637251|ref|YP_977474.1| 159 GEIDGVEQLTRYLELLNRDSVLAPVKGVFAAQQIKPQARILATDRGIRCLTLD--YDTMRGMDSGEYRLF 226
                                    *****************************************************..************987 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-06     0.016       9      45 ..     120     159 ..     114     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                                    HHHTT-EEEEEEEEETTEEEEEEE...TTEEEEEEEEE-. CS
                        UPF0102   9 LekkgyeilernwrcragEiDiia...tevlvfvEVKtRs 45 
                                    L  +gy+++ r++ + +g +D+ +   +   v vE+K R 
  gi|121637251|ref|YP_977474.1| 120 LLGEGYTLVRREYMTAIGPVDLLCrdeRGGSVAVEIKRRG 159
                                    5679**********************95569*******94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1539.64
//
Query:       gi|121637252|ref|YP_977475.1|  [L=98]
Description: hypothetical protein BCG_1383 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 746.08
//
Query:       gi|121637253|ref|YP_977476.1|  [L=152]
Description: hypothetical protein BCG_1384c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-21   74.3   0.0    1.3e-20   73.7   0.0    1.3  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.6e-14   53.5   0.0    3.1e-14   53.2   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.3e-10   41.7   0.0    1.7e-10   41.3   0.0    1.3  1  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.035   14.3   0.0    1.3  1  Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-term


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   2.9e-24   1.3e-20       1     109 []      22     134 ..      22     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 2.9e-24
                                    EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEEEEE CS
                   Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhlaywv 76 
                                    d++gi+V Dl+ a++ + ++lG+    +  +++q+++ a++ + ++  qi+L++pl+++    +fl+++g+g+++la++v
  gi|121637253|ref|YP_977476.1|  22 DHVGIAVADLDVAIEWYHDHLGMILVHEEINDDQGIREALLAVPGSAAQIQLMAPLDESsviaKFLDKRGPGIQQLACRV 101
                                    6*********************98777777899*******9999988************888888888************ PP

                                    S-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                   Glyoxalase_4  77 ddldaavarleeqGfevvqkgvragaagrrfay 109
                                    +dlda ++rl++qG+++v +  r g+a+ r+ +
  gi|121637253|ref|YP_977476.1| 102 SDLDAMCRRLRSQGVRLVYETARRGTANSRINF 134
                                    ********************99***99999876 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0     7e-18   3.1e-14       1     128 []      20     147 ..      20     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 7e-18
                                    EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEE CS
                     Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafi 80 
                                    g+dhv ++v+dl+ ++++Y+++LG+ lv ++     ++g r a + + g  +++ l  + + + +  k++ + + +++ +
  gi|121637253|ref|YP_977476.1|  20 GLDHVGIAVADLDVAIEWYHDHLGMILVHEEI--NDDQGIREALLAVPGSAAQIQLMAPLDESSVIAKFLDKRGPGIQQL 97 
                                    79*****************************9..5667777777777777777777777777777765566589****** PP

                                    EEEHCHHHHHHHHHHHTTGEEEEEEECHH..CTEEEEEEEEETTSEEEEE CS
                     Glyoxalase  81 aldvedvgkaldrlkeagvkvvaepgrhy..fgalysfyfrDpdGillei 128
                                    a  v d++++++rl+++gv+ v e  r++  ++++ +++ +D +G+l+e+
  gi|121637253|ref|YP_977476.1|  98 ACRVSDLDAMCRRLRSQGVRLVYETARRGtaNSRINFIHPKDAGGVLIEL 147
                                    *********************999988761145555669*********96 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.9e-14   1.7e-10       1     114 [.      21     128 ..      21     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.9e-14
                   Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdg..YlEllavdpeapaperprlfgldrlakgegl 78 
                                    lDHv++av dl+ a++++++ lG+ ++      + g++ al+  +++   + l+a+ +e      ++ f ld+  +g+g+
  gi|121637253|ref|YP_977476.1|  21 LDHVGIAVADLDVAIEWYHDHLGMILVHEEINDDQGIREALLAVPGSaaQIQLMAPLDESSV--IAK-F-LDK--RGPGI 94 
                                    8*******************************************664479*****8777765..233.4.344..7**** PP

                   Glyoxalase_3  79 htlalrtddidataarlraaGvd...eagrrvrpdggdl 114
                                     +la+r++d+da+ +rlr++Gv    e++rr      ++
  gi|121637253|ref|YP_977476.1|  95 QQLACRVSDLDAMCRRLRSQGVRlvyETARRG-----TA 128
                                    *********************97555444443.....33 PP

>> Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.8e-06     0.035      50     103 ..      70     123 ..      18     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
                   Glyoxalase_5  50 ginfilneepdsaaakfarehGpsacalafrvkdakkayeralekGakpveket 103
                                    +i+++   +++s +akf  + Gp++  la rv d ++  +r+ ++G + v +++
  gi|121637253|ref|YP_977476.1|  70 QIQLMAPLDESSVIAKFLDKRGPGIQQLACRVSDLDAMCRRLRSQGVRLVYETA 123
                                    688999999********************************9999998776553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1184.07
//
Query:       gi|121637254|ref|YP_977477.1|  [L=389]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-95  319.9   4.6    1.1e-95  319.9   2.7    1.8  2  Thiolase_N     Thiolase, N-terminal domain
    4.9e-43  145.7   1.8    1.1e-42  144.6   1.8    1.6  1  Thiolase_C     Thiolase, C-terminal domain
    9.3e-05   22.1   1.9     0.0002   21.0   0.4    2.3  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
     0.0036   17.1   0.2        4.1    7.3   0.1    2.5  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
  ------ inclusion threshold ------
       0.49   11.1   2.4        9.6    7.0   0.1    2.4  2  DUF4259        Domain of unknown function (DUF4259)


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.9   2.7   3.2e-99   1.1e-95       2     259 ..       1     258 [.       1     259 [. 0.99
   2 ?   -0.7   0.0       0.2   7.2e+02      28      51 ..     290     313 ..     281     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 319.9 bits;  conditional E-value: 3.2e-99
                                    EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                     Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                    +iv++artpigk +gslkd+sa+eL+a+a+k++leka+v+++ v++vi+G+vl+ag+gq++arqaa++agi ++vpa t+
  gi|121637254|ref|YP_977477.1|   1 MIVAGARTPIGKLMGSLKDFSASELGAIAIKGALEKANVPASLVEYVIMGQVLTAGAGQMPARQAAVAAGIGWDVPALTI 80 
                                    59****************************************************************************** PP

                                    EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHH CS
                     Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaen 161
                                    nk+c Sg++a+ala q i+a e+dvvvagG+Esm++ap+  + ++rsg+k+gd ++ d++ +dgl+d+f+++ mG  +e+
  gi|121637254|ref|YP_977477.1|  81 NKMCLSGIDAIALADQLIRAREFDVVVAGGQESMTKAPHLLM-NSRSGYKYGDVTVLDHMAYDGLHDVFTDQPMGALTEQ 159
                                    *****************************************8.************************************* PP

                                    HHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSE.EEE-S-TTS-TT--HHHHHTS-BSSSTTSS-B CS
                     Thiolase_N 162 lakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgk.ktvdkdeairsevtaekLaklkpaFkkeGtvt 240
                                     ++   ++R eqde+A++shqkaaaa+k+g F+de++Pv+++++ g+  ++++de+ir+++ta +La lkpaF+ +Gt+t
  gi|121637254|ref|YP_977477.1| 160 RNDVDMFTRSEQDEYAAASHQKAAAAWKDGVFADEVIPVNIPQRTGDpLQFTEDEGIRANTTAAALAGLKPAFRGDGTIT 239
                                    ******************************************************************************** PP

                                    TTSB--BEEEEEEEEEEEH CS
                     Thiolase_N 241 AgnasqisDGaaavllmse 259
                                    Ag asqisDGaaav++m++
  gi|121637254|ref|YP_977477.1| 240 AGSASQISDGAAAVVVMNQ 258
                                    *****************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHTS-GGGCCEEEEE CS
                     Thiolase_N  28 aealkallekagvdpeevdevivG 51 
                                    a+a++++l++ g++ +++d v + 
  gi|121637254|ref|YP_977477.1| 290 ANAINKALDREGISVDQLDVVEIN 313
                                    78999*******999999988665 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   1.8     3e-46   1.1e-42       2     122 ..     267     387 ..     266     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 3e-46
                                    --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                     Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                    ++la+i ++ +v+ ++++l+ +Pa+ai+k+l+++g++v+++d++EinEAFaa+aLa++++l+l+++ vNvnGGaia+GHP
  gi|121637254|ref|YP_977477.1| 267 TWLAEIGAHGVVAGPDSTLQSQPANAINKALDREGISVDQLDVVEINEAFAAVALASIRELGLNPQIVNVNGGAIAVGHP 346
                                    789***************************************************************************** PP

                                    TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                     Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                    lG+sG+Ri+ +++ +l ++g+ +gvaalC +ggqg+al+++
  gi|121637254|ref|YP_977477.1| 347 LGMSGTRITLHAALQLARRGSGVGVAALCGAGGQGDALILR 387
                                    **************************************986 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   5.6e-08    0.0002     157     210 ..      66     119 ..      24     129 .. 0.85
   2 ?   -1.4   0.1      0.39   1.4e+03     237     253 .]     245     261 ..     220     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.6e-08
                                    HHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHH CS
                  ketoacyl-synt 157 risyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpea 210
                                     ++   g++ p++t+   C S+  a+++a q +r++e dv++aGG e ++++  
  gi|121637254|ref|YP_977477.1|  66 AVAAGIGWDVPALTINKMCLSGIDAIALADQLIRAREFDVVVAGGQESMTKAPH 119
                                    4555689999*************************************9987655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                                    -BB-EEEEEEEEECHHH CS
                  ketoacyl-synt 237 vlGEGvGavvLkrleda 253
                                     +++G++avv++ +e+a
  gi|121637254|ref|YP_977477.1| 245 QISDGAAAVVVMNQEKA 261
                                    5789******9999876 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0012       4.3       3      38 ..      80     115 ..      78     132 .. 0.84
   2 !    7.3   0.1    0.0012       4.1      52      68 ..     246     262 ..     238     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                                    +n+ C + + a+++Ad+li++ ++  v+  g e ++
  gi|121637254|ref|YP_977477.1|  80 INKMCLSGIDAIALADQLIRAREFDVVVAGGQESMT 115
                                    7899*****************988877666666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0012
                                    B-EEEEEEEEEEESSSS CS
                    ACP_syn_III  52 fGDGAgAvvleaseeeg 68 
                                     +DGA+Avv+ ++e+ +
  gi|121637254|ref|YP_977477.1| 246 ISDGAAAVVVMNQEKAQ 262
                                    78********9996544 PP

>> DUF4259  Domain of unknown function (DUF4259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.03   1.1e+02      10      57 ..     137     184 ..     135     228 .. 0.82
   2 ?    7.0   0.1    0.0027       9.6      25      62 ..     286     324 ..     274     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.03
                        DUF4259  10 nDtAaDflaeledakpedrleliiealeevadaeedeyleadegaeal 57 
                                    +++A+D l ++  ++p  +l++++++++ + ++e+dey  a+  ++a 
  gi|121637254|ref|YP_977477.1| 137 DHMAYDGLHDVFTDQPMGALTEQRNDVDMFTRSEQDEYAAASHQKAAA 184
                                    57999999999999999999******************9999887773 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                        DUF4259  25 pedrleliiealee.vadaeedeyleadegaealaaael 62 
                                    + +++++i +al++  +++++ + +e+ e+ +a+a+a +
  gi|121637254|ref|YP_977477.1| 286 QSQPANAINKALDReGISVDQLDVVEINEAFAAVALASI 324
                                    5567899*******99********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2963.66
//
Query:       gi|121637255|ref|YP_977478.1|  [L=304]
Description: thioredoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-16   61.0   0.6    1.1e-16   61.0   0.6    2.7  3  TPR_20         Tetratricopeptide repeat
    1.3e-10   41.2   0.0    2.4e-10   40.3   0.0    1.5  1  Thioredoxin    Thioredoxin
     0.0032   17.9   0.0      0.011   16.2   0.0    1.9  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.045   13.8   0.1    1.9  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem
       0.06   13.9   3.6       0.08   13.5   0.1    2.7  3  TPR_19         Tetratricopeptide repeat
      0.094   13.6   0.2      0.094   13.6   0.2    3.5  4  TPR_14         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         4   1.2e+04      11      20 ..      21      30 ..      13      39 .. 0.52
   2 ?    0.7   0.0      0.22   6.5e+02      75      86 ..     170     181 ..     164     185 .. 0.86
   3 !   61.0   0.6   3.5e-20   1.1e-16      19      90 .]     233     304 .]     217     304 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                         TPR_20 11 leaalaanpd 20
                                   +++++++n +
  gi|121637255|ref|YP_977478.1| 21 IKQRAQQNAA 30
                                   4444444432 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                         TPR_20  75 dplvakyRrkLs 86 
                                    dp+va++R++L 
  gi|121637255|ref|YP_977478.1| 170 DPAVAQARQQLE 181
                                    999*****9995 PP

  == domain 3  score: 61.0 bits;  conditional E-value: 3.5e-20
                         TPR_20  19 pddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkLsslLf 90 
                                     dd+da+++ A++++ ++++ +A+e+L+++++r++++e+ ++r++l+++fe+ +++dp v+++Rr+L+++L+
  gi|121637255|ref|YP_977478.1| 233 SDDIDAAFAAADVQVLNQDVSAAFERLIALVRRTSGEERTRVRTRLIELFELFDPADPEVVAGRRNLANALY 304
                                    69*********************************************************************9 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   8.1e-14   2.4e-10       2     102 ..      45     147 ..      44     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8.1e-14
                                    EEESSHHHHHHHHTT..TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                    Thioredoxin   2 vlvltkenFeeevak..ekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklf 79 
                                    v ++t++nFe+ev    ++ +v+v  ++p    C  l  +l  la + k+k  la v+vd  + +a+ ++v+++Pt++ +
  gi|121637255|ref|YP_977478.1|  45 VTEITEANFEDEVIVrsDEVPVVVLLWSPRSEVCVDLLDTLSGLAAAAKGKWSLASVNVDVAPRVAQIFGVQAVPTVVAL 124
                                    67899****998765447889*********************************************************** PP

                                    ETTEEEEEEESS-HHHHHHHHHH CS
                    Thioredoxin  80 kngkevkkyegarekeklaaflk 102
                                     +g+ +++++g +++++l ++++
  gi|121637255|ref|YP_977478.1| 125 AAGQPISSFQGLQPADQLSRWVD 147
                                    *******************9987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06     0.011       4     108 ..      62     145 ..      59     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt 83 
                                    ++ pv+v+ ++p +  C  l ++l+ l +          k +++ ++v+++ a+ +             a+ +gv+++Pt
  gi|121637255|ref|YP_977478.1|  62 DEVPVVVLLWSPRSEVCVDLLDTLSGLAAA--------AKGKWSLASVNVDVAPRV-------------AQIFGVQAVPT 120
                                    667888999999999999988888888333........566788888888888876.............699******** PP

                  Thioredoxin_2  84 iv.fldgkeivarlpGyvpaeeleal 108
                                    +v +  g+ ++   +G+ pa++l+ +
  gi|121637255|ref|YP_977478.1| 121 VVaLAAGQ-PISSFQGLQPADQLSRW 145
                                    99455565.999**********9987 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.5e-05     0.045      51      84 ..      97     130 ..      78     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                     TrbC_Ftype  51 emekasvqidPllFrqfkitaVPalvlaeedkas 84 
                                    + ++++v++ P++ + f+++aVP++v+ ++ +  
  gi|121637255|ref|YP_977478.1|  97 SLASVNVDVAPRVAQIFGVQAVPTVVALAAGQPI 130
                                    4467899999****************98876655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-05      0.08       2      31 ..     180     209 ..     179     226 .. 0.89
   2 ?   -0.2   0.1      0.49   1.5e+03      22      51 ..     233     262 ..     223     271 .. 0.77
   3 ?   -2.5   0.0       2.5   7.4e+03      17      35 ..     288     303 ..     283     304 .] 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllL 31 
                                    l++gd+ +A + ++++l+++p++ ea+++ 
  gi|121637255|ref|YP_977478.1| 180 LEDGDFVAARKSYQAILDANPGSVEAKAAI 209
                                    899**********************99855 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.49
                         TPR_19  22 pknaearllLAeallalgqldeAealLdal 51 
                                     ++ +a+ + A++++ + ++ +A + L al
  gi|121637255|ref|YP_977478.1| 233 SDDIDAAFAAADVQVLNQDVSAAFERLIAL 262
                                    678888889999999999998887766665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.5
                         TPR_19  17 alqedpknaearllLAeal 35 
                                    a   dp+  + r +LA+al
  gi|121637255|ref|YP_977478.1| 288 A---DPEVVAGRRNLANAL 303
                                    3...666666677888887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.5   1.3e+04      13      29 ..      24      40 ..      16      42 .. 0.69
   2 ?   13.6   0.2   3.1e-05     0.094       6      38 ..     174     206 ..     169     213 .. 0.90
   3 ?   -1.6   0.0       2.4   7.2e+03      21      35 ..     212     226 ..     207     229 .. 0.78
   4 ?    0.8   0.3       0.4   1.2e+03       3      43 ..     238     280 ..     236     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.5
                         TPR_14 13 alGdpdeAiallrrala 29
                                   ++++ ++A + ++ral+
  gi|121637255|ref|YP_977478.1| 24 RAQQNAAASTDADRALS 40
                                   66777777777777776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.1e-05
                         TPR_14   6 alaeallalGdpdeAiallrralalaPddaeaw 38 
                                    a a+  l+ Gd+ +A++ ++++l+++P++ ea 
  gi|121637255|ref|YP_977478.1| 174 AQARQQLEDGDFVAARKSYQAILDANPGSVEAK 206
                                    67899999*********************9986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                         TPR_14  21 iallrralalaPdda 35 
                                    i+ l ra a+ Pd  
  gi|121637255|ref|YP_977478.1| 212 IEFLIRATAQRPDAV 226
                                    567789999999865 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.4
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPdda..eawlllaq 43 
                                    a  a+a++   ++d  +A + l +++++  +++  +++++l +
  gi|121637255|ref|YP_977478.1| 238 AAFAAADVQVLNQDVSAAFERLIALVRRTSGEErtRVRTRLIE 280
                                    6678888888899999999988888887544431156677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2425.26
//
Query:       gi|121637256|ref|YP_977479.1|  [L=603]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-35  121.4  18.5    2.2e-35  120.8  18.5    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8  18.5   1.2e-39   2.2e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.2e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe+l +aa+dla+igs+l aanaaa +ptt++laa+aDeVSaaiA+lf+ah+q+yqa+saq++afh+qfvq+++a
  gi|121637256|ref|YP_977479.1|  1 MSFVIAAPETLVRAASDLANIGSTLGAANAAALGPTTELLAAGADEVSAAIASLFAAHGQAYQAVSAQMSAFHAQFVQTFTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEaa
  gi|121637256|ref|YP_977479.1| 83 GAGAYASAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3820.52
//
Query:       gi|121637257|ref|YP_977480.1|  [L=731]
Description: glycogen branching protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-25   89.5   0.0    2.5e-22   79.0   0.0    2.6  2  CBM_48           Carbohydrate-binding module 48 (Isoamylase N
    6.3e-22   77.9   0.0    1.2e-21   77.0   0.0    1.5  1  Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
    6.3e-16   58.9   0.0    4.2e-10   39.7   0.0    2.4  2  Alpha-amylase    Alpha amylase, catalytic domain
    0.00027   19.3   0.1     0.0013   17.1   0.0    1.8  2  Glyco_hydro_70   Glycosyl hydrolase family 70


Domain annotation for each model (and alignments):
>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00086       3.8       2      83 ..      34     104 ..      33     105 .. 0.74
   2 !   79.0   0.0   5.7e-26   2.5e-22       2      84 .]     130     216 ..     129     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00086
                                    SEEEEESSCEEEEEEEE-TTSSEE.EEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETT.S.CEEE CS
                         CBM_48   2 lGahvsedekgvnfrvwapnAekV.slvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgps.g.ekkl 78 
                                    lGah  +d  ++++r + p+A +V +lv+ +      ++ l+ + ++g + + lp  +   + ++ yr+++++ g e + 
  gi|121637257|ref|YP_977480.1|  34 LGAHEYGD--HTVIRAFRPHAVEVvALVGKD------RFSLQ-HLDSGLFAVALP--FV--D-LIDYRLQVTYeGcEPHT 99 
                                    8****999..***********8871444433......35688.588999999999..44..2.67777777775567788 PP

                                    E--TT CS
                         CBM_48  79 llDPy 83 
                                    ++D+y
  gi|121637257|ref|YP_977480.1| 100 VADAY 104
                                    88888 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 5.7e-26
                                    SEEEEESS.....C.EEEEEEEE-TTSSEEEEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETTSC CS
                         CBM_48   2 lGahvsed.....e.kgvnfrvwapnAekVslvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgpsge 75 
                                    lGah+++        +gv f+vwapnA++Vsl++ fn+w+++e p++    +gvWelf+p d+p+++ +Yk+rv+g +g 
  gi|121637257|ref|YP_977480.1| 130 LGAHPRSFttadgVvSGVSFAVWAPNAKGVSLIGEFNGWNGHEAPMRVLGPSGVWELFWP-DFPCDG-LYKFRVHGADGV 207
                                    8999987788887579********************************9***********.*****8.************ PP

                                    EEEE--TT- CS
                         CBM_48  76 kklllDPya 84 
                                      +++DP+a
  gi|121637257|ref|YP_977480.1| 208 VTDRADPFA 216
                                    *******98 PP

>> Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   2.6e-25   1.2e-21       1      95 [.     633     730 ..     633     731 .] 0.96

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.6e-25
                                    EEEEEETTSSEEEEEECT.TT.EEEEEEE-SSSSEEECEEESSSSSEEEEETTCTTSGCCTTT-SSTSS-EEEECT..TC CS
                Alpha-amylase_C   1 wvsakdeenkviaFeRgd.ge.kllvvfNfhpsnsrqdyrvgvpaagkyrdvlntdaeeyggsglgntgkvvtvdd..dg 76 
                                    w++a+d+ n+v++F+R + ++  l +vfNf + + + dyr+g+p ag++r+vlntda+ y gsg+gn g v ++dd  +g
  gi|121637257|ref|YP_977480.1| 633 WIDANDSANNVLSFMRYGsDGsVLACVFNFAG-AEHRDYRLGLPRAGRWREVLNTDATIYHGSGIGNLGGVDATDDpwHG 711
                                    ****************8876668*********.999******************************************** PP

                                    BSEEEEEEESTTEEEEEEE CS
                Alpha-amylase_C  77 ransltltlpprsalvlkv 95 
                                    r++s+ l lpp sal+l++
  gi|121637257|ref|YP_977480.1| 712 RPASAVLVLPPTSALWLTP 730
                                    ***************9975 PP

>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   9.3e-14   4.2e-10      11      79 ..     280     349 ..     276     378 .. 0.91
   2 !   16.9   0.0   8.4e-07    0.0038     146     217 ..     383     468 ..     375     584 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.3e-14
                                    CCCCCCT-SCEEE-B-CE-S.-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--T CS
                  Alpha-amylase  11 dYlkeLGvtaiwlsPifksp.qadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsd 79 
                                    dY+ + G+t + l P+ + p +   gY ++ y++ + +fGt +d+ +L++++h+ gi vi+D V+ H  +
  gi|121637257|ref|YP_977480.1| 280 DYIVDQGFTHVELLPVAEHPfAGSWGYQVTSYYAPTSRFGTPDDFRALVDALHQAGIGVIVDWVPAHFPK 349
                                    8*****************9944689******************************************755 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.4e-07
                                    TTTCCCCCCCCCCCCCCCTTT.-SEEEETTCCCTTTCCCC.............HCCHCCHHHHHHHHHHHTC.CGTT-EE CS
                  Alpha-amylase 146 teneevrkelkdvvkfwlekg.idGfRlDvvkhvskveal.............esngeflheftqalnetva.srkevmt 210
                                      ++evr+ l   + +wl+++ idG+R+D+v  +   +               ++n e   +f q++n+t++ +   ++t
  gi|121637257|ref|YP_977480.1| 383 FGRPEVRNFLVANALYWLQEFhIDGLRVDAVASMLYLDYSrpeggwtpnvhggRENLE-AVQFLQEMNATAHkVAPGIVT 461
                                    568999999999999****************9999866669999****9998655554.458999999998878889999 PP

                                    EEE-TT- CS
                  Alpha-amylase 211 vgEvssd 217
                                    ++E s +
  gi|121637257|ref|YP_977480.1| 462 IAEESTS 468
                                    9987665 PP

>> Glyco_hydro_70  Glycosyl hydrolase family 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.8e-07    0.0013     633     664 ..     314     345 ..     302     351 .. 0.88
   2 ?   -0.6   0.0     0.061   2.7e+02     151     185 ..     370     414 ..     364     417 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-07
                 Glyco_hydro_70 633 kpnkyGtaddlvdaikalhksGikviadwvpd 664
                                     ++++Gt dd++  + alh+ Gi vi dwvp 
  gi|121637257|ref|YP_977480.1| 314 PTSRFGTPDDFRALVDALHQAGIGVIVDWVPA 345
                                    5679***************************6 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.061
                 Glyco_hydro_70 151 qaeqlnwlyylmnfGs......ivand....adanfdgirvdavd 185
                                    + eql+w  y+++fG       +van      +  +dg+rvdav 
  gi|121637257|ref|YP_977480.1| 370 RGEQLDWGTYVFDFGRpevrnfLVANAlywlQEFHIDGLRVDAVA 414
                                    579***********9644444456775333357788999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 5055.32
//
Query:       gi|121637258|ref|YP_977481.1|  [L=701]
Description: glucanase glgE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-56  191.5   0.0    2.3e-56  190.9   0.0    1.2  1  DUF3416        Domain of unknown function (DUF3416)
    2.2e-08   34.1   0.0    1.3e-06   28.3   0.0    2.2  2  Alpha-amylase  Alpha amylase, catalytic domain
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.044   13.9   0.0    1.3  1  GHL6           Hypothetical glycosyl hydrolase 6


Domain annotation for each model (and alignments):
>> DUF3416  Domain of unknown function (DUF3416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   0.0   3.8e-60   2.3e-56       1     179 []      16     226 ..      16     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 3.8e-60
                        DUF3416   1 griaIedvsPevdgGrfpaKavvGetvpVeAdvfrdGhdalaAtlvlr.......................ragekewqe 57 
                                    gr++I+dv+P+v++G +paKavvGe+vpV+A+v+r+Gh+a+aAtlv+r                        +++ +   
  gi|121637258|ref|YP_977481.1|  16 GRVEIDDVAPVVSCGVYPAKAVVGEVVPVSAAVWREGHEAVAATLVVRylgvryphltdrprarvlptpsePQQRVKPLL 95 
                                    69**********************************************99999999999998888888877444577789 PP

                        DUF3416  58 vpMt.pggndrweasftpdelGryeftveAWvDpfatWrhdlekkveagqdvele...leeGarlleraaeraea..... 128
                                    +pMt  +++ +++++ftpd++G ++f+v++W Dp++tWrh+l +k++agq  ++    l+ Ga lleraa+   +     
  gi|121637258|ref|YP_977481.1|  96 IPMTsGQEPFVFHGQFTPDRVGLWTFRVDGWGDPIHTWRHGLIAKLDAGQGETELsndLLVGAVLLERAATG--Vprglr 173
                                    ****855699***************************************876655555************55..346999 PP

                        DUF3416 129 aalraaaaalrdd..peerlaaalseevaallaryplrelatrseklpveVdR 179
                                    ++l aaaaalr++  p +r a+al++e+++lla yplr+l+tr+e++ v+VdR
  gi|121637258|ref|YP_977481.1| 174 DPLLAAAAALRTPgdPVTRTALALTPEIEELLADYPLRDLVTRGEQFGVWVDR 226
                                    99********887889************************************9 PP

>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.1e-10   1.3e-06      10      92 ..     263     364 ..     254     389 .. 0.89
   2 !    3.5   0.1    0.0072        43     150     174 ..     395     419 ..     379     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-10
                                    CCCCCCCT-SCEEE-B-CE.....................-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EE CS
                  Alpha-amylase  10 LdYlkeLGvtaiwlsPifk.....................spqadhgYdiadytkidpefGtnedlkeLiskahekgikv 68 
                                    L+ + ++G+++++l Pi                       sp    g d     +++p  Gt +d++  +s+a+++g+ v
  gi|121637258|ref|YP_977481.1| 263 LPRIAGMGFDVVYLPPIHPigkvhrkgrnnsptaaptdvgSP-WAIGSDEGGHDTVHPSLGTIDDFDDFVSAARDLGMEV 341
                                    66799*************99**************99999999.899********************************** PP

                                    EEEE--SC--TTSCCCHCCHHSTT CS
                  Alpha-amylase  69 ilDlVvNHtsdehewfkeslkkkg 92 
                                     lDl    ++ +h w++e+++  +
  gi|121637258|ref|YP_977481.1| 342 ALDLALQ-CAPDHPWAREHRQWFT 364
                                    ****995.9******999988555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0072
                                    CCCCCCCCCCCCCCTTT-SEEEETT CS
                  Alpha-amylase 150 evrkelkdvvkfwlekgidGfRlDv 174
                                     +  e+ +vv++w+++g+  fR+D 
  gi|121637258|ref|YP_977481.1| 395 GLYDEVLRVVQHWVNHGVKFFRVDN 419
                                    37788999***************95 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.4e-06     0.044      38     103 ..     316     383 ..     302     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.4e-06
                           GHL6  38 tehpklk.rdllkelvkachregikvvvrvdfska.deriyeqhpeWaavkenGeviiiegervgepg 103
                                    t hp l   d   + v a+++ g+ v   +  ++a d+  +++h +W+   ++G + + e+ + ++++
  gi|121637258|ref|YP_977481.1| 316 TVHPSLGtIDDFDDFVSAARDLGMEVALDLALQCApDHPWAREHRQWFTELPDGTIAYAENPPKKYQD 383
                                    5688885346669********************9868899***************9877776666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4675.45
//
Query:       gi|121637259|ref|YP_977482.1|  [L=863]
Description: glycogen phosphorylase glgP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-36  122.5   0.0    1.9e-35  121.6   0.0    1.5  1  DUF3417        Protein of unknown function (DUF3417)
    4.6e-28   98.0   0.0    2.2e-19   69.2   0.0    3.3  2  Phosphorylase  Carbohydrate phosphorylase


Domain annotation for each model (and alignments):
>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   0.0   2.2e-39   1.9e-35       1     109 []      13     126 ..      13     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 2.2e-39
                        DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksldpelweevghnPvklLeevsqerleelaedeeflarleavveefeeylee 80 
                                    lpe+L++L++L++nl+wsw++++++LF+++dp+lwe++gh+Pv+lL++v+++rl+ela d+efl  l+++++++++yl++
  gi|121637259|ref|YP_977482.1|  13 LPERLAALDQLSTNLRWSWDKPTQDLFAAIDPALWEQCGHDPVALLGAVNPARLDELALDAEFLGALDELAADLNDYLSR 92 
                                    8******************************************************************************* PP

                        DUF3417  81 ktwfqkka.....eeekkeaiAYFsaEfGlhesL 109
                                    + w+q+++     +++ ++ iAYFs EfG++e+L
  gi|121637259|ref|YP_977482.1|  93 PLWYQEQQdagvaAQALPTGIAYFSLEFGVAEVL 126
                                    *******99999999999*************987 PP

>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.6e-09   1.4e-05      23      67 ..     131     176 ..     127     188 .. 0.95
   2 !   69.2   0.0   2.5e-23   2.2e-19     162     577 ..     235     632 ..     203     636 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-09
                                    SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEE CS
                  Phosphorylase  23 GGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqvee 67 
                                    GGLG LA  +l s++ l++p + +g+ Y+ G F+Q++  dg+q+e+
  gi|121637259|ref|YP_977482.1| 131 GGLGILAGDHLKSASDLGVPLIAVGLYYRSGYFRQSLtADGWQHET 176
                                    9************************************88*****97 PP

  == domain 2  score: 69.2 bits;  conditional E-value: 2.5e-23
                                    HHHHHGGGTBSS-SSSSCCHCHHHHHHHHHHHHHHHHHHHHHHHTCTTHGGGHHHHEEEEEESSTTTTHHHHHHHHHHHC CS
                  Phosphorylase 162 kneaeniskvLYPndsteegkeLrLkQqYflvsaslqdilrrfkkkkkdleelpekvaiqlnDtHPalaipelmriLvde 241
                                    +++ +n+++ LY  d+     e r+kQ+ +    +++ i r ++     +e+l+   ++++n+ H  +   e +r Lv++
  gi|121637259|ref|YP_977482.1| 235 EHDLRNVTDRLYGGDQ-----EHRIKQEILAGIGGVRAI-RAYT----AVEKLTPPEVFHMNEGHAGFLGIERIRELVTD 304
                                    5556677777777665.....458999988777777654.5554....7899**************************** PP

                                    C---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHHHHHHHHHHHHHSTT.-HHHHHHHSSEETSC CS
                  Phosphorylase 242 eglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieeinerfleevekklpe.deeklerlsiieeek 320
                                     gl++d+a++++++ + +t ht +p  ++++p+e++++ +           ++  +  ++ lp+  ++++  l   ++  
  gi|121637259|ref|YP_977482.1| 305 AGLDFDTALTVVRSSTVFTTHTPVPAGIDRFPLEMVQRYVN----------DQRGDGRSRLLPGlPADRIVALGAEDDPA 374
                                    ************************************99865..........44444444444553345777777777889 PP

                                    EEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGG..EEE----B-CHHHCCCTSHHHHHHHHHHCSSGGCCSG CS
                  Phosphorylase 321 kvrmanlaivgshsvngvaalhsellkkevlkdfyelypek..fnnktnGitprrwlllanpelaelitekigeewvkdl 398
                                    k +ma++ +  +++ ngv+ lh ++ +    + ++ + p+   +  +tnG+    w   a p+  +l +e  g++ +++ 
  gi|121637259|ref|YP_977482.1| 375 KFNMAHMGLRLAQRANGVSLLHGRVSRAMFNELWAGFDPDEvpIGSVTNGVHAPTW---AAPQWLQLGRELAGSDSLREP 451
                                    **********************997766555557778888733579*****99999...557777777777777777777 PP

                                    GGGGGGGGGCCSHH..HHHHHHHHH.HHHHHHHHH.HHHH.HHSS-.......--TTSEEEEEES-SCCCCTHHHHHHHH CS
                  Phosphorylase 399 eeLkkLekladdke..fleelaeik.qenKerlae.like.kegve.......vdpeslfdvqvkRlheYkRqlLnvLhi 466
                                       ++L+++   +   ++++l+++  ++ ++rl + ++++  ++ e        dp+ l     +R+  YkR +L +   
  gi|121637259|ref|YP_977482.1| 452 VVWQRLHQVDPAHLwwIRSQLRSMLvEDVRARLRQsWLERgATDAElgwiataFDPNVLTVGFARRVPTYKRLTLMLRD- 530
                                    6666666654333211334444332123344443312322222222112222277777777778********9996444. PP

                                    HHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEE CS
                  Phosphorylase 467 itlYneikenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndpevkdklkvvflenynvslaekiipaadls 546
                                      + +++  +   +  p  +i++gk+ p+    k++i+ + + a+     p+ ++  +++fl+ny++s+a  ++ ++d+ 
  gi|121637259|ref|YP_977482.1| 531 PGRLEQLLLD---EQRPIQLIVAGKSHPADDGGKALIQQVVRFADR----PQFRH--RIAFLPNYDMSMARLLYWGCDVW 601
                                    4444444444...479*******************99888777754....55555..689******************** PP

                                    EE---TTTSSS-SHHHHHHHTT-EEEEESST CS
                  Phosphorylase 547 eqistagkeASGTgnmkfmlnGaltigtlDG 577
                                     +  +   eA GT+ mk +lnG+l ++  DG
  gi|121637259|ref|YP_977482.1| 602 LNNPLRPLEACGTSGMKSALNGGLNLSIRDG 632
                                    ***************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (863 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 5254.20
//
Query:       gi|121637260|ref|YP_977483.1|  [L=664]
Description: atp-dependent helicase dinG-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-27   95.9   0.0    4.3e-27   95.4   0.0    1.2  1  Helicase_C_2  Helicase C-terminal domain
    2.2e-09   37.3   2.4    0.00011   22.0   0.0    2.6  3  DEAD          DEAD/DEAH box helicase
    0.00046   20.2   0.0       0.22   11.5   0.0    2.2  2  ResIII        Type III restriction enzyme, res subunit
      0.003   17.2   0.0     0.0058   16.3   0.0    1.4  1  DEAD_2        DEAD_2
  ------ inclusion threshold ------
      0.031   14.0   8.4        2.3    7.9   0.1    4.2  4  AAA_30        AAA domain
       0.11   12.8   2.1       0.63   10.5   0.2    3.4  3  HEAT          HEAT repeat
       0.19   11.0   0.0       0.33   10.2   0.0    1.3  1  DUF3638       Protein of unknown function (DUF3638)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.7e-30   4.3e-27       2     170 ..     480     639 ..     479     640 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.7e-30
                   Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfs 81 
                                    +el+++  g++l +f+S++  + ++e+++e+l   + +++++ ++ s+++++e++++       l++++  +l+ G+d++
  gi|121637260|ref|YP_977483.1| 480 AELITAAGGRTLGLFSSMRAARAATEAMRERL---STPVLCQ-GDDSTSTLVEKFTA--DAATSLFGTL--SLWQGVDVP 551
                                    67899999***********************9...589****.**************..9*********..********* PP

                   Helicase_C_2  82 ddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeir 161
                                    + +l++v+i ++Pfp p+dp ++a+++ ++++g+ n+++++   +a   + Q+ GRl+R  +D+g++ +lD+R+a+++++
  gi|121637260|ref|YP_977483.1| 552 GPSLSLVLIDRIPFPRPDDPLLSARQRAVAARGG-NGFMTVAASHAALLLAQGSGRLLRRVTDRGVVAVLDSRMATARYG 630
                                    **********************************.********************************************* PP

                   Helicase_C_2 162 eklpkwlre 170
                                    e l  +l++
  gi|121637260|ref|YP_977483.1| 631 EFLRASLPP 639
                                    *99998876 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.2e-08   0.00011       5      65 ..      33      89 ..      26     103 .. 0.80
   2 !   14.8   0.0   7.2e-06     0.018      97     171 ..     214     296 ..     191     301 .. 0.64
   3 ?   -3.9   0.2       3.8   9.7e+03     160     170 ..     409     419 ..     393     420 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.2e-08
                                   HHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  5 aeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtln 65
                                   a++ +++ +g++++v+a TG+GK+la+l+p++ +       +   +++ + t +L +q ++
  gi|121637260|ref|YP_977483.1| 33 AAVAHAFETGEHLVVQAGTGTGKSLAYLVPAIIRA----LCDDAPVVVSTATIALQRQLVD 89
                                   44455556999*********************655....4566678888888888888775 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.2e-06
                                    T.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS.....HHHCTTST.TT.SEEEEEESS CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxx.xx.xxxxxxxxx RF
                           DEAD  97 g.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql.....pqitcdgk.lq.rqvivlSAT 168
                                    g +d+vv+++  l+     ++  l + r+lV+DEa++l d   s    ++ +++     ++it     +  +++ + SAT
  gi|121637260|ref|YP_977483.1| 214 GlADVVVTNHALLAIDAVAESAVLPEHRLLVVDEAHELADRVTSVAAAELTSATlgmaaRRITRLVDpKVtQRLQAASAT 293
                                    45889999998887644456678*****************9555554443332200000333333332221347777777 PP

                                    BSH CS
                                    xxx RF
                           DEAD 169 lpk 171
                                    +++
  gi|121637260|ref|YP_977483.1| 294 FSS 296
                                    765 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.8
                                    SEEEEEESSBS CS
                                    xxxxxxxxxxx RF
                           DEAD 160 rqvivlSATlp 170
                                     ++++ SATl+
  gi|121637260|ref|YP_977483.1| 409 ATTVLTSATLT 419
                                    34899999985 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   8.5e-05      0.22       5      71 ..      25      88 ..      23     135 .. 0.81
   2 !    6.5   0.0     0.003       7.7     124     147 ..     231     254 ..     196     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                                   -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH..HHHHHHH-S.....-EEEEESSHHHHHHHH CS
                         ResIII  5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva..aklierllkkgkeekflflvprkslleqtl 71
                                   r  Q+e+  +++ ++  +  +++++++ TGtGK+l +   ++i++l   +    +++   +++l  q+ 
  gi|121637260|ref|YP_977483.1| 25 RRGQQEMAAAVAHAF--ETGEHLVVQAGTGTGKSLAYlvPAIIRALCDDA---PVVVSTATIALQRQLV 88
                                   789*********999..5999*************9884345666666643...4666666666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
                                    ...HHHTTT-SEEEEETGGGTTS. CS
                         ResIII 124 eseellrdrfdviiiDEaHrlgak 147
                                      e++   ++ ++++DEaH l++ 
  gi|121637260|ref|YP_977483.1| 231 VAESAVLPEHRLLVVDEAHELADR 254
                                    66777777889**********995 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.3e-06    0.0058     114     176 .]     208     268 ..     194     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                                    HHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEECTCCCHHHHHHHCC-EEEECHHH CS
                         DEAD_2 114 lsrelledadiiilpYqyLldekireslkgislknsivilDEAhNiedvceeaasveiseesl 176
                                     +r ++  ad+++  +++L    ++es+  +  +   +++DEAh + d ++++a +e+++ +l
  gi|121637260|ref|YP_977483.1| 208 RARGAAGLADVVVTNHALLAIDAVAESA--VLPEHRLLVVDEAHELADRVTSVAAAELTSATL 268
                                    46778889********999999999998..5699************************98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00089       2.3       7      34 ..      32      58 ..      25      92 .. 0.74
   2 ?    1.5   0.3      0.08     2e+02      73     103 ..     222     254 ..     205     268 .. 0.65
   3 ?   -0.3   0.3       0.3   7.7e+02      56      81 ..     257     283 ..     251     377 .. 0.67
   4 ?    6.3   0.0    0.0027         7      25      66 ..     466     507 ..     463     561 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00089
                         AAA_30  7 aaavealltsgdrvavltGpAGtGKtta 34
                                   aaav+++ ++g+   v++++ GtGK+ a
  gi|121637260|ref|YP_977483.1| 32 AAAVAHAFETGE-HLVVQAGTGTGKSLA 58
                                   688999999997.999*********975 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.08
                         AAA_30  73 iakllkrlk..grarlepgtllivDEagmvdtk 103
                                     + ll   +  + a l +++ll+vDEa  ++ +
  gi|121637260|ref|YP_977483.1| 222 NHALLAIDAvaESAVLPEHRLLVVDEAHELADR 254
                                    4444433337544555666*******9776544 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.3
                         AAA_30  56 gkaAkvLa.eelgieastiakllkrlk 81 
                                    + aA++L+ + lg++a++i +l++   
  gi|121637260|ref|YP_977483.1| 257 SVAAAELTsATLGMAARRITRLVDPKV 283
                                    455555542567788888888875544 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0027
                         AAA_30  25 GpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66 
                                    G+ G+G    l++++e+++aaggr +gl ++ +aA++ +e++
  gi|121637260|ref|YP_977483.1| 466 GRDGSGSAEQLTEIAELITAAGGRTLGLFSSMRAARAATEAM 507
                                    7789999**************************999877654 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00025      0.63       1      25 [.      60      84 ..      60      85 .. 0.94
   2 ?   -2.0   0.0       2.5   6.4e+03       9      23 ..     278     292 ..     275     292 .. 0.81
   3 ?   -2.3   0.0       3.2   8.2e+03      13      28 ..     339     354 ..     335     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                                   HHHHHHHHHT-SSHHHHHHHHHHHH CS
                           HEAT  1 llPlllkllsDpspeVReaAakaLg 25
                                   l+P+++++l+D++p V ++A  aL 
  gi|121637260|ref|YP_977483.1| 60 LVPAIIRALCDDAPVVVSTATIALQ 84
                                   79******************99996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                                    HT-SSHHHHHHHHHH CS
                           HEAT   9 lsDpspeVReaAaka 23 
                                    l Dp   +R  Aa a
  gi|121637260|ref|YP_977483.1| 278 LVDPKVTQRLQAASA 292
                                    67999999***9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.2
                                    SHHHHHHHHHHHHHHH CS
                           HEAT  13 speVReaAakaLgala 28 
                                     ++VR+ A   L++++
  gi|121637260|ref|YP_977483.1| 339 TASVRAEAGAVLTEIS 354
                                    578***9999999886 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013      0.33      24      85 ..      25      88 ..       3     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                        DUF3638 24 ReeQaevAkemisp.ssgensvlQLnmGeGKs.svIvPivaaaladgkkLvrvivlkpllkqma 85
                                   R+ Q+e+A+++ ++ ++ge  v+Q   G GKs + +vP ++ al d++ +v  + + +l +q +
  gi|121637260|ref|YP_977483.1| 25 RRGQQEMAAAVAHAfETGEHLVVQAGTGTGKSlAYLVPAIIRALCDDAPVVVSTATIALQRQLV 88
                                   677888888887652689999***********4569**********997766555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4481.09
//
Query:       gi|121637261|ref|YP_977484.1|  [L=448]
Description: nicotinate phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-26   93.4   0.0    2.1e-26   92.8   0.0    1.3  1  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N
    2.3e-06   27.5   0.1    3.7e-06   26.8   0.1    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    0.00024   20.8   0.1    0.00062   19.4   0.1    1.6  1  NAPRTase    Nicotinate phosphoribosyltransferase (NAPRTase) f


Domain annotation for each model (and alignments):
>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.5e-30   2.1e-26       1     125 []      22     144 ..      22     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.5e-30
                     NAPRTase_N   1 LdtDlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieylenlrfteeeieyLkrklpyfkedfleyL 79 
                                    L+tD Y+ltm +a ++ g  +++++fe+f R+ p +++y++vag  + +e l ++rf+ + +e L+   ++++++ + yL
  gi|121637261|ref|YP_977484.1|  22 LLTDKYELTMLAAALRDGSaNRPTTFEVFARRLPTGRRYGVVAGTGRLLEALPQFRFDADACELLA---QFLDPATVRYL 98 
                                    89***************************************************************9...9********** PP

                     NAPRTase_N  80 rtfrfkpsevaveeeevvfpgepeirveGpwieaillEtplLaivn 125
                                    r+frf++++    e+e  fpg+p ++v+G  +e+ llEt +L+i n
  gi|121637261|ref|YP_977484.1|  99 REFRFRGDIDGYAEGELYFPGSPVLSVRGSFAECVLLETLVLSIFN 144
                                    *******************************************987 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   6.1e-10   3.7e-06       1     156 [.     149     325 ..     149     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.1e-10
                                    HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSS........ CS
                      QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaags........ 65 
                                    iA+++armv+aa +     ++ R+t+   ++++ +A++i+G +       ++r+g+    +  ++  ++  +        
  gi|121637261|ref|YP_977484.1| 149 IASAAARMVSAAGGRPLIEMGSRRTHERAAVAAARAAYIAGFAassnlaaQRRYGVPAHGTAAHAFTMLHAQhggptela 228
                                    8****************************************999999999999999999999988665543333444332 PP

                                    HHHHHHHHHHHHTTTSEEEEEESSHHH..HHHHHHHT-SE..EEEES--HHHHHH.HHHHHHHH.STTSEEEEESS--TT CS
                      QRPTase_C  66 iveavksvreavdkevkieveveslee..leevleaeadi..imLDnfsveelkk.aveelkek.nkrvlievSGgvtle 139
                                     + a ++  ea++    + v+++ +    +++v++a+a++  i++D  +   l++ a e+l++  + r +i vSG + + 
  gi|121637261|ref|YP_977484.1| 229 ERAAFRAQVEALGPGTTLLVDTYDVTTgvANAVAAAGAELgaIRIDSGELGVLARqAREQLDRLgATRTRIVVSGDLDEF 308
                                    223333333444444449999986543225666666666444******99776550555565551556************ PP

                                    THHHHHCTT-SEEEECH CS
                      QRPTase_C 140 nveeyaksgvdvisvga 156
                                    ++++++ + vd ++vg+
  gi|121637261|ref|YP_977484.1| 309 SIAALRGEPVDSYGVGT 325
                                    ***************97 PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1     1e-07   0.00062       4     221 ..     166     361 ..     164     376 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1e-07
                                    EE-TSTTSSSHHHHHHHHHHHHHHHTTTEEEESBHHHHHHHT--B--HHHHHHHHHHHHHHCHHHHHCCHHHHHHHHHHH CS
                       NAPRTase   4 hDFGtRrrsslesqeivvkalkkahlvnflGtdnvlaaakysikaaetsahealgkeqelsafrnnlkqfqkdaldlwva 83 
                                     ++G+Rr +++ + +   +    a    f  ++n++a ++y+++a +t ah + + +++        + ++++a  + v+
  gi|121637261|ref|YP_977484.1| 166 IEMGSRRTHERAAVAAARA----AYIAGFAASSNLAAQRRYGVPAHGTAAHAFTMLHAQHGG---PTELAERAAFRAQVE 238
                                    689******9999999999....99********************************99998...888888888888887 PP

                                    HHC.CHIIEEECHCCTHHHHHCCS-CC.HHHSEEEEE-SS-HHHHHHHHHHHHHCTCTTTCCCSEEEEESS-SHHHHHHH CS
                       NAPRTase  84 iek.gnlgiaLtdlvltdaflkdfrle.akaylgvRpDSGdpvevieklaahygstlnskgytkrlifsDgldvekiiei 161
                                    + + g  +   t  v+t  ++  + +   +    +R DSG+   +  ++ +   ++     +  r++ s  ld  +i ++
  gi|121637261|ref|YP_977484.1| 239 ALGpGTTLLVDTYDVTTGVAN--AVAAaGAELGAIRIDSGELGVLARQAREQLDRL---GATRTRIVVSGDLDEFSIAAL 313
                                    776333333333334444444..444446677889999999988888888888888...344566666777998888888 PP

                                    HHHHHHTTCEEEEEESHHHHSSECTTCTTTCCEEEEEEEEEEEEEETTEETTBGG..SSCCG CS
                       NAPRTase 162 lealkkkgfniaFGiGtnltqdlnrdtlefavkasalniviklvevnkdpvakis..drskk 221
                                      +  +     ++G+Gt+l+                 n+v klvev + pv k s  ++s  
  gi|121637261|ref|YP_977484.1| 314 RGEPVD-----SYGVGTSLVTGSGA---------PTANMVYKLVEVDGVPVQKRSsyKESPG 361
                                    777666.....89999999887777.........5566777777777777777665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2387.77
//
Query:       gi|121637262|ref|YP_977485.1|  [L=101]
Description: ATP-dependent Clp protease adaptor protein ClpS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-21   74.5   0.0    5.7e-21   74.1   0.0    1.1  1  ClpS      ATP-dependent Clp protease adaptor protein ClpS


Domain annotation for each model (and alignments):
>> ClpS  ATP-dependent Clp protease adaptor protein ClpS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   3.2e-25   5.7e-21       3      79 ..      25      95 ..      24      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 3.2e-25
                                   X--EEEEEES-S-S-HHHHHHHHHHHSSS-HHHHHHHHHHHHHHSEEEEEEE-HHHHHHHHHHHHH......TT--E CS
                           ClpS  3 pkqYkvvLlNDdvttmefVvevLqkvfgkskeeAteimlevhreGravvgvgtreiaetkveqverlarreghpLkv 79
                                   ++ +++++++D+v+ m++V++v+qk+fg+s+ +At++ml+vh+eG+avv  g+re++e +v+++++       +L++
  gi|121637262|ref|YP_977485.1| 25 DRAWVTIVWDDPVNLMSYVTYVFQKLFGYSEPHATKLMLQVHNEGKAVVSAGSRESMEVDVSKLHA------AGLWA 95
                                   678**************************************************************9......66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 554.96
//
Query:       gi|121637263|ref|YP_977486.1|  [L=218]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-59  198.9   0.2    6.7e-59  198.7   0.2    1.0  1  DUF2017   Domain of unknown function (DUF2017)


Domain annotation for each model (and alignments):
>> DUF2017  Domain of unknown function (DUF2017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.7   0.2   3.7e-63   6.7e-59       2     177 .]      32     215 ..      31     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 3.7e-63
                        DUF2017   2 rrggrivarldeaEaelLrslvaqvlelLeeraasapeeDeLaaltglrtgpaepPeDpaLaRLLPdayred........ 73 
                                    r+g r++++l+++Ea+lL++l+  +++lL++r++s+p +DeL+++tg++tg+a++P Dp+L+RLLPd+yr+d        
  gi|121637263|ref|YP_977486.1|  32 RDGPRFRSSLAPHEAALLKNLAGAMIGLLDDRDSSSP-SDELEEITGIKTGHAQRPGDPTLRRLLPDFYRPDdlddddpt 110
                                    67899********************************.*******************************999999999** PP

                        DUF2017  74 .....eeaaaefRrlteedlraaKraaarvvldtleedggkeveLdeeeaqawlaaLnDvRlalgtrlgieeeedaelee 148
                                         e+ +a++R+l+e+++++aKr aa+++ldt++++gg+ +eL+e +a+aw+aa+nD+Rlalg++l+i    +   e+
  gi|121637263|ref|YP_977486.1| 111 avdgsESFNAALRSLHEPEIIDAKRVAAQQLLDTVPDNGGR-LELTESDANAWIAAVNDLRLALGVMLEIGPRGP---ER 186
                                    ****9**********************************99.*********************************...9* PP

                        DUF2017 149 lpdddpraaavavyewLtvlqesLvealm 177
                                    lp ++p aa+++vy+wLtvlqe+Lv +lm
  gi|121637263|ref|YP_977486.1| 187 LPGNHPLAAHFNVYQWLTVLQEYLVLVLM 215
                                    *************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1242.31
//
Query:       gi|121637264|ref|YP_977487.1|  [L=344]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-72  243.7  10.8    3.7e-72  243.4  10.8    1.0  1  Peptidase_S58   Peptidase family S58


Domain annotation for each model (and alignments):
>> Peptidase_S58  Peptidase family S58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4  10.8   2.1e-76   3.7e-72       1     293 [.       2     330 ..       2     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 2.1e-76
                  Peptidase_S58   1 naitDVaGvrVghatlae.....ge.vrtGvTvilprgnlfkekvvAavdvlnGfgkttgtdqleelglle..tpivLtn 72 
                                    n+itDV G+rVgh ++ +     g+ +++GvTv+lp+     + +v+avd+++G+++t++td+l+++++++  ++++L++
  gi|121637264|ref|YP_977487.1|   2 NSITDVGGIRVGHYQRLDpdaslGAgWACGVTVVLPP----PG-TVGAVDCRGGAPGTRETDLLDPANSVRfvDALLLAG 76 
                                    9**************97789999555**********9....55.9*********************************** PP

                  Peptidase_S58  73 tlsvg.aaadgvvewlleeeee.eearsvvpvVaetnDgvlndiragavkeehvaeala....aAaaa...pvaeGnvGa 143
                                    ++++g aaadgv++wl+e+++  ++++ vvp+V++   +v++d+  g+   ++ ++++a    +A+aa   +va G+vG 
  gi|121637264|ref|YP_977487.1|  77 GSAYGlAAADGVMRWLEEHRRGvAMDSGVVPIVPG---AVIFDLPVGG---WN-CRPTAdfgySACAAagvDVAVGTVGV 149
                                    ******************8766899999*******...*******999...77.55555577755544567********* PP

                  Peptidase_S58 144 GtGmiafglKGGiGtaSrvleegekeytvgalvqaNfggredlriagvpvgkelaeea...................... 201
                                    G+G++a++lKGG+GtaS++l++g   +tvg+l+++N++g+     +g+p+ + l  e                       
  gi|121637264|ref|YP_977487.1| 150 GVGARAGALKGGVGTASATLQSG---VTVGVLAVVNAAGNVVDPATGLPWMADLVGEFalrappaeqiaalaqlssplga 226
                                    ********************766...**************54456788888666555578889999999999******** PP

                  Peptidase_S58 202 ...kdgsiivvvatDapLskrqlkrlakraalGlartgsp.hsngsGDivlafstaekepe.........evledeelde 268
                                         +++i v+a+Da+Ls++ ++r+a +a++Glart++p h++ +GD+v+a++t++   +         +  e + +++
  gi|121637264|ref|YP_977487.1| 227 fntPFNTTIGVIACDAALSPAACRRIAIAAHDGLARTIRPaHTPLDGDTVFALATGAVAVPpeagvpaalS-PETQLVTA 305
                                    *********************************************************99989*****7431.2345599* PP

                  Peptidase_S58 269 lfeaaaeaveeAilnallaAetvtg 293
                                    + +aaa+++++A+l ++l+A+ v+g
  gi|121637264|ref|YP_977487.1| 306 VGAAAADCLARAVLAGVLNAQPVAG 330
                                    **********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1900.73
//
Query:       gi|121637265|ref|YP_977488.1|  [L=146]
Description: hypothetical protein BCG_1396 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-26   91.2   1.6    4.5e-26   91.0   1.6    1.1  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.025   14.6   0.0       0.16   11.9   0.0    1.9  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease
      0.051   13.0   0.0      0.051   13.0   0.0    1.1  1  SpoIIP    Stage II sporulation protein P (SpoIIP)


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   1.6   7.5e-30   4.5e-26       2     116 ..      15     129 ..      14     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 7.5e-30
                       Prok-JAB   2 esvlsalvaharrahpeEtcGlllgkeseseevivvplvnewsn..rfeipdpedslarlkfearerglevvgiwHSHpg 79 
                                    ++++ a+vaharr+hp+E+cG+l+g+e  ++ ++++p+ n+ ++  ++++ d++++l++++ +++++++ +v+i+HSH++
  gi|121637265|ref|YP_977488.1|  15 ADLVNAMVAHARRDHPDEACGVLAGPEGSDRPERHIPMTNAERSptFYRL-DSGEQLKVWR-AMEDADEVPVVIYHSHTA 92 
                                    57889**********************77788888888887787988888.**********.****************** PP

                       Prok-JAB  80 gsarPSetDrrdaaalarvkalliivgd...kaeelrawr 116
                                    ++a+PS+tD + a ++    a++++v++   + +elr++r
  gi|121637265|ref|YP_977488.1|  93 TEAYPSRTDVKLATEP---DAHYVLVSTrdpHRHELRSYR 129
                                    ***************8...9*******9655444445655 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05      0.16       6     107 ..      11     103 ..       7     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                    EEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTTS CS
                            JAB   6 vhleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgre 85 
                                      + ++ +  ++ ha+r      e +G+l G   +d   +   +++ ++++t  +     ld  +  k  + ++   ++e
  gi|121637265|ref|YP_977488.1|  11 LVIRADLVNAMVAHARRDHPD--EACGVLAGPEGSDRPERHIPMTNAERSPTFYR-----LDSGEQLKVWRAMED--ADE 81 
                                    56788999999********99..********998885443344455555555555.....444422233333333..467 PP

                                    EEEEEEEESSSS-SS--HHHHH CS
                            JAB  86 rvvGWYhshpditvwlsevdvr 107
                                      v  Yhsh   ++++s+ dv+
  gi|121637265|ref|YP_977488.1|  82 VPVVIYHSHTATEAYPSRTDVK 103
                                    78889***************97 PP

>> SpoIIP  Stage II sporulation protein P (SpoIIP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.5e-06     0.051      65      95 ..      66     100 ..      23     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-06
                         SpoIIP  65 seeeee....kldkskpevlIYhtHt.tEsYlplls 95 
                                    s e+ +      d+++  v+IYh+Ht tE+Y p+ +
  gi|121637265|ref|YP_977488.1|  66 SGEQLKvwraMEDADEVPVVIYHSHTaTEAY-PSRT 100
                                    333333676677889999*******868***.6553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 831.25
//
Query:       gi|121637266|ref|YP_977489.1|  [L=93]
Description: antigen cfp10A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-18   66.6   0.0    2.5e-18   66.5   0.0    1.0  1  ThiS           ThiS family
     0.0095   16.3   0.0      0.013   15.8   0.0    1.3  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   2.8e-22   2.5e-18       1      77 []       5      93 .]       5      93 .] 0.97

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2.8e-22
                                   EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG...........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEE CS
                           ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela...........lerrvavavNgeivpr.lwldtelkdgDevai 70
                                   v +++ lr  +g ++ + a+g+t+++++  L+++y+++            l+r+v+++vN+e+v++  +l t+++dgD v i
  gi|121637266|ref|YP_977489.1|  5 VSIPTILRPHTGGQKSVSASGDTLGAVISDLEANYSGISerlmdpsspgkLHRFVNIYVNDEDVRFsGGLATAIADGDSVTI 86
                                   6688999***********************************************************88************** PP

                                   EESTTC- CS
                           ThiS 71 lppVaGG 77
                                   lp+VaGG
  gi|121637266|ref|YP_977489.1| 87 LPAVAGG 93
                                   ******9 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-06     0.013      18      86 .]      20      93 .]      11      93 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-06
                  Lambda_tail_I 18 dvveavktleeairalssqldafkellq.rskfavrvagvdVgesvp....vdryaetlkdgkvvtivpvpaGg 86
                                    v  +++tl+ +i  l  +  +  e l   s  +  + +v++    +     + +a ++ dg  vti p +aGg
  gi|121637266|ref|YP_977489.1| 20 SVSASGDTLGAVISDLEANYSGISERLMdPSSPGKLHRFVNIYVNDEdvrfSGGLATAIADGDSVTILPAVAGG 93
                                   567899**********9999888776663444555566666544333111246789*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 617.89
//
Query:       gi|121637267|ref|YP_977490.1|  [L=323]
Description: cysteine synthase b cysM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-60  202.7   0.7      1e-59  202.4   0.7    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.4   0.7   5.6e-64     1e-59       3     286 ..       9     287 ..       7     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 5.6e-64
                                    GCSSS--EEEECCTC.......CCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHH CS
                           PALP   3 lgigpTPlvrlprls.......kelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAa 72 
                                    ++ g+TPlv l+rls       +   v+l++KlE+ nptgS+KdR a+ ++++++     +++ t++e +sGN+g++lA+
  gi|121637267|ref|YP_977490.1|   9 QALGNTPLVGLQRLSprwddgrDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADgllRPGATILEPTSGNTGISLAM 88 
                                    6789***********9999766666666*************************666669********************* PP

                                    HHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHH CS
                           PALP  73 aaallGlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglE 149
                                    aa+l G+++++v+p+++s e+++ll+l+Ga+++++  +g+ ++ava+a+elaa +++++++ q++np++++  y  +g+E
  gi|121637267|ref|YP_977490.1|  89 AARLKGYRLICVMPENTSVERRQLLELYGAQIIFSaaEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDShYCGTGPE 168
                                    *************************************99***************************************** PP

                                    HHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTC CS
                           PALP 150 ileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spsel 228
                                    +l++l ++++++v+++G+ g+++G++++l+e+  +v+++++ep   + +++ +                 ++ g +p+ +
  gi|121637267|ref|YP_977490.1| 169 LLADL-PEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALR----------------NMDEGfVPELY 231
                                    *****.6*************************************999999999................89999888888 PP

                                    CHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC..E CS
                           PALP 229 afelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkeg..d 286
                                    + e+l +     ++v   +a++  r+l ++egi+++ s++a+l+a+  + ag+l++g  +
  gi|121637267|ref|YP_977490.1| 232 DPEILTAR----YSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGerA 287
                                    88888655....55*****************************99977788888877444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2409.20
//
Query:       gi|121637268|ref|YP_977491.1|  [L=240]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-25   90.5  18.5    1.4e-25   90.0  18.5    1.2  1  Rhomboid         Rhomboid family
  ------ inclusion threshold ------
       0.15   12.0   1.1       0.32   11.0   1.1    1.5  1  CBM_1            Fungal cellulose binding domain


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0  18.5   1.6e-29   1.4e-25       3     147 ..      73     220 ..      71     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.6e-29
                                    GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S.......-EESSHHH CS
                       Rhomboid   3 krgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses....plvGaSGa 78 
                                    k   lw ++++ +lHa+w Hl++N++ llv+G  +    G +rf++ +++ +++g+l+++l+ + ++s     ++GaSG 
  gi|121637268|ref|YP_977491.1|  73 KTDGLWGVIFAPLLHANWHHLMANTIPLLVLGFLMTLA-GLSRFVWATAIIWILGGLGTWLIGNVGSScgptDHIGASGL 151
                                    56789****************************97776.**************************999***9******** PP

                                    HHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSS...STTTHHHHHHHHHHHHHHHHHHCC CS
                       Rhomboid  79 ifgllgallvlvprnrkllrkliiallllllfillnlvlgllpra...ggvsnlAHlgGllaGlllgllllr 147
                                    ifg+l++llv++++ rk ++ +i+    ++lf++  ++lg +p     ggvs+++Hl+G++aG+++++ll++
  gi|121637268|ref|YP_977491.1| 152 IFGWLAFLLVFGLFVRKGWDIVIGL---VVLFVYGGILLGAMPVLgqcGGVSWQGHLSGAVAGVVAAYLLSA 220
                                    ********************99999...99999999999999999999********************9976 PP

>> CBM_1  Fungal cellulose binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   3.6e-05      0.32       3      12 ..     194     203 ..     193     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                          CBM_1   3 gQCGGigWtG 12 
                                    gQCGG +W+G
  gi|121637268|ref|YP_977491.1| 194 GQCGGVSWQG 203
                                    8********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1720.69
//
Query:       gi|121637269|ref|YP_977492.1|  [L=271]
Description: glutamate racemase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-30  105.4   0.0    5.2e-30  105.0   0.0    1.2  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   2.9e-34   5.2e-30       1     223 [.       8     216 ..       8     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 2.9e-34
                                    EEEC.SCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CC.S-TCHHHHHCH.T..THH.HHHHHHHHHHCTTESEEEE-- CS
                   Asp_Glu_race   1 IGgm.gpeatlsvlrklveatpaesdqehlplivlndsa.ipdrteaieeesgddpvl.klleaakkLekagadaiviaC 77 
                                    +G++ +++++l+v r+++ ++p+e+      +++++d+   p  + +i     ++ ++ + l+  + L   g++a+viaC
  gi|121637269|ref|YP_977492.1|   8 VGVFdSGVGGLTVARAIIDQLPDED------IVYVGDTGnGPYGPLTI-----PE-IRaHALAIGDDLVGRGVKALVIAC 75 
                                    79***********************......********755444444.....32.44499******************* PP

                                    CHHHHH.HHHHHHH-SSEEEECHHHHHHHHHH.HSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCH CS
                   Asp_Glu_race  78 nTahav.adelqkkikiPvlgiveataealka.tgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqai 155
                                    n+a+++ + + ++  ++Pv+ ++ ++++ + a t+++++g++gTr+t++s++yq++++a+++        e+   v  a+
  gi|121637269|ref|YP_977492.1|  76 NSASSAcLRDARERYQVPVVEVILPAVRRAVAaTRNGRIGVIGTRATITSHAYQDAFAAARDT-------EI-TAV--AC 145
                                    ***866266788**************9988888**************************8444.......32.233..56 PP

                                    C..HHHH.TT-TTSH.HHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHHH CS
                   Asp_Glu_race 156 y..eelk.aGevtee.arrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilaret 223
                                    +  ++ +  G + +   +     +le+l++ ++d+++LGCT++pll   ++ +++e+ v+++++++ +a+e+
  gi|121637269|ref|YP_977492.1| 146 PrfVDFVeLGVTSGRqVLGLAQGYLEPLQRAEVDTLVLGCTHYPLLSGLIQLAMGEN-VTLVSSAEETAKEV 216
                                    65555555888888844445555777888*********************9999985.***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2019.46
//
Query:       gi|121637270|ref|YP_977493.1|  [L=273]
Description: hypothetical protein BCG_1401 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-19   68.2   0.3    8.9e-19   67.8   0.3    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00011   22.2   4.6    0.00013   22.0   3.8    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.3     1e-22   8.9e-19      26     201 .]      65     237 ..      49     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1e-22
                                    --..SEEEEE-SS--HHHHGGGGCCCC......C--EE....EEEEEEHHHHHHCCTTCGHHHCHTT...TTEEEEEE-T CS
                  Lactamase_B_2  26 delppidaVllthaHyDHlaglltlre......lrpkk....lplyapkgvlavleanfvylaleee...pavnvheldw 92 
                                    +++++++ Vll+h H+DH+ +l+ l            +    + ly+p ++++ l a +++   e +   ++ +vh  + 
  gi|121637270|ref|YP_977493.1|  65 ADPASVH-VLLSHLHADHCLDLPGLFVwrryhpS---RpsgkALLYGPSDTWSRLGAASSPYGGEIDdcsDIFDVHHWAD 140
                                    4666677.***********999988655444443...455566799*********9888887777777999999999999 PP

                                    TSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTH CS
                  Lactamase_B_2  93 gesfelgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyipeeigerlggadllllditayedde 171
                                     e+++lg     +t++p   ++++       + +Glri+  +g +++y+gDtg ++ ++ e+ +g+d+ l ++  ++   
  gi|121637270|ref|YP_977493.1| 141 SEPVTLG--A--LTIVPRLVAHPT-------ESFGLRITdPSGASLAYSGDTGICD-QLVELARGVDVFLCEAS-WTHSP 207
                                    9999998..4..788888888888.......89******888999********888.6677***********99.55544 PP

                                    HHHHHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 172 mirhmgHltpeeaveaaadlgakrlvliHi 201
                                        + Hl+  ea  +aa++g++ l+l+Hi
  gi|121637270|ref|YP_977493.1| 208 KHPPDLHLSGTEAGMVAAQAGVRELLLTHI 237
                                    444999***********************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   3.8   1.4e-08   0.00013       5     152 ..      35     182 ..      31     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-08
                                    SSEEEEEE.ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   5 pvnsylie.gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    p++ yl++   +  ++iD G++   a++      ++ +p  v +v+l+HlH+DH+ +l+gl   + +++   + +a  + 
  gi|121637270|ref|YP_977493.1|  35 PASGYLLRaPHTPPLVIDFGGGVLGALQ------RHADPASV-HVLLSHLHADHCLDLPGLFVWRRYHPSRPSGKALLYG 107
                                    667799996679***************9......68888887.79*****************999999999999999999 PP

                                    CHHHHHHHHHCCHH.....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTT CS
                    Lactamase_B  84 meeaddaasrkgll.....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDal 152
                                    +   +   ++ +++     +   +++++ ++ + +++++g    ++  + +++ + ++++++  g++++++GD++
  gi|121637270|ref|YP_977493.1| 108 PSDTWSRLGAASSPyggeiDDCSDIFDVHHWADSEPVTLGALTIVPRLVAHPTESFGLRITDpSGASLAYSGDTG 182
                                    999999999988888888855566666666666666666666666666666666666666665667777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1964.30
//
Query:       gi|121637271|ref|YP_977494.1|  [L=259]
Description: ribonuclease PH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.5e-25   88.4   1.0    8.2e-25   87.8   0.1    1.7  2  RNase_PH    3' exoribonuclease family, domain 1
    9.7e-10   38.3   0.1    1.9e-09   37.4   0.1    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.037   13.8   0.0    1.4  1  COXG        Carbon monoxide dehydrogenase subunit G (CoxG)


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.1   1.4e-28   8.2e-25       1     129 [.      12     142 ..      12     144 .. 0.94
   2 ?   -2.7   0.0       1.3   7.6e+03     113     131 ..     156     174 ..     152     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.4e-28
                                    EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CC.EEEECCCCECCCCEC-C.......S...HH CS
                       RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddae.galdveveyapfasger....rregrpsde 74 
                                    elR++ i  g+ ++  GS+++e+G+tkvl++ ++   + p++ +    + g+l++e+ + p a+++r      +gr s +
  gi|121637271|ref|YP_977494.1|  12 ELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGV-PRWRKaT--GlGWLTAEYAMLPSATHSRsdreSVRGRLSGR 88 
                                    79**********************************99.7888433..359*****************98766699**** PP

                                    HHHHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCT CS
                       RNase_PH  75 eielsrlleralrpsillekkpkstididitvlssdggslldalinaaslALada 129
                                    ++e+srl+ r+lr++i l    ++ti id+ vl++dg ++  a+i++a +ALada
  gi|121637271|ref|YP_977494.1|  89 TQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADG-GTRTAAITGAYVALADA 142
                                    ******************9999***************.****************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                    -CHHHCHHHHHHHHHCTCE CS
                       RNase_PH 113 slldalinaaslALadagi 131
                                     +l+++i+a+s+  +d +i
  gi|121637271|ref|YP_977494.1| 156 RPLSCAIAAVSVGVVDGRI 174
                                    5788999999988887665 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.1   3.2e-13   1.9e-09       2      65 ..     161     225 ..     160     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.2e-13
                                    --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSC.EEHHHHHHHHHHHH CS
                     RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsq.ldeetlleaielAk 65 
                                    +++av+vg+vd+ + +D+ +eE++ +e d++++ + t+  v ++ +g++  + + tl + +++A+
  gi|121637271|ref|YP_977494.1| 161 AIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGAtFARSTLDKLLDMAL 225
                                    689*********************************************99*************96 PP

>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.2e-06     0.037      45      92 ..     165     222 ..     159     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                                    EESSSSEEEE..........EEEEEEEEEETTTEEE..EEEEEE-SSEEEEEEEEEEE CS
                           COXG  45 lkvGplkgsf..........karvelselekensttieikGkGrgagvaidfalvvlv 92 
                                    ++vG + g++          +a+v ++ +  +  t +ei+G+G ga++a ++ +++l+
  gi|121637271|ref|YP_977494.1| 165 VSVGVVDGRIrvdlpyeedsRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLD 222
                                    566666666666668888889************999****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2106.30
//
Query:       gi|121637272|ref|YP_977495.1|  [L=204]
Description: deoxyribonucleotide triphosphate pyrophosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-57  193.4   0.0    3.8e-57  193.3   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.3   0.0   2.1e-61   3.8e-57       1     185 [.       7     195 ..       7     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 2.1e-61
                                    EEEC-S-HHHHHHHHHHTTT...ECCCE.EECCC.CEE----BSSSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTT CS
                     Ham1p_like   1 ivfaTgNkgKlrevkeilae...ellevkslkel.elpeveEtqgtfeenalkKaraaae.aglpvladDsgLevdaLng 75 
                                    +++a++N++Kl+e++++l++   ++l++ sl ++  lpe++Et+ tfe+nal+Kar+a+  +gl+ +adDsgLev aL+g
  gi|121637272|ref|YP_977495.1|   7 LLVASRNRKKLAELRRVLDGaglSGLTLLSLGDVsPLPETPETGVTFEDNALAKARDAFSaTGLASVADDSGLEVAALGG 86 
                                    689***************99777677777888889999999****************99757****************** PP

                                    TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTT.S--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGE CS
                     Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeee.edrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiF 154
                                    +PGv sar++g+ ++d++n a ll++l +++ e+r+A+fv+++al+++ ++e ++++Ge+ G+i++eprg+ggfGyDp+F
  gi|121637272|ref|YP_977495.1|  87 MPGVLSARWSGRYGDDAANTALLLAQLCDVPdERRGAAFVSACALVSG-SGE-VVVRGEWPGTIAREPRGDGGFGYDPVF 164
                                    ****************************9776889***********97.444.69************************* PP

                                    EETT-SS.BTTTS.CHHHHHHSHHHHHHHHHH CS
                     Ham1p_like 155 vpeegek.tfaelskeeknaiShRgkAlekll 185
                                    vp +g++ t a+ls++ek+a+ShRg+Al+ ll
  gi|121637272|ref|YP_977495.1| 165 VP-YGDDrTAAQLSPAEKDAVSHRGRALALLL 195
                                    **.55666********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1480.29
//
Query:       gi|121637273|ref|YP_977496.1|  [L=120]
Description: hypothetical protein BCG_1404c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-23   81.3   5.9      8e-23   81.1   5.9    1.1  1  DUF3817   Domain of unknown function (DUF3817)


Domain annotation for each model (and alignments):
>> DUF3817  Domain of unknown function (DUF3817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   5.9   4.5e-27     8e-23       4      80 ..      28     109 ..      25     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 4.5e-27
                        DUF3817   4 yrviAiiegvslllLlvamilkyl.....lvkvigivHGllfvvYlllalllaskmrWslkrlvllllagvvPflsfive 78 
                                    yr++A+ +g++l++L+ +++++y+       ++ig+vHG++++ Ylll+l+la+k+rW+l++++ +llag++P+l+++ve
  gi|121637273|ref|YP_977496.1|  28 YRIMAWTTGLWLIALCYEIVVRYVvkvdnPPTWIGVVHGWVYFTYLLLTLNLAVKVRWPLGKTAGVLLAGTIPLLGIVVE 107
                                    9****************************6678*********************************************** PP

                        DUF3817  79 rk 80 
                                    + 
  gi|121637273|ref|YP_977496.1| 108 HF 109
                                    86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 843.90
//
Query:       gi|121637274|ref|YP_977497.1|  [L=126]
Description: lipoprotein lprD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    9.0   9.7          3    8.1   3.2    2.4  3  SURF1     SURF1 family


Domain annotation for each model (and alignments):
>> SURF1  SURF1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.2   0.00017         3       2      20 ..      17      35 ..      16      41 .. 0.85
   2 ?    5.1   0.2    0.0013        24     162     175 ..      40      53 ..      35      54 .. 0.84
   3 ?   -2.4   0.0      0.27   4.9e+03     109     109 ..      94      94 ..      63     122 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00017
                          SURF1  2 vpvvvlfgLGtWQlqRlkw 20
                                   ++++ +++LG WQ+ R + 
  gi|121637274|ref|YP_977497.1| 17 IATCGCLALGWWQWTRFQS 35
                                   67789***********987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0013
                          SURF1 162 vlhlgYaltWfgla 175
                                    +++lgYal+W ++a
  gi|121637274|ref|YP_977497.1|  40 FQNLGYALQWPLFA 53 
                                    469*******9998 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.27
                          SURF1 109 k 109
                                    +
  gi|121637274|ref|YP_977497.1|  94 A 94 
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 971.66
//
Query:       gi|121637275|ref|YP_977498.1|  [L=106]
Description: acyl carrier protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-13   50.1   1.8    3.3e-13   49.8   1.8    1.1  1  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   1.8   1.9e-17   3.3e-13       2      67 .]      33      99 ..      32      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.9e-17
                     PP-binding  2 klrelvaevlgvpleeidpdtdlf.dlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                   +l++++++ l+++l +++pd+ l  d GlDS++++  ++a+ee++gv+++ ++l++++t++el a++
  gi|121637275|ref|YP_977498.1| 33 TLLSILRDDLNIDLTRVTPDARLVdDVGLDSVAFAVGMVAIEERLGVALSEEELLTCDTVGELEAAI 99
                                   699*********************77*************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 879.15
//
Query:       gi|121637276|ref|YP_977499.1|  [L=521]
Description: long-chain-fatty-acid--ACP ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-49  167.1   0.0    8.5e-49  166.3   0.0    1.4  1  AMP-binding      AMP-binding enzyme
    4.9e-05   24.2   0.2    0.00011   23.1   0.2    1.6  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
    0.00024   21.3   0.0    0.00044   20.5   0.0    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   0.0   1.4e-52   8.5e-49      19     422 ..      28     420 ..       9     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 1.4e-52
                                    STEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET........TS-HHHHHHHH CS
                    AMP-binding  19 egqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp........tltaeelayil 90 
                                     + +  + e++  ++++Aa+L+   + +   V+++ ++++e+v+a+++++ aGa+v+ l          ++  ++l   l
  gi|121637276|ref|YP_977499.1|  28 LWCRHPWPEVHGLAESVAAWLLD--HDRPAAVGLVGEPTVELVAAIQGAWLAGAAVSILPGpvrgandqRWADATLTRFL 105
                                    56677789999**********64..899999************************9988763333333333333333322 PP

                                    HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--S CS
                    AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGT 170
                                       ++++++   +   l++l++++ +      v++ d         l +++++++       + ++ ++ +a+++ T G+
  gi|121637276|ref|YP_977499.1| 106 -GIGVRTVL--SQGSYLARLRSVDTAG-----VTIGD---------LSTAAHTNR------SATPVASEGPAVLQGTAGS 162
                                    .23444444..2333345554444432.....33333.........333333332......2335899************ PP

                                    SSS-EEEEEEHHHHHHHHHHHHHHHCSC.CTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHH CS
                    AMP-binding 171 TGkPKGVmlshrnlvanvaslkletrfk.lkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllel 248
                                    TG P  ++ls +++++n++ l  ++r +   ++dv +s+lpl+h++gl +++l a l+Ga + l+p++a+ ++p ++l  
  gi|121637276|ref|YP_977499.1| 163 TGAPRTAILSPGAVLSNLRGL--NQRVGtDAATDVGCSWLPLYHDMGL-AFVLSAALAGAPLWLAPTTAFtASPFRWLSW 239
                                    ********************7..5553312359999***********9.*******************99666******* PP

                                    HHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC......EEEEEEEEGGGS CS
                    AMP-binding 249 ieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfge......evlegYGlTEtt 321
                                    +++ ++t++a+++ +++ + + +++ +    + dl++lr++l ggep+  + l++f + + +      +vl +YGl+E t
  gi|121637276|ref|YP_977499.1| 240 LSDSGATMTAAPNFAYNLIGKyARRVS----EVDLGALRVTLNGGEPVDCDGLTRFAEAMAPfgfdagAVLPSYGLAEST 315
                                    *******88888888888877665555....55***************************999***************** PP

                                    SECEE............CHCTTTCTSTTS-BEE-TTEEEEEE..-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHH CS
                    AMP-binding 322 gvvtv............lpleedkkklgsvGkplpgvevkiv..DeetgepvpdgeeGellvrgpgvmkgYlkkpeatae 387
                                    ++vtv            ++ ++  +k    G p+pg+ev+i   D++ g+     e Ge+ +rg+++m gYl++     +
  gi|121637276|ref|YP_977499.1| 316 CAVTVpvpgiglladrvIDGSGA-HKHAVLGNPIPGMEVRIScgDQAAGNA--SREIGEIEIRGASMMAGYLGQ-----Q 387
                                    ***99999999999997443444.344557***********9877776665..5899***************99.....7 PP

                                    HEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 388 afdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                     +d +++w+ TGDlg+l   G l ++gR+k++i +
  gi|121637276|ref|YP_977499.1| 388 PID-PDDWFATGDLGYLG-AGGLVVCGRAKEVISI 420
                                    787.767**********9.8************976 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   1.8e-08   0.00011       1      76 []     429     507 ..     429     507 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-08
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE-.---.--.HHHHHHHHHHHHT-TTTS-SEEEE-.S.---B-TTS CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlk.dgs.ea.leeeLkahvrkelgpyavpkkvvfv.d.elpktrsG 75 
                                    evE + +++ +V+e aVv+  +  +  ++  +V  + +g+ ea  ++eL+++v++e g +  p++vvfv + +lp+t sG
  gi|121637276|ref|YP_977499.1| 429 EVELVAAQVRGVREGAVVALGTGDRSTRPGLVVAAEfRGPdEAnARAELIQRVASECGIV--PSDVVFVsPgSLPRTSSG 506
                                    89****************5555555555555555433364233589**********9985..*******6556******* PP

                                    - CS
                  AMP-binding_C  76 K 76 
                                    K
  gi|121637276|ref|YP_977499.1| 507 K 507
                                    9 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.3e-08   0.00044       1      93 [.     422     512 ..     422     515 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.3e-08
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET..TEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--.EEEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg..elDelevkvEvkegfsdelkelealekkiakklksklgvsv.kvelv 77 
                                    G n+fP+++e v  ++++v +   + + + +  ++  l v  E +    d     ++ ++++ ++++s++g+ + +v +v
  gi|121637276|ref|YP_977499.1| 422 GRNIFPTEVELVAAQVRGVREGAVVALGTGDrsTRPGLVVAAEFRGP--D----EANARAELIQRVASECGIVPsDVVFV 495
                                    78******************999999988761145566666666665..4....4788899999999****98649**** PP

                                    -TT-S----.-----EE CS
                AMP-binding_C_2  78 epgtlprse.gKakrvi 93 
                                    +pg+lpr+  gK++r+ 
  gi|121637276|ref|YP_977499.1| 496 SPGSLPRTSsGKLRRLA 512
                                    *******6527****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3893.14
//
Query:       gi|121637277|ref|YP_977500.1|  [L=386]
Description: acyl-CoA dehydrogenase fadE14 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-32  111.8   8.7    5.2e-32  111.1   8.7    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.1e-15   57.6   0.0    2.1e-15   56.7   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      2e-05   25.2   1.0    0.00011   22.9   0.0    2.6  3  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    0.00014   22.1   2.6    0.00037   20.8   2.6    1.7  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   8.7   1.2e-35   5.2e-32       1     149 [.     224     370 ..     224     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 1.2e-35
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g G++++ ++l+heR+++a + ++ ++ra+  +l+++ +r++fg++l++hq++r ++a+++a+++ +r ++  +ae   +
  gi|121637277|ref|YP_977500.1| 224 GTGLAAISWGLAHERMSIAGQIAASCQRAIGITLARMMSRRQFGQTLFEHQALRLRMADLQARVDLLRYALHGIAE---Q 300
                                    579***********************************************************************97...7 PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTS.GGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyl.eeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    g+ +   a+++K+ a++l +ev++++m+++GgaGyl +e+ + +++rd+++ r+g+Gt+e++++++a+++
  gi|121637277|ref|YP_977500.1| 301 GRLELRTAAAVKVTAARLGEEVISECMHIFGGAGYLvDETTLGKWWRDMKLARVGGGTDEVLWELVAAGM 370
                                    8888888****************************999999**************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   4.7e-19   2.1e-15       1      95 [.     117     211 ..     117     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 4.7e-19
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE..TS---.----EEEEEEE..GGGEEE-- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar..tekpd.rarglslflvprdapgvsvrr 77 
                                    +++++E+++Gsd++ v+t+  +rdg ++ ++G K +++ ++ia++++v+ar   ++p+ r++++ +++vp  a  vsv+ 
  gi|121637277|ref|YP_977500.1| 117 CIGASEESGGSDLQIVETEIRSRDG-GFEVRGVKKFVSLSPIADHIMVVARsvDHDPTsRHGNVAVVAVP--AAQVSVQT 193
                                    99****************8888888.8************************8766666899999999999..7889**99 PP

                                    ---BSS-TTS-EEEEEEE CS
                  Acyl-CoA_dh_M  78 ieeklGlrglptgelvfe 95 
                                      +k+G   l+t+ ++++
  gi|121637277|ref|YP_977500.1| 194 PYRKVGAGPLDTAAVCID 211
                                    99******9999999876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.4e-08   0.00011       6     101 ..       9     101 ..       5     113 .. 0.84
   2 ?   -1.0   0.0      0.59   2.6e+03      45      64 ..     115     134 ..     103     138 .. 0.81
   3 ?   -1.7   0.1      0.98   4.4e+03      56      95 ..     224     259 ..     214     268 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.4e-08
                                    HHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHH CS
                  Acyl-CoA_dh_N   6 alrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvh 85 
                                    ++r  +++ ++e++    ae++++++fpr+l++ l+  G++   + ++     ++ +e a ++ +la a++g+  ++++h
  gi|121637277|ref|YP_977500.1|   9 DFRGLLAKAFDERVVAWTAEAEAQERFPRQLIEHLGVCGVFDAKWATDARPDVGKLVELAFALGQLASAGIGV--GVSLH 86 
                                    6777788888999988999999999************************977679************988886..55889 PP

                                    HHTTHHHHHHHS-HHH CS
                  Acyl-CoA_dh_N  86 sslvapailrfGteeq 101
                                    +s +a ++ rfG  + 
  gi|121637277|ref|YP_977500.1|  87 DSAIA-ILRRFGKSDY 101
                                    99996.899**97665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                                    CTSTTS-GGGTS--S-HHHH CS
                  Acyl-CoA_dh_N  45 llgitvpeeygGagldylea 64 
                                    +l+i   ee gG++l+++e+
  gi|121637277|ref|YP_977500.1| 115 VLCIGASEESGGSDLQIVET 134
                                    6889999******9988775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.98
                                    S--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHH CS
                  Acyl-CoA_dh_N  56 Gagldyleaaivaeelaradaglalllgvhsslvapailr 95 
                                    G gl +++  ++ e ++ a   ++++ +++ ++++ +++r
  gi|121637277|ref|YP_977500.1| 224 GTGLAAISWGLAHERMSIA---GQIAASCQRAIGI-TLAR 259
                                    6666666666666666643...3446667776665.4555 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   2.6   8.2e-08   0.00037      11     127 ..     249     353 ..     239     358 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.2e-08
                                    HHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  11 AraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaala 90 
                                    +++a+  +++++  r +  +g++l +++a+ l+ a+++ar+d +r  l+  a++      ++ e      + a++ +++a
  gi|121637277|ref|YP_977500.1| 249 CQRAIGITLARMMSRRQ--FGQTLFEHQALRLRMADLQARVDLLRYALHGIAEQ------GRLE-----LRTAAAVKVTA 315
                                    56777777888888888..**************************999999999......5555.....46778889*** PP

                                    HHHHHHHHHHHHHHCGGGGGB.TT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  91 velaiaavdalfeaaGgsalr.kesplqRlwRDahaaa 127
                                    ++l  +++++++ ++Gg +++ +e  l   wRD++ a+
  gi|121637277|ref|YP_977500.1| 316 ARLGEEVISECMHIFGGAGYLvDETTLGKWWRDMKLAR 353
                                    *******************8626789*******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2871.34
//
Query:       gi|121637278|ref|YP_977501.1|  [L=210]
Description: hypothetical protein BCG_1409c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-44  151.7   0.2    1.5e-44  151.2   0.2    1.1  1  Acetyltransf_8  Acetyltransferase (GNAT) domain
     0.0016   19.1   0.3     0.0074   17.0   0.3    1.9  1  Acetyltransf_3  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.2   0.2   1.6e-48   1.5e-44       4     144 ..      51     192 ..      49     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 1.6e-48
                                    GGHHHHHHHCTSCCCHHHH-----H.HHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEE CS
                 Acetyltransf_8   4 aDlellhrWmnrprvaewweeagtl.eevrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGi 82 
                                    +D+e+l++Wmnrp++a+ we ++++ ++ ++l a+l+  ++s plig+++g++ gy+e+Ywa++d +++yyda+p+d+G+
  gi|121637278|ref|YP_977501.1|  51 TDAEMLAEWMNRPHLAAAWEYDWPAsRWRQHLNAQLE-GTYSLPLIGSWHGTDGGYLELYWAAKDLISHYYDADPYDLGL 129
                                    7************************999999999997.****************************************** PP

                                    EEEESSHHHCTTTCHHHHHHHHHHHHHC.CTT--EEEE--BTT-HHHHHHHHHTT-EEEEEEE CS
                 Acetyltransf_8  83 Hlligeaeargkglttallralvhylfa.dprtrrvvvEPdvrNerairllekaGfekekevd 144
                                    H +i++ +++++g+++ ll+++v+ +fa +pr+rr++++Pd+rN++ +rl+e aG+++ +e+d
  gi|121637278|ref|YP_977501.1| 130 HAAIADLSKVNRGFGPLLLPRIVASVFAnEPRCRRIMFDPDHRNTATRRLCEWAGCKFLGEHD 192
                                    ***************************7588*****************************988 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   8.3e-07    0.0074       4     138 .]      45     186 ..      44     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.3e-07
                 Acetyltransf_3   4 LrplteeDlealfelrsdpe.vmry.lpepltleeaeewlera..........waeeseeegygwaivlkdtgviGsvgl 71 
                                    Lr ++ +D+e l+e++++p+    + + +p+++  ++   +            w+    +               G+  l
  gi|121637278|ref|YP_977501.1|  45 LRVAQLTDAEMLAEWMNRPHlAAAWeYDWPASRWRQHLNAQLEgtyslpligsWHGT--D--------------GGYLEL 108
                                    7888999*9999********5555787776655555444441122344444444432..2..............344444 PP

                 Acetyltransf_3  72 rdleeedee.........aelgymlaps.fwgkGyateavralleyaf.eelglerlvavidkeNeaSirvleklGfe 138
                                    +++ ++  +         + l   +a+    ++G++   +  ++  +f +e++ +r++   d +N+a +r+ e +G++
  gi|121637278|ref|YP_977501.1| 109 YWAAKDLIShyydadpydLGLHAAIADLsKVNRGFGPLLLPRIVASVFaNEPRCRRIMFDPDHRNTATRRLCEWAGCK 186
                                    433333222333333322666666664323499*******998777775888**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1738.95
//
Query:       gi|121637279|ref|YP_977502.1|  [L=859]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-28  100.1   0.0    2.3e-28   99.4   0.0    1.4  1  ABC_tran        ABC transporter
    2.4e-23   82.9   0.1    5.5e-23   81.7   0.1    1.6  1  SIP             Siderophore-interacting protein
    2.9e-15   56.7   1.4    4.2e-15   56.1   1.4    1.2  1  ABC_membrane    ABC transporter transmembrane region
    4.9e-12   46.1   0.1    2.3e-10   40.7   0.0    2.5  2  FAD_binding_9   Siderophore-interacting FAD-binding domain
    3.2e-06   26.7   0.0     0.0024   17.4   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
    3.1e-05   24.4   0.9    0.00016   22.1   0.7    2.2  2  AAA_16          AAA ATPase domain
    7.5e-05   23.0   0.1    0.00099   19.4   0.1    2.3  1  AAA_22          AAA domain
    0.00095   18.9   0.3     0.0031   17.3   0.3    1.8  1  AAA_30          AAA domain
      0.001   18.8   0.9     0.0029   17.3   0.1    2.2  2  AAA_29          P-loop containing region of AAA domain
     0.0024   17.5   0.1     0.0084   15.7   0.0    1.9  2  AAA_25          AAA domain
      0.003   17.7   0.0      0.007   16.5   0.0    1.7  1  AAA_33          AAA domain
     0.0036   17.1   0.0     0.0064   16.2   0.0    1.4  1  AAA_24          AAA domain
     0.0051   16.1   0.2      0.013   14.8   0.0    1.6  2  Zeta_toxin      Zeta toxin
     0.0094   15.9   0.0      0.017   15.0   0.0    1.3  1  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.012   16.2   0.0      0.029   14.9   0.0    1.6  1  AAA_18          AAA domain
       0.02   14.7   0.0      0.035   13.9   0.0    1.4  1  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      0.034   14.6   0.0       0.46   10.9   0.0    2.2  2  AAA             ATPase family associated with various cellula
      0.096   12.7   0.0       0.24   11.4   0.0    1.6  1  AAA_5           AAA domain (dynein-related subfamily)
       0.11   12.4   0.0       0.21   11.5   0.0    1.4  1  APS_kinase      Adenylylsulphate kinase
       0.13   12.0   0.0       0.25   11.0   0.0    1.4  1  Cytidylate_kin  Cytidylate kinase
       0.15   11.8   0.0        0.2   11.3   0.0    1.1  1  AAA_15          AAA ATPase domain
       0.18   12.3   0.0       0.29   11.6   0.0    1.2  1  AAA_23          AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   2.8e-31   2.3e-28       2     137 .]     627     774 ..     626     774 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.8e-31
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++vsl+l++g+++a+vG++G+GKStL+ lla+ ++ + G i++ g+d+++    +l  ++g++ qe+ql  ++ ++en  
  gi|121637279|ref|YP_977502.1| 627 QDVSLTLRPGTVTALVGPSGSGKSTLATLLARFHDVERGAIRVGGQDIRSLAADELYTRVGFVLQEAQLVHGT-AAENia 705
                                    79**********************************************************************9.89999* PP

                                    ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  +++++i++ + +l + +  dtv+    s LSgG++qr+ +ara+l + ++l+lDE+ta
  gi|121637279|ref|YP_977502.1| 706 lavpdapaeqvqvaAREAQIHDRVLRLPDGY--DTVL-GANSGLSGGERQRLTIARAILGDTPVLILDEATA 774
                                    *****77766654444444444444444444..6666.556*****************************96 PP

>> SIP  Siderophore-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   6.7e-26   5.5e-23       4     119 .]     131     241 ..     128     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 6.7e-26
                            SIP   4 vllagDeTAlPAiaaiLeelpadaqvravievpdaad.elelsapaaveltwlvregaaaagelLaealrelelpagely 82 
                                    +ll+gD +++P +++i+e++p+d+ +++++e +d++d  ++l+++++++++w++r+++    ++Laea+++ ++  +++y
  gi|121637279|ref|YP_977502.1| 131 YLLIGDSASIPGMNGIIETVPNDVPIEMYLEQHDDNDtLIPLAKHPRLRVRWVMRRDE----KSLAEAIENRDW--SDWY 204
                                    8*******************************99999678******************....***********9..**** PP

                            SIP  83 vwvagEaavvkalRrhlvkergldrkqvaamgYWrrg 119
                                    +w++ Eaa++k +R  l++e g+++++++a++YW++g
  gi|121637279|ref|YP_977502.1| 205 AWATPEAAALKCVRVRLRDEFGFPKSEIHAQAYWNAG 241
                                    **********************************976 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   1.4   5.1e-18   4.2e-15       2     263 ..     294     552 ..     293     562 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 5.1e-18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                    +l+ +la+l+++++++  ++l  +   l++ + ++    +v + ++ llg + +++a l   +l+v+  r  ++lr +l+
  gi|121637279|ref|YP_977502.1| 294 VLSGVLAALVTLAQLAPFVLLVELSRLLVSGAGAHR-LFTVGFAAVGLLGTGALLAAALT-LWLHVIDARFARALRLRLL 371
                                    567788888888887766777777777776555555.34444444444444444444444.34489************** PP

                                    HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsavi 161
                                     k+ r+p+++f ++ +G++  ++t+d+  l+ +++  + + + +++  vg+l+++f++ w+++lvl++ +++++ ++  +
  gi|121637279|ref|YP_977502.1| 372 SKLSRLPLGWFTSRGSGSIKKLVTDDTLALHYLVTHAVPDAVAAVVAPVGVLVYLFVVDWRVALVLFGPVLVYLTITSSL 451
                                    **************************************************************************999999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTT.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 162 akilkklkkkeqkavakassvaeEslsgirtVkafgr.eeyflekfekaleeakkagikkaianglligitqllgllsya 240
                                    +  + +   + q   +k++  a   l+g  +++ fg+  + f+++ ++++      ++  a    l+  +t+ +++l  +
  gi|121637279|ref|YP_977502.1| 452 TIQSGPRIVQAQRWAEKMNGEAGSYLEGQPVIRVFGAaSSSFRRRLDEYIGFLVAWQRPLAGKKTLMDLATRPATFLWLI 531
                                    88888888888888888888888888888888888762456777777777777777777777777777777776666666 PP

                                    HHHHHHHHHHHTTSSTHHHHHHH CS
                   ABC_membrane 241 lalwfGttlvisgelsvgdlvvf 263
                                    +a   Gt lv ++ +++ +l+ f
  gi|121637279|ref|YP_977502.1| 532 AA--TGTLLVATHRMDPVNLLPF 552
                                    66..6777777777777775555 PP

>> FAD_binding_9  Siderophore-interacting FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.03        24       2      48 ..      22      68 ..      21      71 .. 0.90
   2 !   40.7   0.0   2.8e-13   2.3e-10      63     115 ..      61     113 ..      53     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                  FAD_binding_9  2 vvrverlspslrrvtltgeelagfksdgtDqhikLllpepgqtepel 48
                                   v ++  ++p+++rv + ++ l + ++  + ++++  +p+p++ ++e+
  gi|121637279|ref|YP_977502.1| 22 VIETISIAPHFVRVRMVSPTLFQDAEAEPAAWLRFWFPDPNGSNTEF 68
                                   778899**********************************9988766 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 2.8e-13
                  FAD_binding_9  63 lpederpvmRtYtvraldaeaeeldidfvlHgdegpaarwAaqAqpGdelaiv 115
                                    +++++    R Yt+++ d++a+++++d vlH+  gpa++wA++++pG ++a++
  gi|121637279|ref|YP_977502.1|  61 PNGSNTEFQRAYTISEADPAAGRFAVDVVLHDPAGPASSWARTVKPGATIAVM 113
                                    566777889****************************************9987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0039       3.2      25      40 ..     637     652 ..     627     658 .. 0.83
   2 !   17.4   0.0   2.9e-06    0.0024     136     210 ..     745     815 ..     672     822 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0039
                                    SEEEEEESTTSSHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnl 40 
                                     +ta+vGp GSGKs l
  gi|121637279|ref|YP_977502.1| 637 TVTALVGPSGSGKSTL 652
                                    589***********87 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.9e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                     LSgGe++     L +A      +p+ +lDe  a  D +    v + l++ + +  ++vi++r +++++ad++v 
  gi|121637279|ref|YP_977502.1| 745 GLSGGERQ----RLTIARAILGDTPVLILDEATAFADPESEYLVQQALNRLTRDRTVLVIAHRLHTITRADQIVV 815
                                    59999998....55666677899************************************************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.9   7.2e+03      93     137 ..     461     511 ..     452     512 .. 0.73
   2 !   22.1   0.7   1.9e-07   0.00016      25     170 .]     637     800 ..     628     800 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.9
                         AAA_16  93 eleawrekleeala......avpelagaeasrllellkrllallsrderpl 137
                                    ++++w+ek  ++++      +v  + ga++s++++ l + + +l   +rpl
  gi|121637279|ref|YP_977502.1| 461 QAQRWAEKMNGEAGsylegqPVIRVFGAASSSFRRRLDEYIGFLVAWQRPL 511
                                    678888888888887777777777777777999999999986665557665 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.9e-07
                         AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql.esaipysalaqalareellrqllde..........aesa 92 
                                     ++ l+G+sG+GKs+l++ l+r    + g+i + g+  ++  ++  y  +  +l + +l+   ++e          ae+ 
  gi|121637279|ref|YP_977502.1| 637 TVTALVGPSGSGKSTLATLLARFHDVErGAIRVGGQDIRSlAADELYTRVGFVLQEAQLVHGTAAEnialavpdapAEQV 716
                                    6789*****************85554413333555555552222223224444444455555555533222222232233 PP

                         AAA_16  93 eleawrekleeala.....................avpelagaeasrllellkrllallsrderplvlvlDdlq.wadea 150
                                    +++          a                     a + l+g e++rl   ++r++      +++ vl+lD++   ad++
  gi|121637279|ref|YP_977502.1| 717 QVA----------AreaqihdrvlrlpdgydtvlgANSGLSGGERQRLT--IARAI-----LGDTPVLILDEATaFADPE 779
                                    333..........244444444447777777666666666666555554..44555.....2445899999999456668 PP

                         AAA_16 151 slqllaaLlrllesk.pllvv 170
                                    s  l ++ l +l+++  +lv+
  gi|121637279|ref|YP_977502.1| 780 SEYLVQQALNRLTRDrTVLVI 800
                                    888877666666664377776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.2e-06   0.00099       5     112 ..     636     791 ..     633     808 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee........................................erpevvf 44 
                                     ++++++G+sG+GK+tl+  l++ +d e  a +                                        +      
  gi|121637279|ref|YP_977502.1| 636 GTVTALVGPSGSGKSTLATLLARFHDVERGAIRvggqdirslaadelytrvgfvlqeaqlvhgtaaenialavP------ 709
                                    57899********************9988888888877777766666643333333333222222222222221...... PP

                         AAA_22  45 vtlpsstsskdllrellralglelka.................................erlsseellealeqalrarav 91 
                                                             +                                 +      l             
  gi|121637279|ref|YP_977502.1| 710 -------------------------DapaeqvqvaareaqihdrvlrlpdgydtvlganS-----GLS-----------G 748
                                    .........................12222222233334444444444444444333221.....121...........0 PP

                         AAA_22  92 ...............ielliiDEaqhlr...s....eealeeL 112
                                                   +++li+DEa  +    s    ++al+ L
  gi|121637279|ref|YP_977502.1| 749 gerqrltiarailgdTPVLILDEATAFAdpeSeylvQQALNRL 791
                                    1111112222234456788888888875443244445555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   3.8e-06    0.0031      17     114 ..     635     789 ..     629     803 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgi...eastiakllkrlk.......... 81 
                                    +  v++l+Gp G+GK+t+ + l++ ++ + g  rv g    + aA++L + +g+   ea+ ++    ++           
  gi|121637279|ref|YP_977502.1| 635 PGTVTALVGPSGSGKSTLATLLARFHDVErGaIRVGGQDIRSLAADELYTRVGFvlqEAQLVHGTAAENIalavpdapae 714
                                    55799*********************999656777788888889999999888766655555555544335666666788 PP

                         AAA_30  82 ..........................................grarlepgtllivDEagmvdtkqlaallkaaek 114
                                                                              +ra l +  +li DEa   +  + + l+++a +
  gi|121637279|ref|YP_977502.1| 715 qvqvaareaqihdrvlrlpdgydtvlgansglsggerqrltiARAILGDTPVLILDEATAFADPESEYLVQQALN 789
                                    888888888888999999999999999999999999999988667777889999999999988888888888765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.8   7.1e+03      21      33 ..     128     139 ..     122     139 .. 0.80
   2 !   17.3   0.1   3.5e-06    0.0029      15      38 ..     629     652 ..     625     656 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.8
                         AAA_29  21 lkgatlltGpsGs 33 
                                    ++g +ll+G+s s
  gi|121637279|ref|YP_977502.1| 128 PAG-YLLIGDSAS 139
                                    567.9*****986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.5e-06
                         AAA_29  15 htieidlkgatlltGpsGsGKSTl 38 
                                     ++++++  +t l+GpsGsGKSTl
  gi|121637279|ref|YP_977502.1| 629 VSLTLRPGTVTALVGPSGSGKSTL 652
                                    5567776679*************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-05    0.0084      30      55 ..     633     658 ..     609     660 .. 0.90
   2 ?   -2.3   0.0       3.5   2.8e+03     142     188 ..     763     802 ..     743     803 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                         AAA_25  30 lpagelallaGapgtGKttlaldlal 55 
                                    l+ g++++l+G++g+GK+tla+ la 
  gi|121637279|ref|YP_977502.1| 633 LRPGTVTALVGPSGSGKSTLATLLAR 658
                                    6679*****************99985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                         AAA_25 142 gvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                    +  ++++D  +++  +d++s+  v++++++l r     + +vl++ H
  gi|121637279|ref|YP_977502.1| 763 DTPVLILDEATAF--ADPESEYLVQQALNRLTR-----DRTVLVIAH 802
                                    4667788876665..466666778888777776.....345555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.6e-06     0.007       1      34 [.     638     675 ..     638     769 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.6e-06
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg....avllssdtlr 34 
                                    ++ lvG++GsGKstla+ l++ ++    a+++   ++r
  gi|121637279|ref|YP_977502.1| 638 VTALVGPSGSGKSTLATLLARFHDvergAIRVGGQDIR 675
                                    5679**************99877766677777666543 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.9e-06    0.0064       5      88 ..     639     786 ..     636     795 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-06
                         AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.............swedfldevvel............ 59 
                                     +++Gpsg+GK+tla+ l   + f d+e+G+ ++ + ++ ++                                      
  gi|121637279|ref|YP_977502.1| 639 TALVGPSGSGKSTLATLL---ARFHDVERGAIRVGGQDIRSLAadelytrvgfvlqE----------Aqlvhgtaaenia 705
                                    689***************...99**************99988666555533333331..........0333555555566 PP

                         AAA_24  60 ....................................................aaeladyktlviDtideleelclaevir 87 
                                                                                        +a l d  +l++D ++ + +  ++++ +
  gi|121637279|ref|YP_977502.1| 706 lavpdapaeqvqvaareaqihdrvlrlpdgydtvlgansglsggerqrltiaRAILGDTPVLILDEATAFADPESEYLVQ 785
                                    66666666666667777777777777777777777777777888888888877777777888888888887777777766 PP

                         AAA_24  88 q 88 
                                    q
  gi|121637279|ref|YP_977502.1| 786 Q 786
                                    6 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.013      19      57 ..     639     677 ..     632     687 .. 0.91
   2 ?   -3.2   0.0       5.1   4.1e+03     129     161 ..     799     829 ..     772     840 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                     Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                      l+G +G+GKs+la+ll++ ++ +++++r+ + d+R+l
  gi|121637279|ref|YP_977502.1| 639 TALVGPSGSGKSTLATLLARFHDVERGAIRVGGQDIRSL 677
                                    5699*********************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                     Zeta_toxin 129 vavkkelSrlgvldRyeeevaegRlvpkeehde 161
                                    v++++ ++++++ + +  +   gR+v+  +h+e
  gi|121637279|ref|YP_977502.1| 799 VIAHRLHTITRADQIVVLD--HGRIVERGTHEE 829
                                    3334455555555444444..457777766666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.017      94     130 ..     630     667 ..     622     672 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                    HHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                    +  l+   +++lvG+SG GKStL   l+  ++++ g++
  gi|121637279|ref|YP_977502.1| 630 SLTLRPgTVTALVGPSGSGKSTLATLLARFHDVERGAI 667
                                    5556665899**************99998777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.6e-05     0.029       3      27 ..     641     685 ..     640     731 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf....................gvn 27 
                                    l G++G+GK+tla  L++ + +                     ++
  gi|121637279|ref|YP_977502.1| 641 LVGPSGSGKSTLATLLARFHDVergairvggqdirslaadelYTR 685
                                    89**************77656666777888444444444444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-05     0.035       1      30 [.     638     667 ..     638     689 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdve 30 
                                    +++l+Gp gsGKS+L  +l  ++++ r ++
  gi|121637279|ref|YP_977502.1| 638 VTALVGPSGSGKSTLATLLARFHDVERGAI 667
                                    69*****************99988733333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00057      0.46       3      53 ..     641     693 ..     639     715 .. 0.75
   2 ?    1.0   0.0      0.64   5.2e+02      53     109 ..     757     801 ..     739     816 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00057
                                    EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkea 53 
                                    l+Gp G GK++la  +a+  +  +  +++ g +++s    e   ++  +++ea
  gi|121637279|ref|YP_977502.1| 641 LVGPSGSGKSTLATLLARFHDveRGAIRVGGQDIRSLAADELYTRVGFVLQEA 693
                                    89***************986511447888888887665555555555555554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.64
                                    HHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                            AAA  53 akeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                    a++   ++ +l++DE+ a+a  +       +e +v+q l+ l + ++      v++++
  gi|121637279|ref|YP_977502.1| 757 ARAILgDTPVLILDEATAFADPE-------SEYLVQQALNRLTRDRT------VLVIA 801
                                    3333344699*******999888.......33344443333333333......34444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.24       4      22 ..     641     659 ..     639     674 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                    EE--SSSSHHHHHHHGGGG CS
                          AAA_5   4 LvGppGtgKselaerlaaa 22 
                                    LvGp+G+gKs+la  la++
  gi|121637279|ref|YP_977502.1| 641 LVGPSGSGKSTLATLLARF 659
                                    9***************986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.21       3      44 ..     637     677 ..     635     695 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                    EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                     APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44 
                                    +v  l G sgsGKst+a+ l+ + ++  + ++++ G+ +R  
  gi|121637279|ref|YP_977502.1| 637 TVTALVGPSGSGKSTLATLLA-RFHDVERGAIRVGGQDIRSL 677
                                    567799************998.57888899999999999964 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.25       2      20 ..     640     658 ..     639     667 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                    EEE-STTSSHHHHHHHHHH CS
                 Cytidylate_kin   2 aiDGPagsGKssvaralae 20 
                                    a+ GP+gsGKs++a +la+
  gi|121637279|ref|YP_977502.1| 640 ALVGPSGSGKSTLATLLAR 658
                                    678**************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024       0.2      14      49 ..     626     662 ..     625     692 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                         AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnn 49 
                                    ++dv++ l +  +t l+G+ +sGKS+++ +l  F + 
  gi|121637279|ref|YP_977502.1| 626 IQDVSLTLRPGtVTALVGPSGSGKSTLATLLARFHDV 662
                                    6888899999899******************999775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00036      0.29      12      36 ..     628     653 ..     622     657 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                         AAA_23  12 dqeidFsk.gltlItGpNGaGKTTil 36 
                                    d+++ + +  +t+++Gp G+GK+T+ 
  gi|121637279|ref|YP_977502.1| 628 DVSLTLRPgTVTALVGPSGSGKSTLA 653
                                    56666666359*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (859 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 5241.86
//
Query:       gi|121637280|ref|YP_977503.1|  [L=579]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-35  123.0   0.0    1.8e-35  122.5   0.0    1.3  1  ABC_tran      ABC transporter
    6.2e-08   32.3   0.2    8.3e-06   25.4   0.2    2.4  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00034   20.3   0.1     0.0011   18.7   0.1    1.8  1  AAA_29        P-loop containing region of AAA domain
      0.001   19.0   0.0      0.014   15.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0025   17.6   1.9      0.014   15.1   1.9    2.2  1  AAA_30        AAA domain
     0.0027   16.6   1.0      0.039   12.8   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0038   17.7   0.1     0.0064   17.0   0.1    1.2  1  AAA_23        AAA domain
     0.0062   16.9   3.6     0.0062   16.9   3.6    2.4  2  AAA_16        AAA ATPase domain
     0.0087   16.3   0.2       0.22   11.8   0.0    2.4  2  AAA_22        AAA domain
     0.0089   16.0   0.0      0.018   14.9   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
       0.03   14.0   1.8      0.042   13.5   1.8    1.2  1  ABC_membrane  ABC transporter transmembrane region
      0.061   13.5   0.2       0.66   10.1   0.1    2.7  2  AAA_33        AAA domain
      0.075   12.9   0.0       0.12   12.2   0.0    1.2  1  Rad17         Rad17 P-loop domain
       0.09   12.0   0.0       0.18   11.0   0.0    1.4  1  Zeta_toxin    Zeta toxin
       0.14   11.8   0.1       0.28   10.8   0.1    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.16   11.5   3.8       0.32   10.5   0.5    2.8  2  AAA_25        AAA domain
       0.18   11.5   0.0       0.25   11.0   0.0    1.1  1  AAA_15        AAA ATPase domain
       0.43   10.8   1.8        6.6    7.0   1.8    2.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.5   0.0   1.8e-38   1.8e-35       1     137 []     349     498 ..     349     498 .. 0.90

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 1.8e-38
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+ l++g+++aivG++G+GKSt+l+l+agl++pt G++l+dg+d+ + + +  ++  +v++q+p lf ++ +r+n 
  gi|121637280|ref|YP_977503.1| 349 LDGVSFCLQPGTTTAIVGPSGCGKSTILALIAGLHQPTRGRVLIDGTDVATLDARAQQAVCSVVFQHPYLFHGT-IRDNv 427
                                    789***********************************************************************.***** PP

                                    ......HHHTC.........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ......xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdee.........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                          +sd++         +++++++l +   ++t+v++ +s LSgG++qrv++arallk++++ll+DE+t+
  gi|121637280|ref|YP_977503.1| 428 faadpgASDDQfaqavrlarVDELIARLPD--GANTIVGEAGSALSGGERQRVSIARALLKAAPVLLVDEATS 498
                                    ******555553333334446666666665..55*************************************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   8.3e-09   8.3e-06      26     210 ..     361     539 ..     352     545 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.3e-09
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                     taivGp G+GKs +l  i    G ++      ++ + li         a++++a  +++f+++     + +++v     
  gi|121637280|ref|YP_977503.1| 361 TTAIVGPSGCGKSTILALI---AGLHQP-----TRGRVLIDGtdvATLDARAQQAVCSVVFQHPYLFHGTIRDNVFAADP 432
                                    689***********99888...564333.....33444444444456678888888888888887764444444444433 PP

                                    EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkgeseykingkevtkkevsellesagiske.....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                      +++  +++   + ++  e+   l++   ++      +LSgGe++ v++a        k ap+ l+De  +aLD++n +
  gi|121637280|ref|YP_977503.1| 433 GASDD--QFAQAVRLARVDELIARLPDGANTIVgeagsALSGGERQRVSIAR----ALLKAAPVLLVDEATSALDAENEA 506
                                    33333..45555556666666666665333222334449*******998864....457999****************** PP

                                    HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 178 kvaellkeksknaQfivislreemlekadklvg 210
                                    +v++ l ++  +   +++++r   +++ad+++ 
  gi|121637280|ref|YP_977503.1| 507 AVVDALAADPRSRTRVIVAHRLASIRHADRVLF 539
                                    *******999998899999**999999999875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.1e-06    0.0011      13      44 ..     350     380 ..     348     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                         AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqa 44 
                                    dg ++ +++  +t ++GpsG GKST+l A++a
  gi|121637280|ref|YP_977503.1| 350 DGVSFCLQPGTTTAIVGPSGCGKSTIL-ALIA 380
                                    567778887779**************9.6655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.014       2      24 ..     362     384 ..     361     404 .. 0.83
   2 ?    1.4   0.0      0.23   2.3e+02     250     294 ..     479     524 ..     466     525 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                                    ++++Gp g+GKS++L ++ +l++
  gi|121637280|ref|YP_977503.1| 362 TAIVGPSGCGKSTILALIAGLHQ 384
                                    89******************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                         AAA_21 250 allralkkg.sllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                    +++ral k+ ++ll+DE  + L+ +  + +++ l +  r ++ vi+
  gi|121637280|ref|YP_977503.1| 479 SIARALLKAaPVLLVDEATSALDAENEAAVVDALAADPRSRTRVIV 524
                                    3444444444********9999999999999988766666777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.9   1.4e-05     0.014      17     114 ..     358     514 ..     352     532 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrvi.....glAptgkaAkvLa............................ 63 
                                    +  +++++Gp G GK+t+l+ ++ +++   grv+     +++  ++a +++                             
  gi|121637280|ref|YP_977503.1| 358 PGTTTAIVGPSGCGKSTILALIAGLHQPTRGRVLidgtdVATLDARAQQAVCsvvfqhpylfhgtirdnvfaadpgasdd 437
                                    556899*********************99655553444345555555555544555555555555555444433333221 PP

                         AAA_30  64 .eelgieastiakllkrlk.................................grarlepgtllivDEagmv.dtkqlaal 108
                                      +  ++ +         +                                 +ra l+++ +l+vDEa  + d+++ aa+
  gi|121637280|ref|YP_977503.1| 438 qFAQAVRLA---------RvdeliarlpdgantivgeagsalsggerqrvsiARALLKAAPVLLVDEATSAlDAENEAAV 508
                                    112223333.........14444445558999999999999999999999987788888899999998665588888888 PP

                         AAA_30 109 lkaaek 114
                                    ++a+++
  gi|121637280|ref|YP_977503.1| 509 VDALAA 514
                                    777665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.068        67     245     268 ..     359     382 ..     352     408 .. 0.74
   2 !   12.8   0.1   3.9e-05     0.039     299     352 ..     445     499 ..     436     513 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.068
                                    S.EEEEEE-TTSSHHHHHHHHHHCC CS
                     ABC_ATPase 245 G.vtlIvGggfhGKsTLLeAlekGv 268
                                    G  t+IvG+   GKsT+L Al +G 
  gi|121637280|ref|YP_977503.1| 359 GtTTAIVGPSGCGKSTIL-ALIAGL 382
                                    54799***********99.555665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.9e-05
                                    EE--TTTB---CCC--STTEEESS-.-HHHHHHHHHHHHHHTT-SEEEEEGGGS- CS
                     ABC_ATPase 299 gvDispFinnLPegkdttkfstedA.SGStsqAanimealeagakllLiDEDtsA 352
                                     + +   i +LP g++t       A SG   q ++i++al   a++lL+DE tsA
  gi|121637280|ref|YP_977503.1| 445 LARVDELIARLPDGANTIVGEAGSAlSGGERQRVSIARALLKAAPVLLVDEATSA 499
                                    5557789**********977777766****************************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.4e-06    0.0064      21      39 ..     361     379 ..     346     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
                         AAA_23  21 ltlItGpNGaGKTTildAi 39 
                                     t+I+Gp G+GK+Til  i
  gi|121637280|ref|YP_977503.1| 361 TTAIVGPSGCGKSTILALI 379
                                    68**************887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       9.9   9.9e+03     130     132 ..     200     202 ..     167     234 .. 0.55
   2 !   16.9   3.6   6.2e-06    0.0062      25     143 ..     360     542 ..     355     555 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.9
                         AAA_16 130 lsr 132
                                    +++
  gi|121637280|ref|YP_977503.1| 200 ART 202
                                    221 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.2e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql....esa..........ipysalaqalareellrqlldeae 90 
                                      + ++G+sG+GKs+++  ++   + ++g +l   +d      + a           py  +  ++ r+ ++++   +++
  gi|121637280|ref|YP_977503.1| 360 TTTAIVGPSGCGKSTILALIAGLHQPTRGRVLIDGTDVAtldaR-AqqavcsvvfqHPY-LFHGTI-RDNVFAADPGASD 436
                                    56789***************975555555553333333313321.12233443443333.233333.4444444444444 PP

                         AAA_16  91 saeleawrekleeala.......................................................avpelagae 115
                                    ++ ++a r +  ++l                                                         v++la++ 
  gi|121637280|ref|YP_977503.1| 437 DQFAQAVRLARVDELIarlpdgantivgeagsalsggerqrvsiarallkaapvllvdeatsaldaeneaaVVDALAADP 516
                                    44444444333333335666666664444334444444444444445555555555555444444444333333333333 PP

                         AAA_16 116 asrllellkrllallsrderplvlvlDd 143
                                    +sr +  +++ la +++ ++  vl++Dd
  gi|121637280|ref|YP_977503.1| 517 RSRTRVIVAHRLASIRH-AD-RVLFVDD 542
                                    35555555555555555.33.4666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00022      0.22       7      29 ..     361     383 ..     357     413 .. 0.80
   2 ?    2.0   0.0      0.23   2.3e+02      81     107 ..     479     503 ..     448     541 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                         AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                     ++++G+sG+GK+t l+ ++  +
  gi|121637280|ref|YP_977503.1| 361 TTAIVGPSGCGKSTILALIAGLH 383
                                    579************99887766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.23
                         AAA_22  81 aleqalraravielliiDEaqh.lrsee 107
                                     +++al ++a   +l++DEa   l+ +e
  gi|121637280|ref|YP_977503.1| 479 SIARALLKAAP--VLLVDEATSaLD-AE 503
                                    56666666666..9******88774.33 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.018      96     122 ..     355     382 ..     341     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                    HCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpe 122
                                     l+   t+++vG+SG GKSt++  +++ 
  gi|121637280|ref|YP_977503.1| 355 CLQPgTTTAIVGPSGCGKSTILALIAGL 382
                                    56655899**************988874 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.8   4.3e-05     0.042       5     267 ..      21     280 ..      17     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   5 illailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkki 84 
                                     lla+++ v+  +  ++l  ++  l++   p+     +++ +l ++++a ++l  +  ++ + +g  + ++ + ++ +++
  gi|121637280|ref|YP_977503.1|  21 ALLAFCSVVARAVGTVLLVPLMAALFG-EAPQR--AWLWLGWLSAATVAGWVLDAVTARIGIELGFAVLNHTQHDVADRL 97 
                                    567777777777888888888888887.55555..577777777777778888888888888888888888888888888 PP

                                    HCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  85 lrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviaki 164
                                        + +f   ++ +  + ++     l  ++ + +  ++ ++l+  ++ + ++ ++w+l ++ la +pl++   +  a +
  gi|121637280|ref|YP_977503.1|  98 PVVRLDWFTAENTATARQAIAATGPELVGLVVNLVTPLTSAILLPAVIALALLPISWQLGVAALAGVPLLLGALWASAAF 177
                                    888888888888888888888888888888888888888888888888888888************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 165 lkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalalw 244
                                     +++     ka+  ++  ++E  +  + ++a +r e  ++   +al + ++a+++ + ++   +  + +++ l+ ++ + 
  gi|121637280|ref|YP_977503.1| 178 ARRADTAADKANTALTERIIEFARTQQALRAARRVEPARSLVGNALASQHTATMRLLGMQIPGQLLFSIASQLALIVLAG 257
                                    *******************************************************9999987777777777777777777 PP

                                    HHHHHHHTTSSTHHHHHHHHHHH CS
                   ABC_membrane 245 fGttlvisgelsvgdlvvflslf 267
                                      ++l i+g+l+v +++++++ +
  gi|121637280|ref|YP_977503.1| 258 TTAALTITGTLTVPEAIALIVVM 280
                                    7889999********99998876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.8   1.7e+03      94     121 ..      90     117 ..      84     127 .. 0.85
   2 ?   10.1   0.1   0.00066      0.66       4      75 ..     364     463 ..     362     541 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
                         AAA_33  94 rlgvpvrivvvetdeetlkeRlakRaan 121
                                    +++v++r+ vv+ d++t++    +R+a 
  gi|121637280|ref|YP_977503.1|  90 QHDVADRLPVVRLDWFTAENTATARQAI 117
                                    799999999*********9999999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                         AAA_33   4 lvGlpGsGKstlaerl...lkklg.avllssdt..........................lrrrlfgtdqqsktdytrvld 53 
                                    +vG++G+GKst +  +   ++++   vl++  +                          +r+++f+ d+    d+   + 
  gi|121637280|ref|YP_977503.1| 364 IVGPSGCGKSTILALIaglHQPTRgRVLIDGTDvatldaraqqavcsvvfqhpylfhgtIRDNVFAADPGASDDQFAQAV 443
                                    79*********876552215555466666554467777788888888888888887777555555543333333222222 PP

                         AAA_33  54 rlyqilnelarkalsagrnvil 75 
                                    rl  ++ el+  +l  g+n+i+
  gi|121637280|ref|YP_977503.1| 444 RLA-RVDELI-ARLPDGANTIV 463
                                    222.233444.24444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.12      50      70 ..     364     384 ..     350     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                          Rad17  50 isGPsGCgkstvvkvLskelg 70 
                                    i GPsGCgkst++  ++  + 
  gi|121637280|ref|YP_977503.1| 364 IVGPSGCGKSTILALIAGLHQ 384
                                    89**********998887665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.18      21      55 ..     364     398 ..     358     412 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlR 55 
                                    ++G +G+GKs++++l++  ++++++ v +d++d+ 
  gi|121637280|ref|YP_977503.1| 364 IVGPSGCGKSTILALIAGLHQPTRGRVLIDGTDVA 398
                                    7899**************************99875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00028      0.28       4      35 ..     348     380 ..     347     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                    HHHHHS-EBT.T-EEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   4 vlDalfpivq.GqrtlipgafgvGktvisqsls 35 
                                    vlD +  + q G +t+i+g +g+Gk++i++ ++
  gi|121637280|ref|YP_977503.1| 348 VLDGVSFCLQpGTTTAIVGPSGCGKSTILALIA 380
                                    567665555549999*************98876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.37   3.7e+02      14      36 ..      44      66 ..      36      69 .. 0.81
   2 ?   10.5   0.5   0.00032      0.32      30      53 ..     356     379 ..     347     507 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.37
                         AAA_25 14 dlaapppprrwlvkgllpagela 36
                                   +l  + p+r wl+ g+l a ++a
  gi|121637280|ref|YP_977503.1| 44 ALFGEAPQRAWLWLGWLSAATVA 66
                                   5667889**********988776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                         AAA_25  30 lpagelallaGapgtGKttlaldl 53 
                                    l  g++++++G++g+GK+t++  +
  gi|121637280|ref|YP_977503.1| 356 LQPGTTTAIVGPSGCGKSTILALI 379
                                    67899**************98654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.25      25      48 ..     361     384 ..     351     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                         AAA_15  25 ltvliGkNnsGKSsilealdlFln 48 
                                    +t ++G+ ++GKS+il ++  + +
  gi|121637280|ref|YP_977503.1| 361 TTAIVGPSGCGKSTILALIAGLHQ 384
                                    79***************9976655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.8    0.0066       6.6      25      89 ..     462     513 ..     444     514 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0066
                        SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     + +  ++lSGGe+q    + +a a   l++          +++ DEA s lD+e+ a+++++l+
  gi|121637280|ref|YP_977503.1| 462 IVGEAGSALSGGERQ---RVSIARA---LLKA-------APVLLVDEATSALDAENEAAVVDALA 513
                                    555566677777773...2333322...3333.......246899***********999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3710.36
//
Query:       gi|121637281|ref|YP_977504.1|  [L=247]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-65  220.4   8.1    2.9e-65  220.1   8.1    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.1e-55  188.2   6.1    1.3e-55  187.9   6.1    1.1  1  adh_short     short chain dehydrogenase
    1.4e-20   73.9   3.7    2.2e-20   73.3   3.7    1.3  1  KR            KR domain
  ------ inclusion threshold ------
       0.21   10.6   1.5       0.26   10.2   1.5    1.2  1  3Beta_HSD     3-beta hydroxysteroid dehydrogenase/isomerase f


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   8.1   6.5e-69   2.9e-65       1     232 [.      14     244 ..      14     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 6.5e-69
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E...EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v...lecDVtdeeqvealveevvekfgklDilvnn 76 
                                    G a+g+G ai +++ +eGa+vvl d+n ea   +e +a++lg + v   ++cDVt+ ++v+ l++++ve+fg+lD++vnn
  gi|121637281|ref|YP_977504.1|  14 GGAQGLGLAIGQRFVAEGARVVLGDVNLEA---TEVAAKRLGGDdValaVRCDVTQADDVDILIRTAVERFGGLDVMVNN 90 
                                    6689*************************9...5555666664443356******************************* PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtry 154
                                    agi+++  + + ++++e+fd++++v l+++++ ++ a+ +m+e+  g+ivn+ssv++++++ +++ y+aaKa+++++t++
  gi|121637281|ref|YP_977504.1|  91 AGITRD--ATMRTMTEEQFDQVIAVHLKGTWNGTRLAAAIMRERkrGAIVNMSSVSGKVGMVGQTNYSAAKAGIVGMTKA 168
                                    ******..9999***************************9998889********************************** PP

                                    HHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    +A+el++ giRvNa++pg+i+  ++++++  +++ ++  a+ p+gr+g+p+eva++a+fLasd++sy+tG++l v gG
  gi|121637281|ref|YP_977504.1| 169 AAKELAHLGIRVNAIAPGLIRSAMTEAMP--QRIWDQKLAEVPMGRAGEPSEVASVAVFLASDLSSYMTGTVLDVTGG 244
                                    ****************************9..89999999**************************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   6.1   2.8e-59   1.3e-55       2     190 ..       9     196 ..       8     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 2.8e-59
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    ++++tG+++G+G+ai +++++eGa+vv+ d + e+ e +ak l+ + + ala+++Dvt++++v+ l+++av+++g+ldv+
  gi|121637281|ref|YP_977504.1|   9 TAVITGGAQGLGLAIGQRFVAEGARVVLGDVNLEATEVAAKRLGGD-DVALAVRCDVTQADDVDILIRTAVERFGGLDVM 87 
                                    79*****************************************985.88******************************* PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                    vnNAGit+++++  ++ee++++vi+v l+g+ + tr+++  m ++++G+Ivn+sSv gkv++ g++ YsA+Ka+++g+t+
  gi|121637281|ref|YP_977504.1|  88 VNNAGITRDATMRTMTEEQFDQVIAVHLKGTWNGTRLAAAIMRERKRGAIVNMSSVSGKVGMVGQTNYSAAKAGIVGMTK 167
                                    ******************************************************************************** PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmakel 190
                                    ++akela  girvna+aPGl++++m+++ 
  gi|121637281|ref|YP_977504.1| 168 AAAKELAHLGIRVNAIAPGLIRSAMTEAM 196
                                    *************************9876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   3.7   4.9e-24   2.2e-20       3     173 ..      10     183 ..       8     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 4.9e-24
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     +itGG+ gLGl++ +  +++gar  v+l+    + e+ +   ++l   ++   +v++Dv+++d+v  l++++ ++++ +
  gi|121637281|ref|YP_977504.1|  10 AVITGGAQGLGLAIGQRFVAEGAR--VVLGDV--NLEATEVAAKRLGGDDVAL-AVRCDVTQADDVDILIRTAVERFGGL 84 
                                    68*********************9..556666..3344444567777766665.679*********************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHH.... CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNa.... 154
                                       ++ Ag++rd+++ +mt+e+++qv+a  +kG+wn  +l +     ++   +v +SS++g +g+ gq+nY+aa a    
  gi|121637281|ref|YP_977504.1|  85 DVMVNNAGITRDATMRTMTEEQFDQVIAVHLKGTWNGTRLAAAimreRKRGAIVNMSSVSGKVGMVGQTNYSAAKAgivg 164
                                    ***********************************9655544333359999***********************872222 PP

                                    HHHHHHHHHHHHHHTEEEE CS
                             KR 155 flDalaeyrrsqglpavsi 173
                                    +  a a++ +++g ++ +i
  gi|121637281|ref|YP_977504.1| 165 MTKAAAKELAHLGIRVNAI 183
                                    3344555555555555555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   5.9e-05      0.26       1      98 [.      11     120 ..      11     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.9e-05
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkle....eale...gvdvv 70 
                                    v+tGga  lG a+ +++v ++    v   D++ + +    +++++ ++    + +Dvt++d+++     a+e   g dv+
  gi|121637281|ref|YP_977504.1|  11 VITGGAQGLGLAIGQRFVAEGA--RVVLGDVNLEATE-VAAKRLGGDDvalAVRCDVTQADDVDilirTAVErfgGLDVM 87 
                                    79******************95..7778887765444.355666666656799********98622224544444789** PP

                      3Beta_HSD  71 ihlaslvd.....vagkltedeimkvnvkGTrn 98 
                                    +  a+++       + + ++d++  v +kGT n
  gi|121637281|ref|YP_977504.1|  88 VNNAGITRdatmrTMTEEQFDQVIAVHLKGTWN 120
                                    999998742221134467788999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1852.06
//
Query:       gi|121637282|ref|YP_977505.1|  [L=109]
Description: hypothetical protein BCG_1413 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 788.08
//
Query:       gi|121637283|ref|YP_977506.1|  [L=123]
Description: hypothetical protein BCG_1414 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 934.03
//
Query:       gi|121637284|ref|YP_977507.1|  [L=261]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-14   52.7   0.0    5.7e-14   52.2   0.0    1.3  1  TetR_C_1  Tetracyclin repressor-like, C-terminal domain
    8.8e-12   44.6   0.0    1.9e-11   43.5   0.0    1.6  1  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_C_1  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   6.3e-18   5.7e-14       5     139 ..      83     222 ..      79     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 6.3e-18
                                    TS.-HHHHHHHHHHHHHHHHHTSTTHHHHHHT-SS--HHHHHH....HHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHH CS
                       TetR_C_1   5 ge.dWrerlrelarslrrallrhrdlarlfagtprlspnelrg....mErlLrllrdaGlsdedavyalslisnFvvGav 79 
                                    ++ dWre lr+ ars+r+++ + + l  l + +  lsp++ r+    mE+ ++ l  aGls+eda+ + s++s  v G+v
  gi|121637284|ref|YP_977507.1|  83 EAgDWRETLRNHARSMRKTFADNPVLCDLILIRAALSPKTARLgaqeMEKAIANLVTAGLSLEDAFDIYSAVSVHVRGSV 162
                                    6669**********************************998755555********************************9 PP

                                    .HHHHHHHSTT--STT-HHHHHHH--TTT-HHHHHHHH...HHT---HHHHHHHHHHHHHH CS
                       TetR_C_1  80 .leeqsgledaeeraeqeavleealepgeypllaealelaeiltsedsdaaFefGLellld 139
                                     l++ s+  + + +   +     a +p++ plla a  ++  +++   ++ Fe GLe +ld
  gi|121637284|ref|YP_977507.1| 163 vLDRLSRKSQSAGSGPSAIEHPVAIDPATTPLLAHATGRGHRIGA-PDETNFEYGLECILD 222
                                    89****99999999999999*****************99999998.55678*********8 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.1e-15   1.9e-11       1      47 []      21      67 ..      21      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.1e-15
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   I+++A el ++  +d+++++ + k++Gv+  ++Y+yF+ K++Ll+a+
  gi|121637284|ref|YP_977507.1| 21 IISGAFELAQQVSIDNLSMPLLGKHLGVGVTSIYWYFRKKDDLLNAM 67
                                   89******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1913.43
//
Query:       gi|121637285|ref|YP_977508.1|  [L=623]
Description: hypothetical protein BCG_1416c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-67  226.1   0.0    8.2e-67  225.2   0.0    1.5  1  EAL           EAL domain
    2.7e-39  134.5   0.0    4.6e-39  133.7   0.0    1.4  1  GGDEF         Diguanylate cyclase, GGDEF domain
    3.7e-08   33.7   0.2    1.2e-07   32.1   0.2    1.9  1  GAF_2         GAF domain
    5.4e-07   30.3   0.2    2.4e-06   28.2   0.0    2.2  2  GAF           GAF domain
     0.0066   16.8   0.1      0.064   13.6   0.0    2.4  2  GAF_3         GAF domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.046   13.2   0.0    1.7  1  Autoind_bind  Autoinducer binding domain


Domain annotation for each model (and alignments):
>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.2   0.0   2.7e-70   8.2e-67       4     238 .]     361     595 ..     358     595 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 2.7e-70
                                    HHHHCCTT-EEEEEEEEEESSS-SSEEEEEEEEEEECTTCEE-CCCCHHHHHHCTCHHHHHHHHHHHHHHHHHHHHCH.T CS
                            EAL   4 lrealenkelalyyQPvvdlktgkvvgleallrwqhpdgglispeeflplaerlgllaeldrwvleqalqdlrrlaeq.l 82 
                                    lr+ +e + l+l+y P vdl+tg++vg eal+rwqhp++gl++p+ f+p+ae+ +l+ eldrwvl++a++++++++++ l
  gi|121637285|ref|YP_977508.1| 361 LRRGIESDALRLVYLPEVDLRTGDIVGTEALVRWQHPTRGLLAPGCFIPVAESINLAGELDRWVLRRACNEFSEWQSAgL 440
                                    8999***********************************************************************85557 PP

                                    T--EEEEEE--CHHCC-CCHHHHHHHHHHCCT-GCC-EEEEEEHHHHHHTHHHHH.HHHHHHHCTT-EEEEEEETSSTCC CS
                            EAL  83 dadiklsinlspasladeefleelrellkqsgpspsrLvleitesellarlealqeevlarLralGirialddfgtgyss 162
                                     +d  l in+s+ +l   +f++ +++ + q+g+++s+++leite+ ++++l++++ + larL++ G++ia+ddfgtgys+
  gi|121637285|ref|YP_977508.1| 441 GHDALLRINVSAGQLVTGGFVDFVADTIGQHGLDASSVCLEITENVVVQDLHTAR-ATLARLKEVGVHIAIDDFGTGYSA 519
                                    999999**********************999999999*****************9.************************ PP

                                    CHHHCCC--SEEEE-HHHHTTTTTSCHHHHHHHHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SEE-STTT--- CS
                            EAL 163 lsylarlppdiiKldrslladleedeeaqalvkalialakelgikvvaegVeteeqlealrelgcdlvQGyllskp 238
                                    +s+l+ lp+d++K+d+ ++++l ++ ++  +v+++ +la+ ++++vvaegVete+ ++ l + +c  +QG+l+s+p
  gi|121637285|ref|YP_977508.1| 520 ISLLQTLPIDTLKIDKTFVRQLGTNTSDLVIVRGIMTLAEGFQLDVVAEGVETEAAARILLDQRCYRAQGFLFSRP 595
                                    ***************************************************************************9 PP

>> GGDEF  Diguanylate cyclase, GGDEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   0.0   1.5e-42   4.6e-39       1     160 [.     184     338 ..     184     339 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 1.5e-42
                                    HSB-CCCGSEEHHHHHHHHHHHHHCCHHCTSEEEEEEEEETTHHHHHHHH-HHHHHHHHHHHHHHHHCCS-TTSEEEEES CS
                          GGDEF   1 aahDslTgLpNRrlleeeleqelqrarreqkslavllldldnFkkindtyGhsvGDevLqevakrLssslrksdlvaRlg 80 
                                    a+hD lTgL+NRr+l ++l+q+l+  +    ++a l+ldld++k+ind +Gh++GD++++ +a+r+ ++l  + l+aRlg
  gi|121637285|ref|YP_977508.1| 184 ADHDDLTGLHNRRALLQHLDQRLAPGQ--PGPVAALFLDLDRLKAINDYLGHAAGDQFIHVFAQRIGDALVGESLIARLG 261
                                    68***********************95..59************************************************* PP

                                    SSEEEEEEECSSHHHHHHHHHHHHHHHHCS-EEETTCCEEE---EEEEEEEE..-TTS-HHHHHHHHHHHHHHHHHCTSS CS
                          GGDEF  81 gdeFaillpetsseeaaelaerirrllaklkepvelsgeelyvtisiGialappeegedleellkeAdealyeaKkagrn 160
                                    gdeF+++  +    +a++++++++rl ++lk++v+++ge l+ t+siG+a+  +  ++++++ll++Ad+a  +aK+ag +
  gi|121637285|ref|YP_977508.1| 262 GDEFVLIPASPM--SADAAQPLAERLRDQLKDHVAIGGEVLTRTVSIGVASG-TPGQHTPSDLLRRADQAALAAKHAGGD 338
                                    ****99955555..58************************************.6**********************9975 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.2     4e-11   1.2e-07       2     136 ..      27     170 ..      26     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4e-11
                                    HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.--...-TT.H.HHHHHHHTS-EEES-. CS
                          GAF_2   2 adleelldlvldelve.lgaalgyillvdddgglrlaawgeaeeefgaaldr.pl...geg.l.vgealrtgrpvilnd. 73 
                                    a+  e+ ++vl +lve lg++++++   d d++ + +++  +++     +d+ +l   +++ + ++ + + ++p+++   
  gi|121637285|ref|YP_977508.1|  27 ATSAEVSQRVLAYLVEqLGVDVSFLRHNDRDRRATRLVAEWPPRLNIPDPDPlRLiyfADAdPvFALCEHAKEPLVFRPe 106
                                    67789*********9989***********999977778888888888888777445666666757777777899998776 PP

                                    GGG.-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                          GAF_2  74 lee.dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136
                                    +++ d+ +  ++a+++++ s +avPl+s++ + G l++  ++++++ e++l  L ++a++ a++
  gi|121637285|ref|YP_977508.1| 107 PATeDYQRLIEEARGVPVTSAAAVPLVSGEITTGLLGFIKFGDRKWHEAELNALMTIATLFAQV 170
                                    666355555555****************878*******9999999**************99975 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.0         6   1.8e+04     118     129 ..      10      21 ..       7      23 .. 0.76
   2 !   28.2   0.0   8.1e-10   2.4e-06       4     131 ..      31     169 ..      28     170 .. 0.68

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 6
                                    HHHHHHHHHHHH CS
                            GAF 118 elellqvladqv 129
                                     +el++++a+q+
  gi|121637285|ref|YP_977508.1|  10 LEELVTTVANQL 21 
                                    578999999987 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 8.1e-10
                                    HHHHHHHHHHHHHHTESEEEEEE.EEETTEEE.............CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGT CS
                            GAF   4 elldtvveelrellgadrvalyl.pdydGlhy.............dipqasrwlfmkngrgicgqvlatgqplvipdstp 69 
                                    e++++v++ l e lg+d   l + +d+d  ++             + p+ +r ++  + +++++ + + ++plv+    p
  gi|121637285|ref|YP_977508.1|  31 EVSQRVLAYLVEQLGVDVSFL-RhNDRDR-RAtrlvaewpprlniPDPDPLRLIYFADADPVFALCEHAKEPLVFR---P 105
                                    688999999999999998888.3223333.2222233233333222223333344444555666999999******...9 PP

                                    STTHHTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE..SSSCSHHHHHHHHHHHHHHHHH CS
                            GAF  70 dprfaqy.nrrdllenmgirsslvvPlvndgelwGllvlhn..psppftreelellqvladqvav 131
                                    +p   +y +  + +++  + s+++vPlv+++ + Gll ++    + +++++el+ l+++a++ a+
  gi|121637285|ref|YP_977508.1| 106 EPATEDYqRLIEEARGVPVTSAAAVPLVSGEITTGLLGFIKfgDR-KWHEAELNALMTIATLFAQ 169
                                    99988876555666666666********98777777777774335.5*************99886 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.1e-05     0.064       4     122 ..      31     166 ..      28     170 .. 0.77
   2 ?    0.1   0.0      0.32   9.4e+02       9      55 ..     281     328 ..     253     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                          GAF_3   4 ellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvse............ps 71 
                                    e+ + +l +lv+ lg++v++l   d+d++  + +a w   p+l  +++ +++l    ++   +v++            p+
  gi|121637285|ref|YP_977508.1|  31 EVSQRVLAYLVEQLGVDVSFLRHNDRDRRATRLVAEW--PPRL--NIPDPDPLRLIYFADADPVFAlcehakeplvfrPE 106
                                    78899999**********9999999999999999***..7777..88888888887777777777778888888666744 PP

                          GAF_3  72 faeedg.........lpdraalavPLvagrqviGvlalastkprafdaedlelleslArq 122
                                     a ed+          p ++a avPLv+g+ + G+l++   ++r++ +++l  l ++A++
  gi|121637285|ref|YP_977508.1| 107 PATEDYqrlieeargVPVTSAAAVPLVSGEITTGLLGFIKFGDRKWHEAELNALMTIATL 166
                                    433333334433334888************999999988888888999999888887765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.32
                          GAF_3   9 llkllvkllgaevgalllldedgnklqvaagwdgkpalsesld.edsa 55 
                                    l+++l + l+  v++ +++ ++  ++ va+g+ g++ +s  l+ +d+a
  gi|121637285|ref|YP_977508.1| 281 LAERLRDQLKDHVAIGGEVLTRTVSIGVASGTPGQHTPSDLLRrADQA 328
                                    566777777777777777777888888888888888888766642222 PP

>> Autoind_bind  Autoinducer binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.046      55     142 ..      84     167 ..      80     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                    GGGT-HHHHHHHHCSSEEEEECGGCCCCCSHHHHHHHHHHHHTT-SEEEEEEEEETTSSEEEEEEEESSSSCCHHHHHH. CS
                   Autoind_bind  55 ylaiDPvvreaarssspfvWsddllaaelspaarrfldeardfGlrsGltvpvhgprgrlaalslageerdldaaeaae. 133
                                    +++ DPv++ + ++ +p+v + ++ +    ++ +r+++ear   ++s  +vp+ + +  +++l ++ +  d+ ++ea   
  gi|121637285|ref|YP_977508.1|  84 FADADPVFALCEHAKEPLVFRPEPAT----EDYQRLIEEARGVPVTSAAAVPLVSGEITTGLLGFI-KFGDRKWHEAELn 158
                                    5678******************9999....5569*****************************995.5555567655444 PP

                                    HHHHHHHHH CS
                   Autoind_bind 134 ararlqlla 142
                                    a++ + +l 
  gi|121637285|ref|YP_977508.1| 159 ALMTIATLF 167
                                    544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 4051.21
//
Query:       gi|121637286|ref|YP_977509.1|  [L=715]
Description: hypothetical protein BCG_1417c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-25   87.8   0.0      9e-25   87.4   0.0    1.2  1  ThiF            ThiF family
    1.5e-06   28.4   3.9      0.021   14.9   0.2    3.2  3  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
       0.14   11.4   0.1       0.28   10.5   0.1    1.4  1  Cellulase-like  Sugar-binding cellulase-like


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   1.5e-28     9e-25       2     144 ..      90     230 ..      89     464 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.5e-28
                                    HHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTT.TEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   2 srqlallgedgqekLrdskvllvGaGglGsellknLalsGv.gkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    +r++ l+  + q++L++ +v +vG+ + G+ ++ +La+ G  g l+l+D+DkielsNlnR +  +  diG +Ka+ aa++
  gi|121637286|ref|YP_977509.1|  90 DRNRHLITAEEQRALHALRVGVVGLSA-GHAIAYTLAAEGAcGTLRLADFDKIELSNLNRVPV-GVFDIGLNKAMIAARR 167
                                    688888889****************87.9*******997754*********************.**************** PP

                                    HHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  81 lqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlg 144
                                    ++e+ p++ v  vt  +++e+ ++e+l ++D+V+  +D++++++++ +a++ +g+p++ a+  +
  gi|121637286|ref|YP_977509.1| 168 IAELDPYLAVDLVTSGLSPES-VDEFLDGLDVVIEECDSLDIKVILRQAACARGVPVLMATSDR 230
                                    *******************98.69********************************99876655 PP

>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   3.6e-06     0.021      24      44 ..     374     394 ..     365     413 .. 0.78
   2 ?    0.8   0.3     0.073   4.4e+02     104     133 ..     406     435 ..     398     441 .. 0.84
   3 !   12.1   0.0   2.5e-05      0.15      83     143 ..     596     646 ..     513     659 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-06
                                    HHHHHTS--GGG---EEEEEE CS
                 Nitroreductase  24 leaarraPsagnlqpwrfvvv 44 
                                     +aa raPs+gn qpw++v+ 
  gi|121637286|ref|YP_977509.1| 374 AQAAIRAPSGGNVQPWHVVAK 394
                                    467899************986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.073
                                    --HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                 Nitroreductase 104 erkaaerayryalldagaaaqnllLaAtal 133
                                    ++ a++ a r +++ +gaa+ n  +aA+a+
  gi|121637286|ref|YP_977509.1| 406 HTSAMDIAFRGSAVAVGAAMFNARVAAAAH 435
                                    56678899999**************99986 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GG CS
                 Nitroreductase  83 aqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggf 143
                                    +++++  + +l ++          + ++a+ ++++  g a+q +++ A+ +Gl+++p++ +
  gi|121637286|ref|YP_977509.1| 596 TNERVSASSALAIV----------YVDGATLTDFARGGSAMQAVWIVAQQHGLAVQPMSPI 646
                                    55555555555555..........77889999999***********************965 PP

>> Cellulase-like  Sugar-binding cellulase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.7e-05      0.28      23      53 ..      74     104 ..      59     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.7e-05
                                    HHHHHHHHTT--EEEEE--HHHHHH-TT-EE CS
                 Cellulase-like  23 rvldelkeRGydavRiDafPHLlaadaerew 53 
                                     v+  l  RG+ avR+D   HL++a+++r  
  gi|121637286|ref|YP_977509.1|  74 MVVAILGPRGFRAVRLDRNRHLITAEEQRAL 104
                                    35566778******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4923.31
//
Query:       gi|121637287|ref|YP_977510.1|  [L=263]
Description: hypothetical protein BCG_1418c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1927.61
//
Query:       gi|121637288|ref|YP_977511.1|  [L=307]
Description: hypothetical protein BCG_1419c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-65  219.0   0.0    7.6e-65  218.8   0.0    1.1  1  EAL       EAL domain


Domain annotation for each model (and alignments):
>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   4.2e-69   7.6e-65       4     237 ..      61     298 ..      58     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 4.2e-69
                                    HHHHCCTT-EEEEEEEEEESSS-SSEEEEEEEEEEECTTCEE-CCCCHHHHHHCTCHHHHHHHHHHHHHHHHHHHHCH.T CS
                            EAL   4 lrealenkelalyyQPvvdlktgkvvgleallrwqhpdgglispeeflplaerlgllaeldrwvleqalqdlrrlaeq.l 82 
                                    +r al+++e++l+yQP+++l++++++g+eallrw+hp++g++ p++f+  ae++gl+  l+ +vleqa++++r+++++  
  gi|121637288|ref|YP_977511.1|  61 MRVALDRGEFFLVYQPIIRLADNRIIGAEALLRWEHPTLGTLLPGRFIDRAENNGLMVPLTAFVLEQACRHVRSWRDHsT 140
                                    6889***********************************************************************95546 PP

                                    T--EEEEEE--CHHCC-CCHHHHHHHHHHCCT-GCC-EEEEEEHHHHHHTHHHHH.HHHHHHHCTT-EEEEEEETSSTCC CS
                            EAL  83 dadiklsinlspasladeefleelrellkqsgpspsrLvleitesellarlealqeevlarLralGirialddfgtgyss 162
                                    d++  +s+n+s++++ d++fl  ++ +l ++g+++ +L le++e++ l+r+e++    l++L+alG+ ia+ddfg g+ss
  gi|121637288|ref|YP_977511.1| 141 DPQPFVSVNVSASTICDPGFLVLVEGVLGETGLPAHALQLELAEDARLSRDEKAV-TRLQELSALGVGIAIDDFGIGFSS 219
                                    777777**********************999999999*****************9.************************ PP

                                    CHHHCCC--SEEEE-HHHH....TTTTTSCHHHHHHHHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SEE-STTT-- CS
                            EAL 163 lsylarlppdiiKldrsll....adleedeeaqalvkalialakelgikvvaegVeteeqlealrelgcdlvQGyllsk 237
                                    l+yl rlp+d++Kl + ++     d++    + ++++a+i+l  +lgi+v a+ Ve+++q+ +lr+ gc  +QG++++k
  gi|121637288|ref|YP_977511.1| 220 LAYLPRLPVDVVKLGGKFIecldGDIQARLANEQITRAMIDLGDKLGITVTAKLVESPSQAARLRAFGCKAAQGWHFAK 298
                                    *******************888888888888999*******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2362.21
//
Query:       gi|121637289|ref|YP_977512.1|  [L=1159]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-16   58.5   0.0    8.2e-16   57.3   0.0    1.7  1  GerE          Bacterial regulatory proteins, luxR family
     0.0002   21.0   0.0    0.00054   19.6   0.0    1.8  1  Sigma70_r4_2  Sigma-70, region 4
    0.00025   21.5   0.2    0.00025   21.5   0.2    3.8  4  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.027   14.6   0.4       0.27   11.3   0.1    2.8  2  ANAPC5        Anaphase-promoting complex subunit 5
      0.027   13.7   0.0      0.078   12.1   0.0    1.8  1  NB-ARC        NB-ARC domain
      0.078   13.4   0.2       0.21   12.1   0.2    1.7  1  HTH_40        Helix-turn-helix domain
       0.22   11.4   3.4       0.23   11.3   0.0    2.9  3  HTH_23        Homeodomain-like domain


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   3.2e-19   8.2e-16       2      56 ..    1099    1153 ..    1098    1154 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.2e-19
                                     SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHH CS
                           GerE    2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrl 56  
                                      L++ E ++ +l++eG+ +k+IA++l++S++TV++h+++i++KL+v+srv+lv+ 
  gi|121637289|ref|YP_977512.1| 1099 ALTPAEHKIVKLVTEGLVTKDIAARLFVSPRTVQTHLTHIYTKLDVTSRVQLVQE 1153
                                     69**************************************************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00054      10      54 .]    1099    1142 ..    1098    1142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                     TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54  
                                     +L++ + +i+ l   egl +k+IA++l +s++tV+++l     kL
  gi|121637289|ref|YP_977512.1| 1099 ALTPAEHKIVKL-VTEGLVTKDIAARLFVSPRTVQTHLTHIYTKL 1142
                                     699*********.89***********************9877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   9.7e-08   0.00025       2      51 ..     270     314 ..     269     473 .. 0.73
   2 ?   -3.3   0.1       4.1   1.1e+04      99     132 ..     621     655 ..     565     659 .. 0.54
   3 ?    0.1   0.1      0.35   8.9e+02      64     122 ..     750     813 ..     715     828 .. 0.66
   4 ?   -1.2   0.2      0.88   2.3e+03     119     156 ..     959     991 ..     832    1010 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.7e-08
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                    +vGR++++++++++l +      +lv l+Ge GvGK++l+ +++ a e +
  gi|121637289|ref|YP_977512.1| 270 FVGRDAQINEVQEVLTNY-----RLVTLRGEGGVGKTRLAIQIAAASEFR 314
                                    9*******9999999865.....8****************8888544433 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.1
                         AAA_16  99 ekleealaavpelagaea.srllellkrllallsr 132
                                    ++l++a a++++l++a   sr +  ++++l+l+s 
  gi|121637289|ref|YP_977512.1| 621 QRLLQAEAEIDNLRAAFTwSRGNGDIAAALQLASA 655
                                    22222222445555554466666666666666665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.35
                         AAA_16  64 esaipysalaqalareellrqlldeaesaeleawrekleeala..........avpelagaeasrllel 122
                                    e+a py  +a+a+   el r+++de + ++ ++w+       +          +++ela+++ +r+   
  gi|121637289|ref|YP_977512.1| 750 EAAQPY--FAEAI---ELARAINDEWTLSQIDYWQVVGIFISGqpiplraaaeQARELADSIGNRFVSR 813
                                    456777..99999...89999999988888888887444444466555544444455555555666555 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.88
                         AAA_16 119 llellkrll.allsrderplvlvlDdlqwadeaslqlla 156
                                     +    +l+ al++r +r + +  D+l +a+++ +++ a
  gi|121637289|ref|YP_977512.1| 959 GW----HLMmALIAR-AR-VAIAQDELGKARDDAHAAVA 991
                                    22....333234444.66.88888888888887776655 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.27      43      87 ..     732     779 ..     725     781 .. 0.76
   2 ?   -1.4   0.0      0.96   2.5e+03      44      73 ..    1054    1085 ..    1040    1089 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                         ANAPC5  43 alLnlaslhadf..ghneeAvk.aleeairlArenkDkscLalalawl 87 
                                    a+L+ a + +    g++ eA +  + eai+lAr  +D+ +L+ +++w 
  gi|121637289|ref|YP_977512.1| 732 AVLARALVACGCgsGCDTEAAQpYFAEAIELARAINDEWTLSQIDYWQ 779
                                    5666666665554466666554279**********************6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.96
                         ANAPC5   44 lLnlaslhadf..ghneeAvkaleeairlAre 73  
                                     +L  a+   df    +e A + l eai+ A+ 
  gi|121637289|ref|YP_977512.1| 1054 ALRDAMGDEDFtaAWAEGAAAPLDEAIAYAQR 1085
                                     55555555566323356788889999999986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     3e-05     0.078       2      45 ..     274     312 ..     273     507 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC   2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksd 45 
                                    ++++++v+e L    +    +v+l G gGvGKt la qi   s+
  gi|121637289|ref|YP_977512.1| 274 DAQINEVQEVLT---NYR--LVTLRGEGGVGKTRLAIQIAAASE 312
                                    567888888888...666..99*****************98843 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     8e-05      0.21       6      40 ..    1108    1142 ..    1103    1157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                         HTH_40    6 lelleeglsieeIAkerglkesTIegHLaelieeg 40  
                                      +l+ egl  ++IA++  +++ T+++HL++++ + 
  gi|121637289|ref|YP_977512.1| 1108 VKLVTEGLVTKDIAARLFVSPRTVQTHLTHIYTKL 1142
                                     68999*************************98873 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       3.1   8.1e+03      30      43 ..      15      29 ..      14      32 .. 0.74
   2 ?   -2.9   0.1       2.7   6.9e+03      15      39 ..      38      63 ..      35      66 .. 0.75
   3 ?   11.3   0.0     9e-05      0.23       9      35 ..    1106    1132 ..    1105    1140 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                         HTH_23 30 srrTvyrw..lkryre 43
                                   sr+   rw  ++r+ +
  gi|121637289|ref|YP_977512.1| 15 SRHSALRWarHRRF-A 29
                                   89999999877777.4 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                         HTH_23 15 aeGlsvreIAreLgvsrrTvy.rwlk 39
                                   +  +   +IAr  +++ r ++  w++
  gi|121637289|ref|YP_977512.1| 38 RSLQIADQIARTGHMPVRRLDlIWIS 63
                                   55566679999999999998877776 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 9e-05
                         HTH_23    9 rillllaeGlsvreIAreLgvsrrTvy 35  
                                     +i++l+ eGl +++IA++L vs+rTv+
  gi|121637289|ref|YP_977512.1| 1106 KIVKLVTEGLVTKDIAARLFVSPRTVQ 1132
                                     58999999999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.82u 0.28s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 7325.87
//
Query:       gi|121637290|ref|YP_977513.1|  [L=250]
Description: transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.009   15.7   0.1      0.018   14.6   0.1    1.6  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     1e-06     0.018      73     153 ..      96     163 ..      34     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-06
                  Guanylate_cyc  73 ahaaklaelaLdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseety 152
                                    aha++++ +aL++ +a           + +r+GihtG+   +++     +  + G t nlA+ +  ++++g+  +s +t 
  gi|121637290|ref|YP_977513.1|  96 AHASDAVACALELHQAP-------LSPIVLRIGIHTGEA--QLV----DERIYAGATMNLAAELRDLAHGGQTVMSGATE 162
                                    55566666666554432.......36899********96..455....233477**********************9997 PP

                  Guanylate_cyc 153 e 153
                                    +
  gi|121637290|ref|YP_977513.1| 163 D 163
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1784.14
//
Query:       gi|121637291|ref|YP_977514.1|  [L=340]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-61  208.5   3.3    1.9e-61  208.2   3.3    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   3.3   1.1e-65   1.9e-61      20     312 ..      15     316 ..       3     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 1.1e-65
                 Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgG 99 
                                      l+++++ a+a+E+ Gfd+ w+ae+       +d+f +l  +a++T+r++lgt + ++++r+P+++A   + L+  s+G
  gi|121637291|ref|YP_977514.1|  15 NQLARAADAAVALERNGFDGGWTAEAS------HDPFLPLLLAAEHTSRLELGTNIAVAFARNPMIVANVGWDLQTYSKG 88 
                                    36999**********************......6********************************************** PP

                 Bac_luciferase 100 RfglglgtggpaveerrfGvdhderyarlrEfvevlrrlw....rgeevdfeGeffsv..kgalllprpgqgpiP.vyva 172
                                    R++lglgt+ ++++e+rf++++  + +r+rEfv +lr++w     g +  feGef++   +++  +p+p++ p+P v++a
  gi|121637291|ref|YP_977514.1|  89 RLILGLGTQIRPHIEKRFSMPWGHPARRMREFVAALRAIWlawqDGTKLCFEGEFYTHkiMTPMFTPEPQPYPVPrVFIA 168
                                    ****************************************888444555******88788*********999999***** PP

                 Bac_luciferase 173 aaspaglelaarhadglllag..eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea......ral 244
                                    a+++a+ e+ +++adg l ++  + ++  +  ++ l  g a+ grd+++++v + ++v+ +++++e  a         a+
  gi|121637291|ref|YP_977514.1| 169 AVGEAMTEMCGEVADGHLGHPmvSKRYLTEVSVPALLRGLARSGRDRSAFEVSCEVMVATGADDAELAAACtatrkqIAF 248
                                    *************************************************************9999999999889888888 PP

                 Bac_luciferase 245 iagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagv 312
                                    + ++++y+   e +g+++   e ++ ++ ++w++++ +++de++ a+a+vG+ +++a +l+   e+ v
  gi|121637291|ref|YP_977514.1| 249 YGSTPAYRKVLEQHGWGDLHPELHRLSKLGEWEAMGGLIDDEMLGAFAVVGPVDTIAGALRNRCEGVV 316
                                    88888******************************************************998666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2552.58
//
Query:       gi|121637292|ref|YP_977515.1|  [L=396]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-59  200.9  29.7    2.4e-59  200.0  23.1    2.6  2  PPE       PPE family
    3.2e-17   63.2  13.5    3.2e-17   63.2  13.5    4.8  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0  23.1   2.6e-63   2.4e-59       1     157 [.       6     162 ..       6     163 .. 0.99
   2 !    4.2   0.5    0.0047        42      41      91 ..     238     288 ..     221     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 2.6e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+nsa++yaGpgs++l+aAa+ Wd++a++l saa++++sv+ +l+ ++W G+s+  m+aaa py+aW+s +a qae
  gi|121637292|ref|YP_977515.1|   6 ALPPEINSARMYAGPGSASLVAAAQMWDSVASDLFSAASAFQSVVWGLTVGSWIGSSAGLMVAAASPYVAWMSVTAGQAE 85 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     +Aaq+++aaaaYe+A+  +vpp++ia+nrael+ l+atn++GqntpaIa++eaey emwaqdaaam +Y+a++a+a
  gi|121637292|ref|YP_977515.1|  86 LTAAQVRVAAAAYETAYGLTVPPPVIAENRAELMILIATNLLGQNTPAIAVNEAEYGEMWAQDAAAMFGYAATAATA 162
                                    *************************************************************************9987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0047
                                    HHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  41 lesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaeeaAaqaeaaaa 91 
                                    l+++++ l++     +s  +ma+    +l+  + aaaqa e+Aaq  ++a+
  gi|121637292|ref|YP_977515.1| 238 LSNIVSMLNNHVSMTNSGVSMASTLHSMLKGFAPAAAQAVETAAQNGVQAM 288
                                    56667777777777889999*************************988876 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -14.6  18.7         2   1.8e+04      26      49 ..      79     102 ..      14     213 .. 0.75
   2 ?    2.4   0.9     0.035   3.1e+02      27      43 ..     270     286 ..     227     308 .. 0.53
   3 !   63.2  13.5   3.6e-21   3.2e-17       1      79 [.     309     391 ..     309     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: -14.6 bits;  conditional E-value: 2
                       PE_PPE_C  26 asaaaaalsgttaaaaaaaagaal 49 
                                    ++a  a l+++++  aaaa ++a+
  gi|121637292|ref|YP_977515.1|  79 VTAGQAELTAAQVRVAAAAYETAY 102
                                    223333333333333333333333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.035
                       PE_PPE_C  27 saaaaalsgttaaaaaa 43 
                                    ++aaa++  t+a+ + +
  gi|121637292|ref|YP_977515.1| 270 APAAAQAVETAAQNGVQ 286
                                    22222222222222222 PP

  == domain 3  score: 63.2 bits;  conditional E-value: 3.6e-21
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaa.aaaaaagaalggmPlaaagagga...aggaaprygfrptv 76 
                                    +A lG+Aa+vG+LSVPp+Waaa++a+++aa+al+ t  + aa+ a+g++lgg+Pl+++ ++g+   ++++a+r+ +r+ v
  gi|121637292|ref|YP_977515.1| 309 AANLGRAASVGSLSVPPAWAAANQAVTPAARALPLTSLTsAAQTAPGHMLGGLPLGQLTNSGGgfgGVSNALRMPPRAYV 388
                                    69*******************************888765155567778888****99999999899999*********** PP

                       PE_PPE_C  77 mpr 79 
                                    mpr
  gi|121637292|ref|YP_977515.1| 389 MPR 391
                                    **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2830.08
//
Query:       gi|121637293|ref|YP_977516.1|  [L=220]
Description: hypothetical protein BCG_1424c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.021   15.2   0.2       0.04   14.2   0.2    1.4  1  DUF3239      Protein of unknown function (DUF3239)
       0.08   13.0   0.0       0.23   11.6   0.0    1.6  1  Phage_TAC_9  Phage tail assemb.y chaperone protein, TAC


Domain annotation for each model (and alignments):
>> DUF3239  Protein of unknown function (DUF3239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   4.5e-06      0.04      10      53 ..     158     201 ..     150     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-06
                                    XXXX-EEEEEEEEE-SS-EEEEEEEE-BSSTTS---EEEEEEEE CS
                        DUF3239  10 YdeyeLvPavvaevnprdvvllaLvdiakdeaaepeyalalrtv 53 
                                      + ++v a v+e +p+  v+l++vd +++++ +p++++a+ +v
  gi|121637293|ref|YP_977516.1| 158 KTTAKVVRAAVSELHPDSAVVLVFVDQSTTSKDSPNPSMAASSV 201
                                    5678999****************************988887665 PP

>> Phage_TAC_9  Phage tail assemb.y chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.5e-05      0.23      75      99 ..     106     132 ..     100     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                    Phage_TAC_9  75 tadGktyrL..kpdrlnehfntrrshl 99 
                                     +dG+  +L  +pd+l++ f t rshl
  gi|121637293|ref|YP_977516.1| 106 ASDGTIALLsySPDTLDQDFATARSHL 132
                                    579999999889**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1696.83
//
Query:       gi|121637294|ref|YP_977517.1|  [L=261]
Description: hypothetical protein BCG_1425c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.2   1.8       0.13   12.6   0.4    1.9  2  PBP1_TM   Transmembrane domain of transglycosylase PBP1 at N-
        3.1    8.2  11.0        7.8    6.9   3.5    3.3  3  Toprim_3  Toprim domain


Domain annotation for each model (and alignments):
>> PBP1_TM  Transmembrane domain of transglycosylase PBP1 at N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.5e-05      0.13      20      78 ..      46     107 ..      34     115 .. 0.50
   2 ?   -1.3   0.0      0.33   2.9e+03      34      56 ..     176     198 ..     159     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                        PBP1_TM  20 parkkasrrrrrdddyddeydd..eedDdddddeeeevprkgkkkkpprkkrrw.lwllikl 78 
                                     +r++ +    +d++  +ey d  + +D+dd+d+ e   + + ++++ r++ r+ l  l  +
  gi|121637294|ref|YP_977517.1|  46 LKREALAMAPAEDENVPEEYADweDAEDYDDYDDYEAADQEAARSASWRRRLRVrLPRLSTI 107
                                    44444444444455555555541134566666666666665444554555544335444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                        PBP1_TM  34 dyddeyddeedDdddddeeeevp 56 
                                    ++ d+++++  D+ +  e+++v 
  gi|121637294|ref|YP_977517.1| 176 EFRDDFQQRAADFTKVVEQSKVV 198
                                    56667888888887666665554 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.5   0.00087       7.8      45      88 ..      20      71 ..       9      77 .. 0.81
   2 ?    0.4   0.0     0.094   8.4e+02      58      87 ..     139     168 ..     119     188 .. 0.52
   3 ?    3.7   0.2    0.0088        79       3      33 ..     197     227 ..     195     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00087
                       Toprim_3 45 viaaDnDaand.Greaaeklaerleaagieavllepaege.......Dwndv 88
                                    +aa ++aa++   +aa+++ +r+++  +ea ++ pae+e       Dw d+
  gi|121637294|ref|YP_977517.1| 20 ALAAEAEAAEAeALAAAARARARAARLKREALAMAPAEDEnvpeeyaDWEDA 71
                                   567777777768999*********************5555566666688885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.094
                       Toprim_3  58 eaaeklaerleaagieavllep.aegeDwnd 87 
                                    +aa+ +a + +   i+++ l+  +++eD+  
  gi|121637294|ref|YP_977517.1| 139 RAAAFAAGAKQ-GVINMTSLDFnKAKEDVAR 168
                                    33322222222.2333333333444444443 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0088
                       Toprim_3   3 iivEGietaLsileartgaaviAllsaanlk 33 
                                    +++EG  +a ++++ +++ av+ +  +++++
  gi|121637294|ref|YP_977517.1| 197 VVTEGTVNATAVESMNEHSAVVLVAATSRVT 227
                                    69**********5555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1537  (0.085727); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2029.73
//
Query:       gi|121637295|ref|YP_977518.1|  [L=653]
Description: hypothetical protein BCG_1426c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-41  141.8   0.2    2.7e-40  138.3   0.1    2.2  2  SpoIIE       Stage II sporulation protein E (SpoIIE)
      6e-14   52.1   1.3    1.3e-13   51.0   1.3    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
    7.9e-13   48.6   0.4    3.2e-12   46.7   0.2    2.2  2  PAS_4        PAS fold
    2.2e-11   44.0   7.7    8.5e-11   42.1   1.7    3.4  3  STAS_2       STAS domain
    4.3e-09   36.0   0.0    8.5e-09   35.1   0.0    1.4  1  STAS         STAS domain
     0.0015   18.5   0.0     0.0029   17.6   0.0    1.5  1  PAS          PAS fold
  ------ inclusion threshold ------
       0.01   16.3   1.2        0.1   13.1   0.7    2.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.022   15.0   0.0      0.041   14.1   0.0    1.5  1  PAS_9        PAS domain


Domain annotation for each model (and alignments):
>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.3   0.1   1.2e-43   2.7e-40       2     192 ..     202     396 ..     201     397 .. 0.87
   2 ?    0.9   0.0      0.16   3.6e+02      21      63 ..     416     456 ..     412     463 .. 0.83

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 1.2e-43
                                    TTEEEEEEEECSSSSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEEEEEE CS
                         SpoIIE   2 dgrlalvvgDvvGhGleAalimgllrsalrelataglepaevlkrlnralardleeeerfaTavlavydpstgkleyana 81 
                                    ++rl+lvvgDvvGhG+eAa++m++lr+alr  ++ g+++ e+l++++r+  ++++ + + aT++++ +d  +g+++y+ a
  gi|121637295|ref|YP_977518.1| 202 GDRLVLVVGDVVGHGVEAAAVMSQLRTALRMQISTGYTVVEALEAVDRFH-KQVPGS-KSATMCVGSLDFTSGEFQYCTA 279
                                    689***********************************************.9****9.********************** PP

                                    SSSSEEEEETTSTEEEEE--SS--TTTSSST-EEEEEEE--TTEEEEEESCCCCSSS..HHHHHHCCCHHCHHHHCT... CS
                         SpoIIE  82 GhpppllvrpdggtklllastglplGilpeadyetaelelepgdtlllyTDGvtEar..dsdgelfgkerllallasa.. 157
                                    Ghpppllv++d ++++++ ++  plG   ++ +++++  l+ gd +l+yTDG++E++    +  + + ++l+a +as   
  gi|121637295|ref|YP_977518.1| 280 GHPPPLLVTADASARYVEPTGAGPLGS--GTGFPVRSEVLNIGDAILFYTDGLIERPgrPLEASTAEFADLAASIASGsg 357
                                    **************************9..999**************************9555555555666655555545 PP

                                    ......HCCHHHHHHHHHHH..HTTSSSSS-EEEEEEEE CS
                         SpoIIE 158 .eges.leelldalveelle..lgsgeleDDitllvlrv 192
                                        + +++ +d+l +++le  l s + +DD+tll++++
  gi|121637295|ref|YP_977518.1| 358 gFVLDaPARPIDRLCSDTLEllLRSTGYNDDVTLLAMQR 396
                                    53333466666666666666665577**********997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCE CS
                         SpoIIE  21 limgllrsalrelataglepaevlkrlnralardleeeerfaT 63 
                                     + ++lr +l e+ +++ + a++++++ +++++ +e+   +aT
  gi|121637295|ref|YP_977518.1| 416 TVRAQLREWLAEIGADHSDIADIVHAISEFVENAVEHG--YAT 456
                                    56689**************************6655555..666 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   1.3   5.8e-17   1.3e-13       3     124 ..     409     522 ..     407     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.8e-17
                    HATPase_c_2   3 adpehvrtvrevaeavlrraglseelldeirlaveEactNavehayleapegpvevrles.deealtvevaDsGpgfdpe 81 
                                    a+    rtvr  ++++l++ g + +++++i  a++E + Naveh+y  + ++ + v++   +++ ++++v D+G++ d +
  gi|121637295|ref|YP_977518.1| 409 ATINAARTVRAQLREWLAEIGADHSDIADIVHAISEFVENAVEHGYATDVSKGIVVEAALaGDGNVRASVIDRGQWKDHR 488
                                    777889********************************************999999955505566***********9998 PP

                    HATPase_c_2  82 tlpdpteeepkeslkegGrGlalikglvDevey..dgegnvvtms 124
                                               + ++ +GrGla+ ++lv e ++  +++g++ t++
  gi|121637295|ref|YP_977518.1| 489 -----------DGARGRGRGLAMAEALVSEARImhGAGGTTATLT 522
                                    ...........456679****************998899998886 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2   1.4e-15   3.2e-12       1     110 []      21     135 ..      21     135 .. 0.96
   2 ?   -3.2   0.0       4.3   9.7e+03      68      88 ..     617     639 ..     606     649 .. 0.60

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.4e-15
                          PAS_4   1 ldslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..... 74 
                                    ++++p++l+ l +pd r++++Naa++     p  + +G++ +e++pe  ++++ + l+rv +++ep++  e +l      
  gi|121637295|ref|YP_977518.1|  21 FEHIPAILVGLeGPDHRFVAVNAAYRG--FSPLLDTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWRLQtdydg 98 
                                    799999999999************999..99999**********************************999888889999 PP

                          PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                     + eer++++ ++P r ++G + gv +i+ D+T r+r
  gi|121637295|ref|YP_977518.1|  99 sGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVR 135
                                    999*******************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                          PAS_4  68 fleelll..pgeerhyelrllPl 88 
                                     +e++l   pg++ h+ l+l+ l
  gi|121637295|ref|YP_977518.1| 617 GTECVLVapPGSPAHHVLSLVQL 639
                                    44444444688888888777544 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.7   8.2e+03      14      38 ..     221     249 ..     216     251 .. 0.54
   2 ?    3.9   0.1      0.03        66       1      24 [.     403     426 ..     403     438 .. 0.84
   3 !   42.1   1.7   3.8e-14   8.5e-11       1      75 [.     559     635 ..     559     640 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                         STAS_2  14 elreqlleal....aagaevvvDlsgver 38 
                                    ++ +ql+ al    ++g +vv  l  v r
  gi|121637295|ref|YP_977518.1| 221 AVMSQLRTALrmqiSTGYTVVEALEAVDR 249
                                    44555555554444777666655555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.03
                         STAS_2   1 LsLsGeldldtaaelreqlleala 24 
                                    L+++ + ++++a+++r+ql+e+la
  gi|121637295|ref|YP_977518.1| 403 LHITLDATINAARTVRAQLREWLA 426
                                    6788899***************95 PP

  == domain 3  score: 42.1 bits;  conditional E-value: 3.8e-14
                         STAS_2   1 LsLsGeldldtaaelreqllealaag.aevvvDlsgvervDsaalalLlalartarargrrlvlrglppalr.rlld 75 
                                    ++++G++d  taa+l +q +   + g a+v++Dls v+ + sa++++L+a+  +ar++g   vl+++p+  + ++l+
  gi|121637295|ref|YP_977518.1| 559 IVVRGDVDSTTAATLDRQIAVESRSGiAPVTIDLSAVTHLGSAGVGALAAACDRARKQGTECVLVAPPGSPAhHVLS 635
                                    5799**************************************************************99874425555 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.8e-12   8.5e-09      17      95 ..     563     632 ..     537     650 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.8e-12
                                    EEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES--HHHHHH CS
                           STAS  17 gpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlvnikpevrek 95 
                                    g++d ++a ++ +++    + +         + ++ +dlsav+++ s+Gv+aL  ++ + +++g e+vlv + ++ +++
  gi|121637295|ref|YP_977518.1| 563 GDVDSTTAATLDRQIAVESRSG---------IAPVTIDLSAVTHLGSAGVGALAAACDRARKQGTECVLVAPPGSPAHH 632
                                    5666666666666666666655.........9****************************************9998887 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0029       1     113 []      15     130 ..      15     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                            PAS   1 edlraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                    ed+r+i+e++p+  +++   d+r++ vNaa++   G+s+  + +g++  ++++e + ++ +e l +++++ge++++ e +
  gi|121637295|ref|YP_977518.1|  15 EDVRRIFEHIPAILVGLEgPDHRFVAVNAAYR---GFSPlLDTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWR 91 
                                    689***************************99...888889***************99********************** PP

                                    EEC....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS  79 fkl....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    + +       ++++++  ++p+r a+g i g+ +++ d+
  gi|121637295|ref|YP_977518.1|  92 LQTdydgSGVEERYFDFVVTPRRRADGSIEGVQLIVDDV 130
                                    ****8877777899999999************9999986 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.3   9.7e+03       5      28 ..     204     227 ..     202     242 .. 0.65
   2 ?   13.1   0.7   4.6e-05       0.1       2     106 ..     434     521 ..     433     527 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                                    HHHHHHHHHHHHHHHHHSTTTEEE CS
                      HATPase_c   5 rLrqiisnlvdNavkfatkageie 28 
                                    rL  ++  +v++ v++a+ +++++
  gi|121637295|ref|YP_977518.1| 204 RLVLVVGDVVGHGVEAAAVMSQLR 227
                                    777788888888888855555543 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.6e-05
                                    HHHHHHHHHHHHHHHHHHHHSTTTEE..EEEEEE...EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkagei..eveika...seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76 
                                    d   + ++is++v+Nav++ ++a+++   + ++a    +++++ sv D G+   k++++              g  g+G 
  gi|121637295|ref|YP_977518.1| 434 DIADIVHAISEFVENAVEH-GYATDVskGIVVEAalaGDGNVRASVIDRGQ--WKDHRD--------------GARGRGR 496
                                    566789*************.7777774445555444433799999***664..343333..............2357777 PP

                                    HHHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                      HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftf 106
                                    Gl+++++lv+    e ++     +Gtt t+
  gi|121637295|ref|YP_977518.1| 497 GLAMAEALVS----EARI-MHGAGGTTATL 521
                                    7777777666....3444.33345666555 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.041       8     103 ..      33     131 ..      25     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                          PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk...kerevevvlirkngetfwvllta 82 
                                     pd+r + +N a + +  +   + +g++ ++++   + ++  e l++++++g+    +e++ ++++  +  e+ ++++ +
  gi|121637295|ref|YP_977518.1|  33 GPDHRFVAVNAAYRGF--SPLLDTVGQPAREVYpeLEGQQIYEMLDRVYQTGEPqsgSEWRLQTDYDGSGVEERYFDFVV 110
                                    5788888888877777..6778999*******9665666666666666666666************************** PP

                          PAS_9  83 spvkdddgelvgiivilrDit 103
                                    +p + +dg + g+ +i+ D+t
  gi|121637295|ref|YP_977518.1| 111 TPRRRADGSIEGVQLIVDDVT 131
                                    ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 4382.52
//
Query:       gi|121637296|ref|YP_977519.1|  [L=128]
Description: hypothetical protein BCG_1427c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-17   62.3   0.0    3.4e-17   62.1   0.0    1.0  1  STAS            STAS domain
    9.8e-09   35.4   0.6    1.3e-08   35.0   0.6    1.2  1  STAS_2          STAS domain
  ------ inclusion threshold ------
      0.034   14.4   0.0      0.064   13.5   0.0    1.5  2  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   5.8e-21   3.4e-17       2     117 .]      19     124 ..      18     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 5.8e-21
                                    EEEEECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT- CS
                           STAS   2 idaeeiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigv 81 
                                    ++++++++ +i++ +g+id+an +++++ +++a++ ++       ++++l+++l +++f+ +++v++L    ++++r+gv
  gi|121637296|ref|YP_977519.1|  19 ATIQHHDSAVIIHARGEIDAANEHTWQDLVTKAAAATT-------APEPLVVNLNGLDFMGCCAVAVLAHKAERCRRRGV 91 
                                    578999******************************96.......9********************************** PP

                                    EEEEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  82 evvlvnikpevreklektgffdeveeeklfltvhdA 117
                                    +v lv+ + +v++ ++++g+ d++   ++++t ++A
  gi|121637296|ref|YP_977519.1|  92 DVRLVSRDRAVARIIHACGYGDVL---PVHPTTESA 124
                                    ************************...999998887 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.6   2.2e-12   1.3e-08       2      78 ..      31     110 ..      30     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.2e-12
                         STAS_2   2 sLsGeldldtaaelreqlleal...aagaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlldlyG 78 
                                    + +Ge+d+++ +++++ + +a+   +a++++vv l g+ ++ + a+a+L++ a+++r+rg  ++l+   +a++r+ +  G
  gi|121637296|ref|YP_977519.1|  31 HARGEIDAANEHTWQDLVTKAAaatTAPEPLVVNLNGLDFMGCCAVAVLAHKAERCRRRGVDVRLVSRDRAVARIIHACG 110
                                    779***************99996654458*********************************************998766 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.064      47     112 ..      29      96 ..      20      98 .. 0.75
   2 ?   -3.0   0.0       1.4   8.1e+03      38      54 ..     107     123 ..     104     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                    EEBTTBSTTSS--HHHHHHHHHHHHHTTSEEEEEE..E-SSEEEEEEE---SS..STS-EEE.EEEEEE CS
                 DNA_pol_B_palm  47 itkkdakseskklkklleklvkklkkkgfltdsLavesgeskfmGvcrlpeee..kkelhrR.iDlklv 112
                                    i + +++ +   +++  ++lv+k  ++    + L v+ ++  fmG+c++   +  +++  rR +D++lv
  gi|121637296|ref|YP_977519.1|  29 IIHARGEID-AANEHTWQDLVTKAAAATTAPEPLVVNLNGLDFMGCCAVAVLAhkAERCRRRgVDVRLV 96 
                                    445555553.357899999999999999999****999*********9887544334444445999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                    SEESSEEEEEEBTTBST CS
                 DNA_pol_B_palm  38 essGDvDvlitkkdaks 54 
                                    + +G  Dvl  ++ ++s
  gi|121637296|ref|YP_977519.1| 107 HACGYGDVLPVHPTTES 123
                                    57888899988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 962.43
//
Query:       gi|121637297|ref|YP_977520.1|  [L=273]
Description: hypothetical protein BCG_1428 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-10   39.6   0.0      9e-10   38.9   0.0    1.3  1  RelA_SpoT  Region found in RelA / SpoT proteins
     0.0037   17.2   0.1        1.7    8.6   0.0    2.6  2  HTH_37     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> RelA_SpoT  Region found in RelA / SpoT proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0     1e-13     9e-10       1     106 [.      76     174 ..      76     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1e-13
                                    EEE--HHHHHHHHHHCT--CCCCCCCSSTSEEEEEEESS.HHHHHHHHHHHHT-SSSEEEEEEETSTSHCTTCCSEEEEE CS
                      RelA_SpoT   1 gRvKslysiieKlerkgikveekfeeitDligiRvivef.kddvyevlelikklwdvkpkrfkdyiaepkengYrslHtv 79 
                                    +R Ks + ++ Kl+r+      ++++i+D++g+R+  +    +  +  + i +++   +   +d  ++p + gYr +H+ 
  gi|121637297|ref|YP_977520.1|  76 SRAKSQDTLLAKLRRRPYL---QLNTIQDIAGVRIDADLlLGEQTRLAREIADHFGADQPAIHDLRDHP-HAGYRAVHVW 151
                                    69*************9966...9************9976467888999999999999999999997777.89******** PP

                                    EEETTEEEEEEEEEEEEEHHHHHHHHH CS
                      RelA_SpoT  80 vssekgeekvlvEiQiRtiamdawaei 106
                                    +    +    +vEiQiRti +  wa++
  gi|121637297|ref|YP_977520.1| 152 L----RLPAGRVEIQIRTILQSLWANF 174
                                    *....777789**************84 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00019       1.7       6      37 ..      41      72 ..      39      91 .. 0.89
   2 !    5.7   0.0    0.0015        14      35      53 ..     121     139 ..     114     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00019
                                   X--HHHHHHHHHHHHHHHHHHHHHCT--HHHH CS
                         HTH_37  6 geedaeelkaKaqlalaiaeliekrelsqsea 37
                                   +++ ae +   a+la+++++ ie+r +s se+
  gi|121637297|ref|YP_977520.1| 41 CPSYAEVMLWHADLAAEVQDRIEGRSWSASEL 72
                                   56678888899*****************9986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0015
                                    HHHHHHHT--HHHHHHHHT CS
                         HTH_37  35 seaaqllgiaqPkvsrllr 53 
                                    +e+a ++g +qP + +l++
  gi|121637297|ref|YP_977520.1| 121 REIADHFGADQPAIHDLRD 139
                                    79**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2162.01
//
Query:       gi|121637298|ref|YP_977521.1|  [L=377]
Description: hypothetical protein BCG_1429c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-65  219.7   1.3    6.9e-65  219.5   1.3    1.0  1  Beta-lactamase   Beta-lactamase
  ------ inclusion threshold ------
      0.067   12.8   0.0       0.18   11.4   0.0    1.7  2  Beta-lactamase2  Beta-lactamase enzyme family


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.5   1.3   7.7e-69   6.9e-65      20     313 ..       1     341 [.       1     353 [. 0.95

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 7.7e-69
                                    EEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTST............... CS
                 Beta-lactamase  20 avvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylP............... 84 
                                    +v+++ k++  + +G++d+++g p++ dtlfriaS+tK++t aa++ lv+eGkl L dp++++ P               
  gi|121637298|ref|YP_977521.1|   1 MVWQREKLLQVNEIGYRDIDAGVPMQRDTLFRIASMTKPVTVAAAMSLVDEGKLALRDPITRWAPelckvavlddaagpl 80 
                                    6899999999999******************************************************************* PP

                                    TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTH.......HHHHHHHHHSBSSSSTTSCEE-SHHHHHHHHHHHH CS
                 Beta-lactamase  85 efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaada.......aellralatlppkyapGtkwgYsntgygllgelle 157
                                    + + p+ ++i ++dLltHtsGl+++f+   ++++a+++       +  l+alatlp++++pG + +Ys + + +lg ++ 
  gi|121637298|ref|YP_977521.1|  81 DRTHPARRAILIEDLLTHTSGLAYGFSVSGPISRAYQRlpfgqgpDVWLAALATLPLVHQPGDRVTYSHAID-VLGVIVS 159
                                    *********************************************************************999.******* PP

                                    HHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC......TTTBEEEEHHHHHHH CS
                 Beta-lactamase 158 kvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae......gagglistardlarf 231
                                    ++ + +l q ++e++l p gm+dt++++ +++++r a++y+ + +++ + ++++p+  +      ++ggl+sta+d++rf
  gi|121637298|ref|YP_977521.1| 160 RIEDAPLYQVIDERVLGPAGMTDTGFYVSADAQRRAATMYRLDEQDRLRHDVMGPPHVTppsfcnAGGGLWSTADDYLRF 239
                                    ******************************************************************************** PP

                                    H..........HHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCH...........TEEEEEEEST CS
                 Beta-lactamase 232 l..........glalegglllsaetlaqltaklssgttrpagiraglglGwvladktga...........pgtfghtGgg 290
                                    +          g++ + ++ ++ +   +lt++++++   +a++  g+g+G++l+  t++            gtf+++G  
  gi|121637298|ref|YP_977521.1| 240 VrmllgdgtvdGVRVLSPESVRLMRTDRLTDEQKRHSFLGAPFWVGRGFGLNLSVVTDPaksrplfgpggLGTFSWPG-A 318
                                    *9999998888888888888888888888999999999999999999*******************************.* PP

                                    EEEEEEEECGGTEEEEEEESBCS CS
                 Beta-lactamase 291 ygtyvfvdpeanlvvavltnrdp 313
                                    ygt++ +dp a+l++ +l +  p
  gi|121637298|ref|YP_977521.1| 319 YGTWWQADPSADLILLYLIQHCP 341
                                    *****************998655 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     2e-05      0.18      10      48 ..      26      64 ..      20     100 .. 0.77
   2 ?   -2.7   0.0      0.41   3.7e+03     127     156 ..     230     264 ..     222     282 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                                   STTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGH CS
                Beta-lactamase2 10 nadeefpaaStiKvpillalleavlegklslderltlta 48
                                   + d+ f  aS+ K + ++a++  v+egkl l +++t  a
  gi|121637298|ref|YP_977521.1| 26 QRDTLFRIASMTKPVTVAAAMSLVDEGKLALRDPITRWA 64
                                   77999******************************9754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.41
                                    EE-HHHHHHHHHHHHHT......TSSHHHHHHHHHH CS
                Beta-lactamase2 127 tttardlarllealarg......ellspeelleils 156
                                    ++ta d+ r+ ++l  +      ++lspe  +++++
  gi|121637298|ref|YP_977521.1| 230 WSTADDYLRFVRMLLGDgtvdgvRVLSPE-SVRLMR 264
                                    57899999999988876444445666664.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 2042.13
//
Query:       gi|121637299|ref|YP_977522.1|  [L=261]
Description: lipoprotein lprF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-70  234.7   4.5      9e-70  234.4   4.5    1.1  1  LppX_LprAFG  LppX_LprAFG lipoprotein


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.4   4.5     5e-74     9e-70       1     192 []      57     256 ..      57     256 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 5e-74
                                    .HHHHHHHHHHHHHT-SEEEEEEEEEC--TTSTEEEEEEEEETTTT.E..EEEEEEEEET..TCEEEEEEEEETTEEEEE CS
                    LppX_LprAFG   1 daakllaesakatkslksvhlaltvngkvdglpvesvegdltnqpaga..akgnakvtla..gqavdvkfvvvdgklyak 76 
                                    +a+++l++s+katk+l+svh+++tvn+ +++lp+esv++d+tnqp+g+  a+gnakv+++  ++ v+++f+v+++++y+k
  gi|121637299|ref|YP_977522.1|  57 EAQQILQDSSKATKGLHSVHVVVTVNN-LSTLPFESVDADVTNQPQGNgqAVGNAKVRMKpnTPVVATEFLVTNKTMYTK 135
                                    599************************.********************************98999*************** PP

                                    ECTTEEEEEEEHGHCHHHHCGG-TTTSHHHHCCTEEEEEEEEEEEETTEEEEEEEEEE-HHHHHHH-CCG-SS.S.EEEE CS
                    LppX_LprAFG  77 lppetwsdlgpaekiydpavlLdpdkGlanvLagvtdakaegreeidGtatvkitGtvdadvvsaivpslked.gtvpit 155
                                    ++ +++ ++gpaekiydp+++Ld+d+Gl++v+ +v++++++gr+ idG atvk++Gt+da+v+++ivp+l++  g++pit
  gi|121637299|ref|YP_977522.1| 136 RG-GDYVSVGPAEKIYDPGIILDKDRGLGAVVGQVQNPTIQGRDAIDGLATVKVSGTIDAAVIDPIVPQLGKGgGRLPIT 214
                                    **.9********************************************************************99****** PP

                                    EEEESS......TT--EEEEEEEECTCEEEEEEEESTT---TT CS
                    LppX_LprAFG 156 lWiaed......gelrlvrvvvdkesgesveltlskwgkpvtv 192
                                    lWi+++      ++++lvr+v+dk++g+ v++tls+wg pvt+
  gi|121637299|ref|YP_977522.1| 215 LWIVDTnastpaPAANLVRMVIDKDQGN-VDITLSNWGAPVTI 256
                                    ****************************.************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1357.56
//
Query:       gi|121637300|ref|YP_977523.1|  [L=317]
Description: hypothetical protein BCG_1431 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.0   0.0    2.1e-17   63.0   0.0    1.5  1  Cyt-b5    Cytochrome b5-like Heme/Steroid binding domain


Domain annotation for each model (and alignments):
>> Cyt-b5  Cytochrome b5-like Heme/Steroid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   1.2e-21   2.1e-17      13      73 ..      28      88 ..       7      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.2e-21
                                   EEEEEETTEEEECTTTCCCSTTCSHHHHTTTTSBBHHHHHHTTGGCHHHHHHHHG.GEEEEE CS
                         Cyt-b5 13 dlwvairgkVYDvskflskhpGgesailkyaGkDateafksvvhsekdaekllkk.ylvGkl 73
                                   d+wv ++g+ YD+s+++skhpGg+++i++++++D+t+++ks++++++++e++l++ y++G+ 
  gi|121637300|ref|YP_977523.1| 28 DVWV-YNGRAYDLSEWISKHPGGAFFIGRTKNRDITAIVKSYHRDPAIVERILQRrYALGRD 88
                                   99*9.*******************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1666.52
//
Query:       gi|121637301|ref|YP_977524.1|  [L=331]
Description: hypothetical protein BCG_1432 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-14   51.9  12.7    1.2e-13   51.5  12.7    1.1  1  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5  12.7   6.9e-18   1.2e-13       1     225 [.      14     245 ..      14     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 6.9e-18
                  FA_desaturase   1 sswlalllalllglfllgitgslaHeaaHgalfkkrklnrwlndllgallglplgisysawrisH.lrHHaytngpdeDp 79 
                                    +sw++l+++++++++l++  ++++H a+H+    +r lnr +n+++    +  +   +    + H l HH yt ++  D+
  gi|121637301|ref|YP_977524.1|  14 PSWMPLWAFVIAMVLLRSSLAGFGHYALHR---AQRGLNRVFNNAF---DLNYV-ALSLVTADGHtLLHHPYTQSE-VDI 85 
                                    68*****55555555777768********7...4556888888888...55554.556699999*******95555.555 PP

                  FA_desaturase  80 dlaplalsrfeglfryllrlllgllvlgwllalvlgl.wlrrlarrrapsksrrrkwrllawlllllawlglwlalllll 158
                                        +      ++ ++l++l++ ++++ +++++ l   ++r+++++r  +k+      +  w+++l+++lg +++ lll 
  gi|121637301|ref|YP_977524.1|  86 KKNVF------TMMMRLPWLYRVPVHTIHKFGHMLSGmAIRIVDVFRITRKVGVE-ESYGSWRAALPHFLGSAGVRLLLV 158
                                    54433......33333333333333333222222222144444444444444433.555555555555533222222222 PP

                  FA_desaturase 159 glall........lwlvplllllfllalvlnyveHyg...........gdwgerqvetsasir.saswllnll.tgnlny 217
                                    + +++         w++++++ l++ +++  +++H +           +dwg +q+e+ ++ + + ++ ++++ + +l+ 
  gi|121637301|ref|YP_977524.1| 159 SELVVfaiagdfwPWALQFVATLWVSTFL-VVASHEFeddtqggavngEDWGVDQLEHANDLTvIGNRYVDCFlSAGLSS 237
                                    22222223344338999999999988888.**********************************9999999999****** PP

                  FA_desaturase 218 HieHHlfP 225
                                    H +HH  P
  gi|121637301|ref|YP_977524.1| 238 HRVHHVLP 245
                                    *****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1782.98
//
Query:       gi|121637302|ref|YP_977525.1|  [L=393]
Description: hypothetical protein BCG_1433 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-23   81.5   0.1    8.1e-23   81.0   0.1    1.1  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
    1.3e-21   77.2   0.0    2.2e-21   76.4   0.0    1.4  1  Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal 
    2.3e-11   43.7   0.4    1.4e-10   41.2   0.1    2.4  3  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    3.1e-11   43.1   0.7    4.6e-11   42.6   0.7    1.2  1  FAE1_CUT1_RppA   FAE1/Type III polyketide synthase-like prote
    1.4e-08   34.5   1.3    2.9e-08   33.4   1.3    1.5  1  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.1   2.3e-26   8.1e-23      14     223 ..      33     235 ..      28     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 2.3e-26
                Chal_sti_synt_N  14 atllalGkalPeqvveqeklvdyylrvtksedlaelkeklerlcdkstvkkryivlteeileenPeltaemapsldarle 93 
                                    a++  l +++P +vv+q++ +d           +  +e++ r+ ++s + +r + +  + l+ + ++  +  +++  r++
  gi|121637302|ref|YP_977525.1|  33 AVIEGLATGTPRRVVNQSDAADRVAELF---LDPGQRERIPRVYQNSRITTRRMAV--DPLDAKFDVFRREPAAIRDRMH 107
                                    6777899**************9755443...33689****************8765..6799999*************** PP

                Chal_sti_synt_N  94 ivnaevlklgkeaalkalkewGrPkskithlvfvsssevelPGadlklakklGlrpsvkrvmlyflGcygGatvlrlakd 173
                                    +  +  + l+ + +++al      +++i  lv  +s++   PG d+ + k lGl+ps+ rv++ f+Gc +   +l +a +
  gi|121637302|ref|YP_977525.1| 108 LFYEHAVPLAVDVSKRALAGLPYRAAEIGLLVLATSTGFIAPGVDVAIVKELGLSPSISRVVVNFMGCAAAMNALGTATN 187
                                    ********************9999******************************************************** PP

                Chal_sti_synt_N 174 iaennkGarvlvvaseitvlgfrgPskdrlddlvGaalfGdGaaaviiGa 223
                                         +  + lvv+ e+  +   +   d ++d+v ++lfGdG+aa +iGa
  gi|121637302|ref|YP_977525.1| 188 YVRAHPAMKALVVCIELCSV--NAVFADDINDVVIHSLFGDGCAALVIGA 235
                                    **************998876..56788999*******************9 PP

>> Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   6.2e-25   2.2e-21       4     148 ..     251     389 ..     248     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6.2e-25
                Chal_sti_synt_C   4 saaqtflPetdgvidgklteeGltfkllrdlPekieenieeflkklleklGieefndlfwivhPGGpaildrleaklkle 83 
                                    s+  ++l +t+  i + ++ +G+t +l ++lP  i   +  +++++l   G +  +  +w++hPGGp i+++    l++ 
  gi|121637302|ref|YP_977525.1| 251 SSFSQLLDNTEDGIVLGVNHNGITCELSENLPGYIFSGVAPVVTEMLWDNGLQISDIDLWAIHPGGPKIIEQSVRSLGIS 330
                                    677899*****************************************999998666669********************* PP

                Chal_sti_synt_C  84 kekleasrkvlseyGnvssatvlyvldelrdkelkkklattgegkewGlllafGPGltietlllr 148
                                     e    s +vl  +Gn+ s ++++vl+++ ++    k          G+ +afGPG+t+e++l+ 
  gi|121637302|ref|YP_977525.1| 331 AELAAQSWDVLARFGNMLSVSLIFVLETMVQQAESAKAI------STGVAFAFGPGVTVEGMLFD 389
                                    *****************************9944333444......46***************975 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.91   3.2e+03      26      45 ..     154     175 ..     151     187 .. 0.79
   2 ?   -1.8   0.0         1   3.6e+03      58      78 ..     236     254 ..     227     255 .. 0.71
   3 !   41.2   0.1   3.9e-14   1.4e-10       3      89 ..     299     389 ..     297     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                                    HHHHHHT--GG..GB--THHHH CS
                  ACP_syn_III_C  26 avakklglpee..kvvvnldey 45 
                                    a++k+lgl++   +vvvn++ +
  gi|121637302|ref|YP_977525.1| 154 AIVKELGLSPSisRVVVNFMGC 175
                                    5789999999977888887655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                    HHHHHTTSS-TT-EEEEEEEE CS
                  ACP_syn_III_C  58 deaveegklkpgdlvllvgfG 78 
                                    ++   ++kl+pg+ v+ ++f 
  gi|121637302|ref|YP_977525.1| 236 SQV--QEKLEPGKVVVRSSFS 254
                                    444..4599****99999985 PP

  == domain 3  score: 41.2 bits;  conditional E-value: 3.9e-14
                                    HTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GG...GB--THHHH-B-GGGHHHHHHHHHHHTT.SS-TT-EEEEEEEE CS
                  ACP_syn_III_C   3 kagltpedidalvphqanlriidavakklglpee...kvvvnldeyGntsaasiplaLdeaveeg.klkpgdlvllvgfG 78 
                                    ++gl+ +did+  +h    +ii++ ++ lg+++e   +    l+++Gn+ ++s++  L+++v++    k+  + + ++fG
  gi|121637302|ref|YP_977525.1| 299 DNGLQISDIDLWAIHPGGPKIIEQSVRSLGISAElaaQSWDVLARFGNMLSVSLIFVLETMVQQAeSAKAISTGVAFAFG 378
                                    689*******************************886666667*******************998689999********* PP

                                    TTTEEEEEEEE CS
                  ACP_syn_III_C  79 aGltwgaallr 89 
                                     G+t+ ++l+ 
  gi|121637302|ref|YP_977525.1| 379 PGVTVEGMLFD 389
                                    *******9985 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.7   1.3e-14   4.6e-11     101     209 ..     131     239 ..     111     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.3e-14
                 FAE1_CUT1_RppA 101 spkdidilvvncslfsptPslsamvvnryklredvksynLsgmGCsAglisidlaknllqvhkntlalvvstEnitlnwY 180
                                    ++++i++lv ++s+   +P +   +v+  +l   ++ + +  mGC+A++ ++  a+n +++h+   alvv  E ++ n+ 
  gi|121637302|ref|YP_977525.1| 131 RAAEIGLLVLATSTGFIAPGVDVAIVKELGLSPSISRVVVNFMGCAAAMNALGTATNYVRAHPAMKALVVCIELCSVNAV 210
                                    789***************************************************************************** PP

                 FAE1_CUT1_RppA 181 vGnersmllanclFRvGgaavllsnksad 209
                                    + ++ + ++  +lF  G aa+++  ++ +
  gi|121637302|ref|YP_977525.1| 211 FADDINDVVIHSLFGDGCAALVIGASQVQ 239
                                    ********************998776654 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   1.3   8.1e-12   2.9e-08       6      65 ..     174     238 ..     170     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 8.1e-12
                                    GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG.CS...-TTTHHHHTTB-EEEEEEEEEEE.S CS
                    ACP_syn_III   6 aCsgfvyalsvAdaliesgaakrvLvigaetlsk.il...DwkdrstavlfGDGAgAvvleas.e 65 
                                    +C++++ al +A++++++  a ++Lv++ e +s   +   D +d   + lfGDG++A+v++as  
  gi|121637302|ref|YP_977525.1| 174 GCAAAMNALGTATNYVRAHPAMKALVVCIELCSVnAVfadDINDVVIHSLFGDGCAALVIGASqV 238
                                    7*******************************98533222335677777*************942 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2174.87
//
Query:       gi|121637303|ref|YP_977526.1|  [L=327]
Description: glycolipid sulfotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-59  200.3   0.0    4.8e-59  200.0   0.0    1.0  1  Sulfotransfer_1  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.0   2.7e-63   4.8e-59       1     260 [.      30     306 ..      30     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 2.7e-63
                                    TTSEEEEESTTSSHHHHHHHHHHHHTTTCCHHHTSSGHCT-.HHHSCBTTHECCTSGCCGTTECCCHHHTTTEEHHHHHH CS
                Sulfotransfer_1   1 dddvlivtypKSGTtwlqellslitsegdfekaeepalfna.rdrspfLelydlyfpnslkppdhlrsyshvaekvvrlr 79 
                                    d d++i++++KSG tw+q+l+sl        +++ p+l+++ +++sp+L++                 +++++e+v++l+
  gi|121637303|ref|YP_977526.1|  30 DGDIIISAPSKSGLTWTQRLVSL-------LVFDGPDLPGPlSTVSPWLDQT----------------IRPIEEVVATLD 86 
                                    579********************.......999*****************93................7999******** PP

                                    HSTSS.EEEE...GGGS.CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBT........................TSTTT- CS
                Sulfotransfer_1  80 alesprllktHlplkllpkslldsnlKiiylvRnpkdvavSryhfsrslk........................klkepe 135
                                    a++++r++ktH+pl++l   +ld+++ +i++ R+p+d+avS++++s++++                        +     
  gi|121637303|ref|YP_977526.1|  87 AQQHRRFIKTHTPLDGL---VLDDRVSYICVGRDPRDAAVSMLYQSANMNedrmrilheavvpfheriapppfaE----- 158
                                    *****************...******************************9999977777775555555555553..... PP

                                    S-HH........HHHHHHHT..............THSTTC-HHHHHHHHHHHTTTTTEEEEEHHHHHHHHHHHHHHHHHH CS
                Sulfotransfer_1 136 tpfe........effdlfle..............grvvcgsyfdhvkswlklrkkgnvlflrYEdlkkdpakeikkiaeF 193
                                                ef+d++                g+++++++++++ +++ +r+ +nv++++Y d+++d+a+e+ ++a++
  gi|121637303|ref|YP_977526.1| 159 ---LgharspteEFRDWMEGpnqpppgigfthlkGIGTLANILHQLGTVWVRRHLPNVALFHYADYQADLAGELLRLARV 235
                                    ...055555555******************************************************************** PP

                                    TT--..HHHHHHHHHHTSHHHHHTETTTSSTTSCTT...TTSTSSEE--TTGGGGTSBH.HHHHHHHHHHH CS
                Sulfotransfer_1 194 lGiplteeelekivkhlsfenmksnpvsnksklskg...ekekffrkgqvgdWkneltv.eqaekldeifq 260
                                    lGi +t+++++++++++++++m+s+ ++ ++++++g   ++e+ffr+g++gdW++ +t+ e+++++++i+q
  gi|121637303|ref|YP_977526.1| 236 LGIAATRDRARDLAQYATLDAMRSRASEIAPNTTDGiwhSDERFFRRGGSGDWQQFFTEaEHLRYYHRINQ 306
                                    *********************************999***********************9********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1804.73
//
Query:       gi|121637304|ref|YP_977527.1|  [L=152]
Description: hypothetical protein BCG_1435c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 885.43
//
Query:       gi|121637305|ref|YP_977528.1|  [L=439]
Description: hypothetical protein BCG_1436 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-56  192.5   6.9    1.4e-56  192.1   6.9    1.1  1  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   6.9   7.9e-61   1.4e-56       1     322 [.     115     423 ..     115     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 7.9e-61
                           YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvr.asyrelegegaldpeelglyseeekdaadfvlepfdpdrpidw 79 
                                    +Gk+a+++aA++sa++E+lE ++ae    + ++ ++ a++r+le++   dp++l+            + + ++++ ++dw
  gi|121637305|ref|YP_977528.1| 115 QGKAASYRAAQVSAVMESLEGWHAE----NVTADLWsATARDLEADLTYDPAQLRHR----------PGSLYHAGVKLDW 180
                                    6**********************99....77888888*****************555..........38*********** PP

                           YcaO  80 vpgwsltdgeevlvPanlvyl.yeppegea.rlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridla 157
                                    + ++ l++g++++vP+ +v +  ++++  + ++f ++++GlA+Gn+++eA+lh+l+E++ER+++a a   + +  +++ +
  gi|121637305|ref|YP_977528.1| 181 MVATTLLTGRRTWVPWTAVLVnVATRDCWEpPMFEMDTTGLASGNCYDEATLHALYEVMERHSVAAAVA-GETMFEVPTD 259
                                    *********************8555555556***********************************955.5577778877 PP

                           YcaO 158 sd..peirellerlreagievrlldatldlgipvvaavlvdpklllva.gaGahldpevAlerAltElaqsrltlisgar 234
                                    ++  ++ ++l+e +r+ag +v l  +    g+ ++aa l++ +l +++ g+G h+dp+vAl+rA+tE+aqsr t isgar
  gi|121637305|ref|YP_977528.1| 260 DVagSDSAHLVEMIRDAGDDVDLARIDVWDGYYCFAAELTSATLEVTFgGFGLHHDPNVALSRAITEAAQSRITAISGAR 339
                                    5577*************************************88888899******************************* PP

                           YcaO 235 edpdf.d.eeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerl.kaagldvlvvdltrpdlg 311
                                    ed      +++ +v t+++a++ + l l++a+++ ++     +    ++l e ++   +++ ++ g ++l+v ++ +d  
  gi|121637305|ref|YP_977528.1| 340 EDLPSaIyHRFGRVHTYAKARK-TSLRLNRARPTPWRVP---DV---DSLPELVASAATAVaNRSGTEPLAVVCDFADAC 412
                                    99988569*********86666.4444477777799995...34...3555555555554425666776655444449** PP

                           YcaO 312 lpvvkvivPgl 322
                                    +pvvkv++Pgl
  gi|121637305|ref|YP_977528.1| 413 VPVVKVLAPGL 423
                                    **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2432.18
//
Query:       gi|121637306|ref|YP_977529.1|  [L=497]
Description: hypothetical protein BCG_1437 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-43  145.3   0.0    1.2e-42  144.4   0.0    1.5  1  TfuA      TfuA-like protein


Domain annotation for each model (and alignments):
>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4   0.0   6.6e-47   1.2e-42       1     120 []      53     172 ..      53     172 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 6.6e-47
                           TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgyeals 80 
                                    DG+f+q+p+v+hkE+l+++++gv+vvG++smGALRAaEl++fGm+g+G ++e yr+g+le+DdeV v+h++a++gy  + 
  gi|121637306|ref|YP_977529.1|  53 DGLFFQQPSVRHKELLTLMADGVRVVGSSSMGALRAAELHPFGMEGYGWVFESYRDGVLEADDEVGVVHGDADDGYPVFV 132
                                    9******************************************************************************* PP

                           TfuA  81 ealvnlratlkaaveegiiseeeaaallelakelyykert 120
                                    +alvn+r+tl++av++g++ +e a++++e+a+++ ++ rt
  gi|121637306|ref|YP_977529.1| 133 DALVNMRHTLARAVATGVVCSELAERIIETARATPFTMRT 172
                                    *************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2747.11
//
Query:       gi|121637307|ref|YP_977530.1|  [L=212]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-22   77.9   0.0    1.4e-21   77.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    7.3e-18   65.0   0.0    9.9e-18   64.6   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    2.6e-15   56.5   0.0    3.1e-15   56.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.1e-14   53.5   0.0      7e-14   52.4   0.0    1.5  2  Methyltransf_12  Methyltransferase domain
    1.3e-12   47.8   0.0    2.2e-12   47.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    4.5e-10   39.6   0.0      2e-09   37.4   0.0    1.8  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    3.9e-08   32.9   0.0      5e-08   32.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    1.3e-07   31.2   0.0    1.6e-07   30.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.3e-07   30.4   0.0    2.9e-07   30.1   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    6.5e-07   29.1   0.0    8.8e-07   28.6   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00026   20.9   0.1    0.00048   20.1   0.1    1.3  1  Methyltransf_18  Methyltransferase domain
    0.00062   19.4   0.0    0.00077   19.1   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0021   17.7   0.0     0.0031   17.2   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0023   17.5   0.1     0.0034   17.0   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0098   15.3   0.1      0.014   14.8   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.041   13.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.13   12.6   0.0       0.22   11.9   0.0    1.3  1  Mur_ligase       Mur ligase family, catalytic domain
       0.31   10.0   0.0       0.41    9.6   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   1.4e-24   1.4e-21       1      96 [.      49     142 ..      49     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.4e-24
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLd+GcG G+++++la+++  ++vtg+Dis+++l +a++ra+++g++v+f +gda++l    g fD v+ +g++h+l+d+
  gi|121637307|ref|YP_977530.1|  49 VLDIGCGLGDNAIYLARNG--YQVTGLDISPTALTTAKRRASDAGVDVKFAVGDATKLTGYTGAFDTVIDCGMFHCLDDD 126
                                    9*****************5..*************************************************999******* PP

                                    HHHHHHHHHHHHEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpg 96 
                                      + + + ++r+++pg
  gi|121637307|ref|YP_977530.1| 127 GKRSYAASVHRATRPG 142
                                    ***************8 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0     1e-20   9.9e-18       1      95 [.      50     146 ..      50     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpe 78 
                                    Ld+GcG G +a +la++g++v+g+D+s+++l++ak++as++g+ v+f v+da+kl    + fD v+   ++h +  +  +
  gi|121637307|ref|YP_977530.1|  50 LDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGVDVKFAVGDATKLTGYTGAFDTVIDCGMFHCLddDGKR 129
                                    8******************************************************88889**************866788 PP

                                    HHHHHHHHHEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                    ++ + ++R  +pg +l+
  gi|121637307|ref|YP_977530.1| 130 SYAASVHRATRPGATLL 146
                                    999**********9886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   3.1e-18   3.1e-15       6     114 ..      48     156 ..      45     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.1e-18
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                     vlD+GCG G+ ++ la++   + +v+G+Dis++a++ A+ +a++ g+d v+F +gd+++l   ++   fD +++ + ++
  gi|121637307|ref|YP_977530.1|  48 DVLDIGCGLGDNAIYLARN---GYQVTGLDISPTALTTAKRRASDAGVD-VKFAVGDATKLTG-YT-GAFDTVIDCGMFH 121
                                    69***************54...678***********************8.**********885.66.9*******99996 PP

                Methyltransf_31  86 alad..pdkileeiervlkpggilliedpr....l 114
                                    +l d  + ++  +++r+ +pg  ll++ ++     
  gi|121637307|ref|YP_977530.1| 122 CLDDdgKRSYAASVHRATRPGATLLLSCFSnampP 156
                                    666533667778*********99999888744443 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0     7e-17     7e-14       1      99 []      50     145 ..      50     145 .. 0.89
   2 ?   -2.3   0.0       7.9   7.9e+03       3      36 ..     173     206 ..     172     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7e-17
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhl 79 
                                    L+iGcG G+++ +l+++  + ++tg+Disp a++ ak++ ++ +      v++ + d+ +l g  ++fD+v+ ++ +h+l
  gi|121637307|ref|YP_977530.1|  50 LDIGCGLGDNAIYLARN--GYQVTGLDISPTALTTAKRRASDAGV----DVKFAVGDATKLTGYtGAFDTVIDCGMFHCL 123
                                    8****************..**************888888888874....77888888777777788************** PP

                Methyltransf_12  80 ..kdirevldnirklLkpgGrl 99 
                                      + +r++ ++++++ +pg+ l
  gi|121637307|ref|YP_977530.1| 124 ddDGKRSYAASVHRATRPGATL 145
                                    9878889************875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.9
                Methyltransf_12   3 iGcGtGsllralleklpdieytgvDispsaieda 36 
                                    + +G G  ++ l++++ + e+ g+++  ++ + +
  gi|121637307|ref|YP_977530.1| 173 VLGGAGWDIESLEPATVRRELDGTEVEMAFWNVR 206
                                    5678888888899998888899998888777444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   2.2e-15   2.2e-12      24     124 ..      47     154 ..      24     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.2e-15
                Methyltransf_23  24 grvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvlrevlehv 95 
                                    g vLdiGcG G ++ +l++ng++vtg D+sp a   a+          k+a+ d +   + +   g fd+++   +++ +
  gi|121637307|ref|YP_977530.1|  47 GDVLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKrrasdagvDVKFAVGDAT---KLTGYTGAFDTVIDCGMFHCL 123
                                    69*****************************9988887765554333333333333...4444677************** PP

                Methyltransf_23  96 pd..ppellrqiatllkpgGylllseplasl 124
                                    +d    ++ +++++ ++pg+ llls + +  
  gi|121637307|ref|YP_977530.1| 124 DDdgKRSYAASVHRATRPGATLLLSCFSNAM 154
                                    *889******************999986544 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0     2e-12     2e-09      42     193 ..      50     189 ..      26     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2e-12
                                    EEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--...........-TTT---SS-..EEEEE CS
                           TPMT  42 lvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeysageiellcgdvFtlraeelgkfdliy 121
                                    l  +CG + +++ lA +g++v G+++s+ A++ + + a         +gv      +++   gd+  l+    g fd++ 
  gi|121637307|ref|YP_977530.1|  50 LDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASD-------AGV------DVKFAVGDATKLTGY-TGAFDTVI 115
                                    5569****************************95332222.......222......235567888776654.579***** PP

                                    EESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEEEE---S.----SS----HHHHHHHHG.GTEEEEEEEETT- CS
                           TPMT 122 draalvAlppelreryakslaelLkpdgeglLvtldypqa.eheGPPfsvpeaelealls.agfkvaeleeeda 193
                                    d +++  l+ + +  ya+s+++  +p++  lL   + ++  ++e P  +v+e++l+ +l+ ag+ +++le + +
  gi|121637307|ref|YP_977530.1| 116 DCGMFHCLDDDGKRSYAASVHRATRPGATLLLSCFSNAMPpDEEWPRSTVSEQTLRDVLGgAGWDIESLEPATV 189
                                    *****************************99999988775166689999**********9899****9997655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0     5e-11     5e-08      66     169 ..      49     152 ..      45     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5e-11
                                    EEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEE.EES-GGG-----SEEEEES-GGGTSGGG CS
                           CMAS  66 lLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvev.klldyedldekvdrvvsvgafehvgken 144
                                    +LdiGcG G  +++ +++ + +v gl +S     +ak+r  +++++ k  v + ++     + +d v+  g+f  +  + 
  gi|121637307|ref|YP_977530.1|  49 VLDIGCGLGDNAIYLARN-GYQVTGLDISPTALTTAKRRASDAGVDVKFAVgDATKLTGYTGAFDTVIDCGMFHCLDDDG 127
                                    8***************99.***********************99988887744556666777****************** PP

                                    HHHHHHHHHHHS-TT-EEEEEEEEE CS
                           CMAS 145 ydtffkklkkllkedGllllhtits 169
                                       + + ++++++++ +lll +   
  gi|121637307|ref|YP_977530.1| 128 KRSYAASVHRATRPGATLLLSCFSN 152
                                    *******************998765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.6e-10   1.6e-07      50     156 ..      48     152 ..      30     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.6e-10
                                    EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG- CS
                Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnv 129
                                    +vlD+ +G gD a+ l++   + ++v++lDi+++ L ++++++ + g+ +++f +++a +L    ++fD+v +  G+   
  gi|121637307|ref|YP_977530.1|  48 DVLDIGCGLGDNAIYLAR---NGYQVTGLDISPTALTTAKRRASDAGV-DVKFAVGDATKLTGYTGAFDTV-IDCGMFHC 122
                                    79************9975...6789******************99986.9*******************97.77787766 PP

                                    S-HH...HHHHHHHHHEEEEEEEEEEEE-- CS
                Ubie_methyltran 130 tDkl...kaLkeayrvlkpGGrlvvlefsk 156
                                     D +       +++r  +pG +l+   fs+
  gi|121637307|ref|YP_977530.1| 123 LDDDgkrSYAASVHRATRPGATLLLSCFSN 152
                                    554311134567888888888887766665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0     3e-10   2.9e-07      32     135 ..      47     149 ..      44     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3e-10
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--.--S-EEEEEEESSGGGS-G CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineak.lderydfilstvvlmflea 110
                                    g vld+gcg g n++yl+ +gy+vt +d   ++++  ++ ++   ++ ++ a+ d  +++     +d ++   ++  l+ 
  gi|121637307|ref|YP_977530.1|  47 GDVLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGVD-VKFAVGDATKLTgYTGAFDTVIDCGMFHCLDD 125
                                    789*********************************99999999998.99999999887637789999999999999999 PP

                                    GGHHHHHHHHHHTEEEEEEEEEEEE CS
                           TehB 111 eripsiienmqectkvggynlivaa 135
                                    +   s  + +++ t++g   l+++ 
  gi|121637307|ref|YP_977530.1| 126 DGKRSYAASVHRATRPGAT-LLLSC 149
                                    9999999999999999875.44444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   8.8e-10   8.8e-07      32     103 ..      46     116 ..      40     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.8e-10
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEEE CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdlivs 103
                                    +g+vlD+GcG G  ++ la++  +  vt +d++  Al+ ak+ +++ +++v++   d+++ +   + fd+++ 
  gi|121637307|ref|YP_977530.1|  46 HGDVLDIGCGLGDNAIYLARNGYQ--VTGLDISPTALTTAKRRASDAGVDVKFAVGDATKLTGyTGAFDTVID 116
                                    578****************98777..9******************************9987665688999886 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   4.9e-07   0.00048      17      91 ..      48     119 ..      44     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.9e-07
                Methyltransf_18  17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk.eeevdtvviaGm 91 
                                     v+DiG+  g  +iyl+++g    v+  Di++ +l++ak+ +++ag++  +++ ++d  +    ++ +dtv+ +Gm
  gi|121637307|ref|YP_977530.1|  48 DVLDIGCGLGDNAIYLARNGYQ--VTGLDISPTALTTAKRRASDAGVD--VKFAVGDATKLTGyTGAFDTVIDCGM 119
                                    589**************99975..9*********************95..67777777666663466********9 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.7e-07   0.00077      45     121 ..      47     125 ..      34     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.7e-07
                           NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkes.shiswivsdvqqfs.tdekfdlivvaevlyyied 121
                                    +d+l++Gc  G  +  la    ++t +d+ + a++ a++r  ++  ++++ v d +++   +  fd+++ + +++ ++d
  gi|121637307|ref|YP_977530.1|  47 GDVLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAgVDVKFAVGDATKLTgYTGAFDTVIDCGMFHCLDD 125
                                    79**************************************9886369********999735789999997776666655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0031      65     126 ..      56     115 ..      34     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                                    HHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                        UPF0020  65 lkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                    l ++a   ar+ +++ g+D+ + ++++a++ a+ agv+  ++f + da+kL+  +g +d+++
  gi|121637307|ref|YP_977530.1|  56 LGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGVD--VKFAVGDATKLTGYTGAFDTVI 115
                                    666777888999***********************997..6788899*****9999999998 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.4e-06    0.0034       4      61 ..      49     104 ..      46     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                    +lD+ +G G n+i +a+++ +v +++i++  l  a++ a   gv+  +++ +gd ++l
  gi|121637307|ref|YP_977530.1|  49 VLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGVD--VKFAVGDATKL 104
                                    89****************99****************999877765..55667776664 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.4e-05     0.014     164     230 ..      48     114 ..      43     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                           PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadvi 230
                                     vlD+G+G G  ai  a+ g  +v+++Di + A++ ak+ a+  +v+ k+ v  + +l+  ++ +d +
  gi|121637307|ref|YP_977530.1|  48 DVLDIGCGLGDNAIYLARNGY-QVTGLDISPTALTTAKRRASDAGVDVKFAVGDATKLTGyTGAFDTV 114
                                    69************9999886.69******************99999999884333333234666666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.2e-05     0.041      28      78 ..      48      92 ..      45     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                Methyltransf_32 28 tvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                   +v+D+G+G g  +  la     ++++v+g+d++    ++a++ra+  g  +
  gi|121637307|ref|YP_977530.1| 48 DVLDIGCGLGDNAIYLAR----NGYQVTGLDISPTALTTAKRRASDAG--V 92
                                   699*******98888888....69********************9998..3 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.22       9      41 ..      53      93 ..      51     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                   SCCHHHHHHHHHHTTSEEEEEESSHC........HHHTT-E CS
                     Mur_ligase  9 grgmsagalflalkGykvdGsdfies........lialGaa 41
                                   g g++  a +la  Gy+v+G d+ +         + ++G+ 
  gi|121637307|ref|YP_977530.1| 53 GCGLGDNAIYLARNGYQVTGLDISPTalttakrrASDAGVD 93
                                   56788899*****************9877777777777765 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00041      0.41     202     248 ..      46      92 ..      34     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00041
                tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaaqyniaanki 248
                                    +gd+l++ cG G+ ++ larn  +v   +i+ +++ +a+    +  +
  gi|121637307|ref|YP_977530.1|  46 HGDVLDIGCGLGDNAIYLARNGYQVTGLDISPTALTTAKRRASDAGV 92 
                                    78********************************9999877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1173.97
//
Query:       gi|121637308|ref|YP_977531.1|  [L=475]
Description: hypothetical protein BCG_1439c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   54.0  31.7    2.5e-14   53.5  31.7    1.2  1  DUF222           Domain of unknown function (DUF222)
      0.002   18.3   0.8     0.0032   17.6   0.8    1.3  1  HNH              HNH endonuclease
  ------ inclusion threshold ------
      0.011   15.6   0.4      0.019   14.8   0.4    1.4  1  HNH_5            HNH endonuclease
        6.1    6.5   9.0        4.3    7.0   0.6    2.2  2  Erythro_esteras  Erythromycin esterase


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5  31.7   5.6e-18   2.5e-14       4     268 ..      71     328 ..      68     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 5.6e-18
                         DUF222   4 aleeleaaarrlaavevllvael.....aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalra 78 
                                    +le+ + aa++ +a++++   +l     a+ +++++  ++ va++va + r s+a++ r +  A+al  ++p + aal  
  gi|121637308|ref|YP_977531.1|  71 ELERVKSAAAAGQARAAAALDKLrrcneADAGVPARRRGRGVASEVALARRDSPARGGRHLGFAKALVYEMPHTLAALEV 150
                                    55566666665555555555555545778899999999****************************************** PP

                         DUF222  79 GdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvr.rdeeaarrreltltkd 157
                                    G++++  ++ I+     l d +d +++d+++ a ++    +  a++a+++++++ rld+ +v  r+++a+++r +t++++
  gi|121637308|ref|YP_977531.1| 151 GRLSEWRATLIVRESACL-DVEDRRALDAELCADMSALDGMGDARIAAAARAIAYRLDAQAVVeRAARAETERTVTIRPA 229
                                    ************999999.******************************************9857777777********* PP

                         DUF222 158 edGmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvhvtae 237
                                     d m++++  l+ + +  + a+L++ a+++  +      R++ q  aD L++ +        ++++a ++  v v+++++
  gi|121637308|ref|YP_977531.1| 230 PDTMTWVTALLPVARGVSVYAALKRAADTTFDD------RTRGQVMADTLVERV--------TGQPAEAAQPVAVNLVLS 295
                                    ****************************99866......***********9987........5889999999******** PP

                         DUF222 238 eltaaagg..aaltgggglLpasdvrrLAkdAt 268
                                    + t  ag   +a+ +g+g++pa+ +r L +dA 
  gi|121637308|ref|YP_977531.1| 296 DETLLAGDraPAVVDGYGPIPAAVARNLVRDAV 328
                                    ***9999999899999***************97 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   7.2e-07    0.0032       3      42 ..     378     412 ..     372     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                            HNH   3 yCgrkfhksealevdHiipisqggaddieNlqllCksCHn 42 
                                    yC+ ++      + dH +p+++gg+++  N    C++C+ 
  gi|121637308|ref|YP_977531.1| 378 YCDAPI-----RHRDHAQPHHRGGPTTATNGLGSCERCNY 412
                                    666665.....466************************95 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   4.3e-06     0.019       4      43 ..     379     414 ..     372     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                          HNH_5   4 Cgkeiaekel.seeHIiPeslGGkltisnlvtlCkkCNqkk 43 
                                    C+ +     + +++H  P  +GG +t +n   +C++CN  k
  gi|121637308|ref|YP_977531.1| 379 CDAP-----IrHRDHAQPHHRGGPTTATNGLGSCERCNYVK 414
                                    3333.....3369*************************766 PP

>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.6   0.00096       4.3      68     113 ..      51      96 ..      40     131 .. 0.68
   2 ?    3.4   2.2     0.012        54     117     201 ..     197     278 ..     150     291 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00096
                                    -EEEEEE-S---HHHHHHHHHHHHC.HCCCCHHHHHHHCCHGGC.S.. CS
                Erythro_esteras  68 vrfyGlDlqslresldavldyLakv.dpelagaareryaclapl.adp 113
                                    v+++G+D    ++sl+a ++ L++v + ++ag+ar++ a+l++l +  
  gi|121637308|ref|YP_977531.1|  51 VSLAGVDSRDDEASLTARIAELERVkSAAAAGQARAA-AALDKLrR-C 96 
                                    99*******99**************545555555555.88888832.2 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                                    .TSSCCCCCHHHHHHHHHHHHCCHGGG.....GG.TSHHHHHHHHHHHHHHHHHHHC..CSSSSSCHHHHHHHHHHHHHH CS
                Erythro_esteras 117 rsaeaaelrscedevvallkellakreeyaaedg.eaeeffsaeqnarlvknaeryyragdeeswnlrllalRDrhMaen 195
                                    + a a  +r  +++vv+  ++ +++r+      + ++++  ++++   +++++  y +  ++ ++++ + + R + Ma++
  gi|121637308|ref|YP_977531.1| 197 AAARAIAYRLDAQAVVERAARAETERT---VTIRpAPDTMTWVTALLPVARGVSVYAAL-KRAADTTFDDRTRGQVMADT 272
                                    223333444445555444444333333...33335789999999999999988777764.344445556788******** PP

                                    HHHHHH CS
                Erythro_esteras 196 lealle 201
                                    l   + 
  gi|121637308|ref|YP_977531.1| 273 LVERVT 278
                                    987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2627.54
//
Query:       gi|121637309|ref|YP_977532.1|  [L=193]
Description: bifunctional pyrimidine regulatory protein PyrR/uracil phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-15   56.8   0.1    2.4e-15   56.4   0.1    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.026   14.0   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   2.7e-19   2.4e-15      14     137 ..      25     163 ..      14     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.7e-19
                                    EEEETTEEEEEE....--GGGE....EEEEEETTTHHHHHHHHHHS......TT-EE-EEEEEE-TTT--EE........ CS
                   Pribosyltran  14 avarlaaeilee....yngkpd....vvvgiargGvpfakiladeL......evplayvrkvkyrpdgseeaargssdes 79 
                                     + r+a++i+e+    ++  pd    v++gi+++Gv++a++la  +       v    ++++ yr+d + + +r +   s
  gi|121637309|ref|YP_977532.1|  25 TISRIAHQIIEKtaldDPVGPDaprvVLLGIPTRGVTLANRLAGNIteysgiHVGHGALDITLYRDDLMIKPPRPLASTS 104
                                    45666666666643334444447777************************998889999999999999999999888888 PP

                                    EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-.BSEEEEEEEEE-HHHHHHHHHH- CS
                   Pribosyltran  80 rlledpagkkVliVDDildtGgTllaalelLkekg.peevriavlvdkpateeevdkna 137
                                     +++ +++  V++VDD+l +G++++ al++L+++g p  v +avlvd++++e++ ++++
  gi|121637309|ref|YP_977532.1| 105 IPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGrPRAVQLAVLVDRGHRELPLRADY 163
                                    8*********************************8577***************998843 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-06     0.026     113     159 ..     103     148 ..      70     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
                        UPRTase 113 nkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsv 159
                                    + +P+   ++  v+l+D v+ +G+s+ +a++ L++ g    + + l+v
  gi|121637309|ref|YP_977532.1| 103 TSIPAGGiDDALVILVDDVLYSGRSVRSALDALRDVG--RPRAVQLAV 148
                                    556666558889***********************55..444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1066.07
//
Query:       gi|121637310|ref|YP_977533.1|  [L=319]
Description: aspartate carbamoyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-40  137.0   0.0    7.5e-40  136.3   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.1e-20   74.3   0.0      3e-20   72.9   0.0    1.7  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   8.4e-44   7.5e-40       1     147 [.       4     152 ..       4     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 8.4e-44
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT..TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk..ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                    rhll+ +dls+++ +++ld a+++ ++      kk ++l+g+t++++F+e+StRTrvSfevA k ++++v+++s+a    
  gi|121637310|ref|YP_977533.1|   4 RHLLTAADLSRDDATAILDDADRFAQALVGrdIKKLPTLRGRTVVTMFYENSTRTRVSFEVAGKWMSADVINVSAA---- 79 
                                    8************************9887667889999************************************66.... PP

                                    TTTGGSTTSSCHHHHHHHHHHHT.SEEEEEESSHHHHHHHHHHH.....SSEEEEEEETSSB-HHHHHHHHHHHH CS
                       OTCace_N  79 lssvskgrkEsleDtarvlsryv.daiviRhpgaeeleelakya.....svpviNagdgdgeHPtQaLaDlltir 147
                                     ssv kg  Esl+Dta +l + + da++iRhp++  ++ la++         viNagdg++eHPtQaL+D+ltir
  gi|121637310|ref|YP_977533.1|  80 GSSVGKG--ESLRDTALTLRAAGaDALIIRHPASGAAHLLAQWTgahndGPAVINAGDGTHEHPTQALLDALTIR 152
                                    6888899..***********************55559999998899999999**********************8 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   3.4e-24     3e-20       2     156 ..     160     305 ..     159     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 3.4e-24
                                    C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                         OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                    g +i++vGd  +++va+s + ll  lg++vvlvaP++l p           +  +g   t+++d  + +  aD v + ++
  gi|121637310|ref|YP_977533.1| 160 GRRIVIVGDiLHSRVARSNVMLLDTLGAEVVLVAPPTLLP-----------VGVTGWPATVSHDFDAELPAADAVLMLRV 228
                                    889*******9**************************666...........23469999********************* PP

                                    SETTCCGGHHHHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  81 vsmgeekereerlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    +    +   + +++++   y +te   ++   +a+vlH+ P++rg+E+t++V ds +s+v +q++N++ +++A+l++
  gi|121637310|ref|YP_977533.1| 229 QAERMNGGFFPSVREYSVrYGLTERRQAMLPGHAVVLHPGPMVRGMEITSSVADSSQSAVLQQVSNGVQVRMAVLFH 305
                                    *444455555999999988********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1765.34
//
Query:       gi|121637311|ref|YP_977534.1|  [L=430]
Description: dihydroorotase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-23   81.9   0.4    2.9e-22   79.5   0.4    1.9  1  Amidohydro_1  Amidohydrolase family
    2.7e-13   50.0   0.0    4.6e-13   49.3   0.0    1.3  1  DHOase        Dihydro-orotase-like
    1.8e-11   44.2   7.6    2.5e-06   27.3   0.7    2.5  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.4   4.9e-26   2.9e-22       1     343 [.      48     421 ..      48     422 .. 0.73

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4.9e-26
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEE CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglril 80 
                                    ++lPG++D+H+Hl+             +p++++ae +e+g ++a  +G t v +m +t++   ++    +++++     +
  gi|121637311|ref|YP_977534.1|  48 VLLPGFVDLHTHLR-------------EPGREYAEDIETGSAAAALGGYTAVFAMANTNPV--ADSPVVTDHVWHRGQQV 112
                                    589**********9.............******************************9744..33333344432221112 PP

                                    EESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH........HHHHHHHHHHHHTTEEEEEE CS
                   Amidohydro_1  81 ggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsde........elkealkeakkrdlpvaiHa 152
                                    g        ++ ++   +   +aga      ++ g+     + +    fsd+         ++ al+ a   ++ +a Ha
  gi|121637311|ref|YP_977534.1| 113 G-------LVDVHPVGAVTVGLAGA----ELTEMGM--MNAGAAQVRMFSDDgvcvhdplIMRRALEYATGLGVLIAQHA 179
                                    2.......44555555555555776....2233334..44666677888888999999999******************* PP

                                    TSSCHHHHHHHHHHT..TTEEEETTTTSTCC......HHTTTHCCEEEHCTCEEEHH.HHHHHHHHHHHHCEE....... CS
                   Amidohydro_1 153 letkgevedaeaafg..etiehgthlevaes......lglldeiklilahgvhltpt.eaellkerlkeagva....... 216
                                     e + +v +  ++++   +   ++  + ae+      + l+++   +++h++h +++ ++e+lk  +k+ g++       
  gi|121637311|ref|YP_977534.1| 180 EEPRLTVGAFAHEGPmaARLGLAGWPRAAEEsivardALLARD-AGARVHICHASAAgTVEILKW-AKDQGISitaevtp 257
                                    9988888555554441134444444555555666666666666.666999999996643444433.36667776688888 PP

                                    .HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT..........TSSCCGGHHHHHHHHHHHHHH CS
                   Amidohydro_1 217 .hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga..........asgnslnlleelrlalklqrg 270
                                     h+  ++ +                +s+  alr+al +G++  ++tD+a                   + + l+l ++ +
  gi|121637311|ref|YP_977534.1| 258 hHLLLDDARlasydgvnrvnpplrEASDAVALRQALADGIIDCVATDHAphaehekcveF-----AAARPGMLGLQTALS 332
                                    844444444556666666777777***************************988555552.....333335555555555 PP

                                    CCTT..TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT..............CGGGTTTCTSEEE CS
                   Amidohydro_1 271 llye..deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi..............laafvglkkdgnv 334
                                    +  +  ++ g ls+ ++ r+++ n+A + +l+d+   +evG +A+l+vvd+d               +++f+ ++ + +v
  gi|121637311|ref|YP_977534.1| 333 VVVQtmVAPGLLSWRDIARVMSENPACIARLPDQGRPLEVGEPANLTVVDPDAtwtvtgadlasrsaNTPFESMSLPATV 412
                                    55555677799*********************99999*************94445668888899**************** PP

                                    EEEEETTEE CS
                   Amidohydro_1 335 kkvivkGkl 343
                                    + + ++Gk+
  gi|121637311|ref|YP_977534.1| 413 TATLLRGKV 421
                                    *******97 PP

>> DHOase  Dihydro-orotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   7.7e-17   4.6e-13       2     138 ..      47     233 ..      46     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 7.7e-17
                         DHOase   2 rllvpglidlavhlrelsgeakeliet...........tvaaygvtfkaP........................aaitve 46 
                                    ++l+pg++dl+ hlre++ e  e iet            v a+++t++                           a+tv+
  gi|121637311|ref|YP_977534.1|  47 HVLLPGFVDLHTHLREPGREYAEDIETgsaaaalggytAVFAMANTNPVAdspvvtdhvwhrgqqvglvdvhpvGAVTVG 126
                                    799*********************************98899999999977888********************9888999 PP

                         DHOase  47 ddsee.............afiltddtvyvtiqllefeglkk.aeLdqalkaiaeDDevtnqsavqdfelarfyGvqLkG. 111
                                      + e               +++dd+v v   l++  +l+  + L+  + ++ae+  +t ++  +++ +a + G  L G 
  gi|121637311|ref|YP_977534.1| 127 LAGAEltemgmmnagaaqVRMFSDDGVCVHDPLIMRRALEYaTGLGVLIAQHAEEPRLTVGAFAHEGPMAARLG--LAGw 204
                                    888889999999999987889*******************9889******************************..***9 PP

                         DHOase 112 ..vCeaekivydvLlakaagcgfyvsiiy 138
                                      + e+  +++d Lla++ag+  ++++ +
  gi|121637311|ref|YP_977534.1| 205 prAAEESIVARDALLARDAGARVHICHAS 233
                                    9999***********************87 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.7   4.1e-10   2.5e-06       1      28 [.      40      67 ..      40     107 .. 0.81
   2 !   21.1   1.0     3e-08   0.00018     347     472 ..     274     422 ..      61     423 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.1e-10
                   Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnl 28
                                   +viDa+G ++lPGFvD HtHl + g ++
  gi|121637311|ref|YP_977534.1| 40 DVIDATGHVLLPGFVDLHTHLREPGREY 67
                                   69******************99988444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3e-08
                   Amidohydro_3 347 srlgperargs..tpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg......evlrpdeelsleealaly 417
                                    +r++p+ +++s   +++  l++g+  + ++D ap +   +  ++ aa ++  + +       + + +   ls++++++ +
  gi|121637311|ref|YP_977534.1| 274 NRVNPPLREASdaVALRQALADGIIDCVATDhAPHAEHEKCVEFAAARPGMLGLQTalsvvvQTMVAPGLLSWRDIARVM 353
                                    456666666665577889999999999999988888888888888887765543338898997777788*********** PP

                   Amidohydro_3 418 TrgpAkalgledrkGt.LevGadADlvvld.adpldvdppelaear.............vrltvvdGrvv 472
                                    +++pA + +l+d  G+ LevG +A+l+v d ++  +v+ ++la+               v +t+ +G+v+
  gi|121637311|ref|YP_977534.1| 354 SENPACIARLPDQ-GRpLEVGEPANLTVVDpDATWTVTGADLASRSantpfesmslpatVTATLLRGKVT 422
                                    ************9.8779************6555677777777777999999999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2538.55
//
Query:       gi|121637312|ref|YP_977535.1|  [L=165]
Description: export or membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 911.21
//
Query:       gi|121637313|ref|YP_977536.1|  [L=376]
Description: carbamoyl phosphate synthase small subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-47  159.5   0.0    5.8e-47  158.7   0.0    1.4  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    9.3e-38  129.9   0.0    1.3e-37  129.5   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    3.1e-09   36.9   0.1    1.6e-07   31.3   0.1    2.4  2  Peptidase_C26    Peptidase C26
     0.0047   16.6   0.7      0.011   15.4   0.7    1.5  1  GP38             Phage tail fibre adhesin Gp38


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.0   1.3e-50   5.8e-47       1     127 [.       3     132 ..       3     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 1.3e-50
                CPSase_sm_chain   1 kavLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedves..ekikvaglv 77 
                                    kavLvLedG+vf+G+ fg +++a GE vf+Tgm+GYqe+ltDpsY++qi+v t+p+iGn+G+n ed es  e+i+vag+ 
  gi|121637313|ref|YP_977536.1|   3 KAVLVLEDGRVFTGRPFGaTGQALGEAVFSTGMSGYQETLTDPSYHRQIVVATAPQIGNTGWNGEDSESrgERIWVAGYA 82 
                                    589***************779**********************************************998889******* PP

                CPSase_sm_chain  78 vrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                    vr+ s ++snwra+ +L++ l +++i+gi+g+DTR ++++lr++g+mk+ 
  gi|121637313|ref|YP_977536.1|  83 VRDPSPRASNWRATGTLEDELIRQRIVGIAGIDTRGVVRHLRSRGSMKAG 132
                                    ***********************************************985 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   2.8e-41   1.3e-37       4     189 ..     189     369 ..     186     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 2.8e-41
                                    ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHH CS
                         GATase   4 DnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQ 82 
                                    D +  ++ n  ++++++g++++v+p ++++e+i   + np+g+++s+Gpg+p+ +++ +++++e+++++iP++GIC+G+Q
  gi|121637313|ref|YP_977536.1| 189 DLG--IKTNTPRNFARRGIRCHVLPASTTFEQIA--ELNPHGVFLSNGPGDPAtADHVVALTREVLGAGIPLFGICFGNQ 264
                                    666..99**************************5..79***************99************************* PP

                                    HHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESG.....CHHHTT.EEEEEEEETTEEEEE CS
                         GATase  83 llaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpk.....elepag.levtakseddeelme 156
                                    +l+ ++g +++k+  ++h+g ++++ d      + ++++  ++++H+++++ +     +  p g  +v++++++d+ +++
  gi|121637313|ref|YP_977536.1| 265 ILGRALGLSTYKMV-FGHRGINIPVVD------HATGRVAVTAQNHGFALQGEagqsfA-TPFGpAVVSHTCANDGVVEG 336
                                    **************.************......9999**************99998633.3444699********99999 PP

                                    EEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                         GATase 157 iiekknpfvgvQFHPEststpegpellfnflik 189
                                    +   + ++++vQ+HPE+  +p+++e+lf+++++
  gi|121637313|ref|YP_977536.1| 337 VKLVDGRAFSVQYHPEAAAGPHDAEYLFDQFVE 369
                                    999999************************997 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.9   8.6e+03     170     184 ..      44      58 ..      34      60 .. 0.72
   2 !   31.3   0.1   3.6e-11   1.6e-07      92     216 .]     240     352 ..     228     352 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                  Peptidase_C26 170 vnslHhqaikelaee 184
                                      s+H+q +   a++
  gi|121637313|ref|YP_977536.1|  44 DPSYHRQIVVATAPQ 58 
                                    468999998877765 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 3.6e-11
                  Peptidase_C26  92 alelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievn 171
                                     + +aL r++l +g+P++giC G q+l  alG ++y+ +  + g++    +  ++a+ +v v+ +         + ++ +
  gi|121637313|ref|YP_977536.1| 240 DHVVALTREVLGAGIPLFGICFGNQILGRALGLSTYKMVFGHRGIN---IPVVDHATGRVAVTAQN--------HGFALQ 308
                                    56689*********************************99522222...22223334444444333........444444 PP

                  Peptidase_C26 172 slHhqaike.laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        q+  +  ++ +    +a+Dgv+E +++ +    +++vQ+HPE
  gi|121637313|ref|YP_977536.1| 309 GEAGQSFATpFGPAVVSHTCANDGVVEGVKLVDG--RAFSVQYHPE 352
                                    4445555442788888888999**********95..599******9 PP

>> GP38  Phage tail fibre adhesin Gp38
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7   2.4e-06     0.011     178     255 ..      16      99 ..      10     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                           GP38 178 GrPfGlgG...sgsklsggaasltapGagsgsgsaytgGnGGdvGaaGgrangknvkeseggaaGkaviGsaP...twqn 251
                                    GrPfG++G   +++ +s+g + ++++ +  ++  ++   +  ++G++G ++ +++++      aG+av   +P   +w++
  gi|121637313|ref|YP_977536.1|  16 GRPFGATGqalGEAVFSTGMSGYQETLTDPSYHRQIVVATAPQIGNTGWNGEDSESRGERIWVAGYAVRDPSPrasNWRA 95 
                                    9*******8877899**********999999*****99999999999999999999999999******988775447999 PP

                           GP38 252 vGti 255
                                    +Gt+
  gi|121637313|ref|YP_977536.1|  96 TGTL 99 
                                    9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2525.25
//
Query:       gi|121637314|ref|YP_977537.1|  [L=1115]
Description: carbamoyl phosphate synthase large subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-102  341.5   0.0      3e-65  219.7   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.4e-36  124.8   0.0    4.8e-36  123.8   0.0    1.5  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
      1e-21   76.9   0.0    3.4e-21   75.2   0.0    2.0  1  MGS              MGS-like domain
    3.9e-13   49.3   0.0    4.5e-08   32.8   0.0    2.3  2  ATP-grasp        ATP-grasp domain
    1.3e-12   47.7   0.0    9.9e-06   25.2   0.0    2.3  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.9e-09   36.7   0.1    5.1e-05   23.0   0.0    2.9  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    1.4e-06   28.5   0.0     0.0003   20.9   0.0    2.5  2  ATP-grasp_3      ATP-grasp domain
    1.7e-06   27.9   0.0     0.0084   15.9   0.0    2.6  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00087   18.9   0.0        0.6    9.6   0.0    2.5  2  ATP-grasp_2      ATP-grasp domain
     0.0009   18.9   0.0      0.019   14.6   0.0    2.7  2  ATP-grasp_4      ATP-grasp domain
      0.003   17.0   0.0       0.15   11.5   0.0    2.4  2  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.0   1.8e-68     3e-65       1     210 [.     133     339 ..     133     340 .. 0.98
   2 !  119.9   0.0   6.4e-38     1e-34       1     209 [.     688     889 ..     688     891 .. 0.94

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 1.8e-68
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    D++++k++++k++ + ++s  +   t+ e+ + ++e+g Pv+++++f++GG+G+++a++++e+  ++ ++la+++    +
  gi|121637314|ref|YP_977537.1| 133 DRQRFKDIVAKAGGESARSRVC--FTMAEVRETVAELGLPVVVRPSFTMGGLGSGIAYSTDEVDRMAGAGLAASP----S 206
                                    9*******************99..9*************************************************7....8 PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-.EEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgv.vga 157
                                    ++vl+e+s+ g+ke E+e++rD ++nv++vc++en++++  +t+++++vAP+ tLtd+e+q++r   ++++revgv +g+
  gi|121637314|ref|YP_977537.1| 207 ANVLIEESIYGWKEFELELMRDGHDNVVVVCSIENVDPMgvHTGDSVTVAPAMTLTDREYQRMRDLGIAILREVGVdTGG 286
                                    89**************************************************************************5578 PP

                                    EEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                    CPSase_L_D2 158 gtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    ++++f+++p++++ +viE+N+R+s++sala+kaTG++++k+aak+a g++L+e
  gi|121637314|ref|YP_977537.1| 287 CNIQFAVNPRDGRLIVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDE 339
                                    9**************************************************97 PP

  == domain 2  score: 119.9 bits;  conditional E-value: 6.4e-38
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    D+ ++ ++l++++ p  +  +a  +t  +a +ia+eigyPv++++++ lGG+Gm ++++ee+l+  +++a++ ++    +
  gi|121637314|ref|YP_977537.1| 688 DRGAFGDLLSAAGLPAPKYGTA--TTFAQARRIAEEIGYPVLVRPSYVLGGRGMEIVYDEETLQGYITRATQLSP----E 761
                                    8889999999999999987777..8*************************************************7....9 PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgag 158
                                    + vlv+++l+   ei+v+ l D ++  i  + +e + +   + +++    P  tL +++ +++r+a+ ++++ +gvvg  
  gi|121637314|ref|YP_977537.1| 762 HPVLVDRFLEDAVEIDVDALCDGAEVYIG-GIMEHIEEAgiHSGDSACALPPVTLGRSDIEKVRKATEAIAHGIGVVGLL 840
                                    **********************9986664.66888887778*************************************** PP

                                    EEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                    CPSase_L_D2 159 tveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                    +v+++l+  ++  yv+E N+R s+  +  +kaT ++l+k+ a+i lg+++ 
  gi|121637314|ref|YP_977537.1| 841 NVQYALK--DDVLYVLEANPRASRTVPFVSKATAVPLAKACARIMLGATIA 889
                                    ******9..599***********************************9976 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0     3e-39   4.8e-36       2     122 .]     429     549 ..     428     549 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 3e-39
                    CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaell. 80 
                                    +l++p + R++ i  alr g++ve+++e++ +dpwF+++++elv+l++el ++   l++ellr+ak+ G+sD+qia+l  
  gi|121637314|ref|YP_977537.1| 429 RLRTPAEGRLYDIELALRLGATVERVAEASGVDPWFIAQINELVNLRNELVAAP-VLNAELLRRAKHSGLSDHQIASLRp 507
                                    799************************************************998.7********************9986 PP

                    CPSase_L_D3  81 .eeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                         e+ vr+lr +lgi+pvyk+vDtcAaeFea+tpY+Ys+Y
  gi|121637314|ref|YP_977537.1| 508 eL-AGEAGVRSLRVRLGIHPVYKTVDTCAAEFEAQTPYHYSSY 549
                                    42.45678**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   2.1e-24   3.4e-21       2      95 .]     986    1078 ..     985    1078 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 2.1e-24
                                     HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH..HHHHHHHTTSCCEEEEE--THHHHHHC CS
                            MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv..eildaikngeidlvintlypfkatvak 77  
                                     lv  +k+l++lgf++lAT+GTa++l+ +gip+ +v ++++   ++g r   + +dai++ge+++vint+y+++  +  
  gi|121637314|ref|YP_977537.1|  986 LVFPVKRLADLGFRVLATEGTAEMLRRNGIPCDDVRKHFEPA-QPG-RPtmSAVDAIRAGEVNMVINTPYGNSGPRI- 1060
                                     67789**************************99999999998.554.4445************************98. PP

                                     HHHHHHHHHHHTTSHEES CS
                            MGS   78 dgykirraaenidIplpt 95  
                                     dgy+ir aa+  +Ip++t
  gi|121637314|ref|YP_977537.1| 1061 DGYEIRSAAVAGNIPCIT 1078
                                     ****************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.6e-05     0.026       9     161 ..     149     310 ..     141     318 .. 0.81
   2 !   32.8   0.0   2.8e-11   4.5e-08       2     160 ..     697     860 ..     696     863 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                    -EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEE CS
                      ATP-grasp   9 prflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvr 84 
                                    +r  +  + +e++e+++elglpvvv+ +     G G+ +  s +++++++ a      + +v++Ee +   kE  +  +r
  gi|121637314|ref|YP_977537.1| 149 ARSRVCFTMAEVRETVAELGLPVVVR-PSFTMGGLGSGIAYSTDEVDRMAGAGlaasPSANVLIEESIYGWKEFELELMR 227
                                    556666677899**************.8888999999999999998888776666778999********999999999** PP

                                    ETTC-EEE--EEEEEEETTEEE...EEEECEE.-SCHHHHHHHHHHHHHHHHHTS.SEEEEEEEEEE.TTCTEEEEEEES CS
                      ATP-grasp  85 saeGetafypvvetvqedgilr...lsvapae.vsekaqkkaeeiakkiveeLgg.vGvfavElFvl.edgellvnElap 158
                                    + + +++++  +e+v   g+     + vapa  +++++ ++ +++   i++e+g+  G   + + v  +dg+l+v E+ p
  gi|121637314|ref|YP_977537.1| 228 DGHDNVVVVCSIENVDPMGVHTgdsVTVAPAMtLTDREYQRMRDLGIAILREVGVdTGGCNIQFAVNpRDGRLIVIEMNP 307
                                    ***************999887532256677651455577788888889999998756888888887767888******** PP

                                    S-- CS
                      ATP-grasp 159 RpH 161
                                    R+ 
  gi|121637314|ref|YP_977537.1| 308 RVS 310
                                    985 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.8e-11
                                    HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEE CS
                      ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekE 77 
                                    +++glp p++ ++++ ++++++aee+g+pv+v+ +     G+G  +v +ee+l+  ++ +     e++v+v  f +  +E
  gi|121637314|ref|YP_977537.1| 697 SAAGLPAPKYGTATTFAQARRIAEEIGYPVLVR-PSYVLGGRGMEIVYDEETLQGYITRAtqlsPEHPVLVDRFLEDAVE 775
                                    5789*****************************.99999***************9998887888899************* PP

                                    EEEEEEEETTC-EEE--EEEEEEETTEEE....EEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEE CS
                      ATP-grasp  78 lsvlvvrsaeGetafypvvetvqedgilr....lsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellv 153
                                    + v +  +   e+++  ++e+++e gi        + p ++ +++ +k+++ ++ i++ +g+vG++ v   ++ d+ l+v
  gi|121637314|ref|YP_977537.1| 776 IDVDALCDGA-EVYIGGIMEHIEEAGIHSgdsaCALPPVTLGRSDIEKVRKATEAIAHGIGVVGLLNVQYALK-DDVLYV 853
                                    *988776554.489999999999988765221156668889999************************98777.777999 PP

                                    EEEESS- CS
                      ATP-grasp 154 nElapRp 160
                                     E  pR 
  gi|121637314|ref|YP_977537.1| 854 LEANPRA 860
                                    9999996 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.3e-07   0.00038      28     174 ..     160     307 ..     149     315 .. 0.84
   2 !   25.2   0.0   6.1e-09   9.9e-06       1     173 [.     695     857 ..     695     865 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHH..HHHTT-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEE CS
                Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaie..eafkydekvlvEeai.egreievavlgneklevsevgei 104
                                    +++ ++elg+pv+V+p+ +   +G   + s++e+ ++     a++  ++vl+Ee i   +e+e  ++ +++ +v +v  i
  gi|121637314|ref|YP_977537.1| 160 VRETVAELGLPVVVRPSFTMGGLGSGIAYSTDEVDRMAGagLAASPSANVLIEESIyGWKEFELELMRDGHDNVVVVCSI 239
                                    678999***********9988899999999999988765116888899********889*********999888888777 PP

                                    E-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT-.-SEEEEEEEE.ETTTEEEEEEEES CS
                Dala_Dala_lig_C 105 vvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldl.rGlaRvDffl.teegeivlnEvNt 174
                                       +        +++d++++    +l++ +++++++l + + + +++ +G + + f +  ++g++++ E+N+
  gi|121637314|ref|YP_977537.1| 240 ENVD----PMGVHTGDSVTVAPAMTLTDREYQRMRDLGIAILREVGVdTGGCNIQFAVnPRDGRLIVIEMNP 307
                                    6544....3344567889999999999999***********9999984699999999977899999999996 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 6.1e-09
                                    HHHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEE CS
                Dala_Dala_lig_C   1 llkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvE 78 
                                    ll+aaGlp ++y + +   + ++     +++ ee+gypv+V+p+      G++ v  ee l+ +i +a +   ++ vlv+
  gi|121637314|ref|YP_977537.1| 695 LLSAAGLPAPKYGTATT--FAQA-----RRIAEEIGYPVLVRPSYVLGGRGMEIVYDEETLQGYITRATQLspEHPVLVD 767
                                    57778888888876543..3444.....4899************999999******************99733577**** PP

                                    E--.ESEEEEEEEEETSS.CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEE CS
                Dala_Dala_lig_C  79 eai.egreievavlgnek.levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaR 156
                                    +++ ++ ei+v  l +++ + +  + e++ + g+       s+d+a    p++l ++  ek++++   + + +++ Gl  
  gi|121637314|ref|YP_977537.1| 768 RFLeDAVEIDVDALCDGAeVYIGGIMEHIEEAGIH------SGDSACALPPVTLGRSDIEKVRKATEAIAHGIGVVGLLN 841
                                    ***99******888766647788888888887775......456666677777777777777777777777777777777 PP

                                    EEEEEETTTEEEEEEEE CS
                Dala_Dala_lig_C 157 vDfflteegeivlnEvN 173
                                    v + l+ ++ +++ E N
  gi|121637314|ref|YP_977537.1| 842 VQYALK-DDVLYVLEAN 857
                                    777776.6677777777 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00028      0.46      55     118 ..     275     342 ..     262     350 .. 0.74
   2 !   23.0   0.0   3.1e-08   5.1e-05      45     111 ..     819     886 ..     761     899 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                   ATPgrasp_Ter  55 rlaeefgld.glvnvQvred.edg.pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteevee 118
                                    ++ +e+g+d g  n+Q+  + +dg + ++E+NpR+s      s ++G  ++++a+kl+ g   +e+++
  gi|121637314|ref|YP_977537.1| 275 AILREVGVDtGGCNIQFAVNpRDGrLIVIEMNPRVSRSSAlASKATGFPIAKIAAKLAIGYTLDEIVN 342
                                    5666777752568999986525557999*******96555156777*************987666665 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.1e-08
                   ATPgrasp_Ter  45 kdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgl 111
                                    + e++ +++e++a+ +g+ gl nvQ+  ++d +++LE NpRas ++   s ++ v l+++ ++ +lg 
  gi|121637314|ref|YP_977537.1| 819 DIEKVRKATEAIAHGIGVVGLLNVQYALKDDVLYVLEANPRASRTVPFvSKATAVPLAKACARIMLGA 886
                                    34567778889999*******************************98526666899999999999885 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        22      31     158 ..     168     309 ..     154     312 .. 0.61
   2 !   20.9   0.0   1.8e-07    0.0003       8     158 ..     693     860 ..     686     863 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                    SSSEEEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET... CS
                    ATP-grasp_3  31 ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdgekvlvlavnrqliekaek 101
                                      ++vv p+  +gg +  ++   +e +++             l+ e i G k++ ++l+ dg++++v++++ + ++    
  gi|121637314|ref|YP_977537.1| 168 GLPVVVRPSFTMGGLGSGIAYSTDEVDRMAGAGLaaspsanvLIEESIYGwKEFELELMRDGHDNVVVVCSIENVDPM-- 245
                                    567888888888888777776666655443332245667777999999997789999999999999999988888763.. PP

                                    .TEEEEEEE...S----H...HHHHHHHHHHHHTTSTT--EEEEEEEE..ESS.SEEEEEEESS- CS
                    ATP-grasp_3 102 efvyaGnvt...pietel...keevvelaeevvekleglaGyvGvDlv..lkdeepyviEvNPRl 158
                                      v +G ++   p+ t      +++++l   +++++    G   + +    +d+ ++viE NPR+
  gi|121637314|ref|YP_977537.1| 246 -GVHTGDSVtvaPAMTLTdreYQRMRDLGIAILREVGVDTGGCNIQFAvnPRDGRLIVIEMNPRV 309
                                    .555555441113333331113344444444444442112333344443345699*********7 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.8e-07
                                    HHHHTTT.S---.......-EESS--....SSSEEEEESS-------B--SS--TTE...............EEEE---. CS
                    ATP-grasp_3   8 ykkLkeagvkvP...tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefie. 71 
                                     + L++ag+++P   t ++ +++++      +++ v p++  gg ++ +v ++e+++  i   +        lv +f+e 
  gi|121637314|ref|YP_977537.1| 693 GDLLSAAGLPAPkygTATTFAQARRIaeeiGYPVLVRPSYVLGGRGMEIVYDEETLQGYITRATqlspehpvLVDRFLEd 772
                                    5678999999997773333333333344569**********************9999888877789999999******94 PP

                                    SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SE CS
                    ATP-grasp_3  72 GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkdeep 149
                                      ++ v++l+dg +v++  + + + e + ++   a  + p+   +   e+v+++ e + + + g++G++ v   lkd+ +
  gi|121637314|ref|YP_977537.1| 773 AVEIDVDALCDGAEVYIGGIMEHIEEAGIHSGDSACALPPVTLGRsdIEKVRKATEAIAHGI-GVVGLLNVQYALKDDVL 851
                                    579************99999888877755544444444555433322444444444455555.99999999999****** PP

                                    EEEEEESS- CS
                    ATP-grasp_3 150 yviEvNPRl 158
                                    yv+E NPR 
  gi|121637314|ref|YP_977537.1| 852 YVLEANPRA 860
                                    ********6 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00056      0.91       6     145 ..     137     268 ..     133     287 .. 0.80
   2 !   15.9   0.0   5.2e-06    0.0084       8     106 ..     694     788 ..     691     861 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00056
                                    HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEE CS
                         GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvvi 85 
                                     kd+++kag ++a+ ++   ++e++e + e++ ++ Vv+++   +g g  +a s++e  +++   l      + +++v+i
  gi|121637314|ref|YP_977537.1| 137 FKDIVAKAGGESARSRVCFTMAEVRETVAELGLPV-VVRPSFTMGGLGSGIAYSTDEVDRMAGAGLA----ASPSANVLI 211
                                    58999999999999999999***************.********************98888887776....567899*** PP

                                    EE---S.EEEEEEEEECTTEEEE---BEEEEEEECCC.EEEEECECEEEES-TTS-HHHHHH CS
                         GARS_A  86 EelleG.eEvsllalvdgktvkplplaqdhkrvlegD.kgpnTGGmGayspapvvteellek 145
                                    Ee + G +E+ l  + dg++ + +  + +     + D  g+ TG   +++pa ++t+ ++++
  gi|121637314|ref|YP_977537.1| 212 EESIYGwKEFELELMRDGHDNVVVVCSIE-----NVDpMGVHTGDSVTVAPAMTLTDREYQR 268
                                    ******77**********98766554422.....2221466666666666666666666665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.2e-06
                                    HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE CS
                         GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEe 87 
                                    dll++ag+p+++y + t  ++a+ + ee + ++  v+++ + +g+g+ ++ +ee    +++   +     + ++ v+++ 
  gi|121637314|ref|YP_977537.1| 694 DLLSAAGLPAPKYGTATTFAQARRIAEEIGYPV-LVRPSYVLGGRGMEIVYDEETLQGYITRATQ----LSPEHPVLVDR 768
                                    68999****************************.9*****************9988888777765....46899****** PP

                                    ---.SEEEEEEEEECTTEEE CS
                         GARS_A  88 lle.GeEvsllalvdgktvk 106
                                    +le   E+ + al+dg +v+
  gi|121637314|ref|YP_977537.1| 769 FLEdAVEIDVDALCDGAEVY 788
                                    **8358**********9986 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00037       0.6       8      71 ..     138     196 ..     135     238 .. 0.83
   2 !    6.4   0.0    0.0036       5.8       9      54 ..     694     738 ..     692     754 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00037
                                    HHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHH CS
                    ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakea 71 
                                    k+i+ak g ++++++v+++  e++e++++lg  + vv+    +GG G +  +  ++s++e+ ++
  gi|121637314|ref|YP_977537.1| 138 KDIVAKAGGESARSRVCFTMAEVRETVAELGLPV-VVRPSFTMGGLGSG--I--AYSTDEVDRM 196
                                    899*****************************99.*********98854..4..3344444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                                    HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCC CS
                    ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRG 54 
                                    ++l+  g+++p+   a++  +a+++a+++g  +  v+     GGRG
  gi|121637314|ref|YP_977537.1| 694 DLLSAAGLPAPKYGTATTFAQARRIAEEIGYPV-LVRPSYVLGGRG 738
                                    589999**************************9.77777788***8 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.019      51     151 ..     205     308 ..     168     314 .. 0.84
   2 ?    0.9   0.0      0.18     3e+02       1      36 [.     722     757 ..     722     859 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                    ATP-grasp_4  51 eeesflvEeyieG.eEfavdayfdeeGepvilnilkkefaseedvsdrlyvtsak.vieetlealeellkevnallglkn 128
                                     ++++l+Ee i G +Ef +++  d + + v++  ++    +  ++ d + v +a  ++  + +++ +l  ++ +++g+  
  gi|121637314|ref|YP_977537.1| 205 PSANVLIEESIYGwKEFELELMRDGHDNVVVVCSIENVDPMGVHTGDSVTVAPAMtLTDREYQRMRDLGIAILREVGVDT 284
                                    47899********88******99877777766666788888888999**9999861566677899*************** PP

                    ATP-grasp_4 129 fpvHiElrvs.edgkiipiEvnpl 151
                                    + + i + v+  dg++i+iE+np+
  gi|121637314|ref|YP_977537.1| 285 GGCNIQFAVNpRDGRLIVIEMNPR 308
                                    *********94568*********6 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                    ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaiee 36 
                                    i +Pv ++Ps   + +G+ ++ +ee ++  + +  +
  gi|121637314|ref|YP_977537.1| 722 IGYPVLVRPSYVLGGRGMEIVYDEETLQGYITRATQ 757
                                    579**************9999999998876655443 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.043        69      15      52 ..     137     174 ..     129     177 .. 0.90
   2 !   11.5   0.0   9.2e-05      0.15      17      51 ..     694     728 ..     688     731 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.043
                    ATP-grasp_5  15 akelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                     k++++  g + +++r++ + +e+ e+++e+g pvv++
  gi|121637314|ref|YP_977537.1| 137 FKDIVAKAGGESARSRVCFTMAEVRETVAELGLPVVVR 174
                                    5788999999999***********************86 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.2e-05
                    ATP-grasp_5  17 elleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                    +ll+a g+p+++   a++ ++a ++aeeigypv +
  gi|121637314|ref|YP_977537.1| 694 DLLSAAGLPAPKYGTATTFAQARRIAEEIGYPVLV 728
                                    69******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 7186.37
//
Query:       gi|121637315|ref|YP_977538.1|  [L=274]
Description: orotidine 5'-phosphate decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-42  143.9   0.0    6.3e-42  143.7   0.0    1.0  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.0   3.5e-46   6.3e-42       2     224 ..      17     259 ..      16     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 3.5e-46
                                    EEEEEE-SSSH..............HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH...HHTHHHHHHHHHTSEEEEEEEE CS
                      OMPdecase   2 nLclalDvata..............relleladkvgpsivvlKthydlvegwgfe..gtgaklaalarkhgflifeDrKf 65 
                                    +Lcl++D++ +               ++++++ ++ + ++v+K++++++e++g++  +++++++a++r+ ++l+++D+K+
  gi|121637315|ref|YP_977538.1|  17 PLCLGIDPHPEllrgwdlattadglAAFCDICVRAFADFAVVKPQVAFFESYGAAgfAVLERTIAELRAADVLVLADAKR 96 
                                    69***************************************************99************************* PP

                                    -S-HHHHHHHHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H...SHHHHHH CS
                      OMPdecase  66 aDIGntvekqatagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k...gytqacv 140
                                    +DIG+t++++ata + ++ ++ad+vt+++++G++s+++l+e+a+++g rg+++la +s+++++++q+  +   +++q +v
  gi|121637315|ref|YP_977538.1|  97 GDIGATMSAYATAWVGDSPLAADAVTASPYLGFGSLRPLLEVAAAHG-RGVFVLAATSNPEGAAVQNaaAdgrSVAQLVV 175
                                    *************999******************************8.*******************962689******* PP

                                    HHHHHHHHH....TTESEEECCCHTHHHHHH..TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHT CS
                      OMPdecase 141 eaarehkae....dfvmGfvaqetlnateed..addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlk 214
                                    +++ +++++     +++G+v+++t + + +d  a + ++l+pg+g+ qgg ++++      ++++   + ++ v R++l+
  gi|121637315|ref|YP_977538.1| 176 DQVGAANEAagpgPGSIGVVVGATAP-QAPDlsAFTGPVLVPGVGV-QGGRPEALGGL--GGAAS--SQLLPAVAREVLR 249
                                    **999998899999************.55556688**********9.*********86..44433..389********** PP

                                    SSSHHHHHHH CS
                      OMPdecase 215 agdpveeaer 224
                                    ag+ v e+++
  gi|121637315|ref|YP_977538.1| 250 AGPGVPELRA 259
                                    **99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1899.24
//
Query:       gi|121637316|ref|YP_977539.1|  [L=102]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-21   75.2   9.9    4.7e-21   74.9   9.9    1.1  1  PE        PE family
  ------ inclusion threshold ------
       0.06   12.5   0.1      0.092   11.9   0.1    1.2  1  MAAL_C    Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   9.9   5.3e-25   4.7e-21       4      92 ..       3      91 ..       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 5.3e-25
                                   XXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  4 vvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaag 85
                                   ++v+Pe la a+a +++++++l+aa+aaaa+ ++av+++++D VS+  A  fs h++++ a++aq+++++ + +  +a++++
  gi|121637316|ref|YP_977539.1|  3 LRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGSQHVAMAAQGVEELGRSGVGVAESGA 84
                                   89******************************************************************************** PP

                                   HHHS--X CS
                             PE 86 sYaaaEa 92
                                   sYaa +a
  gi|121637316|ref|YP_977539.1| 85 SYAARDA 91
                                   ****998 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     1e-05     0.092     198     231 ..      48      81 ..      42      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                         MAAL_C 198 scnetdvsarvsvhvalatrpaqlLakPGlGvDe 231
                                     cn  + s + s hva+a++ ++ L + G+Gv e
  gi|121637316|ref|YP_977539.1|  48 VCNAVEFSVHGSQHVAMAAQGVEELGRSGVGVAE 81 
                                    5******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 783.77
//
Query:       gi|121637317|ref|YP_977540.1|  [L=539]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-51  175.2  16.3      1e-51  175.2  16.3    2.4  2  PPE       PPE family
  ------ inclusion threshold ------
        7.8    6.8  10.4      0.043   14.0   1.4    1.9  2  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.2  16.3   1.1e-55     1e-51       1     157 [.       7     163 ..       7     164 .. 0.99
   2 ?   -5.9   8.5         2   1.8e+04      74      99 ..     419     444 ..     413     455 .. 0.61

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 1.1e-55
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sa+l+ G+g gp+l +a++  +L+a++a+aa+e+e++l  +a+e WqG++++a++aa++p+laWL +a+a++ 
  gi|121637317|ref|YP_977540.1|   7 AFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEGWQGQAAEAFVAAYMPFLAWLIQASADCV 86 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    e+Aaq +a+++aY+aA+  m++  e+aan+ +la+lvatnffG+nt++Ia +eaey emw+++a++ma+Y+++s++a
  gi|121637317|ref|YP_977540.1|  87 EMAAQQHAVIEAYTAAVELMPTQVELAANQIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSA 163
                                    ************************************************************************99876 PP

  == domain 2  score: -5.9 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  74 aaaaqaeeaAaqaeaaaaaYeaAlaa 99 
                                    a aa ++ aAa+ +a+a+a  +A+aa
  gi|121637317|ref|YP_977540.1| 419 AKAAASDSAAAESAAQASARAQARAA 444
                                    44555555555555555555555554 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.4   4.8e-06     0.043      16      54 ..      33      72 ..      26     102 .. 0.75
   2 ?   -4.9   2.0         2   1.8e+04       8      12 ..     431     435 ..     417     445 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHH CS
                         WXG100 16 fqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefe 54
                                    ++ +++  ++ ++++  +  + ++gW+G+aa+af a+++
  gi|121637317|ref|YP_977540.1| 33 NGELSAQYAEAASEVEELLGVVaSEGWQGQAAEAFVAAYM 72
                                   4445555566666666666667667***********9986 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 2
                                    HHHHH CS
                         WXG100   8 elrqa 12 
                                      +qa
  gi|121637317|ref|YP_977540.1| 431 SAAQA 435
                                    12222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3647.52
//
Query:       gi|121637318|ref|YP_977541.1|  [L=190]
Description: integration host factor mihF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.055   13.9   0.7       0.18   12.2   0.0    2.0  2  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2     0.085   1.5e+03     109     123 ..      13      27 ..       9      31 .. 0.84
   2 ?   12.2   0.0     1e-05      0.18       6      54 ..     135     183 ..     131     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.085
                  Ribosomal_S13 109 lRHkrGlkvRGQrTk 123
                                     RH +G + RG r +
  gi|121637318|ref|YP_977541.1|  13 CRHGHGAPSRGLRGR 27 
                                    69*********9876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1e-05
                  Ribosomal_S13   6 didgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeieki 54 
                                    ++ gk+kv+  l a+  +G+ ka++i++++++  + r++ l + + + +
  gi|121637318|ref|YP_977541.1| 135 EVLGKMKVSALLEALPKVGKVKAQEIMTELEIAPTRRLRGLGDRQRKAL 183
                                    7899***********************************9999886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1303.81
//
Query:       gi|121637319|ref|YP_977542.1|  [L=208]
Description: guanylate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-40  136.9   0.0    7.2e-40  136.6   0.0    1.0  1  Guanylate_kin  Guanylate kinase
    9.5e-07   29.3   0.2    1.7e-06   28.5   0.2    1.6  1  AAA_16         AAA ATPase domain
     0.0019   18.1   0.0     0.0037   17.1   0.0    1.6  1  CPT            Chloramphenicol phosphotransferase-like protei
     0.0019   18.7   0.0     0.0033   18.0   0.0    1.6  1  AAA_18         AAA domain
     0.0052   16.9   0.0     0.0076   16.3   0.0    1.5  1  MMR_HSR1       50S ribosome-binding GTPase
     0.0054   16.6   0.0      0.014   15.3   0.0    1.7  2  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.036   14.2   0.2       0.16   12.1   0.2    2.0  1  AAA_33         AAA domain
      0.078   13.3   0.0       0.12   12.6   0.0    1.5  1  AAA_22         AAA domain
      0.084   12.6   0.0       0.37   10.6   0.0    2.1  2  AAA_29         P-loop containing region of AAA domain
      0.092   12.7   0.0       0.13   12.2   0.0    1.2  1  Rad17          Rad17 P-loop domain
       0.17   12.4   0.0       0.24   11.9   0.0    1.3  1  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.0   4.4e-43   7.2e-40       3     179 ..      22     200 ..      20     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 4.4e-43
                                    SEEEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE--HHHHHHHHHTTTEEEEEEETTEEE..E CS
                  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFvskeemekdiskneflEaaefsgnly..g 80 
                                    r vvl+gps +Gks++   L ++ p+   +svs tTr+pr+gevdG dY+F+   ++++ i++ e+lE+ae +g l   g
  gi|121637319|ref|YP_977542.1|  22 RVVVLSGPSAVGKSTVVRCLRERIPN-LHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHrsG 100
                                    89***************999888887.579*****************************************77755444* PP

                                    EEHHHHHHHHHTTSEEEEE--CHHHHHHHHTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHGGG.CS CS
                  Guanylate_kin  81 tsveaieevlekgkiviLDvdiqavkqlrkaelspiivFikppslkelqrrlksrgkeqeeklakrlaaaekelqey.ef 159
                                    t  + +++ +++g  v++ vd+ +++ ++k+++++++vF++pps ++lq rl +rg+e++ +++ rl++a+ el+ + +f
  gi|121637319|ref|YP_977542.1| 101 TLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQgDF 180
                                    *****************************************************************************89* PP

                                    SEEEEESSHHHHHHHHHHHH CS
                  Guanylate_kin 160 dvvivnddleealkklkell 179
                                    d v+vn  le a+++l +ll
  gi|121637319|ref|YP_977542.1| 181 DKVVVNRRLESACAELVSLL 200
                                    ***************98776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2     1e-09   1.7e-06      19     112 ..      12     107 ..       9     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1e-09
                         AAA_16  19 vrsgrp....elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesa 92 
                                    +++g+p    ++v+lsG+s+vGKs++vr+l++++   ++ + +++++ +     + +      ++  + ++ql d+ e  
  gi|121637319|ref|YP_977542.1|  12 TARGQPaavgRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVsATTRAPRP---GEVDGvDYHFIDP-TRFQQLIDQGELL 87 
                                    66778888889*********************999664333333333333...2223323345545.7788888885555 PP

                         AAA_16  93 eleawrekleealaavpela 112
                                    e+++ +  l+++ + +++++
  gi|121637319|ref|YP_977542.1|  88 EWAEIHGGLHRSGTLAQPVR 107
                                    55555555555444333333 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.3e-06    0.0037       1      55 [.      21      90 ..      21     141 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                                   --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGT.................STTSEEEE CS
                            CPT  1 ariilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqd.................eadglefe 55
                                   +r+++L G s  GKs+++r+l+e +++  lh+ v a + a +p  +d                 +++ le++
  gi|121637319|ref|YP_977542.1| 21 GRVVVLSGPSAVGKSTVVRCLRERIPN--LHFSVSATTRAPRPGEVDgvdyhfidptrfqqlidQGELLEWA 90
                                   79********************98865..7777777666666665555555555555555555444445555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06    0.0033       1      43 [.      24      69 ..      24     173 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdp 43
                                   ++l+G+++vGK+t+ + L++r  ++  +v  +  a+  g +++vd 
  gi|121637319|ref|YP_977542.1| 24 VVLSGPSAVGKSTVVRCLRERIpNLhfSVSATTRAPRPGEVDGVDY 69
                                   789******************8666663333333333333333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.6e-06    0.0076       2      52 ..      24      73 ..      23     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvD 52
                                   v++ G + vGKSt+++ l ++      +   tTr ++ g+v+  g +++++D
  gi|121637319|ref|YP_977542.1| 24 VVLSGPSAVGKSTVVRCLRERiPNLHFSVSATTRAPRPGEVD--GVDYHFID 73
                                   7899****************95556688999**********9..88888888 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.7e-06     0.014      99     123 ..      21      45 ..       9      63 .. 0.80
   2 ?   -3.4   0.0       4.8   7.9e+03      76     104 ..     113     139 ..     102     141 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.7e-06
                                    TSEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                    ++++vl G+S vGKSt++  l+++ 
  gi|121637319|ref|YP_977542.1|  21 GRVVVLSGPSAVGKSTVVRCLRERI 45 
                                    689*****************98764 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                                    TSEEEE--TTTHTTHHHHHHHCTTSEEEE CS
                    RsgA_GTPase  76 gyevllvsaktkegleelkellkdktsvl 104
                                    g++vl+    + +g++++k+ + + ++v+
  gi|121637319|ref|YP_977542.1| 113 GVPVLIE--VDLAGARAIKKTMPEAVTVF 139
                                    5555443..23467778888888877777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2    0.0001      0.16       1      24 [.      23      46 ..      23     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg 24
                                   +v+l G++++GKst+++ l ++ +
  gi|121637319|ref|YP_977542.1| 23 VVVLSGPSAVGKSTVVRCLRERIP 46
                                   899*************98766655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.6e-05      0.12       6      31 ..      22      47 ..      19     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                   +++v+ G+s +GK+t++r l+e+ ++
  gi|121637319|ref|YP_977542.1| 22 RVVVLSGPSAVGKSTVVRCLRERIPN 47
                                   6789*****************99875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.37      23      39 ..      21      38 ..      12      41 .. 0.83
   2 ?   -2.9   0.0       3.7     6e+03      36      51 ..     130     145 ..     129     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                         AAA_29 23 g.atlltGpsGsGKSTll 39
                                   g +++l+Gps +GKST++
  gi|121637319|ref|YP_977542.1| 21 GrVVVLSGPSAVGKSTVV 38
                                   44789***********97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                         AAA_29  36 STllDAiqalLvpakk 51 
                                     T+  A+++ L p+++
  gi|121637319|ref|YP_977542.1| 130 KTMPEAVTVFLAPPSW 145
                                    5777799999999885 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.9e-05      0.13      45      67 ..      21      43 ..      12      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                          Rad17 45 kriLLisGPsGCgkstvvkvLsk 67
                                    r++++sGPs  gkstvv+ L  
  gi|121637319|ref|YP_977542.1| 21 GRVVVLSGPSAVGKSTVVRCLRE 43
                                   57999**************9953 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.24      11      34 ..      21      44 ..      18      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                   TSEEEEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 11 gekvaivGenGaGKStLlkllagl 34
                                   g++v++ G++  GKSt++++l + 
  gi|121637319|ref|YP_977542.1| 21 GRVVVLSGPSAVGKSTVVRCLRER 44
                                   899****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1392.07
//
Query:       gi|121637320|ref|YP_977543.1|  [L=110]
Description: DNA-directed RNA polymerase subunit omega [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-14   53.8   0.1    1.9e-14   53.3   0.1    1.2  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   1.1e-18   1.9e-14       1      47 [.      42     104 ..      42     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.1e-18
                                    HHTTSS--HHHHHHHHHHHHHHH........HT............SS-SSSSTTCHHHHTT-S CS
                   RNA_pol_Rpb6   1 rltskvltrYelvriaakRArQieeg.e...sl............etqkpvviAlrEiaegki 47 
                                    +l+++v ++Y lv+ aakRArQi++  +   +             + +kp++iAlrEi+++++
  gi|121637320|ref|YP_977543.1|  42 ELLDRVSSKYALVIYAAKRARQINDYyNqlgEGileyvgplvepgLQEKPLSIALREIHADLL 104
                                    699********************8844324311446677888886256************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 792.04
//
Query:       gi|121637321|ref|YP_977544.1|  [L=418]
Description: bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-65  220.1   1.5    3.2e-65  219.5   0.1    1.8  2  DFP           DNA / pantothenate metabolism flavoprotein
    8.5e-37  126.3   0.3    1.9e-36  125.2   0.1    1.7  2  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
       0.02   14.8   2.6       0.11   12.3   0.1    2.8  3  YjeF_N        YjeF-related protein N-terminus
       0.16   11.9   0.0       0.36   10.7   0.0    1.6  1  Imm61         Immunity protein 61


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.27   1.2e+03      81      97 ..      81      97 ..      26     104 .. 0.81
   2 !  219.5   0.1   7.1e-69   3.2e-65       1     186 []     191     384 ..     191     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                                   TT-SEEEE---S--EEE CS
                            DFP 81 keadivimaAAvaDyrp 97
                                   ++ad+v++a A aD   
  gi|121637321|ref|YP_977544.1| 81 QQADLVVVAPATADLLA 97
                                   67799999999999755 PP

  == domain 2  score: 219.5 bits;  conditional E-value: 7.1e-69
                                    TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS---TT-EEEE--SHHHHHHHHHHH CS
                            DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.sletpegvevvkvesaeemleaveea 79 
                                    l+g+k+lvtaG+TrE+iDpVRfi+NrSSGk+Gya+A+ aa+rGa+Vtl++g++  l +p+gvevv+v+sa+++++av ++
  gi|121637321|ref|YP_977544.1| 191 LAGRKLLVTAGGTREPIDPVRFIGNRSSGKQGYAVARVAAQRGADVTLIAGHTaGLVDPAGVEVVHVSSAQQLADAVSKH 270
                                    689*************************************************846889********************** PP

                                    HTT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-.....EEEEEEE-S.S...-HHH CS
                            DFP  80 lkeadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkq.....llvGFaaet.e...elle 150
                                    +++ad+++maAAvaD+rp+++a+ Kikk   e  +t+el +n d+la + +++++ q      +vGFaaet +   ++l 
  gi|121637321|ref|YP_977544.1| 271 APTADVLVMAAAVADFRPAQVATAKIKKGV-EGPPTIELLRNDDVLAGVVRARAHGQlpnmrAIVGFAAETgDangDVLF 349
                                    ***************************955.5589**************77766445556558*******965899**** PP

                                    HHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                            DFP 151 nareklerkgldlivaNdvskeeagfgsdenevtll 186
                                    +ar+kl+rkg+dl+v+N v++  ++f+ d+n+ +ll
  gi|121637321|ref|YP_977544.1| 350 HARAKLRRKGCDLLVVNAVGEG-RAFEVDSNDGWLL 384
                                    ********************86.99******99985 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   4.3e-40   1.9e-36       1     151 [.       9     174 ..       9     181 .. 0.93
   2 ?   -2.2   0.0      0.66     3e+03      56      56 ..     254     254 ..     220     319 .. 0.62

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 4.3e-40
                                    EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS................TCSSHHHHHHCTTESEE CS
                   Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa............redpilhielrrwadll 68 
                                    k++++g++G++aa+ka  ++++L +++++v+v+ t++A +f+     +++a                + h+ l ++adl+
  gi|121637321|ref|YP_977544.1|   9 KQVIVGVSGGIAAYKACTVVRQLTEASHRVRVIPTESALRFVGAA--TFEAlsgepvctdvfaDVPAVPHVHLGQQADLV 86 
                                    689****************************************66..5555669*******9967789************ PP

                                    EEEEEEHHHHHHHHTT--SSHHHHHHHTHCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.................... CS
                   Flavoprotein  69 viaPasantlakianGiadnlltlilratakkpiliaPamnpamyenpqtlknlekl.eegvtvikPse.....gdigkg 142
                                    v+aPa+a+ la+ a+G ad+llt++l +ta+ p+l+aPam+++m+ +p+t++n+++l ++g +v++P++      d g g
  gi|121637321|ref|YP_977544.1|  87 VVAPATADLLARAAAGRADDLLTATL-LTARCPVLFAPAMHTEMWLHPATVDNVATLrRRGAVVLEPATgrltgADSGAG 165
                                    ***********************999.7888**************************66*********989**999**** PP

                                    .GHHHHHHH CS
                   Flavoprotein 143 kmaeieeiv 151
                                    +++e eei 
  gi|121637321|ref|YP_977544.1| 166 RLPEAEEIT 174
                                    ****99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.66
                                    H CS
                   Flavoprotein  56 i 56 
                                    +
  gi|121637321|ref|YP_977544.1| 254 V 254
                                    2 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.054   2.4e+02      26      59 ..       8      41 ..       2      73 .. 0.86
   2 ?   12.3   0.1   2.5e-05      0.11      31      61 ..     211     241 ..     175     282 .. 0.83
   3 ?   -2.0   0.1      0.66     3e+03      48     109 ..     354     409 ..     316     413 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.054
                         YjeF_N 26 ekkvlvlvGsgnnGgdglaaArhLaqegakVtvl 59
                                   +k+v+v v++g   +++  + r+L +++++V+v+
  gi|121637321|ref|YP_977544.1|  8 PKQVIVGVSGGIAAYKACTVVRQLTEASHRVRVI 41
                                   57899999999999*****************994 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.5e-05
                         YjeF_N  31 vlvGsgnnGgdglaaArhLaqegakVtvlll 61 
                                     ++G+  +G +g+a+Ar  aq+ga+Vt++  
  gi|121637321|ref|YP_977544.1| 211 RFIGNRSSGKQGYAVARVAAQRGADVTLIAG 241
                                    589************************9543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.66
                         YjeF_N  48 hLaqegakVtv.llleeeekldedaeralellkkaggkvveekpeedleeklsapvdlviDAl 109
                                     L+++g++  v   + e + ++ d ++ + l+    ++ +++ ++          +  ++DA+
  gi|121637321|ref|YP_977544.1| 354 KLRRKGCDLLVvNAVGEGRAFEVDSNDGWLLASDGTESALQHGSKTLM-------ASRIVDAI 409
                                    455666654442333344445555555555554444444444444332.......45555555 PP

>> Imm61  Immunity protein 61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     8e-05      0.36      17      67 ..     361     415 ..     350     418 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                                    -EEEE-GGGSEEEEEEEETTEEEE....EEEETT---EEEEEESSHHHHHHHHHH CS
                          Imm61  17 rlilvdeggeirliieakedryll....tkaeraeeeevvlaAasldvverylwg 67 
                                     l++v++ ge r ++ + +d++ll    t++  +++++ ++a+  +d++ ++l g
  gi|121637321|ref|YP_977544.1| 361 DLLVVNAVGEGRAFEVDSNDGWLLasdgTESALQHGSKTLMASRIVDAIVTFLAG 415
                                    47899*******************88888888888888**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2947.10
//
Query:       gi|121637322|ref|YP_977545.1|  [L=403]
Description: S-adenosylmethionine synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-65  219.0   0.0    4.2e-65  217.9   0.0    1.6  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    1.1e-44  151.5   0.0      7e-44  148.9   0.0    2.0  2  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
      1e-37  128.8   0.2    3.1e-37  127.2   0.0    1.9  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
  ------ inclusion threshold ------
      0.064   12.0   0.0       0.12   11.1   0.0    1.4  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.2     1e+04      66      93 ..     185     210 ..     180     229 .. 0.46
   2 !  217.9   0.0   9.3e-69   4.2e-65       1     138 []     253     392 ..     253     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
                                    EEEE-TT-SS-SEEEEEE-S-BSS-HHH CS
                S-AdoMet_synt_C  66 qlsYaigvaepvsisvetfgtekvseee 93 
                                     ++Y    + pv++    + t++ ++ +
  gi|121637322|ref|YP_977545.1| 185 TIAYED--NVPVQLDTVVISTQHAADID 210
                                    333332..23333333333333333333 PP

  == domain 2  score: 217.9 bits;  conditional E-value: 9.3e-69
                                    S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEE CS
                S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepvsis 80 
                                    +Ggp+gdaGltgrkiivdtYgg+a+hgggafsgKdp+kvDrsaaya r+vakn+vaagla++vevq++Yaig a pv ++
  gi|121637322|ref|YP_977545.1| 253 LGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNVVAAGLAERVEVQVAYAIGKAAPVGLF 332
                                    59****************************************************************************** PP

                                    EEE-S-BSS-HHHHHHHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--..T-TTS. CS
                S-AdoMet_synt_C  81 vetfgtekvseeeiaeivkevfdlrpaaiieeldLkkpiykktaayghfgre..elpwek 138
                                    vetfgte+ +  +i++++ evfdlrp+aii++l+L +piy+ taayghfgr+  elpwe+
  gi|121637322|ref|YP_977545.1| 333 VETFGTETEDPVKIEKAIGEVFDLRPGAIIRDLNLLRPIYAPTAAYGHFGRTdvELPWEQ 392
                                    ***************************************************95666**96 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24   1.1e+03      47      96 ..      33      79 ..      20      90 .. 0.65
   2 !  148.9   0.0   1.6e-47     7e-44       2     120 .]     130     251 ..     129     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                S-AdoMet_synt_M 47 ylrpDaKsqvtveY.eeelkpvrvdtvvistqhdeevsqeklredlkekvi 96
                                    l  D +s+v ve   ++++   v +v  s++ +     ++++++++ +++
  gi|121637322|ref|YP_977545.1| 33 LLAADPRSRVAVETlVTTGQVHVVGEVTTSAKEAF----ADITNTVRARIL 79
                                   57789999999998433555556666666655543....445555555444 PP

  == domain 2  score: 148.9 bits;  conditional E-value: 1.6e-47
                S-AdoMet_synt_M   2 igAgDqGimfGYAtdeteelmPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistqhdee 81 
                                    +gAgDqG+mfGYA++ t+elmPlpi+lah+l++rl+e+rk+g l+ylrpD+K+qvt+ Y e++ pv++dtvvistqh+++
  gi|121637322|ref|YP_977545.1| 130 QGAGDQGLMFGYAINATPELMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIAY-EDNVPVQLDTVVISTQHAAD 208
                                    8**********************************************************.599**************998 PP

                S-AdoMet_synt_M  82 vs.qeklredlkekvikkvlk...eelldekktkllinptGkF 120
                                    ++ +++l  d++ekv+++vl+   +e+ld++++++l+nptGkF
  gi|121637322|ref|YP_977545.1| 209 IDlEKTLDPDIREKVLNTVLDdlaHETLDASTVRVLVNPTGKF 251
                                    88458899999999999999545445778889**********9 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0     7e-41   3.1e-37       3      99 .]       7     106 ..       5     106 .. 0.95
   2 ?   -1.7   0.0       1.1   4.8e+03      60      67 ..     208     215 ..     179     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 7e-41
                S-AdoMet_synt_N   3 lftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittkakv...diekivrevikeigYeke 79 
                                    lftsesV+eGHPDk++d isd++lda+l++dp++rva+etlvttg+v+v+ge+tt+ak    di+++vr  i eigY+++
  gi|121637322|ref|YP_977545.1|   7 LFTSESVTEGHPDKICDAISDSVLDALLAADPRSRVAVETLVTTGQVHVVGEVTTSAKEafaDITNTVRARILEIGYDSS 86 
                                    8****************************************************998764455****************** PP

                S-AdoMet_synt_N  80 elgfdaktcevlvaleeqsp 99 
                                    ++gfd  tc v++ + +qsp
  gi|121637322|ref|YP_977545.1|  87 DKGFDGATCGVNIGIGAQSP 106
                                    ******************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                S-AdoMet_synt_N  60 kvdiekiv 67 
                                     +d+ek+ 
  gi|121637322|ref|YP_977545.1| 208 DIDLEKTL 215
                                    23333333 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.7e-05      0.12      25      44 ..      14      33 ..       6      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.7e-05
                                   -TTSHHHHHHHHHHHHHHHH CS
                AdoMet_Synthase 25 GiGHPDsiaDgiaeavsral 44
                                     GHPD+i+D+i+++v  al
  gi|121637322|ref|YP_977545.1| 14 TEGHPDKICDAISDSVLDAL 33
                                   67*************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2782.63
//
Query:       gi|121637323|ref|YP_977546.1|  [L=492]
Description: monoxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-20   71.1   0.0    9.3e-19   67.8   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.2e-12   46.8   0.0      1e-09   38.1   0.0    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.5e-08   33.6   0.2    3.5e-08   33.6   0.2    2.7  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.9e-08   31.9   4.6     0.0031   17.1   1.7    3.2  3  DAO            FAD dependent oxidoreductase
    2.8e-07   29.4   0.1    4.8e-06   25.3   0.1    2.5  1  FMO-like       Flavin-binding monooxygenase-like
    2.2e-06   27.0   0.4    0.00018   20.7   0.0    2.5  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0002   20.6   0.0    0.00032   19.9   0.0    1.4  1  FAD_binding_2  FAD binding domain
    0.00046   20.7   0.3        1.5    9.4   1.0    2.8  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0022   17.1   0.5      0.085   11.9   0.4    2.2  2  GIDA           Glucose inhibited division protein A
     0.0061   16.6   4.3        3.5    7.6   0.0    3.9  4  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.015   14.6   3.1      0.025   13.9   0.3    2.4  3  Amino_oxidase  Flavin containing amine oxidoreductase
      0.053   12.9   0.4      0.093   12.1   0.4    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
      0.093   12.1   0.0       0.16   11.3   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.14   10.9   1.1         13    4.4   0.0    2.6  3  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   7.2e-22   9.3e-19       1     199 [.       8     205 ..       8     214 .. 0.83
   2 ?    0.4   0.0      0.23     3e+02     234     268 ..     312     341 ..     285     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 7.2e-22
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtf.ispsftsekleipdlnaiseetspafslkeekls 79 
                                    +I+GaG  G++aai+l +ag++dyl++E g  +    ++ +   + ++    s ++++ +              +++++ 
  gi|121637323|ref|YP_977546.1|   8 LIVGAGFSGIGAAIKLDRAGFSDYLVVEAGDGVGGTWHWNTYPGIaVDIPSFSYQFSFEQSR----------HWSRTYAP 77 
                                    6*****************************88888888887655413332233444444333..........34677777 PP

                    Pyr_redox_3  80 rkealeYlrevaksfel..piklfeeVesvkkedeg..fevetske.tyeAkkviiAtGefdkPnklnipGeek...lvk 151
                                    ++e+  Y +  ++++ +  +i+l+++V + + +de+   +v+t+ + +++A+++i A G    P++++i G ++     +
  gi|121637323|ref|YP_977546.1|  78 GHELKAYAEHCVDKYGIrsRIRLNTKVLAAEFDDEHslWRVQTDPGgEITARFLISACGILTVPKLPDIDGVDSfegVTM 157
                                    9**************99445*******999986655459*****977*************************97545678 PP

                    Pyr_redox_3 152 hyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgsei 199
                                    h++  ++ ++++g++v +iG + Sav +  e++   ++ tv+ r+  +
  gi|121637323|ref|YP_977546.1| 158 HTARWDHTQDLTGKRVGIIGTGASAVQVIPEMAPIVSHLTVFQRTPIW 205
                                    9999999********************999999999999998887665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                    Pyr_redox_3 234 evkeikekeeeykvktedgkkvevkddvvlatGyk 268
                                     +++i+ +     v t+dg ++e+ d  vlatG+k
  gi|121637323|ref|YP_977546.1| 312 PIDKITPT----AVATTDGASHEI-DVLVLATGFK 341
                                    44455543....678899988777.8899****97 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   8.1e-13     1e-09       2     185 ..       6     214 ..       5     226 .. 0.79
   2 !    6.9   0.0    0.0025       3.2      67     124 ..     306     358 ..     251     450 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.1e-13
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEE...E..TTHCHHHCSHHHHCHHHHHHHHHHHHH................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx...x..xxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlv...e..legtclnggcllskallgvaedaeias................... 57 
                                    + +++G+G+ G+ aa++l +ag+  +lv   +   +gt+++++ +   +++ ++++  ++s                   
  gi|121637323|ref|YP_977546.1|   6 HALIVGAGFSGIGAAIKLDRAGFSDYLVveaGdgVGGTWHWNTYPG--IAVDIPSFSYQFSfeqsrhwsrtyapghelka 83 
                                    568******************9999999544145777777774333..44444444444446679999999*******9* PP

                                    ...HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E..EE-BCTCTTC.TTBEECCSECHH CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ...evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs..sprdlgipGvaenvgklvrtlds 132
                                         v+k++   + +l+++v++ +++  +  l   +++ + +i++  l+ A G    p++++i+Gv  + +++v   + 
  gi|121637323|ref|YP_977546.1|  84 yaeHCVDKYGIRSRIRLNTKVLAAEFDD-EHSLWRVQTDPGGEITARFLISACGIltVPKLPDIDGV--DSFEGVTMHTA 160
                                    *985678888888888888899999888.5566666678889************666999*******..66677666666 PP

                                    HHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                    Pyr_redox_2 133 aealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrll.raldkel 185
                                         ++l+ kr+ ++G G+ +v +  ++a + ++ t+ ++ ++ + +++d  l
  gi|121637323|ref|YP_977546.1| 161 RWDHTQDLTGKRVGIIGTGASAVQVIPEMAPIVSHLTVFQRTPIWCfPKFDVPL 214
                                    6677777777*********************************99989888655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                                    CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCT..TC.TTBE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxx RF
                    Pyr_redox_2  67 ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gip..Gvaenvg 124
                                    ++l+++ ++ ki p +  v      + d+ + + d lvlAtG++  d   ip  +v  ++g
  gi|121637323|ref|YP_977546.1| 306 VRLVTE-PIDKITPTA--VA-----TTDGASHEIDVLVLATGFKVLDTdSIPtyAVTGTGG 358
                                    333333.444444444..22.....245667888899999998888887676434433333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   2.7e-11   3.5e-08       1      65 [.       9      75 ..       9      77 .. 0.88
   2 ?   -2.5   0.3         5   6.4e+03       1       8 [.     175     182 ..     175     184 .. 0.89
   3 ?   -2.5   0.0       4.9   6.3e+03      11      32 ..     398     420 ..     392     446 .. 0.57

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.7e-11
                                   EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG-EECETTCEECTS---E.EETTHHHHCHHHH CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraasyevpgvrvdygahif.hgsgyypnvrrll 65
                                   IvGaG+sG  aA  L +agf d l++e++d++GG ++ +++pg++vd +   + ++++++++++r +
  gi|121637323|ref|YP_977546.1|  9 IVGAGFSGIGAAIKLDRAGFsDYLVVEAGDGVGGTWHWNTYPGIAVDIPSFSYqFSFEQSRHWSRTY 75
                                   9*******************88*************************98554438888777777765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                                    EE--SHHH CS
                  NAD_binding_8   1 IvGaGlsG 8  
                                    I+G+G+s+
  gi|121637323|ref|YP_977546.1| 175 IIGTGASA 182
                                    9****996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                                    HHHHHHCC.TEEEEEE-SSSSSS CS
                  NAD_binding_8  11 aAylLaka.gfdvlllekrdrlG 32 
                                    + +l+  + ++ + +l +++r+G
  gi|121637323|ref|YP_977546.1| 398 YFALIETQaHHIIRCLKRARRTG 420
                                    44444443244455555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.7   2.5e-06    0.0031       1      45 [.       6      49 ..       6      88 .. 0.71
   2 !    9.6   0.0   0.00048      0.62     149     234 ..      81     166 ..      70     295 .. 0.75
   3 ?    5.2   0.0      0.01        13     150     207 ..     295     343 ..     255     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                                   EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllh 45
                                   + +i+G+G  G+++A  L r+g    +++e+gd +g g+ + n+   +
  gi|121637323|ref|YP_977546.1|  6 HALIVGAGFSGIGAAIKLDRAGfsdYLVVEAGDGVG-GTWHWNT---Y 49
                                   579***************999999************.8877776...3 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                                    HHHHHHHHHHT.T-..EEEESECEEEEEEEE.TCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEE CS
                            DAO 149 taalaraaeal.Gv..eilegtevtgleeed.gkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpispvrg 222
                                    ++a+a+ + ++ G+  +i+++t+v + e +d   +w+v +t p ge+ +a+ ++ a+G+ +  +l   +++d  +  + g
  gi|121637323|ref|YP_977546.1|  81 LKAYAEHCVDKyGIrsRIRLNTKVLAAEFDDeHSLWRV-QTDPgGEI-TARFLISACGILTVpKL---PDID-GVDSFEG 154
                                    566666653332434489********977666889***.88887765.4588******9985555...6664.4588999 PP

                                    EEEEEEECCTHS CS
                            DAO 223 qvlvlkplsekl 234
                                      +++++++ ++
  gi|121637323|ref|YP_977546.1| 155 VTMHTARWDHTQ 166
                                    999998776643 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.01
                                    HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH CS
                            DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll 207
                                    + +++++ +  v+++++ ++ ++       + v  tt+g+ +++d +V+a+G  +  l
  gi|121637323|ref|YP_977546.1| 295 NTYLSTFNRDNVRLVTE-PIDKI-T----PTAV-ATTDGASHEIDVLVLATGFKV--L 343
                                    56777788888888888.88888.2....4566.4555988889********763..3 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   3.7e-09   4.8e-06      84     238 ..      79     224 ..       6     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.7e-09
                       FMO-like  84 sklleylklfakefdllkyiqfkttvcsvkkrpdfstsGqwevvtekegkkesavfdavmvctGhhvnphlplesfpGie 163
                                     +l  y +   +++++   i+++t+v++ +   +      w v t+  g   +  f  ++  +G ++ p+lp     G++
  gi|121637323|ref|YP_977546.1|  79 HELKAYAEHCVDKYGIRSRIRLNTKVLAAEFDDEH---SLWRVQTDPGGEITAR-F--LISACGILTVPKLPD--IDGVD 150
                                    56666777777778888888888888876655444...4699888877655443.3..45567999*****95..89*** PP

                       FMO-like 164 kfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvlsrvsdsGypwdmllvtrf 238
                                     f G ++h+  + + + ++gkrv +iG G s+ ++  e++    ++ +  r+  w + + +d   p+ +  + r+
  gi|121637323|ref|YP_977546.1| 151 SFEGVTMHTARWDHTQDLTGKRVGIIGTGASAVQVIPEMAPIVSHLTVFQRTPIWCFPK-FDVPLPTAVRWAMRI 224
                                    *****************************************999999999999998875.466666666655555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.2   2.8e+03       6      32 ..       8      33 ..       5      48 .. 0.62
   2 !   20.7   0.0   1.4e-07   0.00018      92     211 ..      75     190 ..      61     207 .. 0.81
   3 ?    3.9   0.0     0.019        24     322     341 ..     322     341 ..     296     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                    K_oxygenase  6 igiGiGpsnLsLailleevkkelkalf 32
                                    ++G+G s ++ ai l+ +    + l+
  gi|121637323|ref|YP_977546.1|  8 LIVGAGFSGIGAAIKLDRAG-FSDYLV 33
                                   45677777777777776666.555555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.4e-07
                    K_oxygenase  92 lpsRkefedYlrWvasqle..eqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvG..tepkiPev.. 165
                                    + + +e + Y + ++++    +++r +++v + e+d+e+  +l++v++    +   e++ar l+ + G  t pk+P++  
  gi|121637323|ref|YP_977546.1|  75 YAPGHELKAYAEHCVDKYGirSRIRLNTKVLAAEFDDEH--SLWRVQT----DPGGEITARFLISACGilTVPKLPDIdg 148
                                    555578888888888875433789999999999999986..799**97....56789*******9999889*****9843 PP

                    K_oxygenase 166 leklegkervvHsseylerkeellakkriaVvGsGqSaaeifedll 211
                                    ++++e     +H+++  +++  +l++kr+ ++G G Sa +++ +++
  gi|121637323|ref|YP_977546.1| 149 VDSFE--GVTMHTARWDHTQ--DLTGKRVGIIGTGASAVQVIPEMA 190
                                    55555..7999999999887..8****************9987765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.019
                    K_oxygenase 322 esgeeetlevdavvlATGYr 341
                                    ++ +  ++e+d++vlATG++
  gi|121637323|ref|YP_977546.1| 322 ATTDGASHEIDVLVLATGFK 341
                                    56677899**********97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.5e-07   0.00032       2      40 ..       7      46 ..       6     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                                   EEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl.kvavvekeqefggataw 40
                                   ++++G+G++G  AA+++ +aG  + +vve ++ +gg+ +w
  gi|121637323|ref|YP_977546.1|  7 ALIVGAGFSGIGAAIKLDRAGFsDYLVVEAGDGVGGTWHW 46
                                   69***********************************999 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.0    0.0012       1.5       1      34 [.       6      40 ..       6      43 .. 0.87
   2 ?   -2.9   0.0       8.2   1.1e+04      56      71 ..      97     112 ..      84     120 .. 0.76
   3 !    7.4   0.0    0.0049       6.3       1      41 [.     172     213 ..     172     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                                   EEEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelg.kkVtvversdkl 34
                                   ++++vG+G++g+ +A  l + g ++  vve++d +
  gi|121637323|ref|YP_977546.1|  6 HALIVGAGFSGIGAAIKLDRAGfSDYLVVEAGDGV 40
                                   689****************9998888888888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.2
                                    EEECSEEEEEEEEETT CS
                      Pyr_redox  56 evllntkveeiegsed 71 
                                    +++lntkv + e +++
  gi|121637323|ref|YP_977546.1|  97 RIRLNTKVLAAEFDDE 112
                                    5889999988886665 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0049
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHH CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDee 41 
                                    +v ++G G +++ +  ++a + ++ tv++r +  + +++D  
  gi|121637323|ref|YP_977546.1| 172 RVGIIGTGASAVQVIPEMAPIVSHLTVFQRTPIWCfPKFDVP 213
                                    688***************************999888888865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.4   6.6e-05     0.085       3      37 ..       8      42 ..       6      55 .. 0.86
   2 ?    3.0   0.0     0.034        43     105     149 ..     301     339 ..     284     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                                   EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                           GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                    ++G+G +G+ AA+++ r+G++  L+++  d ++ 
  gi|121637323|ref|YP_977546.1|  8 LIVGAGFSGIGAAIKLDRAGFSDYLVVEAGDGVGG 42
                                   69************************999998876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.034
                                    HHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                           GIDA 105 lenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                     +  +n+ +++e ++++ +     ++v t+dg+  + ++ v+atG
  gi|121637323|ref|YP_977546.1| 301 FN-RDNVRLVTEPIDKITP-----TAVATTDGASHEIDVLVLATG 339
                                    44.499***********99.....99******************9 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.011        14       2      18 ..       9      25 ..       8      59 .. 0.82
   2 ?    1.7   0.0      0.18   2.2e+02     100     154 ..      81     136 ..      62     138 .. 0.69
   3 ?   -1.4   0.0       1.6     2e+03       2      15 ..     175     188 ..     174     205 .. 0.83
   4 !    7.6   0.0    0.0027       3.5     106     154 ..     296     339 ..     255     341 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                  NAD_binding_9  2 ivGaGprGlavlerLla 18
                                   ivGaG++G+ ++ +L +
  gi|121637323|ref|YP_977546.1|  9 IVGAGFSGIGAAIKLDR 25
                                   9***********99855 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                  NAD_binding_9 100 lrdlfeellarlpegvtvevhraevvdleeradg..qavlladgaslaadaVvLAlG 154
                                    l++++e+ ++++  + +++ ++++v++ e ++++  ++v ++ g +++a+ ++ A+G
  gi|121637323|ref|YP_977546.1|  81 LKAYAEHCVDKYGIRSRIR-LNTKVLAAEFDDEHslWRVQTDPGGEITARFLISACG 136
                                    4445555555554444555.477788777777663368999999***********99 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.6
                  NAD_binding_9   2 ivGaGprGlavler 15 
                                    i+G G++++ v+ +
  gi|121637323|ref|YP_977546.1| 175 IIGTGASAVQVIPE 188
                                    9*******998755 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0027
                  NAD_binding_9 106 ellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    + l++++++ +v+++++ + +++++    av ++dgas+++d +vLA+G
  gi|121637323|ref|YP_977546.1| 296 TYLSTFNRD-NVRLVTEPIDKITPT----AVATTDGASHEIDVLVLATG 339
                                    555555433.566666666666655....6889***************9 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.9e-05     0.025       1      29 [.      14      43 ..      14      71 .. 0.89
   2 ?    0.2   0.0      0.28   3.6e+02     223     262 ..      96     137 ..      85     153 .. 0.87
   3 ?   -3.0   0.2       2.5   3.2e+03     241     266 ..     319     344 ..     305     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHTT.EEEEEEESSSSSBTT CS
                  Amino_oxidase  1 laGLaaArqLlsaG.fdVtvlEardrvGGR 29
                                   ++G+ aA +L +aG  d +v+Ea d vGG 
  gi|121637323|ref|YP_977546.1| 14 FSGIGAAIKLDRAGfSDYLVVEAGDGVGGT 43
                                   69***************************4 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.28
                                    EEEETSEEEEEEEEETTC..EEEEETTSTEEEESEEEE-S-H CS
                  Amino_oxidase 223 ldirlntrVkeikregdg..vtvtledgevveaDaVvvTvpl 262
                                     +irlnt+V   + +++    +v++  g +++a+  ++++ +
  gi|121637323|ref|YP_977546.1|  96 SRIRLNTKVLAAEFDDEHslWRVQTDPGGEITARFLISACGI 137
                                    689***********66666799999999999********986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.5
                                    EEEEETTSTEEEESEEEE-S-HHHHH CS
                  Amino_oxidase 241 vtvtledgevveaDaVvvTvplgvlk 266
                                     +v ++dg + e D  v+++ + vl 
  gi|121637323|ref|YP_977546.1| 319 TAVATTDGASHEIDVLVLATGFKVLD 344
                                    689999**************999986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   7.2e-05     0.093       3      37 ..       8      43 ..       7      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                   FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGak.vlLveergvlGGl 37
                                   ++vG+g +G+ AAi   raG +  l+ve  + +GG+
  gi|121637323|ref|YP_977546.1|  8 LIVGAGFSGIGAAIKLDRAGFSdYLVVEAGDGVGGT 43
                                   79******************8626678999999997 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.16      27      67 ..     161     201 ..     151     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                    CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                   2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                    +  + ++l+gk+vGiiG+G+ + +v+  ++++  ++++++r
  gi|121637323|ref|YP_977546.1| 161 RWDHTQDLTGKRVGIIGTGASAVQVIPEMAPIVSHLTVFQR 201
                                    4467899*************999998888877777766666 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9     0.017        21       2      33 ..       6      38 ..       5      42 .. 0.77
   2 ?    4.4   0.0    0.0099        13     125     170 ..      97     143 ..      81     149 .. 0.84
   3 ?   -3.7   0.0       2.8   3.6e+03     144     164 ..     320     340 ..     308     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
                                   SEEEE--SHHHHHHHHHHHHTT--.EEEE-SSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkr.Vlllekak 33
                                   + +++G+G +G+ aAi++ ++g +  l++e+++
  gi|121637323|ref|YP_977546.1|  6 HALIVGAGFSGIGAAIKLDRAGFSdYLVVEAGD 38
                                   578***************998865155566655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0099
                                    EEE-S--EEEEECETTE..EEEEE.TTEEEEESEEEE----SS-GGG CS
                    HI0933_like 125 klrletevksvekeedgk.frvktkseeeleadklvlAtGGlSiPkl 170
                                    ++rl+t+v ++e +++++  rv+t+ ++e++a+ l+ A+G l +Pkl
  gi|121637323|ref|YP_977546.1|  97 RIRLNTKVLAAEFDDEHSlWRVQTDPGGEITARFLISACGILTVPKL 143
                                    688999999998877665269************************97 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.8
                                    EEEE.TTEEEEESEEEE---- CS
                    HI0933_like 144 rvktkseeeleadklvlAtGG 164
                                     v+t+++ + e d lvlAtG 
  gi|121637323|ref|YP_977546.1| 320 AVATTDGASHEIDVLVLATGF 340
                                    456668888899999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2745.56
//
Query:       gi|121637324|ref|YP_977547.1|  [L=461]
Description: cytochrome P450 132 cyp132 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-66  223.6   0.0    6.6e-66  223.0   0.0    1.2  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.0   3.7e-70   6.6e-66      35     447 ..      45     444 ..      41     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 3.7e-70
                                    SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTH CS
                           p450  35 pifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltptltsfgklsl 114
                                    +i r++  ++++v +s+p++v +vl+  + + ++  ++  ++    ++ g ++l+++g+ w ++R  l+ t+       l
  gi|121637324|ref|YP_977547.1|  45 DITRFRCAGRRFVSISHPDYVDHVLHEARLKYVKSDEYGPIR----ATAGLNLLTDEGDSWARHRGALNSTFARR-H--L 117
                                    68899999*****************98863333333444444....699************************99.4..5 PP

                                    HHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHTTTSSH..........HHHHHHHHHHHHH.. CS
                           p450 115 eelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdlledek..........lselvkaveelss.. 182
                                    + lv  +++   +     +  + ++d+++ + + +l v+++ lF+  f+ l +++          +    ++ e+l    
  gi|121637324|ref|YP_977547.1| 118 RGLVGLMIDPIADVTAALVPGA-QFDMHQSMVETTLRVVANALFSQDFGPLVQSMhdlatrglrrA----EKLERLGLwg 192
                                    5555555555555555555555.389***********************99999988877754432....3333333322 PP

                                    HHHCHHHHCCCCCHHHTC...CSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSS CS
                           p450 183 llskssvqllllfpllky...lptkllrklkeavkklkdlldklieerretldsakksrrdfldalllakkekkgeskls 259
                                    l+  +++ ++++  +  y    + + lr+++e++ +l+  ++ +i  r ++  ++     d+l++ll+a+    g+    
  gi|121637324|ref|YP_977547.1| 193 LM--PRT-VYDTLIWCIYsgvHLPPPLREMQEITLTLDRAINSVIDRRLAEPTNS----ADLLNVLLSAD----GG-IWP 260
                                    22..332.23333333330013556677777788888888888888777776666....9*********6....65.799 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSST CS
                           p450 260 deelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikEtLRlhpvvp 339
                                    ++ ++ ++l++++aG++Tt++++sw+ y++a nP++ + +  E+d vlg + +pt ddl kl  ++a+++E++R+ + v 
  gi|121637324|ref|YP_977547.1| 261 RQRVRDEALTFMLAGHETTANAMSWFWYLMALNPQARDHMLTELDDVLGMR-RPTADDLGKLAWTTACLQESQRYFSSVW 339
                                    **************************************************6.5*************************** PP

                                    TEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHH CS
                           p450 340 lllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGerlAr 419
                                      + Re+  d  i+g+ i+ Gt+v+++++++h+dp  +p+P++Fdp+RFl+     +r+ +a+lPFG G+R+CiG+ +A 
  gi|121637324|ref|YP_977547.1| 340 -IIAREAVDDDIIDGHRIRRGTTVVIPIHHIHHDPRWWPDPDRFDPGRFLRCPT--DRPRCAYLPFGGGRRICIGQSFAL 416
                                    .9**************************************************76..7*********************** PP

                                    HHHHHHHHHHHHHEEEEESTSTSGGEEE CS
                           p450 420 melklflatlLqnFevelqpetdpppil 447
                                    me+ l+ a + q+F+++l p+  ++   
  gi|121637324|ref|YP_977547.1| 417 MEMVLMAAIMSQHFTFDLAPGYHVELEA 444
                                    ******************9987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 3169.23
//
Query:       gi|121637325|ref|YP_977548.1|  [L=344]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-23   81.7   5.3    1.2e-22   80.9   5.3    1.4  1  Arabinose_bd  Arabinose-binding domain of AraC transcription 
    4.2e-18   65.4   0.4    8.4e-18   64.4   0.4    1.5  1  HTH_18        Helix-turn-helix domain
    7.5e-10   38.7   0.0    1.6e-06   28.0   0.1    2.5  2  HTH_AraC      Bacterial regulatory helix-turn-helix proteins,
    0.00029   20.5   0.0       0.35   10.7   0.0    2.6  2  HTH_23        Homeodomain-like domain
     0.0042   16.8   0.0      0.014   15.2   0.0    1.9  2  HTH_8         Bacterial regulatory protein, Fis family
  ------ inclusion threshold ------
      0.025   14.0   0.8       0.18   11.2   0.0    2.8  3  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> Arabinose_bd  Arabinose-binding domain of AraC transcription regulator, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   5.3   4.1e-26   1.2e-22       1     187 []      28     216 ..      28     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 4.1e-26
                   Arabinose_bd   1 Gldpdallrragldpalladpdarvpl.aqyarlweaaaralgdpalGlrlgrrlrpgslgllgyaalssptlgeAlqrl 79 
                                    G+ ++ +l+++ + pa+l+dpda v + ++++++ +++ar+ +d  +G+++g r+ ++++gl g+a++s+ tl+e l  +
  gi|121637325|ref|YP_977548.1|  28 GVPTADVLAGTAIEPADLDDPDAVVGAlDEITAVRRLLARLPDDAGIGIDVGSRFALTHFGLFGFAVMSCGTLRELLTIA 107
                                    8999*****************999976155555555666666669*********************************** PP

                   Arabinose_bd  80 vrylrllsdalelrleegegdlarlrlevaeilaalraflevlelllaallrllrwllgrrlpllrVefehpapa.daa. 157
                                    +ry++l++  ++++l e+++d + + l+ ++ +a++r f   +e+ +a+++  + +++ + l+++ ++   ++ a da+ 
  gi|121637325|ref|YP_977548.1| 108 MRYFALTTMHVDITLFETADD-CLVELDASHLPADVRGFF--IERDIAGIIATTTSFALP-LAAKYADQVSAELAvDAEl 183
                                    ***************555566.677776666788888888..*****9999999999866.5555555555555555551 PP

                   Arabinose_bd 158 ...eyrrlFgcpvrFgapanalvfdaadldlpl 187
                                        ++ +   +v Fg+++n+++f++a +d pl
  gi|121637325|ref|YP_977548.1| 184 lrpLLELVPVHDVAFGRAHNRVHFPRAMFDEPL 216
                                    1114445555669*****************997 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.4   2.8e-21   8.4e-18       2      81 .]     266     343 ..     265     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.8e-21
                                    HHHHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHHHHH CS
                         HTH_18   2 aaalgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPseyrrr 81 
                                    a +l++++rtL+r++ +  g++++++l + R   A +lL +n gl+v+++  +lG+ + s+Fs+af++++g+ Psey rr
  gi|121637325|ref|YP_977548.1| 266 AGELDMHPRTLRRRLAE-EGTSFRALLGEARSTVAVDLL-RNVGLTVQQVSTRLGYTEVSTFSHAFKRWYGVAPSEYSRR 343
                                    889**************.*******************99.57***********************************886 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.001       3.1      10      40 ..     261     290 ..     261     291 .. 0.91
   2 !   28.0   0.1   5.5e-10   1.6e-06       8      40 ..     307     340 ..     303     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                                    -HHHHHHHTTSSHHHHHHHHHHHSSS-HHHH CS
                       HTH_AraC  10 tiediAdelgfSrsyFsrlFkketGmtPsqy 40 
                                    t +d+A el +++++++r++ +e G ++++ 
  gi|121637325|ref|YP_977548.1| 261 TFTDVAGELDMHPRTLRRRLAEE-GTSFRAL 290
                                    679******************99.9999876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 5.5e-10
                                    T--HHHHHHHTTS.SHHHHHHHHHHHSSS-HHHH CS
                       HTH_AraC   8 nltiediAdelgf.SrsyFsrlFkketGmtPsqy 40 
                                    +lt+ +++  lg+   s+Fs++Fk+++G+ Ps+y
  gi|121637325|ref|YP_977548.1| 307 GLTVQQVSTRLGYtEVSTFSHAFKRWYGVAPSEY 340
                                    589******************************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0017       4.9      21      39 ..     263     281 ..     261     290 .. 0.82
   2 !   10.7   0.0   0.00012      0.35      10      47 ..     299     336 ..     296     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                         HTH_23  21 reIAreLgvsrrTvyrwlk 39 
                                    +++A eL++++rT++r l 
  gi|121637325|ref|YP_977548.1| 263 TDVAGELDMHPRTLRRRLA 281
                                    689************7654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                         HTH_23  10 illllae.GlsvreIAreLg.vsrrTvyrwlkryreeGle 47 
                                    ++ ll++ Gl+v++++++Lg    +T ++  kr+   G++
  gi|121637325|ref|YP_977548.1| 299 AVDLLRNvGLTVQQVSTRLGyTEVSTFSHAFKRW--YGVA 336
                                    67889988************88889999999999..7766 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06     0.014      22      41 ..     263     282 ..     262     282 .. 0.92
   2 ?   -3.5   0.0       3.3   9.8e+03      20      30 ..     309     319 ..     303     320 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                    HHHHHHHTS-HHHHHHHHHH CS
                          HTH_8  22 skAArlLGisRrtLyrKLkk 41 
                                    +++A +L++++rtL+r+L++
  gi|121637325|ref|YP_977548.1| 263 TDVAGELDMHPRTLRRRLAE 282
                                    679***************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                                    -HHHHHHHHTS CS
                          HTH_8  20 nkskAArlLGi 30 
                                     +++++ +LG 
  gi|121637325|ref|YP_977548.1| 309 TVQQVSTRLGY 319
                                    46778888886 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.4   7.1e+03       1       9 [.     214     222 ..     214     222 .. 0.90
   2 ?   11.2   0.0     6e-05      0.18       8      48 ..     240     280 ..     239     283 .. 0.76
   3 ?   -0.8   0.0      0.36   1.1e+03      20      38 ..     299     318 ..     297     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                   HTH_Tnp_ISL3   1 eelPwarrr 9  
                                    e+lP a+r+
  gi|121637325|ref|YP_977548.1| 214 EPLPQADRH 222
                                    89*****97 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6e-05
                   HTH_Tnp_ISL3   8 rrsriTlrleayilelllesrsvkavArqlgvSwtTVwril 48 
                                    rr++iT + + + ++ +    ++++vA +l+ +++T++r+l
  gi|121637325|ref|YP_977548.1| 240 RRRGITALVRSKLFRDSGLFPTFTDVAGELDMHPRTLRRRL 280
                                    5666666666666666333379*****************98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.36
                   HTH_Tnp_ISL3  20 ilellles.rsvkavArqlg 38 
                                    ++ ll++   +v++v+ +lg
  gi|121637325|ref|YP_977548.1| 299 AVDLLRNVgLTVQQVSTRLG 318
                                    57788888899**9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2140.62
//
Query:       gi|121637326|ref|YP_977549.1|  [L=452]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-36  122.0  23.3    1.3e-35  121.6  23.3    1.2  1  PE              PE family
  ------ inclusion threshold ------
       0.14   12.6  14.7       0.22   12.0  14.7    1.2  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  23.3   1.5e-39   1.3e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1.5e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msf+ ++Pe+l aaa+dla+igsa+s+anaaaaa+tt vlaa+aDeVSaa+Aalfs haq+yqals+qaaafh+q+vq+l++
  gi|121637326|ref|YP_977549.1|  1 MSFLFAQPEMLGAAATDLASIGSAISTANAAAAAATTRVLAAGADEVSAAVAALFSGHAQTYQALSTQAAAFHQQIVQTLTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                    ag+Ya+aEaa
  gi|121637326|ref|YP_977549.1| 83 TAGAYASAEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  14.7   2.5e-05      0.22       4      94 ..       3      94 ..       1      97 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                  T7SS_ESX_EspC  4 nLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp..icaatndavaaaeaarraagealaaasteLadkLraA 83
                                    L  +p+ l ++a+++ ++ + i++a+aaaa a+++vl   G+  ++aa+++ ++   ++ +a  ++ aa ++++ + L+++
  gi|121637326|ref|YP_977549.1|  3 FLFAQPEMLGAAATDLASIGSAISTANAAAAAATTRVLAA-GAdeVSAAVAALFSGHAQTYQALSTQAAAFHQQIVQTLTST 83
                                   6899**************************8888888776.543488888888888888888889999999999******** PP

                  T7SS_ESX_EspC 84 AaaYeatDeea 94
                                   A+aY  ++ ++
  gi|121637326|ref|YP_977549.1| 84 AGAYASAEAAN 94
                                   *****999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 2693.97
//
Query:       gi|121637327|ref|YP_977550.1|  [L=133]
Description: hypothetical protein BCG_1458c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-12   46.0   0.0    8.2e-12   45.7   0.0    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   4.6e-16   8.2e-12       1     111 [.       2     108 ..       2     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.6e-16
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleel...eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaei 77 
                                    i++D+ vlia+lrg + a   r++l ++   + l++s+++ aEl+ + +         ae++e++ ll+++++ p ++ i
  gi|121637327|ref|YP_977550.1|   2 ILVDSDVLIAHLRGVVAA---RDWLVSArkdGPLAISVVSTAELIGGMRT--------AERREVWRLLASFRVQPATEVI 70 
                                    79************9988...6666666666*******************........********************** PP

                                    HHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.E CS
                            PIN  78 aeeaaeialkyg.....llpnDaliaAtAkehgikliat 111
                                    a++a++ +++y+     +++ D liaAtA  +g++l  t
  gi|121637327|ref|YP_977550.1|  71 ARRAGDMMRRYRrshnrIGLGDYLIAATADVQGLQLA-T 108
                                    *********************************9988.7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 936.15
//
Query:       gi|121637328|ref|YP_977551.1|  [L=85]
Description: hypothetical protein BCG_1459c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   40.8   0.3    2.1e-10   40.1   0.3    1.3  1  RHH_1     Ribbon-helix-helix protein, copG family
    9.8e-07   28.6   0.1    1.3e-06   28.2   0.1    1.2  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
     0.0018   18.2   0.1     0.0031   17.4   0.1    1.3  1  RHH_3     Ribbon-helix-helix domain
     0.0096   15.8   0.1      0.015   15.1   0.1    1.3  1  RHH_4     Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.041   13.6   0.0    1.1  1  DUF1564   Protein of unknown function (DUF1564)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.3   5.9e-14   2.1e-10       1      38 [.       3      40 ..       3      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 5.9e-14
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                   r++i+ldee  + Ld+la+ +g+Sr elIR +l ++l+
  gi|121637328|ref|YP_977551.1|  3 RTNIYLDEEQTASLDKLAAQEGVSRAELIRLLLNRALT 40
                                   89******************************998875 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   3.6e-10   1.3e-06       1      42 [.       1      42 [.       1      43 [. 0.96

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.6e-10
                          RHH_5  1 SkRvnvtLPeelleeLeewAdeegRsvSnlaafLvekalrea 42
                                   +kR+n++L ee    L+++A++eg+s++ l+ +L+ +al++a
  gi|121637328|ref|YP_977551.1|  1 MKRTNIYLDEEQTASLDKLAAQEGVSRAELIRLLLNRALTTA 42
                                   79*************************************976 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   8.7e-07    0.0031       3      33 ..       2      32 ..       2      32 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.7e-07
                          RHH_3  3 trttvsidpelaekLkaLSekTrIprSklld 33
                                   +rt +++d+e+ ++L+ L ++ ++ r++l++
  gi|121637328|ref|YP_977551.1|  2 KRTNIYLDEEQTASLDKLAAQEGVSRAELIR 32
                                   5899**************************8 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   4.3e-06     0.015      12      55 ..       3      48 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH...HSS.THHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaeidadr...rgeanLas 55
                                   rT i L ++  + L+++A++eg++ ++Li  +  +r   + +  Las
  gi|121637328|ref|YP_977551.1|  3 RTNIYLDEEQTASLDKLAAQEGVSRAELIRLL-LNRaltTAGDDLAS 48
                                   89999999999*******************99.55545433335655 PP

>> DUF1564  Protein of unknown function (DUF1564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.041      81     117 ..       1      37 [.       1      60 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                        DUF1564  81 lkklsvrvntkdWallgvlaaahgvSrCyLfnyLLwl 117
                                    +k+ ++ +++++ a l  laa+ gvSr  L+  LL  
  gi|121637328|ref|YP_977551.1|   1 MKRTNIYLDEEQTASLDKLAAQEGVSRAELIRLLLNR 37 
                                    9******************************999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 604.64
//
Query:       gi|121637329|ref|YP_977552.1|  [L=319]
Description: lipase lipH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-71  240.7   0.2      2e-71  240.2   0.2    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold
    4.1e-15   55.6   2.3    8.9e-15   54.5   2.3    1.4  1  COesterase     Carboxylesterase family
  ------ inclusion threshold ------
      0.027   13.1   1.4       0.33    9.6   0.5    2.1  2  AXE1           Acetyl xylan esterase (AXE1)
      0.034   13.0   0.0      0.079   11.8   0.0    1.5  1  Say1_Mug180    Steryl acetyl hydrolase
      0.068   12.7   2.8        0.3   10.5   0.2    2.3  2  Esterase_phd   Esterase PHB depolymerase
        0.2   11.1   0.1        0.2   11.1   0.1    1.6  2  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.2   0.2   6.5e-75     2e-71       1     210 [.      84     293 ..      84     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 240.2 bits;  conditional E-value: 6.5e-75
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    +vy+HGGG+ lg+ldthd+++r  a  ++a+vvsvdYrlAPehp+Pa ++d++aalrw+ e+a+elg dpsri++aGdSa
  gi|121637329|ref|YP_977552.1|  84 VVYYHGGGWSLGGLDTHDPVARAHAVGAQAIVVSVDYRLAPEHPYPAGIDDSWAALRWVGENAAELGGDPSRIAVAGDSA 163
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                    GGn++a++a+ ard g+p++++q+l+yP t++ + + +s+   +e+ad+p+l r+ +d+f+  y+p+ d++d ++ p   
  gi|121637329|ref|YP_977552.1| 164 GGNISAVMAQLARDVGGPPLVFQLLWYPTTMA-DLSLPSF---TENADAPILDRDVIDAFLAWYVPGLDISDHTMLPTTL 239
                                    ****************************9977.9999***...789********************99999776655533 PP

                                    ...S.-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 161 ...e.dlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                       + dlsglpp+++ +ae+Dplrd+g+ yae l aagv+vel + + mvHg++
  gi|121637329|ref|YP_977552.1| 240 apgNaDLSGLPPAFIGTAEHDPLRDDGACYAELLTAAGVSVELSNEPTMVHGYV 293
                                    355448**********************************************96 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   2.3     3e-18   8.9e-15      92     198 ..      71     167 ..      62     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3e-18
                                    EEEESSSSSTTSSEEEEEEE--STTTS-BGCGS-THHHHHHH..TSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHH CS
                     COesterase  92 vytPkekkeakkklPVlVwihGggfqtgsaseydgsaLaaeg..nvivVtinYRlGvlGFlstgdeeapGNvGllDqvlA 169
                                    vy P   +  + +lPV+V+ hGgg   g   ++d+ a a     + ivV++ YRl +         e p  +G+ D  +A
  gi|121637329|ref|YP_977552.1|  71 VYWP---PVVRDNLPVVVYYHGGGWSLGGLDTHDPVARAHAVgaQAIVVSVDYRLAP---------EHPYPAGIDDSWAA 138
                                    6666...5567888******************9998877776779**********86.........78999********* PP

                                    HHHHHHHGGGGTEEEEEEEEEEETHHHHH CS
                     COesterase 170 LrWVkenIasFGGdpervtlfGesAGaas 198
                                    LrWV en a+ GGdp+r+ ++G+sAG+ +
  gi|121637329|ref|YP_977552.1| 139 LRWVGENAAELGGDPSRIAVAGDSAGGNI 167
                                    **************************975 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.02        59      69     103 ..      67     103 ..      53     121 .. 0.67
   2 ?    9.6   0.5   0.00011      0.33     172     198 ..     152     178 ..     142     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                                    EEEEEEEES.SSSSEEEEEEEE-TT--..GGGHHHHH CS
                           AXE1  69 ikaklvlPkekeeklPavvefhGYegs..rgeihdll 103
                                    i  ++  P   +++lP+vv +hG   s    ++hd +
  gi|121637329|ref|YP_977552.1|  67 IPVRVYWPPVVRDNLPVVVYYHGGGWSlgGLDTHDPV 103
                                    444566677799**********854442155666655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                                    EEEEEEEEEETHHHHHHHHHHHH-SS- CS
                           AXE1 172 DeeRvavlGasqGGalalavaalekri 198
                                    D++R+av+G+s GG ++ ++a l +++
  gi|121637329|ref|YP_977552.1| 152 DPSRIAVAGDSAGGNISAVMAQLARDV 178
                                    99*******************998765 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05     0.079     123     208 ..      82     167 ..      71     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                    Say1_Mug180 123 pvllylHGGgfalklipvtlvfLsnlrklfpdmailv.sDYtvtaakdqskkYplqvleslavydylvkskg.....fkn 196
                                    pv++y+HGGg+ l+   +   +     ++    ai+v +DY +       + Yp  + +s a   ++ +  +        
  gi|121637329|ref|YP_977552.1|  82 PVVVYYHGGGWSLGGLDTHDPVA--RAHAVGAQAIVVsVDYRLAP----EHPYPAGIDDSWAALRWVGENAAelggdPSR 155
                                    9************8666653332..23344456777736999987....7789999999999999987654311122478 PP

                    Say1_Mug180 197 vvvlGdSaGGnl 208
                                    + v GdSaGGn+
  gi|121637329|ref|YP_977552.1| 156 IAVAGDSAGGNI 167
                                    **********96 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.041   1.2e+02       4      25 ..      70      90 ..      67      99 .. 0.84
   2 ?   10.5   0.2    0.0001       0.3      89     120 ..     146     177 ..     130     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.041
                   Esterase_phd  4 rlylppGarrgamplvvmlhGc 25
                                   r+y pp  r   +p+vv  hG 
  gi|121637329|ref|YP_977552.1| 70 RVYWPPVVRD-NLPVVVYYHGG 90
                                   7899997765.9********96 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                   Esterase_phd  89 vdehrvdaarvyvaGlsaGaaladllalhypd 120
                                    + e + d++r+ vaG saG+ ++ ++a+   d
  gi|121637329|ref|YP_977552.1| 146 AAELGGDPSRIAVAGDSAGGNISAVMAQLARD 177
                                    566788*******************9987666 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.4       3.2   9.5e+03      70      76 ..      91      97 ..      90     100 .. 0.85
   2 ?   11.1   0.1   6.6e-05       0.2      45      83 ..     132     173 ..     127     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3.2
                                   EETHHHH CS
                   Peptidase_S9 70 GgSyGGy 76
                                   G+S GG+
  gi|121637329|ref|YP_977552.1| 91 GWSLGGL 97
                                   9*****8 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.6e-05
                                    HHHHHHHHHHHHHTT...S--GGGEEEEEETHHHHHHHHHHH CS
                   Peptidase_S9  45 fdDfiaaaealakeg...yvdserlaitGgSyGGyltgaaln 83 
                                    +dD  aa++++ ++      d++r+a+ G S+GG  +++++ 
  gi|121637329|ref|YP_977552.1| 132 IDDSWAALRWVGENAaelGGDPSRIAVAGDSAGGNISAVMAQ 173
                                    68888888888544432378**************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2096.85
//
Query:       gi|121637330|ref|YP_977553.1|  [L=320]
Description: lipase lipH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-72  241.3   1.3    1.2e-71  240.9   1.3    1.1  1  Abhydrolase_3    alpha/beta hydrolase fold
    1.5e-11   43.9   0.7    4.3e-11   42.4   0.7    1.6  1  COesterase       Carboxylesterase family
     0.0067   15.3   0.0      0.016   14.1   0.0    1.5  1  Say1_Mug180      Steryl acetyl hydrolase
     0.0077   15.2   0.0      0.013   14.4   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme
      0.008   15.7   0.1      0.014   14.9   0.1    1.3  1  Peptidase_S9     Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.013   15.4   0.3      0.034   14.0   0.1    1.8  2  Phage_tail_APC   Phage tail assembly chaperone protein
      0.073   12.7   0.9        1.2    8.7   0.9    2.1  1  Esterase         Putative esterase
       0.11   12.0   1.1       0.14   11.7   0.1    1.6  2  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.9   1.3   5.5e-75   1.2e-71       1     210 [.      87     294 ..      87     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 240.9 bits;  conditional E-value: 5.5e-75
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    ++yfHGGGfv+g+ldthd +cr+ a  ++a+vvsvdYrlAPehp+Paa+eda+aa+rw+ae+  + gad  ri++aGdSa
  gi|121637330|ref|YP_977553.1|  87 VLYFHGGGFVMGDLDTHDGTCRQHAVGADAIVVSVDYRLAPEHPYPAAIEDAWAATRWVAEHGRQVGADLGRIAVAGDSA 166
                                    79************************************************************99**************** PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGST..TTSGG CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddp..laspl 158
                                    GG++aa++a+rard g+p++++q+l+yP t   +++ +s    +e+ad+p+l  +a+++f r y++e d+++p   ++p 
  gi|121637330|ref|YP_977553.1| 167 GGTIAAVIAQRARDMGGPPIVFQLLWYPSTLW-DQSLPSL---AENADAPILDVKAIAAFSRWYAGEIDLHNPpaPMAPG 242
                                    ****************************8855.7778999...789***************************6666777 PP

                                    GCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 159 laedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                    +ae+l++lpp++++va++Dplrd+g++y e l+aagv+ve+++ + +vHg++
  gi|121637330|ref|YP_977553.1| 243 RAENLADLPPAYIAVAGYDPLRDDGIRYGELLAAAGVPVEVHNAQTLVHGYV 294
                                    7889*********************************************986 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.7   1.9e-14   4.3e-11      92     202 ..      72     174 ..      71     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.9e-14
                                    EEEESSSSSTTSSEEEEEEE--STTTS-BGCGS-THHHHHHH..TSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHH CS
                     COesterase  92 vytPkekkeakkklPVlVwihGggfqtgsaseydgsaLaaeg..nvivVtinYRlGvlGFlstgdeeapGNvGllDqvlA 169
                                    +y P + +++ ++ PV+ ++hGggf++g+  ++dg+        + ivV++ YRl +         e p  +++ D  +A
  gi|121637330|ref|YP_977553.1|  72 IYWPPTCPDQAEA-PVVLYFHGGGFVMGDLDTHDGTCRQHAVgaDAIVVSVDYRLAP---------EHPYPAAIEDAWAA 141
                                    6666666666666.****************99887644333345***********86.........789999******** PP

                                    HHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHH CS
                     COesterase 170 LrWVkenIasFGGdpervtlfGesAGaasvsll 202
                                     rWV e+  + G d  r+ ++G+sAG++++++ 
  gi|121637330|ref|YP_977553.1| 142 TRWVAEHGRQVGADLGRIAVAGDSAGGTIAAVI 174
                                    ***************************998765 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   7.1e-06     0.016     113     211 ..      78     173 ..      67     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                    Say1_Mug180 113 vpetfdPkvDpvllylHGGgfalklipvtlvfLsnlrk.lfpdmailv.sDYtvtaakdqskkYplqvleslavydylvk 190
                                     p +      pv+ly+HGGgf+++   +      + r+ +    ai+v +DY +       + Yp  + ++ a   ++ +
  gi|121637330|ref|YP_977553.1|  78 CPDQ---AEAPVVLYFHGGGFVMGDLDTHDG---TCRQhAVGADAIVVsVDYRLAP----EHPYPAAIEDAWAATRWVAE 147
                                    4444...455************987766533...3333034455666636999987....67899999999999998885 PP

                    Say1_Mug180 191 s.....kgfknvvvlGdSaGGnlvLs 211
                                            +  + v GdSaGG++  +
  gi|121637330|ref|YP_977553.1| 148 HgrqvgADLGRIAVAGDSAGGTIAAV 173
                                    322211346799*********98655 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.8e-06     0.013      14     110 ..      81     177 ..      67     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-06
                Chlorophyllase2  14 ageYpvllflhGyl.llnslYs...qlLkhiashgfivvapqlykvaeada.keiksaakvlnWlakgLesvlpeevepd 88 
                                    + e pv+l++hG   ++ +l +   +  +h      ivv++      e+   + i+ a + + W+a++ +     +v +d
  gi|121637330|ref|YP_977553.1|  81 QAEAPVVLYFHGGGfVMGDLDThdgTCRQHAVGADAIVVSVDYRLAPEHPYpAAIEDAWAATRWVAEHGR-----QVGAD 155
                                    456688888887654444443311157788888999*****977755444459**************976.....9**** PP

                Chlorophyllase2  89 lsklalsgHSrGgktafalalg 110
                                    l ++a++g S+Gg +a+ +a  
  gi|121637330|ref|YP_977553.1| 156 LGRIAVAGDSAGGTIAAVIAQR 177
                                    *************999877755 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   6.1e-06     0.014      44      85 ..     134     178 ..     129     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.1e-06
                                    HHHHHHHHHHHHHHTT...S--GGGEEEEEETHHHHHHHHHHHH- CS
                   Peptidase_S9  44 efdDfiaaaealakeg...yvdserlaitGgSyGGyltgaalnqr 85 
                                     ++D  aa++++a++g    +d  r+a+ G S+GG+ +++++ ++
  gi|121637330|ref|YP_977553.1| 134 AIEDAWAATRWVAEHGrqvGADLGRIAVAGDSAGGTIAAVIAQRA 178
                                    57999*********9983345788**************9999865 PP

>> Phage_tail_APC  Phage tail assembly chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.5e-05     0.034      33      51 ..      35      53 ..      20      76 .. 0.80
   2 ?   -2.7   0.0       2.5   5.6e+03      15      35 ..     121     141 ..     115     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHS---SS--S CS
                 Phage_tail_APC 33 lkaYrqaLRDlPeqegfPa 51
                                   ++a rq LRDlP+q+ +P+
  gi|121637330|ref|YP_977553.1| 35 IEAVRQRLRDLPRQPVHPE 53
                                   7899***********9992 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                    THHHHSTTS---HHHHHHHHH CS
                 Phage_tail_APC  15 sDwvqlpDspldeeerqalka 35 
                                    +D+   p  p  +  ++a++a
  gi|121637330|ref|YP_977553.1| 121 VDYRLAPEHPYPAAIEDAWAA 141
                                    667677777777777888887 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.9   0.00055       1.2       9     139 ..      69     181 ..      64     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                                    EEEEEE.CC.GGTTTEEEEEEE--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEEETTC CS
                       Esterase   9 kvqvyLPedyspgrkypvvylldGltgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgarfyenateg 88 
                                    + ++y P+  +++ + pvv++++G      ++ + ++     r++      +v+ +++ +s       ++   y+ a+e 
  gi|121637330|ref|YP_977553.1|  69 GTRIYWPPTCPDQAEAPVVLYFHGGGFVMGDLDTHDGT---CRQH------AVGADAIVVS-------VD---YRLAPEH 129
                                    55666666666666666666666633334455555555...3443......3333333333.......11...3344566 PP

                                    CCCCCHCHHHHTHHHHHHHHHCSEECCC...EEEEEETHHHHHHHHHHHCSTTT CS
                       Esterase  89 pgaeayetfltqeLlplldanfrtapdg...ravaGqSmGGlgALilalkhpdr 139
                                    p+  a e++ +++   +++++ r         avaG+S GG++A ++a ++ d+
  gi|121637330|ref|YP_977553.1| 130 PYPAAIEDAWAAT--RWVAEHGRQVGADlgrIAVAGDSAGGTIAAVIAQRARDM 181
                                    6666666666654..677777666555557789***********9999998876 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.2   4.9e+03       6      24 ..      69      88 ..      68      89 .. 0.87
   2 ?   11.7   0.1   6.2e-05      0.14      81     121 ..     133     177 ..     126     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                                   EEEEEEE...TTSSSEEEEE CS
                  Peptidase_S15  6 avdiyrP.etkskeklPvll 24
                                    ++iy P + ++++++Pv+l
  gi|121637330|ref|YP_977553.1| 69 GTRIYWPpTCPDQAEAPVVL 88
                                   58999999999999***998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.2e-05
                                    THHHHHHHHHHHHHH...C.TTEEEEEEEEEECHHHHHHHHHCTT CS
                  Peptidase_S15  81 deaedgadvidWlak...q.pwsnGkVgmtGiSYlGttqllaaat 121
                                      +ed++++ +W+a+   q     G++++ G S +Gt++ ++a++
  gi|121637330|ref|YP_977553.1| 133 AAIEDAWAATRWVAEhgrQvGADLGRIAVAGDSAGGTIAAVIAQR 177
                                    6789***********998779999***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1951.55
//
Query:       gi|121637331|ref|YP_977554.1|  [L=200]
Description: hypothetical protein BCG_1462 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-47  160.7  20.2    3.1e-47  160.6  20.2    1.0  1  YhhN             YhhN family
     0.0073   15.3   2.8      0.011   14.7   2.8    1.4  1  PNTB             NAD(P) transhydrogenase beta subunit
  ------ inclusion threshold ------
       0.15   11.7   1.8       0.22   11.2   0.2    2.2  2  RhodobacterPufX  Intrinsic membrane protein PufX


Domain annotation for each model (and alignments):
>> YhhN  YhhN family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6  20.2   5.2e-51   3.1e-47       2     183 ..       3     183 ..       2     184 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 5.2e-51
                           YhhN   2 rllfKplpvllLlllvlleskeasryrrlilagLlfsavGDvlLl.kkkkrsfllGlvaFllaHilYivafl...eqrat 77 
                                    + +fK+++++lL++++++  ++ +r+rr+++ +Ll+sa GD+lL+ ++++ +f++Gl+aFllaH+++i a+l   +q+a 
  gi|121637331|ref|YP_977554.1|   3 QPAFKASMAVLLAAAAVA--HPIGRERRWLVPALLLSATGDWLLAiPWWTWAFVFGLGAFLLAHLCFIGALLplaRQAAP 80 
                                    679***************..******************************************************9999** PP

                           YhhN  78 stlslllllllllaaavllalllprlgk..lkipvlvYalvistmvatAlesllslsslaallaalGallFviSDlllai 155
                                    s+ ++++++++++a+a+ll++++p+lgk  l+ipv+vY++++s+mv+tA     +l++l+++++a+Ga++F++SD+++ i
  gi|121637331|ref|YP_977554.1|  81 SRGRVAAVVAMCVASAGLLVWFWPHLGKdnLTIPVTVYIVALSAMVCTA-----LLARLPTIWTAVGAVCFAASDSMIGI 155
                                    **************************5556*******************.....79************************ PP

                           YhhN 156 nkfvrklpaarllvmitYfaaQllIals 183
                                     +f+   +a  + ++++Y+aa +lI+++
  gi|121637331|ref|YP_977554.1| 156 GRFILGNEALAVPIWWSYAAAEILITAG 183
                                    **************************98 PP

>> PNTB  NAD(P) transhydrogenase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.8   1.9e-06     0.011       5      98 ..      60     158 ..      58     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XX..XXXXXXXXXX.XXXXXXXXXXXXXX.X CS
                           PNTB   5 ylvaallfilglkglsspktarrgnllgavgmllavvatlllllkeaasee..lalillalvi.gaviGlllakkvem.t 80 
                                     l+a l+fi +l  l++++   rg + ++v+m +a +  l+ ++ +  + +  + +++ ++++ ++v+ +lla+  ++ t
  gi|121637331|ref|YP_977554.1|  60 FLLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNltIPVTVYIVALsAMVCTALLARLPTIwT 139
                                    6899*******************************999988666666665544222233333303333333443322213 PP

                                    XXXXX.XXXXXXXXXXXXX CS
                           PNTB  81 emPql.vallnslvGlAav 98 
                                    ++  +  a+  s++G+  +
  gi|121637331|ref|YP_977554.1| 140 AVGAVcFAASDSMIGIGRF 158
                                    3333213455555555555 PP

>> RhodobacterPufX  Intrinsic membrane protein PufX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   3.7e-05      0.22      31      62 ..      52      82 ..      48      87 .. 0.77
   2 ?   -2.6   0.1       0.7   4.2e+03      31      35 ..     123     127 ..     108     145 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                RhodobacterPufX 31 Aavfvlvl.lfllvalaliGrlLPeqsrqtPdP 62
                                   A  fv++l  fll+ l +iG lLP   + +P+ 
  gi|121637331|ref|YP_977554.1| 52 A--FVFGLgAFLLAHLCFIGALLPLARQAAPSR 82
                                   4..4444435899*****************985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.7
                RhodobacterPufX  31 Aavfv 35 
                                     a+++
  gi|121637331|ref|YP_977554.1| 123 SAMVC 127
                                    23333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1282.41
//
Query:       gi|121637332|ref|YP_977555.1|  [L=655]
Description: primosome assembly protein PriA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-16   59.8   0.0    3.8e-16   58.8   0.0    1.6  1  PriA_3primeBD  3′ DNA-binding domain (3′BD)
  ------ inclusion threshold ------
        1.1    9.2   3.6       0.94    9.4   2.0    1.7  1  C1_1           Phorbol esters/diacylglycerol binding domain (


Domain annotation for each model (and alignments):
>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   4.2e-20   3.8e-16       4      96 .]       2      96 ..       1      96 [. 0.95

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.2e-20
                  PriA_3primeBD  4 vdlp.ldrtfdYrvpeel..evkiGsrVlVpfgkrklvGiVvalkeeseveeeklkpieevldeepllteellelaewlaey 82
                                   + +p ldr fdY+vp+e   + ++G rV+V f +r + G+V++  ++s+ ++ kl  +++v++ ep+lt e+ +l++ +a++
  gi|121637332|ref|YP_977555.1|  2 LSVPhLDRDFDYLVPAEHsdDAQPGVRVRVRFHGRLVDGFVLERRSDSD-HHGKLGWLDRVVSPEPVLTTEIRRLVDAVAAR 82
                                   67788************9655566*************************.9******************************* PP

                  PriA_3primeBD 83 ylaplgevlkaalP 96
                                   y+ +  +vl++a+P
  gi|121637332|ref|YP_977555.1| 83 YAGTRQDVLRLAVP 96
                                   ************98 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0   0.00011      0.94      10      36 ..     373     401 ..     367     410 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                                    S--B-TTT-SB-..-SSSS-EEEETTT-- CS
                           C1_1  10 qptfCkhCgefl..wgkekqglkCswCkl 36 
                                      ++C  C  +l  +g +++g  C+wC++
  gi|121637332|ref|YP_977555.1| 373 AIARCRSCTGPLslQGAGSPGAVCRWCGR 401
                                    5689********9777***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3954.91
//
Query:       gi|121637333|ref|YP_977556.1|  [L=274]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-18   65.3   0.1    8.8e-18   64.8   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    4.2e-17   62.6   0.0      6e-17   62.1   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    2.3e-11   43.5   0.0    3.4e-11   42.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.3e-08   34.0   0.0    4.1e-08   33.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.9e-06   26.7   0.0      1e-05   26.2   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    0.00012   21.9   0.0    0.00091   19.0   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    0.00024   21.0   0.0    0.00047   20.0   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
     0.0049   16.6   0.0     0.0075   16.0   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.017   14.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.024   14.2   0.0      0.034   13.7   0.0    1.2  1  MTS              Methyltransferase small domain
      0.042   13.1   0.0      0.056   12.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.058   12.8   0.0      0.087   12.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   5.9e-21   8.8e-18       1      97 []      53     145 ..      53     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 5.9e-21
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLd+++G+G++++ +a ++  a+vt+ D+++e+l++a++ra+++gl++ +++++ae+lpf +g+fD+v+s+ ++++   +
  gi|121637333|ref|YP_977556.1|  53 VLDVAAGSGNVSIPAAMAG--AHVTASDLTPELLRRAQARAAAAGLELGWREANAEALPFSAGEFDAVLSTIGVMFA--P 128
                                    9***************995..*************************************************8665554..5 PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    +++++ +e+arv++ gG
  gi|121637333|ref|YP_977556.1| 129 RHQRTADELARVCRRGG 145
                                    67899***********9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0     4e-20     6e-17       1      94 [.      54     147 ..      54     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ldv++G+G ++ + a +ga+v++ Dl++e+l++a+++a  +gl++ +++a+ae lpf  + fD+v+s+  +++ ++++++
  gi|121637333|ref|YP_977556.1|  54 LDVAAGSGNVSIPAAMAGAHVTASDLTPELLRRAQARAAAAGLELGWREANAEALPFSAGEFDAVLSTIGVMFAPRHQRT 133
                                    8**************999*************************999********************************** PP

                                    HHHHHHHEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGll 94 
                                     +e+aRv++ gG++
  gi|121637333|ref|YP_977556.1| 134 ADELARVCRRGGKI 147
                                    ************97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   2.3e-14   3.4e-11      42     153 ..      44     151 ..      40     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.3e-14
                                    H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                    +++ +rg +vlDva+G+g++++     + +  +v+  D+ +++L+ +++++   g  ++ +  anae+Lpf+ + fD v 
  gi|121637333|ref|YP_977556.1|  44 TSGIRRGDRVLDVAAGSGNVSIPA---AMAGAHVTASDLTPELLRRAQARAAAAGL-ELGWREANAEALPFSAGEFDAVL 119
                                    57889**************99864...45567899****************98885.89********************* PP

                                    EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                     + G+   + ++++  e+ rv + GG++  l+
  gi|121637333|ref|YP_977556.1| 120 STIGVMFAPRHQRTADELARVCRRGGKISTLN 151
                                    ***************************99886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   2.7e-11   4.1e-08       2     108 ..      48     148 ..      47     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.7e-11
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                    ++g rvlD+++G+G+ ++ +a     +a+v+  D ++e +++A+++a+  gl+ +  +++++e+l+  ++   fD +ls 
  gi|121637333|ref|YP_977556.1|  48 RRGDRVLDVAAGSGNVSIPAA---MAGAHVTASDLTPELLRRAQARAAAAGLE-LGWREANAEALP--FSAGEFDAVLST 121
                                    57889****************...5689************************7.************..999********8 PP

                Methyltransf_31  82 evlnaladpdkileeiervlkpggill 108
                                      ++  +  + +  e+ rv + gg + 
  gi|121637333|ref|YP_977556.1| 122 IGVMFAPRHQRTADELARVCRRGGKIS 148
                                    777999999999999999999999875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.7e-09     1e-05       1      99 []      54     147 ..      54     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.7e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhl 79 
                                    L++ +G+G+++ + + +  ++++t++D+ p+ + +a+++ a+ +     ++ +++ +++ l+ + + fD+v++   +   
  gi|121637333|ref|YP_977556.1|  54 LDVAAGSGNVSIPAAMA--GAHVTASDLTPELLRRAQARAAAAGL----ELGWREANAEALPFSaGEFDAVLSTIGVMFA 127
                                    8****************..**************888888888886....555555554444444569*****99555555 PP

                Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                    +  +++ d+++++++ gG++
  gi|121637333|ref|YP_977556.1| 128 PRHQRTADELARVCRRGGKI 147
                                    8999*************986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.1e-07   0.00091      17     127 ..      38     120 ..      27     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.1e-07
                                    HHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHH CS
                        UPF0020  17 AaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNa 96 
                                       lv  +g+++g++ lD   GsG + I aa+ ga++                           +sDl ++++++a+  a
  gi|121637333|ref|YP_977556.1|  38 GPILVSTSGIRRGDRVLDVAAGSGNVSIPAAMAGAHVT--------------------------ASDLTPELLRRAQARA 91 
                                    55699*********************************..........................8999999999999888 PP

                                    HHTT-GGGEEEEE--GGG--STTS---EEEE CS
                        UPF0020  97 ekagvgdliefsqadaakLrlkegevdvivt 127
                                     +ag++    +++a+a +L+ + ge+d++++
  gi|121637333|ref|YP_977556.1|  92 AAAGLE--LGWREANAEALPFSAGEFDAVLS 120
                                    888776..56778888888888889999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.2e-07   0.00047      20     115 ..      47     147 ..      17     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.2e-07
                Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae............kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                     r+g rvLd+++G+G+++  ++  g++vt+ Dl pe+  +a+               +a+  +f       ++g fd + 
  gi|121637333|ref|YP_977556.1|  47 IRRGDRVLDVAAGSGNVSIPAAMAGAHVTASDLTPELLRRAQaraaaaglelgwREANAEALPF-------SAGEFDAVL 119
                                    57888*******************************9999988888887766554444444444.......999999999 PP

                Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGyl 115
                                    ++ +    p + ++ + +a+ ++ gG +
  gi|121637333|ref|YP_977556.1| 120 STIGVMFAPRHQRTADELARVCRRGGKI 147
                                    9988888888888888888888888876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     5e-06    0.0075      98     136 ..      47      83 ..      41      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                                    --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHH CS
                         Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPes 136
                                    ++ g++V+dv AG G  +ip+a    +  v a dl Pe 
  gi|121637333|ref|YP_977556.1|  47 IRRGDRVLDVAAGSGNVSIPAAM--AGAHVTASDLTPEL 83 
                                    5789******************9..7888********85 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.017     159     232 ..      47     120 ..      37     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekadviva 232
                                    +++g++vlDv +GSG  +i aa+ ga +v+a D+ +  ++ a++ a+  ++e   + a++e l+ +++++d +++
  gi|121637333|ref|YP_977556.1|  47 IRRGDRVLDVAAGSGNVSIPAAMAGA-HVTASDLTPELLRRAQARAAAAGLELGWREANAEALPfSAGEFDAVLS 120
                                    68899*****************9997.699******999999998888777765543333333333566666665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.034      30     102 ..      48     119 ..      38     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                    CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEE CS
                            MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdliv 102
                                    ++ ++vlD+++G G +++ +a +  +  vt+ d   + l+ a++ ++a +le+  ++ ++ +  ++ ++fd+++
  gi|121637333|ref|YP_977556.1|  48 RRGDRVLDVAAGSGNVSIPAAMAGAH--VTASDLTPELLRRAQARAAAAGLELGWREANAEAlPFSAGEFDAVL 119
                                    46789***************998777..9*********************998887777655234467777776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05     0.056      58     114 ..      45     100 ..      39     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                    TT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-E CS
                           CMAS  58 lelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkv 114
                                     +++ G+++Ld+ +G G++ + a+   +++v +  l  e  ++a++r ++++le   
  gi|121637333|ref|YP_977556.1|  45 SGIRRGDRVLDVAAGSGNVSIPAAMA-GAHVTASDLTPELLRRAQARAAAAGLELGW 100
                                    57889********************9.**********************99987544 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.8e-05     0.087      31     110 ..      50     129 ..      36     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                                    S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S.-EEEEEEESSGGGS- CS
                           TehB  31 pgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklde.rydfilstvvlmfle 109
                                      +vld+  g+g  s+  ++ g +vta d   + +   +  +    l+ +  +  + +++ ++  ++d +lst+ +mf  
  gi|121637333|ref|YP_977556.1|  50 GDRVLDVAAGSGNVSIPAAMAGAHVTASDLTPELLRRAQARAAAAGLE-LGWREANAEALPFSAgEFDAVLSTIGVMFAP 128
                                    5689****************************9999999999999998.99999999999997548************75 PP

                                    G CS
                           TehB 110 a 110
                                    +
  gi|121637333|ref|YP_977556.1| 129 R 129
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1709.42
//
Query:       gi|121637334|ref|YP_977557.1|  [L=160]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-17   63.4   0.0    2.8e-17   62.4   0.0    1.5  1  MarR            MarR family
    1.4e-08   34.5   0.1    1.4e-08   34.5   0.1    2.4  3  MarR_2          MarR family
    5.2e-05   23.7   0.1      0.004   17.6   0.0    2.2  2  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.071   12.7   0.0    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.029   14.6   0.0        0.1   12.8   0.0    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.05   13.8   0.7       0.27   11.4   0.1    2.1  2  TetR_C_35       Bacterial Tetracyclin repressor,  C-terminal 
       0.13   12.1   0.0       0.84    9.6   0.0    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
       0.18   11.6   3.7       0.77    9.6   0.1    3.0  3  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   1.2e-20   2.8e-17       1      58 [.      43     100 ..      43     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.2e-20
                                    --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                           MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58 
                                    +t +qf++L+il+++gp++++ La  lgv++s++ r++drL+ ++li+R ++p  rRe
  gi|121637334|ref|YP_977557.1|  43 ITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRE 100
                                    799******************************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.8   1.1e+04       6      16 ..      23      33 ..      22      35 .. 0.62
   2 !   34.5   0.1   6.3e-12   1.4e-08       3      61 ..      43      99 ..      41     100 .. 0.96
   3 ?    2.0   0.9     0.084   1.9e+02       8      52 ..      99     141 ..      97     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHC CS
                         MarR_2  6 aqarvLaaLgr 16
                                   +  r+L a+ +
  gi|121637334|ref|YP_977557.1| 23 TASRLLVAISA 33
                                   45677777765 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 6.3e-12
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   +t  q+r L  L ++++  ++ + la  lg+ +sa+ r+++rLv a L+ r p p+ +R
  gi|121637334|ref|YP_977557.1| 43 ITIPQFRTLVILSNHGP--INLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRR 99
                                   7999*************..************************************9999 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.084
                                    HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                    + +LaaL  r++ d  v++++++ + + +++    + ++++GLv+
  gi|121637334|ref|YP_977557.1|  99 RELLAALTKRGR-D-VVRQVTEHRRTEIARIVEQMAPAERHGLVR 141
                                    568889988885.4.788888888888888888888888888885 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.8e-06     0.004       5      68 .]      47     109 ..      43     109 .. 0.89
   2 ?    4.1   0.0     0.029        65       9      46 ..     113     150 ..     111     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                         HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    q  +L  +  ++++  la l+  l v+ s++  ++++L+ ++L+ r + +++rre + +lT  G
  gi|121637334|ref|YP_977557.1|  47 QFRTLVILS-NHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRG 109
                                    555666666.7888899*******************************************9887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.029
                         HTH_27   9 Lhlirhrrrrkkladlcgrlnvedshis.yslkkLtekG 46 
                                    ++++  ++rr ++a++++ +     h+   +l + te+G
  gi|121637334|ref|YP_977557.1| 113 VRQVT-EHRRTEIARIVEQMAPAERHGLvRALTAFTEAG 150
                                    67788.99***********99999999989999888887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.071       6      47 ..      48      89 ..      44      90 .. 0.92
   2 ?   -2.1   0.0       1.3   2.9e+03       5      17 ..      98     110 ..      96     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                         HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   ++ L +L  ++ i+ + LA  lg+ ps++ r ++rL+ ++lI
  gi|121637334|ref|YP_977557.1| 48 FRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELI 89
                                   777889******************************988887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                         HTH_24   5 drkILelLqknpr 17 
                                    +r++L +L k +r
  gi|121637334|ref|YP_977557.1|  98 RRELLAALTKRGR 110
                                    6888999888765 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   5.7e+03      15      24 ..       9      18 ..       7      32 .. 0.61
   2 ?   12.8   0.0   4.5e-05       0.1      19      53 ..      56      90 ..      49      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                   HHHHHHSSB- CS
                 Fe_dep_repress 15 tlseekkvvk 24
                                   t++e+ +v++
  gi|121637334|ref|YP_977557.1|  9 TAEESVDVIT 18
                                   3455555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.5e-05
                                   HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   +++++  + la  L+v+ps    m+ +L  +++++
  gi|121637334|ref|YP_977557.1| 56 NHGPINLATLATLLGVQPSATGRMVDRLVGAELID 90
                                   67889999********************9888876 PP

>> TetR_C_35  Bacterial Tetracyclin repressor,  C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.25   5.6e+02      47      70 ..      21      44 ..       3      55 .. 0.71
   2 ?   11.4   0.1   0.00012      0.27      21      77 ..      87     143 ..      70     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                      TetR_C_35 47 leaAsarlaevlaeswpqldeada 70
                                   l +As+ l ++ a+s  q+de+ +
  gi|121637334|ref|YP_977557.1| 21 LLTASRLLVAISAHSIAQVDENIT 44
                                   446777788888888888877655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                      TetR_C_35  21 pLvravltgeakedLlpllTtdseplleaAsarlaevlaeswpqldeadaevladav 77 
                                    +L+ ++ + + +++Ll  lT +++ ++++ +++ ++ +a+   q+ +a+++ l++a+
  gi|121637334|ref|YP_977557.1|  87 ELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRAL 143
                                    57777777779**********************999999999999999999888876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00038      0.84      12      56 ..      49      93 ..      41     108 .. 0.87
   2 ?    0.4   0.0      0.26   5.9e+02      15      52 ..     103     140 ..      99     144 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                   CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   ++ + L ++gp +  ++a  lgv  s   +++ +L+ + l++r +
  gi|121637334|ref|YP_977557.1| 49 RTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLP 93
                                   55566669*********************************9976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.26
                                    HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                           TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlV 52 
                                    +aL k+g+  ++++ e+   + +++ e +   e+ GlV
  gi|121637334|ref|YP_977557.1| 103 AALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLV 140
                                    56667777777777776666666555555555666666 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   3.8e+03      34      43 ..      23      32 ..      23      40 .. 0.68
   2 ?    9.6   0.1   0.00034      0.77      16      49 ..      57      90 ..      49      93 .. 0.83
   3 ?    2.0   0.2     0.082   1.8e+02       4      28 ..     108     128 ..     100     146 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                   HHHHHHHHHH CS
                       HTH_IclR 34 tvhRlLqtLv 43
                                   t++RlL    
  gi|121637334|ref|YP_977557.1| 23 TASRLLVAIS 32
                                   7888887655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00034
                                   BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                    ++ +l+ lA  +g+ +S++ R++  Lv   ++ 
  gi|121637334|ref|YP_977557.1| 57 HGPINLATLATLLGVQPSATGRMVDRLVGAELID 90
                                   45689**********************9877765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.082
                                    HHHHHHCT-CTTBSS-BHHHHHHHH CS
                       HTH_IclR   4 RalaiLdalaeapqeltlselArrt 28 
                                    R+ ++ ++++e+++     e+Ar  
  gi|121637334|ref|YP_977557.1| 108 RGRDVVRQVTEHRRT----EIARIV 128
                                    555666666666664....555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1028.99
//
Query:       gi|121637335|ref|YP_977558.1|  [L=274]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-20   72.9   0.0    7.9e-20   71.3   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    2.9e-20   72.7   0.1    2.5e-19   69.8   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
    2.9e-15   56.3   0.0    4.3e-15   55.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.2e-14   53.5   0.0    3.2e-14   53.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.4e-07   30.6   0.0    7.7e-07   29.8   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    3.8e-06   26.9   0.0    5.9e-06   26.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00013   21.7   0.0    0.00019   21.1   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00076   18.9   0.0     0.0011   18.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.006   16.3   0.2      0.068   12.8   0.2    2.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0062   16.3   0.0      0.012   15.3   0.0    1.4  1  Met_10           Met-10+ like-protein
      0.008   15.6   0.1      0.008   15.6   0.1    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0093   15.5   0.0      0.017   14.7   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.04   13.3   0.0      0.056   12.9   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.15   11.3   0.6          1    8.6   0.2    2.0  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   6.1e-23   7.9e-20       1      94 [.      54     147 ..      54     149 .. 0.98
   2 ?   -1.5   0.0       3.1     4e+03      37      40 ..     224     227 ..     193     266 .. 0.58

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 6.1e-23
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ldv++G+G ++ + ak+ga+v+ +Dl++e+l++++++a ++gl++++++a+a+ lpf+d+ fD v+s   +++ +d+++a
  gi|121637335|ref|YP_977558.1|  54 LDVAAGSGNISLPAAKTGATVISTDLTPELLQRSQARAAQQGLTLQYQEANAQALPFADDEFDTVISAIGVMFAPDHQAA 133
                                    8******************************************************************************* PP

                                    HHHHHHHEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGll 94 
                                     +e++Rv++pgG++
  gi|121637335|ref|YP_977558.1| 134 ADELVRVCRPGGTI 147
                                    ************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                                    HCCH CS
                Methyltransf_11  37 kase 40 
                                    ++ +
  gi|121637335|ref|YP_977558.1| 224 NYGP 227
                                    4433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   1.9e-22   2.5e-19       1      97 []      53     145 ..      53     145 .. 0.95
   2 ?    0.2   0.0      0.98   1.3e+03      15      51 ..     231     267 ..     225     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.9e-22
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLd+++G+G+++l +ak +  a+v+ +D+++e+l++ ++ra+++gl +++++++a++lpf+d++fD v+s+ ++++   +
  gi|121637335|ref|YP_977558.1|  53 VLDVAAGSGNISLPAAKTG--ATVISTDLTPELLQRSQARAAQQGLTLQYQEANAQALPFADDEFDTVISAIGVMF--AP 128
                                    9*****************5..*************************************************866554..46 PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    d+++a +e+ rv++pgG
  gi|121637335|ref|YP_977558.1| 129 DHQAAADELVRVCRPGG 145
                                    889*************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.98
                                    HHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEE CS
                Methyltransf_25  15 lakrlgkakvtgvDiseemleaareraeeegl.nvefv 51 
                                    + +++g+  v++ +++ +++e a++ +++  + ++e++
  gi|121637335|ref|YP_977558.1| 231 AYAHIGDNAVLAAELDRQLVELAAQYLSDG-VmEWEYL 267
                                    44455789999************9999654.3366665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   3.4e-18   4.3e-15      47     153 ..      49     151 ..      40     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 3.4e-18
                                    -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                    +g +vlDva+G+g++++    ++++  +v+  D+ +++L+ +++++ ++g   +++  ana++Lpf dd fD+v  + G+
  gi|121637335|ref|YP_977558.1|  49 PGVRVLDVAAGSGNISLP---AAKTGATVISTDLTPELLQRSQARAAQQGL-TLQYQEANAQALPFADDEFDTVISAIGV 124
                                    6889**********9976...4556679*********************97.69************************** PP

                                    GG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlvvle 153
                                       +D++ a  e+ rv +pGG++ v+ 
  gi|121637335|ref|YP_977558.1| 125 MFAPDHQAAADELVRVCRPGGTIGVIS 151
                                    **********************98875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   2.5e-17   3.2e-14       3     110 ..      49     150 ..      47     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.5e-17
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                     g+rvlD+++G+G++++ +a +  ++a+v++ D ++e +++++++a+++gl+ ++ +++++++l+  ++d+ fD ++s  
  gi|121637335|ref|YP_977558.1|  49 PGVRVLDVAAGSGNISLPAA-K--TGATVISTDLTPELLQRSQARAAQQGLT-LQYQEANAQALP--FADDEFDTVISAI 122
                                    689*****************.4..479************************8.************..***********98 PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggillie 110
                                     ++  +d +++  e+ rv +pgg + + 
  gi|121637335|ref|YP_977558.1| 123 GVMFAPDHQAAADELVRVCRPGGTIGVI 150
                                    88*********************98665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     6e-10   7.7e-07       1      99 []      54     147 ..      54     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6e-10
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvas.nvlhh 78 
                                    L++ +G+G+++ + ++   +++++ +D+ p+ +++ +++ a+++     +  + +   +      + fD+v+++ +v+  
  gi|121637335|ref|YP_977558.1|  54 LDVAAGSGNISLPAAKT--GATVISTDLTPELLQRSQARAAQQGLTLQYQEANAQALPF----AdDEFDTVISAiGVMF- 126
                                    8****************..**************77777777777644444333333333....3459*****8735555. PP

                Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                     +d +++ d++ ++++pgG +
  gi|121637335|ref|YP_977558.1| 127 APDHQAAADELVRVCRPGGTI 147
                                    59*****************75 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.6e-09   5.9e-06      22     115 ..      49     147 ..      18     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.6e-09
                Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp 96 
                                    +g rvLd+++G+G+ +  +++ g++v+  Dl pe+ ++ +     +  + q + +++q  ++ ++ fd++++  +    p
  gi|121637335|ref|YP_977558.1|  49 PGVRVLDVAAGSGNISLPAAKTGATVISTDLTPELLQRSQaraaqQGLTLQYQEANAQALPFADDEFDTVISAIGVMFAP 128
                                    4459******************************9999877777766677777777777788888*************** PP

                Methyltransf_23  97 dppellrqiatllkpgGyl 115
                                    d+ ++ + + + ++pgG +
  gi|121637335|ref|YP_977558.1| 129 DHQAAADELVRVCRPGGTI 147
                                    *****************88 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00019      11     103 ..      47     142 ..      40     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                           MetW  11 ikpgsrvldlGcGdGel.lellkeekqvdgrGl..eldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                    i pg rvld+ +G G++ l   k    v +  l  el +++ a++ ++Gl++  ++++ +   f+d++fd v+ +  +  
  gi|121637335|ref|YP_977558.1|  47 IGPGVRVLDVAAGSGNIsLPAAKTGATVISTDLtpELLQRSQARAAQQGLTLQYQEANAQALPFADDEFDTVISAIGVMF 126
                                    7899***********9756777777888888775688899*********************************9999999 PP

                           MetW  88 trnpkevldellrigr 103
                                      + +   del+r+ r
  gi|121637335|ref|YP_977558.1| 127 APDHQAAADELVRVCR 142
                                    9999999999999976 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.5e-07    0.0011      57     135 ..      44     123 ..      38     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.5e-07
                                    TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-.EEEEES-GGG-----SEEEE.E CS
                           CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk.vevklldyedldekvdrvvs.v 134
                                     +++ pG ++Ld+ +G G++   a++  ++ v++  l  e  +++++r ++++l+ + +e + +     d+++d v+s +
  gi|121637335|ref|YP_977558.1|  44 AAGIGPGVRVLDVAAGSGNISLPAAKT-GATVISTDLTPELLQRSQARAAQQGLTLQyQEANAQALPFADDEFDTVISaI 122
                                    56789********************99.************************9875515555666655667999998734 PP

                                    S CS
                           CMAS 135 g 135
                                    g
  gi|121637335|ref|YP_977558.1| 123 G 123
                                    4 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   5.3e-05     0.068      46     127 ..      67     120 ..      33     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                                    HHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                        UPF0020  46 aallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                    aa  ga+                          ++  Dl ++++q+++  a++a+ g + ++++a+a++L+ +++e+d++
  gi|121637335|ref|YP_977558.1|  67 AAKTGAT--------------------------VISTDLTPELLQRSQ--ARAAQQGLTLQYQEANAQALPFADDEFDTV 118
                                    4444444..........................558999999999876..67778888999**********8888***** PP

                                    EE CS
                        UPF0020 126 vt 127
                                    ++
  gi|121637335|ref|YP_977558.1| 119 IS 120
                                    98 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.6e-06     0.012      98     135 ..      47      82 ..      41      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-06
                                    --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HH CS
                         Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPe 135
                                    + +g +V+dv AG G  ++p+ak   + +v++ dl Pe
  gi|121637335|ref|YP_977558.1|  47 IGPGVRVLDVAAGSGNISLPAAK--TGATVISTDLTPE 82 
                                    678999*****************..8899********8 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.3e-06     0.008     161     234 ..      49     122 ..      42     151 .. 0.80
   2 ?   -3.6   0.1       4.4   5.6e+03     180     201 ..     233     254 ..     231     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                           PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekadvivaNI 234
                                    +g +vlDv +GSG +++ aak ga  v+ +D+ +  ++ +++ a++ +++ + + a+++ l+ ++ ++d +++ I
  gi|121637335|ref|YP_977558.1|  49 PGVRVLDVAAGSGNISLPAAKTGAT-VISTDLTPELLQRSQARAAQQGLTLQYQEANAQALPfADDEFDTVISAI 122
                                    5678*******************95.889******************99999987666666654789**999987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.4
                           PrmA 180 akLgakkvvavDiDevAvkvak 201
                                    a +g + v+a  +D + v+ a+
  gi|121637335|ref|YP_977558.1| 233 AHIGDNAVLAAELDRQLVELAA 254
                                    6788999999999999998876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.017      34     103 ..      52     120 ..      40     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                    EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE CS
                            MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivs 103
                                    +vlD+++G G +++ +ak   +  v  +d   + l+ +++ +++++l +++ + ++ +  +++++fd+++s
  gi|121637335|ref|YP_977558.1|  52 RVLDVAAGSGNISLPAAKTGAT--VISTDLTPELLQRSQARAAQQGLTLQYQEANAQAlPFADDEFDTVIS 120
                                    79***************97776..999*********************99999998773566999**9997 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.3e-05     0.056      25     111 ..      43     130 ..      25     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                                    HCCCS-S-.EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEEEE CS
                           TehB  25 avkivkpg.kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl.derydfilst 102
                                    a+  + pg +vld+  g+g  sl  +  g  v + d   + ++  +  + ++ l+ ++ +  + +++ + d+++d ++s+
  gi|121637335|ref|YP_977558.1|  43 AAAGIGPGvRVLDVAAGSGNISLPAAKTGATVISTDLTPELLQRSQARAAQQGLT-LQYQEANAQALPFaDDEFDTVISA 121
                                    4555566548**************************9999888888888888887.77777777777665789******* PP

                                    SSGGGS-GG CS
                           TehB 103 vvlmfleae 111
                                    + +mf   +
  gi|121637335|ref|YP_977558.1| 122 IGVMFAPDH 130
                                    *****7554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00079         1      38     121 ..      62     144 ..      28     150 .. 0.72
   2 ?    0.8   0.0      0.19   2.4e+02      34      77 ..     192     231 ..     184     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00079
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH...TTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHH CS
                    AlaDh_PNT_C  38 vaGlqAiatakglgakVtvlDvrparleqles...lgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteem 114
                                       l     a++ ga+V  +D+ p+ l++ ++    ++ +++ +++++++l  a  e d vi+++ +  ++  +   +e 
  gi|121637335|ref|YP_977558.1|  62 NISLP----AAKTGATVISTDLTPELLQRSQAraaQQGLTLQYQEANAQALPFADDEFDTVISAIGVMFAPDHQAAADEL 137
                                    44444....55679*************999997544444566688888889999999*******9997776666666666 PP

                                    HHTS-TT CS
                    AlaDh_PNT_C 115 vksMkpg 121
                                    v+  +pg
  gi|121637335|ref|YP_977558.1| 138 VRVCRPG 144
                                    6665555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                                    ESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE CS
                    AlaDh_PNT_C  34 iGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev 77 
                                    +G Gv Gl+   ta+gl  +V+ +D+ +a+  ++++ +g + +e+
  gi|121637335|ref|YP_977558.1| 192 LGDGVTGLK---TARGL-LEVKRFDTAQAVHDYFKNnYGPT-IEA 231
                                    788888875...66676.47899999999999988855544.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1762.41
//
Query:       gi|121637336|ref|YP_977559.1|  [L=312]
Description: methionyl-tRNA formyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-31  109.5   0.0    1.8e-31  109.3   0.0    1.1  1  Formyl_trans_N  Formyl transferase
    7.9e-21   74.2   0.0    1.2e-20   73.7   0.0    1.3  1  Formyl_trans_C  Formyl transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0     2e-35   1.8e-31       3     179 ..       3     179 ..       1     181 [. 0.93

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2e-35
                                    EEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCC...SCCCCCCCHHHHHHHHCTT CS
                 Formyl_trans_N   3 ivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekk...leprsqfeeelaeelkelk 79 
                                    +v+   gt++ + a l +l ++  + dv++v++++d a g++ + ++s++++ ++e +   l+p++    e+++el  l+
  gi|121637336|ref|YP_977559.1|   3 LVFA--GTPEPALASLRRLIESPSH-DVIAVLTRPDAASGRRGKPQPSPVAREAAERGipvLRPSRPNSAEFVAELSDLA 79 
                                    5555..7777777788888887776.9***************************************************** PP

                                    -SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT CS
                 Formyl_trans_N  80 adlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiae 159
                                    ++   +++y+ ll++ l++ ++++ +n+H SLLP+++Gaa++q+a+ aGd+ tG+t ++++  lD G+i+ +    i ++
  gi|121637336|ref|YP_977559.1|  80 PECCAVVAYGALLGGPLLAVPPHGWVNLHFSLLPAWRGAAPVQAAIAAGDTITGATTFQIEPSLDSGPIYGVVTEVIQPT 159
                                    **********************************************************************999999999* PP

                                    --HHHHHHHHHHHHHHHHHH CS
                 Formyl_trans_N 160 dtkeeleqrvadaehkalve 179
                                    dt+++l +r+a  +  +l +
  gi|121637336|ref|YP_977559.1| 160 DTAGDLLKRLAVSGAALLST 179
                                    *********99888777765 PP

>> Formyl_trans_C  Formyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   1.3e-24   1.2e-20       1      99 [.     204     303 ..     204     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.3e-24
                                    ..-GGGGB--TTSBHHHHHHHHHHT-TS--EEEEETTEEEEEEEEEEE-S--SS-...TTSEEETT..TEEEE-SBSEEE CS
                 Formyl_trans_C   1 kikkedgridwnqsaeeihnlvrglspwPgayttlngkrvkllkaevvsesssaes..pGtivavdkggllvacgdgall 78 
                                    ki+ +++r+ w+ +a+ +++++r+++p+Pga+t + + rvkl  ++ + ++  ++   pG  + v+++++ +++g+++++
  gi|121637336|ref|YP_977559.1| 204 KITVANARVRWDLPAAVVERRIRAVTPNPGAWTLIGDLRVKLGPVHLDAAHRPSKPlpPG-GIHVERTSVWIGTGSEPVR 282
                                    7999*****************************************999777776669999.78899999*********** PP

                                    EEEEEETTS--EEHHHHHHH. CS
                 Formyl_trans_C  79 ilelqlegkkamsaedflngl 99 
                                    + ++q++gkk m+a+d+++g+
  gi|121637336|ref|YP_977559.1| 283 LGQIQPPGKKLMNAADWARGA 303
                                    *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2141.96
//
Query:       gi|121637337|ref|YP_977560.1|  [L=457]
Description: fmu protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-66  222.4   0.0    7.1e-66  221.7   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      2e-24   86.4   0.0    2.8e-24   85.9   0.0    1.2  1  NusB             NusB family
    0.00059   20.5   0.0     0.0019   18.9   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
      0.005   16.7   0.0      0.047   13.5   0.0    2.1  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.068   13.8   0.0       0.18   12.4   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
       0.32   11.4   4.1       0.23   11.9   0.8    2.6  2  Phage_TAC_6      Phage tail assembly chaperone protein, TAC


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.0   2.4e-69   7.1e-66       2     200 .]     260     454 ..     259     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.4e-69
                                    HHH---TT-E..EEESS-TTSHHHHHHHHH.TTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                Methyltr_RsmB-F   2 llLapqeeet..ilDlcaaPGgKTthiael.mknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                    l+Lap +++t  +lDlca+PGgKT+++a l ++++++v+Av+ + +R++ va+n+++L+v+   +l++D+r++d + g  
  gi|121637337|ref|YP_977560.1| 260 LTLAPVDGDTgrWLDLCAGPGGKTALLAGLgLQCAARVTAVEPSPHRADLVAQNTRGLPVE---LLRVDGRHTDLDPG-- 334
                                    789*****9999*************************************************...************99.. PP

                                    .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-T CS
                Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkre 158
                                     fDr+L+DaPC+g+g++rr+p++++rr+++d+a+laklq+ellsaai+l+++gGv++Y+TCs +++E++ ++++aL++++
  gi|121637337|ref|YP_977560.1| 335 -FDRVLVDAPCTGLGALRRRPEARWRRQPADVAALAKLQRELLSAAIALTRPGGVVLYATCSPHLAETVGAVADALRRHP 413
                                    .******************************************************************************* PP

                                    TEEEESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                Methyltr_RsmB-F 159 dvelvetelsepkglklgeeagtlrllPhtenkdgffiaklk 200
                                     ++l++++l+ep+ + lge+  +++l+Ph++ +d++f+a+l+
  gi|121637337|ref|YP_977560.1| 414 VHALDTRPLFEPVLAGLGEGP-HVQLWPHRHGTDAMFAAALR 454
                                    *********************.*****************996 PP

>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   9.3e-28   2.8e-24       2     133 ..      15     137 ..      14     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 9.3e-28
                                    HHHHHHHHHHHHHHHH-S-HHHHHHHHHHHT-.......--HHHHHHHHHHHHHHHHTHHHHHHHHHHTTTT--GGGS-H CS
                           NusB   2 kaRelalqalyqveinkedeeekeailqealnklleeedldeedkafltelvkgvlrnleelDeliekllknwplerlsk 81 
                                    +aR++a+++l +v       ++++a+++ +l +ll+++    +d af+tel++g++r +  lD++i   + +++ + +++
  gi|121637337|ref|YP_977560.1|  15 PARRAAFETLRAV-------SARDAYANLVLPALLAQRGIGGRDAAFATELTYGTCRARGLLDAVIGAAA-ERSPQAIDP 86 
                                    69***********.......************************************************88.999999*** PP

                                    HHHHHHHHHHHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHHHHHHHHHHH CS
                           NusB  82 vdraiLrlavyellylddvPakvaineavelakkygdeksakFvNgVLrkva 133
                                    v++ +Lrl++y+ll + +v+a++a++ +ve a +  d   a+FvNgVLr +a
  gi|121637337|ref|YP_977560.1|  87 VLLDLLRLGTYQLLRT-RVDAHAAVSTTVEQAGIEFDSARAGFVNGVLRTIA 137
                                    ****************.********************************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.4e-07    0.0019       2      70 ..     273     340 ..     273     356 .. 0.90
   2 ?   -3.2   0.0       4.7   1.4e+04      82      97 .]     372     387 ..     366     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.4e-07
                                    EEET-TTSHHHHHHHCTS.T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrl.g.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                    Ldl++G+G  t+ la  + + +a+vt+v++s+   + ++++   +gl ve+++ d ++ +++   fD v++
  gi|121637337|ref|YP_977560.1| 273 LDLCAGPGGKTALLAGLGlQcAARVTAVEPSPHRADLVAQNT--RGLPVELLRVDGRHTDLDP-GFDRVLV 340
                                    8**************9976579********************..799*********9999766.8998876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.7
                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    ++++l+ +  +++pgG
  gi|121637337|ref|YP_977560.1| 372 QRELLSAAIALTRPGG 387
                                    4678999999999999 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.6e-05     0.047      12      61 ..     259     311 ..     245     448 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevl....rengfsvtgvDlspeaveiae 61 
                                    +l  l+p +   gr+Ld+ +G G  + +l     ++ + vt+v++sp+  ++++
  gi|121637337|ref|YP_977560.1| 259 AL-TLAPVDGDTGRWLDLCAGPGGKTALLaglgLQCAARVTAVEPSPHRADLVA 311
                                    33.3668899999**********655555143333445*********9877764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.2e-05      0.18       1      65 [.     273     338 ..     273     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                                    EEET-TTSHHHHHHHHTT....SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg....arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlv 65 
                                    Ld+ +G G  ++ la  g    arv++v++s+   +l+ +++++ +  ve+++ d +++ +    fD v
  gi|121637337|ref|YP_977560.1| 273 LDLCAGPGGKTALLAGLGlqcaARVTAVEPSPHRADLVAQNTRGLP--VELLRVDGRHTDLDP-GFDRV 338
                                    7999999999999995555559**********************99..788888888777655.56655 PP

>> Phage_TAC_6  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3   8.8e+03      37      52 ..      10      25 ..       7      26 .. 0.71
   2 ?   11.9   0.8   7.8e-05      0.23      10      38 ..     346     374 ..     342     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                    Phage_TAC_6 37 aagaapLsRadLdaLm 52
                                   +++ +p +Ra+++ L 
  gi|121637337|ref|YP_977560.1| 10 RRPLDPARRAAFETLR 25
                                   5556788899999886 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.8e-05
                    Phage_TAC_6  10 GlggLrLrPeeFWalTPaELalllgaeaa 38 
                                    Glg+Lr rPe+ W+  Pa+ a+l++++++
  gi|121637337|ref|YP_977560.1| 346 GLGALRRRPEARWRRQPADVAALAKLQRE 374
                                    99*********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 3050.32
//
Query:       gi|121637338|ref|YP_977561.1|  [L=232]
Description: ribulose-phosphate 3-epimerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-83  278.4   0.0    2.8e-83  278.2   0.0    1.0  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
     0.0004   20.2   0.0    0.00071   19.4   0.0    1.3  1  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
     0.0078   15.7   0.1      0.057   12.9   0.1    2.0  2  His_biosynth     Histidine biosynthesis protein
     0.0092   15.6   0.1      0.015   14.9   0.1    1.4  1  OMPdecase        Orotidine 5'-phosphate decarboxylase / HUMPS
  ------ inclusion threshold ------
      0.061   12.6   1.4       0.17   11.2   1.2    1.8  2  ThiG             Thiazole biosynthesis protein ThiG
       0.24   10.5   0.1       0.42    9.8   0.0    1.4  2  IGPS             Indole-3-glycerol phosphate synthase
        2.5    7.7   5.3       0.26   10.8   0.6    1.7  2  Staphylcoagulse  Staphylocoagulase repeat


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.2   0.0   1.1e-86   2.8e-83       2     198 .]      13     207 ..      12     207 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.2 bits;  conditional E-value: 1.1e-86
                                    EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT- CS
                 Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeaga 81 
                                    iapS+l+adfarl++e +av+  gad+lHvDvmDghfvpNltig  vve+l ++t++p+d+HLm++++dr++p +aeaga
  gi|121637338|ref|YP_977561.1|  13 IAPSILAADFARLADEAAAVN--GADWLHVDVMDGHFVPNLTIGLPVVESLLAVTDIPMDCHLMIDNPDRWAPPYAEAGA 90 
                                    9*******************9..99******************************************************* PP

                                    SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHH CS
                 Ribul_P_3_epim  82 siisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklid 161
                                     ++++HaEa++++  + ++i++aGakag++++p tple + ++l+++d++l+msvePgfgGQ+Fipevl+k+++vrk++d
  gi|121637338|ref|YP_977561.1|  91 YNVTFHAEATDNPVGVARDIRAAGAKAGISVKPGTPLEPYLDILPHFDTLLVMSVEPGFGGQRFIPEVLSKVRAVRKMVD 170
                                    ******************************************************************************** PP

                                    HHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                 Ribul_P_3_epim 162 ekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                    + el++ +e+DGG+++d+ieq+aeag+d++Vagsav+
  gi|121637338|ref|YP_977561.1| 171 AGELTILVEIDGGINDDTIEQAAEAGVDCFVAGSAVY 207
                                    ***********************************98 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.8e-07   0.00071     114     161 ..     162     209 ..     155     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.8e-07
                                    HHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
                      QRPTase_C 114 lkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsv 161
                                    ++ + +++++ + ++l+e  Gg++++++e+ a+ gvd++  g++++++
  gi|121637338|ref|YP_977561.1| 162 VRAVRKMVDAGELTILVEIDGGINDDTIEQAAEAGVDCFVAGSAVYGA 209
                                    45555555688999****************************999876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11   2.9e+02      40     109 ..      32     103 ..      17     122 .. 0.63
   2 !   12.9   0.1   2.2e-05     0.057      69     106 ..     171     207 ..     158     232 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                    HHT-SEEEEEEHHHHC.TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHH.HHHHCT-SEEEESHHHHH-T CS
                   His_biosynth  40 eegadelhvvDldaak.egreanldlveeiaeevfipvqvGGGIrsledve.elleagadkviigtaavknp 109
                                     +gad+lhv  +d+ +  + ++ l +ve ++  ++ip+     I + ++ +  + eaga +v    +a +np
  gi|121637338|ref|YP_977561.1|  32 VNGADWLHVDVMDGHFvPNLTIGLPVVESLLAVTDIPMDCHLMIDNPDRWApPYAEAGAYNVTFHAEATDNP 103
                                    578999998888888744455667888888888888776655555555432135555555555555555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.2e-05
                                    HHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                   His_biosynth  69 aeevfipvqvGGGIrsledveelleagadkviigtaav 106
                                    a e++i v+++GGI++   +e++ eag+d  + g+a+ 
  gi|121637338|ref|YP_977561.1| 171 AGELTILVEIDGGINDDT-IEQAAEAGVDCFVAGSAVY 207
                                    34567999*******987.****************965 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     6e-06     0.015     182     223 ..     177     217 ..     152     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                    EEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                      OMPdecase 182 qggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                      +  +g++ +t+e++++ ag d +++G ++++a+dp++++ 
  gi|121637338|ref|YP_977561.1| 177 LVEIDGGINDDTIEQAAE-AGVDCFVAGSAVYGADDPAAAVA 217
                                    566789999999999988.99*****************9986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.65   1.7e+03      80     100 ..      21      44 ..      14      52 .. 0.70
   2 ?   11.2   1.2   6.5e-05      0.17     167     223 ..     165     222 ..     156     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.65
                                    HHHHHHHHTT...S-SEEEE--BC CS
                           ThiG  80 riarlarevl...etdliklEvia 100
                                      arla e++   + d++ ++v+ 
  gi|121637338|ref|YP_977561.1|  21 DFARLADEAAavnGADWLHVDVMD 44 
                                    456666665534488999999875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.5e-05
                                    HHHHHHH-SS-BE..EES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHH CS
                           ThiG 167 lkiiieeakvPvi..vDAGigspsdaaqamelGadavllntavaeakdpvamArafkla 223
                                    ++ +++  ++ ++  +D Gi     + qa e G+d  +  +av  a+dp+a  +a++  
  gi|121637338|ref|YP_977561.1| 165 VRKMVDAGELTILveIDGGIND-DTIEQAAEAGVDCFVAGSAVYGADDPAAAVAALRRQ 222
                                    5666665555555115777764.56889**********************999998764 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.5   6.3e+03      69      87 ..     102     121 ..     100     121 .. 0.76
   2 ?    9.8   0.0   0.00016      0.42     198     254 .]     161     219 ..     157     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.5
                                    -HHHHHHHHTTT.-SE.EEE CS
                           IGPS  69 dpaeiAkkyeeagAsa.iSV 87 
                                    +p+ +A++ ++agA+a iSV
  gi|121637338|ref|YP_977561.1| 102 NPVGVARDIRAAGAKAgISV 121
                                    57778999999999753776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                                    HHHHHCHCC-.TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                           IGPS 198 tteeLaklvp.kd.vllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                    +++ ++k+v+  + ++lv   G  + +++e+ +e+gv++f  G+++  ++d ++a+++l
  gi|121637338|ref|YP_977561.1| 161 KVRAVRKMVDaGElTILVEIDGGINDDTIEQAAEAGVDCFVAGSAVYGADDPAAAVAAL 219
                                    667778888842357888888878889*************************9999876 PP

>> Staphylcoagulse  Staphylocoagulase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6    0.0001      0.26      10      20 ..      88      98 ..      84     101 .. 0.84
   2 ?   -2.4   0.4       1.4   3.6e+03      21      27 .]     203     209 ..     202     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                Staphylcoagulse 10 TNAYNVTTHAd 20
                                     AYNVT HA+
  gi|121637338|ref|YP_977561.1| 88 AGAYNVTFHAE 98
                                   56********8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                Staphylcoagulse  21 GtvsYGa 27 
                                    G + YGa
  gi|121637338|ref|YP_977561.1| 203 GSAVYGA 209
                                    8999**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.40
# Mc/sec: 1749.84
//
Query:       gi|121637339|ref|YP_977562.1|  [L=339]
Description: bifunctional riboflavin biosynthesis protein RIBG: diaminohydroxyphosphoribosylaminopyrimidine deaminase + 5-amino-6-(5-phosphoribosylamino) uracil reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-50  171.2   0.1      3e-50  170.8   0.1    1.2  1  RibD_C           RibD C-terminal domain
    3.3e-17   62.2   0.0    5.1e-17   61.6   0.0    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.1e-08   34.0   0.0    3.3e-08   33.4   0.0    1.2  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.1   5.1e-54     3e-50       1     200 []     154     334 ..     154     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 5.1e-54
                                    -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEE CS
                         RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrv 80 
                                    p+v++k+a+S+DG++aaa+g+s+wi++e+ar d+h+ ra adailvG+gtvlad+p+lt+r+++++ a      +qp+rv
  gi|121637339|ref|YP_977562.1| 154 PHVTWKYATSIDGRSAAADGSSQWISSEAARLDLHRRRAIADAILVGTGTVLADDPALTARLADGSLAP-----QQPLRV 228
                                    89***************************************************************9887.....****** PP

                                    EEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCCESE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEE CS
                         RibD_C  81 VvdstlrvpldakvltddaptlvatteeadkekveklkvrvdlkelleeLkergirsllveGGatLagsllraglvDelr 160
                                    Vv ++ ++p++a+vl+d+a+t++++t e              + e+l++L++r   ++l+eGG+tLag++lrag ++++ 
  gi|121637339|ref|YP_977562.1| 229 VVGKR-DIPPEARVLNDEARTMMIRTHE--------------PMEVLRALSDR--TDVLLEGGPTLAGAFLRAGAINRIL 291
                                    *****.69**********6666666664..............***********..************************* PP

                                    EEEESCE--TTSBCSSSSST-SS....EEEEEEEEEEETTEEEE CS
                         RibD_C 161 lyiaPkllGgagktlfdgegfka....lklklvksealgegvvl 200
                                     y+aP+llGg   t +d++g+++    l++++ ++e++g++++l
  gi|121637339|ref|YP_977562.1| 292 AYVAPILLGG-PVTAVDDVGVSNitnaLRWQFDSVEKVGPDLLL 334
                                    **********.*****************************9975 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   8.5e-21   5.1e-17       5     100 ..      10     106 ..       6     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 8.5e-21
                                    HHHHHHHHHHHHHHH..TTTSCSEEEEEEE.TTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE-- CS
                dCMP_cyt_deam_1   5 ekllelalkaakeaq..kcsnfkVGavivk.ngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtleP 81 
                                     +++ la++++ + +  +++n++VGaviv+ ng+i++ g   epagg+   HAEv+A++ a+       +ga+++vt+eP
  gi|121637339|ref|YP_977562.1|  10 DEAMGLAIEHSYQVKgtTYPNPPVGAVIVDpNGRIVGAGG-TEPAGGD---HAEVVALRRAGGL----ATGAIVVVTMEP 81 
                                    567888888888888889************8888888876.5678999...**********944....469********* PP

                                    BHH......HHHHHHHHT-SEEEEE CS
                dCMP_cyt_deam_1  82 Csm......Cakaiiqsgikkvvvg 100
                                    C++      C +a+i++++ +vv++
  gi|121637339|ref|YP_977562.1|  82 CNHygktppCVNALIEARVGTVVYA 106
                                    ***********************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   5.5e-12   3.3e-08      21     107 ..      29     113 ..      16     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.5e-12
                    MafB19-deam  21 kedkigaviv.kdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepC......dmCagaivqag 93 
                                     + ++gaviv  ++++++ g +e       ++HaE+ al++A     +  + +a+++vt epC      ++C  a+++a+
  gi|121637339|ref|YP_977562.1|  29 PNPPVGAVIVdPNGRIVGAGGTE----PAGGDHAEVVALRRA-----GGLATGAIVVVTMEPCnhygktPPCVNALIEAR 99 
                                    56799*****77889******94....569************.....344689**********44444448********* PP

                    MafB19-deam  94 lkklvygagnpksl 107
                                    + ++vy++++p+++
  gi|121637339|ref|YP_977562.1| 100 VGTVVYAVADPNGI 113
                                    *********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2271.79
//
Query:       gi|121637340|ref|YP_977563.1|  [L=518]
Description: aminoglycosides/tetracycline-transport integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-37  129.7  41.2    8.2e-37  126.9  39.1    2.1  2  MFS_1     Major Facilitator Superfamily
    6.5e-10   38.5   7.8    6.5e-10   38.5   7.8    2.8  3  Sugar_tr  Sugar (and other) transporter
    5.7e-08   31.7   5.9    9.1e-08   31.0   5.9    1.3  1  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
      0.084   13.4   0.8      0.084   13.4   0.8    6.6  4  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9  39.1   1.8e-40   8.2e-37       3     352 ..      14     424 ..      12     425 .. 0.81
   2 !    2.8   0.0    0.0099        44     153     184 ..     475     506 ..     441     516 .. 0.76

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 1.8e-40
                          MFS_1   3 laaflsalarsilgpalplalaedlgispse...igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                    la++l al+ +++ +++   ++++ gi   +   i +++t+y lg+++a+++lGr sdrfGr+ +l ++l++f++g+++ 
  gi|121637340|ref|YP_977563.1|  14 LAVLLGALDTYVVVTIMR-DIMNSVGIPINQlhrITWIVTMYLLGYIAAMPLLGRASDRFGRKLMLQVSLAGFIIGSVVT 92 
                                    788899999999999999.999999*99999999******************************************7777 PP

                          MFS_1  80 lfa..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfy 155
                                    ++a   + + +l+++r +qG+++gal+p+ +al ad++++++r+ ++g ++a+  lG++lgpl g +++  +  Wr vf+
  gi|121637340|ref|YP_977563.1|  93 ALAghFGDFhMLIAGRTIQGVASGALLPITLALGADLWSQRNRAGVLGGIGAAQELGSVLGPLYGIFIVwLLHDWRDVFW 172
                                    7666767888***********************************************************88888****** PP

                          MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee......................................kgtgpaplv 197
                                    i+ +++++a+v+  + +  + ++r++++++ ++                                      + ++  +++
  gi|121637340|ref|YP_977563.1| 173 INVPLTAIAMVM--IHFSLPSHDRSTEPERVDLvgglllalalglaviglynpnpdgkhvlpdygapllvgALVAAVAFF 250
                                    *********887..99999999999999999999******************9999999977777766666555555555 PP

                          MFS_1 198 pawkallkdpvl......w....illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrl 267
                                      w+ + + + +      +    ++l a++ ++++++ +l+ + l+ q vl ++   +a+++l  + ++  i+a+ +g++
  gi|121637340|ref|YP_977563.1| 251 G-WERFARTRLIdpagvhFrpflSALGASVAAGAALMVTLVDVELFGQGVLQMD-QAQAAGMLLWFLIALPIGAVTGGWI 328
                                    5.999999996665554422322444444444444444555566699*******.4555544444444444558999999 PP

                          MFS_1 268 sdrlgrrrrlllallllllaalglallavt...........ssavllllvlvliGfglgfvfpsllalasdlappeeagt 336
                                    ++r g r   + +ll+++ ++ ++  ++v             + ++++  lv++G+glg+v ++l +++ +++p  ++g 
  gi|121637340|ref|YP_977563.1| 329 ATRAGDRAVAFAGLLIAAYGYWLISHWPVDlladrhnilglFTVPAMHTDLVVAGLGLGLVIGPLSSATLRVVPSAQHGI 408
                                    9**99866666666666555555555555598886555544444444448888*************************** PP

                          MFS_1 337 asglfntagslggalg 352
                                    as+++ +a+  g+++g
  gi|121637340|ref|YP_977563.1| 409 ASAAVVVARMTGMLIG 424
                                    *************998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0099
                          MFS_1 153 vfyilaivsllafvlfllllpeepperkrksp 184
                                    +f i aiv+++++vl+ll   +++++ +++ +
  gi|121637340|ref|YP_977563.1| 475 IFTITAIVCVFGAVLGLLISGRKEHADEPEVQ 506
                                    79999999999999866665555555554443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   7.8   1.4e-13   6.5e-10      47     187 ..      46     184 ..      14     195 .. 0.80
   2 ?    1.6   4.2     0.022        97      48     125 ..     307     395 ..     281     448 .. 0.70
   3 ?   -2.9   0.4      0.52   2.3e+03      47      67 ..     471     491 ..     457     497 .. 0.59

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.4e-13
                                    HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmy 126
                                    ++++iv ++l+G i+   ++g ++drfGRk  l ++ + f+ig+v++a+a +   + +li+gR + G++ G+   ++  +
  gi|121637340|ref|YP_977563.1|  46 RITWIVTMYLLGYIAAMPLLGRASDRFGRKLMLQVSLAGFIIGSVVTALAGHFGDFHMLIAGRTIQGVASGALLPITLAL 125
                                    789************************************************99*******************99999888 PP

                                    HHTTS-SCCH.HHHHHH...HHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                       Sugar_tr 127 isEiApkklR.galvsl...yqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                     + +  ++ R g l+++   ++l+ ++G l ++++ + l +      wr  +++++ ++ + +++
  gi|121637340|ref|YP_977563.1| 126 GADLWSQRNRaGVLGGIgaaQELGSVLGPLYGIFIVWLLHD------WRDVFWINVPLTAIAMVM 184
                                    88888777775666554222667777777777776666655......555777776665433333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.022
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH.HHHH-TTTT..........SS-TGGGGGHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfviga.vlqaaakgk..........nsvevlivgRvlvGigv 116
                                       ++  fl+   iG++++g++++r G + +  ++ +++  g  +++++  +           ++v ++ +  v++G+g+
  gi|121637340|ref|YP_977563.1| 307 AAGMLLWFLIALPIGAVTGGWIATRAGDRAVAFAGLLIAAYGYwLISHWPVDLladrhnilglFTVPAMHTDLVVAGLGL 386
                                    45566778999999999999999999999999999999888862455666655777665555555555555577777777 PP

                                    HHHHHHHHH CS
                       Sugar_tr 117 GlasvlvPm 125
                                    Gl+ +  + 
  gi|121637340|ref|YP_977563.1| 387 GLVIGPLSS 395
                                    777665555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.52
                                    HHHHHHHTHHHHHHHHHHHHH CS
                       Sugar_tr  47 lsglivsiflvGaiiGslfag 67 
                                     +g i+ i+ +++++G++++ 
  gi|121637340|ref|YP_977563.1| 471 MYGEIFTITAIVCVFGAVLGL 491
                                    445555566666666665544 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   5.9     2e-11   9.1e-08      48     220 ..      15     190 ..       2     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2e-11
                          TRI12  48 afslnvvatyfvlqasasalpnilqdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfv...ilthilglvgaiv 124
                                    a+ l  + ty+v+      +  +   + q    + + t++ +g   ++ ++gr +drfgr+ ++   ++  i+g v + +
  gi|121637340|ref|YP_977563.1|  15 AVLLGALDTYVVVTIMRDIMNSVGIPINQLHRITWIVTMYLLGYIAAMPLLGRASDRFGRKLMLqvsLAGFIIGSVVTAL 94 
                                    34455677899988888888888888889999999*************************98751124556776655555 PP

                          TRI12 125 gctatkfntllaamtllgvaagpagasplfvg.elmsnktkflgllivsipvvvtsglspylgqrla.iqgswrwifyiy 202
                                          f  l+a  t+ gva+g      l +g +l s++ +   l  + +     s l+p +g  +  +  +wr +f+i 
  gi|121637340|ref|YP_977563.1|  95 AGHFGDFHMLIAGRTIQGVASGALLPITLALGaDLWSQRNRAGVLGGIGAAQELGSVLGPLYGIFIVwLLHDWRDVFWIN 174
                                    555677899*****************9**9994566766665555567788888888******87653789********* PP

                          TRI12 203 iitsaiavllivvwyypp 220
                                    + ++aia+++i   +  p
  gi|121637340|ref|YP_977563.1| 175 VPLTAIAMVMI--HFSLP 190
                                    ***99998765..44444 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.9  13.7         4   1.8e+04      31      81 ..     148     213 ..       6     225 .. 0.64
   2 ?   -6.4   8.1         4   1.8e+04      51      51 ..     290     290 ..     203     332 .. 0.55
   3 ?   -6.4  11.4         4   1.8e+04      33      83 ..     380     429 ..     302     439 .. 0.64
   4 ?   13.4   0.8   1.9e-05     0.084       9      44 ..     459     494 ..     457     499 .. 0.94

  Alignments for each domain:
  == domain 1  score: -8.9 bits;  conditional E-value: 4
                           FtsX  31 valviGlglgllaaqllsdvllss...............vfs.selkisidlitvliiivlllllal 81 
                                    +++v+G + g+++ +ll d+ + +               + s ++ + s+ ++ v ++ +lll lal
  gi|121637340|ref|YP_977563.1| 148 LGSVLGPLYGIFIVWLLHDWRDVFwinvpltaiamvmihF-SlPSHDRSTEPERVDLVGGLLLALAL 213
                                    3455555556666666666666663333333333222211.13555555555555555555555555 PP

  == domain 2  score: -6.4 bits;  conditional E-value: 4
                           FtsX  51 l 51 
                                    +
  gi|121637340|ref|YP_977563.1| 290 V 290
                                    1 PP

  == domain 3  score: -6.4 bits;  conditional E-value: 4
                           FtsX  33 lviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllalla 83 
                                     v+Glglgl++  l+s+ l  +  s +  i      v+ + ++l+ +a l+
  gi|121637340|ref|YP_977563.1| 380 VVAGLGLGLVIGPLSSATLRVV-PSAQHGIASAAVVVARMTGMLIGVAALS 429
                                    3556667777766655555544.3344444444444444444444444444 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 1.9e-05
                           FtsX   9 alGmkkkqvlllllteillitlvalviGlglgllaa 44 
                                    a+G++  q + l+++ei+ it++ +v+G +lgll++
  gi|121637340|ref|YP_977563.1| 459 AIGARYQQAFALMYGEIFTITAIVCVFGAVLGLLIS 494
                                    89******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3518.06
//
Query:       gi|121637341|ref|YP_977564.1|  [L=236]
Description: lipoprotein lprG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-78  262.7   2.6    2.3e-78  262.5   2.6    1.0  1  LppX_LprAFG  LppX_LprAFG lipoprotein


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.5   2.6   1.3e-82   2.3e-78       1     192 []      40     230 ..      40     230 .. 1.00

  Alignments for each domain:
  == domain 1  score: 262.5 bits;  conditional E-value: 1.3e-82
                                    .HHHHHHHHHHHHHT-SEEEEEEEEEC--TTSTEEEEEEEEETTTT.EEEEEEEEEETTCEEEEEEEEETTEEEEEECTT CS
                    LppX_LprAFG   1 daakllaesakatkslksvhlaltvngkvdglpvesvegdltnqpagaakgnakvtlagqavdvkfvvvdgklyaklppe 80 
                                    da+ l++e++ +tk+lks+h++ltvngk++gl++++++gdlt++p+ aa+gn+k+tl+g+++d++fvv+dg lya+l+p+
  gi|121637341|ref|YP_977564.1|  40 DAKPLVEEATAQTKALKSAHMVLTVNGKIPGLSLKTLSGDLTTNPT-AATGNVKLTLGGSDIDADFVVFDGILYATLTPN 118
                                    8999******************************************.********************************* PP

                                    EEEEEEEHGHCHHHHCGG-TTTSHHHHCCTEEEEEEEEEEEETTEEEEEEEEEE-HHHHHHH-CCG-SSS.EEEEEEEES CS
                    LppX_LprAFG  81 twsdlgpaekiydpavlLdpdkGlanvLagvtdakaegreeidGtatvkitGtvdadvvsaivpslkedgtvpitlWiae 160
                                    +wsd+gpa++iydpa++L+pd+GlanvLa++ dakaegr++i+G++t++i+G+v+a++v++i+p ++++++vp+t+Wi+e
  gi|121637341|ref|YP_977564.1| 119 QWSDFGPAADIYDPAQVLNPDTGLANVLANFADAKAEGRDTINGQNTIRISGKVSAQAVNQIAPPFNATQPVPATVWIQE 198
                                    ******************************************************************************** PP

                                    STT--EEEEEEEECTCEEEEEEEESTT---TT CS
                    LppX_LprAFG 161 dgelrlvrvvvdkesgesveltlskwgkpvtv 192
                                    +g+++l+++++d++sg+sv++tlskwg++v+v
  gi|121637341|ref|YP_977564.1| 199 TGDHQLAQAQLDRGSGNSVQMTLSKWGEKVQV 230
                                    ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1498.99
//
Query:       gi|121637342|ref|YP_977565.1|  [L=201]
Description: riboflavin synthase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-49  165.0   0.8    1.4e-24   85.9   0.1    2.0  2  Lum_binding    Lumazine binding domain
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.25   11.3   0.0    1.7  2  Phage_T4_gp36  Phage T4 tail fibre


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   4.2e-26   3.7e-22       1      87 []       3      87 ..       3      87 .. 0.89
   2 !   85.9   0.1   1.6e-28   1.4e-24       1      87 []     100     187 ..     100     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.2e-26
                                   -S--SEEEEEEEEE.ECGCTTEETEESGGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEE CS
                    Lum_binding  1 tGiVeevgtvesiekeekledltielpelakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkV 82
                                   tGiVee g+v+  e   ++++lti+ p + ++ + +GdsiavnGvcLTVv + + +++ft+dv++eTl+r++lgel++g++V
  gi|121637342|ref|YP_977565.1|  3 TGIVEERGEVTGREALVDAARLTIRGP-MVTADAGHGDSIAVNGVCLTVV-DVLPDGQFTADVMAETLNRSNLGELRPGSRV 82
                                   8************76678999999777.55556678*************8.43559************************** PP

                                   EEEEE CS
                    Lum_binding 83 NlEra 87
                                   NlEra
  gi|121637342|ref|YP_977565.1| 83 NLERA 87
                                   ***96 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 1.6e-28
                                    -S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEE..EEE.SSEEEEEEEHHHHHHSSGGG-- CS
                    Lum_binding   1 tGiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvt..eeveeeeftvdvipeTlerttlgelk 77 
                                    +G+V+++g++++  ++e++e ++ie+p ++a+y+vekG si+v+G++LTV    +  ++++f+v++ip+T e ttlg+ +
  gi|121637342|ref|YP_977565.1| 100 QGHVDATGEIVARCPSEHWEVVRIEMPaSVARYVVEKG-SITVDGISLTVSGlgA-EQRDWFEVSLIPTTRELTTLGSAA 177
                                    8************88999********************.***********64742.4589******************** PP

                                    TTSEEEEEEE CS
                    Lum_binding  78 vgdkVNlEra 87 
                                    vg++VNlE++
  gi|121637342|ref|YP_977565.1| 178 VGTRVNLEVD 187
                                    ********97 PP

>> Phage_T4_gp36  Phage T4 tail fibre
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.69   6.2e+03      86      98 ..      18      30 ..       3      46 .. 0.58
   2 ?   11.3   0.0   2.8e-05      0.25      67     117 ..      90     158 ..      77     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.69
                  Phage_T4_gp36 86 vpadkkltvkGkv 98
                                      +  lt++G +
  gi|121637342|ref|YP_977565.1| 18 LVDAARLTIRGPM 30
                                   3335667777644 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.8e-05
                  Phage_T4_gp36  67 fdtRsgnintkGkvgigtrvpa..................dkkltvkGkvdllnvkltvsaeatksvsf 117
                                     ++R g    +G+v +++++ a                  ++ +  kG+++++++ ltvs+ ++++  +
  gi|121637342|ref|YP_977565.1|  90 LGSRLGGHIVQGHVDATGEIVArcpsehwevvriempasvARYVVEKGSITVDGISLTVSGLGAEQRDW 158
                                    6788888677***************************9998899999*************988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1411.65
//
Query:       gi|121637343|ref|YP_977566.1|  [L=171]
Description: hypothetical protein BCG_1474 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-15   57.5   0.0    1.6e-15   57.4   0.0    1.0  1  Ala_racemase_N  Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
      0.045   13.2   0.0       0.57    9.6   0.0    2.0  2  AP_endonuc_2    Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   1.8e-19   1.6e-15      76     202 ..      27     157 ..       1     166 [. 0.84

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.8e-19
                                    C.STGGGHHHHHHT.TEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSSSSSBSCHHHHHHHHHHHHTTTEEEEEEE CS
                 Ala_racemase_N  76 g.fspeelaalaey.dltvtvdsleqlealaaaareagkplrvhlkidtgmgRlGftpeeleellealaalpglrleglm 153
                                    g  ++++l++la++ ++ v   + e +    a +++a   ++v+++id+g +R+G+++e++ e++ a+ +  gl+l+g++
  gi|121637343|ref|YP_977566.1|  27 GtRQADRLRQLADRaRIAVGAGTAEGASNTGARLADAAGAIDVLIEIDSGHHRSGVRAEQVLEVAHAVGE-AGLHLVGVF 105
                                    424778888888877999999999999988888888999*****************************98.68******* PP

                                    -S-SSTTSTS...HHHHHHHHHHHHHHHHHHHTTGGGSEEEEESHHHHHHSG CS
                 Ala_racemase_N 154 tHfasadepd...eeteaqlarfeealeelekaglrppvvslanSaaillaa 202
                                    t+++++ +p    e+ e++++++++a+++l + g+++ ++s ++++++ll a
  gi|121637343|ref|YP_977566.1| 106 TFPGHSYAPGkpgEAGEQERRALNDAANALVAVGFPISCRSGGSTPTALLTA 157
                                    *****97666666777779************999**************9875 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0    0.0059        53     110     164 ..      31      77 ..      27      81 .. 0.79
   2 ?    9.6   0.0   6.3e-05      0.57      17      85 ..      76     141 ..      70     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0059
                                    HHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHH CS
                   AP_endonuc_2 110 aeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgH 164
                                    a++l++lad a     ++a+  ++ +g+++ ++ la+   a+d   v + +D gH
  gi|121637343|ref|YP_977566.1|  31 ADRLRQLADRA-----RIAVGAGTAEGASNTGARLADAAGAID---VLIEIDSGH 77 
                                    78999999997.....588888888888777677777777777...999999999 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 6.3e-05
                                    CTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBS CS
                   AP_endonuc_2  17 rdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGap 85 
                                      +++ +    e++ e++ a+ e+gl+++++ +f++++y +   +ea  e+ ++al +a+ +  a+G p
  gi|121637343|ref|YP_977566.1|  76 GHHRSGV--RAEQVLEVAHAVGEAGLHLVGVFTFPGHSYAPGKPGEAG-EQERRALNDAANALVAVGFP 141
                                    4455555..4689999999999********999999999999855555.56677777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1408.88
//
Query:       gi|121637344|ref|YP_977567.1|  [L=133]
Description: hypothetical protein BCG_1475 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-20   72.9   0.2    3.1e-20   72.6   0.2    1.1  1  D-ser_dehydrat  Putative serine dehydratase domain


Domain annotation for each model (and alignments):
>> D-ser_dehydrat  Putative serine dehydratase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.2   1.7e-24   3.1e-20       1      96 []      19     115 ..      19     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.7e-24
                                    -EEEEEEEEEEETTTT....EEES--HHHH-S-S..S--BT-EEE-TTSEEEEB-..EE-SS-EEEE--TT-GGGS-TT- CS
                 D-ser_dehydrat   1 AlavlatVvSrptarr....alvdaGskalslds..sgpgfgkvvagleegwvvsvrrlsdEhgiltleeesaddlrvGd 74 
                                    Al+v+atVvSr++ r     +++d+Gsk l++d+    +gfg++ +++  +++  +++ls++h+++ ++++ a+ ++vG+
  gi|121637344|ref|YP_977567.1|  19 ALTVAATVVSRQDCRSglrrIVLDCGSKILGSDRpaWATGFGRLIDHA--DAR--IAALSEHHATVVWPDD-APLPPVGT 93 
                                    89***********8877778*************653445599998664..555..66***********966.5******* PP

                                    EEEEE-S-HHHHHTT-SEEEEE CS
                 D-ser_dehydrat  75 vvrlipnHaCptvnlhdayvvv 96 
                                    ++r+ipnH+C+t+nl+d + vv
  gi|121637344|ref|YP_977567.1|  94 RLRVIPNHVCLTTNLVDDVAVV 115
                                    *****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1057.24
//
Query:       gi|121637345|ref|YP_977568.1|  [L=425]
Description: bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-84  281.8   0.2    3.5e-84  281.1   0.2    1.3  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas
    2.9e-73  244.8   0.0    6.5e-73  243.7   0.0    1.6  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.2     4e-88   3.5e-84       1     191 [.       8     200 ..       8     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 4e-88
                                    HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT---BB CS
                  DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhktaft 80 
                                    e+a+++++aGk viv+DdedrenegdLi+aAek+tpe vafm+r++sG++cv+l+ + +d+L+L +m++ n+dkh+ta+t
  gi|121637345|ref|YP_977568.1|   8 ERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAVNQDKHGTAYT 87 
                                    689***************************************************************************** PP

                                    --EEESST-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB CS
                  DHBP_synthase  81 vsvdaaegttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicell 160
                                    v+vda++g+ TGIsa+DRa+T+r ladp++ ++df+rPGhv+plra++ggvl+R ghTEaavdLar+agl+pa++ice++
  gi|121637345|ref|YP_977568.1|  88 VTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIV 167
                                    ******************************************************************************** PP

                                    -TT..SCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                  DHBP_synthase 161 ndd..gtmarrdeleefakkhglkiitiedlie 191
                                    +++  g+ma++del+ fa++hgl +iti+dlie
  gi|121637345|ref|YP_977568.1| 168 SQKdeGSMAHTDELRVFADEHGLALITIADLIE 200
                                    9554699************************98 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.57   5.1e+03      64      83 ..       7      25 ..       5      35 .. 0.72
   2 !  243.7   0.0   7.3e-77   6.5e-73       1     163 []     210     381 ..     210     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHH-.EEEEEE- CS
                GTP_cyclohydro2 64 ldealeliaeegrGvlvylr 83
                                   +++a++ ia +g+ v+v  +
  gi|121637345|ref|YP_977568.1|  7 VERAVADIA-AGKAVIVIDD 25
                                   688999998.8988888654 PP

  == domain 2  score: 243.7 bits;  conditional E-value: 7.3e-77
                                    XXEEEEEEEETTEEEEEEEE--.....EEEEEE-.............EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHH CS
                GTP_cyclohydro2   1 ervaeaklptrfgefrliayedkvdgkehlalvkgdi........pvlvRvHsecltgDvlgslrcdcgeqldealelia 72 
                                    ervaea++ptr+gefr+i+y++  ++ eh+alv g+i        +vlvRvHsecltgDv+gs+rcdcg+qld+al+++a
  gi|121637345|ref|YP_977568.1| 210 ERVAEARIPTRHGEFRAIGYTSIYEDVEHVALVRGEIagpnadgdDVLVRVHSECLTGDVFGSRRCDCGPQLDAALAMVA 289
                                    5778*****************************************9*********************************9 PP

                                    HH-.EEEEEE-.-TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHH CS
                GTP_cyclohydro2  73 eegrGvlvylr.qegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaL 151
                                    +egrGv++y+r +egrgigl++kl+ay+lqd g+DTv+anl+lglpadardygi+aqIL dlgv+++rLlTnnp+k  +L
  gi|121637345|ref|YP_977568.1| 290 REGRGVVLYMRgHEGRGIGLMHKLQAYQLQDAGADTVDANLKLGLPADARDYGIGAQILVDLGVRSMRLLTNNPAKRVGL 369
                                    9******************************************************************************* PP

                                    CTT....SEEEE CS
                GTP_cyclohydro2 152 egfgievvervp 163
                                    +g+g+++ ervp
  gi|121637345|ref|YP_977568.1| 370 DGYGLHIIERVP 381
                                    **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3255.03
//
Query:       gi|121637346|ref|YP_977569.1|  [L=154]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-47  161.0   0.4    1.7e-47  160.8   0.4    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.4   9.5e-52   1.7e-47       2     138 ..      12     145 ..      11     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 9.5e-52
                                    EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHH CS
                  DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfey 81 
                                    +r+aiV+++++ +i+d+ll+ga++ ++ +g +  + +vv+V Ga+E+p++a++la++  + dav+alGvvirG+tphf+y
  gi|121637346|ref|YP_977569.1|  12 VRLAIVASSWHGKICDALLDGARKVAAGCGLD--DPTVVRVLGAIEIPVVAQELARN--H-DAVVALGVVIRGQTPHFDY 86 
                                    79****************************85..9*********************5..6.******************* PP

                                    HHHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTC..CCHHHHHHHHHHHHHH CS
                  DMRL_synthase  82 vaeavskglmrvsldtgvPvifgvltvdteeqaleraggka..gnkGeeaaeaaleman 138
                                    v++av++gl+rvsld+++P+++gvlt++teeqal+rag  +  ++kG++a  aal +a 
  gi|121637346|ref|YP_977569.1|  87 VCDAVTQGLTRVSLDSSTPIANGVLTTNTEEQALDRAGLPTsaEDKGAQATVAALATAL 145
                                    **************************************55556************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1001.12
//
Query:       gi|121637347|ref|YP_977570.1|  [L=154]
Description: hypothetical protein BCG_1478 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-24   84.5   2.0    5.9e-24   83.9   2.0    1.3  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   2.0   3.3e-28   5.9e-24       1      71 [.      72     141 ..      72     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 3.3e-28
                          bPH_6   1 RprvrvdpdGvevrnlfrtrrlpWsaiagvrfpegrrlarldlrdgelvplpavqlgddpelvadalrrlr 71 
                                    Rpr+rv+++G+ vrnl++ r + Ws+++gv+fp+g+r+ar+dl+d+e++p++a+q+ d+ +++++a++++r
  gi|121637347|ref|YP_977570.1|  72 RPRLRVGSAGLSVRNLLGDRIVGWSEVIGVSFPGGSRWARIDLADDEYIPVMAIQAVDK-DRAVAAMDTVR 141
                                    9**********************************************************.********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1062.63
//
Query:       gi|121637348|ref|YP_977571.1|  [L=228]
Description: lipoprotein lprH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.078   12.8   0.0    1.6  1  PknH_C    PknH-like extracellular domain
        5.5    7.0  10.7        4.6    7.2   0.2    2.6  2  LPAM_2    Prokaryotic lipoprotein-attachment site


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.7e-06     0.078     107     176 ..     145     211 ..     143     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-06
                                    HHTTTT-EEEEEETTEEEEEEE---B--.TT-EEEEEE.ESSTT--EEEEEEEEETTEEEEEEEEE.SS-S CS
                         PknH_C 107 wrrCagvttttdsggatetwtvgdvsdd.dgvltatvtvtsggdgarcqralavranvvvdvevcgfedgg 176
                                    +  C g  +  +++g ++++++   ++  dgvl++    t + ++++c   lav+   v+   +cgf++g 
  gi|121637348|ref|YP_977571.1| 145 VSHCRGDAVGVSRAGRSTPMRLRYFATLsDGVLVW----TMSNPRWTCDYGLAVVPHAVLVLSACGFKPGF 211
                                    568***99***************************....6678************************7764 PP

>> LPAM_2  Prokaryotic lipoprotein-attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.3     0.018   1.6e+02       3      14 ..      17      28 ..      15      28 .. 0.93
   2 ?    7.2   0.2   0.00051       4.6       7      17 ..     198     208 ..     198     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.018
                         LPAM_2  3 lllallllLaGC 14
                                   l+l+ +l+La+C
  gi|121637348|ref|YP_977571.1| 17 LVLVVVLALAAC 28
                                   899********* PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00051
                         LPAM_2   7 llllLaGCGqK 17 
                                    ++l L++CG K
  gi|121637348|ref|YP_977571.1| 198 AVLVLSACGFK 208
                                    5899*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1696.13
//
Query:       gi|121637349|ref|YP_977572.1|  [L=157]
Description: hypothetical protein BCG_1480 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-18   67.1   0.4    2.1e-18   66.8   0.4    1.1  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain
     0.0014   19.3   3.3       0.31   11.8   0.0    2.9  3  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.4   2.3e-22   2.1e-18       3     127 .]      37     153 ..      35     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 2.3e-22
                                    EEEEETTTGEEEEETTCTTSTEBEEEEE-TSCCGGGEEEEETTSEEEETT.TTEEEEESSSSTTSBEEEEETTTTSG.GG CS
                 Ricin_B_lectin   3 geirnvasgkCLdvegeskagapvglydChgskgkQlwtltkdgeirskaqselCldvsstaegakvvlakChkgkg.nq 81 
                                    ++++++  + CLd++++s+  +p+++++C+g++  Q+w+lt+d++++s+a ++ C++++   +    +l++C   ++ +q
  gi|121637349|ref|YP_977572.1|  37 VQLKSRLGDVCLDAPSGSW-FSPLVINPCNGTDF-QRWNLTDDRQVESVAFPGECVNIG---NALWARLQPCV--NWiSQ 109
                                    789999************9.************99.**********************95...9999******8..566** PP

                                    CEEEETTTTEEEETTTSEEEEESTTSSTTTBEEEEEE.TSSGGGBE CS
                 Ricin_B_lectin  82 rWefdkdgtqirhkksgkCLdvkgasksneklilkkcdsgsdsQkW 127
                                    +W++++dg   ++++ + CL+v g+ +  + + ++ cd+++++Q+W
  gi|121637349|ref|YP_977572.1| 110 HWTVQPDGL--VKSDLDACLTVLGGPDPGTWVSTRWCDPNAPDQQW 153
                                    *****7777..888899********98877888888********** PP

>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   3.5e-05      0.31      10      58 ..      32      78 ..      21      95 .. 0.83
   2 !    4.9   0.3     0.005        45      34      86 ..      98     139 ..      79     142 .. 0.71
   3 !    5.5   1.2    0.0031        28       2      53 ..     108     154 ..     107     157 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                                   TTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCE CS
                RicinB_lectin_2 10 ggdgyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtg 58
                                   ++dg +++k++    +Ld+++gs      ++ ++c+g++ q+W l+d+ 
  gi|121637349|ref|YP_977572.1| 32 SADGPVQLKSRLGDVCLDAPSGSWF--SPLVINPCNGTDFQRWNLTDDR 78
                                   567889*****************99..699**************97654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.005
                                    CTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEECGCS-STTEEE CS
                RicinB_lectin_2  34 anganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdvaggstanGtnv 86 
                                    a     + ++c++  +q+W+++++g     +v    + +L+v  g+ ++Gt v
  gi|121637349|ref|YP_977572.1|  98 A-----RLQPCVNWISQHWTVQPDG-----LVKSDLDACLTVL-GGPDPGTWV 139
                                    3.....6777889999****99888.....6666666788888.666777766 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0031
                                    CGEEEECETTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TT.T-GGCEEE CS
                RicinB_lectin_2   2 nQqWtlgsggdgyytiknvasgkvLdvaggstanganvqqwtcs.gaanqqWr 53 
                                    +Q+Wt+  ++dg   ++      +L+v gg   +g+ v ++ c+ +a+ qqW 
  gi|121637349|ref|YP_977572.1| 108 SQHWTV--QPDG---LVKSDLDACLTVLGGPD-PGTWVSTRWCDpNAPDQQWD 154
                                    577888..3455...33333467888877655.5777777777779******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1201.84
//
Query:       gi|121637350|ref|YP_977573.1|  [L=646]
Description: excinuclease ABC subunit C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-48  164.5   0.0    3.9e-48  163.3   0.0    1.7  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    1.3e-10   41.4   0.0    2.7e-10   40.4   0.0    1.5  1  GIY-YIG     GIY-YIG catalytic domain
    6.3e-10   39.0   0.0    1.5e-09   37.8   0.0    1.6  1  HHH_2       Helix-hairpin-helix motif
      1e-09   38.9   0.0    2.7e-09   37.5   0.0    1.8  1  HHH_5       Helix-hairpin-helix domain
    3.8e-09   36.0   7.0    9.3e-09   34.8   7.0    1.7  1  UVR         UvrB/uvrC motif
    3.7e-07   29.7   0.3    3.8e-06   26.5   0.2    2.6  2  HHH         Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.16   12.5   0.5         28    5.4   0.2    3.2  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.8   1.2e+04      56      73 ..     365     382 ..     361     386 .. 0.78
   2 !  163.3   0.0   1.5e-51   3.9e-48       2     154 .]     404     571 ..     403     571 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.8
                                    HHHHHHHHHHHHHTTS.. CS
                                    xxxxxxxxxxxxxxxxxx RF
                     UvrC_HhH_N  56 DyaamrevlrRrfkrllk 73 
                                    D +a++e+++R  + +l+
  gi|121637350|ref|YP_977573.1| 365 DKRALAETVHRNAEDALQ 382
                                    788999999999888776 PP

  == domain 2  score: 163.3 bits;  conditional E-value: 1.5e-51
                                    HHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS...--HHHHHHHHHHHHHTTS....... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.... RF
                     UvrC_HhH_N   2 ellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvke...gdDyaamrevlrRrfkrllke.... 74 
                                    + lgl+++p riec+D+Sh+qgt++vgs+vvfedg p+ks+yR+f i++  +   +dD+a+++ev rRrf r l++    
  gi|121637350|ref|YP_977573.1| 404 DSLGLADAPLRIECVDVSHVQGTDVVGSLVVFEDGLPRKSDYRHFGIREAAGqgrSDDVACIAEVTRRRFLRHLRDqsdp 483
                                    789*********************************************8777999**************99999889*** PP

                                    .............---SEEEESSSHHHHHHHHHHHHHTT-.---EEEEES............SSSEE........EE--T CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx RF
                     UvrC_HhH_N  75 ...........fsklPdLiliDGGkgqlnaakevleelgl.kipvvglaKdkkrktrakaeereeev........lelkk 134
                                               f++ P+L+++DGG  q+naa +v++elg+ +++v+glaK  ++            v        +++++
  gi|121637350|ref|YP_977573.1| 484 dllsperksrrFAYPPNLYVVDGGAPQVNAASAVIDELGVtDVAVIGLAKRLEE------------VwvpsepdpIIMPR 551
                                    **************************************************3322............222333334***** PP

                                    T-HHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                     UvrC_HhH_N 135 ssealkllqrirdeaHrfAI 154
                                    +se l+llqr+rdeaHrfAI
  gi|121637350|ref|YP_977573.1| 552 NSEGLYLLQRVRDEAHRFAI 571
                                    *******************8 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.1e-13   2.7e-10       2      76 ..      18      92 ..      17      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.1e-13
                                   -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-H.S.STEEEEEEEE----HHHHHHHHHHHHHHTTSS CS
                        GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkk.gkkpfeliileifptksealelEkklikkyksnk 76
                                    gvY +r++++ +iYvG++k+l++Rl +++a+ ++ + r++  +++ + + +++  t+ eal+lE+ +ik++ + +
  gi|121637350|ref|YP_977573.1| 18 PGVYRFRDQHGRVIYVGKAKSLRSRLTSYFADVASLAPRTRqLVTTAAKVEWTVVGTEVEALQLEYTWIKEFDP-R 92
                                   59***************************9999988888888999**************************998.4 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.8e-13   1.5e-09       8      56 ..     590     638 ..     584     643 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.8e-13
                          HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                    ++  Ge+  k+L+++F+s+ +Lk+a+++e+++v++iG  +A+++++ ++
  gi|121637350|ref|YP_977573.1| 590 VPGLGEHRRKALVTHFGSIARLKEATVDEITAVPGIGVATATAVHDALR 638
                                    7889*****************************************9886 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   1.1e-12   2.7e-09       3      56 ..     586     638 ..     584     640 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.1e-12
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                     L sv+G+G+ + +al+ + ++s++ l++a+v+e++++pGiG  tA  + ++l+
  gi|121637350|ref|YP_977573.1| 586 ALDSVPGLGEHRRKALVTH-FGSIARLKEATVDEITAVPGIGVATATAVHDALR 638
                                    589****************.**************************99999987 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   7.0   3.6e-12   9.3e-09       3      35 ..     210     242 ..     208     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3.6e-12
                            UVR   3 likeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                      + Le++m+ Aae++dFE+AA+lRD ++alk+
  gi|121637350|ref|YP_977573.1| 210 FARALEQQMNAAAEQLDFERAARLRDDLSALKR 242
                                    5689***************************96 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.43   1.1e+03      13      21 ..     587     595 ..     583     602 .. 0.81
   2 !   26.5   0.2   1.5e-09   3.8e-06       3      29 ..     609     635 ..     607     636 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.43
                                    HHTSTT-SH CS
                            HHH  13 LlalPGVGp 21 
                                    L ++PG G+
  gi|121637350|ref|YP_977573.1| 587 LDSVPGLGE 595
                                    889****98 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.5e-09
                                    HHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   3 eglipasreeLlalPGVGpktAeaIls 29 
                                     +l++a+++e++a+PG+G +tA a+++
  gi|121637350|ref|YP_977573.1| 609 ARLKEATVDEITAVPGIGVATATAVHD 635
                                    6799*********************97 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4   6.2e+03      48      79 ..     377     405 ..     364     421 .. 0.62
   2 ?    3.8   0.0     0.034        87      20      46 ..     587     613 ..     583     616 .. 0.87
   3 ?    5.4   0.2     0.011        28      16      33 ..     615     632 ..     613     636 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                     5_3_exonuc  48 ldelkekklkekLeenkeearlskkLatiktd 79 
                                    +   ++  +++kL+++ +    s  L  i++ 
  gi|121637350|ref|YP_977573.1| 377 A---EDALQQHKLKRASDFNARSAALQSIQDS 405
                                    2...2233567777777777777777777765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.034
                     5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeile 46 
                                    +  vpg Ge   ++L++++gs++ + e
  gi|121637350|ref|YP_977573.1| 587 LDSVPGLGEHRRKALVTHFGSIARLKE 613
                                    5679******************98866 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.011
                     5_3_exonuc  16 ssDnipGvpgiGektAak 33 
                                    ++D+i  vpgiG  tA++
  gi|121637350|ref|YP_977573.1| 615 TVDEITAVPGIGVATATA 632
                                    68*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4247.14
//
Query:       gi|121637351|ref|YP_977574.1|  [L=301]
Description: hypothetical protein BCG_1482 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   4.2e-140  465.9   0.0   4.7e-140  465.8   0.0    1.0  1  ATP_bind_2  P-loop ATPase protein family
    0.00039   21.0   0.3     0.0085   16.6   0.3    2.2  1  AAA_18      AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_2  P-loop ATPase protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8   0.0  5.2e-144  4.7e-140       1     284 []      17     301 .]      17     301 .] 0.99

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 5.2e-144
                                    EEEEEEEESTTSSHHHHHHHHHHHTXEEEBSXXGGGHHHHHHHHH...TTTXXEEEEESTTTSXSSHHHHHHHHHTSXTT CS
                     ATP_bind_2   1 ielvivsGlsGaGksvalraledlGyyvvdnlPlsllpklvdllkeansreskvavvldvrnreesaelleqaeelleka 80 
                                    i++v+v+GlsGaG+++a+++ledlG+yv+dnlP++l++++vd+  +a+sr++++avv+dvr+r+++++l+++++el+++a
  gi|121637351|ref|YP_977574.1|  17 IDVVLVTGLSGAGRGTAAKVLEDLGWYVADNLPPQLITRMVDFGLAAGSRITQLAVVMDVRSRGFTGDLDSVRNELATRA 96 
                                    79****************************************************************************** PP

                                    SEEEEEEEEXXHHHHHHHCTSSSXSSTTSXXXSSHHHHHHHHHHTHHHHHTXSEEEECTTXXHHHHHHHHHHHHHXXXSS CS
                     ATP_bind_2  81 itprilfleadddtlvrryedtrrshPlsakdlslegiakerelleplraradlildtselsvrelreklrkalagnsek 160
                                    itpr++f+ea+ddtlvrrye++rrshPl+++++++egia+er++l+p+ra+adli+dts+lsv++lr+++++a++g++++
  gi|121637351|ref|YP_977574.1|  97 ITPRVVFMEASDDTLVRRYEQNRRSHPLQGEQTLAEGIAAERRMLAPVRATADLIIDTSTLSVGGLRDSIERAFGGDGGA 176
                                    ******************************************************************************** PP

                                    S-EEEEEEEEGGG---TT-SEEEE-TTS--GGGSTTTTTS-TTSHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSS- CS
                     ATP_bind_2 161 eltvvvesfGfkyGiPldadlvfdvrflPnPhwveelrPltGkdkevaeyvlkrtevaefieklrsllslvlpslkregk 240
                                    +++v+vesfGfkyG+P+dad+v+dvrflPnPhwv+elrPltG++++v++yvl+r+++aef+e++++llslv+++++regk
  gi|121637351|ref|YP_977574.1| 177 TTSVTVESFGFKYGLPMDADMVMDVRFLPNPHWVDELRPLTGQHPAVRDYVLHRPGAAEFLESYHRLLSLVVDGYRREGK 256
                                    ******************************************************************************** PP

                                    SEEEEEEEESSSSSHHHHHHHHHHHHHHHTT-EEE.EEETTTTTX CS
                     ATP_bind_2 241 syltiaiGctGGkhrsvaiaeqladyfrsdgktvv.arhrdlekr 284
                                    +y+tiaiGctGGkhrsvaiae+l++++rsd++++v a hrdl+++
  gi|121637351|ref|YP_977574.1| 257 RYMTIAIGCTGGKHRSVAIAEALMGLLRSDQQLSVrALHRDLGRE 301
                                    ********************************99889*****996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   9.5e-07    0.0085       1     119 [.      20     124 ..      20     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.5e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldkl.ldaleenssaleegknlvi 79 
                                    +l+tG +G+G  t ak L+++   g  + d+++   +  +vd      s++ +  +++ + ++++ +         +  +
  gi|121637351|ref|YP_977574.1|  20 VLVTGLSGAGRGTAAKVLEDL---GWYVADNLPPQLITRMVDFGLAAGSRITQLAVVMDVrSRGFTG---------D--L 85 
                                    79****************998...7777777777666666666633334444444433330444444.........3..8 PP

                         AAA_18  80 dghlaeleseaakdikkvvLtaspeelleRlekRgyeeak 119
                                    d++++el   a + ++ v+++as+++l +R e+ +++ + 
  gi|121637351|ref|YP_977574.1|  86 DSVRNELATRAITPRV-VFMEASDDTLVRRYEQNRRSHPL 124
                                    ****************.***************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2039.11
//
Query:       gi|121637352|ref|YP_977575.1|  [L=342]
Description: hypothetical protein BCG_1483 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-70  237.1   0.0    2.8e-70  236.9   0.0    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.0   1.6e-74   2.8e-70       1     274 [.       5     281 ..       5     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 1.6e-74
                                    EEEEE-CHHHHHHHHHHCCSSCEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH--S-C...HHHHHCH-B-SSS CS
                        UPF0052   1 vvvlgGGtGlskllrglkevtaeltavvtvaDdggssGelrrelgllaigDirnvlvalidder...lleeLfqyRfkgd 77 
                                    +v+lgGG+Gl   l++ +++t+ +tavvtvaDdggssG+lr+el+++++gD+r  l+al+ d +   l++ ++q+Rf g+
  gi|121637352|ref|YP_977575.1|   5 IVALGGGHGLYATLSAARRLTPYVTAVVTVADDGGSSGRLRSELDVVPPGDLRMALAALASDSPhgrLWATILQHRFGGS 84 
                                    8**********************************************************55555588************* PP

                                    SSSTT-BHHHHHHHHHHHHHS-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-E.......EESTTTGGGG-S.. CS
                        UPF0052  78 gdlaghslgnllLaalaeltgsleeaiealskilkvrgrvlPatddpvelsaeledGee.......itgeskisearklk 150
                                    g lagh +gnl+La+l+e+  +  +a+++l +il+v+grvlP++   +++ a ++  e        i+g+ +i+++    
  gi|121637352|ref|YP_977575.1|  85 GALAGHPIGNLMLAGLSEVLADPVAALDELGRILGVKGRVLPMCPVALQIEADVSGLEAdprmfrlIRGQVAIATTPG-- 162
                                    ******************************************************544449999**9*******66666.. PP

                                    .-EEEEEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB--TTTSTT-BHHH CS
                        UPF0052 151 apikrvflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtqkGetdgfsvsd 230
                                     +++rv l p+++ a++++++ai++Adl+vlgpGs++tS+iP++lvpg+a+alr+++a++ lv+n++ ++Get gfsv++
  gi|121637352|ref|YP_977575.1| 163 -KVRRVRLLPTDPPATRQAVDAIMAADLVVLGPGSWFTSVIPHVLVPGLAAALRATSARRALVLNLVAEPGETAGFSVER 241
                                    .9****************************************************************************** PP

                                    HHHHHHHCH-SS....S-SEEEEE-S---HHHHHHHHTTT--B- CS
                        UPF0052 231 hvkaieravgkgvakayvdavlvntsevpeellekyaaegkepv 274
                                    h++ + ++++ g     v +++++ ++vp+e  +++ ++ ++++
  gi|121637352|ref|YP_977575.1| 242 HLHVLAQHAP-G---FTVHDIIIDAERVPSEREREQLRRTATML 281
                                    **********.5...47999999999888877665555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2491.11
//
Query:       gi|121637353|ref|YP_977576.1|  [L=325]
Description: transcriptional regulatory protein whiA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-24   83.7   0.0    1.7e-23   82.5   0.0    1.6  1  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
    2.3e-22   78.8   0.1    5.2e-22   77.7   0.1    1.6  1  WhiA_N          WhiA N-terminal LAGLIDADG-like domain
    2.2e-20   72.8   0.0    3.4e-20   72.1   0.0    1.3  1  HTH_WhiA        WhiA C-terminal HTH domain


Domain annotation for each model (and alignments):
>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   2.8e-27   1.7e-23       2      93 .]     125     216 ..     124     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 2.8e-27
                 LAGLIDADG_WhiA   2 kaflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyvvylKkaeqIvdlLkiigahesll 81 
                                    +a++rGafla+Gs+++p ++ +LE+++p  e+a +l ++++++++ ak +e+r+  +v+++++e+I  lL+ +ga+++ l
  gi|121637353|ref|YP_977576.1| 125 EAAWRGAFLAHGSLTEPGRSSALEVSCPGPEAALALVGAARRLGVGAKAREVRGADRVVVRDGEAIGALLTRMGAQDTRL 204
                                    689***************************************************************************** PP

                 LAGLIDADG_WhiA  82 kfenirilrevr 93 
                                     +e++r +revr
  gi|121637353|ref|YP_977576.1| 205 VWEERRLRREVR 216
                                    **********98 PP

>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.1   8.6e-26   5.2e-22       3      86 .]      19     102 ..      17     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 8.6e-26
                         WhiA_N   3 crkaeLaAllrmnGslslvngklvlevqtenaaiARriykllkelYgieaellvrkknklkknnvYivrvkegveellke 82 
                                    +r+ae+++llr++G+l++v+g++v+e++++ ++iARr++k + elYg+ a ++v++ ++ +k  +Y++rv++++e+l+++
  gi|121637353|ref|YP_977576.1|  19 ARRAEVTSLLRFAGGLHIVGGRVVVEAELDLGSIARRLRKEIFELYGYTAVVHVLSASGIRKSTRYVLRVANDGEALARQ 98 
                                    799***************************************************************************** PP

                         WhiA_N  83 lgll 86 
                                    +gll
  gi|121637353|ref|YP_977576.1|  99 TGLL 102
                                    **96 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   5.7e-24   3.4e-20       1      84 []     219     301 ..     219     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 5.7e-24
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGS-HHHHHHHHHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHH CS
                       HTH_WhiA   1 vnRlvNcetaNlkKtvkaaakqieaielieekkgleklpeklkevaelRlenpdaSLkeLgelleppisKSgvnhrlrkl 80 
                                    +nRl+N++ aNl+++++aa+   +++e+  e  g +++pe+l ++ +lR+e+++aSL+eLg+l++pp++K++v+ r+r+l
  gi|121637353|ref|YP_977576.1| 219 ANRLANFDDANLRRSARAAVAAAARVERALEILG-DTVPEHLASAGKLRVEHRQASLEELGRLADPPMTKDAVAGRIRRL 297
                                    6*******************************99.********************************************* PP

                                    HHHH CS
                       HTH_WhiA  81 kela 84 
                                     ++a
  gi|121637353|ref|YP_977576.1| 298 LSMA 301
                                    9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2211.16
//
Query:       gi|121637354|ref|YP_977577.1|  [L=253]
Description: hypothetical protein BCG_1485c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1743.81
//
Query:       gi|121637355|ref|YP_977578.1|  [L=459]
Description: hypothetical protein BCG_1486 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-90  302.6   0.8    9.7e-89  297.6   0.0    2.0  2  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    6.8e-35  120.2   0.0    1.1e-34  119.5   0.0    1.3  1  DUF1298         Protein of unknown function (DUF1298)
     0.0051   15.5   0.0      0.012   14.3   0.0    1.5  2  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.6   0.0   1.6e-92   9.7e-89       1     264 []       4     264 ..       4     264 .. 0.98
   2 !    3.5   0.4    0.0088        53     150     222 ..     273     351 ..     268     373 .. 0.69

  Alignments for each domain:
  == domain 1  score: 297.6 bits;  conditional E-value: 1.6e-92
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    Ls++Da+f+++e+a ++mhvgala+++p+++++++  ++rlre i +r++++p+lr++v+  plgl++p++vede++D+d
  gi|121637355|ref|YP_977578.1|   4 LSSVDAAFWSAETAGWHMHVGALAICDPSDAPEYS--FQRLRELIIERLPEIPQLRWRVTGAPLGLDRPWFVEDEELDID 81 
                                    799**************************777777..9****************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    +H+Rr+ +paPG++rel elv+rL+s++LDrsrPlWe++viEG+eggriA+l+k+HHA++DGv+g+ l + lld +p+++
  gi|121637355|ref|YP_977578.1|  82 FHIRRIGVPAPGGRRELEELVGRLMSYKLDRSRPLWELWVIEGVEGGRIATLTKMHHAIVDGVSGAGLGEILLDITPEPR 161
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdr.srtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrf 239
                                    p+++++  + + +   +++ra g  ++++ g+++ ++ v+ ++++++++++a+  a + +++f+ap+t +n+p+s++Rr+
  gi|121637355|ref|YP_977578.1| 162 PPQQETVGFVGFQiPGLERRAIG--ALINVGIMTPFRIVRLLEQTVRQQIAALGVAGKPARYFEAPKTRFNAPVSPHRRV 239
                                    ************98888888877..99999************************************************** PP

                 WES_acyltransf 240 aaaslpLadvkavakalgvtiNDvv 264
                                    ++++++La+ kav++a+gv++NDvv
  gi|121637355|ref|YP_977578.1| 240 TGTRVELARAKAVKDAFGVKLNDVV 264
                                    ************************7 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0088
                 WES_acyltransf 150 arlldldpddpprpeppqvpprdr.srtqlrasg....alvglvaglgkvlgsvagvvssagrlleaal..earslvlpf 222
                                    ++ l++ ++ p+ p + q+p ++r ++t+++++     + ++l+ ++   ++++a++ +s+  + e+a+  +a + ++++
  gi|121637355|ref|YP_977578.1| 273 RQYLQKRDELPAKPLIAQIPVSTRsEETKADVGNqvssMTASLATHIEDPAKRLAAIHESTLSAKEMAKalSA-HQIMGL 351
                                    5666666667777778888887776555555544555588899999999999******999999999987533.333333 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.0   1.8e-38   1.1e-34       2     144 ..     305     454 ..     304     455 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 1.8e-38
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl........lsnttlvi 73 
                                    GNq++ + ++L+++++dP++rl+++++++  +K++ +a+++++++ l ++++p+ +++ +++          l  ++lv+
  gi|121637355|ref|YP_977578.1| 305 GNQVSSMTASLATHIEDPAKRLAAIHESTLSAKEMAKALSAHQIMGL-TETTPPGLLQLAARAYtasglshnLAPINLVV 383
                                    9**********************************************.******99988844445567788899****** PP

                        DUF1298  74 SNvpGPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    SNvpGP  +ly+aGa+l++++p+ p + ++alnit++Sy+++l++gl++ +++ +d+++++d++e al+el
  gi|121637355|ref|YP_977578.1| 384 SNVPGPPFPLYMAGARLDSLVPLGPPVMDVALNITCFSYQDYLDFGLVTTPEVANDIDEMADAIEPALAEL 454
                                    ********************************************************************998 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     2e-06     0.012      76     149 ..      76     148 ..      40     157 .. 0.73
   2 ?   -2.4   0.0      0.23   1.4e+03     245     284 ..     254     299 ..     243     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-06
                                    TT-----EEEE-T..TSSSHHHHHHHHHHHHHTC--SCCCS.-SEEEEEEE.SSTTEEEEEEEEECCT--TTTHHH CS
                   Condensation  76 eerevelevleisdleeseeeeaieefaqkdlqepfdLekg.pLfraalfk.iaenrlllllsvHHiivDGvSlgi 149
                                    ee ++++++  i  + +    + +ee++ +    +++L+++ pL+   +++ ++  r   l ++HH ivDGvS   
  gi|121637355|ref|YP_977578.1|  76 EELDIDFHIRRIG-VPAPGGRRELEELVGR--LMSYKLDRSrPLWELWVIEgVEGGRIATLTKMHHAIVDGVSGAG 148
                                    5555555555555.3344444557777775..45688888889**99999735667889999***********655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.23
                                    HSTSS-HHHHHHHHHHHHHHHHHT-SE......EEEEEEEESSTTC CS
                   Condensation 245 keqgvtlndvllaalgllLskytgqdd......ivvgteisgRese 284
                                     + gv+lndv la+++ +  +y +++d      ++  +++s R +e
  gi|121637355|ref|YP_977578.1| 254 DAFGVKLNDVVLALVAGAARQYLQKRDelpakpLIAQIPVSTRSEE 299
                                    5667777777777776555555544332222224555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3178.87
//
Query:       gi|121637356|ref|YP_977579.1|  [L=420]
Description: esterase lipO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-19   69.3   1.4    7.5e-19   68.4   1.4    1.5  1  Abhydrolase_3  alpha/beta hydrolase fold
    3.1e-14   52.7   0.1    1.9e-13   50.1   0.1    1.9  1  COesterase     Carboxylesterase family
    1.5e-12   47.5   0.9    9.2e-12   44.9   0.9    2.2  1  Peptidase_S9   Prolyl oligopeptidase family
      0.005   16.1   0.3      0.024   13.9   0.2    2.0  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.081   12.2   0.0    2.1  3  LIP            Secretory lipase
      0.064   12.8   0.1       0.12   11.9   0.1    1.5  1  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   1.4   2.5e-22   7.5e-19       2     209 ..     182     390 ..     181     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.5e-22
                                    EEE--STTTS--TTTT.HHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   2 vyfHGGGfvlgsldth.dalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    v++ GG++vlg  + +  +l+++la++ g v+vs +Yr +P h +P  + d+ +al w++e+ +++g dp+ +++ G Sa
  gi|121637356|ref|YP_977579.1| 182 VQVPGGAWVLGWRRPQaYPLMSHLAAR-GWVCVSLNYRVSPRHTWPDHIVDVKRALAWVKENIAAYGGDPNFVAISGGSA 260
                                    6777*******9977769999999986.99********************************99**************** PP

                                    HHHHHHHHHHHHHHTT.---.......EEEEEEESE-SSTSSTTSHHHHHCHHT..TTSSSSCHHHHHHHHHHHSSGGGG CS
                  Abhydrolase_3  81 GGnlaaavalrardeg.epk.......vagqvliyPvtdlertesesikkaeel..adgplltraaldlfwrlylpeadr 150
                                    GG+l a +al   d   +p+       va+ v +y   d  +t+ + +   +e+    ++++ ++++    ++++     
  gi|121637356|ref|YP_977579.1| 261 GGHLCALAALTPNDPRfQPGfeqvdtsVAAAVPVYGRYDWFTTDAPGR---REFvgLLETFVVKRKFSTHRDIFV----- 332
                                    *********999997544449999999999999999776645555555...222233334444555665566666..... PP

                                    GSTTTSGGGCS-SST---EEEEEETT-TTH..HHHHHHHHHHHH.TT--EEEEEETTEETTG CS
                  Abhydrolase_3 151 ddplaspllaedlsglpptlvvvaefDplr..degeayaerlra.agvevelieyegmvHgf 209
                                        asp+++   +++pp +v+ + +D l    e+ a+ e+lra  + +v +   + + H+f
  gi|121637356|ref|YP_977579.1| 333 ---DASPIHH-VRADAPPFFVLHGRHDSLIpvAEAHAFVEELRAvSKSPVAYADLPHAQHAF 390
                                    ...4566655.44469************96226888999****9567789999999999998 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   6.3e-17   1.9e-13     101     207 ..     174     273 ..     163     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 6.3e-17
                                    TTSSEEEEEEE--STTTS-BGCG..S-.THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHHHHHHHHG CS
                     COesterase 101 akkklPVlVwihGggfqtgsase..yd.gsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlALrWVkenI 177
                                    ++ k PVlV + Gg+ + g  +   y+  s+Laa+ + + V++nYR+ +    +t  ++      ++D+  AL WVkenI
  gi|121637356|ref|YP_977579.1| 174 RDAKAPVLVQVPGGAWVLGWRRPqaYPlMSHLAAR-GWVCVSLNYRVSPR---HTWPDH------IVDVKRALAWVKENI 243
                                    34556************998865556525677777.***********995...443333......79************* PP

                                    GGGTEEEEEEEEEEETHHHHHHHHHHHSGG CS
                     COesterase 178 asFGGdpervtlfGesAGaasvsllllspl 207
                                    a++GGdp+ v + G sAG+ + +l  l+p 
  gi|121637356|ref|YP_977579.1| 244 AAYGGDPNFVAISGGSAGGHLCALAALTPN 273
                                    ********************9999988875 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.9   3.1e-15   9.2e-12      43     205 ..     230     412 ..     201     415 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.1e-15
                                    HHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH.HHHHH-GGG-S...........EEEEESE---CCCHHCSTTS CS
                   Peptidase_S9  43 nefdDfiaaaealakegyvdserlaitGgSyGGyltg.aalnqrpdlFk...........aavaevpvvdvlrydsdtdl 110
                                    ++++  +a++++ ++ +  d++ +ai GgS+GG l + aal+ ++ +F+           aav +++ +d+ ++d   + 
  gi|121637356|ref|YP_977579.1| 230 VDVKRALAWVKENIAAYGGDPNFVAISGGSAGGHLCAlAALTPNDPRFQpgfeqvdtsvaAAVPVYGRYDWFTTDAPGRR 309
                                    5667778999999********************88661566688889964444444444477888888999999998776 PP

                                    ....THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS- CS
                   Peptidase_S9 111 ....lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdeg 185
                                        l e +    +    ++ + ++sp++++++    pp++++hG +D+ +p+aea  +v++L+   k  v +   p ++
  gi|121637356|ref|YP_977579.1| 310 efvgLLETFVVKRKFSTHRDIFVDASPIHHVRA--DAPPFFVLHGRHDSLIPVAEAHAFVEELRAVSKSpVAYADLPHAQ 387
                                    754422322222222246666777777777777..*****************************777777********** PP

                                    S...STTSSHHHH..HHHHHHHHHH CS
                   Peptidase_S9 186 H...gvgkprakv..eelarllaFl 205
                                    H   ++g+pra+   e +ar+l+++
  gi|121637356|ref|YP_977579.1| 388 HafdVFGSPRAHHtaEAVARFLSWV 412
                                    *998666666554447777888775 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.22   6.7e+02      72      98 ..     245     273 ..     201     281 .. 0.65
   2 !   13.9   0.2   8.1e-06     0.024     192     233 ..     345     386 ..     334     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                    Hydrolase_4  72 ehpel..plfllGhSmGGliallyllryp 98 
                                     +++    + + G S GG + +l++l+  
  gi|121637356|ref|YP_977579.1| 245 AYGGDpnFVAISGGSAGGHLCALAALTPN 273
                                    33333233556799999999888885544 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.1e-06
                    Hydrolase_4 192 lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                     P+++lhG +D +++ +++++++e+l++  k+   y+ l H 
  gi|121637356|ref|YP_977579.1| 345 PPFFVLHGRHDSLIPVAEAHAFVEELRAVSKSPVAYADLPHA 386
                                    59**********************************999996 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.6   4.7e+03      47      74 ..      54      80 ..      29      82 .. 0.69
   2 ?   -0.3   0.0      0.18   5.5e+02      23      59 ..     206     243 ..     199     293 .. 0.56
   3 ?   12.2   0.0   2.7e-05     0.081     167     261 ..     288     390 ..     273     406 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                            LIP 47 sgkavLdsiraalksekvtgiksdakva 74
                                    g +vLd++r  +  +++ g+k +a  a
  gi|121637356|ref|YP_977579.1| 54 LGASVLDALRRGR-RGDFGGLKGKAALA 80
                                   4788999998877.67777777666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.18
                            LIP  23 LkeGyyVvvpDy.eGpkstftvgrqsgkavLdsiraal 59 
                                     ++G+  v+  y + p+ t++   ++ k+ L  ++  +
  gi|121637356|ref|YP_977579.1| 206 AARGWVCVSLNYrVSPRHTWPDHIVDVKRALAWVKENI 243
                                    55666666555533566666666666666665555554 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.7e-05
                            LIP 167 ladalikyagesyltgdkrafekgsdvlkdetikkvlednk.l.......sksavPqiPvlvyhgvidelipikdakkla 238
                                    +a+a+  y   +++t d    ++  ++l++ ++k+ +  ++ +       +   +  +P +v+hg +d+lip+ +a++  
  gi|121637356|ref|YP_977579.1| 288 VAAAVPVYGRYDWFTTDAPGRREFVGLLETFVVKRKFSTHRdIfvdaspiHHVRADAPPFFVLHGRHDSLIPVAEAHAFV 367
                                    5666666666666666666666666666666665544433213444433355566789********************99 PP

                            LIP 239 knwcdkgiaslefaedlssgHla 261
                                    ++  +   + + +a+   ++H  
  gi|121637356|ref|YP_977579.1| 368 EELRAVSKSPVAYADLPHAQHAF 390
                                    99999888889998877777754 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.2e-05      0.12     138     211 ..     338     410 ..     284     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                            DLH 138 eeaakikapilalfgeeDefipadevekleealka.anvdlelkvYpgagHaFandsresyneeaaedawervle 211
                                    ++++  + p ++l+g +D  ip +e++ + e+l+a ++ +++    p a+HaF    ++ ++  a  +a +r+l+
  gi|121637356|ref|YP_977579.1| 338 HHVRADAPPFFVLHGRHDSLIPVAEAHAFVEELRAvSKSPVAYADLPHAQHAFDVFGSPRAHHTA--EAVARFLS 410
                                    55555567999**********************9834667888999*******998888666554..34445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2777.96
//
Query:       gi|121637357|ref|YP_977580.1|  [L=535]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-67  227.3   0.0    3.2e-67  227.0   0.0    1.1  1  AMP-binding      AMP-binding enzyme
      5e-24   85.1   0.2    1.9e-23   83.2   0.2    2.1  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.046   14.0   0.0    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   0.0   5.3e-71   3.2e-67       4     422 ..      48     439 ..      45     440 .. 0.87

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 5.3e-71
                                    HHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                    AMP-binding   4 qaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                    +a++ pd++ l+d  e  tlT+r+lder n+lAa+L++l +++  +V+i+++n   +v alla+ ++Ga +  ln+++  
  gi|121637357|ref|YP_977580.1|  48 AARRCPDRPGLID--ELGTLTWRQLDERGNALAAALQALPAGPPRVVGIMCRNHRGFVDALLAVNRIGAHILLLNTSFAG 125
                                    688999*******..9**************************************************************** PP

                                    HHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEE CS
                    AMP-binding  84 eelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddla 162
                                    ++la +++  ++ +++  +d+e  +   ++ a+k++a+++v  +d+d  l+ e+l ++      a   +++ e + ++  
  gi|121637357|ref|YP_977580.1| 126 PALAEVVTREGVDTVV--YDEEFsATVDRALAEKPQATRIVAWTDEDHDLTVEKLVAAH-----A--GRRP-EHTGSHGK 195
                                    ****************..89999566556666666666666666655555443333333.....2..2122.46788999 PP

                                    EEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                    AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                    +i+ TSGTTG+PKG+ +s + + +  +++ l+++ +  ++++v + ++p++h+ g+ + l la +  +t+v  +++++  
  gi|121637357|ref|YP_977580.1| 196 VILLTSGTTGTPKGARHSGGGIGTL-KAI-LDRTpW--RAEEVTVIVAPMFHAWGF-SQLVLASSLACTIVTRRRFDP-- 268
                                    *********************9888.666.555534..368999***********9.999999999999999886655.. PP

                                    HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGS CS
                    AMP-binding 242 pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEtt 321
                                     ++ l+li+++++t +++vP +++++++ +a+   ++++d  slr++ + g++++p+++ +f + fg+ +++ Y  TE++
  gi|121637357|ref|YP_977580.1| 269 -EATLDLIDRHHATGLVVVPVMFDRIMDLPAEI--RNRYDGRSLRFAAASGSRMRPDVVIAFMDQFGDVIYNNYNATEAG 345
                                    .6679***********************65444..45668889************************************* PP

                                    SECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEE CS
                    AMP-binding 322 gvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDl 401
                                    +++t +++ + ++ + ++G+p  g+e++i+D++   +vp+ge+G ++vr  + + gY       a+ f    +++ +GD+
  gi|121637357|ref|YP_977580.1| 346 MIAT-ATPADLRTAPDTAGRPAEGTEIRILDQQ-FTEVPTGEVGTIYVRNDSQFDGYTSG---AAKDFH-A-GFMSSGDV 418
                                    ***9.66677778999****************9.999*********************65...899997.5.6******* PP

                                    EEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 402 grldedGyleivgRkkdlikl 422
                                    g+lde+G+l++vgR +++i++
  gi|121637357|ref|YP_977580.1| 419 GYLDENGRLFVVGRDDEMIVS 439
                                    *******************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.2   3.2e-27   1.9e-23       1      76 []     448     523 ..     448     523 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.2e-27
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE +l++hp+VaeaaV+Gv+d+  G++l+afVvlk+g++a++e+Lk+hvr++l+ y+vp+++ ++delp+  +GK
  gi|121637357|ref|YP_977580.1| 448 EVEKTLATHPDVAEAAVIGVDDQQYGQRLAAFVVLKPGVSATPETLKQHVRDNLANYKVPRDIAVLDELPRGITGK 523
                                    8***********************************9987899****************************99998 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.6e-06     0.046       1      65 [.     441     502 ..     441     517 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHH CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklk 65 
                                    G n++P ++e+ l + ++v++   i v++++   +l+  v +k+g+s +    e+l+++++++l+
  gi|121637357|ref|YP_977580.1| 441 GENIYPIEVEKTLATHPDVAEAAVIGVDDQQYGQRLAAFVVLKPGVSAT---PETLKQHVRDNLA 502
                                    78******************************************99765...7777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3593.33
//
Query:       gi|121637358|ref|YP_977581.1|  [L=275]
Description: hypothetical protein BCG_1489c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-19   68.0   0.0    8.5e-19   67.5   0.0    1.2  1  Acyltransferase  Acyltransferase
    3.8e-10   39.2   0.0    4.9e-10   38.8   0.0    1.1  1  DAGAT            Diacylglycerol acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   9.5e-23   8.5e-19       2     133 ..      43     171 ..      42     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 9.5e-23
                Acyltransferase   2 vrvtglenlpekgpailvaNHqsy...lDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnar 77 
                                     +v+gl+ +p+ g+a++vaNH+     +Dv+++++ +y++  ++r+v+++  +++l++ l+g+l+r++g+i ++R     
  gi|121637358|ref|YP_977581.1|  43 SQVHGLDSFPP-GGALVVANHSGGmfpMDVPVFSVDFYDKFgYDRPVYTL-SHDILFMGLTGDLFRRTGYIRATR----- 115
                                    589*******9.***********9999**************885555555.5556778*****************..... PP

                Acyltransferase  78 aagsleniselleegklvviFPEG.....trsregel..lpfkkGlvrlaakakkgvpivPva 133
                                         en++++l++g +vv+FP G     + + ++++  ++ +kG+v+ a++a  gvpivP +
  gi|121637358|ref|YP_977581.1| 116 -----ENAAKALRSGGVVVVFPGGdydayRPTFAENVidFNGRKGYVSTAVEA--GVPIVPAV 171
                                    .....999****************8887755555666799*************..******86 PP

>> DAGAT  Diacylglycerol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   5.5e-14   4.9e-10      57     278 ..      49     265 ..      31     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.5e-14
                          DAGAT  57 aeletdrnYliGyhPhgilsvgafvalatdatgvkekfpgirfnlatLa.gqfrtpfrreillllGlievsresieyvLd 135
                                      +++  + ++  h  g++++ +   ++    ++++kf   r+ + tL+  +  + +  +++  +G i ++re+  + L 
  gi|121637358|ref|YP_977581.1|  49 DSFPPGGALVVANHSGGMFPMDV-PVFS---VDFYDKFGYDRP-VYTLShDILFMGLTGDLFRRTGYIRATRENAAKALR 123
                                    55777778899999999999999.7787...78999*877776.666763778888999******************998 PP

                          DAGAT 136 keekGravvlvvGGaeealeahpgketltLkkrkGfvkialktGadLvPvysfGendvykqvenpkgskl.rk..vqe.k 211
                                    +++    vv+ +GG  +a+     ++ +  + rkG+v +a++ G ++vP  s G ++   q+   +g++l r+  +++  
  gi|121637358|ref|YP_977581.1| 124 SGGV---VVVFPGGDYDAYRPTFAENVIDFNGRKGYVSTAVEAGVPIVPAVSIGGQE--SQLYLSRGTWLaRRlgLKRlL 198
                                    7666...***********************************************776..455555566551220122202 PP

                          DAGAT 212 lkkvlglsppilyGrglfnsltlGllPfrkpittvvGkPievtkt..eePtkeeidelhakYv.eaLaeL 278
                                     +++l +s    +G   f++ +   lP+   i + v  Pi+ tk+  e+P  + +de     + +aL++L
  gi|121637358|ref|YP_977581.1| 199 RSDILPISFGFPFG---FSAAIPPNLPLPAKIVMQVLDPINLTKQfgEDPDVDAVDEHVRSVMqQALNDL 265
                                    34455566665566...88888899**9999999999*******75589*99999997665551567776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1820.24
//
Query:       gi|121637359|ref|YP_977582.1|  [L=422]
Description: hypothetical protein BCG_1490 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-17   61.4   0.5    1.4e-16   60.0   0.5    1.8  1  HTH_30    PucR C-terminal helix-turn-helix domain
    2.9e-07   30.7   0.9    2.9e-07   30.7   0.9    2.3  2  GGDEF_2   GGDEF-like domain


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.5   1.6e-20   1.4e-16       1      58 [.     351     408 ..     351     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.6e-20
                                    ...HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHH CS
                         HTH_30   1 LleTLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddpddrlaLylAlr 58 
                                    L+eTLr +l  ++++ atA+a+ +HrnT++yR+ ++ el+g +lddpd+++++++Al+
  gi|121637359|ref|YP_977582.1| 351 LRETLREFLLRNRSYVATADAMILHRNTIQYRVIQAMELCGQNLDDPDAAFRVQMALE 408
                                    79******************************************************97 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.61   5.5e+03      22      41 ..     121     140 ..      85     165 .. 0.59
   2 !   30.7   0.9   3.3e-11   2.9e-07       7     113 ..     177     296 ..     168     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.61
                        GGDEF_2  22 pyvvvvieleedaerllral 41 
                                    ++v  +iel + + rl++ +
  gi|121637359|ref|YP_977582.1| 121 DRVSTIIELVNRSARLVDLV 140
                                    33333334333333333333 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 3.3e-11
                        GGDEF_2   7 ellerarrlgldldgpyvvvvielee.....daer..........llraleealralgpdalvavrgdrlvlllpaedee 71 
                                    ++ ++ r+lg++ldg ++++v+++++     d             l+ +l  +l   + + +v +++ +  l+++ ++  
  gi|121637359|ref|YP_977582.1| 177 DVPRAERALGYRLDGVHIAAVVWVDSavpigD--VvaqfdqvrclLAGELGPELGPVANSLMVPTDEREARLWFSPAPT- 253
                                    77788899****************87665442..144444445666666666666667888888888899999988775. PP

                        GGDEF_2  72 daeallerlarrlgg..lsvriGiGspveglaglrrSyreArrA 113
                                     ++ + +r+++++++  +++r++ G++ +gl+g+r S+++A+r+
  gi|121637359|ref|YP_977582.1| 254 -RAFAPSRIRAAFESagIRARLACGRVGDGLRGFRASLKQAERV 296
                                    .44555677777777778***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2935.27
//
Query:       gi|121637360|ref|YP_977583.1|  [L=528]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-82  274.0   0.4      2e-81  272.8   0.4    1.6  1  PE-PPE         PE-PPE domain
    3.2e-34  117.1  18.9    3.2e-34  117.1  18.9    2.3  3  PE             PE family
     0.0005   20.1   0.5      0.043   13.8   0.0    2.4  2  Cutinase       Cutinase
  ------ inclusion threshold ------
      0.018   15.6   4.3      0.018   15.6   4.3    2.6  2  Abhydrolase_6  Alpha/beta hydrolase family
      0.019   14.8   0.0      0.032   14.1   0.0    1.3  1  Abhydrolase_2  Phospholipase/Carboxylesterase
        0.2   11.3   0.0       0.33   10.6   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
       0.21   10.9   0.0       0.32   10.3   0.0    1.2  1  DUF2235        Uncharacterized alpha/beta hydrolase domain (D


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.8   0.4     8e-85     2e-81       6     227 .]     149     369 ..     145     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.8 bits;  conditional E-value: 8e-85
                         PE-PPE   6 elvsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa..pdqlsf 83 
                                    + +++Pa+f p+tg+ slt+d+SvaeG+  L++ai+++ aag++vvv+G+Sqga va+ e+++la+l   +a  pdqlsf
  gi|121637360|ref|YP_977583.1| 149 SGLYTPAQFQPWTGIPSLTYDQSVAEGAGYLHTAIMQQVAAGNDVVVLGFSQGASVATLEMRHLASLPAGVApsPDQLSF 228
                                    6789****************************************************************999999****** PP

                         PE-PPE  84 vlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvHtnye 163
                                    vl+gnpn+pngg+larfpg l++ +lg+tf+gatp+++ y T+++++qYDg+adfP+yplN+lAdvNa+lGi++ H+ y+
  gi|121637360|ref|YP_977583.1| 229 VLLGNPNNPNGGILARFPG-LYLQSLGLTFNGATPDTD-YATTIYTTQYDGFADFPKYPLNILADVNALLGIYYSHSLYY 306
                                    ******************9.***************999.***************************************** PP

                         PE-PPE 164 tevaeqlpanirttvnsrgakttyylipteelPLlqplrslgvpeplvdaldavLrvlvdlgYd 227
                                      ++eq++++i  +v+s +++tty+l+p+e+lPLlqplr + vpepl+d+++++Lr +++lgYd
  gi|121637360|ref|YP_977583.1| 307 GLTPEQVASGIVLPVSSPDTNTTYILLPNEDLPLLQPLRGI-VPEPLLDLIEPDLRAIIELGYD 369
                                    *****************************************.*********************7 PP

>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1  18.9   1.3e-37   3.2e-34       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -2.0   0.2       1.8   4.5e+03      34      52 ..     181     199 ..     170     214 .. 0.61
   3 ?   -3.9   0.1       6.9   1.8e+04      42      52 ..     430     439 ..     417     445 .. 0.56

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.3e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv ++Pe++aa+a+dla++g+als+a+aaaa ptt+vlaaaaDeVSaaiA+lf+ah+qe+qalsaqa+afh++fv+al+a
  gi|121637360|ref|YP_977583.1|  1 MSFVFAVPEMVAATASDLASLGAALSEATAAAAIPTTQVLAAAADEVSAAIAELFGAHGQEFQALSAQASAFHDRFVRALSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aag Y +aEaa
  gi|121637360|ref|YP_977583.1| 83 AAGWYVDAEAA 93
                                   *********97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                    HHHH----SSSSHHHHHHH CS
                             PE  34 apttavlaaaaDeVSaaiA 52 
                                     ++++ +aa++D V   ++
  gi|121637360|ref|YP_977583.1| 181 TAIMQQVAAGNDVVVLGFS 199
                                    4455566777777655544 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6.9
                                    SSSSHHHHHHH CS
                             PE  42 aaaDeVSaaiA 52 
                                    a+a e S+a+A
  gi|121637360|ref|YP_977583.1| 430 AGA-ELSVAAA 439
                                    332.3444444 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.017        44      87     137 ..      20      74 ..      19      88 .. 0.74
   2 !   13.8   0.0   1.7e-05     0.043      53     124 ..     167     236 ..     145     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                                    THHHHHHHHHHTT......S-HHHHHHEEEEE..EES-TTC.CCCTTS-TTS-GG CS
                       Cutinase  87 SqGaqvidnaiegga.tatlpaavadkvaavv..lfGdpsn.vaglpevsklyas 137
                                    S Ga++ ++++++++ t+++ aa+ad+v+a++  lfG   +  ++l++ + ++ +
  gi|121637360|ref|YP_977583.1|  20 SLGAALSEATAAAAIpTTQVLAAAADEVSAAIaeLFGAHGQeFQALSAQASAFHD 74 
                                    8899999999998885555999********9966788644325555555555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.7e-05
                                    STTSS-HHHHHHHHHHHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.....S-HHHHHH..EEEEEEES-TTC CS
                       Cutinase  53 lyegseeagakeaaalvqslaskCPdtkivlgGYSqGaqvidnaieggatatlpaavadk..vaavvlfGdpsn 124
                                    +y++s ++ga  +++++ + +++   + +v++G+SqGa v++  + +   a+lpa va +    + vl+G+p+n
  gi|121637360|ref|YP_977583.1| 167 TYDQSVAEGAGYLHTAIMQQVAA--GNDVVVLGFSQGASVATLEMRH--LASLPAGVAPSpdQLSFVLLGNPNN 236
                                    67888888888888888777776..688*************999999..6778888874311457888999988 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   4.9       1.2   3.1e+03      73     151 ..      20      91 ..      19     133 .. 0.50
   2 ?   15.6   4.3   7.2e-06     0.018      18     126 ..     133     252 ..     116     297 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                    TCHHHHHHHHHHCC..EE.EEES-..----TTT.S----TTHHHHHHTT-C..CCCHCCHS-HSCCCCHHHCCCCHCHCC CS
                  Abhydrolase_6  73 SlGGalalaaaplalvvg.vlldppptalpagl.laaalelllallallrl..lawlsreplprlfladedadaawrarl 148
                                    SlG+al+ a+a++a+  + vl ++   a+  +  +a ++  + +  ++l +   a++       +f++ ++  aa ++++
  gi|121637360|ref|YP_977583.1|  20 SLGAALSEATAAAAIPTTqVLAAA---ADEVSAaIAELFGAHGQEFQALSAqaSAFHD------RFVRALS--AAAGWYV 88 
                                    899999999888886666788888...5555544444444444444433334335553......3333222..2222222 PP

                                    CGH CS
                  Abhydrolase_6 149 arl 151
                                    ++ 
  gi|121637360|ref|YP_977583.1|  89 DAE 91 
                                    222 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.2e-06
                                    HHHHHHCCTCEEEEE--TTS...T.........S-GGCS--HHH.CHHH.HHHHCCTT.....TTSEEEEEETCHHHHHH CS
                  Abhydrolase_6  18 pLaallaagvhvlapDlpGh...G.........rsdpppldled.ladl.aalldelaa...gggpvvlvGHSlGGalal 80 
                                    ++     +++  +ap + G+   G          +  p l+++  +a+    l +++ +    g++vv++G S+G+++a+
  gi|121637360|ref|YP_977583.1| 133 QV----YDRY--IAPHYLGYafsGlytpaqfqpWTGIPSLTYDQsVAEGaGYLHTAIMQqvaAGNDVVVLGFSQGASVAT 206
                                    44....6677..99999999666666554443322333344433322222334444444777999*************** PP

                                    H.HHHCC...EEEEES-..----TTTS----TTHHHHHHTT-CCCCHC CS
                  Abhydrolase_6  81 a.aapla.lvvgvlldppptalpagllaaalelllallallrllawls 126
                                    +  ++la l +gv+ +p   +l + ll  + ++  + la+++ l++ s
  gi|121637360|ref|YP_977583.1| 207 LeMRHLAsLPAGVAPSP--DQLSFVLLGNPNNPNGGILARFPGLYLQS 252
                                    *6555556556677777..44444443333333333333333322222 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05     0.032      84     126 ..     173     212 ..     134     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT- CS
                  Abhydrolase_2  84 kksaekleelidaelkkgipssriiigGFSqGaalalylaltl 126
                                    ++ a +l+  i +++++g   +++++ GFSqGa +a+  +  l
  gi|121637360|ref|YP_977583.1| 173 AEGAGYLHTAIMQQVAAG---NDVVVLGFSQGASVATLEMRHL 212
                                    555556666666666655...99*************9877665 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.33     100     124 ..     189     213 ..     160     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                           FSH1 100 ngpfdGiiGFSqGaalaallaslle 124
                                     g  + ++GFSqGa +a+l +  l 
  gi|121637360|ref|YP_977583.1| 189 AGNDVVVLGFSQGASVATLEMRHLA 213
                                    3446789**********98776665 PP

>> DUF2235  Uncharacterized alpha/beta hydrolase domain (DUF2235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.32      85     110 ..     180     205 ..     158     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                        DUF2235  85 YeflmrnyepgDeIylfGFSRGAyta 110
                                     + +m++++ g++++++GFS GA +a
  gi|121637360|ref|YP_977583.1| 180 HTAIMQQVAAGNDVVVLGFSQGASVA 205
                                    4679*******************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3565.45
//
Query:       gi|121637361|ref|YP_977584.1|  [L=589]
Description: hypothetical protein BCG_1492 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   4.5e-267  887.1   6.0   5.2e-267  886.9   6.0    1.0  1  DUF3556     Transmembrane protein of unknown function (DUF355
  ------ inclusion threshold ------
       0.12   12.4   0.1        9.8    6.1   0.1    2.2  2  Nipped-B_C  Sister chromatid cohesion C-terminus


Domain annotation for each model (and alignments):
>> DUF3556  Transmembrane protein of unknown function (DUF3556)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  886.9   6.0  5.8e-271  5.2e-267       1     573 []       1     580 [.       1     580 [. 0.99

  Alignments for each domain:
  == domain 1  score: 886.9 bits;  conditional E-value: 5.8e-271
                        DUF3556   1 mGflkpdlpdvdlaefskkplaerlrllarhwvevGfgtpkvvhllYvlkillyvlggvlvvlltsGldgltdvgeWwse 80 
                                    mGflkpdlpdvd++++ ++p+++rl++++r+wve+Gfgtp++v+llY++ki++yv++g+++++lt+Gl+gl+++g+Ww++
  gi|121637361|ref|YP_977584.1|   1 MGFLKPDLPDVDHDTWLTQPRRTRLQVVTRDWVEHGFGTPYAVYLLYLTKIAVYVAAGAAIISLTPGLGGLSRIGDWWTQ 80 
                                    9******************************************************************************* PP

                        DUF3556  81 pivyqkvvlytllfevvglgcsfGPLaakfkPplggilywlrpgtiRLppwPdkvPltkGdkRtvvDvalYaallvslvv 160
                                    pivyqkv+++tllfev+g+gc++GPL+++f+Pp+gg+lywlrp+tiRLp+wPdkvP+t+Gd+RtvvDvalYa++l+  v+
  gi|121637361|ref|YP_977584.1|  81 PIVYQKVIVFTLLFEVLGFGCGSGPLTGRFWPPIGGFLYWLRPNTIRLPAWPDKVPFTQGDTRTVVDVALYAIVLIGGVW 160
                                    ******************************************************************************** PP

                        DUF3556 161 alvspGv....geaaaaetevgllpavqvvaliallvvlgLRDkviflaaRgeqYlllllvflvlafvdmivalklvilv 236
                                    al+spG+    g+ ++a+ +vgl+++v vv++i++l vlgLRDk+iflaaRge+Y+l l+vf++  f+d+i+a+k+++l+
  gi|121637361|ref|YP_977584.1| 161 ALLSPGSpgpgGTPVTAAGDVGLINPVLVVPTIVALGVLGLRDKTIFLAARGEHYWLKLFVFFFP-FTDQIAAFKIIMLC 239
                                    *******99988899999**********************************************9.************** PP

                        DUF3556 237 iWlGaavsklnkhfplvvstmlsnspllrsk...slkralyrnfpdDlrPsklaklvahvagtvvellvPlvLlf.stnk 312
                                    +W+Gaa+skln+hfp+vv++m+sn++llrs+    +k+ lyr++++DlrPs+l+kl+ah +gt++e+lvP +L++ ++++
  gi|121637361|ref|YP_977584.1| 240 LWWGAATSKLNHHFPYVVAVMTSNNALLRSRvfnPIKHLLYRDHANDLRPSWLPKLMAHGGGTTAEFLVPGILVLvADGH 319
                                    ******************************977679**********************************9998879*** PP

                        DUF3556 313 tltlvaavlmvvfhlfilstlplavPleWnvffifavlflflgfagvgvadlssplllalllavlvvvpvlGnlrPdkvs 392
                                     ++++ + +mv+fhl+ils+lp++vPleWnvffif++++lf ++ +++ +dl+spllla+++a +v+v+++Gnl+P+k+s
  gi|121637361|ref|YP_977584.1| 320 PWRWFLIGFMVLFHLNILSNLPMGVPLEWNVFFIFSLCYLFGHYGAITATDLRSPLLLAIVIA-VVAVVIMGNLLPEKIS 398
                                    **********************************************************98887.56678*********** PP

                        DUF3556 393 fLpsmRyYaGnWatalwafkpgaeeklekeivksaklqadqleklyekeaaeivlqkvlafRalhshgrallslllrald 472
                                    fLp+mRyYaGnWat++w+f+ +ae+++e+++vks++l ++ql+kly+  +aei++++v+afRa+h+hgral++ll rald
  gi|121637361|ref|YP_977584.1| 399 FLPAMRYYAGNWATSIWCFRGDAEATMETSVVKSSALVVNQLAKLYDGATAEIMTDQVAAFRAMHTHGRALNGLLPRALD 478
                                    ******************************************************************************** PP

                        DUF3556 473 dedeytlregelvcstlvgwnfGdghlhneqliaavqkrcefepGelvvvllesqpihrqtqeyrvvDaalGvierGyvk 552
                                    de++y++rege+v++ lvgwnfG+ghlhneql+aavq+rc+f++G+l+v++le+qpih q+q yr+vDa++G++e+Gyv+
  gi|121637361|ref|YP_977584.1| 479 DEAHYRIREGEIVAGPLVGWNFGEGHLHNEQLVAAVQRRCNFADGDLRVIILEGQPIHVQKQWYRIVDAKTGLFEAGYVT 558
                                    ******************************************************************************** PP

                        DUF3556 553 vadavaeqPWl.pddeipvevt 573
                                    v+d++++qPW+ p de+pv+vt
  gi|121637361|ref|YP_977584.1| 559 VEDMLSRQPWPePGDEFPVHVT 580
                                    **********99********96 PP

>> Nipped-B_C  Sister chromatid cohesion C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0011       9.8      37      53 ..     181     197 ..     175     203 .. 0.90
   2 ?    3.8   0.0    0.0052        47      26      68 ..     231     275 ..     223     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                                    HT-S-GGGTHHHHHHHT CS
                     Nipped-B_C  37 qGLvhPvqcvptLiale 53 
                                     GL++Pv +vpt++al 
  gi|121637361|ref|YP_977584.1| 181 VGLINPVLVVPTIVALG 197
                                    6**************95 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0052
                                    HHHHHHHHHHHHT-S-GG..GTHHHHHHHTT-SSHHHHHHHHHHH CS
                     Nipped-B_C  26 aAlevvslilrqGLvhPv..qcvptLialetdpdesirsrAdkll 68 
                                    aA++++ l+l  G ++ +  + +p+++a+ t+++  +rsr ++ +
  gi|121637361|ref|YP_977584.1| 231 AAFKIIMLCLWWGAATSKlnHHFPYVVAVMTSNNALLRSRVFNPI 275
                                    66666666666666666522589****************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4244.86
//
Query:       gi|121637362|ref|YP_977585.1|  [L=473]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.5   0.7    1.6e-12   47.5   0.7    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.2e-07   30.5   1.3    5.6e-07   29.2   1.3    1.7  1  Amino_oxidase   Flavin containing amine oxidoreductase
    4.9e-07   29.2   0.3    7.3e-07   28.7   0.3    1.2  1  Thi4            Thi4 family
    6.3e-07   29.3   9.6    8.9e-07   28.8   6.1    2.6  2  DAO             FAD dependent oxidoreductase
    8.1e-07   28.7   0.3    1.2e-06   28.1   0.3    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    7.2e-06   25.5   1.6    1.1e-05   24.9   1.6    1.2  1  FAD_binding_3   FAD binding domain
    3.7e-05   23.1   0.7    7.5e-05   22.1   0.7    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00021   20.1   1.0    0.00031   19.6   1.0    1.2  1  HI0933_like     HI0933-like protein
    0.00063   18.9   2.1    0.00063   18.9   2.1    1.5  2  FAD_binding_2   FAD binding domain
    0.00072   20.1   2.1      0.001   19.6   0.7    1.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00075   18.8   0.8     0.0011   18.3   0.8    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.006   16.6   1.5      0.011   15.7   0.6    1.8  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0081   15.3   1.9      0.012   14.7   1.9    1.2  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.014   14.3   0.1      0.019   13.8   0.1    1.2  1  Trp_halogenase  Tryptophan halogenase
       0.17   10.9   0.9       0.28   10.2   0.9    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.35   10.7   2.1       0.38   10.6   0.5    1.8  2  YjeF_N          YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.7   1.4e-15   1.6e-12       1      50 [.       6      57 ..       6      72 .. 0.89
   2 ?   -2.9   0.8       7.6   8.5e+03       3      13 ..     450     460 ..     450     466 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.4e-15
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE..TTCEECTS-- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev..pgvrvdygah 50
                                   +vGaG  Gl+aA +La++g+dv++le+rd +GG a+s e+  pgv++d+   
  gi|121637362|ref|YP_977585.1|  6 VVGAGPNGLAAAIHLARHGVDVQVLEARDTIGGGARSGELtvPGVIHDHCSA 57
                                   8*************************************9988******9754 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.6
                                    --SHHHHHHHH CS
                  NAD_binding_8   3 GaGlsGlvaAy 13 
                                    GaG+ Gl+  +
  gi|121637362|ref|YP_977585.1| 450 GAGIHGLCGYH 460
                                    99***998655 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   1.3     5e-10   5.6e-07       3      38 ..      13      50 ..      12     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5e-10
                                   HHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET..TE CS
                  Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvGGRirtvrsd..Gy 38
                                   GLaaA +L+++G+dV+vlEard +GG +r+ ++   G+
  gi|121637362|ref|YP_977585.1| 13 GLAAAIHLARHGVDVQVLEARDTIGGGARSGELTvpGV 50
                                   9*************************888876655555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.3   6.6e-10   7.3e-07      20      65 ..       4      48 ..       1      58 [. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.6e-10
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                    v+vGaG+ GL+aa  la++ ++ v +le++ ++GGGa  G     
  gi|121637362|ref|YP_977585.1|  4 AVVVGAGPNGLAAAIHLARH-GVDVQVLEARDTIGGGARSGELTVP 48
                                   599*****************.*****************99976655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   6.1     8e-10   8.9e-07       2     171 ..       4     241 ..       3     258 .. 0.55
   2 ?   -0.7   0.1      0.72   8.1e+02     318     351 ..     412     463 ..     296     464 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8e-10
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE...EEEESSSSTHHSTHHHHHHHHHHHHHHHHHH.HHH CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns...gllhsglrylpeaselarlslealeelrele.eel 75 
                                     v++G+G  Gl++A +Lar+g  V +le++d +g ga ++     g++h +++ +       +l   +  ++++++ +++
  gi|121637362|ref|YP_977585.1|   4 AVVVGAGPNGLAAAIHLARHGvdVQVLEARDTIGGGARSGELtvpGVIHDHCSAFH------PLGVGS-PFWAAIDlQRY 76 
                                    59****************************99998776666557777777765444......777765.77877665667 PP

                                    SSTTSEEEEEEEEEESS............................................................... CS
                            DAO  76 gididyrrtGllslaad............................................................... 92 
                                    g+ + ++   + +  +d                                                               
  gi|121637362|ref|YP_977585.1|  77 GLTWKWPDVDCAHPLDDgtagvlyrsieataaglgpdgkrwqravgdlaagfdelaedllrpvlnmprhpirlarfgpra 156
                                    87787777777776654444444444444444444444444444444444444444444444444443333333333333 PP

                                    ..HHHHHHHH........HHHHHH.......HHTTTTEE.EEEHHHHHHHSTT.ST.TTSEEEEETTEEEEEHHHHHHHH CS
                            DAO  93 ..eeeleald........kllall.......leagldae.lldaeevrelepa.lp.gllgalfypdtgqvdpakltaal 152
                                      +      +                     + a + ++  ld+ +++ l  + l+ g++ ++ +  +g       t+al
  gi|121637362|ref|YP_977585.1| 157 alP------AtamarrfhT----EraralfgG-AAAHVYtRLDRPLTASLGLMiLAsGHRHGWPVARGGS---GSITKAL 222
                                    330......0222222221....112222221.1112221455554444432232235555544555455...6666667 PP

                                    HHHHHHTT-EEEESECEEE CS
                            DAO 153 araaealGveilegtevtg 171
                                    a+a+ a G+++ +g +vt+
  gi|121637362|ref|YP_977585.1| 223 AAALDAYGGTVATGVTVTS 241
                                    7777777777777777766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                                    EEEEEE..................TEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 318 ligetp..................gvkglylatGhsghGltlapatGkllae 351
                                    +ig ++                  gv+g+yl++    +G     ++G ++ae
  gi|121637362|ref|YP_977585.1| 412 IIGGANdrlqvifrprvavdpyaiGVPGVYLCSQSAPPGAGIHGLCGYHAAE 463
                                    3333234555555555666666666777777777777777777777777665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.3   1.1e-09   1.2e-06       3      41 ..       5      43 ..       4      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-09
                   FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41
                                   vVvG+gp G+aAAi  ar+G  v ++e r+ +GG + sg
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHLARHGVDVQVLEARDTIGGGARSG 43
                                   8********************************988666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.6   9.7e-09   1.1e-05       2      36 ..       2      36 ..       1      47 [. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.7e-09
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                   t+ ++VGaGp Gl +a  L+++Gv+v ++e r+t 
  gi|121637362|ref|YP_977585.1|  2 TTAVVVGAGPNGLAAAIHLARHGVDVQVLEARDTI 36
                                   6778**************************99875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.7   6.7e-08   7.5e-05       3      35 ..       4      36 ..       2      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.7e-08
                                   EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                    vv+G+Gp Glaaa++la++g++v ++e+++t+
  gi|121637362|ref|YP_977585.1|  4 AVVVGAGPNGLAAAIHLARHGVDVQVLEARDTI 36
                                   599**********************99877765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.0   2.8e-07   0.00031       2      36 ..       3      37 ..       2      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   + +v+G+G+ Gl aAi++a++g +V +le+ +++g
  gi|121637362|ref|YP_977585.1|  3 TAVVVGAGPNGLAAAIHLARHGVDVQVLEARDTIG 37
                                   579***************************99887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.1   5.7e-07   0.00063       2      36 ..       4      38 ..       3      48 .. 0.91
   2 ?   -2.7   0.0       2.1   2.3e+03     117     117 ..     177     177 ..     114     280 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.7e-07
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   ++V+G+G  GLaAA+ +a++G +v v+e  +  gg
  gi|121637362|ref|YP_977585.1|  4 AVVVGAGPNGLAAAIHLARHGVDVQVLEARDTIGG 38
                                   69**************************9888777 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                    T CS
                  FAD_binding_2 117 G 117
                                    G
  gi|121637362|ref|YP_977585.1| 177 G 177
                                    1 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   9.2e-07     0.001       2      35 ..       4      37 ..       3      43 .. 0.94
   2 ?   -2.2   0.0       5.6   6.2e+03       6      32 ..     214     244 ..     214     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.2e-07
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +vvvG+G  gl +A  la++g +V+v+e++d++ 
  gi|121637362|ref|YP_977585.1|  4 AVVVGAGPNGLAAAIHLARHGVDVQVLEARDTIG 37
                                   69*****************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                                    CSSHHHHHHHHHHHHTT....SEEEEEESSS CS
                      Pyr_redox   6 GgGyiglElAgalaelg....kkVtvversd 32 
                                    G+G i   lA+al ++g      Vtv  r+d
  gi|121637362|ref|YP_977585.1| 214 GSGSITKALAAALDAYGgtvaTGVTVTSRRD 244
                                    6666666778888888766656777777776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.8   9.8e-07    0.0011       1      30 [.       5      33 ..       5      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.8e-07
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                   +++GaGP Glaaai+l ++g+ d+ +lE  
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHLARHGV-DVQVLEAR 33
                                   79*******************.89****76 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6     1e-05     0.011       1      41 [.       5      40 ..       5      46 .. 0.83
   2 ?   -2.2   0.0       3.2   3.6e+03     118     155 ..     166     204 ..     156     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrv 41
                                   ++vGaGp Gla++ +L+++      +++++ + + + g g++
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHLARH-----GVDVQVLEARDTiG-GGA 40
                                   69*****************.....59999999965536.554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                  NAD_binding_9 118 evhraevvdleeradg.qavlladgaslaadaVvLAlGh 155
                                    ++h++++ +l   a+  ++ +l++  +  +   +LA Gh
  gi|121637362|ref|YP_977585.1| 166 RFHTERARALFGGAAAhVYTRLDRPLTASLGLMILASGH 204
                                    678888888777665525777888888889999999998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.9   1.1e-05     0.012       3      35 ..       5      36 ..       3      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                           GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldti 35
                                   +V+G+G  G++AA+++ar G++v  + +  dti
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHLARHGVDVQVL-EARDTI 36
                                   8**********************998.556665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.7e-05     0.019       3      52 ..       5      54 ..       3      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                   EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS..---SS-EE--THHHH.T CS
                 Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseei..gtvgvGeatipsirk.l 52
                                   v+vG+G+ G  aA++la+++   ++v+++e+ ++  g  + Ge t+p + +  
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHLARHG---VDVQVLEARDTigGGARSGELTVPGVIHdH 54
                                   8*******************...9******97653456889999999876644 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00025      0.28       3      36 ..       5      36 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                  Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   vv+GaGp gl+ A +l  a+ g+ v ++ea + +
  gi|121637362|ref|YP_977585.1|  5 VVVGAGPNGLAAAIHL--ARHGVDVQVLEARDTI 36
                                   8***************..99******99998765 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00034      0.38      38      59 ..       9      30 ..       2      42 .. 0.80
   2 ?   -2.0   0.0       2.5   2.8e+03      35      66 ..     212     244 ..     197     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                         YjeF_N 38 nGgdglaaArhLaqegakVtvl 59
                                    G  glaaA hLa++g++V+vl
  gi|121637362|ref|YP_977585.1|  9 AGPNGLAAAIHLARHGVDVQVL 30
                                   46778***************94 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                         YjeF_N  35 sgnnGgdglaaArhLaqegakVtv.llleeeek 66 
                                    +g +G+   a+A+ L   g +V + ++++++++
  gi|121637362|ref|YP_977585.1| 212 RGGSGSITKALAAALDAYGGTVATgVTVTSRRD 244
                                    677888888999999888888888766665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3397.72
//
Query:       gi|121637363|ref|YP_977586.1|  [L=273]
Description: hypothetical protein BCG_1494 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.4   0.3    2.6e-19   69.9   0.3    1.2  1  Big_10    Bacterial Ig domain
    2.7e-13   50.5   0.0    5.5e-13   49.6   0.0    1.4  1  YkuD      L,D-transpeptidase catalytic domain


Domain annotation for each model (and alignments):
>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.3   2.9e-23   2.6e-19      84     160 ..      37     116 ..      23     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.9e-23
                         Big_10  84 vsatltpedgstvGvgqpisikFdkpv...edkaavekalkvttspavegafaWlsdsevdwRpkeYwkpgtkVtvkakl 160
                                    + a++ p+ g++vGv+ p+ ++F++p+   ++++a+e+a++v+++pa++g+f Wl+++ v+w p+ +w+++++V++++  
  gi|121637363|ref|YP_977586.1|  37 AVASVLPTRGQVVGVAHPVVVTFSAPItnpANRHAAERAVEVKSTPAMTGKFEWLDNDVVQWVPDRFWPAHSTVELSVGS 116
                                    567899*********************777789*****************************************998753 PP

>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   6.2e-17   5.5e-13      25     142 ..     167     265 ..     159     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 6.2e-17
                                    EEE-BEBTTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEEECCCTTCECCCCEEE-STTS-EEEE CS
                           YkuD  25 sfpvsvGgkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyldkknskvalgkvkfvfpngsgiyiHg 104
                                     +p+s+G   +++ +TP+G++++ sk+r+    + +s  + +++++++++ +              ++v  +++g y+H 
  gi|121637363|ref|YP_977586.1| 167 VMPASMG---RPEYPTPVGSYTVLSKERSVI--MDSSSVGIPVDDPDGYRLSV------------DYAVRITSRGLYVH- 228
                                    589****...66************9999999..99999999999988864443............45999*********. PP

                                    .ETCSS...CT...HHC.BSSSEEE-HHHHHHHHHHHHTTE CS
                           YkuD 105 tgapdlfergk...garrShGCirlseedakelyelvlvgt 142
                                     +ap++    +    ++ ShGCi ls eda++ y+ v+ +t
  gi|121637363|ref|YP_977586.1| 229 -SAPWAL---PalgLENVSHGCISLSREDAEWYYNAVDMAT 265
                                    .999653...24666777*******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2242.34
//
Query:       gi|121637364|ref|YP_977587.1|  [L=45]
Description: hypothetical protein BCG_1495 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       124  (0.00691617); expected 358.6 (0.02)
Passed bias filter:                       95  (0.00529868); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 372.48
//
Query:       gi|121637365|ref|YP_977588.1|  [L=209]
Description: hypothetical protein BCG_1496c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1374.96
//
Query:       gi|121637366|ref|YP_977589.1|  [L=339]
Description: glyceraldehyde 3-phosphate dehydrogenase gap [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-69  231.1   0.0    6.3e-69  230.6   0.0    1.3  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
    9.2e-32  109.4   0.0    1.7e-31  108.5   0.0    1.5  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0022   18.6   0.3      0.012   16.3   0.3    2.1  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.6   0.0   1.1e-72   6.3e-69       1     158 []     163     318 ..     163     318 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 1.1e-72
                                    HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEEEES CS
                        Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglAvrVP 80 
                                    Laplakvl+d+fgi+kglmtt+hayt+dQ+l+Dgp+ kdlrraraaa ni+ptstgaaka+glV+p+lkgkldg+A+rVP
  gi|121637366|ref|YP_977589.1| 163 LAPLAKVLDDEFGIVKGLMTTIHAYTQDQNLQDGPH-KDLRRARAAALNIVPTSTGAAKAIGLVMPQLKGKLDGYALRVP 241
                                    8**********************************8.9****************************************** PP

                                    SSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEETTTEEEEEEEE CS
                        Gp_dh_C  81 tpnvsvvdlvvelekevtveevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivveenlvkvvawy 158
                                    +p++sv+dl+v+l+ +++v+e+naa+k+aaeg+lkgil+y ++++vssD+v+dphssifd+ +t+v++ ++ kvv+wy
  gi|121637366|ref|YP_977589.1| 242 IPTGSVTDLTVDLSTRASVDEINAAFKAAAEGRLKGILKYYDAPIVSSDIVTDPHSSIFDSGLTKVID-DQAKVVSWY 318
                                    *******************************************************************7.89******9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0   2.9e-35   1.7e-31       1     100 [.       3     109 ..       3     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 2.9e-35
                                    CEEEEESTSHHHHHHHHHHH.....HHTTCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEE.TTEEEETTEEEEEE- CS
                        Gp_dh_N   1 vkvainGfGRIGrlvlrall.....eekelevvaindltdletlayllkyDsvhgrfkgeveae.eealvvngkkikvla 74 
                                    v+v+inGfGRIGr+++rall      + ++evva nd+td++tla+llk+Ds+ gr++ +v  e ++++vv+  kik la
  gi|121637366|ref|YP_977589.1|   3 VRVGINGFGRIGRNFYRALLaqqeqGTADVEVVAANDITDNSTLAHLLKFDSILGRLPCDVGLEgDDTIVVGRAKIKALA 82 
                                    69******************998644459***********************************7778999999****** PP

                                    -SS.GGGS-CHHHTSSEEEE-SSS--S CS
                        Gp_dh_N  75 ekd.peelpwkelgvdlVvestGvftd 100
                                     ++ p++lpw++lgvd+VvestG+ft+
  gi|121637366|ref|YP_977589.1|  83 VREgPAALPWGDLGVDVVVESTGLFTN 109
                                    *999*********************97 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3     2e-06     0.012       1      90 [.       9     127 ..       9     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT...................................HHHHHT-- CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskd...................................rkallase 45 
                                    G+G iG+ + ++l++qq++ ++++  va +d  + ++                                   ++  +++ 
  gi|121637366|ref|YP_977589.1|   9 GFGRIGRNFYRALLAQQEQGTADVEVVAAND--ITDNstlahllkfdsilgrlpcdvglegddtivvgrakiKALAVREG 86 
                                    99*****************999999999999..33333446666766666666666666666665555444333333344 PP

                                    CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S- CS
                  NAD_binding_3  46 altldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtan 90 
                                    +  l++ dl     +dvvVE ++    a  +   L ag   v+ +
  gi|121637366|ref|YP_977589.1|  87 PAALPWGDLG----VDVVVESTGLFTNAAKAKGHLDAGAKKVIIS 127
                                    4444444443....3777777666666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2726.41
//
Query:       gi|121637367|ref|YP_977590.1|  [L=412]
Description: phosphoglycerate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   9.4e-132  439.5   0.0   1.2e-131  439.2   0.0    1.0  1  PGK        Phosphoglycerate kinase
  ------ inclusion threshold ------
       0.15   11.1   0.0       0.24   10.4   0.0    1.2  1  Phage-Gp8  Bacteriophage T4, Gp8


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.2   0.0  1.3e-135  1.2e-131       6     378 .]      14     394 ..       7     394 .. 0.95

  Alignments for each domain:
  == domain 1  score: 439.2 bits;  conditional E-value: 1.3e-135
                                    -TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TT.S-GGG-SHHHHHHHHHHHTT-EE CS
                            PGK   6 lkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkg.ekeklslkpvaerLsellgkeVk 84 
                                    ++g+ vlvR D+Nvpl+++g+itd  ri a++pT+k+ll+++akvv+++Hlgrpk   +++lsl+pva  L e lg++V+
  gi|121637367|ref|YP_977590.1|  14 VSGRGVLVRSDLNVPLDEDGTITDAGRIIASAPTLKALLDADAKVVVAAHLGRPKDgPDPTLSLAPVAVALGEQLGRHVQ 93 
                                    78999*************************************************87588********************* PP

                                    EESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H....HHHHHHHHT...-SEEEE--GGGTTS--TTTTHHHHC CS
                            PGK  85 fvedvvgeeveeaiaelkegevllLeNvrfykeEeknde....elakklasl...advyVnDAFgtahrahaStvgiakv 157
                                    ++ dvvg+++ + ++ l+ g++llLeN+rf k+E+++++    +lak+l +l   + v+V+D+Fg++hr++aS+++ia++
  gi|121637367|ref|YP_977590.1|  94 LAGDVVGADALARAEGLTGGDILLLENIRFDKRETSKNDddrrALAKQLVELvgtGGVFVSDGFGVVHRKQASVYDIATL 173
                                    **********************************7654436777*****99844358*********************** PP

                                    SEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-SEEEEETCHHHHHHHHTT-B-TTSS--GGG CS
                            PGK 158 lsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekvdkliigGgmantFlkaqgleigkslveedk 237
                                    l+++aG l+++E+++l++++++ +rp++++lGG+kvsdk++vie+L++k+d+++igGgm++tFl+aqg+++g+sl+e+d+
  gi|121637367|ref|YP_977590.1| 174 LPHYAGTLVADEMRVLEQLTSSTQRPYAVVLGGSKVSDKLGVIESLATKADSIVIGGGMCFTFLAAQGFSVGTSLLEDDM 253
                                    *99***************************************************************************** PP

                                    HHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS..EEEECCG--TT-EEEEE-HHHHHHHHHHHCC-SEEEEES-SS-T CS
                            PGK 238 lelakellekakkkgvkillpvDvvvakeeaeke.akvveveaipedemalDigpktielfaeaikeaktvvwnGpmGvf 316
                                    +e+++ lle+++   + + lpvD+vv+++ a+++ +++v+v a+p++ m+lDigp +i++f++ +++a t++wnGpmGvf
  gi|121637367|ref|YP_977590.1| 254 IEVCRGLLETYH---DVLRLPVDLVVTEKFAADSpPQTVDVGAVPNGLMGLDIGPGSIKRFSTLLSNAGTIFWNGPMGVF 330
                                    ***********9...89**********996444449******************************************** PP

                                    TSGCCCHHHHHHHHHHHHHCH.TSEEEEESHHHHHHHHHTT-GG.GSSEEESSSHHHHHHHCTS CS
                            PGK 317 eiekfakGTkaiakalaeatk.galsivGGgdsaaaveklglad.kvshvStGGgAsLelLegk 378
                                    e++++a+GT+ +a+a+ +at  ga+s+vGGgdsaaav+++++ +  +sh+StGGgAsLe+Legk
  gi|121637367|ref|YP_977590.1| 331 EFPAYAAGTRGVAEAIVAATGkGAFSVVGGGDSAAAVRAMNIPEgAFSHISTGGGASLEYLEGK 394
                                    ****************998888********************8879*****************8 PP

>> Phage-Gp8  Bacteriophage T4, Gp8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   2.7e-05      0.24     138     199 ..     339     401 ..     324     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.7e-05
                                    ..EEE.SSSTS-SHHHHHHTTS-E.EESS..--SS---SSSSTESSSSS-EEEEEE..EE-HHHH CS
                      Phage-Gp8 138 irgtc.siasltdkdeclklggkwnapsapgrsetipegrgdaietgdgyvweyly..eippdev 199
                                     rg+  +i + t k     +gg  +a   + r ++ipeg    i tg g   eyl   ++p  ev
  gi|121637367|ref|YP_977590.1| 339 TRGVAeAIVAATGKGAFSVVGGGDSAA--AVRAMNIPEGAFSHISTGGGASLEYLEgkTLPGIEV 401
                                    566552578889999988999987444..46***********************94225565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2779.70
//
Query:       gi|121637368|ref|YP_977591.1|  [L=261]
Description: triosephosphate isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-86  288.9   0.0    3.1e-86  288.7   0.0    1.0  1  TIM       Triosephosphate isomerase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.7   0.0   1.7e-90   3.1e-86       2     242 ..       6     251 ..       5     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 288.7 bits;  conditional E-value: 1.7e-90
                                    EEEEE-TBTS-HHHHHHHHHHHHHHCHG...CTSEEEEE--GGGHHHHHHHHTTSSEC..EEES--BSSSSBS-TT--BH CS
                            TIM   2 liagNwKmnktleeakellkklkaklke...ekvevviappflylekvkklleesklk..lgaqnvsaeksGafTGevsa 76 
                                    liagNwKmn ++ ea +l++k++ +l++   ++v+v+++ppf+ l++v++l++++kl+  +gaq++s ++sGa+TG+vs 
  gi|121637368|ref|YP_977591.1|   6 LIAGNWKMNLNHYEAIALVQKIAFSLPDkyyDRVDVAVIPPFTDLRSVQTLVDGDKLRltYGAQDLSPHDSGAYTGDVSG 85 
                                    79********************99999989999********************99998779******************* PP

                                    HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT.HHHHHHHHHHHHTTTS-CCCGG CS
                            TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleereagkteevvkeqlkeilkkldeealk 156
                                    + l++lg++yv++GHsErr++++E+d+lva+K+++alk+gl+pi+C+GE+l+ reag++ +   eql+ +l++l +e++ 
  gi|121637368|ref|YP_977591.1|  86 AFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIG 165
                                    ******************************************************************************** PP

                                    CEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEESS--TTTHHHHHTSTT--EEEESGGGCSH CS
                            TIM 157 nvviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYGGsvnkenakellkqkdidGlLvGgaslka 236
                                    +vv AYePvWAiGtg++a++ +aqev+aairkela++ s ++a+++r+lYGGsvn++n+ ++++q+d+dG+LvGgasl+ 
  gi|121637368|ref|YP_977591.1| 166 SVVTAYEPVWAIGTGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDG 245
                                    ******************************************************************************** PP

                                    HHHHHH CS
                            TIM 237 esFlki 242
                                    e+F+++
  gi|121637368|ref|YP_977591.1| 246 EHFATL 251
                                    ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1832.49
//
Query:       gi|121637369|ref|YP_977592.1|  [L=141]
Description: hypothetical protein BCG_1500c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-12   48.1   0.1    1.9e-12   47.7   0.1    1.1  1  SnoaL_2   SnoaL-like domain
    3.7e-07   30.0   0.0    6.9e-07   29.1   0.0    1.5  1  SnoaL     SnoaL-like polyketide cyclase


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   2.1e-16   1.9e-12       1     101 [.      10     109 ..      10     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.1e-16
                                    HHHHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEET CS
                        SnoaL_2   1 vraflaalnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipa 79 
                                    v+ f + + a  +d+l ++++pdvv+  p  ++++G  a+++ f++ +  +pdl+ e++++ + gd v++e+++ +  + 
  gi|121637369|ref|YP_977592.1|  10 VEGFADFWKAPSPDRLTDHLHPDVVLVRPlSPPRHGLGAAQREFTRILGLLPDLHGEVDRWSQAGDVVFIEFRLIA--RL 87 
                                    78999************************8888*****************************************96..77 PP

                                    TSSEEEEEEEEEEEEETTEEEE CS
                        SnoaL_2  80 tgrgvtvrgvdvfrvrdGkive 101
                                      + v++++vd f +r++k ve
  gi|121637369|ref|YP_977592.1|  88 GSEVVEWPVVDRFLLRGDKAVE 109
                                    8888999***********9987 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   7.7e-11   6.9e-07       4      89 ..      10      95 ..       7     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.7e-11
                                   HHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEB CS
                          SnoaL  4 lrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgef 85
                                   ++ ++++w    +d+l +++++dvv   p + p++Gl +  +++++ +  +PDl+ ev++  ++gd v  + ++ ++  +e+
  gi|121637369|ref|YP_977592.1| 10 VEGFADFWKAPSPDRLTDHLHPDVVLVRPLSPPRHGLGAAQREFTRILGLLPDLHGEVDRWSQAGDVVFIEFRLIARLGSEV 91
                                   56689****************************************************************9999988887777 PP

                                   TTBE CS
                          SnoaL 86 lGip 89
                                   ++ p
  gi|121637369|ref|YP_977592.1| 92 VEWP 95
                                   6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 988.37
//
Query:       gi|121637370|ref|YP_977593.1|  [L=77]
Description: preprotein translocase subunit SecG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.4   9.2    2.3e-14   53.2   9.2    1.0  1  SecG      Preprotein translocase SecG subunit


Domain annotation for each model (and alignments):
>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   9.2   1.3e-18   2.3e-14       2      69 ..       5      72 ..       4      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.3e-18
                                   HHHHHHHHHHHHHHHHHHCHHCCSCCHHTT....SS-SS--SSCCCHHCCHHHHHHHHHHHHHHHHHHC CS
                           SecG  2 llillvivsilLillvLlQsgkgaglsgafggg.asdslfgsrgaekfLtkiTvilavlFfvlslvlal 69
                                   l+i l+++s+l +llvLl++ kg+gls  fggg +s sl gs+ +ek+L+++T ++  +++v+++ +al
  gi|121637370|ref|YP_977593.1|  5 LQITLIVTSVLVVLLVLLHRAKGGGLSTLFGGGvQS-SLSGSTVVEKNLDRLTLFVTGIWLVSIIGVAL 72
                                   899************************999888676.588*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 639.90
//
Query:       gi|121637371|ref|YP_977594.1|  [L=491]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-33  114.9  19.8    2.6e-33  114.2  19.8    1.4  1  PE              PE family
  ------ inclusion threshold ------
       0.11   12.3   0.2        0.2   11.5   0.2    1.3  1  SIS             SIS domain
       0.16   12.5  10.8       0.24   11.9  10.8    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2  19.8   4.3e-37   2.6e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 4.3e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms v+v+P +l+aaaad+a+ig+alsaan aaa++t++vlaa+aDeVSaaiA+lfs +a++yqalsaq+a fh+qfvqal+a
  gi|121637371|ref|YP_977594.1|  1 MSNVMVVPGMLSAAAADVASIGAALSAANGAAAPTTAGVLAAGADEVSAAIASLFSGYARDYQALSAQMARFHQQFVQALTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   + gsYaaaEaa
  gi|121637371|ref|YP_977594.1| 83 SVGSYAAAEAA 93
                                   *********97 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.3e-05       0.2      53     118 ..      46     112 ..      17     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                                    TTCEEEEEESSSHHHHHHHHHHHHHHTTSEE.EEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHH CS
                            SIS  53 eddlvilisfsgetkdlvaaaelakergaki.iaITdskgsplareadlalyinaepetlvastksl 118
                                    e    i+  fsg+++d++a+  ++++++++   a+T s gs +a+ea +a  ++a ++  +a++++ 
  gi|121637371|ref|YP_977594.1|  46 EVSAAIASLFSGYARDYQALSAQMARFHQQFvQALTASVGSYAAAEAANASPLQALEQQVLAAINAP 112
                                    555667777*******************99968**************99999999999855555544 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  10.8     4e-05      0.24       3      99 ..       2      99 ..       1     100 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                  T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp..icaatndavaaaeaarraagealaaasteLadkLra 82
                                    n+ V+p+ l ++aa++ ++ a +++a+ aaa+++a vl   G+  ++aa ++ ++ + ++ +a  +++a+ ++++ + L+a
  gi|121637371|ref|YP_977594.1|  2 SNVMVVPGMLSAAAADVASIGAALSAANGAAAPTTAGVLAA-GAdeVSAAIASLFSGYARDYQALSAQMARFHQQFVQALTA 82
                                   4899***************************9999999887.65459*********************************** PP

                  T7SS_ESX_EspC 83 AAaaYeatDeeaagald 99
                                   + + Y a++ ++a+ l+
  gi|121637371|ref|YP_977594.1| 83 SVGSYAAAEAANASPLQ 99
                                   *************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 3208.58
//
Query:       gi|121637372|ref|YP_977595.1|  [L=766]
Description: biotin sulfoxide reductase bisC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-56  189.6   0.0    1.2e-55  189.3   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    8.4e-23   80.5   0.0    2.4e-22   79.0   0.0    1.8  2  Molydop_binding  Molydopterin dinucleotide binding domain
    1.2e-13   50.8   0.6    5.2e-12   45.6   0.3    2.7  2  Molybdopterin_N  Molybdopterin oxidoreductase N-terminal doma
  ------ inclusion threshold ------
      0.083   12.8   0.0       0.19   11.6   0.0    1.5  1  PS_pyruv_trans   Polysaccharide pyruvyl transferase


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.3   0.0   2.6e-59   1.2e-55       1     431 [.      50     510 ..      50     511 .. 0.87

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 2.6e-59
                                    B--S-EEEC..........TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT CS
                  Molybdopterin   1 RlkyPmvRk..........qargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllg 70 
                                    R+ +P vR           +arg+ +Fv+vsWde  el a++l++t++ yg+++++ +ss+++ s+  ++ ++  + ++ 
  gi|121637372|ref|YP_977595.1|  50 RIANPAVRRgwlqhgpgpsSARGAEEFVEVSWDELIELLASELRRTVDRYGNEAIY-GSSYGWASAGRFHHAQSQVHRFL 128
                                    8999****************************************************.9**************99999999 PP

                                    -EEE-BEECCGGGTTHHHH....CHHCCCCCT..TTS-SS-CCGGGG-SEEEEESS-HHHHSHHH..........HHHHH CS
                  Molybdopterin  71 gknlsfydwyadlppasaq....qtigsdsrs..nyessnpledlensdliilwGsNvreerpil..........narir 134
                                    +  +++  +   ++ ++ +    + +g+ + +  +  +++++  ++++ l +++G  + ++  ++          +   r
  gi|121637372|ref|YP_977595.1| 129 NMLGGYTASRHSYSAGASEvifpHIVGAALFEalAETTTWDV-IVDHTALLVAFGGLPVKNTAVMpggttahpdrDYVGR 207
                                    988888888888887777778884444433220023344444.5***********9999998888999988886554555 PP

                                    HHHHTTC-EEEEECSSB-H......CGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCE CS
                  Molybdopterin 135 kaalkkkakvivigpryae......llkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvt 208
                                    ++a+    ++++++p  ++       l   + wla+ pgtd+a++l++++v+ +e + d +fl +y++g+e ++ +ll++
  gi|121637372|ref|YP_977595.1| 208 YRARG--GRLVSVSPLRDDiaaiagPLDDRCRWLAPVPGTDVAIMLGLAYVLATESLADRAFLGRYCTGYERFERYLLGL 285
                                    55555..599*****9999999999568999************************************************9 PP

                                    ECCS......HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSC CS
                  Molybdopterin 209 leee......tgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGq 282
                                     ++       +++ ++  a   r lar++a+ ++  +i    +l++ ++g+++++++++La+++g++g pgGg++h  G 
  gi|121637372|ref|YP_977595.1| 286 DDGIpktpewAAALSGLAAGDLRDLARRMAEHRT--LITTSLSLQRIEHGEQTVWMAATLAAMLGQIGLPGGGFGH--G- 360
                                    9888888888**********************99..9999************************************..6. PP

                                    TTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCH CS
                  Molybdopterin 283 lilagaaekvgalpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadeneveka 362
                                    ++ +g +++  a +     +  +  ++++      +l + p++++    +ll+  ++k +y++g np+++h++  ++ +a
  gi|121637372|ref|YP_977595.1| 361 YSSNGVGNPPLACGLPALPQGNNPVSTFIPVAAISELLQRPGQRLAYNGRLLELPDIKCVYWAGGNPFHHHQNLPRLRRA 440
                                    5666666666555333333333334455544455566666999999999******************************* PP

                                    HHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEE.EEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 363 lekldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqh.lkqavsppgeaksdwkIlkaLak 431
                                    l + d++vv + ++t  a++aDi+ P++t +E++d+  +   ++   + ++v+p  +a++d+  ++aLa 
  gi|121637372|ref|YP_977595.1| 441 LSRVDTIVVHEQYWTAMAKHADIVVPTTTSFERDDFAASKTNPTLIaMPAMVPPYANARDDYHTFSALAH 510
                                    *************************************999999888799999****************96 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   9.3e+03      25      43 ..     329     348 ..     316     348 .. 0.63
   2 !   79.0   0.0   5.5e-26   2.4e-22       1     106 [.     623     739 ..     623     744 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                    HCSSS.-EEEEEHHHHHHHT CS
                Molydop_binding  25 akpep.evveinpedAaalG 43 
                                    + +++ ++v++ +  Aa lG
  gi|121637372|ref|YP_977595.1| 329 RIEHGeQTVWMAATLAAMLG 348
                                    22333579999999888776 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 5.5e-26
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                    l+Li  +++ +lhsq +++ ++ ++k ++ e ++i+p+dAaa++++dGd+V+v+++rG++ + +++++++rp vv + +g
  gi|121637372|ref|YP_977595.1| 623 LHLIANQPRTRLHSQLDHGGASMASKIRGrEPIRIHPDDAAARELTDGDIVRVFNDRGACLAGVVIDDGLRPKVVQLSTG 702
                                    799***************************************************************************** PP

                                    HCC..............S-GHCTS.--SCSTTT--CS CS
                Molydop_binding  80 wwe.........agekggnaNalt.ddatdplsgtpe 106
                                    +w          +++ +gn Nal  d++t+ l+ + +
  gi|121637372|ref|YP_977595.1| 703 AWFdpadprdpdSMCVHGNPNALSnDSGTSSLAHGST 739
                                    ************************8888888887765 PP

>> Molybdopterin_N  Molybdopterin oxidoreductase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3   1.2e-15   5.2e-12       1      41 []       6      46 ..       6      46 .. 0.98
   2 ?    2.4   0.0     0.035   1.6e+02      13      26 ..     211     224 ..     206     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.2e-15
                Molybdopterin_N  1 tasHWGafraevkdGkivgvrPfegDpdPspllegvpdavy 41
                                   +a+HWG+f+a+v +G+i +v + ++D++P p l+++p+av+
  gi|121637372|ref|YP_977595.1|  6 SATHWGVFTARVHGGDIAAVAALASDTNPAPQLQNLPGAVR 46
                                   79*************************************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.035
                Molybdopterin_N  13 kdGkivgvrPfegD 26 
                                    ++G++v+v P  +D
  gi|121637372|ref|YP_977595.1| 211 RGGRLVSVSPLRDD 224
                                    79********9998 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.19      89     133 ..     406     449 ..     393     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHS-SSEEEE-SEEE..-S-HHHHHHHHHHHHHTTEEEE CS
                 PS_pyruv_trans  89 lrllflakkagkpviilgqgiGpflnealrkllkkilakadlisv 133
                                        +l+++++++++ ++ g  pf++++++++l+++l+++d i v
  gi|121637372|ref|YP_977595.1| 406 AYNGRLLELPDIKCVYWAGGN-PFHHHQNLPRLRRALSRVDTIVV 449
                                    6666789999***********.********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.55
# Mc/sec: 4213.58
//
Query:       gi|121637373|ref|YP_977596.1|  [L=161]
Description: hypothetical protein BCG_1504c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   22.4   3.7    0.00035   20.9   3.7    1.6  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   3.7   1.9e-08   0.00035       5     141 ..      11     157 ..       8     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-08
                                    EEEEEESS-HHHHHHHHTTTTGGG.GT-TTEEEEECSE.STSSS.........TTTEEEEECCCS...........SEEE CS
                Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwp.rWhpevarveleg.gggpa.........rgvegtvrvggr...........gtvr 62 
                                    +++ v+aap+e+Vw +v  +e++  +  p ++ +  +g +g ++         +          r           +  r
  gi|121637373|ref|YP_977596.1|  11 ERQSVVAAPAEQVWQRVVTPEGINdELRPWMTMSVPRGaKGMTVdtvpigapiG----------RawlrlfgvlpfDYDR 80 
                                    67789*****************99778888887766652333334444444321..........1222222234665579 PP

                                    EEEEEEETTTTEEEEEEE.SSS-TSEEEEEEEEECCET.EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  63 eelvevdpegrllsyrivkpvpvanyvatwtvtpdggg.trvtwtgefdagplggpfekpaaakavkgdleagLerLkar 141
                                      + e++p gr+++ + +  +++++   + tvtp+g+  t v+ +++f+ +  g  f +p++a+++++ +    +rL+++
  gi|121637373|ref|YP_977596.1|  81 LSIAELEP-GRRFREDST-MLSMRQWQHERTVTPEGDTkTIVRDRITFQ-TRAGLRFAAPLIAAGLRALFGHRHRRLQRH 157
                                    99******.999999995.577777799********9755566555556.456778889999999999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1237.98
//
Query:       gi|121637374|ref|YP_977597.1|  [L=136]
Description: hypothetical protein BCG_1505c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-06   25.9   2.9     0.0039   17.4   0.8    2.0  2  DUF948           Bacterial protein of unknown function (DUF94
    1.2e-05   25.5   1.0      2e-05   24.8   0.7    1.5  1  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0001   22.6   0.6    0.00023   21.5   0.5    1.7  1  UPF0184          Uncharacterised protein family (UPF0184)
    0.00054   20.0   0.1    0.00067   19.7   0.1    1.2  1  Laminin_II       Laminin Domain II
    0.00064   19.8   3.3      0.027   14.5   0.7    1.6  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0061   16.9   1.8       0.95    9.9   0.5    2.3  2  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0075   16.6   2.5      0.047   14.1   0.4    2.6  3  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0076   16.3   0.2      0.014   15.4   0.2    1.4  1  DUF1664          Protein of unknown function (DUF1664)
     0.0082   16.8   0.1      0.014   16.0   0.1    1.4  1  KfrA_N           Plasmid replication region DNA-binding N-ter
     0.0097   16.3   0.7        0.2   12.1   0.7    2.2  1  NPV_P10          Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.013   15.7   0.2       0.32   11.3   0.1    2.2  2  WXG100           Proteins of 100 residues with WXG
      0.015   15.4   0.4      0.019   15.0   0.4    1.1  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.015   14.7   0.1      0.019   14.4   0.1    1.2  1  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.02   15.4   0.4      0.065   13.7   0.4    1.7  1  DUF16            Protein of unknown function DUF16
       0.02   14.2   0.0      0.024   14.0   0.0    1.1  1  DUF3450          Protein of unknown function (DUF3450)
      0.026   14.2   0.1      0.042   13.5   0.1    1.4  1  RPW8             Arabidopsis broad-spectrum mildew resistance
       0.03   14.5   0.1      0.041   14.0   0.1    1.2  1  Tropomyosin_1    Tropomyosin like
      0.032   13.7   0.9       0.16   11.5   0.3    2.0  2  DegS             Sensor protein DegS
      0.034   14.3   0.7       0.23   11.6   0.5    2.1  3  COG5             Golgi transport complex subunit 5
      0.054   13.9   0.2       0.13   12.7   0.1    1.7  2  Snapin_Pallidin  Snapin/Pallidin
      0.059   13.2   0.4       0.11   12.3   0.4    1.4  1  Nsp1_C           Nsp1-like C-terminal region
       0.06   14.0   0.3       0.21   12.2   0.3    2.1  1  SlyX             SlyX
      0.062   12.9   0.2      0.087   12.4   0.2    1.3  1  DUF4795          Domain of unknown function (DUF4795)
      0.066   13.0   0.5        1.2    9.0   0.2    2.3  3  DASH_Dam1        DASH complex subunit Dam1
      0.072   13.1   0.4       0.26   11.3   0.2    1.9  1  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.073   12.9   0.0        0.1   12.4   0.0    1.3  1  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.075   12.1   0.1      0.081   12.0   0.1    1.1  1  APG17            Autophagy protein Apg17
       0.11   12.6   0.1       0.14   12.2   0.1    1.3  1  DivIVA           DivIVA protein
       0.11   11.4   0.0       0.12   11.3   0.0    1.0  1  DUF812           Protein of unknown function (DUF812)
       0.11   12.7   0.1       0.24   11.7   0.1    1.6  1  DUF5082          Domain of unknown function (DUF5082)
       0.14   12.4   0.8       0.75   10.0   0.2    1.9  2  CHDCT2           CHDCT2 (NUC038) domain
       0.14   11.9   0.2       0.29   10.8   0.2    1.4  1  LXG              LXG domain of WXG superfamily
       0.19   10.6   0.3       0.22   10.3   0.3    1.1  1  Spc7             Spc7 kinetochore protein
        0.6   10.2   2.3         62    3.7   0.0    2.9  3  PspB             Phage shock protein B


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   7.4e-06    0.0039      20      82 ..      20      82 ..      13      84 .. 0.64
   2 !   14.8   0.0   4.8e-05     0.025      24      74 ..      42     102 ..      38     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.4e-06
                         DUF948 20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82
                                   +l +++  +d++ +++e++ + +++++ e++  l++ n ++e +++ l++++   +++ dl++
  gi|121637374|ref|YP_977597.1| 20 TLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAK 82
                                   444444455555555555556777777777777777777777777777777777777777665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.8e-05
                         DUF948  24 lkktldeaaatieele..........kqvdpilkevedllakvnelledvneklekvdplt 74 
                                    l+kt+ e+++++ +l+          ++++++l+ ++dl +   +l+e v+  ++++d ++
  gi|121637374|ref|YP_977597.1|  42 LGKTMAELNSSLSQLNstverledglDHLEGTLHSLDDLAKRLIVLVEPVEAIVDRIDYIV 102
                                    4555555555555555444333377777777888888888888888888888888888776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.7   3.8e-08     2e-05      21      91 ..      17      84 ..      13      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.8e-08
                        BLOC1_2 21 dyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91
                                    +k+L++   +a + +++++dv+++l k++ +ln+   +l+++ + ++++e+ +++Le +   LD   k+L
  gi|121637374|ref|YP_977597.1| 17 RMKTLTQAALNADKTVEQVEDVLDGLGKTMAELNS---SLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRL 84
                                   689999999**************************...*******************************98 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5   4.3e-07   0.00023      26      59 ..      44      77 ..      24      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-07
                        UPF0184 26 eEyeainsmLDqinsaLDalEernDdlnskLrEL 59
                                   + ++++ns+L q+ns+++ lE+  D+l++ L+ L
  gi|121637374|ref|YP_977597.1| 44 KTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSL 77
                                   5699***************************987 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.3e-06   0.00067       5      84 ..      25     107 ..      12     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                     Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdanka...irdArrsvkkLeklapqLldklkelkql 81 
                                    a +a++t+++v+++l +l + + +++++ls++n++ve+ ++ ++ +  +   ++d  +    L + ++ ++d++  +  l
  gi|121637374|ref|YP_977597.1|  25 ALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTlhsLDDLAKRLIVLVEPVEAIVDRIDYIVSL 104
                                    56789999999999999999999999999999999988888777554440004444555555667777888888777766 PP

                                    HHH CS
                     Laminin_II  82 eea 84 
                                     e 
  gi|121637374|ref|YP_977597.1| 105 GET 107
                                    665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.7   5.1e-05     0.027      68     138 ..      24      95 ..      12      97 .. 0.42
   2 !   12.1   0.1   0.00029      0.15      28      88 ..      49     113 ..      39     129 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                   Baculo_PEP_C  68 lltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl.....dlgalsqeledaldtveeil 138
                                    ++ n ++++     +++  L++l + +++L+ss+  +nst++ l   l+ l      l+ l++ l ++++ ve+i+
  gi|121637374|ref|YP_977597.1|  24 AALNADKTVE----QVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLegtlhSLDDLAKRLIVLVEPVEAIV 95 
                                    2223333333....44444444444444444444444444444433332221112233555555555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                   Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLt 88 
                                    +n+++ +ql+++++ +e  L++l+  l+s l +l++rl  l++ +++ + ++       +t+ + L 
  gi|121637374|ref|YP_977597.1|  49 LNSSL-SQLNSTVERLEDGLDHLEGTLHS-LDDLAKRLIVLVEPVEAIVDRIDyivslgETVMSPLS 113
                                    34555.66666666666666666666666.5566666665555555555555544444466665555 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.5    0.0018      0.95      20      69 ..      26      64 ..      15      66 .. 0.50
   2 !    9.2   0.1    0.0028       1.5      23      52 ..      57      86 ..      51      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                            CLZ 20 akagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69
                                    +a ++ +++e+ ++ L            +++ae++ss ++L++ +++LE
  gi|121637374|ref|YP_977597.1| 26 LNADKTVEQVEDVLDGLG-----------KTMAELNSSLSQLNSTVERLE 64
                                   344444444444444444...........555555666666666666655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                            CLZ 23 gaeqkeleekverLessLeaLqtrlarLla 52
                                   +++ + le+ +++Le++L +L++  +rL+ 
  gi|121637374|ref|YP_977597.1| 57 NSTVERLEDGLDHLEGTLHSLDDLAKRLIV 86
                                   466789999999999999999999999976 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.29   1.5e+02       1      34 [.      17      50 ..      15      52 .. 0.74
   2 !   14.1   0.4   8.9e-05     0.047       2      43 ..      46      87 ..      31      91 .. 0.75
   3 ?    4.6   0.1     0.079        42       5      47 ..      63     108 ..      63     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.29
                      FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelk 34
                                   r+++l +   + + ++e v++ ++ l k+  el+
  gi|121637374|ref|YP_977597.1| 17 RMKTLTQAALNADKTVEQVEDVLDGLGKTMAELN 50
                                   5666666666777888888888888888888877 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.9e-05
                      FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenVkdllsL 43
                                   + el + ls+l +++e +++ +++l+ +++ l++  k+l+ L
  gi|121637374|ref|YP_977597.1| 46 MAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVL 87
                                   457778888888888888888888888888888888888776 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.079
                      FlaC_arch   5 lEnklsklst...eletvkkeneelsksveelkenVkdllsLYEvV 47 
                                    lE  l+ l+    +l+ + k +  l + ve + +++  ++sL E+V
  gi|121637374|ref|YP_977597.1|  63 LEDGLDHLEGtlhSLDDLAKRLIVLVEPVEAIVDRIDYIVSLGETV 108
                                    5666677776444556666677777888899999999999998888 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.7e-05     0.014      60     121 ..      17      78 ..      11      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                        DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                      + L++   + dk++++++++   + + ++e+++ ls++++ ve +++   +le++l++++
  gi|121637374|ref|YP_977597.1|  17 RMKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLD 78 
                                    56788888889999999999999999999999999999999999999999999999999886 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.7e-05     0.014      57     113 ..       8      65 ..       2      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-05
                         KfrA_N  57 pelPealaeallaalwqaaleeaee..elaaaraelqaaraaleaeraeaearveelea 113
                                    ++ P+++ + + ++l qaal + ++  +++   + l +++a+l + + +++++ve+le+
  gi|121637374|ref|YP_977597.1|   8 SGRPAPVRRRM-KTLTQAALNADKTveQVEDVLDGLGKTMAELNSSLSQLNSTVERLED 65 
                                    578********.********988878899999************************997 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.7   0.00038       0.2      13      60 ..      46      93 ..      14     112 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00038
                        NPV_P10 13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60
                                    +++++ ++ l++ v+++++ l  ++   + Ld++++ L  l + ve+
  gi|121637374|ref|YP_977597.1| 46 MAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVLVEPVEA 93
                                   334444444444444444444444444444444444444444444444 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0006      0.32       7      40 ..      19      52 ..      14      54 .. 0.91
   2 ?    2.9   0.0      0.25   1.3e+02      54      76 ..      54      76 ..      50      84 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0006
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCG CS
                         WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdalqsg 40
                                   + l+qaa +++k+ e++ed+l+ l +++++l+s+
  gi|121637374|ref|YP_977597.1| 19 KTLTQAALNADKTVEQVEDVLDGLGKTMAELNSS 52
                                   5799***************************775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 54 eewkqaaqklvdaLeeisealkq 76
                                    +++ ++++l d+L+ ++ +l++
  gi|121637374|ref|YP_977597.1| 54 SQLNSTVERLEDGLDHLEGTLHS 76
                                   45555555666665555555544 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   3.6e-05     0.019      46     114 ..      24      92 ..      15      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                 CENP-F_leu_zip  46 eaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekE 114
                                     a ++ ++ve++++ ++ l +++ el++ L++l s  e Le  l +   + ++L+ l   l  l+e  E
  gi|121637374|ref|YP_977597.1|  24 AALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVLVEPVE 92 
                                    56688899***********************************************99888877777666 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.6e-05     0.019      32      78 ..      41      87 ..      19     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                      Mce4_CUP1 32 rlGesltdlnevLdelNprlpqlredireladladvYadaapdllda 78
                                    lG+++++ln+ L++lN+ +++l++ + +l+ + +  +d a+ l+  
  gi|121637374|ref|YP_977597.1| 41 GLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVL 87
                                   689******************************99999999988755 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   0.00012     0.065      32     102 ..      28     101 ..      16     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                                    BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHHHHHH CS
                          DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln...kvdetleliletLqkinkRlDsi 102
                                     ++ ++++e+ +d lg+ +++l+   ++++  +++l+   +  +  l+    + + l +++e +++i +R+D i
  gi|121637374|ref|YP_977597.1|  28 ADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHsldDLAKRLIVLVEPVEAIVDRIDYI 101
                                    56667777788887777777777777777777777777777776666544456667777788888888888866 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.024      50     110 ..      15      75 ..       8      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                        DUF3450  50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                                     +++++l++ + ++++  eq+e++++ + +++a+l+ ++++++ + ++l+  l+ +  +L+
  gi|121637374|ref|YP_977597.1|  15 RRRMKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLH 75 
                                    5688899999999999999999999999999999999999999999888877776655554 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.9e-05     0.042      14      77 ..      19      86 ..      13     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                           RPW8 14 gellkaileakkksldfksilkrLestleritPvvke....ieklnkeldrpreeieeLkklLekaek 77
                                   + l +a l+a k++ +++  l+ L +t+ +++ ++ +    +e+l++ ld  +  +++L +l ++   
  gi|121637374|ref|YP_977597.1| 19 KTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQlnstVERLEDGLDHLEGTLHSLDDLAKRLIV 86
                                   678999999********************999998762222555666666666666666555555444 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.8e-05     0.041       2      65 ..      18      81 ..      15     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-05
                  Tropomyosin_1  2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakeka 65
                                   +++L   a +a + +e++e+ +  l ++  e ++ +++L+  ++ le+ +++le +l+   + a
  gi|121637374|ref|YP_977597.1| 18 MKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLA 81
                                   6666667777777778888888888888888888888888888888888888888887766655 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3    0.0003      0.16     111     154 ..      15      58 ..       8      66 .. 0.62
   2 ?    1.2   0.0      0.42   2.2e+02     108     133 ..      68      93 ..      56     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                           DegS 111 errLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkq 154
                                     rr+k+l + +  A+k v+qv+ vl+ L + + +++++l++l++
  gi|121637374|ref|YP_977597.1|  15 RRRMKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNS 58 
                                    45666666666666666666666666666666666666665543 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                           DegS 108 delerrLkklketierAeklvsqvgv 133
                                    d+le +L++l++ ++r   lv+ v+ 
  gi|121637374|ref|YP_977597.1|  68 DHLEGTLHSLDDLAKRLIVLVEPVEA 93 
                                    56666666666666665555555444 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00043      0.23      56      93 ..      27      65 ..      13      88 .. 0.65
   2 ?    1.2   0.0      0.73   3.8e+02      73     114 ..      66     106 ..      61     120 .. 0.71
   3 ?    0.3   0.0       1.4   7.4e+02      70      98 ..     104     134 ..      76     136 .] 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                                   XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX- CS
                           COG5 56 nhleLlehlskskslss.vlselksslesLsasyerlks 93
                                   n+++  e++++ +   + ++ el+ssl++L++ +erl+ 
  gi|121637374|ref|YP_977597.1| 27 NADKTVEQVEDVLDGLGkTMAELNSSLSQLNSTVERLED 65
                                   566666777777766666777777777777777777765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.73
                                    XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                           COG5  73 vlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                     l+ l++ l+sL    +rl   ++ep e +  +   + +l +
  gi|121637374|ref|YP_977597.1|  66 GLDHLEGTLHSLDDLAKRLIV-LVEPVEAIVDRIDYIVSLGE 106
                                    577888888888888888864.55777777666665555555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                    XXX.XXXXXXXXXXXXXXXXXXXX-.TTHHH CS
                           COG5  70 lss.vlselksslesLsasyerlks.kvlep 98 
                                    l + v+s+l    +++   ++rl++  v+ep
  gi|121637374|ref|YP_977597.1| 104 LGEtVMSPLSVTEHAVRGVLDRLRNrTVHEP 134
                                    4444555555555666666666664235555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         5   2.6e+03      68      85 ..      14      31 ..      12      36 .. 0.69
   2 ?   12.7   0.1   0.00024      0.13      10      69 ..      34      88 ..      21     101 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5
                Snapin_Pallidin 68 ikkrmsslnerlqklkkR 85
                                   +++rm++l +   ++ k 
  gi|121637374|ref|YP_977597.1| 14 VRRRMKTLTQAALNADKT 31
                                   688888888777666655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                Snapin_Pallidin 10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnik 69
                                    +e +ld l ++ +el  s ++L+++++rl + L++le + +      l+  ak+L+ + 
  gi|121637374|ref|YP_977597.1| 34 QVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLH-----SLDDLAKRLIVLV 88
                                   334445555555555555555555555555555555444444.....4444455554444 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00021      0.11      59     106 ..      18      65 ..      15      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                         Nsp1_C  59 IskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleells 106
                                    ++ L +++l+a+++ +++++ L+ + +   eL+s L ++ + +e+l  
  gi|121637374|ref|YP_977597.1|  18 MKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLED 65 
                                    57899************************************9999874 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0004      0.21      15      50 ..      42      77 ..      15      94 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                           SlyX 15 qedtieeLndvvaeqqqqidrlqrqlrllaerlkel 50
                                   + +t+ eLn  + + + +++rl+  l++l+  l +l
  gi|121637374|ref|YP_977597.1| 42 LGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSL 77
                                   335555666666666666666666666666555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00017     0.087       3      52 ..      33      82 ..      14      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                        DUF4795  3 vnsaellkklqeaieklqeelekleekvkelekrledkekklealkkqie 52
                                    +++  l+ l +++ +l  +l++l+++v++le+ l  +e  l +l + ++
  gi|121637374|ref|YP_977597.1| 33 EQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAK 82
                                   45566677777888888888877777777777777777777666666655 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.018       9.6       2      21 ..      43      62 ..      29      63 .. 0.62
   2 ?    9.0   0.2    0.0022       1.2       2      30 ..      43      71 ..      42      77 .. 0.80
   3 ?    7.4   0.1    0.0072       3.8       3      30 ..      58      85 ..      56      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                      DASH_Dam1  2 epafaeLaDsletLdknled 21
                                    +++aeL+ sl++L++ +e+
  gi|121637374|ref|YP_977597.1| 43 GKTMAELNSSLSQLNSTVER 62
                                   34555555555555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                      DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLs 30
                                    +++aeL+ sl++L++ +e+L++  ++L+
  gi|121637374|ref|YP_977597.1| 43 GKTMAELNSSLSQLNSTVERLEDGLDHLE 71
                                   57899999999999999999988766665 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0072
                      DASH_Dam1  3 pafaeLaDsletLdknledLqqihesLs 30
                                    + ++L+D l+ L+  l+ L+++ ++L 
  gi|121637374|ref|YP_977597.1| 58 STVERLEDGLDHLEGTLHSLDDLAKRLI 85
                                   56799******************99986 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00049      0.26      31      70 ..      42      81 ..      30      84 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                     TMF_DNA_bd 31 lnntikkLrkknkelekeikelkkkleklekeleeleerl 70
                                   l +t+ +L++ +++l++++++l++ l+ le  l +l +++
  gi|121637374|ref|YP_977597.1| 42 LGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLA 81
                                   3455555666666666666666666666655555555555 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019       0.1      81     137 ..      28      84 ..      12     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                    HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHH CS
                      MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveav 137
                                    A+++ ++ +++ + + + ++e n+s++ l++t++r e g++  e t ++l +++++ 
  gi|121637374|ref|YP_977597.1|  28 ADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRL 84 
                                    344444444444445577788899999999999999999999999999998887764 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015     0.081     238     299 ..      33      94 ..      14     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHH CS
                          APG17 238 aeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkae 299
                                    +++edV++ l ++++e++++ ++l+++ e++e  l+ l  +l+ l+++ k+l   ++ ++a+
  gi|121637374|ref|YP_977597.1|  33 EQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVLVEPVEAI 94 
                                    68899999999999999999999999999999999999999999998888887777655554 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.14      21      65 ..      33      77 ..      17      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXX CS
                         DivIVA 21 deVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetL 65
                                   ++V++ Ld + k++ +l +  ++l+++v++le+ l++ +    +L
  gi|121637374|ref|YP_977597.1| 33 EQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSL 77
                                   79*********************************9998776665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.12     332     406 ..      18      92 ..       7     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         DUF812 332 leelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalve 406
                                    +++l +   ++++++e++e+ ++ l +++ +++++l +++++ e+le+ ++  + tl+ l+d  + +  L + ve
  gi|121637374|ref|YP_977597.1|  18 MKTLTQAALNADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLDDLAKRLIVLVEPVE 92 
                                    455555555566666666666666666666666666666666666666666666666666555555555555555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00045      0.24      78     122 ..      34      78 ..      17      85 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                        DUF5082  78 syqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                    +++ + d l ++++++++  ++L ++++ ++  ld+l+  l sl+
  gi|121637374|ref|YP_977597.1|  34 QVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSLD 78 
                                    555555555555555555555555555555555555555555543 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2    0.0014      0.75     124     161 ..      27      64 ..      11      67 .. 0.80
   2 ?    1.2   0.0       0.7   3.7e+02     129     160 ..      67      98 ..      63     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                         CHDCT2 124 vlekvLnqleelLsdmkadvsrlpatlsrlrpvaeRLq 161
                                       k ++q+e++L+ + + ++ l ++ls+l++  eRL+
  gi|121637374|ref|YP_977597.1|  27 NADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLE 64 
                                    44588899999999999999999999999999999985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.7
                         CHDCT2 129 LnqleelLsdmkadvsrlpatlsrlrpvaeRL 160
                                    L++le  L  +    +rl+  +  ++++ +R+
  gi|121637374|ref|YP_977597.1|  67 LDHLEGTLHSLDDLAKRLIVLVEPVEAIVDRI 98 
                                    78888888888888899999988888888887 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00055      0.29     147     191 ..      28      72 ..      14      79 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00055
                            LXG 147 lqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLee 191
                                    ++k  ++v++++++l +  +e++s+l++l+s+++ l+ +++ Le+
  gi|121637374|ref|YP_977597.1|  28 ADKTVEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEG 72 
                                    344445555555555555556666666666666655555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00042      0.22     148     193 ..      32      77 ..      14      98 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                           Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeel 193
                                    +e++e+  + L k ++el++ l +l++  ++le+ l++l+   ++l
  gi|121637374|ref|YP_977597.1|  32 VEQVEDVLDGLGKTMAELNSSLSQLNSTVERLEDGLDHLEGTLHSL 77 
                                    4444444444444444444444444444444444444443333333 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.12        66      41      65 ..      16      40 ..      11      45 .. 0.92
   2 ?    3.7   0.0      0.12        62      40      63 ..      50      73 ..      42      76 .. 0.71
   3 ?    2.4   0.1       0.3   1.6e+02      42      66 ..      73      97 ..      67     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                           PspB 41 krLeellekAekleeRietLEriLd 65
                                   +r+++l++ A + ++ +e +E++Ld
  gi|121637374|ref|YP_977597.1| 16 RRMKTLTQAALNADKTVEQVEDVLD 40
                                   78999*******************9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                           PspB 40 ekrLeellekAekleeRietLEri 63
                                   +++L++l  + e+le+ ++ LE  
  gi|121637374|ref|YP_977597.1| 50 NSSLSQLNSTVERLEDGLDHLEGT 73
                                   456788888888888888888765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.3
                           PspB 42 rLeellekAekleeRietLEriLda 66
                                   +L++l + A++l   +e +E+i+d 
  gi|121637374|ref|YP_977597.1| 73 TLHSLDDLAKRLIVLVEPVEAIVDR 97
                                   6899999999999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      914  (0.0509789); expected 358.6 (0.02)
Passed Vit filter:                       208  (0.0116013); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 876.33
//
Query:       gi|121637375|ref|YP_977598.1|  [L=247]
Description: 6-phosphogluconolactonase devB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-75  252.0   0.0    6.6e-75  251.8   0.0    1.0  1  Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phospho


Domain annotation for each model (and alignments):
>> Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.8   0.0   3.7e-79   6.6e-75       2     225 .]      10     235 ..       9     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 251.8 bits;  conditional E-value: 3.7e-79
                                    SHHHHHHHHHHHHHHHHHHHHHHHS-EEEEE--SHCHHHHHHHHHCSG.GGGGS-GGGEEEEESEEESS-TTSTT-HHHH CS
                Glucosamine_iso   2 dkeelaealaarivealeealaergraslalsGGstpkalyealaeeeeaaaaldwskvhvflgDERfVpaddpdsNakl 81 
                                    d++ l++a+ +r+v a+ +a+a+rg+a ++l+GG  + al++ l++++   ++++wskvh+f+gDER+Vp+dd+++N k+
  gi|121637375|ref|YP_977598.1|  10 DSDILVAAAGKRLVGAIGAAVAARGQALIVLTGGGNGIALLRYLSAQA---QQIEWSKVHLFWGDERYVPEDDDERNLKQ 86 
                                    778899***************************************755...37*************************** PP

                                    HHHHTGGGS---GGGEE-S-TTSST...HHHHHHHHHHHHHHHHCC..SSSSSESEEEE---TTS-BTTB-TTCHHHHCS CS
                Glucosamine_iso  82 areallskvkipeanvhpikesaae...apeaaaaayeeelkella..kelpvfDlvlLGmGpDGHtaSLFPgspeleet 156
                                    ar+all++v+ip+++vhp+ +s+ +   +++aaa aye+ l++ +a  ++ p+fD++lLGmGp+GH++SLFP+sp++ e+
  gi|121637375|ref|YP_977598.1|  87 ARRALLNHVDIPSNQVHPMAASDGDfggDLDAAALAYEQVLAASAApgDPAPNFDVHLLGMGPEGHINSLFPHSPAVLES 166
                                    *******************97666688888************99989999****************************** PP

                                    SSSEEEESSBSTSSS-EEEE-HHHHTTCSEEEEEEESHHHHHHHHHHHTT..TTTSGGGGH--SSEEEE CS
                Glucosamine_iso 157 drlvvavedspkpppeRitlTlpvlnsarevlflvaGeeKaealeevlsgedpeelPaalvegqgellw 225
                                    +r+vvav+dspkppp+RitlTlp+++++rev++lv+G +Ka+a+++++ g+dp ++Paa + g++++lw
  gi|121637375|ref|YP_977598.1| 167 TRMVVAVDDSPKPPPRRITLTLPAIQRSREVWLLVSGPGKADAVAAAIGGADPVSVPAAGAVGRQNTLW 235
                                    *************************************************************98899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1984.60
//
Query:       gi|121637376|ref|YP_977599.1|  [L=303]
Description: OXPP cycle protein opcA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-76  255.3   0.4    7.3e-76  255.0   0.4    1.1  1  OpcA_G6PD_assem  Glucose-6-phosphate dehydrogenase subunit


Domain annotation for each model (and alignments):
>> OpcA_G6PD_assem  Glucose-6-phosphate dehydrogenase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.0   0.4   4.1e-80   7.3e-76       1     254 []      52     294 ..      52     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 255.0 bits;  conditional E-value: 4.1e-80
                OpcA_G6PD_assem   1 aneasrehPcRvivlvtddseeedsrldaevraggdagcgEvivlrlygealrhlasvvlpLllpDlpvvvwWpasappn 80 
                                    an+as+ehP+R+iv ++ d  ++ +rlda++r+g+dag+gE +vlrl+g ++ h++svv+p llpD+pvv+wWp+ ap++
  gi|121637376|ref|YP_977599.1|  52 ANDASHEHPSRIIVTMRGDPYADRPRLDAQLRVGADAGAGEFVVLRLSGPLAGHADSVVIPFLLPDIPVVAWWPDIAPAV 131
                                    799************999999999******************************************************** PP

                OpcA_G6PD_assem  81 paedllgrlaeladrrItDslssedpeaalerlrssyapgdsDLaWtRltpWRellAsafDqerrppleeitsvtiegek 160
                                    pa+d lg+la    rrItD++++ dp +a++++ + y++gd+DLaW+R+t WR+ll sa+Dq   pp+e+i+s+ ++g k
  gi|121637376|ref|YP_977599.1| 132 PAQDALGKLA---IRRITDATNAIDPLSAIKSRLAGYGAGDTDLAWSRITYWRALLTSAVDQ---PPHEPIESALVSGLK 205
                                    **********...*************************************************...*************** PP

                OpcA_G6PD_assem 161 eppsalllagWLasrLgwpvtreetegdkgvtsvtleredgdeielel.pdaetatisrpgqieqvvalprrsledllae 239
                                     +p+ + lagWLasr + pv+r       g  +v+l r++++ i l++ +++ tat++r+g+++  v+l rr ++++lae
  gi|121637376|ref|YP_977599.1| 206 TEPALDVLAGWLASRIEGPVRRAV-----GELKVELVRNSET-IVLSRpQEGITATLTRTGKPDALVPLARRVTGECLAE 279
                                    ********************7766.....899**********.*****45577899************************ PP

                OpcA_G6PD_assem 240 eLrrldpdelYeeaL 254
                                     Lrrldpde+Y +aL
  gi|121637376|ref|YP_977599.1| 280 DLRRLDPDEIYCAAL 294
                                    ***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2293.26
//
Query:       gi|121637377|ref|YP_977600.1|  [L=514]
Description: glucose-6-phosphate 1-dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.4e-109  364.2   0.0   5.3e-109  363.9   0.0    1.1  1  G6PD_C    Glucose-6-phosphate dehydrogenase, C-terminal domai
    5.1e-63  212.9   0.0    7.3e-63  212.4   0.0    1.2  1  G6PD_N    Glucose-6-phosphate dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> G6PD_C  Glucose-6-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.9   0.0  5.9e-113  5.3e-109       1     290 []     217     512 ..     217     512 .. 0.97

  Alignments for each domain:
  == domain 1  score: 363.9 bits;  conditional E-value: 5.9e-113
                                    HHHHHS-STTSTTSSTTTEEEEEEEEEESS--TTTHHHHTTTHHHHHTTTTHHHHHHHHHH----SSSSHHHHHHHHHHH CS
                         G6PD_C   1 lvlRfaNalfeplwnrnyidhvqitvketlgvegrggYydeaGalrDvvqnHllqllalvamepPasldaedirdekvkv 80 
                                    l+lRfaN+lf+p+wn +y+dhvqit++e++g++gr+gYyd +Ga rDv+qnHl+qllal+ame+P+s+++ ++++ek+kv
  gi|121637377|ref|YP_977600.1| 217 LALRFANQLFDPIWNAHYVDHVQITMAEDIGLGGRAGYYDGIGAARDVIQNHLMQLLALTAMEEPVSFHPAALQAEKIKV 296
                                    68****************************************************************************** PP

                                    HTTB----G...GG.EEEEEE.....E--TGS-STTSTTS-TT----SEEEEEEEB-STTTTT-EEEEEEESSBSS-EEE CS
                         G6PD_C  81 LkslrplkleevekkvvrGqYaagavkgkevkgYreeegvakdSkteTfvalkleidnerwagVPfylrtGKrLnekkte 160
                                    L++ r  ++  +++++ rGqYaag++ g++v g ++eeg a+dS+teTf+a++le+d++rwagVPfylrtGKrL +++te
  gi|121637377|ref|YP_977600.1| 297 LSATRLAEP--LDQTTSRGQYAAGWQGGEKVVGLLDEEGFAEDSTTETFAAITLEVDTRRWAGVPFYLRTGKRLGRRVTE 374
                                    ******998..99999**************************************************************** PP

                                    EEEEE---SS-SS---......--EEEEEEESS-EEEEEEEEE-SSSE.....EEEEEEHHHHTT..---HHHHHHHHHH CS
                         G6PD_C 161 iriqfkkvpsdlfkkke.....rneLviriqpdeaislklnakkpgleleleeveldlsykerfk..lpeaYerLlldvl 233
                                    i+++f+++p+  f+ ++     +n +vir+qpde+++l++ +k+pg+++e+++v++d+sy ++f   +peaYerL+ldvl
  gi|121637377|ref|YP_977600.1| 375 IALVFRRAPHLPFDATMtdelgTNAMVIRVQPDEGVTLRFGSKVPGTAMEVRDVNMDFSYGSAFAedSPEAYERLILDVL 454
                                    *************443457899****************************************99999************* PP

                                    HT-GTTSB-HHHHHHHHHHHHHHHHHHHH.---EEEETTSSS-HHHHHHHHHHTX.X. CS
                         G6PD_C 234 kgdqtlFvrsdeveaaWkivdpileawee.eklekYeagsrgPeeadellekdgrkwr 290
                                     g+ +lF  + eve aW+i+dp le+w++  ++  Yeag++gPe++ e+l+++gr+wr
  gi|121637377|ref|YP_977600.1| 455 LGEPSLFPVNAEVELAWEILDPALEHWAAhGTPDAYEAGTWGPESSLEMLRRTGREWR 512
                                    ***************************889779************************6 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.0   8.1e-67   7.3e-63       1     177 []      32     215 ..      32     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 8.1e-67
                         G6PD_N   1 vifGasGdLakrkllPaLyelaregllpeevrivgvarsklsdeefrekvkealkkekekeeldeekleeflkrleyvsg 80 
                                    vifG++GdLa++k++Pa+y+la++gllp+++++vg+ar+++s+++f + v +a+ +e+ ++ +++++++++++ +++v g
  gi|121637377|ref|YP_977600.1|  32 VIFGVTGDLARKKVMPAVYDLANRGLLPPTFSLVGFARRDWSTQDFGQVVYNAV-QEHCRTPFRQQNWDRLAEGFRFVPG 110
                                    8****************************************************9.5777889****************** PP

                         G6PD_N  81 dleeeeeyekLkekleelea......nrlfYlavppslfeevaeklkkaglake..eewkrvvvEKPfGkdlesarelne 152
                                    ++++++++++L+e+le+l+a      n++fYla+pp+ f  v+e+l+k+gla+   ++w+rvv+EKPfG+dl+sareln+
  gi|121637377|ref|YP_977600.1| 111 TFDDDDAFAQLAETLEKLDAergtggNHAFYLAIPPKSFPVVCEQLHKSGLARPqgDRWSRVVIEKPFGHDLASARELNK 190
                                    ****************9883455566*************************9888899********************** PP

                         G6PD_N 153 elkkvfkeeqiyrIDhYLGketvqN 177
                                    ++++vf ee ++rIDhYLGketvqN
  gi|121637377|ref|YP_977600.1| 191 AVNAVFPEEAVFRIDHYLGKETVQN 215
                                    ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.81
# Mc/sec: 1915.63
//
Query:       gi|121637378|ref|YP_977601.1|  [L=373]
Description: transaldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-86  287.7   0.0    1.1e-85  287.5   0.0    1.0  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase
  ------ inclusion threshold ------
      0.065   12.6   0.0        0.8    9.0   0.0    2.2  2  Bromo_MP  Bromovirus movement protein
       0.18   11.0   0.0       0.25   10.5   0.0    1.1  1  Asp1      Accessory Sec system protein Asp1


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.5   0.0   1.8e-89   1.1e-85       1     286 [.      18     363 ..      18     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 287.5 bits;  conditional E-value: 1.8e-89
                                    EEEE---HHHHH.....HHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH......................... CS
                        TAL_FSA   1 lvlDtadrelik.....klleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdll.. 73 
                                    ++lD ++r++++     +l+++k + gvTtNPs+++ka+++ + yd++i+e++++g +v++ +++++++d++ a+d+l  
  gi|121637378|ref|YP_977601.1|  18 VWLDDLSRDRLRsgnlqELIDTKSVVGVTTNPSIFQKALSEGHTYDAQIAELAARGADVDATIRTVTTDDVRSACDVLvp 97 
                                    7***************************************999************************************* PP

                                    .......H-S-EEEE-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHH CS
                        TAL_FSA  74 ......gadgrvslEVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqala 147
                                          g+dgrvs+EVd+rl+++te+ti++A +l+++++r+n++IKiPat++G++Ai++  +eGi+vnvTliFs++++++
  gi|121637378|ref|YP_977601.1|  98 qwedsdGVDGRVSIEVDPRLAHETEKTIQQAIELWKIVDRPNLFIKIPATKAGLPAISAVLAEGISVNVTLIFSVQRYRE 177
                                    ******************************************************************************** PP

                                    HHHH.................T-SEEEEBHHHHHTTT..................S-HHHHHHHHHHHHHHH.T...... CS
                        TAL_FSA 148 aaea.................gasviSpFvgRiddll.kkleek.....dklkgkddgvalvkeiynyykkl.g...... 197
                                    +++a                  +sv+S+Fv+R+d+++ k+l++       +l+g+ +gva+++ +y++y+++ +      
  gi|121637378|ref|YP_977601.1| 178 VMDAyltgmekarqaghslskIHSVASFFVSRVDTEIdKRLDRIgsrqaLELRGQ-AGVANARLAYAAYREVfEdsdryr 256
                                    *************999888755***************9999998999999999*9.****************889***** PP

                                    .............-.S-EEEEBS--SHHHHHHHHT-SEE.EE-HHHHHHHT--HHH........................ CS
                        TAL_FSA 198 .............y.sTkvmaasfrnveeveelagcdtv.Tippkllealakhgkts.eklee..eeieklleklfrlgi 259
                                                 + sT+v++++++++ +v+el++++tv T+p+k+++a+a+hg  + ++++   +++++++++l ++gi
  gi|121637378|ref|YP_977601.1| 257 slkvdgarvqrplWaSTGVKNPDYSDTLYVTELVAPHTVnTMPEKTIDAVADHGVIQgDTVTGtaSDAQAVFDQLGAIGI 336
                                    *************99*****************************************98999888899999********** PP

                                    ..........HHHHHHHHHHHHHHHH- CS
                        TAL_FSA 260 nedavaeelldegikkFakdlekllas 286
                                    ++ +v++ l++eg++kF++++++ll++
  gi|121637378|ref|YP_977601.1| 337 DLTDVFAVLEEEGVRKFEASWNELLQE 363
                                    ************************986 PP

>> Bromo_MP  Bromovirus movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00013       0.8     128     167 ..      63     102 ..      29     128 .. 0.83
   2 ?    1.2   0.0     0.033     2e+02     210     265 ..     258     310 ..     252     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                       Bromo_MP 128 rsllakdvakGldlklvvsavasvnanakvGvlyPiweek 167
                                     + +a+ +a+G d++ ++ +v++ +++++  vl P we+ 
  gi|121637378|ref|YP_977601.1|  63 DAQIAELAARGADVDATIRTVTTDDVRSACDVLVPQWEDS 102
                                    3457999*******************************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.033
                       Bromo_MP 210 ldvaaksdekPvlleervklldkaktlfipeGvdvpsttvteiePekdidaGsskg 265
                                    l v     ++P+  +  vk  d   tl++ e v     tv+ + Pek ida +  g
  gi|121637378|ref|YP_977601.1| 258 LKVDGARVQRPLWASTGVKNPDYSDTLYVTELVAP--HTVNTM-PEKTIDAVADHG 310
                                    56666666788889999999999999**9998876..899988.9******88875 PP

>> Asp1  Accessory Sec system protein Asp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.2e-05      0.25     434     506 ..     133     202 ..     106     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.2e-05
                           Asp1 434 dlseqpdlytqiaGisaGipqinlvasdyvehlknGyildsiselekaadyyleglknwnraliysiekikdn 506
                                     + + p+l+ +i    aG+p i  v+++ +    n  ++ s++     +d yl g++   +a  +s+ ki++ 
  gi|121637378|ref|YP_977601.1| 133 KIVDRPNLFIKIPATKAGLPAISAVLAEGIS--VNVTLIFSVQRYREVMDAYLTGMEKARQA-GHSLSKIHSV 202
                                    46789***********************986..5889999****************998877.5899999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2502.55
//
Query:       gi|121637379|ref|YP_977602.1|  [L=700]
Description: transketolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-144  481.0   0.0     2e-144  480.7   0.0    1.1  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    1.6e-44  151.7   0.1    1.1e-43  148.9   0.0    2.5  3  Transket_pyr     Transketolase, pyrimidine binding domain
    1.2e-12   47.8   0.0    3.2e-12   46.4   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.16   11.4   0.0        0.3   10.5   0.0    1.3  1  XFP_C            XFP C-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.7   0.0  4.4e-148    2e-144       2     334 .]      23     358 ..      22     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 480.7 bits;  conditional E-value: 4.4e-148
                                    HHHHHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS-- CS
                Transketolase_N   2 dkkavnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydls 81 
                                    d++av++iRvLa Dav+k ++GhPG++++la++a++lf+++++h+P+d++w++RDRfvLs+Gh+sl+lY++l+L G++l+
  gi|121637379|ref|YP_977602.1|  23 DSAAVDTIRVLAADAVQKVGNGHPGTAMSLAPLAYTLFQRTMRHDPSDTHWLGRDRFVLSAGHSSLTLYIQLYLGGFGLE 102
                                    7899**************************************************************************** PP

                                    HHHHTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHH...HHHHHHHH-BTTB-S----EEEEEEHHHHHS CS
                Transketolase_N  82 ledlksfrqlgsktpGhPelghtagvevttGPLGqGianavglala...ektlaatynkpgfdivdhytyvilgDgclme 158
                                    l+d++s+r++gsktpGhPe++ht+gve+ttGPLGqG+a+avg+a+a   e+ l++ +++pg++ +dhy+yvi++Dg+++e
  gi|121637379|ref|YP_977602.1| 103 LSDIESLRTWGSKTPGHPEFRHTPGVEITTGPLGQGLASAVGMAMAsryERGLFDPDAEPGASPFDHYIYVIASDGDIEE 182
                                    *******************************************9873336789*************************** PP

                                    HHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGGT--S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EE CS
                Transketolase_N 159 GvsseasslagtlkLgkLivlyDdnkisidGeteisftedvakrfeaygWhvievedgedveaikaaieeakaekdkPsl 238
                                    Gv+seassla++++Lg+Liv+yD n+isi+ +t+i+++ed+a+r++aygWhv+eve+ge+v  i++ai++a+a++d+Ps+
  gi|121637379|ref|YP_977602.1| 183 GVTSEASSLAAVQQLGNLIVFYDRNQISIEDDTNIALCEDTAARYRAYGWHVQEVEGGENVVGIEEAIANAQAVTDRPSF 262
                                    ******************************************************************************** PP

                                    EEEE--TTTTSTTTTTSGGGTSS---HHHHHHHHHHTTS-TT-TS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                Transketolase_N 239 iklrtviGygspakagtedvhGapLgedevaalkkklGfdpeksfevpeevydaykekvaegakaeeeWeekfaaykkka 318
                                    i+lrtviGy++p+  +t ++hGa+Lg+devaa+kk +Gfdp+k+f+v+e+v ++++  va+g++a+e+W+ +f+a+++++
  gi|121637379|ref|YP_977602.1| 263 IALRTVIGYPAPNLMDTGKAHGAALGDDEVAAVKKIVGFDPDKTFQVREDVLTHTRGLVARGKQAHERWQLEFDAWARRE 342
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHTT--- CS
                Transketolase_N 319 peeaaelerrlsgelP 334
                                    pe++a l+r l+++lP
  gi|121637379|ref|YP_977602.1| 343 PERKALLDRLLAQKLP 358
                                    **************99 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.72   3.2e+03      23      46 ..     173     196 ..     169     217 .. 0.82
   2 !  148.9   0.0   2.5e-47   1.1e-43       2     175 ..     374     555 ..     373     557 .. 0.98
   3 ?   -2.8   0.1      0.95   4.2e+03      50      71 ..     675     696 ..     645     698 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.72
                                    EEEEESSTHHHHTTCHCCHHEGGT CS
                   Transket_pyr  23 vvligaDvaggtfsvrkgllhdqg 46 
                                    v++++ D+++g+ s+ ++l   q+
  gi|121637379|ref|YP_977602.1| 173 VIASDGDIEEGVTSEASSLAAVQQ 196
                                    899999999999999999888876 PP

  == domain 2  score: 148.9 bits;  conditional E-value: 2.5e-47
                                    EEEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT............TEGEEE--S-HHHHHHHHHHHHH CS
                   Transket_pyr   2 kiawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg............egrvidsgisEqavlgfavGaal 69 
                                    ++a+r+a++ +l++l+ + pe+++++aD+ag++++++kg   + +             gr +++g++E+a+ ++  G+ l
  gi|121637379|ref|YP_977602.1| 374 ALATRAASGAVLSALGPKLPELWGGSADLAGSNNTTIKGADSFGPpsistkeytahwYGRTLHFGVREHAMGAILSGIVL 453
                                    689***************************************999*********************************** PP

                                    HCTTEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHH CS
                   Transket_pyr  70 agpllviveaqFgdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpa 148
                                    +gp ++ ++++F++F++    y+++a+r ++a++ + ++ v+t+++ig+gedGp+hq++e+++ lr+ip l+vvrP+d++
  gi|121637379|ref|YP_977602.1| 454 HGP-TRAYGGTFLQFSD----YMRPAVR-LAALMDIDTIyVWTHDSIGLGEDGPTHQPIEHLSALRAIPRLSVVRPADAN 527
                                    **9.*************....*******.*************************************************** PP

                                    HHHHHHHHHHHS.SS.SEEEEEE-SSEE CS
                   Transket_pyr 149 etkhllrrairr.edrkPvvlrlpksll 175
                                    et+ ++r+ ++r ++++Pv l+l+++ +
  gi|121637379|ref|YP_977602.1| 528 ETAYAWRTILARrNGSGPVGLILTRQGV 555
                                    ***********99************976 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.95
                                    EEE--S-HHHHHHHHHHHHHHC CS
                   Transket_pyr  50 vidsgisEqavlgfavGaalag 71 
                                     +++  +E+++++ av+aa++ 
  gi|121637379|ref|YP_977602.1| 675 DHKTLFREYGFTAEAVAAAAER 696
                                    5677889999999999999876 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   7.2e-16   3.2e-12       8     124 .]     583     690 ..     578     690 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 7.2e-16
                                    TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHC CS
                Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaee 87 
                                    e++dv+l+a+Gs+v+ a++A   L+++ i a+Vv++++++ +  +  +     ++  v+    + r+++++ va+++ + 
  gi|121637379|ref|YP_977602.1| 583 EEPDVILIATGSEVQLAVAAQTLLADNDILARVVSMPCLEWFEAQPYE-----YRDAVLPPTVSARVAVEAGVAQCWHQ- 656
                                    789********************************************9.....**************************. PP

                                    CCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
                Transketolase_C  88 afdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                        l +    ++  +  +e++  ++l +++g++ae++
  gi|121637379|ref|YP_977602.1| 657 ----LVGDTGEIVSIEHyGESADHKTLFREYGFTAEAV 690
                                    ....55555555555555*****************986 PP

>> XFP_C  XFP C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.7e-05       0.3      12      60 ..     562     609 ..     556     627 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.7e-05
                          XFP_C  12 eAeehckkGasiwewastdegeepdvvlagiGdeptlEvlaAvellree 60 
                                    +Ae  ++ G    ++ + + geepdv+l++ G+e+ l ++aA +ll ++
  gi|121637379|ref|YP_977602.1| 562 DAEGVARGGYVLSDAGGLQPGEEPDVILIATGSEVQL-AVAAQTLLADN 609
                                    55555555666666666899**************988.78888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 5194.04
//
Query:       gi|121637380|ref|YP_977603.1|  [L=1399]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-32  111.8  15.2    1.4e-32  111.8  15.2    1.7  2  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8  15.2   7.8e-37   1.4e-32       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -3.2   0.1      0.63   1.1e+04      17      37 ..     444     464 ..     440     465 .. 0.82

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 7.8e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms v+vaPe++aaaa d+a+igs++  an+aaa++tt+vlaa+aDeVSaaiA+lf++ha+eyqa+s+q+aafh++f+q+l+a
  gi|121637380|ref|YP_977603.1|  1 MSLVIVAPETVAAAALDVARIGSSIGVANSAAAGSTTSVLAAGADEVSAAIATLFGSHAREYQAISTQVAAFHDRFAQTLSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a gsY +aEa+
  gi|121637380|ref|YP_977603.1| 83 AVGSYVSAEAT 93
                                   *********95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.63
                                    HHHHHHHHHHHHHHHHHHHHH CS
                             PE  17 dlagigsalsaanaaaaaptt 37 
                                       g gs++ a  aa a+pt+
  gi|121637380|ref|YP_977603.1| 444 GTGGAGSTIGAHGAAGASPTS 464
                                    56678999***9999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.57u 0.34s 00:00:01.91 Elapsed: 00:00:00.62
# Mc/sec: 6822.59
//
Query:       gi|121637381|ref|YP_977604.1|  [L=308]
Description: protoheme IX farnesyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-58  197.2  31.6    4.4e-58  196.5  31.6    1.3  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.5  31.6   2.5e-62   4.4e-58       1     250 [.      35     284 ..      35     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 196.5 bits;  conditional E-value: 2.5e-62
                           UbiA   1 llipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                    ll++a+ +++la +g +++ll+l +l+g+++aa++an+lN+++D++iD+ m+rt++RPl++ ++ +++al++++ l +++
  gi|121637381|ref|YP_977604.1|  35 LLVTAIPAMLLADRGAIHPLLMLNTLVGGMMAATGANTLNCVADADIDKVMKRTARRPLAREAVPTRNALALGLTLTVIS 114
                                    589***************************************************************************** PP

                           UbiA  81 llllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwai 159
                                    +++l+  +n+l+ +l+l+++++y +vYt l+lKrrt ++ v+gg+a+++p+++gw a+tg++ ++al++++++f++t ++
  gi|121637381|ref|YP_977604.1| 115 FFWLWCATNLLAGVLALVTVAFYvFVYT-LWLKRRTSQNVVWGGAAGCMPVMIGWSAITGTIAWPALAMFAIIFFWTPPH 193
                                    ****************************.9************************************************** PP

                           UbiA 160 alandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrda 239
                                     +a ++r +++++ ag+++lp+v+ ++ +   ++l++++l +a +l+l++++++ly ++al++++++l +a++l++  +a
  gi|121637381|ref|YP_977604.1| 194 TWALAMRYKQDYQVAGVPMLPAVATERQVTK-QILIYTWLTVAATLVLALATSWLYGAVALVAGGWFLTMAHQLYAGVRA 272
                                    ************************6555555.366666666666889****************************99999 PP

                           UbiA 240 kkaakff.lfls 250
                                     ++ + + lfl+
  gi|121637381|ref|YP_977604.1| 273 GEPVRPLrLFLQ 284
                                    888887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2140.67
//
Query:       gi|121637382|ref|YP_977605.1|  [L=740]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-33  113.8  15.2    6.1e-33  113.0  15.2    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0  15.2   3.4e-37   6.1e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.4e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms v+vaPe++aaaa d+a+igs++  an+aaa++tt+vlaa+aDeVSaaiA+lf++ha+eyqa+s+q+aafh++f+q+l+a
  gi|121637382|ref|YP_977605.1|  1 MSLVIVAPETVAAAALDVARIGSSIGVANSAAAGSTTSVLAAGADEVSAAIATLFGSHAREYQAISTQVAAFHDRFAQTLSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a gsY +aEa+
  gi|121637382|ref|YP_977605.1| 83 AVGSYVSAEAT 93
                                   *********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.10u 0.35s 00:00:01.45 Elapsed: 00:00:00.55
# Mc/sec: 4032.84
//
Query:       gi|121637383|ref|YP_977606.1|  [L=421]
Description: transcriptional activator protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-15   55.0   1.7    2.1e-14   53.8   0.4    2.2  2  GGDEF_2   GGDEF-like domain
    3.1e-11   42.9   6.1    3.3e-11   42.8   3.5    2.4  3  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.4   2.3e-18   2.1e-14      10     116 .]     187     295 ..     180     295 .. 0.83
   2 ?   -0.8   0.0       0.2   1.8e+03      41      48 ..     328     335 ..     297     403 .. 0.51

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 2.3e-18
                        GGDEF_2  10 erarrlgldldgpyvvvvielee..daerllraleealral..gpdalvavrgd.rlvlllpaedeedaeallerlarrl 84 
                                    ++ +rlg++ld++++++vi+ ++   +++ l+++++a+ ++   p++lv+v g  + +++++ ++   + +l+++++  +
  gi|121637383|ref|YP_977606.1| 187 HAEARLGYPLDRSHTAAVIWGDQaqGDHSHLDRVADAFGHAggCPHPLVVVAGAaTRWVWVKDAPG-FDIDLIHEVLHDI 265
                                    45589****************987666779********9997668888888777455555555554.3448999999999 PP

                        GGDEF_2  85 gglsvriGiGspveglaglrrSyreArrAlrl 116
                                    ++  +ri+iG +++g++g+rrS+r+A++++r+
  gi|121637383|ref|YP_977606.1| 266 PD--ARIAIGATAPGIEGFRRSHRDALTTARM 295
                                    88..************************9985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                        GGDEF_2  41 leealral 48 
                                    +++ l +l
  gi|121637383|ref|YP_977606.1| 328 IQRTLGNL 335
                                    22222222 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.21   1.9e+03      36      56 ..     129     149 ..     127     150 .. 0.86
   2 ?   -3.0   0.0      0.73   6.5e+03      35      50 ..     187     202 ..     186     205 .. 0.76
   3 !   42.8   3.5   3.7e-15   3.3e-11       3      57 ..     344     396 ..     342     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.21
                                    HHHHHS--TTSHHHHHHHHHH CS
                         HTH_30  36 ieellgldlddpddrlaLylA 56 
                                    ++ell+++++ +++ ++  lA
  gi|121637383|ref|YP_977606.1| 129 LHELLDVPFRTANEFVDTTLA 149
                                    689********9999988877 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.73
                                    HHHHHHS--TTSHHHH CS
                         HTH_30  35 rieellgldlddpddr 50 
                                    ++e  lg++ld+  ++
  gi|121637383|ref|YP_977606.1| 187 HAEARLGYPLDRSHTA 202
                                    6788899999987765 PP

  == domain 3  score: 42.8 bits;  conditional E-value: 3.7e-15
                                    .HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSHHHHHHHHHHH CS
                         HTH_30   3 eTLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddpddrlaLylAl 57 
                                     TL +++++++n+s++A+ L+ HrnTl +RL+ +++ll ++l+d+     + +Al
  gi|121637383|ref|YP_977606.1| 344 TTLLTFINQQCNASRAARLLFTHRNTLMNRLETAQRLLPRPLADTT--IHVAVAL 396
                                    7******************************************876..4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2825.19
//
Query:       gi|121637384|ref|YP_977607.1|  [L=328]
Description: quinone reductase qor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-24   86.9   0.0    1.9e-24   86.1   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
      6e-17   62.9   0.1    1.1e-16   62.0   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
      2e-11   43.7   0.0    5.3e-11   42.4   0.0    1.8  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.034   14.0   0.0    1.4  1  ADH_N_2       N-terminal domain of oxidoreductase
      0.044   13.7   0.0        0.1   12.5   0.0    1.6  1  YAcAr         YspA, cpYpsA-related SLOG family
      0.055   13.5   0.1       0.84    9.7   0.1    2.4  2  Cpn10         Chaperonin 10 Kd subunit


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   6.4e-28   1.9e-24       1     102 [.     153     256 ..     153     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 6.4e-28
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET.TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHC CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny.kea.dlverikeltggegvdvvfecvGsgatleaalkl 78 
                                    gvGl++ q+A +lG++vi+++s++ek++l k+ Gad+v++y ++a ++  r++eltgg gv++v++ vG  +t++a+l++
  gi|121637384|ref|YP_977607.1| 153 GVGLILTQWATHLGVRVITTVSTAEKAKLSKDAGADVVLDYpEDAwQFAGRVRELTGGTGVQAVYDGVG-ATTFDASLAS 231
                                    9****************************************99999***********************.********** PP

                                    EEEEEEEEECSCTSSEEE.EEHHHH CS
                     ADH_zinc_N  79 lkpgGrlvvvGggkgeee.fdlrnl 102
                                    l+ +G+l+++G+ +g+ + +d+++l
  gi|121637384|ref|YP_977607.1| 232 LAVRGTLALFGAASGPVPpVDPQRL 256
                                    ************8888777444442 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.1   3.8e-20   1.1e-16       2     133 .]     186     326 ..     185     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 3.8e-20
                                    T-SEEEETTSTTHH......HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.......S-EEE-CHHHCTT CS
                   ADH_zinc_N_2   2 GAdevidyrtedfe......aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp......lsaallkpakkrk 69 
                                    GAd v+dy +++++      + tgg gv++v+d vg +++ +asl+ l+ +G+l   g+ +       +++l++  +   
  gi|121637384|ref|YP_977607.1| 186 GADVVLDYPEDAWQfagrvrELTGGTGVQAVYDGVGATTF-DASLASLAVRGTLALFGAASgpvppvDPQRLNAAGSVY- 263
                                    9**********99999****9***************9999.*******999**96666433344543333333333322. PP

                                    T-EEEE--GGG...-...-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  70 grsvkyeflfsmkas..aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                      ++   f f+  ++  +   + +el++ i ++++++ v+ ++pl++a +Ah++le+++++G +Vl
  gi|121637384|ref|YP_977607.1| 264 -LTRPSLFHFT--RTgeEFSWRAAELFDAIGSEAITVAVGGRYPLADALRAHQDLEARKTVGSVVL 326
                                    .3333333332..2223344446******************************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.8e-14   5.3e-11       2      77 ..      28     104 ..      27     140 .. 0.80
   2 ?   -2.7   0.0       1.7   5.2e+03      49      63 ..     135     149 ..     130     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.8e-14
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS....--TT-EEEE-SEEE-SSSHHHHTT- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkk....lkvGdrVvvepliscgeCaaCkege 77 
                                    ge+lik +a g++  D  + +g  +++++lp+++G E++G+ve+vgp+v+     ++vGdrVv     + + ++ C+  +
  gi|121637384|ref|YP_977607.1|  28 GELLIKAEAIGVNFIDTYFRSG--QYPRELPFVIGSEVCGTVEAVGPGVTAadtaISVGDRVVSA-SANGAYAEFCTAPA 104
                                    799**************99999..7*************************99999*******984.44455566666554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                    T-CS--TT-EEEE-S CS
                          ADH_N  49 evkklkvGdrVvvep 63 
                                    +v  +k Gd V+v++
  gi|121637384|ref|YP_977607.1| 135 SVYPVKRGDTVLVHA 149
                                    6778999***99976 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.034      20      93 ..      17      92 ..       9     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                        ADH_N_2 20 leeeelpelkdGevlvralylSv...DPymRgrmndaksyvepvelgdvmrgg..avgeVveSknpdfkvGdlVvgllg 93
                                    ++++ p+++ Ge+l++a+ ++v   D y R     ++    p+ +g+ + g+  avg  v   + + +vGd Vv+ + 
  gi|121637384|ref|YP_977607.1| 17 HVDQPQPQPGHGELLIKAEAIGVnfiDTYFRSGQYPREL---PFVIGSEVCGTveAVGPGVTAADTAISVGDRVVSASA 92
                                   5678999**************975558888888877777...********996337******************98765 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.5e-05       0.1      29      59 ..     142     171 ..     132     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                          YAcAr  29 pidmvlvhGgakGaDrlAarWAaergvelvr 59 
                                    + d vlvh ga G+  +  +WA + gv +++
  gi|121637384|ref|YP_977607.1| 142 G-DTVLVHAGAGGVGLILTQWATHLGVRVIT 171
                                    3.89***********************9986 PP

>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00028      0.84      37      74 ..      65      97 ..      61     110 .. 0.84
   2 ?    1.0   0.0      0.15   4.5e+02      57      71 ..     138     152 ..     132     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                                   EEEEEE-T........TS-TTS--T-EEEEEGGGTSS- CS
                          Cpn10 37 GvVvaVGegarnekgedvplevkvgdkVlfpkyagtkv 74
                                   G+V aVG+g +       ++ ++vgd+V+  + +g   
  gi|121637384|ref|YP_977607.1| 65 GTVEAVGPGVTAA-----DTAISVGDRVVSASANGAYA 97
                                   99******99974.....678********999988755 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                    TS--T-EEEEEGGGT CS
                          Cpn10  57 evkvgdkVlfpkyag 71 
                                     vk gd+Vl++ +ag
  gi|121637384|ref|YP_977607.1| 138 PVKRGDTVLVHAGAG 152
                                    6999*****999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2433.76
//
Query:       gi|121637385|ref|YP_977608.1|  [L=287]
Description: hypothetical protein BCG_1516 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.04   13.2   0.0      0.074   12.4   0.0    1.5  1  CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB


Domain annotation for each model (and alignments):
>> CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.1e-06     0.074     151     189 ..     152     193 ..      58     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-06
                      CCB2_CCB4 151 dylpentqsvlvqpl..gdegvli.lgsntpraftkkdeaWi 189
                                    + l +  q+vlvqp   gde vl+ lg++ + aftk+  +W 
  gi|121637385|ref|YP_977608.1| 152 AQLHAAGQAVLVQPGgsGDETVLVfLGGEPSHAFTKQADTWR 193
                                    66677789*******996777766489999***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2052.67
//
Query:       gi|121637386|ref|YP_977609.1|  [L=310]
Description: unidentified antibiotic-transport integral membrane ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-11   43.6  47.0    4.6e-09   35.8  46.5    2.8  1  COX15-CtaA       Cytochrome oxidase assembly protein


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8  46.5   2.5e-13   4.6e-09       3     322 ..      17     291 ..      15     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.5e-13
                     COX15-CtaA   3 wlllvlllvllvvvlGgltRltdsGlsitdWppct.GalppltdeeweaefekyketpeykklagmtlaefkaiawiEwi 81 
                                    ++ +v+l   ++ v G+++R t sGl+++ Wp c+ G+  p   +e           p                  +E+ 
  gi|121637386|ref|YP_977609.1|  17 IAAIVILTQGGIAVTGAIVRVTASGLGCPTWPQCFpGSFTPVVVAE----------VP-------------RVHQAVEFG 73 
                                    5667778888999*********************846666666663..........44.............466789*** PP

                     COX15-CtaA  82 HRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllall 161
                                    +R++  ++ +   +++++++++ r ++e+ +++ l+ +  ++Q+++G ++V  gL          +a+HLl++++++ l 
  gi|121637386|ref|YP_977609.1|  74 NRMVTFAVVIAA-ALAVLVVTRARRRTEVLAYAWLMPVSTVVQAMIGGITVRTGL------LWWTVAIHLLASMTMVWLA 146
                                    ***987765544.44555555677788899999999999****************......99***************** PP

                     COX15-CtaA 162 lwlalrllakeaesaeeeaaakklrllallllallllqialGalvagldAglayntfplmggelipdklplceldwrnlf 241
                                    ++l++++ +++   + +e  ++ lr+l++l+ + l++ +++G+lv +  Ag         g++  + ++p ++  +++l+
  gi|121637386|ref|YP_977609.1| 147 VLLYVKIGQPD-DGVVHELVVSPLRALTALSALNLAAVLVTGTLVTA--AGPHA------GDRSPSRTVPRLKVEITTLV 217
                                    *******9995.45778889999**********************75..66666......33333343444444444444 PP

                     COX15-CtaA 242 enpatvqfaHRllAilvllvllllailllrkarspklarlavllaallllQvalGistvllavplslavaHqlgaallll 321
                                    + ++ +     l+A+l ll+ l +   ll    ++++    ++l+al+++Q+a+G +  +++vp +l ++H +gaa++ +
  gi|121637386|ref|YP_977609.1| 218 HMHSSL-----LVAYLALLIGLGF--GLLAVGATRAILVRLAVLLALVATQAAVGTTQYFTGVPAALVAIHVAGAAAVTA 290
                                    433333.....3444444444444..4444444566666667778999****************************9987 PP

                     COX15-CtaA 322 a 322
                                    a
  gi|121637386|ref|YP_977609.1| 291 A 291
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1984.40
//
Query:       gi|121637387|ref|YP_977610.1|  [L=261]
Description: unidentified antibiotic-transport integral membrane ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-12   44.8  16.0    1.4e-11   44.3  16.0    1.2  1  ABC2_membrane    ABC-2 type transporter
    2.5e-08   33.4  16.5    2.5e-08   33.4  16.5    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3  16.0   1.5e-15   1.4e-11      10     209 ..      34     231 ..      28     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.5e-15
                  ABC2_membrane  10 eflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsp 89 
                                    e+++ +r+ +++ll+++i + ll  +  +  g+ g++  +   p +++ +v+ +a ++ +++a+ f+r+ g l+r+ ++p
  gi|121637387|ref|YP_977610.1|  34 ELKLLLRNGEQLLLTMFIPITLLVGLTLLPMGSFGHNRAATFVPVIMALAVISTA-FTGQAIAVAFDRRYGALKRLGATP 112
                                    789999******88888888777777777777666433333469*******9999.9999999***************** PP

                  ABC2_membrane  90 lyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslgllisalapsfedasqlasl 167
                                    l +++ ++++k l+ ++v +lqa+i+ +i + l g+++   +  l   ++ l +  + +lgll++  +  +e +  +a+l
  gi|121637387|ref|YP_977610.1| 113 L-PVWGIIAGKSLAVVAVVFLQAIILGAIGFAL-GWRPAltALTLGAGIIALGTAGFAALGLLLGGTL-RAEIVLAVANL 189
                                    *.******************************9.****865557777778888888888888888766.55777777777 PP

                  ABC2_membrane 168 vllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                    + +++  ++      + +p  ++w+a++ P   ++eal +++
  gi|121637387|ref|YP_977610.1| 190 MWFVFAGFGALTLESNVIPTAFKWVARVTPSGALTEALSQAM 231
                                    777777777777788888*************99999998876 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4  16.5   2.8e-12   2.5e-08     161     342 ..      73     253 ..      57     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.8e-12
                ABC2_membrane_3 161 sflvgliliilifit.asfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfgnlg 239
                                     ++v++i++++++ t ++  a +++++++ ++++++  +++ ++ ++ +k l++++v +lq++++ ++ f+lg+      
  gi|121637387|ref|YP_977610.1|  73 ATFVPVIMALAVISTaFTGQAIAVAFDRRYGALKRLGATPLPVWGIIAGKSLAVVAVVFLQAIILGAIGFALGWRPALTA 152
                                    456776666665555144446678*******************************************8666436666555 PP

                ABC2_membrane_3 240 lll..llfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.ledlpsalkwifsiiPffapglgllrl 316
                                    l+l    + l+   ++alg+ll+   + +  + +++ ++++  ++ fg+l +  + +p+a+kw++++ P+ a++++l + 
  gi|121637387|ref|YP_977610.1| 153 LTLgaGIIALGTAGFAALGLLLGGTLRAE-IVLAVANLMWF-VFAGFGALTLeSNVIPTAFKWVARVTPSGALTEALSQA 230
                                    55555888888999999999999999865.66788999999.777777777745559*********************** PP

                ABC2_membrane_3 317 itgd.plweillsliilalfavvylll 342
                                    +t        +  +++la+ +++  l+
  gi|121637387|ref|YP_977610.1| 231 MTVSvD----WFGIVVLAVWGALAALA 253
                                    964422....33333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1662.27
//
Query:       gi|121637388|ref|YP_977611.1|  [L=313]
Description: unidentified antibiotic-transport ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.3e-25   87.7   0.0    1.3e-24   87.2   0.0    1.2  1  ABC_tran    ABC transporter
    2.5e-11   43.9   0.1    7.8e-08   32.5   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00029   20.3   0.0       0.15   11.4   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0023   17.6   0.0     0.0045   16.6   0.0    1.6  1  AAA_27      AAA domain
     0.0034   17.6   0.1      0.092   13.0   0.1    2.5  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
     0.0041   16.6   0.0      0.008   15.7   0.0    1.4  1  KdpD        Osmosensitive K+ channel His kinase sensor domain
      0.009   15.7   0.4      0.059   13.1   0.1    2.1  2  AAA_30      AAA domain
  ------ inclusion threshold ------
      0.022   15.3   0.0      0.034   14.6   0.0    1.1  1  AAA_23      AAA domain
      0.033   13.9   0.1        0.1   12.4   0.0    1.8  2  AAA_29      P-loop containing region of AAA domain
      0.037   14.1   0.0      0.077   13.0   0.0    1.5  1  GcnA_N      N-acetyl-beta-D-glucosaminidase N-terminal domain
      0.056   13.7   0.1       0.44   10.8   0.1    2.2  1  AAA_22      AAA domain
      0.062   12.9   0.1       0.27   10.8   0.0    2.0  2  SRP54       SRP54-type protein, GTPase domain
      0.075   12.8   0.0       0.12   12.1   0.0    1.3  1  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.089   12.5   0.1        1.1    8.9   0.0    2.1  2  AAA_24      AAA domain
        0.1   12.3   0.1         11    5.7   0.0    2.2  2  IstB_IS21   IstB-like ATP binding protein
       0.35   10.5   0.0        1.2    8.8   0.0    1.7  2  AAA_15      AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   1.2e-27   1.3e-24       2     137 .]      28     166 ..      27     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1.2e-27
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    +n++l+++  e++a++G+nGaGK+t +++  g ++p++G+i++ g d  + +  +lr++igv+ q     p  +++e   
  gi|121637388|ref|YP_977611.1|  28 SNLDLDVHDAEVMALLGPNGAGKTTTVEMCEGFVRPDAGSIEVLGLDPIT-DNARLRARIGVMLQGGGGYPAARAGEMld 106
                                    799**************************************999655555.599************99999999999999 PP

                                    ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                          +   +++ +l++lgl+e + t+     + LSgGq+qr+ala+al+ +p+l++lDEpta
  gi|121637388|ref|YP_977611.1| 107 lvasyaANPLDPHWLLDTLGLTEAARTTY----RRLSGGQQQRLALACALVGRPQLVFLDEPTA 166
                                    99865555555************999998....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00072      0.81       1      14 [.      39      52 ..      39      57 .. 0.89
   2 !   32.5   0.0     7e-11   7.8e-08     231     298 ..     132     196 ..     100     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00072
                         AAA_21  1 lnvliGpNgsGKSn 14
                                   +++l GpNg+GK++
  gi|121637388|ref|YP_977611.1| 39 VMALLGPNGAGKTT 52
                                   579**********9 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 7e-11
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                     +++r lS G+++ lal+ al  ++    l+++DEp +g++ ++   ++el+++l+r g+ v+ltTH 
  gi|121637388|ref|YP_977611.1| 132 RTTYRRLSGGQQQRLALACALVGRP---QLVFLDEPTAGMDAHARVLVWELIDALRRDGVTVVLTTHH 196
                                    678899****************999...99*************************************5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0036         4      24      41 ..      37      54 ..      26      58 .. 0.83
   2 !   11.4   0.0   0.00014      0.15     135     209 ..     136     208 ..     106     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0036
                                   SSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnll 41
                                    ++ a++GpNG+GK+  +
  gi|121637388|ref|YP_977611.1| 37 AEVMALLGPNGAGKTTTV 54
                                   56889*********9866 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00014
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS.HHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr.eemlekadklv 209
                                      LSgG+++ +ala       v +  l++lDe  a +D++ +  v el+++ + + + ++ ++++ +e  e ad+lv
  gi|121637388|ref|YP_977611.1| 136 RRLSGGQQQRLALA----CALVGRPQLVFLDEPTAGMDAHARVLVWELIDALRRDgVTVVLTTHHlKEAEELADRLV 208
                                    579****9866554....44567778999*********************988774444445544144444456665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     4e-06    0.0045       9      45 ..      19      56 ..      13     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4e-06
                         AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrA 45
                                   +ryG++t   +ld++ ++a++  ++GpN AGK+t+++ 
  gi|121637388|ref|YP_977611.1| 19 KRYGSITAVsNLDLDVHDAEVMALLGPNGAGKTTTVEM 56
                                   79****98538***********************9875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   8.2e-05     0.092      27      88 ..     132     180 ..     123     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    ++ +++lSGG++q la  + +               +++lvfLDE  +++D++ +  + el+
  gi|121637388|ref|YP_977611.1| 132 RTTYRRLSGGQQQRLALACAL-------VG------RPQLVFLDEPTAGMDAHARVLVWELI 180
                                    567788888888655433333.......22......589*************9987777765 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.2e-06     0.008      64     153 ..     137     227 ..     103     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.2e-06
                           KdpD  64 eykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidV.ittvnvqhleslndvveki.tgvr 141
                                    + +g + ++l l  +l  +p++v++De      +   +   ++ +++l + g+ V +tt ++++ e+l+d +  i  gv+
  gi|121637388|ref|YP_977611.1| 137 RLSGGQQQRLALACALVGRPQLVFLDEPTAGM-DAHARVLVWELIDALRRDGVTVvLTTHHLKEAEELADRLVIIdHGVT 215
                                    345778999******************87765.55566789************972699999999999998776624688 PP

                           KdpD 142 vretvPdevlee 153
                                    v    P e++++
  gi|121637388|ref|YP_977611.1| 216 VAAGTPAELMRS 227
                                    888888887765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   5.3e-05     0.059      18      96 ..      37     163 ..      32     196 .. 0.57
   2 ?    1.3   0.1      0.22   2.4e+02      39      69 ..     180     212 ..     174     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                         AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgi........eastiakllkrlk...... 81 
                                    + v++l Gp G+GKtt+++  +  ++ + g  +v+gl p    A +L++ +g+        +a++  ++l+  +      
  gi|121637388|ref|YP_977611.1|  37 AEVMALLGPNGAGKTTTVEMCEGFVRPDaGsIEVLGLDPITDNA-RLRARIGVmlqggggyPAARAGEMLDLVAsyaanp 115
                                    45999****************99999884456777777766655.35554443333333335555544444444444555 PP

                         AAA_30  82 .................................grarlepgtllivDE 96 
                                                                     + a + + +l+  DE
  gi|121637388|ref|YP_977611.1| 116 ldphwlldtlglteaarttyrrlsggqqqrlalACALVGRPQLVFLDE 163
                                    555555555555555555555555555666665444445556666666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                         AAA_30  39 reaweaaggrviglAptgkaAkvLaeelgi..e 69 
                                     +a++++g +v++ ++  k A++La+ l i  +
  gi|121637388|ref|YP_977611.1| 180 IDALRRDGVTVVLTTHHLKEAEELADRLVIidH 212
                                    567888899999999999999999975543332 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     3e-05     0.034      12      37 ..      29      55 ..      18      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                         AAA_23 12 dqeidF.skgltlItGpNGaGKTTild 37
                                   + ++d  +  + ++ GpNGaGKTT ++
  gi|121637388|ref|YP_977611.1| 29 NLDLDVhDAEVMALLGPNGAGKTTTVE 55
                                   4444557778999***********987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.1e-05       0.1      16      39 ..      31      54 ..      22      58 .. 0.79
   2 ?   -3.6   0.0       8.7   9.8e+03      39      47 ..     168     176 ..     168     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   +++++ ++++ l Gp+G+GK+T +
  gi|121637388|ref|YP_977611.1| 31 DLDVHDAEVMALLGPNGAGKTTTV 54
                                   455565669************975 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.7
                         AAA_29  39 lDAiqalLv 47 
                                    +DA++ +Lv
  gi|121637388|ref|YP_977611.1| 168 MDAHARVLV 176
                                    79***9997 PP

>> GcnA_N  N-acetyl-beta-D-glucosaminidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.077       6      72 ..     193     256 ..     189     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                         GcnA_N   6 tekqekavelLekqlsLgdveievaqsdqasirikGeeGdyqltyrkPhqLyraLslLaaaLeeG.ek 72 
                                    t    k  e L+ +l + d+ ++va +  a +   G +   ql +  P +L   LslLa+aL eG + 
  gi|121637388|ref|YP_977611.1| 193 TTHHLKEAEELADRLVIIDHGVTVAAGTPAELMRSGAKD--QLRFTAPPRL--DLSLLASALPEGyQA 256
                                    555666778999******************999998876..677889***9..6**********9555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00039      0.44       4      27 ..      36      59 ..      33     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                         AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                   +a ++++ G+ G+GKTt++++   
  gi|121637388|ref|YP_977611.1| 36 DAEVMALLGPNGAGKTTTVEMCEG 59
                                   678899************998665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.27       2      18 ..      38      54 ..      37      71 .. 0.91
   2 ?   -1.1   0.0       1.1   1.2e+03      37      52 ..     222     237 ..     197     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                   EEEEEEESTTSSHHHHH CS
                          SRP54  2 nvillvGlqGaGKTttl 18
                                   +v++l+G++GaGKTtt+
  gi|121637388|ref|YP_977611.1| 38 EVMALLGPNGAGKTTTV 54
                                   5899***********98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                    ESTSSTTHHHHHHHHH CS
                          SRP54  37 aDtfRaaAveQLktla 52 
                                    a  +R +A +QL+  a
  gi|121637388|ref|YP_977611.1| 222 AELMRSGAKDQLRFTA 237
                                    56789******98765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.12       2      44 ..      43      85 ..      42      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaa 44
                                   +Gp G+GKtt v+ +  +++    s++v+ LDP  ++   +a 
  gi|121637388|ref|YP_977611.1| 43 LGPNGAGKTTTVEMCEGFVRPDAGSIEVLGLDPITDNARLRAR 85
                                   7********************************9988776665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001       1.1       4      22 ..      39      57 ..      36      73 .. 0.86
   2 ?    1.4   0.1      0.21   2.3e+02     110     138 ..     175     203 ..     170     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    +++ Gp+g+GKTt++ + 
  gi|121637388|ref|YP_977611.1| 39 VMALLGPNGAGKTTTVEMC 57
                                   689***********99876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                         AAA_24 110 efrrllkklqelrknvifiahektrkded 138
                                     +++l+++l+  + +v+++ h  ++  e 
  gi|121637388|ref|YP_977611.1| 175 LVWELIDALRRDGVTVVLTTHHLKEAEEL 203
                                    57999**************9988877665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0099        11      44      61 ..      34      51 ..      22      60 .. 0.87
   2 ?    4.3   0.0     0.026        29      95     153 ..     142     199 ..     135     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0099
                      IstB_IS21 44 iekkenivllGpsGvGKs 61
                                   ++++e ++llGp G+GK+
  gi|121637388|ref|YP_977611.1| 34 VHDAEVMALLGPNGAGKT 51
                                   678899***********9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                      IstB_IS21  95 rdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfae 153
                                    ++++la a + + +++l+ lD+  +  +d +++ l++e+i++      +++ +  +++e
  gi|121637388|ref|YP_977611.1| 142 QQQRLALACALVGRPQLVFLDEP-TAGMDAHARVLVWELIDALRRDGVTVVLTTHHLKE 199
                                    5678888899999*********7.5789*************987777766666666555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.2      19      46 ..      32      60 ..      21      70 .. 0.78
   2 ?   -1.1   0.0         1   1.2e+03     325     364 ..     157     195 ..     135     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                         AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlF 46
                                   +d+ +  ++ l G+N++GK++ +e+ + F
  gi|121637388|ref|YP_977611.1| 32 LDVHDAeVMALLGPNGAGKTTTVEMCEGF 60
                                   44444469**************9986666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                     +++++EP a     a   +++ l+++++ +   v++tTH
  gi|121637388|ref|YP_977611.1| 157 QLVFLDEPTAGMDAHARVLVWE-LIDALRRDGVTVVLTTH 195
                                    5677777777776655555555.55555555569****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2228.03
//
Query:       gi|121637389|ref|YP_977612.1|  [L=591]
Description: hypothetical protein BCG_1520c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   13.3   1.0       0.26   11.9   0.0    2.3  2  RCR       Chitin synthesis regulation, resistance to Congo re


Domain annotation for each model (and alignments):
>> RCR  Chitin synthesis regulation, resistance to Congo red
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05      0.26       8      59 ..      90     142 ..      85     159 .. 0.80
   2 ?   -3.8   0.3         1   1.8e+04      21      47 ..     296     320 ..     294     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                            RCR   8 iivlillvllltlrvakrRrrrGlqplygtgWlvs.apppPsYgqsqqqynqa 59 
                                    +++++  ++l+ ++  +rR++rG    +   W+ +   +pP Y++  ++y  +
  gi|121637389|ref|YP_977612.1|  90 VMMALAWLMLGRFTLGRRRMSRGELDRTLLLWMLPlLIAPPMYSKDVYSYLAQ 142
                                    45566666677778*******************9988*******987776554 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1
                            RCR  21 rvakrRrrrGlqplygtgWlvsapppP 47 
                                    + a rR + G+ p +g + +   +p P
  gi|121637389|ref|YP_977612.1| 296 IRASRRPELGASPRAGASRA--VKPRP 320
                                    56889999999999998766..44555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3983.84
//
Query:       gi|121637390|ref|YP_977613.1|  [L=268]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-09   35.4   0.1    1.4e-08   34.1   0.1    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    3.4e-08   33.4   2.1    1.3e-07   31.6   0.2    2.7  3  HTH_20         Helix-turn-helix domain
    8.7e-07   28.7   0.1    2.5e-06   27.3   0.0    1.8  2  HTH_5          Bacterial regulatory protein, arsR family
    9.6e-07   28.7   0.1    2.1e-06   27.6   0.1    1.5  1  HTH_11         HTH domain
    4.2e-06   26.5   2.9    0.00031   20.6   0.4    2.9  2  MarR_2         MarR family
    6.2e-05   22.7   1.1    0.00026   20.7   1.1    2.1  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00093   19.1   0.1     0.0049   16.8   0.0    2.1  2  MarR           MarR family
     0.0024   17.6   0.0     0.0062   16.3   0.0    1.7  1  HTH_DeoR       DeoR-like helix-turn-helix domain
     0.0027   17.8   0.0       0.03   14.5   0.0    2.3  2  HTH_34         Winged helix DNA-binding domain
     0.0065   16.3   0.1      0.055   13.3   0.2    2.2  2  HTH_IclR       IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.035   14.1   0.0    1.7  2  PadR           Transcriptional regulator PadR-like family
      0.026   14.4   0.0      0.069   13.0   0.0    1.6  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.029   14.4   0.1      0.043   13.8   0.1    1.2  1  MRP            Mitochondrial RNA binding protein MRP
      0.051   13.6   0.2         11    6.1   0.0    3.2  4  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.12   12.5   0.0       0.27   11.4   0.0    1.6  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
        1.3    9.2   7.6        0.2   11.8   0.5    3.2  5  HTH_28         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   1.3e-11   1.4e-08       4      45 ..      43      84 ..      42      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                         HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                   t+r+I +lL + ++i+  e+ +rlglS + v+r+l+ L+e+G
  gi|121637390|ref|YP_977613.1| 43 TRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   89**************************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   1.2e-10   1.3e-07       6      52 ..      37      84 ..      33      84 .. 0.95
   2 ?   -0.4   0.0       1.1   1.3e+03      47      58 ..     176     187 ..     145     189 .. 0.81
   3 ?   -2.2   0.0       3.9   4.4e+03      27      48 ..     212     234 ..     206     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.2e-10
                                   HHS-.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                         HTH_20  6 ALah.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeag 52
                                   A+++  +Rr+i r+L + +  ta+e+ +rl+ls + +++HL++L eag
  gi|121637390|ref|YP_977613.1| 37 AVSDgHTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   778888****************************************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                    HHHHCTTEEEEC CS
                         HTH_20  47 vLeeagLvevvr 58 
                                    +L++ag+v +++
  gi|121637390|ref|YP_977613.1| 176 ALSKAGYVATTT 187
                                    788888888776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.9
                                    HHHHHHHHTS-HHH.HHHHHHHH CS
                         HTH_20  27 aselaerldlsknt.lsyHLrvL 48 
                                    ++el+e+ + ++++ l  H++ L
  gi|121637390|ref|YP_977613.1| 212 FPELCETEQQAMAEvLGTHVQRL 234
                                    46677776777777666776666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.2e-09   2.5e-06       3      43 ..      43      84 ..      41      84 .. 0.98
   2 ?   -3.5   0.0         9     1e+04      39      45 ..     177     183 ..     176     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.2e-09
                                   HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaG 43
                                   tR+ I++lL e g+ +++e+ + lgls + v++HL +L eaG
  gi|121637390|ref|YP_977613.1| 43 TRRAIVRLLLEsGSITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   9****************************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9
                                    HHHTTSE CS
                          HTH_5  39 LreaGLV 45 
                                    L +aG+V
  gi|121637390|ref|YP_977613.1| 177 LSKAGYV 183
                                    8899*99 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   1.8e-09   2.1e-06       2      43 ..      44      84 ..      43      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-09
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   +++i++lLle+ + i++ e+ ++L++S + vrr+++aL e+g
  gi|121637390|ref|YP_977613.1| 44 RRAIVRLLLESGS-ITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   689*****99998.************************9999 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   2.7e-07   0.00031      10      49 ..      47      84 ..      41      93 .. 0.82
   2 ?    4.9   0.1     0.021        24      36      55 ..     168     187 ..     167     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                   +   L  ++   +t+ge+ +rlgls + v r+l+ L +aG
  gi|121637390|ref|YP_977613.1| 47 IVRLLLESGS--ITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   4555666666..9**************************9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                                    HHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  36 savsrilkrLvaaGLverrp 55 
                                    +a+ ri   L++aG+v +++
  gi|121637390|ref|YP_977613.1| 168 AAAERIATALSKAGYVATTT 187
                                    57789***********9875 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.1   2.3e-07   0.00026       6      41 ..      45      80 ..      43      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                  HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                   r+I+++L e ++i+  e+++r+GlS++ v+r +++L
  gi|121637390|ref|YP_977613.1| 45 RAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDAL 80
                                   89****************************977666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.4e-06    0.0049       7      45 ..      46      84 ..      42      84 .. 0.93
   2 ?   -1.5   0.0       2.2   2.5e+03      33      48 ..     169     184 ..     167     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkG 45
                                    i+r+l e+g+++  e++++lg+s + v r ld+L+++G
  gi|121637390|ref|YP_977613.1| 46 AIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   6899********************************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHTTSEE CS
                           MarR  33 tvtrvldrLekkGlie 48 
                                    ++ r++++L k+G++ 
  gi|121637390|ref|YP_977613.1| 169 AAERIATALSKAGYVA 184
                                    5668999999999985 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.5e-06    0.0062       4      42 ..      46      84 ..      44      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                       HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqg 42
                                   +i+ ll ++g+++  e+ ++lg S a +RR L+ L e+g
  gi|121637390|ref|YP_977613.1| 46 AIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   79*******************************998887 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.7e-05      0.03       2      76 ..      44     123 ..      43     127 .. 0.85
   2 ?    0.3   0.0       0.7   7.9e+02      36      47 ..     175     186 ..     167     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                         HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke.....fkgkkprtllriTpeGreafkkyvkaL 76 
                                    R a++ +L++  ++++ e+ + l+++++    hl++L +ag  e + +     +  ++p   +r+T +Gr++ +   + L
  gi|121637390|ref|YP_977613.1|  44 RRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASAAapwqqVGRGRPAKRYRLTAAGRAKLDHSYDDL 123
                                    668999*************************************998652221145678*************998877766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.7
                         HTH_34  36 kkLekagYievd 47 
                                    ++L kagY+  +
  gi|121637390|ref|YP_977613.1| 175 TALSKAGYVATT 186
                                    78******9865 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   4.9e-05     0.055      10      46 ..      49      84 ..      46      88 .. 0.85
   2 ?   -0.3   0.0      0.88   9.9e+02      34      49 ..     169     184 ..     159     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                                   CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                       HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                   ++l e +   t  e+ +r+gl+ + v+R+L  L+e G
  gi|121637390|ref|YP_977613.1| 49 RLLLESGS-ITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   55566666.7999*********************988 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
                                    HHHHHHHHHHHTTSEE CS
                       HTH_IclR  34 tvhRlLqtLvelGyve 49 
                                    ++ R+   L + Gyv 
  gi|121637390|ref|YP_977613.1| 169 AAERIATALSKAGYVA 184
                                    5778888999999986 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.035      50      74 ..      93     117 ..      80     118 .. 0.90
   2 ?   -2.8   0.0       5.6   6.3e+03      40      52 ..     176     188 ..     173     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                    EEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR  50 eweesgegpprkyYrlTdaGrrela 74 
                                     w++ g+g+p k YrlT+aGr++l 
  gi|121637390|ref|YP_977613.1|  93 PWQQVGRGRPAKRYRLTAAGRAKLD 117
                                    69999****************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                                    HHHHTTSEEEEEE CS
                           PadR  40 rLekeglvesewe 52 
                                     L+k g+v+++ +
  gi|121637390|ref|YP_977613.1| 176 ALSKAGYVATTTR 188
                                    6899999998865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.069      17      56 ..      51      90 ..      48     109 .. 0.89
   2 ?   -3.2   0.0       7.1     8e+03      44      54 ..     175     185 ..     169     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   Ll++g+ ta ei  +lg++ + v + L  L+++G  e + 
  gi|121637390|ref|YP_977613.1| 51 LLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASA 90
                                   88********************************998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.1
                                    HHHHHCTSEEE CS
                           TrmB  44 rsLedkGlVer 54 
                                      L+++G+V +
  gi|121637390|ref|YP_977613.1| 175 TALSKAGYVAT 185
                                    57899999976 PP

>> MRP  Mitochondrial RNA binding protein MRP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.9e-05     0.043      16     113 ..      88     186 ..      78     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                            MRP  16 assaaslkd.raartvkqrrsaskpaFdinHasrkdvssgallrvpvldeslireqtkvdhfwgLdddgdlKggnkaavq 94 
                                    as aa+ ++  + r +k  r +     +  H+ ++  s+++       +e  +r + + +    L d  +  g+++aa++
  gi|121637390|ref|YP_977613.1|  88 ASAAAPWQQvGRGRPAKRYRLTAAGRAKLDHSYDDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALE 167
                                    4444443331233456666655566667889888877777655556789999****9999999***************** PP

                            MRP  95 gngdlavsvalsnvytard 113
                                      +++ +++  +++y+a  
  gi|121637390|ref|YP_977613.1| 168 AAAERIATALSKAGYVATT 186
                                    ****************975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0097        11      21      49 ..      56      84 ..      41      85 .. 0.87
   2 ?   -3.4   0.0         9     1e+04      17      29 ..     113     125 ..     106     127 .. 0.71
   3 ?   -0.8   0.0       1.4   1.5e+03      40      53 ..     172     186 ..     169     194 .. 0.76
   4 ?    3.0   0.0     0.091     1e+02      23      41 ..     219     237 ..     202     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0097
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTT CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreg 49
                                   ++t  e++++lGl+   v r l +L ++g
  gi|121637390|ref|YP_977613.1| 56 SITAGEIGDRLGLSAAGVRRHLDALIEAG 84
                                   57999*****************9999887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9
                                    EEEEEHHHHHHHH CS
                      HTH_Crp_2  17 eielpltqeelAs 29 
                                    + +l+ + ++lAs
  gi|121637390|ref|YP_977613.1| 113 RAKLDHSYDDLAS 125
                                    4568889999997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.4
                                    HHHHHHHHTTSEE.E CS
                      HTH_Crp_2  40 rilseLkreglis.r 53 
                                    ri ++L+++g++  +
  gi|121637390|ref|YP_977613.1| 172 RIATALSKAGYVAtT 186
                                    888999999999843 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.091
                                    HHHHHHHHTTSSHHHHHHH CS
                      HTH_Crp_2  23 tqeelAsmlGltretvsri 41 
                                     q+ +A+ lG++ + +  i
  gi|121637390|ref|YP_977613.1| 219 EQQAMAEVLGTHVQRLATI 237
                                    799********99987665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.27      13      52 ..      42      81 ..      38      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                   THHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHH CS
                          HTH_9 13 evvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLi 52
                                    + +++v++Ll++g  t+ e+  +++Ls   V++ L +Li
  gi|121637390|ref|YP_977613.1| 42 HTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALI 81
                                   55679*******************************9998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   0.00018       0.2       2      42 ..      44      86 ..      43     102 .. 0.87
   2 ?   -2.9   0.0       7.1     8e+03       2      20 ..     107     125 ..     107     132 .. 0.69
   3 ?   -1.7   0.1         3   3.4e+03      33      46 ..     128     142 ..     123     147 .. 0.68
   4 ?   -3.1   0.0         8   8.9e+03      11      22 ..     200     212 ..     200     212 .. 0.84
   5 ?   -0.9   0.0       1.7   1.9e+03      15      31 ..     220     236 ..     216     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                         HTH_28  2 Rleiiklla.aGh.svreaArelgisrrtvyrWikryeegGia 42
                                   R+ i++ll+ +G  ++ e+  +lg+s   v+r + ++ e G+a
  gi|121637390|ref|YP_977613.1| 44 RRAIVRLLLeSGSiTAGEIGDRLGLSAAGVRRHLDALIEAGDA 86
                                   899*****9557799999*******************999975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.1
                         HTH_28   2 RleiikllaaGhsvreaAr 20 
                                    Rl++  +++  hs++++A 
  gi|121637390|ref|YP_977613.1| 107 RLTAAGRAKLDHSYDDLAS 125
                                    6677777776778887664 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3
                         HTH_28  33 ikryee.gGiagLvp 46 
                                    +++++e gG+++ ++
  gi|121637390|ref|YP_977613.1| 128 MRQLREiGGEEAVRT 142
                                    577888677888776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8
                         HTH_28  11 aGh.svreaArel 22 
                                    ++h +v+ +A+e+
  gi|121637390|ref|YP_977613.1| 200 QHHcPVSHVAEEF 212
                                    57889999**997 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.7
                         HTH_28  15 vreaArelgisrrtvyr 31 
                                    + + A+ lg++ +++  
  gi|121637390|ref|YP_977613.1| 220 QQAMAEVLGTHVQRLAT 236
                                    66789*****9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1756.10
//
Query:       gi|121637391|ref|YP_977614.1|  [L=846]
Description: hypothetical protein BCG_1522 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-73  244.8   0.1    4.5e-70  235.7   0.1    2.3  2  UPF0051          Uncharacterized protein family (UPF0051)
    8.7e-06   25.8   0.0    2.5e-05   24.3   0.0    1.8  1  Hom_end_hint     Hom_end-associated Hint
    4.2e-05   23.8   0.0      0.052   13.9   0.0    2.7  2  LAGLIDADG_3      LAGLIDADG-like domain
     0.0005   20.0   0.0     0.0071   16.3   0.0    2.5  3  Intein_splicing  Intein splicing domain
    0.00073   19.8   0.0     0.0017   18.7   0.0    1.6  1  Hint_2           Hint domain
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.043   13.3   0.0    1.5  1  Hint             Hint module


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0016       4.7       2      26 ..     233     261 ..     232     304 .. 0.74
   2 !  235.7   0.1   1.5e-73   4.5e-70      23     218 .]     622     817 ..     596     817 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                        UPF0051   2 qfertlivveegaevtiieeyagc.......g 26 
                                    qfertli+++eg+ v+++   +gc        
  gi|121637391|ref|YP_977614.1| 233 QFERTLIIADEGSYVHYV---EGClpageliT 261
                                    89****************...77755444440 PP

  == domain 2  score: 235.7 bits;  conditional E-value: 1.5e-73
                        UPF0051  23 agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegaeaelnglylak 102
                                    ++ +vvei+v+ +A+++y+++qnws++++nl+tkra+ ++ a++e++++++g+k+t+k+p v ++ge+a++e+ ++++a+
  gi|121637391|ref|YP_977614.1| 622 LHSAVVEIIVKPHARVRYTTIQNWSNNVYNLVTKRARAEAGATMEWIDGNIGSKVTMKYPAVWMTGEHAKGEVLSVAFAG 701
                                    5669**************************************************************************** PP

                        UPF0051 103 gkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvk 182
                                    ++qh+dt+ k+ h +pntss+i+sk+v+++++r+++rg ++v+kga+++++++++++Ll++  +r+dt P++ i++ddv+
  gi|121637391|ref|YP_977614.1| 702 EDQHQDTGAKMLHLAPNTSSNIVSKSVARGGGRTSYRGLVQVNKGAHGSRSSVKCDALLVDTVSRSDTYPYVDIREDDVT 781
                                    ******************************************************************************** PP

                        UPF0051 183 asHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    ++H+Atv+k++e+qlfYLmsRGl+e+eA++++vrgf
  gi|121637391|ref|YP_977614.1| 782 MGHEATVSKVSENQLFYLMSRGLTEDEAMAMVVRGF 817
                                    ***********************************9 PP

>> Hom_end_hint  Hom_end-associated Hint
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   8.4e-09   2.5e-05       4     100 ..     256     345 ..     253     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 8.4e-09
                                    TT-EEEBTTS-EEEGGG--TT-EEEBTTSSEEEEEE--.EEEE.EEEEEEE-SSSBHHSSST-SEEEEETT-EEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Hom_end_hint   4 kgTevlmadGsdksiedievgekvmGkdGkpreVvalp.rgve.tmYevkektkhraeeeesllsfvcnanHkLvlrtpq 81 
                                     g  +  adG+ + ie+i+vg+ v G+dG+p++V+a+  r+ + ++++ + ++           +f ++a+H L   +  
  gi|121637391|ref|YP_977614.1| 256 AGELITTADGDLRPIESIRVGDFVTGHDGRPHRVTAVQvRDLDgELFTFTPMSP--------ANAFSVTAEHPLLAIPRD 327
                                    5666778****************************9852555425666666662........236899999999999999 PP

                                    EEEEEEEEESTEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxx RF
                   Hom_end_hint  82 kiklterklrgkkytsVty 100
                                    ++++ +++ +g   ++V+ 
  gi|121637391|ref|YP_977614.1| 328 EVRVMRKERNGW-KAEVNS 345
                                    999988775554.455555 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0022       6.6       3      44 ..     384     426 ..     382     463 .. 0.83
   2 !   13.9   0.0   1.7e-05     0.052       3      72 ..     483     551 ..     481     557 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                                    HHHHHHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHH CS
                    LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs.isltssskelledvqrlL 44 
                                    + a L+G++ a+G++  +++  +   s+ s + e++edv++  
  gi|121637391|ref|YP_977614.1| 384 EFARLAGYYLAEGHACLTNGCESLiFSFHSDEFEYVEDVRQAC 426
                                    5799***********9999877778888888889999998765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCH CS
                    LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisg 72 
                                     +++  ++  +DG v+ +++  v  ++ ++s+  + ++q +L+rlG  +t+  +++++  +++ + ++++
  gi|121637391|ref|YP_977614.1| 483 LRELVDAYVNGDGNVTRRNGA-VWKRVHTTSRLWAFQLQSILARLGHYATVELRRPGGPGVIMGRNVVRK 551
                                    5777889999*********76.339***************************998888877776666555 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.42   1.2e+03      68     118 ..     259     305 ..     255     314 .. 0.82
   2 ?   -0.5   0.0      0.37   1.1e+03      57      75 ..     310     328 ..     280     338 .. 0.73
   3 !   16.3   0.0   2.4e-06    0.0071      76     134 .]     355     611 ..     345     611 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.42
                                    EEECCTTEEEEEECCC--TT-EEEEEHSCEEEEEEEEEEEEECEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  68 llvvrdegivEkradeLkegdliavpdadvvwdkvksievedeeeyVYdlt 118
                                    l+++ d+++  +  + +++gd+++   +d   ++v  ++v+d +++ + +t
  gi|121637391|ref|YP_977614.1| 259 LITTADGDL--RPIESIRVGDFVT--GHDGRPHRVTAVQVRDLDGELFTFT 305
                                    566767788..88899999**999..7888899999999999999998876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.37
                                    S-EEEEETT-EEEECCTTE CS
                                    xxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  57 grkikaTpeHkllvvrdeg 75 
                                     +   +T+eH+ll++  ++
  gi|121637391|ref|YP_977614.1| 310 ANAFSVTAEHPLLAIPRDE 328
                                    566789*******994444 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.4e-06
                                    EEEEECCC--TT-EEEEE.............................................................. CS
                                    xxxxxxxxxxxxxxxxxx.............................................................. RF
                Intein_splicing  76 ivEkradeLkegdliavp.............................................................. 93 
                                    +    a+++ egd+++ p                                                              
  gi|121637391|ref|YP_977614.1| 355 W--IAAKDVAEGDFLIYPkpkpiphrtvlplefarlagyylaeghacltngceslifsfhsdefeyvedvrqackslyek 432
                                    5..679999*******999************************************************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|121637391|ref|YP_977614.1| 433 sgsvlieehkhsarvtvytkagyaamrdnvgigssnkklsdllmrqdetflrelvdayvngdgnvtrrngavwkrvhtts 512
                                    ******************************************************************************** PP

                                    ..........................................................HSCEEEEEEEEEEEEECEEEEE CS
                                    ..........................................................xxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  94 ..........................................................dadvvwdkvksievedeeeyVY 115
                                                                                              ++d     +k+  v++ +e VY
  gi|121637391|ref|YP_977614.1| 513 rlwafqlqsilarlghyatvelrrpggpgvimgrnvvrkdiyqvqwteggrgpkqardCGDYFAVPIKKRAVREAHEPVY 592
                                    *********************************************************999*999**************** PP

                                    EEEETTT-EEEECTTEEE- CS
                                    xxxxxxxxxxxxxxxxxxx RF
                Intein_splicing 116 dltvednhNFvangiivHN 134
                                     l ve+ + ++a g+ vHN
  gi|121637391|ref|YP_977614.1| 593 NLDVENPDSYLAYGFAVHN 611
                                    ******************9 PP

>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.7e-07    0.0017       2      47 ..     253     299 ..     252     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.7e-07
                         Hint_2   2 CflagtliatpeGe.vaveeLrvGdlVvtadgglqpvrwigsrtlsa 47 
                                    C+ ag li+t++G+ +++e++rvGd V+ +dg +++v+ +  r l+ 
  gi|121637391|ref|YP_977614.1| 253 CLPAGELITTADGDlRPIESIRVGDFVTGHDGRPHRVTAVQVRDLDG 299
                                    9999*********8579*********************999998864 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.043       8      52 ..     249     294 ..     241     392 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                    HXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                           Hint   8 kkggCFpgestvtvedgeqkslseLepGdkVlavdes.gevvfsev 52 
                                       gC p+  ++t++dg  ++++++++Gd V   d+   +v+  +v
  gi|121637391|ref|YP_977614.1| 249 YVEGCLPAGELITTADGDLRPIESIRVGDFVTGHDGRpHRVTAVQV 294
                                    568*****************************99954033443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (846 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5642.16
//
Query:       gi|121637392|ref|YP_977615.1|  [L=397]
Description: hypothetical protein BCG_1523 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-68  229.5   0.0    4.7e-68  229.1   0.0    1.1  1  UPF0051      Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
      0.082   12.2   0.4       0.15   11.3   0.4    1.4  1  Hydrolase_4  Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.1   0.0   5.2e-72   4.7e-68       5     218 .]     135     360 ..     131     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 5.2e-72
                        UPF0051   5 rtlivveegaevtiieey....agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrk 80 
                                    ++++++ee  e+ ++ ++    +  ++ve++v + A+l+ v + +w++d+v+ls ++a+ g+da l+++tv lgg+++r 
  gi|121637392|ref|YP_977615.1| 135 HLQVRIEELGEAVVVIDHrgggTYADNVEFVVDDAARLTAVWIADWADDTVHLSAHHARIGKDAVLRHVTVMLGGDVVRM 214
                                    88899*******9999998776444******************************************************* PP

                        UPF0051  81 epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkd.......earavfrgkikvrkgaqktda 153
                                    +  v++ g g++ael gly+a+++qhl++r++vdh++p+++s++l+kg+l++       +a++v+ g++++r++a++td+
  gi|121637392|ref|YP_977615.1| 215 SAGVRFCGAGGDAELLGLYFADDGQHLESRLLVDHAHPDCKSNVLYKGALQGdpasslpDAHTVWVGDVLIRAQATGTDT 294
                                    ******************************************************************************** PP

                        UPF0051 154 hqenrnLllsdkaradtiPeleidaddvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    ++ nrnL+l+d+arad++P+lei+++++  a+H++++G++d+eqlfYL+sRG++e++Arrl+vrgf
  gi|121637392|ref|YP_977615.1| 295 FEVNRNLVLTDGARADSVPNLEIETGEIVgAGHASATGRFDDEQLFYLRSRGIPEAQARRLVVRGF 360
                                    *****************************************************************9 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   1.7e-05      0.15      10      83 ..     123     190 ..     117     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                    Hydrolase_4  10 vHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                    v G +e + +y +l  +  + G av+ +DhrG G         ++++ +vdD+a ++    +++ +  + l +h
  gi|121637392|ref|YP_977615.1| 123 VTGPGEGAVAYGHLQVRIEELGEAVVVIDHRGGGTY------ADNVEFVVDDAARLTAVWIADWADDTVHLSAH 190
                                    67889999************************8875......79999999999998888888887777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2544.49
//
Query:       gi|121637393|ref|YP_977616.1|  [L=266]
Description: ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-21   75.1   0.0    9.2e-21   74.8   0.0    1.1  1  ABC_tran     ABC transporter
    2.4e-05   24.3   0.1     0.0054   16.6   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.7e-05   23.7   0.0      0.017   14.5   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00058   19.5   0.2     0.0011   18.6   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.007   16.8   0.1      0.058   13.8   0.1    2.1  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.011   15.3   0.2      0.037   13.6   0.2    1.8  1  AAA_25       AAA domain
      0.036   12.7   0.0       0.24   10.0   0.0    1.9  2  AAA_13       AAA domain
      0.062   13.2   0.0        0.1   12.5   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.064   13.7   0.0       0.11   13.0   0.0    1.2  1  AAA_23       AAA domain
       0.15   11.8   0.0       0.32   10.7   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
       0.16   11.5   0.1       0.46   10.0   0.1    1.7  2  AAA_27       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   5.6e-24   9.2e-21       1     135 [.      26     177 ..      26     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 5.6e-24
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                    l+ v+l++k ge++a++G+nG+GKStL  ++ag+ k   t+G+i+ldg+d+      e++r+ +    q p   p++++ 
  gi|121637393|ref|YP_977616.1|  26 LRGVDLTVKSGETHALMGPNGSGKSTLSYAIAGHPKYhvTSGTITLDGADVLAmSIDERARAGLFLAMQYPVEVPGVSMS 105
                                    6789*****************************877666********999998788899999***************877 PP

                                    HH.............HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                    xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en.............esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEp 135
                                    +              + + +++++ + +   +++   +++s  + +SgG+k+r ++ ++ l kpk+ +lDE 
  gi|121637393|ref|YP_977616.1| 106 NFlrsaatairgeppKLRHWVKEVKAAMAALDIDPAFAERSVnEGFSGGEKKRHEILQLELLKPKIAILDET 177
                                    669999999998888555555555555555555555555555599**************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.3e-06    0.0054       3      21 ..      40      58 ..      39      85 .. 0.83
   2 !    5.8   0.0    0.0066        11     252     302 ..     164     214 ..     161     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                   +l GpNgsGKS+L +a+ +
  gi|121637393|ref|YP_977616.1| 40 ALMGPNGSGKSTLSYAIAG 58
                                   688**************76 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0066
                         AAA_21 252 lralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                    l++lk+ ++ ++DE ++gL+  +lr + e + +++++  + ++l TH + +l
  gi|121637393|ref|YP_977616.1| 164 LELLKP-KIAILDETDSGLDVDALRVVSEGVnRYAESQHGGILLITHYTRIL 214
                                    555555.9********************9996555557999******87766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.1e-05     0.017      26      44 ..      38      56 ..      29      61 .. 0.87
   2 !    7.1   0.0     0.002       3.3     137     202 ..     151     214 ..     110     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                     a++GpNGSGKs l  Ai
  gi|121637393|ref|YP_977616.1| 38 THALMGPNGSGKSTLSYAI 56
                                   6799************999 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.002
                                    S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreeml 202
                                    +SgGek+   +   + ++  kp+ + +lDe d+ LD    + v+e ++  ++s++  ++ i++ +++l
  gi|121637393|ref|YP_977616.1| 151 FSGGEKKRHEI---LQLELLKPK-IAILDETDSGLDVDALRVVSEGVNryAESQHGGILLITHYTRIL 214
                                    67777776553...444555665.789******************99933344556688888877666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   6.9e-07    0.0011      15      39 ..      29      53 ..      25      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.9e-07
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    +++++  +++ l+Gp+GsGKSTl 
  gi|121637393|ref|YP_977616.1| 29 VDLTVKSGETHALMGPNGSGKSTLS 53
                                   55677755599************96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   3.5e-05     0.058       3      43 ..      41      85 ..      39     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                   EESSTTSSHHHHHHHHHHHHTHE....EEEEETTTCSSSSTTHHH CS
                            AAA  3 lyGppGtGKTllakavakelgve....fleisgsellskyvgese 43
                                   l+Gp G GK++l  a+a + + +     ++++g+++l + + e++
  gi|121637393|ref|YP_977616.1| 41 LMGPNGSGKSTLSYAIAGHPKYHvtsgTITLDGADVLAMSIDERA 85
                                   89*****************65332233788888888866444443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.3e-05     0.037      29      55 ..      32      58 ..      11     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                         AAA_25 29 llpagelallaGapgtGKttlaldlal 55
                                    +  ge+++l+G+ g+GK+tl + +a 
  gi|121637393|ref|YP_977616.1| 32 TVKSGETHALMGPNGSGKSTLSYAIAG 58
                                   45789***************9988774 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00014      0.24      23      39 ..      43      59 ..      36      85 .. 0.79
   2 ?    0.3   0.0      0.13   2.1e+02     523     578 ..     165     218 ..     159     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                         AAA_13 23 GwNGaGKTtLSrllrsl 39
                                   G NG+GK+tLS +++  
  gi|121637393|ref|YP_977616.1| 43 GPNGSGKSTLSYAIAGH 59
                                   99***********9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                         AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                    e+ k ki ++D   S LD ++l +v+  ++ ++  +++   +++ TH +  ++++ 
  gi|121637393|ref|YP_977616.1| 165 ELLKPKIAILDETDSGLDVDALRVVSEGVNRYA--ESQHGGILLITHYTRILRYIH 218
                                    56789999999999****************998..8888999*****999999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05       0.1      98     127 ..      35      64 ..      17      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                    TTSEEEEECSTTSSHHHHHHHHCTT----- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelkt 127
                                    +++t +l+G+ G GKStL  a++++ + ++
  gi|121637393|ref|YP_977616.1|  35 SGETHALMGPNGSGKSTLSYAIAGHPKYHV 64 
                                    45999**************99998766554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-05      0.11      23      39 ..      40      56 ..      26      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                   ++ GpNG+GK+T+  Ai
  gi|121637393|ref|YP_977616.1| 40 ALMGPNGSGKSTLSYAI 56
                                   678**********8888 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.32      44      68 ..      33      57 ..      11      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   +++ e  +l+Gp G GKs l+ a++
  gi|121637393|ref|YP_977616.1| 33 VKSGETHALMGPNGSGKSTLSYAIA 57
                                   5678999****************97 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00028      0.46      19      46 ..      29      56 ..      27      59 .. 0.85
   2 ?   -2.6   0.0       2.1   3.4e+03     131     154 ..     232     255 ..     229     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                         AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAi 46
                                   +d+  ++ + h ++GpN +GKst+  Ai
  gi|121637393|ref|YP_977616.1| 29 VDLTVKSGETHALMGPNGSGKSTLSYAI 56
                                   5677778889*************99998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                         AAA_27 131 reGGealleaegelgqlLfeasaG 154
                                    ++GG++l ++ ++ g + f+ ++G
  gi|121637393|ref|YP_977616.1| 232 ESGGSELADELDQNGYVRFSPASG 255
                                    689999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1509.45
//
Query:       gi|121637394|ref|YP_977617.1|  [L=417]
Description: cysteine desulfurase csd [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.4e-140  467.2   0.0   3.9e-140  467.0   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
     0.0015   17.6   0.0     0.0023   17.0   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
       0.14   11.3   0.0       0.23   10.6   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
       0.16   10.5   0.0       0.25    9.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.0   0.0  8.7e-144  3.9e-140       2     371 .]      32     403 ..      31     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 467.0 bits;  conditional E-value: 8.7e-144
                                    EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                    Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                    ylds At+q p +Vlda +e++t +n++vhr++h+l +eat+a+e+ r+++a +++a++ +e++ft+++tea+nlv + l
  gi|121637394|ref|YP_977617.1|  32 YLDSGATSQRPLQVLDAEREFLTASNGAVHRGAHQLMEEATDAYEQGRADIALFVGADT-DELVFTKNATEALNLVSYVL 110
                                    9*********************************************************7.******************** PP

                                    CCC.....-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB- CS
                    Aminotran_5  82 ars.....lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiq 156
                                    ++s     + pgd iv+te+ehhanl+pwqela+rtga+++++ ++++g++dld l  +l++++k+va+th+snvtG++ 
  gi|121637394|ref|YP_977617.1| 111 GDSrferaVGPGDVIVTTELEHHANLIPWQELARRTGATLRWYGVTDDGRIDLDSL--YLDDRVKVVAFTHHSNVTGVLT 188
                                    9988888899**********************************************..9********************* PP

                                    -HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET CS
                    Aminotran_5 157 pveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsl 236
                                    pv e++++a+++gal+++Da+q+v+h+p+d+++lgvDf+afsghK+lgP+GiGvly+r+ell +++p+l+gg+m+e+v++
  gi|121637394|ref|YP_977617.1| 189 PVSELVSRAHQSGALTVLDACQSVPHQPVDLHELGVDFAAFSGHKMLGPNGIGVLYGRRELLAQMPPFLTGGSMIETVTM 268
                                    ******************************************************************************** PP

                                    TEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE CS
                    Aminotran_5 237 eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf 316
                                    e++t+a ap++feaGTp++ +++gl+aa++yl +ig++a+e+he+el +++ e+l+ ++gvr++gp++ + r s v+f++
  gi|121637394|ref|YP_977617.1| 269 EGATYAPAPQRFEAGTPMTSQVVGLAAAARYLGAIGMAAVEAHERELVAAAIEGLSGIDGVRILGPTSMRDRGSPVAFVV 348
                                    ******************************************************************************** PP

                                    TTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 317 kgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                    +gvha+dv+++Ld+ g+avr Ghhca pl++r++l++t RaS+++ynt++evdrl
  gi|121637394|ref|YP_977617.1| 349 EGVHAHDVGQVLDDGGVAVRVGHHCALPLHRRFGLAATARASFAVYNTADEVDRL 403
                                    *****************************************************98 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.1e-07    0.0023     198     233 ..     218     253 ..     179     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.1e-07
                                    HHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHH CS
                           SelA 198 ealaeGvdlvsfsGDkllGgpqaGiivGkkeliekl 233
                                    ++ + Gvd  +fsG k+lG    G++ G++el++++
  gi|121637394|ref|YP_977617.1| 218 DLHELGVDFAAFSGHKMLGPNGIGVLYGRRELLAQM 253
                                    56678***************************9997 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.2e-05      0.23      50     187 ..      79     207 ..      32     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH.......HTTT-EEEEEESS-.THH...HHHHHHTTSEEE CS
                  Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllk.......lnpgdeilvpdpty.asy...knilrlsggevv 118
                                    + ++a f+g       +++ ++v++  a+++++++  +l        + pgd+i+  ++ + a+    ++ +r  g++++
  gi|121637394|ref|YP_977617.1|  79 RADIALFVG------ADTD-ELVFTKNATEALNLVSYVLGdsrferaVGPGDVIVTTELEHhANLipwQELARRTGATLR 151
                                    667777888......3333.444444444444444444444444444559999999999762555111556666666666 PP

                                    EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                  Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                     y ++  +d ++dl++l    ++      ++kv++++  +N tG++ +  el+     a++ ++l+++D
  gi|121637394|ref|YP_977617.1| 152 WYGVT--DDGRIDLDSLYL--DD------RVKVVAFTHHSNVTGVLTPVSELVSR---AHQSGALTVLD 207
                                    66655..999****99965..77......99*****************9999877...88888888888 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.6e-05      0.25      90     201 ..     121     236 ..     112     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.6e-05
                                    TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHH...HHCCTTEEEEEEESS-TTTT----HHHHHHHHHHT CS
                Cys_Met_Meta_PP  90 aGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleele...kaikentklvylEtptnpllkvvDiekiaklakka 166
                                     Gd iv+++  +       +++++++g + +++ ++d  ++      +++++k+v +   +n +  ++ + ++++ a++ 
  gi|121637394|ref|YP_977617.1| 121 PGDVIVTTELEHHANLIPWQELARRTGATLRWYGVTDDGRIDldsLYLDDRVKVVAFTHHSNVTGVLTPVSELVSRAHQS 200
                                    56666666666666666677788888888888777776666411145789****************************** PP

                                    T-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTTTT CS
                Cys_Met_Meta_PP 167 gvlvvvDntfaspllqrpl.klgaDivvhSaTKylg 201
                                    g+l+v+D++ + p     l +lg+D    S+ K lg
  gi|121637394|ref|YP_977617.1| 201 GALTVLDACQSVPHQPVDLhELGVDFAAFSGHKMLG 236
                                    **********9996544443799**99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2773.47
//
Query:       gi|121637395|ref|YP_977618.1|  [L=162]
Description: nitrogen fixation-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-36  125.4   0.0    2.1e-36  124.9   0.0    1.2  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.018   14.9   0.0       0.03   14.2   0.0    1.3  1  DUF3261   Protein of unknown function (DUF3261)


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   2.3e-40   2.1e-36       2     128 ..       9     131 ..       8     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 2.3e-40
                                    SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSB CS
                         NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgkt 81 
                                    y+d++ldhyk+P+++G +e   a   ++++++p+cGD+v+L+++++e+++r++d++++++GC++++A++s+lte+v+g++
  gi|121637395|ref|YP_977618.1|   9 YQDVILDHYKHPQHRGLREPFGA---QVYHVNPICGDEVTLRVALSEDGTRVTDVSYDGQGCSISQAATSVLTEQVIGQR 85 
                                    9*********************7...9***************************************************** PP

                                    HHHHCCCCHHHHHHHHTC.SCSSSCHCSCHHHHHHHHHHHHHHHHCTH CS
                         NifU_N  82 leealkitnkeiaeelgg.lpkeklhcsvlaedalkaavkkYkakkke 128
                                    +++a  +++ ++++e+++ ++++  +++vl++ ++ a+v+kY+a+ k+
  gi|121637395|ref|YP_977618.1|  86 VPRA--LNIVDAFTEMVSsRGTVPGDEDVLGDGVAFAGVAKYPARVKC 131
                                    ****..99999**999988**************************987 PP

>> DUF3261  Protein of unknown function (DUF3261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-06      0.03      31      67 ..      48      86 ..      41      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-06
                        DUF3261 31 aglsplGqrlftlsydgqelevers..rrlPdqlkaeqv 67
                                   ++ls+ G+r++++sydgq+ +++++  + l +q+ +++v
  gi|121637395|ref|YP_977618.1| 48 VALSEDGTRVTDVSYDGQGCSISQAatSVLTEQVIGQRV 86
                                   6799******************77767666666556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1136.42
//
Query:       gi|121637396|ref|YP_977619.1|  [L=115]
Description: hypothetical protein BCG_1527 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-19   68.5   0.5    6.2e-19   67.9   0.5    1.3  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.5   3.5e-23   6.2e-19       2      72 ..      13      87 ..      12      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.5e-23
                                   HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T....-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                 FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg....gkVsvditltypacslaeairadaeaalralpgvevveV 72
                                   ++v++a+r+V+DPelg+++v+lglv+++d+++    +++ +d+tlt++ac+l + i+++ ++al     v++ ++
  gi|121637396|ref|YP_977619.1| 13 ADVEEAMRDVVDPELGINVVDLGLVYGLDVQDgdegTVALIDMTLTSAACPLTDVIEDQSRSALVGSGLVDDIRI 87
                                   79******************************999777889***********************98877777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 796.91
//
Query:       gi|121637397|ref|YP_977620.1|  [L=609]
Description: acyl-CoA dehydrogenase fadE15 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-30  104.9   0.1    8.8e-30  103.4   0.0    1.9  2  Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
    4.3e-18   66.0   1.0    3.9e-17   62.8   1.0    2.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    6.3e-18   64.8   0.0    1.4e-17   63.7   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    2.6e-09   36.9   0.0    6.2e-09   35.8   0.0    1.7  1  AcylCoA_DH_N   Acyl-CoA dehydrogenase N terminal
    0.00017   22.2   0.0    0.00046   20.8   0.0    1.8  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.044   14.1   0.0    2.1  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.7   1.1e+04      92     103 ..     452     463 ..     443     466 .. 0.82
   2 !  103.4   0.0   2.9e-33   8.8e-30       2     123 ..     474     604 ..     473     605 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.7
                  Acyl-CoA_dh_C  92 latarfFaervL 103
                                    +++ +fF+++++
  gi|121637397|ref|YP_977620.1| 452 IQALDFFFRKIV 463
                                    78999**99885 PP

  == domain 2  score: 103.4 bits;  conditional E-value: 2.9e-33
                  Acyl-CoA_dh_C   2 laeieatva..raalkelaaaleaalealqeateallakaakg.....dpeealaaavpyLelfGdvvigwlllrqalaA 74 
                                    la+++ tv+  +++lk+ a+ l++al+++ ++t+al ++++++     d +++++++v+yL ++Gd++igw ll  a +A
  gi|121637397|ref|YP_977620.1| 474 LAQVTHTVEniDPSLKPQAELLRTALDDITAMTGALTGYLMSAaqhssDIYKVGLGSVRYLLAVGDLLIGWRLLVLAGVA 553
                                    78999999955559***************************997777777****************************** PP

                  Acyl-CoA_dh_C  75 qakla..agekdaafyegKlatarfFaervLPraaalaaaieagddslmel 123
                                    +a+la   +++d+afy+gK+a+a fFa+++LP++++ +++ie+ dd++m +
  gi|121637397|ref|YP_977620.1| 554 HAALAdgPSQNDEAFYRGKIAVAAFFAKNMLPKLTGVRSVIENIDDDIMRV 604
                                    *****887788999***********************************87 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   1.0   1.3e-20   3.9e-17       2     143 ..     288     455 ..     287     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.3e-20
                                    BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTS............B-CC-BGGGSHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrr............kafgkplidhqlvreklaemaaeleaarl 69 
                                    +G++++ + ++h R+++++ ++g++   + +al++a++r            +a   +++ h+ vr+ l + +a +e++r+
  gi|121637397|ref|YP_977620.1| 288 NGIAQMFTVIEHARMTIGVKSAGTLSTGYLNALAFAKERvqgadltqmtdkTAPRVTIMHHPDVRRSLMTQKAYAEGLRA 367
                                    69999999*******************************7777776665544445689********************** PP

                                    HHHHHHH--------..............HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS CS
                  Acyl-CoA_dh_1  70 lvyraaealdagkpd..............raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige 135
                                    l + aa+++d++  +                   ++K ++se a e+ ++ +q lGg G+l +yp+e+++rda++++++e
  gi|121637397|ref|YP_977620.1| 368 LYLYAAAHQDDAVAQrvsgadhdmahrvdDLLLPIVKGVGSERAYEILTESLQTLGGSGFLVDYPLEQYIRDAKIDSLYE 447
                                    *******99999999999999*****9999999*********************************************** PP

                                    S-HHHHHH CS
                  Acyl-CoA_dh_1 136 Gtseiqrn 143
                                    Gt+ iq +
  gi|121637397|ref|YP_977620.1| 448 GTTAIQAL 455
                                    *****976 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   4.7e-21   1.4e-17       2      95 ..     162     272 ..     161     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 4.7e-21
                                    EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT.....-SEEEEEEE..TS-------EEEEEEE....GG. CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaai.....atlalvlar..tekpdrarglslflvp..rdap. 71 
                                    + lTEp+aGsdv + +t+a+e+ +g + ++G K++i+++       + ++lvlar   ++p +++glslf+vp    +p 
  gi|121637397|ref|YP_977620.1| 162 MVLTEPDAGSDVGAGRTKAFEQPDGTWHIEGVKRFISGGDVgntaeNIFHLVLARpeGAGP-GTKGLSLFYVPnyLFDPd 240
                                    789************************************99766545556*****644444.6**********9866667 PP

                                    ........GEEE-----BSS-TTS-EEEEEEE CS
                  Acyl-CoA_dh_M  72 ........gvsvrrieeklGlrglptgelvfe 95 
                                            gv v+ +e+k+Gl++ pt+el+f 
  gi|121637397|ref|YP_977620.1| 241 tfelgarnGVYVTGLEHKMGLKSSPTCELTFG 272
                                    7999**************************96 PP

>> AcylCoA_DH_N  Acyl-CoA dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.1e-12   6.2e-09       1      32 []       3      34 ..       3      34 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.1e-12
                   AcylCoA_DH_N  1 qYkAPlRDmrFvLyEvLdaealaalPgfadad 32
                                   +Y+A++RD++F+L EvLd+ a++++++++d+d
  gi|121637397|ref|YP_977620.1|  3 HYIANVRDLEFNLLEVLDIGAVLGTGRYSDLD 34
                                   8*****************************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.6e-07   0.00046      28     103 ..      71     148 ..      36     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                    HHT.SGHHHH...HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-HHHHH CS
                  Acyl-CoA_dh_N  28 eeg.efprel...wkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrfGteeqkr 103
                                    ++   +p+el   +++++e+G++ + + ee gG+ + +   a ++ e+ ++  + a +++++  l+ + ++  G++eq+r
  gi|121637397|ref|YP_977620.1|  71 THSiSVPDELaktVQAIKEAGWWRLGLAEEIGGMPA-PPPLAWAVNEMIYCANPSACFFNLGPVLA-QSLYIEGNDEQRR 148
                                    33445887755679********************95.78888899999999999999****99777.89*********97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.044      37     132 ..     354     449 ..     319     451 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                    -HHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT- CS
                  Acyl-CoA_dh_2  37 dpatqlalaeaaarl..dAAralleraaaraealaaagkevtvedraearraaalavelaiaavdalfeaaGgsalrkes 114
                                    + +tq a ae   +l   AA     ++a+r     a+++     d +   + + + +e+a ++  +  ++ Ggs+ + ++
  gi|121637397|ref|YP_977620.1| 354 SLMTQKAYAEGLRALylYAAAHQDDAVAQR-VS-GADHDMAHRVDDLLLPIVKGVGSERAYEILTESLQTLGGSGFLVDY 431
                                    444444444432222002222222222222.11.2222222233334455569999************************ PP

                                    HHHHHHHHHHHHCTSGGG CS
                  Acyl-CoA_dh_2 115 plqRlwRDahaaaaHaal 132
                                    pl+ + RDa++ + ++++
  gi|121637397|ref|YP_977620.1| 432 PLEQYIRDAKIDSLYEGT 449
                                    *********998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 4157.28
//
Query:       gi|121637398|ref|YP_977621.1|  [L=370]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-32  111.9  23.3      2e-32  111.3  23.3    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3  23.3   1.1e-36     2e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv++ e ++ aa++la++gs +saan+aaaa ttav+aa+aDeVSaa+Aalf+ah+q+yq lsaqaaafh qfvqal++
  gi|121637398|ref|YP_977621.1|  1 MSFVVANTEFVSGAAGNLARLGSMISAANSAAAAQTTAVAAAGADEVSAAVAALFGAHGQTYQVLSAQAAAFHSQFVQALSG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a++YaaaEa+
  gi|121637398|ref|YP_977621.1| 83 GAQAYAAAEAT 93
                                   *********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2163.33
//
Query:       gi|121637399|ref|YP_977622.1|  [L=657]
Description: cation transporter P-type atpase D ctpD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-47  160.1   3.0    3.9e-47  160.1   3.0    2.3  3  E1-E2_ATPase  E1-E2 ATPase
    9.3e-36  124.1   1.5    1.7e-35  123.2   1.5    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
     0.0009   19.0   0.1     0.0013   18.5   0.1    1.2  1  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.21   11.9   0.0    1.4  1  DUF1257       Protein of unknown function (DUF1257)
       0.64   10.7   3.0        7.4    7.3   0.4    2.7  2  Cadherin_4    Bacterial cadherin-like domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   3.0   1.1e-50   3.9e-47       2     180 ..     145     324 ..     144     325 .. 0.97
   2 ?   -2.8   0.1         1   3.7e+03     110     161 ..     440     493 ..     431     496 .. 0.52
   3 ?   -1.8   0.1      0.53   1.9e+03     114     139 ..     588     613 ..     555     636 .. 0.65

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 1.1e-50
                                    SS--EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                   E1-E2_ATPase   2 llpptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                    l p++a v+  dg+e+ ++a+elv+GD v++++gdr+paDg +++g + vd+ ++TGEs+pv k +gd+vf+Gtv+ sg 
  gi|121637399|ref|YP_977622.1| 145 LAPDQAVVVqGDGSERVVAASELVVGDRVVVRPGDRIPADGAVLSGASDVDQRSITGESMPVAKARGDEVFAGTVNGSGV 224
                                    678889999899******************************************************************** PP

                                    EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiP 160
                                    ++ vVt+  ++t +++i++lv++a+++k+++q +++k+ + +++ +++++l++++i l+ g +l+  llra++++++a P
  gi|121637399|ref|YP_977622.1| 225 LHLVVTRDPSQTVVARIVELVADASATKAKTQLFIEKIEQRYSLGMVAATLALIVIPLMFGADLRPVLLRAMTFMIVASP 304
                                    ******************************************************************************** PP

                                    TTHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 161 caLplavplalalgarrlak 180
                                    ca +la+   l+ +++++ +
  gi|121637399|ref|YP_977622.1| 305 CAVVLATMPPLLSAIANAGR 324
                                    *******9999999988766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHS.-STTTSSTT.HHHHHHHHHHHHHS-T CS
                   E1-E2_ATPase 110 plqkkldklgkvlvpvvlliallvfli.alllgksla.eallralallvaaiPc 161
                                    pl + +  l++  +++++l+  +++ +  l+ +  +     + a+a l+aa P 
  gi|121637399|ref|YP_977622.1| 440 PLAELAPLLSAGATAAIVLLDGVAIGVlGLTDQLRPDaVESVAAMAALTAAPPV 493
                                    566666666666555555554444444033333333234445566666666655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHHHHHHHHHHHHS-ST CS
                   E1-E2_ATPase 114 kldklgkvlvpvvlliallvfliall 139
                                     l + ++ +v+v l+ia++++++++l
  gi|121637399|ref|YP_977622.1| 588 GLARQARRVVTVNLAIAATFIAVLVL 613
                                    44444555555555555555554444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   1.5   4.7e-39   1.7e-35       3     209 ..     343     554 ..     341     555 .. 0.88

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 4.7e-39
                                    EEEEESBTTTBCHHHHHHHHHHHH........CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.xxx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsa........alalaaaletgsehpigkalvaaakarsgal...tgfatfigrg.aya 70 
                                     v++Dk+GTLt+g p++  v +           l+laaa e +sehp+g+a+va+a  r++a+   ++f++++g+g +++
  gi|121637399|ref|YP_977622.1| 343 IVALDKTGTLTRGIPRLASVAPLDpnvvdarrLLQLAAAAEQSSEHPLGRAIVAEARRRGIAIppaKDFRAVPGCGvHAL 422
                                    699****************999999988877888889999999****************7777777**********8444 PP

                                    HTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE.EEEEEESSEH CS
                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                      Hydrolase  71 igkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagi.evvlltgdnp 145
                                    +g+     a    +     a+   + s+g t+a++  ++ a +v+ + d+  ++p+a+e va+  a    + vlltgdn 
  gi|121637399|ref|YP_977622.1| 423 VGNDFVEIASpqSYRGAPLAELAPLLSAGATAAIVllDGVAIGVLGLTDQ--LRPDAVESVAAMAALTAaPPVLLTGDNG 500
                                    44433333335555555788888899999999998889************..*************99666********** PP

                                    HHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 146 etaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                    + a+r+a+++G          ++++ a  +pe+kv+++r Lq+ +++v+ VGDgvnDa+a+aaA
  gi|121637399|ref|YP_977622.1| 501 RAAWRVARNAG----------ITDVRAALLPEQKVEVVRNLQAGGHQVLLVGDGVNDAPAMAAA 554
                                    ***********..........7777**************************************9 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.7e-07    0.0013     195     244 ..     527     576 ..     524     587 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.7e-07
                                    HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE- CS
                    Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtk 244
                                    ++ +l+    +v+ +GDg ND + + aa  +vAmg + +   + Ad vt 
  gi|121637399|ref|YP_977622.1| 527 VVRNLQAGGHQVLLVGDGVNDAPAMAAARAAVAMGAGADLTLQTADGVTI 576
                                    5678889999************************************9996 PP

>> DUF1257  Protein of unknown function (DUF1257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.9e-05      0.21      49      82 ..     243     274 ..     239     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                        DUF1257  49 elvaDlqfwkqslsveeflnkltqrYAyktvlae 82 
                                    elvaD++ +k   + + f++k++qrY   +v a+
  gi|121637399|ref|YP_977622.1| 243 ELVADASATK--AKTQLFIEKIEQRYSLGMVAAT 274
                                    89***77777..9999*************99887 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0021       7.4      19      61 ..     171     212 ..     146     234 .. 0.75
   2 ?    2.8   0.1      0.05   1.8e+02       8      32 ..     543     569 ..     537     581 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                     Cadherin_4  19 dsatvtedtpltitagnvlandtDvdgddltvtavtvagtyGt 61 
                                    d + v  ++ +   +g vl+ ++Dvd+ ++t  +  va + G 
  gi|121637399|ref|YP_977622.1| 171 DRVVVRPGDRIPA-DGAVLSGASDVDQRSITGESMPVAKARGD 212
                                    4444555555555.49**************9999988887774 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.05
                     Cadherin_4   8 tgvndaPvavddsatvte..dtpltit 32 
                                    +gvndaP  ++  a+v+   ++ lt +
  gi|121637399|ref|YP_977622.1| 543 DGVNDAPAMAAARAAVAMgaGADLTLQ 569
                                    59******6666555544115555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4535.83
//
Query:       gi|121637400|ref|YP_977623.1|  [L=124]
Description: thioredoxin trxA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-18   64.2   0.0      1e-17   64.0   0.0    1.1  1  Thioredoxin    Thioredoxin
    0.00076   19.8   0.0     0.0014   19.0   0.0    1.6  1  Thioredoxin_8  Thioredoxin-like
    0.00089   19.7   0.1      0.016   15.6   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   1.7e-21     1e-17       4      93 ..       5      92 ..       2     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.7e-21
                                   ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                    Thioredoxin  4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkev 85
                                    lt++ F++++++ +++vlv F+Ap C++C  ++P++e+ ++++  +v+  kv++++++dla+  +v+ +Ptl+ fk+gk v
  gi|121637400|ref|YP_977623.1|  5 DLTAAYFQQTISA-NSNVLVYFWAPLCAPCDLFTPTYEASSRKHF-DVVHGKVNIETEKDLASIAGVKLLPTLMAFKKGKLV 84
                                   578899******9.***************************9999.9*********************************88 PP

                                   EEEESS-H CS
                    Thioredoxin 86 kkyegare 93
                                    k  g ++
  gi|121637400|ref|YP_977623.1| 85 FKQAGIAN 92
                                   88888655 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.3e-07    0.0014       4      33 ..      21      52 ..      18      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                                   EEEEE--SSSHHHHHHHHHHHHHHHHHHH..T CS
                  Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkk..k 33
                                   vl+yf+a  c+pc+ ftp+  + ++k+ +  +
  gi|121637400|ref|YP_977623.1| 21 VLVYFWAPLCAPCDLFTPTYEASSRKHFDvvH 52
                                   9********************99999875444 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.7e-06     0.016       5     107 ..      18      98 ..      14     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                    +  vlv+f++p C  C+++  + +              +++f+ ++ ++            ie++++la   gv+ +Pt+
  gi|121637400|ref|YP_977623.1|  18 NSNVLVYFWAPLCAPCDLFTPTYEAS-----------SRKHFDVVHGKVN-----------IETEKDLASIAGVKLLPTL 75 
                                    67899999999999999988876666...........3344333333333...........456678************6 PP

                  Thioredoxin_2  85 v.fldgkeivarlpGyvpaeelea 107
                                      f  gk  v++  G  +++ ++ 
  gi|121637400|ref|YP_977623.1|  76 MaFKKGK-LVFKQAGIANPAIMDN 98 
                                    6488888.8888899999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 789.06
//
Query:       gi|121637401|ref|YP_977624.1|  [L=123]
Description: thioredoxin trxB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.3   0.0    1.7e-25   89.0   0.0    1.1  1  Thioredoxin    Thioredoxin
    1.7e-06   28.4   0.0    8.7e-06   26.2   0.0    1.9  1  Thioredoxin_2  Thioredoxin-like domain
    4.3e-06   27.0   0.0      7e-05   23.1   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    0.00018   21.3   0.0    0.00023   21.0   0.0    1.1  1  Thioredoxin_9  Thioredoxin
      0.007   16.5   0.0      0.012   15.8   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.014   14.8   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
       0.03   14.0   0.0       0.17   11.6   0.0    1.8  2  Redoxin        Redoxin
      0.072   13.0   0.0      0.078   12.9   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
       0.15   12.3   0.0       0.26   11.5   0.0    1.4  1  Glutaredoxin   Glutaredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   8.6e-29   1.7e-25       4     102 ..       5     101 ..       2     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 8.6e-29
                                    ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                    Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                     lt+++F+e++++ ++ vlv+++A+wCg+C+a+aP++++ +e++  +v+ akvd++++++la+  ++++iPt++ fkngk
  gi|121637401|ref|YP_977624.1|   5 DLTAAQFNETIQS-SDMVLVDYWASWCGPCRAFAPTFAESSEKHP-DVVHAKVDTEAERELAAAAQIRSIPTIMAFKNGK 82 
                                    68999********.9******************************.9********************************* PP

                                    EEEEEESS-HHHHHHHHHH CS
                    Thioredoxin  84 evkkyegarekeklaaflk 102
                                       +  ga + ++l++ ++
  gi|121637401|ref|YP_977624.1|  83 LLFNQAGALPPAALESLVQ 101
                                    ********99999988775 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.4e-09   8.7e-06       6     108 ..      19      99 ..      14     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.4e-09
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                      vlv++++++C+ C+++  ++ e             +++ + +++++++++e+           ela + ++r+ Pti 
  gi|121637401|ref|YP_977624.1|  19 DMVLVDYWASWCGPCRAFAPTFAES-----------SEKHPDVVHAKVDTEAER-----------ELAAAAQIRSIPTIM 76 
                                    56899999************99999...........455555666666666666...........7************77 PP

                  Thioredoxin_2  86 .fldgkeivarlpGyvpaeeleal 108
                                     f +gk  +++  G++p++ le l
  gi|121637401|ref|YP_977624.1|  77 aFKNGK-LLFNQAGALPPAALESL 99 
                                    699**9.88899******999875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.5e-08     7e-05       2      32 ..      19      49 ..      18      56 .. 0.87
   2 ?    3.9   0.0     0.035        69      58      88 ..      47      77 ..      44      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.5e-08
                                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHH CS
                  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkk 32
                                   ++vl+ ++aswc pc+af p+  e +ek+ +
  gi|121637401|ref|YP_977624.1| 19 DMVLVDYWASWCGPCRAFAPTFAESSEKHPD 49
                                   689************************9984 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                                   -TTSEE.EE-TT-HHHHTT-S--TT-SEEEE CS
                  Thioredoxin_8 58 kkpwlsvpfddkkrnklkkkynvkaiPtlvv 88
                                   +++ ++  +d +   +l+   ++ +iPt++ 
  gi|121637401|ref|YP_977624.1| 47 HPDVVHAKVDTEAERELAAAAQIRSIPTIMA 77
                                   46778889999999**************875 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07   0.00023      50     128 ..      27     103 ..       6     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                    -TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEESS-HHHHH...HHH CS
                  Thioredoxin_9  50 edwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwgerPaevqe.lvdel 128
                                    + wCg ++++ P +a+ +e  p++    +  +++ el    +    r+iPt++ ++++   +++ g +P ++ e lv++l
  gi|121637401|ref|YP_977624.1|  27 ASWCGPCRAFAPTFAESSEKHPDVVHAKVDTEAERELAAAAQI---RSIPTIMAFKNGKLLFNQAGALPPAALEsLVQQL 103
                                    78***********************************998865...*********9999999999999987777577776 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     6e-06     0.012      17      56 ..      18      53 ..       5      79 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
                                   T--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEE CS
                  Thioredoxin_7 17 gkpvlvffgaswcftCqalerdflsdeevkaalaekfvll 56
                                      vlv+  aswc++C+a++ +f+++ e  +    ++v  
  gi|121637401|ref|YP_977624.1| 18 SDMVLVDYWASWCGPCRAFAPTFAESSEKHP----DVVHA 53
                                   5679****************99999865443....44444 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     7e-06     0.014      46     104 ..      30      80 ..      17     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7e-06
                      OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                    C +Cr f+p f   a+s  k+      +++ akvd +  +++ +  +++s+P ++ f+ 
  gi|121637401|ref|YP_977624.1|  30 CGPCRAFAPTF---AESSEKH-----PDVVHAKVDTEAERELAAAAQIRSIPTIMAFKN 80 
                                    88888888877...5565666.....58*****************************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.3e-05      0.17      29      57 ..      19      46 ..       2      52 .. 0.73
   2 ?    0.1   0.0      0.31   6.1e+02     109     137 ..      65      93 ..      52     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                                   SEEEEEEESTTT-HHHHHTHHHHHTHHHH CS
                        Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklael 57
                                     v+v  +++ +c++C+a +p +++ +e+
  gi|121637401|ref|YP_977624.1| 19 DMVLVDYWAS-WCGPCRAFAPTFAESSEK 46
                                   3588999999.*******99877777665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                                    .GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                        Redoxin 109 aseglrtpryavidedgkvvylevepepe 137
                                    a++++r+  +++  ++gk+   + ++ p+
  gi|121637401|ref|YP_977624.1|  65 AAAQIRSIPTIMAFKNGKLLFNQAGALPP 93 
                                    33348888899999999999999888873 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05     0.078      25      59 ..      18      49 ..       2     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                   TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTT CS
                       AhpC-TSA 25 gkpvvlffypkdwcpvCttelpalaklyeefkerg 59
                                    + v++  +++ wc +C++ +p +a+  e+    +
  gi|121637401|ref|YP_977624.1| 18 SDMVLVDYWAS-WCGPCRAFAPTFAESSEKHP--D 49
                                   35788889999.*************9988776..3 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.26       5      54 ..      26      76 ..      21      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                   ESTSSHHHHHHHHHH.HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                   Glutaredoxin  5 tkptCpyCkkakrlL.kelgvkfeeidvdkdeeireelkelsgvrtvPqvf 54
                                     ++C+ C++   ++ ++     +++    d e+  el + + +r++P+++
  gi|121637401|ref|YP_977624.1| 26 WASWCGPCRAFAPTFaESSEKHPDVVHAKVDTEAERELAAAAQIRSIPTIM 76
                                   4589*****98877725555778**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 894.68
//
Query:       gi|121637402|ref|YP_977625.1|  [L=285]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-48  163.2   0.0    9.2e-48  162.7   0.0    1.1  1  ECH_1     Enoyl-CoA hydratase/isomerase
    4.6e-24   85.5   0.1    5.5e-24   85.3   0.1    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.0     1e-51   9.2e-48       6     250 ..      29     283 ..      26     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 1e-51
                                    EEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC......HHHHHHHCC.HH CS
                          ECH_1   6 vaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek......akqallkee.vl 78 
                                    +a+i+lnrPe +N++   ++  l +al+++  d+svr+vvLtG ++ F++Gad k +    +        +al + e ++
  gi|121637402|ref|YP_977625.1|  29 IAQITLNRPERMNSMAFDVMVPLKEALAQVSYDNSVRVVVLTGAGRGFSSGADHKSAGVVPHvenltrPTYALRSMElLD 108
                                    9*****************************************************98764321111233344444443145 PP

                                    HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CT.TCHHHHHHHHHHHHHHHHHHHT- CS
                          ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipga.ggtqilarkvGkskAeeilllgk 157
                                    +    l+ +  pviaavnG aigGGl lala+Di++a+ +a f ++ ++ Gl++   g++  l+r++G s+A ei+l+g+
  gi|121637402|ref|YP_977625.1| 109 DVILMLRRLHQPVIAAVNGPAIGGGLCLALAADIRVASSSAYFRAAGINNGLTASElGLSYLLPRAIGSSRAFEIMLTGR 188
                                    66778999********************************************99751566678***************** PP

                                    EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHHHH..HHHHHHHCTSHHHH CS
                          ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.dalaeqleae..aklfestfskddik 234
                                     +sa+ea+++Glv++ vp+eqll+   ++a+++a  s+  ++  k  l   l+   l++ ++ae   +lf  +    +++
  gi|121637402|ref|YP_977625.1| 189 DVSAEEAERIGLVSRQVPDEQLLDACYAIAARMAGFSRPGIELTKRTLWSGLDaASLEAHMQAEglGQLFVRLLTA-NFE 267
                                    ***************************************************9988888888877335889888876.899 PP

                                    HHHHHHHTCSH----- CS
                          ECH_1 235 eGlqaflEkrkpefed 250
                                    e + a +E+r p f+d
  gi|121637402|ref|YP_977625.1| 268 EAVAARAEQRAPVFTD 283
                                    *************987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.1   6.1e-28   5.5e-24       2     186 ..      30     219 ..      29     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 6.1e-28
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THH....HHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkee....eeffreeY 77 
                                    + itLnrp+ +N++  +++  lkeal +++ d++v++vvl+gag ++f++G D ++     + ++ ++     + ++   
  gi|121637402|ref|YP_977625.1|  30 AQITLNRPERMNSMAFDVMVPLKEALAQVSYDNSVRVVVLTGAG-RGFSSGADHKSAGVVPHVENLTRptyaLRSMELLD 108
                                    579***************************************99.********987654444432222212245555566 PP

                                    HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT--.--TTHHHHHHCSST.THHHHHHHH-- CS
                          ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlf.PDvGgsyfLsrlpg.elGlylalTGa 155
                                    ++  ++ ++++pv+a ++G ++GgG+ l++ + +rv++ ++ f    ++ Gl+  + G sy+L+r+ g + +  + lTG+
  gi|121637402|ref|YP_977625.1| 109 DVILMLRRLHQPVIAAVNGPAIGGGLCLALAADIRVASSSAYFRAAGINNGLTaSELGLSYLLPRAIGsSRAFEIMLTGR 188
                                    6677889999*****************************************97369*********9883556669***** PP

                                    -B-HHHHHHTTS--EE--GGGHHHHHHHHHT CS
                          ECH_2 156 rlkgadalaaglathyvpseklealeeaLae 186
                                     +++++a  +gl +  vp+e+l +   a+a+
  gi|121637402|ref|YP_977625.1| 189 DVSAEEAERIGLVSRQVPDEQLLDACYAIAA 219
                                    ********************99777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1971.22
//
Query:       gi|121637403|ref|YP_977626.1|  [L=542]
Description: macrolide-transport ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-46  157.4   0.1    5.8e-23   81.9   0.0    2.9  2  ABC_tran         ABC transporter
      7e-24   85.2   4.9    9.9e-07   28.9   0.0    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.2e-09   35.9   0.0      0.049   13.1   0.0    4.2  4  SMC_N            RecF/RecN/SMC N terminal domain
    2.3e-08   34.0   3.5    4.4e-08   33.0   3.5    1.5  1  ABC_tran_Xtn     ABC transporter
      5e-08   33.1   0.3     0.0093   16.2   0.1    3.4  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      6e-06   26.8   0.5       0.36   11.4   0.0    3.2  3  AAA_18           AAA domain
    2.8e-05   23.8   0.3      0.081   12.7   0.0    3.0  3  AAA_29           P-loop containing region of AAA domain
    2.9e-05   24.6   2.0      0.042   14.3   0.0    2.4  2  AAA_23           AAA domain
    8.6e-05   22.1   0.1     0.0038   16.7   0.0    2.3  2  Arf              ADP-ribosylation factor family
    0.00015   21.8   0.0       0.65   10.1   0.0    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
    0.00019   21.1   0.4       0.67    9.6   0.0    2.6  2  SRP54            SRP54-type protein, GTPase domain
     0.0003   19.6   3.5      0.052   12.2   0.0    3.4  4  AAA_13           AAA domain
    0.00033   21.1   9.3       0.13   12.6   0.4    3.5  3  AAA_16           AAA ATPase domain
    0.00042   19.7   1.4    0.00066   19.1   1.4    1.2  1  Herpes_UL36      Herpesvirus UL36 tegument protein
     0.0005   20.3   3.5        0.1   12.8   0.0    3.2  3  AAA_28           AAA domain
    0.00072   18.5   0.0     0.0064   15.4   0.0    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
    0.00073   19.7   4.5       0.17   12.0   0.1    4.1  3  AAA_33           AAA domain
    0.00093   19.5   3.0        2.2    8.5   0.2    3.7  2  AAA_22           AAA domain
      0.002   18.1   0.2       0.76    9.7   0.0    2.6  2  RsgA_GTPase      RsgA GTPase
     0.0023   15.5  10.0      0.015   12.8   0.3    2.8  3  DUF3584          Protein of unknown function (DUF3584)
     0.0051   16.6   0.1          3    7.5   0.0    2.7  2  AAA_24           AAA domain
     0.0061   15.9   0.3        1.1    8.5   0.1    2.7  2  Zeta_toxin       Zeta toxin
     0.0065   16.5   0.1        3.8    7.5   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0094   15.9   2.3       0.94    9.4   0.2    3.0  3  NACHT            NACHT domain
  ------ inclusion threshold ------
       0.01   15.5   0.0        2.9    7.5   0.0    2.6  2  AAA_15           AAA ATPase domain
      0.015   14.9   1.0          1    8.9   0.1    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.028   14.2   0.2        5.5    6.7   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.037   13.9   0.0         10    6.0   0.0    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.09   12.4   0.2          6    6.5   0.0    2.4  2  Thymidylate_kin  Thymidylate kinase
       0.12   12.9   4.3          3    8.3   0.1    3.2  3  AAA              ATPase family associated with various cellul
       0.12   12.5   0.2          7    6.9   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.28    9.3   0.2       0.38    8.9   0.2    1.1  1  Pox_F12L         Poxvirus F12L protein
       0.37   10.5  12.5       0.76    9.5   0.3    3.4  3  AAA_30           AAA domain
       0.66    9.5   5.6        5.4    6.5   0.0    3.4  3  AAA_27           AAA domain
        6.1    6.4   8.1        5.1    6.6   0.2    3.6  3  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0     1e-22   5.3e-20       5     137 .]      23     197 ..      20     197 .. 0.69
   2 !   81.9   0.0   1.1e-25   5.8e-23       3     137 .]     353     481 ..     351     481 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1e-22
                                    EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.... RF
                       ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren.... 79 
                                    +l +++g ++++vG+nGaGK+t l++lag+++p +G++                 eig+lpq+p++ +    +r++    
  gi|121637403|ref|YP_977626.1|  23 DLRVQPGDRIGLVGRNGAGKTTTLRILAGEVEPYAGSV-------------TRAGEIGYLPQDPKVGDLDVlARDRvlsa 89 
                                    6899**********************************.............44566666666655544332133336666 PP

                                    ....................HHHTCHHHHHHHSTTGG.......................TTCBGESTTSGGS-HHHHHH CS
                                    ....................xxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ....................esdeeiekalsklglke.......................lkdtvvksspssLSgGqkqr 116
                                                        ++++e ++a++++g+ e                       l+++v++++ ++LSgGq++r
  gi|121637403|ref|YP_977626.1|  90 rgldvlltdlekqqalmaevADEDERDRAIRRYGQLEerfvalggygaeseagricaslgLPERVLTQRLRTLSGGQRRR 169
                                    6666666555555555555544444444444444444566666666666666666666666669998888********** PP

                                    HHHHHHHH.......HTSSEEEEESTTT CS
                                    xxxxxxxx.......xxxxxxxxxxxxx RF
                       ABC_tran 117 valarall.......kkpkllllDEpta 137
                                    v+lar+l+        +++ lllDEpt+
  gi|121637403|ref|YP_977626.1| 170 VELARILFaasesgaGNSTTLLLDEPTN 197
                                    ******97332222257789*******7 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 1.1e-25
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.. RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.. 79 
                                     v+l + +g++v+i+G nGaGK+tLl+llag ++p+ G +           ++ +  +ig++ qe ++l+++ tv en  
  gi|121637403|ref|YP_977626.1| 353 GVDLAIDRGSRVVILGLNGAGKTTLLRLLAGVEQPDTGVL-----------EPGYGLRIGYFAQEhDTLDNDATVWENvr 421
                                    7999***********************************9...........7899**********9************99 PP

                                    ..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                      + d+  ++++  lg   ++   +++ + +LSgG+k r+ala ++++ +++lllDEpt+
  gi|121637403|ref|YP_977626.1| 422 haAPDAGEQDLRGLLGAFMFTGPQLEQPAGTLSGGEKTRLALAGLVASTANVLLLDEPTN 481
                                    98666667777777888888888888888******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.5e-05     0.018       3      27 ..      33      51 ..      32      72 .. 0.79
   2 !   23.6   0.2   7.9e-08   4.1e-05     229     302 ..     154     228 ..      77     229 .. 0.80
   3 !   17.2   0.1     7e-06    0.0036       3      44 ..     365     400 ..     364     419 .. 0.79
   4 !   28.9   0.0   1.9e-09   9.9e-07     227     299 ..     443     509 ..     403     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldr 27
                                   +l+G+Ng+GK++ L++l      ++
  gi|121637403|ref|YP_977626.1| 33 GLVGRNGAGKTTTLRIL------AG 51
                                   69***************......44 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 7.9e-08
                         AAA_21 229 gqelparelSdGtkrllalltallralkkg....sllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                         +r lS G++r   l+ +l++a ++g    ++ll+DEp n+L+   l  l ++l++++     +++ +H+  l+
  gi|121637403|ref|YP_977626.1| 154 VLTQRLRTLSGGQRRRVELARILFAASESGagnsTTLLLDEPTNHLDADSLGWLRDFLRLHTG---GLVVISHNVDLV 228
                                    555667889******99999999999999999**************************99998...9******98776 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 7e-06
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44 
                                    v+ G Ng+GK++LL++l ++       +++t +l +g g+r+
  gi|121637403|ref|YP_977626.1| 365 VILGLNGAGKTTLLRLLAGV------EQPDTGVLEPGYGLRI 400
                                    99***************555......6666666666666554 PP

  == domain 4  score: 28.9 bits;  conditional E-value: 1.9e-09
                         AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    g   e pa  lS G k  lal+ ++++++    +ll+DEp n+L+P+  + +l+ l++ +     v+l+TH+p
  gi|121637403|ref|YP_977626.1| 443 GPQLEQPAGTLSGGEKTRLALAGLVASTA---NVLLLDEPTNNLDPASREQVLDALRSYRG---AVVLVTHDP 509
                                    556788999********************...89*******************99988866...********9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.19        96      29      39 ..      34      44 ..      26      49 .. 0.86
   2 !   10.4   0.0   0.00063      0.32     136     205 ..     161     231 ..      83     245 .. 0.82
   3 ?    4.4   0.0     0.041        21      27      41 ..     364     378 ..     351     382 .. 0.82
   4 !   13.1   0.0   9.5e-05     0.049     136     194 ..     452     504 ..     407     515 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                                   EEESTTSSHHH CS
                                   xxxxxxxxxxx RF
                          SMC_N 29 ivGpNGSGKsn 39
                                   +vG+NG+GK+ 
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTT 44
                                   89*******96 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00063
                                    CS-HHHHHHHHHH.HHHHHHC..CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvala.LlfAiqk..vkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                    +LSgG++  v la +lfA  +  +  +   llDe   +LD+     + ++l+ ++    ++vis++ ++++++
  gi|121637403|ref|YP_977626.1| 161 TLSGGQRRRVELArILFAASEsgAGNSTTLLLDEPTNHLDADSLGWLRDFLRLHT--GGLVVISHNVDLVADV 231
                                    7******99999857889665125678999**********************999..8899999998887655 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.041
                                    EEEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnll 41 
                                     +i+G NG+GK+ ll
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLL 378
                                    5899********986 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 9.5e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194
                                    +LSgGekt +ala l+A      a + llDe   +LD + +++v + l++ +    ++ 
  gi|121637403|ref|YP_977626.1| 452 TLSGGEKTRLALAGLVAS----TANVLLLDEPTNNLDPASREQVLDALRSYR--GAVVL 504
                                    69******9999988775....57799********************99887..33444 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   3.5   8.6e-11   4.4e-08       5      76 ..     242     314 ..     238     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.6e-11
                   ABC_tran_Xtn   5 ngklteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLekl.ekiekp 76 
                                    +g++  Y+  +++y+  ++ ++++  +++++ +++ + l++  ++++aka+ka +aq++ ++ +++   ++++
  gi|121637403|ref|YP_977626.1| 242 RGQVDVYNMGWQRYVDARATDEQRRIRERANAERKAAALRAQAAKLGAKATKAVAAQNMLRRADRMmAALDEE 314
                                    899***************************************************************5333333 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00035      0.18      25      88 ..     154     211 ..     146     212 .. 0.73
   2 !   16.2   0.1   1.8e-05    0.0093      26      89 ..     446     496 ..     440     497 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00035
                        SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                     l ++ +tlSGG+++ +    +++a++           +  +++LDE  + lD++s+  l ++l
  gi|121637403|ref|YP_977626.1| 154 VLTQRLRTLSGGQRRRVELARILFAASESGAG------NSTTLLLDEPTNHLDADSLGWLRDFL 211
                                    578999*******9666555455444444444......3579*************998776665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.8e-05
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    l++ +gtlSGGek         +ala l+ s      +  +++LDE  ++lD+ s++++l++l+
  gi|121637403|ref|YP_977626.1| 446 LEQPAGTLSGGEK-------TRLALAGLVAS------TANVLLLDEPTNNLDPASREQVLDALR 496
                                    78999********.......33344455555......3568********************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00069      0.36       1     114 [.      32     163 ..      32     176 .. 0.74
   2 ?    0.5   0.0       1.6   8.3e+02      76     120 ..     235     277 ..     187     287 .. 0.58
   3 !   11.1   0.0   0.00086      0.44       1      40 [.     364     412 ..     364     437 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00069
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvake.nglllevdpe.....aldeskrldedkldklldaleenssaleeg 74 
                                    I+l G  G+GKtt  + L+ +       ++v +  +  +l++dp+      l + ++l    ld+ll+ le++ +     
  gi|121637403|ref|YP_977626.1|  32 IGLVGRNGAGKTTTLRILAGEV--EPYAGSVTRAgEIGYLPQDPKvgdldVLARDRVLSARGLDVLLTDLEKQQA----- 104
                                    8999**************8886..333334333303334455555666769999999999999999999999765..... PP

                         AAA_18  75 knlvidghlaeleseaakdikk......................vvLtaspeelleRlekRg 114
                                       ++  +  e e ++a+++++                        L +++ +l +Rl++ +
  gi|121637403|ref|YP_977626.1| 105 ---LMAEVADEDERDRAIRRYGqleerfvalggygaeseagricASLGLPERVLTQRLRTLS 163
                                    ...88888888887777777777888887777888888888888888888888888888765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.6
                         AAA_18  76 nlvidghlaeleseaakdikk.......vvLtaspeelleRlekRgyeeaki 120
                                    ++ +d ++++                   +++a+     +R+++R + e+k 
  gi|121637403|ref|YP_977626.1| 235 VWFLDAVRGQV---------DvynmgwqRYVDARATDEQRRIRERANAERKA 277
                                    33444444333.........03333333566777777777888888777665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00086
                         AAA_18   1 IlltGtpGvGKttlakeL....skrlgf.........gvnlrdvakengllle 40 
                                    +++ G  G+GKttl + L    +              g +++  a+e+++l+ 
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLagveQ----PdtgvlepgyGLRIGYFAQEHDTLDN 412
                                    789***************44332....13333555556666666666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0064       3.3      17      39 ..      24      46 ..      19      49 .. 0.80
   2 ?   -1.7   0.0       4.8   2.5e+03      28      38 ..     179     189 ..     161     193 .. 0.69
   3 !   12.7   0.0   0.00016     0.081      12      39 ..     351     378 ..     349     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0064
                         AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                   +++++ + + l+G++G+GK+T l
  gi|121637403|ref|YP_977626.1| 24 LRVQPGDRIGLVGRNGAGKTTTL 46
                                   56676677889*********965 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.8
                         AAA_29  28 tGpsGsGKSTl 38 
                                    + +sG+G ST 
  gi|121637403|ref|YP_977626.1| 179 ASESGAGNSTT 189
                                    557999*9995 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00016
                         AAA_29  12 fdghtieidlkgatlltGpsGsGKSTll 39 
                                    f+g ++ id+ + +++ G +G+GK+Tll
  gi|121637403|ref|YP_977626.1| 351 FTGVDLAIDRGSRVVILGLNGAGKTTLL 378
                                    8888999997779**************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.5    0.0032       1.6      24      38 ..      34      48 ..      32      51 .. 0.86
   2 !   14.3   0.0   8.3e-05     0.042      22      39 ..     364     381 ..     345     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0032
                         AAA_23 24 ItGpNGaGKTTildA 38
                                   ++G NGaGKTT l+ 
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRI 48
                                   79*********9975 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.3e-05
                         AAA_23  22 tlItGpNGaGKTTildAi 39 
                                    ++I G NGaGKTT+l+ +
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLL 381
                                    59*************876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.14        73      16      35 ..      31      50 ..      25      56 .. 0.85
   2 !   16.7   0.0   7.5e-06    0.0038      12      36 ..     359     383 ..     349     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                   EEEEEESTTSSHHHHHHHHH CS
                            Arf 16 rilllGLDnaGKtTilkklk 35
                                   ri l+G  +aGKtT l  l 
  gi|121637403|ref|YP_977626.1| 31 RIGLVGRNGAGKTTTLRILA 50
                                   67799**********98776 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.5e-06
                                    TTEEEEEEEESTTSSHHHHHHHHHH CS
                            Arf  12 kkelrilllGLDnaGKtTilkklkl 36 
                                    ++  r+++lGL +aGKtT+l  l  
  gi|121637403|ref|YP_977626.1| 359 DRGSRVVILGLNGAGKTTLLRLLAG 383
                                    6788****************98865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0013      0.65       1      22 [.      31      52 ..      31      99 .. 0.82
   2 !    9.2   0.0    0.0025       1.3       1      21 [.     363     383 ..     363     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                                   EEEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltge 22
                                   ++++vGr  +GK+t ++ l ge
  gi|121637403|ref|YP_977626.1| 31 RIGLVGRNGAGKTTTLRILAGE 52
                                   699****************996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
                                    EEEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg 21 
                                    +v+i+G   +GK+tL++ l g
  gi|121637403|ref|YP_977626.1| 363 RVVILGLNGAGKTTLLRLLAG 383
                                    699**************9987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0013      0.67       5      23 ..      33      51 ..      30      60 .. 0.86
   2 !    9.0   0.0     0.002         1       4      22 ..     364     382 ..     362     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                   EEEESTTSSHHHHHHHHHH CS
                          SRP54  5 llvGlqGaGKTttlaKLaa 23
                                    lvG +GaGKTttl  La 
  gi|121637403|ref|YP_977626.1| 33 GLVGRNGAGKTTTLRILAG 51
                                   59***********998885 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                                    EEEEESTTSSHHHHHHHHH CS
                          SRP54   4 illvGlqGaGKTttlaKLa 22 
                                    ++++Gl+GaGKTt l  La
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLA 382
                                    7899*********998887 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.013       6.4      23      38 ..      36      51 ..      31      66 .. 0.88
   2 ?   -2.0   0.5       1.9     1e+03     329     357 ..     272     300 ..     248     324 .. 0.42
   3 !   12.2   0.0    0.0001     0.052      20      41 ..     365     386 ..     353     393 .. 0.89
   4 ?   -0.1   0.0      0.52   2.7e+02     494     510 ..     447     463 ..     439     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G+NGaGKTt  r+l+ 
  gi|121637403|ref|YP_977626.1| 36 GRNGAGKTTTLRILAG 51
                                   9********9999985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                         AAA_13 329 eaealeeqLkglqraleaKrkepfksvel 357
                                    +ae  +++L++   +l aK ++ ++  ++
  gi|121637403|ref|YP_977626.1| 272 NAERKAAALRAQAAKLGAKATKAVAAQNM 300
                                    22222222333333333332222222222 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0001
                         AAA_13  20 liYGwNGaGKTtLSrllrslel 41 
                                    +i G NGaGKTtL rll+ +e+
  gi|121637403|ref|YP_977626.1| 365 VILGLNGAGKTTLLRLLAGVEQ 386
                                    799***************9976 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.52
                         AAA_13 494 sqaaetLSeGEktaIaf 510
                                    +q+a+tLS GEkt  a+
  gi|121637403|ref|YP_977626.1| 447 EQPAGTLSGGEKTRLAL 463
                                    799**********8886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00069      0.35      29     169 ..      34     220 ..      24     221 .. 0.61
   2 ?    1.0   0.1      0.96   4.9e+02      54     122 ..     236     319 ..     225     337 .. 0.51
   3 !   12.6   0.4   0.00026      0.13      22      52 ..     359     399 ..     353     505 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00069
                         AAA_16  29 lsGesGvGKsslvrellralekdggiflrgkcdql.esa........ipysalaqalareellrqlldeaesaeleawre 99 
                                    l+G  G GK++ +r l+ ++e   g ++r+    + +++        ++++ +++a   + ll++l+ +++  +  a   
  gi|121637403|ref|YP_977626.1|  34 LVGRNGAGKTTTLRILAGEVEPYAGSVTRAGEIGYlPQDpkvgdldvLARDRVLSARGLDVLLTDLEKQQALMAEVA--- 110
                                    89***************988877555555555555333322223333233333333333444444444422222222... PP

                         AAA_16 100 kleeala............................................avpelagaea........srllellkrll 127
                                                                                                         +r + +l+r+l
  gi|121637403|ref|YP_977626.1| 111 ------DederdrairrygqleerfvalggygaeseagricaslglpervlT--------QrlrtlsggQRRRVELARIL 176
                                    ......2333333334666788888899999999999997777766444441........03446666688888999999 PP

                         AAA_16 128 .allsrderp.lvlvlDd.lqwadeaslqllaaLlrlleskpllv 169
                                     a +++++   + l+lD+    +d++sl +l+ +lrl + + l+v
  gi|121637403|ref|YP_977626.1| 177 fAASESGAGNsTTLLLDEpTNHLDADSLGWLRDFLRLHT-GGLVV 220
                                    6666665555788888862669***********999977.46666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.96
                         AAA_16  54 if...lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala.....avpelagaea.......sr 118
                                    +f   +rg+ d + ++  +++ a+a ++ + +r+ ++++++a++ +++++ ++a a     a++ l++a++       +r
  gi|121637403|ref|YP_977626.1| 236 WFldaVRGQVDVYNMGWQRYVDARATDEQRRIRERANAERKAAALRAQAAKLGAKAtkavaAQNMLRRADRmmaaldeER 315
                                    45566788888887775555544555455555555555333333333333333222244443333333322433444455 PP

                         AAA_16 119 llel 122
                                    ++++
  gi|121637403|ref|YP_977626.1| 316 VADK 319
                                    5555 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00026
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd...........g 52 
                                    +r++ v++ G  G GK++l+r l+  +e+            +
  gi|121637403|ref|YP_977626.1| 359 DRGSRVVILGLNGAGKTTLLRLLA-GVEQPdtgvlepgyglR 399
                                    5667899***************99.56666344443333332 PP

>> Herpes_UL36  Herpesvirus UL36 tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.4   1.3e-06   0.00066     139     221 ..     226     308 ..     219     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                    Herpes_UL36 139 elvlelsgdLlqvpaLaeyvdFyrrsYekfldiraaLeelradvrrAlgrvalelaaAlEevaevrrdpeaAkealeeGv 218
                                    +lv  + +++  + a+++ vd y+ ++++++d ra+ e++r + r  ++r+a  l a + ++ +   +  aA+++l++ +
  gi|121637403|ref|YP_977626.1| 226 DLVADVVNKVWFLDAVRGQVDVYNMGWQRYVDARATDEQRRIRERANAERKAAALRAQAAKLGAKATKAVAAQNMLRRAD 305
                                    6788888899999999***********************************9999888888888887899*******999 PP

                    Herpes_UL36 219 sii 221
                                    +++
  gi|121637403|ref|YP_977626.1| 306 RMM 308
                                    865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.013       6.6       2      22 ..      32      52 ..      31      68 .. 0.79
   2 ?   -1.5   0.3       5.2   2.7e+03     123     149 ..     261     288 ..     234     321 .. 0.67
   3 !   12.8   0.0    0.0002       0.1       1      21 [.     363     385 ..     363     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                         AAA_28  2 ivitGgestGKTtlleaLaar 22
                                   i ++G  ++GKTt+l+ La +
  gi|121637403|ref|YP_977626.1| 32 IGLVGRNGAGKTTTLRILAGE 52
                                   678999************954 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.2
                         AAA_28 123 ddgeRre.dleereaiderlrealrelg 149
                                    +d++Rr  + +++e+ +++lr+   +lg
  gi|121637403|ref|YP_977626.1| 261 TDEQRRIrERANAERKAAALRAQAAKLG 288
                                    4444443122334444444444444444 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.0002
                         AAA_28   1 kivitGgestGKTtlleaLa..a 21 
                                    ++vi+G  ++GKTtll+ La  +
  gi|121637403|ref|YP_977626.1| 363 RVVILGLNGAGKTTLLRLLAgvE 385
                                    79*****************9442 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.45   2.3e+02      27      54 ..      31      58 ..      25      87 .. 0.83
   2 !   15.4   0.0   1.3e-05    0.0064      23      71 ..     359     412 ..     348     433 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.45
                           DLIC 27 svlvlGedgsGkttliaklqGveeekkG 54
                                    + ++G +g+Gktt +  l G  e+  G
  gi|121637403|ref|YP_977626.1| 31 RIGLVGRNGAGKTTTLRILAGEVEPYAG 58
                                   56789**********9999997776666 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                           DLIC  23 PsgksvlvlGedgsGkttliaklqGveeekkG.....rGleylyldvkdedrdd 71 
                                      g  v++lG +g+Gkttl+  l Gve++  G      Gl   y+  + +  d+
  gi|121637403|ref|YP_977626.1| 359 DRGSRVVILGLNGAGKTTLLRLLAGVEQPDTGvlepgYGLRIGYFAQEHDTLDN 412
                                    56789***********************97652222168888887766555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.059        30       4      21 ..      34      51 ..      32      59 .. 0.85
   2 ?    1.4   0.3      0.64   3.3e+02      44     120 ..     266     305 ..     193     326 .. 0.60
   3 !   12.0   0.1   0.00034      0.17       2      32 ..     364     395 ..     364     514 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.059
                         AAA_33  4 lvGlpGsGKstlaerllk 21
                                   lvG +G+GK+t ++ l+ 
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRILAG 51
                                   79*********9997765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.64
                         AAA_33  44 sktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                    +++++++++ ++ + l++ a+k                                    +  ++  ++++++  +Ra+
  gi|121637403|ref|YP_977626.1| 266 RIRERANAERKA-AALRAQAAK------------------------------------LGAKATKAVAAQNMLRRAD 305
                                    222211111111.122222222....................................2233333333444444433 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00034
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.avllssdt 32 
                                    v++ Gl+G+GK+tl++ l+  ++  + + ++ 
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLAGVEQpDTGVLEPG 395
                                    6789************9976555533333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2    0.0051       2.6      10      32 ..      34      56 ..      30     227 .. 0.68
   2 !    8.5   0.2    0.0043       2.2       8      26 ..     364     382 ..     358     506 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0051
                         AAA_22 10 vtGesGtGKTtllrrlleqldee 32
                                   ++G  G+GKTt+lr l+ + + +
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRILAGEVEPY 56
                                   79************999887544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                         AAA_22   8 lvvtGesGtGKTtllrrll 26 
                                    +v+ G  G+GKTtllr l+
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLA 382
                                    7899************987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.027        14     103     132 ..      33      62 ..      25      68 .. 0.82
   2 !    9.7   0.0    0.0015      0.76     100     127 ..     362     389 ..     353     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                                    EEECSTTSSHHHHHHHHCTT-----S---- CS
                    RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevse 132
                                     lvG  G+GK+t +  l++e e   g+v +
  gi|121637403|ref|YP_977626.1|  33 GLVGRNGAGKTTTLRILAGEVEPYAGSVTR 62 
                                    589***************998877776665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                                    SEEEEECSTTSSHHHHHHHHCTT----- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelkt 127
                                    + +v++G  G+GK+tL+  l++ ++  t
  gi|121637403|ref|YP_977626.1| 362 SRVVILGLNGAGKTTLLRLLAGVEQPDT 389
                                    6789****************99777666 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00064      0.33      14      37 ..      26      49 ..      21      50 .. 0.87
   2 ?   -1.2   0.8      0.53   2.7e+02     815     856 ..     261     302 ..     239     329 .. 0.50
   3 !   12.8   0.3     3e-05     0.015      18      37 ..     362     381 ..     352     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00064
                        DUF3584 14 ldldghtnieGtNaaGKTtLlrLi 37
                                   +++ ++  ++G N+aGKTt+lr++
  gi|121637403|ref|YP_977626.1| 26 VQPGDRIGLVGRNGAGKTTTLRIL 49
                                   677788999*************86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.53
                        DUF3584 815 eerpalkeqveelesaaeeleqeltrliedtklerkkleker 856
                                       +++  + ++ e++a+ l+ + ++l +++++  ++ ++ r
  gi|121637403|ref|YP_977626.1| 261 TDEQRRIRERANAERKAAALRAQAAKLGAKATKAVAAQNMLR 302
                                    333333333334444444444444443333333333333222 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 3e-05
                        DUF3584  18 ghtnieGtNaaGKTtLlrLi 37 
                                     ++ i G N+aGKTtLlrL+
  gi|121637403|ref|YP_977626.1| 362 SRVVILGLNGAGKTTLLRLL 381
                                    57899**************7 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.016       8.4       4      22 ..      31      49 ..      29      56 .. 0.86
   2 !    7.5   0.0    0.0058         3       3      22 ..     362     381 ..     360     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   +i ++G +g+GKTt+++ l
  gi|121637403|ref|YP_977626.1| 31 RIGLVGRNGAGKTTTLRIL 49
                                   799***********99865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0058
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                     +++i G +g+GKTtl++ l
  gi|121637403|ref|YP_977626.1| 362 SRVVILGLNGAGKTTLLRLL 381
                                    689*************9987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0021       1.1      21      47 ..      34      60 ..      29      63 .. 0.87
   2 ?    4.4   0.0     0.039        20      19      39 ..     364     384 ..     358     393 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                     Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvv 47
                                   l+G  GAGK+++++ l+ e+e++ + v
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRILAGEVEPYAGSV 60
                                   89****************999776665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                     Zeta_toxin  19 illgGqpGAGKselaellkde 39 
                                    +++ G  GAGK++l++ll+  
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLAGV 384
                                    5666889*********99865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.017       8.7      19      42 ..      29      52 ..      10      61 .. 0.82
   2 !    7.5   0.0    0.0074       3.8      19      59 ..     361     402 ..     337     416 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                   TEEEEEEESTTSSHHHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglaka 42
                                   gd i L G  GaGKTt  r la +
  gi|121637403|ref|YP_977626.1| 29 GDRIGLVGRNGAGKTTTLRILAGE 52
                                   66799************9998866 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0074
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--.----TTTTSEEEE CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve.evkSPTFtlveeY 59 
                                    g+ +++ G  GaGKTtl r la   + +  v  P + l   Y
  gi|121637403|ref|YP_977626.1| 361 GSRVVILGLNGAGKTTLLRLLAGVEQPDtGVLEPGYGLRIGY 402
                                    4558888999*********99866555556777777665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.036        19       3      21 ..      32      50 ..      30      55 .. 0.84
   2 ?   -2.7   0.0       9.4   4.8e+03      42      84 ..     264     308 ..     263     313 .. 0.77
   3 !    9.4   0.2    0.0018      0.94       2      21 ..     363     382 ..     362     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.036
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   + l G++G GKTt l+ la
  gi|121637403|ref|YP_977626.1| 32 IGLVGRNGAGKTTTLRILA 50
                                   5689*********999887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.4
                                    TTTTTTS-...-HCHHHCCCCTS--SSS-C..CHHHHCCSCCCEE CS
                          NACHT  42 lrelsrsgnarsladllfsqlpepaapvse..vwavllelperlL 84 
                                    +r+++++ na + a  l++q  +++a+ ++    +++l++++r++
  gi|121637403|ref|YP_977626.1| 264 QRRIRERANAERKAAALRAQAAKLGAKATKavAAQNMLRRADRMM 308
                                    678888888888888999999999999888766778888888876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0018
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                     v++ G +G GKTtLl+ la
  gi|121637403|ref|YP_977626.1| 363 RVVILGLNGAGKTTLLRLLA 382
                                    699*************9775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0058       2.9      28      43 ..      34      49 ..      30      50 .. 0.93
   2 ?    4.9   0.0     0.034        18      25      43 ..     363     381 ..     345     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                         AAA_15 28 liGkNnsGKSsileal 43
                                   l+G+N++GK++ l++l
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRIL 49
                                   8************998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                         AAA_15  25 ltvliGkNnsGKSsileal 43 
                                      v+ G N++GK+++l++l
  gi|121637403|ref|YP_977626.1| 363 RVVILGLNGAGKTTLLRLL 381
                                    56899***********998 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.065        33       4      20 ..      33      49 ..      31      60 .. 0.84
   2 ?    8.9   0.1     0.002         1       3      21 ..     364     382 ..     362     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.065
                                   EEEESTTCCHHHHHHHH CS
                           cobW  4 vltGflGsGKTtLlnhl 20
                                   +l+G  G+GKTt l+ l
  gi|121637403|ref|YP_977626.1| 33 GLVGRNGAGKTTTLRIL 49
                                   78999*******99866 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    +v+ G  G+GKTtLl+ l 
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLA 382
                                    6899***********9765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.035        18       3      24 ..      31      52 ..      29      61 .. 0.85
   2 ?    6.7   0.0     0.011       5.5       2      23 ..     362     383 ..     361     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.035
                      PduV-EutP  3 killiGkvgsGKttLtqalkge 24
                                   +i l+G+ g+GKtt  + l ge
  gi|121637403|ref|YP_977626.1| 31 RIGLVGRNGAGKTTTLRILAGE 52
                                   7889**********99998887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkg 23 
                                    ++++++G  g+GKttL + l g
  gi|121637403|ref|YP_977626.1| 362 SRVVILGLNGAGKTTLLRLLAG 383
                                    5899************999877 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.031        16       2      23 ..      32      53 ..      31     135 .. 0.75
   2 ?    6.0   0.0      0.02        10       2      21 ..     364     383 ..     363     430 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                           MobB  2 lgivgksgsGKTtLleklipel 23
                                   +g+vg++g+GKTt l  l  e+
  gi|121637403|ref|YP_977626.1| 32 IGLVGRNGAGKTTTLRILAGEV 53
                                   799**********998887665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                           MobB   2 lgivgksgsGKTtLleklip 21 
                                    + i g +g+GKTtLl  l  
  gi|121637403|ref|YP_977626.1| 364 VVILGLNGAGKTTLLRLLAG 383
                                    56899*********987754 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.11        55       3      18 ..      36      51 ..      35      63 .. 0.85
   2 ?    6.5   0.0     0.012         6       3      17 ..     368     382 ..     366     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                                   ESTTSSHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellke 18
                                   G +GaGKtt +++l+ 
  gi|121637403|ref|YP_977626.1| 36 GRNGAGKTTTLRILAG 51
                                   779********99975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                                    ESTTSSHHHHHHHHH CS
                Thymidylate_kin   3 GlDGaGKttqaellk 17 
                                    Gl+GaGKtt ++ll+
  gi|121637403|ref|YP_977626.1| 368 GLNGAGKTTLLRLLA 382
                                    9**********9997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0059         3       3      23 ..      34      54 ..      32      71 .. 0.85
   2 ?   -1.8   0.1       7.8     4e+03      70     127 ..      81     128 ..      75     130 .. 0.63
   3 ?    4.7   0.1     0.074        38       2      19 ..     365     382 ..     364     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0059
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   l+G  G GKT++ + +a e++
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRILAGEVE 54
                                   89***************9975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.8
                                    HHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEE CS
                            AAA  70 laksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrk 127
                                    la++r       + r +++Llt l++++       +++   ++d+ d+a++r g ++++
  gi|121637403|ref|YP_977626.1|  81 LARDR-----VLSARGLDVLLTDLEKQQA------LMAEVADEDERDRAIRRyGQLEER 128
                                    55555.....4556667777777776666......455556677778888877777766 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.074
                                    EEESSTTSSHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakava 19 
                                    ++ G  G GKT+l + +a
  gi|121637403|ref|YP_977626.1| 365 VILGLNGAGKTTLLRLLA 382
                                    67899**********998 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.18        92       2      18 ..      32      48 ..      31      61 .. 0.82
   2 ?    6.9   0.0     0.014         7       1      19 [.     363     381 ..     363     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                                   EEEESSTTSSHHHHHHC CS
                            Roc  2 vvlvGdsgvGKtsllkr 18
                                   + lvG +g+GKt+ l+ 
  gi|121637403|ref|YP_977626.1| 32 IGLVGRNGAGKTTTLRI 48
                                   779*********98764 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                                    EEEEESSTTSSHHHHHHCH CS
                            Roc   1 KvvlvGdsgvGKtsllkrf 19 
                                    +vv++G +g+GKt+ll+ +
  gi|121637403|ref|YP_977626.1| 363 RVVILGLNGAGKTTLLRLL 381
                                    69*************9755 PP

>> Pox_F12L  Poxvirus F12L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00074      0.38     295     383 ..     215     303 ..     204     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00074
                       Pox_F12L 295 dkgWtliged.tlvsrdglkvlllDlakFspslslseYvehWaraevelpkdlitkaeakrkakalekassaaaklLyea 373
                                      g ++i+++  lv    +kv +lD+ + ++++  + + ++ + ++++ ++ ++ +a+a+rka+al +++++      +a
  gi|121637403|ref|YP_977626.1| 215 TGGLVVISHNvDLVADVVNKVWFLDAVRGQVDVYNMGWQRYVDARATDEQRRIRERANAERKAAALRAQAAKLGAKATKA 294
                                    567788888888****************999999999999999999999999********************99999999 PP

                       Pox_F12L 374 vlaqsaaLne 383
                                    v aq   L++
  gi|121637403|ref|YP_977626.1| 295 VAAQNM-LRR 303
                                    988864.444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0035       1.8      23      44 ..      34      55 ..      26      68 .. 0.81
   2 ?   -2.4   2.1       6.6   3.4e+03      47     184 ..     265     298 ..     254     321 .. 0.47
   3 ?    9.5   0.3    0.0015      0.76      19      45 ..     362     388 ..     354     517 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                         AAA_30 23 ltGpAGtGKttalkalreawea 44
                                   l+G+ G+GKtt+l+ l+  +e 
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLRILAGEVEP 55
                                   79************99876665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.6
                         AAA_30  47 grviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDer 126
                                    +r+   A  ++ A++L++++                                                            
  gi|121637403|ref|YP_977626.1| 265 RRIRERANAERKAAALRAQAA----------------------------------------------------------- 285
                                    444555555555555553322........................................................... PP

                         AAA_30 127 QlasVeaGgvlrdlveaagigtaeLtevvRqkeseeraaalalregdae...ealealadr 184
                                                                                    +   +a +a+a++
  gi|121637403|ref|YP_977626.1| 286 ------------------------------------------------KlgaKATKAVAAQ 298
                                    ................................................1112222222222 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa 45 
                                      +v+ G  G+GKtt+l+ l+ + + +
  gi|121637403|ref|YP_977626.1| 362 SRVVILGLNGAGKTTLLRLLAGVEQPD 388
                                    457899************998776655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.08        41      31      44 ..      34      47 ..      23      51 .. 0.87
   2 ?   -1.9   1.4         4     2e+03     160     203 ..     275     317 ..     266     320 .. 0.77
   3 ?    6.5   0.0     0.011       5.4      14      44 ..     351     379 ..     343     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.08
                         AAA_27 31 iyGpNEAGKstalr 44
                                   ++G N AGK+t+lr
  gi|121637403|ref|YP_977626.1| 34 LVGRNGAGKTTTLR 47
                                   58**********98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                         AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelreaqvr 203
                                    +  +aL+a+a +l ++ +++  a+++ l++ +++ ++l e+ v 
  gi|121637403|ref|YP_977626.1| 275 RKAAALRAQAAKLGAKATKAV-AAQNMLRRADRMMAALDEERVA 317
                                    566789999999998888888.8888888888888888777765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                         AAA_27  14 ftdrsldfsaeeadlhliyGpNEAGKstalr 44 
                                    ft+  l+++  + +  +i+G N AGK+t+lr
  gi|121637403|ref|YP_977626.1| 351 FTGVDLAID--RGSRVVILGLNGAGKTTLLR 379
                                    555555555..4455699**********998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.19        99      33      51 ..      29      47 ..      23      59 .. 0.82
   2 ?   -2.1   1.6       4.8   2.5e+03      85     136 ..     266     319 ..     259     326 .. 0.55
   3 ?    6.6   0.2    0.0099       5.1      30      54 ..     358     382 ..     354     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                         AAA_25 33 gelallaGapgtGKttlal 51
                                   g+ + l+G+ g+GKtt + 
  gi|121637403|ref|YP_977626.1| 29 GDRIGLVGRNGAGKTTTLR 47
                                   677789*********9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                         AAA_25  85 elrrRlravgeal...rddarllvldlagv.eslpLfakdrggtlltadvdaleaa 136
                                    ++r+R+ a ++a+   ++ a+l +   + v  +++L+ +dr +++l+++  +++++
  gi|121637403|ref|YP_977626.1| 266 RIRERANAERKAAalrAQAAKLGAKATKAVaAQNMLRRADRMMAALDEE--RVADK 319
                                    5555555555444444334444444444555677788778777776665..34444 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0099
                         AAA_25  30 lpagelallaGapgtGKttlaldla 54 
                                    + +g+ +++ G  g+GKttl+  la
  gi|121637403|ref|YP_977626.1| 358 IDRGSRVVILGLNGAGKTTLLRLLA 382
                                    7899****************87666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 3744.06
//
Query:       gi|121637404|ref|YP_977627.1|  [L=63]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.1   0.1      0.068   12.7   0.1    1.1  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.12   12.5   1.7       0.22   11.5   1.7    1.6  1  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.6e-06     0.068       7      40 ..      10      45 ..       6      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-06
                         HTH_24  7 kILelLqk..nprisqreLAerlglSpstvnrrlkr 40
                                   ++L++L+   +++ s+r LA  +g S + ++  l++
  gi|121637404|ref|YP_977627.1| 10 QLLRELRNayEGGASIRNLAATTGRSYGSIHSMLRE 45
                                   6899999999*********************99985 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   2.5e-05      0.22       5      35 ..      15      45 ..      13      63 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                         HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkr 35
                                   l++++eG+ +++++A+ +g s+ ++   l+ 
  gi|121637404|ref|YP_977627.1| 15 LRNAYEGGASIRNLAATTGRSYGSIHSMLRE 45
                                   689999*99****************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 428.81
//
Query:       gi|121637405|ref|YP_977628.1|  [L=187]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-17   62.7   0.2    4.2e-17   61.7   0.2    1.6  1  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.038   14.6   4.7      0.021   15.5   2.4    1.7  2  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.2   4.7e-21   4.2e-17       1      47 []      16      62 ..      16      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.7e-21
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Ild+Ar++fae+Gyd++tvr++ ++ G+s+ga++++F++K++L+ al
  gi|121637405|ref|YP_977628.1| 16 ILDGARRCFAEYGYDKATVRRLEQAIGMSRGAIFHHFRDKDALFFAL 62
                                   9*******************************************986 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   2.4   2.3e-06     0.021      28     119 ..      25     130 ..       4     138 .. 0.70
   2 ?   -1.8   0.0      0.51   4.6e+03      89     105 ..     159     170 ..     147     185 .. 0.43

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-06
                                    HHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...........CCC.HHHHHHHHHHHHHHHHHHHHHHHHC CS
                    Hemerythrin  28 aevhga...lrklaelldelvdeleaHhaaEEellfPlle..........drpggravldvlereHdeirelleelrell 94 
                                    ae  ++    r+l+++++  + ++ +H++++++l+f l +           r+g  +v++++ +  d+++ l+ +l+ + 
  gi|121637405|ref|YP_977628.1|  25 AEYGYDkatVRRLEQAIGMSRGAIFHHFRDKDALFFALARedtermaavaSREGLIGVMRDMLAAPDQFDWLATRLEIAR 104
                                    222233566999****************************9999999999999999999999999999999999998555 PP

                                    HTCG.GSTCHHHHHHHHHHHHHHHHH CS
                    Hemerythrin  95 kgle.epsaaafaelleeladllreH 119
                                    k  + +  ++ +ae+ +ela++  + 
  gi|121637405|ref|YP_977628.1| 105 KLRNdPDFSRGWAERSAELAAATTDR 130
                                    55552334444555555554444443 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.51
                                    HHH.HHCHTCGGSTCHHH CS
                    Hemerythrin  89 elr.ellkgleepsaaaf 105
                                    +l  +l+ g +      +
  gi|121637405|ref|YP_977628.1| 159 GLLaRLASGED------P 170
                                    33312222211......1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1338.94
//
Query:       gi|121637406|ref|YP_977629.1|  [L=943]
Description: aconitate hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.5e-179  596.0   0.0   7.9e-179  595.5   0.0    1.2  1  Aconitase    Aconitase family (aconitate hydratase)
      3e-41  140.8   0.0    4.8e-41  140.1   0.0    1.3  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.5   0.0  8.8e-183  7.9e-179       4     461 .]      67     606 ..      55     606 .. 0.94

  Alignments for each domain:
  == domain 1  score: 595.5 bits;  conditional E-value: 8.8e-183
                      Aconitase   4 wdahlveeegiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknled 78 
                                    wd +++ + +i+y+p+rv++qd+tgv+++vdla++rea+++lgg+++++++l+p+dlvidhsv     g+++a+e+n+e 
  gi|121637406|ref|YP_977629.1|  67 WDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPADLVIDHSViadlfGRADAFERNVEI 146
                                    554433332399******************************************************************** PP

                      Aconitase  79 efernkeryefLksaakaf.girvvppgqGIvHqvnlEy.........glalpgktvvgtDSHTtmigglGvlaiGvGgi 148
                                    e++rn ery+fL++++ af +++vvppg+GIvHqvn+Ey         g+a+p+ t+vgtDSHTtm++glGvl++GvGgi
  gi|121637406|ref|YP_977629.1| 147 EYQRNGERYQFLRWGQGAFdDFKVVPPGTGIVHQVNIEYlasvvmtrdGVAYPD-TCVGTDSHTTMVNGLGVLGWGVGGI 225
                                    ******************************************************.************************* PP

                      Aconitase 149 eaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvG 228
                                    eaea++lgqp+++ ip+vvg++ltG++++gvta+D+vl+v+++lr++gvvgk+vEf+Gegv++ +l++raT+ NM++E+G
  gi|121637406|ref|YP_977629.1| 226 EAEAAMLGQPVSMLIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLGNMSPEFG 305
                                    ******************************************************************************** PP

                      Aconitase 229 AttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselv 307
                                    +t+++fp+de+t++YL+ tgr++++v lveay+kaq++++ + ++++e+++ lel+ls+++ps+agpkrPqd+++l + +
  gi|121637406|ref|YP_977629.1| 306 STAAIFPIDEETIKYLRFTGRTPEQVaLVEAYAKAQGMWH-DPKHEPEFSEYLELNLSDVVPSIAGPKRPQDRIALAQAK 384
                                    *************************99************6.556688*****************************6665 PP

                      Aconitase 308 kkefkeele......................................................keaaekaley..klkeg 331
                                     ++f+e++                                                       + ++++ +++  ++  +
  gi|121637406|ref|YP_977629.1| 385 -STFREQIYhyvgngspdsphdphskldevveetfpasdpgqltfanddvatdetvhsaaahaDGRVSNPVRVksDELGE 463
                                    .579998889***********************************************99998844444445554255569 PP

                      Aconitase 332 tklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvga 410
                                    + l++g+v+iaai+SCTN+sn++v++ a+lla +avekgl+ kp+vkt++aPGS+vv++y++++Gl+++Lek+Gf +vg+
  gi|121637406|ref|YP_977629.1| 464 FVLDHGAVVIAAITSCTNTSNPEVMLGAALLArNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLGFYLVGY 543
                                    99****************************************************************************** PP

                      Aconitase 411 gCstCignsdrle........ege....aivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                    gC+tCigns++l+        + +    ++v+s+NRNFegR++p++++ yLaSP+lv+a+AlaG
  gi|121637406|ref|YP_977629.1| 544 GCTTCIGNSGPLPeeiskavnD-NdlsvTAVLSGNRNFEGRINPDVKMnYLASPPLVIAYALAG 606
                                    ************9777776643.26999***********************************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.1   0.0   5.4e-45   4.8e-41       2     130 ..     735     865 ..     734     866 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 5.4e-45
                                    CCCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEE..TTTTEEEEHHHHHHHHHHTT--EEEE CS
                    Aconitase_C   2 ekllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttd..lddgekedvvdaaerykkegaklvvi 79 
                                    +++l ++G++++d +s ++++++++++++gt+ani+l+n+l++++  + t+d  ++ g++  ++daa++y  + ++lvv 
  gi|121637406|ref|YP_977629.1| 735 ARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLDDVSGGYTRDftQPGGPQAFIYDAAQNYAAQHIPLVVF 814
                                    6899****************************************999888872256789999****************** PP

                                    --SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                    Aconitase_C  80 agknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                    +gk++G+GSSR++AAk+++llG++aviaeSFerI+++nli++g++pl+f+e
  gi|121637406|ref|YP_977629.1| 815 GGKEYGSGSSRDWAAKGTLLLGVRAVIAESFERIHRSNLIGMGVIPLQFPE 865
                                    *************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (943 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 6484.91
//
Query:       gi|121637407|ref|YP_977630.1|  [L=186]
Description: hypothetical protein BCG_1538 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   11.9   0.0      0.095   11.9   0.0    1.1  1  DUF4336   Domain of unknown function (DUF4336)


Domain annotation for each model (and alignments):
>> DUF4336  Domain of unknown function (DUF4336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-06     0.095      15      63 ..      16      64 ..       5     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-06
                        DUF4336 15 yvavpiRmtvvkLekggLlvyaPvapTkellelvkeleaehgevkyivl 63
                                   y+   + mt vk e  +L v aP a+T+ lle+v++ ++e  ++k + l
  gi|121637407|ref|YP_977630.1| 16 YIPQDVDMTAVKAEVAALGVSAPPAATPGLLEVVQHARDEGIDLKIVLL 64
                                   5666799*****************************9988877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1440.84
//
Query:       gi|121637408|ref|YP_977631.1|  [L=472]
Description: invasion protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-31  106.2   0.0    1.5e-30  105.3   0.0    1.5  1  NLPC_P60        NlpC/P60 family
  ------ inclusion threshold ------
       0.23   10.8  12.6        0.2   11.0   0.4    2.1  2  GAS             Growth-arrest specific micro-tubule binding
       0.33   10.9   1.4       0.82    9.6   0.8    1.9  2  SCO1-SenC       SCO1/SenC
       0.36    9.7  14.3          1    8.2   1.6    2.1  2  Spc7            Spc7 kinetochore protein
       0.41   10.8   6.6       0.26   11.4   2.1    2.3  2  Cep57_CLD_2     Centrosome localisation domain of PPC89
        9.5    6.9  15.6         12    6.6   6.9    2.4  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   4.9e-34   1.5e-30       1     103 [.     355     469 ..     355     471 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 4.9e-34
                                    T-BB-TT--BTT.............EB-HHHHHHHHHHTTT----SSHHHHCCCSEE..EEGGG--TTEEEEESGTGGES CS
                       NLPC_P60   1 gkpYrwGGksps.............gfDCsglvryafakagielprssgeqeaagkkkeiskselkrGDLvffktkkgis 67 
                                    g+pY+wGG++ +             gfDCsglv y+fa +gi+lp++sg+q++ g+k  i++s+++rGD++f+++ +g++
  gi|121637408|ref|YP_977631.1| 355 GVPYSWGGGNAAgpskgidsgagtvGFDCSGLVLYSFAGVGIKLPHYSGSQYNLGRK--IPSSQMRRGDVIFYGP-NGSQ 431
                                    79********999********************************************..****************.**** PP

                                    EEEEEEETTEEEEEE..TTEEEEEETTSTTBHSCEEEC CS
                       NLPC_P60  68 HvgiYlgngkmlhas..sekvsvsslsekywkkrllgv 103
                                    Hv+iYlgng+ml+a+  + kv+v ++++++++++++++
  gi|121637408|ref|YP_977631.1| 432 HVTIYLGNGQMLEAPdvGLKVRVAPVRTAGMTPYVVRY 469
                                    ***************9999999**********999876 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   6.8e-05       0.2      43     117 ..      44     118 ..      36     123 .. 0.90
   2 ?    3.6   6.5     0.013        38      52     132 ..     151     232 ..     144     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.8e-05
                            GAS  43 ernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfek 117
                                    +    +++++++ n+rl++   ++++e e  +k++ + e  +   ++++  l+++++ +kd        ++rf++
  gi|121637408|ref|YP_977631.1|  44 DTIAALIADVAKANQRLQDLSDEVQAEQESVNKAMVDVETARDNAAAAEDDLEVSQRAVKDANAAIAAAQHRFDT 118
                                    56667899*****************************************************99999999999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                            GAS  52 isqenkrlkepLkkaeeeveeLrk..qlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                    +s+  +  + +L++a+ e+ + +   +l++++ d ++ + +ka    +   l++++ + +  +++++++ +erd+ +++ 
  gi|121637408|ref|YP_977631.1| 151 LSASSQAVMANLQRARTERVNTESaaRLAKQKAD-KAAADAKASQDAAVAALTETRRKFDEQREEVQRLAAERDAAQARL 229
                                    5667778889999999999888873244444444.556789999999999999999999999999999999***999998 PP

                            GAS 130 eaa 132
                                    +aa
  gi|121637408|ref|YP_977631.1| 230 QAA 232
                                    875 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00027      0.82      62     113 ..      36      87 ..      27     102 .. 0.79
   2 ?    5.7   0.3    0.0044        13      41     106 ..      57     119 ..      48     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                      SCO1-SenC  62 fiTvDPerDtpevlkeyleafdpriigltGskeeiakaakefrvyvekvede 113
                                      T DP++Dt ++l + +++ ++r++ l+++ ++ ++ +++ +v ve+++d+
  gi|121637408|ref|YP_977631.1|  36 LATADPQTDTIAALIADVAKANQRLQDLSDEVQAEQESVNKAMVDVETARDN 87 
                                    679************************9997777666666666666655554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0044
                      SCO1-SenC  41 lanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriigltGskeeiakaakefrvy 106
                                     ++++++ d++++e+e+v+  ++ v  +rD+ ++ ++ le  ++    + + +++ia+a ++f  +
  gi|121637408|ref|YP_977631.1|  57 NQRLQDLSDEVQAEQESVNKAMVDVETARDNAAAAEDDLEVSQRA---VKDANAAIAAAQHRFDTF 119
                                    57899999************************9999888855444...455566666666666555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.6   0.00035         1     158     220 ..      53     114 ..      41     123 .. 0.64
   2 ?    6.8   5.4   0.00091       2.7     156     253 ..     149     232 ..     132     239 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00035
                           Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                    ++k ++ l++l +e+++e++++++ + + ++a+++ ++  +++Le  ++++++++a i++ + 
  gi|121637408|ref|YP_977631.1|  53 VAKANQRLQDLSDEVQAEQESVNKAMVDVETARDN-AAAAEDDLEVSQRAVKDANAAIAAAQH 114
                                    45666666666666666666666666666665554.555666666666666666666665554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00091
                           Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                    ++L+++ + +++ l++ ++e+ + e+ ++  +++a++ ++  k++  ++               + l+e +++ +e++e+
  gi|121637408|ref|YP_977631.1| 149 KTLSASSQAVMANLQRARTERVNTESAARLAKQKADKAAADAKASQDAA--------------VAALTETRRKFDEQREE 214
                                    4444444555555555555555444444444444333333333333333..............33444444444444444 PP

                           Spc7 236 ieelkeqkseleeeiaea 253
                                    ++ l+++++ +++++++a
  gi|121637408|ref|YP_977631.1| 215 VQRLAAERDAAQARLQAA 232
                                    444444444444444443 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.18   5.3e+02      43      59 ..      56      72 ..      51      89 .. 0.78
   2 ?   11.4   2.1   8.6e-05      0.26      12      45 ..     201     234 ..     199     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                    Cep57_CLD_2 43 AyeelneLkaevealrk 59
                                   A ++l++L++ev a ++
  gi|121637408|ref|YP_977631.1| 56 ANQRLQDLSDEVQAEQE 72
                                   67788888888888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.6e-05
                    Cep57_CLD_2  12 LdsltrklqvheeelkrLnkERdsalrqLgvAye 45 
                                    L+ ++rk  ++ ee +rL++ERd a  +L+ A++
  gi|121637408|ref|YP_977631.1| 201 LTETRRKFDEQREEVQRLAAERDAAQARLQAARL 234
                                    67789**************************985 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.4     0.012        35       9      72 ..      51     113 ..      48     127 .. 0.69
   2 ?    6.6   6.9    0.0039        12       3      72 ..     161     233 ..     148     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                 HIP1_clath_bdg   9 AevtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlk 72 
                                    A+v+k  +  +   +ev++e++ +++ + +++  +++  +  +  le  +r +++ +a +a ++
  gi|121637408|ref|YP_977631.1|  51 ADVAKANQRLQDLSDEVQAEQESVNKAMVDVETARDNAAA-AEDDLEVSQRAVKDANAAIAAAQ 113
                                    7888888888888899999999999888888777666544.23334444555555555555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0039
                 HIP1_clath_bdg   3 dLLrKnAevtkqlsvarqaqee...verekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlk 72 
                                    +L r  +e +   s+ar a++     ++  k  ++   ++  e++rk +eq+ee+++L +e  a +a+l+ ++
  gi|121637408|ref|YP_977631.1| 161 NLQRARTERVNTESAARLAKQKadkAAADAKASQDAAVAALTETRRKFDEQREEVQRLAAERDAAQARLQAAR 233
                                    566666666666666665554400044445555666666778999***********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1878  (0.104747); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 3206.59
//
Query:       gi|121637409|ref|YP_977632.1|  [L=241]
Description: invasion protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-31  107.0   0.0    6.2e-31  106.6   0.0    1.2  1  NLPC_P60  NlpC/P60 family
     0.0022   17.7   0.0       0.71    9.5   0.0    2.1  2  DUF1175   Protein of unknown function (DUF1175)
  ------ inclusion threshold ------
       0.12   12.3   0.3       0.15   12.0   0.3    1.2  1  NrfD_2    Polysulfide reductase


Domain annotation for each model (and alignments):
>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0     1e-34   6.2e-31       1     103 [.     124     238 ..     124     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1e-34
                                    T-BB-TT--BTT.............EB-HHHHHHHHHHTTT----SSHHHHCCCSEE..EEGGG--TTEEEEESGTGGES CS
                       NLPC_P60   1 gkpYrwGGksps.............gfDCsglvryafakagielprssgeqeaagkkkeiskselkrGDLvffktkkgis 67 
                                    g+pY+wGG+s +             gfDCsglvryafa +g+ +pr sg+q++ag++  ++ +e+krGDL+f+++ +g +
  gi|121637409|ref|YP_977632.1| 124 GVPYSWGGGSLQgpskgvdsgantvGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRH--VPPAEAKRGDLIFYGP-GGGQ 200
                                    79*********9*********************************************..****************.**** PP

                                    EEEEEEETTEEEEEE..TTEEEEEETTSTTBHSCEEEC CS
                       NLPC_P60  68 HvgiYlgngkmlhas..sekvsvsslsekywkkrllgv 103
                                    Hv++Ylgng+ml+as   +kv+vs+++++++++ ++++
  gi|121637409|ref|YP_977632.1| 201 HVTLYLGNGQMLEASgsAGKVTVSPVRKAGMTPFVTRI 238
                                    ***************9999************9998876 PP

>> DUF1175  Protein of unknown function (DUF1175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0012       7.1      54      64 ..     150     160 ..     139     163 .. 0.85
   2 !    9.5   0.0   0.00012      0.71     140     167 ..     184     208 ..     173     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0012
                        DUF1175  54 rDCaglvryav 64 
                                     DC+glvrya 
  gi|121637409|ref|YP_977632.1| 150 FDCSGLVRYAF 160
                                    5********96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00012
                        DUF1175 140 eqAkpgDllFfdqeddelPyHlmiylge 167
                                    ++Ak gDl+F+ ++  +   H+ +ylg+
  gi|121637409|ref|YP_977632.1| 184 AEAKRGDLIFYGPGGGQ---HVTLYLGN 208
                                    5799*************...*******9 PP

>> NrfD_2  Polysulfide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.5e-05      0.15     113     162 ..       4      54 ..       1      98 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                         NrfD_2 113 arewaGvlvlvsavvlay.tGvllaanaarplwdhlllaiflasalllala 162
                                    +r+ +  l++++avv +   Gv+  a+a    wd+ l+a+  a a    la
  gi|121637409|ref|YP_977632.1|   4 TRFHPIKLAWITAVVAGLmVGVATPADAEPGQWDPTLPALVSAGAPGDPLA 54 
                                    699999*********996379*****888889********99987544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1850.02
//
Query:       gi|121637410|ref|YP_977633.1|  [L=377]
Description: transcriptional regulatory protein moxR1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-60  203.1   0.0    2.1e-60  202.3   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    1.4e-17   63.3   0.1    3.5e-17   62.0   0.1    1.7  1  AAA_lid_2        AAA lid domain
    7.2e-16   58.4   0.0    1.5e-15   57.4   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00027   20.7   0.1     0.0025   17.5   0.0    2.3  3  Sigma54_activat  Sigma-54 interaction domain
     0.0082   15.3   0.0      0.031   13.4   0.0    1.9  2  MCM              MCM P-loop domain
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.052   14.0   0.0    1.9  1  AAA              ATPase family associated with various cellul
      0.052   13.3   0.2        2.8    7.7   0.2    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.14   11.5   0.2        3.3    7.0   0.1    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3   0.0   9.5e-64   2.1e-60       1     131 []      73     203 ..      73     203 .. 1.00

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 9.5e-64
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqs 80 
                                    hvllegvPG+aktl+v+++a++++ +f+riqftpdl+P+di+Gt+++++ ++ef+++ Gpv+an+lladeinrap+k+qs
  gi|121637410|ref|YP_977633.1|  73 HVLLEGVPGVAKTLAVETFARVVGGTFSRIQFTPDLVPTDIIGTRIYRQGREEFDTELGPVVANFLLADEINRAPAKVQS 152
                                    9******************************************************************************* PP

                          AAA_3  81 alleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                    alle+m+er+v+++g+t+++p+pflv+atqnPie+eG+yplpeaq drfl+
  gi|121637410|ref|YP_977633.1| 153 ALLEVMQERHVSIGGRTFPMPSPFLVMATQNPIEHEGVYPLPEAQRDRFLF 203
                                    *************************************************96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.1   1.6e-20   3.5e-17       5      70 ..     276     342 ..     273     345 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.6e-20
                      AAA_lid_2   5 ahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiv 70 
                                    +++ +++g+s+r a+l ++ aAr lA+++grdyV+p+Dv e++p VL+HRl+  +++ a++ + e ++
  gi|121637410|ref|YP_977633.1| 276 VKSWVAFGASPR-ASLGIIAAARSLALVRGRDYVIPQDVIEVIPDVLRHRLVltYDALADEISPEIVI 342
                                    567799******.***************************************9999999887766555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   6.7e-19   1.5e-15       1     138 []      73     201 ..      73     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 6.7e-19
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttsl..vdsplvraaregeilvlDEverae 78 
                                    +vlL G pG++K+  +e +a++++ ++  +q+t d+ ++d++g r +++g++++  + +p+v     +  l+ DE++ra+
  gi|121637410|ref|YP_977633.1|  73 HVLLEGVPGVAKTLAVETFARVVGGTFSRIQFTPDLVPTDIIGTRIYRQGREEFdtELGPVV-----ANFLLADEINRAP 147
                                    79**********************************************88888733568888.....99*********** PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                     +v+++Ll ++ er++++  +++ +  +       f v+at np +  ++ +l +a r+Rf
  gi|121637410|ref|YP_977633.1| 148 AKVQSALLEVMQERHVSIGGRTFPMPSP-------FLVMATQNPIEhEGVYPLPEAQRDRF 201
                                    *****************88888888554.......***********999999999*99999 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.28   6.3e+02      19      41 ..      68      90 ..      56     103 .. 0.78
   2 !   17.5   0.0   1.1e-06    0.0025      96     147 ..     137     187 ..     130     207 .. 0.81
   3 ?   -3.1   0.0       2.5   5.6e+03     128     143 ..     252     267 ..     238     271 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.28
                                   CTSSS-EEEECSTTSSHHHHHHH CS
                Sigma54_activat 19 aktdlsvlitGesGtGKellara 41
                                     ++ +vl++G  G+ K+l  ++
  gi|121637410|ref|YP_977633.1| 68 LLSKGHVLLEGVPGVAKTLAVET 90
                                   567789***********987665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.1e-06
                                    EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HHH CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedlee 147
                                     l+ Dei++ p+++Q+ Ll+v+qe++v+  G + +++  + +++at++ +e+
  gi|121637410|ref|YP_977633.1| 137 FLLADEINRAPAKVQSALLEVMQERHVSIGGRTFPMPSPF-LVMATQNPIEH 187
                                    5788**********************98666666666555.66777776665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.5
                                    SSEEE--EEEEEEESS CS
                Sigma54_activat 128 skeikvdvriiaatne 143
                                    ++ ++  vr+++at +
  gi|121637410|ref|YP_977633.1| 252 HALVDYVVRVVFATRK 267
                                    5556677999999976 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.4e-05     0.031      55     174 ..      69     185 ..      52     193 .. 0.75
   2 ?   -2.8   0.0       1.2   2.8e+03      14      45 ..     328     358 ..     326     363 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                    CSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGG CS
                            MCM  55 rgdinvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcciDefd 131
                                     ++ +vll g pg+aK+  +++ ++++  +++  ++ +     +++  +    +  +ef +e G +v      ++ De++
  gi|121637410|ref|YP_977633.1|  69 LSKGHVLLEGVPGVAKTLAVETFARVV-GGTFSRIQFTPDlvpTDIIGTRIYRQGREEFDTELGPVVAN---FLLADEIN 144
                                    567799999999999998888877554.45555555544311134444445556677899999999975...7899**** PP

                                    GSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                            MCM 132 kmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                    +   + +sal+E+m + ++si  +G +  +++   v+a  np+
  gi|121637410|ref|YP_977633.1| 145 RAPAKVQSALLEVMQERHVSI--GGRTFPMPSPFLVMATQNPI 185
                                    *******************99..56677788888888888887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHSSTTSSS-HHHHHHHHHHHH---E CS
                            MCM  14 iieklvksiapsiyghedvkkaillqlfggvk 45 
                                    +++ l++ i p+i+ ++ v ++++l ++ +v 
  gi|121637410|ref|YP_977633.1| 328 TYDALADEISPEIVINR-VLQTVALPQVNAVP 358
                                    57899999999999775.45567776666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.052       1     131 [.      74     208 ..      74     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHH.HHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvges.ekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                    vll G pG+ KTl+++  a+ +g +f +i+  ++l+  +++g +  ++ re f++   +        l+ DEi +   + 
  gi|121637410|ref|YP_977633.1|  74 VLLEGVPGVAKTLAVETFARVVGGTFSRIQFtPDLVpTDIIGTRiYRQGREEFDT---ELgpvVANFLLADEINRAPAK- 149
                                    79************************99996267775555554413444555543...222433478999999988444. PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEETT CS
                            AAA  75 sgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkieie 131
                                              v+++Ll+++++   +         s+++v+++ n      +  l++a + +Rf  ki+++
  gi|121637410|ref|YP_977633.1| 150 ----------VQSALLEVMQERHVSiggrtfpmPSPFLVMATQNPiehegVYPLPEAQR-DRFLFKINVG 208
                                    ..........5999999999999999999999866677766666655444445666666.8888777765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0013       2.8      34      61 ..      72      99 ..      54     168 .. 0.65
   2 ?    0.9   0.0      0.15   3.4e+02      84     142 ..     229     288 ..     218     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                         RuvB_N 34 dhvllyGpPGlGkttlakiiakelgvkl 61
                                    hvll G PG+ kt   +  a+ +g ++
  gi|121637410|ref|YP_977633.1| 72 GHVLLEGVPGVAKTLAVETFARVVGGTF 99
                                   6************987777777776654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                         RuvB_N  84 ekdvlfideihrlsra.veevlysamedfrldivigkGpsarsikldlpkftlvgattra 142
                                    +k++l   ++ rl++  ++++++ a+ d+ + +v  + +  +    d++ +   ga+ ra
  gi|121637410|ref|YP_977633.1| 229 AKQILSTGDLLRLQEIaANNFVHHALVDYVVRVVFATRKPEQLGMNDVKSWVAFGASPRA 288
                                    56778888888998751678999*********9998877777777777777777777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0015       3.3       5      45 ..      54      94 ..      51     101 .. 0.89
   2 ?    2.2   0.0     0.046     1e+02     109     159 ..     137     185 ..     126     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                   Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                   ++Gq++  + + +    + ++ll G pG  Kt+  + ++ +
  gi|121637410|ref|YP_977633.1| 54 IVGQDQLVERMLVGLLSKGHVLLEGVPGVAKTLAVETFARV 94
                                   78999999999*********************998877655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.046
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                     L+ DE+    +kv  +L e +++++v+i    +++  p+ f ++a+ Np 
  gi|121637410|ref|YP_977633.1| 137 FLLADEINRAPAKVQSALLEVMQERHVSIG--GRTFPMPSPFLVMATQNPI 185
                                    5788**********************9996..4567789999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2450.79
//
Query:       gi|121637411|ref|YP_977634.1|  [L=317]
Description: hypothetical protein BCG_1542 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-18   66.4   0.0    5.3e-18   65.1   0.0    1.7  1  DUF58     Protein of unknown function DUF58
    5.9e-05   23.7   0.0    0.00027   21.5   0.0    1.9  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   5.9e-22   5.3e-18       1      82 [.      56     137 ..      56     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 5.9e-22
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqllde 80 
                                    g+++ + R Y+pgD++rr+dW +tARt +++vr++ a r+ +++lv+d s++ ++g++ +ek + av+aaa++       
  gi|121637411|ref|YP_977634.1|  56 GSEPGESRLYQPGDDVRRMDWAVTARTTHPHVRQMIADRELETWLVVDMSASLDFGTACCEKRDLAVAAAAAITFLNSGG 135
                                    578999*****************************************************************987665555 PP

                          DUF58  81 gd 82 
                                    g+
  gi|121637411|ref|YP_977634.1| 136 GN 137
                                    55 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.25   2.2e+03      10      43 ..      14      52 ..      13      82 .. 0.72
   2 !   21.5   0.0     3e-08   0.00027       2     105 ..      99     204 ..      98     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                          VWA_2 10 Smrngdygptrleaakdaveallksl.....pgdrvglv 43
                                   Sm +gd    +l+aa + +e  +k+      +gd++gl+
  gi|121637411|ref|YP_977634.1| 14 SMLRGDIDDPKLAAALRTLELTVKQKldgvlHGDHLGLI 52
                                   677777777777777777777777554666567777776 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3e-08
                          VWA_2   2 vfvlDtSgSmrngdy..gptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleak.gggtnl 78 
                                     +v+D+S+S   g+   +++ l+ a++a++++l+s  g+r+g +  ++ + + +p  +++++  + lr + ++ +    +
  gi|121637411|ref|YP_977634.1|  99 WLVVDMSASLDFGTAccEKRDLAVAAAAAITFLNSGGGNRLGALIANGAAMTRVPARTGRQHQHTMLRTIATMpQAPAGV 178
                                    69********98866669*****************99*******************999999999999999887677888 PP

                          VWA_2  79 aaaLqlarkalkkrrkgekrvivlitD 105
                                       L  a +al++    ++  +v+i+D
  gi|121637411|ref|YP_977634.1| 179 RGDLAVAIDALRRPE-RRRGMAVIISD 204
                                    889999999998665.88999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1653.92
//
Query:       gi|121637412|ref|YP_977635.1|  [L=335]
Description: hypothetical protein BCG_1543 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-21   74.6   0.1    1.9e-20   73.5   0.1    1.5  1  VWA_2     von Willebrand factor type A domain
    9.6e-18   65.0   0.0    1.4e-17   64.5   0.0    1.1  1  VWA       von Willebrand factor type A domain
    9.1e-06   26.0   8.7    9.1e-06   26.0   8.7    2.4  2  BatA      Aerotolerance regulator N-terminal
     0.0068   16.2   0.0      0.014   15.2   0.0    1.5  2  Ssl1      Ssl1-like
  ------ inclusion threshold ------
      0.046   13.5   2.7        1.3    8.8   0.2    2.7  2  DUF588    Domain of unknown function (DUF588)
       0.23   11.8   1.7        6.9    7.1   0.1    2.7  3  SPOR      Sporulation related domain
        6.5    6.4  10.0       0.23   11.1   1.1    2.3  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.1   7.5e-24   1.9e-20       1     107 []      99     212 ..      99     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 7.5e-24
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnla 79 
                                    +++v+D+S+Smr++d++p+r+ aa++a++++ ++l pg ++gl++++++++vl+++t+++++ +nal++l+  ++ t ++
  gi|121637412|ref|YP_977635.1|  99 VMLVIDVSQSMRATDVEPSRMVAAQEAAKQFADELtPGINLGLIAYAGTATVLVSPTTNREATKNALDKLQF-ADRTATG 177
                                    79*******************************9967**********************************8.5****** PP

                          VWA_2  80 aaLqlarkalkkrr.......kgekrvivlitDge 107
                                    +a+ +a +a+           +  +++ivl++Dg+
  gi|121637412|ref|YP_977635.1| 178 EAIFTALQAIATVGavigggdTPPPARIVLFSDGK 212
                                    ********9965556666666889*********95 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   5.3e-21   1.4e-17       2     173 ..      99     291 ..      99     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 5.3e-21
                                    EEEEEE-STTSCHHHHH.....HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                            VWA   2 ivfvlDgSgsmgeenfe.....kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgg 76 
                                    +++v+D+S+sm++ ++e      ++e++k+++++l+   +g+++gl+ +++++++ +s ++   +e+ ++al++l +   
  gi|121637412|ref|YP_977635.1|  99 VMLVIDVSQSMRATDVEpsrmvAAQEAAKQFADELT---PGINLGLIAYAGTATVLVSPTTN--REATKNALDKL-QFAD 172
                                    799********77777666666**************...**********************5..599*******7.6666 PP

                                    SSC-HHHHHHHHHHHHHHHHGT.....SSTTSEEEEEEEESS--CS.S......HTHHHHHHHHGCTEEEEEEEE..... CS
                            VWA  77 gttntgkalkyaleklfkssag.....aRenakkviilltdGksnd.g......dpkeaaneakeqgikvfavGv..... 139
                                     t+ tg+a+  al+ + +  a           +  i+l++dGk+++ +         +aa++ak+qg+ + ++ +     
  gi|121637412|ref|YP_977635.1| 173 RTA-TGEAIFTALQAIATVGAVigggdT--PPPARIVLFSDGKETMpTnpdnpkGAYTAARTAKDQGVPISTISFgtpyg 249
                                    677.899999999988887777666433..469*************669997777778999999**************** PP

                                    ..........SSSHHHHHHHHHSSSSCHHCEEEESSHHHHHHHH CS
                            VWA 140 ..........gnadekelLnkiasepgeghvftvtdfeeleelf 173
                                                +d+++ ++k a+ +g g+ +++++ +el+ ++
  gi|121637412|ref|YP_977635.1| 250 fveiddqrqpVPVDDET-MKKVAQLSG-GNSYNAATLAELRAVY 291
                                    ********998899999.*****9999.9999999999887665 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   8.7   3.6e-09   9.1e-06       3      77 .]      13      86 ..       9      86 .. 0.88
   2 ?    0.7   1.6      0.28   7.1e+02      62      75 ..     312     325 ..     306     334 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.6e-09
                           BatA  3 pFlnPllLlallllplpiillyllkrrpqev..vfsslrlleevekdeealqrlkknllllLrllalallvlalArP 77
                                    F++ +++l+l++++ +++l+ l++  +q++  +f++++lle+v +++ +   + ++++ +L +l l+l  +a+A+P
  gi|121637412|ref|YP_977635.1| 13 GFAHSWFFLFLFVVAGLVALYILMQLARQRRmlRFANMELLESVAPKRPS---RWRHVPAILLVLSLLLFTIAMAGP 86
                                   69999*999999999877777777777777788*****************...999*******************99 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.28
                           BatA  62 LrllalallvlalA 75 
                                    Lrl alal+  alA
  gi|121637412|ref|YP_977635.1| 312 LRLGALALALAALA 325
                                    44444444444444 PP

>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06     0.014       1      74 [.     102     171 ..     102     193 .. 0.81
   2 ?   -3.3   0.0       2.6   6.6e+03      47      72 ..     263     288 ..     260     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                    EEE-SGGGGSSSSSS-HHHHHHHHHHHHHHHHHHHSTT-EEEEEEEETTEEEEEEEEES-HHHHHHHHHHHTTS CS
                           Ssl1   1 vlDlsrameekdlkpsrlavviklleefveeffdqnPisqlgliavkdkkaekltelsGnprkhikaLkslrev 74 
                                    v+D+s++m  +d++psr++   +++++f +e     P   lglia  +++a  l + + n +  ++aL++l+ +
  gi|121637412|ref|YP_977635.1| 102 VIDVSQSMRATDVEPSRMVAAQEAAKQFADEL---TPGINLGLIAY-AGTATVLVSPTTNREATKNALDKLQFA 171
                                    89***************************986...68899999986.678888888889999999999887633 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                                    ETTEEEEEEEEES-HHHHHHHHHHHT CS
                           Ssl1  47 kdkkaekltelsGnprkhikaLkslr 72 
                                     d++ +k+++lsG       +L +lr
  gi|121637412|ref|YP_977635.1| 263 DDETMKKVAQLSGGNSYNAATLAELR 288
                                    56677888999888777777777666 PP

>> DUF588  Domain of unknown function (DUF588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00051       1.3      44      76 ..      14      46 ..       9      85 .. 0.81
   2 ?    4.0   0.2     0.016        40      10      30 ..     311     331 ..     304     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                         DUF588 44 fsdlpafvylvvanaiaavYsllqlvlsvvslv 76
                                   f ++  f +l+v+++++a+Y l+ql+++   l+
  gi|121637412|ref|YP_977635.1| 14 FAHSWFFLFLFVVAGLVALYILMQLARQRRMLR 46
                                   6667779******************99875554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                         DUF588  10 vLRlaavvlalaaavvmatnk 30 
                                     LRl a++lalaa++ +  n+
  gi|121637412|ref|YP_977635.1| 311 WLRLGALALALAALAALLINR 331
                                    69************9998886 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0027       6.9      15      66 ..     123     171 ..     120     181 .. 0.74
   2 ?   -3.7   0.0       6.4   1.6e+04      14      32 ..     221     239 ..     220     247 .. 0.64
   3 ?    3.1   0.2     0.049   1.3e+02      13      52 ..     282     318 ..     276     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0027
                                    HHHHHHHHHHCCHHT--...EEECCSSSCEEEEESSBCTCCHHHHHHHHCH.H CS
                           SPOR  15 eanAerlaakLrakgfaaavavvsgggglyrVrvGpfasreeAqaalkkLk.a 66 
                                    +++A+++a++L+  g++      +   g  +V+v p ++re+ ++al+kL+ a
  gi|121637412|ref|YP_977635.1| 123 QEAAKQFADELTP-GIN---LGLIAYAGTATVLVSPTTNREATKNALDKLQfA 171
                                    4455555555553.233...88888899999*******************953 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.4
                                    -HHHHHHHHHHCCHHT--. CS
                           SPOR  14 seanAerlaakLrakgfaa 32 
                                    +++ A ++a+  +++g ++
  gi|121637412|ref|YP_977635.1| 221 NPKGAYTAARTAKDQGVPI 239
                                    5667777777777777664 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.049
                                    S-HHHHHHHHHHCCHH.T--...EEECCSSSCEEEEESSBC CS
                           SPOR  13 sseanAerlaakLrak.gfaaavavvsgggglyrVrvGpfa 52 
                                    ++ a+ +++++ L+++ g+     +++g+ ++ ++r+G+ a
  gi|121637412|ref|YP_977635.1| 282 ATLAELRAVYSSLQQQiGY----ETIKGDASVGWLRLGALA 318
                                    47899999********888....799999999999999854 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1     9e-05      0.23       4      83 ..      18     113 ..      14     151 .. 0.65
   2 ?   -0.3   2.2      0.28   7.1e+02       7      24 ..     311     328 ..     307     335 .] 0.39

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                        DUF4131   4 plalvllalllllllllllllrr.................rprrrvllllllllllallgfalrapqpnandlsqllesg 66 
                                    ++ l+l+++++l++l++l++l r                  +r+ ++ ++ ++ll+++l ++  a   +++d     + +
  gi|121637412|ref|YP_977635.1|  18 WFFLFLFVVAGLVALYILMQLARqrrmlrfanmellesvaPKRPSRWRHVPAILLVLSLLLFTIAMAGPTHDVRIPRN-R 96 
                                    344455555555555555555558889999999999999966677777777777766666655555555444443333.5 PP

                        DUF4131  67 qeviveGvvaslpeltg 83 
                                      v+++  v++  + t+
  gi|121637412|ref|YP_977635.1|  97 AVVMLVIDVSQSMRATD 113
                                    56666667766666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.28
                        DUF4131   7 lvllalllllllllllll 24 
                                    ++ l++l+l+l++l++ll
  gi|121637412|ref|YP_977635.1| 311 WLRLGALALALAALAALL 328
                                    333333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.60
# Mc/sec: 1674.16
//
Query:       gi|121637413|ref|YP_977636.1|  [L=280]
Description: hypothetical protein BCG_1544c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00011   22.3   0.7    0.00019   21.5   0.7    1.4  1  MTES_1575  REase_MTES_1575
  ------ inclusion threshold ------
       0.11   12.9   0.2       0.27   11.5   0.2    1.7  1  AbiEi_1    AbiEi antitoxin C-terminal domain


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.7   2.2e-08   0.00019      14      79 ..     200     263 ..     189     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-08
                      MTES_1575  14 ykvkpqvgvggfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLe.rlGWkilRiwssd 79 
                                    + v++++g ++  +D+ ++d    ++a e dgd++ +s+  +++di+r+e  + r GW ++R+  +d
  gi|121637413|ref|YP_977636.1| 200 IAVRNEWGWAEAHLDMGWQDI---KVAAEYDGDHHLTSRYHYRKDILRHEKVQhRYGWIVVRVVAED 263
                                    568889999999*****9999...9***********************998887*********9876 PP

>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.1e-05      0.27      23     130 ..      61     160 ..      44     171 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                        AbiEi_1  23 llsAawlhGaahrqpqriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeatavdlatrpsavgg 102
                                    ++sA  +hGa+   +     ++++++++ p  ++ +e++        p +++    +g++v++Pe+ta+dl  r     +
  gi|121637413|ref|YP_977636.1|  61 GYSASAFHGAKWIDADLPAAIIDTNRRRAPGLQVWEERI-------EP-DEI-CVIEGMRVTTPERTALDLTSR----FP 127
                                    566777777766666666666665555555555555555.......23.344.67789*************887....47 PP

                        AbiEi_1 103 ldnvlevLdelaee.....vkpeeLeellsgrp 130
                                    ld ++++ d+l+++     ++ e+L e+ +gr+
  gi|121637413|ref|YP_977636.1| 128 LDPAVAAVDALIQAtdlkvADVEPLIERYRGRR 160
                                    888888888887764444344455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1522.09
//
Query:       gi|121637414|ref|YP_977637.1|  [L=247]
Description: 3-oxoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-57  192.5   5.7    1.7e-56  191.4   5.7    1.4  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    6.5e-49  166.0   4.1    1.3e-48  165.1   4.1    1.5  1  adh_short       short chain dehydrogenase
    5.9e-19   68.7   2.8    1.9e-15   57.3   0.1    2.2  2  KR              KR domain
    4.7e-09   36.1   0.7    1.7e-08   34.3   0.7    1.9  1  Epimerase       NAD dependent epimerase/dehydratase family
    0.00033   19.9   0.2    0.00062   19.0   0.2    1.4  1  RmlD_sub_bind   RmlD substrate binding domain
    0.00059   19.8   1.6    0.00084   19.3   1.6    1.3  1  NAD_binding_10  NAD(P)H-binding
     0.0077   15.1   0.3       0.01   14.7   0.3    1.2  1  DUF917          Protein of unknown function (DUF917)
  ------ inclusion threshold ------
      0.017   14.7   0.2      0.076   12.6   0.0    1.9  2  Amdase          Arylmalonate decarboxylase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   5.7   7.5e-60   1.7e-56       4     233 ..      25     243 ..      21     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 7.5e-60
                                    TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                   adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                    +gIG aiA++la+ G +v++t ++  a           +  + +ecDVtd ++v++++ +v+e+ g + +lv nag + +
  gi|121637414|ref|YP_977637.1|  25 RGIGLAIAQRLAADGHKVAVTHRGSGA---P-------KGLFgVECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSAD 94 
                                    8*********************99998...1.......223459************************************ PP

                                    CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHG CS
                   adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelg 160
                                      + ++ +++e+f+++++ nl+++f++a++a + m+++  g+++ + sv+++ ++ n++ y+a+Ka++++++r++A+el 
  gi|121637414|ref|YP_977637.1|  95 --AFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNkfGRMIFIGSVSGSWGIGNQANYAASKAGVIGMARSIARELS 172
                                    ..99999**************************999988***************************************** PP

                                    GGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                   adh_short_C2 161 pkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                    + +++ N+v+pg+i+T+++++++  +++++ + + +p +r+gtp eva ++ fLas++asyi+G+++ vDgG+
  gi|121637414|ref|YP_977637.1| 173 KANVTANVVAPGYIDTDMTRALD--ERIQQGALQFIPAKRVGTPAEVAGVVSFLASEDASYISGAVIPVDGGM 243
                                    **********************8..99*********************************************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   4.1   5.8e-52   1.3e-48       2     192 ..      17     196 ..      16     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 5.8e-52
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                     vlvtG+ +GIG+aia++la++G kv+v+ r + +        k     ++ +++Dvtd+++v++++ +++++ g+++vL
  gi|121637414|ref|YP_977637.1|  17 SVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGSGAP-------KG----LFGVECDVTDSDAVDRAFTAVEEHQGPVEVL 85 
                                    59**************************99997765.......33....899**************************** PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                    v NAG++ ++   +++ee++e+vi+ Nltg+f +++ + + m +++ Gr ++++Sv g  +  ++a Y+AsKa+v+g++r
  gi|121637414|ref|YP_977637.1|  86 VSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAGVIGMAR 165
                                    ******************************************************************************** PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmakelre 192
                                    s+a+el++ +++ n+vaPG++dTdm+++l e
  gi|121637414|ref|YP_977637.1| 166 SIARELSKANVTANVVAPGYIDTDMTRALDE 196
                                    **************************99876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   8.2e-05      0.18       3      27 ..      18      42 ..      17      54 .. 0.85
   2 !   57.3   0.1   8.4e-19   1.9e-15      58     165 ..      58     169 ..      55     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.2e-05
                                   EEEETTTSHHHHHHHHHHHHHHS-E CS
                             KR  3 ylitGGlGgLGlelarwlaekgarh 27
                                   +l+tGG  g+Gl++a+ la++g + 
  gi|121637414|ref|YP_977637.1| 18 VLVTGGNRGIGLAIAQRLAADGHKV 42
                                   79*******************9764 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 8.4e-19
                                    ----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEE CS
                             KR  58 vaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvl 133
                                    v++Dv+d+dav +++++++++++p++  +  Ag+++d+ l++mt+e++e+v+++ ++Ga  + +  ++    ++   +++
  gi|121637414|ref|YP_977637.1|  58 VECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRsmqrNKFGRMIF 137
                                    68*********************************************************999887665565578888*** PP

                                    EEEHHHHH--TT-HHHHHHHHHHHHHHHHHHH CS
                             KR 134 fSSiagllgsagqanYaaaNaflDalaeyrrs 165
                                    + S++g +g   qanYaa  a + ++a++ ++
  gi|121637414|ref|YP_977637.1| 138 IGSVSGSWGIGNQANYAASKAGVIGMARSIAR 169
                                    ******************98877776666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.7   7.4e-12   1.7e-08       1     116 [.      18     141 ..      18     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 7.4e-12
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHH...HH.T-SEEEE-.-S-- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfk...ee.qpdavihl.Aavg 75 
                                    +lVtG++  iG a++++l++ g++v +  r s     ++ + l  ve+d+td++a++r+f    e+ +p +v+   A+ +
  gi|121637414|ref|YP_977637.1|  18 VLVTGGNRGIGLAIAQRLAADGHKVAVTHRGS-----GAPKGLFGVECDVTDSDAVDRAFTaveEHqGPVEVLVSnAGLS 92 
                                    79***********************9999993.....334455889***********99852224446777766646555 PP

                                    -....HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT....EEEEEEEG CS
                      Epimerase  76 g....vaassedpadfieknlqgtlnlleaarkagvk....rllflsSs 116
                                          + + e+ +++i++nl g+ ++++ a+++  +    r++f++S+
  gi|121637414|ref|YP_977637.1|  93 AdaflMRMTEEKFEKVINANLTGAFRVAQRASRSMQRnkfgRMIFIGSV 141
                                    412224567888899**************999663333446******94 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   2.7e-07   0.00062       2      91 ..      17     125 ..      16     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-07
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--S.....EEEE--.----.. CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpd.....vvvnaA.Ayta.. 63 
                                     +lvtG+n  +G ++a++la++g++v  ++r           e+d+td++av++++ +++ +     v+v+ A    +  
  gi|121637414|ref|YP_977637.1|  17 SVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGsgapkglfgvECDVTDSDAVDRAFTAVEEHqgpveVLVSNAgLSADaf 96 
                                    58*********************9998888889**********************9665544333445554440444422 PP

                                    .HHHHHHSHHHHHHHHTHHHHHHHHHHHH CS
                  RmlD_sub_bind  64 .vDkaEseeeaayavnaeavealAeaaaa 91 
                                     +   E++ e+  ++n +++ ++A+ a++
  gi|121637414|ref|YP_977637.1|  97 lMRMTEEKFEKVINANLTGAFRVAQRASR 125
                                    23467888888888888999999988865 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.6   3.7e-07   0.00084       1     146 [.      22     186 ..      22     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.7e-07
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES---TCC CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk.......gadaVvsalggggk 73 
                                    G++ ++G +++++l+a+g h+v  ++ + + ++     +gl  ve dvtd++++ +a++        +++ vs++g +++
  gi|121637414|ref|YP_977637.1|  22 GGNRGIGLAIAQRLAADG-HKVA-VTHRGSGAP-----KGLFGVECDVTDSDAVDRAFTaveehqgPVEVLVSNAGLSAD 94 
                                    99***************5.9985.555555555.....58999**************99666666556788888865555 PP

                                    .......HHHH................HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCH.HHHHHHHHHHH CS
                 NAD_binding_10  74 .......deeg................aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellk.aylaakraaee 129
                                           +                   a+++ + +++++  R+++++++      +g  ++ n+ + k  ++   r  ++
  gi|121637414|ref|YP_977637.1|  95 aflmrmtE--EkfekvinanltgafrvAQRASRSMQRNKFGRMIFIGSVSGS---WGIGNQANYAASKaGVIGMARSIAR 169
                                    56555431..034555777778888889999999999999999999986533...2222222223333033333445566 PP

                                    HHHHSSSEEEEEEE-CE CS
                 NAD_binding_10 130 llrasgldwTivrpggL 146
                                    +l + +++  +v pg++
  gi|121637414|ref|YP_977637.1| 170 ELSKANVTANVVAPGYI 186
                                    66666666666666666 PP

>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   4.5e-06      0.01     156     256 ..      97     203 ..      59     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-06
                                    EEE.---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--.....-SHHHHHHHHHH.. CS
                         DUF917 156 lkkaqsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaeareak...dvveailealgg.. 230
                                    l +  ++++ E+++ a l+ +   a  a + m+ +++ r++  g++s ++ iG + + a +++    ++++i+++l +  
  gi|121637414|ref|YP_977637.1|  97 LMR-MTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAgviGMARSIARELSKan 175
                                    444.34457999999999999999999******************************99988556788999999999888 PP

                                    .-EEEEEEEEE-.-------------EE CS
                         DUF917 231 .gakvlfkGkiv.dverrteggfdvgev 256
                                     +a v+  G i  d++r +++  + g +
  gi|121637414|ref|YP_977637.1| 176 vTANVVAPGYIDtDMTRALDERIQQGAL 203
                                    8888899999876888877777666665 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.4e-05     0.076     142     216 ..      61     135 ..      56     136 .. 0.94
   2 ?   -0.5   0.1      0.34   7.7e+02      82     110 ..     160     188 ..     151     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                         Amdase 142 kvtaeelvelgkkavaaapeadallisCGGLrtldvvreledelglpvvssalAGlwdavrlagldaraagegrl 216
                                    +vt+++ v+ +  av++++ +  +l+s  GL++ +   ++ +e    v+ + l G++ ++++a+++ + +  gr+
  gi|121637414|ref|YP_977637.1|  61 DVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRM 135
                                    7999999*********************************************************99999888886 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.34
                         Amdase  82 attmssavvealralgarRvAvataYide 110
                                    +  m++++ ++l +  +    va  Yid+
  gi|121637414|ref|YP_977637.1| 160 VIGMARSIARELSKANVTANVVAPGYIDT 188
                                    56789999999999999988899999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1341.05
//
Query:       gi|121637415|ref|YP_977638.1|  [L=269]
Description: enoyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-56  189.9   0.0    6.4e-56  189.5   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.3e-11   44.3   0.0    1.9e-11   43.8   0.0    1.2  1  adh_short     short chain dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.0   7.1e-60   6.4e-56       3     234 .]      16     265 ..      14     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 7.1e-60
                                    T..TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHH...SSEEEEEE CS
                   adh_short_C2   3 a..sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekf...gklDilvn 75 
                                       s+I+++iA+ ++e+Ga++vlt +++ +   +++++++l+a++  le+DV++ee++++l+ +v+e +   +klD++v+
  gi|121637415|ref|YP_977638.1|  16 ItdSSIAFHIARVAQEQGAQLVLTGFDRLR--LIQRITDRLPAKAplLELDVQNEEHLASLAGRVTEAIgagNKLDGVVH 93 
                                    5569***********************998..8*********99667********************9977679****** PP

                                    -----EG...CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                   adh_short_C2  76 nagiapk...lkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealt 152
                                    ++g++p+     +pf +++ +++ + +++++ys++++aka+lp+m++ggsiv + +   +r++p yn++++aK ale++ 
  gi|121637415|ref|YP_977638.1|  94 SIGFMPQtgmGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP-SRAMPAYNWMTVAKSALESVN 172
                                    *******998899********************************************5.5******************** PP

                                    HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.....HHH......HHHHHHHHSTTSS-B.-HHHHHHHHHHHCSGGGT CS
                   adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.....fde......lleelearaplgrlg.tpeevaeaalfLasdeas 220
                                    r +A+e g++g+R N v++gpi+Tla+s+i g     + +      l+e +++rap+g+++ +++ va++++ L+sd+  
  gi|121637415|ref|YP_977638.1| 173 RFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGgalgeE-AgaqiqlLEEGWDQRAPIGWNMkDATPVAKTVCALLSDWLP 251
                                    **************************999977666541.14445558899*********99899**************** PP

                                    T--SEEEEESTTGG CS
                   adh_short_C2 221 yitGqtlvvDgGlt 234
                                    ++tG ++++DgG +
  gi|121637415|ref|YP_977638.1| 252 ATTGDIIYADGGAH 265
                                    ************87 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.1e-15   1.9e-11       9     186 ..      18     198 ..       8     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.1e-15
                                    TSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHH...SSESEEEE- CS
                      adh_short   9 ssGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkkl...gkldvLvnN 84 
                                    +s I   ia+   ++Ga++v+++    +l   ++ + +   aka  +++Dv+++e +  l  ++ + +    kld +v+ 
  gi|121637415|ref|YP_977638.1|  18 DSSIAFHIARVAQEQGAQLVLTGFDRLRL---IQRITDRlPAKAPLLELDVQNEEHLASLAGRVTEAIgagNKLDGVVHS 94 
                                    567999***************77665554...55555555778**********************99977789******* PP

                                    --S.....S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  85 AGi.....tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                     G       g +pf +   +++ + i++   ++ ++++a+lp m    +G+Iv +    +  +++ +   + +K a+++ 
  gi|121637415|ref|YP_977638.1|  95 IGFmpqtgMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMN--PGGSIVGMDFDPS-RAMPAYNWMTVAKSALESV 171
                                    ***999888889999****************************98..******9875555.44555555589******** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHH CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdm 186
                                     r +a+e  ++g+r n va G+++T  
  gi|121637415|ref|YP_977638.1| 172 NRFVAREAGKYGVRSNLVAAGPIRTLA 198
                                    ************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1768.32
//
Query:       gi|121637416|ref|YP_977639.1|  [L=344]
Description: ferrochelatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-93  311.6   0.0    6.6e-93  311.3   0.0    1.0  1  Ferrochelatase  Ferrochelatase
  ------ inclusion threshold ------
      0.017   15.4   0.0        5.1    7.5   0.0    2.5  2  CbiX            CbiX


Domain annotation for each model (and alignments):
>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.3   0.0   7.3e-97   6.6e-93       2     314 ..       4     296 ..       3     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 311.3 bits;  conditional E-value: 7.3e-97
                                    EEEEEEE----SSCCCHHHHHHHHCT-TTTS-S-TTTHHHHHHHHHHHHHHHHHHHHHHTTSS-SHHHHHHHHHHHHHHH CS
                 Ferrochelatase   2 tavLLlnlGgPekpedvrpflenllsdrrvielplllqkllaklilkerlekvaekYekigggSPlneitrkqaealeke 81 
                                    +avLLl++GgPe+pe+vrpflen++++r+v+                erl  vae+Y ++gg SP+n i+r ++++le++
  gi|121637416|ref|YP_977639.1|   4 DAVLLLSFGGPEGPEQVRPFLENVTRGRGVPA---------------ERLDAVAEHYLHFGGVSPINGINRTLIAELEAQ 68 
                                    69******************************...............*******************************99 PP

                                    HHHH---EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHH.TT-SSEEEEE---TT- CS
                 Ferrochelatase  82 laergidvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkk.kreapevrvirqfydh 160
                                          +++vy+++r+weP++eda+++++++gv+r+ v+++++++++s++ +++e+++ra+++ +r+ape+ ++r ++dh
  gi|121637416|ref|YP_977639.1|  69 Q-----ELPVYFGNRNWEPYVEDAVTAMRDNGVRRAAVFATSAWSGYSSCTQYVEDIARARRAaGRDAPELVKLRPYFDH 143
                                    8.....59*****************************************************666**************** PP

                                    HHHHHHHHHHHHHHHTTS-HC.C-EEEEEEE--BHHHHT.TT-S..HHHHHHHHHHHHHHHTTT-S-EEEEEE---SS.. CS
                 Ferrochelatase 161 pgyiealaesikealeelpeekkakllfsaHglPeravkkkgdp..YqqqveetarlvaealglkeevelayqSrvGp.. 236
                                    p ++e++a++i++a ++  +++ a+l+f+aH++P++a+++ g p  Y++qv  ++rlva+a+g+ + ++la+qSr+Gp  
  gi|121637416|ref|YP_977639.1| 144 PLFVEMFADAITAAAATV-RGD-ARLVFTAHSIPTAADRRCG-PnlYSRQVAYATRLVAAAAGYCD-FDLAWQSRSGPpq 219
                                    ****************99.777.9**************9999.558*******************9.************* PP

                                    S-BSSSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHH CS
                 Ferrochelatase 237 eeWlePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlve 314
                                    ++WlePd+ d l  la +g++a++v+pigFv+Dh+E++++ld+e+r +ae+ag+  ++r++t+n++p+f+++ + l+ 
  gi|121637416|ref|YP_977639.1| 220 VPWLEPDVTDQLTGLAGAGINAVIVCPIGFVADHIEVVWDLDHELRLQAEAAGI-AYARASTPNADPRFARLARGLID 296
                                    ******************************************************.***************99988876 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0022        20      14      58 ..      60     102 ..      56     152 .. 0.73
   2 ?    7.5   0.0   0.00057       5.1      37      89 ..     224     273 ..     208     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0022
                                    HHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEE CS
                           CbiX  14 klaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvv 58 
                                    +l++el+++++  pv  g     ep++e+a+++++++gv+r +v+
  gi|121637416|ref|YP_977639.1|  60 TLIAELEAQQE-LPVYFGN-RNWEPYVEDAVTAMRDNGVRRAAVF 102
                                    56677777777.7777776.5579*****************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00057
                                    ECCSCCSSHHHHC-SBSEEEEEEE.SSSSSHHHHTHHHHHCT--SSSS-TTEEE CS
                           CbiX  37 epsleealrelaeqgvkrivvvPl.flfaGvhvkeDIpeeleeaeeahpkdvei 89 
                                    ep++ ++l+ la  g++ ++v P+ f+++ + v  D+ +el++ +ea +    i
  gi|121637416|ref|YP_977639.1| 224 EPDVTDQLTGLAGAGINAVIVCPIgFVADHIEVVWDLDHELRLQAEAAG----I 273
                                    7**********************88999999999999999999998877....4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2413.81
//
Query:       gi|121637417|ref|YP_977640.1|  [L=323]
Description: hypothetical protein BCG_1548c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2286.28
//
Query:       gi|121637418|ref|YP_977641.1|  [L=144]
Description: hypothetical protein BCG_1549 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-19   70.2   2.3    2.9e-19   69.2   2.3    1.5  1  NfeD          NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.17   11.8   0.1    1.3  1  Orthoreo_P10  Orthoreovirus membrane fusion protein p10


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   2.3   3.3e-23   2.9e-19       1      82 [.      53     140 ..      53     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.3e-23
                                    XXXXXXXXXXXXXXXXS---SSS--S..S---GGTTSEEEEEE-B...S-EEEEETTEEEEEE-...SS.B-TT-EEEEE CS
                           NfeD   1 ifavvsvlllvllrplllkklkkkek.ktnaealiGkegvvledi...gtGrvkvdGeeWsars..ege.iekgerVrVv 73 
                                    +f++vsvlllvl+rp ++++l++++  + + eal Gk++vvl ++   g G+vk+dG+ W+ar   +g+ +e+g+ V+Vv
  gi|121637418|ref|YP_977641.1|  53 VFLLVSVLLLVLVRPAVRRRLTQTKGvQLGIEALEGKKAVVLGRVardG-GQVKLDGQVWTARPlnDGDvFEPGDSVTVV 131
                                    79*****************9966554667889*************9644.*************8545559********** PP

                                    EE-SSSEEE CS
                           NfeD  74 eveGltliV 82 
                                    +++G+t++V
  gi|121637418|ref|YP_977641.1| 132 QIDGATAVV 140
                                    ********9 PP

>> Orthoreo_P10  Orthoreovirus membrane fusion protein p10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.9e-05      0.17      29      73 ..      31      76 ..      28      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                   Orthoreo_P10 29 ggdlqa.tssliaywpylaagggliviilllallycckakvkadav 73
                                   gg l a  ss +  wp  a g  ++++ +ll +l+   ++ +  ++
  gi|121637418|ref|YP_977641.1| 31 GGALAAsVSSWLLAWPMWADGAVFLLVSVLLLVLVRPAVRRRLTQT 76
                                   77887725889999*********99998876666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 983.83
//
Query:       gi|121637419|ref|YP_977642.1|  [L=381]
Description: hypothetical protein BCG_1550 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-30  105.0   3.6    4.3e-30  105.0   3.6    1.8  2  Band_7        SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.017   15.0   3.8      0.089   12.6   0.2    2.7  3  Asp_Glu_race  Asp/Glu/Hydantoin racemase
      0.075   12.7   0.0       0.11   12.1   0.0    1.2  1  Band_7_1      SPFH domain-Band 7 family
        0.1   12.9   3.6      0.085   13.2   1.4    2.0  2  Ntox1         Putative RNase-like toxin, toxin_1
       0.48   10.4   4.0          1    9.4   4.0    1.5  1  OppC_N        N-terminal TM domain of oligopeptide transport 
        9.8    6.3   8.4        8.5    6.5   3.7    2.4  2  Caudo_TAP     Caudovirales tail fibre assembly protein, lambd


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   3.6   1.4e-33   4.3e-30       3     176 ..      29     208 ..      27     210 .. 0.94
   2 ?   -2.1   1.2       1.1   3.4e+03     157     177 ..     222     242 ..     201     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.4e-33
                         Band_7   3 ieegevgvvvrfGklsrvlepGlhfilPfgrsvt.vvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                    i++ e++v++r G++sr++   l + +Pf+++v  +v++r ++++++  ++v+t D+l ++id++v+++v + + ++v++
  gi|121637419|ref|YP_977642.1|  29 IPQAEAAVIERLGRYSRTVSGQLTLLVPFIDRVRaRVDLRERVVSFPP-QPVITEDNLTLNIDTVVYFQV-TVPQAAVYE 106
                                    899**************99999999***********************.*********************.********* PP

                         Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakq 161
                                    +     n+   +++++  +lr+v++ mtle+ l +r++++++l+  l e+  ++G+ v +v +++idppp +++++++ +
  gi|121637419|ref|YP_977642.1| 107 I----SNYIVGVEQLTTTTLRNVVGGMTLEQTLTSRDQINAQLRGVLDEATGRWGLRVARVELRSIDPPPSIQASMEKQM 182
                                    *....*************************************************************************** PP

                         Band_7 162 aaeaea...........qaeiaraea 176
                                    +a++e+           +a+i++ae+
  gi|121637419|ref|YP_977642.1| 183 KADREKramiltaegtrEAAIKQAEG 208
                                    ******66666666666666666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                         Band_7 157 laakqaaeaeaqaeiaraeae 177
                                    +aa  aaea++q +  ra++e
  gi|121637419|ref|YP_977642.1| 222 QAAILAAEADRQSRMLRAQGE 242
                                    344556666667777777766 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   1.4e+03       1      26 [.     126     151 ..     126     155 .. 0.89
   2 ?    3.0   0.1     0.026        77     104     135 ..     180     211 ..     168     216 .. 0.83
   3 ?   12.6   0.2     3e-05     0.089     106     188 ..     215     294 ..     208     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                    EEECSCCCCHHHHHHHHHHBTTSSGG CS
                   Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdq 26 
                                    +Ggm+ e tl+   ++++++++  d+
  gi|121637419|ref|YP_977642.1| 126 VGGMTLEQTLTSRDQINAQLRGVLDE 151
                                    7*****************99987765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                                    HHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHH CS
                   Asp_Glu_race 104 ealkatgvkkvglLgTrgtlksglyqkelean 135
                                    +++ka++ k+  +L+ +gt ++++ q+e +++
  gi|121637419|ref|YP_977642.1| 180 KQMKADREKRAMILTAEGTREAAIKQAEGQKQ 211
                                    58999*****************9999988875 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 3e-05
                                    HHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHCHHHHTT-TTSH.HHHHHHHHHHHHHTTT- CS
                   Asp_Glu_race 106 lkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqaiyeelkaGevtee.arrailkllerlaerga 184
                                    l+a+g+k+ ++L+ ++  +s++ +++ e+++ +     +++ q +  + + +++kaG+ t+e  +++ l+ l ++a+ +a
  gi|121637419|ref|YP_977642.1| 215 LAAEGAKQAAILAAEADRQSRMLRAQGERAAAY----LQAQGQAKAIEKTFAAIKAGRPTPEmLAYQYLQTLPEMARGDA 290
                                    4559************************97666....666666655566668999***999999999999999999*999 PP

                                    SEEE CS
                   Asp_Glu_race 185 davi 188
                                    ++v 
  gi|121637419|ref|YP_977642.1| 291 NKVW 294
                                    9986 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05      0.11     154     209 ..     129     184 ..      91     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                       Band_7_1 154 ipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    +++ +  +  +++ ++l+ +l+e+  + Gl + ++e+++i+ p++++  ++k+ ++
  gi|121637419|ref|YP_977642.1| 129 MTLEQTLTSRDQINAQLRGVLDEATGRWGLRVARVELRSIDPPPSIQASMEKQMKA 184
                                    455566677899****************************************9876 PP

>> Ntox1  Putative RNase-like toxin, toxin_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   2.8e-05     0.085      25      87 ..     163     225 ..     159     235 .. 0.87
   2 ?   -1.0   0.2      0.79   2.4e+03      45      83 ..     227     265 ..     221     273 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                          Ntox1  25 vekCsppPCPvlrveYkkelaaddelkeeneevealRkldaklaadeaakLiqaletarlngg 87 
                                    ve+ s  P P ++   +k+++ad e ++   + e+ R+++ k a  + +  i a e a++ + 
  gi|121637419|ref|YP_977642.1| 163 VELRSIDPPPSIQASMEKQMKADREKRAMILTAEGTREAAIKQAEGQKQAQILAAEGAKQAAI 225
                                    677788999*******************************99998888888888899988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.79
                          Ntox1  45 aaddelkeeneevealRkldaklaad.eaakLiqaletar 83 
                                    aa+ + +  +   ++ R ++  l+a+ +a+ + +   +++
  gi|121637419|ref|YP_977642.1| 227 AAEADRQSRMLRAQGERAAA-YLQAQgQAKAIEKTFAAIK 265
                                    45555555555666666444.4444415555544444444 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.0   0.00034         1      15      32 ..       3      20 ..       2      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00034
                         OppC_N 15 lAvvglvilllllliaif 32
                                    Av+glv+l++l+++ai+
  gi|121637419|ref|YP_977642.1|  3 GAVAGLVFLAVLVIFAII 20
                                   59**************98 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.7    0.0028       8.5      19      80 ..     153     219 ..     138     231 .. 0.74
   2 ?    0.6   3.2       0.2     6e+02      59      81 ..     220     242 ..     210     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0028
                      Caudo_TAP  19 ggelpesvvevsdineelkiqpkgkflvsdgeglpawvedk.........keeqiqqAeqekqqllaqAse 80 
                                     g +  +v+ v+    +++i+p+ +++ s ++ ++a+ e++         +e+ i+qAe +kq+ + +A+ 
  gi|121637419|ref|YP_977642.1| 153 TGRWGLRVARVE----LRSIDPPPSIQASMEKQMKADREKRamiltaegtREAAIKQAEGQKQAQILAAEG 219
                                    556666666666....6677888888888888888877766777777788888899999999888888765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                      Caudo_TAP  59 kkeeqiqqAeqekqqllaqAseq 81 
                                    +k++ i +Ae+ +q+++  A+ +
  gi|121637419|ref|YP_977642.1| 220 AKQAAILAAEADRQSRMLRAQGE 242
                                    37888999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 2367.60
//
Query:       gi|121637420|ref|YP_977643.1|  [L=118]
Description: hypothetical protein BCG_1551 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-11   42.4   8.1    7.8e-11   42.0   8.1    1.1  1  DoxX_2          DoxX-like family
  ------ inclusion threshold ------
      0.075   12.6   3.7       0.08   12.5   3.7    1.1  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   8.1   8.7e-15   7.8e-11       4     100 ..      11     106 ..       9     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.7e-15
                         DoxX_2   4 vllalffllsGvakllraeevvakfaqlgfpssfvrllGvvellgalgLllplvtaprltplAavglallmvgAiathlr 83 
                                    ++la++ ++++va  +  + +++ ++ l++p s++ +l vv+ ++a+gLl   +++p+l+ l+ ++l+l++++A+ +h+r
  gi|121637420|ref|YP_977643.1|  11 AVLAALQAGDAVACAIPLPPIARLLDDLDVPVSVRPVLPVVKAASAVGLLSV-TRFPALARLTTAMLTLYFILAVGAHVR 89 
                                    78999*********************************************97.58************************* PP

                         DoxX_2  84 rgdpkavalpavllala 100
                                    ++d    a+pa+ ++ +
  gi|121637420|ref|YP_977643.1|  90 VRDRVVNAIPAASFLTL 106
                                    ****6555555443332 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.7   8.9e-06      0.08     144     207 ..      40     108 ..       7     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-06
                 Virul_fac_BrkB 144 a.....pllglglelsellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvk 207
                                    +     p+l++  + s+++ll+++r+++++ l++++++l + ++  ++vr+r+ ++ a+ aa +++l+ 
  gi|121637420|ref|YP_977643.1|  40 VpvsvrPVLPVVKAASAVGLLSVTRFPALARLTTAMLTLYFILAVGAHVRVRDRVVNAIPAASFLTLFA 108
                                    2445567778777777777********999999******************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 637.26
//
Query:       gi|121637421|ref|YP_977644.1|  [L=76]
Description: hypothetical protein BCG_1552 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-05   22.3   0.1    4.8e-05   22.1   0.1    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.7e-09   4.8e-05     441     484 ..       5      49 ..       2      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-09
                  MM_CoA_mutase 441 elevlkide.eveerqaerlealraerdeaavkaaLaalgeaars 484
                                    e+evlk+++ +v+++q ++l +lr++rd+ +v+aaLa+l++aa  
  gi|121637421|ref|YP_977644.1|   5 EVEVLKVENsRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAA 49 
                                    6899*****9*******************************7763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 408.46
//
Query:       gi|121637422|ref|YP_977645.1|  [L=435]
Description: hypothetical protein BCG_1553 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.1    7.4   8.1       0.78    9.4   0.0    2.8  2  DUF4956   Domain of unknown function (DUF4956)


Domain annotation for each model (and alignments):
>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.4     0.036   6.4e+02      12      61 ..     168     214 ..     156     226 .. 0.57
   2 ?    9.4   0.0   4.3e-05      0.78      84     125 ..     373     414 ..     327     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.036
                        DUF4956  12 lYykrhrrrdlvftflllnvgvfavvlllasvevsiglglGLfgvlsilR 61 
                                    ++++r + +    t ++l+++  + +++la ++ +i l ++L +vl+i+ 
  gi|121637422|ref|YP_977645.1| 168 IFLTRAHTSR---TRVILSTLYGLTMAVLALIHEAIPLEFALGAVLAIIV 214
                                    4444433333...2333333333344444444666777777778888875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 4.3e-05
                        DUF4956  84 inglaslslvellvlnvlivlvlallesprllkkerrklvtl 125
                                    i++++ + ++ +++l+v+iv +l+ +++p + +  +r+ v++
  gi|121637422|ref|YP_977645.1| 373 ITAVDWTRWWVMITLDVAIVYILYAIDRPEIEQPPSRRNVQV 414
                                    667899999*********************999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2378.37
//
Query:       gi|121637423|ref|YP_977646.1|  [L=252]
Description: hypothetical protein BCG_1554c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-23   82.0   8.7    4.5e-23   82.0   8.7    2.0  2  SNARE_assoc      SNARE associated Golgi protein
      0.004   17.3   8.0      0.004   17.3   8.0    2.4  3  ECF_trnsprt      ECF transporter, substrate-specific componen
  ------ inclusion threshold ------
       0.15   11.9   0.8       0.39   10.6   0.8    1.6  1  Arg_repressor_C  Arginine repressor, C-terminal domain


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.42   2.5e+03      30      35 ..      38      43 ..      16      79 .. 0.68
   2 !   82.0   8.7   7.5e-27   4.5e-23       1     119 [.      84     200 ..      84     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.42
                    SNARE_assoc 30 Gaslay 35
                                   G ++  
  gi|121637423|ref|YP_977646.1| 38 GITVLV 43
                                   222222 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 7.5e-27
                    SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpiv 80 
                                    +P +++++aaG+lfg ++g++++++g++++a++a ll+r  g  +l++ l+ ++++++l++ ++++g+la+l lrl+p+v
  gi|121637423|ref|YP_977646.1|  84 FPRTAFTLAAGLLFGSVVGVFIAVVGSTASAVIAMLLVRATG-WQLNS-LVRRRAINRLDERLRERGWLAILSLRLIPVV 161
                                    6999**************************************.77777.999**************************** PP

                    SNARE_assoc  81 PrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                    P++++ny+aG+++v++  F++at++G +p +  ++ lG+
  gi|121637423|ref|YP_977646.1| 162 PFAAINYAAGASGVRILSFAWATLAGLLPGTAAVVILGD 200
                                    ***********************************9997 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.8      0.16   9.6e+02     107     124 ..      32      49 ..       9      82 .. 0.59
   2 !   17.3   8.0   6.7e-07     0.004      32     123 ..      88     197 ..      64     214 .. 0.82
   3 ?    0.8   2.5     0.079   4.7e+02      50      99 ..     177     235 ..     160     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.16
                                    HHHHCCCCCHHHHHHHCC CS
                    ECF_trnsprt 107 ilagvlgtivatllvlli 124
                                    i+++v+g  v +++ ll+
  gi|121637423|ref|YP_977646.1|  32 IVGTVVGITVLVVVALLV 49 
                                    333333333333333333 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.7e-07
                                    HHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH...........................HHHHHHHHCHH CS
                    ECF_trnsprt  32 ihipvllggllfGpikGailgiitsvlkailtggtgalssfv...........................piaflsrilig 84 
                                     + ++  +gllfG ++G+++++++s+++a++  +     ++v                           + a+ls  li+
  gi|121637423|ref|YP_977646.1|  88 AFTLA--AGLLFGSVVGVFIAVVGSTASAVIA-M-----LLVratgwqlnslvrrrainrlderlrergWLAILSLRLIP 159
                                    33344..5**********************92.3.....23345679999****************************** PP

                                    HHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHC CS
                    ECF_trnsprt  85 liagllykkgkkknlkeivvsfilagvlgtivatllvll 123
                                    +++    ++    +  + ++sf++a+++g + +t  v+ 
  gi|121637423|ref|YP_977646.1| 160 VVPFAAINYAAGASGVR-ILSFAWATLAGLLPGTAAVVI 197
                                    ****9998888888888.9***********999988654 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.079
                                    HHHHHHHHHHHHCHT-SSTTHHHH........HHHHHHHHCHHHHHH..HHHHCCCHTTH CS
                    ECF_trnsprt  50 ilgiitsvlkailtggtgalssfv........piaflsriligliag..llykkgkkknl 99 
                                    il++ + +l+ +l +gt+a+++++        p  +l+++++g +    l+y++++++++
  gi|121637423|ref|YP_977646.1| 177 ILSFAWATLAGLL-PGTAAVVILGdafagsgsPLLILVSVCTGALGLtgLVYEIRNYRRQ 235
                                    4556688888888.8888887777888888887777777777765434499998888776 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   6.6e-05      0.39      18      53 ..      11      45 ..       8      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.6e-05
                                   E-STTHHHHHHHHHHH-..TTEEEEEE-SSEEEEEE CS
                Arg_repressor_C 18 kTlpGaAqavAaaiDslelpeilGtiAGdDTilvil 53
                                    T+ G A +++a+  +++lp i+Gt+ G  T+lv++
  gi|121637423|ref|YP_977646.1| 11 ETVHGIATSLGAVARQASLPRIVGTVVGI-TVLVVV 45
                                   5999**********************997.566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1384.56
//
Query:       gi|121637424|ref|YP_977647.1|  [L=615]
Description: methylmalonyl-CoA mutase small subunit mutA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-124  416.9   0.0   1.4e-124  416.5   0.0    1.1  1  MM_CoA_mutase  Methylmalonyl-CoA mutase


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.5   0.0    8e-129  1.4e-124       1     504 [.      48     524 ..      48     528 .. 0.96

  Alignments for each domain:
  == domain 1  score: 416.5 bits;  conditional E-value: 8e-129
                  MM_CoA_mutase   1 kTaegievkplYtaedleekklgeslPGefPftRGvkatmyrgrpWtirqyag.fstaeetnerykklLeaGqtglsvaf 79 
                                    +Ta+g++++ lYta d     ++  lPG++Pf+RG ++ ++++++W++++ +   +  ++tn++++++L +G+++l +  
  gi|121637424|ref|YP_977647.1|  48 QTADGFAIRALYTAFDE---LPEPPLPGQWPFVRGGDPLRDVHSGWKVAEAFPaNGATADTNAAVLAALGEGVSALLI-- 122
                                    599*************6...46788*************************9993556788******************.. PP

                  MM_CoA_mutase  80 dlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqg.vdleklsgti 158
                                                     +vG++Gva d    + +ll+g++l+ ++v ++++a+  p+++++la++++ +  ++++ls+ +
  gi|121637424|ref|YP_977647.1| 123 -----------------RVGESGVAPDR---LTALLSGVYLNLAPVILDAGADYRPACDVMLALVAQLDpGQRDTLSIDL 182
                                    .................8**********...99*****************************999998868999****** PP

                  MM_CoA_mutase 159 qnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvralleaGld 238
                                    ++D+L++ l       +p+p +++++++++ aa   + +++i+v+g ++++ Gata+ ElA+t+a++v+Y+r l+e+Gl 
  gi|121637424|ref|YP_977647.1| 183 GADPLTASLRD-----RPAPPIEEVVAVASRAAG-ERGLRAITVDGPAFHNLGATAATELAATVAAAVAYLRVLTESGLV 256
                                    *********99.....89*************999.789****************************************** PP

                  MM_CoA_mutase 239 vdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilRttlealaA 318
                                    v+++++++sF++a+++d+f++ Ak+RA R+lWar+++ ++g       ++ vha+Ts  ++t++dp+vN+lR tl+a++A
  gi|121637424|ref|YP_977647.1| 257 VSDALRQISFRLAADDDQFMTLAKMRALRQLWARVAE-VVGDP--GGGAAVVHAETSLPMMTQRDPWVNMLRCTLAAFGA 333
                                    *************************************.76765..469******************************** PP

                  MM_CoA_mutase 319 vlggtqslhtnsfDeal.....alPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklfqeieea 393
                                    ++gg++++ +++fD a+     +++  f++riArntql+l eEs+v +v+DP+gGS++vE+LTd+la++aw+ fq+ie++
  gi|121637424|ref|YP_977647.1| 334 GVGGADTVLVHPFDVAIpggfpGTAAGFARRIARNTQLLLLEESHVGRVLDPAGGSWFVEELTDRLARRAWQRFQAIEAR 413
                                    *******************9999********************************************************* PP

                  MM_CoA_mutase 394 GGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealrae......rd 467
                                    GG+++a +  +++ +iae+aarr+++i++r+ +i+GvN++ pn  e +l+  + + +  +r+a+ +ealr++      r+
  gi|121637424|ref|YP_977647.1| 414 GGFVEAHD--FLAGQIAECAARRADDIAHRRLAITGVNEY-PNLGEPALPPGDPT-SPVRRYAAGFEALRDRsdhhlaRT 489
                                    ******98..******************************.****9988888877.8899******************** PP

                  MM_CoA_mutase 468 eaavkaaLaalgeaarsenllaraveaaralatlG.ei 504
                                    +a+++++L +lg++a+++    r+++a+++la++G e+
  gi|121637424|ref|YP_977647.1| 490 GARPRVLLLPLGPLAEHN---IRTTFATNLLASGGiEA 524
                                    ****************99...9*************775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 3285.80
//
Query:       gi|121637425|ref|YP_977648.1|  [L=750]
Description: methylmalonyl-CoA mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.8e-229  760.9   0.2   7.1e-229  760.6   0.2    1.1  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
    6.3e-15   55.3   0.8    1.4e-14   54.1   0.8    1.7  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  760.6   0.2  7.9e-233  7.1e-229       2     513 .]      52     576 ..      51     576 .. 0.98

  Alignments for each domain:
  == domain 1  score: 760.6 bits;  conditional E-value: 7.9e-233
                  MM_CoA_mutase   2 TaegievkplYtaedl...eek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsv 77 
                                    T+egi+v p+Y a+d    e++  + +s+PGe Pf+RG+++tmy+++pWtirqyagfsta+++n++y+++L+aGq+glsv
  gi|121637425|ref|YP_977648.1|  52 TPEGIDVTPVYIAADRaaaEAEgYPLHSFPGEPPFVRGPYPTMYVNQPWTIRQYAGFSTAADSNAFYRRNLAAGQKGLSV 131
                                    99*************999855567888***************************************************** PP

                  MM_CoA_mutase  78 afdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgt 157
                                    afdl+t+rgyDsdhpr++g+vG+aGvaids+ dm++l+dgidl++vsvsmt+n+a+lp+la+y++aaeeqgv++e+l gt
  gi|121637425|ref|YP_977648.1| 132 AFDLATHRGYDSDHPRVQGDVGMAGVAIDSILDMRQLFDGIDLSTVSVSMTMNGAVLPILALYVVAAEEQGVAPEQLAGT 211
                                    ******************************************************************************** PP

                  MM_CoA_mutase 158 iqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvralleaGl 237
                                    iqnDiLke+++r+tyiypp+ps+r+i di++y+++++pkfn+is+sgyhi+eaGata  ElA+tladGv+Y+ra+l+aGl
  gi|121637425|ref|YP_977648.1| 212 IQNDILKEFMVRNTYIYPPKPSMRIISDIFAYTSAKMPKFNSISISGYHIQEAGATADLELAYTLADGVDYIRAGLNAGL 291
                                    ******************************************************************************** PP

                  MM_CoA_mutase 238 dvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilRttleala 317
                                    d+d+faprlsFf++ig++ff+e+AklRA R lW+++v  +f +k+ ksl+lr+h qTsg+sltaqd+++N++Rt++ea+a
  gi|121637425|ref|YP_977648.1| 292 DIDSFAPRLSFFWGIGMNFFMEVAKLRAGRLLWSELVA-QFAPKSAKSLSLRTHSQTSGWSLTAQDVFNNVARTCIEAMA 370
                                    **************************************.9**************************************** PP

                  MM_CoA_mutase 318 AvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklfqeieeaGGml 397
                                    A+ g+tqslhtn++DealalPt+fsariArntql+l++Esg ++ +DP+gGSyyvE+LT++la++a ++++e+ e+GGm+
  gi|121637425|ref|YP_977648.1| 371 ATQGHTQSLHTNALDEALALPTDFSARIARNTQLVLQQESGTTRPIDPWGGSYYVEWLTHRLARRARAHIAEVAEHGGMA 450
                                    ******************************************************************************** PP

                  MM_CoA_mutase 398 kaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkide.eveerqaerlealraerdeaavkaaLa 476
                                    +ai++G+++ +i+e+aar+q++i+s+++ +vGvNk++   e++e+evlk+++ +v+++q ++l++lra rde av+aaLa
  gi|121637425|ref|YP_977648.1| 451 QAISDGIPKLRIEEAAARTQARIDSGQQPVVGVNKYQ-VPEDHEIEVLKVENsRVRAEQLAKLQRLRAGRDEPAVRAALA 529
                                    ************************************6.555679********9*************************** PP

                  MM_CoA_mutase 477 algeaarse..........nllaraveaaralatlGeisdaleevfg 513
                                    +l++aa ++          nlla+a++aara+at+Geis+ale+v+g
  gi|121637425|ref|YP_977648.1| 530 ELTRAAAEQgragadglgnNLLALAIDAARAQATVGEISEALEKVYG 576
                                    ****6665569**********************************98 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.8   1.6e-18   1.4e-14       2     117 ..     618     731 ..     617     735 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.6e-18
                    B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel.lkrirp 80 
                                    ++l+a+ g+d h++G +v+a a+ d gf+V++  +  ++e++++++++++++v+g+S+l   +l+ v +l ++ ++  rp
  gi|121637425|ref|YP_977648.1| 618 RILIAKMGQDGHDRGQKVIATAFADIGFDVDVGSLFSTPEEVARQAADNDVHVIGVSSLAAGHLTLVPALRDAlAQVGRP 697
                                    789***************************888888888**********************************7777899 PP

                    B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedal 117
                                    ++ +vvGG++p  d +e+ +   g + +++  g+  +
  gi|121637425|ref|YP_977648.1| 698 DIMIVVGGVIPPGDFDELYA--AG-ATAIFPPGTVIA 731
                                    ***********999999664..78.888998888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.81u 0.39s 00:00:01.20 Elapsed: 00:00:00.60
# Mc/sec: 3765.18
//
Query:       gi|121637426|ref|YP_977649.1|  [L=100]
Description: hypothetical protein BCG_1557 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 733.64
//
Query:       gi|121637427|ref|YP_977650.1|  [L=105]
Description: hypothetical protein BCG_1558 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-14   54.5   0.0    1.5e-14   54.3   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   8.3e-19   1.5e-14       2     110 ..       6      99 ..       5     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 8.3e-19
                                    TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCH.SEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCCE CS
                     PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnek.ntvivvpltskdkdkkklpfhveleseildlngldkdswvkldqi 80 
                                    rG+++ +dl+  +     +  p ++vsn+a+n++ + v+ v lt+++  +++ p++v + ++ ++l+     ++v++d i
  gi|121637427|ref|YP_977650.1|   6 RGQVYRCDLG--Y-----GAKPWLIVSNNARNRHtADVVAVRLTTTR--RTI-PTWVAMGPS-DPLT-----GYVNADNI 69 
                                    89*******3..2.....466***********9989********999..666.******997.5555.....9******* PP

                                    EEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                     PemK_toxin  81 rtvdkarlrkkigklsredlaevqralakl 110
                                     t+ k++l++++g++++++++++++ala +
  gi|121637427|ref|YP_977650.1|  70 ETLGKDELGDYLGEVTPATMNKINTALATA 99 
                                    ***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 777.53
//
Query:       gi|121637428|ref|YP_977651.1|  [L=334]
Description: arginine/ornithine transport system ATPase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.9e-124  412.1   1.1   8.2e-124  411.9   1.1    1.0  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    2.6e-07   30.4   0.9    1.6e-06   27.9   0.9    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    6.7e-05   23.0   0.0    0.00013   22.1   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00013   21.8   0.0     0.0017   18.2   0.0    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00013   21.7   0.3    0.00027   20.7   0.2    1.6  1  AAA_30           AAA domain
      0.001   18.8   0.0     0.0018   18.0   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
      0.001   18.8   0.0     0.0032   17.2   0.0    1.8  2  IstB_IS21        IstB-like ATP binding protein
     0.0016   19.0   0.2     0.0039   17.7   0.2    1.7  1  AAA_18           AAA domain
     0.0024   17.5   0.1      0.034   13.8   0.1    2.5  2  SRP54            SRP54-type protein, GTPase domain
     0.0027   16.9   0.1     0.0052   16.0   0.1    1.4  1  ArsA_ATPase      Anion-transporting ATPase
      0.003   17.1   1.2       0.72    9.4   0.1    2.3  2  Hpr_kinase_C     HPr Serine kinase C-terminal domain
      0.004   17.6   0.1     0.0096   16.3   0.1    1.7  1  AAA_16           AAA ATPase domain
     0.0056   16.8   0.7       0.04   14.0   0.7    2.2  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0064   16.5   0.4        2.1    8.3   0.0    2.4  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0095   15.9   0.1      0.018   15.0   0.1    1.4  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.028   13.9   0.0    1.4  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
      0.019   15.2   0.0      0.045   14.0   0.0    1.6  1  AAA_22           AAA domain
      0.021   14.2   0.6       0.25   10.6   0.6    2.1  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.034   13.9   0.0      0.066   12.9   0.0    1.6  1  AAA_24           AAA domain
       0.04   13.3   0.2      0.084   12.3   0.2    1.4  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.044   13.7   0.0      0.078   12.9   0.0    1.4  1  AAA_31           AAA domain
      0.056   13.0   0.3       0.38   10.3   0.0    2.1  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.059   13.3   0.0        8.6    6.2   0.0    2.3  2  RsgA_GTPase      RsgA GTPase
       0.11   12.3   0.2       0.19   11.4   0.2    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   11.9   0.0       0.21   11.0   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.17   11.6   0.0       0.38   10.5   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.9   1.1  1.2e-126  8.2e-124       1     266 [.      26     298 ..      26     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 411.9 bits;  conditional E-value: 1.2e-126
                                    HHHHHHHHH--SH....HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------- CS
                           MeaB   1 Laraitlveserp....eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsi 76 
                                    L+raitlves+rp    +a++ll rll+++G+a++vG+tGvPG+Gkst++ealg++l++rG+rvavlavDPss++tGGsi
  gi|121637428|ref|YP_977651.1|  26 LPRAITLVESTRPdhreQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGSI 105
                                    79**************9*************************************************************** PP

                                    -------HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTT CS
                           MeaB  77 lGDklRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGD 156
                                    lGDk+R+++lav+++++iR++p++G+lGG++++tre+v+lleaaGfDv+lietvGvGqsev+va++vdtfv+l+l+++GD
  gi|121637428|ref|YP_977651.1| 106 LGDKTRMARLAVHPNAYIRPSPTSGTLGGVTRATRETVVLLEAAGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGD 185
                                    ******************************************************************************** PP

                                    TTTT--CCCHHH-SEEEEE---...HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHH CS
                           MeaB 157 elqgikkGileiaDiivvnkaD...kkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehrevlk 233
                                    +lqgikkG+le+aDi+vvnkaD   +kea+ aarel+aa++l +++e+ Wrp+vl++saveg+G++el+d++e+hr+vl+
  gi|121637428|ref|YP_977651.1| 186 QLQGIKKGVLELADIVVVNKADgehHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLT 265
                                    ************************99****************************************************** PP

                                    HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHC-H CS
                           MeaB 234 ktGllekrrrerakeelrelvedellkrvkaae 266
                                     +G++++rrr+++++++++lv+d++l+rv++++
  gi|121637428|ref|YP_977651.1| 266 GAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNP 298
                                    *****************************9986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.9   2.3e-09   1.6e-06       3     158 ..      61     214 ..      59     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.3e-09
                                    EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT............EEEETTTTECCHCTT-H CS
                           cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve...........ivelenGciCctlredl 69 
                                    +++tG +G GK+t +++l     ++g ++av+  + +++   +++l +++ +                         +  
  gi|121637428|ref|YP_977651.1|  61 VGITGVPGVGKSTAIEALGmhLIERGHRVAVLAVDPSSTRTGGSILGDKTRMarlavhpnayiR------------PSPT 128
                                    679*************998887889*********************888554455444444321............2222 PP

                                    HHHHHHHHHHH.........TT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHH CS
                           cobW  70 lkelealeere.........erldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqla 140
                                    + +l  + +           + +dviliEt+G+ +             +  +d+ v +  a    + +++ +   +  l+
  gi|121637428|ref|YP_977651.1| 129 SGTLGGVTRATretvvlleaAGFDVILIETVGVGQSEVA--------VANMVDTFVLLTLA----RTGDQLQGIKKGVLE 196
                                    2222222222222245555557**********9998877........46778898888888....789999999999*** PP

                                    TSSEEEEE-HHHHCHC.. CS
                           cobW 141 aadllvlnKtDlldeeal 158
                                     ad++v+nK+D   +++ 
  gi|121637428|ref|YP_977651.1| 197 LADIVVVNKADGEHHKEA 214
                                    ***********9888843 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-07   0.00013       9      92 ..      68     214 ..      63     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep................................. 54 
                                    GvGK+t   +L+  l +rg+rV+++ +Dp ++ +   + g++ + ++                                 
  gi|121637428|ref|YP_977651.1|  68 GVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGsILGDKTRMARlavhpnayirpsptsgtlggvtratretvvlle 147
                                    9*****************************88877467777777777********************************* PP

                                    ...............................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TT CS
                                    ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ...............................dlkrllellealgkkkalllkiagvvlnrvdgeneetl 92 
                                                                   +l r +  l+ ++k+  +l +   vv+n+ dge+++++
  gi|121637428|ref|YP_977651.1| 148 aagfdvilietvgvgqsevavanmvdtfvllTLARTGDQLQGIKKG--VLELADIVVVNKADGEHHKEA 214
                                    ********************99999999888777777777777776..4467778999*****976654 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.5e-06    0.0017       1      37 [.      63      99 ..      63     102 .. 0.94
   2 ?    1.4   0.0      0.33   2.3e+02     155     175 ..     195     214 ..     160     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                   ++G++G+GK+t ++al  +l +rg +vav+  DP + 
  gi|121637428|ref|YP_977651.1| 63 ITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSST 99
                                   68********************************875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.33
                     ATP_bind_1 155 lelPhvvvlnkfDllkeklek 175
                                    lel  +vv+nk+D+   ++e 
  gi|121637428|ref|YP_977651.1| 195 LELADIVVVNKADGEH-HKEA 214
                                    68899*********55.2333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   3.9e-07   0.00027       6      82 ..      45     134 ..      40     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.9e-07
                         AAA_30   6 Qaaavealltsgdrv.avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk... 81 
                                    Q+ +++ l  sg+   + +tG++G GK+ta++al  ++ ++g+rv++lA      ++ +  lg +++     ++ ++   
  gi|121637428|ref|YP_977651.1|  45 QQLLLRLLPDSGNAHrVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPNAyir 124
                                    5555555555655541459***************999999*********9877777766666666666666666555666 PP

                         AAA_30  82 .........g 82 
                                             g
  gi|121637428|ref|YP_977651.1| 125 psptsgtlgG 134
                                    6666666643 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0018       2      44 ..      64     107 ..      63     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                                    EESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHH CS
                Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegik.vvltrepggteiGekire 44 
                                     G+ G+GK+t +e+l  +l e+g++ +vl   p++t++G +i +
  gi|121637428|ref|YP_977651.1|  64 TGVPGVGKSTAIEALGMHLIERGHRvAVLAVDPSSTRTGGSILG 107
                                    6999***********************************99865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.7e-06    0.0032      45      80 ..      56      91 ..      19      96 .. 0.73
   2 ?   -2.8   0.0       6.3   4.4e+03      50      66 ..     153     169 ..     151     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-06
                      IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlf 80
                                    +++ + ++G +GvGKs    alg++ +++g++v  
  gi|121637428|ref|YP_977651.1| 56 GNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAV 91
                                   56777899*************************975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                      IstB_IS21  50 ivllGpsGvGKshlaia 66 
                                    ++l+   GvG s +a+a
  gi|121637428|ref|YP_977651.1| 153 VILIETVGVGQSEVAVA 169
                                    56677778888877776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   5.7e-06    0.0039       1      22 [.      61      82 ..      61     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.7e-06
                         AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                   +++tG+pGvGK+t  ++L  +l
  gi|121637428|ref|YP_977651.1| 61 VGITGVPGVGKSTAIEALGMHL 82
                                   78****************7776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   4.9e-05     0.034       6      99 ..      63     166 ..      59     179 .. 0.65
   2 ?   -0.6   0.0       1.3   8.7e+02      75     117 ..     189     233 ..     185     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                    EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES..TSSTTHH.....HHHHHHHHHTTEEEEE....SSTTSCHHHHHHH CS
                          SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD..tfRaaAv.....eQLktlaeklgvpvik....kkeeadpaavake 74 
                                    + G+ G+GK t++  L  +l ++g++v++ a+D    R +         ++ la + ++  i+    + +       ++e
  gi|121637428|ref|YP_977651.1|  63 ITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDpsSTRTGGSilgdkTRMARLAVHPNAY-IRpsptSGTLGGVTRATRE 141
                                    689******************************444576653222223444444444422.2223222222245556666 PP

                                    HHHHHHHTTSSEEEEEE--SSTTHH CS
                          SRP54  75 avekakeekidvvlvDTaGrlqndk 99 
                                    +v   ++ ++dv+l+ T G  q++ 
  gi|121637428|ref|YP_977651.1| 142 TVVLLEAAGFDVILIETVGVGQSEV 166
                                    6666677777777777777666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                    HHHHHHHTTSSEEEEEE-.-SSTTHHHHH.HHHHHHHHHHSSSEE CS
                          SRP54  75 avekakeekidvvlvDTa.Grlqndkelm.eelkkikkvvkpdev 117
                                    +++k   e +d+v+v  a G ++++++l  +el++  + + p e 
  gi|121637428|ref|YP_977651.1| 189 GIKKGVLELADIVVVNKAdGEHHKEARLAaRELSAAIRLIYPREA 233
                                    667777777899998877588888887752688888888887775 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   7.6e-06    0.0052       6      40 ..      63      97 ..      59     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.6e-06
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                    ArsA_ATPase  6 vgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                   ++G  GVGK+t+  a++++l e g++v ++++DP 
  gi|121637428|ref|YP_977651.1| 63 ITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPS 97
                                   78999*****************************6 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1     0.001      0.72      23      45 ..      63      89 ..      58     114 .. 0.79
   2 !    6.5   0.1     0.008       5.5      10      36 ..     142     168 ..     135     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                                   EEESTCHHHHH....HHHHHHTTT-EE CS
                   Hpr_kinase_C 23 itGesgvGKse....laleLikrghrL 45
                                   itG  gvGKs     l++ Li+rghr+
  gi|121637428|ref|YP_977651.1| 63 ITGVPGVGKSTaieaLGMHLIERGHRV 89
                                   89********633235789******95 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.008
                                    ESEEEEETTEEEEEEESTCHHHHHHHH CS
                   Hpr_kinase_C  10 hGvlvdvygvGvLitGesgvGKselal 36 
                                      vl++  g+ v+++ + gvG se+a+
  gi|121637428|ref|YP_977651.1| 142 TVVLLEAAGFDVILIETVGVGQSEVAV 168
                                    5699*********************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05    0.0096       5      55 ..      41      89 ..      37     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                         AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                   Re+ ++ Ll++l    sg  + v ++G +GvGKs+ +++l  +l ++g  +
  gi|121637428|ref|YP_977651.1| 41 REQAQQLLLRLLP--DSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRV 89
                                   7777777777774..66777999****************999998885333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.7   5.8e-05      0.04       1      35 [.      60     101 ..      60     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                                    EEEEEESTTSSHHHHHHHHH......TS.TEEESSSTTSSSS CS
                       MMR_HSR1   1 evaivGrpNvGKStLinalt......ge.kaivsdkpgtTrd 35 
                                    +v+i G p vGKSt i al       g  +a  +  p  Tr+
  gi|121637428|ref|YP_977651.1|  60 RVGITGVPGVGKSTAIEALGmhlierGHrVAVLAVDPSSTRT 101
                                    69****************952333321212333444444444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0031       2.1       6      34 ..      73     101 ..      70     130 .. 0.65
   2 ?    6.3   0.1     0.013       8.9       2      34 ..     133     166 ..     132     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                 Glyco_transf_4   6 rhvleLaraLarrGheVtvvtpgddgple 34 
                                    + ++ L  +L +rGh+V v++ +++    
  gi|121637428|ref|YP_977651.1|  73 TAIEALGMHLIERGHRVAVLAVDPSSTRT 101
                                    67889999************655554433 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                 Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv.tpgddgple 34 
                                    GGv r ++e +  L ++G++V ++ t g+++ + 
  gi|121637428|ref|YP_977651.1| 133 GGVTRATRETVVLLEAAGFDVILIeTVGVGQSEV 166
                                    9**********************97666665554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.6e-05     0.018       1      31 [.      60      90 ..      60     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   +v iTG pGvGK+T ++ +   l ++g +v+
  gi|121637428|ref|YP_977651.1| 60 RVGITGVPGVGKSTAIEALGMHLIERGHRVA 90
                                   589***************9999999998875 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.028       2      43 ..      60     101 ..      59     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                      Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43 
                                    ++ i G  G+Gkst++  l + l e+g++v ++  DP +  t
  gi|121637428|ref|YP_977651.1|  60 RVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRT 101
                                    57889999*****************************98766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.6e-05     0.045      10      57 ..      63     106 ..      56     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-05
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdll 57 
                                    +tG +G+GK+t ++ l + l     +e+ +r+ v+ v+++s  +  ++l
  gi|121637428|ref|YP_977651.1|  63 ITGVPGVGKSTAIEALGMHL-----IERgHRVAVLAVDPSSTRTGGSIL 106
                                    89*****************9.....344579999999999888776665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00037      0.25      42     150 ..      61     173 ..      49     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                    EEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS.SC.GGGTT-TTBSS.....S-B-SHHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  42 llvaGatgsGKStalntLilSlatthtPeeVqliliDykgv.el.salediphlls....vavatdperalraleeLvke 115
                                    + + G +g GKSta+ +L + l+     ++V+ + +D++++ +  s l d ++++     ++    p   + +l  ++ +
  gi|121637428|ref|YP_977651.1|  61 VGITGVPGVGKSTAIEALGMHLIE--RGHRVAVLAVDPSSTrTGgSILGDKTRMARlavhPNAYIRPSPTSGTLGGVTRA 138
                                    4599**************998887..89**********998644134444444433333577777788888888888888 PP

                                    HHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B- CS
                   FtsK_SpoIIIE 116 meeryalfreagvrsiaaydgeiaedpldifgdvf 150
                                     +e   l+++ag++ i     +++++++   ++v+
  gi|121637428|ref|YP_977651.1| 139 TRETVVLLEAAGFDVILIETVGVGQSEVAVANMVD 173
                                    88888888888888877744444444444444333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.6e-05     0.066       3      43 ..      59     106 ..      57     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                         AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkf 43 
                                     ++ i+G +g+GK+t +  l       g +++++ ++ ++ ++ +  +
  gi|121637428|ref|YP_977651.1|  59 HRVGITGVPGVGKSTAIEALgmhlierGHRVAVLAVDPSSTRTGGSIL 106
                                    6899****************9999999999999999999988877655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00012     0.084      13      41 ..      67      95 ..      61     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                           ParA 13 GGVGKStvavnlAlaLakkglkvgllDaD 41
                                    GVGKSt    l ++L ++g++v++l +D
  gi|121637428|ref|YP_977651.1| 67 PGVGKSTAIEALGMHLIERGHRVAVLAVD 95
                                   6*************************998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.078      12      47 ..      68     103 ..      65     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg 47 
                                    GvGK+T   +l++ l ++g++v +  +Dp +  t g
  gi|121637428|ref|YP_977651.1|  68 GVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGG 103
                                    9****************************9888765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.55   3.8e+02       5      26 ..      60      81 ..      57     110 .. 0.83
   2 ?   10.3   0.0   0.00055      0.38     122     191 ..     196     260 ..     132     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                                   EEEEEESTTSSHHHHHHHHHHH CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdrLlyk 26
                                    +gi g    GK+T +++L ++
  gi|121637428|ref|YP_977651.1| 60 RVGITGVPGVGKSTAIEALGMH 81
                                   6899999999*******99755 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00055
                                    TTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 122 gvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    ++  iv++NK+D   ++e +  ++e++  +         y+ ++    pv+ +Sa++g g+ +l +++ ++
  gi|121637428|ref|YP_977651.1| 196 ELADIVVVNKADGEhHKEARLAARELSAAI------RLIYPREALWRPPVLTMSAVEGRGLAELWDTVERH 260
                                    33459*******997888888999999888......3334555545789*****************99887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.012       8.6     100     121 ..      59      80 ..      36     101 .. 0.79
   2 ?    4.8   0.0     0.035        24      47     106 ..     197     266 ..     140     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                                    SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                    + + + G  GvGKSt i+al  
  gi|121637428|ref|YP_977651.1|  59 HRVGITGVPGVGKSTAIEALGM 80 
                                    55668999*********99865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                                    -EEEEEEE-GGG--HHH..........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEEC CS
                    RsgA_GTPase  47 iepvivlnKiDlleeee..........eleelkeelealgyevllvsaktkegleelkellkdktsvlvG 106
                                    +  ++v+nK+D  +++e          +++ +  + + +  +vl++sa +++gl+el + ++ +  vl G
  gi|121637428|ref|YP_977651.1| 197 LADIVVVNKADGEHHKEarlaarelsaAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTG 266
                                    4558999999999999988987776666666666677788999******************999999998 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00028      0.19       3      21 ..      63      81 ..      61     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                Viral_helicase1  3 vhGvpGcGKStlirkllrt 21
                                   + GvpG GKSt+i  l  +
  gi|121637428|ref|YP_977651.1| 63 ITGVPGVGKSTAIEALGMH 81
                                   78***********887644 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.21       6      36 ..      63      93 ..      61     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                   EE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                          KTI12  6 ltGlPssGKstrakeLakaleeekrsvvvid 36
                                   +tG+P +GKst+ + L  +l e++ +v v+ 
  gi|121637428|ref|YP_977651.1| 63 ITGVPGVGKSTAIEALGMHLIERGHRVAVLA 93
                                   8**********************99999976 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00056      0.38      26      44 ..      62      80 ..      54      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00056
                         AAA_29 26 lltGpsGsGKSTllDAiqa 44
                                    +tG  G+GKST + A+ +
  gi|121637428|ref|YP_977651.1| 62 GITGVPGVGKSTAIEALGM 80
                                   49************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2346.98
//
Query:       gi|121637429|ref|YP_977652.1|  [L=429]
Description: esterase lipL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-58  196.7   4.4    8.4e-58  196.2   4.4    1.1  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2   4.4   4.7e-62   8.4e-58      10     314 ..      45     382 ..      32     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 4.7e-62
                                    HHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTCTTG CS
                 Beta-lactamase  10 aqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPefagp 89 
                                    + +++ G a+av+ dg++v+d + G+ad++g  p++ad+  +++S+tK +ta+++++l+++G++d+ +pV++y+P+f+++
  gi|121637429|ref|YP_977652.1|  45 G-RRFGGGALAVYLDGQPVVDVWKGWADRAGWVPWSADSAPMVFSATKGMTATVIHRLADRGLIDYEAPVAEYWPAFGAN 123
                                    4.7899************************************************************************** PP

                                    GGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHH.HHHHHHHHHHTSHHHHHH CS
                 Beta-lactamase  90 gkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgyg.llgellekvtgrsleqll 168
                                    gk+++T+rd+++H++Gl++l  +++++++  d+  + ++la++ p +  G+   Y+++++g l+  l+++vtg++++ l+
  gi|121637429|ref|YP_977652.1| 124 GKATLTVRDVMRHQAGLSGL--RGATQQDLLDHVVMEERLAAAVPGRLLGKSA-YHALTFGwLMSGLARAVTGKDMRLLF 200
                                    *****************999..999999**9***************9888886.************************** PP

                                    HHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC................................ CS
                 Beta-lactamase 169 reeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae................................ 216
                                    ree+++pL+    +lg p++++p++ a    +++ a   +a l    +                                
  gi|121637429|ref|YP_977652.1| 201 REELAEPLDTDGLHLGRPPADAPTRVAEIIMPQDIAA--NAVL----Tcamrrlahrfsggfrsmyfpgaiaavqgeapl 274
                                    *******************998887776633222222..2222....2333356888*********************** PP

                                    .....TTTBEEEEHHHHHHHHHHHHHCCSSSSHHHHHHH......HHHHTSEEEECTTEEEECECSSEEEEECCHTEEEE CS
                 Beta-lactamase 217 .....gagglistardlarflglalegglllsaetlaql......taklssgttrpagiraglglGwvladktgapgtfg 285
                                         +a+++++tar lar +g  ++gg++ + + l++       + +++  ++r+ +++ ++ lG++ ++ ++ + +fg
  gi|121637429|ref|YP_977652.1| 275 ldaeiPAANGVATARALARMYGAIANGGEIDGIRFLSRElvtgltRNRRQVLPDRNLLVPLNFHLGYHGMPIGNVMPGFG 354
                                    *********************777777777666666666322223555555555555566666666666666666***** PP

                                    EEESTEEEEEEEECGGTEEEEEEESBCSS CS
                 Beta-lactamase 286 htGggygtyvfvdpeanlvvavltnrdpp 314
                                    h G  +g+  + dpe+++++a++ nr  +
  gi|121637429|ref|YP_977652.1| 355 HVG-LGGSIGWTDPETGVAFALVHNRLLS 382
                                    ***.*********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3011.65
//
Query:       gi|121637430|ref|YP_977653.1|  [L=205]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-24   85.2   0.0    1.4e-23   83.3   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
      2e-20   73.3   0.0    1.7e-19   70.3   0.0    2.1  1  Methyltransf_25  Methyltransferase domain
    1.7e-19   70.1   0.0    2.8e-19   69.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.5e-15   57.7   0.0    2.1e-15   57.3   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    6.6e-14   52.1   0.0    7.8e-14   51.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.2e-07   31.3   0.0    6.5e-07   28.9   0.0    1.8  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00014   21.5   0.0    0.00022   20.8   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0063   15.7   0.0     0.0078   15.4   0.0    1.1  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.012   14.7   0.0    1.1  1  Pox_MCEL         mRNA capping enzyme
       0.01   15.3   0.0      0.043   13.3   0.0    1.8  2  Methyltransf_4   Putative methyltransferase
      0.011   15.4   0.0      0.016   14.9   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.06   13.2   0.0       0.38   10.6   0.0    2.1  2  Methyltransf_8   Hypothetical methyltransferase
      0.069   12.4   0.0        0.2   10.9   0.0    1.7  1  CMAS             Mycolic acid cyclopropane synthetase
      0.093   11.3   0.0       0.14   10.6   0.0    1.2  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.095   12.1   0.0       0.37   10.2   0.0    1.8  1  TehB             Tellurite resistance protein TehB
        0.1   12.2   0.0        7.8    6.0   0.0    2.1  2  MetW             Methionine biosynthesis protein MetW
       0.17   11.2   0.0       0.18   11.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.23   10.9   0.0       0.72    9.3   0.0    1.8  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   1.4e-26   1.4e-23       1      96 []       2     117 ..       2     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.4e-26
                                    EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEE................TTEECCCTSS-TT- CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvef................vvadaeklpfedns 61 
                                    LdvGcG+Gr+a +l+ +    +r+ g+D+s++++++++e++  ++++++f                +  d+ ++p++d+s
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALPLTGYLnseGRYAGFDISQKAIAWCQEHITSAHPNFQFevsdiynslynpkgkyQSLDF-RFPYPDAS 80 
                                    8**************5556689**********************996666667777777777766344444.49****** PP

                                    EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  62 fDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                    fD+v++++v++h+  +d+e++l+ei RvLkpgG++++
  gi|121637430|ref|YP_977653.1|  81 FDVVFLTSVFTHMfpPDVEHYLDEISRVLKPGGRCLC 117
                                    **********************************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.7e-22   1.7e-19       2      97 .]       2     113 ..       1     113 [. 0.84

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-22
                                    EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC...........CGB....SSSTTTE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgda...........edl....pfedgsf 65 
                                    Ld+GcG+Gr++l l   l+ ++++ g+Dis+++++ ++e++ ++++n++f++ d+           ++l    p++d+sf
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALPLTGYLNsEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVSDIynslynpkgkyQSLdfrfPYPDASF 81 
                                    9**************999559*********************************954433333332222222247***** PP

                                    EEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  66 DlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    D+v+++ ++ h+ ++d+e++l+ei+rvLkpgG
  gi|121637430|ref|YP_977653.1|  82 DVVFLTSVFTHMFPPDVEHYLDEISRVLKPGG 113
                                    *****8779997789****************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   2.9e-22   2.8e-19       7     128 ..       1     136 [.       1     159 [. 0.87

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 2.9e-22
                Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklled............. 72 
                                    +lD+GCG+G+ ++ l   l++++++ G+Dis++ai  ++e+  +    n++Fe++di + l +   +             
  gi|121637430|ref|YP_977653.1|   1 MLDVGCGSGRMALPLTGYLNSEGRYAGFDISQKAIAWCQEHITSAHP-NFQFEVSDIYNsLYN---Pkgkyqsldfrfpy 76 
                                    79***************************************998888.9********996643...2344677******* PP

                Methyltransf_31  73 ..ekfDlilsnevl..naladpdkileeiervlkpggilliedprllaelpakveeeska 128
                                      ++fD+++  +v+  +  +d + +l ei+rvlkpgg++l++++ l +e +a++ e   a
  gi|121637430|ref|YP_977653.1|  77 pdASFDVVFLTSVFthMFPPDVEHYLDEISRVLKPGGRCLCTYFLLNDESLAHIAEGKSA 136
                                    **************5444478889*********************999999999988773 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   2.1e-18   2.1e-15       1      98 [.       2     114 ..       2     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.1e-18
                Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg............ssf 67 
                                    L++GcG+G+++ +l  +l ++ +y g Dis++ai+  +e++ + ++n+  +v    ++l + +g+            +sf
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALPLTGYLnSEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVSDIYNSLYNPKGKyqsldfrfpypdASF 81 
                                    8**************9999***************9999999999998888888777777777777*************** PP

                Methyltransf_12  68 Dlvvasnvlhhl..kdirevldnirklLkpgGr 98 
                                    D+v++ +v+ h+  +d++ +ld+i ++LkpgGr
  gi|121637430|ref|YP_977653.1|  82 DVVFLTSVFTHMfpPDVEHYLDEISRVLKPGGR 114
                                    ********************************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   7.8e-17   7.8e-14      27     125 ..       2     134 ..       1     169 [. 0.73

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.8e-17
                Methyltransf_23  27 LdiGcGtGillevlrengf...svtgvDlspeaveiaekakkaqkdqfdeqeaae.......................pq 80 
                                    Ld+GcG+G+++  l  +      ++g+D+s +a+++ ++ +++ + +f+ +   +                       p+
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALPLTGYLNsegRYAGFDISQKAIAWCQEHITSAHPNFQFE---VsdiynslynpkgkyqsldfrfpyPD 78 
                                    9*************555333589*************995555555444111...01233344444444444444555588 PP

                Methyltransf_23  81 gkfdlIvlrevlehvp..dppellrqiatllkpgGylllseplasl.........k 125
                                    ++fd++ l+ v+ h+   d++++l+ i + lkpgG++l++++l ++         k
  gi|121637430|ref|YP_977653.1|  79 ASFDVVFLTSVFTHMFppDVEHYLDEISRVLKPGGRCLCTYFLLNDeslahiaegK 134
                                    8*************96459**********************987764455443333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   6.5e-10   6.5e-07      51     152 ..       1     118 [.       1     123 [. 0.75

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.5e-10
                                    EEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS..........TEEEE.......E--TTT-TTS CS
                Ubie_methyltran  51 vlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki..........niefl.......qanaeeLpfe 113
                                    +lDv +G+g +a+ l+  ++++g+  + Di+++ +   ++++                +   l       q+   ++p+ 
  gi|121637430|ref|YP_977653.1|   1 MLDVGCGSGRMALPLTGYLNSEGRYAGFDISQKAIAWCQEHITSAHPNfqfevsdiynS---LynpkgkyQSLDFRFPYP 77 
                                    69**************************************9987654344544422221...111111113333456789 PP

                                    -T-EEEE..EEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                Ubie_methyltran 114 ddsfDvv..tvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                    d sfDvv  t  f     +D ++ L e+ rvlkpGGr ++ 
  gi|121637430|ref|YP_977653.1|  78 DASFDVVflTSVFTHMFPPDVEHYLDEISRVLKPGGRCLCT 118
                                    *****98335567777789******************9996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.2e-07   0.00022      36      94 ..       2      61 ..       1      68 [. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                                   EEET-TTSHHHHHHHH.HTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST CS
                            MTS 36 lDlGcGaGvlgaalak.espeaevtlvdvdarAlesakenleanklevevvasdvleeve 94
                                   lD+GcG G +++ l    ++e +   +d++ +A++ ++e +++ + + ++  sd+++ + 
  gi|121637430|ref|YP_977653.1|  2 LDVGCGSGRMALPLTGyLNSEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVSDIYNSLY 61
                                   9***********99751567777********************************99865 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.8e-06    0.0078      65     179 ..       1     117 [.       1     129 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.8e-06
                Methyltransf_33  65 lvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealealaaeyp..sleveglvgdyedglewlaslpea...e 139
                                    +++ G+Gs++    L   l+++    +Y  +D+s++a++   e +++++p  + ev+ +  + ++   + +sl+ +    
  gi|121637430|ref|YP_977653.1|   1 MLDVGCGSGRMALPLTGYLNSE---GRYAGFDISQKAIAWCQEHITSAHPnfQFEVSDIYNSLYNPKGKYQSLDFRfpyP 77 
                                    5799***************655...78***********************444555566654433334444444336656 PP

                Methyltransf_33 140 derrlvlflGssigNlepeeaaafLrklraalgpgdllLl 179
                                    d +  v+fl s+++ + p++ ++ L ++++ l+pg + L 
  gi|121637430|ref|YP_977653.1|  78 DASFDVVFLTSVFTHMFPPDVEHYLDEISRVLKPGGRCLC 117
                                    7788899**********************99999887765 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05     0.012      69     186 ..       2     119 ..       1     143 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                       Pox_MCEL  69 LdldcgkGg...DLeKyekgeIsklvatDiaeesieeckeRYnklrsekkskyykFdaelirsdsfvssvrevfedyelk 145
                                    Ld++cg G     L+ y   e  ++ + Di++++i+ c+e  ++ + + + +       l+  +   +s++ +f  +++ 
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRmalPLTGYLNSE-GRYAGFDISQKAIAWCQEHITSAHPNFQFEVSDIYNSLYNPKGKYQSLDFRFPYPDAS 80 
                                    777777775222355555544.6899**************99666655555544544589999999********99**** PP

                       Pox_MCEL 146 fdivslQFaiHYsFeseekartvlrNvaellasGGkvlgTt 186
                                    fd+v l  ++   F +  +    l  ++++l++GG+ l T 
  gi|121637430|ref|YP_977653.1|  81 FDVVFLTSVFTHMFPPDVEH--YLDEISRVLKPGGRCLCTY 119
                                    **********9****98776..9***************995 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.3e-05     0.043       5      83 ..       1      77 [.       1      80 [. 0.89
   2 ?   -0.6   0.0      0.78   7.8e+02      98     112 ..     100     114 ..      98     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                   EEEET-TTSHHHHHHH.HHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES--- CS
                 Methyltransf_4  5 vleiGcGkGeflvalA.kknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilFPDP 83
                                   +l++GcG+G++ + l    n +  + G +i++k +a + ++i   +  N++   +d  + l  + ++g+ + + + FP P
  gi|121637430|ref|YP_977653.1|  1 MLDVGCGSGRMALPLTgYLNSEGRYAGFDISQKAIAWCQEHITSAH-PNFQFEVSDIYNSL--YNPKGKYQSLDFRFPYP 77
                                   58*********999962689*********************98765.6999999**99999..77999999999999987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.78
                                    HHHHHHHHHEEEEEE CS
                 Methyltransf_4  98 ellkelarvLkkgGv 112
                                    + l+e+ rvLk+gG 
  gi|121637430|ref|YP_977653.1| 100 HYLDEISRVLKPGGR 114
                                    789999******996 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.016      57     154 ..      20     117 ..       4     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                    BTTEEEEEE-S-HHHHHHHHHHHTT.SGG.GGGEEEE--...........-TTT---SS-..EEEEEEESSTTTS-GGGH CS
                           TPMT  57 eqgrevvGvelselAvekffeeanl.epk.vkelsgvkeysageiellcgdvFtlraeelgkfdliydraalvAlppelr 134
                                    + + + +G ++s++A++   e   + +p+   e+s+  ++  +  + +++  F ++  +  +fd+++   +++ + p + 
  gi|121637430|ref|YP_977653.1|  20 NSEGRYAGFDISQKAIAWCQEHITSaHPNfQFEVSDIYNSLYNPKGKYQSLDFRFPYPDA-SFDVVFLTSVFTHMFPPDV 98 
                                    4566789*********99644444467774446777777777788888888899888887.99***************** PP

                                    HHHHHHHHHHEEEEEE..EE CS
                           TPMT 135 eryakslaelLkpdgeglLv 154
                                    e+y +++ ++Lkp+g+  L+
  gi|121637430|ref|YP_977653.1|  99 EHYLDEISRVLKPGGRC-LC 117
                                    ***************94.44 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.46   4.6e+02      77      88 ..       2      13 ..       1      33 [. 0.83
   2 ?   10.6   0.0   0.00038      0.38     115     153 ..      73     114 ..      56     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                                   EEES-TT-HHHH CS
                 Methyltransf_8 77 adlGcGeakiae 88
                                    d+GcG  ++a 
  gi|121637430|ref|YP_977653.1|  2 LDVGCGSGRMAL 13
                                   69*******994 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                                    S-S--TT-EEEEEEE...S---SS-HHHHHHHHHHHEEEEEE CS
                 Methyltransf_8 115 kvPledesvdvavfc...lslmgtnladflkeanrvlkvGGl 153
                                    + P  d s dv+ +      +   +++++l e+ rvlk+GG 
  gi|121637430|ref|YP_977653.1|  73 RFPYPDASFDVVFLTsvfTHMFPPDVEHYLDEISRVLKPGGR 114
                                    6799999999976531113466789****************6 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002       0.2      66     173 ..       1     126 [.       1     143 [. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                    EEEES-TTSHHHHHHHHHH..--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEE.........ES-GGG---.......- CS
                           CMAS  66 lLdiGcGWGslvrravery..dvkvvglTlSkeqaklakkrvdeldlerkvevk.........lldyedlde.......k 127
                                    +Ld+GcG G ++         + +  g  +S++  +++++++ ++  + + ev+           +y+ ld         
  gi|121637430|ref|YP_977653.1|   1 MLDVGCGSGRMALPLTGYLnsEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVSdiynslynpKGKYQSLDFrfpypdaS 80 
                                    69********9986655441166789**************9999887776666422222111123577666555666678 PP

                                    -SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HH CS
                           CMAS 128 vdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkk 173
                                    +d v    +f h+     +++ ++++++lk++G+ l       +++
  gi|121637430|ref|YP_977653.1|  81 FDVVFLTSVFTHMFPPDVEHYLDEISRVLKPGGRCLCTYFLLNDES 126
                                    99999999999999999999**********9999987766655555 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.14     174     214 ..      73     114 ..      70     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                Methyltransf_29 174 rlpyPsrsfdlihCsrCridwteed.gilllevdRvlRpgGy 214
                                    r+pyP +sfd++  +    +    d   +l e+ Rvl+pgG 
  gi|121637430|ref|YP_977653.1|  73 RFPYPDASFDVVFLTSVFTHMFPPDvEHYLDEISRVLKPGGR 114
                                    89**********99888887665552789***********93 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00037      0.37      35     129 ..       2     114 ..       1     131 [. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                    EEES-TTSHHHH....HHHHTT-EEEEEES-HHHHHHHHHHHHHT......T-TTEEEEE--....GGG---.....-S- CS
                           TehB  35 ldlgcgqgrnsl....ylsllgydvtawdknensiafleeikeke......nlknistalyd....ineakl.....der 95 
                                    ld+gcg+gr +l    yl+  g     +d  +++ia  +e +         ++++i  +ly+     +++++     d  
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALpltgYLNSEGR-YAGFDISQKAIAWCQEHITSAhpnfqfEVSDIYNSLYNpkgkYQSLDFrfpypDAS 80 
                                    9********99855556666653.45688888888887775543311111122334444444111112222222222345 PP

                                    EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEE CS
                           TehB  96 ydfilstvvlmfleaeripsiienmqectkvggy 129
                                    +d ++ t v+  + +  + + ++++ +  k+gg 
  gi|121637430|ref|YP_977653.1|  81 FDVVFLTSVFTHMFPPDVEHYLDEISRVLKPGGR 114
                                    5666666666666666666666666666666665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0078       7.8      18      53 ..       2      39 ..       1      53 [. 0.82
   2 ?    4.2   0.0     0.029        29      71     101 ..      76     108 ..      67     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0078
                           MetW 18 ldlGcGdGellellkeekqvdgr..Gleldeegvaecv 53
                                   ld+GcG G +   l    + +gr  G +++++++a c 
  gi|121637430|ref|YP_977653.1|  2 LDVGCGSGRMALPLTGYLNSEGRyaGFDISQKAIAWCQ 39
                                   9********98888887777775559999999999886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                           MetW  71 fedksfdyvvlsqtlqatrnp..kevldellri 101
                                    ++d sfd+v l+  +  +  p  ++ lde+ r+
  gi|121637430|ref|YP_977653.1|  76 YPDASFDVVFLTSVFTHMFPPdvEHYLDEISRV 108
                                    99**********999888766224788888777 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.18     166     216 ..       2      54 ..       1     141 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                           PrmA 166 lDvGtGSGiLaiaaa.kLg.akkvvavDiDevAvkvakeNaelNkveakleva 216
                                    lDvG+GSG +a+     L+   +  + Di + A+   +e ++  + + ++ev 
  gi|121637430|ref|YP_977653.1|   2 LDVGCGSGRMALPLTgYLNsEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVS 54 
                                    8*******988864424550557889*************99999888888873 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.68   6.7e+02      37      82 ..       3      40 ..       1      68 [. 0.68
   2 ?    9.3   0.0   0.00072      0.72     132     170 ..      76     114 ..      20     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.68
                                   EES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHH CS
                           CheR 37 sagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAka 82
                                    +gc+sG  +  l   l+++         +  + Di++k+++ +++
  gi|121637430|ref|YP_977653.1|  3 DVGCGSGRMALPLTGYLNSE----G----RYAGFDISQKAIAWCQE 40
                                   57888887666665555551....1....23466777777766655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00072
                                    GGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEE CS
                           CheR 132 svlgklDvifcrnvliYfdeetqekvlerfaeklkpggl 170
                                     +  ++Dv+f+  v+  + +++ e+ l+++++ lkpgg+
  gi|121637430|ref|YP_977653.1|  76 YPDASFDVVFLTSVFTHMFPPDVEHYLDEISRVLKPGGR 114
                                    45679********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1559.64
//
Query:       gi|121637431|ref|YP_977654.1|  [L=63]
Description: hypothetical protein BCG_1562c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-25   87.7   0.0    4.8e-25   87.6   0.0    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   2.7e-29   4.8e-25       4      64 .]       1      61 [.       1      61 [. 0.98

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 2.7e-29
                                   EEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                        Dodecin  4 vielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                   +ie+vG+Sp+++++Aiq ++a+A++t+r ++w+eV+ +r+h+ dg +a++qvt+kvgFrle
  gi|121637431|ref|YP_977654.1|  1 MIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLE 61
                                   59*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 495.31
//
Query:       gi|121637432|ref|YP_977655.1|  [L=132]
Description: hypothetical protein BCG_1563 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 920.84
//
Query:       gi|121637433|ref|YP_977656.1|  [L=342]
Description: glycosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-39  133.6   0.0    8.1e-39  133.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    5.1e-05   22.9   0.0    8.3e-05   22.2   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00049   20.1   0.0    0.00078   19.4   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0   1.4e-42   8.1e-39       1     168 [.       4     198 ..       4     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1.4e-42
                                    EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                    s+v+++y+ e+++le++++++a   +  pd+eii+vDDgS++ + +++ +l ++dp+vrvi++++n+G+++a+++gl++a
  gi|121637433|ref|YP_977656.1|   4 SIVTTMYMSEPYVLEFYRRARAAadKITPDVEIIFVDDGSPEAALQQAVSLLDSDPCVRVIQLSRNFGHHKAMMTGLAHA 83 
                                    8******************************************************************************* PP

                                    -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.........................E CS
                Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.........................g 133
                                    tgd+++++D+D+e dp  le+++e+l  +gadvv+g++ r++g++ ++  +k +                         +
  gi|121637433|ref|YP_977656.1|  84 TGDLVFLIDSDLEEDPALLEPFYEKLISTGADVVFGCHARRPGGWLRNFGPKIHyrasallcdpplhentltvrlmtadY 163
                                    ******************************************************************************** PP

                                    EEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
                Glycos_transf_2 134 enerlyfkerkrslkgnlsfeigsaallrrealee 168
                                     ++ ++++er+ s+ g +++  +++  ++++ +++
  gi|121637433|ref|YP_977656.1| 164 VRSLVQHQERELSIAGLWQITGFYQVPMSVNKAWK 198
                                    **************************999998876 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.4e-08   8.3e-05      13      91 ..      14      94 ..       4     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                Glyco_tranf_2_2 13 hyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaD 91
                                   +y+ e     +  a    +++e+i+vddgS+e  l++  s+ d    v + +   + ++  +a   G  +a +dlv+ +D+D
  gi|121637433|ref|YP_977656.1| 14 PYVLEFYrraRAAADKITPDVEIIFVDDGSPEAALQQAVSLLDSDPCVRVIQL-SRNFGHHKAMMTGLAHATGDLVFLIDSD 94
                                   67777662113344444789*************************99976666.789***********************99 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-07   0.00078       5     106 ..       4     103 ..       2     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
                Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqe..y.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                    +++ + +  e++++e  + + a +    p+ve+++v+d+s +++l+ a  l +  p   vrv++ +rn g      a+  
  gi|121637433|ref|YP_977656.1|   4 SIVTTMYMSEPYVLEFYRRARAAAdkItPDVEIIFVDDGSPEAALQQAVSLLDSDPC--VRVIQLSRNFG---HHKAMMT 78 
                                    555556666666666655555332224699*************99977776555555..79******866...567899* PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlk 106
                                    +l ++++dlv l+D+D   +P +l+
  gi|121637433|ref|YP_977656.1|  79 GLAHATGDLVFLIDSDLEEDPALLE 103
                                    ****************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2433.49
//
Query:       gi|121637434|ref|YP_977657.1|  [L=273]
Description: hypothetical protein BCG_1565 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-33  114.3   0.0    1.1e-32  114.0   0.0    1.1  1  PhyH            Phytanoyl-CoA dioxygenase (PhyH)
    0.00042   20.7   0.0     0.0007   20.0   0.0    1.3  1  2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
  ------ inclusion threshold ------
      0.038   14.9   0.0      0.066   14.1   0.0    1.3  1  2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> PhyH  Phytanoyl-CoA dioxygenase (PhyH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   1.8e-36   1.1e-32       3     210 ..      21     209 ..      19     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 1.8e-36
                                    HHSEEEETTSS-HHHHHHHHHHHHHHHHHCHTTCCSEEEEECEEESTTCCCEECCCHHCHHHHTTHHHHHHHHHHHHTSC CS
                           PhyH   3 edGylviegflsaeevealraeiealldralesgdkidfffeekaaadedglleksinkvghflhprkvadlvrailgqd 82 
                                      Gy+v+e++l++++++a r++++++ ++++ ++ +++ ++++++ +  +  ++ +++++  +  p +v ++v+++l+++
  gi|121637434|ref|YP_977657.1|  21 CVGYAVVEDVLDEASLAATRDRMYRV-QERILTEIGKERLARAGELGVLRLMMKYDPHFFTFLEIP-EVLSIVDRVLSET 98 
                                    57***********************8.**************************************9.************* PP

                                    EEEEEEEEEEEEEEEE-TTTCB-E..EEEE-SGGGSTEESGCCEEEEEEESS-B-TTBT-EEEETTGGGS-CCGTCCHHC CS
                           PhyH  83 vyvaavlqsmyqdifkqpkiGgev..qpwHqDstflptdpeesvvgvwialedateenGclrfiPGSHkweegplrrrlp 160
                                    ++   +lq  +    ++p + + v  ++ HqD +++    + ++v++++a++++t++ G++ ++PGSH++ e+      p
  gi|121637434|ref|YP_977657.1|  99 AIL--HLQNGFILPSFPPFSTPDVfqNAFHQDFPRVLSG-YIASVNIMFAIDPFTRDTGATLVVPGSHQRIEK------P 169
                                    *97..68888866889999999999999*********88.8*****************************777......5 PP

                                    SGCCTTSCCCTTTGHGSCEEEE.BTTTEEEEEETTSEEEE-TB.SSSXEE CS
                           PhyH 161 eddteaeddeakkedeeeavpvevkaGdavlfhgrllHgsgaNrsdksRr 210
                                    ++ + a+          +avpv+++aG++++f+++l+H++g+N+s k R 
  gi|121637434|ref|YP_977657.1| 170 DHTYLAR----------NAVPVQCAAGSLFVFDSTLWHAAGRNTSGKDRL 209
                                    7777777..........******************************995 PP

>> 2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-07    0.0007      58      98 ..     171     211 ..     146     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                 2OG-FeII_Oxy_5  58 akeenqslvdvkpkeGdlvlFPswlrHevlpnegeeeRisi 98 
                                    +    +++v v+  +G l++F s l+H++ +n++ ++R+ i
  gi|121637434|ref|YP_977657.1| 171 HTYLARNAVPVQCAAGSLFVFDSTLWHAAGRNTSGKDRLAI 211
                                    3345689999****************************988 PP

>> 2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.066      15      93 ..     126     213 ..     119     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                    E-SS----TT.-.EEEEEEEEE......ET-B--EEE.......................---TT-EEEEE-..B-TEEE CS
                 2OG-FeII_Oxy_3  15 HvDnfekeegsgqrrltvllyLne..keseeGGelelyekdk.............eavkikpkkgrlvlFesdellpHev 79 
                                    H+D+ +     +  +++v +++     + ++G  l++ + ++             +av ++  +g+l +F+s+   +H++
  gi|121637434|ref|YP_977657.1| 126 HQDFPRVL---SGYIASVNIMFAIdpFTRDTGATLVV-PGSHqriekpdhtylarNAVPVQCAAGSLFVFDSTL--WHAA 199
                                    88876433...44666666666434333357888888.444458999999999888888888**********65..5*** PP

                                    --B.-SS-EEEEEE CS
                 2OG-FeII_Oxy_3  80 lpvtkggeRlsltg 93 
                                     + t+g++Rl++++
  gi|121637434|ref|YP_977657.1| 200 GRNTSGKDRLAINH 213
                                    **99988****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2220.41
//
Query:       gi|121637435|ref|YP_977658.1|  [L=299]
Description: hypothetical protein BCG_1566 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-05   23.4   0.2      0.004   16.5   0.1    2.2  2  BNR_2           BNR repeat-like domain
    0.00031   20.2   0.2    0.00069   19.0   0.2    1.6  1  Glyco_hydro_43  Glycosyl hydrolases family 43


Domain annotation for each model (and alignments):
>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0015        13     235     273 ..     115     157 ..      90     161 .. 0.75
   2 !   16.5   0.1   4.5e-07     0.004     137     201 ..     178     248 ..     168     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0015
                                    EEEEEEESTT-..GGG--..--EEEEEEE...EEEEEEEEEEE CS
                          BNR_2 235 kpLtvalskdn..gkswk..evltLekgpkseysYPsliqaed 273
                                    +   va+s+ +   + w+  +v+ L++ + + +sYP++iq++ 
  gi|121637435|ref|YP_977658.1| 115 NTIGVAISEAGapFERWStfPVVALDERDPFSLSYPWVIQDGG 157
                                    556677777753346677667999***999**********975 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.5e-07
                                    EEEEEEESSTTSS-EE----S......SSEEEEEEEE.EEETT.EEEEEEEE...EEEEEEESSTTSS-EEE CS
                          BNR_2 137 rallelsddggktWkkgrvve......qisgeiqpsilvekdg.slvalaRsrkaaileseSedgGetWskv 201
                                    +++ + ++ +g++W+k++ v+      ++s ++ p +++++   ++ + aR  k +i+ ++Sed G tW+++
  gi|121637435|ref|YP_977658.1| 178 HVIRYAQSRDGVHWEKQDRVHidtsgsDNSAACRPCVVRDAGVyRMWFCARGAKYRIYCATSED-GLTWRQL 248
                                    5666778899*********99******999*******877666888888998888999999999.****985 PP

>> Glyco_hydro_43  Glycosyl hydrolases family 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   7.7e-08   0.00069      12     139 ..     149     284 ..     132     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.7e-08
                                    SEEEEEETTCEEEEEEEBTEE........SEEEEEEESSSSSCEEEEECEESTTTCSTTTEECTEEEEEEEETTEEEEEE CS
                 Glyco_hydro_43  12 DpsilrvgedyYlvtstfewf........pglrifhSkdLvnWkqvgrvlerrsqlsmkgknasWAPeiskhdgkyylyy 83 
                                     p+++++g++y++ ++++             +r  +S+d v+W++ +rv  ++s+ +   +     P++ +  g y + +
  gi|121637435|ref|YP_977658.1| 149 YPWVIQDGGTYRMWYGSNLGWgegtdeipHVIRYAQSRDGVHWEKQDRVHIDTSGSDNSAAC---RPCVVRDAGVYRMWF 225
                                    36899*****99888776555699999988899***********************955554...5************** PP

                                    EEEETTCCCSEEEEEEESSTTS--EECEESSCS.......TSSECE.EEEEEETTSEEEEEEEE CS
                 Glyco_hydro_43  84 tatkkgeakqgifvvtadspeGpwsdpiklkts.......gssgiD.pslfedddGkkYlvwgq 139
                                    +   +  ak +i+ +t+++   +w +++k           +s +i  p++f +  G++++++++
  gi|121637435|ref|YP_977658.1| 226 C---ARGAKYRIYCATSEDGL-TWRQLGKDEGIdvspdswDSDMIEyPCVFDHR-GQRFMLYSG 284
                                    *...6888999***9999876.68888776444556767777777645555555.888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2340.04
//
Query:       gi|121637436|ref|YP_977659.1|  [L=382]
Description: TDP-4-oxo-6-deoxy-D-glucose transaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-86  289.3   0.0    5.5e-86  289.1   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.9e-06   26.7   0.0      6e-06   25.7   0.0    1.5  2  Aminotran_1_2    Aminotransferase class I and II
     0.0058   15.6   0.0     0.0085   15.1   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.022   13.3   0.0      0.035   12.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.066   12.5   0.0       0.11   11.8   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.1   0.0   1.5e-89   5.5e-86       5     360 ..      16     374 ..      12     375 .. 0.93

  Alignments for each domain:
  == domain 1  score: 289.1 bits;  conditional E-value: 1.5e-89
                                    HHHHHHHHHHTSS-SSS.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHT CS
                DegT_DnrJ_EryC1   5 eeleaveevlksgwlts.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlel 83 
                                    +el+++ e+   g l   gp++++  + + + +g + a+ + s+taAl+++   l++++gdeVI ps+tFv+tana +  
  gi|121637436|ref|YP_977659.1|  16 RELAYIAEAHSCGHLAGdGPFTRRSHAWLEQQTGCRKALLTPSCTAALEMMALLLDIEEGDEVILPSYTFVSTANAFVLR 95 
                                    56677777777787777799999999999**********************99*************************** PP

                                    T-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
                DegT_DnrJ_EryC1  84 gakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                    g +pvfvD+ pdt+nid  +i  ait+rtkaI+pVh++G +++mda+ +ia++h+l v+eDaA++  a+y+g+ +G++gd
  gi|121637436|ref|YP_977659.1|  96 GGVPVFVDIRPDTLNIDETRIVDAITPRTKAIVPVHYAGVACEMDAIMKIATHHNLAVVEDAAQGAMASYRGRALGSIGD 175
                                    ******************************************************************************** PP

                                    EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCS......S---B-B-BHHHHHHHHHHHCTH CS
                DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgev......elGynyrlteiqAAiglaqLerl 237
                                    ++++SF++tKn+  GeGGa++ n+e+   +a++lr +G +r++    ++ev      + G++y  +e+ AA + aq+e+ 
  gi|121637436|ref|YP_977659.1| 176 LGALSFHETKNVISGEGGALLVNSEDFLLRAEILREKGTNRSR--FLRNEVdkytwqDKGSSYLPSELVAAFLWAQFEEA 253
                                    **************************************99743..44444455788889********************* PP

                                    HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSS..SEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGS CS
                DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketk..khawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrq 315
                                    ++++  R +++++y+e +++le++  l+ p   +  +h+ h y vl+  +  ++r+e++++l+++gig+  hy +plh  
  gi|121637436|ref|YP_977659.1| 254 ERITRIRLDLWNRYHESFESLEQRGLLRRPIIPQgcSHNAHMYYVLLAPS--ADREEVLARLTSKGIGAVFHY-VPLHDS 330
                                    ***********************999999999987669999999999987..57*******************.8***** PP

                                    CCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                DegT_DnrJ_EryC1 316 pvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                    p+ +++  +++g+l++++++a+r + Lp++++l+e d+ rVveal
  gi|121637436|ref|YP_977659.1| 331 PAGRRYG-RTNGNLTVTNDVASRLIRLPMWVGLQEVDQSRVVEAL 374
                                    *998885.66889******************************98 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-09     6e-06      70     193 ..      52     162 ..      19     185 .. 0.82
   2 ?   -3.5   0.0       1.2   4.3e+03     298     315 ..     235     253 ..     209     307 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                    GEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETE CS
                  Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkkt 149
                                      ++++ ++a++e+ + ll+++ gde+++p+ t+ s  n++ l+gg  v + ++ +++ ++d   + +a++       +t
  gi|121637436|ref|YP_977659.1|  52 KALLTPSCTAALEMMALLLDIEEGDEVILPSYTFVSTANAFVLRGGVPVFVDIR-PDTLNIDETRIVDAITP------RT 124
                                    34455555556666666777********************************88.9***************9......99 PP

                                    EEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                  Aminotran_1_2 150 kvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                    k i+   p +  G+++  + + k+   a+ +nl ++ D a +++
  gi|121637436|ref|YP_977659.1| 125 KAIV---PVHYAGVACEMDAIMKI---ATHHNLAVVEDAAQGAM 162
                                    9998...89999999999999999...99999999988875555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                    EEECCS.CSSEEEEEETHH CS
                  Aminotran_1_2 298 kvlasq.sgmflltdlsae 315
                                    ++l+s+  + fl+  ++++
  gi|121637436|ref|YP_977659.1| 235 SYLPSElVAAFLWAQFEEA 253
                                    4444444344444433333 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-06    0.0085      63     181 ..      52     162 ..      37     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                                    GEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEE CS
                    Aminotran_5  63 eiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektkl 142
                                    + + t ++t a++++al l   +++gde+++ +    ++ +   +   r g+ v v    ++ ++d  ++ ++++++tk+
  gi|121637436|ref|YP_977659.1|  52 KALLTPSCTAALEMMALLL--DIEEGDEVILPSYTFVSTAN---AFVLRGGVPVFVDIRPDTLNIDETRIVDAITPRTKA 126
                                    5677889999******999..6*************999993...33347899997766667889**************** PP

                                    EEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                    Aminotran_5 143 vaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                    +   h     G+  ++++i k+a  ++  v+ Daaq+++
  gi|121637436|ref|YP_977659.1| 127 IVPVHY---AGVACEMDAIMKIATHHNLAVVEDAAQGAM 162
                                    999996...7999***********************987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.7e-06     0.035      66     175 ..      49     158 ..      39     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-06
                                    T-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHH..THHH.TTCEEEEESTTSHHHHHHHCCTTEEEE CS
                Cys_Met_Meta_PP  66 ggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkk..vlkk.lgievkfvdtsdleelekaikentklv 141
                                    g  +al+++s +aA++++ l l +++Gde+++ ++ + +t + +     ++  + i+ +  +  d+ ++  ai+++tk++
  gi|121637436|ref|YP_977659.1|  49 GCRKALLTPSCTAALEMMALLLdIEEGDEVILPSYTFVSTANAFVLrgGVPVfVDIRPDTLNI-DETRIVDAITPRTKAI 127
                                    56899*********976655554899**************99774311222224445555554.56678899******99 PP

                                    EEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
                Cys_Met_Meta_PP 142 ylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                                + + +i+k+a ++++ vv D++
  gi|121637436|ref|YP_977659.1| 128 VP---VHYAGVACEMDAIMKIATHHNLAVVEDAA 158
                                    64...44444455677888888888888877765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05      0.11      29     221 ..      32     205 ..      13     300 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                    T--HHHHHHHHHHHHHTT-SEEEEES-HHHH.HHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT. CS
                Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaA.nsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea. 106
                                    g+ + ++r  + +++ +g  +al +p+ taA + ++l + ++ g+evi+  p+ ++  ++ a +  +gv ++ ++++ + 
  gi|121637436|ref|YP_977659.1|  32 GDGPFTRRSHAWLEQQTGCRKALLTPSCTAAlEMMALLLDIEEGDEVIL--PSYTFVSTANAFVLRGGV-PVFVDIRPDt 108
                                    566666777777888999999********99666667777799999987..678888888888777777.8888877743 PP

                                    TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH CS
                Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemf 186
                                     ++d  ++ +ai+++ +  + +++ +  v+++           ++++ +ia  +++ ++ D+A  a a+       + + 
  gi|121637436|ref|YP_977659.1| 109 LNIDETRIVDAITPRTK--AIVPVHYAGVACE-----------MDAIMKIATHHNLAVVEDAAQGAMAS--Y--RGRALG 171
                                    56666777778888655..5555555555555...........6889999*************988777..2..223344 PP

                                    TTSS..EEEEESSSTT--SS-EEEEE-HH....HHHH CS
                Beta_elim_lyase 187 syvD..svtmslkKdllanvGgvlafrddeledylae 221
                                    s  D   +++  +K+++   Gg l+++ +   d+l +
  gi|121637436|ref|YP_977659.1| 172 SIGDlgALSFHETKNVISGEGGALLVNSE---DFLLR 205
                                    44441156666678888888877777777...44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2899.63
//
Query:       gi|121637437|ref|YP_977660.1|  [L=221]
Description: hypothetical protein BCG_1568c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-17   62.9  13.7    1.8e-06   27.4   0.4    3.8  5  Hexapep    Bacterial transferase hexapeptide (six repeats)
    2.7e-07   30.2   5.9    4.1e-06   26.4   0.5    3.6  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase
     0.0049   17.5   0.0       0.12   13.0   0.0    2.3  2  PglD_N     PglD N-terminal domain


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   7.2e-09   4.3e-05       3      36 .]     108     141 ..     106     141 .. 0.95
   2 !   22.9   0.7   8.4e-09     5e-05       2      31 ..     125     154 ..     124     159 .. 0.91
   3 !   16.7   0.1   7.2e-07    0.0043       1      34 [.     142     175 ..     142     176 .. 0.95
   4 !   27.4   0.4     3e-10   1.8e-06       1      34 [.     160     193 ..     160     195 .. 0.94
   5 ?   -2.2   0.0      0.69   4.1e+03      19      23 ..     201     205 ..     199     207 .. 0.48

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.2e-09
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    +IG+nv++    +i + V IG+nv++++g  ig+
  gi|121637437|ref|YP_977660.1| 108 RIGENVFLLEDNTIQPFVSIGNNVTLWSGNHIGH 141
                                    6****************************99986 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 8.4e-09
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgag 31 
                                    + IG+nv+++++ +ig++ +I+d++ ++++
  gi|121637437|ref|YP_977660.1| 125 VSIGNNVTLWSGNHIGHHSTIHDHCFLASH 154
                                    68************************9986 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 7.2e-07
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    +++I++++++ +  v+ g+V+I + + Ig ++++
  gi|121637437|ref|YP_977660.1| 142 HSTIHDHCFLASHIVVSGGVVIEEQSFIGVNATL 175
                                    689**************************99997 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 3e-10
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    ++vI++ ++Ig +a+++++++IG+++++gag+ +
  gi|121637437|ref|YP_977660.1| 160 GVVIEEQSFIGVNATLRDHITIGSRCVVGAGALL 193
                                    689****************************987 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 0.69
                                    TEEE- CS
                        Hexapep  19 nVkIG 23 
                                    +V IG
  gi|121637437|ref|YP_977660.1| 201 GVYIG 205
                                    34443 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.4    0.0069        41       4      26 ..     109     133 ..     108     140 .. 0.68
   2 ?   -1.9   0.0      0.49   2.9e+03       3      11 ..     138     146 ..     136     151 .. 0.65
   3 !   26.4   0.5   6.8e-10   4.1e-06       2      30 ..     161     191 ..     160     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0069
                                    E-TT-EE-TT-EE.S.EEE-TT-EE CS
                      Hexapep_2   4 IGdnCliGanagi.G.vslGdncvv 26 
                                    IG+n+++  + +i + vs+G+n+++
  gi|121637437|ref|YP_977660.1| 109 IGENVFLLEDNTIqPfVSIGNNVTL 133
                                    7777777666555556888888877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.49
                                    EE-TT-EE- CS
                      Hexapep_2   3 iIGdnCliG 11 
                                    +IG  + i+
  gi|121637437|ref|YP_977660.1| 138 HIGHHSTIH 146
                                    677777776 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 6.8e-10
                                    EEE-TT-EE-TT-EE.S.EEE-TT-EE-TT- CS
                      Hexapep_2   2 viIGdnCliGanagi.G.vslGdncvvgaGv 30 
                                    v I++ ++iG+na+    +++G +cvvgaG 
  gi|121637437|ref|YP_977660.1| 161 VVIEEQSFIGVNATLrDhITIGSRCVVGAGA 191
                                    89************9855************6 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     2e-05      0.12       2      67 ..       5      72 ..       4      86 .. 0.77
   2 ?    2.3   0.0     0.045   2.7e+02      53      70 ..     115     132 ..      85     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                         PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkktevegypvlgk..aiellkslseeeyevviAIGn 67
                                   +vI+G G  ++       +  eye+++f+ d++  +v ++++l+    +e ++++ +e+  +++A+  
  gi|121637437|ref|YP_977660.1|  5 LVIFGSGDIAQLAHYYFTRDSEYEVVAFTVDRDYASVSEFCGLPLvaFDEVAQRFPPESHAMFVALAY 72
                                   89*************************99998767677666665411467778888888889999874 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.045
                         PglD_N  53 slseeeyevviAIGnnkv 70 
                                     l+ ++++ +++IGnn +
  gi|121637437|ref|YP_977660.1| 115 LLEDNTIQPFVSIGNNVT 132
                                    4445567789*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1585.23
//
Query:       gi|121637438|ref|YP_977661.1|  [L=254]
Description: hypothetical protein BCG_1569 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-64  216.1  29.6    4.3e-64  215.9  29.6    1.0  1  SfLAP     Sap, sulfolipid-1-addressing protein


Domain annotation for each model (and alignments):
>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9  29.6   2.4e-68   4.3e-64       1     213 [.       5     251 ..       5     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 2.4e-68
                          SfLAP   1 llvlAlvvalsPlrlgvavlllsrprpvlnllaFlvgwlvvlvalglivlfvlrslls.....gasaa.......pssai 68 
                                    +l+l+l++a++P rlg+av++lsr+rp+lnl+aF+vg++v++v+++l+vl+++r+++      ++saa       +  a+
  gi|121637438|ref|YP_977661.1|   5 VLLLGLGMAIDPARLGLAVVMLSRRRPMLNLFAFWVGGMVAGVGIALAVLVFMRDVALaaiqgVVSAAnefreavGILAG 84 
                                    799*******************************************************8888833333667777899*** PP

                          SfLAP  69 kalqivlGvlllllaaveavrr......................pkassrselprllsrleslleggalwvAlvlgllsa 126
                                    ++l+iv+Gv++lllaa+++ r+                       +++ +  ++rl  r++++l+g+++w A+v+g++s 
  gi|121637438|ref|YP_977661.1|  85 GRLHIVIGVIMLLLAARMVARAraqvgvpvgpvgvadggmsalaLAQRPPGLVARLEVRTQQMLQGDVVWPAFVVGVASS 164
                                    ********************************************9*********************************** PP

                          SfLAP 127 kplllylaalaaigasgasvgtqvvalvvFvvvalavveipllaylvapertqavlerlkdwlrsnrrlilavilgvvGl 206
                                     p+++ ++al++i+asga++gtq++a+vvF++++lav+eipl+ayl+ p++tq+v+ r++dw+rsnrr+i ++il+ vG+
  gi|121637438|ref|YP_977661.1| 165 APPFESVVALTVIMASGAEIGTQFGAFVVFTLLVLAVIEIPLVAYLAIPQQTQQVMLRFQDWVRSNRRQISLTILIGVGF 244
                                    ******************************************************************************** PP

                          SfLAP 207 lllakGl 213
                                    l+l++G+
  gi|121637438|ref|YP_977661.1| 245 LFLYQGV 251
                                    ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1903.01
//
Query:       gi|121637439|ref|YP_977662.1|  [L=319]
Description: hypothetical protein BCG_1570 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-23   84.0   0.0    1.5e-23   83.5   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-14   54.9   0.1      2e-14   54.0   0.1    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.9e-06   28.0   0.6    2.8e-06   27.4   0.6    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.8e-06   27.0   0.0    0.00012   21.7   0.0    2.0  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.042   14.4   0.1       0.36   11.4   0.0    2.4  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   4.2e-27   1.5e-23       1     142 [.      20     156 ..      20     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 4.2e-27
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    sv+ip+yN  +t++++l+s+l+q +  +fei+vvDD S+D++++i+      +p+ r++r+e + G+ ++ n+ l+ a+g
  gi|121637439|ref|YP_977662.1|  20 SVCIPMYNNGATIERCLRSILEQ-EGVEFEIVVVDDDSSDDCAAIAATML--RPGDRLLRNEPRLGLNRNHNKCLEVARG 96 
                                    8**********************.*************************7..6*********999*************** PP

                                    SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCC CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfke 142
                                     +i f+  Dd   p+ l+ l +++e++ ++++++ r++ +++ ++ +r  rv  ++r+++ +
  gi|121637439|ref|YP_977662.1|  97 GLIQFVHGDDRLLPGALQTLSRRFEDPSVGMAFAPRRVESDDIKWQQRYGRV--HTRFRKLR 156
                                    **************************77777777777777777777666553..33333333 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.1   5.7e-18     2e-14       4     208 ..      19     226 ..      17     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 5.7e-18
                Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                    ++v +p +n+ ++++++l+s+l qe  ++e+vvv+d s+++ ++ a ++  +++d   r+++n+ +lg     r+ n  l
  gi|121637439|ref|YP_977662.1|  19 ISVCIPMYNNGATIERCLRSILEQEGVEFEIVVVDDDSSDDCAAIA-ATMLRPGD---RLLRNEPRLG---LNRNHNKCL 91 
                                    79*********************************99999977755.66788888...5776655455...46889**** PP

                Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs.tlvsalgalefaerhlrflaar.......... 152
                                    + +++ l+ +v++D+++ P++l+ l + f++p+vg++ +p++++ ++ ++++++g++++  r+lr + +           
  gi|121637439|ref|YP_977662.1|  92 EVARGGLIQFVHGDDRLLPGALQTLSRRFEDPSVGMAFAPRRVESDDiKWQQRYGRVHTRFRKLRDRNHGpslvlqmvlh 171
                                    ********************************************988577665555554444444444446666666654 PP

                Glyco_tranf_2_3 153 ralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa 208
                                     a+   +  ++ +++rr++  + +g++   +   D++ +lrl+ +   +++vp+ +
  gi|121637439|ref|YP_977662.1| 172 GAKENWIGEPTAVMFRRQLALDAGGFRTDIYQLVDVDFWLRLMLRS-AVCFVPHEL 226
                                    4444444467899999999999999999666668999999988765.466666655 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.6   7.8e-10   2.8e-06       4     129 ..     101     235 ..      98     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.8e-10
                Glyco_trans_2_3   4 llDaDtvlppdclreiaaelaspevaivqgpvlvm....nvanwleelaalf...faedhgkdilvrealgrvvpsv.Gs 75 
                                    ++  D++l p  l  + + +++p v+++  p  v+     ++  + ++++ f   ++++hg + + ++ l++    + G 
  gi|121637439|ref|YP_977662.1| 101 FVHGDDRLLPGALQTLSRRFEDPSVGMAFAPRRVEsddiKWQQRYGRVHTRFrklRDRNHGPSLVLQMVLHGAKENWiGE 180
                                    6789***************************9985567999***********5555999999999999999988866587 PP

                Glyco_trans_2_3  76 ga..flrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksplt 129
                                     +  ++rr+++ ++gg++  +     D d++lrl+ +  +++  +e  v++++  t
  gi|121637439|ref|YP_977662.1| 181 PTavMFRRQLALDAGGFR-TDIYQLVDVDFWLRLMLRSAVCFVPHELSVRRHTAAT 235
                                    642289************.4467779*********997666665555445544444 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.2e-08   0.00012       1      94 [.      20     108 ..      20     120 .. 0.86
   2 ?    3.4   0.0     0.012        44     167     219 ..     183     232 ..     145     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.2e-08
                Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska 80 
                                    sv ip++++  +  ie  ++ +  +   e+e++vvdd Ss++ +    ++     +  l++e+    +l + +N+  + a
  gi|121637439|ref|YP_977662.1|  20 SVCIPMYNNGAT--IERCLRSILEQEGVEFEIVVVDDDSSDDCAAIAATMLRPGDR-LLRNEP--RLGLNRNHNKCLEVA 94 
                                    799******999..99999999999999**************88777777665555.457774..689************ PP

                Glyco_tranf_2_2  81 esdlvlFlDaDcfi 94 
                                     + l+ F+ +D+  
  gi|121637439|ref|YP_977662.1|  95 RGGLIQFVHGDDRL 108
                                    ***********965 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                Glyco_tranf_2_2 167 silinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykara 219
                                     ++ +r+  l  GG+   +      D d+ lRl ++       p el+ + ++
  gi|121637439|ref|YP_977662.1| 183 AVMFRRQLALDAGGFRTDI--YQLVDVDFWLRLMLRSAVC-FVPHELSVRRHT 232
                                    57788999999****9999..8999********9997766.789999987775 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.9e-05      0.36       2      39 ..      27      66 ..      26     100 .. 0.82
   2 ?   -0.6   0.0      0.54   1.9e+03      45      77 ..     228     259 ..     214     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-05
                Glyco_tranf_2_4  2 neadiLpeflahh.lalgfd.rilvydndstDgtrailke 39
                                   n  ++++++l+ + ++ g++ +i+v+d+ds+D+ +ai + 
  gi|121637439|ref|YP_977662.1| 27 NNGATIERCLRSIlEQEGVEfEIVVVDDDSSDDCAAIAAT 66
                                   78899******87355678768************999876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
                Glyco_tranf_2_4  45 llhvdksyederrqvellkallaryaeadwvlv 77 
                                    + +++ + ++  r ++ ++++l+r++  +w++v
  gi|121637439|ref|YP_977662.1| 228 VRRHTAA-TETTRVMATRRNVLDRQRILTWLIV 259
                                    4444444.4467778999999999998999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2286.79
//
Query:       gi|121637440|ref|YP_977663.1|  [L=89]
Description: hypothetical protein BCG_1571 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-05   24.6   0.0    1.5e-05   24.5   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.17   11.9   0.1    1.1  1  RadC             RadC-like JAB domain


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.7e-09   1.5e-05     311     358 ..      34      79 ..      22      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.7e-09
                                    HGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHH CS
                DegT_DnrJ_EryC1 311 plhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVve 358
                                     lh++ + ae   ++s+dl+++e++++r++sLp++++++ +dv rVv+
  gi|121637440|ref|YP_977663.1|  34 TLHSLATNAEL--VESADLTVTEDICSRIVSLPVHDHMAIADVARVVA 79 
                                    45555555555..56679****************************97 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.9e-05      0.17      58     110 ..      23      73 ..      21      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                    HHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHHHHHHHHT-EEEEEEEEES CS
                           RadC  58 ealklnAaavilaHnhPsgdlepSeeDieltkrlkealkllgiellDhiIigd 110
                                     al + A a  ++H    +     ++D+++t+ ++   ++++++++Dh+ i+d
  gi|121637440|ref|YP_977663.1|  23 PALTCTAVATRTLHSLATNAELVESADLTVTEDIC--SRIVSLPVHDHMAIAD 73 
                                    6999999999999*****9999**********995..699**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 667.96
//
Query:       gi|121637441|ref|YP_977664.1|  [L=346]
Description: sugar transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-23   83.5   0.1    3.6e-23   82.2   0.1    1.7  1  Glycos_transf_2  Glycosyl transferase family 2
    5.9e-07   29.6   0.1    1.1e-06   28.7   0.1    1.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.4e-06   25.5   0.0    1.3e-05   24.8   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.1     6e-27   3.6e-23       1     128 [.       2     131 ..       2     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 6e-27
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraat 79 
                                    s+v ++yN e++++e+l+  +aq +   +e+i++DD+StD t+ i+ e+a+ +++ +r i r  n G ++++   l+aa+
  gi|121637441|ref|YP_977664.1|   2 SIVSISYNQEEYIREALDGFAAQRTEFPVEVIIADDASTDATPRIIGEYAArYPQLFRPILRQTNIGVHANFKDVLSAAR 81 
                                    8999***********************************************8888899********************** PP

                                    SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCH CS
                Glycos_transf_2  80 gdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeier 128
                                    g+y++++  Dd++++  +l+k v++l+++++  v+ +++r  +e++ +  
  gi|121637441|ref|YP_977664.1|  82 GEYLALCEGDDYWTDPlKLSKQVKYLDRHPETTVCFHPVRVIYEDGAKDS 131
                                    **************999********************9999999877665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.9e-10   1.1e-06      10     126 ..       7     122 ..       2     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.9e-10
                Glyco_tranf_2_3  10 tfneedvlgevlesllaqe.yprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravks 88 
                                    ++n e++++e l+ ++aq  + +vev++ +d s+++t + + e aa++p+   r + ++ n g  +   + +++l+a+++
  gi|121637441|ref|YP_977664.1|   7 SYNQEEYIREALDGFAAQRtEFPVEVIIADDASTDATPRIIGEYAARYPQL-FRPILRQTNIG--VH-ANFKDVLSAARG 82 
                                    68999*************74699**************************85.67777777666..45.6699******** PP

                Glyco_tranf_2_3  89 dlvllvDdDtvv.ePdtlkrllqff.ltpkvgavgtpvfl 126
                                    ++++l ++D+ + +P  l +++ ++ ++p+ ++   pv++
  gi|121637441|ref|YP_977664.1|  83 EYLALCEGDDYWtDPLKLSKQVKYLdRHPETTVCFHPVRV 122
                                    ************88988********888877665555555 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.2e-09   1.3e-05       9     155 ..       9     151 ..       2     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-09
                Glyco_tranf_2_2   9 seerhyieerv....lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdl 84 
                                    ++ ++yi+e +     q++ +    +e+i+ dd S++ +   +    +   + + +   ++  +  a      s a +++
  gi|121637441|ref|YP_977664.1|   9 NQ-EEYIREALdgfaAQRTEF---PVEVIIADDASTDATPRIIGEYAARYPQLFRPILRQTNIGVHANFKDVLSAARGEY 84 
                                    33.449***997665556666...89***************************99************9999********* PP

                Glyco_tranf_2_2  85 vlFlDaDcfis.sDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaaks 155
                                    +  +++D++++ + k+ k++k      l + ++++v +  v  + ed  +  +   l ++ ++  d+l a++
  gi|121637441|ref|YP_977664.1|  85 LALCEGDDYWTdPLKLSKQVK-----YLDRHPETTVCFHPVRVIYEDGAKDSEFPPLSWRRDLSVDALLARN 151
                                    **********92346666666.....9***********9999**9999999999999999999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2699.04
//
Query:       gi|121637442|ref|YP_977665.1|  [L=583]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-72  242.8   0.0    6.1e-72  242.5   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.5   0.0   3.4e-76   6.1e-72       2     422 ..      13     471 ..      12     472 .. 0.84

  Alignments for each domain:
  == domain 1  score: 242.5 bits;  conditional E-value: 3.4e-76
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                    +e+a  +p++ al++       +g  +tlT+++l++r+ +lAa Lr++G   gdr +il+p+ +++vv+++a l+aG+v+
  gi|121637442|ref|YP_977665.1|  13 RERASFQPNDKALTFidyerswDGVEETLTWSQLYRRTLNLAAQLREHG-STGDRALILAPQILDYVVSFIASLQAGIVA 91 
                                    6788889999999888899999999*********************966.569*************************** PP

                                    EEEET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                    AMP-binding  75 vplnp...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                    vpl+    +   e+   +++d+ + +++  + s  ++++ e  + ++ + +  v++ d+l+    +  +++s+++     
  gi|121637442|ref|YP_977665.1|  92 VPLSIpqgGAHDERTVSVFADTAPAIVL--TASSVVDNVVEYVQPQPGQNAPAVIEVDRLDLD--ARPSSGSRSA----- 162
                                    ***998888889****************..766666667776666667777777777665544..2222222221..... PP

                                    CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC....SCCTT.T-EEEESS-TTSCHHHHHHHHHHHH CS
                    AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr....fklke.ddvvlsilplahifglilelllall 226
                                       +    d++y++YTSG+T +P GVm+s +nl an  ++  + +     k+ + +++v+s+lp++h++g++l+l+l++l
  gi|121637442|ref|YP_977665.1| 163 ---AHGHPDILYLQYTSGSTRTPAGVMVSNKNLFANFEQIM-TSYygvyGKVAPpGSTVVSWLPFYHDMGFVLGLILPIL 238
                                    ...234569***************************99996.3332444553336************************* PP

                                    TT-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHH CS
                    AMP-binding 227 sGatvvllpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffra 305
                                    +G   vl ++  +l+ p++++++++  +   ++++P ++  l++ ++++++++  dl++++ +l g e+++p +l++f +
  gi|121637442|ref|YP_977665.1| 239 AGIPAVLTSPIGFLQrPARWIQMLA-SNTLAFTAAPNFAFDLASRKTKDEDMEGLDLGGVHGILNGSERVQPVTLKRFID 317
                                    *************666*********.66666777787777777743333678889************************* PP

                                    HHTC......EEEEEEEEGGGSSECEE..................CHCTTTCTSTTS-BEE-......TTEEEEEE-TTT CS
                    AMP-binding 306 lfge......evlegYGlTEttgvvtv..................lpleedkkklgsvGkpl......pgvevkivDeet 355
                                    +f +      ++  +YG++E+t+ v++                  +   + +++ +  G+pl        + v+ivD++t
  gi|121637442|ref|YP_977665.1| 318 RFAPfnldpkAIRPSYGMAEATVYVATrkagqppkivqfdpqklpD--GQAERTESDGGTPLvsygivDTQLVRIVDPDT 395
                                    ***9*****99**************888999**********99541..333333334466655555547889******** PP

                                    SCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.........TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 356 gepvpdgeeGellvrgpgvmkgYlkkpeataeafds.........egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                    g + p g+ Ge++v+g +v+ gY++kpeat+++f +         + + wlrTGD g+l  +G+l+i+gR+kdl+++
  gi|121637442|ref|YP_977665.1| 396 GIERPAGTIGEIWVHGDNVAIGYWQKPEATERTFSAtivnpsegtPAGpWLRTGDSGFLS-EGELFIMGRIKDLLIV 471
                                    **********************************978999999874455********999.9***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4267.62
//
Query:       gi|121637443|ref|YP_977666.1|  [L=1107]
Description: transmembrane transport protein mmpL12 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.3e-194  644.8  44.9   5.6e-100  334.5  16.7    4.3  5  MMPL            MMPL family
    0.00019   21.3   3.5    0.00019   21.3   3.5    2.6  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
  ------ inclusion threshold ------
      0.014   13.4   4.4      0.056   11.4   0.0    3.2  4  Prominin        Prominin
       0.03   14.3   4.7        1.6    8.8   1.9    2.7  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        1.8    6.5  12.5         20    3.1   0.0    2.2  2  Patched         Patched family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.8     0.089   3.2e+02     279     305 ..      25      52 ..      13      56 .. 0.84
   2 !  334.5  16.7  1.6e-103  5.6e-100       3     331 ..      57     382 ..      55     384 .. 0.99
   3 ?   -2.0   0.0      0.37   1.3e+03       4      39 ..     413     447 ..     411     468 .. 0.82
   4 ?   -0.3   0.1      0.11   3.9e+02       7      86 ..     521     631 ..     515     663 .. 0.50
   5 !  323.5   7.5  3.6e-100   1.3e-96      25     331 ..     676    1018 ..     651    1020 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.089
                           MMPL 279 aialGvlvdvlivlTll.PAllvllGra 305
                                     i +G  ++v+++lTll P l + + ++
  gi|121637443|ref|YP_977666.1|  25 LIVIGCWIAVAAALTLLlPTLQAQAAKR 52 
                                    56789999*********9*998877766 PP

  == domain 2  score: 334.5 bits;  conditional E-value: 1.6e-103
                           MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafvS 82 
                                    +p++a+s++  ++++aaf+e+ +++++ +v+l ++++ lg+ a+ea++++l+++l++dt++  +v+dfl+ p++++++ S
  gi|121637443|ref|YP_977666.1|  57 LPPGAPSMVLQKEMSAAFQEKIETSALLLVLL-TNENGLGP-ADEAVYRKLIENLRADTQDKISVQDFLAVPEMKELLAS 134
                                    699*****************999999999999.********.************************************** PP

                           MMPL  83 kDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLli 162
                                    kD+ka+ +++t++gd++s+e+++++++++a+v+++++ ++l+v+++Gp at+adl++++++d+++ie+ t+v +l+iL++
  gi|121637443|ref|YP_977666.1| 135 KDNKAWNLPITFAGDAASPETQAAFKRVAAIVKQTVAGTSLTVHLSGPIATVADLTELGEKDVRIIEIGTAVSVLIILIL 214
                                    ******************************************************************************** PP

                           MMPL 163 vyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavir 242
                                    vyr+lv++l+pl+t++ s+++a+g+++ la + gl+++++++ ++++++i++GtDYa++L+sRy++++++ge+++ av +
  gi|121637443|ref|YP_977666.1| 215 VYRNLVTMLVPLATIGASVVTAQGTLSGLAEF-GLAVNMQAIVFMSAVMIGAGTDYAVFLISRYHDYVRHGEKSDMAVKK 293
                                    *************************9999998.9********************************************** PP

                           MMPL 243 avastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrrl 322
                                    a++s+gkv+ta+++tva+++l++v+++l+v+++vG+aia+++ v++l ++TllPA+l+l+Gr++++kprr++++r+Wrr+
  gi|121637443|ref|YP_977666.1| 294 ALMSIGKVITASAATVAVTFLAMVFTKLEVFSAVGPAIAVAITVSLLGAVTLLPAILTLTGRRGWIKPRRDLTSRMWRRS 373
                                    ******************************************************************************** PP

                           MMPL 323 grlvvrrPl 331
                                    g+++vrrP+
  gi|121637443|ref|YP_977666.1| 374 GVRIVRRPT 382
                                    ********8 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.37
                           MMPL   4 padaesvkamdrleaafpeeadsdkiivvvlaegde 39 
                                    p+  esvk  + ++++fp    ++++++ +++++d 
  gi|121637443|ref|YP_977666.1| 413 PQHVESVKGYEAMNRHFPM-NAMTPMVLFIKSPRDL 447
                                    678899*************.8889999999988875 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.11
                           MMPL   7 aesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdel...vdelkkdtkhv.gevsdf........... 70 
                                     ++++a+ ++++++++ +a+s+ i+ +++a+ d + g+ ++ +++++    v ++++ ++++ g v d+           
  gi|121637443|ref|YP_977666.1| 521 HQLADALAQIRNEINGaVASSSGIVNTLQAMMDLMGGD-KTIRQLENAsqyVGRMRALGDNLsGTVTDAeqiatwaspmv 599
                                    56778888999999999999999999988887777766.33333332200022222222221123333344444344444 PP

                           MMPL  71 ................lsdpdvaaafvSkDgk 86 
                                                     s+ ++aa ++++D+ 
  gi|121637443|ref|YP_977666.1| 600 nalnsspvcnsdpacrTSRAQLAAIVQAQDDG 631
                                    44333333333333333333355555555544 PP

  == domain 5  score: 323.5 bits;  conditional E-value: 3.6e-100
                           MMPL   25 dsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf......................lsdpd...va 77  
                                       +k++++ ++ ++ a+gsaa +a+v+elvd++kk++++++e++df                      +s+++   +a
  gi|121637443|ref|YP_977666.1|  676 LPTKLAQMQQGANALADGSAALAAGVQELVDQVKKMGSGLNEAADFllgikrdadkpsmagfnippqiFSRDEfkkGA 753 
                                     4468899999************************************999999999999999998888877777788** PP

                           MMPL   78 aafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdasdrdlklievvt 152 
                                     + f+S+Dg+aar+ v+ +++p++tea+++v++i +++++ar   +le++++ ++G++++l+d+rd++++d+k+i+++t
  gi|121637443|ref|YP_977666.1|  754 QIFLSADGHAARYFVQSALNPATTEAMDQVNDILRVADSARpntELEDATIGLAGVPTALRDIRDYYNSDMKFIVIAT 831 
                                     *****************************************9999********************************* PP

                           MMPL  153 lvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyree 229 
                                     +v++++iL+i++r+lva+++++++v++s+l alg+ +l+++l+lg+e++++ +gl+++ll+a+G+DY++lL+sR+r+e
  gi|121637443|ref|YP_977666.1|  832 IVIVFLILVILLRALVAPIYLIGSVLISYLSALGIgTLVFQLILGQEMHWSLPGLSFILLVAIGADYNMLLISRIRDE 909 
                                     ****************************************************************************** PP

                           MMPL  230 laagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraa 306 
                                     + +g++   +vir+v+stg+v+t aGl++a++m+gLv a+++++aq G++i++G+++d+++v+T++ PAl++++Gra+
  gi|121637443|ref|YP_977666.1|  910 SPHGIRI--GVIRTVGSTGGVITSAGLIFAASMFGLVGASINTMAQAGFTIGIGIVLDTFLVRTVTvPALTTMIGRAN 985 
                                     *******..********************************************************************8 PP

                           MMPL  307 .la.....kprrkrkk.......rwW.rrlgrlvvrrPl 331 
                                      ++     +               +W rr+  + ++ P 
  gi|121637443|ref|YP_977666.1|  986 wWPselgrD------PstpptkaDRWlRRVKGHRRKAPI 1018
                                     555444441......223444455554777777777775 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.5   5.4e-08   0.00019       9     146 ..     222     364 ..     215     370 .. 0.81
   2 ?    4.1   2.4      0.01        37      14     137 ..     854     981 ..     844     986 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.4e-08
                                    HHHHHHHHHCCHHHHCCHH...HHHHHHHHHHHHHHHHHHHHHHCHHC.CHHCHHHHHHHHTTTCHHHHHHHHHHHHCCC CS
                 Sterol-sensing   9 glagviivllsvasslgll...aylgltltliilevlPflvlavgvdn.ifvlvkavqrtsrsldeseriaealgevgps 84 
                                    +l+ ++++++sv+ + g l   a +gl ++++ +  +  + +  g+d  +f++ + ++ + + ++ +  +++al ++g  
  gi|121637443|ref|YP_977666.1| 222 MLVPLATIGASVVTAQGTLsglAEFGLAVNMQAIVFMSAVMIGAGTDYaVFLISRYHDYVRHGEKSDMAVKKALMSIGKV 301
                                    56667889999999887761114577888887777777788899999625666666666666677799************ PP

                                    CHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH.HCTXXT CS
                 Sterol-sensing  85 illtsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre.eserld 146
                                    i+++++t ++++l  ++t++ + ++     ava++v+ l  +t+  a+L+l  rr   + r d
  gi|121637443|ref|YP_977666.1| 302 ITASAATVAVTFLAMVFTKLEVFSAVGPAIAVAITVSLLGAVTLLPAILTLTGRRGwIKPRRD 364
                                    *************888***999999999**************************976665555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.01
                                    HHHHCCHHHHCCHHHH.HHHHH...HHHHHHHHHH.HHHHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHH CS
                 Sterol-sensing  14 iivllsvasslgllay.lgltl...tliilevlPf.lvlavgvd.nifvlvkavqrtsrsldeseriaealgevgpsill 87 
                                      vl+s++s+lg+ ++ ++l l    +++l  l f l++a+g d n++++    +r ++ +     + +++g++g  i++
  gi|121637443|ref|YP_977666.1| 854 GSVLISYLSALGIGTLvFQLILgqeMHWSLPGLSFiLLVAIGADyNMLLI-SR-IRDESPHGIRIGVIRTVGSTGGVITS 931
                                    5688889999888654244433111334444455625679****555555.44.4445555667889999***9999998 PP

                                    CCCH.HHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                 Sterol-sensing  88 tslt.ellall.lgaltdvpavqeFclfaavavlvdFllqitfFvavLsldi 137
                                      l   + ++  +ga+++  a   F +   +++++d +l  t+ v  L+  i
  gi|121637443|ref|YP_977666.1| 932 AGLIfAASMFGlVGASINTMAQAGFTI--GIGIVLDTFLVRTVTVPALTTMI 981
                                    866515555658898888888888876..89999999998888888877665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1      0.73   2.6e+03     401     436 ..     183     218 ..     156     220 .. 0.76
   2 ?   11.4   0.0   1.6e-05     0.056     245     405 ..     496     650 ..     490     670 .. 0.79
   3 ?    0.5   0.1     0.032   1.1e+02     664     704 ..     671     711 ..     632     723 .. 0.53
   4 ?    1.4   0.1     0.016        58     406     438 ..     815     847 ..     784     851 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.73
                       Prominin 401 sktfddvvekyekyrwliglivcsllllivvililg 436
                                    + t  d  e  ek+ ++i + +++++l+i+++++  
  gi|121637443|ref|YP_977666.1| 183 IATVADLTELGEKDVRIIEIGTAVSVLIILILVYRN 218
                                    566777788888999999999999999999888755 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.6e-05
                       Prominin 245 lenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldqlpnvdevl 324
                                    + +l ea ++Le+    + +L   ++qL d+l ++++++n a++++ +    ++++  ++   +  +k+++ql+n ++++
  gi|121637443|ref|YP_977666.1| 496 GGKLDEATTLLEEHGGELDQLTGGAHQLADALAQIRNEINGAVASSSG--IVNTLQAMMDL--MGGDKTIRQLENASQYV 571
                                    56788999999999999****************************655..77777777777..99*************** PP

                       Prominin 325 ealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktf 404
                                     +++ +  +nls +v+++ +     + +v+   ++ v +   a ++ r+q+  + ++  ++ l + i++l  t ++++++
  gi|121637443|ref|YP_977666.1| 572 GRMRAL-GDNLSGTVTDAEQIATWASPMVNALNSSPVCNSDPACRTSRAQLAAIVQAQ-DDGLLRSIRALAVTLQQTQEY 649
                                    ***987.999999998887766666666666666667777777777777777777666.666666666666666666666 PP

                       Prominin 405 d 405
                                    +
  gi|121637443|ref|YP_977666.1| 650 Q 650
                                    5 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.032
                       Prominin 664 elvlplessvkklkksvkkldeensdlqesikkllaavera 704
                                    + v+ l ++++++++  ++l + +  l++ +++l+++v++ 
  gi|121637443|ref|YP_977666.1| 671 KAVDGLPTKLAQMQQGANALADGSAALAAGVQELVDQVKKM 711
                                    23455666666666666666666666666666666666655 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.016
                       Prominin 406 dvvekyekyrwliglivcsllllivvililgLl 438
                                    d  ++y+++ + i++ ++++++li+vil+ +L+
  gi|121637443|ref|YP_977666.1| 815 DIRDYYNSDMKFIVIATIVIVFLILVILLRALV 847
                                    667899***********************9997 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0048        17      48     100 ..     500     551 ..     485     587 .. 0.75
   2 ?    8.8   1.9   0.00045       1.6      24     110 ..     640     703 ..     613     722 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0048
                   Baculo_PEP_C  48 nalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                    ++ ++ l++   eld +l+  +++L dal+++ ++++ +  +   i+++L++ 
  gi|121637443|ref|YP_977666.1| 500 DEATTLLEEHGGELD-QLTGGAHQLADALAQIRNEINGAVASSSGIVNTLQAM 551
                                    333333333333332.6777788999999999999999999999999999875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00045
                   Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnlnsiltnL 97 
                                    a+ lq++q    la+++ ++++qL+++ + lk+ +  l t   ++++ +++L d  +al+   +                
  gi|121637443|ref|YP_977666.1| 640 AVTLQQTQEYQTLARTVSTLDGQLKQVVSTLKA-VDGLPTklaQMQQGANALADGSAALAagvQ---------------- 702
                                    233344444444444444444444444444443.333333344333334444444444432222................ PP

                   Baculo_PEP_C  98 lssvtNinstLnn 110
                                                 
  gi|121637443|ref|YP_977666.1| 703 ------------E 703
                                    ............2 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6  14.0      0.07   2.5e+02     660     808 ..     202     352 ..     195     355 .. 0.73
   2 ?    3.1   0.0    0.0055        20     429     534 ..     366     469 ..     360     474 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.07
                        Patched 660 iqnivlallcmfvvallfipelitvlvitlsivsidigviGflsl.WgvdLDpismitiimsiGfsvdlsaHia..yafv 736
                                    i ++v+ l+++++v   ++  l+ ++ i  s+v+ +  + G+  +   v++ +i+ ++ +m iG   d++   +  y+ +
  gi|121637443|ref|YP_977666.1| 202 IGTAVSVLIILILVYRNLVTMLVPLATIGASVVTAQGTLSGLAEFgLAVNMQAIVFMSAVM-IGAGTDYAVFLIsrYHDY 280
                                    5566666777777777777777777777777777665555555543369******999999.9********997344445 PP

                        Patched 737 rsekddakeRvvealealgwPvvqgalSTi.lgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPillsl 808
                                      ++++++  v++al  +g  v+ ++  T+ +  l ++f    +      ++   ++++ll ++ +lP +l+l
  gi|121637443|ref|YP_977666.1| 281 VRHGEKSDMAVKKALMSIGK-VITASAATVaVTFLAMVFTKLEVFSAVGPAIAVAITVSLLGAVTLLPAILTL 352
                                    5666699************7.55555555414445555556666666678999*****************986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0055
                        Patched 429 kskffreiyapfllnksvrlvvlllfvvylaiaiyGc.vnikegLepkklvledsplvevlkliekei.wkeglqvevvv 506
                                    +s+++r + +  + ++  +lv  l+ +    +a+ Gc + i+ + +  k v +  + v+ ++ +++++ ++  + +  ++
  gi|121637443|ref|YP_977666.1| 366 TSRMWRRSGVRIVRRPTIHLVGSLIVL----VALAGCtLLIRFNYDDLKTVPQHVESVKGYEAMNRHFpMNAMTPMVLFI 441
                                    566666666666666666655544444....4555652567888899999*****************956777889999* PP

                        Patched 507 nNppdltikesrdrleelveefentpya 534
                                    + p dl+++   + +e +  e++++p++
  gi|121637443|ref|YP_977666.1| 442 KSPRDLRTPGALADIEMMSREIAELPNI 469
                                    *******************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.43
# Mc/sec: 7760.84
//
Query:       gi|121637444|ref|YP_977667.1|  [L=347]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-24   85.9   0.0    3.9e-24   85.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.4e-22   79.0   0.0    6.3e-22   78.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.5e-17   62.6   0.0    5.5e-17   62.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.1e-14   53.7   0.0    3.1e-14   53.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-13   50.8   0.0    3.6e-13   50.1   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.8e-10   40.5   0.0    2.7e-10   40.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.3e-06   24.5   0.0    1.2e-05   24.0   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    0.00058   19.5   0.0    0.00091   18.8   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0029   17.5   0.0     0.0046   16.8   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
      0.003   17.4   0.0     0.0095   15.7   0.0    1.8  1  DUF938           Protein of unknown function (DUF938)
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.023   14.3   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
      0.031   13.6   0.0      0.046   13.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.032   15.3   0.0       0.07   14.2   0.0    1.6  1  Methyltransf_24  Methyltransferase domain
       0.28   10.3   0.0        3.1    6.8   0.0    2.0  2  Pox_MCEL         mRNA capping enzyme


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0     3e-27   3.9e-24       1      95 [.     165     259 ..     165     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 3e-27
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                    L+v cG+G  a ++a++   a+++g+Dl+++ ++l+++k + +g  ++fv++da++lpf+d+sfD+vv  e+ h  +d +
  gi|121637444|ref|YP_977667.1| 165 LEVSCGAGGGASYIARNLgpASYTGLDLNPASIDLCRAKHRLPG--LQFVQGDAQNLPFPDESFDAVVNVEASHQYPDFR 242
                                    899************6666*************************..89******************************** PP

                                    HHHHHHHHHEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                     +l+e+aRvL+pgG+++
  gi|121637444|ref|YP_977667.1| 243 GFLAEVARVLRPGGHFL 259
                                    **************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   4.9e-25   6.3e-22       1      97 []     164     256 ..     164     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.9e-25
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vL++ cG G  + ++a++lg a++tg+D++++ ++ +r++++   + ++fvqgda++lpf+d+sfD+vv + a h +  +
  gi|121637444|ref|YP_977667.1| 164 VLEVSCGAGGGASYIARNLGPASYTGLDLNPASIDLCRAKHR--LPGLQFVQGDAQNLPFPDESFDAVVNVEASHQY--P 239
                                    9******************99********************4..458***********************9886555..5 PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    d + +l+e+arvL+pgG
  gi|121637444|ref|YP_977667.1| 240 DFRGFLAEVARVLRPGG 256
                                    99**************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   4.3e-20   5.5e-17       4     114 ..     161     272 ..     158     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.3e-20
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    g++vl++ CG+G  +  +a++lgp a ++G+D ++ +i l+r+   k+ l  ++F qgd+++l+  + de+fD ++  e+
  gi|121637444|ref|YP_977667.1| 161 GKEVLEVSCGAGGGASYIARNLGP-ASYTGLDLNPASIDLCRA---KHRLPGLQFVQGDAQNLP--FPDESFDAVVNVEA 234
                                    789****************99998.99****************...79999999**********..************** PP

                Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr.......l 114
                                     +  +d   +l e+ rvl+pgg++l +d r       +
  gi|121637444|ref|YP_977667.1| 235 SHQYPDFRGFLAEVARVLRPGGHFLYTDSRrnpvvaeW 272
                                    ****************************9966644432 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   2.4e-17   3.1e-14       7     125 ..     144     271 ..     138     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.4e-17
                Methyltransf_23   7 eelsdklerll.pklraggrvLdiGcGtGillevlren.gf.svtgvDlspeaveiae...kakkaqkdqfdeqeaaepq 80 
                                    +++ +++++++ + + +g++vL++ cG G  ++++++n g  s+tg Dl+p+ +++ +     +  q++q d+q+ ++p+
  gi|121637444|ref|YP_977667.1| 144 RYCIQLYHQTAsQVDLTGKEVLEVSCGAGGGASYIARNlGPaSYTGLDLNPASIDLCRakhRLPGLQFVQGDAQNLPFPD 223
                                    4566788777735599*******************9987556**************9999999999************** PP

                Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl...k 125
                                    ++fd +v+ e  +  pd+   l+ +a+ l+pgG++l +++ ++    +
  gi|121637444|ref|YP_977667.1| 224 ESFDAVVNVEASHQYPDFRGFLAEVARVLRPGGHFLYTDSRRNPvvaE 271
                                    **************************************9966543322 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.8e-16   3.6e-13       1      99 []     165     258 ..     165     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.8e-16
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le+ cG G  +++++++l +++ytg+D++p++i d  +  ++  +++  +v+ +a++l   d+  sfD+vv  ++ h  +
  gi|121637444|ref|YP_977667.1| 165 LEVSCGAGGGASYIARNLGPASYTGLDLNPASI-DLCRAKHRLPGLQ--FVQGDAQNLPFPDE--SFDAVVNVEASHQYP 239
                                    8********************************.4444445555544..56666666555554..*************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d r +l++++++L+pgG++
  gi|121637444|ref|YP_977667.1| 240 DFRGFLAEVARVLRPGGHF 258
                                    *****************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.1e-13   2.7e-10      43     151 ..     156     260 ..     148     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.1e-13
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                    + +++g++vl+v++G+g  a  +++++g     ++lD+n+  ++  ++k +  g   ++f+q++a++Lpf d+sfD v  
  gi|121637444|ref|YP_977667.1| 156 QVDLTGKEVLEVSCGAGGGASYIARNLGPAS-YTGLDLNPASIDLCRAKHRLPG---LQFVQGDAQNLPFPDESFDAVVN 231
                                    56789**********************9975.789*************999877...68*****************9998 PP

                                    ES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                           +D    L e+ rvl+pGG+++ 
  gi|121637444|ref|YP_977667.1| 232 VEASHQYPDFRGFLAEVARVLRPGGHFLY 260
                                    88999********************9875 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   9.7e-09   1.2e-05     111     220 ..     155     263 ..     140     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.7e-09
                Methyltransf_29 111 liaaggkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaL.eRgvpailavlg.tkrlpyPsrsfdlihCs 188
                                    + + + + + vl+v Cg    ga  + r++   s +  D   a + +      +p +  v g ++ lp+P +sfd +   
  gi|121637444|ref|YP_977667.1| 155 S-QVDLTGKEVLEVSCGA-GGGASYIARNLGPASYTGLDLNPASIDLCRaKHRLPGLQFVQGdAQNLPFPDESFDAVVNV 232
                                    3.56777899******95.56888999******************997514579999999983578*************9 PP

                Methyltransf_29 189 rCridwteedgilllevdRvlRpgGyfvlsap 220
                                        ++ +  g +l ev RvlRpgG+f+++ +
  gi|121637444|ref|YP_977667.1| 233 EASHQYPDFRG-FLAEVARVLRPGGHFLYTDS 263
                                    99999999999.589*************9754 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.1e-07   0.00091      31     138 ..     160     261 ..     148     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.1e-07
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STT CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfha 109
                                    + ++vl + cGaG  +  +a++   a+ t +d + ++++++++  +  +l  ++v+ d+ +  +++++fd++v     h+
  gi|121637444|ref|YP_977667.1| 160 TGKEVLEVSCGAGGGASYIARNLGPASYTGLDLNPASIDLCRAKHRLPGL--QFVQGDAQNlPFPDESFDAVVNVEASHQ 237
                                    5678**************************************98888885..888888877356799*****97443333 PP

                                    TCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                            MTS 110 gkatelavaeeliaeAkeaLkegGeLliV 138
                                         +   + ++ae +++L++gG++l  
  gi|121637444|ref|YP_977667.1| 238 -----YPDFRGFLAEVARVLRPGGHFLYT 261
                                    .....555999999999999999998765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.6e-06    0.0046     108     155 ..     211     259 ..     172     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                                    EEES-TTS-S--TT-EEEEEEE.S---SS-HHHHHHHHHHHEEEEEEEE CS
                 Methyltransf_8 108 vvacdlakvPledesvdvavfc.lslmgtnladflkeanrvlkvGGllk 155
                                     v  d +++P  des d +v    s    +++ fl e+ rvl++GG++ 
  gi|121637444|ref|YP_977667.1| 211 FVQGDAQNLPFPDESFDAVVNVeASHQYPDFRGFLAEVARVLRPGGHFL 259
                                    577899***********999763688999*****************986 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.4e-06    0.0095      19      68 ..     154     203 ..     135     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.4e-06
                         DUF938  19 ksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaaw 68 
                                     s+++ t+++vLE++ G+G  A ++A +l ++ +   d ++   +  +a 
  gi|121637444|ref|YP_977667.1| 154 ASQVDLTGKEVLEVSCGAGGGASYIARNLGPASYTGLDLNPASIDLCRAK 203
                                    478999999**************************999998776555553 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.8e-05     0.023      14     101 ..     161     251 ..     151     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                           MetW  14 gsrvldlGcGdGellellkeekqvdg.rGleldeegvaecvak....Glsviqgdldkdlenfedksfdyvvlsqtlqat 88 
                                    g +vl++ cG G   ++++ + +  +  Gl+l+ +++  c ak    Gl+ +qgd+++    f+d+sfd vv   +  + 
  gi|121637444|ref|YP_977667.1| 161 GKEVLEVSCGAGGGASYIARNLGPASyTGLDLNPASIDLCRAKhrlpGLQFVQGDAQN--LPFPDESFDAVVNVEASHQY 238
                                    678********99998888777755516************99888889*******975..479********987776666 PP

                           MetW  89 rnpkevldellri 101
                                     + +  l e+ r+
  gi|121637444|ref|YP_977667.1| 239 PDFRGFLAEVARV 251
                                    6666666666665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.6e-05     0.046      62     164 ..     160     260 ..     148     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                                    TT-EEEEES-TTSHHHHHHHHHH-.-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGT CS
                           CMAS  62 pGmtlLdiGcGWGslvrraveryd.vkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehv 140
                                     G+++L++ cG G+ + + +++ + ++  gl l      l++++    +l+  v+ + ++    de +d+vv v+a  + 
  gi|121637444|ref|YP_977667.1| 160 TGKEVLEVSCGAGGGASYIARNLGpASYTGLDLNPASIDLCRAKHRLPGLQ-FVQGDAQNLPFPDESFDAVVNVEASHQ- 237
                                    599******************99857889***********99999888865.56777777777789*********9764. PP

                                    SGGGHHHHHHHHHHHS-TT-EEEE CS
                           CMAS 141 gkenydtffkklkkllkedGllll 164
                                     +  +  f +++ ++l+++G +l 
  gi|121637444|ref|YP_977667.1| 238 -YPDFRGFLAEVARVLRPGGHFLY 260
                                    .68899**************9986 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.5e-05      0.07       3     103 ..     169     260 ..     167     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.5e-05
                Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiD.llfiDgghaa 81 
                                    +G  +G  + +++r l      +++ +d +p   +   l r ++    ++++++d++++   + ++s+D ++ + ++h++
  gi|121637444|ref|YP_977667.1| 169 CG--AGGGASYIARNLGP---ASYTGLDLNP---ASIDLCRAKHRLPGLQFVQGDAQNL--PFPDESFDaVVNVEASHQY 238
                                    67..77777777755544...4578999999...5555666655556699999999999..677899996788******* PP

                Methyltransf_24  82 eavledleallprlapggvvlf 103
                                     + + +l  + ++l+pgg +l 
  gi|121637444|ref|YP_977667.1| 239 PDFRGFLAEVARVLRPGGHFLY 260
                                    ******************9876 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0024       3.1      51     106 ..     147     203 ..     143     218 .. 0.84
   2 ?    1.2   0.0      0.12   1.6e+02     167     185 ..     243     261 ..     234     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0024
                       Pox_MCEL  51 iseyasktkldesnklkvLdldcgkGgDLeKy.ekgeIsklvatDiaeesieeckeR 106
                                    i++y + +++ +    +vL+++cg Gg      +  + +++ + D + +si+ c+ +
  gi|121637444|ref|YP_977667.1| 147 IQLYHQTASQVDLTGKEVLEVSCGAGGGASYIaRNLGPASYTGLDLNPASIDLCRAK 203
                                    89999999999999***********99876542456778999999999999999865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                       Pox_MCEL 167 tvlrNvaellasGGkvlgT 185
                                      l+ va++l++GG++l T
  gi|121637444|ref|YP_977667.1| 243 GFLAEVARVLRPGGHFLYT 261
                                    57899************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2381.49
//
Query:       gi|121637445|ref|YP_977668.1|  [L=414]
Description: glycosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-09   35.7   0.0    1.6e-08   34.7   0.0    1.5  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
      0.004   16.0   0.0     0.0093   14.8   0.0    1.6  1  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.02   14.9   0.0    1.3  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   2.7e-12   1.6e-08       1      85 [.       3      85 ..       3     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.7e-12
                                   EEEEE-SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHH CS
                Glyco_transf_28  1 ivllggGTgGhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakk 82
                                   +v++  GT+G+++P  A+  eL+++gh+V  l+ +++l  ++ e+agl  +  + +  +++l +++l +++k+ + ++  ++
  gi|121637445|ref|YP_977668.1|  3 FVVASYGTRGDIEPCAAVGLELQRRGHDVC-LAVPPNLIGFV-ETAGLSAVAYGSRDSQEQLDEQFLHNAWKLQNPIKLLRE 82
                                   588999************************.**********9.*****************************9888777776 PP

                                   HHH CS
                Glyco_transf_28 83 ilk 85
                                    + 
  gi|121637445|ref|YP_977668.1| 83 AMA 85
                                   665 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-06    0.0093     249     407 ..     222     378 ..     220     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-06
                          UDPGT 249 figglnckpakplpkeleefvqssGehGvvvfSlGsmvseipeekanaiAsaLakipqkvlWrfdgkkPstLa..kntll 326
                                    f+g l  + a +   e+  ++ +  +   ++f +Gsm      +++ +i +a a+++++ l          +       +
  gi|121637445|ref|YP_977668.1| 222 FVGALTMESATDADDEVASWIAA--DTPPIYFGFGSMPIGSLADRVAMISAACAELGERALICSGPSDATGIPqfDHVKV 299
                                    56666666666666666666666..6666788888886666666678888888888887776443322222220023466 PP

                          UDPGT 327 vkWlPqndlLgHPktkAFvtHaGangvyEaisnGvPmvglPlFgdqrdNikrmeakgaavtlnvkemtsedllnAlkevi 406
                                    v+ +   ++   P  +A v H+Ga +   ++  G+P  +l + +dq+  ++++++   +    ++  t+e l   l++++
  gi|121637445|ref|YP_977668.1| 300 VRVVSHAAV--FPTCRAVVHHGGAGTTAAGLRAGIPTLILWVTSDQPIWAAQIKQLKVGRGRRFSSATKESLIADLRTIL 377
                                    666666666..5*****************************************999888888999999999999999888 PP

                          UDPGT 407 n 407
                                     
  gi|121637445|ref|YP_977668.1| 378 A 378
                                    6 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.3e-06      0.02      60     154 ..     300     389 ..     278     404 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                    EESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHH CS
                Glyco_tran_28_C  60 fefidkmaeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeall 139
                                    ++ +  +a++      v+ ++Gagt a  l++g p+++    +    +q   a+++ + +++++ + + +t e+L++ l+
  gi|121637445|ref|YP_977668.1| 300 VRVVS-HAAVFPTCRAVVHHGGAGTTAAGLRAGIPTLILWVTS----DQPIWAAQIKQLKVGRGRRFSSATKESLIADLR 374
                                    55555.666666677899******************9999999....9******************************** PP

                                    HHCCS---S---SSC CS
                Glyco_tran_28_C 140 elaaeklrlaekska 154
                                    +++a++    ++  a
  gi|121637445|ref|YP_977668.1| 375 TILAPDYVTRAREIA 389
                                    **9998765444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3074.40
//
Query:       gi|121637446|ref|YP_977669.1|  [L=261]
Description: rhamnosyl transferase wbbL2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0088   16.0   0.2      0.017   15.1   0.1    1.6  2  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.25   4.5e+03       4      24 ..       8      28 ..       7      38 .. 0.80
   2 !   15.1   0.1   9.2e-07     0.017     150     216 ..     133     203 ..      68     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.25
                Glyco_tranf_2_3  4 lavlVptfneedvlgevlesl 24
                                   l + Vp+f+ +++ ++++++l
  gi|121637446|ref|YP_977669.1|  8 LMITVPVFGQHEYTHALVADL 28
                                   568899999999999888765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.2e-07
                Glyco_tranf_2_3 150 aarralgvltlnGsgslirrevlkelegldp....lflltdDyelglrlrragfrtayvpgaavrevfpss 216
                                     ++r+ +v+++ G+ +++ r+++++ +g d     +   + D++l+lr+r+ g+  ++ + a +++  +++
  gi|121637446|ref|YP_977669.1| 133 PRARYRKVPAVEGTALVMSRDCWDAVGGMDLstfgRYGWGLDLDLALRARKSGYGLYTTEMAYINHFGRKT 203
                                    5667888********************65554343355559**************9999999999986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1870.72
//
Query:       gi|121637447|ref|YP_977670.1|  [L=426]
Description: glycosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-09   35.5   0.0    1.7e-08   34.6   0.0    1.4  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
       0.15   10.8   0.1       0.49    9.1   0.0    1.8  2  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas


Domain annotation for each model (and alignments):
>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.9e-12   1.7e-08       1      51 [.       3      51 ..       3      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.9e-12
                                   EEEEE-SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEE CS
                Glyco_transf_28  1 ivllggGTgGhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefe 51
                                   +vl++ GT+G+v+P  A+  eL+++gh V+ ++ +++l e++ e+agl+ +
  gi|121637447|ref|YP_977670.1|  3 FVLAVHGTRGDVEPCAAVGVELRRRGHAVH-MAVPPNLIEFV-ESAGLTGV 51
                                   699***************************.**********9.99999755 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.11   9.4e+02     123     169 ..     111     157 ..      95     163 .. 0.67
   2 ?    9.1   0.0   5.5e-05      0.49     279     406 ..     252     379 ..     223     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.11
                          UDPGT 123 ladpvlpcgellAellkiptvyllrdvpgqaaekvsGkllsppsyvp 169
                                      ++   +++ +Ae+ +ip+ +l ++  +   + +   +++p ++v 
  gi|121637447|ref|YP_977670.1| 111 TGQTYHGVAANVAEYYDIPAAALHHFPMQVNGQIAIPSIPTPATLVR 157
                                    445566678999*******9988776655555555556666666665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 5.5e-05
                          UDPGT 279 vfSlGsmvseipeekanaiAsaLakipqkvlWrfdgkkPstLakntllvkWlPq.ndlLgHPktkAFvtHaGangvyEai 357
                                    +f +Gs   ++p + + +i +  a+++++ l      +   + ++   vk +   n     Pk +A v H+Ga +   ++
  gi|121637447|ref|YP_977670.1| 252 YFGFGSTPVQTPVQTLAMISDVCAQLGERALIYSPAANSTRIRHADH-VKRVGLvNYSTILPKCRAVVHHGGAGTTAAGL 330
                                    66666666666666666666666666666554333333333332222.2222220222234******************* PP

                          UDPGT 358 snGvPmvglPlFgdqrdNikrmeakgaavtlnvkemtsedllnAlkevi 406
                                      G+P  +l   +dq+  +  ++    + +  ++++t   ll+ l++++
  gi|121637447|ref|YP_977670.1| 331 RAGMPTLILWDVADQPIWAGAVQRLKVGSAKRFTNITRGSLLKELRSIL 379
                                    ****************999999998888888888999988888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2909.26
//
Query:       gi|121637448|ref|YP_977671.1|  [L=2108]
Description: polyketide synthase pks5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-102  343.7   4.2   1.8e-102  343.1   4.2    1.3  1  Acyl_transf_1    Acyl transferase domain
      8e-90  300.8   0.0    2.5e-89  299.2   0.0    1.9  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    5.9e-58  195.7   2.4    2.6e-57  193.6   0.2    2.6  2  KR               KR domain
    3.9e-48  164.2   6.6    9.3e-48  163.0   6.6    1.7  1  PS-DH            Polyketide synthase dehydratase
    3.9e-38  130.1   1.0    3.9e-38  130.1   1.0    2.0  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      6e-21   74.8   0.6    4.9e-20   71.8   0.1    2.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
    1.1e-17   65.3   0.0    1.1e-16   62.1   0.0    2.8  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    4.1e-12   46.5   0.0    1.3e-11   44.9   0.0    1.9  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    2.2e-09   37.1   0.2    1.5e-08   34.3   0.0    2.4  2  adh_short        short chain dehydrogenase
    3.2e-08   33.8   0.4    8.3e-08   32.5   0.4    1.8  1  PP-binding       Phosphopantetheine attachment site
      2e-07   30.7   0.2    4.9e-07   29.4   0.2    1.6  1  Thiolase_N       Thiolase, N-terminal domain
    4.9e-07   29.6   0.0    1.6e-06   28.0   0.0    1.9  1  ADH_N            Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.053   12.6   0.5        0.3   10.2   0.1    2.2  2  RmlD_sub_bind    RmlD substrate binding domain
       0.44   10.4   1.2         19    5.1   0.2    2.5  2  PPTA             Protein prenyltransferase alpha subunit repe


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.1   4.2  1.4e-105  1.8e-102       1     317 [.     546     861 ..     546     863 .. 0.97

  Alignments for each domain:
  == domain 1  score: 343.1 bits;  conditional E-value: 1.4e-105
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    v+vfsGqGsQwaGMG++Ll+t+++faa+ia+ ++ +++++gfsv++++++ +   +++i+ vqp L+a+q+ala+++ks+
  gi|121637448|ref|YP_977671.1| 546 VWVFSGQGSQWAGMGADLLATEPVFAATIAAIEPLIAAESGFSVTEAMTAPE--VVTGIDRVQPTLFAMQVALAATMKSY 623
                                    7***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.....HHHHHHH..TT.EEEEEEECC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel....aeeeeklrcqddvvgavanspr 156
                                    Gv+p+av+GHSlGE+Aaavvagal +e++++++++rs lm+++ag+g+ma+vel    + +e+++r  +d v+av++sp+
  gi|121637448|ref|YP_977671.1| 624 GVAPGAVIGHSLGESAAAVVAGALCLEDGVRVICRRSALMTRIAGAGAMASVELpaqqVLSELMARGVNDAVVAVVASPQ 703
                                    *******************************************************9877899****999*********** PP

                                    CCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHH CS
                  Acyl_transf_1 157 rvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaey 236
                                    ++vi+g ++++r+lv+ +++++v a++++v+va+hspqvd+i d+la+ala+i p +p+++++s+ts+d+++e+ ++a y
  gi|121637448|ref|YP_977671.1| 704 STVIGGATQTVRDLVAAWEQRDVLAREVAVDVASHSPQVDPILDELAEALAEISPLQPEIPYYSATSFDPREEPYCDAYY 783
                                    ******************************************************************************** PP

                                    HHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT CS
                  Acyl_transf_1 237 wvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltg 316
                                    wv+nlr +vrfa+av++a+e++++vf e+ pH+ll++a+ +t +s  d++ a+l+G ++r++    + +++l++ +  +g
  gi|121637448|ref|YP_977671.1| 784 WVDNLRHTVRFAAAVQAALEDGYRVFTELTPHPLLTHAVDQTARS-LDMSAAALAG-MRREQPL-PHGLRALAGDLYAAG 860
                                    ********************************************7.**********.*****99.888888887777666 PP

                                    - CS
                  Acyl_transf_1 317 s 317
                                    +
  gi|121637448|ref|YP_977671.1| 861 A 861
                                    5 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.2   0.0   1.9e-92   2.5e-89       3     253 .]      16     263 ..      14     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 299.2 bits;  conditional E-value: 1.9e-92
                                    -EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispr 80 
                                    pva++Gmg+r+Pgg d ++ +we+Ll+g d ++e+padrwd d++ydp++ ++g++++k+g++ld v dfdpeffgi ++
  gi|121637448|ref|YP_977671.1|  16 PVAVIGMGCRLPGGIDsPDRLWEALLRGDDLVTEIPADRWDIDEYYDPEPGVPGRTDCKWGAYLDnVGDFDPEFFGIGEK 95 
                                    8***************9*************************************************************** PP

                                    HHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHH CS
                  ketoacyl-synt  81 eaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagrisy 160
                                    ea a+dpq+rllle++wea+e+ gltp++   sr+gvf+G+ + dy  + ++ +++  +  +   +g+ +a++++gr++y
  gi|121637448|ref|YP_977671.1|  96 EAIAIDPQHRLLLETSWEAMEHGGLTPNQ-MASRTGVFVGLVHTDY--ILVHADNQTFEGPYG-NTGT-NACFASGRVAY 170
                                    ***************************77.6679**********99..334443342333444.6676.*********** PP

                                    HHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB- CS
                  ketoacyl-synt 161 alglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlGE 240
                                    a+gl+Gp++tvdtACsS+l+a+h+a++sl++ge+d+alaGGv ++l+p+ +a+ sa+g+ls++grc+afd +adGfv GE
  gi|121637448|ref|YP_977671.1| 171 AMGLQGPAITVDTACSSGLTAIHLACRSLHDGESDIALAGGVYVMLEPRRFASGSALGMLSATGRCHAFDVSADGFVSGE 250
                                    ******************************************************************************** PP

                                    EEEEEEEEECHHH CS
                  ketoacyl-synt 241 GvGavvLkrleda 253
                                    G+ ++ Lkrl da
  gi|121637448|ref|YP_977671.1| 251 GCVMLALKRLPDA 263
                                    **********887 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       0.3   3.8e+02      17      77 ..     683     751 ..     676     758 .. 0.70
   2 !  193.6   0.2     2e-60   2.6e-57       1     179 [.    1765    1942 ..    1765    1943 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.3
                                    HHHHHHHH.S-EEEEE-SS........--HHHHHHHHHHHHTT-EEEE----TT-HH.HHHHHHHHHHH CS
                             KR  17 arwlaekg.arhlvllsRsa......aadedskaliaelealgaevevvaaDvsdkd.avealleeika 77 
                                       l+++g +  +v +  s+       a+++ ++l+a++e++++  + va+Dv++++ +v  +l+e+ +
  gi|121637448|ref|YP_977671.1| 683 LSELMARGvNDAVVAVVASPqstvigGATQTVRDLVAAWEQRDVLAREVAVDVASHSpQVDPILDELAE 751
                                    5556666644444444444345777778889999*******************9865367777776665 PP

  == domain 2  score: 193.6 bits;  conditional E-value: 2e-60
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     g+y+itGGlGgLGl la+ +a+ ga ++vl sRs ++++++ ++i+ ++a g +v v   D++++d   +l+++++a+
  gi|121637448|ref|YP_977671.1| 1765 GSYIITGGLGGLGLFLAEKMANAGAGRIVLSSRS-QPSQKALETIELVRAIGSDVVVECGDIAQPDTADRLVTAATAT 1841
                                     89********************************.88999999*********************************** PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     + p++Gv+haA v++d++l++ t+e +e+  apK  Gaw+Lh++++d++ld+f  fSS+a+l+gs+gq++YaaaN++l
  gi|121637448|ref|YP_977671.1| 1842 GLPLRGVLHAAAVVEDATLANITDELIERDWAPKAYGAWQLHRATADQPLDWFCSFSSAAALVGSPGQGAYAAANSWL 1919
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BT CS
                             KR  157 Dalaeyrrsqglpavsinwglwa 179 
                                     D++ ++rr+q lpa+si+wg+w 
  gi|121637448|ref|YP_977671.1| 1920 DTFTHWRRAQDLPATSIAWGAWG 1942
                                     **********************6 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   6.6   7.3e-51   9.3e-48       1     292 [.     905    1186 ..     905    1192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 7.3e-51
                                     BTTB.-EE--..-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B CS
                          PS-DH    1 hpllGsrvrsa.sdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvl 77  
                                     hpllGs+vr + +++++v++ ++ +  +pwL+DH+++g + lPga+y emal+Aar + ge+   e+rd++++++l l
  gi|121637448|ref|YP_977671.1|  905 HPLLGSHVRLPeEPERHVWQGEVGTVTQPWLADHQIHGAAALPGAAYCEMALAAARAVLGEA--SEVRDIRFEQMLLL 980 
                                     9**********99**********************************************877..9************* PP

                                     --SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-----.....--B--HHHHHHHS-SEE... CS
                          PS-DH   78 pedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaa.....aaavdlealqarcaepaslr 150 
                                     ++++p+ v+ ++e+ +   +      ++ +  +g    t+  ++ +++ ++a+     +++  +++        +++ 
  gi|121637448|ref|YP_977671.1|  981 DDETPIGVTATVEAPG--VV----PLTVETSHDGR--YTRQLAAVLHVVREADdapdqPPQKNIAE-----LLASHPH 1045
                                     **99*******99994..33....55555544444..47888888887777664333334444444.....4555566 PP

                                     .E-HHHHHHHHHHHSEEE-GGG--EEEEEEE...TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----- CS
                          PS-DH  151 svssaefYerlaargleyGpsFqglralwrg...dgealaelrlpeelaggesayvlhPallDaalQllaaalsaeae 225 
                                     +v++ae+ + l++rg  +Gp+F gl +++      + +lae++lp  l+++ +ay +hP+llDa++Q++aa    +  
  gi|121637448|ref|YP_977671.1| 1046 KVDGAEVRQWLDKRGHRLGPAFAGLVDAYIAegaGDTVLAEVNLPGPLRSQVKAYGVHPVLLDACFQSVAAHPAVQGM 1123
                                     69*************************9999554558******************************88666655678 PP

                                     -----EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE-- CS
                          PS-DH  226 kadaaylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrve 292 
                                     +++ + lP+++ rlr y+   +a++  ++ +++++ g  +++adl+++de G vv+ ++gl+l    
  gi|121637448|ref|YP_977671.1| 1124 ADGGLLLPLGVRRLRSYG---SARHARYCCTTVTACG-VGVEADLDVLDEHGAVVLAVRGLQLGTGA 1186
                                     9999*************8...5677888888888776.49*********************986655 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   1.0     3e-41   3.9e-38       1     117 [.     271     384 ..     271     385 .. 0.99
   2 ?   -3.4   0.3       7.4   9.5e+03      86     106 ..     630     649 ..     626     653 .. 0.66

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 3e-41
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +avi+g+a+n+dg++  + +p+ +aq +a+++al+ agvdp++v++veahg gtp+gDpiE+++l++v+g+++   p+a+
  gi|121637448|ref|YP_977671.1| 271 LAVIRGTAANQDGHTVNIATPSRSAQVAAYREALDVAGVDPATVGMVEAHGPGTPVGDPIEYASLAEVYGNDG---PCAL 347
                                    69*********************************************************************98...9*** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                     SvK+n GH+++AaG+++l+k+vlal+hgv+p++l++
  gi|121637448|ref|YP_977671.1| 348 ASVKTNFGHTQSAAGALGLMKAVLALQHGVVPQNLHF 384
                                    ************************************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                                    HH-B-GGGHHHHHHHHHHHHH CS
                Ketoacyl-synt_C  86 niGHleaAaGvaelikvvlal 106
                                     iGH+++ +++a ++  +l+l
  gi|121637448|ref|YP_977671.1| 630 VIGHSLGESAAAVVAG-ALCL 649
                                    69**998877665444.4455 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.1   3.8e-23   4.9e-20       1     115 [.    1570    1684 ..    1570    1701 .. 0.86
   2 ?   -0.6   0.1      0.92   1.2e+03       1      41 [.    1775    1822 ..    1775    1844 .. 0.65

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 3.8e-23
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalk 77  
                                     gvG+aa+++A+a+Ga+++a++++e++++l++++G ++v+++ +  ++ e+i++ t g gvd+v++ v  ga+  a lk
  gi|121637448|ref|YP_977671.1| 1570 GVGQAAIAIARAAGAQIYATAGNEKRRDLLRDMGIEHVYDS-RSvEFAEQIRRDTAGYGVDIVLNSVT-GAAQLAGLK 1645
                                     9****************************************.655***********************.********* PP

                                     CEEEEEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SS CS
                     ADH_zinc_N   78 llkpgGrlvvvGg..gkgeeefdlrnlllkeksilGsllg 115 
                                     ll+ gGr+  +G    + ++ + l + +++++ ++G  lg
  gi|121637448|ref|YP_977671.1| 1646 LLALGGRFIEIGKrdIYSNTRLELLP-FRRNLAFYGLDLG 1684
                                     ************98888877766655.3566666555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.92
                                     HHHHHHHHHHHHTT-.EEEEEESSHHHH......HHHHHTTESEEEET CS
                     ADH_zinc_N    1 gvGlaavqlAkalGa.eviavdsseekl......elakklGadeviny 41  
                                     g+Gl++ +  + +Ga +++  ++s+         el++ +G d+v+  
  gi|121637448|ref|YP_977671.1| 1775 GLGLFLAEKMANAGAgRIVLSSRSQPSQkaletiELVRAIGSDVVVEC 1822
                                     778888888888888888887666543312444466666677777654 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         4   5.1e+03      78      99 ..     461     485 ..     433     531 .. 0.64
   2 !   62.1   0.0   8.3e-20   1.1e-16       2     133 .]    1603    1741 ..    1602    1741 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4
                                    GGG...-....-HHHHHHHHHHHHH CS
                   ADH_zinc_N_2  78 lfsmkas...aqadileelaaliee 99 
                                    lf ++as   a +++ ++la+++++
  gi|121637448|ref|YP_977671.1| 461 LFALSASsqdALRQTAARLADWVDA 485
                                    4444444334334445666666665 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 8.3e-20
                                     T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEE CS
                   ADH_zinc_N_2    2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvk 74  
                                     G ++v+d+r+ +f+    ++t g gvD+vl++v g+a   a lk+l+ gGr+++ig +++ s++ l++  +r++ +++
  gi|121637448|ref|YP_977671.1| 1603 GIEHVYDSRSVEFAeqirRDTAGYGVDIVLNSVTGAAQ-LAGLKLLALGGRFIEIGkRDIYSNTRLELLPFRRNLAFY 1679
                                     899******999999***9999************9999.7777999888*******7777555555555556666677 PP

                                     E--GGG...-....-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   75 yeflfsmkas...aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                        l  m+ s   a +++l ++ +l  eG l ++ + ++pl+eaa+A+r + ++ ++GK++l
  gi|121637448|ref|YP_977671.1| 1680 GLDLGLMSVShpaAVRELLSTVYRLTVEGVLPMPQSTHYPLAEAATAIRVMGAAEHTGKLIL 1741
                                     666665555567877777*************9999999**********************97 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0     1e-14   1.3e-11      10     108 ..     395     509 ..     389     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1e-14
                 KAsynt_C_assoc  10 egrlkVvteptpwpggi......vgvNsfGfGGsnvHviLksnkkekrkeesk.......eeslprLlvlsgrteeavea 76 
                                    e++l V++e tpwpg        ++v+s+G+ G+nvH+i+++++ + +++ ++         +   L++ls+ +++a+++
  gi|121637448|ref|YP_977671.1| 395 ETNLFVPQEITPWPGADqetprrAAVSSYGMTGTNVHAIVEQAPVPAPESGAPgdtpatpGIDGALLFALSASSQDALRQ 474
                                    57899*********9999999***********************7777777777777777899999************** PP

                 KAsynt_C_assoc  77 llekleeh.lldaellsllneilseeisr..lpyR 108
                                    ++++l+++  ++ ++l+ ++ +++ +++r   p+R
  gi|121637448|ref|YP_977671.1| 475 TAARLADWvDAQGPELAPADLAYTLARRRghRPVR 509
                                    ********666688888887777777666535555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.72   9.3e+02       3      37 ..    1562    1596 ..    1560    1610 .. 0.87
   2 !   34.3   0.0   1.2e-11   1.5e-08       4     161 ..    1768    1924 ..    1766    1937 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.72
                                     EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHH CS
                      adh_short    3 vlvtGassGIGraiakelakeGakvvvvdrseekl 37  
                                     vl+  a++G+G+a      ++Ga++++++ +e++ 
  gi|121637448|ref|YP_977671.1| 1562 VLIHSATGGVGQAAIAIARAAGAQIYATAGNEKRR 1596
                                     89999********9999999*******99887765 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.2e-11
                                     EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT...TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee...gakalaiqvDvtdreevealvekavkklgkl 78  
                                     ++tG+ +G+G+ +a+++a++Ga  +v+++++++ +++++ ++     g+++++  +D+++ + +++lv +a +   +l
  gi|121637448|ref|YP_977671.1| 1768 IITGGLGGLGLFLAEKMANAGAGRIVLSSRSQPSQKALETIELVraiGSDVVVECGDIAQPDTADRLVTAATATGLPL 1845
                                     8*************************999999999999887755557999**************************** PP

                                     SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                      adh_short   79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156 
                                       + + A++ ++++ +++++e +er  +    g+ +l ra +++            sS a++v+++g+ aY+A+   +
  gi|121637448|ref|YP_977671.1| 1846 RGVLHAAAVVEDATLANITDELIERDWAPKAYGAWQLHRATADQ----PLDWFCSFSSAAALVGSPGQGAYAAANSWL 1919
                                     *********88888888888888888888888877777777766....55678999*****************99999 PP

                                     HHHHH CS
                      adh_short  157 agltr 161 
                                     + +t+
  gi|121637448|ref|YP_977671.1| 1920 DTFTH 1924
                                     88887 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.4   6.5e-11   8.3e-08       1      66 [.    2029    2093 ..    2029    2094 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.5e-11
                     PP-binding    1 eklrelvaevlgvpleeidpdtd..lfdlGlDSllavellaaleeefgveiplsdlfehptlaelaay 66  
                                     ++lr+l++++ g+ l + + dtd  l+++GlDSl++ el a++e+e g++i+ +++  ++t++ la++
  gi|121637448|ref|YP_977671.1| 2029 DRLRRLLSKQVGLILRR-TIDTDrlLSEYGLDSLSSQELRARVEAETGIRISATEI--NTTVRGLADL 2093
                                     58999*******97766.555555588***************************99..7***999986 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   3.8e-10   4.9e-07      66     115 ..     168     215 ..     155     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.8e-10
                                    HHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEES CS
                     Thiolase_N  66 aalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsm 115
                                    +a ++g+  + pa+tv+ +csSgl+a++la++s+  ge+d+++agGv  m
  gi|121637448|ref|YP_977671.1| 168 VAYAMGL--QGPAITVDTACSSGLTAIHLACRSLHDGESDIALAGGVYVM 215
                                    5556666..889**********************************9776 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.2e-09   1.6e-06       1      67 [.    1446    1512 ..    1446    1526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE- CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplisc 67  
                                     pge+ + v+a++i+  D+ +  g+ ++       lG +++G+v++vgp+v++lkvGdrV       c
  gi|121637448|ref|YP_977671.1| 1446 PGEIEVAVTASSINFADVLVTFGRYQTLDGRQPQLGTDFAGVVSAVGPGVSELKVGDRVGGMSPNGC 1512
                                     589***************99999855555555589************************98777777 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.38   4.9e+02       2      48 ..    1561    1609 ..    1560    1615 .. 0.79
   2 ?   10.2   0.1   0.00023       0.3       4      75 ..    1768    1839 ..    1766    1865 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                                     EEEEESTTSHHHHHHHHHCTTTSEEEEEE..-TTT--TTSHHHHHHHHH CS
                  RmlD_sub_bind    2 kilvtGanGqlGseLakqlaeeglevlal..treeldltdaeavaellk 48  
                                     k+l+  a+G +G++ ++ ++++g++++a+  ++++ dl +   ++++ +
  gi|121637448|ref|YP_977671.1| 1561 KVLIHSATGGVGQAAIAIARAAGAQIYATagNEKRRDLLRDMGIEHVYD 1609
                                     6899999999***999999999999999954566778877777776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00023
                                     EEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHH CS
                  RmlD_sub_bind    4 lvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaay 75  
                                     ++tG+ G lG  La+++a++g+  + l++++   ++a +  el++++  dvvv+++   + D a     aa 
  gi|121637448|ref|YP_977671.1| 1768 IITGGLGGLGLFLAEKMANAGAGRIVLSSRSQPSQKALETIELVRAIGSDVVVECGDIAQPDTADRLVTAAT 1839
                                     79*************************99999999999999*********************9987655554 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.015        19      18      26 ..     881     889 ..     881     890 .. 0.88
   2 ?    3.4   0.0     0.052        67       4      20 ..    1863    1881 ..    1862    1885 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                    HHHHHHHHH CS
                           PPTA  18 aWnyRrwll 26 
                                    +Wn+Rr ll
  gi|121637448|ref|YP_977671.1| 881 TWNHRRLLL 889
                                    5******99 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.052
                                     HHHHHHHH-..TT-CHHHH CS
                           PPTA    4 ltekliekd..pkNYsaWn 20  
                                      t++lie+d  pk Y aW+
  gi|121637448|ref|YP_977671.1| 1863 ITDELIERDwaPKAYGAWQ 1881
                                     5899**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 1.09u 0.29s 00:00:01.38 Elapsed: 00:00:00.49
# Mc/sec: 12969.83
//
Query:       gi|121637449|ref|YP_977672.1|  [L=165]
Description: polyketide synthase associated protein papA4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1095.22
//
Query:       gi|121637450|ref|YP_977673.1|  [L=584]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-73  246.9   0.0    3.5e-73  246.6   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.0     2e-77   3.5e-73       2     422 ..      11     472 ..      10     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 2e-77
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                    +e+a  +p+  a+++        g  +tlT+++l++r  ++A  Lr+ G++ gdr +il+p+++e+vv +l++l+aG ++
  gi|121637450|ref|YP_977673.1|  11 RERASVHPNGAAITYidyeqdwAGVAETLTWSQLYRRMLNVAEPLRHVGAT-GDRAVILAPQGIEYVVGFLGALQAGRIA 89 
                                    68899999999998888999998899*********************8987.99************************** PP

                                    EEEET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                    AMP-binding  75 vplnp...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                    vpl     +   e+   +l+d+ + v++  + s +++ ++e+a+ ++ +++  +++ d l+  +++ +++  +       
  gi|121637450|ref|YP_977673.1|  90 VPLPVphaGAHDERTISVLSDTSPAVIL--TTSGAVDDVRECAQPQPGQSAPSIVELDLLDLDSRQRSRS--PG----A- 160
                                    ***876668899****************..7777789999**9988888888888876666553333333..22....2. PP

                                    CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHCSC.CTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                    AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk...letrfk.lkeddvvlsilplahifglilelllalls 227
                                    ++   +  ++ay++YTSG+T +P GVm+s +n+ an  ++    + ++ + + +d +v+s+lpl+h++gl l+ ++++l+
  gi|121637450|ref|YP_977673.1| 161 RPTGRDTPETAYLQYTSGSTRTPAGVMVSNKNVFANFEQIVadfFAPEGGvVPPDLTVVSWLPLYHDMGLLLGAIMPILA 240
                                    2234566678**************************9*998777666655366699************************ PP

                                    T-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHH CS
                    AMP-binding 228 Gatvvllpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffral 306
                                    G   vl ++  +l+ p+++++l+++ + t+ ag++ ++e  +++ + +  ++  dl +++++l g e++ p++l++f ++
  gi|121637450|ref|YP_977673.1| 241 GVPTVLTSPVGFLQrPARWIQLLARNGRTISAGPNFAFELAVRKTSDD-GMDGLDLAGVHTILNGSERVHPATLKRFAER 319
                                    ************666**************************9965555.35677************************** PP

                                    HTC......EEEEEEEEGGGSSECEE........................CHCTTTCTSTTS-BEE-TTEEEEEE-TTTS CS
                    AMP-binding 307 fge......evlegYGlTEttgvvtv........................lpleedkkklgsvGkplpgvevkivDeetg 356
                                    fg+      ++  +YG++E+t+ +++                        +p +++ + l s+G p + + v+ivD++t 
  gi|121637450|ref|YP_977673.1| 320 FGRfnfaaaALRPAYGMAEATVYIATrnvneppeivdfeseklpagqairCP-SGSGTPLVSYGVP-RSQLVRIVDPDTC 397
                                    ********99**************778889****999999997777766544.3444455566666.799********** PP

                                    CBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE..........TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 357 epvpdgeeGellvrgpgvmkgYlkkpeataeafds..........egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                     ++p+g +Ge++v+g +v++gY+ kpe+ +++f +          e   wlrTGD g++   G+l+i+gR+kdl+++
  gi|121637450|ref|YP_977673.1| 398 IECPQGSVGEIWVQGGNVASGYWHKPEESKRTFGArivtpsagtpE-ApWLRTGDSGFVS-GGELFIIGRIKDLLIV 472
                                    *********************************9889999999853.45**********9.8***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4042.71
//
Query:       gi|121637451|ref|YP_977674.1|  [L=367]
Description: alcohol dehydrogenase adh [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-25   89.0   0.3    3.3e-25   88.1   0.3    1.5  1  ADH_N           Alcohol dehydrogenase GroES-like domain
    2.4e-20   72.8   3.1    4.1e-20   72.1   3.1    1.3  1  ADH_zinc_N      Zinc-binding dehydrogenase
    0.00046   19.7   0.3    0.00068   19.2   0.3    1.2  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
      0.029   14.5   0.1       0.05   13.7   0.1    1.3  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.061   14.4   3.1       0.13   13.3   2.1    2.0  3  ADH_zinc_N_2    Zinc-binding dehydrogenase
        0.2   12.0   1.4       0.32   11.4   0.1    2.0  2  GHMP_kinases_C  GHMP kinases C terminal
       0.47    9.7   6.6          1    8.6   6.6    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.3   1.3e-28   3.3e-25       2     106 ..      31     147 ..      30     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.3e-28
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS...--TT-EEEE-SEEE-SSSHHHHTT-G CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkk...lkvGdrVvvepliscgeCaaCkegee 78 
                                    +++l++v+a+g+Cg+D + ++g  el   + +++GHE+vG+++++gp+ ++   ++ GdrV+ve+++sc +Ca+C+ ge+
  gi|121637451|ref|YP_977674.1|  31 DDALVRVEACGLCGTDHEQYTG--ELAGGFAFVPGHETVGTIAAIGPRAEQrwgVSAGDRVAVEVFQSCRQCANCRGGEY 108
                                    789******************9..7999**********************9999************************** PP

                                    GG-TTBEETTTS..........S-SSSBSE.EEECGGGE CS
                          ADH_N  79 nlCeeakllgvs..........ldGgfaey.vvvpekkl 106
                                    + C +++l +++          l+Gg+aey +++p++++
  gi|121637451|ref|YP_977674.1| 109 RRCVRHGLADMYgfipvdrepgLWGGYAEYqYLAPDSMV 147
                                    ***999999999999999************445556655 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   3.1   1.6e-23   4.1e-20       3     129 ..     193     325 ..     192     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.6e-23
                                    HHHHHHHHHHTT-.EEEEEE...SSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSC.SHHHHHHHH CS
                     ADH_zinc_N   3 GlaavqlAkalGa.eviavd...sseeklelakklGadevinykea.dlverikeltggegvdvvfecvG.sgatleaal 76 
                                    Gl+a ++Ak +Ga  v+++    +++++l+la+++Gad +++     d+v+++ e tg + +dvv+++++ ++a++ +a+
  gi|121637451|ref|YP_977674.1| 193 GLCAAAAAKGAGAgFVMVTGlgpRDADRLALAAQFGADLAVDV-AIdDPVAALTEQTG-GLADVVVDVTAkAPAAFAQAI 270
                                    99***********97777662224566****************.6669*********5.5**********99******** PP

                                    HCEEEEEEEEECSC...TSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  77 kllkpgGrlvvvGg...gkgeee.fdlrnlllkeksilGsllgslreefkealdlla 129
                                    +l++p G++vv G+   g+g  + f++  +++ke+++lG l+ +   ++++aldll+
  gi|121637451|ref|YP_977674.1| 271 ALARPAGTVVVAGTrgvGSG-APgFSPDVVVFKELRVLGALGVD-ATAYRAALDLLV 325
                                    **************984444.446********************.9*******9986 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   2.7e-07   0.00068      33     175 ..     183     325 ..     176     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-07
                    Glu_dehyd_C  33 salvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatY.vdsr.etpvdeipease.emdlvvEaTG 109
                                     + vlG G  GL a+a+ +    g+  v+ lg rd    ++ l ++ Ga   vd +  +pv  ++e++    d+vv+ T 
  gi|121637451|ref|YP_977674.1| 183 VVAVLGPGIRGLCAAAAAKGAGAGFVMVTGLGPRD--ADRLALAAQFGADLaVDVAiDDPVAALTEQTGgLADVVVDVTA 260
                                    678***********999998888887676666555..5666789****986245442578998877665157******** PP

                    Glu_dehyd_C 110 sakhafeaieala.pnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLa 175
                                    +a++af++  ala p+G ++ +G       +   g   + +v +   ++G+   ++++++aa+d L 
  gi|121637451|ref|YP_977674.1| 261 KAPAAFAQAIALArPAGTVVVAGTRGVG--SGAPGFSPDVVVFKELRVLGALGVDATAYRAALDLLV 325
                                    *****9765555439******9987655..3345555566677888888888888888888888775 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.9e-05      0.05      50     101 ..     229     287 ..     192     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                    SS.--S-BEBSSHHHHHHH....-SEEEE-S..-HHHHHHHHHHHHHTT-EEEE--SS- CS
                         DapB_N  50 lg.klgvavtddleevlek....advliDFT..tpeavlenlklalekgvklViGTTGl 101
                                     +  ++va+ d +++++e+    adv++D T  +p+a+ + ++la  +g+ +V GT G+
  gi|121637451|ref|YP_977674.1| 229 ADlAVDVAIDDPVAALTEQtgglADVVVDVTakAPAAFAQAIALARPAGTVVVAGTRGV 287
                                    44467888888888888888889********66699999999999999********996 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.5   1.4e+04      47      73 ..     181     205 ..     171     224 .. 0.53
   2 ?   13.3   2.1   5.1e-05      0.13       2      55 ..     228     285 ..     227     328 .. 0.76
   3 ?   -1.7   0.0       2.3   5.8e+03      30      53 ..     310     333 ..     298     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.5
                                    EEEEE----.S-EEE-CHHHCTTT-EE CS
                   ADH_zinc_N_2  47 Grlvsiggpplsaallkpakkrkgrsv 73 
                                    G++v ++gp ++   l  a+ +kg++ 
  gi|121637451|ref|YP_977674.1| 181 GDVVAVLGPGIRG--LCAAAAAKGAGA 205
                                    7777777653222..222222333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.1e-05
                                    T-SEEEETT.STTHH...HHH-TT-EEEEEES-H.HHHH.HHHHHHEEEEEEEEE---- CS
                   ADH_zinc_N_2   2 GAdevidyr.tedfe...aatggegvDvvldtvg.gealleaslkvlpggGrlvsiggp 55 
                                    GAd ++d   ++ ++   ++tgg   Dvv+d ++  +a++++++++ ++ G++v+ g +
  gi|121637451|ref|YP_977674.1| 228 GADLAVDVAiDDPVAaltEQTGG-LADVVVDVTAkAPAAFAQAIALARPAGTVVVAGTR 285
                                    78888877777777777688855.5*******999555558888777888***998843 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                                    -H.HHHH.HHHHHHEEEEEEEEE-- CS
                   ADH_zinc_N_2  30 vg.gealleaslkvlpggGrlvsig 53 
                                    +g  +++++a+l++l   Gr++  +
  gi|121637451|ref|YP_977674.1| 310 LGvDATAYRAALDLLVS-GRYLFAS 333
                                    55544455888888855.7775544 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013      0.32      25      60 ..     180     215 ..     153     215 .. 0.88
   2 ?   -1.9   0.1       1.8   4.6e+03      29      59 ..     259     290 ..     256     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                 GHMP_kinases_C  25 lkavvgilppeleellealselGalgaklsGaGgGp 60 
                                    + +vv++l p ++ l+ a+ + Ga ++++  +G+Gp
  gi|121637451|ref|YP_977674.1| 180 PGDVVAVLGPGIRGLCAAAAAKGAGAGFVMVTGLGP 215
                                    67799******************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                 GHMP_kinases_C  29 vgilppeleellealselG.algaklsGaGgG 59 
                                    +++ p ++ +++ +++ +G +  a+  G G+G
  gi|121637451|ref|YP_977674.1| 259 TAKAPAAFAQAIALARPAGtVVVAGTRGVGSG 290
                                    66778889999999999998555555555446 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.6   0.00039         1      22      77 ..     174     233 ..     164     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00039
                                    EETCB---EEE.EESTSHHHHHHHHHHHHTT-...EEEEEESSHHHHHHHHH.TTTCECEE CS
                    AlaDh_PNT_C  22 gvpgvepakvl.viGgGvaGlqAiatakglga...kVtvlDvrparleqles.lgakfvev 77 
                                    ++p+++p+ v+ v+G G+ Gl A+a+akg ga    Vt l  r a +  l + +ga  + v
  gi|121637451|ref|YP_977674.1| 174 TIPETKPGDVVaVLGPGIRGLCAAAAAKGAGAgfvMVTGLGPRDADRLALAAqFGAD-LAV 233
                                    7899999987559******************94333444444444333333346666.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:01.03
# Mc/sec: 1072.11
//
Query:       gi|121637452|ref|YP_977675.1|  [L=188]
Description: hypothetical protein BCG_1583 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   60.5   0.0    2.4e-16   59.5   0.0    1.5  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   1.3e-20   2.4e-16       1      84 [.      40     122 ..      40     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.3e-20
                                    HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHH CS
                            CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAl 80 
                                    p l+r++++l   +l+ +g Ld ++reL+++++ ++++c+y++  H r A   Gv+++++  v ++    +++pa++a+l
  gi|121637452|ref|YP_977675.1|  40 PRLARTFNDLLATMLW-HGTLDSRLRELVIMRIGWLTDCDYEWTQHWRVASGLGVSADDLLGVRDWQGYNGFGPAEQAVL 118
                                    7899************.*************************************************************** PP

                                    HHHH CS
                            CMD  81 aaae 84 
                                    aa++
  gi|121637452|ref|YP_977675.1| 119 AATD 122
                                    9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1270.57
//
Query:       gi|121637453|ref|YP_977676.1|  [L=144]
Description: hypothetical protein BCG_1584c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-12   46.6   0.4    4.2e-12   46.3   0.4    1.2  1  4HBT      Thioesterase superfamily
    5.5e-10   39.5   0.0    6.5e-10   39.3   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
    0.00067   20.0   0.1    0.00072   19.9   0.1    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.4     7e-16   4.2e-12       4      78 ..      59     134 ..      56     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 7e-16
                                    B-HHHHHHHHHHHHHHHHHHTTST..TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                           4HBT   4 vhgGvylallDeaagaalrslggr..gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                     hgGv+++ +D+a++aa++s +++  g+++++v++si++  +++   +l+++ar  r  +   ++e++ +d dg  v
  gi|121637453|ref|YP_977676.1|  59 FHGGVIASVMDTAGAAAAWSNHDFdrGTRAATVAMSIQYTGAAKRC-DLLCHARTARRRKELTFTEITATDPDGNIV 134
                                    6*********************************************.8***********************999866 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.1e-13   6.5e-10       9     130 ..      20     141 ..      12     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.1e-13
                                    HHHHSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHH..S-TTEEEEEEEEEEEE-S CS
                        DUF4442   9 vslkaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeat..lpdthrwipkgmevdYla 86 
                                    ++ + P++g++g+ +e+ ep+ +++rl+ r ++ N  + +H++ i++++++a  + a  +  + ++ r    +m+++Y+ 
  gi|121637453|ref|YP_977676.1|  20 LMPRTPFIGGLGIVFERYEPDDVVIRLPFRTDLTNDGTYFHGGVIASVMDTAGAAAAWSNhdFDRGTRAATVAMSIQYTG 99 
                                    45589**********************************************98877755422777**************7 PP

                                    -.--S-EEEEEE-TTS-TT--EEEEEEEEEEETTE.EEEEEEEEE CS
                        DUF4442  87 k.atgdltavaelepedvgekeelvvevevrdekgeevvraeitl 130
                                      ++ dl ++a++ ++   +ke    e++++d +g+ v++a  t 
  gi|121637453|ref|YP_977676.1| 100 AaKRCDLLCHARTARR---RKELTFTEITATDPDGNIVAHAVQTY 141
                                    73689******99865...355677799999*9999999998775 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.2e-07   0.00072     157     245 ..      54     140 ..      12     143 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-07
                                    TTS-SSHHHHHHHHTT-..-GGGGTSS-......SB--EEEEEEEE-S--S-...EEEEEE-SEEETTEEEEEEEEE-TT CS
                         4HBT_3 157 eggepahlaaLaylsDsf.pvprvhglrldaeasgwmpsldltiyfhrepaedeWllleaetpwagdgrglvearlwded 235
                                    ++g+ +h   +a ++D    +++ +++ +d ++   ++++ ++i+   +  +   ll+ a+t + +   +++e +  d d
  gi|121637453|ref|YP_977676.1|  54 NDGTYFHGGVIASVMDTAgAAAAWSNHDFD-RG-TRAATVAMSIQYTGAA-KRCDLLCHARTARRRKELTFTEITATDPD 130
                                    344455555666666664343444444443.22.3566777777776643.34567777777777777777777777777 PP

                                    S-EEEEEEEE CS
                         4HBT_3 236 GrlvAtstQe 245
                                    G++vA ++Q+
  gi|121637453|ref|YP_977676.1| 131 GNIVAHAVQT 140
                                    7777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1047.74
//
Query:       gi|121637454|ref|YP_977677.1|  [L=375]
Description: hypothetical protein BCG_1585 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-56  191.4   0.1      4e-56  190.8   0.1    1.2  1  NMO            Nitronate monooxygenase
    4.8e-10   39.0   3.3    7.8e-10   38.3   3.3    1.2  1  FMN_dh         FMN-dependent dehydrogenase
    1.1e-05   24.7   0.0    0.00017   20.7   0.2    2.0  2  IMPDH          IMP dehydrogenase / GMP reductase domain
     0.0067   15.7   0.2      0.013   14.8   0.2    1.5  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
  ------ inclusion threshold ------
      0.035   13.4   1.0      0.053   12.8   1.0    1.2  1  ThiG           Thiazole biosynthesis protein ThiG
      0.044   13.3   0.1      0.071   12.6   0.1    1.4  1  His_biosynth   Histidine biosynthesis protein
          1    8.5   4.6          6    5.9   4.6    2.0  1  Glu_synthase   Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.1   1.6e-59     4e-56      26     331 .]      23     361 ..       3     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 1.6e-59
                            NMO  26 rLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdk.Pfgvnlflpkkdaadra.....ekykkeleeaa....leln 95 
                                    + +aavsnaGg G+l++  +++ rl+ e++ +++ t   P+gv ++lp k  + ++     +++++ ++e        l 
  gi|121637454|ref|YP_977677.1|  23 DVVAAVSNAGGFGILGAVAHSPKRLESELTWIEEHTGGkPYGVDVLLPPKYIGAEQggidaQQARELIPEGHrtfvDDLL 102
                                    789*********************************877********999887776677767778877765411114566 PP

                            NMO  96 ieegvr....................fyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvear 155
                                    +++g++                    ++  ++v   +  +++  ++g+p++++v+r ++ +v++  +++++++ar  +a+
  gi|121637454|ref|YP_977677.1| 103 VRYGIPavtdrqrsssagglhispkgYQPLLDVAFAHDIRLIASALGPPPPDLVERAHNHDVLVAALAGTAQHARRHAAA 182
                                    778888*******************888889999999******************************************* PP

                            NMO 156 GaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdak 234
                                    G D +++qG eaGGh+G  ev+   ++ Lvp+v+dav+  Pv+AaGGi ++r++aaaLalGA+gv  g+ +L t+e++++
  gi|121637454|ref|YP_977677.1| 183 GVDLIVAQGTEAGGHTG--EVA---TMVLVPEVVDAVSpTPVLAAGGIARGRQIAAALALGAEGVWCGSVWLTTEEAETP 257
                                    *****************..775...9****************************************************** PP

                            NMO 235 dahkkklleaklddteltsavsGrpaRalatelleelee.akiatlalpeahelakk....iraalvea..gnteegllw 307
                                    +++k k l a   dt+  +   G+paR l+t ++ e ++     +l++p +  l       i +a+++     +e   ++
  gi|121637454|ref|YP_977677.1| 258 PVVKDKFLAATSSDTVRSRSLTGKPARMLRTAWTDEWDRpDSPDPLGMPLQSALVSDpqlrINQAAGQPgaKARELATYF 337
                                    **************************************9767789999999988877788899999997556788899** PP

                            NMO 308 agqgidrldkiisvkeLiesLvee 331
                                    +gq+ ++ld++ s++ ++ ++vee
  gi|121637454|ref|YP_977677.1| 338 VGQVVGSLDRVRSARSVVLDMVEE 361
                                    ******************999975 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   3.3     3e-13   7.8e-10     226     305 ..     172     250 ..     169     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3e-13
                                    SHHHHHHHHHTTESEEEE..--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 226 taedakraveaGvdgivv..SNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                    ta+ a+r ++aGvd iv      GG+   g +at+   pe+v+av   ++vl+ gGi rG  ++ AlalGA++v+ G  +
  gi|121637454|ref|YP_977677.1| 172 TAQHARRHAAAGVDLIVAqgTEAGGHT--GEVATMVLVPEVVDAVS-PTPVLAAGGIARGRQIAAALALGAEGVWCGSVW 248
                                    578899999******998445678876..999*************8.9*****************************988 PP

                                    HH CS
                         FMN_dh 304 ly 305
                                    l 
  gi|121637454|ref|YP_977677.1| 249 LT 250
                                    76 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.024        61      53     136 ..      27     205 ..      21     215 .. 0.69
   2 !   20.7   0.2   6.8e-08   0.00017     206     248 ..     215     257 ..     194     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.024
                                    HHHHTTSEEEE-SS.S-HHHHHHHHHHHHTS................................................. CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx................................................. RF
                          IMPDH  53 alareGgigvihkn.lsieeqaeevkkvkrs................................................. 82 
                                    a++++Gg g++     s+++  +e++ + ++                                                 
  gi|121637454|ref|YP_977677.1|  27 AVSNAGGFGILGAVaHSPKRLESELTWIEEHtggkpygvdvllppkyigaeqggidaqqarelipeghrtfvddllvryg 106
                                    56667777777654145555566677777667777777777777777777777777777777777777777777777777 PP

                                    ...............................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHT CS
                                    ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  83 ...............................................pnaakdekgrllvgaavgvkedalervkalvea 115
                                                                                   +   + +++ +lv+a  g+     +++++ ++a
  gi|121637454|ref|YP_977677.1| 107 ipavtdrqrsssagglhispkgyqplldvafahdirliasalgppppDLVERAHNHDVLVAALAGTA----QHARRHAAA 182
                                    7777777777777777777777777777777778888888888877434445566777777777777....466666789 PP

                                    T-SEEEEE..-STSSSHHHHHHH CS
                                    xxxxxxxx..xxxxxxxxxxxxx RF
                          IMPDH 116 gvdvlvvd..sahghsekvleav 136
                                    gvd++v     a gh+ +v ++v
  gi|121637454|ref|YP_977677.1| 183 GVDLIVAQgtEAGGHTGEVATMV 205
                                    99999987224667877777665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6.8e-08
                                    CT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 206 agvpviaDGGikysgdivkAlaaGadavmlGsllagteEspge 248
                                       pv+a GGi   ++i+ Ala+Ga+ v +Gs+   teE+ + 
  gi|121637454|ref|YP_977677.1| 215 SPTPVLAAGGIARGRQIAAALALGAEGVWCGSVWLTTEEAETP 257
                                    3589***********************************9875 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   4.9e-06     0.013     140     193 ..     154     206 ..     153     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                  PEP_hydrolase 140 elikkAheldllttayvfneeearamaeaGadvivahlGlttggsigaktalsl 193
                                    +l+++Ah++d+l  a + +++ ar+ a+aG+d+iva+ G  +gg++g   ++ l
  gi|121637454|ref|YP_977677.1| 154 DLVERAHNHDVLVAALAGTAQHARRHAAAGVDLIVAQ-GTEAGGHTGEVATMVL 206
                                    5799*****************************9986.9999999998766554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   2.1e-05     0.053     136     205 ..     175     246 ..     162     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHTT-SEBEEBSSSTTS----S-HHHH.HHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESH CS
                           ThiG 136 larrleevGcaavmPlaapiGsglGllnkeal.kiiieea.kvPvivDAGigspsdaaqamelGadavllnt 205
                                     arr   +G+  ++  ++  G   G +++++l   +++ +   Pv+   Gi +  ++a+a+ lGa++v   +
  gi|121637454|ref|YP_977677.1| 175 HARRHAAAGVDLIVAQGTEAGGHTGEVATMVLvPEVVDAVsPTPVLAAGGIARGRQIAAALALGAEGVWCGS 246
                                    699999*******************77665542678888878*************************97655 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.8e-05     0.071      55     106 ..     197     249 ..     159     273 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                    CTTHHHHHHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                   His_biosynth  55 kegreanldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaav 106
                                    ++g+ a   lv e++++v+  pv   GGI +  +++++l +ga+ v  g++ +
  gi|121637454|ref|YP_977677.1| 197 HTGEVATMVLVPEVVDAVSpTPVLAAGGIARGRQIAAALALGAEGVWCGSVWL 249
                                    34555555566666666666666666666666666666666666444444433 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.6    0.0024         6     277     307 ..     219     249 ..     155     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0024
                                    EEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                   Glu_synthase 277 liadGglktgadvvkalalGAdavgigtaal 307
                                    + a+Gg+  g++++ alalGA+ v  g++ l
  gi|121637454|ref|YP_977677.1| 219 VLAAGGIARGRQIAAALALGAEGVWCGSVWL 249
                                    6799********************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2806.87
//
Query:       gi|121637455|ref|YP_977678.1|  [L=225]
Description: transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-20   70.9   1.2    1.8e-19   69.3   1.2    1.9  1  TetR_N     Bacterial regulatory proteins, tetR family
    4.5e-06   27.4   3.1    4.5e-06   27.4   3.1    2.4  3  TetR_C_15  Tetracyclin repressor-like, C-terminal domain
    3.5e-05   24.0   0.4    9.2e-05   22.7   0.4    1.7  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   1.2     3e-23   1.8e-19       1      47 []      24      70 ..      24      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 3e-23
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Il+aA  +fa++G++attv++IAk+AG++ g++Y+yF+sK++L++al
  gi|121637455|ref|YP_977678.1| 24 ILAAAKIVFAHKGFHATTVADIAKQAGLAYGLIYWYFDSKDDLFHAL 70
                                   9*******************************************996 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.1   1.2e+04      84      99 ..      10      27 ..       4      33 .. 0.53
   2 ?    0.6   0.1      0.16   9.3e+02      81     102 ..      66      88 ..      60      90 .. 0.81
   3 !   27.4   3.1   7.5e-10   4.5e-06       1     103 [.      96     203 ..      96     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                      TetR_C_15 84 laleedp..adrealiae 99
                                   +a+++++  ++r+++ a 
  gi|121637455|ref|YP_977678.1| 10 RAVSDEDksQRRDEILAA 27
                                   344444435555555544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                      TetR_C_15  81 llhlaleedp.adrealiaelkr 102
                                    l+h++++ ++ a r+++ ael+r
  gi|121637455|ref|YP_977678.1|  66 LFHALMAGEEeALRAHVAAELAR 88 
                                    78888888888999999999987 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 7.5e-10
                      TetR_C_15   1 pLeealdalvdallaahrenpalrrvlleeapslgel..elvealeqriaealaalL..arrrpelppedlelaafvave 76 
                                    pL+++l+a v+a ++++++++a  ++l+++a++lg+   e+    ++r+++ ++a++  a+rr e++++  ++aa+++ +
  gi|121637455|ref|YP_977678.1|  96 PLRALLQAAVQATFEFFETDKATVKLLFRDAYALGGRfeEHLGGIYERFIDDIEAVVvaAQRRGEVVEAPSRMAAYTLAA 175
                                    9******************************9999888777899***********8644789999999************ PP

                      TetR_C_15  77 aveallhlaleedp.adrealiaelkrl 103
                                    +v +l h+ l+ d+  +++++ +  + l
  gi|121637455|ref|YP_977678.1| 176 LVGQLAHRRLNTDDnVTAAQVADFVVSL 203
                                    ************9988888777655555 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   1.5e-08   9.2e-05       6     114 .]      99     208 ..      94     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
                                    HHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHH CS
                      TetR_C_24   6 erLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmln 85 
                                    + L+a+v+a  e++ ++++++ +l+r+  aL +   e++    +++ + +++++ +++++ge+ ++  ++aa+++  ++ 
  gi|121637455|ref|YP_977678.1|  99 ALLQAAVQATFEFFETDKATVKLLFRDAYALGGRFEEHLGGIYERFIDDIEAVVVAAQRRGEVVEAPSRMAAYTLAALVG 178
                                    5699*************************************************************************998 PP

                                    CHH.HC--TTSSS-HHHHHHHHHHHHHH-S CS
                      TetR_C_24  86 wvy.rWyrpdGplspeeiadqyadlllrgl 114
                                    +++ r  + d  ++++++ad +++l+l+gl
  gi|121637455|ref|YP_977678.1| 179 QLAhRRLNTDDNVTAAQVADFVVSLVLDGL 208
                                    875267899999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1536.33
//
Query:       gi|121637456|ref|YP_977679.1|  [L=78]
Description: hypothetical protein BCG_1587 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 563.32
//
Query:       gi|121637457|ref|YP_977680.1|  [L=1041]
Description: isoleucyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.8e-180  599.3   0.0   8.8e-180  598.9   0.0    1.1  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      1e-23   83.9   0.0    1.8e-23   83.2   0.0    1.3  1  Anticodon_1   Anticodon-binding domain of tRNA
    3.4e-18   65.6   0.3    1.3e-06   27.4   0.0    3.9  3  tRNA-synt_1g  tRNA synthetases class I (M)
    0.00013   21.5   0.0    0.00088   18.7   0.0    2.0  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.9   0.0    2e-183  8.8e-180       2     597 ..      23     653 ..      22     657 .. 0.94

  Alignments for each domain:
  == domain 1  score: 598.9 bits;  conditional E-value: 2e-183
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                    +++ W  +d+f+++ + ++ ++e++++dgPP+++G +H+Gh l+  +kdiv ry++m+G++v++++GwD++Gl+ e +ve
  gi|121637457|ref|YP_977680.1|  23 VLDYWSRDDTFRASIARRDGAPEYVFYDGPPFANGLPHYGHLLTGYVKDIVPRYRTMRGYKVERRFGWDTHGLPAELEVE 102
                                    6899**************************************************************************** PP

                    tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkk 161
                                    ++lg+++k++ + +g ++f++ +r+ + +y++e++  v+r  ++vDfd++y+Tld  ++e+v+++f++l dkgl y+g +
  gi|121637457|ref|YP_977680.1| 103 RQLGITDKSQIEAMGIAAFNDACRASVLRYTDEWQAYVTRQARWVDFDNDYKTLDLAYMESVIWAFKQLWDKGLAYEGYR 182
                                    ******************************************************************************** PP

                    tRNA-synt_1 162 lvnwstklktalselEv.....eykdkkdalihvafpladkee......vklviaTTtPeTllgdtavavnpeldyv... 227
                                    +++++++ +t+ls+ E       y+  +d++++v f++ +++       ++l ++TTtP+Tl++++avav p++ yv   
  gi|121637457|ref|YP_977680.1| 183 VLPYCWRDETPLSNHELrmdddVYQSRQDPAVTVGFKVVGGQPdngldgAYLLVWTTTPWTLPSNLAVAVSPDITYVqvq 262
                                    *****************66555566777**********55544455667****************************988 PP

                    tRNA-synt_1 228 itkeklilaeallkslvkke.sekkiledergkeLegkevelpl.....vnrkipiiaddyvdkeaGtGvVkiaPahded 301
                                    + +++++laea+l + +++  +e  +l ++rg+eL g ++ +p+       ++++++a+d+v+++ GtG+V++aPa++ed
  gi|121637457|ref|YP_977680.1| 263 AGDRRFVLAEARLAAYARELgEEPVVLGTYRGAELLGTRYLPPFayfmdWPNAFQVLAGDFVTTDDGTGIVHMAPAYGED 342
                                    889*************999967779*******************99988889**************************** PP

                    tRNA-synt_1 302 Dyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekg........lllkaekiehsvpfcerskkpii 373
                                    D  v++  ++ +++++d++g+++ ++a+++g++vfda+ ++v++lk +         +l+++e+ eh +p+c+r  +p+i
  gi|121637457|ref|YP_977680.1| 343 DMVVAEAVGIAPVTPVDSKGRFDVTVADYQGQHVFDANAQIVRDLKTQSgpaavngpVLIRHETYEHPYPHCWRCRNPLI 422
                                    *********************************************987434444445799******************** PP

                    tRNA-synt_1 374 yrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelk.el 451
                                    yr++++Wfvrv++++d +++ +++++++p+  k+ ++ +wl+ ++dW iSR+r+WG++ip++ s++    + r ++  +l
  gi|121637457|ref|YP_977680.1| 423 YRSVSSWFVRVTDFRDRMVELNQQITWYPEHvKDGQFGKWLQGARDWSISRNRYWGTPIPVWKSDDPA--YPRIDVYgSL 500
                                    ******************************98999*****************************9966..7766665144 PP

                    tRNA-synt_1 452 vagreeeeaekkalekeakdkl.......kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGl 524
                                     + +    ++ ++l++  +d+l        +++ ++++++dvlDvWF+Sgs+p+++++yp+e+ + ++  +p d+++e +
  gi|121637457|ref|YP_977680.1| 501 DELERDFGVRPANLHRPYIDELtrpnpddPTGRSTMRRIPDVLDVWFDSGSMPYAQVHYPFENLDWFQGHYPGDFIVEYI 580
                                    45455567888999********999998888999********************************************** PP

                    tRNA-synt_1 525 DiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgr 597
                                     ++rgW+++l +l++al+++  fk+ + hg+v+  +G+KmSKsl N++d ++v ++ g da+R++l+ s+ +r
  gi|121637457|ref|YP_977680.1| 581 GQTRGWFYTLHVLATALFDRPAFKTCVAHGIVLGFDGQKMSKSLRNYPDVTEVFDRDGSDAMRWFLMASPILR 653
                                    *******************************************************************998876 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   3.9e-27   1.8e-23       1     148 [.     701     839 ..     701     844 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.9e-27
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    dr+il++l+ l  + +e++e y++  a+ +l +f +++l +wy++ +++r++ e+a+       +l++vle  +rl aP 
  gi|121637457|ref|YP_977680.1| 701 DRYILAKLAVLRDDLSESMEVYDIPGACEHLRQF-TEALTNWYVRRSRSRFWAEDADAI----DTLHTVLEVTTRLAAPL 775
                                    9********************************7.999**************9987555....***************** PP

                    Anticodon_1  81 mPfitEelwqreeeelgkkesimlaewpekaeel..ekeleeeevellkeivkairklrselkikpssel 148
                                    +P itE +w    + l +++s++l +wp +++ l  +++l  ++++ ++++++a+ +lr+ +k+  + +l
  gi|121637457|ref|YP_977680.1| 776 LPLITEIIW----RGLTRERSVHLTDWP-APDLLpsDADL-VAAMDQVRDVCSAASSLRKAKKLRVRLPL 839
                                    *********....99*************.56555666666.88*******************99887775 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     3e-10   1.3e-06       8      72 ..      53     118 ..      50     205 .. 0.75
   2 !   17.2   0.1   3.7e-07    0.0017     167     239 ..     412     485 ..     403     492 .. 0.82
   3 !   15.3   0.0   1.4e-06    0.0065     271     356 ..     566     648 ..     540     656 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3e-10
                                    B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHHHHHHHH CS
                   tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeelvekvhe 72 
                                    p+ang +H Ghll+    Di+ Ry+ +rg++v    g D+hG p el+ e++ g+t +  +e +  
  gi|121637457|ref|YP_977680.1|  53 PFANGLPHYGHLLTGYVKDIVPRYRTMRGYKVERRFGWDTHGLPAELEVERQlGITDKSQIEAMGI 118
                                    89***********9999******************************9875437777766655544 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.7e-07
                                    ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..T CS
                   tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..g 239
                                    p++  + +  ++++ +++f ++ +f++++ e  ++ +   e+    +  +wl+   +d++isr+  wG p+P  +
  gi|121637457|ref|YP_977680.1| 412 PHCWRCRNPLIYRSVSSWFVRVTDFRDRMVELNQQITWYPEHVKDGQFGKWLQG-ARDWSISRNRYWGTPIPvwK 485
                                    8999999999*********************99555533445555688999976.9****************542 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.4e-06
                                    GGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE-.-EEE--------------HHHHHHHH-HHH CS
                   tRNA-synt_1g 271 kwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvahe.yltvegkKlSkSrgvvvkakealerldadl 349
                                     ++ ++   +   +v+ ig+    F t+   a+ l  +  + k+ vah+  l ++g+K+SkS ++  +++e+ +r  +d+
  gi|121637457|ref|YP_977680.1| 566 WFQGHY---PGDFIVEYIGQTRGWFYTLHVLATALFDRPAF-KTCVAHGiVLGFDGQKMSKSLRNYPDVTEVFDRDGSDA 641
                                    455555...33456777777777777776666655555444.455555516789************************** PP

                                    HHHHHHH CS
                   tRNA-synt_1g 350 lRYylaa 356
                                    +R++l+a
  gi|121637457|ref|YP_977680.1| 642 MRWFLMA 648
                                    *****97 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.13   5.7e+02      21      49 ..      57      85 ..      46      86 .. 0.87
   2 !   18.7   0.0     2e-07   0.00088     230     282 ..     595     648 ..     591     652 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
                                   S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                   tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                      h Gh  +  + Di+ r+  ++gY+v+
  gi|121637457|ref|YP_977680.1| 57 GLPHYGHLLTGYVKDIVPRYRTMRGYKVE 85
                                   578***********************995 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2e-07
                                    HHHSSS--EEE.EEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                   tRNA-synt_1e 230 eaafdkqlvky.flhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                    +a+fd++  k    h  +l ++g+kmsksL+n+  + +v+ +  + ++R++l+ 
  gi|121637457|ref|YP_977680.1| 595 TALFDRPAFKTcVAHGIVLGFDGQKMSKSLRNYPDVTEVFDRDGSDAMRWFLMA 648
                                    68888555555055666789*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1041 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 5966.76
//
Query:       gi|121637458|ref|YP_977681.1|  [L=463]
Description: DNA polymerase IV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-35  121.9   0.0    4.9e-35  120.7   0.0    1.6  2  IMS       impB/mucB/samB family
    2.8e-19   70.0   0.1    1.9e-18   67.3   0.1    2.1  2  IMS_C     impB/mucB/samB family C-terminal domain
    1.5e-07   31.4   0.0    3.3e-07   30.2   0.0    1.7  1  IMS_HHH   IMS family HHH motif
     0.0065   16.2   2.5      0.036   13.8   1.2    2.3  2  DUF3553   Protein of unknown function (DUF3553)


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   1.1e-38   4.9e-35       1     149 [.       4     151 ..       4     152 .. 0.96
   2 ?   -3.0   0.0       1.4   6.3e+03     100     121 ..     248     268 ..     235     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 1.1e-38
                                    EEETTHHHHHHHHHT.T-TTS-EEEEET....TEEEEE-HHHHTTT--TTSBHHHHHTTHTT.-EEEEEE-HHHHHHHHH CS
                            IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsekrgiviavsyeArayGvkrgmrikeakklcpd.livvkvdlekyrraskk 79 
                                    +DmdaF+asve++ +p L+g+Pv v++    rg+v+ +syeArayG +++m++++a++l    ++v++++   y  as++
  gi|121637458|ref|YP_977681.1|   4 LDMDAFFASVEQLTRPTLRGRPVLVGGLGG-RGVVAGASYEARAYGARSAMPMHQARRLIGVtAVVLPPRGVVYGIASRR 82 
                                    7**************************977.6*****************************559**************** PP

                                    HHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                            IMS  80 ileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                    ++++++   +p ve++s+DEa+++  +l+   +++++ ++++lr+++ +e+gl +s+G +s k +AK+as
  gi|121637458|ref|YP_977681.1|  83 VFDTVRGL-VPVVEQLSFDEAFAEPPQLAGAVAEDVETFCERLRRRVRDETGLIASVGAGSGKQIAKIAS 151
                                    ********.66*************999888888888*********************************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                    EEEE-HHHHHHHH-SHHHHHHH CS
                            IMS 100 ayldltgleelaesegaalake 121
                                    + +dlt +e+l+e+   ++a+ 
  gi|121637458|ref|YP_977681.1| 248 FAVDLTTMEQLHEAI-DSIAEH 268
                                    456888888777773.666554 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.39   1.8e+03      15      45 ..     101     132 ..      92     155 .. 0.70
   2 !   67.3   0.1   4.2e-22   1.9e-18       2     112 ..     233     343 ..     232     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.39
                          IMS_C  15 ktfpepydesk...lkkelreLaeelarrLrdkg 45 
                                      f+e   +++   + + ++ ++e+l rr rd+ 
  gi|121637458|ref|YP_977681.1| 101 EAFAE--PPQLagaVAEDVETFCERLRRRVRDET 132
                                    44554..222234566678899999999988875 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 4.2e-22
                          IMS_C   2 vearpepksissektfpe.pydesklkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreil 79 
                                    v +r e k+is+e tf+   ++ ++l++ +   ae ++ rL ++g+ artit+kl++sd +  +rsat+p+pt d+++++
  gi|121637458|ref|YP_977681.1| 233 VVERAEAKQISAESTFAVdLTTMEQLHEAIDSIAEHAHQRLLRDGRGARTITVKLKKSDMStLTRSATMPYPTTDAGALF 312
                                    67899************94444555999999*********999999**********999889****************** PP

                          IMS_C  80 eaalkLlrrlide.pglpirligvsasnlvekae 112
                                      a++Ll    d  +  pirl+gv++s+l++ ++
  gi|121637458|ref|YP_977681.1| 313 TVARRLL---PDPlQIGPIRLLGVGFSGLSDIRQ 343
                                    *******...33358***************6554 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   7.5e-11   3.3e-07       2      32 .]     165     195 ..     164     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.5e-11
                        IMS_HHH   2 ddvkefLwplpitkipGiGgklgekLeklGi 32 
                                    ++++++L+ lp++ ++GiG++ +ekL+ lGi
  gi|121637458|ref|YP_977681.1| 165 AEEQALLSGLPVRRLWGIGPVAEEKLHRLGI 195
                                    6789**************************9 PP

>> DUF3553  Protein of unknown function (DUF3553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.098   4.4e+02      10      27 ..     175     192 ..     173     196 .. 0.71
   2 !   13.8   1.2   7.9e-06     0.036      11      36 ..     385     410 ..     380     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.098
                        DUF3553  10 PkqpdWGlGqVqSaiagr 27 
                                    P +  WG+G V     +r
  gi|121637458|ref|YP_977681.1| 175 PVRRLWGIGPVAEEKLHR 192
                                    56677****997665555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.9e-06
                        DUF3553  11 kqpdWGlGqVqSaiagrvtvnFenaG 36 
                                    ++p+ G G Vq+a  g vtv+Fe +G
  gi|121637458|ref|YP_977681.1| 385 AHPELGHGWVQGAGHGVVTVRFETRG 410
                                    46899*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3104.19
//
Query:       gi|121637459|ref|YP_977682.1|  [L=326]
Description: L-aparaginase ansA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-44  150.3   0.0    6.6e-44  149.7   0.0    1.2  1  Asparaginase    Asparaginase, N-terminal
    3.7e-19   69.0   1.5    2.8e-18   66.2   0.7    2.5  3  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   7.4e-48   6.6e-44       2     170 ..      15     180 ..      14     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 7.4e-48
                                    EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEE CS
                   Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfV 80 
                                    + v++tGGTi+ ++ ++g  l+p+  +++l++ l+      ++e+ +l+ +dSs++tpadw ++ +a++ea+++ +dg+V
  gi|121637459|ref|YP_977682.1|  15 LTVITTGGTISTTAGPDG-VLRPTHCGATLIAGLD---MDSDIEVVDLMALDSSKLTPADWDRIGAAVQEAFRGgADGVV 90 
                                    789**************8.9***999999999993...33489*****************************777***** PP

                                    EE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGG.TTSECEEEETTEEEETTTEEE- CS
                   Asparaginase  81 vlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasse.riagvlvvfngkllranrvtKv 159
                                    ++hGTDTl++tA  L+l+ ++ ++pvvltG++++++++++Dgp+Nl dAl+vaa+++ r  gvlv f+g++l+    +Kv
  gi|121637459|ref|YP_977682.1|  91 ITHGTDTLEETALWLDLTYAG-SRPVVLTGAMLSADAPGADGPANLRDALAVAADPAaRDLGVLVSFGGRVLQPLGLHKV 169
                                    *********************.**********************************99********************** PP

                                    BSSSSS-EEET CS
                   Asparaginase 160 htssldaFesp 170
                                       +l  F   
  gi|121637459|ref|YP_977682.1| 170 ANPDLCGFAGE 180
                                    99999888654 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.13   1.2e+03      73     109 ..      34      70 ..       7      74 .. 0.75
   2 ?   -1.4   0.0       0.3   2.7e+03      16      30 ..      78      92 ..      75     101 .. 0.81
   3 !   66.2   0.7   3.2e-22   2.8e-18       1     109 [.     210     320 ..     210     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                                    ...HHHHHTEEE-TT--HHHHHHHHHHHCTT---HHH CS
                 Asparaginase_C  73 agkelerlgvisaddmtpeaarikLmlllgkgldpae 109
                                     ++  + + +i++ dm     ++ Lm l +++l+pa+
  gi|121637459|ref|YP_977682.1|  34 LRPTHCGATLIAGLDMDSDIEVVDLMALDSSKLTPAD 70 
                                    4566788999999999999999999999999888886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                                   HHHHHHTT--EEEEE CS
                 Asparaginase_C 16 lkallkkgakGvvle 30
                                   ++++++ ga+Gvv+ 
  gi|121637459|ref|YP_977682.1| 78 VQEAFRGGADGVVIT 92
                                   66778889****996 PP

  == domain 3  score: 66.2 bits;  conditional E-value: 3.2e-22
                                    -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT...-EEEEEESSSBS-----H.....HH CS
                 Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakarg...ivvvatsqcpsgsvsnseyeagkel 77 
                                    rV++++++pg d+  ++a++++ga++vvle+ G+Gn+  a++e +++  + g   +v+ +++++   +v ++ y+ g++l
  gi|121637459|ref|YP_977682.1| 210 RVDIVAVYPGSDAVAMDACVAAGARAVVLEALGSGNAGAAVIEGVRRHCRDGsdpVVIAVSTRVAGARVGAG-YGPGHDL 288
                                    8***********************************************988655578888888888888888.89***** PP

                                    HHHTEEE-TT--HHHHHHHHHHHCTT---HHH CS
                 Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgkgldpae 109
                                     ++g++  + + p +ar++Lm +l+ +   a+
  gi|121637459|ref|YP_977682.1| 289 VEAGAVMVPRLPPSQARVLLMAALAANSPVAD 320
                                    *************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1705.39
//
Query:       gi|121637460|ref|YP_977683.1|  [L=202]
Description: lipoprotein signal peptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-30  105.0   2.9    4.3e-30  104.8   2.9    1.0  1  Peptidase_A8  Signal peptidase (SPase) II
  ------ inclusion threshold ------
      0.064   13.6   0.0       0.15   12.3   0.0    1.7  1  SH3_3         Bacterial SH3 domain


Domain annotation for each model (and alignments):
>> Peptidase_A8  Signal peptidase (SPase) II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   2.9   4.7e-34   4.3e-30       2     141 .]      40     178 ..      39     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 4.7e-34
                   Peptidase_A8   2 allllllDqltKllvvenlkte.svevipgffkltyveNrgaafgllesgakrkllillslvvilllivlllkkkkkskl 80 
                                    a+++l lD +tK+++v+ l     v++i + + +t+v+N+gaaf++ ++   +++l+l++  v+++++++ ++    s +
  gi|121637460|ref|YP_977683.1|  40 AVVVLTLDIVTKVVAVQLLPPGqPVSIIGDTVTWTLVRNSGAAFSMATG--YTWVLTLIATGVVVGIFWMGRRL--VSPW 115
                                    799*********9997777766789999*****************7443..46999999988888898877655..479* PP

                   Peptidase_A8  81 lrialalilgGalGNliDrlly......gkVvDfldfsleliefpvFNvADvaitvGvilliiallf 141
                                    ++++l++ilgGa+GNl+Dr+++      g+VvDfl++      +pvFNvAD  ++ G+ill+i ++f
  gi|121637460|ref|YP_977683.1| 116 WALGLGMILGGAMGNLVDRFFRapgplrGHVVDFLSVG----WWPVFNVADPSVVGGAILLVILSIF 178
                                    ********************96666666********86....47*****************998876 PP

>> SH3_3  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05      0.15      19      42 ..      58      79 ..      54      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                          SH3_3 19 lpyGekVevleetgggeWykvrtd 42
                                   lp+G++V+++++t    W  vr++
  gi|121637460|ref|YP_977683.1| 58 LPPGQPVSIIGDTVT--WTLVRNS 79
                                   89*************..****665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.59
# Mc/sec: 1036.13
//
Query:       gi|121637461|ref|YP_977684.1|  [L=308]
Description: hypothetical protein BCG_1592 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.5   0.0    4.7e-29  101.5   0.0    1.9  2  PseudoU_synth_2  RNA pseudouridylate synthase
    0.00012   21.7   0.0    0.00026   20.6   0.0    1.6  1  S4               S4 domain


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.2   1.8e+03      38      56 ..      42      60 ..      26      73 .. 0.75
   2 !  101.5   0.0   5.2e-33   4.7e-29       2     160 .]      90     243 ..      89     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                PseudoU_synth_2 38 kkelklvhRLDkatsGlll 56
                                   + +  + ++ D+ +sG ll
  gi|121637461|ref|YP_977684.1| 42 ELNGVPAGKSDRLVSGALL 60
                                   5556678999******998 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 5.2e-33
                PseudoU_synth_2   2 lvvvnKPagvpvqpeakdgsekekettatssrae...eekkelklvhRLDkatsGllllAksseaanklakafeerkvrK 78 
                                    +v+v+KPa v+ +        ++ +  a+++ +    +  +++++vhRLD++tsG++++A s+ a   l +af+ r+v K
  gi|121637461|ref|YP_977684.1|  90 IVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRIttsGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVDK 169
                                    78999999999999998333344444444444443338899*************************************** PP

                PseudoU_synth_2  79 kYlalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhl 158
                                    +Y alv+g+p +++g+i+++i +   ++    + a +++g+ + t++ +l+ +      ++sl+ ++letGr+hQiRvh+
  gi|121637461|ref|YP_977684.1| 170 RYHALVQGHPDPSSGTIDAPIGR---HRGHEWKFAITKNGRHSLTHYDTLEAF-----VAASLLDVHLETGRTHQIRVHF 241
                                    ***********************...5555555678889**************.....********************** PP

                PseudoU_synth_2 159 aa 160
                                    aa
  gi|121637461|ref|YP_977684.1| 242 AA 243
                                    96 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.9e-08   0.00026       1      44 [.      15      56 ..      15      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-08
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-T CS
                             S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkp 44
                                   +R d+ larl+  s r  A  l e+G V +NG ++   s+r+ +
  gi|121637461|ref|YP_977684.1| 15 MRVDTGLARLLGLS-RTAAAALAEEGAVELNGVPAG-KSDRLVS 56
                                   8*******777776.*******************99.6666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1686.47
//
Query:       gi|121637462|ref|YP_977685.1|  [L=197]
Description: lipoprotein lprI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   50.5   0.0    2.8e-13   49.6   0.0    1.4  1  MliC      Membrane-bound lysozyme-inhibitor of c-type lysozym
    0.00011   22.8   6.2    0.00018   22.1   6.2    1.3  1  LprI      Lysozyme inhibitor LprI


Domain annotation for each model (and alignments):
>> MliC  Membrane-bound lysozyme-inhibitor of c-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   3.1e-17   2.8e-13       1      63 [.     125     190 ..     125     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.1e-17
                                    EEECCCE.EEEEEEE.CTTEEEEEEECCTEEEEEEEEETSSSEEEEE..TEEEEEETTEEEEEETTT CS
                           MliC   1 YqCdsga.evtvtyi.agdpsfavlrlggktltLaqavSaSGarYsa..nyewWtkGdeAtLtwggg 63 
                                    Y+C  +  ++t++++ + dp++avl+++g++++   ++S+SGarY    ++e+W++++e++L  +g+
  gi|121637462|ref|YP_977685.1| 125 YRCPTQDgPLTAQFYnQFDPKTAVLNWKGDQVIVFVELSGSGARY-GrqGIEYWEHQGEVRLDFHGA 190
                                    99*99999*************************************.667*************98876 PP

>> LprI  Lysozyme inhibitor LprI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   6.2     2e-08   0.00018      10     103 .]      42     110 ..      35     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-08
                                    H..HHHHHHHHHHHHHHHHHHH.HHHHHHHHHTT....HHHHHHHHHHHHHHHHHHHHHHHTTTS-TTSHHH....HHHH CS
                           LprI  10 tqanqCasaalkaadaeLnkay.kalkeekekkavssearkaLkdaqraWikyRdaeCalakspakegsgaggsmeplay 88 
                                     q+  C +++l + d +L++ay +al++         +  +aL++aq  W   Rda +            ++     +  
  gi|121637462|ref|YP_977685.1|  42 VQQLVCHDRQLTSLDHRLSTAYqQALAH---------RRSAALEAAQSSWTMLRDACA------------QD-----TDP 95 
                                    33389*****************555553.........33469**************55............44.....777 PP

                                    HHHHHHHHHHHHHHH CS
                           LprI  89 asClarltqeRiaeL 103
                                     +C  ++ q+R+ +L
  gi|121637462|ref|YP_977685.1|  96 RTCVQEAYQTRLVQL 110
                                    888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1090.51
//
Query:       gi|121637463|ref|YP_977686.1|  [L=136]
Description: hemoglobin glbN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-35  119.7   0.0    8.5e-35  119.5   0.0    1.0  1  Bac_globin   Bacterial-like globin
  ------ inclusion threshold ------
      0.024   14.5   0.0       0.04   13.8   0.0    1.4  1  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Bac_globin  Bacterial-like globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.0   9.5e-39   8.5e-35       1     120 [.      14     127 ..      14     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 9.5e-39
                                    -HHHHHTHHHHHHHHHHHHHHHHHT-CCCCCCGGGTTSSHHHHHHHHHHHHHHHTTSSSHHHHHHSS-.HHHHHTTS--B CS
                     Bac_globin   1 tlydaiGgeatveelvdrfYervdedeeealseifsgtdlegsreklveFlvqalgGPelYverrGhPrlrkrHapfeit 80 
                                    ++yd+iGg++++e +v++fY rv +d++  ls++fsgt++++ + k+veF+++algGPe Y+   G+P ++++H++++it
  gi|121637463|ref|YP_977686.1|  14 SIYDKIGGHEAIEVVVEDFYVRVLADDQ--LSAFFSGTNMSRLKGKQVEFFAAALGGPEPYT---GAP-MKQVHQGRGIT 87 
                                    69**************************..*******************************6...***.*********** PP

                                    HHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHC CS
                     Bac_globin  81 aaerdawlkhlaeAleetgvssedreeklellealahaaq 120
                                    +++++ ++ hla+Al+++gv+se+ +e+l +++ la++++
  gi|121637463|ref|YP_977686.1|  88 MHHFSLVAGHLADALTAAGVPSETITEILGVIAPLAVDVT 127
                                    ***********************************99886 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-06      0.04      31      77 ..      23      68 ..      21     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                                   HCHHHHHHHHHHHHCTSHHHHHHHCHHCHHHHHHHHHHHHHHHCCCS CS
                    Protoglobin 31 alipavvdafYekllsfpetarifetssqierlkdflksyllklfsg 77
                                   ++i+ vv++fY ++l  ++++ +f+   ++ rlk  + +++   + g
  gi|121637463|ref|YP_977686.1| 23 EAIEVVVEDFYVRVLADDQLSAFFSG-TNMSRLKGKQVEFFAAALGG 68
                                   689**********************9.9*******999988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 940.49
//
Query:       gi|121637464|ref|YP_977687.1|  [L=341]
Description: fatty acyl-CoA reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-46  157.5   0.3    3.7e-46  157.1   0.3    1.1  1  adh_short        short chain dehydrogenase
    1.5e-31  109.7   0.2    2.3e-31  109.2   0.2    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.7e-13   50.9   0.5    2.8e-13   50.2   0.5    1.3  1  KR               KR domain
    0.00025   21.0   0.5    0.00057   19.8   0.5    1.5  1  NAD_binding_10   NAD(P)H-binding
    0.00057   19.4   0.3     0.0064   16.0   0.3    2.3  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0033   17.4   0.0     0.0061   16.5   0.0    1.4  1  Ribosomal_S6e    Ribosomal protein S6e
     0.0038   16.8   0.8     0.0065   16.1   0.8    1.3  1  LDcluster4       SLOG cluster4 family
  ------ inclusion threshold ------
      0.079   13.1   0.0       0.19   11.9   0.0    1.7  1  Abi_C            Abortive infection C-terminus
        0.1   12.4   0.1       0.22   11.3   0.1    1.5  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.3   1.8e-49   3.7e-46       1     188 [.      54     246 ..      54     250 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 1.8e-49
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT...TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee...gakalaiqvDvtdreevealvekavkklgk 77 
                                    kvvl+tG+ssGIG a ak++a++G +vv+v+r+ e+le+va+ +++    g +a+++++D++d++++  + +++  +lg+
  gi|121637464|ref|YP_977687.1|  54 KVVLITGGSSGIGAAAAKKIAEAGGTVVLVARTLENLENVANDIRAIrgnGGTAHVYPCDLSDMDAIAVMADQVLGDLGG 133
                                    89*******************************************99988999*************************** PP

                                    ESEEEE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                      adh_short  78 ldvLvnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                    +d+L+nNAG    +s + s     +++r++++N+ g+++l+  ++p m +++ G+IvnvsSv  + + + + aY AsKaa
  gi|121637464|ref|YP_977687.1| 134 VDILINNAGRsiRRSLELSYDRIHDYQRTMQLNYLGAVQLILKFIPGMRERHFGHIVNVSSVGVQTRAPRFGAYIASKAA 213
                                    **********54444444445556699***************************************************** PP

                                    HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmak 188
                                    +++l ++l+ e   +++r ++v+ +lv+T+m  
  gi|121637464|ref|YP_977687.1| 214 LDSLCDALQAETVHDNVRFTTVHMALVRTPMIS 246
                                    ******************************975 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.2   1.1e-34   2.3e-31       3     183 ..      62     249 ..      60     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.1e-34
                                    TTSHHHHHHHHHHHTT-EEEEEESSGGH....HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea....kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnna 77 
                                     sgIG+a+Ak++ae+G +vvl+ +  e+    +++++++  ++g++ v++cD +d ++++ ++++v  ++g++Dil+nna
  gi|121637464|ref|YP_977687.1|  62 SSGIGAAAAKKIAEAGGTVVLVARTLENlenvANDIRAIRGNGGTAhVYPCDLSDMDAIAVMADQVLGDLGGVDILINNA 141
                                    59********************99988851123344444445554458******************************** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    g + + + ++      +++r+++ n  ++++l+  ++p m+e+  g ivn+ssvg +   p   ay a+Kaal +l+ +l
  gi|121637464|ref|YP_977687.1| 142 GRSIRRSLELSYDRIHDYQRTMQLNYLGAVQLILKFIPGMRERhfGHIVNVSSVGVQTRAPRFGAYIASKAALDSLCDAL 221
                                    *****444444446689*********************777777************************************ PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGST CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgik 183
                                     +e  ++++R  +v+  +++T++ s  +
  gi|121637464|ref|YP_977687.1| 222 QAETVHDNVRFTTVHMALVRTPMISPTT 249
                                    ***********************87655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.5   1.4e-16   2.8e-13       2     168 ..      55     226 ..      54     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.4e-16
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeepp 81 
                                    ++litGG  g+G + a+ +ae g  ++vl++R+ ++ e+ ++ i++++ +g + +v+++D+sd da++ + +++  + + 
  gi|121637464|ref|YP_977687.1|  55 VVLITGGSSGIGAAAAKKIAEAGG-TVVLVARTLENLENVANDIRAIRGNGGTAHVYPCDLSDMDAIAVMADQVLGDLGG 133
                                    579******************996.68999***9999******************************************* PP

                                    --EEEE---------TT..T--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR  82 ikGvihaAgvlrdklle..emtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaf 155
                                    +   i+ Ag +  + le       d+++ ++    Ga +L   + +    ++  ++v +SS++  + ++  ++Y a  a 
  gi|121637464|ref|YP_977687.1| 134 VDILINNAGRSIRRSLElsYDRIHDYQRTMQLNYLGAVQLILKFIPgmreRHFGHIVNVSSVGVQTRAPRFGAYIASKAA 213
                                    *********8776665411566789************998765544466699999************************* PP

                                    HHHHHHHHHHHHH CS
                             KR 156 lDalaeyrrsqgl 168
                                    lD+l++  +++  
  gi|121637464|ref|YP_977687.1| 214 LDSLCDALQAETV 226
                                    *****99887765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.5   2.9e-07   0.00057       1     126 [.      60     222 ..      60     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.......CT.TTCEEEE--TT-CCHHHHHHT.......T-SEEE CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele.......ae.eglevvegdvtdvedlaealk.......gadaVv 65 
                                    G++ ++G +++k+++++g  +v++++R+ e l++++        +   ++v   d++d +++a   +       g+d+ +
  gi|121637464|ref|YP_977687.1|  60 GGSSGIGAAAAKKIAEAG-GTVVLVARTLENLENVAndirairGNgGTAHVYPCDLSDMDAIAVMADqvlgdlgGVDILI 138
                                    8999*************6.79*******9999855422222223324667778899988887766666667777889988 PP

                                    ES---TCC.......HHHH..................HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH.HCCHH CS
                 NAD_binding_10  66 salggggk.......deeg..................aknivdaakeagvkRfvlvsaigvgdevpgefgewnk.ellka 119
                                     ++g++ +       d                       + +  ++e +  ++v vs++gv+ ++p+ fg +   ++  +
  gi|121637464|ref|YP_977687.1| 139 NNAGRSIRrslelsyD--RihdyqrtmqlnylgavqlILKFIPGMRERHFGHIVNVSSVGVQTRAPR-FGAYIAsKAALD 215
                                    8887766655666551..0455566778888997777777799*******************76665.554433133333 PP

                                    HHHHHHH CS
                 NAD_binding_10 120 ylaakra 126
                                     l +  +
  gi|121637464|ref|YP_977687.1| 216 SLCDALQ 222
                                    3333444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   3.2e-06    0.0064       1      82 [.      56     150 ..      56     243 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.2e-06
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES.-STTTTCHHCHHC........EEEE--TT-HHHHH....HHHHHH.T-S CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldr.lssasntarledl........elveldltdrsale....rlfkee.qpd 66 
                                    +l+tG++  iG+a +k+++e+g +v+ ++r l++ +n a++ ++        +++ +dl d +a++    +++ +  ++d
  gi|121637464|ref|YP_977687.1|  56 VLITGGSSGIGAAAAKKIAEAGGTVVLVARtLENLENVANDIRAirgnggtaHVYPCDLSDMDAIAvmadQVLGDLgGVD 135
                                    79********************99666655055555555444449******************77611114444445666 PP

                                    EEEE--S---HHHHHH CS
                      Epimerase  67 avihlAavggvaasse 82 
                                    + i+ A+  ++++s e
  gi|121637464|ref|YP_977687.1| 136 ILINNAG-RSIRRSLE 150
                                    6666655.33444444 PP

>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.1e-06    0.0061      22      77 ..      29      84 ..      13      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                                   HCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                  Ribosomal_S6e 22 klrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77
                                   + r ++ +++ + v+g  l++  kg v+ itggs   G    +++ ++g + +L++
  gi|121637464|ref|YP_977687.1| 29 RYRPFYLRNLLDAVQGRNLNDAVKGKVVLITGGSSGIGAAAAKKIAEAGGTVVLVA 84
                                   5789999********************************99999999888777765 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   3.3e-06    0.0065      31      81 ..      52     100 ..      48     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                     LDcluster4  31 kegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiy 81 
                                    k ++vl+tGg +G+  aa+k + eagG++v + +  ++ e++++  di  +
  gi|121637464|ref|YP_977687.1|  52 KGKVVLITGGSSGIGAAAAKKIAEAGGTVVLVARTLENLENVAN--DIRAI 100
                                    5679*************************988888777666666..66555 PP

>> Abi_C  Abortive infection C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.5e-05      0.19      28      54 ..      83     109 ..      68     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                          Abi_C  28 ikqilsglasivqglgeLRNkggtaHG 54 
                                    + + l +l+++++ + ++R +ggtaH 
  gi|121637464|ref|YP_977687.1|  83 VARTLENLENVANDIRAIRGNGGTAHV 109
                                    678999********************5 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.22      37      57 ..      49      70 ..      17      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                   --..-SEEEEESTSSHHHHHHH CS
                Eno-Rase_NADH_b 37 ek.gpkkvLviGaStGYGLAsr 57
                                   +  + k vL+ G+S+G G A+ 
  gi|121637464|ref|YP_977687.1| 49 DAvKGKVVLITGGSSGIGAAAA 70
                                   222469************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2492.66
//
Query:       gi|121637465|ref|YP_977688.1|  [L=32]
Description: hypothetical protein BCG_1596 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   12.7   0.0      0.093   12.4   0.0    1.2  1  TGBp3     Triple gene block 3


Domain annotation for each model (and alignments):
>> TGBp3  Triple gene block 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-06     0.093      22      36 ..       5      19 ..       1      20 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-06
                          TGBp3 22 sssegCvivITGesv 36
                                    ++++ ++vITG+sv
  gi|121637465|ref|YP_977688.1|  5 KPNNQTTVVITGASV 19
                                   678999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 230.87
//
Query:       gi|121637466|ref|YP_977689.1|  [L=231]
Description: ketoacyl reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-31  106.9   0.0    1.1e-30  106.6   0.0    1.1  1  adh_short     short chain dehydrogenase
    9.5e-20   71.2   0.0    1.1e-19   70.9   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    0.00066   19.6   0.0     0.0011   18.9   0.0    1.4  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.9e-34   1.1e-30      29     188 ..       2     160 ..       1     166 [. 0.96

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.9e-34
                                    EEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHH CS
                      adh_short  29 vvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseeewerviev 107
                                    +v+r+ e+l e+a++l++e    + ++++D++d ++  +l ++   + + +  L n AG   sg f el  ++  + + +
  gi|121637466|ref|YP_977689.1|   2 LVARRRERLDELADQLRQEhCVGVEVLPLDLADTQARAQLADRL--RSDAIAGLCNSAGFGTSGRFWELPFARESEEVVL 79 
                                    6899**************99889*********************..7799***********************999999* PP

                                    HTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                      adh_short 108 NltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdma 187
                                    N  ++++lt+a+lp m+k+ +G++ n++S+ag++p + +a+YsA+Ka+v  +++++++el+ tg++v+a++PG+v T+ a
  gi|121637466|ref|YP_977689.1|  80 NALALMELTHAALPGMVKRGAGAVLNIASIAGFQPIPYMAVYSATKAFVLTFSEAVQEELHGTGVSVTALCPGPVPTEWA 159
                                    *****************************************************************************987 PP

                                    H CS
                      adh_short 188 k 188
                                    +
  gi|121637466|ref|YP_977689.1| 160 E 160
                                    5 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.8e-23   1.1e-19      27     212 ..       7     184 ..       1     199 [. 0.83

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.8e-23
                                    SGGHHHHHHHHHHHT..TSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTH CS
                   adh_short_C2  27 neeakkrveelaeel..gaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnly 104
                                    +e++++ +++l +e+  g evl++D +d+++ ++l+++++++   + +l+n+ag+ ++  g+f e++ +   + +  n+ 
  gi|121637466|ref|YP_977689.1|   7 RERLDELADQLRQEHcvGVEVLPLDLADTQARAQLADRLRSD--AIAGLCNSAGFGTS--GRFWELPFARESEEVVLNAL 82 
                                    333344455555543113446******************987..6*************..******************** PP

                                    HHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGS CS
                   adh_short_C2 105 slfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgi 182
                                    +l+ l++aalp ++k+g g+++n++s+++ + +p  ++y+a+Ka +  ++ ++  el   g+ v a +pgp+ T+ a+ +
  gi|121637466|ref|YP_977689.1|  83 ALMELTHAALPgMVKRGaGAVLNIASIAGFQPIPYMAVYSATKAFVLTFSEAVQEELHGTGVSVTALCPGPVPTEWAEIA 162
                                    ***********8888889*******************************************************9987644 PP

                                    TTHHHHHHHHHHHSTTSS-B-HHHHHHHHH CS
                   adh_short_C2 183 kgfdelleelearaplgrlgtpeevaeaal 212
                                    +       + + ++pl + ++p++vaeaa+
  gi|121637466|ref|YP_977689.1| 163 S-------AERFSIPLAQ-VSPHDVAEAAI 184
                                    3.......4445678877.88888887764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.9e-07    0.0011      30     165 ..       2     137 ..       1     151 [. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                                    EE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHH CS
                             KR  30 llsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqv 108
                                    l++R+   +e+ ++l ++l++   + vev+++D++d +a ++l ++++++  +i+G  ++Ag+   + + e+  ++  + 
  gi|121637466|ref|YP_977689.1|   2 LVARR---RERLDELADQLRQEhCVGVEVLPLDLADTQARAQLADRLRSD--AIAGLCNSAGFGTSGRFWELPFARESEE 76 
                                    56666...455567889998873559*********************955..5*************99999987665554 PP

                                    HTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHHH CS
                             KR 109 lapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalaeyrrs 165
                                    +     ++  L ++  +    +    ++ ++Siag+   +  a Y+a+ af+ ++ e  ++
  gi|121637466|ref|YP_977689.1|  77 VVLNALALMELTHAALPgmvkRGAGAVLNIASIAGFQPIPYMAVYSATKAFVLTFSEAVQE 137
                                    44444555555444443376678889999********************999888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1690.86
//
Query:       gi|121637467|ref|YP_977690.1|  [L=75]
Description: hypothetical protein BCG_1598 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 602.74
//
Query:       gi|121637468|ref|YP_977691.1|  [L=143]
Description: hypothetical protein BCG_1599 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-24   84.5   0.5    8.8e-24   84.4   0.5    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.5   4.9e-28   8.8e-24       1     141 [.       1     141 [.       1     143 [] 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.9e-28
                                    EEEEEEEEEESS-HHHHHHHHTTTTGGGGT..-TTEEEEECSE..STSSSTTTEEEEECCCS.SEEEEEEEEEETTTTEE CS
                Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprW..hpevarveleg..gggpargvegtvrvggr.gtvreelvevdpegrll 75 
                                    m++v+ s++++ +p++ w++vs ++++ +W  ++e  r+el++  g+g   +++g+ r++g+ ++v+++++++dp ++ +
  gi|121637468|ref|YP_977691.1|   1 MASVELSADVPISPQDTWDHVSELSELGEWlvIHEGWRSELPDqlGEGV--QIVGVARAMGMrNRVTWRVTKWDP-PHEV 77 
                                    789***************************9966777788988444444..889****9999999**********.**** PP

                                    EEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  76 syrivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkar 141
                                    ++++ + +++++y +t+tv p+ gg+ +  + e+ + +l+gp+ + aaa+avkgd+e++L++++++
  gi|121637468|ref|YP_977691.1|  78 AMTG-SGKGGTKYGVTLTVRPTKGGSALGLRLELGGRALFGPL-GSAAARAVKGDVEKSLKQFAEL 141
                                    ****.48********************9999999988999**8.7889**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1078.30
//
Query:       gi|121637469|ref|YP_977692.1|  [L=1184]
Description: DNA polymerase III subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-92  307.3   0.0    2.6e-91  305.8   0.0    1.7  2  DNA_pol3_alpha   Bacterial DNA polymerase III alpha NTPase do
    1.8e-61  206.3   0.0    2.6e-61  205.8   0.0    1.2  1  DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit f
    2.1e-46  158.3   0.0    3.8e-46  157.4   0.0    1.5  1  PHP              PHP domain
      1e-23   83.3   0.0    3.1e-23   81.8   0.0    1.9  1  HHH_6            Helix-hairpin-helix motif
    2.6e-06   27.3   0.0    8.9e-06   25.6   0.0    2.0  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.8   0.0   7.2e-95   2.6e-91       2     260 .]     320     590 ..     319     590 .. 0.95
   2 ?   -2.3   0.0      0.74   2.7e+03     142     216 ..     716     790 ..     710     797 .. 0.70

  Alignments for each domain:
  == domain 1  score: 305.8 bits;  conditional E-value: 7.2e-95
                                    HHHHHHHHHHHHHSTT---TTHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHTT--B-S--GGGGG-HHHHHTTS--- CS
                 DNA_pol3_alpha   2 yLrklveeglkerlkeelpeevkerlekElevIekmgfadyflivadlvkaakkkgilvGpgRGSaagslvayllgiTei 81 
                                    +Lr++v  gl++r++++ p+ ++er  +E++vI ++gf++yflivadl+++a++ gi+vGpgRGSaagslvay+lgiT+i
  gi|121637469|ref|YP_977692.1| 320 WLRHEVDAGLRRRFPAGPPDGYRERAAYEIDVICSKGFPSYFLIVADLISYARSAGIRVGPGRGSAAGSLVAYALGITDI 399
                                    89****************************************************************************** PP

                                    -HHHHT--HHHHS-TTS-------EEEEGGGHHHHHHHHHHHH-TTTEEEEEEEEE--HHHHHHHHHHH.H-GG.HHHHH CS
                 DNA_pol3_alpha  82 dPlkydllFerFlnpervsmPDiDidfekerreevidyvkekyGkenvaqiitfgtlaakaairdvgra.lglp.lkevd 159
                                    dP+ ++llFerFlnper+smPDiDidf+++rr e+++y+++k+G+++vaq+itfgt+++kaa++d +r+ +g p ++++d
  gi|121637469|ref|YP_977692.1| 400 DPIPHGLLFERFLNPERTSMPDIDIDFDDRRRGEMVRYAADKWGHDRVAQVITFGTIKTKAALKDSARIhYGQPgFAIAD 479
                                    ********************************************************************9677776899** PP

                                    HHHHTS---.SS..--.......GGGG-----SHHHHHHH-HHHHHHHHHHHTTTT-EEEEEEEEEEEEE-SS-GGGTS- CS
                 DNA_pol3_alpha 160 klaklipke.lg..it.......lekaleeekelkelieedeevkrlvelakkleglkrntgqHaaGvvispkeltdlvP 229
                                    +++k++p   ++  i+        ++ ++e++e++ lie+d++v++++++a++legl rn+g+Ha++v++s+++lt+ +P
  gi|121637469|ref|YP_977692.1| 480 RITKALPPAiMAkdIPlsgitdpSHERYKEAAEVRGLIETDPDVRTIYQTARGLEGLIRNAGVHACAVIMSSEPLTEAIP 559
                                    *******995223444666667778888889************************************************* PP

                                    EEE-TTT--EEESS-HHHHHTTT-EEEEEEE CS
                 DNA_pol3_alpha 230 lqkaekeeevvtqfdmedledlgllKlDfLG 260
                                    l+k+ ++++++t +d+ ++e++gllK+DfLG
  gi|121637469|ref|YP_977692.1| 560 LWKRPQDGAIITGWDYPACEAIGLLKMDFLG 590
                                    ******************************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.74
                                    HHHHHHHHHH-GGHHHHHHHHHTS---SS--GGGG-----SHHHHHH.H-HHHHHHHHHHHTTTT-EEEEEEEEEE CS
                 DNA_pol3_alpha 142 aairdvgralglplkevdklaklipkelgitlekaleeekelkelie.edeevkrlvelakkleglkrntgqHaaG 216
                                    + +r + ++ +++l+ +d l k++ k+++  lek++e  ++  +    + + +k l++++  + + + n + HaaG
  gi|121637469|ref|YP_977692.1| 716 QIMRIAQKVASYSLARADILRKAMGKKKREVLEKEFEGFSDGMQANGfSPAAIKALWDTILPFADYAFNKS-HAAG 790
                                    56677889999999999999999999977568888887444433333356667777777777777666665.5655 PP

>> DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.0   7.3e-65   2.6e-61       1     166 []     593     762 ..     593     762 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 7.3e-65
                                    HHHHHHHHHHHHHHHH-----GGG--S--HHHHHHHHHT--TTSTT--SHHHHHHHHHH---SHHHHHHHHHHSSHHHHH CS
                DNA_pol3_finger   1 tltiirralklikekkgkeidleeipleDkkvykllskgdtlGvfqlesrgmrqllkrlkPktfeDlvalvaLyRpgpvq 80 
                                    +ltii +a++++++++g+++dle++pl+Dk++y+ll++gdtlGvfql+++ mr+ll+r++P+ feD+va++aLyRpgp+ 
  gi|121637469|ref|YP_977692.1| 593 NLTIIGDAIDNVRANRGIDLDLESVPLDDKATYELLGRGDTLGVFQLDGGPMRDLLRRMQPTGFEDVVAVIALYRPGPMG 672
                                    79****************************************************************************** PP

                                    TTHHHHHHHHHTTSS----SSH....HHTTTTTTTTT---BHHHHHHHHHHHH---HHHHHHHHHHHHH--HHHHHHHHH CS
                DNA_pol3_finger  81 ggnvddyikrkngeekveyihp....eleeiLketygvivyQEqvmqiaqvlagfslgeAdllrramgkkkeeeleklke 156
                                    ++ ++dy++rkn++++++ ihp     l+eiL+etyg+ivyQEq+m+iaq++a +sl++Ad lr+amgkkk+e+lek+ e
  gi|121637469|ref|YP_977692.1| 673 MNAHNDYADRKNNRQAIKPIHPeleePLREILAETYGLIVYQEQIMRIAQKVASYSLARADILRKAMGKKKREVLEKEFE 752
                                    **********************88888999************************************************** PP

                                    HHHHHHHHTT CS
                DNA_pol3_finger 157 kfiegakeng 166
                                     f +g+++ng
  gi|121637469|ref|YP_977692.1| 753 GFSDGMQANG 762
                                    *******986 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.0   1.1e-49   3.8e-46       1     167 []      12     198 ..      12     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 1.1e-49
                                    EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse....... 73 
                                    +lH+Hteys+ldga++i+ +++++++lg++a+++TDhgn+fg+ efy+ a    kagikpiiG+eay+a++s+       
  gi|121637469|ref|YP_977692.1|  12 HLHNHTEYSMLDGAAKITPMLAEVERLGMPAVGMTDHGNMFGASEFYNSA---TKAGIKPIIGVEAYIAPGSRfdtrril 88 
                                    9*************************************************...8999*********************** PP

                                    .......................E....EHHHHHHHHHHHHH...........HHHHHHS..................TT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  74 .............kerpshltllaknqeGyknllkllskaylegf.yrkpridkellekhsegLivlsgclkGevfeald 139
                                                 +  ++hlt++a+n +G++nl+kl+s+a +eg+  +  r+d el+++h+eg+i+++gc +Gev++ l+
  gi|121637469|ref|YP_977692.1|  89 wgdpsqkaddvsgSGSYTHLTMMAENATGLRNLFKLSSHASFEGQlSKWSRMDAELIAEHAEGIIITTGCPSGEVQTRLR 168
                                    *********************************************9********************************** PP

                                    GGHHHHHHHHHHHHHHHC....T-EEEEEGC CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                            PHP 140 lieveekaeealeelakif...gdyiEints 167
                                    l++ +e a ea+ ++++i+   ++++E++++
  gi|121637469|ref|YP_977692.1| 169 LGQDRE-ALEAAAKWREIVgpdNYFLELMDH 198
                                    ******.999*******99*********987 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   8.6e-27   3.1e-23       1      88 [.     835     922 ..     835     924 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 8.6e-27
                          HHH_6   1 gvevlppdvnrSeadftveeedgairlGLaaikglgeaaaerivaeRekegpfksledlarrvds..lnkrqleaLakaG 78 
                                    g++vlppdvn+S+ +f     +++ir+GL+a++++g++++ +++++R+++g+f++++d ++++d   +nk++ e+L+kaG
  gi|121637469|ref|YP_977692.1| 835 GITVLPPDVNESGLNFASV--GQDIRYGLGAVRNVGANVVGSLLQTRNDKGKFTDFSDYLNKIDIsaCNKKVTESLIKAG 912
                                    89**************987..566****************************************99************** PP

                          HHH_6  79 aldslglnRr 88 
                                    a+dslg+ R+
  gi|121637469|ref|YP_977692.1| 913 AFDSLGHARK 922
                                    *******997 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2     8e+03      37      72 ..     113     148 ..     106     150 .. 0.79
   2 !   25.6   0.0   2.5e-09   8.9e-06       1      75 [.    1024    1100 ..    1024    1101 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                                    HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                tRNA_anti-codon  37 eeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                    e+at l + +k  ++   +G+++++ + + el++e 
  gi|121637469|ref|YP_977692.1| 113 ENATGLRNLFKLSSHASFEGQLSKWSRMDAELIAEH 148
                                    578888899999999999999999977778998876 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.5e-09
                                     EEEEEEEEEEE...EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                tRNA_anti-codon    1 VtvaGrvtsis...drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75  
                                     V+v G + s+     ++g   ++++l+D tg i+v++f+  ++++  ++  + vv v  +v  r+++ + l+++++++
  gi|121637469|ref|YP_977692.1| 1024 VRVGGILASVNrrvNKNGMPWASAQLEDLTGGIEVMFFPHTYSSYGADIVDDAVVLVNAKVAVRDDR-IALIANDLTV 1100
                                     67778888888878899999***********************************************.******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 7352.59
//
Query:       gi|121637470|ref|YP_977693.1|  [L=678]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-81  266.1 331.6    4.7e-12   45.6  20.7   13.3 13  Pentapeptide_2  Pentapeptide repeats (8 copies)
    3.2e-57  193.0  27.5    5.1e-57  192.4  27.5    1.3  1  PPE             PPE family
  ------ inclusion threshold ------
       0.76   10.1   6.5        1.4    9.2   6.5    1.4  1  WXG100          Proteins of 100 residues with WXG
        8.9    7.1  17.0       0.96   10.1  12.4    1.8  2  TPR_16          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  14.2   3.6e-08   0.00016       5      40 .]     189     224 ..     185     224 .. 0.85
   2 !   45.6  20.7   1.1e-15   4.7e-12       1      40 []     220     259 ..     220     259 .. 0.98
   3 !   39.5  27.9   8.4e-14   3.8e-10       1      39 [.     260     298 ..     260     299 .. 0.99
   4 !   27.8  38.7   3.8e-10   1.7e-06       1      40 []     300     339 ..     300     339 .. 0.98
   5 !   31.7  30.5   2.3e-11     1e-07       1      39 [.     335     373 ..     335     374 .. 0.97
   6 !   31.3  34.8   3.1e-11   1.4e-07       3      40 .]     379     416 ..     377     416 .. 0.97
   7 !   17.7   6.7   5.5e-07    0.0025      13      38 ..     433     458 ..     425     460 .. 0.70
   8 !   32.9  19.3   9.7e-12   4.3e-08       3      39 ..     453     489 ..     452     490 .. 0.98
   9 !   29.1  18.1   1.5e-10   6.7e-07       6      40 .]     490     524 ..     489     524 .. 0.94
  10 !   42.2  23.6   1.2e-14   5.4e-11       1      38 [.     515     552 ..     515     554 .. 0.97
  11 !   14.2  10.6   6.5e-06     0.029       6      32 ..     558     584 ..     553     585 .. 0.71
  12 !   18.0   5.6   4.4e-07     0.002      11      37 ..     596     622 ..     593     625 .. 0.55
  13 !   12.7   7.2     2e-05     0.091       9      38 ..     629     659 ..     626     661 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.6e-08
                 Pentapeptide_2   5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +l +G++ +G fNl sgN G +NlGs+N Gs ntGs
  gi|121637470|ref|YP_977693.1| 189 FLDLGNVTIGGFNLASGNLGLGNLGSFNPGSANTGS 224
                                    567899999999999999999999999999999995 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 1.1e-15
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtGs+N+G++N+G++NlGsgN+Gs+NlG gNtG++n+Gs
  gi|121637470|ref|YP_977693.1| 220 ANTGSVNLGNANIGDLNLGSGNIGSYNLGGGNTGDLNPGS 259
                                    6*************************************96 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 8.4e-14
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gNtG+lN+GsgN+G++NlG gN Gs+NlGsgNtG++n+G
  gi|121637470|ref|YP_977693.1| 260 GNTGTLNWGSGNIGSYNLGGGNLGSYNLGSGNTGDTNFG 298
                                    8*************************************9 PP

  == domain 4  score: 27.8 bits;  conditional E-value: 3.8e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gNtG+lN+G gNtG+ N G+gNtG+ N+G+gNtG++n+Gs
  gi|121637470|ref|YP_977693.1| 300 GNTGNLNVGGGNTGNSNFGFGNTGNVNFGNGNTGDTNFGS 339
                                    8**************************************6 PP

  == domain 5  score: 31.7 bits;  conditional E-value: 2.3e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+Gs+N+GsgN+Gf+N Gs N+G++N+G++N+G+g tG
  gi|121637470|ref|YP_977693.1| 335 TNFGSGNLGSGNIGFGNKGSHNIGFGNSGNNNIGFGLTG 373
                                    6************************************99 PP

  == domain 6  score: 31.3 bits;  conditional E-value: 3.1e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G lNsGsgN+Gf+N+G+gN+G+fN+G++N+G+gn+G+
  gi|121637470|ref|YP_977693.1| 379 FGALNSGSGNLGFGNSGNGNIGFFNSGNNNIGMGNSGN 416
                                    8************************************6 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 5.5e-07
                 Pentapeptide_2  13 tGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +Gf+N+G  +tG +N+G   tG +n+
  gi|121637470|ref|YP_977693.1| 433 SGFGNSGELSTGIGNSGQLSTGWFNS 458
                                    57777777777777777777777775 PP

  == domain 8  score: 32.9 bits;  conditional E-value: 9.7e-12
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    tG +Ns ++ tG+fN+G++NtG+fN+G+ NtG+gn+G
  gi|121637470|ref|YP_977693.1| 453 TGWFNSATTSTGWFNSGTTNTGWFNSGTTNTGIGNSG 489
                                    89**********************************9 PP

  == domain 9  score: 29.1 bits;  conditional E-value: 1.5e-10
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +N+ +g +G+fN+G +NtGsfN+Gs NtG++n+G+
  gi|121637470|ref|YP_977693.1| 490 GNLVTGSMGLFNSGHTNTGSFNAGSMNTGDFNSGN 524
                                    6888999**************************96 PP

  == domain 10  score: 42.2 bits;  conditional E-value: 1.2e-14
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +NtG++NsG++NtG fN+G+ NtG+fN+G+ NtG +n+
  gi|121637470|ref|YP_977693.1| 515 MNTGDFNSGNVNTGYFNSGNINTGFFNSGDLNTGLFNS 552
                                    5************************************7 PP

  == domain 11  score: 14.2 bits;  conditional E-value: 6.5e-06
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgN 32 
                                     NsG  +tG+ N+G +N G fN+G+ N
  gi|121637470|ref|YP_977693.1| 558 QNSGWLHTGTNNSGYANAGTFNSGFDN 584
                                    477777777777777777777777655 PP

  == domain 12  score: 18.0 bits;  conditional E-value: 4.4e-07
                 Pentapeptide_2  11 gNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    gN+G++N+G+ N G  N+G+  +G+ n
  gi|121637470|ref|YP_977693.1| 596 GNSGLANVGNYNAGIINVGDHLSGFRN 622
                                    555555555555555555555555544 PP

  == domain 13  score: 12.7 bits;  conditional E-value: 2e-05
                 Pentapeptide_2   9 GsgNt.GffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    G++N+ Gf+N G+   G+fN+Gs  +G+ n+
  gi|121637470|ref|YP_977693.1| 629 GTANIsGFVNAGTSISGFFNFGSLMSGFANF 659
                                    7777558888888888888888888888886 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4  27.5   1.1e-60   5.1e-57       1     157 [.       5     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 1.1e-60
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+nsal++aG+g+gp+laAa+aW+gLa +l saaa++++v+++la+++WqGp+saam+  aa y++WL++aaaqae
  gi|121637470|ref|YP_977693.1|   5 VLPPEINSALMFAGAGPGPMLAAASAWTGLAGDLGSAAASFSAVTSQLATGSWQGPASAAMTGVAASYARWLTTAAAQAE 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA qa+aa++a+eaAlaa+v+p  + anr +l++lva+n++Gqn+paIaa+ea ye+mwa+d+aam +Y+  ++a+
  gi|121637470|ref|YP_977693.1|  85 QAAGQAQAAVSAFEAALAATVHPGAVSANRGRLRSLVASNLLGQNAPAIAAVEAVYEQMWAADVAAMLGYHGEASAV 161
                                    *************************************************************************9997 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.5   0.00032       1.4       9      84 ..      24     100 ..      19     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00032
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   9 lrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                    + +aa++  + a++l ++ ++  a  ++l +++W+G a+ a  ++ + + + +++ +++ e+ + + ++a +afe a
  gi|121637470|ref|YP_977693.1|  24 MLAAASAWTGLAGDLGSAAASFSAVTSQLaTGSWQGPASAAMTGVAASYARWLTTAAAQAEQAAGQAQAAVSAFEAA 100
                                    88999999******************************************999999999999999999999999975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.8   1.3e+04      10      22 ..      35      47 ..      25      51 .. 0.63
   2 ?   10.1  12.4   0.00021      0.96       2      62 ..      79     141 ..      78     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.8
                         TPR_16 10 agdyddAaaalea 22
                                   agd   Aaa + a
  gi|121637470|ref|YP_977693.1| 35 AGDLGSAAASFSA 47
                                   3555555555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00021
                         TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq...grlaeAaalyraalr 62 
                                    a+a+a  +ag+ ++A+ a+eaal++  ++P a+ A  ++ +++ +    g  a+A+a+++a ++
  gi|121637470|ref|YP_977693.1|  79 AAAQAEQAAGQAQAAVSAFEAALAAT-VHPGAVSANRGRLRSLVASnllGQNAPAIAAVEAVYE 141
                                    799***********************.*********9999999988788999999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4466.89
//
Query:       gi|121637471|ref|YP_977694.1|  [L=647]
Description: fatty-acid-CoA ligase FadD11 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-90  303.5   0.1      3e-90  302.9   0.1    1.3  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.9   0.1   1.7e-94     3e-90       1     421 [.      53     497 ..      53     499 .. 0.85

  Alignments for each domain:
  == domain 1  score: 302.9 bits;  conditional E-value: 1.7e-94
                                    HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                    ++++a   pd+val   g++qt+T+r++ ++v+r+AagL  lGv++gd+V +++ n++e++ ++++++ +Ga+   +++t
  gi|121637471|ref|YP_977694.1|  53 FQRTAVMDPDAVALRTPGGNQTMTWRDYAAQVRRVAAGLAGLGVRRGDTVSLMMANRIEFYPLDVGAQHVGATSFSVYNT 132
                                    7899999*******88999************************************************************* PP

                                    S-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS....-TSCCCS- CS
                    AMP-binding  81 ltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae....kpeeeeel 156
                                    l+ae+l y++++++ kv+i  ++++ +++   ++a+    ++++++d +++ + +  +  + ++   +     + + +++
  gi|121637471|ref|YP_977694.1| 133 LPAEQLTYVFDNAGTKVVI--CEQQYVDR---VRASGVPIEHIVCVDGAPPGTLSLTDLYAAAS---GdffdFESTWRAV 204
                                    *******************..99988555...55566678999999988877654333333222...134454557889* PP

                                    BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TT CS
                    AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpk 236
                                    +p+d++++iYTSGTTG+PKGV ++h+nl++  ++++  +  +++ +d+v s+lp ahi+  +++l+l  + G +v  +  
  gi|121637471|ref|YP_977694.1| 205 QPEDIVTLIYTSGTTGNPKGVEMTHANLLFEGYAID--EVLGIRFGDRVTSFLPSAHIADRMTGLYLQEMFGTQVTAVAD 282
                                    *******************************99985..44555568*****************************99884 PP

                                    CGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH..............HHCCCHHCHHHHC...................... CS
                    AMP-binding 237 daaldpklllelieklkvtviagvPrvleal..............lesgalkaakkak...................... 280
                                      +     +++++ + ++tv+ +vPrv+e+l              +         k++                      
  gi|121637471|ref|YP_977694.1| 283 ART-----IAAALPDVRPTVWGAVPRVWEKLkagieftvaretdeM---------KRQalawamsvagkranallagesm 348
                                    433.....578999*****************888776643332221.........1113455555566677777777777 PP

                                    .......................CGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTT CS
                    AMP-binding 281 .......................dlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklg 337
                                                            ++ lr +l+g++p+++e+l ff  ++++ + e++G++E ++v+t + +++d  +lg
  gi|121637471|ref|YP_977694.1| 349 sdqlvaewakadesvlsklrerlGFGELRWALSGAAPIPKETLAFFAGIGIP-IAEIWGMSELSCVAT-ASHPRD-GRLG 425
                                    877777777777777777666665567999*******************986.**************9.775555.689* PP

                                    S-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECC CS
                    AMP-binding 338 svGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkk 417
                                    +vGk lpg + ki+++           Ge lvrgp vmkgY k+p++taea+d +++wl+TGD+  +d dGyl++v+Rkk
  gi|121637471|ref|YP_977694.1| 426 TVGKLLPGLQGKIAED-----------GEYLVRGPLVMKGYRKEPAKTAEAID-SDGWLHTGDVFDIDSDGYLRVVDRKK 493
                                    *************987...........9999*********************9.757*********************** PP

                                    CEEE CS
                    AMP-binding 418 dlik 421
                                    +li+
  gi|121637471|ref|YP_977694.1| 494 ELII 497
                                    **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4198.30
//
Query:       gi|121637472|ref|YP_977695.1|  [L=621]
Description: glycerol-3-phosphate acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-08   33.0   0.0      1e-07   31.7   0.0    1.7  1  Acyltransferase  Acyltransferase
  ------ inclusion threshold ------
       0.48   10.3   2.1       0.36   10.7   0.1    1.9  2  HNH_repeat       Homing endonuclease repeat


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.1e-11     1e-07       4     134 ..     105     241 ..     103     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.1e-11
                Acyltransferase   4 vtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidR..ksnaraags 81 
                                    +t+l +l +k  + ++  H+sylD +ll  +  ++++  +  + ++++l +   +g  ++++g+ifi+R  k+  +++ +
  gi|121637472|ref|YP_977695.1| 105 ITQLRKLDRKATLAFAFSHRSYLDGMLLPEAILANRL-SPALTFGGANLNF-FPMGAWAKRTGAIFIRRqtKDIPVYRFV 182
                                    56677788888888999************88866666.7888889999666.667888999********55555555555 PP

                Acyltransferase  82 leniselleegkl.vviFPEGtrsregellpfkkGlvrlaakak.....kgvpivPvai 134
                                    l  ++  l ++ + +    EG+r+r+g+l+p+  G+ r + +a+       v++vP +i
  gi|121637472|ref|YP_977695.1| 183 LRAYAAQLVQNHVnLTWSIEGGRTRTGKLRPPVFGILRYITDAVdeidgPEVYLVPTSI 241
                                    55555577777888*****************************9999999999999877 PP

>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1     4e-05      0.36       5      18 ..      46      59 ..      46      59 .. 0.91
   2 ?   -3.5   0.2       1.1   9.9e+03       8      13 ..     598     603 ..     598     603 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4e-05
                     HNH_repeat  5 ElvQkqAaELGRtP 18
                                   E+++++A+ELGR P
  gi|121637472|ref|YP_977695.1| 46 ERLRALADELGRDP 59
                                   89**********65 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                     HNH_repeat   8 QkqAaE 13 
                                    Q++A+E
  gi|121637472|ref|YP_977695.1| 598 QQFADE 603
                                    9***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3706.11
//
Query:       gi|121637473|ref|YP_977696.1|  [L=583]
Description: fumarate reductase flavoprotein subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.9e-113  378.7   0.1   5.4e-113  378.2   0.1    1.2  1  FAD_binding_2   FAD binding domain
    8.5e-36  122.8   0.0    1.4e-35  122.1   0.0    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    2.4e-07   30.3   0.8    0.00021   20.6   0.3    3.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00053   19.7   1.4     0.0021   17.7   1.5    2.0  1  DAO             FAD dependent oxidoreductase
     0.0011   18.3   1.5     0.0031   16.8   0.2    2.0  2  Thi4            Thi4 family
     0.0069   15.1   0.7      0.017   13.9   0.0    1.9  3  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.013   14.6   0.5      0.039   13.0   0.3    1.8  2  GIDA            Glucose inhibited division protein A
      0.078   13.8   0.1       0.17   12.7   0.1    1.6  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.082   11.9   0.5       0.13   11.3   0.5    1.2  1  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.2   0.1  2.7e-116  5.4e-113       2     417 .]       7     394 ..       6     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 378.2 bits;  conditional E-value: 2.7e-116
                                    EEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-H CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaae.aGl.kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladq 79 
                                    ++ViG+G+AGL+AA+++ae + + +va+v+k+ +++++t+ ++Gg++av        g++ds+++h++dt++++d+l+dq
  gi|121637473|ref|YP_977696.1|   7 IVVIGGGGAGLRAAIAIAEtNPHlDVAIVSKVYPMRSHTVSAEGGAAAVT-------GDDDSLDEHAHDTVSGGDWLCDQ 79 
                                    79*****************75556**************************.......677******************** PP

                                    HHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEE CS
                  FAD_binding_2  80 plveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdf 158
                                    ++veafv++ap+++ +Le++g+p+sr++dg+v+vr++Gg+++  rt++ aad+      tg++ll++l+++++ +  v  
  gi|121637473|ref|YP_977696.1|  80 DAVEAFVAEAPKELVQLEHWGCPWSRKPDGRVAVRPFGGMKKL-RTWF-AADK------TGFHLLHTLFQRLLTYSdVMR 151
                                    *******************************************.****.****......********************* PP

                                    EESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTS CS
                  FAD_binding_2 159 qerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalraga 238
                                    +++++a++L+v+dgrv G v+ ++++gr+++i a+av+l tgG+gr          ++  ttna + tGdg ala+raga
  gi|121637473|ref|YP_977696.1| 152 YDEWFATTLLVDDGRVCGLVAIELATGRIETILADAVILCTGGCGR----------VFPFTTNANIKTGDGMALAFRAGA 221
                                    **********************************************..........************************ PP

                                    SEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH................GGGS-HHHHHHHHH.H CS
                  FAD_binding_2 239 alnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm................nelasrdvvsrailek 302
                                    +l+d  me+vq+hPt+l+     +giLitea+r eGg+l++kdG r+                 +el +rd++s+a++ +
  gi|121637473|ref|YP_977696.1| 222 PLKD--MEFVQYHPTGLP----FTGILITEAARAEGGWLLNKDGYRYLqdydlgkptpeprlrsMELGPRDRLSQAFV-H 294
                                    ****..************....********************************************************.9 PP

                                    HHHTTTS.....CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEE CS
                  FAD_binding_2 303 eiaeggs.....eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGve 377
                                    e+++g++     ++ vyld++h l+a+ ++a+l+ ++e +++  +      idp  + +p       v+p +hy+mgGv+
  gi|121637473|ref|YP_977696.1| 295 EHNKGRTvdtpyGPVVYLDLRH-LGADLIDAKLPFVRELCRDYQH------IDPVVELVP-------VRPVVHYMMGGVH 360
                                    99999999**************.*******************888......*********.......************* PP

                                    BETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                  FAD_binding_2 378 tdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                    td ng +      ++pGLYAaGe+a+++++ganrlg+nsl
  gi|121637473|ref|YP_977696.1| 361 TDINGAT------TLPGLYAAGETACVSINGANRLGSNSL 394
                                    *******......*************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.0   6.8e-39   1.4e-35       1     128 []     455     581 ..     455     581 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 6.8e-39
                                    .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTT CS
                 Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGa 80 
                                    r ++++++++ +g++R++ +L++a++e++ l+er+   +++d+s+++N+el+  lel  +l++A ai++s l+R+ESrGa
  gi|121637473|ref|YP_977696.1| 455 RADMQATLESAAGIYRDGPTLTKAVEEIRVLQERFATAGIDDHSRTFNTELTALLELSGMLDVALAIVESGLRREESRGA 534
                                    679***************************************************************************** PP

                                    BEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                 Succ_DH_flav_C  81 HaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                    H r+dfp+rdDe++l htl+  ++++++ ++ y pv+++  +p eR+Y
  gi|121637473|ref|YP_977696.1| 535 HQRTDFPNRDDEHFLAHTLV-HRESDGTLRVGYLPVTITRWPPGERVY 581
                                    ********************.5567799******************99 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3     1e-07   0.00021       2     115 ..       6     200 ..       5     235 .. 0.65
   2 !    5.3   0.0     0.005        10     256     279 ..     357     384 ..     352     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                                    SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...................... CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias...................... 57 
                                    ++vviGgG AGl+aa+ +a+    ++v++v   +  + +   +s +  ++a  ++  s                      
  gi|121637473|ref|YP_977696.1|   6 NIVVIGGGGAGLRAAIAIAEtnPHLDVAIV--SKVYPMRSHTVSAEGGAAAVTGDDDSldehahdtvsggdwlcdqdave 83 
                                    89******************75599*****..555555555554433333333333334566677777777777888888 PP

                                    ......................................................HHHHCHHHHCCCCHCCT.CEEEE..E CS
                                    ......................................................xxxxxxxxxxxxxxxxx.xxxxx..x RF
                    Pyr_redox_2  58 ......................................................evvkklnqgielllgee.vvkid..p 80 
                                                                                               l   +++ll+ + v+++d  +
  gi|121637473|ref|YP_977696.1|  84 afvaeapkelvqlehwgcpwsrkpdgrvavrpfggmkklrtwfaadktgfhllhT----L---FQRLLTYSdVMRYDewF 156
                                    8888888888899999999999999999999999999998888888766644331....2...33333322255554323 PP

                                    SCEEEEETEEEC.........TCEEEEEESEEEE---EEE-BCT CS
                                    xxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  81 gkkkvklekkke.........gdeekiaydklvlAtGssprdlg 115
                                    +   +++  +++         g  e+i +d+++l+tG+  r ++
  gi|121637473|ref|YP_977696.1| 157 ATTLLVDDGRVCglvaielatGRIETILADAVILCTGGCGRVFP 200
                                    33233333333377777777799999999999999997444442 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.005
                                    TEEE--TTSBESSTTEEE-GGGC....T CS
                                    xxxxxxxxxxxxxxxxxxxxxxx....x RF
                    Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva....g 279
                                    gg+ +d +++t+ pg+ya+G  a    +
  gi|121637473|ref|YP_977696.1| 357 GGVHTDINGATTLPGLYAAGETAcvsiN 384
                                    89999***************99966662 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.5     1e-06    0.0021       2     111 ..       7     133 ..       6     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                                    EEEECTSHHHHHHHHHHHHTT....EEEEESSSSTTSSGGGSSEEEEESSS...STHHSTH................HHH CS
                            DAO   2 vviiGGGiiGlstAyeLarrg....VtllekgdiagsgaSgrnsgllhsgl...rylpeas................ela 58 
                                    +v+iGGG +Gl +A + a+ +    V+++ k     s++ ++ +g  +      + l   +                ++ 
  gi|121637473|ref|YP_977696.1|   7 IVVIGGGGAGLRAAIAIAETNphldVAIVSKVYPMRSHTVSAEGGAAAVTGdddS-LD--EhahdtvsggdwlcdqdAVE 83 
                                    9*****************885589********66667999999999988765432.22..1356999999*****98777 PP

                                    HHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEES.SHHHHHHHHHHHHHHHHTTT CS
                            DAO  59 rlslealeelreleeelgididyrrtGllslaa.deeelealdkllallleagl 111
                                     +++ea +el +le   g ++  ++ G + +   +   + +l+ ++a+ +  g 
  gi|121637473|ref|YP_977696.1|  84 AFVAEAPKELVQLEHW-GCPWSRKPDGRVAVRPfG--GMKKLRTWFAADK-TGF 133
                                    9*********999964.877777778888774233..4777777777642.443 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   1.5e-06    0.0031      16      49 ..       3      37 ..       1      53 [. 0.89
   2 ?   -0.2   0.1      0.24   4.8e+02     210     233 ..     367     391 ..     356     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                   TEEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                           Thi4 16 aesDvvivGaGssGLtaayylakk.pdlkvailer 49
                                   a+ ++v++G+G +GL aa  +a+  p l vai+ +
  gi|121637473|ref|YP_977696.1|  3 AQHNIVVIGGGGAGLRAAIAIAETnPHLDVAIVSK 37
                                   5779******************999******9865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
                                    EEETTEEE-TH.HHHHHHT-EB--S CS
                           Thi4 210 evvpnlyvaGm.evaevdganRmGp 233
                                      +p+ly+aG  +   ++ganR+G+
  gi|121637473|ref|YP_977696.1| 367 TTLPGLYAAGEtACVSINGANRLGS 391
                                    5689******6256789******96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.3e-06     0.017       2      60 ..       6      66 ..       5     116 .. 0.68
   2 ?   -3.9   0.1       2.1   4.2e+03     147     164 ..     177     194 ..     172     198 .. 0.80
   3 ?   -1.9   0.0       0.5     1e+03     358     384 ..     357     378 ..     355     385 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-06
                                   SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEE CS
                    HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekakklgrKilisGgGrcNvTnlseepeell 60
                                   +++viGgG AGl aAi++   +   +V+++ k   + +    + gG   vT  + +++e +
  gi|121637473|ref|YP_977696.1|  6 NIVVIGGGGAGLRAAIAIaeTNPHLDVAIVSKVYPMRSHTVSAEGGAAAVTGDDDSLDEHA 66
                                   79***************93334557788888877777776666777777776666665555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
                                    E.TTEEEEESEEEE---- CS
                    HI0933_like 147 tkseeeleadklvlAtGG 164
                                    t   e++ ad+++l tGG
  gi|121637473|ref|YP_977696.1| 177 TGRIETILADAVILCTGG 194
                                    55568899*********9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.5
                                    EEE-GGGB-TTT-BBTTSTTEEE-GGG CS
                    HI0933_like 358 GGVdlkevssktmeskkvpgLffaGEv 384
                                    GGV+++   + t     +pgL+ aGE 
  gi|121637473|ref|YP_977696.1| 357 GGVHTDINGATT-----LPGLYAAGET 378
                                    677665433444.....6*******95 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3     2e-05     0.039       2      22 ..       7      27 ..       6      47 .. 0.88
   2 ?   -1.5   0.0       0.5     1e+03     121     166 ..     160     210 ..     142     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                   EEEE-SSHHHHHHHHHHHHTT CS
                           GIDA  2 viViGgGhAGceAAlaaarlG 22
                                   ++ViGgG AG+ AA+a+a+ +
  gi|121637473|ref|YP_977696.1|  7 IVVIGGGGAGLRAAIAIAETN 27
                                   89****************876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.5
                                    EEECTTEEEE...EE..ETTS-EEEECEEEE--TT-BT-EEEETTEEEESS CS
                           GIDA 121 liveekkvkg...vv..tedgetikakavviatGtflkgkihigekelsaG 166
                                    l+v++++v+g   +   t + eti a+av++ tG   +  + + + ++++G
  gi|121637473|ref|YP_977696.1| 160 LLVDDGRVCGlvaIElaTGRIETILADAVILCTGGCGRVFPFTTNANIKTG 210
                                    555566666532122113445689999*******97776666666666666 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.8e-05      0.17       2      61 ..       6      65 ..       5      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp 61
                                   ++++iG+G +g + + ++ e++++++v+ + +  + r+++v+++ g++a++  ++ l++ 
  gi|121637473|ref|YP_977696.1|  6 NIVVIGGGGAGLRAAIAIAETNPHLDVAIVSKVYPMRSHTVSAEGGAAAVTGDDDSLDEH 65
                                   79************99*************************9999999887766555544 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   6.4e-05      0.13       2      30 ..       7      35 ..       6      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvli 30
                                   +vviG+G Agl+ A  ++e +p l v ++
  gi|121637473|ref|YP_977696.1|  7 IVVIGGGGAGLRAAIAIAETNPHLDVAIV 35
                                   8**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3934.72
//
Query:       gi|121637474|ref|YP_977697.1|  [L=376]
Description: fumarate reductase frdC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-39  133.9   8.1    4.9e-39  133.3   8.1    1.2  1  Fumarate_red_C  Fumarate reductase subunit C
      2e-32  111.4   0.0    3.3e-32  110.7   0.0    1.3  1  Fer2_3          2Fe-2S iron-sulfur cluster binding domain
    2.8e-12   46.9   0.7    4.8e-12   46.1   0.7    1.4  1  Fer4_8          4Fe-4S dicluster domain
    4.2e-09   36.4   1.4    7.7e-09   35.5   1.4    1.4  1  Fer4_10         4Fe-4S dicluster domain
      2e-07   31.5   2.1    4.3e-07   30.4   2.1    1.6  1  Fer4_7          4Fe-4S dicluster domain
    2.6e-07   31.1   0.9    6.2e-07   29.9   1.0    1.6  1  Fer4_17         4Fe-4S dicluster domain
    6.3e-06   27.0   0.6    1.1e-05   26.2   0.6    1.5  1  Fer4_16         4Fe-4S double cluster binding domain
    7.2e-06   25.6   8.1    1.8e-05   24.3   0.5    2.5  2  Fer4            4Fe-4S binding domain
    2.1e-05   24.6   5.1    0.00053   20.1   6.1    2.3  2  Fer4_9          4Fe-4S dicluster domain
    0.00037   20.5  11.5     0.0011   18.9   3.5    2.5  2  Fer4_6          4Fe-4S binding domain
     0.0017   18.7   0.7     0.0017   18.7   0.7    2.3  2  Fer4_4          4Fe-4S binding domain
     0.0049   16.9   1.3     0.0049   16.9   1.3    2.6  2  Fer4_2          4Fe-4S binding domain
     0.0055   16.8   3.3      0.028   14.5   0.9    2.2  2  Fer4_21         4Fe-4S dicluster domain
      0.006   16.8   0.5        3.1    8.0   0.2    2.2  2  Fer4_18         4Fe-4S dicluster domain
     0.0078   16.0   0.3        1.6    8.5   0.1    2.2  2  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
  ------ inclusion threshold ------
      0.029   15.3  12.5       0.19   12.7   4.3    2.6  2  Fer4_3          4Fe-4S binding domain
        2.3    8.8   9.5       0.07   13.7   1.9    2.2  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
        6.5    7.6   5.8         45    4.9   2.1    2.3  2  Fer4_15         4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   8.1     5e-42   4.9e-39       5     126 ..     253     374 ..     250     375 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 5e-42
                 Fumarate_red_C   5 pYvremkktWWkknpfYrfYmlrEatavlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLaaallhavT 84 
                                    +Y++++++ WW++++ Y  +mlrE ++++va+f+l+l+l l a+ +g ++y++fl+f +nP+v++ln++aL ++llhavT
  gi|121637474|ref|YP_977697.1| 253 AYRQPVERYWWARRRSYLRFMLREISCIFVAWFVLYLVLVLRAVGAGGNSYQRFLDFSANPVVVVLNVVALSFLLLHAVT 332
                                    7******************************************************************************* PP

                 Fumarate_red_C  85 wfelaPkavkivvkgeklpeevivkalwaalvvvsvvvlvlv 126
                                    wf  aP+a++i v+g+++p++++ ++++aa++vvsv+v ++v
  gi|121637474|ref|YP_977697.1| 333 WFGSAPRAMVIQVRGRRVPARAVLAGHYAAWLVVSVIVAWMV 374
                                    ***************************************998 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   3.3e-35   3.3e-32       2     108 ..       7     110 ..       6     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 3.3e-35
                         Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlak 81 
                                    ++v R++p+  ++++ +q yev+ ++e+ vld L++ik+++d tl+fr+sCr giCGs +++inG p+laC + + d+  
  gi|121637474|ref|YP_977697.1|   7 MEVSRYRPEI-ESAPTFQAYEVPLTREWAVLDGLTYIKDHLDGTLSFRWSCRMGICGSSGMTINGDPKLACATFLADYLP 85 
                                    689*****66.55*****************************************************************96 PP

                         Fer2_3  82 qkseieleplpkfpvirDLvvDideml 108
                                       ++++ep+++fpvirDLvvDi++++
  gi|121637474|ref|YP_977697.1|  86 G--PVRVEPMRNFPVIRDLVVDISDFM 110
                                    6..5*******************9986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.7   4.8e-15   4.8e-12       2      65 .]     146     219 ..     145     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.8e-15
                         Fer4_8   2 lekCieCgaCqsaCpvlrr...........tk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                    ++ Ci+C++C saCpv+              + + +ld+r++ a+   +++vl +++++w+Ct  g+C+++Cp+g+
  gi|121637474|ref|YP_977697.1| 146 FSMCINCMLCYSACPVYALdpdflgpaaiaLGqRYNLDSRDQGAA--DRRDVLAAADGAWACTLVGECSTACPKGV 219
                                    789***********9887755555555555443666666666555..55566677******************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   1.4   7.7e-12   7.7e-09       6      56 .]     146     216 ..     142     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.7e-12
                        Fer4_10   6 ddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     + Ci+C  C +aCP+++                    +++++ + + +  a  ++ ++Ct +g+C  aCP
  gi|121637474|ref|YP_977697.1| 146 FSMCINCMLCYSACPVYAldpdflgpaaialgqrynldSRDQGAADRRDVLAAADGAWACTLVGECSTACP 216
                                    568**********************************9888899999999999999**************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   2.1   4.3e-10   4.3e-07       2      52 .]     149     219 ..     148     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.3e-10
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.................gtekv...eidpekClgCgaCvavCPtga 52 
                                    Ci+C  C +aCpv+a++ d    ++                  +++v   +  ++ C+  g+C ++CP+g+
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACPVYALDPDFLGPAAialgqrynldsrdqgaaDRRDVlaaADGAWACTLVGECSTACPKGV 219
                                    *****************996322222232222222222222222233331333678999999******996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.0   6.2e-10   6.2e-07       2      61 .]     149     220 ..     148     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.2e-10
                        Fer4_17   2 CiqCgyClpeCpsyeaydn..epk..kllraakl.......glleeaeke.......ekaslCieCgeCerkCPqgld 61 
                                    Ci+C  C  +Cp y+  ++   p+   l ++++l       ++      +       + a  C+  geC+++CP+g+d
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACPVYALDPDflGPAaiALGQRYNLdsrdqgaAD------RrdvlaaaDGAWACTLVGECSTACPKGVD 220
                                    ****************877443552233344444554433322......1234544489****************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.6   1.1e-08   1.1e-05       2      66 ..     149     217 ..     148     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-08
                        Fer4_16   2 CgtCgkCaevCPtnaikek....kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    C++C  C ++CP+ a++ +    ++  + +r + ++++++  d ++  ++ + ++a+t  + C ++CP 
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACPVYALDPDflgpAAIALGQRYNLDSRDQGAADRRDVLAAADGAWACTLVGECSTACPK 217
                                    *****************8844223333333334444666666666777777778**************6 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.8e-08   1.8e-05       6      23 ..     147     164 ..     143     165 .. 0.91
   2 ?    4.5   1.7     0.034        34      12      21 ..     209     218 ..     204     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-08
                                    TTSSS-THHHHHSTTTEE CS
                           Fer4   6 ekCigCGaCvevCPvgAI 23 
                                    ++Ci+C++C+++CPv A+
  gi|121637474|ref|YP_977697.1| 147 SMCINCMLCYSACPVYAL 164
                                    79*************997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
                                    THHHHHSTTT CS
                           Fer4  12 GaCvevCPvg 21 
                                    G+C  +CP g
  gi|121637474|ref|YP_977697.1| 209 GECSTACPKG 218
                                    89******88 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.2   2.3e-05     0.023      31      48 ..     143     161 ..     124     164 .. 0.70
   2 !   20.1   6.1   5.4e-07   0.00053       2      49 ..     149     218 ..     148     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                         Fer4_9  31 ase.eaCigCgaCveaCpk 48 
                                    +++ + Ci C+ C+ aCp 
  gi|121637474|ref|YP_977697.1| 143 FKQfSMCINCMLCYSACPV 161
                                    222567***********97 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.4e-07
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                    C++C  C +aCp  +  +d  +  a    +++                      +aC+  g+C  aCpkg
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACPVYALDPDFLGPAAIALGQRYnldsrdqgaadrrdvlaaadgaWACTLVGECSTACPKG 218
                                    ***********9999999888887777666667899999999999***********************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.5   1.1e-06    0.0011       8      24 .]     148     164 ..     147     164 .. 0.92
   2 ?    6.1   1.1     0.013        13      13      22 ..     209     218 ..     204     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         Fer4_6   8 kCigCgdCvrvCPegai 24 
                                     Ci C+ C+++CP +a+
  gi|121637474|ref|YP_977697.1| 148 MCINCMLCYSACPVYAL 164
                                    7************9996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                         Fer4_6  13 gdCvrvCPeg 22 
                                    g+C ++CP g
  gi|121637474|ref|YP_977697.1| 209 GECSTACPKG 218
                                    89******55 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.7   1.7e-06    0.0017       3      16 ..     148     161 ..     146     170 .. 0.91
   2 ?   -0.2   0.6         2     2e+03       8      16 ..     209     217 ..     204     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                     Ci+C+ C++aCP+
  gi|121637474|ref|YP_977697.1| 148 MCINCMLCYSACPV 161
                                    7************5 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                         Fer4_4   8 gsCvaaCPq 16 
                                    g C  aCP 
  gi|121637474|ref|YP_977697.1| 209 GECSTACPK 217
                                    578899995 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.3     5e-06    0.0049       9      21 ..     148     160 ..     142     161 .. 0.91
   2 ?    3.3   1.2      0.11   1.1e+02      14      21 ..     209     216 ..     201     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                         Fer4_2   9 rCigCgaCvsaCP 21 
                                    +Ci+C  C+saCP
  gi|121637474|ref|YP_977697.1| 148 MCINCMLCYSACP 160
                                    8************ PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                         Fer4_2  14 gaCvsaCP 21 
                                    g C +aCP
  gi|121637474|ref|YP_977697.1| 209 GECSTACP 216
                                    78*****9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   2.9e-05     0.028       7      53 ..     148     161 ..     141     166 .. 0.62
   2 ?    2.0   0.1      0.23   2.3e+02      41      52 ..     205     216 ..     190     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                        Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                    +Ci+C +C+ aC+                                 v
  gi|121637474|ref|YP_977697.1| 148 MCINCMLCYSACP---------------------------------V 161
                                    5555555555555.................................4 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.23
                        Fer4_21  41 CvGCnlCssvCP 52 
                                    C+    Cs+ CP
  gi|121637474|ref|YP_977697.1| 205 CTLVGECSTACP 216
                                    333344566665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0032       3.1      56      72 ..     144     160 ..     129     165 .. 0.59
   2 !    6.9   0.0     0.007         7      50      79 ..     194     223 ..     174     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0032
                        Fer4_18  56 kgagdcidcescvkvcP 72 
                                    k+ + ci+c  c + cP
  gi|121637474|ref|YP_977697.1| 144 KQFSMCINCMLCYSACP 160
                                    44445555555555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.007
                        Fer4_18  50 keerkekgagdcidcescvkvcPtgidirk 79 
                                      + +++ga  c+  + c + cP g+d   
  gi|121637474|ref|YP_977697.1| 194 DVLAAADGAWACTLVGECSTACPKGVDPAG 223
                                    33456677889***************9655 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0016       1.6      10      46 ..     135     169 ..     129     175 .. 0.82
   2 ?    5.4   0.0     0.015        15      15      60 ..     193     239 ..     179     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                    ----HHHHHHHHTT----TT-HHHHCSTT---HHHHH CS
                        Fer4_20  10 lglteeealeeAsRClqCkkapcvkgCPveidipefi 46 
                                    ++  e +a ++ s C++C    c ++CPv    p+f+
  gi|121637474|ref|YP_977697.1| 135 QTPAELDAFKQFSMCINC--MLCYSACPVYALDPDFL 169
                                    4555668999999*****..89*******99888886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                                    HHHHHHHTT----T.T-HHHHCSTT---HHHHHHHHHTT-HHHHHHH CS
                        Fer4_20  15 eealeeAsRClqCk.kapcvkgCPveidipefikkiaegnleeaaki 60 
                                    +++l+ A+    C+   +c+++CP  +d  + i++ +    ++a+k 
  gi|121637474|ref|YP_977697.1| 193 RDVLAAADGAWACTlVGECSTACPKGVDPAGAIQRYKLTAATHALKK 239
                                    556667777778875678***********999998888877777765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.3   0.00019      0.19       1      15 []     149     163 ..     149     163 .. 0.94
   2 ?    6.9   1.1     0.014        14       5      14 ..     209     218 ..     203     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C++C++C  +CPv A
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACPVYA 163
                                    ************976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                         Fer4_3   5 gaCvevCPvg 14 
                                    g C  +CP+g
  gi|121637474|ref|YP_977697.1| 209 GECSTACPKG 218
                                    58******98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.9     7e-05      0.07       6      26 ..     149     168 ..     147     201 .. 0.67
   2 ?   -1.5   1.1       3.7   3.7e+03       6      18 ..     205     217 ..     203     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-05
                        Fer4_13   6 CiacgaCvelaPdvFeeddeg 26 
                                    Ci+c++C++++P v++ d++ 
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACP-VYALDPDF 168
                                    ************.88888875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.7
                        Fer4_13   6 CiacgaCvelaPd 18 
                                    C+  g C  ++P+
  gi|121637474|ref|YP_977697.1| 205 CTLVGECSTACPK 217
                                    888899*999996 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.1     0.045        45       8      59 ..     149     205 ..     147     205 .. 0.67
   2 ?    4.7   0.7     0.053        53       6      21 ..     203     218 ..     198     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.045
                        Fer4_15   8 CigcglCvaeapevfelded..glasvl......lddgeiaegevpddeeeaaqeAaraC 59 
                                    Ci c lC+ ++p v  ld d  g a +       ld   +++g  +  ++ aa + a aC
  gi|121637474|ref|YP_977697.1| 149 CINCMLCYSACP-VYALDPDflGPAAIAlgqrynLDS--RDQGAADRRDVLAAADGAWAC 205
                                    ***********9.888888866777776655554432..235566666666666666666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.053
                        Fer4_15   6 daCigcglCvaeapev 21 
                                    +aC+ +g C +++p+ 
  gi|121637474|ref|YP_977697.1| 203 WACTLVGECSTACPKG 218
                                    69***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1959.80
//
Query:       gi|121637475|ref|YP_977698.1|  [L=125]
Description: fumarate reductase subunit D [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-32  111.5   6.4    2.5e-32  111.3   6.4    1.0  1  Fumarate_red_D  Fumarate reductase subunit D
    0.00089   19.3   3.5     0.0011   19.0   3.5    1.2  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr


Domain annotation for each model (and alignments):
>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   6.4   2.8e-36   2.5e-32       2     114 .]      11     123 ..      10     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 2.8e-36
                 Fumarate_red_D   2 pkrsdepifwlLFgaGGmvaAlvlpvlililglllplGlldsdalsyekvlafaqswigklvllvviilplwhalhrihh 81 
                                    ++rs ep++wlLF+aGGmv+Alv+pvl+l++gl +plG+ld  a ++ ++la+++++i+klv+lv+++l+l+ha+hr+++
  gi|121637475|ref|YP_977698.1|  11 RRRSAEPFLWLLFSAGGMVTALVAPVLLLLFGLAFPLGWLD--APDHGHLLAMVRNPITKLVVLVLVVLALFHAAHRFRF 88 
                                    58*************************************97..88*********************************** PP

                 Fumarate_red_D  82 glhd.lkihvkkaaklif.YglAallsvvalilll 114
                                    +l++ l++ + ++  +++ Yg+A+l s++a ++ll
  gi|121637475|ref|YP_977698.1|  89 VLDHgLQLGRFDRVIALWcYGMAVLGSATAGWMLL 123
                                    **88899999877776656***********99985 PP

>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   3.5   1.3e-07    0.0011      22     116 ..      19     113 ..       3     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                        Sdh_cyt  22 lsilhritGvallv.glllllvwlllalsls.spesfarvvallaspiklilllllllallyHllnGiRhllwDlglgle 99 
                                    l++l    G + ++ + +lll+++l+ +++  ++ ++ ++ a + +pi+++++l+l++++l+H+++  R++l     gl+
  gi|121637475|ref|YP_977698.1|  19 LWLLFSAGGMVTALvAPVLLLLFGLAFPLGWlDAPDHGHLLAMVRNPITKLVVLVLVVLALFHAAHRFRFVLD-H--GLQ 95 
                                    66666666666666555666666666665543777889999999999999999999999999*******9987.4..556 PP

                        Sdh_cyt 100 lesarksalavl.alava 116
                                    l +  +  ++++ ++av+
  gi|121637475|ref|YP_977698.1|  96 LGRFDRVIALWCyGMAVL 113
                                    655555555554144444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 691.49
//
Query:       gi|121637476|ref|YP_977699.1|  [L=202]
Description: regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-26   90.6   1.3      1e-25   90.3   0.1    1.7  2  TetR_C_11    Tetracyclin repressor-like, C-terminal domain
      4e-16   58.5   0.3      1e-15   57.2   0.2    1.7  2  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.031   14.3   0.0    1.6  1  TetR_C_7     AefR-like transcriptional repressor, C-terminal 
      0.028   14.6   0.2       0.12   12.6   0.0    2.1  2  TetR_C_31    Tetracyclin repressor-like, C-terminal domain
      0.074   13.7   0.1       0.42   11.3   0.1    2.2  1  ParE_toxin   ParE toxin of type II toxin-antitoxin system, pa
       0.11   12.7   0.0       0.75   10.0   0.0    2.0  2  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas


Domain annotation for each model (and alignments):
>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.93   2.8e+03      22      40 ..      33      51 ..      21      75 .. 0.53
   2 !   90.3   0.1   3.3e-29     1e-25       1     113 []      82     192 ..      82     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.93
                      TetR_C_11 22 laspragallrallaeaqr 40
                                   l+++   +l  + +a+++r
  gi|121637476|ref|YP_977699.1| 33 LQEHGYDRLTVDAVAASAR 51
                                   4444444444444444433 PP

  == domain 2  score: 90.3 bits;  conditional E-value: 3.3e-29
                      TetR_C_11   1 vpDtGslrgDLrallralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadve 80 
                                    +p tG+lr+DL++l + +++++ +   ++++ra+l e++r+p+l + l+ ++++ r+a ++ +l++Av+rGe++  a  +
  gi|121637476|ref|YP_977699.1|  82 PPNTGNLRDDLLRLGELICREVGQ--HASTIRAVLVEVSRNPALNDVLQHQFVDHRKALIQYILQQAVDRGEISSAAISD 159
                                    79**********************..6***************************************************** PP

                      TetR_C_11  81 lvldlllgpllyrllltgeplddafaerlvdav 113
                                     + dll+g l++r ++  +p++++++++lvd+v
  gi|121637476|ref|YP_977699.1| 160 ELWDLLPGYLIFRSIIPNRPPTQDTVQALVDDV 192
                                    *******************************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.2   3.4e-19     1e-15       1      47 []      25      71 ..      25      71 .. 0.97
   2 ?   -2.9   0.0         2   6.1e+03      11      22 ..     102     113 ..     100     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.4e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+++++l++e+Gyd++tv+++A++A  sk+++Yr++psK+eL++a+
  gi|121637476|ref|YP_977699.1| 25 LLAVTLRLLQEHGYDRLTVDAVAASARASKATVYRRWPSKAELVLAA 71
                                   799*****************************************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                                    HHHTTT--HHHH CS
                         TetR_N  11 erGydattvreI 22 
                                    e G +a t+r++
  gi|121637476|ref|YP_977699.1| 102 EVGQHASTIRAV 113
                                    567788888876 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.031       9      67 ..      94     154 ..      86     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                    HHHHHHT-H..HHHHHHHHHHHHHHT-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB-S CS
                       TetR_C_7   9 allalllsp..evlalaRlviaeaerfPelarafyeagpgrveealaayLeaavaaGrLri 67 
                                    +l +l++++  ++++++R v+ e++r+P+l +   ++    +++ ++ +L++av++G++  
  gi|121637476|ref|YP_977699.1|  94 RLGELICREvgQHASTIRAVLVEVSRNPALNDVLQHQFVDHRKALIQYILQQAVDRGEISS 154
                                    5566777763357899*********************999999999999********9864 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.41   1.2e+03      64      64 ..      51      51 ..      19      96 .. 0.57
   2 ?   12.6   0.0   4.1e-05      0.12      30     105 ..     113     193 ..      95     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.41
                                   S CS
                      TetR_C_31 64 l 64
                                   +
  gi|121637476|ref|YP_977699.1| 51 R 51
                                   2 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.1e-05
                                    HHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCSS-HH.HHHHH...HHHHHHHHHHHHHHSGTS-H.HHHHHHHHHHH CS
                      TetR_C_31  30 lfleaarrPeLraalarlrralrealaallaalGlpdpe.eaarl...lvaaldGllldrLagpaadp.raevrellral 104
                                     ++e +r+P+L ++l++++ + r al+++  +  +++ e ++a+    l  +l G l+ r + p+++p ++ v +l++++
  gi|121637476|ref|YP_977699.1| 113 VLVEVSRNPALNDVLQHQFVDHRKALIQYILQQAVDRGEiSSAAIsdeLWDLLPGYLIFRSIIPNRPPtQDTVQALVDDV 192
                                    679****************9999998888776666444433333334599999999998888886666678888888877 PP

                                    T CS
                      TetR_C_31 105 l 105
                                    +
  gi|121637476|ref|YP_977699.1| 193 I 193
                                    5 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00014      0.42      10      60 ..      48     100 ..      40     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHH..CC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEE CS
                     ParE_toxin  10 dlkkiadyia..rdgpaakrfldaleealellaenpalgrprrelglkglrri 60 
                                       ++ + ++  r+++ a+ +l+a+ e ++++a++p  g  r++l+  g++ +
  gi|121637476|ref|YP_977699.1|  48 ASARASKATVyrRWPSKAELVLAAFIEGIRQVAVPPNTGNLRDDLLRLGELIC 100
                                    44555555554355559************************999985566655 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00025      0.75      17      52 ..      31      67 ..      26      77 .. 0.87
   2 ?    0.2   0.0      0.26   7.7e+02      56      84 ..     124     152 ..      96     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                   HHHHHHHH--S-HHHHHHHHTS-HHHHHH.HHH-HHH CS
                    HTH_Tnp_1_2 17 ellvendyekltldeiaeevgvsrsTlyk.WkkkkeF 52
                                    ll e+ y++lt+d +a+    s++T y+ W +k e 
  gi|121637476|ref|YP_977699.1| 31 RLLQEHGYDRLTVDAVAASARASKATVYRrWPSKAEL 67
                                   689999**********************548888775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                                    HHHHHHHHHHTTHHHHHHHHHHHHHSSS- CS
                    HTH_Tnp_1_2  56 vnelaeefleeeraevykaLlrkilkgrs 84 
                                     + l  +f+++ +a +   L ++++ g  
  gi|121637476|ref|YP_977699.1| 124 NDVLQHQFVDHRKALIQYILQQAVDRGEI 152
                                    45667788888888888888888887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1130.59
//
Query:       gi|121637477|ref|YP_977700.1|  [L=148]
Description: membrane protein mmpS6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-60  202.4   0.5    2.9e-60  202.2   0.5    1.0  1  Mycobact_memb  Mycobacterium membrane protein


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.2   0.5   1.6e-64   2.9e-60       1     138 [.      10     147 ..      10     148 .] 0.99

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.6e-64
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEEB-B----TT-----B---TTS------S CS
                  Mycobact_memb   1 lkrlWiplvivvvvvvggltvsrlhsifgsekrasvadklaedskpfnPkkvkyevfGpagtvadisyldadaepqridg 80 
                                    +kr W+ lv v+vv+v+g++v+rlh+ifgs++ +s+a   a+d+kpfnPk+v+ evfG++gtva i+yld+da+p+++ +
  gi|121637477|ref|YP_977700.1|  10 VKRGWMVLVAVAVVAVAGFSVYRLHGIFGSHDTTSTAGGVANDIKPFNPKQVTLEVFGAPGTVATINYLDVDATPRQVLD 89 
                                    69****************************************************************************** PP

                                    -SS--B--EE-SSS------B--SS-S------BBTTB---------S-TTSSS--S- CS
                  Mycobact_memb  81 aalPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevnaltyClvks 138
                                    ++lPWs ti+ttl+av +nvvaqg+s+sigCri+v+gvvkder++nev+a+t+Cl ks
  gi|121637477|ref|YP_977700.1|  90 TTLPWSYTITTTLPAVFANVVAQGDSNSIGCRITVNGVVKDERIVNEVRAYTFCLDKS 147
                                    ******************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 818.15
//
Query:       gi|121637478|ref|YP_977701.1|  [L=967]
Description: transmembrane transport protein mmpL6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   8.6e-214  708.6  31.6     6e-112  373.8   5.8    2.7  3  MMPL       MMPL family
  ------ inclusion threshold ------
       0.17   11.8   1.0        0.3   11.0   1.0    1.4  1  Sec34      Sec34-like family
       0.17   12.2   0.6       0.46   10.8   0.6    1.7  1  kleA_kleC  Uncharacterized KorC regulated protein A


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.8   5.8    1e-115    6e-112       3     333 .]      52     379 ..      50     379 .. 0.99
   2 ?   -1.0   0.1      0.11   6.6e+02      17     126 ..     421     520 ..     407     564 .. 0.56
   3 !  342.9  14.4  2.7e-106  1.6e-102       2     331 ..     599     934 ..     598     936 .. 0.98

  Alignments for each domain:
  == domain 1  score: 373.8 bits;  conditional E-value: 1e-115
                           MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafvS 82 
                                    s +d +s +am+r+++ f+e  dsd+++++vl egd+ lg+ +a++++d+l+++l++dtkhv++v+df++dp +aa+ +S
  gi|121637478|ref|YP_977701.1|  52 SSPDDPSLQAMKRIGKVFHE-FDSDSAAMIVL-EGDKPLGN-DAHRFYDTLLRNLSNDTKHVEHVQDFWGDPLTAAGSQS 128
                                    67899***************.***********.********.************************************** PP

                           MMPL  83 kDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLli 162
                                     Dgkaa+++v+l+g++g+ +++esv+a+r++v++++p++g+k++vtG a+++ad+ +++++ +++++ +tlvvi+v+Ll 
  gi|121637478|ref|YP_977701.1| 129 TDGKAAYVQVYLAGNQGEALSIESVDAVRDIVAHTPPPAGVKAYVTGAAPLMADQFQVGSKGTAKVTGITLVVIAVMLLF 208
                                    ******************************************************************************** PP

                           MMPL 163 vyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavir 242
                                    vyrS+v+++l+l+tv+++l+aa+g+v++l ++ +++lst +++ll++l+ia+GtDYa+++++Ry+e++ a +dre+a+++
  gi|121637478|ref|YP_977701.1| 209 VYRSVVTMVLVLITVLIELAAARGIVAFLGNAGVIGLSTYSTNLLTLLVIAAGTDYAIFVLGRYHEARYAAQDRETAFYT 288
                                    ******************************************************************************** PP

                           MMPL 243 avastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrrl 322
                                    ++++t++vv+++Gltva+a+++L+++rlp+++++G+++++Gv+++++++l+l P++l l +r++ ++p+r++++r Wrr+
  gi|121637478|ref|YP_977701.1| 289 MYRGTAHVVLGSGLTVAGAVYCLSFTRLPYFQSLGIPASIGVMIALAAALSLAPSVLILGSRFGCFEPKRRMRTRGWRRI 368
                                    ******************************************************************************** PP

                           MMPL 323 grlvvrrPlpv 333
                                    g+++vr+P p+
  gi|121637478|ref|YP_977701.1| 369 GTAIVRWPGPI 379
                                    ********985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.11
                           MMPL  17 eaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafvSkDgkaaralvtleg 96 
                                    e++fp+ a  ++  ++++ +++++ ++ a++  +d++++++  + +++g v+++     ++ + +  D++++ ++++++ 
  gi|121637478|ref|YP_977701.1| 421 ERHFPQ-ARLNPELLMIE-TDHDMRNP-ADMLILDRIAKAV-FHLPGIGLVQAM-----TRPLGTPIDHSSIPFQISMQS 491
                                    556666.55555444444.33333333.6666666666666.555556666666.....555555666666666666665 PP

                           MMPL  97 dpgsteadesvaairaaveearpleglkve 126
                                      + +  + + ++ ++ +++a+   g ++e
  gi|121637478|ref|YP_977701.1| 492 VGQIQNLKYQRDRAADLLKQAE-ELGKTIE 520
                                    5555555566666666666665.3333333 PP

  == domain 3  score: 342.9 bits;  conditional E-value: 2.7e-106
                           MMPL   2 lspadaesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.......... 70 
                                    l +++a++++++d+l+a  p+ +a  ++ i   + +++ al + a+++++ ++ ++l ++++++g+++d+          
  gi|121637478|ref|YP_977701.1| 599 LGEQLASVTVTLDKLAAIQPQlVALLPDEIASQQINRELALANYATMSGIYAQTAALIENAAAMGQAFDAaknddsfylp 678
                                    67899*****************************************************************9999999999 PP

                           MMPL  71 ...lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdas 141
                                       +++pd   + ++f+S+Dgkaar+++++egdp+++e++++++ai++a++ea+   p++g+ ++++G+aat++d++d++
  gi|121637478|ref|YP_977701.1| 679 peaFDNPDfqrGLKLFLSADGKAARMIISHEGDPATPEGISHIDAIKQAAHEAVkgtPMAGAGIYLAGTAATFKDIQDGA 758
                                    99999**99999******************************************************************** PP

                           MMPL 142 drdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYal 220
                                    ++dl ++++++l +il+i++i++rSlvaal++++tv++sl+a++gl vl++++llg++l++ vl+l+v+ll+avG+DY+l
  gi|121637478|ref|YP_977701.1| 759 TYDLLIAGIAALSLILLIMMIITRSLVAALVIVGTVALSLGASFGLsVLVWQHLLGIQLYWIVLALAVILLLAVGSDYNL 838
                                    ******************************************************************************** PP

                           MMPL 221 lLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAll 299
                                    lL+sR++ee++ag ++  ++ira+a+tg+vvtaaGl++a++m ++v+++l+vl+q+G++i+lG+l+d+l+v++++ P+++
  gi|121637478|ref|YP_977701.1| 839 LLISRFKEEIGAGLNT--GIIRAMAGTGGVVTAAGLVFAATMSSFVFSDLRVLGQIGTTIGLGLLFDTLVVRAFMtPSIA 916
                                    ****************..************************************************************** PP

                           MMPL 300 vllGraalakprrkrkkrwWrrlgrlvvrrPl 331
                                    vllGr+           +wW+++   v++rP+
  gi|121637478|ref|YP_977701.1| 917 VLLGRW-----------FWWPQR---VRPRPA 934
                                    ******...........***999...888887 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0     5e-05       0.3       3      71 ..     496     564 ..     494     570 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                          Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyF 71 
                                    ++L+ ++++  +ll+q++e+ +++e l+ ++   +e   + he++e+ ++    ++el + i +  ++F
  gi|121637478|ref|YP_977701.1| 496 QNLKYQRDRAADLLKQAEELGKTIEILQRQYALQQELAAATHEQAESFHQTIATVKELRDRIANFDDFF 564
                                    78999********************************************************99866666 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   7.7e-05      0.46      17      48 ..     496     527 ..     488     552 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
                      kleA_kleC  17 tdlvarRdkiAaklaeAeeLvrqaeeLRakvy 48 
                                    ++l+ +Rd+ A++l++AeeL + +e L  +  
  gi|121637478|ref|YP_977701.1| 496 QNLKYQRDRAADLLKQAEELGKTIEILQRQYA 527
                                    78999********************9965433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (967 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1266  (0.0706119); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.03u 0.35s 00:00:01.38 Elapsed: 00:00:00.56
# Mc/sec: 5183.57
//
Query:       gi|121637479|ref|YP_977702.1|  [L=148]
Description: hypothetical protein BCG_1610 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-58  194.5   0.5      7e-58  194.4   0.5    1.0  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.5   3.9e-62     7e-58       1     130 []      14     143 ..      14     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 3.9e-62
                                    XXXXXXXXXXXXXXXXTTXTTS---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEE CS
                F420H2_quin_red   1 llReqvaiyrrtegkvgrrlegvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevq 80 
                                    ++Req+++y++++g++g++l+g+pv+lLtt+G+ktgk+rktpl++v+++++y++vas+gGapk+p+wy+N+ +nPrve+q
  gi|121637479|ref|YP_977702.1|  14 WSREQADTYMKSGGTEGTQLQGKPVILLTTVGAKTGKLRKTPLMRVEHDGQYAIVASLGGAPKNPVWYHNVVKNPRVELQ 93 
                                    79****************************************************************************** PP

                                    ETTEEEEEEEEE--HHHHHHHHHHHHHH-THHHHHHHHHSSTS-EEEEE- CS
                F420H2_quin_red  81 vgakkldvtAreveddekarlwklvvenspsYadyqsktdreipvvVlep 130
                                    +g+++ d++Arev +deka +w+++v+++p+Ya+yq+ktdr+ipv+Vl+p
  gi|121637479|ref|YP_977702.1|  94 DGTVTGDYDAREVFGDEKAIWWQRAVAVWPDYASYQTKTDRQIPVFVLTP 143
                                    ***********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 803.65
//
Query:       gi|121637480|ref|YP_977703.1|  [L=429]
Description: threonine dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-76  256.4   7.4    4.2e-76  256.2   7.4    1.1  1  PALP            Pyridoxal-phosphate dependent enzyme
    1.9e-29  101.3   0.0    2.9e-29  100.7   0.0    1.3  1  Thr_dehydrat_C  C-terminal regulatory domain of Threonine deh
  ------ inclusion threshold ------
       0.21   11.2   0.9       0.37   10.4   0.9    1.4  1  DAGK_cat        Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.2   7.4   7.1e-80   4.2e-76       2     294 .]      30     323 ..      29     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 256.2 bits;  conditional E-value: 7.1e-80
                                    GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                           PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                    +++++pTPl +++rls+ +g+ ++lK+E+l+   S+K+Rga++ll +l  ++ a +vv++s+GNh+++ A+a++ lG+  
  gi|121637480|ref|YP_977703.1|  30 APVVTPTPLQPSDRLSAITGATVYLKREDLQTVRSYKLRGAYNLLVQLSDEELAAGVVCSSAGNHAQGFAYACRCLGVHG 109
                                    68899******************************************88888**************************** PP

                                    EEEEETTS-HHHHHHHHHTT-EEEEE...CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTE CS
                           PALP  82 tivvpadaspekvallrllGaevvev...ggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkp 158
                                    +++vpa+++++k++++r +G e +     g++yd a+aaa e  ++ +ga+lv++fd+   i+g+gti+ E+l ql ++p
  gi|121637480|ref|YP_977703.1| 110 RVYVPAKTPKQKRDRIRYHGGEFIDLivgGSTYDLAAAAALEDVER-TGATLVPPFDDLRTIAGQGTIAVEVLGQLEDEP 188
                                    *********************99999996666888888888*****.********************************* PP

                                    EEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEE CS
                           PALP 159 davvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvd 238
                                    d vvvpvGgGg iaGi ++l+er +++ v+gvep+g++a+ ++l+ag++vt+++ d+++dg av+++++l+ ++l++ +d
  gi|121637480|ref|YP_977703.1| 189 DLVVVPVGGGGCIAGITTYLAERTTNTAVLGVEPAGAAAMMAALAAGEPVTLDHVDQFVDGAAVNRAGTLTYAALAAAGD 268
                                    ***************************************************************************99999 PP

                                    ..EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                           PALP 239 ..eivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                         tv++ +++ am  l+++egi++ep++a ++a+l     +++++g++vv++++g
  gi|121637480|ref|YP_977703.1| 269 mvSLTTVDEGAVCTAMLDLYQNEGIIAEPAGALSVAGL---LEADIEPGSTVVCLISG 323
                                    88899*********************************...***************98 PP

>> Thr_dehydrat_C  C-terminal regulatory domain of Threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   4.9e-33   2.9e-29       1      91 []     336     428 ..     336     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 4.9e-33
                                    HHHTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 Thr_dehydrat_C   1 eraevgegleallavefpeqpGaLkkFlellggrnd.iTlfeYrkage.kngkvLvgvevsqaeeldelierleklgykv 78 
                                    er++v+ gl+++++v+fp++pGaL++Fl++++g+nd iTlfeY+k+++ ++g++Lvg+e+ +a++ld l +r+++++++v
  gi|121637480|ref|YP_977703.1| 336 ERSLVHLGLKHYFLVDFPQEPGALRRFLDDVLGPNDdITLFEYVKRNNrETGEALVGIELGSAADLDGLLARMRATDIHV 415
                                    89****************************************************************************** PP

                                    XXXXXXXXXXXXX CS
                 Thr_dehydrat_C  79 edlsknellkehl 91 
                                    e l+++++++++l
  gi|121637480|ref|YP_977703.1| 416 EALEPGSPAYRYL 428
                                    *********9997 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   6.3e-05      0.37      44      98 ..     177     231 ..     147     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.3e-05
                                    HHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHH CS
                       DAGK_cat  44 akelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdlar 98 
                                    a e++ ++++e   ++v +GG G +  +   l+e++ ++  lg+ P+G +  +a 
  gi|121637480|ref|YP_977703.1| 177 AVEVLGQLEDEPDLVVVPVGGGGCIAGITTYLAERTTNTAVLGVEPAGAAAMMAA 231
                                    556677777877789999****************9999999*******9877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2765.11
//
Query:       gi|121637481|ref|YP_977704.1|  [L=72]
Description: hypothetical protein BCG_1612 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-19   67.1   0.1    1.3e-18   66.7   0.1    1.1  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1   7.1e-23   1.3e-18       1      43 [.       7      49 ..       7      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 7.1e-23
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------HH CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkree 43
                                   +rtnI+iDDeL ae++r++gl+tKr+aV+lALr+L++++ ++e
  gi|121637481|ref|YP_977704.1|  7 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSRE 49
                                   59************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 508.84
//
Query:       gi|121637482|ref|YP_977705.1|  [L=134]
Description: hypothetical protein BCG_1613 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.9   2.5    2.2e-17   63.7   2.5    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.037   14.8   0.3      0.056   14.2   0.3    1.4  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   2.5   2.5e-21   2.2e-17       1     121 [.       2     124 ..       2     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.5e-21
                                    EEE-HHHHHHHH..TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCHH CS
                            PIN   1 ivlDTsvliall..rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp.idae 76 
                                    i++DTs++++++   g+  a ++r+ll e   ++++++ ++ E+l ++       +  ++l++l   l++l++ + id +
  gi|121637482|ref|YP_977705.1|   2 ILIDTSAWVEYFraTGSIAAVEVRRLLSEEaARIAMCEPIAMEILSGALD----DNTHTTLERLVNGLPSLNVDDaIDFR 77 
                                    79**************************99********************....6666666666666*******99**** PP

                                    HHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  77 iaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvak 121
                                    +a+ +++ a+++g   +++nD+liaA+A++hg++++ ++D df+ +a+
  gi|121637482|ref|YP_977705.1|  78 AAAGIYRAARRAGetvRSINDCLIAALAIRHGARIV-HRDADFDVIAR 124
                                    *********************************999.******99885 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   6.3e-06     0.056       2     105 ..       2     108 ..       1     118 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-06
                          PIN_3   2 vvlDtnvlldallfdsp.aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvaler..kav 78 
                                    +++Dt+ ++++++  ++ aa  ++++l ++a ++ +++ +  E+   + +  +    ++    +  l  ++a++   +a 
  gi|121637482|ref|YP_977705.1|   2 ILIDTSAWVEYFRATGSiAAVEVRRLLSEEAARIAMCEPIAMEILSGALDDNTHTTLERLVNGLPSLNVDDAIDFraAAG 81 
                                    689**********9999**************************9976666655555555555555555555544432222 PP

                          PIN_3  79 apdaelrpllkcrDpdDqkvlelAlaa 105
                                       a+ r+   +r  +D  +++lA+ +
  gi|121637482|ref|YP_977705.1|  82 IYRAARRAGETVRSINDCLIAALAIRH 108
                                    222223334445566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1039.96
//
Query:       gi|121637483|ref|YP_977706.1|  [L=186]
Description: maltooligosyltrehalose trehalohydrolase TreZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.5   0.2    5.8e-16   58.6   0.0    1.5  2  DUF3459   Domain of unknown function (DUF3459)


Domain annotation for each model (and alignments):
>> DUF3459  Domain of unknown function (DUF3459)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.64   1.1e+04      12      22 ..      42      52 ..      40      65 .. 0.56
   2 !   58.6   0.0   3.2e-20   5.8e-16       1      90 [.      97     179 ..      97     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.64
                                   HCCCTT--CGG CS
                        DUF3459 12 ePaLadarrgg 22
                                   eP+La++  +g
  gi|121637483|ref|YP_977706.1| 42 EPELAHSTVAG 52
                                   57777764433 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.2e-20
                                    HHHHHHHHHHHHCCCTT--CGGEEEEEEECTCEEEEEEEETTEEEEEEEE-SSCGCCS-SS---SEEEEECT--S....S CS
                        DUF3459   1 lyrdLLaLRreePaLadarrgglevavlgdgallvrwrlgdgrllrllaNLgdepvtlppegaagkllfsseaaraggda 80 
                                    +yrdL+aLR++e +Lad++ ++l v+++++++++v++r    ++l +++NLg+ep  +p   + g+l++++e++  g+ +
  gi|121637483|ref|YP_977706.1|  97 FYRDLIALRHNEADLADPWLDHLMVDYDEQQRWVVMRR----GQLMIACNLGAEPTCVP---VSGELVLAWESPIIGDNS 169
                                    7*************************************....699**************...**************999* PP

                                    SEE-TTEEEE CS
                        DUF3459  81 grlppesvvv 90 
                                    ++l+++s ++
  gi|121637483|ref|YP_977706.1| 170 TELAAYSLAI 179
                                    ****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1223.52
//
Query:       gi|121637484|ref|YP_977707.1|  [L=394]
Description: maltooligosyltrehalose trehalohydrolase TreZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.6   0.0      7e-13   48.9   0.0    2.1  2  Alpha-amylase  Alpha amylase, catalytic domain
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.051   13.9   0.0    1.6  1  CBM_48         Carbohydrate-binding module 48 (Isoamylase N-t


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   7.8e-17     7e-13       1      94 [.     112     209 ..     112     217 .. 0.90
   2 !   13.7   0.0   3.8e-06     0.034     148     182 ..     221     256 ..     218     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.8e-17
                                    --CHHHHCTCCCCCCCT-SCEEE-B-CE.-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--T CS
                  Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifk.spqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsd 79 
                                    G+++  iekLdYl +LG++ + l P+ + + +   gYd   ++++++ +G  + l + i+++h + + v++D+V+NH + 
  gi|121637484|ref|YP_977707.1| 112 GTFDAAIEKLDYLVDLGIDFVELMPVNSfAGTRGWGYDGVLWYSVHEPYGGPDGLVRFIDACHTRRLGVLIDAVFNHLGP 191
                                    5666679*******************9989999*********************************************** PP

                                    TSCC...CHCCHHSTTSG CS
                  Alpha-amylase  80 ehew...fkeslkkkgep 94 
                                    + ++   f ++l++  +p
  gi|121637484|ref|YP_977707.1| 192 SGNYlprFGPYLSSASNP 209
                                    999977777777777666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.8e-06
                                    TCCCCCCCCCCCCCCCTTT.-SEEEETTCCCTTTCC CS
                  Alpha-amylase 148 neevrkelkdvvkfwlekg.idGfRlDvvkhvskve 182
                                    ++evr+++ d + +w++++ +dG+RlD+v+ +  ++
  gi|121637484|ref|YP_977707.1| 221 SDEVRHYIIDCALRWMRDFhADGLRLDAVHALVDTT 256
                                    689****************9*********9987733 PP

>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-06     0.051      15      70 ..       4      50 ..       2      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
                                   EEEE-TTSSEEEEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEE CS
                         CBM_48 15 frvwapnAekVslvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvk 70
                                   frvwap+   V+l     + ++  + ++ r+ +g+W+ ++    p + +rY+y ++
  gi|121637484|ref|YP_977707.1|  4 FRVWAPKPALVRL-----DVNGAVHAMT-RSADGWWHTTVA--APAD-ARYGYLLD 50
                                   8999998877766.....335679****.69**********..5555.5****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2956.83
//
Query:       gi|121637485|ref|YP_977708.1|  [L=765]
Description: maltooligosyltrehalose synthase TreY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-20   72.7   0.0    1.4e-15   57.7   0.0    3.2  3  Alpha-amylase  Alpha amylase, catalytic domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   7.6e-20   1.4e-15      10      79 ..      31     101 ..      27     138 .. 0.88
   2 !    3.6   0.0    0.0023        42     137     178 ..     202     244 ..     177     263 .. 0.86
   3 !    7.3   0.0   0.00017       3.1     304     329 ..     605     630 ..     594     637 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 7.6e-20
                                    CCCCCCCT-SCEEE-B-CE.-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--T CS
                  Alpha-amylase  10 LdYlkeLGvtaiwlsPifk.spqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsd 79 
                                    LdYl +LGv+ ++lsPi +    ++hgYd++d t++ pe G  + l +L+++a+++g+ +i+D+V+ H + 
  gi|121637485|ref|YP_977708.1|  31 LDYLDDLGVSHLYLSPILTaVGGSTHGYDVTDPTTVSPELGGSDGLARLSAAARSRGMGLIVDIVPSHVGV 101
                                    9****************99556799*******************************************984 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0023
                                    S-TTS-BB-TTTCCCCCCCCCCCCCCCTTT.-SEEEETTCCCT CS
                  Alpha-amylase 137 flkklpdLnteneevrkelkdvvkfwlekg.idGfRlDvvkhv 178
                                     + +l+ L  e  +v  +    v +w+ +g +dG R+D  + +
  gi|121637485|ref|YP_977708.1| 202 SITSLAGLRQEDRAVFDASHAEVARWFTEGlVDGVRVDHLDGL 244
                                    5678999999999999999998889999999*******77655 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHCCCTSSSEEEEETTCCC CS
                  Alpha-amylase 304 ekklklaaillltlrGvpviYyGeEi 329
                                    e  + +a +l lt++Gvp +Y+G E+
  gi|121637485|ref|YP_977708.1| 605 ESDALAAKLLALTVPGVPDVYQGSEL 630
                                    445566788999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 5067.38
//
Query:       gi|121637486|ref|YP_977709.1|  [L=721]
Description: maltooligosyltrehalose synthase TreX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-21   75.6   0.0    7.7e-21   74.2   0.0    1.8  1  CBM_48         Carbohydrate-binding module 48 (Isoamylase N-t
    3.8e-15   56.3   0.0      2e-06   27.6   0.0    2.5  2  Alpha-amylase  Alpha amylase, catalytic domain


Domain annotation for each model (and alignments):
>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   8.6e-25   7.7e-21       1      84 []      26     112 ..      26     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 8.6e-25
                                    TSEEEEESSCEEEEEEEE-TTSSEEEEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETT....S.. CS
                         CBM_48   1 plGahvsedekgvnfrvwapnAekVslvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgps....g.. 74 
                                    plGa++++   g+nf+++++ AekV+l+l +++  +++ipl+ + +g+vW+++lp ++++g +rY++rv+gp+    g  
  gi|121637486|ref|YP_977709.1|  26 PLGATYDGA--GTNFSLFSEIAEKVELCLIDEDGVESRIPLD-EVDGYVWHAYLP-NITPG-QRYGFRVHGPFdpaaGhr 100
                                    7*****998..*******************************.69**********.56658.6**********8887467 PP

                                    ..CEEEE--TT- CS
                         CBM_48  75 ..ekklllDPya 84 
                                      ++klllDPy+
  gi|121637486|ref|YP_977709.1| 101 cdPSKLLLDPYG 112
                                    77*********5 PP

>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.2e-10     2e-06      10      81 ..     207     295 ..     196     318 .. 0.82
   2 !   26.0   0.0   6.8e-10   6.1e-06     140     333 ..     328     549 ..     307     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.2e-10
                                    CCCCCCCT-SCEEE-B-CE..........-S-TTTTSS-SCECCE-CCC--C.......CCCCCHHHHHHCTT-EEEEEE CS
                  Alpha-amylase  10 LdYlkeLGvtaiwlsPifk..........spqadhgYdiadytkidpefGtn.......edlkeLiskahekgikvilDl 72 
                                    +d l eL vta+ l P+ +             ++ gY +  + + + ++  +       +++k++++ +he gi vilD+
  gi|121637486|ref|YP_977709.1| 207 IDHLNELNVTAVELMPVHQflhdsrlldlGLRNYWGYNTFGFFAPHHQYASTrqagsavAEFKTMVRSLHEAGIEVILDV 286
                                    688999***********99999*99999955579999998888888888654222222268******************* PP

                                    --SC--TTS CS
                  Alpha-amylase  73 VvNHtsdeh 81 
                                    V NHt++ +
  gi|121637486|ref|YP_977709.1| 287 VYNHTAEGN 295
                                    *****9865 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.8e-10
                                    TS-BB-TTTCCCCCCCCCCCCCCCTTT.-SEEEETTCCCTTTCCCC.................................. CS
                  Alpha-amylase 140 klpdLnteneevrkelkdvvkfwlekg.idGfRlDvvkhvskveal.................................. 184
                                    +   Ln +++++ + + d +++w+ +  +dGfR D ++ ++ + ++                                  
  gi|121637486|ref|YP_977709.1| 328 TGNSLNARHPHTLQLIMDSLRYWVIEMhVDGFRFDLASTLARELHDvdrlsaffdlvqqdpvvsqvkliaepwdvgeggy 407
                                    55689******************98877************995554999******************************8 PP

                                    ..HCCHCCHHHHHHHHHHHTC..CGTT-EEEEE-TT-SCCCHCCCC-CGG-SICECCITTCGGGCC-CTSTTSB-SS-HH CS
                  Alpha-amylase 185 ..esngeflheftqalnetva..srkevmtvgEvssdasedlrvyttearlelemvldfphldvaqkakikeqlksisak 260
                                       +    ++e++ +   tv+   r e  t+gE+ s  +    +y  ++r  +    ++ ++ ++ ++   ++l s++ k
  gi|121637486|ref|YP_977709.1| 408 qvGNFPGLWTEWNGKYRDTVRdyWRGEPATLGEFASRLTGSSDLYEATGRRPSA---SINFVTAHDGFT-LNDLVSYNDK 483
                                    8756667899999999998887778999************99999999999998...555555555555.5677776766 PP

                                    HHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTTTTHHHHHHHHHCCCTSSSEEEEETTCCCT--- CS
                  Alpha-amylase 261 klkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsaeaekklklaaillltlrGvpviYyGeEigmtg 333
                                    + ++  +++++  + + +++  + g  D + il   +++        +++ + l+ ++G+p+i  G+Eig t 
  gi|121637486|ref|YP_977709.1| 484 HNEANGENNRDGESYNRSWNCGVEGPTDDPDILALRARQM-------RNMWATLMVSQGTPMIAHGDEIGRTQ 549
                                    66666666666666689***************99877766.......788888899**************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5084.51
//
Query:       gi|121637487|ref|YP_977710.1|  [L=729]
Description: hypothetical protein BCG_1618c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-16   60.7  30.5    2.5e-16   59.7  30.5    1.5  1  Acyl_transf_3  Acyltransferase family
  ------ inclusion threshold ------
      0.095   12.4   0.1        3.6    7.3   0.0    2.7  3  Neurensin      Neurensin


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7  30.5   2.8e-20   2.5e-16       1     335 [.      32     373 ..      32     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.8e-20
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxx RF
                  Acyl_transf_3   1 laylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla...........amlyrrr 69 
                                    +++lD+lRg+Ai lV ++H++                         + gv++F+ lSGff+             +l++  
  gi|121637487|ref|YP_977710.1|  32 RHDLDGLRGVAIALVAVFHVWF---------------------GRVSGGVDVFLALSGFFFGgkilraalnpdLSLSPIA 90 
                                    69********************.....................78999*****************997764433333333 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  70 glsklikrRilrlliplliwllliillialvaghiqanasanvtlfdet...........kglmfllfefpatghlWfLw 138
                                     +++l    i+rll +l+++l  ++ll+  +   + + a an +l+                    +    +  h W+++
  gi|121637487|ref|YP_977710.1|  91 EVIRL----IRRLLPALVVVLAGCALLTIAIQPQTRWEAFANQSLASLGyyqnwelastvSNYLRAGEAVSPLQHIWSMS 166
                                    44444....444444444444444444444444455555555555433366668****975555666668899******* PP

                                    xxxxxxxxxxxx........xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 139 alfvlylllpll........lrllrkvrkshl.....llllilllllslvfirhelfgpatsvgllplpsvlallfflfG 205
                                    +  ++yl+++ll         rl+r+ r ++l     +ll +l+l+++ ++i +++ ++at +++ +      ++ +l+G
  gi|121637487|ref|YP_977710.1| 167 VQGQFYLAFLLLvagcayllRRLFRGPRAPYLrtmfvVLLSTLTLASFIYAIVAHHAYQATAYYNTFAR----AWELLAG 242
                                    ****************99986666666555541111144455555566666666666666666665554....9****** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                  Acyl_transf_3 206 alladaddrdrnlsrglkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllfalpsrsafk. 284
                                    al++   ++ r   + + +++ ++l++++  ++++ g++           +   ++lv +g+ +l++l+ a+++      
  gi|121637487|ref|YP_977710.1| 243 ALVGAVVPHVRWPMWLRTAVATAALAAILSCGALIDGVK----------EFPGPWALVPVGATMLMILAGANRQGHPGTr 312
                                    **********99999999999999999999999999999..........5666666666666666666666666664445 PP

                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 285 .............llrylgkiSygiYliHlpllmllqkllrdwglnlgevlllvlllvvsvivs 335
                                                  l+ lg ++y+ Yl+H+pll ++ ++  + + n   ++   ++l+vs +++
  gi|121637487|ref|YP_977710.1| 313 drlplpnrllataPLVALGAMAYSWYLWHWPLLIFWLSYTGHRHAN---FVEGAAVLLVSGLLA 373
                                    888999999*********************************9666...444444444444444 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.024   2.2e+02      46      76 ..     100     130 ..      82     153 .. 0.84
   2 ?   -2.0   0.0       0.3   2.7e+03      43      60 ..     165     186 ..     133     187 .. 0.71
   3 ?    7.3   0.0    0.0004       3.6      34      72 ..     401     439 ..     380     463 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.024
                      Neurensin  46 vvgtlvlllGvtallvGylvprrlelvkseg 76 
                                      +++v+l+G + l++    ++r e++ +++
  gi|121637487|ref|YP_977710.1| 100 LPALVVVLAGCALLTIAIQPQTRWEAFANQS 130
                                    567899************9999***994444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.3
                      Neurensin  43 v....slvvgtlvlllGvtall 60 
                                          + +++l+l++G + ll
  gi|121637487|ref|YP_977710.1| 165 MsvqgQFYLAFLLLVAGCAYLL 186
                                    2334478889999999998875 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0004
                      Neurensin  34 qksesllwkvslvvgtlvlllGvtallvGylvprrlelv 72 
                                     ++ + l + ++v+g +v llGv+  ++++++ +++ + 
  gi|121637487|ref|YP_977710.1| 401 IPWRLRLRRPTIVLGSVVALLGVALTATSFTWREHVIVQ 439
                                    345555555599*********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.81u 0.38s 00:00:01.19 Elapsed: 00:00:00.58
# Mc/sec: 3785.71
//
Query:       gi|121637488|ref|YP_977711.1|  [L=230]
Description: inv protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-26   92.3   0.0    2.7e-26   91.6   0.0    1.3  1  NLPC_P60   NlpC/P60 family
  ------ inclusion threshold ------
       0.62   10.0   2.6        6.1    6.8   0.1    2.1  2  Flu_C_NS1  Influenza C non-structural protein (NS1)


Domain annotation for each model (and alignments):
>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0     3e-30   2.7e-26       1     104 [.      55     167 ..      55     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 3e-30
                                    T-BB-TT--BTT.............EB-HHHHHHHHHHTTT----SSHHHHCCCSEE..EEGGG--TTEEEEESGTGGES CS
                       NLPC_P60   1 gkpYrwGGksps.............gfDCsglvryafakagielprssgeqeaagkkkeiskselkrGDLvffktkkgis 67 
                                    g+p++w+G+  s             gfD+sgl++ya+a ag++lprssg+++++g+k  ++ +++++GDL+f+++ +g++
  gi|121637488|ref|YP_977711.1|  55 GVPFSWAGGGISgptrgtgtgintvGFDASGLIQYAYAGAGLKLPRSSGQMYKVGQK--VLPQQARKGDLIFYGP-EGTQ 131
                                    789***999999999******************************************..****************.**** PP

                                    EEEEEEETTEEEEEETTEEEEEETTSTTBHSCEEECC CS
                       NLPC_P60  68 HvgiYlgngkmlhassekvsvsslsekywkkrllgvr 104
                                     v++Ylg+g+ml+  ++ v+vs++++++++++l++v+
  gi|121637488|ref|YP_977711.1| 132 SVALYLGKGQMLEV-GDVVQVSPVRTNGMTPYLVRVL 167
                                    *************9.*****************99875 PP

>> Flu_C_NS1  Influenza C non-structural protein (NS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1   0.00068       6.1      13      51 ..     155     194 ..     140     197 .. 0.75
   2 ?    3.7   0.3     0.006        54      29      53 ..     197     221 ..     193     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00068
                      Flu_C_NS1  13 esptmtpasvemkgkk.fpidfapsniapigqnpiylspc 51 
                                     +  mtp  v + g +  p++ ap + ap+ q p+  +p+
  gi|121637488|ref|YP_977711.1| 155 RTNGMTPYLVRVLGTQpTPVQQAPVQPAPVQQAPVQQAPV 194
                                    45679*****99986538****************998885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.006
                      Flu_C_NS1  29 fpidfapsniapigqnpiylspcip 53 
                                     p++ ap + ap+ q p+  +p+ p
  gi|121637488|ref|YP_977711.1| 197 APVQQAPVQQAPVQQAPVQQAPVQP 221
                                    5778888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1257.36
//
Query:       gi|121637489|ref|YP_977712.1|  [L=94]
Description: hypothetical protein BCG_1620c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   10.2   0.2       0.28   10.0   0.2    1.1  1  DUF1177   Protein of unknown function (DUF1177)


Domain annotation for each model (and alignments):
>> DUF1177  Protein of unknown function (DUF1177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   1.5e-05      0.28     191     220 ..      56      85 ..      34      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 1.5e-05
                        DUF1177 191 nsilqPavatkaPvvgvAittetvvpGcat 220
                                     s+l+ + ++  P++ +A++t t ++G+a 
  gi|121637489|ref|YP_977712.1|  56 VSMLKGWYMSFWPIISIAVITVTSIAGYAI 85 
                                    58899999999****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 532.63
//
Query:       gi|121637490|ref|YP_977713.1|  [L=437]
Description: adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-112  376.6   0.0   1.4e-112  376.4   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0044   16.2   0.0     0.0086   15.3   0.0    1.4  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.4   0.0  1.5e-116  1.4e-112      10     404 ..      35     428 ..      27     430 .. 0.95

  Alignments for each domain:
  == domain 1  score: 376.4 bits;  conditional E-value: 1.5e-116
                                    CEEEEEEEBTEEE.ETTS-..EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                    Aminotran_3  10 llvitkaeGvylt.dvdgk..rylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                    ++v+  a+G++lt   dg+  ++lD++ss++ +++Gh hP++ +a+ +q+  + hv+fg lt+epa++la+ l++++p g
  gi|121637490|ref|YP_977713.1|  35 PVVAVAAHGAWLTlIRDGQpiEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAG 114
                                    47888899999995345544499********************************************************* PP

                                    .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGG CS
                    Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdee 166
                                    ld vf+ +sGs +ve+A K+a +y r ++ + k ++++++g++HG+t++a+s+++++ ++++l+ ++l+ +v++++    
  gi|121637490|ref|YP_977713.1| 115 LDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVP-- 192
                                    *********************************************************************999999874.. PP

                                    GTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-S.CETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSS CS
                    Aminotran_3 167 vlkeneeeeaalleelealekkkkdevaAvivEp.iqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklf 245
                                          + + a + ++ea  ++++ e+aAv+vEp +qg+gG+ +++p +l+ lr++c++++vlli+DE++tGfGrTG+lf
  gi|121637490|ref|YP_977713.1| 193 -----RDYDPAYSAAFEAQLAQHAGELAAVVVEPvVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALF 267
                                    .....33456778899999999********************************************************** PP

                                    GGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS.....B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHH CS
                    Aminotran_3 246 AlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs.....hgsTfgGnplacavalavleiieeekllenaqe 319
                                    A++hagvspD+m+++KaltgG l+l+a+l+ta+v+++++ g      hg+Tf++nplacav++a++e++  +++  ++ e
  gi|121637490|ref|YP_977713.1| 268 AADHAGVSPDIMCVGKALTGGyLSLAATLCTADVAHTISAGAagalmHGPTFMANPLACAVSVASVELLLGQDWRTRITE 347
                                    **************************************99999************************************* PP

                                    HHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHH CS
                    Aminotran_3 320 lgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidell 399
                                    l a l++gL  + + +  + +vR  G++++ie+  +++      + +a++ Gv+++++  n+++ +pp+i t +ei +++
  gi|121637490|ref|YP_977713.1| 348 LAAGLTAGLDTARALP-AVTDVRVCGAIGVIECDRPVDLA--VATPAALDRGVWLRPFR-NLVYAMPPYICTPAEITQIT 423
                                    *************999.*********************66..7899*************.*******************9 PP

                                    HHHHH CS
                    Aminotran_3 400 eilkk 404
                                    +++++
  gi|121637490|ref|YP_977713.1| 424 SAMVE 428
                                    99876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.6e-07    0.0086     170     295 ..     237     359 ..     231     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-07
                                    HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHH CS
                  Aminotran_1_2 170 leklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrp 249
                                    l++l d++++y++ll++De+  gf  +   ++a +a+v++++       ++Ka+    + ++++l++a+v+ ++   +++
  gi|121637490|ref|YP_977713.1| 237 LHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIM-----CVGKALTGGYLSLAATLCTADVAHTISAGAAG 311
                                    7788888********************9999899999999866.....45676522222356666677999999999999 PP

                                    HTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                  Aminotran_1_2 250 fls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael 295
                                     l   ++ ++  +a a+s a  +    ++ r r+ +++  l+++L+ +
  gi|121637490|ref|YP_977713.1| 312 ALMhgPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTA 359
                                    999999999998888888877666699999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 2369.89
//
Query:       gi|121637491|ref|YP_977714.1|  [L=386]
Description: 8-amino-7-oxononanoate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-57  193.8   0.0    5.5e-57  193.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.8e-07   30.4   0.0    2.7e-07   29.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      1e-06   28.4   0.0    1.6e-06   27.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.8e-06   25.1   0.0    7.9e-06   24.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0018   17.7   0.0     0.0042   16.4   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0024   16.6   0.0      0.003   16.3   0.0    1.2  1  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.6   0.0   1.8e-60   5.5e-57       4     359 ..      43     373 ..      40     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 193.6 bits;  conditional E-value: 1.8e-60
                                    EESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    ++L+sn+ylg+s++p + +   ++ +  ga+a+g++  +g++++++++e +la+f+g        + a ++++sG++a++
  gi|121637491|ref|YP_977714.1|  43 LDLASNDYLGLSRHPAVIDGGVQALRiwGAGATGSRLVTGDTKLHQQFEAELAEFVG--------AAAGLLFSSGYTANL 114
                                    79************8888877777778******************************........999************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                     a+  l    pg+  ++++ ++as  +++rls++ vv  p       h d++a+++al++  e+++   v+++ s+++ +
  gi|121637491|ref|YP_977714.1| 115 GAVVGLSG--PGSLLVSDARSHASLVDACRLSRARVVVTP-------HRDVDAVDAALRSRDEQRA---VVVTDSVFSAD 182
                                    *******9..******************************.......*************999999...*********** PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH..HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavat..ranveeepnllivgslsKafGlaGeRvGyilgnaav 239
                                    G++a+  el ++   ++++++ll+vDea++ +v g  +   +   ++++ +p+++ +++lsKa+G+ G   G +lg   v
  gi|121637491|ref|YP_977714.1| 183 GSLAPVRELLEV---CRRHGALLLVDEAHGLGVRGGGRG--LlyELGLAGAPDVVMTTTLSKALGSQG---GVVLGPTPV 254
                                    ************...********************7632..2459***********************...********* PP

                                    HHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHH CS
                  Aminotran_1_2 240 vsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetake 319
                                    + +l +++rpf++++ l++a++ a+++al++ +    + q + +++ el   +   g++ ++  s+m+++ ++++e+a +
  gi|121637491|ref|YP_977714.1| 255 RAHLIDAARPFIFDTGLAPAAVGAARAALRVLQAEPWRPQAVLNHAGELARMC---GVAAVPD-SAMVSVILGEPESAVA 330
                                    *****************************************************...9999985.**************** PP

                                    HHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHH CS
                  Aminotran_1_2 320 lskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleel 359
                                    ++ ++l+  gv v  ++++tv   ++rlR+t  A+l++ ele +
  gi|121637491|ref|YP_977714.1| 331 AAAACLDA-GVKVGCFRPPTVpagTSRLRLTArASLNAGELELA 373
                                    ********.*****************************999876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0     9e-11   2.7e-07      39     180 ..      81     210 ..      55     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 9e-11
                                    HHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE CS
                    Aminotran_5  39 keatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv 118
                                    +  tk  ++ ++++ae+++a+    ++f sG t  + +v       l+   + +v++a  ha l   +++++   a+v+v
  gi|121637491|ref|YP_977714.1|  81 TGDTKLHQQFEAELAEFVGAAA--GLLFSSGYTANLGAV--VG---LSGPGSLLVSDARSHASL---VDACRLSRARVVV 150
                                    55588999*************6..*********444444..33...56678999**********...5555556789988 PP

                                    EEBETTSCBE.GGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT CS
                    Aminotran_5 119 ipldeegeld.ldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav 180
                                     p  +   +d +d++    +e+ ++v    v ++ G + pv e+ ++++++gal+lvD a ++
  gi|121637491|ref|YP_977714.1| 151 TPHRD---VDaVDAALRSRDEQRAVVVTDSVFSADGSLAPVRELLEVCRRHGALLLVDEAHGL 210
                                    77733...333556677778999999999*****************************99876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   5.2e-10   1.6e-06      22     156 ..      84     217 ..      72     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.2e-10
                                    SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-G CS
                DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidp 101
                                     +  ++FE+++a+++g++  + +ssG +A++ a   l+ gpg  ++  + + ++ + a + + a++v           d+
  gi|121637491|ref|YP_977714.1|  84 TKLHQQFEAELAEFVGAAAGLLFSSGYTANLGAVVGLS-GPGSLLVSDARSHASLVDACRLSRARVVVTP------HRDV 156
                                    45679************************987765543.5899999999999999999999999988642......3477 PP

                                    GGCGGG--TTE..EEEEEB-GG....GB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTE CS
                DegT_DnrJ_EryC1 102 aaieaaitert..kaIlpVhly....GqvadmdalkaiaakhglkvieDaAhAlGatykgk 156
                                    +a+ aa+ +r   +a+++ + +    G  a + +l +++++hg  ++ D Ah+lG +  g+
  gi|121637491|ref|YP_977714.1| 157 DAVDAALRSRDeqRAVVVTDSVfsadGSLAPVRELLEVCRRHGALLLVDEAHGLGVRGGGR 217
                                    777777777766677777653323339****************************987775 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.6e-09   7.9e-06      54     176 ..      87     208 ..      80     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-09
                                    HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHH CS
                Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleeleka 133
                                    ++ +e+++a+  g++a+l++ssG +A   a++ l   G+ +v++   + +  + ++    ++ + + + d++ +++  + 
  gi|121637491|ref|YP_977714.1|  87 HQQFEAELAEFVGAAAGLLFSSGYTANLGAVVGLSGPGSLLVSDARSHASLVDACRLSRARV-VVTPHRDVDAVDAALRS 165
                                    6899*******************************************999999999888887.55667899999999999 PP

                                    CCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 134 ikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                     +e+  +v ++++ +   +++ +++++++++ +g+l++vD + 
  gi|121637491|ref|YP_977714.1| 166 RDEQRAVVVTDSVFSADGSLAPVRELLEVCRRHGALLLVDEAH 208
                                    99999***********************************876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-06    0.0042      28     169 ..      81     207 ..      68     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                    CT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTT CS
                Beta_elim_lyase  28 YgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaG 107
                                     g+ k  +++e+++ae +g++a+l + +G  An  ++  l  +g+  + + ++h     +  ++      +r + +++  
  gi|121637491|ref|YP_977714.1|  81 TGDTKLHQQFEAELAEFVGAAAGLLFSSGYTANLGAVVGLSGPGSLLVSDARSHASLVDACRLSR-----ARVVVTPH-- 153
                                    677888999*******************************9999999999999998776655533.....34445555.. PP

                                    BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                      d++++ aa++   +  ++ +++++t  + +a G   sl+ +re+ ++++++g  l++D A
  gi|121637491|ref|YP_977714.1| 154 -RDVDAVDAALRS--R--DEQRAVVVTDSVFSADG---SLAPVRELLEVCRRHGALLLVDEA 207
                                    .589*********..5..66888999999998777...56778999999*********9977 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.9e-07     0.003     187     314 ..     164     292 ..      85     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-07
                                    CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT....TTTSSSSGGGGCTS--SEE...EE CS
                    Aminotran_3 187 kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf....GrTGklfAlehagvspDlm...tl 259
                                    +  +++ a v++  + ++ G  ++    +++l e+c++h++ll+vDE   G+    G  G l+ l     +pD++   tl
  gi|121637491|ref|YP_977714.1| 164 RSRDEQRAVVVTDSVFSADGSLAP----VRELLEVCRRHGALLLVDEAH-GLgvrgGGRGLLYELGL-AGAPDVVmttTL 237
                                    566677777777778888887766....578889*************65.66113333344444443.457998533357 PP

                                    -GGGG..TTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHH CS
                    Aminotran_3 260 aKalt..gGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekll 314
                                    +Kal+  gG  l  + ++a + +a +p    +     p a  +a+a+l++++ e + 
  gi|121637491|ref|YP_977714.1| 238 SKALGsqGGVVLGPTPVRAHLIDAARPFIFDTGL--APAAVGAARAALRVLQAEPWR 292
                                    8***854569999999999999998776655544..488888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2618.13
//
Query:       gi|121637492|ref|YP_977715.1|  [L=226]
Description: dithiobiotin synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-28   97.4   0.1    1.2e-27   97.1   0.1    1.1  1  AAA_26       AAA domain
    1.7e-06   28.1   0.0    3.4e-06   27.1   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0011   18.3   5.0     0.0035   16.7   2.2    2.5  3  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
  ------ inclusion threshold ------
       0.14   11.6   2.2       0.16   11.4   0.5    1.8  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
       0.15   11.5   1.2       0.25   10.7   1.2    1.3  1  ParA         NUBPL iron-transfer P-loop NTPase
       0.87    8.7   2.3        1.5    8.0   2.3    1.3  1  ArsA_ATPase  Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.1   3.9e-31   1.2e-27       3     186 ..       4     190 ..       2     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 3.9e-31
                         AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.dedselikellgldqtyelpeplalsaplspelaarq 81 
                                    ++vtgt+tgvGKTvv+++L++a ++ g+ v++ KP+qtg+ + d+d + + +l+g++q   l+   ++ +p++p +aa++
  gi|121637492|ref|YP_977715.1|   4 LVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARgDDDLAEVGRLAGVTQLAGLA---RYPQPMAPAAAAEH 80 
                                    79***************************************9788999999999888765533...67777777777777 PP

                         AAA_26  82 egedid.lekiv...kelekdadivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealrqkn 156
                                     g ++   ++iv    +l    ++++VEGaggl+v ++e   +  d+a    a  ++V++++lgt+n++ lt+eal  ++
  gi|121637492|ref|YP_977715.1|  81 AGMALPaRDQIVrliADLDRPGRLTLVEGAGGLLVELAEPgVTLRDVAVDVAAVALVVVTADLGTLNHTKLTLEALAAQQ 160
                                    775555344444555999999***************999968888*********************************** PP

                         AAA_26 157 vrvlGvilNkvrnpenvetlekksgipvlG 186
                                    v  +G+++  +++p  + ++++ s +  ++
  gi|121637492|ref|YP_977715.1| 161 VSCAGLVIGSWPDPPGLVAASNRSALARIA 190
                                    ***********9995555554444443333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.1e-09   3.4e-06       1      68 [.       4     100 ..       4     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.1e-09
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep......................... 54 
                                    +++++t  GvGKT+++a+La a  ++g +V++ + +++    +a     ++d +                          
  gi|121637492|ref|YP_977715.1|   4 LVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKpVQTG---TA-----RGDDDLaevgrlagvtqlaglarypqpmapa 75 
                                    589*****************************9955555...22.....2222223356666777777777777777777 PP

                                    ...........CCHCCCHHHHHHCH CS
                                    ...........xxxxxxxxxxxxxx RF
                           CbiA  55 ...........dlkrllellealgk 68 
                                                ++++++l+++l++
  gi|121637492|ref|YP_977715.1|  76 aaaehagmalpARDQIVRLIADLDR 100
                                    7777777777777777777777765 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.2   1.2e-06    0.0035      14      56 ..       3      45 ..       1      59 [. 0.89
   2 ?    0.5   0.0       0.1     3e+02      75     109 ..      91     124 ..      87     142 .. 0.74
   3 ?    0.5   0.1      0.11   3.2e+02      59     130 ..     120     185 ..     107     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                        DUF1611 14 rvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili 56
                                   +++v GT+  vGK + + +l+ a++++G+++a++   qtg   
  gi|121637492|ref|YP_977715.1|  3 ILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTAR 45
                                   67899*****************************999999765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                        DUF1611  75 veglvkkaaeeeepdlilveGQgsLt.hpaysgvtl 109
                                    + +l+ ++++     l lveG g+L+   a +gvtl
  gi|121637492|ref|YP_977715.1|  91 IVRLIADLDR-PG-RLTLVEGAGGLLvELAEPGVTL 124
                                    5567777775.45.7899999999986555566766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.11
                        DUF1611  59 egvvldavvvdfvaGaveglvkkaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkh 130
                                     gv l  v vd +a a+  ++ ++   ++   + +e   +L  +  s+  +gl++Gs Pd   L+ + +r++
  gi|121637492|ref|YP_977715.1| 120 PGVTLRDVAVDVAAVALVVVTADLGTLNH-TKLTLE---ALAAQQVSC--AGLVIGSWPDPPGLVAASNRSA 185
                                    55555555555555555555555554333.333333...233333333..5677777777666666666555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   5.5e-05      0.16       1      34 [.       1      34 [.       1      38 [. 0.92
   2 ?   -1.2   0.0      0.39   1.2e+03     131     163 ..     125     159 ..     110     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                       CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvl 34
                                   m++l+++G   GvG+t + aaLa a ++ g  v 
  gi|121637492|ref|YP_977715.1|  1 MTILVVTGTGTGVGKTVVCAALASAARQAGIDVA 34
                                   99***********************999887775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                       CBP_BcsQ 131 trellaladlvllvvepdanc..hvrLhqqalpaa 163
                                       ++ +a + l vv++d  +  h +L  +al+a+
  gi|121637492|ref|YP_977715.1| 125 RDVAVDVAAVALVVVTADLGTlnHTKLTLEALAAQ 159
                                    55567788899999999977444888877777765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   8.5e-05      0.25       6      37 ..       3      35 ..       1      38 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.5e-05
                           ParA  6 iavlSgKG.GVGKStvavnlAlaLakkglkvgl 37
                                   i+v+ g G GVGK+ v + lA a ++ g++v++
  gi|121637492|ref|YP_977715.1|  3 ILVVTGTGtGVGKTVVCAALASAARQAGIDVAV 35
                                   778888887*********************997 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.3   0.00049       1.5       1      32 [.       1      33 [.       1      37 [. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00049
                                   -EEEEEEEST.TSSHHHHHHHHHHHHHHTTS-E CS
                    ArsA_ATPase  1 lkvilvgGKG.GVGKttvsaatavklsekgkkv 32
                                   +++++v+G G GVGKt v aa+a    + g +v
  gi|121637492|ref|YP_977715.1|  1 MTILVVTGTGtGVGKTVVCAALASAARQAGIDV 33
                                   678999**999***********98877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1566.72
//
Query:       gi|121637493|ref|YP_977716.1|  [L=169]
Description: hypothetical protein BCG_1624 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-07   30.1   0.0    4.4e-07   29.9   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.5e-11   4.4e-07      16     121 ..      28     134 ..       9     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.5e-11
                2_5_RNA_ligase2  16 lydkayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFehkksvvylsvsdsealqalraalleal 95 
                                      + + p+ +pH++L+    + +   +++e l ++a++  p+++ ++++  F++ + v ++ v ++++l al+a++ + +
  gi|121637493|ref|YP_977716.1|  28 GIPSQAPASRPHVSLAVAERIAP---EVDEPLGAVARR-LPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLC 103
                                    4566789999******9988885...788888888854.57***********976666666668**************** PP

                2_5_RNA_ligase2  96 peagdkeds.....geftPHlTiaqsadsts 121
                                    +++ +         g++t H+T+a++    +
  gi|121637493|ref|YP_977716.1| 104 GPHLAPAPManslpGQWTAHVTLARRVGGHQ 134
                                    ***77766588899**********9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1175.57
//
Query:       gi|121637494|ref|YP_977717.1|  [L=318]
Description: hypothetical protein BCG_1625c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-64  217.2   3.4    4.3e-64  216.9   3.4    1.1  1  DUF222    Domain of unknown function (DUF222)
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.015   15.5   0.1    2.4  3  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   3.4   4.8e-68   4.3e-64     103     301 .]       2     223 ..       1     223 [. 0.97

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 4.8e-68
                         DUF222 103 atvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltk.dedGmsrisgeldaeaaaaldavLd 181
                                    +t+++aea+l+++aa+++p+eLa+ ++r++++l+pDg+ +d+e+ar+r++tl++ + dGmsr+sg+l+++a+a+++avL+
  gi|121637494|ref|YP_977717.1|   2 STRQAAEADLAGKAAQYRPDELARYAQRVMDWLHPDGDLTDTERARKRGITLSNqQYDGMSRLSGYLTPQARATFEAVLA 81 
                                    799***************************************************9************************* PP

                         DUF222 182 slaap.vcap..............dgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvhvtaeeltaaagga 246
                                    +laap   +p              ++++D+Rs+aqr++D+Lla+lr+++a+g+l++h+g+p+++vv++t+++l++ ag+ 
  gi|121637494|ref|YP_977717.1|  82 KLAAPgATNPddhtpvidttpdaaAIDRDTRSQAQRNHDGLLAGLRALIASGELGQHNGLPVSIVVTTTLTDLQTGAGK- 160
                                    *****88888*********************************************************************. PP

                         DUF222 247 altgggglLpasdvrrLAkdAt..........laifdepagrpldlgrtkrtasaalrralraRD 301
                                    + tggg+lLp++dv+r+ ++A+           aifd+  g+pl+l++tkr+as+a+r++l a D
  gi|121637494|ref|YP_977717.1| 161 GFTGGGTLLPMADVIRMTSHAHhyspasgrypQAIFDH--GTPLALYHTKRLASPAQRIMLFAND 223
                                    **************************999986668888..*********************9877 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.69   6.2e+03      14      23 ..     179     188 ..     174     203 .. 0.63
   2 ?   15.5   0.1   1.6e-06     0.015       4      42 ..     226     266 ..     224     271 .. 0.85
   3 ?   -4.9   4.0         2   1.8e+04      13      27 ..     297     309 ..     289     317 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.69
                            HNH  14 levdHiipis 23 
                                    ++ +H  p s
  gi|121637494|ref|YP_977717.1| 179 SHAHHYSPAS 188
                                    5666655543 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-06
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHn 42 
                                    C +++ +   + ++ +H+  +   g++di +l+l+C   ++
  gi|121637494|ref|YP_977717.1| 226 CTKPGCDApaYHSQAHHVTGWTSTGRTDITDLTLACDPDNR 266
                                    6666666666889***********************98887 PP

  == domain 3  score: -4.9 bits;  conditional E-value: 2
                            HNH  13 alevdHiipisqgga 27 
                                     ++ +H + + +  +
  gi|121637494|ref|YP_977717.1| 297 TNTFHHHEKLLR--H 309
                                    567777766663..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2353.56
//
Query:       gi|121637495|ref|YP_977718.1|  [L=222]
Description: hypothetical protein BCG_1626c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-19   70.4   2.5    2.1e-19   70.2   2.5    1.2  1  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   2.5   1.1e-23   2.1e-19       3      98 ..      38     143 ..      36     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.1e-23
                         DUF222   3 aaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lpa 71 
                                    + le+le + rrl+av+++l+++l+ ++s+ee g++ ++ ++a+rlri+  +A+ r++ A++l++r           L+a
  gi|121637495|ref|YP_977718.1|  38 RSLERLECLVRRLPAVGHTLINQLDTQASEEELGGT-LCCALANRLRITKPDAALRIADAADLGPRraltgeplapqLTA 116
                                    6799********************************.******************************************* PP

                         DUF222  72 vaaalraGdidlrqvrvIaartdllpd 98 
                                    +a+a+r+G i++ +++vI+a ++   +
  gi|121637495|ref|YP_977718.1| 117 TATAQRQGLIGEAHIKVIRALFRPPAR 143
                                    *******************99886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1548.57
//
Query:       gi|121637496|ref|YP_977719.1|  [L=349]
Description: biotin synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-15   56.0   0.1    1.9e-14   54.4   0.1    1.8  2  Radical_SAM  Radical SAM superfamily
    6.6e-12   45.4   0.0    1.7e-11   44.1   0.0    1.7  1  BATS         Biotin and Thiamin Synthesis associated domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   2.2e-18   1.9e-14       4     165 ..      82     239 ..      80     241 .. 0.81
   2 ?    0.6   0.0     0.074   6.7e+02      91     116 ..     235     261 ..     228     302 .. 0.68

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.2e-18
                                    ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE....SSTGGGSTTHHHHHHHHHHTCCCTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilg....ggepllypdfvellerlaklavpgi 78 
                                    t gC+ +C+fC+++   ++ +r++ l++ +++e +k+  a+ g ++++i+      +e l+ +  +  +e+++    +++
  gi|121637496|ref|YP_977719.1|  82 TGGCPEDCHFCSQSGLFASPVRSAWLDIPSLVEAAKQT-AKSGaTEFCIVAavrgPDERLM-AQVAAGIEAIR----NEV 155
                                    68************999999999999999999999999.7999666666665543333333.32322222222....589 PP

                                    EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                    +i + ++ ++++ e+++ l+ +gv r++++le+a ++ + + +  +ht+ee++++l + r+ag+++++ +i+g+ Ge+ +
  gi|121637496|ref|YP_977719.1| 156 EINIACSLGMLTAEQVDQLAARGVHRYNHNLETARSF-FANVV-TTHTWEERWQTLSMVRDAGMEVCCGGILGM-GETLQ 232
                                    999999999999*************************.*****.9********************666666666.59998 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 159 eleelle 165
                                    ++ e++ 
  gi|121637496|ref|YP_977719.1| 233 QRAEFAA 239
                                    8888775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.074
                                    HHHHHHHHHTT-SEEEEEEBSSSHH.H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                    Radical_SAM  91 eeklerllelgvdrvslgleaadde.k 116
                                     e++++l+elg+d v l+   + +  +
  gi|121637496|ref|YP_977719.1| 235 AEFAAELAELGPDEVPLNFLNPRPGtP 261
                                    589999999999999998877777652 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.9e-15   1.7e-11       1      83 [.     250     338 ..     250     340 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.9e-15
                                    E--B----TCCCC...........HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH..HHHCCT--EEE-C---TTTGGGSE CS
                           BATS   1 siprlrpikdtpl...........lkiiaalRlllPkag.illsgResaefrdq..lllklGansisagsktevggyafl 66 
                                    ++++l+p ++tp+           lk +aa+Rl+lP+++ ++++gRe    +      +  G+n++++g+        +l
  gi|121637496|ref|YP_977719.1| 250 PLNFLNPRPGTPFadlevmpvgdaLKAVAAFRLALPRTMlRFAGGREITLGDLGakRGILGGINAVIVGN--------YL 321
                                    89*********************************************9998766554458**********........** PP

                                    SSTT-TCCCCHHHHHHT CS
                           BATS  67 ttdgrsleedvkmleel 83 
                                    tt gr +e d+++l el
  gi|121637496|ref|YP_977719.1| 322 TTLGRPAEADLELLDEL 338
                                    *************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2356.98
//
Query:       gi|121637497|ref|YP_977720.1|  [L=79]
Description: hypothetical protein BCG_1628 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   14.9   0.3      0.029   14.3   0.3    1.4  1  Nudix_N_2        Nudix N-terminal
      0.021   14.5   4.7      0.062   13.0   4.7    1.8  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.063   12.8   0.0      0.098   12.2   0.0    1.3  1  DmpG_comm        DmpG-like communication domain
       0.11   13.0   0.4       0.19   12.3   0.4    1.3  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


Domain annotation for each model (and alignments):
>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   6.5e-06     0.029       1      17 [.      42      58 ..      42      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-06
                                   -B-TTT--B-EEE--TT CS
                      Nudix_N_2  1 kFCsqCGtpvelripdg 17
                                   +FC qCG ++  ++ ++
  gi|121637497|ref|YP_977720.1| 42 RFCAQCGRRMVVQVRPD 58
                                   8********77665443 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.7   1.4e-05     0.062       4      24 ..      42      64 ..      42      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                  zf-NADH-PPase  4 rFCgrCGaptepa..eggwarvC 24
                                   rFC++CG +++++  ++gw  +C
  gi|121637497|ref|YP_977720.1| 42 RFCAQCGRRMVVQvrPDGWWARC 64
                                   9*********8651266888888 PP

>> DmpG_comm  DmpG-like communication domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05     0.098       5      47 ..      10      53 ..       7      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                      DmpG_comm  5 reslvlGyaGVYSsFl.lhaeraaerygvdardilvelGrrklv 47
                                   r+ ++ G ++VY + l   a   a+r g+++     ++Grr +v
  gi|121637497|ref|YP_977720.1| 10 RAPVAAGVYNVYTGELaDTATPTAARMGLEPPRFCAQCGRRMVV 53
                                   56678899999988661567889******************998 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   4.2e-05      0.19       7      32 ..      43      67 ..      43      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkrhyY.rCsty 32
                                   +C++CG++m+++ r   +  + rCs++
  gi|121637497|ref|YP_977720.1| 43 FCAQCGRRMVVQVRP--DGWWaRCSRH 67
                                   7*********98663..3344466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 539.78
//
Query:       gi|121637498|ref|YP_977721.1|  [L=221]
Description: hypothetical protein BCG_1629 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-78  263.1   9.4    1.2e-78  262.9   9.4    1.1  1  DUF2567   Protein of unknown function (DUF2567)
  ------ inclusion threshold ------
        3.7    8.0  10.1        4.7    7.7   6.6    2.6  2  MerC      MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> DUF2567  Protein of unknown function (DUF2567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.9   9.4   1.4e-82   1.2e-78       1     166 []      32     198 ..      32     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 1.4e-82
                        DUF2567   1 lavvGvlvGalWawiaPpvhavvaltrsgervkaylGnesdrffvaaalllgllavlavvaavlvWqaRahRGpvmvaal 80 
                                    l+++GvlvG+lWawiaPp+havva+tr+gerv++ylG+es++ff+a+++llgll+vlavva+ l+Wq+R+hRGp+mva+l
  gi|121637498|ref|YP_977721.1|  32 LSATGVLVGGLWAWIAPPIHAVVAITRAGERVHEYLGSESQNFFIAPFMLLGLLSVLAVVASALMWQWREHRGPQMVAGL 111
                                    5789**************************************************************************** PP

                        DUF2567  81 aiglvaaaalaaevGallvklRygaldvdavpvse.earvayvveaPpvffgdgplqiavtlllpaaiaalvYallavas 159
                                    +igl++aaa+aa+vGal+v+lRygald+d+vp+s+ ++ ++yv++aPpvff+++plqia+tl++pa+ia+lvYalla+ +
  gi|121637498|ref|YP_977721.1| 112 SIGLTTAAAIAAGVGALVVRLRYGALDFDTVPLSRgDHALTYVTQAPPVFFARRPLQIALTLMWPAGIASLVYALLAAGT 191
                                    ***********************************99******************************************* PP

                        DUF2567 160 ardDLGa 166
                                    ardDLG+
  gi|121637498|ref|YP_977721.1| 192 ARDDLGG 198
                                    *****96 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.6   0.00052       4.7      38      80 ..      79     121 ..      24     158 .. 0.83
   2 ?    0.2   0.1      0.11     1e+03      63      83 ..     168     188 ..     150     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00052
                           MerC  38 lhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillva 80 
                                    +  + l+ v+a+   al++ +r+hr +++++ + +Gl+  ++ 
  gi|121637498|ref|YP_977721.1|  79 FMLLGLLSVLAVVASALMWQWREHRGPQMVAGLSIGLTTAAAI 121
                                    4556667789999999********************9977643 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                           MerC  63 ktsvlvlgalGllillvalfl 83 
                                    +  ++++  +G++ l++al++
  gi|121637498|ref|YP_977721.1| 168 QIALTLMWPAGIASLVYALLA 188
                                    334444444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1732.28
//
Query:       gi|121637499|ref|YP_977722.1|  [L=446]
Description: hypothetical protein BCG_1630c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.9e-105  351.7   0.0   3.6e-105  351.4   0.0    1.1  1  LIP           Secretory lipase
  ------ inclusion threshold ------
       0.27   10.7   0.8          6    6.3   0.2    2.1  2  Peptidase_S9  Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.4   0.0    4e-109  3.6e-105       2     285 ..     129     406 ..     128     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 351.4 bits;  conditional E-value: 4e-109
                            LIP   2 qfksklstvatqaelllivplLkeGyyVvvpDyeGpkstftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgG 81 
                                    ++++k+ +++tq+ell+i+++L+eG++V+vpD+eGpk+++++++++g++vLd+iraal+se+v g++++++++lwGYSgG
  gi|121637499|ref|YP_977722.1| 129 RRRAKALGSLTQMELLMISAALAEGWAVSVPDHEGPKGLWGSPYEPGYRVLDGIRAALNSERV-GLSPATPIGLWGYSGG 207
                                    6789999********************************************************.**************** PP

                            LIP  82 slAsawAaelqpeYAPelelvGaalGgfvanltavaeavdgtvfaGlialalnglaneypelkkilkeevneearealek 161
                                    +lAsawAae+++eYAP+l++vGa+lG++v++l++++++++gt++aGl+al++++l+++yp l++++ke++n+e+r+ le+
  gi|121637499|ref|YP_977722.1| 208 GLASAWAAEACGEYAPDLDIVGAVLGSPVGDLGHTFRRLNGTLLAGLPALVVAALQHSYPGLARVIKEHANDEGRQLLEQ 287
                                    ******************************************************************************** PP

                            LIP 162 lsencladalikyagesyltgdkrafekgsdvlkdetikkvlednklsksavPqiPvlvyhgvidelipikdakklaknw 241
                                    l+e++++da+i++ag+++  gd+ + e+ +d+l+++++++v+ d+kl +savP++Pvl++++v+d+li+++d+++la+++
  gi|121637499|ref|YP_977722.1| 288 LTEMTTVDAVIRMAGRDM--GDFLD-EPLEDILSTPEVSHVFGDTKL-GSAVPTPPVLIVQAVHDYLIDVSDIDALADSY 363
                                    *****************9..99999.*********************.******************************** PP

                            LIP 242 cdkgiaslefaedlssgHlaetlvgapaaltWitdRfsgkpavd 285
                                    +++g a++++++dl+s+H++ ++++ap++l+W+tdRf+gkp++d
  gi|121637499|ref|YP_977722.1| 364 TAGG-ANVTYHRDLFSEHVSLHPLSAPMTLRWLTDRFAGKPLTD 406
                                    *999.6***********************************986 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2   0.00067         6      65      83 ..     198     216 ..     179     221 .. 0.85
   2 ?    2.6   0.0    0.0092        82     142     190 ..     336     384 ..     309     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00067
                                    GEEEEEETHHHHHHHHHHH CS
                   Peptidase_S9  65 rlaitGgSyGGyltgaaln 83 
                                     ++++G S GG+ +++a++
  gi|121637499|ref|YP_977722.1| 198 PIGLWGYSGGGLASAWAAE 216
                                    689**************97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0092
                                    ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTS CS
                   Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgk 190
                                     +pp+L++++ +D+ + ++    l++  +  g nv ++ +  + H++  
  gi|121637499|ref|YP_977722.1| 336 PTPPVLIVQAVHDYLIDVSDIDALADSYTAGGANVTYHRDLFSEHVSLH 384
                                    589***************9999999999999999999999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2824.44
//
Query:       gi|121637500|ref|YP_977723.1|  [L=236]
Description: hypothetical protein BCG_1631c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   34.8   0.0    2.2e-08   34.2   0.0    1.3  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.035   14.2   0.1      0.074   13.1   0.1    1.6  1  PapA_C    Phthiocerol/phthiodiolone dimycocerosyl transferase
       0.15   11.7   0.0       0.21   11.1   0.0    1.2  1  NUDIX_2   Nucleotide hydrolase


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   3.7e-12   2.2e-08      16     127 ..      32     136 ..      17     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.7e-12
                                    EEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE..EEEEEEEEEEEE CS
                          NUDIX  16 evLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd..eheilyvfleev 92 
                                     vLl +r+k p +g W+lPgG+++ +E+    +rR l+E + l     + l++l+ la + +p++    ++i  ++l+ v
  gi|121637500|ref|YP_977723.1|  32 NVLLWQRAKEPQRGaWSLPGGRLRNDEDMTSSVRRQLAEKVDL-----RELAHLEQLAVFSDPHRLpgIRMIASTYLGVV 106
                                    39999***999999****************************9.....66777778888889999877777778888666 PP

                                    CSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHH CS
                          NUDIX  93 egelepndenevsevrwvpleellkeklaaesrkl 127
                                     +  +p+ +++    rw+p+  l  +++a ++ ++
  gi|121637500|ref|YP_977723.1| 107 PSPATPELPAD---TRWHPVSSL--PPMAFDHGPM 136
                                    66666665555...689999999..6656655555 PP

>> PapA_C  Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.2e-05     0.074       8      74 ..      60     128 ..      58     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHCTHHHHC--BGGGGGG-.S-SSS--...EEEE-S---TT----TTEEEEEEE......... CS
                         PapA_C   8 vsaqlradLadGvvqqsllhpaeqlaa.akpglPp...vvitNlGvipalrlPegLevedfrsviaselga 74 
                                    ++  +r+ La+ v ++ l+h  + ++  ++ +lP    ++ t lGv+p++++Pe    ++  ++++s+l++
  gi|121637500|ref|YP_977723.1|  60 MTSSVRRQLAEKVDLRELAHLEQLAVFsDPHRLPGirmIASTYLGVVPSPATPELPADTR--WHPVSSLPP 128
                                    667789999999999999998888776656666667779**************9544444..444444444 PP

>> NUDIX_2  Nucleotide hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.6e-05      0.21      59      98 ..      32      75 ..      12      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                        NUDIX_2 59 hvLlLqielq....efkLpggklksgedeiegLkrkLakklske 98
                                    vLl q++++     + Lpgg+l+++ed  + ++r+La+k+  +
  gi|121637500|ref|YP_977723.1| 32 NVLLWQRAKEpqrgAWSLPGGRLRNDEDMTSSVRRQLAEKVDLR 75
                                   478888755544557************************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1849.48
//
Query:       gi|121637501|ref|YP_977724.1|  [L=349]
Description: quinolinate synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.7e-107  359.1   0.0   1.9e-107  358.9   0.0    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.9   0.0  1.1e-111  1.9e-107       2     299 .]      37     341 ..      36     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 358.9 bits;  conditional E-value: 1.1e-111
                                    HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HH CS
                           NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsl 81 
                                    ei++l + + a++laHnYq ++iq++ad+vGDSl+L+r aae+ +++ivfcGVhFMaetakiLsp+k+vl+pd++agCsl
  gi|121637501|ref|YP_977724.1|  37 EIRRLAHLRGATVLAHNYQLPAIQDVADHVGDSLALSRVAAEAPEDTIVFCGVHFMAETAKILSPHKTVLIPDQRAGCSL 116
                                    79999999************************************************************************ PP

                                    HCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS.-SEEEEES-HHHHHHHHHHH.SEEEEE CS
                           NadA  82 admitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealk.ekkilflPDqnLgryvakklgekkiil 160
                                    ad+it +e++++k+e+p+a+vv+YvN++a+vKal+di+cTSsnav+vv +++ ++++lf+PDq+Lg++v++ +g+k++++
  gi|121637501|ref|YP_977724.1| 117 ADSITPDELRAWKDEHPGAVVVSYVNTTAAVKALTDICCTSSNAVDVVASIDpDREVLFCPDQFLGAHVRRVTGRKNLHV 196
                                    ***************************************************55*************************** PP

                                    SSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS...........-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-T CS
                           NadA 161 wkgaCsvHeefkaeeveelkeehpdakvlvHPEc...........keevveaadvvgSTsqiikavkeseakefiigTel 229
                                    w+g+C+vH+ ++ +e+++  ++hpda+++vHPEc           + +  +++  + ST ++++a+++++a++++++Te+
  gi|121637501|ref|YP_977724.1| 197 WAGECHVHAGINGDELADQARAHPDAELFVHPECgcatsalylagEGAFPAERVKILSTGGMLEAAHTTRARQVLVATEV 276
                                    ********************************************999999****************************** PP

                                    HHHHHHHHH-TTSEEE.....ECS.SSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                           NadA 230 glverlkkeapekefialsaeaae.eavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                    g++++l+++ape +f a     ++ +a+C++Mk+it++ ll++L e ++ e++vd+ +a++ +++++rm+e
  gi|121637501|ref|YP_977724.1| 277 GMLHQLRRAAPEVDFRA-----VNdRASCKYMKMITPAALLRCLVEGAD-EVHVDPGIAASGRRSVQRMIE 341
                                    ****************3.....343789*******************99.*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2376.30
//
Query:       gi|121637502|ref|YP_977725.1|  [L=527]
Description: L-aspartate oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-88  296.4  17.0    3.7e-88  296.4  17.0    1.9  2  FAD_binding_2   FAD binding domain
    4.2e-08   33.2   0.5    2.6e-05   24.2   0.2    2.3  2  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.9e-07   30.6   9.2     0.0019   17.5   4.5    4.0  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.9  11.3    0.00028   20.6  11.0    1.8  1  DAO             FAD dependent oxidoreductase
    0.00011   21.6   2.4    0.00011   21.6   2.4    1.7  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00015   20.6   4.8    0.00086   18.1   1.9    2.4  2  HI0933_like     HI0933-like protein
     0.0002   20.9   6.4     0.0002   20.9   6.4    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00075   19.7   0.8    0.00075   19.7   0.8    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0018   17.4   3.9     0.0018   17.4   3.9    2.7  3  GIDA            Glucose inhibited division protein A
     0.0033   16.7   0.7     0.0094   15.2   0.3    1.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.004   16.5   2.1      0.013   14.8   1.7    2.0  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.053   12.6   0.8       0.11   11.6   0.8    1.5  1  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.4  17.0   2.4e-91   3.7e-88       1     417 []      11     381 ..      11     381 .. 0.95
   2 ?   -5.1   5.2       8.6   1.3e+04       5      24 ..     387     405 ..     385     412 .. 0.83

  Alignments for each domain:
  == domain 1  score: 296.4 bits;  conditional E-value: 2.4e-91
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-H CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.atawsqGgidavlspeqkkagikdspelhrtdtlkaldeladq 79 
                                    Dv+ViG+G+AGLaAAl+a +aG++v+v++k+ ++   at+++qGgi++vl p +     +ds+++h+ dtl+a+++l+d+
  gi|121637502|ref|YP_977725.1|  11 DVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQTHVtATHYAQGGIAVVL-PDN-----DDSVDAHVADTLAAGAGLCDP 84 
                                    9**********************************99*************.555.....6******************** PP

                                    HHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEE CS
                  FAD_binding_2  80 plveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdf 158
                                    ++v  +v+ + +av+ L   g++++++  g++++++ Gg+s++ r++h  +da      tg ++  +l ++a   g +d+
  gi|121637502|ref|YP_977725.1|  85 DAVYSIVADGYRAVTDLVGAGARLDESVPGRWALTREGGHSRR-RIVHAGGDA------TGAEVQRALQDAA---GmLDI 154
                                    **************************9999*************.****9***9......***********99...44*** PP

                                    EESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTS CS
                  FAD_binding_2 159 qerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalraga 238
                                    ++ + a+++++++  vtG  v  p++ +   i a  v+latgG g+           +  ttn+++ tGdg+al+l+ag+
  gi|121637502|ref|YP_977725.1| 155 RTGHVALRVLHDGTAVTGLLVVRPDGCG--IISAPSVILATGGLGH----------LYSATTNPAGSTGDGIALGLWAGV 222
                                    ***********999********555555..56799***********..........************************ PP

                                    SEES..TT-EEEEEEEET....TTTB...B--THHHHTT-EEE-TTSSBTH......GGGS-HHHHHHHHH.HHHHTTTS CS
                  FAD_binding_2 239 alnddrmeevqfhPtslvpirdgsgi...LitealrgeGgilvdkdGrrFm......nelasrdvvsrailekeiaeggs 309
                                    a+ d  +e++qfhPt l+  r   g+   Litea+rgeG+ilvd++G+  +      ++la+rdvv++ai  +  + +g 
  gi|121637502|ref|YP_977725.1| 223 AVSD--LEFIQFHPTMLFAGRA--GGrrpLITEAIRGEGAILVDRQGNSITagvhpmGDLAPRDVVAAAID-ARLKATGD 297
                                    ****..************4333..33569********************99********************.66667777 PP

                                    CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEE CS
                  FAD_binding_2 310 eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldadg 389
                                     ++vylda++    eg++++++++   ++  ++      idp ++pip       vvp++hy++gG++td  g++     
  gi|121637502|ref|YP_977725.1| 298 -PCVYLDARG---IEGFASRFPTVTASCRA-AG------IDPVRQPIP-------VVPGAHYSCGGIVTDVYGQT----- 354
                                    .9********...899*************9.99......*********.......********************..... PP

                                    ESSBTEEE-STCEESSSSTTS--TTHHH CS
                  FAD_binding_2 390 qpipGLYAaGevaaggvhganrlgGnsl 417
                                      + GLYAaGeva +g+hganrl++nsl
  gi|121637502|ref|YP_977725.1| 355 -ELLGLYAAGEVARTGLHGANRLASNSL 381
                                    .*************************98 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 8.6
                                    E--SHHHHHHHHHHHHTTT- CS
                  FAD_binding_2   5 iGsGlAGLaAAleaaeaGlk 24 
                                    + +G AG aAA+ aa aG++
  gi|121637502|ref|YP_977725.1| 387 V-GGRAGKAAAAHAAAAGRS 405
                                    5.5899***********985 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0034         5       2      31 ..     425     454 ..     424     467 .. 0.88
   2 !   24.2   0.2   1.8e-08   2.6e-05      60      88 ..     470     498 ..     465     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHHSSSSB-HHHHHHHHHHHHHH CS
                 Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkel 31 
                                     +L+++m ++++++R ++gL++ ++ l+  
  gi|121637502|ref|YP_977725.1| 425 GDLQRAMSRDASMYRAAAGLHRLCDSLSGA 454
                                    689*******************99998765 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.8e-08
                                    HHHHHHHHHHHHHH--S-BTTBEBTTS-S CS
                 Succ_DH_flav_C  60 llelAeaiaksAlaRkESrGaHaredfpe 88 
                                    l  +A+ ++++AlaR+ESrG+H+r ++p 
  gi|121637502|ref|YP_977725.1| 470 LTLVAQSVTAAALARTESRGCHHRAEYPC 498
                                    56789*********************984 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.5   1.2e-06    0.0019       2      36 ..      11      46 ..      10     200 .. 0.86
   2 ?    1.0   0.0      0.13   1.9e+02     255     288 ..     256     288 ..     246     294 .. 0.82
   3 !   11.2   0.0    0.0001      0.15     255     279 ..     343     371 ..     320     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.legtcl 36
                                   dvvviG G+AGlaaal + +ag  v++++ + +t++
  gi|121637502|ref|YP_977725.1| 11 DVVVIGTGVAGLAAALAADRAGRSVVVLSkAAQTHV 46
                                   8**************************974333333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                    TTEEE--TTSBESSTTEEE-GGGCTECCSS--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDvaggkggpelaq 288
                                     g+i+vd+++++   g+   GD a ++++++ a 
  gi|121637502|ref|YP_977725.1| 256 EGAILVDRQGNSITAGVHPMGDLA-PRDVVAAAI 288
                                    799*********************.555555554 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0001
                                    TTEEE--TTSBESSTTEEE-GGGC....T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx....x RF
                    Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDva....g 279
                                     ggiv+d +++t+  g+ya+G va    +
  gi|121637502|ref|YP_977725.1| 343 CGGIVTDVYGQTELLGLYAAGEVArtglH 371
                                    59**********************65441 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  11.0   1.8e-07   0.00028       1     201 [.      11     194 ..      11     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    dvv+iG G++Gl++A+++ r+g  V++l k+ + +  a++ ++g ++  l +  +   +   ++++l+  + l++  ++ 
  gi|121637502|ref|YP_977725.1|  11 DVVVIGTGVAGLAAALAADRAGrsVVVLSKAAQTHVTATHYAQGGIAVVLPDNDD--SVDAHVADTLAAGAGLCDPDAV- 87 
                                    9*****************99999********99999***********96644442..2336666666666666644222. PP

                                    TSEEEEEEEEEESSHHHHHHHHHHHHHH..HHTTTTEEE.EEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHH CS
                            DAO  79 idyrrtGllslaadeeelealdkllall..leagldael.ldaeevrelepalpgllgalfypdtgqvdpakltaalara 155
                                          G+  +           +l++++  l+  ++ ++ l++e          g+     ++ +g +  a++ +al++a
  gi|121637502|ref|YP_977725.1|  88 YSIVADGYRAV----------TDLVGAGarLDESVPGRWaLTRE------G---GHSRRRIVHAGGDATGAEVQRALQDA 148
                                    33333444444..........33333331133445667766665......2...22333333344666667777777777 PP

                                    HHHTT-EEEESECEEEEEEEETCEEEEE..EECT.EEEEEEEEEEE--G CS
                            DAO 156 aealGveilegtevtgleeedgkvwgve..rttp.gendaadavVnaaG 201
                                    a  l  +i++g+ + ++ +++  v+g+   r    g++ +a  v++a+G
  gi|121637502|ref|YP_977725.1| 149 AGML--DIRTGHVALRVLHDGTAVTGLLvvRPDGcGII-SAPSVILATG 194
                                    7444..88888777776555455666655433333543.3355999998 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.4   7.4e-08   0.00011      28      71 ..       9      52 ..       3      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.4e-08
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT CS
                    AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslg 71
                                   +a v+viG GvaGl+A+ +a + g +V+vl + +++     ++ 
  gi|121637502|ref|YP_977725.1|  9 AADVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQTHVTATHYA 52
                                   799**************************999888877666633 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.9   5.8e-07   0.00086       2      34 ..      11      43 ..      10      47 .. 0.93
   2 ?    2.6   0.1      0.03        45     147     190 ..     178     227 ..     142     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.8e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                   dv+viG G AGl aA++a ++g++V++l ka +
  gi|121637502|ref|YP_977725.1| 11 DVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQ 43
                                   8***************************99876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.03
                                    E.TTEEEEESEEEE----S......S-GGGT--SHHHHHHHHTT--EEEE CS
                    HI0933_like 147 tkseeeleadklvlAtGGl......SiPklGstgkgyklaeqfghtivpl 190
                                     ++ + ++a +++lAtGGl           Gstg+g+ l   +g+ + +l
  gi|121637502|ref|YP_977725.1| 178 PDGCGIISAPSVILATGGLghlysaTTNPAGSTGDGIALGLWAGVAVSDL 227
                                    456678999*********73333112345699999999988888888765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   6.4   1.3e-07    0.0002       1      30 [.      11      40 ..      11      44 .. 0.95
   2 ?   -4.9   7.4       8.6   1.3e+04       4      24 ..     386     405 ..     385     407 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                   DvvV+G g+aG+aAA+aA raG++v+++++
  gi|121637502|ref|YP_977725.1| 11 DVVVIGTGVAGLAAALAADRAGRSVVVLSK 40
                                   9*************************9986 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 8.6
                   FAD_oxidored   4 VvGGgpaGvaAAiaAaraGak 24 
                                    VvGG  aG aAA  Aa aG++
  gi|121637502|ref|YP_977725.1| 386 VVGG-RAGKAAAAHAAAAGRS 405
                                    6665.6788888888888876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.8     5e-07   0.00075       1      42 [.      14      55 ..      14      65 .. 0.85
   2 ?   -3.5   0.1       8.7   1.3e+04      10      18 ..     477     485 ..     476     500 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5e-07
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETT CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpg 42
                                   ++G+G++Gl+aA ++ +ag++v++l k+ ++   a+ y  +g
  gi|121637502|ref|YP_977725.1| 14 VIGTGVAGLAAALAADRAGRSVVVLSKAAQTHVTATHYAQGG 55
                                   8**************************998766666666666 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.7
                                    HHHHHHHCC CS
                  NAD_binding_8  10 vaAylLaka 18 
                                    v+A++La+ 
  gi|121637502|ref|YP_977725.1| 477 VTAAALART 485
                                    677777763 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.9   1.2e-06    0.0018       1      34 [.      11      44 ..      11      61 .. 0.82
   2 ?   -0.5   0.0      0.34   5.1e+02     110     150 ..     151     195 ..     128     224 .. 0.64
   3 ?   -4.6   5.4       5.9   8.8e+03       7      22 ..     388     403 ..     385     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                   dv+ViG G AG++AAlaa r+G +v+ + +  +t
  gi|121637502|ref|YP_977725.1| 11 DVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQT 44
                                   79***********************999443333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.34
                                    TEEEEES-EEEEEECT.TEEEE..EEETTS.-EEEECEEEE--TT CS
                           GIDA 110 nleiieeeveelivee.kkvkg..vvtedg.etikakavviatGt 150
                                     l+i+++ v+  ++++ + v+g  vv  dg  +i+a +v++atG 
  gi|121637502|ref|YP_977725.1| 151 MLDIRTGHVALRVLHDgTAVTGllVVRPDGcGIISAPSVILATGG 195
                                    4666666665433333355666443333441578888*******8 PP

  == domain 3  score: -4.6 bits;  conditional E-value: 5.9
                                    SSHHHHHHHHHHHHTT CS
                           GIDA   7 gGhAGceAAlaaarlG 22 
                                    gG AG +AA++aa +G
  gi|121637502|ref|YP_977725.1| 388 GGRAGKAAAAHAAAAG 403
                                    79***********998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   6.3e-06    0.0094       1      35 [.      13      46 ..      13      55 .. 0.84
   2 ?   -1.6   0.0      0.83   1.2e+03     122     136 ..     183     197 ..     171     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnigns 35
                                   ++iG G aGlaaa+++ +ag  ++++l k++ ++ 
  gi|121637502|ref|YP_977725.1| 13 VVIGTGVAGLAAALAADRAGR-SVVVLSKAAQTHV 46
                                   79******************9.7******966554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                    Pyr_redox_3 122 tyeAkkviiAtGefd 136
                                     ++A++vi+AtG  +
  gi|121637502|ref|YP_977725.1| 183 IISAPSVILATGGLG 197
                                    678999999999755 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.7   8.5e-06     0.013       2      39 ..      10      47 ..       9      56 .. 0.93
   2 ?   -2.1   0.0       1.2   1.7e+03     107     161 ..     141     192 ..     137     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-06
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                   +dV+++G+G aGl +al   +aG +vv++ k ++t+v+
  gi|121637502|ref|YP_977725.1| 10 ADVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQTHVT 47
                                   69*******************************99986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                  FAD_binding_3 107 leriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                    ++r+L ++   +g l++r ++  + +++d++ vt  +  + +g    ++a  ++ a
  gi|121637502|ref|YP_977725.1| 141 VQRALQDA---AGmLDIRTGHVALRVLHDGTAVTGLLVVRPDGCG-IISAPSVILA 192
                                    66666666...677999999999999*******999988887766.6666655555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8     7e-05      0.11       1      38 [.      11      46 ..      11      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                   DvvviG G Agl+ A      ++g +vv++  +++   
  gi|121637502|ref|YP_977725.1| 11 DVVVIGTGVAGLAAALAA--DRAGRSVVVLSKAAQTHV 46
                                   9**********9877666..999999999976666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3975.61
//
Query:       gi|121637503|ref|YP_977726.1|  [L=285]
Description: nicotinate-nucleotide pyrophosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-62  208.5   0.1    7.5e-62  208.1   0.1    1.2  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
    1.2e-20   73.3   0.0    2.1e-20   72.5   0.0    1.4  1  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.49   10.6   0.0    2.0  1  DUF1153    Protein of unknown function (DUF1153)
       0.45   11.2   4.3       0.42   11.3   0.7    2.4  2  TPR_16     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.1   1.7e-65   7.5e-62       1     169 []     117     284 ..     117     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 1.7e-65
                                    HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTT CS
                      QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdke 80 
                                    iAt+ta++v+a++++k++i dTRkt+Pglr+l+kyAv++GGg nhrlgL d++likdnh+aaags+v+a+++vr+a+++ 
  gi|121637503|ref|YP_977726.1| 117 IATATAAWVDAVRGTKAKIRDTRKTLPGLRALQKYAVRTGGGVNHRLGLGDAALIKDNHVAAAGSVVDALRAVRNAAPDL 196
                                    9****************************************************************************999 PP

                                    SEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHT CS
                      QRPTase_C  81 vkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalths 160
                                      +evev+sle+l++vl +++++i+LDnf v+++++av+++++++++v++e+SGg++l++ ++ya++gvd+++vgalths
  gi|121637503|ref|YP_977726.1| 197 P-CEVEVDSLEQLDAVLPEKPELILLDNFAVWQTQTAVQRRDSRAPTVMLESSGGLSLQTAATYAETGVDYLAVGALTHS 275
                                    6.****************************************************************************** PP

                                    B----EEEE CS
                      QRPTase_C 161 vkalDislk 169
                                    v++lDi l+
  gi|121637503|ref|YP_977726.1| 276 VRVLDIGLD 284
                                    ******996 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   4.7e-24   2.1e-20       4      89 .]      27     115 ..      24     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 4.7e-24
                                    --HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHH...TTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHH CS
                      QRPTase_N   4 gDlttealipeekkakaeiiakeegvvaGlevaeevfell...pglevellvkDGervekgdvlleieGnarallsaERv 80 
                                     D+tt a++p++++ +a+++++e+gvvaGl+va  +++ +   +g++v   v+DG+rv +g+ l+++e+++r ll+aER+
  gi|121637503|ref|YP_977726.1|  27 PDVTTLATVPASATTTASLVTREAGVVAGLDVALLTLDEVlgtNGYRVLDRVEDGARVPPGEALMTLEAQTRGLLTAERT 106
                                    7************************************9999*************************************** PP

                                    HHHHHHHHH CS
                      QRPTase_N  81 aLnllqrlS 89 
                                    +Lnl+ +lS
  gi|121637503|ref|YP_977726.1| 107 MLNLVGHLS 115
                                    *******98 PP

>> DUF1153  Protein of unknown function (DUF1153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.49      17      54 ..      30      68 ..      21      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                   EETTTS--SS.-S---HHHHHHHHHHHHCTTS-HHHHHH CS
                        DUF1153 17 ltradLPppn.tkrWvarRKaevvaavrggLlsleeale 54
                                    t+a +P++  t+   + R a vva+++  Ll+l+e+l 
  gi|121637503|ref|YP_977726.1| 30 TTLATVPASAtTTASLVTREAGVVAGLDVALLTLDEVLG 68
                                   577888876515567899******************975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.25   1.1e+03      12      25 ..       5      18 ..       1      24 [. 0.57
   2 ?   11.3   0.7   9.3e-05      0.42      21      62 ..     146     188 ..     142     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                         TPR_16 12 dyddAaaaleaalk 25
                                   d++ Aaa++ +a+ 
  gi|121637503|ref|YP_977726.1|  5 DWELAAARAAIARG 18
                                   55555555555544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                         TPR_16  21 eaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalr 62 
                                    +a+ k++ ++   +  +l+lgdaal + ++ +Aa  +++a+ +
  gi|121637503|ref|YP_977726.1| 146 RALQKYAVRTGGGVNHRLGLGDAALIKDNHVAAAgSVVDALRA 188
                                    455555555588999*******************898888763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2503.13
//
Query:       gi|121637504|ref|YP_977727.1|  [L=252]
Description: hypothetical protein BCG_1635 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-06   28.1   0.0    1.1e-05   25.9   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
     0.0014   19.3   0.0     0.0035   18.0   0.0    1.8  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.3e-09   1.1e-05       1      95 [.      53     140 ..      53     141 .. 0.86
   2 ?   -1.0   0.0      0.33   2.9e+03      32      64 ..     170     198 ..     158     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.3e-09
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ld+ +G+G +++   +   + v+++ ++   ++a ++ ++ g  v ++ +d   lpf+d+ fDlv+s++         + 
  gi|121637504|ref|YP_977727.1|  53 LDLETGGGEVLAGAGNFPPTMVATEAWPPNAAMATRRLHPMGA-VVVITGDKPPLPFADAAFDLVTSRH------PSTRW 125
                                    677778888888888777999*****************99996.8889999999**************8......45556 PP

                                    HHHHHHHEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllv 95 
                                    + eiaRvL+ gG  +
  gi|121637504|ref|YP_977727.1| 126 WTEIARVLRAGGSYF 140
                                    78*********9865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                                    HHHHHHCCHHT-EEEETTEECCCTSS-TT-EEE CS
                Methyltransf_11  32 klakekaseeglkvefvvadaeklpfednsfDl 64 
                                    +++++++ ++g  +e+v   +e+  ++ + fD+
  gi|121637504|ref|YP_977727.1| 170 QVVRTCITDAG--LEIVDLQMER--LRVEFFDV 198
                                    34455555555..5556666665..33344444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.9e-07    0.0035       2      97 .]      53     137 ..      52     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-07
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ldl +G G++++ + +  +  ++++++  +   + a +r++  g  v +++gd   lpf+d+ fDlv+s+    h     
  gi|121637504|ref|YP_977727.1|  53 LDLETGGGEVLAGAGNF-P-PTMVATEAWPPNAAMATRRLHPMG-AVVVITGDKPPLPFADAAFDLVTSR----HP---- 121
                                    77778888777776644.4.899999999999999999995443.9999********************5....42.... PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                      +   eiarvL+ gG
  gi|121637504|ref|YP_977727.1| 122 STRWWTEIARVLRAGG 137
                                    2467899*****9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1791.05
//
Query:       gi|121637505|ref|YP_977728.1|  [L=136]
Description: hypothetical protein BCG_1636c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-05   24.5   0.1    2.5e-05   24.4   0.1    1.1  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.4e-09   2.5e-05       3      81 ..      23      95 ..      20     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-09
                                   XXXXXXXXXXXXXXTTXTTS---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEE CS
                F420H2_quin_red  3 ReqvaiyrrtegkvgrrlegvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqv 81
                                   R+qv+  +r    + r l+g  ++ ++ +Grk+gkp +t ++  r+++ ++++  +g    + +w+ N+ a  ++ v+ 
  gi|121637505|ref|YP_977728.1| 23 RLQVKYINRALKPIARYLPG--TATIEHRGRKSGKPYQTIVTAYRKDGVLAIALAHG----KTDWVKNVLAAGEADVHF 95
                                   78888888888889999999..8889*******************************....99********98888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 889.88
//
Query:       gi|121637506|ref|YP_977729.1|  [L=438]
Description: histidinol dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.4e-154  513.8   3.9   3.8e-154  513.6   3.9    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.6   3.9  2.1e-158  3.8e-154       3     409 .]      23     436 ..      21     436 .. 0.97

  Alignments for each domain:
  == domain 1  score: 513.6 bits;  conditional E-value: 2.1e-158
                                    ------HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC CS
                  Histidinol_dh   3 rseedseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaq 82 
                                    r  +d+e+v  tv++i+++v e+G ea l++ + FD+v+ ++++rv+++++++al+ ld ++ eal++++e+ r++h+ q
  gi|121637506|ref|YP_977729.1|  23 RGGADVEAVLPTVRPIVAAVAERGAEAALDFGASFDGVR-PHAIRVPDAALDAALAGLDCDVCEALQVMVERTRAVHSGQ 101
                                    66788999****************************775.689************************************* PP

                                    ----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS...GG.--HHHHHHHHH CS
                  Histidinol_dh  83 keseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq...dgkvnpavlaaakl 159
                                    +++ + +++  pg++++++++p+ervGlYvPgG+a+ypS+v+mn+vpA+ Agv+++vv++Ppq   dg ++p++laaa+l
  gi|121637506|ref|YP_977729.1| 102 RRT-DVTTTLGPGATVTERWVPVERVGLYVPGGNAVYPSSVVMNVVPAQAAGVDSLVVASPPQaqwDGMPHPTILAAARL 180
                                    *86.456699****************************************************99888************* PP

                                    CT-SEEEE--HHHHHHHHHH-.....-SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHH CS
                  Histidinol_dh 160 agvdeiykvGGaqAiaalAyG.....tesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvA 234
                                    +gvde+++vGGaqA+a lAyG      + +++vd+i+GPGniyV+aAKrl++++vgiD+ aGP+E++++aD+tadp +vA
  gi|121637506|ref|YP_977729.1| 181 LGVDEVWAVGGAQAVALLAYGgtdtdGAALTPVDMITGPGNIYVTAAKRLCRSRVGIDAEAGPTEIAILADHTADPVHVA 260
                                    *********************877655679************************************************** PP

                                    HHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCC.H-EEEE-SSHHHHHHHHHHH--SEEEEE CS
                  Histidinol_dh 235 aDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslek.qsaiilvedleeaielaneyApEHlelq 313
                                    aDL+sqaEHde a++vlvt+se+la+a+++e++ ql+++ ++e+++++l+  qsai+lv+d+++a+ ++n+yA+EHle+q
  gi|121637506|ref|YP_977729.1| 261 ADLISQAEHDELAASVLVTPSEDLADATDAELAGQLQTTVHRERVTAALTGrQSAIVLVDDVDAAVLVVNAYAAEHLEIQ 340
                                    *************************************************9989*************************** PP

                                    STTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHH CS
                  Histidinol_dh 314 vedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlA 393
                                    ++d+ +++++i++aGaif+G++sp+slgDY+aG+nhvLPT+g+Ar+ssglsv++Fl+ i+v+e++++alk+++ +v+tlA
  gi|121637506|ref|YP_977729.1| 341 TADAPQVASRIRSAGAIFVGPWSPVSLGDYCAGSNHVLPTAGCARHSSGLSVQTFLRGIHVVEYTEAALKDVSGHVITLA 420
                                    ******************************************************************************** PP

                                    HHTT-HHHHHHHHHHH CS
                  Histidinol_dh 394 eaEgLeaHaeavkvRl 409
                                    +aE+L+aH eav+ R+
  gi|121637506|ref|YP_977729.1| 421 TAEDLPAHGEAVRRRF 436
                                    *************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3146.04
//
Query:       gi|121637507|ref|YP_977730.1|  [L=380]
Description: histidinol-phosphate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-53  181.6   0.0    3.2e-53  181.2   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.2   0.0   1.8e-57   3.2e-53       4     356 ..      34     355 ..      32     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 1.8e-57
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    + L++ne+++   +  +++v++  +e   a  +l++y++ d + +l+ +la +l  + +++l  e +++  +G++++++ 
  gi|121637507|ref|YP_977730.1|  34 VRLNTNENPHPPTRALVDDVVRSVRE---AAIDLHRYPDRD-AVALRADLAGYLTAQTGIQLGVE-NIWAANGSNEILQQ 108
                                    57999*****9666777777777765...9999********.***********************.************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    l +++   pg+  + + p+y+++  i    + e+++ +   ++df+ld++   +a+ +      k+ v++++sp+NP+G+
  gi|121637507|ref|YP_977730.1| 109 LLQAF-GGPGRSAIGFVPSYSMHPIISDGTHTEWIEAS--RANDFGLDVDVAVAAVVDR-----KPDVVFIASPNNPSGQ 180
                                    *****.7*******************************..67*******9888887773.....88************** PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsq 242
                                      +l++l+klld+a     + +vDeaY++f +++    +++++vee+p  l++++++sKaf+ aG R+Gy+++++av+++
  gi|121637507|ref|YP_977730.1| 181 SVSLPDLCKLLDVAP---GIAIVDEAYGEFSSQP----SAVSLVEEYPSkLVVTRTMSKAFAFAGGRLGYLIATPAVIDA 253
                                    **********99999...7*************94....3499************************************** PP

                                    HHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHH CS
                  Aminotran_1_2 243 lrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelsk 322
                                    +  +  p+  ss++qaa+ aal++++    ++  +++ l+++r++++ +L++ g+ v++s+++++l+ ++  +   ++++
  gi|121637507|ref|YP_977730.1| 254 MLLVRLPYHLSSVTQAAARAALRHSD----DTLSSVAALIAERERVTTSLNDMGFRVIPSDANFVLFGEFADA--PAAWR 327
                                    **************************....7899*************************************88..***** PP

                                    HHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHH CS
                  Aminotran_1_2 323 kLleevgvyvtpgtsftvpgrlRitvAglteeel 356
                                      le  g++++    +++pg lR t  gl ee +
  gi|121637507|ref|YP_977730.1| 328 RYLEA-GILIRD---VGIPGYLRATT-GLAEE-N 355
                                    *****.******...78888999999.55444.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2750.17
//
Query:       gi|121637508|ref|YP_977731.1|  [L=210]
Description: imidazoleglycerol-phosphate dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-57  194.4   0.8    1.4e-57  194.0   0.8    1.1  1  IGPD      Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.024   14.6   0.0    1.5  1  Fae       Formaldehyde-activating enzyme (Fae)


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   0.8   1.6e-61   1.4e-57       1     144 []      40     190 ..      40     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 1.6e-61
                                    ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE-- CS
                           IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldls 80 
                                    Tg++f+dhmL++l +h++fdl+v+++gd+e+++Hht+ed++ialG+al +algdkrgi+Rfg+a++pmDe+la++a+dls
  gi|121637508|ref|YP_977731.1|  40 TGVPFYDHMLTALGSHASFDLTVRATGDVEIEAHHTIEDTAIALGTALGQALGDKRGIRRFGDAFIPMDETLAHAAVDLS 119
                                    9******************************************************************************* PP

                                    SS-EEE--.....-SB--TT.....--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                           IGPD  81 grpylvleae...lkrekig....eldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                    grpy+v+++e   l++++i      ++t + +++fesla++a+i+lhv+vl+g++ hhi+ea++Ka+araL
  gi|121637508|ref|YP_977731.1| 120 GRPYCVHTGEpdhLQHTTIAgssvPYHTVINRHVFESLAANARIALHVRVLYGRDPHHITEAQYKAVARAL 190
                                    ******997767777777765666699*******************************************8 PP

>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-06     0.024      95     148 ..     148     204 ..     142     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                            Fae  95 iipkeeaddlviivsvfidpea...kdkkkiyeynyeAtklAikrAlkeePsidevl 148
                                    +i+++  + l   + + ++ ++   +d ++i e +y+A+ +A+++A++  P+++ v 
  gi|121637508|ref|YP_977731.1| 148 VINRHVFESLAANARIALHVRVlygRDPHHITEAQYKAVARALRQAVEPDPRVSGVP 204
                                    67777788888888999999999999*************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1506.83
//
Query:       gi|121637509|ref|YP_977732.1|  [L=206]
Description: imidazole glycerol phosphate synthase subunit HisH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-17   63.7   0.0    2.3e-17   63.4   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    0.00011   21.9   0.1    0.00015   21.4   0.1    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00041   20.2   0.0     0.0079   16.1   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
     0.0025   17.6   0.8      0.018   14.8   0.3    2.1  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.092   12.6   0.4       0.13   12.1   0.4    1.2  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   6.5e-21   2.3e-17       2     183 ..       8     199 ..       7     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.5e-21
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT........TTTHHHHHHHHCTSTS- CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg........vegkieaikearenkiP 73 
                                    ++D+++++ ++  +al ++g++vev   d++a        ++dg++v +G+g+ +        + g+  ++++++  + P
  gi|121637509|ref|YP_977732.1|   8 VLDYGSGNLRSAQRALQRVGAEVEVTA-DTDAAM------TADGLVV-PGVGAFAacmaglrkISGERIIAERVAA-GRP 78 
                                    89**********************998.554444......4899877.6899999898888776677677777777.9** PP

                                    EEEETHHHHHHHHHTTT.............EEE..EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHH CS
                         GATase  74 iLGICLGmQllaiefgr.............kvv..kekekehhggtmrlgddetallyglknevierhrHryevnpkele 138
                                    +LG+C GmQ+l+    +              v+  ++   +h+g++    + ++al++gl+ + + ++ H+y++++ e  
  gi|121637509|ref|YP_977732.1|  79 VLGVCVGMQILFACGVEfgvqtpgcghwpgAVIrlEAPVIPHMGWNVVDSAAGSALFKGLDVDARFYFVHSYAAQRWEGS 158
                                    ***********9766666556666666666444888888********9999999*********************85656 PP

                                    HTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHH CS
                         GATase 139 paglevtakseddeelmeiiekknpfvgvQFHPEststpegpell 183
                                    p+ l    + +    + +++e+   + ++QFHPE++   + +++l
  gi|121637509|ref|YP_977732.1| 159 PDALLT--WATYRAPFLAAVEDGA-LAATQFHPEKSGDAG-AAVL 199
                                    665554..4445557899998887.9********976554.5555 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   4.3e-08   0.00015      27      88 ..      31      89 ..      11     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.3e-08
                       GATase_3 27 vrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88
                                      +   d++ +  ad +++pG    ++ +a lr+ + ++ i+e ++ag+pvlg+C G+q+L
  gi|121637509|ref|YP_977732.1| 31 EVTA---DTDAAMTADGLVVPGVGAFAACMAGLRKISGERIIAERVAAGRPVLGVCVGMQIL 89
                                   2223...33333459**********************************************9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.2e-06    0.0079       6      81 ..      14      89 ..       9     100 .. 0.83
   2 ?    2.2   0.0     0.038   1.4e+02     155     174 ..     174     193 ..     124     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                                   SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-..HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHH CS
                            SNO  6 GaveehveaikkclaenktvkrkedlaevdaliiPGGe..stamskliertglyedllefvknsekvvlGtCaGlill 81
                                   G+++  ++a+++++ae  +  +++     d+l++PG    +++m+ l +  g    + e v+ + ++vlG C G+ +l
  gi|121637509|ref|YP_977732.1| 14 GNLRSAQRALQRVGAEVEVTADTDAAMTADGLVVPGVGafAACMAGLRKISG-ERIIAERVAAG-RPVLGVCVGMQIL 89
                                   77888999***********9***************95411455777777777.77788889888.**********765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.038
                                    EEEEETTEEEESS-GGGSTT CS
                            SNO 155 vvakqkkilatsfhPelaed 174
                                     +++ + + at fhPe + d
  gi|121637509|ref|YP_977732.1| 174 AAVEDGALAATQFHPEKSGD 193
                                    3455778999******8866 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   4.9e-06     0.018      95     122 ..      66      92 ..      55     106 .. 0.84
   2 ?    1.0   0.0     0.082     3e+02     205     216 .]     178     189 ..     121     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                  Peptidase_C26  95 laLiraalergvPilgiCrGlqllnval 122
                                      +i++ +++g P+lg+C G+q+l  a 
  gi|121637509|ref|YP_977732.1|  66 ERIIAERVAAGRPVLGVCVGMQIL-FAC 92 
                                    56899999***************9.555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.082
                  Peptidase_C26 205 kafvlgvQwHPE 216
                                    +  + + Q+HPE
  gi|121637509|ref|YP_977732.1| 178 DGALAATQFHPE 189
                                    5678899****9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   3.6e-05      0.13      45     113 ..      27      95 ..       6     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                                    SEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHH..HHHHHHHHHTT-EEEEETTTHHHHHHTTTT CS
                      DJ-1_PfpI  45 GlkvtvdaslddvkaaeyDalvlpGGragperlrenekv..velvkefaekgklvaaICagpqlLaaagvl 113
                                    G++v v+a  d  +a + D lv+pG  a + +++   k+    ++ e + +g++v  +C g q+L a gv 
  gi|121637509|ref|YP_977732.1|  27 GAEVEVTADTD--AAMTADGLVVPGVGAFAACMAGLRKIsgERIIAERVAAGRPVLGVCVGMQILFACGVE 95 
                                    55555555444..33478*******8888999998887733589**********************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1593.26
//
Query:       gi|121637510|ref|YP_977733.1|  [L=245]
Description: phosphoribosyl isomerase A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-59  200.8   1.2    2.4e-59  200.6   1.2    1.0  1  His_biosynth  Histidine biosynthesis protein
      6e-08   32.4   1.8     0.0012   18.3   0.1    2.1  2  NMO           Nitronate monooxygenase
    1.7e-06   27.4   0.0      0.048   12.7   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.016   14.2   0.3        0.8    8.6   0.0    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
       0.81    8.7   4.6       0.32   10.0   0.4    2.0  2  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   1.2   6.7e-63   2.4e-59       2     229 .]       6     235 ..       5     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 6.7e-63
                                    EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS CS
                   His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG 81 
                                    ++pa+D+ +G++Vrlv+G+  ++++ +g+ v++a  ++++ga+++h+vDldaa+ gr+ n++l++e++ +++++v++ GG
  gi|121637510|ref|YP_977733.1|   6 LLPAVDVVEGRAVRLVQGKAGSQTE-YGSAVDAALGWQRDGAEWIHLVDLDAAF-GRGSNHELLAEVVGKLDVQVELSGG 83 
                                    68******************66555.5999***********************8.************************* PP

                                    SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE..C.EEEEETTTTEEEEEEHHHHHHHHHH CS
                   His_biosynth  82 IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr..g.ykvaikgwreetgldavelakklee 158
                                    Ir+ e+++++l  g+ +v +gtaa++np+++ +++ ++g+ +++v++D++   g +++  +gw+ + g d+ +++++l++
  gi|121637510|ref|YP_977733.1|  84 IRDDESLAAALATGCARVNVGTAALENPQWCARVIGEHGD-QVAVGLDVQIidGeHRLRGRGWETD-GGDLWDVLERLDS 161
                                    ****************************************.*******999874699******999.************* PP

                                    TT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHH...HTTCSEEEESHHHHTTSS- CS
                   His_biosynth 159 lgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelk...segvdavivgsalyegelt 229
                                     g++++++tdi +dGtl Gp+l+l+  +a++++ pviasGGv+sl+dl++++     gv+++ivg+aly +++t
  gi|121637510|ref|YP_977733.1| 162 EGCSRFVVTDITKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLDDLRAIAtltHRGVEGAIVGKALYARRFT 235
                                    *************************************************9998889999**********99875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.4e-07    0.0012     180     226 ..      62     108 ..      53     118 .. 0.91
   2 !   13.7   0.2   8.4e-06      0.03     181     225 ..     182     229 ..     156     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                            NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                    + ++L+++v+  +d+ v   GGi d + +aaaLa G + v +gt+ L
  gi|121637510|ref|YP_977733.1|  62 SNHELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAAL 108
                                    6799****************************************976 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.4e-06
                            NMO 181 lfaLvpqvldavdiPviAaGGii...drrgvaaaLalGAsgvqigtrf 225
                                     + L++ v+d  d PviA GG+    d r +a+   +G +g+ +g ++
  gi|121637510|ref|YP_977733.1| 182 NLDLLAGVADRTDAPVIASGGVSsldDLRAIATLTHRGVEGAIVGKAL 229
                                    467999***************872225566677777899999999775 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   1.3e-05     0.048     175     224 ..      67     115 ..      57     128 .. 0.88
   2 !   12.7   0.0   1.4e-05      0.05     132     219 ..     144     232 ..     137     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                    HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHH CS
                            Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfa 224
                                     +ev  ++ + v   G+I+d e++ a+l+  G+  v +g +al+nP   a
  gi|121637510|ref|YP_977733.1|  67 LAEVVGKLDVQVELSGGIRDDESLAAALAT-GCARVNVGTAALENPQWCA 115
                                    577888999*******************98.***************9877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.4e-05
                                    ESSTTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHH..HHHH--SE CS
                            Dus 132 giddeeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqai..leetGadg 209
                                    g++ +  ++ ++ +++  +G+  ++v   t+     g  +++  + v ++   pvia G++ +++d++ai  l + G++g
  gi|121637510|ref|YP_977733.1| 144 GWETDGGDLWDVLERLDSEGCSRFVVTDITKDGTL-GGPNLDLLAGVADRTDAPVIASGGVSSLDDLRAIatLTHRGVEG 222
                                    56666667888888889999999988666655444.455888899999****************998865338999**** PP

                                    EEESCHHCCS CS
                            Dus 210 vmigrgalgn 219
                                     ++g++ + +
  gi|121637510|ref|YP_977733.1| 223 AIVGKALYAR 232
                                    *****99875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00022       0.8     200     237 ..      68     105 ..      60     116 .. 0.91
   2 ?    3.5   0.1    0.0079        28     201     228 ..     188     214 ..     181     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00022
                                    HHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 200 aeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                    ae++ k +v+v   GGi+ ++ ++ Ala G   v +G 
  gi|121637510|ref|YP_977733.1|  68 AEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGT 105
                                    67788999**************************9996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0079
                                    HHHCTCT-EEEEES---SHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 201 eaakkagvpviaDGGikysgdivkAlaa 228
                                     +a++++ pvia GG+++  d+ +A+a 
  gi|121637510|ref|YP_977733.1| 188 GVADRTDAPVIASGGVSSLDDL-RAIAT 214
                                    578999**********988775.56664 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4     9e-05      0.32     259     304 ..      65     108 ..      59     128 .. 0.84
   2 ?   -0.0   0.4     0.096   3.5e+02     258     300 ..     183     226 ..     179     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9e-05
                                    HCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                         FMN_dh 259 dvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                    + L e+v +++  ++v ++gGir  +  + Ala G   v +G ++l
  gi|121637510|ref|YP_977733.1|  65 ELLAEVVGKLD--VQVELSGGIRDDESLAAALATGCARVNVGTAAL 108
                                    56677777665..9***************************98775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.096
                                    HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHT....T-SEEEES CS
                         FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlal....GAdavllG 300
                                    +d L  ++++ +  ++v+++gG+++  D l+A+a     G ++ ++G
  gi|121637510|ref|YP_977733.1| 183 LDLLAGVADRTD--APVIASGGVSSLDD-LRAIATlthrGVEGAIVG 226
                                    567777777765..99999999987555.566663233355555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1716.38
//
Query:       gi|121637511|ref|YP_977734.1|  [L=270]
Description: inositol-monophosphatase impA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-50  170.8   0.1    5.2e-50  170.5   0.1    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   0.1   2.9e-54   5.2e-50      18     264 ..      16     258 ..       4     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 2.9e-54
                                    HHHHHHTTTSEEEESTTT..CCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEET CS
                     Inositol_P  18 evlreefsenelvieeks..kegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDG 95 
                                    ++l+ +     + ++++s   ++ +d++t++d a+e+ +++al +   + ++ gee ++++      +++++w++DPiDG
  gi|121637511|ref|YP_977734.1|  16 AILDAATALFLVGHRADSavRKKGNDFATEVDLAIERQVVAALVAAT-GIEVHGEEFGGPAV-----DSRWVWVLDPIDG 89 
                                    444444443334444444555567******************88887.78899********9.....788********** PP

                                    HHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETC.EEEEECTTSEGGGTEEEEEESSSSSSHHHH CS
                     Inositol_P  96 TknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflng.eklplsrappiseallvtlfavssrkdtse 174
                                    T n + g+p  a+++gll++g+pv+G+ ++P+++q+y+a++g     ng  + pl +a+ ++  + v++f+ +sr +++ 
  gi|121637511|ref|YP_977734.1|  90 TINHAAGSPLAAILLGLLHDGVPVAGLTWMPFTDQRYTAVAGGPLIKNGvPQPPLADAELANVLVGVGTFSADSRGQFPG 169
                                    *************************************************87799************************** PP

                                    CHHHHHHHCCCCCH.EEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEEEESSSCSSSTTSSEEEE CS
                     Inositol_P 175 asllekvesavsae.gvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGGvvtdakgegrlllargiia 253
                                    +  l+ +e++ +   ++r++gs++++l+ va+G +   ++fg  + WDhAAG+a++++aGGvvtd++g+++++++r+ +a
  gi|121637511|ref|YP_977734.1| 170 RYRLAVLEKLSRVSsRLRMHGSTGIDLVFVADGILGGAISFG-GHVWDHAAGVALVRAAGGVVTDLAGQPWTPASRSALA 248
                                    ***99999998888789*************************.************************************* PP

                                    ESCHHHHHHHH CS
                     Inositol_P 254 anqkelaella 264
                                    ++  + +++++
  gi|121637511|ref|YP_977734.1| 249 GP-LRVHAQIL 258
                                    99.44455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2087.32
//
Query:       gi|121637512|ref|YP_977735.1|  [L=267]
Description: imidazole glycerol phosphate synthase subunit HisF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-86  287.3   0.5    8.4e-86  287.1   0.5    1.0  1  His_biosynth  Histidine biosynthesis protein
    2.8e-07   30.3  11.8     0.0021   17.5   0.9    2.1  2  NMO           Nitronate monooxygenase
    4.2e-07   29.5   6.2     0.0049   16.2   0.7    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    1.3e-05   24.6   2.7      0.022   14.1   0.1    2.2  2  TMP-TENI      Thiamine monophosphate synthase
    1.6e-05   24.1   5.1     0.0032   16.5   0.7    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    1.9e-05   24.2   0.8     0.0099   15.3   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    3.7e-05   23.1   1.2      0.049   12.9   0.1    2.2  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.011   14.9   0.1        2.5    7.1   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
       0.64    8.8   1.9        1.2    8.0   1.9    1.4  1  DUF5423       Family of unknown function (DUF5423)
        5.8    5.8  19.7        1.1    8.2   1.2    2.6  3  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.1   0.5   4.7e-89   8.4e-86       1     229 []      16     251 ..      16     251 .. 0.98

  Alignments for each domain:
  == domain 1  score: 287.1 bits;  conditional E-value: 4.7e-89
                                    EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEES CS
                   His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGG 80 
                                    r+ip+lD++dG+vV   kG++f++lr+agdpvela  y++egadel+++D++a+++gr ++l++v+++ae+vfip++vGG
  gi|121637512|ref|YP_977735.1|  16 RVIPCLDVDDGRVV---KGVNFENLRDAGDPVELAAVYDAEGADELTFLDVTASSSGRATMLEVVRRTAEQVFIPLTVGG 92 
                                    79************...*************************************************************** PP

                                    SSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C.....EEEEETTTTEEEEEEHH CS
                   His_biosynth  81 GIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g.....ykvaikgwreetgldav 150
                                    G+r++ dv++ll+agadkv ++taa+ + +l+ ++a++fgsq+iv+++Dar            ++v+++g+r+ tg+dav
  gi|121637512|ref|YP_977735.1|  93 GVRTVADVDSLLRAGADKVAVNTAAIACLDLLADMARQFGSQCIVLSVDARTvpvgsAptpsgWEVTTHGGRRGTGMDAV 172
                                    ****************************************************98865055666***************** PP

                                    HHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS- CS
                   His_biosynth 151 elakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegelt 229
                                    ++a + ++lg+geill+++d+dGt++G+dl l++++++av++pviasGG+g +e+++ ++++g+dav+++s+++++elt
  gi|121637512|ref|YP_977735.1| 173 QWAARGADLGVGEILLNSMDADGTKAGFDLALLRAVRAAVTVPVIASGGAGAVEHFAPAVAAGADAVLAASVFHFRELT 251
                                    ***************************************************************************9975 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   1.2e-06    0.0021     180     231 ..      72     123 ..      62     133 .. 0.83
   2 !   17.5   4.1   1.2e-06    0.0021     182     225 ..     202     245 ..     167     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                            NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                      +++v + ++ v iP+   GG+ +  +v+  L++GA  v++ t+ +++ + 
  gi|121637512|ref|YP_977735.1|  72 TMLEVVRRTAEQVFIPLTVGGGVRTVADVDSLLRAGADKVAVNTAAIACLDL 123
                                    45566777777777*******************************9999775 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.2e-06
                            NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                    +aL+  v+ av +PviA GG    +  a a a+GA +v  ++ f
  gi|121637512|ref|YP_977735.1| 202 LALLRAVRAAVTVPVIASGGAGAVEHFAPAVAAGADAVLAASVF 245
                                    6899**********************************988776 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   2.9e-06    0.0051     165     221 ..      75     132 ..      61     148 .. 0.80
   2 !   16.2   0.7   2.7e-06    0.0049     158     205 ..     197     243 ..     168     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                                    HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH.HHTSSSHHHHHHHHH CS
                           ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllnta.vaeakdpvamArafk 221
                                    e+++   e++ +P+ v  G+++  d+   +  Gad v +nta +a  +  + mAr f 
  gi|121637512|ref|YP_977735.1|  75 EVVRRTAEQVFIPLTVGGGVRTVADVDSLLRAGADKVAVNTAaIACLDLLADMARQFG 132
                                    445566778899****************************972555555678999885 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.7e-06
                                    ----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESH CS
                           ThiG 158 glGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnt 205
                                      G  + + l+ +++ ++vPvi   G g  ++ a a+  Gadavl ++
  gi|121637512|ref|YP_977735.1| 197 KAGF-DLALLRAVRAAVTVPVIASGGAGAVEHFAPAVAAGADAVLAAS 243
                                    4454.35679999********************************886 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.3e-05     0.022     136     180 ..      71     116 ..      44     117 .. 0.85
   2 !   10.7   0.5   0.00013      0.23     116     177 ..     178     241 ..     162     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                       TMP-TENI 136 plgleglkelaealeiPvvaiGGit.lenvaevleagadgvavvsa 180
                                    +  le ++++ae++ iP+ + GG++  ++v+++l+agad vav +a
  gi|121637512|ref|YP_977735.1|  71 ATMLEVVRRTAEQVFIPLTVGGGVRtVADVDSLLRAGADKVAVNTA 116
                                    5668999999**************6269**************9765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                       TMP-TENI 116 gadYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGitl.envaevleagadgvav 177
                                    gad +gvG i   +   d   +  +l++l+++++a+++Pv+a GG  + e+ a +++agad v  
  gi|121637512|ref|YP_977735.1| 178 GAD-LGVGEILLNSMDADGtkAGFDLALLRAVRAAVTVPVIASGGAGAvEHFAPAVAAGADAVLA 241
                                    555.5777777666666663345678899****************97547888999999998865 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3   0.00021      0.38     126     172 ..      64     113 ..      27     119 .. 0.65
   2 !   16.5   0.7   1.8e-06    0.0032     203     240 ..     209     246 ..     194     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                                    TSSSHHHHHHHHHHHHHTTTSEE...EEEEE-SHHHHHHHHHTT-SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 126 hghsekvleavkeikkkveevev...iaGnvataegakaLieagadavkv 172
                                     + s++  ++++ +++++e+v +   ++G v t + + +L++agad v v
  gi|121637512|ref|YP_977735.1|  64 TASSSGRATMLEVVRRTAEQVFIpltVGGGVRTVADVDSLLRAGADKVAV 113
                                    23334444444444444444322222788888888888888888888766 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.8e-06
                                    HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGslla 240
                                     +   vpvia GG    ++ + A+aaGadav+  s++ 
  gi|121637512|ref|YP_977735.1| 209 RAAVTVPVIASGGAGAVEHFAPAVAAGADAVLAASVFH 246
                                    45568***************************999885 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.5e-06    0.0099     126     168 ..      72     114 ..      70     118 .. 0.91
   2 !    7.4   0.1    0.0014       2.6     130     166 ..     204     240 ..     199     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                                    GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                   G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                    ++ +v++++ +++ ip+  GG ++t  dv+++l+aGa+ v++ 
  gi|121637512|ref|YP_977735.1|  72 TMLEVVRRTAEQVFIPLTVGGGVRTVADVDSLLRAGADKVAVN 114
                                    6899**********************************99875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                                    HHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
                   G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealkaGaiavs 166
                                    ++++++ ++++p+ia+G     e+   a++aGa+av 
  gi|121637512|ref|YP_977735.1| 204 LLRAVRAAVTVPVIASGGAGAVEHFAPAVAAGADAVL 240
                                    57889999***************************96 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   2.7e-05     0.049     229     276 ..      72     117 ..      50     125 .. 0.92
   2 !    9.2   0.1   0.00034      0.61     232     283 ..     203     252 ..     199     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                    HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                         DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                    + l+v+r+ ++++   ip+   GG+ +  D+   ++aGA  v+v ta 
  gi|121637512|ref|YP_977735.1|  72 TMLEVVRRTAEQVF--IPLTVGGGVRTVADVDSLLRAGADKVAVNTAA 117
                                    56889999999999..******************************97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00034
                                    HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCH CS
                         DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpki 283
                                    +++r++++ +   +p+I++GG  + e     + aGA +v   + ++f++ +i
  gi|121637512|ref|YP_977735.1| 203 ALLRAVRAAVT--VPVIASGGAGAVEHFAPAVAAGADAVLAASVFHFRELTI 252
                                    67888888888..********************************9998765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0032       5.8     170     216 ..      72     117 ..      38     131 .. 0.77
   2 ?    7.1   0.0    0.0014       2.5     170     213 ..     200     242 ..     168     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0032
                                    --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
                            Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrga 216
                                      +e ++   ++v ip+ + G+++++ d++  l+  Gad v +  +a
  gi|121637512|ref|YP_977735.1|  72 TMLEVVRRTAEQVFIPLTVGGGVRTVADVDSLLRA-GADKVAVNTAA 117
                                    34677888899999*******************99.***99886665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                                    --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                            Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                     d++  ++v+ av++pvia G+   +e    +++  Gad+v+++
  gi|121637512|ref|YP_977735.1| 200 FDLALLRAVRAAVTVPVIASGGAGAVEHFAPAVAA-GADAVLAA 242
                                    57777899*********************999999.****9876 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.9   0.00065       1.2      79     126 ..     207     255 ..     163     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00065
                        DUF5423  79 dtvaavslpfiltgtaaglmfsaiavggga.vilanplflmgsmtlgfa 126
                                       aav++p+i +g a  +   a av  ga  +la  +f +  +t+g  
  gi|121637512|ref|YP_977735.1| 207 AVRAAVTVPVIASGGAGAVEHFAPAVAAGAdAVLAASVFHFRELTIGQV 255
                                    34599*********99999888777776653689999**9999999965 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2   0.00063       1.1     260     302 ..      72     116 ..      61     126 .. 0.77
   2 ?   -1.7   1.4      0.64   1.1e+03     272     295 ..     156     180 ..     113     198 .. 0.54
   3 ?    2.7  10.6     0.028        51     252     307 ..     194     249 ..     157     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00063
                                    CHHHHHHHH..S..S-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                         FMN_dh 260 vLpeiveavggr..ievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                    ++ e+v++ +++  i++ v gG+r+ +Dv   l  GAd v++  +
  gi|121637512|ref|YP_977735.1|  72 TMLEVVRRTAEQvfIPLTVGGGVRTVADVDSLLRAGADKVAVNTA 116
                                    455666666554459************************998665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.64
                                    S-EEEESS--.SHHHHHHHHHTT-S CS
                         FMN_dh 272 ievlvDgGir.rGsDvlkAlalGAd 295
                                     ev   gG r +G D+++  a GAd
  gi|121637512|ref|YP_977735.1| 156 WEVTTHGGRRgTGMDAVQWAARGAD 180
                                    4444455544345566666666665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.028
                                    TT---HHH..CHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHH CS
                         FMN_dh 252 dgapatid..vLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflygl 307
                                    dg+ a +d   L ++++av   ++v+++gG    ++ + A+a GAdavl +  f++  
  gi|121637512|ref|YP_977735.1| 194 DGTKAGFDlaLLRAVRAAVT--VPVIASGGAGAVEHFAPAVAAGADAVLAASVFHFRE 249
                                    66666655215778888886..***************************998887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1715.03
//
Query:       gi|121637513|ref|YP_977736.1|  [L=115]
Description: phosphoribosyl-AMP cyclohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-34  116.8   0.8    3.8e-34  116.4   0.8    1.2  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.8   2.1e-38   3.8e-34       1      73 [.      33     105 ..      33     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 2.1e-38
                                    EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS- CS
                         PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCF 73 
                                    m+a+mn+eal++tl+t++a+yySrsr++ W+KG+tSg++q+v+++rlDcD+Da+ll+v+q g aCHtg +sCF
  gi|121637513|ref|YP_977736.1|  33 MVAWMNDEALARTLQTREATYYSRSRAEQWVKGATSGHTQHVHSVRLDCDGDAVLLTVDQVGGACHTGDHSCF 105
                                    9************************************************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 800.63
//
Query:       gi|121637514|ref|YP_977737.1|  [L=360]
Description: ionic transporter integral membrane protein chaA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-27   93.8  37.0    5.1e-14   52.5  14.3    2.2  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4  14.7     1e-16   1.8e-12       7     150 ..      33     183 ..      27     184 .. 0.85
   2 !   52.5  14.3   2.8e-18   5.1e-14       2     150 ..     216     358 ..     215     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTT...HHHHHHHHHHHHHHHHHTHH CS
                       Na_Ca_ex   7 ilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltge...vdlaignvlGsnifnlllvi 83 
                                    +l+ +l++ +    v++ae++a      g+++G ++lA +++ +E++++++ +++g    ++la+++v++++++ ++++ 
  gi|121637514|ref|YP_977737.1|  33 LLAAVLLAGAVLAAVNHAEVVA---ARVGEPFGSLVLAVAVTTIEVALIVALMVSGGddaATLARDTVFAAVMITTNGIA 109
                                    4455555566777789999999...89999*************************88899******************** PP

                                    HHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHH........HTEEHHHHHHHHHHHHHHHHHHHH CS
                       Na_Ca_ex  84 Glialigslkvdseslkldlgllllvallllllvlllllplfv........pgrltvleglvllllYalylvlsl 150
                                    Gl++l+gs  +++ +l + +g    +a + +l++l l+lp+f+        +  + ++ g++ l+lY+l+l+ ++
  gi|121637514|ref|YP_977737.1| 110 GLSLLLGS-LRYGVTLFNPHGSGAALATVTTLATLSLVLPTFTtsqsgpelSPGQLIFAGAASLGLYVLFLFTQT 183
                                    ********.5555554344477778888888889999****99********8888899**************997 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 2.8e-18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHT CS
                       Na_Ca_ex   2 lfvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlll 81 
                                    +++l++++l++++ la++ ++ +ee+++  g ++s++G+ ++A+ + lpE++++  aa++g  + +++ ++Gs+++ ++l
  gi|121637514|ref|YP_977737.1| 216 SLGLLLVALVAVVGLAKVESPVIEEVVSAAGFPQSFVGV-VIATLVLLPETLAAARAARQGRLQTSLNLAYGSAMASIGL 294
                                    67899***********************9**********.99************************************** PP

                                    HHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                       Na_Ca_ex  82 viGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                    +i++ial + +   ++   l lg+++lv+l+l+++v++l+    vpgr t+l+g v+l+l a+yl+l++
  gi|121637514|ref|YP_977737.1| 295 TIPTIALASLWLSGPL--QLGLGAIQLVLLVLTVVVSVLT---VVPGRATRLQGEVHLVLLAAYLFLAV 358
                                    ********77555554..5888888888888888888877...558*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2640.12
//
Query:       gi|121637515|ref|YP_977738.1|  [L=154]
Description: peroxidoxin bcpB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-30  104.8   0.0    3.3e-30  104.5   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    6.3e-21   74.6   0.0    7.4e-21   74.4   0.0    1.0  1  Redoxin     Redoxin
     0.0007   19.7   0.0    0.00092   19.3   0.0    1.2  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   5.5e-34   3.3e-30       2     121 ..       4     127 ..       3     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 5.5e-34
                                    TSB----EEESTTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                       AhpC-TSA   2 gdkapdfelknadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                    gd + dfel+++ g++ +ls + ++ pvvlffyp++ +p+Ct+e++ +++l++ef+e  +  +g+s+d++ +++kf+e  
  gi|121637515|ref|YP_977738.1|   4 GDTVADFELPDQTGTPRRLSVLlSDGPVVLFFYPAAMTPGCTKEACHFRDLAKEFAEVRASRVGISTDPVRKQAKFAEVR 83 
                                    8999******************9778****************************************************** PP

                                    H.SSEEEE-TTSHHHHHTT-EETT...TTECSCEEEEE-TTSBE CS
                       AhpC-TSA  81 slnfpllsDeegkvakaygvlkee...kglalratfvidkegki 121
                                    ++ +pllsD +g+va ++gv +      +   r+tfvid++ k+
  gi|121637515|ref|YP_977738.1|  84 RFDYPLLSDAQGTVAAQFGVKRGLlgkLMPVKRTTFVIDTDRKV 127
                                    *********************988997677789********998 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.2e-24   7.4e-21       1     146 [.       2     144 ..       2     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.2e-24
                                    -TTSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHH CS
                        Redoxin   1 kagdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkef 79 
                                    k gd++ df+lp+  + g++  ls  + +++vv++f+p+a +P C++e++ +++la++++e   + v++++d    + +f
  gi|121637515|ref|YP_977738.1|   2 KTGDTVADFELPD--QTGTPRRLSVlLSDGPVVLFFYPAAMTPGCTKEACHFRDLAKEFAEVRASRVGISTDPVRKQAKF 79 
                                    579********99..***************************************************************** PP

                                    HHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHHH CS
                        Redoxin  80 wgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaeav 146
                                    ++    ++p+lsD+++ +++++G++     + +   ++++vid d kv  ++  +++   ++ a+++
  gi|121637515|ref|YP_977738.1|  80 AEVRRFDYPLLSDAQGTVAAQFGVKRGLLGKLMPVKRTTFVIDTDRKVLDVISSEFSM--DAHADKA 144
                                    ***********************8844444444677789***********99998883..5666655 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.5e-07   0.00092       3      67 ..      52     117 ..      50     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-07
                     AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkrglklklaplslq 67 
                                    +++++e+++ + + v+i+ + + +  kF++   f+++l+ D+++++ +++g+krgl +kl+p + +
  gi|121637515|ref|YP_977738.1|  52 RDLAKEFAEVRASRVGISTDPVrKQAKFAEVRRFDYPLLSDAQGTVAAQFGVKRGLLGKLMPVKRT 117
                                    55678888889999999*****77************************************987643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1156.23
//
Query:       gi|121637516|ref|YP_977739.1|  [L=516]
Description: anthranilate synthase component I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-93  312.3   0.0    8.6e-93  310.6   0.0    1.7  2  Chorismate_bind  chorismate binding enzyme
      4e-34  117.9   0.0    1.2e-31  109.8   0.0    2.9  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.12   1.1e+03      26      78 ..      26      80 ..      16     100 .. 0.66
   2 !  310.6   0.0   9.5e-97   8.6e-93       3     258 .]     234     492 ..     232     492 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.12
                                   EEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEE..EETT.....EEEEEEESSEEEEEE CS
                Chorismate_bind 26 lsrrlkaeleaavdplalyralrarnpapysfll..eled.....sellgaSPElllkve 78
                                   ++r++ a    + +pl++yr+l a+ p  + +    +  +      +++ga   + l+v+
  gi|121637516|ref|YP_977739.1| 26 VTRKVLAD---SETPLSAYRKLAANRPGTFLLESaeN--GrswsrWSFIGAGAPTALTVR 80
                                   44444444...457899******99988876655330..233333555666555555555 PP

  == domain 2  score: 310.6 bits;  conditional E-value: 9.5e-97
                                    CHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETT......EEEEEEESSEEEE CS
                Chorismate_bind   3 edYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleled......sellgaSPElllk 76 
                                    e+Y + ve ++++i+ag+ ++vv+s+r+++   ++vdp+++yr lr +np+py++ll++++      ++++g+SPE l++
  gi|121637516|ref|YP_977739.1| 234 EEYGAIVEYLVDQIAAGEAFQVVPSQRFEMD--TDVDPIDVYRILRVTNPSPYMYLLQVPNsdgavdFSIVGSSPEALVT 311
                                    799****************************..99**********************888888888899*********** PP

                                    EETTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEE CS
                Chorismate_bind  77 veggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlv 156
                                    v++g  ++t+piaGTr rg+t+ ed  le+ell+d+KeraEhlm+vdl rndLg+v++pg+v+v+++ ++erys+v+hlv
  gi|121637516|ref|YP_977739.1| 312 VHEG-WATTHPIAGTRWRGRTDDEDVLLEKELLADDKERAEHLMLVDLGRNDLGRVCTPGTVRVEDYSHIERYSHVMHLV 390
                                    **77.*************************************************************************** PP

                                    EEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEE CS
                Chorismate_bind 157 stiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrl 236
                                    st++g+l e+ ++ld++ a+fP+g+++GaPk rame+i+e+E++rRg+Y+G+vgyld+ g+a++a++IRta+++++++++
  gi|121637516|ref|YP_977739.1| 391 STVTGKLGEGRTALDAVTACFPAGTLSGAPKVRAMELIEEVEKTRRGLYGGVVGYLDFAGNADFAIAIRTALMRNGTAYV 470
                                    ******************************************************************************** PP

                                    EEEEEEETT--HHHHHHHHHHH CS
                Chorismate_bind 237 gaGaGIvadSdpeaEyeEtlaK 258
                                    +aG+G+vadS+   Ey+E ++K
  gi|121637516|ref|YP_977739.1| 471 QAGGGVVADSNGSYEYNEARNK 492
                                    ******************9988 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   1.3e-35   1.2e-31       1     142 []      33     177 ..      33     177 .. 0.92
   2 !    4.1   0.0    0.0054        49       2      54 ..     266     320 ..     265     353 .. 0.79
   3 ?   -0.4   0.0      0.13   1.2e+03      86      98 ..     434     446 ..     420     449 .. 0.73

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.3e-35
                  Anth_synt_I_N   1 ddltplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeee.pldalrellerfr 78 
                                    d++tpls+y+kla+++  +flLeSaen  +++r+Sfig+     l++++g++ + g+  +++ ++  pl al+ +le + 
  gi|121637516|ref|YP_977739.1|  33 DSETPLSAYRKLAANRpGTFLLESAENGRSWSRWSFIGAGAPTALTVREGQAVWLGAVPKDAPTGGdPLRALQVTLELLA 112
                                    789************9**********99999*************************66666666557*********9999 PP

                  Anth_synt_I_N  79 saedse.ptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtlivfDhkerrlyl 142
                                     a +++ p+ +p++gG+vG+++YD+vr +e+lp++a ddl lpd+ l+l  ++ ++Dh+e++++l
  gi|121637516|ref|YP_977739.1| 113 TADRQSePGLPPLSGGMVGFFAYDMVRRLERLPERAVDDLCLPDMLLLLATDVAAVDHHEGTITL 177
                                    6544447*****************************************************99886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0054
                  Anth_synt_I_N   2 dltplsvylklaeee...hkflLeSaeneggegrySfigldpflelkskngeveve 54 
                                    d++p+ vy+ l+ ++   + +lL    n+ g   +S++g +p + +++++g ++++
  gi|121637516|ref|YP_977739.1| 266 DVDPIDVYRILRVTNpspYMYLLQVP-NSDGAVDFSIVGSSPEALVTVHEGWATTH 320
                                    57899999998887778899999988.589999*********99999988876665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.13
                  Anth_synt_I_N  86 telpfvgGlvGyl 98 
                                    t   ++gG+vGyl
  gi|121637516|ref|YP_977739.1| 434 TRRGLYGGVVGYL 446
                                    444589******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4050.93
//
Query:       gi|121637517|ref|YP_977740.1|  [L=235]
Description: hypothetical protein BCG_1648 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-45  153.3  26.4    6.7e-45  153.1  26.4    1.0  1  Trp_oprn_chp   Tryptophan-associated transmembrane protein (T
  ------ inclusion threshold ------
        7.9    5.4  15.5        2.9    6.9   5.8    2.0  2  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1  26.4   7.5e-49   6.7e-45       1     180 []      22     224 ..      22     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 7.5e-49
                   Trp_oprn_chp   1 llllalgAallllasrltWvtvtvsdalggprtvalsGadwapaltalAlvllAaavAvlavrglgrrvvgvllalagag 80 
                                    +lll+++A++l++a+rl+Wv + ++d+lg+p++v+l+Ga+w++al +lAl++lAaavA+lavrg+ +r+++vlla+a+++
  gi|121637517|ref|YP_977740.1|  22 QLLLVVAAGALWMAARLPWVVIGSFDELGPPKEVTLTGASWSTALLPLALLMLAAAVAALAVRGWPLRALAVLLAAASFA 101
                                    589***************************************************************************** PP

                   Trp_oprn_chp  81 aavaalslltdpadaaraaaaaatgvasaaaaveltawpvlalaggvllllagvllllra...rswpamssrYerpaarr 157
                                    +++ ++sl++ p+ aar+a+ a   v + + ++++  ++v+a++++v++lla+v+l+ +a   +s+++  +rY +p+arr
  gi|121637517|ref|YP_977740.1| 102 VGYLGISLWVVPDVAARGADLAHVPVVTLVGSARHYWGAVAAVLAAVCALLAAVFLMSSAairGSAGEDMARYAAPRARR 181
                                    ********************555555577777777789********************99887788899*********** PP

                   Trp_oprn_chp 158 aeaeae....................dserdlWdaLdrGeDPT 180
                                    + a+++                    +ser++W+aLd+G+DPT
  gi|121637517|ref|YP_977740.1| 182 SIARRQhsnaagraapqddgpdmgprMSERMIWEALDEGRDPT 224
                                    *999999***********************************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.8   0.00032       2.9      94     181 ..      25     108 ..      12     120 .. 0.75
   2 ?    4.2   2.2    0.0022        19     298     338 ..     122     157 ..     122     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00032
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3  94 illialvaghiqanasanvtlfdetkglmfllfefpatghlWfLwalfvlylllplllrllrkvrkshlllllillllls 173
                                    +++ a   ++    +++   +f    +  ++  e ++tg++W+ ++l +  l+l+  +++l++++++ ++l+++l+++++
  gi|121637517|ref|YP_977740.1|  25 LVVAAGALWMAARLPWVVIGSF----DELGPPKEVTLTGASWSTALLPLALLMLAAAVAALAVRGWPLRALAVLLAAASF 100
                                    3444444444444444444444....669999999************999999999999999999999999999999999 PP

                                    xxxxxxxx RF
                  Acyl_transf_3 174 lvfirhel 181
                                    +v ++   
  gi|121637517|ref|YP_977740.1| 101 AVGYLGIS 108
                                    99887665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0022
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 298 liHlpllmllqkllrdwglnlgevlllvlllvvsvivsvvl 338
                                    l+H+p++ l++++   w      ++++vl+ v +++++v l
  gi|121637517|ref|YP_977740.1| 122 LAHVPVVTLVGSARHYW-----GAVAAVLAAVCALLAAVFL 157
                                    89***************.....7778888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1774.34
//
Query:       gi|121637518|ref|YP_977741.1|  [L=272]
Description: indole-3-glycerol-phosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-78  263.0   0.0    2.5e-78  262.8   0.0    1.0  1  IGPS       Indole-3-glycerol phosphate synthase
    0.00029   20.5   0.1    0.00041   20.0   0.1    1.3  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
     0.0015   17.6   5.9      0.051   12.6   3.7    2.3  2  FMN_dh     FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.0   4.1e-82   2.5e-78       1     254 []       7     258 ..       7     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 4.1e-82
                                    HHHCHHHHHHHHHHHHCCS-GGCCCCG..-SS-SS-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT CS
                           IGPS   1 lekivaekkeevaeakkrqsladleaavklakpkrsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkyeea 80 
                                    l++i++  +++va++++++sl++++aa+ +a+p  + + aLre    +++iaEvK+aSPs g +++ +dpa++A++y+++
  gi|121637518|ref|YP_977741.1|   7 LDSILEGVRADVAAREASVSLSEIKAAAAAAPPPLDVMAALRE--PGIGVIAEVKRASPSAGALATIADPAKLAQAYQDG 84 
                                    789****************************************..9********************************** PP

                                    .-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-E CS
                           IGPS  81 gAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslgle 160
                                    gA ++SV te++ FqGsl+dL +vr++vs+pvlrKdF++++yqi+eara+gad+ LLiv++le++ l ++ +  +slg+ 
  gi|121637518|ref|YP_977741.1|  85 GARIVSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDFVVQPYQIHEARAHGADMLLLIVAALEQSVLVSMLDRTESLGMT 164
                                    ******************************************************************************** PP

                                    EEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHH CS
                           IGPS 161 vLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGes 240
                                    +LvEvh+e+e +ralk+gak+iGvN R+L tl+vd + + ++a+ +p++v+ +aeSG++ ++d+ +++ +g++a+LvGe 
  gi|121637518|ref|YP_977741.1| 165 ALVEVHTEQEADRALKAGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEG 244
                                    ******************************************************************************** PP

                                    HHC-TTHHHHHHHH CS
                           IGPS 241 lmrqedvekairel 254
                                    l+ + d ++a+++l
  gi|121637518|ref|YP_977741.1| 245 LVTSGDPRAAVADL 258
                                    ********999876 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   6.9e-08   0.00041      97     223 ..     135     256 ..      61     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.9e-08
                                    HHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTHHHHHHTTCSCEEEH CS
                      OMPdecase  97 GkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetlnateedaddfihltp 176
                                    G +++  ++ a+e++    + +l+++ s g  +l e   t++ +++a ++   ++v+G+ a   +  ++ d d f  + p
  gi|121637518|ref|YP_977741.1| 135 GADMLLLIVAALEQS--VLVSMLDRTESLGMTALVE-VHTEQEADRALKAG--AKVIGVNARDLMT-LDVDRDCFARIAP 208
                                    455555555555555..48999*********99999.78899999999999..78*******9999.777889******* PP

                                    HHTTEEEEECTTCCGGGHHHHH.HHTTCSEEEESHHHHTSSSHHHHHH CS
                      OMPdecase 177 gigleqggdgkgqqyntpekli.giagadiiivGRgIlkagdpveeae 223
                                    g    +   ++   + t++ l+   agad + vG g++++gdp++++ 
  gi|121637518|ref|YP_977741.1| 209 GLPSSVIRIAESGVRGTADLLAyAGAGADAVLVGEGLVTSGDPRAAVA 256
                                    **9955555554444444443313489*****************9985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0017        10     176     241 ..      72     139 ..      16     144 .. 0.77
   2 !   12.6   3.7   8.6e-06     0.051     223     303 ..     168     245 ..     157     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0017
                                    STSGSCCTTH..THHHH..HHCCCHB-TC--HHHHHHHHHHHSSEEEEEE.E-SHHHHHHHHHTTESEE CS
                         FMN_dh 176 akpewaaealkkasaaa..efvgkqldpsltwddikwlreqtklplvvKG.vltaedakraveaGvdgi 241
                                    a+p+  a+a ++  a    ++v++q + + + dd++ +r+ +++p++ K  v+++  +++a ++G+d +
  gi|121637518|ref|YP_977741.1|  72 ADPAKLAQAYQDGGA-RivSVVTEQRRFQGSLDDLDAVRASVSIPVLRKDfVVQPYQIHEARAHGADML 139
                                    344444444312222.234777777778889******************8579*************976 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.6e-06
                                    EE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                         FMN_dh 223 GvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                    +v t+++a+ra++aG++ i v    +R l +     d+  +i+  +++++  ++ +G+r  +D l     GAdavl+G  
  gi|121637518|ref|YP_977741.1| 168 EVHTEQEADRALKAGAKVIGVN---ARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTADLLAYAGAGADAVLVGEG 244
                                    68999**************994...89********************999999*************************76 PP

                                    H CS
                         FMN_dh 303 f 303
                                    +
  gi|121637518|ref|YP_977741.1| 245 L 245
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2073.93
//
Query:       gi|121637519|ref|YP_977742.1|  [L=410]
Description: tryptophan synthase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-51  175.4   3.4      2e-51  175.2   3.4    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.33   11.2   0.0    1.7  1  Gmad2     Immunoglobulin-like domain of bacterial spore germi


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.2   3.4   2.2e-55     2e-51       3     294 .]      65     391 ..      63     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 2.2e-55
                                    GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHH.HHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                           PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgae.yllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                    ++ +p+Pl ++ rls++ g + +flK+E+ln+tgS+K++ +   +l++ + g ++++++e+++G+hg+a+A a+allGl+
  gi|121637519|ref|YP_977742.1|  65 YAGRPSPLYEATRLSQHAGSArIFLKREDLNHTGSHKINNVLgQALLARRMG-KTRVIAETGAGQHGVATATACALLGLD 143
                                    5789*************************************95555556666.*************************** PP

                                    EEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH....STTCEE--TTT.....SHHHHHH.HHTHH CS
                           PALP  81 vtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae....gegaylvsqfd.....nptvieg.ygtig 147
                                    ++i++   ++   + +va++rllGaevv v+++ ++ ++a++e+ ++     ++ y++  +       pt +   +  ig
  gi|121637519|ref|YP_977742.1| 144 CVIYMGGIDTarqALNVARMRLLGAEVVAVQTGSKTLKDAINEAFRDwvanADNTYYCFGTAagphpFPTMVRDfQRIIG 223
                                    ******99995556****************988888888877777777777455555444444564434455555***** PP

                                    HHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B........... CS
                           PALP 148 lEil....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs.......... 213
                                    +E       q g+ pdavv++vGgG+++ Gi +++ + +p vr++g e++     ++++++gr+  + ++          
  gi|121637519|ref|YP_977742.1| 224 MEARvqiqGQAGRLPDAVVACVGGGSNAIGIFHAFLD-DPGVRLVGFEAA-----GDGVETGRHAATFTAgspgafhgsf 297
                                    ***955555555************************6.899******999.....444444444444444455567777* PP

                                    ..............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHH CS
                           PALP 214 ..............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklrea 279
                                                  ++i  gl+ + +++++  l ++   ++  ++d ea++a  ll+r egi++   sa+a+a++ l+  
  gi|121637519|ref|YP_977742.1| 298 syllqdedgqtiesHSISAGLDYPGVGPEHAWLKEAGRVDYRPITDSEAMDAFGLLCRMEGIIPAIESAHAVAGA-LKLG 376
                                    *************9**********55555555556666669**********************************.**** PP

                                    HCCTTCEEEEEEE-B CS
                           PALP 280 gelkegdrvvviltg 294
                                     el++g+++vv l+g
  gi|121637519|ref|YP_977742.1| 377 VELGRGAVIVVNLSG 391
                                    ************998 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.33      20      57 ..     287     324 ..     280     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                          Gmad2  20 sGkarvFEatvnvrlrddagevlaegfvtAdegapkfg 57 
                                    +G+  +F +++++ l+d++g+ +  ++++A+  +p+ g
  gi|121637519|ref|YP_977742.1| 287 AGSPGAFHGSFSYLLQDEDGQTIESHSISAGLDYPGVG 324
                                    68889*************************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2789.20
//
Query:       gi|121637520|ref|YP_977743.1|  [L=270]
Description: tryptophan synthase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-68  230.3   0.0      2e-68  230.1   0.0    1.0  1  Trp_syntA      Tryptophan synthase alpha chain
     0.0014   18.1   0.2     0.0023   17.4   0.2    1.2  1  PcrB           PcrB family
     0.0041   16.6   0.3     0.0072   15.8   0.3    1.3  1  His_biosynth   Histidine biosynthesis protein
     0.0053   16.2   0.5      0.013   15.0   0.2    1.7  2  BtpA           BtpA family
  ------ inclusion threshold ------
      0.037   13.8   0.2        6.1    6.6   0.2    2.2  2  KDGP_aldolase  KDGP aldolase


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   0.0   5.5e-72     2e-68       1     236 [.      16     249 ..      16     266 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 5.5e-72
                                    HHHHHCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHH CS
                      Trp_syntA   1 faklkaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelvee 80 
                                    f +++a+nraa++ y+  g+pd+  s+ +++al ++g d+iE+G+p+sdP +dGP+I +a++ aL+ gv+++++l  ve+
  gi|121637520|ref|YP_977743.1|  16 FDSCRANNRAALIGYLPTGYPDVPASVAAMTALVESGCDIIEVGVPYSDPGMDGPTIARATEAALRGGVRVRDTLAAVEA 95 
                                    67899*************************************************************************** PP

                                    HHHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHH CS
                      Trp_syntA  81 vrkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevv 160
                                    +  ++     v++ty n+vl+yg ++f ++l+ ag  gli pDl ++ea++  +a +++ l+ +flvap+++ erl+  v
  gi|121637520|ref|YP_977743.1|  96 ISIAG--GRAVVMTYWNPVLRYGVDAFARDLAAAGGLGLITPDLIPDEAQQWLAASEEHRLDRIFLVAPSSTPERLAATV 173
                                    **555..45699******************************************************************** PP

                                    HH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCT CS
                      Trp_syntA 161 eqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieee 236
                                    e+++gfvY+ s +GvTga++av++   elv r+k++++ Pv vG G+++++q++q+a+ adGvivGSalv+++ e 
  gi|121637520|ref|YP_977743.1| 174 EASRGFVYAASTMGVTGARDAVSQAAPELVGRVKAVSDIPVGVGLGVRSRAQAAQIAQYADGVIVGSALVTALTEG 249
                                    ***********************************************************************99875 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   6.3e-07    0.0023     170     211 ..     202     242 ..     185     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.3e-07
                                    HHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHH CS
                           PcrB 170 evialkkklekarlivGGGirsaEkAkevveaADvivvGnvv 211
                                    +v   +k ++++ + vG G+rs+ +A++++++AD ++vG ++
  gi|121637520|ref|YP_977743.1| 202 LV-GRVKAVSDIPVGVGLGVRSRAQAAQIAQYADGVIVGSAL 242
                                    33.345677899999************************987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3     2e-06    0.0072      59     107 ..     197     244 ..     185     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-06
                                    HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                   His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                    +a  +lv ++    +ipv vG G+rs  +++++ +  ad vi+g+a v+
  gi|121637520|ref|YP_977743.1| 197 QAAPELVGRVKAVSDIPVGVGLGVRSRAQAAQIAQY-ADGVIVGSALVT 244
                                    45568999************************9999.*********987 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.52   1.9e+03      62      76 ..      39      53 ..      32      62 .. 0.74
   2 !   15.0   0.2   3.6e-06     0.013     176     230 ..     186     242 ..     165     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.52
                           BtpA 62 petvaamtvivkevk 76
                                   p+ vaamt +v+   
  gi|121637520|ref|YP_977743.1| 39 PASVAAMTALVESGC 53
                                   778999999987654 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.6e-06
                           BtpA 176 vilsGkatGgevdl.eelklaketvkvkvlvgsGvse.enlekllsiadGvivgtsi 230
                                    + ++G +   +  + e + ++k + +++v vg Gv     ++++ ++adGvivg+ +
  gi|121637520|ref|YP_977743.1| 186 MGVTGARDAVSQAApELVGRVKAVSDIPVGVGLGVRSrAQAAQIAQYADGVIVGSAL 242
                                    55677665555555045556666666*********7615788999*********986 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0051        18      22      67 ..      20      65 ..      13      79 .. 0.85
   2 ?    6.6   0.2    0.0017       6.1      14      77 ..     173     233 ..     159     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0051
                                   HHTTT-EEEEEEGGGSSSHHHHHHHHHHHHHCTTT-EEEE-STT-G CS
                  KDGP_aldolase 22 eaaeghvviGvlsknyetveeavedvkkykkevdnaisvGLGaGdp 67
                                    a +  ++iG l + y++v ++v ++ ++ ++  + i vG+   dp
  gi|121637520|ref|YP_977743.1| 20 RANNRAALIGYLPTGYPDVPASVAAMTALVESGCDIIEVGVPYSDP 65
                                   5667789*********************999988899999877666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                    HHHHHHHHHHTTT-EEEEEEGGGSSSHHHHHHHHHHHHHCTTT-EEEE-STT-GGGHHHHHHHC CS
                  KDGP_aldolase  14 ienakeiyeaaeghvviGvlsknyetveeavedvkkykkevdnaisvGLGaGdpeqskmvaeis 77 
                                    +e ++  + aa     +Gv  +  +  ++a e v + k++ d ++ vGLG    +q++++a+ +
  gi|121637520|ref|YP_977743.1| 173 VEASRGFVYAAS---TMGVTGARDAVSQAAPELVGRVKAVSDIPVGVGLGVRSRAQAAQIAQYA 233
                                    333333333333...3566666667777777888889999999********9999999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1842.42
//
Query:       gi|121637521|ref|YP_977744.1|  [L=468]
Description: prolipoprotein diacylglyceryl transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-57  192.6  11.2    7.4e-57  192.4  11.2    1.1  1  LGT       Prolipoprotein diacylglyceryl transferase


Domain annotation for each model (and alignments):
>> LGT  Prolipoprotein diacylglyceryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4  11.2   4.1e-61   7.4e-57       4     241 ..      16     273 ..      13     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 4.1e-61
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx...xxxxxxxx RF
                            LGT   4 fsigpleirwYgllialgfllavllakrrakkeglkeekdkvddlliyavilgiiGaRlgyvl....fY...ylsnplei 76 
                                    + +gpl++r Y++++++g+++a+l+  rr++ +g ++     +d++++av++g+iG+Rl+++     +Y     + +++ 
  gi|121637521|ref|YP_977744.1|  16 WYLGPLPVRAYAVCVITGIIVALLIGDRRLTARGGERGM--TYDIALWAVPFGLIGGRLYHLAtdwrTYfgdGGAGLAAA 93 
                                    67899***************************9888855..9*********************99987745422778*** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                            LGT  77 lkiwegGlaihGgligvllalllyakkkklsflkvlDivapvvalgqaigRlGNfingelyGkptdlpwg.......... 146
                                    l+iw+gGl i+G++  +++++++ +++ ++++  +lD+vap+v+l+qaigRlGN++n+elyG++t++pwg          
  gi|121637521|ref|YP_977744.1|  94 LRIWDGGLGIWGAVTLGVMGAWIGCRRCGIPLPVLLDAVAPGVVLAQAIGRLGNYFNQELYGRETTMPWGleifyrrdps 173
                                    *************************777******************************************9888877777 PP

                                    .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                            LGT 147 .......lvfkkaeelplprhPtqlYeslenlllflilllllskkkkkkkkdgevfglylilyglgRffiEflRtds.ll 218
                                           l  ++++++++ ++Pt+lYe ++n+l+f+ l++ + ++      +g++fg+y+++y +gRf++E+lR d   l
  gi|121637521|ref|YP_977744.1| 174 gfdvpnsLDGVSTGQVAFVVQPTFLYELIWNVLVFVALIY-IDRRF--IIGHGRLFGFYVAFYCAGRFCVELLRDDPaTL 250
                                    7766665555555555577*******************99.54333..4679**********************995244 PP

                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                            LGT 219 lgslrmgqllsiplvlagialli 241
                                    ++++r++ ++s ++++ +++++i
  gi|121637521|ref|YP_977744.1| 251 IAGIRINSFTSTFVFIGAVVYII 273
                                    6*****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3015.31
//
Query:       gi|121637522|ref|YP_977745.1|  [L=146]
Description: hypothetical protein BCG_1653 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-11   43.2   8.4      5e-11   42.7   8.4    1.2  1  TM2       TM2 domain


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   8.4   2.8e-15     5e-11       2      50 ..      72     126 ..      71     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.8e-15
                            TM2   2 kksklvaylLwf..fLGglGvHRFYlGktgsGvlqlltfv....Gglgiwwlidl 50 
                                    +ksk+va+lL +  ++G+ G+ R+YlG+tg G++qll+++     g+ iw++id 
  gi|121637522|ref|YP_977745.1|  72 DKSKTVAGLLQLlgLFGIAGIGRIYLGHTGLGIAQLLVGWvtcgLGAVIWGVIDA 126
                                    7*********99566*************************888555777888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1211.03
//
Query:       gi|121637523|ref|YP_977746.1|  [L=132]
Description: hypothetical protein BCG_1654 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-19   67.2   1.2    9.8e-19   67.2   1.2    2.1  2  DUF2752   Protein of unknown function (DUF2752)
  ------ inclusion threshold ------
      0.014   14.4   0.6      0.014   14.4   0.6    1.7  1  FecCD     FecCD transport family
       0.12   12.0  10.0       0.35   10.4  10.0    1.6  1  DUF998    Protein of unknown function (DUF998)
       0.53    9.9   2.6        2.7    7.6   0.9    2.0  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   1.2   2.2e-22   9.8e-19       1      48 [.      41      88 ..      41      89 .. 0.97
   2 ?   -1.5   0.2      0.61   2.7e+03      37      45 ..     105     113 ..      95     117 .. 0.52

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.2e-22
                        DUF2752  1 CpfkaltGipCPGCGltRavhallhgdfaaAfrynplgvlllplllll 48
                                   C+fk ltG++CP+CG++R++h+llhg++aa+++ n+++++ +p+l+ +
  gi|121637523|ref|YP_977746.1| 41 CLFKLLTGWNCPACGGLRMIHDLLHGELAASINDNVFLLVGVPVLASW 88
                                   ********************************************9865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.61
                        DUF2752  37 lgvlllpll 45 
                                    ++ ++++++
  gi|121637523|ref|YP_977746.1| 105 MIAVAVAVI 113
                                    223333333 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   3.1e-06     0.014     231     307 ..      12      86 ..      10      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                          FecCD 231 ltavavalvGpigFvGLivPhiarllvgadhrkllp..lsallGallllladllarlllsptelpvgivtaliGapffi 307
                                    +++++v l+G +g++GL+ Ph    l  +   kll    +  +G+l ++   l ++l++s ++     v  l+G+p+++
  gi|121637523|ref|YP_977746.1|  12 AAGSVVLLAGALGYIGLVDPHNSNSLYPPCLFKLLTgwNCPACGGLRMIHDLLHGELAAS-IN---DNVFLLVGVPVLA 86 
                                    799*******************99999966666664213455555555444444444443.33...3566677777766 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  10.0   7.8e-05      0.35      64     159 ..       6     122 ..       2     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.8e-05
                         DUF998  64 argragragrlllavaglglvlagvfptdpgggsp...................slsglvH..glasavaflalavavll 122
                                    +++r ++ag+++l +++lg ++ +  p +  + +p                     ++l+H   +as+   + l+v+v +
  gi|121637523|ref|YP_977746.1|   6 RQRRYAAAGSVVLLAGALGYIGLV-DPHNSNSLYPpclfklltgwncpacgglrMIHDLLHgeLAASINDNVFLLVGVPV 84 
                                    678889999999999999999998.4444444444799999999999999999999*****7778999999999999999 PP

                         DUF998 123 la.saarrrawallrlvggvallllvaalvwllaaald 159
                                    la +   rr+++ l+l + v+++++va+++w+++++l 
  gi|121637523|ref|YP_977746.1|  85 LAsWVLLRRRHGDLALPIPVMIAVAVAVIAWTVLRNLP 122
                                    99999****************************99444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.029   1.3e+02      29      58 ..       7      36 ..       3      48 .. 0.65
   2 ?    7.6   0.9   0.00061       2.7       5      54 ..      74     120 ..      70     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.029
                        DUF4131 29 rrrvllllllllllallgfalrapqpnand 58
                                   +rr++++ +++ll+++lg+   ++ +n+n+
  gi|121637523|ref|YP_977746.1|  7 QRRYAAAGSVVLLAGALGYIGLVDPHNSNS 36
                                   556666666666666666666665555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00061
                        DUF4131   5 lalvllalllllllllllllrrrprrrvllllllllllallgfalrapqp 54 
                                     +++ll+ + +l+ + ll+   r++   +l + + +++a++++a++++++
  gi|121637523|ref|YP_977746.1|  74 DNVFLLVGVPVLASWVLLR---RRHGDLALPIPVMIAVAVAVIAWTVLRN 120
                                    5677888888888888887...99********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1020.40
//
Query:       gi|121637524|ref|YP_977747.1|  [L=472]
Description: pyruvate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   4.4e-118  394.1   2.5   5.8e-118  393.7   2.5    1.1  1  PK         Pyruvate kinase, barrel domain
    2.3e-23   82.7   0.0      1e-22   80.5   0.0    2.1  2  PK_C       Pyruvate kinase, alpha/beta domain
    2.5e-05   23.5   3.0    0.00047   19.4   1.7    2.9  3  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.7   2.5  9.7e-122  5.8e-118       2     340 ..       3     335 ..       2     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 393.7 bits;  conditional E-value: 9.7e-122
                                    --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCS CS
                             PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgk 81 
                                    rr kivctlGPa+++++ +++l+eaG++v+r+nfshG++++h+   e+vr a +++g+ v++l D++Gp+ir g ++ g+
  gi|121637524|ref|YP_977747.1|   3 RRGKIVCTLGPATQRDDLVRALVEAGMDVARMNFSHGDYDDHKVAYERVRVASDATGRAVGVLADLQGPKIRLGRFASGA 82 
                                    899***************************************************************************99 PP

                                    SSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-B CS
                             PK  82 kdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkg 161
                                       +  eg+++++++ +      +++ ++ +yk + +d  +G+++lvdDG+++l v +v+ +  ++++v  +g ++++kg
  gi|121637524|ref|YP_977747.1|  83 --THWAEGETVRITVGACEG---SHDRVSTTYKRLAQDAVAGDRVLVDDGKVALVVDAVEGDD-VVCTVVEGGPVSDNKG 156
                                    ..7789*******9987544...5799********************************9999.**************** PP

                                    EE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHHSS CS
                             PK 162 vnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeileasD 241
                                    + lpg +v +palsekD +dl f+++ gvd++a+sfvr+ +Dv+ v ev++  g+++ +iak+e+ e+++nl+ i+ a D
  gi|121637524|ref|YP_977747.1| 157 ISLPGMNVTAPALSEKDIEDLTFALNLGVDMVALSFVRSPADVELVHEVMDRIGRRVPVIAKLEKPEAIDNLEAIVLAFD 236
                                    ******************************************************************************** PP

                                    EEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTS CS
                             PK 242 gimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakG 321
                                    ++mvarGDlG+e+p e+v+lvqk+ i++++   kpvi+atqml+smi+n rptrae+sDvanavlDG+Da+mLsget+ G
  gi|121637524|ref|YP_977747.1| 237 AVMVARGDLGVELPLEEVPLVQKRAIQMARENAKPVIVATQMLDSMIENSRPTRAEASDVANAVLDGADALMLSGETSVG 316
                                    ******************************************************************************** PP

                                    S-HHHHHHHHHHHHHHHHH CS
                             PK 322 kyPveavkamaevaleaek 340
                                    kyP  av++m+++    e+
  gi|121637524|ref|YP_977747.1| 317 KYPLAAVRTMSRIICAVEE 335
                                    ***********99877665 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.74   4.4e+03       7      25 ..     261     278 ..     257     290 .. 0.72
   2 !   80.5   0.0   1.7e-26     1e-22       3     117 .]     354     465 ..     353     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.74
                                    HHHHHHHHT-SEEEEE-SS CS
                           PK_C   7 aveaaeelgakaIvvltes 25 
                                    a+++a+e +ak ++v+t+ 
  gi|121637524|ref|YP_977747.1| 261 AIQMARE-NAKPVIVATQM 278
                                    6677774.68888888875 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 1.7e-26
                                    HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHH CS
                           PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreav 82 
                                    i++aa+++ e l+aka v++t+sG+t+r+++++   +p++a+t  +++  qla+ +G  ++ v+k    +std ++r++ 
  gi|121637524|ref|YP_977747.1| 354 ISYAARDIGERLDAKALVAFTQSGDTVRRLARLHTPLPLLAFTAWPEVRSQLAMTWGTETFIVPK---MQSTDGMIRQVD 430
                                    789**********************************************************9997...788********* PP

                                    HHHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                           PK_C  83 kvakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                    k ++e    k+gd+vv++aG p g+ g+tN+++V+
  gi|121637524|ref|YP_977747.1| 431 KSLLELARYKRGDLVVIVAGAPPGTVGSTNLIHVH 465
                                    *****999************************997 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.7   7.8e-08   0.00047      73     185 ..     169     274 ..     162     304 .. 0.73
   2 ?    1.3   0.0     0.026   1.5e+02      13      33 ..     295     315 ..     289     338 .. 0.81
   3 ?    0.2   0.0     0.057   3.4e+02      80     111 ..     406     438 ..     397     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.8e-08
                                    HHHHHGG....HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEE CS
                      HpcH_HpaI  73 likqdle....vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgv 147
                                    l ++d+e    +l+lg++ v + +v ++++++ v +++ ++         +++++a +E  e+++n+e+I+ a    d+v
  gi|121637524|ref|YP_977747.1| 169 LSEKDIEdltfALNLGVDMVALSFVRSPADVELVHEVMDRIG-------RRVPVIAKLEKPEAIDNLEAIVlA---FDAV 238
                                    44444444449******************************9.......89*******************966...5777 PP

                                    EE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEE CS
                      HpcH_HpaI 148 flGaeDlsadlgtkrspegtevldareriltaaraagi 185
                                    +++  Dl ++l +++ p  ++   a+++ +  a++  +
  gi|121637524|ref|YP_977747.1| 239 MVARGDLGVELPLEEVPLVQK--RAIQMARENAKPVIV 274
                                    888889998888877554443..455555555555544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.026
                                    HHHHHCTC--SEEEEESSTSS CS
                      HpcH_HpaI  13 laekaaiagaDsvliDlEdav 33 
                                     + +a + gaD++++ +E +v
  gi|121637524|ref|YP_977747.1| 295 DVANAVLDGADALMLSGETSV 315
                                    56788899***********99 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.057
                                    HHHTTSSEEEESS--SHH.HHHHHHHHTSHTTT CS
                      HpcH_HpaI  80 vldlgaqvvlvPkvetae.ealevvsalrepek 111
                                    +++ g ++++vPk ++ + ++++v++ l e  +
  gi|121637524|ref|YP_977747.1| 406 AMTWGTETFIVPKMQSTDgMIRQVDKSLLELAR 438
                                    5677999*******9877356788887776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3190.48
//
Query:       gi|121637525|ref|YP_977748.1|  [L=300]
Description: acyl-CoA thioesterase II tesB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-61  204.1   0.1    2.3e-47  160.2   0.0    3.1  2  Acyl_CoA_thio  Acyl-CoA thioesterase
    2.7e-44  152.3   1.1    3.2e-44  152.0   1.1    1.1  1  4HBT_3         Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> Acyl_CoA_thio  Acyl-CoA thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   4.9e-13   4.4e-09       2     128 ..      23     111 ..      22     120 .. 0.90
   2 !  160.2   0.0   2.6e-51   2.3e-47       2     132 .]     154     285 ..     153     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.9e-13
                                    CCTCCEC-.SEEEECSSSSBTTCHHHHHEECCCCCCCCTS-TTHCCCCCHHHHHTTSSSGGGGGGGGTTTSTTEEEEEEE CS
                  Acyl_CoA_thio   2 akelfeleypvevrpkelkrefgGqvvaekqsllrakktvPddallhsvllaYlSDltllltalttHelledslqvsldH 81 
                                    a++lf++++p +++   l r+fgGq++a  qs++++++t+++++l++s++                              
  gi|121637525|ref|YP_977748.1|  23 ASDLFTGSHPSKNP---L-RTFGGQLMA--QSFVASSRTLTRHHLPPSAF------------------------------ 66 
                                    78899999994433...3.79*******..*******************5.............................. PP

                                    EEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEE......ECTTEEEEEEE CS
                  Acyl_CoA_thio  82 svyFlrpgdlnewilydvespsasggrgLrqGriFs......tqdgkliasvq 128
                                    sv+F+++gd++++i ++v +        Lr++r+F+      +qdg+l++s++
  gi|121637525|ref|YP_977748.1|  67 SVHFINGGDTAKDIEFQVIR--------LRDERRFAnrrvdaVQDGTLLSSAM 111
                                    ********************........9******9999999*******9965 PP

  == domain 2  score: 160.2 bits;  conditional E-value: 2.6e-51
                                    CCTCCEC-.SEEEECSSSSBTTCHHHHHEECCCCCCCCTS-TTHCCCCCHHHHHTTSSSGGGGGGGGT..TTSTTEEE.E CS
                  Acyl_CoA_thio   2 akelfeleypvevrpkelkrefgGqvvaekqsllrakktvPddallhsvllaYlSDltllltalttHe..lledslqv.s 78 
                                    +++l+ +e++++++p++++r+ +G+++a+++++++a++++Pdd++lh+++l+Y+SD+t+l++++ttH+  + +d++++ s
  gi|121637525|ref|YP_977748.1| 154 VNALQPIEWRYANDPAWIMRD-KGDRLAYNRVWVKALGEMPDDPVLHTATLLYSSDTTVLDSVITTHGlsWGFDRIFAaS 232
                                    68899****************.********************************************************** PP

                                    EEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEEEEEEEEEEE CS
                  Acyl_CoA_thio  79 ldHsvyFlrpgdlnewilydvespsasggrgLrqGriFstqdgkliasvqqeGl 132
                                    ++Hsv+F+r++++++w+ly+++sp+a+++rgL +G++F +++gklia+v+qeG+
  gi|121637525|ref|YP_977748.1| 233 ANHSVWFHRQVNFDDWVLYSTSSPVAADSRGLGSGHFF-DRSGKLIATVVQEGV 285
                                    **************************************.*************96 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   1.1   3.6e-48   3.2e-44       3     247 ..      32     285 ..      30     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 3.6e-48
                                    GGGECTTC.-HHHHHHHHHHHHHHT.-S.SS..EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETTEEEEEE CS
                         4HBT_3   3 ppwtpggagyGGyvlAlalraaqrtvpdprl..hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqggrpifta 79 
                                    p+ +p ++ +GG+++A+   a  rt+++ +l   +++v+F++ gd++  ++++v r+rd r+f+ r+v + q+g    +a
  gi|121637525|ref|YP_977748.1|  32 PSKNPLRT-FGGQLMAQSFVASSRTLTRHHLppSAFSVHFINGGDTAkDIEFQVIRLRDERRFANRRVDAVQDGTLLSSA 110
                                    55556666.****************954456889********************************************** PP

                                    EEEEE---T....---EE-------.GGGE---...--SSGGGSGG..TEEEE-HHT---S..........S-EEEEEEE CS
                         4HBT_3  80 tasfgraestgwelepaaapppvpppdeaalaad..eaplplfrrvpgflepfeprpaegg...kpdspagpkrvrqWvr 154
                                    ++s+++ +  g  le+a  pp+v +p + ++  +  +  ++ ++++ + l+p+e+r+a  +   ++d+++  +  r+Wv+
  gi|121637525|ref|YP_977748.1| 111 MVSYMAGGR-G--LEHALDPPQVAEPHTRPPIGEllRGYEETVPHFVNALQPIEWRYANDPawiMRDKGDRLAYNRVWVK 187
                                    *****9886.4..566666788888777766433433333334477899*********5444765566666778899*** PP

                                    ET...TTS-SSHHHHHHHHTT-....-GGGGTSS-......SB--EEEEEEEE-S--S-...EEEEEE-SEEETTEEEEE CS
                         4HBT_3 155 lr...eggepahlaaLaylsDs.f..pvprvhglrldaeasgwmpsldltiyfhrepaedeWllleaetpwagdgrglve 228
                                    +    ++++ +h a+L+y sD      v ++hgl++  ++  +++s +++++fhr+ + d+W+l+ +++p+a+d rgl +
  gi|121637525|ref|YP_977748.1| 188 ALgemPDDPVLHTATLLYSSDTtVldSVITTHGLSWGFDR-IFAASANHSVWFHRQVNFDDWVLYSTSSPVAADSRGLGS 266
                                    *887777799************769*999****9998777.8*************986589******************* PP

                                    EEEE-TTS-EEEEEEEEEE CS
                         4HBT_3 229 arlwdedGrlvAtstQegl 247
                                    ++++d++G+l+At++Qeg+
  gi|121637525|ref|YP_977748.1| 267 GHFFDRSGKLIATVVQEGV 285
                                    *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2200.99
//
Query:       gi|121637526|ref|YP_977749.1|  [L=484]
Description: hypothetical protein BCG_1657 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-66  225.0   0.0    1.2e-66  224.7   0.0    1.1  1  DUF2156   Uncharacterised conserved protein (DUF2156)


Domain annotation for each model (and alignments):
>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.7   0.0   6.8e-71   1.2e-66       3     297 ..     160     459 ..     158     460 .. 0.95

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 6.8e-71
                                    CCCTSSGGGGHHHHHHCCHCCEEEECCTTEEEEEEEECTCEEEECS-EE.CCGHHHHHHHHHHHHHHCTSEEEEEEE-HH CS
                        DUF2156   3 llersgsedslsnlalwrdksyyfspsgdalvayrvkggvalalgdPvGdpeawpeaieeflelaaehgwrpafygvsee 82 
                                    l++ +  +dsl+ +a++ +ks++fs +g+a++ayr++ g a+++gdP+Gd++++p+++++f ++++ hgwr++++g+se+
  gi|121637526|ref|YP_977749.1| 160 LINATR-ADSLAPFAMQAGKSHHFSAAGTAALAYRTRIGYAVVSGDPIGDEAQFPQLVADFAAMCHMHGWRIVVVGCSER 238
                                    556666.8****************88****************************************************** PP

                                    HHHHHHHCT.....EEEECCCEEEEEEHHHHHTTSGGGHHHHHHHHHHHHCTECEEEEEGGGH-HHHHHHHHHHHHHHHH CS
                        DUF2156  83 laellaelg.....lsalrlgeeavvdledftLsGkkfrnvRnainraeraGytveverisdlspellaelkeiseeWlk 157
                                     + l+ + +     l+++ +g ++v+d+++f+++G++frn+R+a++r ++ G+t+e++  ++l+++  ael+e+ ++  +
  gi|121637526|ref|YP_977749.1| 239 RLGLWSDPMvvgqsLRPIPIGRDVVIDVSNFEMTGRRFRNLRQAVKRTHNFGVTTEIVAEQQLDDQRQAELAEVLAASPS 318
                                    *******77899*******************************************************************9 PP

                                    H.TTCHHHHCCCHHHHCHHHH..TSEEEEEEE.TTEEEEEEEEEEECTTTEEEEEEEEE-TT.STTHHHHHHHHHHHHCH CS
                        DUF2156 158 q.keatEkgfslglfdelddl..dlrglvvrdeegrivAftsfeplngkdglsldlmRrdpdapnGlmefliaelaeelk 234
                                    + +  t++gf+++l   l+++  + +++++rd+ gr+++f  + + +g   +sld+ +r++ apnG+ e l a +++++k
  gi|121637526|ref|YP_977749.1| 319 GaR--TDRGFCMNLDGVLEGRypGIQLIIARDASGRVQGFHRYATAGGGSDMSLDVPWRRRGAPNGIDERLSADMIAAAK 396
                                    955..*******9877666654499**********************99******************************* PP

                                    HTT-SEEEEEEE...............HHHHHHHHHHHHHTTTCHHHHHHHCT--CEEEEEEE CS
                        DUF2156 235 eegveyvsLgfaplaglgeregagllerllrllleflerdygfegLrrfKlkyqPeweprYla 297
                                    + gv+++sL+fa++  l  +++ g l+r+ r l++ l +++ +e+L+r+ +k++   e+rY++
  gi|121637526|ref|YP_977749.1| 397 DAGVQRLSLAFAAFPDLFGANQLGRLQRVCRALIHILDPLIALESLYRYLRKFHALDERRYVL 459
                                    *****************7777789*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3713.65
//
Query:       gi|121637527|ref|YP_977750.1|  [L=576]
Description: cytochrome assembly ABC transporter ATP-binding protein CydC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-25   88.4   0.0    9.4e-25   87.7   0.0    1.3  1  ABC_tran      ABC transporter
    1.1e-06   28.7   0.1      0.017   14.9   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.8e-06   25.4   0.1    9.8e-06   25.4   0.1    1.8  2  ABC_membrane  ABC transporter transmembrane region
      6e-05   23.5   0.3      6e-05   23.5   0.3    2.3  2  AAA_16        AAA ATPase domain
     0.0086   15.8   0.1      0.026   14.3   0.1    1.8  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.028   13.8   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.021   15.1   0.2      0.084   13.1   0.0    2.1  2  AAA_28        AAA domain
      0.027   13.9   0.0      0.067   12.6   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.03   14.6   0.8       0.22   11.8   0.8    2.2  1  AAA_22        AAA domain
       0.12   12.3   0.4       0.31   11.0   0.2    1.8  2  NACHT         NACHT domain
       0.13   12.9   0.0       0.27   11.8   0.0    1.6  1  AAA_18        AAA domain
       0.13   12.4   0.0       0.38   10.8   0.0    1.8  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
       0.23   11.1   0.0       0.39   10.4   0.0    1.3  1  AAA_24        AAA domain
        4.5    7.4  13.7      0.049   13.7   5.4    2.1  1  DUF3742       Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   7.3e-28   9.4e-25       4     136 ..     361     506 ..     359     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 7.3e-28
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.... 79 
                                    v+++l +g ++a++G +GaGK+tLl++lagll p  G++lldg++l++ ++ +lr+ ++++ +++++f ++ vr+n    
  gi|121637527|ref|YP_977750.1| 361 VTIDLPPGARLAVTGASGAGKTTLLMTLAGLLPPVHGRVLLDGTNLSDFDEDELRSAVSFFAEDAHIFATT-VRDNllta 439
                                    7899****************************************************************999.****9999 PP

                                    ...HHHTCHHHHHHHSTTGG.......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...esdeeiekalsklglke.......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         d+e+ +al+++gl +          tv+  +++ +S Gq++r+ lara+l+ ++++llDEp 
  gi|121637527|ref|YP_977750.1| 440 rgdCPDDELIEALDRVGLCGwlaglpeGLSTVLIGGAQAVSAGQRRRLLLARAVLSPARIVLLDEPV 506
                                    9988888899999999999977777765555555666*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00013      0.17       3      26 ..     372     398 ..     371     436 .. 0.69
   2 !   14.9   0.0   1.3e-05     0.017     237     298 ..     479     540 ..     476     545 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         AAA_21   3 vliGpNgsGKSnLLdaldllarl...d 26 
                                    +++G+ g+GK++LL +l +l      +
  gi|121637527|ref|YP_977750.1| 372 AVTGASGAGKTTLLMTLAGLLPPvhgR 398
                                    689**************9995434442 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.3e-05
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr...ngaQviltTHS 298
                                    +S G++r l l+ a+l+ +   +++l+DEp  +L+ +    l +ll  +s        v+++TH 
  gi|121637527|ref|YP_977750.1| 479 VSAGQRRRLLLARAVLSPA---RIVLLDEPVEHLDAANADLLRDLLAPNSGimsAMRTVVVATHH 540
                                    7999999999999999888...************************7777777667899****96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   7.7e-09   9.8e-06       5     162 ..      28     187 ..      27     203 .. 0.83
   2 ?   -2.3   1.0       2.1   2.7e+03     126     155 ..     266     294 ..     257     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.7e-09
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHSS..TCCHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   5 illailagvlsplfplvlgrildtlldk..gdpet...ealnvysllllllglaqfilallqsyllnvtgerlskrlrrk 79 
                                    il+a++ gvls+  +l l+ +  +l++   +        +l+v  +++ ++++ +++l +      + t+ r+  r r+ 
  gi|121637527|ref|YP_977750.1|  28 ILAAVALGVLSLGSALALAGVSAWLITRawQ---MppvLDLSVAVVAVRAFAISRGVLHYCERLATHDTALRAAGRARTL 104
                                    6788899999999999999999999985432...3346889999999999999999999999999888************ PP

                                    HHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  80 lfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsa 159
                                    +++++ + p +     ++G+l +r+  dv+ l ++l + l+ +  + ++ v++ +v+  +++  ++vl ++l++  +v+ 
  gi|121637527|ref|YP_977750.1| 105 IYHRLAHGPAAAAVGLHSGDLAARVGADVDELANMLVRALVPIAVAAVLAVAATAVVAAVSVPAAVVLAVCLLVAGVVAP 184
                                    **********************************************************9999865555555544444444 PP

                                    HHH CS
                   ABC_membrane 160 via 162
                                    ++a
  gi|121637527|ref|YP_977750.1| 185 WLA 187
                                    444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                   ABC_membrane 126 lltfvgglivmfylgwkltlvllailplii 155
                                    l  +v+g++++ ++ +  tl++l +lpl +
  gi|121637527|ref|YP_977750.1| 266 LGAVVAGIGMAPTVAPT-TLAILMLLPLSA 294
                                    55689999999999996.999999999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.0       1.3   1.6e+03     106     137 ..     202     239 ..     133     255 .. 0.60
   2 !   23.5   0.3   4.7e-08     6e-05      27     160 ..     371     522 ..     360     536 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                         AAA_16 106 a....avpelagaea......srllellkrllallsrderpl 137
                                    +     ++ +    a       r++ +l++ +a ++r+++ +
  gi|121637527|ref|YP_977750.1| 202 RgmrdTSAMI----AlehapeLRVAGALRNVIADSQRRQHAW 239
                                    1222222222....1333466888889999998888888854 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 4.7e-08
                         AAA_16  27 vllsGesGvGKsslvrellralekdggif.lrgkcdql......esaipy....sa.laqalareellrqllde.aesae 93 
                                    + ++G+sG GK++l+ +l+  l   +g + l g++ +       +sa+++    ++ +a++  r+ ll++ +d  +++  
  gi|121637527|ref|YP_977750.1| 371 LAVTGASGAGKTTLLMTLAGLLPPVHGRVlLDGTNLSDfdedelRSAVSFfaedAHiFATTV-RDNLLTARGDCpDDELI 449
                                    679****************7777666666433333333432244666777555422244444.54555555544322223 PP

                         AAA_16  94 leawrekleeala..........avpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlr 160
                                     + +r  l+++la          ++++ a ++ +r + ll+r++  ls+ +r +vl+ + ++ +d+a ++ll+ Ll+
  gi|121637527|ref|YP_977750.1| 450 EALDRVGLCGWLAglpeglstvlIGGAQAVSAGQRRRLLLARAV--LSP-AR-IVLLDEPVEHLDAANADLLRDLLA 522
                                    33344444444449999996666444444444489999999999..676.77.8888889*************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     2e-05     0.026      17      48 ..     363     394 ..     357     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                         AAA_29  17 ieidlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                    i++ +     +tG+sG+GK+Tll  ++ lL p
  gi|121637527|ref|YP_977750.1| 363 IDLPPGARLAVTGASGAGKTTLLMTLAGLLPP 394
                                    5555444789************9777777765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05     0.028      29      59 ..     359     388 ..     347     392 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                                    -EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  29 nplvldlkkmashllvaGatgsGKStalntL 59 
                                    + +++dl++ a  l v Ga+g GK+t l+tL
  gi|121637527|ref|YP_977750.1| 359 IRVTIDLPPGA-RLAVTGASGAGKTTLLMTL 388
                                    5689999***9.******************8 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.1   2.7e+03     109     146 ..     207     244 ..     176     255 .. 0.54
   2 ?   13.1   0.0   6.5e-05     0.084       2      22 ..     371     391 ..     370     434 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                         AAA_28 109 ydlvfllppapei.dddgeRredleereaiderlrealr 146
                                      +++ l++ape+ +  + R    ++ ++ +++  +al+
  gi|121637527|ref|YP_977750.1| 207 TSAMIALEHAPELrVAGALRNV-IADSQRRQHAWADALD 244
                                    4557777777777445555543.4444555555555444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.5e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                     ++tG++++GKTtll  La  
  gi|121637527|ref|YP_977750.1| 371 LAVTGASGAGKTTLLMTLAGL 391
                                    689*************99965 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-05     0.067      16      59 ..     362     405 ..     347     423 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                   Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevak 59 
                                    +i    g  l ++G++G+GKt l   l++llpp++ +  l+ ++
  gi|121637527|ref|YP_977750.1| 362 TIDLPPGARLAVTGASGAGKTTLLMTLAGLLPPVHGRVLLDGTN 405
                                    455556678999*********************99887777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   0.00018      0.22       8      31 ..     371     394 ..     368     543 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                         AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                    l+vtG sG+GKTtll +l+  l+ 
  gi|121637527|ref|YP_977750.1| 371 LAVTGASGAGKTTLLMTLAGLLPP 394
                                    68*************999988864 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00024      0.31       3      22 ..     371     390 ..     369     394 .. 0.88
   2 ?   -2.8   0.0       4.2   5.4e+03      90     116 ..     502     524 ..     472     542 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    ++++G++G GKTtLl  la 
  gi|121637527|ref|YP_977750.1| 371 LAVTGASGAGKTTLLMTLAG 390
                                    789*************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.2
                                    STT-SS-TCH.........HHHHHCTT CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkk 116
                                    lDe v++l++    +  +lL++l+  +
  gi|121637527|ref|YP_977750.1| 502 LDEPVEHLDA----ANADLLRDLLAPN 524
                                    5666666666....5566777777654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.27       2      35 ..     372     413 ..     371     455 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                         AAA_18   2 lltGtpGvGKttlakeLskrl.gf.......gvnlrdvaken 35 
                                    ++tG++G+GKttl   L+ +l  +       g+nl+d   ++
  gi|121637527|ref|YP_977750.1| 372 AVTGASGAGKTTLLMTLAGLLpPVhgrvlldGTNLSDFDEDE 413
                                    59***************9998666877888888887766543 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.38       4      24 ..     373     393 ..     371     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                    EESSTTSSHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   4 astkGGvGKTtlaanLarala 24 
                                    + + +G+GKTtl+ +La +l 
  gi|121637527|ref|YP_977750.1| 373 VTGASGAGKTTLLMTLAGLLP 393
                                    6799*************9985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.39       3      23 ..     369     392 ..     368     443 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                         AAA_24   3 lkiliyGpsgiGKTtlakel...g 23 
                                    ++++++G sg+GKTtl+ +l    
  gi|121637527|ref|YP_977750.1| 369 ARLAVTGASGAGKTTLLMTLaglL 392
                                    6899*************9985551 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.4   3.8e-05     0.049      25     102 ..     131     208 ..     108     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                        DUF3742  25 lrlerraaswlvakGvpaavatavlwvvklavlGvllyvafWlal.llvvvvlvawaarsvdtsdeeksgdeeelrnge 102
                                    + ++ ++a++lv++ vp ava ++ +++ ++v  v + +a  la+ llv+ v++ w+a+++ + +e    ++  +r++ 
  gi|121637527|ref|YP_977750.1| 131 ADVD-ELANMLVRALVPIAVAAVLAVAATAVVAAVSVPAAVVLAVcLLVAGVVAPWLAGRTAAAQEAIARQHRGMRDTS 208
                                    4443.57899***********************************8889999999*****9998888776677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3775.59
//
Query:       gi|121637528|ref|YP_977751.1|  [L=527]
Description: cytochrome assembly ABC transporter ATP-binding protein CydD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-27   94.3   0.0    1.4e-26   93.6   0.0    1.3  1  ABC_tran      ABC transporter
    1.1e-13   51.5   0.2    1.7e-13   50.9   0.2    1.2  1  ABC_membrane  ABC transporter transmembrane region
    3.6e-09   36.9   0.5    9.1e-05   22.4   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      7e-08   32.2   0.0     0.0013   18.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    1.9e-05   24.3   0.1    5.1e-05   22.9   0.1    1.7  1  AAA_29        P-loop containing region of AAA domain
    0.00028   21.5   0.1    0.00041   20.9   0.1    1.1  1  AAA_23        AAA domain
     0.0069   16.1   0.0       0.01   15.5   0.0    1.2  1  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.2  12.3      0.019   14.7   7.1    3.0  2  AAA_30        AAA domain
      0.025   14.2   0.0      0.049   13.2   0.0    1.4  1  AAA_27        AAA domain
      0.032   14.1   0.1      0.084   12.8   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
      0.053   13.3   0.2      0.053   13.3   0.2    1.6  2  MukB          MukB N-terminal
       0.11   12.8   0.1       0.32   11.3   0.0    1.8  2  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.0   9.4e-30   1.4e-26       4     137 .]     334     477 ..     332     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 9.4e-30
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.... 79 
                                    ++ ++++g++++++G+nGaGKSt l+++agl+ p +G+i++ g d+++     + +++++lpq p l p++ vr n    
  gi|121637528|ref|YP_977751.1| 334 LTADIEPGRVTVLTGRNGAGKSTTLQAIAGLTAPSSGRITVAGVDVTNLAPAAWWRQLSWLPQRPVLVPGT-VRHNlvll 412
                                    7889********************************************999999999**************.******** PP

                                    .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              + + ++++l++l      dtv+++++  LS Gq+qr+ laral + + +lllDEpta
  gi|121637528|ref|YP_977751.1| 413 gpvddleraCAAAGFDAVLDELPRGL--DTVLGRGGVGLSLGQRQRLGLARALGSPAAVLLLDEPTA 477
                                    99876654333344999999998766..*************************************97 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.2   1.1e-16   1.7e-13      16     258 ..      12     256 ..       2     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.1e-16
                                    HHHHHHHHHHHHHHHSSTCCHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHH CS
                   ABC_membrane  16 plfplvlgrildtlldkgdpet...ealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsff 92 
                                    +  ++vl++i+  ++d ++p      +    + +ll+l  +++ + +lq +l    ++ ++ +l  +++ ++     s  
  gi|121637528|ref|YP_977751.1|  12 IGSAIVLASIVAGVIDPANPGMaglRRWLGPLSILLVLWGLRASIQWLQARLAQRGASAVIADLSGQVLTAVTARRPSQL 91 
                                    55667777777777776666665555555556677778888899999************************998866666 PP

                                    HH.SCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  93 dt.nsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkk 171
                                       +++  +  ++t+ ++ lr  ++  l +++ + ++  ++++v+ ++  k + +++++lpli +++++i+  +++ +  
  gi|121637528|ref|YP_977751.1|  92 AAqRDAAAV--LITRGLDGLRPYFTGYLPTLLLAAILTPATVAVIGLYDLKSMAIVVITLPLIPIFMVLIGLATTNPSAA 169
                                    663777666..8******************************************************************** PP

                                    HHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHH CS
                   ABC_membrane 172 eqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalal.wfGttlv 250
                                       a+  + + + + + gi t++a+gr +  ++++ + + +++++++  ++++ l+  +++ll++l +al++  +G  lv
  gi|121637528|ref|YP_977751.1| 170 ALAAMTAVQARLLDLIAGIPTLRALGRASGPEQRIAELSADHRRSAMATLRIAFLSALVLELLATLGVALVAvGIGLRLV 249
                                    ***********************************************************************633444444 PP

                                    HTTSSTHH CS
                   ABC_membrane 251 isgelsvg 258
                                      ge+s+ 
  gi|121637528|ref|YP_977751.1| 250 -FGEMSLT 256
                                    .3666554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   6.1e-08   9.1e-05       1      23 [.     343     365 ..     343     387 .. 0.87
   2 !   12.6   0.0     6e-05      0.09     237     296 ..     449     505 ..     447     509 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.1e-08
                         AAA_21   1 lnvliGpNgsGKSnLLdaldlla 23 
                                    ++vl+G+Ng+GKS+ L+a+ +l 
  gi|121637528|ref|YP_977751.1| 343 VTVLTGRNGAGKSTTLQAIAGLT 365
                                    79*****************9995 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6e-05
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltT 296
                                    lS G+++ l+l+ al + +   ++ll+DEp ++L+ +   ++l+ + +++++ ga v+++ 
  gi|121637528|ref|YP_977751.1| 449 LSLGQRQRLGLARALGSPA---AVLLLDEPTAHLDARTEQHVLGAIvERARA-GATVLVVA 505
                                    6777777777777777777...**************9988888888455555.88888765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   9.6e-05      0.14      25      44 ..     342     361 ..     331     370 .. 0.87
   2 !   18.2   0.0   8.6e-07    0.0013     152     213 ..     460     522 ..     449     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                                    SEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                    ++t+++G+NG+GKs  l+Ai
  gi|121637528|ref|YP_977751.1| 342 RVTVLTGRNGAGKSTTLQAI 361
                                    589****************9 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 8.6e-07
                                    HHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH.HHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 152 AiqkvkpaplyllDeidaaLDeknvkkvaellk.eksknaQfivislreemlekadklvgvtk 213
                                    A    +pa++ llDe  a+LD++  + v   +  +++  a ++v+++r+++ +  d++v v +
  gi|121637528|ref|YP_977751.1| 460 ARALGSPAAVLLLDEPTAHLDARTEQHVLGAIVeRARAGATVLVVAHRQQVAAAGDRVVEVNS 522
                                    555568999*************99998876665155666*******************99975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.4e-08   5.1e-05      16      50 ..     335     369 ..     332     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.4e-08
                         AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                    t++i++  +t+ltG++G+GKST l Ai+ l  p++
  gi|121637528|ref|YP_977751.1| 335 TADIEPGRVTVLTGRNGAGKSTTLQAIAGLTAPSS 369
                                    56788777*******************99988876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.8e-07   0.00041      20      40 ..     342     362 ..     331     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-07
                         AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                     +t++tG NGaGK+T l+Ai 
  gi|121637528|ref|YP_977751.1| 342 RVTVLTGRNGAGKSTTLQAIA 362
                                    59******************7 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     7e-06      0.01      18      44 ..     335     362 ..     329     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7e-06
                         AAA_15  18 eidlsee.ltvliGkNnsGKSsileald 44 
                                    + d+++  +tvl G+N++GKS+ l+a+ 
  gi|121637528|ref|YP_977751.1| 335 TADIEPGrVTVLTGRNGAGKSTTLQAIA 362
                                    55666667******************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.73   1.1e+03      49      72 ..     158     181 ..     154     197 .. 0.87
   2 ?   14.7   7.1   1.3e-05     0.019      17     130 ..     340     512 ..     335     516 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.73
                         AAA_30  49 viglAptgkaAkvLaeelgieast 72 
                                    +iglA t+  A++La+ + ++a+ 
  gi|121637528|ref|YP_977751.1| 158 LIGLATTNPSAAALAAMTAVQARL 181
                                    589999999999999999998875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.3e-05
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLa.........................e 64 
                                    + rv+vltG+ G+GK+t+l+a++ + + + g       +v  lAp +   ++L+                          
  gi|121637528|ref|YP_977751.1| 340 PGRVTVLTGRNGAGKSTTLQAIAGLTAPSsGritvagVDVTNLAPAAWW-RQLSwlpqrpvlvpgtvrhnlvllgpvddL 418
                                    4579*******************99999866766666666666665443.445455555555555554444444444221 PP

                         AAA_30  65 elgieastiakllkrlk........................grarlepgtllivDEagmv.....dtkqlaallkaaeka 115
                                    e   +a+  + +l++l                         +ra  +p+ +l+ DE          ++ l a++++a++ 
  gi|121637528|ref|YP_977751.1| 419 ERACAAAGFDAVLDELPrgldtvlgrggvglslgqrqrlglARALGSPAAVLLLDEPTAHldartEQHVLGAIVERARA- 497
                                    3334555555555555589999999999999999999999855555677999999976555555466677778888877. PP

                         AAA_30 116 gakvilvGDerQlas 130
                                    ga+v++v  ++Q a+
  gi|121637528|ref|YP_977751.1| 498 GATVLVVAHRQQVAA 512
                                    999999999999987 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.3e-05     0.049      25      49 ..     340     364 ..     330     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                         AAA_27  25 eadlhliyGpNEAGKstalrAisdl 49 
                                      +++++ G N AGKst+l+Ai  l
  gi|121637528|ref|YP_977751.1| 340 PGRVTVLTGRNGAGKSTTLQAIAGL 364
                                    567899***************9866 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05     0.084      86     122 ..     327     364 ..     308     375 .. 0.79
   2 ?   -3.0   0.0         4   5.9e+03      88     112 ..     425     449 ..     421     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                    THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    ++++  +l++ ++  +++vl G  G+GKSt + a+++ 
  gi|121637528|ref|YP_977751.1| 327 DGRAPYDLTADIEPgRVTVLTGRNGAGKSTTLQAIAGL 364
                                    555566788888877*****************999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                    TTHHHHHHHCTTSEEEEECSTTSSH CS
                    RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGK 112
                                    +g++++ ++l   + +++G  GvG 
  gi|121637528|ref|YP_977751.1| 425 AGFDAVLDELPRGLDTVLGRGGVGL 449
                                    57788888999999999******96 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.6e-05     0.053      27      52 ..     342     367 ..     332     380 .. 0.83
   2 ?   -3.0   0.1       3.4   5.1e+03      96     117 ..     498     520 ..     486     522 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                                    HHHHHHS--SHHHHHHHHHHHHHHS- CS
                           MukB  27 lvttlsGgnGaGksttmaafvtaliP 52 
                                     vt l G nGaGkstt+ a+     P
  gi|121637528|ref|YP_977751.1| 342 RVTVLTGRNGAGKSTTLQAIAGLTAP 367
                                    69***************998765555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                                    S-EEEEEEEEEE-SS.TTT-EEE CS
                           MukB  96 eqrllvgvrleqvag.rdkkvdi 117
                                    +  +lv  + +qva+  d+ v++
  gi|121637528|ref|YP_977751.1| 498 GATVLVVAHRQQVAAaGDRVVEV 520
                                    34566666777876515777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.32       5      27 ..     341     363 ..     337     391 .. 0.81
   2 ?   -3.1   0.0       5.8   8.7e+03      70      91 ..     478     500 ..     455     504 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         AAA_22   5 agilvvtGesGtGKTtllrrlle 27 
                                     +++v+tG  G+GK+t+l+ ++ 
  gi|121637528|ref|YP_977751.1| 341 GRVTVLTGRNGAGKSTTLQAIAG 363
                                    6799**************98875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                         AAA_22  70 a.erlsseellealeqalrarav 91 
                                    +    +++++l a+ + +ra a+
  gi|121637528|ref|YP_977751.1| 478 HlDARTEQHVLGAIVERARAGAT 500
                                    13334555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3383.97
//
Query:       gi|121637529|ref|YP_977752.1|  [L=346]
Description: integral membrane cytochrome D ubiquinol oxidase (subunit II) cydB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-100  335.9  37.9   2.6e-100  335.7  37.9    1.0  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.7  37.9  1.5e-104  2.6e-100       1     303 []       3     326 ..       3     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 1.5e-104
                Cyt_bd_oxida_II   1 lqliwflligvllagYvvldGfDlGvGillpll.....akkdeerrlllnsigpvWdgnevWLvtaggalfaaFPlayat 75 
                                    lq++wf +i+ l++g+++l+GfD+GvG+l+  +     +  +++rr++ln+igpvWdgnevWL+tag+a+faaFP +yat
  gi|121637529|ref|YP_977752.1|   3 LQELWFGVIAALFLGFFILEGFDFGVGMLMAPFahvgmGDPETHRRTALNTIGPVWDGNEVWLITAGAAIFAAFPGWYAT 82 
                                    799**************************98886775445677************************************* PP

                Cyt_bd_oxida_II  76 lfsglylpllliLlglilRgvafefrskaeskrwrklwdlaffigSllaalllGvalgnllqGvpfdad.eyg.flsdll 153
                                    +fs+lylpll+iL+g+ilR+va+e+r+k+++++wr+  d+ +++gS+l+all+Gva++ l++G+p+da+ +++  + d+l
  gi|121637529|ref|YP_977752.1|  83 VFSALYLPLLAILFGMILRAVAIEWRGKIDDPKWRTGADFGIAAGSWLPALLWGVAFAILVRGLPVDANgHVAlSIPDVL 162
                                    ******************************************************************988655468889** PP

                Cyt_bd_oxida_II 154 npfallvglllvalflllGalylalktegelqerarrlalvlalvllvllvvvllwtll........lvllllavlalll 225
                                    n ++ll+gl++  lf l Ga+++alkt+g+++++a r+a +l+l+++ l++ ++lwt l        lvl++++ + +++
  gi|121637529|ref|YP_977752.1| 163 NAYTLLGGLATAGLFSLYGAVFIALKTSGPIRDDAYRFAVWLSLPVAGLVAGFGLWTQLaygkdwtwLVLAVAGCAQAAA 242
                                    *********************************************************99*****8855676677777777 PP

                Cyt_bd_oxida_II 226 avlllrkkreglaflasaltvllvvlllavslfPyllpss......ltianaasseytlkvmlivalillplvlaytawl 299
                                    +vl++r+ ++g+af++++++v++vv+ll+++l+P+l+ps+      lti+na+s++ytlk+m++v++++ pl +ay++w+
  gi|121637529|ref|YP_977752.1| 243 TVLVWRRVSDGWAFMCTLIVVAAVVVLLFGALYPNLVPSTlnpqwsLTIHNASSTPYTLKIMTWVTAFFAPLTVAYQTWT 322
                                    778888899*********************************************************************** PP

                Cyt_bd_oxida_II 300 yrvf 303
                                    y+vf
  gi|121637529|ref|YP_977752.1| 323 YWVF 326
                                    ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2409.59
//
Query:       gi|121637530|ref|YP_977753.1|  [L=485]
Description: integral membrane cytochrome D ubiquinol oxidase (subunit I) cydA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.2e-162  540.5  26.9   2.5e-162  540.3  26.9    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.3  26.9  1.4e-166  2.5e-162       1     418 []       6     460 ..       6     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: 540.3 bits;  conditional E-value: 1.4e-166
                 Cyt_bd_oxida_I   1 laRlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysr 80 
                                    ++R+qf++t+v+Hf+fvplt+Gla l+a+++tl+++t+++++++l+kf+gklf+inFa+Gv+tGiv+efqfg+nWseysr
  gi|121637530|ref|YP_977753.1|   6 ISRWQFGITTVYHFIFVPLTIGLAPLIAVMQTLWVVTDNPAWYRLTKFFGKLFLINFAIGVATGIVQEFQFGMNWSEYSR 85 
                                    69****************************************************************************** PP

                 Cyt_bd_oxida_I  81 fvGdifgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvGaelnpdtgra 160
                                    fvGd+fgapLa+Egl AFf+Estf+gl++fgw+r+++ +hl+++w+vai+ ++Sa++I+aans+mq+PvGa++np+tgra
  gi|121637530|ref|YP_977753.1|  86 FVGDVFGAPLAMEGLAAFFFESTFIGLWIFGWNRLPRLVHLACIWIVAIAVNVSAFFIIAANSFMQHPVGAHYNPTTGRA 165
                                    ******************************************************************************** PP

                 Cyt_bd_oxida_I 161 eltdflavlfnpsalakflHtvlaalltaaffvagvsawyllr........rekefarkslkialvvalvaallqallGd 232
                                    el++++ +l+n++a+a+f+Htv++allta++fva+vsaw+l+r        ++++++r +  ++++val+a++  +++Gd
  gi|121637530|ref|YP_977753.1| 166 ELSSIVVLLTNNTAQAAFTHTVSGALLTAGTFVAAVSAWWLVRsstthadsDTQAMYRPATILGCWVALAATAGLLFTGD 245
                                    ********************************************99876644444************************* PP

                 Cyt_bd_oxida_I 233 lsgkevaetqpaKlAAmeglwetee.aplslfgipdeeeeknefa.ieiPgllsllatgsldge.vkGlndlpk...... 303
                                    ++gk ++++qp+K+A++e l++t++  ++s++++ ++++ ++  + ie+P++l +la+g+++g  ++G+ dl++      
  gi|121637530|ref|YP_977753.1| 246 HQGKLMFQQQPMKMASAESLCDTQTdPNFSVLTVGRQNNCDSLTRvIEVPYVLPFLAEGRISGVtLQGIRDLQQeyqqrf 325
                                    ************************999*******999655444447***************986599*****98****** PP

                 Cyt_bd_oxida_I 304 ...eevPpvalvfwsfrimvglgvlllllallalll.........rwllrllllaiplpfiaveaGWivtevGRqPWivy 371
                                       +++P++++++wsfr+m+gl+ + +l+al+al+l         rw+ +l+ll++p+pf+a++aGW++te+GRqPW+v 
  gi|121637530|ref|YP_977753.1| 326 gpnDYRPNLFVTYWSFRMMIGLMAIPVLFALIALWLtrggqipnqRWFSWLALLTMPAPFLANSAGWVFTEMGRQPWVVV 405
                                    *********************************************9*********************************9 PP

                 Cyt_bd_oxida_I 372 ....g....llrtadavspvsagevllslilflllylvLlvvevylllklikkgp 418
                                        g     l+++++vs++sa+ v++sl++f+l+y+vL+v++++ll ++i +gp
  gi|121637530|ref|YP_977753.1| 406 pnptGdqlvRLTVKAGVSDHSATVVATSLLMFTLVYAVLAVIWCWLLKRYIVEGP 460
                                    66661555599****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.22s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3512.20
//
Query:       gi|121637531|ref|YP_977754.1|  [L=195]
Description: hypothetical protein BCG_1662c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-23   80.4  60.1    2.4e-11   43.8  20.7    3.0  3  DUF308    Short repeat of unknown function (DUF308)
  ------ inclusion threshold ------
        4.4    6.9  16.3        4.1    7.0   3.5    2.9  3  TMEM100   Transmembrane protein 100
        6.6    7.0  22.8       0.86    9.9   0.6    3.0  3  DUF2189   Predicted integral membrane protein (DUF2189)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  20.7     4e-15   2.4e-11       2      72 ..      30      99 ..      29     100 .. 0.93
   2 !   28.4  15.3   2.6e-10   1.5e-06       1      72 [.      86     155 ..      86     156 .. 0.90
   3 !   33.7   8.1   5.8e-12   3.5e-08       2      50 ..     143     191 ..     142     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4e-15
                         DUF308  2 lGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                   +Gil+++lG+l+l++P++++l+ ++ fG++ll+ G++q++ af+ +  + ggr+l +++G+ +li+++l++
  gi|121637531|ref|YP_977754.1| 30 SGILSLILGVLVLAWPGISILVAAMAFGVYLLITGVAQVAFAFSLHV-SAGGRILLFISGAASLILAVLAF 99
                                   8******************************************8887.555699**************987 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.6e-10
                         DUF308   1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72 
                                    ++G  +++l++la+ + + a+l l++++Gi +++ G++  ++a++     +  r +++++G+++liaG++++
  gi|121637531|ref|YP_977754.1|  86 ISGAASLILAVLAFRHFGDAVLLLAIWIGIGFIFRGVATTVSAISDPMLPG--RGWSIFVGVISLIAGIVVM 155
                                    6899****************************************5555444..448*************986 PP

  == domain 3  score: 33.7 bits;  conditional E-value: 5.8e-12
                         DUF308   2 lGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkkn 50 
                                    +G++++++Gi++++ P+ ++ +l+l++Gi+l+v G+ +i+++fa rk +
  gi|121637531|ref|YP_977754.1| 143 VGVISLIAGIVVMASPFESIWILALVVGIWLVVIGACEIASSFAIRKAS 191
                                    8******************************************988754 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.18   1.1e+03      56      71 ..      26      41 ..      23      44 .. 0.77
   2 ?    7.0   3.5   0.00069       4.1      57     105 ..      53      97 ..      46     102 .. 0.66
   3 ?    6.2   2.8    0.0012       7.2      60     103 ..     143     184 ..     139     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                        TMEM100 56 CviPfgvvvLvaGvvv 71
                                    ++  g+++L+ Gv v
  gi|121637531|ref|YP_977754.1| 26 STLASGILSLILGVLV 41
                                   5677899999999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00069
                        TMEM100  57 viPfgvvvLvaGvvvtavaytfnshgsvisvlglvLLsaGlvllassav 105
                                     + fgv  L+ Gv+   va++f  h s      ++L+ +G   l+ +++
  gi|121637531|ref|YP_977754.1|  53 AMAFGVYLLITGVAQ--VAFAFSLHVSA--GGRILLFISGAASLILAVL 97 
                                    678*********975..77777777666..2334455556555555555 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0012
                        TMEM100  60 fgvvvLvaGvvvtavaytfnshgsvisvlglvLLsaGlvllass 103
                                     gv++L+aG+vv a    f s   +  v+g+ L+  G   +ass
  gi|121637531|ref|YP_977754.1| 143 VGVISLIAGIVVMAS--PFESIWILALVVGIWLVVIGACEIASS 184
                                    69*********9765..566666666677777777776666655 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   9.1    0.0021        13      42     114 ..      24      99 ..      15     102 .. 0.75
   2 ?    9.9   0.6   0.00014      0.86      96     124 ..     106     134 ..     101     135 .. 0.92
   3 ?   -0.2   0.5      0.19   1.1e+03      40      59 ..     154     173 ..     141     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0021
                        DUF2189  42 ranassllllglllallfllWvraaallfallfgtapl.eslsa..fledvlltpeglaflivgllvGavlAalvF 114
                                    ++   + ++l+l+l +l+l+W  ++ l+ a+ fg   l + +++  f+  +  ++ g  +l++  ++ ++lA+l+F
  gi|121637531|ref|YP_977754.1|  24 WKSTLASGILSLILGVLVLAWPGISILVAAMAFGVYLLiTGVAQvaFAFSLHVSAGGRILLFISGAASLILAVLAF 99 
                                    4555578899***********************9444444444310344466677788889999999999999999 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                        DUF2189  96 laflivgllvGavlAalvFaisvvslPll 124
                                    + +l++++ +G+++  ++ ++s++s P+l
  gi|121637531|ref|YP_977754.1| 106 VLLLAIWIGIGFIFRGVATTVSAISDPML 134
                                    6799************************8 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.19
                        DUF2189  40 alranassllllglllallf 59 
                                    ++ ++ +s+++l+l++ + +
  gi|121637531|ref|YP_977754.1| 154 VMASPFESIWILALVVGIWL 173
                                    45555555665555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1363.43
//
Query:       gi|121637532|ref|YP_977755.1|  [L=418]
Description: membrane-anchored adenylyl cyclase cya [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-58  197.7   0.0      2e-58  197.0   0.0    1.3  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
      0.024   14.1   0.1      0.036   13.5   0.1    1.2  1  HNOBA          Heme NO binding associated
       0.11   12.3   0.3       0.28   11.0   0.0    1.8  2  RVT_3          Reverse transcriptase-like


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.0   3.4e-62     2e-58       3     182 ..     219     397 ..     217     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 3.4e-62
                  Guanylate_cyc   3 aesydevtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaela 82 
                                    a +yde ++lFadIvgft+ +s + p ++v++L  ly+ fdel+d+++++k+k+ Gd+ymvvsg+p+++++h++ la++a
  gi|121637532|ref|YP_977755.1| 219 ADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFA 298
                                    5789**************************************************************************** PP

                  Guanylate_cyc  83 LdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellkeeqfel 162
                                    Ldm++ + + +  + + + +rvG+ tGpvvagv+G +++ ydvwG++vn+Asrmest   g+iqv +e+ye lk ++f l
  gi|121637532|ref|YP_977755.1| 299 LDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLK-DDFVL 377
                                    **************************************************************************.***** PP

                  Guanylate_cyc 163 tergevevkGkgkletyfle 182
                                    +erg+++vkGkg + t++l 
  gi|121637532|ref|YP_977755.1| 378 RERGHINVKGKGVMRTWYLI 397
                                    *****************986 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.1e-06     0.036     195     221 .]     184     210 ..     176     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-06
                          HNOBA 195 mkeleeekkrtdeLLysmiPkevAerL 221
                                     + +e e  r+++LL +m+P ++AerL
  gi|121637532|ref|YP_977755.1| 184 EAVMEAEHDRSEALLANMLPASIAERL 210
                                    445899*******************98 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4      0.89   5.3e+03      44      56 ..     119     131 ..     117     140 .. 0.54
   2 ?   11.0   0.0   4.8e-05      0.28      54      91 ..     261     298 ..     260     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.89
                          RVT_3  44 ElqALlrGLqlal 56 
                                    E++AL  GL +++
  gi|121637532|ref|YP_977755.1| 119 EHTALAVGLAAVA 131
                                    5556666655443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.8e-05
                          RVT_3  54 lalklgirrlvvegDsktvvqllngrekvksselanll 91 
                                    l++++g++++ v gDs++vv+ + +  + +++ la + 
  gi|121637532|ref|YP_977755.1| 261 LVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFA 298
                                    6789******************9999985665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2650.69
//
Query:       gi|121637533|ref|YP_977756.1|  [L=205]
Description: two-component system transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-30  105.6   0.3    2.5e-30  104.9   0.3    1.3  1  Response_reg  Response regulator receiver domain
    1.7e-19   69.4   2.9    3.8e-19   68.3   0.8    2.3  2  ANTAR         ANTAR domain
  ------ inclusion threshold ------
      0.057   13.1   0.1      0.083   12.6   0.1    1.3  1  RE_XamI       XamI restriction endonuclease


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.3   4.1e-34   2.5e-30       1     111 [.      16     125 ..      16     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 4.1e-34
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vli++D+ l+r+ l+++l+eegye v+ea dg+ea+el++ +k+dl+++D++mp+ dG+++++ei  +    p+++lta 
  gi|121637533|ref|YP_977756.1|  16 VLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASKR-IAPIVVLTAF 94 
                                    8****************************************************************9987.89******** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    s+ + +++a +aga+ +l+Kpf++++L+ a+
  gi|121637533|ref|YP_977756.1|  95 SQRDLVERARDAGAMAYLVKPFSISDLIPAI 125
                                    ***************************9887 PP

>> ANTAR  ANTAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.11   6.6e+02       6      18 ..      93     105 ..      91     106 .. 0.81
   2 !   68.3   0.8   6.4e-23   3.8e-19       2      54 .]     144     196 ..     143     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHH CS
                          ANTAR   6 aleeRklieqAkg 18 
                                    a   R+l+e+A +
  gi|121637533|ref|YP_977756.1|  93 AFSQRDLVERARD 105
                                    66789*****975 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 6.4e-23
                                    HHHHHHHHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHCTTTS-HHHHHHHH- CS
                          ANTAR   2 qLeealeeRklieqAkgiLmeryglsedeAfrlLrklSmdsnvklrevAeavv 54 
                                     L e+le+Rkl+e+Akg+L +++g++e++Af+++++++md++++++ vAe v+
  gi|121637533|ref|YP_977756.1| 144 TLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKRVAEVVL 196
                                    6899*********************************************9875 PP

>> RE_XamI  XamI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.4e-05     0.083      44     108 ..     134     199 ..      91     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                        RE_XamI  44 lvksle.eekrlkkrmeaakldeelrkvaeiilrlaDrdiFtWleeerepteaeieraavivadrL 108
                                     ++ le e   l++r+e+ kl e ++ + ++   ++++d F W+++ +    + ++r a +v + L
  gi|121637533|ref|YP_977756.1| 134 EITALEgEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKRVAEVVLETL 199
                                    4566665667899***********************************999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1632.29
//
Query:       gi|121637534|ref|YP_977757.1|  [L=402]
Description: lipid-transfer protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.0   0.0    5.7e-09   35.7   0.0    2.1  1  Thiolase_N       Thiolase, N-terminal domain
    2.3e-06   27.4   3.3    9.8e-06   25.3   3.3    1.9  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
      5e-05   23.1   1.3     0.0024   17.7   0.2    2.6  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
      0.031   14.3   0.2        0.9    9.6   0.0    2.8  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.3e-12   5.7e-09       1     260 []       9     227 ..       9     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.3e-12
                                    EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEEE CS
                     Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqniarqaalkagipeevpav 79 
                                    v+i +a + p gk          +e +  a++a+l +agvd  +v+ v+ +  + +   g       a k+g    vp++
  gi|121637534|ref|YP_977757.1|   9 VYILGAGMHPWGK-----WGNDFTEYGVVAARAALRDAGVDWRHVQLVAGADTIRNgYPGFVAGATFAQKLGW-TGVPVS 82 
                                    5667777777777.....3334566788899******************999998868999999999******.9***** PP

                                    EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                     Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlta 159
                                        +c+Sg +a+  a  +i ag +dv++++G+ +    p+    + + g + gd   + + +      a+n +  +l a
  gi|121637534|ref|YP_977757.1|  83 SSYAACASGSQALQSARAQILAGFCDVALVIGADTT---PKGFF-APVGGERKGDPDWQRFHLIG----ATNTVYFALLA 154
                                    ********************************9863...33333.45677777777777776544....89999****** PP

                                    HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS- CS
                     Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtv 239
                                    ++  + y+++ e+ +++ vk+ +++ ++++a  +++e               + d+ + s+v+ ++L+ l          
  gi|121637534|ref|YP_977757.1| 155 RRRMDLYGATVEDFAQVKVKNSRHGLDNPNAR-YRKEN--------------SIDDVLASPVVSDPLRLL---------- 209
                                    *******************************9.88876..............89****************.......... PP

                                    BTTSB--BEEEEEEEEEEEHH CS
                     Thiolase_N 240 tAgnasqisDGaaavllmses 260
                                       + +  sDGaaa++++s+s
  gi|121637534|ref|YP_977757.1| 210 ---DICATSDGAAALIVASKS 227
                                    ...**************9975 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   3.3   2.2e-09   9.8e-06     153     204 ..      65     117 ..      11     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.2e-09
                                    HHHHHHHHHHT--SSEEEEE.SGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE- CS
                  ketoacyl-synt 153 viagrisyalglrGpsvtvd.tACsSslvavhaavqslrsgeadvalaGGvel 204
                                    v+ +  +++lg++G+ v+ + +AC+S+  a++ a  ++ +g +dval+ G+++
  gi|121637534|ref|YP_977757.1|  65 VAGATFAQKLGWTGVPVSSSyAACASGSQALQSARAQILAGFCDVALVIGADT 117
                                    344456788*****8887655*****************************995 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   5.5e-07    0.0024       5      39 ..      86     120 ..      84     123 .. 0.94
   2 ?    3.4   0.0     0.015        69      52      65 ..     214     229 ..     204     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-07
                                    -GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                    ACP_syn_III   5 aaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                    aaC++  +al+ A+a i +g +  +Lviga+t+ k
  gi|121637534|ref|YP_977757.1|  86 AACASGSQALQSARAQILAGFCDVALVIGADTTPK 120
                                    89*****************************9865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                                    B-EEEEEEEEEEE..S CS
                    ACP_syn_III  52 fGDGAgAvvleas..e 65 
                                     +DGA+A+++  +  +
  gi|121637534|ref|YP_977757.1| 214 TSDGAAALIVASKsfT 229
                                    58********987432 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.075   3.3e+02      29      52 ..      33      56 ..      27      57 .. 0.87
   2 ?    9.6   0.0    0.0002       0.9      14      56 ..     266     308 ..     261     318 .. 0.89
   3 ?   -2.9   0.0       1.5   6.6e+03      72      91 ..     377     396 ..     368     398 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.075
                                   HHHHHHHHHT--GGGEEEEE-SS- CS
                Ketoacyl-synt_C 29 aiekalaeagvdpedvdyveahgt 52
                                   a ++al++agvd + v++v   +t
  gi|121637534|ref|YP_977757.1| 33 AARAALRDAGVDWRHVQLVAGADT 56
                                   5789*************9987665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                                    STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHH CS
                Ketoacyl-synt_C  14 ahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtpl 56 
                                    +++ ++ap+     +++ +a+aeag+ ped ++ e  + +t+l
  gi|121637534|ref|YP_977757.1| 266 STAAVPAPERVFKDQILDAAYAEAGIGPEDLSLAEVYDLSTAL 308
                                    5678899999999***************************987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                                    GGGSCTSEEE-THHHH-B-G CS
                Ketoacyl-synt_C  72 karkqplavgSvKsniGHle 91 
                                    +  ++++ v++   + GH+ 
  gi|121637534|ref|YP_977757.1| 377 QVADAKVGVTANQGLFGHGS 396
                                    33367788888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3075.88
//
Query:       gi|121637535|ref|YP_977758.1|  [L=163]
Description: hypothetical protein BCG_1666c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-13   49.7   0.3    4.2e-13   49.1   0.3    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.3e-10   40.1   1.5    3.7e-10   39.5   1.5    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00023   20.7   1.3    0.00036   20.1   1.3    1.2  1  zf-tcix        Putative treble-clef, zinc-finger, Zn-binding
  ------ inclusion threshold ------
      0.019   14.4   5.3      0.083   12.3   5.5    1.9  2  zf-ribbon_3    zinc-ribbon domain
      0.099   13.0   0.0       0.14   12.5   0.0    1.2  1  Rhodanese_C    Rhodanase C-terminal


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.3   1.2e-16   4.2e-13       3      63 ..      59     125 ..      57     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.2e-16
                                    EE-GG-EEEEEEEEEE-T....TS-EEEEEEEEEEEE-TT....-EE-EEEEEEES...TT-B-EEE CS
                  OB_aCoA_assoc   3 elsgrGtvysftvvhrap....pgfaeeaPyvvgvVeLde.gvrimarlvgvdpde.vriGmrVrav 63 
                                     ls rG+++s+t  ++ap    p+ ++++P++v+vVeL++ g  +++ +v+   ++ +++Gm+++++
  gi|121637535|ref|YP_977758.1|  59 GLSTRGKLWSYTENRYAPpppyPAPDPFEPFAVAVVELADeGLIVLGKVVDGTLAAdLKVGMEMELT 125
                                    589***********************************887999********96666*******987 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.5     1e-13   3.7e-10       3      37 .]      19      56 ..      17      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1e-13
                        DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPr.avC..phCgsddle 37
                                    a  ++L+g++Cp CGt++fPPr   C  p Cgsd+le
  gi|121637535|ref|YP_977758.1| 19 KAGNPHLLGGKCPQCGTYVFPPRaDNCpnPACGSDTLE 56
                                   566789*****************999**********98 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.3     1e-07   0.00036      12      33 ..      29      51 ..      22      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                        zf-tcix 12 kCpkCGtyN.GtRglsCkNkaCd 33
                                   kCp+CGty  + R+  C N+aC 
  gi|121637535|ref|YP_977758.1| 29 KCPQCGTYVfPPRADNCPNPACG 51
                                   9*******66************7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.5   2.3e-05     0.083       4      23 ..      29      51 ..      29      54 .. 0.85
   2 ?    0.2   0.1      0.16   5.6e+02       6      10 ..      48      52 ..      48      57 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                    zf-ribbon_3  4 rCPnCGa.plssddnvCpy..CG 23
                                   +CP+CG+ +  +++ +Cp+  CG
  gi|121637535|ref|YP_977758.1| 29 KCPQCGTyVFPPRADNCPNpaCG 51
                                   6****************984466 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                    zf-ribbon_3  6 PnCGa 10
                                   P+CG+
  gi|121637535|ref|YP_977758.1| 48 PACGS 52
                                   66775 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.14      19      45 ..      28      54 ..      12      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                    Rhodanese_C 19 gkCieCgkpvdelrkrnCanedCnelv 45
                                   gkC +Cg+ v   r+ nC n++C    
  gi|121637535|ref|YP_977758.1| 28 GKCPQCGTYVFPPRADNCPNPACGSDT 54
                                   89*********99**********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1305.79
//
Query:       gi|121637536|ref|YP_977759.1|  [L=904]
Description: DNA polymerase I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.4e-145  483.8   0.0   4.6e-145  483.4   0.0    1.1  1  DNA_pol_A        DNA polymerase family A
    4.5e-54  182.7   0.0    9.5e-54  181.6   0.0    1.6  1  5_3_exonuc_N     5'-3' exonuclease, N-terminal resolvase-like
    2.2e-26   92.3   0.0    5.2e-26   91.1   0.0    1.7  1  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
     0.0059   16.6   0.0      0.027   14.4   0.0    2.0  2  NYN_YacP         YacP-like NYN domain
     0.0076   16.8   0.1      0.048   14.3   0.0    2.4  2  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.031   14.1   0.0      0.094   12.6   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.052   13.7   0.0       0.15   12.2   0.0    1.7  1  HHH_2            Helix-hairpin-helix motif
        0.1   12.9   0.0       0.29   11.5   0.0    1.8  1  Transposase_20   Transposase IS116/IS110/IS902 family
       0.18   12.0   0.1          2    8.6   0.0    2.5  2  Sep15_SelM       Sep15/SelM redox domain
        0.6   10.0   5.6       0.14   12.0   1.1    2.4  2  DUF4880          Domain of unknown function (DUF4880)


Domain annotation for each model (and alignments):
>> DNA_pol_A  DNA polymerase family A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.4   0.0  2.6e-148  4.6e-145       4     375 ..     527     900 ..     525     901 .. 0.98

  Alignments for each domain:
  == domain 1  score: 483.4 bits;  conditional E-value: 2.6e-148
                                    HHHHHHHHHHHHHHHHHHHHHHSS.C-STTTCCCCHHHHTCCCCS.TTSBETTSBTTTCCHHHHHT.S...CHHHHHHHH CS
                      DNA_pol_A   4 leelseeleeeleeleeeiyelag.efnlnSpkqlaevLfeklklpekkktktgystdeevLekla.k..hplakliley 79 
                                    l+el+++++++++++ e +y ++g ++nl+Spkql+ vLf++l++p++k+tktgy+td+++L++l  k  hp+++++l +
  gi|121637536|ref|YP_977759.1| 527 LTELQSQFGDQIRDAAEAAYGVIGkQINLGSPKQLQVVLFDELGMPKTKRTKTGYTTDADALQSLFdKtgHPFLQHLLAH 606
                                    78999*******************77***************************************96479********** PP

                                    HHHHHHHHHTTTTGGGCCBTTTSEE--EEESSSSSSSS-EEESS-GGGS-TTSCCHHHHHHTBCG.TTCCEEEEEEETTH CS
                      DNA_pol_A  80 relsklkstyvdallklinkktgrihtsfnqtvtatGrlsssepnlqnipirteegrriRkafvaeegghvllsaDysqi 159
                                    r++++lk t vd+ll+ +   +griht+fnqt++atGrlss+epnlqnipirt+ grriR+afv+ +g+  l++aDysqi
  gi|121637536|ref|YP_977759.1| 607 RDVTRLKVT-VDGLLQAVA-ADGRIHTTFNQTIAATGRLSSTEPNLQNIPIRTDAGRRIRDAFVVGDGYAELMTADYSQI 684
                                    *******99.8*******5.79*********************************************9999********* PP

                                    HHHHHHHHCT.HHHHHHHHTTH-HHHHHHHHHCTS.GGGHHHHHHHHHHHHHHHHHTT--HHHHHHHHTSSHHHHHHHHH CS
                      DNA_pol_A 160 ELRilAhlsgdeklieafkegeDiHsktAsevfgvpveevtkeqRrqaKainfGiiYGagakgLaeqlgiseeeAkefie 239
                                    E+Ri+Ahlsgde lieaf++geD+Hs +As+ fgvp++evt e Rr++Ka+ +G+ YG++a+gL++ql+is+eeA+e ++
  gi|121637536|ref|YP_977759.1| 685 EMRIMAHLSGDEGLIEAFNTGEDLHSFVASRAFGVPIDEVTGELRRRVKAMSYGLAYGLSAYGLSQQLKISTEEANEQMD 764
                                    ******************************************************************************** PP

                                    HHHHHSHHHHHHHHHHHHHCCCECCEEETTCSEEEECTTT-CCHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      DNA_pol_A 240 kyferypgvksyleetleeakekgyvetllgrrrylpeiksknaalrekaeraavNapiQGsAaDiiklamikieealke 319
                                    +yf+r+ gv++yl+ ++e+a+++gy++t+lgrrrylpe++s+n+++re+aeraa+NapiQGsAaDiik+ami++++al+e
  gi|121637536|ref|YP_977759.1| 765 AYFARFGGVRDYLRAVVERARKDGYTSTVLGRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMIQVDKALNE 844
                                    ******************************************************************************** PP

                                    TT-SEEEEEEETTEEEEEEECCCHHHHHHHHHHHHHHHHHSSS--EEEEEEESSCC CS
                      DNA_pol_A 320 eklkarlllqvHDElvfevpeeeveevaelvkeamesaveldvplkvevkvGknWg 375
                                    ++l +r+llqvHDEl+fe+++ e+e+v++lv+++m  a+ ldvpl+v+v++G++W+
  gi|121637536|ref|YP_977759.1| 845 AQLASRMLLQVHDELLFEIAPGERERVEALVRDKMGGAYPLDVPLEVSVGYGRSWD 900
                                    *******************************************************7 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.0   5.3e-57   9.5e-54       2     159 .]      17     184 ..      16     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 5.3e-57
                   5_3_exonuc_N   2 llLiDgsslifRayyal....lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKanReetpe 77 
                                    l+L+Dg+sl+fRa+yal    ++t+ g  tnavygf+ ml++ll++e+pth+a++fD +++tfR + ypeYKanR++tp+
  gi|121637536|ref|YP_977759.1|  17 LMLLDGNSLAFRAFYALpaenFKTRGGLTTNAVYGFTAMLINLLRDEAPTHIAAAFDVSRQTFRLQRYPEYKANRSSTPD 96 
                                    89**************999999999********************************8899******************* PP

                   5_3_exonuc_N  78 elkeqlplikevlealgikvlevegyEADDvigtlakraeeeg..vvivsgDkDllQlvednvrvld....vkkeellde 151
                                    e++ q+++ kevl algi+vl+ +g+EADD+i+tla++ae+eg  v +v+gD+D+lQlv+d+v+vl+    v++ +++++
  gi|121637536|ref|YP_977759.1|  97 EFAGQIDITKEVLGALGITVLSEPGFEADDLIATLATQAENEGyrVLVVTGDRDALQLVSDDVTVLYprkgVSELTRFTP 176
                                    **************************************9976668**********************9887666567*** PP

                   5_3_exonuc_N 152 eevaekyg 159
                                    e+v+ekyg
  gi|121637536|ref|YP_977759.1| 177 EAVVEKYG 184
                                    ******98 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   2.9e-29   5.2e-26       2      96 ..     186     279 ..     185     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 2.9e-29
                     5_3_exonuc   2 kPeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelkekklkekLeenkeearlskkLatiktdvp 81 
                                    +P+q++d++aL+GD+sDn+pG+pg+GektAak+++eygsl ++++n+d +++ k+ ++L++n  ++  +++L+ +++dvp
  gi|121637536|ref|YP_977759.1| 186 TPRQYPDFAALRGDPSDNLPGIPGVGEKTAAKWIAEYGSLRSLVDNVDAVRG-KVGDALRANLASVVRNRELTDLVRDVP 264
                                    8***********************************************9886.*************************** PP

                     5_3_exonuc  82 leleledlklkepde 96 
                                    l  + + l+l+++d+
  gi|121637536|ref|YP_977759.1| 265 LAQTPDTLRLQPWDR 279
                                    ***********9986 PP

>> NYN_YacP  YacP-like NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.5e-05     0.027      71     111 ..     116     156 ..     105     167 .. 0.90
   2 ?   -2.2   0.0         2   3.6e+03     100     136 ..     416     452 ..     402     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                    EE--TT--HHHHHHHHHHHC--TT--EEEE---CSSCTGGG CS
                       NYN_YacP  71 vytkegetADsvIeklvaelrkekeevvVvTSDraeqlvvf 111
                                    v ++ g +AD++I  l++++++e  +v VvT Dr+  ++v+
  gi|121637536|ref|YP_977759.1| 116 VLSEPGFEADDLIATLATQAENEGYRVLVVTGDRDALQLVS 156
                                    55778889**************************9988876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                    E---CSSCTGGGGCTEEEE-HHHHHHHHHHHHHHHHH CS
                       NYN_YacP 100 vTSDraeqlvvfgkGAlrlsarelveevkeaekeikk 136
                                    vTSD a  ++ ++ G    +  +l  +  + e ++++
  gi|121637536|ref|YP_977759.1| 416 VTSDTALAAYLVRPGQRSFTLDDLSLRYLRRELRAET 452
                                    8999999999999999998888887666665555543 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.7e-05     0.048      26      54 ..     193     221 ..     174     224 .. 0.76
   2 ?   -2.2   0.4       3.6   6.5e+03      17      40 ..     474     495 ..     472     496 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                    HHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                          HHH_5  26 vedlaaadveeLakipGiGkktAeriile 54 
                                    +++l     + L  ipG+G+ktA ++i e
  gi|121637536|ref|YP_977759.1| 193 FAALRGDPSDNLPGIPGVGEKTAAKWIAE 221
                                    33344445578999*************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                                    HHHTTT--SHHHHHHS-HHHHHTS CS
                          HHH_5  17 allsaGiesvedlaaadveeLaki 40 
                                    ++l+a  + v dla+a  +eLa+i
  gi|121637536|ref|YP_977759.1| 474 TILRA--RAVIDLADALDAELARI 495
                                    57888..9999***9988999887 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.094       5      21 ..     206     223 ..     203     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                DNA_pol_lambd_f   5 kvyGVGpktAkkwyak.G 21 
                                    ++ GVG ktA kw+a+ G
  gi|121637536|ref|YP_977759.1| 206 GIPGVGEKTAAKWIAEyG 223
                                    799***********9864 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05      0.15       7      30 ..     206     229 ..     204     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                          HHH_2   7 GIrhVGektAklLakrFksldaLk 30 
                                    GI+ VGektA +   +++sl  L 
  gi|121637536|ref|YP_977759.1| 206 GIPGVGEKTAAKWIAEYGSLRSLV 229
                                    9*******************9985 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.29       4      27 ..     204     227 ..     201     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                 Transposase_20   4 LesipGiGpvtaaallaeigdlrr 27 
                                    L  ipG+G+ taa ++ae g lr 
  gi|121637536|ref|YP_977759.1| 204 LPGIPGVGEKTAAKWIAEYGSLRS 227
                                    778****************99864 PP

>> Sep15_SelM  Sep15/SelM redox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0011         2      55      74 ..     270     289 ..     266     291 .. 0.87
   2 ?   -0.2   0.0      0.63   1.1e+03      43      60 ..     457     474 ..     447     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                    EEEE-SSS-HHHHHHHHHHH CS
                     Sep15_SelM  55 erislekwdrdeieelleek 74 
                                    ++++l++wdrd+i++l+++ 
  gi|121637536|ref|YP_977759.1| 270 DTLRLQPWDRDHIHRLFDDL 289
                                    5899*************875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.63
                                    EEEEE-SSS---EEEE-S CS
                     Sep15_SelM  43 kLilldedgeeverisle 60 
                                    +L lld+d++  e+i+  
  gi|121637536|ref|YP_977759.1| 457 QLSLLDDDDTDAETIQTT 474
                                    699***********9865 PP

>> DUF4880  Domain of unknown function (DUF4880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       3.3   5.9e+03      24      30 ..     327     333 ..     326     334 .. 0.82
   2 ?   12.0   1.1   7.9e-05      0.14      10      41 ..     370     400 ..     368     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.3
                        DUF4880  24 qaWlaad 30 
                                    ++Wla++
  gi|121637536|ref|YP_977759.1| 327 RQWLAEH 333
                                    69**998 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.9e-05
                        DUF4880  10 LrsgeasaadraafqaWlaadPrHarAwqrae 41 
                                    L+ ++++++d aa++aWl adP+  +A ++a 
  gi|121637536|ref|YP_977759.1| 370 LDTATLTPDDDAALAAWL-ADPAKPKALHEAK 400
                                    777899************.99**999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (904 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 6272.19
//
Query:       gi|121637537|ref|YP_977760.1|  [L=481]
Description: 30S ribosomal protein S1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-83  272.5  28.2    2.3e-26   91.9   1.8    4.1  4  S1             S1 RNA binding domain
    1.3e-06   28.2   0.9       0.17   11.4   0.1    3.2  3  DUF2110        Uncharacterized protein conserved in archaea (
    1.9e-06   27.8   6.0      0.025   14.6   0.0    4.8  4  S1_2           S1 domain
     0.0035   18.1   8.7       0.52   11.1   0.1    4.3  5  PCB_OB         Penicillin-binding protein OB-like domain
  ------ inclusion threshold ------
      0.021   14.7   4.6       0.73    9.8   0.3    3.5  3  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
        0.1   12.8   0.1         20    5.4   0.1    2.4  2  RGCC           Response gene to complement 32 protein family
        1.4    9.0   8.5        3.3    7.7   0.0    4.5  5  CsrA           Global regulator protein family
        2.5    8.7   6.4       0.25   11.9   1.5    1.9  2  EFTUD2         116 kDa U5 small nuclear ribonucleoprotein com


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   2.7   3.5e-20   7.8e-17       2      75 .]      33     105 ..      32     105 .. 0.97
   2 !   55.8   0.6   1.9e-18   4.2e-15       3      75 .]     121     188 ..     119     188 .. 0.97
   3 !   91.9   1.8     1e-29   2.3e-26       2      75 .]     206     277 ..     205     277 .. 0.98
   4 !   79.9   1.8   5.9e-26   1.3e-22       2      75 .]     291     363 ..     290     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.5e-20
                                    STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                    ++ g++veG++++v+++ +  ++g++ eg +pa els + ++ dp+ev++vGdev++ vl  +++++r+ils+k
  gi|121637537|ref|YP_977760.1|  33 FNDGDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSIK-HDVDPNEVVSVGDEVEALVLTKEDKEGRLILSKK 105
                                    689************************************.********************************86 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 1.9e-18
                                    TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                    ek+e v+G+V++v+kgG++ ++g   +gf+pas+++++   +++d + ++G+e+++k++++dk+r++++ls++
  gi|121637537|ref|YP_977760.1| 121 EKDEAVKGTVIEVVKGGLILDIG--LRGFLPASLVEMR---RVRDLQPYIGKEIEAKIIELDKNRNNVVLSRR 188
                                    89*********************..***********88...9*****************************86 PP

  == domain 3  score: 91.9 bits;  conditional E-value: 1e-29
                                    STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                    ++kg++ +G+V+s++++GafV+lg gv+g+v++sels++ ++++p+ev++vGdev v+vl+vd+dr+r++ls+k
  gi|121637537|ref|YP_977760.1| 206 LQKGTIRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWK-HIDHPSEVVQVGDEVTVEVLDVDMDRERVSLSLK 277
                                    589*********************.**************.********************************86 PP

  == domain 4  score: 79.9 bits;  conditional E-value: 5.9e-26
                                    STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                    +++g++v G+Vt+++++GafV++++g+eg+v++sel+ + +ve+pd+v+ vGd   vkv+++d +rrri+ls+k
  gi|121637537|ref|YP_977760.1| 291 HAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAER-HVEVPDQVVAVGDDAMVKVIDIDLERRRISLSLK 363
                                    789************************************.********************************86 PP

>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   7.8e-05      0.17      62     103 ..      27      70 ..       9      96 .. 0.77
   2 !   11.0   0.0   0.00011      0.24      58      98 ..     110     150 ..     104     163 .. 0.88
   3 ?    2.5   0.0     0.041        92      66     156 ..     200     290 ..     180     304 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.8e-05
                        DUF2110  62 geitkeveegevyvGtlesldedgfvldigve..vripkdelkp 103
                                    ++  k +++g+++ Gt+ ++d+d+ +ldig +    ip+ el+ 
  gi|121637537|ref|YP_977760.1|  27 DKTIKYFNDGDIVEGTIVKVDRDEVLLDIGYKteGVIPARELSI 70 
                                    5556669***********************98334578887774 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                        DUF2110  58 reefgeitkeveegevyvGtlesldedgfvldigvevripk 98 
                                    ++ +g+i++  e++e ++Gt+ ++ + g +ldig +   p+
  gi|121637537|ref|YP_977760.1| 110 ERAWGTIEALKEKDEAVKGTVIEVVKGGLILDIGLRGFLPA 150
                                    578*******************************9866555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.041
                        DUF2110  66 ke....veegevyvGtlesldedgfvldigve.vripkdelkpLgegspeqiaerFGlvqhlpleveveeveeeekeiea 140
                                    +e    +++g + +G+++s+ + g  +d g     ++ +el+   +++++   e   + +++ +e  v +v+ +++ +  
  gi|121637537|ref|YP_977760.1| 200 SEflnnLQKGTIRKGVVSSIVNFGAFVDLGGVdGLVHVSELS---WKHIDHPSEVVQVGDEVTVE--VLDVDMDRERVSL 274
                                    4455558999999*******9999999998652555555555...33333333333333444444..4446666777778 PP

                        DUF2110 141 rltdeqvdrlyewkkg 156
                                    +l  +q d +++++++
  gi|121637537|ref|YP_977760.1| 275 SLKATQEDPWRHFART 290
                                    8888888888888775 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.045     1e+02       2      57 ..      36     101 ..      36     105 .. 0.56
   2 ?   -2.2   0.0       2.1   4.7e+03       5      22 ..     126     143 ..     124     154 .. 0.77
   3 !    9.1   0.1    0.0006       1.3       2      46 ..     209     260 ..     208     262 .. 0.75
   4 !   14.6   0.0   1.1e-05     0.025       1      44 [.     293     337 ..     293     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.045
                           S1_2   2 GkintlkvlretdfgyfLqkdesgevlLpkkevp........eeleiGdeveVFvYt..Dsedrli 57 
                                    G i++ ++++ +   + L+ + ++e   p +e+         e + +Gdeve  v t  D+e+rli
  gi|121637537|ref|YP_977760.1|  36 GDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSikhdvdpnEVVSVGDEVEALVLTkeDKEGRLI 101
                                    566777777777777777777777777777766432111122445666666655543226666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                           S1_2   5 ntlkvlretdfgyfLqkd 22 
                                    ++ +v++  + g+ L+ +
  gi|121637537|ref|YP_977760.1| 126 VKGTVIEVVKGGLILDIG 143
                                    578999999999999866 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0006
                           S1_2   2 GkintlkvlretdfgyfLqkdesgevlLpkkevp........eeleiGdeveV 46 
                                    G+i++  v  + +fg+f++ ++ ++ l++ +e+         e +++Gdev+V
  gi|121637537|ref|YP_977760.1| 209 GTIRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSwkhidhpsEVVQVGDEVTV 260
                                    99*****************999.898888888754222223344567777766 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 1.1e-05
                           S1_2   1 iGkintlkvlretdfgyfLqkdesgevlLpkkevp.eeleiGdev 44 
                                    iG+i+  kv++  +fg+f+  +e+ e l++ +e+  +++e+ d+v
  gi|121637537|ref|YP_977760.1| 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAeRHVEVPDQV 337
                                    8*********************************75778887776 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.006        13      18      92 ..      23      85 ..       9     104 .. 0.77
   2 ?   -0.4   0.1      0.85   1.9e+03      31      54 ..      82     105 ..      73     135 .. 0.71
   3 !   11.1   0.1   0.00023      0.52      18      99 ..     195     264 ..     183     277 .. 0.81
   4 ?    3.2   0.1     0.067   1.5e+02      17      95 ..     280     346 ..     270     365 .. 0.70
   5 ?   -3.6   0.1         8   1.8e+04      18      37 ..     411     430 ..     403     438 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                                   HHHHHHHCCTSSTCTTEEEEEEEEEETTEEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEE CS
                         PCB_OB 18 eealeealkklpdsgelrpAvVlsvseksarvglrdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdv 92
                                    +a++ +  k+ + g+++++ +++v+ +++ + +  + +g+ip+++l++   v           ++++v+++Gd 
  gi|121637537|ref|YP_977760.1| 23 LAAID-KTIKYFNDGDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSIKHDV-----------DPNEVVSVGDE 85
                                   55554.444677889*******************************9998884...........56667777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.85
                                    CTTEEEEEEEEEETTEEEEEETTS CS
                         PCB_OB  31 sgelrpAvVlsvseksarvglrdg 54 
                                    +g+ ++A+Vl  ++k+ r+ l+++
  gi|121637537|ref|YP_977760.1|  82 VGDEVEALVLTKEDKEGRLILSKK 105
                                    566677888888888888777544 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00023
                                    HHHHHHHCCTSSTCTTEEEEEEEEEETTEEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEEEEEE CS
                         PCB_OB  18 eealeealkklpdsgelrpAvVlsvseksarvglrdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdvvlvrk 97 
                                    +++++++  +  + g +r++vV s+ + +a v l +g  g + +++l+w              + +s+v+++Gd v v+ 
  gi|121637537|ref|YP_977760.1| 195 QSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHI-----------DHPSEVVQVGDEVTVEV 262
                                    445555566666889*******************.**************887...........789***********998 PP

                                    -T CS
                         PCB_OB  98 ee 99 
                                     +
  gi|121637537|ref|YP_977760.1| 263 LD 264
                                    76 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.067
                                    .HHHHHHHCCTSSTCTTEEEEEEEEEETTEEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEEEE CS
                         PCB_OB  17 deealeealkklpdsgelrpAvVlsvseksarvglrdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdvvlv 95 
                                    +e+ + ++ + ++  g+++p+ V++  + +a v +++g +g + +++l+  ++          ++ +++v+++Gd  +v
  gi|121637537|ref|YP_977760.1| 280 QEDPW-RHFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA--ER---------HVEVPDQVVAVGDDAMV 346
                                    44455.367778889999*****************99999999888764..33.........23456666666665555 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 8
                                    HHHHHHHCCTSSTCTTEEEE CS
                         PCB_OB  18 eealeealkklpdsgelrpA 37 
                                    ++++e+  +++++  ++++A
  gi|121637537|ref|YP_977760.1| 411 RAEWEARYAEAERRHKMHTA 430
                                    44455555555555555444 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.82   1.8e+03       2      19 ..      85     102 ..      84     104 .. 0.86
   2 ?    9.8   0.3   0.00033      0.73      35      57 ..     253     275 ..     247     277 .. 0.90
   3 ?    4.5   0.3     0.015        34      33      57 ..     337     361 ..     308     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.82
                  RNase_II_C_S1   2 tFdAvVvdvddrggtVql 19 
                                    + +A V+  +d++g++ l
  gi|121637537|ref|YP_977760.1|  85 EVEALVLTKEDKEGRLIL 102
                                    689********9999887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                  RNase_II_C_S1  35 plGervrVrLveADvatrrvrFe 57 
                                     +G++v+V++ ++D ++ rv ++
  gi|121637537|ref|YP_977760.1| 253 QVGDEVTVEVLDVDMDRERVSLS 275
                                    68******************876 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.015
                  RNase_II_C_S1  33 glplGervrVrLveADvatrrvrFe 57 
                                     +++G++  V++ + D+++rr+ ++
  gi|121637537|ref|YP_977760.1| 337 VVAVGDDAMVKVIDIDLERRRISLS 361
                                    4789*****************9876 PP

>> RGCC  Response gene to complement 32 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.014        31     105     133 ..       2      30 ..       1      32 [. 0.91
   2 ?    5.4   0.1    0.0089        20      25      85 ..     397     457 ..     385     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                           RGCC 105 ssplvvsrkakLGDtkeLedfiaDLDrtL 133
                                     sp+v+s++  + D    edf+a +D+t+
  gi|121637537|ref|YP_977760.1|   2 PSPTVTSPQVAVNDIGSSEDFLAAIDKTI 30 
                                    5799999********************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0089
                           RGCC  25 addLsdvLcefdavledfesPvekrhfrYeehLkelkrrssasvsDsGisdsesadslnrs 85 
                                    +++ ++ L  f++  +++e+   + + r++ h  ++ + ++a     G +d  sa+s + +
  gi|121637537|ref|YP_977760.1| 397 DAETNEWLEGFEKQRAEWEARYAEAERRHKMHTAQMEKFAAAETAGRGADDQSSASSAPSE 457
                                    56778889999999999999999999999***************************98765 PP

>> CsrA  Global regulator protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.81   1.8e+03      16      32 ..      37      53 ..      32      56 .. 0.65
   2 ?   -0.6   0.0      0.58   1.3e+03       8      32 ..      76     100 ..      74     103 .. 0.81
   3 ?    0.3   0.1      0.31     7e+02      14      29 ..     165     180 ..     163     186 .. 0.87
   4 ?    7.7   0.0    0.0015       3.3       9      36 ..     249     278 ..     247     281 .. 0.79
   5 ?    1.2   0.1      0.16   3.6e+02       9      32 ..     335     358 ..     333     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.81
                                   TTEEEEEEEEETTEEEE CS
                           CsrA 16 ddIeitvlevegnqvrl 32
                                   d +e t+++v+ ++v l
  gi|121637537|ref|YP_977760.1| 37 DIVEGTIVKVDRDEVLL 53
                                   55666677777776655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.58
                                    TT-EEEETTTEEEEEEEEETTEEEE CS
                           CsrA   8 kgEsIvIgddIeitvlevegnqvrl 32 
                                    ++E + +gd++e  vl  e+++ rl
  gi|121637537|ref|YP_977760.1|  76 PNEVVSVGDEVEALVLTKEDKEGRL 100
                                    6899999999999999888877776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.31
                                    ETTTEEEEEEEEETTE CS
                           CsrA  14 IgddIeitvlevegnq 29 
                                    Ig++Ie +++e ++n+
  gi|121637537|ref|YP_977760.1| 165 IGKEIEAKIIELDKNR 180
                                    9**********99886 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0015
                                    T-EEEETTTEEEEEEEEETTE..EEEEEE- CS
                           CsrA   9 gEsIvIgddIeitvlevegnq..vrlgIeA 36 
                                     E + +gd++++ vl+v+ ++  v l ++A
  gi|121637537|ref|YP_977760.1| 249 SEVVQVGDEVTVEVLDVDMDRerVSLSLKA 278
                                    68899************9777447777666 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.16
                                    T-EEEETTTEEEEEEEEETTEEEE CS
                           CsrA   9 gEsIvIgddIeitvlevegnqvrl 32 
                                    ++ + +gdd  ++v++++ ++ r+
  gi|121637537|ref|YP_977760.1| 335 DQVVAVGDDAMVKVIDIDLERRRI 358
                                    677889***********9888777 PP

>> EFTUD2  116 kDa U5 small nuclear ribonucleoprotein component N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.2         8   1.8e+04      86      97 ..      83      95 ..      77      97 .. 0.69
   2 ?   11.9   1.5   0.00011      0.25       2      49 ..     382     432 ..     381     463 .. 0.43

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8
                                   -SSSEEEE.--S- CS
                         EFTUD2 86 Gkdvetlv.qeeD 97
                                   G++ve lv  +eD
  gi|121637537|ref|YP_977760.1| 83 GDEVEALVlTKED 95
                                   7888888723444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                         EFTUD2   2 dlYDEFGNyiGpelesdeeeeseeeeeeeeeeeeeeeeee....eaekaeed 49 
                                    d YDE GNyi pe  + e  ++  e  e++++e e++ +e    ++ ++++ 
  gi|121637537|ref|YP_977760.1| 382 DSYDEQGNYIFPEGFDAET-NEWLEGFEKQRAEWEARYAEaerrHKMHTAQM 432
                                    89********666543322.12222222222211111111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3306.17
//
Query:       gi|121637538|ref|YP_977761.1|  [L=407]
Description: dephospho-CoA kinase/protein folding accessory domain-containing protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-61  206.2   0.0    5.7e-61  205.3   0.0    1.5  1  CoaE             Dephospho-CoA kinase
    2.5e-40  138.3   0.0    3.9e-40  137.7   0.0    1.3  1  GrpB             GrpB protein
  ------ inclusion threshold ------
      0.089   12.9   0.6       0.22   11.6   0.3    1.9  2  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3   0.0   9.6e-65   5.7e-61       3     176 ..       4     178 ..       2     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 9.6e-65
                                    EEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-HHHHHHHHHTSHHHHHHH CS
                           CoaE   3 vgltGgiasGKstvanlfadlgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdReaLrkkvFadpeekkaL 82 
                                    +gltGgi++GKs+++ +f+++g  +vD D++Ar+vv+pg+e l+++v++Fg +il +dG+LdR+aL+ k F+d+e++ +L
  gi|121637538|ref|YP_977761.1|   4 IGLTGGIGAGKSLLSTTFSQCGGIVVDGDVLAREVVQPGTEGLASLVDAFGRDILLADGALDRQALAAKAFRDDESRGVL 83 
                                    9******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHH--S.SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS--HH CS
                           CoaE  83 nallhPlirreikkelakles.kyvlldvPLLvEkqlekliervlvvdvelelqveRlvardgvseeevkaiiaaQlsee 161
                                    n+++hPl++r+  + +a+++  ++v+ d+PLLvE++++ l+  v+vv++++el+v+Rlv+++g++e++++a+iaaQ+s++
  gi|121637538|ref|YP_977761.1|  84 NGIVHPLVARRRSEIIAAVSGdAVVVEDIPLLVESGMAPLFPLVVVVHADVELRVRRLVEQRGMAEADARARIAAQASDQ 163
                                    *******************998999******************************************************* PP

                                    HHHHH-SEEEE-.SS CS
                           CoaE 162 erlaladvvldNdss 176
                                    +r+a+adv+ldN++s
  gi|121637538|ref|YP_977761.1| 164 QRRAVADVWLDNSGS 178
                                    ************987 PP

>> GrpB  GrpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   6.5e-44   3.9e-40       2     160 .]     211     395 ..     210     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 6.5e-44
                                    X--BS--THHHHHHHHHHHHHHHHH....EEEEEESGGGSTT...--B-S-EEEEEEES-SGGGGGGHHHHHHTT-EE.- CS
                           GrpB   2 velveydpeWpeqferekarlraal....isieHiGSTsvpg...laAKpiiDilvvvedledeeelveaLeaagyellr 74 
                                     +lv+ dp+Wp+q++r+ +rl+ a+    ++++HiGST+v+g   + AK++iDi+v+ve+l+ ++el+e+L aagy    
  gi|121637538|ref|YP_977761.1| 211 ARLVPADPSWPDQARRIVNRLKIACghkaLRVDHIGSTAVSGfpdFLAKDVIDIQVTVESLDVADELAEPLLAAGYPR-- 288
                                    689**********************999559*********6633378************9999999**********66.. PP

                                    T.......................TTTSTTEEEEEE-SSS..--EEEEEEETT-HHHHHHHHHHHHHHH-HHHHHHHHHH CS
                           GrpB  75 g.......................epgiperrlfvkgedeeertvhlhvveagspelerhllfrdyLrahpearaeYaal 131
                                                            + +++++r+++++ d+ +r++++h++++g+p+++++llf d+L a+p ar++Y ++
  gi|121637538|ref|YP_977761.1| 289 LehitqdtektdarstvgrydhtdSAALWHKRVHASA-DP-GRPTNVHLRVHGWPNQQFALLFVDWLAANPGAREDYLTV 366
                                    2347778899999999****99988889*******98.55.69************************************* PP

                                    HHHHHTT-SS-HHHH----HHHHHHHHHH CS
                           GrpB 132 KrelaakaeedidaYteaKeefikeilkr 160
                                    K ++ ++a+ ++++Y++aKe+++ ++++r
  gi|121637538|ref|YP_977761.1| 367 KCDADRRADGELARYVTAKEPWFLDAYQR 395
                                    ************************99986 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   3.7e-05      0.22     117     155 ..     127     167 ..     124     212 .. 0.89
   2 ?   -2.3   0.0      0.69   4.1e+03     139     154 ..     298     313 ..     267     338 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                Cytidylate_kin2 117 rvfltapledrvkrvaereglseeeareki..ketDkrrak 155
                                     v ++a+ e rv+r+ e++g+ e++ar +i  ++ D++r++
  gi|121637538|ref|YP_977761.1| 127 VVVVHADVELRVRRLVEQRGMAEADARARIaaQASDQQRRA 167
                                    5899*****************99888887722566777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                Cytidylate_kin2 139 eeearekiketDkrra 154
                                    + +ar+++ + D++ +
  gi|121637538|ref|YP_977761.1| 298 KTDARSTVGRYDHTDS 313
                                    2233333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2794.03
//
Query:       gi|121637539|ref|YP_977762.1|  [L=147]
Description: hypothetical protein BCG_1670c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-16   57.9   0.3    1.3e-15   57.3   0.3    1.3  1  DUF402    Protein of unknown function (DUF402)


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.3   7.3e-20   1.3e-15       1      68 []      28      95 ..      28      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 7.3e-20
                                   S-EEEEE-.TT-SEEEEEEEETTTEEEEEEEEEES...--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                         DUF402  1 ylelwllp.lglwynvfhfldgdgrlqglYvDiat...ppevgegawktiDlyLDlvvspdgevevlDedEL 68
                                   yle+wllp lgl+++vfhf + ++r++++Y+D+ +   +    + +w+ +D+yLD+ v   g  e+ D+dEL
  gi|121637539|ref|YP_977762.1| 28 YLESWLLPsLGLRATVFHFNPSHKRDHDYYLDVGEytpG----PSVWRSEDHYLDIEVRTGGGAELADVDEL 95
                                   89********************99***********5432....467***********9999**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1026.62
//
Query:       gi|121637540|ref|YP_977763.1|  [L=698]
Description: excinuclease ABC subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-33  113.6   0.0    2.1e-32  111.1   0.0    2.2  2  UvrB_inter     UvrB interaction domain
      4e-22   77.8   1.8      4e-22   77.8   1.8    1.9  2  UvrB           Ultra-violet resistance protein B
    7.3e-17   61.7   0.1    1.6e-16   60.7   0.1    1.6  1  Helicase_C     Helicase conserved C-terminal domain
    2.4e-09   37.5   0.0    1.8e-08   34.6   0.0    2.1  2  ResIII         Type III restriction enzyme, res subunit
    3.7e-07   29.7   5.1    3.7e-07   29.7   5.1    2.4  2  UVR            UvrB/uvrC motif
    2.5e-05   24.1   0.0    0.00033   20.5   0.0    2.8  3  DEAD           DEAD/DEAH box helicase
     0.0003   21.2   0.0        0.1   12.9   0.0    2.6  2  AAA_19         AAA domain
    0.00059   19.6   0.0      0.054   13.2   0.0    2.7  2  AAA_30         AAA domain
     0.0013   18.8   0.0     0.0097   15.9   0.0    2.4  2  AAA_5          AAA domain (dynein-related subfamily)
     0.0032   17.3   0.0      0.011   15.6   0.0    1.9  1  Helicase_RecD  Helicase
     0.0034   17.7   0.0      0.066   13.5   0.0    2.7  2  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.035   14.2   0.0    1.6  1  DUF87          Helicase HerA, central domain
      0.029   14.8   1.1       0.16   12.3   0.0    2.7  2  AAA_16         AAA ATPase domain
      0.099   13.2   0.0        1.4    9.4   0.0    2.3  2  ABC_tran       ABC transporter
       0.11   12.0   0.0       0.21   11.1   0.0    1.4  1  AAA_7          P-loop containing dynein motor region
       0.14   11.5   0.0       0.27   10.5   0.0    1.5  1  AIG1           AIG1 family
       0.22   10.9   1.2        8.2    5.7   0.0    3.0  3  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.75    9.6   4.2        0.8    9.5   0.2    2.8  3  CdvA           CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.0   2.1e-35   2.1e-32       1      91 []     161     250 ..     161     250 .. 0.99
   2 ?   -0.8   0.0       1.8   1.8e+03      51      76 ..     469     494 ..     464     501 .. 0.81

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 2.1e-35
                     UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgkslekl 80 
                                    +elkvg++++r+ llr Lv++qY+rnd+ ++rG+FrvrGdtvei+p++ ee a+rieffgdeie +++++pltg++++++
  gi|121637540|ref|YP_977763.1| 161 VELKVGEEVPRDGLLRLLVDVQYTRNDMSFTRGSFRVRGDTVEIIPSY-EELAVRIEFFGDEIEALYYLHPLTGEVIRQV 239
                                    58**********************************************.8****************************** PP

                     UvrB_inter  81 eeitifPakhf 91 
                                    +++ ifPa+h+
  gi|121637540|ref|YP_977763.1| 240 DSLRIFPATHY 250
                                    **********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                     UvrB_inter  51 evairieffgdeiesireidpltgks 76 
                                    e  ir+     e++++r+++ l +  
  gi|121637540|ref|YP_977763.1| 469 EMGIRVRYLHSEVDTLRRVELLRQLR 494
                                    56799999999999999999887765 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.8   5.8e+03      13      20 ..      22      29 ..      21      29 .. 0.91
   2 !   77.8   1.8     4e-25     4e-22       1      42 [.     553     594 ..     553     595 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.8
                                   HHHHHHHH CS
                           UvrB 13 AideTerR 20
                                   Aide erR
  gi|121637540|ref|YP_977763.1| 22 AIDELERR 29
                                   9******9 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 4e-25
                                    EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
                           UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                                    +YADkiTdSM++AideTerRR++Q+aYNe++gI P+ ++Kki
  gi|121637540|ref|YP_977763.1| 553 MYADKITDSMREAIDETERRRAKQIAYNEANGIDPQPLRKKI 594
                                    9****************************************9 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   1.6e-19   1.6e-16      11     109 ..     442     545 ..     431     547 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.6e-19
                                    HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                     Helicase_C  11 kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                    ++   ++++l+ + t++++e+ +++ll + gi+v +lh+e  +  r e l+q + g++dvL+  + + +G+d+p+v+lV 
  gi|121637540|ref|YP_977763.1| 442 TRADADQRVLVTTLTKKMAEDlTDYLL-EMGIRVRYLHSEVDTLRRVELLRQLRLGDYDVLVGINLLREGLDLPEVSLVA 520
                                    566778999********9998889985.447************************************************* PP

                                    ESSSS.....SSHHHHHHHHTTSSS CS
                     Helicase_C  90 nfdlp.....rnvtsyiqriGRtgR 109
                                    ++d++     r+ +s+iq iGR++R
  gi|121637540|ref|YP_977763.1| 521 ILDADkegflRSSRSLIQTIGRAAR 545
                                    *****88888889***********9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.8e-11   1.8e-08       7     137 ..      18     140 ..      13     141 .. 0.82
   2 ?   -0.1   0.0       0.8     8e+02     135     169 ..     335     397 ..     319     398 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.8e-11
                                    HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GE CS
                         ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeig 86 
                                     Q  ai++l+  ++  +++ +++  aTGtGK+ + a lierl++      +l+++p+k+l  q+ +e++++l+ ++  ++
  gi|121637540|ref|YP_977763.1|  18 DQPAAIDELERRIN-AGERDVVLLGATGTGKSATTAWLIERLQR-----PTLVMAPNKTLAAQLANELREMLPHNA--VE 89 
                                    5999*********9.****************************9.....8***********************987..45 PP

                                    EEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEE CS
                         ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdvii 137
                                     +vs   + + e  + +++ ++++ +s++ d e+ +   +++l +r dv++
  gi|121637540|ref|YP_977763.1|  90 YFVSYYDYYQPEAYIAQTDTYIEKDSSINDDVERLRHSATSALLSRRDVVV 140
                                    554444444445555689999999999999996556666667777777666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.8
                                    EEEEETGGGTTS............T...................TTHHHHHT---SEEEEEESS- CS
                         ResIII 135 viiiDEaHrlgak...........k...................swreilekfkeavllglTATp 169
                                    +++iDE+H +  +           k                   +w+e ++ +     ++l+ATp
  gi|121637540|ref|YP_977763.1| 335 LLVIDESHVTVPQiggmyegdisrKrnlveygfrlpsacdnrplTWEEFADRIG--QTVYLSATP 397
                                    8999***98877655555444433033333444444444455556666555554..455555665 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       8.7   8.6e+03       7      17 ..     558     568 ..     556     570 .. 0.73
   2 !   29.7   5.1   3.7e-10   3.7e-07       3      35 ..     655     687 ..     653     688 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.7
                            UVR   7 LeeemeeAaen 17 
                                    +++ m eA+++
  gi|121637540|ref|YP_977763.1| 558 ITDSMREAIDE 568
                                    55669999997 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.7e-10
                            UVR   3 likeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                    lik+L+++m  Aa++++FE+AA++RD+i+ lk+
  gi|121637540|ref|YP_977763.1| 655 LIKDLTAQMMAAARDLQFELAARFRDEIADLKR 687
                                    8****************************9996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.3e-07   0.00033      13      75 ..      33      87 ..      18     141 .. 0.74
   2 ?   -1.0   0.0       1.3   1.3e+03     124     168 ..     335     396 ..     333     402 .. 0.55
   3 ?   -1.7   0.0       2.2   2.2e+03      51     103 ..     451     503 ..     425     526 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                                   TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                                   g++dv++ ++TG+GK++     +++++       +  +l+++P + La q +n+l++++ +  
  gi|121637540|ref|YP_977763.1| 33 GERDVVLLGATGTGKSAT-TAWLIERL-------QRPTLVMAPNKTLAAQLANELREMLPHNA 87
                                   679************987.55666566.......3457******************9987543 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                                    EEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTT................SEEEEEESS CS
                                    xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxx RF
                           DEAD 124 flVlDEadrlldq...gfsdfinrilnqlpqitcdgklq................rqvivlSAT 168
                                    +lV+DE +    q    ++ +i+r  n + +   + + +                 q++ lSAT
  gi|121637540|ref|YP_977763.1| 335 LLVIDESHVTVPQiggMYEGDISRKRNLV-EYGFRLP-SacdnrpltweefadriGQTVYLSAT 396
                                    58999999887776655666666644433.2222222.12344444455555554556666666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.2
                                    EEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH...HHHHHHHHTT.CSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.xxxxxx RF
                           DEAD  51 livePtreLaeqtlnnlkkfkkyidlrvlliiggvaa...rdqlskldng.vdivvg 103
                                    l+ + t+++ae+    l+ ++ ++++rv  + ++v++    + l++l+ g +d++vg
  gi|121637540|ref|YP_977763.1| 451 LVTTLTKKMAED----LTDYLLEMGIRVRYLHSEVDTlrrVELLRQLRLGdYDVLVG 503
                                    444444444444....44444444444444433333300033344444334666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0    0.0001       0.1       9     110 ..      33     143 ..      27     152 .. 0.73
   2 ?    5.4   0.0     0.022        22      40      78 ..     445     498 ..     431     616 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...................a 69 
                                     e+ +++++  GtGK+ ++   ++ l++ +       l++a+++  a +l+++l++++ +                   a
  gi|121637540|ref|YP_977763.1|  33 GERDVVLLGATGTGKSATTAWLIERLQRPT-------LVMAPNKTLAAQLANELREMLPHnaveyfvsyydyyqpeayiA 105
                                    5677999***********999888887665.......6666666666666666555444455568888888888888877 PP

                         AAA_19  70 tTiHrlalldfddlltealelleeaeeekklqeeellivDE 110
                                    +T  ++   + d+ +++ +e l++++++  l ++++++v  
  gi|121637540|ref|YP_977763.1| 106 QTDTYI---EKDSSINDDVERLRHSATSALLSRRDVVVVAS 143
                                    776666...88888888999999888888887777888855 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                         AAA_19  40 vkpeeillvaftgrAakelrerlaalgaeatTiHrlal................l 78 
                                     + +++l+ ++t++ a+ l++ l ++g + + +H+  +                 
  gi|121637540|ref|YP_977763.1| 445 DADQRVLVTTLTKKMAEDLTDYLLEMGIRVRYLHSE-VdtlrrvellrqlrlgdY 498
                                    234899***************999999986666644.112333333444444440 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.4e-05     0.054      14      67 ..      30      80 ..      16     141 .. 0.76
   2 ?    3.2   0.0     0.061        61      44      82 ..     445     491 ..     435     511 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                         AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                                   ++ g+r +vl G+ GtGK+ + + l e ++   ++ +++Ap+++ A++La+el 
  gi|121637540|ref|YP_977763.1| 30 INAGERDVVLLGATGTGKSATTAWLIERLQ---RPTLVMAPNKTLAAQLANELR 80
                                   455667799**********99888776666...788*************99875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.061
                         AAA_30  44 aaggrviglAptgkaAkvLae...elgieastiakllkrlk.....g 82 
                                    +a +rv++ + t+k+A++L++   e+gi+ + +++ +++l+     +
  gi|121637540|ref|YP_977763.1| 445 DADQRVLVTTLTKKMAEDLTDyllEMGIRVRYLHSEVDTLRrvellR 491
                                    34689***************877799999999999998888666553 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.7e-06    0.0097       1      42 [.      36      76 ..      36     138 .. 0.72
   2 ?   -0.8   0.0       1.4   1.4e+03      65      95 ..     542     572 ..     512     595 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlk 42
                                   dv+L+G++GtgKs  +  l ++l+r++++++ ++ + +++l 
  gi|121637540|ref|YP_977763.1| 36 DVVLLGATGTGKSATTAWLIERLQRPTLVMAPNKTL-AAQLA 76
                                   69************************9999887744.44454 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                    G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                          AAA_5  65 egeilvlDEveraesevlnsLlslleerrll 95 
                                    +++  v +Ev++  +++++s+   ++e +++
  gi|121637540|ref|YP_977763.1| 542 RAARNVSGEVHMYADKITDSMREAIDETERR 572
                                    5555566899999999999999999998877 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.011       1      97 [.      38     142 ..      38     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                  Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke...............eekkkkae 65 
                                    vl ++ G+GKSa+ + ++++l +      lv ap+k+ +++l + l++ l +  +++               ++++  ++
  gi|121637540|ref|YP_977763.1|  38 VLLGATGTGKSATTAWLIERLQRP----TLVMAPNKTLAAQLANELREMLPHNAVEYfvsyydyyqpeayiaQTDTYIEK 113
                                    688999********9999998887....79********************999999899999999888887666666666 PP

                  Helicase_RecD  66 kaelrvrkqrieyiapdellklkeqadllvvD 97 
                                    + +++ + +r+++ a ++ll+++   d++vv 
  gi|121637540|ref|YP_977763.1| 114 DSSINDDVERLRHSATSALLSRR---DVVVVA 142
                                    67777779999999999999865...888885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.6e-05     0.066       8      90 ..      37     136 ..      31     144 .. 0.67
   2 ?    0.6   0.0      0.64   6.4e+02      37      70 ..     568     604 ..     553     668 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................. 70 
                                    +v+ G +GtGK+ + ++l e+l+        rp+  +v +p++t  ++l++el + l +++ +                 
  gi|121637540|ref|YP_977763.1|  37 VVLLGATGTGKSATTAWLIERLQ--------RPT--LVMAPNKTLAAQLANELREMLPHNAVEyfvsyydyyqpeayiaq 106
                                    5899******************4........444..56778888788888888888887776677777755555555555 PP

                         AAA_22  71 ..........erlsseellealeqalrara 90 
                                               +++ e+l++  + al +r+
  gi|121637540|ref|YP_977763.1| 107 tdtyiekdssINDDVERLRHSATSALLSRR 136
                                    555555555555555555544444444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.64
                         AAA_22  37 e...erpevvfvtlpsstsskdllrellralglelka 70 
                                    e   +r++++ ++ +++ +++ l+++++ +l++   +
  gi|121637540|ref|YP_977763.1| 568 EterRRAKQIAYNEANGIDPQPLRKKIADILDQVYRE 604
                                    1335899999999999999999999999999875554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.035      26      48 ..      37      59 ..      30      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                          DUF87 26 lAilgsTGsGKSntvavLleell 48
                                   +  lg TG+GKS t+a L+e+l 
  gi|121637540|ref|YP_977763.1| 37 VVLLGATGTGKSATTAWLIERLQ 59
                                   5679*****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.16      14      52 ..      25      62 ..      18     143 .. 0.74
   2 ?   -0.5   0.4       1.4   1.4e+03      63      95 ..     642     673 ..     518     696 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                         AAA_16 14 salervrsgrpelvllsGesGvGKsslvrellralekdg 52
                                   ++ +r+++g+ + v+l G+ G+GKs+    l ++l++  
  gi|121637540|ref|YP_977763.1| 25 ELERRINAGE-RDVVLLGATGTGKSATTAWLIERLQRPT 62
                                   4456788887.99**************998888998883 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                         AAA_16  63 l.esaipysalaqalareellrqlldeaesaele 95 
                                      +sa+p++ la+++ + +l +q+ ++a++ ++e
  gi|121637540|ref|YP_977763.1| 642 RdTSAMPRAELADLI-K-DLTAQMMAAARDLQFE 673
                                    223334444444444.3.4444444443333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0014       1.4       4      36 ..      26      59 ..      23     128 .. 0.83
   2 ?    1.0   0.0      0.57   5.6e+02      26      67 ..     535     583 ..     534     633 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                                   EEEEEETTSE.EEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  4 vslklkegek.vaivGenGaGKStLlkllagllk 36
                                   ++  +++ge+ v+++G +G+GKS   + l++ l+
  gi|121637540|ref|YP_977763.1| 26 LERRINAGERdVVLLGATGTGKSATTAWLIERLQ 59
                                   5567888886699**********88777665544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.57
                                    HHHHHHTTSS--SEEEEEETTCEGGG.......B-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                       ABC_tran  26 tLlkllagllkpteGeilldgkdlke.......qeleslrkeigvlpqe 67 
                                    +L++++ +  ++ +Ge+++  +++++       +++++  k+i++ + +
  gi|121637540|ref|YP_977763.1| 535 SLIQTIGRAARNVSGEVHMYADKITDsmreaidETERRRAKQIAYNEAN 583
                                    5788888888889999988888888866666544444444555544443 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.21      32      81 ..      33      82 ..      22      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                          AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdi 81
                                    ++ v+l G tGtGK++++  l+++l++ +++++  +  a   an+l+++
  gi|121637540|ref|YP_977763.1| 33 GERDVVLLGATGTGKSATTAWLIERLQRPTLVMAPNKTLAAQLANELREM 82
                                   57899*****************9999977666655555555555555555 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00027      0.27       2      22 ..      36      56 ..      35      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                   EEEEESSTTSSHHHHHHHHHT CS
                           AIG1  2 tivlvGktgnGkSaTgNsilg 22
                                    +vl+G tg+GkSaT   +++
  gi|121637540|ref|YP_977763.1| 36 DVVLLGATGTGKSATTAWLIE 56
                                   69*************876665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0082       8.2      40      60 ..      35      55 ..       6      58 .. 0.78
   2 ?    2.0   0.0      0.11   1.1e+02      75     127 ..     226     279 ..     224     305 .. 0.73
   3 ?   -0.8   0.4      0.77   7.7e+02     102     164 ..     555     616 ..     541     694 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0082
                                   .SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE 40 shllvaGatgsGKStalntLi 60
                                     ++++Gatg+GKS +   Li
  gi|121637540|ref|YP_977763.1| 35 RDVVLLGATGTGKSATTAWLI 55
                                   6799**********9877666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                    EEE-TTSS.SCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                   FtsK_SpoIIIE  75 iliDykgv.elsalediphllsvavatdperalraleeLvkemeeryalfreag 127
                                    + + + ++  +++++ + +  ++  +++per + a+ ++++e+ er a ++++g
  gi|121637540|ref|YP_977763.1| 226 YYLHPLTGeVIRQVDSLRIFPATHYVAGPERMAHAVSAIEEELAERLAELESQG 279
                                    555666665577777777777888999999999999999999999986555443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.77
                                    HHHHHHHHHHHHHHHHHHH.HHHHHTT-SSHHH..HHHHHHHHHHTT---B-TT-........... CS
                   FtsK_SpoIIIE 102 peralraleeLvkemeery.alfreagvrsiaa..ydgeiaedpldifgdvflvlDnyddlaaene 164
                                    +++++  ++e ++e e+r  + ++   ++ i+    +++i    +di   v+   D+++ +++ + 
  gi|121637540|ref|YP_977763.1| 555 ADKITDSMREAIDETERRRaKQIAYNEANGIDPqpLRKKI----ADILDQVYREADDTAVVEVGGS 616
                                    5677788888888888877667777777777774333333....3333345555555555555444 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00081       0.8      37      91 ..     260     314 ..     255     316 .. 0.86
   2 ?   -1.7   0.1       2.4   2.4e+03      19      54 ..     536     571 ..     531     577 .. 0.68
   3 ?   -0.6   0.0       1.1   1.1e+03      19      61 ..     652     694 ..     644     697 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00081
                           CdvA  37 kakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairell 91 
                                      +++ e+l +rl+ele+q k le   + ++ +y +  +    + s ie +++++
  gi|121637540|ref|YP_977763.1| 260 AVSAIEEELAERLAELESQGKLLEAQRLRMRTNYDIEMMRQVGFCSGIENYSRHI 314
                                    567899****************************999998888888888877765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                           CdvA  19 tyeeikekleealkklkekakelkeklkkrlkeled 54 
                                      + i +  ++ + ++   a+++ + +++ ++e e 
  gi|121637540|ref|YP_977763.1| 536 LIQTIGRAARNVSGEVHMYADKITDSMREAIDETER 571
                                    555566666666677777788888888888888775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.1
                           CdvA  19 tyeeikekleealkklkekakelkeklkkrlkeledqikslek 61 
                                     ++ ik    + +++ ++ + el+ + + ++++l+ +++ ++ 
  gi|121637540|ref|YP_977763.1| 652 LADLIKDLTAQMMAAARDLQFELAARFRDEIADLKRELRGMDA 694
                                    3444444455555666777778888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 4629.15
//
Query:       gi|121637541|ref|YP_977764.1|  [L=471]
Description: drug efflux membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-32  111.2  67.4    5.2e-32  111.1  64.2    2.2  1  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.55    8.5   5.9        4.7    5.4   1.6    2.4  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1  64.2   5.8e-36   5.2e-32       3     353 .]      27     423 ..      25     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 5.8e-36
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                     +++l+a++ ++++++lp+++  d g     + +++tly +g++va+  +  +  r+G+r+ +l+gl++f+l++l+++ a
  gi|121637541|ref|YP_977764.1|  27 GGVALYATNEFLTISLLPSTI-ADIG-GSRLYAWVTTLYLVGSVVAATTVNTMLLRVGARSSYLMGLAVFGLASLVCAAA 104
                                    57889999999*******766.6667.78889*****************************************7777745 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    +s+ +l+++r lqG+++g+l+ +g+ali    pk+  +r+ +l+sa++++++++gp+ ggl+a+++ Wr++f +++++++
  gi|121637541|ref|YP_977764.1| 105 PSMQILVAGRTLQGIAGGLLAGLGYALINSTLPKSLWTRGSALVSAMWGVATLIGPATGGLFAQLGLWRWAFGVMTLLTA 184
                                    8888***********************************************************9999************* PP

                          MFS_1 163 lafvlfllllpeepperkrkspkeee...............................................kgtgpap 195
                                    l+++l+ + l + ++ ++ ++p+                                                   ++ +a+
  gi|121637541|ref|YP_977764.1| 185 LMAMLVPVALGAGRVGPGGETPVGSThkvpvwslllmgaaalaisvaalpnylvqtagllaaaallvavfvvvDWRIHAA 264
                                    **********999999999988888888999999*******************999999999998888888877777777 PP

                          MFS_1 196 lvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275
                                    ++p   +++ + +l  +++   ++ ++ +++ t++pl+  ++lg  + + ag+l a+la+++ ++ + ++ l      r 
  gi|121637541|ref|YP_977764.1| 265 VLP--PSVFGSGPLK-WIYLTMSVQMIAAMVDTYVPLF-GQRLGHLTPVAAGFLGAALAVGWTVGEVASASLNSA---RV 337
                                    777..5666666663.5666666666***********9.666666625777777777777777775555555533...55 PP

                          MFS_1 276 rlllallllllaalglallavt........ssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntags 346
                                    +  +  ++ l++a glal avt          a+++l +l++iG+g g+++p l++ a+d++  p e+ +a++++n+++ 
  gi|121637541|ref|YP_977764.1| 338 IGHVVAAAPLVMASGLALGAVTqradapvgIIALWAL-ALLIIGTGIGIAWPHLTVRAMDSVaDPAESSAAAAAINVVQL 416
                                    5555555555555555555555555333214444443.8999******************998889999*********** PP

                          MFS_1 347 lggalgp 353
                                    ++ga+g+
  gi|121637541|ref|YP_977764.1| 417 ISGAFGA 423
                                    ****996 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.6   0.00053       4.7     131     188 ..     106     167 ..      58     175 .. 0.80
   2 ?    4.9   0.1   0.00071       6.3     131     193 ..     368     431 ..     207     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00053
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkkn....splylgilyalrilGpalGfllG 188
                                     + +++++ +l+Gi++ ++  lG++ i     k+     s+l  +++ +++++Gpa G l++
  gi|121637541|ref|YP_977764.1| 106 SMQILVAGRTLQGIAGGLLAGLGYALINSTLPKSLwtrgSALVSAMWGVATLIGPATGGLFA 167
                                    45699************************999975111155666666666677777665554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.00071
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 131 lvllfflaqlllGiGatpiyt.lGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                    ++ l  la l++G G    ++ l +  +d  +++ +s+   +++ +++++  a+G  l++++++
  gi|121637541|ref|YP_977764.1| 368 IIALWALALLIIGTGIGIAWPhLTVRAMDSVADPAESSAAAAAINVVQLISGAFGAGLAGVVVN 431
                                    6678999999**99988887659***********************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2930.39
//
Query:       gi|121637542|ref|YP_977765.1|  [L=556]
Description: hypothetical protein BCG_1673c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-08   33.0  18.6    6.2e-08   33.0  18.6    2.7  3  PMT_2          Dolichyl-phosphate-mannose-protein mannosyltra
  ------ inclusion threshold ------
       0.82    9.0   1.6        1.6    8.0   1.6    1.4  1  Sarcoglycan_1  Sarcoglycan complex subunit protein


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  18.6   6.9e-12   6.2e-08       5     154 ..     114     265 ..     111     270 .. 0.91
   2 ?   -2.8   0.1      0.75   6.7e+03     141     156 ..     305     320 ..     282     324 .. 0.57
   3 ?   -0.6   4.5      0.15   1.3e+03      75     109 ..     364     396 ..     330     406 .. 0.47

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.9e-12
                          PMT_2   5 liawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwal 84 
                                    l++ l++ ++++f  +el+ rl+s+la+  +++++   a+++ g+++a+ a +  a++p ++  + + +  a+ v++ ++
  gi|121637542|ref|YP_977765.1| 114 LYYLLMHGWFAIFPPTELWSRLPSCLAIGAAAAGVVVFAKQFSGRTTAVCAGAVFAILPRVTWAGIEARSSALSVAAAVW 193
                                    78999******************************************************8888888************** PP

                          PMT_2  85 alylllraleknklkywllagvlfGlgflsKytaallliaall..yllisarrilkekkpyl.alllalllfs 154
                                    ++ ll+ a+  n  + wll ++++ l++l+  + all++a++    ll+s ++  k+++++  +++ a+l ++
  gi|121637542|ref|YP_977765.1| 194 LTVLLVAAVRCNTQRRWLLYALVLMLSILVSINLALLVPAYATmvPLLAS-GKSRKSPVIWWtVVTAAALGAM 265
                                    **********9999*************************96666788889.8999999999966666665554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.75
                          PMT_2 141 kpylalllalllfspv 156
                                     ++la+l++++ ++++
  gi|121637542|ref|YP_977765.1| 305 FAILAGLIVAAGIAAH 320
                                    3333555555555555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.15
                          PMT_2  75 daplvllwalalylllraleknklkywllagvlfG 109
                                    + +l++  a++++++  ++  +k   wl+agv+f 
  gi|121637542|ref|YP_977765.1| 364 YLILTAPAAAVILAVCVVTIARK--PWLIAGVVFL 396
                                    22222222333333333333333..2444444443 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.6   0.00018       1.6       7      31 ..     207     231 ..     204     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00018
                  Sarcoglycan_1   7 rrkrclyllvllLlllaivnLalti 31 
                                     r+++ly lvl+L +l+ +nLal +
  gi|121637542|ref|YP_977765.1| 207 QRRWLLYALVLMLSILVSINLALLV 231
                                    69********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3599.49
//
Query:       gi|121637543|ref|YP_977766.1|  [L=146]
Description: hypothetical protein BCG_1674 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-25   88.7   3.8    5.8e-25   88.4   3.8    1.1  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.089   12.5   0.0       0.14   11.9   0.0    1.2  1  Binary_toxB_2  Clostridial binary toxin B/anthrax toxin PA do


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   3.8   6.5e-29   5.8e-25       2     141 .]       4     144 ..       3     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 6.5e-29
                                    -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTT CS
                            Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeagg 79 
                                    yk+++V++Dgs++s +A+++A++ a a +a+li++ +  p+  +a+++   + e      ++  +e +   +++a++ag 
  gi|121637543|ref|YP_977766.1|   4 YKTVVVGTDGSDSSMRAVDRAAQIAGA-DAKLIIASAYLPQHEDARAADILKDESYKVTGTAPIYEILHdaKERAHNAGA 82 
                                    9**************************.79****9999988888887777777766666666666655567********* PP

                                    CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    ++ve    +g p ++++ +a+ee+adl+VvG  g+s+++++llGSv  +v r+a+++Vl+V+
  gi|121637543|ref|YP_977766.1|  83 KNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVH 144
                                    ************************************************************96 PP

>> Binary_toxB_2  Clostridial binary toxin B/anthrax toxin PA domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05      0.14      61     120 ..       7      71 ..       3      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                                    EBTSCES-EEEEEEEEESESSSSEESH..HHHHT--TTSBEE...EEEEEEEEE-SSS-BESEEE CS
                  Binary_toxB_2  61 vsagfsnsnsstvaidhslslagertw..aetmglntadtar...lnaniryvntgtapiynvlp 120
                                    v  g   s+ss  a+d +  +ag  +     +  l   + ar   +  +  y  tgtapiy++l 
  gi|121637543|ref|YP_977766.1|   7 VVVGTDGSDSSMRAVDRAAQIAGADAKliIASAYLPQHEDARaadILKDESYKVTGTAPIYEILH 71 
                                    7788999**************997653114444555555555111556678***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1015.78
//
Query:       gi|121637544|ref|YP_977767.1|  [L=264]
Description: hypothetical protein BCG_1675c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-10   40.3   5.5    6.1e-10   39.4   5.5    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00025   20.6   1.9    0.00065   19.3   1.9    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00036   20.1   0.0    0.00052   19.6   0.0    1.2  1  Lactamase_B_5  Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.017   15.0   0.6      0.053   13.4   0.6    1.9  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   5.5   1.4e-13   6.1e-10       2     173 ..      72     225 ..      71     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.4e-13
                                    CCCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                    Lactamase_B   2 gpdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                    gp   n+yl++    g+++LiD+  ++e    +     +++   ++  ++ +H H+DH  +l  ++ at++p++a++++a
  gi|121637544|ref|YP_977767.1|  72 GPMDNNAYLVTcsATGETLLIDAANDAEVLIDL-----VRRYAPKLALIVTSHQHFDHWQALQAVAAATGAPTAAHPIDA 146
                                    56678*******999****************98.....9999999*********************************** PP

                                    HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCE.....EEECTTTSS CS
                    Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkv.....lftGDalla 154
                                      l+                        + +  +d+ + g +++ v++  gh++g++ + +gg  +     lftGD l++
  gi|121637544|ref|YP_977767.1| 147 DPLPVKPD--------------------RLLTHGDSVRIGELTFDVIHLRGHTPGSIALALGGPVTggvtqLFTGDCLFP 206
                                    ********....................******************************9998776656666********* PP

                                    HHCCCCCC.TTCEEE-SHC CS
                    Lactamase_B 155 getgridltlrgaevrdps 173
                                    g  g++  + ++ + +d++
  gi|121637544|ref|YP_977767.1| 207 GGVGKTWQPADFTQLLDDV 225
                                    **99999933333333333 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.9   1.4e-07   0.00065       3     160 ..      90     219 ..      88     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-07
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                    +LiDa  d        l     r+  p++++++ +h+H+DH + l  +++ ++        +  +  ++a   +   +  
  gi|121637544|ref|YP_977767.1|  90 LLIDAANDAEVL--IDL----VRRYAPKLALIVTSHQHFDHWQALQAVAAATG-------APTAAHPIDADPLPVKPD-- 154
                                    799999993322..222....345579***************98888888332.......223333333332222222.. PP

                                    TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE...CTTEEEEEESS-S---HHHHHHHCT-SE CS
                  Lactamase_B_2  83 pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie...gggkrvyyigDtgyipeeigerlggadl 159
                                         + l+ g+s+++g  +l++ ++ +r+ ++          ++l+++   +gg + +++gD+  +p+ +g+  ++ad 
  gi|121637544|ref|YP_977767.1| 155 -----RLLTHGDSVRIG--ELTFDVIHLRGHTPG--------SIALALGgpvTGGVTQLFTGDCL-FPGGVGKTWQPADF 218
                                    .....458899*****9..689999999999999........55566555555999999999998.88888988888887 PP

                                    E CS
                  Lactamase_B_2 160 l 160
                                    +
  gi|121637544|ref|YP_977767.1| 219 T 219
                                    5 PP

>> Lactamase_B_5  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-07   0.00052      56     129 ..     111     189 ..      73     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                  Lactamase_B_5  56 vawivltns...dhlraakeiaeltyakiagpaaeketfpiacdrwlsdgdelvsg...lkvlelkgsktpgelalllee 129
                                       +++t     dh +a +++a  t+a  a+   + + +p++ dr l+ gd +  g   ++v++l+g +tpg +al l +
  gi|121637544|ref|YP_977767.1| 111 KLALIVTSHqhfDHWQALQAVAAATGAPTAAHPIDADPLPVKPDRLLTHGDSVRIGeltFDVIHLRG-HTPGSIALALGG 189
                                    555566654122778999************9999******************977743346888998.69*****99864 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   1.2e-05     0.053       9      81 ..      89     173 ..      74     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                  Lactamase_B_3   9 sflleta.garilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql.................aenvkvleeges 70 
                                    ++l++ a +a++l+D       +++ a++  l++ s+++ dH+++ +  ++                  +  ++l++g+s
  gi|121637544|ref|YP_977767.1|  89 TLLIDAAnDAEVLIDL------VRRYAPKLALIVTSHQHFDHWQALQAVAAatgaptaahpidadplpVKPDRLLTHGDS 162
                                    4455553245555554......457889**************98755444457777776666666666444456666777 PP

                  Lactamase_B_3  71 levggleirav 81 
                                    +++g+l +  +
  gi|121637544|ref|YP_977767.1| 163 VRIGELTFDVI 173
                                    77777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1797.07
//
Query:       gi|121637545|ref|YP_977768.1|  [L=972]
Description: excinuclease ABC subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-41  139.2   0.1    1.4e-40  137.7   0.0    1.8  1  UvrA_inter       UvrA interaction domain
    3.5e-35  120.7   0.0    1.2e-32  112.6   0.0    3.5  3  UvrA_DNA-bind    UvrA DNA-binding domain
      2e-17   64.0   0.0    1.1e-08   35.7   0.0    4.4  3  ABC_tran         ABC transporter
    3.1e-08   34.2   0.3      0.013   15.9   0.0    3.0  2  AAA_16           AAA ATPase domain
    7.2e-08   32.1   0.0        0.7    9.3   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.5e-07   31.1   0.1     0.0021   17.8   0.1    2.5  2  AAA_29           P-loop containing region of AAA domain
    1.7e-06   28.1   0.9       0.04   13.7   0.0    4.0  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.5e-05   24.7   0.7      0.075   12.6   0.0    3.0  2  AAA_25           AAA domain
    2.6e-05   24.2   0.2      0.066   13.1   0.2    2.3  2  RsgA_GTPase      RsgA GTPase
    0.00019   21.6   0.4          1    9.5   0.0    3.3  3  AAA_33           AAA domain
    0.00052   19.9   0.0     0.0012   18.8   0.0    1.5  1  DUF2083          Predicted transcriptional regulator (DUF2083
    0.00053   19.9   0.1       0.51   10.2   0.0    2.7  2  APS_kinase       Adenylylsulphate kinase
    0.00069   20.2   0.0        1.3    9.5   0.0    2.4  2  AAA_23           AAA domain
     0.0038   17.8   0.0          3    8.4   0.0    2.7  2  AAA_18           AAA domain
     0.0044   17.3   0.0        2.6    8.3   0.0    3.2  3  AAA_22           AAA domain
      0.005   17.2   4.8       0.21   12.0   0.3    3.8  4  DnaJ_CXXCXGXG    DnaJ central domain
  ------ inclusion threshold ------
      0.016   15.2   0.0       0.61   10.0   0.0    2.4  2  NACHT            NACHT domain
      0.033   13.8   1.9       0.41   10.2   0.1    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.05   13.3   0.0        0.5   10.1   0.1    2.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.067   13.6   0.0        3.5    8.1   0.0    2.4  2  RNA_helicase     RNA helicase
      0.084   12.6   0.0         30    4.2   0.0    3.3  4  AAA_15           AAA ATPase domain
      0.086   12.7   0.0       0.24   11.2   0.0    1.9  1  DUF1421          UBA-like domain (DUF1421)
      0.089   12.9   0.6        3.8    7.6   0.1    2.8  2  MMR_HSR1         50S ribosome-binding GTPase
       0.12   11.4   0.1        3.9    6.4   0.1    2.4  2  T2SSE            Type II/IV secretion system protein
       0.27   10.4   0.1        5.6    6.1   0.1    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.29   11.3  10.9        2.1    8.5   0.0    4.7  5  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0     2e-43   1.4e-40       1     108 [.     131     238 ..     131     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 2e-43
                     UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydldedieldknkkhsievvvDrlvv 80 
                                    Q+++qIvdq+l+++egt++l+laPvvr rkgef +l+++l+ +G++rvr+Dg ++ l++ ++l+k++kh+ievvvDrl+v
  gi|121637545|ref|YP_977768.1| 131 QTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFADLFDKLNAQGYSRVRVDGVVHPLTDPPKLKKQEKHDIEVVVDRLTV 210
                                    9******************************************************************************* PP

                     UvrA_inter  81 kkeersrlaesvetAlklgeglvivsev 108
                                    k   ++rl++svetAl+l++g+v+ ++v
  gi|121637545|ref|YP_977768.1| 211 KAAAKRRLTDSVETALNLADGIVVLEFV 238
                                    ***********************99876 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.4   2.8e+02      79     108 ..      37      66 ..      27      68 .. 0.85
   2 !  112.6   0.0   1.7e-35   1.2e-32       1     109 [.     295     404 ..     295     405 .. 0.97
   3 ?    1.3   0.0      0.64   4.4e+02      22      70 ..     463     511 ..     442     520 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.4
                                    ......---HHHHHHHHHH-------HHHH CS
                  UvrA_DNA-bind  79 rsyektfeGvipnlerryreteSeavreel 108
                                     + +  f+ +  + +rry e+ S ++r+ l
  gi|121637545|ref|YP_977768.1|  37 GKSSLAFDTIFAEGQRRYVESLSAYARQFL 66 
                                    5667789999999**************966 PP

  == domain 2  score: 112.6 bits;  conditional E-value: 1.7e-35
                                    -S----.-----------GGG...TT-HHHHHHHHHHHTTTS------------S-THHHHH----.............. CS
                  UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapw.sskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggrkr 79 
                                    Dp+lvvpdp+++la+gA+apw + ++ +y+ ++++++ e +g+d+dtp+++Lp+++++++L G++e++ +++++++gr+r
  gi|121637545|ref|YP_977768.1| 295 DPELVVPDPDRTLAQGAVAPWsNGHTAEYFTRMMAGLGEALGFDVDTPWRKLPAKARKAILEGADEQVHVRYRNRYGRTR 374
                                    9********************999999**************************************9998888888***** PP

                                    .....---HHHHHHHHHH-------HHHHH CS
                  UvrA_DNA-bind  80 syektfeGvipnlerryreteSeavreele 109
                                    sy++ feGv+  l+r++ +teSe+++e++e
  gi|121637545|ref|YP_977768.1| 375 SYYADFEGVLAFLQRKMSQTESEQMKERYE 404
                                    ****************************98 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.64
                                    ..TT-HHHHHHHHHHHTTTS------------S-THHHHH----..... CS
                  UvrA_DNA-bind  22 sskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikv 70 
                                      +++ +  q+l+++  ++g+ ld+ ++ L+ +   + L G + ++i+ 
  gi|121637545|ref|YP_977768.1| 463 GPREQAIAGQVLKEIRSRLGFLLDVGLEYLSLSRAAATLSGGEAQRIRL 511
                                    667888999******************************9999988876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00035      0.24       1      28 [.      15      42 ..      15      52 .. 0.92
   2 !    9.9   0.0    0.0014      0.98      97     135 ..     489     529 ..     386     531 .. 0.81
   3 !   35.7   0.0   1.6e-11   1.1e-08       1     136 [.     637     873 ..     637     874 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                                   EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                   l+ v+l+l ++ +++++G +G+GKS+L+
  gi|121637545|ref|YP_977768.1| 15 LRSVDLDLPRDALIVFTGLSGSGKSSLA 42
                                   57899*********************95 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                    TTCBGESTTSGGS-HHHHHHHHHHHHHHHT..SSEEEEEST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran  97 lkdtvvksspssLSgGqkqrvalarallkk..pkllllDEp 135
                                    l+   +++ +++LSgG+ qr+ la  + +     l++lDEp
  gi|121637545|ref|YP_977768.1| 489 LEYLSLSRAAATLSGGEAQRIRLATQIGSGlvGVLYVLDEP 529
                                    45555666679*************99877622468888988 PP

  == domain 3  score: 35.7 bits;  conditional E-value: 1.6e-11
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE...................EETTCEGGGB-HHHCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx...................xxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei...................lldgkdlkeqeleslrk 59 
                                    l+ +++++  g ++ ++G +G+GKStL++ ++  +     +G                     ++d+ ++ +++++    
  gi|121637545|ref|YP_977768.1| 637 LRGIDVSFPLGVLTSVTGVSGSGKSTLVNDILAAVLAnrLNGARqvpgrhtrvtgldyldklvRVDQSPIGRTPRSNPAT 716
                                    578999**********************9887766543445554667777888888888888888888888888888888 PP

                                    CEEEE-SS--S-TTSBHHHH............................................................ CS
                                    xxxxxxxxxxxxxxxxxxxx............................................................ RF
                       ABC_tran  60 eigvlpqepqlfpeltvren............................................................ 79 
                                      gv+ +  +lf  +t ++                                                             
  gi|121637545|ref|YP_977768.1| 717 YTGVFDKIRTLFAATTEAKVrgyqpgrfsfnvkggrceactgdgtikiemnflpdvyvpcevcqgarynretlevhykgk 796
                                    888888888888888744447***********************************************999999999998 PP

                                    ..........HHHTC.......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT...SSEEEEESTT CS
                                    ..........xxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                       ABC_tran  80 ..........esdee.......iekalsklglkelkdtvvksspssLSgGqkqrvalarallkk...pkllllDEpt 136
                                              e+ +e       ++++l++l +++l   ++++ + +LSgG+ qrv+la  l k+   +++++lDEpt
  gi|121637545|ref|YP_977768.1| 797 tvsevldmsiEEAAEffepiagVHRYLRTLVDVGLGYVRLGQPAPTLSGGEAQRVKLASELQKRstgRTVYILDEPT 873
                                    888888777633333677777799****************9999****************987622268*******9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.9e-05     0.027      25      86 ..      26      90 ..      12     176 .. 0.80
   2 !   15.9   0.0   1.9e-05     0.013      26      59 ..     649     685 ..     639     711 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
                         AAA_16 25 elvllsGesGvGKsslv.rellralekdggif..lrgkcdql..esaipysalaqalareellrqll 86
                                    l++++G sG+GKssl+ ++++ + ++   ++  l++ ++q+  +++ p + +++ l+    + q  
  gi|121637545|ref|YP_977768.1| 26 ALIVFTGLSGSGKSSLAfDTIFAEGQR--RYVesLSAYARQFlgQMDKPDVDFIEGLSPAVSIDQKS 90
                                   5799*************9999964444..46666999999999999999777988886655555444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.9e-05
                         AAA_16  26 lvllsGesGvGKsslvrellralekd...ggiflrgk 59 
                                    l+ ++G sG+GKs+lv+ +l a+ ++   g+  + g+
  gi|121637545|ref|YP_977768.1| 649 LTSVTGVSGSGKSTLVNDILAAVLANrlnGARQVPGR 685
                                    5789****************99888844333334444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.022        15       4      51 ..       4      52 ..       1      69 [. 0.74
   2 !    9.3   0.0     0.001       0.7     135     211 ..     349     574 ..     126     580 .. 0.67
   3 ?    5.2   0.1     0.018        12      26      44 ..     649     667 ..     627     681 .. 0.83
   4 !    7.5   0.0    0.0035       2.4     136     209 ..     842     915 ..     711     922 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.022
                                   EEEEESETTEECEEEEEETTSS.EEEEEESTTSSHHHH.HHHHHHHCTT. CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          SMC_N  4 rleienFksyagktvilpfsks.ftaivGpNGSGKsnl.ldAilFvLGer 51
                                   rl++++ +  + ++v+l++ +  + + +G  GSGKs+l +d i F  G+r
  gi|121637545|ref|YP_977768.1|  4 RLIVKGAREHNLRSVDLDLPRDaLIVFTGLSGSGKSSLaFDTI-FAEGQR 52
                                   6777777777777777777654156678*********945777.776654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                                    T............................................................................... CS
                                    x............................................................................... RF
                          SMC_N 135 e............................................................................... 135
                                    +                                                                               
  gi|121637545|ref|YP_977768.1| 349 Karkailegadeqvhvryrnrygrtrsyyadfegvlaflqrkmsqteseqmkeryegfmrdvpcpvcagtrlkpeilavt 428
                                    05555555555555555555555555555555555555555555555555566666666666666666666666666666 PP

                                    .......................................................................CS-HHHHHH CS
                                    .......................................................................xxxxxxxxx RF
                          SMC_N 136 .......................................................................lLSgGektL 144
                                                                                                           +LSgGe + 
  gi|121637545|ref|YP_977768.1| 429 lageskgehgaksiaevcelsiadcadflnaltlgpreqaiagqvlkeirsrlgflldvgleylslsraaaTLSGGEAQR 508
                                    66666666666666666666666666666666666667777777777777777777777777777777777899999887 PP

                                    HHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 145 valaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                    + la    i +     ly+lDe    L ++  +++ e l + ++    +iv+ ++e+++e+ad +v +
  gi|121637545|ref|YP_977768.1| 509 IRLATQ--IGSGLVGVLYVLDEPSIGLHQRDNRRLIETLTRLRDLgNTLIVVEHDEDTIEHADWIVDI 574
                                    766665..55556678******************999999988875889*************998876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.018
                                    EEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAi 44 
                                    +t+++G  GSGKs l++ i
  gi|121637545|ref|YP_977768.1| 649 LTSVTGVSGSGKSTLVNDI 667
                                    699***********99877 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0035
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklv 209
                                    +LSgGe + v la  +  ++   + +y+lDe    L +  ++k+ ++++   ++   +ivi ++ ++++ +d ++
  gi|121637545|ref|YP_977768.1| 842 TLSGGEAQRVKLASELQ-KRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKgNTVIVIEHNLDVIKTSDWII 915
                                    79****99999998864.45567899***********************776665899*****999999887665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00052      0.36      17      38 ..      20      41 ..      11      52 .. 0.75
   2 !   17.8   0.1     3e-06    0.0021      23      50 ..     647     675 ..     634     681 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                         AAA_29 17 ieidlkgatlltGpsGsGKSTl 38
                                   +++ ++  +++tG sGsGKS+l
  gi|121637545|ref|YP_977768.1| 20 LDLPRDALIVFTGLSGSGKSSL 41
                                   44444448899*********98 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3e-06
                         AAA_29  23 g.atlltGpsGsGKSTllDAiqalLvpak 50 
                                    g  t +tG sGsGKSTl+  i a  ++++
  gi|121637545|ref|YP_977768.1| 647 GvLTSVTGVSGSGKSTLVNDILAAVLANR 675
                                    44899*************77666666554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.46   3.2e+02       2      15 ..      28      41 ..      27      73 .. 0.92
   2 ?    5.9   0.1     0.014       9.3     237     295 ..     501     558 ..     475     565 .. 0.82
   3 ?    2.4   0.1      0.16   1.1e+02       1      19 [.     649     667 ..     649     692 .. 0.78
   4 !   13.7   0.0   5.8e-05      0.04     237     298 ..     843     904 ..     835     909 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                         AAA_21  2 nvliGpNgsGKSnL 15
                                    v++G  gsGKS+L
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSL 41
                                   7999********98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                    lS G  + ++l+t + + l    l+++DEp  gLH +  rrl+e l +l++ g  +i++
  gi|121637545|ref|YP_977768.1| 501 LSGGEAQRIRLATQIGSGLVG-VLYVLDEPSIGLHQRDNRRLIETLTRLRDLGNTLIVV 558
                                    566665555788888887777.799***********99999999999999888888875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.16
                         AAA_21   1 lnvliGpNgsGKSnLLdal 19 
                                    l+ ++G  gsGKS+L   +
  gi|121637545|ref|YP_977768.1| 649 LTSVTGVSGSGKSTLVNDI 667
                                    57799*********98666 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 5.8e-05
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    lS G  +  +l++ l  +   ++++++DEp +gLH   +r+ll +++ l ++g  vi+  H+
  gi|121637545|ref|YP_977768.1| 843 LSGGEAQRVKLASELQKRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGNTVIVIEHN 904
                                    5555555557888888888888**********************998888888888886555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0014      0.95      30      53 ..      22      45 ..       9      50 .. 0.87
   2 !   12.6   0.0   0.00011     0.075      30      65 ..     644     678 ..     624     693 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                         AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                   lp+++l++++G +g+GK+ la d 
  gi|121637545|ref|YP_977768.1| 22 LPRDALIVFTGLSGSGKSSLAFDT 45
                                   79*******************986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                         AAA_25  30 lpagelallaGapgtGKttlaldlalavatGkpwlg 65 
                                     p+g l+ ++G +g+GK+tl+ d+ +av+  + + g
  gi|121637545|ref|YP_977768.1| 644 FPLGVLTSVTGVSGSGKSTLVNDILAAVLANR-LNG 678
                                    599*************************9765.556 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0025       1.7      88     116 ..      13      42 ..       3      60 .. 0.77
   2 !   13.1   0.2   9.5e-05     0.066     101     140 ..     649     687 ..     628     693 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                                    TTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                    RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLi 116
                                    ++l+++   l    ++v+ G SG GKS+L 
  gi|121637545|ref|YP_977768.1|  13 HNLRSVDLDLPRdALIVFTGLSGSGKSSLA 42 
                                    5555665555444899************95 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.5e-05
                                    EEEEECSTTSSHHHHHHHHCTT-.----S------------ CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel.elktgevseklgrGkhT 140
                                    ++ + G SG GKStL+n +l      + +   +++  G+hT
  gi|121637545|ref|YP_977768.1| 649 LTSVTGVSGSGKSTLVNDILAAVlANRLNG--ARQVPGRHT 687
                                    56789*************998631444444..444678887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0031       2.2       1      16 [.      27      42 ..      27      67 .. 0.91
   2 ?   -2.8   0.0       9.6   6.6e+03      81     113 ..     535     567 ..     520     568 .. 0.58
   3 !    9.5   0.0    0.0015         1       4      28 ..     652     676 ..     649     732 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                         AAA_33  1 lvllvGlpGsGKstla 16
                                   l+++ Gl+GsGKs la
  gi|121637545|ref|YP_977768.1| 27 LIVFTGLSGSGKSSLA 42
                                   799**********998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.6
                         AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlke 113
                                    +r++r+ +  l r  +   +++vve de+t+++
  gi|121637545|ref|YP_977768.1| 535 QRDNRRLIETLTRLRDLGNTLIVVEHDEDTIEH 567
                                    334444444444444555778888888888876 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                         AAA_33   4 lvGlpGsGKstlaerllkklgavll 28 
                                    + G++GsGKstl+  +l++  a +l
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAAVLANRL 676
                                    78***********998866555555 PP

>> DUF2083  Predicted transcriptional regulator (DUF2083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-06    0.0012      32      84 ..     111     164 ..      98     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                        DUF2083  32 fqfarfgg.aCPlwnvheafetpgrilvqlaelpdgeryltiartvekesgafg 84 
                                    + +ar+g  +CP      a +tp++i+ q++ +p+g+r+l++a  v++++g+f+
  gi|121637545|ref|YP_977768.1| 111 LLYARAGTpHCPTCGERVARQTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFA 164
                                    556666653799999999****************************99998876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00074      0.51       3      20 ..      26      43 ..      24      56 .. 0.85
   2 !    6.9   0.1    0.0079       5.4       6      27 ..     651     672 ..     646     692 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
                                   EEEEEESSTTSSHHHHHH CS
                     APS_kinase  3 vvvwltGlsgsGKstian 20
                                   + + +tGlsgsGKs++a+
  gi|121637545|ref|YP_977768.1| 26 ALIVFTGLSGSGKSSLAF 43
                                   6799************97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0079
                                    EEESSTTSSHHHHHHHHHHHHH CS
                     APS_kinase   6 wltGlsgsGKstianalekkLv 27 
                                     +tG+sgsGKst+ n +  ++ 
  gi|121637545|ref|YP_977768.1| 651 SVTGVSGSGKSTLVNDILAAVL 672
                                    68**********9887654443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0019       1.3       1      35 [.       4      41 ..       4      46 .. 0.85
   2 !    8.4   0.0    0.0042       2.9      21      42 ..     649     670 ..     627     753 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                         AAA_23  1 kLkienfrsf..rdqeidF.skgltlItGpNGaGKTTi 35
                                   +L +++ r +  r +++d+  + l ++tG  G+GK+++
  gi|121637545|ref|YP_977768.1|  4 RLIVKGAREHnlRSVDLDLpRDALIVFTGLSGSGKSSL 41
                                   68889999996666777778889*************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                         AAA_23  21 ltlItGpNGaGKTTildAikla 42 
                                    lt +tG  G+GK+T+++ i  a
  gi|121637545|ref|YP_977768.1| 649 LTSVTGVSGSGKSTLVNDILAA 670
                                    8999************655554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.019        13       1      15 [.      28      42 ..      28      60 .. 0.95
   2 !    8.4   0.0    0.0043         3       3      18 ..     652     667 ..     651     723 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                         AAA_18  1 IlltGtpGvGKttla 15
                                   I+ tG +G+GK++la
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSLA 42
                                   899**********98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0043
                         AAA_18   3 ltGtpGvGKttlakeL 18 
                                    +tG++G+GK+tl + +
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDI 667
                                    8***********9877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.05        34       6      22 ..      26      42 ..      23      64 .. 0.91
   2 !    8.3   0.0    0.0037       2.6       8      28 ..     650     670 ..     648     694 .. 0.84
   3 ?   -1.9   0.0       5.4   3.7e+03      81     103 ..     852     876 ..     833     901 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.05
                         AAA_22  6 gilvvtGesGtGKTtll 22
                                    ++v tG sG+GK+ l+
  gi|121637545|ref|YP_977768.1| 26 ALIVFTGLSGSGKSSLA 42
                                   57999*********986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                         AAA_22   8 lvvtGesGtGKTtllrrlleq 28 
                                    + vtG sG+GK+tl++ +l  
  gi|121637545|ref|YP_977768.1| 650 TSVTGVSGSGKSTLVNDILAA 670
                                    579***********9988765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.4
                         AAA_22  81 aleqalrarav.ielliiDEaqh.l 103
                                    +l+  l++r++ + + i+DE    l
  gi|121637545|ref|YP_977768.1| 852 KLASELQKRSTgRTVYILDEPTTgL 876
                                    4566677777788999999976666 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.2   4.3e+03      16      21 ..     120     125 ..     114     141 .. 0.62
   2 ?    2.8   0.0      0.22   1.5e+02      16      25 ..     281     290 ..     270     301 .. 0.72
   3 ?    1.0   0.0      0.79   5.5e+02      41      50 ..     409     418 ..     390     424 .. 0.60
   4 !   12.0   0.3    0.0003      0.21      16      51 ..     752     783 ..     740     789 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.2
                  DnaJ_CXXCXGXG  16 tCktCk 21 
                                    +C+tC+
  gi|121637545|ref|YP_977768.1| 120 HCPTCG 125
                                    366664 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.22
                  DnaJ_CXXCXGXG  16 tCktCkGsGv 25 
                                     C++C+G G 
  gi|121637545|ref|YP_977768.1| 281 ACPECSGLGI 290
                                    5888888773 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.79
                  DnaJ_CXXCXGXG  41 qstCpeCeGt 50 
                                      +Cp C Gt
  gi|121637545|ref|YP_977768.1| 409 DVPCPVCAGT 418
                                    3456666655 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.0003
                  DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                                    +C++C G G+++ e++    f   +  +C+ C+G  
  gi|121637545|ref|YP_977768.1| 752 RCEACTGDGTIKIEMN----FLPDVYVPCEVCQGAR 783
                                    7********7666653....45566789*****975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.19   1.3e+02       2      17 ..      27      42 ..      26      60 .. 0.83
   2 ?   10.0   0.0   0.00088      0.61       5      32 ..     652     679 ..     649     683 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                                   CEEEEC-TTTCHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLl 17
                                   l++ +G +GsGK+ L+
  gi|121637545|ref|YP_977768.1| 27 LIVFTGLSGSGKSSLA 42
                                   68999*********98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00088
                                    EEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                          NACHT   5 lqGeaGsGKTtLlqklalawaegklpqg 32 
                                    ++G +GsGK+tL+  +  a  +++l++ 
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAAVLANRLNGA 679
                                    89**************999888888775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16   1.1e+02       3      21 ..      28      46 ..      26      56 .. 0.78
   2 ?   10.2   0.1   0.00059      0.41       3      22 ..     650     669 ..     648     680 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                                   EEEEESTTCCHHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhll 21
                                   +v+tG  GsGK++L   ++
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSLAFDTI 46
                                   799**********977766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00059
                                    EEEEESTTCCHHHHHHHHHC CS
                           cobW   3 tvltGflGsGKTtLlnhlle 22 
                                    t +tG  GsGK+tL+n +l+
  gi|121637545|ref|YP_977768.1| 650 TSVTGVSGSGKSTLVNDILA 669
                                    789**************994 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   7.6e+02       1      15 [.      28      42 ..      28      84 .. 0.80
   2 ?   10.1   0.1   0.00072       0.5       3      21 ..     652     670 ..     650     692 .. 0.85
   3 ?   -2.8   0.0       6.1   4.2e+03     110     135 ..     849     874 ..     846     897 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                Viral_helicase1  1 ivvhGvpGcGKStli 15
                                   iv  G  G+GKS+l 
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSLA 42
                                   678999******975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00072
                Viral_helicase1   3 vhGvpGcGKStlirkllrt 21 
                                    v Gv G+GKStl+ ++l  
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAA 670
                                    99*************9977 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.1
                Viral_helicase1 110 llahlpsslshrvgrrttyllpsdva 135
                                    ++ +l s+l++r++ rt+y+l + ++
  gi|121637545|ref|YP_977768.1| 849 QRVKLASELQKRSTGRTVYILDEPTT 874
                                    56677788888888888888876665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.19   1.3e+02       1      17 [.      28      44 ..      28      66 .. 0.85
   2 ?    8.1   0.0    0.0051       3.5       3      25 ..     652     674 ..     650     698 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.19
                   RNA_helicase  1 iwlyGpsgeGKStlake 17
                                   i+++G sg GKS+la +
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSLAFD 44
                                   7899*********9976 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0051
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkk 25 
                                    ++G sg GKStl++++ +a+l +
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAAVLAN 674
                                    7899***********88887744 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.79   5.5e+02      15      40 ..      16      42 ..      13      69 .. 0.86
   2 ?    4.2   0.0     0.043        30     325     356 ..     522     553 ..     505     563 .. 0.87
   3 ?   -2.6   0.1       4.8   3.3e+03      17      41 ..     642     665 ..     636     673 .. 0.77
   4 ?    3.1   0.0     0.093        64     320     365 ..     860     904 ..     847     908 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.79
                         AAA_15 15 kdveidlsee.ltvliGkNnsGKSsil 40
                                   ++v++dl  + l v+ G  +sGKSs++
  gi|121637545|ref|YP_977768.1| 16 RSVDLDLPRDaLIVFTGLSGSGKSSLA 42
                                   566677777779*************84 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.043
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnk 356
                                    v+++++EP + LH    + li++l +l + ++
  gi|121637545|ref|YP_977768.1| 522 VLYVLDEPSIGLHQRDNRRLIETLTRLRDLGN 553
                                    799*********************99987776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.8
                         AAA_15  17 veidlseeltvliGkNnsGKSsile 41 
                                    v+ +l   lt + G  +sGKS++++
  gi|121637545|ref|YP_977768.1| 642 VSFPLGV-LTSVTGVSGSGKSTLVN 665
                                    4555666.89999999******986 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.093
                         AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    +++   +++++EP + LH +  + l + +  l+++++  vi+  H+
  gi|121637545|ref|YP_977768.1| 860 RSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGN-TVIVIEHN 904
                                    45556799****************************9.67766666 PP

>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00035      0.24       2      42 ..     164     209 ..     163     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                        DUF1421   2 ddlidkvasMGfrrDqVrsvvqrmve.....aGqpvDfNvvlDkLs 42 
                                     dl+dk+ + G++r +V++vv ++++      ++  D  vv D+L 
  gi|121637545|ref|YP_977768.1| 164 ADLFDKLNAQGYSRVRVDGVVHPLTDppklkKQEKHDIEVVVDRLT 209
                                    59**********************9733333566677777777775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.27   1.8e+02       2      15 ..      28      41 ..      27      56 .. 0.90
   2 ?    7.6   0.1    0.0056       3.8       4      22 ..     652     670 ..     650     694 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                                   EEEEESTTSSHHHH CS
                       MMR_HSR1  2 vaivGrpNvGKStL 15
                                   +++ G + +GKS+L
  gi|121637545|ref|YP_977768.1| 28 IVFTGLSGSGKSSL 41
                                   7899*********9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0056
                                    EEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   4 ivGrpNvGKStLinaltge 22 
                                    + G + +GKStL+n ++ +
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAA 670
                                    7899***********9875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.13        86     127     146 ..      23      42 ..       2      53 .. 0.75
   2 ?    6.4   0.1    0.0057       3.9     134     154 ..     652     672 ..     641     677 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.13
                          T2SSE 127 rerglilvsGgTgsGKttll 146
                                     +  li+++G  gsGK+ l+
  gi|121637545|ref|YP_977768.1|  23 PRDALIVFTGLSGSGKSSLA 42 
                                    47789***********9876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0057
                          T2SSE 134 vsGgTgsGKttllyallkein 154
                                    v+G  gsGK+tl++ +l+ + 
  gi|121637545|ref|YP_977768.1| 652 VTGVSGSGKSTLVNDILAAVL 672
                                    9**************999875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.15   1.1e+02       2      24 ..      26      48 ..      25      66 .. 0.78
   2 ?    6.1   0.1    0.0082       5.6       5      25 ..     651     671 ..     648     690 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                        DUF2075  2 avvlVtGvaGtGKtvvllnllae 24
                                   a+++ tG +G+GK+ +++  +++
  gi|121637545|ref|YP_977768.1| 26 ALIVFTGLSGSGKSSLAFDTIFA 48
                                   57899*********999976654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0082
                        DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                     VtGv+G+GK+ + + +la++
  gi|121637545|ref|YP_977768.1| 651 SVTGVSGSGKSTLVNDILAAV 671
                                    59**************99987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.003       2.1      26      39 ..     117     131 ..     104     132 .. 0.77
   2 ?   -1.5   0.0         4   2.8e+03      19      36 ..     249     265 ..     246     268 .. 0.70
   3 ?    2.6   0.5      0.22   1.5e+02      22      38 ..     274     292 ..     257     294 .. 0.75
   4 ?    1.7   0.1      0.41   2.8e+02      26      35 ..     409     419 ..     392     421 .. 0.71
   5 ?    1.2   0.4      0.58     4e+02       7      37 ..     752     785 ..     752     787 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.003
                    Zn-ribbon_8  26 lta.CPeCgsevrrv 39 
                                     t+ CP+Cg++v r+
  gi|121637545|ref|YP_977768.1| 117 GTPhCPTCGERVARQ 131
                                    3455******99996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4
                    Zn-ribbon_8  19 qsisdapltaCPeCgs.ev 36 
                                    q++s+  + aCP+ ++ +v
  gi|121637545|ref|YP_977768.1| 249 QRFSE--KLACPNGHAlAV 265
                                    55663..566**9998555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.22
                    Zn-ribbon_8  22 s.dapltaCPeCgs.evrr 38 
                                    s  +p  aCPeC +   r+
  gi|121637545|ref|YP_977768.1| 274 SfNSPYGACPECSGlGIRK 292
                                    43666667****9877776 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.41
                    Zn-ribbon_8  26 ltaCPeCgs.e 35 
                                    +++CP C + +
  gi|121637545|ref|YP_977768.1| 409 DVPCPVCAGtR 419
                                    556****9855 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.58
                    Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs.evr 37 
                                    rCe+C  + ++  +++  ++  + C  C++ +  
  gi|121637545|ref|YP_977768.1| 752 RCEACTGDGTIKIEMNfLPDVYVpCEVCQGaRYN 785
                                    799999999977778866777778****986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (972 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.82u 0.25s 00:00:01.06 Elapsed: 00:00:00.43
# Mc/sec: 6787.29
//
Query:       gi|121637546|ref|YP_977769.1|  [L=85]
Description: hypothetical protein BCG_1677c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 648.20
//
Query:       gi|121637547|ref|YP_977770.1|  [L=489]
Description: hypothetical protein BCG_1678c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-11   42.6   0.0    9.5e-11   41.8   0.0    1.4  1  Esterase      Putative esterase
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.037   13.5   0.1    1.6  2  Peptidase_S9  Prolyl oligopeptidase family
      0.096   11.9   0.0       0.19   10.9   0.0    1.5  1  Hydrolase_4   Serine aminopeptidase, S33
        6.8    6.3  17.3          6    6.5   7.4    2.5  2  DUF4131       Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   2.1e-14   9.5e-11      12     194 ..     200     392 ..     194     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.1e-14
                                    EEE.CC..........GGTTTEEEEEEE--T....THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSB CS
                       Esterase  12 vyLPedy.........spgrkypvvylldGl....tgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlg 78 
                                    vyLP+ +         +p  ++p+v++  G+     +w + ++a ++l++ a+ +    +++v+v+ gg+ ++++++   
  gi|121637547|ref|YP_977770.1| 200 VYLPPAWfdrehrsenPPPPQLPTVMMIGGQfntpADWARAGNAVKTLDDFAAAHSGNAPVVVFVDSGGAFNNDTECV-- 277
                                    88898888888776666777899***********************************************96666655.. PP

                                    B.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCC..EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC... CS
                       Esterase  79 arfyenategpgaeayetfltqeLlplldanfrtapdg..ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps... 153
                                             ++ + +  + lt+ ++p+  ++f ++p++    ++G SmGG+ A+ l + hp++F+     ++  +p    
  gi|121637547|ref|YP_977770.1| 278 ---------NGRRGNAADHLTKDVVPYMVSKFGVSPEQtsWGIVGWSMGGTCAVDLTVMHPTLFSAFVDIAGDFYPNagn 348
                                    .........4456666789*******************8889**********************7777777666666555 PP

                                    .....HCHHHC...TTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTB CS
                       Esterase 154 .....namWgq...eekeawqendpvllakelsaslkalriyldvGtse 194
                                              +    +++aw + dp+  + +   s+++l+ ++ + ++ 
  gi|121637547|ref|YP_977770.1| 349 ktqtiV----RlfgGNEDAWSAFDPTTVITR-HGSYTGLSGWFAISSPG 392
                                    544443....134335666777777766643.56666665555555555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.3e-06     0.037      51      96 ..     292     339 ..     261     358 .. 0.84
   2 ?   -3.3   0.0       1.1     5e+03      78     101 ..     426     449 ..     424     454 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
                                    HHHHHHHTT..S--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEES CS
                   Peptidase_S9  51 aaealakeg..yvdserlaitGgSyGGyltgaalnqrpdlFkaavaev 96 
                                    ++ ++++++    +++  +i G+S GG+ +  +  ++p lF+a v  +
  gi|121637547|ref|YP_977770.1| 292 VVPYMVSKFgvSPEQTSWGIVGWSMGGTCAVDLTVMHPTLFSAFVDIA 339
                                    5667777773334455689************9999********98655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                                    HHHHHHH-GGG-SEEEEESE---C CS
                   Peptidase_S9  78 tgaalnqrpdlFkaavaevpvvdv 101
                                    +++al++++ ++ a+v + + +d+
  gi|121637547|ref|YP_977770.1| 426 ALCALGRANGIYCAVVPQPGKHDW 449
                                    5788999999999***99999999 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.3e-05      0.19      47     125 ..     279     356 ..     237     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.3e-05
                    Hydrolase_4  47 gkrghvpsfddyvdDlaaf.vekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllkl 125
                                    g+rg  +  d++++D+  + v+k+    +++   ++G SmGG+ a+ ++ ++p  +++++ +a  + ++a  k++ +++l
  gi|121637547|ref|YP_977770.1| 279 GRRG--NAADHLTKDVVPYmVSKFGVSPEQTSWGIVGWSMGGTCAVDLTVMHPTLFSAFVDIAGDFYPNAGNKTQTIVRL 356
                                    6666..6677888887755367777777777899********************999**999999998887666666665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.3    0.0048        22       3      50 ..      31      76 ..      29      85 .. 0.51
   2 ?    6.5   7.4    0.0013         6       4      56 ..      90     144 ..      87     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0048
                        DUF4131  3 lplalvllalllllllllllllrrrprrrvllllllllllallgfalr 50
                                    pla+ ++ +++l+l++ +      ++rr+l +++++ ++++ g  ++
  gi|121637547|ref|YP_977770.1| 31 VPLAVQVVTAVVLVLAAGWRSR--HWQRRWLPTAAAIGATLAWGTRWY 76
                                   4555555555555444444442..455555555555555555554444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0013
                        DUF4131   4 plalvllalllllllllllllrrrprrrv..llllllllllallgfalrapqpna 56 
                                    +l++++ ++++++++l+l +   r++rr   ll++ l+ll a+l + l++ + ++
  gi|121637547|ref|YP_977770.1|  90 TLWIWVALTGAAATVLILGWRSARWWRRGasLLAVPLCLLSATLTLNLWVGYFPT 144
                                    6788888888888888877754444444445888888888888888888776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3145.03
//
Query:       gi|121637548|ref|YP_977771.1|  [L=1172]
Description: lysyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-102  343.1   0.0   1.5e-102  342.6   0.0    1.2  1  DUF2156          Uncharacterised conserved protein (DUF2156)
    1.1e-80  270.4  23.7      2e-80  269.6  23.7    1.4  1  tRNA-synt_2_TM   Transmembrane region of lysyl-tRNA synthetas
    3.1e-66  223.6   0.0    4.3e-66  223.1   0.0    1.2  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.2e-11   44.4   0.0    2.5e-11   43.4   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0022   17.5   0.0       0.33   10.4   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.054   13.6   0.0       0.11   12.5   0.0    1.4  1  BOF              Bacterial OB fold (BOF) protein
        2.2    7.5   4.9        3.5    6.8   4.9    1.2  1  Peptidase_U4     Sporulation factor SpoIIGA
        6.8    7.1   8.0         41    4.6   7.9    2.5  1  MFS_MOT1         Molybdate transporter of MFS superfamily


Domain annotation for each model (and alignments):
>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.6   0.0  6.7e-106  1.5e-102       2     298 .]     309     607 ..     308     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.6 bits;  conditional E-value: 6.7e-106
                                    CCCCTSSGGGGHHHHHHCCHCCEEEECCTTEEEEEEEECTCEEEECS-EE.CCGHHHHHHHHHHHHHHCTSEEEEEEE-H CS
                        DUF2156   2 allersgsedslsnlalwrdksyyfspsgdalvayrvkggvalalgdPvGdpeawpeaieeflelaaehgwrpafygvse 81 
                                     ll+ +g++dsl+++a++rdks++f+ sg+a+++yrv+ gv+la+gdPvGd  awp+a++++l+l++++gw p ++g+s 
  gi|121637548|ref|YP_977771.1| 309 GLLDLYGKDDSLGYFATRRDKSVVFASSGRACITYRVEVGVCLASGDPVGDHRAWPQAVDAWLRLCQTYGWAPGVMGASS 388
                                    689999*******************88***************************************************** PP

                                    HHHHHHHHCTEEEECCCEEEEEEHHHHHTTSGGGHHHHHHHHHHHHCTECEEEEEGGGH-HHHHHHHHHHHHHHHHHTTC CS
                        DUF2156  82 elaellaelglsalrlgeeavvdledftLsGkkfrnvRnainraeraGytveverisdlspellaelkeiseeWlkqkea 161
                                    ++a++++e+gl+al+lg+ea+++++df+LsG ++r vR+a+ ra+raG+tv+++r++d++++++a+    +++W++++  
  gi|121637548|ref|YP_977771.1| 389 QGAQTYREAGLTALELGDEAILRPADFKLSGPEMRGVRQAVTRARRAGLTVRIRRHRDIAEDEMAQTITRADSWRDTE-- 466
                                    ******************************************************************************.. PP

                                    HHHHCCCHHHHCHHHHTSEEEE..EEE.TTEEEEEEEEEEECTTTEEEEEEEEE-TT.STTHHHHHHHHHHHHCHHTT-S CS
                        DUF2156 162 tEkgfslglfdelddldlrglv..vrdeegrivAftsfeplngkdglsldlmRrdpdapnGlmefliaelaeelkeegve 239
                                    tE+gfs++l++++d++d ++l+  ++d+ +++ A++s++p++  +g+sldlmRr+p++pnG++e+++ ela+++++ g++
  gi|121637548|ref|YP_977771.1| 467 TERGFSMALGRLGDPADSDCLLveAIDPHNQVLAMLSLVPWG-TTGVSLDLMRRSPQSPNGTIELMVSELALHAESLGIT 545
                                    **********************55566788************.7************************************ PP

                                    EEEEEEE..................HHHHHHHHHHHHHTTTCHHHHHHHCT--CEEEEEEEE CS
                        DUF2156 240 yvsLgfaplagl...geregagllerllrllleflerdygfegLrrfKlkyqPeweprYlay 298
                                    ++sL+fa+++ +   g++ gag+++rl+r+ll f++r++++e L+r+++kyqPew+prY +y
  gi|121637548|ref|YP_977771.1| 546 RISLNFAVFRAAfeqGAQLGAGPVARLWRGLLVFFSRWWQLETLYRSNMKYQPEWVPRYACY 607
                                    **************99*********************************************8 PP

>> tRNA-synt_2_TM  Transmembrane region of lysyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.6  23.7     9e-84     2e-80       1     217 []      76     290 ..      76     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 269.6 bits;  conditional E-value: 9e-84
                 tRNA-synt_2_TM   1 rlaevPaiaglivgvlavlsllasvspllrrlikvvrevvddylfnvPdtslawavvLllLAaAlaarkriAwwllvvyl 80 
                                    r+++vPa+ag++vgv+a+lsllasvspl+r++ikv+re+++dylfn+Pdt++aw++vL+lLAaAl arkriAw++l++ +
  gi|121637548|ref|YP_977771.1|  76 RYHWVPAAAGWTVGVIATLSLLASVSPLIRWIIKVPREFINDYLFNFPDTNFAWSFVLALLAAALTARKRIAWLVLLANM 155
                                    689***************************************************************************** PP

                 tRNA-synt_2_TM  81 vlllllnavllvasdlreqvaedinelvglavqvvvlvlLllarkeFyarvrrGallkAllvlvaglavatllgwgLvel 160
                                    vl++++na++++a  + +++ae + e +g+av+vv++v+L+l ++eF+a+vrrGal++A++v++ag +v+++ +wgLvel
  gi|121637548|ref|YP_977771.1| 156 VLAAVVNAAEIAA--GGNTAAESFGENLGFAVHVVAIVVLVLGYREFWAKVRRGALFRAAAVWLAGAVVGIVASWGLVEL 233
                                    *************..***************************************************************** PP

                 tRNA-synt_2_TM 161 fPgsLeeeeRllwalnrvlglalvdeesfeghphvfvnvllgllgalaLlaaaivLF 217
                                    fPgsL+++eRl +a+nrv+g+al+d++ f+g+phvf+n+++gl+ga+aL+ aaivLF
  gi|121637548|ref|YP_977771.1| 234 FPGSLAPDERLGYAANRVVGFALADPDLFTGRPHVFLNAIFGLFGAFALIGAAIVLF 290
                                    ********************************************************9 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.0   1.9e-69   4.3e-66       3     312 ..     822    1168 ..     820    1170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 1.9e-69
                                     CHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                     xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2    3 elrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79  
                                     e r++ ryldl  +++ ++ + +rs+v++avr+ l+ +gf+e+etPiL++ ++++ ar+F+++ ++ + ++f L+++p
  gi|121637548|ref|YP_977771.1|  822 EARVRTRYLDLaVNAESRALITARSSVLRAVRETLFAKGFVEVETPILQQLHGGATARPFVTHINTYSMDLF-LRIAP 898 
                                     7899**********************************************************9999988999.***** PP

                                     HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTT CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvi 157 
                                     +lyl++l v+g++rvf+++raFR+E ++ ++++ EFt +ea+ + + + + ++   eli++ ++ + ++    ++  +
  gi|121637548|ref|YP_977771.1|  899 ELYLKRLCVGGVERVFELGRAFRNEGVDFSHNP-EFTLLEAYQAHAGYLEWIDGCRELIQNAAQAA-NGAPIAMRPRT 974 
                                     *********************************.******************************99.65545554444 PP

                                     TTTS.........EE-SSS-EEEEHHHHHHHHHTS-SS--H..HHHHHHHH.........................HS CS
                                     xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.........................xx RF
                    tRNA-synt_2  158 rrns.........kdlkkpfkrltykeaieklneigkdldk..aderalvk.........................ke 199 
                                     ++ s          d++  ++  t ++ai+++ ++  d d+    +r l++                           
  gi|121637548|ref|YP_977771.1|  975 DKGSdgtrhhlepVDISGIWPVRTVHDAISEALGERIDADTglTTLRKLCDaagvpyrtqwdagavvlelyehlveCR 1052
                                     444488999998888888899999999999987774444431145555555888888888888888889999888566 PP

                                     --SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH.....SSSGGGGHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx RF
                    tRNA-synt_2  200 knepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld.....eeaeekfsw 272 
                                       +p+f +dfP +++p++++++++   ++e++Dl+  g+El+++++++ dp e++++l+++ l       ea+e +++
  gi|121637548|ref|YP_977771.1| 1053 TEQPTFYIDFPTSVSPLTRPHRSK-RGVAERWDLVAWGIELGTAYSELTDPVEQRRRLQEQSLLaaggdPEAMELDED 1129
                                     789*********************.8*************************************99999999******* PP

                                     HHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-X CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  273 ylealeyGapphgGlglGldRlvmlllgsesIrdviaFPk 312 
                                     +l+a+ey +pp+gGlg+G+dR+vml++g  sIr++++FP 
  gi|121637548|ref|YP_977771.1| 1130 FLQAMEYAMPPTGGLGMGIDRVVMLITGR-SIRETLPFPL 1168
                                     ***************************97.*********7 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.1e-14   2.5e-11       1      76 []     726     804 ..     726     804 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.1e-14
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.....HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.....eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                    V+v Gr+++i  r+ g+v+f++lrD +g++qv l++     + a +++   + Gd+v+ tG  +++++g ++l+v+ ++l
  gi|121637548|ref|YP_977771.1| 726 VSVSGRIMRI--RNYGGVLFAQLRDWSGEMQVLLDNsrldqGCAAEFNAATDLGDLVEMTGHMGASKTGTPSLIVSGWRL 803
                                    89********..**************************************************************998877 PP

                                    E CS
                tRNA_anti-codon  76 l 76 
                                    +
  gi|121637548|ref|YP_977771.1| 804 I 804
                                    5 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00015      0.33     103     130 ..     912     939 ..     909     974 .. 0.89
   2 ?    4.4   0.1      0.01        23     200     227 ..    1131    1157 ..    1126    1164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                    EEEEEEEEEBSST-SSSB-SEEEEEEEE CS
                   tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqvegl 130
                                    +++ +gr+fR++ vD +h +eF+ +e  
  gi|121637548|ref|YP_977771.1| 912 RVFELGRAFRNEGVDFSHNPEFTLLEAY 939
                                    7999******************998875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                                     HHHTT-.TTSEEEEEEEEHHHHHHHHHT CS
                   tRNA-synt_2d  200 leavgideevsgfafGlGveRlamlkyg 227 
                                     l+a+++    +  ++G+G++R+ ml +g
  gi|121637548|ref|YP_977771.1| 1131 LQAMEY-AMPPTGGLGMGIDRVVMLITG 1157
                                     666666.55667789**********987 PP

>> BOF  Bacterial OB fold (BOF) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05      0.11      19      71 ..     708     763 ..     698     786 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                    ------HHHHTTS-SSEEEEEEEEEEE..EEETTEEE.EEETTEEEEEE--GGGST CS
                            BOF  19 nakvttvkaAlsaaDdasvslrGnivk..riddDeyv.FrDasGeikveiddrvfn 71 
                                     +   tv +Al a  +asvs+ G i++  + ++  +   rD sGe++v +d+ + +
  gi|121637548|ref|YP_977771.1| 708 RPPSHTVAQALAADHQASVSVSGRIMRirNYGGVLFAqLRDWSGEMQVLLDNSRLD 763
                                    56778********************761155566664369********99987765 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.9    0.0016       3.5      11     116 ..     126     278 ..     122     302 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                   Peptidase_U4  11 Nllmdyll.LlltakllklkikklrlllaAllGalyvvlvlflp...klesillsillkilvsllmvliafgpkslkefl 86 
                                    N++  ++l Ll++a +++++i +l ll+  +l+a+  ++ +      + es+  ++ + + v +++vl + g+++++  +
  gi|121637548|ref|YP_977771.1| 126 NFAWSFVLaLLAAALTARKRIAWLVLLANMVLAAVVNAAEIAAGgntAAESFGENLGFAVHVVAIVVL-VLGYREFWAKV 204
                                    66666655267777777777777755544445555544444442221333344444444444444444.59********* PP

                   Peptidase_U4  87 kalllfylvsfllgGilfalsyll............lkskn...................................l 116
                                    +  +lf +++++l+G+++++                    +                                    
  gi|121637548|ref|YP_977771.1| 205 RRGALFRAAAVWLAGAVVGIVASWglvelfpgslapD---ErlgyaanrvvgfaladpdlftgrphvflnaifglfG 278
                                    ***************9999887556666655554440...1444444455555555566666666664333333332 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.9     0.018        41      17      86 ..     131     199 ..     120     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                       MFS_MOT1  17 lvialaalaslsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaagillGlvllllgltg 86 
                                    +v+al a a    +++++ v l+n++++ + +    + +g  aa+  fg+++g a+ ++++v+l+lg+  
  gi|121637548|ref|YP_977771.1| 131 FVLALLAAALTARKRIAWLVLLANMVLAAVVNAAEIAAGGNTAAE-SFGENLGFAVHVVAIVVLVLGYRE 199
                                    567777777666799999999**9999988887766555555555.59*******************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.45
# Mc/sec: 7801.18
//
Query:       gi|121637549|ref|YP_977772.1|  [L=201]
Description: translation initiation factor IF-3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-32  110.5   0.1    4.2e-32  110.0   0.1    1.2  1  IF3_C     Translation initiation factor IF-3, C-terminal doma
    1.9e-29  101.7   0.1    3.3e-29  100.9   0.1    1.4  1  IF3_N     Translation initiation factor IF-3, N-terminal doma
  ------ inclusion threshold ------
       0.19   11.8   0.0       0.83    9.7   0.0    1.8  2  Wzt_C     Wzt C-terminal domain


Domain annotation for each model (and alignments):
>> IF3_C  Translation initiation factor IF-3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.1     7e-36   4.2e-32       2      85 ..      84     167 ..      83     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 7e-36
                                    -EEEEEEESS--HHHHHHHHHHHHHHHHHT-EEEEEEE--S-TTSHHHHHHHHHHHHHHHTTTTEEEEEEEEE-SSEEEE CS
                          IF3_C   2 evKEiklrpkidehDlevKlknarkFLeegdkvKvtlrfrGReiahkelgkevleriaeeleevakvekkpklegrqmim 81 
                                     vKE klrpkid+hD+e+K  ++ +FLe g kvKvt++frGRe +++elg ++l+r+ +++++++ +e+++k++gr+m+m
  gi|121637549|ref|YP_977772.1|  84 VVKEQKLRPKIDDHDYETKKGHVVRFLEAGSKVKVTIMFRGREQSRPELGYRLLQRLGADVADYGFIETSAKQDGRNMTM 163
                                    69****************************************************************************** PP

                                    EEEE CS
                          IF3_C  82 vlap 85 
                                    vlap
  gi|121637549|ref|YP_977772.1| 164 VLAP 167
                                    ***9 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.1   5.6e-33   3.3e-29       1      69 [.       7      75 ..       7      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 5.6e-33
                                   ETTS--SSEEEEE-SSS-EEEEEEHHHHHHHHHHHTSEEEEEESSSSS-EEEEE-HHHHHHHHHHHHHH CS
                          IF3_N  1 iNeqIrarevrlvdedGeqlGvistreAlrlaeekgldLVevspnaepPVcrimdygkfrYeqkkkeke 69
                                   +Ne+Ir++evrl++  Geq+G++++++ lr a +++ldLVev+pna pPVc+imdygk++Ye+ +k++e
  gi|121637549|ref|YP_977772.1|  7 VNERIRVPEVRLIGPGGEQVGIVRIEDSLRVAADADLDLVEVAPNARPPVCKIMDYGKYKYEAAQKARE 75
                                   7******************************************************************98 PP

>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.2   1.2e+03       7      39 ..       8      40 ..       3      50 .. 0.83
   2 ?    9.7   0.0   0.00014      0.83      12      63 ..      94     144 ..      88     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.2
                          Wzt_C  7 sgeaeIedvelldaegeetstfesgeevtlrik 39
                                   + ++++ +v+l++  ge++ +++  +++++  +
  gi|121637549|ref|YP_977772.1|  8 NERIRVPEVRLIGPGGEQVGIVRIEDSLRVAAD 40
                                   678889999999999999999999999888765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                          Wzt_C  12 Iedvelldaegeetstfesgeevtlrikvkahedvedpvfgfaikdrngqev 63 
                                    I d    +++g+ ++ +e g++v++ i ++  e+  +p +g+ +  r+g +v
  gi|121637549|ref|YP_977772.1|  94 IDDHDYETKKGHVVRFLEAGSKVKVTIMFRGREQS-RPELGYRLLQRLGADV 144
                                    6666667899*******************987666.9************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1482.81
//
Query:       gi|121637550|ref|YP_977773.1|  [L=64]
Description: 50S ribosomal protein L35 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-24   84.1   6.1    7.6e-24   84.0   6.1    1.0  1  Ribosomal_L35p  Ribosomal protein L35


Domain annotation for each model (and alignments):
>> Ribosomal_L35p  Ribosomal protein L35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   6.1   4.2e-28   7.6e-24       1      61 []       2      62 ..       2      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 4.2e-28
                 Ribosomal_L35p  1 PKmKThkgakKRfkvtgsGkikrkkagkrHlltkKstkrkrrlrktalvskadakrlkklL 61
                                   PK KTh+ga+KRf++tg+Gki r+ka++rHll++K ++r+rrl + ++v+++d+kr+  lL
  gi|121637550|ref|YP_977773.1|  2 PKAKTHSGASKRFRRTGTGKIVRQKANRRHLLEHKPSTRTRRLDGRTVVAANDTKRVTSLL 62
                                   9********************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 484.99
//
Query:       gi|121637551|ref|YP_977774.1|  [L=129]
Description: 50S ribosomal protein L20 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-42  141.5   8.8      1e-41  141.3   8.8    1.0  1  Ribosomal_L20  Ribosomal protein L20


Domain annotation for each model (and alignments):
>> Ribosomal_L20  Ribosomal protein L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   8.8   5.7e-46     1e-41       1     107 []       3     109 ..       3     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 5.7e-46
                                    XXX.XXXXXXXXXXXXX--SSS---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT--HHHHHHH CS
                  Ribosomal_L20   1 RvkrgvaarkrrkkilklakgyrgrrsklyrvakqavekalqyayrdRkkkkrdfrklwitrinaaarenglsYskfing 80 
                                    Rvkr+v+a+k+r+ ilk+++gyrg+rs+lyr ak++  ++l+yayrdR+++k +frklwi+rinaaar n+++Y+++i+g
  gi|121637551|ref|YP_977774.1|   3 RVKRAVNAHKKRRSILKASRGYRGQRSRLYRKAKEQQLHSLNYAYRDRRARKGEFRKLWIARINAAARLNDITYNRLIQG 82 
                                    9******************************************************************************* PP

                                    HCCTTS---HHHHHHHHHH-HHHHHHH CS
                  Ribosomal_L20  81 LkkanielnRkvLadlAindpeaFkal 107
                                    Lk a++e++Rk Lad+Ai+dp+aF+al
  gi|121637551|ref|YP_977774.1|  83 LKAAGVEVDRKNLADIAISDPAAFTAL 109
                                    ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 902.90
//
Query:       gi|121637552|ref|YP_977775.1|  [L=260]
Description: 23S rRNA methyltransferase tsnR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-37  128.2   0.1    5.7e-37  127.0   0.0    1.6  2  SpoU_methylase  SpoU rRNA Methylase family
    4.7e-08   33.2   0.1    9.1e-08   32.3   0.1    1.4  1  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
  ------ inclusion threshold ------
      0.034   14.2   0.9      0.059   13.4   0.9    1.5  1  PA              PA domain


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.67     4e+03      29      60 ..      67      98 ..      58     103 .. 0.71
   2 !  127.0   0.0   9.6e-41   5.7e-37       2     142 .]     109     251 ..     108     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.67
                                   EEEEESGSSCTCGSHHHHHHCTTHHHHHHEEE CS
                 SpoU_methylase 29 elvlvkprsadllnpeakraaagalevlelkv 60
                                    ++lv +r+a+ l++++  a++ a   l++++
  gi|121637552|ref|YP_977775.1| 67 SVHLVTERAAKALSDTVTPAGLVAVCDLPATR 98
                                   67888888888888888877777776666655 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 9.6e-41
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvat 81 
                                    li v vei++pgN G+++R a+a+ga +++l + rs+d++n + +ra++g+ + ++++v++++ +a+++l+ +g++++at
  gi|121637552|ref|YP_977775.1| 109 LIAVTVEIREPGNAGTVIRIADAMGAAAVILAG-RSVDPYNGKCLRASTGSIFAIPVVVAPDVGAAIADLRAAGLQVLAT 187
                                    68899*********************9999977.9********************************************* PP

                                    STT-S.EGCCS..HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  82 slkgk.slsei..dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                      +g+  l+++   l+e++a++fG+E +Gls e+ +lad+ v+Ipmsg +eSLNva A+ai+ly
  gi|121637552|ref|YP_977775.1| 188 AVDGEmALDDAdrLLAEPTAWLFGPEAHGLSAEIAALADHRVHIPMSGGAESLNVAAAAAICLY 251
                                    *966625666633667***********************************************9 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.5e-11   9.1e-08       1      71 [.      28      93 ..      28      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.5e-11
                  SpoU_sub_bind  1 liyGlhaVleaLksgrriekllvtegradkrleellklakkrgikvelvdkekLdklsgtanHQGvvaevk 71
                                   l +G ++V +aL+ g  +++++vte +a ++  ell +a ++  +v+lv+++  ++ls+t+++ G+va+++
  gi|121637552|ref|YP_977775.1| 28 LAEGPNLVAAALARGL-VREVFVTEVAARRH--ELLLAAHEA--SVHLVTERAAKALSDTVTPAGLVAVCD 93
                                   679***********95.*********55555..999999777..*************************98 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   9.9e-06     0.059      22      80 ..      83     166 ..      60     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-06
                             PA  22 vdvkGkivLvqr..tf........................aeKarnAqaaGAagviiv.......ndgelgaatgasgne 68 
                                    v+ +G +++++   t+                        ++ +r A a GAa+vi++       n ++l a+t      
  gi|121637552|ref|YP_977775.1|  83 VTPAGLVAVCDLpaTRledvlagspqliavtveirepgnaGTVIRIADAMGAAAVILAgrsvdpyNGKCLRAST------ 156
                                    4556667777423322444566666667777788888888999***************8874333222244444...... PP

                             PA  69 gepdgitiPavg 80 
                                       + + iP+v 
  gi|121637552|ref|YP_977775.1| 157 --GSIFAIPVVV 166
                                    ..5568888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1961.31
//
Query:       gi|121637553|ref|YP_977776.1|  [L=351]
Description: hypothetical protein BCG_1684c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-53  180.1   1.6    7.4e-53  180.1   1.6    1.5  2  DUF2236   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   1.6   4.1e-57   7.4e-53       1     221 [.      19     250 ..      19     254 .. 0.94
   2 ?   -2.6   0.2      0.29   5.2e+03     192     192 ..     292     292 ..     258     336 .. 0.51

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 4.1e-57
                        DUF2236   1 wryagdelilllgalaalllqaahplvltgvldhstf.adplrRllrTaqfiltvvygsgeeaeaaaarVrllHaavrgt 79 
                                    w+y+gd+++ ++g ++ + +q++ p +++gv +hs + ++pl+R+ r++  i++vvy+ g++a +++++++ +H++++g+
  gi|121637553|ref|YP_977776.1|  19 WKYFGDLRTGMMG-VWIGAIQNMYPELGAGVEEHSILlREPLQRVARSVYPIMGVVYD-GDRAAQTGQQIKGYHRTIKGV 96 
                                    9**********98.7778889**************88688******************.9******************** PP

                        DUF2236  80 dasgerygainpedllwvhatfsasflraygrtvgpltaeeeeayyhewrrvgrllGvpdrllpatraafdayldemvla 159
                                    da+g+ry+a+np++++w+hatf++++++++++++g lt++e+ ++++e +r++r++G+++r +p+++++f++y+d+++++
  gi|121637553|ref|YP_977776.1|  97 DAEGRRYHALNPDTFYWAHATFFMLVIKVAEYFCGGLTEAEKHQLFEEHVRWYRMYGMSMRPVPKSWEDFQDYWDRVCRD 176
                                    *********************************999******************************************** PP

                        DUF2236 160 elevdeearelgdarll..............parpalpllrvitrgllppalrellglpvpwssrdellvvalral 221
                                    +le++ ++ ++ ++r+               +++p+ +  r+i++gl  pa+re+ g++  w++ de+l +++  +
  gi|121637553|ref|YP_977776.1| 177 KLEINQATVDILQMRIPkprfvlmptpiwdqLFKPLIAGQRWIAAGLFDPAVREKAGMH--WTPGDEVLLRVFGKV 250
                                    ******9999955555588888888999899****************************..********5555444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.29
                        DUF2236 192 l 192
                                    +
  gi|121637553|ref|YP_977776.1| 292 M 292
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2948.14
//
Query:       gi|121637554|ref|YP_977777.1|  [L=310]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-29  101.4  16.7    5.6e-29  100.3  16.7    1.6  1  PE             PE family
  ------ inclusion threshold ------
        1.9    9.0   9.6        5.1    7.6   9.6    1.8  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3  16.7   6.3e-33   5.6e-29       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 6.3e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msf++vaP++++aaa++l+++gsal++a+aaaa++t +++a+aaD+VSa +Aa+++a+a+++q +saq a fh+qfv al++
  gi|121637554|ref|YP_977777.1|  1 MSFLTVAPDMVTAAAGNLESVGSALNEAAAAAAPATVGLAAPAADRVSAVVAAMLGAYARDFQGISAQIAGFHNQFVGALRG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a++Ya+aEaa
  gi|121637554|ref|YP_977777.1| 83 GAAAYASAEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.6   0.00056       5.1       4      94 ..       3      94 ..       1     108 [. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00056
                  T7SS_ESX_EspC  4 nLsVdpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAA 84
                                    L+V pd + ++a  +++v + ++ a+aaa   ++   ++    ++a +++++ a+ ++ ++  +++a+ ++++   Lr  A
  gi|121637554|ref|YP_977777.1|  3 FLTVAPDMVTAAAGNLESVGSALNEAAAAAaPATVGLAAPAADRVSAVVAAMLGAYARDFQGISAQIAGFHNQFVGALRGGA 84
                                   79*************************999344567778889999999********************************** PP

                  T7SS_ESX_EspC 85 aaYeatDeea 94
                                   aaY  ++ ++
  gi|121637554|ref|YP_977777.1| 85 AAYASAEAAN 94
                                   ****999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2439.11
//
Query:       gi|121637555|ref|YP_977778.1|  [L=316]
Description: hypothetical protein BCG_1686 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-12   45.4   0.0    1.2e-11   44.5   0.0    1.4  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
      0.042   13.6   0.0      0.065   13.0   0.0    1.3  1  GGDEF          Diguanylate cyclase, GGDEF domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.4e-15   1.2e-11       7     162 ..     127     265 ..     122     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.4e-15
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                     evt++F+d+vgf + s +    + ++lL ++   +++ l   ++  vk +Gd +m+v+  p    + a +++ +a d +
  gi|121637555|ref|YP_977778.1| 127 PEVTLVFTDLVGFSTWSLHAGDDATLTLLRQVARAVESPLLDAGGHIVKRLGDGIMAVFRNP----TVALRAVLVAQDAV 202
                                    68***********99998888899*************************************9....44445555554444 PP

                  Guanylate_cyc  87 ealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellkeeqfel 162
                                       ++ +v+     ++r+GihtG+        ++   d  G +vn+A+r+   + +g i++s+ t +l    q el
  gi|121637555|ref|YP_977778.1| 203 ---KSLEVQG-YTPRMRIGIHTGR-------PQRLAADWLGVDVNIAARVMERATKGGIMISQPTLDLIP--QSEL 265
                                    ...5555555.4559********8.......789999****************************99876..4444 PP

>> GGDEF  Diguanylate cyclase, GGDEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-06     0.065      18     132 ..     115     221 ..     110     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-06
                                    HHHHHHHCCHHCTSEEEEEEEEETTHHHHHHHH-HHHHHHHHHHHHHHHHCCS-T..TSEEEEESSSEEEEEEECSSHHH CS
                          GGDEF  18 eleqelqrarreqkslavllldldnFkkindtyGhsvGDevLqevakrLssslrk..sdlvaRlggdeFaillpetssee 95 
                                     l+++++r    + ++++++ dl  F +   + G +++  +L++va++ +s l +  +++v Rl gd ++ ++ + +   
  gi|121637555|ref|YP_977778.1| 115 ALTEAVSRRPA-NPEVTLVFTDLVGFSTWSLHAGDDATLTLLRQVARAVESPLLDagGHIVKRL-GDGIMAVFRNPTV-- 190
                                    56667777643.6899***********************************9998877777777.5777777788774.. PP

                                    HHHHHHHHHHHHHCS-EEETTCCEEE---EEEEEEEE CS
                          GGDEF  96 aaelaerirrllaklkepvelsgeelyvtisiGiala 132
                                    a ++  +++ +++ l+ +        + ++ iGi + 
  gi|121637555|ref|YP_977778.1| 191 ALRAVLVAQDAVKSLEVQ------GYTPRMRIGIHTG 221
                                    588888888888887763......3344555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2292.77
//
Query:       gi|121637556|ref|YP_977779.1|  [L=268]
Description: hypothetical protein BCG_1687 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.4   0.5       0.18   12.4   0.5    2.4  3  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2      0.43   7.8e+03      47      63 ..       7      23 ..       2      32 .. 0.61
   2 ?   -1.9   0.1      0.29   5.2e+03      38      42 ..      99     103 ..      72     118 .. 0.55
   3 ?   12.4   0.5   9.9e-06      0.18       9      54 ..     179     224 ..     175     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.43
                         PAP2_C 47 iiasrkHYtvDVllgly 63
                                   ++++r ++tv  + +l 
  gi|121637556|ref|YP_977779.1|  7 CLLARIRFTVGYVAALA 23
                                   66777777776555554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.29
                         PAP2_C  38 llall 42 
                                    ++  +
  gi|121637556|ref|YP_977779.1|  99 VVGHI 103
                                    22222 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 9.9e-06
                         PAP2_C   9 GHtvvltlavlfileyspkklailkvillllallglfliiasrkHY 54 
                                    GHtv+l+l +l+   +++   ++l  ++ll +++g++l++++++ +
  gi|121637556|ref|YP_977779.1| 179 GHTVALLLGMLVTACFTRPARWTLGRCALLAVASGFCLVLLAHSWW 224
                                    9****************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1916.18
//
Query:       gi|121637557|ref|YP_977780.1|  [L=341]
Description: phenylalanyl-tRNA synthetase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-96  321.1   0.0    5.3e-96  320.8   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.2e-15   56.3   0.7    4.1e-15   55.5   0.7    1.4  1  Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-termin
  ------ inclusion threshold ------
      0.024   14.1   0.0       0.31   10.4   0.0    2.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
       0.12   12.6   0.1        3.1    8.1   0.0    2.3  2  LpqV             Putative lipoprotein LpqV


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8   0.0   1.2e-99   5.3e-96       2     242 ..      95     334 ..      94     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 1.2e-99
                                    .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESE CS
                   tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekl 81 
                                    idvtlp++r+ ag++hp+  ++e+++++f+++g+e +egpeve+e +nfdaLn+p dhpaR  qdtFy+  p   +++++
  gi|121637557|ref|YP_977780.1|  95 IDVTLPSTRVPAGARHPIIMLAEHVADTFIAMGWELAEGPEVETEQFNFDALNFPADHPARGEQDTFYI-AP---EDSRQ 170
                                    7********************************************************************.44...4579* PP

                                    EE-SSTHHHHHHHHTTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEE CS
                   tRNA-synt_2d  82 lLRthttavqirtlekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrf 161
                                    lLRtht++vqirtl ++++p++iisigr+fR+d++Dath++ Fhqvegl+vd+++s+a+l g+l++++++ fg ++++r+
  gi|121637557|ref|YP_977780.1| 171 LLRTHTSPVQIRTLLARELPVYIISIGRTFRTDELDATHTPIFHQVEGLAVDRGLSMAHLRGTLDAFARAEFGPSARTRI 250
                                    ******************************************************************************** PP

                                    EECEETTEEEEEEEEEEE..CCSSSSEEEEEEEEEE-HHHHHHTT-..TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT. CS
                   tRNA-synt_2d 162 rpsyfpftePsaevdvyl..vekkkkwlEllgaGmvrpevleavgid.eevsgfafGlGveRlamlkygieDiRelvend 238
                                    rp++fpftePsaevdv++     + +w+E++g+Gmv+p+vl+a+gid + +sgfafG+G+eR+  +++gi+D+R++ve d
  gi|121637557|ref|YP_977780.1| 251 RPHFFPFTEPSAEVDVWFanKIGGADWVEWGGCGMVHPNVLRATGIDpDLYSGFAFGMGLERTLQFRNGIPDMRDMVEGD 330
                                    ******************66557899****************************************************** PP

                                    HHHH CS
                   tRNA-synt_2d 239 lrfl 242
                                    +rf 
  gi|121637557|ref|YP_977780.1| 331 VRFS 334
                                    **96 PP

>> Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.7   9.1e-19   4.1e-15       2      69 .]      23      90 ..      22      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 9.1e-19
                                   CCCCCCCCHHHHHCCCCCCCCCCCTTTTCCCCTTTHHHHCCHHHHCCCCCCCCCHHHCCHCCHHHHHC CS
                Phe_tRNA-synt_N  2 dleeLeelRvkyLGkkGeltellkelgklppeeRkeaGkliNelKqeieealeerkeeleaaeleakl 69
                                   +l+ L  +++++LG++++l+ + + l  lp+e+R+eaGk++N+++++++ +++er + l+a++++a l
  gi|121637557|ref|YP_977780.1| 23 TLDVLARVKTEHLGDRSPLALARQALAVLPKEQRAEAGKRVNAARNAAQRSYDERLATLRAERDAAVL 90
                                   7899**********************************************************999865 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.9e-05      0.31       1     207 [.      95     300 ..      95     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.9e-05
                tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGl.....nEvitysfvsekeldkll.eddderkavelanPlsedqsvl 74 
                                    I  tlP++ +++g++++   l ++++d+ +++G+      Ev t  f  ++ +  +      e+++  +a    + +++l
  gi|121637557|ref|YP_977780.1|  95 IDVTLPSTRVPAGARHPIIMLAEHVADTFIAMGWelaegPEVETEQFNFDALNFPADhPARGEQDTFYIA--PEDSRQLL 172
                                    6678888888888888888888888888888888444444777777776666666654444555555554..36677888 PP

                tRNA_synthFbeta  75 RtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgiveal 153
                                    Rt   p  + +l   lar+++ v +  ig++f+ d  + +     +++ ++++ +             ++++l g+++a+
  gi|121637557|ref|YP_977780.1| 173 RTHTSPVQIRTL---LARELP-VYIISIGRTFRTDeLDATHTPIFHQVEGLAVDRG-----------LSMAHLRGTLDAF 237
                                    888888877777...788888.9999999999999433333333445555555555...........9999999999999 PP

                tRNA_synthFbeta 154 le.slgi.ekvefepaehpalhpgrsAeikvdgk.......evGvlGelhpevleafdlkqrv 207
                                    ++ ++g  ++ +++p   p+ +p    ++ + +k       e G  G +hp+vl+a +++   
  gi|121637557|ref|YP_977780.1| 238 ARaEFGPsARTRIRPHFFPFTEPSAEVDVWFANKiggadwvEWGGCGMVHPNVLRATGIDPDL 300
                                    96258888889999999999999999999988888888999***************9998765 PP

>> LpqV  Putative lipoprotein LpqV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.055   2.4e+02      27      42 ..       2      17 ..       1      20 [. 0.87
   2 ?    8.1   0.0   0.00069       3.1      75     105 ..      62      92 ..      51      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.055
                           LpqV 27 vsPgGvttavdvpaes 42
                                   +sP+  ttavd++ ++
  gi|121637557|ref|YP_977780.1|  2 LSPEALTTAVDAAQQA 17
                                   79*********98775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00069
                           LpqV  75 slqssdsagpgtfntpWaeLtparqaavivA 105
                                     + ++ +a++ +++++ a L ++r aav+vA
  gi|121637557|ref|YP_977780.1|  62 RVNAARNAAQRSYDERLATLRAERDAAVLVA 92 
                                    6788899999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2339.72
//
Query:       gi|121637558|ref|YP_977781.1|  [L=831]
Description: phenylalanyl-tRNA synthetase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-56  190.9   0.0    2.1e-56  190.3   0.0    1.3  1  B3_4             B3/4 domain
    1.2e-51  175.3   0.0    1.6e-51  174.8   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    9.1e-25   86.9   0.0    1.5e-24   86.2   0.0    1.4  1  FDX-ACB          Ferredoxin-fold anticodon binding domain
      1e-19   70.4   0.0    1.7e-19   69.7   0.0    1.4  1  tRNA_bind        Putative tRNA binding domain
    1.3e-15   57.4   0.0      1e-14   54.6   0.0    2.4  2  B5               tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   5.9e-60   2.1e-56       3     174 .]     224     395 ..     222     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 5.9e-60
                                    SEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT--EEEEEGGGTBTEEEEEE--TTEEEEBTTS- CS
                           B3_4   3 pryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgqPlhafDldkiqgdivvrlakegeklvtldgk 82 
                                    +r+a r + g++++a sp+wlqrrL  +gir   ++VD+tNyvmlelg+P+ha+D ++i+g++ vr+a++ge+ vtldg 
  gi|121637558|ref|YP_977781.1| 224 RRFALRPVIGIDPAAVSPWWLQRRLLLCGIRATCPAVDVTNYVMLELGHPMHAHDRNRISGTLGVRFARSGETAVTLDGI 303
                                    89****************************************************************************** PP

                                    EEEE-TTSEEEETEEEEEEETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHHTT---HHHHHHHH---TTTHHHHH CS
                           B3_4  83 ereldeedlviadsekpvslagvmggeeskvsedTknvfleaaafdpvsirktarrlglrseaskrfergvdpekleaal 162
                                    er+ld  d++i+d+    ++ gvmg ++++v +d+++v+leaa++dp+++ +t+rrl+l sea++r+er+vdp+   aal
  gi|121637558|ref|YP_977781.1| 304 ERKLDTADVLIVDDAATAAIGGVMGAASTEVRADSTDVLLEAAIWDPAAVSRTQRRLHLPSEAARRYERTVDPAISVAAL 383
                                    *************99999************************************************************** PP

                                    HHHHHHHHHHH- CS
                           B3_4 163 dravallselcg 174
                                    dr+++ll++++g
  gi|121637558|ref|YP_977781.1| 384 DRCARLLADIAG 395
                                    ********9986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.8   0.0   4.3e-55   1.6e-51       1     214 []     487     722 ..     487     722 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.8 bits;  conditional E-value: 4.3e-55
                tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll..eddderkavelanPlsedqsvlRtsL 78 
                                    Ips+lP ap+++g l+  q++rr++ + la +G++E++  +f  + ++d +   +dd++r + +++nPl +d++ l t+L
  gi|121637558|ref|YP_977781.1| 487 IPSVLPPAPAGRG-LTAGQQRRRTIGRSLALSGYVEILPTPFLPAGVFDLWGleADDSRRMTTRVLNPLEADRPQLATTL 565
                                    9************.***************************************88889999******************* PP

                tRNA_synthFbeta  79 lpglLevlarNlargnedvrlFEigkvflkdseeel......................peeerhlaivltgkreeeswse 136
                                    lp lLe+l rN++rg+ dv+lF i++v+++++++++                      p++++h+a+vl+g re++++++
  gi|121637558|ref|YP_977781.1| 566 LPALLEALVRNVSRGLVDVALFAIAQVVQPTEQTRGvglipvdrrptddeiamldaslPRQPQHVAAVLAGLREPRGPWG 645
                                    ******************************9444448999999999999999999999********************** PP

                tRNA_synthFbeta 137 karavdfydlkgivealleslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                    ++r+v+ +d+ ++v+ ++++ ++ +v+++pa++ ++hpgr+A++ v++  vG++G+lhp+v e+ +l++ ++++El+l
  gi|121637558|ref|YP_977781.1| 646 PGRPVEAADAFEAVRIIARASRV-DVTLRPAQYLPWHPGRCAQVFVGESSVGHAGQLHPAVIERSGLPKGTCAVELNL 722
                                    ***********************.****************************************************97 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   4.2e-28   1.5e-24       1      94 []     737     830 ..     737     830 .. 0.99

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 4.2e-28
                                    -SS--EEEEEEEEEESSS-HHHHHHHHHHHH-TTEEEEEEEEEEESTTS-SSEEEEEEEEEE--SSS---HHHHHHHHHH CS
                        FDX-ACB   1 SkfPaverDlalvvdekveaaelleavreaagellesvqlfDvYrgkklaegkkSlalrltlqskertLtdeevnaaiek 80 
                                    S +Pav +D++lvv ++++a+++ +avr+ ag+lle++ lfDv++g++++e++kSl+++l +++++rtLt+++ +aa + 
  gi|121637558|ref|YP_977781.1| 737 SPYPAVFQDVSLVVAADIPAQAVADAVRAGAGDLLEDIALFDVFTGPQIGEHRKSLTFALRFRAPDRTLTEDDASAARDA 816
                                    78****************************************************************************** PP

                                    HHHHHHTT.T-BES CS
                        FDX-ACB  81 vvealekklgaelR 94 
                                     v++ ++++ga lR
  gi|121637558|ref|YP_977781.1| 817 AVQSAAERVGAVLR 830
                                    ************99 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   4.8e-23   1.7e-19       1      95 [.      50     152 ..      50     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.8e-23
                                    EEEEEEEEEEEETTSST.EEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESE..........EETTEEESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadk.LlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpk..........klrGveSeG 69 
                                    ++vG+v ++ee+ +++k ++ + vd+G++++r+i++ga+n++       +++vvva+++++          k +G +S+G
  gi|121637558|ref|YP_977781.1|  50 VTVGRVADIEELTGYKKpIRACAVDIGDRQYREIICGATNFAV------GDLVVVALPGATlpggftisarKAYGRNSDG 123
                                    68*****************************************......9999999999999999999************ PP

                                    EE-EEEC...CESSCEEEEEESST--TTC CS
                      tRNA_bind  70 Milsaee...ldekevgilelpadveaGe 95 
                                    Mi+sa+e   +++++  ++ +p+++e+G+
  gi|121637558|ref|YP_977781.1| 124 MICSAAElnlGADHSGILVLPPGAAEPGA 152
                                    *********87888888888999999996 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.51   1.8e+03      13      33 ..      18      38 ..      15     102 .. 0.83
   2 !   54.6   0.0   2.8e-18     1e-14       5      67 .]     423     484 ..     419     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.51
                                   TS---HHHHHHHHHHTT-E.E CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                             B5 13 GidlseeeiikiLkrlgceri 33
                                   G d+++ e +++L r+g+e++
  gi|121637558|ref|YP_977781.1| 18 GWDVTPGELEQTLLRIGHEVE 38
                                   788999999999999999953 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.8e-18
                                    HHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5   5 vekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                    v+   +++G+ +++ ++++ L ++g  + ++d+d+l+Vt+PswR+Dl++++Dl+EEv+Rl G+
  gi|121637558|ref|YP_977781.1| 423 VDVPDRIAGVAYPQGTTARRLAQIGAVV-THDGDTLTVTPPSWRPDLRQPADLVEEVLRLEGL 484
                                    666789********************87.*******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5543.67
//
Query:       gi|121637559|ref|YP_977782.1|  [L=1018]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-30  104.1  15.4    3.8e-30  104.1  15.4    3.1  3  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1  15.4   2.1e-34   3.8e-30       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -1.9   0.3      0.23   4.2e+03      38      57 ..     798     817 ..     792     822 .. 0.80
   3 ?   -1.6   5.2       0.2   3.6e+03      15      59 ..     889     933 ..     887     939 .. 0.76

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 2.1e-34
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msf+ v+P++++aaaa+lagi+sals+a+aaa+ ptta+++a+aDeVSaa+++lf+a++q++qal+a+aa+fh++fv  l++
  gi|121637559|ref|YP_977782.1|  1 MSFLLVEPDLVTAAAANLAGIRSALSEAAAAASTPTTALASAGADEVSAAVSRLFGAYGQQFQALNARAATFHAEFVSLLNG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a++Y+ aEaa
  gi|121637559|ref|YP_977782.1| 83 GAAAYTGAEAA 93
                                   *********97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.23
                                    ----SSSSHHHHHHHHHHHH CS
                             PE  38 avlaaaaDeVSaaiAalfsa 57 
                                    a+ a aa +VS a+  +++a
  gi|121637559|ref|YP_977782.1| 798 ALQALAAGDVSGAVTDVLGA 817
                                    57788999999999888776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHH CS
                             PE  15 aadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsaha 59 
                                    a  l+++gs +++a a a+++t+ v a  a    aa+Aal++a a
  gi|121637559|ref|YP_977782.1| 889 AMTLNAVGSPITTAIAFAESTTAFVSAVQAGNLQAAAAALVGAPA 933
                                    567788888888888888888887777788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1018 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.01u 0.32s 00:00:01.33 Elapsed: 00:00:00.52
# Mc/sec: 5887.35
//
Query:       gi|121637560|ref|YP_977783.1|  [L=352]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-26   92.2   0.0    7.7e-26   91.3   0.0    1.5  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      3e-20   72.8   0.0    5.9e-20   71.9   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   8.6e-30   7.7e-26       3     184 .]     169     323 ..     167     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 8.6e-30
                                    HHHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
                Semialdhyde_dhC   3 PLlda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                    P l+a l+e+  v+v++++++SGaG++                 a+++  g+++ g++ +y+   +++++pe+++ l+av
  gi|121637560|ref|YP_977783.1| 169 PALAAdLIEPA-VTVVAVSGTSGAGRA-----------------ATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAV 230
                                    66666577775.**************7.................************************************ PP

                                    HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTCSSSEEEE CS
                Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaapevkvvvneeedrPtpaavaggtnsvsVG 161
                                     ++ + ++ft+      v++P+ rG+++++t++++    ++++++e+ ++a e++++ ++e++ P + av+g +n+++++
  gi|121637560|ref|YP_977783.1| 231 TDRDVSVSFTP------VLIPASRGILATCTARTRSPLSQLRAAYEKAYHA-EPFIYLMPEGQLPRTGAVIG-SNAAHIA 302
                                    ***********......*****************855579***********.*******************9.9****** PP

                                    EEEEETTCTTEEEEEEEEETTTT CS
                Semialdhyde_dhC 162 RirkdemgdeglklvvvgDNllk 184
                                     + +de+ ++ +++++++DNl+k
  gi|121637560|ref|YP_977783.1| 303 -VAVDEDAQT-FVAIAAIDNLVK 323
                                    .*****9986.**********97 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   6.6e-24   5.9e-20       1     113 [.      11     140 ..      11     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 6.6e-24
                                    EEEEETTTSHHHHHHHHHHHCTSS.....EEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpe.....velvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalp 75 
                                    kva+ Ga+Gy G e+lrlL  hp      + + +l++ ++ aG++l e++++l+  +  +ve+++++ l + d vflalp
  gi|121637560|ref|YP_977783.1|  11 KVAVAGASGYAGGEILRLLLGHPAyadgrLRIGALTAATS-AGSTLGEHHPHLTPLAHRVVEPTEAAVLGGHDAVFLALP 89 
                                    7*********************983333355667777666.*************************************** PP

                                    HHHHHHHHHHHHHTTSEEEESSSTTTTST..............TSEBE-HHH CS
                 Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkd..............davyvlpev 113
                                    +g s+ la++l + ++ +iD  +dfRl d               ++y+lpe+
  gi|121637560|ref|YP_977783.1|  90 HGHSAVLAQQL-SPETLIIDCGADFRLTDaavwerfygsshagSWPYGLPEL 140
                                    **********9.88889**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2366.51
//
Query:       gi|121637561|ref|YP_977784.1|  [L=404]
Description: bifunctional ornithine acetyltransferase/N-acetylglutamate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-127  424.8   6.0   2.6e-127  424.6   6.0    1.0  1  ArgJ      ArgJ family
  ------ inclusion threshold ------
        0.7   10.5   3.7         17    6.0   0.1    3.4  3  FlgT_N    Flagellar assembly protein T, N-terminal domain


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.6   6.0  2.9e-131  2.6e-127       2     376 .]      24     404 .]      23     404 .] 0.95

  Alignments for each domain:
  == domain 1  score: 424.6 bits;  conditional E-value: 2.9e-131
                                    EEEEXXSSS...SXXEEEEEEEEEEEE.EEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHH CS
                           ArgJ   2 aagvaagikkk.kkdlalivseepasa.aavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeem 79 
                                    aagvaagik++ + dlal+++e p  a a+vfT+n+vkAapv ++++vl++++ +rav++nsg ANa+tg +G++d++++
  gi|121637561|ref|YP_977784.1|  24 AAGVAAGIKASgALDLALVFNEGPDYAaAGVFTRNQVKAAPVLWTQQVLTTGR-LRAVILNSGGANACTGPAGFADTHAT 102
                                    899******777***********877659********************8776.************************** PP

                                    HHHHHHHH.....TSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETE CS
                           ArgJ  80 aeavaeal.....gikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgk 148
                                    aeava+al     ++ + ev+v+sTG+iG rlpm+k++ag++++v++++      +eaa+AimTTD vpK++a++   ++
  gi|121637561|ref|YP_977784.1| 103 AEAVAAALsdwgtETGAIEVAVCSTGLIGDRLPMDKLLAGVAHVVHEMHgglvggDEAAHAIMTTDNVPKQVALHH--HD 180
                                    *******97775444466****************************9978888999******************88..59 PP

                                    EEEEEEEEEXSSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHH CS
                           ArgJ 149 evtiagiaKGaGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedlee 228
                                    ++t++g+aKGaGm++P++aTmL+++ttDaa +++al+++l++a++ +F+++++Dg  STnDtvlll++ga+ e  +++++
  gi|121637561|ref|YP_977784.1| 181 NWTVGGMAKGAGMLAPSLATMLCVLTTDAAAEPAALERALRRAAAATFDRLDIDGSCSTNDTVLLLSSGAS-EIPPAQAD 259
                                    **********************************************************************9.459999** PP

                                    HHHHHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS---T CS
                           ArgJ 229 feealtevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeldp 308
                                    ++ea+ +v+ +L+ q+ +D+EG+tk v+v+V+ga++e++A  +a+++a++sLvKtAlfG+D+nwGR+laavG+a+++ldp
  gi|121637561|ref|YP_977784.1| 260 LDEAVLRVCDDLCAQLQADAEGVTKRVTVTVTGAATEDDALVAARQIARDSLVKTALFGSDPNWGRVLAAVGMAPITLDP 339
                                    ******************************************************************************** PP

                                    TS-EE..TTEEEEETTEE----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                           ArgJ 309 ekvsvllgevkvlekgepeevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                    +++sv++++  v+ +g  +     + +  l++++++i+vdlg g+++a++ t+DLs+ Yv+ N++Y++
  gi|121637561|ref|YP_977784.1| 340 DRISVSFNGAAVCVHGVGA---PGAREVDLSDADIDITVDLGVGDGQARIRTTDLSHAYVEENSAYSS 404
                                    ****************974...6788999*************************************86 PP

>> FlgT_N  Flagellar assembly protein T, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0019        17      16      42 ..      95     121 ..      79     145 .. 0.80
   2 ?    2.9   0.1     0.019   1.7e+02      14      42 ..     207     238 ..     203     254 .. 0.61
   3 ?    0.2   0.1      0.13   1.2e+03       2      31 ..     287     316 ..     286     319 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0019
                         FlgT_N  16 diAreqAredAlkqAllyagaqvgsis 42 
                                     +A+++A+++A+  Al++ g + g i+
  gi|121637561|ref|YP_977784.1|  95 GFADTHATAEAVAAALSDWGTETGAIE 121
                                    6899***************99988654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
                         FlgT_N  14 nddiAreqAredAlkq..Allyagaqvg.sis 42 
                                     d +A  +A+e+Al+   A  +  ++++ s s
  gi|121637561|ref|YP_977784.1| 207 TDAAAEPAALERALRRaaAATFDRLDIDgSCS 238
                                    45567777888888773334444555555555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.13
                         FlgT_N   2 wveaqGeAsIinnd..diAreqAredAlkqAl 31 
                                    +v+++G A+  ++d   +Ar+ Ar+  +k Al
  gi|121637561|ref|YP_977784.1| 287 TVTVTGAAT--EDDalVAARQIARDSLVKTAL 316
                                    588999993..333123467777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2851.39
//
Query:       gi|121637562|ref|YP_977785.1|  [L=294]
Description: acetylglutamate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-47  159.9   1.4    9.4e-47  159.6   1.4    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   1.4   5.2e-51   9.4e-47       1     241 []      29     270 ..      29     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 5.2e-51
                                    TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHH CS
                      AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrd 80 
                                    k+vVvK GG+++td      r++a++ a l++ g+++vvVhGgg+++ ++l++  g++ +++  g r+t  e ++va+++
  gi|121637562|ref|YP_977785.1|  29 KVVVVKYGGNAMTDDTL--RRAFAADMAFLRNCGIHPVVVHGGGPQITAMLRR-LGIEGDFKG-GFRVTTPEVLDVARMV 104
                                    689**********7766..7*********************************.*********.**************** PP

                                    HHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE............HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEE CS
                      AA_kinase  81 alaslgerlvaallaaglpavglsaaaldateagr..........degsdgnvesvdaeaieelleagvvpvltgfigld 150
                                    + +++g++lv  + a+g  avg+++++  +++a r          d g +g+v +v+++a+ +l++ag +pv++ ++  d
  gi|121637562|ref|YP_977785.1| 105 LFGQVGRELVNLINAHGPYAVGITGEDAQLFTAVRrsvtvdgvatDIGLVGDVDQVNTAAMLDLVAAGRIPVVSTLA-PD 183
                                    ***************************************************************************97.99 PP

                                    TTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHH CS
                      AA_kinase 151 eegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaa 230
                                     +g + ++++Dt+aa++AealgA+kl+ ltd+dG+y++ p+ +    l++ei+  ++++        Gm +k++a+l+a+
  gi|121637562|ref|YP_977785.1| 184 ADGVVHNINADTAAAAVAEALGAEKLLMLTDIDGLYTRWPDRD---SLVSEIDTGTLAQ-LLPTLESGMVPKVEACLRAV 259
                                    999999*************************************...9*****9999998.6678899************* PP

                                    HCTT-EEEEEE CS
                      AA_kinase 231 rrggipvvItn 241
                                     +g+  ++I++
  gi|121637562|ref|YP_977785.1| 260 IGGVPSAHIID 270
                                    ***99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2213.11
//
Query:       gi|121637563|ref|YP_977786.1|  [L=400]
Description: acetylornithine aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-105  352.6   0.1   2.7e-105  352.3   0.1    1.0  1  Aminotran_3      Aminotransferase class-III
     0.0011   18.3   0.1      0.002   17.5   0.1    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0044   16.0   0.0      0.013   14.5   0.0    1.7  2  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.3   0.1  4.5e-109  2.7e-105       5     405 ..      22     392 ..      18     393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 352.3 bits;  conditional E-value: 4.5e-109
                                    TB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT CS
                    Aminotran_3   5 eednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklap 84 
                                    ++   ++++  ++G+++tdvdg++y+Dl+++iav+ lGh+hP+v++av  q+ +l h+s +++++ep ++lae+l++l++
  gi|121637563|ref|YP_977786.1|  22 NYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTS-NLYATEPGIALAEELVALLG 100
                                    45555689999************************************************.******************** PP

                                    -..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                    Aminotran_3  85 kgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                     +   +vf++nsG+eA+e+A+Kl+r        t +tk++a ++afHGrt+g+l++tg+ +  +t f p++ +v+++ y 
  gi|121637563|ref|YP_977786.1| 101 ADQRtRVFFCNSGAEANEAAFKLSRL-------TGRTKLVAAHDAFHGRTMGSLALTGQ-PAKQTPFAPLPGDVTHVGYG 172
                                    95548********************9.......**************************.999***************** PP

                                    BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSS CS
                    Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGk 243
                                    d                 + al ++ +d++aAv +Epi ge Gvvv+++++la++r+++++ ++ll+ DEvqtG+GrTG+
  gi|121637563|ref|YP_977786.1| 173 D-----------------VDALAAAVDDHTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGA 235
                                    9.................999*********************************************************** PP

                                    SSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                    Aminotran_3 244 lfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaa 323
                                    +fA++h+g++pD++tlaK+l+gGlp+ a la    ++ l+pg hgsTfgGnp+ +a+alavl++++ + l+++a+ lg++
  gi|121637563|ref|YP_977786.1| 236 FFAHQHDGITPDVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLGKS 315
                                    ******************************************************************************** PP

                                    HHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHHH CS
                    Aminotran_3 324 lkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidelleilk 403
                                    l++g e+l +    i +vRg+Gl+++i l++++    k+  + a+++G l+  a ++virl+pplii ++++d ++ +l 
  gi|121637563|ref|YP_977786.1| 316 LRHGIEALGHP--LIDHVRGRGLLLGIALTAPHA---KDAEATARDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFVAALP 390
                                    *********66..7****************9999...468899******************************9998876 PP

                                    HH CS
                    Aminotran_3 404 ka 405
                                    ++
  gi|121637563|ref|YP_977786.1| 391 AI 392
                                    65 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.3e-07     0.002      12     167 ..      67     224 ..      62     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-07
                                    HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-S...EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTT CS
                Beta_elim_lyase  12 eamsdaqaaamlGdesYgedktvnrLedavaelfgke...aalfvpqGtaAnsillkillqrgeevivtepahihfdetg 88 
                                    ea++++++++    + Y++++++  L++++ +l+g++    ++f+ +G  An+ ++k+    g  ++v  +  +h ++ g
  gi|121637563|ref|YP_977786.1|  67 EAVTRQMSTLGHTSNLYATEPGIA-LAEELVALLGADqrtRVFFCNSGAEANEAAFKLSRLTGRTKLVAAHDAFHGRTMG 145
                                    455566665555556699999985.777777788888332355999**********877777778888888778888888 PP

                                    HHHHCC--EEEEE-EBTT.......TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HH.HHHHHHHHHHHC CS
                Beta_elim_lyase  89 aiaelagvklrdlknkea.......GkmdlekleaaikevgaheekiklisltvTnntagGqvvsle.elrevaaiakky 160
                                     +a  ++  +++ + +         G+ d+++l+aa+++       ++++ l+  +    G vv+++ +l+++++i+ ++
  gi|121637563|ref|YP_977786.1| 146 SLALTGQP-AKQTPFAPLpgdvthvGYGDVDALAAAVDD------HTAAVFLEPIMGE-SGVVVPPAgYLAAARDITARR 217
                                    88766433.333333333345558899**********99......4679999988885.6888876548999999**999 PP

                                    T-EEEEE CS
                Beta_elim_lyase 161 giplhlD 167
                                    g  l+lD
  gi|121637563|ref|YP_977786.1| 218 GALLVLD 224
                                    9999999 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.42   2.5e+03     245     264 ..      18      37 ..       5      39 .. 0.75
   2 !   14.5   0.0   2.2e-06     0.013      48     181 ..      91     230 ..      60     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.42
                                    TGGGS.SS--HHHHHHHHHH CS
                    Aminotran_5 245 pskfeaGTpnvagiiglgaa 264
                                     ++ + GTp++a + g ga+
  gi|121637563|ref|YP_977786.1|  18 VMMNNYGTPPIALASGDGAV 37 
                                    5667889****999887766 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-06
                                    HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE....EBET CS
                    Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi....plde 123
                                      e++ +l++a+++ ++ f+ +++ea++++ +    +l  +++ v  +   h+ ++   +l  +   +  ++     +++
  gi|121637563|ref|YP_977786.1|  91 LAEELVALLGADQRTRVFFCNSGAEANEAAFKLS--RLTGRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAplpgDVTH 168
                                    4556667999****************99988766..37777777777777788776666555443333333311125788 PP

                                    TSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH....TT-EEEEE-TTTTT CS
                    Aminotran_5 124 egeldldelekllnektklvaithvsnvtGtiqpveeigklakk....kgalvlvDaaqavg 181
                                     g  d+d+l++++++ t++v++  +  ++G++ p +   ++a++    +gal+++D +q+ +
  gi|121637563|ref|YP_977786.1| 169 VGYGDVDALAAAVDDHTAAVFLEPIMGESGVVVPPAGYLAAARDitarRGALLVLDEVQTGM 230
                                    89999**************************887666555555433226**********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2920.03
//
Query:       gi|121637564|ref|YP_977787.1|  [L=307]
Description: ornithine carbamoyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-52  177.5   0.0      3e-52  176.8   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.2e-47  161.6   0.0    1.9e-47  161.0   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.0   3.4e-56     3e-52       2     156 ..     148     302 ..     147     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 3.4e-56
                                    C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SS CS
                         OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwv 81 
                                    gl++ + Gd+ nn+a+sl+ + +  g++v+++aP+g+ pd+ v + a+  a+ +g+s+t+t d  +a++gaDv++td+w+
  gi|121637564|ref|YP_977787.1| 148 GLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAAPEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWT 227
                                    78999*************************************************************************** PP

                                    ETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  82 smgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    smg+e++ ++r+k ++++q+++ ll+la++daivlHcLPa+rg+E+td V+d+p+s+v+++aeNrlh++kAllv+
  gi|121637564|ref|YP_977787.1| 228 SMGQENDGLDRVKPFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALLVW 302
                                    *************************************************************************97 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   2.1e-51   1.9e-47       1     148 []       3     141 ..       3     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 2.1e-51
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT.-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkg.ktlallFeepStRTrvSfevAakrlGgkvlslseaediql 79 
                                    rh+l+ +dls++e  e+l+laaelk+++    +++ l+g + +a++F ++StRTr+Sfe+++++lGg++++++ + ++ql
  gi|121637564|ref|YP_977787.1|   3 RHFLRDDDLSPAEQAEVLELAAELKKDPV---SRRPLQGpRGVAVIFDKNSTRTRFSFELGIAQLGGHAVVVD-SGSTQL 78 
                                    8************************9996...677777779********************************.768888 PP

                                    TTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                       OTCace_N  80 ssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                    +     r+E+l+Dta+vlsryvdaiv+R++g+e+l+++a+ a+vpviNa+ +d+ HP+Q+LaDl+ti e
  gi|121637564|ref|YP_977787.1|  79 G-----RDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVINAL-SDEFHPCQVLADLQTIAE 141
                                    8.....88******************************************.****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2324.79
//
Query:       gi|121637565|ref|YP_977788.1|  [L=170]
Description: arginine repressor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-26   91.7   0.0    2.4e-26   91.3   0.0    1.2  1  Arg_repressor    Arginine repressor, DNA binding domain
    1.5e-24   85.6   0.0    2.4e-24   85.0   0.0    1.3  1  Arg_repressor_C  Arginine repressor, C-terminal domain
     0.0059   16.6   0.3      0.013   15.5   0.3    1.5  1  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.043   13.4   0.2      0.066   12.8   0.2    1.2  1  AA_kinase        Amino acid kinase family
      0.092   12.7   0.0       0.15   12.0   0.0    1.3  1  Type2_restr_D3   Type-2 restriction enzyme D3 domain


Domain annotation for each model (and alignments):
>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   6.7e-30   2.4e-26       1      69 [.      16      85 ..      16      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 6.7e-30
                                   SSHHHHHHHHHHHHHHS---SHHHHHHHHHTTT----HHHHHHHHHHHT-EEEE.TTSTSEEEE-B-SS- CS
                  Arg_repressor  1 ikkeerqklikkiikeekissQkelvelLkeeGidvtQatvSRdLkelglvkvr.aengeyvYvlpaets 69
                                   ++++ rq++i +i+++++++sQ+el++lL++eGi+vtQat+SRdL+elg+vk+r a++g+ +Yv+p+++s
  gi|121637565|ref|YP_977788.1| 16 ANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRgADGGTGIYVVPEDGS 85
                                   5899**************************************************99**********9975 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.0   6.6e-28   2.4e-24       2      67 ..     102     167 ..     101     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 6.6e-28
                                    HHH-SEEEEETTEEEEE-STTHHHHHHHHHHH-..TTEEEEEE-SSEEEEEE-TTS-HHHHHHHHH CS
                Arg_repressor_C   2 relvvsidsaenlvvikTlpGaAqavAaaiDslelpeilGtiAGdDTilvilrseedaeelaeklk 67 
                                     el+vs d ++nl+v++T+pGaA+++A+aiD++ lp+++GtiAGdDTilv++r+++++++la  ++
  gi|121637565|ref|YP_977788.1| 102 GELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFE 167
                                    6899*******************************************************9987765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   3.6e-06     0.013      12      54 ..      22      66 ..      20      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTE CS
                         HTH_20 12 RrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLv 54
                                   ++ri + L++a+ ++ +ela++l     +++++tls+ L++L    +v
  gi|121637565|ref|YP_977788.1| 22 QARIVAILSSAQVRSQNELAALLaaegiEVTQATLSRDLEELG---AV 66
                                   689********************877666************94...44 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.8e-05     0.066      68     171 ..      14     105 ..       2     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                    E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEE CS
                      AA_kinase  68 stleeagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfi 147
                                    + ++ ag  a+ +a++s ++  +++ laa+l+a g+ + + ++++         ++e++ a +++       + v+++++
  gi|121637565|ref|YP_977788.1|  14 VAANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSR---------DLEELGAVKLRGADGGTGIYVVPEDG 84 
                                    5566777788889****************************9765.........667999999999986657******85 PP

                                    EEETTTEEEEE-HHHHHHHHHHHC CS
                      AA_kinase 148 gldeegelgrgssDtiaallAeal 171
                                     +++ g    g++D++a+ll+e+l
  gi|121637565|ref|YP_977788.1|  85 -SPVRGV--SGGTDRMARLLGELL 105
                                    .999999..89**********987 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.15      14      57 ..      21      63 ..      18      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                 Type2_restr_D3 14 RRtiilkylleskkrrsleeikayLklagleEdveTIkDDiqgl 57
                                   R + i+ +l+ ++ +rs +e+ a L++ g+e + +T+  D++ l
  gi|121637565|ref|YP_977788.1| 21 RQARIVAILSSAQ-VRSQNELAALLAAEGIEVTQATLSRDLEEL 63
                                   7889999996666.***********************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1197.96
//
Query:       gi|121637566|ref|YP_977789.1|  [L=398]
Description: argininosuccinate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-185  616.8   0.0   2.1e-185  616.5   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
      0.039   13.5   0.0      0.062   12.8   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.5   0.0  2.4e-189  2.1e-185       1     387 [.       6     392 ..       6     393 .. 1.00

  Alignments for each domain:
  == domain 1  score: 616.5 bits;  conditional E-value: 2.4e-189
                Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYed 80 
                                    +LaysGGlDtsv+i+++ +++g+ev+ava+d+Gq++e++d ++++al++gav++vvvDa++ef+e y++p++ +nalY+d
  gi|121637566|ref|YP_977789.1|   6 ILAYSGGLDTSVAISWIGKETGREVVAVAIDLGQGGEHMDVIRQRALDCGAVEAVVVDARDEFAEGYCLPTVLNNALYMD 85 
                                    79****************************************************************************** PP

                Arginosuc_synth  81 rYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgip 160
                                    rY+l++a++RPli+k+lv++a+++g+ +vahGctGkGnDqvRfev+++slaPdl+v+aPvR++++tRe++i++a+e++ip
  gi|121637566|ref|YP_977789.1|  86 RYPLVSAISRPLIVKHLVAAAREHGGGIVAHGCTGKGNDQVRFEVGFASLAPDLEVLAPVRDYAWTREKAIAFAEENAIP 165
                                    ******************************************************************************** PP

                Arginosuc_synth 161 vevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvleliekln 240
                                    ++vtk++p+siD+n++gr++e+g+Le+++nap++diy++t+dp+ ++  p+ev ++fe+GvPv++dg+++s+l++ie+ln
  gi|121637566|ref|YP_977789.1| 166 INVTKRSPFSIDQNVWGRAVETGFLEHLWNAPTKDIYAYTEDPTINWGVPDEVIVGFERGVPVSVDGKPVSMLAAIEELN 245
                                    ******************************************************************************** PP

                Arginosuc_synth 241 eiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkeald 320
                                    ++ag++GvGR+D+vedRlvg+ksReiYeap+a+vLi+ah++le++tlere+ +fk+++++++aelvY+Glw+sPlk+al+
  gi|121637566|ref|YP_977789.1| 246 RRAGAQGVGRLDVVEDRLVGIKSREIYEAPGAMVLITAHTELEHVTLERELGRFKRQTDQRWAELVYDGLWYSPLKAALE 325
                                    ******************************************************************************** PP

                Arginosuc_synth 321 afiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqakly 387
                                    af++ktqe+v+G+vr+ l+ G+++v+gR+s+eslYd++la+yde d+fdq++a+Gf+++hgl++kl+
  gi|121637566|ref|YP_977789.1| 326 AFVAKTQEHVSGEVRLVLHGGHIAVNGRRSAESLYDFNLATYDEGDSFDQSAARGFVYVHGLSSKLA 392
                                    ***************************************************************9975 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-06     0.062       2      44 ..       5      47 ..       4      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-06
                                   EEEE--SSHHHHHHHHHH.HHH-SEEEEEEEESS-T.TSHHHHHH CS
                           QueC  2 avvllSGGlDSttvlala.kkegkevealtfdYgqr.hkkeleaa 44
                                   +++  SGGlD ++++ +  k++g ev a+ +d gq  ++  +++ 
  gi|121637566|ref|YP_977789.1|  5 VILAYSGGLDTSVAISWIgKETGREVVAVAIDLGQGgEH--MDVI 47
                                   67789*****9999887626778***********98433..3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2640.04
//
Query:       gi|121637567|ref|YP_977790.1|  [L=470]
Description: argininosuccinate lyase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-59  200.3   0.0    7.4e-59  199.7   0.0    1.3  1  Lyase_1   Lyase
    4.1e-24   85.1   0.2    3.4e-23   82.2   0.1    2.5  2  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.0   8.3e-63   7.4e-59       6     312 .]      16     306 ..      11     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 8.3e-63
                                    ETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHH CS
                        Lyase_1   6 kadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnm 85 
                                      +   ++ +++  ++  l  +d +a+ a +  +  a+++++e+ +  +++ld +++++  +  f   v +e+ + a+++
  gi|121637567|ref|YP_977790.1|  16 GPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRDGLLAGLDSLAQDVADG-SFGPLVTDEDVHAALER 94 
                                    44555678899999999***9*****************************************.77777889********* PP

                                    HHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEE CS
                        Lyase_1  86 nlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtP 165
                                     l + +g       +  + +  g+S+nDqv+  +r++l++a+  ++ + + + + al e+a ++ + +++G Thlq A+P
  gi|121637567|ref|YP_977790.1|  95 GLIDRVG------PDLGGRLRAGRSRNDQVAALFRMWLRDAV-RRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQP 167
                                    *******......9****************************.66*********************************** PP

                                    EEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHH CS
                        Lyase_1 166 vtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDav 245
                                    + l++ l a+a+ l rd+ r+ +  kr  v++ g+g+++g  l+ dp    ++a+ l+ ++     a+ns++a+++rD+ 
  gi|121637567|ref|YP_977790.1| 168 ILLAHHLLAHAHPLLRDLDRIVDFDKRAAVSPYGSGALAGSSLGLDPD---AIAADLG-FSA---AADNSVDATAARDFA 240
                                    ************************************************...*******.888...9************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                        Lyase_1 246 vellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                    +e++++ +++a++Ls++aeD+++ ss+e+g+v+l +  s+ GSSiMP+K+NP+ +El +g++gr +G
  gi|121637567|ref|YP_977790.1| 241 AEAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWST-GSSIMPQKKNPDIAELARGKSGRLIG 306
                                    ****************************************.***********************988 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.27   2.4e+03      46      63 ..      74      93 ..      44      94 .. 0.67
   2 !   82.2   0.1   3.8e-27   3.4e-23       1      68 [.     369     436 ..     369     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                                   HHH.HH-TT--.GGGGGGSS CS
                         ASL_C2 46 elk.eisplle.edveeaLd 63
                                     + ++ pl++ edv++aL+
  gi|121637567|ref|YP_977790.1| 74 VADgSFGPLVTdEDVHAALE 93
                                   33334458988899999985 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 3.8e-27
                                    STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--GGGGGGSSHHHHT CS
                         ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplleedveeaLdpeasV 68 
                                    +++ATdlA++Lvr+G+pFR AHe++g+avr+ae++g+ l+elt +el++isp l+++v+e+L++e+sV
  gi|121637567|ref|YP_977790.1| 369 YTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPELTPQVREVLTIEGSV 436
                                    789****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3408.04
//
Query:       gi|121637568|ref|YP_977791.1|  [L=353]
Description: chalcone synthase pks10 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-20   72.1   0.0    7.3e-20   71.4   0.0    1.3  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
    7.3e-17   61.8   0.0    1.3e-16   60.9   0.0    1.4  1  Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal 
      1e-14   54.5   0.0    2.6e-14   53.2   0.0    1.6  2  FAE1_CUT1_RppA   FAE1/Type III polyketide synthase-like prote
    9.5e-10   38.5   0.0    5.6e-08   32.8   0.0    2.3  2  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.6e-23   7.3e-20      22     220 ..      10     196 ..       2     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.6e-23
                Chal_sti_synt_N  22 alPeqvveqeklvdyylrvtksedlaelkeklerlcdkstvkkryivlteeileenPeltaemapsldarleivnaevlk 101
                                    alP     q +l+d ++ +   e   +    +++l   + v  r++vl    le++P+lt  +++     ++i  ++ ++
  gi|121637568|ref|YP_977791.1|  10 ALPPYRYSQRELTDSFVSIPDFEGYED---IVRQLHASAKVNSRHLVLP---LEKYPKLTDFGEA-----NKIFIEKAVD 78 
                                    788888889999999999888888554...45667788999******97...88******99987.....58999999** PP

                Chal_sti_synt_N 102 lgkeaalkalkewGrPkskithlvfvsssevelPGadlklakklGlrpsvkrvmlyflGcygGatvlrlakdiaennkGa 181
                                    lg +a ++al e G   +++  l+  + +++ +P  d  +a +lGlr++v+rv l+ lGc +Ga+++    d     +  
  gi|121637568|ref|YP_977791.1|  79 LGVQALAGALDESGLRPEDLDVLITATVTGLAVPSLDARIAGRLGLRADVRRVPLFGLGCVAGAAGVARLHDYLRGAPDG 158
                                    **************999***********************************************9988888887777777 PP

                Chal_sti_synt_N 182 rvlvvaseitvlgfrgPskdrlddlvGaalfGdGaaavi 220
                                       +v+ e+  l++ g     l  lvG alf dGaaav+
  gi|121637568|ref|YP_977791.1| 159 VAALVSVELCSLTYPGYK-PTLPGLVGSALFADGAAAVV 196
                                    7778899******97765.56779*************97 PP

>> Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   2.9e-20   1.3e-16       8     148 ..     219     351 ..     212     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.9e-20
                Chal_sti_synt_C   8 tflPetdgvidgklteeGltfkllrdlPekieenieeflkklleklGieefndlfwivhPGGpaildrleaklklekekl 87 
                                    ++ P++  ++   +  +G+++ l rdl   +e+ + + +++ l+  G +  +   w+ hPGGp i++++ ++l+l ++ l
  gi|121637568|ref|YP_977791.1| 219 HLYPDSLRTMGYDVGSAGFELVLSRDLAAVVEQYLGNDVTTFLASHGLSTTDVGAWVTHPGGPKIINAITETLDLSPQAL 298
                                    6678888889999999*********************************99999************************** PP

                Chal_sti_synt_C  88 easrkvlseyGnvssatvlyvldelrdkelkkklattgegkewGlllafGPGltietlllr 148
                                    e + + l e Gn+ssa+vl+vl   rd+ +k   +        Gl++a+GPG+  e +llr
  gi|121637568|ref|YP_977791.1| 299 ELTWRSLGEIGNLSSASVLHVL---RDTIAKPPPS-----GSPGLMIAMGPGFCSELVLLR 351
                                    ******************9986...7733333332.....358*************99997 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   5.7e-18   2.6e-14      88     204 ..      81     198 ..      60     207 .. 0.90
   2 ?   -2.3   0.0      0.49   2.2e+03     248     268 ..     240     260 ..     230     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 5.7e-18
                 FAE1_CUT1_RppA  88 fgavdellaktkvspkdidilvvncslfsptPslsamvvnryklredvksynLsgmGCsAglisidlaknllqvhkntla 167
                                    ++a++  l +++++p+d+d+l++++ +  + Psl a++  r +lr dv+ + L g+GC Ag   +   ++ l+ +++ +a
  gi|121637568|ref|YP_977791.1|  81 VQALAGALDESGLRPEDLDVLITATVTGLAVPSLDARIAGRLGLRADVRRVPLFGLGCVAGAAGVARLHDYLRGAPDGVA 160
                                    5677788999********************************************************************** PP

                 FAE1_CUT1_RppA 168 lvvstEnitlnwYvGnersm..llanclFRvGgaavlls 204
                                     +vs+E ++l +Y G + ++  l++ +lF  G+aav+ +
  gi|121637568|ref|YP_977791.1| 161 ALVSVELCSL-TYPGYKPTLpgLVGSALFADGAAAVVAA 198
                                    ******9987.69998877656*************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.49
                 FAE1_CUT1_RppA 248 slskdlvkvagealkknlttl 268
                                     ls+dl++v+ + l +++tt+
  gi|121637568|ref|YP_977791.1| 240 VLSRDLAAVVEQYLGNDVTTF 260
                                    478999999999999888875 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.018        82       1      22 [.      88     109 ..      88     160 .. 0.67
   2 !   32.8   0.0   1.3e-11   5.6e-08       1      90 []     261     352 ..     261     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                                    HHHTT--GGG-SEEEE-SSSHH CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlr 22 
                                    L+++gl+ped+d+l+   +   
  gi|121637568|ref|YP_977791.1|  88 LDESGLRPEDLDVLITATVTGL 109
                                    789***********98776544 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 1.3e-11
                                    HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GG...GB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEE CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpee...kvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgf 77 
                                    L+ +gl++ d+ a v h    +ii+a+ + l+l+++    +  +l e+Gn+s+as++  L + ++ +   +g   l++++
  gi|121637568|ref|YP_977791.1| 261 LASHGLSTTDVGAWVTHPGGPKIINAITETLDLSPQaleLTWRSLGEIGNLSSASVLHVLRDTIA-KPPPSGSPGLMIAM 339
                                    6889******************************996634555679*******************.7899********** PP

                                    ETTTEEEEEEEE- CS
                  ACP_syn_III_C  78 GaGltwgaallrw 90 
                                    G G+    +llrw
  gi|121637568|ref|YP_977791.1| 340 GPGFCSELVLLRW 352
                                    *****99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2530.66
//
Query:       gi|121637569|ref|YP_977792.1|  [L=2126]
Description: polyketide synthase pks7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-92  310.9   0.2      2e-92  310.1   0.2    1.4  1  Acyl_transf_1    Acyl transferase domain
    2.2e-91  306.0   1.0    7.2e-91  304.3   1.0    2.0  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    2.9e-59  200.0   1.7    2.9e-59  200.0   1.7    3.3  3  KR               KR domain
    2.5e-52  178.0   3.6    7.9e-52  176.3   3.6    1.9  1  PS-DH            Polyketide synthase dehydratase
    9.8e-43  144.9   0.6      3e-42  143.3   0.6    1.9  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    2.2e-19   70.8   0.4    1.3e-16   61.8   0.1    3.4  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    2.9e-16   59.9   0.0    5.9e-15   55.7   0.0    2.5  2  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.1e-13   51.2   0.2    6.1e-12   45.6   0.0    3.5  3  ADH_zinc_N       Zinc-binding dehydrogenase
    8.8e-13   48.4   0.1    2.5e-12   47.0   0.1    1.9  1  PP-binding       Phosphopantetheine attachment site
    1.3e-11   44.4   6.5    2.2e-11   43.6   0.3    3.1  3  adh_short        short chain dehydrogenase
    8.4e-09   34.9   5.4    8.4e-09   34.9   5.4    2.0  2  PikAIV_N         Narbonolide/10-deoxymethynolide synthase Pik
      1e-07   31.7   0.2    1.9e-07   30.8   0.2    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.8e-06   27.5   1.5    3.6e-06   26.6   0.2    2.1  3  Thiolase_N       Thiolase, N-terminal domain
    3.4e-05   24.1   0.4     0.0001   22.6   0.4    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    5.5e-05   23.0   2.6    0.00014   21.7   2.6    1.7  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    0.00016   20.9   0.0    0.00028   20.1   0.0    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0011   18.5   0.0     0.0017   17.9   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0073   15.3   0.0      0.012   14.7   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
       0.12   12.0   1.0         12    5.5   1.9    2.6  2  SAT              Starter unit:ACP transacylase in aflatoxin b
       0.26   11.0   2.6        1.9    8.2   0.2    2.7  2  MoCF_biosynth    Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.1   0.2   2.3e-95     2e-92       2     317 ..     564     884 ..     563     886 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.1 bits;  conditional E-value: 2.3e-95
                                    EEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--T.TGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   2 fvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpe.glldaiqfvqpaLaavqialaellksk 80 
                                    fvf+GqG+Qw GMG++L +t ++fa+ i+r+++a++++  +s+ldvlr +p  + ld++++vqpaL av+++lael++s 
  gi|121637569|ref|YP_977792.1| 564 FVFPGQGAQWLGMGAQLCATAPVFAEHIHRCERALREHVEWSLLDVLRGAPGaPGLDRVDVVQPALWAVMVSLAELWRSV 643
                                    9*************************************************97689************************* PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS....HHHHHHH..TT.EEEEEEECCC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel...aeeeeklrcqddvvgavansprr 157
                                    Gv p+av+GHS+GE+Aaa+vagals+ +a+ +v+lrsrl  +l g+g+m +++    ++e+++ ++ d++  a++n+ ++
  gi|121637569|ref|YP_977792.1| 644 GVVPDAVIGHSQGEIAAAYVAGALSLWDAAAVVALRSRLLVRLGGAGGMVSLACgqpQAEKLASQWGDRLNIAAVNGVSS 723
                                    **************************************************999995555555556*************** PP

                                    CECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHH CS
                  Acyl_transf_1 158 vvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeyw 237
                                    vv++g+++a+ el++r+++eg++a++++v++a+hs+qvdai+++l +al  i pr+++va+ s+++ + +++  + aeyw
  gi|121637569|ref|YP_977792.1| 724 VVLAGETDAVTELMQRCEAEGIRARRIDVDYASHSAQVDAIREELIAALRGIEPRTSTVAFFSTVTGELMDTAGVNAEYW 803
                                    ******************************************************************************** PP

                                    HHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCC..CCCTEETTSS-HHHCHHHHHHHHHHC CS
                  Acyl_transf_1 238 vanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksat..lvGklkrdltdflvtflyllakahlt 315
                                    ++++r+pv+f+ av++a++ +++vfve spH++l a++e+tl + + +++ +  ++++l rd ++ + +f  ++++ah++
  gi|121637569|ref|YP_977792.1| 804 YRSIRQPVQFERAVRNAFDGGYRVFVESSPHPVLIAGIEETLVDCDRGATGEpiVIPTLGRDDGG-VGRFWLSAGQAHVA 882
                                    *******************************************9666655433399*********.*************9 PP

                                    T- CS
                  Acyl_transf_1 316 gs 317
                                    g+
  gi|121637569|ref|YP_977792.1| 883 GV 884
                                    98 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.3   1.0     8e-94   7.2e-91       2     253 .]      35     284 ..      34     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.3 bits;  conditional E-value: 8e-94
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadklydpparaagkiktklggfld.vddfdpeffgis 78 
                                    epva+vGmg+r+Pgg+d +e++wel+ +grda+se+padr wd+ +l+dp+++a gk++t+ ggfl+ v+ fd+effgi 
  gi|121637569|ref|YP_977792.1|  35 EPVAVVGMGCRYPGGVDsPETLWELVAHGRDAVSEFPADRgWDVAGLFDPDPDAVGKSYTRCGGFLTdVAGFDAEFFGIA 114
                                    89****************************************************************************** PP

                                    HHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHH CS
                  ketoacyl-synt  79 preaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagri 158
                                    p+ea amdpqqrllle++weale+ag++p +l+gs++gvf+Gv +g+y+++     d    + +    g+ + +v++gr+
  gi|121637569|ref|YP_977792.1| 115 PSEALAMDPQQRLLLEVSWEALERAGIDPITLRGSQTGVFAGVFHGSYGGQGRVPGDL---ERYG-LRGS-TLSVASGRV 189
                                    ************************************************9877777555...4455.4465.89******* PP

                                    HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-B CS
                  ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvl 238
                                    +y lgl+Gp+v+vdtACsSslva+h+avqslr ge+d+al+GGv+++ tp  ++ fs++++ls+dgrcka++ +adG+ +
  gi|121637569|ref|YP_977792.1| 190 AYVLGLQGPAVSVDTACSSSLVALHLAVQSLRLGECDLALVGGVTVMATPAMFIEFSRQRALSADGRCKAYAGAADGTAF 269
                                    ******************************************************************************** PP

                                    B-EEEEEEEEECHHH CS
                  ketoacyl-synt 239 GEGvGavvLkrleda 253
                                    +EG+G++vL rl+da
  gi|121637569|ref|YP_977792.1| 270 AEGAGVLVLARLADA 284
                                    ************997 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.85   7.6e+02      23      75 ..     719     768 ..     687     778 .. 0.66
   2 ?   -1.0   0.0       1.5   1.4e+03       4      55 ..    1505    1573 ..    1503    1579 .. 0.70
   3 !  200.0   1.7   3.2e-62   2.9e-59       1     179 [.    1694    1872 ..    1694    1873 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.85
                                    HHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HH.HHHHHHHHH CS
                             KR  23 kgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkd.avealleei 75 
                                    +g +++vl + +    ++ ++l++++ea g++ + +++D ++++ +v a+ ee+
  gi|121637569|ref|YP_977792.1| 719 NGVSSVVLAGET----DAVTELMQRCEAEGIRARRIDVDYASHSaQVDAIREEL 768
                                    445555555555....66777999999999999988888665540444444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                     EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS...................--HHHHHHHHHHHHTT-EE CS
                             KR    4 litGGlGgLGlelarwlaekgarhlvllsRsa.................aadedskaliaelealgaev 55  
                                     l+  G+Gg+G++ +      ga+  v  sR +                 ++ e ++a++++ e +g++v
  gi|121637569|ref|YP_977792.1| 1505 LVHAGTGGVGMAAVSLARYWGAEVFVTASRAKwdtlramgfddihisdsRSLEFEEAFLRATEGSGVDV 1573
                                     78889*****99988877889999999999976666666666666555544444555666666666665 PP

  == domain 3  score: 200.0 bits;  conditional E-value: 3.2e-62
                                     SEEEEETTTSHHHHHHHHHHHH.HHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlae.kgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77  
                                     gt+++tGG+G  G ++a++l++ +g ++lvl+sRs+++ +++++  a l++ ga+v vv++Dv+d+da++all+ ++ 
  gi|121637569|ref|YP_977792.1| 1694 GTVVVTGGTGMAGSAVATHLVRrHGVANLVLVSRSGEQADRAAEVAALLREGGAQVAVVSCDVADRDALAALLAGLDP 1771
                                     899******************6377**********88888888888888999************************95 PP

                                     HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR   78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaf 155 
                                     +  p+kGv+haAgvl+d+ ++ +t +++++vl++Kv+GawnLhel+ed +l  fv+fSS+ag++g++ q+nYaaaNaf
  gi|121637569|ref|YP_977792.1| 1772 RY-PLKGVFHAAGVLDDAVITGLTPDRVDTVLRAKVDGAWNLHELTEDMDLSAFVVFSSMAGIVGTPAQGNYAAANAF 1848
                                     55.*************************************************************************** PP

                                     HHHHHHHHHHHHHTEEEEEE--BT CS
                             KR  156 lDalaeyrrsqglpavsinwglwa 179 
                                     lD+l++yrrs+gl+++s++wglw+
  gi|121637569|ref|YP_977792.1| 1849 LDGLVAYRRSRGLAGLSVAWGLWE 1872
                                     ***********************8 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   3.6   8.8e-55   7.9e-52       1     297 [.     934    1204 ..     934    1205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 8.8e-55
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlp 78  
                                     h ll + v+ +++  vv   r+++   pwL+DH+v+  v++Pg+g++e+al A+ ++     + +l++++++++lvlp
  gi|121637569|ref|YP_977792.1|  934 HGLLAAVVQRPDSGGVVLTGRISVVAAPWLADHAVGPVVLFPGTGFVELALRAGDEVG----CSVLQELTLQAPLVLP 1007
                                     66888889999**********************************************9....999************* PP

                                     -SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HHH CS
                          PS-DH   79 edepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrsvssae 156 
                                       ++v+vq+++   e++ +r+++ ++ + +++++ +wt+ha+G + ++  ++     +++l  + ++p+ +r++++a+
  gi|121637569|ref|YP_977792.1| 1008 -ADGVRVQVVVGGVEQSGTRNVWVYSAAGQADSSPGWTLHAQGVLGVGSVQP-----AAEL--SVWPPVGARAMDVAD 1077
                                     .789********998888888888888888888888**********998777.....3444..6679999999***** PP

                                     HHHHHHHHSEEE-GGG--EEEEEEETTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEEE CS
                          PS-DH  157 fYerlaargleyGpsFqglralwrgdgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylPv 234 
                                      Y+ laarg+ yGp+F+gl+alwr+  e++a ++lpe +  +   + +hPa+lDaal++ ++      e++++++lP+
  gi|121637569|ref|YP_977792.1| 1078 GYQVLAARGYGYGPAFRGLQALWRRGAEVFADVTLPEGVPIRG--FGIHPAVLDAALHAWGI-----VEGEQQTMLPF 1148
                                     ************************************9999664..*************8843.....489******** PP

                                     EEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XXXXX CS
                          PS-DH  235 aierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrvereals 297 
                                     +++ + ++       + ++v++rl+  g  + ++ ++l d +G +v+++++l +r+v+++als
  gi|121637569|ref|YP_977792.1| 1149 SWQGVCLHA-----SGAARVRVRLAPVG--RGAVPVELADPQGLPVLSVRQLMVRPVSAAALS 1204
                                     ********5.....3579******9998..899**************************9987 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   0.6   3.4e-45     3e-42       1     117 [.     292     408 ..     292     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 3.4e-45
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a ++gsavn+dga+n+l +png aq+r+i++ala+a++  +dvd+ve hgtgt+lgDpiE++a+ +++g++  ++pl++
  gi|121637569|ref|YP_977792.1| 292 LALVRGSAVNQDGASNGLATPNGPAQQRVITAALASARLGVADVDVVEGHGTGTTLGDPIEAQAILATYGQRPADRPLWL 371
                                    689***************************************************************************** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    gS+KsniGH+ aAaGva++ik+v+a++hgv+p+tl++
  gi|121637569|ref|YP_977792.1| 372 GSIKSNIGHTSAAAGVAGVIKMVQAMRHGVLPKTLHV 408
                                    ************************************8 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.1   1.5e-19   1.3e-16       7     133 .]    1549    1679 ..    1543    1679 .. 0.81
   2 ?    5.3   0.0     0.044        39      44     106 ..    1692    1751 ..    1688    1763 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.5e-19
                                     E..ETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--G CS
                   ADH_zinc_N_2    7 i..dyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyefl 78  
                                        d+r+ +fe    +at+g gvDvvl++++ge + +asl++lp gGr++++g++ ++++    ++  +g + ++  l
  gi|121637569|ref|YP_977792.1| 1549 HisDSRSLEFEeaflRATEGSGVDVVLNSLAGEFT-DASLRLLPSGGRFIELGKTDIRDGQTVAER-HRGVRYRAFDL 1624
                                     445999999999999****************9977.*******988*******7544444333333.44455555555 PP

                                     GG...-...-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   79 fsmkas..aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                     +++  +  + a +l e++ l+++G l   + ++f+   a+ A+r + ++r++GK+Vl
  gi|121637569|ref|YP_977792.1| 1625 VEA--GpdRIAAMLSEVVGLLAAGVLARLPVKTFDARCAPAAYRFVSQARHIGKVVL 1679
                                     544..45566666*************999999************************8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.044
                                     EEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH----E CS
                   ADH_zinc_N_2   44 pggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGklrpvv 106 
                                     +g G++v+ gg+ ++    +  + r +++v    l+s++   qad+ +e+aal+ eG  ++ v
  gi|121637569|ref|YP_977792.1| 1692 AG-GTVVVTGGTGMAGSAVATHLVR-RHGVANLVLVSRSGE-QADRAAEVAALLREGGAQVAV 1751
                                     55.9999999876777666666644.555555566655555.***************988877 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   6.6e-18   5.9e-15       1     112 []     411     528 ..     411     528 .. 0.89
   2 ?    1.3   0.0       0.5   4.5e+02      58      84 ..    2046    2072 ..    2034    2097 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 6.6e-18
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeesk.eeslprLlvlsgrteeave 75 
                                    P p+++ ++ g + + tep pw+       +gv+sfG++G+n+HviL++++  ++  +++ +++    +vls+r+++a++
  gi|121637569|ref|YP_977792.1| 411 PTPHVD-WSAGAVSLLTEPRPWHVPGrprrAGVSSFGISGTNAHVILEEAPAVEPVGAAHgNDPVAVPWVLSARSAQALT 489
                                    99****.***************54444578*********************998888888678888999*********** PP

                 KAsynt_C_assoc  76 allekleehlldaellsllneilseeisr..lpyRGyav 112
                                    +++ +l ++   +e ++ l+   s   +r  +++R+ +v
  gi|121637569|ref|YP_977792.1| 490 NQARRLLAWVGADENVRPLDVGWSLVNTRslFDHRAVVV 528
                                    *******************99998776666799998876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.5
                 KAsynt_C_assoc   58 eslprLlvlsgrteeaveallekleeh 84  
                                     +  +rL+++sg +++++++ ++++   
  gi|121637569|ref|YP_977792.1| 2046 HLDSRLVTASGSDQQSLSDRVDDITRE 2072
                                     4578**************999998776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   6.8e-15   6.1e-12       1      90 [.    1512    1601 ..    1512    1623 .. 0.88
   2 ?   -1.2   0.1       2.1   1.9e+03      31      33 ..    1715    1717 ..    1692    1771 .. 0.51
   3 ?    0.7   0.0      0.55     5e+02      19      76 ..    1995    2047 ..    1981    2050 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 6.8e-15
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEE.EETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadev.inykea.dlverikeltggegvdvvfecvGsgatleaal 76  
                                     gvG+aav lA+ +Gaev++++s + k + ++ +G d + i  ++  +++e+  ++t+g gvdvv++ ++ g+  +a+l
  gi|121637569|ref|YP_977792.1| 1512 GVGMAAVSLARYWGAEVFVTASRA-KWDTLRAMGFDDIhISDSRSlEFEEAFLRATEGSGVDVVLNSLA-GEFTDASL 1587
                                     9*******************9999.69*******7765155578889**********************.******** PP

                                     HCEEEEEEEEECSC CS
                     ADH_zinc_N   77 kllkpgGrlvvvGg 90  
                                     +ll  gGr+   G 
  gi|121637569|ref|YP_977792.1| 1588 RLLPSGGRFIELGK 1601
                                     *********99995 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                     HHT CS
                     ADH_zinc_N   31 kkl 33  
                                     ++ 
  gi|121637569|ref|YP_977792.1| 1715 RRH 1717
                                     222 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.55
                                     EEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N   19 avdsseeklelakklGadevinykeadlverikeltg.gegvdvvfecvGsgatleaal 76  
                                      vd++++  +  ++lG d +      +l  r+k +tg +  + ++f+++  +atl + l
  gi|121637569|ref|YP_977792.1| 1995 SVDINAH--KAFQDLGFDSLTAV---ELRNRLKTATGlTLSPTLIFDYPT-PATLAEHL 2047
                                     5788888..68889999999999...79999999999999**********.*9998765 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   2.8e-15   2.5e-12       5      67 .]    1984    2047 ..    1980    2047 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.8e-15
                     PP-binding    5 elvaevlgv.pleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     + +a vlg+ +  +i+++  + dlG+DSl+avel ++l+ + g++++++ +f++pt+a la++l
  gi|121637569|ref|YP_977792.1| 1984 SNAAAVLGRsSSVDINAHKAFQDLGFDSLTAVELRNRLKTATGLTLSPTLIFDYPTPATLAEHL 2047
                                     5678899996666799999*******************************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.095        85      23      77 ..     719     774 ..     714     777 .. 0.84
   2 ?   -0.7   0.1      0.92   8.3e+02       2      33 ..    1503    1534 ..    1502    1542 .. 0.87
   3 !   43.6   0.3   2.4e-14   2.2e-11       2     160 ..    1695    1853 ..    1694    1859 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.095
                                    TT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT.SHHHHHHHHHHHHHHHSS CS
                      adh_short  23 eGakvvvvdrseekleevakelkeegakalaiqvDvt.dreevealvekavkklgk 77 
                                    +G++ vv++ + +++ e+++ +++eg +a  i vD + ++++v+a+ e+ ++ l +
  gi|121637569|ref|YP_977792.1| 719 NGVSSVVLAGETDAVTELMQRCEAEGIRARRIDVDYAsHSAQVDAIREELIAALRG 774
                                    68888999999999*********************996777888888877777665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.92
                                     EEEEESTTSHHHHHHHHHHHHTT-EEEEEESC CS
                      adh_short    2 vvlvtGassGIGraiakelakeGakvvvvdrs 33  
                                      vlv  +++G+G a +      Ga+v+v++++
  gi|121637569|ref|YP_977792.1| 1503 KVLVHAGTGGVGMAAVSLARYWGAEVFVTASR 1534
                                     699**************9999******97665 PP

  == domain 3  score: 43.6 bits;  conditional E-value: 2.4e-14
                                     EEEEESTTSHHHHHHHHHHHHT.T-EEEE.EESCHH...HHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                      adh_short    2 vvlvtGassGIGraiakelake.Gakvvv.vdrsee...kleevakelkeegakalaiqvDvtdreevealvekavkk 74  
                                     +v+vtG+++  G a+a +l+++ G+  +v v+rs e   +++eva+ l+e ga++ ++++Dv+dr+++ al++    +
  gi|121637569|ref|YP_977792.1| 1695 TVVVTGGTGMAGSAVATHLVRRhGVANLVlVSRSGEqadRAAEVAALLREGGAQVAVVSCDVADRDALAALLAGLDPR 1772
                                     69*****************98636555544888766111556666677776************************888 PP

                                     HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short   75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152 
                                     + +l  + + AG+  ++ +  l+ ++++ v+   + g+ +l ++ ++ m+     + v  sS+ag v+ + +  Y+A+
  gi|121637569|ref|YP_977792.1| 1773 Y-PLKGVFHAAGVLDDAVITGLTPDRVDTVLRAKVDGAWNLHEL-TEDMD---LSAFVVFSSMAGIVGTPAQGNYAAA 1845
                                     7.7***********************************999766.66666...6677888****************** PP

                                     HHHHHHHH CS
                      adh_short  153 Kaavaglt 160 
                                      a+++gl+
  gi|121637569|ref|YP_977792.1| 1846 NAFLDGLV 1853
                                     ****9997 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   5.4   9.3e-12   8.4e-09       3      29 ..       5      31 ..       3      32 .. 0.93
   2 ?   -2.9   0.5       5.9   5.3e+03       4      11 ..     766     773 ..     765     773 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 9.3e-12
                       PikAIV_N  3 deklVeALRaSLkEnERLRqqNrrLtA 29
                                   +e lV+ALR SLk nERL+++Nr L A
  gi|121637569|ref|YP_977792.1|  5 PEDLVKALRRSLKQNERLKRENRDLLA 31
                                   799**********************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                       PikAIV_N   4 eklVeALR 11 
                                    e+l++ALR
  gi|121637569|ref|YP_977792.1| 766 EELIAALR 773
                                    899****9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.2   2.2e-10   1.9e-07       1     123 [.    1696    1838 ..    1696    1861 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.2e-10
                                     EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHHHT-SE CS
                      Epimerase    1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl.........elveldltdrsalerlfkeeqpda 67  
                                     ++VtG+tG+ Gsa++ +l +++   +++ ++r  ++  +a++  +          +v +d+ dr+al++l++  +p +
  gi|121637569|ref|YP_977792.1| 1696 VVVTGGTGMAGSAVATHLVRRHgvANLVLVSRSGEQADRAAEVAAllreggaqvAVVSCDVADRDALAALLAGLDPRY 1773
                                     68****************9988766688888886666655555559**************************998876 PP

                                     ....EEE--S---HHH....HHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSCS CS
                      Epimerase   68 ....vihlAavggvaa....ssedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkda 123 
                                         v+h+A+v + a+    + ++   ++++ + g++nl e   + ++  ++ +sS + + G +a
  gi|121637569|ref|YP_977792.1| 1774 plkgVFHAAGVLDDAVitglTPDRVDTVLRAKVDGAWNLHELTEDMDLSAFVVFSSmAGIVGTPA 1838
                                     6666****9955443311115556667889**************************666666555 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.7     6e+03      24      45 ..     125     146 ..     119     159 .. 0.84
   2 !   26.6   0.2     4e-09   3.6e-06      70     117 ..     193     238 ..     180     257 .. 0.87
   3 ?   -3.3   0.1         5   4.4e+03     137     181 ..    1710    1754 ..    1704    1760 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.7
                                    HHHHHHHHHHHHHHHTS-GGGC CS
                     Thiolase_N  24 eeLlaealkallekagvdpeev 45 
                                    + Ll e+ +++le+ag+dp ++
  gi|121637569|ref|YP_977792.1| 125 QRLLLEVSWEALERAGIDPITL 146
                                    6789999**********99765 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4e-09
                                    TTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTT CS
                     Thiolase_N  70 agipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsn 117
                                    +g+  + pav v+ +csS+l a++la+qs++ ge+d +++gGv  m +
  gi|121637569|ref|YP_977792.1| 193 LGL--QGPAVSVDTACSSSLVALHLAVQSLRLGECDLALVGGVTVMAT 238
                                    555..779***********************************99976 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5
                                     EEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHH CS
                     Thiolase_N  137 akdllipdgladafneehmGltaenlakkykisReeqdefAvksh 181 
                                     a  l+ ++g+a+ +     G  a++ a+  ++ Re  +++Av s 
  gi|121637569|ref|YP_977792.1| 1710 ATHLVRRHGVANLVLVSRSGEQADRAAEVAALLREGGAQVAVVSC 1754
                                     55566667888888888899999************9999999885 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.4   1.1e-07    0.0001       1      69 [.    1696    1768 ..    1696    1771 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                                     EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....TTTCEEEEE--TTTHHHHHHHHHTT CS
                Sacchrp_dh_NADP    1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.....lgvrfeaialdaenyeavLaallke 69  
                                     v++ G+ G+ G+ava  l+r++ v a++++++rs e+++++a+ a      g ++  +++d+++++a Laall++
  gi|121637569|ref|YP_977792.1| 1696 VVVTGGtGMAGSAVATHLVRRHGV-ANLVLVSRSGEQADRAAEVAallreGGAQVAVVSCDVADRDA-LAALLAG 1768
                                     6777888****************9.6***************99989*********************.***9986 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.6   1.6e-07   0.00014       2      60 ..    1395    1449 ..    1394    1455 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                                     TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                          ADH_N    2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60  
                                     g+v++ v a+g++  D+ ++ g      + +  lG + +G+v+evgp+v++l+vGdrV+
  gi|121637569|ref|YP_977792.1| 1395 GQVRVAVGAVGVNFRDVLVALG----MYPGGGELGVDGAGVVVEVGPGVTGLAVGDRVM 1449
                                     79*******************9....5777888*************************8 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.1e-07   0.00028       1     128 [.    1696    1829 ..    1696    1841 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.1e-07
                                     EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                Polysacc_synt_2    1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77  
                                     v+vtG++G  Gs++ ++++++  +++++l++r+  + ++ ++   + l++     ++++v +dv+d++ l+ +l  l+
  gi|121637569|ref|YP_977792.1| 1696 VVVTGGTGMAGSAVATHLVRRhGVANLVLVSRSGEQADRAAEVA-ALLREGGA--QVAVVSCDVADRDALAALLAGLD 1770
                                     79***************9998799********988887777653.44555444..556889*************9777 PP

                                     -SE....EEE------....HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2   78 vdv....vfhaAAlKh....VPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128 
                                     + +    vfhaA +        l    +  +++  v g+ n+ e + +++ +++v+ S+
  gi|121637569|ref|YP_977792.1| 1771 PRYplkgVFHAAGVLDdaviTGLTPDRVDTVLRAKVDGAWNLHELTEDMDLSAFVVFSS 1829
                                     6544444*****87551111234455666778889999999999999999999999886 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.9e-06    0.0017       2      77 ..    1698    1772 ..    1697    1783 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                     EETTTSHHHHHHHHHHHHC.T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                  GDP_Man_Dehyd    2 iTGiaGfiGsylaelLlek.gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77  
                                     +TG++G  Gs +a +L+++ g    ++v r s  +++r +++a   + e   ++ ++++D+ D+++l  lla  +p+
  gi|121637569|ref|YP_977792.1| 1698 VTGGTGMAGSAVATHLVRRhGVANLVLVSR-SGEQADRAAEVAALLR-EGGAQVAVVSCDVADRDALAALLAGLDPR 1772
                                     9****************9834444444444.4456777777776554.45789******************988875 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.012       1     122 [.    1697    1836 ..    1697    1847 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                      3Beta_HSD    1 vvtGgaGFlGralvkeLvrleelkevrvlD.....lrespelleelskvnvkk.....viegDvtdkdkleealegvd 68  
                                     vvtGg+G  G+a+  +Lvr++ + ++  +       +   e+   l++          v+ +Dv d d l + l g d
  gi|121637569|ref|YP_977792.1| 1697 VVTGGTGMAGSAVATHLVRRHGVANLVLVSrsgeqADRAAEVAALLRE----GgaqvaVVSCDVADRDALAALLAGLD 1770
                                     8*******************9977665544333332222333333333....1333579***************9975 PP

                      3Beta_HSD   69 ......vvihlaslvd...vag..kltedeimkvnvkGTrnvleacvkagvrvlvYtSsa.evvgp 122 
                                            v+h a++ d   ++g   ++ d++ ++ v G  n+ e   ++++ ++v  Ss+ ++vg 
  gi|121637569|ref|YP_977792.1| 1771 pryplkGVFHAAGVLDdavITGltPDRVDTVLRAKVDGAWNLHELTEDMDLSAFVVFSSMaGIVGT 1836
                                     33333279*****9884423342234456667779****************988766665156665 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.9     0.014        12     105     148 ..     648     691 ..     624     710 .. 0.78
   2 ?    3.1   0.0     0.075        67     194     239 ..     711     756 ..     698     757 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                            SAT 105 tylvGlCtGllaAaavacskslseLvplaveavrvafrlGleva 148
                                      ++G+++G +aAa va + sl +  ++     r+++rlG +  
  gi|121637569|ref|YP_977792.1| 648 DAVIGHSQGEIAAAYVAGALSLWDAAAVVALRSRLLVRLGGAGG 691
                                    479****************9999887777777778888886655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.075
                            SAT 194 srvyisavssss.vtisGpPstleallksskakkkkkksklpiyapy 239
                                     r+ i+av++ s v+++G  +++ +l+++++a+  + + ++++  + 
  gi|121637569|ref|YP_977792.1| 711 DRLNIAAVNGVSsVVLAGETDAVTELMQRCEAEGIRAR-RIDVDYAS 756
                                    7999*****9777********************99987.88876655 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0021       1.9      46      83 ..    1264    1301 ..    1248    1394 .. 0.84
   2 ?    1.6   0.2      0.22     2e+02      59      85 ..    1695    1721 ..    1689    1755 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0021
                                     HHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHHS CS
                  MoCF_biosynth   46 ikeallaaleeadviittGGtGptpdDvtpealaklfe 83  
                                     +++ l++ + +  v++t G +Gp +dDvt  a a++ +
  gi|121637569|ref|YP_977792.1| 1264 LQSWLASDATGLGVVVTRGAVGPVDDDVTDLAGAAVWG 1301
                                     4444444444448****************999887765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                     EEEEESS-SSSTT--HHHHHHHHHSEE CS
                  MoCF_biosynth   59 viittGGtGptpdDvtpealaklfeke 85  
                                      +++tGGtG++   v    +++ +   
  gi|121637569|ref|YP_977792.1| 1695 TVVVTGGTGMAGSAVATHLVRRHGVAN 1721
                                     599*******98888887777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 1.10u 0.32s 00:00:01.42 Elapsed: 00:00:00.48
# Mc/sec: 13408.38
//
Query:       gi|121637570|ref|YP_977793.1|  [L=1601]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-91  304.5   1.1    1.5e-90  303.2   1.1    1.7  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    2.3e-58  198.2   1.3    3.7e-58  197.5   1.3    1.3  1  Acyl_transf_1    Acyl transferase domain
    3.8e-52  177.4   5.6    7.6e-52  176.4   5.6    1.5  1  PS-DH            Polyketide synthase dehydratase
    8.3e-43  145.2   0.5    2.5e-42  143.6   0.5    1.9  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    8.2e-14   52.0   0.0    3.3e-13   50.1   0.0    2.0  2  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.8e-12   47.4   0.0      6e-12   45.7   0.0    2.0  1  ADH_zinc_N       Zinc-binding dehydrogenase
    5.5e-08   32.5   0.1    4.7e-07   29.4   0.2    2.3  2  Thiolase_N       Thiolase, N-terminal domain
    3.4e-07   31.4   0.0    2.4e-06   28.6   0.0    2.5  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    4.8e-07   29.3   7.3    1.1e-06   28.1   7.3    1.6  1  Docking          Erythronolide synthase docking
    1.4e-06   28.1   0.3    4.3e-06   26.6   0.3    1.8  1  ADH_N            Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.2   1.1   8.5e-94   1.5e-90       2     253 .]      34     281 ..      33     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 303.2 bits;  conditional E-value: 8.5e-94
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadklydpparaagkiktklggfld.vddfdpeffgis 78 
                                    epva+vGmg+r+Pgg+d +e++wel+ +grda+s++padr wd+++l+dp+++a gk++t++g+fl+ + dfd+ ffgi 
  gi|121637570|ref|YP_977793.1|  34 EPVAVVGMGCRYPGGVDsPETLWELVAQGRDAVSDFPADRgWDVYGLFDPDPDACGKMYTRRGTFLEhAGDFDAGFFGIG 113
                                    89****************************************************************************** PP

                                    HHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHH CS
                  ketoacyl-synt  79 preaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagri 158
                                    p+ea amdpqqrllle++weale+ g++p++l+gs++gvf+Gv ++ y++  +l+  g e +++   +g+ + +v++gr+
  gi|121637570|ref|YP_977793.1| 114 PSEALAMDPQQRLLLEVSWEALERTGIDPTKLRGSATGVFAGVIHAGYGG--QLS--G-ELEGYG-LTGS-TLSVASGRV 186
                                    **********************************************9976..454..3.467899.9999.9******** PP

                                    HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-B CS
                  ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvl 238
                                    +y lgl+Gp+v+vdtACsSslva+h+avqslrsge+d+alaGGv+++ tp a++ fs++++l++dgrck ++ +adG+ +
  gi|121637570|ref|YP_977793.1| 187 AYVLGLEGPAVSVDTACSSSLVALHLAVQSLRSGECDLALAGGVTVMATPAAFVEFSRQRALARDGRCKVYAGAADGTAW 266
                                    ******************************************************************************** PP

                                    B-EEEEEEEEECHHH CS
                  ketoacyl-synt 239 GEGvGavvLkrleda 253
                                    +EG+G++v++rl da
  gi|121637570|ref|YP_977793.1| 267 SEGAGVLVVERLVDA 281
                                    ***********9886 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5   1.3     2e-61   3.7e-58       1     317 [.     561     871 ..     561     873 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 2e-61
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfvf+GqG+Qw GMG++L+++ ++fa + ++ +e +  +  + + +vl + +e ll++++f+qpaL+a+++ala ll+  
  gi|121637570|ref|YP_977793.1| 561 VFVFPGQGAQWVGMGAQLYAELPLFALAFDAVAEELDRHLRLPLRNVLWEGDEALLTSTEFAQPALFAIEVALATLLQHW 640
                                    8******************************************************************************* PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECCCCEC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavansprrvvi 160
                                    G  p+ ++GHS+GE+Aaa+ ag ls+ +a+  v+ r+rlm++l   g m  v+ +eee      d   +a++n p++vv+
  gi|121637570|ref|YP_977793.1| 641 GISPDFLIGHSVGEIAAAHLAGVLSLTDAAGLVAARGRLMAELPAGGVM-VVAASEEEVLPVLVDGANLAAVNAPHSVVV 719
                                    ******************************************9665555.555546666666****************** PP

                                    CEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHHHH CS
                  Acyl_transf_1 161 sgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywvan 240
                                    sg ++a++++  + +++g+++++ +v+ a+hs  ++++  +     a i   kp+++  s ++ + + ++  +++ywv+ 
  gi|121637570|ref|YP_977793.1| 720 SGCEAAVSDIADHFARRGRRVHRLAVSHAFHSLLMEPMLAEFTRIAAGISVSKPRIPLVSNVTGQMAGAGYGDGQYWVEH 799
                                    *********************************************9********************************** PP

                                    HHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT- CS
                  Acyl_transf_1 241 lrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltgs 317
                                     r pvrf e v+ + +++   fve+ p   l+a +e+ l       +a  v  ++r++ + ++ +l + a+++++g+
  gi|121637570|ref|YP_977793.1| 800 ARRPVRFVEGVQLLNAVGATRFVEVGPGGGLTALVEQSLP----LGEALSVAMMRREHPE-VSSVLGAVATLFTAGA 871
                                    **************************************99....789999999*******.9999999999999887 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   5.6   4.2e-55   7.6e-52       1     294 [.     920    1187 ..     920    1191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 4.2e-55
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlp 78  
                                     h llG+ v++++++ vv   rl++ e+ wL+DH++ g v+l ga+++e+al Aa q+     + +++++++ ++lvlp
  gi|121637570|ref|YP_977793.1|  920 HGLLGAVVEQPDSDVVVLTGRLSVGEQRWLADHVIAGVVLLAGAAFVELALRAADQVD----CGVVEELTVVTPLVLP 993 
                                     789*******************************************************....778************* PP

                                     -SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT..EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HH CS
                          PS-DH   79 edepvevqlslepeedgadrawvefeifSregggee.wtehatGtvrlaegaaaaavdlealqarcaepaslrsvssa 155 
                                       ++v++q+++   e g+      ++i+Sr+++++  w++ha+G + + + a+  a+dl+ +++  a+p     v+++
  gi|121637570|ref|YP_977793.1|  994 TVGGVQLQVVVGVGEMGQR----PVSIYSRNAESDSgWVLHARGVLGAKAVAP--AADLSVWPPLGAAP-----VDVD 1060
                                     ***************9999....***********99***********765555..89999997777777.....5566 PP

                                     HHHHHHHHHSEEE-GGG--EEEEEEETTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEE CS
                          PS-DH  156 efYerlaargleyGpsFqglralwrgdgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylP 233 
                                       Y+r+a+ g+eyG +Fqgl+a+wr+++e +a +++p++++ + s + +hP +lDaal+++++       ++ a++lP
  gi|121637570|ref|YP_977793.1| 1061 GAYQRFAELGYEYGRAFQGLTAMWRRESELFADVAVPDDVDVTLSGFGIHPLVLDAALHAMGM-----VGEQAATMLP 1133
                                     6**********************************************************9854.....3589****** PP

                                     EEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XX CS
                          PS-DH  234 vaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrvere 294 
                                     ++++ ++++       +  +v+ar++ +g  + +++++l d++G +v++++ l +r+v+++
  gi|121637570|ref|YP_977793.1| 1134 FSWQGVSLHA-----AGASRVRARIAPAG--DGTVSVELADQAGLPVLSVQALVMRSVSSQ 1187
                                     *********6.....34578999998887..6799***********************987 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.5   1.4e-45   2.5e-42       1     117 [.     289     404 ..     289     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.4e-45
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a ++gsavn+dga+n+ltapng +q+r+i++ala+a++++ +vd+ve hgtgt lgDpiE++al +++g+++  +pl++
  gi|121637570|ref|YP_977793.1| 289 LALVRGSAVNQDGASNGLTAPNGPSQQRVIRAALASARLRAVEVDVVEGHGTGTMLGDPIEAQALLATYGQDR-VEPLWL 367
                                    689********************************************************************99.78**** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    gS+KsniGH+ aAaGva++ik+v+a++hgv+p+tl++
  gi|121637570|ref|YP_977793.1| 368 GSIKSNIGHTSAAAGVAGVIKMVQAMRHGVMPKTLHV 404
                                    ************************************8 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.8e-16   3.3e-13       1     112 []     407     526 ..     407     526 .. 0.87
   2 ?   -1.7   0.0       2.1   3.9e+03      59     100 ..     712     752 ..     705     757 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.8e-16
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnk...kekrkeeskeeslprLlvlsgrteea 73 
                                    P p+++ ++ g + + t+p  w+ +     +gv+sfG++G+n+HviL++++   +  ++ +s+++ +   +vls+r+e+a
  gi|121637570|ref|YP_977793.1| 407 PTPHVD-WSVGAVSLLTQPRAWSVHGrprrAGVSSFGISGTNAHVILEQAPvveSVVPEVASPTAASAVPWVLSARSEQA 485
                                    99****.***************87666788*********************65533333344477889999********* PP

                 KAsynt_C_assoc  74 veallekleehlldaellsllneilseeisr..lpyRGyav 112
                                    +  ++++l +  + +++l+ ++   s   +r  +++R+ +v
  gi|121637570|ref|YP_977793.1| 486 LAGQAQRLLAFVAANPDLDPIDVGWSLVKTRamFEHRAVVV 526
                                    *********************99998877777799998876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                 KAsynt_C_assoc  59 slprLlvlsgrteeaveallekleehlldaellsllneilse 100
                                    + p+ +v+sg  e+av++++++++ + +  ++l++ +  +s 
  gi|121637570|ref|YP_977793.1| 712 NAPHSVVVSGC-EAAVSDIADHFARRGRRVHRLAVSHAFHSL 752
                                    56888999998.89**********999999999998888875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.4e-15     6e-12       1      90 [.    1490    1579 ..    1490    1593 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.4e-15
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTES..EEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGad..evinykea.dlverikeltggegvdvvfecvGsgatleaa 75  
                                     gvG+aavqlA+ +G ev+a++s   k + +  +G+d  +v ++ ++  ++e  +  t+g+gvdvv++ ++ g+  +a+
  gi|121637570|ref|YP_977793.1| 1490 GVGMAAVQLARLWGLEVFATASRG-KWDTLHTMGCDntHVADS-RTlAFEETFWLTTEGRGVDVVLNSLA-GEFTDAS 1564
                                     9******************99888.69*******761155555.8889**********************.******* PP

                                     HHCEEEEEEEEECSC CS
                     ADH_zinc_N   76 lkllkpgGrlvvvGg 90  
                                     l+ll +gGr+  +G 
  gi|121637570|ref|YP_977793.1| 1565 LRLLPRGGRFIEMGK 1579
                                     **********99996 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.45     8e+02      23      51 ..     123     151 ..     113     166 .. 0.80
   2 !   29.4   0.2   2.6e-10   4.7e-07      68     117 ..     188     235 ..     173     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.45
                                    HHHHHHHHHHHHHHHHTS-GGGCCEEEEE CS
                     Thiolase_N  23 aeeLlaealkallekagvdpeevdevivG 51 
                                     + Ll e+ +++le++g+dp ++   + G
  gi|121637570|ref|YP_977793.1| 123 QQRLLLEVSWEALERTGIDPTKLRGSATG 151
                                    5789999*************998766555 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 2.6e-10
                                    HHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTT CS
                     Thiolase_N  68 lkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsn 117
                                      +g+  e pav v+ +csS+l a++la+qs+++ge+d ++agGv  m +
  gi|121637570|ref|YP_977793.1| 188 YVLGL--EGPAVSVDTACSSSLVALHLAVQSLRSGECDLALAGGVTVMAT 235
                                    55555..789***********************************99976 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-09   2.4e-06       4      55 ..    1526    1580 ..    1523    1598 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-09
                                     SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE---- CS
                   ADH_zinc_N_2    4 devidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggp 55  
                                     ++v d+rt +fe      t+g+gvDvvl++++ge + +asl++lp gGr++++g++
  gi|121637570|ref|YP_977793.1| 1526 THVADSRTLAFEetfwLTTEGRGVDVVLNSLAGEFT-DASLRLLPRGGRFIEMGKT 1580
                                     699***********9988889***********9977.*******888******963 PP

>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   7.3   6.1e-10   1.1e-06       6      26 .]       7      27 ..       4      27 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6.1e-10
                        Docking  6 LRdYLKRvTaDLrqtRrRLrE 26
                                   ++dYLKR TaDLr+tRrRL++
  gi|121637570|ref|YP_977793.1|  7 HVDYLKRLTADLRRTRRRLSD 27
                                   68*****************85 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   2.4e-09   4.3e-06       1      60 [.    1372    1427 ..    1372    1436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-09
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60  
                                     pg+v+i+v+a g++  D+ ++ g   ++ +    lG E +G+v evgp+v++l+vGd V+
  gi|121637570|ref|YP_977793.1| 1372 PGQVRIEVRALGVNFRDVLVALG--IYPGA--AELGAEGAGVVTEVGPGVTGLAVGDPVM 1427
                                     589*******************9..44444..459***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.92u 0.27s 00:00:01.19 Elapsed: 00:00:00.47
# Mc/sec: 10294.44
//
Query:       gi|121637571|ref|YP_977794.1|  [L=502]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-59  198.4   3.8    1.4e-58  197.8   3.8    1.3  1  KR               KR domain
    2.3e-14   53.5   0.0    5.1e-14   52.4   0.0    1.7  1  PP-binding       Phosphopantetheine attachment site
    1.6e-12   47.3   1.1    2.9e-12   46.4   1.1    1.4  1  adh_short        short chain dehydrogenase
    2.7e-12   46.7   0.4    4.2e-12   46.1   0.4    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.7e-09   36.9   1.6    5.1e-09   36.0   1.6    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    7.4e-08   31.9   0.1    1.1e-07   31.3   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.7e-07   29.8   0.0    5.5e-07   29.3   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.3e-06   25.2   0.1    1.1e-05   24.7   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.1e-05   26.5   0.3    3.9e-05   24.7   0.1    2.1  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    0.00045   20.2   4.2    0.00081   19.3   4.2    1.4  1  NAD_binding_10   NAD(P)H-binding
     0.0038   17.3   0.3      0.019   15.0   0.2    2.0  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0081   15.4   0.6      0.084   12.0   0.4    2.5  3  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
       0.14   12.4   0.0        0.4   10.9   0.0    1.8  1  PAC4             Proteasome assembly chaperone 4
       0.14   12.0   0.4        9.6    6.1   0.0    3.1  3  Tnp_DNA_bind     Transposase DNA-binding
       0.18   10.8   0.2       0.35    9.8   0.2    1.4  1  PDH              Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   3.8   1.2e-61   1.4e-58       1     179 [.      64     239 ..      64     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1.2e-61
                                    SEEEEETTTSHHHHHHHHHHHH.HHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                             KR   1 gtylitGGlGgLGlelarwlae.kgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                    gt+litGG+G  G ++ar+l++  g r++vl sR ++ +e+ +al++el + ga+v+vv++Dv+d+dav+ l+++     
  gi|121637571|ref|YP_977794.1|  64 GTVLITGGTGMAGSAVARHLVSrYGVRQVVLASRAGEHTESVAALVDELGSAGARVQVVSCDVADRDAVAGLVASQ---- 139
                                    89*******************7258********************************************9999876.... PP

                                    S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                             KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaflDal 159
                                    p ++ v+haAgvl+d+ ++ +t e++++vl++Kv+GawnLhel+++ ++  fvlfSS+ag++g++gqanYaaaNaflD+l
  gi|121637571|ref|YP_977794.1| 140 PDLTAVFHAAGVLDDAVITGLTPERVDKVLRAKVDGAWNLHELTRHLDVSAFVLFSSMAGIVGAPGQANYAAANAFLDGL 219
                                    79****************************************************************************** PP

                                    HHHHHHHHHTEEEEEE--BT CS
                             KR 160 aeyrrsqglpavsinwglwa 179
                                    a+yrrs+gl+a+s++wglw+
  gi|121637571|ref|YP_977794.1| 220 AAYRRSRGLAALSVAWGLWE 239
                                    *******************8 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   4.3e-17   5.1e-14       4      67 .]     347     410 ..     340     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 4.3e-17
                     PP-binding   4 relvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67 
                                    ++ +a vlg +  eid++  + dlG+DSl+avel ++l+ + g+++p++ +f++pt aela++l
  gi|121637571|ref|YP_977794.1| 347 CSNAAIVLGHSGTEIDAHKAFQDLGFDSLTAVELRNRLKTATGLTLPPTLIFDYPTAAELAEHL 410
                                    4445557888999*************************************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   1.1   2.5e-15   2.9e-12       2     160 ..      65     220 ..      64     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.5e-15
                                    EEEEESTTSHHHHHHHHHHHH.TT-EEEE.EESCH...HHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                      adh_short   2 vvlvtGassGIGraiakelak.eGakvvv.vdrse...ekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                    +vl+tG+++  G a+a++l++  G++ vv ++r     e ++++++el+++ga++ ++++Dv+dr++v  lv+       
  gi|121637571|ref|YP_977794.1|  65 TVLITGGTGMAGSAVARHLVSrYGVRQVVlASRAGehtESVAALVDELGSAGARVQVVSCDVADRDAVAGLVASQ----P 140
                                    69****************986269988874666551114455666777777**************9988888776....9 PP

                                    SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                      adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156
                                     l ++ + AG+  ++ +  l+ e++++v+   + g+ +l ++ +++++     + v  sS+ag v+ +g+a Y+A+ a++
  gi|121637571|ref|YP_977794.1| 141 DLTAVFHAAGVLDDAVITGLTPERVDKVLRAKVDGAWNLHEL-TRHLD---VSAFVLFSSMAGIVGAPGQANYAAANAFL 216
                                    9***********************************998765.88866...8889999********************** PP

                                    HHHH CS
                      adh_short 157 aglt 160
                                    +gl+
  gi|121637571|ref|YP_977794.1| 217 DGLA 220
                                    9997 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.4   3.5e-15   4.2e-12       1     122 [.      66     204 ..      66     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.5e-15
                                    EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHH.T-SE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl...........elveldltdrsalerlfkee.qpda 67 
                                    +l+tG+tG+ Gsa++++l ++  ++ ++l+++  +++t++ + l           ++v +d+ dr+a++ l++++ + +a
  gi|121637571|ref|YP_977794.1|  66 VLITGGTGMAGSAVARHLVSRYgVRQVVLASRA-GEHTESVAALvdelgsagarvQVVSCDVADRDAVAGLVASQpDLTA 144
                                    79*****************99876655555552.44444444446899*************************999999* PP

                                    EEE--S---H....HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSC CS
                      Epimerase  68 vihlAavggv....aassedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkd 122
                                    v+h+A+v +     + + e+  +++++ + g++nl e  r  +v  ++ +sS + + G++
  gi|121637571|ref|YP_977794.1| 145 VFHAAGVLDDavitGLTPERVDKVLRAKVDGAWNLHELTRHLDVSAFVLFSSmAGIVGAP 204
                                    *****9555411114567788899****************************56666654 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.6   4.3e-12   5.1e-09       7     153 ..      76     221 ..      72     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.3e-12
                                    HHHHHHHHH.HTT-E.EEEEESSGGHHHHHHHHHHHTTSE...E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   7 GraiAkala.eeGae.vvltdlneeakkrveelaeelgae...v..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                    G a+A++l  + G + vvl+ +  e  ++v++l++elg++   v  + cDV+d+++v+ lv+        l  ++++ag+
  gi|121637571|ref|YP_977794.1|  76 GSAVARHLVsRYGVRqVVLASRAGEHTESVAALVDELGSAgarVqvVSCDVADRDAVAGLVAS----QPDLTAVFHAAGV 151
                                    566777654155765499999999999**********966544366*********99998876....67899******** PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtr 153
                                     ++  + ++ ++ e +d++l  ++ ++++l +  ++l  + ++ v  ss+++ ++ p+++ y+aa a l +l+ 
  gi|121637571|ref|YP_977794.1| 152 LDD--AVITGLTPERVDKVLRAKVDGAWNLHELTRHL--DVSAFVLFSSMAGIVGAPGQANYAAANAFLDGLAA 221
                                    ***..99999*******************98888776..5589************************9999875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   9.2e-11   1.1e-07       1     128 [.      66     196 ..      66     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.2e-11
                                    EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT...T- CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale.elkv 78 
                                    vl+tG++G  Gs++ r+++++  +++++l +r+  +  +++  + +el +   +v+  +v +dv+d++ ++ ++  + + 
  gi|121637571|ref|YP_977794.1|  66 VLITGGTGMAGSAVARHLVSRyGVRQVVLASRAGEHTESVAALV-DELGSAGARVQ--VVSCDVADRDAVAGLVAsQPDL 142
                                    89***************999889***********9999999976.56666667666..7889*********988614577 PP

                                    SEEEE------....HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  79 dvvfhaAAlKh....VPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                     +vfhaA +        l  e + ++++  v g+ n+ e + + +v+++vl S+
  gi|121637571|ref|YP_977794.1| 143 TAVFHAAGVLDdaviTGLTPERVDKVLRAKVDGAWNLHELTRHLDVSAFVLFSS 196
                                    89*****986512113455677888999***********************996 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   4.6e-10   5.5e-07       1      85 [.      67     151 ..      67     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.6e-10
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEE.EEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.T-SE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgiv.rrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.qpde 78 
                                    LiTG++G  Gs +a++L+++ y v  +v    +  +t+++++l ++   ++  +++++++D+ D++++  l+a+  + ++
  gi|121637571|ref|YP_977794.1|  67 LITGGTGMAGSAVARHLVSR-YGVRQVVlASRAGEHTESVAALVDEL-GSAGARVQVVSCDVADRDAVAGLVASQpDLTA 144
                                    9******************9.44444430444556899999998765.56789******************997658889 PP

                                    EEE--S- CS
                  GDP_Man_Dehyd  79 vynLAAq 85 
                                    v++ A+ 
  gi|121637571|ref|YP_977794.1| 145 VFHAAGV 151
                                    9998775 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   8.8e-09   1.1e-05       1     122 [.      67     202 ..      67     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.8e-09
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD.....lrespelleelskvnvkk.viegDvtdkdkleeale...gvdvvi 71 
                                    ++tGg+G  G+a+ ++Lv++  +++v  +       +    l +el + + +  v+ +Dv d d +   +    +  +v+
  gi|121637571|ref|YP_977794.1|  67 LITGGTGMAGSAVARHLVSRYGVRQVVLASragehTESVAALVDELGSAGARVqVVSCDVADRDAVAGLVAsqpDLTAVF 146
                                    69*******************999997777554443334445566655555546*********99876554112789*** PP

                      3Beta_HSD  72 hlaslvd...vag..kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                    h a++ d   ++g    + d++ ++ v G  n+ e  ++ +v ++v  Ss+  + +
  gi|121637571|ref|YP_977794.1| 147 HAAGVLDdavITGltPERVDKVLRAKVDGAWNLHELTRHLDVSAFVLFSSMAGIVG 202
                                    ****9984423342233456666779********************9999865543 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   3.3e-08   3.9e-05      86     133 .]       8      55 ..       1      55 [. 0.92

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.3e-08
                                    -HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  86 qadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                     a++l+el++l++ ++l+  + ++++   a+eA+r l ++r++GK+Vl
  gi|121637571|ref|YP_977794.1|   8 IAQMLAELVELFKTEALHRLPVKSWDVRHAREAYRFLSQARHVGKVVL 55 
                                    5778**************99999************************8 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   4.2   6.8e-07   0.00081       1     123 [.      70     221 ..      70     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.8e-07
                                    TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCH.......HHH.CTTTCEEEE--TT-CCHHHHHHTT-...SEEEES- CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpekla.......ele.aeeglevvegdvtdvedlaealkga...daVvsal 68 
                                    G+tG  G++++++l++r    +v++  R  e+++       el  a ++++vv+ dv d +++a  ++ +    aV+ a+
  gi|121637571|ref|YP_977794.1|  70 GGTGMAGSAVARHLVSRYgVRQVVLASRAGEHTEsvaalvdELGsAGARVQVVSCDVADRDAVAGLVASQpdlTAVFHAA 149
                                    9****************9555788888988888733344434434458********************664225999999 PP

                                    --TCC.........HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHH CS
                 NAD_binding_10  69 ggggk.........deeg..........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaa 123
                                    g  ++         +  +          a n+ +  +  +v+ fvl s++     +pg+ +  + +++ + laa
  gi|121637571|ref|YP_977794.1| 150 GVLDDavitgltpeR--VdkvlrakvdgAWNLHELTRHLDVSAFVLFSSMAGIVGAPGQANYAAANAFLDGLAA 221
                                    655444444444330..133445555668888899999999999999886433345666665555555555555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.6e-05     0.019      14      56 ..      65     109 ..      55     139 .. 0.81
   2 ?   -0.8   0.0       1.2   1.4e+03      37      83 ..     153     196 ..     133     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                    EEEEE.S-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH CS
                   Shikimate_DH  14 kvlli.GaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel 56 
                                    +vl+  G+G+ ++ va+hL+++ gv++vv a R  e+ +++a  +
  gi|121637571|ref|YP_977794.1|  65 TVLITgGTGMAGSAVARHLVSRyGVRQVVLASRAGEHTESVAALV 109
                                    56666369************999***********99998887655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                    CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH  37 kkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83 
                                    ++ v+++ t er++++ +   +    a +l+el+++l+ +  v+ + 
  gi|121637571|ref|YP_977794.1| 153 DDAVITGLTPERVDKVLRAKVDG---AWNLHELTRHLDVSAFVLFSS 196
                                    56688888999998875544333...699999999998776655444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.4   7.1e-05     0.084       1     137 [.      68     198 ..      68     214 .. 0.68
   2 ?   -0.8   0.0      0.57   6.9e+02      56     104 ..     372     426 ..     350     435 .. 0.77
   3 ?   -2.0   0.0       1.4   1.7e+03      41      72 ..     438     469 ..     427     470 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                    EE-TTSHHHHHHHHHHHHHS-.T.EEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGG..GG-- CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpev.kiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlsepr..lGLs 77 
                                    +TG+TG+ G+ + + L+++   v +++l  Ra + ++  + l +e     l s     +  r++vv+ D+++ +   GL 
  gi|121637571|ref|YP_977794.1|  68 ITGGTGMAGSAVARHLVSRYG-VrQVVLASRAGEHTESVAALVDE-----LGS-----AGARVQVVSCDVADRDavAGLV 136
                                    8****************9997.77********9886666655333.....333.....3468899999998887443443 PP

                                    HHHHHHHHHH--EEEE--SS-S........STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.G CS
                  NAD_binding_4  78 eedlqelaeevdviihsaAtvn.......fdepykellrvNveGtrevlelakklkklkvllhvST.a 137
                                    +++       +++++h a+ ++         e+++++lr+ v+G+ ++ el + l    +++ +S+ a
  gi|121637571|ref|YP_977794.1| 137 ASQ-----PDLTAVFHAAGVLDdavitglTPERVDKVLRAKVDGAWNLHELTRHLDVS-AFVLFSSmA 198
                                    333.....33445555555444222111134588888888888888888888888777.777777753 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.57
                                    H......HHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.STTS CS
                  NAD_binding_4  56 k......elaerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfdepy 104
                                           el++r+k  +G +  p l  +  ++ elae++d+ + +a  v++d+p 
  gi|121637571|ref|YP_977794.1| 372 FdsltavELRNRLKTATGLTLPPTLIFDYPTAAELAEHLDIQLANAPAVTVDQPN 426
                                    122223467999999999999999999**************99999999998875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.4
                                    HHHHT-SS-HHHHHHH.HHTTTEEEEE--TTSG CS
                  NAD_binding_4  41 leeelekkelfsallk.elaerikvveGDlsep 72 
                                    l ++l +++ ++   k +l +r++++ +D++ p
  gi|121637571|ref|YP_977794.1| 438 L-QALLDQPNWNPDDKtRLIKRLQAILTDCTAP 469
                                    4.777888888888668999*********9876 PP

>> PAC4  Proteasome assembly chaperone 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033       0.4      27      76 ..      49      94 ..      33      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                           PAC4 27 plgslvvAmpsrtnkktptisTtLlgdgsdeaserlAqrLArRlg.kqvfv 76
                                    +g +v+ mp+        + T L+++g++ a +++A+ L++R+g +qv++
  gi|121637571|ref|YP_977794.1| 49 HVGKVVLTMPDAWA-----AGTVLITGGTGMAGSAVARHLVSRYGvRQVVL 94
                                   46899999999887.....79***********************9556665 PP

>> Tnp_DNA_bind  Transposase DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.13   1.6e+02      22      56 ..      13      47 ..       4      48 .. 0.71
   2 ?   -2.1   0.0         3   3.6e+03      16      33 ..      86     103 ..      85     106 .. 0.84
   3 ?    6.1   0.0    0.0081       9.6      15      47 ..     453     485 ..     450     488 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                   Tnp_DNA_bind 22 vklaeslaekpgasiPqacqdwaetkAaYrFldne 56
                                   ++l+e +  +   ++P  + d   ++ aYrFl++ 
  gi|121637571|ref|YP_977794.1| 13 AELVELFKTEALHRLPVKSWDVRHAREAYRFLSQA 47
                                   5566666666667777777777788889****986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                   Tnp_DNA_bind  16 RltkRlvklaeslaekpg 33 
                                    R   R+v la++ +e+++
  gi|121637571|ref|YP_977794.1|  86 RYGVRQVVLASRAGEHTE 103
                                    7778*******9999876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0081
                   Tnp_DNA_bind  15 kRltkRlvklaeslaekpgasiPqacqdwaetk 47 
                                    +Rl kRl +++++  + p +s P+++ d+ ++ 
  gi|121637571|ref|YP_977794.1| 453 TRLIKRLQAILTDCTAPPASSGPSTTHDDEDIT 485
                                    6************************99888765 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00029      0.35      84     176 ..      52     144 ..      48     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                                    HHHHHHHHHCC..GCEE.EEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE..--HHH CS
                            PDH  84 kvvreleellkegksfv.gghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvil..mspee 160
                                    kvv ++ + ++ g+ ++ gg  maG+    v+    + +  + v+L   + + +e ++ + + l   garv +  ++ ++
  gi|121637571|ref|YP_977794.1|  52 KVVLTMPDAWAAGTVLItGGTGMAGS---AVARHLVSRYGVRQVVLASRAGEHTESVAALVDELGSAGARVQVvsCDVAD 128
                                    56778888888888877467889999...89999999*******************************998761155678 PP

                                    HHHHHHHHTHHHHHHH CS
                            PDH 161 HDrvvavvshlphvva 176
                                     D v ++v   p + a
  gi|121637571|ref|YP_977794.1| 129 RDAVAGLVASQPDLTA 144
                                    8889999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.59
# Mc/sec: 2568.74
//
Query:       gi|121637572|ref|YP_977795.1|  [L=1017]
Description: polyketide synthase pks9 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-63  215.4   3.0      2e-63  214.8   3.0    1.2  1  Acyl_transf_1    Acyl transferase domain
    5.8e-62  209.6   0.3    4.4e-59  200.1   0.3    2.8  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    6.8e-39  132.5   1.8    1.5e-38  131.4   1.8    1.7  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    2.6e-14   53.6   0.0    5.4e-14   52.6   0.0    1.5  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    2.4e-07   31.0   0.0    9.9e-07   29.0   0.0    2.2  2  PP-binding       Phosphopantetheine attachment site
     0.0001   21.7   0.5    0.00038   19.9   0.1    1.9  2  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   3.0   6.8e-67     2e-63       1     274 [.     504     777 ..     504     797 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 6.8e-67
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfvf+GqGsQw GMG++L+    +fa + ++   ++  q  +sv +v+  ++ gll++++f+qpaL++vq+ala+ll+  
  gi|121637572|ref|YP_977795.1| 504 VFVFPGQGSQWLGMGRQLYGRYSVFARAFDEVVAVLDGQLRLSVRQVMWGADAGLLESTEFAQPALFVVQVALAALLQDW 583
                                    8******************************************************************************* PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECCCCEC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavansprrvvi 160
                                    Gv p++v+GHS+GE+Aaa+vagals+ +a+++v+ r+rlm+ l   g m av+ +e e +   ++ v  a++n p++vvi
  gi|121637572|ref|YP_977795.1| 584 GVLPDLVMGHSVGEIAAAYVAGALSLVDAARVVAARGRLMQALPAGGVMVAVAASEDEVAPLLTEGVCIAAVNAPESVVI 663
                                    ******************************************************99999999****************** PP

                                    CEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHHHH CS
                  Acyl_transf_1 161 sgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywvan 240
                                    sg+q+a+  +v r+   g+++++ +v+ a+hs  +d++ ++ ++ lad+  r p++   s ++ + + ++  s +ywv+ 
  gi|121637572|ref|YP_977795.1| 664 SGEQAAVGVVVDRLVGLGRRVRRLAVSHAFHSVLMDPMVEEFSKVLADVCVRAPRIGLVSNVTGQLAGAGYGSPAYWVEH 743
                                    ******************************************************************************** PP

                                    HHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCC CS
                  Acyl_transf_1 241 lrspvrfaeavlsaaetiplvfveispHslllaa 274
                                    +r+pvrf + v  a   + +vfve+ p + l a 
  gi|121637572|ref|YP_977795.1| 744 VRKPVRFFDGVGLAESLGARVFVEVGPGAGLEAS 777
                                    *************9999********998777665 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.1   0.3   1.5e-62   4.4e-59       4     252 ..       6     221 ..       4     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 1.5e-62
                                    EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTSTHHHHHHHC CS
                  ketoacyl-synt   4 vaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfldvddfdpeffgispreae 83 
                                    +ai+G+++rfP  +++ ++w+lL++gr+a++++++       +                     +dfd+ ff+ sprea 
  gi|121637572|ref|YP_977795.1|   6 IAIIGLACRFPTVVSPGDLWDLLRDGREATGSIDN-------V---------------------ADFDADFFNLSPREAS 57 
                                    9******************************9992.......3.....................57************** PP

                                    TS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHHHHT CS
                  ketoacyl-synt  84 amdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagrisyalg 163
                                    amdp qrl+le +we leda + pe+l+g+ ++v++G+++ dya   +l    ++v+ +  + g+ ++++ia+r+s a+g
  gi|121637572|ref|YP_977795.1|  58 AMDPRQRLALELTWELLEDAFVVPETLRGQPIAVYLGAMNDDYAV-LTLA--ADRVDHHA-FAGT-SRAIIANRVSFAFG 132
                                    *****************************************9954.4444..44478888.8898.9************* PP

                                    --SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB-EEE CS
                  ketoacyl-synt 164 lrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlGEGvG 243
                                    lrGpsvt+d+  sSslvavh+a++s+r+gea +a+aGGv l l  e+ ++ ++ g++sp+g++ afd++adG+v+G+G G
  gi|121637572|ref|YP_977795.1| 133 LRGPSVTIDSGQSSSLVAVHLACESVRTGEAPLAIAGGVHLNLARETAMLEQEFGAVSPSGHTYAFDERADGYVPGDGGG 212
                                    ******************************************************************************** PP

                                    EEEEEECHH CS
                  ketoacyl-synt 244 avvLkrled 252
                                    +v+Lk+ + 
  gi|121637572|ref|YP_977795.1| 213 LVLLKPVQA 221
                                    *****9875 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   1.8   5.1e-42   1.5e-38       1     117 [.     230     346 ..     230     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 5.1e-42
                                    SEEEEEEEEEE--.STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSE CS
                Ketoacyl-synt_C   1 yavikgsavnsdg.ahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqpla 79 
                                    +a+i+gsav + g ++++lt p+ ++q ++i++a++ agvd ++v+yveahgtgt++gDpiE++al ++f++++ ++p+ 
  gi|121637572|ref|YP_977795.1| 230 HAIIRGSAVGNAGhSATGLTVPSVAGQVDVIRRAMSGAGVDCHQVHYVEAHGTGTKIGDPIEARALGEIFAARQ-RRPVS 308
                                    599**********999********************************************************99.77*** PP

                                    EE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  80 vgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    vgSvK+niGH+ +AaG+a+l+k+vla+++ vipp+ln+
  gi|121637572|ref|YP_977795.1| 309 VGSVKTNIGHTGGAAGIAGLLKAVLAIENAVIPPSLNY 346
                                    ************************************97 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.8e-17   5.4e-14       5     112 .]     351     469 ..     349     469 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.8e-17
                 KAsynt_C_assoc   5 ipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeesk......eeslprLlvlsgrteeav 74 
                                    i+ l+++ l+V t  tpwp       +gv+sfG+GG+n+HviL++ ++++++  ++      +++    +vl++r+++a+
  gi|121637572|ref|YP_977795.1| 351 ID-LDSLGLRVDTALTPWPVADeprrAGVSSFGMGGTNAHVILEQGPTQSPEIVESvaaagsNAPVAVPWVLAARSPQAL 429
                                    78.9999***********98877889*********************8888777777888767778888899******** PP

                 KAsynt_C_assoc  75 eallekleehlldaellsllneilseeisr..lpyRGyav 112
                                    ++++ +l +hl  ++ l+ l+   s   +r  +++R+ +v
  gi|121637572|ref|YP_977795.1| 430 TNQAGRLLAHLTADDGLTALDVGWSLVSTRsvFDHRAVVV 469
                                    ********************99999887777899998876 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.8   1.4e+04      38      46 ..     179     187 ..     174     191 .. 0.83
   2 !   29.0   0.0   3.3e-10   9.9e-07      10      67 .]     877     938 ..     868     938 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.8
                     PP-binding  38 laaleeefg 46 
                                    +a+le+efg
  gi|121637572|ref|YP_977795.1| 179 TAMLEQEFG 187
                                    689*****8 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 3.3e-10
                     PP-binding  10 vlgv.pleeidpdtdlfdlGlDSllavellaaleeef...gveiplsdlfehptlaelaayl 67 
                                    vlg+ +  +idp+  + dlG+DS++ vel ++l+ +    g+++p + +f++pt ++la++l
  gi|121637572|ref|YP_977795.1| 877 VLGRkSSHDIDPECAFQDLGFDSMSGVELRNRLQMAIglpGLSLPRTLIFDYPTASALAECL 938
                                    67776667899**************************55555*****************975 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.3e-07   0.00038      58     112 ..     119     171 ..     105     196 .. 0.89
   2 ?   -1.3   0.0      0.37   1.1e+03      27      61 ..     572     607 ..     562     622 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                                    STSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  58 egqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                    + ++ia+ ++++ g+    p+vt++   sS+l av+la++s+++gea  ++agGv
  gi|121637572|ref|YP_977795.1| 119 SRAIIANRVSFAFGL--RGPSVTIDSGQSSSLVAVHLACESVRTGEAPLAIAGGV 171
                                    445699999999999..99***********************************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC CS
                     Thiolase_N  27 laealkallekagvdpeevdevivGnvlqa.gegqn 61 
                                     + al all++ gv p+ v    vG++++a ++g+ 
  gi|121637572|ref|YP_977795.1| 572 VQVALAALLQDWGVLPDLVMGHSVGEIAAAyVAGAL 607
                                    5789999******************99999777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1017 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.56
# Mc/sec: 5455.43
//
Query:       gi|121637573|ref|YP_977796.1|  [L=353]
Description: chalcone synthase pks11 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-22   77.5   0.0    1.4e-21   77.0   0.0    1.2  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
    7.6e-17   61.7   0.0    1.3e-16   61.0   0.0    1.4  1  Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal 
    1.7e-14   53.8   0.0    2.4e-14   53.3   0.0    1.1  1  FAE1_CUT1_RppA   FAE1/Type III polyketide synthase-like prote
    9.2e-12   45.0   0.0    2.4e-10   40.4   0.0    2.3  2  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
      0.026   13.9   0.0      0.055   12.8   0.0    1.4  1  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   3.9e-25   1.4e-21      21     221 ..       9     197 ..       2     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 3.9e-25
                Chal_sti_synt_N  21 kalPeqvveqeklvdyylrvtksedlaelkeklerlcdkstvkkryivlteeileenPeltaemapsldarleivnaevl 100
                                     alP +   q++++d ++     ++     e ++rl   + v  r++vl    l+++P lt  + +     +ei  ++ +
  gi|121637573|ref|YP_977796.1|   9 GALPPHRYSQSEITDSFVEFPGLKE---HEEIIRRLHAAAKVNGRHLVLP---LQQYPSLTDFGDA-----NEIFIEKAV 77 
                                    58999999999****9998876555...567788999999********97...99*****999876.....69******* PP

                Chal_sti_synt_N 101 klgkeaalkalkewGrPkskithlvfvsssevelPGadlklakklGlrpsvkrvmlyflGcygGatvlrlakdiaennkG 180
                                    +lg ea l+al +     s+i  +   + ++v +P  d  +a +lGlrp+v+r+ l+ lGc +Ga+++   +d     + 
  gi|121637573|ref|YP_977796.1|  78 DLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPD 157
                                    **************9999*************************************************9999999999999 PP

                Chal_sti_synt_N 181 arvlvvaseitvlgfrgPskdrlddlvGaalfGdGaaavii 221
                                       ++v+ e+  l++ +  k  + +lvG+alfGdGaaav+ 
  gi|121637573|ref|YP_977796.1| 158 DVAVLVSVELCSLTY-PAVKPTVSSLVGTALFGDGAAAVVA 197
                                    9999999*******9.66788899**************984 PP

>> Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   3.6e-20   1.3e-16       8     148 ..     219     351 ..     212     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.6e-20
                Chal_sti_synt_C   8 tflPetdgvidgklteeGltfkllrdlPekieenieeflkklleklGieefndlfwivhPGGpaildrleaklklekekl 87 
                                     + P++ + +   +  +Gl ++l  dl ++ie  + + +++ l+    ++ +   w+ hPGGp ++d++ + l l +e l
  gi|121637573|ref|YP_977796.1| 219 SLYPDSLHIMGWDVGSHGLRLRLSPDLTNLIERYLANDVTTFLDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEAL 298
                                    56678888888889999************************99987777666668************************* PP

                Chal_sti_synt_C  88 easrkvlseyGnvssatvlyvldelrdkelkkklattgegkewGlllafGPGltietlllr 148
                                    e + + l e Gn+ssa++l++l   rd  ++k+  +       Gl+la+GPG+  e +llr
  gi|121637573|ref|YP_977796.1| 299 ELTWRSLGEIGNLSSASILHIL---RD-TIEKRPPSG----SAGLMLAMGPGFCTELVLLR 351
                                    ******************9997...66.444444444....68*************99998 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   6.7e-18   2.4e-14      94     205 ..      87     199 ..      55     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 6.7e-18
                 FAE1_CUT1_RppA  94 llaktkvspkdidilvvncslfsptPslsamvvnryklredvksynLsgmGCsAglisidlaknllqvhkntlalvvstE 173
                                     l  ++++p+did++ +++ +  + Psl a++  r +lr dv+ + L g+GC Ag   +   ++ l+ +++ +a++vs+E
  gi|121637573|ref|YP_977796.1|  87 ALDDANLRPSDIDMIATATVTGVAVPSLDARIAGRLGLRPDVRRMPLFGLGCVAGAAGVARLRDYLRGAPDDVAVLVSVE 166
                                    456789************************************************************************** PP

                 FAE1_CUT1_RppA 174 nitlnwYvGn.ersmllanclFRvGgaavllsn 205
                                     ++l + + + + s l++++lF  G+aav+   
  gi|121637573|ref|YP_977796.1| 167 LCSLTYPAVKpTVSSLVGTALFGDGAAAVVAVG 199
                                    ***998765526799*************97543 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.05   1.8e+02       1      20 [.      88     107 ..      88     165 .. 0.67
   2 !   40.4   0.0   6.7e-14   2.4e-10       1      90 []     261     352 ..     261     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.05
                                    HHHTT--GGG-SEEEE-SSS CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqan 20 
                                    L++a+l+p+did++    + 
  gi|121637573|ref|YP_977796.1|  88 LDDANLRPSDIDMIATATVT 107
                                    7899********98776554 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 6.7e-14
                                    HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GG...GB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEE CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpee...kvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgf 77 
                                    L+++ lt++di a v h    ++idava  l lp+e    +  +l e+Gn+s+asi+  L + +e ++  +g   l++++
  gi|121637573|ref|YP_977796.1| 261 LDAHRLTKDDIGAWVSHPGGPKVIDAVATSLALPPEaleLTWRSLGEIGNLSSASILHILRDTIE-KRPPSGSAGLMLAM 339
                                    78999*******************************77344556699******************.789*********** PP

                                    ETTTEEEEEEEE- CS
                  ACP_syn_III_C  78 GaGltwgaallrw 90 
                                    G G+    +llrw
  gi|121637573|ref|YP_977796.1| 340 GPGFCTELVLLRW 352
                                    ********99999 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.055      22     121 ..      75     174 ..      61     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                                    -HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE.EHGGGHHHHHHHHHHHHHH CS
                     Thiolase_N  22 saeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv.nkvcsSglkavalaaqsia 100
                                    +a++L+ eal ++l++a++ p+++d ++ ++v   +  +  ar  a ++g+  +v  + +    c  g+++va+  + ++
  gi|121637573|ref|YP_977796.1|  75 KAVDLGVEALLGALDDANLRPSDIDMIATATVTGVAVPSLDARI-AGRLGLRPDVRRMPLfGLGCVAGAAGVARLRDYLR 153
                                    689***************************99887666665554.45556655554444315679999999999999999 PP

                                    TTSHSEEEEEEEEESTTS-EE CS
                     Thiolase_N 101 ageadvvvagGvEsmsnapta 121
                                        dv+v++ vE  s ++ a
  gi|121637573|ref|YP_977796.1| 154 GAPDDVAVLVSVELCSLTYPA 174
                                    999999999999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2298.26
//
Query:       gi|121637574|ref|YP_977797.1|  [L=430]
Description: cytochrome P450 139 CYP139 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-62  211.6   0.0    2.3e-62  211.3   0.0    1.0  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.3   0.0   1.3e-66   2.3e-62      33     445 ..      16     404 ..       4     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 211.3 bits;  conditional E-value: 1.3e-66
                                    H-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTT CS
                           p450  33 ygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltptltsfgkl 112
                                     gp+ +  +g++  ++l g+ea + v+ + + +fs    + +++++   +  + +++++g+++++ R+++ p l+++  +
  gi|121637574|ref|YP_977797.1|  16 RGPLINAGVGGHGYTYLLGAEANRFVFANAD-AFSW---SQTFESLVPVDGPTALIVSDGADHRRRRSVVAPGLRHHHVQ 91 
                                    58999999999999************99997.4444...35666666689999************************555 PP

                                    THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCC CS
                           p450 113 sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdlledeklselvkaveelssllskssvqll 192
                                    ++++++ + ++ +++ +++  g++  ldi++ l  a+  + ++ lFg r+    ++++  l ++ + l++l+     ++ 
  gi|121637574|ref|YP_977797.1|  92 RYVATMVSNIDTVIDGWQP--GQR--LDIYQELRSAVRRSTAESLFGQRLA--VHSDF--LGEQLQPLLDLT----RRPP 159
                                    9**************9986..677..99*********************77..33335..677777887666....3577 PP

                                    CCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHH CS
                           p450 193 llfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdfldalllakkekkgesklsdeelaatvlellf 272
                                    ++++l + + ++ +r++ +a+k+++dl+d+ i + r   +++     ++l  l++    ++g+ +lsd+e++ ++  l++
  gi|121637574|ref|YP_977797.1| 160 QVMRLQQRVNSPGWRRAMAARKRIDDLIDAQIADARTAPRPD----DHMLTTLISGC-SEEGT-TLSDNEIRDSIVSLIT 233
                                    778888899****************************99999....45677777775.56666.9*************** PP

                                    HHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEE CS
                           p450 273 aGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvi 352
                                    aG++Tts +l+wa+y L++ P + e    E+ +vlg+ r p  ddl+ l+yl+ v++EtLRl+++ +    R+v++d+ +
  gi|121637574|ref|YP_977797.1| 234 AGYETTSGALAWAIYALLTVPGTWESAASEVARVLGG-RVPAADDLSALTYLNGVVHETLRLYSPGV-ISARRVLRDLWF 311
                                    ***********************************99.69***************************.555********* PP

                                    TTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTS.CTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHH CS
                           p450 353 rgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekg.nskrksfaflPFGaGpRnCiGerlArmelklflatlLq 431
                                    +g+ i++G   i+++y +hr pe++p+P eF+p R++++ +   k  +++f+PF+ G + CiG  +A+ e+ ++la+l+ 
  gi|121637574|ref|YP_977797.1| 312 DGHRIRAGRLLIFSAYVTHRLPEIWPEPTEFRPLRWDPNAAdYRKPAPHEFIPFSGGLHRCIGAVMATTEMTVILARLVA 391
                                    ***************************************9974457799******************************9 PP

                                    HEEEEESTSTSGGE CS
                           p450 432 nFevelqpetdppp 445
                                    +  ++l+  ++ + 
  gi|121637574|ref|YP_977797.1| 392 RAMLQLP-AQRTHR 404
                                    9988884.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2962.89
//
Query:       gi|121637575|ref|YP_977798.1|  [L=591]
Description: macrolide ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-47  161.0   0.0    4.5e-22   79.0   0.0    2.9  2  ABC_tran      ABC transporter
    1.6e-12   47.9  12.9    0.00079   19.3   0.2    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.4e-07   28.6   0.5        5.5    6.4   0.4    4.1  4  SMC_N         RecF/RecN/SMC N terminal domain
    2.8e-06   27.5   2.0    2.8e-06   27.5   2.0    2.2  2  ABC_tran_CTD  ABC transporter C-terminal domain
    4.4e-06   26.7   0.1       0.14   12.3   0.0    2.7  2  MMR_HSR1      50S ribosome-binding GTPase
    6.9e-06   26.0   0.0    2.4e-05   24.3   0.0    1.9  2  ABC_tran_Xtn  ABC transporter
    3.2e-05   23.6   1.1      0.042   13.6   0.1    2.4  2  AAA_29        P-loop containing region of AAA domain
    7.6e-05   23.3   0.7      0.054   14.0   0.1    2.6  2  AAA_23        AAA domain
    0.00017   20.7   2.4      0.019   13.9   0.3    2.3  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    0.00028   20.8   0.5       0.43   10.5   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
     0.0056   16.8   1.6       0.24   11.4   0.2    2.5  2  DUF87         Helicase HerA, central domain
  ------ inclusion threshold ------
      0.012   15.7   0.6        3.3    7.7   0.0    2.5  2  Dynamin_N     Dynamin family
       0.04   13.6   0.1        8.5    6.0   0.2    2.6  3  AAA_15        AAA ATPase domain
       0.17   11.4   0.1         15    5.1   0.0    2.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.17   12.5   1.5       0.35   11.5   0.9    1.9  1  FOXP-CC       FOXP coiled-coil domain
        0.3   11.5   9.6        0.1   13.0   0.4    3.1  4  AAA_16        AAA ATPase domain
        1.4    8.8   4.3        7.2    6.5   0.6    2.8  3  NACHT         NACHT domain
        2.1    9.0   4.5         60    4.4   1.1    3.3  2  SlyX          SlyX
        2.4    8.4   5.8        1.5    9.0   0.3    3.3  3  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   5.4e-25   5.1e-22       2     137 .]      21     151 ..      20     151 .. 0.93
   2 !   79.0   0.0   4.8e-25   4.5e-22       1     137 []     305     441 ..     305     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 5.4e-25
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + v+l ++ g +++ivG+nG GKS+Ll ll+g+l+p++G++           ++++  ++  l+q+++l+p+ tv+ +  
  gi|121637575|ref|YP_977798.1|  21 EAVTLGVNDGARIGIVGRNGDGKSSLLGLLTGQLRPDSGRV-----------TRRSGLRVNALSQTDTLDPNRTVGWTli 89 
                                    5799*************************************...........7899*******************99999 PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            + + +i ++++ l  +   dt+v    s+LSgGq++rv+la +l+ + +++ lDEpt+
  gi|121637575|ref|YP_977798.1|  90 gdqpehqwAGNPRIRDVVAGLVSDIAWDTPV----STLSGGQRRRVQLASLLVGEWDVIALDEPTN 151
                                    9977666555555999999999999999999....******************************8 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 4.8e-25
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvre 78 
                                    l+++++ + +ge+++ivG nGaGKStLl l+ag ++p  G++  +gk ++   l +    ++ +  +  +          
  gi|121637575|ref|YP_977798.1| 305 LRDIEWRIGPGERIGIVGANGAGKSTLLGLIAGTVQPGVGRV-KRGKTVRLAVLDQHGDDLAPFADDriAD--------- 374
                                    67999*************************************.2234444434444444444444443322......... PP

                                    H...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 +++ ++++l++lg      + ++ +   LSgGq++r++l+ +ll++p++lllDEpt+
  gi|121637575|ref|YP_977798.1| 375 VlgrlrggyqveGREVTPTQLLERLGFRR---DQLSARVDDLSGGQRRRLQLMLTLLSEPNVLLLDEPTN 441
                                    24555566666677777999999999655...6677788******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0018       1.7       3      41 ..      34      66 ..      33      97 .. 0.75
   2 !   12.6   0.0   9.4e-05     0.089     232     298 ..     118     182 ..      89     187 .. 0.87
   3 !   13.2   1.6   6.2e-05     0.059       3      20 ..     319     336 ..     318     353 .. 0.87
   4 !   19.3   0.2   8.4e-07   0.00079     227     303 .]     403     473 ..     354     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                   +++G+Ng GKS+LL +l +       ++++    ++++g
  gi|121637575|ref|YP_977798.1| 34 GIVGRNGDGKSSLLGLLTGQ------LRPDSGRVTRRSG 66
                                   69***************554......4444444444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.4e-05
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                    +p++ lS G++r   l+++l       +++++DEp n+L+ + ++ l++ l++  + n + ++++TH+
  gi|121637575|ref|YP_977798.1| 118 TPVSTLSGGQRRRVQLASLLVGEW---DVIALDEPTNHLDIQGITWLADHLRRRWArNTGGLLVVTHD 182
                                    688889999999999999999877...9*************999999988844444588999999997 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 6.2e-05
                         AAA_21   3 vliGpNgsGKSnLLdald 20 
                                    +++G+Ng+GKS+LL ++ 
  gi|121637575|ref|YP_977798.1| 319 GIVGANGAGKSTLLGLIA 336
                                    69************9984 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 8.4e-07
                         AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr....ngaQviltTHSplll 302
                                     d     +++lS G++r l l + ll+ +    +ll+DEp n  + ++l+          +    + + +i+++H+ +ll
  gi|121637575|ref|YP_977798.1| 403 RDQLSARVDDLSGGQRRRLQLMLTLLSEP---NVLLLDEPTNDVDTEMLTATE-------DlldsWAGTLIVVSHDRYLL 472
                                    45555567889***************999...89************4444444.......34445889********9998 PP

                         AAA_21 303 d 303
                                    +
  gi|121637575|ref|YP_977798.1| 473 E 473
                                    5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.3    0.0095         9      28      41 ..      34      47 ..      21      68 .. 0.87
   2 ?    5.2   0.0     0.013        12     136     205 ..     122     189 ..      69     198 .. 0.84
   3 !    6.4   0.4    0.0059       5.5      28      41 ..     319     332 ..     311     337 .. 0.87
   4 !    5.6   0.0    0.0097       9.1     111     211 ..     383     482 ..     373     488 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0095
                                   EEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnll 41
                                    ivG+NG GKs+ll
  gi|121637575|ref|YP_977798.1| 34 GIVGRNGDGKSSLL 47
                                   69**********97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH..CTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek..sknaQfivislreemleka 205
                                    +LSgG++  v la l     v    +  lDe   +LD + ++ +a+ l+++  +++  ++v+++++ +l ++
  gi|121637575|ref|YP_977798.1| 122 TLSGGQRRRVQLASL----LVGEWDVIALDEPTNHLDIQGITWLADHLRRRwaRNTGGLLVVTHDRWFLDEV 189
                                    799999998887765....467777899********************965225668899999998777665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0059
                                    EEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnll 41 
                                     ivG+NG+GKs ll
  gi|121637575|ref|YP_977798.1| 319 GIVGANGAGKSTLL 332
                                    69*********987 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0097
                                    EEETTEEE-HHHHHHHH..HCTT-..STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 111 ykingkevtkkevsell..esagi..skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                    y+++g+evt +++ e l  ++ ++    + LSgG++  + l L   +   +   + llDe     D +  ++  +ll++ 
  gi|121637575|ref|YP_977798.1| 383 YQVEGREVTPTQLLERLgfRRDQLsaRVDDLSGGQRRRLQLMLT--L--LSEPNVLLLDEPTNDVDTEMLTATEDLLDSW 458
                                    666666666666555542223333013458******87666555..3..34445679********************999 PP

                                    CTTSEEEEE-SSHHHCCC-.SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          SMC_N 187 sknaQfivislreemleka.dklvgv 211
                                         +iv+s+++ +le++ d+ + +
  gi|121637575|ref|YP_977798.1| 459 A--GTLIVVSHDRYLLERVtDQQYAI 482
                                    8..889********999886666665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.6       3.6   3.4e+03      45      65 ..     220     240 ..     211     241 .. 0.86
   2 !   27.5   2.0     3e-09   2.8e-06       7      69 .]     527     588 ..     522     588 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.6
                   ABC_tran_CTD  45 elsaeleeleaeLeelyerWe 65 
                                    +l+a  e+ ++ L +++  W+
  gi|121637575|ref|YP_977798.1| 220 RLTAAAEAKRQNLLRKELAWL 240
                                    688999999999999999997 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3e-09
                   ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLee 69 
                                    ++el+++++++++L  + a+ ++ela+ +  sd+  +++l+++l  l++  ++++ rW+eL+e
  gi|121637575|ref|YP_977798.1| 527 EKELAAVDRQLARLADRVAAKHTELAEHD-QSDHVGITRLTQQLRVLQDHVAAMENRWLELSE 588
                                    79***************************.5899***************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00014      0.14       1      23 [.      32      55 ..      32      88 .. 0.80
   2 !   11.6   0.0   0.00023      0.22       1      23 [.     317     340 ..     317     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                   EEEEEESTTSSHHHHHHHHHTS.T CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltge.k 23
                                   +++ivGr   GKS+L+  ltg+ +
  gi|121637575|ref|YP_977798.1| 32 RIGIVGRNGDGKSSLLGLLTGQlR 55
                                   69******************9752 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                                    EEEEEESTTSSHHHHHHHHHTS.T CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.k 23 
                                    +++ivG   +GKStL+  + g+ +
  gi|121637575|ref|YP_977798.1| 317 RIGIVGANGAGKSTLLGLIAGTvQ 340
                                    69**************99988643 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.5e-08   2.4e-05       1      56 [.     194     247 ..     194     274 .. 0.84
   2 ?   -2.5   0.2       5.7   5.3e+03      37      56 ..     523     540 ..     519     557 .. 0.48

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.5e-08
                   ABC_tran_Xtn   1 velengklteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakk 56 
                                    +e+++g ++ ++G Y +y+ ++ er +  ++a++k+q+ ++k+ ++ +r +   ++
  gi|121637575|ref|YP_977798.1| 194 WEVHDGIVEPFEGGYAAYVLQRVERDRLTAAAEAKRQNLLRKELAWLRRGAP--AR 247
                                    699**********************************************875..34 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                   ABC_tran_Xtn  37 qkeikkleefIerfrakakk 56 
                                     +  +k+ + ++r  a  + 
  gi|121637575|ref|YP_977798.1| 523 RRATEKELAAVDRQLA--RL 540
                                    3344444444444443..22 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0022         2      23      39 ..      30      47 ..      19      60 .. 0.76
   2 !   13.6   0.1   4.5e-05     0.042      17      39 ..     310     332 ..     305     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                         AAA_29 23 g.atlltGpsGsGKSTll 39
                                   g  + ++G++G GKS+ll
  gi|121637575|ref|YP_977798.1| 30 GaRIGIVGRNGDGKSSLL 47
                                   446679***********8 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.5e-05
                         AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                    ++i + + + ++G++G+GKSTll
  gi|121637575|ref|YP_977798.1| 310 WRIGPGERIGIVGANGAGKSTLL 332
                                    6777777788************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0065       6.1      23      40 ..      34      51 ..      26      78 .. 0.84
   2 !   14.0   0.1   5.8e-05     0.054      24      40 ..     320     336 ..     318     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0065
                         AAA_23 23 lItGpNGaGKTTildAik 40
                                    I+G NG GK+++l  ++
  gi|121637575|ref|YP_977798.1| 34 GIVGRNGDGKSSLLGLLT 51
                                   59***********97665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.8e-05
                         AAA_23  24 ItGpNGaGKTTildAik 40 
                                    I+G NGaGK+T+l  i 
  gi|121637575|ref|YP_977798.1| 320 IVGANGAGKSTLLGLIA 336
                                    9***********97775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0042       3.9      27      60 ..      28      61 ..      10      92 .. 0.84
   2 !   13.9   0.3     2e-05     0.019      14      49 ..     300     335 ..     290     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0042
                                   S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                           MeaB 27 GraqvvGltGvPGaGkstlvealglelrrrGkrv 60
                                       ++G+ G  G Gks l+  l+ +lr    rv
  gi|121637575|ref|YP_977798.1| 28 NDGARIGIVGRNGDGKSSLLGLLTGQLRPDSGRV 61
                                   55689*******************9999776666 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2e-05
                                    HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB  14 eakellerllakaGraqvvGltGvPGaGkstlveal 49 
                                      + +l+ +  + G  +++G+ G  GaGkstl+  +
  gi|121637575|ref|YP_977798.1| 300 GGRPVLRDIEWRIGPGERIGIVGANGAGKSTLLGLI 335
                                    568899*************************98654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0022       2.1     100     133 ..      31      64 ..       3      76 .. 0.76
   2 !   10.5   0.1   0.00046      0.43     102     131 ..     318     347 ..     282     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                                    SEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevsek 133
                                      + +vG  G GKS+L+  l+++l+   g v ++
  gi|121637575|ref|YP_977798.1|  31 ARIGIVGRNGDGKSSLLGLLTGQLRPDSGRVTRR 64 
                                    556699****************988777777665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00046
                                    EEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevs 131
                                    + +vG  G+GKStL+  ++++ +  +g v+
  gi|121637575|ref|YP_977798.1| 318 IGIVGANGAGKSTLLGLIAGTVQPGVGRVK 347
                                    5689****************9998888886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.04        38      25      47 ..      32      54 ..      22      61 .. 0.86
   2 !   11.4   0.2   0.00026      0.24      25      63 ..     317     362 ..     315     575 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.04
                          DUF87 25 HlAilgsTGsGKSntvavLleel 47
                                   +++i+g+ G GKS + ++L  +l
  gi|121637575|ref|YP_977798.1| 32 RIGIVGRNGDGKSSLLGLLTGQL 54
                                   789**************998665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                          DUF87  25 HlAilgsTGsGKSntvavLleelle.......kkgatililDpHGE 63 
                                    +++i+g  G+GKS++ +++   +          k +++ +lD HG+
  gi|121637575|ref|YP_977798.1| 317 RIGIVGANGAGKSTLLGLIAGTVQPgvgrvkrGKTVRLAVLDQHGD 362
                                    789**************88765555888987677779999999997 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0035       3.3       1      22 [.      33      54 ..      33      96 .. 0.82
   2 ?    5.8   0.2     0.014        13       1      20 [.     318     337 ..     318     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0035
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                   i +vG   +GKSS+l  L+g+ 
  gi|121637575|ref|YP_977798.1| 33 IGIVGRNGDGKSSLLGLLTGQL 54
                                   789*************999985 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                                    EEEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlg 20 
                                    i +vG+  +GKS++l  + g
  gi|121637575|ref|YP_977798.1| 318 IGIVGANGAGKSTLLGLIAG 337
                                    789************98887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.031        29      28      43 ..      35      50 ..      29      53 .. 0.92
   2 ?   -2.7   0.0       3.9   3.7e+03     325     368 ..     142     185 ..     140     186 .. 0.85
   3 ?    6.0   0.2     0.009       8.5      28      43 ..     320     335 ..     316     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
                         AAA_15 28 liGkNnsGKSsileal 43
                                   ++G+N+ GKSs+l +l
  gi|121637575|ref|YP_977798.1| 35 IVGRNGDGKSSLLGLL 50
                                   8***********9776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    ++++++EP +hL +q  + l++ l++    n + +++ TH  ++
  gi|121637575|ref|YP_977798.1| 142 DVIALDEPTNHLDIQGITWLADHLRRRWARNTGGLLVVTHDRWF 185
                                    6899********99999999999998888887789999998776 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.009
                         AAA_15  28 liGkNnsGKSsileal 43 
                                    ++G+N++GKS++l ++
  gi|121637575|ref|YP_977798.1| 320 IVGANGAGKSTLLGLI 335
                                    8***********9776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.015        15       5      55 ..      32      87 ..      29      91 .. 0.76
   2 ?    3.8   0.0     0.037        35       6      24 ..     318     336 ..     316     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                   EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.....HCHSHHHHHHTSC CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.....lDtlkeErergiT 55
                                    igi+g    GK++L++ L+ ++  +s + +++++ rv     +Dtl+  r  g T
  gi|121637575|ref|YP_977798.1| 32 RIGIVGRNGDGKSSLLGLLTGQLRPDSGRVTRRSGLRVnalsqTDTLDPNRTVGWT 87
                                   689**************999999998887777743333444557777777766666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                                    EEEEESTTSSHHHHHHHHH CS
                       GTP_EFTU   6 igiighvDhGKtTLtdrLl 24 
                                    igi+g   +GK+TL++ + 
  gi|121637575|ref|YP_977798.1| 318 IGIVGANGAGKSTLLGLIA 336
                                    89*************9775 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00037      0.35      14      55 ..     543     584 ..     540     591 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                        FOXP-CC  14 kvledveeflkhlnseHalddkstaqlrvqmqvvqqlekqlv 55 
                                    +v+ +++e+ +h +s+H    + t qlrv ++ v ++e++  
  gi|121637575|ref|YP_977798.1| 543 RVAAKHTELAEHDQSDHVGITRLTQQLRVLQDHVAAMENRWL 584
                                    6788999*******************************9865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.08        76      29      57 ..      35      63 ..      22      87 .. 0.82
   2 ?   -3.0   0.0       8.5     8e+03      86      86 ..     213     213 ..     159     263 .. 0.52
   3 ?   13.0   0.4   0.00011       0.1      25     142 ..     316     437 ..     305     472 .. 0.59
   4 ?   -1.6   0.2       3.3   3.1e+03     110     128 ..     517     542 ..     466     575 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.08
                         AAA_16 29 lsGesGvGKsslvrellralekdggiflr 57
                                   ++G  G GKssl+  l  +l+ d g ++r
  gi|121637575|ref|YP_977798.1| 35 IVGRNGDGKSSLLGLLTGQLRPDSGRVTR 63
                                   89999************999999666644 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.5
                         AAA_16  86 l 86 
                                    l
  gi|121637575|ref|YP_977798.1| 213 L 213
                                    1 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00011
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql....esa...ipy..salaqalareellrqlldeaesaele 95 
                                    e + ++G+ G GKs+l+  ++  ++   g + rgk+++l    + +   +p+  + +a++l r +   q++       +e
  gi|121637575|ref|YP_977798.1| 316 ERIGIVGANGAGKSTLLGLIAGTVQPGVGRVKRGKTVRLavldQHGddlAPFadDRIADVLGRLRGGYQVE------GRE 389
                                    566799***************88887745555566555533321112226655323555553333333333......444 PP

                         AAA_16  96 awrekleeala........avpelagaeasrllellkrllallsrderplvlvlD 142
                                      +++l+e+l+         v++l+g +++rl +l+  ll   s   +p vl+lD
  gi|121637575|ref|YP_977798.1| 390 VTPTQLLERLGfrrdqlsaRVDDLSGGQRRRL-QLMLTLL---S---EPNVLLLD 437
                                    55555555555655544446666666655444.3333333...2...35566666 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.3
                         AAA_16 110 elagaea.......srllellkrlla 128
                                    +++ga++        ++ ++l+rl++
  gi|121637575|ref|YP_977798.1| 517 AMSGAQRratekelAAVDRQLARLAD 542
                                    33333333333333333333333332 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.12   1.1e+02       4      20 ..      34      50 ..      31      63 .. 0.84
   2 ?   -2.9   0.0       5.9   5.6e+03     106     121 ..     158     173 ..     129     192 .. 0.65
   3 ?    6.5   0.6    0.0076       7.2       3      24 ..     318     339 ..     316     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                                   EEEC-TTTCHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqkl 20
                                    + G++G GK+ Ll  l
  gi|121637575|ref|YP_977798.1| 34 GIVGRNGDGKSSLLGLL 50
                                   589**********9765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                                    ...HHHHHCTTTTT-- CS
                          NACHT 106 rtlLselirkkllpea 121
                                     t+L++ +r+   +++
  gi|121637575|ref|YP_977798.1| 158 ITWLADHLRRRWARNT 173
                                    3444444444444444 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0076
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    + + G++G GK+tLl  +a + 
  gi|121637575|ref|YP_977798.1| 318 IGIVGANGAGKSTLLGLIAGTV 339
                                    5689***********9888665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4     0.095        89      30      58 ..     527     555 ..     524     560 .. 0.75
   2 ?    4.4   1.1     0.063        60      33      52 ..     562     581 ..     550     590 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.095
                                    HHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                           SlyX  30 qqqidrlqrqlrllaerlkeleessgase 58 
                                    ++++++  rql++la+r+++  ++ ++++
  gi|121637575|ref|YP_977798.1| 527 EKELAAVDRQLARLADRVAAKHTELAEHD 555
                                    67889999999999999977776665444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.063
                                    HHHHHHHHHHHHHT-XXXXX CS
                           SlyX  33 idrlqrqlrllaerlkelee 52 
                                    i+rl++qlr l+++++++e+
  gi|121637575|ref|YP_977798.1| 562 ITRLTQQLRVLQDHVAAMEN 581
                                    67788888888888777765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7   2.5e+03       1      20 [.      32      51 ..      32      65 .. 0.81
   2 ?    9.0   0.3    0.0016       1.5       1      26 [.     317     342 ..     317     442 .. 0.83
   3 ?    0.0   0.2      0.95     9e+02     121     154 ..     517     550 ..     510     580 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                         AAA_28  1 kivitGgestGKTtlleaLa 20
                                   +i i+G  + GK++ll  L+
  gi|121637575|ref|YP_977798.1| 32 RIGIVGRNGDGKSSLLGLLT 51
                                   57799999*******99887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0016
                         AAA_28   1 kivitGgestGKTtlleaLaargypv 26 
                                    +i i+G+ ++GK+tll  +a +  p 
  gi|121637575|ref|YP_977798.1| 317 RIGIVGANGAGKSTLLGLIAGTVQPG 342
                                    6789************9998664433 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.95
                         AAA_28 121 idddgeRredleereaiderlrealrelgipvii 154
                                    + + ++Rr +++e +a+d++l  + ++   + ++
  gi|121637575|ref|YP_977798.1| 517 AMSGAQRRATEKELAAVDRQLARLADRVAAKHTE 550
                                    4467778888888888888887777766555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 3741.64
//
Query:       gi|121637576|ref|YP_977799.1|  [L=120]
Description: hypothetical protein BCG_1707 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 914.82
//
Query:       gi|121637577|ref|YP_977800.1|  [L=115]
Description: hypothetical protein BCG_1708 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-29  100.9   0.0    3.1e-29  100.7   0.0    1.1  1  NTP_transf_9  Domain of unknown function (DUF427)


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   1.8e-33   3.1e-29       1      92 [.       2      91 ..       2      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.8e-33
                                   EEEE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEETTE...EEEEEEEEESS--T CS
                   NTP_transf_9  1 vrvklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslavdgk...evkdaaWsYpeptp 79
                                   +r+++ngtv+ae+ ++v+ve+     ++Yfppe+++ e+l +s tt++CpwKG a+yy+++vdg    +++daaW+Y++p+p
  gi|121637577|ref|YP_977800.1|  2 IRAVWNGTVLAEAPRTVRVEG-----NHYFPPESLHREHLIESPTTSICPWKGLAHYYNVVVDGPygpVNPDAAWYYRRPSP 78
                                   6899*****************.....************************************9999999************* PP

                                   T-GGGTT-BEE-T CS
                   NTP_transf_9 80 eaaeikgyvaFya 92
                                    a++ik++vaF++
  gi|121637577|ref|YP_977800.1| 79 LARRIKNHVAFWH 91
                                   ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 823.33
//
Query:       gi|121637578|ref|YP_977801.1|  [L=130]
Description: hypothetical protein BCG_1709 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.054   13.5   6.6      0.069   13.2   6.6    1.2  1  MerT             MerT mercuric transport protein


Domain annotation for each model (and alignments):
>> MerT  MerT mercuric transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   6.6   3.9e-06     0.069      14     107 ..      28     121 ..      18     130 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-06
                           MerT  14 gglaailaslcclgplvllllgvsga...wignltvlepyrpifiaaalvalffawrriyrpveacepgevcavpqvrkt 90 
                                    g ++ ++  lcc+gp +l l+g+  a   +     + + y   f +  l++l +  +  +r  + c   +v a+ ++r +
  gi|121637578|ref|YP_977801.1|  28 GIISGLVGMLCCVGPTILALVGIISAataFAWANDLYDNYAWWFRVSGLAVLAILVWWALRHRNRC---SVNAIRRLRWR 104
                                    778889999*************854312244445678999999*9999999988777667766555...45666666666 PP

                           MerT  91 ykvifwlvavlvlvava 107
                                       ++ + + +  v+ a
  gi|121637578|ref|YP_977801.1| 105 LMAVLAIAVGTYGVLSA 121
                                    66666666655545444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 951.37
//
Query:       gi|121637579|ref|YP_977802.1|  [L=443]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-35  120.8  49.6    3.9e-32  111.6  41.5    2.0  2  MFS_1     Major Facilitator Superfamily
    1.3e-05   24.6  43.6    8.3e-05   22.0  43.6    1.8  1  MFS_4     Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6  41.5   4.3e-36   3.9e-32       1     315 [.      24     348 ..      24     361 .. 0.80
   2 !   13.6  12.3   2.6e-06     0.023      71     197 ..     319     440 ..     309     443 .] 0.78

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 4.3e-36
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l++++++++ +r+++++a+  a++ dl +s++++g+++++++lg++++++p+ +   rfG+ r+l + +l++++++++ +
  gi|121637579|ref|YP_977802.1|  24 LFVLYVINFVDRANISVAAL-AMNADLRLSATAYGTAAGVFFLGYVLFQVPANAALARFGAGRTLTAVVLAWGVCSAATA 102
                                    6899***************9.******************************************************55555 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wrav 153
                                    +  ++  +l+++r+  G+++g++fp+++a+++ wfp  +r+ra++ + +++ ++  +g +l+gl++ ++       Wra+
  gi|121637579|ref|YP_977802.1| 103 L-VTSAhTLYLARFALGVAEGGFFPGVIAYLTVWFPCAQRARAVATFLLAIPVANTVGLPLSGLIVGHVHmaglpgWRAM 181
                                    5.455558**********************************************************8888999******* PP

                          MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp....awkallkdpvl.......w...illialllf 219
                                    f+i a+ +ll++ l   llp++p + ++ +p+e+     + +++     +                 w   ++ ++  + 
  gi|121637579|ref|YP_977802.1| 182 FVIEALPALLLAPLLRRLLPDNPQRASWLTPEERA----ELSARLtedtPAP-------TgrssgagWdlvLFAVVYGGL 250
                                    **********************************4....4443332222111.......122333337743233333333 PP

                          MFS_1 220 ffgfsglltllplylqevlglsglllaglllallalvgailallagrls.drlgr...rrrlllallllllaalglalla 295
                                     f++++l ++lp ++ +  + ++ l+a++l al++ v+a ++l ++  s dr g+   +++l  + ++ +++ ++l +++
  gi|121637579|ref|YP_977802.1| 251 YFALYALQFFLPQLVASLAHGTATLTAATLAALPYGVAALAMLAWSHRSiDRSGAqagHITLPTTAAGSAALGAALSPMS 330
                                    557777*******8555555556799999*********999999999998*96655556777777777777777777777 PP

                          MFS_1 296 vtssavllllvlvliGfglg 315
                                    ++ + ++l +  +++G+ ++
  gi|121637579|ref|YP_977802.1| 331 PIVTLSWLTI--AVAGILAA 348
                                    7745555544..44444222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.6e-06
                          MFS_1  71 lfalglllll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                    + alg ++l+ + s++  l ++  +++G+  +a+ +     +a+++ + + + ai+ ++a +sl++  gp + g l ++ 
  gi|121637579|ref|YP_977802.1| 319 SAALG-AALSpM-SPIVtLSWLTIAVAGIL-AAMPAFWSRCTAALAGP-RVAVAIATVNAVASLASFAGPYATGHLKDAT 394
                                    33333.333334.88887888888899998.79999999999999999.****************************777 PP

                          MFS_1 149 g.Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplv 197
                                    g ++++ + +a+v++ a+ + lll  + ++  +++s++ +     p+p++
  gi|121637579|ref|YP_977802.1| 395 GtYHLALLTVAAVLAAAAACSLLLRHAGRTVCANDSEIML----HPSPAT 440
                                    77***************99977887777766666666666....666655 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  43.6   9.3e-09   8.3e-05      18     360 ..      44     413 ..      43     416 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.3e-09
                          MFS_4  18 allaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAv 97 
                                    a+ a++ ls+++ g  a + +lGY +  + a  al++  +  +l a +la  +  +a al++s  ++ l+Rf++Gva + 
  gi|121637579|ref|YP_977802.1|  44 AMNADLRLSATAYGTAAGVFFLGYVLFQVPANAALARFGAGRTLTAVVLAWGVCSAATALVTSAHTLYLARFALGVAEGG 123
                                    58999********************9999998888776666669999******************************998 PP

                          MFS_4  98 vl...vfgsslv..lahaaaarrervgallfaGvGlGiavsgllvllllqlglsassl.Wlalavlsavllllvalllp. 170
                                     +   ++  ++    a+ a a + +++a+  a   +G  +sgl+v  ++ +gl +  +  ++ a+ +++l  l+  llp 
  gi|121637579|ref|YP_977802.1| 124 FFpgvIAYLTVWfpCAQRARAVATFLLAIPVAN-TVGLPLSGLIVGHVHMAGLPGWRAmFVIEALPALLLAPLLRRLLPd 202
                                    765424444444244444555567777777764.6999********9999999865551555555566666666777774 PP

                          MFS_4 171 ...........raalrea..s......aaaeaakaeqkslpllalllaYglaGfGYiitatFlvaiardgaggal...le 228
                                               +     a  s      ++a+  +   +   l+ ++++Yg   f++ +   Fl++++++ a+g +   ++
  gi|121637579|ref|YP_977802.1| 203 npqraswltpeE----RAelSarltedTPAPTGRSSGAGWDLVLFAVVYGGLYFALYALQFFLPQLVASLAHGTAtltAA 278
                                    333332222211....1111111111133344444455556788999**********************98877522134 PP

                          MFS_4 229 allWllvGlaaivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivs....svllGltflaitalvlqla 304
                                     l+ l +G+aa +++l+w +++  +  ++a  ++l + a+g ++  +  sp+++iv      + + +   a+ a+  + +
  gi|121637579|ref|YP_977802.1| 279 TLAALPYGVAA-LAMLAWSHRSIDRSGAQAGHITLPTTAAGSAALGAALSPMSPIVTlswlTIAVAGILAAMPAFWSRCT 357
                                    45566689986.56788888877777778888888888777777666666666666511112334444556667777888 PP

                          MFS_4 305 relappatrrllglmTasfgigQilGpllasllaeatgslalallvaaaalvlaal 360
                                      la+p +  +++ + a+  +   +Gp++++ l++atg+++lall  aa+l+ aa+
  gi|121637579|ref|YP_977802.1| 358 AALAGPRVAVAIATVNAVASLASFAGPYATGHLKDATGTYHLALLTVAAVLAAAAA 413
                                    899999999999*********************************88888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2782.39
//
Query:       gi|121637580|ref|YP_977803.1|  [L=310]
Description: hypothetical protein BCG_1711c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-25   88.4   0.0    7.1e-25   87.6   0.0    1.4  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0     4e-29   7.1e-25       1     112 []     133     244 ..     133     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 4e-29
                 Transglut_core   1 ralaeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgyls 80 
                                    r+la+++++ +++ple+a++iy++v + ++y+ +++++   + e++l++  Gnc d+ +lfv+l+R++ ipaR+v g   
  gi|121637580|ref|YP_977803.1| 133 RTLAQDVVGPETNPLEQARRIYDYVTGAMDYD-ATKQSFLGSTEHALTCSVGNCNDIHALFVSLCRSVDIPARFVLGQAL 211
                                    689*****************************.888899999**********************************9987 PP

                 Transglut_core  81 .geeekeqsvasedaHawvevylegygWvplDp 112
                                      ++ ++q  ++ ++H+w+e+++ g gW+p+D+
  gi|121637580|ref|YP_977803.1| 212 eLPQPGAQDCEVCGYHCWAEFFVAGLGWLPADA 244
                                    34555555999********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1946.45
//
Query:       gi|121637581|ref|YP_977804.1|  [L=218]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-13   49.3   0.0      9e-13   48.7   0.0    1.3  1  Rhodanese   Rhodanese-like domain
    6.6e-09   35.5   1.3    1.5e-08   34.4   0.2    2.2  3  HTH_5       Bacterial regulatory protein, arsR family
    9.3e-09   35.2   5.7    2.4e-08   33.9   1.5    2.9  3  HTH_20      Helix-turn-helix domain
    1.4e-05   25.1   6.3    1.8e-05   24.7   1.8    2.7  3  DprA_WH     DprA winged helix domain
    0.00022   21.1   0.0    0.00071   19.4   0.0    1.8  2  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0022   17.9   3.7     0.0079   16.1   1.8    2.5  3  MarR_2      MarR family
      0.004   17.5   0.0     0.0095   16.3   0.0    1.6  1  Rrf2        Transcriptional regulator
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.087   13.1   0.0    1.8  1  PaaX        PaaX-like protein
      0.033   14.1   0.1      0.085   12.8   0.0    1.6  2  MarR        MarR family
      0.049   13.6   0.1       0.12   12.4   0.1    1.7  1  HTH_Crp_2   Crp-like helix-turn-helix domain
      0.058   13.9   0.1       0.12   12.9   0.1    1.5  1  HTH_27      Winged helix DNA-binding domain
      0.063   12.8   0.1        0.3   10.7   0.0    2.0  2  HTH_24      Winged helix-turn-helix DNA-binding
       0.08   12.7   4.1        0.1   12.4   2.7    1.9  2  HTH_IclR    IclR helix-turn-helix domain
       0.15   11.8   0.7        2.7    7.8   0.1    2.3  2  FtsK_gamma  Ftsk gamma domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0     7e-16     9e-13       2     106 ..     120     210 ..     119     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 7e-16
                      Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaa 81 
                                     +el+++ ++g+v +lDvRp+ eY++gh+pgAv++             pl+el e+l el    +  +v  c+g  +  a
  gi|121637581|ref|YP_977804.1| 120 RDELQARVAAGSVLVLDVRPAMEYAAGHLPGAVSI-------------PLDELAERLDEL--PSGIDIVACCRGPYCVYA 184
                                    6899********99*********************.............***********9..***************444 PP

                      Rhodanese  82 a..aallkklGyknvsvldGGfkawke 106
                                         ll+  G    + ldGGf++w +
  gi|121637581|ref|YP_977804.1| 185 YdaLELLRPNG-FSARRLDGGFSEWLA 210
                                    4324466669*.79***********86 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.2   1.2e-11   1.5e-08       4      47 .]      24      67 ..      21      67 .. 0.97
   2 ?   -1.5   0.0       1.9   2.4e+03       5      23 ..      87     106 ..      85     107 .. 0.76
   3 ?   -3.7   0.0       9.1   1.2e+04      12      18 ..     176     182 ..     176     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                                   HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   Rl++L lL +ge++v  la++ gl+ ++ S+HL +Lr aGLV++
  gi|121637581|ref|YP_977804.1| 24 RLELLDLLVQGERSVDALARASGLTFANASQHLLQLRRAGLVTS 67
                                   9*****************************************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                    HHHHHHHTTSS.EEHHHHHH CS
                          HTH_5   5 lkILklLaege.lcvcelae 23 
                                    ++ ++++ae++ ++v+ l++
  gi|121637581|ref|YP_977804.1|  87 VRAVRAVAERNlASVGSLVR 106
                                    67789999955489998876 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.1
                                    TTSSEEH CS
                          HTH_5  12 aegelcv 18 
                                    ++g++cv
  gi|121637581|ref|YP_977804.1| 176 CRGPYCV 182
                                    689***9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   1.5   1.8e-11   2.4e-08       5      61 .]      17      72 ..      11      72 .. 0.95
   2 ?    0.2   0.0      0.62     8e+02       3      25 ..      74      93 ..      73     129 .. 0.74
   3 ?    0.8   0.0      0.42   5.3e+02      18      35 ..     147     164 ..     146     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.8e-11
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                    AL++  R+++l++L   +++++ +la++ +l+ +++s+HL +L++agLv+++r g+
  gi|121637581|ref|YP_977804.1| 17 QALSSGHRLELLDLL-VQGERSVDALARASGLTFANASQHLLQLRRAGLVTSRRDGK 72
                                   79*************.**************************************985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.62
                                   HHHHHS-HHHHHHHHHHSTCTTB CS
                         HTH_20  3 iaeALahPvRrrilraLaraegl 25
                                   +++AL++P   ++ ra    +++
  gi|121637581|ref|YP_977804.1| 74 VIYALSDPQVWDVVRAV---RAV 93
                                   78999999999999888...333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.42
                                    HHSTCTTB-HHHHHHHHT CS
                         HTH_20  18 aLaraegltaselaerld 35 
                                    +L++a    + elaerld
  gi|121637581|ref|YP_977804.1| 147 HLPGAVSIPLDELAERLD 164
                                    677888888999***997 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.8   1.4e-08   1.8e-05      11      59 ..      21      69 ..      15      71 .. 0.90
   2 ?   -1.5   0.0       2.3   2.9e+03      24      35 ..     116     127 ..     114     130 .. 0.71
   3 ?    1.1   0.0      0.33   4.3e+02      23      35 ..     151     163 ..     147     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                        DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverlp 59
                                   ++ +  +L++L +  ++vD+L+r++gl++a  s +Ll+L  aGlv+++ 
  gi|121637581|ref|YP_977804.1| 21 SGHRLELLDLLVQGERSVDALARASGLTFANASQHLLQLRRAGLVTSRR 69
                                   5667789**************************************9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                        DprA_WH  24 ePvhvDqLvrrt 35 
                                    eP++ D+L +r+
  gi|121637581|ref|YP_977804.1| 116 EPISRDELQARV 127
                                    678888887765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.33
                        DprA_WH  23 pePvhvDqLvrrt 35 
                                    + ++++D+L++r+
  gi|121637581|ref|YP_977804.1| 151 AVSIPLDELAERL 163
                                    5578999999996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.5e-07   0.00071      15      67 ..      28      81 ..      26      82 .. 0.90
   2 ?   -1.8   0.0       2.3     3e+03      39      54 ..     184     199 ..     183     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.5e-07
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                   l Ll +g+ ++d +a+++g+  +++ + L +L ++GlV+ ++ g++ +Y   dp
  gi|121637581|ref|YP_977804.1| 28 LDLLVQGERSVDALARASGLTFANASQHLLQLRRAGLVTSRRdGKRVIYALSDP 81
                                   6899***********************************998455668888777 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHCTSEEE CS
                           TrmB  39 vYevLrsLedkGlVer 54 
                                    +Y++L+ L   G+  r
  gi|121637581|ref|YP_977804.1| 184 AYDALELLRPNGFSAR 199
                                    7999999999998665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   6.1e-06    0.0079      10      61 ..      27      73 ..      18      74 .. 0.84
   2 ?    0.7   0.0       0.4   5.1e+02       4      30 ..      80     107 ..      76     115 .. 0.77
   3 ?   -3.0   0.0       5.7   7.3e+03      23      31 ..     155     163 ..     146     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-06
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   +L  L  +++   +v +lar+ gl+ +++s++l  L +aGLv+ r++   kR
  gi|121637581|ref|YP_977804.1| 27 LLDLLVQGER---SVDALARASGLTFANASQHLLQLRRAGLVTSRRD--GKR 73
                                   6666666664...******************************9987..555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.4
                                    -HHHHHHHHHHHCTTTSEE.EHHHHHHH CS
                         MarR_2   4 tpaqarvLaaLgrrpgrdl.tvgelarr 30 
                                    +p+ ++v  a+++  +r+l +vg l+r 
  gi|121637581|ref|YP_977804.1|  80 DPQVWDVVRAVRAVAERNLaSVGSLVRQ 107
                                    4899999999999999977788888775 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.7
                                    EHHHHHHHH CS
                         MarR_2  23 tvgelarrl 31 
                                       ela+rl
  gi|121637581|ref|YP_977804.1| 155 PLDELAERL 163
                                    445677766 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.4e-06    0.0095      26      83 .]      36      90 ..      23      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET.TT-TCEEESSHCCCSBHHHHHHHH CS
                           Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvr.GkgGGyrLakppeeItlldvvrav 83
                                    s++++a+  ++    +++ l +Lr+aglv+s+r Gk+  y+L+      +++dvvrav
  gi|121637581|ref|YP_977804.1| 36 RSVDALARASGLTFANASQHLLQLRRAGLVTSRRdGKRVIYALSD----PQVWDVVRAV 90
                                   47999***************************9857766666644....4677777775 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.8e-05     0.087      46      68 ..      58      80 ..      53      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                           PaaX 46 RlakaGwlvrekegrrsfYrLsd 68
                                    l +aG++++ ++g+r++Y+Lsd
  gi|121637581|ref|YP_977804.1| 58 QLRRAGLVTSRRDGKRVIYALSD 80
                                   5889******************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.6e-05     0.085      11      52 ..      29      70 ..      21      72 .. 0.91
   2 ?   -3.6   0.0       8.9   1.1e+04      18      27 ..     154     163 ..     153     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                   HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                    l  qg+ sv  La+++g++ ++++  l +L ++Gl++++++
  gi|121637581|ref|YP_977804.1| 29 DLLVQGERSVDALARASGLTFANASQHLLQLRRAGLVTSRRD 70
                                   5667888999****************************9997 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.9
                                    EEHHHHHHHH CS
                           MarR  18 lsvseLakkl 27 
                                    + + eLa++l
  gi|121637581|ref|YP_977804.1| 154 IPLDELAERL 163
                                    5678999987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.2e-05      0.12      25      56 ..      39      73 ..      20      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-05
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET..EE CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rg..rr 56
                                   + lA+  Glt    s+ l +L+r+gl++ r+  +r
  gi|121637581|ref|YP_977804.1| 39 DALARASGLTFANASQHLLQLRRAGLVTsRRdgKR 73
                                   679*************************7542244 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.3e-05      0.12      20      66 ..      37      80 ..      25      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                         HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                   +  +l+++  ++ +++s  l +L ++GLv   ++++d++++ ++l+d
  gi|121637581|ref|YP_977804.1| 37 SVDALARASGLTFANASQHLLQLRRAGLV---TSRRDGKRVIYALSD 80
                                   556788889999999**************...88899******9987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024       0.3      16      48 .]      34      66 ..      23      66 .. 0.86
   2 ?   -0.8   0.0      0.88   1.1e+03      18      27 ..     154     163 ..     153     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                         HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +  s   LA+++gl+ ++ +++l +L ++Gl++
  gi|121637581|ref|YP_977804.1| 34 GERSVDALARASGLTFANASQHLLQLRRAGLVT 66
                                   6668889************************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.88
                         HTH_24  18 isqreLAerl 27 
                                    i+  eLAerl
  gi|121637581|ref|YP_977804.1| 154 IPLDELAERL 163
                                    6778****98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.7   7.8e-05       0.1       6      50 ..      25      67 ..      24      69 .. 0.92
   2 ?   -2.5   0.0       3.7   4.8e+03      20      29 ..     155     164 ..     148     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   l++Ld+l ++ +   +  lAr++gl+ ++++ +L  L + G+v+ 
  gi|121637581|ref|YP_977804.1| 25 LELLDLLVQGERS--VDALARASGLTFANASQHLLQLRRAGLVTS 67
                                   6789999999995..9***************************85 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.7
                                    BHHHHHHHHT CS
                       HTH_IclR  20 tlselArrtg 29 
                                     l elA+r++
  gi|121637581|ref|YP_977804.1| 155 PLDELAERLD 164
                                    5789999975 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0021       2.7      17      57 ..      33      72 ..      27      77 .. 0.86
   2 ?    2.0   0.1      0.14   1.8e+02       9      28 ..      88     107 ..      86     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                     FtsK_gamma 17 egkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegskp 57
                                   +g+ S+  l R   + ++ A++ + qL ++G+V++    ++
  gi|121637581|ref|YP_977804.1| 33 QGERSVDALARASGLTFANASQHLLQLRRAGLVTSRRD-GK 72
                                   67789****************************98764.33 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                     FtsK_gamma   9 eavelvveegkaStSllQRr 28 
                                    +av+ v e + aS+ +l R+
  gi|121637581|ref|YP_977804.1|  88 RAVRAVAERNLASVGSLVRQ 107
                                    699*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1589.55
//
Query:       gi|121637582|ref|YP_977805.1|  [L=244]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-18   66.7   0.0    2.2e-18   66.1   0.0    1.3  1  cNMP_binding  Cyclic nucleotide-binding domain
    1.4e-11   44.2   1.1    1.4e-11   44.2   1.1    1.9  2  HTH_Crp_2     Crp-like helix-turn-helix domain
     0.0013   18.6   0.5     0.0013   18.6   0.5    3.2  4  MarR_2        MarR family
  ------ inclusion threshold ------
      0.032   14.2   0.2       0.08   12.9   0.2    1.6  1  HTH_37        Helix-turn-helix domain
      0.042   13.5   0.1       0.16   11.6   0.2    1.9  2  GntR          Bacterial regulatory proteins, gntR family
      0.061   13.4   0.0       0.24   11.5   0.0    2.0  1  HTH_29        Winged helix-turn helix
       0.11   12.8   0.0       0.32   11.3   0.0    1.7  1  ParBc         ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   8.5e-22   2.2e-18       2      89 .]      60     146 ..      59     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 8.5e-22
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    ++f++g v+f+++++ad+++iv+ G +++  + +  ++ v+++l+pGd+ G++ ll + p+ +t +Alt++++l+l+r++
  gi|121637582|ref|YP_977805.1|  60 KEFAPGAVVFHADQTADGVWIVRHGLIELA-VGSRRRRAVVNILHPGDVDGDIPLLLEMPMVYTGRALTQATCLFLDRQA 138
                                    68***************************6.99999999*****************99********************** PP

                                    HHHHHHH- CS
                   cNMP_binding  82 flellqqd 89 
                                    f++ll+++
  gi|121637582|ref|YP_977805.1| 139 FERLLATH 146
                                    ****9876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   5.7e+03      47      55 ..      82      93 ..      81     104 .. 0.52
   2 !   44.2   1.1   5.4e-15   1.4e-11       3      67 ..     180     241 ..     178     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                                   HTTSEE..ET.E CS
                      HTH_Crp_2 47 reglis..rg.r 55
                                   r+gli+   g r
  gi|121637582|ref|YP_977805.1| 82 RHGLIElaVGsR 93
                                   678888652222 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 5.4e-15
                                    HHHHHHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES-HHHHHH CS
                      HTH_Crp_2   3 lArfLlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglisrgrr.irildleaLra 67 
                                    +A++Ll+ a +a    ++ l q+ lA+mlG+ r ++++il+e++r+ li+ g+  i+i+d  +Lra
  gi|121637582|ref|YP_977805.1| 180 VAQLLLDEAIDA----RIELAQRTLAAMLGAQRPSINKILKEFERDRLITVGYAvIEITDQHGLRA 241
                                    899998865542....5899******************************99778*********97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.62   1.6e+03      21      32 ..      48      58 ..      16      62 .. 0.66
   2 ?   -0.3   0.2       0.4     1e+03      46      62 .]      81      97 ..      80      97 .. 0.83
   3 ?   -2.3   0.0       1.7   4.3e+03      31      43 ..     132     144 ..     129     153 .. 0.66
   4 !   18.6   0.5   4.9e-07    0.0013       4      52 ..     162     225 ..     159     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.62
                                   EEEHHHHHHHHT CS
                         MarR_2 21 dltvgelarrlg 32
                                   d  v++la++l+
  gi|121637582|ref|YP_977805.1| 48 D-DVSALAETLQ 58
                                   2.5666766665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                                   HHTTSEEEEESSSSSSS CS
                         MarR_2 46 vaaGLverrpgpeDkRa 62
                                   v++GL+e   g++ +Ra
  gi|121637582|ref|YP_977805.1| 81 VRHGLIELAVGSRRRRA 97
                                   789****9999888875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.7
                                    HTSSHHHHHHHHH CS
                         MarR_2  31 lglsksavsrilk 43 
                                    l l+++a  r+l+
  gi|121637582|ref|YP_977805.1| 132 LFLDRQAFERLLA 144
                                    6677777666654 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 4.9e-07
                                    -HHHHHHHHHHHCTTTS...............EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2   4 tpaqarvLaaLgrrpgr...............dltvgelarrlglsksavsrilkrLvaaGLve 52 
                                    + aq r+++ Lgr  +                +l+++ la+ lg  ++++++ilk++++  L++
  gi|121637582|ref|YP_977805.1| 162 STAQIRLMGMLGRPLPAqvaqllldeaidariELAQRTLAAMLGAQRPSINKILKEFERDRLIT 225
                                    5688888888888888899999999999998889*****************************6 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.1e-05      0.08      23      61 ..     185     220 ..     176     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                    HHHHHHHC.T--HHHHHHHHT--HHHHHHHHTT--TT--H CS
                         HTH_37  23 iaeliekr.elsqseaaqllgiaqPkvsrllrgklsrfsl 61 
                                    + e i++r el+q+ +a++lg ++P+++++l+    +f+ 
  gi|121637582|ref|YP_977805.1| 185 LDEAIDARiELAQRTLAAMLGAQRPSINKILK----EFER 220
                                    6666766658*********************7....4444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.9   7.3e+03       9      22 ..      53      66 ..      51      67 .. 0.75
   2 ?   11.6   0.2   6.2e-05      0.16       9      56 ..     180     226 ..     175     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                                   HHHHHHTTSS-TTS CS
                           GntR  9 LredIlsgelrpGd 22
                                   L e + ++e++pG+
  gi|121637582|ref|YP_977805.1| 53 LAETLQAKEFAPGA 66
                                   66778888899885 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.2e-05
                                    HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           GntR   9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56 
                                    + +++l+  + +   L ++r Laa++g  r+++++ L++ e++ l+++
  gi|121637582|ref|YP_977805.1| 180 VAQLLLDEAIDARIEL-AQRTLAAMLGAQRPSINKILKEFERDRLITV 226
                                    5677777777777889.9***************************986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.3e-05      0.24       6      41 ..     183     223 ..     180     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                         HTH_29   6 lllaeGvs.....tvsqiAkllglsrrtvyrwlkrfeegGl 41 
                                    lll+e+ +       + +A++lg  r++++++lk fe ++l
  gi|121637582|ref|YP_977805.1| 183 LLLDEAIDarielAQRTLAAMLGAQRPSINKILKEFERDRL 223
                                    66666666666667899********************9985 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.32      20      62 ..      47      99 ..      39     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                          ParBc 20 pekieelvasIkkkGllqPiivrktr..........qgryeiiaGerRlrAak 62
                                   ++++ +l++++++k + + ++v + +           g++e+  G rR+rA+ 
  gi|121637582|ref|YP_977805.1| 47 RDDVSALAETLQAKEFAPGAVVFHADqtadgvwivrHGLIELAVGSRRRRAVV 99
                                   7999*************99999999999999999999**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1743.33
//
Query:       gi|121637583|ref|YP_977806.1|  [L=234]
Description: hypothetical protein BCG_1714 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.1e-08   32.2   0.0    1.7e-07   31.2   0.0    1.6  1  AhpC-TSA    AhpC/TSA family
    2.5e-05   24.4   0.0    4.2e-05   23.6   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
    0.00024   20.9   0.0       0.01   15.6   0.0    2.3  2  Redoxin     Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.9e-11   1.7e-07       2     123 ..      51     205 ..      50     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.9e-11
                                    TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                       AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                    g  +p   l++ + ++v++ +  g  + l f +++ cp C  +l+++a++++e ++ g++ +       +++    + ++
  gi|121637583|ref|YP_977806.1|  51 GATVPTRRLQDINDQPVDVPAATG-RTHLQFRRFAACPICHLHLRSFANRHQEVADSGITEVVFFHSAADAL----RGYQ 125
                                    56778889999999**********.99*******************************98877777766644....4444 PP

                                    ...SSEEEE-TTSHHHHHTT-EETT....................................TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  82 ..lnfpllsDeegkvakaygvlkee....................................kglalratfvidkegkiry 123
                                      l+f +++D+++   +++gv k+                                     + l l+a f++d++g++++
  gi|121637583|ref|YP_977806.1| 126 slLPFAVIADPDRVQYREFGVEKSLgaithpralwaavrgsaamlhrndperagvgfgdgtTHLGLPADFLLDADGTVAA 205
                                    559*******************999***********************************999**************986 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     7e-09   4.2e-05       4     112 ..      98     210 ..      93     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7e-09
                     AhpC-TSA_2   4 rdkpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqalglkrglklklaplslqkalenllkrlkeigi 82 
                                    ++ +e+++ g++ v+ ++  ++ ++ ++     pf +++Dp++  y+++g++++l    +p++l++a++ ++ +l++   
  gi|121637583|ref|YP_977806.1|  98 NRHQEVADSGITEVVFFHSAADaLRGYQ--SLLPFAVIADPDRVQYREFGVEKSLGAITHPRALWAAVRGSAAMLHRN-D 174
                                    4567788899999999999996599999..789*****************************************9997.3 PP

                     AhpC-TSA_2  83 pgdl......ageltqrGGtflfdkqgelvyehrdr 112
                                    p+++      ++  + + + fl+d++g ++  h+ r
  gi|121637583|ref|YP_977806.1| 175 PERAgvgfgdGTTHLGLPADFLLDADGTVAAVHYGR 210
                                    333345554466667777999999999999999876 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-06      0.01       3     104 ..      51     147 ..      49     162 .. 0.79
   2 ?    3.0   0.0     0.013        77     112     136 ..     187     212 ..     176     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                    TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH CS
                        Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk 82 
                                    g+++P+ +l++   + ++v++ + +g++  + f + a cP C   ++ +++  ++ +++g++ v+   +  +  +   + 
  gi|121637583|ref|YP_977806.1|  51 GATVPTRRLQD--INDQPVDVPAATGRT-HLQFRRFAACPICHLHLRSFANRHQEVADSGITEVVFFHSAADALRGYQSL 127
                                    78899999988..899999999999***.67777777*******999*****9999*****9987766666665555443 PP

                                    TT-TSEEEE-TTSHHHHHTT-T CS
                        Redoxin  83 eglkfpvlsDgsaaftkalGlr 104
                                      l+f v++D++    +++G++
  gi|121637583|ref|YP_977806.1| 128 --LPFAVIADPDRVQYREFGVE 147
                                    ..35888888888888888855 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.013
                                    G.EEE-EEEEEEETTEEEEEEESSSC CS
                        Redoxin 112 g.lrtpryavidedgkvvylevepep 136
                                    + l++p+ +++d+dg v +++++   
  gi|121637583|ref|YP_977806.1| 187 ThLGLPADFLLDADGTVAAVHYGRHA 212
                                    34899999************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1563.28
//
Query:       gi|121637584|ref|YP_977807.1|  [L=182]
Description: lipoprotein dsbF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-14   52.4   0.0    5.9e-14   52.1   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    1.3e-10   41.2   0.0    1.7e-10   40.8   0.0    1.1  1  Redoxin        Redoxin
    7.4e-08   32.3   0.0    6.9e-06   26.0   0.1    2.2  2  Thioredoxin    Thioredoxin
      2e-06   28.2   0.0    3.4e-06   27.5   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
    4.4e-06   26.9   0.0    6.1e-06   26.5   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
    1.3e-05   25.2   0.0    5.5e-05   23.1   0.0    1.9  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0     2e-17   5.9e-14       7     122 ..      53     161 ..      44     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2e-17
                                    --EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES.SSCHHHHHHHHH-H..SS CS
                       AhpC-TSA   7 dfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv.dspeshkkfiekes.lnf 84 
                                    +f++k+ dg +++ + + gkp+vl f++  wcp C+ e+p   +++       v+ +gv   d++ ++++f++k+   +f
  gi|121637584|ref|YP_977807.1|  53 QFSAKTLDGHDFHGESLLGKPAVLWFWAP-WCPTCQGEAPVVGQVAASHP--EVTFVGVAGlDQVPAMQEFVNKYPvKTF 129
                                    6****************************.****************9988..8999***998**************679* PP

                                    EEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
                       AhpC-TSA  85 pllsDeegkvakaygvlkeekglalratfvidkegkir 122
                                    + l+D++g v  ++gv       +++a  ++d++g++ 
  gi|121637584|ref|YP_977807.1| 130 TQLADTDGSVWANFGVT------QQPAYAFVDPHGNVD 161
                                    *****************......99**********996 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   5.8e-14   1.7e-10       2     127 ..      44     160 ..      40     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 5.8e-14
                                    TTSBB-...--ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEE.EESSSHHHH CS
                        Redoxin   2 agdkaP...dftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvav.vadndafvk 77 
                                    ag+++P    f+    + dg +++ +++ gk++v+ f++  +cPtC+ e+p + ++a+      v++v+v   d+ + ++
  gi|121637584|ref|YP_977807.1|  44 AGQTVPaqlQFSA--KTLDGHDFHGESLLGKPAVLWFWAP-WCPTCQGEAPVVGQVAAS--HPEVTFVGVaGLDQVPAMQ 118
                                    6888885333444..459999999999*************.**********99999888..56699999944556666** PP

                                    HHHHHTT-TSEE.EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEE CS
                        Redoxin  78 efwgkeglkfpv.lsDgsaaftkalGlrleedaseglrtpryavidedgkv 127
                                    ef++k+ +k +  l+D ++++ +++G++           p+ya +d +g+v
  gi|121637584|ref|YP_977807.1| 119 EFVNKYPVKTFTqLADTDGSVWANFGVT---------QQPAYAFVDPHGNV 160
                                    *****66555444*************88.........67********9988 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   2.3e-09   6.9e-06      18      71 ..      71     127 ..      55     133 .. 0.69
   2 !    6.1   0.0    0.0036        11      38     101 ..     115     176 ..     113     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.3e-09
                                    SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEE...E.TTTSHHHHHHTT-S CS
                    Thioredoxin  18 kklvlveFyApwCghCkalaPeleklaeelkdkvklakv...d.vdenedlakkyeve 71 
                                     k+ ++ F+ApwC+ C+  aP++ ++a  +  +v+++ v   d v + ++ ++ky v+
  gi|121637584|ref|YP_977807.1|  71 GKPAVLWFWAPWCPTCQGEAPVVGQVAASHP-EVTFVGVaglDqVPAMQEFVNKYPVK 127
                                    488999************************9.77777661113233344445555554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHH CS
                    Thioredoxin  38 PeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaafl 101
                                    P ++++ +++   vk     +d+  ++ ++++v++ P+  ++    +v+ + g  ++++l + +
  gi|121637584|ref|YP_977807.1| 115 PAMQEFVNKYP--VKTFTQLADTDGSVWANFGVTQQPAYAFVDPHGNVDVVRGRMSQDELTRRV 176
                                    67777777887..5544445677778999*****************************998776 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.1e-09   3.4e-06       5     107 ..      71     174 ..      67     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.1e-09
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkel....ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd.ieenvelarkygv 78 
                                    gkp +++f++p+Cp C+    ++ ++    ++vt+    ++ l++   p+++++  +  + k+f++  ++   +   +gv
  gi|121637584|ref|YP_977807.1|  71 GKPAVLWFWAPWCPTCQGEAPVVGQVaashPEVTFV--GVAgLDQV--PAMQEFVNKYPV-KTFTQlADTDGSVWANFGV 145
                                    8****************9888999996655666555..55577776..777777666666.56677555666666679** PP

                  Thioredoxin_2  79 rgtPtivfldgkeivarlpGyvpaeelea 107
                                    +  P+  f d+   v++++G ++++el+ 
  gi|121637584|ref|YP_977807.1| 146 TQQPAYAFVDPHGNVDVVRGRMSQDELTR 174
                                    ************8899**********986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     2e-09   6.1e-06       1      95 []      71     160 ..      71     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2e-09
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S-- CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynv 80 
                                    gk  +L f+a wcp c+   p + ++  ++     v +v v    +  +++++++k   p   ++   +    ++ +++v
  gi|121637584|ref|YP_977807.1|  71 GKPAVLWFWAPWCPTCQGEAPVVGQVAASHP---EVTFVGVAGLDQVPAMQEFVNKY--PVKTFTQLADTDGSVWANFGV 145
                                    57889*************************6...9******877778**********..66666655566889999**** PP

                                    TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  81 kaiPtlvvldkngev 95 
                                    ++ P    +d++g+v
  gi|121637584|ref|YP_977807.1| 146 TQQPAYAFVDPHGNV 160
                                    *************98 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.8e-08   5.5e-05     131     223 ..      73     176 ..      67     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-08
                           TraF 131 ygLlfFyrgkcpyceaqapilqafadky.glevraVs.vdgrplpe.lpn..........arvdkgqaarlgvkrtPalv 197
                                     + l F ++ cp c+ +ap++ ++a ++ + + + V+ +d+ p  + + n          a  d +  a++gv++ Pa  
  gi|121637584|ref|YP_977807.1|  73 PAVLWFWAPWCPTCQGEAPVVGQVAASHpEVTFVGVAgLDQVPAMQeFVNkypvktftqlADTDGSVWANFGVTQQPAYA 152
                                    56788999*****************99977777777656777764454445665666656667778889*********** PP

                           TraF 198 lvdpksqkvvpvaaGllsldeleeri 223
                                    +vdp+ ++v  v  G +s+del++r+
  gi|121637584|ref|YP_977807.1| 153 FVDPH-GNV-DVVRGRMSQDELTRRV 176
                                    *****.666.7889**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1314.54
//
Query:       gi|121637585|ref|YP_977808.1|  [L=300]
Description: hypothetical protein BCG_1716 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          2    7.4   4.2        3.2    6.8   4.2    1.6  1  LMF1      Lipase maturation factor


Domain annotation for each model (and alignments):
>> LMF1  Lipase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.2   0.00018       3.2      67     127 ..      56     115 ..      24     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00018
                           LMF1  67 dLtaldyhyetqplPtplawyahqlpswlhkletvvtlvvelvvpfllllPirklrlfggv 127
                                    dL  +++     p+ tp++w + +++  +  +  +++l++e ++ +lll++ + +rl++ +
  gi|121637585|ref|YP_977808.1|  56 DLYHFTHLAVEHPVFTPFSWVIEHAVLPYFTAFGWGVLFAESALAVLLLTG-TAVRLAALI 115
                                    555666666678999************************************.788876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2237.71
//
Query:       gi|121637586|ref|YP_977809.1|  [L=373]
Description: acyl-CoA dehydrogenase fadE16 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-15   55.4   1.1    1.4e-14   54.5   1.1    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.9e-12   45.6   0.0    1.4e-11   44.4   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      6e-12   46.0   5.0      6e-12   46.0   5.0    2.0  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    9.9e-10   39.1   2.0    1.8e-09   38.3   0.4    2.1  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
       0.14   11.8   0.1       0.23   11.1   0.1    1.2  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   1.1     4e-18   1.4e-14       1     135 [.     215     353 ..     215     367 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 4e-18
                                    TBHHHHHTTT.T--S-----..-SHHHHHHHHHHHHHHHTS..B-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                  Acyl-CoA_dh_1   1 gkGfrvamet.lnheRlavaaaalglarraleealeyarrr..kafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                    g Gf ++m+t l +  l++aa +lgla +a   a++++ +   +  g+ l++ + +r ++a+m + l+a +++++ aa+ 
  gi|121637586|ref|YP_977809.1| 215 GGGFGIMMQTvLPWFNLGNAAVSLGLATAATGAAVKHVGTArlEHLGGSLAELPTIRAQIARMGTTLAAQKAYLEVAANS 294
                                    579*******9***************************988556778*******************************99 PP

                                    -------.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS CS
                  Acyl-CoA_dh_1  78 ldagkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige 135
                                    ++  +++    +  +K+ + ++a +++++am ++Gga+++++ p+er++rdar+ ++++
  gi|121637586|ref|YP_977809.1| 295 VSSPDDTtLTHVLGVKASVNDAALTITESAMRVCGGAAFSKHLPIERAFRDARAGSVMA 353
                                    88888884556666***************************************988775 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0     4e-15   1.4e-11       2      92 ..     111     199 ..     110     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4e-15
                                    EE---SS-SS-GGG---EE.EEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE----- CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvktta.aerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrriee 80 
                                    +a++Ep++ s+  +  +ta a++dg  ++++  K w+t+a+ a++++v + +++ + a+++ l +vp+d+pg++v  + +
  gi|121637586|ref|YP_977809.1| 111 LAFSEPGSRSHFWAPVSTAsADGDG--IAVRADKSWVTSAGFADVYVVSVGSADGA-AGDVDLYAVPADTPGLRVAGTFT 187
                                    799*****99988888745555555..************************65566.9*****************9999* PP

                                    BSS-TTS-EEEE CS
                  Acyl-CoA_dh_M  81 klGlrglptgel 92 
                                     +Glrg +++ +
  gi|121637586|ref|YP_977809.1| 188 GMGLRGNASAPM 199
                                    ******998876 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2   4.3e+03      95     110 ..      60      75 ..      58      81 .. 0.85
   2 !   46.0   5.0   1.7e-15     6e-12       2     127 ..     232     350 ..     231     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHCGGGGG CS
                  Acyl-CoA_dh_2  95 iaavdalfeaaGgsal 110
                                    +++v +l +a+G++a+
  gi|121637586|ref|YP_977809.1|  60 TEVVAQLSAACGSTAM 75 
                                    5789999999999986 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 1.7e-15
                                    HHHHHHHHHHHHHHHHHHHHHH.HHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelar.ervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    g aav lG+A aa  ++v++++ +r +   g +la+ p++ +++a++ + l A +a le aa++    +   +     + 
  gi|121637586|ref|YP_977809.1| 232 GNAAVSLGLATAATGAAVKHVGtARLE-HLGGSLAELPTIRAQIARMGTTLAAQKAYLEVAANS----VSSPDDT---TL 303
                                    679*******************66666.99**********************************....6666665...44 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                    +     +a + + a  +++++++++Gg a  k  p++R++RDa+a++
  gi|121637586|ref|YP_977809.1| 304 THVLGVKASVNDAALTITESAMRVCGGAAFSKHLPIERAFRDARAGS 350
                                    4455567888999999****************************986 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.4     5e-13   1.8e-09      18      90 ..      13      85 ..       5      91 .. 0.88
   2 ?   -1.3   0.1      0.93   3.3e+03      55      96 ..     216     252 ..     202     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 5e-13
                                   HTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTH CS
                  Acyl-CoA_dh_N 18 elaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslva 90
                                    +a+ha+++d++ +fp e++++l + Gllg+ +p e gG+g +++e   v+ +l++a+ ++a+++ +h++ ++
  gi|121637586|ref|YP_977809.1| 13 VAAEHAERVDTDCAFPAEAVDALRKTGLLGLVLPREIGGMGSGPVEFTEVVAQLSAACGSTAMIYLMHMAAAV 85
                                   3467899998888**************************************************9999987664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.93
                                    TS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHH CS
                  Acyl-CoA_dh_N  55 gGagldyleaaivaeelaradaglalllgvhsslvapailrf 96 
                                    gG g  ++++++    l+ a ++l+l+ ++     + a+ + 
  gi|121637586|ref|YP_977809.1| 216 GGFGI-MMQTVLPWFNLGNAAVSLGLATAA----TGAAVKHV 252
                                    33342.777777777787766665553322....22244455 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.3e-05      0.23     175     228 ..     132     182 ..     123     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                                    -SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEE CS
                         HpaB_N 175 tddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlkl 228
                                    + dGi Vr  k   T a +ad  +v   +a  +++d d     avp+d+pGl++
  gi|121637586|ref|YP_977809.1| 132 DGDGIAVRADKSWVTSAGFADVYVVSVGSADGAAGDVD---LYAVPADTPGLRV 182
                                    669************************96665555555...689*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3014.27
//
Query:       gi|121637587|ref|YP_977810.1|  [L=274]
Description: hypothetical protein BCG_1718 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-30  105.1   0.0    5.4e-30  104.8   0.0    1.1  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0028   17.6   0.1      0.021   14.8   0.1    2.3  1  NMT1            NMT1/THI5 like
  ------ inclusion threshold ------
      0.052   13.0   0.0       0.23   10.9   0.0    1.9  1  SBP_bac_3       Bacterial extracellular solute-binding protei
       0.14   11.4   0.0       0.22   10.9   0.0    1.3  1  ERG2_Sigma1R    ERG2 and Sigma1 receptor like protein


Domain annotation for each model (and alignments):
>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   1.2e-33   5.4e-30      28     241 ..      35     256 ..      15     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.2e-33
                                    SSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-..EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG CS
                 Phosphonate-bd  28 GvevelvvatdyaavvealragqvDiaflgplayvqardqag..veplatrvrsdGsasyrsviivradsdiqsledLkg 105
                                    + ++++v +++ya +v +l ag++Dia+ ++layv+ + q g  ++pla+r     +  y +v++++a+sd++  +d++g
  gi|121637587|ref|YP_977810.1|  35 DTQMDFVLYSNYARLVDSLIAGHIDIAWNTNLAYVRTVLQTGgrCTPLAQRDT---DVDYTTVFVAHAGSDLHGAKDIAG 111
                                    678999******************************99887522699999998...99********************** PP

                                    -EEEE--TT-TTTTHHHHHHTCCCCT--HH........HHSSEE.EE-.-HHHHHHHHHTTSSSEEEEEHHHHHHHHHH- CS
                 Phosphonate-bd 106 ktiafvspsStsGylvpaalLvkeagldpe........ddfsev.fsg.shdaavlavlsgdadaaavsadaledlvaeg 175
                                    k++a++s++S+ + ++p+++L ++ag+  +        +d++++  +g s   av+avl+g+ad+aa+ ++++  + a+ 
  gi|121637587|ref|YP_977810.1| 112 KRLALGSADSAHAAILPLYYL-RRAGIAESdlqvirfdTDIGKHgDTGrSELDAVDAVLAGEADVAAIGSSTWAAMGAA- 189
                                    *********************.8****77745555554689998877669999***********************987. PP

                                    HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHH---.SHHHHHHHHHTTEEEEEE--GG CS
                 Phosphonate-bd 176 pedkdelrviassppipndpvvvrkelseelkekiqdallslae.teegkkllealgiegfvpadds 241
                                    +   ++l+ +++++ +   ++ +  +l++e  +   d ll+++  ++e++k+le  g  ++vp   +
  gi|121637587|ref|YP_977810.1| 190 ELMGESLTEVWRTDGYCHCMFTALDTLPAERYQPWLDRLLAMSWdDSEHRKILELEGLRRWVPPHLD 256
                                    6899***************************************967999999999999999997665 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   4.6e-06     0.021      74     131 ..      92     150 ..      24     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-06
                                    -EEEEEECCC--SSGGGGTTSEEEE-S-TTHHHHH..HHHHHHTT--GGG-EEEE-.TT- CS
                           NMT1  74 lsglivlkdsgikspkDLkGkrigyvgspfekall..kallakdggdpsdvtlvnvggts 131
                                    ++ ++++++s+++  kD++Gkr+++  ++ + a +     l+ +g+ +sd+++++ +  +
  gi|121637587|ref|YP_977810.1|  92 TTVFVAHAGSDLHGAKDIAGKRLALGSADSAHAAIlpLYYLRRAGIAESDLQVIRFDT-D 150
                                    678999999***************88877766655125679*************9843.3 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.1e-05      0.23      40     164 ..      38     184 ..      31     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                                    EEEEE-.SGGGHHHHHHTTSSSEEESSEB-.......-HHHHTTEEEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTS CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3  40 vefvpv.swdelipalksgkvDiaiaaiti.......tpeReekvdFsqpyfsagqvllvrkkdaskissiksladLkgk 111
                                    ++fv + +++ l+++l +g++Dia+++          t  R++ ++  +   + ++v+++++++     ++ + +d++gk
  gi|121637587|ref|YP_977810.1|  38 MDFVLYsNYARLVDSLIAGHIDIAWNTNLAyvrtvlqTGGRCTPLAQRDTDVDYTTVFVAHAGS-----DLHGAKDIAGK 112
                                    67888779999999999*****999765446777788777777777777777777888888553.....577777***** PP

                                    EEEEETT.SHHHHHHHHHHHC.......TSEE...........EEESSHHHHHHHHHTTSSSEEEEEHHHHH CS
                                    xxxxxxx.xxxxxxxxxxxxx.......xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 112 kvgvqag.staeellkeelkk.......gaei...........vefdtleealqaLkngrvdavvadspvla 164
                                    +++   + s+++++l  ++ +       + ++            +  +  +a+ a+ +g++d+++  s++ a
  gi|121637587|ref|YP_977810.1| 113 RLALGSAdSAHAAILPLYYLRragiaesDLQVirfdtdigkhgDTGRSELDAVDAVLAGEADVAAIGSSTWA 184
                                    ***766626666665554444455555533335555555654434566667777888888888877777665 PP

>> ERG2_Sigma1R  ERG2 and Sigma1 receptor like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.22      95     129 ..     144     178 ..     135     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                   ERG2_Sigma1R  95 lilFGtavgteGhtGrhladdyftiLkGeqlaakp 129
                                    +i F t +g +G tGr   d  + +L Ge   a+ 
  gi|121637587|ref|YP_977810.1| 144 VIRFDTDIGKHGDTGRSELDAVDAVLAGEADVAAI 178
                                    788*************************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2136.29
//
Query:       gi|121637588|ref|YP_977811.1|  [L=330]
Description: molybdopterin biosynthesis protein moeX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-20   72.0   0.0    1.2e-19   71.3   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    5.2e-07   30.0   0.0      8e-07   29.4   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
     0.0074   16.4   0.0      0.012   15.7   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0     2e-23   1.2e-19       7     144 ..      87     217 ..      85     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2e-23
                                    ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                    Cnl C +C+++++  +  ++r+l  e+i ++v e+ a++gv+e++l+ggep+l pd+  +++ ++k     + +tv tng
  gi|121637588|ref|YP_977811.1|  87 CNLCCDYCCVSSS--PSTPHRELGAERIGRIVGEA-ARWGVRELFLTGGEPFLLPDIDTIIATCVKQ----LPTTVLTNG 159
                                    ***********97..********************.8**********************99999995....********* PP

                                    SCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                    xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  87 tlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                    ++     + + + l++g   ++++l++a++e  ++ +++ +t+ + +++++++ ++g+++
  gi|121637588|ref|YP_977811.1| 160 MVFKgrGRRALESLPRG-LALQISLDSATPE-LHDAHRGAGTWVKAVAGIRLALSLGFRV 217
                                    ****9977888888878.*************.**************************96 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.3e-10     8e-07       4      97 ..      75     163 ..      73     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.3e-10
                        Fer4_12   4 eGvrlslf.vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                    +Gvrl l+    Cnl C++C   +    + ++e   e + +i+ +++   +++l l+GGEP+l    +++  ++  + ++
  gi|121637588|ref|YP_977811.1|  75 PGVRLWLYtNFHCNLCCDYCC-VSSSPSTPHRELGAERIGRIVGEAARWGVRELFLTGGEPFL---LPDIDTIIATCVKQ 150
                                    79******5459********9.677777888999999*********9****************...99************ PP

                        Fer4_12  83 kpekdiwlytgytle 97 
                                     p  + +l++g  ++
  gi|121637588|ref|YP_977811.1| 151 LP--TTVLTNGMVFK 163
                                    *9..78999999986 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-06     0.012       7      88 ..      86     158 ..      81     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                        Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                     Cnl C  C  +++ +    +    e + +i+   ++ +   ++l ltGGeP++    +++++++   +++    + ++ 
  gi|121637588|ref|YP_977811.1|  86 HCNLCCDYCCVSSSPSTPHRELG-AERIGRIV--GEAARWGVRELFLTGGEPFLL---PDIDTIIATCVKQL---PTTVL 156
                                    59999999988885555555555.55566999..6777777799*********55...67777776666666...44555 PP

                        Fer4_14  87 tn 88 
                                    tn
  gi|121637588|ref|YP_977811.1| 157 TN 158
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2425.35
//
Query:       gi|121637589|ref|YP_977812.1|  [L=305]
Description: coiled-coil structural protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-06   27.3   7.2    3.1e-06   27.3   7.2    3.3  3  DivIVA           DivIVA protein
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.012   15.4   0.2    4.2  3  DivIC            Septum formation initiator
      0.051   13.9   2.8        1.9    8.9   0.0    3.5  2  TSC22            TSC-22/dip/bun family
      0.051   13.9   1.0      0.051   13.9   1.0    2.8  2  zf-C4H2          Zinc finger-containing protein
       0.14   12.7  30.8        1.3    9.7   0.3    4.5  3  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
       0.48   10.9  10.0       0.99    9.9   0.9    3.0  3  IZUMO            Izumo sperm-egg fusion, Ig domain-associated
        2.1    8.7   5.0        6.8    7.0   0.1    3.4  2  DUF948           Bacterial protein of unknown function (DUF94
        2.1    8.7  10.7        1.6    9.0   4.0    2.9  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
        7.4    6.6  20.3         15    5.7   7.2    4.0  3  SOAR             STIM1 Orai1-activating region


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   7.2   1.6e-09   3.1e-06      10     117 ..      34     148 ..      31     155 .. 0.68
   2 ?    3.7   5.2     0.031        61      76     117 ..     154     195 ..     148     209 .. 0.67
   3 ?    1.6   6.4      0.14   2.8e+02      60     124 ..     204     268 ..     181     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.6e-09
                                    ---EEEEEEEHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  10 eFkkklrGYdedeVdeFLdqvak.......dyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkan 82 
                                    +F+++  GYd+  V+ ++++++        ++e+l  e ++lk++ ++l+++  + + + + + k+l +a +   +++++
  gi|121637589|ref|YP_977812.1|  34 RFQRTRSGYDPVAVNHYIAELVLrqqaqhcEIETLKAEIASLKDENAALKDTSPSAQAVTDRMAKMLRLAVDEVFQMQSE 113
                                    69999**************9987111112234455555555555555555555556666777888888888888888888 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  83 akkeaeliikeAekkaekiveeaeeeakkiaeeie 117
                                    a++ea +++++A+++ae++  + +e +++++++  
  gi|121637589|ref|YP_977812.1| 114 ARAEAATLVSAARDEAEAVRTQKREMLADMNARQR 148
                                    88888888888888888887766666666666555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  76 aeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeie 117
                                      +v + a++eae+++++A+++ e++    +++ +k+++e++
  gi|121637589|ref|YP_977812.1| 154 HADVMRRAREEAEQLVAQATAEVERMRVIDARRREKAEQELD 195
                                    456777888899999988888888886644445555555554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  60 eleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqar 124
                                    +++ ++ + l ++q+  e+   +ak ea+  ++ A+++ e+ ++ea++ +++i+++   + +q +
  gi|121637589|ref|YP_977812.1| 204 DAQFQIDDQLQATQQECEKRLGEAKIEADRRLHVADEQIEHGLSEARRTLEEISQRRVGILEQLA 268
                                    44556666777778888888888888888888888888888888999999988877666555555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   5.8e-06     0.012      16      45 ..      55      84 ..      49     100 .. 0.89
   2 ?   -7.5  10.4         9   1.8e+04      23      23 ..     166     166 ..     122     231 .. 0.65
   3 ?   -2.1   0.1       1.7   3.4e+03      24      40 ..     254     260 ..     241     282 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.8e-06
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC 16 llaykqlkqeiaalqaelaklkaeneeLea 45
                                   +l++++++ ei++l+ae+a+lk+en++L++
  gi|121637589|ref|YP_977812.1| 55 VLRQQAQHCEIETLKAEIASLKDENAALKD 84
                                   6789999*********************97 PP

  == domain 2  score: -7.5 bits;  conditional E-value: 9
                                    H CS
                          DivIC  23 k 23 
                                    +
  gi|121637589|ref|YP_977812.1| 166 E 166
                                    1 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHHHH CS
                          DivIC  24 qeiaalqaelaklkaen 40 
                                    +ei           +++
  gi|121637589|ref|YP_977812.1| 254 EEIS----------QRR 260
                                    3333..........333 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00094       1.9      15      34 ..      64      83 ..      55      93 .. 0.68
   2 ?    2.7   0.8     0.077   1.5e+02       8      34 ..     121     147 ..     119     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00094
                          TSC22 15 eVevLkekIkeLeernsele 34
                                   e+e+Lk +I+ L ++n++l+
  gi|121637589|ref|YP_977812.1| 64 EIETLKAEIASLKDENAALK 83
                                   56666666666666666554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.077
                          TSC22   8 LmfAVrEeVevLkekIkeLeernsele 34 
                                    L+ A r+e e  +++ +e+++++++ +
  gi|121637589|ref|YP_977812.1| 121 LVSAARDEAEAVRTQKREMLADMNARQ 147
                                    677999999999999888877776544 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.3  14.5         9   1.8e+04      22     106 ..     128     208 ..      57     237 .. 0.58
   2 ?   13.9   1.0   2.6e-05     0.051      27      90 ..     240     303 ..     218     305 .] 0.89

  Alignments for each domain:
  == domain 1  score: -7.3 bits;  conditional E-value: 9
                        zf-C4H2  22 eveal.ekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeks.lekakklyeeykklkeevnel 99 
                                    e ea+ ++++++l ++++    Le+E   H++ +r  ++   + E+ + +a  e e++ +  a++  +  ++l  e+ +l
  gi|121637589|ref|YP_977812.1| 128 EAEAVrTQKREMLADMNARQRALESE---HADVMRRARE---EAEQLVAQATAEVERMrVIDARRREKAEQELDAEIIRL 201
                                    33332023333444444444444443...4555554443...34444444444443331234444455555566666666 PP

                        zf-C4H2 100 rselgle 106
                                    r++   +
  gi|121637589|ref|YP_977812.1| 202 RTDAQFQ 208
                                    6654444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.6e-05
                        zf-C4H2  27 ekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeyk 90 
                                    e+ e+ l+e +++le+++q +   +e+L  Iha ++++   +++a++++++ l++++ +++e++
  gi|121637589|ref|YP_977812.1| 240 EQIEHGLSEARRTLEEISQRRVGILEQLARIHAQLENIPALLESARHSETEPLQSINGAVAELR 303
                                    567889*************************************************999988876 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00066       1.3      46      89 ..      57     100 ..      47     106 .. 0.85
   2 ?    1.6  11.1      0.21   4.2e+02       9      72 ..     116     180 ..     113     193 .. 0.68
   3 ?    7.5   6.2    0.0031       6.2       8      84 ..     195     273 ..     193     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00066
                 HIP1_clath_bdg  46 kleeqkeelekLkreleakraelarlkssLesseqsgeqlssql 89 
                                    + + q+ e+e+Lk+e+++ ++e a lk +  s +   +++++ l
  gi|121637589|ref|YP_977812.1|  57 RQQAQHCEIETLKAEIASLKDENAALKDTSPSAQAVTDRMAKML 100
                                    568999**********************9998888888777655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                 HIP1_clath_bdg   9 Aevtkqlsvarqaqeeverekkeleeelerlkeeaerkle....eqkeelekLkreleakraelarlk 72 
                                    Ae ++++s+ar + e v ++k+e+  ++++ ++  e++ +      +ee e+L    ++  ae++r++
  gi|121637589|ref|YP_977812.1| 116 AEAATLVSAARDEAEAVRTQKREMLADMNARQRALESEHAdvmrRAREEAEQLV---AQATAEVERMR 180
                                    999*********************999998776655554422214455555554...44445555544 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0031
                 HIP1_clath_bdg   8 nAevtkqlsvar.qaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlk.ssLesseqsgeq 84 
                                    +Ae++++ + a+ q  ++++++++e e++l ++k ea+r+l+   e++e+  +e  ++ +e+++ + + Le+ ++  +q
  gi|121637589|ref|YP_977812.1| 195 DAEIIRLRTDAQfQIDDQLQATQQECEKRLGEAKIEADRRLHVADEQIEHGLSEARRTLEEISQRRvGILEQLARIHAQ 273
                                    799******99955677899*********************99999988766666666666655432345555555555 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.062   1.2e+02      55     110 ..      62     117 ..      48     123 .. 0.85
   2 ?    9.9   0.9   0.00049      0.99      25      77 ..     148     203 ..     129     206 .. 0.83
   3 ?    3.2   0.3     0.059   1.2e+02      24      91 ..     206     269 ..     200     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.062
                                    EEEHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          IZUMO  55 vvdeetlekvasslkkelkrltdsdlkgelllkeLlwllqkqkkklkealkefqke 110
                                      + etl+    slk+e   l+d++   + + +++ ++l+ +++++ ++ +e + e
  gi|121637589|ref|YP_977812.1|  62 HCEIETLKAEIASLKDENAALKDTSPSAQAVTDRMAKMLRLAVDEVFQMQSEARAE 117
                                    567789999999****************************9999988887777666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00049
                                    S...GGHHHHHHHHHHHHHTTT---SGGGGGGSEEEHHHHHHHHHHHHHHHHHHHH CS
                          IZUMO  25 l...ehreklleraealledlsekelaenkflgvvdeetlekvasslkkelkrltd 77 
                                        +++ ++++ra+++ e+l  +  ae + ++v+d ++ ek+ ++l  e+ rl++
  gi|121637589|ref|YP_977812.1| 148 RaleSEHADVMRRAREEAEQLVAQATAEVERMRVIDARRREKAEQELDAEIIRLRT 203
                                    23456899***************************************999998875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.059
                                    HSGGHHHHHHHHHHHHHTTT---SGGGGGGSEEEHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHH CS
                          IZUMO  24 elehreklleraealledlsekelaenkflgvvdeetlekvasslkkelkrltdsdlkgelllkeLlw 91 
                                    +++ +++l++ +++  ++l e +++ +  l v d e++e+  s+ +++l+++++  +    +l++L  
  gi|121637589|ref|YP_977812.1| 206 QFQIDDQLQATQQECEKRLGEAKIEADRRLHVAD-EQIEHGLSEARRTLEEISQRRV---GILEQLAR 269
                                    5667889999999999999999999999997665.5799999999999999998765...44555444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.0      0.34   6.7e+02      31      58 ..     118     145 ..      64     182 .. 0.61
   2 ?    7.0   0.1    0.0034       6.8      30      77 ..     230     277 ..     211     303 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                         DUF948  31 aaatieelekqvdpilkevedllakvne 58 
                                    aa+ +   +++++++ ++ +++la +n+
  gi|121637589|ref|YP_977812.1| 118 AATLVSAARDEAEAVRTQKREMLADMNA 145
                                    3333333334444444444444444444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0034
                         DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                    ea +++++  +q++  l e++++l+++ +   ++ e+l+++ +  e++
  gi|121637589|ref|YP_977812.1| 230 EADRRLHVADEQIEHGLSEARRTLEEISQRRVGILEQLARIHAQLENI 277
                                    566666666677777777777777777765555555555555555554 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.0   0.00082       1.6       8     127 ..      44     177 ..      42     179 .. 0.84
   2 ?    2.4   0.5     0.092   1.8e+02      56     115 ..     186     245 ..     184     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00082
                       Gp-FAR-1   8 PsevvealknltdeekaqlkevvknykgyknedellaalKkkspaLyekaeklqaklkekvd...kLspeakeFvkkli. 83 
                                    P  v  ++ +l   ++aq  e+ +  ++  + ++  aalK+ sp+  +   ++ ++l+  vd   +++ ea++ +  l+ 
  gi|121637589|ref|YP_977812.1|  44 PVAVNHYIAELVLRQQAQHCEIETLKAEIASLKDENAALKDTSPSAQAVTDRMAKMLRLAVDevfQMQSEARAEAATLVs 123
                                    556777788888888888888888889999999999********999988888888887776222578999988888889 PP

                       Gp-FAR-1  84 ..........akgrkleaqvlagekpdlselkkvaktifnkykslseeakaele 127
                                               + r++ a++ a ++   se   v++   +++++l+++a ae+e
  gi|121637589|ref|YP_977812.1| 124 aardeaeavrTQKREMLADMNARQRALESEHADVMRRAREEAEQLVAQATAEVE 177
                                    999999999999999999999999999999999999999999999999998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.092
                       Gp-FAR-1  56 kaeklqaklkekvdkLspeakeFvkkliakgrkleaqvlagekpdlselkkvaktifnky 115
                                    + ek +++l++++  L+ +a+  +++ ++  ++  +++l ++k++ +++  va +++++ 
  gi|121637589|ref|YP_977812.1| 186 RREKAEQELDAEIIRLRTDAQFQIDDQLQATQQECEKRLGEAKIEADRRLHVADEQIEHG 245
                                    568899999999999999999777766665555556668889999999999999998874 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.2    0.0074        15       4      93 ..      93     182 ..      90     184 .. 0.81
   2 ?    3.3   2.0      0.04        80      33      58 ..     158     183 ..     145     206 .. 0.57
   3 ?    4.6   2.7     0.015        30      10      58 ..     212     271 ..     204     296 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0074
                           SOAR   4 peeLqqlLqlTyelElkylnkkkqeaekqlqeAkeeveklkkkrssllgslrlahssslddvdkkileakqaleevtkel 83 
                                    ++++ ++L+l     ++  ++ ++ea++ +++A++e+e ++ +++ +l+ +   +    ++  + + +a+++ e++ +++
  gi|121637589|ref|YP_977812.1|  93 TDRMAKMLRLAVDEVFQMQSEARAEAATLVSAARDEAEAVRTQKREMLADMNARQRALESEHADVMRRAREEAEQLVAQA 172
                                    67888999999999999999******************************998765555555556778888888888877 PP

                           SOAR  84 kerqeRWqqi 93 
                                    + + eR + i
  gi|121637589|ref|YP_977812.1| 173 TAEVERMRVI 182
                                    7777777666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.04
                           SOAR  33 lqeAkeeveklkkkrssllgslrlah 58 
                                    +++A+ee+e+l  + +  +  +r++ 
  gi|121637589|ref|YP_977812.1| 158 MRRAREEAEQLVAQATAEVERMRVID 183
                                    44555555555555555555555554 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.015
                           SOAR  10 lLqlTyelElkylnkkkqeaekqlqeAke...........eveklkkkrssllgslrlah 58 
                                     Lq T +   k+l + k ea ++l++A e            +e + ++r  +l +l  +h
  gi|121637589|ref|YP_977812.1| 212 QLQATQQECEKRLGEAKIEADRRLHVADEqiehglsearrTLEEISQRRVGILEQLARIH 271
                                    577777666677777778888888887773333333333355555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2172  (0.121145); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 1975.80
//
Query:       gi|121637590|ref|YP_977813.1|  [L=999]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-28   98.6   0.0    4.8e-28   97.9   0.0    1.3  1  AMP-binding    AMP-binding enzyme
    1.2e-07   32.5   5.0    1.2e-07   32.5   5.0    3.4  2  Abhydrolase_6  Alpha/beta hydrolase family
    2.4e-07   30.7   0.0    5.3e-07   29.5   0.0    1.6  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00093   19.1   0.0     0.0016   18.4   0.0    1.4  1  Palm_thioest   Palmitoyl protein thioesterase
     0.0012   18.4   0.0     0.0022   17.5   0.0    1.4  1  PHB_depo_C     PHB de-polymerase C-terminus
  ------ inclusion threshold ------
      0.099   11.1   0.1       0.16   10.3   0.1    1.3  1  DUF3141        Protein of unknown function (DUF3141)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   1.6e-31   4.8e-28       2     414 ..     455     861 ..     454     870 .. 0.74

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.6e-31
                                    HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                    AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                    +eqa   p+  +l +  +g+  TY+ +++r+n++ +gL + Gv++gdrV++l++++p  +va+ a+ ++Gav+v+++p++
  gi|121637590|ref|YP_977813.1| 455 DEQAHDAPKGEFLLF--DGRVHTYEAVNRRINNVVRGLIAVGVRQGDRVGVLMETRPSALVAIAALSRLGAVAVVMRPDT 532
                                    678889998888999..99**********************************************************987 PP

                                    -HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS............. CS
                    AMP-binding  82 taeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae............. 148
                                        l+  ++  +++ ++  +d ++l+++++       + +v+vl  +e+++  +l++++ ++ +               
  gi|121637590|ref|YP_977813.1| 533 D---LSASVRLGRVTEIL--TDPTNLDAARQL------PGQVLVLGGGESRDL-DLPADALEQGQVIdmekidpdavelp 600
                                    5...67788889999999..888774443333......455666665555544.55555544433213556778889988 PP

                                    ...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHH CS
                    AMP-binding 149 ...kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllal 225
                                       +   +++  + dla+i ++S   G   + +++   + ++v+++    +  l+++d+v++  pl+h  +l ++l +a+
  gi|121637590|ref|YP_977813.1| 601 awyR---PNPGLARDLAFIAFSS-ADGDLVAKQITN--YRWAVSAFGTASTAALGRRDTVYCLTPLHHESALLVSLGGAV 674
                                    6533...457899********88.678765555555..5555555433345667789**************978888888 PP

                                    HTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHH CS
                    AMP-binding 226 lsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffr 304
                                    + G ++ l+++    +p+++++ +++++vtv+ ++ ++l+ +++++a+         ++ +rl  + g+ ++  l++++ 
  gi|121637590|ref|YP_977813.1| 675 VGGTRIALSRGL---RPDRFVAEVRQYGVTVVSYTWAMLRDVVDDPAFV----L-HGNHpVRL--FIGSGMPTGLWERVV 744
                                    888888886633...467899***********************87665....1.22333666..89************* PP

                                    HHHTC.EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T.TEEEEEE..-TTTSCBEETTSEEEEEEEETTS-SEBTT CS
                    AMP-binding 305 alfge.evlegYGlTEttgvvtvlpleedkkklgsvGkplp.gvevkiv..DeetgepvpdgeeGellvrgpgvmkgYlk 380
                                    + f + +v+e +  T   +v++++      +k+gs G+plp   +v++   D e   ++ ++  G + v g +     l 
  gi|121637590|ref|YP_977813.1| 745 EAFAPaHVVEFFATTDGQAVLANVA----GAKIGSKGRPLPgAGRVELGayDAE-HDLILENDRGFVQVAGVNQVGVLLA 819
                                    ****999*************98333....3469*******95334554443777.5555577888888888887777776 PP

                                    -......HHHHHHHEEE...T.CCEEEEEEEEEEETTSEEEEEE CS
                    AMP-binding 381 k......peataeafds...e.grwlrTGDlgrldedGyleivg 414
                                    +      p  ta++      + + w  T +l ++d+dG +++ g
  gi|121637590|ref|YP_977813.1| 820 QsrgpidP--TASVKRGvfaPaDTWISTDYLFWRDDDGDYWLAG 861
                                    64553333..3333221333545588888888888888888776 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   5.0   4.1e-11   1.2e-07       1     210 [.      71     341 ..      71     358 .. 0.58
   2 ?  -12.0  15.3         6   1.8e+04      68      96 ..     514     577 ..     344     959 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4.1e-11
                                    EEEE--GC.....G...C.HHHHHHHHCCTCEEEEE--TTSTS-GGCS....--HHH.CHHHHHHHCCTT...TTSEEEE CS
                  Abhydrolase_6   1 vlllHGagssassW...l.vapLaallaagvhvlapDlpGhGrsdppp....ldled.ladlaalldelaa.gggpvvlv 70 
                                    vl++H   +sa++W   +  + +  l a+g  ++++D+ G   +d        +l+d +++l++++d +++  g++v+ v
  gi|121637590|ref|YP_977813.1|  71 VLMVHPMMMSADMWdvtReDGAVGILHASGLDPWVIDF-GS--PDEVEggmrRNLADhIVALSEAVDTVKDaTGHDVHFV 147
                                    7999999999****654244466777778888899***.88..6555512225554443333444444444679****** PP

                                    EETCHHHHHHHHHHCC.....EE.EEES-.........----TTTS----TTHHHHHHTT-C.CCCHCCH.......... CS
                  Abhydrolase_6  71 GHSlGGalalaaapla...lvvg.vlldppp.......talpagllaaalelllallallrl.lawlsre.......... 128
                                    G+S+GG+   +aa++    ++++ v+  +p+       ++ pa ++aa++ +++    ++ + + w++r+          
  gi|121637590|ref|YP_977813.1| 148 GYSQGGMFCYQAAAYRrskDIASvVAFGSPVdtlaalpMGIPANMGAAVADFMADHVFNRLDiPSWMARMgfqmmdplkt 227
                                    *******9999888888876666777777666664444677777788888888877776666689997544554444444 PP

                                    .....S-HSCCCCHHH....C.......CCCHCHCCCGHH...........HHCCHHC..HTTCCHHTT-TTGCEEE.CT CS
                  Abhydrolase_6 129 .....plprlfladed....a.......daawrarlarla...........allaglg..llpaaawadlpvpllvl.gg 178
                                         ++ r++++ e+    +        + w a+  ++            + ++g +        ++d+++p+l + g+
  gi|121637590|ref|YP_977813.1| 228 akarvDFVRQLHDREAllprEqqrrfleSEGWIAWSGPAIsellkqfiahnRMMTGGFaiSGQMVTLTDITCPILAFvGE 307
                                    44444333344443332221011222223333333333335444433332211111112222355888888888533388 PP

                                    T-C....HHHHCHHCCCHSTTEEETCE...SSS-HH CS
                  Abhydrolase_6 179 eDp....lvprllerllaqagarlpvvlpgaGHlph 210
                                     D+    +  r ++r++  +++++ + l +aGH+ +
  gi|121637590|ref|YP_977813.1| 308 VDDigqpASVRGIRRAAP-NSEVY-ECLIRAGHFGL 341
                                    888433333344666666.88888.89999999765 PP

  == domain 2  score: -12.0 bits;  conditional E-value: 6
                                    EEEEET.CHHHHHHHHHHCC.............EEEEES-........................... CS
                  Abhydrolase_6  68 vlvGHS.lGGalalaaapla...........lvvgvlldp..........................p 96 
                                     + + S lG++ + +    +           +v  +l dp                          p
  gi|121637590|ref|YP_977813.1| 514 AIAALSrLGAVAVVM---RPdtdlsasvrlgRVTEILTDPtnldaarqlpgqvlvlgggesrdldlP 577
                                    444444444443333...2223333333332222255555333333333222222222211111110 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.8e-10   5.3e-07      55     252 ..     125     340 ..      56     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.8e-10
                                    SHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHH.GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHH CS
                  Abhydrolase_1  55 gtasvaddldrildalgddkltlvGhSmGGmialayaaey.perVkalvllgaidpaaslieaqrqqaksfpdffdgyaa 133
                                    +++++ + +d ++da+g d ++ vG+S+GGm++ ++aa    + ++++v+ g+   + ++  a ++ ++   +++  ++ 
  gi|121637590|ref|YP_977813.1| 125 HIVALSEAVDTVKDATGHD-VHFVGYSQGGMFCYQAAAYRrSKDIASVVAFGS---PVDTLAALPMGIPANMGAAVADFM 200
                                    7788999**********87.89****************999999*********...666666666666666666666666 PP

                                    HHHHHHHHHHHHCCSCHHHHHHHHHHHHHH................HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCH CS
                  Abhydrolase_1 134 dcarnpagplladelaaleqrhrlvdalkf................pdkskrfpssgsdnasslatgalksieqwpttds 197
                                    ++ + +  ++ + ++++ +q  ++++  k                 +++ +rf +s+ ++a s+ + + + ++ ++ + +
  gi|121637590|ref|YP_977813.1| 201 ADHVFNRLDIPSWMARMGFQMMDPLKTAKArvdfvrqlhdreallpREQQRRFLESEGWIAWSGPAISELLKQFIAHNRM 280
                                    6666667777777777777777766655558888888888******9********9999999999999999999999999 PP

                                    HHHHHHHHC....THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSSH CS
                  Abhydrolase_1 198 aklllrlre....lknvlaptlvisgtsDplvppkaledlaqllpk.krlvvisdagHla 252
                                    +     + +    l+++++p+l + g+ D +  p + + ++++ p+ + ++ +  agH+ 
  gi|121637590|ref|YP_977813.1| 281 MTGGFAISGqmvtLTDITCPILAFVGEVDDIGQPASVRGIRRAAPNsEVYECLIRAGHFG 340
                                    999999999*************************99999999988855555566677765 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.3e-07    0.0016      51     109 ..     129     184 ..      70     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.3e-07
                   Palm_thioest  51 lndqveavckklelangfhaiGfSQGglflRaliercddkknvrnlislggpqaGvfgl 109
                                    l + v+ v ++  + + +h++G+SQGg+f+   +    +k+ + +++ +g+p    ++l
  gi|121637590|ref|YP_977813.1| 129 LSEAVDTVKDA--TGHDVHFVGYSQGGMFCYQAAAYRRSKD-IASVVAFGSPVDTLAAL 184
                                    44444445333..5789*************99998886666.**********8877775 PP

>> PHB_depo_C  PHB de-polymerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.3e-07    0.0022     105     200 ..     270     360 ..     202     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.3e-07
                     PHB_depo_C 105 tveevfqefalakgklkvegkrvdlkkikrvalltveGenDDisglGqtkaaldlctgipesrkahylqegvGhyGvfsG 184
                                     +++   + ++  g ++++g+ v+l++i+ + +l+  Ge DDi   Gq ++++ + ++ p+s+        +Gh+G+  G
  gi|121637590|ref|YP_977813.1| 270 LLKQFIAHNRMMTGGFAISGQMVTLTDIT-CPILAFVGEVDDI---GQPASVRGIRRAAPNSEVY-ECLIRAGHFGLVVG 344
                                    45555666788899999**********97.8999999*****8...8999999999999988755.556789******** PP

                     PHB_depo_C 185 srfreeivPrvrdfir 200
                                    sr  ++  P v+d++r
  gi|121637590|ref|YP_977813.1| 345 SRAAQQSWPTVADWVR 360
                                    ************9987 PP

>> DUF3141  Protein of unknown function (DUF3141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   5.5e-05      0.16      51     314 ..      50     315 ..      40     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.5e-05
                        DUF3141  51 YaLlrilppedvevDp.akrPfvvidPRaGhgpGiGGfkedseiGvalraGhPvYfvsf.lpepvpgqtledvveaeaaf 128
                                    Y+L r  pp++++  p    P++++ P    +      +ed  +G+   +G   + + f +p+ v+g +  ++++  +a 
  gi|121637590|ref|YP_977813.1|  50 YKLRRYFPPDNRPGQPpVGPPVLMVHPMMMSADMWDVTREDGAVGILHASGLDPWVIDFgSPDEVEGGMRRNLADHIVAL 129
                                    77888888888665541457777888888777777778888888888888888888888557778888888888888888 PP

                        DUF3141 129 lrkvaelhpeae.kPvvignCqaGwavlmlaala.pelvGpiivaGaPlsywaGvrgknpmRYagGllGGsWltaltsDL 206
                                     ++v  +   +      +g  q+G     +aa +  + +  ++  G+P+   a      pm   + +  G+ ++ +++D 
  gi|121637590|ref|YP_977813.1| 130 SEAVDTVKDATGhDVHFVGYSQGGMFCYQAAAYRrSKDIASVVAFGSPVDTLA----ALPMGIPANM--GAAVADFMADH 203
                                    88888777766646678999999988887777651567788888899999888....6788877766..78889999999 PP

                        DUF3141 207 GnGrfD.GawLv.qnfeklnPantlwskqynlyakvdte.......aerylefekwWGghvllnkeeieyivdnLfvGnr 277
                                       r D  +w+  + f+ ++P +t  ++   + +  d e       ++r+le e w    +   +  i  + ++    nr
  gi|121637590|ref|YP_977813.1| 204 VFNRLDiPSWMArMGFQMMDPLKTAKARVDFVRQLHDREallpreqQRRFLESEGW----IAWSGPAISELLKQFIAHNR 279
                                    99999944677624799999988877665544444444311111116799999988....455667788888998899** PP

                        DUF3141 278 latgelvtsdgvriDlrnirsPivvfaskgDnitPPq 314
                                    ++tg  +   g+++ l +i  Pi+ f  + D+i  P+
  gi|121637590|ref|YP_977813.1| 280 MMTGGFA-ISGQMVTLTDITCPILAFVGEVDDIGQPA 315
                                    ****985.56999********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (999 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 7050.24
//
Query:       gi|121637591|ref|YP_977814.1|  [L=74]
Description: hypothetical protein BCG_1722 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-09   35.9   0.2    5.8e-08   33.2   0.2    2.0  1  Trm112p   Trm112p-like protein


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2   3.2e-12   5.8e-08       1      68 []       3      44 ..       3      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.2e-12
                                   BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                        Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                   ++ ll iL+Cpa++gpL                        + l+e d + ++L++p+ +raY+I+dG
  gi|121637591|ref|YP_977814.1|  3 DEALLAILVCPADRGPL------------------------V-LVE-DGDIQVLYNPRLRRAYRIEDG 44
                                   5789*************........................3.222.33349***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 587.88
//
Query:       gi|121637592|ref|YP_977815.1|  [L=207]
Description: hypothetical protein BCG_1723c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-25   89.7   0.1    2.4e-25   88.8   0.0    1.5  2  TetR_C_16  Tetracyclin repressor-like, C-terminal domain
    2.4e-16   59.2   1.3    3.6e-16   58.7   1.3    1.3  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.089   13.0   0.0       0.17   12.1   0.0    1.4  1  DUF3572    Protein of unknown function (DUF3572)


Domain annotation for each model (and alignments):
>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   7.3e+03      49      52 ..      42      45 ..      19      62 .. 0.52
   2 !   88.8   0.0   4.1e-29   2.4e-25       1     107 []      90     197 ..      90     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                   HHHC CS
                      TetR_C_16 49 lapl 52
                                   ++++
  gi|121637592|ref|YP_977815.1| 42 IRAV 45
                                   2222 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 4.1e-29
                                    TTHHHHHHHHHHHHHHHHT-HHHHHHHHH--------HHHHHHHHHHHHHHCTTTS-ST..THHHHHHHHHHHHHHHHHH CS
                      TetR_C_16   1 eelGerlvravlevwepearepllallrsalsseeaaellrefleeqvlaplaarlggp..daelRaalvasqllGlala 78 
                                    eelG +l + +l  w++e ++ l a+lrs   s+ +  l+r+flee+v+ +l +r+++p  + + R++ vasql+G+++a
  gi|121637592|ref|YP_977815.1|  90 EELGYKLPSLLLPIWDSELGAGLIATLRSL-ISGSDVGLARSFLEEVVTVELGSRVDNPpgTGKIRTQFVASQLMGVVMA 168
                                    89****************************.566799**********************9******************** PP

                                    HHTS--TTCCCS-HHHHHHHHHHHHHHHH CS
                      TetR_C_16  79 RyvlrleplasasreelvalvgptlqryL 107
                                    Ry++r+ep+as+++e++v++++p+lqryL
  gi|121637592|ref|YP_977815.1| 169 RYIVRIEPFASLPAEQIVQTIAPNLQRYL 197
                                    ****************************8 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   1.3     6e-20   3.6e-16       1      47 []      24      70 ..      24      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 6e-20
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Il+ Arelfa++G+d+t++r++A++AGv ++++++yF++K++L++a+
  gi|121637592|ref|YP_977815.1| 24 ILSSARELFAHNGIDRTSIRAVAAKAGVDAALVHHYFGTKQQLFAAA 70
                                   9*******************************************996 PP

>> DUF3572  Protein of unknown function (DUF3572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.17      24      74 ..      30      80 ..      26      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                        DUF3572 24 rFLaltGlepadLRaaaaepeflaavLdFllsdealllafaeaaglkpeev 74
                                   ++ a+ G++  ++Ra aa+ ++ aa++ +     + l a a +  ++p  +
  gi|121637592|ref|YP_977815.1| 30 ELFAHNGIDRTSIRAVAAKAGVDAALVHHYFGTKQQLFAAAIHIPIDPMVI 80
                                   578999*************************************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1534.26
//
Query:       gi|121637593|ref|YP_977816.1|  [L=226]
Description: integral membrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-29  101.9  20.0    4.7e-29  101.3  20.0    1.2  1  ABC2_membrane    ABC-2 type transporter
    6.9e-17   61.6  12.9    6.9e-17   61.6  12.9    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
      1e-08   34.8  16.1    1.4e-08   34.4  16.1    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
      0.003   17.6  10.1      0.003   17.6  10.1    2.3  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.042   12.7   1.3      0.059   12.2   1.3    1.2  1  DUF5423          Family of unknown function (DUF5423)
       0.16   12.2   0.0       0.27   11.4   0.0    1.3  1  PilN             Fimbrial assembly protein (PilN)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3  20.0   1.6e-32   4.7e-29      26     207 ..       3     188 ..       1     189 [. 0.91

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 1.6e-32
                  ABC2_membrane  26 liqplllalvfgtvfgnlg...nsedglnr..pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlak 100
                                    l+ p+l+++++ ++f n +    + +g+n   + ll+ + lf++ + +t++ + +er  g+ler l++pl ++ + ++++
  gi|121637593|ref|YP_977816.1|   3 LLVPILIITLMYFMFENFPhrpGTPSGFNTacLVLLGLFPLFVM-FVITAITMQRERASGTLERILTTPL-RRLDLLAGY 80 
                                    56788888889999998776664444443456777777777777.9999999******************.********* PP

                  ABC2_membrane 101 vlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGff 179
                                     +++ + +++qa++  +++++++g+d   + +++++++++ a+++++lgll sa+a+++ +a+q+++lv++p lll+G++
  gi|121637593|ref|YP_977816.1|  81 GTAFSIAAAAQATLACIVAFWFLGFDTAgSPVWVFAIAIVNAVLGVGLGLLCSAFARTEFQAVQFIPLVMVPQLLLAGII 160
                                    ***************************9777************************************************* PP

                  ABC2_membrane 180 ipidsmpkwlqwiaylnPltyavealrs 207
                                    +p+  mp wl wi+ + P +ya+eal++
  gi|121637593|ref|YP_977816.1| 161 VPRALMPTWLEWISNVMPASYALEALQQ 188
                                    *************************986 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   2.4    0.0097        29       6      25 ..       1      20 [.       1      28 [. 0.84
   2 !   61.6  12.9   2.3e-20   6.9e-17     157     344 ..      28     218 ..      24     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0097
                ABC2_membrane_3  6 itlllPiilvlllglifsns 25
                                   ++ll+Pi++++l++++f n 
  gi|121637593|ref|YP_977816.1|  1 MILLVPILIITLMYFMFENF 20
                                   5799************9876 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 2.3e-20
                ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgi 233
                                    s+++  +++l+ ++++f++++++a  + +E+ s+++e++l++++++l ++ +  ++  ++++ q+ l++++   ++g  +
  gi|121637593|ref|YP_977816.1|  28 SGFNTACLVLLGLFPLFVMFVITAITMQRERASGTLERILTTPLRRLDLLAGYGTAFSIAAAAQATLACIVafwFLG--F 105
                                    5677778889999********9**9****************************************998885234555..4 PP

                ABC2_membrane_3 234 pfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglg 312
                                    +   + ++++   ++ + + + lg+l+s++ +++  a ++i++v+++ +++ g+++p   +p++l wi+ + P ++  ++
  gi|121637593|ref|YP_977816.1| 106 DTAgSPVWVFAIAIVNAVLGVGLGLLCSAFARTEFQAVQFIPLVMVPQLLLAGIIVPRALMPTWLEWISNVMPASYALEA 185
                                    44448889**************************************9999999999999********************* PP

                ABC2_membrane_3 313 llrlitgdplweil.lsliilalfavvylllal 344
                                    l +++    l  i+ +++++ + fav+ l+la+
  gi|121637593|ref|YP_977816.1| 186 LQQVGAHPELTGIAvRDVVVVLSFAVASLCLAA 218
                                    ****85444566777999999999999999997 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4  16.1   4.7e-12   1.4e-08      84     285 ..      40     223 ..       2     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.7e-12
                ABC2_membrane_2  84 lipvi.aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledll 162
                                    l+p++   +++a    +E+++gTl++ L++P  R ++l+g   g + +   ia a+ at l+ ++    lg  +a++ + 
  gi|121637593|ref|YP_977816.1|  40 LFPLFvMFVITAITMQRERASGTLERILTTPLRRLDLLAG--YGTAFS---IAAAAQAT-LACIVAFWFLGFDTAGSPVW 113
                                    3443334456666678***********************9..466666...77777777.55566666677777777777 PP

                ABC2_membrane_2 163 llvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsay 242
                                    ++++a+v  +l    ++lgll S++ar+  +a    + l++v ++l    l+g++ + a +     +   +s + p+s+ 
  gi|121637593|ref|YP_977816.1| 114 VFAIAIVNAVL---GVGLGLLCSAFARTEFQAV-QFIPLVMVPQLL----LAGIIVPRALMPT---WLEWISNVMPASYA 182
                                    77777776666...79***********444444.444455555444....4444444443333...44445555555555 PP

                ABC2_membrane_2 243 ntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                      +l+++ a  +l   g+++  ++++l  ++++l l++v ++r
  gi|121637593|ref|YP_977816.1| 183 LEALQQVGAHPEL--TGIAVRDVVVVLSFAVASLCLAAVTLRR 223
                                    5555555555544..59*********************99887 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  10.1   9.9e-07     0.003      19     168 ..       3     147 ..       1     151 [. 0.58
   2 ?    3.0   1.7     0.029        88     103     156 ..     115     169 ..     111     185 .. 0.55
   3 ?   -4.0   0.3       4.2   1.3e+04     152     152 ..     211     211 ..     200     221 .. 0.38

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.9e-07
                ABC2_membrane_4  19 vlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaK 98 
                                    +l+++l+  l+ + f+ + ++   p++f +  +  + l l+  +++ +i+++ ++rE+ ++tl  +lt P  r  ll++ 
  gi|121637593|ref|YP_977816.1|   3 LLVPILIITLMYFMFENFPHRPGTPSGFNT--ACLVLLGLFPLFVMFVITAITMQRERASGTLERILTTPLRRLDLLAG- 79 
                                    334444434444445455544444555544..333333455667788899*************************9987. PP

                ABC2_membrane_4  99 livllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi.ialvllkksyvlp 168
                                    + + + ++++ +  ++l+++++ +++gf ++ +++v+ +   ++  +l+v + +l   +a + ++  +++p
  gi|121637593|ref|YP_977816.1|  80 YGTAFSIAAAAQ--ATLACIVAFWFLGF-DTAGSPVWVFAIAIVNAVLGVGLGLLCSaFARTEFQAVQFIP 147
                                    555555444444..44555555566664.455666666666666666666555443313334455555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.029
                ABC2_membrane_4 103 lllsvllmlvtflitvlfallsgfvgfsvklvl..ellkkclelgllvffavlpii 156
                                    + ++++  ++ + + +l++ ++  ++f++ +++   ++ ++l+ g++v  a++p +
  gi|121637593|ref|YP_977816.1| 115 FAIAIVNAVLGVGLGLLCSAFAR-TEFQAVQFIplVMVPQLLLAGIIVPRALMPTW 169
                                    44445555555555555544443.44554444411344478888888888888876 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.2
                ABC2_membrane_4 152 v 152
                                    v
  gi|121637593|ref|YP_977816.1| 211 V 211
                                    1 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3     2e-05     0.059       2      71 ..      61     138 ..      60     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                        DUF5423   2 gllsrfltapdrhpklryvy....dialiai.silcivsiilw...tqgsglalfaiapalaigalgvtllvsdlaes 71 
                                    g l r+lt+p r   l   y     ia  a  ++ civ+  +    t gs + +faia   a+  +g+ ll s +a +
  gi|121637593|ref|YP_977816.1|  61 GTLERILTTPLRRLDLLAGYgtafSIAAAAQaTLACIVAFWFLgfdTAGSPVWVFAIAIVNAVLGVGLGLLCSAFART 138
                                    7899*******9999977661111455555414669998754333499*************************99865 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     9e-05      0.27       3      34 ..     170     201 ..     168     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                           PilN   3 ldeLsravPkgvwltsisqegnqltitGsAvs 34 
                                    l+ +s+++P +  l+ ++q g+  ++tG+Av 
  gi|121637593|ref|YP_977816.1| 170 LEWISNVMPASYALEALQQVGAHPELTGIAVR 201
                                    6779**************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1684.80
//
Query:       gi|121637594|ref|YP_977817.1|  [L=255]
Description: ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-30  105.6   0.0    4.2e-30  105.0   0.0    1.3  1  ABC_tran      ABC transporter
      5e-12   46.2   0.0    4.3e-06   26.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0029   17.5   0.2     0.0049   16.8   0.2    1.3  1  RsgA_GTPase   RsgA GTPase
     0.0044   17.6   0.1     0.0065   17.0   0.1    1.2  1  AAA_23        AAA domain
     0.0058   17.0   0.3     0.0082   16.5   0.3    1.6  1  AAA_16        AAA ATPase domain
      0.006   16.3   0.1      0.012   15.3   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.01   16.0   0.0      0.023   14.9   0.0    1.7  1  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.038   13.4   0.0        2.5    7.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.044   13.2   0.1       0.24   10.7   0.1    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.054   13.3   0.1       0.11   12.3   0.1    1.6  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain
      0.074   12.8   0.4       0.22   11.2   0.4    1.8  1  AAA_30        AAA domain
      0.081   12.5   0.7       0.15   11.7   0.7    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.9   1.8       0.29   11.4   0.7    2.4  2  AAA_22        AAA domain
       0.13   11.7   0.0       0.26   10.7   0.0    1.6  2  PhoH          PhoH-like protein
       0.18   12.1   0.6       0.32   11.3   0.6    1.7  1  AAA_19        AAA domain
       0.19   10.5   0.3       0.28    9.9   0.3    1.2  1  Adeno_IVa2    Adenovirus IVa2 protein
       0.22   11.6   0.3       0.51   10.4   0.3    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
       0.28   11.1   0.8        1.1    9.1   0.1    2.1  2  ATPase_2      ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   4.3e-33   4.2e-30       1     136 [.      33     170 ..      33     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 4.3e-33
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vs+ +  g++++++G++G+GK+tL++++ g    ++G++ + g++  +    +lr+++g++pq+p++ ++l+v +n 
  gi|121637594|ref|YP_977817.1|  33 LQDVSVRVACGTITGLLGPSGSGKTTLIRCIVGSQIIASGSVSVLGQPAGS---AELRHRVGYMPQDPTIYNDLRVIDNi 109
                                    789********************************************9999...99************************ PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             +++ ++++++ ++l + ++ ++    ++LSgGq+ rv+la+al+ +p+ll+lDEpt
  gi|121637594|ref|YP_977817.1| 110 ryfaelcgVDRQAADEVIEAVDLRDHRTARC----ANLSGGQRARVSLACALVGRPDLLVLDEPT 170
                                    *****99777777************888888....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0026       1      23 [.      45      67 ..      45     114 .. 0.78
   2 !   26.8   0.0   4.3e-09   4.3e-06     242     297 ..     147     200 ..     134     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   +++l Gp gsGK++L++++ + +
  gi|121637594|ref|YP_977817.1| 45 ITGLLGPSGSGKTTLIRCIVGSQ 67
                                   799****************6543 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 4.3e-09
                         AAA_21 242 krllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    +r+ ++ +a++    + +ll++DEp  gL+P l  +l++ + +l+r+g+ +++++H
  gi|121637594|ref|YP_977817.1| 147 QRA-RVSLACALVGRP-DLLVLDEPTIGLDPVLRVELWDRFTALARRGTTLLVSSH 200
                                    444.555555555555.*************************************** PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   4.9e-06    0.0049      99     131 ..      43      75 ..      21      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.9e-06
                                    TSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevs 131
                                    + ++ l+G+SG GK+tLi  +++++ ++ g+vs
  gi|121637594|ref|YP_977817.1|  43 GTITGLLGPSGSGKTTLIRCIVGSQIIASGSVS 75 
                                    47899******************9999999887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.6e-06    0.0065      21      39 ..      45      63 ..      28      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
                         AAA_23 21 ltlItGpNGaGKTTildAi 39
                                   +t + Gp G+GKTT++++i
  gi|121637594|ref|YP_977817.1| 45 ITGLLGPSGSGKTTLIRCI 63
                                   8999**************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   8.2e-06    0.0082      25      52 ..      44      72 ..      25     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-06
                         AAA_16 25 elvllsGesGvGKsslvrell.ralekdg 52
                                    ++ l G+sG+GK++l+r++   ++ ++g
  gi|121637594|ref|YP_977817.1| 44 TITGLLGPSGSGKTTLIRCIVgSQIIASG 72
                                   677899************99734555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-05     0.012      16      39 ..      37      60 ..      31      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++++    +t l GpsGsGK+Tl+
  gi|121637594|ref|YP_977817.1| 37 SVRVACGTITGLLGPSGSGKTTLI 60
                                   55565445899************8 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-05     0.023       5      68 ..      49     121 ..      46     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                         AAA_33   5 vGlpGsGKstlaerllkklg.....avllssdt....lrrrlfg.tdqqsktdytrvldrlyqilnelarkals 68 
                                     G++GsGK+tl++ ++  +      + +l +++    lr r+ +  +++++ +  rv d+++++  el+   ++
  gi|121637594|ref|YP_977817.1|  49 LGPSGSGKTTLIRCIVGSQIiasgsVSVLGQPAgsaeLRHRVGYmPQDPTIYNDLRVIDNIRYFA-ELCGVDRQ 121
                                    6************9976555666689999999966654444444444556666667888888875.66644444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0025       2.5      25      44 ..      44      63 ..      19      72 .. 0.74
   2 ?    4.2   0.0     0.025        25     136     185 ..     142     187 ..      84     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                    +t ++Gp GSGK+ l+  i
  gi|121637594|ref|YP_977817.1| 44 TITGLLGPSGSGKTTLIRCI 63
                                   5899***********99887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                    +LSgG+++ v+la       v +  l +lDe    LD   + ++ +++ +
  gi|121637594|ref|YP_977817.1| 142 NLSGGQRARVSLACA----LVGRPDLLVLDEPTIGLDPVLRVELWDRFTA 187
                                    8******98887754....4556668888888888887766666665554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00024      0.24       2      43 ..      23      64 ..      22      73 .. 0.88
   2 ?   -0.3   0.0       0.6     6e+02       4      34 ..     142     172 ..     135     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                   Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43
                                   l+ ++G++ a + + + +a g    l+Gp+GsGKt l++++ 
  gi|121637594|ref|YP_977817.1| 23 LRVIRGKRLALQDVSVRVACGTITGLLGPSGSGKTTLIRCIV 64
                                   5678999999999999999999999*************9985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.6
                   Mg_chelatase   4 dvkGqeeakraleiaaaGgHnlllvGppGsG 34 
                                    ++ G ++a+  l  a  G+ +ll++  p  G
  gi|121637594|ref|YP_977817.1| 142 NLSGGQRARVSLACALVGRPDLLVLDEPTIG 172
                                    6789999999999999999999998888666 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011      0.11      22     104 ..      19     108 ..      16     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                    EE-TTS-EEEEEEEGGGHHHHHTT-E..EE-.GGGGG--TTS---TT-S-SSS--EEEEE-GGG....-EEE---SSTTS CS
                   Gln-synt_N_2  22 yvdlaGvtrGkalplasLeekLasGi..Glt.katlalserdlidevedlgpvGelrLvpdPas....avalpyaPdaaa 94 
                                     +d   v+rGk l+l  +  ++a G   Gl  ++ +  +++      +++ + G + +++ Pa     ++++ y+P+  +
  gi|121637594|ref|YP_977817.1|  19 IIDQLRVIRGKRLALQDVSVRVACGTitGLLgPSGSGKTTLIRCIVGSQIIASGSVSVLGQPAGsaelRHRVGYMPQDPT 98 
                                    56788899999999999999999885224431333444444444456889999*********9634446999******** PP

                                    EEEEEE-TTS CS
                   Gln-synt_N_2  95 llgdlvevdg 104
                                    ++ dl+ +d+
  gi|121637594|ref|YP_977817.1|  99 IYNDLRVIDN 108
                                    ******9997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00022      0.22      20      52 ..      45      77 ..      34     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvigl 52
                                   ++ l Gp G+GKtt+++ ++     a g+v +l
  gi|121637594|ref|YP_977817.1| 45 ITGLLGPSGSGKTTLIRCIVGSQIIASGSVSVL 77
                                   67899************9965444443344444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00015      0.15       2      21 ..      45      64 ..      44      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                   EEEEEESTTCCHHHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnhll 21
                                   +t+l G+ GsGKTtL++ ++
  gi|121637594|ref|YP_977817.1| 45 ITGLLGPSGSGKTTLIRCIV 64
                                   68899***********9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   0.00029      0.29       8      26 ..      46      64 ..      42     169 .. 0.87
   2 ?   -1.5   0.0       2.7   2.7e+03      82     103 ..     185     208 ..     172     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                         AAA_22  8 lvvtGesGtGKTtllrrll 26
                                   + + G+sG+GKTtl+r ++
  gi|121637594|ref|YP_977817.1| 46 TGLLGPSGSGKTTLIRCIV 64
                                   5578***********9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                         AAA_22  82 leqalrarav..ielliiDEaqhl 103
                                    ++  +r+  +  ++  + DEa++ 
  gi|121637594|ref|YP_977817.1| 185 FTALARRGTTllVSSHVMDEADRC 208
                                    444444444455566678888874 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.26      19     110 ..      43     132 ..      22     139 .. 0.71
   2 ?   -3.3   0.0       5.2   5.2e+03     114     128 ..     191     205 ..     189     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                                    -SEEEEE--TTSSTTHH.HHHHHHHHHHTTS-SEEEEEE-S--T..T----SS---------TTTHHHHHHHTTTS-TTC CS
                           PhoH  19 ndivfaiGpaGtGKtyl.avalavealkkkkvkriiltrpavea..geelGflpgdleekvdpylrplydaLkdllgaek 95 
                                     +i+  +Gp+G+GKt l  + ++ +++ +++v+  +l +pa +a    ++G++p d + + d     ++d+++ + +   
  gi|121637594|ref|YP_977817.1|  43 GTITGLLGPSGSGKTTLiRCIVGSQIIASGSVS--VLGQPAGSAelRHRVGYMPQDPTIYNDL---RVIDNIRYFAELCG 117
                                    579999********8651677899999999998..7777777554489999999885443332...45666666666666 PP

                                    HHHHHHTTSEEEEEG CS
                           PhoH  96 vekllekgkievapl 110
                                    v++   +++ie ++l
  gi|121637594|ref|YP_977817.1| 118 VDRQAADEVIEAVDL 132
                                    666666666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.2
                                    TT--B-SEEEEE-SG CS
                           PhoH 114 RGrTlndafvilDEA 128
                                    RG Tl  +  ++DEA
  gi|121637594|ref|YP_977817.1| 191 RGTTLLVSSHVMDEA 205
                                    999999999999999 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00032      0.32      11      33 ..      44      66 ..      34     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                         AAA_19 11 kvllvtaGpGtGKTrvlkhival 33
                                   ++  ++++ G+GKT+++++iv  
  gi|121637594|ref|YP_977817.1| 44 TITGLLGPSGSGKTTLIRCIVGS 66
                                   567799*************9965 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00028      0.28      92     114 ..      48      70 ..      32      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                     Adeno_IVa2  92 iyGPtGsGksqllrnlissklis 114
                                    + GP GsGk+ l+r ++ s++i 
  gi|121637594|ref|YP_977817.1|  48 LLGPSGSGKTTLIRCIVGSQIIA 70 
                                    469*****************997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00051      0.51       3      26 ..      47      70 ..      45      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                                   EEEESTTSSHHHHHHHHHTSTEEE CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltgekaiv 26
                                   +++G + +GK+tLi+ ++g++ i+
  gi|121637594|ref|YP_977817.1| 47 GLLGPSGSGKTTLIRCIVGSQIIA 70
                                   799****************97665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.69   6.9e+02     111     131 ..       7      27 ..       2      34 .. 0.81
   2 ?    9.1   0.1    0.0011       1.1      25      41 ..      48      64 ..      32      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.69
                       ATPase_2 111 ekikkkgkkiiiiiDelqkli 131
                                    +++ ++g  +++iiD l  ++
  gi|121637594|ref|YP_977817.1|   7 DELLRDGADPAVIIDQLRVIR 27 
                                    567789999******998776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                       ATPase_2 25 iYGpegsGKtaLlkeii 41
                                   + Gp gsGKt+L++ i+
  gi|121637594|ref|YP_977817.1| 48 LLGPSGSGKTTLIRCIV 64
                                   67************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1637.65
//
Query:       gi|121637595|ref|YP_977818.1|  [L=203]
Description: 3-methyladenine DNA glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-54  183.5   0.0    2.8e-54  183.2   0.0    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   1.5e-58   2.8e-54       6     175 .]       9     185 ..       5     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 1.5e-58
                  Pur_DNA_glyco   6 dalevAkeLLGkvlvreleegkvagrivEtEAYlg.....eeDpAshayrgrternavmFgppgtlYvYliygihhclnv 80 
                                    d+++ A++LLG+++  +     v++++vE+EAY+g     + D A+h+yrgr+ rn+vmFgppg+lY Y+++gih c+nv
  gi|121637595|ref|YP_977818.1|   9 DPVAAAHRLLGATIAGR----GVRAMVVEVEAYGGvpdgpWPDAAAHSYRGRNGRNDVMFGPPGRLYTYRSHGIHVCANV 84 
                                    78899**********99....9*************9999999************************************** PP

                  Pur_DNA_glyco  81 vteeegeasaVLiRalevveglelmrarrg.......lanGPgkLcqaLgidkelngadlle.seelvlekeeaeeeeiv 152
                                     ++++g+a+aVL+Ra+++ +g+el+++rrg       la+GPg+Lc+aLgi++++ng dl++ s++++l+   +++++ +
  gi|121637595|ref|YP_977818.1|  85 ACGPDGTAAAVLLRAAAIEDGAELATSRRGqtvravaLARGPGNLCAALGITMADNGIDLFDpSSPVRLR--LNDTHRAR 162
                                    *************************************************************999999999..5789999* PP

                  Pur_DNA_glyco 153 agpRiGiskaaelpwRfyikgnp 175
                                    +gpR+G+s+aa++pwR +++g+p
  gi|121637595|ref|YP_977818.1| 163 SGPRVGVSQAADRPWRLWLTGRP 185
                                    *******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1374.21
//
Query:       gi|121637596|ref|YP_977819.1|  [L=424]
Description: tyrosyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-82  274.6   0.0    1.2e-81  274.3   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
    7.7e-05   22.3   0.0    0.00015   21.4   0.0    1.5  1  S4            S4 domain
  ------ inclusion threshold ------
       0.08   12.8   0.5        1.5    8.6   0.5    2.2  1  TyrRSs_C      Tyrosyl-tRNA synthetase C-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.3   0.0     2e-85   1.2e-81       3     292 ..      30     325 ..      28     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 274.3 bits;  conditional E-value: 2e-85
                                    HS--EEEEEEETSSS.-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH..HHHHHHHT CS
                   tRNA-synt_1b   3 erplrvysGidPTgk.lHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena..ikaqlakg 79 
                                    ++p++vy+G+dPT++ lH G+lvpl +l+++q+agh++++l ++++++igdp++  er+l+++++v+e++  i+ ql+++
  gi|121637596|ref|YP_977819.1|  30 RGPMTVYAGFDPTAPsLHAGHLVPLLTLRRFQRAGHRPIVLAGGATGMIGDPRDVGERSLNEADTVAEWTerIRGQLERF 109
                                    5799**************************************************************************** PP

                                    CHTTT....EEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS... CS
                   tRNA-synt_1b  80 ldpek....aevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad... 152
                                    +d+++    a v ++ ew  +l+ +e+lrd+gk++s+n ml+++++++rl+  egis++ef+Y lLqa+D++ l+ +   
  gi|121637596|ref|YP_977819.1| 110 VDFDDspmgAIVENNLEWTGSLSAIEFLRDIGKHFSVNVMLARDTIRRRLAG-EGISYTEFSYLLLQANDYVELHRRhgc 188
                                    *****998888*****************************************.7************************** PP

                                    .EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC CS
                   tRNA-synt_1b 153 .lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde 231
                                     l++gG DQ++ni++g+ l+r+        ++++ltvpl+t +dG+ K++KS g++ ++Ld++ +s+++++q++v++ d+
  gi|121637596|ref|YP_977819.1| 189 tLQIGGADQWGNIIAGVRLVRQKLGA----TVHALTVPLVTAADGT-KFGKSTGGGSLWLDPQMTSPYAWYQYFVNTADA 263
                                    ***********************999....****************.********************************* PP

                                    SHHHHHHHHHTHHHCHHHHHHHHCCSEE.ESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 232 evekllklktelsnelierleavsgkkp.kreaeellaeevtklvhggdlkkalaealnell 292
                                    +v ++l+++t+ls +++ +le+ + + p +r+a+  la+e t lvhg+++  a+++a+++l+
  gi|121637596|ref|YP_977819.1| 264 DVIRYLRWFTFLSADELAELEQATAQRPqQRAAQRRLASELTVLVHGEAATAAVEHASRALF 325
                                    ***********************************************************998 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.5e-08   0.00015       4      40 ..     359     395 ..     357     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                                    HHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT- CS
                             S4   4 dkvlarlglassrreArqlIehGrVlVNGkvvkdpsy 40 
                                     ++l+++gl  s+  Ar+ I +G+V VN+ +v++  +
  gi|121637596|ref|YP_977819.1| 359 VDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEW 395
                                    678999**************************98766 PP

>> TyrRSs_C  Tyrosyl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5   0.00026       1.5      26      57 ..     361     392 ..     355     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                                    HHHHTTS-STHHHHHHHHHHT-EEEEE--S-- CS
                       TyrRSs_C  26 iLyaaGLasskseghrliakkgayvgsrpgkk 57 
                                    +L a GL++sk  ++r i++ g+ v   + ++
  gi|121637596|ref|YP_977819.1| 361 LLVASGLSASKGAARRTIHEGGVSVNNIRVDN 392
                                    79999*****************9998765534 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3017.06
//
Query:       gi|121637597|ref|YP_977820.1|  [L=127]
Description: lipoprotein lprJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-20   72.4   1.6      4e-20   72.0   1.6    1.1  1  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   1.6   2.3e-24     4e-20       3      93 ..      26     116 ..      24     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.3e-24
                         DUF732   3 aallaaalllaapAaAdsaddaFlaalnqagiaygspdaaialGkavCkkl.dsGksaeavvaevkndnsglspeqaaqf 81 
                                    a ++++a+ +aap +Ad   +aFl+al++agiay++p+ ++alG++vC+++ + G ++e++++++++  +g+s+++a++f
  gi|121637597|ref|YP_977820.1|  26 AGVFGGAASCAAPIQADMMGNAFLTALTNAGIAYDQPATTVALGRSVCPMVvAPGGTFESITSRMAE-INGMSRDMASTF 104
                                    67889999*******************************************99*************9.9999******** PP

                         DUF732  82 vgaAvsayCPeq 93 
                                    +  A+ +yCP+ 
  gi|121637597|ref|YP_977820.1| 105 TIVAIGTYCPAV 116
                                    **********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 861.26
//
Query:       gi|121637598|ref|YP_977821.1|  [L=250]
Description: hypothetical protein BCG_1729 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-06   27.0  14.7    0.00062   20.4   3.3    3.7  3  TPR_16    Tetratricopeptide repeat
    8.3e-05   23.0  17.7     0.0045   17.5   0.9    4.1  5  TPR_19    Tetratricopeptide repeat
    0.00018   21.7  14.0      0.039   14.2   0.2    4.1  4  TPR_12    Tetratricopeptide repeat
    0.00034   20.8   0.1        0.3   11.4   0.0    3.0  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
    0.00046   20.1  14.2       0.26   11.5   1.4    4.8  5  TPR_2     Tetratricopeptide repeat
    0.00046   20.4   1.7     0.0013   19.0   1.7    1.7  1  TPR_5     Tetratrico peptide repeat
    0.00071   18.9   7.3     0.0024   17.2   7.3    1.9  1  TPR_15    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   15.1   0.3         21    4.9   0.0    3.6  3  TPR_11    TPR repeat
      0.015   15.9   1.8      0.015   15.9   1.8    5.9  5  TPR_4     Tetratricopeptide repeat
       0.03   14.5   0.2        6.5    7.2   0.3    3.3  3  TPR_8     Tetratricopeptide repeat
      0.053   14.4  27.7      0.087   13.7   1.2    5.4  5  TPR_14    Tetratricopeptide repeat
        1.8    8.5  11.7          2    8.4   0.5    3.7  4  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   9.0   0.00018      0.27      12      68 .]      73     126 ..      71     126 .. 0.95
   2 !   20.4   3.3   4.2e-07   0.00062       4      59 ..      99     150 ..      96     161 .. 0.92
   3 !   19.5   3.7   7.8e-07    0.0012       3      66 ..     168     232 ..     166     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                         TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                    d+++A++ ++aa+ r+   ++ a+ + + g aa+r g++a A+a +raa r ++++p
  gi|121637598|ref|YP_977821.1|  73 DPEAALRHARAARVRA---SRIAAVREAVGIAAYRCGDWAQALAELRAARRMGSKSP 126
                                    799*************...******************************99998876 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.2e-07
                         TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                    + aa+r gd+++A+a l+aa++++++sP+    l l +d+   +gr ++A++l r 
  gi|121637598|ref|YP_977821.1|  99 GIAAYRCGDWAQALAELRAARRMGSKSPL----LALIADCERGLGRPQRAIELARG 150
                                    78999***********************7....******************99885 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 7.8e-07
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                    +a a++++g+ ++A+ +l +   + +++   aa+  +++++++l++gr +eA++++++ ++a+ d
  gi|121637598|ref|YP_977821.1| 168 AAGARADLGQLEQALTVLSTPQLDPGRTGStAARLFYAYAEILLALGRGDEALQWFLRSAAADID 232
                                    68999*************9988888888889***************************9888765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.46   6.9e+02      14      34 ..      63      83 ..      51      88 .. 0.74
   2 ?    5.4   3.0     0.018        27       4      66 ..      71     132 ..      63     134 .. 0.79
   3 !   11.4   0.3   0.00023      0.34       5      47 ..     106     147 ..     102     149 .. 0.92
   4 !   11.0   0.8   0.00032      0.48       5      52 ..     139     189 ..     137     202 .. 0.85
   5 !   17.5   0.9     3e-06    0.0045       5      54 ..     176     229 ..     176     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                         TPR_19 14 leqalqedpknaearllLAea 34
                                   l +a +   +++ea+l+ A+a
  gi|121637598|ref|YP_977821.1| 63 LVAAGELIDDDPEAALRHARA 83
                                   556666777888888888887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                         TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                    + d+++Al++ ++a   +   a++r +  +a +  g++++A a L a+ ++  +++ + +L+A
  gi|121637598|ref|YP_977821.1|  71 DDDPEAALRHARAARVRASRIAAVREAVGIAAYRCGDWAQALAELRAARRMGSKSPLL-ALIA 132
                                    56899999999999777777888888889999*************9999998884444.4665 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00023
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                    gd a+Ala l++a     k++ ++l  A++   lg+++ A++l
  gi|121637598|ref|YP_977821.1| 106 GDWAQALAELRAARRMGSKSPLLAL-IADCERGLGRPQRAIEL 147
                                    89***********999888888888.**************986 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00032
                         TPR_19   5 gdyaeAlalleq..alqedpk.naearllLAeallalgqldeAealLdalp 52 
                                    g++++A++l +   a + + +  +e+r+  A a   lgql++A  +L++ +
  gi|121637598|ref|YP_977821.1| 139 GRPQRAIELARGseAVELSGDaADELRIVAAGARADLGQLEQALTVLSTPQ 189
                                    899999777777668899999899***********************8755 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 3e-06
                         TPR_19   5 gdyaeAlalleqalqedpk.....naearllLAeallalgqldeAealLdalpee 54 
                                    g++++Al  l+   q dp+      a++ +++Ae+llalg+ deA +   +  ++
  gi|121637598|ref|YP_977821.1| 176 GQLEQALTVLST-PQLDPGrtgstAARLFYAYAEILLALGRGDEALQWFLRSAAA 229
                                    788888888888.6899999997777777899**************987776665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.2     0.018        27      10      67 ..      65     121 ..      58     125 .. 0.61
   2 !   11.1   1.4   0.00026      0.38       3      69 ..      92     149 ..      90     154 .. 0.80
   3 ?   -0.0   0.0      0.74   1.1e+03      11      25 ..     170     184 ..     164     187 .. 0.72
   4 !   14.2   0.2   2.6e-05     0.039       3      32 ..     200     229 ..     197     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                         TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                    aa ++   + + Al++ ++a+ +a+r+    ++++ ++ +  g++ +al ++++A+++
  gi|121637598|ref|YP_977821.1|  65 AAGELIDDDPEAALRHARAARVRASRIA-AVREAVGIAAYRCGDWAQALAELRAARRM 121
                                    5555556667777777777766666663.44666666666666666666666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                    a++   ++ + +r g++++Al+ l++a+++       ++pl    l  ++++ r lgr++ A+el +
  gi|121637598|ref|YP_977821.1|  92 AAVREAVGIAAYRCGDWAQALAELRAARRMG-----SKSPL----LALIADCERGLGRPQRAIELAR 149
                                    56666789999****************7777.....55544....7889999999999999999876 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.74
                         TPR_12  11 avlrrlgrydeAlel 25 
                                     + + lg++++Al+ 
  gi|121637598|ref|YP_977821.1| 170 GARADLGQLEQALTV 184
                                    556678888888875 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 2.6e-05
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                    a++ + +a++l++lgr deAl+++ ++ ++
  gi|121637598|ref|YP_977821.1| 200 ARLFYAYAEILLALGRGDEALQWFLRSAAA 229
                                    667778999999999999999999988765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0002       0.3      24      80 ..     125     186 ..     107     188 .. 0.77
   2 ?    5.7   0.0     0.012        18      57      79 ..     201     223 ..     190     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                    HHHHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3  24 edayll.AlclylngqykrAyellrka.klnsksl...gcrylfAqcllkLkkyeeAiaaLe 80 
                                    + +++l A c   +g+ +rA+el+r +   + +     + r+++A +  +L+++e+A+++L+
  gi|121637598|ref|YP_977821.1| 125 SPLLALiADCERGLGRPQRAIELARGSeAVELSGDaadELRIVAAGARADLGQLEQALTVLS 186
                                    4444445999999**************6555555578899********************96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHTT-HHHHHHHH CS
                         ANAPC3  57 gcrylfAqcllkLkkyeeAiaaL 79 
                                    +  y +A+ ll+L++ +eA++ +
  gi|121637598|ref|YP_977821.1| 201 RLFYAYAEILLALGRGDEALQWF 223
                                    45677889999999999998765 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.3   1.9e+03      15      27 ..      72      84 ..      58      87 .. 0.77
   2 !    9.4   0.7   0.00081       1.2       7      28 ..      98     119 ..      92     122 .. 0.88
   3 ?    3.9   0.0     0.049        73       4      23 ..     128     147 ..     126     149 .. 0.85
   4 ?   -0.1   0.0      0.91   1.4e+03      12      22 ..     173     183 ..     168     186 .. 0.80
   5 !   11.5   1.4   0.00017      0.26       1      29 [.     200     228 ..     200     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                          TPR_2 15 gdyeeAleafekA 27
                                   +d+e Al++ ++A
  gi|121637598|ref|YP_977821.1| 72 DDPEAALRHARAA 84
                                   7889999999887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00081
                          TPR_2   7 lGlayyklgdyeeAleafekAl 28 
                                     G a+y+ gd+++Al+ +++A 
  gi|121637598|ref|YP_977821.1|  98 VGIAAYRCGDWAQALAELRAAR 119
                                    699***************9996 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.049
                          TPR_2   4 lynlGlayyklgdyeeAlea 23 
                                    l  ++++ + lg++++A+e+
  gi|121637598|ref|YP_977821.1| 128 LALIADCERGLGRPQRAIEL 147
                                    567899999*********97 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.91
                          TPR_2  12 yklgdyeeAle 22 
                                    + lg++e+Al 
  gi|121637598|ref|YP_977821.1| 173 ADLGQLEQALT 183
                                    67999**9986 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00017
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                    a++ y+ ++++++lg+ +eAl++f ++ +
  gi|121637598|ref|YP_977821.1| 200 ARLFYAYAEILLALGRGDEALQWFLRSAA 228
                                    6789********************99876 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.7   8.4e-07    0.0013      14     104 ..     138     230 ..     129     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.4e-07
                          TPR_5  14 tGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaL..vLsdlgrer 91 
                                     G++++a++l r + a  L+g  +  + i  a +   lG++e+al++L + + +p+   + a + f a   +L +lgr  
  gi|121637598|ref|YP_977821.1| 138 LGRPQRAIELARGSEAVELSGDAADELRIVAAGARADLGQLEQALTVLSTPQLDPGRTGSTAARLFYAYaeILLALGRGD 217
                                    69***********************************************99999999999998988765337******** PP

                          TPR_5  92 eavsivllalaeh 104
                                    ea++  l + a+ 
  gi|121637598|ref|YP_977821.1| 218 EALQWFLRSAAAD 230
                                    ******9998875 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.3   1.6e-06    0.0024      88     243 ..      69     229 ..      37     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                         TPR_15  88 lydaepkeaarlaekgwrrfrsprlLssalel.lerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAl 166
                                    l d++p++a+r a ++  r  +     +a+ + ++r +d+ +    l++l +  ++ + +  l++ a  +r  g++++A+
  gi|121637598|ref|YP_977821.1|  69 LIDDDPEAALRHARAARVRASRIAAVREAVGIaAYRCGDWAQ---ALAELRAARRMGSKSPLLALIADCERGLGRPQRAI 145
                                    467888888888888877777777777777641467777755...67777779999999********************* PP

                         TPR_15 167 rdyr..eAlalapds.selraallWlliDlgrraeLrellkawkara....esdasLwgplaaAlllLgrpkkALeylrk 239
                                    +++r  eA++l++d  +elr     +  Dlg+ +++  +l++ + +     ++ a+L  ++a  ll+Lgr ++AL+++ +
  gi|121637598|ref|YP_977821.1| 146 ELARgsEAVELSGDAaDELRIVAAGARADLGQLEQALTVLSTPQLDPgrtgSTAARLFYAYAEILLALGRGDEALQWFLR 225
                                    ***977899999874157887778888899988877777776666669999****************************9 PP

                         TPR_15 240 qake 243
                                     a++
  gi|121637598|ref|YP_977821.1| 226 SAAA 229
                                    9885 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.024        36       5      20 ..     103     118 ..      99     126 .. 0.89
   2 ?    4.9   0.0     0.014        21       5      18 ..     173     186 ..     171     187 .. 0.84
   3 ?    1.6   0.1      0.16   2.3e+02       3      19 ..     209     225 ..     206     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.024
                         TPR_11   5 yeqGkyeeAieaYkkA 20 
                                    y  G++ +A++++++A
  gi|121637598|ref|YP_977821.1| 103 YRCGDWAQALAELRAA 118
                                    889**********998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                         TPR_11   5 yeqGkyeeAieaYk 18 
                                     ++G++e+A+++++
  gi|121637598|ref|YP_977821.1| 173 ADLGQLEQALTVLS 186
                                    689*******9875 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.16
                         TPR_11   3 ayyeqGkyeeAieaYkk 19 
                                    ++ ++G+ +eA++++ +
  gi|121637598|ref|YP_977821.1| 209 ILLALGRGDEALQWFLR 225
                                    788999999**999865 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.4      0.13   1.9e+02      15      26 .]      72      83 ..      58      83 .. 0.90
   2 ?    8.4   4.3    0.0026       3.9       8      26 .]      99     117 ..      92     117 .. 0.88
   3 ?   -0.6   0.5         2     3e+03      13      25 ..     137     149 ..     132     149 .. 0.84
   4 ?    8.0   1.2    0.0034       5.1       4      24 ..     165     185 ..     163     186 .. 0.90
   5 ?   15.9   1.8     1e-05     0.015       2      24 ..     201     223 ..     200     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                          TPR_4 15 GdldeAraller 26
                                    d+++A++++++
  gi|121637598|ref|YP_977821.1| 72 DDPEAALRHARA 83
                                   59********95 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                          TPR_4   8 ArallalGdldeAraller 26 
                                    + a+++ Gd+++A+a l++
  gi|121637598|ref|YP_977821.1|  99 GIAAYRCGDWAQALAELRA 117
                                    789**************95 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2
                          TPR_4  13 alGdldeAralle 25 
                                     lG++ +A +l++
  gi|121637598|ref|YP_977821.1| 137 GLGRPQRAIELAR 149
                                    58***99999887 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0034
                          TPR_4   4 llaLArallalGdldeArall 24 
                                    +++ A a ++lG+l++A+++l
  gi|121637598|ref|YP_977821.1| 165 RIVAAGARADLGQLEQALTVL 185
                                    8899999***********987 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1e-05
                          TPR_4   2 rallaLArallalGdldeArall 24 
                                    r+ +a+A+ llalG+ deA++++
  gi|121637598|ref|YP_977821.1| 201 RLFYAYAEILLALGRGDEALQWF 223
                                    66799****************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.12   1.8e+02       2      22 ..     126     146 ..     125     150 .. 0.87
   2 ?   -0.3   0.0       1.2   1.7e+03      13      22 ..     174     183 ..     168     186 .. 0.80
   3 ?    7.2   0.3    0.0043       6.5       1      27 [.     200     226 ..     200     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                    CHHHHHHHHHHHTT-HHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAke 22 
                                    +++ +++++ + lg+ + A+e
  gi|121637598|ref|YP_977821.1| 126 PLLALIADCERGLGRPQRAIE 146
                                    578899*************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                    HTT-HHHHHH CS
                          TPR_8  13 klgdyeeAke 22 
                                    +lg++e+A  
  gi|121637598|ref|YP_977821.1| 174 DLGQLEQALT 183
                                    8999999976 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0043
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyeka 27 
                                    a++ y  + i+l lg+ +eA +++ + 
  gi|121637598|ref|YP_977821.1| 200 ARLFYAYAEILLALGRGDEALQWFLRS 226
                                    6899*******************9875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.5      0.26   3.9e+02      11      34 ..      68      91 ..      52      99 .. 0.75
   2 ?    6.4   2.9     0.012        19       6      34 ..      97     125 ..      92     132 .. 0.78
   3 ?    4.9   0.4     0.039        58       4      28 ..     128     152 ..     125     169 .. 0.68
   4 ?    3.3   0.3      0.13   1.9e+02       5      24 ..     166     185 ..     161     187 .. 0.82
   5 ?   13.7   1.2   5.8e-05     0.087       2      30 ..     201     229 ..     200     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.26
                         TPR_14 11 llalGdpdeAiallrralalaPdd 34
                                   +l  +dp++A++++r+a  +a   
  gi|121637598|ref|YP_977821.1| 68 ELIDDDPEAALRHARAARVRASRI 91
                                   455678999******997766555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                         TPR_14   6 alaeallalGdpdeAiallrralalaPdd 34 
                                    a + a ++ Gd+++A+a lr+a + + ++
  gi|121637598|ref|YP_977821.1|  97 AVGIAAYRCGDWAQALAELRAARRMGSKS 125
                                    568899****************8765554 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.039
                         TPR_14   4 llalaeallalGdpdeAiallrral 28 
                                    l+++a+ ++ lG+p++Ai+l+r   
  gi|121637598|ref|YP_977821.1| 128 LALIADCERGLGRPQRAIELARGSE 152
                                    44456666779*********99743 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                         TPR_14   5 lalaeallalGdpdeAiall 24 
                                      +a a + lG++++A+++l
  gi|121637598|ref|YP_977821.1| 166 IVAAGARADLGQLEQALTVL 185
                                    557888999********998 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 5.8e-05
                         TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                    ++ +a+ae+llalG+ deA++ + r  a+
  gi|121637598|ref|YP_977821.1| 201 RLFYAYAEILLALGRGDEALQWFLRSAAA 229
                                    689******************99997664 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.6    0.0094        14       7      30 ..      97     120 ..      91     124 .. 0.83
   2 ?   -0.8   0.1         1   1.5e+03      15      26 ..     138     149 ..     135     156 .. 0.80
   3 ?   -3.3   0.0       6.4   9.6e+03      15      22 ..     175     182 ..     171     184 .. 0.60
   4 ?    8.4   0.5    0.0013         2       9      30 ..     207     228 ..     204     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0094
                         TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                      ++a ++ g++++A+a l+ a +
  gi|121637598|ref|YP_977821.1|  97 AVGIAAYRCGDWAQALAELRAARR 120
                                    5699**************999865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                         TPR_10  15 rgrydeAealle 26 
                                    +gr ++A +l++
  gi|121637598|ref|YP_977821.1| 138 LGRPQRAIELAR 149
                                    789999988876 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.4
                         TPR_10  15 rgrydeAe 22 
                                    +g++++A+
  gi|121637598|ref|YP_977821.1| 175 LGQLEQAL 182
                                    55555554 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0013
                         TPR_10   9 analrqrgrydeAealleeala 30 
                                    a +l ++gr+deA++++ ++ a
  gi|121637598|ref|YP_977821.1| 207 AEILLALGRGDEALQWFLRSAA 228
                                    67899***********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1783.06
//
Query:       gi|121637599|ref|YP_977822.1|  [L=353]
Description: phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-20   71.5   6.0    5.5e-20   71.5   6.0    2.4  2  GNAT_like       GCN5-related N-acetyltransferase like domain
    4.9e-18   65.1   0.1    1.2e-17   63.8   0.0    1.7  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    2.5e-16   59.5   0.1    6.9e-16   58.1   0.1    1.8  1  Hydrolase_like  HAD-hyrolase-like
    0.00039   20.8   0.7     0.0006   20.2   0.7    1.3  1  Hydrolase       haloacid dehalogenase-like hydrolase
     0.0095   16.0   0.0      0.021   14.9   0.0    1.5  1  HAD_2           Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> GNAT_like  GCN5-related N-acetyltransferase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6       2.1   7.6e+03      42      49 ..     137     144 ..     129     154 .. 0.56
   2 !   71.5   6.0   1.5e-23   5.5e-20       1      62 []     269     340 ..     269     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                      GNAT_like  42 rplrvdag 49 
                                    ++l+++ag
  gi|121637599|ref|YP_977822.1| 137 AALAIRAG 144
                                    33455555 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 1.5e-23
                      GNAT_like   1 cggWrvevdggaltvsgtga.......gdpldglRAlaaAvWa...aagdgrplrvdagDdaArkaLarlgL 62 
                                    ++gW+++v+gga+tv ++g+       +d+l+++RA+a+AvW+   a+ ++rplr++agD++Ar+aL+r++L
  gi|121637599|ref|YP_977822.1| 269 QPGWQIDVGGGAVTVCANGDvddlefiDDGLSIVRAVASAVWEaraADLHQRPLRIEAGDERARAALQRWSL 340
                                    8******************556799******************8888899*********************8 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   3.4e-21   1.2e-17       1     100 [.      11     108 ..      11     109 .. 0.96
   2 ?   -2.8   0.0       1.9   6.9e+03       5      29 ..     152     176 ..     148     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.4e-21
                                    EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH.SX CS
                    Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr.ka 79 
                                    +l+D+dG++  g+++  ga++ l ++r+++   +++TNn+s+s +e+a++l +lg+ +t e+vvtsa++aa++l+ +  +
  gi|121637599|ref|YP_977822.1|  11 LLIDLDGTVFCGRQPTGGAVQSLSQVRSRK---LFVTNNASRSADEVAAHLCELGFTATGEDVVTSAQSAAHLLAGQlAP 87 
                                    589************************996...7*****************************************99889 PP

                                    XXEEEEESXHHHHHHHHHTTX CS
                    Hydrolase_6  80 dkkvlvigeeglreelkeagf 100
                                    + +vl++g+e+l++e+ ++g+
  gi|121637599|ref|YP_977822.1|  88 GARVLIVGTEALANEVAAVGL 108
                                    ****************99997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                                    STTTSEETTEE-TTHHHHHHHHHHT CS
                    Hydrolase_6   5 idGvLwrgdkaipgaaealnalraa 29 
                                    +d +L  ++ ++pg   ++ alr a
  gi|121637599|ref|YP_977822.1| 152 VDPTLPTERGLLPGNGSMVAALRTA 176
                                    5667778889999999999999865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   1.9e-19   6.9e-16       2      74 ..     184     256 ..     183     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.9e-19
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHH..HHHHHT---SEEES CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedlee..pehkptyvaddlae 74 
                                    +gKP+p ++ +a+++   d+++ l++GDrl+tDi+gAn+aG+ s++VltGv+++ d+    p  +pty+  dl+ 
  gi|121637599|ref|YP_977822.1| 184 AGKPAPALMTEAVAR--GDFRAALVVGDRLDTDIEGANAAGLPSLMVLTGVNSAWDAVYaePVRRPTYIGHDLRS 256
                                    7*************9..699*******************************9986654422668*****999975 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.7   1.7e-07    0.0006       2     210 .]       9     222 ..       8     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.HHCHHHHHHHHHHHHHHHHH..HHHHHETTTEHHHHTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg.sehpigkalvaaakarsgal..tgfatfigrgayaigkpewlt 78 
                                    +++++D+dGT+  g++    +++s+   +++ l++  +    +  ++a  +++++    +++ t       a     +l+
  gi|121637599|ref|YP_977822.1|   9 DCLLIDLDGTVFCGRQPTGGAVQSLSQVRSRKLFVTnNASRSADEVAAHLCELGFTAtgEDVVT------SAQSAAHLLA 82 
                                    6899***********8888999999444444444444555666666666666644441233333......2222222222 PP

                                    HHHCHHHHHHHHHHHHHHCHHHHHH........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      Hydrolase  79 aldippdlgaaigsaqsqgrtvall........qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae. 149
                                     +   p  +  i   ++ + +va +        ++r +av+      + + ++aea  +++ ag  ++++ + +p+ +  
  gi|121637599|ref|YP_977822.1|  83 GQ-LAPGARVLIVGTEALANEVAAVglrpvrrfEDRPDAVVQGLSMTTGWSDLAEAALAIR-AGA-LWVAANVDPTLPTe 159
                                    22.34444445555555555555556777777788*******************8888877.777.66666666655553 PP

                                    HHHHH.TT.GGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                    xxxxx.xx.xxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 150 raanq.lG.ddyf.daviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                    r +    G + +      + d      +kp p  + +a+ +   +    ++VGD++  D++++ aAg
  gi|121637599|ref|YP_977822.1| 160 RGLLPgNGsMVAAlRTATGMD--PrvAGKPAPALMTEAVARGDFRA--ALVVGDRLDtDIEGANAAG 222
                                    666664554222213333333..256***************76666..******************8 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.9e-06     0.021     127     178 .]     178     228 ..     171     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                          HAD_2 127 tsedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                    +++     KP+p+++ +a+ + ++    +++vGD   tDie+a +ag+ +++v
  gi|121637599|ref|YP_977822.1| 178 GMDPRVAGKPAPALMTEAVARGDFR--AALVVGDRLdTDIEGANAAGLPSLMV 228
                                    55666678************99886..5799****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2502.04
//
Query:       gi|121637600|ref|YP_977823.1|  [L=58]
Description: hypothetical protein BCG_1731 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 450.33
//
Query:       gi|121637601|ref|YP_977824.1|  [L=268]
Description: cytotoxin/hemolysin TlyA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-22   80.3   0.0    2.3e-22   79.9   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
    1.5e-07   31.0   0.4    4.4e-07   29.5   0.1    2.0  2  S4               S4 domain
  ------ inclusion threshold ------
      0.049   14.3   0.0      0.091   13.4   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.062   14.0   0.0       0.13   13.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   5.2e-26   2.3e-22       1     175 [.      62     243 ..      62     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 5.2e-26
                                    CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....HHH..TTEEEE.CS-CCCS CS
                           FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....apl..pgvtti.qgditdp 73 
                                    ++sR+a+KL  ++e+f +   g++++D ga++Gg+++vll r ga ++vva D++ +    +++  p+v ++ +++ +  
  gi|121637601|ref|YP_977824.1|  62 WVSRGAHKLVGALEAFAIAVAGRRCLDAGASTGGFTEVLLDR-GA-AHVVAADVGYGqlawSLRndPRVVVLeRTNARGL 139
                                    69***************888**********************.88.9**********77763446699999999999888 PP

                                    SHHHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHH........CCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHH CS
                           FtsJ  74 etiekikealserkvdlvvsDgapdvsgvhdldeylq........sqLllaalelalkllkpggtfvlkifrgeeteall 145
                                    + +  i       +vdlvv+D++ ++s+ ++l++++         + L+++++e++  +++pgg++    +r +++ a++
  gi|121637601|ref|YP_977824.1| 140 TPEA-IG-----GRVDLVVADLS-FISLATVLPALVGcasrdadiVPLVKPQFEVGKGQVGPGGVVHDPQLRARSVLAVA 212
                                    6665.44.....37*********.************9*******99********************************** PP

                                    HH.HHCCEEEEEEEE-SS--CCG-EEEEEEE CS
                           FtsJ 146 kq.lkkfFekvsvvkPkssrsesseeflvcr 175
                                    ++  + ++++v v  ++  +++++ e+++++
  gi|121637601|ref|YP_977824.1| 213 RRaQELGWHSVGVKASPLPGPSGNVEYFLWL 243
                                    99666**********************9876 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   9.8e-11   4.4e-07       2      42 ..       6      46 ..       5      50 .. 0.92
   2 ?   -3.2   0.0       1.6   7.4e+03      35      46 ..     181     191 ..     181     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.8e-11
                                   EHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE CS
                             S4  2 RLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrV 42
                                   R d  l+r gla sr +A +lI +G+V+++G ++ +p++ V
  gi|121637601|ref|YP_977824.1|  6 RVDAELVRRGLARSRQQAAELIGAGKVRIDGLPAVKPATAV 46
                                   88999**************************9998888776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                                    E--TT-EE-TTC CS
                             S4  35 vkdpsyrVkpgD 46 
                                    vk p ++V+ g 
  gi|121637601|ref|YP_977824.1| 181 VK-PQFEVGKGQ 191
                                    67.999999986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.091       1      73 [.      87     159 ..      87     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.S.S-TT-EEEEEEES-CCC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl.p.fednsfDlvvssevlhh 73 
                                    Ld+G+ tG ++e l +rg a+vv+ D+   +l+++ ++ ++    v + + +a+ l p    + +Dlvv+  ++  
  gi|121637601|ref|YP_977824.1|  87 LDAGASTGGFTEVLLDRGaAHVVAADVGYGQLAWSLRNDPRV---VVLERTNARGLtPeAIGGRVDLVVADLSFIS 159
                                    8*******************************8887666665...4456666666544244578888888776655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.8e-05      0.13       2      71 ..      87     154 ..      86     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS..SSTTTEEEEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp..fedgsfDlvvss 71 
                                    Ld+G+ tG +t+ l++r g+a+v++ D+  ++l+   ++     +  v +++ +a+ l      g++Dlvv+ 
  gi|121637601|ref|YP_977824.1|  87 LDAGASTGGFTEVLLDR-GAAHVVAADVGYGQLAWSLRND----PrVVVLERTNARGLTpeAIGGRVDLVVAD 154
                                    9****************.69********999999877776....42444566667666522466788888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2126.46
//
Query:       gi|121637602|ref|YP_977825.1|  [L=307]
Description: inorganic polyphosphate/ATP-NAD kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-77  260.8   0.1    1.5e-77  260.7   0.1    1.0  1  NAD_kinase  ATP-NAD kinase
     0.0026   17.4   0.2     0.0065   16.1   0.2    1.7  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.7   0.1   1.7e-81   1.5e-77       2     291 ..       7     283 ..       6     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.7 bits;  conditional E-value: 1.7e-81
                                    EEEEESSCGGTCSHHHHHHHHHHHCT.-..EEEEECCGGCCSSSTT--HHHHTTTT--.......EEECCC-TTTTTSSS CS
                     NAD_kinase   2 vgivvnpikkeaieraeevarwLlda.lsrvlevtveeklgeslaeaaefrsevisvlkkvkttddtrkaleafadagvd 80 
                                    v++vv++ ++ea+e+a++v ++L d+ +  +l+v+ +e+++++  + a++++++++v+        +  +++++a +g++
  gi|121637602|ref|YP_977825.1|   7 VLLVVHTGRDEATETARRVEKVLGDNkI--ALRVLSAEAVDRGSLHLAPDDMRAMGVE-------IEVVDADQHAADGCE 77 
                                    89************************55..**************************99.......99************* PP

                                    EEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE......E CS
                     NAD_kinase  81 liivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskgeediadi 160
                                    l++v+GGDGT+l++a+l ++a+iPvlgvn+G++gfl+e e ea++ +le+++++++rve+r++ld+v++++ +      i
  gi|121637602|ref|YP_977825.1|  78 LVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGR------I 151
                                    *************************************************************************......* PP

                                    EEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS--- CS
                     NAD_kinase 161 viensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssr 240
                                    v++ ++lnev +++gp+  ++ + +++d+++++a+++dg++vstPtGstay++saGgp+++P+++ail+vp+++h+l  r
  gi|121637602|ref|YP_977825.1| 152 VNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGR 231
                                    ******************************************************************************** PP

                                    -EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                     NAD_kinase 241 piVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                    p+V s++ ++ i+++ ++++al+++dG++e+ ++ g +++vt++ +++k+ r
  gi|121637602|ref|YP_977825.1| 232 PMVTSPEATIAIEIEaDGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWAR 283
                                    ***********************************************99987 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   7.2e-07    0.0065      10      77 ..      13      97 ..       6     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.2e-07
                                   CTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTH...............HHHH..HHHHHHCC-SEEEEEESHHHHHHHHHH CS
                       DAGK_cat 10 sGkgkgekllrkvrelleeagvelelieteepgd...............akel..akeakeegvdlivvaGGDGtvsevlng 74
                                    G+ ++ +++r+v+++l ++++ l++   e  +                + e+  a +++++g +l++v+GGDGt+  +++ 
  gi|121637602|ref|YP_977825.1| 13 TGRDEATETARRVEKVLGDNKIALRVLSAEAVDRgslhlapddmramgvEIEVvdADQHAADGCELVLVLGGDGTFLRAAEL 94
                                   6788888888999999999999888888886666778888888888866333345777778899***********9888765 PP

                                   HCT CS
                       DAGK_cat 75 lle 77
                                     +
  gi|121637602|ref|YP_977825.1| 95 ARN 97
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2115.42
//
Query:       gi|121637603|ref|YP_977826.1|  [L=587]
Description: DNA repair protein recN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-15   54.9   0.0      1e-14   54.5   0.0    1.1  1  SMC_N     RecF/RecN/SMC N terminal domain
    1.5e-05   25.6   0.0    2.8e-05   24.7   0.0    1.4  1  AAA_23    AAA domain
    0.00012   22.4   0.4    0.00084   19.6   0.4    2.6  1  AAA_22    AAA domain
    0.00073   19.4   0.0       0.45   10.3   0.0    2.4  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.052   13.3   0.0          2    8.0   0.0    2.1  2  AAA_15    AAA ATPase domain
      0.075   13.5   1.2       0.14   12.6   0.1    2.0  2  Spectrin  Spectrin repeat
      0.078   13.2   0.0       0.27   11.5   0.0    1.9  2  CotJB     CotJB protein
      0.098   12.2   0.2       0.21   11.2   0.2    1.5  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.1   0.1       0.25   11.1   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   5.1e-18     1e-14       4     212 ..       4     535 ..       1     541 [. 0.91

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 5.1e-18
                                    EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT...TTTTTTCHCCCCCC--BTTCSSTTEEEE.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGer..sakklrseklsdlihkskekasvkkaev.. 79 
                                    +l+ie    +  + ++ +f+++ft+++G+ G GK+ ++  + ++LG +  +a+ +rs   ++++  + +   ++ a+v  
  gi|121637603|ref|YP_977826.1|   4 ELRIESLGAI--SVATAEFDRGFTVLTGETGTGKTMVVTGL-HLLGGAraDATRVRSGADRAVVEGRFTTTDLDDATVag 80 
                                    5666666666..467889***********************.99997623556778888888999955666666666611 PP

                                    .EEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT....................... CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                          SMC_N  80 .eitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske....................... 135
                                     + ++d ++++ + e+ +v   r+++r+g s+ ++ g+ v  k +s + ++     +                       
  gi|121637603|ref|YP_977826.1|  81 lQAVLDSSGAE-RDEDGSVIALRSISRDGPSRAYLGGRGVPAKSLSGFTNELLT-LHgqndqlrlmrpdeqrgaldrfaa 158
                                    15666777776.67777789999*********************9987666544.4447899****************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637603|ref|YP_977826.1| 159 ageavqryrklrdawltarrdlvdrrnrarelaqeadrlkfalneidtvdpqpgedvalvadiarlseldtlreaattar 238
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637603|ref|YP_977826.1| 239 atlcgtpdadafdrgavdslgraraalqssddaalrglaeqvgealtvvvdavaelgayldelpadasaldaklarqaql 318
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|121637603|ref|YP_977826.1| 319 rtltrkyaadidgvlrwadeararlaqldvseeglaalerrtgelahelgqaavdlstirrkaakrlakevsaelsalam 398
                                    ******************************************************************************** PP

                                    .........................................................CS-HHHHHHHHHHH..HHHHHCC CS
                                    .........................................................xxxxxxxxxxxxxx..xxxxxxx RF
                          SMC_N 136 .........................................................lLSgGektLvalaL..lfAiqkv 156
                                                                                             + SgGe + v+l+L  ++A+ + 
  gi|121637603|ref|YP_977826.1| 399 adaeftigvtteladhgdpvalalasgelaragadgvdavefgfvahrgmtvlplakSASGGELSRVMLSLevVLATSRK 478
                                    ***************************************************************98777665438888777 PP

                                    S--.SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 157 kpa.plyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                    + a   +++Deida        ++ ++l +   + Q+iv+++  ++ + ad  + v+
  gi|121637603|ref|YP_977826.1| 479 QAAgTTMVFDEIDAGVGGWAAVQIGRRLARLARTHQVIVVTHLPQVAAYADVHLMVQ 535
                                    76625789*************************************999999887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.4e-08   2.8e-05       2     195 ..       5     204 ..       4     233 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                         AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.......grgfeksdveiesegkvkay 74 
                                    L+ie ++ ++  + +F++g+t++tG++G+GKT ++  ++l  + ++  ++ +s       +++f + d   ++ +  +a+
  gi|121637603|ref|YP_977826.1|   5 LRIESLGAISVATAEFDRGFTVLTGETGTGKTMVVTGLHLLGGARADATRVRSgadravvEGRFTTTDLDDATVAGLQAV 84 
                                    78888999999999*************************97777665555544333333322233333322222333333 PP

                         AAA_23  75 velt..fenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefel.kdk 151
                                    ++ +   +++    + s+   r+ s++   ++    ++++  + l  f++ell+   ++ +l l+ ++e+   +++ ++ 
  gi|121637603|ref|YP_977826.1|  85 LDSSgaERDE----DGSVIALRSISRDGP-SRAYLGGRGVPAKSLSGFTNELLTLHGQNDQLRLMRPDEQRGALDRfAAA 159
                                    3333322222....345656666666544.44444556666677899999988888887777777777774333333445 PP

                         AAA_23 152 kerleelekelee.ledekkllekleqekekekeleeleeeleei 195
                                     e+++ ++k  +  l+++++l+++++++ e  +e + l+ +l+ei
  gi|121637603|ref|YP_977826.1| 160 GEAVQRYRKLRDAwLTARRDLVDRRNRARELAQEADRLKFALNEI 204
                                    556666666655555566666666666666666655555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.4   4.2e-07   0.00084       3      51 ..      20      74 ..      18     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-07
                         AAA_22  3 ktagilvvtGesGtGKTtllrrlleqldeeakaee....erpevv..fvtlpsst 51
                                   +++g++v+tGe+GtGKT+++  l+    ++a+a++    +++ vv  ++t + + 
  gi|121637603|ref|YP_977826.1| 20 FDRGFTVLTGETGTGKTMVVTGLHLLGGARADATRvrsgADRAVVegRFTTTDLD 74
                                   579*****************99999998888888887766666665655555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0028       5.6       1      33 [.      24      52 ..      24      88 .. 0.72
   2 !   10.3   0.0   0.00023      0.45     246     300 ..     470     523 ..     460     526 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdveglt 33
                                   ++vl+G  g+GK+ +   l ll ++    + + 
  gi|121637603|ref|YP_977826.1| 24 FTVLTGETGTGKTMVVTGLHLLGGA----RADA 52
                                   89*****************999765....2222 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                         AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                     +++a  r    g++ ++DE+++g   ++   + + l +l+r   Qvi++TH p 
  gi|121637603|ref|YP_977826.1| 470 EVVLATSRKQAAGTTMVFDEIDAGVGGWAAVQIGRRLARLAR-THQVIVVTHLPQ 523
                                    5677777777788************************99999.9********886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.001         2       1      45 [.       1      44 [.       1      65 [. 0.93
   2 ?    3.4   0.0     0.025        50     303     367 ..     463     523 ..     368     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                         AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl 45
                                   M +++++i+  ++++ ++ +++  +tvl G+ ++GK+ ++  l l
  gi|121637603|ref|YP_977826.1|  1 M-LTELRIESLGAISVATAEFDRGFTVLTGETGTGKTMVVTGLHL 44
                                   7.89999******************************99988765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.025
                         AAA_15 303 rllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                    + + l+l+ + a  +  k++   + +++E++a     a  ++ + l++la+++  Qvi+ TH p 
  gi|121637603|ref|YP_977826.1| 463 SRVMLSLEVVLATSR--KQAAGTTMVFDEIDAGVGGWAAVQIGRRLARLARTH--QVIVVTHLPQ 523
                                    556667777777766..777777888888888888888888889999******..*******765 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.8   5.5e+03      48      67 ..     178     197 ..     161     206 .. 0.58
   2 ?   12.6   0.1   7.2e-05      0.14       3      70 ..     322     388 ..     320     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.8
                                    HHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  48 aelaaqqervkalnelaekl 67 
                                    ++l ++++r ++l + a++l
  gi|121637603|ref|YP_977826.1| 178 RDLVDRRNRARELAQEADRL 197
                                    44555555555555555544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHT CS
                       Spectrin   3 lqqfaqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkaln.elaekllde 70 
                                     +++a d+d ++ W +e+++ l++ d+  + e++ al+++  +l +el ++   + ++  + a++l++e
  gi|121637603|ref|YP_977826.1| 322 TRKYAADIDGVLRWADEARARLAQLDV--SEEGLAALERRTGELAHELGQAAVDLSTIRrKAAKRLAKE 388
                                    589*******************99999..*****************************95555555444 PP

>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.8   1.4e+04      21      41 ..     153     173 ..     153     179 .. 0.71
   2 ?   11.5   0.0   0.00014      0.27      13      50 ..     290     327 ..     278     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.8
                          CotJB  21 LDthPddkealelfnkyskkr 41 
                                    LD +    ea++ ++k+++  
  gi|121637603|ref|YP_977826.1| 153 LDRFAAAGEAVQRYRKLRDAW 173
                                    677777788888888877665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                          CotJB  13 avvdlnLYLDthPddkealelfnkyskkrkelkkeYee 50 
                                    av +l  YLD  P d+ al++    ++++++l+++Y+ 
  gi|121637603|ref|YP_977826.1| 290 AVAELGAYLDELPADASALDAKLARQAQLRTLTRKYAA 327
                                    899*********************************87 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00011      0.21       3      47 ..      25      79 ..      23      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                   EEEEESTTCCHHHHHHHHH..........CT--SS-EEEEESS-SSCHCCCCCCH CS
                           cobW  3 tvltGflGsGKTtLlnhll..........enraglklavivNefgevsiDaellr 47
                                   tvltG  G+GKT++++ l           + r+g + av+++ f ++++D + ++
  gi|121637603|ref|YP_977826.1| 25 TVLTGETGTGKTMVVTGLHllggaradatRVRSGADRAVVEGRFTTTDLDDATVA 79
                                   89*************866556**99999989999****************99885 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.25      12      39 ..      13      39 ..       2      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                         AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                   ++  t+e+d +g+t+ltG++G+GK+ ++
  gi|121637603|ref|YP_977826.1| 13 ISVATAEFD-RGFTVLTGETGTGKTMVV 39
                                   555788999.789***********9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4007.48
//
Query:       gi|121637604|ref|YP_977827.1|  [L=393]
Description: hypothetical protein BCG_1735 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-18   64.5   4.5    1.7e-17   63.2   4.5    1.7  1  TPPK_C         Thiamine pyrophosphokinase C terminal
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.033   14.3   0.0    1.5  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   4.5   1.9e-21   1.7e-17       1      51 [.     334     384 ..     334     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.9e-21
                         TPPK_C   1 KGVsrLYrsrisggallllvlAaLvAvavallvspagqsfldllidtwnll 51 
                                    K+V++LYr++isgga++ll+l++L+A++val+vs +  ++l ++id+wn++
  gi|121637604|ref|YP_977827.1| 334 KAVATLYRNHISGGAIALLALTMLIAIIVALWVSRTDGVVLHWIIDYWNRF 384
                                    9************************************************98 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-06     0.033      11      62 ..     209     274 ..     201     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
                  TPK_catalytic  11 rvcaDgGanrlyeeekerlellpdvivGDlDSirpevke...................fyeskgteivkkp 62 
                                     v +  Ga  l+     +++++p++ivGD D i++ev++                   ++++ g+  +  p
  gi|121637604|ref|YP_977827.1| 209 LVGVGTGADVLR-----KAGYRPQLIVGDPDQISTEVLKcgaqvvlpadadghapgleRIQDLGVGAMTFP 274
                                    566667888888.....999*****************9955555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2649.26
//
Query:       gi|121637605|ref|YP_977828.1|  [L=314]
Description: hypothetical protein BCG_1736 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-93  313.2  18.3    2.7e-93  313.1  18.3    1.0  1  MctB      Copper transport outer membrane protein, MctB
  ------ inclusion threshold ------
       0.15   12.3   0.1       0.27   11.4   0.1    1.3  1  JIP_LZII  JNK-interacting protein  leucine zipper II


Domain annotation for each model (and alignments):
>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.1  18.3     3e-97   2.7e-93       1     305 [.       1     311 [.       1     312 [. 0.98

  Alignments for each domain:
  == domain 1  score: 313.1 bits;  conditional E-value: 3e-97
                           MctB   1 MIdfRyhlvSlvAvfLALavGivlGsgvlsdnlldtlegqveelreekeelraeadaleaqleaaddfaaavaprlvagr 80 
                                    MI++R+h+vSl+AvfLALa G+vlGsg+ sd+ll++l++++++l ++ ++l++++dal+++l+aad+f+ +v+ r+v+++
  gi|121637605|ref|YP_977828.1|   1 MISLRQHAVSLAAVFLALAMGVVLGSGFFSDTLLSSLRSEKRDLYTQIDRLTDQRDALREKLSAADNFDIQVGSRIVHDA 80 
                                    9******************************************************************************* PP

                           MctB  81 LtgrsVavvttpdadeedvdavtelleqAGAtvtgtvtltdkfvdpdeadklrslaaq.vlp.gaqlspeaadpgekaga 158
                                    L g+sV++++tpda ++d++av++ + qAG+ vt+tv+lt++fv++++a+klrs++++ +lp g qls++ +d+g++ag+
  gi|121637605|ref|YP_977828.1|  81 LVGKSVVIFRTPDAHDDDIAAVSKIVGQAGGAVTATVSLTQEFVEANSAEKLRSVVNSsILPaGSQLSTKLVDQGSQAGD 160
                                    **********************************************************9999****************** PP

                           MctB 159 llgaallt....aeeeasseeraavlaaLreaglvtv.edetvapadavvvvteaegstsedaekaaailarlaaalder 233
                                    llg all+    a++++++++r++vlaaLre+g++t+   + +  a+a vvvt   g+ s da++++ ++ar+aaal+ r
  gi|121637605|ref|YP_977828.1| 161 LLGIALLSnadpAAPTVEQAQRDTVLAALRETGFITYqPRDRIGTANATVVVT--GGALSTDAGNQGVSVARFAAALAPR 238
                                    ************999**********************88999***********..45679******************** PP

                           MctB 234 gagvVlaGragaaaeggliavvradealaaavSTVDnvdtaaGrvatvlAlaeqlagk.aGaYGtgegakall 305
                                    g+g+ laGr+g+a+  +++av rad+++aa++STVD++d ++Gr++++lAl++ ++g+ +G+YGtg+ga +++
  gi|121637605|ref|YP_977828.1| 239 GSGTLLAGRDGSANRPAAVAVTRADADMAAEISTVDDIDAEPGRITVILALHDLINGGhVGHYGTGHGAMSVT 311
                                    *********************************************************99**********9987 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     3e-05      0.27      28      62 ..      41      75 ..      36      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                       JIP_LZII 28 kddLIarvdeLtsereiLreEleslqkakerlesr 62
                                   k+dL +++d Lt +r++Lre l++  +   ++ sr
  gi|121637605|ref|YP_977828.1| 41 KRDLYTQIDRLTDQRDALREKLSAADNFDIQVGSR 75
                                   99*******************99987766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.60
# Mc/sec: 1579.30
//
Query:       gi|121637606|ref|YP_977829.1|  [L=586]
Description: CTP synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.3e-119  396.7   0.0   5.7e-119  396.3   0.0    1.2  1  CTP_synth_N    CTP synthase N-terminus
    3.4e-44  150.9   0.0    5.5e-44  150.2   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    2.2e-07   30.9   0.2    1.1e-06   28.6   0.1    2.2  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.043   13.9   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.3   0.0  1.3e-122  5.7e-119       1     265 []      10     278 ..      10     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 396.3 bits;  conditional E-value: 1.3e-122
                                    EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT-- CS
                    CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldik 80 
                                    k+++v+GGv+S+lGkG++a+slg+ll++rgl+vt++k+DPYlnvd+gt++p++hGEvfv++dGaetDlD+G+YeRfld +
  gi|121637606|ref|YP_977829.1|  10 KHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDVGHYERFLDRN 89 
                                    789***************************************************************************** PP

                                    --GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.H.C...T-SEEEEEE-S-TTSGGGHHHHHHH CS
                    CTP_synth_N  81 ltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakk.v...eadvviveigGtvgdieslpfleai 156
                                    l  + n+ttG++y++vi kerrG+ylG+tvqviph+tdeik+ri ++a+      ++dvvi+eigGtvgdies+pflea 
  gi|121637606|ref|YP_977829.1|  90 LPGSANVTTGQVYSTVIAKERRGEYLGDTVQVIPHITDEIKRRILAMAQPdAdgnRPDVVITEIGGTVGDIESQPFLEAA 169
                                    **********************************************9987446655************************ PP

                                    HHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEE CS
                    CTP_synth_N 157 rqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavis 236
                                    rq+++ lg+e+v+++hv+lvp+l+ +gelktkptqhsv +lrs+Gi+pd +++r++++++e++k+kial+c+v+ + vis
  gi|121637606|ref|YP_977829.1| 170 RQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHSVAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVIS 249
                                    ******************************************************************************** PP

                                    EE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                    CTP_synth_N 237 vkdvesiyevpllleeqglaelileklkl 265
                                    ++d+ siy++p++l++++l+ +++++l+l
  gi|121637606|ref|YP_977829.1| 250 TPDAPSIYDIPKVLHREELDAFVVRRLNL 278
                                    **************************987 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   0.0   1.2e-47   5.5e-44       2     188 ..     313     542 ..     312     544 .. 0.90

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 1.2e-47
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                    l D+y sv e+l   + + ++kve+ ++ ++  e+ +    +l +++g+l++gG+g +g+egki ai +ar +++P+LG 
  gi|121637606|ref|YP_977829.1| 313 LSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSgaaaALGDVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGL 392
                                    78*****************************999977776459************************************* PP

                                    THHHHHHHHHTTTEEE...........................EEECEEEEEEEEEEEETTT........CGGTTTTSEE CS
                         GATase  78 CLGmQllaiefgrkvv...........................kekekehhggtmrlgddet........allyglknev 122
                                    CLG+Q+++ie +r+v                             +  + ++ggtmrlg++++        a++y++  +v
  gi|121637606|ref|YP_977829.1| 393 CLGLQCIVIEAARSVGltnansaefdpdtpdpviatmpdqeeiVAG-EADLGGTMRLGSYPAvlepdsvvAQAYQT-TQV 470
                                    *************666666666666666666666888888887778.89*********************999999.999 PP

                                    EEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT...T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                         GATase 123 ierhrHryevnpk...elepaglevtakseddeelmeiiekkn...p.fvgvQFHPEststpegpellfnfli 188
                                     erhrHryevn++   ++ ++gl+++++s d+ +l+e++e +    p +vg+Q HPE +s+p++p++lf  ++
  gi|121637606|ref|YP_977829.1| 471 SERHRHRYEVNNAyrdKIAESGLRFSGTSPDG-HLVEFVEYPPdrhPfVVGTQAHPELKSRPTRPHPLFVAFV 542
                                    ***********99****************998.688887754335699*********************9887 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.82   3.7e+03      51      67 ..     350     366 ..     345     370 .. 0.82
   2 !   28.6   0.1   2.5e-10   1.1e-06      98     216 .]     379     526 ..     374     526 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.82
                  Peptidase_C26  51 dvkaildkldgllltGg 67 
                                     ++a+l  ++g+l++Gg
  gi|121637606|ref|YP_977829.1| 350 GAAAALGDVHGVLIPGG 366
                                    56788999********9 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.5e-10
                  Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.................q.....saashavkvek 155
                                    i+ a +rg+P+lg C+Glq + +    ++     + s++ d   ++                 +        s    +e+
  gi|121637606|ref|YP_977829.1| 379 IAYARARGLPVLGLCLGLQCIVIEAARSVGLTNAN-SAEFDPDTPDpviatmpdqeeivageaDlggtmRLGSYPAVLEP 457
                                    5668899*************988665444433332.2222222222346667777766666551445557778888899* PP

                  Peptidase_C26 156 gsllaellgseeievnslHhqaike......laeelrveAvaeDg.viEaieseeak.afvlgvQwHPE 216
                                    +s++a+++++++++    H+  +++       +++lr + +++Dg ++E++e + ++  fv+g Q HPE
  gi|121637606|ref|YP_977829.1| 458 DSVVAQAYQTTQVSERHRHRYEVNNayrdkiAESGLRFSGTSPDGhLVEFVEYPPDRhPFVVGTQAHPE 526
                                    ********999988899999999989999978889********9867*****9876659*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-06     0.043       8      55 ..      20     118 ..      15     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                                    TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                           CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................. 54 
                                    +  GK  +a +L+++l  rgl+V + ++Dp  n +    g+ n  +                                  
  gi|121637606|ref|YP_977829.1|  20 SSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDP---GTMNPFQHgevfvtedgaetdldvghyerfldrnlpgsanv 96 
                                    677***************************999887...55554444555555555555665555555555555555555 PP

                                    .....................C CS
                                    .....................x RF
                           CbiA  55 .....................d 55 
                                                         +
  gi|121637606|ref|YP_977829.1|  97 ttgqvystviakerrgeylgdT 118
                                    5555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3929.57
//
Query:       gi|121637607|ref|YP_977830.1|  [L=207]
Description: hypothetical protein BCG_1738 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-13   48.4   0.2    1.6e-12   47.6   0.2    1.4  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.2   8.9e-17   1.6e-12       5     116 ..      45     156 ..      41     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 8.9e-17
                                    EEEEEEEETTSEEEEEEESSSSTTT...EESSEEECB.TTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   5 avgvvllnekgevLlvrrskkpfpg...WelPgGkve.pgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                    av++v ++++g + +v ++ +++ g   WelP+G ++ +gE p  +A+REl+EE+Gl+a ++++l +l++    +g+ + 
  gi|121637607|ref|YP_977830.1|  45 AVAIVAMDDNGNIPMVYQY-RHTYGrrlWELPAGLLDvAGEPPHLTAARELREEVGLQASTWQVLVDLDT---APGFSD- 119
                                    89999*******7777777.5555557**********6699999***************99999995544...333333. PP

                                    EEEEEEEEE.EEECSGCSSTSTTTEEEEE..EEEHHHHH CS
                          NUDIX  81 eheilyvfl.eevegelepndenevsevr..wvpleell 116
                                    e   +y+ +  ++ g++e    +e ++    w+p++e++
  gi|121637607|ref|YP_977830.1| 120 ESVRVYLATgLREVGRPEAH--HEEADMTmgWYPIAEAA 156
                                    44455555555555554444..555555346*****993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1449.62
//
Query:       gi|121637608|ref|YP_977831.1|  [L=311]
Description: site-specific tyrosine recombinase XerD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-46  157.4   0.0    4.4e-46  156.8   0.0    1.3  1  Phage_integrase  Phage integrase family
    1.1e-25   89.7   0.1      3e-25   88.3   0.1    1.8  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
     0.0062   17.0   0.0      0.012   16.1   0.0    1.5  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.024   14.7   0.5       0.14   12.3   0.1    2.4  2  Integrase_1      Integrase


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.8   0.0   9.9e-50   4.4e-46       2     169 ..     120     294 ..     119     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.8 bits;  conditional E-value: 9.9e-50
                                    HHHHHHHHHHHHCCGC......HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHH CS
                Phage_integrase   2 vltedeverllaalee......slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplsee 75 
                                     lt dev +ll+ +        +l +r++++lelly+tG+RisE+++L+++d+d+  + +l+   +gKg+k+r vp+++ 
  gi|121637608|ref|YP_977831.1| 120 SLTIDEVLSLLEGAGGdkpsdgPLTLRNRAVLELLYSTGARISEAVGLDLDDIDTHARSVLL---RGKGGKQRLVPVGRP 196
                                    57889999999988878888899***************************************...*************** PP

                                    HHHHHHHHHHHH....CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHH CS
                Phage_integrase  76 alellkellska....leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvv 151
                                    a+++l  +l +      ++  ++ ++f+++rg +lsrq+++++++ a+e+agi+  ++pH+lRhsfat+Lle g+d+rvv
  gi|121637608|ref|YP_977831.1| 197 AVHALDAYLVRGrpdlARRGRGTAAIFLNARGGRLSRQSAWQVLQDAAERAGITAGVSPHMLRHSFATHLLEGGADVRVV 276
                                    ************999888889999******************************************************** PP

                                    HHHHT-SSCCHHHHHHCC CS
                Phage_integrase 152 qkllGHssisttqiYthv 169
                                    q+llGH+s+ ttqiYt v
  gi|121637608|ref|YP_977831.1| 277 QELLGHASVTTTQIYTLV 294
                                    ***************976 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.1   6.6e-29     3e-25       1      84 []       8      98 ..       8      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 6.6e-29
                                   HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----.......-----HHHHHHHHHH CS
                Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg.......lsatslarrlsalrs 75
                                   l+++l++L++erg+++nTl++YrrdLrr++k+l+erg+ +l++++++dv++fl++l++ +       lsa s+ar+l+a+r+
  gi|121637608|ref|YP_977831.1|  8 LQGYLDHLTIERGVAANTLSSYRRDLRRYSKHLEERGITDLAKVGEHDVSEFLVALRRGDpdsgtaaLSAVSAARALIAVRG 89
                                   789*******************************************************99********************** PP

                                   HHHHHHHTT CS
                Phage_int_SAM_1 76 Ffqflvreg 84
                                   +++f+ +eg
  gi|121637608|ref|YP_977831.1| 90 LHRFAAAEG 98
                                   *****9997 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.7e-06     0.012       5      67 ..      11      83 ..       7     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                Phage_int_SAM_4  5 frealrl.aglserTiksYlsaikrflrflkkk...apeeltkedieaYlnyLanerk.......lsastqkna 67
                                   ++++l+  +g + +T  sY + ++r+ ++l+++     ++++++d+ ++l  L++          lsa ++ +a
  gi|121637608|ref|YP_977831.1| 11 YLDHLTIeRGVAANTLSSYRRDLRRYSKHLEERgitDLAKVGEHDVSEFLVALRRG-DpdsgtaaLSAVSAARA 83
                                   55666666899999999************998877777888999999999999833.23555555555555555 PP

>> Integrase_1  Integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     3e-05      0.14      35     148 ..     149     264 ..     145     265 .. 0.65
   2 ?   -2.8   0.0       1.4   6.1e+03     130     147 ..     287     304 ..     282     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                    Integrase_1  35 avlqLarvlGLRseEAvqlakslktWkkaLergeerlrvvfGTKGgrpRevtile.............realksava.la 100
                                    avl+L ++ G R  EAv l        ++++  +    v    KGg++R v++               r  l++  + +a
  gi|121637608|ref|YP_977831.1| 149 AVLELLYSTGARISEAVGLD------LDDIDTHAR--SVLLRGKGGKQRLVPVGRpavhaldaylvrgRPDLARRGRgTA 220
                                    77888888888888888885......233333222..3444459999999998877655555555555333333222123 PP

                    Integrase_1 101 ikvaeernGkLidkpdlslipdryreilrrlgltgessphslRyayaq 148
                                        + r+G+L    +++++ ++++  ++r+g+t+ +sph lR+++a 
  gi|121637608|ref|YP_977831.1| 221 AIFLNARGGRL----SRQSAWQVLQDAAERAGITAGVSPHMLRHSFAT 264
                                    33445555655....567777799999999****************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                    Integrase_1 130 rlgltgessphslRyaya 147
                                     +++   + +h+lR  +a
  gi|121637608|ref|YP_977831.1| 287 TTQIYTLVTVHALREVWA 304
                                    457778889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1940.49
//
Query:       gi|121637609|ref|YP_977832.1|  [L=454]
Description: hypothetical protein BCG_1740c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-106  354.8   7.9   5.1e-106  354.6   7.9    1.1  1  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.6   7.9  2.8e-110  5.1e-106       1     301 []      36     361 ..      36     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 354.6 bits;  conditional E-value: 2.8e-110
                         DUF222   1 llaaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........L 69 
                                    +la+l+++e+++rrl+a+e+ ++++la++++++e g++ +  ++a+rl+isr+eAsrr+++A++l++r           L
  gi|121637609|ref|YP_977832.1|  36 CLAMLQRCEKIRRRLPAAEHPFINKLADQTDQTELGGK-LPFALAERLHISRGEASRRIHEAADLGPRrtltgqplpplL 114
                                    5789**********************************.***************************************** PP

                         DUF222  70 pavaaalraGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarr 149
                                    +a+aaa+raG+++  +v+vI++++++lp++vdl+t++kaea+l++   +++p++L+kl+++l+++l+pDg+++d+++arr
  gi|121637609|ref|YP_977832.1| 115 TATAAAQRAGHLGPAHVQVIRCFLHQLPHHVDLPTREKAEAELATLGGRFRPDQLHKLATKLADCLNPDGNYNDTDRARR 194
                                    ******************************************************************************** PP

                         DUF222 150 reltltk.dedGmsrisgeldaeaaaaldavLdslaap.vcap..............dgtkDpRspaqrraDALlallrl 213
                                    r++ l++ + dGms+isg+l++ea+a++davL++laap + +p              +++ D+Rs+ qr++D+Lla+lr+
  gi|121637609|ref|YP_977832.1| 195 RSIILGNqGPDGMSAISGYLTPEARATVDAVLAKLAAPgMANPaddtpclagtpsqaAIEADTRSAGQRHHDGLLAALRA 274
                                    **************************************99999************************************* PP

                         DUF222 214 alaagaldchagvpatvvvhvtaeeltaaaggaaltgggglLpasdvrrLAkdAt..laifdepagrpldlgrtkrtasa 291
                                    +l++g+l++h+g+pa ++v+++++el+++ag+ altggg+lLp+sdv+rLA++A+  l+ifd+  gr l+l++tkr+as+
  gi|121637609|ref|YP_977832.1| 275 LLCSGELGQHNGLPAAIIVSTSLTELQSRAGH-ALTGGGTLLPMSDVIRLASHANhyLRIFDH--GRELALYHTKRLASP 351
                                    ********************************.**********************9999**99..*************** PP

                         DUF222 292 alrralraRD 301
                                    ++r++l+a+D
  gi|121637609|ref|YP_977832.1| 352 GQRIVLYAKD 361
                                    *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3061.49
//
Query:       gi|121637610|ref|YP_977833.1|  [L=196]
Description: catechol-o-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-15   56.0   0.0    3.4e-15   55.8   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    6.8e-13   49.6   0.2    9.6e-13   49.1   0.2    1.2  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.041   14.0   0.0      0.063   13.4   0.0    1.2  1  DUF531           Protein of unknown function (DUF531)
      0.084   13.6   0.0       0.14   12.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   7.7e-19   3.4e-15      22     159 ..      11     151 ..       1     169 [. 0.87

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7.7e-19
                                    TST.TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGE CS
                 Methyltransf_3  22 kktdlsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaeki 101
                                    +k     ++v+ ++g +L+  v+  +    le+G++ Gys+L +a a Pe  ++ +++  + ++  a++++ +agv++++
  gi|121637610|ref|YP_977833.1|  11 EKS--MLINVGDEKGTLLDAAVRRADPALALELGTYLGYSALRIARAAPE-ARVYSVELAEANASNARRIWAHAGVDDRV 87 
                                    443..45689999***********************************98.69**************************9 PP

                                    EEEE...S-HHHHHHHHHTSSS.---EEEEEE-S-GGGHHHHHHHHHH..TEEEEEEEEEE-TT CS
                 Methyltransf_3 102 elie...gdalkvLeelvkdkk.lpefDfifvDaDkssyvnyyeklle..LvkvGgliaiDntL 159
                                       +   gd+ ++L+ l+++   ++ +Df+f+D Dk++y    + +l+   ++ G +++ Dn+ 
  gi|121637610|ref|YP_977833.1|  88 VCVVgtiGDGGRTLDALTEHGFaTGTLDFVFLDHDKKAYLPDLQSILDrgWLHPGSIVVADNVR 151
                                    8765222799*********997699**************9999999974469999999999985 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   2.2e-16   9.6e-13       1     106 []      39     150 ..      39     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.2e-16
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikads......eealasla.....ag 68 
                                    +E+G+y G+s+l ++ra+ +++   +++v+  ++ a++a+++++ ag+ddrv  ++++        +al         +g
  gi|121637610|ref|YP_977833.1|  39 LELGTYLGYSALRIARAAPEAR---VYSVELAEAnASNARRIWAHAGVDDRVVCVVGTIgdggrtLDAL---TehgfaTG 112
                                    7****************99986...89999977656779999999***********9996665554444...144477** PP

                Methyltransf_24  69 siDllfiDgghaaeavledleallp..rlapggvvlfdDi 106
                                    + D++f+D  h+++a+l+dl+ +l+  +l+pg++v+ d++
  gi|121637610|ref|YP_977833.1| 113 TLDFVFLD--HDKKAYLPDLQSILDrgWLHPGSIVVADNV 150
                                    ********..99***********97558*********985 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.063      23      75 ..      52     108 ..      47     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                         DUF531  23 iARaapicyafdfnLalldFplk...keekelvdvva.ekttiGesGkylkelaekn 75 
                                    iARaap + +++++La  + +       +  + d v+    tiG+ G+ l +l+e++
  gi|121637610|ref|YP_977833.1|  52 IARAAPEARVYSVELAEANASNArriWAHAGVDDRVVcVVGTIGDGGRTLDALTEHG 108
                                    9***************9998776444356667776553899************9976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05      0.14       2      71 ..      39     120 ..      38     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC....CGBS......SSTTTEEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda....edlp......fedgsfDlvv 69 
                                    L+lG+  G  +l++a++ ++a+v+ v+++e+   +ar+  +++g+  +v +v+g +    ++l+      f+ g+ D+v+
  gi|121637610|ref|YP_977833.1|  39 LELGTYLGYSALRIARAAPEARVYSVELAEANASNARRIWAHAGVddRVVCVVGTIgdggRTLDaltehgFATGTLDFVF 118
                                    8999999**********999**********************99999888888877444533433334456777777777 PP

                                    EE CS
                Methyltransf_25  70 ss 71 
                                    + 
  gi|121637610|ref|YP_977833.1| 119 LD 120
                                    64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1472.94
//
Query:       gi|121637611|ref|YP_977834.1|  [L=556]
Description: D-serine/alanine/glycine transporter protein cycA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-97  326.2  45.2    3.7e-97  325.9  45.2    1.1  1  AA_permease    Amino acid permease
      6e-42  144.0  53.2    7.7e-42  143.6  53.2    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.9  45.2  4.1e-101   3.7e-97       1     431 [.      25     433 ..      25     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: 325.9 bits;  conditional E-value: 4.1e-101
                    AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                    h+++ia+gg+iGtglf+g+g ++s aGp +++++y ++g+++f+v +++ge+   + +  +f  +a++ lgp++Gf++G+
  gi|121637611|ref|YP_977834.1|  25 HIQLIAIGGAIGTGLFMGSGRTISLAGP-AVMVVYGIIGFFVFFVLRAMGELLLSNLNYKSFVDFAADLLGPAAGFFVGW 103
                                    99**************************.99************************************************* PP

                    AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivg.ii 159
                                    +y+f w+++ +++l+a+ ++  fw   + lp +wv ++v+++++l++nl++v+ +ge ef++alik+ ai+ +i vg i 
  gi|121637611|ref|YP_977834.1| 104 SYWFAWVVTGIADLVAITSYARFW--WPGLP-IWVPALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGaIL 180
                                    ************************..*****.*********************************************655 PP

                    AA_permease 160 llaggkpnkga..gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkail 237
                                    + ++    +g   ++++l+++ +    ++p g        f++++s+f+i++fa+ G elv+++a+E++dP++++P+ai+
  gi|121637611|ref|YP_977834.1| 181 VATNFVSPHGVhaTIENLWNDNG----FFPTG--------FLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAIN 248
                                    55555555555555656555555....7****........**************************************** PP

                    AA_permease 238 qvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlys 317
                                     v +r+++fY+++ll+i ++vp+    + +      spfv++++ +g++++a+++n+v+ taa ssans+ +s+ R+l+ 
  gi|121637611|ref|YP_977834.1| 249 AVPLRVAVFYIGALLAILAVVPWRQFASGE------SPFVTMFSLAGLAAAASVVNFVVVTAAASSANSGFFSTGRMLFG 322
                                    *************************66666......9******************************************* PP

                    AA_permease 318 lakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyq 397
                                    la++g+aP+ +  ++++gvP+ a+ll++ + l ++ l ++  ++  +f+ + ++s l +++vw +ii+syl++R+    +
  gi|121637611|ref|YP_977834.1| 323 LADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRR---H 399
                                    ***********************************8888888888*******************************...6 PP

                    AA_permease 398 grsieelgfkaallplgvilvlaaliiillilal 431
                                      ++ ++ +k+++++ +++ vl+++ +++ +l+ 
  gi|121637611|ref|YP_977834.1| 400 PQRHTDSVYKMPGGVVMCWAVLVFFAFVIWTLTT 433
                                    666679******************9999877665 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6  53.2   8.6e-46   7.7e-42       8     418 ..      28     449 ..      25     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 8.6e-46
                  AA_permease_2   8 alvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaEl..ssalprsgGiyvytkaafgkkvaflsawf 83 
                                    +++ig +ig+g f+ +   +  +gpa+++++ i+ + + + vl ++ El  s+   + +  + +++ + g+ ++f+++w+
  gi|121637611|ref|YP_977834.1|  28 LIAIGGAIGTGLFMGSgrTISLAGPAVMVVYGIIGFFV-FFVLRAMGELllSN--LNYKSFVDFAADLLGPAAGFFVGWS 104
                                    589************99777779999776666655555.46999999998777..66778999***************** PP

                  AA_permease_2  84 nwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilg 163
                                    +wfa+v++  +   va+ +++ ++ p l     ++ + a + ++l+ ++n++++++ + + ++ +++k+   ++ li++g
  gi|121637611|ref|YP_977834.1| 105 YWFAWVVTG-IADLVAITSYARFWWPGL-----PIWVPALVTVALILAVNLFSVRHFGELEFWFALIKV-AAIVCLIAVG 177
                                    *******88.555666666677675766.....4556666778888899********************.699******* PP

                  AA_permease_2 164 litvdgggfssl........stetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvl 233
                                     i+v  +  s +         ++++ ffp+g  gv++g+ i++++++G+e +   + e  ++++++p+ai+ + l v+v+
  gi|121637611|ref|YP_977834.1| 178 AILVATNFVSPHgvhatienLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAEtaDPRRTLPRAINAVPLRVAVF 257
                                    ****99887766777766553333349999999*************************877779**************** PP

                  AA_permease_2 234 yllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffa 313
                                    y++  +a+l+vvp+ ++a+ ++   ++  +f  +g  ++a++v+++++ +++ ++n+ ++++ r+l+ la +g  P  f+
  gi|121637611|ref|YP_977834.1| 258 YIGALLAILAVVPWRQFASGES---PFVTMFSLAGLAAAASVVNFVVVTAAASSANSGFFSTGRMLFGLADEGHAPAAFH 334
                                    ******************7554...699**************************************************** PP

                  AA_permease_2 314 kvnkfgspiraiiltaivslillllfllas...saaynfllsvsslgliisyllliigalilrkkrphlkr......pgk 384
                                    + n+ g p  a+ lta +  + ++ +l+a      a++++++vssl+++++++++ii++l++r++ p++ +      pg 
  gi|121637611|ref|YP_977834.1| 335 QLNRGGVPAPALLLTAPLL-LTSIPLLYAGrsvIGAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTdsvykmPGG 413
                                    ****************995.7888888777677789*******************************9966675434555 PP

                  AA_permease_2 385 ilvaiigalfllfllvalffppkgpa..tqssliyt 418
                                    +++ +  ++f+ f++ +l   +++++  ++++l++ 
  gi|121637611|ref|YP_977834.1| 414 VVMCWAVLVFFAFVIWTLTTETETATalAWFPLWFV 449
                                    555555555555555555544444444566665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3627.54
//
Query:       gi|121637612|ref|YP_977835.1|  [L=385]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-64  214.6  25.9    7.7e-64  214.6  25.9    3.0  3  PPE       PPE family
    1.4e-23   83.6  11.4    1.4e-23   83.6  11.4    5.6  5  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6  25.9   8.5e-68   7.7e-64       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?    1.9   2.3     0.024   2.2e+02      18      50 ..     174     206 ..     169     237 .. 0.69
   3 ?   -0.1   0.6       0.1     9e+02      48      65 ..     267     284 ..     261     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 8.5e-68
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPEvns ++y Gpgs+p++aAa+aW+gLaael+ aa  +e+v+++l++e+W Gp+s+ m++a+apy+aW++a+a qae
  gi|121637612|ref|YP_977835.1|   5 ALPPEVNSGRMYCGPGSAPMVAAASAWNGLAAELSVAAVGYERVITTLQTEEWLGPASTLMVEAVAPYVAWMRATAIQAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA+qa+aaaaaYe+A+aa+vpp++iaanra+l++lv+ n+fGqnt++Iaatea+y+emwaqda am++Y+ +sa+a
  gi|121637612|ref|YP_977835.1|  85 QAASQARAAAAAYETAFAAIVPPPLIAANRARLTSLVTHNVFGQNTASIAATEAQYAEMWAQDAMAMYGYAGSSATA 161
                                    *************************************************************************9987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT. CS
                            PPE  18 gpllaAaaaWdgLaaelasaaaelesvlaelaa 50 
                                    ++ +aAa++++++a+   ++a + +s +ael a
  gi|121637612|ref|YP_977835.1| 174 TSPSAAATQLSAVAKAAGTSAGAAQSAIAELIA 206
                                    667889999999999999988888888888863 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.1
                                    TT.TTS-SHHHHHHHHHT CS
                            PPE  48 laaeaWqGpssaamaaaa 65 
                                     +a  W Gp +a++aaaa
  gi|121637612|ref|YP_977835.1| 267 WRALGWIGPEAAEAAAAA 284
                                    555566676666666654 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.5      0.25   2.2e+03      35      56 ..      21      42 ..       4      55 .. 0.59
   2 ?   -8.5  14.1         2   1.8e+04      19      62 ..      75     117 ..      55     169 .. 0.67
   3 ?   -6.6  14.1         2   1.8e+04      14      60 ..     168     197 ..     144     230 .. 0.51
   4 ?    0.2   3.5      0.16   1.4e+03      40      55 ..     277     293 ..     264     298 .. 0.38
   5 !   83.6  11.4   1.5e-27   1.4e-23       1      80 []     299     381 ..     299     381 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                       PE_PPE_C 35 gttaaaaaaaagaalggmPlaa 56
                                   +++++aaa+a++++++ + +aa
  gi|121637612|ref|YP_977835.1| 21 SAPMVAAASAWNGLAAELSVAA 42
                                   3334444444444444444443 PP

  == domain 2  score: -8.5 bits;  conditional E-value: 2
                       PE_PPE_C  19 WaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagagga 62 
                                    W + a a++a  aa ++ +aaaa ++a aa+   Pl aa +++ 
  gi|121637612|ref|YP_977835.1|  75 W-MRATAIQAEQAASQARAAAAAYETAFAAIVPPPLIAANRARL 117
                                    5.334444444444444444444444444444555555555444 PP

  == domain 3  score: -6.6 bits;  conditional E-value: 2
                       PE_PPE_C  14 SVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagag 60 
                                      Pp+ +++++aa+++                 +a++ +++++aga+
  gi|121637612|ref|YP_977835.1| 168 APPPNTTSPSAAATQL-----------------SAVAKAAGTSAGAA 197
                                    2222222222222221.................22222222222222 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.16
                       PE_PPE_C  40 aaaaaagaalg.gmPla 55 
                                    aa+aaa+a ++ g++++
  gi|121637612|ref|YP_977835.1| 277 AAEAAAAAPAAvGAAVG 293
                                    11111111111122222 PP

  == domain 5  score: 83.6 bits;  conditional E-value: 1.5e-27
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasa...aaaal.....sgttaaaaaaaagaalggmPlaaagaggaaggaaprygf 72 
                                    sAglG+Aat+G+LSVPp+Wa+a+p++++   +   +     s+++++++a+aag++lggmPla++g+g++  ga+prygf
  gi|121637612|ref|YP_977835.1| 299 SAGLGNAATIGKLSVPPNWAGASPSLAPtvgS---AsaplvSDIVEQPEAGAAGNLLGGMPLAGSGTGTG--GAGPRYGF 373
                                    8**********************999995540...334446**********************9999999..******** PP

                       PE_PPE_C  73 rptvmprp 80 
                                    r tvm+rp
  gi|121637612|ref|YP_977835.1| 374 RVTVMSRP 381
                                    *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2908.60
//
Query:       gi|121637613|ref|YP_977836.1|  [L=394]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-63  212.2  25.2    4.1e-63  212.2  25.2    2.4  2  PPE       PPE family
    6.3e-11   43.0  12.9    6.3e-11   43.0  12.9    5.8  5  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.2  25.2   4.5e-67   4.1e-63       1     157 [.      41     198 ..      41     199 .. 0.97
   2 ?   -5.1   8.0         2   1.8e+04      24      80 ..     300     357 ..     280     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 212.2 bits;  conditional E-value: 4.5e-67
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT..TTS-SHHHHHHHHHTHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaa.eaWqGpssaamaaaaapylaWLsaaaaqa 79 
                                    alpPE+ns ++y+Gpgsgpl+aAaaaWdgLaael+saa+ + + ++el++   W+Gp+s++m+aa++p++ WLs++a+ a
  gi|121637613|ref|YP_977836.1|  41 ALPPEINSGRMYSGPGSGPLMAAAAAWDGLAAELSSAATGYGAAISELTNmRWWSGPASDSMVAAVLPFVGWLSTTATLA 120
                                    79**********************************************9615689************************* PP

                                    HHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  80 eeaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    e+aA+qa+aaaaa+eaA+a++vpp+ iaanr+ l++lv tn+fGqntpaIa+te +y+emwaqdaaam++Y++a+a a
  gi|121637613|ref|YP_977836.1| 121 EQAAMQARAAAAAFEAAFAMTVPPPAIAANRTLLMTLVDTNWFGQNTPAIATTESQYAEMWAQDAAAMYGYASAAAPA 198
                                    *************************************************************************99876 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHHHHHHHHHTTTT..TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE  24 aaaWdgLaaelasaaaelesvlaela.aeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                     +aW++L a   +a a+l++ +  ++    W+ p ++  a+ +a+ +  ++ aa+ ae
  gi|121637613|ref|YP_977836.1| 300 WSAWSQLGAGPVAASATLAAKIGPMSvPPGWSAPPATPQAQTVARSIPGIRSAAEAAE 357
                                    479***************9999987734689999999999999988888888877776 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -12.2  18.7         2   1.8e+04       5      60 ..      80     136 ..      35     157 .. 0.61
   2 ?   -6.8  12.8         2   1.8e+04      34      61 ..     203     230 ..     157     237 .. 0.51
   3 ?    2.9   1.9     0.024   2.2e+02       4      25 ..     217     238 ..     214     256 .. 0.92
   4 ?   -5.0  10.7         2   1.8e+04      19      57 ..     278     314 ..     266     316 .. 0.54
   5 !   43.0  12.9     7e-15   6.3e-11       1      78 [.     312     388 ..     312     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: -12.2 bits;  conditional E-value: 2
                       PE_PPE_C   5 GqAatvGaLSVPpsWaaaapaasa.aaaal.sgttaaaaaaaagaalggmPlaaagag 60 
                                    G +a++ +L     W+++a+  +  a+     g+  ++a+ a +aa+++ ++aaa ++
  gi|121637613|ref|YP_977836.1|  80 GYGAAISELTNMRWWSGPASDSMVaAVL-PfVGWLSTTATLAEQAAMQARAAAAAFEA 136
                                    5555555555555564444332220222.23444444444444444443333222222 PP

  == domain 2  score: -6.8 bits;  conditional E-value: 2
                       PE_PPE_C  34 sgttaaaaaaaagaalg....gmPlaaagagg 61 
                                    + ++++ +++a     g    ++++aa+ +++
  gi|121637613|ref|YP_977836.1| 203 PFAPPPQTTNAT----GlvghATAVAALRGQH 230
                                    222222222222....1232355555554444 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.024
                       PE_PPE_C   4 lGqAatvGaLSVPpsWaaaapa 25 
                                    +G+A++v aL   +sWaaa+p 
  gi|121637613|ref|YP_977836.1| 217 VGHATAVAALRGQHSWAAAIPW 238
                                    8******************996 PP

  == domain 4  score: -5.0 bits;  conditional E-value: 2
                       PE_PPE_C  19 WaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaa 57 
                                    W++a ++a aa aa+++   aa+ +a+++++ + P+aa+
  gi|121637613|ref|YP_977836.1| 278 WSTALAEAGAAEAAAGAG-GAAGWSAWSQLG-AGPVAAS 314
                                    555555544444444333.334444444433.5555554 PP

  == domain 5  score: 43.0 bits;  conditional E-value: 7e-15
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsW..aaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmp 78 
                                    +A++  Aa++G +SVPp W    a+p+a+++a++++g+  aa+aa+ +++l g+P+ + +++++    + ryg+r tvm+
  gi|121637613|ref|YP_977836.1| 312 AASATLAAKIGPMSVPPGWsaPPATPQAQTVARSIPGIRSAAEAAETSVLLRGAPTPGRSRAAH---MGRRYGRRLTVMA 388
                                    689999*************6556779999999999*********************88888888...************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2826.59
//
Query:       gi|121637614|ref|YP_977837.1|  [L=55]
Description: hypothetical protein BCG_1745c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 422.49
//
Query:       gi|121637615|ref|YP_977838.1|  [L=486]
Description: hypothetical protein BCG_1746 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-65  220.2  38.0    2.2e-40  138.6   5.7    2.4  3  Sulfate_transp  Sulfate permease family
    6.7e-09   35.4   0.0    1.6e-08   34.2   0.0    1.7  1  STAS            STAS domain
    4.9e-07   30.0   2.2    2.1e-06   28.0   0.1    2.7  2  STAS_2          STAS domain
  ------ inclusion threshold ------
       0.34    9.7  12.6        2.1    7.1   0.2    2.9  2  HCO3_cotransp   HCO3- transporter family
       0.92    8.4   4.5        0.1   11.5   0.4    1.6  2  PalH            PalH/RIM21
        6.8    6.9   5.2        1.3    9.2   0.3    2.1  2  DUF5534         Family of unknown function (DUF5534)


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1  19.7   9.9e-30     3e-26       3     133 ..       7     133 ..       5     138 .. 0.95
   2 !  138.6   5.7   7.4e-44   2.2e-40     174     379 ..     141     353 ..     133     354 .. 0.85
   3 ?   -3.9   0.1       1.5   4.4e+03     249     261 ..     364     376 ..     355     390 .. 0.47

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 9.9e-30
                 Sulfate_transp   3 gDliaGitvallaiPqalayal.lagl..ppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakvaeeepek 79 
                                     +l++G+ va++a+P+a+a+++ ++g    ++ gLy+++++++++a+fG+++ ++ Gp++ ++++++++ia+        
  gi|121637615|ref|YP_977838.1|   7 RELLSGVAVAIVALPLAIAFGItATGTsqGALIGLYGAIFAGFFAAVFGGTPGQVTGPTGPITVVATATIAEH------- 79 
                                    6799******************77776879*****************************************77....... PP

                 Sulfate_transp  80 gieiattltllaGviqvllGllRLgflveflseavlsGfiaGaaivillsqikv 133
                                    g+e a+ + +laGv+q+l+G  RLg l+++++++v+sGf++G+ai i+++q+ +
  gi|121637615|ref|YP_977838.1|  80 GLEGAFFAFILAGVFQILFGACRLGSLIRYVPHPVISGFMGGIAILIIMTQLDQ 133
                                    ***************************************************976 PP

  == domain 2  score: 138.6 bits;  conditional E-value: 7.4e-44
                 Sulfate_transp 174 vLlvtkellkklkkllvipapael.vavivatlvsaif...elkreagvki......vgeipsglpelslpkvdwsllsa 243
                                    vL+++  ll+    ++   +p  l v+v+v+ ++ +++   + +r   v+i      +geip+ +p++ +p+v  s++ +
  gi|121637615|ref|YP_977838.1| 141 VLVTVVLLLAS--GRFIKAIPPSLlVLVLVSSVLPLAApwlRDLRAGPVSInrtvdyIGEIPQAMPSFDFPQVANSTMLQ 218
                                    33333333221..235555555550555555555544479877777788867777779********************** PP

                 Sulfate_transp 244 llpdalaialvglleaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvsa 323
                                    +l+ a+aial+g+l+++++s+++d+++g+++ snkEL+++G+ Ni+++lfggl+ +ga++rs+vn+++G++t+ls   ++
  gi|121637615|ref|YP_977838.1| 219 VLLSAVAIALLGSLDSLLTSLVMDNIRGTRHRSNKELIGQGIGNIAAGLFGGLAGAGATVRSVVNVRNGGQTALSAATHS 298
                                    ******************************************************************************** PP

                 Sulfate_transp 324 lvvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklskldflilla 379
                                    +v+++++  l+ +++yiP avL++i+i++++g + +++++ k++   + d+++++ 
  gi|121637615|ref|YP_977838.1| 299 VVLFVFVAGLGAVVQYIPLAVLSGILILVAVG-MFDWHAMRKAHVSPRGDVIVMFT 353
                                    ********************************.9******9999999999999876 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.5
                 Sulfate_transp 249 laialvglleaia 261
                                     +  +vg++ +++
  gi|121637615|ref|YP_977838.1| 364 TIAVMVGIALSLL 376
                                    3333333333332 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   5.5e-12   1.6e-08       6     110 ..     390     479 ..     385     486 .] 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.5e-12
                                    ECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEE CS
                           STAS   6 eiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvl 85 
                                    ++++   +r+dgp+ f +++++  +l++  ++             + ldl++v+++D+sG++aL  ++   ++ gv v +
  gi|121637615|ref|YP_977838.1| 390 TQDDTGTYRIDGPLSFLSVDGVFGSLRDGRED-------------VSLDLQHVTYLDTSGAQALLYFIDHSEKDGVAVSI 456
                                    5677789******************9998776.............67********************************* PP

                                    ES--HHHHHHHHHTTCGGCC..SEE CS
                           STAS  86 vnikpevreklektgffdeveeekl 110
                                      i p+++  l+   ++d ++++kl
  gi|121637615|ref|YP_977838.1| 457 KRIPPRLESQLT--ALADNEQRDKL 479
                                    ******999655..44555555555 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.32   9.6e+02      39      54 ..     212     227 ..     210     230 .. 0.87
   2 !   28.0   0.1   7.1e-10   2.1e-06      23      75 ..     415     468 ..     406     471 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                         STAS_2  39 vDsaalalLlalarta 54 
                                    ++s+ l++Ll++++ a
  gi|121637615|ref|YP_977838.1| 212 ANSTMLQVLLSAVAIA 227
                                    6899********9877 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 7.1e-10
                         STAS_2  23 laag.aevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlld 75 
                                    l++g ++v +Dl++v+++D++++++Ll +  + ++ g  +++++ pp+l + l 
  gi|121637615|ref|YP_977838.1| 415 LRDGrEDVSLDLQHVTYLDTSGAQALLYFIDHSEKDGVAVSIKRIPPRLESQLT 468
                                    567779*******************************************99875 PP

>> HCO3_cotransp  HCO3- transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.2    0.0023       6.9      47     105 ..      21      76 ..      13     139 .. 0.68
   2 ?    7.1   0.2   0.00069       2.1     438     468 ..     301     331 ..     272     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0023
                  HCO3_cotransp  47 spaitFGgLlgeategaigvseslvsaaisgilfalfagqpllilgstgPllvfekily 105
                                      ai+FG    +at   +g+   l++a ++g++ a+f+g p  + g tgP+ v  ++  
  gi|121637615|ref|YP_977838.1|  21 PLAIAFGI---TATGTSQGALIGLYGAIFAGFFAAVFGGTPGQVTGPTGPITVVATATI 76 
                                    55788885...678888999999****************************99776543 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00069
                  HCO3_cotransp 438 liglsvlltpvlklIPmpVLyGvFLYmgvts 468
                                    l  +   l  v+++IP++VL G+++ ++v +
  gi|121637615|ref|YP_977838.1| 301 LFVFVAGLGAVVQYIPLAVLSGILILVAVGM 331
                                    22233337789*************9999865 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       1.2   3.7e+03     163     191 ..     122     149 ..     105     172 .. 0.57
   2 ?   11.5   0.4   3.5e-05       0.1     246     295 ..     288     361 ..     195     368 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                           PalH 163 laqvqivirlfsrqkekriiilvGlalii 191
                                    +a + i+++l +  ++  + +lv+++l++
  gi|121637615|ref|YP_977838.1| 122 IAILIIMTQLDQV-RSSSLLVLVTVVLLL 149
                                    4444444444422.333333444443333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.5e-05
                           PalH 246 m.......................ketilllilnllvillpvvff.ildisnadvaewkeliiwvlkllitviv 295
                                                             + i+l++l+ ++il+ v +f +  + +a+v+  +++i+++++++itv+v
  gi|121637615|ref|YP_977838.1| 288 GqtalsaathsvvlfvfvaglgavVQYIPLAVLSGILILVAVGMFdWHAMRKAHVSPRGDVIVMFTTMIITVVV 361
                                    055555555566666666666666899***********9999998455666*********************98 PP

>> DUF5534  Family of unknown function (DUF5534)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.7         1     3e+03      79      95 ..      13      29 ..       6      31 .. 0.82
   2 ?    9.2   0.3   0.00044       1.3      78     105 ..     355     382 ..     337     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                        DUF5534 79 iliacvalsialicGia 95
                                   + +a val +a+ +Gi+
  gi|121637615|ref|YP_977838.1| 13 VAVAIVALPLAIAFGIT 29
                                   67999999999999997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00044
                        DUF5534  78 viliacvalsialicGiaisyviYrLvq 105
                                    +i+   v l+ia+++Gia+s +++rL  
  gi|121637615|ref|YP_977838.1| 355 MIITVVVDLTIAVMVGIALSLLVHRLRS 382
                                    57778899*****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2983.15
//
Query:       gi|121637616|ref|YP_977839.1|  [L=318]
Description: initiation inhibitor protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-61  205.1   0.0    9.5e-61  204.8   0.0    1.1  1  AAA_31       AAA domain
    2.3e-25   89.1   0.0    9.1e-25   87.2   0.0    1.8  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-10   41.5   0.0    5.4e-10   39.2   0.0    1.9  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    8.6e-09   35.2   0.0    1.5e-07   31.1   0.0    2.1  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.4e-07   30.3   0.5     0.0003   20.2   0.1    2.1  2  MipZ         ATPase MipZ
    3.3e-07   30.0   0.1    1.1e-06   28.3   0.1    1.8  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.9e-06   27.3   0.1    3.7e-06   26.3   0.1    1.7  1  ArsA_ATPase  Anion-transporting ATPase
      3e-05   23.4   0.2    0.00018   20.9   0.1    2.0  2  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.033   13.4   0.0    1.6  1  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
      0.027   13.5   0.3      0.057   12.4   0.3    1.5  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.26   10.9   0.2       0.92    9.1   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.8   0.0   5.8e-64   9.5e-61       2     177 .]      65     241 ..      64     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.8 bits;  conditional E-value: 5.8e-64
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkven 80 
                                    kvIa+ nqKGGvGKTT+++nl+aal ++g +vLlvD+DpQ++++ glg+ + e++kt+++vl+  +++i++++i+++v+n
  gi|121637616|ref|YP_977839.1|  65 KVIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSAGLGVPHYELDKTIHNVLVePRVSIDDVLIHSRVKN 144
                                    9*************************************************************9899************** PP

                         AAA_31  81 ldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleql 160
                                    +dl+ps+idL++aei+lv+   +e++l ++l  v d+YDy++iDc+PsLgllt+n+L+  d viip+++e+++l+Gl+ l
  gi|121637616|ref|YP_977839.1| 145 MDLVPSNIDLSAAEIQLVNEVGREQTLARALYPVLDRYDYVLIDCQPSLGLLTVNGLACTDGVIIPTECEFFSLRGLALL 224
                                    ******************************************************************************** PP

                         AAA_31 161 lktieevkkklnpklei 177
                                    ++t+++v+++lnpkl+i
  gi|121637616|ref|YP_977839.1| 225 TDTVDKVRDRLNPKLDI 241
                                    **************987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   5.6e-28   9.1e-25       1     128 []      67     292 ..      67     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 5.6e-28
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    ia++++kGGvGKTt ++nL++al + g+rVllvD+Dpq+ ++a   gl   + +                          
  gi|121637616|ref|YP_977839.1|  67 IAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSA---GLGVPHYEldktihnvlveprvsiddvlihsrvk 143
                                    799***************************************9...4444444445699999****************** PP

                                    ............................................................................CCHC CS
                                    ............................................................................xxxx RF
                           CbiA  55 ............................................................................dlkr 58 
                                                                                                                +l  
  gi|121637616|ref|YP_977839.1| 144 nmdlvpsnidlsaaeiqlvnevgreqtlaralypvldrydyvlidcqpslglltvnglactdgviipteceffslrGLAL 223
                                    ******************************************************************************** PP

                                    CCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                           CbiA  59 llellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlg.viprdeavaeapargepv 128
                                    l  ++ +++ +++++l+i g++++r+d++  + + +e ++++ +r+g+ v++ vi r+++++e    gep+
  gi|121637616|ref|YP_977839.1| 224 LTDTVDKVRDRLNPKLDISGILITRYDPR--TVNSREVMARVVERFGDLVFDtVITRTVRFPETSVAGEPI 292
                                    *****************************..9*******************************99999886 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   3.3e-13   5.4e-10       2     230 ..      65     309 ..      64     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
                       CBP_BcsQ   2 kvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieq.regwaraeldga.pwrqaal.eyapg 78 
                                    kv+a+   +GGvG+t+ +  L+ al e g +vl++D+ p+  L     v++ + +++  + +++ +  + +  +    ++
  gi|121637616|ref|YP_977839.1|  65 KVIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSAGLGVPHYElDKTIHNVLVEPRvSIDDVLIhSRVKN 144
                                    578888889*************************************9999865256677777765415555544156799 PP

                       CBP_BcsQ  79 ldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc....... 151
                                    +dl+P     ++ + +l +   ++++l++al  +  +y+++l+D++     lt + la +d v+  +e +  +       
  gi|121637616|ref|YP_977839.1| 145 MDLVPSNIDLSAAEIQLVNEVGREQTLARALYPVLDRYDYVLIDCQPSLGLLTVNGLACTDGVIIPTECEFFSlrglall 224
                                    *****875444444446667778999******************************999998886655543321110000 PP

                       CBP_BcsQ 152 .....hvrLhqqalpaaellLiNqfeaasqlqqDllqlWlqslrrll.PlvihrDealaEalaakqPlgeyrpdslaaee 225
                                         +vr + ++  + + +Li ++++     ++++    + + +l+   vi r   ++E+ +a  P+++++p+s+ a +
  gi|121637616|ref|YP_977839.1| 225 tdtvdKVRDRLNPKLDISGILITRYDPRTVNSREVMARVVERFGDLVfDTVITRTVRFPETSVAGEPITTWAPKSAGALA 304
                                    00000333333344445556666666666666666666665555544144666666666666666666666666666666 PP

                       CBP_BcsQ 226 vktLa 230
                                     + La
  gi|121637616|ref|YP_977839.1| 305 YRALA 309
                                    66665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   9.2e-11   1.5e-07       7     246 ..      72     314 ..      65     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 9.2e-11
                      Fer4_NifH   7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaD.strlll.ggkaqetvldtlrekgavedvkvedvvkkGyggvkcv 84 
                                     kGG+Gk+t++ nl aal e g++vl+v  DP+   s+ l + +  + +t+ ++l e      v ++dv+ +    vk +
  gi|121637616|ref|YP_977839.1|  72 QKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGAlSAGLGVpHYELDKTIHNVLVEP----RVSIDDVLIH--SRVKNM 145
                                    59******************************96525655441445556666666554....5899999988..788999 PP

                      Fer4_NifH  85 esGGPepGvGCaGrgvitaielleel..gayd..d.lDfvlyDv...LGDvvCGGfalPiredkaqevyivtsgelmaly 156
                                    +    +     a   +++ +   + l    y   d +D+vl D    LG     G+a        + v+i t++e+ +l 
  gi|121637616|ref|YP_977839.1| 146 DLVPSNIDLSAAEIQLVNEVGREQTLarALYPvlDrYDYVLIDCqpsLGLLTVNGLAC------TDGVIIPTECEFFSLR 219
                                    9988888888888888877754333211344333459****99755577777777774......689************* PP

                      Fer4_NifH 157 aanniakgiekyaksgg..vrlgGliinsr..kvddereliekfaeelgtkvlevv.Prdeivrkaelrkktvieyapes 231
                                        ++ ++ k + + +  + ++G++i     ++++ re++ + +e+ g  v+++v  r+    +++++ + ++ +ap+s
  gi|121637616|ref|YP_977839.1| 220 GLALLTDTVDKVRDRLNpkLDISGILITRYdpRTVNSREVMARVVERFGDLVFDTViTRTVRFPETSVAGEPITTWAPKS 299
                                    **********99876544599***9987322258999************999986516677788999************* PP

                      Fer4_NifH 232 eqakeyrelarkile 246
                                      a  yr+lar++++
  gi|121637616|ref|YP_977839.1| 300 AGALAYRALARELID 314
                                    ***********9987 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.8e-07    0.0003       2      39 ..      66     103 ..      65     111 .. 0.94
   2 !    8.5   0.0   0.00068       1.1      58     142 ..     143     224 ..     126     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.8e-07
                                    EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                           MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39 
                                    vi + n+kGG Gk+t ++ +  aL + G rv  +d+d 
  gi|121637616|ref|YP_977839.1|  66 VIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDP 103
                                    899*********************************96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00068
                                    HT------EEE-SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHC CS
                           MipZ  58 kglsLplpealalseaeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfd 137
                                    k+++L  p+ + ls ae + v+e   ++  +l++++  +  ++d+++id+  s   l+  + +  d ++ P    f  + 
  gi|121637616|ref|YP_977839.1| 143 KNMDLV-PSNIDLSAAEIQLVNEVGREQ--TLARALYPVLDRYDYVLIDCQPSLGLLTVNGLACTDGVIIPTECEFFSLR 219
                                    566664.455588888877777766665..9**************************************99988887776 PP

                                    CCEEE CS
                           MipZ 138 llgkv 142
                                     l+ +
  gi|121637616|ref|YP_977839.1| 220 GLALL 224
                                    66555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   6.8e-10   1.1e-06       4      44 ..      65     105 ..      63     151 .. 0.91
   2 ?   -1.1   0.0      0.63     1e+03     111     141 ..     181     209 ..     160     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.8e-10
                           ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyG 44 
                                    kvia++  KGGVGK+t ++nl +aL + g +v l+D+D  G
  gi|121637616|ref|YP_977839.1|  65 KVIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQG 105
                                    79999*********************************887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.63
                           ParA 111 elDyLiiDlPPGtgDeqltvaqklplagavi 141
                                      Dy++iD+ P  g   ltv     ++g++i
  gi|121637616|ref|YP_977839.1| 181 RYDYVLIDCQPSLG--LLTVNGLACTDGVII 209
                                    579******99987..455555554455444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   2.3e-09   3.7e-06       6      50 ..      70     114 ..      64     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.3e-09
                                    EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS- CS
                    ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqk 50 
                                       KGGVGKtt+   +++ l e g++vll+  DP   ls  +   
  gi|121637616|ref|YP_977839.1|  70 CNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSAGLGVP 114
                                    456*******************************99999777664 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.1e-07   0.00018       2      43 ..      65     106 ..      64     110 .. 0.91
   2 ?    0.2   0.0      0.23   3.7e+02      83     115 ..     181     213 ..     168     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                          VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43 
                                    k+i++c  kGG Gktt+ + l +al   g+rv l + d    
  gi|121637616|ref|YP_977839.1|  65 KVIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGA 106
                                    6899********************************997655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                          VirC1  83 GfdyaladtrgGsselnntiiassdllliPtml 115
                                     +dy+l+d +     l    +a +d ++iPt  
  gi|121637616|ref|YP_977839.1| 181 RYDYVLIDCQPSLGLLTVNGLACTDGVIIPTEC 213
                                    589999999998888888889999999999865 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.033      12      62 ..      64     114 ..      56     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                        DUF1611  12 akrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgiliagegvv 62 
                                    ak++++      vGK t +++l +al e+G ++ +v ++++g+l ag gv+
  gi|121637616|ref|YP_977839.1|  64 AKVIAMCNQKGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSAGLGVP 114
                                    6666666666779**********************************9997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   3.5e-05     0.057      26      74 ..      61     110 ..      57     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                    -S-SEEEEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                           MeaB  26 aGraqvvGltGv.PGaGkstlvealglelrrrGkrvavlavDPsspftGG 74 
                                     G a+v+ +     G+Gk t + +lg+ l + G+rv ++ +DP    + G
  gi|121637616|ref|YP_977839.1|  61 HGPAKVIAMCNQkGGVGKTTSTINLGAALGEYGRRVLLVDMDPQGALSAG 110
                                    577788887654168****************************9887766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00057      0.92       4      38 ..      67     102 ..      64     107 .. 0.83
   2 ?   -1.7   0.0       1.1   1.8e+03     136     153 ..     235     252 ..     224     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00057
                                    EEEEEST.TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54   4 illvGlq.GaGKTttlaKLaallkkegkkvllvaaD 38 
                                    i+++  + G+GKTt++  L a l + g++vllv +D
  gi|121637616|ref|YP_977839.1|  67 IAMCNQKgGVGKTTSTINLGAALGEYGRRVLLVDMD 102
                                    555555416************************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                    HHHHSSCSEEEEESTTSS CS
                          SRP54 136 FkeavgitgviltklDgd 153
                                     + +++i+g+ +t+ D +
  gi|121637616|ref|YP_977839.1| 235 LNPKLDISGILITRYDPR 252
                                    567899********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.60
# Mc/sec: 1602.35
//
Query:       gi|121637617|ref|YP_977840.1|  [L=278]
Description: hypothetical protein BCG_1748 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-86  288.9   0.1    4.3e-86  288.7   0.1    1.0  1  SMC_ScpA         Segregation and condensation protein ScpA
      0.001   18.7   0.0     0.0015   18.2   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.7   0.1   4.8e-90   4.3e-86       1     241 []      40     264 ..      40     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 288.7 bits;  conditional E-value: 4.8e-90
                                    HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelrdkLia 80 
                                    Li+a++ldvt+va+++vtd+f+ay+k+++++lelee+t++lvia+tl++lKaa+Llp++qv++eed++  l+e+rd+L+a
  gi|121637617|ref|YP_977840.1|  40 LIFAHQLDVTEVALHQVTDDFIAYTKAIGARLELEETTAFLVIAATLLDLKAARLLPAGQVDDEEDLA--LLEVRDLLFA 117
                                    89****************************************************************99..99******** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...HH CS
                       SMC_ScpA  81 rLleYrkykeeaklfkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakivalaekqiselei 160
                                    rLl+Yr++k++a++f+elea++l+s+++a+s+++ f+ +++ev++++++++f++i+a+++++++a++va++++  +el++
  gi|121637617|ref|YP_977840.1| 118 RLLQYRAFKHVAEMFAELEATALRSYPRAVSLEDGFVGLLPEVMLGVDAHRFAEIAAIALTPRPAPTVATEHL--HELMV 195
                                    ************************************************************************9..***** PP

                                    HHHHHHHHHH...............HHHTS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEEEE CS
                       SMC_ScpA 161 sieeqleellaqleqflqarlkevLldlrswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeeflddLqvsl 240
                                    s++eq+e+lla    +l+ar++      ++w+++seL+ad  +++++e+vg+FlAlLeL++++ava+eQ+e+l++Lqvs+
  gi|121637617|ref|YP_977840.1| 196 SVPEQAEHLLA----MLKARGS------GQWASFSELVAD--CTAPIEIVGRFLALLELYRTRAVAFEQSEPLGALQVSW 263
                                    **********9....*******......99**********..*************************************9 PP

                                    - CS
                       SMC_ScpA 241 l 241
                                    +
  gi|121637617|ref|YP_977840.1| 264 T 264
                                    5 PP

>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-07    0.0015      25     123 ..     115     208 ..     104     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-07
                                    EEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEEEECEEEEEEHSSSHHHHHHH CS
                Chorismate_bind  25 vlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrrietepiaGTrargktpeedeal 104
                                     ++r l+++  a  + ++++++l+a+   +y  +++le  +++g  PE++l v+++r +e+ +ia T  r +  +   + 
  gi|121637617|ref|YP_977840.1| 115 LFARLLQYR--AFKHVAEMFAELEATALRSYPRAVSLE-DGFVGLLPEVMLGVDAHRFAEIAAIALTP-RPAP-TVATEH 189
                                    566667777..667889*********999999999996.66*************99***********5.5554.456666 PP

                                    HHHHHCCHHHHHHHHHHHH CS
                Chorismate_bind 105 eeelledeKeraEhlmivd 123
                                     +el+ +  e+aEhl+ + 
  gi|121637617|ref|YP_977840.1| 190 LHELMVSVPEQAEHLLAML 208
                                    79************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.59
# Mc/sec: 1421.44
//
Query:       gi|121637618|ref|YP_977841.1|  [L=231]
Description: hypothetical protein BCG_1749 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-49  166.0   0.1    6.5e-49  165.6   0.1    1.2  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
    0.00037   20.4   6.2     0.0066   16.4   1.2    2.7  2  HTH_15    Helix-turn-helix domain of alkylmercury lyase
  ------ inclusion threshold ------
      0.035   14.2   2.8      0.035   14.2   2.8    2.4  2  DprA_WH   DprA winged helix domain
      0.084   13.4   0.2        0.2   12.2   0.2    1.7  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   0.1   1.5e-52   6.5e-49       2     159 ..      31     187 ..      30     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 1.5e-52
                       SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktrL 81 
                                    ++EA+L+v ++p+++++La+++e    +v++ l+ +++e++ +d+g+ l+++ +g+r++t++++a++v+kl+ +  +t+L
  gi|121637618|ref|YP_977841.1|  31 VLEALLLVIDTPVTADALAAATEQPVYRVAAKLQLMADELTGRDSGIDLRHTSEGWRMYTRARFAPYVEKLLLDGARTKL 110
                                    69********************999******************************************************* PP

                       SMC_ScpB  82 sqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksleeLpk 159
                                    ++aaletLa++ay+qpvtra+++++RGvn+d+v+rtLl+rgli+e+g++  +g +++++tTe Fle++gl+sl+eLp+
  gi|121637618|ref|YP_977841.1| 111 TRAALETLAVVAYRQPVTRARVSAVRGVNVDAVMRTLLARGLITEVGTDADTG-AVTFATTELFLERLGLTSLSELPD 187
                                    **************************************************999.***********************8 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.2   1.5e-06    0.0066      29      61 ..      36      68 ..      17      75 .. 0.83
   2 !    5.8   0.3    0.0029        13      31      58 ..     122     149 ..      97     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                         HTH_15 29 lLakGepVtveeLAaatgrsveevrqaLaalps 61
                                   lL+   pVt + LAaat ++v +v++ L+ +++
  gi|121637618|ref|YP_977841.1| 36 LLVIDTPVTADALAAATEQPVYRVAAKLQLMAD 68
                                   466789***********************9998 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0029
                         HTH_15  31 akGepVtveeLAaatgrsveevrqaLaa 58 
                                    a  +pVt++++ a  g  v+ v + L a
  gi|121637618|ref|YP_977841.1| 122 AYRQPVTRARVSAVRGVNVDAVMRTLLA 149
                                    4568******************998865 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.8   7.9e-06     0.035       6      46 ..      20      63 ..      15      73 .. 0.87
   2 ?   -0.5   0.1       0.3   1.3e+03      24      47 ..     125     148 ..     105     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.9e-06
                        DprA_WH  6 aepplddlerrvLaaL...gpePvhvDqLvrrtglpaaevsaaL 46
                                   +++ ++d+ +rvL+aL     +Pv+ D+L+++t  p+ +v+a L
  gi|121637618|ref|YP_977841.1| 20 PAELDADELKRVLEALllvIDTPVTADALAAATEQPVYRVAAKL 63
                                   566678999*****9988889********************988 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                        DprA_WH  24 ePvhvDqLvrrtglpaaevsaaLl 47 
                                    +Pv+   +++  g+ +++v+++Ll
  gi|121637618|ref|YP_977841.1| 125 QPVTRARVSAVRGVNVDAVMRTLL 148
                                    677777788888888999999987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   4.4e-05       0.2      37      66 ..     142     171 ..     110     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                         HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTd 66 
                                     +++ L ++GL+++ g +ad ++++++ T+
  gi|121637618|ref|YP_977841.1| 142 AVMRTLLARGLITEVGTDADTGAVTFATTE 171
                                    6899*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1273.75
//
Query:       gi|121637619|ref|YP_977842.1|  [L=254]
Description: hypothetical protein BCG_1750 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-20   72.5   0.0    1.1e-19   71.1   0.0    1.7  1  PseudoU_synth_2  RNA pseudouridylate synthase
    2.8e-13   49.3   0.5    2.8e-13   49.3   0.5    1.8  2  S4               S4 domain
  ------ inclusion threshold ------
      0.083   12.7   0.1       0.17   11.7   0.1    1.5  1  S4_2             S4 domain
      0.084   13.2   0.1       0.15   12.4   0.1    1.3  1  TruB_N           TruB family pseudouridylate synthase (N term


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.5e-23   1.1e-19       2     160 .]      76     211 ..      75     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.5e-23
                PseudoU_synth_2   2 lvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkYl 81 
                                    ++++nKP g++++  +      +    +   r+ + +k+l +v+RLD +t+Gl+ll++++e+a++l++  ++++v K+Yl
  gi|121637619|ref|YP_977842.1|  76 YLALNKPRGMHSTMSD---DRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLMLLTNDGELAHRLMH--PSHEVPKTYL 150
                                    899*************...888899999999999**********************************..********** PP

                PseudoU_synth_2  82 alvfgapeee.egaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhlaa 160
                                    a+v+g  +     ++++ i+               +dg   v  + v++        + +lv+++l++Gr++ +R+ laa
  gi|121637619|ref|YP_977842.1| 151 ATVTGSVPRGlGRTLRAGIEL--------------DDGPAFVDDFAVVDAI-----PGKTLVRVTLHEGRNRIVRRLLAA 211
                                    ***843333303445555555..............8***************.....********************9986 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.5   6.2e-17   2.8e-13       2      44 ..      15      56 ..      14      60 .. 0.96
   2 ?   -2.3   0.2      0.85   3.8e+03      28      35 ..      61      68 ..      61      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 6.2e-17
                                   EHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-T CS
                             S4  2 RLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkp 44
                                   RL+kvl+++g+as rr A+++I +GrV V+G vv+  ++rV+p
  gi|121637619|ref|YP_977842.1| 15 RLQKVLSQAGIAS-RRAAEKMIVDGRVEVDGHVVTELGTRVDP 56
                                   ************9.***************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.85
                                   EEETTEEE CS
                             S4 28 VlVNGkvv 35
                                   V+V+G +v
  gi|121637619|ref|YP_977842.1| 61 VRVDGARV 68
                                   9****987 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.7e-05      0.17       8      52 ..      14      57 ..       9      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                           S4_2  8 ItLgqlLKlaglvesGgeaKafiaegeVkvNGevetrRgkKlraG 52
                                   I+L+++L  ag+++   +a  +i +g V+v+G+v t+ g ++ + 
  gi|121637619|ref|YP_977842.1| 14 IRLQKVLSQAGIASR-RAAEKMIVDGRVEVDGHVVTELGTRVDPQ 57
                                   999*****9999998.56667889************999888765 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.3e-05      0.15       1      49 [.     104     154 ..     104     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                    HHHTT-S-EEESS---TT-EEEEEEEEGG..GGGGHHHCTTS-EEEEEEEE CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavge..aTklleylleadKeYeatir 49 
                                    +++ ++kk  h G LD   +G++++  +   a +l++  +e +K+Y at++
  gi|121637619|ref|YP_977842.1| 104 RKVRGTKKLFHVGRLDADTEGLMLLTNDGelAHRLMHPSHEVPKTYLATVT 154
                                    677899****************999876446899999999******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1521.37
//
Query:       gi|121637620|ref|YP_977843.1|  [L=230]
Description: cytidylate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-82  274.8   1.3    5.5e-82  274.6   1.3    1.0  1  Cytidylate_kin   Cytidylate kinase
    2.6e-07   31.0   0.1    6.9e-07   29.6   0.1    1.7  1  Cytidylate_kin2  Cytidylate kinase-like family
    2.9e-07   31.1   0.0    6.6e-07   29.9   0.0    1.6  1  AAA_18           AAA domain
    6.5e-05   23.1   0.0     0.0075   16.4   0.0    2.2  2  SKI              Shikimate kinase
    8.5e-05   22.4   2.0      0.016   14.9   0.1    2.2  2  AAA_30           AAA domain
     0.0001   22.5   0.4    0.00045   20.4   0.4    2.3  1  AAA_33           AAA domain
    0.00057   20.2   0.0     0.0017   18.6   0.0    1.7  2  AAA_22           AAA domain
     0.0031   17.9   0.5     0.0056   17.1   0.5    1.8  1  AAA_16           AAA ATPase domain
     0.0069   16.7   0.0      0.016   15.5   0.0    1.6  1  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.025   15.0   0.0    1.6  1  AAA              ATPase family associated with various cellul
      0.016   15.1   0.0      0.059   13.3   0.0    1.8  2  NACHT            NACHT domain
      0.026   14.9   0.0       0.15   12.5   0.0    2.1  3  AAA_17           AAA domain
      0.032   14.2   0.1       0.17   11.9   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
      0.055   13.9   0.0      0.094   13.1   0.0    1.3  1  RNA_helicase     RNA helicase
      0.089   11.7   0.0       0.17   10.8   0.0    1.4  1  AAA_6            Hydrolytic ATP binding site of dynein motor 


Domain annotation for each model (and alignments):
>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.6   1.3   4.6e-85   5.5e-82       1     210 [.       9     223 ..       9     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 274.6 bits;  conditional E-value: 4.6e-85
                                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEE....EEEETTEE- CS
                 Cytidylate_kin   1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfeae....kvllngedv 76 
                                    +aiDGPag+GKssv+r+la++lg+++ldtga+YR+++la+lr+  d+ d+aa++++a++v++s+  +    +++l+gedv
  gi|121637620|ref|YP_977843.1|   9 VAIDGPAGTGKSSVSRRLARELGARFLDTGAMYRIVTLAVLRAGADPSDIAAVETIASTVQMSLGYDpdgdSCYLAGEDV 88 
                                    79**************************************************************9999999********* PP

                                    TTGGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT CS
                 Cytidylate_kin  77 eeelrsdevekavSavaaipavRailvkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakg 155
                                    + e+r d+v++avSav+++pavR++lv+++r++++  +++vveGRDigtvvfpda++Kifl+As+e+Ra+RR++q+ a+g
  gi|121637620|ref|YP_977843.1|  89 SVEIRGDAVTRAVSAVSSVPAVRTRLVELQRTMAEgPGSIVVEGRDIGTVVFPDAPVKIFLTASAETRARRRNAQNVAAG 168
                                    ***********************************8899***************************************** PP

                                    ----HHHHHHHHHHHHHHHHCTSSS-S---TT-EEEETTTS-HHHHHHHHHHHHH CS
                 Cytidylate_kin 156 tsvsleellaeikeRDklDkerevgpLklaedaliidtskltieevvekilelik 210
                                     +++++ +la++++RD+lD++r+v+pL++a da+i+dts++t +evv+++lel++
  gi|121637620|ref|YP_977843.1| 169 LADDYDGVLADVRRRDHLDSTRAVSPLQAAGDAVIVDTSDMTEAEVVAHLLELVT 223
                                    ***************************************************9886 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   5.7e-10   6.9e-07       1     134 [.       8     163 ..       8     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.7e-10
                Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr....eiieevakelglseeeveevde.rsrlssflskllaarvagdtl.. 73 
                                    +++I++  G+g++ + ++LA +Lg +f+d     +i++ ++ ++g +++ +++v+  +s++++ l      +  gd    
  gi|121637620|ref|YP_977843.1|   8 VVAIDGPAGTGKSSVSRRLARELGARFLDTgamyRIVTLAVLRAGADPSDIAAVETiASTVQMSL----GYDPDGDSCyl 83 
                                    799**************************954444667777889999999999999655544443....33333344466 PP

                Cytidylate_kin2  74 ...................deklddelfeaqervirela.aeesvVivGR.gadliLkdrpnvlrvfltapledrvkrva 132
                                                         ++  +++ +  ++ r++a    s+V+ GR  + +++ d p  +++flta+ e r++r  
  gi|121637620|ref|YP_977843.1|  84 agedvsveirgdavtravsAVSSVPAVRTRLVELQRTMAeGPGSIVVEGRdIGTVVFPDAP--VKIFLTASAETRARRRN 161
                                    7788999*******9999766666667777799999999534589999**569******99..*************9865 PP

                Cytidylate_kin2 133 er 134
                                    ++
  gi|121637620|ref|YP_977843.1| 162 AQ 163
                                    54 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   5.5e-10   6.6e-07       1     114 [.       9     164 ..       9     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.5e-10
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.........................gvnlrdvakenglllevdpe.......alde 48 
                                    +++ G++G+GK++++++L+++lg                             +  +a+  +++l++dp+         d 
  gi|121637620|ref|YP_977843.1|   9 VAIDGPAGTGKSSVSRRLARELGArfldtgamyrivtlavlragadpsdIAAVETIASTVQMSLGYDPDgdscylaGEDV 88 
                                    6788*****************96669*********************998889999999999999999999985444445 PP

                         AAA_18  49 skrldedkldklldaleenss..............aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                    s +++ d + ++++a+    s                e ++++v++g+    +   +   k ++Ltas e++++R ++++
  gi|121637620|ref|YP_977843.1|  89 SVEIRGDAVTRAVSAVS---SvpavrtrlvelqrtMAEGPGSIVVEGRDIGTVVFPDAPVK-IFLTASAETRARRRNAQN 164
                                    55555555555555555...4555*********9866677888****99988877777777.*************88765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.2e-06    0.0075       2      23 ..      16      37 ..      15      44 .. 0.93
   2 ?    4.7   0.0     0.024        29      89     156 ..     147     221 ..     122     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                   TSSHHHHHHHHHHHHTSEEEEH CS
                            SKI  2 GaGKstvGkllAkklglefiDl 23
                                   G+GKs+v ++lA++lg +f+D+
  gi|121637620|ref|YP_977843.1| 16 GTGKSSVSRRLARELGARFLDT 37
                                   9********************8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                                    EEEE--HHHHHHHHHHTTSSGGGCSCHH....HHHHHHHHH.HH..HHHHCCSSCEEEECTSSHHHHHHHHHHHH CS
                            SKI  89 iyLdvsleellerlkadkeRPllqeksk....eeelleela.er..eplyeeaadvvvdeseeskeevaeeilea 156
                                    i+L +s e+ ++r +a++  + l ++      + +++++l  +r   pl +  ++v+vd+s+ +++ev++++le 
  gi|121637620|ref|YP_977843.1| 147 IFLTASAETRARRRNAQNVAAGLADDYDgvlaDVRRRDHLDsTRavSPLQAAGDAVIVDTSDMTEAEVVAHLLEL 221
                                    7888888888888877777443433333466644444444444411455666699***************99985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.4e-05     0.016      18      60 ..       6      54 ..       2     101 .. 0.76
   2 !    7.3   0.2    0.0028       3.4      81     118 ..     181     228 ..     140     230 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaag......grviglAptgkaAk 60
                                   + v+++ GpAGtGK+ + + l++ + a+       +r++ lA   + A+
  gi|121637620|ref|YP_977843.1|  6 AAVVAIDGPAGTGKSSVSRRLARELGARFldtgamYRIVTLAVLRAGAD 54
                                   45999************99997666655335777788888887666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0028
                         AAA_30  81 k.........grarlepg.tllivDEagmvdtkqlaallkaaekagak 118
                                    +         +   l+++ + +ivD + m+ ++ +a+ll+ +++++  
  gi|121637620|ref|YP_977843.1| 181 RrrdhldstrAVSPLQAAgDAVIVDTSDMTEAEVVAHLLELVTRRSEA 228
                                    1333444454334556666***********************997655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   3.8e-07   0.00045       1      35 [.       8      42 ..       8     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.8e-07
                         AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlrr 35
                                   +v + G++G+GKs +++rl+++lga +l++ +++r
  gi|121637620|ref|YP_977843.1|  8 VVAIDGPAGTGKSSVSRRLARELGARFLDTGAMYR 42
                                   67788********************9999988655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0017       5      65 ..       6      69 ..       3     107 .. 0.72
   2 ?   -1.2   0.0       1.9   2.3e+03      74     112 ..     182     218 ..     130     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdl..lrellralg 65
                                   a ++++ G++GtGK+ + rrl+++l ++   +  + + v +  l ++ +++d+   + +++ ++
  gi|121637620|ref|YP_977843.1|  6 AAVVAIDGPAGTGKSSVSRRLARELGARFLDTGaMYRIVTLAVLRAGADPSDIaaVETIASTVQ 69
                                   67899********************877776665444444555555556666644555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                         AAA_22  74 sseell.ealeqalraravielliiDEaqhlrseealeeL 112
                                    ++++l  ++    l+a+++  ++i+D  +   ++e++ +L
  gi|121637620|ref|YP_977843.1| 182 RRDHLDsTRAVSPLQAAGD--AVIVDTSDMT-EAEVVAHL 218
                                    3333333444444444444..5666655555.44444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   4.6e-06    0.0056      26      52 ..       8      42 ..       2     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                         AAA_16 26 lvllsGesGvGKsslvrellralekd........g 52
                                   +v + G++G+GKss+ r+l+r+l ++        +
  gi|121637620|ref|YP_977843.1|  8 VVAIDGPAGTGKSSVSRRLARELGARfldtgamyR 42
                                   57889****************99998444443331 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.016       8     128 ..       4     225 ..       1     229 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp..eeillvaftgrAakelrerlaalgaeatTiH.rlal....... 77 
                                    l++ v+++ +++GtGK+ v +   ++l ++        +i+ +a+ +  a+     +aa++  a+T+  +l+        
  gi|121637620|ref|YP_977843.1|   4 LSAAVVAIDGPAGTGKSSVSRRLARELGARFLDTGamYRIVTLAVLRAGADPSD--IAAVETIASTVQmSLGYdpdgdsc 81 
                                    5678999************99999988776533331267777777666665543..446788899998455559999999 PP

                         AAA_19  78 ................................................................................ 77 
                                                                                                                    
  gi|121637620|ref|YP_977843.1|  82 ylagedvsveirgdavtravsavssvpavrtrlvelqrtmaegpgsivvegrdigtvvfpdapvkifltasaetrarrrn 161
                                    9999***********************************************************************99999 PP

                         AAA_19  78 ................ldfddlltealelle......eaeeekklqeee.llivDEfqdvd.elqyrLlkallge 128
                                                            +     +      +++  ++lq++  ++ivD + +++ e+  +Ll+ ++ +
  gi|121637620|ref|YP_977843.1| 162 aqnvaagladdydgvlA-------DV----RrrdhldSTRAVSPLQAAGdAVIVDTSDMTEaEVVAHLLELVTRR 225
                                    99999888744443221.......11....12333436778889988878***********9999***9988855 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.1e-05     0.025       4      29 ..      12      37 ..       9      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                   ESSTTSSHHHHHHHHHHHHTHEEEEE CS
                            AAA  4 yGppGtGKTllakavakelgveflei 29
                                    Gp GtGK+++ + +a+elg++fl +
  gi|121637620|ref|YP_977843.1| 12 DGPAGTGKSSVSRRLARELGARFLDT 37
                                   59******************999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05     0.059       2      49 ..       8      56 ..       7      77 .. 0.79
   2 ?   -0.8   0.0       1.1   1.3e+03      41      71 ..     152     182 ..     141     226 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS- CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsg 49
                                   +v++ G+aG GK+   ++la+++ ++ l+ ga ++ v +  lr+  +++
  gi|121637620|ref|YP_977843.1|  8 VVAIDGPAGTGKSSVSRRLARELGARFLDTGAmYRIVTLAVLRAGADPS 56
                                   799********************99999888766666666666655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                    ETTTTTTS-...-HCHHHCCCCTS--SSS-C CS
                          NACHT  41 slrelsrsgnarsladllfsqlpepaapvse 71 
                                    s  ++ r+ na  +a  l+++++   a+v++
  gi|121637620|ref|YP_977843.1| 152 SAETRARRRNAQNVAAGLADDYDGVLADVRR 182
                                    4556666666677777777777777777777 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.15       2      31 ..      13      42 ..      13      63 .. 0.91
   2 ?   -0.9   0.0       1.7     2e+03     105     121 ..     146     162 ..     126     177 .. 0.69
   3 ?   -3.2   0.0         9   1.1e+04      72      82 ..     200     210 ..     180     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHH CS
                         AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllr 31
                                   G+ G GK+ ++++l++++g  +l +G + r
  gi|121637620|ref|YP_977843.1| 13 GPAGTGKSSVSRRLARELGARFLDTGAMYR 42
                                   899***********************8766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                    EEEEE--HHHHHHHHHH CS
                         AAA_17 105 iilleadpeeilerrlk 121
                                     i+l a++e+  +rr  
  gi|121637620|ref|YP_977843.1| 146 KIFLTASAETRARRRNA 162
                                    46788888877777654 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9
                                    SEEEEEE-SEE CS
                         AAA_17  72 kgvlvdghpri 82 
                                    + v+vd+  ++
  gi|121637620|ref|YP_977843.1| 200 DAVIVDTSDMT 210
                                    44555555554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.17       5      27 ..      12      34 ..       9      58 .. 0.87
   2 ?   -0.4   0.0      0.89   1.1e+03      65      92 ..     198     225 ..     172     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                   E--SSSSHHHHHHHGGGGBS--E CS
                          AAA_5  5 vGppGtgKselaerlaaalnrev 27
                                    Gp GtgKs++++rla+ l++++
  gi|121637620|ref|YP_977843.1| 12 DGPAGTGKSSVSRRLARELGARF 34
                                   6****************997665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.89
                                    G-SEEEEESGGG--HHHHHHHHHHHHSS CS
                          AAA_5  65 egeilvlDEveraesevlnsLlslleer 92 
                                     g+ +++D  ++ e ev++ Ll l  +r
  gi|121637620|ref|YP_977843.1| 198 AGDAVIVDTSDMTEAEVVAHLLELVTRR 225
                                    6777777777888888888887776655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.8e-05     0.094       2      26 ..      10      34 ..       9      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                    + Gp+g+GKS+++++La++l  ++
  gi|121637620|ref|YP_977843.1| 10 AIDGPAGTGKSSVSRRLARELGARF 34
                                   578******************9877 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.17      36      60 ..      10      34 ..       4      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                          AAA_6 36 apaGpagtGKtEtvkdLakalakqv 60
                                   a+ GpagtGK+   + La++l+  +
  gi|121637620|ref|YP_977843.1| 10 AIDGPAGTGKSSVSRRLARELGARF 34
                                   789******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1620.80
//
Query:       gi|121637621|ref|YP_977844.1|  [L=463]
Description: GTP-binding protein EngA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-45  151.7   0.0    1.3e-21   76.8   0.0    2.2  2  MMR_HSR1        50S ribosome-binding GTPase
    3.5e-26   91.6   0.0    1.8e-14   53.6   0.0    2.2  2  FeoB_N          Ferrous iron transport protein B
    4.2e-25   87.9   0.0    9.4e-25   86.7   0.0    1.6  1  KH_dom-like     KH-domain-like of EngA bacterial GTPase enzym
    2.7e-19   69.5   0.1    2.8e-07   30.3   0.0    4.7  5  GTP_EFTU        Elongation factor Tu GTP binding domain
    5.3e-11   42.7   0.5      0.011   15.6   0.0    3.3  3  RsgA_GTPase     RsgA GTPase
    6.7e-11   42.5   0.1     0.0098   16.0   0.0    4.1  4  Dynamin_N       Dynamin family
    8.5e-09   35.0   0.0    1.3e-05   24.6   0.0    2.1  2  AIG1            AIG1 family
    2.4e-08   34.6   1.4      0.013   15.9   0.2    3.3  3  AAA_16          AAA ATPase domain
    1.4e-07   31.7   0.1       0.01   16.1   0.0    3.4  2  Roc             Ras of Complex, Roc, domain of DAPkinase
    3.8e-06   26.1   3.6      0.041   12.9   0.0    3.5  3  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
    5.3e-06   26.1   0.0     0.0042   16.7   0.0    3.0  2  Ras             Ras family
    3.4e-05   24.2   0.7      0.022   15.0   0.0    3.2  3  AAA_28          AAA domain
     0.0001   22.8   0.0       0.77   10.3   0.0    2.4  2  ABC_tran        ABC transporter
    0.00012   22.1   0.3     0.0039   17.1   0.4    2.2  2  Ploopntkinase3  P-loop Nucleotide Kinase3
    0.00077   19.1   0.5        8.1    6.0   0.1    3.9  4  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0008   18.9   0.0        1.4    8.2   0.0    2.4  2  TniB            Bacterial TniB protein
     0.0016   18.4   0.0      0.063   13.2   0.0    2.2  2  ATPase_2        ATPase domain predominantly from Archaea
     0.0017   18.7   0.1       0.95    9.7   0.0    2.8  2  AAA_22          AAA domain
     0.0022   18.6   0.0        3.5    8.2   0.0    2.5  2  AAA_18          AAA domain
     0.0026   17.5   0.0        1.7    8.3   0.0    2.4  2  AAA_24          AAA domain
     0.0034   17.3   0.1       0.85    9.5   0.0    2.7  2  NTPase_1        NTPase
     0.0058   17.0   0.0        4.9    7.6   0.0    2.3  2  RNA_helicase    RNA helicase
  ------ inclusion threshold ------
      0.016   14.7   0.0        1.4    8.3   0.0    3.0  2  SRPRB           Signal recognition particle receptor beta sub
      0.016   15.4   2.4       0.23   11.6   0.0    2.7  2  AAA_33          AAA domain
      0.021   14.3   0.1         14    5.1   0.0    3.2  3  Arf             ADP-ribosylation factor family
      0.022   14.5   0.0        3.9    7.3   0.0    2.6  2  AAA_29          P-loop containing region of AAA domain
       0.03   14.8   0.0        5.2    7.5   0.0    2.7  2  AAA             ATPase family associated with various cellula
       0.03   13.6   0.1          6    6.0   0.0    2.5  2  GBP             Guanylate-binding protein, N-terminal domain
      0.031   13.4   0.0       0.95    8.6   0.0    2.2  2  NB-ARC          NB-ARC domain
      0.044   13.6   0.0        8.7    6.1   0.0    3.1  4  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.08   12.9   0.0         18    5.2   0.0    3.0  3  NACHT           NACHT domain
      0.093   12.7   0.0        2.2    8.3   0.0    2.3  2  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
       0.11   12.2   0.0         26    4.5   0.0    3.2  3  PduV-EutP       Ethanolamine utilisation - propanediol utilis


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   2.3e-24   1.3e-21       2     114 .]      29     143 ..      28     143 .. 0.85
   2 !   73.0   0.0   3.6e-23     2e-20       1     114 []     201     319 ..     201     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2.3e-24
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS.HHHHHH..HHHHHHHHHHCTS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie.gaseek..glgkaflaleead 77 
                                    va+vGrpNvGKStL+n+++g+ +a v+d+pg+Trd + +   + g+++++ Dt G  e +a+  +    ++a  a++ ad
  gi|121637621|ref|YP_977844.1|  29 VAVVGRPNVGKSTLVNRILGRrEAVVQDIPGVTRDRVCYDALWTGRRFVVQDTGG-WEpNAKGLQrlVAEQASVAMRTAD 107
                                    89******************967999**************9999***********.76333333323445555557779* PP

                                    EEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +++lvvda   + ++ de  +++l +++kp++l++nk
  gi|121637621|ref|YP_977844.1| 108 AVILVVDAG-VGATAADEAAARILLRSGKPVFLAANK 143
                                    *******88.45889999*****999*********98 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 3.6e-23
                                    EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS...HHHHHH..HHHHHHHHHH CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie...gaseek..glgkaflale 74 
                                    +va+vG+pNvGKS+L+n+l g+ ++ v + +gtT d++   ++l+g+ +++vDt+Gl     +as ++     ++ +a++
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDqRSVVHEAAGTTVDPVDSLIELGGDVWRFVDTAGLRRkvgQASGHEfyASVRTHAAID 280
                                    69*******************979999*****************************632343333333446677777777 PP

                                    CTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  75 eadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +a+++++++das + l+++d ++ ++  ea++ l+l++nk
  gi|121637621|ref|YP_977844.1| 281 SAEVAIVLIDAS-QPLTEQDLRVISMVIEAGRALVLAYNK 319
                                    89********99.7799999999999999*******9998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   8.1e-12   4.4e-09       3     117 ..      29     146 ..      27     181 .. 0.78
   2 !   53.6   0.0   3.2e-17   1.8e-14       2     153 ..     201     362 ..     200     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 8.1e-12
                                    EEEEESTTSSHHHHHHHHHTTSEE.EEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHH.HHCTSSS CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqk.vgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardf.lleeepd 80 
                                    va+vG pnvGk+tl+n++ g ++  v   pGvt ++      ++g+++ + D  G ++ +a   +  va++  ++ +++d
  gi|121637621|ref|YP_977844.1|  29 VAVVGRPNVGKSTLVNRILGRREAvVQDIPGVTRDRVCYDALWTGRRFVVQDTGG-WEPNAKGLQRLVAEQAsVAMRTAD 107
                                    89******************99762679************************966.7899999999999876266899** PP

                                    EEEEEEEGGGHHH..HHHHHHHHHHTTSSEEEEEETHHH CS
                         FeoB_N  81 vvvnvvdatnler..nLyLtlqllelgvpvvlalnmide 117
                                    +v+ vvda       +      ll  g+pv la n++d 
  gi|121637621|ref|YP_977844.1| 108 AVILVVDAGVGATaaDEAAARILLRSGKPVFLAANKVDS 146
                                    *******96433300334444556666777777777665 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 3.2e-17
                                    EEEEEESTTSSHHHHHHHHHTTSEE.EEESTTSSSEEEEEEEEETTEEEEEEE----.SSSSSSSHHHHHH..HHHHHCT CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqk.vgNwpGvtvekkegklklkgkeveivDlPGi.Yslsayseeekva..rdfllee 77 
                                    +valvG+pnvGk++l+n+l+g + + v   +G+tv+     ++l g+  ++vD  G   ++ + s  e  a  r+  + +
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSvVHEAAGTTVDPVDSLIELGGDVWRFVDTAGLrRKVGQASGHEFYAsvRTHAAID 280
                                    69*******************8866167899*************************944678889888766225666679 PP

                                    SSSEEEEEEEGGG..HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT....S-EEEEBTTTTBTHHH CS
                         FeoB_N  78 epdvvvnvvdatn..lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg....vpvvktsakkkegiee 151
                                    +++v + ++da++   e++L ++  ++e g  +vla n++d +++++ e+ +++++++L      + v++sak+++ +++
  gi|121637621|ref|YP_977844.1| 281 SAEVAIVLIDASQplTEQDLRVISMVIEAGRALVLAYNKWDLVDEDRRELLQREIDRELVqvrwAQRVNISAKTGRAVHK 360
                                    99*********9854599****************************9999999988887422224568888998888888 PP

                                    HH CS
                         FeoB_N 152 ll 153
                                    l+
  gi|121637621|ref|YP_977844.1| 361 LV 362
                                    76 PP

>> KH_dom-like  KH-domain-like of EngA bacterial GTPase enzymes, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   1.7e-27   9.4e-25       1      80 []     375     453 ..     375     453 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.7e-27
                                    ---HHHHHHHHHHHHCCS--SET.TCC-EEEEEEEEETTTTEEEEEECSCCCS-HHHHHHHHHHHHHHCT-TTS--EEEE CS
                    KH_dom-like   1 RistseLnrvleeavekhpppvk.gkrlkiyyatqvgtrpptfvlfvndpelvkesykryLenqlreafgfegtPirlkf 79 
                                    Ri t+ Ln++l e+++++pppv+ gk+++i +atq+++rpptfvlf++    ++  y+r+Le++lre+fgf+g+Pir+ +
  gi|121637621|ref|YP_977844.1| 375 RIATGPLNTWLTEVTAATPPPVRgGKQPRILFATQATARPPTFVLFTTG--FLEAGYRRFLERRLRETFGFDGSPIRVNV 452
                                    89*******************9989**********************95..**************************998 PP

                                    E CS
                    KH_dom-like  80 R 80 
                                    R
  gi|121637621|ref|YP_977844.1| 453 R 453
                                    7 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.013       6.9       6      28 ..      29      51 ..      26      62 .. 0.86
   2 !   23.4   0.0   6.7e-08   3.6e-05      88     135 ..     100     147 ..      96     158 .. 0.91
   3 ?   -0.0   0.0         1   5.4e+02     172     193 ..     166     187 ..     160     188 .. 0.89
   4 ?    2.3   0.0      0.19     1e+02       4      30 ..     200     226 ..     199     246 .. 0.81
   5 !   30.3   0.0   5.1e-10   2.8e-07      78     192 ..     265     369 ..     247     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                                   EEEEESTTSSHHHHHHHHHHHTT CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyktg 28
                                   ++++g  + GK+TL+ r+l + +
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRILGRRE 51
                                   789***************96655 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.7e-08
                                    HHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST CS
                       GTP_EFTU  88 irglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl 135
                                    + ++r++D ++lvvda  G ++  e  +r++l+ g p++++ NK+D  
  gi|121637621|ref|YP_977844.1| 100 SVAMRTADAVILVVDAGVGATAADEAAARILLRSGKPVFLAANKVDSE 147
                                    678*******************************************86 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1
                                    EEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 172 fgSalkgegvktllealvellp 193
                                     +Sa++g gv +ll+ +   lp
  gi|121637621|ref|YP_977844.1| 166 AISAMHGRGVADLLDGVLAALP 187
                                    68*************9998887 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.19
                                    EEEEEEESTTSSHHHHHHHHHHHTTSS CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgai 30 
                                    r ++++g  + GK++L+ +L  +   +
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLAGDQRSV 226
                                    67899**************98666554 PP

  == domain 5  score: 30.3 bits;  conditional E-value: 5.1e-10
                                    SSSGGGHHHHHHH.HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  78 PGHvdFskevirg.lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkee 155
                                     GH+ + +  +++ +  +++a++++da++  ++q  +v+ ++++ g  ++++ NK D + +++ + +++e+ ++l     
  gi|121637621|ref|YP_977844.1| 265 SGHEFYASVRTHAaIDSAEVAIVLIDASQPLTEQDLRVISMVIEAGRALVLAYNKWDLVdEDRRELLQREIDREL----- 339
                                    69999988766654999******************************************6566667788999999..... PP

                                    HHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                       GTP_EFTU 156 klekygekgekevpvvfgSalkgegvktllealvell 192
                                     +++ ++++      v +Sa++g +v +l+ a+ + l
  gi|121637621|ref|YP_977844.1| 340 -VQVRWAQR------VNISAKTGRAVHKLVPAMEDAL 369
                                    .88888775......899*****99999999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-05     0.011      92     130 ..      19      57 ..       9      63 .. 0.86
   2 !   14.7   0.1   3.9e-05     0.021     100     129 ..     200     229 ..     191     236 .. 0.85
   3 !    8.6   0.1     0.003       1.6      20      99 ..     286     367 ..     268     371 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                                    HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                    e++e  +  ++++vG   vGKStL+n++l++ e+ ++++
  gi|121637621|ref|YP_977844.1|  19 EIAESGAAPVVAVVGRPNVGKSTLVNRILGRREAVVQDI 57 
                                    566666778999******************999999987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.9e-05
                                    SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktge 129
                                    + ++lvG+  vGKS+L+n+l+++++  ++e
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLAGDQRSVVHE 229
                                    56899*****************98777665 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.003
                                    EEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTT.SEEEE--TTTHTTHHHHHH CS
                    RsgA_GTPase  20 livvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee...eleelkeelealg.yevllvsaktkegleelke 95 
                                    ++++ +++p +++    r++ ++ e+g  +v++ nK Dl++e++     +e+  el ++   + + +sakt++++++l +
  gi|121637621|ref|YP_977844.1| 286 IVLIDASQPLTEQ--DLRVISMVIEAGRALVLAYNKWDLVDEDRrelLQREIDRELVQVRwAQRVNISAKTGRAVHKLVP 363
                                    3333334333333..3499999999999**************99766344444555544425678899999999999998 PP

                                    HCTT CS
                    RsgA_GTPase  96 llkd 99 
                                    +++d
  gi|121637621|ref|YP_977844.1| 364 AMED 367
                                    8877 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.8e-05    0.0098       1      29 [.      29      57 ..      29      65 .. 0.85
   2 ?    2.3   0.0      0.29   1.6e+02     101     148 ..      74     125 ..      64     144 .. 0.71
   3 !   15.2   0.0     3e-05     0.017       1      29 [.     202     230 ..     202     239 .. 0.83
   4 ?    3.9   0.0     0.093        50     105     151 ..     251     304 ..     244     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S---SS CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpn 29
                                   +avvG  + GKS+++n +lg++  +++ +
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRILGRREAVVQDI 57
                                   89******************997666665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.29
                                    -SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS-CCC-CHH CS
                      Dynamin_N 101 kgltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhdlsnseal 148
                                     + ++ D+ G   ++k+ q    e +  +++ ad++++v++a + ++ ++  
  gi|121637621|ref|YP_977844.1|  74 RRFVVQDTGGWEPNAKGLQrlvaEQASVAMRTADAVILVVDAGVGATAADEA 125
                                    55667799999999999996665555556799**********9977755543 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3e-05
                                    EEEEEBTTTTHHHHHHHHHTS--S---SS CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpn 29 
                                    +a+vG+ + GKSS+ln+L g++  ++++ 
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGDQRSVVHEA 230
                                    799*****************997776655 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.093
                                    EEE---B-SSSGTTS.......HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHH CS
                      Dynamin_N 105 lvDlPGldsvnkrdq.......elvkeyikkadiilavtsanhdlsnsealfla 151
                                    +vD+ Gl +   +           ++ +i++a + +++ +a++ l++++ + ++
  gi|121637621|ref|YP_977844.1| 251 FVDTAGLRRKVGQASghefyasVRTHAAIDSAEVAIVLIDASQPLTEQDLRVIS 304
                                    79999999955555567799844455666*****************99987665 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.4e-08   1.3e-05       4     107 ..      30     130 ..      28     135 .. 0.89
   2 !    8.3   0.0    0.0023       1.3       2     105 ..     201     304 ..     200     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.4e-08
                                    EEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT- CS
                           AIG1   4 vlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseeg 83 
                                     +vG+  +GkS+ +N ilg++    +    +vt+    + + w g++ +V DT g   ++ +a+ +++ + +  ++++  
  gi|121637621|ref|YP_977844.1|  30 AVVGRPNVGKSTLVNRILGRREAVVQ-DIPGVTRDRVCYDALWTGRRFVVQDTGG---WEPNAKGLQRLVAEQASVAMRT 105
                                    58******************998877.789***********************99...567777777888888899999* PP

                                    ESEEEEEEETT.B-SHHHHHHHHHH CS
                           AIG1  84 ihalllvlslg.rfteedekalktl 107
                                     +a++lv+++g   t+ de+a++ l
  gi|121637621|ref|YP_977844.1| 106 ADAVILVVDAGvGATAADEAAARIL 130
                                    ***********99999999998766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                    EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCT..TCCHHCHHHHHHHHHHH CS
                           AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdl..svsadkiskeivrclll 79 
                                    ++ lvGk  +GkS+  N + g++    + +a++ t  +  +  +  g     +DT gl     ++s  + + ++     +
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSVVH-EAAGTTVDPVDSLIELGGDVWRFVDTAGLRRKvgQASGHEFYASVRTHAAI 279
                                    789*****************99986666.567777777777778888888888888884331133555555555554444 PP

                                    CTT-ESEEEEEEETTB-SHHHHHHHH CS
                           AIG1  80 seegihalllvlslgrfteedekalk 105
                                     +  + ++l++   + +te+d  +++
  gi|121637621|ref|YP_977844.1| 280 DSAEVAIVLIDA-SQPLTEQDLRVIS 304
                                    444343333332.2356666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00024      0.13      20      62 ..      22      63 ..      15      80 .. 0.75
   2 ?    3.3   0.0      0.18        95      17      65 ..      99     148 ..      88     193 .. 0.74
   3 !   15.9   0.2   2.3e-05     0.013      19     156 ..     194     332 ..     180     345 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdq 62
                                    sg  ++v ++G + vGKs+lv+++l    ++++++  + g +++
  gi|121637621|ref|YP_977844.1| 22 ESGAAPVVAVVGRPNVGKSTLVNRILG---RREAVVqdIPGVTRD 63
                                   577789****************99994...444555456665555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                         AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqles 65 
                                     +v++ +  +v+l+ ++GvG ++  ++++r l ++g  +fl+++ +++e+
  gi|121637621|ref|YP_977844.1|  99 ASVAMRTADAVILVVDAGVGATAADEAAARILLRSGkPVFLAANKVDSEK 148
                                    456666678999******************99999889998887777733 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.3e-05
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdql.esaipysa.laqalareellrqlldeaesael 94 
                                     +sg+p+ v l+G + vGKssl+++l+    +++ ++  ++g++++  +s i++   +++  ++ +l r++++++     
  gi|121637621|ref|YP_977844.1| 194 SASGGPRRVALVGKPNVGKSSLLNKLAG---DQRSVVheAAGTTVDPvDSLIELGGdVWRFVDTAGLRRKVGQASGHEFY 270
                                    578899********************94...4444443466665555455688866677777777888888888444443 PP

                         AAA_16  95 eawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwadeaslqlla 156
                                    +  r++     a+v+ +  ++++ l e+  r + + ++  +r lvl     + +de+ ++ll+
  gi|121637621|ref|YP_977844.1| 271 ASVRTHAAIDSAEVAIVLIDASQPLTEQDLRVIsMVIEA-GRALVLAYNKWDLVDEDRRELLQ 332
                                    333333333333344444444478888888888777777.66788888888888888888876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00046      0.25       2      67 ..      29      85 ..      28     146 .. 0.52
   2 !   16.1   0.0   1.8e-05      0.01       1      39 [.     201     240 ..     201     322 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGG CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqe 67
                                   v +vG  +vGK++l++r++ +  +   + + gv+  +  +   + +   ++    ++ + Dt+G e
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRILGR-REAVVQDIPGVTRDRV-C--YDAL---WTG--RRFVVQDTGGWE 85
                                   679**************9954.4444555555554322.2..1221...222..245566666644 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-05
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEET.TTTEEEEEE CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekeks.tigvdfltk 39 
                                    +v lvG+ +vGK+sll+++  d+ s  +++  + vd +++
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSVVHEAaGTTVDPVDS 240
                                    589*****************99998654430344444433 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.5e-05     0.041      23      49 ..      20      46 ..      10      54 .. 0.88
   2 !   10.9   0.3    0.0003      0.16      24      68 ..     194     238 ..     185     249 .. 0.88
   3 ?    0.5   0.2      0.44   2.4e+02     175     227 ..     318     367 ..     277     379 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                   GGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB 23 lakaGraqvvGltGvPGaGkstlveal 49
                                   +a++G a vv + G P +Gkstlv+++
  gi|121637621|ref|YP_977844.1| 20 IAESGAAPVVAVVGRPNVGKSTLVNRI 46
                                   6789********************997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0003
                                    GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                           MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68 
                                    + +G  ++v l G P +Gks l+++l+   r+  +  a   vDP 
  gi|121637621|ref|YP_977844.1| 194 SASGGPRRVALVGKPNVGKSSLLNKLAGDQRSVVHEAAGTTVDPV 238
                                    5688999**********************9999999999999996 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.44
                                    E---HHHHHHHHHHHHHHHHHCSTT.BTTB--EEEEEBCCCTBSHHHHHHHHHH CS
                           MeaB 175 nkaDkkeaekaarelraaleleeek.ekeWrpkvlktsavegeGidelvdaiee 227
                                    nk D+ + ++  rel +  e+++e  +  W  +v ++sa++g+ +++lv a+e+
  gi|121637621|ref|YP_977844.1| 318 NKWDLVDEDR--RELLQR-EIDRELvQVRWAQRV-NISAKTGRAVHKLVPAMED 367
                                    5555433332..333222.233333367787765.7899999999999988876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014       7.4       2      20 ..      29      47 ..      28     177 .. 0.77
   2 !   16.7   0.0   7.8e-06    0.0042       2     153 ..     202     362 ..     201     370 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                                   EEEEESTTSSHHHHHHHHH CS
                            Ras  2 lvlvGdsavGKtslllrfv 20
                                   + +vG  +vGK++l++r  
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRIL 47
                                   579************9965 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.8e-06
                                    EEEEESTTSSHHHHHHHHHHSSCS..SSCTTTSSEEEEEEEEEET........TEEEEEEEEEETTSGGGHHHHHHH.HT CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFk..eeyesTigvdfytkeievd........gkevkleiwDTAGqeefkslrely.yr 70 
                                    + lvG+ +vGK+sll++ + d+ +  +e   T  vd   + ie+            ++ ++    G e + s+r+   + 
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGDQRSvvHEAAGTT-VDPVDSLIELGgdvwrfvdTAGLRRKVGQASGHEFYASVRTHAaID 280
                                    789***************987654114444455.6888888887733444433444555666666789999998765166 PP

                                    TESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG...G-SS-HHHHHHHHHHHTSEEEEEBTTTTC CS
                            Ras  71 daegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee...kravsteegeelakelglkfletSAktne 147
                                    +ae+++++ d ++  + ++    ++ i++v e   ++vL  nK Dl +   ++ +++e  +el +   ++ +++SAkt  
  gi|121637621|ref|YP_977844.1| 281 SAEVAIVLIDASQPLTEQD----LRVISMVIEAGRALVLAYNKWDLVDedrRELLQREIDRELVQVRWAQRVNISAKTGR 356
                                    7788888877666655444....44556666666789*********9877544455555566666666889999999999 PP

                                    THHHHH CS
                            Ras 148 nveeaf 153
                                     v++++
  gi|121637621|ref|YP_977844.1| 357 AVHKLV 362
                                    998865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.023        13       2      85 ..      29     120 ..      28     126 .. 0.55
   2 !   15.0   0.0   4.1e-05     0.022       1      35 [.     201     235 ..     201     268 .. 0.93
   3 ?   -1.7   0.1       5.4   2.9e+03      20      56 ..     316     351 ..     311     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaare.ileekl.....akgedalpwvedllafaervleeqleeeaaaaa 72 
                                    ++++G +  GK+tl++++  r    ++ +p + r+ ++ + l     +  +d+  w+    +  +r+++eq++ + ++a+
  gi|121637621|ref|YP_977844.1|  29 VAVVGRPNVGKSTLVNRILGRreaVVQDIPGVTRDrVCYDALwtgrrFVVQDTGGWE-PNAKGLQRLVAEQASVAMRTAD 107
                                    789999*********998855233222234444421333333221112222444453.4444445555566666666677 PP

                         AAA_28  73 nkvlfcDrglldt 85 
                                      +l++D g+ +t
  gi|121637621|ref|YP_977844.1| 108 AVILVVDAGVGAT 120
                                    7777777776655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.1e-05
                         AAA_28   1 kivitGgestGKTtlleaLaargypvvpEaareil 35 
                                    +++++G +  GK++ll++La ++ +vv+Eaa + +
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSVVHEAAGTTV 235
                                    799***************************98765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.4
                         AAA_28  20 aargypvvpEaareileeklakgedalpwvedllafa 56 
                                    a +++  v E  re+l+ + +++  + +w+ +++++ 
  gi|121637621|ref|YP_977844.1| 316 AYNKWDLVDEDRRELLQREIDRELVQVRWA-QRVNIS 351
                                    455777888888888888888888888885.555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017       0.9      13      36 ..      28      51 ..      23      81 .. 0.89
   2 !   10.3   0.0    0.0014      0.77      13      36 ..     201     224 ..     197     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                                   EEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                   +va+vG+   GKStL++ ++g  +
  gi|121637621|ref|YP_977844.1| 28 VVAVVGRPNVGKSTLVNRILGRRE 51
                                   79*****************99866 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
                                    EEEEEESTTSSHHHHHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllk 36 
                                    +va+vG+   GKS+Ll+ lag  +
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQR 224
                                    89*****************99876 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.23   1.2e+02       6      23 ..      29      46 ..      25      66 .. 0.85
   2 !   17.1   0.4   7.2e-06    0.0039       4     152 ..     200     349 ..     198     376 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                 Ploopntkinase3  6 iylvGqPGaGkstlmael 23
                                   + +vG P  Gkstl+  +
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRI 46
                                   679***********9765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.2e-06
                 Ploopntkinase3   4 rliylvGqPGaGkstlmaeltkgfdrskveqee.etv.phdvlvdrttGev....vgaelGkrreafsGtdalassiidk 77 
                                    r + lvG+P  Gks l+ +l+ g +rs v+++  +tv p d+l++   G+v     +a l ++ ++ sG +  as     
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLA-GDQRSVVHEAAgTTVdPVDSLIE-LGGDVwrfvDTAGLRRKVGQASGHEFYASVRTHA 277
                                    7789***************96.66788887776666625666665.56665221146777777789*****999987777 PP

                 Ploopntkinase3  78 avPwvetkPydlllaeGar.lank..rfldaaleaGyevtlalldhdqadawrka.rskklgrvqneswvkgrlsasrk 152
                                    a+   ++    ++l + ++ l+++  r +   +eaG ++ la+ + d +d+ r++   ++++r+     v+ r +   +
  gi|121637621|ref|YP_977844.1| 278 AI---DSAEVAIVLIDASQpLTEQdlRVISMVIEAGRALVLAYNKWDLVDEDRRElLQREIDRE----LVQVRWAQRVN 349
                                    75...66677788877765355434499**************9999999876654134555554....44444433333 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.023        12       1      25 [.      27      51 ..      27      63 .. 0.85
   2 ?    2.0   0.0      0.24   1.3e+02      87     123 ..      77     117 ..      67     157 .. 0.64
   3 ?    0.1   0.0      0.93   5.1e+02       4      22 ..     203     222 ..     201     234 .. 0.79
   4 ?    6.0   0.1     0.015       8.1     112     164 ..     282     333 ..     260     346 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.023
                                   EEEEEEESTTCCHHHHHHHHHCT-- CS
                           cobW  1 pvtvltGflGsGKTtLlnhllenra 25
                                   pv+ ++G +  GK+tL+n++l +r+
  gi|121637621|ref|YP_977844.1| 27 PVVAVVGRPNVGKSTLVNRILGRRE 51
                                   689999***************4443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                                    EEEECTTTTHHHH.HTT...SHHHHHCCCECEEEEEEETTT CS
                           cobW  87 liEttGlaePapv.aft...eeelksdltldavvavvDakn 123
                                    ++  tG  eP+   + +   e+   +  t+dav+ vvDa  
  gi|121637621|ref|YP_977844.1|  77 VVQDTGGWEPNAKgLQRlvaEQASVAMRTADAVILVVDAGV 117
                                    666677777776642224436666678899********933 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.93
                                    EEEESTTCCHHHHHHHHH.C CS
                           cobW   4 vltGflGsGKTtLlnhll.e 22 
                                     l+G +  GK++Lln+l  +
  gi|121637621|ref|YP_977844.1| 203 ALVGKPNVGKSSLLNKLAgD 222
                                    57888899********9852 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.015
                                    ECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHH CS
                           cobW 112 ldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeealleklee 164
                                    +++ ++++Da++  +e++     +  +   a +l  nK+Dl+de++  e l++
  gi|121637621|ref|YP_977844.1| 282 AEVAIVLIDASQPLTEQDLRVISMVIEAGRALVLAYNKWDLVDEDRR-ELLQR 333
                                    566789999988776666666666666666777778*******9944.44433 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.003       1.7      35      56 ..      26      47 ..      18      66 .. 0.82
   2 !    8.2   0.0    0.0027       1.4      35      64 ..     199     228 ..     180     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.003
                           TniB 35 mpnlllvGdsnnGKtmivekFa 56
                                    p + +vG++n+GK+++v++  
  gi|121637621|ref|YP_977844.1| 26 APVVAVVGRPNVGKSTLVNRIL 47
                                   68899*************9976 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                           TniB  35 mpnlllvGdsnnGKtmivekFarlhppekd 64 
                                    ++ + lvG++n+GK+++++k a ++++  +
  gi|121637621|ref|YP_977844.1| 199 PRRVALVGKPNVGKSSLLNKLAGDQRSVVH 228
                                    56799***************9988766544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00012     0.063      13      45 ..      19      51 ..      18      64 .. 0.92
   2 ?    2.7   0.0      0.19     1e+02      18      42 ..     198     221 ..     188     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                       ATPase_2 13 eilerepneiyfiYGpegsGKtaLlkeiienle 45
                                   ei+e++ ++++ + G+ ++GK++L+++i+ ++e
  gi|121637621|ref|YP_977844.1| 19 EIAESGAAPVVAVVGRPNVGKSTLVNRILGRRE 51
                                   799*************************99886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                       ATPase_2  18 epneiyfiYGpegsGKtaLlkeiie 42 
                                    +p+++ ++ G  ++GK++Ll++++ 
  gi|121637621|ref|YP_977844.1| 198 GPRRVALV-GKPNVGKSSLLNKLAG 221
                                    55555554.99**********9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0018      0.95       6      32 ..      27      53 ..      22     115 .. 0.76
   2 ?    6.0   0.0     0.026        14       8      70 ..     202     258 ..     197     318 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldee 32
                                    +++v+G + +GK+tl++r+l + +++
  gi|121637621|ref|YP_977844.1| 27 PVVAVVGRPNVGKSTLVNRILGRREAV 53
                                   6789***************99887554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka 70 
                                    ++++G + +GK+ ll++l+               vv      t+    s+ +l  ++ r+++  + +
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGDQRS----------VVheaaGTTVDPVDSLIELGGDVWRFVDTAGLR 258
                                    579**************9976422..........222222333333334444444444444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0064       3.5       1      25 [.      29      59 ..      29     142 .. 0.61
   2 !    8.0   0.0    0.0074         4       1      21 [.     202     222 ..     202     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0064
                         AAA_18  1 IlltGtpGvGKttlakeL.skrlgf.....g 25
                                   +++ G p vGK+tl +++  +r+++     g
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRIlGRREAVvqdipG 59
                                   6899**********98874444344344442 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0074
                         AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                    ++l G+p vGK++l + L+  
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGD 222
                                    6899************99644 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0076       4.2       3      23 ..      27      49 ..      25     110 .. 0.88
   2 !    8.3   0.0    0.0031       1.7       3      23 ..     200     221 ..     198     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0076
                         AAA_24  3 lkiliyGpsgiGKTtlakel..g 23
                                     ++++G + +GK+tl++++   
  gi|121637621|ref|YP_977844.1| 27 PVVAVVGRPNVGKSTLVNRIlgR 49
                                   5799*************998643 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0031
                         AAA_24   3 lkiliyGpsgiGKTtlakel.g 23 
                                    ++++++G++ +GK++l+++l g
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLaG 221
                                    689**************99952 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0016      0.85       2      22 ..      29      49 ..      28      83 .. 0.82
   2 ?    5.0   0.0     0.039        21       1      23 [.     201     223 ..     201     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                                   EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                   v++ G+p vGK+Tlv+++l  
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRILGR 49
                                   7899*************9865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                                    EEEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   1 kvfiTGppGvGKtTlvkkvlell 23 
                                    +v++ G+p vGK+ l++k++   
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQ 223
                                    58899*************98765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.013       6.9       2      19 ..      30      47 ..      29      71 .. 0.86
   2 !    7.6   0.0     0.009       4.9       2      21 ..     203     222 ..     202     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                   RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                    ++G++++GKStl++++ 
  gi|121637621|ref|YP_977844.1| 30 AVVGRPNVGKSTLVNRIL 47
                                   689***********9964 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.009
                   RNA_helicase   2 wlyGpsgeGKStlakeLaka 21 
                                     l+G++++GKS+l ++La +
  gi|121637621|ref|YP_977844.1| 203 ALVGKPNVGKSSLLNKLAGD 222
                                    689*************9865 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.16        86       4      26 ..      27      49 ..      24     148 .. 0.61
   2 ?    8.3   0.0    0.0026       1.4       4     145 ..     200     343 ..     198     362 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                   -EEEEE-STTSSHHHHHHHHHHS CS
                          SRPRB  4 pavllvGlsdsGKTslftrLttd 26
                                   p v +vG  + GK +l +r++  
  gi|121637621|ref|YP_977844.1| 27 PVVAVVGRPNVGKSTLVNRILGR 49
                                   77889999999999999998754 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
                                    -EEEEE-STTSSHHHHHHHHHHS..S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEE CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttd..svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvf 81 
                                    ++v lvG  + GK sl+++L  d  sv +  +      ++++ +  g  ++++D  G  +   + +  +   +s+++   
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLAGDqrSVVHEAAGTTVDPVDSLIELGGDVWRFVDTAGLRRKVGQAS-GHEFYASVRTH-A 277
                                    57899***************9995433333333333333333455666677777766333222222.22344444443.3 PP

                                    EEETTS-HHHHHHHHHHHHH..HHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHHHHHHHH CS
                          SRPRB  82 vvDStidpkevkevAEllye..illiteklkdavdiliACnKqelflakspklikdaLEkElnkii 145
                                     +DS+     + +    l+e  + +i++ ++ +  +++A nK +l+     +l++ ++++El +++
  gi|121637621|ref|YP_977844.1| 278 AIDSAEVAIVLIDASQPLTEqdLRVISMVIEAGRALVLAYNKWDLVDEDRRELLQREIDRELVQVR 343
                                    466666666666666666532245555556666667777777777766666667777777766666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00043      0.23       1      78 [.      28     116 ..      28     150 .. 0.62
   2 ?    3.3   0.0      0.15        82       2      23 ..     202     223 ..     202     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                         AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg.........tdqqsktdytrvldrlyqilnelarkalsag 70 
                                    +v +vG p +GKstl+ r+l ++ av+ + + + r r+++           q++  + +  ++ l + ++e a  a++ +
  gi|121637621|ref|YP_977844.1|  28 VVAVVGRPNVGKSTLVNRILGRREAVVQDIPGVTRdRVCYdalwtgrrfVVQDTGGWEP-NAKGLQRLVAEQASVAMRTA 106
                                    7999****************999888766666544466654444222221122222222.33345666666666666666 PP

                         AAA_33  71 rnvil..dat 78 
                                     +vil  da+
  gi|121637621|ref|YP_977844.1| 107 DAVILvvDAG 116
                                    6666655555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                         AAA_33   2 vllvGlpGsGKstlaerllkkl 23 
                                    v lvG p +GKs l+ +l+  +
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGDQ 223
                                    5689***********9998655 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.025        14      19      69 ..      31      85 ..      24     171 .. 0.67
   2 ?    4.8   0.0     0.032        18      16      53 ..     201     238 ..     192     258 .. 0.88
   3 ?   -0.5   0.1       1.3   7.2e+02     117     158 ..     312     352 ..     278     368 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                                   EEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE....TTEEEEEEEE-SSG CS
                            Arf 19 llGLDnaGKtTilkklkleelvttvPTigfnveelei....knlkftvwDvGGqe 69
                                   ++G  n GK+T+++++   + + ++   g + +++ +     + +f v D GG e
  gi|121637621|ref|YP_977844.1| 31 VVGRPNVGKSTLVNRILGRREAVVQDIPGVTRDRVCYdalwTGRRFVVQDTGGWE 85
                                   789999*********9988877777777888888888444455689999999854 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                                    EEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEE CS
                            Arf  16 rilllGLDnaGKtTilkklkleelvttvPTigfnveel 53 
                                    r+ l+G  n GK+ +l+kl  ++ + +    g +v+ +
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSVVHEAAGTTVDPV 238
                                    78899****************99998888888887766 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                                    EEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBT CS
                            Arf 117 allvlaNKqDlpealseeelrellgleelkgkrkleiqkcsa 158
                                    al++  NK Dl +   +e l+++++ e ++  r  + ++ sa
  gi|121637621|ref|YP_977844.1| 312 ALVLAYNKWDLVDEDRRELLQREIDRELVQ-VRWAQRVNISA 352
                                    455566999999988887777776655544.33333333334 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0073       3.9      15      39 ..      19      43 ..       8      47 .. 0.72
   2 ?    4.3   0.0      0.06        33      25      39 ..     202     216 ..     191     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0073
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                   + +e   + ++ ++G+  +GKSTl+
  gi|121637621|ref|YP_977844.1| 19 EIAESGAAPVVAVVGRPNVGKSTLV 43
                                   444444333899************8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.06
                         AAA_29  25 tlltGpsGsGKSTll 39 
                                    + l+G+  +GKS+ll
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLL 216
                                    789**********98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.068        37       2      21 ..      30      49 ..      29     123 .. 0.86
   2 ?    7.5   0.0    0.0095       5.2       2      34 ..     203     235 ..     202     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.068
                                   EEESSTTSSHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavake 21
                                    ++G p +GK++l++ +   
  gi|121637621|ref|YP_977844.1| 30 AVVGRPNVGKSTLVNRILGR 49
                                   589***********998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0095
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTC CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsel 34 
                                     l+G p +GK++l + +a +  + + e  g+++
  gi|121637621|ref|YP_977844.1| 203 ALVGKPNVGKSSLLNKLAGDQRSVVHEAAGTTV 235
                                    69****************997665555555544 PP

>> GBP  Guanylate-binding protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.011         6      23      46 ..      28      51 ..      19      74 .. 0.90
   2 ?    4.9   0.1     0.024        13      24      44 ..     202     237 ..     200     369 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                                   EEEEEEBTTSSHHHHHHHHHTBSS CS
                            GBP 23 vvaivGlyRkGksfLlnklarkkk 46
                                   vva+vG    Gks L+n+++++++
  gi|121637621|ref|YP_977844.1| 28 VVAVVGRPNVGKSTLVNRILGRRE 51
                                   9*******************9886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.024
                                    EEEEEBTTSSHHHHHHHHHT...............B CS
                            GBP  24 vaivGlyRkGksfLlnklar...............k 44 
                                    va+vG    Gks Llnkla+               +
  gi|121637621|ref|YP_977844.1| 202 VALVGKPNVGKSSLLNKLAGdqrsvvheaagttvdP 237
                                    89999999***********95555555555555550 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0018      0.95      22      43 ..      28      49 ..      17      61 .. 0.82
   2 ?    2.4   0.0      0.14        75      22      47 ..     201     226 ..     186     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                   EEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                   vva+vG++ vGK+tl++ il  
  gi|121637621|ref|YP_977844.1| 28 VVAVVGRPNVGKSTLVNRILGR 49
                                   9****************99866 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                                    EEEEEESTTSSHHHHHHHHCCSHCCC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdev 47 
                                     valvG++ vGK+ l+++   +  +v
  gi|121637621|ref|YP_977844.1| 201 RVALVGKPNVGKSSLLNKLAGDQRSV 226
                                    699*************9988776655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.11        62       1      17 [.      31      47 ..      31      57 .. 0.85
   2 ?   -0.9   0.0       2.2   1.2e+03     148     180 ..     126     158 ..      97     186 .. 0.82
   3 ?   -2.6   0.0       6.8   3.7e+03       2      16 ..     205     219 ..     204     222 .. 0.88
   4 ?    6.1   0.0     0.016       8.7     125     201 ..     284     362 ..     262     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                     ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                   vvG + +GK+t+v+++ 
  gi|121637621|ref|YP_977844.1| 31 VVGRPNVGKSTLVNRIL 47
                                   89***********9986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                     ATP_bind_1 148 alsamlrlelPhvvvlnkfDllkeklekeleff 180
                                    a +++lr + P   + nk+D  k +++ +  + 
  gi|121637621|ref|YP_977844.1| 126 AARILLRSGKPVFLAANKVDSEKGESDAAALWS 158
                                    6789999999**********9886666665555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.8
                     ATP_bind_1   2 vGpaGsGKttfvgal 16 
                                    vG + +GK+++ ++l
  gi|121637621|ref|YP_977844.1| 205 VGKPNVGKSSLLNKL 219
                                    79999*****99987 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                     ATP_bind_1 125 vvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.......eky 197
                                    v+++L+D+    +     ++ l  +s++++++   v ++nk Dl++e++++ l++  d e ++    +         +++
  gi|121637621|ref|YP_977844.1| 284 VAIVLIDASQPLT-----EQDLRVISMVIEAGRALVLAYNKWDLVDEDRRELLQREIDRELVQVRWAQRVnisaktgRAV 358
                                    5666666544443.....4445567899******************9966666666666655554444432343333333 PP

                     ATP_bind_1 198 kkla 201
                                    +kl 
  gi|121637621|ref|YP_977844.1| 359 HKLV 362
                                    3444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.083        45       2      21 ..      28      47 ..      27      51 .. 0.91
   2 ?    5.2   0.0     0.033        18       1      21 [.     200     220 ..     200     228 .. 0.90
   3 ?   -1.7   0.0       4.3   2.4e+03      35      85 ..     266     315 ..     250     341 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.083
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   +v++ G++ +GK+tL+ ++ 
  gi|121637621|ref|YP_977844.1| 28 VVAVVGRPNVGKSTLVNRIL 47
                                   6899*************995 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                                    SCEEEEC-TTTCHHHHHHHHH CS
                          NACHT   1 rlvilqGeaGsGKTtLlqkla 21 
                                    r v+l G++ +GK+ Ll kla
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLA 220
                                    6799***************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.3
                                    SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEE CS
                          NACHT  35 klvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelperlLl 85 
                                     + F+ s+r+   +  a  +a +l +  +++ ++  +v+++++e  + l+l
  gi|121637621|ref|YP_977844.1| 266 GHEFYASVRTHAAIDSA-EVAIVLIDASQPLTEQDLRVISMVIEAGRALVL 315
                                    56688889998888888.777777777777777777788888887777666 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.37     2e+02      57     100 ..     136     182 ..     132     187 .. 0.70
   2 ?    8.3   0.0    0.0041       2.2      59     100 ..     314     365 ..     275     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.37
                   MMR_HSR1_Xtn  57 pclyvlNKiDlisle.eldelare..pnsvviSaekelnldeLkeki 100
                                    p++++ NK+D+ + e +  +l +    +   iSa ++ ++ +L++ +
  gi|121637621|ref|YP_977844.1| 136 PVFLAANKVDSEKGEsDAAALWSLglGEPHAISAMHGRGVADLLDGV 182
                                    778899****9544303444444344588889999999999998866 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
                   MMR_HSR1_Xtn  59 lyvlNKiDlisleeldelare..........pnsvviSaekelnldeLkeki 100
                                    ++++NK Dl++++  + l+re           + v iSa+++  + +L+ ++
  gi|121637621|ref|YP_977844.1| 314 VLAYNKWDLVDEDRRELLQREidrelvqvrwAQRVNISAKTGRAVHKLVPAM 365
                                    679***************9977878888776688889999999888887665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.72   3.9e+02       4      23 ..      29      48 ..      27      53 .. 0.86
   2 ?    2.4   0.0      0.23   1.2e+02      63     139 ..     105     180 ..      92     183 .. 0.73
   3 ?    4.5   0.0     0.048        26       2      25 ..     200     223 ..     199     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.72
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   + ++G+ ++GK tL +++ g
  gi|121637621|ref|YP_977844.1| 29 VAVVGRPNVGKSTLVNRILG 48
                                   5689**********999865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.23
                      PduV-EutP  63 eadvialvqdateeesvfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellk 139
                                     ad + lv+da    +   ++ a+++ +    +   ++++ d+e+ e     L s G  +   +sa++  g+ +ll+
  gi|121637621|ref|YP_977844.1| 105 TADAVILVVDAGVGATAADEAAARILLRSGKPVFLAANKV-DSEKGESDAAALWSLGLGEPHAISAMHGRGVADLLD 180
                                    5777888888888888777777887776555555555555.45555666678999*****************99875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.048
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                    +++ l+Gk ++GK +L ++l g++
  gi|121637621|ref|YP_977844.1| 200 RRVALVGKPNVGKSSLLNKLAGDQ 223
                                    6899****************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2916.65
//
Query:       gi|121637622|ref|YP_977845.1|  [L=270]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-49  167.6   1.6    3.7e-49  167.4   1.6    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.3e-35  121.8   0.6    2.9e-35  121.5   0.6    1.1  1  adh_short        short chain dehydrogenase
    8.8e-15   55.1   2.1    1.3e-14   54.5   2.1    1.2  1  KR               KR domain
  ------ inclusion threshold ------
      0.026   14.0   0.4      0.051   13.0   0.4    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.038   13.1   0.0      0.049   12.8   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.19   11.2   0.2       0.26   10.8   0.2    1.4  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   1.6   1.2e-52   3.7e-49       1     234 []      29     268 ..      29     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 1.2e-52
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT...SEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelg...aevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                    Ga  ++Gr +A+ala++Ga++ l+  n ++   ++el++  g   a+v+ c   + ++ +++ve++  ++g+lD+++ + 
  gi|121637622|ref|YP_977845.1|  29 GATGSLGRVAARALADAGARLTLAGGNSAG---LAELVNGAGiddAAVVTCRPDSLADAQQMVEAALGRYGRLDGVLVAS 105
                                    8999**************************...666666666432447******************************** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSB.STTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaerv.vpnynaygaaKaalealtr 153
                                    g  +   +p++e+  e+fd ++d n+++++l+++aa + l+++g  gs+v +ssv++  +  ++y+ay+ +Ka+   l++
  gi|121637622|ref|YP_977845.1| 106 GSNHV--APITEMAVEDFDAVMDANVRGAWLVCRAAGRvLLEQGqgGSVVLVSSVRGGLGnAAGYSAYCPSKAGTDLLAK 183
                                    *9999..*******************************76676689*********776665999**************** PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTT....HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikg....fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                    +lA+e+g +giRvNa +p + +   ++ +       ++ +e++ ar+pl+r+++pe+   a ++L+sd++s+ tGq+++ 
  gi|121637622|ref|YP_977845.1| 184 TLAAEWGGHGIRVNALAPTVFRSAVTEWMFTddpkGRATREAMLARIPLRRFAEPEDFVGALIYLLSDASSFYTGQVMYL 263
                                    *******************99988766553322226679999************************************** PP

                                    STTGG CS
                   adh_short_C2 230 DgGlt 234
                                    DgG+t
  gi|121637622|ref|YP_977845.1| 264 DGGYT 268
                                    ****8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.6   9.8e-39   2.9e-35       1     188 [.      23     210 ..      23     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 9.8e-39
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    k +l+tGa++ +Gr  a++la +Ga++++++ +++ l+e+++  +   ++a ++++   + ++++++ve+a  ++g+ld 
  gi|121637622|ref|YP_977845.1|  23 KSILITGATGSLGRVAARALADAGARLTLAGGNSAGLAELVNGAGI--DDAAVVTCRPDSLADAQQMVEAALGRYGRLDG 100
                                    679**********************************999999886..5799999999999******************* PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvag.kvpvagvaaYsAsKaavag 158
                                    +    G ++++p+ e+  e++++v++ N+ g+ l++ra+ + +l ++++G++v vsSv g +   ag++aY+ sKa+ + 
  gi|121637622|ref|YP_977845.1| 101 VLVASGSNHVAPITEMAVEDFDAVMDANVRGAWLVCRAAGRVLLeQGQGGSVVLVSSVRGgLGNAAGYSAYCPSKAGTDL 180
                                    ******************************************9978899*********9945566899************ PP

                                    HHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 159 ltrslakelaptgirvnavaPGlvdTdmak 188
                                    l+++la e+  +girvna+aP ++++++++
  gi|121637622|ref|YP_977845.1| 181 LAKTLAAEWGGHGIRVNALAPTVFRSAVTE 210
                                    ***********************9988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   2.1   4.3e-18   1.3e-14       3     163 ..      25     185 ..      24     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 4.3e-18
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     litG++G+LG++ ar la+ gar  +  + s    +  ++l++     +a v +++ D  + ++ ++++e++  + +++
  gi|121637622|ref|YP_977845.1|  25 ILITGATGSLGRVAARALADAGARLTLAGGNS----AGLAELVNGAGIDDAAVVTCRPD--SLADAQQMVEAALGRYGRL 98 
                                    69********************9855555555....44556777777778888888888..8888999999999999*** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--T.T-HHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsa.gqanYaaaNafl 156
                                     Gv+ a g  + ++++em  ed+++v+ + v+Gaw + ++  +      +   +vl+SS+ g lg+a g ++Y    a  
  gi|121637622|ref|YP_977845.1|  99 DGVLVASGSNHVAPITEMAVEDFDAVMDANVRGAWLVCRAAGRvlleqGQGGSVVLVSSVRGGLGNAaGYSAYCPSKAGT 178
                                    *************************************9976654444488899********9999752788999988888 PP

                                    HHHHHHH CS
                             KR 157 Dalaeyr 163
                                    D la++ 
  gi|121637622|ref|YP_977845.1| 179 DLLAKTL 185
                                    8888765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.7e-05     0.051       1     102 [.      25     139 ..      25     159 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......................EEEE--TT-HHHHH CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......................elveldltdrsale 57 
                                    il+tGatG +G+  ++al+++g +++    +s + ++     l                       ++ve+ l       
  gi|121637622|ref|YP_977845.1|  25 ILITGATGSLGRVAARALADAGARLTLAGGNSAGLAE-----LvngagiddaavvtcrpdsladaqQMVEAALGRYG--- 96 
                                    8*********************987665554222222.....11222355565544444433333333333333333... PP

                                    HHHHHHT-SEEEE--S---HH....HHHHSHHHHHHHHTHHHHHHHHHH CS
                      Epimerase  58 rlfkeeqpdavihlAavggva....assedpadfieknlqgtlnlleaa 102
                                          + d v+ + +  +va      +ed  +++++n++g++ ++ aa
  gi|121637622|ref|YP_977845.1|  97 ------RLDGVLVASGSNHVApiteMAVEDFDAVMDANVRGAWLVCRAA 139
                                    ......3444444433333321111345555566666666666666666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.049       1     118 [.      25     142 ..      25     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT...T-S CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.kvd 79 
                                    +l+tGa+Gs+G+   r ++    +++ l   +   l e+ +     +++  + +     ++d +  + +e al ++ + d
  gi|121637622|ref|YP_977845.1|  25 ILITGATGSLGRVAARALA-DAGARLTLAGGNSAGLAELVNGA--GIDDAAVVTCRPDSLADAQ--QMVEAALGRYgRLD 99 
                                    89*********87666655.56678999999999999998875..3455444222233455443..45666777663689 PP

                                    EEEE------H.HHHHHSHHH...HHHHHHHHHHHHHHHHHHT CS
                Polysacc_synt_2  80 vvfhaAAlKhV.Plveenple...aiktNvlgtenvieaaiea 118
                                     v+ a    hV P+ e+ + +   +++ Nv g+  v++aa + 
  gi|121637622|ref|YP_977845.1| 100 GVLVASGSNHVaPITEMAVEDfdaVMDANVRGAWLVCRAAGRV 142
                                    9999999999977777765432226789999999999998655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   8.9e-05      0.26       1      25 [.      25      49 ..      25     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.9e-05
                                   EEESSTTSHHHHHHHHHHHHHT-EE CS
                           NmrA  1 IlviGaTGrqGksvvrallkaghkv 25
                                   Il++GaTG++G+  +ral++ag + 
  gi|121637622|ref|YP_977845.1| 25 ILITGATGSLGRVAARALADAGARL 49
                                   89******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1985.45
//
Query:       gi|121637623|ref|YP_977846.1|  [L=304]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-48  163.0   3.9    5.2e-47  160.1   3.9    2.0  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      6e-21   74.9   0.0    1.3e-20   73.8   0.0    1.6  1  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    2.5e-07   31.0   0.4    4.9e-07   30.1   0.4    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0011   19.0   0.4      0.002   18.2   0.4    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0096   15.6   0.4      0.018   14.7   0.4    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.012   15.6   0.4      0.025   14.5   0.4    1.6  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.013   14.8   4.5      0.021   14.1   4.5    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.021   14.9   0.3      0.038   14.1   0.3    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.037   13.6   0.1      0.059   12.9   0.1    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.073   13.6   1.4       0.17   12.4   1.4    1.7  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.077   13.3   1.6       0.16   12.2   1.6    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.14   12.4   3.3       0.29   11.4   3.3    1.5  1  TrkA_N           TrkA-N domain
       0.18   11.2   1.5       0.54    9.6   1.4    1.8  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.18   11.9   0.0       0.28   11.3   0.0    1.2  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
       0.45    9.7   5.4       0.17   11.1   2.4    1.7  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
        7.1    6.9   7.2        2.3    8.5   1.0    2.6  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   3.9   4.6e-50   5.2e-47       2     179 ..      10     174 ..       9     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 4.6e-50
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-S CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dad 80 
                                     av+GaG+mG+ ia v+asagl+V ++d+++e+l++a+ ++++    ++ +g+            + +++dl++a+ dad
  gi|121637623|ref|YP_977846.1|  10 AAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAAAVEAAR----VAGAGR----------GSVAAAADLAAAIpDAD 75 
                                    69*********************************99888775....444454..........5588999********** PP

                                    EEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHH CS
                        3HCDH_N  81 lviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetv 160
                                    lviEavvEnl++K+++f++l+++a pda+la+nTS l+i +++e++++ +rvig+HF+nPp+l+++vEvv++++T+++t 
  gi|121637623|ref|YP_977846.1|  76 LVIEAVVENLAVKQELFERLATLA-PDAVLATNTSVLPIGAVTERVEDGSRVIGTHFWNPPDLIPVVEVVPSARTAPDTA 154
                                    ********************9987.9****************************************************** PP

                                    HHHHHHHHHTT-EEEEE.CS CS
                        3HCDH_N 161 atvvelakkigktpvvv.kd 179
                                    ++vv+l++++gk pv+v +d
  gi|121637623|ref|YP_977846.1| 155 DRVVALLTQVGKLPVRVgRD 174
                                    ****************9776 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   1.2e-23   1.3e-20       1      97 []     177     275 ..     177     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.2e-23
                                    TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHS...SCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                          3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlp...mGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                    GF+ nR++ +l++ea++lv+egv++p+++D ++r+ +Gl+   +Gp+e +d++gld+ ++i +++   l+ +  +pspll
  gi|121637623|ref|YP_977846.1| 177 GFIGNRLQHALWREAIALVAEGVCDPKTVDLVVRNTIGLRlatLGPLENADYIGLDLTLAIHDAVIPSLNHD-PHPSPLL 255
                                    9***************************************77779******************777776666.5568*** PP

                                    HHHHHTT--BGGGTBSSSBC CS
                          3HCDH  78 eklveagrlgrktgkgfyky 97 
                                    ++lv ag+lg +tg gf+++
  gi|121637623|ref|YP_977846.1| 256 RELVAAGQLGARTGHGFLDW 275
                                    *****************986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   4.3e-10   4.9e-07       3      94 ..      11     112 ..       9     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.3e-10
                                    EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                  NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasldvvitmvkagkavdev 72 
                                    +++G G MG+ +a  l++ag +va+ + ++e + +++ e           + aa+++++++ ++d+vi  v ++ av++ 
  gi|121637623|ref|YP_977846.1|  11 AVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAAAVEAarvagagrgsVAAAADLAAAIPDADLVIEAVVENLAVKQE 90 
                                    89*************************9998777666665567778888888888888888888**************** PP

                                    HHSHCCC--TT-EEEE-S---H CS
                  NAD_binding_2  73 iegllealkkgdilidgstssp 94 
                                    +++ l++l+++++l   +++ p
  gi|121637623|ref|YP_977846.1|  91 LFERLATLAPDAVLATNTSVLP 112
                                    ***999999*999998888766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   1.8e-06     0.002      13      97 ..       8      94 ..       2     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                   -EEEEES-SHHHHHHHHHHHCCT-CEEEEE..ESSHHHHHHH.HHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB CS
                   Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvva..NRtlerakel.aeel.kgeeiealkleelkellaeadvvisataseepil 90
                                   +++ ++GaG m++++a  L+++g++ v+++  N ++ +a+++ a ++ ++ + ++ +  +l +++ +ad+vi a+   +  +
  gi|121637623|ref|YP_977846.1|  8 SRAAVVGAGLMGRRIAGVLASAGLD-VAITdtNAEILHAAAVeAARVaGAGRGSVAAAADLAAAIPDADLVIEAVVE-NLAV 87
                                   5789*******************99.7776115555566665323333556678999****************9864.4455 PP

                                   -HHHHHC CS
                   Shikimate_DH 91 ekeevee 97
                                   ++e +e+
  gi|121637623|ref|YP_977846.1| 88 KQELFER 94
                                   5665555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   1.6e-05     0.018       2      47 ..      11      57 ..      10     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                   EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                           ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                                   a++GaG +G+ +a+ La ag dv + + ++  l a   +  r+ + g
  gi|121637623|ref|YP_977846.1| 11 AVVGAGLMGRRIAGVLASAGLDVAITDTNAeILHAAAVEAARVAGAG 57
                                   79*********************999988854544555555555555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   2.3e-05     0.025       3      81 ..      11      85 ..       9     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                   EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH CS
                 NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa 81
                                   av+GaG  G  +A vla++g +v +   ++e +++   e   v+         ++ a +dla+a+ +ad+++ +v  + 
  gi|121637623|ref|YP_977846.1| 11 AVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAAAVEAARVAGAG----RGSVAAAADLAAAIPDADLVIEAVVENL 85
                                   8************************9999988887777777666555....589******************9886653 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.5   1.9e-05     0.021      30      99 ..       9      81 ..       4      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE....HCHHHHHHHHHHHH-SEEEE-- CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev....lksqeellaeavkeadvvigtv 99
                                   +  v+G+G  G   + + ++ g +V ++D++++ l+      a+ v        + ++ la a+ +ad+vi +v
  gi|121637623|ref|YP_977846.1|  9 RAAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAAAVEAAR-VAGagrgSVAAAADLAAAIPDADLVIEAV 81
                                   6789*****************************99988776666.333477799999**************998 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   3.4e-05     0.038       3      76 ..      10      82 ..       8     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                                   EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.STTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S- CS
                         DapB_N  3 vavvGasGrmGkevvkaveeaedlelvaavdrke.selegkdagellglgklgvavtddleevlekadvliDFTt 76
                                    avvGa G mG++++ ++ + ++l ++    + e  ++ + +a +++g g+ +va  +dl++++ +ad +i+  +
  gi|121637623|ref|YP_977846.1| 10 AAVVGA-GLMGRRIAGVLAS-AGLDVAITDTNAEiLHAAAVEAARVAGAGRGSVAAAADLAAAIPDADLVIEAVV 82
                                   68***9.********99998.6666554433333445566778899999999*******************9765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.2e-05     0.059       2      38 ..       9      45 ..       8      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdk 38
                                   + +v+G+G +G   a vla++g +v + D ++e  ++
  gi|121637623|ref|YP_977846.1|  9 RAAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHA 45
                                   669****************************986655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4   0.00015      0.17       1      36 [.       9      44 ..       9      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                   +++vvG+G+ g   Ag+la  g +V + + + ++l 
  gi|121637623|ref|YP_977846.1|  9 RAAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILH 44
                                   579****************************99993 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.6   0.00014      0.16       3      80 ..      12      84 ..      10      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80
                                   ++GaG +G+ +a +la  +    ++++ d + e l+a+a +a    + a    ++  ++ Laa++ ++dlv+ +++  
  gi|121637623|ref|YP_977846.1| 12 VVGAGLMGRRIAGVLASAGL---DVAITDTNAEILHAAAVEA-ARVAGAGRGSVAAAAD-LAAAIPDADLVIEAVVEN 84
                                   89***************985...6*********999988664.4457788888888889.*************99876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3   0.00026      0.29       2      89 ..      11     101 ..      10     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                    EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE...EEES-TTSHHHHHHTTGGGESEEEE-SSSH.HHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle...vvvgdatdeevLeeagiekadaviaatgdd.eani 77 
                                    +++G+G +Gr++a  L ++g dv + d++ e ++ ++ e ++   +  g+++  + L +a i +ad+vi a+ ++ +++ 
  gi|121637623|ref|YP_977846.1|  11 AVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAAAVEAARvagAGRGSVAAAADL-AAAIPDADLVIEAVVENlAVKQ 89 
                                    79****************6657**********9999988876423444444444444.4578899988855443337777 PP

                                    HHHHHHHHHTSS CS
                         TrkA_N  78 lavllakelnpk 89 
                                     + + + +l p+
  gi|121637623|ref|YP_977846.1|  90 ELFERLATLAPD 101
                                    777777777765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4   0.00048      0.54      38      73 ..       9      44 ..       3      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00048
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                   + +++G+G +G+++a +l++ g++v ++d++ +  +
  gi|121637623|ref|YP_977846.1|  9 RAAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILH 44
                                   679**************************9977444 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.28      25      98 ..      28     100 ..      10     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                    HCT-EEEEES-TT..SSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHHHHHHHHCC CS
                         OTCace  25 rlgmdvvlvaPkg..lepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekereerlkklkd 98 
                                      g+dv +   ++  l+   + + ea+  a +  gs+    dl++a+ +aD v+  v+  ++ ++e +erl+ l++
  gi|121637623|ref|YP_977846.1|  28 SAGLDVAITDTNAeiLHA--AAV-EAARVAGAGRGSVAAAADLAAAIPDADLVIEAVVENLAVKQELFERLATLAP 100
                                    555555555555532222..223.333334444599***********************************99886 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4   0.00015      0.17     144     181 ..       9      46 ..       2      58 .. 0.84
   2 ?   -1.4   0.3      0.97   1.1e+03       5      22 ..      53      70 ..      49      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllral 181
                                    r++vvG+G+ G  +A++la++g +v + + + ++l a 
  gi|121637623|ref|YP_977846.1|   9 RAAVVGAGLMGRRIAGVLASAGLDVAITDTNAEILHAA 46 
                                    79****************************99999433 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.97
                                   EE--SHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  5 viGgGpAGlaaaltlaqa 22
                                   v G+G + +aaa +la+a
  gi|121637623|ref|YP_977846.1| 53 VAGAGRGSVAAAADLAAA 70
                                   569999******999985 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0    0.0021       2.3       1      30 [.      12      41 ..      12      49 .. 0.93
   2 ?    0.9   0.7      0.47   5.3e+02       1      18 [.      53      70 ..      53      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                   +vGaGl G  +A  La ag+dv + +++  
  gi|121637623|ref|YP_977846.1| 12 VVGAGLMGRRIAGVLASAGLDVAITDTNAE 41
                                   8***********************998765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.47
                                   EE--SHHHHHHHHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka 18
                                   + GaG ++ +aA+ La a
  gi|121637623|ref|YP_977846.1| 53 VAGAGRGSVAAAADLAAA 70
                                   56***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1964.95
//
Query:       gi|121637624|ref|YP_977847.1|  [L=276]
Description: hypothetical protein BCG_1755 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-35  120.6   0.4    7.5e-35  120.1   0.4    1.2  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.4   4.2e-39   7.5e-35       1     136 []      17     168 ..      17     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 4.2e-39
                        Cyclase   1 idLshplsedtpvwp..dp..................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvsa 58 
                                    +dLshp+ ++ p+wp  +                   i++ +h+GTH+Dap+H++e    +de+pl+ ++g +vv+++ +
  gi|121637624|ref|YP_977847.1|  17 YDLSHPWGHGAPAWPyfEDvqierlhgmaksrvltqkITTVMHSGTHIDAPAHVVEgtPFLDEIPLSAFFGTGVVVSIPK 96 
                                    7*************7672257788999999************************9976678*****************44 PP

                        Cyclase  59 kaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkeky..rnpglseeaaewlaekgvkavGvDtlsvDa 136
                                        +++ ++taedl++a      +i+pgdiv+++Tgw+++++d+++y    pg++++a ew+a kgvkavG+Dt ++D+
  gi|121637624|ref|YP_977847.1|  97 ----GKWGMVTAEDLQNAT----PDIRPGDIVVVNTGWHHKYADSAEYyaYSPGFDKKAGEWFAAKGVKAVGTDTQALDH 168
                                    ....577899*****9983....4699**************97776666888*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2020.40
//
Query:       gi|121637625|ref|YP_977848.1|  [L=116]
Description: hypothetical protein BCG_1756 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.7   0.1    1.6e-08   34.1   0.1    1.3  1  Cupin_2          Cupin domain
  ------ inclusion threshold ------
      0.024   14.3   0.1       0.03   14.0   0.1    1.2  1  Cupin_3          Protein of unknown function (DUF861)
      0.079   13.9   0.1      0.099   13.5   0.1    1.2  1  Glyco_hydro_79C  Glycosyl hydrolase family 79 C-terminal beta


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   2.7e-12   1.6e-08       2      70 ..      40     107 ..      39     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.7e-12
                                    EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                        Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                    l ++ pG++a++   ++e  +++Vl+Ge+++tvdg e++l+  dsv+  +g+   ++N++d +a llv 
  gi|121637625|ref|YP_977848.1|  40 LSVYRPGGTAEPAPTREE-TVYVVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVT 107
                                    56789***9998887887.9******************************************9999875 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.1e-06      0.03      10      59 ..      39      89 ..      30     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-06
                                   EEEEEECEEEEECESS.EEEE.EEEECEEEEEETTTEEEEEETTEEEEE-TT CS
                        Cupin_3 10 giwectpGkfrltyee.dEfc.yileGevkvtpeggetvelraGDlvvlpkg 59
                                   g+    pG+ +   ++ +E++  +l Ge  vt+ +g++  l+  D+v l kg
  gi|121637625|ref|YP_977848.1| 39 GLSVYRPGGTAEPAPTrEETVyVVLDGELVVTV-DGAETVLGWLDSVHLAKG 89
                                   5555667777777766699*95578********.777777777777777666 PP

>> Glyco_hydro_79C  Glycosyl hydrolase family 79 C-terminal beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.7e-05     0.099      42     103 .]      17      78 ..       2      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                Glyco_hydro_79C  42 gksvkvkrLtapgvdadanitwaGqsfn.nksdeldggeeeetvvvvsdGkvtvdVpaseavL 103
                                     ++v+  rL++  +   ++  w G+s+   +++  +  ++eetv vv dG++ v+V  +e vL
  gi|121637625|ref|YP_977848.1|  17 HHEVSTMRLQGREA-GRTERFWVGLSVYrPGGTAEPAPTREETVYVVLDGELVVTVDGAETVL 78 
                                    57889999999953.333479999876504445555555999999999************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 926.10
//
Query:       gi|121637626|ref|YP_977849.1|  [L=207]
Description: hypothetical protein BCG_1757 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-58  198.8   0.0    1.2e-58  198.5   0.0    1.0  1  BKACE     beta-keto acid cleavage enzyme


Domain annotation for each model (and alignments):
>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.0     7e-63   1.2e-58       2     200 ..       3     193 ..       2     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 7e-63
                                    B-EEEE-S-SSS-CCC-TTS--SHHHHHHHHHHHHHHTESEEEE-EE-TTTS-EE--HHHHHHHHHHHHHHHTTSEEEE- CS
                          BKACE   2 viitvavtGavttkednpavPvtpeeiaeeaveaaeaGAaivHlHaRdpedgrpsldpelyrevlarirekepdviinlt 81 
                                    ++itva+tG+++tk+dnpa+P++peeia+++ +a+ aGAa++H+H Rd e++rp+ dp++ r++++ i e ++ ++i+l+
  gi|121637626|ref|YP_977849.1|   3 IVITVAPTGPIATKADNPALPTSPEEIATAVEQAYHAGAAVAHIHLRD-ENERPTADPNIARRAMDLIGE-RCPILIQLS 80 
                                    79**********************************************.89*******************.8******** PP

                                    SSTTTTG-HHHHHTHHHHH--SEEEEE-S-EEEB-SGCEE---HHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHHHHT CS
                          BKACE  82 tggastmsaeerlavlealkpemasldlgslnfglkdlvfentpedieellrrmaeagvkpeievfdvghlrnvkrliee 161
                                    tg + t+ +e+r + +e+ +p ma+l++ s+ f  +   f+n+p+ +++l++rm+e+++kpe+e++d+ghl+ + rl++e
  gi|121637626|ref|YP_977849.1|  81 TGVGLTVPFEQREQLVEL-RPRMATLNPCSMSF--GAGEFRNPPQAVRRLAARMRELDIKPELEIYDTGHLEACLRLWAE 157
                                    **8889999***999999.**************..6777***************************************** PP

                                    TSS-SSEEEEEEE--CTS--S-HHHHHHHHHHHHHHTTC CS
                          BKACE 162 Gllkgpllvqfvlgvpggapatpenllflkemadrlpeg 200
                                     ll +pl +++vlgv gg+ at++nll    m++rlp+g
  gi|121637626|ref|YP_977849.1| 158 DLLAEPLQFSIVLGVRGGMAATADNLLT---MVRRLPPG 193
                                    ***************************5...88888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1520.91
//
Query:       gi|121637627|ref|YP_977850.1|  [L=259]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-35  122.0   0.0    3.2e-35  120.8   0.0    1.6  2  IclR            Bacterial transcriptional regulator
    3.8e-13   49.0   1.5    6.5e-13   48.3   0.7    1.8  1  HTH_IclR        IclR helix-turn-helix domain
    2.1e-11   43.2   0.1      4e-11   42.3   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-10   40.0   0.4    7.3e-10   38.6   0.4    1.7  1  MarR_2          MarR family
    1.3e-09   37.9   0.4    6.2e-09   35.7   0.1    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.1e-08   32.7   0.0    9.1e-08   31.9   0.0    1.4  1  MarR            MarR family
    1.1e-06   28.2   0.1    2.6e-06   27.0   0.1    1.6  1  HTH_23          Homeodomain-like domain
    5.9e-06   26.5   0.2    1.1e-05   25.7   0.2    1.5  1  Rrf2            Transcriptional regulator
    3.4e-05   23.6   0.2    0.00013   21.7   0.2    2.1  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    4.2e-05   23.8   0.8    0.00018   21.8   0.8    2.3  1  HTH_31          Helix-turn-helix domain
     0.0001   22.3   2.8    0.00017   21.6   0.4    2.3  2  HTH_20          Helix-turn-helix domain
    0.00011   22.1   0.0    0.00024   20.9   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00012   22.1   0.0    0.00024   21.1   0.0    1.6  1  HTH_3           Helix-turn-helix
    0.00012   22.1   0.4    0.00073   19.6   0.1    2.4  2  HTH_28          Helix-turn-helix domain
    0.00017   21.4   0.0    0.00043   20.1   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00018   21.4   0.1    0.00042   20.3   0.1    1.6  1  HTH_29          Winged helix-turn helix
    0.00022   20.8   0.1    0.00042   19.9   0.1    1.5  1  Crp             Bacterial regulatory proteins, crp family
    0.00037   20.2   0.0    0.00086   19.0   0.0    1.6  1  HTH_38          Helix-turn-helix domain
     0.0004   20.3   0.0    0.00084   19.2   0.0    1.5  1  HTH_11          HTH domain
    0.00051   19.5   0.1     0.0014   18.1   0.1    1.8  1  Sigma70_r4      Sigma-70, region 4
     0.0032   17.1   0.3     0.0088   15.7   0.3    1.8  1  GntR            Bacterial regulatory proteins, gntR family
     0.0044   17.2   0.0     0.0088   16.2   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0079   15.7   0.2       0.02   14.5   0.1    1.7  2  HTH_CodY        CodY helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   16.0   1.3      0.025   14.7   1.3    1.6  1  Metal_resist    Heavy-metal resistance
      0.011   16.3   0.0      0.022   15.2   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
      0.015   15.2   0.0      0.027   14.4   0.0    1.4  1  HTH_36          Helix-turn-helix domain
      0.024   14.3   0.0      0.051   13.2   0.0    1.5  1  RP-C            Replication protein C N-terminal domain
      0.044   13.4   0.0      0.081   12.6   0.0    1.4  1  CENP-B_N        CENP-B N-terminal DNA-binding domain
      0.047   13.4   0.4        0.3   10.8   0.0    2.2  2  Sigma70_r4_2    Sigma-70, region 4
      0.065   13.2   0.0       0.13   12.2   0.0    1.5  1  HTH_37          Helix-turn-helix domain
       0.07   12.7   0.0       0.12   12.0   0.0    1.3  1  HTH_47          winged helix-turn-helix
      0.083   12.8   0.0       0.19   11.6   0.0    1.6  1  TFIIE_alpha     TFIIE alpha subunit
        0.1   12.0   0.0       0.14   11.5   0.0    1.1  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
       0.13   12.3   0.0       0.24   11.5   0.0    1.4  1  HTH_7           Helix-turn-helix domain of resolvase
       0.14   12.1   0.0        0.3   11.1   0.0    1.4  1  BLACT_WH        Beta-lactamase associated winged helix domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.5   4.4e+03       7      30 ..      36      59 ..      34      64 .. 0.80
   2 !  120.8   0.0   6.3e-38   3.2e-35       1     127 [.     127     253 ..     127     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.5
                                   TSTT-EEEGGGSHHHHHHHHTS-H CS
                           IclR  7 saiGtrlplyataiGKalLaalde 30
                                    +iG+r+ +  + + ++l a +de
  gi|121637627|ref|YP_977850.1| 36 AEIGERVGMARSTVSRILNALEDE 59
                                   479999999999999999888766 PP

  == domain 2  score: 120.8 bits;  conditional E-value: 6.3e-38
                                    CSEEETTSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEE CS
                           IclR   1 lrlravsaiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvr 80 
                                    +rlravsa+G+++ply++a+GKalLaal++e++ ++l +  l++lt +Titd+++L++eL+++R +G+a+dreE++eg++
  gi|121637627|ref|YP_977850.1| 127 QRLRAVSAVGESFPLYCCANGKALLAALPPERQARALPS-RLAPLTANTITDRAALRDELNRIRVDGVAYDREEQTEGIC 205
                                    5899************************66665555555.5*************************************** PP

                                    EEEEEEE-TTSSEEEEEEEEEETTTSHHHHHHH..HHHHHHHHHHHHHH CS
                           IclR  81 ciAapifdasgevvaAvsvsgptarlteeelke..ellalvreaArkis 127
                                    +++a++++  +  ++Avsv++p++r++ +e++   +lla+v++++++++
  gi|121637627|ref|YP_977850.1| 206 AVGAVLRG-VSVELVAVSVPVPAQRFYGREAELagALLAWVSKVDAWFN 253
                                    ********.9999*************9877665559*******999876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.7   1.3e-15   6.5e-13       2      50 ..      16      64 ..      15      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.3e-15
                                   HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   ++Ra+++L+ l ++p++l+ +e+ +r g+++Stv+R+L+ L+ +G+v  
  gi|121637627|ref|YP_977850.1| 16 IARAAELLRVLQAHPGGLSQAEIGERVGMARSTVSRILNALEDEGLVAS 64
                                   79********************************************975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1   7.8e-14     4e-11       8      47 ..      22      62 ..      21      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 7.8e-14
                         HTH_24  8 ILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +L++Lq++p+ +sq+e+ er+g+ +stv+r l+ Le+eGl+
  gi|121637627|ref|YP_977850.1| 22 LLRVLQAHPGgLSQAEIGERVGMARSTVSRILNALEDEGLV 62
                                   79*************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.4   1.4e-12   7.3e-10       8      54 ..      20      65 ..      16      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.4e-12
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   a +L +L ++pg+ l+++e+ +r g+ +s+vsril+ L++ GLv  r
  gi|121637627|ref|YP_977850.1| 20 AELLRVLQAHPGG-LSQAEIGERVGMARSTVSRILNALEDEGLVASR 65
                                   679*********9.******************************877 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   1.2e-11   6.2e-09      21      54 ..      32      66 ..      17      73 .. 0.79
   2 ?   -1.4   0.0       4.6   2.3e+03      58      67 ..     174     183 ..     171     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-11
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                    l+q+e+++++G+ r+tvsril++L++egl+  rg
  gi|121637627|ref|YP_977850.1| 32 GLSQAEIGERVGMARSTVSRILNALEDEGLVAsRG 66
                                   48*****************************9666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.6
                                    EES-HHHHHH CS
                      HTH_Crp_2  58 rildleaLra 67 
                                    +i+d++aLr+
  gi|121637627|ref|YP_977850.1| 174 TITDRAALRD 183
                                    79******97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.8e-10   9.1e-08       7      49 ..      21      64 ..      17      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.8e-10
                                   HHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR  7 viLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieR 49
                                   ++Lr l  +++ ls++e+++++g+ +stv+r+l +Le++Gl+ +
  gi|121637627|ref|YP_977850.1| 21 ELLRVLQAHPGgLSQAEIGERVGMARSTVSRILNALEDEGLVAS 64
                                   689999999988*****************************976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   5.2e-09   2.6e-06      10      48 ..      19      63 ..      14      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.2e-09
                         HTH_23 10 illllae......GlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                   ++ ll++      Gls++eI ++ g+ r+Tv+r+l++ + eGl +
  gi|121637627|ref|YP_977850.1| 19 AAELLRVlqahpgGLSQAEIGERVGMARSTVSRILNALEDEGLVA 63
                                   4444443446777************************97799865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   2.1e-08   1.1e-05      10      69 ..      19      75 ..      14      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.1e-08
                                   HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                           Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak 69
                                   a  +l +L++++++  +s +ei er+++ +s +++il+ L+ +glv s rG++G yrL  
  gi|121637627|ref|YP_977850.1| 19 AAELLRVLQAHPGG--LSQAEIGERVGMARSTVSRILNALEDEGLVAS-RGARGPYRLGP 75
                                   67788889999995..7*****************************88.8******9964 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   2.5e-07   0.00013       7      42 .]      21      57 ..      20      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.5e-07
                  HTH_AsnC-type  7 kILeaLqed.aRisyaeLAervGlSestvlrRvrrLe 42
                                    +L+ Lq+  + +s ae++ervG+++stv r +++Le
  gi|121637627|ref|YP_977850.1| 21 ELLRVLQAHpGGLSQAEIGERVGMARSTVSRILNALE 57
                                   59***************************99777765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.8   3.6e-07   0.00018       2      39 ..      19      57 ..      13      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.6e-07
                         HTH_31  2 LGalLralRera.GLsqeevAerlgvsestlsrlEqGrr 39
                                    ++lLr l +   GLsq+e +er+g+ +st+sr+ ++ +
  gi|121637627|ref|YP_977850.1| 19 AAELLRVLQAHPgGLSQAEIGERVGMARSTVSRILNALE 57
                                   57889999988855********************99755 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   3.2e-07   0.00017      14      58 ..      21      66 ..      19      68 .. 0.91
   2 ?   -0.4   0.1       2.5   1.3e+03      19      34 ..     163     179 ..     148     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.2e-07
                                   HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                   ++lr L a ++gl+ +e+ er++++++t+s+ L++Le+ gLv +++
  gi|121637627|ref|YP_977850.1| 21 ELLRVLqAHPGGLSQAEIGERVGMARSTVSRILNALEDEGLVASRG 66
                                   567888888*********************************9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                                    H.STCTTB-HHHHHHHH CS
                         HTH_20  19 L.araegltaselaerl 34 
                                    L +r ++lta+ + +r 
  gi|121637627|ref|YP_977850.1| 163 LpSRLAPLTANTITDRA 179
                                    25666888888888876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.7e-07   0.00024      21      58 ..      31      68 ..      22      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.7e-07
                                   CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   g ++  ei e++g  rs+v ++L+ Led GlV  +  r
  gi|121637627|ref|YP_977850.1| 31 GGLSQAEIGERVGMARSTVSRILNALEDEGLVASRGAR 68
                                   567788**************************987655 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.7e-07   0.00024       8      32 ..      31      55 ..      22      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.7e-07
                                   TTHHHHHHHHHHTSSHHHHHHHHTT CS
                          HTH_3  8 lglsqeeLAeklGvsrstisriEnG 32
                                    glsq+e+ e++G+ rst+sri n 
  gi|121637627|ref|YP_977850.1| 31 GGLSQAEIGERVGMARSTVSRILNA 55
                                   59********************996 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.4e-06   0.00073      11      49 ..      27      66 ..      13      70 .. 0.76
   2 ?   -0.7   0.0       3.2   1.6e+03       5      19 ..     206     220 ..     204     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                         HTH_28 11 a...Gh.svreaArelgisrrtvyrWikryeegGiagLvprrr 49
                                   +   G+ s++e+ +++g+ r+tv+r ++++e +G+   v  r+
  gi|121637627|ref|YP_977850.1| 27 QahpGGlSQAEIGERVGMARSTVSRILNALEDEGL---VASRG 66
                                   2455566**********************999664...66555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                         HTH_28   5 iikllaaGhsvreaA 19 
                                    ++ ++++G+sv  +A
  gi|121637627|ref|YP_977850.1| 206 AVGAVLRGVSVELVA 220
                                    8999*****997666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.4e-07   0.00043      18      46 ..      35      63 ..      20      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.4e-07
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVe 46
                                     e+ e +g+ +stvS+ L++L+++GLV 
  gi|121637627|ref|YP_977850.1| 35 QAEIGERVGMARSTVSRILNALEDEGLVA 63
                                   5689999*********************6 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   8.2e-07   0.00042       3      53 ..      24      71 ..      23      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-07
                         HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrp 53
                                   ++l+++  G+s  ++i +++g+ r+tv r+l++ e +Gl a +  r  g +
  gi|121637627|ref|YP_977850.1| 24 RVLQAHPGGLS-QAEIGERVGMARSTVSRILNALEDEGLVASRGAR--GPY 71
                                   68999999*98.**************************87775433..444 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   8.1e-07   0.00042       3      31 ..      33      61 ..      32      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.1e-07
                                   --HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                            Crp  3 mSRqdIAdylGlTrETVSRlLtrLrekGL 31
                                   +S  +I++ +G +r TVSR L  L+ +GL
  gi|121637627|ref|YP_977850.1| 33 LSQAEIGERVGMARSTVSRILNALEDEGL 61
                                   7999************************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06   0.00086      20      41 ..      32      53 ..      25      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                         HTH_38 20 GlslreIArrLgrspsTIsREl 41
                                   Gls++eI+ r+g ++sT+sR l
  gi|121637627|ref|YP_977850.1| 32 GLSQAEIGERVGMARSTVSRIL 53
                                   89******************87 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-06   0.00084       1      47 [.      18      62 ..      18      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                         HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                   R+  +l+ L ++ g +s +e+ e+ ++ r+tv r + aLe+ g  ++
  gi|121637627|ref|YP_977850.1| 18 RAAELLRVLQAHPGGLSQAEIGERVGMARSTVSRILNALEDEG--LV 62
                                   677899999666666***************************9..33 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.7e-06    0.0014      20      41 ..      32      53 ..      22      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                                   T--HHHHHHHHTS-HHHHHHHH CS
                     Sigma70_r4 20 glTleEIgerlgiSrerVrqie 41
                                   gl+++EIger g+ r++V++i+
  gi|121637627|ref|YP_977850.1| 32 GLSQAEIGERVGMARSTVSRIL 53
                                   89******************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.7e-05    0.0088      24      61 ..      33      69 ..      16      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                                   ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                           GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                   L s+ e+ ++ g  r+tv + L+ Le eglv +r  rG
  gi|121637627|ref|YP_977850.1| 33 L-SQAEIGERVGMARSTVSRILNALEDEGLVASRGARG 69
                                   6.889***************************999887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-05    0.0088      24      59 ..      34      69 ..      23      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                 Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                   +++++ er + + s+Vs  l+ Le++G+v   + +g
  gi|121637627|ref|YP_977850.1| 34 SQAEIGERVGMARSTVSRILNALEDEGLVASRGARG 69
                                   6789*************************8777665 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.8e-05      0.02       3      40 ..      31      66 ..      29      72 .. 0.88
   2 ?   -2.9   0.0        10   5.1e+03       5      13 ..     170     178 ..     169     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                       HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiiesrsLG 40
                                   G L  ++i +r+G++rs +   L  Le  G++ sr  G
  gi|121637627|ref|YP_977850.1| 31 GGLSQAEIGERVGMARSTVSRILNALEDEGLVASR--G 66
                                   6688899***************************9..3 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 10
                       HTH_CodY   5 LtaskiaDr 13 
                                    Lta +i Dr
  gi|121637627|ref|YP_977850.1| 170 LTANTITDR 178
                                    899****99 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.3     5e-05     0.025      61     105 ..     152     196 ..     147     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-05
                                    HHHHHHHHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHHHHHHHHH CS
                   Metal_resist  61 elralrrelraarrelaallaaepfDaaaieaalaeiraaqaalr 105
                                    ++ + +r++ra   +la l a+  +D+aa++++l++ir   +a +
  gi|121637627|ref|YP_977850.1| 152 AALPPERQARALPSRLAPLTANTITDRAALRDELNRIRVDGVAYD 196
                                    667899*******************************98777655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   4.3e-05     0.022       6      58 ..      20      66 ..      16      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-05
                         HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                   a +L++++   ++ ++a++ +r+ +  s++s +l++L+  GLv      a+r+
  gi|121637627|ref|YP_977850.1| 20 AELLRVLQAHPGGLSQAEIGERVGMARSTVSRILNALEDEGLV------ASRG 66
                                   778999998889999****************************......3333 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-05     0.027      27      54 ..      34      61 ..      26      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                         HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                   sq+ + +r g+ ++Tvsr+++ Le+ G+
  gi|121637627|ref|YP_977850.1| 34 SQAEIGERVGMARSTVSRILNALEDEGL 61
                                   999*********************9997 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.051      73     104 ..      34      65 ..      33      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                           RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirr 104
                                    s a++ +++g+++st++r+l aL + Gl++ r
  gi|121637627|ref|YP_977850.1|  34 SQAEIGERVGMARSTVSRILNALEDEGLVASR 65 
                                    6678889**********************987 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016     0.081      19      45 ..      29      55 ..      21      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                   HHCTT-HHHHHHHHT--CCHHHHHHHC CS
                       CENP-B_N 19 leegeSkaelarrfnvpestlsdilkn 45
                                      g S ae++ r +  +st+s+il++
  gi|121637627|ref|YP_977850.1| 29 HPGGLSQAEIGERVGMARSTVSRILNA 55
                                   44455********************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00058       0.3      26      44 ..      32      50 ..      28      54 .. 0.92
   2 ?   -0.4   0.2       1.8   9.2e+02       6      16 ..     149     159 ..     148     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                                   ---HHHHHHHHT--HHHHH CS
                   Sigma70_r4_2 26 glsykEIAellgisegtVk 44
                                   gls++EI e+ g+  +tV 
  gi|121637627|ref|YP_977850.1| 32 GLSQAEIGERVGMARSTVS 50
                                   9*****************6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                    HHHTTS-HHHH CS
                   Sigma70_r4_2   6 ealaeLperqr 16 
                                    ++la+Lp++++
  gi|121637627|ref|YP_977850.1| 149 ALLAALPPERQ 159
                                    589*****987 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.13      31      54 ..      32      55 ..       4      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                   T--HHHHHHHHT--HHHHHHHHTT CS
                         HTH_37 31 elsqseaaqllgiaqPkvsrllrg 54
                                   +lsq+e+ ++ g+a++ vsr+l++
  gi|121637627|ref|YP_977850.1| 32 GLSQAEIGERVGMARSTVSRILNA 55
                                   7********************985 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.12      31      77 ..      17      63 ..       7      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                   --HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 31 qaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   +++ +ll vL    G  s  +i er+g+   +v  i++aL+++gl+a
  gi|121637627|ref|YP_977850.1| 17 ARAAELLRVLQAHPGGLSQAEIGERVGMARSTVSRILNALEDEGLVA 63
                                   567899***************************************96 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00037      0.19      16      63 ..      20      68 ..      13      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                                   HHHHHHHHCT.TSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
                    TFIIE_alpha 16 vlvldvLlek.gevteedlakelkidlnelrklLnrLyearlvkykrrr 63
                                   ++ l vL  + g ++  ++ + +++ +  + ++Ln+L +++lv  + +r
  gi|121637627|ref|YP_977850.1| 20 AELLRVLQAHpGGLSQAEIGERVGMARSTVSRILNALEDEGLVASRGAR 68
                                   5667777655488999***************************988776 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.14     102     135 ..      32      65 ..      25      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                    XEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEE CS
                  RNA_pol_Rpc34 102 GIwsrtiksklnLhksvvkkcLksLeskkyiksv 135
                                    G  +++i ++++++ s v ++L  Le +++++s+
  gi|121637627|ref|YP_977850.1|  32 GLSQAEIGERVGMARSTVSRILNALEDEGLVASR 65 
                                    899****************************986 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00048      0.24      13      44 ..      24      55 ..      16      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                                   GGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                          HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRylad 44
                                   rv++ +  G s ++I ++v+ +RsTv R+l++
  gi|121637627|ref|YP_977850.1| 24 RVLQAHPGGLSQAEIGERVGMARSTVSRILNA 55
                                   67777778899999****************97 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00058       0.3      20      42 ..      44      66 ..      40      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                       BLACT_WH 20 aAergvlahLeKLeeeGkVkreg 42
                                   +A+ +v  +L+ Le+eG+V++ g
  gi|121637627|ref|YP_977850.1| 44 MARSTVSRILNALEDEGLVASRG 66
                                   9******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1891.83
//
Query:       gi|121637628|ref|YP_977851.1|  [L=129]
Description: hypothetical protein BCG_1759c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-06   28.2   0.0      3e-06   27.8   0.0    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.6e-10     3e-06       1     117 [.       2     116 ..       2     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.6e-10
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar...rkskrekaaelvelllllsalkilpidaei 77 
                                    ivlD+s+ ++l+   +  +a++++l + e+++ +a+   E++  ++    r++ ++++  +v ++ l   ++ +p  ++ 
  gi|121637628|ref|YP_977851.1|   2 IVLDASAAVELMLTTPAGAAVARRLRG-ETVHAPAHFDVEVIGAIRQavvRQLISDHEGLVVVVNFLSLPVRRWP-LKPF 79 
                                    79***********************98.*******************9987777777777777788888899988.8999 PP

                                    HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                            PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfr 117
                                    + +a+++++ +  +++D   +A+A+  g +li t+D +++
  gi|121637628|ref|YP_977851.1|  80 TQRAYQLRSTH--TVADGAYVALAEGLGVPLI-TCDGRLA 116
                                    99999****99..*******************.***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 853.21
//
Query:       gi|121637629|ref|YP_977852.1|  [L=75]
Description: hypothetical protein BCG_1760c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.7   0.1      0.018   15.4   0.1    1.2  1  ParD      Antitoxin ParD
       0.02   14.8   0.8       0.02   14.8   0.8    2.9  2  RHH_1     Ribbon-helix-helix protein, copG family
      0.024   14.5   2.3      0.098   12.6   0.4    2.4  2  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1     3e-06     0.018       8      54 ..      10      56 ..       4      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
                           ParD  8 itpeqhqrlkAvAAlqGksikeYvLerlleepkeadedealkeLeal 54
                                   + +e   +lkA AA q  s+ ++ L+rl e ++e + d+ l++L+al
  gi|121637629|ref|YP_977852.1| 10 VPDELLHELKARAAAQRMSLSDFLLARLAEIAEEPALDDVLDRLAAL 56
                                   66788899********************9777666778888888776 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8   3.4e-06      0.02       6      31 ..      10      35 ..       9      43 .. 0.90
   2 ?    1.5   0.8     0.051   3.1e+02      10      19 ..      46      55 ..      43      72 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
                                   EEHHHHHHHHHHHHHHTSSHHHHHHH CS
                          RHH_1  6 ldeellerLdelarrrgrSrSelIRe 31
                                   +++ell++L ++a+++++S S+++ +
  gi|121637629|ref|YP_977852.1| 10 VPDELLHELKARAAAQRMSLSDFLLA 35
                                   79********************9865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.051
                                   HHHHHHHHHH CS
                          RHH_1 10 llerLdelar 19
                                   l++ Ld+la+
  gi|121637629|ref|YP_977852.1| 46 LDDVLDRLAA 55
                                   5555666664 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.6e-05     0.098       8      30 ..      10      32 ..       9      41 .. 0.91
   2 ?    1.1   0.0     0.063   3.8e+02      14      38 ..      48      72 ..      44      73 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                          RHH_5  8 LPeelleeLeewAdeegRsvSnl 30
                                   +P+ell eL+  A++++ s+S +
  gi|121637629|ref|YP_977852.1| 10 VPDELLHELKARAAAQRMSLSDF 32
                                   8*******************976 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.063
                          RHH_5 14 eeLeewAdeegRsvSnlaafLveka 38
                                   + L+++A+  +R++   aa Lv++a
  gi|121637629|ref|YP_977852.1| 48 DVLDRLAALPRRDLGASAAELVDEA 72
                                   4577777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 550.56
//
Query:       gi|121637630|ref|YP_977853.1|  [L=494]
Description: biotin carboxylase-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00061   19.9   0.0      0.001   19.1   0.0    1.3  1  ATP-grasp_3  ATP-grasp domain
     0.0019   17.7   0.0       0.15   11.6   0.0    2.2  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-07     0.001     103     160 ..     267     325 ..     229     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-07
                                    TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEE..ESS.SEEEEEEESS--G CS
                    ATP-grasp_3 103 fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlv..lkdeepyviEvNPRltt 160
                                     v++G + p++t+ ++e+v+   +v+++  g +Gy+ vDl+  l  +e+y+ EvNPRl +
  gi|121637630|ref|YP_977853.1| 267 DVWRGALPPAQTRAAREMVAKLGDVLSRE-GYRGYFEVDLLhdLDADELYLGEVNPRLSG 325
                                    5789**********************998.***********776779**********987 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0     0.004        35       4      58 ..     145     201 ..     142     213 .. 0.82
   2 !   11.6   0.0   1.6e-05      0.15     140     191 ..     283     334 ..     272     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.004
                                    HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-S..SEEEEETTCCTTTTEEEES CS
                    CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigy..PviikaafglGGkGmrvar 58 
                                     +++++++++vp vp +++ v++ +e  a+a+  g     ++ aa+g  G+ + ++r
  gi|121637630|ref|YP_977853.1| 145 VMTRLADEAGVPSVPHVIGRVSSYDELSALAHGAGLgdDLVVEAAYGNAGSATFFVR 201
                                    5677899*******************99998876652279*******9998877776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHH CS
                    CPSase_L_D2 140 alreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaT 191
                                    ++ ++   v++  g++g   v+ l d + +e y+ EvN+Rls  s++++ +T
  gi|121637630|ref|YP_977853.1| 283 EMVAKLGDVLSREGYRGYFEVDLLHDLDADELYLGEVNPRLSGASPMTNLTT 334
                                    44455567788889**********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3521.56
//
Query:       gi|121637631|ref|YP_977854.1|  [L=415]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-42  144.4   1.1    6.1e-42  144.0   1.1    1.1  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   1.1   3.4e-46   6.1e-42       7     329 ..      70     387 ..      64     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 3.4e-46
                                    HHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTC CS
                 Beta-lactamase   7 elmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPef 86 
                                    + ma  +++   +av+++g +v+++++          + ++t++ ++Sv+K+++aa+v +l+ +G+++Ld+pV+ y+P++
  gi|121637631|ref|YP_977854.1|  70 AVMA--ATATDGWAVAHRGALVAEQYLD--------GLGPRTRHLLFSVSKSLVAAVVGALHGAGAIELDAPVTAYVPAL 139
                                    5555..5666679**************9........******************************************** PP

                                    TTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTH...............HHHHHHHHHSBSSSSTTSCEE-SHHHHHH CS
                 Beta-lactamase  87 agpgkgkiTlrdLltHtsGlpdlfasdlleeaaada...............aellralatlppkyapGtkwgYsntgygl 151
                                    a+ g+++ T+r+Ll+++sG++  + +d++  + + +               a l+++l tl+ k+a+G  ++Y  +  ++
  gi|121637631|ref|YP_977854.1| 140 ADCGYAGATVRHLLDMRSGVAFSENYDDPAAEIHVReqvigwapkrgpdlpATLRDYLLTLRRKSAHGGPFEYRSCETDV 219
                                    ********************99977777777766669******************************************* PP

                                    HHHHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEEEHHHHHHH CS
                 Beta-lactamase 152 lgellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglistardlarf 231
                                    lg ++e+++g+++ +l++e +++  g +  ++   + + ++ +                       +gg+ ++++d+ rf
  gi|121637631|ref|YP_977854.1| 220 LGWICEAAAGQPMPELMSELLWSRIGAQCDATIALDVAGAAGTGIF--------------------DGGISACLTDMIRF 279
                                    **************************99999999888889999999....................68************ PP

                                    HHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCH....TEEEEEEE.......STEEEEEEEECG CS
                 Beta-lactamase 232 lglalegglllsaetlaqltaklssgttrpagiraglglGwvladktga....pgtfghtG.......ggygtyvfvdpe 300
                                    + l l++g  l++++  ++ a+   ++++++  r+++      ++ +g+    + +f ++G       g+ g+ ++v+++
  gi|121637631|ref|YP_977854.1| 280 GSLYLRDGVSLAGQQVVPA-AWIADTFDGGPDSRQAFAASPDDNPMPGGmyrnQVWFPYPGsnvalcvGMCGQLIYVNRA 358
                                    *555555555555555554.7777777777777777755555555555555559************************** PP

                                    GTEEEEEEESBCSSHHHHHHHHHHHHHHH CS
                 Beta-lactamase 301 anlvvavltnrdppnedaaedarlialaa 329
                                    a++v+a l+++ +++e++  d+ ++++a+
  gi|121637631|ref|YP_977854.1| 359 AEVVAAKLSTQPHSHEPHMLDTLRAFDAV 387
                                    *******************9999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2947.14
//
Query:       gi|121637632|ref|YP_977855.1|  [L=139]
Description: hypothetical protein BCG_1763c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.6   0.1      0.047   14.1   0.1    1.2  1  LPD5      Large polyvalent protein-associated domain 5


Domain annotation for each model (and alignments):
>> LPD5  Large polyvalent protein-associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.6e-06     0.047      47     113 ..      60     127 ..      49     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-06
                           LPD5  47 erkeekpkkkikfdvYrrratkevfigkki.gkkklkLke.gFksvkeAreylkenqeeLeqklkklke 113
                                    + ++ kp+ ki++++  +r + +vf+++ + +k   kL +   + v++A + ++++q+ L+ kl+++++
  gi|121637632|ref|YP_977855.1|  60 Q-RQLKPSPKIDISLLDDRIRFSVFVSTDVsAKDLCKLDDaVYNAVRNAGRAIENEQAALDHKLAEVRK 127
                                    3.46788899********************99999*****445779*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1081.26
//
Query:       gi|121637633|ref|YP_977856.1|  [L=236]
Description: hypothetical protein BCG_1764c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-27   93.3   0.0    8.8e-27   92.8   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix
    0.00034   21.4   3.7      0.084   13.7   0.0    2.4  2  MDMPI_C   MDMPI C-terminal domain
  ------ inclusion threshold ------
      0.029   14.4   0.6       0.05   13.7   0.6    1.4  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   1.5e-30   8.8e-27       1      89 [.      16     101 ..      16     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 1.5e-30
                                    HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                           HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80 
                                    l+g++W+lli++ell+g+ Rf+e++r lp+is+++LaqrLr+L++d++ie+++ ++ +    Y++t +G++l+pvlq+l 
  gi|121637633|ref|YP_977856.1|  16 LLGDRWTLLIVRELLFGPLRFTEIERGLPGISRSVLAQRLRRLQHDRIIEAVPEHTGGG---YRFTVAGEELRPVLQTLG 92 
                                    69*****************************************************9999...****************** PP

                                    HHHHHHHHC CS
                           HxlR  81 kwgeeylee 89 
                                    +w++++l++
  gi|121637633|ref|YP_977856.1|  93 DWVSRWLMA 101
                                    ******986 PP

>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   1.6    0.0015       8.7      24      89 ..      75     144 ..      50     146 .. 0.63
   2 !   13.7   0.0   1.4e-05     0.084      56      84 ..     166     199 ..     149     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                        MDMPI_C  24 srvvlelegprtvhlhatdggrarlalwadg...ad.atvrGtaadlllllwGRlspddt........levdGdrall 89 
                                     r++++ e+ r+v  + +d        w  +   ad +  +++++ l+l+  +R+  ++             G+r+l+
  gi|121637633|ref|YP_977856.1|  75 YRFTVAGEELRPVLQTLGD--------WVSRwlmADpTPAECDPELLTLWISRRVNTEALpgrrvvveFRYHGERPLW 144
                                    3444444444444444444........4444555330679****************9987777766555556666666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                        MDMPI_C  56 datvrGtaadlllllwGRlspddt.....levdG 84 
                                    d tvrG + dl+++  GR + +++     +e+dG
  gi|121637633|ref|YP_977856.1| 166 DLTVRGHPRDLYRVYSGRSTLAAEisaerIELDG 199
                                    68*******************9986666666666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   8.4e-06      0.05       2      59 ..      12      69 ..      11      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-06
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.TS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerl.dlskntlsyHLrvLeeagLvevvre 59
                                   ++ae+L+++  + i r+L   ++l ++e+ + l ++s++ l ++Lr L+   ++e v e
  gi|121637633|ref|YP_977856.1| 12 RAAELLGDRWTLLIVREL-LFGPLRFTEIERGLpGISRSVLAQRLRRLQHDRIIEAVPE 69
                                   567888888888899999.999***********99*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1907.80
//
Query:       gi|121637634|ref|YP_977857.1|  [L=461]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-29   99.9   6.2    2.1e-28   98.8   6.2    1.6  1  FAD_binding_4  FAD binding domain
    1.5e-13   50.6   1.0    6.3e-13   48.6   0.1    2.3  3  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   6.2   2.4e-32   2.1e-28       1     137 [.      42     175 ..      42     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 2.4e-32
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    pa++++++++ +v+++lr a +ag+   vrGgG++++g a+++ggvv+dls+++  +++d+++g+++v++G+tl+dl++a
  gi|121637634|ref|YP_977857.1|  42 PALIATCHDACDVRTVLRRAVDAGMVTAVRGGGHNVAGTALCDGGVVIDLSAMRA-VSLDPATGRVRVQGGATLADLDHA 120
                                    7899*********************************99999********99**9.8*********************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvr 137
                                    + +  ++++   g +++++vGG+++++++G++ ++ Gl++dn++ +++v+a G  + 
  gi|121637634|ref|YP_977857.1| 121 TVPFARVAP--AGIVTTTGVGGLTLGGGVGWTTRRFGLSCDNLVAVRLVTAAGDYLS 175
                                    *********..9*****************************************9876 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.17   1.5e+03      13      30 ..     148     165 ..     134     166 .. 0.86
   2 ?   -4.4   0.2         2   1.8e+04      16      23 ..     319     326 ..     316     326 .. 0.60
   3 !   48.6   0.1   7.1e-17   6.3e-13       1      46 []     413     458 ..     413     458 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.17
                                    HHHHHHHGGGHHHHHHHH CS
                            BBE  13 ewgerYFggNferLvkvK 30 
                                     w++r Fg   ++Lv v+
  gi|121637634|ref|YP_977857.1| 148 GWTTRRFGLSCDNLVAVR 165
                                    6*************9985 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2
                                    HHHHGGGH CS
                            BBE  16 erYFggNf 23 
                                    + Y+++++
  gi|121637634|ref|YP_977857.1| 319 RYYWKSDY 326
                                    45667766 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 7.1e-17
                                    --TTS--GGG-HHHHHHHHG.GGHHHHHHHHHHH-TT--S--TT--- CS
                            BBE   1 aYvNyrdldlgkewgerYFg.gNferLvkvKtkyDPdNvFrneqsIp 46 
                                    aYvN+   d + +++e+ ++  +f+rLv +K++ DPdNvFrn+++I+
  gi|121637634|ref|YP_977857.1| 413 AYVNFTADDAP-MHVETLYStTEFSRLVTLKNRLDPDNVFRNNHNIR 458
                                    8**********.********888**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3539.89
//
Query:       gi|121637635|ref|YP_977858.1|  [L=189]
Description: hypothetical protein BCG_1766 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   49.7   3.3      6e-13   49.7   3.3    2.4  2  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.028   14.4   0.0    1.4  1  DinB      DinB family
      0.031   14.8   0.1      0.044   14.3   0.1    1.4  1  DinB_2    DinB superfamily


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   3.3     1e-16     6e-13       3     141 .]       9     130 ..       7     130 .. 0.87
   2 ?    0.9   0.5      0.11   6.8e+02      37      88 ..     142     181 ..     131     189 .] 0.47

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1e-16
                        MDMPI_N   3 eewaalaalvagLtdeqwaapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaasla 82 
                                    e+ ++l alv++++ +  + p+pc+ W+v+ l++H   s +a+aaa+++  a+ ++              ++v  +a   
  gi|121637635|ref|YP_977858.1|   9 EAEQRLVALVSSIDADSYSSPTPCDRWDVRALLSHALASIDAFAAAVDG--APGPD-------------MAQVFSGADIV 73 
                                    7889******************************************998..33332.............67888888888 PP

                        MDMPI_N  83 peallaafraavtrlaaalaalppdaiadrlgipggprslgeflrtrlvEavvHglDla 141
                                    +++ l a ++ ++r +aa+  + +   +  +    g++++g++l++ ++ +vvHg+Dla
  gi|121637635|ref|YP_977858.1|  74 GDDPLGATQRITRRSQAAWSTVRDLNAELST--FIGVMPAGQALAIITFSTVVHGWDLA 130
                                    9999999999999999999987776666666..899999999***************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                        MDMPI_N  37 Hlarsaralaaalaaegaesalardaaaalvtaad.........aeavdlaaslapealla 88 
                                    Hla +a+ +aa l                               a +vdla +++p++ l+
  gi|121637635|ref|YP_977858.1| 142 HLAEAAQQVAAEL---------------------VpvlrprglfAHDVDLAGEATPTQRLV 181
                                    3333333333332.....................022223344455555555555555555 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.7e-06     0.028      10      65 ..       3      63 ..       1     111 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHHHHHHHHHHCT--CCCTT--SSTTS--HHHHHHHHHHHHHHHHHHHHH...... CS
                           DinB 10 llqynqwardrtldaiaaLpdeelkaengegfqsvkqtlnHvldveelwlsrleg.....e 65
                                   l++++++a +r+  ++ ++++++++ +     + v+ +l+H l+++ ++ ++ +g      
  gi|121637635|ref|YP_977858.1|  3 LYSNLVEAEQRLVALVSSIDADSYSSPTPCDRWDVRALLSHALASIDAFAAAVDGapgpdM 63
                                   7999**********************************************99998554441 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   7.4e-06     0.044       2      69 ..       7      96 ..       6     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                         DinB_2  2 lerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlrgeeap......................rpgld 61
                                   l +a +rl al++ ++++ +  + + ++w ++ ll H  ++ + +++++ g++ p                      ++++ 
  gi|121637635|ref|YP_977858.1|  7 LVEAEQRLVALVSSIDADSYSSPTPCDRWDVRALLSHALASIDAFAAAVDGAPGPdmaqvfsgadivgddplgatqrITRRS 88
                                   67899*********************************************86666666664444433333222222222222 PP

                         DinB_2 62 pltppsaa 69
                                   ++++ +++
  gi|121637635|ref|YP_977858.1| 89 QAAWSTVR 96
                                   22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1477.46
//
Query:       gi|121637636|ref|YP_977859.1|  [L=256]
Description: hypothetical protein BCG_1767c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1944.97
//
Query:       gi|121637637|ref|YP_977860.1|  [L=312]
Description: hypothetical protein BCG_1768c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-64  216.5   0.1    3.8e-64  216.1   0.1    1.2  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.1   0.1   2.1e-68   3.8e-64       1     188 []      19     203 ..      19     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.1 bits;  conditional E-value: 2.1e-68
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    a++va++ral+++ + +gli+Dp+ae+lv+a+gl+l+++++d+el+ ++    + + a+++  g avRt++fdd+l +a+
  gi|121637637|ref|YP_977860.1|  19 ATIVAVGRALATKDP-RGLINDPFAEPLVRAVGLDLFTKMMDGELDMSTIADVSPAVAQAMVYGNAVRTKYFDDYLLNAT 97 
                                    789***********9.*******************************9965677899*********************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     a girqv iL++GlD+rayRlpw+ +++v+E+Dqp+v+efK++tl++lgaep+a +r vp+Dlr  dwp+aL+aagfd+
  gi|121637637|ref|YP_977860.1|  98 -AGGIRQVAILASGLDSRAYRLPWPTRTVVYEIDQPKVMEFKTTTLADLGAEPSAIRRAVPIDLR-ADWPTALQAAGFDS 175
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleaia 188
                                    ++ptaw+aeG+l+YL+p+++d+l+++i+
  gi|121637637|ref|YP_977860.1| 176 AAPTAWLAEGLLIYLKPQTQDRLFDNIT 203
                                    *************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2223.07
//
Query:       gi|121637638|ref|YP_977861.1|  [L=517]
Description: penicillin-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-69  234.1   4.6      4e-69  233.4   4.6    1.3  1  Beta-lactamase  Beta-lactamase
  ------ inclusion threshold ------
          1   10.0   6.3        8.4    7.1   0.2    4.4  5  SnoaL_2         SnoaL-like domain


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.4   4.6   4.4e-73     4e-69       1     314 [.      60     383 ..      60     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 233.4 bits;  conditional E-value: 4.4e-73
                                    HHHHHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGG CS
                 Beta-lactamase   1 ldrlvrelmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVs 80 
                                    ld+ + ++m+ ++ipGvavav+ +g++ ++ + Gv +++++ pv+ dt+fri+S+tKtft++++++lve+Gk+dLd pV 
  gi|121637638|ref|YP_977861.1|  60 LDAKINAGMKAYAIPGVAVAVWAGGQEYVKGY-GVTNVDHPMPVDGDTVFRIGSTTKTFTGTVMMRLVERGKVDLDSPVR 138
                                    5788999********************87766.9********************************************** PP

                                    GTST...TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHHHHHHHHH CS
                 Beta-lactamase  81 kylP...efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgygllgelle 157
                                    +y+P     + ++ +++T+r+Ll+Ht+G ++ +  d  ++++   a  ++a+ +lp+  +pGt+++Y+n g  ++g+++e
  gi|121637638|ref|YP_977861.1| 139 RYIPdfaVADESASATVTVRQLLNHTAGWDGRNGQDFGRGDD-AVALYVKAMTRLPQLTPPGTAFAYNNSGLVVAGRIIE 217
                                    ****998778899999*************8884444444443.458********************************** PP

                                    HHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC..TTTBEEEEHHHHHHHH... CS
                 Beta-lactamase 158 kvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae..gagglistardlarfl... 232
                                     v+g+++e  +++ +l+pL + +t + +++    ++aa+++  +  + a+++   +++   + ggl+stard +r++   
  gi|121637638|ref|YP_977861.1| 218 LVAGTTYESTVQRLLLDPLQLAHTRYFSDQIIGLNVAASHSVVDGKPIAVTDFWTFPRScnPTGGLMSTARDQLRYAqfh 297
                                    ****************************************5544444444444444444******************555 PP

                                    ...HHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEEC.....ECSSEEEEECCHTEEEEEEE..STEEEEEEEECGGT CS
                 Beta-lactamase 233 ...glalegglllsaetlaqltaklssgttrpagiragl.....glGwvladktgapgtfghtG..ggygtyvfvdpean 302
                                       g a +g+++ls+++l++++++  +g t        +     g  w+l ++  + +++ h+G   g ++ ++++p++n
  gi|121637638|ref|YP_977861.1| 298 lgdGRAPNGEQILSRQSLKAMRSNPGAGGTLW------VeltgmGVTWMLRPSAENVTIVEHGGtwKGQRSGFVMVPDRN 371
                                    55555555555555555555555555555555......144444999999999999************************ PP

                                    EEEEEEESBCSS CS
                 Beta-lactamase 303 lvvavltnrdpp 314
                                     +++vltn+d++
  gi|121637638|ref|YP_977861.1| 372 FAMTVLTNSDGG 383
                                    *********985 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00094       8.4      31      98 ..      18      85 ..       8      86 .. 0.79
   2 ?   -1.1   0.1      0.35   3.1e+03      58      94 ..      98     125 ..      91     132 .. 0.59
   3 ?    0.4   0.0      0.12   1.1e+03      15      52 ..     156     194 ..     137     227 .. 0.71
   4 ?   -1.1   0.0      0.34   3.1e+03      47      74 ..     245     274 ..     238     297 .. 0.68
   5 ?    1.1   0.0     0.068   6.1e+02      15      93 ..     386     475 ..     374     480 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00094
                                   SEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEETTE CS
                        SnoaL_2 31 gelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrvrdGk 98
                                   g+++Gr+ + +++ral +   ++   + + v + d  a+  +++++i a  +++ ++gv+v  +++G+
  gi|121637638|ref|YP_977861.1| 18 GTRHGRAVVTEYVRALDRLPHEIATAVVETVNCADPGAAFDELDAKINAGMKAYAIPGVAVAVWAGGQ 85
                                   559*************9977777777777776666666665555568**************9999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.35
                                    EEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEE CS
                        SnoaL_2  58 hdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrv 94 
                                    h + +dgd+v+  +  t          t++g+ ++r+
  gi|121637638|ref|YP_977861.1|  98 HPMPVDGDTVFRIGSTT---------KTFTGTVMMRL 125
                                    55677888886555444.........34555555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.12
                                    HHHHTEEEEEEEEETTSE..EESHHHHHHHHHHHHHHEEE CS
                        SnoaL_2  15 alaalfapdvvwedpgge..lrGreairaffralfaafpd 52 
                                    ++++l+   + w +  g+   rG +a++ +++a+ + +p+
  gi|121637638|ref|YP_977861.1| 156 TVRQLLNHTAGWDGRNGQdfGRGDDAVALYVKAMTR-LPQ 194
                                    456888888888888555599999999999999875.444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.34
                                    HHHEEEEEEEEEEEEEETTEEEEE..EEEE CS
                        SnoaL_2  47 faafpdlrfeihdvvadgdrvave..wtvt 74 
                                     +++ +l++   + v+dg  +av   wt+ 
  gi|121637638|ref|YP_977861.1| 245 SDQIIGLNVAASHSVVDGKPIAVTdfWTFP 274
                                    445677778888888888888876557764 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.068
                                    HHHHTEEEEEEEE.......ET.TSEEESHHHHHH....HHHHHHHHEEEEEEEEEEE.EEETTEEEEEEEEEEEEETTS CS
                        SnoaL_2  15 alaalfapdvvwe.......dp.ggelrGreaira....ffralfaafpdlrfeihdv.vadgdrvavewtvtgtipatg 81 
                                     + +lfa d+ ++        p ++++ G  +++     ++++  a+ +dl+ ++ d+ + dg+ +    t +    ++g
  gi|121637638|ref|YP_977861.1| 386 MINDLFASDWALQrfaglsnLPaTPQRLGAVDLAPyegrYIAKQVAQNGDLETTVIDFrARDGQLAGSMSTDD--ANPDG 463
                                    5566666666666555544333222244444444433345566666777777777777444555443333333..57888 PP

                                    SEEEEEEEEEEE CS
                        SnoaL_2  82 rgvtvrgvdvfr 93 
                                    +   + g +++r
  gi|121637638|ref|YP_977861.1| 464 QNSANLGLAFYR 475
                                    877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3754.14
//
Query:       gi|121637639|ref|YP_977862.1|  [L=518]
Description: succinate-semialdehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.5e-137  456.6   0.1   9.1e-137  456.3   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.3   0.1  5.1e-141  9.1e-137      12     462 .]      29     481 ..      19     481 .. 0.95

  Alignments for each domain:
  == domain 1  score: 456.3 bits;  conditional E-value: 5.1e-141
                                    EETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHH CS
                         Aldedh  12 inPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaev 90 
                                    i+ + tg++++++p +ta+dv+aa+a+A++a+  wak p+ eRa+++r+ +dl+ e++e l++l+++e+Gk  + a++e+
  gi|121637639|ref|YP_977862.1|  29 IDEVfTGKPLTTIPVGTAADVEAAFAEARAAQTDWAKRPVIERAAVIRRYRDLVIENREFLMDLLQAEAGKARWAAQEEI 108
                                    555559************************************************************************** PP

                                    HHHHHHHHHHHHHHHH.HSE.EEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHH CS
                         Aldedh  91 eeaidvlryyaelaek.leg.evlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpl 167
                                     + i  ++yya+ + + l+  ++ p      +++v ++P Gvvg+I+PWN+P+ l++   +pal+aGN+vvlKP ++tp 
  gi|121637639|ref|YP_977862.1| 109 VDLIANANYYARVCVDlLKPrKAQPLlPGIGKTTVCYQPKGVVGVISPWNYPMTLTVSDSVPALVAGNAVVLKPDSQTPY 188
                                    *************99966664445554467788999******************************************** PP

                                    HHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TT CS
                         Aldedh 168 salllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivled 247
                                    +al++ael+ +aglP+ +  +v+g+gs vg a++++  +d ++ftGs+++g ++a++a+++l  +++ElGGknp+iv   
  gi|121637639|ref|YP_977862.1| 189 CALACAELLYRAGLPRALYAIVPGPGSVVGTAITDN--CDYLMFTGSSATGSRLAEHAGRRLIGFSAELGGKNPMIVARG 266
                                    **********************************96..99**************************************** PP

                                    SHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHH CS
                         Aldedh 248 aDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveea 327
                                    a+ldk+++a+ +++f+naGQ Ci+++r++v+++i++ef+ k+ +a++++k+g + d ++d+G+liseaql++v ++v++a
  gi|121637639|ref|YP_977862.1| 267 ANLDKVAKAATRACFSNAGQLCISIERIYVEKDIAEEFTRKFGDAVRNMKLGTAYDFSVDMGSLISEAQLKTVSGHVDDA 346
                                    ******************************************************************************** PP

                                    HHTTSEEEE-TTE.SB-SSST.TEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBH CS
                         Aldedh 328 keegaklllGgereeaglekg.yfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdl 406
                                    +++gak++ Gg   +a+++ g  f+ePtvl+nv p+m++a +E+FGPV+s++++ d++ea+e+aNdt+yGL+a+v++ + 
  gi|121637639|ref|YP_977862.1| 347 TAKGAKVIAGG---KARPDIGpLFYEPTVLTNVAPEMECAANETFGPVVSIYPVADVDEAVEKANDTDYGLNASVWAGST 423
                                    ***********...55566666********************************************************** PP

                                    HHHHHHHHHS-SSEEEESSSST--TTT..SEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 407 eraervaerleaGnvyiNdsttgaaea..lpfgGvkqSglGreggkegleeytevktv 462
                                    ++ +r+a+rl+ G+v++ +  ++a  +  +p+gG++ Sg+Gr +g+egl +yte +t+
  gi|121637639|ref|YP_977862.1| 424 AEGQRIAARLRSGTVNVDEGYAFAWGSlsAPMGGMGLSGVGRRHGPEGLLKYTESQTI 481
                                    ********************8887776667************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3590.91
//
Query:       gi|121637640|ref|YP_977863.1|  [L=182]
Description: hypothetical protein BCG_1771c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-20   72.3   0.0    4.2e-20   71.9   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    6.4e-16   58.4   0.0    7.8e-16   58.1   0.0    1.1  1  Redoxin        Redoxin
     0.0026   18.2   0.0     0.0045   17.4   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0     7e-24   4.2e-20       2     123 ..      11     134 ..      10     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 7e-24
                                    TSB----EEE.STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH........H CS
                       AhpC-TSA   2 gdkapdfelk.nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe........s 72 
                                    g +ap+f+l+  a g tvsl+++ g  +v+ f+++ +cp+ ++ +  la l  +++++gv ++g+s++++         +
  gi|121637640|ref|YP_977863.1|  11 GTPAPSFTLPqPATGATVSLDELTGPALVVTFICN-HCPYVQHVAAGLATLGRDLADQGVPMVGISSNDVVtypqdgpdQ 89 
                                    899*******66679********************.*******************************999999*****9* PP

                                    HHHHHHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  73 hkkfiekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                    + + +++++++fp+l+De+++va+a+ +       +++ tfv+d +  ++y
  gi|121637640|ref|YP_977863.1|  90 MVAEARRHGWTFPYLYDETQDVARAFSAA------CTPDTFVFDGQRRLVY 134
                                    *****************************......*********9998887 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.3e-19   7.8e-16       3     138 ..      11     143 ..       9     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.3e-19
                                    TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH....... CS
                        Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf....... 75 
                                    g +aP+ftlp+ +  g +vsl+e++g  +v + + +++cP+ ++ +  l++l + l++ gv +v++++++          
  gi|121637640|ref|YP_977863.1|  11 GTPAPSFTLPQ-PATGATVSLDELTGPALV-VTFICNHCPYVQHVAAGLATLGRDLADQGVPMVGISSNDVVTypqdgpd 88 
                                    899******99.99**********999855.555566*******999*****8888**********88887777888856 PP

                                    HHHHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                        Redoxin  76 vkefwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                    ++  +++   +g +fp+l+D+++++++a+ ++         +tp ++v+d + ++vy+++ +++++
  gi|121637640|ref|YP_977863.1|  89 QM--VAEarrHGWTFPYLYDETQDVARAFSAA---------CTPDTFVFDGQRRLVYRGQLDDSRP 143
                                    44..444447********************88.........******************9998855 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.5e-07    0.0045       5     101 ..      35     139 ..      32     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.5e-07
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfp...lkpsfepkavaiwcakekkkafkd............... 65 
                                    g  ++v f  ++Cpy +   + l +l +d+ +    +p   ++++ + +               d               
  gi|121637640|ref|YP_977863.1|  35 GPALVVTFICNHCPYVQHVAAGLATLgRDLADQ--GVPmvgISSN-DVVTYPQ-----------Dgpdqmvaearrhgwt 100
                                    667899999****************98888888..6665455444.2222222...........2222233356678999 PP

                  Thioredoxin_2  66 ....ieenvelarkygvrgtPtivfldgkeivarlpGyvp 101
                                        ++e++++ar++    tP+++++dg+ + ++++G ++
  gi|121637640|ref|YP_977863.1| 101 fpylYDETQDVARAFSAACTPDTFVFDGQ-RRLVYRGQLD 139
                                    9****************************.7778999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1248.83
//
Query:       gi|121637641|ref|YP_977864.1|  [L=210]
Description: hypothetical protein BCG_1772c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1527.36
//
Query:       gi|121637642|ref|YP_977865.1|  [L=80]
Description: hypothetical protein BCG_1773c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-09   35.2   0.0    9.5e-09   35.0   0.0    1.0  1  2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catal


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   5.3e-13   9.5e-09     154     223 ..       2      71 ..       1      75 [. 0.95

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.3e-13
                                    E---------------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHH CS
                   2-oxoacid_dh 154 sNlGmlGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkk 223
                                    +N+G  Gv+ +  +i ppqva + +g+  +r  +++g++ v  ++  +l aDH   d + +a F   +++
  gi|121637642|ref|YP_977865.1|   2 TNVGDQGVDAVFGVIYPPQVALVSFGKPAQRVCAVDGAIHVMTTVLATLPADHGCSDDHRGALFFLSINE 71 
                                    9***************************999999****************************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 578.91
//
Query:       gi|121637643|ref|YP_977866.1|  [L=165]
Description: hypothetical protein BCG_1774c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-10   38.3  13.7      1e-09   38.1  13.7    1.0  1  SLAC1     Voltage-dependent anion channel


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1  13.7   5.8e-14     1e-09     212     323 ..       1     117 [.       1     118 [. 0.83

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.8e-14
                          SLAC1 212 lGplgqgalallllgkaapk.aaevlkvlalllalflwglglfwll.vavlsvlslpv...rlkfslswWaftFPlgala 286
                                    +G+ ++++la   + + a++ +a v+  l   +++++w++g ++++ ++++s+++++v   +l++  + W+++FPlg++ 
  gi|121637643|ref|YP_977866.1|   1 MGATAITVLAGAHIVEMADApMAIVTSGLVAGASVVFWAFGPWLIPpLVAASIWKHVVhrvPLRYEATLWSVVFPLGMYG 80 
                                    79999999999888777766434444445555899**********72567778884335679****************** PP

                          SLAC1 287 latielgkaleseafkvlgtillvllvlvwllvlvgt 323
                                    +++++lg a++++ ++ +g +  +++++vw++++v +
  gi|121637643|ref|YP_977866.1|  81 VGAYRLGLAAHLPIVESIGEFEGWVALAVWTITFVAM 117
                                    *******99999999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1194.27
//
Query:       gi|121637644|ref|YP_977867.1|  [L=652]
Description: nitrate reductase NarX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-85  285.0  12.6    4.9e-85  284.5  12.6    1.2  1  Nitrate_red_gam  Nitrate reductase gamma subunit
    1.4e-31  110.0   0.0    1.8e-31  109.5   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.8e-08   33.9   0.0    4.4e-08   33.2   0.0    1.3  1  Nitrate_red_del  Nitrate reductase delta subunit
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.043   13.8   0.1    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
       0.34   11.4   5.1       0.93   10.0   3.9    2.5  2  DUF3681          Protein of unknown function (DUF3681)


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.5  12.6   1.4e-88   4.9e-85       2     219 .]     419     639 ..     418     639 .. 0.97

  Alignments for each domain:
  == domain 1  score: 284.5 bits;  conditional E-value: 1.4e-88
                Nitrate_red_gam   2 tllfvvlPYvalavlvvgsllryrydqftwtskSsqllekklLrlgsplFHvGilvvllgHlvGlliPksvtealgvsee 81 
                                    +l+++v+PYv+++++ vgs++ryryd+f+wt++Ssql+e++lLr++sp+FH+Gilvv++gH +Gl+iP+s+t+a g+se 
  gi|121637644|ref|YP_977867.1| 419 ELFWTVVPYVTMTIVAVGSWWRYRYDKFGWTTRSSQLYESRLLRIASPMFHFGILVVIVGHGIGLVIPQSWTQAAGLSEG 498
                                    589***************************************************************************** PP

                Nitrate_red_gam  82 lyqllalvaGliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsal....dygseretisp 157
                                    +y+++a+v+G+iag+++l+G++lL++RR+t+  v++at+++Dkv++l+L+++i++Gl +t + +      y + ret+s 
  gi|121637644|ref|YP_977867.1| 499 AYHVQAVVLGSIAGITTLAGVTLLIYRRRTRGPVFMATTVNDKVMYLVLVAAIVAGLGATALGSGvvgeAY-NYRETVSV 577
                                    ************************************************************99998565522.44****** PP

                Nitrate_red_gam 158 wlrslltlqpdaellaevplifklHvllglllfalfPFtrLvHvlsapleYllrpyqvvrsr 219
                                    w+rs+++lqp+ +l+ae+pl++++Hvl+gl+lfal+PFtrLvH++sap++Yl+rpy+++rsr
  gi|121637644|ref|YP_977867.1| 578 WFRSVWVLQPRGDLMAEAPLYYQIHVLIGLALFALWPFTRLVHAFSAPIGYLFRPYIIYRSR 639
                                    ************************************************************97 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   5.1e-35   1.8e-31       1     103 [.     118     252 ..     118     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 5.1e-35
                                    B--S-EEEC..................................TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEE CS
                  Molybdopterin   1 RlkyPmvRk..................................qargeGkFvrvsWdeAleliaaslkytikkygpdrva 46 
                                    R+++P+ R+                                   arg+G++vrvsW eA e+iaa+++ ti +ygpdrva
  gi|121637644|ref|YP_977867.1| 118 RVRHPYARGvlvemyreakarlgdpvaawadiqadprrrrryqRARGKGGLVRVSWAEATEMIAAAHVHTISTYGPDRVA 197
                                    8999999999999999999999999999999999999999*999************************************ PP

                                    EEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-S CS
                  Molybdopterin  47 gfssgplmsmeslaslkkllsllggknlsfydwyadlppasaqqtigsdsrsnyess 103
                                    gfs++p+msm+s+a+++++++l+gg ++sfydwyadlp as+q  + +d+++++es+
  gi|121637644|ref|YP_977867.1| 198 GFSPIPAMSMVSHAAGSRFVELIGGVMTSFYDWYADLPVASPQ--VFGDQTDVPESG 252
                                    ******************************************5..445556666655 PP

>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.2e-11   4.4e-08      12     134 ..     292     406 ..     274     409 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.2e-11
                Nitrate_red_del  12 laelaealaaededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrqaglevaeefneppDHla 91 
                                    l+  ++ l  +++d l  a+ Y+++F+   r++a +y +++++++  + +g++ l++++ yr+++++ +++    pD+l+
  gi|121637644|ref|YP_977867.1| 292 LGRTVSEL--RRADPLTAATRYVDTFD--LRGRATLYLTYWTAGDT-RNRGREMLAFAQTYRSTDVAPPRGE--TPDFLP 364
                                    33344445..999**************..8*************777.7888888*************55553..5***** PP

                Nitrate_red_del  92 veLeflahLaereaeaeeaeeaealleaqkafleehllpWlpe 134
                                    v+Lef a+   ++  ++    ++ +++a+ + l+e  lp+++ 
  gi|121637644|ref|YP_977867.1| 365 VVLEFAATVDPEAGRRLL-SGYRVPIAALCNALTEAALPYAHT 406
                                    *******87766655333.578889999999999988888765 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.2e-05     0.043       6      52 ..      58     112 ..      53     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                    EE-S.SBTT--EEEEEEETTEEEEEEE-TTSTTTT.......T---HHHHTCHHC CS
                 Molybdop_Fe4S4   6 taCp.yCgvgCglevhvkdgkivkvegdpdhpvne.......grlCvKGrtller 52 
                                    ++   +C+ +C+ +++vkdg i++  + +d+p+          r C++G++   +
  gi|121637644|ref|YP_977867.1|  58 STHGvNCTGSCSWKIYVKDGIITWETQETDYPSVGpdrpeyePRGCPRGAAFSWY 112
                                    555559*****************6666666665555555555*******986655 PP

>> DUF3681  Protein of unknown function (DUF3681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   9.4e+03      55      72 ..     319     336 ..     316     343 .. 0.71
   2 ?   10.0   3.9   0.00026      0.93       8      73 ..     506     573 ..     500     586 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                        DUF3681  55 GlaeasvgfWvsgdperr 72 
                                    G a   + +W +gd+++r
  gi|121637644|ref|YP_977867.1| 319 GRATLYLTYWTAGDTRNR 336
                                    556677889999998555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                        DUF3681   8 aLiagGvvkaaaalllalfr.sp.ggvflrhgkallylYYgiLvavvvfGlaeasvgfWvsgdp.errr 73 
                                    +L +++ +++ a ++l+++r    g vf+  +++   + Y++Lva++v+Gl   ++g  v g+  + r+
  gi|121637644|ref|YP_977867.1| 506 VLGSIAGITTLAGVTLLIYRrRTrGPVFM-ATTVNDKVMYLVLVAAIVAGLGATALGSGVVGEAyNYRE 573
                                    56665555555566666655233599999.77788899***************9999988887414444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4389.66
//
Query:       gi|121637645|ref|YP_977868.1|  [L=395]
Description: nitrate/nitrite transporter narK2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-36  125.2  49.7    4.1e-36  124.6  49.7    1.3  1  MFS_1       Major Facilitator Superfamily
    1.8e-06   27.1  10.6    0.00027   19.9   0.5    3.0  2  MFS_1_like  MFS_1 like family
    0.00066   18.7  26.8      0.005   15.7  14.4    2.4  2  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
        2.7    6.2   7.3       0.19   10.0   0.1    2.4  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6  49.7   9.1e-40   4.1e-36       4     350 ..      14     346 ..      11     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 9.1e-40
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                    + +++++a++++gp+ +  +a+d  +s +e++ll+++  l+ a++ +++G+l+drfG r +l++  l+++l  +l++ +a
  gi|121637645|ref|YP_977868.1|  14 ISVVNFWAWNLIGPLST-SYARDMSLSSAEASLLVATPILVGALGRIVTGPLTDRFGGRAMLIAVTLASILP-VLAVgVA 91 
                                    5789*************.9****************************************************9.3333344 PP

                          MFS_1  83 ..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                       +++ ll+++ ++ G++ g++f++g+ ++  w+ + +rg+ +g++++g  +G++l + + + ++    W ++f  +ai
  gi|121637645|ref|YP_977868.1|  92 atMGSYaLLVFFGLFLGVA-GTIFAVGIPFANNWYQPARRGFSTGVFGMG-MVGTALSAFFTPRFV---RWFGLFTTHAI 166
                                    4744555***********9.8***************************95.577777777777777...56667777777 PP

                          MFS_1 160 vslla...fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylq 235
                                    v++ +   +v+++++l++ p  r++  p           ++p +ka  + pv w + ++ +++f+ gf +++ +lp+y+ 
  gi|121637645|ref|YP_977868.1| 167 VAAALastAVVAMVVLRDAPYFRPNADP-----------VLPRLKAAARLPVTWeMSFLYAIVFG-GFVAFSNYLPTYIT 234
                                    7777733355555555555555555544...........44579**********98888888887.************** PP

                          MFS_1 236 evlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglg 315
                                    + +g+s  + ag+  a +al+++ +++++g+lsdr+ +r   l +l++++l+a++ al +++   v++++ ++++ ++lg
  gi|121637645|ref|YP_977868.1| 235 TIYGFS-TVDAGARTAGFALAAVLARPVGGWLSDRIAPRHVVLASLAGTALLAFAAALQPPP--EVWSAATFITLAVCLG 311
                                    ******.677777777777777777*************************************..**************** PP

                          MFS_1 316 fvfpsllalasdlappeeagtasglfntagslgga 350
                                    + ++ ++a++++ ap+   g+++g++  ag+lgg 
  gi|121637645|ref|YP_977868.1| 312 VGTGGVFAWVARRAPAASVGSVTGIVAAAGGLGGY 346
                                    *********************************85 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   3.3   4.1e-05      0.19      20      75 ..      27      82 ..      12     182 .. 0.89
   2 !   19.9   0.5     6e-08   0.00027       2      87 ..     209     294 ..     208     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
                     MFS_1_like 20 PYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilsllls 75
                                   P  t y ++  l+ +e  ++++   l+  l++ ++g+l Drfg+r+ +++++l   
  gi|121637645|ref|YP_977868.1| 27 PLSTSYARDMSLSSAEASLLVATPILVGALGRIVTGPLTDRFGGRAMLIAVTLASI 82
                                   6778899999***********************************99877665443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6e-08
                     MFS_1_like   2 islkilyFfffaalgsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80 
                                    + +++ly ++f+ + ++  Yl  y++   g++  + g  t+   l ++l++p+ g+l+Dr++ r  v++  +  ++++f+
  gi|121637645|ref|YP_977868.1| 209 WEMSFLYAIVFGGFVAFSNYLPTYITtIYGFSTVDAGARTAGFALAAVLARPVGGWLSDRIAPRHVVLASLAGTALLAFA 288
                                    8899*********************9456*********************************998877766666666666 PP

                     MFS_1_like  81 sllfipp 87 
                                    + l  pp
  gi|121637645|ref|YP_977868.1| 289 AAL-QPP 294
                                    544.344 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  14.4   1.1e-06     0.005      43     197 ..      37     188 ..       9     192 .. 0.85
   2 !    8.7   3.8   0.00015      0.67     272     371 ..     225     318 ..     202     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                    H....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                       Sugar_tr  43 e.ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                    + ss   +l+v+  ++++++G +++g+l+drfG +  l+++++ ++   +  ++a    s+ +l++  +++G++  ++ v
  gi|121637645|ref|YP_977868.1|  37 SlSSAEASLLVATPILVGALGRIVTGPLTDRFGGRAMLIAVTLASILPVLAVGVAATMGSYALLVFFGLFLGVAGTIFAV 116
                                    25677889***********************************************9999********************* PP

                                    HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                       Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPry 197
                                     +P +++    ++ Rg+ ++++ ++++   l a+++  ++  ++    +     +++++a + ++++++l++ P++
  gi|121637645|ref|YP_977868.1| 117 GIP-FANNWYQPARRGFSTGVFGMGMVGTALSAFFTPRFVRWFGL---FTTHAIVAAALASTAVVAMVVLRDAPYF 188
                                    **9.5777778888*********9987666666666655566666...999999999999999999*****99998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00015
                                    HHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...C CS
                       Sugar_tr 272 aimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaas 349
                                    +  y++++i+   g+s+    + t+++    ++a  v+ +l+dr+  R ++l ++ag a++++  +    + ++      
  gi|121637645|ref|YP_977868.1| 225 FSNYLPTYITTIYGFSTVdaGARTAGFALAAVLARPVGGWLSDRIAPRHVVLASLAGTALLAFAAA--LQPPPEV----- 297
                                    44677888999999999998899*******************************999999988886..3333332..... PP

                                    HHHHHHHHHHHHHHHTTTTHHH CS
                       Sugar_tr 350 ivaivfialfialfalgwgpvp 371
                                      a +fi l ++l ++g g+v+
  gi|121637645|ref|YP_977868.1| 298 WSAATFITLAVCL-GVGTGGVF 318
                                    2233333333333.33555554 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.6     0.077   3.5e+02     326     378 ..      37      86 ..      34     101 .. 0.69
   2 ?   -2.0   0.4      0.18     8e+02     131     184 ..      97     147 ..      89     162 .. 0.66
   3 ?   10.0   0.1   4.3e-05      0.19     301     368 ..     213     279 ..     190     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.077
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 326 slsaseAnlltGvvvipgaalGillgGllvkklklsakklaklvlvvsllsll 378
                                    sls++eA+ll+++ + +++alG ++ G l+ ++  +a  ++  v+++s+l +l
  gi|121637645|ref|YP_977868.1|  37 SLSSAEASLLVATPI-LVGALGRIVTGPLTDRFGGRA--MLIAVTLASILPVL 86 
                                    678999999987755.567899********9986554..44444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.18
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalG 184
                                    + ll+f++ + lG+++t  +++Gi++  +  ++ +  +  g+ + + ++G al 
  gi|121637645|ref|YP_977868.1|  97 YALLVFFGLF-LGVAGTI-FAVGIPFANNWYQPARRGFSTGV-FGMGMVGTALS 147
                                    4555666644.5777665.78888888888887777777665.45666666654 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 4.3e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 301 lssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklakl 368
                                    +  ++ + ++ +f+ +lp y+ t ++ s+  A   t+ +++ +a+l   +gG+l  ++ ++   la l
  gi|121637645|ref|YP_977868.1| 213 FLYAIVFGGFVAFSNYLPTYITTIYGFSTVDAGARTAGFAL-AAVLARPVGGWLSDRIAPRHVVLASL 279
                                    4445556677788899*******************999887.6788999*******999987666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 2879.31
//
Query:       gi|121637646|ref|YP_977869.1|  [L=94]
Description: hypothetical protein BCG_1777 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-33  112.6   0.4    7.2e-33  112.4   0.4    1.0  1  DUF1876   Domain of unknown function (DUF1876)


Domain annotation for each model (and alignments):
>> DUF1876  Domain of unknown function (DUF1876)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.4     4e-37   7.2e-33       1      81 [.      11      90 ..      11      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 4e-37
                                   ----EEEEEEEETTEEEEEEEEE.ETTEEEEEEEEEES-SSS---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-XXX CS
                        DUF1876  1 kewtveleldEddgrTrAearlrltdetelrgvGlArrnpaDedvpeiGdElAaaRALsdLaeqLleaaaedieavthrpa 81
                                   ++wtv++++dE++g TrA+arlr ++e+el+gvGlAr npaD++vpeiGdEl++aRALsdL++++l+ +++dieavth+pa
  gi|121637646|ref|YP_977869.1| 11 QHWTVDISIDEHEGLTRAKARLR-WREKELVGVGLARLNPADRNVPEIGDELSVARALSDLGKRMLKVSTHDIEAVTHQPA 90
                                   59*********************.9******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 721.57
//
Query:       gi|121637647|ref|YP_977870.1|  [L=560]
Description: sulfate-transport transmembrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.5e-104  347.7  23.0   8.4e-104  347.3  23.0    1.1  1  Sulfate_transp  Sulfate permease family
    8.2e-18   64.1   0.0    1.3e-17   63.5   0.0    1.3  1  STAS            STAS domain


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.3  23.0  9.3e-108  8.4e-104       1     380 []      25     392 ..      25     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 347.3 bits;  conditional E-value: 9.3e-108
                 Sulfate_transp   1 lkgDliaGitvallaiPqalayallaglppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakvaeeepekg 80 
                                    l+gD++aG+tva+++iPqa+aya++aglpp +gL++s+ p ++yal+G+srql++Gp+++++l++++++a +a+ + +++
  gi|121637647|ref|YP_977870.1|  25 LRGDVLAGLTVAAYLIPQAMAYATVAGLPPAAGLWASIAPLAIYALLGSSRQLSIGPESATALMTAAVLAPMAAGDLRRY 104
                                    789***************************************************************************** PP

                 Sulfate_transp  81 ieiattltllaGviqvllGllRLgflveflseavlsGfiaGaaivillsqikvllglervskkeslvsvlsslftnlekv 160
                                      +a+tl ll+G+i++l+G+ RLgfl+++ls++vl+G++aG+a+v++ sq+ +++g++   + ++++s ++s+ t++++v
  gi|121637647|ref|YP_977870.1| 105 AVLAATLGLLVGLICLLAGTARLGFLASLLSRPVLVGYMAGIALVMISSQLGTITGTS--VEGNEFFSEVHSFATSVTRV 182
                                    *********************************************************9..99999*************** PP

                 Sulfate_transp 161 nlakvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaifelkreagvkivgeipsglpelslpkvdwsl 240
                                    +++++vl++++l++L++ ++        ++++ap++++av++at+++a++ +++ +g++ivg+ipsglp++++p v++++
  gi|121637647|ref|YP_977870.1| 183 HWPTFVLAMSVLALLTMLTR--------WAPRAPGPIIAVLAATMLVAVM-SLDAKGIAIVGRIPSGLPTPGVPPVSVED 253
                                    ********************........799*******************.8999************************* PP

                 Sulfate_transp 241 lsallpdalaialvglleaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsgl 320
                                    l+al++ a+ ia+v++++++++++++++++g++v++n EL A+G++Ni+++l++g+p++++ sr+a+   +G++tql +l
  gi|121637647|ref|YP_977870.1| 254 LRALIIPAAGIAIVTFTDGVLTARAFAARRGQEVNANAELRAVGACNIAAGLTHGFPVSSSSSRTALADVVGGRTQLYSL 333
                                    ******************************************************************************** PP

                 Sulfate_transp 321 vsalvvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklskldflillat 380
                                    +   +v++v++++++ll+++P+a+L+a++++a+++ L++l+e+ +l +++++++++ lat
  gi|121637647|ref|YP_977870.1| 334 IALGLVVIVMVFASGLLAMFPIAALGALVVYAALR-LIDLSEFRRLARFRRSELMLALAT 392
                                    ***********************************.******************999876 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   1.5e-21   1.3e-17       1     117 []     443     553 ..     443     553 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.5e-21
                                    EEEEEECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT CS
                           STAS   1 yidaeeiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrig 80 
                                    y++a++ +g +++r d+p++fanae+f+++   +v+++p +      ++ ++l+ +    +D +++ aL ++++el r+g
  gi|121637647|ref|YP_977870.1| 443 YPQAKRVPGLVVYRYDAPLCFANAEDFRRRALTVVDQDPGQ------VEWFVLNAESNVEVDLTALDALDQLRTELLRRG 516
                                    899***********************************966......6******************************** PP

                                    -EEEEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  81 vevvlvnikpevreklektgffdeveeeklfltvhdA 117
                                    + ++++ +k+++re l+++ ++d+++e+++f+t+ +A
  gi|121637647|ref|YP_977870.1| 517 IVFAMARVKQDLRESLRAASLLDKIGEDHIFMTLPTA 553
                                    *********************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3576.52
//
Query:       gi|121637648|ref|YP_977871.1|  [L=70]
Description: hypothetical protein BCG_1779 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-17   62.8   1.1    4.2e-17   62.7   1.1    1.0  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   1.1   2.3e-21   4.2e-17      16      82 .]       2      69 ..       1      69 [. 0.98

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.3e-21
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--HHHHHHHHHHHHHTS--SS-SSTTSTTTXXXXXXX CS
                  PSK_trans_fac 16 eLarltgeskteAvrrAleerlerlrre.raepllerllallrraaakaekedrspdekllyDeeglp 82
                                   eLa+++ge++t+Av  A++e+l+r+  + r+ +l+e+l+a+ rr+aa ++ ++r +d++l+yDe+glp
  gi|121637648|ref|YP_977871.1|  2 ELAARMGETLTQAVVVAVREQLARRTGRtRSISLREELAAIGRRCAALPVLDTRAADTILGYDERGLP 69
                                   8***********************99999**************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 533.22
//
Query:       gi|121637649|ref|YP_977872.1|  [L=82]
Description: hypothetical protein BCG_1780 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-05   23.4   0.0    7.3e-05   23.3   0.0    1.2  1  PIN             PIN domain
      0.002   17.8   0.0     0.0075   15.9   0.0    1.9  1  End_N_terminal  N terminal extension of bacteriophage endosia


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.2e-09   7.3e-05       1      47 [.       1      47 [.       1      76 [. 0.88

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.2e-09
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS CS
                            PIN  1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar 47
                                   +v+DTs+l+a+l++e++a +++ +++++  +++s +++ E++ v++ 
  gi|121637649|ref|YP_977872.1|  1 MVIDTSALVAMLNDEPEAQRFEIAVAADHVWLMSTASYPEMATVIET 47
                                   69******************************************998 PP

>> End_N_terminal  N terminal extension of bacteriophage endosialidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.4e-07    0.0075       9      66 ..       4      71 ..       2      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.4e-07
                                   -HHHHHHHHHHS-TTS-EE-TT-EEEE.....SS---GGGEES-EEEE....-.SSTT--EEEE-BTS CS
                 End_N_terminal  9 DtdalsevlaaapvgkkidGrGltykv.....ssLPDisrfknarfvy....e.RiaGqPLyYvseef 66
                                   Dt+al ++l++ p+ ++ + + +   v     +s P++   + +rf      e +++GqPL Y  ++f
  gi|121637649|ref|YP_977872.1|  4 DTSALVAMLNDEPEAQRFEIAVAADHVwlmstASYPEMATVIETRFGEpggrEpKVSGQPLLYTGDDF 71
                                   89999******999999887665544333332689***********632222248************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 594.11
//
Query:       gi|121637650|ref|YP_977873.1|  [L=221]
Description: hypothetical protein BCG_1781 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1672.97
//
Query:       gi|121637651|ref|YP_977874.1|  [L=566]
Description: transmembrane serine/threonine-protein kinase E pknE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-42  146.3   0.0    1.4e-42  145.9   0.0    1.1  1  Pkinase         Protein kinase domain
    3.9e-27   95.2   0.0    5.3e-27   94.7   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    3.4e-08   33.8   0.0    5.7e-08   33.1   0.0    1.3  1  Thioredoxin_4   Thioredoxin
    9.4e-06   25.7   3.7      0.012   15.6   0.0    3.0  3  APH             Phosphotransferase enzyme family
    1.7e-05   24.3   0.0    3.2e-05   23.4   0.0    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00068   19.5   0.4     0.0082   15.9   0.2    2.5  2  DSBA            DSBA-like thioredoxin domain
     0.0014   17.5   0.0     0.0022   16.8   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.9   0.0   5.4e-46   1.4e-42       1     212 [.      16     229 ..      16     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 5.4e-46
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    y+  + +G+G++G Vy+a ++ +++ivA+K +++   ++    ++++rE +   +l+ p++v + ++ e + +ly+ + +
  gi|121637651|ref|YP_977874.1|  16 YRLRRLVGRGGMGDVYEAEDTVRERIVALKLMSETLSSDPVFrTRMQREARTAGRLQEPHVVPIHDFGEIDGQLYVDMRL 95 
                                    566789*************************9988766544449************************************ PP

                                    -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS..BCTT CS
                        Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk..ltsf 157
                                    ++g +la +l+r+g l++ +a  i++qi ++l+  H++g  HrD+KpeNiL++ ++   ++DFG+a+  + ++   l + 
  gi|121637651|ref|YP_977874.1|  96 INGVDLAAMLRRQGPLAPPRAVAIVRQIGSALDAAHAAGATHRDVKPENILVSADDFAYLVDFGIASATTDEKLtqLGNT 175
                                    ********************************************************************99988777899* PP

                                    TSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHT CS
                        Pkinase 158 vgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldq 212
                                    vgt +Y+APE  +e++ +  +D+++l ++lye ltg+pp++g++  + + ++++q
  gi|121637651|ref|YP_977874.1| 176 VGTLYYMAPERFSESHATYRADIYALTCVLYECLTGSPPYQGDQL-SVMGAHINQ 229
                                    *****************************************4433.323333333 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   2.1e-30   5.3e-27       3     249 ..      18     260 ..      16     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.1e-30
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeepllivt 80 
                                    l + +G+G  G+V+e++ +     +e  Va+K ++e+ +++   ++++ +ea++  +l+ p++v ++ +   +++l++ +
  gi|121637651|ref|YP_977874.1|  18 LRRLVGRGGMGDVYEAEDT----VRERIVALKLMSETLSSDPvfRTRMQREARTAGRLQEPHVVPIHDFGEIDGQLYVDM 93 
                                    67889***********988....8999*******9998888777999********************************* PP

                                    E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEE CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyv 160
                                     +++g dL  +Lr++   +l   + + ++ q+ ++++  ++    Hrd+   N+L+s ++++ + DfG+a+++ +d++ +
  gi|121637651|ref|YP_977874.1|  94 RLINGVDLAAMLRRQ--GPLAPPRAVAIVRQIGSALDAAHAAGATHRDVKPENILVSADDFAYLVDFGIASAT-TDEKLT 170
                                    **************8..9*****************************************************99.999999 PP

                                    ETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEE..S-BBTTSBHHHHHHH CS
                    Pkinase_Tyr 161 kkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkr..lekpekcpeelyelm 238
                                    + +++   + +mapE ++e++ t ++D+++   +l+E +t g+ py+g + + + +++++      +    +p ++  ++
  gi|121637651|ref|YP_977874.1| 171 QLGNTVGTLYYMAPERFSESHATYRADIYALTCVLYECLT-GSPPYQGDQLSVMGAHINQAIPrpSTVRPGIPVAFDAVI 249
                                    ****************************************.*******99999888886543311233455777777888 PP

                                    HHHT-SSGGGS CS
                    Pkinase_Tyr 239 kkcweedpeeR 249
                                     + ++++pe+R
  gi|121637651|ref|YP_977874.1| 250 ARGMAKNPEDR 260
                                    88888888887 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   2.2e-11   5.7e-08       5     164 ..     389     565 ..     386     566 .] 0.64

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.2e-11
                                    SEEES-TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-....-..--S.TTTHHHHHHHTT--TT.. CS
                  Thioredoxin_4   5 diviGnpdApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdf..pld..kek.eslkaamaarcagees.. 77 
                                    ++++G++ Ap t++++    Cp C  f +++   +  ++ + ++ ++++ +    d    k +s++a+ a+ c++ ++  
  gi|121637651|ref|YP_977874.1| 389 GVFVGSSVAPTTIDIFNEPICPPCGSFIRSYASDIDTAVADKQLAVRYHLLnfLDDqsHSKnYSTRAVAASYCVAGQNdp 468
                                    6789****************************777777888876666666622444322235899999999996666444 PP

                                    HHHHHHHHHHHHTH...HHHTTS-..HHHHH.......HHHHHTS-------HHHHHHHHHHH....HHHT--SS-EEEE CS
                  Thioredoxin_4  78 peaflaikallysq...qeewaes..lkela..aealdkdekfeacleeekldalveaeskea....kkagiestPtfii 146
                                    + + ++++al+ s    qe++a +   +ela  a+++  + +  +c++++    ++++  ++a       + ++tP f+ 
  gi|121637651|ref|YP_977874.1| 469 KLYASFYSALFGSDfqpQENAASDrtDAELAhlAQTVGAEPTAISCIKSGADLGTAQTKATNAsetlAGFNASGTP-FVW 547
                                    4456788888777653333333334422233333355555555556666655555555555554100444555777.555 PP

                                    TTEEE-TT--HHHHHHHH CS
                  Thioredoxin_4 147 ngekveepqtyeelkali 164
                                    +g +v ++q+++ l +li
  gi|121637651|ref|YP_977874.1| 548 DGSMVVNYQDPSWLARLI 565
                                    888888899988888777 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5     6e-05      0.15      13     109 ..      30     134 ..      19     136 .. 0.77
   2 !   15.6   0.0   4.6e-06     0.012     164     198 ..     131     163 ..     127     165 .. 0.81
   3 ?   -0.8   0.0      0.46   1.2e+03      29      58 ..     269     301 ..     255     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6e-05
                                    EEEEEETT--EE..EEEE-TT..S-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS... CS
                            APH  13 tylvttpagryv..lrrnppa..raaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr... 84 
                                    +y+ +++ ++ +  l++ ++     + +  r++++ r   ++   +v  ++++++ d++++  ++li +v+ + +lr   
  gi|121637651|ref|YP_977874.1|  30 VYEAEDTVRERIvaLKLMSETlsSDPVFRTRMQREARTAGRLQEpHVVPIHDFGEIDGQLYVDMRLINGVDLAAMLRrqg 109
                                    677777775444245565555634444445777777776666556787888999************************** PP

                                    HHHHHHHHHHHHHHHHHHCCHHCH. CS
                            APH  85 klsaaqlpellealgeflaalhqvd 109
                                    +l ++ + ++++++g++l a h+++
  gi|121637651|ref|YP_977874.1| 110 PLAPPRAVAIVRQIGSALDAAHAAG 134
                                    **********************985 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.6e-06
                                    S-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                     +++ +H+D +p N+lv +dd    +++Df+ a++
  gi|121637651|ref|YP_977874.1| 131 HAAGATHRDVKPENILVSADDFA--YLVDFGIASA 163
                                    578899************55555..6*****9875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.46
                                    -TTS-HHHHHHHHHHHHHHHHTT-...B--B-C CS
                            APH  29 pparaaeeirrevallrlLakagv...pvPevl 58 
                                    ++a+aa  ++++ +  + L+++ v   pvP  +
  gi|121637651|ref|YP_977874.1| 269 AAAHAALATADQDRATDILRRSQVaklPVPSTH 301
                                    445889999999999999999999988888776 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   3.2e-05      99     167 ..      95     159 ..      89     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
                            Kdo  99 legaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    l +  dL+++l++   la  +  a+++++g +    h+ag  H+d+ + nil+ +++     ++l+D+ 
  gi|121637651|ref|YP_977874.1|  95 LINGVDLAAMLRRQGPLAPPRAVAIVRQIGSALDAAHAAGATHRDVKPENILVSADD----FAYLVDFG 159
                                    667789******966699999**********************************99....89999996 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.6   4.1e+03      84     106 ..     265     287 ..     237     290 .. 0.62
   2 !   15.9   0.2   3.2e-06    0.0082       1     191 [.     400     564 ..     400     566 .] 0.73

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHHHGHHHHH CS
                           DSBA  84 knstraarlllaagaeglaekvv 106
                                    ++++ aa+++la++ +++a +++
  gi|121637651|ref|YP_977874.1| 265 GDLSAAAHAALATADQDRATDIL 287
                                    36777777778877777666555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.2e-06
                                    EEEEEEBTTBHHHHHHHHHHHHHHHHC...CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT.... CS
                           DSBA   1 tvdeffDvlCPyCylgkerleklaars...pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplr 77 
                                    t+d+f + +CP C  + + + + +      +++ v+++ +++  ++ +s+n+                            
  gi|121637651|ref|YP_977874.1| 400 TIDIFNEPICPPCGSFIRSYASDIDTAvadKQLAVRYHLLNFLDDQSHSKNY---------------------------- 451
                                    799**********9999888877777777668*************9999988............................ PP

                                    GGSSHHHHHHHHHHHHHHHHHHH..GHHHHHHHHHHHHHTSSS-T...SSHHHHHHHHHHTTS.HHHHHHHHTS...HHH CS
                           DSBA  78 fpkdklknstraarlllaagaeg..laekvvrelfealwsegqai...tddqellevaekaGldaeeldeales...eav 149
                                           +++ +a+ + +ag+ +  l++ ++++lf   ++ +++    ++d+el+ +a+ +G + +++    ++   + +
  gi|121637651|ref|YP_977874.1| 452 -------STRAVAASYCVAGQNDpkLYASFYSALFGSDFQPQENAasdRTDAELAHLAQTVGAEPTAISCIKSGadlGTA 524
                                    .......6666666666666666777777777777777766665522245667**********99996555555212555 PP

                                    HHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                           DSBA 150 keavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                    + +     +  +  +++G+P+ v+dg+ mv+  +++  la+ 
  gi|121637651|ref|YP_977874.1| 525 QTKATNASETLAGFNASGTPF-VWDGS-MVVNYQDPSWLARL 564
                                    555555666677789*****5.68999.99888887777765 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.6e-07    0.0022     325     397 ..     132     198 ..     118     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.6e-07
                 Pkinase_fungal 325 kagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgeeHsyrhDL 397
                                     ag  HrD+  +Nil+      +++   L+D+ +a+ + d ++  + ++ +GTl++ma e  ++++ +yr D+
  gi|121637651|ref|YP_977874.1| 132 AAGATHRDVKPENILVS-----ADDFAYLVDFGIASATTD-EKLTQLGNTVGTLYYMAPERFSESHATYRADI 198
                                    67889************.....8999************97.6666779***************7777999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3800.44
//
Query:       gi|121637652|ref|YP_977875.1|  [L=133]
Description: hypothetical protein BCG_1783c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 906.66
//
Query:       gi|121637653|ref|YP_977876.1|  [L=176]
Description: isopentenyl-diphosphate delta-isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-18   66.6   0.0    2.6e-18   66.3   0.0    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.5e-22   2.6e-18       2     130 ..      39     170 ..      38     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.5e-22
                                    EEEEEEEEEEETTSEEEEEEES..SSSTTT.EE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   2 lrravgvvllnekgevLlvrrs..kkpfpg.We.lPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgp 77 
                                    l+ a++ ++++ ++++L++rr+  k+++p+ W+  ++G+  pgE++  A rR+l+ E+Gl+++ ++l+      +  ++ 
  gi|121637653|ref|YP_977876.1|  39 LHLAFSSYVFDLHDQLLITRRAatKRTWPAvWTnSCCGHPLPGESLPGAIRRRLAAELGLTPDRVDLILPGFRYRAAMAD 118
                                    799*****************************88**********888***************999999855555555555 PP

                                    EEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                          NUDIX  78 ygdeheilyvfleevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                     + e+ei+ v++ +v+ +++pn ++ev+++rw++ e+++++  a   +++ pw
  gi|121637653|ref|YP_977876.1| 119 GTVENEICPVYRVQVDQQPRPN-SDEVDAIRWLSWEQFVRDVTAGVIAPVSPW 170
                                    555******************9.***************777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1322.43
//
Query:       gi|121637654|ref|YP_977877.1|  [L=476]
Description: anchored-membrane serine/threonine-protein kinase pknF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-39  133.5   0.0    1.1e-38  133.1   0.0    1.1  1  Pkinase         Protein kinase domain
    1.1e-23   83.8   0.0    1.5e-23   83.4   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    2.1e-05   23.5   0.0    3.3e-05   22.8   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.022   14.1   0.0       0.23   10.8   0.0    2.2  2  APH_6_hur       Aminoglycoside/hydroxyurea antibiotic resista
      0.027   13.8   0.0      0.057   12.8   0.0    1.5  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.068   13.1   4.5      0.044   13.7   1.2    2.3  2  APH             Phosphotransferase enzyme family
       0.27   10.1   0.1       0.38    9.6   0.1    1.1  1  STT3            Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0   4.4e-42   1.1e-38       2     205 ..      13     226 ..      12     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 4.4e-42
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE-- CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyv 80 
                                    + +++lG+G++G+Vy a++ +  ++ A+K+++ +   + +   ++ rE    ++l hp+iv + +  e + +l++ +++v
  gi|121637654|ref|YP_977877.1|  13 TIVRQLGSGGMGEVYLARHPRLPRQDALKVLRADVSADGEYrARFNREADAAASLWHPHIVAVHDRGEFDGQLWIDMDFV 92 
                                    6789****************************999888887799************************************ PP

                                    TTEBHHHHHHHHSS..--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE....EEE-SGTTSEESSSSCS. CS
                        Pkinase  81 eggeladllerkgs..lseeeakkiakqilegleylHskgiiHrDlKpeNiLidekge....lKitDFGlakelesssk. 153
                                    +g++  +ll+++    ++  e+ +i++ ++e+l+y H+++++HrD+Kp+NiLi + +     ++++DFG+a  ++  s  
  gi|121637654|ref|YP_977877.1|  93 DGTDTVSLLRDRYPngMPGPEVTEIITAVAEALDYAHERRLLHRDVKPANILIANPDSpdrrIMLADFGIAGWVDDPSGl 172
                                    ****9999994443349999**********************************74445677*************99999 PP

                                    ..BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHH CS
                        Pkinase 154 ..ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkek 205
                                      ++  vgt  Y APE l +ne +  +D ++l+ + + lltg+ppf++ +    
  gi|121637654|ref|YP_977877.1| 173 taTNMTVGTVSYAAPEQLMGNELDGRADQYALAATAFHLLTGSPPFQHANPAVV 226
                                    99999******************************************7776554 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   5.8e-27   1.5e-23       2     218 ..      13     230 ..      12     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 5.8e-27
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEEST..TSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlke..eateeekeelleeakimkklkhpnivkllgvctkeeplliv 79 
                                    ++ ++lG+G  G+V+ ++      +   + a+K+l++  +a+ e ++++ +ea+   +l hp+iv+++     +++l+i 
  gi|121637654|ref|YP_977877.1|  13 TIVRQLGSGGMGEVYLARHP----RLPRQDALKVLRAdvSADGEYRARFNREADAAASLWHPHIVAVHDRGEFDGQLWID 88 
                                    57799************999....45555677777651145556699*************************9******* PP

                                    EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE....TTEEEE-STTTHEETTT CS
                    Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse....nkvvkisDfGLardiek 155
                                    +++v+g d  + Lr++  + +   +++++++ vA++++y ++++l+Hrd+   N+L+++    ++ + ++DfG+a  + +
  gi|121637654|ref|YP_977877.1|  89 MDFVDGTDTVSLLRDRYPNGMPGPEVTEIITAVAEALDYAHERRLLHRDVKPANILIANpdspDRRIMLADFGIAGWVDD 168
                                    **********************************************************9888899*************99 PP

                                    SSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH CS
                    Pkinase_Tyr 156 ddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevlekl 218
                                     +  ++++ +   v + apE l+ +++  ++D ++ + + + ++t g+ p+++ +++ v+++ 
  gi|121637654|ref|YP_977877.1| 169 PSGLTATNMTVGTVSYAAPEQLMGNELDGRADQYALAATAFHLLT-GSPPFQHANPAVVISQH 230
                                    9999*****************************************.******99888877665 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.3e-08   3.3e-05     323     389 ..     129     193 ..     113     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.3e-08
                 Pkinase_fungal 323 flkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkge 389
                                    + + ++LHrD+   Nili ++ + ++r+ +L+D+ +a  ++d+s   + +  +GT+ + a e l+g+
  gi|121637654|ref|YP_977877.1| 129 H-ERRLLHRDVKPANILIANP-DSPDRRIMLADFGIAGWVDDPSGLTATNMTVGTVSYAAPEQLMGN 193
                                    3.7899*************66.5569******************99999********9999888865 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.1e-05      0.23     142     175 ..     114     147 ..     101     173 .. 0.87
   2 ?    0.5   0.0      0.12   3.1e+02     112     146 ..     241     272 ..     230     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                      APH_6_hur 142 yveaaaiaaeLleepselrpLHgdlhhenvLage 175
                                    + e+++++ae l+ ++e r+LH d++ +n+L ++
  gi|121637654|ref|YP_977877.1| 114 VTEIITAVAEALDYAHERRLLHRDVKPANILIAN 147
                                    57788999**********************9875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                      APH_6_hur 112 plPpLlpleevfealfreaasdagagasrlyveaa 146
                                     +P+L+pl+ vf++  +++++d+   ++r +++a 
  gi|121637654|ref|YP_977877.1| 241 RVPELTPLDPVFAKALAKQPKDR---YQRCVDFAR 272
                                    5799********99999887754...344444444 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.057     121     166 ..     115     160 ..      92     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                            Kdo 121 rallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                     +++ av+ +    h++ + H+d+ + nil+ + ++ +++i+l D+
  gi|121637654|ref|YP_977877.1| 115 TEIITAVAEALDYAHERRLLHRDVKPANILIANPDSPDRRIMLADF 160
                                    57899****************************************9 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   1.7e-05     0.044     147     198 ..     113     165 ..      26     167 .. 0.58
   2 ?   -1.8   0.1      0.96   2.4e+03      89     107 ..     258     277 ..     194     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC....TTEEEEE---TT-EE CS
                            APH 147 eleeqvlaalaallpgelptvllHgDlhpgNllvd..pddgrvtGviDfedagl 198
                                    e++e ++ a+a+ l+ + +++llH+D +p N+l+   + ++r + + Df+ ag+
  gi|121637654|ref|YP_977877.1| 113 EVTE-IITAVAEALDYAHERRLLHRDVKPANILIAnpDSPDRRIMLADFGIAGW 165
                                    3333.55555555555779***************98844444335777777766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.96
                                    HHHHHHHHHHHHHHCCH.HC CS
                            APH  89 aqlpellealgeflaal.hq 107
                                    +q ++ ++++++f +al h+
  gi|121637654|ref|YP_977877.1| 258 KQPKDRYQRCVDFARALgHR 277
                                    33334444444443333233 PP

>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00015      0.38      98     127 ..     302     331 ..     291     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                                    HHHHHHHCCHHHHHHHHCHHHHHHHHHHS- CS
                           STT3  98 sirevclwlpallgsLlaIpiyflvrelks 127
                                    s++++++++pa+l++Ll++++  +vre+++
  gi|121637654|ref|YP_977877.1| 302 SLLRTAVIVPAVLAMLLVMAVAVTVREFQR 331
                                    7999***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3384.83
//
Query:       gi|121637655|ref|YP_977878.1|  [L=865]
Description: transmembrane ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-31  108.5   0.0    5.7e-31  107.9   0.0    1.3  1  ABC_tran         ABC transporter
      1e-29  102.6   1.2    4.7e-15   55.7   0.1    2.6  2  FHA              FHA domain
    3.5e-24   84.9   0.0    1.4e-12   47.7   0.0    2.8  2  Yop-YscD_cpl     Inner membrane component of T3SS, cytoplasmi
    6.4e-20   71.5   6.3    1.1e-19   70.7   6.3    1.4  1  ABC2_membrane    ABC-2 type transporter
    1.4e-11   44.8   0.3    6.1e-08   32.8   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-06   27.7   5.4    2.6e-06   26.8   5.4    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
    7.4e-05   22.3   0.0     0.0085   15.5   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00068   19.9   0.3     0.0034   17.7   0.3    2.0  1  AAA_22           AAA domain
     0.0033   17.8   0.0     0.0069   16.8   0.0    1.6  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.054   13.3   0.1    1.8  1  AAA_29           P-loop containing region of AAA domain
      0.031   14.0   0.1       0.26   11.0   0.0    2.2  2  Cytidylate_kin   Cytidylate kinase
       0.05   13.5   0.0      0.098   12.6   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
       0.07   13.4   0.5       0.84    9.9   0.0    2.6  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.072   13.3   0.0       0.16   12.2   0.0    1.5  1  AAA_33           AAA domain
        0.1   12.8   0.0       0.25   11.6   0.0    1.6  1  AAA_28           AAA domain
       0.15   12.5   0.1       0.38   11.2   0.1    1.8  1  AAA              ATPase family associated with various cellul
       0.17   11.6   0.8       0.58    9.9   0.8    1.9  1  AAA_30           AAA domain
       0.25   10.6   9.4       0.85    8.8   9.0    1.9  2  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   5.7e-34   5.7e-31       1     137 []     335     482 ..     335     482 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 5.7e-34
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ +sl+ ++g ++a++G++GaGKStL++l+ag ++pt G+++++g++++  e  slr++ig++pq++ +  +ltv+   
  gi|121637655|ref|YP_977878.1| 335 LDGISLTARPGMLTAVIGPSGAGKSTLARLVAGYTHPTDGTVTFEGHNVHA-EYASLRSRIGMVPQDDVVHGQLTVKHAl 413
                                    789************************************************.**************************9* PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   ++++ ++++l++l++++  dt+v     +LSgGq++r ++a  ll+ p+ll+lDEpt+
  gi|121637655|ref|YP_977878.1| 414 myaaelrlppdttkdDRTQVVARVLEELEMSKHIDTRV----DKLSGGQRKRASVALELLTGPSLLILDEPTS 482
                                    **********9965444444999999999999999999....*****************************96 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1   7.5e-15   7.4e-12       1      69 []      29      92 ..      29      92 .. 0.95
   2 !   55.7   0.1   4.7e-18   4.7e-15       1      69 []     230     293 ..     230     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 7.5e-15
                                   EEEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA  1 vtiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69
                                   v++GR+ ++d+++ +p iSr H+l++fd+g  ++  +D gS nG ++N++r++    v++ +  ++++G
  gi|121637655|ref|YP_977878.1| 29 VVVGRDLRADVRVAHPLISRAHLLLRFDQG--RWVAIDNGSLNGLYLNNRRVPV---VDIYDAQRVHIG 92
                                   579***************************..********************97...999999988887 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 4.7e-18
                                    EEEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   1 vtiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                    v+iGR++d+div+++   Sr+Ha+++ ++g  + +++D +S nGtfvNg r+     + L++gdv+++G
  gi|121637655|ref|YP_977878.1| 230 VRIGRANDNDIVIPEVLASRHHATLVPTPG--GTEIRDNRSINGTFVNGARVDA---ALLHDGDVVTIG 293
                                    68****************************..*********************9...**********98 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.4e-11   2.4e-08       9      83 ..      18      93 ..      11      95 .. 0.91
   2 !   47.7   0.0   1.4e-15   1.4e-12      13      90 ..     224     301 ..     221     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.4e-11
                                   T-EEEE.TTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC--TTSEEEETT CS
                   Yop-YscD_cpl  9 GaeveL.eegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveelelrpgdvlelGt 83
                                   G+e +  ++++vv+G+d ++D+ +  + +sr+hl L++++ ++++ d gs ngl++n++rv    + + +++ +G+
  gi|121637655|ref|YP_977878.1| 18 GSERTFaAGHDVVVGRDLRADVRVAHPLISRAHLLLRFDQGRWVAIDNGSLNGLYLNNRRVPVVDIYDAQRVHIGN 93
                                   66666657889**************************************************988899999999995 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 1.4e-15
                                    EETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC--TTSEEEETTEEEEEEE CS
                   Yop-YscD_cpl  13 eLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveelelrpgdvlelGttelalvk 90 
                                    eL  g+v+iG+++d+Div+     sr+h++L  +  ++ ++d +s ng++vng rv+ + l++gdv+++G++ l++++
  gi|121637655|ref|YP_977878.1| 224 ELPPGAVRIGRANDNDIVIPEVLASRHHATLVPTPGGTEIRDNRSINGTFVNGARVDAALLHDGDVVTIGNIDLVFAD 301
                                    6899****************************************************9999*************99875 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   6.3   1.1e-22   1.1e-19       1     205 [.     596     810 ..     596     814 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.1e-22
                  ABC2_membrane   1 tqikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedgl.nrpgllffsvlflafsaltsvapv. 74 
                                    +q+ ++ +r++++++ d+ ++ ++  + p++++ + ++v g++g    n  + + n+pg +  ++   a+++ t++ ++ 
  gi|121637655|ref|YP_977878.1| 596 RQFSTIARRQLRLIVSDRGYF-VFLALLPFIMGALSMSVPGDVGfgfpNPMGDApNEPGQILVLLNVGAVFMGTAL-TIr 673
                                    59*******************.99******************8888888776666888888888888886666665.441 PP

                  ABC2_membrane  75 .ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls......rf.flflllllltalaass 146
                                      + er ++ re + +l s+ ay++akv+v+ +++++q++i+++iv++  g + +      +  + +++ + +t +a+  
  gi|121637655|ref|YP_977878.1| 674 dLIGERAIFRREQAVGL-STTAYLIAKVCVYTVLAVVQSAIVTVIVLVGKGGPTQgavalsKPdLELFVDVAVTCVASAM 752
                                    1578*************.******************************8777777766455449**************** PP

                  ABC2_membrane 147 lgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyaveal 205
                                    lgl++sa+a+s e+++ l  + ++  l++sG +ip++     l  ++++ P ++++ a 
  gi|121637655|ref|YP_977878.1| 753 LGLALSAIAKSNEQIMPLLVVAVMSQLVFSGGMIPVTGRV-PLDQMSWVTPARWGFAAS 810
                                    ***************************************5.5999**********9875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00057      0.57       1      22 [.     347     368 ..     347     398 .. 0.78
   2 !   32.8   0.1   6.1e-11   6.1e-08     220     300 ..     437     514 ..     408     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                         AAA_21   1 lnvliGpNgsGKSnLLdaldll 22 
                                    l+++iGp g+GKS+L ++  + 
  gi|121637655|ref|YP_977878.1| 347 LTAVIGPSGAGKSTLARLVAGY 368
                                    699************9988665 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 6.1e-11
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                     +  le+++  ++ +++lS G+++ + +++ ll  +   sll++DEp +gL+P+l r ++++l++l++ g  v+++THS 
  gi|121637655|ref|YP_977878.1| 437 VLEELEMSKHIDTRVDKLSGGQRKRASVALELLTGP---SLLILDEPTSGLDPALDRQVMTMLRQLADAGRVVLVVTHSL 513
                                    566678888888899999*******88888888877...*****************************77777******6 PP

                         AAA_21 300 l 300
                                    +
  gi|121637655|ref|YP_977878.1| 514 T 514
                                    5 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   5.4   2.6e-09   2.6e-06     170     340 ..     662     853 ..     652     856 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.6e-09
                ABC2_membrane_3 170 ilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afgl......gipfgnlgl.l 241
                                     ++f++ + +++ ++ E+    +e q   g+s+++y+++k++ + +++++q+++++++ ++g       ++  +   l l
  gi|121637655|ref|YP_977878.1| 662 GAVFMGTALTIRDLIGERAIFRRE-Q-AVGLSTTAYLIAKVCVYTVLAVVQSAIVTVIvLVGKggptqgAVALSKPDLeL 739
                                    556777777777888887763333.3.557***********************999975666689999966666665536 PP

                ABC2_membrane_3 242 lllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.ledlp....salkwifsiiPffapglgllrl 316
                                    ++ + + + a+++lg++ls++ k+ e  + l+++  ++ ++f+gg++p +  +p    s++  + + +  +a ++ l++l
  gi|121637655|ref|YP_977878.1| 740 FVDVAVTCVASAMLGLALSAIAKSNEQIMPLLVVAVMSQLVFSGGMIPvTGRVPldqmSWVTPARWGFAASAATVDLIKL 819
                                    7888889****************999998885555555999999999954445563444444455555555555555555 PP

                ABC2_membrane_3 317 i.........tgdplwe....il.lsliilalfavvyl 340
                                    +              w      +  ++++l++++v+y+
  gi|121637655|ref|YP_977878.1| 820 VpgpltpkdsH----WHhtasAWwFDMAMLVALSVIYV 853
                                    45555442220....22555533477777777777776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.02        20      26      40 ..     347     361 ..     327     366 .. 0.82
   2 !   15.5   0.0   8.6e-06    0.0085     132     209 ..     449     523 ..     408     530 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.02
                                    EEEEEESTTSSHHHH CS
                                    xxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnl 40 
                                    +ta++Gp G+GKs l
  gi|121637655|ref|YP_977878.1| 347 LTAVIGPSGAGKSTL 361
                                    69***********87 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.6e-06
                                    -STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 132 iskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklv 209
                                       + LSgG+++ +++aL          +l +lDe  + LD +  ++v ++l++  +    ++v++++ + l  +d+++
  gi|121637655|ref|YP_977878.1| 449 TRVDKLSGGQRKRASVALE----LLTGPSLLILDEPTSGLDPALDRQVMTMLRQLADAgRVVLVVTHSLTYLDVCDQVL 523
                                    23459**********9987....467789*************************9998466789999999998888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   3.4e-06    0.0034       6     130 ..     346     510 ..     342     515 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..................................erpevv........ 43 
                                     +++v+G+sG+GK+tl+r ++   +    +++                                       v        
  gi|121637655|ref|YP_977878.1| 346 MLTAVIGPSGAGKSTLARLVAGYTH----PTDgtvtfeghnvhaeyaslrsrigmvpqddvvhgqlT----Vkhalmyaa 417
                                    5789**************9987653....22245667999999999999999999977777744441....344423344 PP

                         AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseellealeqalrarav...........ielliiDEaqh.lr...seea 108
                                    +  lp +t  kd +++++  + +el+     s+++ +++ + +  +++           ++lli+DE    l+     ++
  gi|121637655|ref|YP_977878.1| 418 ELRLPPDT-TKDDRTQVVARVLEELEM----SKHIDTRVDKLSGGQRKrasvalelltgPSLLILDEPTSgLDpalDRQV 492
                                    55555555.444444444444445555....3333333333333333333455555888889999999999976554888 PP

                         AAA_22 109 leeLrsllnlsrkgvqliLvGt 130
                                    ++ Lr+l++      +++Lv t
  gi|121637655|ref|YP_977878.1| 493 MTMLRQLAD----AGRVVLVVT 510
                                    888888888....555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     7e-06    0.0069      24      66 ..     344     388 ..     332     509 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7e-06
                         AAA_16  24 p.elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa 66 
                                    p  l+ ++G+sG GKs+l+r ++ +   ++g + ++g++++ e a
  gi|121637655|ref|YP_977878.1| 344 PgMLTAVIGPSGAGKSTLARLVAGYTHPTDGTVtFEGHNVHAEYA 388
                                    346889*****************8777776555377777777222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.4e-05     0.054      23      38 ..     345     361 ..     329     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                         AAA_29  23 g.atlltGpsGsGKSTl 38 
                                    g  t ++GpsG+GKSTl
  gi|121637655|ref|YP_977878.1| 345 GmLTAVIGPSGAGKSTL 361
                                    44899***********8 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.26       2      20 ..     349     367 ..     348     454 .. 0.88
   2 ?    0.2   0.0      0.51   5.1e+02     180     206 ..     497     523 ..     488     527 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                                    EEE-STTSSHHHHHHHHHH CS
                 Cytidylate_kin   2 aiDGPagsGKssvaralae 20 
                                    a+ GP+g+GKs++ar++a 
  gi|121637655|ref|YP_977878.1| 349 AVIGPSGAGKSTLARLVAG 367
                                    677*************995 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.51
                                    S-S---TT-EEEETTTS-HHHHHHHHH CS
                 Cytidylate_kin 180 gpLklaedaliidtskltieevvekil 206
                                     +L  a  ++++ t +lt  +v++++l
  gi|121637655|ref|YP_977878.1| 497 RQLADAGRVVLVVTHSLTYLDVCDQVL 523
                                    4677788899***************98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.8e-05     0.098     100     122 ..     346     368 ..     292     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.8e-05
                                    SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                     +++++G+SG+GKStL   +++ 
  gi|121637655|ref|YP_977878.1| 346 MLTAVIGPSGAGKSTLARLVAGY 368
                                    6899************9887765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00084      0.84      22      89 ..     443     497 ..     426     498 .. 0.75
   2 ?   -2.9   0.1       8.7   8.7e+03      42      58 ..     749     765 ..     747     772 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00084
                        SbcCD_C  22 kekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     +k++++++ +lSGG++ + a++al      l+       + ++l++LDE  s+lD+   ++++ +l+
  gi|121637655|ref|YP_977878.1| 443 MSKHIDTRVDKLSGGQR-KRASVALE-----LL-------TGPSLLILDEPTSGLDPALDRQVMTMLR 497
                                    45557778888888888.66666665.....33.......3589********************9998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.7
                        SbcCD_C  42 aylalaaalaalyssae 58 
                                    a+ +l++al+a  +s+e
  gi|121637655|ref|YP_977878.1| 749 ASAMLGLALSAIAKSNE 765
                                    6788999***9999975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.16       2      20 ..     348     366 ..     347     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                         AAA_33   2 vllvGlpGsGKstlaerll 20 
                                    + ++G++G+GKstla+ ++
  gi|121637655|ref|YP_977878.1| 348 TAVIGPSGAGKSTLARLVA 366
                                    6789***********9876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.25       3      32 ..     349     389 ..     347     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                         AAA_28   3 vitGgestGKTtlleaLa..ar.........gypvvpEaar 32 
                                    +++G++++GK+tl++  a   +         g++v++E+a 
  gi|121637655|ref|YP_977878.1| 349 AVIGPSGAGKSTLARLVAgyTHptdgtvtfeGHNVHAEYAS 389
                                    79****************76335664455556666666664 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00038      0.38       3      23 ..     350     370 ..     348     518 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                    EESSTTSSHHHHHHHHHHHHT CS
                            AAA   3 lyGppGtGKTllakavakelg 23 
                                    ++Gp G GK++la+ va  ++
  gi|121637655|ref|YP_977878.1| 350 VIGPSGAGKSTLARLVAGYTH 370
                                    79***************9874 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   0.00058      0.58      14      64 ..     341     392 ..     338     512 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00058
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Lae 64 
                                    ++ + +++++ Gp G+GK+t+ + ++   +   g+v    ++  a  + L+ 
  gi|121637655|ref|YP_977878.1| 341 TARPGMLTAVIGPSGAGKSTLARLVAGYTHPTDGTVTFEGHNVHAEYAsLRS 392
                                    56677899*************9999888877765665444443333333443 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.65   6.5e+02       2      31 ..     600     629 ..     599     670 .. 0.86
   2 ?    8.8   9.0   0.00085      0.85     118     275 ..     694     852 ..     687     858 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.65
                ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidval 31 
                                    +ia++ +r +v +r + ++ +llp+i +al
  gi|121637655|ref|YP_977878.1| 600 TIARRQLRLIVSDRGYFVFLALLPFIMGAL 629
                                    6899999999999*********99995554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00085
                ABC2_membrane_2 118 eillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaa 196
                                    ++l++K+  + +++++  a+  +++vl++ +   ++ ++l+  dl l+v ++v+ ++    ++lgl+lS++a+ s+e++ 
  gi|121637655|ref|YP_977878.1| 694 AYLIAKVCVYTVLAVVqSAIV-TVIVLVGKGGPTQGAVALSKPDLELFVDVAVTCVA---SAMLGLALSAIAK-SNEQIM 768
                                    568888888888866644333.33335545555555555555555555555554444...599**********.777766 PP

                ABC2_membrane_2 197 lalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlna.............lgstat 263
                                      l++ v+ ++++++   +v+             d +s+++p+++  ++ ++     +l                 + ++
  gi|121637655|ref|YP_977878.1| 769 PLLVVAVMSQLVFSGGMIPVTGRVP--------LDQMSWVTPARWGFAASAATVDLIKLVPgpltpkdshwhhtASAWWF 840
                                    6677777776666665545444444........55558888888855554444444433334555555555555555555 PP

                ABC2_membrane_2 264 nllilllllavl 275
                                     +++l++l +++
  gi|121637655|ref|YP_977878.1| 841 DMAMLVALSVIY 852
                                    555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 5520.31
//
Query:       gi|121637656|ref|YP_977879.1|  [L=243]
Description: hypothetical protein BCG_1787 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   12.6   6.7       0.16   12.6   1.7    2.2  2  DUF4439   Domain of unknown function (DUF4439)


Domain annotation for each model (and alignments):
>> DUF4439  Domain of unknown function (DUF4439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.012   2.2e+02      81     105 ..      74      97 ..      58     106 .. 0.80
   2 ?   12.6   1.7     9e-06      0.16      15      68 ..     164     217 ..     150     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.012
                        DUF4439  81 elEedlaaayaalvaaddadlRsta 105
                                    ++E+d+a  ++a+++a +a++R+ a
  gi|121637656|ref|YP_977879.1|  74 TVENDAA-RWRAITRAVEAHERTDA 97 
                                    6777755.69999999999999876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9e-06
                        DUF4439  15 gYgvvsarldgarraaarealaaHrarrdalaallsargatppaaeaaYelpfe 68 
                                    +++ ++a +  +rr+  +++ ++  ar++ l +++s++gat++++e aY+l+ +
  gi|121637656|ref|YP_977879.1| 164 AFDTAEAEAMRRRRTGFSREEQQRLARAQSLLRVASDAGATAQERERAYRLART 217
                                    677888999999999999*********************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1761.39
//
Query:       gi|121637657|ref|YP_977880.1|  [L=185]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0033   17.5   1.7      0.013   15.5   0.0    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
       0.09   13.1   1.9       0.19   12.0   0.2    2.0  2  DUF4064          Protein of unknown function (DUF4064)
       0.16   11.5   4.1        1.9    8.0   0.8    2.3  2  PMT              Dolichyl-phosphate-mannose-protein mannosylt
       0.72    9.3   5.4       0.57    9.6   0.9    2.1  2  DUF4173          Domain of unknown function (DUF4173)


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.9e-06     0.013      42      84 ..      20      73 ..       6      81 .. 0.67
   2 ?    0.9   0.5       0.1   4.6e+02      40      72 ..     104     124 ..      93     173 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
                Phage_holin_3_6 42 aagvlallalllllvala...........lalaa..lwlaalivaavllvlagvla 84
                                   + g++++++++++l++++           +  ++  lw+  liv++v ++ ag  +
  gi|121637657|ref|YP_977880.1| 20 GVGMFTIVGVIVALIGAFvqsrrhrhrpaA--DIhmLWWMVLIVGVVSIIGAGYHV 73
                                   345555666666666663355555666431..22458*************999755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                Phage_holin_3_6  40 lgaagvlallalllllvalalalaalwlaaliv 72 
                                     +++++   +                wla+++v
  gi|121637657|ref|YP_977880.1| 104 GVVGLMAYRFRGH------------FWLATIVV 124
                                    2222222223333............33333332 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.3e-05      0.19      64     102 ..      21      67 ..       5      68 .. 0.76
   2 ?    0.3   0.1      0.19   8.4e+02       7      39 ..     105     137 ..     101     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                        DUF4064  64 lgvialiaivlgivgalllkknkk........vsGilfiiaailslf 102
                                     g++ ++  ++ ++ga++ ++ ++        + +++++i++++s++
  gi|121637657|ref|YP_977880.1|  21 VGMFTIVGVIVALIGAFVQSRRHRhrpaadihMLWWMVLIVGVVSII 67 
                                    4666777777777777777766666677*****************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                        DUF4064   7 iLglIGgilgillglllllflfllssgefsqel 39 
                                    + gl++  +   ++l+++++l ++  g+ + + 
  gi|121637657|ref|YP_977880.1| 105 VVGLMAYRFRGHFWLATIVVLTIQYVGDAAGHI 137
                                    566666667777777777777777666666665 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8   0.00042       1.9     182     228 ..      19      66 ..      15      75 .. 0.87
   2 ?    4.6   0.1    0.0048        21      59     105 ..      85     131 ..      70     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00042
                            PMT 182 Kwvglftvllvgllliwelwqllgdkslllksi.vkhllaralalivi 228
                                    K+vg+ft++ v + li   +q +  + ++ + i + ++++ ++ ++ i
  gi|121637657|ref|YP_977880.1|  19 KGVGMFTIVGVIVALIGAFVQSRRHRHRPAADIhMLWWMVLIVGVVSI 66 
                                    9***********************999999999988888888888766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0048
                            PMT  59 LagkdgnftfesigaeyypenvpyvslRlfsallgslivplvyltll 105
                                    ++  dg f++e++ ++  ++ v  +++R+   +  ++iv+l+ + + 
  gi|121637657|ref|YP_977880.1|  85 YTRGDGGFQWENAMGDLAIGVVGLMAYRFRGHFWLATIVVLTIQYVG 131
                                    4556899**********************999999999999988776 PP

>> DUF4173  Domain of unknown function (DUF4173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.031   1.4e+02      54      85 ..      30      61 ..      19      74 .. 0.47
   2 ?    9.6   0.9   0.00013      0.57     115     170 ..      98     152 ..      94     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.031
                        DUF4173 54 vvlvalrlakrekakkrkllrvlllvlialtl 85
                                   +v+++  +++ ++ ++r +  + +l +++l +
  gi|121637657|ref|YP_977880.1| 30 IVALIGAFVQSRRHRHRPAADIHMLWWMVLIV 61
                                   33333333333344444444444444444332 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00013
                        DUF4173 115 llllalvlllvlvkilkrkfklfraalvaaavlllvlafinpdalIarynverye.t 170
                                    +  la+++++++++ ++ +f+l+ +  v++++ +++ a  ++ ++++++n++ y+ +
  gi|121637657|ref|YP_977880.1|  98 MGDLAIGVVGLMAYRFRGHFWLATI--VVLTIQYVGDAAGHIYYWVVENNTNPYNiG 152
                                    666899***************9765..6678899*****************999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1370.54
//
Query:       gi|121637658|ref|YP_977881.1|  [L=532]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-53  182.0   0.1    1.8e-53  181.7   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    3.6e-08   34.3   0.0    1.2e-07   32.6   0.0    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.1     2e-57   1.8e-53      12     422 ..      18     407 ..       9     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 2e-57
                                    EEEEECCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHH CS
                    AMP-binding  12 valvdsgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayil 90 
                                    +a+ +  +g ++T++++ +++ + Aa+L   ++ ++ ++++ ll n+pe+++ l a+   G v+  ln+t + ++la  +
  gi|121637658|ref|YP_977881.1|  18 IAVKY--GGLQWTWSQYLAESAARAAALItIADPQRPTHIGSLLGNTPEMLAQLAAAGLGGYVLCGLNTTRRGDALAADV 95 
                                    67777..8999*********9999999998899********************9999999******************** PP

                                    HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--S CS
                    AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGT 170
                                    + +++++++  +d++     ++  + l+  +   +ld+  ++ +e + ++   + +     + +e++  d+ ++i+TSGT
  gi|121637658|ref|YP_977881.1|  96 RRADCQIVV--TDADH----RALLDGLDL-AGARILDTSTPRWAELVAGDG--AFV-----PYREVDTMDPFMMIFTSGT 161
                                    *********..66555....333333333.344568877777776666666..333.....334689************* PP

                                    SSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHH CS
                    AMP-binding 171 TGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelie 250
                                     G+PK+V +sh  ++++ +sl  ++rf+l+e+d++++ +pl+h+ +++++   a++sGa++  ++ ++a   + +l++++
  gi|121637658|ref|YP_977881.1| 162 SGNPKAVPVSHLMATFAGRSL--TERFGLTEQDTCYVSMPLFHSNAVVAGWAPAVVSGAAIAPAT-FSA---TGFLDDVR 235
                                    ***********9999998995..77899*******************888888888888776655.555...3367**** PP

                                    HHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHC CS
                    AMP-binding 251 klkvtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpl 329
                                    ++++t++++v   l ++l+ ++++      d    lr++   g+  + + +++f+++fg +v +g+G TE++++v+  + 
  gi|121637658|ref|YP_977881.1| 236 RYHATYMNYVGKPLAYILATPERD-----DDADNpLRVA--FGNEANDKDIEEFSRRFGVQVEDGFGSTENAVIVI-RE- 306
                                    *******************87666.....367777**94..57777777778999999999*************99.44. PP

                                    TTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE...........TTSEEEEE.EEETTS-SEBTT-HHHHHHHEEETCCEEE CS
                    AMP-binding 330 eedkkklgsvGkplpgvevkivDeetgepvp...........dgeeGell.vrgpgvmkgYlkkpeataeafdsegrwlr 397
                                      + + +gs+G+  +gv v+  +  t+  v+           d+  Gel+   g g + gY+++pea+ae++  + +++ 
  gi|121637658|ref|YP_977881.1| 307 --PGTPPGSIGRGAHGVAVYNGETVTECAVArfdahgaltnaDEAIGELVnTTGSGFFTGYYNDPEANAERMR-H-GMYW 382
                                    ..3336999**88877776666666666665777777777768888****7889******************8.6.6*** PP

                                    EEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 398 TGDlgrldedGyleivgRkkdlikl 422
                                    +GDl+++d +G +++ gR+ d + +
  gi|121637658|ref|YP_977881.1| 383 SGDLAYRDSEGWIYLAGRTADWMRV 407
                                    *******************998865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.4e-11   1.2e-07       2      76 .]     417     493 ..     416     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.4e-11
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHH..HT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrk..elgpyavpkkvvfvdelpktrsGK 76 
                                    +E +l++ +a++ +aV++vpde  G  ++a  vl++g + +  +++ +a++ +   l + a+p+++++ ++lp t++ K
  gi|121637658|ref|YP_977881.1| 417 IERILLRYKAINRVAVYAVPDEYVGDQVMAALVLRAGdTfD--PDAFEAFLDAqpDLSTKARPRYIRIAADLPSTATHK 493
                                    89********************************8884333..68888888555699999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3723.57
//
Query:       gi|121637659|ref|YP_977882.1|  [L=460]
Description: hypothetical protein BCG_1790 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-78  263.8   0.0      3e-78  263.5   0.0    1.0  1  FAD_binding_3   FAD binding domain
    3.5e-11   43.3   0.7      7e-06   25.9   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    2.9e-06   27.4   0.3    7.1e-06   26.2   0.3    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.4e-06   26.2   0.3      0.048   12.5   0.0    3.0  3  Trp_halogenase  Tryptophan halogenase
    6.4e-06   25.5   5.1     0.0068   15.5   0.6    3.0  3  FAD_binding_2   FAD binding domain
    3.6e-05   23.2   0.0    9.9e-05   21.7   0.0    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00021   20.1   0.1    0.00044   19.1   0.1    1.5  1  HI0933_like     HI0933-like protein
    0.00043   20.8   0.1     0.0021   18.6   0.0    2.1  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0016   17.8   0.0     0.0023   17.3   0.0    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0032   16.9   1.7      0.026   13.9   0.5    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0041   16.2   0.0       0.25   10.4   0.0    2.1  2  SE              Squalene epoxidase
     0.0059   15.7   1.9       0.22   10.5   0.2    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0069   15.5   0.1      0.011   14.8   0.1    1.3  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.19   11.3   0.5        0.5   10.0   0.2    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.5   0.0   2.3e-81     3e-78       2     347 ..      53     393 ..      51     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 263.5 bits;  conditional E-value: 2.3e-81
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                    t+ +I+G+GpaG++l+llL++aGv+v+l+ek+ +  +++r+d+++++tm+ll++lGl++r++a  +++  ++++++n   
  gi|121637659|ref|YP_977882.1|  53 TTCAIIGGGPAGMVLGLLLARAGVQVTLLEKHGDFLRDFRGDTVHPTTMRLLDELGLWERFAALPYSEVRTATLHSNG-- 130
                                    4566**************************************************************************.. PP

                                    CCCEEEEEHH...CHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEE CS
                  FAD_binding_3  82 dtpkaradle...lesspervtvypqteleriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvrakY 157
                                       +a ++++   l++ +++v+++pq++l+++L+e+a++++ +++r+ktev++l++++ +vt + ++ ++g   ++ra+ 
  gi|121637659|ref|YP_977882.1| 131 ---RAVTYIDferLHQPYPYVAMVPQWDLLNLLAEAAQAEPsFTLRMKTEVTGLLREGGKVTGVRYQGAEGPG-ELRAEL 206
                                    ...888888887999*********************************************************9.****** PP

                                    EEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC....CEEEEECCTTEEEEEECCE.TEEEEEEEEE CS
                  FAD_binding_3 158 lvGaDGgrStvrktlgiefegeetvyeagvldvlfda.dlsdivep....lvlilsaesrgvmviPlen.tlerfyvqve 231
                                    +v++DG +S++r+++g++         a+ + v+fd+ +++ ++e+    ++l + ++ +g+ viP+e  ++ +++    
  gi|121637659|ref|YP_977882.1| 207 TVACDGRWSIARHEAGLK---------AREFPVNFDVwWFKLPREGdaefSFLPRFSPGKGLGVIPREGyFQIAYLGPKG 277
                                    ****************88.........78899*********999999*999***************************** PP

                                    CCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHH CS
                  FAD_binding_3 232 araekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDa 311
                                    ++a+ +er  ++++++v++ l+e++++ ++ ++ +ev++++v+ +  ++++ + ++++GDAaH+++P++G+G+N+a+qDa
  gi|121637659|ref|YP_977882.1| 278 TDAQLRERGIEEFRRDVSELLPEATASVAALASTDEVKHLNVKVNRLRRWHIDGLLCIGDAAHAMSPVAGVGINLAVQDA 357
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHTTSS-GGGGHHHHHHHHHHHHHHHH CS
                  FAD_binding_3 312 vnLawkLaavlkGeAkeelLdtYeeerravaqavvd 347
                                    v  a+ La+ l++++ ++++ +  ++rra+ +av++
  gi|121637659|ref|YP_977882.1| 358 VAAATILAEPLREHRVSSRHLAAVRRRRAFPTAVTQ 393
                                    *********************************997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   6.2e-06    0.0079       3      30 ..      56      85 ..      54      97 .. 0.93
   2 !   25.9   0.0   5.5e-09     7e-06     144     299 ..     152     301 ..     137     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                                   EEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgd 30
                                   +iiGGG +G+   + Lar+g  Vtllek+ 
  gi|121637659|ref|YP_977882.1| 56 AIIGGGPAGMVLGLLLARAGvqVTLLEKHG 85
                                   8***************************94 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 5.5e-09
                                    EHHHHHHHHHHHHHHTT.-EEEESECEEEEEEEETCEEEEE..EECT.EEEEEEEEEEE--GGGHHHHHTT.CTTTSEEE CS
                            DAO 144 dpakltaalaraaealG.veilegtevtgleeedgkvwgve..rttp.gendaadavVnaaGawsdllgll.keldlpis 218
                                      + l++ la+aa+a    +++ +tevtgl +e+gkv+gv+   ++  ge + a+  V + G ws  ++++   l+ +  
  gi|121637659|ref|YP_977882.1| 152 PQWDLLNLLAEAAQAEPsFTLRMKTEVTGLLREGGKVTGVRyqGAEGpGELR-AELTVACDGRWS--IARHeAGLKAREF 228
                                    556789999****999758**********98999******998555557654.477********7..5444455654558 PP

                                    EEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG CS
                            DAO 219 pvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPq 298
                                    pv   v+ + +l+++    a    +p +  +g+g+ v+pr+ g + +   +  ++g+d  +  e+ i+e+++ +++l+P+
  gi|121637659|ref|YP_977882.1| 229 PVNFDVWWF-KLPREG--DAEFSFLP-RFSPGKGLGVIPRE-GYFQIAYLG--PKGTDA-QLRERGIEEFRRDVSELLPE 300
                                    899999888.444422..22333333.999*********96.875544444..467788.9******************9 PP

                                    G CS
                            DAO 299 l 299
                                     
  gi|121637659|ref|YP_977882.1| 301 A 301
                                    4 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.3   5.6e-09   7.1e-06       1      30 [.      57      86 ..      57      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.6e-09
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                   I+G+G +G+v+  lLa+ag++v+llek+ +
  gi|121637659|ref|YP_977882.1| 57 IIGGGPAGMVLGLLLARAGVQVTLLEKHGD 86
                                   9**************************976 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   3.8e-05     0.048       3      64 ..      56     114 ..      54     154 .. 0.83
   2 ?    1.0   0.0      0.11   1.4e+02     159     211 ..     159     215 ..     155     226 .. 0.77
   3 !    8.9   0.0   0.00045      0.58     296     356 ..     309     370 ..     293     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                                    EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S.SS---SS-EE--THHHHTHHHHT--HHHHC CS
                 Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlvese.eigtvgvGeatipsirkllrlLgideeefl 64 
                                     i+GGG+aG +   +la+a+   ++vtl+e+  ++ +   G+   p++  ll+ Lg+ e+ f 
  gi|121637659|ref|YP_977882.1|  56 AIIGGGPAGMVLGLLLARAG---VQVTLLEKHgDFLRDFRGDTVHPTTMRLLDELGLWER-FA 114
                                    79******************...9******973566777788888888889999999887.54 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                    HHHHHHHHC.T-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG- CS
                 Trp_halogenase 159 fLrrvaear.Gvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrg 211
                                    +L + a+a+   t +  + v+  l+e g+v+++r++      e+ a+l + c G  +
  gi|121637659|ref|YP_977882.1| 159 LLAEAAQAEpSFTLRMKTEVTGLLREGGKVTGVRYQGaegPGELRAELTVACDGRWS 215
                                    5666666665666666777788999**********98765347*********99766 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00045
                                    TTTS-.EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT-- CS
                 Trp_halogenase 296 leaep.rkirfttGrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksde 356
                                    + +++ ++++++++r ++    +++ +G+a+ ++ P+ + +i l+ +++   +++l++   e
  gi|121637659|ref|YP_977882.1| 309 ASTDEvKHLNVKVNRLRRWHIDGLLCIGDAAHAMSPVAGVGINLAVQDAVAAATILAEPLRE 370
                                    33444499*************************************99888888888776555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   5.3e-06    0.0068       3      32 ..      56      85 ..      54      88 .. 0.93
   2 !   10.3   0.0   0.00021      0.27     136     193 ..     149     205 ..     111     235 .. 0.81
   3 ?   -1.2   0.0      0.65   8.4e+02     388     411 ..     325     344 ..     315     352 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                                   EEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                    +iG+G AG++ +l +a+aG +v+++ek +
  gi|121637659|ref|YP_977882.1| 56 AIIGGGPAGMVLGLLLARAGVQVTLLEKHG 85
                                   69*************************976 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                                    ...HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES CS
                  FAD_binding_2 136 tlvtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirak 193
                                    ++v+   ll  l+e+a++ +  +++ +te++ L++e+g+vtG+  +  e+++e r  a 
  gi|121637659|ref|YP_977882.1| 149 AMVPQWDLLNLLAEAAQAEPsFTLRMKTEVTGLLREGGKVTGVRYQGAEGPGELR--AE 205
                                    56677788999999998888***********************999665555544..54 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.65
                                    EEESSBTEEE-STCEESSSSTTS- CS
                  FAD_binding_2 388 dgqpipGLYAaGevaaggvhganr 411
                                       +i+GL ++G +a    h + +
  gi|121637659|ref|YP_977882.1| 325 RRWHIDGLLCIGDAA----HAMSP 344
                                    5568**********9....33333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.7e-08   9.9e-05     143     181 ..      53      91 ..      16     116 .. 0.73
   2 ?   -2.8   0.0       2.2   2.8e+03      22      86 ..     129     189 ..     121     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.7e-08
                                    SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllral 181
                                      ++++GgG+ G++l   la++g++vtl+e    +lr +
  gi|121637659|ref|YP_977882.1|  53 TTCAIIGGGPAGMVLGLLLARAGVQVTLLEKHGDFLRDF 91 
                                    456777777777777777777777777777777777544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                    HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEE CS
                                    xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  22 agakvtlve...legtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvk 86 
                                    +g  vt ++   l +  +++ ++++  ll+  ++a +a+        +++l++++ev+++ ++ +kv+
  gi|121637659|ref|YP_977882.1| 129 NGRAVTYIDferLHQPYPYVAMVPQWDLLNLLAEAAQAEP-------SFTLRMKTEVTGLLREGGKVT 189
                                    5666666655555666666666666666666666654442.......456666666666666666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.4e-07   0.00044       3      39 ..      55      91 ..      53      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-07
                                   EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                    HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                    ++iGgG+AG+   + +a++g +V+llek   ++r +
  gi|121637659|ref|YP_977882.1| 55 CAIIGGGPAGMVLGLLLARAGVQVTLLEKHGDFLRDF 91
                                   68***************************99988865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0021       3      42 ..      56      95 ..      54     109 .. 0.78
   2 ?   -2.0   0.0       4.3   5.4e+03      56      78 ..     171     193 ..     159     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                   EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHH CS
                      Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeea 42
                                   +++GgG  g+ l+  la+ g +Vt++e +  +lr +  ++
  gi|121637659|ref|YP_977882.1| 56 AIIGGGPAGMVLGLLLARAGVQVTLLEKHGDFLRDFRGDT 95
                                   8********************************5554443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                    EEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox  56 evllntkveeiegsedgvesvkl 78 
                                    +++++t+v+ +  ++ +v++v+ 
  gi|121637659|ref|YP_977882.1| 171 TLRMKTEVTGLLREGGKVTGVRY 193
                                    78889999999988888999986 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0023       2      30 ..      57      84 ..      56     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                   IiG+GPaG+  ++ l +ag+ +++ lEk+
  gi|121637659|ref|YP_977882.1| 57 IIGGGPAGMVLGLLLARAGV-QVTLLEKH 84
                                   9*******************.79****97 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5     2e-05     0.026       3     142 ..      56     210 ..      55     222 .. 0.63
   2 ?   -2.4   0.0       1.8   2.3e+03     405     430 ..     300     325 ..     298     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                   FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiaref....lerlrq....rgga. 73 
                                     ++GGgpaG++  +  araG +v L+e++g     + +  v + ++         g++++f    ++++r      +g  
  gi|121637659|ref|YP_977882.1|  56 AIIGGGPAGMVLGLLLARAGVQVTLLEKHGDFLRDFRGDTVHPTTMRLLD---ELGLWERFaalpYSEVRTatlhSNGRa 132
                                    59*************************98544334444444333333322...233333331111333333111111112 PP

                   FAD_oxidored  74 .rlkkrskwn...............tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAk 137
                                                             + + + ++ ++e+  ae+  t+ ++t++++  +eg+++++v+ +  eg  ++rA+
  gi|121637659|ref|YP_977882.1| 133 vT-------YidferlhqpypyvamVPQWDLLNLLAEAAQAEPSFTLRMKTEVTGLLREGGKVTGVRYQGAEGPGELRAE 205
                                    21.......02233333344555544555555666666669999999999999999999999999999888899999999 PP

                   FAD_oxidored 138 vfiDA 142
                                    +++ +
  gi|121637659|ref|YP_977882.1| 206 LTVAC 210
                                    88866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                   FAD_oxidored 405 qAaGvaAalaleegvaprdvdvkelq 430
                                    +A++ +Aala  ++v+  +v+v++l+
  gi|121637659|ref|YP_977882.1| 300 EATASVAALASTDEVKHLNVKVNRLR 325
                                    79999**********99999999998 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.02        26       2      18 ..     204     220 ..     203     231 .. 0.87
   2 !   10.4   0.0   0.00019      0.25     111     166 ..     311     366 ..     286     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                             SE   2 AkltvvcDGifsklRke 18 
                                    A+ltv cDG +s  R+e
  gi|121637659|ref|YP_977882.1| 204 AELTVACDGRWSIARHE 220
                                    99**********99876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                             SE 111 egklrsmpnkflpasknekkGlillGDalnmRHPltggGmtvalnDivllskllkp 166
                                    +++++ ++ k+   ++ +  Gl+ +GDa     P+ g G+  a++D+v  + +l +
  gi|121637659|ref|YP_977882.1| 311 TDEVKHLNVKVNRLRRWHIDGLLCIGDAAHAMSPVAGVGINLAVQDAVAAATILAE 366
                                    44667777777777777889***************************988887765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   0.00017      0.22       3      35 ..      56      86 ..      55      93 .. 0.89
   2 ?    4.6   0.1     0.011        14     259     309 ..     333     386 ..     320     428 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                  Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieasps 35
                                   ++iG+GpAg+ l   l  a++g++v+l+e   +
  gi|121637659|ref|YP_977882.1| 56 AIIGGGPAGMVLGLLL--ARAGVQVTLLEKHGD 86
                                   79**************..**********97665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                  Lycopene_cycl 259 laiGaaaglvhPaTGYsvarslaeapllasaiaaalres...slsarawatlwp 309
                                    l iG aa ++ P  G  +  +++ a   a  +a+ lre+   s++  a ++  +
  gi|121637659|ref|YP_977882.1| 333 LCIGDAAHAMSPVAGVGINLAVQDAVAAATILAEPLREHrvsSRHLAAVRRRRA 386
                                    679*************99999999998888999999987554222222222222 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   8.8e-06     0.011       2      33 ..      55      86 ..      54      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkld 33
                                   + +iGgG AG+   l +ar+G++v+L+ ++ d
  gi|121637659|ref|YP_977882.1| 55 CAIIGGGPAGMVLGLLLARAGVQVTLLEKHGD 86
                                   78*************************88776 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00039       0.5       2      29 ..      56      83 ..      55      96 .. 0.90
   2 ?   -2.7   0.0       3.3   4.2e+03      17      47 ..     160     192 ..     157     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                                   EEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                           ApbA  2 ailGaGaiGsllaakLakagadvtlilr 29
                                   ai+G G  G +l+  La+ag +vtl+ +
  gi|121637659|ref|YP_977882.1| 56 AIIGGGPAGMVLGLLLARAGVQVTLLEK 83
                                   8************************966 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                                    HHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                           ApbA  17 Lak.agadvtlilrsr.rlealkknGlrltseg 47 
                                    La+ a a++ + lr + ++  l ++G ++t+++
  gi|121637659|ref|YP_977882.1| 160 LAEaAQAEPSFTLRMKtEVTGLLREGGKVTGVR 192
                                    677788889999999988888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3116.53
//
Query:       gi|121637660|ref|YP_977883.1|  [L=149]
Description: hypothetical protein BCG_1791 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1152.01
//
Query:       gi|121637661|ref|YP_977884.1|  [L=1026]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-56  188.3  32.6    9.5e-56  188.3  32.6    1.6  2  PPE             PPE family
    2.6e-41  139.2 261.8    3.1e-11   43.0  23.0   10.4 10  Pentapeptide_2  Pentapeptide repeats (8 copies)
  ------ inclusion threshold ------
       0.14   11.5   0.6       0.19   11.0   0.6    1.1  1  PAD_porph       Porphyromonas-type peptidyl-arginine deiminas
        3.1    8.2   5.9        6.7    7.1   5.9    1.5  1  DUF3144         Protein of unknown function (DUF3144)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3  32.6   2.1e-59   9.5e-56       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -4.0   0.8       3.2   1.4e+04      70      84 ..     180     194 ..     172     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 2.1e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+nsal++aG+g++p+ aAa+aWdgLa elasaaa++ sv+++l ++aWqG+ss amaaaaapy+aWL+aaa qae
  gi|121637661|ref|YP_977884.1|   5 VLPPEINSALIFAGAGPEPMAAAATAWDGLAMELASAAASFGSVTSGLVGGAWQGASSSAMAAAAAPYAAWLAAAAVQAE 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    ++Aaqa+a++a +ea  +a+v+p ++aanra l++lv++n+fGqn+paIaa ea ye+mwa+d++am+aY+a ++a+
  gi|121637661|ref|YP_977884.1|  85 QTAAQAAAMIAEFEAVKTAVVQPMLVAANRADLVSLVMSNLFGQNAPAIAAIEATYEQMWAADVSAMSAYHAGASAI 161
                                    *************************************************************************9986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHHHHHH CS
                            PPE  70 aWLsaaaaqaeeaAa 84 
                                    aWL+  a  a+ +Aa
  gi|121637661|ref|YP_977884.1| 180 AWLASGAPAAAMTAA 194
                                    444444444444433 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  31.3   2.3e-08    0.0001       2      40 .]     208     246 ..     206     246 .. 0.95
   2 !   17.8  36.6   4.9e-07    0.0022       2      39 ..     238     275 ..     232     276 .. 0.82
   3 !   23.8  34.5   6.6e-09   2.9e-05       2      40 .]     268     306 ..     267     306 .. 0.97
   4 !   30.5  33.7   5.6e-11   2.5e-07       3      40 .]     311     348 ..     309     348 .. 0.97
   5 !   34.5  28.0   3.1e-12   1.4e-08       1      40 []     339     378 ..     339     378 .. 0.98
   6 !   43.0  23.0     7e-15   3.1e-11       1      40 []     379     418 ..     379     418 .. 0.98
   7 !   30.3  20.6   6.2e-11   2.8e-07       1      38 [.     409     446 ..     409     447 .. 0.95
   8 ?    0.5  21.4      0.13   5.8e+02       4      38 ..     926     962 ..     923     963 .. 0.82
   9 !    7.9  10.1   0.00064       2.9       2      29 ..     970     997 ..     969     999 .. 0.79
  10 ?    1.8   0.3     0.051   2.3e+02      14      24 ..    1009    1019 ..    1001    1022 .. 0.49

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-08
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N G++N+G gN+G++N G +N+G++NlG++N+Gsgn+G+
  gi|121637661|ref|YP_977884.1| 208 NLGIANVGGGNVGNANNGLANIGNANLGNYNFGSGNFGN 246
                                    99**********************************996 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.9e-07
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+Gs+N+G+ N+G++ lG+ N+G++NlGs+N+G gn+G
  gi|121637661|ref|YP_977884.1| 238 NFGSGNFGNSNIGSASLGNNNIGFGNLGSNNVGVGNLG 275
                                    88888888888888888888888888888888888888 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 6.6e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+G+ NtGf+N+G gN+G++N+G++N+G+g tG+
  gi|121637661|ref|YP_977884.1| 268 NVGVGNLGNLNTGFANTGLGNFGFGNTGNNNIGIGLTGN 306
                                    9************************************96 PP

  == domain 4  score: 30.5 bits;  conditional E-value: 5.6e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G lNsG+gN+G+fN+GsgN+G+fN+G+gN+G+gn+G+
  gi|121637661|ref|YP_977884.1| 311 IGGLNSGTGNFGLFNSGSGNVGFFNSGNGNFGIGNSGN 348
                                    89***********************************6 PP

  == domain 5  score: 34.5 bits;  conditional E-value: 3.1e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++NsG++NtG +N+G gNtG+fN+Gs+NtG++ +G+
  gi|121637661|ref|YP_977884.1| 339 GNFGIGNSGNFNTGGWNSGHGNTGFFNAGSFNTGMLDVGN 378
                                    8***********************************9996 PP

  == domain 6  score: 43.0 bits;  conditional E-value: 7e-15
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtGslN+Gs N+G+fN Gs NtG fN+G++NtG++n+G+
  gi|121637661|ref|YP_977884.1| 379 ANTGSLNTGSYNMGDFNPGSSNTGTFNTGNANTGFLNAGN 418
                                    6*************************************96 PP

  == domain 7  score: 30.3 bits;  conditional E-value: 6.2e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +NtG+lN+G+ NtG fN+G  N G fN+G+ N G +  
  gi|121637661|ref|YP_977884.1| 409 ANTGFLNAGNINTGVFNIGHMNNGLFNTGDMNNGVFYR 446
                                    6*********************************9865 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 0.13
                 Pentapeptide_2   4 GslNsGsg.NtGffNlGs.gNtGsfNlGsgNtGsgnt 38 
                                    G++Ns+++  +GffN+G  gN G++N Gsg +G +nt
  gi|121637661|ref|YP_977884.1| 926 GYFNSSTApSSGFFNSGAgGNSGFGNNGSGLSGWFNT 962
                                    8888888756899999963699999999999999997 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.00064
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlG 29 
                                     +G+ N+G   +Gf NlGsg  G++N G
  gi|121637661|ref|YP_977884.1| 970 GSGYQNFGGLSSGFSNLGSGVSGFANRG 997
                                    5788888888888888888888888877 PP

  == domain 10  score: 1.8 bits;  conditional E-value: 0.051
                 Pentapeptide_2   14 GffNlGsgNtG 24  
                                     Gf+N+G+   G
  gi|121637661|ref|YP_977884.1| 1009 GFANIGTNLAG 1019
                                     33333333333 PP

>> PAD_porph  Porphyromonas-type peptidyl-arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   4.3e-05      0.19      23      86 ..      74     154 ..      56     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                                    GC.GGGHHHHHHHHHHHHHHHHTTSEEEEEESSHH.HHHHHHHC...............EEEEE---SSS-HHHHS-EEE CS
                      PAD_porph  23 dw.eekleeaqeefaelakaiaefepvtllvedee.aeearell...............velveiptndlWlRDtgpifv 85 
                                     w +  + +a+++ a+ a+ iaefe v+ +v +   +++ r+ l               +  +e++++++W+ D+ ++  
  gi|121637661|ref|YP_977884.1|  74 AWlAAAAVQAEQTAAQAAAMIAEFEAVKTAVVQPMlVAANRADLvslvmsnlfgqnapaIAAIEATYEQMWAADVSAMSA 153
                                    4524568899******************999555544554555568999*************************999876 PP

                                    E CS
                      PAD_porph  86 v 86 
                                     
  gi|121637661|ref|YP_977884.1| 154 Y 154
                                    6 PP

>> DUF3144  Protein of unknown function (DUF3144)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.9    0.0015       6.7      22      61 ..      59      97 ..      52     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                        DUF3144 22 geVsaallyAaARfnafvaaskfeskedlaaekeealeyf 61
                                   g+ s+a+  AaA ++a++aa+++ ++e+ aa+  ++++ f
  gi|121637661|ref|YP_977884.1| 59 GASSSAMAAAAAPYAAWLAAAAV-QAEQTAAQAAAMIAEF 97
                                   66799************999999.7777788777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1026 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.25s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 7095.11
//
Query:       gi|121637662|ref|YP_977885.1|  [L=563]
Description: hypothetical protein BCG_1793c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-119  399.1   4.4   1.6e-119  398.8   4.4    1.1  1  DUF4185         Domain of unknown function (DUF4185)


Domain annotation for each model (and alignments):
>> DUF4185  Domain of unknown function (DUF4185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.8   4.4  8.9e-124  1.6e-119       2     313 .]     234     559 ..     233     559 .. 0.97

  Alignments for each domain:
  == domain 1  score: 398.8 bits;  conditional E-value: 8.9e-124
                        DUF4185   2 spnrtdsrfgvsgTDLGimwdngkg...rvlivfGDtfgekavgsgkgdWrsnvllrssdrdlsdgl.........tfdg 69 
                                    spn+t +rfg+sgTDLGi+wdng+    +vl++fGDtfg  av ++  +Wr+n+l+rs+drdl +g+         +++g
  gi|121637662|ref|YP_977885.1| 234 SPNKTLERFGISGTDLGIPWDNGDPanrQVLMIFGDTFGYCAVDGH--QWRYNTLFRSQDRDLGNGVhvtsgdasnRYSG 311
                                    89*******************9955666***********9998887..****************************9*** PP

                        DUF4185  70 avgdaggkakqlipseklkgvevtviPtagisvggtqylsymsvrswgapgewttnysaiaksdDngetWekvpesvrtn 149
                                    ++ +++g++kqli+s k+++ e+++iPtagi+vg+tqy+++ms+r+wg++gewttnys+ia+s+Dng+tW ++p+++r +
  gi|121637662|ref|YP_977885.1| 312 SPVRQPGFSKQLINSIKWARDETGIIPTAGIAVGKTQYVNFMSIRNWGRDGEWTTNYSGIAVSKDNGQTWGVFPGTIRAS 391
                                    *******************************************************************************9 PP

                        DUF4185 150 sd........tagnenfqqvafvk.ddgyvYvfgtpngRsgaayLarvpeadildlsayeywkgggeaWvkaeeaaatpv 220
                                    +         + gnenfq++a++k +dgy+Y fgtp gR+g+ayLarvp++ ++dl++y+yw+g++++Wv+++++aatpv
  gi|121637662|ref|YP_977885.1| 392 GPdsggkarfVPGNENFQMGAYLKsNDGYLYSFGTPPGRGGSAYLARVPQRFVPDLTKYQYWNGDSNSWVPNKPDAATPV 471
                                    99********9************99*************************************999888************ PP

                        DUF4185 221 lagpvgElSvqyneklgkwvllyldeeknsivlrtadspegpwsepktlvssaqvpg.lYgpyihPwstlksktgkdlyf 299
                                    ++gpvgE+Svqyn++l+++++ly++   n++v rta++p+gpws++++lvss q+pg +Y+p++hPw    s tgkd+yf
  gi|121637662|ref|YP_977885.1| 472 IPGPVGEMSVQYNTYLKQYLALYTNGM-NDVVARTAPAPQGPWSAEQMLVSSWQMPGgIYAPMMHPW----S-TGKDVYF 545
                                    *************************87.***************************************....6.8999*** PP

                        DUF4185 300 llSqWntYnvmlmr 313
                                     lS W+ Ynvmlm+
  gi|121637662|ref|YP_977885.1| 546 SLSLWSAYNVMLMH 559
                                    *************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3752.22
//
Query:       gi|121637663|ref|YP_977886.1|  [L=514]
Description: phospholipase C 4 plcD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.9e-129  430.1   0.0   8.2e-129  429.8   0.0    1.0  1  Phosphoesterase  Phosphoesterase family


Domain annotation for each model (and alignments):
>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.8   0.0  4.6e-133  8.2e-129       1     356 []      50     429 ..      50     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 429.8 bits;  conditional E-value: 4.6e-133
                Phosphoesterase   1 ikhvViivqENrsfdhlfGtlkgvrgiddasplaqqdG..vkkqalnkaevsapfsldtakg.lsaqvvvedpehsfqai 77 
                                    i+h+V  +qENrsfdh+fGtl+g++g++++spl+qq+G  +++qal+ + v++p+++dt++g + ++++v+dp+hs+ a+
  gi|121637663|ref|YP_977886.1|  50 IEHFVFFMQENRSFDHYFGTLSGTDGFNTVSPLFQQKGwnPMTQALDATGVTMPYRFDTTRGpFLDGACVNDPDHSWVAM 129
                                    89*************************************************************99*************** PP

                Phosphoesterase  78 qeqwnggrndkfvaaaese.......lvmgyfkredipvlwelaqeftlcDryFssvlggtepNrlflisgtsdpsGteg 150
                                    +e+wngg nd++++a++++       +vmgy++r+dip+++ la++ft+cDryF+svlg+t pNrl+++s+t+dp+G++g
  gi|121637663|ref|YP_977886.1| 130 HESWNGGVNDNWLPAQAKTrsaahtpTVMGYYTRQDIPIHYLLADAFTVCDRYFCSVLGPTLPNRLYWLSATIDPDGQNG 209
                                    ***************999559*********************************************************** PP

                Phosphoesterase 151 gpsladpkktvlkgftqktigerLsekgvswaiYqealdnlakskvapfnyyvrklkklearrkalkqlglaakqlekfk 230
                                    gp+l++p+ ++++ f +++++++Ls++gvsw++Y +++     s+v ++   v+++k+++++r++l ++g+a++++++f+
  gi|121637663|ref|YP_977886.1| 210 GPELQSPTFQPVRRFGWRIMPQNLSDAGVSWKVYRNKT-LGPISSVLTYGSLVTSFKQSADPRSDLVRFGVAPSYPASFA 288
                                    *************************************9.33334444899****************************** PP

                Phosphoesterase 231 kdvkngkLPqvsfikpngandeHpgadvaagdklikevlealtsspq.waktllivtyDEngGfyDhVappvapvsdpdg 309
                                    +dv +++LP+vs+++pn+ ++eHp+++ aag+ +i+++l+ l ++p+ w+kt+liv+yDEngGf+DhV+p++ap+ +p++
  gi|121637663|ref|YP_977886.1| 289 ADVLANRLPRVSWVIPNVLESEHPAVPAAAGAFAIVNILRILLANPAvWEKTALIVSYDENGGFFDHVVPATAPAGTPGE 368
                                    ******************************************************************************** PP

                Phosphoesterase 310 l.........kGd.....pyglgvrvPllviSpyakkgtvdhelfdhtSvlrfiekrfglp 356
                                    +          G+     p+glg+rvP++viSpy+++++++h++fdhtS+lr++e+rfg+p
  gi|121637663|ref|YP_977886.1| 369 YvtvpdidqvPGSggirgPIGLGFRVPCFVISPYSRGPQMVHDTFDHTSQLRLLETRFGVP 429
                                    *99999998844466899*****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.22s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3531.15
//
Query:       gi|121637664|ref|YP_977887.1|  [L=394]
Description: hypothetical protein BCG_1795c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-25   87.7   0.0    9.2e-25   87.1   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    8.2e-22   78.1   0.1    1.5e-21   77.2   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.6e-09   36.1   0.2    1.4e-08   35.0   0.2    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.2e-05   25.4   1.7    1.5e-05   25.1   0.2    1.9  3  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.017   15.2   0.0       0.45   10.6   0.0    2.2  2  DUF3880          DUF based on E. rectale Gene description (DU


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   2.6e-28   9.2e-25      13     165 ..     210     357 ..     202     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 2.6e-28
                                    TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHHHH CS
                Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleellk 91 
                                     ++ +++  grl+ eK  d+ i+a+a l+++   +++lviaG+g+ +++l+++a  l +     f+g++s r+++  ll 
  gi|121637664|ref|YP_977887.1| 210 PTQILLVHCGRLSVEKHADRSIDALAALCDA-GVDARLVIAGEGPLRARLERKATGLPI----DFTGFISdRHAVAGLLA 284
                                    567889999*********************9.********************9888887....***************** PP

                                    CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.HHHHHH CS
                Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede.elrerl 165
                                    +ad++++p   E fG+++lE++a+g+p+++s ++ + e+++    G++ ++  +ea+a a+r +++ +  +r+r+
  gi|121637664|ref|YP_977887.1| 285 SADVALAPGPHETFGLAALESLACGTPAVVSRTSALTEIITADS-GACADNR-PEAIAHAVRTIVSRPeRHRRRC 357
                                    *****************************************999.9999988.**************95455555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.1   4.1e-25   1.5e-21       3     132 ..     214     347 ..     212     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 4.1e-25
                                    EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHTT-T.TEEEE---TH...HHHHHHH-SEE CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaagleerveftGfved...laellaaadvf 76 
                                     ++++Grl   +k +d  ++a+++l ++  d+rlvi+G+gp r ++le++a gl   + ftGf++d   +a lla+adv+
  gi|121637664|ref|YP_977887.1| 214 LLVHCGRL-SVEKHADRSIDALAALCDAgvDARLVIAGEGPlR-ARLERKATGLP--IDFTGFISDrhaVAGLLASADVA 289
                                    5899****.545**********999988666**********66.5***8888985..*******55567*********** PP

                                    EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLl 132
                                    +aP   e+fgl++lE++a+g+p V+++++++ e++  ++g +++ + pea+a a+ +++
  gi|121637664|ref|YP_977887.1| 290 LAPGphETFGLAALESLACGTPAVVSRTSALTEIItADSGACAD-NRPEAIAHAVRTIV 347
                                    *****9**********************9******989998887.45********9876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   3.8e-12   1.4e-08       2      91 ..     289     375 ..     288     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.8e-12
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlae 80 
                                    +L+p  +e++ l  +E +acG++a+++++++l e++t + ++ +++  +e +a ++r  ++ pe+ r  ++ ar+r  + 
  gi|121637664|ref|YP_977887.1| 289 ALAPGPHETFGLAALESLACGTPAVVSRTSALTEIITAD-SGACADnRPEAIAHAVRTIVSRPERHR--RRCARRR-AEI 364
                                    57777788999999***********************99.889999788888888888887777755..5677777.678 PP

                Glyco_trans_1_2  81 htydhraeqll 91 
                                    +t++++a+ +l
  gi|121637664|ref|YP_977887.1| 365 FTWQRAAASML 375
                                    9***9999887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   4.2e-09   1.5e-05      38     169 ..      64     192 ..      38     193 .. 0.78
   2 ?   -2.6   0.0       1.3   4.7e+03      14      45 ..     236     260 ..     231     315 .. 0.49
   3 ?   -2.8   0.0       1.5   5.3e+03      40      64 ..     343     367 ..     323     379 .. 0.50

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.2e-09
                 Glyco_transf_4  38 elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye.krllkarl 116
                                      vvr++ +   +++  +++  ++ ++r +l+  +pD + + +  +l   +++ r  +g+ +V   H   +        +
  gi|121637664|ref|YP_977887.1|  64 TGVVRITLPAKHIPYTGGYRAVMPGAVRTVLETLRPDTLEVSDRLTLRSLGRWGRE-HGVTTVMISHERLDrFAGQLLPR 142
                                    3466666666667777778888888999999999************9999999997.*************8533333455 PP

                 Glyco_transf_4 117 kplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                    + +++++    +r++ + d v++++ ++++e+ +  g  + + +++p GvDl+
  gi|121637664|ref|YP_977887.1| 143 RAAQKFADFANARTAANYDTVVCTTGFAREEFDR-IG--ATNTVTVPLGVDLK 192
                                    56666777777788********************.88..566*********96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                 Glyco_transf_4  14 aLarrGheVtvvtpgddgpleeevelvvrvpr 45 
                                    aL+++G++ ++v  g ++  ++        +r
  gi|121637664|ref|YP_977887.1| 236 ALCDAGVDARLVIAGEGPLRARL-------ER 260
                                    55666666665544433332222.......22 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.5
                 Glyco_transf_4  40 vvrvprvplpllkrllrslaflrrl 64 
                                    v+ ++++p ++++r+ r+ a ++ +
  gi|121637664|ref|YP_977887.1| 343 VRTIVSRPERHRRRCARRRAEIFTW 367
                                    4444444444444444433333333 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.45      15      64 ..     156     205 ..     150     216 .. 0.83
   2 ?    1.9   0.0     0.066   2.4e+02      13      40 ..     355     382 ..     351     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                        DUF3880  15 iandcnyiftfDkeqyeelkelGvknvyylPLAanverldpleaeaekee 64 
                                    +a ++++++ +     ee+ + G++n + +PL+++ + ++p ++ a+ ++
  gi|121637664|ref|YP_977887.1| 156 TAANYDTVVCTTGFAREEFDRIGATNTVTVPLGVDLKTFHPRRRCARVRQ 205
                                    5667888888888889************************9998776555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.066
                        DUF3880  13 ksiandcnyiftfDkeqyeelkelGvkn 40 
                                    +++a +   ift+++  ++ l+ lG+  
  gi|121637664|ref|YP_977887.1| 355 RRCARRRAEIFTWQRAAASMLATLGAMA 382
                                    667778889************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2818.14
//
Query:       gi|121637665|ref|YP_977888.1|  [L=379]
Description: sulfite oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-54  182.0   0.0    1.1e-53  181.3   0.0    1.3  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain
    1.7e-22   79.9   0.0    3.1e-22   79.1   0.0    1.5  1  Mo-co_dimer     Mo-co oxidoreductase dimerisation domain
    0.00038   21.2   0.0    0.00086   20.0   0.0    1.6  1  Big_7           Bacterial Ig domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.3   0.0   1.9e-57   1.1e-53       1     171 [.      59     235 ..      59     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.3 bits;  conditional E-value: 1.9e-57
                                    SS----.GCCC-EEEEESTCSSEEEEEHHHHHH.C-EEEEEEEEE-TTTTHHHHCHH.--SS-.---TTSEEEEEEEEEE CS
                 Oxidored_molyb   1 hgavpkvdpekwrlevdglvekplslslddLka.lpavevtatlqCagnrrkelnkk.kvkgl.qwgagavsnaeWtGvr 77 
                                    hg+vp++ p++wrl+v glv++pl+++++ L + ++++ v+atl+Cagnrr+el ++ +  g   w +ga+s+a+W Gvr
  gi|121637665|ref|YP_977888.1|  59 HGPVPDIAPQHWRLTVGGLVDNPLTVTYERLTTeFDQHCVVATLACAGNRRAELLRVrQIPGKePWAHGAISTAQWCGVR 138
                                    89***99*************************99*****************99986556666548*************** PP

                                    HHHHHHHTTB-ETT..EEEEEEEEE-T...CCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGS CS
                 Oxidored_molyb  78 lrdvLekagvkkpearhvvfegadeel...eeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgars 154
                                    l+d+L++a v+ +e  hv f++ d  +     ++yg+sipl+kal+ +vlLA++mn epLp+ hG P+R+vvpg++gars
  gi|121637665|ref|YP_977888.1| 139 LADILQAADVHIDEGLHVAFDAPDVAEearPIQPYGSSIPLSKALSPEVLLAWQMNSEPLPRAHGGPVRVVVPGFIGARS 218
                                    **********98999*******986666656789***********99********************************* PP

                                    BTTEEEEEEESS---SH CS
                 Oxidored_molyb 155 vKwlkrievsdeesegy 171
                                    vKw++ i+v++ +s++y
  gi|121637665|ref|YP_977888.1| 219 VKWVTAITVQPGASQNY 235
                                    **************998 PP

>> Mo-co_dimer  Mo-co oxidoreductase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   5.2e-26   3.1e-22       6     136 ..     263     377 ..     259     379 .] 0.91

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 5.2e-26
                                    S---EEEE-SS-SEEEE-S....EEEEEEEEEE-STT--EEEEEEESSTTSS-EE-EEESSSSS---..SSTTS-TTS-E CS
                    Mo-co_dimer   6 dlnvnsvicspeheekvklkeaeetytikGyaysGgGrritrvevsldkGksWklaeieyeedkereakeesretafcwv 85 
                                     l +n+ i  p++ + v  ++    +ti+Gy+ +G Gr ++rv+vs+d+G +W+ a+++ + +             ++w 
  gi|121637665|ref|YP_977888.1| 263 SLALNCDILDPTDGDDVPAGA----LTIRGYGMAGDGRSVERVDVSVDDGLTWQQADLHAAPS------------QWSWR 326
                                    678899999999999999965....*********************************99833............5**** PP

                                    EEEEEEEESS...E.EEEEEEEETT--B--S..HHH--TT-------EEEEEE CS
                    Mo-co_dimer  86 fweldvevselakekeilvravDealnvqPe..emiwnvlgmlnnawfrvkik 136
                                     w+l+v+v+       i++ra+D++ ++qPe   ++wn +g  nnaw rv+++
  gi|121637665|ref|YP_977888.1| 327 PWSLTVDVEPG--PLGITARAWDDTGALQPEsaVSLWNPRGYGNNAWARVALR 377
                                    *********95..788***************77789**************986 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.4e-07   0.00086       5      58 ..     270     327 ..     267     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                                    EEE--TT--EBTSEEEEE..EEEE-SS-EEEEEEEETTEE...EEEE-SSSEEEEEE- CS
                          Big_7   5 itsPangatvsggtvtis..asAsddggvskVefyvdgtl.g.lgtdtsapysltwtt 58 
                                    i  P++g+ v++g +ti+  + A d  +v++V+++vd+ l +  +   +ap +++w +
  gi|121637665|ref|YP_977888.1| 270 ILDPTDGDDVPAGALTIRgyGMAGDGRSVERVDVSVDDGLtWqQADLHAAPSQWSWRP 327
                                    889**************944568888**************886444456888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2720.78
//
Query:       gi|121637666|ref|YP_977889.1|  [L=945]
Description: transmembrane transport protein mmpL14 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.8e-177  588.2  39.2    6.6e-94  314.5  17.0    2.5  2  MMPL         MMPL family
     0.0067   16.9   0.0        4.4    7.9   0.0    3.2  3  NPV_P10      Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.062   11.5   0.0      0.087   11.0   0.0    1.1  1  Myosin_head  Myosin head (motor domain)
        1.8    8.9   7.3         15    5.9   7.3    2.8  1  DUF5464      Family of unknown function (DUF5464)


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.5  17.0   1.5e-97   6.6e-94       2     333 .]      44     376 ..      43     376 .. 0.99
   2 !  279.1  14.2   8.9e-87     4e-83       3     332 ..     597     942 ..     595     943 .. 0.97

  Alignments for each domain:
  == domain 1  score: 314.5 bits;  conditional E-value: 1.5e-97
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    +spa++++++a++r +aaf++ a +d+i ++vl e++  l++ +++a++d+lv +l++d++hv ev+d++++p +a+++ 
  gi|121637666|ref|YP_977889.1|  44 FSPAGTATSRAVERSAAAFSQ-APGDNIGYLVL-ERNGVLND-QDRAYYDALVVALRRDSRHVIEVVDWWGTPAIAEVAR 120
                                    689******************.***********.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    S+D++a++a +++ g+ g+++a es++a r++v++++p++gl+v vtGp+at+ d   a dr+++li+++t+vv+l++Ll
  gi|121637666|ref|YP_977889.1| 121 SDDHHAVTAALRFGGMVGTSQAGESITAARSIVTQLHPPDGLHVFVTGPGATIVDEFAAIDRQTQLITATTIVVLLILLL 200
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                    ivyrS ++a++pll+vvvsl++a ++v++l + +++++s f+lgl+v++++++Gt +a++L++Ry+e++++++  ++a++
  gi|121637666|ref|YP_977889.1| 201 IVYRSAITATVPLLSVVVSLAVAKPIVSVLVDRDFIGISLFSLGLSVAVVVGAGTGFAMFLIGRYHERRRQHIAPAAALA 280
                                    ******************************************************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlg...LvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.lakprrkrkkr 317
                                    +a++++++++++a+++v++++ +   L++ar++++a++G+ +++Gvl + l++lTl+PAl++l++ra+ l++p++kr +r
  gi|121637666|ref|YP_977889.1| 281 DAYRGVAPAIAGATFIVVTSLGAvgwLSLARIGMFATTGILCSIGVLAVGLAALTLTPALVALASRANlLKPPQHKRIQR 360
                                    *********************99999******************************************999********* PP

                           MMPL 318 wWrrlgrlvvrrPlpv 333
                                     +rrlg++v+r+P+p+
  gi|121637666|ref|YP_977889.1| 361 QFRRLGTHVARWPAPI 376
                                    *************985 PP

  == domain 2  score: 279.1 bits;  conditional E-value: 8.9e-87
                           MMPL   3 spadaesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf........... 70 
                                    + ++a+++ ++ r  a++ + +++++ +  ++++ g++ ++ ++++a+v+el++++   ++ ++e+ d+           
  gi|121637666|ref|YP_977889.1| 597 CAKLADAAGQLARGIADVASaTSGVSGLPNALDGIGGQLAQVRESAAGVQELLNNV--GAAPLRELPDYlrelaavsqsa 674
                                    568899999999999999999999********************************..8999*******89988888888 PP

                           MMPL  71 ...........lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaat 133
                                               l+dp+   v ++fvS++g+a+r+lv+ +g+++ ++++++++ai +av+e +   +l++++ve+tG++++
  gi|121637666|ref|YP_977889.1| 675 pgvdlyaarriLTDPNmraVLDYFVSPNGHATRLLVYGDGSEWGDDGAQRARAIVTAVAEETdegTLRPTAVELTGVGPA 754
                                    88888888888889999999**************************************999999**************** PP

                           MMPL 134 ladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlli 212
                                    ++dl+d++ +dl+l+ v+tl+vi++i ++++rS++a l++++t+++s+++alg  v+i++++lg +l+++vl++++vlli
  gi|121637666|ref|YP_977889.1| 755 TRDLQDLVGSDLTLLAVITLAVIFAIAALLLRSPLAGLVVVGTIATSYICALGAsVVIWKHILGDNLHWSVLPIAFVLLI 834
                                    ******************************************************************************** PP

                           MMPL 213 avGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                    +vG++Y+ll+  R+ree+ ag+++  +vira+a tg+vvtaaG+++ ++m++L++++  ++aq+Gv++++G+l+d+l+++
  gi|121637666|ref|YP_977889.1| 835 SVGSAYNLLFALRIREESPAGPRT--SVIRAFAATGMVVTAAGIVFGTTMFALAASTSLSVAQIGVTVGMGLLLDALVIR 912
                                    ************************..****************************************************** PP

                           MMPL 293 Tll.PAllvllGraalakprrkrkkrwWrrlgrlvvrrPlp 332
                                     ++ PAl+vllGr+            wW+r+++ ++++P+p
  gi|121637666|ref|YP_977889.1| 913 GFVlPALMVLLGRW-----------LWWPRRSVSNRQVPEP 942
                                    **************...........**************97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        71      31      65 ..     488     519 ..     473     525 .. 0.62
   2 ?    0.2   0.0      0.24   1.1e+03      15      45 ..     535     565 ..     526     576 .. 0.80
   3 !    7.9   0.0   0.00097       4.4      23      67 ..     607     654 ..     592     664 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                        NPV_P10  31 qenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                     ++   ++e +++L + +a+ ++le++v ++ + L
  gi|121637666|ref|YP_977889.1| 488 GDQ---LDEFSDQLTSRQATFTNLEAAVRDVVSAL 519
                                    333...34456777777777777777777766655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                        NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLd 45 
                                    +v+  V  +qq+++++q    dv ++ + L 
  gi|121637666|ref|YP_977889.1| 535 QVSLAVRLMQQAITKLQGSAGDVFDIFDPLR 565
                                    5677789999*****9999999988877665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00097
                        NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn...p 67 
                                    l   ++dv++    v+ l + Ld++  qLa++ ++   +q++Ln   +
  gi|121637666|ref|YP_977889.1| 607 LARGIADVASATSGVSGLPNALDGIGGQLAQVRESAAGVQELLNnvgA 654
                                    6677899999**********************************4431 PP

>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.9e-05     0.087     256     315 ..     447     506 ..     441     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHHHHCTSSEEEECTTSSEEESSHHHHHHHHHHHTS-HHHHHHHHHSEEEEET CS
                    Myosin_head 256 eifrivaailhlGniefkkeakdeqavledeeklekaaellgvdaeelekalvkrriktg 315
                                     i ri+aai+ +G +++ ++a++ +++++++++l++ a  lg +  e++  l++r+ +  
  gi|121637666|ref|YP_977889.1| 447 AIERITAAIMAIGGVRMVQSASHPNGMVSKQAALTASAGNLGDQLDEFSDQLTSRQATFT 506
                                    6889**************************************************997655 PP

>> DUF5464  Family of unknown function (DUF5464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.3    0.0034        15      11      51 .]     773     813 ..     762     813 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0034
                        DUF5464  11 alaailtlayilavyPqvalvvvGaCylaavCaCvWsivnW 51 
                                    +la i+++a +l   P   lvvvG+   + +Ca   s+v W
  gi|121637666|ref|YP_977889.1| 773 TLAVIFAIAALLLRSPLAGLVVVGTIATSYICALGASVVIW 813
                                    46667777777777899*****************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (945 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 5876.16
//
Query:       gi|121637667|ref|YP_977890.1|  [L=218]
Description: cutinase cut1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-48  165.6   0.1    1.2e-48  165.4   0.1    1.0  1  Cutinase       Cutinase
  ------ inclusion threshold ------
      0.022   14.6   0.2      0.034   14.0   0.2    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.024   14.5   0.1      0.038   13.8   0.1    1.3  1  Abhydrolase_2  Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.1     2e-52   1.2e-48       1     177 [.      28     216 ..      28     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 2e-52
                                    ---SEEEEEE--TT--TTTSSHHHHHHHHHHHH.TTT-EEEEE------CGGSTTSS-HHHHHHHHHHHHHHHHH-TT-E CS
                       Cutinase   1 sckdvevifArgttepgglgsvGeavvsalesavgsksvavqgvnYpAdleqlyegseeagakeaaalvqslaskCPdtk 80 
                                    +c+dvev+fArgt+ep+g+g +Ge + +al+s++g+ks++v+gv+YpA+++     ++ ag+ +a ++v+++a++CP++k
  gi|121637667|ref|YP_977890.1|  28 ACPDVEVVFARGTGEPPGVGGIGEDFIDALRSKIGEKSMGVYGVDYPATTDF---PTAMAGIYDAGTHVEQTAANCPQSK 104
                                    6*************************************************96...7999********************* PP

                                    EEEEEETHHHHHHHHHHTT.............S-HHHHHHEEEEEEES-TTC..CCCTT....S-TTS-GGGEEEE--TT CS
                       Cutinase  81 ivlgGYSqGaqvidnaiegga......tat..lpaavadkvaavvlfGdpsn..vaglp....evsklyaskikslCdag 146
                                    +vlgG+SqGa+v+  ++++++      +a   +p++vad+vaav lfG ps   +++++     + +lya+k+++lC++g
  gi|121637667|ref|YP_977890.1| 105 LVLGGFSQGAAVMGFVTAAAIpdgaplDAPrpMPPEVADHVAAVTLFGMPSVafMHSIGappiVIGPLYAEKTIQLCAPG 184
                                    ************98887776677777733368*******************97744444566699*************** PP

                                    -GGGTS----GGGG-GGGG..HHHHHHHHHHH CS
                       Cutinase 147 DpiCgsgneleaHlsYvsey.ttqaakFvvsk 177
                                    Dp+C sg +++aH +Y++++ ++qaa F++ +
  gi|121637667|ref|YP_977890.1| 185 DPVCSSGGNWAAHNGYADDGmVEQAAVFAAGR 216
                                    ********************99******9876 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   5.8e-06     0.034      31      97 ..      67     129 ..      55     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                    EEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT- CS
                  Abhydrolase_3  31 vvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardege 97 
                                     v+ vdY     + fP+a+  +++a  +++++  ++++ +s++vl+G S G+  +  v+ +a  +g 
  gi|121637667|ref|YP_977890.1|  67 GVYGVDYPA--TTDFPTAMAGIYDAGTHVEQT--AANCPQSKLVLGGFSQGAAVMGFVTAAAIPDGA 129
                                    577788864..678*****************9..689****************99999988877654 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.4e-06     0.038     100     118 ..      98     116 ..      82     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                    TT--GGGEEEEEETHHHHH CS
                  Abhydrolase_2 100 kgipssriiigGFSqGaal 118
                                    +  p+s+ ++gGFSqGaa+
  gi|121637667|ref|YP_977890.1|  98 ANCPQSKLVLGGFSQGAAV 116
                                    34899************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1486.60
//
Query:       gi|121637668|ref|YP_977891.1|  [L=802]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                       91  (0.00507558); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.10u 0.32s 00:00:01.42 Elapsed: 00:00:00.51
# Mc/sec: 4706.86
//
Query:       gi|121637669|ref|YP_977892.1|  [L=94]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-32  110.7  15.4    3.8e-32  110.5  15.4    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5  15.4   2.1e-36   3.8e-32       1      84 [.       1      84 [.       1      86 [. 0.99

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.1e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pe++aaaa+dla +gs+++ anaaaaa tt++laa+aDe+SaaiAalf+ah+++yqa+sa+aaafh +fvqal++
  gi|121637669|ref|YP_977892.1|  1 MSFVIAVPETIAAAATDLADLGSTIAGANAAAAANTTSLLAAGADEISAAIAALFGAHGRAYQAASAEAAAFHGRFVQALTT 82
                                   9********************************************************************************9 PP

                                   HH CS
                             PE 83 aa 84
                                   ++
  gi|121637669|ref|YP_977892.1| 83 GG 84
                                   87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 647.17
//
Query:       gi|121637670|ref|YP_977893.1|  [L=509]
Description: hypothetical protein BCG_1801 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-87  293.4   0.0    2.4e-87  293.0   0.0    1.1  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    2.1e-16   60.2   0.0    4.4e-16   59.1   0.0    1.5  1  DUF1298         Protein of unknown function (DUF1298)
  ------ inclusion threshold ------
       0.03   13.0   0.0      0.046   12.4   0.0    1.2  1  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.0   0.0   4.1e-91   2.4e-87       1     264 []      38     298 ..      38     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 293.0 bits;  conditional E-value: 4.1e-91
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    Ls+lDa+fl++e++++p++v+++  l++++++ g+ ++ r++ a+e++ ++ap++r+k+++++l+l++pvWv+d++f+++
  gi|121637670|ref|YP_977893.1|  38 LSGLDAFFLYMETPSQPLNVCCVLELDTSTMPGGY-TYGRFHAALEKYVKAAPEFRMKLADTELNLDHPVWVDDDNFQIR 116
                                    899**************************999999.9******************************************* PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEG.leggriAillkvHHAliDGvgglkllarlldldpdd 159
                                    +H+Rrva+paPG++rel+e+++++a  pLDr+rPlWe++viEG ++++++A++lkvHHA++DGv+g++ll++l++l+pd+
  gi|121637670|ref|YP_977893.1| 117 HHLRRVAMPAPGGRRELAEICGYIAGLPLDRDRPLWEMWVIEGgARSDTVAVMLKVHHAVVDGVAGANLLSHLCSLQPDA 196
                                    ******************************************989*********************************** PP

                 WES_acyltransf 160 pprpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrf 239
                                    p+++ ++ +  ++   +q++asg lvg++++  +++++v+++v +++r+l +a+e r++++pf+ap+tp+n pl+r R++
  gi|121637670|ref|YP_977893.1| 197 PAPQPVRGTGGGN--VLQIAASG-LVGFASRPVRLATVVPATVLTLVRTLLRAREGRTMAAPFSAPPTPFNGPLGRLRNI 273
                                    *****99988888..9****998.******************************************************** PP

                 WES_acyltransf 240 aaaslpLadvkavakalgvtiNDvv 264
                                    a+++l+++dvk+v++++gvtiNDvv
  gi|121637670|ref|YP_977893.1| 274 AYTQLDMRDVKRVKDRFGVTINDVV 298
                                    ************************7 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   7.4e-20   4.4e-16       3     101 ..     339     443 ..     338     455 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 7.4e-20
                        DUF1298   3 NqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl.......lsnttlviSN 75 
                                    Nq +++++ +p +++dP++r+r++ + ++++K   +a+ ++ll ++ +++ ++ ++ a+++ l       ++  +l++SN
  gi|121637670|ref|YP_977893.1| 339 NQATWMFCRVPSQISDPAQRIRTIAAGNTVAKDHAAAIGPTLLHDW-IQFGGSTMFGAAMRILphisithSPAYNLILSN 417
                                    999*******************************************.************98889999999********** PP

                        DUF1298  76 vpGPqeelylaGaplkaiypvvpglp 101
                                    vpGPq +ly++G ++++++p+ p l+
  gi|121637670|ref|YP_977893.1| 418 VPGPQAQLYFLGCRMDSMFPLGPSLA 443
                                    *********************99876 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.6e-06     0.046      41     147 ..      74     182 ..      52     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-06
                                    HHHHHHHHHHHHHH-SSCCEEEEE....TTEEEEEE-TT-----EEEE-T..TSSSHHHH..HHHHHHHHHTC--SCCCS CS
                   Condensation  41 lerlekalqelierhdaLRtvflee..engepvQvileerevelevleisdleeseeeea..ieefaqkdlqepfdLekg 116
                                      r++ al++ ++  + +R+ +     + ++pv v  +++++++   +++++++ +      + e+    +  ++ L+++
  gi|121637670|ref|YP_977893.1|  74 YGRFHAALEKYVKAAPEFRMKLADTelNLDHPVWV--DDDNFQI-RHHLRRVAMPAPGGRreLAEICG--YIAGLPLDRD 148
                                    56899999999999999999997642233444433..5555555.33444444444322222555555..7889*****9 PP

                                    .-SEEEEEEESSTTE..EEEEEEEECCT--TTTH CS
                   Condensation 117 .pLfraalfkiaenr..lllllsvHHiivDGvSl 147
                                     pL+ + +++  +++  + ++l+vHH +vDGv  
  gi|121637670|ref|YP_977893.1| 149 rPLWEMWVIEGGARSdtVAVMLKVHHAVVDGVAG 182
                                    9********9766551166799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3554.16
//
Query:       gi|121637671|ref|YP_977894.1|  [L=127]
Description: hypothetical protein BCG_1802c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-72  239.0   2.1    8.8e-72  238.8   2.1    1.0  1  DUF5073         Domain of unknown function (DUF5073)
     0.0099   16.4   0.0      0.014   15.9   0.0    1.2  1  Pro_dh-DNA_bdg  DNA-binding domain of Proline dehydrogenase


Domain annotation for each model (and alignments):
>> DUF5073  Domain of unknown function (DUF5073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.8   2.1   9.9e-76   8.8e-72       1     121 []       1     121 [.       1     121 [. 0.99

  Alignments for each domain:
  == domain 1  score: 238.8 bits;  conditional E-value: 9.9e-76
                                    --S---HHHHHHHHHHHHSHHHHHHHHHHHHS-SSS---SSSSS--S--SS--S----SSHHHHHGGGSSSTTTTHHHHH CS
                        DUF5073   1 mtafdservsdavaaalagpggvalvvkvfagvpgvvhtparrgllrseperiqigdwryevtsdgrlsaahlvngivia 80 
                                    m++fd+ervs+avaaal+gpggvalvvkvfag+pgv+htparrg++rs+periqigdwryev++dgrl+aah+vngivia
  gi|121637671|ref|YP_977894.1|   1 MSDFDTERVSRAVAAALVGPGGVALVVKVFAGLPGVIHTPARRGFFRSNPERIQIGDWRYEVAHDGRLLAAHMVNGIVIA 80 
                                    99****************************************************************************** PP

                                    HSHHHHTT-TTHHHHTHHHHHHHH--STTHHHHHHHHHHT- CS
                        DUF5073  81 edvlaaeevgphiaralgqivsrygatvlpnidaalevlet 121
                                    ed+l+ae+vgph+aralgqivsrygatv+pni+aa+evl+t
  gi|121637671|ref|YP_977894.1|  81 EDALIAEAVGPHLARALGQIVSRYGATVIPNINAAIEVLGT 121
                                    **************************************986 PP

>> Pro_dh-DNA_bdg  DNA-binding domain of Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.6e-06     0.014      41     110 ..      51     121 ..      37     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                                    HTTTTS-HHHHHHHHHHCTT-GGG----------...-SS----HHHHHHHHHH-HHHHHHHHHHHHHHHHH CS
                 Pro_dh-DNA_bdg  41 dklakgdwkehlgksesllvnaatwgLlltgkll..eekeeeleealkklvkrlgepvirkaveqamkllge 110
                                    ++++ gdw+ +++++  ll+     g+++++  l  e+   +l++al ++v+r g++vi   +++a+++lg+
  gi|121637671|ref|YP_977894.1|  51 ERIQIGDWRYEVAHDGRLLAAHMVNGIVIAEDALiaEAVGPHLARALGQIVSRYGATVIP-NINAAIEVLGT 121
                                    68999*************************99888888999***************9996.58999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 831.25
//
Query:       gi|121637672|ref|YP_977895.1|  [L=262]
Description: hypothetical protein BCG_1803c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-20   73.7   2.4    2.6e-09   37.6   0.1    2.2  2  YbjQ_1    Putative heavy-metal-binding
  ------ inclusion threshold ------
       0.11   12.2   0.0        1.5    8.7   0.0    2.3  2  GPHH      Voltage-dependent L-type calcium channel, IQ-associ


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   2.9e-13   2.6e-09      46     103 ..      64     122 ..      43     123 .. 0.93
   2 !   36.2   0.2   8.3e-13   7.4e-09      21     103 ..     161     244 ..     156     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.9e-13
                         YbjQ_1  46 elkayeeeleeareeAlerlkeeAeelGAnAvvgvrldtseige.kgmlevlayGTAVk 103
                                    el+ ++e+ ++ar +A++r+++eA +l A+ +vgvrl+ ++ ge ++ le +a+GTAV+
  gi|121637672|ref|YP_977895.1|  64 ELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEgGEHLEFMAVGTAVR 122
                                    56778999**********************************9999************7 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 8.3e-13
                         YbjQ_1  21 vtgetvrsrnvlkdilaglrslvG.GelkayeeeleeareeAlerlkeeAeelGAnAvvgvrldtseige.kgmlevlay 98 
                                    v+g++v     ++ ++++lr++    e+ ++++  ++are A++r+++eAe+ GA  vvgv++  s+ +    ++e    
  gi|121637672|ref|YP_977895.1| 161 VMGNCVFHIA-VQGFMQTLRQIGRnMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWgVHTVEFYTA 239
                                    6666666543.5678888888854368999**************************************776799999*** PP

                         YbjQ_1  99 GTAVk 103
                                    GTAV+
  gi|121637672|ref|YP_977895.1| 240 GTAVR 244
                                    ***96 PP

>> GPHH  Voltage-dependent L-type calcium channel, IQ-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.051   4.6e+02       8      20 ..       5      17 ..       4      19 .. 0.86
   2 ?    8.7   0.0   0.00017       1.5      16      46 ..     141     172 ..     137     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.051
                           GPHH  8 eyDPeAtgrikvq 20
                                     DP A++r +++
  gi|121637672|ref|YP_977895.1|  5 SLDPVASERLSHA 17
                                   67********996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00017
                           GPHH  16 rikvqdmyellrrlspPLGfGk.kcPsrvayk 46 
                                    + + qdm++llr+ ++P+ f   +c + +a +
  gi|121637672|ref|YP_977895.1| 141 HLSGQDMVTLLRSGFAPVAFVMgNCVFHIAVQ 172
                                    56789*************99556888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 1429.71
//
Query:       gi|121637673|ref|YP_977896.1|  [L=155]
Description: hypothetical protein BCG_1804c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.091   11.5   0.0       0.11   11.3   0.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        0.1   12.2   4.5       0.19   11.4   4.5    1.4  1  DUF4131          Domain of unknown function (DUF4131)
        0.2    9.6   0.0       0.24    9.3   0.0    1.0  1  Prominin         Prominin
       0.29   11.2   5.3       0.22   11.5   2.7    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.11     341     434 ..      50     140 ..      29     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                        DUF2207 341 kyakkskk.kakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllil 419
                                     +a+k ++ +++++ + ++++ +a +k  ++ ++k+  +++  ++ + l++++l++ +i + +       ++l  ++l++
  gi|121637673|ref|YP_977896.1|  50 ADATKRRAnLQRTIDARIDDLIDAADK--SHALRKAAMSYRGNWRDIVLLVCVLLFTIIWWNVNHGR--ANWLPTFVLLI 125
                                    344443333666777777777777777..99999999999999999999999999998877755443..44444444444 PP

                        DUF2207 420 lliaiivlllfsrll 434
                                    ll+a+ +++ +++ l
  gi|121637673|ref|YP_977896.1| 126 LLAAVTAVYALRGAL 140
                                    444444444444444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.5   4.2e-05      0.19      10      59 ..      94     146 ..      89     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.2e-05
                        DUF4131  10 lalllllllllllllrr...rprrrvllllllllllallgfalrapqpnandl 59 
                                    ++ll+++ll+ +++++    r ++   ++ll+ll+++++++alr + ++a++l
  gi|121637673|ref|YP_977896.1|  94 IVLLVCVLLFTIIWWNVnhgRANWLPTFVLLILLAAVTAVYALRGALRAATSL 146
                                    44555555555555555599999999999999999999999999988887765 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   5.3e-05      0.24     368     433 ..      45     109 ..      33     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.3e-05
                       Prominin 368 lakgreqikklakkiprealdavisdlenterssktfddvvekyekyrwliglivcsllllivvil 433
                                    l++ ++   k   ++ ++++da i+dl +  ++s++  +    y  +++ i+l+vc+ll+ i+  +
  gi|121637673|ref|YP_977896.1|  45 LDRLPADATKRRANL-QRTIDARIDDLIDAADKSHALRKAAMSYRGNWRDIVLLVCVLLFTIIWWN 109
                                    566666666777788.99*******************************************99766 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.26   1.2e+03      71      81 ..      16      26 ..       5      45 .. 0.66
   2 ?   11.5   2.7     5e-05      0.22      49      92 ..      96     143 ..      74     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.26
                Phage_holin_3_6 71 ivaavllvlag 81
                                   i ++++l++a+
  gi|121637673|ref|YP_977896.1| 16 IFGGAMLAIAA 26
                                   44444444443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5e-05
                Phage_holin_3_6  49 lalllllvalalalaa.....lwlaalivaavllvlagvlalvglkklk 92 
                                    l + +ll++++++  +      wl ++++ ++l+++++v al+g  +++
  gi|121637673|ref|YP_977896.1|  96 LLVCVLLFTIIWWN-VnhgraNWLPTFVLLILLAAVTAVYALRGALRAA 143
                                    34455555555555.2356778999888888888888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1101.11
//
Query:       gi|121637674|ref|YP_977897.1|  [L=50]
Description: hypothetical protein BCG_1805c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 365.26
//
Query:       gi|121637675|ref|YP_977898.1|  [L=479]
Description: hypothetical protein BCG_1806c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-48  165.4   4.8    3.6e-48  164.6   4.8    1.4  1  DUF222    Domain of unknown function (DUF222)
    1.5e-11   43.9   1.4    1.5e-11   43.9   1.4    2.6  2  HTH_IclR  IclR helix-turn-helix domain
      2e-07   31.1   1.9    3.7e-07   30.2   1.9    1.4  1  HNH       HNH endonuclease
    1.9e-05   24.4   3.2    4.4e-05   23.3   1.0    2.7  2  MarR_2    MarR family
    0.00036   20.4   0.0    0.00062   19.6   0.0    1.4  1  IclR      Bacterial transcriptional regulator
  ------ inclusion threshold ------
      0.027   14.6   2.1       0.18   12.0   1.8    2.4  2  HNH_2     HNH endonuclease
      0.027   14.1   0.1      0.067   12.8   0.1    1.6  1  RP-C      Replication protein C N-terminal domain
      0.038   13.7   0.0      0.075   12.8   0.0    1.4  1  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.062   13.2   0.1       0.35   10.8   0.1    2.2  2  HTH_5     Bacterial regulatory protein, arsR family
      0.081   13.0   1.6       0.17   11.9   0.3    2.4  2  HTH_20    Helix-turn-helix domain
        1.2    9.9   4.0        1.6    9.4   0.0    2.8  3  zf-ISL3   zinc-finger of transposase IS204/IS1001/IS1096/IS11


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   4.8   2.2e-51   3.6e-48      71     301 .]     151     367 ..      99     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 2.2e-51
                         DUF222  71 avaaalraGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrr 150
                                    + a a  +G+++l+qv vIa r+ + +da++++ +  a++++lr+a kl+p++            +p++   d ++++r+
  gi|121637675|ref|YP_977898.1| 151 KAALAALEGRLSLDQVGVIAGRAGEGSDAHYAQLAGVATVNQLRTALKLEPRP------------EPEP---DFRPEPRP 215
                                    44567779********************************************9............8888...799***** PP

                         DUF222 151 eltltkdedGmsrisgeldaeaaaaldavLdslaapvcap........dgtkDpRspaqrraDALlallrlalaagaldc 222
                                    ++t ++ ++++s+++++l++++aa++da+L+s+ ++++a+        dg++D+R+p + + +A+l+l++++++a+ +++
  gi|121637675|ref|YP_977898.1| 216 SITRSA-DEQFSCWRIKLPHVEAAKFDAALQSHLDALIAEykrdhdnsDGVSDQRPPLPGNVEAFLRLVEAGWDAEVARR 294
                                    ******.9************************************************************************ PP

                         DUF222 223 hagvpatvvvhvtaeeltaaaggaaltgggglLpasdvrrLAkdAtlaifdepagrpldlgrtkrtasaalrralraRD 301
                                    ++g+++tvv+h++++e+ a  ++      g+lL++s++r+L++dAt++ ++e++g+ +++grt+r+++++lrral++RD
  gi|121637675|ref|YP_977898.1| 295 PHGQHTTVVMHLDVQERAAGLHL------GPLLSESERRYLLCDATFEAWFERDGQVIGCGRTTRQINRRLRRALEHRD 367
                                    ***********************......9************************************************9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   1.4     9e-15   1.5e-11       2      51 ..      19      68 ..      18      69 .. 0.96
   2 ?   -0.2   0.2      0.56   9.1e+02      15      35 ..     431     451 ..     429     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 9e-15
                                   HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                   l Ra+a Ld +a++p+ l+l +l++r+gl+kSt++RlL  Lve G+v  d
  gi|121637675|ref|YP_977898.1| 19 LRRAVAALDEIAAEPGHLRLVDLCERLGLAKSTTRRLLVGLVEVGLVSVD 68
                                   78*********************************************866 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.56
                                    TBSS-BHHHHHHHHTS-HHHH CS
                       HTH_IclR  15 apqeltlselArrtglpkStv 35 
                                    a+++l+   lAr++  p+++v
  gi|121637675|ref|YP_977898.1| 431 AGRPLSAGSLARASTKPPPAV 451
                                    78999*********9999987 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.9   2.3e-10   3.7e-07       4      46 ..     375     413 ..     370     414 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.3e-10
                            HNH   4 CgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                    Cg +      l+ +Hi ++ +gga+++ Nl+l+C+  H+++h+
  gi|121637675|ref|YP_977898.1| 375 CGAT----RGLHAHHIRHWQDGGATELANLVLVCPYHHRAHHR 413
                                    6666....5799***************************9997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.0   2.7e-08   4.4e-05       8      52 ..      23      66 ..      17      74 .. 0.90
   2 ?   -1.7   0.0       1.7   2.7e+03      14      31 ..     427     444 ..     425     451 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.7e-08
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                     +L +++++pg  l+  +l++rlgl ks++ r+l  Lv+ GLv 
  gi|121637675|ref|YP_977898.1| 23 VAALDEIAAEPGH-LRLVDLCERLGLAKSTTRRLLVGLVEVGLVS 66
                                   5689********8.9****************************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                    HHCTTTSEEEHHHHHHHH CS
                         MarR_2  14 Lgrrpgrdltvgelarrl 31 
                                    ++++ gr+l++g lar+ 
  gi|121637675|ref|YP_977898.1| 427 VADSAGRPLSAGSLARAS 444
                                    577888899*****9976 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.8e-07   0.00062       2      29 ..     131     158 ..     130     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
                                    SEEETTSTT-EEEGGGSHHHHHHHHTS- CS
                           IclR   2 rlravsaiGtrlplyataiGKalLaald 29 
                                    rlravsa+G r+pl+ ta+GKa Laal+
  gi|121637675|ref|YP_977898.1| 131 RLRAVSAVGLRFPLNGTANGKAALAALE 158
                                    789**********************995 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9   6.4e+03      11      19 ..      84      92 ..      68     115 .. 0.80
   2 ?   12.0   1.8   0.00011      0.18       1      71 [.     370     418 ..     370     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                          HNH_2 11 lleaAHIiP 19
                                   +++ AHI  
  gi|121637675|ref|YP_977898.1| 84 SVTGAHIAA 92
                                   788999965 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                          HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfaf 71 
                                    Cv+ g+ + + l+a+HI            +++ +                +N+ l +p +H++++++l+++
  gi|121637675|ref|YP_977898.1| 370 CVVPGCGATRGLHAHHIRH----------WQDGG------------ATELANLVLVCPYHHRAHHRGLITI 418
                                    8896766666899999999..........55555............789********************98 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.1e-05     0.067      76     103 ..      40      67 ..      38      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                           RP-C  76 qLsralglsestlrrhlaaLveaGliir 103
                                    +L+++lgl++st rr+l  Lve+Gl+  
  gi|121637675|ref|YP_977898.1|  40 DLCERLGLAKSTTRRLLVGLVEVGLVSV 67 
                                    5899*********************975 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05     0.075      11      44 ..      32      65 ..      24      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                       HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                   + g+l++ +l+e+lg ++ T RR L  L+e gl+
  gi|121637675|ref|YP_977898.1| 32 EPGHLRLVDLCERLGLAKSTTRRLLVGLVEVGLV 65
                                   569***********************99999985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00021      0.35      19      46 ..      39      66 ..      29      67 .. 0.90
   2 ?   -1.6   0.0       1.6   2.6e+03      14      32 ..     433     451 ..     431     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 19 celaeelglsqstvShHLkkLreaGLVe 46
                                    +l+e lgl +st+++ L  L e GLV+
  gi|121637675|ref|YP_977898.1| 39 VDLCERLGLAKSTTRRLLVGLVEVGLVS 66
                                   59*************************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                    SSEEHHHHHHHHTS-HHHH CS
                          HTH_5  14 gelcvcelaeelglsqstv 32 
                                    ++l+++ la++  +++++v
  gi|121637675|ref|YP_977898.1| 433 RPLSAGSLARASTKPPPAV 451
                                    7999*******99999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00011      0.17      29      61 .]      40      72 ..      23      72 .. 0.92
   2 ?   -3.8   0.0         9   1.5e+04      22      32 ..     432     442 ..     430     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   HHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvregr 61
                                   +l+erl+l+k+t ++ L  L+e+gLv v  +gr
  gi|121637675|ref|YP_977898.1| 40 DLCERLGLAKSTTRRLLVGLVEVGLVSVDSHGR 72
                                   79**************************99886 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9
                                    CTTB-HHHHHH CS
                         HTH_20  22 aegltaselae 32 
                                    +++l+a+ la+
  gi|121637675|ref|YP_977898.1| 432 GRPLSAGSLAR 442
                                    68999999998 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00099       1.6      12      37 ..     292     317 ..     288     318 .. 0.88
   2 ?   -1.5   0.0       2.6   4.3e+03       7      18 ..     347     358 ..     346     364 .. 0.79
   3 ?   -0.3   0.7       1.1   1.8e+03       6      25 ..     373     391 ..     368     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00099
                        zf-ISL3  12 tvvkhgkkerrvrhlpiggkrvyLrl 37 
                                     ++ hg++++ v+hl+++++ + L+l
  gi|121637675|ref|YP_977898.1| 292 ARRPHGQHTTVVMHLDVQERAAGLHL 317
                                    6689****************999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                        zf-ISL3   7 nCgsktvvkhgk 18 
                                    +Cg++t++++ +
  gi|121637675|ref|YP_977898.1| 347 GCGRTTRQINRR 358
                                    6****9998854 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                        zf-ISL3   6 PnCgsk.tvvkhgkkerrvrh 25 
                                    P+Cg++  ++ h    r +++
  gi|121637675|ref|YP_977898.1| 373 PGCGATrGLHAHH--IRHWQD 391
                                    89***95556554..888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3362.94
//
Query:       gi|121637676|ref|YP_977899.1|  [L=446]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-30  104.5   1.3    5.2e-30  104.0   1.3    1.3  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.33   11.1   0.0    1.6  1  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   1.3   5.8e-34   5.2e-30       1     138 [.      35     169 ..      35     170 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 5.8e-34
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    p+++v++ s++++++a+r+a+ +g++v v++gG+s++ + +++g+v+ld+sr+++  +id+++g+a+v++G  ++ l ++
  gi|121637676|ref|YP_977899.1|  35 PEVIVQAVSADDIVSAIRYATVNGHKVSVVSGGHSFAASHLRDGAVLLDVSRIDH-ASIDADKGRAVVGPGKGGSVLMAE 113
                                    789**********************************88888*************.9*********************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                    l+a+gl+++   g++  +++GG+++++++G++s++yG+ ++ v gl+v++adG  +++
  gi|121637676|ref|YP_977899.1| 114 LEAQGLFFP--GGHCRGVCLGGYLLQGGYGWNSRIYGPACESVIGLDVITADGAQIHC 169
                                    *********..9*****************************************99998 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.7e-05      0.33      23      41 ..     423     441 ..     405     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                                    HHHHHHHHHHH-TT--S-- CS
                            BBE  23 ferLvkvKtkyDPdNvFrn 41 
                                     ++L +v+++yDPd +F++
  gi|121637676|ref|YP_977899.1| 423 MAKLDRVRAEYDPDGLFNS 441
                                    689**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3349.31
//
Query:       gi|121637677|ref|YP_977900.1|  [L=272]
Description: hypothetical protein BCG_1808 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-66  223.3   0.0    3.4e-66  223.0   0.0    1.0  1  DAPG_hydrolase  DAPG hydrolase PhiG domain


Domain annotation for each model (and alignments):
>> DAPG_hydrolase  DAPG hydrolase PhiG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.0   1.9e-70   3.4e-66       5     225 .]      50     267 ..      47     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 1.9e-70
                 DAPG_hydrolase   5 ledlnrllepgylkvenGycllpdgtayvasrtkmpgvtaeMldWWfaWhsleseRYklWhpeaHvdasvsdedrlsdes 84 
                                    ++d++ ++++gy+++enGy++l dg++ v++rt+mpgvt++M+ WWf Wh++++ RYklWhp+aH++a+++d d+ s   
  gi|121637677|ref|YP_977900.1|  50 FDDAASIVDEGYQQTENGYGILGDGSMQVSVRTDMPGVTPAMWAWWFGWHGSDTRRYKLWHPRAHLSARWKDGDQDSGAG 129
                                    7999********************************************************************99999999 PP

                 DAPG_hydrolase  85 lsleerylgnthyvtEdvgeglekleirFvdpeelGldeeklkekkvaaavcaevglgeepelklalmvHlvretegGle 164
                                        +ry+g+ +++ E++g++++ ++i+Fv+p+ +Gl++++ ++    +++ca++g++++p ++++++vH+vr t+gG+e
  gi|121637677|ref|YP_977900.1| 130 RRGAQRYVGRWSMISEYIGSTKLGAAIQFVEPAAMGLPDDSDDT----VSICARLGSADAP-VDAGWFVHQVRSTPGGSE 204
                                    9*************************************998885....89******97777.9***************** PP

                 DAPG_hydrolase 165 lrSrfwlgerv.arvaglekaaklvk.alsegeavleelakellvHdvkEftnLasiLPelYa 225
                                    +rSrfw+g  + a  ++ e a+k+v+  +s+   v e++a++llv +++E+++La +L +l++
  gi|121637677|ref|YP_977900.1| 205 MRSRFWMGGPHiAVRKAPEVASKAVRpIASKLIGVSESTARNLLVYCAQEMNHLAGFLADLWE 267
                                    ********999544445566777888444555678999**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2148.59
//
Query:       gi|121637678|ref|YP_977901.1|  [L=186]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.0   0.1    2.6e-07   30.3   0.1    1.4  1  TetR_N    Bacterial regulatory proteins, tetR family
     0.0032   17.5   0.1     0.0061   16.6   0.1    1.4  1  HTH_7     Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.065   13.2   0.0       0.18   11.8   0.0    1.7  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   4.3e-11   2.6e-07       1      43 [.      20      62 ..      20      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4.3e-11
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeL 43
                                   I +aA  l+ ++G +a+ ++++A++++ s++++Yr+ ++K+++
  gi|121637678|ref|YP_977901.1| 20 IYAAATDLITRYGLNALDIDKLAREVHCSRATIYRRAGGKAQI 62
                                   789*************************************998 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     1e-06    0.0061      24      40 ..      38      54 ..      28      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                                   STTTSSSS---SSSS-- CS
                          HTH_7 24 iskIAkevnisRsTvYR 40
                                   i k+A+ev +sR+T+YR
  gi|121637678|ref|YP_977901.1| 38 IDKLAREVHCSRATIYR 54
                                   789*************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.1e-05      0.18      18      35 ..      38      55 ..      32      56 .. 0.89
   2 ?   -3.0   0.0       1.2   7.5e+03      32      40 ..      78      86 ..      77      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                         HTH_11 18 geeLAeeLnvSrrtvrrd 35
                                   +++LA+e ++Sr+t++r+
  gi|121637678|ref|YP_977901.1| 38 IDKLAREVHCSRATIYRR 55
                                   689*************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                         HTH_11 32 vrrdIkaLe 40
                                   vr d+++L+
  gi|121637678|ref|YP_977901.1| 78 VRSDVETLR 86
                                   899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1416.20
//
Query:       gi|121637679|ref|YP_977902.1|  [L=434]
Description: cytochrome p450 144 CYP144 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-23   81.0   0.0    3.6e-20   72.1   0.0    3.0  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.3   0.0    0.0062   1.1e+02      83     125 ..     116     158 ..      73     164 .. 0.80
   2 !   72.1   0.0     2e-24   3.6e-20     238     434 ..     242     407 ..     231     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.0062
                                    TTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHH CS
                           p450  83 kgkgvlfangekwkklRrfltptltsfgklsleelveeeaedl 125
                                     +  +++a+ + +  +R++++++l  + ++ +e+++ + a++l
  gi|121637679|ref|YP_977902.1| 116 PTHVLATADDPAHAVHRKLVLRHLAAKRIRVMEQFTVQAADRL 158
                                    5566788899*****************8889***999999887 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 2e-24
                                    SCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHH CS
                           p450 238 rrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptydd 317
                                    +rd l   l +    +g  +l+    +  + +l++aG + t++ l  a   La++P++q+++r +               
  gi|121637679|ref|YP_977902.1| 242 PRDNLLGELATA-CASG--ELDTLTAQVMMVTLFAAGGESTAALLGSAVWILATRPDIQQQVRAN--------------- 303
                                    555555555553.3333..4777778888899******************************998............... PP

                                    CCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTES CS
                           p450 318 lqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskr 397
                                        ++l a+i+EtLR+ p+   +  R v + ++++g  +p++++ ++  +a +rdp++f+ P eF+ +R   +      
  gi|121637679|ref|YP_977902.1| 304 ---PELLGAFIEETLRYEPPFR-GQYRHVRNATTLDGTELPADSHLLLLWGAANRDPAQFEAPGEFRLDRAGGK------ 373
                                    ...369****************.********************************************9984333...... PP

                                    SCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEE CS
                           p450 398 ksfaflPFGaGpRnCiGerlArmelklflatlLqnFe 434
                                        ++ FG G++ C+G  lAr+e +++l +lL + +
  gi|121637679|ref|YP_977902.1| 374 ---GHISFGKGAHFCVGAALARLEARIVLRLLLDRTS 407
                                    ...59***************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3101.19
//
Query:       gi|121637680|ref|YP_977903.1|  [L=149]
Description: hypothetical protein BCG_1811c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1034.73
//
Query:       gi|121637681|ref|YP_977904.1|  [L=597]
Description: hypothetical protein BCG_1812c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-54  185.8   5.3    1.1e-54  185.8   5.3    1.8  2  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.8   5.3   6.2e-59   1.1e-54       8     297 ..      35     318 ..      32     319 .. 0.98
   2 ?   -1.3   2.3     0.063   1.1e+03     203     231 ..     327     370 ..     314     415 .. 0.45

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 6.2e-59
                        DUF4407   8 serkkyagiGavvlltallAalsgayAlytvlkspll...lallvGllwgllIfnlDRfivssikkrakkrrelalalpR 84 
                                    +er+ +a +G++v++ a+lA+l +++A++ ++++p+    +a+  +l+ gll+ ++ R   s         r +a++++R
  gi|121637681|ref|YP_977904.1|  35 HERSTHAVAGVIVAVGAALAGLLASLAVSEAAQGPISspiGAASLALVLGLLVGAVTRGTASGP------ARGRAGVTGR 108
                                    8***********************************99*************************9......********** PP

                        DUF4407  85 lllAvligvvisepleLkiFekeIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaq 164
                                      +Av +g+v++e   L++F+++Id++l+e++  +a++  + ++  ++a l+++++ ++al+++++ a+ rld++   a+
  gi|121637681|ref|YP_977904.1| 109 ASVAVAVGFVVGELAALVMFSGAIDRRLDEQAMHSADATPAAVQ--ASASLQQARNARTALDSAVERARGRLDDALVVAR 186
                                    ********************************************..999******************************* PP

                        DUF4407 165 keldgtk...gtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaadd 241
                                    +e+++t+   +t++tgv+G+gp+++++++ l++aq+el+++ a   ++++ +al+a++a   +e+a ++ +++  a+a +
  gi|121637681|ref|YP_977904.1| 187 CEYHPTPacpQTRITGVPGRGPETRTANQLLADAQRELDNALAA--RDHQAPALDAKMAH--DEQALAEVRQAVVADAGR 262
                                    ********************************************..**************..999999************ PP

                        DUF4407 242 GllarlealdrltkedatallarlllfllflaiellPvlvKllspkgayDrllaae 297
                                    Gl+ r+ a+++lt ++a+al+ar+l +++f ++ llP++++l+++ +++Dr++aa+
  gi|121637681|ref|YP_977904.1| 263 GLGSRWVAMNDLTLASAGALTARMLAIAFFALLYLLPLILRLWRGDTTHDRHAAAR 318
                                    ****************************************************9986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.063
                        DUF4407 203 kakld................atarlaalraelaeleaerakera 231
                                    +a+                  a+++l++ r  ++  +ae+++e++
  gi|121637681|ref|YP_977904.1| 327 EADTAiaikraevrraaeimwAEHQLTQTRLAIEA-QAEIDREQQ 370
                                    22222222222233333333322222222222222.222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3923.24
//
Query:       gi|121637682|ref|YP_977905.1|  [L=187]
Description: hypothetical protein BCG_1813 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1360.76
//
Query:       gi|121637683|ref|YP_977906.1|  [L=724]
Description: 4-alpha-glucanotransferase malQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.2e-121  406.9   0.0   1.6e-121  406.5   0.0    1.1  1  Glyco_hydro_77  4-alpha-glucanotransferase


Domain annotation for each model (and alignments):
>> Glyco_hydro_77  4-alpha-glucanotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.5   0.0  8.8e-126  1.6e-121       1     464 [.     179     687 ..     179     690 .. 0.94

  Alignments for each domain:
  == domain 1  score: 406.5 bits;  conditional E-value: 8.8e-126
                                    E-GGGSB-SSSSSS--SSHHHHHHHHHH.HTT--EEEES--SE..........ST..--TTS-SESSSE-GGGS-CHG.H CS
                 Glyco_hydro_77   1 lplsSLrskksyGiGdlgdlkefvdfla.kagqklwqilPlndt.........ep.dtsPYsslSafalnplyidlealp 69 
                                    ++l+S+rs++s+GiGdl+dl++++ + a ++g+ ++ ++Pl+++         +p ++sPY ++S++++nply+++ea+p
  gi|121637683|ref|YP_977906.1| 179 VQLYSVRSRQSWGIGDLTDLANLALWSAsAHGAGYVLVNPLHAAtlpgpagrsKPiEPSPYLPTSRRFVNPLYLRVEAIP 258
                                    69************************9867899**********988887765544455********************** PP

                                    HH.........HHHHHTTSSHGGGSSB--HHHHHHHHHHHHHHHHHTHHH.HHSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Glyco_hydro_77  70 el.........aelaeegllakeelervdyekvielklkllrkaferfkekkkakeskefeeFveenaewledyalFmal 140
                                    el         ++l+ +++++ ++l+++d ++++++k+++l+ +++  +   +a ++ ++++F ++++++l+d+a+++al
  gi|121637683|ref|YP_977906.1| 259 ELvdlpkrgrvQRLRTNVQQHADQLDTIDRDSAWAAKRAALKLVHRVPR---SAGRELAYAAFRTREGRALDDFATWCAL 335
                                    **9****999999999999999999*******************97544...677899********************** PP

                                    HHHCT-SSGGGS-HHHHTTTHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEE..EEEESS--SSSHHH CS
                 Glyco_hydro_77 141 kekfegaswseWpeelrkrkeealekakkelaeeiefykflQylfdkqlkelkeyanekgieli..gDlpigvardSadv 218
                                     e+++  +w++Wp++lr+++++ ++++ +++a+ ++f+++lQ+++d+ql++++++a ++g++l+   Dl++gv++++ad+
  gi|121637683|ref|YP_977906.1| 336 AETYG-DDWHRWPKSLRHPDASGVADFVDKHADAVDFHRWLQWQLDEQLASAQSQALRAGMSLGimADLAVGVHPNGADA 414
                                    99965.89******************************************************9888************** PP

                                    HHCGGGB-BTTTSEESSBSSSTT-EEEEEE-B-HHHHHHTTTHHHHHHHHHHHTT-SEEEETTGGGGTEEEEEETT-SSC CS
                 Glyco_hydro_77 219 WanpelFkldesaGaPPDafsatGQnWgnPlynweelekdgyawwikrlraalklfdalRIDHvlGffrlWeipaeekta 298
                                    Wa +++++   +aGaPPD+f++ GQ+W +P++++++l++++y++++++++aal++++a+RIDH++G+frlW+ip +    
  gi|121637683|ref|YP_977906.1| 415 WALQDVLAQGVTAGAPPDEFNQLGQDWSQPPWRPDRLAEQEYRPFRALIQAALRHAGAVRIDHIIGLFRLWWIPDG-APP 493
                                    ***************************************************************************9.899 PP

                                    TC-EEEE--HHHHHHHHHHHHHHCT-EEEE---SS--HHHHHHHHHTT-BEEEEGGGTTSTT..TT..TTSGGGS-SSEE CS
                 Glyco_hydro_77 299 lngeyvkypgeelfevlkeelqkgkllviaEDLGvvpdevrelleelgilgmkvlqfafede..en.efylphnypensv 375
                                    ++g+yv+y++++++ +++ e++++ ++v++EDLG+v+++vr++l   g+lg+++l+f+++++     ++ + ++++e ++
  gi|121637683|ref|YP_977906.1| 494 TQGTYVRYDHDAMIGIVALEAHRAGAVVVGEDLGTVEPWVRDYLLLRGLLGTSILWFEQDRDcgPAgTPLPAERWREYCL 573
                                    9**********************************************************988852257899999****** PP

                                    EES--TTS--HHHHHT.....................HHHHHHHHHHHHHHHHTT.....CCS-GGGHHHHHHHHHHHSS CS
                 Glyco_hydro_77 376 vytgtHDndtlrgwwe.....................eerakekealleylkeeg.....peeaeeeivealirlalasv 429
                                     +++tHD+++++g+++                     e+++++++a+++ l++ g      e  +ee+v al+r++ +++
  gi|121637683|ref|YP_977906.1| 574 SSVTTHDLPPTAGYLAgdqvrlreslglltnpveaelESARADRAAWMAELRRVGlladgAEPDSEEAVLALYRYLGRTP 653
                                    *********************************998766667999999999999999887667889************** PP

                                    SSEEEEEHHHHTTTGGG-S--TT-SSSSTTS-B-- CS
                 Glyco_hydro_77 430 aklailplqDlllgeeeriNvPgtveeepnWrwrl 464
                                    ++l+ + l D+  g+++++N+Pgt++e+pnWr+ l
  gi|121637683|ref|YP_977906.1| 654 SRLLAVALTDA-VGDRRTQNQPGTTDEYPNWRVPL 687
                                    ***********.********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 4604.50
//
Query:       gi|121637684|ref|YP_977907.1|  [L=506]
Description: hypothetical protein BCG_1815 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-154  515.7   3.5   1.2e-154  515.6   3.5    1.0  1  T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM


Domain annotation for each model (and alignments):
>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.6   3.5  6.5e-159  1.2e-154       2     473 ..      16     494 ..      15     495 .. 0.98

  Alignments for each domain:
  == domain 1  score: 515.6 bits;  conditional E-value: 6.5e-159
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSSEEEETTT-- CS
                 T7SS_ESX1_EccB   2 qlttrdqvsgyrFllrRlehAlvrrdvrmlddplrsqsrallvGvvlavvvlagaavlallkPqgkvgdskivadkesga 81 
                                    +l+tr+qv+gy+Fl rR++ Al+r  vrm  +p r+q+ a++++v  a+v++ ga+++++++P+g++++s i+ad++sga
  gi|121637684|ref|YP_977907.1|  16 GLSTRTQVTGYQFLARRTAMALTRWHVRMEIEPGRRQTLAVVASVSAALVICLGALLWSFISPSGQLNESPIIADRDSGA 95 
                                    589***************************************************************************** PP

                                    EEEEETTEEEEES-HHHHHHHCTS-B--EEE-HHHHHTS-B--EBS-TTS-S---B-SS.SSCEEEEEEEECSTTSS... CS
                 T7SS_ESX1_EccB  82 lYvvvdgtLhPvlNlaSArLilgkaakpttvkdseLdklprGplvGIpgAPealpqsadldeskWtvCDtvssaasa... 158
                                    lYv+v+++L+P+lNlaSArLi+g++++p+ v++s+++++prGplvGIpgAP++++ ++    s+W vCDtv++++s    
  gi|121637684|ref|YP_977907.1|  96 LYVRVGDRLYPALNLASARLITGRPDNPHLVRSSQIATMPRGPLVGIPGAPSSFSPKSP-PASSWLVCDTVATSSSIgsl 174
                                    *******************************************************9999.9**********998877899 PP

                                    -EEEEEEEES----BTTEEE--TTEEEEEEETTEEEEEETTEEEEE-TTSHHHHHCCT--...TS--EE--HHHHHHS-E CS
                 T7SS_ESX1_EccB 159 savettviagklalgaraaelaadqavLvsadgktyLvydgkraeidladravtrAlgle...gakprpvsagllnalpe 235
                                    + v++tvi g+++l+ + + l+ ++av+ +++g+++++ +g+r++i++++rav   lgl+     ++rp+s++l++alp 
  gi|121637684|ref|YP_977907.1| 175 QGVTVTVIDGTPDLTGHRQILSGSDAVVLRYGGDAWVIREGRRSRIEPTNRAVLLPLGLTpeqVSQARPMSRALFDALPV 254
                                    ************************************************************8866778************* PP

                                    EEESS----TTTTSB-TTSS-TTSBTT-EEEEEET.TEEEEEEEETTEEEEE-HHHHHHHHHHT-TT-SS--EE-CCHCC CS
                 T7SS_ESX1_EccB 236 vpplkaPaipgaGkpaglelggkarvGsvvkvsdadgeeeyYvvlsdglqrvtevvadllrnansqgltepptvepdvla 315
                                    +p+l +P++p+aG pa+++ +  + +G+v+ + + +g ++y +vl dg+q++ ++va++l+na s g+t+p tvep++la
  gi|121637684|ref|YP_977907.1| 255 GPELLVPEVPNAGGPATFPGAPGP-IGTVIVTPQISGPQQYSLVLGDGVQTLPPLVAQILQNAGSAGNTKPLTVEPSTLA 333
                                    ******************988877.******************************************************* PP

                                    CS-E-----...--SS--EEE-TTTS-EEEEEEEE-STTSS-EEEEEEESS-SS-..GCCGEEE-TTSSEE......EEE CS
                 T7SS_ESX1_EccB 316 klpvveelpvdayPekppkivdvkeapvlCaswekgagdarakvallagaalPvp..ekaktvelvsadgsgatvdavyl 393
                                    k+pvv++l+ +ayP++p+++vd +e+p +C+ we++ag++ra+v++++g ++Pv+  e++k v+lv+ad+sg+++d+vy 
  gi|121637684|ref|YP_977907.1| 334 KMPVVNRLDLSAYPDNPLEVVDIREHPSTCWWWERTAGENRARVRVVSGPTIPVAatEMNKVVSLVKADTSGRQADQVYF 413
                                    *******************************************************9999********************* PP

                                    SSBE..EEEEEECSTT..CEEEEEEEETTSEEEEE-SH.HHHHHCT--S.-EE--HHHHTTSEEEEEE-CCCCT-EESSX CS
                 T7SS_ESX1_EccB 394 ppgtgalvqatgaepaseargslfyvsdtGvRYgipde.etakaLGlkeepepaPwsilkllpaGPtLsradAlvahDgl 472
                                     p+++++v +tg++p++++++sl++v+d G R+g++d+ e+ +aLGl+ +p+ aPw  l+llp+GPtLsradAlv+hD+l
  gi|121637684|ref|YP_977907.1| 414 GPDHANFVAVTGNNPGAQTSESLWWVTDAGARFGVEDSkEARDALGLTLTPSLAPWVALRLLPQGPTLSRADALVEHDTL 493
                                    ************************************9967889************************************9 PP

                                    X CS
                 T7SS_ESX1_EccB 473 p 473
                                    p
  gi|121637684|ref|YP_977907.1| 494 P 494
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3627.70
//
Query:       gi|121637685|ref|YP_977908.1|  [L=1391]
Description: hypothetical protein BCG_1816 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.8e-114  379.7   0.0    4.5e-82  275.1   0.0    4.8  5  FtsK_SpoIIIE     FtsK/SpoIIIE family
    1.2e-10   42.0   0.0      0.008   16.6   0.0    3.6  3  AAA_16           AAA ATPase domain
    6.8e-08   31.7   0.0    2.9e-06   26.3   0.0    2.2  2  Adeno_IVa2       Adenovirus IVa2 protein
      3e-07   30.5   0.1      0.021   14.7   0.0    3.1  3  NACHT            NACHT domain
    5.9e-07   29.8   0.0       0.13   12.5   0.0    4.0  3  AAA_22           AAA domain
    3.3e-06   26.8   0.5       0.15   11.9   0.0    3.0  3  AAA_29           P-loop containing region of AAA domain
      7e-06   26.0   0.1      0.073   12.8   0.1    3.0  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.9e-05   25.0   0.5       0.02   15.2   0.0    3.8  3  AAA_19           AAA domain
    3.7e-05   24.3   1.1        1.3    9.5   0.2    3.3  3  ABC_tran         ABC transporter
    0.00021   21.3   0.0        9.6    6.2   0.0    3.9  3  AAA_14           AAA domain
      0.001   19.2   1.4       0.16   12.0   0.1    2.5  2  DUF87            Helicase HerA, central domain
     0.0027   17.9   0.0        2.4    8.3   0.0    3.3  3  AAA_33           AAA domain
     0.0028   16.6   3.0        2.4    7.0   0.0    3.4  4  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.003   16.6   4.2        0.7    8.9   0.1    3.1  3  T2SSE            Type II/IV secretion system protein
     0.0033   17.9   0.6        6.1    7.3   0.0    4.3  4  AAA              ATPase family associated with various cellul
     0.0038   17.6   0.1        6.4    7.2   0.0    3.4  3  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   14.5   0.3        1.2    8.0   0.0    2.6  3  AAA_10           AAA-like domain
      0.013   14.6   0.1        1.1    8.3   0.0    2.9  3  G-alpha          G-protein alpha subunit
      0.014   15.3   0.0         10    6.0   0.0    3.5  3  ATPase_2         ATPase domain predominantly from Archaea
      0.016   15.0   0.6        2.1    8.0   0.0    2.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.016   14.8   0.7        2.4    7.7   0.0    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.028   13.9   0.8        9.7    5.7   0.1    3.0  3  AAA_7            P-loop containing dynein motor region
       0.03   14.9   0.1        8.9    6.9   0.0    2.8  2  AAA_18           AAA domain
      0.046   13.4   3.0        1.2    8.9   0.0    3.0  3  AAA_30           AAA domain
      0.073   12.8   0.0        8.3    6.1   0.1    2.6  2  AAA_24           AAA domain
       0.08   12.1   0.1          4    6.5   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
      0.083   13.4   0.8        7.8    6.9   0.0    2.4  2  AAA_23           AAA domain
      0.087   12.6   0.0        2.3    8.0   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
      0.088   12.4   4.7       0.67    9.5   0.0    3.8  2  AAA_25           AAA domain
        0.1   12.6   0.1         15    5.7   0.0    3.2  2  MMR_HSR1         50S ribosome-binding GTPase
       0.11   11.7   0.1         11    5.0   0.0    2.4  2  NB-ARC           NB-ARC domain
       0.21   12.0   0.5         21    5.6   0.2    2.5  2  AAA_17           AAA domain
       0.21   10.8   1.4        4.4    6.5   0.1    2.6  2  Zeta_toxin       Zeta toxin
       0.24   11.3   4.1        3.5    7.5   0.2    3.2  3  NTPase_1         NTPase
       0.25   10.6   1.4          9    5.5   0.0    2.8  3  Septin           Septin
       0.26   11.3   0.3        5.7    7.0   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.37   10.5   4.6       0.73    9.5   4.6    1.4  1  Yip1             Yip1 domain
       0.69   10.1   5.5         10    6.3   0.3    3.1  3  AAA_28           AAA domain
        5.2    5.6   6.4        6.5    5.2   0.0    3.0  4  DUF853           Bacterial protein of unknown function (DUF85


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00055      0.25      56     123 ..     234     301 ..     232     327 .. 0.83
   2 !   79.3   0.0     6e-25   2.7e-22      16     206 ..     463     671 ..     451     697 .. 0.81
   3 !  275.1   0.0   9.8e-85   4.5e-82       2     242 ..     824    1096 ..     823    1097 .. 0.98
   4 !    8.2   0.0    0.0031       1.4      30      63 ..    1163    1195 ..    1143    1203 .. 0.84
   5 ?   -2.2   0.0       4.6   2.1e+03     148     185 ..    1281    1322 ..    1270    1351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                                    HHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHH.HHH CS
                   FtsK_SpoIIIE  56 lntLilSlatthtPeeVqliliDykgvelsalediphllsvavatdperalraleeLvkemeery.alf 123
                                    ++++i+ la+ h P++Vq+i++     +   ++ +ph +  + + d+   +r++   v e    + +lf
  gi|121637685|ref|YP_977908.1| 234 MRAIICQLAFSHGPDHVQMIVVSSDLDQWDWVKWLPHFGD-SRRHDAAGNARMVYTSVREFAAEQaELF 301
                                    689*******************99988**********999.8888888888887766666554444555 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 6e-25
                                    -TTEEEEEEET.TS-EEEEEGGGS-......SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS.SCGGGT CS
                   FtsK_SpoIIIE  16 sqlpvalgkei.sgnplvldlkkma.....shllvaGatgsGKStalntLilSlatthtPeeVqliliDykgv.elsale 88 
                                    s+l   +g     g+ l ld k+       +h++  G+tgsGKSt ++t i Sl++ h Pee+q++l D kg+ + + + 
  gi|121637685|ref|YP_977908.1| 463 SRLRAPFGNRSdNGELLFLDMKSLDeggdgPHGVMSGTTGSGKSTLVRTVIESLMLSHPPEELQFVLADLKGGsAVKPFA 542
                                    5556666666666777777888877888889************************************************* PP

                                    T-TTBSS...S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT-.....--B-TT-........ CS
                   FtsK_SpoIIIE  89 diphlls..vavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldif.....gdvflvlDnyddlaa 161
                                    ++ph+    +   +d     r+l++L  e+ +r+a+ ++agv++ + y+++ a+  + ++     +++++v+D+    ++
  gi|121637685|ref|YP_977908.1| 543 GVPHVSRiiTDLEEDQALMERFLDALWGEIARRKAICDSAGVDDAKEYNSVRARMRARGQdmaplPMLVVVIDEF---YE 619
                                    *****998778888899999***************************9999988877665111123456777764...43 PP

                                    .....................-----------B-----EEEEEEC-HHHHHH CS
                   FtsK_SpoIIIE 162 ene.......ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrl 206
                                     +           s+  qg +y +h++++++    +   l+ + + r+ L  
  gi|121637685|ref|YP_977908.1| 620 WFRimptavdVLDSIGRQGRAYWIHLMMASQTIESRAEKLMENMGYRLVLKA 671
                                    333444677666678899**********99998889999**99999987765 PP

  == domain 3  score: 275.1 bits;  conditional E-value: 9.8e-85
                                     HHHHHTSHHHHT---TTEEEEEEET.TS-EEEEEGGGS-........SEEEE--TTSSHHHHHHHHHHHHHTT--TTT CS
                   FtsK_SpoIIIE    2 Llevleskkfrtessqlpvalgkei.sgnplvldlkkma.......shllvaGatgsGKStalntLilSlatthtPee 71  
                                     L++++ ++++++e++++++++++ + +++p+++d+++++       +++l++Ga gsGK+tal+tLi+S+a+thtP++
  gi|121637685|ref|YP_977908.1|  824 LVNRFLGRPWHKEYGSACNLVFPIGiIDRPYKHDQPPWTvdtsgpgANVLILGAGGSGKTTALQTLICSAALTHTPQQ 901 
                                     899*************************************************************************** PP

                                     EEEEEE-TTSSSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH.....HHHHHHHHHHT CS
                   FtsK_SpoIIIE   72 VqliliDykgvelsalediphllsvavatdperalraleeLvkemeeryalfreagvrsiaa.....ydgeiaedpld 144 
                                     Vq+++++y++++l+++++iph+++va++tdp+ ++r+++eL+++++er+++f e+g++s+++     + ge++++p+d
  gi|121637685|ref|YP_977908.1|  902 VQFYCLAYSSTALTTVSRIPHVGEVAGPTDPYGVRRTVAELLALVRERKRSFLECGIASMEMfrrrkFGGEAGPVPDD 979 
                                     ****************************************************************************** PP

                                     T---B-TT-..........................-----------B-----EEEEEEC-HHHHHHHHHHH....... CS
                   FtsK_SpoIIIE  145 ifgdvflvlDnyddlaaene....ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkds....sv 214 
                                     +fgdv+lv+Dny++la+ene    ++++++nqgps+gvhv+vta+re+e rp++++++++rieLrlaa +d+    s+
  gi|121637685|ref|YP_977908.1|  980 GFGDVYLVIDNYRALAEENEvlieQVNVIINQGPSFGVHVVVTADRESELRPPVRSGFGSRIELRLAAVEDAklvrSR 1057
                                     ****************************************************************************** PP

                                     .HHHHHHHHHHH......CG.....GGTEEEEEEES--- CS
                   FtsK_SpoIIIE  215 lvedaivRlark......gr.....aaglHlllatqrls 242 
                                     +++d++v+++r+      +r     +aglH+l+a+++l+
  gi|121637685|ref|YP_977908.1| 1058 FAKDVPVKPGRGmvavnyVRldsdpQAGLHTLVARPALG 1096
                                     ************99887767999************9876 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0031
                                     EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHH CS
                   FtsK_SpoIIIE   30 plvldlkkmashllvaGatgsGKStalntLilSl 63  
                                     p++l+ +++  hl+v G+ + G +t+l t++  +
  gi|121637685|ref|YP_977908.1| 1163 PVYLNFAENS-HLMVTGRRECGRTTTLATIMSEI 1195
                                     6777777777.******************99765 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 4.6
                                     -B-TT-..........................---------- CS
                   FtsK_SpoIIIE  148 dvflvlDnyddlaaene....ritsLsnqgpsygvhvlvtag 185 
                                      +fl++D+ ++l   +     + +  +n+    g hv+vt++
  gi|121637685|ref|YP_977908.1| 1281 EIFLIVDDIQQLPPGFDsplhKAVPFVNRAADVGLHVIVTRT 1322
                                     57899999999998888889899999************9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-05     0.008      22     144 ..     490     617 ..     479     635 .. 0.64
   2 !   11.8   0.1    0.0005      0.23      21      46 ..     865     891 ..     862     954 .. 0.76
   3 !    9.0   0.0    0.0036       1.6      25     146 ..    1172    1319 ..    1164    1348 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-05
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                    g+++  + sG  G+GKs+lvr++ ++l  +    +  f+ ++ +  ++  p+   a +   ++++++l+++  +a+ e++
  gi|121637685|ref|YP_977908.1| 490 GDGPHGVMSGTTGSGKSTLVRTVIESLMLShppeELQFVLADLKGGSAVKPF---AGVPHVSRIITDLEED--QALMERF 564
                                    555777899****************777776665677777777776555665...3333333455555544..2234444 PP

                         AAA_16  98 rekleeala......avpelagaea.srllellkrllallsrderplvlvlDdl 144
                                     ++l +++a      +++ +++a++ +++++ +++  + +++  + lv+v+D++
  gi|121637685|ref|YP_977908.1| 565 LDALWGEIArrkaicDSAGVDDAKEyNSVRARMRARGQDMAP-LPMLVVVIDEF 617
                                    444444444333323222233333368888888888877776.334******98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0005
                         AAA_16  21 sgrp.elvllsGesGvGKsslvrellr 46 
                                    +++p  +vl+ G+ G+GK++ +++l  
  gi|121637685|ref|YP_977908.1| 865 TSGPgANVLILGAGGSGKTTALQTLIC 891
                                    4555689***************88763 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0036
                         AAA_16   25 elvllsGesGvGKsslvrellralekdggiflrgkcdql..esaipysalaqalareellrqlldeaesaeleawrek 100 
                                     + ++++G + +G ++ + +++ ++ + +   + g         ++p ++++ +  r++ll++l+++     +e+++  
  gi|121637685|ref|YP_977908.1| 1172 SHLMVTGRRECGRTTTLATIMSEIGRLY---APGASSAPppAPGRPSAQVWLVDPRRQLLTALGSD----YVERFAYN 1242
                                     6799*****************9888763...22222222222346666777777788999999988....89999999 PP

                         AAA_16  101 leealaavpelagaea..srllellkrll.allsrderplvlvlDdlq............................w 146 
                                     l++++a  +ela+a+a  +    l ++ l +++   ++ + l++Dd+q                             
  gi|121637685|ref|YP_977908.1| 1243 LDGVVAMMGELAAALAgrEPPPGLSAEELlSRSWWSGPEIFLIVDDIQqlppgfdsplhkavpfvnraadvglhviV 1319
                                     999999888888888888555555555554555564555*********66665555555555555555555555550 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.3e-09   2.9e-06       6     123 ..     401     528 ..     396     534 .. 0.80
   2 ?    3.0   0.0      0.08        37      91     122 ..     873     904 ..     869     910 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.3e-09
                     Adeno_IVa2   6 veaveelydrveelk..davkslnraillkPlkdfasyeellslggvdak.lveeneevkdiekldakl..lrddGel.. 78 
                                    + + ee+ +++ +++  +a +++ + ++    +d  sy  +   g +d + l   +++  +  +l a++   +d+Gel  
  gi|121637685|ref|YP_977908.1| 401 IAEAEEFAQKLAQWRlaEAYEEIGQRVAHIGARDILSYYGIDDPGNIDFDsLWASRTDTMGRSRLRAPFgnRSDNGELlf 480
                                    56778999999998633778899888888899999999999999999964277788899999999999943468998723 PP

                     Adeno_IVa2  79 ...sslnyglqPviGviyGPtGsGksqllrnlissklisPiPetvifi 123
                                        sl+ g +   Gv++G tGsGks l+r++i s ++s +Pe + f+
  gi|121637685|ref|YP_977908.1| 481 ldmKSLDEGGDGPHGVMSGTTGSGKSTLVRTVIESLMLSHPPEELQFV 528
                                    33256777778889*****************************99887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.08
                     Adeno_IVa2  91 viyGPtGsGksqllrnlissklisPiPetvif 122
                                    +i G  GsGk+  l++li s  +  +P+ v f
  gi|121637685|ref|YP_977908.1| 873 LILGAGGSGKTTALQTLICSAALTHTPQQVQF 904
                                    5899************************9988 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00033      0.15       4      38 ..     496     529 ..     495     531 .. 0.88
   2 !   14.7   0.0   4.6e-05     0.021       3      39 ..     872     905 ..     870     926 .. 0.83
   3 ?   -2.1   0.0       6.8   3.1e+03       4      28 ..    1175    1199 ..    1173    1205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                                    EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEE CS
                          NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvF 38 
                                    ++ G  GsGK+tL++ +++ +  +++p++  ++v+
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLMLSHPPEE-LQFVL 529
                                    578**********************9996.47765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.6e-05
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEE CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFf 39 
                                    v++ G+ GsGKTt lq l+  +a  + pq+ +++  +
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLICSAALTHTPQQ-VQF--Y 905
                                    899***********************9995.333..3 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.8
                                     EEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT    4 ilqGeaGsGKTtLlqklalawaegk 28  
                                     +++G+  +G Tt l+ +++++ + +
  gi|121637685|ref|YP_977908.1| 1175 MVTGRRECGRTTTLATIMSEIGRLY 1199
                                     68888889**********9987655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00028      0.13       6      38 ..     493     542 ..     488     628 .. 0.56
   2 !    7.7   0.0    0.0087         4       8      53 ..     872     913 ..     867    1026 .. 0.70
   3 ?    4.4   0.0     0.093        43       5      38 ..    1171    1214 ..    1169    1320 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................e 38 
                                     ++v  G +G+GK+tl+r++ e+l     +                     +
  gi|121637685|ref|YP_977908.1| 493 PHGVMSGTTGSGKSTLVRTVIESLMLS--HPPeelqfvladlkggsavkpfA 542
                                    578999****************99533..33312444444444444444441 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0087
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstss 53 
                                    +++ G  G+GKTt l++l  ++        + p++v f++l+ s++ 
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLICSAALT-----HTPQQVqFYCLAYSSTA 913
                                    6899**************9997322.....44444434444433333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.093
                         AAA_22    5 agilvvtGesGtGKTtllrrlleqldeeakaee...........e 38  
                                      ++l+vtG   +G+Tt+l++++++  + +++             +
  gi|121637685|ref|YP_977908.1| 1171 NSHLMVTGRRECGRTTTLATIMSEIGRLYAP-GassapppapgrP 1214
                                     57999**************999987543333.2365444333331 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00045      0.21      24      40 ..     494     510 ..     482     526 .. 0.81
   2 !   11.9   0.0   0.00032      0.15      17      48 ..     861     892 ..     854     901 .. 0.77
   3 ?   -1.4   0.0       4.3     2e+03      20      39 ..    1169    1188 ..    1164    1193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                         AAA_29  24 atlltGpsGsGKSTllD 40 
                                      +++G++GsGKSTl+ 
  gi|121637685|ref|YP_977908.1| 494 HGVMSGTTGSGKSTLVR 510
                                    45899**********95 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00032
                         AAA_29  17 ieidlkg...atlltGpsGsGKSTllDAiqalLvp 48 
                                    +++d++g   ++l+ G+ GsGK+T l   q+l+++
  gi|121637685|ref|YP_977908.1| 861 WTVDTSGpgaNVLILGAGGSGKTTAL---QTLICS 892
                                    66676666689*************76...666655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.3
                         AAA_29   20 dlkgatlltGpsGsGKSTll 39  
                                      +++  ++tG+ + G +T l
  gi|121637685|ref|YP_977908.1| 1169 AENSHLMVTGRRECGRTTTL 1188
                                     5555789**********987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0024       1.1       2      26 ..     496     518 ..     495     534 .. 0.81
   2 !   12.8   0.1   0.00016     0.073       2      25 ..     873     895 ..     872     920 .. 0.80
   3 ?   -0.3   0.0       1.6   7.4e+02      65      81 ..    1283    1299 ..    1270    1305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                Viral_helicase1   2 vvhGvpGcGKStlirkllrtslilt 26 
                                    v++G  G+GKStl+r+++++   + 
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIES--LML 518
                                    889**************988..333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                Viral_helicase1   2 vvhGvpGcGKStlirkllrtslil 25 
                                    ++ G++G+GK+t++++l+++   l
  gi|121637685|ref|YP_977908.1| 873 LILGAGGSGKTTALQTLICSA-AL 895
                                    799***************993.33 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.6
                Viral_helicase1   65 ililDEylllhaGyill 81  
                                     +li+D++++l++G    
  gi|121637685|ref|YP_977908.1| 1283 FLIVDDIQQLPPGFDSP 1299
                                     89**********98655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.071        33      13      38 ..     495     520 ..     489     539 .. 0.81
   2 !   15.2   0.0   4.4e-05      0.02      11      59 ..     870     918 ..     863    1006 .. 0.85
   3 ?   -0.9   0.0         4   1.8e+03       9      36 ..    1170    1197 ..    1166    1204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.071
                         AAA_19  13 llvtaGpGtGKTrvlkhivallvelg 38 
                                     ++ +  G+GK+++++++++ l   +
  gi|121637685|ref|YP_977908.1| 495 GVMSGTTGSGKSTLVRTVIESLMLSH 520
                                    5778999*************998776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.4e-05
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelr 59 
                                     ++l+++  G+GKT+ l++ +  +  +++ +  +++++a+ + A   ++
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTLICSAALTHTPQQVQFYCLAYSSTALTTVS 918
                                    67999******************999999999*********99988776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4
                         AAA_19    9 kekvllvtaGpGtGKTrvlkhivallve 36  
                                     ++++l+vt+   +G T++l +i++++ +
  gi|121637685|ref|YP_977908.1| 1170 ENSHLMVTGRRECGRTTTLATIMSEIGR 1197
                                     678899999999**********988765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0039       1.8      15      33 ..     496     514 ..     491     525 .. 0.85
   2 !    9.5   0.2    0.0029       1.3      10      32 ..     868     890 ..     865     903 .. 0.89
   3 ?    2.2   0.0      0.53   2.4e+02       3      34 ..    1163    1194 ..    1161    1198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0039
                                    EEEESTTSSHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllag 33 
                                    ++ G +G+GKStL++++++
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIE 514
                                    567***********99876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0029
                                    TTSEEEEEESTTSSHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  10 egekvaivGenGaGKStLlklla 32 
                                    +g  v i+G  G+GK+t l++l+
  gi|121637685|ref|YP_977908.1| 868 PGANVLILGAGGSGKTTALQTLI 890
                                    7899***************9986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.53
                                     EEEEEEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran    3 nvslklkegekvaivGenGaGKStLlkllagl 34  
                                      v l++ e++ + ++G+  +G +t l++++ +
  gi|121637685|ref|YP_977908.1| 1163 PVYLNFAENSHLMVTGRRECGRTTTLATIMSE 1194
                                     57789999*******************99876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.046        21       6      32 ..     496     524 ..     492     558 .. 0.82
   2 ?    4.7   0.0     0.062        29       5      27 ..     872     894 ..     869     916 .. 0.80
   3 ?    6.2   0.0     0.021       9.6       4      25 ..    1173    1194 ..    1170    1201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.046
                         AAA_14   6 vitGaRrvGKTtllkqlikell..vkkes 32 
                                    v++G   +GK+tl++++i++l+   ++e+
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLMlsHPPEE 524
                                    5789999***********99887655544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.062
                         AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                    ++i Ga  +GKTt l++li +  
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLICSAA 894
                                    7899*************996655 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                         AAA_14    4 ilvitGaRrvGKTtllkqlike 25  
                                      l++tG R +G Tt l ++++e
  gi|121637685|ref|YP_977908.1| 1173 HLMVTGRRECGRTTTLATIMSE 1194
                                     589*************999876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00035      0.16      30      48 ..     499     517 ..     494     534 .. 0.87
   2 ?    5.6   0.2     0.033        15      26      48 ..     872     894 ..     870     900 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                          DUF87  30 gsTGsGKSntvavLleell 48 
                                    g+TGsGKS++v+  +e+l+
  gi|121637685|ref|YP_977908.1| 499 GTTGSGKSTLVRTVIESLM 517
                                    99**************997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.033
                          DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                    ++ilg  GsGK++    L+ +++
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLICSAA 894
                                    68****************98875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0052       2.4       3      23 ..     496     516 ..     496     528 .. 0.89
   2 ?    4.7   0.0     0.066        30       2      20 ..     872     890 ..     872     951 .. 0.85
   3 ?   -0.3   0.0       2.3   1.1e+03      62     112 ..    1306    1358 ..    1290    1363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0052
                         AAA_33   3 llvGlpGsGKstlaerllkkl 23 
                                    ++ G  GsGKstl++ +++ l
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESL 516
                                    589************998765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.066
                         AAA_33   2 vllvGlpGsGKstlaerll 20 
                                    vl+ G+ GsGK+t ++ l+
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLI 890
                                    6788**********99985 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.3
                         AAA_33   62 larkalsagrnvildatn..lsrrerarflklarrlgvpvrivvvetdeetlk 112 
                                     ++++a+  g +vi+  t+  +s +  + +l++++++++p ++++ ++de  ++
  gi|121637685|ref|YP_977908.1| 1306 FVNRAADVGLHVIVTRTFggWSSAGSDPMLRALHQANAPLLVMDADPDEGFIR 1358
                                     666777788999998886336678889*************9999999997665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0051       2.4      17      40 ..     494     517 ..     485     544 .. 0.72
   2 !    6.8   0.3    0.0058       2.7      17      38 ..     871     892 ..     864     898 .. 0.89
   3 ?   -3.7   0.0       8.8   4.1e+03     258     285 ..    1002    1029 ..     984    1030 .. 0.75
   4 ?    0.3   0.0      0.56   2.6e+02      13      39 ..    1169    1195 ..    1162    1198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0051
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrair 40 
                                    h ++ GttGsGK++ ++  ++++ 
  gi|121637685|ref|YP_977908.1| 494 HGVMSGTTGSGKSTLVRTVIESLM 517
                                    889**********99888877654 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllra 38 
                                     +li+G+ GsGKt+al+ l+ +
  gi|121637685|ref|YP_977908.1| 871 NVLILGAGGSGKTTALQTLICS 892
                                    689***************9965 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8.8
                  TrwB_AAD_bind  258 leelksllaegRkfGgavvlglqsiaql 285 
                                     +e+++ ++++g +fG+ vv+++   + l
  gi|121637685|ref|YP_977908.1| 1002 IEQVNVIINQGPSFGVHVVVTADRESEL 1029
                                     78999999************99877766 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.56
                  TrwB_AAD_bind   13 retqhilivGttGsGKtqalekllrai 39  
                                     +e++h++++G    G+t++l  ++ +i
  gi|121637685|ref|YP_977908.1| 1169 AENSHLMVTGRRECGRTTTLATIMSEI 1195
                                     699*********************987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0015       0.7     133     153 ..     496     516 ..     494     524 .. 0.88
   2 ?    5.9   0.5     0.012       5.6     130     150 ..     870     890 ..     866     900 .. 0.87
   3 ?    0.8   0.0      0.44     2e+02     128     153 ..    1170    1195 ..    1160    1198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                          T2SSE 133 lvsGgTgsGKttllyallkei 153
                                    ++sG+TgsGK+tl+ ++++ +
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESL 516
                                    68************9998765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                          T2SSE 130 glilvsGgTgsGKttllyall 150
                                     ++l+ G+ gsGKtt l +l+
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTLI 890
                                    589**************9886 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.44
                          T2SSE  128 erglilvsGgTgsGKttllyallkei 153 
                                     e+  ++v+G    G+tt+l ++++ei
  gi|121637685|ref|YP_977908.1| 1170 ENSHLMVTGRRECGRTTTLATIMSEI 1195
                                     567899****************9998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.013       6.1       3      37 ..     497     540 ..     496     629 .. 0.67
   2 ?    2.3   0.0      0.47   2.2e+02       1      22 [.     872     893 ..     872     951 .. 0.77
   3 ?    1.5   0.0      0.81   3.7e+02      67     131 ..     991    1044 ..     977    1045 .. 0.72
   4 ?    0.5   0.0       1.6   7.5e+02       2      23 ..    1175    1196 ..    1174    1207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                                    EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS CS
                            AAA   3 lyGppGtGKTllakavakel.........gvefleisgsellsk 37 
                                    ++G+ G GK++l++ v+++l         ++ +  ++g + ++ 
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRTVIESLmlshppeelQFVLADLKGGSAVKP 540
                                    68*****************7444433322344566666666644 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.47
                                    EEEESSTTSSHHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel 22 
                                    vl+ G  G GKT++ + ++ ++
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLICSA 893
                                    6899*********998887765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.81
                                     GGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                            AAA   67 idalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131 
                                       ala+++        e +++q    +++  +    v v++++ r+++l p+++ + f ++ie++
  gi|121637685|ref|YP_977908.1|  991 YRALAEEN--------EVLIEQVNVIINQGPSF--GVHVVVTADRESELRPPVR-SGFGSRIELR 1044
                                     55554444........55555555555555553..599****************.9999998875 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.6
                                     EEESSTTSSHHHHHHHHHHHHT CS
                            AAA    2 llyGppGtGKTllakavakelg 23  
                                     +++G   +G+T++   +++e+g
  gi|121637685|ref|YP_977908.1| 1175 MVTGRRECGRTTTLATIMSEIG 1196
                                     78999************99986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.014       6.4       3      23 ..     497     517 ..     496     533 .. 0.85
   2 ?    5.1   0.0     0.062        28       1      36 [.     872     906 ..     872     918 .. 0.73
   3 ?    0.4   0.0       1.8   8.3e+02       2      23 ..    1175    1196 ..    1174    1214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                   RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                    ++G +g GKStl+++++++l+
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRTVIESLM 517
                                    79*************999988 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.062
                   RNA_helicase   1 iwlyGpsgeGKStlake.Lakallkklklkkkdsvys 36 
                                    +++ G+ g GK+t+ ++ +++a l++   +++ ++y+
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTlICSAALTHT--PQQVQFYC 906
                                    5789************93445555555..66667776 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.8
                   RNA_helicase    2 wlyGpsgeGKStlakeLakall 23  
                                     +++G++ +G +t+  ++++++ 
  gi|121637685|ref|YP_977908.1| 1175 MVTGRRECGRTTTLATIMSEIG 1196
                                     799*************999886 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.064        29      22      47 ..     493     518 ..     486     543 .. 0.85
   2 ?    8.0   0.0    0.0025       1.2     243     305 ..     611     673 ..     608     680 .. 0.83
   3 ?   -2.6   0.0       4.4     2e+03      23      47 ..     871     895 ..     868     900 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.064
                         AAA_10  22 sasliiGdlGnGKSvlakllvlyisl 47 
                                    ++ +++G +G GKS l+++++  ++l
  gi|121637685|ref|YP_977908.1| 493 PHGVMSGTTGSGKSTLVRTVIESLML 518
                                    67899**************9877766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                         AAA_10 243 vvifDEaw.iftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretd 305
                                    vv++DE +  f  ++    +l+++ R+GR+y   +++++q  +    e+l +n+g++l+ ++ +
  gi|121637685|ref|YP_977908.1| 611 VVVIDEFYeWFRIMPTAVDVLDSIGRQGRAYWIHLMMASQTIE-SRAEKLMENMGYRLVLKART 673
                                    6788887625777888899********************9876.678999*******9988665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                         AAA_10  23 asliiGdlGnGKSvlakllvlyisl 47 
                                    ++li+G  G GK    ++l+  ++l
  gi|121637685|ref|YP_977908.1| 871 NVLILGAGGSGKTTALQTLICSAAL 895
                                    579************9999887766 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.44     2e+02      28      42 ..     497     511 ..     495     527 .. 0.85
   2 ?    8.3   0.0    0.0024       1.1      24      44 ..     870     890 ..     861     918 .. 0.83
   3 ?    0.9   0.0      0.44     2e+02      23      44 ..    1171    1192 ..    1164    1210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.44
                                    EEESTTSSHHHHHHH CS
                        G-alpha  28 llGqseSGKsTilkq 42 
                                    + G+ +SGKsT+++ 
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRT 511
                                    679*********986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                                    EEEEEEESTTSSHHHHHHHHH CS
                        G-alpha  24 vkllllGqseSGKsTilkqlk 44 
                                     ++l+lG+++SGK+T l+ l 
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTLI 890
                                    589*************99875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.44
                                     EEEEEEEESTTSSHHHHHHHHH CS
                        G-alpha   23 evkllllGqseSGKsTilkqlk 44  
                                     + +l++ G  e+G++T+l  + 
  gi|121637685|ref|YP_977908.1| 1171 NSHLMVTGRRECGRTTTLATIM 1192
                                     458999**********987764 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.022        10      24      45 ..     496     517 ..     482     621 .. 0.82
   2 ?    2.2   0.0      0.31   1.4e+02      18      45 ..     867     894 ..     863     923 .. 0.74
   3 ?    2.2   0.0       0.3   1.4e+02      15      43 ..    1166    1194 ..    1157    1199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                       ATPase_2  24 fiYGpegsGKtaLlkeiienle 45 
                                    +  G  gsGK++L++ +ie l 
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLM 517
                                    56699**************984 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.31
                       ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienle 45 
                                    +p   ++i G  gsGKt+ l+ +i    
  gi|121637685|ref|YP_977908.1| 867 GPGANVLILGAGGSGKTTALQTLICSAA 894
                                    5666789*************99986653 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.3
                       ATPase_2   15 lerepneiyfiYGpegsGKtaLlkeiien 43  
                                     l+  +n+ ++++G++ +G t+ l  i+++
  gi|121637685|ref|YP_977908.1| 1166 LNFAENSHLMVTGRRECGRTTTLATIMSE 1194
                                     5566788899***********99988765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0047       2.1       2      23 ..     498     519 ..     497     524 .. 0.88
   2 ?    4.5   0.1     0.055        25       1      23 [.     874     896 ..     874     903 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0047
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelr 23 
                                     G+ GsGK+t+v++++e l+l+
  gi|121637685|ref|YP_977908.1| 498 SGTTGSGKSTLVRTVIESLMLS 519
                                    59*************9988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.055
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                    ++G  GsGKtt  ++l+  + l+
  gi|121637685|ref|YP_977908.1| 874 ILGAGGSGKTTALQTLICSAALT 896
                                    6899**********998877766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0053       2.4       4      22 ..     496     514 ..     493     526 .. 0.88
   2 ?    5.3   0.2     0.029        13       4      21 ..     873     890 ..     870     902 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0053
                                    EEEESTTCCHHHHHHHHHC CS
                           cobW   4 vltGflGsGKTtLlnhlle 22 
                                    v++G  GsGK+tL+++++e
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIE 514
                                    789*************995 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                                    EEEESTTCCHHHHHHHHH CS
                           cobW   4 vltGflGsGKTtLlnhll 21 
                                    ++ G  GsGKTt l++l+
  gi|121637685|ref|YP_977908.1| 873 LILGAGGSGKTTALQTLI 890
                                    678999**********99 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.046        21      37      58 ..     496     517 ..     491     528 .. 0.84
   2 ?    5.7   0.1     0.021       9.7      34      69 ..     870     904 ..     865     920 .. 0.67
   3 ?   -0.3   0.0       1.4   6.6e+02      31      57 ..    1169    1195 ..    1164    1201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                          AAA_7  37 llvGptGtGKtviikdllkkld 58 
                                    ++ G+tG+GK++++++++++l 
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLM 517
                                    679************9998875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                          AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinf 69 
                                     +vl+ G  G+GKt+ +++l+ +    ++++ +++f
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTLICSAA-LTHTPQQVQF 904
                                    68****************9554443.3333333333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                          AAA_7   31 knkkpvllvGptGtGKtviikdllkkl 57  
                                     +++ +++++G   +G+t+++ ++++++
  gi|121637685|ref|YP_977908.1| 1169 AENSHLMVTGRRECGRTTTLATIMSEI 1195
                                     67899***************9999876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.019       8.9       4      22 ..     498     516 ..     496     582 .. 0.74
   2 ?    4.9   0.1     0.076        35       1      18 [.     872     889 ..     872     918 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                         AAA_18   4 tGtpGvGKttlakeLskrl 22 
                                    +Gt G+GK+tl + + ++l
  gi|121637685|ref|YP_977908.1| 498 SGTTGSGKSTLVRTVIESL 516
                                    7**********99886665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.076
                         AAA_18   1 IlltGtpGvGKttlakeL 18 
                                    +l+ G+ G+GKtt  + L
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTL 889
                                    799**********99988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.11        50      22      40 ..     496     514 ..     490     537 .. 0.88
   2 ?   -1.5   0.2       3.9   1.8e+03      38      62 ..     656     680 ..     650     692 .. 0.80
   3 ?    8.9   0.0    0.0025       1.2      20      60 ..     871     915 ..     855     955 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    v+ G  G+GK+t+++++ e
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIE 514
                                    789************9966 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                         AAA_30  38 lreaweaaggrviglAptgkaAkvL 62 
                                    +++++e+ g+r+++ A t+ aA++ 
  gi|121637685|ref|YP_977908.1| 656 AEKLMENMGYRLVLKARTAGAAQAA 680
                                    56788888*************9975 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0025
                         AAA_30  20 vavltGpAGtGKttalkal..reaweaaggrvi..glAptgkaAk 60 
                                     +++ G+ G+GKttal++l   +a+++  ++v    lA +++a  
  gi|121637685|ref|YP_977908.1| 871 NVLILGAGGSGKTTALQTLicSAALTHTPQQVQfyCLAYSSTALT 915
                                    57899************9977777777765554227777777655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        48       6      47 ..     496     548 ..     492     625 .. 0.70
   2 ?    6.1   0.1     0.018       8.3       3      22 ..     870     889 ..     869     902 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                         AAA_24   6 liyGpsgiGKTtlakel...........gpkplfidtekGlksldadkfpdie 47 
                                    ++ G  g+GK+tl+++            + ++++ d+ +G++   ++ +p ++
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVieslmlshppeELQFVLADLKGGSAVKPFAGVPHVS 548
                                    67799***********9555555554333333344888888766666666554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    +++li G  g+GKTt + +l
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTL 889
                                    689************99987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0087         4      51      77 ..     490     516 ..     476     529 .. 0.82
   2 ?    2.7   0.0      0.13        58      52      75 ..     868     891 ..     864     902 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0087
                         DUF815  51 lpannvLLwGarGtGKSslvkallney 77 
                                        + ++ G+ G+GKS+lv+++++++
  gi|121637685|ref|YP_977908.1| 490 GDGPHGVMSGTTGSGKSTLVRTVIESL 516
                                    555677899*************99876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                         DUF815  52 pannvLLwGarGtGKSslvkalln 75 
                                    p  nvL+ Ga G+GK + +++l+ 
  gi|121637685|ref|YP_977908.1| 868 PGANVLILGAGGSGKTTALQTLIC 891
                                    6789************99988765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.13        58      24      37 ..     497     510 ..     490     513 .. 0.87
   2 ?    6.9   0.0     0.017       7.8      22      39 ..     872     889 ..     852     913 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                         AAA_23  24 ItGpNGaGKTTild 37 
                                     +G +G+GK+T+++
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVR 510
                                    689********985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                         AAA_23  22 tlItGpNGaGKTTildAi 39 
                                    +lI G  G+GKTT l+ +
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTL 889
                                    49************9754 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.33   1.5e+02      17      31 ..     495     509 ..     483     531 .. 0.76
   2 ?    8.0   0.0    0.0049       2.3      14      45 ..     869     901 ..     861    1256 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                                    EEEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                           DEAD  17 vlvaaeTGsGKTlaf 31 
                                     ++++ TGsGK++  
  gi|121637685|ref|YP_977908.1| 495 GVMSGTTGSGKSTLV 509
                                    5899*******9874 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                                    TCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                           DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyet.kgk 45 
                                    g +vl+ ++ GsGKT+a +  ++++ +++  ++
  gi|121637685|ref|YP_977908.1| 869 GANVLILGAGGSGKTTALQTLICSAALTHtPQQ 901
                                    789**************9999997765532222 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.8      0.42   1.9e+02      38     152 ..     497     618 ..     491     628 .. 0.53
   2 ?    9.5   0.0    0.0014      0.67      24      59 ..     861     895 ..     852     908 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.42
                         AAA_25  38 laGapgtGKttlaldlalavatGkpwlg...............pvap.eqgkVlyvsaEdsedelrrRlravgealrdda 101
                                      G +g+GK+tl+  +  ++++ +p  +               p+a   ++  ++ ++E++++ ++r l a+  ++   +
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRTVIESLMLSHPPEElqfvladlkggsavkPFAGvPHVSRIITDLEEDQALMERFLDALWGEI--AR 574
                                    5677777777776555555553333222333334444444444444346677777777777755555555555555..46 PP

                         AAA_25 102 rllvldlagveslpLfakdrggtlltadvdaleaaieeveg..vrlvviDpls 152
                                    r +++d agv         ++ +  +++ ++++a+ ++++     +vviD ++
  gi|121637685|ref|YP_977908.1| 575 RKAICDSAGV---------DDAKEYNSVRARMRARGQDMAPlpMLVVVIDEFY 618
                                    7777777776.........2222234444444444444444335566677665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                         AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavat 59 
                                    w v+     g+ +l+ Ga+g+GKtt++  l ++ a+
  gi|121637685|ref|YP_977908.1| 861 WTVDTS-GPGANVLILGAGGSGKTTALQTLICSAAL 895
                                    555555.4588899****************999994 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.033        15       5      22 ..     498     515 ..     495     643 .. 0.56
   2 ?    2.8   0.0      0.26   1.2e+02       1      26 [.     871     896 ..     871     909 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                                    EESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   5 vGrpNvGKStLinaltge 22 
                                     G + +GKStL+++ +++
  gi|121637685|ref|YP_977908.1| 498 SGTTGSGKSTLVRTVIES 515
                                    59999********99974 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.26
                                    EEEEEESTTSSHHHHHHHHHTSTEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaiv 26 
                                    +v+i+G   +GK+t +++l+ ++a +
  gi|121637685|ref|YP_977908.1| 871 NVLILGAGGSGKTTALQTLICSAALT 896
                                    589****************9876544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.025        11      25      45 ..     497     516 ..     483     570 .. 0.81
   2 ?    4.0   0.0     0.053        24      23      41 ..     872     890 ..     863     913 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                                    EEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  25 lvGmgGvGKttlakqilnksd 45 
                                    ++G  G+GK+tl++ ++++  
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRTVIES-L 516
                                    68*************9987.4 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                                    EEEEESTTSSHHHHHHHHC CS
                         NB-ARC  23 valvGmgGvGKttlakqil 41 
                                    v + G gG+GKtt ++  +
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLI 890
                                    7799*********887655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.12        56       2      23 ..     499     520 ..     498     523 .. 0.90
   2 ?    5.6   0.2     0.045        21       1      23 [.     875     897 ..     875     899 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                                    E-TTSSHHHHHHHHHHHHTEEE CS
                         AAA_17   2 GgPGsGKgtqceklvekygfth 23 
                                    G  GsGK+t+++++ e + ++h
  gi|121637685|ref|YP_977908.1| 499 GTTGSGKSTLVRTVIESLMLSH 520
                                    889***********99998777 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
                                    EE-TTSSHHHHHHHHHHHHTEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfth 23 
                                    lG  GsGK+t++++l     +th
  gi|121637685|ref|YP_977908.1| 875 LGAGGSGKTTALQTLICSAALTH 897
                                    6999***********99888887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0095       4.4      20      40 ..     496     516 ..     488     522 .. 0.90
   2 ?    2.3   0.2      0.19        88      19      36 ..     872     889 ..     862     902 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0095
                     Zeta_toxin  20 llgGqpGAGKselaellkdel 40 
                                    +++G +G+GKs+l + + ++l
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESL 516
                                    79*************999886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                     Zeta_toxin  19 illgGqpGAGKselaell 36 
                                    +l+ G+ G+GK+++++ l
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTL 889
                                    78889********99876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0076       3.5       3      24 ..     496     517 ..     494     520 .. 0.89
   2 ?    2.0   0.1      0.37   1.7e+02       2      21 ..     872     891 ..     871     901 .. 0.86
   3 ?    1.1   0.0      0.69   3.2e+02       1      23 [.    1173    1195 ..    1173    1199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0076
                                    EEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                    +++G  G+GK+Tlv+ v+e l 
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLM 517
                                    578****************985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.37
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    v+i G  G+GKtT ++ +++
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTLIC 891
                                    7899**********998876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.69
                                     EEEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1    1 kvfiTGppGvGKtTlvkkvlell 23  
                                     ++++TG+   G tT +  +++++
  gi|121637685|ref|YP_977908.1| 1173 HLMVTGRRECGRTTTLATIMSEI 1195
                                     689*************9998876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.2        90       9      29 ..     497     517 ..     495     529 .. 0.84
   2 ?    5.5   0.0      0.02         9       5      32 ..     870     897 ..     866     912 .. 0.83
   3 ?   -0.7   0.1       1.5   6.9e+02       6      26 ..    1173    1193 ..    1171    1196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.2
                                    EEEBTTSSCCCCCCTTSSSS- CS
                         Septin   9 vvGesglGkttlintlfetdl 29 
                                    + G+ g Gk+tl++t++e+ +
  gi|121637685|ref|YP_977908.1| 497 MSGTTGSGKSTLVRTVIESLM 517
                                    5799***********998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                                    EEEEEEEBTTSSCCCCCCTTSSSS---- CS
                         Septin   5 ftlmvvGesglGkttlintlfetdliee 32 
                                     ++++ G+ g Gktt ++tl+ +   ++
  gi|121637685|ref|YP_977908.1| 870 ANVLILGAGGSGKTTALQTLICSAALTH 897
                                    599*****************88776655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                                     EEEEEEBTTSSCCCCCCTTSS CS
                         Septin    6 tlmvvGesglGkttlintlfe 26  
                                      lmv G+   G+tt + t+++
  gi|121637685|ref|YP_977908.1| 1173 HLMVTGRRECGRTTTLATIMS 1193
                                     59************9999876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.012       5.7      23      45 ..     496     518 ..     480     525 .. 0.87
   2 ?    1.4   0.1      0.64   2.9e+02      21      43 ..     871     893 ..     861     903 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                                    EEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  23 lLeGdLGaGKTtlvrglakalgv 45 
                                    +++G  G+GK+tlvr ++++l +
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRTVIESLML 518
                                    689***************99865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.64
                                    EEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakal 43 
                                     +l+ G  G+GKTt  + l+ + 
  gi|121637685|ref|YP_977908.1| 871 NVLILGAGGSGKTTALQTLICSA 893
                                    57888999******999988654 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.6    0.0016      0.73      20      93 ..      35      90 ..      20      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                           Yip1 20 rapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhliakllgg 93
                                   + ++l+++ +++++ll g +a+                  + + g+ ++g +g++++l+ + +++  + + +gg
  gi|121637685|ref|YP_977908.1| 35 KPWWLIVVGVVVVGLLGGMVAM------------------VFASGSHVFGGIGSIFPLFMMVGIMMMMFRGMGG 90
                                   5699999999999999999999..................6777777888888888999999999999999995 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       9.1   4.2e+03     109     155 ..     380     430 ..     360     435 .. 0.57
   2 ?    5.0   0.1     0.057        26       3      18 ..     496     511 ..     495     539 .. 0.87
   3 ?    6.3   0.3     0.023        10       2      19 ..     872     889 ..     871     902 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.1
                         AAA_28 109 ydlvfllppapei..dddgeRredleereaiderlre.....alrelgipviiv 155
                                     d + + +  +++   +d++   + +e+e+++++l +     a++e+g +v+ +
  gi|121637685|ref|YP_977908.1| 380 RDTWMVIDDKAWFfaLTDQV---SIAEAEEFAQKLAQwrlaeAYEEIGQRVAHI 430
                                    55566666655553334444...4444444444433322222888888777766 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.057
                         AAA_28   3 vitGgestGKTtllea 18 
                                    v++G+ ++GK+tl++ 
  gi|121637685|ref|YP_977908.1| 496 VMSGTTGSGKSTLVRT 511
                                    789**********986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.023
                         AAA_28   2 ivitGgestGKTtlleaL 19 
                                    + i+G+ ++GKTt l+ L
  gi|121637685|ref|YP_977908.1| 872 VLILGAGGSGKTTALQTL 889
                                    89************9987 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.014       6.5      23      59 ..     494     534 ..     485     555 .. 0.79
   2 ?    2.0   0.5      0.14        62      25      42 ..     873     890 ..     861     899 .. 0.89
   3 ?   -3.2   0.0         5   2.3e+03     274     328 ..     998    1050 ..     993    1058 .. 0.83
   4 ?   -1.7   0.0       1.7     8e+02      20      43 ..    1170    1193 ..    1160    1198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                         DUF853  23 hGliaGatGtGktvtLqvlaeslsea....GvpvfladvkG 59 
                                    hG+++G tG Gk   ++++ esl           +lad+kG
  gi|121637685|ref|YP_977908.1| 494 HGVMSGTTGSGKSTLVRTVIESLMLShppeELQFVLADLKG 534
                                    ********************998544111145566777777 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                         DUF853  25 liaGatGtGktvtLqvla 42 
                                    li Ga G Gkt +Lq+l 
  gi|121637685|ref|YP_977908.1| 873 LILGAGGSGKTTALQTLI 890
                                    899************995 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5
                         DUF853  274 pkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkd 328 
                                      ++l+e+v+ ++    s Gv v   +   ++l   v + +G+r+   l a   +d
  gi|121637685|ref|YP_977908.1|  998 NEVLIEQVNVIINQGPSFGVHVVVTADRESELRPPVRSGFGSRIELRLAA--VED 1050
                                     67999********99********9999****************9855554..444 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.7
                         DUF853   20 anrhGliaGatGtGktvtLqvlae 43  
                                      n h +++G    G+t tL ++  
  gi|121637685|ref|YP_977908.1| 1170 ENSHLMVTGRRECGRTTTLATIMS 1193
                                     699***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 1.01u 0.32s 00:00:01.33 Elapsed: 00:00:00.49
# Mc/sec: 8607.52
//
Query:       gi|121637686|ref|YP_977909.1|  [L=393]
Description: cytochrome P450 143 cyp143 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-19   69.8   0.0    2.4e-09   36.5   0.0    3.1  2  p450       Cytochrome P450
  ------ inclusion threshold ------
        3.1    8.0   8.7       0.35   11.1   0.2    3.1  4  TetR_C_31  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   2.7e-13   2.4e-09     244     373 ..     206     313 ..     174     315 .. 0.83
   2 !   24.8   0.0   9.3e-10   8.3e-06     398     459 ..     328     390 ..     320     393 .] 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.7e-13
                                    HHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HH CS
                           p450 244 alllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpy 323
                                    +l + +   +  + ls+ e+      l++aG dT ++++ + L+eLa++P++ ++lr + ++                  
  gi|121637686|ref|YP_977909.1| 206 VLSQVQ-IGE--DPLSEIEVLGLSHLLILAGLDTVTAAVGFSLLELARRPQLRAMLRDNPKQ------------------ 264
                                    333332.333..369*******************************************9444.................. PP

                                    HHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT- CS
                           p450 324 ldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrd 373
                                     + +i+E+ Rl p +p   pR++t++v+++g ++p+G+ v +++ a++rd
  gi|121637686|ref|YP_977909.1| 265 IRVFIEEIVRLEPSAP-VAPRVTTEPVTVGGMTLPAGSPVRLCMAAVNRD 313
                                    4567************.*******************************98 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 9.3e-10
                                    SCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHE.EEEESTSTSGGEEESSCSSEEESSSS CS
                           p450 398 ksfaflPFGaGpRnCiGerlArmelklflatlLqnF.evelqpetdpppileksglllppkpi 459
                                    k +++ +FG Gp+ C+G +lAr+el l+++  L +  ++el p+ +p+ +++ ++++l++ p+
  gi|121637686|ref|YP_977909.1| 328 KVHRHWGFGGGPHRCLGSHLARLELTLLVGEWLNQIpDFELAPDYAPEIRFPSKSFALKNLPL 390
                                    567899************************999764356666788888888887888888776 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       1.5   1.4e+04      26      38 ..      51      63 ..      49      65 .. 0.57
   2 ?    1.3   0.2     0.044     4e+02      31      68 ..     167     205 ..     146     212 .. 0.63
   3 ?   11.1   0.2   3.9e-05      0.35      31      60 ..     245     274 ..     229     290 .. 0.85
   4 ?   -2.9   0.1       0.9     8e+03      24      32 ..     346     354 ..     344     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHCCSC CS
                      TetR_C_31 26 AryelfleaarrP 38
                                    r e  l+a r+P
  gi|121637686|ref|YP_977909.1| 51 TRREDVLAALRNP 63
                                   4555556666666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                                    HHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCS.S-HH CS
                      TetR_C_31  31 fleaarrPeLraalarlrralrealaallaalGl.pdpe 68 
                                     ++ + rP   +a  ++ r+l+e l+a++a+  + p+p+
  gi|121637686|ref|YP_977909.1| 167 VIAMSDRPHPTEADVAAARELLEYLTAMVAERRRnPGPD 205
                                    445555555555556666777777777777666666665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 3.9e-05
                                    HHHHCCSCHHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_31  31 fleaarrPeLraalarlrralrealaalla 60 
                                    +le arrP+Lra l++   ++r  ++++++
  gi|121637686|ref|YP_977909.1| 245 LLELARRPQLRAMLRDNPKQIRVFIEEIVR 274
                                    69**************99999888888776 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.9
                                    HHHHHHHHH CS
                      TetR_C_31  24 tlAryelfl 32 
                                    +lAr+el l
  gi|121637686|ref|YP_977909.1| 346 HLARLELTL 354
                                    89****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 2146.92
//
Query:       gi|121637687|ref|YP_977910.1|  [L=67]
Description: ferredoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-12   47.9   0.1    1.9e-12   47.7   0.1    1.1  1  Fer4_15   4Fe-4S single cluster domain
    3.2e-09   37.2   0.1    4.1e-09   36.8   0.1    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.033   14.3   0.0    1.2  1  Fer4_19   Divergent 4Fe-4S mono-cluster
       0.22   11.7   2.3         10    6.4   0.1    2.4  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   4.3e-16   1.9e-12       1      65 [.       3      60 ..       3      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 4.3e-16
                        Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65
                                   V++D ++C g+++C+a++p++f +d+ g + +l+      e+ev +++++ +++ ++aCP+ A++
  gi|121637687|ref|YP_977910.1|  3 VRLDPSRCVGHAQCYAVDPDLFPIDDSGNS-ILA------EHEVRPEDMQLTRDGVAACPEMALI 60
                                   899**********************99998.774......79********************986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   9.2e-13   4.1e-09       2      55 ..       6      58 ..       5      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 9.2e-13
                        Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPves 55
                                   D ++C+++++C+++ Pd+F +dd  g s+ ae+++ +e+ ++ ++ ++aCP  +
  gi|121637687|ref|YP_977910.1|  6 DPSRCVGHAQCYAVDPDLFPIDDS-GNSILAEHEVRPEDMQLTRDGVAACPEMA 58
                                   7899*******************8.679999********************865 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.4e-06     0.033       7      59 ..       2      59 ..       1      64 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                        Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrk.pwi....kpdeasteeiievverCPSGAL 59
                                   ++  +++ C + ++C   +p++F  ++    i    + + ++ +  +  v+ CP  AL
  gi|121637687|ref|YP_977910.1|  2 KVRLDPSRCVGHAQCYAVDPDLFPIDDSgNSIlaehEVRPEDMQLTRDGVAACPEMAL 59
                                   788899*****************99998434446555566677888999999997766 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0022        10       4      13 ..       5      17 ..       2      19 .. 0.69
   2 ?    5.1   0.2    0.0056        25      16      24 .]      51      59 ..      51      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                         Fer4_6  4 idpdkCi...gCg 13
                                    dp++C+   +C+
  gi|121637687|ref|YP_977910.1|  5 LDPSRCVghaQCY 17
                                   59*****444476 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0056
                         Fer4_6 16 vrvCPegai 24
                                   v++CPe a+
  gi|121637687|ref|YP_977910.1| 51 VAACPEMAL 59
                                   78****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 463.76
//
Query:       gi|121637688|ref|YP_977911.1|  [L=364]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-62  208.2  28.4      7e-62  208.2  28.4    2.2  3  PPE       PPE family
    1.5e-17   64.3   3.9    1.5e-17   64.3   3.9    4.3  5  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2  28.4   7.8e-66     7e-62       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -2.8   0.6      0.67     6e+03      15      38 ..     177     200 ..     174     204 .. 0.64
   3 ?   -1.3   0.0      0.23   2.1e+03     100     127 ..     269     296 ..     264     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 7.8e-66
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+ns ++y Gpgsgp+laAaaaWdg+a el  aa+ ++sv+ael+++ W G++s +m+aaa+py+aWLs+aaa+ae
  gi|121637688|ref|YP_977911.1|   5 ALPPEINSGRMYCGPGSGPMLAAAAAWDGVAVELGLAATGYASVIAELTGAPWVGAASLSMVAAATPYVAWLSQAAARAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a++qa+aaaaaYeaA+ ++vpp++i+anr  +++l+atnffGqn++aIa++ea+y+emwaqda am++Y+aasa+a
  gi|121637688|ref|YP_977911.1|  85 QAGMQAAAAAAAYEAAFVMTVPPPVITANRVLVMTLIATNFFGQNSAAIAVAEAQYAEMWAQDAVAMYGYAAASASA 161
                                    *************************************************************************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.67
                                    --SHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  15 pgsgpllaAaaaWdgLaaelasaa 38 
                                    +g    +aA aa  gL + l+saa
  gi|121637688|ref|YP_977911.1| 177 AGVVAQVAAVAAMPGLLQRLSSAA 200
                                    555566666666666666666666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.23
                                    S--HHHHHHHHHHHHHHHHT-TTSTTHH CS
                            PPE 100 mvppaeiaanraelaalvatnffGqntp 127
                                    +++ a + a ra  a+l+ +n +G+ ++
  gi|121637688|ref|YP_977911.1| 269 TPQFAGLGASRAVSASLARANKIGALSV 296
                                    7788888999999999999999998765 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5      0.65   5.8e+03      40      54 ..      26      42 ..      15      57 .. 0.51
   2 ?   -4.4  16.2         2   1.8e+04      17      61 ..      55     100 ..      40     119 .. 0.54
   3 ?   -3.8   9.0         2   1.8e+04      25      58 ..     157     190 ..     128     204 .. 0.54
   4 ?   -3.3   0.2         2   1.8e+04      44      48 ..     259     263 ..     238     279 .. 0.54
   5 !   64.3   3.9   1.6e-21   1.5e-17       1      80 []     282     360 ..     282     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.65
                       PE_PPE_C 40 aaaaaagaalg..gmPl 54
                                   aaaaa+++++   g+++
  gi|121637688|ref|YP_977911.1| 26 AAAAAWDGVAVelGLAA 42
                                   33333332222333333 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2
                       PE_PPE_C  17 psWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagagg 61 
                                    + W +aa+  + aaa+   ++  +aaa a +a+++++++aaa +++
  gi|121637688|ref|YP_977911.1|  55 APWVGAASLSMVAAATPyVAWLSQAAARAEQAGMQAAAAAAAYEAA 100
                                    4587777655555555525665555555555555444444444443 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2
                       PE_PPE_C  25 aasaaaaal.sgttaaaaaaaagaalggmPlaaag 58 
                                    a ++a++ l + ++++ +++ ag++++ +++aa++
  gi|121637688|ref|YP_977911.1| 157 ASASASR-LiPFAAPPKTTNSAGVVAQVAAVAAMP 190
                                    2222222.244444444444444444433333333 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2
                       PE_PPE_C  44 aagaa 48 
                                    +ag++
  gi|121637688|ref|YP_977911.1| 259 TAGSG 263
                                    22222 PP

  == domain 5  score: 64.3 bits;  conditional E-value: 1.6e-21
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmprp 80 
                                    sA+l++A+++GaLSVPpsW  +++ +++ a a+s+ +++ ++++++++l g+Pl++  ++++ g+ a+rygfr++v++rp
  gi|121637688|ref|YP_977911.1| 282 SASLARANKIGALSVPPSWVKTTALTEPGAHAVSANPTVGSSHGPHGLLRGLPLGSRITRRS-GAFAHRYGFRHSVVARP 360
                                    8************************************************************9.****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2937.96
//
Query:       gi|121637689|ref|YP_977912.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-35  118.9  21.6    1.1e-34  118.7  21.6    1.1  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7  21.6   5.9e-39   1.1e-34       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 5.9e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pealaaaa+ l+gigsal+a+naaaa ptt+v++aaaDeVSa +Aa+f+ahaq yqa+saqaaa he+fv++l+ 
  gi|121637689|ref|YP_977912.1|  1 MSFVTTQPEALAAAAGSLQGIGSALNAQNAAAATPTTGVVPAAADEVSALTAAQFAAHAQIYQAVSAQAAAIHEMFVNTLQM 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++gsYaa+Eaa
  gi|121637689|ref|YP_977912.1| 83 SSGSYAATEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 734.95
//
Query:       gi|121637690|ref|YP_977913.1|  [L=393]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-64  214.9  34.2    5.9e-64  214.9  34.2    2.0  2  PPE       PPE family
    1.5e-19   70.6  17.3    1.5e-19   70.6  17.3    5.4  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
       0.33   10.8   2.5       0.48   10.3   2.5    1.2  1  RIFIN     Rifin


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.9  34.2     1e-67   5.9e-64       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -0.5   0.2      0.19   1.1e+03      29      39 ..     185     195 ..     168     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 1e-67
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPEvns ++yaGpgs+p++aAa+aW+gLaael+saa+ +e+v+++l++e W Gp+saama+a+apy+aW+saaaaqae
  gi|121637690|ref|YP_977913.1|   5 ALPPEVNSVRMYAGPGSAPMVAAASAWNGLAAELSSAATGYETVITQLSSEGWLGPASAAMAEAVAPYVAWMSAAAAQAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA+qa+aaaaa+eaA+aa+vpp++iaanra l++l++tn+fGqnt+aIaa+ea+y emwaqd+aam+aY+ +sa+a
  gi|121637690|ref|YP_977913.1|  85 QAATQARAAAAAFEAAFAATVPPPLIAANRASLMQLISTNVFGQNTSAIAAAEAQYGEMWAQDSAAMYAYAGSSASA 161
                                    ************************************************************************99876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHH CS
                            PPE  29 gLaaelasaaa 39 
                                    ++a+   +a++
  gi|121637690|ref|YP_977913.1| 185 AVATAAGTAQS 195
                                    12222222222 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -19.0  31.3         3   1.8e+04      18      54 ..      56      93 ..       5     157 .. 0.65
   2 ?    0.7  10.2      0.17     1e+03       3      55 ..     157     207 ..     155     214 .. 0.75
   3 ?    4.6   2.7      0.01        62      34      61 ..     281     308 ..     271     311 .. 0.74
   4 !   70.6  17.3   2.6e-23   1.5e-19       1      80 []     312     389 ..     312     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: -19.0 bits;  conditional E-value: 3
                       PE_PPE_C 18 sWaaaapaasa.aaaalsgttaaaaaaaagaalggmPl 54
                                    W ++a+aa+a a+a+  ++  aaaa+a +aa ++ ++
  gi|121637690|ref|YP_977913.1| 56 GWLGPASAAMAeAVAPYVAWMSAAAAQAEQAATQARAA 93
                                   34333333333133333444333333333333332222 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                       PE_PPE_C   3 glGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPla 55 
                                    + ++A++v   S Pp+   a+p+a+ + aa+ +t+a +a+++  +++ g+P a
  gi|121637690|ref|YP_977913.1| 157 SSASASAVTPFSTPPQI--ANPTAQGTQAAAVATAAGTAQSTLTEMITGLPNA 207
                                    6788***********86..6666666666666676777777888888888865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.01
                       PE_PPE_C  34 sgttaaaaaaaagaalggmPlaaagagg 61 
                                     g++a+aa aaag a+ g+P+ +   gg
  gi|121637690|ref|YP_977913.1| 281 IGSAAPAAVAAAGDAAKGLPGLGGMLGG 308
                                    57888999999999999***96554444 PP

  == domain 4  score: 70.6 bits;  conditional E-value: 2.6e-23
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapa.asaaaaalsgttaa.aaaaaagaalggmPlaaagaggaaggaaprygfrptvmp 78 
                                    +AglG+Aa+vG+LSVPp W+++ p  +++ aa+l+ +t++ a +aa+g++lgg+Pla+ag++ga    +prygfrptvm+
  gi|121637690|ref|YP_977913.1| 312 AAGLGNAASVGKLSVPPVWSGPLPGsVTPGAAPLPVSTVSaAPEAAPGSLLGGLPLAGAGGAGA----GPRYGFRPTVMA 387
                                    6********************9985266788888665555055666778999****99999999....************ PP

                       PE_PPE_C  79 rp 80 
                                    rp
  gi|121637690|ref|YP_977913.1| 388 RP 389
                                    *8 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.5     8e-05      0.48     131     262 ..      72     198 ..      52     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8e-05
                          RIFIN 131 vaawkkaalaaaieaaieage.aagikaviellkkllk..lselkekkleslitatnyknvtslvkaikeeyeescllkl 207
                                    ++aw++aa+a+a +aa++a + aa+ +a+   + +++   l   ++ +l +li+++ + ++ts + a +++y e+ ++++
  gi|121637690|ref|YP_977913.1|  72 YVAWMSAAAAQAEQAATQARAaAAAFEAA---FAATVPppLIAANRASLMQLISTNVFGQNTSAIAAAEAQYGEMWAQDS 148
                                    45699999999999999944424455555...2333332233335688999999*****************987665433 PP

                          RIFIN 208 kkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaeataeae 262
                                    +++ a      + ++++as+ + +++  + ++ +a+ ++aaa a+aa +a+++++
  gi|121637690|ref|YP_977913.1| 149 AAMYAY-----AGSSASASAVTPFSTPPQIANPTAQGTQAAAVATAAGTAQSTLT 198
                                    333322.....22222222222222222222223333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 3262.21
//
Query:       gi|121637691|ref|YP_977914.1|  [L=350]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-62  209.2  28.4    6.4e-62  208.3  28.4    1.4  1  PPE       PPE family
    2.9e-17   63.3   5.2    2.9e-17   63.3   5.2    4.1  5  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.3  28.4   7.1e-66   6.4e-62       1     157 [.       5     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 7.1e-66
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+ns ++y Gpgsgp+laAaaaWdg+a el  aa+ ++sv+ael+++ W G++s +m+aaa+py+aWLs+aaa+ae
  gi|121637691|ref|YP_977914.1|   5 ALPPEINSGRMYCGPGSGPMLAAAAAWDGVAVELGLAATGYASVIAELTGAPWVGAASLSMVAAATPYVAWLSQAAARAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a++qa+aaaaaYeaA+ ++vpp++i+anr  +++l+atnffGqn++aIa++ea+y+emwaqda am++Y+aasa+a
  gi|121637691|ref|YP_977914.1|  85 QAGMQAAAAAAAYEAAFVMTVPPPVITANRVLVMTLIATNFFGQNSAAIAVAEAQYAEMWAQDAVAMYGYAAASASA 161
                                    *************************************************************************9986 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.7      0.67     6e+03      40      54 ..      26      42 ..      17      59 .. 0.49
   2 ?   -4.2  16.1         2   1.8e+04      17      61 ..      55     100 ..      40     119 .. 0.54
   3 ?   -1.0   3.7      0.38   3.4e+03      51      62 ..     153     164 ..     122     191 .. 0.46
   4 ?   -3.5   0.2         2   1.8e+04      45      49 ..     245     249 ..     229     264 .. 0.51
   5 !   63.3   5.2   3.2e-21   2.9e-17       1      79 [.     267     345 ..     267     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.67
                       PE_PPE_C 40 aaaaaagaalg..gmPl 54
                                   aaaaa+++++   g+++
  gi|121637691|ref|YP_977914.1| 26 AAAAAWDGVAVelGLAA 42
                                   33333332222333333 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2
                       PE_PPE_C  17 psWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagagg 61 
                                    + W +aa+  + aaa+   ++  +aaa a +a+++++++aaa +++
  gi|121637691|ref|YP_977914.1|  55 APWVGAASLSMVAAATPyVAWLSQAAARAEQAGMQAAAAAAAYEAA 100
                                    4587777655555555525665555555555555444444444443 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.38
                       PE_PPE_C  51 gmPlaaagagga 62 
                                    g ++a+a+a++ 
  gi|121637691|ref|YP_977914.1| 153 GYAAASASASRL 164
                                    333333332222 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2
                       PE_PPE_C  45 agaal 49 
                                    ag+++
  gi|121637691|ref|YP_977914.1| 245 AGSGG 249
                                    22222 PP

  == domain 5  score: 63.3 bits;  conditional E-value: 3.2e-21
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalg..gmPlaaagaggaaggaaprygfrptvmp 78 
                                    sA+l++A +vG+LSVPpsWa aapa +  ++a +   +  +a+  g+++   g+Pla ag++++  + a+rygfr++v++
  gi|121637691|ref|YP_977914.1| 267 SASLARAEPVGRLSVPPSWAVAAPAFAEKPEAGTPMSVIGEASSCGQGGLlrGIPLARAGRRTG--AFAHRYGFRHSVIT 344
                                    8********************************9999999999999888899****99999999..*************9 PP

                       PE_PPE_C  79 r 79 
                                    r
  gi|121637691|ref|YP_977914.1| 345 R 345
                                    9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2876.72
//
Query:       gi|121637692|ref|YP_977915.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-34  117.4  23.9    3.3e-34  117.1  23.9    1.1  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1  23.9   1.8e-38   3.3e-34       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.8e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pealaaaaa+l+gig++++a+naaaaaptt+v++aaaDeVSa +Aa+f+ahaq yq++saqaaa he+fv++l a
  gi|121637692|ref|YP_977915.1|  1 MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAAHAQMYQTVSAQAAAIHEMFVNTLVA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   ++gsYaa+Eaa
  gi|121637692|ref|YP_977915.1| 83 SSGSYAATEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 739.05
//
Query:       gi|121637693|ref|YP_977916.1|  [L=98]
Description: hypothetical protein BCG_1824 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-20   71.7   3.7    5.1e-20   71.5   3.7    1.0  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.017   15.4   0.2      0.019   15.3   0.2    1.1  1  DUF5082   Domain of unknown function (DUF5082)


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   3.7   5.7e-24   5.1e-20       2      86 .]       5      90 ..       4      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 5.7e-24
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82
                                   +++dp ++r++a rf  +a+++ede +r+ a+ +++ ++gWsG+a  +  +++++++qa++++v++L+++++ l + an++e
  gi|121637693|ref|YP_977916.1|  5 FMTDPHAMRDMAGRFEVHAQTVEDEARRMWASAQNIsGAGWSGQAEATSLDTMTQMNQAFRNIVNMLHGVRDGLVRDANNYE 86
                                   689******************************************************************************* PP

                                   HHHC CS
                         WXG100 83 daDe 86
                                   ++++
  gi|121637693|ref|YP_977916.1| 87 QQEQ 90
                                   **97 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.1e-06     0.019      49     112 ..      34      97 ..      16      98 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                        DUF5082  49 klekplnssesWkGkeennydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvld 112
                                    + + + +s + W G++e++  +   ++ ++ +++v  l  + d + ++ +++e+q + +q++l+
  gi|121637693|ref|YP_977916.1|  34 WASAQNISGAGWSGQAEATSLDTMTQMNQAFRNIVNMLHGVRDGLVRDANNYEQQEQASQQILS 97 
                                    55566677779**********************************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 791.68
//
Query:       gi|121637694|ref|YP_977917.1|  [L=94]
Description: ESAT-6 like protein 5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-14   54.2   2.5    1.5e-14   54.0   2.5    1.0  1  WXG100     Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.035   14.6   0.0      0.084   13.4   0.0    1.6  1  Nup214_FG  Nucleoporin Nup214 phenylalanine-glycine (FG) doma


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   2.5   1.6e-18   1.5e-14       2      86 .]       3      87 ..       2      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.6e-18
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83
                                   i++++ +++++ a +++qa++le+e+q++ ++v a ++ W Ga ++a+q++++++ +++q ++++ + +++++++a+n++++
  gi|121637694|ref|YP_977917.1|  3 INYQFGDVDAHGAMIRAQAASLEAEHQAIVRDVLAAGDFWGGAGSVACQEFITQLGRNFQVIYEQANAHGQKVQAAGNNMAQ 84
                                   89******************************************************************************** PP

                                   HHC CS
                         WXG100 84 aDe 86
                                   +D+
  gi|121637694|ref|YP_977917.1| 85 TDS 87
                                   *95 PP

>> Nup214_FG  Nucleoporin Nup214 phenylalanine-glycine (FG) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.4e-06     0.084      28      44 ..      37      53 ..      29      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.4e-06
                      Nup214_FG 28 psGtfsaGgGsvasqGf 44
                                   ++G f  G+Gsva+q f
  gi|121637694|ref|YP_977917.1| 37 AAGDFWGGAGSVACQEF 53
                                   79*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 737.94
//
Query:       gi|121637695|ref|YP_977918.1|  [L=300]
Description: hypothetical protein BCG_1826 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-50  171.1   7.3    3.5e-50  170.9   7.3    1.0  1  ESX-1_EspG  EspG family


Domain annotation for each model (and alignments):
>> ESX-1_EspG  EspG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   7.3     2e-54   3.5e-50       2     244 ..      14     283 ..      13     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 2e-54
                                    HHHHHHHHHHHT----CGGGCC--STSSHHHHHHHHHHHHHHHHHT.TSBETTEB-HHHHHHHHHHHS-SEEEEEEEEE. CS
                     ESX-1_EspG   2 vdeldvlwealglgelPvpLevpspgataeeraalreraaaeLaer.GLadgrrvdpeladaLrlLarpdrevdarvvr. 79 
                                    vd++++l+++l++++    L+++++++ ++++++l+e+  ++ +++ G++++++v++++a+++++La+pd+ev+a+++r 
  gi|121637695|ref|YP_977918.1|  14 VDGFWMLQALLDIRHVAPELRCRPYVS-TDSNDWLNEHPGMAVMREqGIVVNDAVNEQVAARMKVLAAPDLEVVALLSRg 92 
                                    89*************888*****9999.999*******999965555********************************* PP

                                    ................--STTCEEEEEEEEETTEEEEEEEETTEEEEEEE-T.SG..HHHHHHTTSH....--B-SS--E CS
                     ESX-1_EspG  80 ................rdlgdeelralvarrgrqavlavrdgddvtlepvrp.ds..laaalvalLp...eappgrgrsv 137
                                                    rd++d+e+r+++arrg+++v avr g+d+t+++v+  ds  +aa ++++L    +a+p+++++v
  gi|121637695|ref|YP_977918.1|  93 kllygviddenqppgsRDIPDNEFRVVLARRGQHWVSAVRVGNDITVDDVTVsDSasIAALVMDGLEsihHADPAAINAV 172
                                    ****************************************************666***********9999********** PP

                                    EEEHHHHHHHHHHHHT.....GHHHHHHHHT--CCCHHHHHHHTSSTSEEEEEEEEEEECCCECEEECESS-EEEEEETT CS
                     ESX-1_EspG 138 slpadeleeaaerara.....alaaalralgasaadaralarllasprsrvgqfivavardrggrrtradrplswfDtea 212
                                    ++p++e+ ea +  ++      ++++lr++g+saa+++al+++l++p + v++++ ++ rd++  ++ +  +ls  D + 
  gi|121637695|ref|YP_977918.1| 173 NVPMEEMLEATKSWQEsgfnvFSGGDLRRMGISAATVAALGQALSDPAAEVAVYARQY-RDDAKGPSAS--VLSLKDGSG 249
                                    ***********887779****8899***************************777777.6664545555..********* PP

                                    EE..EEEEEEEETTS--EEEEEE--HHHHHHHHH CS
                     ESX-1_EspG 213 GR..ylvspsraadgeewltvaPadparlarale 244
                                    GR  +++++++a++ge+wl+++Pa+p+ ++  ++
  gi|121637695|ref|YP_977918.1| 250 GRiaLYQQARTAGSGEAWLAICPATPQLVQVGVK 283
                                    **877899********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2614.86
//
Query:       gi|121637696|ref|YP_977919.1|  [L=503]
Description: hypothetical protein BCG_1827 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-13   48.6   0.4    2.6e-12   47.2   0.4    1.8  1  YukD            WXG100 protein secretion system (Wss), protei
  ------ inclusion threshold ------
      0.028   14.8   0.7      0.028   14.8   0.7    2.0  2  PG_isomerase_N  Phosphoglucose isomerase N-terminal domain
        8.9    5.0  18.8       0.12   11.2   4.5    2.2  2  PigN            Phosphatidylinositolglycan class N (PIG-N)


Domain annotation for each model (and alignments):
>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.4   4.4e-16   2.6e-12       4      76 .]      23     103 ..      20     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 4.4e-16
                                    EEEE.-TTTEEEEEEETTSBTTHHHHHHHHHS-..........--S---TT-EEEEGGGEEEETTSBCGGGT--TT-EEE CS
                           YukD   4 Vtvl.agnrrvDlaLPadvpvaellpalvrllg.......epddeagrpggwsLarvggapLsgdrtLaeagVrDGdlLv 75 
                                    V v  +++ ++ + L a+ pv+ + + l+++++       e+  ea+++g+w+L+ v+gapL  +++L+e++V+DGd+L+
  gi|121637696|ref|YP_977919.1|  23 VGVMaGEGVQIGVLLDANAPVSVMTDPLLKVVNsrlrelgEAPLEATGRGRWALCLVDGAPLRATQSLTEQDVYDGDRLW 102
                                    566635566*******************************99999**********************************8 PP

                                    E CS
                           YukD  76 L 76 
                                    +
  gi|121637696|ref|YP_977919.1| 103 I 103
                                    6 PP

>> PG_isomerase_N  Phosphoglucose isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2         3   1.8e+04      79      91 ..      13      25 ..       3      36 .. 0.45
   2 ?   14.8   0.7   4.7e-06     0.028      10      70 ..     215     275 ..     208     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3
                                   EEEESSTT-SEE- CS
                 PG_isomerase_N 79 vRvGfrdevdvlv 91
                                     v ++++v v v
  gi|121637696|ref|YP_977919.1| 13 EGVASPQAVVVGV 25
                                   3333333333322 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.7e-06
                                    T-S---SS---SSEEEEEECCCHHHHHHH-S-.....-SSSEEEEEEESS-TTCHCCCHHH CS
                 PG_isomerase_N  10 gsyagpteaedgPygvvGvGegtlaaeLaetlvaaelteeGtqFvlesaddlgaAadaael 70 
                                     + a+p  +  +P +v+G+G  t+aa La  ++ ++l+   t  ++++ + l+a a ++++
  gi|121637696|ref|YP_977919.1| 215 AAAAAPPGPVGSPQAVLGFGVLTVAAALALRFTGRRLGIYTTIVIIDALTMLAALARMVAA 275
                                    56788999999*****************************999999988777766655544 PP

>> PigN  Phosphatidylinositolglycan class N (PIG-N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   6.3     0.064   3.8e+02     159     286 ..     159     307 ..     101     315 .. 0.50
   2 ?   11.2   4.5     2e-05      0.12     139     262 ..     355     478 ..     345     493 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.064
                           PigN 159 gtsflkknslls..llWllsclllsvFpll.pvektenltlvvlggllilliglllllksl...............skks 220
                                    g+ ++ +n+ l+  ++ ++ +l+l+v +ll    kt+  + v   +l+++++++++ +                      
  gi|121637696|ref|YP_977919.1| 159 GWWRWHHNTWLTtiYTAVIGVLVLAVAMLLlMRAKTDADRRVADIMLMSAIMPVTVAA--AaappgpvgspqavlgF--- 233
                                    3333444443330033344556666666664444444333333333333444444411..11233333322222321... PP

                           PigN 221 vsrallvqvllvvlsl...........lvtrssvsslqakqglpllnqvasWiilvlslv.l...pllksskp...lsRl 282
                                            vl v+++l           ++t  +   l     l  ++ + s ++l++sl+ +    ++         +Rl
  gi|121637696|ref|YP_977919.1| 234 -------GVLTVAAALalrftgrrlgiYTTIVIIDALTMLAALARMVAATSAVTLLSSLLlIcvvAYHA---ApalSRRL 303
                                    .......22222222222333333333677777777777777777777777777777777332222222...13446666 PP

                           PigN 283 lsif 286
                                    + i 
  gi|121637696|ref|YP_977919.1| 304 AGIR 307
                                    6655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2e-05
                           PigN 139 fhreilsvlfvllalwpllygtsflkknsllsllWllsclllsvFpll.pvektenltlvvlggllilliglllllksls 217
                                      r++ls l++ l+++ +++ ts++  ++ + +l l++  ++s F+ll    +++  + ++l+g ++++++++++ +   
  gi|121637696|ref|YP_977919.1| 355 RARSFLSGLLTGLGVMVVVCMTSLCDPHTGQRWLPLILAGFTSGFLLLrGRSYVDRWQSITLAGTAVIIAAAVCV-RYA- 432
                                    6799**********9999*99****************************99****99999999988888888873.221. PP

                           PigN 218 kksvsrall...vqvllvvlsllvtrssvsslqakqglpllnqvasWi 262
                                      + s+ l    v ++lv+l  ++  + ++++ +    pl+ + + Wi
  gi|121637696|ref|YP_977919.1| 433 -LELSSPLAvsiVAAILVLL-PAAGMAAAAHVPHTIYSPLFRKFVEWI 478
                                    .1122222201223333333.222223333333555566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3453.38
//
Query:       gi|121637697|ref|YP_977920.1|  [L=585]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-24   86.2   4.2    6.3e-20   71.6   0.1    2.9  2  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.4   1.6e-06     0.029       1      78 [.     100     154 ..     100     159 .. 0.70
   2 !   71.6   0.1   3.5e-24   6.3e-20      81     298 .]     268     513 ..     259     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-06
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEET..T-SS-TT-SC-SSS....HHHHHHHHHH-B..S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngad..settstnwarddngnsieHGthvAGiaaanape 78 
                                    g+gv+vav+DtGv + hp+l                    + g+d  +  ++  +++d       HGt vA+++aa  p 
  gi|121637697|ref|YP_977920.1| 100 GDGVKVAVIDTGV-TPHPRLPRL-----------------IPGGDyvMAGGDGLSDCDA------HGTLVASMIAAV-PA 154
                                    79***********.559998832.................4444400444555555555......**********98.44 PP

  == domain 2  score: 71.6 bits;  conditional E-value: 3.5e-24
                                    SSB-SSTTSEEE............EEE-SSTTSB-HH.....HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH CS
                                    xxxxxxxxxxxx............xxxxxxxxxxxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  81 ekngvapgakil............svkvldtsggsmet..g.teliraieeaaedkvdvinmslgestslpktgrsieal 145
                                     ++g+apg++i+            +   +d++ +++++  + ++++rai  aa+ ++ vin+s     s  ++ +  +al
  gi|121637697|ref|YP_977920.1| 268 AFSGIAPGVEIIsirqssqafglkDPYTGDEDPQTAQKidNvETMARAIVHAANMGASVINISDVMCMSARNVID-QRAL 346
                                    567788888888666666666555444445444444432146788888999999999999999884444444443.3445 PP

                                    ..HHHHHH.CCT-EEEEE--SS-T-HH...............EEE-TTCEECTTTST.TCEEEEEESTTSS.B-TT--B- CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxx RF
                   Peptidase_S8 146 ..ainravnkkgvlvviSaGNngktgs...............slqagspvgtpstsk.nvitvgayttegk.iapfSsrG 206
                                      a+ +a  +k+ ++v++aG  +k++                  +a  +v tps +   v+tvga++ +g+ ++  S  G
  gi|121637697|ref|YP_977920.1| 347 gaAVHYAAVDKDAVIVAAAGDGSKKDCkqnpifdplqpddprAWNAVTTVVTPSWFHdYVLTVGAVDANGQpLSKMSIAG 426
                                    679999999************99554477899999999999999**********99889********7776267888888 PP

                                    TT.......-EEEE-S-CCCCCCCCCHHHTTTHH........EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 207 pssdgklkpdivapGgnivstwsrqsnnsaglss........yqsmsGTSmAsPnaagaaAlllsalpkltpetvraall 278
                                    p +      +i+apG+++v   +r++       +        +    GTS++++ ++g+aAl++ ++p+l+++++   l+
  gi|121637697|ref|YP_977920.1| 427 PWV------SISAPGTDVVGLSPRDD-GLI---NaidgpdnsLLVPAGTSFSAAIVSGVAALVRAKFPELSAYQIINRLI 496
                                    865......9*******554444444.222...2344666898899********************************** PP

                                    CCS-EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 279 ntAqdlgkadniesfaqGaG 298
                                    +tA++   + +++++++G+G
  gi|121637697|ref|YP_977920.1| 497 HTARP---PARGVDNQVGYG 513
                                    ***65...5789******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4222.22
//
Query:       gi|121637698|ref|YP_977921.1|  [L=406]
Description: hypothetical protein BCG_1829 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-23   82.6   2.5    1.9e-23   82.6   2.5    1.8  2  EccE      Putative type VII ESX secretion system translocon, 
     0.0082   16.5   0.2      0.022   15.1   0.2    1.6  1  ORF_12_N  ORF 12 gene product N-terminal


Domain annotation for each model (and alignments):
>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   2.5   2.1e-27   1.9e-23       2      99 .]     201     292 ..     200     292 .. 0.98
   2 ?   -2.7   0.1      0.88   7.9e+03       6      24 ..     315     333 ..     312     361 .. 0.65

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.1e-27
                           EccE   2 aaqRttWlalrldpeenvaalsaRgggtegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaapadvr 81 
                                    a +R+tWl+lr++p++nvaa++ R    +++a +++aa++Rl++ L++q ++ar+++a+el++++ a+++ l+++++  r
  gi|121637698|ref|YP_977921.1| 201 ADRRRTWLVLRMNPQRNVAAVACR----DSLASTLVAATERLVQDLDGQSCAARPVTADELTEVDSAVLADLEPTWS--R 274
                                    679*********************....*************************************************..* PP

                           EccE  82 eewrtirtrdgylttYav 99 
                                      wr++++ +gy t+++v
  gi|121637698|ref|YP_977921.1| 275 PGWRHLKHFNGYATSFWV 292
                                    *****************7 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.88
                           EccE   6 ttWlalrldpeenvaalsa 24 
                                    tt +++rl  +    alsa
  gi|121637698|ref|YP_977921.1| 315 TTVVTVRLTTRVGSPALSA 333
                                    5677777776655555554 PP

>> ORF_12_N  ORF 12 gene product N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.5e-06     0.022       3      76 ..     198     270 ..     197     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-06
                       ORF_12_N   3 dtpaGeqarWvldalnsdapiaaeevaerfsaeflaevpaeelaevla.qlraagPftvtsyegvesaavvtles 76 
                                    +t a ++  W++  +n + ++aa   ++ ++ +++a+   e+l++ l+ q  aa+P t+ ++++v+sa+++ le 
  gi|121637698|ref|YP_977921.1| 198 RTVADRRRTWLVLRMNPQRNVAAVACRDSLASTLVAA--TERLVQDLDgQSCAARPVTADELTEVDSAVLADLEP 270
                                    68899999*****************************..9999999999********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3073.05
//
Query:       gi|121637699|ref|YP_977922.1|  [L=610]
Description: hypothetical protein BCG_1830 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-17   62.2   0.0    1.3e-16   61.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.8e-12   45.9   0.2    1.6e-11   44.2   0.2    2.0  1  AAA_lid_6        AAA lid domain
    6.9e-07   29.8  12.2    0.00094   19.8   0.8    4.4  3  TPR_16           Tetratricopeptide repeat
    6.3e-06   26.2   0.0    1.5e-05   25.0   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-05   24.5   3.2     0.0051   17.1   0.3    3.4  2  TPR_12           Tetratricopeptide repeat
    7.7e-05   23.1   0.0    0.00037   20.9   0.0    2.2  1  AAA_16           AAA ATPase domain
    0.00015   21.6   7.0       0.13   12.5   0.0    5.4  4  TPR_2            Tetratricopeptide repeat
    0.00058   20.1   0.1     0.0024   18.1   0.1    2.1  1  AAA_22           AAA domain
    0.00095   19.6   3.8        3.1    8.4   0.4    4.1  3  TPR_19           Tetratricopeptide repeat
     0.0032   16.9   0.0     0.0062   16.0   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0059   16.3   0.2        1.1    8.9   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0065   16.6   0.1       0.02   15.1   0.0    1.9  1  AAA_33           AAA domain
     0.0075   16.1   0.0      0.013   15.2   0.0    1.3  1  AAA_11           AAA domain
     0.0082   16.3   0.0      0.018   15.1   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.018   14.5   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.012   15.4   0.1      0.029   14.1   0.1    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.015   15.9   0.0      0.039   14.5   0.0    1.8  1  AAA_18           AAA domain
      0.019   15.1   0.0       0.07   13.2   0.0    1.8  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.022   15.1   0.4      0.065   13.6   0.4    1.8  1  AAA_19           AAA domain
      0.024   15.2   2.7      0.087   13.5   0.0    3.3  2  TPR_6            Tetratricopeptide repeat
      0.025   14.3   0.0      0.061   13.1   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.034   14.8   0.2        9.9    6.9   0.1    2.8  2  Methyltransf_11  Methyltransferase domain
      0.052   13.4   0.0          4    7.4   0.0    3.6  4  TPR_1            Tetratricopeptide repeat
      0.052   13.3   0.0      0.099   12.3   0.0    1.5  1  AAA_24           AAA domain
      0.058   13.4   1.3       0.16   12.0   1.3    1.8  1  TPR_3            Tetratricopeptide repeat
      0.062   13.3   0.1        6.5    6.7   0.1    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.072   12.2   0.0       0.15   11.2   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.099   12.9   0.3        1.8    9.0   0.0    3.2  2  TPR_8            Tetratricopeptide repeat
       0.13   11.2   0.0       0.26   10.1   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.17   11.0   0.1       0.31   10.2   0.1    1.3  1  TIP49            TIP49 P-loop domain
       0.21   11.8   4.0       0.25   11.6   0.1    2.9  3  AAA_28           AAA domain
       0.84    9.6   7.1         14    5.7   0.1    3.7  3  TPR_10           Tetratricopeptide repeat
        8.6    7.5  20.2        5.8    8.0   0.1    5.6  5  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   2.3e-19   1.3e-16       2     130 ..     354     486 ..     353     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.3e-19
                                    EEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA   2 llyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                    ll GppGtGKT++a+a  k+l       +  ++e+s ++ll  y+ ++ek+++e+++ a   a    +f+DE++ l+++ 
  gi|121637699|ref|YP_977922.1| 354 LLLGPPGTGKTSVARAFTKQLcgltvlrKPLVVETSRTKLLGRYMADAEKNTEEMLEGALGGA----VFFDEMHTLHEKG 429
                                    89******************865555544558************************9986555....************* PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                            AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnr.....pdkldpallrgRfdrkiei 130
                                     ++ +  ++ ++n+Ll  +++ ++   +++v ga++      + ++++ l+ +Rf+ +ie+
  gi|121637699|ref|YP_977922.1| 430 YSQGDPYGNAIINTLLLYMENHRD---ELVVFGAGYAkamekMLEVNQGLR-RRFSTVIEF 486
                                    999*********************...599999998877433333444455.799988876 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.2     3e-14   1.6e-11      15      62 .]     538     596 ..     512     596 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3e-14
                      AAA_lid_6  15 rrdenfGNARfVRnllekairrqadRlatt........ddseltredlmt...LtaeDi 62 
                                    r ++ +GNA+fVRn++eka+++++ Rl+++        d +e ++++l +   Lt+eD+
  gi|121637699|ref|YP_977922.1| 538 RGIDLLGNAGFVRNVVEKARDHRSFRLDDEdldavlasDLTEFSEDQLRRfkeLTREDL 596
                                    56777*******************************************99999*****7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.057        31      11      43 ..      33      62 ..      31      79 .. 0.77
   2 !    8.7   1.7     0.005       2.7       6      50 ..     121     163 ..     116     173 .. 0.60
   3 !   19.8   0.8   1.7e-06   0.00094       6      62 ..     192     248 ..     186     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.057
                         TPR_16 11 gdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                    +++ Aa ++++a+++d   P   +A+l++ +a
  gi|121637699|ref|YP_977922.1| 33 HNPQVAAQMFTTATRLD---PKMCDAWLARLLA 62
                                   5899*************...8866666665544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.005
                         TPR_16   6 aalragdyddAaaaleaalkrdpssPdaae.Allllgdaalrqgrl 50 
                                     +++a++y++Aa++l+a+  r+   P++ae  ++ +g++++r +r+
  gi|121637699|ref|YP_977922.1| 121 VLAEAKRYQEAAELLDATDPRH---PFDAElVSYVRGVLYFRTKRW 163
                                    4566666666666665554444...654431466666666666665 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.7e-06
                         TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                    a++ +g +++A +++++a++ d+++ +a  Al+  g ++ + gr +eA++l+r+ + 
  gi|121637699|ref|YP_977922.1| 192 ALASLGVFEEAFRRAQEAIEGDRVPGAANIALYTQGMCLRHVGREEEAVELLRRVYS 248
                                    555666699*********************************************984 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.8e-08   1.5e-05       1      78 [.     352     426 ..     352     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.8e-08
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                    + lL+GppGtgK+++a+ + + l + +v+ + l   t++++l+gr+     +++    ++  ++  g  +++DE ++++
  gi|121637699|ref|YP_977922.1| 352 HTLLLGPPGTGKTSVARAFTKQLcGLTVLRKPLVVETSRTKLLGRYMA---DAEKNTEEML-EGALGGAVFFDEMHTLH 426
                                    679********************9**********************96...4444444444.45556667777777665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.033        18       8      27 ..     117     136 ..     110     138 .. 0.67
   2 !   17.1   0.3   9.3e-06    0.0051      14      74 ..     194     249 ..     180     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                         TPR_12   8 nlaavlrrlgrydeAlelle 27 
                                     +aavl++++ry+eA ell+
  gi|121637699|ref|YP_977922.1| 117 AYAAVLAEAKRYQEAAELLD 136
                                    45777777777777777765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.3e-06
                         TPR_12  14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                    + lg ++eA++  ++a+e   r++G  +    ++l++ g+++r  gr eeA+ell++++ +
  gi|121637699|ref|YP_977922.1| 194 ASLGVFEEAFRRAQEAIEGD-RVPGAAN----IALYTQGMCLRHVGREEEAVELLRRVYSR 249
                                    44677777777777777777.5655444....589**********************9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.7e-07   0.00037      24      50 ..     345     376 ..     325     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.7e-07
                         AAA_16  24 p.....elvllsGesGvGKsslvrellralek 50 
                                    p     + +ll G++G+GK+s++r++ ++l++
  gi|121637699|ref|YP_977922.1| 345 PvpvtsRHTLLLGPPGTGKTSVARAFTKQLCG 376
                                    55555699********************9985 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       1.1   6.2e+02      16      33 ..      34      51 ..      32      52 .. 0.89
   2 ?    3.8   1.9      0.14        73       6      25 ..     117     136 ..     114     137 .. 0.86
   3 ?    1.2   0.0      0.92     5e+02       5      20 ..     151     166 ..     148     175 .. 0.82
   4 !   12.5   0.0   0.00023      0.13       2      29 ..     221     248 ..     220     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                          TPR_2 16 dyeeAleafekAleldPn 33
                                   +++ A++ f  A +ldP+
  gi|121637699|ref|YP_977922.1| 34 NPQVAAQMFTTATRLDPK 51
                                   778899***********6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.14
                          TPR_2   6 nlGlayyklgdyeeAleafe 25 
                                    + + +++++++y+eA+e+++
  gi|121637699|ref|YP_977922.1| 117 AYAAVLAEAKRYQEAAELLD 136
                                    578999**********9875 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.92
                          TPR_2   5 ynlGlayyklgdyeeA 20 
                                    y +G +y++ +++ + 
  gi|121637699|ref|YP_977922.1| 151 YVRGVLYFRTKRWPDV 166
                                    789*********9765 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00023
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                     aly +G+++++ g+ eeA+e+++++ +
  gi|121637699|ref|YP_977922.1| 221 IALYTQGMCLRHVGREEEAVELLRRVYS 248
                                    59**********************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.5e-06    0.0024       5      40 ..     350     377 ..     348     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.5e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                     +++++ G++GtGKT ++r +++ql+        + 
  gi|121637699|ref|YP_977922.1| 350 SRHTLLLGPPGTGKTSVARAFTKQLC--------GL 377
                                    5799********************96........33 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0       0.1        57       6      35 ..      34      61 ..      19      63 .. 0.80
   2 !    8.4   0.4    0.0057       3.1      30      60 ..     117     147 ..     111     153 .. 0.84
   3 ?    5.1   0.0     0.058        32       8      57 ..     200     252 ..     194     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                         TPR_19  6 dyaeAlalleqalqedpknaearllLAeal 35
                                   +++ A+++++ a   dpk+ +a+l  A++l
  gi|121637699|ref|YP_977922.1| 34 NPQVAAQMFTTATRLDPKMCDAWL--ARLL 61
                                   7999**************666666..4433 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0057
                         TPR_19  30 lLAeallalgqldeAealLdalpeedpddar 60 
                                    ++A +l ++++++eA +lLda  +  p da+
  gi|121637699|ref|YP_977922.1| 117 AYAAVLAEAKRYQEAAELLDATDPRHPFDAE 147
                                    58999***************99998888765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.058
                         TPR_19   8 aeAlalleqalqe..dpknaearllL..AeallalgqldeAealLdalpeedpd 57 
                                    +eA ++ ++a++    p+ a+++l +    +l   g+ +eA +lL ++   d++
  gi|121637699|ref|YP_977922.1| 200 EEAFRRAQEAIEGdrVPGAANIAL-YtqGMCLRHVGREEEAVELLRRVYSRDAK 252
                                    566666666654422566666666.24688888889999999999887666554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0062      10      50 ..     339     378 ..     334     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                   Mg_chelatase  10 eakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                    +ak  l + ++ +H ll +GppG+GKt +a+++++ l+ l+
  gi|121637699|ref|YP_977922.1| 339 RAKMGLPVPVTSRHTLL-LGPPGTGKTSVARAFTKQLCGLT 378
                                    67888888888888865.6*************999887765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.002       1.1      21      44 ..     349     372 ..     326     387 .. 0.81
   2 ?    5.1   0.1      0.03        17      80     107 ..     400     427 ..     392     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                    SSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraihe 44 
                                    t+ ++l++G  GtGK+ +ara  +
  gi|121637699|ref|YP_977922.1| 349 TSRHTLLLGPPGTGKTSVARAFTK 372
                                    55799***************9765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                                    TTSS-BEHHHHHTTTSEEEEETGGGS-H CS
                Sigma54_activat  80 GAekekkGlfekadgGtlfLDeigelpl 107
                                    +Aek+ + ++e a gG +f+De+++l  
  gi|121637699|ref|YP_977922.1| 400 DAEKNTEEMLEGALGGAVFFDEMHTLHE 427
                                    688889999***************9976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.7e-05      0.02       3      38 ..     354     390 ..     353     480 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlf 38 
                                    ll G+pG+GK+ +a+   k+l   ++l+++ + ++ +
  gi|121637699|ref|YP_977922.1| 354 LLLGPPGTGKTSVARAFTKQLCgLTVLRKPLVVETSR 390
                                    678******************9899999998655443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.013      15      42 ..     349     375 ..     340     412 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                         AAA_11  15 seseitliqGPPGtgKTktivellsqll 42 
                                    ++++ tl+ GPPGtgKT++  ++ +ql 
  gi|121637699|ref|YP_977922.1| 349 TSRH-TLLLGPPGTGKTSVARAFTKQLC 375
                                    5666.9******************9996 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-05     0.018       6     105 ..     353     450 ..     350     452 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                                    EEEE--TTSSHHHHHHHHHHHTT-......-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfv..kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpk 83 
                                     lllgp g+Gkt +a+a  + l      +k+l++   ++ l      ++ +  + + + + + + gG v++DE+   h+k
  gi|121637699|ref|YP_977922.1| 353 TLLLGPPGTGKTSVARAFTKQLCGltVLRKPLVVETSRTKLL----GRYMADAEKNTEEMLEGALGGAVFFDEMHTLHEK 428
                                    5899*********99988887753423345555555555555....8888888888888889999*************** PP

                                    ---------HHHHHHHHHHHH- CS
                          AAA_2  84 essgadvSregVqrdLLqileg 105
                                    + s+ d  ++ + + LL  +e+
  gi|121637699|ref|YP_977922.1| 429 GYSQGDPYGNAIINTLLLYMEN 450
                                    ****************987775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.4e-05     0.018      33     111 ..     350     424 ..     338     489 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnm 111
                                    ++++ll Gp GtGKt++++ ++k+l    +++l   +   ts ++l    ++  ek +++++  + g    vF D+++ 
  gi|121637699|ref|YP_977922.1| 350 SRHTLLLGPPGTGKTSVARAFTKQLC--GLTVLRKPLVVETSRTKLLGRYMADAEKNTEEMLEGALGG--AVFFDEMHT 424
                                    6899*******************998..7777777777777777777777777777777776655554..455566665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.3e-05     0.029      32      57 ..     349     374 ..     310     428 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                         RuvB_N  32 aldhvllyGpPGlGkttlakiiakel 57 
                                    +  h+ll GpPG Gkt++a+  +k+l
  gi|121637699|ref|YP_977922.1| 349 TSRHTLLLGPPGTGKTSVARAFTKQL 374
                                    457****************9988876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.3e-05     0.039       2      26 ..     354     387 ..     354     458 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.3e-05
                         AAA_18   2 lltGtpGvGKttlakeLskrl.gf........gv 26 
                                    ll G+pG+GKt++a++  k l g+        ++
  gi|121637699|ref|YP_977922.1| 354 LLLGPPGTGKTSVARAFTKQLcGLtvlrkplvVE 387
                                    589**************99986667666665544 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013      0.07      25      83 ..     354     427 ..     348     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                    EEEEETT--HHHHHHCC--TTS-EE...--SSTTHHHH-H............HHHHHHTTTSEEEEEE-TT--H CS
                Sigma54_activ_2  25 fltGekGsgkelvArlLhknsgpwl...eifvverlaklp............ldlleqakggtLylkdiadlsk 83 
                                    +l+G++G+gk++vAr++ k+ ++     ++ vve++ +               ++le a gg  ++ +++ l +
  gi|121637699|ref|YP_977922.1| 354 LLLGPPGTGKTSVARAFTKQLCGLTvlrKPLVVETSRTKLlgrymadaekntEEMLEGALGGAVFFDEMHTLHE 427
                                    799*****************998541124455544443225777777778889999999**9999999998876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   0.00012     0.065       9      41 ..     349     381 ..     345     517 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvk 41 
                                    ++++ l++++pGtGKT v ++  + l  l+ + 
  gi|121637699|ref|YP_977922.1| 349 TSRHTLLLGPPGTGKTSVARAFTKQLCGLTVLR 381
                                    67899*************999999887776553 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.9       7.9   4.3e+03      10      24 ..     122     136 ..     114     137 .. 0.68
   2 ?   13.5   0.0   0.00016     0.087       2      28 ..     222     248 ..     221     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 7.9
                                    HHHHHHHHHHHHHHH CS
                          TPR_6  10 yrklgdtdkAleale 24 
                                    + +++++++A e+l+
  gi|121637699|ref|YP_977922.1| 122 LAEAKRYQEAAELLD 136
                                    334479999999985 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                    Aly +++++r  g+ ++A+e+l+r+ +
  gi|121637699|ref|YP_977922.1| 222 ALYTQGMCLRHVGREEEAVELLRRVYS 248
                                    9**********66***********965 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.061      50      72 ..     353     375 ..     346     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                      IstB_IS21  50 ivllGpsGvGKshlaialgveav 72 
                                     +llGp+G+GK+ +a a+ ++ +
  gi|121637699|ref|YP_977922.1| 353 TLLLGPPGTGKTSVARAFTKQLC 375
                                    689****************9988 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.087        47      19      86 ..      58     127 ..      42     130 .. 0.81
   2 ?    6.9   0.1     0.018       9.9      51      86 ..     558     593 ..     540     594 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.087
                                    SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C....CHHHHHHHHHH CS
                Methyltransf_11  19 arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve....dpekalkeiaR 86 
                                    ar+++ D s e+l+ a +++++ g   e ++  +++l+f+ +  D  +++ +++ v+      +++l+e++R
  gi|121637699|ref|YP_977922.1|  58 ARLLAGDQSIEVLAGAWAAVRTFG--WETRRLGVTDLQFRPEVSDGLFLRLAITSVDslacAYAAVLAEAKR 127
                                    677888888888888888888888..678999************************6344477888888887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.018
                                    ECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHH CS
                Methyltransf_11  51 daeklpfednsfDlvvssevlhhvedpekalkeiaR 86 
                                    d +++ + d+  D+v++s   ++ ed+ + +ke+ R
  gi|121637699|ref|YP_977922.1| 558 DHRSFRLDDEDLDAVLASDLTEFSEDQLRRFKELTR 593
                                    4456789**************************988 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.8   4.2e+03      20      33 ..      38      51 ..      38      52 .. 0.87
   2 ?   -0.1   0.3       1.8   9.6e+02       9      22 ..     120     133 ..     119     136 .. 0.80
   3 ?   -0.4   0.0       2.1   1.1e+03       5      19 ..     151     165 ..     149     170 .. 0.81
   4 ?    7.4   0.0    0.0074         4       3      27 ..     222     246 ..     221     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.8
                                   HHHHHHHHHHHSTT CS
                          TPR_1 20 AleyyekALelnPn 33
                                   A + +  A +l+P+
  gi|121637699|ref|YP_977922.1| 38 AAQMFTTATRLDPK 51
                                   6788999******7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                                    HHHHHTT-HHHHHH CS
                          TPR_1   9 nayfklgkydeAle 22 
                                    +++ + ++y+eA e
  gi|121637699|ref|YP_977922.1| 120 AVLAEAKRYQEAAE 133
                                    6778899*****88 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.1
                                    HHHHHHHHHTT-HHH CS
                          TPR_1   5 ynlGnayfklgkyde 19 
                                    y +G++yf+ +++ +
  gi|121637699|ref|YP_977922.1| 151 YVRGVLYFRTKRWPD 165
                                    679*****9999866 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0074
                                    HHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                    aly  G+++++ g+ +eA+e  +++
  gi|121637699|ref|YP_977922.1| 222 ALYTQGMCLRHVGREEEAVELLRRV 246
                                    89******************99987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018     0.099       4      30 ..     352     387 ..     349     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                         AAA_24   4 kiliyGpsgiGKTtlakel.........gpkplfid 30 
                                      l+ Gp+g+GKT++a+ +           kpl++ 
  gi|121637699|ref|YP_977922.1| 352 HTLLLGPPGTGKTSVARAFtkqlcgltvLRKPLVVE 387
                                    6799**************976666666666666665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3    0.0003      0.16       6      25 ..     117     136 ..     117     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                                    HHHHHHHHTT-HHHHHHH.. CS
                          TPR_3   6 syAaefynkkkyqeArelfs 25 
                                    +yAa++   k+yqeA+el++
  gi|121637699|ref|YP_977922.1| 117 AYAAVLAEAKRYQEAAELLD 136
                                    7*****************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.012       6.5      22      56 ..     348     382 ..     292     407 .. 0.76
   2 ?    4.4   0.0     0.063        34     122     152 ..     402     432 ..     384     449 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....- CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeek 56 
                                       ++ l+  + GtGKT va +++++l      +k
  gi|121637699|ref|YP_977922.1| 348 VTSRHTLLLGPPGTGKTSVARAFTKQLCGLTVLRK 382
                                    55678999999**********99999976655555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.063
                                    .....HHHTTT-S.EEEEETGGGTTS.TTTHH CS
                         ResIII 122 eeeseellrdrfd.viiiDEaHrlgakkswre 152
                                    e+++ee+l+++    +++DE H l++ k + +
  gi|121637699|ref|YP_977922.1| 402 EKNTEEMLEGALGgAVFFDEMHTLHE-KGYSQ 432
                                    555666666655579**********9.66654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.15      51      83 ..     348     381 ..     295     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg.Lr 83 
                                     ++++ LL G  GtGK s+ +a +++++  + Lr
  gi|121637699|ref|YP_977922.1| 348 VTSRHTLLLGPPGTGKTSVARAFTKQLCGLTvLR 381
                                    35789*******************9998765444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       6.9   3.8e+03      18      31 ..     123     136 ..     117     139 .. 0.70
   2 ?    9.0   0.0    0.0034       1.8       3      33 ..     222     252 ..     222     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.9
                                    HHHHHHHHHHHHHH CS
                          TPR_8  18 eeAkeyyekaleld 31 
                                     eAk y e a  ld
  gi|121637699|ref|YP_977922.1| 123 AEAKRYQEAAELLD 136
                                    57777777776655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    a+y  g++++  g+ eeA+e ++++ + d +
  gi|121637699|ref|YP_977922.1| 222 ALYTQGMCLRHVGREEEAVELLRRVYSRDAK 252
                                    68999********************999976 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00048      0.26       5      38 ..     340     373 ..     336     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                  TrwB_AAD_bind   5 agvplpkeretqhilivGttGsGKtqalekllra 38 
                                    a++ lp+    +h+l++G  G+GKt +++++ ++
  gi|121637699|ref|YP_977922.1| 340 AKMGLPVPVTSRHTLLLGPPGTGKTSVARAFTKQ 373
                                    56667777889****************9998776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00056      0.31      25      75 ..     315     375 ..     294     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                                    XXXXXXXXXXXXXXX.....XXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  25 glvGqkkareaagvi.....velikekk.....laGravLlaGpsgtGktalaiaiskelg 75 
                                    +++G ++a++   +i     v+l ++k      ++ r  Ll Gp+gtGkt++a a +k+l 
  gi|121637699|ref|YP_977922.1| 315 AMLGMEQAKKEIKLIksttkVNLARAKMglpvpVTSRHTLLLGPPGTGKTSVARAFTKQLC 375
                                    666666666666555222223444443222222568999*****************99985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.4     3e+03     112     138 ..     267     294 ..     244     317 .. 0.60
   2 ?   11.6   0.1   0.00047      0.25       3      27 ..     354     380 ..     352     420 .. 0.71
   3 ?   -0.5   0.1       2.3   1.3e+03     110     146 ..     568     605 ..     522     608 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                         AAA_28 112 vfllppap.eidddgeRredleereaid 138
                                     +l++p+  e+++d + +++   r++++
  gi|121637699|ref|YP_977922.1| 267 LILTDPETiEARTDPWDPDSAPTRAQTE 294
                                    4555554447777777765444443332 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00047
                         AAA_28   3 vitGgestGKTtlleaLaar..gypvv 27 
                                     ++G+++tGKT++++a++++  g +v+
  gi|121637699|ref|YP_977922.1| 354 LLLGPPGTGKTSVARAFTKQlcGLTVL 380
                                    589***************988854433 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.3
                         AAA_28 110 dl.vfllppapeidddgeRredleereaiderlrealr 146
                                    dl  +l     e+++d+ Rr ++  re+++e lr+a+ 
  gi|121637699|ref|YP_977922.1| 568 DLdAVLASDLTEFSEDQLRRFKELTREDLAEGLRAAVA 605
                                    55566666667778999999999999999999888876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6     0.057        31       9      26 ..     119     136 ..     116     138 .. 0.89
   2 ?    0.5   0.1       1.1     6e+02      11      30 ..     192     211 ..     191     214 .. 0.81
   3 ?    5.7   0.1     0.027        14      12      30 ..     230     248 ..     227     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.057
                         TPR_10   9 analrqrgrydeAealle 26 
                                    a++l + +ry+eA +ll+
  gi|121637699|ref|YP_977922.1| 119 AAVLAEAKRYQEAAELLD 136
                                    8899***********986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                         TPR_10  11 alrqrgrydeAealleeala 30 
                                    al ++g ++eA + ++ea++
  gi|121637699|ref|YP_977922.1| 192 ALASLGVFEEAFRRAQEAIE 211
                                    67788889999999999986 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.027
                         TPR_10  12 lrqrgrydeAealleeala 30 
                                    lr++gr +eA++ll+++++
  gi|121637699|ref|YP_977922.1| 230 LRHVGREEEAVELLRRVYS 248
                                    7899***********9986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       1.3   6.8e+02      16      40 ..      34      61 ..      29      64 .. 0.72
   2 ?    7.1   0.8     0.022        12       6      36 ..     117     147 ..     112     153 .. 0.84
   3 ?    1.4   0.4       1.4   7.8e+02       9      29 ..     191     211 ..     183     225 .. 0.74
   4 ?    8.0   0.1     0.011       5.8       4      40 ..     223     259 ..     219     260 .. 0.83
   5 ?   -1.2   0.7       9.8   5.3e+03      19      42 ..     294     318 ..     290     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                         TPR_14 16 dpdeAiallrralalaP...ddaeawll 40
                                   +p+ A++++  a +l+P   d + a+ll
  gi|121637699|ref|YP_977922.1| 34 NPQVAAQMFTTATRLDPkmcDAWLARLL 61
                                   78889************44333444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.022
                         TPR_14   6 alaeallalGdpdeAiallrralalaPddae 36 
                                    a+a++l+++ +++eA++ll++   ++P dae
  gi|121637699|ref|YP_977922.1| 117 AYAAVLAEAKRYQEAAELLDATDPRHPFDAE 147
                                    79*****************997667776655 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.4
                         TPR_14   9 eallalGdpdeAiallrrala 29 
                                     al+ lG ++eA + +++a++
  gi|121637699|ref|YP_977922.1| 191 TALASLGVFEEAFRRAQEAIE 211
                                    578889999999999999988 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.011
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    l+  +  l++ G+ +eA++llrr+ +++ ++  a+ +
  gi|121637699|ref|YP_977922.1| 223 LYTQGMCLRHVGREEEAVELLRRVYSRDAKFTPAREA 259
                                    66667778999***************99998887766 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 9.8
                         TPR_14  19 eAiallrrala.laPddaeawllla 42 
                                    eA+++++ a + la +dae++ +l+
  gi|121637699|ref|YP_977922.1| 294 EAARHAEMAAKyLAEGDAELNAMLG 318
                                    7788888887777788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 4039.40
//
Query:       gi|121637700|ref|YP_977923.1|  [L=63]
Description: lipoprotein lppT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 491.91
//
Query:       gi|121637701|ref|YP_977924.1|  [L=655]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-77  258.0   5.0    7.1e-77  258.0   5.0    1.8  2  PE-PPE    PE-PPE domain
    1.5e-55  187.6  27.0    1.5e-55  187.6  27.0    1.8  2  PPE       PPE family


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.29   2.6e+03      46      71 ..     147     172 ..      94     208 .. 0.73
   2 !  258.0   5.0     8e-81   7.1e-77       1     226 [.     245     469 ..     245     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.29
                         PE-PPE  46 agekvvvfGySqgalvasnekarlaa 71 
                                    a ++++ +Gy  ga  +++++a+  +
  gi|121637701|ref|YP_977924.1| 147 AQDAAAMAGYYVGASAVATQLASWLQ 172
                                    66777778888888877777766544 PP

  == domain 2  score: 258.0 bits;  conditional E-value: 8e-81
                         PE-PPE   1 PgadaelvsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaapdq 80 
                                    Pg+ a+++ +P+ ++pv  +k+lt+d+Sva+G+  Le+air++ aag++v+vfGySq+a++ s  +a+laa+ +p +pd+
  gi|121637701|ref|YP_977924.1| 245 PGVIAQALVTPQGLYPVVVIKNLTFDSSVAQGAVILESAIRQQIAAGNNVTVFGYSQSATISSLVMANLAASADPPSPDE 324
                                    78999*************************************************************************** PP

                         PE-PPE  81 lsfvlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialvHt 160
                                    lsf+l+gnpn+pngg+++rfpg +  p+lg+t tgatp++  y+T++++++YDgvadfP+yplN+++++Nai+G+++vH+
  gi|121637701|ref|YP_977924.1| 325 LSFTLIGNPNNPNGGVATRFPG-ISFPSLGVTATGATPHNL-YPTKIYTIEYDGVADFPRYPLNFVSTLNAIAGTYYVHS 402
                                    *********************9.******************.************************************** PP

                         PE-PPE 161 nyetevaeqlpanirttvnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgY 226
                                    ny   ++eq +a+++ t++   ++t+yy+++te+lPLl+plrs++ v++pl+++++++L+v+v+lgY
  gi|121637701|ref|YP_977924.1| 403 NYFILTPEQIDAAVPLTNTVGPTMTQYYIVRTENLPLLEPLRSVPiVGNPLANLVQPNLKVIVNLGY 469
                                    *****************999999******************************************** PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6  27.0   1.7e-59   1.5e-55       1     157 [.       7     163 ..       7     164 .. 0.99
   2 ?   -3.3   0.1      0.98   8.8e+03      35      53 ..     555     573 ..     548     586 .. 0.55

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 1.7e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPEvnsa+++aG+gs+p+laAaaaWd La+el+ aa ++ sv+++l  + WqG++saam++aaa y+ WLs+ aa+ae
  gi|121637701|ref|YP_977924.1|   7 VLPPEVNSARVFAGAGSAPMLAAAAAWDDLASELHCAAMSFGSVTSGLVVGWWQGSASAAMVDAAASYIGWLSTSAAHAE 86 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aA  a+aa++++e+Alaa+v+pa++aanra++a+lva+n+fGqn+paIaa+e  ye mwaqdaaama+Y   ++a+
  gi|121637701|ref|YP_977924.1|  87 GAAGLARAAVSVFEEALAATVHPAMVAANRAQVASLVASNLFGQNAPAIAALESLYEWMWAQDAAAMAGYYVGASAV 163
                                    **********************************************************************9999987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.98
                                    HHHHHHHHHHHTTTT.TTS CS
                            PPE  35 asaaaelesvlaelaaeaW 53 
                                    + a+++l+++++++aa+++
  gi|121637701|ref|YP_977924.1| 555 QVANRNLANTISKVAATSY 573
                                    5555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4614.81
//
Query:       gi|121637702|ref|YP_977925.1|  [L=423]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-64  215.5  24.6      4e-64  215.5  24.6    2.6  3  PPE       PPE family
    3.8e-08   34.1  26.1    3.8e-08   34.1  26.1    5.4  2  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5  24.6   4.5e-68     4e-64       2     157 ..       6     160 ..       5     161 .. 0.99
   2 ?   -2.4   0.5       0.5   4.5e+03      81      89 ..     184     192 ..     173     228 .. 0.59
   3 ?   -5.7   5.9         2   1.8e+04      62      62 ..     392     392 ..     340     417 .. 0.46

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 4.5e-68
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPE+ns ++y+Gpg+gp+laAa+aWdgLa el+++aa ++s l++l+ +aW+Gpss++ma+aaapy+aW+sa+a +ae 
  gi|121637702|ref|YP_977925.1|   6 LPPEINSGRMYTGPGPGPMLAAATAWDGLAVELHATAAGYASELSALT-GAWSGPSSTSMASAAAPYVAWMSATAVHAEL 84 
                                    8***********************************************.******************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    a+aqa+ a+aaYeaA+aa+vpp++iaanra+l++l+atn+fGqntpaI+ tea+y emwaqdaaam++Y+ +sa+a
  gi|121637702|ref|YP_977925.1|  85 AGAQARLAIAAYEAAFAATVPPPVIAANRAQLMVLIATNIFGQNTPAIMMTEAQYMEMWAQDAAAMYGYAGSSATA 160
                                    ***********************************************************************99986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.5
                                    HHHHHHHHH CS
                            PPE  81 eaAaqaeaa 89 
                                    ++A+ a++a
  gi|121637702|ref|YP_977925.1| 184 AVAQTAATA 192
                                    222222222 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 2
                                    H CS
                            PPE  62 a 62 
                                     
  gi|121637702|ref|YP_977925.1| 392 G 392
                                    2 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -28.9  37.5         2   1.8e+04      18      63 ..      55      84 ..      25     234 .. 0.72
   2 !   34.1  26.1   4.2e-12   3.8e-08       1      67 [.     318     388 ..     318     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: -28.9 bits;  conditional E-value: 2
                       PE_PPE_C 18 sWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagagga.a 63
                                   +W++++++ +a+aaa                 + ++ ++a a +a  
  gi|121637702|ref|YP_977925.1| 55 AWSGPSSTSMASAAA-----------------PYVAWMSATAVHAeL 84
                                   344444333333333.................322222222222210 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 4.2e-12
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal....sgttaaaaaaaagaalggmPlaaagaggaaggaa 67 
                                    sAg G+A +vG+LSVP+ W+ aap++ + aaal     ++++ aa+ +aga+lggm+l ++++++aag+++
  gi|121637702|ref|YP_977925.1| 318 SAGIGRAGLVGKLSVPQGWTVAAPEIPSPAAALqatrLAAAPIAATDGAGALLGGMALSGLAGRAAAGSTG 388
                                    8***************************99999455544555555566666666*********99955444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2659.18
//
Query:       gi|121637703|ref|YP_977926.1|  [L=463]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-63  212.6  31.1      3e-63  212.6  31.1    2.8  3  PPE       PPE family
    4.8e-11   43.4  19.0    4.8e-11   43.4  19.0    4.7  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
      0.055   13.7   6.4       0.26   11.5   6.4    2.2  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6  31.1   5.1e-67     3e-63       1     157 [.       5     160 ..       5     161 .. 0.99
   2 ?   -1.7   1.0      0.47   2.8e+03      48      88 ..     183     223 ..     172     234 .. 0.62
   3 ?   -0.3   1.6      0.17     1e+03      83     126 ..     330     373 ..     323     380 .. 0.77

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 5.1e-67
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns ++yaGpgsgp+laAaaaWdgLa+el+s+aa + sv++ l+ + W+G+ss  maaaaapy+aW+sa+aa a+
  gi|121637703|ref|YP_977926.1|   5 VLPPEINSGRMYAGPGSGPMLAAAAAWDGLATELQSTAADYGSVISVLT-GVWSGQSSGTMAAAAAPYVAWMSATAALAR 83 
                                    59***********************************************.****************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    eaAaqa+aaaaaYeaA+aa+vpp+++aanraela+l+atn+fGqnt aIaa+ea y+emwaqdaaam++Y+ +s+ a
  gi|121637703|ref|YP_977926.1|  84 EAAAQASAAAAAYEAAFAATVPPPVVAANRAELAVLAATNIFGQNTGAIAAAEARYAEMWAQDAAAMYGYAGSSSVA 160
                                    ************************************************************************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.47
                                    TT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  48 laaeaWqGpssaamaaaaapylaWLsaaaaqaeeaAaqaea 88 
                                    +a ++  G+s+  + + +   l++L++a+++ +++ a +  
  gi|121637703|ref|YP_977926.1| 183 VAVAQAVGASAGNARSLVSEVLEFLATAGTNYNKTVASLMN 223
                                    44445556666666666666666666666666666555444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTH CS
                            PPE  83 AaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqnt 126
                                       ++++aa+++++ ++ vp+a i +     ++++a+   G+  
  gi|121637703|ref|YP_977926.1| 330 TPAIRTVAAVFSSTGLQAVPAAAISEGSLLSQMALASVAGGALG 373
                                    45689999************999999888888877777666655 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -18.3  30.6         3   1.8e+04      18      46 ..      73     101 ..      16     163 .. 0.65
   2 ?   -2.0  10.9       1.2   7.1e+03      27      65 ..     158     195 ..     141     233 .. 0.71
   3 !   43.4  19.0     8e-15   4.8e-11       1      70 [.     308     379 ..     308     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: -18.3 bits;  conditional E-value: 3
                       PE_PPE_C  18 sWaaaapaasaaaaalsgttaaaaaaaag 46 
                                    +W +a++a++  aaa  +++aaa +aa++
  gi|121637703|ref|YP_977926.1|  73 AWMSATAALAREAAAQASAAAAAYEAAFA 101
                                    23222222222222222222222222222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                       PE_PPE_C  27 saaaaalsgttaaaaaaaagaalggmPlaaagaggaagg 65 
                                    s a + ++ ++++++++aag a +g+++a+a +++a g+
  gi|121637703|ref|YP_977926.1| 158 SVATQVTPFAAPPPTTNAAGLATQGVAVAQAVGASA-GN 195
                                    223333477888888888888888999988877777.22 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 8e-15
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalg...gmPlaaagaggaaggaapry 70 
                                    sAg+ qA +vG++SVPpsWaaa+pa++++aa  s+t+ +a +aaa ++++    m+la++++g+  ggaa r 
  gi|121637703|ref|YP_977926.1| 308 SAGASQAGSVGGMSVPPSWAAATPAIRTVAAVFSSTGLQAVPAAAISEGSllsQMALASVAGGAL-GGAAARA 379
                                    8******************************************9999988999*********999.7777664 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.4   4.4e-05      0.26       9      84 ..      24      99 ..      21      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  9 lrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84
                                   + +aaa+ ++ a+el++  ++  + ++ l++ WsG+++ + +a+ + + + +   +++  e + +  +aa+a+e a
  gi|121637703|ref|YP_977926.1| 24 MLAAAAAWDGLATELQSTAADYGSVISVLTGVWSGQSSGTMAAAAAPYVAWMSATAALAREAAAQASAAAAAYEAA 99
                                   7899*********************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2395.81
//
Query:       gi|121637704|ref|YP_977927.1|  [L=540]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                       90  (0.0050198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.92u 0.37s 00:00:01.29 Elapsed: 00:00:00.61
# Mc/sec: 2678.33
//
Query:       gi|121637705|ref|YP_977928.1|  [L=87]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-29  101.9  12.9    1.9e-29  101.8  12.9    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8  12.9   1.1e-33   1.9e-29       2      84 ..       4      86 ..       3      87 .] 0.98

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.1e-33
                                   XXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  2 sfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaa 83
                                   s ++vaP  + aaa+dla+igsa+s ana a  p+ta+l+a+aD+VSaaiAalf++h+q+yq+lsa+a+afheqfvq ++a+
  gi|121637705|ref|YP_977928.1|  4 SQMIVAPAFVDAAAKDLATIGSAISRANAEALVPITALLPAGADDVSAAIAALFATHGQAYQELSAHAVAFHEQFVQLMSAG 85
                                   789*****************************************************************************99 PP

                                   H CS
                             PE 84 a 84
                                   a
  gi|121637705|ref|YP_977928.1| 86 A 86
                                   8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 580.38
//
Query:       gi|121637706|ref|YP_977929.1|  [L=108]
Description: hypothetical protein BCG_1837c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-25   89.7   0.0    1.4e-25   89.5   0.0    1.0  1  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0   7.6e-30   1.4e-25       5      94 ..       9     100 ..       5     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 7.6e-30
                         DUF732   5 llaaalllaapAaAd.sadda.FlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaaqfv 82 
                                     + ++++la pA+A  s dda Fla+l++agi+y++pd+aia+GkavC+ ++sG+s  +vv+e++++n+g+s++   +f+
  gi|121637706|ref|YP_977929.1|   9 SIPLMIGLAVPAHAGpSGDDAvFLASLERAGITYSHPDQAIASGKAVCALVESGESGLQVVNELRTRNPGFSMDGCCKFA 88 
                                    56689*********65566666********************************************************** PP

                         DUF732  83 gaAvsayCPeql 94 
                                    ++++++yCP+q+
  gi|121637706|ref|YP_977929.1|  89 AISAHVYCPHQI 100
                                    *********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 731.09
//
Query:       gi|121637707|ref|YP_977930.1|  [L=115]
Description: hypothetical protein BCG_1838c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 816.34
//
Query:       gi|121637708|ref|YP_977931.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-27   93.7  19.6    7.2e-27   93.6  19.6    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6  19.6     4e-31   7.2e-27       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 4e-31
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   M fv v P+ala aa++l ++gs ++a na aa++t+++++aaaDeVSa +A++f+ ha+ yqa++aqa+a+ e fv++l a
  gi|121637708|ref|YP_977931.1|  1 MAFVLVCPDALAIAAGQLRHVGSVIAARNAVAAPATAELAPAAADEVSALTATQFNFHAAMYQAVGAQAIAMNEAFVAMLGA 82
                                   99******************************************************************************** PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a+sYaa+Eaa
  gi|121637708|ref|YP_977931.1| 83 SADSYAATEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 550.73
//
Query:       gi|121637709|ref|YP_977932.1|  [L=399]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-63  211.0  33.1    9.3e-63  211.0  33.1    2.1  2  PPE       PPE family
    5.7e-21   75.2  16.5    5.7e-21   75.2  16.5    6.1  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.0  33.1     1e-66   9.3e-63       2     157 ..       6     161 ..       5     162 .. 0.99
   2 ?   -2.0   2.3      0.37   3.3e+03      29      58 ..     189     217 ..     170     228 .. 0.50

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 1e-66
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPE+nsa++y+G+gs+p+laAa+aW+gL+ael+++a +++svl++l++e+W+Gp+sa+m+aaaapy+aW+s +a +ae+
  gi|121637709|ref|YP_977932.1|   6 LPPEINSARMYSGAGSAPMLAAASAWHGLSAELRASALSYSSVLSTLTGEEWHGPASASMTAAAAPYVAWMSVTAVRAEQ 85 
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    a+aqaeaaaaaYeaA+aa+vpp++i anra+l+al+atn++Gqn+paIaatea+y+emw qda am++Y+ asaaa
  gi|121637709|ref|YP_977932.1|  86 AGAQAEAAAAAYEAAFAATVPPPVIEANRAQLMALIATNVLGQNAPAIAATEAQYAEMWSQDAMAMYGYAGASAAA 161
                                    *************************************************************************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHHHTTTT.TTS-SHHH CS
                            PPE  29 gLaaelasaaaelesvlaelaaeaWqGpss 58 
                                    +  a+  +++++l++++a++  +  qG ss
  gi|121637709|ref|YP_977932.1| 189 ATGASAGAQQTTLSQLIAAIP-SVLQGLSS 217
                                    223334444444555555554.55555554 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5      0.41   3.6e+03      49      60 ..      19      30 ..       4      47 .. 0.49
   2 ?  -37.3  47.9         2   1.8e+04      19      61 ..      57     100 ..      18     239 .. 0.79
   3 ?    0.1   2.0      0.18   1.6e+03      40      62 ..     281     311 ..     265     316 .. 0.54
   4 !   75.2  16.5   6.3e-25   5.7e-21       1      80 []     317     395 ..     317     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.41
                       PE_PPE_C 49 lggmPlaaagag 60
                                   +g +P+ aa+++
  gi|121637709|ref|YP_977932.1| 19 AGSAPMLAAASA 30
                                   223333333322 PP

  == domain 2  score: -37.3 bits;  conditional E-value: 2
                       PE_PPE_C  19 Waaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagagg 61 
                                    W ++a+a ++aaaa   ++  ++a  a +a++++ ++aaa +++
  gi|121637709|ref|YP_977932.1|  57 WHGPASASMTAAAAPyVAWMSVTAVRAEQAGAQAEAAAAAYEAA 100
                                    77777666666666643333333333333333322222222222 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.18
                       PE_PPE_C  40 aaaaaagaalg........gmPlaaagagga 62 
                                    aaa aag +lg        g+ +a++g++g+
  gi|121637709|ref|YP_977932.1| 281 AAADAAGDVLGeatsgglgGALVAPLGSAGG 311
                                    4444444444445555454555555555555 PP

  == domain 4  score: 75.2 bits;  conditional E-value: 6.3e-25
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmprp 80 
                                    +AglG+AatvG LSVPpsW+aaap as++++al+gt+++a + a +a+++gmP++ +g++g  g a+p+ygfrp  ++rp
  gi|121637709|ref|YP_977932.1| 317 AAGLGNAATVGTLSVPPSWTAAAPLASPLGSALGGTPMVAPPPAVAAGMPGMPFGTMGGQGF-GRAVPQYGFRPNFVARP 395
                                    6*************************************************************.****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2473.42
//
Query:       gi|121637710|ref|YP_977933.1|  [L=409]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-64  215.7  24.2    3.4e-64  215.7  24.2    2.9  4  PPE       PPE family
    5.2e-09   36.9  15.4    5.2e-09   36.9  15.4    5.5  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.7  24.2   3.8e-68   3.4e-64       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -5.7   7.4         2   1.8e+04       8      42 ..     183     217 ..     174     244 .. 0.49
   3 ?   -2.6   0.0      0.57   5.2e+03     135     151 ..     324     340 ..     311     346 .. 0.70
   4 ?   -3.2   0.2      0.92   8.2e+03      13      25 ..     344     356 ..     335     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 3.8e-68
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+ns ++yaGpgsgpllaAaaaWd+Laael saaa++ s++++l+ + W Gpss  maaa+apy+aW+s +a qae
  gi|121637710|ref|YP_977933.1|   5 ALPPEINSGRMYAGPGSGPLLAAAAAWDALAAELYSAAASYGSTIEGLTVAPWMGPSSITMAAAVAPYVAWISVTAGQAE 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a+aqa++aa +Ye+A+aa+vpp++i anra l++lvatn+fGqntpaIaatea+y+emwaqdaaam++Y+ +sa+a
  gi|121637710|ref|YP_977933.1|  85 QAGAQAKIAAGVYETAFAATVPPPVIEANRALLMSLVATNIFGQNTPAIAATEAHYAEMWAQDAAAMYGYAGSSATA 161
                                    ************************************************************************99986 PP

  == domain 2  score: -5.7 bits;  conditional E-value: 2
                                    HHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE   8 sallyaGpgsgpllaAaaaWdgLaaelasaaaele 42 
                                    sa++ + +g++  +   a++++L + l s+ ++l+
  gi|121637710|ref|YP_977933.1| 183 SAVVAQAAGAAASSDITAQLSQLISLLPSTLQSLA 217
                                    33333333333333333333333333333333333 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.57
                                    HHHHHHHHHHHHHHHHH CS
                            PPE 135 eyeemwaqdaaamaaYe 151
                                    +  + wa++a +m+a +
  gi|121637710|ref|YP_977933.1| 324 SVPQGWAEAAPVMRAVA 340
                                    55678999999998765 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 0.92
                                    HS--SHHHHHHHH CS
                            PPE  13 aGpgsgpllaAaa 25 
                                     G g++p laA+a
  gi|121637710|ref|YP_977933.1| 344 PGTGAAPALAAEA 356
                                    5889999999875 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -31.9  39.9         2   1.8e+04       4       4 ..     158     158 ..      17     239 .. 0.69
   2 ?   -6.8   8.9         2   1.8e+04      16      51 ..     256     303 ..     217     315 .. 0.65
   3 !   36.9  15.4   5.7e-13   5.2e-09       2      71 ..     312     382 ..     311     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: -31.9 bits;  conditional E-value: 2
                       PE_PPE_C   4 l 4  
                                     
  gi|121637710|ref|YP_977933.1| 158 S 158
                                    1 PP

  == domain 2  score: -6.8 bits;  conditional E-value: 2
                       PE_PPE_C  16 PpsWaaaapaasaaaaalsgttaaaaaaaagaalg............g 51 
                                    P  W  +  ++  +a+ ++g +a  +++aa++al+             
  gi|121637710|ref|YP_977933.1| 256 PGGWWLTFGQILGLAQNAPGVAALLGPKAAAGALSplaplrggyiadI 303
                                    555555555555556666666665555555555543444444444444 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 5.7e-13
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaa..aaaaagaalggmPlaaagaggaaggaapryg 71 
                                    +g ++A  vG+LSVP+ Wa+aap ++a+a+ l+gt+aa+  aa+a+ga++g m+l ++++++  +g+a r g
  gi|121637710|ref|YP_977933.1| 312 GGIARAIYVGSLSVPQGWAEAAPVMRAVASVLPGTGAAPalAAEAPGALFGEMALSSLAGRAL-AGTAVRSG 382
                                    57899***************************7666655226889999999***********9.77777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2540.46
//
Query:       gi|121637711|ref|YP_977934.1|  [L=187]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-61  206.6  25.3    2.6e-61  206.3  25.3    1.1  1  PPE             PPE family
  ------ inclusion threshold ------
       0.03   15.2   2.0       0.03   15.2   2.0    1.7  2  Nucleoporin_FG  Nucleoporin FG repeat region


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.3  25.3   2.9e-65   2.6e-61       3     157 ..       7     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 2.9e-65
                                    -HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHH CS
                            PPE   3 pPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaeea 82 
                                    pPE++s  +y Gpg+gp+laAa aWdgLaael+s+aa+++s+++++a+e+W Gpssa maaaaapy++W+s ++aqa++a
  gi|121637711|ref|YP_977934.1|   7 PPEITSGEMYLGPGAGPMLAAAVAWDGLAAELQSMAASYASIVEGMASESWLGPSSAGMAAAAAPYVTWMSGTSAQAKAA 86 
                                    9******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  83 AaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    A qa+aa+ aYe+A+aa+vpp++iaanr +l +lvatn+fGqnt+aIaateaey emwaqd  am +Y+++sa+a
  gi|121637711|ref|YP_977934.1|  87 ADQARAAVVAYETAFAAVVPPPQIAANRSQLISLVATNIFGQNTAAIAATEAEYGEMWAQDTMAMFGYASSSATA 161
                                    **********************************************************************99986 PP

>> Nucleoporin_FG  Nucleoporin FG repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.5   1.3e+04      61      61 ..      80      80 ..      59      92 .. 0.53
   2 ?   15.2   2.0   3.3e-06      0.03      12      64 ..     123     186 ..     116     187 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                 Nucleoporin_FG 61 t 61
                                   +
  gi|121637711|ref|YP_977934.1| 80 S 80
                                   1 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.3e-06
                 Nucleoporin_FG  12 gglFGststt............atstgglFGasstatatasggglfgatsqtaasgglFGstnat 64 
                                    +++FG+++++            a+ t  +FG  ++++atas  + f a+ qt++++gl G+++at
  gi|121637711|ref|YP_977934.1| 123 TNIFGQNTAAiaateaeygemwAQDTMAMFGY-ASSSATASRLTPFTAPPQTTNPSGLAGQAAAT 186
                                    78999999998888888888888899999993.33444444446999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1271.03
//
Query:       gi|121637712|ref|YP_977935.1|  [L=118]
Description: hypothetical protein BCG_1844 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-24   85.8   3.8    2.4e-24   85.5   3.8    1.0  1  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   3.8   1.4e-28   2.4e-24       2      94 ..      19     113 ..      18     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 1.4e-28
                         DUF732   2 aaallaaalllaapAaAd.sadda.FlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaa 79 
                                    +++ +a++++laap +Ad + dda Flaal+qagi+y++p +ai+++ka+C   ++G++  ++va++++ n+gl+++ aa
  gi|121637712|ref|YP_977935.1|  19 LLLSAATMIGLAAPGKADpTGDDAaFLAALDQAGITYADPGHAITAAKAMCGLCANGVTGLQLVADLRDYNPGLTMDSAA 98 
                                    57789*************7444446*******************************************99********** PP

                         DUF732  80 qfvgaAvsayCPeql 94 
                                    +f+++A  ayCPe+l
  gi|121637712|ref|YP_977935.1|  99 KFAAIASGAYCPEHL 113
                                    *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 800.41
//
Query:       gi|121637713|ref|YP_977936.1|  [L=234]
Description: Mg2+ transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-32  111.5  13.1    4.5e-32  111.0  13.1    1.2  1  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0  13.1   2.5e-36   4.5e-32       1     119 [.      13     132 ..      13     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 2.5e-36
                           MgtC   1 LllAlllGlliGleRelrekaaGlRTfaLvalgaalfvllslelae...srvaaqvvsgigflgagvilkekegakvkgl 77 
                                    L++ + +G++iGleR++r ++aGlRT+aLva ga+lfvl ++ + +   +rva++vvsgigflg+gvil  +eg +v+gl
  gi|121637713|ref|YP_977936.1|  13 LAVGVGCGAIIGLERQWRARMAGLRTNALVATGATLFVLYAVATEDsspTRVASYVVSGIGFLGGGVIL--REGFNVRGL 90 
                                    678999**********************************88876699*********************..9999***** PP

                           MgtC  78 TTaaslwvtaaiGllvglglyllavvatvlvllllallrele 119
                                    +Taa+lw++aa+G+l++ g+++  +++t +++++  l r+l 
  gi|121637713|ref|YP_977936.1|  91 NTAATLWCSAAVGVLAASGHLVFTLIGTGTIVAVHLLGRPLG 132
                                    **********************************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1649.97
//
Query:       gi|121637714|ref|YP_977937.1|  [L=400]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-50  171.6   1.1    2.5e-50  171.4   1.1    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.7e-08   33.0   0.6    2.6e-05   24.7   0.0    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    7.2e-08   32.4  11.3       0.04   13.5   0.4    4.1  4  DAO            FAD dependent oxidoreductase
    1.8e-05   24.8   5.4      0.062   13.3   0.1    4.1  4  NAD_binding_9  FAD-NAD(P)-binding
     0.0016   17.6   4.7       0.45    9.5   0.2    3.5  3  GIDA           Glucose inhibited division protein A
     0.0027   16.8   8.2      0.005   16.0   1.0    3.3  4  FAD_binding_2  FAD binding domain
     0.0056   16.9   2.8        1.1    9.6   0.1    2.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
       0.03   13.0   3.0       0.72    8.5   0.1    3.3  4  HI0933_like    HI0933-like protein
      0.044   13.1   5.4        2.2    7.6   0.6    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.052   12.8   0.2       0.28   10.4   0.0    1.9  2  Amino_oxidase  Flavin containing amine oxidoreductase
        0.5    9.7   4.0       0.42    9.9   0.5    2.2  2  FAD_oxidored   FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   1.1   1.5e-53   2.5e-50       2     293 ..       3     312 ..       2     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.5e-53
                                    SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCH CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielll 71 
                                    +vvviG+G+AGl+aal +a+   ++ v     + +++ ++++    ++++++d + ++               +g+  ++
  gi|121637714|ref|YP_977937.1|   3 RVVVIGSGFAGLWAALGAARrlDELAVPAGTVDVMVVSNKPFHDIRVRNYEADLSACRiplgdvlgP------AGVAHVT 76 
                                    8*******************6556666666799999*******************999*99866542......4799999 PP

                                    CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                    Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp......... 142
                                    + ev++id + ++v+      + + ++ yd+lvlA+Gs+  ++ +pG+ae ++++ +t+d a +l+++l+          
  gi|121637714|ref|YP_977937.1|  77 A-EVTAIDADGRRVTT-----STGASYSYDRLVLASGSHVVKPALPGLAEFGFDV-DTYDGAVRLQQHLQGlaggpltsa 149
                                    9.9*************.....56789**********************8888766.************************ PP

                                    .SEEEEES-SHHHHHHHHHH....HHHT-..........EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEE CS
                                    .xxxxxxxxxxxxxxxxxxx....xxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 .krivvvGgGyiGvElAaal....aklgk..........evtlveardrllraldkelsaaleealekeGvevklgtsvk 207
                                     + +vvvG+G++G+E+A++l    +   +          +v+l+++++ + + ++ +++  +e+al ++Gve+++g sv 
  gi|121637714|ref|YP_977937.1| 150 aATVVVVGAGLTGIETACELpgrlH---AlfargdgvtpRVVLIDHNPFVGSDMGLSARPVIEQALLDNGVETRTGVSVA 226
                                    *******************754442...133357788989***************************************9 PP

                                    EEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBES.STTEEE-GGGC.....TEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.....xxx RF
                    Pyr_redox_2 208 eidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtn.vpgiyaiGDva.....ggk 281
                                    ++ + g    v+l++ge+++a +vv+++G+r+s+ +  e+l ++ d+ g+++vd++lr+  vp ++a+GDva     +++
  gi|121637714|ref|YP_977937.1| 227 AVSPGG----VTLSSGERLAAATVVWCAGMRASRLT--EQLPVARDRLGRLQVDDYLRVIgVPAMFAAGDVAaarmdDEH 300
                                    999888....79*********************855..9*******************977***********99998888 PP

                                    CSS--HHHHHHH CS
                                    xxxxxxxxxxxx RF
                    Pyr_redox_2 282 ggpelaqaAvqq 293
                                     +++++q+   +
  gi|121637714|ref|YP_977937.1| 301 LSVMSCQHGRPM 312
                                    888888887665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0092        15       1      19 [.       3      21 ..       3      49 .. 0.82
   2 !   24.7   0.0   1.6e-08   2.6e-05       2      69 ..     153     231 ..     152     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0092
                                   EEEEECSSHHHHHHHHHHH CS
                      Pyr_redox  1 kvvvvGgGyiglElAgala 19
                                   +vvv+G+G+ gl +A  +a
  gi|121637714|ref|YP_977937.1|  3 RVVVIGSGFAGLWAALGAA 21
                                   79*********98886654 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.6e-08
                                    EEEECSSHHHHHHHHHH...........HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                      Pyr_redox   2 vvvvGgGyiglElAgal...........aelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                    vvvvG+G++g+E A++l                +V +++ ++ + + ++  a+ ++++ l +ng+e +++ +v+++   
  gi|121637714|ref|YP_977937.1| 153 VVVVGAGLTGIETACELpgrlhalfargDGVTPRVVLIDHNPFVGSDMGLSARPVIEQALLDNGVETRTGVSVAAVSPG 231
                                    9****************9999777654333447*****************************************99854 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   4.7e-05     0.077       1      22 [.       3      25 ..       3      45 .. 0.76
   2 ?    4.2   0.0     0.017        27     160     204 ..      71     110 ..      65     127 .. 0.77
   3 !   13.5   0.4   2.5e-05      0.04       2      33 ..     153     197 ..     152     207 .. 0.82
   4 !    7.3   0.3    0.0018         3     154     216 ..     210     262 ..     206     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                                   EEEEECTSHHHHHHHHHHHHT.T CS
                            DAO  1 dvviiGGGiiGlstAyeLarr.g 22
                                   +vv+iG+G +Gl++A+ +arr  
  gi|121637714|ref|YP_977937.1|  3 RVVVIGSGFAGLWAALGAARRlD 25
                                   59****************99852 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                    T-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGH CS
                            DAO 160 Gveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaws 204
                                    Gv  ++  evt+++++   + +v  tt+ g+  ++d +V+a G ++
  gi|121637714|ref|YP_977937.1|  71 GVAHVTA-EVTAIDAD---GRRV--TTStGASYSYDRLVLASGSHV 110
                                    5555665.9****665...6788..888899867799******884 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.5e-05
                                    EEEECTSHHHHHHHHHH........HHTT......EEEEESSSSTT CS
                            DAO   2 vviiGGGiiGlstAyeL........arrg......Vtllekgdiag 33 
                                    vv++G+G +G+ tA eL        a rg      V+l++ ++++g
  gi|121637714|ref|YP_977937.1| 153 VVVVGAGLTGIETACELpgrlhalfA-RGdgvtprVVLIDHNPFVG 197
                                    9****************888776543.4456999******998888 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0018
                                    HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSE CS
                            DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlp 216
                                    +a+ ++Gve ++g  v +++      +gv  t + ge+ aa +vV +aG  ++ l+   ++l  p
  gi|121637714|ref|YP_977937.1| 210 QALLDNGVETRTGVSVAAVS-----PGGV--TLSsGERLAAATVVWCAGMRASrLT---EQL--P 262
                                    67889********9999994.....3445..334488756688********98665...444..3 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.024        39       1      36 [.       5      44 ..       5      61 .. 0.78
   2 !   13.3   0.1   3.8e-05     0.062     116     155 ..      71     108 ..      63     109 .. 0.87
   3 !    5.7   0.1    0.0084        14       1      37 [.     154     197 ..     154     215 .. 0.83
   4 ?    1.5   0.1      0.16   2.6e+02     135     155 ..     232     252 ..     210     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.024
                  NAD_binding_9  1 aivGaGprGlavlerLlara....kkkspleitlfdpsep 36
                                   +++G G++Gl ++   ++r      ++  ++++++ ++++
  gi|121637714|ref|YP_977937.1|  5 VVIGSGFAGLWAALGAARRLdelaVPAGTVDVMVVSNKPF 44
                                   69********999999998877667778889988877776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.8e-05
                  NAD_binding_9 116 tvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                     v +++aev++++   dg++v++++gas+ +d++vLA G 
  gi|121637714|ref|YP_977937.1|  71 GVAHVTAEVTAIDA--DGRRVTTSTGASYSYDRLVLASGS 108
                                    48999*******95..56779****************995 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0084
                  NAD_binding_9   1 aivGaGprGlavlerLlara......kkkspleitlfdpsep.g 37 
                                    ++vGaG +G+ ++ +L  r        ++   ++ l+d +++ g
  gi|121637714|ref|YP_977937.1| 154 VVVGAGLTGIETACELPGRLhalfarGDGVTPRVVLIDHNPFvG 197
                                    69************998888777766667779999999999855 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.16
                  NAD_binding_9 135 avlladgaslaadaVvLAlGh 155
                                     v+l++g++laa  Vv + G+
  gi|121637714|ref|YP_977937.1| 232 GVTLSSGERLAAATVVWCAGM 252
                                    4899**************996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00028      0.45       2      21 ..       4      23 ..       3      30 .. 0.93
   2 ?    0.8   0.0      0.12     2e+02     116     151 ..      77     109 ..      70     123 .. 0.80
   3 !    6.6   0.3    0.0021       3.5       1      17 [.     152     168 ..     152     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00028
                                   EEEE-SSHHHHHHHHHHHHT CS
                           GIDA  2 viViGgGhAGceAAlaaarl 21
                                   v+ViG G AG+ AAl aar+
  gi|121637714|ref|YP_977937.1|  4 VVVIGSGFAGLWAALGAARR 23
                                   9****************995 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                                    S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT- CS
                           GIDA 116 eeveeliveekkvkgvvtedgetikakavviatGtf 151
                                    +ev+ ++      + v+t++g+ ++ +  v+a+G+ 
  gi|121637714|ref|YP_977937.1|  77 AEVTAIDA---DGRRVTTSTGASYSYDRLVLASGSH 109
                                    56666644...66779******************94 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0021
                                    CEEEE-SSHHHHHHHHH CS
                           GIDA   1 dviViGgGhAGceAAla 17 
                                    +v+V+G+G+ G+e A +
  gi|121637714|ref|YP_977937.1| 152 TVVVVGAGLTGIETACE 168
                                    59************986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   3.1e-06     0.005       2      21 ..       4      23 ..       3      35 .. 0.89
   2 ?   -2.4   0.0       1.2   1.9e+03     216     293 ..      73     100 ..      65     109 .. 0.56
   3 ?    3.3   0.1     0.021        35       2      18 ..     153     169 ..     152     174 .. 0.89
   4 ?   -0.7   0.0      0.34   5.6e+02     376     407 ..     271     297 ..     262     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                                   EEEE--SHHHHHHHHHHHHT CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaea 21
                                   v+ViGsG+AGL AAl aa++
  gi|121637714|ref|YP_977937.1|  4 VVVIGSGFAGLWAALGAARR 23
                                   9****************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                    SSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTHGGGS-HH CS
                  FAD_binding_2 216 eaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFmnelasrd 293
                                    ++ t  + a++ dg +++ ++ga+                                                  +s+d
  gi|121637714|ref|YP_977937.1|  73 AHVTAEVTAIDADGRRVTTSTGAS--------------------------------------------------YSYD 100
                                    555555555555555555555554..................................................3444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.021
                                    EEEE--SHHHHHHHHHH CS
                  FAD_binding_2   2 viViGsGlAGLaAAlea 18 
                                    v+V+G+Gl G   A e+
  gi|121637714|ref|YP_977937.1| 153 VVVVGAGLTGIETACEL 169
                                    9**********999876 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.34
                                    EEBETTSBESTTEEESSBTEEE-STCEESSSS CS
                  FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvh 407
                                    +++d+ +rv       +p ++AaG vaa+ ++
  gi|121637714|ref|YP_977937.1| 271 LQVDDYLRV-----IGVPAMFAAGDVAAARMD 297
                                    678888888.....78999********98875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.4    0.0063        10       1      18 [.       6      23 ..       6      39 .. 0.85
   2 !    9.6   0.1   0.00066       1.1       1      35 [.     155     200 ..     155     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0063
                                   EE--SHHHHHHHHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka 18
                                   ++G+G++Gl aA  +a++
  gi|121637714|ref|YP_977937.1|  6 VIGSGFAGLWAALGAARR 23
                                   8**********9877764 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00066
                                    EE--SHHHHHHHHHHH.......CC..TE..EEEEE-SSSSSSGGG CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLa.......ka..gf..dvlllekrdrlGGra 35 
                                    +vGaGl+G  +A++L         +  g+  +v+l+++++ +G ++
  gi|121637714|ref|YP_977937.1| 155 VVGAGLTGIETACELPgrlhalfARgdGVtpRVVLIDHNPFVGSDM 200
                                    8*************96333333312457777899999999988444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00044      0.72       2      22 ..       3      23 ..       2      30 .. 0.86
   2 ?    1.8   0.0     0.047        77     128     165 ..      75     109 ..      70     124 .. 0.80
   3 ?    0.8   0.1     0.097   1.6e+02       2      19 ..     152     169 ..     151     205 .. 0.66
   4 ?   -2.6   0.0         1   1.6e+03     119     159 ..     212     247 ..     206     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00044
                                   SEEEE--SHHHHHHHHHHHHT CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakr 22
                                   +v+viG G AGl aA+ aa+r
  gi|121637714|ref|YP_977937.1|  3 RVVVIGSGFAGLWAALGAARR 23
                                   79**************99887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.047
                                    -S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 128 letevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    +  ev+++  ++dg  rv+t+++ +++ d+lvlA+G+ 
  gi|121637714|ref|YP_977937.1|  75 VTAEVTAI--DADG-RRVTTSTGASYSYDRLVLASGSH 109
                                    55677777..4455.6788889*************986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.097
                                    SEEEE--SHHHHHHHHHH CS
                    HI0933_like   2 dviviGgGaAGlmaAisa 19 
                                    +v+v+G+G  G+ +A ++
  gi|121637714|ref|YP_977937.1| 152 TVVVVGAGLTGIETACEL 169
                                    69*********9999876 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1
                                    HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                    HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklv 159
                                    l ++gv+ r+  +v++v  + +g   v+++s+e+l+a+++v
  gi|121637714|ref|YP_977937.1| 212 LLDNGVETRTGVSVAAV--SPGG---VTLSSGERLAAATVV 247
                                    55666666666666666..3333...344445555555555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0015       2.5      30      49 ..       3      23 ..       1      35 [. 0.80
   2 ?    7.6   0.6    0.0013       2.2      16      44 ..     139     166 ..     128     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                                   EEEEESTSHHHHHHHH.HHHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAia.takg 49
                                   +v+viG G aGl A+  +a++
  gi|121637714|ref|YP_977937.1|  3 RVVVIGSGFAGLWAALgAARR 23
                                   8**********9877504455 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                                    EEETTCEETCB---EEEEESTSHHHHHHH CS
                    AlaDh_PNT_C  16 kgtlaGgvpgvepakvlviGgGvaGlqAi 44 
                                    +g+ aGg    ++a+v+v+G+G  G++ +
  gi|121637714|ref|YP_977937.1| 139 QGL-AGGPLTSAAATVVVVGAGLTGIETA 166
                                    334.444444889************9865 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.28     227     275 ..      75     116 ..      62     128 .. 0.83
   2 ?   -0.3   0.0       0.3     5e+02     221     274 ..     215     261 ..     201     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                    TSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCS CS
                  Amino_oxidase 227 lntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplp 275
                                    + ++V+ i+  +dg +vt+++g ++++D+ v+++   v+k     P lp
  gi|121637714|ref|YP_977937.1|  75 VTAEVTAID--ADGRRVTTSTGASYSYDRLVLASGSHVVK-----PALP 116
                                    445556665..5999*************************.....5444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.3
                                    TTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCC CS
                  Amino_oxidase 221 rgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPpl 274
                                     g++ r++  V  ++      +vtl++ge + a  Vv ++ +++ +   ++ +l
  gi|121637714|ref|YP_977937.1| 215 NGVETRTGVSVAAVSP----GGVTLSSGERLAAATVVWCAGMRASR---LTEQL 261
                                    6778888888888887....5666689**********999999888...44444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00026      0.42       2      21 ..       4      23 ..       3      25 .. 0.96
   2 ?    0.4   0.2       0.2   3.2e+02       2      16 ..     153     167 ..     152     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAara 21
                                   vvV+G+g aG+ AA+ Aar+
  gi|121637714|ref|YP_977937.1|  4 VVVIGSGFAGLWAALGAARR 23
                                   9*****************95 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.2
                   FAD_oxidored   2 vvVvGGgpaGvaAAi 16 
                                    vvVvG+g+ G+  A 
  gi|121637714|ref|YP_977937.1| 153 VVVVGAGLTGIETAC 167
                                    9*********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2969.84
//
Query:       gi|121637715|ref|YP_977938.1|  [L=143]
Description: hypothetical protein BCG_1847c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-15   58.0   3.3    1.4e-15   57.6   3.3    1.2  1  DUF4189   Domain of unknown function (DUF4189)


Domain annotation for each model (and alignments):
>> DUF4189  Domain of unknown function (DUF4189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   3.3   7.7e-20   1.4e-15       1      97 []      58     142 ..      58     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.7e-20
                        DUF4189   1 ygaiavspstgkvgasvnyssreeAeaaAlkeCakkggsdCkvvvsfknacgAvaeskkkaaagvgsgasleeaeeaAlk 80 
                                    ygaia++ps++  g ++ +++ + Ae+ Al++C   g++ Ckvv +f ++cgAva++ +  +++ g+g ++++ae++A++
  gi|121637715|ref|YP_977938.1|  58 YGAIAYAPSGA-SGKAWHQRTPARAEQVALEKC---GDKTCKVVSRF-TRCGAVAYNGS--KYQGGTGLTRRAAEDDAVN 130
                                    9*********8.9********************...***********.**********9..7****************** PP

                        DUF4189  81 kCkkkggseCkvvasaC 97 
                                    +++       ++v +aC
  gi|121637715|ref|YP_977938.1| 131 RLEG-----GRIVNWAC 142
                                    9887.....45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1065.06
//
Query:       gi|121637716|ref|YP_977939.1|  [L=300]
Description: membrane-bound C-5 sterol desaturase erg3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-25   88.7   8.9    3.9e-25   88.7   8.9    1.6  2  FA_hydroxylase  Fatty acid hydroxylase superfamily


Domain annotation for each model (and alignments):
>> FA_hydroxylase  Fatty acid hydroxylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.14   2.5e+03      68      97 ..      67      95 ..      43      96 .. 0.49
   2 !   88.7   8.9   2.2e-29   3.9e-25       1     133 []      94     227 ..      94     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                 FA_hydroxylase 68 plsalllvlvlaallelliHsglhvslgwl 97
                                   +  all ++++ a+l+ ++ s+ h++++w+
  gi|121637716|ref|YP_977939.1| 67 KSLALLGYAAIYAYLAPWQLSA-HRWYTWV 95
                                   2222222555555555566666.5666665 PP

  == domain 2  score: 88.7 bits;  conditional E-value: 2.2e-29
                 FA_hydroxylase   1 lllallledfveYwvHrllHrvkllwrrlHkvHHsseaptalaalrahplealllallllllllllg.plsalllvlvla 79 
                                    +++a+++ d+++Y +Hr+ Hrv+l+w+  H+ HHsse  ++ +alr+++ ++    +l++++l l+g p+++++  ++l+
  gi|121637716|ref|YP_977939.1|  94 WVIAIVGVDLLYYSYHRIAHRVRLIWA-THQAHHSSEYFNFATALRQKWNNSG--EILMWVPLPLMGlPPWMVFCSWSLN 170
                                    5899******************99***.********************97764..46667777778878999999***** PP

                 FA_hydroxylase  80 allelliHsglhvslgwllerllatpraHrlHHskneeg...nfgvllslwDrlfgT 133
                                     ++++++H+++  +l+++ e++++tp++Hr+HH  ++ +   n+g +l +wDrlfg+
  gi|121637716|ref|YP_977939.1| 171 LIYQFWVHTERIDRLPRWFEFVFNTPSHHRVHHGMDPVYldkNYGGILIIWDRLFGS 227
                                    **********6667777779****************977888*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2325.97
//
Query:       gi|121637717|ref|YP_977940.1|  [L=221]
Description: hypothetical protein BCG_1849 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.6   0.6          2    8.1   0.4    2.1  2  Trypsin   Trypsin


Domain annotation for each model (and alignments):
>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0   0.00054       9.7      18      65 ..      36      89 ..      18     118 .. 0.71
   2 ?    8.1   0.4   0.00011         2     172     196 ..     163     191 ..     132     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00054
                                   EEETTCEEEEEEEEEETT.EEE.EEGGGTTT....GGGEEEEESE.SBTTSCTTT CS
                        Trypsin 18 lsvksgkhlCgGslisen.wvl.TAaHCvsn....asdvkvvlge.hnlkksegk 65
                                   +++++ +h+C+   +++   +  TA+HC  +    ++d+kv +g  ++++ + ++
  gi|121637717|ref|YP_977940.1| 36 MEIRQDNHVCTLGYVDPAlKIAfTAGHCRGGgavtSRDYKV-IGHlRAFRDNTPS 89
                                   45555589999999999884545*****9999998889988.6665666665554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00011
                                    SSSBCTTTTTTSEEEETTT....EEEEEE CS
                        Trypsin 172 ggkdacqGDSGGPlvcsdg....elvGiv 196
                                     g+ +++GDSGGP+         ++vGi 
  gi|121637717|ref|YP_977940.1| 163 HGVLSEKGDSGGPVYLAPDggpaQIVGIF 191
                                    477899*******9876555777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1528.77
//
Query:       gi|121637718|ref|YP_977941.1|  [L=234]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-24   87.1   1.2    1.8e-24   86.5   0.3    1.7  2  TetR_C_33  Tetracyclin repressor-like, C-terminal domain
      3e-07   30.1   0.1    1.6e-06   27.8   0.0    2.1  2  TetR_N     Bacterial regulatory proteins, tetR family
     0.0012   18.6   0.1     0.0032   17.2   0.1    1.8  1  HTH_23     Homeodomain-like domain
     0.0019   18.0   0.1     0.0043   16.8   0.1    1.6  1  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.018   14.8   0.1      0.042   13.6   0.1    1.6  1  HTH_38     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   4.2e+03      78      83 ..      48      53 ..      19      87 .. 0.58
   2 !   86.5   0.3     5e-28   1.8e-24       2     102 ..      96     225 ..      95     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                   HHHHHH CS
                      TetR_C_33 78 lvsLel 83
                                   +vs  +
  gi|121637718|ref|YP_977941.1| 48 MVSSAV 53
                                   333333 PP

  == domain 2  score: 86.5 bits;  conditional E-value: 5e-28
                                    HHHHHHHHHHHHH-HHHHHHCCSS--TT-S-H.GHHCCCCHHHHHHHHHHHGGG---TH..................... CS
                      TetR_C_33   2 ralarayrrfAlahpaeYallfgspvpgyaap.delaaagarvlalllaalaalvaagl..................... 59 
                                     a+ara+r +A+++pa++all+gspvpgy+ap d++a  ++rv++++++a+aa  a+g                      
  gi|121637718|ref|YP_977941.1|  96 IAIARAVRGWAVTNPARWALLYGSPVPGYHAPpDRTAGVATRVVGAFFDAIAAGIATGDirltddvapqpmssdfekirq 175
                                    79*****************************768******************999************************* PP

                                    ....--CC.HHHHHHHHHHHHHHHHHHHHCTTT..TSSS-HHHHHHHHHH CS
                      TetR_C_33  60 ....ppad.avaaaralwaalhGlvsLelfghf..glpadpdalferlvd 102
                                        p++d +v  +++lwa + G++sLe+fg++  ++ +dp  +f+++ +
  gi|121637718|ref|YP_977941.1| 176 efgfPGDDrVVTKCFLLWAGVVGAISLEVFGQYgaDMLTDPGVVFDAQTR 225
                                    ***987777************************9888********99876 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.4e-10   1.6e-06       1      44 [.      21      64 ..      21      67 .. 0.95
   2 ?   -0.9   0.0      0.41   1.5e+03       6      17 ..     202     213 ..     199     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.4e-10
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLl 44
                                   I++ +r+ + ++G +++++r+IA+ +G+  +a+Yry +s++eLl
  gi|121637718|ref|YP_977941.1| 21 IVELGRRQLLDHGAAGLSLRAIARNLGMVSSAVYRYVSSRDELL 64
                                   788899*************************************8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                                    HHHHHHHHTTT- CS
                         TetR_N   6 relfaerGydat 17 
                                    +e+f+++G d +
  gi|121637718|ref|YP_977941.1| 202 LEVFGQYGADML 213
                                    79******8855 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   8.9e-07    0.0032       2      39 ..      13      58 ..      12      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.9e-07
                         HTH_23  2 asereRlrillllae........GlsvreIAreLgvsrrTvyrwlk 39
                                   a+e++ ++i+ l ++        Gls r+IAr Lg+  + vyr+++
  gi|121637718|ref|YP_977941.1| 13 AREQIEAKIVELGRRqlldhgaaGLSLRAIARNLGMVSSAVYRYVS 58
                                   56666666666666445556667********************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-06    0.0043      11      40 ..      29      58 ..      28      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                                   T-CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLq 40
                                   +l +++ +l+l+ +Ar++g+  S+v+R+++
  gi|121637718|ref|YP_977941.1| 29 LLDHGAAGLSLRAIARNLGMVSSAVYRYVS 58
                                   68889999********************86 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.042      18      39 ..      34      55 ..      26      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                         HTH_38 18 aeGlslreIArrLgrspsTIsR 39
                                   a+Glslr+IAr Lg   s ++R
  gi|121637718|ref|YP_977941.1| 34 AAGLSLRAIARNLGMVSSAVYR 55
                                   79************98888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1792.35
//
Query:       gi|121637720|ref|YP_977943.1|  [L=487]
Description: hypothetical protein BCG_1852 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-51  174.9   3.5    3.5e-51  174.6   3.5    1.1  1  FAD_binding_2  FAD binding domain
    9.1e-12   45.2   5.4    3.2e-11   43.4   5.4    1.8  1  DAO            FAD dependent oxidoreductase
    1.1e-08   34.9   1.1    2.2e-07   30.6   1.7    2.0  2  FAD_oxidored   FAD dependent oxidoreductase
    1.9e-07   30.2   5.7     0.0075   15.0   0.0    2.1  2  HI0933_like    HI0933-like protein
    1.1e-06   28.2   0.9    5.1e-05   22.6   0.0    2.7  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.015   14.6   2.2      0.015   14.6   2.2    1.8  2  Thi4           Thi4 family
      0.063   12.6   3.3       0.12   11.7   3.3    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.067   12.4   2.5        3.5    6.8   2.3    2.1  2  FAD_binding_3  FAD binding domain
      0.098   12.9   6.9       0.28   11.4   6.9    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.48    9.4  12.2        6.4    5.7   9.2    2.1  2  GIDA           Glucose inhibited division protein A
        1.5    9.4   3.3        8.1    7.1   0.0    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
        2.8    7.8   4.0        5.5    6.8   4.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   3.5   2.3e-54   3.5e-51       1     404 [.      22     452 ..      22     471 .. 0.85

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 2.3e-54
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT...SSGGSTC.CHHHHHHHHHHHHTTT-S-H CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl.speqkkagikdspelhrtdtlkaldeladq 79 
                                    Dv ViG G+AG +AA++aa aG++v+v+e + + gg+ta ++G + + + ++ q + g  dspe++ ++++++++e  d+
  gi|121637720|ref|YP_977943.1|  22 DVTVIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTTALAGGHFYLGGgTTVQLATGHPDSPEEMYKYLVAVSREP-DH 100
                                    899****************************************9988642788899999***************977.** PP

                                    HHHHHHHHTHHHHHHHHHHTT----B...........CCTSSB-EEE-TT-SST.............EEEE-.STT-... CS
                  FAD_binding_2  80 plveafveaapeavdeLeelgvpfsr...........tedgpvdvrelGglsat.............artlhdaadarre 135
                                    + ++a+++ + e  ++Le lg++f r           +          G +                a  +h+++++   
  gi|121637720|ref|YP_977943.1| 101 DKIRAYCDGSVEHFNWLEGLGFQFERsyfpgkaviqpN--------TEGLMFTGnekvwpflelavpAPRGHKVPVP--G 170
                                    **************************666555555552........3333333344444555544444447778888..7 PP

                                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEEC.TTEEEEEEEEETTTTCEEEEEESEEEE-----GG.......... CS
                  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLive.dgrvtGavvenpesgrevrirakavvlatgGfgr..allkellg 212
                                      +    ++  l+++a ++g++++ +t a+eLiv+ +g+vtG++ +  + +++ +i+ak v++a+gGf    +++ ++++
  gi|121637720|ref|YP_977943.1| 171 DTGGAAMVIDLLLKRAASLGIQIRYETGATELIVDgTGKVTGVMWK--RFSETGAIKAKSVIIAAGGFVMnpDMVAKYTP 248
                                    77888888899***********************7466******99..999999****************9*99999999 PP

                                    ..GSSSBSSGT.T-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTHGGGS- CS
                  FAD_binding_2 213 aaaeaettnap.avtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFmnelas 291
                                    ++ae+  +      +G g++l+++ag+a +   m+++ +  +  +    +s +L         gi+v+k G+rF++e  s
  gi|121637720|ref|YP_977943.1| 249 KLAEKPFVLGNtYDDGLGIRLGVSAGGATQH--MDQMFITAPPYP----PSILLT--------GIIVNKLGQRFVAED-S 313
                                    99988887777699**************888..998888777777....666655........**************9.* PP

                                    HHHHHHHHH.HHHHTTTSCCBEEEE-TT............................SSHHHHHHHSHHHHHHHHHCCT.. CS
                  FAD_binding_2 292 rdvvsrailekeiaeggseanvyldash...........................gldaegleatleaineeaangldkd 344
                                    ++  ++ ++   ++++ s+a  yl+++                            g+++ +l+atl+++n  aa+g+d+d
  gi|121637720|ref|YP_977943.1| 314 YHSRTAGFI---MEQPDSAA--YLIVDEahlehpkmplvplidgwetvvemeaalGIPPGNLAATLDRYNAYAARGADPD 388
                                    *****9999...67777744..55555556************************************************** PP

                                    ....S-TTTSEEE.......EEEEE....EEES-EEEBETTSBESTTEEESSBTEEE-STCEES CS
                  FAD_binding_2 345 fgrgidpadrpipgpfyavkvvpaq....hytmgGvetdengrvldadgqpipGLYAaGevaag 404
                                    f+++ +  +    gp+ a +++ +      +t+gG++t  +g+vl++dg +++GLYA+G++a+ 
  gi|121637720|ref|YP_977943.1| 389 FHKQPEFLAAQDNGPWGAFDMSLGKamyaGFTLGGLATSVDGQVLRDDGAVVAGLYAVGACASN 452
                                    99764433332339********998766678*******************************43 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   5.4   2.2e-14   3.2e-11       1     204 [.      22     237 ..      22     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.2e-14
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS........STHHSTH.........HHHHHH CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl........rylpeas.........elarls 61 
                                    dv +iG Gi+G ++A  +a++g  V++le++  ag g++  ++g+++ g               +          l+ +s
  gi|121637720|ref|YP_977943.1|  22 DVTVIGFGIAGGCAAVSAAAAGarVLVLERAAAAG-GTTALAGGHFYLGGgttvqlatG-----HpdspeemykYLVAVS 95 
                                    89*****************************6666.**********9888777544330.....3455666777777999 PP

                                    HHH.HHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEH.HHHHHHSTTST...TTSEE.. CS
                            DAO  62 lea.leelreleeelgididyrrtGllslaadeeelealdkllallleagldaellda.eevrelepalp...gllga.. 134
                                    +e  ++ +r++++    ++ + +    + +++   +++  + ++ ++  gl   ++++ e   +++p l+   +   +  
  gi|121637720|ref|YP_977943.1|  96 REPdHDKIRAYCDGSVEHFNWLEGLGFQFERS--YFPGK-AVIQ-PNTEGL---MFTGnE---KVWPFLElavPAPRGhk 165
                                    99999*******99888888888777787754..56663.3333.334555...788834...78887334453333311 PP

                                    EEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEE....EECTEEEEEEEEEEE--GGGH CS
                            DAO 135 lfypdtgqvdpakltaalaraaealGveilegtevtgleeed.gkvwgve....rttpgendaadavVnaaGaws 204
                                    + +p+  +  +a ++  l+++a++lG++i+++t +t+l  ++ gkv+gv      +t g++ +a+ v++aaG ++
  gi|121637720|ref|YP_977943.1| 166 VPVPG-DTGGAAMVIDLLLKRAASLGIQIRYETGATELIVDGtGKVTGVMwkrfSET-GAI-KAKSVIIAAGGFV 237
                                    34555.444889999999999****************866557******88855433.764.4477******884 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.7   1.5e-10   2.2e-07       1      48 [.      22      69 ..      22     116 .. 0.88
   2 ?    1.6   0.0     0.093   1.4e+02      85     140 ..     171     230 ..     143     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.5e-10
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig 48
                                   Dv V+G g+aG +AA++Aa aGa+vl++e+    GG+++ +++   +g
  gi|121637720|ref|YP_977943.1| 22 DVTVIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTTALAGGHFYLG 69
                                   9************************************99988877666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.093
                   FAD_oxidored  85 epevakavleeml...aeagvtvllntrlvevekeg.kriesvtveskegrktirAkvfi 140
                                    +   a+ v++ +l   a  g+++ ++t ++e +++g +++++v  ++ +++ +i+Ak +i
  gi|121637720|ref|YP_977943.1| 171 DTGGAAMVIDLLLkraASLGIQIRYETGATELIVDGtGKVTGVMWKRFSETGAIKAKSVI 230
                                    55667778888888776779**************97456****9977668*******998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   5.0   1.3e-05     0.019       2      44 ..      22      64 ..      21      69 .. 0.94
   2 !   15.0   0.0     5e-06    0.0075     107     166 ..     174     237 ..     163     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGG CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGg 44
                                   dv viG G AG  aA+saa++g+rVl+le+a ++g   +++Gg
  gi|121637720|ref|YP_977943.1| 22 DVTVIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTTALAGG 64
                                   89*******************************9998888886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5e-06
                                    -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE----SS CS
                    HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvkt.k...seeeleadklvlAtGGlS 166
                                     a+ ++d+llk++ + g+++r+et  +++  + +gk++  + k   ++++++a+++++A GG  
  gi|121637720|ref|YP_977943.1| 174 GAAMVIDLLLKRAASLGIQIRYETGATELIVDGTGKVTGVMwKrfsETGAIKAKSVIIAAGGFV 237
                                    6899************************988777655432223333999*************65 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.4e-08   5.1e-05       2     119 ..      22     245 ..      21     273 .. 0.85
   2 ?    2.7   0.1      0.04        59     249     279 ..     423     453 ..     417     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.4e-08
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHHHCHHHHHHHHHHHHH............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcllskallgvaedaeias............. 57 
                                    dv viG G+AG  aa  +a+aga+v+++e           ++g++ +gg    + ++g ++ +e++              
  gi|121637720|ref|YP_977943.1|  22 DVTVIGFGIAGGCAAVSAAAAGARVLVLEraaaaggttalAGGHFYLGGGTTVQLATGHPDSPEEMYkylvavsrepdhd 101
                                    89**************************8888988999999999999999999999999999998889************ PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                    Pyr_redox_2  58 ................................................................................ 57 
                                                                                                                    
  gi|121637720|ref|YP_977943.1| 102 kiraycdgsvehfnwleglgfqfersyfpgkaviqpnteglmftgnekvwpflelavpaprghkvpvpgdtggaamvidl 181
                                    ******************************************************************************99 PP

                                    ..HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEEC.TCEEEEEESEEEE---EEE-BCTCTTC CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ..evvkklnqgielllgeevvkidpgk.kkvklekkke.gdeekiaydklvlAtGssprdlgipGv 119
                                      +   +l+ +i++ +g  +++++ +  +kv+    k+ +++  i+++++++A G+   ++++ + 
  gi|121637720|ref|YP_977943.1| 182 llKRAASLGIQIRYETG--ATELIVDGtGKVTGVMWKRfSETGAIKAKSVIIAAGGFVMNPDMVAK 245
                                    87554555555555555..888775555899986666588899************99988866544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.04
                                    T-EEEETTEEE--TTSBESSTTEEE-GGGC..T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                    Pyr_redox_2 249 glelderggivvdeflrtnvpgiyaiGDva..g 279
                                    gl++  +g+++ d+     v g+ya+G++a   
  gi|121637720|ref|YP_977943.1| 423 GLATSVDGQVLRDDGA--VVAGLYAVGACAsnI 453
                                    6666667777777766..489*********440 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.2   9.7e-06     0.015      17      64 ..      20      66 ..       8      68 .. 0.88
   2 ?   -3.4   0.0         3   4.5e+03     203     223 ..     431     451 ..     425     455 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.7e-06
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64
                                   + Dv ++G G +G  aa   a + + +v++ler  + GG + l G  f
  gi|121637720|ref|YP_977943.1| 20 DVDVTVIGFGIAGGCAAVSAAAA-GARVLVLERAAAAGGTTALAGGHF 66
                                   579**********9999999988.***************999877666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3
                                    HHHHHECEEETTEEE-THHHH CS
                           Thi4 203 aivkktrevvpnlyvaGmeva 223
                                    +++++  +vv +ly+ G  ++
  gi|121637720|ref|YP_977943.1| 431 QVLRDDGAVVAGLYAVGACAS 451
                                    566777777777777776555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.3   7.9e-05      0.12      30      62 ..      22      54 ..       8      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.9e-05
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                    v+viG G+aG  A+  a++ ga+V vl+  +a
  gi|121637720|ref|YP_977943.1| 22 DVTVIGFGIAGGCAAVSAAAAGARVLVLERAAA 54
                                   79*************************998766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.3    0.0024       3.5       1      35 [.      20      54 ..      20      60 .. 0.93
   2 ?    3.6   0.0     0.021        32     106     163 ..     177     234 ..     172     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0024
                                   EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   ++dV ++G G aG  +a   + aG rv+++e+ + 
  gi|121637720|ref|YP_977943.1| 20 DVDVTVIGFGIAGGCAAVSAAAAGARVLVLERAAA 54
                                   689*****************************875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                                    HHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                  FAD_binding_3 106 eleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                    ++  +L+++a++ g+q+r +t  + l  d++g  + v  k+  e+  ++ak ++ a G
  gi|121637720|ref|YP_977943.1| 177 MVIDLLLKRAASLGIQIRYETGATELIVDGTGKVTGVMWKRFSETGAIKAKSVIIAAG 234
                                    67789**********************9999988888888888888999998876655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.9   0.00019      0.28       1      35 [.      25      59 ..      25      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                   ++G G++G +aA  +a ag++vl+le++   GG  
  gi|121637720|ref|YP_977943.1| 25 VIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTT 59
                                   8999****************************975 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.2    0.0043       6.4       1      28 [.      22      49 ..      22      64 .. 0.87
   2 ?    4.5   0.0      0.01        16     117     153 ..     199     238 ..     183     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0043
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   dv+ViG G AG  AA+ aa +Ga+vl +
  gi|121637720|ref|YP_977943.1| 22 DVTVIGFGIAGGCAAVSAAAAGARVLVL 49
                                   79***********************988 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                                    -EEEEEECTTEEEEEEET...TS-EEEECEEEE--TT-BT CS
                           GIDA 117 eveeliveekkvkgvvte...dgetikakavviatGtflk 153
                                      e +++ ++kv+gv+ +   +  +ikak+v+ia+G f+ 
  gi|121637720|ref|YP_977943.1| 199 ATELIVDGTGKVTGVMWKrfsETGAIKAKSVIIAAGGFVM 238
                                    33444444599***98761114567999********9975 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.4      0.57   8.6e+02       2      32 ..      23      53 ..      22      59 .. 0.92
   2 ?    7.1   0.0    0.0054       8.1      44      76 ..     180     213 ..     175     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.57
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                   v+v+G G  g  +A  +a+ g++V v+er+ 
  gi|121637720|ref|YP_977943.1| 23 VTVIGFGIAGGCAAVSAAAAGARVLVLERAA 53
                                   79**************************985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                      Pyr_redox  44 kilqeklekngievllntkveeiegsedg.vesv 76 
                                    ++l ++   +gi+++++t ++e+  ++ g v++v
  gi|121637720|ref|YP_977943.1| 180 DLLLKRAASLGIQIRYETGATELIVDGTGkVTGV 213
                                    67889999*******************9999998 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.0    0.0037       5.5       2      34 ..      23      55 ..      22      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0037
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v+viG G+ G   a  +a+ag +V +++++++a
  gi|121637720|ref|YP_977943.1| 23 VTVIGFGIAGGCAAVSAAAAGARVLVLERAAAA 55
                                   9**************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3435.54
//
Query:       gi|121637721|ref|YP_977944.1|  [L=501]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-36  123.4  21.7    5.2e-36  122.9  21.7    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9  21.7   2.9e-40   5.2e-36       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 2.9e-40
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv+ Pealaa+a+dlagigs++ +anaaaa ptt+vlaaaaDeVSaa+Aalfs haq+yqalsaqaa fheqfv+al+a
  gi|121637721|ref|YP_977944.1|  1 MSFVVTIPEALAAVATDLAGIGSTIGTANAAAAVPTTTVLAAAADEVSAAMAALFSGHAQAYQALSAQAALFHEQFVRALTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +agsYaaaEaa
  gi|121637721|ref|YP_977944.1| 83 GAGSYAAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 3419.98
//
Query:       gi|121637722|ref|YP_977945.1|  [L=639]
Description: drugs-transport transmembrane ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-99  330.3   1.3    1.3e-98  329.7   1.3    1.3  1  ABC_membrane_2  ABC transporter transmembrane region 2
    1.2e-26   93.9   5.0    2.9e-26   92.6   5.0    1.5  1  SbmA_BacA       SbmA/BacA-like family
    3.3e-15   56.8   0.0    6.8e-15   55.8   0.0    1.6  1  ABC_tran        ABC transporter
    7.5e-05   23.2   0.2    0.00018   21.9   0.2    1.6  1  AAA_16          AAA ATPase domain
    0.00035   20.8   0.0    0.00062   20.1   0.0    1.5  1  AAA_22          AAA domain
    0.00084   19.3   0.2     0.0038   17.1   0.0    1.9  2  NACHT           NACHT domain
     0.0011   18.7   0.0     0.0025   17.5   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
     0.0018   18.0   0.0     0.0031   17.3   0.0    1.3  1  AAA_30          AAA domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.036   13.6   0.0    1.5  1  AAA_25          AAA domain
      0.018   15.5   0.0      0.031   14.8   0.0    1.2  1  AAA_23          AAA domain
      0.046   12.8   0.0      0.078   12.0   0.0    1.2  1  T2SSE           Type II/IV secretion system protein
      0.047   13.9   0.1      0.089   13.0   0.1    1.4  1  AAA_28          AAA domain
      0.048   13.6   0.0      0.081   12.8   0.0    1.2  1  RsgA_GTPase     RsgA GTPase
      0.077   12.6   0.0       0.13   11.8   0.0    1.3  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.095   12.5   0.1       0.29   10.9   0.0    1.8  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
       0.11   12.4   0.0        0.2   11.5   0.0    1.3  1  NTPase_1        NTPase
       0.12   13.0   0.0       0.22   12.1   0.0    1.4  1  AAA_18          AAA domain


Domain annotation for each model (and alignments):
>> ABC_membrane_2  ABC transporter transmembrane region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7   1.3  1.2e-101   1.3e-98       1     269 []      54     358 ..      54     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 1.2e-101
                 ABC_membrane_2   1 Llkili.pklkskeallllvlllllvlrtllsvlvaqldgklvkalva..............knvraFvlsllkfallav 65 
                                    ++++++ ++++++++l+l+vlll++vl+++l+vl++++ +++++al++              ++vr+F++s+++f+++av
  gi|121637722|ref|YP_977945.1|  54 ITRAYFvGPNSVRVWLMLGVLLLSVVLAVRLNVLFSYQGNDMYTALQKafegiasgdgtvkrSGVRGFWMSIGVFSVMAV 133
                                    7899999************************************************************************* PP

                 ABC_membrane_2  66 pasfvnsalkYltqkLalafRkrLtkhllseYlknrtyYkvsnlderidnpDqritqDvekFt...........s.slss 133
                                    +++++++a++Yltq++++a+R++Lt+hl++++l++r+yY+  ++de+idnpDqri+qDv++Ft           + ++s+
  gi|121637722|ref|YP_977945.1| 134 LHVTRVMADIYLTQRFIIAWRVWLTHHLTQDWLDGRAYYRDLFIDETIDNPDQRIQQDVDIFTagaggtpnapsNgTAST 213
                                    *************************************************************************956**** PP

                 ABC_membrane_2 134 LlsglvkpildvilftfiLwslsgtlgl..........lllllyvllatvilriigpplgklvaeeeklegefRylhsrl 203
                                    Ll+g+v++i++vi+ft+iLw+lsgtl++          +++l+yv++atvi +iig+pl++l++++ekl+++fRy+++rl
  gi|121637722|ref|YP_977945.1| 214 LLFGAVQSIISVISFTAILWNLSGTLNIfgvsipramfWTVLVYVFVATVISFIIGRPLIWLSFRNEKLNAAFRYALVRL 293
                                    ******************************************************************************** PP

                 ABC_membrane_2 204 itnaEeIAFyrGeevEkkqlqrrfkslidnlrrilsrrlrlgiieafvlkYlasilgyvlvalpif 269
                                    +++aE+++FyrGe+vE +qlqrrf+++idn+rr+++r++++++++ +v ++++++l++v++a+++f
  gi|121637722|ref|YP_977945.1| 294 RDAAEAVGFYRGERVEGTQLQRRFTPVIDNYRRYVRRSIAFNGWNLSV-SQTIVPLPWVIQAPRLF 358
                                    ************************************************.**************998 PP

>> SbmA_BacA  SbmA/BacA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   5.0   2.8e-29   2.9e-26       7     306 ..      68     400 ..      62     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 2.8e-29
                      SbmA_BacA   7 WsilgtalilfvlyfqvevsvkvnaWygpfydliqkala.......apekvtieefyaelldfllialvavviavlnaff 79 
                                    W +lg  ++l+++ + v+++v   +   ++y  +qka+        + +++ ++ f+ ++  f+++a++ v+  +   ++
  gi|121637722|ref|YP_977945.1|  68 WLMLG--VLLLSVVLAVRLNVLFSYQGNDMYTALQKAFEgiasgdgTVKRSGVRGFWMSIGVFSVMAVLHVTRVMADIYL 145
                                    54444..556666677777777777777888889988642111111233456789*****************9999**** PP

                      SbmA_BacA  80 vshyifrWrtamneyyiskw.......dkl...reieGasqrvqedtmrfak............iledlGvslvkaimtl 137
                                    ++ +i  Wr  ++++ ++ w         l   ++i+   qr+q+d+  f+             +   l    v++i+ +
  gi|121637722|ref|YP_977945.1| 146 TQRFIIAWRVWLTHHLTQDWldgrayyRDLfidETIDNPDQRIQQDVDIFTAgaggtpnapsngTASTLLFGAVQSIISV 225
                                    *****************99943332221223356899**********99975233323222233556777889******* PP

                      SbmA_BacA 138 iaflPvlfelskkvkvlpilgeiekslviaalvwslgGtvlllvvGiklpglefnnqkveaayrkelvygeddv...... 211
                                    i+f+ +l++ls +++++    +i++++ ++ lv+ ++ tv+++++G+ l  l f+n k +aa+r  lv   d +      
  gi|121637722|ref|YP_977945.1| 226 ISFTAILWNLSGTLNIF--GVSIPRAMFWTVLVYVFVATVISFIIGRPLIWLSFRNEKLNAAFRYALVRLRDAAeavgfy 303
                                    ************99944..448**********************************************988876223333 PP

                      SbmA_BacA 212 ..drakpatlkelfkdvrknyfrlylhylyfniarilylqldnlfallllapsivagkitlGvlkqitnafgkvreslqy 289
                                      +r++ ++l+  f+ v  ny r  ++ + fn ++   +q+ +  + ++ ap ++ag+i +G + q +++fg++++sl++
  gi|121637722|ref|YP_977945.1| 304 rgERVEGTQLQRRFTPVIDNYRRYVRRSIAFNGWNLSVSQTIVPLPWVIQAPRLFAGQIDFGDVGQTATSFGNIHDSLSF 383
                                    3357889999********************************************************************** PP

                      SbmA_BacA 290 linsWttivellsiykr 306
                                    + n++ +   +++   r
  gi|121637722|ref|YP_977945.1| 384 FRNNYDAFASFRAAIIR 400
                                    ***99987776665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   6.4e-18   6.8e-15       2     137 .]     444     579 ..     443     579 .. 0.73

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 6.4e-18
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + +++ l +g  ++i+G++GaGK+tLl+ la+l   ++G+++  g +    +++ + +++ ++p   +l + + ++ n  
  gi|121637722|ref|YP_977945.1| 444 DPLDVRLDRGGSLVITGRSGAGKTTLLRSLAELWPYASGTLHRPGGE----NETMFLSQLPYVPLG-TLRDVV-CYPNsa 517
                                    5688999**********************************554322....333444444444444.222222.333355 PP

                                    ..HHHTCHHHHHHHSTTGGTTCBGESTTS..GGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..esdeeiekalsklglkelkdtvvkssp..ssLSgGqkqrvalarallkkpkllllDEpta 137
                                        d+ + + l+k+ l  l d+  ++++  + LS G++qrva ar+ll+kpk ++lDE t+
  gi|121637722|ref|YP_977945.1| 518 aaIPDATLRDTLTKVALAPLCDRLDEERDwaKVLSPGEQQRVAFARILLTKPKAVFLDESTS 579
                                    656666677777777777755555444336699**************************995 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   1.7e-07   0.00018      19     161 ..     448     595 ..     440     603 .. 0.47

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd..............ggiflrgkcdqlesaipy...........sa.l 72 
                                    vr +r+++++++G sG GK++l+r+l++ +  +                           s++py           ++  
  gi|121637722|ref|YP_977945.1| 448 VRLDRGGSLVITGRSGAGKTTLLRSLAELWPYAsgtlhrpggenetmF-----------LSQLPYvplgtlrdvvcYPnS 516
                                    6667789********************988888322222222222220...........222444222222222221212 PP

                         AAA_16  73 aqalareellrqlldeaesaeleawrekleeala........avpelagaea..........srllellkrllallsrde 134
                                    a a+  +  lr+ l++               ++         +        +          ++ + +++r+l  l+   
  gi|121637722|ref|YP_977945.1| 517 AAAI-PDATLRDTLTK---------------VALaplcdrldE--------ErdwakvlspgEQQRVAFARIL--LT--- 567
                                    3333.11222222222...............222222211110........0112223322233334444444..22... PP

                         AAA_16 135 rplvlvlDdlqwadeaslql.laaLlrl 161
                                    +p  ++lD+   a ++ l++ l++Llr+
  gi|121637722|ref|YP_977945.1| 568 KPKAVFLDESTSALDTGLEFaLYQLLRS 595
                                    3456777777777777777777777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.8e-07   0.00062       4      28 ..     452     476 ..     448     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.8e-07
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleq 28 
                                    + g+lv+tG sG+GKTtllr l+e 
  gi|121637722|ref|YP_977945.1| 452 RGGSLVITGRSGAGKTTLLRSLAEL 476
                                    689*******************986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.6e-06    0.0038       3      24 ..     456     477 ..     455     498 .. 0.91
   2 ?   -0.6   0.1       1.1   1.1e+03      83     139 ..     571     619 ..     513     623 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.6e-06
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    ++++G++G GKTtLl++la++w
  gi|121637722|ref|YP_977945.1| 456 LVITGRSGAGKTTLLRSLAELW 477
                                    689******************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                    EEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTS CS
                          NACHT  83 lLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeql 139
                                    ++++  +   l t         ++  L +l+r +l+ +  + ++ rp   r  e ql
  gi|121637722|ref|YP_977945.1| 571 AVFLDESTSALDT--------GLEFALYQLLRSELPDCIVVSVSHRPALERLHENQL 619
                                    4454333333444........444489999999999998888888887665555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0025      16      40 ..     447     471 ..     442     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                         AAA_29  16 tieidlkgatlltGpsGsGKSTllD 40 
                                    ++++d+ g+ ++tG+sG+GK+Tll 
  gi|121637722|ref|YP_977945.1| 447 DVRLDRGGSLVITGRSGAGKTTLLR 471
                                    57899889***************95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.9e-06    0.0031      21      45 ..     456     480 ..     448     519 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                         AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                     v+tG+ G+GKtt+l++l+e+w  a
  gi|121637722|ref|YP_977945.1| 456 LVITGRSGAGKTTLLRSLAELWPYA 480
                                    69********************876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.036       8      54 ..     425     474 ..     419     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                         AAA_25   8 savsvadlaapppprrwlvkg...llpagelallaGapgtGKttlaldla 54 
                                    ++v+ +d++++ p  + l++     l +g+  +++G++g+GKttl+ +la
  gi|121637722|ref|YP_977945.1| 425 ESVELNDIEVRTPAGDRLIDPldvRLDRGGSLVITGRSGAGKTTLLRSLA 474
                                    56788899999999999999766789*******************99887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.9e-05     0.031      20      39 ..     454     473 ..     441     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                         AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                    g  +ItG  GaGKTT+l+ +
  gi|121637722|ref|YP_977945.1| 454 GSLVITGRSGAGKTTLLRSL 473
                                    7889*************876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.4e-05     0.078      93     150 ..     417     474 ..     408     482 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                          T2SSE  93 lviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                    +  R ++ ++++l+d+ ++    +++ + l   + + g+++++G  g GKttll +l 
  gi|121637722|ref|YP_977945.1| 417 VLTRPSDDESVELNDIEVRTPAGDRLIDPLDVRLDRGGSLVITGRSGAGKTTLLRSLA 474
                                    5567888899999999999999999999999999********************8765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.4e-05     0.089       3      22 ..     457     476 ..     455     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
                         AAA_28   3 vitGgestGKTtlleaLaar 22 
                                    vitG +++GKTtll+ La+ 
  gi|121637722|ref|YP_977945.1| 457 VITGRSGAGKTTLLRSLAEL 476
                                    9****************974 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.7e-05     0.081      91     120 ..     444     474 ..     422     485 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.7e-05
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinall 120
                                    + l  +l+     v+ G SG+GK+tL+ +l+
  gi|121637722|ref|YP_977945.1| 444 DPLDVRLDRgGSLVITGRSGAGKTTLLRSLA 474
                                    55666666657899*************9997 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.13       3      21 ..     456     474 ..     455     480 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    +v+tG  G+GKTtLl++l 
  gi|121637722|ref|YP_977945.1| 456 LVITGRSGAGKTTLLRSLA 474
                                    69*************9986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.29       3      39 ..     457     490 ..     455     500 .. 0.77
   2 ?   -1.9   0.0       2.2   2.3e+03     234     285 ..     547     596 ..     540     611 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgg 39 
                                    v++G+ g+GK++LL+ l  l   ++++ g+ + ++g 
  gi|121637722|ref|YP_977945.1| 457 VITGRSGAGKTTLLRSLAEL---WPYASGTLHRPGGE 490
                                    9**************99766...66666666665555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                         AAA_21 234 arel.SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                    ++++ S G ++  a++ +ll  +   + +++DE  + L+  l   l++ll+++
  gi|121637722|ref|YP_977945.1| 547 WAKVlSPGEQQRVAFARILLTKP---KAVFLDESTSALDTGLEFALYQLLRSE 596
                                    55555777777767777777766...679999999888888888888888655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019       0.2       2      21 ..     456     475 ..     455     479 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    ++iTG++G GKtTl++ ++e
  gi|121637722|ref|YP_977945.1| 456 LVITGRSGAGKTTLLRSLAE 475
                                    78*************99887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.22       2      22 ..     457     477 ..     456     506 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                         AAA_18   2 lltGtpGvGKttlakeLskrl 22 
                                    ++tG +G+GKttl + L+++ 
  gi|121637722|ref|YP_977945.1| 457 VITGRSGAGKTTLLRSLAELW 477
                                    69***************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4055.25
//
Query:       gi|121637723|ref|YP_977946.1|  [L=547]
Description: hypothetical protein BCG_1855 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-46  156.1   0.8      5e-45  153.2   1.0    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      9e-31  106.7   0.0    2.1e-30  105.6   0.0    1.7  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    5.5e-21   74.7   0.1    1.5e-20   73.4   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.086   12.6   0.0       0.16   11.7   0.0    1.3  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   1.0   1.1e-48     5e-45       1     164 [.      11     172 ..      11     178 .. 0.98
   2 ?   -0.7   0.0       0.2   9.1e+02     119     146 ..     497     524 ..     457     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 1.1e-48
                                    EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                   TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                    m+++++++r+Lka g+++vf++ G+++ +++d ++ee gir++ +rhEq+aafaA+g++++t+ pgv+++t+gpG+tn++
  gi|121637723|ref|YP_977946.1|  11 MHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREE-GIRLIDTRHEQTAAFAAEGWSKVTRVPGVAALTAGPGITNGM 89 
                                    67899********************************.7***************************************** PP

                                    HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                   TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                     a+a A+++++Pl+vl g++p+ + g g lq e+d++ +++pv+++a + +s+e++  ++++A+++a s+++g++++++p
  gi|121637723|ref|YP_977946.1|  90 SAMAAAQQNQSPLVVLGGRAPALRWGMGSLQ-EIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFP 168
                                    *******************************.************************************************ PP

                                    HHHC CS
                   TPP_enzyme_N 161 kdvl 164
                                    +d+ 
  gi|121637723|ref|YP_977946.1| 169 MDHA 172
                                    **85 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                    HHCCCSSEEEE-SSGGGHHHHHHHHHHH CS
                   TPP_enzyme_N 119 lfrpvtkyaervtspeelpealrrAirt 146
                                    ++r +  + e v+ p+el++al+rA++ 
  gi|121637723|ref|YP_977946.1| 497 VVRALGGHGELVSVPAELRPALERAFAS 524
                                    4556666677788899999999999875 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.0   4.6e-34   2.1e-30       1     153 []     385     532 ..     385     532 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 4.6e-34
                                    ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEE CS
                   TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvl 80 
                                    d+G++  +a r+++ + p+ +l+sg +g++G g ++A++akla+p+r+vv + GDG+f ++++e  t vr+n+ ++ v+ 
  gi|121637723|ref|YP_977946.1| 385 DAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIG 464
                                    7899999999********************************************************************** PP

                                    E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                    nN+++g+ ++ +e  +g + +++     + +++ ++++alG +g  v+++  +el++al++a++++ pa+++v
  gi|121637723|ref|YP_977946.1| 465 NNGIWGLEKHPMEALYGYSVVAEL---RPGTRYDEVVRALGGHGELVSVP--AELRPALERAFASGLPAVVNV 532
                                    ****************98887766...899***************999**..*******************97 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.7   7.6e+03       9      22 ..      96     109 ..      91     111 .. 0.80
   2 !   73.4   0.0   3.3e-24   1.5e-20       1     137 []     199     326 ..     199     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                                    HH-SSEEEEE-CHH CS
                   TPP_enzyme_M   9 kaakrpvilvGggv 22 
                                    ++ + p++++Gg++
  gi|121637723|ref|YP_977946.1|  96 QQNQSPLVVLGGRA 109
                                    688999***99976 PP

  == domain 2  score: 73.4 bits;  conditional E-value: 3.3e-24
                                    HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SE CS
                   TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDl 80 
                                    +++aa ll++a+rpvi++G  v++ +a+++l +l+e+ +iPv+   m++gv+p dh l         s+a+++al eaD+
  gi|121637723|ref|YP_977946.1| 199 LDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGVVPADHRLA-------FSRARSKALGEADV 271
                                    589******************************************************87.......59************ PP

                                    EEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                   TPP_enzyme_M  81 vlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                     l++G+ +d+   +g    f + +++i  d  +    + ++v+ +++gd+++tl+aL
  gi|121637723|ref|YP_977946.1| 272 ALIVGVPMDFRLGFGG--VFGSTTQLIVADRVEPAREHPRPVAAGLYGDLTATLSAL 326
                                    **********776663..45556679999988888888889*************997 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.5e-05      0.16      24      70 ..     198     244 ..     194     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                    -SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET CS
                          CO_dh  24 alkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata 70 
                                    al  +a ++++a+rP+++ G +v +   e a  +  +e++++v + +
  gi|121637723|ref|YP_977946.1| 198 ALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNG 244
                                    5678999********************99999*********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3784.85
//
Query:       gi|121637724|ref|YP_977947.1|  [L=808]
Description: preprotein translocase subunit SecA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-82  275.0   0.1      1e-81  274.4   0.1    1.2  1  SecA_DEAD     SecA DEAD-like domain
    1.2e-21   77.5   0.3    3.9e-21   75.8   0.3    1.9  1  SecA_PP_bind  SecA preprotein cross-linking domain
    1.3e-19   71.1   1.5    3.7e-14   53.2   0.1    2.5  2  SecA_SW       SecA Wing and Scaffold domain
  ------ inclusion threshold ------
      0.088   12.8   0.1       0.97    9.4   0.0    2.5  2  ResIII        Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.4   0.1   2.3e-85     1e-81       4     288 ..      49     423 ..      46     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 274.4 bits;  conditional E-value: 2.3e-85
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD   4 llgsknerelkklkkiveeineleeelkalsdeeLrakteelkerlaegealdellpeafalvreaakrvlgmrhydvQl 83 
                                    llg+++e++ ++  + v++ +e ++e ++lsde+Lr+ +  l+    ++   +  +p+ +a+ reaa+r +g+r++dvQl
  gi|121637724|ref|YP_977947.1|  49 LLGASTEKNRSRSLADVTASAEYDKEAADLSDEKLRKAAGLLNLDDLAE---SADIPQFLAIAREAAERRTGLRPFDVQL 125
                                    667788888888888888899999**************99998433333...345899********************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  84 iGglvlhegkiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerre 163
                                    +G+l +  g++ em+TGEGKtl+ +++a+  al+g+ vhvvt+ndYLa+rdaewmgp+ +++Gl+vg+i+++ +++err+
  gi|121637724|ref|YP_977947.1| 126 LGALRMLAGDVIEMATGEGKTLAGAIAAAGYALAGRHVHVVTINDYLARRDAEWMGPLLDAMGLTVGWITADSTPDERRT 205
                                    ******************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 164 aYeaditYgtnnelgfdyLrDnlalskeelvqrglnfaivDEvDsvLiDeArtpLiisgpaeeeselyeeakklvkelee 243
                                    aY+ d+tY++ ne+gfd LrD+l+++ ++lv  + ++a++DE+DsvL+DeA  pL+++g +++e+  +e   +lv+el  
  gi|121637724|ref|YP_977947.1| 206 AYDRDVTYASVNEIGFDVLRDQLVTDVNDLVSPNPDVALIDEADSVLVDEALVPLVLAGTTHRETPRLEI-IRLVAELVG 284
                                    ***********************************************************76665554443.344444444 PP

                                    xxx............................................................................. RF
                      SecA_DEAD 244 eed............................................................................. 246
                                    ++d                                                                             
  gi|121637724|ref|YP_977947.1| 285 DKDadeyfatdsdnrnvhltehgarkvekalggidlyseehvgttltevnvalhahvllqrdvhyivrddavhlinasrg 364
                                    44445567788888889999999999****************************************************** PP

                                    .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 247 .................akegveieeesqtlatitlqnffrlYeklaGmtGTaeteaee 288
                                                     akeg+e +e+ ++l tit+q + ++Y  ++GmtGTa  + e+
  gi|121637724|ref|YP_977947.1| 365 riaqlqrwpdglqaaveAKEGIETTETGEVLDTITVQALINRYATVCGMTGTALAAGEQ 423
                                    *****************************************************877665 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.3   8.6e-25   3.9e-21      14     111 .]     284     381 ..     273     381 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 8.6e-25
                                    CCCHTTCCECCCTTTSEEEESHHHHHHHHHCCT-SSSTTSCCHC.CHHHHHHHHHHHHHCSTTTTTEEECTTCEEEBSTT CS
                   SecA_PP_bind  14 kklkeeedyevdekkktveltekGvekvekllkvkeelydeenl.elvhhvnqaLkAhtlferdvdYivkdgeviivDef 92 
                                     + +++e+++ d+ +++v+lte+G +kvek+l+   +ly+ee++ +++  vn aL+Ah l++rdv+Yiv+d+ v +++ +
  gi|121637724|ref|YP_977947.1| 284 GDKDADEYFATDSDNRNVHLTEHGARKVEKALGG-IDLYSEEHVgTTLTEVNVALHAHVLLQRDVHYIVRDDAVHLINAS 362
                                    4456678*************************77.799988885378999****************************** PP

                                    TSSEBTS--SSTTHHHHHH CS
                   SecA_PP_bind  93 tGRlmegrrysdGLhqaie 111
                                     GR+ + +r+ dGL+ a+e
  gi|121637724|ref|YP_977947.1| 363 RGRIAQLQRWPDGLQAAVE 381
                                    *****************98 PP

>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   9.3e-07    0.0042       9      53 ..     622     666 ..     614     673 .. 0.87
   2 !   53.2   0.1   8.3e-18   3.7e-14     107     187 ..     670     752 ..     666     764 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.3e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                        SecA_SW   9 ksienaQkkvEernfdiRknlleYDdVmnkQRkviYkqRrevLeg 53 
                                    + +++aQ+  E+r  d+  n+ +Y + + +QR +i ++R+ +L++
  gi|121637724|ref|YP_977947.1| 622 SLLDHAQRVAEGRLLDVHANTWRYNQLIAQQRAIIVERRNTLLRT 666
                                    56899**************************************44 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 8.3e-18
                                    HHHHHHHHHHHHHHHHHHC..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSSSS-CCHHHHHHHHHHHHHHH CS
                        SecA_SW 107 aeellekaekayekkeeei..ellrelervvlLevlDkaWkehLdamdeLregiglrgygqkdPlqeYkkegfelFeeml 184
                                    +eel e a k+ye+ ++++  e l+++ r+++L  lD+ W +hL  + ++re+i+lr++g ++Pl e+++ +++ F ++ 
  gi|121637724|ref|YP_977947.1| 670 REELAELAPKRYEELSDKVseERLETICRQIMLYHLDRGWADHLAYLADIRESIHLRALGRQNPLDEFHRMAVDAFASLA 749
                                    78899999999999999999767******************************************************998 PP

                                    HHH CS
                        SecA_SW 185 ari 187
                                    a+ 
  gi|121637724|ref|YP_977947.1| 750 ADA 752
                                    875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00022      0.97      28      58 ..     136     166 ..     127     255 .. 0.87
   2 ?    0.0   0.2      0.17   7.5e+02      46      96 ..     643     695 ..     639     763 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                                    EEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                         ResIII  28 likmaTGtGKTlvaaklierllkkgkeekfl 58 
                                    +i+maTG GKTl  a +++ ++ +g+  +++
  gi|121637724|ref|YP_977947.1| 136 VIEMATGEGKTLAGAIAAAGYALAGRHVHVV 166
                                    699*********9999999888887755554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                                    HHH-S.....-EEEEESSHHHHHHHH..HHGGGGTGG....GEEEESSS-B-- CS
                         ResIII  46 erllkkgkeekflflvprkslleqtl..eefkkflseaykeigkkvsgdkkka 96 
                                    +r+ +   +++++++  r++ll      ee+++++++ y+e + kvs+++ + 
  gi|121637724|ref|YP_977947.1| 643 WRYNQLIAQQRAIIVERRNTLLRTVTarEELAELAPKRYEELSDKVSEERLET 695
                                    66666666667777777777777655557788888888777777766665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 5458.73
//
Query:       gi|121637725|ref|YP_977948.1|  [L=209]
Description: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase pgsA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   51.4   0.3    1.3e-13   51.4   0.3    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.059   14.3   0.5      0.059   14.3   0.5    2.7  2  PIG-Y            Phosphatidylinositol N-acetylglucosaminyltra


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.3   1.5e-17   1.3e-13       2      66 .]      13      77 ..      12      77 .. 0.93
   2 ?   -2.8   4.5       1.3   1.2e+04      16      34 ..     161     179 ..      82     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.5e-17
                                   -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   +Pn+++++rl+l+ + ++++l+++   +++++l++++++D+ DGk+AR lnq+s+lG+llD+ +D
  gi|121637725|ref|YP_977948.1| 13 VPNMLSVIRLALIPAFVYVVLSAHANGWGVAILVFSGVSDWADGKIARLLNQSSRLGALLDPAVD 77
                                   7***********999888888888899999999*******************888*******998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                                    HHHHGGGS-H..HHHHHHH CS
                CDP-OH_P_transf  16 lailllltyyplvlailll 34 
                                      ++l++ +y +++a++l+
  gi|121637725|ref|YP_977948.1| 161 GWAFLIWGMYAYLWAFVLY 179
                                    2222232333345555554 PP

>> PIG-Y  Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7      0.12   1.1e+03      36      50 ..      65      87 ..      22     101 .. 0.44
   2 ?   14.3   0.5   6.6e-06     0.059       2      25 ..     155     178 ..     154     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                          PIG-Y 36 v........laddryYcylvpll 50
                                   +         a dr Y + vp++
  gi|121637725|ref|YP_977948.1| 65 SsrlgalldPAVDRLYMVTVPIV 87
                                   23333332211335777777753 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.6e-06
                          PIG-Y   2 yallltsvllfivgmyavlfskll 25 
                                    ++ll++++ ++i gmya l+ ++l
  gi|121637725|ref|YP_977948.1| 155 HVLLACGWAFLIWGMYAYLWAFVL 178
                                    589****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1491.97
//
Query:       gi|121637726|ref|YP_977949.1|  [L=307]
Description: hypothetical protein BCG_1858 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-34  119.5   0.0    1.9e-34  118.6   0.0    1.4  1  DUF881    Bacterial protein of unknown function (DUF881)


Domain annotation for each model (and alignments):
>> DUF881  Bacterial protein of unknown function (DUF881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0     1e-38   1.9e-34       2     145 .]     150     303 ..     149     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 1e-38
                         DUF881   2 leelkllaGltpveGpGvtitlddakkaeeeaeee...........vhdedLldvvneLraaGAeaIsingqRivatsai 70 
                                    l+ l+l+a+  pv GpG+t+t++d+ ++ + ++             + d+dL+ vvn L+++GAeaIsi+g+Ri+++ +i
  gi|121637726|ref|YP_977949.1| 150 LDVLSLAAASAPVVGPGLTVTVTDPGASPNLSD-VskqrvsgsqqiILDRDLQLVVNSLWESGAEAISIDGVRIGPNVTI 228
                                    778999*******************87755444.2589****************************************** PP

                         DUF881  71 rcagnailvdgrrispPyeikaIGdpekLesalniseavggllellke.glsvtvekseevtipayrgplelkyak 145
                                    r+ag+ailvd+++ s+Py+i a+G p+++++ +++s+++ +l+ l+++ g+ v+v+  + + +pa  ++ ++k+ak
  gi|121637726|ref|YP_977949.1| 229 RQAGGAILVDNNPTSSPYTILAVGPPHAMQDVFDRSAGLYRLRLLETSyGVGVSVNVGDGLALPA-GATRDVKFAK 303
                                    ************************************99999999999879***************.5566888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2240.48
//
Query:       gi|121637727|ref|YP_977950.1|  [L=121]
Description: hypothetical protein BCG_1859 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-33  114.1   3.8    3.6e-33  113.5   3.8    1.3  1  DUF1290    Protein of unknown function (DUF1290)
  ------ inclusion threshold ------
       0.21   11.1   0.1       0.21   11.1   0.1    1.8  2  DUF1129    Protein of unknown function (DUF1129)
       0.52   10.8   6.7          1    9.8   6.7    1.6  1  FtsX       FtsX-like permease family
        1.1    9.5   0.1        1.1    9.5   0.1    3.0  3  HIG_1_N    Hypoxia induced protein conserved region
          5    6.7   6.0          4    7.0   0.5    2.0  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> DUF1290  Protein of unknown function (DUF1290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   3.8     1e-36   3.6e-33       1      86 []      32     119 ..      32     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 1e-36
                        DUF1290   1 ipaayskylsvailaaldsvfGgiraslekkFdekvfisgffsnvllAalLvylGdklgv..dlylaavvvfgirifqnl 78 
                                    +p+ +++yl++a++aald+vfGg+ra+le+ Fd kvf+++f++nvl+Aal+vy+Gd+lgv  +l++a++vv+girif n 
  gi|121637727|ref|YP_977950.1|  32 VPEVIQPYLPIAVVAALDAVFGGLRAYLERIFDPKVFVVSFVFNVLVAALIVYVGDQLGVgtQLSTAIIVVLGIRIFGNT 111
                                    6999********************************************************99****************** PP

                        DUF1290  79 aiirrlll 86 
                                    a++rr l+
  gi|121637727|ref|YP_977950.1| 112 AALRRRLF 119
                                    *****986 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.7e-05      0.21     151     200 ..      12      62 ..       4      66 .. 0.76
   2 ?   -0.6   0.3      0.21   7.7e+02     173     199 ..      90     116 ..      65     118 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                        DUF1129 151 lilllllvvwlvlftlval.lpaviNpvLpplvliiigviafvvryylkkk 200
                                    +i +++l+v +vl +++   +p+vi p Lp  v +++ ++ +++r yl + 
  gi|121637727|ref|YP_977950.1|  12 MIGIAALAVGIVLGLVFHPgVPEVIQPYLPIAVVAALDAVFGGLRAYLERI 62 
                                    34444445555555555555***************************9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                        DUF1129 173 viNpvLpplvliiigviafvvryylkk 199
                                     +  +L+  + +++g+ +f+    l++
  gi|121637727|ref|YP_977950.1|  90 GVGTQLSTAIIVVLGIRIFGNTAALRR 116
                                    234556666666666666666655555 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.7   0.00029         1      26      85 ..      11      84 ..       5     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                           FtsX 26 llitlvalviGlglgllaaqllsdvllss...........vfs...selkisidlitvliiivlllllallagl 85
                                    +i++ al++G++lgl++   +  v++ +           vf+     l   +d+  +++ +v+ +l+a l+++
  gi|121637727|ref|YP_977950.1| 11 RMIGIAALAVGIVLGLVFHPGVPEVIQPYlpiavvaaldaVFGglrAYLERIFDPKVFVVSFVFNVLVAALIVY 84
                                   589***********************999555555554442225789999999999999999999999999854 PP

>> HIG_1_N  Hypoxia induced protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.0      0.16   5.9e+02       3      20 ..       9      26 ..       8      28 .. 0.73
   2 ?    9.5   0.1   0.00031       1.1       2      26 ..      37      61 ..      37      70 .. 0.93
   3 ?   -0.0   0.1       0.3   1.1e+03      12      23 ..      97     108 ..      91     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
                        HIG_1_N  3 plvpiGilatvgalvrgl 20
                                   p  +iGi+a ++  v+gl
  gi|121637727|ref|YP_977950.1|  9 PARMIGIAALAVGIVLGL 26
                                   556788888888777776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00031
                        HIG_1_N  2 eplvpiGilatvgalvrglrsmkrg 26
                                   +p+ pi+++a + a++ glr++  +
  gi|121637727|ref|YP_977950.1| 37 QPYLPIAVVAALDAVFGGLRAYLER 61
                                   699******************9865 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.3
                        HIG_1_N  12 tvgalvrglrsm 23 
                                    t++++v+g+r +
  gi|121637727|ref|YP_977950.1|  97 TAIIVVLGIRIF 108
                                    777777788766 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0011         4     144     169 ..      10      35 ..       5      59 .. 0.76
   2 ?    2.9   0.7     0.021        77      97     130 ..      68     102 ..      53     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                      CPP1-like 144 avlltlvgLvvGlllGsllasllqvd 169
                                    a ++++++L+vG++lG ++ + +++ 
  gi|121637727|ref|YP_977950.1|  10 ARMIGIAALAVGIVLGLVFHPGVPEV 35 
                                    6789**************99988654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.021
                      CPP1-like  97 liraavflvlavltlvapaes.vpalllalglgas 130
                                     + ++vf vl++ ++v+  ++ +++ +l++++++ 
  gi|121637727|ref|YP_977950.1|  68 FVVSFVFNVLVAALIVYVGDQlGVGTQLSTAIIVV 102
                                    44455555555555555544449999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 936.75
//
Query:       gi|121637728|ref|YP_977951.1|  [L=292]
Description: hypothetical protein BCG_1860 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-36  125.0   3.1    3.1e-36  124.4   0.3    2.2  2  DUF881     Bacterial protein of unknown function (DUF881)
  ------ inclusion threshold ------
       0.22   10.9   2.0       0.41   10.1   2.0    1.3  1  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative


Domain annotation for each model (and alignments):
>> DUF881  Bacterial protein of unknown function (DUF881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.047   4.2e+02      43      54 ..     106     117 ..      79     139 .. 0.50
   2 !  124.4   0.3   3.5e-40   3.1e-36       2     145 .]     151     289 ..     150     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.047
                         DUF881  43 ldvvneLraaGA 54 
                                    l +++ Lr+ +A
  gi|121637728|ref|YP_977951.1| 106 LVLLDSLRQREA 117
                                    444444444433 PP

  == domain 2  score: 124.4 bits;  conditional E-value: 3.5e-40
                         DUF881   2 leelkllaGltpveGpGvtitlddakkaeeeaeeevhdedLldvvneLraaGAeaIsing....qRivatsaircagnai 77 
                                    l++l++l G++ ++GpGv it+dd+  +       v +e ++dv+neLraaGAeaI+in+    +R++ +++++ + + +
  gi|121637728|ref|YP_977951.1| 151 LAALSILVGAVGATGPGVMITIDDPGPG-------VAPEVMIDVINELRAAGAEAIQINDahrsVRVGVDTWVVGVPGSL 223
                                    7899*********************999.......****************************************999** PP

                         DUF881  78 lvdgrrispPyeikaIGdpekLesalniseavggllellke.glsvtvekseevtipayrgplelkyak 145
                                    +vd++ +spPy+i aIGdp +L++a+ni+   gg ++ +k+ g ++ v+++++v+++a+r+p++ +ya+
  gi|121637728|ref|YP_977951.1| 224 TVDTKVLSPPYSILAIGDPPTLAAAMNIP---GGAQDGVKRvGGRMVVQQADRVDVTALRQPKQHQYAQ 289
                                    *****************************...88888888768************************96 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.0   4.5e-05      0.41      73     124 ..     103     154 ..      87     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.5e-05
                      Mce4_CUP1  73 pdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngdnLirl 124
                                     dll  Ld++++  +T++++  +L++ l a+   +nt +  le+ +++L+ l
  gi|121637728|ref|YP_977951.1| 103 ADLLVLLDSLRQREATLNAEVIDLQNTLNALQASGNTDQAALESAQARLAAL 154
                                    49********************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2124.30
//
Query:       gi|121637729|ref|YP_977952.1|  [L=134]
Description: glycine cleavage system protein H [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-39  133.9   0.0    2.8e-39  133.8   0.0    1.0  1  GCV_H          Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.019   14.8   0.0       0.04   13.7   0.0    1.6  2  Biotin_lipoyl  Biotin-requiring enzyme
       0.05   13.6   0.1      0.079   12.9   0.1    1.3  1  RnfC_N         RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8   0.0   4.7e-43   2.8e-39       1     118 [.       8     131 ..       8     134 .] 0.88

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 4.7e-43
                                    -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT CS
                          GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNeklee 80 
                                    l+yt ehew++  +d++++vGitd+aq++lgdvvfv+lp  gt+v +ge+++ vEs K++s++yap+sG+v  vN++l+ 
  gi|121637729|ref|YP_977952.1|   8 LHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSAVNSDLDG 87 
                                    68****************************************************************************** PP

                                    -TTHHHH-TTTTT--EEEEE..S-GGGGGG....SEEHHHHHHH CS
                          GCV_H  81 epeliNkdpyeegWliklkl..snleelee....Llsaeeyekl 118
                                     p+l+N+dpy+ gWl+ +++  s++  le+    Ll+ae+y+ +
  gi|121637729|ref|YP_977952.1|  88 TPQLVNSDPYGAGWLLDIQVdsSDVAALESalttLLDAEAYRGT 131
                                    ****************9999663443333331146777777665 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   7.8e+03      18      25 ..      15      22 ..       3      28 .. 0.60
   2 ?   13.7   0.0   6.8e-06      0.04      24      58 ..      49      83 ..      36      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                                   SESSSTTC CS
                  Biotin_lipoyl 18 evlvkvGd 25
                                   e++   Gd
  gi|121637729|ref|YP_977952.1| 15 EWIRRSGD 22
                                   55555555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.8e-06
                                   TCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESS CS
                  Biotin_lipoyl 24 GdkVkagqvlaeveamKmemeieapkaGvvkeilv 58
                                   G +V+ag++  eve+ K + ++ ap +G+v+ +  
  gi|121637729|ref|YP_977952.1| 49 GTAVTAGETFGEVESTKSVSDLYAPISGKVSAVNS 83
                                   889***************************99865 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.3e-05     0.079      49      84 ..      49      85 ..      42      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                         RnfC_N 49 gdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrl 84
                                   g  V+ G+  +e e+    +  +a++sG+V a+++ l
  gi|121637729|ref|YP_977952.1| 49 GTAVTAGETFGEVEStKSVSDLYAPISGKVSAVNSDL 85
                                   7789********998444678***********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 996.91
//
Query:       gi|121637730|ref|YP_977953.1|  [L=162]
Description: hypothetical protein BCG_1862 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-19   69.5   0.1    3.2e-19   69.1   0.1    1.2  1  FHA           FHA domain
      5e-18   65.2   0.0    7.5e-18   64.7   0.0    1.3  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
  ------ inclusion threshold ------
      0.014   14.5   0.0      0.018   14.2   0.0    1.2  1  PBP_like      PBP superfamily domain


Domain annotation for each model (and alignments):
>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.1   5.3e-23   3.2e-19       2      69 .]      78     140 ..      77     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 5.3e-23
                                    EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                    + GR++d+di ldd ++Sr+Ha+++ +++  ++ ++D+gS nGt+vN++++ +   + L++gd++++G
  gi|121637730|ref|YP_977953.1|  78 SAGRHPDSDIFLDDVTVSRRHAEFRLENN--EFNVVDVGSLNGTYVNREPVDS---AVLANGDEVQIG 140
                                    57***************************..*********************9...**********98 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.2e-21   7.5e-18       4      88 ..      62     146 ..      59     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.2e-21
                                    CCCCTT-EEEETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC--TTSEEEETT CS
                   Yop-YscD_cpl   4 sGpdkGaeveLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveelelrpgdvlelGt 83 
                                    +Gp++G+++ L++     G+++d+Di L+D +vsr+h++ ++e+++  + d+gs ng++vn e+v+++ l+ gd++++G 
  gi|121637730|ref|YP_977953.1|  62 RGPNAGSRFLLDQAITSAGRHPDSDIFLDDVTVSRRHAEFRLENNEFNVVDVGSLNGTYVNREPVDSAVLANGDEVQIGK 141
                                    8****************************************************************9999*********** PP

                                    EEEEE CS
                   Yop-YscD_cpl  84 telal 88 
                                    ++l++
  gi|121637730|ref|YP_977953.1| 142 FRLVF 146
                                    *9987 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-06     0.018      76     121 ..      38      85 ..      27     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-06
                                    HCCHHHS--BGGGC.-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT.E CS
                       PBP_like  76 akgnpkkitnwkdl.adaplrlvnRetGSGtrdlfdellkkegisk.s 121
                                    ++g + ++++++ l + + l +v+R+  +G+r l+d++++ +g  + s
  gi|121637730|ref|YP_977953.1|  38 QAGTESAVSGVEGLpPGSALLVVKRGPNAGSRFLLDQAITSAGRHPdS 85 
                                    5667778999999988899********************998877652 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1245.32
//
Query:       gi|121637731|ref|YP_977954.1|  [L=247]
Description: hypothetical protein BCG_1863 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.1   0.0    2.6e-10   39.9   0.0    1.8  1  MerR      MerR family regulatory protein
    1.6e-08   34.5   0.0    2.1e-07   30.9   0.0    2.3  2  MerR_1    MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.9e-14   2.6e-10       7      38 .]      24      54 ..      13      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.9e-14
                                   HHHTTTHHHHHHHHHTTSSTSEEETTTSSEEE CS
                           MerR  7 eltGvsprtLRyYEreGLipppeRtegGyRlY 38
                                   ++++v+++++R++E eGL+ +p+R ++GyR++
  gi|121637731|ref|YP_977954.1| 24 DFPDVTISKIRFLEAEGLV-TPRRASSGYRRF 54
                                   689****************.***********8 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.4e-11   2.1e-07      12      67 ..      28      84 ..      12      86 .. 0.91
   2 ?    1.2   0.0     0.045   4.1e+02      33      60 ..     157     183 ..     145     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.4e-11
                                   S-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHHHHHHHHH.TT--GGG---XXX CS
                         MerR_1 12 vtthtlrywekegllkpkrteggrryYtdedierLklikyLlk.rGltlkgikklln 67
                                   vt + +r+ e egl+ p r + g+r++t  d++rL++i + +  + l+lk i+  l+
  gi|121637731|ref|YP_977954.1| 28 VTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRdHYLPLKVIRAQLD 84
                                   7999***********************************99999********98776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.045
                                    TS-EEEEHHHHHHHHHHHHHHHTT--GG CS
                         MerR_1  33 ggrryYtdedierLklikyLlkrGltlk 60 
                                     g  +++++ +  L+  ++L + G+  +
  gi|121637731|ref|YP_977954.1| 157 PG-GFFDEHAVVILQCARALAEYGVEPR 183
                                    44.7888999999999998888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.58
# Mc/sec: 1289.82
//
Query:       gi|121637732|ref|YP_977955.1|  [L=164]
Description: hypothetical protein BCG_1864 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-47  158.9   0.0    5.5e-47  158.6   0.0    1.1  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   0.0   3.1e-51   5.5e-47       2     126 ..       6     127 ..       5     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 3.1e-51
                                    EEEEEEETTTTEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEE CS
                    DNase-RNase   2 vagialdassqspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtf 81 
                                    v gi++++++++pv+lLre++g+r+lpIwig++ea+aial+++g+eppRPlthDL+++l+ alg+++++v+I dl++gtf
  gi|121637732|ref|YP_977955.1|   6 VVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDLIRDLIAALGHSLKEVRIVDLQEGTF 85 
                                    89********************99******************************************************** PP

                                    EEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-E CS
                    DNase-RNase  82 yAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeasi 126
                                    yA+l++++ +  +++ aRpSD++a+Alr+g+pIyvee vl++a++
  gi|121637732|ref|YP_977955.1|  86 YADLIFDR-N--IKVSARPSDSVAIALRVGVPIYVEEAVLAQAGL 127
                                    *******9.5..9*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 864.04
//
Query:       gi|121637733|ref|YP_977956.1|  [L=225]
Description: hypothetical protein BCG_1865 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-13   48.8   0.0    8.4e-13   48.2   0.0    1.3  1  MerR_1    MerR HTH family regulatory protein
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.051   13.4   0.0    1.8  1  MerR      MerR family regulatory protein


Domain annotation for each model (and alignments):
>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   9.4e-17   8.4e-13       5      66 ..      69     134 ..      65     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 9.4e-17
                                    HHHHHHTS-HHHHHHHHHHTT-S-EE....-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XX CS
                         MerR_1   5 evakilgvtthtlrywekegllkpkr....teggrryYtdedierLklikyLlkrGltlkgikkll 66 
                                     +++i+g+t+++l yw +  l++p++     +g +r+Y+ +di +Lk +k+Ll+ G++l +i+ + 
  gi|121637733|ref|YP_977956.1|  69 SACQIAGITYRQLDYWARTSLVVPSIrsaaGSGSQRLYSFKDILVLKIVKRLLDTGISLHNIRVAV 134
                                    5899*****************99999899888888***************************9765 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.7e-06     0.051       5      34 ..      70      99 ..      69     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                                   HHHHHTTTHHHHHHHHHTTSSTSEEETTTS CS
                           MerR  5 vAeltGvsprtLRyYEreGLipppeRtegG 34
                                   +++++G++ r L y+ r  L+ p++R+++G
  gi|121637733|ref|YP_977956.1| 70 ACQIAGITYRQLDYWARTSLVVPSIRSAAG 99
                                   6899***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1252.41
//
Query:       gi|121637734|ref|YP_977957.1|  [L=85]
Description: hypothetical protein BCG_1866 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.8   0.0       0.09   12.5   0.0    1.1  1  DUF4872   Domain of unknown function (DUF4872)


Domain annotation for each model (and alignments):
>> DUF4872  Domain of unknown function (DUF4872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-06      0.09     122     164 ..      42      83 ..      32      85 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-06
                        DUF4872 122 elseamteaadaWtelAalaaeasksreardlaeaadaleela 164
                                    + ++ +++++++W+ lA l ++ +k  + + ++++a+ l++la
  gi|121637734|ref|YP_977957.1|  42 RTARDYDASGKRWRPLAVLTRRWGKAIHLT-VDRVAESLRRLA 83 
                                    67899**********************987.********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 481.67
//
Query:       gi|121637735|ref|YP_977958.1|  [L=941]
Description: glycine dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-198  659.5   0.0   1.2e-184  614.1   0.0    2.3  3  GDC-P            Glycine cleavage system P-protein
    1.2e-07   31.1   0.1    2.1e-05   23.7   0.0    2.4  2  Aminotran_5      Aminotransferase class-V
    0.00015   21.1   0.2    0.00041   19.7   0.0    1.8  2  Beta_elim_lyase  Beta-eliminating lyase
     0.0045   15.6   0.2        1.2    7.6   0.2    2.7  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.17   10.5   0.0       0.29    9.8   0.0    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  614.1   0.0  3.5e-188  1.2e-184       1     430 []       9     438 ..       9     438 .. 0.99
   2 !   42.9   0.0   7.8e-15   2.8e-11      46     286 ..     461     720 ..     444     722 .. 0.81
   3 ?   -4.2   0.0       1.5   5.4e+03     335     363 ..     750     778 ..     747     782 .. 0.87

  Alignments for each domain:
  == domain 1  score: 614.1 bits;  conditional E-value: 3.5e-188
                                    HHH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S-------........--HHHHHHHHHHHHTTB---EE--BT CS
                          GDC-P   1 erhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleap........ksEeellaelekiasknkvvksfiGa 72 
                                    +rhig +++++ +mL+++G++slddl+ kavP+ i  + +++ +ap        +sE+e+lael+++a++n+v+ s+iG+
  gi|121637735|ref|YP_977958.1|   9 DRHIGLDSQAVATMLAVIGVDSLDDLAVKAVPAGILDTLTDTGAAPgldslppaASEAEALAELRALADANTVAVSMIGQ 88 
                                    69****************************************************************************** PP

                                    TB------HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SS CS
                          GDC-P  73 GyydtilPaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskk 152
                                    Gyydt++P+v++rni+enp+wytaYtPYq+EisqGrLeallnfqtlv+dltGl+ianas+lDegtAaaEA++l++ra+++
  gi|121637735|ref|YP_977958.1|  89 GYYDTHTPPVLLRNIIENPAWYTAYTPYQPEISQGRLEALLNFQTLVTDLTGLEIANASMLDEGTAAAEAMTLMHRAARG 168
                                    ******************************************************************************** PP

                                    S--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-...S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEE CS
                          GDC-P 153 kakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtdkekevagvlvqypnteGriedlkelvekakkkkslvvv 232
                                     +k+vvvd++v++qt++vl trak+lgieiv++dl++   +    e++g + q+p+++Gri+d+++lv++a+++ +lv+v
  gi|121637735|ref|YP_977958.1| 169 PVKRVVVDADVFTQTAAVLATRAKPLGIEIVTADLRAGLPD---GEFFGAIAQLPGASGRITDWSALVQQAHDRGALVAV 245
                                    **********************************9998888...6*********************************** PP

                                    EE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEEEEE-CCGSHHC CS
                          GDC-P 233 aadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkralrlalqtREqHi 312
                                     adllaLtl++pPge+gaD+++G++qrfGvP+g+GGPhag++Av++k++R++PGRlvGvs D++g++a+rlalqtREqHi
  gi|121637735|ref|YP_977958.1| 246 GADLLALTLIAPPGEIGADVAFGTTQRFGVPMGFGGPHAGYLAVHAKHARQLPGRLVGVSVDSDGTPAYRLALQTREQHI 325
                                    ******************************************************************************** PP

                                    CHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSSEEEEE--TTTHHHHH CS
                          GDC-P 313 rRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffdtllieveekaaekvl 392
                                    rRdkAtsniCtaq+LlA+laa+ya yhG+ gl++iarr+h+++e++a +l    +++l+++k+fdt+l++v  +a  +vl
  gi|121637735|ref|YP_977958.1| 326 RRDKATSNICTAQVLLAVLAAMYASYHGAGGLTAIARRVHAHAEAIAGAL----GDALVHDKYFDTVLARVPGRAD-EVL 400
                                    *************************************************9....668***************9998.9** PP

                                    HHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS
                          GDC-P 393 kkaekeglnlrkvelktvgialdEtvtkedieallkvl 430
                                    ++a+++g+nl++v++++v++a+dE++t+++++ +l+++
  gi|121637735|ref|YP_977958.1| 401 ARAKANGINLWRVDADHVSVACDEATTDTHVAVVLDAF 438
                                    *********************************99876 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 7.8e-15
                                    -.....--HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGGG-HHHH.HHHHHHHHH CS
                          GDC-P  46 p.....ksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaEisqGrL.eallnfqtl 118
                                    p      +E+ +++ l+++a+k+    +s+i  G   ++l a+ + + +  pe+  +  P+ +      L + + + q+ 
  gi|121637735|ref|YP_977958.1| 461 PaftqyRTETSMMRYLRALADKDIAlDRSMIPLGSCTMKLNAAAEMESITWPEFGRQH-PFAPASDTAGLrQLVADLQSW 539
                                    34444489***************99789******************99*****98775.88877665555155669**** PP

                                    HHHHHT-SEE-S-BS-HHHHHHHHHHHH.HHH-SSS--EEEEETTS-HHHHHHH.HHHHGGGT-EEEEE-GGG--S-... CS
                          GDC-P 119 vadltGldianasllDegtAaaEAvlla.araskkkakkvvvdkkvhpqtlevl.ktrakglgieivevdlteekvtd.. 194
                                    ++ +tG d    sl  ++   +E + l+  +  +  + +   d  + p +++      a   g+ +v+vd+++++  d  
  gi|121637735|ref|YP_977958.1| 540 LVLITGYDA--VSLQPNAGSQGEYAGLLaIHEYHASRGEPHRDICLIPSSAHGTnAASAALAGMRVVVVDCHDNGDVDld 617
                                    ******995..6999999999996655414444444445555555556555443045677889********999999899 PP

                                    ..........S-EEEEEEEES-TTSB-.---HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT-- CS
                          GDC-P 195 ........kekevagvlvqypnteGri.edlkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv.vGsaqrfGvP 263
                                            +++ ++++++ yp+t+G   +d+ e+ +++++    v v  a+l aL+ l+ Pg++g D+  +   + f +P
  gi|121637735|ref|YP_977958.1| 618 dlrakvgeHAERLSALMITYPSTHGVYeHDIAEICAAVHDAGGQVYVdGANLNALVGLARPGKFGGDVShLNLHKTFCIP 697
                                    9***99999999*************87357**********9988887469999***************84677889**** PP

                                    -GGG----EEEEE-GGGGGG--S CS
                          GDC-P 264 lgyGGPhagffAvkeklkRkiPG 286
                                     g GGP +g +Av+++l+  +PG
  gi|121637735|ref|YP_977958.1| 698 HGGGGPGVGPVAVRAHLAPFLPG 720
                                    *****************999999 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GDC-P 335 yavyhGkeglkeiarrihkkteilakelk 363
                                    y+ + G+egl++ +    ++++++a+ l 
  gi|121637735|ref|YP_977958.1| 750 YIRMMGAEGLRAASLTAITSANYIARRLD 778
                                    777899*****************999886 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0032        11     145     209 ..     216     280 ..     200     378 .. 0.70
   2 !   23.7   0.0   5.8e-09   2.1e-05      77     207 ..     566     699 ..     558     783 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0032
                                    EESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-E CS
                    Aminotran_5 145 ithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiG 209
                                    i++   ++G i +  +++++a+++galv+v a   ++       ++g+D+++ +++ +  P G G
  gi|121637735|ref|YP_977958.1| 216 IAQLPGASGRITDWSALVQQAHDRGALVAVGADLLALTLIAPPGEIGADVAFGTTQRFGVPMGFG 280
                                    56666789**********************99999999999999999999999999999998875 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 5.8e-09
                                    HHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-...-TTEEEEEEESBETTT CS
                    Aminotran_5  77 valslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll...nektklvaithvsnvt 152
                                    +++ + +s  +p + i +  +  h++  + ++     g++v+v+   ++g +dld+l++++   +e+ ++++it  s ++
  gi|121637735|ref|YP_977958.1| 566 AIHEYHASrGEPHRDICLIPSSAHGTNAASAA---LAGMRVVVVDCHDNGDVDLDDLRAKVgehAERLSALMITYPS-TH 641
                                    55566555667777777777777777734444...45************************5544666667777665.58 PP

                                    TE.B--HHHHHHHHHHTT-EEEEE-TT.TTTTS---HHHHTESEEEEETTT.TTSSTT CS
                    Aminotran_5 153 Gt.iqpveeigklakkkgalvlvDaaq.avghipidvkklgvDflafsghK.llgPtG 207
                                    G+  ++++ei+++++++g  v vD+a  +++       k+g D+  +  hK ++ P G
  gi|121637735|ref|YP_977958.1| 642 GVyEHDIAEICAAVHDAGGQVYVDGANlNALVGLARPGKFGGDVSHLNLHKtFCIPHG 699
                                    9989**********************84567777788899999999999998888865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.7   6.2e+03      41      88 ..     135     185 ..     127     194 .. 0.63
   2 !   19.7   0.0   1.1e-07   0.00041      44     169 ..     543     667 ..     501     689 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
                                    HHHHTT-SEEE..EES-HHHH.HHHHHHHH--TTEEEEEETT-HHHHSSTT CS
                Beta_elim_lyase  41 vaelfgkeaal..fvpqGtaA.nsillkillqrgeevivtepahihfdetg 88 
                                    v++l+g e a    +  GtaA +++ l+  + rg+ + v  +a ++++++ 
  gi|121637735|ref|YP_977958.1| 135 VTDLTGLEIANasMLDEGTAAaEAMTLMHRAARGPVKRVVVDADVFTQTAA 185
                                    566666664332255677764266666666688887777777777777765 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-07
                                    HTT-SEEEE....ES-HHHHHHHHH.HHH--TT..EEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHH CS
                Beta_elim_lyase  44 lfgkeaalf....vpqGtaAnsill.killqrg..eevivtepahihfdetgaiaelagvklrdlknkeaGkmdleklea 116
                                    ++g++a+        qG  A  +++ ++++ rg  +  i+ +p+  h  ++ a a+lag++++ ++  ++G++dl++l+a
  gi|121637735|ref|YP_977958.1| 543 ITGYDAVSLqpnaGSQGEYAGLLAIhEYHASRGepHRDICLIPSSAHG-TNAASAALAGMRVVVVDCHDNGDVDLDDLRA 621
                                    777777776222233677777777777788776225679999988875.566777899********9999********** PP

                                    HS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                Beta_elim_lyase 117 aikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                    ++ e   h+e+ +++++t          v    ++e+ a +++ g ++ +DgA
  gi|121637735|ref|YP_977958.1| 622 KVGE---HAERLSALMITYPSTH----GVYEHDIAEICAAVHDAGGQVYVDGA 667
                                    ****...8899999998876664....366788*******************9 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2   0.00033       1.2      57     124 ..     134     203 ..     126     273 .. 0.82
   2 !    4.6   0.0    0.0028        10     135     192 ..     627     686 ..     590     692 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00033
                                    HHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TT..EEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST CS
                Cys_Met_Meta_PP  57 leeriaaLeggeaalavssGmaAiaaailallkaG..deivvsddlYggtqrllkkvlkklgievkfvdt 124
                                    l   ++ Le ++a+++     aA a+++++ +  G  +++vv+ d++  t ++l + +k lgie+   d 
  gi|121637735|ref|YP_977958.1| 134 LVTDLTGLEIANASMLDEGTAAAEAMTLMHRAARGpvKRVVVDADVFTQTAAVLATRAKPLGIEIVTADL 203
                                    445566677777777777677778888999999884457*************************999886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0028
                                    CTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT..TTS-GGGGT-SEE CS
                Cys_Met_Meta_PP 135 kentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp..llqrplklgaDiv 192
                                     e+ +++ +  p+   +  +Di++i++++++ag  v vD + +     l rp k+g D++
  gi|121637735|ref|YP_977958.1| 627 AERLSALMITYPSTHGVYEHDIAEICAAVHDAGGQVYVDGANLNAlvGLARPGKFGGDVS 686
                                    34666777777888888899*******************988877334789999999987 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   8.1e-05      0.29     109     183 ..     587     654 ..     571     667 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.1e-05
                                    EETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHHHHHC CS
                        SepSecS 109 idekSslkavelaGleialvekvlegDelitdvedveeiiekkreevilavlstlsffaprspDdvkeiakiCae 183
                                     ++     ++ laG+++++v+  ++gD   +d++d  +++ ++ e   + +++++s+      D    ia+iCa+
  gi|121637735|ref|YP_977958.1| 587 SAHGTNAASAALAGMRVVVVDCHDNGD---VDLDDLRAKVGEHAERLSALMITYPSTHGVYEHD----IAEICAA 654
                                    56667778999***********99999...89********999999999999****99999999....9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.55
# Mc/sec: 5120.72
//
Query:       gi|121637736|ref|YP_977959.1|  [L=286]
Description: haloalkane dehalogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-27   94.4   0.1    1.3e-20   74.2   0.2    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.1e-17   63.2   6.0    6.2e-17   62.9   6.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.6e-08   34.1   0.0    2.2e-08   33.6   0.0    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.03   13.0   0.0      0.039   12.7   0.0    1.2  1  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.2   2.8e-24   1.3e-20       1     106 [.      35     134 ..      35     152 .. 0.93
   2 !   18.4   0.0   2.9e-07    0.0013     211     257 .]     227     274 ..     178     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 2.8e-24
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p+++++hG p +s +++   ++ aL + +f+++++D +G+g S++++      y+++ +a+++  ++d+lg+d+   +G+
  gi|121637736|ref|YP_977959.1|  35 PPILLCHGNPTWSFLYRD--IIVALRD-RFRCVAPDYLGFGLSERPSG---FGYQIDEHARVIGEFVDHLGLDRYLSMGQ 108
                                    89***********99999..*****98.********************...***************************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllga 106
                                    ++GG i++a+a e  +rV+++vl ++
  gi|121637736|ref|YP_977959.1| 109 DWGGPISMAVAVERADRVRGVVLGNT 134
                                    ***********************998 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.9e-07
                                    HSEEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 211 laptlvisgtsDplvpp.kaledlaqllpkkrlvvisdagHlaflegp 257
                                    ++ptl+i+g++D ++ p   + +l + +p++ lv +++a H+++ + p
  gi|121637736|ref|YP_977959.1| 227 TKPTLLIWGMKDVAFRPkTIIPRLSATFPDHVLVELPNAKHFIQEDAP 274
                                    34******************************************9875 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   6.0   1.4e-20   6.2e-17       1     220 []      37     280 ..      37     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.4e-20
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTST...S-GGCS--HHHCHHH.HHHHCCTT..TTSEEE.EEETCH CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhG...rsdpppldledladl.aalldelaagggpvvl.vGHSlG 75 
                                    +ll+HG ++  +s+l++ +  +l+++++++apD+ G+G   r+++  +  ++ a++  +++d+l   g + +l +G ++G
  gi|121637736|ref|YP_977959.1|  37 ILLCHGNPT--WSFLYRDIIVALRDRFRCVAPDYLGFGlseRPSGFGYQIDEHARViGEFVDHL---GLDRYLsMGQDWG 111
                                    89****998..445699*********************766666666777774555599*****...5666666****** PP

                                    HHHHHHHHHCC.......EEEEES-..----TTTS----TTHHHHHHTT-C.CCCHCCH.S-HSCCCCHHH.....C... CS
                  Abhydrolase_6  76 Galalaaapla.....lvvgvlldppptalpagllaaalelllallallrl.lawlsre.plprlfladed.....a... 140
                                    G +++a   +a     +v+gv+l     ++ ++    a++ + +++++ +  +a l+r+ ++ rl+ a+++     a   
  gi|121637736|ref|YP_977959.1| 112 GPISMA---VAveradRVRGVVLGN---TWFWPADTLAMKAFSRVMSSPPVqYAILRRNfFVERLIPAGTEhrpssAvma 185
                                    *99999...4444456777799999...9999999999999999999777733444444444445555555443331334 PP

                                    .CCCHCHCCCGHHHHCCHHC....HTT.CCHHTT-TTGC..........EEEC.TT-C......HHHHCHHCCCH.STTE CS
                  Abhydrolase_6 141 .daawrarlarlaallaglg....llp.aaawadlpvpl..........lvlg.geDp......lvprllerlla.qaga 196
                                     ++a++++ a+ +  + ++     ++p +a++a+               l+++  +D       ++prl     a  ++ 
  gi|121637736|ref|YP_977959.1| 186 hYRAVQPNAAARRGVAEMPKqilaARPlLARLAR----EvpatlgtkptLLIWgMKDVafrpktIIPRL----SAtFPDH 257
                                    4455555555555444444432221111112222....1344456667744452556666555555544....4455889 PP

                                    EETCE...SSS-HHHHSHHHHHHH CS
                  Abhydrolase_6 197 rlpvvlpgaGHlphleepdevaea 220
                                    +l v+lp+a H++++++pd++a+a
  gi|121637736|ref|YP_977959.1| 258 VL-VELPNAKHFIQEDAPDRIAAA 280
                                    99.************999***986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0     5e-12   2.2e-08       7     232 ..      37     267 ..      35     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5e-12
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    ++l+HG    s  y +++ aL ++ f ++a D+ G+G se   g   ++d++ + + +fv+++  +    +   +G+ +G
  gi|121637736|ref|YP_977959.1|  37 ILLCHGNPTWSFLYRDIIVALRDR-FRCVAPDYLGFGLSERPSGFGYQIDEHARVIGEFVDHLGLD----RYLSMGQDWG 111
                                    789******************876.***************99999999999999999999999844....46679***** PP

                    Hydrolase_4  87 GliallyllrypdkvaglilsaPalkikakl......kappllkl.......llkllgkllpklqv....snnlkadsls 149
                                    G i+++++ +++d+v+g++l +++++++  l      +      +        + l  +++ +  +    +++  ++ + 
  gi|121637736|ref|YP_977959.1| 112 GPISMAVAVERADRVRGVVLGNTWFWPADTLamkafsR------VmssppvqYAILRRNFFVERLIpagtEHRPSSAVMA 185
                                    ***************************98764433331......322233224445555555555555544445555555 PP

                    Hydrolase_4 150 rdpevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeas.relyerlgskdktlklyp 228
                                    ++++v+   +a   v ++++  l++  l a  + e  a+  t P+ll+ G +D    p+    +l ++ +  d  l   p
  gi|121637736|ref|YP_977959.1| 186 HYRAVQPNAAARRGVAEMPKQILAARPLLARLAREVPATLGTKPTLLIWGMKDVAFRPKTIiPRLSATFP--DHVLVELP 263
                                    5555555555555555555544444444444444444555569999999999998888776333333333..66666666 PP

                    Hydrolase_4 229 glyH 232
                                    ++ H
  gi|121637736|ref|YP_977959.1| 264 NAKH 267
                                    6666 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.7e-06     0.039      82     228 ..      84     236 ..      75     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-06
                                    HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---.S---HHHHHHHHHH.......TTTS- CS
                            Ndr  82 lddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinits.kaagwvewakeKlsskllkkvgltdl 160
                                    +d+ a  + + +dh+ l+  +++G+  G  i +  a++  +rv g+vL n+    a+ +   a ++++s+    v+ + l
  gi|121637736|ref|YP_977959.1|  84 IDEHARVIGEFVDHLGLDRYLSMGQDWGGPISMAVAVERADRVRGVVLGNTWFwPADTLAMKAFSRVMSS--PPVQYAIL 161
                                    67788899999*************************************9875313444444444555542..23333444 PP

                                    HHHHHHHHHS-HHHHHH.T-HHHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSS......S-EEEEEET CS
                            Ndr 161 lkdlllahkFgkeekse.nsdlvreyrkllkerlnsknlelyleaynkRrdleierkkle......vkvllvvGd 228
                                      +++++++    ++++ +s ++++yr    ++  ++ +++  + +   r+l   +  +        ++ll+ G+
  gi|121637736|ref|YP_977959.1| 162 RRNFFVERLIPAGTEHRpSSAVMAHYRAVQPNAAARRGVAEMPKQILAARPLLARLAREVpatlgtKPTLLIWGM 236
                                    455566665555444443555666666666666666666666666555555555444444445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1584.06
//
Query:       gi|121637737|ref|YP_977960.1|  [L=288]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-17   63.2   9.8    6.6e-17   62.8   9.8    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    9.1e-15   55.0   0.0    2.3e-13   50.4   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    6.2e-08   32.2   0.0    8.6e-08   31.7   0.0    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.23   11.0   0.0       0.35   10.3   0.0    1.2  1  DUF900         Alpha/beta hydrolase of unknown function (DUF9


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   9.8   1.5e-20   6.6e-17       2     220 .]      36     281 ..      35     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.5e-20
                                    EEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTST.S-GGCS--HHHCHHHHHHHCCTT....TTSEEEEEETCHHH CS
                  Abhydrolase_6   2 lllHGagssassWlvapLaallaag.vhvlapDlpGhG.rsdpppldledladlaalldelaa..gggpvvlvGHSlGGa 77 
                                    lllHG  +++ss+ ++ + + l+++ +  +++D+ G+G ++ p+p+ ++  +++a+l++ ++a  ++g+vv+++H++G++
  gi|121637737|ref|YP_977960.1|  36 LLLHG--YPSSSFDFRAVIPHLTGQaW--VTMDFLGFGlSDKPRPHRYSL-LEQAHLVETVVAhtVTGAVVVLAHDMGTS 110
                                    9****..66677755588888888867..89******9766677777766.8888888888877889************* PP

                                    HHHHHHHCC..........EE.EEES-..----TTT.S----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHCHC CS
                  Abhydrolase_6  78 lalaaapla........lvvg.vlldppptalpagl.laaalelllallallrllawlsreplprlfladedadaawrar 147
                                    + +++++          l ++ vl ++   +   +  l+++ ++l+ +l++ ++ +++sr+ ++r+f +  +  +a    
  gi|121637737|ref|YP_977960.1| 111 VTTELLARDldgrlpfdL-RRaVLSNG--SVILERAsLRPIQKVLRSPLGPVAA-RLVSRGGFTRGFGRIFS--PAHPLS 184
                                    ****55555789999854.44488888..4333333344444444444444444.55555544444444444..666666 PP

                                    CCGHHHHCCHHCHTTCCHHTT-TTGC.......................EEECTT-CHHHHCHHCCCH.....STTEEET CS
                  Abhydrolase_6 148 larlaallaglgllpaaawadlpvpl.......................lvlggeDplvprllerlla.....qagarlp 199
                                     ++++a++  l ++   ++++l+ ++                       +v +g D+ v+      l      +++a + 
  gi|121637737|ref|YP_977960.1| 185 AQEAQAQWELLCYNDGNRIPHLLISYlderirhaqrwhgavrdwpkplgFV-WGLDDPVA--TTNVLNglrelRPSAAV- 260
                                    666666666555555444444444444444444444445555545555555.88888555..22222222235599999. PP

                                    CE...SSS-HHHHSHHHHHHH CS
                  Abhydrolase_6 200 vvlpgaGHlphleepdevaea 220
                                    v+lpg GH+p+ e+p+++aea
  gi|121637737|ref|YP_977960.1| 261 VELPGLGHYPQVEAPKAYAEA 281
                                    *******************96 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   5.2e-17   2.3e-13       1     256 [.      33     274 ..      33     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.2e-17
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p++++lhG+p ss  +++  ++p+L   g+  +++D +G+g S+++     ++y++   a  ++ +++++  + +++++h
  gi|121637737|ref|YP_977960.1|  33 PTMLLLHGYPSSSFDFRA--VIPHLT--GQAWVTMDFLGFGLSDKPRP---HRYSLLEQAHLVETVVAHTVTGAVVVLAH 105
                                    689********9999999..*****9..*******************9...***************************** PP

                                    THHHHHHHHHHHHH.....GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHH CS
                  Abhydrolase_1  81 SmGGmialayaaey.....perVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrh 155
                                    +mG+ + ++++a+      p   ++ vl ++   +  l++a ++ ++++ +   g +a+  + ++g   ++   +++ + 
  gi|121637737|ref|YP_977960.1| 106 DMGTSVTTELLARDldgrlPFDLRRAVLSNG---SVILERASLRPIQKVLRSPLGPVAARLVSRGGFTRGFGRIFSPAH- 181
                                    *******************************...999999999999999999999999999999999888877777666. PP

                                    HHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHH CS
                  Abhydrolase_1 156 rlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaq 235
                                     l+    +++++  ++++g ++++ l  + ++ i +++  + a   +++ +      p  +++g +Dp+++ ++l  l++
  gi|121637737|ref|YP_977960.1| 182 PLSAQEAQAQWELLCYNDGNRIPHLLISYLDERIRHAQRWHGAV--RDWPK------PLGFVWGLDDPVATTNVLNGLRE 253
                                    12222222888888888888888877777777777777655543..33344......999******************** PP

                                    CHTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 236 llpkkrlvvisdagHlafleg 256
                                    l p++ +v +++ gH+ + e 
  gi|121637737|ref|YP_977960.1| 254 LRPSAAVVELPGLGHYPQVEA 274
                                    ***************999886 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.9e-11   8.6e-08       6     207 ..      34     245 ..      31     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.9e-11
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                    +++l+HG+ ++s  +  ++ +L+ q  a +++D  G+G s+  r h  s   +++  a +ve+v+++  +  +++l+h m
  gi|121637737|ref|YP_977960.1|  34 TMLLLHGYPSSSFDFRAVIPHLTGQ--AWVTMDFLGFGLSDKPRPHRYS---LLEQ-AHLVETVVAHTVTGAVVVLAHDM 107
                                    6899******************855..7899*********977764433...3343.456688888888999******** PP

                    Hydrolase_4  86 GGliallyllrypd.....kvaglilsaPalkikaklkappllklllkllgkllpklqv............snnlkadsl 148
                                    G  +++++l+r  d     ++++++ls+  + ++    ++p++k+l+  lg+++ +l              s    + s 
  gi|121637737|ref|YP_977960.1| 108 GTSVTTELLARDLDgrlpfDLRRAVLSNGSVILERAS-LRPIQKVLRSPLGPVAARLVSrggftrgfgrifSP-AHPLSA 185
                                    *********6666666777999*******99998764.*******9999999999998899999999988533.333344 PP

                    Hydrolase_4 149 srdpevva.ayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdp 207
                                    ++ +++ + ++ +d   + ++ ++ l e ++ ++r +  + ++  Pl ++ G +D+v   
  gi|121637737|ref|YP_977960.1| 186 QEAQAQWElLCYNDGNRIPHLLISYLDERIRHAQRWHGAVRDWPKPLGFVWGLDDPVATT 245
                                    444444443678888889999999999999999999999999999999999999999865 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.8e-05      0.35      74     113 ..      78     117 ..      67     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                         DUF900  74 easrdalekllrylatkksakkihllaHSmGtwlvlealr 113
                                    ++s  + ++l++++  ++    + +laH mGt +++e l 
  gi|121637737|ref|YP_977960.1|  78 RYSLLEQAHLVETVVAHTVTGAVVVLAHDMGTSVTTELLA 117
                                    566667788999999999999**************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1591.25
//
Query:       gi|121637738|ref|YP_977961.1|  [L=628]
Description: hypothetical protein BCG_1870c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-76  256.0   0.4    5.9e-76  255.6   0.4    1.1  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    3.5e-40  138.3   0.0    5.1e-40  137.8   0.0    1.2  1  PepX_C         X-Pro dipeptidyl-peptidase C-terminal non-cata
     0.0053   16.1   0.0     0.0079   15.5   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.11   11.9   0.1       0.18   11.3   0.1    1.3  1  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.6   0.4   1.3e-79   5.9e-76       1     268 [.      38     351 ..      38     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 255.6 bits;  conditional E-value: 1.3e-79
                                    TS-EEEEEEEEE...TTSSSEEEEEEEESS-CCT.CCCCHTTCHHCCHGGGHH........HHHTT-EEEEEE-TTSTTS CS
                  Peptidase_S15   1 DGvrLavdiyrP.etkskeklPvlltrtPYgkndelasdkalaleelelqdkv........fvarGYavVvqdvrGtggS 71 
                                    DGvr+a+d+y+P + +s+++lP++l++t+Y+++ +l++ +++ l++++lq+++        fva+GYa+V +dvrG+g+S
  gi|121637738|ref|YP_977961.1|  38 DGVRIAIDLYLPaGLTSAARLPAILHQTRYYRSLQLRWPLRMLLGGKPLQHIAadkrrrrrFVASGYAWVDVDVRGSGAS 117
                                    9******************************************************************************* PP

                                    -S---TT.TTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCSECTTEEB CS
                  Peptidase_S15  72 eGeftvg.dsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyyregGlvr 150
                                     G+++++ +sde++dga+++dW+++qpw+nG+V+++G+SY+Gt + l++++++pa+++i+p+++++d+y+d++++gG+++
  gi|121637738|ref|YP_977961.1| 118 FGARVCEwSSDEIRDGAEIVDWIVRQPWCNGTVAALGNSYDGTSAELLLVNQHPAVRVIAPCFSLFDVYTDIAFPGGIHA 197
                                    *******99*********************************************************************** PP

                                    CCHHHHH.....................HHHHCCCCHHTSSS-STTHHHHHHHH................HHCHCCCCCC CS
                  Peptidase_S15 151 apgglsw.....................edldllaealtsrradegdalkaaar................yeaasdella 193
                                    a+++++w                     ++++ ++ ++++r+++ +d++ aa+r                + +asd +++
  gi|121637738|ref|YP_977961.1| 198 AWFTDTWgrynealdrnalhevvgwwakLPVTGMQPVQEDRDRSLRDGAIAAHRgnydvhqiagsltfrdDVSASDPYRG 277
                                    ******************************************************************************** PP

                                    TTHHH.....THHHHCCCC--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTCCHHHHHHHHHCCTT-EEEEECECTT CS
                  Peptidase_S15 194 eldrq.....tpveselletgdydafWkdrnlsedadkvkapvllvgGwnDwnvkngaiklyealkapgvklilgpwtHv 268
                                    + d++     tp+es +++  + +++W+d ++s      +a++++++Gw+D++++++aik + ++++pg++lilgpw+H+
  gi|121637738|ref|YP_977961.1| 278 QPDARlepigTPIESGSINLISPHNYWRDVQAS------GAAIYSYSGWFDGGYAHAAIKRFLTVSTPGSHLILGPWNHT 351
                                    *******************************99......9***************************************8 PP

>> PepX_C  X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   0.0   1.1e-43   5.1e-40       2     195 ..     387     601 ..     386     614 .. 0.93

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 1.1e-43
                         PepX_C   2 gvertppvrlqvldggsgstwrtedawpspntkattlylsqrgagstgdgtlsaasplsdeaaaseedlydptnp..... 76 
                                    g+ ++ppv ++ + ++   +w++ d+wp+p+t    +yls       +d++l+  +p +d  a  +e+++d t       
  gi|121637738|ref|YP_977961.1| 387 GIGSEPPVHYFTMVEN---RWKSADTWPPPATTQ-SYYLS-------ADRQLRPDAPDCDSGA--DEYVVDQTAGtgers 453
                                    67789********888...4************66.*****.......***************9..899999966667777 PP

                         PepX_C  77 ............ldqdqreeradslafttaplaedtelvGapkakLrvssdapdadlsvtLvdvdpdGeatlitkGwlrl 144
                                                +  d + ++a  l++t+apl++++e++G++ ++L+ +s+ +d++++v+L dvdp+G+   it+G+lr+
  gi|121637738|ref|YP_977961.1| 454 rwrsqvgigghvCYPDRKAQDAKLLTYTSAPLDHPLEVTGHVVVTLFITSTSSDGTFFVYLEDVDPRGRVAYITEGQLRA 533
                                    777777777777777779************************************************************** PP

                         PepX_C 145 snRasdeep.................eplePGevydleieLqptayrfpkGhrlrlsvsssdfpmilp 195
                                     +R++++ p                  pl PGe+++l+++L pt+y f++Ghr+r+ ++++d  ++ +
  gi|121637738|ref|YP_977961.1| 534 IHRRLSDGPppyrqvvpyrtfasgdaWPLVPGEIARLTFDLLPTSYLFQPGHRIRIAIAGADASHFAI 601
                                    ***************************************************************99976 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06    0.0079      25     104 ..      97     176 ..      87     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                    Hydrolase_4  25 eaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvk.eehpelplfllGhSmGGliallyl.lrypdkva 102
                                    ++++a G+a + +D rG G s g+r+ ++  +d ++D a++v+ ++ +++ +  +  lG S  G+ a l+l  ++p+ v+
  gi|121637738|ref|YP_977961.1|  97 RRFVASGYAWVDVDVRGSGASFGARV-CEWSSDEIRDGAEIVDWIVrQPWCNGTVAALGNSYDGTSAELLLvNQHPA-VR 174
                                    6899**********************.88888889999999998887999999********9877776666366666.54 PP

                    Hydrolase_4 103 gl 104
                                     +
  gi|121637738|ref|YP_977961.1| 175 VI 176
                                    44 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     4e-05      0.18       9     103 ..      99     187 ..      91     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                                    HHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG CS
                   Peptidase_S9   9 lladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdl 88 
                                    ++ + Gy+ v +++rGsg    +f  ++  ++ + e++D  +++++++ + ++ +  +a+ G Sy G+ +  +l +++  
  gi|121637738|ref|YP_977961.1|  99 FV-ASGYAWVDVDVRGSG---ASFGARV-CEWSSDEIRDGAEIVDWIVRQPWC-NGTVAALGNSYDGTSAELLLVNQHPA 172
                                    44.89***********98...6666544.57**********************.6789*******999998888755555 PP

                                    -SEEEEESE---CCC CS
                   Peptidase_S9  89 Fkaavaevpvvdvlr 103
                                     ++++   + +dv +
  gi|121637738|ref|YP_977961.1| 173 VRVIAPCFSLFDVYT 187
                                    555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 3505.24
//
Query:       gi|121637739|ref|YP_977962.1|  [L=677]
Description: hypothetical protein BCG_1871c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-17   62.5  10.5    4.8e-17   62.5  10.5    1.7  2  SBP_bac_11   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.24   11.3   0.0    1.6  1  VWA_3        von Willebrand factor type A domain
        0.2   11.6   0.1        0.4   10.7   0.1    1.4  1  Consortin_C  Consortin C-terminus
        1.2    9.5   4.5        3.6    7.9   0.7    2.9  3  DUF3040      Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5  10.5   1.1e-20   4.8e-17       3     230 .]     163     444 ..     161     444 .. 0.81
   2 ?   -3.3   0.0       1.4   6.1e+03     113     146 ..     482     524 ..     471     544 .. 0.71

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.1e-20
                                    EEE-SSTHHHHHHHHHHHHHHH-......--EEEEESSHHHHHHHH......HHH..-SEEEESSH.HHHHHHHHGGGGG CS
                     SBP_bac_11   3 vaaagslaaalrelaaaFeahtg......vkvevsaggsgklarqi......adgarpDvwipassawlellaaaglvqa 70 
                                    v a +s+a  ++e a+ + a  g      v v+v+++gs ++++        + g +p +wip ss   ++l  a   qa
  gi|121637739|ref|YP_977962.1| 163 VIADPSIADQVKESADSYNASAGpvgdrcVAVAVTSAGSDAVINGFigkwptELGGQPGLWIPSSSISAARLTGAAGSQA 242
                                    88999*************88777779999***************886666655555*********999999976644444 PP

                                    .GG-EEEEEEEEEEEESTT-..TT---SHHHHHHS................S--EEEE--T-TTTTHH.HHHHGGG--.. CS
                     SBP_bac_11  71 .esavplassplviavpkgn..pkkikgwadLlkp................glklavadPttspsGlaalalleaaga.. 129
                                     +++++l++sp+ +av+++   +   ++wa+L +                 +l+la+++  +  +++ a ++++aa a  
  gi|121637739|ref|YP_977962.1| 243 iSDSRSLVISPVLLAVRPELqqALANQNWAALPGLqtnpnslsgldlpawgSLRLAMPSSGNGDAAYLAGEAVAAASApa 322
                                    78*****************9554478899998775567899999999988777******999999999999999884445 PP

                                    .......HHHHHHHHHTEEEEESSHHHHHHH..HHTTT.....-SEEEEEHHHHH.......HSTTSSEEEE--TTT--. CS
                     SBP_bac_11 130 .......qellkalekkvvklgessrqllta..veage.....adagivyeseakaa.....engdkleavylpeglnld 190
                                            + +++l +  +kl+++s +++ +  ++ g+     + a++++e+++ ++     +++  l  + +p    + 
  gi|121637739|ref|YP_977962.1| 323 gapatagIGAVRTLMGARPKLADDSLTAAMDtlLKPGDvatapVHAVVTTEQQLFQRgqslsDAENTLGSWLPPGPAAV- 401
                                    556666677************9999776666685556522222669999999997666666566667777766666665. PP

                                    ..EEEEEEEE-T....T--HHHHHHHHHTTSHHHHHHHHHTT-B CS
                     SBP_bac_11 191 pldypaavlkka....akreaAraFlafLrspeaqailrkyGfr 230
                                     +dyp ++l++a     +  aA aF+++L+ pe+ a l+++Gfr
  gi|121637739|ref|YP_977962.1| 402 -ADYPTVLLSGAwlsqEQTSAASAFARYLHKPEQLAKLARAGFR 444
                                    .89****9998888768889***********************8 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                    -TTTTHH.HHHHGGG.....--....HHHHHHHHHTEEEEESS CS
                     SBP_bac_11 113 tspsGlaalalleaa.....ga....qellkalekkvvklges 146
                                    t+++G aa  +l+++     g+    +  + ale+++  + +s
  gi|121637739|ref|YP_977962.1| 482 TASAGVAATIMLDQSmpndeGGnsrlSNVVAALENRIKAMPPS 524
                                    6788888888888766665522456667888888887766555 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-05      0.24      18     154 ..     508     658 ..     487     659 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                          VWA_3  18 klvkdaLsvalrqLptndkiavllfgt....kprplfpgsravsaaelqeal.qkikelelslgasnlegaLkealrqp. 91 
                                      v++aL + ++++p++  + +  f+     + +p  p ++ v+ + + +al +++ ++  s g+     +L+ + +   
  gi|121637739|ref|YP_977962.1| 508 SNVVAALENRIKAMPPSSVVGLWTFDGregrTEVPAGPLADPVNGQPRPAALtAALGKQYSSGGGAVSFTTLRLIYQEMl 587
                                    56666666666666666666666666544434445555566666666655441445554444444444566665554334 PP

                          VWA_3  92 ..akpgevrsvilltDgss.aqge.....ervsdlisrarekirfhalglgsslsaamlqaLAeasgGtye 154
                                       ++g++ sv+++t+g   +q+      ++++ +  + ++ i +  + +g++ + a  +a+A+ sgG+y+
  gi|121637739|ref|YP_977962.1| 588 anYHVGQANSVLVITAGPHtDQTLdgpglQDFIRKSADPAKPIAVNIIDFGADPDRATWEAVAQLSGGSYQ 658
                                    44899**********999856654777778888888777788***************************97 PP

>> Consortin_C  Consortin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.8e-05       0.4      60      86 ..     119     145 ..     106     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                    Consortin_C  60 lllclvtvvisvGGtalycalgdvess 86 
                                    +++ lv+vv+ v G  l+c +gd+ s+
  gi|121637739|ref|YP_977962.1| 119 VIVALVAVVVMVAGVILWCFFGDALSN 145
                                    7889*******************9997 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7   0.00081       3.6      37      64 ..     107     134 ..      93     140 .. 0.74
   2 ?    1.7   0.0     0.072   3.2e+02      21      63 ..     165     208 ..     163     217 .. 0.74
   3 ?   -3.2   0.1       2.4   1.1e+04      40      58 ..     471     489 ..     457     493 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00081
                        DUF3040  37 rrrslrrlavlavllfvaGllllvlGva 64 
                                    r+   rr + ++v++++++++++v+Gv+
  gi|121637739|ref|YP_977962.1| 107 RSADGRRGVSIGVIVALVAVVVMVAGVI 134
                                    344457777888888888********75 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.072
                        DUF3040  21 eDPklaaalrggaar..arrrslrrlavlavllfvaGllllvlGv 63 
                                     DP  a++++++a +  a+++ + + + +av++  aG  +++ G+
  gi|121637739|ref|YP_977962.1| 165 ADPSIADQVKESADSynASAGPVGD-RCVAVAVTSAGSDAVINGF 208
                                    69*******7777777666666666.7777777777877777774 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.4
                        DUF3040  40 slrrlavlavllfvaGlll 58 
                                    s+r ++   ++++ aG+++
  gi|121637739|ref|YP_977962.1| 471 SMRATLADTMVTASAGVAA 489
                                    3333333333333334443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4201.09
//
Query:       gi|121637740|ref|YP_977963.1|  [L=741]
Description: malate synthase G [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     6e-190  632.0   0.0   6.8e-190  631.8   0.0    1.0  1  Malate_synthase  Malate synthase


Domain annotation for each model (and alignments):
>> Malate_synthase  Malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  631.8   0.0  3.8e-194  6.8e-190       1     526 []      17     699 ..      17     699 .. 0.99

  Alignments for each domain:
  == domain 1  score: 631.8 bits;  conditional E-value: 3.8e-194
                                    CCCCCHHTHHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHS............HHHCCTCCCH-TSS CS
                Malate_synthase   1 vdfvkeevleaaeilteealefvaelvrdltprrrelLeeRdelqaeidkgeln............dflketkylreepe 68 
                                    +dfv++e+l++++i++++++++v+++v+dltp++++lL++Rdelqa+idk++++            +fl e++yl++ep+
  gi|121637740|ref|YP_977963.1|  17 YDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQALLNARDELQAQIDKWHRRrviepidmdayrQFLTEIGYLLPEPD 96 
                                    689*************************************************777**********9999*********** PP

                                    ---S-........................................................................... CS
                Malate_synthase  69 wktat........................................................................... 73 
                                    ++t t                                                                           
  gi|121637740|ref|YP_977963.1|  97 DFTITtsgvdaeitttagpqlvvpvlnarfalnaanarwgslydalygtdvipetdgaekgptynkvrgdkviayarkfl 176
                                    ***5559************************************************************************* PP

                                    ............................................................EECCCCE-TCCCCCCC-CCH CS
                Malate_synthase  74 ............................................................lhielqdrrveiiGkadrkm 93 
                                                                                                lhie+ +++++ +G +dr++
  gi|121637740|ref|YP_977963.1| 177 ddsvplssgsfgdatgftvqdgqlvvalpdkstglanpgqfagytgaaesptsvllinhgLHIEILIDPESQVGTTDRAG 256
                                    ******************************************************************************** PP

                                    CCCCCCCSSSEEEEESSTTS--...........HHHHHHCCHHCCCHCCTTT-EEEET-TSEEEEETTS....ESSSSEE CS
                Malate_synthase  94 iinalnesaittiaDfEDsvap...........nwenlvkGqlnledavrgrisfrkenkdksYklndg....legrsll 158
                                    ++++++esaitti+DfEDsva+           nw +l+kG+l   ++++g+ ++r +n+d++Y++  g    l+grsl+
  gi|121637740|ref|YP_977963.1| 257 VKDVILESAITTIMDFEDSVAAvdaadkvlgyrNWLGLNKGDLAAAVDKDGTAFLRVLNRDRNYTAPGGgqftLPGRSLM 336
                                    *******************************************************************889********** PP

                                    EEE---TTTEEEEEE.CTTCEEEHHHHHH...HHHHHHHHHHC......SCCTTSSEEEEE-S-SSHHHHHHHHHHHHHH CS
                Malate_synthase 159 fvRnrGwhltekhil.vdGeeisegilDf...gliffhnakel......klsrgggpyivlPKmegpqEaalwnevFsra 228
                                    fvRn+G+++t+++i+ +dG e++egi+D+   gli++h++k+        +sr+g++yiv+PKm+gp+E+a+++e+Fsr+
  gi|121637740|ref|YP_977963.1| 337 FVRNVGHLMTNDAIVdTDGSEVFEGIMDAlftGLIAIHGLKASdvngplINSRTGSIYIVKPKMHGPAEVAFTCELFSRV 416
                                    ***************9**************************99999999****************************** PP

                                    HHHCTSSTTSCEEEEEE-SHHHHTTHHHHHHCTTTTEEEEEE-CHHHHHHHHHHTCCCCGCB...CGGGGCCSHHHHHHH CS
                Malate_synthase 229 edllglprgtikatvliEtlraslnldeiiyelrdrvaglNcGrlDyifseiktlreagdmvLPdRkavtktapfikaYe 308
                                    ed+lglp++t+k+++++E++r+++nl+++i++++drv+++N+G+lD++++ei+t++eag+mv   Rk ++k++p+i aYe
  gi|121637740|ref|YP_977963.1| 417 EDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMV---RKGTMKSQPWILAYE 493
                                    **************************************************************...*************** PP

                                    HHHHHHHHHTT.CCCCCCCTCSEECCCEHHHCCCHHHHHHHCHHHHHCT-SEEEESSHHHHHHHHHHHHHCHCHCHHCCH CS
                Malate_synthase 309 kllvktchkrgvhamgGlaakipikkdmeaneellekvredKlrevraGadgaWvahPtlatlaaevfeevdvapnQiel 388
                                    +++v++      ++++G++++++++k+m+ ++el+++++e K+ ++raGa +aWv++Pt+atl+a ++++vdva++Q+ l
  gi|121637740|ref|YP_977963.1| 494 DHNVDA------GLAAGFSGRAQVGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGL 567
                                    ******......******************************************************************** PP

                                    HTTTHHHHHHHHCS.--BB.......HHHHHHHHHHHHHHHHHHHHHH.CT-SS..EEETT...EEESHHHHHHHHHHHH CS
                Malate_synthase 389 akeevritaddLltkipea.......eeteeglrnnvqvglqYvvaWl.rgvGc..vpiih...LmEDaATaeiSrqqla 455
                                    a ++ r+t ++Llt ip a        e++e+++nn+q++l+Yvv+W+ +gvGc  vp+ih   LmED+AT++iS+q la
  gi|121637740|ref|YP_977963.1| 568 AGKR-RATIEQLLT-IPLAkelawapDEIREEVDNNCQSILGYVVRWVdQGVGCskVPDIHdvaLMEDRATLRISSQLLA 645
                                    9995.********8.***************************************************************** PP

                                    HHHHTTSC-CCHSHCHHHHHHHHHHHHHCCHHHHHHHCCTTHHHCHHHHHHHHHTTTCCC-CHHHHHCCHH CS
                Malate_synthase 456 qWirhgvvlkeqgvkvslelmaklvdeenarleelgkedeayreaakllkkeataeefadfltlkaykeli 526
                                    +W+rhgv+++ + v++sle+ma lvd++na       +d ayr++         a++f+d+++++a++eli
  gi|121637740|ref|YP_977963.1| 646 NWLRHGVITSAD-VRASLERMAPLVDRQNA-------GDVAYRPM---------APNFDDSIAFLAAQELI 699
                                    ***********7.*****************.......9*******.........***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 5000.45
//
Query:       gi|121637741|ref|YP_977964.1|  [L=131]
Description: hypothetical protein BCG_1873c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-17   62.6   0.1    5.4e-17   62.4   0.1    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.14   11.2   0.0       0.15   11.1   0.0    1.0  1  MMS22L_C  S-phase genomic integrity recombination mediator, C


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.1     6e-21   5.4e-17       1     119 [.       2     124 ..       2     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 6e-21
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                    i++D+++  +l+  ++++   a +lle++    e+lvt a vl+E+++ + +   kr +a++   + ++    ++lpi  
  gi|121637741|ref|YP_977964.1|   2 ILVDSNIPMYLVgASHPHKLDAQRLLESAlsggERLVTDAEVLQEICHRYVA--IKRREAIQPAFDAIIGVVDEVLPIER 79 
                                    79**************************************************..9999********************** PP

                                    HHHHHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  76 eiaeeaaeialkyg.llpnDaliaAtAkehgikliatfDedfrrv 119
                                     ++e+a++  l+y+ l++ Dal++A++ +h+i+ +++fD+ f+ +
  gi|121637741|ref|YP_977964.1|  80 TDVEHARDALLRYQtLSARDALHIAVMAHHDITRLMSFDRGFDSY 124
                                    *****************************************9865 PP

>> MMS22L_C  S-phase genomic integrity recombination mediator, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.7e-05      0.15     212     276 ..      40     109 ..       4     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                       MMS22L_C 212 rklilevlvenflefkgsap.pprlasvlafilellkrlndskeleaelllll....lppvleclllvne 276
                                     + +l+ ++  ++++k++++ +p + +++ ++ e+l   +++ e  +++ll++    +   l  +++ + 
  gi|121637741|ref|YP_977964.1|  40 DAEVLQEICHRYVAIKRREAiQPAFDAIIGVVDEVLPIERTDVEHARDALLRYqtlsARDALHIAVMAHH 109
                                    5679**************999**************97555554555555555555774445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 913.16
//
Query:       gi|121637742|ref|YP_977965.1|  [L=87]
Description: hypothetical protein BCG_1874c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00054   19.8   3.4    0.00054   19.8   3.4    2.2  3  RHH_1           Ribbon-helix-helix protein, copG family
     0.0014   18.5   3.2     0.0022   17.8   1.2    2.0  2  RHH_4           Ribbon-helix-helix domain
     0.0069   16.7   0.2     0.0084   16.4   0.2    1.0  1  DUF2383         Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
       0.11   12.6   1.1       0.28   11.4   0.3    1.9  2  MatP_C          MatP C-terminal ribbon-helix-helix domain
       0.18   11.7   0.4       0.24   11.3   0.4    1.2  1  DEDD_Tnp_IS110  Transposase
        0.9   10.3   7.4        1.9    9.3   7.4    1.6  1  PSK_trans_fac   Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   3.4   1.8e-07   0.00054       1      39 []       4      42 ..       4      42 .. 0.96
   2 ?   -2.2   0.2       1.5   4.6e+03      29      35 ..      55      61 ..      55      62 .. 0.77
   3 ?   -1.5   0.1      0.91   2.7e+03       9      16 ..      70      77 ..      69      86 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-07
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyler 39
                                   r+++ ld ++ e+L+e+arr + ++Se +R+ lre++er
  gi|121637742|ref|YP_977965.1|  4 RLQVLLDPDEWEELREIARRHRTTVSEWVRRTLREARER 42
                                   78999*******************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                   HHHHHHH CS
                          RHH_1 29 IReAlre 35
                                   +R+A+r+
  gi|121637742|ref|YP_977965.1| 55 VRAAARH 61
                                   6999987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.91
                                   HHHHHHHH CS
                          RHH_1  9 ellerLde 16
                                   ++le++++
  gi|121637742|ref|YP_977965.1| 70 QMLEEIER 77
                                   56777765 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.2   7.3e-07    0.0022      15      43 ..       7      35 ..       3      55 .. 0.80
   2 ?    0.9   0.0      0.14   4.3e+02      35      48 ..      67      80 ..      52      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.3e-07
                                   EEEEHHHHHHHHHHHHHTT--HHHHHHHH CS
                          RHH_4 15 irLEpafWdaLeeiArregltvnaLiaei 43
                                   + L p  W++L+eiArr  +tv++ + + 
  gi|121637742|ref|YP_977965.1|  7 VLLDPDEWEELREIARRHRTTVSEWVRRT 35
                                   668999*****************999876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                   -HHHHHHHH.HHHH CS
                          RHH_4 35 tvnaLiaeidadrr 48
                                    v+++++ei++ r+
  gi|121637742|ref|YP_977965.1| 67 DVEQMLEEIERGRG 80
                                   57788888877773 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   2.8e-06    0.0084      35      97 ..      16      78 ..       9      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                                   HHHHHHHHHHHHHHHHHHHHHHCT----------------------------HHHHHHHHHHH CS
                        DUF2383 35 lleriaeereeaaeeLqseiralggepedggslagklhrawvdlksaltsndeeaileeleeg 97
                                    l++ia+ ++ +++e   +  ++ +e e +g+l  kl+ + ++ ++ + + d e +lee+e+g
  gi|121637742|ref|YP_977965.1| 16 ELREIARRHRTTVSEWVRRTLREAREREPRGDLDMKLRSVRAAARHEFPTADVEQMLEEIERG 78
                                   6899*********************************************************98 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   9.3e-05      0.28       9      43 ..       9      43 ..       3      57 .. 0.86
   2 ?    0.3   0.0      0.27   8.1e+02      32      42 ..      68      78 ..      47      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                         MatP_C  9 LdyavWqrLsklsqrrgsTLSetivqLieeaerke 43
                                   Ld   W+ L + ++r+ +T Se + + + ea ++e
  gi|121637742|ref|YP_977965.1|  9 LDPDEWEELREIARRHRTTVSEWVRRTLREARERE 43
                                   56667*******************99888876655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                         MatP_C 32 ivqLieeaerk 42
                                   ++q++ee er 
  gi|121637742|ref|YP_977965.1| 68 VEQMLEEIERG 78
                                   68999999885 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   8.1e-05      0.24     110     144 ..       3      36 ..       1      40 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.1e-05
                 DEDD_Tnp_IS110 110 grlrplklddeayaeLrqltrqredlvkertrlkn 144
                                    +rl+ l ld+++++eLr+++r++++ v e++r + 
  gi|121637742|ref|YP_977965.1|   3 KRLQVL-LDPDEWEELREIARRHRTTVSEWVRRTL 36 
                                    566666.78899******************99775 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.4   0.00062       1.9      15      47 ..      18      63 ..      10      86 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.............XX-- CS
                  PSK_trans_fac 15 reLarltgeskteAvrrAleerlerlrre.............raep 47
                                   re+ar+  ++  e vrr l+e+ er+ r              r+e 
  gi|121637742|ref|YP_977965.1| 18 REIARRHRTTVSEWVRRTLREAREREPRGdldmklrsvraaaRHEF 63
                                   9************************976544444333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 603.29
//
Query:       gi|121637743|ref|YP_977966.1|  [L=272]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-35  119.7  22.8    4.9e-35  119.7  22.8    2.6  3  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7  22.8   2.8e-39   4.9e-35       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -0.0   1.1     0.063   1.1e+03      38      54 ..     174     190 ..     169     196 .. 0.79
   3 ?   -2.9   1.5      0.51   9.1e+03      49      68 ..     249     254 ..     227     265 .. 0.51

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.8e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv+aPe++ aaa+dlagigsa+ aanaaaa pt++vlaa+aDeVSaa+A lf+ahaq+yqalsaqaa fheqfv+a++a
  gi|121637743|ref|YP_977966.1|  1 MSFVVAAPEVVVAAASDLAGIGSAIGAANAAAAVPTMGVLAAGADEVSAAVADLFGAHAQAYQALSAQAALFHEQFVHAMTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya aEaa
  gi|121637743|ref|YP_977966.1| 83 GAGAYAGAEAA 93
                                   *********97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.063
                                    ----SSSSHHHHHHHHH CS
                             PE  38 avlaaaaDeVSaaiAal 54 
                                     v++a++ + S a+Aa+
  gi|121637743|ref|YP_977966.1| 174 PVVPAGSADCSSATAAT 190
                                    48999999999998886 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHHHHHHHHHH CS
                             PE  49 aaiAalfsahaqeyqalsaq 68 
                                    +a+A              a+
  gi|121637743|ref|YP_977966.1| 249 TATA--------------AT 254
                                    2222..............22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2046.34
//
Query:       gi|121637744|ref|YP_977967.1|  [L=349]
Description: hypothetical protein BCG_1877c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-40  137.1   4.4    6.4e-40  136.7   4.4    1.1  1  DUF21         Cyclin M transmembrane N-terminal domain
    1.9e-13   50.6   1.1    7.4e-06   26.3   0.4    2.5  2  CBS           CBS domain
  ------ inclusion threshold ------
      0.064   11.5   0.5      0.089   11.1   0.5    1.2  1  Silic_transp  Silicon transporter


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   4.4   1.1e-43   6.4e-40       1     176 []       8     202 ..       8     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 1.1e-43
                          DUF21   1 liivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvella 80 
                                    l+++ll++++aff+gaE+Al+s++r rle+lae+gk+ a ++ +  +++  +L+ +++g+t+++ill+ ++++++v+ll+
  gi|121637744|ref|YP_977967.1|   8 LLALLLIGANAFFVGAEFALISARRDRLEALAEQGKATAVTVIRAGEQLPAMLTGAQLGVTVSSILLGRVGEPAVVKLLQ 87 
                                    578999*************************************************************************9 PP

                          DUF21  81 e............galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil.. 146
                                                 ++l++++a++iv+ l++++gE++Pk++al+ +e++a++l+pp  v+ +l +P++++ + ++n+il  
  gi|121637744|ref|YP_977967.1|  88 LsfglsgvppallHTLSLAVALAIVVALHVLLGEMVPKNIALAGPERTAMLLVPPYLVYVRLARPFIAFYNNCANAILrl 167
                                    9******************************************************************************* PP

                          DUF21 147 .....esesepavseeelkklveeseeegvieeee 176
                                         ++e + avs +el ++++es +eg +++ee
  gi|121637744|ref|YP_977967.1| 168 vgvqpKDELDIAVSTAELSEMIAESLSEGLLDHEE 202
                                    ********************************998 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     2e-08   0.00012      23      53 ..     246     276 ..     239     279 .. 0.86
   2 !   26.3   0.4   1.2e-09   7.4e-06       6      54 ..     290     338 ..     284     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                                    HHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS  23 elmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    + ++++g+sr+PVVd  g+++G+++ +D+l 
  gi|121637744|ref|YP_977967.1| 246 QALAQTGYSRFPVVDRGGRFIGYLHIKDVLT 276
                                    4467789*******9999***********96 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.2e-09
                                    BSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHH CS
                            CBS   6 trdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllra 54 
                                     r+++ vp + +l++al +mr+ + s+l +V+ ++g +vG+v l+D+++ 
  gi|121637744|ref|YP_977967.1| 290 VRPLPRVPQSLPLADALSRMRRIN-SHLaLVTADNGSVVGMVALEDVVED 338
                                    578999**************8744.477448889************9875 PP

>> Silic_transp  Silicon transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   1.5e-05     0.089     262     352 ..       7      93 ..       2     128 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.5e-05
                   Silic_transp 262 vvlfflllsvvGlleGmqiaffavaklrkeerGesffakktvellfkgeGknlpgflvGrqltvvlcffiiarvttldie 341
                                    v+l +ll+    ++ G + a+++  + r e   e   +k t  + + + G+ lp++l G ql v+++  +++rv  + + 
  gi|121637744|ref|YP_977967.1|   7 VLLALLLIGANAFFVGAEFALISARRDRLEALAE--QGKAT-AVTVIRAGEQLPAMLTGAQLGVTVSSILLGRVGEPAVV 83 
                                    5555555566666666665555544433333333..24444.4555568*************************998874 PP

                   Silic_transp 342 vGvdenifGvs 352
                                      + +  fG+s
  gi|121637744|ref|YP_977967.1|  84 -KLLQLSFGLS 93 
                                    .3444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2663.49
//
Query:       gi|121637745|ref|YP_977968.1|  [L=455]
Description: hypothetical protein BCG_1878c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-35  120.2   1.8    1.3e-34  119.5   1.8    1.3  1  DUF21      Cyclin M transmembrane N-terminal domain
    7.3e-20   70.8   0.0    2.2e-19   69.2   0.0    1.9  1  CorC_HlyC  Transporter associated domain
    2.2e-10   40.8   0.4    0.00044   20.6   0.0    2.7  2  CBS        CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   1.8   2.1e-38   1.3e-34       2     174 ..      12     203 ..      10     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 2.1e-38
                          DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellae 81 
                                    +i++l+++ ++f++aE++l++l+r+++e+ a+ g+++ +++++ ++++++ Ls +++g+++++++++ l+++l++el ++
  gi|121637745|ref|YP_977968.1|  12 AILALTAGTGVFVAAEFSLTALDRSTVEANARGGTSRDRFIQRAHHRLSFQLSGAQLGISITTLATGYLTEPLVAELPHP 91 
                                    678888************************************************************************99 PP

                          DUF21  82 ............galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil... 146
                                                ++l  + a+vivt l +vfgE++Pk la+++++++a+ ++    +++ ll+P+++l +  +n+i+   
  gi|121637745|ref|YP_977968.1|  92 glvavgmsdrvaDGLITFFALVIVTSLSMVFGELVPKYLAVARPLRTARSVVAGQVLFSLLLTPAIRLTNGAANWIVrrl 171
                                    ***********9999999************************************************************** PP

                          DUF21 147 ....esesepavseeelkklveeseeegviee 174
                                         +e ++a +++el +lv++s+++g+++ 
  gi|121637745|ref|YP_977968.1| 172 giepAEELRSARTPQELVSLVRSSARSGALDD 203
                                    ****99**********************9975 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   3.8e-23   2.2e-19       4      78 ..     357     441 ..     354     444 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.8e-23
                                    CTTEEEEETT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEE...EETT.........EEEEEEEEETTC CS
                      CorC_HlyC   4 degsylvdGslpldeleeelglelpeedyeTlgGlllellgriPkegesvev...dleg.........lrftVlemdgrr 71 
                                    +++ ++v+G l++de+++++g + p++ yeT+gGl+l++lg+iP  ge+ve+   d            +  tV +mdgrr
  gi|121637745|ref|YP_977968.1| 357 AGNGWRVSGLLRIDEVASATGYRAPDGPYETIGGLVLRELGHIPVAGETVELtalD--QdglpddsmrWLATVIQMDGRR 434
                                    7899********************************************88775551..1456666767************ PP

                                    EEEEEEE CS
                      CorC_HlyC  72 Ikkvrve 78 
                                    I+++++ 
  gi|121637745|ref|YP_977968.1| 435 IDSLELI 441
                                    ***9886 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.4e-08   0.00044       2      53 ..     221     275 ..     220     279 .. 0.84
   2 !   17.6   0.1   6.5e-07    0.0039       8      56 ..     292     340 ..     285     341 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.4e-08
                                    HHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                            CBS   2 gdimtr..dvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                    +++mt+  ++v +  d+t+++++   + +g+sr+PVV  d d   vGiv+ + +++
  gi|121637745|ref|YP_977968.1| 221 EELMTPrsKIVALQTDDTIADLVAAAAASGFSRFPVVegDLD-ATVGIVHVKQVFE 275
                                    6787776699***************98999*******74444.5******998876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.5e-07
                                    SCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllrall 56 
                                    +v +vp + +   ++ + r ++  +++ VVde+g   G+vtl+Dl++ ++
  gi|121637745|ref|YP_977968.1| 292 PVAVVPSTLDGDAVMAQVRASAlQTAM-VVDEYGGTAGMVTLEDLIEEIV 340
                                    455555556666777778666655577.******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3116.12
//
Query:       gi|121637746|ref|YP_977969.1|  [L=479]
Description: inosine 5-monophosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.9e-102  342.8   0.1   4.4e-102  341.6   0.1    1.5  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    8.7e-10   38.9   2.0    3.7e-05   24.1   0.2    2.7  2  CBS           CBS domain
    1.5e-05   24.5   0.8     0.0015   18.1   0.0    2.5  3  His_biosynth  Histidine biosynthesis protein
    8.1e-05   21.8  10.9     0.0023   17.0  10.6    2.8  2  FMN_dh        FMN-dependent dehydrogenase
    0.00013   21.5  12.9     0.0004   19.9   0.0    3.2  3  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.032   13.4   2.4      0.032   13.4   1.2    1.5  2  Glu_synthase  Conserved region in glutamate synthase
       0.12   11.8   2.7       0.33   10.3   1.4    2.1  2  Aldolase      KDPG and KHG aldolase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.6   0.1  1.7e-105  4.4e-102       2     344 ..      14     474 ..      13     475 .. 0.96

  Alignments for each domain:
  == domain 1  score: 341.6 bits;  conditional E-value: 1.7e-105
                                    --GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH   2 ltfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvk 80 
                                    lt++dv++vp++sev+++ +vdl+t   +    +iP+v a+m +v++++mA ++ar+Ggi ++ ++l i +  ++v+ vk
  gi|121637746|ref|YP_977969.1|  14 LTYNDVFIVPNRSEVASRfDVDLSTADGSG--TTIPVVVANMTAVAGRRMAETVARRGGIVILPQDLPIPAVKQTVAFVK 91 
                                    8*****************9*****998877..689********************************************* PP

                                    TS.............................................................................. CS
                                    xx.............................................................................. RF
                          IMPDH  81 rs.............................................................................. 82 
                                    +                                                                               
  gi|121637746|ref|YP_977969.1|  92 SRdlvldtpvtlapddsvsdamalihkrahgvavvilegrpiglvressclgvdrftrvrdiavtdyvtapagteprkif 171
                                    99****************************************************************************** PP

                                    ..................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSS CS
                                    ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  83 ..................................pnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahgh 128
                                                                       + a+d+ grl++gaavg++ d  ++++al+eagvdvlv+d+ahgh
  gi|121637746|ref|YP_977969.1| 172 dllehapvdvavltdadgtlagvlsrtgairagiYTPATDSAGRLRIGAAVGINGDVGAKARALAEAGVDVLVIDTAHGH 251
                                    *********************************977789***************************************** PP

                                    SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 129 sekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagv 208
                                    + k+l+a+k++ +    + + aGnv++aeg+++L++aga++vkvG+GpG++Cttr+++gvG+pq++Av+e+a+aa++ g 
  gi|121637746|ref|YP_977969.1| 252 QVKTLDAIKAVSALDLGLPLAAGNVVSAEGTRDLLKAGANVVKVGVGPGAMCTTRMMTGVGRPQFSAVLECASAARQLGG 331
                                    ************98878*************************************************************** PP

                                    EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEET.TEEEEEEEETTSHHHH.HH-SS-TTS-...--SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxx RF
                          IMPDH 209 pviaDGGikysgdivkAlaaGadavmlGsllagteEspgevilie.grkyKeyrGmgslgam.kkgskdryfq.kkeklv 285
                                    +++aDGGi++ +d++ AlaaGa+ vm+Gs++agt Espg+++  + ++ yKe  Gm+s +a+ +++ +d+ f+ +++ l+
  gi|121637746|ref|YP_977969.1| 332 HIWADGGIRHPRDVALALAAGASNVMIGSWFAGTYESPGDLMRDRdDQPYKESYGMASKRAVvARTGADNPFDrARKALF 411
                                    ******************************************9876899*************6556777777734779** PP

                                    -SBEEEEE....E--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS- CS
                                    xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 286 peGvegrv....pykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshv 344
                                    +eG++++     p++g v+++++++++g+rs+++y+Ga++++el+e+a +  ++ ag++e+h+
  gi|121637746|ref|YP_977969.1| 412 EEGISTSRmgldPDRGGVEDLIDHITSGVRSTCTYVGASNLAELHERAVVGVQSGAGFAEGHP 474
                                    ****976556669************************************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   1.4e-08   3.7e-05       7      50 ..      98     140 ..      90     145 .. 0.79
   2 !   13.6   0.1   2.7e-05      0.07       1      54 [.     150     203 ..     150     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                                    SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHH CS
                            CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrD 50 
                                    + +vt+ pd+++++a+ l+ +k+ +++ VV  +g+++G+v ++ 
  gi|121637746|ref|YP_977969.1|  98 DTPVTLAPDDSVSDAMALI-HKRAHGVAVVILEGRPIGLVRESS 140
                                    4468***************.7777788765268*******8876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.7e-05
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEE.EETTTBEEEEEEHHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPV.VdedgklvGivtlrDllra 54 
                                    V+di  +d+vt+p  t  +++++l+ e++ v  + V +d dg l G+++++  +ra
  gi|121637746|ref|YP_977969.1| 150 VRDIAVTDYVTAPAGTEPRKIFDLL-EHApV-DVAVlTDADGTLAGVLSRTGAIRA 203
                                    799999*******************.77778.44463699**********977775 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.5   6.3e+03     166     178 ..     184     194 ..     156     214 .. 0.66
   2 !    4.4   0.3    0.0084        22      29     102 ..     226     296 ..     220     311 .. 0.81
   3 !   18.1   0.0   5.7e-07    0.0015      67     105 ..     324     362 ..     307     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                                    EEETTTTTTSS-- CS
                   His_biosynth 166 ltdidrdGtlsGp 178
                                    lt  d+dGtl+G+
  gi|121637746|ref|YP_977969.1| 184 LT--DADGTLAGV 194
                                    44..467777776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0084
                                    TSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS.SSSHHHHHHHHHCT-SEEEES CS
                   His_biosynth  29 gdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG.Irsledveelleagadkviig 102
                                    gd+ + a++++e+g+d l+   +d a+ ++ + ld+++++    ++ + +  G + s e  ++ll+aga+ v +g
  gi|121637746|ref|YP_977969.1| 226 GDVGAKARALAEAGVDVLV---IDTAHGHQVKTLDAIKAVSAL-DLGLPLAAGnVVSAEGTRDLLKAGANVVKVG 296
                                    6666677788888888776...688999999999**9998765.8888888888999999*********977665 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 5.7e-07
                                    HHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                   His_biosynth  67 eiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                      a+++  +++ +GGIr+  dv+ +l aga++v+ig++ 
  gi|121637746|ref|YP_977969.1| 324 SAARQLGGHIWADGGIRHPRDVALALAAGASNVMIGSWF 362
                                    467788899****************************85 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  10.6   9.1e-07    0.0023     215     302 ..     267     361 ..     223     367 .. 0.64
   2 ?    0.7   0.0     0.081   2.1e+02     313     346 ..     427     460 ..     424     462 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                                    HSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH...SS-EEEESS--SHHHHH CS
                         FMN_dh 215 tklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg.rievlvDgGirrGsDvl 287
                                    + lpl    v++ae  + +++aG++ + v    G     R + g+  + +++  e++ a+++    +++DgGir+  Dv+
  gi|121637746|ref|YP_977969.1| 267 LGLPLAAGNVVSAEGTRDLLKAGANVVKVGVGPGamcttRMMTGVgRPQFSAVLECASAARQlGGHIWADGGIRHPRDVA 346
                                    335555555666666666666666666665555555555555544234456666666666664589************** PP

                                    HHHHTT-SEEEESHH CS
                         FMN_dh 288 kAlalGAdavllGRp 302
                                     Ala GA+ v++G  
  gi|121637746|ref|YP_977969.1| 347 LALAAGASNVMIGSW 361
                                    ************965 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.081
                                    HHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCGGE CS
                         FMN_dh 313 eGvervleilraelertmallGvksvaeldrsll 346
                                     Gve++++ +++ +++t + +G++++ael+++++
  gi|121637746|ref|YP_977969.1| 427 GGVEDLIDHITSGVRSTCTYVGASNLAELHERAV 460
                                    69***************************98765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.2    0.0097        25       9      41 ..      43      75 ..      38     127 .. 0.83
   2 ?   -0.5   7.0      0.25   6.4e+02     148     222 ..     231     296 ..     198     305 .. 0.84
   3 !   19.9   0.0   1.6e-07    0.0004     196     234 ..     333     371 ..     314     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0097
                            NMO  9 kikppvvqpgmggiskarLaaavsnaGgLGvla 41
                                   ++  pvv + m  +++ r+a  v+  Gg+ +l 
  gi|121637746|ref|YP_977969.1| 43 GTTIPVVVANMTAVAGRRMAETVARRGGIVILP 75
                                   5678999*********************98776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                            NMO 148 earkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqig 222
                                    +ar+++++G D+l+++   a Ghq   +     ++  + ++++a+d  +P +AaG ++ ++g    L +GA+ v++g
  gi|121637746|ref|YP_977969.1| 231 KARALAEAGVDVLVID--TAHGHQV--K-----TLDAI-KAVSALDlgLP-LAAGNVVSAEGTRDLLKAGANVVKVG 296
                                    6899999999999997..5668998..2.....33334.45577776778.69*********************998 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1.6e-07
                            NMO 196 viAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdak 234
                                    + A GGi   r+va aLa+GAs v ig+ f +t es+  
  gi|121637746|ref|YP_977969.1| 333 IWADGGIRHPRDVALALAAGASNVMIGSWFAGTYESPGD 371
                                    5699*******************************9865 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.97   2.5e+03     216     238 ..     228     250 ..     217     277 .. 0.69
   2 ?   13.4   1.2   1.3e-05     0.032     224     304 ..     286     360 ..     253     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.97
                                    HHHHHHHHHHTT-SEEEEE-TT- CS
                   Glu_synthase 216 vetiaagvakanadiilidGleG 238
                                    v++ a  +a+a++d+++id  +G
  gi|121637746|ref|YP_977969.1| 228 VGAKARALAEAGVDVLVIDTAHG 250
                                    45556668999999999997776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    HHTT-SEEEEE-TT---SSEE.HHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE- CS
                   Glu_synthase 224 akanadiilidGleGGTGAsp.kssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgi 302
                                     ka+a+++++ G   G GA   + ++  +G P   a+ e   + ++ g     ++ adGg++ ++dv++ala GA +v i
  gi|121637746|ref|YP_977969.1| 286 LKAGANVVKV-G--VGPGAMCtTRMMTGVGRPQFSAVLECASAARQLGG----HIWADGGIRHPRDVALALAAGASNVMI 358
                                    5666666665.2..25555430445666788888888877776655543....589************************ PP

                                    SH CS
                   Glu_synthase 303 gt 304
                                    g+
  gi|121637746|ref|YP_977969.1| 359 GS 360
                                    97 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.4   0.00013      0.33      21      84 ..     227     293 ..     220     309 .. 0.81
   2 ?   -0.3   0.0      0.24   6.2e+02     154     180 ..     336     363 ..     323     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                    GHHHHHHHHHHTT--EEEEETTSTT...HHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHCT-SEE CS
                       Aldolase  21 dalplaeaLvagGlrvlevtlrtea...aldairvlrkerpdllvgaGtvlnaeqlaeakeaGaqfv 84 
                                    d+   a aL++ G+ vl +     +   +ldai+++ +   +l ++aG v++ae   +  +aGa+ v
  gi|121637746|ref|YP_977969.1| 227 DVGAKARALAEAGVDVLVIDTAHGHqvkTLDAIKAVSALDLGLPLAAGNVVSAEGTRDLLKAGANVV 293
                                    5666799*********999665443122789***9999999***********************976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                                    BSS-.-TTTHHHHHTSTTBS-EEESCCC CS
                       Aldolase 154 tGGi.spanvrdylalpsvlvvgGswlv 180
                                     GGi +p +v   la+++  v+ Gsw+ 
  gi|121637746|ref|YP_977969.1| 336 DGGIrHPRDVALALAAGASNVMIGSWFA 363
                                    5777568888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3072.10
//
Query:       gi|121637747|ref|YP_977970.1|  [L=685]
Description: 6-phosphogluconate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-89  299.7   0.0    3.1e-89  299.2   0.0    1.1  1  6PGD           6-phosphogluconate dehydrogenase, C-terminal d
    2.4e-44  151.3   0.0    3.9e-44  150.6   0.0    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
       0.06   13.4   0.0       0.13   12.3   0.0    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.2   0.0   5.2e-93   3.1e-89       1     219 [.     166     384 ..     166     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 299.2 bits;  conditional E-value: 5.2e-93
                           6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgelesyLieitakilrkkdeedgkplvdkilDka 80 
                                    Gh+VKmvHNGiey+dmqli+Eay+l++++lgl++  ia+vF+eWn+g+l+syL+eita++lr++d+++gkplvd+i+D+a
  gi|121637747|ref|YP_977970.1| 166 GHFVKMVHNGIEYSDMQLIGEAYQLMRDGLGLTAPAIADVFTEWNNGDLDSYLVEITAEVLRQTDAKTGKPLVDVIVDRA 245
                                    9******************************************************************************* PP

                           6PGD  81 gqkGTgkwtvqealelgvpvptiaeavfaRllSslkeervkaskllkeeeekeeedkeefiedlrkAlyaskivsYaqgl 160
                                    +qkGTg+wtv++al+lgvpv+ iaeavfaR+lS +  +r +as l +++  ++ +d ++f+ed+r+Alyaskiv+Yaqg+
  gi|121637747|ref|YP_977970.1| 246 EQKGTGRWTVKSALDLGVPVTGIAEAVFARALSGSVGQRSAASGLASGKLGEQPADPATFTEDVRQALYASKIVAYAQGF 325
                                    ********************************************998766699999************************ PP

                           6PGD 161 ellkaaskeygwnlnlaeiariWrgGCiIrakfldkikeafeknpelenllldpefake 219
                                    ++++a s+e+gw+++ +++a+iWrgGCiIrakfl++ikeaf+++p+l++l+++p+f++ 
  gi|121637747|ref|YP_977970.1| 326 NQIQAGSAEFGWDITPGDLATIWRGGCIIRAKFLNHIKEAFDASPNLASLIVAPYFRAP 384
                                    ********************************************************875 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   6.5e-48   3.9e-44      10     158 .]       1     161 [.       1     161 [. 0.97

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 6.5e-48
                                    HHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHSHCCC-- CS
                  NAD_binding_2  10 MGsnmalnllkagykvavynrtkekveelvaeg.....akaaesieelvasl...dvvitmvkagkavdeviegllealk 81 
                                    MGsn+a+n++++gy+vav+nr+ +k+++l++e+     ++  e+i e++a+l   + v++mvkag+a+d+vi++l++a++
  gi|121637747|ref|YP_977970.1|   1 MGSNIARNFARHGYTVAVHNRSVAKTDALLKEHssdgkFVRSETIPEFLAALekpRRVLIMVKAGEATDAVINELADAME 80 
                                    ********************************9999999999**********999************************* PP

                                    TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE......EEEE CS
                  NAD_binding_2  82 kgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga......kvth 155
                                    +gdi+idg+++ ++dt +++k+++e+gl+f++a++SGGeegA +G+ sim+GG++e+++++ p+le+i+a      ++th
  gi|121637747|ref|YP_977970.1|  81 PGDIIIDGGNALYTDTMRREKAMRERGLHFVGAGISGGEEGALNGP-SIMPGGPAESYQSLGPLLEEISAhvdgvpCCTH 159
                                    **********************************************.***********************8888888774 PP

                                    E-E CS
                  NAD_binding_2 156 viG 158
                                     iG
  gi|121637747|ref|YP_977970.1| 160 -IG 161
                                    .35 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.2e-05      0.13      23      74 ..       1      50 [.       1      74 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH CS
                   Shikimate_DH 23 maelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkella 74
                                   m++ +a++++++g++ v+v NR++++ ++l +e++++  ++++ e + e la
  gi|121637747|ref|YP_977970.1|  1 MGSNIARNFARHGYT-VAVHNRSVAKTDALLKEHSSD-GKFVRSETIPEFLA 50
                                   8999***********.*****************9655.55666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4575.78
//
Query:       gi|121637748|ref|YP_977971.1|  [L=316]
Description: hypothetical protein BCG_1881c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-10   41.1   0.6      9e-10   38.6   0.1    2.1  2  Peptidase_M48  Peptidase family M48
      1e-05   24.9   0.3    2.4e-05   23.7   0.3    1.6  1  Peptidase_M56  BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1     1e-13     9e-10      26      90 ..     144     206 ..     134     225 .. 0.80
   2 ?    0.1   0.0     0.067     6e+02     137     163 ..     227     252 ..     224     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1e-13
                                    EEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  26 kvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivslla 90 
                                    ++ v++  +  A++l+g  ++r+v+++g l ++l ++e+aa+l HE +H+ +rh +v   ++ + 
  gi|121637748|ref|YP_977971.1| 144 DLRVLDVAQPLAYCLPGV-RSRVVVSEGTL-TALADAEVAAILTHERAHLRARHDLVLEAFTAVH 206
                                    56677888889*******.88*********.***********************98874444333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.067
                                    HHHHHHHHHHTTT.HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 137 EyqADeagvellkrakdlvraliklak 163
                                    E+ AD a+v+++  +  l+ral+  a+
  gi|121637748|ref|YP_977971.1| 227 ELLADDAAVRAAG-RTPLARALVACAS 252
                                    8889******999.9999999987665 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   2.6e-09   2.4e-05     176     220 ..     160     205 ..      79     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-09
                  Peptidase_M56 176 llkprIvlPadflkklsdeeleyillHElaHlk.rkDllvnllvav 220
                                     +++r+v+++  l+ l+d+e + il+HE+aHl+ r+Dl+ +++ av
  gi|121637748|ref|YP_977971.1| 160 GVRSRVVVSEGTLTALADAEVAAILTHERAHLRaRHDLVLEAFTAV 205
                                    4799****************************8689***9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2195.03
//
Query:       gi|121637749|ref|YP_977972.1|  [L=138]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.0   0.1    1.3e-29  102.8   0.1    1.0  1  Penicillinase_R  Penicillinase repressor
     0.0027   17.6   0.0      0.005   16.7   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
        1.2    8.8   4.5        3.5    7.3   0.9    2.9  3  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.1   2.2e-33   1.3e-29       1     114 [.       7     120 ..       7     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 2.2e-33
                                    ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXX. CS
                Penicillinase_R   1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkq. 78 
                                    lg+lE++vm++lw++ e +tv++v+e+l+++++lay+TV+t+l+rL kK+l+ + ++ ra++Y+p++ ++e+va+ + + 
  gi|121637749|ref|YP_977972.1|   7 LGDLERAVMDHLWSRTEpQTVRQVHEALSARRDLAYTTVMTVLQRLAKKNLVLQIRDDRAHRYAPVHGRDELVAGLMVDa 86 
                                    79*************999*******************************************************9977651 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  79 lldklfegsvkelvaafveeeklseddleeLrelle 114
                                    l +  ++gs+++++++fve+  + +d++++Lr++l+
  gi|121637749|ref|YP_977972.1|  87 LAQAEYSGSRQAALVHFVER--VGADEADALRRALA 120
                                    667789**************..**********9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.3e-07     0.005      21      66 ..      23      73 ..      10      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.3e-07
                                   CCCHHCHHCCCT....TSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                           TrmB 21 gpatadeiaeel....gvprskvYevLrsLedkGlVerek.grpklYravd 66
                                   +p t+++++e+l    ++ +++v  vL++L +k lV  ++  r ++Y +v+
  gi|121637749|ref|YP_977972.1| 23 EPQTVRQVHEALsarrDLAYTTVMTVLQRLAKKNLVLQIRdDRAHRYAPVH 73
                                   6778888877772222566799999***********888835588**9985 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.073   4.4e+02      38      51 ..      24      37 ..      20      41 .. 0.83
   2 ?    7.3   0.9   0.00059       3.5      30      55 ..      34      59 ..      26      66 .. 0.81
   3 ?    1.0   0.2     0.056   3.4e+02      41      50 ..     115     124 ..     111     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHT CS
                           GntR 38 rttvReALrrLeae 51
                                    +tvR+++  L+a+
  gi|121637749|ref|YP_977972.1| 24 PQTVRQVHEALSAR 37
                                   57999999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00059
                                   HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           GntR 30 LaaefgVsrttvReALrrLeaeglve 55
                                   L+a+ +   ttv+ +L+rL+ ++lv 
  gi|121637749|ref|YP_977972.1| 34 LSARRDLAYTTVMTVLQRLAKKNLVL 59
                                   5666666679*************995 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.056
                                    HHHHHHHHHH CS
                           GntR  41 vReALrrLea 50 
                                    +R+AL +Lea
  gi|121637749|ref|YP_977972.1| 115 LRRALAELEA 124
                                    89*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 746.39
//
Query:       gi|121637750|ref|YP_977973.1|  [L=140]
Description: hypothetical protein BCG_1883 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-16   58.4   0.4    8.7e-16   58.0   0.4    1.2  1  4HBT      Thioesterase superfamily
      1e-05   25.7   0.0    1.4e-05   25.2   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
    0.00014   22.2   0.1    0.00016   22.0   0.1    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.4   1.5e-19   8.7e-16       2      79 .]      48     127 ..      47     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.5e-19
                                    SSB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                           4HBT   2 GvvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                    GvvhgGvy a+++++a++a++ +  +   g  vv+v+ + dflr++  g  ++ +a++l+ gr+ + + v+++d+++r+v
  gi|121637750|ref|YP_977973.1|  48 GVVHGGVYCAMIESIASMAAFAWLNShgeGGSVVGVNNNTDFLRSISSG-MVYGTAEPLHRGRRQQLWLVTITDDTDRVV 126
                                    9*********************9999999********************.***************************998 PP

                                    E CS
                           4HBT  79 a 79 
                                    a
  gi|121637750|ref|YP_977973.1| 127 A 127
                                    5 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.4e-09   1.4e-05      10     130 ..      12     133 ..       9     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-09
                                    HHHSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-T...TEEEEEEEEEEEE-S CS
                        DUF4442  10 slkaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpd...thrwipkgmevdYla 86 
                                    ++++P+   +g++++el p+ a+++l  r+++    g vH++  c++ E  +++ a a l +   +  ++  + + d+l+
  gi|121637750|ref|YP_977973.1|  12 NVTVPFDSELGLQFTELGPDGARAQLDVRPKLLQLTGVVHGGVYCAMIESIASMAAFAWLNShgeGGSVVGVNNNTDFLR 91 
                                    67899999************************************************99999866678899999******9 PP

                                    ---S-.EEEEEE-TTS-TT--EEEEEEEEEEETTE.EEEEEEEEE CS
                        DUF4442  87 katgd.ltavaelepedvgekeelvvevevrdekgeevvraeitl 130
                                       ++ +  +a  ep  +g++++l   v+++d+ +++v+r++++l
  gi|121637750|ref|YP_977973.1|  92 SISSGmVYGTA--EPLHRGRRQQLW-LVTITDDTDRVVARGQVRL 133
                                    96655055555..566666555554.59999****9****99875 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.7e-08   0.00016       9      87 ..      48     137 ..      39     140 .] 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.7e-08
                                    TC.-HHHHHHHHHHHHHHT...........-S.SS.EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEET.TEEE CS
                         4HBT_3   9 gagyGGyvlAlalraaqrtv..........pdprl.hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqg.grpi 76 
                                    g+++GG+  A++ + a  +            ++ +  +   +Flr +++g v  ++e++ +Gr+ +++ v+++ + +r++
  gi|121637750|ref|YP_977973.1|  48 GVVHGGVYCAMIESIASMAAfawlnshgegGSV-VgVNNNTDFLRSISSGMVYGTAEPLHRGRRQQLWLVTITDDtDRVV 126
                                    3359****9999999997756899888776443.46799**********************************9889*** PP

                                    EEEEEEEE--- CS
                         4HBT_3  77 ftatasfgrae 87 
                                    +++++ ++++e
  gi|121637750|ref|YP_977973.1| 127 ARGQVRLQNLE 137
                                    *****999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 772.26
//
Query:       gi|121637751|ref|YP_977974.1|  [L=100]
Description: urease subunit gamma [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-48  160.7   0.2    9.8e-48  160.5   0.2    1.0  1  Urease_gamma  Urease, gamma subunit


Domain annotation for each model (and alignments):
>> Urease_gamma  Urease, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   0.2   5.5e-52   9.8e-48       1      99 []       1      99 [.       1      99 [. 1.00

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 5.5e-52
                                   ----HHHHHHHHHHHHHHHHHHHHHTT--B-HHHHHHHHHHHHHHHHHCTS-HHHHHHHHCCSS-CCCB-TTCHHH-SEEEE CS
                   Urease_gamma  1 mkLtpreldkLllfaaaelAqkrlarGlkLnhpEavaliasevlelardgksvaelmelgkklLtredvldgvaelleevqv 82
                                   m+Ltp+e+++Lll++aaelA++r+arGl+LnhpEa+a+ia+++le+ardg++vaelm+ g+++L+r+dv++gv+e+l evqv
  gi|121637751|ref|YP_977974.1|  1 MRLTPHEQERLLLSYAAELARRRRARGLRLNHPEAIAVIADHILEGARDGRTVAELMASGREVLGRDDVMEGVPEMLAEVQV 82
                                   9********************************************************************************* PP

                                   EEEETTEEEEEEEES-S CS
                   Urease_gamma 83 eatfpdgtkLvtvhdpi 99
                                   eatfpdgtkLvtvh+pi
  gi|121637751|ref|YP_977974.1| 83 EATFPDGTKLVTVHQPI 99
                                   ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 764.24
//
Query:       gi|121637752|ref|YP_977975.1|  [L=104]
Description: urease subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-35  120.9   0.0    1.9e-35  120.8   0.0    1.0  1  Urease_beta  Urease beta subunit


Domain annotation for each model (and alignments):
>> Urease_beta  Urease beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.0   1.1e-39   1.9e-35       1      93 [.       3      96 ..       3     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.1e-39
                                   TT-EE-SSSEEETTTT-.--EEEEEEE-SSS-EEEETTS-GGGS-TTEES-HHHHTTEEE-SSTT-EEEE-TT-EEEEEEEE CS
                    Urease_beta  1 pgeiiteegeielnagr.etiklkvantgdrpiqvgshyhflevnkaLefdRekalGlrldipagtavrfepgeekevelve 81
                                   pgei++ +g+ie+na   +++++++ n gdrp+qvgsh+h+ ++n+aL+fdR++a+G+rldipa+tavrfepg  + v lv+
  gi|121637752|ref|YP_977975.1|  3 PGEIFYGSGDIEMNAAAlSRLQMRIINAGDRPVQVGSHVHLPQANRALSFDRATAHGYRLDIPAATAVRFEPGIPQIVGLVP 84
                                   8*************986599************************************************************** PP

                                   -STT-EE-STTS CS
                    Urease_beta 82 laGerkvyGlng 93
                                   l+G+r+v Gl+ 
  gi|121637752|ref|YP_977975.1| 85 LGGRREVPGLTL 96
                                   *********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 718.30
//
Query:       gi|121637753|ref|YP_977976.1|  [L=577]
Description: urease subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-69  233.2   1.1    7.2e-69  232.7   1.1    1.2  1  Amidohydro_1  Amidohydrolase family
    5.7e-53  178.4   0.9      1e-52  177.5   0.9    1.5  1  Urease_alpha  Urease alpha-subunit, N-terminal domain
    1.6e-06   27.9   6.4    9.1e-06   25.4   1.7    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.7   1.1   1.2e-72   7.2e-69       1     334 [.     132     458 ..     132     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.7 bits;  conditional E-value: 1.2e-72
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH....HHHHHHHHHHTSSSE CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst....giealleaaeelplg 76 
                                    iv++G +D HvHl              ++p+++ eal+ g++t +++Gt+++ ++ att+t    +++++le+++  p++
  gi|121637753|ref|YP_977976.1| 132 IVTAGTVDCHVHL--------------ICPQIIVEALAAGTTTIIGGGTGPAEGTKATTVTpgewHLARMLESLDGWPVN 197
                                    79***********..............***************************************************** PP

                                    EEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TS CS
                   Amidohydro_1  77 lrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa..le 154
                                    + +lg+      g++ ++ a++e+l+ ga             ++++ he+++ ++++++ +l +a+ ++++va H   l+
  gi|121637753|ref|YP_977976.1| 198 FALLGK------GNTVNPDALWEQLRGGA-------------SGFKLHEDWGSTPAAIDTCLAVADVAGVQVALHSdtLN 258
                                    ******......*****************.............************************************** PP

                                    SCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE...HH...HHHHHHHHHHHHCEE.........HHH CS
                   Amidohydro_1 155 tkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt...pt...eaellkerlkeagva.........hcp 219
                                    ++g+ved++ a++++ +h++h+e+a++++++d+i+++++ +v+++   pt   ++++l+e+l++ +v+         +++
  gi|121637753|ref|YP_977976.1| 259 ETGFVEDTIGAIAGRSIHAYHTEGAGGGHAPDIITVAAQPNVLPSstnPTrphTVNTLDEHLDMLMVChhlnpripeDLA 338
                                    *********************************************77744777*************************** PP

                                    HHHHHSEHHHHHHHHHHHH.TSCEEEEEECTTSSCCGGHHHH...HHHHHHHHHHCCTT.....TTHCHCHHHHHHHHHT CS
                   Amidohydro_1 220 fsnsilrsgrealrkalde.GvkvglgtDgaasgnslnllee...lrlalklqrgllye.....deegglslkealrmaT 290
                                    f++s++r+ ++a++++l++ G+++++g+D++a+g++++++ +   +++ +k +rg l +     +++++ ++ ++++++T
  gi|121637753|ref|YP_977976.1| 339 FAESRIRPSTIAAEDVLHDmGAISMIGSDSQAMGRVGEVVLRtwqTAHVMKARRGALEGdpsgsQAADNNRVRRYIAKYT 418
                                    *************************************999999**************999999999************** PP

                                    HHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEE CS
                   Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnv 334
                                    i +A+a+g+d+ +Gs+evGk ADlv++     +af+g+ +    
  gi|121637753|ref|YP_977976.1| 419 ICPAIAHGMDHLIGSVEVGKLADLVLW----EPAFFGVRPHVVL 458
                                    ***************************....*****99884443 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   0.9   1.8e-56     1e-52       2     121 .]       3     126 ..       2     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 1.8e-56
                   Urease_alpha   2 klsreeyaelyGptvgDrvrLadtellievekDlt....vyGeevkfGggkviRdgmgqssaakeeealDlvitnavilD 77 
                                    +lsre+ya+lyGpt+gDr+rLadt+ll+ev++D       +G+e++fGggkv+R++mgq +a+++++a D+vit+avi+D
  gi|121637753|ref|YP_977976.1|   3 RLSRERYAQLYGPTTGDRIRLADTNLLVEVTEDRCggpgLAGDEAVFGGGKVLRESMGQGRASRADGAPDTVITGAVIID 82 
                                    699******************************9988889**************************************** PP

                   Urease_alpha  78 atgivkadigikdgrivaiGkagnpdvmdgvdeelvigastevi 121
                                    ++gi+kadigi+dgriv+iGkagnpd+m gv+++lv+g+ste+i
  gi|121637753|ref|YP_977976.1|  83 YWGIIKADIGIRDGRIVGIGKAGNPDIMTGVHRDLVVGPSTEII 126
                                    ******************************************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2    0.0032        19       8      62 ..     131     184 ..     126     197 .. 0.84
   2 !   25.4   1.7   1.5e-09   9.1e-06     263     455 ..     234     455 ..     189     464 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0032
                   Amidohydro_3   8 rlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt.pkgrwiv 62 
                                    r+v++G vD H Hl+  ++ +  l  +    t + g +  +++ ++tt  +g+w++
  gi|121637753|ref|YP_977976.1| 131 RIVTAGTVDCHVHLICPQIIVEALAAGT--TTIIGGGTGPAEGTKATTvTPGEWHL 184
                                    78*************9998888888888..88888888888888888877777764 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.5e-09
                   Amidohydro_3 263 ealaelvaaadergldvaihaigdaavd...dvldafeaa....aekngnqdrr.....rlehaegv............. 317
                                    +a+  ++a ad +g++va+h+++   +    d++ a++ +     + +g  + +     ++                   
  gi|121637753|ref|YP_977976.1| 234 AAIDTCLAVADVAGVQVALHSDTLNETGfveDTIGAIAGRsihaYHTEGAGGGHapdiiTV-----Aaqpnvlpsstnpt 308
                                    4588899999999999999999988888788889998888766644444444444544422.....13355578878888 PP

                   Amidohydro_3 318 tesqiervaalqvaagvqpvfnf....edelldsrlgperargstpvkellnagvkvalgsD....apvgpfdpwpriga 389
                                    ++++++ + +      v++ +n+    +  +++sr+   r++++++   l ++g   + gsD     +vg +      +a
  gi|121637753|ref|YP_977976.1| 309 RPHTVNTLDEHLDMLMVCHHLNPripeDLAFAESRI---RPSTIAAEDVLHDMGAISMIGSDsqamGRVGEVVLRTWQTA 385
                                    888888888888888888888889998888888888...88999999999999999999999764444444444444456 PP

                   Amidohydro_3 390 avmrktrrgg.....evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdpp 455
                                    +vm+  r+ +        ++     ++  +a yT  pA a g+++  G++evG+ ADlv+++ + + v p 
  gi|121637753|ref|YP_977976.1| 386 HVMKARRG-AlegdpSGSQAADNNRVRRYIAKYTICPAIAHGMDHLIGSVEVGKLADLVLWEPAFFGVRPH 455
                                    66655544.35999988888888899999**********************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 4152.55
//
Query:       gi|121637754|ref|YP_977977.1|  [L=211]
Description: urease accessory protein uref [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-13   50.0   2.3    6.8e-13   49.4   2.3    1.3  1  UreF      UreF
  ------ inclusion threshold ------
      0.029   14.4   0.4        0.2   11.7   0.1    2.3  2  TetR_C_7  AefR-like transcriptional repressor, C-terminal dom


Domain annotation for each model (and alignments):
>> UreF  UreF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   2.3   7.6e-17   6.8e-13       4     131 ..      38     171 ..      35     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 7.6e-17
                                    HHHHHHHHHHHHTTHHHHTHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHH-....... CS
                           UreF   4 easlaawledqLllglarldlavlarayraaragdaaalrelddwllatretaelrlaseqmGrsllrllrkl....... 76 
                                     a+l+a+l+ +  ++ + l + ++a+++r        a+++ d++ +a ++++ +r as+++Gr l+rl+r++       
  gi|121637754|ref|YP_977977.1|  38 LATLEAFLKRR-VRTHGLLTASIAAAVHRGE-----LAVDDADRETDARTPAPAARHASRSQGRGLIRLARRVwpdsgwe 111
                                    57888888888.5566666666666666554.....48***********************************8877766 PP

                                    ......-HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHT CS
                           UreF  77 .t....hypvafglaaaalgipleeallaylfswaenlvsAavklvplGqtagqrilarl 131
                                          h++v+ g + a  g+ +e+ +l +++ ++++ + Aa +l+ l++ +   + ++l
  gi|121637754|ref|YP_977977.1| 112 eLgprpHLAVVAGRVGALSGLAPEHNALHLVYITMTGSAIAAQRLLALDPAEVTVVTFQL 171
                                    505567********************************************9998888776 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.2e-05       0.2      38      71 ..      42      74 ..      29      78 .. 0.90
   2 ?   -0.0   0.0     0.095   8.6e+02      50      71 ..     172     193 ..     165     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                   CCHHHT.T----HHHHHHHHHHHHTTSB-SS-HH CS
                       TetR_C_7 38 rafyeagpgrveealaayLeaavaaGrLridDpe 71
                                   +af+++   r++  l+a ++aav++G+L++dD++
  gi|121637754|ref|YP_977977.1| 42 EAFLKR-RVRTHGLLTASIAAAVHRGELAVDDAD 74
                                   678888.8899999******************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.095
                                    HHHHHHHHHHHHTTSB-SS-HH CS
                       TetR_C_7  50 ealaayLeaavaaGrLridDpe 71 
                                    ++l + +++++ aG  +  Dp 
  gi|121637754|ref|YP_977977.1| 172 SELCEQIAQEATAGLADLSDPL 193
                                    6789999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1573.84
//
Query:       gi|121637755|ref|YP_977978.1|  [L=224]
Description: urease accessory protein ureG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-35  120.0   0.1    9.6e-35  119.8   0.1    1.1  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
    3.4e-05   23.0   1.4       0.09   11.7   0.4    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0016   18.9   0.0     0.0026   18.2   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0062   17.1   0.0      0.011   16.3   0.0    1.5  1  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.054   13.6   0.0    2.0  1  MMR_HSR1      50S ribosome-binding GTPase
      0.037   13.0   0.0      0.048   12.6   0.0    1.2  1  DUF463        YcjX-like family, DUF463
      0.044   13.8   0.0      0.076   13.0   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
      0.064   12.5   0.0       0.11   11.8   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.079   13.1   0.0       0.11   12.6   0.0    1.3  1  AAA_33        AAA domain
      0.082   12.8   0.1        7.5    6.5   0.0    2.2  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.086   13.3   0.0       0.15   12.5   0.0    1.4  1  AAA           ATPase family associated with various cellular 
       0.14   12.6   0.0       0.17   12.4   0.0    1.3  1  ABC_tran      ABC transporter
       0.24   11.8   0.0        0.5   10.8   0.0    1.5  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.1     7e-38   9.6e-35       3     174 ..      28     196 ..      26     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 7e-38
                                    EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCCCT.....EEEETTTTECCH.CTT-HHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellretgve....ivelenGciCct.lredllkeleal 76 
                                    ++++G++GsGKT+L+ +l+ + r +l+lav++N+++ + +Da++lr+++v     i  +++G++++t +r+d++++l+a+
  gi|121637755|ref|YP_977978.1|  28 IGVGGPVGSGKTALVAALCrQLRGELSLAVLTNDIY-TTEDADFLRTHAVLpddrIAAVQTGGCPHTaIRDDITANLDAI 106
                                    679****************99999************.***********7777888***********************99 PP

                                    HHHH...TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                           cobW  77 eere...erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                     e+    + ld+il+E++G +++++++         +  +da ++v+D+    a ++k ++k++ +++++dllv+nKtDl
  gi|121637755|ref|YP_977978.1| 107 DELMaahDALDLILVESGGdNLTATFS---------SGLVDAQIFVIDV----AGGDKVPRKGGPGVTYSDLLVVNKTDL 173
                                    999888899***********9999999.........99***********....99************************* PP

                                    HCHC...HHHHHHHHHHHHTTS- CS
                           cobW 153 ldee.allekleerlrqlnpeak 174
                                    +  + a+l+++++++++++++ +
  gi|121637755|ref|YP_977978.1| 174 AALVgADLAVMARDADAVRDGRP 196
                                    ****************9998776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00016      0.22      23      56 ..      19      52 ..       4      67 .. 0.84
   2 !   11.7   0.4   6.5e-05      0.09     121     181 ..     115     175 ..      85     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                   GGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCT CS
                           MeaB 23 lakaGraqvvGltGvPGaGkstlvealglelrrr 56
                                   + k G+  ++G+ G  G+Gk  lv al  +lr +
  gi|121637755|ref|YP_977978.1| 19 VRKPGEPLRIGVGGPVGSGKTALVAALCRQLRGE 52
                                   5678999*********************999754 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.5e-05
                                    T-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHH CS
                           MeaB 121 GfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkke 181
                                      D +l+e  G     +    +vd  + ++  ++GD++       +  +D++vvnk+D+++
  gi|121637755|ref|YP_977978.1| 115 ALDLILVESGGDNLTATFSSGLVDAQIFVIDVAGGDKVPRKGGPGVTYSDLLVVNKTDLAA 175
                                    3699********9999*9*******************98765556789**********654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.9e-06    0.0026      22      76 ..      23      77 ..      16     148 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd...ggif..lrgkcdqlesaipysalaqal 76
                                   g+p  + + G+ G+GK++lv +l r+l+++    +++  +++     ++++ ++    +l
  gi|121637755|ref|YP_977978.1| 23 GEPLRIGVGGPVGSGKTALVAALCRQLRGElslAVLTndIYT-----TEDADFLRTHAVL 77
                                   55588889********************99433111122222.....2333333333344 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.8e-06     0.011       1      61 [.      28      86 ..      28     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.8e-06
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldkll 61
                                   I++ G+ G+GKt l  +L + l    +l+  +  n++++++d++ l+ + +l +d+ ++++
  gi|121637755|ref|YP_977978.1| 28 IGVGGPVGSGKTALVAALCRQL--RGELSLAVLTNDIYTTEDADFLRTHAVLPDDRIAAVQ 86
                                   89****************8887..7777777777777777777746666666666655554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.9e-05     0.054       1      57 [.      27     106 ..      27     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                    EEEEEESTTSSHHHHHHHHHT....S..TEEESSSTTSSSSEEEEEEE..ETTEEEEEEECGGC...............S CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg....e..kaivsdkpgtTrdinegrvk..lkgkeielvDtpGl...............i 57 
                                    ++++ G   +GK+ L+ al++    e   a  ++   tT d  + r +  l +++i  v t G                i
  gi|121637755|ref|YP_977978.1|  27 RIGVGGPVGSGKTALVAALCRqlrgElsLAVLTNDIYTTEDADFLRTHavLPDDRIAAVQTGGCphtairdditanldaI 106
                                    58999***************944442436677999999999988887766556788888888862222222222222220 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.048       1      25 [.      26      50 ..      26      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                         DUF463  1 lrlavTGLsraGKtvfitsLvnqLl 25
                                   lr++v G  ++GKt+++++L +qL 
  gi|121637755|ref|YP_977978.1| 26 LRIGVGGPVGSGKTALVAALCRQLR 50
                                   79**********************7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-05     0.076       6      88 ..      32     112 ..      30     144 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                                    --SSSSHHHHHHHGGGGBS--EEEEE--TT..--HH.HHH--B--.........--------...G-SEEEEESGGG--H CS
                          AAA_5   6 GppGtgKselaerlaaalnreveyvqltrd..ttee.dlkgrreikngttslvdsplvraar...egeilvlDEveraes 79 
                                    Gp G+gK+ l+  l++ l+ e+    lt d  tte+ d++          +l d  +  a++    +++++ D+++ a+ 
  gi|121637755|ref|YP_977978.1|  32 GPVGSGKTALVAALCRQLRGELSLAVLTNDiyTTEDaDFLRTHA------VLPDDRIA-AVQtggCPHTAIRDDIT-ANL 103
                                    9*****************66666665555521333313333333......33333333.33333366677777776.667 PP

                                    HHHHHHHHH CS
                          AAA_5  80 evlnsLlsl 88 
                                    +++++L+  
  gi|121637755|ref|YP_977978.1| 104 DAIDELMAA 112
                                    777666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.7e-05      0.11      13      54 ..      22      63 ..      13      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-05
                     Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                     +P  i +gG  G+GK++l ++l ++l+ + +  +l  D +
  gi|121637755|ref|YP_977978.1| 22 PGEPLRIGVGGPVGSGKTALVAALCRQLRGELSLAVLTNDIY 63
                                   47899999******************9987777777777755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.2e-05      0.11       5      33 ..      31      63 ..      28     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                         AAA_33  5 vGlpGsGKstlaerllkklg....avllssdtl 33
                                    G+ GsGK+ l+  l+++l       +l+ d++
  gi|121637755|ref|YP_977978.1| 31 GGPVGSGKTALVAALCRQLRgelsLAVLTNDIY 63
                                   599****************97777777777774 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0055       7.5       3      25 ..      29      51 ..      27      65 .. 0.84
   2 ?    4.2   0.0     0.027        37      76      97 ..     101     122 ..      83     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0055
                           MobB  3 givgksgsGKTtLleklipelka 25
                                   g+ g  gsGKT+L+  l ++l+ 
  gi|121637755|ref|YP_977978.1| 29 GVGGPVGSGKTALVAALCRQLRG 51
                                   6678889***********99975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
                           MobB  76 eaelsleellarlsevDlvlvE 97 
                                    ++  +++el+a  +++Dl+lvE
  gi|121637755|ref|YP_977978.1| 101 ANLDAIDELMAAHDALDLILVE 122
                                    444568899999999******9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.15       4      25 ..      31      52 ..      28      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                   ESSTTSSHHHHHHHHHHHHTHE CS
                            AAA  4 yGppGtGKTllakavakelgve 25
                                    Gp G GKT+l+ a++++l  e
  gi|121637755|ref|YP_977978.1| 31 GGPVGSGKTALVAALCRQLRGE 52
                                   59****************8543 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.17      13      38 ..      27      52 ..      21     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                   EEEEEESTTSSHHHHHHHHTTSS--S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpt 38
                                   ++++ G+ G+GK+ L+++l+++l+ +
  gi|121637755|ref|YP_977978.1| 27 RIGVGGPVGSGKTALVAALCRQLRGE 52
                                   57889****************99853 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036       0.5       4      36 ..      31      64 ..      28      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                   RNA_helicase  4 yGpsgeGKStlakeLakallkkl.klkkkdsvys 36
                                    Gp g GK+ l+  L+++l ++l     ++++y+
  gi|121637755|ref|YP_977978.1| 31 GGPVGSGKTALVAALCRQLRGELsLAVLTNDIYT 64
                                   5788****************98842333466666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1513.74
//
Query:       gi|121637756|ref|YP_977979.1|  [L=208]
Description: urease accessory protein ureD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-15   57.2   0.9    2.6e-15   56.9   0.9    1.2  1  UreD      UreD urease accessory protein


Domain annotation for each model (and alignments):
>> UreD  UreD urease accessory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.9   1.4e-19   2.6e-15       1     135 [.      27     158 ..      27     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.4e-19
                                    EEEEE-SS-B-TT-EEEEEEEE-TT-EEEEEE-S-EEE---T.TS-EEEEEEEEE-TT-EEEE----EEE-TT-EEEEEE CS
                           UreD   1 vyllsygGGlvgGDrldldvevgpgarlllttqgatkiyksraekvsrqtlrvrvaagatLellPdpvipfagsryeqtq 80 
                                    v+l+s ++  +gGD+++++v v+ ga+l l++ +at + +    ++ + + + +++  +tL++  +p+++ a++r+  + 
  gi|121637756|ref|YP_977979.1|  27 VHLVSAAATPLGGDTMRIRVIVERGAQLRLRSAAATVALPG--VDTLTSHAHWEIDVTGTLDVDLEPTVVAASARHLSHA 104
                                    689*************************************9..346999******************************* PP

                                    EEEE-TT-EEEEEEEEE-S-CCCT--S-SSEEEEEEEE.EETTEEEEEEEEEE-....T CS
                           UreD  81 rfeLapgasllllDwvtsGrtargErwafdryrsrnevwvgdgrlllrDrllle....p 135
                                    +++L++++++ l + v  Gr    E +    ++s ++ ++  gr+llr r+ l     +
  gi|121637756|ref|YP_977979.1| 105 TLRLHDDGRVRLRERVQIGRCNEREGF----WSSSLQADR-HGRPLLRHRVELGagslA 158
                                    ********************7666666....*********.9***********943330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1630.84
//
Query:       gi|121637757|ref|YP_977980.1|  [L=463]
Description: NADH dehydrogenase ndh [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-59  200.4   0.8    4.5e-59  200.1   0.8    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      1e-12   48.4   1.2    3.5e-07   30.7   0.4    2.9  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      4e-07   29.5   1.0       0.02   14.0   0.1    4.1  4  GIDA           Glucose inhibited division protein A
     0.0002   21.1   4.8      0.091   12.3   0.1    3.7  4  DAO            FAD dependent oxidoreductase
    0.00067   19.8   1.5      0.016   15.4   0.0    3.1  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0025   17.1   0.0          1    8.5   0.0    2.8  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0056   16.0   2.0       0.39    9.9   0.0    2.4  2  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.012   14.7   0.2      0.054   12.6   0.0    2.0  2  FAD_binding_2  FAD binding domain
      0.052   13.5   0.2        9.9    6.1   0.0    2.7  2  NAD_binding_9  FAD-NAD(P)-binding
      0.058   12.6   0.2       0.98    8.6   0.0    2.3  2  Thi4           Thi4 family
      0.071   13.5   0.0        0.2   12.1   0.0    1.7  1  DUF732         Protein of unknown function (DUF732)
       0.13   12.7   0.1       0.46   10.9   0.0    2.0  2  NAD_binding_7  Putative NAD(P)-binding
       0.18   11.4   1.0        2.3    7.9   0.0    2.6  3  ApbA           Ketopantoate reductase PanE/ApbA
       0.55    8.9   2.4        3.7    6.2   0.0    3.0  4  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.1   0.8   3.5e-62   4.5e-59       1     293 [.      15     339 ..      15     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 3.5e-62
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCCTCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..evvkklnqgielllgeevvki 78 
                                    ++vv+iG+G++Gl+aa++l++a +++ l+ +++t++++++ll+++++g+ +++eia   +vv + + ++++llg +v++i
  gi|121637757|ref|YP_977980.1|  15 HRVVIIGSGFGGLNAAKKLKRADVDIKLI-ARTTHHLFQPLLYQVATGIISEGEIAPptRVVLRKQRNVQVLLG-NVTHI 92 
                                    58***************************.*****************************888889999******.***** PP

                                    EESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.......TCTTC.......TTBEECCSECHHHHHHCCSS-TSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdl.......gipGv......aenvgklvrtldsaealklkllpkri 145
                                    d + ++v+  ++  g++ +  yd+l++A G+ +  +         pG+       e  g+ ++++++ae+ ++ ++++++
  gi|121637757|ref|YP_977980.1|  93 DLAGQCVVS-ELL-GHTYQTPYDSLIVAAGAGQSYFgndhfaeFAPGMksiddaLELRGRILSAFEQAERSSDPERRAKL 170
                                    *99978887.555.999**************7777733323444445599999999999999999999999999999555 PP

                                    ...EEES-SHHHHHHHHHHHHHT-...............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEE CS
                                    ...xxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 146 ...vvvGgGyiGvElAaalaklgk...............evtlveardrllraldkelsaaleealekeGvevklgtsvk 207
                                       +vvG+G++GvE+A+++a+l++               +v l++a++ +l++++ +l+++++++l+k Gve++lg++v+
  gi|121637757|ref|YP_977980.1| 171 ltfTVVGAGPTGVEMAGQIAELAEhtlkgafrhidstkaRVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVT 250
                                    555*******************999999999999999999**************************************** PP

                                    EEEETTEEEEEEETTSCE..EEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--TTSBES.STTEEE-GGGCTECC CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 208 eidgngeklevvledgee..idadlvvvavGvrpstelle..eklglelderggivvdeflrtn.vpgiyaiGDvaggkg 282
                                    ++d+ng   +v+++dg++  i+  + v+++Gv++s+ +++  e++ +eld++g+++v + l     p+++++GD+a  +g
  gi|121637757|ref|YP_977980.1| 251 DVDRNGI--TVKDSDGTVrrIESACKVWSAGVSASRLGRDlaEQSRVELDRAGRVQVLPDLSIPrYPNVFVVGDMAAVEG 328
                                    ******7..99999999999*******************9*********************9977***********999* PP

                                    SS--HHHHHHH CS
                                    xxxxxxxxxxx RF
                    Pyr_redox_2 283 gpelaqaAvqq 293
                                    +p  aq A+q 
  gi|121637757|ref|YP_977980.1| 329 VPGVAQGAIQG 339
                                    ********986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.024       1      35 [.      16      50 ..      16      61 .. 0.91
   2 !   30.7   0.4   2.7e-10   3.5e-07       3      70 ..     174     256 ..     172     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +vv++G+G+ gl +A+ l++   +++++ r  + l
  gi|121637757|ref|YP_977980.1| 16 RVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHL 50
                                   79**************************9987655 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.7e-10
                                    EEECSSHHHHHHHHHHHHTT...............SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
                      Pyr_redox   3 vvvGgGyiglElAgalaelg...............kkVtvversdkllrllDeeaskilqeklekngievllntkveeie 67 
                                    +vvG+G +g+E+Ag +ael+               ++V ++++++ +l+ ++++++++ + +l+k+g+e+ l++ v+ ++
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAELAehtlkgafrhidstkARVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVD 253
                                    7***************88888888888888888889*******************************************9 PP

                                    EET CS
                      Pyr_redox  68 gse 70 
                                     ++
  gi|121637757|ref|YP_977980.1| 254 RNG 256
                                    766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.5e-05      0.02       2      35 ..      17      50 ..      16      69 .. 0.87
   2 !    4.8   0.0    0.0096        12     103     164 ..      74     132 ..      62     150 .. 0.79
   3 !    4.9   0.2    0.0089        11       3      25 ..     174     196 ..     172     203 .. 0.88
   4 ?    1.0   0.0      0.14   1.8e+02     345     383 ..     304     341 ..     295     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                   v++iG G  G+ AA +++r+ ++++Li+  ++++
  gi|121637757|ref|YP_977980.1| 17 VVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHL 50
                                   9**************************8777766 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0096
                                    HHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEEC..EEEE--TT-BT-EEEETTEEEE CS
                           GIDA 103 eklenepnleiieeeveeliveekkvkgvvtedgetikak..avviatGtflkgkihigekels 164
                                     +l+++ n++++ ++v+++++  +   +v    g+t+++   + ++a+G+   g++++g+++++
  gi|121637757|ref|YP_977980.1|  74 VVLRKQRNVQVLLGNVTHIDLAGQC--VVSELLGHTYQTPydSLIVAAGA---GQSYFGNDHFA 132
                                    57899**************994444..455556666666556********...88888888765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0089
                                    EEE-SSHHHHHHHHHHHHTT--E CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakv 25 
                                    +V+G+G  G+e A ++a+l  ++
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAELAEHT 196
                                    7***************9986655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.14
                                    GB-TTSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHH CS
                           GIDA 345 qllntLetkkvkgLflAGqinGteGYeEaaaqGllAGin 383
                                    q+l++L++ + +++f+ G++  +eG +  +aqG + G  
  gi|121637757|ref|YP_977980.1| 304 QVLPDLSIPRYPNVFVVGDMAAVEG-VPGVAQGAIQGAK 341
                                    788999999************9999.6789999998875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        22       1      27 [.      16      44 ..      16      48 .. 0.82
   2 ?    4.0   0.0     0.024        31     158     203 ..      79     122 ..      73     160 .. 0.77
   3 ?   -1.2   0.1       0.9   1.2e+03       3      20 ..     174     191 ..     172     220 .. 0.59
   4 !   12.3   0.1   7.1e-05     0.091     147     213 ..     227     293 ..     224     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtlle 27
                                   +vviiG+G  Gl +A  L r+   + l+ 
  gi|121637757|ref|YP_977980.1| 16 RVVIIGSGFGGLNAAKKLKRADvdIKLIA 44
                                   59****************76666666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                                    HTT-EEEESECEEEEEEEETCEEEEEEECT.EEE..EEEEEEEE--GGG CS
                            DAO 158 alGveilegtevtgleeedgkvwgverttp.gen..daadavVnaaGaw 203
                                    ++ v++l+g +vt+++  +   + v + +  g++  + +d +++aaGa+
  gi|121637757|ref|YP_977980.1|  79 QRNVQVLLG-NVTHIDLAG---QCV-VSELlGHTyqTPYDSLIVAAGAG 122
                                    788******.*****7753...333.233335543236788******98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.9
                                    EEECTSHHHHHHHHHHHH CS
                            DAO   3 viiGGGiiGlstAyeLar 20 
                                     ++G+G +G+  A + a+
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAE 191
                                    69*******988877754 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 7.1e-05
                                    HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HTT.CTT CS
                            DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gll.kel 213
                                    kl +  a+++++lGvei +g+ vt+++++   + +v  + + g++++++    V +aG+ ++ l + l ++ 
  gi|121637757|ref|YP_977980.1| 227 KLGQRAAARLQKLGVEIQLGAMVTDVDRN---GITV--KDSdGTVRRIESacKVWSAGVSASRLgRDLaEQS 293
                                    677788999*****************776...7888..4454876433334599999999884433333333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.016       1      25 [.      19      43 ..      19      49 .. 0.91
   2 ?    2.0   0.1       0.2   2.5e+02       1      16 [.     175     190 ..     175     220 .. 0.68
   3 ?   -1.8   0.0       2.9   3.7e+03      11      24 ..     232     245 ..     229     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                   I+G+G++Gl aA  L++a++d+ l+
  gi|121637757|ref|YP_977980.1| 19 IIGSGFGGLNAAKKLKRADVDIKLI 43
                                   9********************9997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                                    EE--SHHHHHHHHHHH CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                                    +vGaG +G  +A  +a
  gi|121637757|ref|YP_977980.1| 175 VVGAGPTGVEMAGQIA 190
                                    8*******98886665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                                    HHHHHHCCTEEEEE CS
                  NAD_binding_8  11 aAylLakagfdvll 24 
                                    aA++L+k g++++l
  gi|121637757|ref|YP_977980.1| 232 AAARLQKLGVEIQL 245
                                    89*******99976 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00081         1     157     198 ..       7      48 ..       1     121 [. 0.86
   2 !    5.4   0.1    0.0074       9.5       2      19 ..     175     192 ..     174     198 .. 0.83
   3 ?   -1.1   0.0      0.69   8.9e+02     227     305 .]     241     321 ..     225     321 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00081
                    Pyr_redox_3 157 kefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                    + +++ + ++vv+iG +  +  aA +l r++ +++++ r+++
  gi|121637757|ref|YP_977980.1|   7 PTAQPPRRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTH 48 
                                    566777889999999999999999999999999999998875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0074
                    Pyr_redox_3   2 IiGaGPaGlaaaielkka 19 
                                    ++GaGP G+++a ++ ++
  gi|121637757|ref|YP_977980.1| 175 VVGAGPTGVEMAGQIAEL 192
                                    8**********9877665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.69
                    Pyr_redox_3 227 ikvlfnaevkeikekeeeykvktedgkkvev..kddvvlatGykpd...lsflkkslfeldedgrpvlteeteetnvpgl 301
                                    +++   a v++++++   ++vk +dg+  ++    + v   G + +    ++ ++s +eld+ gr+++ ++     +p++
  gi|121637757|ref|YP_977980.1| 241 VEIQLGAMVTDVDRN--GITVKDSDGTVRRIesACK-VWSAGVSASrlgRDLAEQSRVELDRAGRVQVLPDLSIPRYPNV 317
                                    555555556666654..3444444444333310222.3334444432212344446666666666666666666666666 PP

                    Pyr_redox_3 302 flaG 305
                                    f++G
  gi|121637757|ref|YP_977980.1| 318 FVVG 321
                                    6665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0003      0.39       3      35 ..      16      48 ..      14      54 .. 0.89
   2 ?    4.8   0.7     0.011        14       5      79 ..     174     262 ..     171     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                    V+I+G+G  Gl +a+ L++a v+  l+ + + 
  gi|121637757|ref|YP_977980.1| 16 RVVIIGSGFGGLNAAKKLKRADVDIKLIARTTH 48
                                   69**********************999998765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                    EEE--SHHHHHHHH...HHHHTTHH............EEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEEC CS
                  FAD_binding_3   5 lIVGaGpaGlmlal...lLseaGvr............vvlvekrsttvvlpradglnqrtmellrqlGledrilaegapn 69 
                                     +VGaGp+G+  a    +L+e+  +            v+l++  + +v  p +  l qr    l++lG+e ++ a+ +  
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGqiaELAEHTLKgafrhidstkarVILLDA-APAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDV 252
                                    59*******9666512246665555888888888864444443.334444588888888888888888888888888888 PP

                                    CCCEEEEEEE CS
                  FAD_binding_3  70 elmgealyne 79 
                                    + +g++++ +
  gi|121637757|ref|YP_977980.1| 253 DRNGITVKDS 262
                                    8888888777 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05     0.054       2      31 ..      17      46 ..      16      51 .. 0.88
   2 ?   -0.5   0.0       0.4   5.1e+02     135     180 ..     220     260 ..     172     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavveke 31
                                   v++iGsG++GL AA ++++a  ++ ++  +
  gi|121637757|ref|YP_977980.1| 17 VVIIGSGFGGLNAAKKLKRADVDIKLIART 46
                                   9******************99988877665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.4
                                    ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                  FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                                    +    g +l  r +++++k+gv++q  + ++++ +     +G++v+
  gi|121637757|ref|YP_977980.1| 220 VLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVDR-----NGITVK 260
                                    45556666667777777777777777666666633.....344444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.024        30       1      28 [.      18      40 ..      18      56 .. 0.80
   2 ?    6.1   0.0    0.0077       9.9       2      20 ..     175     193 ..     174     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.024
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkksplei 28
                                   +i+G G+ Gl ++++L +       ++i
  gi|121637757|ref|YP_977980.1| 18 VIIGSGFGGLNAAKKLKRAD-----VDI 40
                                   7**************97763.....444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0077
                  NAD_binding_9   2 ivGaGprGlavlerLlara 20 
                                    +vGaGp+G+ ++ ++++ a
  gi|121637757|ref|YP_977980.1| 175 VVGAGPTGVEMAGQIAELA 193
                                    8***********9999987 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00076      0.98      20      48 ..      17      44 ..      13      48 .. 0.86
   2 ?    1.4   0.1      0.13   1.6e+02      21      38 ..     174     191 ..     169     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00076
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvaile 48
                                   vvi+G+G  GL aa+ l ++ d+ + ++ 
  gi|121637757|ref|YP_977980.1| 17 VVIIGSGFGGLNAAKKLKRA-DVDIKLIA 44
                                   9****************999.88777775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                                    EEE--SHHHHHHHHHHHH CS
                           Thi4  21 vivGaGssGLtaayylak 38 
                                     +vGaG++G+  a  +a+
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAE 191
                                    59*********9999987 PP

>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016       0.2      25      79 ..     248     301 ..     219     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                         DUF732  25 FlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaa 79 
                                     +++++++gi+++++d +++  +++Ck +++G+sa+ + +++++ +s ++ + a+
  gi|121637757|ref|YP_977980.1| 248 MVTDVDRNGITVKDSDGTVRRIESACKVWSAGVSASRLGRDLAE-QSRVELDRAG 301
                                    6899**************************************99.6665656555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.46       6      43 ..      13      50 ..      10     118 .. 0.84
   2 ?   -2.2   0.0       4.5   5.8e+03       9      26 ..     172     189 ..     167     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                  NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkee 43
                                   ++ +v+++G G  +++ ++kl +a+ +++++a +++  
  gi|121637757|ref|YP_977980.1| 13 RRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHL 50
                                   5789****************************996443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.5
                  NAD_binding_7   9 kvlvvGgGevAarkvrkl 26 
                                    +  vvG+G+ + + + ++
  gi|121637757|ref|YP_977980.1| 172 TFTVVGAGPTGVEMAGQI 189
                                    578999999987766555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0018       2.3       1      33 [.      17      50 ..      17      85 .. 0.90
   2 ?   -2.7   0.0       3.1     4e+03       2      23 ..     174     196 ..     173     206 .. 0.79
   3 ?    1.2   0.0       0.2   2.5e+02       9      59 ..     228     276 ..     225     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rl 33
                                   ++i+G+G  G   a kL++a  d+ li+r+  +l
  gi|121637757|ref|YP_977980.1| 17 VVIIGSGFGGLNAAKKLKRADVDIKLIARTThHL 50
                                   68****************************9776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                                    EEES-SHHHHHHHHHHHH.HTHC CS
                           ApbA   2 ailGaGaiGsllaakLak.agad 23 
                                    +++GaG  G  +a+++a+ a ++
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAElAEHT 196
                                    69999999999999998877665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT.CEEEEEECEEEC CS
                           ApbA   9 iGsllaakLakagadvtlilrsrrlealkknGlrltseg.geeilrppeals 59 
                                    +G+  aa+L+k g ++ l +    + ++ +nG+++++++ + ++++   +++
  gi|121637757|ref|YP_977980.1| 228 LGQRAAARLQKLGVEIQLGAM---VTDVDRNGITVKDSDgTVRRIESACKVW 276
                                    688999999999999888766...5589999999999996666666665555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0029       3.7       2      31 ..      16      45 ..      15      50 .. 0.90
   2 ?    0.5   0.1      0.15   1.9e+02       4      21 ..     174     191 ..     171     197 .. 0.78
   3 ?   -0.8   0.0      0.38   4.9e+02     117     171 ..     234     286 ..     230     299 .. 0.64
   4 ?   -3.3   0.0       2.1   2.7e+03     374     392 ..     313     331 ..     309     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0029
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                   +v++iG G  Gl aA ++++++ ++ l+ +
  gi|121637757|ref|YP_977980.1| 16 RVVIIGSGFGGLNAAKKLKRADVDIKLIAR 45
                                   79********************99999876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                                    EEE--SHHHHHHHHHHHH CS
                    HI0933_like   4 iviGgGaAGlmaAisaak 21 
                                     v+G+G+ G+  A ++a+
  gi|121637757|ref|YP_977980.1| 174 TVVGAGPTGVEMAGQIAE 191
                                    79********88887766 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.38
                                    HHHHHHT-EEE-S--EEEEECETTE.EEEEE...TTEEEEESEEEE----SS-GGGT CS
                    HI0933_like 117 kelkeagvklrletevksvekeedgkfrvkt.k.seeeleadklvlAtGGlSiPklG 171
                                    ++l++ gv+++l   v++v++  +g ++vk  + + +++e++  v +  G S+ +lG
  gi|121637757|ref|YP_977980.1| 234 ARLQKLGVEIQLGAMVTDVDR--NG-ITVKDsDgTVRRIESACKVWS-AGVSASRLG 286
                                    68999**************44..55.445541212333443333333.455555555 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.1
                                    TSTTEEE-GGGBSEEE-TT CS
                    HI0933_like 374 kvpgLffaGEvlDvegvtG 392
                                    + p++f++G +  vegv G
  gi|121637757|ref|YP_977980.1| 313 RYPNVFVVGDMAAVEGVPG 331
                                    679*********9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3082.20
//
Query:       gi|121637758|ref|YP_977981.1|  [L=307]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-49  168.2   4.2    5.7e-47  160.7   1.3    2.0  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7   1.3   3.2e-51   5.7e-47      19     233 ..      21     242 ..       3     245 .. 0.92
   2 !    8.7   0.1   5.8e-05         1     286     313 ..     250     278 ..     243     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 3.2e-51
                 Bac_luciferase  19 saslrylvelaraaEelGfdavwvaehhggpgga..........ldaftllaalaaaTerirlgtavtplytrhPavlAq 88 
                                       +  ++++ar+aE++G+d+++v++h                 l+a+t l+ala aTer++lg+ vt  + r+P++lA+
  gi|121637758|ref|YP_977981.1|  21 L--FPSVIAQAREAEAAGYDSLFVMDHFYQ---LpmlgtpdqpmLEAYTALGALATATERLQLGALVTGNTYRSPTLLAK 95 
                                    4..78899*******************973...23579999*************************************** PP

                 Bac_luciferase  89 qaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqg 165
                                     + tLd +s GR++lg+g+g+++ e+r+ G     +++r +rl+E++++l+ + +ge+++f G++++++ a   pr +++
  gi|121637758|ref|YP_977981.1|  96 IITTLDVVSAGRAILGIGAGWFELEHRQLGFefgTFSDRFNRLEEALQILEPMVKGERPTFFGDWYTTESAMAEPRYRDR 175
                                    *****************************************************************************999 PP

                 Bac_luciferase 166 piPvyvaaas.paglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadt 233
                                     iP+++++++  ++ ++aar+ad l ++    +e+ ++++ l+a+  eagrd++++++ + ltv++++t
  gi|121637758|ref|YP_977981.1| 176 -IPILIGGGGeKKTFAIAARFADHLNIVA-AVDELPRKMRALAARCDEAGRDRSTLQTSLLLTVMIDET 242
                                    .*********9*************99998.788888889999999999*******************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 5.8e-05
                 Bac_luciferase 286 elvaatalvGtpeqvaerlaa.yaeagvd 313
                                    + + + ++vG+p+q+a++++a + +agvd
  gi|121637758|ref|YP_977981.1| 250 AEMSGRVVVGSPAQIADQIQAkVLDAGVD 278
                                    45667788*************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2344.23
//
Query:       gi|121637759|ref|YP_977982.1|  [L=225]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-19   69.6   0.2    1.5e-17   63.9   0.2    2.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    8.5e-14   51.5   0.1    1.3e-13   50.8   0.1    1.2  1  adh_short     short chain dehydrogenase
     0.0014   18.8   0.1     0.0053   17.0   0.1    1.8  2  TrkA_N        TrkA-N domain
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.069   13.1   0.0    1.5  1  KR            KR domain
      0.042   13.3   0.0      0.053   13.0   0.0    1.1  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.2   4.2e-21   1.5e-17       6     232 ..      14     219 ..      11     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.2e-21
                                    HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG.CS CS
                   adh_short_C2   6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapk.lk 84 
                                    +Gr +A+ + + G +v l+ +++ +   +e +a+el+ +++ cD td+++++++     +   +lD +vn  + + +  +
  gi|121637759|ref|YP_977982.1|  14 LGRTMAEGFRNDGHKVTLVGARRGD---LEVAAKELDVDAVVCDTTDPTSLTEARGLFPR---HLDTIVNVPAPSWDaGD 87 
                                    699****************999998...9999******************9988777665...58999***999999844 PP

                                    S-GGGH..-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGG CS
                   adh_short_C2  85 gpflet..sreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgpk 162
                                     ++ ++  + + +++ald  + s++l+++ +  ++++ggsiv +         p   a +a Kaal + +   A+ +g +
  gi|121637759|ref|YP_977982.1|  88 PRAYSVsdTANAWRNALDATVLSVVLTVQSVGDHLRSGGSIVSVVAE----NPPAGGAESAIKAALSNWIAGQAAVFGTR 163
                                    444444337899*****************************976544....55777899********************* PP

                                    TEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 163 giRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    gi++N+v+ g    +  +g++         +  ap+       e+a++alfL  ++a+ itGqtl+v  G
  gi|121637759|ref|YP_977982.1| 164 GITINTVACGRSVQTGYEGLS---------HTPAPVA-----AEIARLALFLTTPAARHITGQTLHVSHG 219
                                    *********987755555554.........4455555.....5************************988 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.1   3.7e-17   1.3e-13       3     181 ..       5     174 ..       4     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.7e-17
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    vlvtG++  +Gr +a+ + ++G kv++v+ +  +le +akel      + a+ +D td +++ ++         +ld +v
  gi|121637759|ref|YP_977982.1|   5 VLVTGGDTDLGRTMAEGFRNDGHKVTLVGARRGDLEVAAKELD-----VDAVVCDTTDPTSLTEARGLF---PRHLDTIV 76 
                                    89***************************************99.....89*********9988766555...37899999 PP

                                    E---S...S--SSGGGCSHHH..HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
                      adh_short  83 nNAGi...tgsgpfselseee..wervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                                    n  +    +g+  + ++s+++  w++ ++  + +v+l++++v +++  +s+G+Iv v    +++p + + a sA Kaa+ 
  gi|121637759|ref|YP_977982.1|  77 NVPAPswdAGDPRAYSVSDTAnaWRNALDATVLSVVLTVQSVGDHL--RSGGSIVSVV---AENP-PAGGAESAIKAALS 150
                                    98777677444444445444447**********************5..5*****9665...5444.5555669******* PP

                                    HHHHHHHHHHGGGTEEEEEEEESS CS
                      adh_short 158 gltrslakelaptgirvnavaPGl 181
                                     ++   a  + ++gi++n+va+G 
  gi|121637759|ref|YP_977982.1| 151 NWIAGQAAVFGTRGITINTVACGR 174
                                    **********************95 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.5e-06    0.0053       8      58 ..      13      64 ..       5      67 .. 0.89
   2 ?   -1.3   0.0      0.69   2.5e+03      11      48 ..     116     156 ..     114     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHT CS
                         TrkA_N  8 rvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeea 58
                                   ++Gr++ae +++ g+ +v+++  ++  +e +++e  +++vv d td+  L ea
  gi|121637759|ref|YP_977982.1| 13 DLGRTMAEGFRNdGH-KVTLVGARRGDLEVAAKELdVDAVVCDTTDPTSLTEA 64
                                   68**********555.7**************99999**************998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.69
                                    HHHHHHHHHTTEEEEEEESSHHH..HHHHHHTT.SEEEES- CS
                         TrkA_N  11 rslaeeLseggkdvvvidkdeer..veelreeg.levvvgd 48 
                                    +s+ + L++gg+ v+v+  ++ +  +e++ +    +++ g+
  gi|121637759|ref|YP_977982.1| 116 QSVGDHLRSGGSIVSVVAENPPAggAESAIKAAlSNWIAGQ 156
                                    56778899955449999999865445544433324566655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.069       3      78 ..       5      71 ..       4     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78
                                   +l+tGG   LG+++a+   ++g +  ++ +R++           e++a++ +v++v +D +d+++++++   + ++
  gi|121637759|ref|YP_977982.1|  5 VLVTGGDTDLGRTMAEGFRNDGHKVTLVGARRGD---------LEVAAKELDVDAVVCDTTDPTSLTEARGLFPRH 71
                                   69********************988888888832.........245677889999999999999999887666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.053       1      71 [.       5      78 ..       5     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-S.TTTTCHHCHHCEEEE--TT-HHHHHHH...HHHHT-SEEEE- CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrls.sasntarledlelveldltdrsalerl...fkeeqpdavihl 71
                                   +lVtG+   +G+ +++ + + g++v+ +  ++ + +  a++ d++ v +d td+++l+++   f + + d+++++
  gi|121637759|ref|YP_977982.1|  5 VLVTGGDTDLGRTMAEGFRNDGHKVTLVGARRgDLEVAAKELDVDAVVCDTTDPTSLTEArglFPR-HLDTIVNV 78
                                   79**********************877776630333344444449*********977665111443.67777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1947.48
//
Query:       gi|121637760|ref|YP_977983.1|  [L=261]
Description: molybdate-binding lipoprotein modA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-43  149.2   6.2    1.9e-43  148.9   6.2    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    1.5e-20   74.4   1.1    2.5e-19   70.4   1.1    2.4  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    3.3e-06   26.4   0.4    7.3e-06   25.2   0.4    1.6  1  PBP_like    PBP superfamily domain
     0.0003   20.5   6.0    0.00053   19.8   6.1    1.5  1  PBP_like_2  PBP superfamily domain
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.55    9.6   0.0    2.1  2  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   6.2   5.2e-47   1.9e-43       1     229 [.      41     258 ..      41     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 5.2e-47
                                    .EEEE-SSTHHHHHHHHHHHHH.HH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEE CS
                     SBP_bac_11   1 ltvaaagslaaalrelaaaFea.htgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplass 79 
                                    + v+aa+sl+ a++++ ++F+a ++gv+v++ ++gs++la q+++ga +Dv+++a++a+++++a+agl++ ++++++a++
  gi|121637760|ref|YP_977983.1|  41 IVVFAAASLQSAFTQIGEQFKAgNPGVNVNFAFAGSSELATQLTQGATADVFASADTAQMDSVAKAGLLA-GHPTNFATN 119
                                    579*****************7769**********************************************.********* PP

                                    EEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT- CS
                     SBP_bac_11  80 plviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveagea 159
                                    ++vi++ +gnpkki+++adL++pgl+++v +P + p G a+  + +a g       +  + v ++ s++++l+ v +g+a
  gi|121637760|ref|YP_977983.1| 120 TMVIVAAAGNPKKIRSFADLTRPGLNVVVCQP-SVPCGSATRRIEDATG-------IHLNPVSEELSVTDVLNKVITGQA 191
                                    ********************************.78************99.......566777777789************ PP

                                    SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                     SBP_bac_11 160 dagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                    dag+vy s+a+  + ++k++ v+ pe   +   +y++avlk++++++ Ar F+a ++ +++++il + Gf
  gi|121637760|ref|YP_977983.1| 192 DAGLVYVSDAL--SVATKVTCVRFPEAAGV-VNVYAIAVLKRTSQPALARQFVAMVTAAAGRRILDQSGF 258
                                    **********9..6899******9999988.45************************************9 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   1.1   6.9e-23   2.5e-19       2     313 ..      47     249 ..      46     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.9e-23
                                    GSHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHH CS
                      SBP_bac_1   2 gsltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvka 80 
                                    +sl++  a+ ++  ++f++ +pg++V++ + gs++la+    ++ +G+  aDv+a+ d+++++  akagll+   + ++ 
  gi|121637760|ref|YP_977983.1|  47 ASLQS--AFTQIG-EQFKAGNPGVNVNFAFAGSSELAT----QLTQGA-TADVFASaDTAQMDSVAKAGLLAGHPTNFAT 118
                                    78888..******.************************....******.55*****999999999999999999998888 PP

                                    TTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEE...ETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHC CS
                      SBP_bac_1  81 ylapgvkdaadklsssvlpkildskvlyvPlyaargliY...NkdlfekagldppwtWdelveaakklkekgkkpiggar 157
                                    ++  +v                                    N+++          ++ +l++++ +++   ++      
  gi|121637760|ref|YP_977983.1| 119 NTMVIV--------------------------------AaagNPKKIR--------SFADLTRPGLNVVVCQPSV----- 153
                                    854443................................2333444444........*****************99..... PP

                                    CEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSE CS
                      SBP_bac_1 158 ggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaam 237
                                                                              + +   ++ +t  + ++++e+ +++++l+ + +G+a++
  gi|121637760|ref|YP_977983.1| 154 ----------------------------------------PCGSATRRIEDATGIHLNPVSEELSVTDVLNKVITGQADA 193
                                    ........................................33444445555667899*********************** PP

                                    EEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                      SBP_bac_1 238 aivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspea 313
                                    ++v+ ++al+++ + + v f++++  +                    ++y +a++k +++p+ A++F+++++++++
  gi|121637760|ref|YP_977983.1| 194 GLVYVSDALSVATKVTCVRFPEAAGVV--------------------NVYAIAVLKRTSQPALARQFVAMVTAAAG 249
                                    *******76666666666666666666....................*************************9987 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4     2e-09   7.3e-06       2     151 ..      58     197 ..      57     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2e-09
                                    HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---.CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHH CS
                       PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldk.eteeynapalrkaldgievvlvnlarreqglvvakgnp 80 
                                    e++++ npgv v++a+ Gs++  ++l +g    a ++++++ +t + +  a   +l+g++    n+a+  + +v a+gnp
  gi|121637760|ref|YP_977983.1|  58 EQFKAGNPGVNVNFAFAGSSELATQLTQG----ATADVFASaDTAQMDSVAKAGLLAGHP---TNFATNTMVIVAAAGNP 130
                                    789999*************9988888888....556665541333334444444567776...9**************** PP

                                    HS--BGGGC-S-B-EEEEE-T....TSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCC CS
                       PBP_like  81 kkitnwkdladaplrlvnRet....GSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgi 151
                                    kki++++dl++++l +v  +     GS tr   d            ++ + +e+ s  +v   V +g+ad+g+  
  gi|121637760|ref|YP_977983.1| 131 KKIRSFADLTRPGLNVVVCQPsvpcGSATRRIEDATG-------IHLNPV-SEELSVTDVLNKVITGQADAGLVY 197
                                    ****************988864444677776533333.......335666.488999999999999999999733 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   6.1   1.5e-07   0.00053       2     106 ..      31     132 ..      30     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-07
                     PBP_like_2   2 aaaeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngd.vdfagsdrplteseia.agwaa 79 
                                    +a+ ++++++i++ ++ ++++a+++  ++f+  +pg+ vn a  GS++   +l +g+ +d+ +s + ++ + +a ag  a
  gi|121637760|ref|YP_977983.1|  31 PAGPTQGARSIVVFAAASLQSAFTQIGEQFKAGNPGVNVNFAFAGSSELATQLTQGAtADVFASADTAQMDSVAkAGLLA 110
                                    5677788888**********************************************996666666666555553332222 PP

                     PBP_like_2  80 ngaggliqvpvaigaialvvnkdnpln 106
                                          + + +a++  ++v    np++
  gi|121637760|ref|YP_977983.1| 111 -----GHPTNFATNTMVIVAAAGNPKK 132
                                    .....2356666666666666665555 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        41      20      85 ..      88     144 ..      79     159 .. 0.61
   2 ?    9.6   0.0   0.00015      0.55     135     214 ..     182     258 ..     171     261 .] 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                      SBP_bac_6  20 eeglfqpldpanlpnvnkdfaeeglkdp.dgkyypygvgplvlavnkdrlkgrpvPksWaDLldPey 85 
                                    ++++f+  d+a++++v+k    +gl  +   +++  +++ +  a n +++      +s+aDL++P +
  gi|121637760|ref|YP_977983.1|  88 TADVFASADTAQMDSVAK----AGLLAGhPTNFATNTMVIVAAAGNPKKI------RSFADLTRPGL 144
                                    566777666666666664....6666553344444444444444555555......78888888765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                      SBP_bac_6 135 aagslesgepavsvvpyffadilpekkkgknlkvv.wPedGalvspifmlvkkg.kkkelakafidfllspevqailaka 212
                                     +++++ g+  ++ +  + +d+l       ++  v  Pe  ++v++++++v k  ++++la++f+   + + +++il  +
  gi|121637760|ref|YP_977983.1| 182 VLNKVITGQ--ADAGLVYVSDALSVAT---KVTCVrFPEAAGVVNVYAIAVLKRtSQPALARQFVAMVTAAAGRRILDQS 256
                                    567777777..5555555566666665...4444416777****************************999999999888 PP

                      SBP_bac_6 213 gg 214
                                    g+
  gi|121637760|ref|YP_977983.1| 257 GF 258
                                    76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1731.85
//
Query:       gi|121637761|ref|YP_977984.1|  [L=264]
Description: molbdenum-transport integral membrane protein ABC transporter modB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-18   65.8  13.9    3.9e-18   65.8  13.9    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   2.3     0.087   1.6e+03      31      43 ..      14      30 ..       7      68 .. 0.50
   2 !   65.8  13.9   2.2e-22   3.9e-18       1     174 [.      69     249 ..      65     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.087
                   BPD_transp_1 31 Psfv....laillvlvf 43
                                   P ++    +a++lv+++
  gi|121637761|ref|YP_977984.1| 14 PAIAgivfVAMPLVAIA 30
                                   33333333455555333 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 2.2e-22
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf............vilsilghlilpviillllsaapyv 68 
                                    g+++++++a +++++l + lrpli ++l lP++v +i l+++f            +   ++ ++  +v+++ ++ ++py 
  gi|121637761|ref|YP_977984.1|  69 GVPMALVLA-RSRGRLVRSLRPLILLPLVLPPVVGGIALLYAFgrlgligryleaA-GISIAFSTAAVVLAQTFVSLPYL 146
                                    567777777.99999999***********************************963.4457788889************* PP

                   BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw.pGlgtllleailg 147
                                    ++  ++a r+   d++ +a +lGa++ ++ ++v+lP++lp +++g +laf+++lg++ ++++++++ +G++++l   i  
  gi|121637761|ref|YP_977984.1| 147 VISLEGAARTAGADYEVVAATLGARPGTVWWRVTLPLLLPGVVSGSVLAFARSLGEFGATLTFAGSrQGVTRTLPLEIYL 226
                                    *********************************************************99887775514455555555555 PP

                   BPD_transp_1 148 ydyseisnggvlalviavlllnlvadi 174
                                    + ++       +a+++++ll++++a +
  gi|121637761|ref|YP_977984.1| 227 QRVTDPD----AAVALSLLLVVVAALV 249
                                    5555444....3333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2013.43
//
Query:       gi|121637762|ref|YP_977985.1|  [L=369]
Description: molybdenum-transport ATP-binding protein ABC transporter modC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-32  111.3   0.0    7.2e-32  110.8   0.0    1.2  1  ABC_tran  ABC transporter
    1.3e-14   54.3   0.2    4.1e-14   52.6   0.2    2.0  1  TOBE      TOBE domain
    2.7e-09   37.3   0.1    0.00029   20.8   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0018   17.9   0.1     0.0059   16.3   0.0    1.8  2  AAA_29    P-loop containing region of AAA domain
     0.0042   16.9   0.1      0.013   15.3   0.0    1.8  2  MukB      MukB N-terminal
     0.0046   16.6   0.0     0.0076   15.9   0.0    1.3  1  AAA_27    AAA domain
  ------ inclusion threshold ------
      0.043   13.5   0.3      0.084   12.6   0.3    1.6  1  AAA_30    AAA domain
      0.045   14.2   0.0       0.06   13.8   0.0    1.1  1  AAA_23    AAA domain
      0.069   12.6   0.0        1.3    8.4   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
       0.11   12.2   0.0       0.72    9.5   0.0    1.9  2  AAA_15    AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0     4e-35   7.2e-32       3     136 ..      16     166 ..      15     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 4e-35
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvre 78 
                                    +v++++++ge++a++G+nGaGKSt l ++agll+p++G ++l ++ l++     +    ++++g l q+p lfp+l+v++
  gi|121637762|ref|YP_977985.1|  16 DVEFSVSAGEVLAVLGPNGAGKSTALHVIAGLLRPDAGLVRLGDRVLTDteagVNVATHDRRVGLLLQDPLLFPHLSVAK 95 
                                    699****************************************9999999999899999********************* PP

                                    H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    n               + +  + al++l+ ++ +++ ++++p++LSgGq qrva+aral+ +p++lllDEp 
  gi|121637762|ref|YP_977985.1|  96 NvafgpqcrrgmfgsGRARTRASALRWLREVN-AEQFADRKPRQLSGGQAQRVAIARALAAEPDVLLLDEPL 166
                                    ******99999999845555666666666666.666666667*****************************6 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.2   2.3e-17   4.1e-14       2      64 .]     295     359 ..     294     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.3e-17
                           TOBE   2 sarNqlpgtVvvveplgseveVrvdlggga..tLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                    s+rN++  tV +v ++g+ v+Vr + ++g    L+A++t ++a+eL++apG++V++++ka++v+l
  gi|121637762|ref|YP_977985.1| 295 SPRNIVGLTVAEVDTRGPMVLVRGHDQPGGapGLAACITVDAATELRVAPGSRVWFSVKAQEVAL 359
                                    99****************************9******************************9975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.3e-05     0.023       3      25 ..      28      50 ..      26      70 .. 0.81
   2 !   20.8   0.0   1.6e-07   0.00029     232     300 ..     134     200 ..      73     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   ++ GpNg+GKS+ L  + +l r 
  gi|121637762|ref|YP_977985.1| 28 AVLGPNGAGKSTALHVIAGLLRP 50
                                   789***************99874 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.6e-07
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                    + +r+lS G+ +  a++ al++ +   ++ll+DEp +gL+ ++ + +  +l +  +r g  v+ltTH+ l
  gi|121637762|ref|YP_977985.1| 134 RKPRQLSGGQAQRVAIARALAAEP---DVLLLDEPLTGLDVAAAAGIRSVLrSVVARSGCAVVLTTHDLL 200
                                    557888888887778888888877...9***********************5444559*********965 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0059      17      49 ..      19      51 ..      12      55 .. 0.81
   2 ?   -3.5   0.0         5     9e+03      16      31 ..     304     320 ..     301     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   ++++  ++  + Gp+G+GKST l  i+ lL p+
  gi|121637762|ref|YP_977985.1| 19 FSVSAGEVLAVLGPNGAGKSTALHVIAGLLRPD 51
                                   4555444999*************9999999886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                         AAA_29  16 tieidlkg.atlltGps 31 
                                    ++e+d++g ++l+ G+ 
  gi|121637762|ref|YP_977985.1| 304 VAEVDTRGpMVLVRGHD 320
                                    67889999999999975 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.4e-06     0.013      28      75 ..      26      77 ..      15      95 .. 0.82
   2 ?   -2.1   0.0       1.5   2.7e+03      88     109 ..     337     358 ..     330     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-06
                                   HHHHHS--SHHHHHHHHHHHHHHS--TTT-----....-------------- CS
                           MukB 28 vttlsGgnGaGksttmaafvtaliPdlsllhfrn....tteaGatsgsrdkG 75
                                   v ++ G nGaGkst++  +   l Pd  l+++ +     teaG + ++ d+ 
  gi|121637762|ref|YP_977985.1| 26 VLAVLGPNGAGKSTALHVIAGLLRPDAGLVRLGDrvltDTEAGVNVATHDRR 77
                                   67788*********************99998754222158999999999985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                    EEEEE-TTS-EEEEEEEEEE-S CS
                           MukB  88 vlevvnsreqrllvgvrleqva 109
                                    + e   + + r++++v+ ++va
  gi|121637762|ref|YP_977985.1| 337 ATELRVAPGSRVWFSVKAQEVA 358
                                    5677788899********9998 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.2e-06    0.0076      19      50 ..      17      48 ..       2      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-06
                         AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   ++fs ++ ++  ++GpN AGKstal+ i  ll
  gi|121637762|ref|YP_977985.1| 17 VEFSVSAGEVLAVLGPNGAGKSTALHVIAGLL 48
                                   467888999999**************998886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   4.7e-05     0.084      16      46 ..      22      53 ..      14     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa.g 46
                                   s   v ++ Gp G+GK+tal +++ +++ + g
  gi|121637762|ref|YP_977985.1| 22 SAGEVLAVLGPNGAGKSTALHVIAGLLRPDaG 53
                                   4556999****************999887744 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05      0.06      13      40 ..      15      45 ..       3      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                         AAA_23 13 qeidF...skgltlItGpNGaGKTTildAik 40
                                    +++F      + ++ GpNGaGK+T l  i 
  gi|121637762|ref|YP_977985.1| 15 LDVEFsvsAGEVLAVLGPNGAGKSTALHVIA 45
                                   5666666333578899*********998776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00073       1.3      25      44 ..      25      44 ..      11      52 .. 0.81
   2 ?    2.1   0.0     0.062   1.1e+02     135     185 ..     137     183 ..      73     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                   ++ a++GpNG+GKs  l  i
  gi|121637762|ref|YP_977985.1| 25 EVLAVLGPNGAGKSTALHVI 44
                                   46799*********877665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.062
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                     +LSgG+ + va+a  +A +   p  + llDe    LD +  + + ++l++
  gi|121637762|ref|YP_977985.1| 137 RQLSGGQAQRVAIARALAAE---PD-VLLLDEPLTGLDVAAAAGIRSVLRS 183
                                    58*******99999888743...33.3466777677776666666666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0004      0.72      17      48 ..      19      49 ..      13      66 .. 0.83
   2 ?    0.5   0.0      0.22   3.9e+02     323     365 ..     156     198 ..     146     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0004
                         AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFln 48
                                   ++++  e +  + G+N++GKS++l+++  +l 
  gi|121637762|ref|YP_977985.1| 19 FSVSAGE-VLAVLGPNGAGKSTALHVIAGLLR 49
                                   4555566.89999************9977665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    ++++ll++EP + L   a   +   l++++  + + v++tTH 
  gi|121637762|ref|YP_977985.1| 156 EPDVLLLDEPLTGLDVAAAAGIRSVLRSVVARSGCAVVLTTHD 198
                                    67899999999999999999999*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2534.03
//
Query:       gi|121637763|ref|YP_977986.1|  [L=325]
Description: hypothetical protein BCG_1896 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.7e-141  469.2  46.7   5.7e-141  469.2  46.7    2.0  2  FAP       Fibronectin-attachment protein (FAP)
  ------ inclusion threshold ------
        2.5    8.2   0.0        2.5    8.2   0.0    3.6  3  MelC1     Tyrosinase co-factor MelC1


Domain annotation for each model (and alignments):
>> FAP  Fibronectin-attachment protein (FAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2  46.7  6.4e-145  5.7e-141       1     297 [.       1     297 [.       1     298 [. 0.99
   2 ?   -4.4  13.6       1.1     1e+04      60     106 ..     293     317 ..     292     325 .] 0.41

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 6.4e-145
                            FAP   1 mdqvdaeskrrkglsktlaiaavagasavalalPavanadpePaPppPstaeaapaeaaaapaPaapapaPapadpnape 80 
                                    m+qvd + +rrkg+ ++laiaa+a+as+v++a+Pa+anadpePaPp+P+ta+++p++aaa+paPa+p+++P+pa++n+p+
  gi|121637763|ref|YP_977986.1|   1 MHQVDPNLTRRKGRLAALAIAAMASASLVTVAVPATANADPEPAPPVPTTAASPPSTAAAPPAPATPVAPPPPAAANTPN 80 
                                    99****************************************************************************** PP

                            FAP  81 aaPapadPnapapppadPnapappavdPnapepgrvdnavGGfsyvvPaGwkvsdatqlsyGqallski...ppegaqpp 157
                                    a+P  +dPna+ pppadPnap+pp+++Pnap+p+r+dn+vGGfs+++PaGw++sda++l+yG+allsk+   pp ++qpp
  gi|121637763|ref|YP_977986.1|  81 AQP--GDPNAA-PPPADPNAPPPPVIAPNAPQPVRIDNPVGGFSFALPAGWVESDAAHLDYGSALLSKTtgdPPFPGQPP 157
                                    999..*****6.999******************************************************9999******9 PP

                            FAP 158 ..andtsvllGrldlklfasaeadnakaavrlasdmGeffmPfPGtrinqetvplnangltGsasyyevkftdankPnGq 235
                                      andt+++lGrld+kl+asaea+++kaa+rl+sdmGef+mP+PGtrinqetv+l+ang++Gsasyyevkf+d++kPnGq
  gi|121637763|ref|YP_977986.1| 158 pvANDTRIVLGRLDQKLYASAEATDSKAAARLGSDMGEFYMPYPGTRINQETVSLDANGVSGSASYYEVKFSDPSKPNGQ 237
                                    9******************************************************************************* PP

                            FAP 236 iwagvvGepvasgtdrGqraperwfvvwlGtannPvdkeaavalaesirpwtaPppappaap 297
                                    iw+gv+G+p+a+++d+G  +p+rwfvvwlGtannPvdk+aa+alaesirp++aPppap++ap
  gi|121637763|ref|YP_977986.1| 238 IWTGVIGSPAANAPDAG--PPQRWFVVWLGTANNPVDKGAAKALAESIRPLVAPPPAPAPAP 297
                                    *****************..****************************************998 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 1.1
                            FAP  60 aapaPaapapaPapadpnapeaaPapadPnapapppadPnapappav 106
                                    +apaPa+papaPapa   ap+                      p + 
  gi|121637763|ref|YP_977986.1| 293 PAPAPAEPAPAPAPAGEVAPT----------------------PTTP 317
                                    344455555444444444433......................3221 PP

>> MelC1  Tyrosinase co-factor MelC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -11.1  14.3         2   1.8e+04       3      34 ..      22      53 ..      15      94 .. 0.64
   2 ?    8.2   0.0   0.00028       2.5      14      69 ..     172     227 ..     165     230 .. 0.90
   3 ?   -2.2   2.5      0.47   4.2e+03      17      37 ..     288     306 ..     271     311 .. 0.53

  Alignments for each domain:
  == domain 1  score: -11.1 bits;  conditional E-value: 2
                          MelC1  3 ataatagaalaglaaasasaaeapakaegsae 34
                                   a+a ++ +++a  a+a a+  +ap   +++a+
  gi|121637763|ref|YP_977986.1| 22 AMASASLVTVAVPATANADPEPAPPVPTTAAS 53
                                   33333333333344444444444444444444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00028
                          MelC1  14 glaaasasaaeapakaegsaepesFDevyrGrRiqGlpaeggahghaehgagyqvl 69 
                                    + + asa+a+++ a a+  ++  +F   y G Ri+  + +  a+g  + ++ y+v 
  gi|121637763|ref|YP_977986.1| 172 QKLYASAEATDSKAAARLGSDMGEFYMPYPGTRINQETVSLDANGVSGSASYYEVK 227
                                    66789999999999999999999***********************9999999995 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.47
                          MelC1  17 aasasaaeapakaegsaepes 37 
                                    a  +  a+apa ae++++p++
  gi|121637763|ref|YP_977986.1| 288 A--PPPAPAPAPAEPAPAPAP 306
                                    2..333466666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2279.33
//
Query:       gi|121637764|ref|YP_977987.1|  [L=101]
Description: hypothetical protein BCG_1897 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-12   45.1  13.4    8.6e-12   45.1  13.4    2.4  2  Transgly_assoc   Transglycosylase associated protein
  ------ inclusion threshold ------
       0.73    8.6   3.5       0.76    8.6   3.5    1.2  1  DUF5423          Family of unknown function (DUF5423)
        7.8    6.3  11.9        3.3    7.5   0.2    3.0  3  FeoB_C           Ferrous iron transport protein B C terminus


Domain annotation for each model (and alignments):
>> Transgly_assoc  Transglycosylase associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.9      0.16   9.7e+02      10      12 ..      31      33 ..       9      49 .. 0.62
   2 !   45.1  13.4   1.4e-15   8.6e-12       1      49 []      51     100 ..      51     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.16
                 Transgly_assoc 10 vGg 12
                                   ++g
  gi|121637764|ref|YP_977987.1| 31 IAG 33
                                   333 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.4e-15
                 Transgly_assoc   1 IilGivGAfvGgfllgllgi.gvgggelaslivaiiGAiILLfivrlvrr 49 
                                    +++G+vGAf +g++l++lg+  ++gg + +++va+ GA++LL+iv++vr+
  gi|121637764|ref|YP_977987.1|  51 VVIGVVGAFGAGLVLNALGVdVNHGGYWFTFFVALGGAVVLLWIVGMVRK 100
                                    69**********************************************96 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.5   0.00013      0.76      86     130 ..      23      68 ..       9      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00013
                        DUF5423  86 lpfiltgtaaglmfsaiavgggavilanplf.lmgsmtlgfalmsl 130
                                    l +i+ g  ag + s i  ggg+ il n ++ ++g++  g+ l +l
  gi|121637764|ref|YP_977987.1|  23 LGYIVIGGIAGWLASKIVKGGGSGILMNVVIgVVGAFGAGLVLNAL 68 
                                    789************************9876478998888888765 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00056       3.3       9      33 ..      26      49 ..      22      51 .. 0.86
   2 ?    3.8   1.5    0.0079        47       5      21 ..      51      67 ..      47      72 .. 0.87
   3 ?    1.8   0.7     0.032   1.9e+02       5      22 ..      77      94 ..      75     101 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00056
                         FeoB_C  9 ilvallvalllkkttlkgepspfvm 33
                                   i++  ++++l++k+  kg  s+ +m
  gi|121637764|ref|YP_977987.1| 26 IVIGGIAGWLASKI-VKGGGSGILM 49
                                   78888********9.**99888887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0079
                         FeoB_C  5 Yllgilvallvalllkk 21
                                    ++g++ a+ ++l+l+ 
  gi|121637764|ref|YP_977987.1| 51 VVIGVVGAFGAGLVLNA 67
                                   69*************97 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.032
                         FeoB_C  5 Yllgilvallvalllkkt 22
                                   Y + ++val  a +l ++
  gi|121637764|ref|YP_977987.1| 77 YWFTFFVALGGAVVLLWI 94
                                   678899999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 713.92
//
Query:       gi|121637765|ref|YP_977988.1|  [L=346]
Description: alcohol dehydrogenase adhA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-28   99.3   1.3    1.7e-28   98.7   1.3    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    3.3e-07   30.3   0.3    1.2e-06   28.5   0.2    1.9  1  ADH_zinc_N    Zinc-binding dehydrogenase
     0.0036   18.4   0.1     0.0074   17.3   0.0    1.6  2  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   1.3   2.8e-32   1.7e-28       2     107 ..      39     149 ..      38     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2.8e-32
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS.....--TT-EEEE-SEEE.-SSSHHHHT CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkk.....lkvGdrVvveplis.cgeCaaCke 75 
                                     e+l+ v+a+g+C++Dlh+ +g + + ++  +i+GHE+vGev evg++v       +  GdrV + +l + cg C++C++
  gi|121637765|ref|YP_977988.1|  39 SELLVAVHACGVCRTDLHVTEG-DLPVHRERVIPGHEVVGEVIEVGSAVGAaaggeFDRGDRVGIAWLRHtCGVCKYCRR 117
                                    689*******************.79999999******************9899999***********9999********* PP

                                    T-GGG-TTBEETTTSS-SSSBSEEEECGGGEE CS
                          ADH_N  76 geenlCeeakllgvsldGgfaeyvvvpekklv 107
                                    g+enlC++ +++g++ dGg+ae ++vp+++++
  gi|121637765|ref|YP_977988.1| 118 GSENLCPQSRYTGWDADGGYAEFTTVPAAFAH 149
                                    ***************************87765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   2.1e-10   1.2e-06       4     129 ..     195     310 ..     189     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.1e-10
                                    HHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEE CS
                     ADH_zinc_N   4 laavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgG 83 
                                    +++ q+A a Gae++++ + ++ ++la +lGa  + ++         ++   + ++d+++ ++ +g+ +  al++l++gG
  gi|121637765|ref|YP_977988.1| 195 HITAQVALAQGAEIHVMTRGARARKLALQLGAASAQDA---------ADRP-PVPLDAAILFAPVGDLVLPALEALDRGG 264
                                    6789****************************999999.........2333.33555555555555************** PP

                                    EEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  84 rlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                     l++ G+ +++  +++ ++ l++e++i+ ++  + r + ++++d++a
  gi|121637765|ref|YP_977988.1| 265 ILAIAGIhLTDIPDLNYQQHLFQERQIRSVTSNT-RADARAFFDFAA 310
                                    *******9999888**************999999.999999988865 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   1.2e+04      44      69 ..     180     204 ..     172     239 .. 0.53
   2 !   17.3   0.0   1.2e-06    0.0074      40     133 .]     257     344 ..     224     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                                    EEEEEEEE--.--.S-EEE-CHHHCTT CS
                   ADH_zinc_N_2  44 pggGrlvsig.gpplsaallkpakkrk 69 
                                    p+gGrl  +g g   sa + ++ + + 
  gi|121637765|ref|YP_977988.1| 180 PPGGRLGLYGfGG--SAHITAQVALAQ 204
                                    5556666555442..222222222232 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-06
                                    HHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHH CS
                   ADH_zinc_N_2  40 lkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAh 119
                                    l++l+  G ++ i+g +  +++++++    ++ ++   + s++++ +ad  ++ +++ ++++++++   ++pl +a +A+
  gi|121637765|ref|YP_977988.1| 257 LEALDR-GGILAIAG-IHLTDIPDLN--YQQHLFQERQIRSVTSNTRAD-ARAFFDFAAQHHIEVTTP-EYPLGQADRAL 330
                                    456644.55555554.1222233332..334566666666666675788.*****************9.7********** PP

                                    HHHHSS--SSEEEE CS
                   ADH_zinc_N_2 120 rylesgrarGKiVl 133
                                     +l +gr  G  Vl
  gi|121637765|ref|YP_977988.1| 331 GDLSAGRIAGAAVL 344
                                    *******9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2492.41
//
Query:       gi|121637766|ref|YP_977989.1|  [L=256]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-16   58.3   6.9    7.5e-16   58.3   6.9    2.9  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   8.3         1   1.8e+04      38      60 ..      33      77 ..      14     120 .. 0.57
   2 !   58.3   6.9   4.2e-20   7.5e-16       7      91 ..     132     242 ..     126     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHCSGGGHHH.H.....................H CS
                           CPBP 38 tlailissilFglaHlpngps.v.....................l 60
                                   ++++l+  +   +aH+ + ++ +                     +
  gi|121637766|ref|YP_977989.1| 33 AVVVLVLVLTNLIAHFTTPWAsIatvpaaavglvilvrsrglgwA 77
                                   556666666677888888666333333333333333333333330 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 4.2e-20
                                    HHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-.HHHHHHHHHHHHHCSGGG........................HHHH.. CS
                           CPBP   7 vfllalllapllEEllfRglllqllqergss.tlailissilFglaHlpn........................gpsv.. 59 
                                     ++++ l + + EEl fRg+l  +l++  +  + + ++ s+lFgl+H+++                        g  v  
  gi|121637766|ref|YP_977989.1| 132 SMVMIPLQTVIPEELAFRGVLHGALNRA-WGfRGVAVAGSVLFGLWHIATslgltssnvgftrlfgggiiglvaG--Vml 208
                                    56778888999**************999.88678888889**********8887777666666666655555552..055 PP

                                    ..HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           CPBP  60 ..llaalaGlvlgylylktgsllaaillHallnl 91 
                                      l++ +aG+v+++l++++gsl+a+i+lH+ ln 
  gi|121637766|ref|YP_977989.1| 209 avLATGVAGFVFSWLRRRSGSLIAPIALHWSLNG 242
                                    55*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1873.17
//
Query:       gi|121637767|ref|YP_977990.1|  [L=251]
Description: hypothetical protein BCG_1900c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-23   81.0   0.0    1.2e-22   80.4   0.0    1.3  1  MOSC      MOSC domain
  ------ inclusion threshold ------
       0.49   10.3   3.1       0.61   10.0   1.8    1.8  2  3-alpha   3-alpha domain


Domain annotation for each model (and alignments):
>> MOSC  MOSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   1.3e-26   1.2e-22       2     131 .]      80     193 ..      79     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.3e-26
                                    XX---GGGGSEEEEETHHHHHHHHHS..GGGGG-STTTT--SEEE.S-.......-TTT-BTT-E.EEETT......... CS
                           MOSC   2 rkihggdekavllisresldalneelkegrsveldpgrfreNivv.ggaaafeEdtwkelrigdrrfrlggacsRcqmvn 80 
                                    +k+hggd++av++++re+lda++++l   r   l  g f+eN+++ g+       + + +rig+r +r+g+         
  gi|121637767|ref|YP_977990.1|  80 PKLHGGDDQAVYAYAREDLDAWETQL--HR--TLHNGMFGENLTTsGV-------DVTYARIGER-WRIGS--------- 138
                                    789***********************..65..69***********777.......**********.****9......... PP

                                    ............EE----THHHHH...TTHHHHHHHHT---EEEEEEE-EEEETTS-EE CS
                           MOSC  81 vdqetga.....rprepcktlakf...rrvdkrvkgkgrfGvylrvleegtvrvGdeve 131
                                         g       pr pc+t+a+f   r + k ++++   G+ylrv+++gtvr+Gd+++
  gi|121637767|ref|YP_977990.1| 139 ----DGLvlevsAPRIPCRTFAAFldlRYWIKTFTRAAKPGAYLRVIAPGTVRAGDTIT 193
                                    ....34467789***********77*******************************996 PP

>> 3-alpha  3-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.5   1.4e+04      10      17 ..     195     202 ..     193     203 .. 0.81
   2 ?   10.0   1.8   6.8e-05      0.61      13      40 ..     211     238 ..     208     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.5
                                    HHTS---H CS
                        3-alpha  10 lyhdkldr 17 
                                     y+++++ 
  gi|121637767|ref|YP_977990.1| 195 DYRPEHNV 202
                                    699*9996 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.8e-05
                                    S---HHHHHHHHTSTT--HHHHHHHHHH CS
                        3-alpha  13 dkldrealrrllelpaLspsWrktfekR 40 
                                    ++ + e l +ll+++aL+++ ++++++R
  gi|121637767|ref|YP_977990.1| 211 RTSESELLPQLLAADALAAELKAYARER 238
                                    567889999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1729.22
//
Query:       gi|121637768|ref|YP_977991.1|  [L=286]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-45  153.6   0.1    5.9e-45  153.1   0.1    1.2  1  adh_short       short chain dehydrogenase
    1.3e-37  129.6   0.1    1.8e-37  129.2   0.1    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    0.00012   22.0   0.5    0.00085   19.3   0.5    2.0  1  KR              KR domain
  ------ inclusion threshold ------
      0.043   13.6   0.1       0.11   12.2   0.1    1.7  1  AIM24           Mitochondrial biogenesis AIM24
      0.061   13.4   0.0       0.11   12.6   0.0    1.3  1  Acetyltransf_9  Acetyltransferase (GNAT) domain
      0.061   13.3   0.3       0.14   12.1   0.2    1.6  1  ADH_zinc_N      Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.1     2e-48   5.9e-45       1     186 [.      18     199 ..      18     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2e-48
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv+ +tG+++GIG+a+a +l + Gakv++ d+ e+ ++e  + l       ++ ++Dvtd ++ + ++++++ +lg++dv
  gi|121637768|ref|YP_977991.1|  18 KVIAITGGARGIGLATAAALHNLGAKVAIGDIDEAMAKESGADLD----LDMYGKLDVTDPDSFSGFLDAVERQLGPIDV 93 
                                    89***************************9999887766666666....479**************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    LvnNAGi  +g + +  +  ++r++++N+ gv+l ++++++ m+ + +G+++nv+S ag+    gva Y+AsK+av+++t
  gi|121637768|ref|YP_977991.1|  94 LVNNAGIMPVGRIVDEPDPVTRRILDINVYGVILGSKLAAQRMVPRGRGHVINVASLAGEIYAVGVATYCASKHAVVAFT 173
                                    ******************************************************************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdm 186
                                    +s++ e+++ g++ ++v P +v+T++
  gi|121637768|ref|YP_977991.1| 174 DSARLEYRSAGVKFSMVLPSFVNTEL 199
                                    ************************97 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.1     6e-41   1.8e-37       1     204 [.      24     228 ..      24     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 6e-41
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                    G a+gIG a+A al++ Ga+v++ d++e+    ++e  ++l+ ++  ++DVtd+++   + ++v++++g +D+lvnnagi
  gi|121637768|ref|YP_977991.1|  24 GGARGIGLATAAALHNLGAKVAIGDIDEAM---AKESGADLDLDMyGKLDVTDPDSFSGFLDAVERQLGPIDVLVNNAGI 100
                                    669**************************9...89999999988559********************************* PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                    +p   g++++ ++   +r+ld+n+y+++l +k a++ ++ +g g ++n++s+++e++  + + y+a+K+a++a+t ++  
  gi|121637768|ref|YP_977991.1| 101 MPV--GRIVDEPDPVTRRILDINVYGVILGSKLAAQrMVPRGrGHVINVASLAGEIYAVGVATYCASKHAVVAFTDSARL 178
                                    ***..******************************95666669************************************* PP

                                    HHGGGTEEEEEEEE--BHCTG...GGGSTTHHHHHHHHHHHSTTSS-B-H CS
                   adh_short_C2 158 elgpkgiRvNavspgpikTla...asgikgfdelleelearaplgrlgtp 204
                                    e+ + g++   v p++++T++   + gikgf++ + +  a a +g ++ p
  gi|121637768|ref|YP_977991.1| 179 EYRSAGVKFSMVLPSFVNTELiagTGGIKGFKNAEPADIADAIVGLIVHP 228
                                    ********************955555677788887777777777766666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   2.8e-07   0.00085       4     163 ..      21     176 ..      19     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-07
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EE.EE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaev.evvaaDvsdkdavealleeikaeeppi 82 
                                     itGG+ g+Gl++a  l + ga+  v ++     ++ +k      +  + +  ++ ++Dv+d+d+ +  l++++++ +pi
  gi|121637768|ref|YP_977991.1|  21 AITGGARGIGLATAAALHNLGAK--VAIGDI--DEAMAK-----ESGADLDLdMYGKLDVTDPDSFSGFLDAVERQLGPI 91 
                                    69*******************99..455555..222222.....2222223314679*********************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDa 158
                                       ++ Ag++  + + +  +   +++l   v G+    +l ++    +   +++ ++S+ag + + g a+Y a  + + a
  gi|121637768|ref|YP_977991.1|  92 DVLVNNAGIMPVGRIVDEPDPVTRRILDINVYGVILGSKLAAQrmvpRGRGHVINVASLAGEIYAVGVATYCASKHAVVA 171
                                    ******************99999*******9999888877777555567789999******999*******999888777 PP

                                    HHHHH CS
                             KR 159 laeyr 163
                                    + ++ 
  gi|121637768|ref|YP_977991.1| 172 FTDSA 176
                                    76654 PP

>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.8e-05      0.11     128     185 ..     139     264 ..     114     268 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                                    ESSSEE..EEEEECSEEEEEEE.EEEEEEEGGGEEEEETTEEEEEEEET............................... CS
                          AIM24 128 tGrGlv..alsgyGaiyeielkageelvvdpghlvafsgslkfdiervg............................... 174
                                    +GrG v  + s  G+iy + +    ++ + + ++vaf++s +++ +++g                               
  gi|121637768|ref|YP_977991.1| 139 RGRGHVinVASLAGEIYAVGV---ATYCASKHAVVAFTDSARLEYRSAGvkfsmvlpsfvnteliagtggikgfknaepa 215
                                    588888545555899999999...57999999999999999998888855566666666666666666666666666666 PP

                                    ......................................T---STTTTS- CS
                          AIM24 175 ......................................glkrrligGeg 185
                                                                          + ++rl+gGe 
  gi|121637768|ref|YP_977991.1| 216 diadaivglivhpkprvrvtkaagsmivaqrfmprqvsEGLNRLLGGEH 264
                                    6666666666666666666655566666665555555544566666665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.6e-05      0.11      42     115 ..     120     193 ..     107     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                                    SEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--S CS
                 Acetyltransf_9  42 srvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfPs 115
                                     +v+g+  + +l++q ++ + + +v +    a+ +++V+va     ++ + ++++ a  e+r+ g+++s+  Ps
  gi|121637768|ref|YP_977991.1| 120 INVYGVILGSKLAAQRMVPRGRGHVINVASLAGEIYAVGVATYCASKHAVVAFTDSARLEYRSAGVKFSMVLPS 193
                                    48999999**************************************************************9996 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.7e-05      0.14       1      67 [.      28      99 ..      28     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET.........TTC.HHHHHHHHHTTTSSEEEEEESSC CS
                     ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny.........kea.dlverikeltggegvdvvfecvG 67
                                   g+Gla+ ++++ lGa+v   d++e    +ak+ Gad  ++          ++   + +++++  g  ++dv ++ +G
  gi|121637768|ref|YP_977991.1| 28 GIGLATAAALHNLGAKVAIGDIDEA---MAKESGADLDLDMygkldvtdpDSFsGFLDAVERQLG--PIDVLVNNAG 99
                                   8***********************5...*******998888666665555444446666666663..6777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2210.48
//
Query:       gi|121637769|ref|YP_977992.1|  [L=778]
Description: hypothetical protein BCG_1902 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.3e-162  540.3   0.7    2.1e-93  313.4   0.1    2.0  2  CoA_transf_3  CoA-transferase family III
  ------ inclusion threshold ------
       0.16   11.5   0.0        4.8    6.7   0.0    2.2  2  DeoC          DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.8   0.1   9.7e-71   8.7e-67      18     367 ..       2     352 ..       1     353 [. 0.95
   2 !  313.4   0.1   2.4e-97   2.1e-93       2     367 ..     376     746 ..     375     747 .. 0.95

  Alignments for each domain:
  == domain 1  score: 225.8 bits;  conditional E-value: 9.7e-71
                   CoA_transf_3  18 atslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkrLvakADVvieNfrpgv 97 
                                    +t+lLAdlGA+V kv+pp +g p R+v+p+   g+s  f++ n nKrs +l+  +e +r+ +++L+a+AD+v++   pg+
  gi|121637769|ref|YP_977992.1|   2 VTRLLADLGADVLKVQPP-GGSPGRHVRPTLA-GTSIGFAMHNANKRSAVLNPLDESDRRRFLDLAASADIVVDCGLPGQ 79 
                                    689***************.**********998.*********************************************** PP

                   CoA_transf_3  98 lerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvgvplgDivtgllaavail 177
                                    ++++g + +el+ +  +L+ +s++ +G  Gp++++++ D+v+ a+sG +s +g   g+Pv +  +++ +++++ aa+a+l
  gi|121637769|ref|YP_977992.1|  80 AAAYGASCAELADRYRHLVALSITDFGAAGPRSSWRATDPVLYAMSGALSRSGPTAGTPVLPPDGIASATAAVQAAWAVL 159
                                    ******************************************************************************** PP

                   CoA_transf_3 178 aallarertGkGqvidvslleaalallapqlley..latgevperq.gnrdpaaapygvyrtkdgwvaiaaatdkqwaal 254
                                     a+++r r G+G+ id s ++a++  l+p +  +  +a+g   + +   r  +   y +y+++dg+v +++  ++qw+ l
  gi|121637769|ref|YP_977992.1| 160 VAYFNRLRCGTGDYIDFSRFDAVVMALDPPFGAHgqVAAGIRSTGRwRGRPKNQDAYPIYPCRDGYVRFCVMAPRQWRGL 239
                                    *******************************9998744444444232445557778************************ PP

                   CoA_transf_3 255 ckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntleevlddpqlaarglvvevd 334
                                     + lg+pe  +dp++    +rl++  ++  ++a+ +ae+t++e++++ +a gvp+++v t++ +l++++++a g +++ +
  gi|121637769|ref|YP_977992.1| 240 RRWLGEPEDFQDPKYDVIGARLAAWPQISVLVAKLCAEKTMKELVAAGQALGVPITAVLTPSRILASEHFQAVGAITDAE 319
                                    ********88********************************************************************** PP

                   CoA_transf_3 335 dpdygevpvvglpvrlsetparvkraaPklGed 367
                                         ++ v++  + +++ +a ++++aP+ G+d
  gi|121637769|ref|YP_977992.1| 320 LVPGVRTGVPTGYFVVDGKRAGFRTPAPAAGQD 352
                                    999888**************************9 PP

  == domain 2  score: 313.4 bits;  conditional E-value: 2.4e-97
                   CoA_transf_3   2 aGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkr 81 
                                    +G+r+ldl+ ++aG   ++l++dlGAeVIkvE+ +  D +R+++   ++ +s  f++ +rn   + lDl++ eg++++ r
  gi|121637769|ref|YP_977992.1| 376 EGLRILDLGIIVAGGELSRLFGDLGAEVIKVESADHPDGLRQTRV--GDAMSESFAWTHRNHLALGLDLRNSEGKAIFGR 453
                                    8*****************************************955..458****************************** PP

                   CoA_transf_3  82 LvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsl.tgepdgp..... 155
                                    Lva++D v  Nf+pg+l +lg++y+ l+a nPr+++a  s++G++Gp+++r gy++++ aa+G++ + t ++ +p     
  gi|121637769|ref|YP_977992.1| 454 LVAESDAVFANFKPGTLTSLGFSYDVLHAFNPRIVLAGSSAFGNRGPWSTRMGYGPLVRAATGVTRVwTSDEAQPdnsrh 533
                                    *******************************************************************7766655566677 PP

                   CoA_transf_3 156 P.vkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvy 234
                                    P + + + + D+v g ++a+ +laal++r+rtG G ++ +s++e +++ l+  ++   a  +  +   + +p++  + vy
  gi|121637769|ref|YP_977992.1| 534 PfYDATTIFPDHVVGRVGALLALAALIHRDRTGGGAHVHISQAEVVVNQLDTMFVAEAARATDVA---EIHPDTSVHAVY 610
                                    5478889999*******************************************987744444444...59********** PP

                   CoA_transf_3 235 rt.kdg.wvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapv 312
                                    ++ +d+ w++i++ +d++w++   ++g+pela+dprf +++sr++nr el a++++w+++rt  +++ +l+aagv+a+p+
  gi|121637769|ref|YP_977992.1| 611 PCaGDDeWCVISIRSDDEWRRATSVFGQPELANDPRFGASRSRVANRSELVAAVSAWTSTRTPVQAAGALQAAGVAAGPM 690
                                    **86778************************************************************************* PP

                   CoA_transf_3 313 ntleevlddpqlaarglvvevddpdyge.vpvvglpvrlsetparvkraaPklGed 367
                                    n+++++l+dpql +r+l++++ +p + + +p+ + p+ ++  p++++r+aP  G+d
  gi|121637769|ref|YP_977992.1| 691 NRPSDILEDPQLIERNLFRDMVHPLIARpLPAETGPAPFRHIPQAPQRPAPLPGQD 746
                                    *************************9888**************************9 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00053       4.8     157     174 ..       3      22 ..       2     114 .. 0.85
   2 ?    2.3   0.0     0.012   1.1e+02     155     173 ..     391     409 ..     390     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00053
                                    HHHHTCCT-SEEEE--S..S CS
                           DeoC 157 arvsaelGaDiiKvevp..k 174
                                    +r+ a+lGaD++Kv+ p   
  gi|121637769|ref|YP_977992.1|   3 TRLLADLGADVLKVQPPggS 22 
                                    7999************9441 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.012
                                    HHHHHHTCCT-SEEEE--S CS
                           DeoC 155 eAarvsaelGaDiiKvevp 173
                                    e +r++ +lGa +iKve +
  gi|121637769|ref|YP_977992.1| 391 ELSRLFGDLGAEVIKVESA 409
                                    6799************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 5497.02
//
Query:       gi|121637770|ref|YP_977993.1|  [L=494]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-26   91.1   0.8      6e-26   90.2   0.8    1.5  1  TLP1_add_C      Thiolase-like protein type 1 additional C-ter
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.21   11.3   0.0    1.3  1  Thiolase_C      Thiolase, C-terminal domain
       0.14   12.8   0.1       0.73   10.5   0.0    2.2  3  Asp_protease_2  Aspartyl protease


Domain annotation for each model (and alignments):
>> TLP1_add_C  Thiolase-like protein type 1 additional C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.8     1e-29     6e-26       1      83 []     409     490 ..     409     490 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1e-29
                     TLP1_add_C   1 plqeevdavpvpevveeaeGeatvEtyTvefnRdgePekgfvvgRltsdgaRfLAneadeetlealvsedveGakvrVrq 80 
                                    ++q +vd++p+ +  +e+eG +tvE++T+++nRdg+Pek+f+++R t+dg+R LA+++d + ++a+v+ed++G kv V  
  gi|121637770|ref|YP_977993.1| 409 DMQPAVDREPTGDGLVEWEGIGTVEAWTTPVNRDGQPEKAFLAVR-TPDGSRSLAVITDPASVQATVREDIAGVKVAVAP 487
                                    789******************************************.********************************** PP

                     TLP1_add_C  81 Dgt 83 
                                    Dgt
  gi|121637770|ref|YP_977993.1| 488 DGT 490
                                    *97 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.5e-05      0.21      26     109 ..     297     384 ..     277     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G....GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCT CS
                     Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl....ekvNvnGGaialGHPlGasGaRivvtllselkkeg 101
                                     a  ++l+ agl ++di+++++   F + + ++a +l+ld+    + + v GG    G P     +  ++t+++ l  + 
  gi|121637770|ref|YP_977993.1| 297 IAGARALELAGLGLDDIEYVDLYSCFPSAVQVAAIELGLDTddpaRPLTVTGGLTFAGGPWSNYVTHSIATMAELLAANP 376
                                    466799********************98888888888888866777899****999999999999999999999999999 PP

                                    TSEEEEEE CS
                     Thiolase_C 102 gklgvaal 109
                                    g+ g++++
  gi|121637770|ref|YP_977993.1| 377 GRRGLITA 384
                                    99999886 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         3   1.8e+04      37      56 ..      77      96 ..      71     103 .. 0.73
   2 ?   10.5   0.0   0.00012      0.73      13      68 ..     243     302 ..     240     318 .. 0.87
   3 ?   -3.4   0.0       2.7   1.6e+04      30      46 ..     332     348 ..     325     355 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                 Asp_protease_2 37 eseltvrvsgaggevkarlv 56
                                   + ++t+ +sg+gg+++ +lv
  gi|121637770|ref|YP_977993.1| 77 ARTFTTGYSGVGGNMPQSLV 96
                                   55567788999998887665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00012
                 Asp_protease_2  13 llDTGasttlispelaeklglkvreseltvrvsgagge.vkarlvrlds...lklggltl 68 
                                    ++D Ga  +l s e a++l+++ ++  +++ ++ a+ +   a+++rl++   ++++g+++
  gi|121637770|ref|YP_977993.1| 243 MVDQGAALLLTSVERATRLRIPAERWVYPQAGTDAHDTpAVADRHRLHRstaIRIAGARA 302
                                    89*********************************9998999999999655688877765 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.7
                 Asp_protease_2  30 klglkvreseltvrvsg 46 
                                    +lgl++++ +++ +v+g
  gi|121637770|ref|YP_977993.1| 332 ELGLDTDDPARPLTVTG 348
                                    78898888776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 2611.18
//
Query:       gi|121637771|ref|YP_977994.1|  [L=699]
Description: hypothetical protein BCG_1904 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-06   27.6   0.7    2.3e-06   27.6   0.7    2.0  2  NAD_binding_10  NAD(P)H-binding
    0.00041   19.9   1.0     0.0018   17.8   0.1    2.4  3  Epimerase       NAD dependent epimerase/dehydratase family
     0.0029   17.2   0.3      0.007   15.9   0.3    1.6  1  NmrA            NmrA-like family
     0.0036   16.4   0.5     0.0069   15.5   0.5    1.5  1  RmlD_sub_bind   RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.7   5.2e-10   2.3e-06       2     100 ..       8     104 ..       8     126 .. 0.84
   2 ?   -2.0   0.1      0.64   2.8e+03      55      73 ..     549     567 ..     537     590 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.2e-10
                                    TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.....--TCCHHH CS
                 NAD_binding_10   2 AtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal.....ggggkdee 76 
                                    AtG vGr ++++l+a+ gh+v  ++ +p+++     +++++ v +++ ++  l+e    adaV+  +     ++gg   +
  gi|121637771|ref|YP_977994.1|   8 ATGAVGRSVTRQLIAA-GHTVSGIAQHPHDAL----DPRVDYVCASLRNP-VLQELAGEADAVIHLApvdtsAPGGVGIT 81 
                                    9***************.5************97....49*********976.78999999*****9998888655555778 PP

                                    HHHHHHHHHHHCT--EEEEEEETT CS
                 NAD_binding_10  77 gaknivdaakeagvkRfvlvsaig 100
                                    g +++++aa +ag  R+++vs + 
  gi|121637771|ref|YP_977994.1|  82 GLAHVANAAARAGA-RLLFVSQAA 104
                                    8************9.777777654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                                    HHHHTT-SEEEES---TCC CS
                 NAD_binding_10  55 aealkgadaVvsalggggk 73 
                                    a a + +daV++ +g++g 
  gi|121637771|ref|YP_977994.1| 549 APAAAAVDAVIARIGHRGL 567
                                    5688899****99998876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.1e-07    0.0018       1      74 [.       3      70 ..       3     115 .. 0.78
   2 ?   -0.7   0.0      0.18     8e+02     213     231 ..     161     179 ..     157     191 .. 0.85
   3 ?   -3.5   0.0       1.3   5.8e+03      64     110 ..     580     626 ..     569     628 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.1e-07
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAav 74
                                   ilVt atG +G+ ++++l ++g++v g+++     + a++++++ v + l++++ l++l    ++davihlA v
  gi|121637771|ref|YP_977994.1|  3 ILVTDATGAVGRSVTRQLIAAGHTVSGIAQH---PHDALDPRVDYVCASLRNPV-LQELAG--EADAVIHLAPV 70
                                   89*****************************...44445555567777777666.788777..79******754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                                    EEHHHHHHHHHHHHHHHTT CS
                      Epimerase 213 lyveDvaeaillvlehvda 231
                                    l+ +D+++ ++l+l+  ++
  gi|121637771|ref|YP_977994.1| 161 LHLDDLVRFLVLALNTDRN 179
                                    899***********99544 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.3
                                    T-SEEEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEE CS
                      Epimerase  64 qpdavihlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrl 110
                                    +p   +  Aa ++  +a   +pa +i++ ++gt+   e a+ + + r+
  gi|121637771|ref|YP_977994.1| 580 DPALLLKTAAeIAARPAGPAHPATLIQRLAAGTRSARELAHGTTI-RF 626
                                    677778888889999999999999999999999888888877666.55 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.6e-06     0.007       1     102 [.       3     103 ..       3     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                                    EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG..... CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy..... 75 
                                    Ilv+ aTG+ G+sv+r l++agh+v  +   ++  l        v  v+++l +  +l+e+  ++d+v+   ++      
  gi|121637771|ref|YP_977994.1|   3 ILVTDATGAVGRSVTRQLIAAGHTVSGIAQHPHDALD-----PRVDYVCASLRN-PVLQELAGEADAVIHLAPVDtsapg 76 
                                    89***********************999888865543.....335666777765.4677777777777777776666666 PP

                                    S-HHHHHHHHHHHHHHHS-SEEEEEE- CS
                           NmrA  76 skeiedgkklvdAakeaGvkhfiySsl 102
                                    +  i    ++++Aa++aG + ++ S+ 
  gi|121637771|ref|YP_977994.1|  77 GVGITGLAHVANAAARAGARLLFVSQA 103
                                    666666667777777777666666655 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   1.5e-06    0.0069       1     100 [.       1     101 [.       1     104 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-06
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------..HHHHHHSHHHHHHHH CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAyta..vDkaEseeeaayavn 78 
                                    m+ilvt a+G++G+ +++ql ++g+ v ++ ++  d  d+ +v+ + ++ +  v+ ++A   +  +  a  +  a   v 
  gi|121637771|ref|YP_977994.1|   1 MQILVTDATGAVGRSVTRQLIAAGHTVSGIAQHPHDALDP-RVDYVCASLRNPVLQELAGEADavIHLAPVDTSAPGGVG 79 
                                    89*******************************9999998.5888888888889999987654224567888899999** PP

                                    THHHHHHHHHHHHCT-EEEEEE CS
                  RmlD_sub_bind  79 aeavealAeaaaavgalLihvS 100
                                     ++ +++A+aaa++ga L++vS
  gi|121637771|ref|YP_977994.1|  80 ITGLAHVANAAARAGARLLFVS 101
                                    ********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 3846.04
//
Query:       gi|121637772|ref|YP_977995.1|  [L=411]
Description: reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-65  219.4   0.3    7.9e-65  219.0   0.3    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-20   73.8   1.2    7.8e-18   64.8   0.3    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      8e-13   48.8   0.2    6.5e-12   45.9   0.0    2.7  2  Reductase_C     Reductase C-terminal
    3.8e-09   36.2   0.0    2.9e-08   33.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-08   34.3   3.4     0.0094   14.7   0.1    3.7  4  HI0933_like     HI0933-like protein
    1.9e-07   30.7   0.2     0.0012   18.2   0.2    2.3  2  Amino_oxidase   Flavin containing amine oxidoreductase
    1.7e-06   27.8  10.5      0.027   14.1   0.4    4.0  4  DAO             FAD dependent oxidoreductase
    2.1e-06   27.8   4.3      0.002   18.3   0.3    3.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.7e-06   24.9   3.7       0.14   11.2   1.2    3.5  4  GIDA            Glucose inhibited division protein A
      0.001   19.0   0.7     0.0019   18.1   0.7    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.002   18.1   8.5        2.1    8.3   0.3    4.1  4  NAD_binding_9   FAD-NAD(P)-binding
     0.0036   16.5   0.3       0.42    9.7   0.0    2.8  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0061   15.7  14.5       0.34   10.0   1.4    4.1  4  FAD_binding_2   FAD binding domain
     0.0078   15.6   0.4      0.018   14.4   0.0    1.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.017   15.5   0.1       0.43   11.0   0.2    2.3  2  NAD_binding_7   Putative NAD(P)-binding
      0.044   12.8   4.4        2.6    7.0   0.4    3.0  3  Lycopene_cycl   Lycopene cyclase protein
       0.05   13.2   0.2       0.11   12.1   0.1    1.6  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.059   12.6  11.5       0.83    8.9   5.8    2.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.063   13.5   1.3       0.71   10.1   0.1    2.3  2  TrkA_N          TrkA-N domain
       0.18   11.0   3.5        0.7    9.1   0.4    2.4  2  FAD_binding_3   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.3   8.8e-68   7.9e-65       3     293 ..       7     304 ..       5     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 8.8e-68
                                    EEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHH.CCCCHCCTCEEE CS
                                    xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxx RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.evvkklnqg.ielllgeevvki 78 
                                     v++GgG AG +a + l++   g++++l+++e+++++++++lsk++l+ ++  + ++ +  + ++ + ++++lg+ v ++
  gi|121637772|ref|YP_977995.1|   7 FVIVGGGLAGAKAVEALRRsdFGGRIILFGDEEHLPYDRPPLSKEFLAGKKSLSDFTiQTSDWYRDHdVDVRLGVRVSSL 86 
                                    69*****************767********************************99994455555556************ PP

                                    EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                    Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiGvEl 157
                                    d+ +++v+l      d+  + ydkl+lAtGs pr+++ipG    +++ +r++++a al++ l++  +++vvG+G iG+E+
  gi|121637772|ref|YP_977995.1|  87 DRSAHTVEL-----PDGAAVRYDKLLLATGSAPRRPPIPGSDAAGVHYLRSYNDAVALNSVLVQgSSLAVVGAGWIGLEV 161
                                    *********.....78899**********************99999999***************9*************** PP

                                    HHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 158 Aaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvav 235
                                    Aa +++ g++vt+ve + ++l  al++++++  ++ ++++Gv+++l+t+ +ei++ + k++ ++  dg++++ad v+vav
  gi|121637772|ref|YP_977995.1| 162 AASARQRGVDVTVVETAIQPLlAALGEAVGKVFADLHRDQGVDLRLQTQLEEITAADGKATgLKMRDGSTVAADAVLVAV 241
                                    ********************99***********************************98889****************** PP

                                    -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqq 293
                                    G +p+ el+ +++gl++   gg++vd +lrt++p+iya+GD+a       g++ + e++ +A +q
  gi|121637772|ref|YP_977995.1| 242 GAKPNVELA-QQAGLAM-GEGGVLVDASLRTSDPDIYAVGDIAaaehpllGTRVRTEHWANALKQ 304
                                    *********.*******.99999********************9999999999999999999876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.017        15       2      28 ..       7      35 ..       6      45 .. 0.77
   2 ?   -1.4   0.0         4   3.6e+03      51      72 ..      71      92 ..      65      97 .. 0.80
   3 !   64.8   0.3   8.7e-21   7.8e-18       2      80 ..     149     228 ..     148     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                                   EEEECSSHHHHHHHHHHHH..TTSEEEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalae..lgkkVtvv 28
                                    v+vGgG+ g  + +al++  +g ++ ++
  gi|121637772|ref|YP_977995.1|  7 FVIVGGGLAGAKAVEALRRsdFGGRIILF 35
                                   59***************553377777666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4
                                   HHTTEEEECSEEEEEEEEETTS CS
                      Pyr_redox 51 ekngievllntkveeiegsedg 72
                                   +++ ++v+l+ +v +++ s+ +
  gi|121637772|ref|YP_977995.1| 71 RDHDVDVRLGVRVSSLDRSAHT 92
                                   7888999999999999988765 PP

  == domain 3  score: 64.8 bits;  conditional E-value: 8.7e-21
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvklkd 80 
                                    ++vvG+G+iglE+A+ +++ g +Vtvve + ++l  +l+e+++k++++ ++++g++++l+t++eei+  + + +++k++d
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASARQRGVDVTVVETAIQPLlAALGEAVGKVFADLHRDQGVDLRLQTQLEEITAADGKATGLKMRD 228
                                    79*****************************************************************8888899999987 PP

>> Reductase_C  Reductase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.3   4.7e+03      33      50 ..     220     237 ..     213     247 .. 0.81
   2 !   45.9   0.0   7.2e-15   6.5e-12       3      84 ..     326     408 ..     324     409 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.3
                                    EEEEEEEETTEEEEEEEE CS
                    Reductase_C  33 afsvfylrdgrlvaveav 50 
                                    + + + +rdg  va++av
  gi|121637772|ref|YP_977995.1| 220 KATGLKMRDGSTVAADAV 237
                                    566678899999999987 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 7.2e-15
                                    EEEETTEEEEEEE--TT--EEEEEEETTTTEEEEEEE.ETTEEEEEEEES-HHHHHHHHHHTTTT----HHHHH-TTS-H CS
                    Reductase_C   3 WSDqydlklQiaGlatgadevvvRgdpeerafsvfyl.rdgrlvaveavnrprdlmaarrliaagasvdpaalaDpavdL 81 
                                     +Dqydl ++++G+a   d+vv Rg+ + r+f  f+l  d r++a   vn    +  ++ li +g +vd ++l+Dp+ +L
  gi|121637772|ref|YP_977995.1| 326 FTDQYDLGMEYVGHAPSCDRVVFRGNVAGREFLSFWLdGDSRVLAGMNVNVWDVVDDVKGLIRSGNPVDVDRLVDPQWPL 405
                                    58************************999********77889************************************** PP

                                    HH. CS
                    Reductase_C  82 kkl 84 
                                     +l
  gi|121637772|ref|YP_977995.1| 406 ADL 408
                                    987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.37   3.3e+02       1      21 [.       8      28 ..       8      39 .. 0.85
   2 !   33.3   0.0   3.3e-11   2.9e-08      92     305 .]      71     279 ..      47     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl 21
                                   +I+G+G aG +a  +l+++++
  gi|121637772|ref|YP_977995.1|  8 VIVGGGLAGAKAVEALRRSDF 28
                                   7**********9999998876 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 3.3e-11
                    Pyr_redox_3  92 ksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskv.kefhk.....yagq 165
                                    + ++++++l  +V s+++++++ e+  + + ++ +k+++AtG    P+++ ipG++   +hy    +++       ++g 
  gi|121637772|ref|YP_977995.1|  71 RDHDVDVRLGVRVSSLDRSAHTVELP-DGAAVRYDKLLLATGS--APRRPPIPGSDAAGVHYLRSyNDAVAlnsvlVQGS 147
                                    66778888888888888887665553.5568999********9..***********988888432133222111227899 PP

                    Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey 245
                                     ++V+G++  + ++A    ++g +Vtvv      +       + l   + + +++l + + +++  +++++ei+  + + 
  gi|121637772|ref|YP_977995.1| 148 SLAVVGAGWIGLEVAASARQRGVDVTVVETAI--Q----PLLAALGEAVGKVFADLHRDQGVDLRLQTQLEEITAADGKA 221
                                    9***************************9874..2....357789999999****999988*************998877 PP

                    Pyr_redox_3 246 .kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                      +k++dg++v   d v++a+G kp++++ ++++++  e g   l ++   t  p+++ +G
  gi|121637772|ref|YP_977995.1| 222 tGLKMRDGSTVA-ADAVLVAVGAKPNVELAQQAGLAMGEGGV--LVDASLRTSDPDIYAVG 279
                                    257888887766.59999*************99998855553..33444555566666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.41   3.7e+02       3      27 ..       7      33 ..       5      41 .. 0.68
   2 !    7.8   0.0    0.0013       1.2     119     184 ..      70     134 ..      63     141 .. 0.82
   3 !    9.5   0.4   0.00038      0.34       3      33 ..     149     179 ..     147     184 .. 0.91
   4 !   14.7   0.1     1e-05    0.0094     114     165 ..     193     244 ..     184     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.41
                                   EEEE--SHHHHHHHHHH..HHTT--EE CS
                    HI0933_like  3 viviGgGaAGlmaAisa..akrgkrVl 27
                                    +++GgG AG  a +++  ++ g r++
  gi|121637772|ref|YP_977995.1|  7 FVIVGGGLAGAKAVEALrrSDFGGRII 33
                                   69********98766663244455555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                                    HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS..-GGGT--SHHHHHHHHTT CS
                    HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS..iPklGstgkgyklaeqfg 184
                                     ++ +v++rl  +v+s+++   ++++v++ ++ +++ dkl+lAtG++    P  Gs+ +g++ +++++
  gi|121637772|ref|YP_977995.1|  70 YRDHDVDVRLGVRVSSLDR---SAHTVELPDGAAVRYDKLLLATGSAPrrPPIPGSDAAGVHYLRSYN 134
                                    578899***********44...447899999**************97522477799999999888765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00038
                                    EEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekak 33 
                                    ++v+G+G  Gl  A+sa++rg +V+++e a 
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASARQRGVDVTVVETAI 179
                                    78*************************9875 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 1e-05
                                    HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    ++    +++gv+lrl+t+++++++ ++++  +k++++++++ad++++A+G +
  gi|121637772|ref|YP_977995.1| 193 VFADLHRDQGVDLRLQTQLEEITAADGKATGLKMRDGSTVAADAVLVAVGAK 244
                                    55666789*****************************************986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00035      0.31     195     266 ..      25     116 ..      11     143 .. 0.73
   2 !   18.2   0.2   1.3e-06    0.0012     215     262 ..     196     243 ..     158     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                    HHHHTSCCCEE....................TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEE CS
                  Amino_oxidase 195 legfggslllp....................rgGlsqlpealae..elrgldirlntrVkeikregdgvtvtledgevve 252
                                    +++fgg ++l                     ++ ls    + ++  + +++d+rl+ rV++++r++++v  +l dg  v+
  gi|121637772|ref|YP_977995.1|  25 RSDFGGRIILFgdeehlpydrpplskeflagKKSLSDFTIQTSDwyRDHDVDVRLGVRVSSLDRSAHTV--ELPDGAAVR 102
                                    5566666555566666666666666666555555666666666688899***************66665..558****** PP

                                    ESEEEE-S-HHHHH CS
                  Amino_oxidase 253 aDaVvvTvplgvlk 266
                                    +D+ ++++  +  +
  gi|121637772|ref|YP_977995.1| 103 YDKLLLATGSAPRR 116
                                    ***99999877665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
                                    HHHHTTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-H CS
                  Amino_oxidase 215 alaeelrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvpl 262
                                     l+ +  g+d+rl t + ei+  +g   +++++dg++v aDaV+v+v  
  gi|121637772|ref|YP_977995.1| 196 DLH-RDQGVDLRLQTQLEEITAaDGKATGLKMRDGSTVAADAVLVAVGA 243
                                    344.499***************66666*******************975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.13   1.1e+02       2      21 ..       7      25 ..       6      40 .. 0.70
   2 ?    2.4   0.0      0.11        95     157     202 ..      71     112 ..      60     134 .. 0.78
   3 !   11.8   2.3   0.00015      0.13       2      29 ..     149     178 ..     148     193 .. 0.89
   4 !   14.1   0.4     3e-05     0.027     153     207 ..     195     249 ..     185     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                                   EEEECTSHHHHHHHHHHHHT CS
                            DAO  2 vviiGGGiiGlstAyeLarr 21
                                    vi+GGG +G+ +  +L rr
  gi|121637772|ref|YP_977995.1|  7 FVIVGGGLAGAKAVEAL-RR 25
                                   69********9776666.44 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                    HHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GG CS
                            DAO 157 ealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGa 202
                                    +++ v++++g +v +l++    +++v  + p g+ +++d++ +a+G 
  gi|121637772|ref|YP_977995.1|  71 RDHDVDVRLGVRVSSLDRS---AHTV--ELPdGAAVRYDKLLLATGS 112
                                    66789***********876...8999..455587755688*****95 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00015
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                    ++++G+G iGl +A  + +rg  Vt++e +
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASARQRGvdVTVVETA 178
                                    58***************999********86 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 3e-05
                                    HHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH CS
                            DAO 153 araaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll 207
                                    a+  +++Gv+++++t+ +++ + dgk++g+  + + g+++aadav +a Ga  + +l
  gi|121637772|ref|YP_977995.1| 195 ADLHRDQGVDLRLQTQLEEITAADGKATGL--KMRdGSTVAADAVLVAVGAKPNvEL 249
                                    6667899*************9999******..4444888889********9877644 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.3   0.00088      0.79       1      25 [.       9      35 ..       9      41 .. 0.81
   2 !   18.3   0.3   2.2e-06     0.002       1      29 [.     151     179 ..     151     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00088
                                   EE--SHHHHHHHHHHHCCTE..EEEEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagf..dvlll 25
                                   IvG+Gl+G+ a  +L++ +f  ++ l+
  gi|121637772|ref|YP_977995.1|  9 IVGGGLAGAKAVEALRRSDFggRIILF 35
                                   9****************9664477776 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                    +vGaG  Gl  A+ ++++g+dv+++e++ 
  gi|121637772|ref|YP_977995.1| 151 VVGAGWIGLEVAASARQRGVDVTVVETAI 179
                                    8*************************975 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0     0.009         8       3      21 ..       8      26 ..       6      44 .. 0.70
   2 ?   -2.6   0.0       2.5   2.2e+03     126     150 ..      88     112 ..      80     121 .. 0.82
   3 !   11.2   1.2   0.00016      0.14       3      32 ..     150     179 ..     148     192 .. 0.84
   4 !    6.4   0.1    0.0046       4.1     114     150 ..     207     243 ..     188     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.009
                                   EEE-SSHHHHHHHHHHHHT CS
                           GIDA  3 iViGgGhAGceAAlaaarl 21
                                   +++GgG+AG  A  a+ r+
  gi|121637772|ref|YP_977995.1|  8 VIVGGGLAGAKAVEALRRS 26
                                   89*********95555443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                    TEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 126 kkvkgvvtedgetikakavviatGt 150
                                    ++ + v + dg++++ ++  +atG+
  gi|121637772|ref|YP_977995.1|  88 RSAHTVELPDGAAVRYDKLLLATGS 112
                                    5677899999999***********8 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00016
                                    EEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkl 32 
                                     V+G+G+ G+e A+ a ++G++v+ +   +
  gi|121637772|ref|YP_977995.1| 150 AVVGAGWIGLEVAASARQRGVDVTVVETAI 179
                                    7**********************9995444 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0046
                                    EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    ++ + ee+   ++k +g++++dg+t+ a+av +a G+
  gi|121637772|ref|YP_977995.1| 207 LQTQLEEITAADGKATGLKMRDGSTVAADAVLVAVGA 243
                                    367899999999************************8 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.7   2.1e-06    0.0019       2      68 ..     149     215 ..     148     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-06
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH.HHHHHHHHCCTTTTSS-HHHHCCCHHCEE CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekal.ekieksleklvekgklkeeeveaalaris 68 
                                    +av+GaG +G ++aa + ++g++V++v+++ + l +al e++ k ++ l++++ ++    +++l++i+
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASARQRGVDVTVVETAIQPLLAALgEAVGKVFADLHRDQGVD-LRLQTQLEEIT 215
                                    69**************************9877665555144455556655555555.55555555555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012        11       1      32 [.       8      36 ..       8      50 .. 0.81
   2 ?    4.4   0.0     0.037        33     124     155 ..      83     112 ..      65     113 .. 0.78
   3 ?    2.2   0.2      0.18   1.6e+02       1      33 [.     150     177 ..     150     187 .. 0.81
   4 !    8.3   0.3    0.0024       2.1     103     155 ..     193     243 ..     183     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfd 32
                                   +ivG+G +G+ ++e+L ++   +   +i lf 
  gi|121637772|ref|YP_977995.1|  8 VIVGGGLAGAKAVEALRRS---DFGGRIILFG 36
                                   7***************998...5777777774 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.037
                  NAD_binding_9 124 vvdleeradgqavlladgaslaadaVvLAlGh 155
                                    v +l+++a   +v l dga +++d++ LA+G 
  gi|121637772|ref|YP_977995.1|  83 VSSLDRSAH--TVELPDGAAVRYDKLLLATGS 112
                                    444444443..6899***************96 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.18
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp 33 
                                    a+vGaG  Gl v++   +r      +++t+++ 
  gi|121637772|ref|YP_977995.1| 150 AVVGAGWIGLEVAASARQR-----GVDVTVVET 177
                                    79********999875555.....688888886 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0024
                  NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    +f++l ++   +++++   +e+++ + +a+g  +  +dg+++aadaV +A+G 
  gi|121637772|ref|YP_977995.1| 193 VFADLHRDQGVDLRLQTQLEEITAADGKATG--LKMRDGSTVAADAVLVAVGA 243
                                    5555555554455555555566666666666..6779**************95 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.058        52     191     216 ..       4      29 ..       1      68 [. 0.73
   2 !    9.7   0.0   0.00046      0.42     146     217 ..     100     172 ..      73     189 .. 0.73
   3 ?    0.2   0.0      0.36   3.2e+02     295     339 ..     203     242 ..     191     252 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.058
                    K_oxygenase 191 kkriaVvGsGqSaaeifedllrrqkk 216
                                    + ++++vG+G  +a  +e l r+   
  gi|121637772|ref|YP_977995.1|   4 PTTFVIVGGGLAGAKAVEALRRSDFG 29 
                                    56789***********9999887544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                    K_oxygenase 146 elearnlvlgvGtepkiPevleklegkervvHss.eylerkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                                     ++  +l+l++G+ p  P++  +     + + s  ++   ++ l ++ ++aVvG+G  + e++  + +r  +v
  gi|121637772|ref|YP_977995.1| 100 AVRYDKLLLATGSAPRRPPIPGSDAAGVHYLRSYnDAVALNSVLVQGSSLAVVGAGWIGLEVAASARQRGVDV 172
                                    5666799***********998875533333333213333333499*****************99988885543 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.36
                    K_oxygenase 295 lrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                    + l+ ++++e+++a   +++ l++r+      +t+ +dav++A G
  gi|121637772|ref|YP_977995.1| 203 VDLRLQTQLEEITAADGKATGLKMRD-----GSTVAADAVLVAVG 242
                                    55555555555555554455555555.....34444444444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.047        42       3      14 ..       8      19 ..       6      40 .. 0.74
   2 !   10.0   1.4   0.00037      0.34       3      30 ..     150     177 ..     148     182 .. 0.93
   3 !    8.3   0.5    0.0012       1.1     140     207 ..     187     250 ..     180     260 .. 0.82
   4 ?    1.6   0.0      0.13   1.1e+02     374     403 ..     260     283 ..     252     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.047
                                   EEE--SHHHHHH CS
                  FAD_binding_2  3 iViGsGlAGLaA 14
                                   +++G+GlAG  A
  gi|121637772|ref|YP_977995.1|  8 VIVGGGLAGAKA 19
                                   9********877 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00037
                                    EEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvek 30 
                                     V+G+G  GL  A++a+++G +v+vve 
  gi|121637772|ref|YP_977995.1| 150 AVVGAGWIGLEVAASARQRGVDVTVVET 177
                                    7*************************96 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                  FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr.all 207
                                    g a+ +++++  r+ gvd++ +t+++e++  dg++tG  ++   +g++v  +a+av++a g+ ++ +l+
  gi|121637772|ref|YP_977995.1| 187 GEAVGKVFADLHRDQGVDLRLQTQLEEITAADGKATGLKMR---DGSTV--AADAVLVAVGAKPNvELA 250
                                    6777888888999999*********************9888...66655..599*****9998885444 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.13
                                    -EEEBETTSBESTTEEESSBTEEE-STCEE CS
                  FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGevaa 403
                                    gGv +d+++r+        p+ YA+G  aa
  gi|121637772|ref|YP_977995.1| 260 GGVLVDASLRT------SDPDIYAVGDIAA 283
                                    8**********......99*******9995 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.2   3.8e+03      38      64 ..       6      34 ..       3      40 .. 0.74
   2 !   14.4   0.0     2e-05     0.018      30      70 ..     140     180 ..     128     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                                   EEEEES-SHHHHHHHHHHH..HTT-EEEE CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk..afgmkvia 64
                                   t  i+G G  G ++ + l+   fg ++i 
  gi|121637772|ref|YP_977995.1|  6 TFVIVGGGLAGAKAVEALRrsDFGGRIIL 34
                                   78899999999999888874456666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
                                    SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                     +  ++g+ ++++G+G IG +va  +++ g++v+++++  +
  gi|121637772|ref|YP_977995.1| 140 NSVLVQGSSLAVVGAGWIGLEVAASARQRGVDVTVVETAIQ 180
                                    566789***************************99987655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.29   2.6e+02       9      29 ..       6      26 ..       2      72 .. 0.83
   2 ?   11.0   0.2   0.00048      0.43       5      46 ..     144     201 ..     141     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.29
                  NAD_binding_7  9 kvlvvGgGevAarkvrkllea 29
                                   + ++vGgG  +a+ v+ l ++
  gi|121637772|ref|YP_977995.1|  6 TFVIVGGGLAGAKAVEALRRS 26
                                   689*****9999999888764 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00048
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele................e 46 
                                    ++g +  vvG+G ++++ + +  + g +vtvv  ++++ l                 +
  gi|121637772|ref|YP_977995.1| 144 VQGSSLAVVGAGWIGLEVAASARQRGVDVTVVETAIQPLLAalgeavgkvfadlhrdQ 201
                                    5788899*************************99975555544444444443333331 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.21   1.9e+02       3      29 ..       8      34 ..       7      46 .. 0.75
   2 ?    7.0   0.4    0.0029       2.6       2      37 ..     149     182 ..     148     186 .. 0.88
   3 ?    4.8   0.1     0.014        12     104     177 ..     206     281 ..     191     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                  Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvl 29
                                   v++G+G+Ag +  + l ++  g +++l
  gi|121637772|ref|YP_977995.1|  8 VIVGGGLAGAKAVEALRRSDFGGRIIL 34
                                   8********988777766666666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0029
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                    ++v+GaG  gl +Aa     + g+ v+++e++ ++l
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASA--RQRGVDVTVVETAIQPL 182
                                    78*************99..999*******9876665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.014
                  Lycopene_cycl 104 lleakvesveeeeageslvvleggrkirarlvvdarglaslk..karrlglQtfy.GvevevdnppfdldkmvlMDf 177
                                    +l+ + e++++++   +   + +g ++ a +v++a g a+++   a++ gl +   Gv+v  +    d+d   + D 
  gi|121637772|ref|YP_977995.1| 206 RLQTQLEEITAADGKATGLKMRDGSTVAADAVLVAVG-AKPNveLAQQAGLAMGEgGVLVDASLRTSDPDIYAVGDI 281
                                    57888999999999888999*****************.444435444444444332677888777778877766665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.11       3      30 ..     149     176 ..     147     182 .. 0.92
   2 ?   -3.0   0.0         5   4.5e+03      69      86 ..     226     243 ..     207     253 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                    EEEE--STTHHHHHHHHHHCTSEEEEE- CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvD 30 
                                    ++v+G+G++Gl  aa   ++g++v++v 
  gi|121637772|ref|YP_977995.1| 149 LAVVGAGWIGLEVAASARQRGVDVTVVE 176
                                    68***********************996 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                                    -HHHHHHC-SEEEE---- CS
                 UDPG_MGDP_dh_N  69 dvekaveeadvifiaVgT 86 
                                      + +  +ad++++aVg 
  gi|121637772|ref|YP_977995.1| 226 MRDGSTVAADAVLVAVGA 243
                                    444456789999999985 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0043       3.8      28      48 ..       4      24 ..       1      32 [. 0.86
   2 ?    8.9   5.8   0.00093      0.83      18      64 ..     137     182 ..     124     270 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                                   --EEEEESTSHHHHHHHHHHH CS
                    AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatak 48
                                   p + +++GgG aG +A+++ +
  gi|121637772|ref|YP_977995.1|  4 PTTFVIVGGGLAGAKAVEALR 24
                                   7889************98765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00093
                                    ETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                    AlaDh_PNT_C  18 tlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                    +++  v  v+ +   v+G+G  Gl+ +a a++ g +Vtv+++ ++ l
  gi|121637772|ref|YP_977995.1| 137 VALNSVL-VQGSSLAVVGAGWIGLEVAASARQRGVDVTVVETAIQPL 182
                                    5566666.889999***************************987654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.27   2.4e+02       1      20 [.       7      26 ..       7      40 .. 0.83
   2 ?   10.1   0.1    0.0008      0.71       2      36 ..     150     184 ..     149     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                                   EEEES-SHHHHHHHHHHHHT CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLseg 20
                                   ++i+G G  G + +e L+++
  gi|121637772|ref|YP_977995.1|  7 FVIVGGGLAGAKAVEALRRS 26
                                   79***************984 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
                                    EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeervee 36 
                                    +++G+G +G ++a   +++g dv+v+++  + +  
  gi|121637772|ref|YP_977995.1| 150 AVVGAGWIGLEVAASARQRGVDVTVVETAIQPLLA 184
                                    79****************7768*****98776555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.075        68       3      22 ..       6      25 ..       4      33 .. 0.84
   2 ?    9.1   0.4   0.00078       0.7       5      35 ..     150     180 ..     147     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.075
                                   EEEEE--SHHHHHHHHHHHH CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLse 22
                                   + +IVG+G+aG+ +   L++
  gi|121637772|ref|YP_977995.1|  6 TFVIVGGGLAGAKAVEALRR 25
                                   568********999888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00078
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                    ++VGaG  Gl  a   +++Gv+v++ve   +
  gi|121637772|ref|YP_977995.1| 150 AVVGAGWIGLEVAASARQRGVDVTVVETAIQ 180
                                    69************************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2562.27
//
Query:       gi|121637773|ref|YP_977996.1|  [L=222]
Description: hypothetical protein BCG_1906c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1576.43
//
Query:       gi|121637774|ref|YP_977997.1|  [L=129]
Description: hypothetical protein BCG_1907c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-39  134.1   0.1    3.4e-39  133.9   0.1    1.0  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.1   1.9e-43   3.4e-39       2     129 ..       8     128 ..       7     129 .] 0.97

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.9e-43
                                    XXXXXXXXXXXXX.XXTTXTTS---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEE CS
                F420H2_quin_red   2 lReqvaiyrrteg.kvgrrlegvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevq 80 
                                    +Re+v++++r+ +  +gr+l++   ++L+t+Grktg+pr+t++g++  ++++++v+++g   +h+++++N+kanP+v+v+
  gi|121637774|ref|YP_977997.1|   8 KREFVHRVQRFVVnPIGRQLPM---TMLETIGRKTGQPRRTAVGGRVVDNQFWMVSEHG---EHSDYVYNIKANPAVRVR 81 
                                    69**********999*****99...**********************************...****************** PP

                                    ETTEEEEEEEEE--.HHHHHHHHHHHHHH-THHHHHHHHHSSTS-EEEEE CS
                F420H2_quin_red  81 vgakkldvtAreve.ddekarlwklvvenspsYadyqsktdreipvvVle 129
                                    +g++++++tA+ ++ dd+++rl+ l++ ns++  +++++td  ++++V++
  gi|121637774|ref|YP_977997.1|  82 IGGRWRSGTAYLLPdDDPRQRLRGLPRLNSAG--VRAMGTD-LLTIRVDL 128
                                    **************999***************..*******.9*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 931.15
//
Query:       gi|121637775|ref|YP_977998.1|  [L=414]
Description: L-lactate dehydrogenase (cytochrome) lldD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.3e-123  411.6   0.0   2.7e-123  411.4   0.0    1.0  1  FMN_dh        FMN-dependent dehydrogenase
     0.0021   17.5   1.4     0.0035   16.8   1.4    1.3  1  NMO           Nitronate monooxygenase
     0.0023   17.0   1.5      0.049   12.6   0.8    2.5  3  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0038   16.4   0.2      0.006   15.8   0.2    1.2  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.4   0.0    6e-127  2.7e-123       1     347 [.      44     402 ..      44     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.4 bits;  conditional E-value: 6e-127
                                    HHCCS-HHHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHH CS
                         FMN_dh   1 ArkrlpkkafayvaggagdevtlrenraaferirlrprvlrdvskvdlsttllGqklslPvliaPvglaklahpdgelal 80 
                                    A++r p++af+y +g+a+de ++++ r+ f++i+++p +lrdv++v +  ++lGq+  lP++iaP+g+++l+h +ge+a 
  gi|121637775|ref|YP_977998.1|  44 AKRRTPRAAFDYADGAAEDELSIARARQGFRDIEFHPTILRDVTTVCAGWNVLGQPTVLPFGIAPTGFTRLMHTEGEIAG 123
                                    89****************************************************************************** PP

                                    HHHHHHHTS-EEEETT-SS-HHHHHHH.HTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT CS
                         FMN_dh  81 araaakagipfvlstvastsleevaaa.aegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerdlrng 159
                                    araaa+agipf lst+a++++e+++ a  +g++wfqly+++dr+ +++l++ra+aag++++++tvD+pv+g R rd+rng
  gi|121637775|ref|YP_977998.1| 124 ARAAAAAGIPFSLSTLATCAIEDLVIAvPQGRKWFQLYMWRDRDRSMALVRRAAAAGFDTMLVTVDVPVAGARLRDVRNG 203
                                    ***********************98752667************************************************* PP

                                    --BSTT-T.G.TTGGGSTSGSCCTTH.............THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE-SHH CS
                         FMN_dh 160 fslppklklrnllqelakpewaaeal...........kkasaaaefvgkqldpsltwddikwlreqtklplvvKGvltae 228
                                    +s+pp+l+lr++l+++++p+w  + l           +   + +e++++++dpslt+dd++w+++q++++lvvKG++t +
  gi|121637775|ref|YP_977998.1| 204 MSIPPALTLRTVLDAMGHPRWWFDLLtteplafasldRWPGTVGEYLNTVFDPSLTFDDLAWIKSQWPGKLVVKGIQTLD 283
                                    ************************999*****999844444445************************************ PP

                                    HHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                         FMN_dh 229 dakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                    da+ +v+ Gvdgiv+SNHGGRqld ap +++ Lp++++++g+++e+lvD Gi++G+D++ A+alGA++ l+GR++lygl+
  gi|121637775|ref|YP_977998.1| 284 DARAVVDRGVDGIVLSNHGGRQLDRAPVPFHLLPHVARELGKHTEILVDTGIMSGADIVAAIALGARCTLIGRAYLYGLM 363
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCGGEE CS
                         FMN_dh 309 agGeeGvervleilraelertmallGvksvaeldrslls 347
                                    agGe+Gv+r++eil++ + rtm+llGv+ ++el++++++
  gi|121637775|ref|YP_977998.1| 364 AGGEAGVNRAIEILQTGVIRTMRLLGVTCLEELSPRHVT 402
                                    ***********************************9986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.4   7.9e-07    0.0035     137     227 ..     273     360 ..     262     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.9e-07
                            NMO 137 vvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLal 214
                                     +++  i + ++ar+v  rG D +++  ++ GG q ++++     f+L+p+v+  +     ++   Gi+ + ++ aa+al
  gi|121637775|ref|YP_977998.1| 273 KLVVKGIQTLDDARAVVDRGVDGIVL--SNHGGRQLDRAPV---PFHLLPHVARELGkhTEILVDTGIMSGADIVAAIAL 347
                                    57788999*****************9..589****988874...8*******998877899999**************** PP

                            NMO 215 GAsgvqigtrfLl 227
                                    GA    ig ++L 
  gi|121637775|ref|YP_977998.1| 348 GARCTLIGRAYLY 360
                                    **********996 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.023     1e+02     134     170 ..     261     296 ..     256     305 .. 0.82
   2 !   12.6   0.8   1.1e-05     0.049     207     238 ..     326     357 ..     314     372 .. 0.85
   3 ?   -1.6   0.0      0.23     1e+03     298     327 ..     369     398 ..     360     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.023
                                    HHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 134 eavkeikkkveeveviaGnvataegakaLieagadav 170
                                    + +++ik++++  ++++  + t + a+a+++ g+d++
  gi|121637775|ref|YP_977998.1| 261 DDLAWIKSQWP-GKLVVKGIQTLDDARAVVDRGVDGI 296
                                    67889999996.556666699999*********9998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                                    T-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 207 gvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                      +++ D Gi +  div A+a+Ga + ++G+ 
  gi|121637775|ref|YP_977998.1| 326 HTEILVDTGIMSGADIVAAIALGARCTLIGRA 357
                                    468999************************85 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.23
                                    -HHHHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 298 svkevveqlvgglrsgmgylGaktieelke 327
                                     v++ +e l +g+  +m  lG++ +eel  
  gi|121637775|ref|YP_977998.1| 369 GVNRAIEILQTGVIRTMRLLGVTCLEELSP 398
                                    57889999*****************99975 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.3e-06     0.006     269     307 ..     321     359 ..     317     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    TT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                   Glu_synthase 269 eglrdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                     +l ++ ++ +d g+++gad+v a+alGA    ig+a l
  gi|121637775|ref|YP_977998.1| 321 RELGKHTEILVDTGIMSGADIVAAIALGARCTLIGRAYL 359
                                    67889999************************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2938.33
//
Query:       gi|121637776|ref|YP_977999.1|  [L=145]
Description: hypothetical protein BCG_1909 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-55  186.4   0.0    2.1e-55  186.2   0.0    1.0  1  DUF1810   Protein of unknown function (DUF1810)


Domain annotation for each model (and alignments):
>> DUF1810  Protein of unknown function (DUF1810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2   0.0   1.2e-59   2.1e-55       2     136 .]       8     142 ..       7     142 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 1.2e-59
                                    T-THHHHHHHTTTHHHHHHHHHTT---SS-HHHHS--BTTS--SHHHHHTSB-SHHHHHHHHHSTTHHHHHHHHHHHHHH CS
                        DUF1810   2 fdlerFveaqekvyetalaelkaGrkrshwmWfvFPqlkglgksetaerYaiesleearaylahpvLgkrlreitealla 81 
                                    fdl+rFv aq+ vy+++++el+aGrkr hwmWfvFPql+glg+s+ a rY+i+sleea+ayl+h++Lg+rl+e+t ++++
  gi|121637776|ref|YP_977999.1|   8 FDLKRFVYAQAPVYRSVVEELRAGRKRGHWMWFVFPQLRGLGSSPLAVRYGISSLEEAQAYLQHDLLGPRLHECTGLVNQ 87 
                                    89****************************************************************************** PP

                                    --S--HHHHS-TTHHHHHHHHHHHHHHH-S--HHHHHHHHHHSTT---HHHHHHH CS
                        DUF1810  82 leeksaeeilGsidalKlrssmtLFaevaedekvfkevldkyfdgerdeaTlell 136
                                    ++++s+eei+G +d+lKl+ssmtLFa+++++++ f ++l+ky+ g +d++T++ll
  gi|121637776|ref|YP_977999.1|  88 VQGRSIEEIFGPPDDLKLCSSMTLFARATDANQDFVALLAKYYGGGEDRRTVALL 142
                                    ***************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 801.82
//
Query:       gi|121637777|ref|YP_978000.1|  [L=228]
Description: hypothetical protein BCG_1910 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   27.3   0.1    5.9e-05   24.1   0.0    2.1  2  EthD      EthD domain
  ------ inclusion threshold ------
      0.087   13.3   0.0       0.14   12.6   0.0    1.4  1  MmlI      Methylmuconolactone methyl-isomerase
       0.17   11.9   0.0       0.25   11.4   0.0    1.2  1  RTX_C     RTX C-terminal domain


Domain annotation for each model (and alignments):
>> EthD  EthD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   1.1e+03       9      64 ..       9      62 ..       3      80 .. 0.69
   2 !   24.1   0.0   9.9e-09   5.9e-05       2      80 ..     121     193 ..     120     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                   HHHHHHTHHHHHCTSTT.............--EEEEEEEEEBTTC--SEEEEEEEEE CS
                           EthD  9 rdyweevHaplvkdllg.girryvlratktrpateagvalagpgsdadyDgiaelwf 64
                                    d+ +++ a+++ +llg g+   + +    r+ t +   +++++  ++  +++ lw 
  gi|121637777|ref|YP_978000.1|  9 DDWCARQRAQVADALLGlGVAGLSIN---VRDSTVRDSLMTLTTLYPPVAAVVSLWT 62
                                   56667777788888888667777766...6677777777899999999999999997 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 9.9e-09
                                    -S-HHHHHHHHHHTHHHHHCTSTT............--EEEEEEEEEBTTC--SEEEEEEEEE.....SSHHHHHHHHCS CS
                           EthD   2 glspeeFrdyweevHaplvkdllggirryvlratktrpateagvalagpgsdadyDgiaelwf.....dsleaflaafad 76 
                                    gl+++++ ++w++ H++++++ ++           t+ +t++ v++a++++ ++  gi+e +f      +l af+ a +d
  gi|121637777|ref|YP_978000.1| 121 GLDQATWLTRWQRDHTQVAIEAQA-----------TFGYTQNWVVRALTPEAPGIAGIVEELFpvaatTDLKAFFGAADD 189
                                    89**********************...........899*************************88665588888888888 PP

                                    HHHH CS
                           EthD  77 peya 80 
                                     + +
  gi|121637777|ref|YP_978000.1| 190 NDLR 193
                                    7765 PP

>> MmlI  Methylmuconolactone methyl-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05      0.14       4      48 ..     112     156 ..     110     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                           MmlI   4 rlgllsrredlsheqflahwrevhaplvhavtGlrryqqnrvvde 48 
                                    +++ll r+++l +  +l++w++ h +++ +      y qn vv  
  gi|121637777|ref|YP_978000.1| 112 NIALLRRPDGLDQATWLTRWQRDHTQVAIEAQATFGYTQNWVVRA 156
                                    6899*************************************9975 PP

>> RTX_C  RTX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.25     119     143 ..     188     211 ..     174     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                          RTX_C 119 qkknlsndieklisstsaftssska 143
                                    + ++l+n i+++++stsaf++++  
  gi|121637777|ref|YP_978000.1| 188 DDNDLRNRISRMVASTSAFGANQ-N 211
                                    5689****************987.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.59
# Mc/sec: 1172.10
//
Query:       gi|121637778|ref|YP_978001.1|  [L=147]
Description: hypothetical protein BCG_1911 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-09   37.6   0.1    3.5e-09   36.7   0.1    1.4  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.9e-13   3.5e-09       3      87 ..       6      91 ..       4      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.9e-13
                                   HHHHHHHHHSSEEEEEEEETTSEEEEEEEE..EEEETTT.TEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEE CS
                 Putative_PNPOx  3 eelreflaeskavvlATvdedGrPnvspvl..lkagdgr.dgivfatnadsrklrnleenprvallflddelgrgvrieGta 81
                                   e+++ + ae+ ++v++Tv++dG++++s+v+  l +++   +  + +t +   kl+nl++ p+ a++f +    ++ ++eG+a
  gi|121637778|ref|YP_978001.1|  6 EAAALAAAERGLAVVSTVRADGTVQASLVNvgLLPHPVSgEPSLGFTTYGKVKLGNLRARPQLAVTFRNGW--QWATVEGRA 85
                                   55566667889*****************994455555557666778899******************9999..9******** PP

                                   EEESCH CS
                 Putative_PNPOx 82 elvsdg 87
                                   +lv ++
  gi|121637778|ref|YP_978001.1| 86 QLVGPD 91
                                   **9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 798.39
//
Query:       gi|121637779|ref|YP_978002.1|  [L=159]
Description: bacterioferritin bfrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-35  121.1   3.1    3.6e-35  121.0   3.1    1.0  1  Ferritin  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   3.1     2e-39   3.6e-35       3     141 ..      10     143 ..       8     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 2e-39
                                    HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS.SH CS
                       Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg.sv 81 
                                    +Lneql+ elta++qy+ ++ + +++g+ +la++ + ++ +e+ ha+++ +ril l+g p+ +r+   +i      g ++
  gi|121637779|ref|YP_978002.1|  10 LLNEQLTSELTAINQYFLHSKMQDNWGFTELAAHTRAESFDEMRHAEEITDRILLLDGLPNYQRIGSLRI------GqTL 83 
                                    8*********************************************************************......99** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                    +e++ea+l+ e++v ++l+ +i +++e++D ++a +le++++++eeh++ le++le +++
  gi|121637779|ref|YP_978002.1|  84 REQFEADLAIEYDVLNRLKPGIVMCREKQDTTSAVLLEKIVADEEEHIDYLETQLELMDK 143
                                    ********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 883.57
//
Query:       gi|121637780|ref|YP_978003.1|  [L=511]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-34  117.8  36.7    3.4e-33  115.0  36.7    1.8  1  MFS_1        Major Facilitator Superfamily
    4.4e-16   58.8  12.6    4.4e-16   58.8  12.6    1.6  2  Sugar_tr     Sugar (and other) transporter
    7.1e-13   47.8  18.9    1.5e-12   46.8  18.9    1.4  1  TRI12        Fungal trichothecene efflux pump (TRI12)
    2.9e-05   23.1   5.7    5.5e-05   22.2   5.7    1.4  1  MFS_1_like   MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0  36.7   7.6e-37   3.4e-33       1     231 [.      33     264 ..      33     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 7.6e-37
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l+++++++a++ +i+ palp ++  +lg++++ +++++t y lg  v ++++G l+d +Gr rvll ++++f++g++l+ 
  gi|121637780|ref|YP_978003.1|  33 LVFGVLVAATGQTIVVPALP-TIVAELGSTVD-QSWAVTSYLLGGTVVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCG 110
                                    57999***************.9******5555.6*****************************************66666 PP

                          MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                    +++++++l+++r+lqG+gaga+  +++al+a+++p ++rgr+ g+l+a f++ ++ gpllgg+l+++l+Wr++f+i+ +v
  gi|121637780|ref|YP_978003.1| 111 LSQTMTMLAISRALQGVGAGAISVTAYALAAEVVPLRDRGRYQGVLGAVFGVNTVTGPLLGGWLTDYLSWRWAFWINVPV 190
                                    666777************************************************************************** PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeee........kgtgpaplvpawkallkdpvlw..illialllfffgfsglltll 230
                                    s+ ++ +++  +p+ ++++k++ +            +    +++    ++       w  + +++ll+++++  g++++l
  gi|121637780|ref|YP_978003.1| 191 SIAVLTVAATAVPALARPPKPVIDYLGIlviavattALIMATSWGG-TTYA------WgsATIVGLLIGAAVALGFFVWL 263
                                    ****885555555555555555444442333222222222222222.3333......45447777777777777777777 PP

                          MFS_1 231 p 231
                                     
  gi|121637780|ref|YP_978003.1| 264 E 264
                                    5 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8  12.6   9.7e-20   4.4e-16      44     187 ..      60     197 ..      26     204 .. 0.83
   2 ?   -5.5   2.7       3.2   1.4e+04     349     349 ..     242     242 ..     216     263 .. 0.34

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 9.7e-20
                                    ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                       Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                    s+v++++ v ++l+G+++  ++ag+lgd +GR  +ll ++v+fv+g+vl+++++   ++ +l+++R l G+g+G++sv++
  gi|121637780|ref|YP_978003.1|  60 STVDQSWAVTSYLLGGTVVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCGLSQ---TMTMLAISRALQGVGAGAISVTA 136
                                    89****************************************************...9********************** PP

                                    HHHHHTTS-SCCH....HHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                       Sugar_tr 124 PmyisEiApkklR....galvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                      +++E+ p + R    g l+ ++ + +++G l++ ++     ++ +   wr+ +++++  ++++l +
  gi|121637780|ref|YP_978003.1| 137 YALAAEVVPLRDRgryqGVLGAVFGVNTVTGPLLGGWL----TDYLS---WRWAFWINVPVSIAVLTV 197
                                    *********99993333456777777777777777665....45555...999999999988887655 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 3.2
                                    C CS
                       Sugar_tr 349 s 349
                                    +
  gi|121637780|ref|YP_978003.1| 242 G 242
                                    1 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8  18.9   3.3e-16   1.5e-12      51     292 ..      37     265 ..      18     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3.3e-16
                          TRI12  51 lnvvatyfvlqasasalpnilqdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatk 130
                                    + v+at         alp i+ ++g + ++s   t + +g +v ++v g+l d +gr  +++ + ++ +vg+++   ++ 
  gi|121637780|ref|YP_978003.1|  37 VLVAATG--QTIVVPALPTIVAELGSTVDQSWAVTSYLLGGTVVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCGLSQT 114
                                    4444443..3345679*****************************************99999999999999877555555 PP

                          TRI12 131 fntllaamtllgvaagpagaspl.fvgel..msnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsa 207
                                    +  l  + +l gv ag    +   +  e+  + ++ ++ g+l     v +++  +p lg  l+   swrw f+i + +s 
  gi|121637780|ref|YP_978003.1| 115 MTMLAISRALQGVGAGAISVTAYaLAAEVvpLRDRGRYQGVLGAVFGVNTVT--GPLLGGWLTDYLSWRWAFWINVPVS- 191
                                    55555567899*****988766514567723468899***998776665555..9*******************98776. PP

                          TRI12 208 iavllivvwyyppsfaqlhgkkvrkreelakldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvf 287
                                    iavl +      p++a         r     +d++gi++++v ++ +++  swgg     w sa ++gl+   + +l  f
  gi|121637780|ref|YP_978003.1| 192 IAVLTVAATAV-PALA---------RPPKPVIDYLGILVIAVATTALIMATSWGGTT-YAWGSATIVGLLIGAAVALGFF 260
                                    78876655444.4443.........4555679***********************86.57**********9999999888 PP

                          TRI12 288 alyev 292
                                       e 
  gi|121637780|ref|YP_978003.1| 261 VWLEG 265
                                    87765 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   5.7   1.2e-08   5.5e-05     275     383 ..      77     184 ..      60     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-08
                     MFS_1_like 275 plfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgll 354
                                    ++ ++a kl + lG  ++l+ +++++++  +l ++ + + ++ +  +L+g+  g++ ++a   +++++p + ++++qg+l
  gi|121637780|ref|YP_978003.1|  77 VVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCGLSQTMTMLAISRALQGVGAGAISVTAYALAAEVVPLRDRGRYQGVL 156
                                    6678999************************************************************************9 PP

                     MFS_1_like 355 sglyfglGralGsliGGllwdlksaiflF 383
                                     ++ fg+ +  G l+GG l d+ s +++F
  gi|121637780|ref|YP_978003.1| 157 GAV-FGVNTVTGPLLGGWLTDYLSWRWAF 184
                                    877.*****************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3048.97
//
Query:       gi|121637781|ref|YP_978004.1|  [L=404]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-05   24.0  20.8      4e-05   22.7  19.9    1.8  2  MFS_1     Major Facilitator Superfamily
     0.0014   17.2   3.4     0.0058   15.1   3.3    1.9  1  TRI12     Fungal trichothecene efflux pump (TRI12)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7  19.9   4.5e-09     4e-05     214     352 ..       4     142 ..       1     143 [. 0.82
   2 ?   -0.3   0.0     0.044   3.9e+02     152     174 ..     199     219 ..     174     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.5e-09
                          MFS_1 214 ialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                                    + +++++f++ g+lt++p+yl  v g s +  +gl    + ++ +i++  +g l+ r+gr  + ++ +++++l+a++++l
  gi|121637781|ref|YP_978004.1|   4 VLSFVVGFAMLGALTFVPIYLGYVDGAS-ATASGLRTLPMVIGLLIASTGTGVLVGRTGR--YKIFPVAGMALMAVAFLL 80 
                                    456677779999****************.455555555555555555669*******999..899999999999999999 PP

                          MFS_1 294 lavt...ssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    ++     + ++l  l lv++G g g+ +  l  ++++  + e  g a++ +++++ +g+++g
  gi|121637781|ref|YP_978004.1|  81 MSQMdewTPPLLQSLYLVVLGAGIGLSMQVLVLIVQNTSSFEDLGVATSGVTFFRVVGASFG 142
                                    99996556666666699999999999999999999999999******************998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.044
                          MFS_1 152 avfyilaivsllafvlfllllpe 174
                                     vf+ +  v++++f+l  +ll++
  gi|121637781|ref|YP_978004.1| 199 QVFLCAVSVTVVGFIL--ALLLR 219
                                    4666666677777666..33333 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.3   6.4e-07    0.0058     413     480 ..      98     165 ..      49     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.4e-07
                          TRI12 413 vlsgfvvawaqditmllvqfittdedlgvafavvaaarpfagsiftaafislysnrypkelashlssa 480
                                    v+ g  ++ + ++ +l+vq  ++ edlgva + v+  r +  s  ta+f +l+ n   + l+s l+s 
  gi|121637781|ref|YP_978004.1|  98 VVLGAGIGLSMQVLVLIVQNTSSFEDLGVATSGVTFFRVVGASFGTATFGALFVNFLDRRLGSALTSG 165
                                    44577788999999**************************99***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2795.54
//
Query:       gi|121637782|ref|YP_978005.1|  [L=450]
Description: glutamine synthetase glnA3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-65  221.9   0.0    1.7e-65  221.3   0.0    1.2  1  Gln-synt_C  Glutamine synthetase, catalytic domain
  ------ inclusion threshold ------
       0.13   12.2   1.5       0.28   11.0   0.9    1.8  2  R_equi_Vir  Rhodococcus equi virulence-associated protein


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.3   0.0   1.9e-69   1.7e-65       2     333 ..     112     432 ..     111     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.3 bits;  conditional E-value: 1.9e-69
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                    ++ R +l r +a la+ G+++v+g E+EF+l+d + ++                p++  + + va v e+e ++r++ +a
  gi|121637782|ref|YP_978005.1| 112 ACSRGTLSRIEAALADAGIDAVIGHEVEFLLVDADGQRL---------------PSTLWAQYGVAGVLEHEAFVRDVNAA 176
                                    689******************************887743...............34456779999999************ PP

                                    HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT CS
                     Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg 161
                                    ++a+gi +e++h E++  Q+Ei+l ++ +++aaD++v+++ ++  +Ar+hgl++++ p p++g+ Gsg H h+Sl   ++
  gi|121637782|ref|YP_978005.1| 177 ATAAGIAIEQFHPEYGANQFEISLAPQPPVAAADQLVLTRLIIGRTARRHGLRVSLSPAPFAGSIGSGAHQHFSLT-MSE 255
                                    ****************************************************************************.777 PP

                                    EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-...TSGGCST CS
                     Gln-synt_C 162 knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa...skekakr 238
                                      lf++ +++ ++++ ++ +++G+l+ +++   +++ ++ S  R+ pg +a+++++wg++NR+a++R +    +++ +  
  gi|121637782|ref|YP_978005.1| 256 GMLFSGGTGAAGMTSAGEAAVAGVLRGLPDAQGILCGSIVSGLRMRPGNWAGIYACWGTENREAAVRFVKggaGSAYGGN 335
                                    88*******999*******************************************************999888888999* PP

                                    EEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-H CS
                     Gln-synt_C 239 vElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlge 316
                                    vE++++d+saNPYLa Aa+l  +ldG+++k  ++ +++ d  +ls+ +r  +gi +l+a+  +A+  l++++ll+ +lg+
  gi|121637782|ref|YP_978005.1| 336 VEVKVVDPSANPYLASAAILGLALDGMKTKAVLPSETTVDPTQLSDVDRdrAGILRLAADQADAIAVLDSSKLLRCILGD 415
                                    *********************************************999999***************************** PP

                                    HHHHHHHHHHHHCHHHH CS
                     Gln-synt_C 317 evieaylalkraEleel 333
                                     v++a +a+++ E e++
  gi|121637782|ref|YP_978005.1| 416 PVVDAVVAVRQLEHERY 432
                                    *************9998 PP

>> R_equi_Vir  Rhodococcus equi virulence-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   3.1e-05      0.28      87     119 ..     246     280 ..     238     285 .. 0.90
   2 ?   -3.3   0.0      0.79   7.1e+03      17      44 ..     350     377 ..     338     392 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                                    EEEEEEEECT--EEEEEEE..CEE-SEEEEEEEEE CS
                     R_equi_Vir  87 YqklkisvdggktFdGdaG..GlsiPGaaalwGtL 119
                                     q++++++ +g+ F G +G  G++  G aa++G+L
  gi|121637782|ref|YP_978005.1| 246 HQHFSLTMSEGMLFSGGTGaaGMTSAGEAAVAGVL 280
                                    69**************877669***********99 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.79
                                    XXXXXX..XXXXXXXXXXXXXXXXXXXX CS
                     R_equi_Vir  17 aaaivlllapagvanarvlassatsalq 44 
                                    a a++l la+ g+++ +vl s++t++ +
  gi|121637782|ref|YP_978005.1| 350 ASAAILGLALDGMKTKAVLPSETTVDPT 377
                                    3444455799999999999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3008.43
//
Query:       gi|121637783|ref|YP_978006.1|  [L=378]
Description: hypothetical protein BCG_1916 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-13   48.7   1.7    1.9e-12   47.6   1.7    1.6  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   1.7     1e-16   1.9e-12     132     291 .]     216     375 ..     139     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1e-16
                                    HHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCE CS
                   Amidohydro_2 132 rpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyv 211
                                    r ++  + +lg p+++h+G      fg+++++++  +pl+l +++r   n++ivl H+       r+a +l+  ++nvy+
  gi|121637783|ref|YP_978006.1| 216 RFGLHQALRLGKPLQFHVG------FGDRDADLHKANPLYLLDFLRQSGNTPIVLLHCYPY---EREAGYLAQAFNNVYL 286
                                    4444445569*********......*********************************777...***************9 PP

                                    EECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH..............SSHHHH CS
                   Amidohydro_2 212 klsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval..............lsdeer 277
                                    + +      +     +  p ++ rl+e+++  +i+++sD + p++ + ++a  ++ ++++                  ++
  gi|121637783|ref|YP_978006.1| 287 DGGL-----SVHYLGARSPAFIGRLLELAPFRKIVYSSDGFGPAELHFLGATLWRSGIQRvlrgfverddwcetDALRVV 361
                                    9977.....555667777888********************************99999999**********999999999 PP

                                    HHHHTHHHHHHCTB CS
                   Amidohydro_2 278 ekilggNAarlygl 291
                                    + i++g+Aar+y+l
  gi|121637783|ref|YP_978006.1| 362 DLIAHGTAARIYRL 375
                                    ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2609.94
//
Query:       gi|121637784|ref|YP_978007.1|  [L=438]
Description: cytochrome p450 140 CYP140 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  113.2   0.1    3.9e-28   98.4   0.4    3.0  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0   0.00029       5.2      87     134 ..     111     158 ..      95     178 .. 0.87
   2 !   98.4   0.4   2.2e-32   3.9e-28     227     433 ..     226     402 ..     206     406 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00029
                                    STTCGHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCC CS
                           p450  87 vlfangekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkag 134
                                    +l  +++++++ R+++ + +ts  +  +l++lve+ a +l++++ ++ g
  gi|121637784|ref|YP_978007.1| 111 LLAVEPPDHTRYRKTVSAVFTSR-AVsALRDLVEQTAINLLDRFAEQPG 158
                                    55667799***************.666****************999866 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 2.2e-32
                                    HHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHH CS
                           p450 227 rretldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidev 306
                                    + ++l+ a     d+++ l++  +  ++e++l+++el+a ++ +l+aG++Tt + l  ++  L+++Pe+ + lr+     
  gi|121637784|ref|YP_978007.1| 226 HLQQLRHA--PGDDLMSQLIQIAESGDNETQLDETELRAIAGLVLVAGFETTVNLLGNGIRMLLDTPEHLATLRQH---- 299
                                    66667777..77899999999984455558*******************************************987.... PP

                                    CCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GG CS
                           p450 307 lgdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpe 386
                                                   ++  ++++E+LRl ++v  l+ R++ +dv++ g+ i+ G +v+++l a +rdp+vfp+P++Fd+e
  gi|121637784|ref|YP_978007.1| 300 --------------PELWPNTVEEILRLDSPVQ-LTARVACRDVEVAGVRIKRGEVVVIYLAAANRDPAVFPDPHRFDIE 364
                                    ..............368999*************.99******************************************** PP

                                    GGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHE CS
                           p450 387 RFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnF 433
                                    R +           ++l+F++G++ C+G  lAr e ++ l t++ +F
  gi|121637784|ref|YP_978007.1| 365 RPNAG---------RHLAFSTGRHFCLGAALARAEGEVGLRTFFDRF 402
                                    *9888.........47***************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3003.08
//
Query:       gi|121637785|ref|YP_978008.1|  [L=140]
Description: lipoprotein lppE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-28   98.2   0.1    5.2e-28   97.7   0.1    1.3  1  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
  ------ inclusion threshold ------
        2.8    7.9   6.3       0.25   11.2   1.8    1.6  2  LPAM_2       Prokaryotic lipoprotein-attachment site


Domain annotation for each model (and alignments):
>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1   5.8e-32   5.2e-28       2     116 .]      27     140 .]      26     140 .] 0.96

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 5.8e-32
                    Myco_19_kDa   2 aapagtatvtvdGqdlqttgsvtCtqaggaltiaigdgasgvsavlt.dgdeptvesvgigdvdGftltyaegtgggsae 80 
                                    + p+++a++t+dG + +tt++ tC+q++++ ti+i++++s+v+av+  +gd++  ++v+i++vdGf++++++g +g+ a+
  gi|121637785|ref|YP_978008.1|  27 TVPRKAARLTIDGVT-HTTRPATCSQEHSYRTIDIRNHDSTVQAVVLlSGDRVIPQWVKIRNVDGFNGSFWHGGVGN-AR 104
                                    67899********99.67*****************989*********9*************************9998.** PP

                    Myco_19_kDa  81 vtkdgntYtitGtaegadsanpaqpvtktFeievtC 116
                                    + +++ntYt+ G+a+g+ s++p++ v+++F+i ++C
  gi|121637785|ref|YP_978008.1| 105 ADRARNTYTVAGSAYGISSKKPNTVVSTDFNILAEC 140
                                    **********************************99 PP

>> LPAM_2  Prokaryotic lipoprotein-attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   2.8e-05      0.25       4      16 ..      12      24 ..      11      24 .. 0.90
   2 ?   -3.0   0.2      0.85   7.7e+03       8      13 ..      70      75 ..      69      75 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                         LPAM_2  4 llallllLaGCGq 16
                                   +++ +++L++CGq
  gi|121637785|ref|YP_978008.1| 12 AMVVAAGLSACGQ 24
                                   7899********9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.85
                         LPAM_2  8 lllLaG 13
                                   + lL+G
  gi|121637785|ref|YP_978008.1| 70 VVLLSG 75
                                   556666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1031.73
//
Query:       gi|121637786|ref|YP_978009.1|  [L=277]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-44  149.6   0.0    8.9e-44  149.3   0.0    1.1  1  adh_short     short chain dehydrogenase
    1.2e-33  116.7   0.3    1.4e-33  116.4   0.3    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    0.00038   20.4   0.1    0.00071   19.5   0.1    1.4  1  KR            KR domain
  ------ inclusion threshold ------
      0.084   12.8   0.2       0.17   11.7   0.2    1.5  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.0     2e-47   8.9e-44       1     193 [.       2     194 ..       2     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 2e-47
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH.HHHHH.SSE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvek.avkkl.gkl 78 
                                    k++++tGa+sG+Gr+ a  + ++G++v ++dr+e+ l+++  +l++e  +++a +vDvtd++++e ++++ ++ ++ g+l
  gi|121637786|ref|YP_978009.1|   2 KAIFITGAGSGMGREGATLFHANGWRVGAIDRNEDGLAALRVQLGAE--RLWARAVDVTDKAALEGALADfCAGNVgGGL 79 
                                    789******************************************96..8**************98776615555599** PP

                                    SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHH CS
                      adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavag 158
                                    d++ nNAGi + g f+++  e+  rv++vN+++v+  + a+lp+++k+ +     +sS  g ++++  a+YsA+K+av+g
  gi|121637786|ref|YP_978009.1|  80 DMMWNNAGIGEGGWFEDVPYEAAVRVVDVNFKAVLTGAYAALPYLKKAPGSLMFSTSSSSGTYGMPRIAVYSATKHAVKG 159
                                    ********************************************99999999999************************* PP

                                    HHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                      adh_short 159 ltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                    lt++l+ e++++g+rv  v PGl+dT++ +++r++
  gi|121637786|ref|YP_978009.1| 160 LTEALSVEWQRHGVRVADVLPGLIDTAILTSTRQH 194
                                    ****************************9998876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.3   3.2e-37   1.4e-33       1     184 [.       8     193 ..       8     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 3.2e-37
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHH..SSEEEEEE CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v..lecDVtdeeqvealveevvekf..gklDilvn 75 
                                    Ga sg+Gr+ A +++++G++v + d+ne++   +++l  +lgae +   ++DVtd++++e + ++  +    g+lD++ n
  gi|121637786|ref|YP_978009.1|   8 GAGSGMGREGATLFHANGWRVGAIDRNEDG---LAALRVQLGAErLwaRAVDVTDKAALEGALADFCAGNvgGGLDMMWN 84 
                                    889***************************...999999999887346************877765544448******** PP

                                    -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEE.EEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsiv.nlssvgaervvpnynaygaaKaalealtr 153
                                    nagi +   g f++++ e   r++dvn+++++  a aalp++k+  gs++  +ss +++ ++p  ++y+a+K+a+++lt 
  gi|121637786|ref|YP_978009.1|  85 NAGIGEG--GWFEDVPYEAAVRVVDVNFKAVLTGAYAALPYLKKApGSLMfSTSSSSGTYGMPRIAVYSATKHAVKGLTE 162
                                    *******..*******************************998888886515678889999******************* PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikg 184
                                    +l ve+ ++g+Rv  v pg+i+T + ++ ++
  gi|121637786|ref|YP_978009.1| 163 ALSVEWQRHGVRVADVLPGLIDTAILTSTRQ 193
                                    ***********************99766654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.6e-07   0.00071       5     161 ..       6     162 ..       3     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                                    EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-.EEEE----TT-HHHHHHHHHHHHHHS..S CS
                             KR   5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.ga.evevvaaDvsdkdavealleeikaee..p 80 
                                    itG+  g+G+e a+   ++g r +  + R+       ++ +a+l+ + ga +  ++a+Dv+dk+a+e +l+++ a +  +
  gi|121637786|ref|YP_978009.1|   6 ITGAGSGMGREGATLFHANGWR-VGAIDRN-------EDGLAALRVQlGAeRLWARAVDVTDKAALEGALADFCAGNvgG 77 
                                    6666666666666666666644.3444444.......44566666554765788999****************9988889 PP

                                    ---EEEE---------TTT--HHHHHHH....HTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  81 pikGvihaAgvlrdklleemtaedleqv....lapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156
                                     +    + Ag+ + + +e++  e+  +v    +++ ++Ga     +l++ +  ++  +SS +g++g++  a Y+a+ + +
  gi|121637786|ref|YP_978009.1|  78 GLDMMWNNAGIGEGGWFEDVPYEAAVRVvdvnFKAVLTGAYAALPYLKKAPGSLMFSTSSSSGTYGMPRIAVYSATKHAV 157
                                    9**********************99998222235567888888899999**************************99988 PP

                                    HHHHH CS
                             KR 157 Dalae 161
                                     +l e
  gi|121637786|ref|YP_978009.1| 158 KGLTE 162
                                    77765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.9e-05      0.17       3      44 ..       5      47 ..       3      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                   EEE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N  3 aviGaGt.mGagiaavfasagleVvlvdiseealekalekiek 44
                                    + GaG  mG++ a++f ++g +V  +d++e+ l++ + ++ +
  gi|121637786|ref|YP_978009.1|  5 FITGAGSgMGREGATLFHANGWRVGAIDRNEDGLAALRVQLGA 47
                                   67899966************************99988777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1831.20
//
Query:       gi|121637787|ref|YP_978010.1|  [L=158]
Description: hypothetical protein BCG_1920c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-19   69.2   1.1    5.3e-19   68.9   1.1    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
      1e-11   45.2   0.0    1.2e-11   45.0   0.0    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   1.1   5.9e-23   5.3e-19       5     143 .]      10     156 ..       7     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.9e-23
                                    EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSE.STSSS...TTTEEEEECCCS...SEEEEEEEEEETTTTEEEE CS
                Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleg.gggpa...rgvegtvrvggr...gtvreelvevdpegrllsy 77 
                                    +++v+ aapp+k+w l++d +n  r +pe  ++e+ +   gpa   r++ g+vr +g     ++++e+++ +p gr +++
  gi|121637787|ref|YP_978010.1|  10 SATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDgATGPAlgaRFR-GHVRRNGIgpvYWTVCEVTACEP-GREFGF 87 
                                    789*******************************8875777779*6655.*******98886799999999**.****** PP

                                    EEE..SSS-TSEEEEEEEEECCETEEEEEEEEEEE........E--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  78 riv.kpvpvanyvatwtvtpdgggtrvtwtgefda........gplggpfekpaaakavkgdleagLerLkarle 143
                                     +  +++pv+   + +++tp+++gt+vt ++ + +          +gg+++     +   +d++++L+r+k ++e
  gi|121637787|ref|YP_978010.1|  88 AVLlGDRPVN--NWHYRLTPTADGTEVTESFRLPPsvlttvyyRVFGGWLR----QRRNIRDMTKTLQRIKDLVE 156
                                    **889*****..9****************9977753332222223334443....34555559999999998887 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   1.3e-15   1.2e-11       1     124 [.      15     138 ..      15     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.3e-15
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE....E.....EEECSTTSSCEEEEEEEEEEETTTEEECTTCCCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes.glsa.....dlevgfggltesftarvtldppeeitfklvegdf 74 
                                    ++ap+d+++ l+adv +  +f+p+  ++e+l+ a+  +l a       ++g g++  + ++   ++p +  +f +   + 
  gi|121637787|ref|YP_978010.1|  15 MAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGpALGArfrghVRRNGIGPVYWTVCEVTACEPGR--EFGFAVLLG 92 
                                    68*********************************8754455543333444444444445555555555..5******** PP

                                    CEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  75 kslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervlde 124
                                    ++ +++W+ +  p+   +++t+v+ ++++ + s l  +  + ++++ +++
  gi|121637787|ref|YP_978010.1|  93 DRPVNNWHYRLTPT---ADGTEVTESFRL-PPSVLTTVYYRVFGGWLRQR 138
                                    *************8...************.77777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1239.89
//
Query:       gi|121637788|ref|YP_978011.1|  [L=176]
Description: resuscitation-promoting factor rpfC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-34  116.6   7.5    8.8e-34  116.0   7.5    1.3  1  Transglycosylas  Transglycosylase-like domain
  ------ inclusion threshold ------
      0.081   12.6   0.0       0.17   11.5   0.0    1.6  1  SLT              Transglycosylase SLT domain


Domain annotation for each model (and alignments):
>> Transglycosylas  Transglycosylase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   7.5   9.8e-38   8.8e-34       4      77 .]      70     140 ..      67     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 9.8e-38
                                    HHHHHHHHHHHHSS-TT-TTSSSEBTTTTBEHHHHHHTTCCST.SCGGGS-HHHHHHHHHHHHHHHCGGGSTTC CS
                Transglycosylas   4 esnwdaiAqcEsggnwaintgnGyyGglqfsqstWeavggekyapsaaqAsreqQiavAekvlatqGagaWptc 77 
                                    + nwda+AqcEsggnwa+ntgnG yGglqf+++tW+a+gg++   ++a+AsreqQiavA++vla+qG++aWptc
  gi|121637788|ref|YP_978011.1|  70 SPNWDAVAQCESGGNWAANTGNGKYGGLQFKPATWAAFGGVG---NPAAASREQQIAVANRVLAEQGLDAWPTC 140
                                    689***************************************...****************************9 PP

>> SLT  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.9e-05      0.17      19      53 ..      75     109 ..      63     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHTT-TT-B-TTSEBTTTTBETTTHHHHHH CS
                            SLT  19 aiaqvESgfnpkAvsksgavGLmQimpstakrlgl 53 
                                    a+aq ESg+n  A  ++g +G  Q+ p+t  ++g 
  gi|121637788|ref|YP_978011.1|  75 AVAQCESGGNWAANTGNGKYGGLQFKPATWAAFGG 109
                                    89***************************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1199.21
//
Query:       gi|121637789|ref|YP_978012.1|  [L=199]
Description: chorismate mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.7   0.2    4.6e-10   39.7   0.1    1.9  2  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1   2.6e-14   4.6e-10      10      75 .]      41     110 ..      40     110 .. 0.92
   2 ?   -1.1   0.0      0.14   2.5e+03       1      13 [.     134     146 ..     134     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.6e-14
                                    HHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                           CM_2  10 eileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75 
                                    e+++  aeR+e+a+ v+++K +++lp++d +R +++l++l e+a    +d+++++r+f + i+a  a+++
  gi|121637789|ref|YP_978012.1|  41 ELVDAAAERLEVADPVAAFKWRAQLPIEDSGRVEQQLAKLGEDArsqhIDPDYVTRVFDDQIRATEAIEY 110
                                    899*****************98899*****************555567***************9999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHH CS
                           CM_2   1 RkeIdeiDdeile 13 
                                    R+ Id++++++l 
  gi|121637789|ref|YP_978012.1| 134 RSAIDSLNNRMLS 146
                                    8899999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1503.59
//
Query:       gi|121637790|ref|YP_978013.1|  [L=325]
Description: hypothetical protein BCG_1923c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-75  251.4   0.5    1.1e-74  251.2   0.5    1.0  1  Esterase  Putative esterase


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.2   0.5   6.4e-79   1.1e-74       1     251 []      55     318 ..      55     318 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.2 bits;  conditional E-value: 6.4e-79
                                    ETTTTEEEEEEEEE.CC.GGTTTEEEEEEE--T......THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSB CS
                       Esterase   1 SealgreikvqvyLPedyspgrkypvvylldGl......tgwdqnfrakelleslaregeiaeviivvvprggessfysd 74 
                                    S ++gr+ikvq++     s g++ p+vylldGl      +gwd+n++a+e++++++ +        +v+p+gg+ssfysd
  gi|121637790|ref|YP_978013.1|  55 SPSMGRDIKVQFQ-----SGGNNSPAVYLLDGLraqddyNGWDINTPAFEWYYQSGLS--------IVMPVGGQSSFYSD 121
                                    789**********.....99**************************************........************** PP

                                    TTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC. CS
                       Esterase  75 wdlgarfyenategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps. 153
                                    w+ +    +++++g++++++et lt+eL+++l an+ ++p+g a++G Sm+G++A+ila++hp++F +++s+S++++ps 
  gi|121637790|ref|YP_978013.1| 122 WYSP----ACGKAGCQTYKWETLLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSq 197
                                    ****....************************************************************************ PP

                                    ...................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCC CS
                       Esterase 154 ...................namWgqeekeawqendpvllakelsaslkalriyldvGtseddlgeqlsveilevlarnre 214
                                                       + mWg+++++aw++ndp+ ++++l+a++++l++y+ +Gt+++ +g + ++e+le+++r+++
  gi|121637790|ref|YP_978013.1| 198 gmgpsliglamgdaggykaADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSN 277
                                    ******************************************************************************** PP

                                    HHHHCCCCCCTT-SCCCC....--SSHHHHHHHHHHCHHHH CS
                       Esterase 215 lkeqlaargvegedheyd....GghsweyWraqLiaaladl 251
                                    lk+q a+++ +g++ +++    G+hsweyW aqL+a+++dl
  gi|121637790|ref|YP_978013.1| 278 LKFQDAYNAAGGHNAVFNfppnGTHSWEYWGAQLNAMKGDL 318
                                    *************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2364.43
//
Query:       gi|121637791|ref|YP_978014.1|  [L=380]
Description: hypothetical protein BCG_1924 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.62   10.5   0.0    2.1  1  DUF1964   Domain of unknown function (DUF1964)
        1.1    9.5   3.4         13    6.1   0.2    2.5  2  YbgS      YbgS-like protein


Domain annotation for each model (and alignments):
>> DUF1964  Domain of unknown function (DUF1964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.9e-05      0.62      16      49 ..      72     106 ..      62     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.9e-05
                                    EEEEEE-S.S-EEEEEE-GGGC-STT--S--EEEE CS
                        DUF1964  16 itfaWkge.tssatLtfePkrGlGvdnaapvasLr 49 
                                    i  +W++e +++a+L  e   G G dn  pv  Lr
  gi|121637791|ref|YP_978014.1|  72 IGVTWNAEaSAQAALLVESLTGAGFDNVVPVRRLR 106
                                    6789***95569*******************8886 PP

>> YbgS  YbgS-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3    0.0089        80      11      40 ..     208     233 ..     202     247 .. 0.68
   2 ?    6.1   0.2    0.0014        13       6      36 ..     260     290 ..     256     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0089
                           YbgS  11 aaltlgsGaalaadsnnGqansaadaGava 40 
                                    a +t++ Gaalaa++    + + +da  va
  gi|121637791|ref|YP_978014.1| 208 AQVTVARGAALAAAQ----STEFTDAQLVA 233
                                    6789********974....44444444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0014
                           YbgS   6 ilfltaaltlgsGaalaadsnnGqansaada 36 
                                     + + a+l+l+ G  la ++++G+a ++a+ 
  gi|121637791|ref|YP_978014.1| 260 AVTFVASLSLAVGIQLAPHNDTGTAKHGAHK 290
                                    566789*******************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2546.28
//
Query:       gi|121637792|ref|YP_978015.1|  [L=239]
Description: hypothetical protein BCG_1925c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-21   74.8  19.2    5.6e-13   48.6   7.6    2.7  3  DUF4389          Domain of unknown function (DUF4389)


Domain annotation for each model (and alignments):
>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   7.6   3.1e-17   5.6e-13       3      74 ..      22      95 ..      20      96 .. 0.92
   2 ?   -1.5   0.1      0.14   2.4e+03       8      23 ..     125     140 ..     119     151 .. 0.62
   3 !   33.9   0.9   1.2e-12   2.2e-08      21      73 ..     158     210 ..     139     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.1e-17
                        DUF4389  3 avwlRlllmllfaivlslaslvlwvvvvvqflivLvtgrpnepLrdfgksllrYiarilrflt..lnseekPfp 74
                                   + +++++l ++++ivl +++++++vv+v+ f+++L+tgr +++L+df  ++ r+ +r++ +++  l ++++P++
  gi|121637792|ref|YP_978015.1| 22 QWLVKWFLAIPHYIVLFFLHVAAVVVTVIAFFAILFTGRYPRTLFDFNVGVMRWRWRVAFYALsaLGTDRYPPF 95
                                   568899*****************************************************99863378*****65 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.14
                        DUF4389   8 lllmllfaivlslasl 23 
                                    +ll ++++ +l++  +
  gi|121637792|ref|YP_978015.1| 125 WLLAIPHYLILAVFLS 140
                                    4666777666666544 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 1.2e-12
                        DUF4389  21 aslvlwvvvvvqflivLvtgrpnepLrdfgksllrYiarilrfltlnseekPf 73 
                                    + ++l+++++v ++++L+tgr +  L+++  ++ r+  r+ ++ tl  +e+P+
  gi|121637792|ref|YP_978015.1| 158 WPSLLVILLLVAVVALLFTGRYPIGLYNLVIGVNRWALRVRAYTTLMRDEYPP 210
                                    567899**********************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1726.45
//
Query:       gi|121637793|ref|YP_978016.1|  [L=57]
Description: hypothetical protein BCG_1926c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   63.2   0.0    3.2e-17   63.1   0.0    1.0  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   1.8e-21   3.2e-17     139     188 .]       1      49 [.       1      49 [. 0.97

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.8e-21
                                    EEE--TTSHHHHHHHHHHTT-TTSEEEEEEESSGGGS-HHHHHHHHHHHH CS
                            LCM 139 yvpvDlrdddwpeaLaaagfdpekptawvaeGvlvYLtpeasdalleaia 188
                                    +vpvDlr  dwp+ L++agfdp++p+aw+aeG+l++L+p+a+d+ll++i+
  gi|121637793|ref|YP_978016.1|   1 MVPVDLR-RDWPTPLRQAGFDPNQPSAWLAEGLLAFLPPDAQDRLLDNIT 49 
                                    59*****.***************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 410.09
//
Query:       gi|121637794|ref|YP_978017.1|  [L=118]
Description: hypothetical protein BCG_1927c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-28   98.9   1.9    3.6e-28   98.8   1.9    1.0  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   1.9     2e-32   3.6e-28       1     101 [.      19     118 .]      19     118 .] 0.98

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 2e-32
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHG.CHCCCCT--HHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekek.eeekkekkapelnrgiavRtrffddllkaa 79 
                                    a++vaaara+++r++ ++lidDp+ae+lv+a+g ++++r+a++++++ + ++++  +  ++l++ +a+Rtr+fd+++++a
  gi|121637794|ref|YP_978017.1|  19 ATMVAAARAVATRAD-NPLIDDPFAEPLVRAVGIDFFTRWAAGNIKATDvDDPDGTWGLQRLADLLAARTRYFDAFFRDA 97 
                                    79************9.*********************************99***************************** PP

                                    HHCTTESEEEEET-TT--HHHH CS
                            LCM  80 lsaagirqvViLGAGlDtrayR 101
                                    + +agirq+ViL++GlD+rayR
  gi|121637794|ref|YP_978017.1|  98 T-SAGIRQAVILASGLDARAYR 118
                                    *.6******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 916.59
//
Query:       gi|121637795|ref|YP_978018.1|  [L=203]
Description: hypothetical protein BCG_1928c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-12   45.6   0.0    1.3e-11   45.3   0.0    1.1  1  YceI      YceI-like domain


Domain annotation for each model (and alignments):
>> YceI  YceI-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   7.2e-16   1.3e-11      23     144 ..      53     197 ..      26     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.2e-16
                                    EEEECTECCEEEE..TTT..EEEEEEEEGGGEES........S.HCH...HHHHHCT...CTT-TTT--EEEECCCCEE. CS
                           YceI  23 tGrfkkvsgelsvdeddp.essvevtidvasidt........gnakr...dehlksa...dffdvakyPtatFvstsve. 86 
                                    t  ++++++ ++  + dp +  +e++ +v+s++         g   +   +++l+ a   + +++ ++P+++F+   ++ 
  gi|121637795|ref|YP_978018.1|  53 TIAMTRWQALVNWSGTDPvA--GELVAEVDSFEVmrgeggvkG---LsepEKALVRAnalKTLNASRFPHIRFTTEAIAq 127
                                    33334444444444445544..555556666666555553331...2444555555545567***********9999888 PP

                                    ......EEEEEEETTEEEEEEEEEEEEE..EECCEECEEEEEGGGGTC........TTTC-SEEEEEEEE CS
                           YceI  87 ....akvtGdLtikGvtkpvtlpvtvng..aaagfsatgtidrtdFGlkr......galvgdeveleiel 144
                                        +++tG+L i+G++++  +++  +   aa + sa++t++++++G+k          v+dev + +++
  gi|121637795|ref|YP_978018.1| 128 tgngYRLTGKLHIRGKSREHVIDLHTEDlgAAWRISADTTVRQSNYGVKPysllmgSIRVADEVSVAFTA 197
                                    ****88******************998522334478***********855888888889*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1427.21
//
Query:       gi|121637796|ref|YP_978019.1|  [L=135]
Description: hypothetical protein BCG_1929 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 858.84
//
Query:       gi|121637797|ref|YP_978020.1|  [L=103]
Description: hypothetical protein BCG_1930 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0067   16.5   4.1     0.0088   16.1   4.1    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   4.1   4.9e-07    0.0088      41     105 ..      32      95 ..      24     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-07
                Phage_holin_3_6  41 gaagvlallalllllvalalala.a....lwlaali.vaavllvlagvlalvglkklkkakp.lpertieel 105
                                    ++ag++ +  l++l        + +    + l+ +i +a+++l l g++++vgl+++ ++ +  pe+ +++l
  gi|121637797|ref|YP_978020.1|  32 IGAGFFFAPVLAVL--------SpWptitAVLWWIIgLAGLWLGLLGIAMAVGLARVLRSGAeIPEAYWRTL 95 
                                    33333333333333........32233332333345589999999999999999999887777999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 764.00
//
Query:       gi|121637798|ref|YP_978021.1|  [L=72]
Description: hypothetical protein BCG_1931 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   16.0   7.9       0.14   12.5   0.6    2.3  2  MT0933_antitox  MT0933-like antitoxin protein
      0.087   12.3   0.8        2.5    7.5   0.0    2.0  2  DUF2884         Protein of unknown function (DUF2884)


Domain annotation for each model (and alignments):
>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.5   0.00072       6.5       5      30 ..       6      30 ..       5      34 .. 0.73
   2 ?   12.5   0.6   1.6e-05      0.14       6      39 ..      37      69 ..      34      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00072
                 MT0933_antitox  5 kdlaekhedkvdqgiDKAgdavddkt 30
                                   kd+++   d++  +++KA d v+  +
  gi|121637798|ref|YP_978021.1|  6 KDAVDAVRDIAANAVEKASDIVE-NA 30
                                   56666666888889999999888.44 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                 MT0933_antitox  6 dlaekhedkvdqgiDKAgdavddktGgKysdkId 39
                                   d a+ ++ +v++ iD A  avd +t++ +  k d
  gi|121637798|ref|YP_978021.1| 37 DIAGGASGIVKDSIDIATHAVD-RTKEVFTGKTD 69
                                   7899******************.***99988876 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2    0.0035        32      64      86 ..      11      33 ..       6      45 .. 0.80
   2 ?    7.5   0.0   0.00028       2.5      67      92 ..      44      69 ..      41      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0035
                        DUF2884 64 evaelasdgvdlAsdaldevlte 86
                                    v ++a ++v+ Asd+++++   
  gi|121637798|ref|YP_978021.1| 11 AVRDIAANAVEKASDIVENAGHI 33
                                   68899************987655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00028
                        DUF2884 67 elasdgvdlAsdaldevltellgeds 92
                                    +++d++d+A+ a+d++ + ++g+ +
  gi|121637798|ref|YP_978021.1| 44 GIVKDSIDIATHAVDRTKEVFTGKTD 69
                                   589******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 526.20
//
Query:       gi|121637799|ref|YP_978022.1|  [L=376]
Description: hypothetical protein BCG_1932c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-44  151.7   0.7    1.8e-43  149.2   0.7    1.8  1  NMO           Nitronate monooxygenase
      4e-06   26.1   4.6    6.7e-06   25.4   4.6    1.3  1  FMN_dh        FMN-dependent dehydrogenase
    0.00062   19.1   1.4    0.00091   18.6   1.4    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
     0.0072   15.4   1.3      0.015   14.3   1.3    1.7  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
       0.18   11.2   1.6       0.19   11.1   0.3    1.6  2  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.7     5e-47   1.8e-43      24     285 ..      21     311 ..       3     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 5e-47
                            NMO  24 karLaaavsnaGgLGvlasgyltaDrlakeirkvka.ltdkPfgvnlflpkkdaadraekykkeleeaalelnieegvr. 101
                                      + + avs+aGg Gvl++   t+ +l+ e++ + + + d+P+gv + +p+k ++ + +  ++el+++   +  +e    
  gi|121637799|ref|YP_978022.1|  21 CRDVVVAVSKAGGFGVLGAVGFTPEQLEIELNWIDEhIGDHPYGVDIVIPNKYEGMDSQLSADELAKTLRSMVPQEHLDf 100
                                    467899************999*************6528899********9997766555555555544433333333334 PP

                            NMO 102 .............................fyrkvevvlde.kvevvsfgfglpteevvarlkeagvvliptissvkeark 151
                                                                    +v+  l++ k  +v  ++g p+ +++++ +++g  +  + +s  +ark
  gi|121637799|ref|YP_978022.1| 101 arkiladhgvpvedadedslqllgwteatATPQVDAALKHpKMTMVANALGTPPADMIKHIHDSGRKVAALCGSPSQARK 180
                                    44488888999*************999988889*****9999************************************** PP

                            NMO 152 vearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                     + +G D++i+qG+eaGGh G  ev   g + L pqv++ v+ +Pv+AaGGi  ++++aaaLalG +g+  g+ +L+ +e
  gi|121637799|ref|YP_978022.1| 181 HADAGVDIIIAQGGEAGGHCG--EV---GSIVLWPQVVKEVApVPVLAAGGIGSGQQIAAALALGTQGAWTGSQWLMVEE 255
                                    *********************..77...69********99999************************************* PP

                            NMO 231 sdakdahkkklleaklddteltsavsGrpaRalatelleelee.akiatlalpeah 285
                                    +   ++ ++++++a   dt+  + + G+paR l+++++e  e+    ++l++p + 
  gi|121637799|ref|YP_978022.1| 256 AANTAVQQAAYVKATSRDTVRSRSFTGKPARMLRNDWTEAWEQpESPKPLGMPLQY 311
                                    ******************************************96444555555543 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   4.6   1.9e-09   6.7e-06     226     309 ..     174     256 ..     168     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.9e-09
                                    SHHHHHHHHHTTESEEEE..--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 226 taedakraveaGvdgivv..SNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                    ++  a++ ++aGvd+i+      GG+   g + +i   p++v++v+  ++vl+ gGi +G+ ++ AlalG ++ + G ++
  gi|121637799|ref|YP_978022.1| 174 SPSQARKHADAGVDIIIAqgGEAGGHC--GEVGSIVLWPQVVKEVA-PVPVLAAGGIGSGQQIAAALALGTQGAWTGSQW 250
                                    578899********9998333567765..8999************9.9*******************************9 PP

                                    HHHHHH CS
                         FMN_dh 304 lyglaa 309
                                    l+   a
  gi|121637799|ref|YP_978022.1| 251 LMVEEA 256
                                    876554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.4   2.5e-07   0.00091     133     206 ..     174     249 ..     134     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-07
                                    -HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHH..HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH CS
                           ThiG 133 DlvlarrleevGcaavmPlaapiGsglGllnkeal..kiiieeakvPvivDAGigspsdaaqamelGadavllnta 206
                                     +  ar+  ++G+  ++  +   G   G +   +l  +++ e a vPv+   Gigs +++a+a+ lG+++    + 
  gi|121637799|ref|YP_978022.1| 174 SPSQARKHADAGVDIIIAQGGEAGGHCGEVGSIVLwpQVVKEVAPVPVLAAGGIGSGQQIAAALALGTQGAWTGSQ 249
                                    57789************************999988656777788************************99776664 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.3   4.1e-06     0.015     200     253 ..     210     263 ..      22     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
                                    HHHHCTC.T-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEET CS
                                    xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 200 aeaakka.gvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevilie 253
                                     +++k+   vpv+a GGi + ++i+ Ala+G++    Gs    +eE+    +  +
  gi|121637799|ref|YP_978022.1| 210 PQVVKEVaPVPVLAAGGIGSGQQIAAALALGTQGAWTGSQWLMVEEAANTAVQ-Q 263
                                    455555426******************************99999999766554.4 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   5.3e-05      0.19     186     221 ..     212     248 ..     177     254 .. 0.84
   2 ?   -3.0   0.0       1.1   4.1e+03     135     159 ..     339     363 ..     317     366 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
                                    HHHHH.SSEEEEESS--SHHHHHHHHHTTCSEEEESH CS
                   His_biosynth 186 laeav.kipviasGGvgsledlkelksegvdavivgs 221
                                    + ++v  +pv+a+GG+gs + ++++ + g +++ +gs
  gi|121637799|ref|YP_978022.1| 212 VVKEVaPVPVLAAGGIGSGQQIAAALALGTQGAWTGS 248
                                    4555549*************************99998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                                    EEEETTTTEEEEEEHHHHHHHHHHT CS
                   His_biosynth 135 kvaikgwreetgldavelakkleel 159
                                     v + +  e+t+  ++ +++++ e+
  gi|121637799|ref|YP_978022.1| 339 VVGQFTKVEKTATVIERWVQEYLEA 363
                                    4555566666667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2650.85
//
Query:       gi|121637800|ref|YP_978023.1|  [L=107]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-22   79.1   2.6    2.4e-22   78.9   2.6    1.1  1  ADH_N        Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.051   13.5   0.0    1.5  1  ADH_N_assoc  Alcohol dehydrogenase GroES-associated


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   2.6   2.7e-26   2.4e-22       2      74 ..      26      96 ..      25     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2.7e-26
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHH CS
                          ADH_N  2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCk 74
                                   + v++ v+aagiCgsDlh+++g  e++   p++lGHE+vG+++e+gp+v+++ vGd V+v+ +  cg C+ C+
  gi|121637800|ref|YP_978023.1| 26 DGVVVAVTAAGICGSDLHFYEG--EYPFTEPVALGHEAVGTIVEAGPQVRTVGVGDLVMVSSVAGCGVCPGCE 96
                                   779******************9..7***********************************************7 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.7e-06     0.051       1      21 [.       1      21 [.       1      22 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                    ADH_N_assoc  1 MKAVTyqGpkdVrVeeVPDPk 21
                                   M+AV+  G  +VrV + PDP 
  gi|121637800|ref|YP_978023.1|  1 MRAVVIDGAGSVRVNTQPDPA 21
                                   ********************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 747.47
//
Query:       gi|121637801|ref|YP_978024.1|  [L=234]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-20   73.7   0.0    1.8e-20   73.2   0.0    1.2  1  ADH_zinc_N    Zinc-binding dehydrogenase
    5.4e-07   30.7   0.0    8.7e-07   30.0   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    4.3e-05   23.1   0.2    8.1e-05   22.2   0.2    1.4  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
     0.0037   16.6   0.8     0.0037   16.6   0.8    1.5  2  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
     0.0064   16.4   2.6      0.018   15.0   2.6    1.9  1  PGF-CTERM     PGF-CTERM motif


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0     5e-24   1.8e-20       1     129 [.      69     194 ..      69     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5e-24
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    +vGl+a+  A + Ga +v+avd+ + +l+ a+  Ga+ +  +      e i ++t+g+g+d v+++vG+ a++++al+++
  gi|121637801|ref|YP_978024.1|  69 AVGLCALRSAFIHGAaTVFAVDRVKGRLQRAATWGATPIPSP----AAETILAATRGRGADSVIDAVGTDASMSDALNAV 144
                                    69****************************************....89******************************** PP

                                    EEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                    +pgG++ vvG+   ++ ++++  +ll++++++ ++    +++++e+++ll+
  gi|121637801|ref|YP_978024.1| 145 RPGGTVSVVGVhDLQPFPLPALTCLLRSITLRMTMAPV-QRTWPELIPLLQ 194
                                    **********866666668888899*********9999.********9986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.4e-10   8.7e-07      11     120 ..     112     218 ..     102     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.4e-10
                                    STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHH CS
                   ADH_zinc_N_2  11 tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyeflfsmkasaqadi 89 
                                    +e + aat+g+g D v+d+vg++a ++++l+++++gG++ ++g      +  + pa+     +  +  ++ m +  q+  
  gi|121637801|ref|YP_978024.1| 112 AETILAATRGRGADSVIDAVGTDASMSDALNAVRPGGTVSVVGvH--DLQPFPLPALTC-LLRSITLRMT-MAPV-QRT- 185
                                    444447999************99999*******887999777744..455566666633.3333333444.7787.888. PP

                                    HHHHHHHHHHHH---..-EEEEEEGGGHHHHHH CS
                   ADH_zinc_N_2  90 leelaalieeGklrp..vvdrvfpleeaaeAhr 120
                                      el  l+++G+l +    + ++pl+eaa+ ++
  gi|121637801|ref|YP_978024.1| 186 WPELIPLLQSGRLDVdgIFTTTLPLDEAAKGYA 218
                                    ************8752266777******98665 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   2.3e-08   8.1e-05      24     136 ..      53     159 ..      33     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-08
                    Glu_dehyd_C  24 rsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdl 103
                                    r+  ++  + + v+G G++GL al       +g  +v+ ++r +    +++  +  Gat + s  ++    +   +  d 
  gi|121637801|ref|YP_978024.1|  53 RADISFG-SAVAVIGLGAVGLCALRSAFI--HGAATVFAVDRVKG---RLQRAATWGATPIPSPAAETILAATRGRGADS 126
                                    3333333.345699*********876655..68888999997544...5556799********9998888889999**** PP

                    Glu_dehyd_C 104 vvEaTGsakhafeaiealapnGvaaLlGvpeds 136
                                    v++a G+ + + +a++a++p G +  +Gv   +
  gi|121637801|ref|YP_978024.1| 127 VIDAVGTDASMSDALNAVRPGGTVSVVGVHDLQ 159
                                    *****************************8655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5         1   3.6e+03      32      42 ..       1      11 [.       1      21 [. 0.77
   2 !   16.6   0.8     1e-06    0.0037      29     100 ..      60     132 ..      41     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                   EEESTSHHHHH CS
                    AlaDh_PNT_C 32 lviGgGvaGlq 42
                                   +++G+Gv G +
  gi|121637801|ref|YP_978024.1|  1 MIFGAGVLGGA 11
                                   689***98854 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-06
                                    -EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE--- CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvl 100
                                    + v viG G +Gl A++ a   ga +V ++D  + rl++  ++ga+ +   +++  l a + + ad vi +v 
  gi|121637801|ref|YP_978024.1|  60 SAVAVIGLGAVGLCALRSAFIHGAaTVFAVDRVKGRLQRAATWGATPIPSPAAETILAATRGRGADSVIDAVG 132
                                    5699****************99963799********************9999999999999999999998875 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.6   5.1e-06     0.018       4      22 ..      58      76 ..      58      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.1e-06
                      PGF-CTERM  4 FGavlAlaGLLaaalLaRR 22
                                   FG+++A++GL a++l a R
  gi|121637801|ref|YP_978024.1| 58 FGSAVAVIGLGAVGLCALR 76
                                   ****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1715.92
//
Query:       gi|121637802|ref|YP_978025.1|  [L=303]
Description: hypothetical protein BCG_1935c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-56  190.2   0.0    4.1e-56  189.9   0.0    1.1  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   0.0   2.3e-60   4.1e-56       1     187 [.      26     201 ..      26     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 2.3e-60
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    al va +ral++  + ++l++D++a++++ a+++ +le   ++        ++++++ +++ r + v+trffdd+++ a 
  gi|121637802|ref|YP_978025.1|  26 ALLVAGWRALHTTGP-KPLVQDEYAKHFITASADPYLEGLLAN--------PRTSEDGTAFPRLYGVQTRFFDDFFNCAD 96 
                                    7899***********.****************88875444433........5566789*********************9 PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     +agirq+Vi++AGlD rayRl+w  g++vfE+D p+vlefK+++l e ga pka++  vp+Dlr +dwp+ L+aagfdp
  gi|121637802|ref|YP_978025.1|  97 -EAGIRQAVIVAAGLDCRAYRLDWQPGTTVFEIDVPKVLEFKARVLSERGAVPKAHRVAVPADLR-TDWPTPLTAAGFDP 174
                                    .7***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleai 187
                                    ++p+aw++eG+l+YLt +a+ al+++i
  gi|121637802|ref|YP_978025.1| 175 QRPSAWSVEGLLPYLTGDAQYALFARI 201
                                    ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2554.02
//
Query:       gi|121637803|ref|YP_978026.1|  [L=143]
Description: D-tyrosyl-tRNA(Tyr) deacylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-49  166.4   0.0    6.1e-49  166.3   0.0    1.0  1  Tyr_Deacylase  D-Tyr-tRNA(Tyr) deacylase
  ------ inclusion threshold ------
       0.05   13.5   0.3       0.12   12.3   0.3    1.7  1  SPDY           Domain of unknown function (DUF317)


Domain annotation for each model (and alignments):
>> Tyr_Deacylase  D-Tyr-tRNA(Tyr) deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   0.0   6.8e-53   6.1e-49       1     144 []       2     142 ..       2     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 6.8e-53
                                    EEEEEEEEEEEEEETTEEEEEE...SSEEEEEEE-BTT--HHHHHHHHHHHHH-EEEEETTSSEEEETTTTT-EEEEEE- CS
                  Tyr_Deacylase   1 raviqrvksAsvtvegevvgsi...gkGllvlvgvekedteedleklakkilnlrifedeegkmnlsvkdvggevLvVsq 77 
                                    r+++qrv+sA+v+v+g+vvg+i   g+Gl+++vgv+++d+ +++++la+k++nlr++       ++s++d+++++Lv+sq
  gi|121637803|ref|YP_978026.1|   2 RVLVQRVSSAAVRVDGRVVGAIrpdGQGLVAFVGVTHGDDLDKARRLAEKLWNLRVLAG-----EKSASDMHAPILVISQ 76 
                                    89********************9999*******************************98.....69************** PP

                                    GGGGSBTSSSSS-BGTTB--HHHHHHHHHHHHHHHHHCTCTTEEE--TTS-EEEEEEEEEEEEEEEE CS
                  Tyr_Deacylase  78 ftLyadtrkGrrpsfhkaakpeeaeelyekfveklrerlgekvetGeFgadmkvslvndGPvtilld 144
                                    ftLyadt+kGrrps+++aa++++a++l+++f+++lr+  g++ve G+Fga+m+v+lvndGPvt++l+
  gi|121637803|ref|YP_978026.1|  77 FTLYADTAKGRRPSWNAAAPGAVAQPLIAAFAAALRQL-GAHVEAGVFGAHMQVELVNDGPVTVMLE 142
                                    ************************************85.78************************97 PP

>> SPDY  Domain of unknown function (DUF317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   1.3e-05      0.12      26      56 ..      80     111 ..      66     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                           SPDY  26 earp.aadgpaWhatFtaatPaelvaaftaaL 56 
                                     a + ++ +p W+a + +a+ ++l+aaf+aaL
  gi|121637803|ref|YP_978026.1|  80 YADTaKGRRPSWNAAAPGAVAQPLIAAFAAAL 111
                                    56666899***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1251.72
//
Query:       gi|121637804|ref|YP_978027.1|  [L=102]
Description: hypothetical protein BCG_1937 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-29  101.8   0.9    1.6e-29  101.7   0.9    1.0  1  Thiamine_BP     Thiamine-binding protein
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.023   15.2   0.0    1.2  1  Ykof            YKOF-related Family
      0.024   15.1   0.5       0.03   14.8   0.5    1.1  1  Phage_H_T_join  Phage head-tail joining protein
      0.038   14.1   3.1      0.054   13.6   3.1    1.2  1  DUF4235         Protein of unknown function (DUF4235)


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.9   3.5e-33   1.6e-29       1      92 []       5      95 ..       5      95 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 3.5e-33
                                   EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS- CS
                    Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdke 81
                                   v++sv+Plg+ ge v ++V+++++v+++sgl++++ +m+T+ieg+ + evm+vv++a ea++++ a+Rvs vik+d+r++++
  gi|121637804|ref|YP_978027.1|  5 VAFSVTPLGV-GEGVGEIVTEAIRVVRDSGLPNQTDAMFTVIEGDtWAEVMAVVQRAVEAVAAR-APRVSAVIKVDWRPGVT 84
                                   79********.*****************************************************.***************** PP

                                   --HHHHHHHHH CS
                    Thiamine_BP 82 qtleeKvksve 92
                                     +++Kv++ve
  gi|121637804|ref|YP_978027.1| 85 DAMTQKVATVE 95
                                   ********996 PP

>> Ykof  YKOF-related Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.1e-06     0.023       5      65 ..       6      68 ..       3      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                                   EEEEEETTSTTHHHHHH.HHHHHCHHTTSEEEEETTEEEEECBH.HHHHHHHHHHHHHHHCCS CS
                           Ykof  5 qfsLYpmgadDyvdvIl.galdlldkskvrvetdhiatrlrGdv.eevFdalkavflkaaqsv 65
                                    fs  p+g +  v++I+ +a++++  s++ ++td + t+++Gd+  ev  +++ +  ++a+ +
  gi|121637804|ref|YP_978027.1|  6 AFSVTPLGVGEGVGEIVtEAIRVVRDSGLPNQTDAMFTVIEGDTwAEVMAVVQRAVEAVAARA 68
                                   5889999999999988538************************84578888887777776655 PP

>> Phage_H_T_join  Phage head-tail joining protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   6.7e-06      0.03      28      72 ..      47      91 ..      21      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.7e-06
                 Phage_H_T_join 28 atvwAeveslsgreaiaagaeqaettvritiRyrkditadmrivf 72
                                   +  wAev  + +r   a +a   +++++i + +r+++t+ m++++
  gi|121637804|ref|YP_978027.1| 47 GDTWAEVMAVVQRAVEAVAARAPRVSAVIKVDWRPGVTDAMTQKV 91
                                   369*******999999999999999****************9875 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.1   1.2e-05     0.054       7      67 ..       9      68 ..       4      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                        DUF4235  7 vlglvaGavagkafaavWkkvtgedaPkdpkdedvslrevllfAaisGavlavvrvaadRg 67
                                   v++l+ G  +g +++++ + v+ +  P +++d+  ++ e  ++A + ++v  +v ++a R+
  gi|121637804|ref|YP_978027.1|  9 VTPLGVGEGVGEIVTEAIRVVRDSGLP-NQTDAMFTVIEGDTWAEVMAVVQRAVEAVAARA 68
                                   67888888999999999999*******.********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 786.44
//
Query:       gi|121637805|ref|YP_978028.1|  [L=358]
Description: lipoprotein lppD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-27   93.9   0.0    9.8e-27   93.3   0.0    1.3  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0   5.5e-31   9.8e-27       2     118 .]     208     317 ..     207     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 5.5e-31
                                    EEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHHHH CS
                          Macro   2 nAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeellaka 81 
                                    nAaN+rl + ggva+ai+ra+g++l++e++e     +++ lGeav t+a+++pa+yvih+   +++  ++ ++ e +++a
  gi|121637805|ref|YP_978028.1| 208 NAANTRLRHAGGVAAAIARAGGPELQRESTEK----APIGLGEAVETTAGDMPARYVIHA--ATME-LGGPTSGEIITAA 280
                                    9*******************************....99**********************..8886.79*********** PP

                                    HHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                          Macro  82 yknalelaeekgiksvafPaistGifgvpweeaarva 118
                                    +   l++a+e g++s+a+ a +tG++g+p+++aar++
  gi|121637805|ref|YP_978028.1| 281 TAATLRKADELGCRSLALVAFGTGVGGFPLDDAARLM 317
                                    **********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2692.06
//
Query:       gi|121637806|ref|YP_978029.1|  [L=462]
Description: lignin peroxidase lipJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-14   53.9   0.3    1.5e-13   50.8   0.3    2.0  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    6.7e-09   35.8   0.0    4.5e-07   29.8   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.3   1.6e-17   1.5e-13       9     173 ..     296     445 ..     291     454 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-17
                  Guanylate_cyc   9 vtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdmlea 88 
                                     ti+F+dIvg+t+ ++a       +lL ++ + + + +++ ++ +v+t Gd +++++ +p    ++a  +a       ++
  gi|121637806|ref|YP_978029.1| 296 ATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSP----SAAIACA-------DD 364
                                    59****************999***************************************....3333333.......33 PP

                  Guanylate_cyc  89 l.eevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellkeeqfelterge 167
                                    + + va+    g++vr+Gih G+v ++         dv G +v + +r+ +++ ++++ vs++++++      ++ erge
  gi|121637806|ref|YP_978029.1| 365 IvDAVAAL---GIEVRIGIHAGEVEVRDA---SHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGE 438
                                    32444444...699**********98866...8899******************************************** PP

                  Guanylate_cyc 168 vevkG.k 173
                                     e+kG +
  gi|121637806|ref|YP_978029.1| 439 QELKGvP 445
                                    ****954 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   5.1e-11   4.5e-07      31     113 ..      63     146 ..      57     161 .. 0.88
   2 !    3.7   0.0    0.0044        40     208     254 ..     222     267 ..     185     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.1e-11
                                    EEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE...C CS
                  Abhydrolase_1  31 dvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga...i 107
                                    +vi lD+rGvg Ss+  a   ++ g    a d  +++da g ++ t+ + S+  m +l +aa+yperV++l+ +++   +
  gi|121637806|ref|YP_978029.1|  63 RVIRLDHRGVGLSSRLAAI--TTLGPKFWAQDAIAVMDAVGCEQATIFAPSFHAMNGLVLAADYPERVRSLIVVNGsarP 140
                                    79***************98..7777777999999*****************************************97766 PP

                                    SSCCHH CS
                  Abhydrolase_1 108 dpaasl 113
                                     +a+++
  gi|121637806|ref|YP_978029.1| 141 LWAPDY 146
                                    665555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0044
                                    HHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHH CS
                  Abhydrolase_1 208 knvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafl 254
                                      + aptl+++     ++p +++++la+++ + +++v+ ++  ++++
  gi|121637806|ref|YP_978029.1| 222 GHIEAPTLILHRVGSTYIPVGHGRYLAEHIAG-SRLVELPGTDTLYW 267
                                    33555***************************.55555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3544.41
//
Query:       gi|121637807|ref|YP_978030.1|  [L=430]
Description: competence damage-inducible protein A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-54  182.6   1.3    5.6e-54  181.9   1.3    1.3  1  CinA           Competence-damaged protein
    3.6e-38  130.4   0.1      3e-36  124.2   0.0    2.4  2  MoCF_biosynth  Probable molybdopterin binding domain
     0.0087   16.2   0.1      0.054   13.7   0.0    2.5  2  CinA_KH        Damage-inducible protein CinA KH domain


Domain annotation for each model (and alignments):
>> CinA  Competence-damaged protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   1.3   9.4e-58   5.6e-54       4     155 .]     273     423 ..     270     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 9.4e-58
                           CinA   4 laeevvkllkkkgltlatAEScTGGllaaaltsvpGaSavfeggvvtYsneaKeelLgvseetleehgavSeevaeemae 83 
                                    + e v+kll  +g+++atAEScT+Gllaa+lt+ pG+S+++ g+vv+YsneaK++lLgv+++++e+hgavSe+va++ma+
  gi|121637807|ref|YP_978030.1| 273 VDELVAKLL--TGRRIATAESCTAGLLAARLTDRPGSSKYVAGAVVAYSNEAKAQLLGVDPALIEAHGAVSEPVAQAMAA 350
                                    566677777..8999***************************************************************** PP

                           CinA  84 garerlgadiavavtGiAGpsggteekpvGtvyialagkgg.veveklefegdreeireaavkaALellrell 155
                                    ga++ +gad a a+tGiAGpsggt+ekpvGtv++ +  ++g +++++++++g+r++ire++++ A++llr++l
  gi|121637807|ref|YP_978030.1| 351 GALQGFGADTATAITGIAGPSGGTPEKPVGTVCFTVLLDDGrTTTRTVRLPGNRSDIRERSTTVAMHLLRRTL 423
                                    *************************************99999***************************9986 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.0   5.1e-40     3e-36       1     138 [.       8     178 ..       8     184 .. 0.95
   2 !    4.0   0.0    0.0058        35      99     137 ..     374     414 ..     305     421 .. 0.84

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 5.1e-40
                                    EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTSSEEEEESS-SSSTT--HHHHH CS
                  MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeal..laaleeadviittGGtGptpdDvtpeal 78 
                                    +++++G+e+l+g+++D+ngp++a++l elgve++++t+++D +++i+++l  +a+ +++d+i+t+GG+Gpt+dD+t+e++
  gi|121637807|ref|YP_978030.1|   8 GIVITGTEVLTGRVQDRNGPWIADRLLELGVELAHITICGDRPADIEAQLrfMAE-QGVDLIVTSGGLGPTADDMTVEVV 86 
                                    699***********************************************64444.666********************* PP

                                    HHHHSEE-HHHHHHHHHHHHHHCC..................................TTSHGGGGGGE.EETTE.EEEE CS
                  MoCF_biosynth  79 aklfekelegfeeafrrvslkpgk..................................pvgvapgailsravgkt.iigL 123
                                    a+ +++el++++e+ +r+++  +k                                  pvg+apg ++ ++   + +++L
  gi|121637807|ref|YP_978030.1|  87 ARYCGRELVLDDELENRIANILKKlmgrnpaiepanfdsiraanrkqamipagsqvidPVGTAPGLVVPGR---PaVMVL 163
                                    **********************99*****************************************999876...7699** PP

                                    -SSHHHHHHHHHHHH CS
                  MoCF_biosynth 124 PGspkavkealeeil 138
                                    PG p++ + ++ + +
  gi|121637807|ref|YP_978030.1| 164 PGPPRELQPIWSKAI 178
                                    ***********9887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0058
                                    HHCCTTSHGGGGGGE.EE.TTE.EEEE-SSHHHHHHHHHHH CS
                  MoCF_biosynth  99 kpgkpvgvapgailsrav.gkt.iigLPGspkavkealeei 137
                                     p+kpvg++++++l +    +t  + LPG+ + ++e   ++
  gi|121637807|ref|YP_978030.1| 374 TPEKPVGTVCFTVLLDDGrTTTrTVRLPGNRSDIRERSTTV 414
                                    6778******999988775444799******9988765555 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.97   5.8e+03      11      22 ..     101     112 ..      96     120 .. 0.51
   2 !   13.7   0.0     9e-06     0.054       2      40 ..     196     238 ..     195     267 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.97
                                    HHHHHHHHGGGS CS
                        CinA_KH  11 ESavaekladli 22 
                                    E ++a+ l+ l+
  gi|121637807|ref|YP_978030.1| 101 ENRIANILKKLM 112
                                    334444444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9e-06
                                    EEEEE-S--HHHHHHHHGGGS-B....SSSEEEEEEETTEEEE CS
                        CinA_KH   2 rvLktfGigESavaekladlidr....enptlAiyakegevtv 40 
                                     ++++fG+ ES++a+ l+d  +     +  ++ +  ++ge++ 
  gi|121637807|ref|YP_978030.1| 196 ETIRIFGLPESSLADTLRDAEAAipgfDLVEITTCLRRGEIEM 238
                                    79****************9865544333346666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2972.06
//
Query:       gi|121637808|ref|YP_978031.1|  [L=422]
Description: sialic acid-transport integral membrane protein nanT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-39  135.2  21.2    2.6e-25   89.2   7.2    2.0  2  Sugar_tr  Sugar (and other) transporter
    1.8e-35  122.5  39.8    9.3e-26   90.6  17.1    2.0  2  MFS_1     Major Facilitator Superfamily
    1.2e-05   24.8  20.1    7.1e-05   22.3  20.1    2.1  1  MFS_4     Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   7.2   4.4e-29   2.6e-25       7     213 ..      18     210 ..      12     225 .. 0.82
   2 !   51.7   6.4     1e-17   6.1e-14      36     189 ..     247     396 ..     221     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 4.4e-29
                                    HHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                       Sugar_tr   7 lgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavl 85 
                                    + g ++  +d++++  +++ ++     +  ++      +++++ +++ ++l+ + +G+l++gl++dr+GR+  l++ + +
  gi|121637808|ref|YP_978031.1|  18 FLGwTMDAFDYFLVVLVYADIA-----TTFHH------TKTDVAFLTTATLAMRPVGALLFGLWADRVGRRVPLMVDVSF 86 
                                    4444444444444443333333.....22222......33345699999***************************6666 PP

                                    HHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS CS
                       Sugar_tr  86 fvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnkts 165
                                    +++ ++l+a+a+   ++ vl++ R+l Gig+G++ +l   +  E  p++ Rg + +l q +++fG l+a++  l++ +  
  gi|121637808|ref|YP_978031.1|  87 YSVIGFLCAFAP---NFTVLVILRLLYGIGMGGEWGLGAALSMEKVPAERRGVFSGLLQEGYAFGYLLASVAALVVMNWL 163
                                    666667777777...7************************************************************9988 PP

                                    -TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHH CS
                       Sugar_tr 166 nadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlak 213
                                    +   wr+l+gl+++pal+ li+++ + ES  +   +++   +k+ +++
  gi|121637808|ref|YP_978031.1| 164 G-LSWRWLFGLSIIPALISLIIRYRVKESEVWEAAQDRMRLTKTRIRD 210
                                    8.89*****************************999998877776666 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 1e-17
                                    -SHHHHHH.....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHH CS
                       Sugar_tr  36 ksksskee..ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvG 113
                                    ++++++ +  ss++  +iv i+++GaiiG+l +g+l++rf+R+++++++a+l +    l a +    +  +l++g +l+ 
  gi|121637808|ref|YP_978031.1| 247 TATTDHGAglSSLTARWIVVIYNIGAIIGGLAFGTLSQRFSRRYTIVFCAALGLPIVPLFAYSR---TAAMLCLGSFLMQ 323
                                    2333333366899999********************************9999887777777777...89*********** PP

                                    HHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                       Sugar_tr 114 igvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                    ++v +a +++P  + E++p+++Rg    +  + +++G l+aa+   + ++  ++ g+++ l+ ++vp ll++++l+
  gi|121637808|ref|YP_978031.1| 324 VFVQGAWGVIPAHLTEMSPDAIRGV---YPGVTYQLGNLLAAFNLPIQERLAESHGYPFALAATIVPVLLVVAVLT 396
                                    ***********************96...66788999*****9877777999999*************999888776 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6  17.1   1.6e-29   9.3e-26       6     226 ..      22     238 ..      13     253 .. 0.81
   2 !   38.1  15.5   1.4e-13   8.3e-10      23     170 ..     248     395 ..     233     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.6e-29
                          MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfassl 85 
                                     + a++++++ +++   +a++++ +++ + +l+t+  +   v++l++G ++dr+Grr  l++ + ++++ ++l++fa+++
  gi|121637808|ref|YP_978031.1|  22 TMDAFDYFLVVLVYA-DIATTFHHTKTDVAFLTTATLAMRPVGALLFGLWADRVGRRVPLMVDVSFYSVIGFLCAFAPNF 100
                                    334444444444444.******************************************9999999999998999998898 PP

                          MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivsll 163
                                    ++l++lr+l G+g+g+ + +gaal  + +p e+rg   gll+ g+++G++l+ +++ +++ +lg  Wr++f +  i +l+
  gi|121637808|ref|YP_978031.1| 101 TVLVILRLLYGIGMGGEWGLGAALSMEKVPAERRGVFSGLLQEGYAFGYLLASVAALVVMNWLGlsWRWLFGLSIIPALI 180
                                    8******************************************************************************* PP

                          MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..illialllfffgfsg..l 226
                                    +++   + ++++++e +  ++ +      +   +  ++ +l +p +   ++ ++ll+++f +++  +
  gi|121637808|ref|YP_978031.1| 181 SLI---IRYRVKESEVWEAAQDRM-----RLTKTR-IRDVLGNPAIVrrFVYLVLLMTAFNWMShgT 238
                                    *88...788888888888876666.....555555.8999999988553233333333333333543 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 1.4e-13
                          MFS_1  23 laedlg..ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslw.lllvlrvlqGlg 98 
                                     ++d+g  +s  ++ +++++y +ga+++ l +G ls+rf+rr +++++++l +    ++lfa s    +l+++ +l+ ++
  gi|121637808|ref|YP_978031.1| 248 ATTDHGagLSSLTARWIVVIYNIGAIIGGLAFGTLSQRFSRRYTIVFCAALGLPI--VPLFAySRTAaMLCLGSFLMQVF 325
                                    4455444488889**************************9999999999988888..44445588888************ PP

                          MFS_1  99 agalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                      +++ ++ a +++++p+  rg + g+ +   +l a++  ++   la+s g++ +  +  +  ll+  +++l
  gi|121637808|ref|YP_978031.1| 326 VQGAWGVIPAHLTEMSPDAIRGVYPGVTYQLGNLLAAFNLPIQERLAESHGYPFALAATIVPVLLV--VAVL 395
                                    ***************************************************987755555555544..2223 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3  20.1   1.2e-08   7.1e-05      21     355 ..      40     386 ..      27     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-08
                          MFS_4  21 aegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlv 100
                                    ++ + + +++++l +a ++   vGall+   + +   R+ l++ +    +  + +a++ +f++++++R+l G++ +    
  gi|121637808|ref|YP_978031.1|  40 TTFHHTKTDVAFLTTATLAMRPVGALLFGLWADRVGRRVPLMVDVSFYSVIGFLCAFAPNFTVLVILRLLYGIGMGGEWG 119
                                    5667788999******************7777777788889999999999999*************************** PP

                          MFS_4 101 fgsslvlahaaaarrervgallfaGvGlGiavsgllvllllq.lglsasslW.lalavlsavllllvalllpraal.rea 177
                                    +g++l+++++ a rr+   +ll  G  +G +++++++l++++ lgls+   W ++l+++ a++ l++   +++++  ++a
  gi|121637808|ref|YP_978031.1| 120 LGAALSMEKVPAERRGVFSGLLQEGYAFGYLLASVAALVVMNwLGLSWR--WlFGLSIIPALISLIIRYRVKESEVwEAA 197
                                    *******************************999988765441455544..62467888888888888888866551455 PP

                          MFS_4 178 saaaeaakaeqksl...pllalllaY...glaGfGYi......itatFlvaiardg.aggalleallWllvGlaaivgvl 244
                                    +  ++ +k+  +++   p++    +Y    + +f ++      ++ tFl a   +g + ++l +  + +++ ++ai+g l
  gi|121637808|ref|YP_978031.1| 198 QDRMRLTKTRIRDVlgnPAIVRRFVYlvlLMTAFNWMshgtqdVYPTFLTATTDHGaGLSSLTARWIVVIYNIGAIIGGL 277
                                    55566655554443222333323333111345666653333346779****999974445555555667899*******9 PP

                          MFS_4 245 vwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappatrrllglmTasfg 324
                                    +   +++r   r  ++   ++    v l   s + ++l ++s l+ ++  +   +  +   e++p+a r +   +T  + 
  gi|121637808|ref|YP_978031.1| 278 AFGTLSQRFSRRYTIVFCAALGLPIVPLFAYSRTAAMLCLGSFLMQVFVQGAWGVIPAHLTEMSPDAIRGVYPGVT--YQ 355
                                    9999999865555544444444445666677889999********9999999999999999999999999988776..78 PP

                          MFS_4 325 igQilGpllasllaeatgslalallvaaaal 355
                                    +g +l++    +    + s  ++ ++aa ++
  gi|121637808|ref|YP_978031.1| 356 LGNLLAAFNLPIQERLAESHGYPFALAATIV 386
                                    8999999888888777777777777777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 2324.04
//
Query:       gi|121637809|ref|YP_978032.1|  [L=134]
Description: hypothetical protein BCG_1942 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-30  103.3  19.5    1.1e-29  103.1  19.5    1.0  1  Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily
  ------ inclusion threshold ------
        1.5    8.1   7.3        6.1    6.1   0.5    2.0  2  OST3_OST6        OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1  19.5   1.3e-33   1.1e-29       3     105 .]       4     119 ..       2     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 1.3e-33
                Phage_holin_4_2   3 fllrllvnalallvaalllpgvevas.......fltallaalvlgllnalvkpilkllslpltiltlGlftlvinalmll 75 
                                    fl+r +v+++al+v++l++pg+++a+       +  ++++a+++gl+na++kpi+++ls+pl+iltlGlf +v+na ml+
  gi|121637809|ref|YP_978032.1|   4 FLMRAAVTGFALWVVTLFVPGMRFAGgdttlqrVAIIFVVAVIFGLVNAFIKPIVQILSIPLYILTLGLFHVVVNASMLW 83 
                                    89***************99**988555777776777899***************************************** PP

                Phage_holin_4_2  76 laaalvsg.....fevdgf.wsallgaliisvvsav 105
                                    l+a+++++     +++d+f w+a+++a+++s+vs++
  gi|121637809|ref|YP_978032.1|  84 LTAWITEHtthwgLQIDHFwWTAIWAAILLSIVSWI 119
                                    ******6677788****99567*************7 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.3   0.00092       8.2     240     281 ..       9      54 ..       4      60 .. 0.87
   2 ?    6.1   0.5   0.00068       6.1     235     284 ..      70     123 ..      66     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00092
                      OST3_OST6 240 gllallvilLiklvprikn....akvqrvlvivllvlifllfslll 281
                                    ++ ++++++++ +vp ++     ++ qrv++i+++++if l+++++
  gi|121637809|ref|YP_978032.1|   9 AVTGFALWVVTLFVPGMRFaggdTTLQRVAIIFVVAVIFGLVNAFI 54 
                                    5678999999999999998888899**************9998876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00068
                      OST3_OST6 235 vallygllallvilLiklvprikn....akvqrvlvivllvlifllfslllslf 284
                                     +l+++++ ++++ L+ ++ + +     +  + +++++++++++ ++s++lsl 
  gi|121637809|ref|YP_978032.1|  70 LGLFHVVVNASMLWLTAWITEHTThwglQIDHFWWTAIWAAILLSIVSWILSLL 123
                                    67888999999999999998777778878889999***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 925.26
//
Query:       gi|121637810|ref|YP_978033.1|  [L=143]
Description: hypothetical protein BCG_1943 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-13   49.8   0.0    2.7e-13   49.6   0.0    1.1  1  STAS      STAS domain
    1.3e-05   25.4   0.1    2.3e-05   24.6   0.1    1.4  1  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0     3e-17   2.7e-13       4     117 .]      32     135 ..      29     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3e-17
                                    EEECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EE CS
                           STAS   4 aeeiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvev 83 
                                    +e + + +++++ g+id+ n   +++ +++ ++         +++ ++++d+ +++f+ s++ ++L +   +++r+gv++
  gi|121637810|ref|YP_978033.1|  32 TECTGSAVVVHVGGDIDASNEVAWQRLVSKSAAIA-------IAPGPFVIDIRDLDFMGSCAYAVLAQESVRCRRRGVNM 104
                                    56778889*************************98.......599*********************************** PP

                                    EEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  84 vlvnikpevreklektgffdeveeeklfltvhdA 117
                                     lv+ +p v++++ ++g+ + +   +l+  v++A
  gi|121637810|ref|YP_978033.1| 105 RLVSNQPIVARTIAACGLRRLI---PLYAMVETA 135
                                    **********************...999988876 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   2.6e-09   2.3e-05       1      79 [.      41     122 ..      41     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-09
                         STAS_2   1 LsLsGeldldtaaelreqlleal....aagaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlldl 76 
                                    +++ G++d+++  ++++ + + +    a+g + v+D +++ ++ s a a+L++   ++r+rg  ++l+   p ++r+ + 
  gi|121637810|ref|YP_978033.1|  41 VHVGGDIDASNEVAWQRLVSKSAaiaiAPG-PFVIDIRDLDFMGSCAYAVLAQESVRCRRRGVNMRLVSNQPIVARTIAA 119
                                    688999999999998888888555777999.*****************************************9**99999 PP

                         STAS_2  77 yGl 79 
                                     Gl
  gi|121637810|ref|YP_978033.1| 120 CGL 122
                                    988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 994.14
//
Query:       gi|121637811|ref|YP_978034.1|  [L=320]
Description: D-amino acid oxidase aao [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-33  115.7   4.9    3.9e-33  115.5   4.9    1.0  1  DAO            FAD dependent oxidoreductase
    5.9e-06   25.6   0.7    8.8e-06   25.0   0.7    1.3  1  FAD_binding_2  FAD binding domain
     0.0044   16.2   0.5     0.0062   15.7   0.5    1.2  1  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.011   15.0   0.3      0.017   14.3   0.3    1.3  1  Thi4           Thi4 family
      0.015   14.6   0.1      0.022   14.0   0.1    1.2  1  FAD_binding_3  FAD binding domain
      0.025   14.8   0.6      0.057   13.7   0.6    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.066   11.9   0.5       0.11   11.1   0.5    1.3  1  HI0933_like    HI0933-like protein
       0.12   11.6   0.1       0.18   11.0   0.1    1.3  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.13   11.5   0.1       0.25   10.6   0.1    1.5  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   4.9     2e-36   3.9e-33       2     351 ..       8     315 ..       7     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 2e-36
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTT CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgidi 79 
                                    v++iG+G+ Gl+ A  La++g  V +  ++  + + +S  +++++ +    +++  ++  + +++l+ +r+l+++  + +
  gi|121637811|ref|YP_978034.1|   8 VIVIGAGVSGLTSAICLAEAGwpVRVWAAA-LPQQTTSAVAGAVWGP-RP-KEPVAKVRGWIEQSLHVFRDLAKD--PAT 82 
                                    9*****************************.9985666666555555.54.55543666**************97..66* PP

                                    SEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.ST.TTSEEEEETTEEEEEHHHHHHHHHHHHH CS
                            DAO  80 dyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lp.gllgalfypdtgqvdpakltaalaraae 157
                                    ++r+t  ls++ d     ++ +  a+  + gl  el+    vr  +pa +p g++++++ +    +d  +++  l ++++
  gi|121637811|ref|YP_978034.1|  83 GVRMTPALSVG-D-----RI-ETGAM--PPGL--ELIPD--VRPADPAdVPgGFRAGFHATL-PMIDMPQYLDCLTQRLA 148
                                    **********8.4.....45.22333..5676..47754..999999875579999999888.999************** PP

                                    HTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEEEEECCTHSTG CS
                            DAO 158 alGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkeldlpispvrgqvlvlkplseklvs 236
                                    a G+ei ++ + ++l      +        ++   a  v+n+aG++++ l+   ++    + p+ gq++vl ++ ++++ 
  gi|121637811|ref|YP_978034.1| 149 ATGCEIETR-PLRSL------AEAA-----EA---APIVINCAGLGAReLA---GDA--TVWPRFGQHVVLTNPGLEQL- 207
                                    ********9.****9......3344.....33...678********99666...655..99**********66555332. PP

                                    SGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCG..EEEEEEEEEEETT CS
                            DAO 237 paailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgd..vlrkwaGlrplpd 314
                                           ++ +++g   +++    +rv++Gg    ++++d+ ++++e  +++l+++r++ P+l++  v ++ +Glrp ++
  gi|121637811|ref|YP_978034.1| 208 -------FIERTGGSEWICYFAHPQRVVCGGIS-IPGRWDT-TPEPEITERILQRCRRIQPRLAEaaVIETITGLRPDRP 278
                                    .......3355555555666555689**99987.8888888.********************95544779*******333 PP

                                    S.....SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 315 g.....lpligetpgvkglylatGhsghGltlapatGkllae 351
                                           p ig+       ++++Gh+g G+tl++++++ +++
  gi|121637811|ref|YP_978034.1| 279 SvrveaEP-IGR----ALCIHNYGHGGDGVTLSWGCAREVVN 315
                                    31222133.344....479*******************9987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.7   4.4e-09   8.8e-06       2      49 ..       8      54 ..       7      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.4e-09
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl 49
                                   viViG+G++GL++A+ +aeaG  v v   + +++ ++a + G ++ ++
  gi|121637811|ref|YP_978034.1|  8 VIVIGAGVSGLTSAICLAEAGWPVRVWAAALPQQTTSAVA-GAVWGPR 54
                                   9*******************************99888888.5667666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   3.1e-06    0.0062       1      30 [.       7      36 ..       7      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                   +viViG+G +G+  A+ +a++G +v   + 
  gi|121637811|ref|YP_978034.1|  7 QVIVIGAGVSGLTSAICLAEAGWPVRVWAA 36
                                   69***********************98843 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   8.7e-06     0.017      16      44 ..       4      31 ..       1      52 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                                   TEEEEEEE--SHHHHHHHHHHHHCTTS-E CS
                           Thi4 16 aesDvvivGaGssGLtaayylakkpdlkv 44
                                    e+ v+++GaG sGLt+a  la++ +  v
  gi|121637811|ref|YP_978034.1|  4 GEQQVIVIGAGVSGLTSAICLAEA-GWPV 31
                                   5889******************98.4444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.1e-05     0.022       2      29 ..       6      33 ..       5      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEE CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvl 29
                                    +V+++GaG +Gl++a  L+eaG  v++
  gi|121637811|ref|YP_978034.1|  6 QQVIVIGAGVSGLTSAICLAEAGWPVRV 33
                                   58*********************77765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   2.9e-05     0.057       1      25 [.      10      34 ..      10      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                   ++GaG+sGl+ A  La+ag  v ++
  gi|121637811|ref|YP_978034.1| 10 VIGAGVSGLTSAICLAEAGWPVRVW 34
                                   8*****************9888776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   5.7e-05      0.11       2      28 ..       7      33 ..       6      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEE CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVll 28
                                   +viviG+G +Gl  Ai +a++g  V +
  gi|121637811|ref|YP_978034.1|  7 QVIVIGAGVSGLTSAICLAEAGWPVRV 33
                                   79******************9988876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.8e-05      0.18       2      29 ..       7      34 ..       6      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlv 29
                                   +v+viG+G+ Gl+ a+ la+ag  v + 
  gi|121637811|ref|YP_978034.1|  7 QVIVIGAGVSGLTSAICLAEAGWPVRVW 34
                                   79*****************999888765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00012      0.25     164     196 ..       5      37 ..       1      79 [. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                    Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrg 196
                                    +q+v+ViG++ S+   A+ l+++g  V+v    
  gi|121637811|ref|YP_978034.1|   5 EQQVIVIGAGVSGLTSAICLAEAGWPVRVWAAA 37 
                                    689999999999999999999999888876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2063.88
//
Query:       gi|121637812|ref|YP_978035.1|  [L=156]
Description: hypothetical protein BCG_1945c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1134.32
//
Query:       gi|121637813|ref|YP_978036.1|  [L=215]
Description: hypothetical protein BCG_1946c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-32  112.6   0.1      2e-32  112.1   0.1    1.2  1  DUF4262   Domain of unknown function (DUF4262)


Domain annotation for each model (and alignments):
>> DUF4262  Domain of unknown function (DUF4262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.1   1.1e-36     2e-32       5     127 .]      84     197 ..      81     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1.1e-36
                        DUF4262   5 yGwavqaveaedeeeppfaYTvGltetfghpElivfGlppelahalLnevadrvregerlleggeleddvlegypvklle 84 
                                    +Gwavq+ve    e+ pfaYTvGlt++ g+pEl+v+Gl+p+  ++lLn +a+r+  g+ l++g +++      +   +++
  gi|121637813|ref|YP_978036.1|  84 HGWAVQHVEC---ERRPFAYTVGLTRR-GLPELVVTGLSPRRGQRLLNIAARRALVGDLLTPGMQTTL----PAGPLVET 155
                                    9*******75...79************.*****************************99999999995....34444455 PP

                        DUF4262  85 veesayeeylgvAlafygeedvpalQlvwpDreGrfPwepgyd 127
                                    v+ ++++++l +A+a++g++ v alQlvw+Dr+Gr+Pw +++d
  gi|121637813|ref|YP_978036.1| 156 VQVTHPDAHLYCAIAIFGDK-VTALQLVWADRRGRWPWAADFD 197
                                    55589**************7.******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1791.55
//
Query:       gi|121637814|ref|YP_978037.1|  [L=740]
Description: catalase-peroxidase-peroxynitritase T katG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.9e-88  293.8   0.0    1.3e-47  162.4   0.0    2.3  2  peroxidase  Peroxidase


Domain annotation for each model (and alignments):
>> peroxidase  Peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.0   7.3e-52   1.3e-47       9     226 ..      91     397 ..      77     400 .. 0.90
   2 !  129.2   0.0     1e-41   1.9e-37       2     228 ..     406     713 ..     405     714 .. 0.88

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 7.3e-52
                                    CCC.TTTHCHHHHHHHHHHHTT.......SSTTSCHHHTCCHHCSGGGTTTHHHHHHHHHHHHHCTT.....S-HHHHHH CS
                     peroxidase   9 lka.drdmgpsllrlafhdcfv.......gGcdgsvlllepektapaNaslrkgldvldaikakleaacpgvvScADlia 80 
                                    + a ++++gp ++r+a+h +++       gG+ g++++++p +++p+Nasl+k++++l+++k+k++++    +S+ADli+
  gi|121637814|ref|YP_978037.1|  91 WPAdYGHYGPLFIRMAWHAAGTyrihdgrGGAGGGMQRFAPLNSWPDNASLDKARRLLWPVKKKYGKK----LSWADLIV 166
                                    3335899*********************9*************************************95....******** PP

                                    HHHHHHHHCTT--..--EE---S-SSGGGS-S........................................-.-TS-HH CS
                     peroxidase  81 laardavelaggplvpvslGRrDatessasev.snl....................................Pdptasvd 123
                                    +a+++a+e +g +++ + +GR D++e++++++ ++                                     Pdp a + 
  gi|121637814|ref|YP_978037.1| 167 FAGNCALESMGFKTFGFGFGRVDQWEPDEVYWgKEAtwlgderysgkrdlenplaavqmgliyvnpegpngnPDPMAAAV 246
                                    *************99*****************65559****************************99999999******* PP

                                    HHHHHHHHHT--HHHHHHH.HGGGGC-EESHH................SS-GGGT......HHS..............EE CS
                     peroxidase 124 elrdkfarkgltdeelvaL.sGaHtiGkahcssfsrly.a....aadpaldaayaae..kCasgnte......lvdldtp 189
                                    ++r++f+r+ ++d e+ aL +G+Ht+Gk+h++  + l       a+ ++++ +++++  +  +g+++      +v ++tp
  gi|121637814|ref|YP_978037.1| 247 DIRETFRRMAMNDVETAALiVGGHTFGKTHGAGPADLVgPepeaAPLEQMGLGWKSSygT-GTGKDAitsgieVVWTNTP 325
                                    ******************************8755566642688888889******88652.23333345577677777** PP

                                    TS-STHHHHHHCC...................................T-EEEHHHHHHHHSCCCHHHHHHC CS
                     peroxidase 190 tkfdnsyfknlle...................................krgllrsDqvllsdsetralveky 226
                                    tk+dns+ + l                                     + ++l++D++l  d+ ++ + ++ 
  gi|121637814|ref|YP_978037.1| 326 TKWDNSFLEILYGyeweltkspagawqytakdgagagtipdpfggpgrSPTMLATDLSLRVDPIYERITRRW 397
                                    *********9999**************************************************999998875 PP

  == domain 2  score: 129.2 bits;  conditional E-value: 1e-41
                                    HHHHHHCCCC.TTTHCHHH.........HHHHHHH......................................HTT.... CS
                     peroxidase   2 rafvkaalka.drdmgpsl.........lrlafhd......................................cfv.... 29 
                                    ++f+ka++k  +rdmgp            +l ++d                                      + +    
  gi|121637814|ref|YP_978037.1| 406 DEFAKAWYKLiHRDMGPVArylgplvpkQTLLWQDpvpavshdlvgeaeiaslksqilasgltvsqlvstawaA-Assfr 484
                                    6899*************66677999999**********************999999999999988888776651.15566 PP

                                    .....SSTTSCHHHTCCHHCSGGGT...TTHHHHHHHHHHHHHCTT.......S-HHHHHHHHHHHHHHCT....T--.. CS
                     peroxidase  30 .....gGcdgsvlllepektapaNa...slrkgldvldaikakleaacpg..vvScADlialaardavela....ggp.l 94 
                                         gG++g++++l+p+  ++ N+    lrk++++l++i++++++a pg  +vS+ADl++l++++a+e+a    g+  +
  gi|121637814|ref|YP_978037.1| 485 gsdkrGGANGGRIRLQPQVGWEVNDpdgDLRKVIRTLEEIQESFNSAAPGniKVSFADLVVLGGCAAIEKAakaaGHNiT 564
                                    88999*********************99**********************855*****************8888666677 PP

                                    .--EE---S-SSGGG.S-S...................-.-TS-HHH.HHHHHHHHT--HHHHHHH.HGGGGC-EESHH. CS
                     peroxidase  95 vpvslGRrDatessa.sev.snl...............Pdptasvde.lrdkfarkgltdeelvaL.sGaHtiGkahcss 155
                                    vp+++GR+Da+++++ +e+ + l               P     ++  l+dk++ ++l+++e+++L +G++++G++++  
  gi|121637814|ref|YP_978037.1| 565 VPFTPGRTDASQEQTdVESfAVLepkadgfrnylgkgnP---LPAEYmLLDKANLLTLSAPEMTVLvGGLRVLGANYK-- 639
                                    8**************888855558666666666655443...5688889****************************3.. PP

                                    ..........SS-GGGT....HHS........EETS-STHHHHHHCC........................T-EEEHHHH CS
                     peroxidase 156 fsrlyaaadpaldaayaaekCasgntelvdldtptkfdnsyfknlle........................krgllrsDq 211
                                      rl                        v+++ +++++n++f+nll+                        k++ +r+D+
  gi|121637814|ref|YP_978037.1| 640 --RLPL---------------------GVFTEASESLTNDFFVNLLDmgitwepspaddgtyqgkdgsgkvKWTGSRVDL 696
                                    ..3321.....................45666789********************************************* PP

                                    HHHHSCCCHHHHHHCCC CS
                     peroxidase 212 vllsdsetralvekyae 228
                                    v++s+se+ralve+y +
  gi|121637814|ref|YP_978037.1| 697 VFGSNSELRALVEVYGA 713
                                    ***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 5168.83
//
Query:       gi|121637815|ref|YP_978038.1|  [L=150]
Description: ferric uptake regulation protein furA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-18   65.2   0.0    7.1e-18   64.9   0.0    1.1  1  FUR        Ferric uptake regulator family
     0.0026   17.6   0.0     0.0047   16.8   0.0    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.038   13.8   0.0        0.1   12.4   0.0    1.7  2  PASTA      PASTA domain
      0.059   13.9   0.0      0.091   13.3   0.0    1.3  1  HTH_27     Winged helix DNA-binding domain
        0.1   12.5   0.3       0.37   10.7   0.3    1.9  1  MarR_2     MarR family
       0.12   12.3   0.4       0.12   12.3   0.4    2.2  2  Nudix_N_2  Nudix N-terminal


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   2.4e-21   7.1e-18       2     110 ..      17     124 ..      16     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.4e-21
                                    TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEE CS
                            FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhdhl 81 
                                    a+l++T++R ++le  + +  h + e ++  ++   p++s   VY +L+ l+ aglv++++ +++ +rye + +++h+h+
  gi|121637815|ref|YP_978038.1|  17 ADLRVTRPRVAVLEAVNAH-PHADTETIFGVVRFALPDVSRQAVYDVLHALTAAGLVRKIQPSGSVARYESRVGDNHHHI 95 
                                    579***********98765.4*********************************************************** PP

                                    EETTT--EEEE--HHHHHHHHHHHHHTT- CS
                            FUR  82 icekCgkviefkddeiekiqeeiaekegf 110
                                    +c++Cg + +++    e+   ++++++gf
  gi|121637815|ref|YP_978038.1|  96 VCRSCGVIADVDCAVGEAPCLTASDHNGF 124
                                    **********9876555555555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.6e-06    0.0047      33      58 ..      53      78 ..      51      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                                   TSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 33 gvprskvYevLrsLedkGlVerekgr 58
                                   +v+r+ vY+vL  L  +GlV++++ +
  gi|121637815|ref|YP_978038.1| 53 DVSRQAVYDVLHALTAAGLVRKIQPS 78
                                   699*******************9844 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.91   2.7e+03      11      27 ..       7      23 ..       5      32 .. 0.72
   2 ?   12.4   0.0   3.5e-05       0.1       3      42 ..      51      83 ..      49      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHTT--CCC CS
                          PASTA 11 vdeAkatLkalGlkikt 27
                                   + ++ ++L+ + l+++ 
  gi|121637815|ref|YP_978038.1|  7 IPDYAEQLRTADLRVTR 23
                                   55778888888886655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.5e-05
                                   --TTTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTBEEE CS
                          PASTA  3 vPdvtGmsvdeAkatLkalGlkiktveetsddvpeGtVis 42
                                    Pdv  + v ++  +L+a+Gl       + + +p+G+V++
  gi|121637815|ref|YP_978038.1| 51 LPDVSRQAVYDVLHALTAAGL-------VRKIQPSGSVAR 83
                                   7********************.......889999999875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05     0.091       1      50 [.      21      74 ..      21      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                         HTH_27  1 ltrqqalvLhlir...hrrrrkkladlcgrlnvedshis.yslkkLtekGLver 50
                                   +tr+ ++vL+ ++   h + + +   ++++l   + +++  +l +Lt++GLv +
  gi|121637815|ref|YP_978038.1| 21 VTRPRVAVLEAVNahpHADTETIFGVVRFALPDVSRQAVyDVLHALTAAGLVRK 74
                                   799***********7776677777*******666666666************44 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00013      0.37      32      54 ..      53      75 ..      19      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                   TSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 32 glsksavsrilkrLvaaGLverr 54
                                   ++s++av  +l  L aaGLv++ 
  gi|121637815|ref|YP_978038.1| 53 DVSRQAVYDVLHALTAAGLVRKI 75
                                   69******************986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   3.9e-05      0.12      12      31 ..      84     103 ..      79     104 .. 0.82
   2 ?   -1.0   0.2      0.56   1.7e+03      25      29 ..     137     141 ..     136     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                    EE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2  12 lripdgDnreRlvCpaCgti 31 
                                    ++   gDn++  vC +Cg i
  gi|121637815|ref|YP_978038.1|  84 YESRVGDNHHHIVCRSCGVI 103
                                    55667*************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.56
                                    ETTTT CS
                      Nudix_N_2  25 CpaCg 29 
                                    Cp+C+
  gi|121637815|ref|YP_978038.1| 137 CPDCS 141
                                    88885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.57
# Mc/sec: 798.62
//
Query:       gi|121637816|ref|YP_978039.1|  [L=197]
Description: hypothetical protein BCG_1949c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-21   76.9   0.0    2.5e-21   76.3   0.0    1.2  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   1.4e-25   2.5e-21       2     132 .]      69     195 ..      68     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.4e-25
                                    --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC.....EE-B-TTSSCCC CS
                            PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega.....vqgknslgeese 74 
                                    +p++y  +g n++Ppl+ws         alvv DpDap ++  ++Hw+v++i + + s ++g+     +++ ns+g+   
  gi|121637816|ref|YP_978039.1|  69 IPEQYtcKGANIAPPLTWSA----PFGGALVVDDPDAP-REP-YVHWIVIGIAPGAGSTADGEtpgggISLPNSSGQ--- 139
                                    7888888999*********8....45679********9.444.9**********99999999999999999999999... PP

                                    CS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                            PBP  75 sgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                     +Y gpcPp+g+g+H+Y f+ly+l +      ag +  ++ + ia+++  +a+l g+Y
  gi|121637816|ref|YP_978039.1| 140 PAYTGPCPPAGTGTHHYRFTLYHLPAVP--PLAGLAGTQAARVIAQAATMQARLIGTY 195
                                    9*********************976664..3344443455555777777788888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1253.15
//
Query:       gi|121637817|ref|YP_978040.1|  [L=201]
Description: lipoprotein lppC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-28   98.8   0.0      4e-28   98.4   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   2.2e-32     4e-28       2     132 .]      69     199 ..      68     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.2e-32
                                    --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC.....EE-B-TTSSCCC CS
                            PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega.....vqgknslgeese 74 
                                    +p+++  +g n++Ppl+ws+ p+g+ ++alvv DpDa   +  ++Hw+vt+i +   s ++g+      ++ ns g+   
  gi|121637817|ref|YP_978040.1|  69 IPVQFscKGANVAPPLTWSS-PAGAAELALVVDDPDAV-GG-LYVHWIVTGIAPGSGSTADGQtpaggHSVPNSGGR--- 142
                                    7888888999*********9.****************8.33.3**********999999999897666666666666... PP

                                    CS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                            PBP  75 sgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                    +gY+gpcPp+g+g+H+Y f+ly+l v+  +l++g+t  ++ +aia+++ ++a+l+g++
  gi|121637817|ref|YP_978040.1| 143 QGYFGPCPPAGTGTHHYRFTLYHLPVAL-QLPPGATGVQAAQAIAQAASGQARLVGTF 199
                                    9*************************95.799999999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1449.29
//
Query:       gi|121637818|ref|YP_978041.1|  [L=334]
Description: oxidoreductase fadB5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-26   93.3   0.0    2.2e-26   92.4   0.0    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    3.8e-18   66.8   0.0    1.1e-17   65.4   0.0    1.8  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.6e-08   34.4   0.0    3.7e-08   33.2   0.0    1.6  1  ADH_N         Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   3.6e-30   2.2e-26       1     129 [.     152     290 ..     152     291 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 3.6e-30
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                    gvG+aavq+Aka++aev++++s + k ++++++G+d++i+y   + + +++ l    ++dvv++++G g++l+++++ll+
  gi|121637818|ref|YP_978041.1| 152 GVGIAAVQFAKAAKAEVHGTASPQ-KHQKLAEFGVDRAIDY---RRDGWWQGLG---PYDVVLDALG-GTSLRRSYTLLR 223
                                    9******************87655.57**************...68********...**********.************ PP

                                    EEEEEEECSC..TSSEEE................EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  81 pgGrlvvvGg..gkgeee................fdlrnlllkeksilGsllgslreefkealdlla 129
                                    pgGrlv +G+  ++++e+                f+l+++l ++k+++G ++ +l+++ +++ +++a
  gi|121637818|ref|YP_978041.1| 224 PGGRLVGYGIsnMQHGEKrsmrrvaphalsmlrgFNLMKQLEESKTVIGLNMLRLWDDRRTLEPWIA 290
                                    ***********98888889*******************************************99986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   1.8e-21   1.1e-17       2     133 .]     184     332 ..     183     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.8e-21
                                    T-SEEEETTSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--...................S-EEE- CS
                   ADH_zinc_N_2   2 GAdevidyrtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp..................lsaall 62 
                                    G+d +idyr++ +  + g + +Dvvld++gg++l ++s ++l++gGrlv +g + +                  l+   l
  gi|121637818|ref|YP_978041.1| 184 GVDRAIDYRRDGW--WQGLGPYDVVLDALGGTSL-RRSYTLLRPGGRLVGYGiSNMqhgekrsmrrvaphalsmLRGFNL 260
                                    99*******7777..556688***********99.*******888*******8776888666666666665553222222 PP

                                    CHHHCTTT-EEEE--GGG...-.................-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS- CS
                   ADH_zinc_N_2  63 kpakkrkgrsvkyeflfsmkas................aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgr 126
                                    ++++ ++              s                  +  ++ l++ + +G++ p v    p++ea+eAhr l+++ 
  gi|121637818|ref|YP_978041.1| 261 MKQL-EE--------------SktviglnmlrlwddrrTLEPWIAPLTKALNDGTILPIVHAIVPFAEAPEAHRILAARE 325
                                    3323.22..............2444444344444344444444599********************************** PP

                                    -SSEEEE CS
                   ADH_zinc_N_2 127 arGKiVl 133
                                     +GK+Vl
  gi|121637818|ref|YP_978041.1| 326 NVGKVVL 332
                                    ******8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   6.1e-12   3.7e-08       2      64 ..      29      91 ..      28     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6.1e-12
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SE CS
                          ADH_N  2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepl 64
                                   g++++ v+aag++  D     g      klp ++G E++G+ve+vg++v+  +vG+rV++   
  gi|121637818|ref|YP_978041.1| 29 GQLRVAVRAAGVNFADHLARVGLYPDAPKLPAVVGYEVAGTVEAVGDGVDPNRVGERVLAGTR 91
                                   7899*************99999899999******************************98543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2420.59
//
Query:       gi|121637819|ref|YP_978042.1|  [L=250]
Description: hypothetical protein BCG_1952 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-20   74.0   9.4    2.6e-20   73.3   9.4    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.6e-06   26.3   2.1    2.5e-05   23.9   2.1    2.1  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   9.4   2.9e-24   2.6e-20       2     193 ..      18     212 ..      17     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2.9e-24
                                    CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                    Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                    +++ v++ l++g +g +L+DtGt+  +a a  +   + + + +v++v+lTH H+DH+ g   + +a  ++  +v e++++
  gi|121637819|ref|YP_978042.1|  18 PFCDVTVGLVRGRTGILLVDTGTTLGEATAI-AADVKQIAGCQVTHVVLTHKHFDHVLGSSVFDQAEVFCAPEVVEYLRS 96 
                                    5788999**********************97.5*********************************************** PP

                                    CHCHHHHHHHHHCCHH....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEET......TCCEEEECTT CS
                    Lactamase_B  82 lfmeeaddaasrkgll....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyg......ggkvlftGDa 151
                                     +++ ++da s++ +     +a++  ++p++ + + ++++g+r  + +++g gh+  ++vv ++      g +v+ftGD+
  gi|121637819|ref|YP_978042.1|  97 ATDRLREDALSYGADTaevdRAIAALKPPQHGIYDAAVDLGDRTVTITHPGSGHTTADLVVVAPatghadGPTVVFTGDL 176
                                    ************9999********************************************9766222222678******* PP

                                    TSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEE CS
                    Lactamase_B 152 llagetgridltlrgaevrdpsdaekyldsllklaglkaevl 193
                                    + +   ++id       + d + +  +ld++l + g++a+++
  gi|121637819|ref|YP_978042.1| 177 VEESADPDIDA------DSDLAAWPATLDRVLAIGGPDASYV 212
                                    ***********......***************9999999887 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   2.1   2.7e-09   2.5e-05       3      82 ..      34     106 ..      33     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.7e-09
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                    +L+D+g+ l +  +     v++ +   ++  V+lth+H+DH+ g   + +     +++++ ++v ++l++ +++l  +  
  gi|121637819|ref|YP_978042.1|  34 LLVDTGTTLGEA-TAIAADVKQIAG-CQVTHVVLTHKHFDHVLGSSVFDQ-----AEVFCAPEVVEYLRSATDRLREDAL 106
                                    589999997666.433344543333.48999*************888888.....579***********99877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1759.54
//
Query:       gi|121637820|ref|YP_978043.1|  [L=135]
Description: hypothetical protein BCG_1953c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1123.32
//
Query:       gi|121637821|ref|YP_978044.1|  [L=766]
Description: isocitrate lyase aceA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.1e-119  400.3   0.0    2.4e-70  237.5   0.0    2.0  2  ICL         Isocitrate lyase family
    3.1e-11   43.2   0.0    1.2e-10   41.3   0.0    2.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.5   0.0   2.7e-74   2.4e-70       1     263 [.      21     285 ..      21     319 .. 0.95
   2 !  160.9   0.1   4.6e-51   4.1e-47     284     525 ..     360     599 ..     333     600 .. 0.89

  Alignments for each domain:
  == domain 1  score: 237.5 bits;  conditional E-value: 2.7e-74
                                    HHHXHHHHHTSGGGGG---SS-HHHHHHH--SS----T.HHHHHHHHHHHHHHHHHHT--EEEEB--SHHHHHHHHHH.- CS
                            ICL   1 evaevkkwwsdsrwrktkrvysaedivskrGnlkieya.sseqakklfklleeheaektasktfGaldpvqvtqmaky.l 78 
                                    +va+ ++++++sr+    r y+a+++v++rG++ +++  + e a  +++ l+e +a +++ +tfG   p q   m +  +
  gi|121637821|ref|YP_978044.1|  21 DVAATQRYFDSSRFAGIIRLYTARQVVEQRGTIPVDHIvAREAAGAFYERLRELFAARKSITTFGPYSPGQAVSMKRMgI 100
                                    68999*****************************98761556677899***********************999988659 PP

                                    S-EEE-HHHHHHH--TT----SS-S-S-TTHHHHHHHHHHHHHHHHHHHHHHHHHSS-HHHHTTS--------EEEE-TT CS
                            ICL  79 dtiyvsGwqssstastsnepspdladypmdtvpnkvehlflaqlfhdrkqkeerlkvkkeereklanvdylrpiiadadt 158
                                    ++iy+ Gw +s+  s++++p+pdla yp+  vp+    l  a l  dr q+  rl++++ +r+ ++  d+   iiadadt
  gi|121637821|ref|YP_978044.1| 101 EAIYLGGWATSAKGSSTEDPGPDLASYPLSQVPDDAAVLVRALLTADRNQHYLRLQMSERQRAATPAYDFRPFIIADADT 180
                                    **********************************************************************999******* PP

                                    -SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE--GGGEEE CS
                            ICL 159 GhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvartdseaatl 238
                                    GhGG   v  l + f+e G  G hiedq +gtkkcGh  Gkvlvp +e i rl a+r q di+ +  ++vartd+eaa+l
  gi|121637821|ref|YP_978044.1| 181 GHGGDPHVRNLIRRFVEVGVPGYHIEDQRPGTKKCGHQGGKVLVPSDEQIKRLNAARFQLDIMRVPGIIVARTDAEAANL 260
                                    ******************************************************************************** PP

                                    ES-TT-GGGGGGEEEE--TTS--HH CS
                            ICL 239 itstidtrdhafilGatnpdleela 263
                                    i s  d+rd  f+lGat  d+ ++ 
  gi|121637821|ref|YP_978044.1| 261 IDSRADERDQPFLLGATKLDVPSYK 285
                                    ******************9997665 PP

  == domain 2  score: 160.9 bits;  conditional E-value: 4.6e-51
                                    HHHHHHS-EE-SHHHHHHHHHTSS-S-HHHHH..HHHHHHHTT--HH...HHHHHHHHHHSS----BTTSS--TT--EEE CS
                            ICL 284 dewlkkaglklfeeavvdeieksklsnkkeli..kkftkkvkplselsnkearklakellgkdiffdwelprvreGyyry 361
                                      w  +agl ++ eav d++e ++ + +   +  +++ + +    + s + ar+ akel g d  +d el+++ eGyy+ 
  gi|121637821|ref|YP_978044.1| 360 AAWEDDAGLMTYGEAVADVLEFGQSEGEPIGMapEEWRAFA---ARASLHAARAKAKEL-GADPPWDCELAKTPEGYYQI 435
                                    57*******************99876655444114555444...456678999999998.56889*************** PP

                                    --SHHHHHHHHHHHTTS-SEEE---SS--HHHHHHHHHHHHTT-TT-EEEEE--SSS-GGGTS-HHH.HHSHHHHHHHTT CS
                            ICL 362 kGgtqcsvvravafapyadliwmesklpdyaqakefaeGvkakvpeqklaynlspsfnwkkamsade.qetyikrlaklG 440
                                    +Gg+  ++ +++a ap+ad++wme+k+ d+a+a++fae ++a +p+q+laynlspsfnw++++++de ++ + + l+k+G
  gi|121637821|ref|YP_978044.1| 436 RGGIPYAIAKSLAAAPFADILWMETKTADLADARQFAEAIHAEFPDQMLAYNLSPSFNWDTTGMTDEeMRRFPEELGKMG 515
                                    ************************************************************998877659*********** PP

                                    EEEEEETTHHHHHHHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHT-GGGSHHHHHTHHHHHHHHHHHH--XXXXXXXXXX CS
                            ICL 441 yvwqfitlaGlhtnalisdkfakdyakrGmkaygeevqeeeidnGvdvvkhqkwsGaeyidellklvtGGvsstaamGkG 520
                                    +v++fit +G   + +++++fa +  ++Gm a ++ +q++ +       + q   G    d  l   +G  ++t amGkG
  gi|121637821|ref|YP_978044.1| 516 FVFNFITYGGHQIDGVAAEEFATALRQDGMLALAR-LQRKMRLVESPYRTPQTLVGGPRSDAALAASSGRTATTKAMGKG 594
                                    ********************************985.677766666778899***************************** PP

                                    XXXXX CS
                            ICL 521 vtedq 525
                                     t++q
  gi|121637821|ref|YP_978044.1| 595 STQHQ 599
                                    **998 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.3e-14   1.2e-10       9     147 ..      79     256 ..      71     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.3e-14
                     PEP_mutase   9 eplvlpnawDalsakiveeagfkalatsSlavaaslGv.....pDgeelpleellaavraiaevvs.............. 69 
                                    + +     ++++ a  ++++g++a+ ++++a++a         pD    pl+++ + ++ +++++               
  gi|121637821|ref|YP_978044.1|  79 KSITTFGPYSPGQAVSMKRMGIEAIYLGGWATSAKGSStedpgPDLASYPLSQVPDDAAVLVRALLtadrnqhylrlqms 158
                                    56666677777777777888877777777777665432111114557777777766666666665456667777778888 PP

                     PEP_mutase  70 .............lPlivDledGygespeevaetvrrliaaGvvgvniEDk.....kknd.aerqlldieefaekiaaar 130
                                                   +i+D+++G+g +p +v++ +rr++++Gv g +iED+     k++  +++ l++ +e+ ++++aar
  gi|121637821|ref|YP_978044.1| 159 erqraatpaydfrPFIIADADTGHGGDP-HVRNLIRRFVEVGVPGYHIEDQrpgtkKCGHqGGKVLVPSDEQIKRLNAAR 237
                                    88888888888844469********966.**********************9986544453666666************* PP

                     PEP_mutase 131 aaaeeag..fvinARtdal 147
                                     + +      +i+ARtda 
  gi|121637821|ref|YP_978044.1| 238 FQLDIMRvpGIIVARTDAE 256
                                    99999888889******94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4949.15
//
Query:       gi|121637822|ref|YP_978045.1|  [L=1835]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-83  274.9 440.0    5.8e-11   42.1  26.1   17.4 18  Pentapeptide_2  Pentapeptide repeats (8 copies)
    2.1e-57  193.7  25.3    3.2e-57  193.0  25.3    1.3  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   9.0   4.2e-08   0.00038       6      39 ..     204     237 ..     201     237 .. 0.73
   2 !   26.5  35.9   4.7e-10   4.2e-06       2      39 ..     235     272 ..     233     273 .. 0.97
   3 !   26.6  30.1   4.3e-10   3.9e-06       3      39 ..     278     314 ..     276     315 .. 0.96
   4 !   39.8  24.9   3.3e-14   2.9e-10       2      40 .]     318     356 ..     317     356 .. 0.98
   5 !   42.1  26.1   6.4e-15   5.8e-11       2      40 .]     348     386 ..     347     386 .. 0.98
   6 !   34.5  30.9   1.6e-12   1.4e-08       2      40 .]     358     396 ..     357     396 .. 0.98
   7 !   24.9  26.0   1.5e-09   1.3e-05       2      39 ..     368     405 ..     367     406 .. 0.95
   8 ?    1.7  20.4     0.027   2.4e+02       4      38 ..     943     979 ..     941     982 .. 0.82
   9 !    9.5   7.5   9.8e-05      0.88       1      28 [.     984    1011 ..     981    1014 .. 0.70
  10 !   36.2  23.4   4.4e-13   3.9e-09       1      39 [.    1050    1088 ..    1050    1089 .. 0.97
  11 !   19.5  29.4   7.6e-08   0.00068       1      36 [.    1080    1115 ..    1080    1117 .. 0.83
  12 !   28.4  30.5   1.3e-10   1.1e-06       2      39 ..    1122    1159 ..    1121    1160 .. 0.97
  13 !   34.3  33.6   1.7e-12   1.6e-08       3      40 .]    1165    1202 ..    1163    1202 .. 0.97
  14 !   39.5  24.5   4.1e-14   3.7e-10       2      39 ..    1204    1241 ..    1203    1242 .. 0.98
  15 !   41.5  13.6     1e-14   8.9e-11       1      40 []    1243    1282 ..    1243    1282 .. 0.97
  16 ?    3.0   9.6     0.011        97       4      35 ..    1733    1766 ..    1732    1769 .. 0.72
  17 !    8.4   7.0   0.00022         2      14      38 ..    1780    1804 ..    1777    1807 .. 0.65
  18 !    4.2   1.6    0.0044        39      22      39 ..    1815    1832 ..    1811    1834 .. 0.46

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.2e-08
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    l +G +N+Gf+ +G +N G  NlGs N G +n+G
  gi|121637822|ref|YP_978045.1| 204 LSLGLANSGFGQMGAANLGILNLGSLNPGGNNFG 237
                                    5677777888888888888888888887777777 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.7e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G +N+Gs N+G++N+G+gN+G++N+G+gN+G+g tG
  gi|121637822|ref|YP_978045.1| 235 NFGLGNVGSNNVGLGNTGNGNIGFGNTGNGNIGFGLTG 272
                                    9***********************************99 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 4.3e-10
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G  NsG+gN+G+fN+G+gN+G +N+G+gN+G+gn+G
  gi|121637822|ref|YP_978045.1| 278 FGGWNSGTGNIGLFNSGTGNIGIGNTGTGNFGIGNSG 314
                                    8999********************************9 PP

  == domain 4  score: 39.8 bits;  conditional E-value: 3.3e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG++N+G +NtGffN G +NtG +N+G++NtGs+n+Gs
  gi|121637822|ref|YP_978045.1| 318 NTGIGNTGQANTGFFNAGIANTGIGNTGNYNTGSFNLGS 356
                                    *************************************96 PP

  == domain 5  score: 42.1 bits;  conditional E-value: 6.4e-15
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtGs+N+Gs+NtG+fN+Gs NtG+fN G+ NtG gntG+
  gi|121637822|ref|YP_978045.1| 348 NTGSFNLGSFNTGDFNTGSSNTGFFNPGNLNTGVGNTGN 386
                                    **************************************6 PP

  == domain 6  score: 34.5 bits;  conditional E-value: 1.6e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG++N+Gs NtGffN G+ NtG +N+G++NtG +n+G+
  gi|121637822|ref|YP_978045.1| 358 NTGDFNTGSSNTGFFNPGNLNTGVGNTGNVNTGGFNSGN 396
                                    **************************************6 PP

  == domain 7  score: 24.9 bits;  conditional E-value: 1.5e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N G+ NtG +N+G++NtG fN+G++  G++  G
  gi|121637822|ref|YP_978045.1| 368 NTGFFNPGNLNTGVGNTGNVNTGGFNSGNYSNGFFWRG 405
                                    **********************************9776 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.027
                 Pentapeptide_2   4 GslNsGsg.NtGffNlGsgNt.GsfNlGsgNtGsgnt 38 
                                    G++Ns ++  +GffN+G+g t G++N+Gsg +G+ n+
  gi|121637822|ref|YP_978045.1| 943 GFGNSTTTpSSGFFNSGTGGTsGFGNVGSGGSGFWNI 979
                                    677766553789*****998669*******9999986 PP

  == domain 9  score: 9.5 bits;  conditional E-value: 9.8e-05
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNl 28  
                                     gN+G+lN+G   +G +N G++  G +N+
  gi|121637822|ref|YP_978045.1|  984 GNSGFLNVGPLTSGILNFGNTVSGLYNT 1011
                                     5777777777777777777777777765 PP

  == domain 10  score: 36.2 bits;  conditional E-value: 4.4e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     +N G+lN+G++N+G++N+GsgN+Gs+N+GsgN+G+g +G
  gi|121637822|ref|YP_978045.1| 1050 ANDGTLNLGNANLGDYNVGSGNVGSYNFGSGNIGNGSFG 1088
                                     699**********************************99 PP

  == domain 11  score: 19.5 bits;  conditional E-value: 7.6e-08
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36  
                                     gN+G++ +G gN+G+ N G+gN+Gs+NlG++NtG g
  gi|121637822|ref|YP_978045.1| 1080 GNIGNGSFGFGNIGSNNFGFGNVGSNNLGFANTGPG 1115
                                     789999999999999999999999999999999865 PP

  == domain 12  score: 28.4 bits;  conditional E-value: 1.3e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N+G++N+G  N+Gf+N+G+gN+G++N+G+gN+G+g tG
  gi|121637822|ref|YP_978045.1| 1122 NIGFGNIGGNNYGFANIGNGNIGFGNTGTGNIGIGLTG 1159
                                     9***********************************99 PP

  == domain 13  score: 34.3 bits;  conditional E-value: 1.7e-12
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +G lNsGsgN+GffN+G+gN+G+fN+G+gN+G+gn+G+
  gi|121637822|ref|YP_978045.1| 1165 FGALNSGSGNIGFFNSGNGNIGFFNSGNGNVGIGNSGN 1202
                                     8************************************6 PP

  == domain 14  score: 39.5 bits;  conditional E-value: 4.1e-14
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     NtG +N+G++NtG+fN+G++NtG +N+Gs+NtGs n+G
  gi|121637822|ref|YP_978045.1| 1204 NTGLGNVGNANTGLFNTGNVNTGIGNAGSYNTGSYNAG 1241
                                     *************************************9 PP

  == domain 15  score: 41.5 bits;  conditional E-value: 1e-14
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +NtG+lN G++NtG +NlG  NtG++N+G+ NtG++ +Gs
  gi|121637822|ref|YP_978045.1| 1243 TNTGDLNPGNANTGYLNLGDLNTGWGNIGDLNTGALISGS 1282
                                     6************************************996 PP

  == domain 16  score: 3.0 bits;  conditional E-value: 0.011
                 Pentapeptide_2    4 GslNsGsg.NtGffNlGsgN.tGsfNlGsgNtGs 35  
                                     G++Ns ++  +GffN+G g+  G++N+G g +G 
  gi|121637822|ref|YP_978045.1| 1733 GFGNSTTTpSSGFFNSGDGSaSGFGNVGPGISGL 1766
                                     6677665536899999999745999999887765 PP

  == domain 17  score: 8.4 bits;  conditional E-value: 0.00022
                 Pentapeptide_2   14 GffNlGsgNtGsfNlGsgNtGsgnt 38  
                                     G +N+G    G +NlG+  +G++nt
  gi|121637822|ref|YP_978045.1| 1780 GIYNVGQLASGVANLGNTVSGFNNT 1804
                                     6666666666666666666666665 PP

  == domain 18  score: 4.2 bits;  conditional E-value: 0.0044
                 Pentapeptide_2   22 NtGsfNlGsgNtGsgntG 39  
                                     N G +N+G    G++ +G
  gi|121637822|ref|YP_978045.1| 1815 NSGVNNIGQMLLGFFSPG 1832
                                     444444444444444443 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0  25.3   3.6e-61   3.2e-57       2     158 .]       6     162 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 3.6e-61
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPE+nsal++ G+gs+p++aAa aWd+La elasaaa+++sv+++l +e+W Gpssaamaaa+apyl WL+aaaaqa++
  gi|121637822|ref|YP_978045.1|   6 LPPEINSALIFGGAGSEPMSAAAVAWDQLAMELASAAASFNSVTSGLVGESWLGPSSAAMAAAVAPYLGWLAAAAAQAQR 85 
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     A+qa+a++a +ea +aamv+pa++aanr  l++lv +nffGqn+paIaa ea+ye+mwa d+++m+aY+a ++a+a
  gi|121637822|ref|YP_978045.1|  86 SATQAAALVAEFEAVRAAMVQPALVAANRSDLVSLVFSNFFGQNAPAIAAIEAAYEQMWAIDVSVMSAYHAGASAVA 162
                                    *************************************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.01u 0.35s 00:00:01.36 Elapsed: 00:00:00.59
# Mc/sec: 9447.79
//
Query:       gi|121637823|ref|YP_978046.1|  [L=625]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-58  196.2  26.3    7.5e-58  195.1  26.3    1.6  1  PPE             PPE family
    2.2e-55  184.2 334.7    1.3e-12   47.4  18.9    7.8 10  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1  26.3   8.4e-62   7.5e-58       1     157 [.       5     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 8.4e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+nsal++aG+gsgp+laAa+aWdgLa+elasaa ++ sv+a+l +++WqG ss amaaaaapy+ WL+aaa+qae
  gi|121637823|ref|YP_978046.1|   5 VLPPEINSALIFAGAGSGPMLAAASAWDGLATELASAAVSFGSVTAGLVGGSWQGRSSVAMAAAAAPYAGWLAAAATQAE 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA+qa++++a +ea ++amv+pa++aanr  l +lv +n+fGqn+paIaa+ea+yeemwa d++amaaY++ ++a+
  gi|121637823|ref|YP_978046.1|  85 QAATQAQVMVAEFEAVRLAMVQPALVAANRSGLISLVISNLFGQNAPAIAAAEAAYEEMWALDVSAMAAYHSGASAV 161
                                    *************************************************************************9997 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  29.8   1.1e-06      0.01       4      37 ..     208     241 ..     204     241 .. 0.75
   2 !   24.8  30.8   1.6e-09   1.5e-05       1      39 [.     230     268 ..     230     269 .. 0.98
   3 !   26.3  29.1   5.5e-10   4.9e-06       1      39 [.     240     278 ..     240     278 .. 0.99
   4 !   25.2  31.4   1.2e-09   1.1e-05       2      40 .]     266     304 ..     265     304 .. 0.97
   5 !   31.0  31.8     2e-11   1.7e-07       3      40 .]     309     346 ..     307     346 .. 0.97
   6 !   38.2  26.5   1.1e-13   9.8e-10       1      39 [.     317     355 ..     317     356 .. 0.98
   7 !   35.0  23.4   1.1e-12   9.8e-09       1      40 []     337     376 ..     337     376 .. 0.98
   8 !   47.4  18.9   1.4e-16   1.3e-12       1      39 [.     357     395 ..     357     396 .. 0.99
   9 !   38.0  23.7   1.2e-13   1.1e-09       2      39 ..     398     435 ..     397     436 .. 0.98
  10 !   32.4  17.4   6.7e-12     6e-08       1      38 [.     407     444 ..     407     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    G +N+G gN+G++N G gN+G++NlG++N Gsgn
  gi|121637823|ref|YP_978046.1| 208 GLANVGGGNLGNANNGLGNIGNANLGNNNLGSGN 241
                                    7778888888888888888888888888888777 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N G+ N+GsgN+G+fN+Gs+N G +N+G gN G++n+G
  gi|121637823|ref|YP_978046.1| 230 ANLGNNNLGSGNFGSFNIGSANLGGNNIGIGNAGANNFG 268
                                    6*************************************9 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 5.5e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+Gs+N+Gs+N+G  N+G gN G +N+G +N G++ntG
  gi|121637823|ref|YP_978046.1| 240 GNFGSFNIGSANLGGNNIGIGNAGANNFGLANLGNLNTG 278
                                    8*************************************9 PP

  == domain 4  score: 25.2 bits;  conditional E-value: 1.2e-09
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G +N+G+ NtGf+N G gN+G +N+G++N+G+g tG+
  gi|121637823|ref|YP_978046.1| 266 NFGLANLGNLNTGFANAGIGNFGIANTGNNNIGNGLTGN 304
                                    9************************************96 PP

  == domain 5  score: 31.0 bits;  conditional E-value: 2e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G lNsG+gN+G+fN Gs+N+G+fN+G+gN+G+gn+G+
  gi|121637823|ref|YP_978046.1| 309 IGGLNSGNGNVGLFNAGSANIGFFNSGNGNFGIGNSGN 346
                                    89***********************************6 PP

  == domain 6  score: 38.2 bits;  conditional E-value: 1.1e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G +N+Gs+N+GffN+G+gN+G +N+G++ tG +n+G
  gi|121637823|ref|YP_978046.1| 317 GNVGLFNAGSANIGFFNSGNGNFGIGNSGNFSTGLFNPG 355
                                    8*************************************9 PP

  == domain 7  score: 35.0 bits;  conditional E-value: 1.1e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++NsG++ tG+fN G gNtG+ N+Gs+NtG++ +G+
  gi|121637823|ref|YP_978046.1| 337 GNFGIGNSGNFSTGLFNPGHGNTGFLNAGSFNTGMFDVGN 376
                                    8*************************************96 PP

  == domain 8  score: 47.4 bits;  conditional E-value: 1.4e-16
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gNtG+lN+Gs+NtG+f++G++NtGsfN+G++N+G++n+G
  gi|121637823|ref|YP_978046.1| 357 GNTGFLNAGSFNTGMFDVGNANTGSFNVGHYNFGAFNPG 395
                                    8*************************************9 PP

  == domain 9  score: 38.0 bits;  conditional E-value: 1.2e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N+G +NtG+fN+Gs NtG fN+G+ N G +ntG
  gi|121637823|ref|YP_978046.1| 398 NTGTFNTGGANTGWFNTGSINTGAFNIGDMNNGLFNTG 435
                                    *************************************9 PP

  == domain 10  score: 32.4 bits;  conditional E-value: 6.7e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +NtG +N+Gs NtG fN+G  N G fN+G+ N G +  
  gi|121637823|ref|YP_978046.1| 407 ANTGWFNTGSINTGAFNIGDMNNGLFNTGDMNNGVFYR 444
                                    6*********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3348.57
//
Query:       gi|121637824|ref|YP_978047.1|  [L=154]
Description: hypothetical protein BCG_1958c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-21   77.5   2.9    1.3e-21   77.4   2.9    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.034   14.3   0.1    1.7  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   2.9   1.5e-25   1.3e-21       2     143 .]       6     148 ..       5     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.5e-25
                                    EEEEEEEEESS-HHHHHHHHTTTTGGGGT.-TTEEEEECSESTSSSTTTEEEEECCCSSE..EEEEEEEEETTTTEEEEE CS
                Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprW.hpevarveleggggpargvegtvrvggrgt..vreelvevdpegrllsyr 78 
                                    ++++v+++  ap+++ ++lv+d +nw++W +p va++ ++ +g+pa g  g +r+ g+++  v+ee ve++   r++ y+
  gi|121637824|ref|YP_978047.1|   6 FSFEVTKTSSAPAATLFRLVTDGGNWATWaKPIVAQSSWARRGDPAPGGIGAIRKLGMWPvfVQEETVEYEQ-DRRHVYK 84 
                                    6899999**********************999999*****9999995566*******95567********96.7888888 PP

                                    EE..SSS-TSEEEEEEEEECC.ETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  79 iv.kpvpvanyvatwtvtpdg.ggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                    +v +  pv +y +++ +tp + ggt+++w+g f     +  +++p++++a++g+++    +L +++e
  gi|121637824|ref|YP_978047.1|  85 LVgARTPVQDYFGEVVLTPNAsGGTDLRWSGSFTE---KVRGTGPVMRAALGGAVRFFAGQLVKAAE 148
                                    87789**************99778**********3...45557899*************99999887 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.8e-06     0.034       2      35 ..      15      49 ..      14     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-06
                                   SS-HHHHHHHHTTTGGCCSCCCCEEE.EEE.SSSE CS
                 Polyketide_cyc  2 papadqvyalvadvesypeflphcss.vevleeae 35
                                   +apa+++++lv+d  ++ ++ ++++  +++ ++ +
  gi|121637824|ref|YP_978047.1| 15 SAPAATLFRLVTDGGNWATWAKPIVAqSSWARRGD 49
                                   69*******************99985355554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 865.30
//
Query:       gi|121637825|ref|YP_978048.1|  [L=287]
Description: hypothetical protein BCG_1959 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   63.5   0.0    2.1e-17   63.0   0.0    1.2  1  Acyltransferase  Acyltransferase
      4e-10   39.1   0.0    4.9e-10   38.8   0.0    1.1  1  DAGAT            Diacylglycerol acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   2.3e-21   2.1e-17       2     133 ..      47     172 ..      46     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.3e-21
                Acyltransferase   2 vrvtglenlpekgpailvaNHqsy..lDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraa 79 
                                     +v+g en+p+ ++a+lv NH++   +D++ll++ l++++  r v+ ++++++++ip++++++ ++g++  +R       
  gi|121637825|ref|YP_978048.1|  47 PKVYGIENVPT-ERALLVGNHNTLglVDAPLLAAELWERG--RIVRSLGDHAHFKIPGWRDALTRTGVVEGTR------- 116
                                    589*******8.***********999**********9999..89*****************************....... PP

                Acyltransferase  80 gsleniselleegklvviFPEG.....trsregel..lpfkkGlvrlaakakkgvpivPva 133
                                       e +sel+++g+lv++FP G     +r++e++   ++ + G++rla+++  g+pivP+a
  gi|121637825|ref|YP_978048.1| 117 ---EITSELMRRGELVIVFPGGarevnKRKNERYKlvWKNRLGFARLAIQH--GYPIVPFA 172
                                    ...999****************8777655555444599*************..******97 PP

>> DAGAT  Diacylglycerol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   5.4e-14   4.9e-10     106     218 ..      95     204 ..      53     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.4e-14
                          DAGAT 106 gqfrtpfrreillllGlievsresieyvLdkeekGravvlvvGGaeealeahpgketltLkkrkGfvkialktGadLvPv 185
                                    ++f++p  r+ l+ +G++e +re    ++ +   G+ v++ +GGa+e  + +++  +l+ k+r Gf ++a+++G ++vP 
  gi|121637825|ref|YP_978048.1|  95 AHFKIPGWRDALTRTGVVEGTREITSELMRR---GELVIVFPGGAREVNKRKNERYKLVWKNRLGFARLAIQHGYPIVPF 171
                                    789*******************977766654...557999**************************************** PP

                          DAGAT 186 ysfGendvykqvenpkgsklrkvqeklkkvlgl 218
                                     s G ++  + v  ++   l  vq   +k lg 
  gi|121637825|ref|YP_978048.1| 172 ASVGAEHGIDIVLDNESPLLAPVQFLAEKLLGT 204
                                    ****98877777777777777788777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1643.24
//
Query:       gi|121637826|ref|YP_978049.1|  [L=423]
Description: lipoprotein lppF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-11   44.0   0.7      2e-07   31.6   0.2    2.8  2  HAD        haloacid dehalogenase-like hydrolase
    6.2e-05   23.4   0.4    0.00017   21.9   0.1    1.8  2  Hydrolase  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00014       1.3       1      42 [.      72     118 ..      72     126 .. 0.84
   2 !   31.6   0.2   2.2e-11     2e-07      73     183 ..     217     339 ..     168     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                            HAD   1 alfDfDgTLldgdsle.....lllrfllrrgaprlwralreklllal 42 
                                    a+fD+D T + +d ++     +l + l+ ++a ++w a+ ++l  a 
  gi|121637826|ref|YP_978049.1|  72 AIFDWDNTVVKNDIGYatnyyMLQHSLVLQPANQDWHAASRYLTDAA 118
                                    79**************9998888888889999999999988876655 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 2.2e-11
                            HAD  73 lerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlatelevdd..rltgelglegkp 148
                                    ++ ++         +p++++l+   +a G+ ++vvS++++p+v+ ++ e+g   ++v++ +   d+  +lt++l + g++
  gi|121637826|ref|YP_978049.1| 217 VDGYI-------RVYPQMKDLIGTLQAHGIDTWVVSASPEPIVKVWAGEVGldDQHVVGVRSVADQsgKLTAHLVGCGGV 289
                                    22222.......266********999*********************999999999*9996555556*999998888888 PP

                            HAD 149 vrgegkv.....................aalrewlaaegegidleevvayGDspsD 183
                                      g++ v                     +      a +  ++d+  v a GDs sD
  gi|121637826|ref|YP_978049.1| 290 RDGDDSVmtyldgkrcwanqvifgvtgpQ------AFNQLAADRRQVLAAGDSNSD 339
                                    88888888888887666666664333333......555566777779999999999 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.9e-08   0.00017       2     158 ..      70     264 ..      69     282 .. 0.69
   2 ?   -2.0   0.0       0.4   3.6e+03     182     204 ..     319     341 ..     315     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-08
                                    SEEEEESBTTTBCHH........HHHHHHHHHH....................CHHHHHHHHHH......HHCHHHHHHH CS
                                    xxxxxxxxxxxxxxx........xxxxxxxxxx....................xxxxxxxxxxx......xxxxxxxxxx RF
                      Hydrolase   2 ktvvfDkdGTLttge........psvedvivsa....................alalaaaletg......sehpigkalv 47 
                                    k+ +fD d+T+++          +        +                    + a a al ++      + +p+     
  gi|121637826|ref|YP_978049.1|  70 KVAIFDWDNTVVKNDigyatnyyM--------LqhslvlqpanqdwhaasrylTDAAANALSVAcgkvvpAGKPLPTGSN 141
                                    678999999999777433322221........133334445566666666655333333333335555886666666666 PP

                                    HHHHHH......HHHHHHHHHETTTE.HHHHTHHHHHHHH...HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTH CS
                                    xxxxxx......xxxxxxxxxxxxxx.xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  48 aaakar......sgaltgfatfigrg.ayaigkpewltal...dippdlgaaigsaqsqgrtvallqaralavftiadpl 117
                                    a + ++      ++ +tg  +f g++ + + g   w +al      ++l    ++a +q   + +   + ++   +   +
  gi|121637826|ref|YP_978049.1| 142 ALCANEilslldGETTTGQPAFVGNNvRRLAGPYAWSNALsagYTAEELAGFADQAKKQNLAADVGATQQVGTQQVDGYI 221
                                    66666656666444446666677777999999999****9988777777777777777777777777899999999999* PP

                                    HBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                      Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..dd 158
                                    +v+p +++++ +L+a gi++++++ + +  ++  a ++G  d+
  gi|121637826|ref|YP_978049.1| 222 RVYPQMKDLIGTLQAHGIDTWVVSASPEPIVKVWAGEVGldDQ 264
                                    ************************9999999999999994322 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.4
                                    HHHHHTSTGGGEEEEESSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 182 aireLqgkpeevamVGDgvnDaa 204
                                    a ++L ++ ++v++ GD+  Da 
  gi|121637826|ref|YP_978049.1| 319 AFNQLAADRRQVLAAGDSNSDAT 341
                                    56788889999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2302.38
//
Query:       gi|121637827|ref|YP_978050.1|  [L=371]
Description: lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-62  209.1   1.1    1.2e-61  208.7   1.1    1.1  1  Beta-lactamase   Beta-lactamase
  ------ inclusion threshold ------
      0.086   12.4   0.1       0.19   11.3   0.0    1.6  1  Beta-lactamase2  Beta-lactamase enzyme family


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   1.1   1.4e-65   1.2e-61      13     320 ..      58     363 ..      43     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 1.4e-65
                                    TESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTCTTGGGT CS
                 Beta-lactamase  13 gipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPefagpgkg 92 
                                    + pG ++av + gkv++  + G adl++g++ t+dt+f+iaSv+K fta+a+l lve+Gkl+Lddp+s+y+Pe   ++++
  gi|121637827|ref|YP_978050.1|  58 DEPGCSAAVGVEGKVIWSGVRGIADLASGAKITTDTVFDIASVSKQFTATAILLLVEAGKLTLDDPISQYVPE-LPDWAQ 136
                                    57*********************************************************************88.566667 PP

                                    TEBHHHHHTTHSSCSSSSTSTTCTSHHHTH....HHHHHHHHHSB.SSSSTTSCEE-SHHHHHHHHHHHHHHHTSHHHHH CS
                 Beta-lactamase  93 kiTlrdLltHtsGlpdlfasdlleeaaada....aellralatlp.pkyapGtkwgYsntgygllgellekvtgrsleql 167
                                    ++T+++L+  tsG+pd+ a  ++++++       ae+++ala++p ++++pGt++ Ysn +y llge++++++g++l ++
  gi|121637827|ref|YP_978050.1| 137 TVTVEQLMHQTSGIPDYVALLAARGYQVSDrtieAEARQALAAAPeLQFKPGTRFDYSNSNYLLLGEIVHRASGQPLPEF 216
                                    7****************9999999999888****8888888765539999****************************** PP

                                    HHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC.TTTBEEEEHHHHHHHHHHHHHCCSSSSHHH CS
                 Beta-lactamase 168 lreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae.gagglistardlarflglalegglllsaet 246
                                    l+ ei++pLg+  + + p    + +  ++ +g+g ++ + ++ +pa+++ g+gg+ +t++ lar++    ++ ++ s   
  gi|121637827|ref|YP_978050.1| 217 LSAEIFQPLGLA-MVVDPVGKVPNKAVSYEKGTGGNRSEYRVGNPAWEQiGDGGIQTTPSQLARWA----DNYRTGSVGG 291
                                    ********8775.556666666666666666666777777777777777*****************....4566666777 PP

                                    HHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE..STEEEEEEEECGGTEEEEEEESBCSSHHHHHH CS
                 Beta-lactamase 247 laqltaklssgttrpagiraglglGwvladktgapgtfghtG..ggygtyvfvdpeanlvvavltnrdppnedaae 320
                                    l+ l a l +     +g+++++g G v        gt+ h G   g+ t++ +  +++  va+ +n+d+p++ a +
  gi|121637827|ref|YP_978050.1| 292 LKLLEAQLAGAVETEPGGGDRYGAGIVSRA----DGTLDHAGawAGFVTAFHISSDRRTSVAISCNTDKPDPVAMA 363
                                    8888889999999999**********8886....7889*******************************9444433 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.1e-05      0.19       8      45 ..      88     125 ..      84     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                                    EESTTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEE CS
                Beta-lactamase2   8 gvnadeefpaaStiKvpillalleavlegklslderlt 45 
                                    ++  d++f  aS+ K + + a l  v++gkl ld+++ 
  gi|121637827|ref|YP_978050.1|  88 KITTDTVFDIASVSKQFTATAILLLVEAGKLTLDDPIS 125
                                    56789******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2023.78
//
Query:       gi|121637828|ref|YP_978051.1|  [L=446]
Description: lipase lipD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-62  210.0   4.8    6.9e-62  209.6   4.8    1.1  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   4.8   3.9e-66   6.9e-62      11     312 ..      59     394 ..      46     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 3.9e-66
                                    HTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTCTTGG CS
                 Beta-lactamase  11 qggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPefagpg 90 
                                     +++ G a+ v+ d++ v+d + G++d++g+ p+tadt  +++S+tK ++a+++++lv++G+l++d+pV++y+Pef+++g
  gi|121637828|ref|YP_978051.1|  59 GRKFGGGALSVYIDDRQVVDVWTGWSDRQGKVPWTADTGAMVFSATKGLAATVIHRLVDRGLLSYDAPVAEYWPEFGANG 138
                                    57789*************************************************************************** PP

                                    GTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHH.HHHHHHHHHHTSHHHHHHH CS
                 Beta-lactamase  91 kgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgyg.llgellekvtgrsleqllr 169
                                    k ++T+ d+l+H+sGl++l    + +e + d+  + ++la++p+++++G+   Y++++yg ll  l+++vtg+ +++l+r
  gi|121637828|ref|YP_978051.1| 139 KSEVTVSDVLRHRSGLAHL-KGVDKDEVM-DHLLMEQKLAAAPLNRQHGKLA-YHAVTYGwLLSGLARAVTGKGMRELFR 215
                                    ****************888.333333333.568999*************997.*************************** PP

                                    HHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC................................. CS
                 Beta-lactamase 170 eeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae................................. 216
                                    ee++rpL+   ++lg p+++ p+ aa      p+a++p++ l++ a                                  
  gi|121637828|ref|YP_978051.1| 216 EELARPLNTDGIHLGRPPADSPTKAAQTLL--PQAKVPTPLLDFIAPkvaglsfsgllgavyfpgilsllqddmpfldge 293
                                    ********************9999998855..5555555555555556699***************************** PP

                                    .TTTBEEEEHHHHHHHH.....HHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEEST CS
                 Beta-lactamase 217 .gagglistardlarfl.....glalegglllsaetlaqltaklssgttrpagiraglglGwvladktgapgtfghtGgg 290
                                     +a +++ tar la+ +     +++++g++lls ++ + lt k   +++ + g + ++  G++ ++ +g   ++gh G  
  gi|121637828|ref|YP_978051.1| 294 vPAVNGVVTARALAKTYgalanDGVIDGTRLLSSQAVRGLTGKSELWPDLNLGLPFTYHQGYQSSPVPGLLEGYGHIG-L 372
                                    **********************777999999999999999**************************************.* PP

                                    EEEEEEEECGGTEEEEEEESBC CS
                 Beta-lactamase 291 ygtyvfvdpeanlvvavltnrd 312
                                    +gt  ++dpe++ ++ ++ nr 
  gi|121637828|ref|YP_978051.1| 373 GGTIGWADPETGSAFGYVHNRL 394
                                    ********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2540.63
//
Query:       gi|121637829|ref|YP_978052.1|  [L=126]
Description: hypothetical protein BCG_1963c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 876.44
//
Query:       gi|121637830|ref|YP_978053.1|  [L=620]
Description: fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-61  207.4   0.0    3.6e-61  207.0   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   0.0     2e-65   3.6e-61      22     421 ..      68     506 ..      42     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 2e-65
                                    EEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET...TS-HHHHHHHHHHHTESEE CS
                    AMP-binding  22 tlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp...tltaeelayiledseakvl 98 
                                     +T+ ++  r  +++a+ ++  +++gdrVail+p+++++v  ++a+ kaG v+vpl +      ae+l  +l+dse+ v+
  gi|121637830|ref|YP_978053.1|  68 EVTWTQFGMRLAAIGAHVQR-FAGPGDRVAILAPQGIDYVCGFYAAIKAGTVAVPLFApelPGHAERLDTALRDSEPAVI 146
                                    68*****************9.89*********************************987444456*************** PP

                                    EETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEE CS
                    AMP-binding  99 iatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVm 178
                                    +  + +++ ++++    ++++ ++ +vl  d++++       e++         ++el+ d +  ++YTSG+T  P GV 
  gi|121637830|ref|YP_978053.1| 147 L--TTAAAKNAVEGFLNNVPRLRKPTVLVIDQIPDR------EGEL-----F-VPVELDIDAVSHLQYTSGSTRPPVGVE 212
                                    *..555556667777777777777777776665544......3223.....2.3457899******************** PP

                                    EEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-S.. CS
                    AMP-binding 179 lshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvt.. 255
                                    ++hr++ +n+ ++ l+  + l+++   +s+lpl+h++gl + + ++ + G+   l++++a+ ++p ++++++++ + t  
  gi|121637830|ref|YP_978053.1| 213 ITHRAVGTNLVQMILSI-DLLNRNTHGVSWLPLYHDMGL-SMIGFPAVYGGHSTLMSPTAFvRRPLRWIQALSEGSRTgr 290
                                    ******99999975332.335566777***********9.777777777888888999999788*********8776544 PP

                                    EEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC......EEEEEEEEGGGSSECEE... CS
                    AMP-binding 256 viagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge......evlegYGlTEttgvvtv... 326
                                    v++++P ++  +++++ l a+ ++ dls + l+ +g ep+s ++++ f++ f +      ++  +YG +E+t  v++   
  gi|121637830|ref|YP_978053.1| 291 VVTAAPNFAYEWAAQRGLPAQGDDVDLSNVVLI-IGSEPVSIDAVTTFNKAFAPyglprtAFKPSYGIAEATLLVATidh 369
                                    999*********997777745555688887774.7******************9*****99**************66688 PP

                                    ......................CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBE....ETTSEEEEEEEETTS-SEBTT CS
                    AMP-binding 327 ......................lpleedkkklgsvGkplpgvevkivDeetgepv....pdgeeGellvrgpgvmkgYlk 380
                                                          +p+  + ++  s+G + +   + ivD++tg +     pdge Ge++++g +v++gY++
  gi|121637830|ref|YP_978053.1| 370 aaeptvvyldpeqlgaghatrvAPDAPNAVVHVSCGHVARSLWAVIVDPDTGPEAgaelPDGEIGEVWLQGDNVARGYWG 449
                                    9999999**************9776777788899**************999765533337******************** PP

                                    -HHHHHHHEEE...............T.CC.EEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 381 kpeataeafds...............e.gr.wlrTGDlgrldedGyleivgRkkdlik 421
                                    +pe+t+ +f +                 ++ wlrTGDlg++  dG+l+i+gR+ dl+ 
  gi|121637830|ref|YP_978053.1| 450 RPEETRMTFGArlqsplaegshadgsAiDDtWLRTGDLGVYL-DGELYITGRIADLLT 506
                                    *********9889999********9835566**********9.9**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4300.52
//
Query:       gi|121637831|ref|YP_978054.1|  [L=159]
Description: immunogenic protein mpt63 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-51  172.5   1.3    4.4e-51  172.1   1.3    1.2  1  DUF1942   Domain of unknown function (DUF1942)
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.034   14.4   0.0    1.3  1  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF1942  Domain of unknown function (DUF1942)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1   1.3   4.9e-55   4.4e-51       2     125 .]      33     157 ..      32     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 4.9e-55
                                    EEEETT-EEEEEETTTTEEEEEEEEEEEE------.S---SEEEEEEEEEEEEES-B---GGGEEEE-TT--EEEB--SS CS
                        DUF1942   2 tvkklGseaeltdagGavvqeytvsdLkpssdvip.yevagklweatatveavsgtvtPivsnlnaraangetYrvlkev 80 
                                     + klGse ++td++G+vv +++vsdLk+s++vip y+vag++weatatv+a++g+vtP+vs++nar+a+g +Yrvl++ 
  gi|121637831|ref|YP_978054.1|  33 ITGKLGSELTMTDTVGQVVLGWKVSDLKSSTAVIPgYPVAGQVWEATATVNAIRGSVTPAVSQFNARTADGINYRVLWQA 112
                                    6789**************************************************************************** PP

                                    S-TTB-----B-TT-EEEEEEEEEE-SS---EEEEE-SSSEEEEE CS
                        DUF1942  81 atpqginpatlaqgekstGklYFdvtGeaPdsvvyndggedllvW 125
                                    a p++i++at++qge+stGk+YFdvtG++P+ v +n+g+edll+W
  gi|121637831|ref|YP_978054.1| 113 AGPDTISGATIPQGEQSTGKIYFDVTGPSPTIVAMNNGMEDLLIW 157
                                    ********************************************* PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-06     0.034      58     103 ..      93     137 ..      82     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                                    GGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEE CS
                        DUF4352  58 ssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklvFdv 103
                                     sqf  +++dg +y+   +a   + +  + t+ +G+++tGk++Fdv
  gi|121637831|ref|YP_978054.1|  93 VSQFNARTADGINYRVLWQAAGPD-TISGATIPQGEQSTGKIYFDV 137
                                    579999*********999985554.59******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1055.71
//
Query:       gi|121637832|ref|YP_978055.1|  [L=257]
Description: hypothetical protein BCG_1966 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-60  204.8   0.1    1.4e-60  204.6   0.1    1.0  1  DUF2071   Uncharacterized conserved protein (COG2071)


Domain annotation for each model (and alignments):
>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6   0.1   7.8e-65   1.4e-60       2     211 ..      36     246 ..      35     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 7.8e-65
                        DUF2071   2 qeWrdllflhwpvdpealapllPaglelDtf.dGkayvslvpFrmedvrvrglpavpglstfpelNvRtYvrdkegrrGV 80 
                                    q+W+dl+f+hwpv pe++a   P+g+++D+f dG +yv+lvpFrm+ +++ +++++p++ tfpe+NvR+Y+ d++gr+GV
  gi|121637832|ref|YP_978055.1|  36 QRWTDLTFIHWPVLPESVAGSYPPGTRPDVFaDGMTYVGLVPFRMSSTKLGTALPIPYVGTFPETNVRLYSIDNAGRHGV 115
                                    9******************************************************************************* PP

                        DUF2071  81 vFlsldadrllivlvarllfglpYvtarmrveeeegeveyksrr....sparfaatyrptaeveeaepgsleeflteryr 156
                                    +F sl+++rl++v + r+ +g+pY+++rmr+ +++++++y+s r    ++ r+ +t+++++ ve+   ++le +lt+r+ 
  gi|121637832|ref|YP_978055.1| 116 LFRSLETARLTVVPLTRIGLGIPYAWSRMRMMRSGKHITYHSVRrwprRGLRSLLTITIGDLVEP---TPLEVWLTARWG 192
                                    ********************************9*******8885588788888888888888765...7*********** PP

                        DUF2071 157 lYtrrrgrlleyeveHepwplqeaellelentlleaaglplkpss.eplvlyspgv 211
                                     +tr++gr++++++eH+pwpl+ ae+ el+++l++a+g++  p+  +  +l+spgv
  gi|121637832|ref|YP_978055.1| 193 AHTRKAGRTWWVPNEHKPWPLRAAEIAELNDELIDASGVQ--PTGdRLRALFSPGV 246
                                    ***************************************9..43334557888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1972.37
//
Query:       gi|121637833|ref|YP_978056.1|  [L=255]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-69  231.5   0.4    1.1e-68  231.3   0.4    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.8e-56  190.1   3.3    3.2e-56  189.9   3.3    1.0  1  adh_short        short chain dehydrogenase
    1.1e-11   45.0   2.9    1.4e-11   44.6   2.9    1.1  1  KR               KR domain
  ------ inclusion threshold ------
      0.011   15.0   1.1       0.12   11.6   0.0    2.4  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.015   14.3   1.1      0.022   13.8   1.1    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.072   13.2   1.0        0.2   11.7   0.1    2.1  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.095   12.2   2.2      0.071   12.7   0.5    1.6  2  NmrA             NmrA-like family
       0.14   11.9   1.6       0.43   10.4   0.1    2.2  2  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.3   0.4   4.9e-72   1.1e-68       1     234 []      18     253 ..      18     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 231.3 bits;  conditional E-value: 4.9e-72
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga  gIG+ +A a+ e+Ga+v+++ ++ +a +k ++e+ +++g+ v + cDV++ +qv+++ ++v++++g++Di+v nag
  gi|121637833|ref|YP_978056.1|  18 GASTGIGKRVALAYVEAGAQVAIAARHLDAlEKLADEIGTSGGKVVpVCCDVSQHQQVTSMLDQVTAELGGIDIAVCNAG 97 
                                    899************************99988888888888888889********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSB.STTTT.HHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaerv.vpnyn.aygaaKaalealtr 153
                                    i +   +p+l+++ eef+r +++n++++fl+a+aa+++m ++   g i+n++s++++++ vp++  +y+a+Kaa+++lt+
  gi|121637833|ref|YP_978056.1|  98 IITV--TPMLDMPLEEFQRLQNTNVTGVFLTAQAAAKAMVKQgqgGVIINTASMSGHIInVPQQVsHYCASKAAVIHLTK 175
                                    ****..*******************************7666558899*******999886777778************** PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                    ++Avel+p++iRvN+vspg+i T++++ ++   e +  +e ++plgrlg+pee a ++l+Las+++sy+tG+++v+DgG+
  gi|121637833|ref|YP_978056.1| 176 AMAVELAPHKIRVNSVSPGYILTELVEPYT---EYQPLWEPKIPLGRLGRPEELAGLYLYLASEASSYMTGSDIVIDGGY 252
                                    *************************99997...78889****************************************** PP

                                    G CS
                   adh_short_C2 234 t 234
                                    t
  gi|121637833|ref|YP_978056.1| 253 T 253
                                    8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   3.3   1.4e-59   3.2e-56       1     192 [.      12     206 ..      12     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 1.4e-59
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    k +l+tGas GIG+ +a +++++Ga+v++++r+ ++le++a+e++  g k++++ +Dv+++++v  +++++ ++lg++d+
  gi|121637833|ref|YP_978056.1|  12 KRALITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKLADEIGTSGGKVVPVCCDVSQHQQVTSMLDQVTAELGGIDI 91 
                                    679***************************************************************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGG..TSB-TTBHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvag..kvpvagvaaYsAsKaava 157
                                     v NAGi  ++p+ ++  ee++r+ ++N+tgvfl+++a+++am+ ++++G I+n++S+ g   +   +v+ Y+AsKaav+
  gi|121637833|ref|YP_978056.1|  92 AVCNAGIITVTPMLDMPLEEFQRLQNTNVTGVFLTAQAAAKAMVkQGQGGVIINTASMSGhiINVPQQVSHYCASKAAVI 171
                                    ********************************************778899**********4334556889********** PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakelre 192
                                    +lt+++a elap++irvn+v PG++ T+++++ +e
  gi|121637833|ref|YP_978056.1| 172 HLTKAMAVELAPHKIRVNSVSPGYILTELVEPYTE 206
                                    *****************************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   2.9   6.4e-15   1.4e-11       4     153 ..      15     166 ..      13     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 6.4e-15
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    litG+  g+G+ +a   +e ga+ +++ +R+    ++ ++l +e+  +g +v  v +Dvs++++v+++l++++ae + i 
  gi|121637833|ref|YP_978056.1|  15 LITGASTGIGKRVALAYVEAGAQ-VAIAARH--L-DALEKLADEIGTSGGKVVPVCCDVSQHQQVTSMLDQVTAELGGID 90 
                                    9********************96.7889999..4.4455699************************************** PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHH.HH--TT-HHHHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiag.llgsagqanYaaaN 153
                                      +  Ag++  +++ +m  e+++++ +  v+G+    ++ ++      +  +++ ++S++g ++  ++q+++ +a+
  gi|121637833|ref|YP_978056.1|  91 IAVCNAGIITVTPMLDMPLEEFQRLQNTNVTGVFLTAQAAAKamvkqGQGGVIINTASMSGhIINVPQQVSHYCAS 166
                                    ********************************99988887775665577889999999999677777887666555 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05      0.12      33      76 ..       8      51 ..       4      57 .. 0.90
   2 ?    1.4   0.3      0.08   1.8e+02      23      65 ..      75     122 ..      62     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                                   --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                  THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76
                                   +l+gk++++ G+s+ +gk +al   e++a V ++ ++ + l+++
  gi|121637833|ref|YP_978056.1|  8 DLHGKRALITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKL 51
                                   899******************************99988777765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.08
                                    HHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT.....T-EEEE CS
                  THF_DHG_CYH_C  23 vvellketgielegkkvvvvGrsnivgkplallLlek.....natVtv 65 
                                    v+++l++ + el g +++v +++ i   p+  + le+     n  Vt 
  gi|121637833|ref|YP_978056.1|  75 VTSMLDQVTAELGGIDIAVCNAGIITVTPMLDMPLEEfqrlqNTNVTG 122
                                    677888888888888888888887777777666554333333555554 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   9.9e-06     0.022       1     108 [.      15     135 ..      15     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.9e-06
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleeale.......gvdvvih 72 
                                    ++tG++  +G+++  + v+++    + +  l+  ++l +e+ +++ k   +++Dv ++++++  l+       g+d+ + 
  gi|121637833|ref|YP_978056.1|  15 LITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKLADEIGTSGGKVvPVCCDVSQHQQVTSMLDqvtaelgGIDIAVC 94 
                                    69*******************9999999999999******9999988879*********998887722222224566677 PP

                      3Beta_HSD  73 laslvdvagkl.....tedeimkvnvkGTrnvleacvkagv 108
                                     a+++ v+ +l     +++++++ nv G     +a+ ka v
  gi|121637833|ref|YP_978056.1|  95 NAGIITVTPMLdmpleEFQRLQNTNVTGVFLTAQAAAKAMV 135
                                    77777766543112225677777777777666666666666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.8e-05       0.2       9      59 ..       8      58 ..       2      67 .. 0.87
   2 ?   -1.5   0.0       1.1   2.5e+03      23      41 ..     126     144 ..     109     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.8e-05
                                   ..TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                   Shikimate_DH  9 slkekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                   +l++k++l+ Ga   ++++va + +++g++ v++a R l+  ++la+e+++ 
  gi|121637833|ref|YP_978056.1|  8 DLHGKRALITGASTgIGKRVALAYVEAGAQ-VAIAARHLDALEKLADEIGTS 58
                                   6999********7648999*********99.*****************9765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHCCT-CEEEE CS
                   Shikimate_DH  23 maelvakhLlakgvkkvvv 41 
                                    +a+ +ak+++++g   v++
  gi|121637833|ref|YP_978056.1| 126 TAQAAAKAMVKQGQGGVII 144
                                    4555555555555554444 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   3.2e-05     0.071       2      66 ..      15      83 ..      14      87 .. 0.93
   2 ?   -2.7   0.0       1.5   3.4e+03      59      73 ..     132     147 ..     109     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT-S CS
                           NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvealkgvd 66
                                   l++Ga+  +Gk v+ a ++ag +v +  R +   ++la+++ ++G ++v  + d+ +++ + + l++v 
  gi|121637833|ref|YP_978056.1| 15 LITGASTGIGKRVALAYVEAGAQVAIAARHLdaLEKLADEIGTSGGKVVpvCCDVSQHQQVTSMLDQVT 83
                                   799**************************887689**********9999989************99996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                    HHHHTT-S.EEEE--- CS
                           NmrA  59 vealkgvd.vvfsvtg 73 
                                    ++ +k+ + +v+++t+
  gi|121637833|ref|YP_978056.1| 132 KAMVKQGQgGVIINTA 147
                                    3333333212444444 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00019      0.43      40      66 ..      11      36 ..       5      42 .. 0.79
   2 ?    0.1   0.1      0.31   6.9e+02       6      37 ..     139     171 ..     134     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                                   -SEEEEESTSSHHHHHHHHHHHHS.S-- CS
                Eno-Rase_NADH_b 40 pkkvLviGaStGYGLAsriaaafg.aga 66
                                    k++L+ GaStG G   r+a+a+  aga
  gi|121637833|ref|YP_978056.1| 11 GKRALITGASTGIG--KRVALAYVeAGA 36
                                   59*********988..799999874444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                                    EETTEESS--HHHHHHHHHHHHH.HHHHS---- CS
                Eno-Rase_NADH_b   6 irgficltahPaGcaknveeqie.yvksqkkie 37 
                                      g+i+ ta   G   nv +q++ y+ s++++ 
  gi|121637833|ref|YP_978056.1| 139 QGGVIINTASMSGHIINVPQQVShYCASKAAVI 171
                                    568899999999999999988862555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1553.54
//
Query:       gi|121637834|ref|YP_978057.1|  [L=214]
Description: hypothetical protein BCG_1968c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-06   27.6   3.6    1.2e-05   26.1   3.6    1.9  1  MDMPI_C   MDMPI C-terminal domain
     0.0004   21.1   5.5      0.029   15.0   0.7    2.5  2  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai


Domain annotation for each model (and alignments):
>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   3.6   1.3e-09   1.2e-05      47      90 ..     163     205 ..     114     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                        MDMPI_C  47 rlalwadgadatvrGtaadlllllwGRlspddtlevdGdralla 90 
                                    r++ +  +++a+++G++++lll+++GR+++++ +ev+G++++ a
  gi|121637834|ref|YP_978057.1| 163 RVRVRSGEPTARLTGPPGELLLYVFGRRAVAR-VEVSGPLEAIA 205
                                    3333333389*********************9.*****998765 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.7   3.3e-06     0.029      11      47 ..      14      50 ..       8      59 .. 0.82
   2 !    7.8   0.4   0.00056       5.1      90     141 .]      60     115 ..      58     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
                        MDMPI_N 11 lvagLtdeqwaapspcpGWtvadlvaHlarsaralaa 47
                                   l++ L++   a  ++ +GWt +dl+aH++  +r l a
  gi|121637834|ref|YP_978057.1| 14 LCDLLEELGPAVATLIEGWTAHDLAAHIVLRERDLVA 50
                                   5666677778999**************9988888765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00056
                        MDMPI_N  90 fraavtrlaaalaalppdaiadrl...gipggprslge.flrtrlvEavvHglDla 141
                                    f++ ++r++a+la+  +  + +     g+p+g  + g+   ++ l E +vH+ D++
  gi|121637834|ref|YP_978057.1|  60 FQRFAERRRARLAQSKDFTWLVARirsGPPMGFFRIGWvRTLANLNEFFVHHEDVR 115
                                    5566788888888888888866551135555555666655667889********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1640.19
//
Query:       gi|121637835|ref|YP_978058.1|  [L=174]
Description: hypothetical protein BCG_1969c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-06   28.6   0.0    2.9e-05   23.9   0.0    2.2  2  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.0    0.0049        88       2      26 ..       3      27 ..       2      36 .. 0.83
   2 !   23.9   0.0   1.6e-09   2.9e-05     113     161 ..      37      86 ..      28      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0049
                                   EEEEEEETTBEHHHHHHHHHHHHHT CS
                      DJ-1_PfpI  2 kvlvlladgvedvElivpvdvlkra 26
                                   +++++   gv  ++++ p++vl++ 
  gi|121637835|ref|YP_978058.1|  3 QIAFVAYPGVTALDVVGPYEVLRNL 27
                                   5889999***************985 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.6e-09
                                    TTTSEE--SGGGHHHHHHTTSE.E-SSSEEEETTEEEESSGGGHHHHHHH CS
                      DJ-1_PfpI 113 lkgrrvTsypavkdklekagak.yvdkrvvvdgnlvTsrgpgaaiefale 161
                                    l+grr+Ts++   ++l++ ga  + d+r+v  +n+vTs+g+ a +++al 
  gi|121637835|ref|YP_978058.1|  37 LRGRRATSHWLTLPALKAFGAIpVADERIVHQDNIVTSAGVSAGLDLALW 86 
                                    89**************88887527788****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1225.36
//
Query:       gi|121637836|ref|YP_978059.1|  [L=259]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.2e-23   80.5   0.7    2.7e-22   78.8   1.0    1.7  2  HTH_18     Helix-turn-helix domain
    2.7e-12   46.4   0.0    3.9e-05   23.6   0.0    2.5  2  HTH_AraC   Bacterial regulatory helix-turn-helix proteins, Ar
    1.5e-07   31.4   0.1    2.6e-07   30.6   0.1    1.3  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.85   5.1e+03      52      77 ..      42      67 ..      31      67 .. 0.71
   2 !   78.8   1.0   4.4e-26   2.7e-22       1      80 [.     178     256 ..     178     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.85
                                   HHHTT-S-HHHHHHHHHHHHSS-HHH CS
                         HTH_18 52 AlalGFsdlsrFsrafrklfgetPse 77
                                   A ++    +++F +a   l+g tPs+
  gi|121637836|ref|YP_978059.1| 42 ARRVVTVCTGAFLAAEAGLLGRTPSD 67
                                   55555556677888888888888885 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 4.4e-26
                                    HHHHHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHHHH CS
                         HTH_18   1 laaalgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPseyrr 80 
                                    la+++++s+r+++r+f +++g  p +y+ r+R e+Arr+L e+t+++v +iA+++GF+++ +++r f ++ g++P +yr+
  gi|121637836|ref|YP_978059.1| 178 LAQRAAMSPRHFTRVFSDEVGEAPGRYVERIRTEAARRQL-EETHDTVVAIAARCGFGTAETMRRSFIRRVGISPDQYRK 256
                                    89**************************************.78************************************8 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   6.6e-09   3.9e-05      11      40 ..     175     204 ..     173     206 .. 0.94
   2 !   20.4   0.0   6.7e-08    0.0004      10      42 .]     223     256 ..     217     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.6e-09
                                    HHHHHHHTTSSHHHHHHHHHHHSSS-HHHH CS
                       HTH_AraC  11 iediAdelgfSrsyFsrlFkketGmtPsqy 40 
                                    i+++A+ + +S+++F+r+F+ e+G+ P  y
  gi|121637836|ref|YP_978059.1| 175 IGELAQRAAMSPRHFTRVFSDEVGEAPGRY 204
                                    89*************************998 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 6.7e-08
                                    -HHHHHHHTTS.SHHHHHHHHHHHSSS-HHHHHH CS
                       HTH_AraC  10 tiediAdelgf.SrsyFsrlFkketGmtPsqyrt 42 
                                    t+  iA+ +gf    +++r F +++G++P qyr+
  gi|121637836|ref|YP_978059.1| 223 TVVAIAARCGFgTAETMRRSFIRRVGISPDQYRK 256
                                    8889****************************96 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   4.3e-11   2.6e-07      62     114 ..      11      62 ..       7      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.3e-11
                                    -SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTT CS
                      DJ-1_PfpI  62 yDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlk 114
                                     D+++lpGG    +  r +++++++vk +   +++v+++C+g++l a+ag+l 
  gi|121637836|ref|YP_978059.1|  11 VDTVILPGGAG-VDAARSEPALIDWVKAVSGTARRVVTVCTGAFLAAEAGLLG 62 
                                    79*******88.********************************999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2001.00
//
Query:       gi|121637837|ref|YP_978060.1|  [L=165]
Description: thiol peroxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-26   91.0   0.0    6.8e-26   90.7   0.0    1.0  1  Redoxin   Redoxin
    5.6e-15   55.4   0.0    6.9e-15   55.1   0.0    1.1  1  AhpC-TSA  AhpC/TSA family


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   7.6e-30   6.8e-26       2     147 .]      20     160 ..      19     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 7.6e-30
                                    TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHH CS
                        Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefw 80 
                                    +g++aP+ftl++   d   +s ++f+gk+v++n++p+ ++P+C +++   ++++e+++++g +v  +v+++ +f +k+f+
  gi|121637837|ref|YP_978060.1|  20 VGSPAPAFTLTG--GDLGVISSDQFRGKSVLLNIFPSVDTPVCATSV---RTFDERAAASGATV-LCVSKDLPFaQKRFC 93 
                                    89*******966..*******************************99...***********999.999999999****** PP

                                    HHTT-TSEEEE-T.TSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHHHH CS
                        Redoxin  81 gkeglkfpvlsDg.saaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaeavl 147
                                    g+eg  +++ +++   +f +++G++++    +gl++++ +vi +dg+v y+e++pe  + e+n+ea+l
  gi|121637837|ref|YP_978060.1|  94 GAEGTENVMPASAfRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQ-EPNYEAAL 160
                                    *********999659**************9999************************87.****9987 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   7.7e-19   6.9e-15       1     123 [.      20     143 ..      20     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 7.7e-19
                                    TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                       AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                    vg +ap f+l+ +d + +s ++++gk v+l+++p+ ++pvC t ++ + +++   ++ g++v+ vs d p+++k+f+ +e
  gi|121637837|ref|YP_978060.1|  20 VGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERA---AASGATVLCVSKDLPFAQKRFCGAE 96 
                                    799********************************************99987...7889********************* PP

                                    H.....SSEEEE-TTSHHHHHTT-EETT...TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  81 s....lnfpllsDeegkvakaygvlkee...kglalratfvidkegkiry 123
                                    +    ++   + D    + ++ygv   +   +gl  ra +vi ++g+++y
  gi|121637837|ref|YP_978060.1|  97 GtenvMPASAFRD---SFGEDYGVTIADgpmAGLLARAIVVIGADGNVAY 143
                                    *655555555555...8899****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1232.79
//
Query:       gi|121637838|ref|YP_978061.1|  [L=363]
Description: acyl-CoA dehydrogenase fadE18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-34  119.3   5.1    2.3e-34  118.8   5.1    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-17   63.9   0.1    3.9e-17   62.9   0.1    1.5  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.1e-09   37.2   4.5    6.4e-09   36.2   4.5    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    0.00091   19.4   0.0      0.002   18.3   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   5.1   5.1e-38   2.3e-34       7     149 ..     215     358 ..     209     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 5.1e-38
                                    HTTT.T--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------H CS
                  Acyl-CoA_dh_1   7 amet.lnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdr 85 
                                     me+ l++ R+++aa +lg a+++l+ a++ya rr++f +p++++q+v++ +a+m++e++a+r++v+ aa  + +g++ +
  gi|121637838|ref|YP_978061.1| 215 DMERvLDVARVLLAAEMLGGAEACLDLAVQYAGRRTQFDRPIGSFQAVKHACADMMIEIDATRATVMFAAMSAANGDELQ 294
                                    56666*************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  86 aeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                      a +aK++++e+++ +a +a+q++G+ ++++e+ ++ +yr+a++++ + G+s   r ++a+r+
  gi|121637838|ref|YP_978061.1| 295 TVAPLAKAQTAETFVLCAGSALQIHGAIAFTWEHDLHLYYRRAKTTEALFGSSARNRALLAERA 358
                                    *************************************************************996 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   8.7e-21   3.9e-17       2     112 ..       7     113 ..       6     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 8.7e-21
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHH.HHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkkl.aelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                     eq+++r+++r f+ + + p ++e+ +++  +r lw++l  el l +++vp e+gG+g++ +e+ai++ el+ra ++   
  gi|121637838|ref|YP_978061.1|   7 TEQDDFRASLRGFLGRGA-P-VREMAAADGSDRRLWQRLcTELELPALHVPPEHGGLGATLVETAIAFAELGRALTP--- 81 
                                    79**************88.5.88888666668999****569*******************************9999... PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasg 112
                                    ++ + +  +++ailr+G +eq++r L  l++g
  gi|121637838|ref|YP_978061.1|  82 IPFAATVFAIEAILRMGDDEQRKRLLAGLLTG 113
                                    56677888899******************998 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   4.5   1.4e-12   6.4e-09       3     126 ..     227     340 ..     225     345 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.4e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    +aa +lG A+a+l+ +v++a++r++  + +++  ++a+++a a++  ++dA ra++  aa +    aa+g+e+     + 
  gi|121637838|ref|YP_978061.1| 227 LAAEMLGGAEACLDLAVQYAGRRTQ--FDRPIGSFQAVKHACADMMIEIDATRATVMFAAMS----AANGDEL----QTV 296
                                    7999*********************..******************************99999....9999997....777 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaa 126
                                    a +a+a ++e+ + ++ ++ +++G+ a + e+ l  ++R a+++
  gi|121637838|ref|YP_978061.1| 297 APLAKAQTAETFVLCAGSALQIHGAIAFTWEHDLHLYYRRAKTT 340
                                    88888889999999999999999999999988888888877775 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.5e-07     0.002       9      78 ..     122     186 ..     119     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.5e-07
                                    -SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE--- CS
                  Acyl-CoA_dh_M   9 aGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrri 78 
                                    +G+dvas +t  a r +g  +l+Ge + + +++ a+l++v a      +++++ l +v +dapgv+v+++
  gi|121637838|ref|YP_978061.1| 122 SGHDVASATTVRAVRRDGRPALTGECTPVLHGHVADLFVVPAV-----ADGSIVLHVVAADAPGVTVTPL 186
                                    699******9886666669************************.....4799*9*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:01.98
# Mc/sec: 555.45
//
Query:       gi|121637839|ref|YP_978062.1|  [L=409]
Description: acyl-CoA dehydrogenase fadE17 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-28   98.8   0.1    6.1e-28   97.7   0.1    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.1e-22   79.1   0.0    3.3e-22   78.5   0.0    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.2e-20   74.3   0.2    2.5e-20   73.2   0.1    1.7  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1     1e-31   6.1e-28       2     113 .]       7     124 ..       6     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 1e-31
                                    HHHHHHHHHHHHHHHHHTHH.....HHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelap.....haaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                    +e ea+rd++ref++e+l+p      a   +e++ef r+++++la +Gl+++++p+eygG gl+++e++++aee+ara+a
  gi|121637839|ref|YP_978062.1|   7 PEAEAFRDRIREFVAEHLPPgwpgpGALPPHEREEFARHWRRALAGAGLVAVSWPTEYGGGGLSPMEQVVLAEEFARAGA 86 
                                    899****************954444588889999********************************************** PP

                                    HHHH.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  77 glal.llgvhsslvapailrfGteeqkrryLpklasge 113
                                    + ++    ++ +l ++++++ G+e+qkr++Lp+++sge
  gi|121637839|ref|YP_978062.1|  87 PERAeNDLLGIDLLGNTLIALGSEAQKRHFLPRILSGE 124
                                    9888544457788889*********************8 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   5.6e-26   3.3e-22       1      94 [.     128     219 ..     128     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 5.6e-26
                                    EEE---SS-SS-GGG---EE.EEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE-- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvktta.aerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvrr 77 
                                    + +++Ep+aGsd+asv+t+   ++d+  +v+nG+Kiw + +++a+++++lart+ p+  ++rgls++lvp d+pgv vr+
  gi|121637839|ref|YP_978062.1| 128 CQGFSEPEAGSDLASVRTRGvLDGDE--WVINGHKIWTSAGTTANWIFLLARTD-PSaaKHRGLSFLLVPMDQPGVVVRP 204
                                    7899**************87666666..************************44.44489******************** PP

                                    ---BSS-TTS-EEEEEE CS
                  Acyl-CoA_dh_M  78 ieeklGlrglptgelvf 94 
                                    i +  G    +++e+++
  gi|121637839|ref|YP_978062.1| 205 IVNAAGHS--SFSEVFL 219
                                    *9888876..4556555 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   1.4e+04     117     129 ..      38      50 ..      31      52 .. 0.78
   2 !   73.2   0.1   4.2e-24   2.5e-20       1     150 []     234     397 ..     234     397 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                                    GGGHHHHHHHHTH CS
                  Acyl-CoA_dh_1 117 eeypverlyrdar 129
                                    e+++++r++r+a+
  gi|121637839|ref|YP_978062.1|  38 EREEFARHWRRAL 50 
                                    5677999999987 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 4.2e-24
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G+  am+ l +eR +++a+a+  ++r l+++ e+ar+r         ++ vr+ la ++a+++ +r   yr   ++ +
  gi|121637839|ref|YP_978062.1| 234 GDGWSTAMTLLGFERGSHIATAAIDFERDLQRLCELARDRGLHT-----DPRVRDGLAWCYARVQIMRYRGYRDLTLALT 308
                                    79**************************************9855.....9****************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT....................SGGGH...HHHHHHHTHHHHHSSS- CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGy....................leeyp...verlyrdarvlrigeGt 137
                                    g+p++aea+++K+ +se +++ +dla+++lG +++                    +   p   ++  +  ar+ +i++G+
  gi|121637839|ref|YP_978062.1| 309 GRPPGAEAAITKVIWSEYFRRYTDLAVEILGLEALgprgpgnggarlvpeagtpnS---PacwMDE-LLYARAATIYAGS 384
                                    ***********************************************998763322...3442444.5789********* PP

                                    HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1 138 seiqrniiarrll 150
                                    s+iqrn+i++rll
  gi|121637839|ref|YP_978062.1| 385 SQIQRNVIGERLL 397
                                    **********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2857.12
//
Query:       gi|121637840|ref|YP_978063.1|  [L=318]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-37  127.8   0.0    5.5e-23   81.6   0.0    2.0  2  ECH_1     Enoyl-CoA hydratase/isomerase
    2.7e-15   56.7   0.0      4e-15   56.2   0.0    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.2e-15   1.1e-11       5      62 ..      36      93 ..      33     108 .. 0.92
   2 !   81.6   0.0   6.1e-27   5.5e-23      52     210 ..     109     262 ..     102     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-15
                                   TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHH CS
                          ECH_1  5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkem 62
                                    +a i+l+rP++ Na +  +l El +a+e +e d +vr+v+L   + aF+aG dl  +
  gi|121637840|ref|YP_978063.1| 36 RIAAITLDRPKQRNAQTRGMLVELGAAFELAEADDTVRVVILRAAGPAFSAGHDLGSA 93
                                   599***************************************************9765 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 6.1e-27
                                    EEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-.GGGGGTS CS
                          ECH_1  52 aFaaGadlkemaeeekakqallkeevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfgl.nelklGl 130
                                    + + Ga++  +  ++     + ++ ++e+ ++ +++ k++ia v Ga++ +Gl la +cD+++a+++ +f+    ++lG+
  gi|121637840|ref|YP_978063.1| 109 YRCNGATFGGVESRN----RQEWHYYFENTKRWRNLRKITIAQVHGAVLSAGLMLAWCCDLIVASEDTVFADvVGTRLGM 184
                                    558888888887764....44566666666677778899*******************************9614566665 PP

                                    --CTTCHHHH..HHHHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH CS
                          ECH_1 131 ipgaggtqil..arkvGkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnak 208
                                    +     ++++  + + G +k +e+ll+g+ i+a+ea   G+v+kv+p+++l   ++e a+++a+ +  a+  +ke++n++
  gi|121637840|ref|YP_978063.1| 185 CG----VEYFghPWEFGPRKTKELLLTGDCIGADEAHALGMVSKVFPADELATSTIEFARRIAKVPTMAALLIKESVNQT 260
                                    55....544322678************************************************9999999999*****99 PP

                                    HH CS
                          ECH_1 209 le 210
                                    ++
  gi|121637840|ref|YP_978063.1| 261 VD 262
                                    98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   4.4e-19     4e-15       2     198 ..      38     248 ..      37     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 4.4e-19
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS................ CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakeg................ 65 
                                    + itL+rpk+ Na +  m+ +l +a++  e+dd+v++v+l++ag  af+AG D+ +  + ++++                
  gi|121637840|ref|YP_978063.1|  38 AAITLDRPKQRNAQTRGMLVELGAAFELAEADDTVRVVILRAAG-PAFSAGHDLGSADDIRERSpgpdqhpsyrcngatf 116
                                    679***************************************99.8********99988888779999999998888777 PP

                                    ...-THHHHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE.--GGGGT----TTHHHHHHC CS
                          ECH_2  66 ...kkeeeeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfA.mPEtaIGlfPDvGgsyfLsr 141
                                       ++++++ ++  ++  ++  +++k ++a ++G v+  G+ l+  + + v++e+tvfA +  t++G+   +G+ yf   
  gi|121637840|ref|YP_978063.1| 117 ggvESRNRQEWHYYFENTKRWRNLRKITIAQVHGAVLSAGLMLAWCCDLIVASEDTVFAdVVGTRLGM---CGVEYFGHP 193
                                    764333488999999999*****************************************667999999...699999887 PP

                                    SST..THHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT........--- CS
                          ECH_2 142 lpg..elGlylalTGarlkgadalaaglathyvpseklealeeaLaelessdeeaveev 198
                                     +   +  + l lTG+ +++ +a a+g+ ++++p+++l++ + ++a+   +    v ++
  gi|121637840|ref|YP_978063.1| 194 WEFgpRKTKELLLTGDCIGADEAHALGMVSKVFPADELATSTIEFARRIAK----VPTM 248
                                    632236678899************************998766555553222....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2055.89
//
Query:       gi|121637841|ref|YP_978064.1|  [L=369]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-43  147.4   1.8    7.8e-43  147.1   1.8    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   1.8   4.3e-47   7.8e-43       1     311 [.       1     322 [.       1     324 [. 0.87

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 4.3e-47
                 Bac_luciferase   1 mefgvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga.ldaftllaalaaaTerirlgtavtply 79 
                                    me+g+fl  +++++++ +  + r  ++++++a++lG+  +wv+eh ++p      +  lla ++ +T++i+l  +++ l+
  gi|121637841|ref|YP_978064.1|   1 MEIGIFLMPAHPPERTLYD-ATRWDLDVIELADQLGYVEAWVGEHFTVPWEPiCAPDLLLAQALLRTQQIKLAPGAHLLP 79 
                                    899********99999999.889999*********************98777888999********************** PP

                 Bac_luciferase  80 trhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGv..dhderyarlrEfvevlrrlwrgeev.dfeGeffsv... 153
                                     +hP+ lA  +a +dhl++GRf lg+g++g + + + + v     e  +++rE++e++ r+w+++e+ +++G+++++   
  gi|121637841|ref|YP_978064.1|  80 YHHPVELAHRVAYFDHLAQGRFMLGVGASGIPGDWALYDVdgKNGEHREMTREALEIMLRIWTEDEPwEHRGKYWNAngi 159
                                    **********************************99997777899*******************999************* PP

                 Bac_luciferase 154 .......kgalllprpgqgpiPvyvaaas..paglelaarhadglllageppeeaaelierlragaaeagrdpadirvgi 224
                                           ++ +++p ++++ +P+ v + s   ++l+la++++ + ++     e +a + + +++ga + gr+p++ +  +
  gi|121637841|ref|YP_978064.1| 160 apmfeglMRRHIKPYQKPH-PPIGVTGFSagSETLKLAGERGYIPMSLDLNTEYVATHWDAVEEGALRSGRTPDRRDWRL 238
                                    ****988888888888777.8899999887789*********************************************** PP

                 Bac_luciferase 225 sltvivadteeeAraearaliagld.fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatal.vGtpeqvae 302
                                     + v va+t+e+A ++a + +   + ++  + +++ +     + + ++++++     d v++e++a+++  vG+ ++v++
  gi|121637841|ref|YP_978064.1| 239 VREVLVAETDEQAFRYAVDGT---MgRAMREYVLPTFR---MFGMTKFYKHNPSVPDDEVTPEYLAENTFvVGSVQTVVD 312
                                    *****************5555...22333344444444...455555555555555555655555555545********* PP

                 Bac_luciferase 303 rlaa.yaeag 311
                                    +l+a y + g
  gi|121637841|ref|YP_978064.1| 313 KLEAtYDQVG 322
                                    ***9666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2537.71
//
Query:       gi|121637842|ref|YP_978065.1|  [L=839]
Description: oxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-21   75.9   0.0    9.9e-21   74.0   0.0    2.0  2  FAD_binding_6   Oxidoreductase FAD-binding domain
    1.5e-17   64.2   0.0      4e-17   62.8   0.0    1.7  2  NAD_binding_1   Oxidoreductase NAD-binding domain
    1.5e-13   50.5   4.4    3.1e-13   49.5   4.4    1.5  1  Fer2            2Fe-2S iron-sulfur cluster binding domain
      0.001   18.0   0.1       0.57    9.0   0.0    3.2  3  Trp_halogenase  Tryptophan halogenase
     0.0018   17.5   0.1       0.26   10.3   0.1    2.3  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.028   13.7   1.1       0.87    8.8   1.1    2.4  1  FAD_binding_3   FAD binding domain
      0.043   13.0   0.7       0.33   10.1   0.1    2.6  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.054   13.1   2.5       0.33   10.5   0.3    2.8  3  DAO             FAD dependent oxidoreductase
      0.099   12.0   0.0       0.21   10.9   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
        0.2   10.9   0.8       0.94    8.7   0.2    2.1  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   5.5e-24   9.9e-21       3      99 .]     108     202 ..     106     202 .. 0.93
   2 ?   -2.0   0.0       2.6   4.7e+03      58      86 ..     260     298 ..     243     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 5.5e-24
                                    EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH.HC CS
                  FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaL.de 81 
                                    ++t++e vs++t+i+r++++ ++  l++++Gq+   +l+++g++v+R+Y+ +   + +Ge+e++++ +p+G+ms++L d+
  gi|121637842|ref|YP_978065.1| 108 VVTAVELVSPSTAILRVDTSGMAGALRYRAGQFA--QLQVPGTNVWRNYSYAHPADGRGECEFIIRLLPDGVMSNYLrDR 185
                                    68999***************************55..55555*********99999**********************999 PP

                                    S-TT-EEEEEEEE-SEEC CS
                  FAD_binding_6  82 lkigdtleikGPlGkfeY 99 
                                    +++gd++++++++G+f Y
  gi|121637842|ref|YP_978065.1| 186 AQPGDHIALRCSKGSF-Y 202
                                    ***************9.5 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                                    TECCEEEEEEE--........TT-HHHHHHHC..S-TT- CS
                  FAD_binding_6  58 nekGelellvkvy........pgGkmsqaLde..lkigd 86 
                                       G+le++v v         + G ++ +Lde  l+ gd
  gi|121637842|ref|YP_978065.1| 260 RRVGRLEVHVVVArpdpdwdgRTGLVTDLLDErmLASGD 298
                                    567899999988899999999999999999764555555 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   2.2e-20     4e-17       1     108 [.     212     314 ..     212     315 .. 0.93
   2 ?   -2.7   0.0       5.3   9.5e+03      11      41 ..     563     595 ..     560     602 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.2e-20
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqda 80 
                                    ++agGtG++ ++++ + + ++    ++v+l+yG++++edl   +el el+++  + l+v  vv r++ +w+g++g v+d 
  gi|121637842|ref|YP_978065.1| 212 LVAGGTGLSAILAMAQSLDAD--VAHPVYLLYGVERTEDLCKLDELTELRRRVGR-LEVHVVVARPDPDWDGRTGLVTDL 288
                                    79***************9997..778***********************666665.88888899**************** PP

                                    HHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  81 lleellslkkeethvyvCGppgMikavr 108
                                    l e +l   +++++vy+CGp +M++a+r
  gi|121637842|ref|YP_978065.1| 289 LDERMLA--SGDADVYLCGPVAMVDAAR 314
                                    ***9999..***************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                                    HHHHHHHHHHHCT..TCSEEEEEEEESSGCGST CS
                  NAD_binding_1  11 vrsvlraileeak..dktkvvlvyGnrteedll 41 
                                    ++s++++++  +   +++ +v+ y++r  ed +
  gi|121637842|ref|YP_978065.1| 563 FYSTMQHRVPPERrwQDKVMVICYAYRPFEDTY 595
                                    788899888863366668888899998887766 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   4.4   1.7e-16   3.1e-13       3      78 .]      11      84 ..      10      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.7e-16
                                   TTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCECTT.SSSSTHHHHHTTEEEEGGGSEES CS
                           Fer2  3 idgkevevevadgettlldaaeenggidipysCggggCgtClvevlegevqsd.etelegeeldegklrlaCqtivt 78
                                    dg+  + +v  ++t +ldaaee  g++i  +C+ g CgtC++++++g++q +  + l++ e++++k  l+Cqt+vt
  gi|121637842|ref|YP_978065.1| 11 SDGTHKTMPVRCDQT-VLDAAEEH-GVAIVNECQSGICGTCVATCTAGRYQMGrTEGLSDVERAARKI-LTCQTFVT 84
                                   579999999999999.******98.*************************666677788888777777.*****997 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0097        17       3      34 ..     365     393 ..     363     405 .. 0.86
   2 ?    0.2   0.0      0.14   2.5e+02     196     212 ..     524     540 ..     490     545 .. 0.67
   3 !    9.0   0.0   0.00032      0.57     301     378 ..     659     735 ..     651     746 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0097
                                    EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                 Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlvese 34 
                                    v++GG +aG  aA +l+++++   +v ++e++
  gi|121637842|ref|YP_978065.1| 365 VVIGGSIAGIAAAKMLSETFD---RVIVLEKD 393
                                    89******************4...57777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                                    -EEE-SEEEE-SGGG-I CS
                 Trp_halogenase 196 reveadlfiDcsGfrgl 212
                                    ++v a++++D+sG + +
  gi|121637842|ref|YP_978065.1| 524 QVVPAEFVVDASGKNTR 540
                                    7899*********8766 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00032
                                    EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HH.HHHHHHHHHHHHHHHHHHHH CS
                 Trp_halogenase 301 rkirfttGrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepa.aiaefnrevarelervrdfi 378
                                    +++r++  + k+   + ++a+G+a+ + +P+ + ++ l+ + +r++ all++ +     +  ++ r++a++ ++  +f+
  gi|121637842|ref|YP_978065.1| 659 NMLRLRYEK-KRNLPRALLAVGDAYTSADPVSGLGMSLALKEVREMQALLAKYGAGHRdLPRRYYRAIAKMADT-AWFV 735
                                    555555544.445667899********************************99887552667788888776654.4555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00015      0.26       2      44 ..     364     409 ..     363     414 .. 0.83
   2 !    4.8   0.0    0.0069        12     112     205 ..     448     543 ..     421     558 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS...GGGG--S- CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg...atawsqGg 44 
                                    ++ViG+ +AG aAA  ++e   +v+v+ek ++ +       ++qG+
  gi|121637842|ref|YP_978065.1| 364 AVVIGGSIAGIAAAKMLSETFDRVIVLEKDGPHRRregRPGAAQGW 409
                                    69***************************99866433366666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0069
                                    -EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT..EEEEESEEEEEEEEC..TTEEEEEEEEET..TTT CS
                  FAD_binding_2 112 dvrelGglsatartlhdaadarretlvtghallarlvesarkag..vdfqerteadeLive..dgrvtGavvenp..esg 185
                                    ++r  G+++++     +++d   e +  g+ ll+  v++ ++ +  +df+ + e+++L  +  ++ ++G+ v n   ++g
  gi|121637842|ref|YP_978065.1| 448 RIRLGGTWKKP-----GTSDI--EIVCAGRPLLEWCVRRRLDDEprIDFRYESEVADLAFDraNNAIVGVAVDNGdaDGG 520
                                    55555555555.....45555..66778999999888887777779*************974466*******98886444 PP

                                    CEE.EEEESEEEE-----GG... CS
                  FAD_binding_2 186 rev.rirakavvlatgGfgr..a 205
                                         + a  vv+a+g   r  +
  gi|121637842|ref|YP_978065.1| 521 DGLqVVPAEFVVDASGKNTRvpE 543
                                    44414455599999988776443 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1   0.00049      0.87       5     325 ..     365     714 ..     362     732 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00049
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS......S-....-EEEHHHHHHHHHT.T-HHHHHHHSEECCCCE CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp......ra....dglnqrtmellrql.Gledrilaegapnelmg 73 
                                    +++G++ aG+ +a++Lse   rv+++ek     +        ++    + l+   +el r   G+ d + +ega +  m+
  gi|121637842|ref|YP_978065.1| 365 VVIGGSIAGIAAAKMLSETFDRVIVLEKDGPHRRREgrpgaaQGwhlhHLLTAGQIELERIFpGIVDDMVREGAFKVDMA 444
                                    69999999999999999998889999997654433222232211111122233333433321255555555555555555 PP

                                    EEEEEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEE.....ECCT CS
                  FAD_binding_3  74 ealynelsdtpkaradlelesspervtvypqteleriLvehaeerg.lqvrfktevesleqdeegvtaevr.....dket 147
                                       + +l++t k +      +s  ++   + + le  ++ ++  ++ +++r + ev  l  d  + + +       d ++
  gi|121637842|ref|YP_978065.1| 445 AQYRIRLGGTWKKPG-----TSDIEIVCAGRPLLEWCVRRRLDDEPrIDFRYESEVADLAFDRANNAIVGVavdngD-AD 518
                                    555555444422222.....333445556777777777777777788888888887766666555322222333421.22 PP

                                    TEE..EEEEEEEEEE--GTT-HHH...HHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC....CEEEEECCTTEEEEE CS
                  FAD_binding_3 148 gee..etvrakYlvGaDGgrStvr...ktlgiefegeetvyeagvldvlfda.dlsdivep....lvlilsaesrgvmvi 217
                                    g +  + v a+++v a G +++v    ++lg+  ++ e++++  + +++    + ++ +++    +++ +++ ++  +  
  gi|121637842|ref|YP_978065.1| 519 GGDglQVVPAEFVVDASGKNTRVPeflERLGVGAPEAEQDIINCFYSTMQHRvPPERRWQDkvmvICYAYRPFEDTYAAQ 598
                                    22245677888888888888888522257788855555555555555555554666666667777777777777765444 PP

                                    ECCE.TEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEE..EEEEEEEEEEEEEEESSSEETT.....EEE- CS
                  FAD_binding_3 218 Plen.tlerfyvqvearaekeersekfteeevkarlreivgektldv..eieevsawtvaqrvaekyrkgr.....vfla 289
                                     + +  ++     + a++  +  +++++ +  ++ +++ v  + +d   + + +  ++  +++  +y+k r     ++ +
  gi|121637842|ref|YP_978065.1| 599 YYTDsSRTILSTSLVAYNCYSPPRTAREFRAFADLMPSPVIGENIDGlePASPIYNFRYPNMLRLRYEKKRnlpraLLAV 678
                                    44442222222233333333333444444445555555555555554434555666666666666666654344445567 PP

                                    GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTS CS
                  FAD_binding_3 290 GDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGe 325
                                    GDA     P+ G+G+ +a++ + ++   La+   G+
  gi|121637842|ref|YP_978065.1| 679 GDAYTSADPVSGLGMSLALKEVREMQALLAKYGAGH 714
                                    888888888888888888888888888888765554 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39     7e+02     179     204 ..      16      41 ..       4      44 .. 0.84
   2 ?   -2.1   0.0      0.96   1.7e+03     261     278 ..     290     308 ..     282     320 .. 0.80
   3 ?   10.1   0.1   0.00019      0.33       3      33 ..     364     394 ..     362     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                    TTS-HHHHHHHHHHHHHTTEEEEESC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 179 raldkelsaaleealekeGvevklgt 204
                                    ++++ ++ +++ +a e++Gv+++ ++
  gi|121637842|ref|YP_978065.1|  16 KTMPVRCDQTVLDAAEEHGVAIVNEC 41 
                                    6788999**************98765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.96
                                    -TTS.BESSTTEEE-GGGC CS
                                    xxxx.xxxxxxxxxxxxxx RF
                    Pyr_redox_2 261 defl.rtnvpgiyaiGDva 278
                                    de++ ++ + ++y++G va
  gi|121637842|ref|YP_978065.1| 290 DERMlASGDADVYLCGPVA 308
                                    777746669*******999 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00019
                                    EEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlveleg 33 
                                     vviGg +AG+aaa+ l++   +v+++e++g
  gi|121637842|ref|YP_978065.1| 364 AVVIGGSIAGIAAAKMLSETFDRVIVLEKDG 394
                                    59*****************988888887443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.92   1.6e+03     145     168 ..      19      42 ..       7      76 .. 0.80
   2 ?   10.5   0.3   0.00018      0.33       2      38 ..     364     404 ..     363     425 .. 0.77
   3 ?    0.2   0.0      0.25   4.4e+02     270     314 ..     539     593 ..     499     617 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.92
                                    HHHHHHHHHHHHHHTT-EEEESEC CS
                            DAO 145 pakltaalaraaealGveilegte 168
                                    p +  + +++aae++Gv i+++++
  gi|121637842|ref|YP_978065.1|  19 PVRCDQTVLDAAEEHGVAIVNECQ 42 
                                    55666778999********99976 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                                    EEEECTSHHHHHHHHHHHHT.T.EEEEESSSSTT...SSGGG CS
                            DAO   2 vviiGGGiiGlstAyeLarr.g.Vtllekgdiag...sgaSg 38 
                                     v+iGG i+G+++A  L++    V++lek+  ++   +g  g
  gi|121637842|ref|YP_978065.1| 364 AVVIGGSIAGIAAAKMLSETfDrVIVLEKD-GPHrrrEGRPG 404
                                    59***************998658******9.77733334444 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.25
                                    E......EETTCSSTSCSHHHHHHHHHHHHHHSGGG....CGEEE.EEEEEEEETT CS
                            DAO 270 d......eesgdddpevdeedidellealrklfPql....gdvlr.kwaGlrplpd 314
                                    +      e+ g + pe++++ i+ +++ +++++P      ++v   ++a +rp  d
  gi|121637842|ref|YP_978065.1| 539 TrvpeflERLGVGAPEAEQDIINCFYSTMQHRVPPErrwqDKVMViCYA-YRPFED 593
                                    14555556677778999****************8842343335444888.999545 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.21       3     145 ..     365     537 ..     364     539 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                   FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLve...ergvlGGlltsglvatdignkaee.....qvvtgiareflerlrq..rgg 72 
                                    vV+GG +aG+aAA    +   +v+++e   ++++  G   ++ +  + +  +++     ++  gi+++++++ +   +  
  gi|121637842|ref|YP_978065.1| 365 VVIGGSIAGIAAAKMLSETFDRVIVLEkdgPHRRREGRPGAAQGWHLHHLLTAGqieleRIFPGIVDDMVREGAFkvD-- 442
                                    8**************************555344556666666666666655555677778888999998888876442.. PP

                   FAD_oxidored  73 a....rlkkrskw.n.........tfepevakavleeml.aeagvtvllntrlveveke..gkriesvtveske..g... 130
                                         r++   +w +         +     ++ ++   l +e++++  +++++ +   +  ++ i +v v + +  g   
  gi|121637842|ref|YP_978065.1| 443 MaaqyRIRLGGTWkKpgtsdieivCAGRPLLEWCVRRRLdDEPRIDFRYESEVADLAFDraNNAIVGVAVDNGDadGgdg 522
                                    334334446666642566644555444444444444444899***********887776336779999997643322356 PP

                   FAD_oxidored 131 rktirAkvfiDATgd 145
                                     +++ A++++DA+g+
  gi|121637842|ref|YP_978065.1| 523 LQVVPAEFVVDASGK 537
                                    8999********985 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.35   6.3e+02      32      55 ..     210     234 ..     189     236 .. 0.87
   2 ?    8.7   0.2   0.00053      0.94      28      60 ..     361     393 ..     346     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                                    EEESTSHHHHHHH.HHHHHTT-EEE CS
                    AlaDh_PNT_C  32 lviGgGvaGlqAi.atakglgakVt 55 
                                    +++ +G  Gl+Ai a+a++l+a+V 
  gi|121637842|ref|YP_978065.1| 210 VILVAGGTGLSAIlAMAQSLDADVA 234
                                    67778889****8689******995 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00053
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                    +++ +viGg +aG++A+++ ++   +V vl+++
  gi|121637842|ref|YP_978065.1| 361 RGTAVVIGGSIAGIAAAKMLSETFDRVIVLEKD 393
                                    6789****************9999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (839 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 5209.67
//
Query:       gi|121637843|ref|YP_978066.1|  [L=356]
Description: epoxide hydrolase ephB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-25   90.5   1.6    6.7e-24   84.9   0.6    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.8e-16   60.0  18.0    3.6e-11   44.1   9.3    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
    1.2e-14   54.2   0.4    1.8e-14   53.6   0.4    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0036   16.0   0.0      0.016   13.9   0.0    1.8  2  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.6   1.5e-27   6.7e-24       1     106 [.      28     129 ..      28     153 .. 0.97
   2 !    4.7   0.0    0.0044        20     193     255 ..     275     338 ..     236     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.5e-27
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p++v+lhG+p+s+++w+    +paLa +g++v+++D+rG+g+Ss+   +  + y++  +  d+  +ld++g ++  +vGh
  gi|121637843|ref|YP_978066.1|  28 PLVVLLHGFPESWYSWRH--QIPALAGAGYRVVAIDQRGYGRSSKYRVQ--KAYRIKELVGDVVGVLDSYGAEQAFVVGH 103
                                    78****************..*****************************..***************************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllga 106
                                    ++G  +a+++a ++p+r++++v ++ 
  gi|121637843|ref|YP_978066.1| 104 DWGAPVAWTFAWLHPDRCAGVVGISV 129
                                    **********************9987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0044
                                    HHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHC..HTS.EEEEEEETCSSSHHHH CS
                  Abhydrolase_1 193 pttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaql..lpk.krlvvisdagHlafle 255
                                     ++d++ l +++++    + p+l+i+g++D  + ++a+   +++   p+    + i+d gH+++ e
  gi|121637843|ref|YP_978066.1| 275 IDNDWHDLADQQGK--PLTPPALFIGGQYDVGTIWGAQAIERAHevMPNyRGTHMIADVGHWIQQE 338
                                    45566666666555..5566*************9987777777778999788999*******9966 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   9.3     8e-15   3.6e-11       1     116 [.      30     149 ..      30     189 .. 0.59
   2 !   20.0   4.5   1.9e-07   0.00086      38     219 ..     145     345 ..     139     346 .. 0.55

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8e-15
                                    EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.......CHHHHHHHCCTT..TTSEEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhGrsdpppldled.......ladlaalldelaagggpvvlvGH 72 
                                    v+llHG++ s +sW +  ++ al++ag++v+a+D +G+Grs  + + ++        + d++ +ld+   g+ ++++vGH
  gi|121637843|ref|YP_978066.1|  30 VVLLHGFPESWYSWrH--QIPALAGAGYRVVAIDQRGYGRS--SKYRVQKayrikelVGDVVGVLDSY--GAEQAFVVGH 103
                                    8*******77777766..*********************55..4433333111111234445555555..69999***** PP

                                    TCHHHHHHHHHHCC.......EEEEES-...........----TTTS----TTHHHHH CS
                  Abhydrolase_6  73 SlGGalalaaapla.....lvvgvlldppp.........talpagllaaalelllall 116
                                    ++G+ +a+     a     + +gv+  + p         ++ p+g+         +++
  gi|121637843|ref|YP_978066.1| 104 DWGAPVAWT---FAwlhpdRCAGVVGISVPfagrgviglPGSPFGE---------RRP 149
                                    *********...6666644445544444221222221111222222.........222 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.9e-07
                                    TS-GGCS--HHH.......CHHHHHHHCCTT...TTSE..EEEEETCH....HHHHHHHHHCC..EEEEES-..----TT CS
                  Abhydrolase_6  38 Grsdpppldled.......ladlaalldelaa.gggpv..vlvGHSlG....Galalaaaplalvvgvlldppptalpag 103
                                    G++ p++++le        ++d+ a+ d++++    +   +l+G  +     G++a+   ++a+++gv l++   ++p++
  gi|121637843|ref|YP_978066.1| 145 GERRPSDYHLELagpgrvwYQDYFAVQDGIITeIEEDLrgWLLGLTYTvsgeGMMAAT--KAAVDAGVDLES---MDPID 219
                                    5444444444443333333477755555554431333355777777665546664444..2558899*****...88888 PP

                                    T.......S----TTHHHHHHTT-CCCCHCCH...........S-HSCCCCHHH.CCCCHCHCCCGHHHHCCHHCHTTCC CS
                  Abhydrolase_6 104 l.......laaalelllallallrllawlsre...........plprlfladed.adaawrarlarlaallaglgllpaa 164
                                            +a  ++l +a+  +++ +aw++++           +   +f ++++ ++ + +++++ + ++ ++l   p+a
  gi|121637843|ref|YP_978066.1| 220 ViragplcMAEGARLKDAFVYPETMPAWFTEAdldfytgeferS---GFGGPLSfYHNIDNDWHDLADQQGKPLT--PPA 294
                                    85444444555555555555577779999754344333332220...2222222222444444433333333333..333 PP

                                    HHTT-TTGCEEECTT-CHHHHCHHCCCHSTTEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 165 awadlpvpllvlggeDplvprllerllaqagarlpvvlpgaGHlphleepdevae 219
                                     + +    + +++g+ ++ +  + + +  + +++ + +++ GH++++e+p+e+++
  gi|121637843|ref|YP_978066.1| 295 LFIGGQYDVGTIWGAQAIER--AHEVMP-NYRGT-HMIADVGHWIQQEAPEETNR 345
                                    55555555545589999999..669998.99999.****************9986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.4   4.1e-18   1.8e-14       6     108 ..      29     128 ..      24     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 4.1e-18
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrg.hvpsfddyvdDlaafvekvkeehpelplfllGhS 84 
                                    +vvl+HG+ e+     + + aLa +G+ v+a+D+rG+Grs   r+ +  +++++v D+  +++        ++ f++Gh 
  gi|121637843|ref|YP_978066.1|  29 LVVLLHGFPESWYSWRHQIPALAGAGYRVVAIDQRGYGRSSKYRVqKAYRIKELVGDVVGVLDSYG----AEQAFVVGHD 104
                                    79***************************************99987899***********997666....5579****** PP

                    Hydrolase_4  85 mGGliallyllrypdkvaglilsa 108
                                    +G+ +a +++  +pd++ag++ ++
  gi|121637843|ref|YP_978066.1| 105 WGAPVAWTFAWLHPDRCAGVVGIS 128
                                    ********************9776 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.6e-06     0.016      82     139 ..      79     136 ..      66     140 .. 0.90
   2 ?   -0.7   0.0       0.1   4.6e+02     234     278 ..     309     353 ..     268     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-06
                                    HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---H CS
                            Ndr  82 lddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagw 139
                                    +++l  +++ vld +  +++  +G   GA +   fa  hp+r  g+v i++    +g+
  gi|121637843|ref|YP_978066.1|  79 IKELVGDVVGVLDSYGAEQAFVVGHDWGAPVAWTFAWLHPDRCAGVVGISVPFAGRGV 136
                                    7889999****************************************99987666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.1
                                    HHHHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHHHH CS
                            Ndr 234 devvevnskldkkkttllkvadsgglvleeqPdklaeslklflkG 278
                                     +++e ++++ +++     +ad+g  +++e+P+   + l  fl G
  gi|121637843|ref|YP_978066.1| 309 AQAIERAHEVMPNYRGTHMIADVGHWIQQEAPEETNRLLLDFLGG 353
                                    4555666666666666777999*99*******9999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2305.68
//
Query:       gi|121637844|ref|YP_978067.1|  [L=171]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-29  100.8   0.0    8.5e-29  100.6   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.49   10.4   0.0    1.6  1  DUF1815        Domain of unknown function (DUF1815)


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   9.4e-33   8.5e-29       4     154 ..      27     168 ..      24     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 9.4e-33
                                    S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCC CS
                  Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtd 83 
                                    ++ +v  v +   +++p g+ +ssfts+s dPplv++++++ s t+ +l++  ++ +++l+e + a++ ++s+    ++ 
  gi|121637844|ref|YP_978067.1|  27 FPCGVIAVCA-MVDDQPVGMAASSFTSVSVDPPLVSICVQNCSTTWPKLRDRPRLGVSVLAEGHDAACMSLSR----KEG 101
                                    6777777777.56999*********************************************************....677 PP

                                    CCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEEEE CS
                  Flavin_Reduct  84 dksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrryagl 154
                                    ++  fag+ w+e   g  +++ga a+l+C+   ++++gdh + ++e+ av+ + +  ++pL+++ +r+++l
  gi|121637844|ref|YP_978067.1| 102 NR--FAGVFWSELSSGGVVIAGAGAWLDCRPYAEIPAGDHLIALLEICAVRADPE--TPPLVFHGSRFRRL 168
                                    99..**********************************************99998..469********976 PP

>> DUF1815  Domain of unknown function (DUF1815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.4e-05      0.49      29      77 ..      29      80 ..      24      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.4e-05
                        DUF1815 29 rGvlascytcgde...aesasfvvdlgdghlvrflvsdlgiswvesrddrel 77
                                   +Gv+a c   +d+   + ++sf +   d  lv + v +++ +w  +rd   l
  gi|121637844|ref|YP_978067.1| 29 CGVIAVCAMVDDQpvgMAASSFTSVSVDPPLVSICVQNCSTTWPKLRDRPRL 80
                                   799********9988778889999999******************9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1183.13
//
Query:       gi|121637845|ref|YP_978068.1|  [L=353]
Description: riboflavin biosynthesis protein ribA1 (GTP cyclohydrolase II) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-58  194.9   0.2    1.3e-57  194.4   0.2    1.2  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas
    3.8e-22   78.6   0.0    9.4e-21   74.1   0.0    2.2  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.2   1.5e-61   1.3e-57       2     192 .]      10     194 ..       9     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 1.5e-61
                                    HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT---BB- CS
                  DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhktaftv 81 
                                    +ai+a++ G+ v+++ d++  ++g L++aA+++tp+ vaf +rh+sG++ val+ +++++L+Lp+m   ++    t+ +v
  gi|121637845|ref|YP_978068.1|  10 RAITAMAGGHAVVLTGDPN--GDGYLVFAAQAATPRLVAFAVRHTSGYLRVALPGAECERLHLPPMC--DR---DTTHCV 82 
                                    79*************9866..89********************************************..33...4688** PP

                                    -EEESST-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB- CS
                  DHBP_synthase  82 svdaaegttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicelln 161
                                    svd++ gt TGIsa+DRa Ti +la++++ ++df+rPGhv+p++a+ +gvl Rrg +EaavdLarla+ +paa++ce+++
  gi|121637845|ref|YP_978068.1|  83 SVDVR-GTGTGISASDRAWTIAALASATSVAADFQRPGHVVPVQAQADGVLGRRGPAEAAVDLARLAERRPAAALCEIVS 161
                                    *****.************************************************************************** PP

                                    TT..SCB-BHHHHHHHHHHHT-EEEEHHHHHHH CS
                  DHBP_synthase 162 dd..gtmarrdeleefakkhglkiitiedliey 192
                                     d   +ma+++e +efa +hgl +++i +l++y
  gi|121637845|ref|YP_978068.1| 162 PDnpVQMAHHAESVEFAVEHGLAMVSIGELVAY 194
                                    886768*************************98 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0     1e-24   9.4e-21       5      86 ..     207     292 ..     203     309 .. 0.92
   2 ?    2.2   0.0     0.014   1.2e+02     126     140 ..     314     328 ..     303     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1e-24
                                    EEEEEETTEEEEEEEE--.....EEEEEE-.........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH-.EEEE CS
                GTP_cyclohydro2   5 eaklptrfgefrliayedkvdgkehlalvkgdi....pvlvRvHsecltgDvlgslrcdcgeqldealeliaeegrGvlv 80 
                                     a+lpt  g  r+i+++d  d  ehla++ g +    pv+  vH ecltgDv+gs  c cge+l+ al++++++g+Gv++
  gi|121637845|ref|YP_978068.1| 207 AATLPTWAGASRVIGFRDVYDLGEHLAVIVGAVgagvPVPLHVHIECLTGDVFGSTACRCGEELNGALARMSAQGSGVVL 286
                                    689********************************************************************99******* PP

                                    EE--TT CS
                GTP_cyclohydro2  81 ylrqeg 86 
                                    ylr  g
  gi|121637845|ref|YP_978068.1| 287 YLRPPG 292
                                    **9655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.014
                                    HHHHHHHTT--EEEE CS
                GTP_cyclohydro2 126 aaqILkdlgvkkirL 140
                                     + IL+dlgv  irL
  gi|121637845|ref|YP_978068.1| 314 VTWILRDLGVYAIRL 328
                                    567***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2706.80
//
Query:       gi|121637846|ref|YP_978069.1|  [L=256]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-59  199.8  10.0    5.9e-59  199.5  10.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.5e-50  171.3   4.2      2e-50  171.0   4.2    1.1  1  adh_short     short chain dehydrogenase
    4.7e-12   46.2   3.4      8e-12   45.4   3.4    1.4  1  KR            KR domain
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.019   14.3   0.1    1.5  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
      0.022   14.2   0.4      0.038   13.4   0.3    1.5  1  Epimerase     NAD dependent epimerase/dehydratase family
      0.056   13.3   4.6      0.084   12.8   3.5    1.7  2  YjeF_N        YjeF-related protein N-terminus
      0.077   11.6   1.0        0.1   11.1   1.0    1.2  1  DUF853        Bacterial protein of unknown function (DUF853)
       0.18   11.7   0.3       0.36   10.7   0.3    1.5  1  UPF0146       Uncharacterised protein family (UPF0146)
       0.23   11.3   1.7       0.43   10.5   1.7    1.5  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.5  10.0     3e-62   5.9e-59       1     232 [.      15     250 ..      15     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 3e-62
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    Ga  gIG a+A++la+eG++v+++d++ +a +++++ +  +ga+++++DV+de+q+ a+v+++v+ fg++D lv nag++
  gi|121637846|ref|YP_978069.1|  15 GAGAGIGLAVARRLADEGCHVLCADIDGDA-ADAAATKIGCGAAACRVDVSDEQQIIAMVDACVAAFGGVDKLVANAGVV 93 
                                    8889*************************9.34444444566778*********************************** PP

                                    EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    +   +++++t+ e+fdr++++nl++++l++k+a+p ++++g g+ivnlss++++++v ++ ayg++Ka++++l+r  A+e
  gi|121637846|ref|YP_978069.1|  94 HL--ASLIDTTVEDFDRVIAINLRGAWLCTKHAAPrMIERGgGAIVNLSSLAGQVAVGGTGAYGMSKAGIIQLSRITAAE 171
                                    **..*******************************7777778************************************** PP

                                    HGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHHHHHST....TSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTla.asgikgfdelleelearap....lgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    l + giR N+  p +++T++ +++++ fd  l +  ar++     gr++ pee+a +++fL+sd+as+itG+t ++DgG
  gi|121637846|ref|YP_978069.1| 172 LRSSGIRSNTLLPAFVDTPMqQTAMAMFDGALGAGGARSMiarlQGRMAAPEEMAGIVVFLLSDDASMITGTTQIADGG 250
                                    ********************55566679999888887777223357789*****************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   4.2     1e-53     2e-50       1     190 [.       9     195 ..       9     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 1e-53
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv++vtGa++GIG+a+a++la eG++v+++d+  +++ ++a++++     a a++vDv+d++++ a+v+++v+ +g++d 
  gi|121637846|ref|YP_978069.1|   9 KVAIVTGAGAGIGLAVARRLADEGCHVLCADIDGDAADAAATKIGCG---AAACRVDVSDEQQIIAMVDACVAAFGGVDK 85 
                                    89*****************************************9974...9***************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    Lv+NAG+ + ++  +++ e+++rvi++Nl g+ l+t++++p m+++ +G+Ivn sS ag+v+v g+ aY+ sKa++++l+
  gi|121637846|ref|YP_978069.1|  86 LVANAGVVHLASLIDTTVEDFDRVIAINLRGAWLCTKHAAPRMIERGGGAIVNLSSLAGQVAVGGTGAYGMSKAGIIQLS 165
                                    ******************************************************************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmakel 190
                                    r  a el+++gir n++ P++vdT+m++++
  gi|121637846|ref|YP_978069.1| 166 RITAAELRSSGIRSNTLLPAFVDTPMQQTA 195
                                    ***************************976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   3.4     4e-15     8e-12       4     151 ..      12     156 ..       9     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4e-15
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    ++tG+  g+Gl++ar la++g + l  ++     d d++   a+ ++ g+   ++++Dvsd++++ a+++++ a ++ + 
  gi|121637846|ref|YP_978069.1|  12 IVTGAGAGIGLAVARRLADEGCHVL--CADI---DGDAA--DAAATKIGCGAAACRVDVSDEQQIIAMVDACVAAFGGVD 84 
                                    8********************8754..4433...22222..2445789******************************** PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                      +  Agv++ + l ++t ed+++v+a  ++Gaw   +  ++    +    +v +SS+ag +   g ++Y  
  gi|121637846|ref|YP_978069.1|  85 KLVANAGVVHLASLIDTTVEDFDRVIAINLRGAWLCTKHAAPrmieRGGGAIVNLSSLAGQVAVGGTGAYGM 156
                                    ***********************************99988883444555689********999999999975 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.4e-06     0.019      32      74 ..       4      48 ..       1      89 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.4e-06
                                   S-GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHH.C CS
                   2-Hacid_dh_C 32 kelsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkee.e 74
                                    +l+gk   + G+G+ IG ava+rl+  g++v++ d   ++ + +
  gi|121637846|ref|YP_978069.1|  4 PDLAGKVAIVTGAGAgIGLAVARRLADEGCHVLCADIDGDAADaA 48
                                   58999*********77********************998877622 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.9e-05     0.038       2      61 ..      12      74 ..      11     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHH CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfk 61
                                   +VtGa   iG a++++l+++g +v++ d + +a   a+ + +      +++d+ d++++ ++++
  gi|121637846|ref|YP_978069.1| 12 IVTGAGAGIGLAVARRLADEGCHVLCADIDGDAADAAATK-IgcgaAACRVDVSDEQQIIAMVD 74
                                   8***************************997776665544.26999888888888886665554 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.5   4.2e-05     0.084      28     139 ..       9     112 ..       4     115 .. 0.72
   2 ?   -1.5   0.0         1     2e+03      95     117 ..     188     210 ..     161     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                         YjeF_N  28 kvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedleeklsapvdlviD 107
                                    kv +++G g   g gla+Ar La eg++V +      +++d+da++a +    +g      + +++  +++ a+vd ++ 
  gi|121637846|ref|YP_978069.1|   9 KVAIVTGAG--AGIGLAVARRLADEGCHVLC------ADIDGDAADAAATKIGCGAAACRVDVSDE--QQIIAMVDACVA 78 
                                    566777766..699*****************......79999999999999999988886666554..455677999999 PP

                         YjeF_N 108 AllGiglrgelre..elaeliewlnsseapvlav 139
                                    A+ G+    +  +  +la+li++  ++   v+a+
  gi|121637846|ref|YP_978069.1|  79 AFGGVDKLVANAGvvHLASLIDTTVEDFDRVIAI 112
                                    9988843322222224666666666665556665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                         YjeF_N  95 eeklsapvdlviDAllGiglrge 117
                                    +  ++++++ + D+ lG g +++
  gi|121637846|ref|YP_978069.1| 188 DTPMQQTAMAMFDGALGAGGARS 210
                                    33455666777777777766655 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   5.3e-05       0.1      24      67 ..       8      50 ..       2      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
                         DUF853 24 GliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiaka 67
                                   G +a  tG+G  + L  +a  l++ G  v++ad+ Gd ++ a++
  gi|121637846|ref|YP_978069.1|  8 GKVAIVTGAGAGIGLA-VARRLADEGCHVLCADIDGDAADAAAT 50
                                   6788899999999996.79******************9987765 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00018      0.36      17      49 ..      13      45 ..       5      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                   EEEET-TT--HHHHHHHHHS-EEEEE-SS-S.. CS
                        UPF0146 17 vvEvGiGrkldvaealakrgvdlvatDikekka 49
                                   v   G+G  l+va+ la  g+ ++  Di+   a
  gi|121637846|ref|YP_978069.1| 13 VTGAGAGIGLAVARRLADEGCHVLCADIDGDAA 45
                                   44569999********************87743 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   0.00021      0.43       4      44 ..      13      54 ..       9      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                   EE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N  4 viGaGt.mGagiaavfasagleVvlvdiseealekalekiek 44
                                   v GaG  +G  +a  +a +g++V   di+ +a+++a+ ki  
  gi|121637846|ref|YP_978069.1| 13 VTGAGAgIGLAVARRLADEGCHVLCADIDGDAADAAATKIGC 54
                                   45888669****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1789.96
//
Query:       gi|121637847|ref|YP_978070.1|  [L=109]
Description: hypothetical protein BCG_1981c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-14   53.7   0.1    2.6e-14   53.6   0.1    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.1   1.5e-18   2.6e-14       2     109 ..       7     103 ..       6     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.5e-18
                                    TTEEEEEEE-S--TTS--SEEEEEE-S-H.HHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCCE CS
                     PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsnd.afnekntvivvpltskdkdkkklpfhveleseildlngldkdswvkldqi 80 
                                    rGe+++++       e ++rRpvvV+s+d a+++    +v+p t++++       +v le++ ++    ++ s v+ld +
  gi|121637847|ref|YP_978070.1|   7 RGEVWWCEM-----AE-IGRRPVVVLSRDaAIPRLRRALVAPCTTTIRGL---ASEVVLEPGSDPI---PRRSAVNLDSV 74 
                                    9********.....35.9***********7777779***********655...889***9973333...467******** PP

                                    EEEEGGGEEEEEEE--HHHHHHHHHHHHH CS
                     PemK_toxin  81 rtvdkarlrkkigklsredlaevqralak 109
                                     +v+ a l +++g+l + +++++ +al  
  gi|121637847|ref|YP_978070.1|  75 ESVSVAVLVNRLGRLADIRMRAICTALEV 103
                                    *************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 829.12
//
Query:       gi|121637848|ref|YP_978071.1|  [L=125]
Description: hypothetical protein BCG_1982c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.5   0.8      0.019   14.9   0.8    1.2  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
       0.15   12.5   0.3       0.23   11.9   0.3    1.3  1  CcdA            Post-segregation antitoxin CcdA


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8   2.1e-06     0.019       7      45 ..      57      95 ..      55      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX-------HH.. CS
                 VapB_antitoxin  7 iDDeLlaeAirltglktKrEaVnlALreLiqrrkreeld 45
                                   +D +Ll  A  +    t  +++++AL +L++r++++e d
  gi|121637848|ref|YP_978071.1| 57 VDAALLTSARDMRAGITDAALIDEALAALLARHRSAEVD 95
                                   7889999999999999******************99765 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.6e-05      0.23       3      42 ..      52      93 ..      50     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                           CcdA  3 avnlsldsdllaqAralgiNl..SatleeaLaeevkeekaer 42
                                   +++ ++d++ll  Ar++   +  +a+++eaLa+ ++++++++
  gi|121637848|ref|YP_978071.1| 52 RLSTTVDAALLTSARDMRAGItdAALIDEALAALLARHRSAE 93
                                   57889**********886555338999*********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 934.51
//
Query:       gi|121637849|ref|YP_978072.1|  [L=196]
Description: hypothetical protein BCG_1983c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-10   38.8   9.5    1.2e-09   37.9   9.5    1.5  1  SEC-C     SEC-C motif


Domain annotation for each model (and alignments):
>> SEC-C  SEC-C motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   9.5   6.6e-14   1.2e-09       1      18 [.     168     185 ..     168     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 6.6e-14
                          SEC-C   1 RNdpCPCGSGkKYKkCCg 18 
                                    RN++C+CGSG+KYKkCC+
  gi|121637849|ref|YP_978072.1| 168 RNQQCWCGSGHKYKKCCA 185
                                    9****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1446.61
//
Query:       gi|121637850|ref|YP_978073.1|  [L=454]
Description: hypothetical protein BCG_1984 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-99  333.2  14.2    2.1e-99  332.8  14.2    1.1  1  DUF222    Domain of unknown function (DUF222)
    9.6e-05   22.5   0.3    0.00022   21.3   0.3    1.6  1  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.8  14.2  2.3e-103   2.1e-99       2     301 .]      37     361 ..      36     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 332.8 bits;  conditional E-value: 2.3e-103
                         DUF222   2 laaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lp 70 
                                    la+l++le  +rr+ a+e++l+++la+++++ee g++ +++++a+rl+i+++eAsrr+++A++l+er           L+
  gi|121637850|ref|YP_978073.1|  37 LACLQRLEVERRRQGAAEHALINQLAGQACEEELGGT-LRTALANRLHITPGEASRRIAEAEDLGERraltgeplpaqLT 115
                                    6899*********************************.****************************************** PP

                         DUF222  71 avaaalraGdidlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrr 150
                                    a+aaa+r+G+i+ ++++ I+a++++l++avdl  +++aea+l++ a++ +p++L+ l+++l+++l+pDg+++d+e+ar+r
  gi|121637850|ref|YP_978073.1| 116 ATAAAQREGKIGREHIKEIQAFFKELSAAVDLGIREAAEAQLAELATSRRPDHLHGLATQLMDWLHPDGNFSDQERARKR 195
                                    ******************************************************************************** PP

                         DUF222 151 eltltk.dedGmsrisgeldaeaaaaldavLdslaap.vcap..............dgtkDpRspaqrraDALlallrla 214
                                    ++t++k + dGmsrisg l++e +a+++avL++laap  c+p              + ++D+Rs+aqr++DA+la+lr +
  gi|121637850|ref|YP_978073.1| 196 GITMGKqEFDGMSRISGLLTPELRATIEAVLAKLAAPgACNPddqtplvddtpdadAVRRDTRSQAQRNHDAFLAALRGL 275
                                    ******9************************************************999********************** PP

                         DUF222 215 laagaldchagvpatvvvhvtaeeltaaaggaaltgggglLpasdvrrLAkdAt..laifdepagrpldlgrtkrtasaa 292
                                    la+g+l++h+g+p+t+vv++t++el+aa+g+ ++tggg+++p+sd +r+A++A+  la+fd   ++pl+l++tkr+as+a
  gi|121637850|ref|YP_978073.1| 276 LASGELGQHKGLPVTIVVSTTLKELEAATGK-GVTGGGSRVPMSDLIRMASNANhyLALFDG--AKPLALYHTKRLASPA 352
                                    *******************************.**********************99999999..**************** PP

                         DUF222 293 lrralraRD 301
                                    +r++l+a+D
  gi|121637850|ref|YP_978073.1| 353 QRIMLYAKD 361
                                    ********9 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   2.4e-08   0.00022       4      42 ..     364     404 ..     362     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-08
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHn 42 
                                    C r++ +   + +ev+H+ p+    ++di++l+l+C   ++
  gi|121637850|ref|YP_978073.1| 364 CSRPGCDApaYHSEVHHVTPWTTTHRTDINDLTLACGPDNR 404
                                    7777777777899***********************88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3020.20
//
Query:       gi|121637851|ref|YP_978074.1|  [L=150]
Description: lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1056.41
//
Query:       gi|121637852|ref|YP_978075.1|  [L=133]
Description: hypothetical protein BCG_1986 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1042.61
//
Query:       gi|121637853|ref|YP_978076.1|  [L=116]
Description: hypothetical protein BCG_1987c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 760.90
//
Query:       gi|121637854|ref|YP_978077.1|  [L=300]
Description: hypothetical protein BCG_1988c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2292.00
//
Query:       gi|121637855|ref|YP_978078.1|  [L=63]
Description: hypothetical protein BCG_1989c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 474.61
//
Query:       gi|121637856|ref|YP_978079.1|  [L=98]
Description: hypothetical protein BCG_1990c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 711.91
//
Query:       gi|121637857|ref|YP_978080.1|  [L=71]
Description: hypothetical protein BCG_1991 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.055   13.3   0.0    1.2  1  Arc       Arc-like DNA binding domain


Domain annotation for each model (and alignments):
>> Arc  Arc-like DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-06     0.055      11      43 ..       5      37 ..       2      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-06
                                   CEHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                            Arc 11 lPeevrekvkevAeengRSmNSEilqrveeslk 43
                                   lPe+ +  ++ +A  ++ S+  E  +++   l+
  gi|121637857|ref|YP_978080.1|  5 LPEGTKAALRVRAARHHHSVEAEARAILTAGLL 37
                                   8**********************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 562.45
//
Query:       gi|121637858|ref|YP_978081.1|  [L=103]
Description: hypothetical protein BCG_1992 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.8   0.1     0.0082   16.6   0.1    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.019   14.9   0.0    1.1  1  DUF1045   Protein of unknown function (DUF1045)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   9.1e-07    0.0082       1      60 [.       3      63 ..       3      84 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.1e-07
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHH CS
                            PIN  1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelve 60
                                   +vlDT+v+ al     ++ a++++ +++   e ++ a++laE+ +++ +++++   + e ++
  gi|121637858|ref|YP_978081.1|  3 YVLDTNVVSALR-VPGRHPAVAAWADSVqvAEQFVVAITLAEIERGVIAKERTDPTQSEHLR 63
                                   79******9666.33334444555555578*****************993333333333333 PP

>> DUF1045  Protein of unknown function (DUF1045)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.1e-06     0.019      44     109 ..      10      76 ..       3      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                        DUF1045  44 flALvpaapsealqalAaacvraldefraplseaelarr..raerLsarqealLerWGyPyVldeFrF 109
                                    + AL+  ++++a++a A++ v+  ++f   ++ ae++r   ++er +++q ++L+rW +  Vl  F F
  gi|121637858|ref|YP_978081.1|  10 VSALRVPGRHPAVAAWADS-VQVAEQFVVAITLAEIERGviAKERTDPTQSEHLRRWFDDKVLRIFVF 76 
                                    5688888999999999876.7999**************877999*************88888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 774.20
//
Query:       gi|121637859|ref|YP_978082.1|  [L=173]
Description: hypothetical protein BCG_1993c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1300.65
//
Query:       gi|121637860|ref|YP_978083.1|  [L=170]
Description: hypothetical protein BCG_1994 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-15   57.1   0.1    1.9e-15   56.8   0.1    1.1  1  Gp49      Phage derived protein Gp49-like (DUF891)


Domain annotation for each model (and alignments):
>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.1   1.1e-19   1.9e-15       1      90 []      72     158 ..      72     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.1e-19
                           Gp49   1 eeldalpkkarakilaaldlleeggpdlgkplvkkledglwElrpksaggiiRvlyafdpgrkvilLhafqKktqktpkk 80 
                                    +e+d+lp++ara+++ ++++   g  dl+   +k +++++ Elr+++a++++Rvl++   ++  + L af K++qktpk+
  gi|121637860|ref|YP_978083.1|  72 KEFDKLPDQARAALIVLMQRYLVG--DLAAGSIKPIRGDILELRWHEANNHFRVLFFRWGQH-PVALTAFYKNQQKTPKT 148
                                    689*****************9655..6****************************9988777.999************** PP

                           Gp49  81 eielAekrlk 90 
                                    +ie+A++r k
  gi|121637860|ref|YP_978083.1| 149 KIETALDRQK 158
                                    ******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1287.31
//
Query:       gi|121637861|ref|YP_978084.1|  [L=149]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-10   40.4   0.0    3.2e-10   39.9   0.0    1.3  1  HTH_3       Helix-turn-helix
    3.8e-08   33.6   0.6    3.8e-08   33.6   0.6    1.7  2  HTH_31      Helix-turn-helix domain
    6.1e-08   32.5   0.0      1e-07   31.8   0.0    1.4  1  HTH_37      Helix-turn-helix domain
    3.3e-05   23.8   0.0    5.2e-05   23.2   0.0    1.3  1  HTH_19      Helix-turn-helix domain
     0.0016   18.8   0.0     0.0028   18.1   0.0    1.4  1  HTH_26      Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.022   14.3   0.2      0.084   12.4   0.0    2.0  2  Sigma70_r4  Sigma-70, region 4
      0.063   12.9   0.0       0.16   11.5   0.0    1.6  1  HTH_24      Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.3e-13   3.2e-10       3      50 ..      44      91 ..      42      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.3e-13
                                   HHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                          HTH_3  3 elRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50
                                   +lRk   lsq e+A+++Gv + t+s  E+  + P l+tl+++a+aL+ 
  gi|121637861|ref|YP_978084.1| 44 ALRKHCQLSQVEVAKRMGVRQPTVSGFEKEPSDPKLSTLQRYARALDA 91
                                   79********************************************85 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.6   1.5e-11   3.8e-08       2      60 ..      38      95 ..      37      99 .. 0.91
   2 ?   -3.0   0.0       3.7   9.6e+03      42      47 ..     106     111 ..     103     124 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.5e-11
                         HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpae 60
                                   L + L alR+ + Lsq evA+r gv + t+s  E    + p++++l ++aral++   +
  gi|121637861|ref|YP_978084.1| 38 LVDALIALRKHCQLSQVEVAKRMGVRQPTVSGFEKEPSD-PKLSTLQRYARALDARLRL 95
                                   5677889*******************************7.**************97655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                         HTH_31  42 pspavl 47 
                                    p+++ l
  gi|121637861|ref|YP_978084.1| 106 PTWHRL 111
                                    555544 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     4e-11     1e-07      17      79 ..      36      97 ..      21      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4e-11
                                   HHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTEEEEEEE CS
                         HTH_37 17 aqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGqkveivv 79
                                   ++l+ a+++l+++ +lsq e+a+++g+ qP vs  ++ + s+  l++L +++ al+ ++ +v+
  gi|121637861|ref|YP_978084.1| 36 RRLVDALIALRKHCQLSQVEVAKRMGVRQPTVSGFEK-EPSDPKLSTLQRYARALDARLRLVL 97
                                   689999******************************8.99******************99986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     2e-08   5.2e-05       6      53 ..      44      90 ..      40      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                         HTH_19  6 eaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53
                                   ++R++++l+q e+a+r g+++   s +E++ + +p+ ++l+++a+al+
  gi|121637861|ref|YP_978084.1| 44 ALRKHCQLSQVEVAKRMGVRQPTVSGFEKEPS-DPKLSTLQRYARALD 90
                                   79****************************99.***********9985 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0028      10      52 ..      50      91 ..      42      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                         HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgc 52
                                   ++++ e+a++ g+ ++t+s++ k+ p+ ++l+tL++ ++aL+ 
  gi|121637861|ref|YP_978084.1| 50 QLSQVEVAKRMGVRQPTVSGFEKE-PSDPKLSTLQRYARALDA 91
                                   459999*****************8.79**************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.3e-05     0.084      13      38 ..      43      68 ..      40      73 .. 0.87
   2 ?   -1.4   0.1      0.68   1.7e+03       4      13 ..      88      97 ..      83      99 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                   HHHHHTTT--HHHHHHHHTS-HHHHH CS
                     Sigma70_r4 13 lelrfgeglTleEIgerlgiSrerVr 38
                                   + lr    l++ E+++r+g+ + +V+
  gi|121637861|ref|YP_978084.1| 43 IALRKHCQLSQVEVAKRMGVRQPTVS 68
                                   899*****************999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
                                   HS-HHHHHHH CS
                     Sigma70_r4  4 sLpererevl 13
                                    L++r r vl
  gi|121637861|ref|YP_978084.1| 88 ALDARLRLVL 97
                                   4666666666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.3e-05      0.16       9      35 ..      42      68 ..      38      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                         HTH_24  9 LelLqknprisqreLAerlglSpstvn 35
                                   L +L+k+  +sq e+A+r g+ ++tv+
  gi|121637861|ref|YP_978084.1| 42 LIALRKHCQLSQVEVAKRMGVRQPTVS 68
                                   789*****************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1124.60
//
Query:       gi|121637862|ref|YP_978085.1|  [L=181]
Description: hypothetical protein BCG_1996 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.9   0.0      0.003   17.5   0.0    1.3  1  SecB      Preprotein translocase subunit SecB


Domain annotation for each model (and alignments):
>> SecB  Preprotein translocase subunit SecB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.6e-07     0.003      69     127 ..      96     160 ..      50     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-07
                           SecB  69 ktlFlvevkyaGiftie......nipeeqlepllliecPrilFPyaReivsdlvreggfppllLe 127
                                    + +  ++ ++a++f  +      + +ee+l+ +  ++    l+Py+Re v dl+ +  +ppl Le
  gi|121637862|ref|YP_978085.1|  96 QDVATADFEFAALFDYHlqegedDPTEEELTAYAATTGRFALYPYIREYVYDLTGRLALPPLTLE 160
                                    44455666666666543322211344555666666666668*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1464.75
//
Query:       gi|121637863|ref|YP_978086.1|  [L=204]
Description: hypothetical protein BCG_1997c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1373.91
//
Query:       gi|121637864|ref|YP_978087.1|  [L=98]
Description: hypothetical protein BCG_1998c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-23   82.5   0.1    2.8e-23   82.3   0.1    1.0  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.1   1.6e-27   2.8e-23       1      89 [.       5      93 ..       5      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.6e-27
                                   EEEEHHHHHHHHHHHHHHH.CC-H.HHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEE CS
                     ParE_toxin  1 vrltprAlkdlkkiadyia.rdgp.aakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvi 80
                                   + l+p+A+++l++i+d ++ r+g  +a+++l +l+ a+++ a np++gr ++e+++ g+r++  g + ++Yr+ +e+++  +
  gi|121637864|ref|YP_978087.1|  5 YLLSPAAQAHLEEIWDCTYdRWGVdQAEQYLRELQHAIDRAAANPRIGRACDEIRP-GYRKLSAGSHTLFYRVTGEGTID-V 84
                                   579********************88******************************9.****************8665555.* PP

                                   EEEEEHHHH CS
                     ParE_toxin 81 lrvlhrsed 89
                                   +rvlh+++d
  gi|121637864|ref|YP_978087.1| 85 VRVLHQRMD 93
                                   *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 732.54
//
Query:       gi|121637865|ref|YP_978088.1|  [L=83]
Description: hypothetical protein BCG_1999c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-43  144.8   0.5    8.6e-43  144.7   0.5    1.0  1  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t
  ------ inclusion threshold ------
       0.01   15.7   1.4      0.039   13.9   0.2    2.2  2  RHH_1           Ribbon-helix-helix protein, copG family
      0.012   15.4   0.0      0.015   15.1   0.0    1.1  1  CdvA            CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.5   1.4e-46   8.6e-43       1      80 [.       1      80 [.       1      81 [. 0.98

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 1.4e-46
                                   XXX-EEE---HHHHHHHHHHHCTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-EESS--HHHHHHHCCHXXX CS
                 ParD_antitoxin  1 mskntsvvLgehfsafidsqvaaGrYgsaseviraaLrLLeeretklkaLreaLeegeqsGeaepfDldafleeksreaa 80
                                   m+knts+vL+eh+safid+++aaGrY+sasevir+aLrLLe+ret+l+aLreaLe+ge+sG+++pfD+d+fl++k+++a+
  gi|121637865|ref|YP_978088.1|  1 MGKNTSFVLDEHYSAFIDGEIAAGRYRSASEVIRSALRLLEDRETQLRALREALEAGERSGSSTPFDFDGFLGRKRADAS 80
                                   89**************************************************************************9987 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.5e-06     0.039      12      39 .]      15      43 ..       4      43 .. 0.75
   2 ?    0.7   0.1     0.091   5.5e+02      32      38 ..      49      55 ..      46      62 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                                   HHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                          RHH_1 12 erLdelarrrg.rSrSelIReAlreyler 39
                                   + +d  +++++ rS Se+IR Alr + +r
  gi|121637865|ref|YP_978088.1| 15 AFIDGEIAAGRyRSASEVIRSALRLLEDR 43
                                   556667778888************98775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.091
                                   HHHHHHH CS
                          RHH_1 32 Alreyle 38
                                   Alre+le
  gi|121637865|ref|YP_978088.1| 49 ALREALE 55
                                   4444433 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-06     0.015      70     115 ..      16      61 ..      11      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-06
                           CdvA  70 yasGEidEeaYksaieairellesaleekeeikklleklsklelee 115
                                    ++ GEi    Y+sa+e ir++l+ ++++ ++++ l e l++ e + 
  gi|121637865|ref|YP_978088.1|  16 FIDGEIAAGRYRSASEVIRSALRLLEDRETQLRALREALEAGERSG 61 
                                    889************************************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 569.91
//
Query:       gi|121637866|ref|YP_978089.1|  [L=164]
Description: hypothetical protein BCG_2000 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1173.77
//
Query:       gi|121637867|ref|YP_978090.1|  [L=135]
Description: hypothetical protein BCG_2001c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-15   58.1   2.3    1.4e-15   57.9   2.3    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   2.3   7.6e-20   1.4e-15       1     121 [.       2     122 ..       2     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 7.6e-20
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeia 78 
                                    i+l Ts+l++l+r e++++a++++l++    +++tsal+  El + +++        + l ++   l++l  ++ida i+
  gi|121637867|ref|YP_978090.1|   2 IYLETSALVKLIRIEVESDALADWLDDRteLRWITSALTEVELSRAIRA-----VSPEGLPAVPSVLARLDRFEIDAVIR 76 
                                    79************************99*********************.....888888888888999999999***** PP

                                    HHHHHHHHHHHSBHHHHHHHHHHHHHT-E....EE.ESSTHHHHHHH CS
                            PIN  79 eeaaeialkygllpnDaliaAtAkehgik....liatfDedfrrvak 121
                                     +aa++ + + l+++Da+++AtA+  g      +++t+D++++++a+
  gi|121637867|ref|YP_978090.1|  77 STAAAYPNPA-LRSLDAIHLATAQTAGSVapltALVTYDNRLKEAAE 122
                                    *********9.****************999999555*******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1063.76
//
Query:       gi|121637868|ref|YP_978091.1|  [L=90]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-06   27.3   0.1    3.3e-06   26.8   0.1    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.8e-10   3.3e-06       1      43 [.       1      42 [.       1      50 [. 0.97

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-10
                                   CEEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHH CS
                PhdYeFM_antitox  1 mkivsiseakanlselldeveegeepviItrrGkpvaVlvsle 43
                                   m++vsi+ + +  s++l +v++gee + +t rGk  a++++++
  gi|121637868|ref|YP_978091.1|  1 MNEVSIRTLNQETSKVLARVKRGEE-INLTERGKVIARIIPAS 42
                                   99***********************.***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 689.78
//
Query:       gi|121637869|ref|YP_978092.1|  [L=406]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-32  108.7   3.4    8.1e-17   60.7   0.6    2.6  2  TetR_N       Bacterial regulatory proteins, tetR family
      6e-08   32.9   2.7    9.7e-05   22.6   0.1    3.0  3  TetR_C_24    Tetracyclin repressor-like, C-terminal domain
     0.0098   16.0   0.0      0.022   14.9   0.0    1.6  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
  ------ inclusion threshold ------
      0.031   14.5   0.8       0.33   11.2   0.2    2.4  2  DUF4031      Protein of unknown function (DUF4031)
      0.058   13.5   0.0       0.59   10.3   0.0    2.3  2  HTH_AraC     Bacterial regulatory helix-turn-helix proteins, 


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.6   2.3e-20   8.1e-17       1      47 []      19      65 ..      19      65 .. 0.98
   2 !   48.2   0.1   1.9e-16   6.9e-13       1      47 []     223     269 ..     223     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 2.3e-20
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Ild A+ lf+erG++++ +++IA++AGv+++alYr++++K++Ll+++
  gi|121637869|ref|YP_978092.1| 19 ILDQAVGLFIERGFHSVKLEDIAEAAGVTARALYRHYDNKQALLAEA 65
                                   9*******************************************986 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1.9e-16
                                    HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N   1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47 
                                    +l+a+++lf  +Gy a+ ++eI k AG++ + lYr F+sK+++l+al
  gi|121637869|ref|YP_978092.1| 223 LLAAGARLFRAQGYPAVNTSEIGKGAGIAGPGLYRSFSSKQAILDAL 269
                                    79******************************************996 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.64   2.3e+03      30      65 ..      37      72 ..      11      79 .. 0.60
   2 !    9.2   0.0    0.0004       1.4      12      57 ..      95     140 ..      90     151 .. 0.89
   3 !   22.6   0.1   2.7e-08   9.7e-05       3      81 ..     290     366 ..     288     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.64
                                   HHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      TetR_C_24 30 lrelraLspehreeiralrreyerllrdlieeGvaa 65
                                   l+++    +  ++++ +  ++ ++ll+++i+ G+++
  gi|121637869|ref|YP_978092.1| 37 LEDIAEAAGVTARALYRHYDNKQALLAEAIRTGQDQ 72
                                   555555555555555555555566666666666654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0004
                                    HHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_24  12 vrahveviaeereeaavllrelraLspehreeiralrreyerllrd 57 
                                    +++++++ + +r+ +++ +re r+L++++r+++r++ +++ + +rd
  gi|121637869|ref|YP_978092.1|  95 LEDLIAAAVASRALTVLWQREARYLNEDDRTAVRRRINAIVAGMRD 140
                                    67788999999************************99999888876 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 2.7e-08
                                    SHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHH CS
                      TetR_C_24   3 spaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalail 81 
                                    ++a+rLr lv+ hv++ ++ ++ +av ++el + s e r+ + + + + e+++ dli + v a ++++   +l++ a +
  gi|121637869|ref|YP_978092.1| 290 QAAQRLRGLVQGHVRISLDAPDLVAVSVTELSHASVEVRDGYLRNQGDREAVWIDLIGKLVPATSVAQ--GRLLVAAAI 366
                                    689*******************************************************9999988744..444544444 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.1e-06     0.022      10      53 ..      16      62 ..       8      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.1e-06
                                   HHHH..HHHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH.H-HHHH CS
                    HTH_Tnp_1_2 10 akQk..kaaellvendyekltldeiaeevgvsrsTlykWk.kkkeFi 53
                                   +kQ+  +a+ l +e+ ++ + l++iae  gv  + ly+   +k++  
  gi|121637869|ref|YP_978092.1| 16 KKQIldQAVGLFIERGFHSVKLEDIAEAAGVTARALYRHYdNKQALL 62
                                   5665448999****************************985666655 PP

>> DUF4031  Protein of unknown function (DUF4031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   9.1e-05      0.33      26      69 ..      37      75 ..      33      82 .. 0.88
   2 ?    1.0   0.0      0.15   5.2e+02      49      67 ..     213     231 ..     205     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.1e-05
                        DUF4031 26 LhafAarlGvprrafqrktskdHYDvpeerraeavalGAvevss 69
                                   L ++A+++Gv +ra  r     HYD  ++  aea+++G  + +s
  gi|121637869|ref|YP_978092.1| 37 LEDIAEAAGVTARALYR-----HYDNKQALLAEAIRTGQDQYQS 75
                                   8899***********99.....****************877665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                        DUF4031  49 YDvpeerraeavalGAvev 67 
                                     Dv  +r++ ++a+GA+  
  gi|121637869|ref|YP_978092.1| 213 ADVLFSRYETLLAAGARLF 231
                                    59999***********865 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00017      0.59       7      31 ..      33      57 ..      32      59 .. 0.91
   2 ?    0.4   0.0      0.21   7.6e+02      11      23 ..     369     381 ..     369     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                   CT--HHHHHHHTTSSHHHHHHHHHH CS
                       HTH_AraC  7 tnltiediAdelgfSrsyFsrlFkk 31
                                   ++ ++ediA+++g+  + ++r + +
  gi|121637869|ref|YP_978092.1| 33 HSVKLEDIAEAAGVTARALYRHYDN 57
                                   6899*****************9876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                                    HHHHHHHTTSSHH CS
                       HTH_AraC  11 iediAdelgfSrs 23 
                                    ied+A ++++ r+
  gi|121637869|ref|YP_978092.1| 369 IEDVARTWHLTRY 381
                                    89*******9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2875.91
//
Query:       gi|121637870|ref|YP_978093.1|  [L=134]
Description: integral membrane protein YrbE3a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.1   0.2      0.077   12.7   0.2    1.2  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   4.3e-06     0.077       3      54 ..      49     100 ..      47     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-06
                           MlaE   3 eqlefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvr 54 
                                     q++fv+  s ++ +l++++  ++ ++ + ++l+++ga ++ g+  a+++v 
  gi|121637870|ref|YP_978093.1|  49 LQCWFVARVSTLPGVLMTIPWAVISGFLFNVLLTDIGAADFSGTGCAIFTVN 100
                                    69******************************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 907.12
//
Query:       gi|121637871|ref|YP_978094.1|  [L=174]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   40.8   0.0    6.1e-10   38.6   0.0    1.8  1  RrnaAD    Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
       0.18   11.5   0.0       0.29   10.8   0.0    1.2  1  UPF0020   Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   6.8e-14   6.1e-10      55     195 ..      52     167 ..      44     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.8e-14
                                    EEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEE CS
                         RrnaAD  55 vvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkml 134
                                    vv++El +r + +l++++     ++vvh+D+    +p          ++f+vvan Py+is+ l   ll ++  glv + 
  gi|121637871|ref|YP_978094.1|  52 VVAVELHPRRVGVLRERFP---GITVVHADAASIRLPG---------RPFRVVANPPYGISSRLLRTLL-APNSGLVAAD 118
                                    899*************665...9**************9.........**********************.59999***** PP

                                    EEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-S CS
                         RrnaAD 135 lwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPppkvdsalvelerkd 195
                                    l+lq+  + + ++r  + +r +l+v +           +++++f Ppp vdsa++  +r++
  gi|121637871|ref|YP_978094.1| 119 LVLQRALVCKFASR--NARRFTLTVGL----------MLPRRAFLPPPHVDSAVLVVRRRK 167
                                    **********9997..23555555544..........46***************9999986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.2e-05      0.29     105     134 ..      72     100 ..      68     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                                    EEEEE--GGG--STTS---EEEE------- CS
                        UPF0020 105 iefsqadaakLrlkegevdvivtnpPYGer 134
                                    i+++ adaa++rl+   +  +v+npPYG++
  gi|121637871|ref|YP_978094.1|  72 ITVVHADAASIRLPGRPF-RVVANPPYGIS 100
                                    678999******777677.89*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1236.24
//
Query:       gi|121637872|ref|YP_978095.1|  [L=186]
Description: hypothetical protein BCG_2005c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-15   55.5   0.8    7.2e-15   55.2   0.8    1.1  1  RES       RES domain


Domain annotation for each model (and alignments):
>> RES  RES domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.8     4e-19   7.2e-15       2     128 ..      25     148 ..      24     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 4e-19
                            RES   2 lyRirksdylaaapfsgpgaaagggRfnsa.gigvlYaAssvatAlaEvlvhrgrfldataglpll.lprdlrlldlevp 79 
                                    +yR ++    +++++sg+ga+++ggR+n++  ++++Y+A+s + ++ Ev        +a+   + + l   +rl +++v 
  gi|121637872|ref|YP_978095.1|  25 CYRYTGA---HRDALSGEGARRFGGRWNPPlLFPAIYLADSAQACMVEVER----AAQAASTTAEKmLEAAYRLHTIDVT 97 
                                    6888667...99*************************************55....3333333333359999999999999 PP

                            RES  80 darlvdldrgaalerlpkwadpas...dysatqaiadalraagidGilypSa 128
                                    d +++dl++++a+e ++ ++ ++    d s +qa++ a++ ++ +G+l+p a
  gi|121637872|ref|YP_978095.1|  98 DLAVLDLTTPQAREAVG-LENDDIygdDWSGCQAVGHAAWFLHMQGVLVPAA 148
                                    *******5577888888.666644666999********************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1471.70
//
Query:       gi|121637873|ref|YP_978096.1|  [L=113]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-07   30.1   1.1    4.9e-07   29.7   0.3    1.7  2  DUF2384          Protein of unknown function (DUF2384)
  ------ inclusion threshold ------
      0.025   14.9   0.2      0.045   14.1   0.2    1.4  1  HTH_31           Helix-turn-helix domain
      0.064   13.3   0.0       0.12   12.5   0.0    1.5  1  HTH_3            Helix-turn-helix
      0.095   12.5   0.0       0.11   12.3   0.0    1.1  1  DUF4447          Domain of unknown function (DUF4447)
      0.097   12.7   0.0       0.11   12.5   0.0    1.2  1  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
       0.12   12.2   0.0       0.29   11.0   0.0    1.6  1  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3   6.8e+03       8      15 ..      31      38 ..      24      38 .. 0.69
   2 !   29.7   0.3   1.6e-10   4.9e-07      10      51 .]      70     110 ..      55     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                        DUF2384  8 deeraarW 15
                                   +++ +arW
  gi|121637873|ref|YP_978096.1| 31 SPRSVARW 38
                                   47888888 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-10
                        DUF2384  10 eraarWLrrPnpaLggrtPldlldteaGarlVedyLdrirgG 51 
                                    ++a  W+ +Pn+ L++r+P+dl++ ++  ++V  ++d+++ G
  gi|121637873|ref|YP_978096.1|  70 DQANVWMFSPNRLLEHRKPADLVR-DGEYQRVLALIDAMAEG 110
                                    34455*******************.**************998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.5e-05     0.045      11      54 ..      15      63 ..      12      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                         HTH_31 11 eraGLsqeevAerlgvsestlsrlEqGrrgrp......spavlealaral 54
                                   er GL+ eev++ +  s+  + r+  G+  +p      ++  l+ +a+al
  gi|121637873|ref|YP_978096.1| 15 ERLGLTYEEVGDIVDASPRSVARWTAGQV-VPqrlnkqRLIELAYVADAL 63
                                   799**************************.69444333333555555554 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05      0.12       6      45 ..      15      57 ..      13      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                   HHTTHHHHHHHHHHTSSHHHHHHHHTT...SSCSBHHHHHHHH CS
                          HTH_3  6 kqlglsqeeLAeklGvsrstisriEnG...ernPsletlkkla 45
                                   + lgl+ ee+ + ++ s+++++r+  G    ++ + ++l++la
  gi|121637873|ref|YP_978096.1| 15 ERLGLTYEEVGDIVDASPRSVARWTAGqvvPQRLNKQRLIELA 57
                                   689************************7665556666666665 PP

>> DUF4447  Domain of unknown function (DUF4447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05      0.11      17      61 ..      15      59 ..       2      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                   HHTT--HHHHHHHHTS-HHHHHHHHTTSS---HHHHHHHHHHHHH CS
                        DUF4447 17 qslglsaaqvgeltkaseedvlaweageaeapelaqkklleidei 61
                                   + lgl+ ++vg++ +as   v  w ag+     l +++l+e+  +
  gi|121637873|ref|YP_978096.1| 15 ERLGLTYEEVGDIVDASPRSVARWTAGQVVPQRLNKQRLIELAYV 59
                                   579*************************9999999999*998765 PP

>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.6e-05      0.11      39      73 ..      28      62 ..      25     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT- CS
                S-AdoMet_synt_C 39 vDrsaayaaryvaknlvaaglakkvevqlsYaigv 73
                                   vD s   +ar+ a ++v ++l k+ +++l+Y+ + 
  gi|121637873|ref|YP_978096.1| 28 VDASPRSVARWTAGQVVPQRLNKQRLIELAYVADA 62
                                   8999999************************8765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.7e-05      0.29      16      37 ..      16      38 ..       7      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                         HTH_23 16 e.GlsvreIAreLgvsrrTvyrw 37
                                   + Gl+++e+ ++ + s+r v rw
  gi|121637873|ref|YP_978096.1| 16 RlGLTYEEVGDIVDASPRSVARW 38
                                   359******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 850.63
//
Query:       gi|121637874|ref|YP_978097.1|  [L=111]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.045   13.2   0.4        0.3   10.5   0.1    2.0  2  adh_short  short chain dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   1.7e-05       0.3       1      29 [.       7      35 ..       7      63 .. 0.79
   2 ?    1.1   0.0     0.013   2.3e+02      16      41 ..      73      98 ..      71     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.7e-05
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE CS
                      adh_short  1 kvvlvtGassGIGraiakelakeGakvvv 29
                                   kv+++tG ++G Gr  a +la  +a+ + 
  gi|121637874|ref|YP_978097.1|  7 KVAFITGVARGQGRSHAVRLADGQARALG 35
                                   89*******************99988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.013
                                   HHHHHHHTT-EEEEEESCHHHHHHHH CS
                      adh_short 16 iakelakeGakvvvvdrseekleeva 41
                                    ++++a++G++vv +  s+++l e  
  gi|121637874|ref|YP_978097.1| 73 ACRRVARQGIRVVGLPVSQRELVEPE 98
                                   69999*******99888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 981.36
//
Query:       gi|121637875|ref|YP_978098.1|  [L=114]
Description: hypothetical protein BCG_2008c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-23   80.9   0.0    9.5e-23   80.7   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   5.3e-27   9.5e-23       2     111 .]       5     112 ..       4     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 5.3e-27
                                    TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCH..SEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCC CS
                     PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnek..ntvivvpltskdkdkkklpfhveleseildlngldkdswvkldq 79 
                                    r eI+++dl+p++gs+ +krRpv+V+++d +n++  +tvi + +ts+    +++p +v l+++   ++ l++ds+v++  
  gi|121637875|ref|YP_978098.1|   5 RAEIYWADLGPPSGSQPAKRRPVLVIQSDPYNASrlATVIAAVITSNTA-LAAMPGNVFLPAT---TTRLPRDSVVNVTA 80 
                                    88*********99*******************77567********9997.5566******976...6667899******* PP

                                    EEEEEGGGEEEEEEE--HHHHHHHHHHHHHHC CS
                     PemK_toxin  80 irtvdkarlrkkigklsredlaevqralakll 111
                                    i t++k  l +++g++++ ++ ev+r l+++l
  gi|121637875|ref|YP_978098.1|  81 IVTLNKTDLTDRVGEVPASLMHEVDRGLRRVL 112
                                    ****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 852.33
//
Query:       gi|121637876|ref|YP_978099.1|  [L=771]
Description: metal cation transporter P-type atpase G ctpG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-40  138.7   6.4    1.4e-40  138.7   6.4    2.6  2  E1-E2_ATPase  E1-E2 ATPase
      2e-40  139.3  11.1    4.5e-40  138.2  11.1    1.6  1  Hydrolase     haloacid dehalogenase-like hydrolase
     0.0015   18.9   2.7       0.02   15.3   0.8    3.3  3  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.035   13.8   0.7      0.093   12.5   0.3    1.7  2  Hydrolase_3   haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   6.4   3.2e-44   1.4e-40       2     180 ..     262     439 ..     261     440 .. 0.98
   2 ?    0.4   0.2     0.091   4.1e+02     103     141 ..     694     733 ..     675     749 .. 0.66

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 3.2e-44
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                    l p++a+v+r+gte+ +++ el++GD  ++k+g+r ++Dg+i  g + +d sa+TGEs+pve+  gd+vf+G+++  g +
  gi|121637876|ref|YP_978099.1| 262 LVPDQATVLREGTETIVASTELHVGDQMIVKPGERLATDGIIRAGRTALDVSAITGESVPVEVGPGDEVFAGSINGLGVL 341
                                    7899**************************************************************************** PP

                                    EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-T CS
                   E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPc 161
                                    ++ Vtat+ ++ l++i++ ve+++ +k   q+ +d +++ lvp ++++a+l++ +  +lg++l  ++ ral++lvaa Pc
  gi|121637876|ref|YP_978099.1| 342 QVGVTATAANNSLARIVHIVEAEQVRKGASQRLADCIARPLVPSIMIAAALIAGTGSVLGNPL-VWIERALVVLVAAAPC 420
                                    ******************************************************999988888.9*************** PP

                                    THHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 162 aLplavplalalgarrlak 180
                                    aL++avp++++++++++++
  gi|121637876|ref|YP_978099.1| 421 ALAIAVPVTVVASIGAASR 439
                                    *************999876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.091
                                    ---.----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                   E1-E2_ATPase 103 eak.skktplqkkldklgkvlvpvvlliallvflialllg 141
                                    +a  +++ + q +++++g  l+++ +l+ l++f i+ l  
  gi|121637876|ref|YP_978099.1| 694 QALdHARRSRQIMVQNVGLSLSIITVLMPLALFGILGLAA 733
                                    4444677777888888888888888888888888765544 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2  11.1   9.9e-44   4.5e-40       1     210 []     456     663 ..     456     663 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 9.9e-44
                                    SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE....... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakarsgaltgfatfigrg....... 67 
                                    i++v++Dk+GTLt  +p+v dv   +       la aaale  sehp++ a+ aa +a + a +++++++g g       
  gi|121637876|ref|YP_978099.1| 456 IRAVALDKTGTLTANRPVVIDVATTNgatreeVLAVAAALEARSEHPLAVAVLAATQA-TTAASDVQAVPGAGligrldg 534
                                    799******************9999988888899999999999*********655555.68889**************** PP

                                    .HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSE CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 .ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdn 144
                                     ++  g+p wl+a     +l + +   q++g t++l+  ++++l+ +++ d+  ++peaae+va L+  g++v +ltgdn
  gi|121637876|ref|YP_978099.1| 535 rVVRLGRPGWLDAA----ELADHVACMQQAGATAVLVerDQQLLGAIAVRDE--LRPEAAEVVAGLRTGGYQVTMLTGDN 608
                                    **************....*******************9988***********..************************** PP

                                    HHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHT.STGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 145 petaeraanqlGddyfdaviasdiet.vakpspegkvaaireLq.gkpeevamVGDgvnDaaalaaAg 210
                                    ++ta ++a q+G           ie  +a+  pe+k +++ +L+  +p  +amVGDgvnDa+alaaA+
  gi|121637876|ref|YP_978099.1| 609 HATAAALAAQAG-----------IEQvHAELRPEDKAHLVAQLRaRQP--TAMVGDGVNDAPALAAAD 663
                                    ************...........8888****************84557..*****************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.23     1e+03      44     108 ..     223     280 ..     198     291 .. 0.69
   2 ?    0.1   0.0       0.2   8.9e+02       7     107 ..     465     567 ..     461     567 .. 0.62
   3 !   15.3   0.8   4.4e-06      0.02      65     187 ..     566     659 ..     544     660 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.23
                            HAD  44 rellrldraglaelleallaglseelaaelerfvaevirpklldpgalellaahraaGdrvvvvS 108
                                      l++l +a++ ++l ++ +gl+e+  a+ +r +++      l p+  ++l+    +G +++v S
  gi|121637876|ref|YP_978099.1| 223 VALGELGEAATLAFLFSISEGLEEYATARTRRGLRALLS---LVPDQATVLR----EGTETIVAS 280
                                    368899999999999999999999999998888832222...3355555555....555555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                            HAD   7 gTLldgdsle..lllrfllrrgaprlwralrek....lllalfrellrldraglaelleallaglseelaaelerfvaev 80 
                                    gTL+++ +    + ++  ++++++ l+ a++ +      la++  ++++   ++  +++   agl ++l+ ++ r++   
  gi|121637876|ref|YP_978099.1| 465 GTLTANRPVVidV-ATTNGATREEVLAVAAALEarseHPLAVAVLAATQATTAASDVQAVPGAGLIGRLDGRVVRLG--- 540
                                    5666664444432.222333333333222222211224444467777777778888888889999999999999999... PP

                            HAD  81 irpklldp.galellaahraaGdrvvvv 107
                                     rp +ld  ++ + +a+ ++aG + v+v
  gi|121637876|ref|YP_978099.1| 541 -RPGWLDAaELADHVACMQQAGATAVLV 567
                                    .777555569999999999999988887 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 4.4e-06
                            HAD  65 lseelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelgl 144
                                    l e++ + l+++    +r   l+p+a e++a  r  G++v++++g +   + +l+a+ g+++v a+           l++
  gi|121637876|ref|YP_978099.1| 566 LVERDQQLLGAIA---VRDE-LRPEAAEVVAGLRTGGYQVTMLTGDNHATAAALAAQAGIEQVHAE-----------LRP 630
                                    4455555555555...3444.67********999*************************6666555...........222 PP

                            HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                    e+k        a lr+      + +    +  +GD+++D p+l
  gi|121637876|ref|YP_978099.1| 631 EDKAHLV----AQLRA------RQP----TAMVGDGVNDAPAL 659
                                    2322222....34444......222....67777777777776 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.41   1.9e+03      16      55 ..     583     622 ..     580     626 .. 0.86
   2 ?   12.5   0.3   2.1e-05     0.093     204     230 ..     644     670 ..     634     684 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.41
                                    --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                    Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                    + ++++e+++ l+  g++v+  TG ++ ++  ++ + g++
  gi|121637876|ref|YP_978099.1| 583 LRPEAAEVVAGLRTGGYQVTMLTGDNHATAAALAAQAGIE 622
                                    56788899999999*************9999999998887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                                    GGEEEEESSGGGHHHHHHSSEEEEETT CS
                    Hydrolase_3 204 eeviafGDgeNDieMLeaaglgvAmgn 230
                                    + ++ +GDg ND + L aa+lg+Amg 
  gi|121637876|ref|YP_978099.1| 644 QPTAMVGDGVNDAPALAAADLGIAMGA 670
                                    668999*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5514.05
//
Query:       gi|121637877|ref|YP_978100.1|  [L=90]
Description: hypothetical protein BCG_2010c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-39  133.0   8.3    3.3e-39  132.8   8.3    1.0  1  DUF1490   Protein of unknown function (DUF1490)


Domain annotation for each model (and alignments):
>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   8.3   1.8e-43   3.3e-39       1      86 [.       1      86 [.       1      88 [. 0.98

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 1.8e-43
                        DUF1490  1 mvvqgllakaattvvtGvvGvaayevlrkavakaplreaaVaatalglrgaRkaeeaaEsarLkvaDvvaeAreriGeeapp 82
                                   mv+++ll+kaa++v+tG+vGv+aye+lrka+ +ap+r+a+V+++++glrg+R+ae+aaEsarL+vaDvvaeAr+riGeeap 
  gi|121637877|ref|YP_978100.1|  1 MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAESARLTVADVVAEARGRIGEEAPL 82
                                   9********************************************************************************* PP

                        DUF1490 83 pava 86
                                   pa a
  gi|121637877|ref|YP_978100.1| 83 PAGA 86
                                   *976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 690.79
//
Query:       gi|121637878|ref|YP_978101.1|  [L=118]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.1e-17   60.8   0.1    1.5e-16   59.9   0.1    1.4  1  HTH_5      Bacterial regulatory protein, arsR family
    2.1e-11   43.7   0.7    3.5e-11   43.0   0.2    1.6  2  HTH_20     Helix-turn-helix domain
      6e-06   26.1   0.1    1.1e-05   25.2   0.1    1.6  1  MarR_2     MarR family
    0.00035   20.3   1.3    0.00048   19.9   0.1    1.9  3  HTH_IclR   IclR helix-turn-helix domain
    0.00055   19.9   0.0     0.0018   18.2   0.0    1.8  2  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.0   0.7       0.18   11.5   0.1    2.1  3  RP-C       Replication protein C N-terminal domain
      0.056   13.3   0.0       0.08   12.8   0.0    1.2  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.084   12.4   0.1       0.18   11.4   0.1    1.7  1  HTH_24     Winged helix-turn-helix DNA-binding
        0.1   12.9   0.1       0.69   10.2   0.0    2.1  2  PaaX       PaaX-like protein


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.1   7.8e-20   1.5e-16       1      45 [.      20      64 ..      20      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7.8e-20
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   dptR++IL +L +g ++ ++la++lgl++s+vS HL++Lr +GLV
  gi|121637878|ref|YP_978101.1| 20 DPTRCRILVALLDGVCYPGQLAAHLGLTRSNVSNHLSCLRGCGLV 64
                                   8*******************************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.2   1.8e-14   3.5e-11       3      60 ..      14      70 ..      12      71 .. 0.91
   2 ?   -2.4   0.0       2.5   5.1e+03      42      45 ..      83      86 ..      75     100 .. 0.55

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.8e-14
                                   HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   + +ALa+P+R+ril aL  ++   +++la+ l+l+++++s+HL  L+  gLv  + eg
  gi|121637878|ref|YP_978101.1| 14 LGRALADPTRCRILVAL-LDGVCYPGQLAAHLGLTRSNVSNHLSCLRGCGLVVATYEG 70
                                   568**************.****************************999998776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                                   HHHH CS
                         HTH_20 42 syHL 45
                                    + L
  gi|121637878|ref|YP_978101.1| 83 ARAL 86
                                   2222 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   5.5e-09   1.1e-05       4      52 ..      20      65 ..      16      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.5e-09
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   +p+  r+L aL ++    + +g+la++lgl++s+vs++l  L   GLv+
  gi|121637878|ref|YP_978101.1| 20 DPTRCRILVALLDGV---CYPGQLAAHLGLTRSNVSNHLSCLRGCGLVV 65
                                   59999******9998...8*****************************6 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.3   8.6e+03      12      17 ..      11      16 ..       8      22 .. 0.56
   2 !   19.9   0.1   2.4e-07   0.00048      22      49 ..      38      65 ..      24      67 .. 0.94
   3 ?   -2.9   0.0       3.1   6.2e+03      24      29 ..      82      87 ..      77      91 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                                   -CTTBS CS
                       HTH_IclR 12 laeapq 17
                                   la+ ++
  gi|121637878|ref|YP_978101.1| 11 LARLGR 16
                                   444443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyve 49
                                    +lA+++gl++S+v+++L+ L  +G+v 
  gi|121637878|ref|YP_978101.1| 38 GQLAAHLGLTRSNVSNHLSCLRGCGLVV 65
                                   68************************95 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.1
                                   HHHHHT CS
                       HTH_IclR 24 lArrtg 29
                                   lAr++g
  gi|121637878|ref|YP_978101.1| 82 LARALG 87
                                   444444 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.8e-07    0.0018      26      55 ..      39      71 ..      37      80 .. 0.84
   2 ?   -1.9   0.0       1.7   3.4e+03      37      46 ..      81      90 ..      76      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.8e-07
                                   HHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TE CS
                      HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.r..gr 55
                                   +lA++lGltr+ vs  ls L+  gl+  +  gr
  gi|121637878|ref|YP_978101.1| 39 QLAAHLGLTRSNVSNHLSCLRGCGLVVaTyeGR 71
                                   8************************98743233 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                   HHHHHHHHHH CS
                      HTH_Crp_2 37 tvsrilseLk 46
                                   ++ r+l+eL 
  gi|121637878|ref|YP_978101.1| 81 HLARALGELV 90
                                   6677777775 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.9   7.7e+03      83      97 ..       6      20 ..       4      22 .. 0.71
   2 ?   11.5   0.1   8.9e-05      0.18      76     116 ..      39      79 ..      37      87 .. 0.89
   3 ?    2.6   0.0     0.048        95      82     107 ..      76     101 ..      72     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.9
                           RP-C 83 lsestlrrhlaaLve 97
                                   + es+l r+ +aL++
  gi|121637878|ref|YP_978101.1|  6 MRESALARLGRALAD 20
                                   677777777777765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.9e-05
                           RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRyarrd 116
                                    qL+  lgl++s +++hl+ L  +Gl++      + Rya  d
  gi|121637878|ref|YP_978101.1|  39 QLAAHLGLTRSNVSNHLSCLRGCGLVVATYEGRQVRYALAD 79 
                                    79999**********************99999999998655 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.048
                           RP-C  82 glsestlrrhlaaLveaGliirrDsp 107
                                     l++s l r l +Lv++ l +  D p
  gi|121637878|ref|YP_978101.1|  76 ALADSHLARALGELVQVVLAVDTDQP 101
                                    68999**************9999998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05      0.08      24      65 ..      36      78 ..      24      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                   HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE- CS
                           TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYrav 65
                                      ++a +lg+ rs+v + L+ L  +GlV    +    +Y  +
  gi|121637878|ref|YP_978101.1| 36 YPGQLAAHLGLTRSNVSNHLSCLRGCGLVVATYEGrQVRYALA 78
                                   5568999**********************99885525577665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.3e-05      0.18      20      41 ..      37      58 ..      20      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                         HTH_24 20 qreLAerlglSpstvnrrlkrL 41
                                     +LA +lgl++s+v+ +l  L
  gi|121637878|ref|YP_978101.1| 37 PGQLAAHLGLTRSNVSNHLSCL 58
                                   569***************9755 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00035      0.69      29      69 ..      40      80 ..      39      81 .. 0.92
   2 ?   -0.2   0.0      0.61   1.2e+03      23      40 ..      86     103 ..      83     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                           PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69
                                   l a lG+  s v   ls l   G++v++ egr++ Y+L+d 
  gi|121637878|ref|YP_978101.1| 40 LAAHLGLTRSNVSNHLSCLRGCGLVVATYEGRQVRYALADS 80
                                   778999999999999***********************995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.61
                           PaaX  23 lgsLirllaelGiseslv 40 
                                    lg+L++ + +++ ++  v
  gi|121637878|ref|YP_978101.1|  86 LGELVQVVLAVDTDQPCV 103
                                    799****99999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 776.99
//
Query:       gi|121637879|ref|YP_978102.1|  [L=255]
Description: hypothetical protein BCG_2012 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-19   70.7  14.3    1.7e-13   51.3   2.9    2.2  2  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   2.9   9.4e-18   1.7e-13       4     131 .]      69     201 ..      66     201 .. 0.87
   2 !   32.2   3.7   7.8e-12   1.4e-07       2      81 ..     139     223 ..     138     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 9.4e-18
                                    HHHHHHHHHHHHHHHHHHHHHHH..HHHHCCC..HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHH CS
                    Hemerythrin   4 ealdeeHralrallerlralada..aaevhga..lrklaelldelvdeleaHhaaEEellfPlledrpggravldvlere 79 
                                    e l++eH  l++ l   r+  ++  a+++ +a  l + a++++++ ++   H + EE+++fP le+++  ++ ++vl+ +
  gi|121637879|ref|YP_978102.1|  69 EDLMREHGVLKRILLIYREGIRRlqADDQSPApaLNESAQIIRRFIED--YHGQLEEQYVFPKLEQAGKLTDITSVLRTQ 146
                                    56899**********9977777753333333378*********99998..9***************************** PP

                                    HHHHHHHHHHHH.HHCHTCG..GSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
                    Hemerythrin  80 Hdeirelleelr.ellkgle..epsaaafaelleeladllreHiakEesilfpll 131
                                    H++ r l +++  ++++ ++  +p+ +++a+++++++++++ H a+E+ ++fp+l
  gi|121637879|ref|YP_978102.1| 147 HQRGRVLTDRVLaATTAAAAfdQPARDTLAQDMAAYIRMFEPHEAREDTVVFPAL 201
                                    *****99999995555555587999999999**********************86 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 7.8e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC.HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH....CCC.HHHHHHHH CS
                    Hemerythrin   2 ivealdeeHralrallerlraladaaaevhga.lrklaelldelvdeleaHhaaEEellfPlle...drpggravldvle 77 
                                    i+ +l+++H++ r l++r+ a+++aaa  +++ ++ la+ ++++ + +e+H+a+E++++fP+l+    ++++r++ +  e
  gi|121637879|ref|YP_978102.1| 139 ITSVLRTQHQRGRVLTDRVLAATTAAAAFDQPaRDTLAQDMAAYIRMFEPHEAREDTVVFPALRdvmSAVEFRDMAETFE 218
                                    6789*************9977777744444445*******************************8888888888888777 PP

                                    H.HHH CS
                    Hemerythrin  78 r.eHd 81 
                                      eH+
  gi|121637879|ref|YP_978102.1| 219 DeEHR 223
                                    51455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1728.24
//
Query:       gi|121637880|ref|YP_978103.1|  [L=317]
Description: hypothetical protein BCG_2013 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-47  161.4   5.5    4.7e-24   85.5   2.5    2.2  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   2.5   2.6e-28   4.7e-24       5     141 .]      10     159 ..       8     159 .. 0.92
   2 !   76.7   0.1   1.4e-25   2.5e-21       5     141 .]     172     308 ..     169     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.6e-28
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.............. CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.............. 70 
                                    I+V+vDgs++s+ A+ewA++ a++r+ +l+++ v++p   +++++a+e ++ +e++++e  ++ +               
  gi|121637880|ref|YP_978103.1|  10 IVVGVDGSPCSHTAVEWAARDAQMRNVALRVVQVVPPVITAPEGWAFEYSRFQEAQKREIVEHSYLvaqahqiveqahkv 89 
                                    9******************************************************************************7 PP

                                    .HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  71 .akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                     ++a   ++ ++ + +v++g+  ++++ +  ++++ ++V+G rg+++++++llGSvs++++rha+ pV v++
  gi|121637880|ref|YP_978103.1|  90 aLEASSSGRAAQITGEVLHGQIVPTLANI--SRQVAMVVLGYRGQGAVAGALLGSVSSSLVRHAHGPVAVIP 159
                                    77777777777777777777777766666..667************************************86 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 1.4e-25
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCC...CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasga...vsdadeeaeeeeleleeaeleadaakaaaeaggvk 81 
                                    ++V++Dgs++s  A+e A+++a +rg +l++lh+++++ +       +a+ e +  e e+e++ ++++     ++++ ++
  gi|121637880|ref|YP_978103.1| 172 VVVGIDGSPTSGLAAEIAFDEASRRGVDLVALHAWSDMGPLDfprLNWAPIEWRNLEDEQEKMLARRL---SGWQDRYPD 248
                                    89*********************************976555400045555555555555555555554...577777777 PP

                                    EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    v+v+ ++   +++  +++ ++ a+l+VvGs+gr+g+ ++ lGSvs++v+++ + pV+v r
  gi|121637880|ref|YP_978103.1| 249 VVVHKVVVCDRPAPRLLELAQTAQLVVVGSHGRGGFPGMHLGSVSRAVVNSGQAPVIVAR 308
                                    7777777777777777777777***********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2258.47
//
Query:       gi|121637881|ref|YP_978104.1|  [L=905]
Description: metal cation transporter P-type atpase A ctpF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-54  182.8   1.8    4.1e-54  182.8   1.8    2.3  2  E1-E2_ATPase     E1-E2 ATPase
    5.7e-39  133.7   9.6    5.7e-39  133.7   9.6    1.6  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    7.3e-19   68.9  10.5    2.2e-18   67.3   8.0    3.0  2  Hydrolase        haloacid dehalogenase-like hydrolase
      2e-18   66.2   0.0    4.4e-18   65.1   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    4.7e-18   64.6   0.0    9.4e-18   63.7   0.0    1.5  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    7.7e-05   22.6   1.1    9.4e-05   22.3   0.2    1.5  2  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   1.8   1.4e-57   4.1e-54       2     181 .]     119     311 ..     118     311 .. 0.99
   2 ?   -3.8   1.7       2.7   8.1e+03     144     174 ..     714     745 ..     698     751 .. 0.49

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 1.4e-57
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G-TT CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............ekgd 68 
                                    +  ++akv+r+g e++++++elvpGD+vll agd+vpaD r+v ++  +v+esaLTGEs+pv+k            ++++
  gi|121637881|ref|YP_978104.1| 119 MVHTHAKVVREGHEHTMPSDELVPGDLVLLAAGDKVPADLRLVRQTGlSVNESALTGESTPVHKdevalpegtpvaDRRN 198
                                    56789**********************************************************************99*** PP

                                    EE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHH CS
                   E1-E2_ATPase  69 mvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeal 148
                                     ++sGt v++g+  ++V+atg +telg+i rlv +a+   tpl+ kl  ++k+l++++l +a+l+f + ll++++++e++
  gi|121637881|ref|YP_978104.1| 199 IAYSGTLVTAGHGAGIVVATGAETELGEIHRLVGAAEVVATPLTAKLAWFSKFLTIAILGLAALTFGVGLLRRQDAVETF 278
                                    ******************************************************************************** PP

                                    HHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 149 lralallvaaiPcaLplavplalalgarrlakk 181
                                    + a+al+v+aiP++Lp+av+++la+g++r+ak+
  gi|121637881|ref|YP_978104.1| 279 TAAIALAVGAIPEGLPTAVTITLAIGMARMAKR 311
                                    *******************************96 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                                    TTHHHHHHHHHHHHHS-TTHH.HHHHHHHHHH CS
                   E1-E2_ATPase 144 laeallralallvaaiPcaLp.lavplalalg 174
                                    l+     a+++++ ++P  +  + +++a+alg
  gi|121637881|ref|YP_978104.1| 714 LVILAAIAVGVALPILPTQILwINMTTAIALG 745
                                    33333345556666666654213344444444 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.4   7.3e+03     127     140 ..     251     264 ..     238     287 .. 0.57
   2 !  133.7   9.6   1.9e-42   5.7e-39       2     177 ..     726     892 ..     725     897 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                Cation_ATPase_C 127 llllaillslllqv 140
                                    +l +ail+ ++l++
  gi|121637881|ref|YP_978104.1| 251 FLTIAILGLAALTF 264
                                    33333333333322 PP

  == domain 2  score: 133.7 bits;  conditional E-value: 1.9e-42
                Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgisek 81 
                                    lp+ ++qiLwin+ t + ++l+La+ep+e++im+rpPr++++pl+++ ++rr+l++++l+++++ ++f++ l  +g+  +
  gi|121637881|ref|YP_978104.1| 726 LPILPTQILWINMTTAIALGLMLAFEPKEAGIMTRPPRDPDQPLLTGWLVRRTLLVSTLLVASAWWLFAWEL-DNGAGLH 804
                                    799*****************************************************************5555.5777777 PP

                Cation_ATPase_C  82 enklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplslee 161
                                    e       a+t+a++ +v+++ f+++++rs+++s+++  g+f n++++l++ ++++ q++i+y p +n vf+tap+++  
  gi|121637881|ref|YP_978104.1| 805 E-------ARTAALNLFVVVEAFYLFSCRSLTRSAWR-LGMFANRWIILGVSAQAIAQFAITYLPAMNMVFDTAPIDIGV 876
                                    7.......*****************************.****************************************** PP

                Cation_ATPase_C 162 wlialllalvvllvde 177
                                    w+ ++++a ++++v+ 
  gi|121637881|ref|YP_978104.1| 877 WVRIFAVATAITIVVA 892
                                    ********99999875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   4.7e+03     136     156 ..     144     165 ..      75     186 .. 0.65
   2 !   67.3   8.0   7.5e-22   2.2e-18       3     210 .]     329     655 ..     327     655 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                                    EEEEEESSEHHHHH.HHHHHTT CS
                                    xxxxxxxxxxxxxx.xxxxxxx RF
                      Hydrolase 136 evvlltgdnpetae.raanqlG 156
                                    ++vll  +++ +a+ r+ +q G
  gi|121637881|ref|YP_978104.1| 144 DLVLLAAGDKVPADlRLVRQTG 165
                                    3667777777777778888887 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 7.5e-22
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH..............HHCHHHHHHHHHHHHH.....HHHHHHHHHE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxx.....xxxxxxxxxx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg..............sehpigkalvaaakar.....sgaltgfatf 63 
                                    +++ Dk+GTLt+ ++ v  ++       +++ +tg              +  p   +      a+      ga+++ a++
  gi|121637881|ref|YP_978104.1| 329 VICADKTGTLTENQMTVQSIWTPH----GEIRATGtgyapdvllcdtddA--PVPVNA---NAALrwsllAGACSNDAAL 399
                                    7999********************....5555555557777777655332..222222...2222122345555666665 PP

                                    TTTE..................HHHHTHHHHHHHH.....HCH.HHHHHHHHHHHHHCHHHHHH................ CS
                                    xxxx..................xxxxxxxxxxxxx.....xxx.xxxxxxxxxxxxxxxxxxxx................ RF
                      Hydrolase  64 igrg..................ayaigkpewltal.....dip.pdlgaaigsaqsqgrtvall................ 103
                                       g                  a a  +pe l+        ip +  ++ + ++ ++g ++++l                
  gi|121637881|ref|YP_978104.1| 400 VRDGtrwqivgdptegamlvvaAKAGFNPERLATTlpqvaAIPfSSERQYMATLHRDGTDHVVLakgavermldlcgtem 479
                                    55556666666667777777774444444444444455542221333445555555555555556777777777777777 PP

                                    ..................................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT CS
                                    ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 104 ..................................................qaralavftiadplkvkpeaaeavasLkaa 133
                                                                                      +  + ++ +++dp  ++  aa ava+ ++a
  gi|121637881|ref|YP_978104.1| 480 gadgalrpldratvlratemltsrglrvlatgmgagagtpddfdenvipgSLALTGLQAMSDP--PRAAAASAVAACHSA 557
                                    7777777777777778999999999999999*********999999999988***********..*************** PP

                                    TEEEEEEESSEHHHHHHHHHHTT...............GGGESEEEEHHCES......STTTSHHHHHHHHHHHTSTGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 134 gievvlltgdnpetaeraanqlG...............ddyfdaviasdiet......vakpspegkvaaireLqgkpee 192
                                    gi v ++tgd+  ta ++a ++G               ++  + + +++ e+      +a +spe+k+++++ Lq++++ 
  gi|121637881|ref|YP_978104.1| 558 GIAVKMITGDHAGTATAIATEVGlldntepaagsvltgAELAALSADQYPEAvdtasvFARVSPEQKLRLVQALQARGHV 637
                                    ************************9999777776666533334444444444888999********************** PP

                                    EEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxx RF
                      Hydrolase 193 vamVGDgvnDaaalaaAg 210
                                    vam GDgvnDa+al++A+
  gi|121637881|ref|YP_978104.1| 638 VAMTGDGVNDAPALRQAN 655
                                    ****************96 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.5e-21   4.4e-18       3      90 ..     394     477 ..     392     478 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.5e-21
                  Cation_ATPase   3 cNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApe 82 
                                     N+aa+    +  +++++G++tE A+lv+a+k+g ++e+l    ++v+ ipF+s+r +m+++++  +   ++++ KGA e
  gi|121637881|ref|YP_978104.1| 394 SNDAAL--VRDGTRWQIVGDPTEGAMLVVAAKAGFNPERLATTLPQVAAIPFSSERQYMATLHR--DGTDHVVLAKGAVE 469
                                    467777..88999***************************************************..67************ PP

                  Cation_ATPase  83 iilkrCth 90 
                                    ++l+ C++
  gi|121637881|ref|YP_978104.1| 470 RMLDLCGT 477
                                    ******86 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   3.1e-21   9.4e-18       2      68 ..      12      78 ..      11      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3.1e-21
                Cation_ATPase_N  2 halsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                   h l+++ev   Le+d+ +GL++ eaa+rl+++GpN+l+   + sl++++l+qf +pl+++Llva+ +
  gi|121637881|ref|YP_978104.1| 12 HGLPAHEVVLLLESDPYHGLSDGEAAQRLERFGPNTLAVVTRASLLARILRQFHHPLIYVLLVAGTI 78
                                   7899************************************************************987 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       3.4     1e+04      21      54 ..     548     581 ..     545     593 .. 0.79
   2 !   22.3   0.2   3.2e-08   9.4e-05     195     246 ..     627     679 ..     624     686 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.4
                                    HHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                    Hydrolase_3  21 keaikklkekgikvviATGRslravlpvleelgl 54 
                                    ++a++ ++++gi v   TG +  ++  ++ e+gl
  gi|121637881|ref|YP_978104.1| 548 ASAVAACHSAGIAVKMITGDHAGTATAIATEVGL 581
                                    5788999999999999999998888888888876 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.2e-08
                                    HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHH.HHHSSEEE--G CS
                    Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseev.kkaAdyvtksn 246
                                    l++ l+     v+  GDg ND + L +a++gvAmg +  ev k aAd+v ++ 
  gi|121637881|ref|YP_978104.1| 627 LVQALQARGHVVAMTGDGVNDAPALRQANIGVAMGRGGTEVaKDAADMVLTDD 679
                                    678888888899999********************976555278888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (905 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 5331.91
//
Query:       gi|121637882|ref|YP_978105.1|  [L=258]
Description: hypothetical protein BCG_2015c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-60  204.6   0.1    1.8e-60  204.4   0.1    1.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
      0.063   12.4   0.0        0.1   11.7   0.0    1.4  1  HpcH_HpaI   HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.4   0.1     2e-64   1.8e-60       1     238 [.       3     229 ..       3     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 2e-64
                     PEP_mutase   1 lraLhakgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGy 80 
                                    +++Lh++g p+vlpnawD+ sa +  + gf a++t+S++v+ s G+pDg+++++  ++a+++a+a  +++ ++vD+edGy
  gi|121637882|ref|YP_978105.1|   3 FHDLHHQGVPFVLPNAWDVPSALAYLAEGFTAIGTTSFGVSSSGGHPDGHRATRGANIALAAALAP-LQCYVSVDIEDGY 81 
                                    789*************************************************************99.9************ PP

                     PEP_mutase  81 gespeevaetvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeaie 160
                                    +++p+ +a++v++l     +g+niED+    + ++l+d++ +a+ki a+++  +e  +++nAR+d+++l+++a+ + +i+
  gi|121637882|ref|YP_978105.1|  82 SDEPDAIADYVAQLST---AGINIEDS----SAEKLIDPALAAAKIVAIKQRNPE--VFVNARVDTYWLRQHADTTSTIQ 152
                                    **********999887...679*****....6789**************887666..*********************** PP

                     PEP_mutase 161 RaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvaelaelGvarislgnhllraalaalreaaeei 238
                                    Ra +Y++AGAdgvfvp +++++e+ael++++++p+n +p +g l++a+l elGvar+s+g+ ++ a l a+++aa+++
  gi|121637882|ref|YP_978105.1| 153 RALRYVDAGADGVFVPLANDPDELAELTRNIPCPVNTLPVPG-LTIADLGELGVARVSTGSVPYSAGLYAAAHAARAV 229
                                    ***************************************776.************************99999999876 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05       0.1      61     106 ..     138     183 ..      89     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                                    EEEEE-SSTTHHHHHHHGGHHHTTSSEEEESS--SHHHHHHHHHHT CS
                      HpcH_HpaI  61 evvVRvnsldselikqdlevldlgaqvvlvPkvetaeealevvsal 106
                                    +  +R  + ++ +i++ l+++d+ga++v vP  + ++e++e+ + +
  gi|121637882|ref|YP_978105.1| 138 TYWLRQHADTTSTIQRALRYVDAGADGVFVPLANDPDELAELTRNI 183
                                    5678888889999999999********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1750.94
//
Query:       gi|121637883|ref|YP_978106.1|  [L=440]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-46  156.8  34.6    9.5e-46  156.5  34.6    1.1  1  AA_permease_2   Amino acid permease
    9.3e-35  120.1  35.3    1.2e-34  119.8  34.5    1.5  1  AA_permease     Amino acid permease
    0.00093   18.1   1.1     0.0014   17.5   1.1    1.3  1  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
      0.011   14.5  25.9      0.004   15.9  16.2    3.2  2  Aa_trans        Transmembrane amino acid transporter protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5  34.6   2.1e-49   9.5e-46       1     404 [.      18     399 ..      18     415 .. 0.88

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 2.1e-49
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                    l+ll+a+++ +gs+ig+gif++   +a+++g  l+l + +a+++  ++ ++  a l+++ p sgG yvy++   g ++++
  gi|121637883|ref|YP_978106.1|  18 LGLLDAVVIGLGSMIGAGIFAALapAAYAAGSGLLLGLAVAAVVA-YCNAISSARLAARYPASGGTYVYGRMRLGDFWGY 96 
                                    799******************989888889999999999999998.9*********999********************* PP

                  AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                    l++w ++++  +++       a++ l+ +g  ++ ++ ++  +a+a+++ ++++n+ gi++sa+++  ++ +++ ++l+ 
  gi|121637883|ref|YP_978106.1|  97 LAGWGFVVGKTASC-------AAMALT-VG--FYVWPAQAHAVAVAVVVALTAVNYAGIQKSAWLTRSIVAVVL-VVLTA 165
                                    ********999988.......222222.34..234899999*********************************.58888 PP

                  AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyll 236
                                    ++++++  + ++ +       d  +    +g+l + +  +++f+G+  +a   eev+   +++p+ai+++l+i+l +y l
  gi|121637883|ref|YP_978106.1| 166 VVVAAYGSGAADPAR-----LDIGVDAHVWGMLQAAGLLFFAFAGYARIATLGEEVRDpaRTIPRAIPLALGITLAVYAL 240
                                    888999999999997.....4443444555777777778****************7766599****************** PP

                  AA_permease_2 237 vniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn 316
                                    v++a+++v+++  +a  +    +++  ++ +g  ++  +v+i++a+++lg+++++++g+sr+  a+ard+ lPr++a v+
  gi|121637883|ref|YP_978106.1| 241 VAVAVIAVLGPQRLARAAA---PLSEAMRVAGVNWLIPVVQIGAAVAALGSLLALILGVSRTTLAMARDRHLPRWLAAVH 317
                                    **************97554...79999***************************************************** PP

                  AA_permease_2 317 .kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfl 395
                                     +f+ p+ra  ++  v+ +l+     a +a++      ss+g++++y+++ ++al l  ++ + +r  ++lv++ig+++l
  gi|121637883|ref|YP_978106.1| 318 pRFKVPFRAELVVGAVVAALA-----A-TADIRGAIGFSSFGVLVYYAIANASALTLGLDEGRPRRL-IPLVGLIGCVVL 390
                                    *********999999984432.....2.5789****************************6665554.589********* PP

                  AA_permease_2 396 lfllvalff 404
                                     f+l +  +
  gi|121637883|ref|YP_978106.1| 391 AFALPLSSV 399
                                    **9966554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8  34.5   2.6e-38   1.2e-34       1     360 [.      22     346 ..      22     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 2.6e-38
                    AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                    +++vi lg++iG+g+f +l+ ++ +aG  g+ll++++a vv ++ ++s + +a  +p sgg+y+y +  lg+ +G+  G+
  gi|121637883|ref|YP_978106.1|  22 DAVVIGLGSMIGAGIFAALAPAAYAAGS-GLLLGLAVAAVVAYCNAISSARLAARYPASGGTYVYGRMRLGDFWGYLAGW 100
                                    579************************9.99************************************************* PP

                    AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiil 160
                                         ++++ ++ ++a++ +++f   v  +  a+++++ ++v+l+++n++g+  ++   +  ++++++ ++ + +v + +
  gi|121637883|ref|YP_978106.1| 101 G----FVVGKTASCAAMALTVGFY--VWPAQ-AHAVAVAVVVALTAVNYAGIQKSAW--LTRSIVAVVLVVLTAVVVAAY 171
                                    *....8999999999999999999..66555.789999999***********99987..445555666666666666666 PP

                    AA_permease 161 laggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvv 240
                                     +g++  ++         ++i  +             + +++ ++  ++faf+G+  +a++++Ev+dP+++iP+ai  ++
  gi|121637883|ref|YP_978106.1| 172 GSGAADPAR---------LDIGVDAH-----------VWGMLQAAGLLFFAFAGYARIATLGEEVRDPARTIPRAIPLAL 231
                                    666666666.........44333333...........6669999999********************************* PP

                    AA_permease 241 iritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslak 320
                                     +++ +Y l++++++++++ + l   +       p+  +++ +gv+ l p++ ++  +aal+s+++++   sR+  ++a+
  gi|121637883|ref|YP_978106.1| 232 GITLAVYALVAVAVIAVLGPQRLARAA------APLSEAMRVAGVNWLIPVVQIGAAVAALGSLLALILGVSRTTLAMAR 305
                                    *******************99955554......4999******************************************* PP

                    AA_permease 321 dglaP.kvlkkvskrgvPlraillsmiisllalllaslnla 360
                                    d+++P + ++++ + +vP ra l++ ++++++   a +  a
  gi|121637883|ref|YP_978106.1| 306 DRHLPrWLAAVHPRFKVPFRAELVVGAVVAALAATADIRGA 346
                                    *****888999***********9987777766634443333 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   3.1e-07    0.0014       8     256 ..      24     271 ..      17     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.1e-07
                 Spore_permease   8 fvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektliellkkilg.kwLGsllsilfi 86 
                                    +v+    ++G+gi  +++ +a +a+     ++ll++ ++ ++++     + + +    ++  + + g   LG + + l  
  gi|121637883|ref|YP_978106.1|  24 VVIGLGSMIGAGIFAALAPAAYAAG----SGLLLGLAVAAVVAYCNAISSARLAARYPASGGTYVYGrMRLGDFWGYLAG 99 
                                    5556678999999999998888883....489****************9999999999*999*****556********** PP

                 Spore_permease  87 lyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslar..eflfiivilliilllillfslklaei 164
                                      F++  +     ++  + +++ +    ++ +++++++++ + + Gi++ a     ++++v +++  +++    ++ a++
  gi|121637883|ref|YP_978106.1| 100 WGFVVGKTASCAAMALTVGFYVWPAQAHAVAVAVVVALTA-VNYAGIQKSAWltRSIVAVVLVVLTAVVVAAYGSGAADP 178
                                    ***********************99888777777776665.456777775542224444455555555666677889999 PP

                 Spore_permease 165 knlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkv.kkaallgvlistllyllttlivilvlsveqlkkat 243
                                      l+  ++  +  +l+++    ++f g   +  l + ++d+ ++  +a+ l+++i+  +y+l+ + vi+vl+ + l +a 
  gi|121637883|ref|YP_978106.1| 179 ARLDIGVDAHVWGMLQAAGLLFFAFAGYARIATLGEEVRDPARTiPRAIPLALGITLAVYALVAVAVIAVLGPQRLARAA 258
                                    9999888888999**************9999999999999876527999******************************9 PP

                 Spore_permease 244 wptlsllkvievp 256
                                     p+ + ++v  v+
  gi|121637883|ref|YP_978106.1| 259 APLSEAMRVAGVN 271
                                    9999999887665 PP

>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9  16.2   8.8e-07     0.004       5     283 ..      20     285 ..      16     293 .. 0.71
   2 ?   -0.2   0.7      0.07   3.1e+02     346     364 ..     377     395 ..     374     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.8e-07
                       Aa_trans   5 alsavlnlikaivGaGvLa.L.PyA.fkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGpk 81 
                                     l+av+  + +++GaG++a L P A  +  Gl++Gl++ ++va+++ +++  L+  +     + + + Yg +    lG  
  gi|121637883|ref|YP_978106.1|  20 LLDAVVIGLGSMIGAGIFAaLaPAAyAAGSGLLLGLAVAAVVAYCNAISSARLAARYPA---SGGTYVYGRM---RLGDF 93 
                                    57788899999******974435554456699999999999999999999999988874...4588888888...88998 PP

                       Aa_trans  82 gkliidlailvqlfGvgvsyliligdllpaifesffdtlllsnvyfilisaliiipLslipnlskLsylSllalvsslyy 161
                                    + ++ +  ++v     + +  +++g    ++++      + + v + +++al  +  + i++ + L+  S++a+v++   
  gi|121637883|ref|YP_978106.1|  94 WGYLAGWGFVVGKTASCAAMALTVGF---YVWPA-----QAHAVAVAVVVALTAVNYAGIQKSAWLT-RSIVAVVLV--- 161
                                    88888888888888888888777774...44554.....2234455555555555555555544443.356666666... PP

                       Aa_trans 162 ivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtkvlllsiilatvl 241
                                     v++++vva ++++ +     + +  + +++g+++a+g + FAf+g a + ++ +e++dp+   ++ +++ l+  ++ ++
  gi|121637883|ref|YP_978106.1| 162 -VLTAVVVAAYGSGAADPARLD-IGVDAHVWGMLQAAGLLFFAFAGYARIATLGEEVRDPAR--TIPRAIPLALGITLAV 237
                                    .455666666666655554444.4468899********************************..689************* PP

                       Aa_trans 242 yilvGlvGYltFGnevkgnillnlpkss......ilivivnlllvlhl 283
                                    y+lv++++ ++ G++    +   l++        +li +v++  ++++
  gi|121637883|ref|YP_978106.1| 238 YALVAVAVIAVLGPQRLARAAAPLSEAMrvagvnWLIPVVQIGAAVAA 285
                                    ******998888877555444444333333344456666666555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.07
                       Aa_trans 346 kvlslvGatsstplsfilP 364
                                    ++++lvG ++++ l+f lP
  gi|121637883|ref|YP_978106.1| 377 RLIPLVGLIGCVVLAFALP 395
                                    5899**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 2816.87
//
Query:       gi|121637884|ref|YP_978107.1|  [L=537]
Description: hypothetical protein BCG_2017 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-06   28.4   0.0    1.9e-05   24.8   0.0    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0001   21.7   0.0        0.4    9.9   0.0    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0039   16.5   0.0      0.016   14.4   0.0    1.8  2  Thi4           Thi4 family
     0.0074   16.3   0.0       0.71    9.9   0.0    2.3  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.033   14.2   0.1        2.1    8.3   0.0    2.9  3  NAD_binding_9  FAD-NAD(P)-binding
      0.088   13.4   0.0        6.9    7.3   0.0    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.13   12.5   0.0          5    7.4   0.1    2.4  2  TrkA_N         TrkA-N domain
       0.16   11.2   0.3       0.33   10.2   0.1    1.5  2  FAD_binding_3  FAD binding domain
        0.2   11.3   0.3       0.39   10.4   0.1    1.5  2  ApbA           Ketopantoate reductase PanE/ApbA
       0.21   10.3   0.1       0.36    9.5   0.1    1.3  1  HI0933_like    HI0933-like protein
       0.23   10.6   0.0       0.53    9.4   0.0    1.5  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.24   10.6   0.0         15    4.7   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.3e-08   1.9e-05       1      38 [.      79     117 ..      79     134 .. 0.88
   2 ?    0.7   0.0      0.41   6.1e+02       1      17 [.     251     268 ..     251     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.3e-08
                                    EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSSSGGG-EE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLaka.gfdvlllekrdrlGGraasy 38 
                                    ++GaG+ G+++  +L  + g++v+ ++++ ++GG+++++
  gi|121637884|ref|YP_978107.1|  79 VIGAGAMGMAFTDTLITEsGARVVMIDRACQPGGHWTTA 117
                                    8***********8876555*****************996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.41
                                    EE--SHHHH.HHHHHHHC CS
                  NAD_binding_8   1 IvGaGlsGl.vaAylLak 17 
                                    +vGaG +G+ v+ +lL++
  gi|121637884|ref|YP_978107.1| 251 VVGAGKTGMdVCLWLLRN 268
                                    8*******9777788876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00027       0.4       2      33 ..      76     106 ..      70     128 .. 0.78
   2 !    9.6   0.0   0.00032      0.49     142     166 ..     241     270 ..     198     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                    SEEEE--SHHHHHHHHHHHH.HTS-EEEEETTH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq.agakvtlveleg 33 
                                    d++viG+G+ G+a+  tl + +ga+v++++  +
  gi|121637884|ref|YP_978107.1|  76 DYLVIGAGAMGMAFTDTLITeSGARVVMID--R 106
                                    788999999999999999887799999994..2 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00032
                                    T.....SEEEEES-SHHHHHHHHHHHHHT- CS
                                    x.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 142 p.....krivvvGgGyiGvElAaalaklgk 166
                                    p     +r vvvG+G +G++++  l +  +
  gi|121637884|ref|YP_978107.1| 241 PklgtrDRYVVVGAGKTGMDVCLWLLRNDV 270
                                    234445899*************99865544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.016      14      59 ..      71     115 ..      66     123 .. 0.88
   2 ?   -1.3   0.0      0.72   1.1e+03      21      38 ..     250     267 ..     243     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                    HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                           Thi4  14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59 
                                    k +e+D +++GaG+ G++ + +l ++ + +v++++r   pGG  w 
  gi|121637884|ref|YP_978107.1|  71 KTIETDYLVIGAGAMGMAFTDTLITESGARVVMIDRACQPGG-HWT 115
                                    5689******************99999*********999976.565 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.72
                                    EEE--SHHHHHHHHHHHH CS
                           Thi4  21 vivGaGssGLtaayylak 38 
                                    v+vGaG +G+     l +
  gi|121637884|ref|YP_978107.1| 250 VVVGAGKTGMDVCLWLLR 267
                                    89*******987766655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00048      0.71      14      45 ..      76     107 ..      68     115 .. 0.87
   2 ?    3.9   0.0     0.035        53      12      34 ..     246     268 ..     235     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                                    EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRt 45 
                                      l+iGaG m+   +  L++++  +vv + R 
  gi|121637884|ref|YP_978107.1|  76 DYLVIGAGAMGMAFTDTLITESGARVVMIDRA 107
                                    679****************9988889999886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                                    T-EEEEES-SHHHHHHHHHHHCC CS
                   Shikimate_DH  12 ekkvlliGaGemaelvakhLlak 34 
                                    + + +++GaG+++  v+  Ll++
  gi|121637884|ref|YP_978107.1| 246 RDRYVVVGAGKTGMDVCLWLLRN 268
                                    46789********9999888766 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0014       2.1       2      45 ..      79     117 ..      78     188 .. 0.83
   2 ?    2.1   0.0      0.11   1.7e+02       1      20 [.     250     269 ..     250     279 .. 0.87
   3 ?   -0.8   0.0      0.88   1.3e+03      59      78 ..     460     479 ..     454     516 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtd 45 
                                    ++GaG+ G+a+++ L+ +    s  ++ ++d+  +pg  + w t+
  gi|121637884|ref|YP_978107.1|  79 VIGAGAMGMAFTDTLITE----SGARVVMIDRaCQPG--GHWTTA 117
                                    8*****************....599*******44555..667665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    ++vGaG +G+ v+  Ll++ 
  gi|121637884|ref|YP_978107.1| 250 VVVGAGKTGMDVCLWLLRND 269
                                    69**************9985 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.88
                  NAD_binding_9  59 mslftddpptfaeWlrerga 78 
                                    m l++ d  +f++Wl++ + 
  gi|121637884|ref|YP_978107.1| 460 MRLMHSDLGNFQRWLNDPDL 479
                                    56666667777777776553 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0046       6.9       3      34 ..      78     110 ..      76     115 .. 0.90
   2 ?    3.6   0.0     0.067     1e+02       2      15 ..     249     262 ..     248     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                                    EEECSSHHHHHHHHHH.HHTTSEEEEEESSSSS CS
                      Pyr_redox   3 vvvGgGyiglElAgal.aelgkkVtvversdkl 34 
                                    +v+G+G  g+ +  +l +e g++V +++r+ ++
  gi|121637884|ref|YP_978107.1|  78 LVIGAGAMGMAFTDTLiTESGARVVMIDRACQP 110
                                    7***************999*********98665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.067
                                    EEEECSSHHHHHHH CS
                      Pyr_redox   2 vvvvGgGyiglElA 15 
                                     vvvG+G +g+++ 
  gi|121637884|ref|YP_978107.1| 249 YVVVGAGKTGMDVC 262
                                    69*********985 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0033         5       1      29 [.      77     106 ..      77     109 .. 0.89
   2 ?    2.6   0.0      0.11   1.6e+02       1      19 [.     249     267 ..     249     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0033
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                    +++iG+G +G++ +++L + +g +vv id+
  gi|121637884|ref|YP_978107.1|  77 YLVIGAGAMGMAFTDTLITeSGARVVMIDR 106
                                    68****************966677****97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                    EEEES-SHHHHHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse 19 
                                    ++++G+G++G+ ++  L +
  gi|121637884|ref|YP_978107.1| 249 YVVVGAGKTGMDVCLWLLR 267
                                    79*********99977776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00022      0.33       1      33 [.      74     107 ..      74     112 .. 0.86
   2 ?   -3.1   0.0       2.4   3.6e+03       5      20 ..     250     265 ..     250     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                    EEEEEEE--SHHHHHHHHHH.HHTTHHEEEEESS CS
                  FAD_binding_3   1 etdVlIVGaGpaGlmlallL.seaGvrvvlvekr 33 
                                    etd l++GaG  G+  +  L +e G rvv++++ 
  gi|121637884|ref|YP_978107.1|  74 ETDYLVIGAGAMGMAFTDTLiTESGARVVMIDRA 107
                                    6899**********9886652789********96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                    EEE--SHHHHHHHHHH CS
                  FAD_binding_3   5 lIVGaGpaGlmlallL 20 
                                    ++VGaG +G+   l L
  gi|121637884|ref|YP_978107.1| 250 VVVGAGKTGMDVCLWL 265
                                    59*******9766665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00026      0.39       2      30 ..      78     107 ..      77     111 .. 0.90
   2 ?   -3.6   0.0       5.3   7.9e+03       2      19 ..     250     267 ..     249     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                    EEES-SHHHHHHHHHHHH.HTHCEEEE-SC CS
                           ApbA   2 ailGaGaiGsllaakLak.agadvtlilrs 30 
                                    +++GaGa+G  +  +L    ga v++i+r 
  gi|121637884|ref|YP_978107.1|  78 LVIGAGAMGMAFTDTLITeSGARVVMIDRA 107
                                    79**************655********995 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                                    EEES-SHHHHHHHHHHHH CS
                           ApbA   2 ailGaGaiGsllaakLak 19 
                                    +++GaG  G  ++  L +
  gi|121637884|ref|YP_978107.1| 250 VVVGAGKTGMDVCLWLLR 267
                                    799999999888777765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00024      0.36       2      36 ..      76     111 ..      75     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                                    SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS- CS
                    HI0933_like   2 dviviGgGaAGlmaAisa.akrgkrVlllekakklg 36 
                                    d +viG+Ga G+  + ++  + g+rV+++++a ++g
  gi|121637884|ref|YP_978107.1|  76 DYLVIGAGAMGMAFTDTLiTESGARVVMIDRACQPG 111
                                    679*********88887779***********98887 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.0       5.2   7.8e+03       5      35 ..      77     106 ..      75     114 .. 0.59
   2 ?    9.4   0.0   0.00036      0.53     188     227 ..     243     283 ..     233     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 5.2
                    K_oxygenase   5 ligiGiGpsnLsLailleevkkelkalfler 35 
                                       iG+G++ +++  +l   +   +++ ++r
  gi|121637884|ref|YP_978107.1|  77 YLVIGAGAMGMAFTDTLITES-GARVVMIDR 106
                                    556666666666665555555.555555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00036
                    K_oxygenase 188 llakkriaVvGsGqSaaeifedllrr.qkkvelklvtrsea 227
                                    l +++r +VvG+G+++ +++  llr+     +l++++ +++
  gi|121637884|ref|YP_978107.1| 243 LGTRDRYVVVGAGKTGMDVCLWLLRNdVCPDKLTWIMPRDS 283
                                    6678899******************955579*****98865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.021        32       1      31 [.      78     108 ..      73     122 .. 0.77
   2 ?    4.7   0.0      0.01        15     163     188 ..     245     270 ..     198     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.021
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgn 31 
                                    ++iGaG+ G+a+  +l      +++ +++++
  gi|121637884|ref|YP_978107.1|  78 LVIGAGAMGMAFTDTLITESGARVVMIDRAC 108
                                    5899999999998776555555788888874 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                    Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkga 188
                                    + +++vV+G++ +++D+ l l r++ 
  gi|121637884|ref|YP_978107.1| 245 TRDRYVVVGAGKTGMDVCLWLLRNDV 270
                                    5789***************9999863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3506.48
//
Query:       gi|121637885|ref|YP_978108.1|  [L=250]
Description: hypothetical protein BCG_2018 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-36  125.6   0.0    2.3e-36  125.4   0.0    1.0  1  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   1.3e-40   2.3e-36       1     219 [.      18     227 ..      18     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 1.3e-40
                    Acyl-ACP_TE   1 gkvfkekyevrvyevdvngtakleallnllqdvaanqveelGlsddkflkklnlvWvvakyeieierlpefgdkveietw 80 
                                    g+v+++ + ++  ++d +++++l+ +++++q+v+a+++  +       l++ ++ W+v ++ i++  ++e+ + ++ ++w
  gi|121637885|ref|YP_978108.1|  18 GYVYTTGWRLATTDIDEHQQLRLDGVARYIQEVGAEHLADAQ------LAEVHPHWIVLRTVIDVINPIELPSDITFHRW 91 
                                    689**********************************98777......9******************************* PP

                    Acyl-ACP_TE  81 aesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilaey.eeeseeklkkkpktkvleakeeseekel 159
                                    +++ + ++c +++++++ +g   ie + +++ ++++t  +sr+td+ +a + +++++++lk+ p      +  + +e+ +
  gi|121637885|ref|YP_978108.1|  92 CAALSTRWCSMRVQLQGSAG-GHIETEGFWICVNKDTLTPSRLTDDCIARFgSTTENHRLKWRPW--LTGPNIDGTETPF 168
                                    *****************666.47899*************************8889999******9..78888899***** PP

                    Acyl-ACP_TE 160 kvrysDlDlnqHvNNvkYlewilevlpleilkkhelkkitlkYekevqlgdkveilteia 219
                                    + r++D+D ++HvNN+ Y+  + e l  +i +   + ++ l+Y+ +++ g+ ++i +e++
  gi|121637885|ref|YP_978108.1| 169 PLRRTDIDPFEHVNNTIYWHGVHEILC-QIPTLTAPYRAVLEYRSPIKSGEPLTIRYEQH 227
                                    ***********************9885.799999*******************9887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1718.43
//
Query:       gi|121637886|ref|YP_978109.1|  [L=260]
Description: 20-beta-hydroxysteroid dehydrogenase fabG3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-62  211.4   2.2    1.6e-62  211.1   2.2    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    6.2e-56  189.0   0.7    7.7e-56  188.6   0.7    1.1  1  adh_short     short chain dehydrogenase
    8.7e-09   35.5   0.8    1.3e-08   35.0   0.8    1.2  1  KR            KR domain
  ------ inclusion threshold ------
       0.06   12.8   0.0       0.12   11.8   0.0    1.5  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.1   2.2   3.7e-66   1.6e-62       1     232 [.      14     237 ..      14     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.1 bits;  conditional E-value: 3.7e-66
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                    G a+g+G+  ++a+ +eGa+vv+ d+ +e+ k+ ++ela+   a+++++DVt+++q++a+v+++v  fg+l++lvnnagi
  gi|121637886|ref|YP_978109.1|  14 GGARGMGASHVRAMVAEGAKVVFGDILDEEgKAVAAELAD--AARYVHLDVTQPAQWTAAVDTAVTAFGGLHVLVNNAGI 91 
                                    669**************************96666666666..4678********************************** PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                     +   g +++    e++r+ldvnl+++fl ++a+++ mke   gsi+n+ss+ +  ++   + y+a+K a+ +lt++ A 
  gi|121637886|ref|YP_978109.1|  92 LNI--GTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAgrGSIINISSIEGLAGTVACHGYTATKFAVRGLTKSTAL 169
                                    ***..*******************************7777669************************************* PP

                                    HHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    elgp giRvN+++pg++kT++++ ++  +++      ++ lgr+++p ev +++++Lasde+sy tG+++vvDgG
  gi|121637886|ref|YP_978109.1| 170 ELGPSGIRVNSIHPGLVKTPMTDWVP--EDI-----FQTALGRAAEPVEVSNLVVYLASDESSYSTGAEFVVDGG 237
                                    ************************99..344.....4578*********************************** PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.7   1.7e-59   7.7e-56       1     189 [.       8     193 ..       8     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 1.7e-59
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv+lv G+++G+G   ++++++eGakvv+ d+ +e+ ++va+el ++   a ++++Dvt+ +++ a+v++av  +g+l+v
  gi|121637886|ref|YP_978109.1|   8 KVALVSGGARGMGASHVRAMVAEGAKVVFGDILDEEGKAVAAELADA---ARYVHLDVTQPAQWTAAVDTAVTAFGGLHV 84 
                                    89*******************************************97...****************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    LvnNAGi + g+++++  +ew+r+++vNltgvfl +rav++ m+++ +G+I+n+sS+ g+ +      Y+A+K+av+glt
  gi|121637886|ref|YP_978109.1|  85 LVNNAGILNIGTIEDYALTEWQRILDVNLTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGLT 164
                                    ******************************************************************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmake 189
                                    +s a el p+girvn+++PGlv+T+m+  
  gi|121637886|ref|YP_978109.1| 165 KSTALELGPSGIRVNSIHPGLVKTPMTDW 193
                                    **************************975 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.8   2.9e-12   1.3e-08       3     153 ..      10     157 ..       8     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.9e-12
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     l+ GG+ g+G + +r ++++ga+  v+++     de+ ka  ael++     ++v++Dv+++++ +a+++++ + ++ +
  gi|121637886|ref|YP_978109.1|  10 ALVSGGARGMGASHVRAMVAEGAK--VVFGDI--LDEEGKAVAAELAD---AARYVHLDVTQPAQWTAAVDTAVTAFGGL 82 
                                    59*********************9..667887..78888989999998...789999*********************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHH....HHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGa....wnLhelledesldffvlfSSiagllgsagqanYaaaN 153
                                    +  ++ Ag+l+ +++e+    +++++l   ++G+    + + + +++     ++ +SSi gl g+     Y+a+ 
  gi|121637886|ref|YP_978109.1|  83 HVLVNNAGILNIGTIEDYALTEWQRILDVNLTGVflgiRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATK 157
                                    *****************************9998621114455555557778999999*99999999999999875 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.12      25      75 ..     113     163 ..      97     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                                    --EETTTHHHHHHHHHHTT-EEEEEGGGEET--SSHHHHHHHHH.TT-SEE CS
                   G3P_antiterm  25 legdilnlkeiveklkkagkkvfvhiDlieGlskdeaaveflkkeikvdGi 75 
                                    l+g  l ++ +v+ +k+ag+  +++i +ieGl+   a+  + ++++ v G+
  gi|121637886|ref|YP_978109.1| 113 LTGVFLGIRAVVKPMKEAGRGSIINISSIEGLAGTVACHGYTATKFAVRGL 163
                                    556677899********************************9999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1378.72
//
Query:       gi|121637887|ref|YP_978110.1|  [L=285]
Description: hypothetical protein BCG_2020c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-10   40.2   0.1    7.2e-10   39.4   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    1.9e-08   34.3   0.0    3.2e-08   33.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.6e-07   31.9   0.1    3.3e-07   30.9   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    8.5e-05   23.2   0.0    0.00018   22.2   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.8   0.3       0.03   14.4   0.0    1.9  2  DUF2059          Uncharacterized protein conserved in bacteri
       0.11   11.8   0.0       0.26   10.6   0.0    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   2.4e-13   7.2e-10       1      96 []     102     187 ..     102     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.4e-13
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    L++G+GtGr+a  l       +g+D+s  +l  a+++++          a  e +pf +  f +v++ ++l++v dp+++
  gi|121637887|ref|YP_978110.1| 102 LEIGVGTGRFADLLG----VRFGLDPSRDALMFARRRGVLV------ANAVGEAVPFVSRHFGAVLMAFTLCFVTDPAAI 171
                                    89*************....5579********9999998876......57888889************************* PP

                                    HHHHHHHEEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                    ++e +R+L  gG lvi
  gi|121637887|ref|YP_978110.1| 172 FRETRRLLADGGGLVI 187
                                    ************9886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-11   3.2e-08      27     164 ..     102     235 ..      83     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                Methyltransf_23  27 LdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrq 104
                                    L+iG GtG+++++l  +     g D+s+ a   a+  +   a+ + +     ++ +++f  + + ++l+ v dp++ +r 
  gi|121637887|ref|YP_978110.1| 102 LEIGVGTGRFADLLGVR----FGLDPSRDALMFARrrGVLVANAVGE---AVPFVSRHFGAVLMAFTLCFVTDPAAIFRE 174
                                    9***********99666....79999998777776553333333333...4556779*********************** PP

                Methyltransf_23 105 iatllkpgGylllseplaslkedrllldwlylvpag.rhisffsarslkelleeaGlevve 164
                                     ++ll++gG l++    +  +++ l+   ++  + g r  +f++a +l++ll ++G++v++
  gi|121637887|ref|YP_978110.1| 175 TRRLLADGGGLVIGFLPRGTPWADLYALRAARGQPGyRDARFYTAAELEQLLADSGFRVIA 235
                                    ********99888887566566666554444444445666******************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   1.1e-10   3.3e-07       2      97 .]     102     183 ..     102     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.1e-10
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    L++G GtGr++  l  r+      g+D+s ++l  ar+r       v + ++  e++pf +++f +v+++++l++++d  
  gi|121637887|ref|YP_978110.1| 102 LEIGVGTGRFADLLGVRF------GLDPSRDALMFARRRG------VLVANAVGEAVPFVSRHFGAVLMAFTLCFVTD-- 167
                                    89**********999887......9**************9......67777777****************99999985.. PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                     +++++e +r+L +gG
  gi|121637887|ref|YP_978110.1| 168 PAAIFRETRRLLADGG 183
                                    569************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.2e-08   0.00018       1      99 []     102     185 ..     102     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.2e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    LeiG GtG++++ l  +       g+D+s++a+      +a+r++  ++n   ea    ++    +f +v+++++l+ + 
  gi|121637887|ref|YP_978110.1| 102 LEIGVGTGRFADLLGVR------FGLDPSRDAL-----MFARRRGVLVANAVGEAVPFVSR----HFGAVLMAFTLCFVT 166
                                    8*************999......9*********.....66666666666666666665555....9************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d+++++++ r+lL++gG l
  gi|121637887|ref|YP_978110.1| 167 DPAAIFRETRRLLADGGGL 185
                                    ****************965 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05      0.03      25      51 ..      72      99 ..      57     103 .. 0.91
   2 ?   -1.9   0.1       1.2   3.5e+03      15      25 ..     217     227 ..     214     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                   HHHHSHHHHHHHHHHHHHHHHHHH.HHH CS
                        DUF2059 25 aFYkSPlGkkllekepaataesmq.aaq 51
                                   a+Y SP+G+ +l+ e aa + + +  aq
  gi|121637887|ref|YP_978110.1| 72 AWYDSPTGRPILATEVAALRPLIEvFAQ 99
                                   8*******************99997777 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                    S-HHHHHHHHH CS
                        DUF2059  15 fteaelkaila 25 
                                    +t ael+++la
  gi|121637887|ref|YP_978110.1| 217 YTAAELEQLLA 227
                                    89999999986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.6e-05      0.26     104     151 ..     140     187 ..     125     192 .. 0.90
   2 ?   -2.8   0.0       1.1   3.2e+03     198     216 ..     216     234 ..     214     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.6e-05
                                    E--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 104 qanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                    +a +e++pf    f  v ++f l  vtD    ++e +r l  GG lv+
  gi|121637887|ref|YP_978110.1| 140 NAVGEAVPFVSRHFGAVLMAFTLCFVTDPAAIFRETRRLLADGGGLVI 187
                                    45689***************************************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                    S--HHHHHHHHHHTTEEEE CS
                Ubie_methyltran 198 fPdqetlkeliedaGfksv 216
                                    f  + +l++l+ d+Gf+ +
  gi|121637887|ref|YP_978110.1| 216 FYTAAELEQLLADSGFRVI 234
                                    5667899********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1538.65
//
Query:       gi|121637888|ref|YP_978111.1|  [L=498]
Description: hypothetical protein BCG_2021c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-15   57.5   0.6    4.9e-15   55.9   0.1    2.0  2  AAA_33          AAA domain
    4.7e-05   22.8   0.9    8.7e-05   21.9   0.0    1.8  2  Zeta_toxin      Zeta toxin
    0.00017   22.2   0.0    0.00048   20.7   0.0    1.7  1  AAA_18          AAA domain
     0.0012   19.3   0.1     0.0033   17.8   0.0    1.8  2  AAA             ATPase family associated with various cellula
     0.0017   18.8   0.2      0.017   15.5   0.0    2.6  2  AAA_17          AAA domain
      0.002   18.5   0.7     0.0046   17.3   0.2    1.9  2  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.2   0.5      0.032   13.9   0.1    2.0  2  AAA_30          AAA domain
      0.015   15.4   0.0      0.039   14.0   0.0    1.6  1  ADK             Adenylate kinase
      0.056   13.2   0.0       0.14   11.8   0.0    1.6  1  Cytidylate_kin  Cytidylate kinase
      0.072   13.1   0.0       0.24   11.4   0.0    1.8  2  AAA_5           AAA domain (dynein-related subfamily)
      0.097   12.9   0.9       0.66   10.3   0.1    2.3  2  AAA_22          AAA domain
       0.15   11.3   0.6       0.37   10.0   0.0    1.9  2  ATP_bind_2      P-loop ATPase protein family
       0.27   11.0   0.8       0.41   10.4   0.1    1.7  2  RuvB_N          Holliday junction DNA helicase RuvB P-loop do


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.2   4.5e+03      67      85 ..      39      58 ..      14      74 .. 0.50
   2 !   55.9   0.1   3.5e-18   4.9e-15       2     130 ..     325     460 ..     324     470 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.2
                         AAA_33 67 lsagrnvildat.nlsrrer 85
                                    +a+++v++d   ++++++r
  gi|121637888|ref|YP_978111.1| 39 FKAKKPVVTDFCdFRTAEQR 58
                                   24444444444422222333 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 3.5e-18
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg....tdqqskt........dytrvldrlyqilnelarkalsa 69 
                                     l+ G pG+GKstla+++++  ga+++s+d++rrrl+     t+    +        ++      +yq   + ar  l +
  gi|121637888|ref|YP_978111.1| 325 ALVGGNPGTGKSTLARGVAELVGAQVISTDDVRRRLRDcgviTG----EpgvldsglYSRANVVAVYQEALRKARLLLGS 400
                                    57889**************9999***************666633....33333444255545566888888********* PP

                         AAA_33  70 grnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpe 130
                                    g +vild t+ +++ ra  ++la + ++++    +++  +++++R+ +Ra  g++++ ++ 
  gi|121637888|ref|YP_978111.1| 401 GHSVILDGTWGDPQMRACARRLAADTHSAIVEFRCSATVDVMADRIVARAG-GNSDATAEI 460
                                    ************************9998888888999999**********9.555544433 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       1.2   1.6e+03     136     173 ..     122     160 ..     119     177 .. 0.68
   2 !   21.9   0.0   6.3e-08   8.7e-05      18     120 ..     324     425 ..     311     468 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                     Zeta_toxin 136 SrlgvldRyeeevaegRlvpkeehdeaf.eglresveal 173
                                    ++ +vl+R+ ++++++R ++ +    a+ ++  e++++l
  gi|121637888|ref|YP_978111.1| 122 AIAEVLARFHQRAQRNRCIDTQGEVGAVaRRWHENLAEL 160
                                    567889999999888899988766544414555555554 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 6.3e-08
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilka.dpkkaseltqkdaselvekllqea...ie 93 
                                    l l+gG pG GKs+la+ +++ +    ++ ++++Dd+R++ ++   i  +  + +   + ++ +  + +++l +a   + 
  gi|121637888|ref|YP_978111.1| 324 LALVGGNPGTGKSTLARGVAELV----GAQVISTDDVRRRLRDCGVITGEpGVLDSGLYSRANVVAVYQEALRKArllLG 399
                                    789*****************998....67789**************99998999999999999999*9*99999844458 PP

                     Zeta_toxin  94 ngyniivegtlrspdvvkklaealkka 120
                                     g ++i++gt  +p+  +  a++l+++
  gi|121637888|ref|YP_978111.1| 400 SGHSVILDGTWGDPQMRA-CARRLAAD 425
                                    9************99766.66666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.4e-07   0.00048       2     113 ..     326     449 ..     326     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-07
                         AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvak.englllevdpe..aldeskrldedkldklldaleenssaleegknlv 78 
                                    l+ G pG+GK+tla+ ++++ g  v+++d ++   + +   + e   ld+ +  + +++++ ++al++++  l++g++++
  gi|121637888|ref|YP_978111.1| 326 LVGGNPGTGKSTLARGVAELVGAQVISTDDVRrRLRDCGVITGEpgVLDSGLYSRANVVAVYQEALRKARLLLGSGHSVI 405
                                    589****************9866333333333033333333333679**********************99********* PP

                         AAA_18  79 idghlaeleseaakdikk.......vvLtasp..eelleRlekR 113
                                    +dg  +++   a  ++         v  ++s   +++++R+ +R
  gi|121637888|ref|YP_978111.1| 406 LDGTWGDPQMRACARRLAadthsaiVEFRCSAtvDVMADRIVAR 449
                                    ***99887644443333344666665555555556666666666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.4e-06    0.0033       2      30 ..     326     354 ..     325     393 .. 0.92
   2 ?   -3.0   0.0       6.7   9.3e+03      14      36 ..     418     440 ..     417     462 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                            AAA   2 llyGppGtGKTllakavakelgvefleis 30 
                                    l+ G+pGtGK++la+ va+ +g+++++++
  gi|121637888|ref|YP_978111.1| 326 LVGGNPGTGKSTLARGVAELVGAQVISTD 354
                                    778******************99999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.7
                                    HHHHHHHHHTHEEEEEETTTCSS CS
                            AAA  14 lakavakelgvefleisgsells 36 
                                    +a+ +a ++++ ++e+ +s  ++
  gi|121637888|ref|YP_978111.1| 418 CARRLAADTHSAIVEFRCSATVD 440
                                    68889999999999999998873 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.89   1.2e+03      70      89 ..     195     214 ..     154     238 .. 0.75
   2 !   15.5   0.0   1.3e-05     0.017       2     126 ..     329     452 ..     328     460 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.89
                                    HSSEEEEEE-SEEEETTEEE CS
                         AAA_17  70 kkkgvlvdghprikeqagfl 89 
                                     k+g +vdgh+ + +++ fl
  gi|121637888|ref|YP_978111.1| 195 IKEGCIVDGHADLLADDIFL 214
                                    45678888888766655554 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                                    E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH....HSSEEEEE CS
                         AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea....kkkgvlvd 77 
                                    G PG GK+t+++ ++e +g +++s+ d+ r   +++g ++ +  + +  l  +  + +  +e++++++    + + v++d
  gi|121637888|ref|YP_978111.1| 329 GNPGTGKSTLARGVAELVGAQVISTDDVRRRL-RDCGVITGEPGVLDSGLYSRANVVAVYQEALRKARlllgSGHSVILD 407
                                    88**********************98876665.67776444433444444455555555555555544444455668888 PP

                                    E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HH.HHHHHHHHHTTST CS
                         AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpe.eilerrlkdrtrg 126
                                    g     +++    +l     ++   +ai+ + +++  ++++ r+  r  g
  gi|121637888|ref|YP_978111.1| 408 GTWGDPQMRACARRLA----ADT-HSAIVEFRCSATvDVMADRIVARAGG 452
                                    8776433333333333....332.45566666665544555554444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.4     1e+04     124     130 ..     128     134 ..     100     168 .. 0.57
   2 !   17.3   0.2   3.4e-06    0.0046      22      52 ..     319     362 ..     304     433 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.4
                         AAA_16 124 krllall 130
                                    +r+ +++
  gi|121637888|ref|YP_978111.1| 128 ARFHQRA 134
                                    2222222 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.4e-06
                         AAA_16  22 grp.elvllsGesGvGKsslvrellralekd............g 52 
                                    + + +l l+ G++G+GKs+l+r +++ + ++            +
  gi|121637888|ref|YP_978111.1| 319 HATvRLALVGGNPGTGKSTLARGVAELVGAQvistddvrrrlrD 362
                                    4445999******************7666664444444444432 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.6   6.3e+03     114     125 ..      26      37 ..      21      38 .. 0.75
   2 ?   13.9   0.1   2.3e-05     0.032      10      45 ..     314     349 ..     311     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                         AAA_30 114 kagakvilvGDe 125
                                    ++ a v+l+GD+
  gi|121637888|ref|YP_978111.1|  26 THTAVVVLAGDR 37 
                                    356999****97 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.3e-05
                         AAA_30  10 vealltsgdrvavltGpAGtGKttalkalreaweaa 45 
                                     ++l + + r+a++ G +GtGK+t+ ++++e++ a+
  gi|121637888|ref|YP_978111.1| 314 TQHLQHATVRLALVGGNPGTGKSTLARGVAELVGAQ 349
                                    56777778889*******************998765 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-05     0.039       3     129 ..     329     461 ..     327     476 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                    ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCH....GTTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                            ADK   3 GaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeeleke....dkkkgfl 78 
                                    G Pg+GK t a+ +++  g++ +st d+ R     g  +G+    v+d g   +   vv++ +e+l+k        +  +
  gi|121637888|ref|YP_978111.1| 329 GNPGTGKSTLARGVAELVGAQVISTDDVRRRLRDCGVITGEP--GVLDSGL-YSRANVVAVYQEALRKArlllGSGHSVI 405
                                    99**************************99999999999985..6888885.5666667889999998744444678899 PP

                                    EESB...-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT..GSHHHHH CS
                                    xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                            ADK  79 lDGf...PRtveqaealeelleeekvkldlvleldvpeevlveRltg..Dneetvk 129
                                    lDG    P   + a++l +  ++++v+  +  ++dv  + +v R  g  D + +++
  gi|121637888|ref|YP_978111.1| 406 LDGTwgdPQMRACARRLAADTHSAIVEFRCSATVDVMADRIVARAGGnsDATAEIA 461
                                    99853336666666666665555555555555555555555555444665555555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.14       5      35 ..     329     359 ..     325     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                    -STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                 Cytidylate_kin   5 GPagsGKssvaralaeklglkyldtgalYRa 35 
                                    G  g+GKs++ar +ae +g+++++t  + R 
  gi|121637888|ref|YP_978111.1| 329 GNPGTGKSTLARGVAELVGAQVISTDDVRRR 359
                                    7789*********************988775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.24       4      27 ..     327     350 ..     325     358 .. 0.87
   2 ?   -2.7   0.0       3.9   5.3e+03      53      73 ..     384     408 ..     366     410 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                    EE--SSSSHHHHHHHGGGGBS--E CS
                          AAA_5   4 LvGppGtgKselaerlaaalnrev 27 
                                    + G+pGtgKs+la+ +a++++++v
  gi|121637888|ref|YP_978111.1| 327 VGGNPGTGKSTLARGVAELVGAQV 350
                                    569***************997655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                                    ....--------....G-SEEEEES CS
                          AAA_5  53 slvdsplvraar....egeilvlDE 73 
                                    + v +++ r+ar    +g+ ++lD+
  gi|121637888|ref|YP_978111.1| 384 VAVYQEALRKARlllgSGHSVILDG 408
                                    4456666667777777777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00048      0.66       7      29 ..     324     346 ..     319     360 .. 0.83
   2 ?    0.1   0.1      0.66   9.1e+02       4      16 ..     360     372 ..     356     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                         AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                    + +v G +GtGK+tl+r ++e  
  gi|121637888|ref|YP_978111.1| 324 LALVGGNPGTGKSTLARGVAELV 346
                                    67889************988865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.66
                         AAA_22   4 tagilvvtGesGt 16 
                                     + ++v+tGe+G+
  gi|121637888|ref|YP_978111.1| 360 LRDCGVITGEPGV 372
                                    5789********7 PP

>> ATP_bind_2  P-loop ATPase protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00027      0.37      91     133 ..      92     135 ..      89     168 .. 0.85
   2 ?   -2.5   0.1       1.8   2.5e+03       2      21 ..     323     342 ..     322     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                                    XHHHHHHHCTSSSXSSTTSXXXSSHHH.HHHHHHHTHHHHHTXS CS
                     ATP_bind_2  91 dddtlvrryedtrrshPlsakdlsleg.iakerelleplrarad 133
                                    +  +++rry+d++r+  + + +l++eg +++  e+l+  ++ra+
  gi|121637888|ref|YP_978111.1|  92 EPVVVMRRYRDKQRLASMVTAGLPVEGaLDAIAEVLARFHQRAQ 135
                                    556789*********************9***********99997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                    EEEEEEESTTSSHHHHHHHH CS
                     ATP_bind_2   2 elvivsGlsGaGksvalral 21 
                                     l +v G  G+Gks+ +r +
  gi|121637888|ref|YP_978111.1| 323 RLALVGGNPGTGKSTLARGV 342
                                    57899*********988865 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       7.5     1e+04      86     103 ..     166     183 ..     155     185 .. 0.72
   2 ?   10.4   0.1    0.0003      0.41      22      64 ..     311     353 ..     298     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.5
                         RuvB_N  86 dvlfideihrlsraveev 103
                                    +v+  d i r++++v+e+
  gi|121637888|ref|YP_978111.1| 166 KVVSGDVIRRIEHMVDEF 183
                                    566668888888888886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0003
                         RuvB_N  22 fieaakkreealdhvllyGpPGlGkttlakiiakelgvklkit 64 
                                    +i++ + ++ ++   l+ G PG Gk+tla+ +a+ +g+++ +t
  gi|121637888|ref|YP_978111.1| 311 IIATQHLQHATVRLALVGGNPGTGKSTLARGVAELVGAQVIST 353
                                    4444445556666778899***************999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2714.51
//
Query:       gi|121637889|ref|YP_978112.1|  [L=295]
Description: hypothetical protein BCG_2022c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-52  176.8  10.6    4.4e-26   92.1   3.7    2.0  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.6   1.9e-29   3.4e-25       5     141 .]      10     148 ..       8     148 .. 0.93
   2 !   92.1   3.7   2.5e-30   4.4e-26       5     141 .]     162     293 ..     159     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.9e-29
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHHHHCTTC CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaaaeaggv 80 
                                    ++V+vDgs es++A+ w++  a++r+ +l+++hv+ ++  ++ +++ +e+   ++e+e+++ +a+a    ++a  ++++ 
  gi|121637889|ref|YP_978112.1|  10 VVVGVDGSLESDAAACWGATDAAMRNIPLTVVHVVNADVATWPPMPYPETWGVWQEDEGRQIVANAvklaKEAVGADRKL 89 
                                    89****************************************************************88877777777788 PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +v+ ++++  p ++ +e+ +e  a+++V+Gs+gr++l+r llGSvs++++r+a cpV v++
  gi|121637889|ref|YP_978112.1|  90 SVKSELVFSTPVPTMVEISNE--AEMVVLGSSGRGALARGLLGSVSSSLVRRAGCPVAVIH 148
                                    888888888888888888776..***********************************985 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 2.5e-30
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                    +lV++Dgs+ s+ A   A+++a +rg eli++h++++ +  + + +d +a ++e+el++ae+ a      ++++ ++v v
  gi|121637889|ref|YP_978112.1| 162 VLVGIDGSPVSELATAVAFDEASRRGVELIAVHAWSDVEVVELPGLDFSAVQQEAELSLAERLA-----GWQERYPDVPV 236
                                    9*************************************************************85.....67999999999 PP

                                    EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                     +++   +++  +v ++ +a+l+VvGs+gr+gl ++llGSvs++vl+ a +pV+v r
  gi|121637889|ref|YP_978112.1| 237 SRVVVCDRPARKLVQKSASAQLVVVGSHGRGGLTGMLLGSVSNAVLHAARVPVIVAR 293
                                    99999999999999****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1646.97
//
Query:       gi|121637890|ref|YP_978113.1|  [L=1327]
Description: trehalose-6-phosphate phosphatase otsB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.3e-156  519.6   0.0   5.7e-156  519.2   0.0    1.2  1  Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalyt
    4.2e-69  232.2   0.0    6.2e-69  231.7   0.0    1.3  1  Trehalose_PPase  Trehalose-phosphatase
    2.2e-68  230.3   0.3    4.1e-68  229.4   0.3    1.5  1  Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal dom
    5.6e-11   42.2   1.3    1.5e-10   40.8   0.0    2.4  3  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom
    6.4e-05   23.3   0.6      0.038   14.3   0.0    3.1  2  Hydrolase        haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.2   0.0  1.6e-159  5.7e-156       1     387 []     847    1259 ..     847    1259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 519.2 bits;  conditional E-value: 1.6e-159
                Glyco_hydro_65m    1 rlalfhllqtlaaadarld..vgakGltGegYrGhvfWDtElfvlPlylltepevarnlLeyRynrleaArekAkekg 76  
                                     rl+l+hllqt+++++a+ld  v+a+Gl+Ge+YrGhvfWD+ lfv P+++l++p+var+lL+yRy+rl+aAr++A+++g
  gi|121637890|ref|YP_978113.1|  847 RLHLLHLLQTISPHTAELDagVPARGLNGEAYRGHVFWDA-LFVAPVLSLRMPKVARSLLDYRYRRLPAARRAAHRAG 923 
                                     79*************************************6.************************************* PP

                Glyco_hydro_65m   77 lkGAlyPwesasdGeEesqelhlnirsgewepdaseeeiHvnaaiayavvqYveatgDeefleeeglellvetarfWa 154 
                                     + GA+yPw+s+sdG+E+sq+lhln+rsg+w+pd s++++Hv++a+ay++++Y+++tgD+++l ++g+ellve+arfW+
  gi|121637890|ref|YP_978113.1|  924 HLGAMYPWQSGSDGSEVSQQLHLNPRSGRWTPDPSDRAHHVGLAVAYNAWHYYQVTGDRQYLVDCGAELLVEIARFWV 1001
                                     ****************************************************************************** PP

                Glyco_hydro_65m  155 sraeldkdkgryeidgviGPdEYe........envdnNaytnliaawnlelalealeeleeea.....eklevkeeel 219 
                                      +a+ld+++gry i+gviGPdE++        +++dnNaytn++a w++ +a+eal+ l+ ++     ekl+++++e 
  gi|121637890|ref|YP_978113.1| 1002 GLAKLDDSRGRYLIRGVIGPDEFHsgypgneyDGIDNNAYTNVMAVWVILRAMEALDLLPLTDrrhliEKLGLTTQER 1079
                                     **************************************************************999************* PP

                Glyco_hydro_65m  220 ekwekvleklylpideelgviaqkdgflelaeldleeykalagdet..dlllkaegdkvlesqviKQaDvllllyl.. 293 
                                     ++w++v++++++p+++  gvi+q++g++elaeld+++y++++g+++  d++l+aegd+v+++q++KQaD+l+llyl  
  gi|121637890|ref|YP_978113.1| 1080 DQWDDVSRRMFVPFHD--GVISQFEGYSELAELDWDHYRHRYGNIQrlDRILEAEGDSVNNYQASKQADALMLLYLls 1155
                                     ****************..**************************9999****************************** PP

                Glyco_hydro_65m  294 ..........lkeefseeqikanldfYeprtvhdSslSalvhaivaaelgklekalelfkeaariDl.daqerstedG 360 
                                               l ++f+++qi  ++d+Y++rt+++S+lSa+vha+v+a++++ ++a+e+f++++r+D+ d+q+++t++G
  gi|121637890|ref|YP_978113.1| 1156 sdeligllarLGYRFAPTQIPGTVDYYLARTSDGSTLSAVVHAWVLARANR-SNAMEYFRQVLRSDIaDVQGGTTQEG 1232
                                     ***************************************************.************************** PP

                Glyco_hydro_65m  361 iHiaslagtleaivqgfaglrlregel 387 
                                     iH+a++ag++++++++++gl+lr+++l
  gi|121637890|ref|YP_978113.1| 1233 IHLAAMAGSIDLLQRCYSGLELRDDRL 1259
                                     ************************986 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.7   0.0   1.7e-72   6.2e-69       1     231 [.     285     510 ..     285     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 1.7e-72
                                    EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-H CS
                Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenq 80 
                                    flD+dGTls+ive+p+aa++ + + ++L++La++++  va++SGr+l++++++vkv++l+la++HG+e+ +p+g++++n 
  gi|121637890|ref|YP_978113.1| 285 FLDFDGTLSDIVERPEAATLVDGAAEALRALAAQCP--VAVISGRDLADVRNRVKVDGLWLAGSHGFELVAPDGSHHQNA 362
                                    89**********************************..****************************************** PP

                                    HHHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT..THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S CS
                Trehalose_PPase  81 aevedlewlkevkeileektertpGsyiEekkfalsvHyrnaddeelqakelaehlesvltdkpdlevtqgkkvvevrpq 160
                                    a++++++ l e++++l ++++++ G+++E+k+fa++vHyrn++d+  ++++l ++++++ ++  +l+vt+g+kvve+rp+
  gi|121637890|ref|YP_978113.1| 363 AATAAIDGLAEAAAQLADALREIAGAVVEHKRFAVAVHYRNVADD--SVDNLIAAVRRLGHAA-GLRVTTGRKVVELRPD 439
                                    *********************************************..***********99999.**************** PP

                                    ---.HHHHHHHHHHTS---..-----EEEEEE-SSTTHHHHTTS-TT...-EEEEE--TTS---EES-SEEESS CS
                Trehalose_PPase 161 gvs.KGkaverlleslgsa..dseddfvlciGDdrtDedmFsvlrktkesgvsievsavevgskpskakyslds 231
                                    +++ KGka++++ e+lg a  +++ +++++iGDd+tDed+F+++r t   gv+i+v++ e+g+++s+a+++l++
  gi|121637890|ref|YP_978113.1| 440 IAWdKGKALDWIGERLGPAevGPDLRLPIYIGDDLTDEDAFDAVRFT---GVGIVVRHNEHGDRRSAATFRLEC 510
                                    *******************9**************************9...*********************986 PP

>> Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.4   0.3   1.2e-71   4.1e-68       3     228 .]     540     793 ..     538     793 .. 0.93

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 1.2e-71
                                    .....S--HHHHHHT-EE-SSEEE----TT.TT--....-EEETT-EE-T........TSSS-EE----EEEEEEEEETT CS
                Glyco_hydro_65N   3 tgfdpeeeglrEslftlGNGylGtRgafee.eysd...pgtyiaGvYdreiseeanGypeeneelvnlpdwlglrlrvdg 78 
                                    +g+dp +e+lrE+l+++GNGylG Rg ++e ++s+   pgty+aGvY++  + +++G +++ne+lvnlp+wl l++r+dg
  gi|121637890|ref|YP_978113.1| 540 HGYDPGQERLREALCAVGNGYLGSRGCAPEsAESEahyPGTYVAGVYNQL-TDHIEGCTVDNESLVNLPNWLSLTFRIDG 618
                                    79****************************533446789***********.99*************************** PP

                                    EE.--GGGSEEEEEEEEEETTTTEEEEEEEEE-TTS-EEEEEEEEEE-SSSTTEEEEEEEEEESS--EEEEEEEEEETT- CS
                Glyco_hydro_65N  79 ee.ldldegeildyereLdlreGvltrsltwrspagkevrveserfvsladrhlaairlevtplnfsgevevesgldgdv 157
                                    +  +++d++e+l+y+++ dlr+++ltrsl++r+++g+ +++++erf+s+++++l+a++++++++n+sg+v+++s +dg v
  gi|121637890|ref|YP_978113.1| 619 GAwFNVDTVELLSYRQTFDLRRATLTRSLRFRDAGGRVTTMTQERFASMNRPNLVALQTRIESENWSGTVDFRSLVDGGV 698
                                    999***************************************************************************** PP

                                    -B...............................EEEEETTSS-EEEEEEEEEEEETTEE--SEE......SEEEEEEEEE CS
                Glyco_hydro_65N 158 an..........ekh.kdprka...........levrtresgitvavaartrveasgeklevee......ekiaqtlsve 209
                                    +n          ++h +                l+++t++sgi +avaar+++  +g++++++       ++ +++++v+
  gi|121637890|ref|YP_978113.1| 699 HNtlvdryrqlsSQHlT----TaeievladsvlLRTQTSQSGIAIAVAARSTLWRDGQRVDAQYrvardtNRGGHDIQVT 774
                                    **999876666533442....133457888999*************************9999779*************** PP

                                    E-TT-EEEEEEEEEEEETT CS
                Glyco_hydro_65N 210 lkagetvtleKyvavatsr 228
                                    l+ag++vtleK+++++tsr
  gi|121637890|ref|YP_978113.1| 775 LSAGQSVTLEKVATIFTSR 793
                                    ******************8 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   5.9e+03       4      14 ..     607     616 ..     605     616 .. 0.84
   2 ?   -2.6   0.0       1.5   5.5e+03      28      42 ..     769     783 ..     767     784 .. 0.71
   3 !   40.8   0.0   4.1e-14   1.5e-10       1      50 [.    1263    1314 ..    1263    1315 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                    -TT-SEEEEEE CS
                Glyco_hydro_65C   4 PeeWdglsFrl 14 
                                    P +W +l+Fr+
  gi|121637890|ref|YP_978113.1| 607 P-NWLSLTFRI 616
                                    5.9******98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    SEEEEEEESSSTEEE CS
                Glyco_hydro_65C  28 eevtvtlesgeplti 42 
                                    + ++vtl +g+ +t+
  gi|121637890|ref|YP_978113.1| 769 HDIQVTLSAGQSVTL 783
                                    567788888888887 PP

  == domain 3  score: 40.8 bits;  conditional E-value: 4.1e-14
                                     ----TT-SEEEEEEEETTEEEEEEEESSEEEEEEESSS..TEEEEETTEEEE CS
                Glyco_hydro_65C    1 PrLPeeWdglsFrlryRGrrLrVrvtpeevtvtlesge..pltievyGeevt 50  
                                     P++Pe+++ l+F++ yR ++L +r++  ++t+t+esg+  p+++e++G + +
  gi|121637890|ref|YP_978113.1| 1263 PQWPEALGPLEFPFVYRRHQLSLRISGRSATLTAESGDaePIEVECRGHVQR 1314
                                     99**********************************5555********9876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.038     124     209 ..     131     219 ..     118     220 .. 0.82
   2 !    5.9   0.2    0.0037        13       3      62 ..     283     351 ..     225     439 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 124 aeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet....vakpspegkvaaireLqgkpeevamVGD 198
                                    a + ++L+ ag++v+  t  +++++ ++++  G ++ f++ +++ +++     a+p+p g+ +++++L+++p ++++++ 
  gi|121637890|ref|YP_978113.1| 131 ASFARRLQVAGVRVAAHT--SHRNYGHTLDATGlAEVFAVFVDGAVTAelglPAEPNPAGLIETAKRLGANPGRCVVIDS 208
                                    566778888999888888..55667788999999888866666665556888**************************99 PP

                                    SHHHHHHHHHT CS
                                    xxxxxxxxxxx RF
                      Hydrolase 199 gvnDaaalaaA 209
                                      +++ a+++ 
  gi|121637890|ref|YP_978113.1| 209 CQTGLRAGRNG 219
                                    88888888775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0037
                                    EEEEESBTTTBCHH..HHHHHHHHHHCHHHHHHHHHH.....HHCHHHHHH.HHHHHHHHHHH.HHHHH CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx.xxxxxxxxxxx.xxxxx RF
                      Hydrolase   3 tvvfDkdGTLttge..psvedvivsaalalaaaletg.....sehpigkal.vaaakarsgal.tgfat 62 
                                    +v++D+dGTL +    p+  ++++ aa al+a  +       s + ++      + ++++ a  +gf+ 
  gi|121637890|ref|YP_978113.1| 283 AVFLDFDGTLSDIVerPEAATLVDGAAEALRALAAQCpvaviSGRDLADVRnRVKVDGLWLAGsHGFEL 351
                                    688899999998877788888888884444433333333344544444444333333334444445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.01u 0.34s 00:00:01.35 Elapsed: 00:00:00.56
# Mc/sec: 7155.04
//
Query:       gi|121637891|ref|YP_978114.1|  [L=114]
Description: ferredoxin fdxA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-08   32.7  17.7    1.1e-06   28.2   5.0    2.7  2  Fer4      4Fe-4S binding domain
    0.00012   22.1   8.2     0.0015   18.6   0.3    2.2  2  Fer4_21   4Fe-4S dicluster domain
    0.00048   20.7  11.5    0.00076   20.0   1.5    2.2  3  Fer4_7    4Fe-4S dicluster domain
     0.0048   17.3   6.1      0.019   15.4   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
     0.0057   17.6   5.7       0.14   13.1   0.5    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
      0.007   16.5  11.9      0.016   15.4  11.9    1.6  1  Fer4_9    4Fe-4S dicluster domain
     0.0078   16.3   9.9     0.0085   16.1   2.8    2.6  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.022   14.8   2.4      0.022   14.8   2.4    2.2  2  Fer4_10   4Fe-4S dicluster domain
      0.026   14.6   4.7      0.026   14.6   4.7    2.5  2  Fer4_6    4Fe-4S binding domain
      0.051   14.1   4.1      0.051   14.1   4.1    2.7  3  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.5   8.3e-05      0.15      13      24 .]      16      27 ..      12      27 .. 0.89
   2 !   28.2   5.0   6.1e-10   1.1e-06       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                                   HHHHHSTTTEEE CS
                           Fer4 13 aCvevCPvgAIt 24
                                    Cv+ CPv++I+
  gi|121637891|ref|YP_978114.1| 16 SCVQECPVDCIY 27
                                   7*********96 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 6.1e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                   +i+++ C+ CGaC  +C v+AI+
  gi|121637891|ref|YP_978114.1| 34 YINPDECVDCGACKPACRVEAIY 56
                                   8********************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   2.8    0.0041       7.3      36      57 ..       4      26 ..       1      28 [. 0.74
   2 !   18.6   0.3   8.4e-07    0.0015       3      27 ..      35      56 ..      33      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                        Fer4_21 36 vvedeCvGC..nlCssvCPvedci 57
                                   v+ +eCv    + C++ CPv dci
  gi|121637891|ref|YP_978114.1|  4 VIGSECVDVmdKSCVQECPV-DCI 26
                                   5567777653368******9.9*9 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 8.4e-07
                        Fer4_21  3 idedkCigCgkCliaCedtshqaie 27
                                   i++d+C++Cg C  aC+   ++ai 
  gi|121637891|ref|YP_978114.1| 35 INPDECVDCGACKPACR---VEAIY 56
                                   99**************9...67774 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.3     0.024        43      37      51 ..       8      24 ..       2      25 .. 0.71
   2 !   12.2  14.4   0.00012      0.21       6      52 .]      15      54 ..       7      54 .. 0.86
   3 !   20.0   1.5   4.2e-07   0.00076       2      22 ..      40      60 ..      39      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                         Fer4_7 37 kClgCga..CvavCPtg 51
                                   +C++     Cv++CP++
  gi|121637891|ref|YP_978114.1|  8 ECVDVMDksCVQECPVD 24
                                   566654444******97 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                         Fer4_7  6 gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   + Cv+ Cpv++i+   +        ++i+p++C++CgaC  +C ++a
  gi|121637891|ref|YP_978114.1| 15 KSCVQECPVDCIYEGAR-------MLYINPDECVDCGACKPACRVEA 54
                                   58**********98554.......59*****************9876 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 4.2e-07
                         Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                   C+ CgaC +aC v+ai+++ +
  gi|121637891|ref|YP_978114.1| 40 CVDCGACKPACRVEAIYWEGD 60
                                   *****************9854 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.5     0.051        92      53      64 ..      13      24 ..       5      25 .. 0.75
   2 !   15.4   0.1   1.1e-05     0.019       4      17 ..      39      52 ..      36      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.051
                         Fer4_8 53 tcgaCtevCpvg 64
                                   + ++C+++Cpv+
  gi|121637891|ref|YP_978114.1| 13 MDKSCVQECPVD 24
                                   5578******86 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                         Fer4_8  4 kCieCgaCqsaCpv 17
                                   +C+ CgaC+ aC v
  gi|121637891|ref|YP_978114.1| 39 ECVDCGACKPACRV 52
                                   79999999999953 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.5    0.0051       9.2       6      20 ..      15      29 ..       8      38 .. 0.83
   2 !   13.1   0.5   7.7e-05      0.14       2      18 ..      40      56 ..      39      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0051
                        Fer4_16  6 gkCaevCPtnaikek 20
                                   + C++ CP+++i e 
  gi|121637891|ref|YP_978114.1| 15 KSCVQECPVDCIYEG 29
                                   57*********9887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-05
                        Fer4_16  2 CgtCgkCaevCPtnaik 18
                                   C++Cg+C  +C ++ai 
  gi|121637891|ref|YP_978114.1| 40 CVDCGACKPACRVEAIY 56
                                   **************995 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  11.9   8.9e-06     0.016       6      51 .]      15      55 ..       7      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.9e-06
                         Fer4_9  6 gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   ++Cv+ Cp + + e a   +++ +     +C++CgaC  aC  +ai
  gi|121637891|ref|YP_978114.1| 15 KSCVQECPVDCIYEGARMLYINPD-----ECVDCGACKPACRVEAI 55
                                   68**********999999999974.....4***********99876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.034        62      14      21 ..      15      22 ..       7      23 .. 0.80
   2 !   16.1   2.8   4.7e-06    0.0085       3      20 ..      33      50 ..      30      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.034
                         Fer4_2 14 gaCvsaCP 21
                                   ++Cv+ CP
  gi|121637891|ref|YP_978114.1| 15 KSCVQECP 22
                                   58****** PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.7e-06
                         Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                    ++++d C+ CgaC  aC
  gi|121637891|ref|YP_978114.1| 33 LYINPDECVDCGACKPAC 50
                                   789***********9999 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  13.3    0.0012       2.2      13      55 ..      15      50 ..       3      51 .. 0.87
   2 ?   14.8   2.4   1.2e-05     0.022       2      19 ..      33      50 ..      32      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                        Fer4_10 13 gkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                   + Cv+ CP+         ++++  +  +++++C +cgaC  aC
  gi|121637891|ref|YP_978114.1| 15 KSCVQECPV-------DCIYEGARMLYINPDECVDCGACKPAC 50
                                   68*******.......888888899999***********9999 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.2e-05
                        Fer4_10  2 vvidddtCirCgkCvkaC 19
                                   ++i++d C+ Cg+C+ aC
  gi|121637891|ref|YP_978114.1| 33 LYINPDECVDCGACKPAC 50
                                   589*************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   3.3      0.33   5.9e+02      15      23 ..      17      25 ..       8      30 .. 0.76
   2 ?   14.6   4.7   1.4e-05     0.026       4      24 .]      35      55 ..      33      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.33
                         Fer4_6 15 CvrvCPega 23
                                   Cv  CP + 
  gi|121637891|ref|YP_978114.1| 17 CVQECPVDC 25
                                   999***765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.4e-05
                         Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                   i+pd C++Cg+C  +C   ai
  gi|121637891|ref|YP_978114.1| 35 INPDECVDCGACKPACRVEAI 55
                                   89**************88887 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       6.7   1.2e+04      10      12 ..       9      11 ..       7      12 .. 0.65
   2 ?    2.8   1.5      0.12   2.2e+02       8      16 ..      15      23 ..      14      27 .. 0.77
   3 ?   14.1   4.1   2.9e-05     0.051       1      15 [.      37      51 ..      37      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.7
                         Fer4_4 10 Cva 12
                                   Cv+
  gi|121637891|ref|YP_978114.1|  9 CVD 11
                                   776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                         Fer4_4  8 gsCvaaCPq 16
                                   +sCv  CP+
  gi|121637891|ref|YP_978114.1| 15 KSCVQECPV 23
                                   578888886 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.9e-05
                         Fer4_4  1 qerCigCgsCvaaCP 15
                                   ++ C++Cg+C  aC 
  gi|121637891|ref|YP_978114.1| 37 PDECVDCGACKPACR 51
                                   689***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 630.24
//
Query:       gi|121637892|ref|YP_978115.1|  [L=441]
Description: hypothetical protein BCG_2025c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   82.3   0.0      4e-23   81.9   0.0    1.2  1  DUF4143   Domain of unknown function (DUF4143)
    1.3e-15   57.6   0.0    2.4e-15   56.7   0.0    1.4  1  AAA_14    AAA domain
    0.00012   22.5   0.1     0.0024   18.3   0.0    2.7  2  AAA_16    AAA ATPase domain
    0.00036   20.4   0.0    0.00086   19.2   0.0    1.6  1  HTH_11    HTH domain
     0.0027   18.0   0.1        1.2    9.4   0.0    2.5  2  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.013   15.3   0.7       0.04   13.7   0.7    1.9  1  HTH_IclR  IclR helix-turn-helix domain
       0.16   12.0   0.0        0.3   11.1   0.0    1.3  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.5e-26     4e-23       1     121 [.     227     381 ..     227     382 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.5e-26
                                    xxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143   1 erDirklagvrdpeelrk.......................................glverlppwsespnskkrlrksp 41 
                                    erD+++l+ +  ++++r+                                        +v++l pw  ++n +kr+r+sp
  gi|121637892|ref|YP_978115.1| 227 ERDLAQLGVRIPAATMRRawtmlahyhgqlfsgaelarsldvaqttarryldaltdaLVVRQLTPW--FANIGKRQRRSP 304
                                    68999999888888888899999999999999999999999999999999999999**********..************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  42 KlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                    K+y+ DtGLl+ llg+d++  le+++ +Ga +E +V+++L +        lyy+r+++ aE+D+ +el +g+ +++E+K 
  gi|121637892|ref|YP_978115.1| 305 KIYIRDTGLLHRLLGIDDRLALERNPKLGASWEGFVLEQLAA--LLAPNPLYYWRTQQDAELDLYVEL-SGRPYGFEIKR 381
                                    *****************************************9..44578******************8.77999****96 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   9.3e-19   2.4e-15       3     128 ..      72     186 ..      70     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 9.3e-19
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpeweka 82 
                                    +++++tG+R++GKTtl + + k+         + ++d e+  +++      + +l++ ++    ++ +DE+q++p+++ +
  gi|121637892|ref|YP_978115.1|  72 PVVLLTGPRQAGKTTLSRLVGKSAP-------ECTFDAENPVDATRL---ADPMLAL-SG-LSGLITIDEAQRIPDLFPV 139
                                    689*************877775555.......666666555443333...3334443.22.3459*************** PP

                         AAA_14  83 lkslvdeg.knldvivtGSnskllskeiatslagrvaeielyplsfa 128
                                    l+ lvd+     ++++ GS+s +l   +++slagrv+ +el  l+++
  gi|121637892|ref|YP_978115.1| 140 LRVLVDRPvMPARFLILGSASPDLVGLASESLAGRVELVELSGLTVR 186
                                    ******998889*****************************999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.3e-07    0.0024       2      49 ..      54      96 ..      53     154 .. 0.88
   2 ?    1.2   0.1      0.16   4.2e+02      72     107 ..     335     379 ..     223     413 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.3e-07
                         AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellrale 49
                                   l+ R++  ++L++al+r+     ++vll+G++  GK++l r + +++ 
  gi|121637892|ref|YP_978115.1| 54 LIERRDAAARLRRALHRA-----PVVLLTGPRQAGKTTLSRLVGKSAP 96
                                   677899999999999988.....9****************99988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                         AAA_16  72 laqalareellrqlldeaesaeleawrekleeala.............a 107
                                     ++ +     l+ql++ ++ + l +wr++ +++l              +
  gi|121637892|ref|YP_978115.1| 335 SWEGFV----LEQLAALLAPNPLYYWRTQQDAELDlyvelsgrpygfeI 379
                                    333332....233333333345666666666666555555555555551 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.4e-07   0.00086       8      43 ..     248     284 ..     243     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.4e-07
                         HTH_11   8 lLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                    +L + +g+ +sg+eLA+ L+v  +t rr+++aL++++
  gi|121637892|ref|YP_978115.1| 248 MLAHYHGQlFSGAELARSLDVAQTTARRYLDALTDAL 284
                                    788889999************************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00046       1.2       4      31 ..      70      97 ..      65     114 .. 0.84
   2 !    6.0   0.0    0.0052        13      92     117 ..     122     145 ..     107     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00046
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqlde 31
                                   +a ++++tG+  +GKTtl r + ++++e
  gi|121637892|ref|YP_978115.1| 70 RAPVVLLTGPRQAGKTTLSRLVGKSAPE 97
                                   67789***************99988865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0052
                         AAA_22  92 ielliiDEaqhlrseealeeLrslln 117
                                     +l+ iDEaq++  ++++  Lr l++
  gi|121637892|ref|YP_978115.1| 122 SGLITIDEAQRI--PDLFPVLRVLVD 145
                                    589*********..777777777777 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   1.5e-05      0.04      12      50 ..     249     288 ..     247     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                    -CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  12 laeapqel.tlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    la+  + l + +elAr ++++ +t++R+L  L+    v+q
  gi|121637892|ref|YP_978115.1| 249 LAHYHGQLfSGAELARSLDVAQTTARRYLDALTDALVVRQ 288
                                    666666666779********************98766666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012       0.3       9      41 ..      59      93 ..      55     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                   HHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE  9 algkklakal..gdvilLeGdLGaGKTtlvrglak 41
                                   +++++l +al  + v+lL+G+  aGKTtl+r + k
  gi|121637892|ref|YP_978115.1| 59 DAAARLRRALhrAPVVLLTGPRQAGKTTLSRLVGK 93
                                   566677776655668***************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2916.99
//
Query:       gi|121637893|ref|YP_978116.1|  [L=80]
Description: hypothetical protein BCG_2026 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-17   62.3   0.4      4e-17   61.9   0.4    1.2  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.4   2.2e-21     4e-17       1      42 [.       7      48 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.2e-21
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------H CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkre 42
                                   +rtnIeiDDeL+a A+r+++l  Kr aV+lALr+L++++ ++
  gi|121637893|ref|YP_978116.1|  7 SRTNIEIDDELVAAAQRMYRLDSKRSAVDLALRRLVGEPLGR 48
                                   59************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 514.90
//
Query:       gi|121637894|ref|YP_978117.1|  [L=132]
Description: hypothetical protein BCG_2027 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-15   55.1   1.4    1.2e-14   54.9   1.4    1.0  1  PIN       PIN domain
     0.0019   18.5   0.0      0.002   18.4   0.0    1.2  1  PIN_4     PIN domain
     0.0076   16.8   0.0     0.0085   16.6   0.0    1.2  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   1.4   1.9e-18   1.2e-14       1     119 [.       1     120 [.       1     122 [. 0.88

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.9e-18
                                    EEE-HHHHHHHH..TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCHHH CS
                            PIN   1 ivlDTsvliall..rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp.idaei 77 
                                    +++DTsv+ia+l  +++  +++++++++++++++++++v+ Ell++ +        +++  +++ ll ++ i p    ++
  gi|121637894|ref|YP_978117.1|   1 MIVDTSVWIAYLstSESLASRWLADRIAADSTVIVPEVVMMELLIGKTD-------EDTAALRRRLLQRFAIEPlAPVRD 73 
                                    68**********988888889999999999*******************.......66666666677777777755899* PP

                                    HHHHHHHHHHHH......SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  78 aeeaaeialkyg......llpnDaliaAtAkehgikliatfDedfrrv 119
                                    ae aa+i+++ +      ++++D+ +aA+A++ g ++  ++D+d + +
  gi|121637894|ref|YP_978117.1|  74 AEDAAAIHRRCRrggdtvRSLIDCQVAAMALRIGVAVA-HRDRDYEAI 120
                                    **********99***********************777.*****8765 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-07     0.002       1      44 [.       1      58 [.       1     112 [. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-07
                          PIN_4  1 fVlDTnvlLhdpealksf.........keehdvviPitVleELdklKkgsse.....r 44
                                   +++DT+v++  ++  +s+           +  v++P +V+ EL   K+++++     r
  gi|121637894|ref|YP_978117.1|  1 MIVDTSVWIAYLSTSESLasrwladriAADSTVIVPEVVMMELLIGKTDEDTaalrrR 58
                                   699***********9*99*********99**************999999996444331 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.4e-06    0.0085       2      46 ..       2      44 ..       1      78 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                         PIN_12  2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEfl 46
                                   ++DT++++   + ++ e+  ++ l++  + + ++ivp++v++E+l
  gi|121637894|ref|YP_978117.1|  2 IVDTSVWIA--YLSTSESLASRWLADRIAADSTVIVPEVVMMELL 44
                                   68******5..66666656666656666668************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 955.90
//
Query:       gi|121637895|ref|YP_978118.1|  [L=143]
Description: hypothetical protein BCG_2028c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-10   40.9   2.5    2.9e-10   39.9   0.7    2.3  2  MarR_2     MarR family
    2.1e-05   24.5   0.1    6.9e-05   22.8   0.1    2.0  2  HTH_29     Winged helix-turn helix
     0.0097   15.9   1.4      0.062   13.3   0.1    2.5  3  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.03   14.2   0.0    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.019   14.7   0.7      0.057   13.2   0.3    2.0  2  HTH_IclR   IclR helix-turn-helix domain
      0.039   14.1   0.0       0.11   12.7   0.0    1.8  1  HTH_17     Helix-turn-helix domain
       0.19   11.8   0.1       0.19   11.8   0.1    2.6  3  HTH_20     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.4     1e+03      43      55 ..      11      23 ..       6      30 .. 0.73
   2 !   39.9   0.7   1.1e-13   2.9e-10       4      60 ..      33      86 ..      30      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.4
                                   HHHHHTTSEEEEE CS
                         MarR_2 43 krLvaaGLverrp 55
                                   + ++ aGL++r+ 
  gi|121637895|ref|YP_978118.1| 11 DVFELAGLLRRSG 23
                                   5678899999984 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.1e-13
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                                   t a +++L ++ +r    ltv + arrlg++++ v+r+ ++Lv  GL e r +p+++
  gi|121637895|ref|YP_978118.1| 33 TQARWQLLSVVSDRA---LTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHR 86
                                   7899**********9...9********************************999886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.7e-08   6.9e-05       9      51 ..      45      86 ..      36      95 .. 0.82
   2 ?   -3.0   0.0       3.1   7.9e+03      22      33 ..     124     135 ..     122     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.7e-08
                         HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                   ++++ tv q+A++lg++r+ v+r+ ++ +  Gla l++++ ++
  gi|121637895|ref|YP_978118.1| 45 DRAL-TVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHR 86
                                   4455.9******************************8876544 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                         HTH_29  22 lglsrrtvyrwl 33 
                                    l+ +r++ +r +
  gi|121637895|ref|YP_978118.1| 124 LQATRDSLRRMI 135
                                    556777777765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.4e-05     0.062      21      52 ..      47      78 ..      15      87 .. 0.78
   2 ?   -0.7   0.0      0.58   1.5e+03      40      66 ..      99     125 ..      95     127 .. 0.60
   3 ?    0.6   0.1      0.23   5.9e+02      31      48 ..     124     141 ..     122     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                    lt  + A++lG+tr+ v r+ ++L   gl +
  gi|121637895|ref|YP_978118.1| 47 ALTVPQAARRLGVTRQGVQRVANDLVVCGLAE 78
                                   5777789******************9888877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.58
                                    HHHHHHHHTTSEEETEE.EEES-HHHHH CS
                      HTH_Crp_2  40 rilseLkreglisrgrr.irildleaLr 66 
                                    r+l++  ++ ++ ++ r     d++aL+
  gi|121637895|ref|YP_978118.1|  99 RVLQAITERAIVVNN-RlADAVDPAALQ 125
                                    566666666666655.225566666666 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.23
                                    TTSSHHHHHHHHHHHHHT CS
                      HTH_Crp_2  31 lGltretvsrilseLkre 48 
                                    l +tr ++ r++ +Lk e
  gi|121637895|ref|YP_978118.1| 124 LQATRDSLRRMIVALKAE 141
                                    7899*******9999976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05      0.03      16      58 ..      41      83 ..      38      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                    +++   +t+ + a++lgv r+ v++v + L+ +Gl e ++  
  gi|121637895|ref|YP_978118.1| 41 SVVSDRALTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNP 83
                                   678889999****************************988765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   2.2e-05     0.057      16      50 ..      45      79 ..      38      81 .. 0.94
   2 ?   -2.4   0.0       1.7   4.3e+03       5      15 ..      97     107 ..      94     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                   BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   +++lt+ + Arr+g+++  v R  + Lv +G+ e 
  gi|121637895|ref|YP_978118.1| 45 DRALTVPQAARRLGVTRQGVQRVANDLVVCGLAEL 79
                                   6889****************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                    HHHHHCT-CTT CS
                       HTH_IclR   5 alaiLdalaea 15 
                                    + ++L+a++e+
  gi|121637895|ref|YP_978118.1|  97 GRRVLQAITER 107
                                    55788888765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05      0.11       2      21 ..      48      67 ..      47      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                         HTH_17  2 ltveEaAelLgvsrstvyrl 21
                                   ltv +aA+ Lgv r+ v+r 
  gi|121637895|ref|YP_978118.1| 48 LTVPQAARRLGVTRQGVQRV 67
                                   9****************995 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.5   3.8e+03      49      57 ..      14      22 ..       4      24 .. 0.68
   2 ?   11.8   0.1   7.4e-05      0.19      12      42 ..      36      65 ..      31      80 .. 0.85
   3 ?   -0.2   0.1      0.42   1.1e+03      28      28 ..     122     122 ..      93     138 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                   HHCTTEEEE CS
                         HTH_20 49 eeagLvevv 57
                                   e agL+++ 
  gi|121637895|ref|YP_978118.1| 14 ELAGLLRRS 22
                                   447777765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.4e-05
                                   HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHH CS
                         HTH_20 12 RrrilraLaraegltaselaerldlskntls 42
                                   R  +l+   ++++lt+++ a+rl+++++ + 
  gi|121637895|ref|YP_978118.1| 36 RWQLLSVV-SDRALTVPQAARRLGVTRQGVQ 65
                                   55677778.9*****************9886 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.42
                                    H CS
                         HTH_20  28 s 28 
                                    +
  gi|121637895|ref|YP_978118.1| 122 A 122
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1028.08
//
Query:       gi|121637896|ref|YP_978119.1|  [L=164]
Description: hypothetical protein BCG_2029 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-10   38.5   0.0    1.5e-09   37.9   0.0    1.3  1  DUF1398   Protein of unknown function (DUF1398)


Domain annotation for each model (and alignments):
>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   8.3e-14   1.5e-09      12     114 ..      44     147 ..      35     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.3e-14
                                    --HHHHHHHHHH-SSEEEEETTTSEEEEE-SSS-EEE..EE-STT-----S---HHHHHHHHHHHHHT---HHHHHHHHH CS
                        DUF1398  12 dfpafiqelkrlgvskYeyfvadgnvkyvgendevve..vkakrellkvaekknaelikaalkkhqqgettfetfcedlA 89 
                                     fp++++ l+r gv+  + ++ + +  y ++ + v++  v     + +v +  +++++ +al++ q+g+t+f++f   + 
  gi|121637896|ref|YP_978119.1|  44 GFPHLAETLRRAGVRTNTWWLPAMQSLYETDYGPVLDqgVPLIDGVAEVPA-FDRTALVTALRADQAGQTSFREFAAAAW 122
                                    688888888888888888888888888887777777622344555555544.4566677899****************** PP

                                    HTT--EEEEETTTTEEEEE-TT--E CS
                        DUF1398  90 kaGvekWivdleektrtYydkdnsl 114
                                    +aGv +++vdle++t+tY+  +++ 
  gi|121637896|ref|YP_978119.1| 123 RAGVLRYVVDLENRTCTYFGLHDQT 147
                                    *******************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1148.32
//
Query:       gi|121637897|ref|YP_978120.1|  [L=205]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-28   97.1   0.0      1e-27   96.9   0.0    1.1  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   5.8e-32     1e-27      13     155 .]       2     142 ..       1     142 [. 0.97

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 5.8e-32
                 DEDD_Tnp_IS110  13 cvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvnplavkrlrkly.lrk 91 
                                    +++da g+++ + +++++ +gl++lle  +++ag  +v++e       ++v  lleagitvvv+ p + k+lr +y + +
  gi|121637897|ref|YP_978120.1|   2 SIVDARGREVRRATIEHNAAGLRELLEL-LSRAGAREVAIERPDG---PVVDTLLEAGITVVVISPNQLKNLRGRYgSAG 77 
                                    799************************9.99**********9987...789**********************9995678 PP

                 DEDD_Tnp_IS110  92 aKtDakDAkvIAdllr.drgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdqvfp 155
                                    +K+D+ DA+v+Ad+lr dr+rlrpl +d+ a+a Lr+ +r r+dlv+ r++l n+lra+L+ vfp
  gi|121637897|ref|YP_978120.1|  78 NKDDRFDAFVLADTLRtDRSRLRPLLPDTPATATLRRTCRPRKDLVAHRVALANQLRAHLRVVFP 142
                                    ****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 1065.59
//
Query:       gi|121637898|ref|YP_978121.1|  [L=196]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-18   65.9   0.5    5.4e-18   65.1   0.0    1.7  2  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.47   8.5e+03      62      76 ..      22      36 ..      18      45 .. 0.56
   2 !   65.1   0.0     3e-22   5.4e-18       2      86 ..      57     141 ..      56     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.47
                 Transposase_20 62 rrlRraLyeaAlaai 76
                                   +++ ra++ a ++++
  gi|121637898|ref|YP_978121.1| 22 AHITRAMVAALTSVA 36
                                   555555555554444 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 3e-22
                 Transposase_20   2 elLesipGiGpvtaaallaeigdl.rrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairanp 80 
                                    ++++s+p  G+v aa+llaeigd+  rf+++++la++aG+ap+++qSGk k+  +++++ +++lR a++ +A  + ran 
  gi|121637898|ref|YP_978121.1|  57 HIFTSLPRSGTVRAARLLAEIGDCrARFPTPESLACLAGVAPSTRQSGKVKH-VGFRWAADKQLRDAVCDFAGDSRRANL 135
                                    7899********************888**********************998.99************************8 PP

                 Transposase_20  81 elrayy 86 
                                    +++++y
  gi|121637898|ref|YP_978121.1| 136 WAADRY 141
                                    888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1246.23
//
Query:       gi|121637899|ref|YP_978122.1|  [L=418]
Description: hypothetical protein BCG_2032c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-73  248.1   4.7    2.1e-73  247.4   4.7    1.3  1  DUF222    Domain of unknown function (DUF222)
    1.6e-07   31.3   1.9    3.1e-07   30.5   1.9    1.5  1  HNH       HNH endonuclease
  ------ inclusion threshold ------
      0.029   14.5   1.9       0.16   12.1   1.9    2.1  1  HNH_2     HNH endonuclease
        0.8   10.4   4.0        1.4    9.7   0.0    2.9  3  zf-ISL3   zinc-finger of transposase IS204/IS1001/IS1096/IS11


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.4   4.7   4.7e-77   2.1e-73       2     301 .]      22     306 ..      21     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 247.4 bits;  conditional E-value: 4.7e-77
                         DUF222   2 laaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalraGdi 81 
                                    +++l+el+ +++++++++v++vael++++ ++ +ga++va lva+++++s+++A+++ ++Ar+l e +p++a+ +r+G++
  gi|121637899|ref|YP_978122.1|  22 FEELAELAGQRNAIDGRIVEIVAELDRDGLWGVTGARSVAGLVAWKMGCSSGNAHTIATVARRLPE-FPRCARGMREGRL 100
                                    689***************************************************************.************* PP

                         DUF222  82 dlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltkdedGm 161
                                    +l+qv vIa r+ + +da++++ +  a++++lr+a kl+p++            +p++   d ++++r+++t ++ ++++
  gi|121637899|ref|YP_978122.1| 101 SLDQVGVIAGRAGEGSDAHYAQLAGVATVNQLRTALKLEPRP------------EPEP---DFRPEPRPSITRSA-DEQF 164
                                    *****************************************9............8888...799***********.9*** PP

                         DUF222 162 srisgeldaeaaaaldavLdslaapvcap........dgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvh 233
                                    s+++++l++++aa++da+L+s+ ++++a+        dg++D+R+p + + +A+l+l++++++a+ +++++g+++tvv+h
  gi|121637899|ref|YP_978122.1| 165 SCWRIKLPHVEAAKFDAALQSHLDALIAEykrdhdnsDGVSDQRPPLPGNVEAFLRLVEAGWDAEVARRPHGQHTTVVMH 244
                                    ******************************************************************************** PP

                         DUF222 234 vtaeeltaaaggaaltgggglLpasdvrrLAkdAtlaifdepagrpldlgrtkrtasaalrralraRD 301
                                    ++++e+ a  ++      g+lL++s++r+L++dAt++ ++e++g+ +++grt+r+++++lrral++RD
  gi|121637899|ref|YP_978122.1| 245 LDVQERAAGLHL------GPLLSESERRYLLCDATFEAWFERDGQVIGCGRTTRQINRRLRRALEHRD 306
                                    ************......9************************************************9 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   1.9   6.9e-11   3.1e-07       4      46 ..     314     352 ..     309     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6.9e-11
                            HNH   4 CgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                    Cg +      l+ +Hi ++ +gga+++ Nl+l+C+  H+++h+
  gi|121637899|ref|YP_978122.1| 314 CGAT----RGLHAHHIRHWQDGGATELANLVLVCPYHHRAHHR 352
                                    6666....6799***************************9997 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.9   3.6e-05      0.16       1      71 [.     309     357 ..     309     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                          HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfaf 71 
                                    Cv+ g+ + + l+a+HI            +++ +                +N+ l +p +H++++++l+++
  gi|121637899|ref|YP_978122.1| 309 CVVPGCGATRGLHAHHIRH----------WQDGG------------ATELANLVLVCPYHHRAHHRGLITI 357
                                    8996766666899999999..........55555............789********************98 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0003       1.4      12      37 ..     231     256 ..     227     257 .. 0.88
   2 ?   -1.3   0.0      0.82   3.7e+03       7      18 ..     286     297 ..     285     303 .. 0.79
   3 ?   -0.1   0.7      0.35   1.5e+03       6      25 ..     312     330 ..     307     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                        zf-ISL3  12 tvvkhgkkerrvrhlpiggkrvyLrl 37 
                                     ++ hg++++ v+hl+++++ + L+l
  gi|121637899|ref|YP_978122.1| 231 ARRPHGQHTTVVMHLDVQERAAGLHL 256
                                    6689****************999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.82
                        zf-ISL3   7 nCgsktvvkhgk 18 
                                    +Cg++t++++ +
  gi|121637899|ref|YP_978122.1| 286 GCGRTTRQINRR 297
                                    6****9998854 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.35
                        zf-ISL3   6 PnCgsk.tvvkhgkkerrvrh 25 
                                    P+Cg++  ++ h    r +++
  gi|121637899|ref|YP_978122.1| 312 PGCGATrGLHAHH--IRHWQD 330
                                    89***95556554..888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3091.60
//
Query:       gi|121637900|ref|YP_978123.1|  [L=191]
Description: hypothetical protein BCG_2033 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   10.9   0.0       0.31   10.5   0.0    1.1  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.7e-05      0.31       6      52 ..      26      73 ..      17      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.7e-05
                                   .S-EEE......-THHHHCTB--..........-------HHHH.... CS
                          RVT_1  6 pgsyRpisllsvdykalnkliakrLkdvl.ekllsenqpgfrpgrstl 52
                                   + ++Rp   +++  ++l++li++r++ +l   + s++ + ++++  t 
  gi|121637900|ref|YP_978123.1| 26 MRNWRPGWFPTMHSRCLSNLIHDRIWAHLvTLIASNPGTSIKDKGATR 73
                                   679***77********************95555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1345.83
//
Query:       gi|121637901|ref|YP_978124.1|  [L=346]
Description: regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-23   81.7   0.0    6.5e-23   81.0   0.0    1.3  1  Peptidase_M78    IrrE N-terminal-like domain
    2.7e-16   59.4   0.0    6.4e-16   58.1   0.0    1.7  1  HTH_3            Helix-turn-helix
    6.8e-14   52.0   0.0    6.8e-14   52.0   0.0    2.7  4  HTH_31           Helix-turn-helix domain
    1.9e-08   34.2   0.0    4.9e-08   32.9   0.0    1.8  1  HTH_19           Helix-turn-helix domain
      4e-05   23.5   0.0      0.044   13.7   0.0    3.2  3  HTH_37           Helix-turn-helix domain
     0.0004   19.9   0.1    0.00097   18.6   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00075   19.6   0.0     0.0016   18.5   0.0    1.5  1  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
     0.0023   18.3   0.1     0.0091   16.4   0.0    2.0  2  HTH_26           Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
       0.05   13.6   0.0          4    7.5   0.0    2.9  3  Phage_lysozyme2  Phage tail lysozyme


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   3.2e-26   6.5e-23       2     122 ..     154     264 ..     153     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 3.2e-26
                  Peptidase_M78   2 erlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlereanaf 81 
                                    e  g  v+++d++ + +dg + +  + +v+++n+n +p r+r tlaHElgHl+lh+++           +e +e ea+af
  gi|121637901|ref|YP_978124.1| 154 EAAGCLVFEEDFATQRIDGLSQWVDDYPVMLINANAAPDRKRLTLAHELGHLVLHSTN----------PTENMETEATAF 223
                                    78899*****************************************************..........89********** PP

                  Peptidase_M78  82 AaelllPeeaflalaatqrkdleerlaeyfgVSkeavavrl 122
                                    Aae+l+Pe ++++ + +      ++l++++gVS++a+  r+
  gi|121637901|ref|YP_978124.1| 224 AAEFLMPESEIRPELRRLDLGKLLELKREWGVSMQALLERA 264
                                    ***********88888777777779***********99885 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   3.2e-19   6.4e-16       4      54 ..      11      61 ..       8      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.2e-19
                                   HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                          HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                   +Rk++gl+q eLAe++G+++ +i+r+E+G+r P++ ++ kla+ Lgv+ d 
  gi|121637901|ref|YP_978124.1| 11 ARKARGLTQIELAELVGLTQPAINRYESGDRDPDQHIVAKLAEILGVTDDL 61
                                   8**********************************************9775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   3.4e-17   6.8e-14       2      61 ..       4      62 ..       3      64 .. 0.96
   2 ?   -3.2   0.0       5.6   1.1e+04      31      54 ..      89      99 ..      83     105 .. 0.54
   3 ?   -2.5   0.1       3.5     7e+03      30      30 ..     253     253 ..     235     285 .. 0.57
   4 ?   -2.9   0.0       4.5   9.1e+03      12      26 ..     314     328 ..     308     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.4e-17
                         HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpaer 61
                                   LG+ L+ +R+++GL+q e+Ae++g+++  ++r+E+G r+ p  + +++la++lg++++++
  gi|121637901|ref|YP_978124.1|  4 LGDVLAVARKARGLTQIELAELVGLTQPAINRYESGDRD-PDQHIVAKLAEILGVTDDLL 62
                                   8*************************************7.****************9975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.6
                         HTH_31 31 lsrlEqGrrgrpspavlealaral 54
                                   +++lE             a +++l
  gi|121637901|ref|YP_978124.1| 89 WRQLE-------------ARLNLL 99
                                   44444.............444444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.5
                         HTH_31  30 t 30 
                                    +
  gi|121637901|ref|YP_978124.1| 253 W 253
                                    2 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.5
                         HTH_31  12 raGLsqeevAerlgv 26 
                                     +G + +++A+ +g+
  gi|121637901|ref|YP_978124.1| 314 SRGFTDQQAAAIAGY 328
                                    467788888877775 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.5e-11   4.9e-08       3      62 ..       7      65 ..       5      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.5e-11
                         HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                    L  aR+ +gltq elae +g ++  i+ +E+g + +p+ + + k+ae+lg++ + l++g
  gi|121637901|ref|YP_978124.1|  7 VLAVARKARGLTQIELAELVGLTQPAINRYESGDR-DPDQHIVAKLAEILGVTDDLLIHG 65
                                   56779******************************.****************99988887 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.2e-05     0.044      25      54 ..      10      39 ..       3      56 .. 0.88
   2 ?   -1.5   0.0       1.3   2.5e+03      17      35 ..     271     290 ..     251     293 .. 0.62
   3 !    5.9   0.0    0.0064        13      14      46 ..     299     331 ..     292     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                   HHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                         HTH_37 25 eliekrelsqseaaqllgiaqPkvsrllrg 54
                                     +++r+l+q e+a+l g +qP ++r + g
  gi|121637901|ref|YP_978124.1| 10 VARKARGLTQIELAELVGLTQPAINRYESG 39
                                   57899*******************998866 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                    HHHHHH.HHHHHHHCT--HH CS
                         HTH_37  17 aqlala.iaeliekrelsqs 35 
                                    ++ a++ +++ + +r+++++
  gi|121637901|ref|YP_978124.1| 271 SAEARTkLYKAMNARGWKTK 290
                                    33344467778888887766 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0064
                                    HHHHHHHHHHHHHHHHCT--HHHHHHHHT--HH CS
                         HTH_37  14 kaKaqlalaiaeliekrelsqseaaqllgiaqP 46 
                                    + K +l + i  ++++r+ ++++aa++ g+a P
  gi|121637901|ref|YP_978124.1| 299 REKPSLPAHIGMTLRSRGFTDQQAAAIAGYANP 331
                                    56777777888999****************998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.9e-07   0.00097       8      37 ..       7      36 ..       5      36 .. 0.90
   2 ?   -3.6   0.0       4.4   8.7e+03      22      30 ..      50      58 ..      49      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.9e-07
                         HTH_24  8 ILelLqknprisqreLAerlglSpstvnrr 37
                                   +L + +k  +++q eLAe +gl+++++nr+
  gi|121637901|ref|YP_978124.1|  7 VLAVARKARGLTQIELAELVGLTQPAINRY 36
                                   6777788889******************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.4
                         HTH_24 22 eLAerlglS 30
                                    LAe lg++
  gi|121637901|ref|YP_978124.1| 50 KLAEILGVT 58
                                   599*99975 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     8e-07    0.0016      74     126 ..       8      61 ..       3      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8e-07
                 MqsA_antitoxin  74 iarvrkkleldqreaaeifGgGvnafsryekGkvrpplalv.kllklldrhPel 126
                                    +a  rk+ +l+q e+ae+ G    a +rye+G   p++ +v kl ++l    +l
  gi|121637901|ref|YP_978124.1|   8 LAVARKARGLTQIELAELVGLTQPAINRYESGDRDPDQHIVaKLAEILGVTDDL 61 
                                    55679999****************************998774677777666666 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.6e-06    0.0091       2      53 ..       8      58 ..       7      64 .. 0.89
   2 ?   -1.8   0.0       2.3   4.5e+03       1      15 [.     277     291 ..     277     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-06
                         HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct 53
                                   L ++ ++rg+t+ eLa+ +g++++ ++r+ +g  + ++ +  +k++++Lg+t
  gi|121637901|ref|YP_978124.1|  8 LAVARKARGLTQIELAELVGLTQPAINRYESGD-RDPDQHIVAKLAEILGVT 58
                                   5667799*************************9.89999***********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                         HTH_26   1 kLrelmadrgitkse 15 
                                    kL ++m +rg +++e
  gi|121637901|ref|YP_978124.1| 277 KLYKAMNARGWKTKE 291
                                    68899******8876 PP

>> Phage_lysozyme2  Phage tail lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   2.2e+02      72     126 ..      95     146 ..      73     179 .. 0.72
   2 ?    0.1   0.0      0.36   7.2e+02      49      89 ..     171     211 ..     137     228 .. 0.72
   3 ?    7.5   0.0     0.002         4       6      27 ..     308     329 ..     306     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                Phage_lysozyme2  72 nwkdlevqlefllkelknqysssektakkalksatsveeaakaflksferpgdes 126
                                    + + l+v   fl++e+     +se+++ ++  + t++e+aa+ + +++  p ++ 
  gi|121637901|ref|YP_978124.1|  95 RLNLLRVHASFLFEEVAI---NSEQHVPAFDPEFTAAEDAARLVRAQWRMPMGPV 146
                                    445666777777777776...4555555555577889999999999998887764 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                Phage_lysozyme2  49 yGlvQWtgsrrtallkyakakgknwkdlevqlefllkelkn 89 
                                     Gl QW ++   +l+++ +a + +  +l+ +l  l+ + +n
  gi|121637901|ref|YP_978124.1| 171 DGLSQWVDDYPVMLINANAAPDRKRLTLAHELGHLVLHSTN 211
                                    48889998888888887777777777888777777766666 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.002
                Phage_lysozyme2   6 iynyliskglskeaaAGilGni 27 
                                    i   l+s+g+++++aA+i G  
  gi|121637901|ref|YP_978124.1| 308 IGMTLRSRGFTDQQAAAIAGYA 329
                                    567899************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2559.15
//
Query:       gi|121637902|ref|YP_978125.1|  [L=239]
Description: hypothetical protein BCG_2035 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-11   41.4   0.0    3.5e-10   39.6   0.0    2.0  2  DUF433        Protein of unknown function (DUF433)
     0.0067   15.8   0.0      0.013   14.9   0.0    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
  ------ inclusion threshold ------
       0.03   14.1   0.0        4.8    7.1   0.0    2.5  2  HTH_23        Homeodomain-like domain
       0.12   12.6   0.2       0.95    9.6   0.0    2.4  3  HTH_28        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   5.8e+03      34      41 ..     151     158 ..     145     163 .. 0.73
   2 !   39.6   0.0   7.9e-14   3.5e-10       1      53 [.     183     234 ..     183     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                    HHHHHHHH CS
                         DUF433  34 ieeiledy 41 
                                    ++ei+e+y
  gi|121637902|ref|YP_978125.1| 151 FKEIVEHY 158
                                    67888888 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 7.9e-14
                                    EEE-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHH CS
                         DUF433   1 ItidpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaal 53 
                                    ++ dp+   G+Pv+ g  ++V+++l+ l+aG++++ +++dy ++t++++++al
  gi|121637902|ref|YP_978125.1| 183 VVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDY-GVTPDQLRDAL 234
                                    5789*************************************.**********9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     3e-06     0.013      24      51 ..     210     237 ..     206     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-06
                   HTH_Tnp_ISL3  24 llesrsvkavArqlgvSwtTVwrildry 51 
                                    l+ +++++avA+++gv+++ ++++ld++
  gi|121637902|ref|YP_978125.1| 210 LRAGATFQAVADDYGVTPDQLRDALDAI 237
                                    56779*******************9986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0083        37      16      43 ..      13      40 ..       7      47 .. 0.83
   2 ?    7.1   0.0    0.0011       4.8      10      38 ..     206     234 ..     200     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0083
                         HTH_23 16 e.GlsvreIAreLgvsrrTvyrwlkryre 43
                                   +  ++ +e++r L v+r T+  w   y e
  gi|121637902|ref|YP_978125.1| 13 VpLYTLAEASRYLVVPRATLATWADGY-E 40
                                   467999*****************9988.3 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                         HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwl 38 
                                    +l  l+ G++ +++A+ +gv++ +++  l
  gi|121637902|ref|YP_978125.1| 206 VLGPLRAGATFQAVADDYGVTPDQLRDAL 234
                                    5667888***************9998766 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.37   1.7e+03      16      37 ..      19      40 ..      16      42 .. 0.76
   2 ?   -3.4   0.0       2.4   1.1e+04       4      12 ..     153     161 ..     152     165 .. 0.79
   3 ?    9.6   0.0   0.00021      0.95       4      34 ..     205     235 ..     204     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.37
                         HTH_28 16 reaArelgisrrtvyrWikrye 37
                                   +ea+r l + r t+  W   ye
  gi|121637902|ref|YP_978125.1| 19 AEASRYLVVPRATLATWADGYE 40
                                   566666667899*****99998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                         HTH_28   4 eiikllaaG 12 
                                    ei+++++++
  gi|121637902|ref|YP_978125.1| 153 EIVEHYLQQ 161
                                    899999986 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00021
                         HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWik 34 
                                     ++ +l aG +  ++A  +g++++++++ + 
  gi|121637902|ref|YP_978125.1| 205 DVLGPLRAGATFQAVADDYGVTPDQLRDALD 235
                                    6899***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1884.81
//
Query:       gi|121637903|ref|YP_978126.1|  [L=138]
Description: hypothetical protein BCG_2036 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-17   63.1   0.1    3.2e-17   62.5   0.1    1.2  1  PIN_10    PIN like domain


Domain annotation for each model (and alignments):
>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   1.8e-21   3.2e-17       2      83 ..      13      95 ..      13      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.8e-21
                         PIN_10  2 kfflDenlppa.lakaLrelleeeghevvhlrdkf....aagtkDeeWiaalaeggwvvltkDrrirkrpaEraalreaglr 78
                                   ++f+D++l+   +++ Lr     +g++++++r+++    a++++D++Wia  ae gw+  +kD++ir++  Er+ ++++g+r
  gi|121637903|ref|YP_978126.1| 13 HIFVDRSLGAVqVPQLLR----DAGFRLTTMREHYgetqAQSVSDHKWIAMTAECGWIGFHKDANIRRNAVERRTVLDTGAR 90
                                   69********99******....************************************************************ PP

                         PIN_10 79 vfila 83
                                   +f++ 
  gi|121637903|ref|YP_978126.1| 91 LFCVP 95
                                   ***86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1199.43
//
Query:       gi|121637904|ref|YP_978127.1|  [L=99]
Description: hypothetical protein BCG_2037c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.8e-10   38.1   0.0    1.1e-09   37.7   0.0    1.1  1  Type_ISP_C  Type ISP C-terminal specificity domain


Domain annotation for each model (and alignments):
>> Type_ISP_C  Type ISP C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   6.3e-14   1.1e-09     304     343 .]      38      78 ..      36      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6.3e-14
                     Type_ISP_C 304 ksaleWlkdrykrktdkasgilndpnewak.leeteellel 343
                                    +sal W+++ry+++tdkasgi+ndpn+w+  +++++++++l
  gi|121637904|ref|YP_978127.1|  38 RSALGWIIERYRVTTDKASGIVNDPNDWCDeHDDPTYIVDL 78 
                                    89****************************9*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 879.84
//
Query:       gi|121637905|ref|YP_978128.1|  [L=101]
Description: hypothetical protein BCG_2038c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-13   49.5   0.3    3.6e-13   49.3   0.3    1.1  1  HTH_37      Helix-turn-helix domain
    2.2e-10   40.4   0.2    2.9e-10   40.0   0.2    1.1  1  HTH_3       Helix-turn-helix
    3.5e-10   40.1   0.9    5.5e-10   39.4   0.9    1.3  1  HTH_31      Helix-turn-helix domain
      2e-07   30.9   0.0    2.9e-07   30.4   0.0    1.2  1  HTH_19      Helix-turn-helix domain
    3.4e-06   26.8   0.2      5e-06   26.3   0.2    1.3  1  HTH_25      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.025   14.1   0.9      0.051   13.1   0.3    1.9  2  Sigma70_r4  Sigma-70, region 4
      0.028   14.9   0.0      0.042   14.3   0.0    1.3  1  HTH_26      Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.3   1.4e-16   3.6e-13      20      80 .]      32      92 ..      15      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.4e-16
                                   HHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTEEEEEEEE CS
                         HTH_37 20 alaiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGqkveivvk 80
                                   a +++el++++ l+q ++a+l +i q++vs++++g++ +  +++L++++ alG+++ i v+
  gi|121637905|ref|YP_978128.1| 32 AFRLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGGELDITVR 92
                                   344*******************************************************996 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.1e-13   2.9e-10       1      53 [.      35      88 ..      35      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.1e-13
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHHTSEHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaLgvsld 53
                                   l+elR ++ l+q ++A+++ + +s +s iEnG + +  + tl k+  aLg +ld
  gi|121637905|ref|YP_978128.1| 35 LRELRAAQSLTQVQVAALAHIRQSRVSSIENGdIGSAQVNTLRKYVSALGGELD 88
                                   89************************************************8876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.9   2.1e-13   5.5e-10       5      56 ..      34      85 ..      32      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.1e-13
                         HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                                   +Lr+lR+++ L+q +vA+++++ +s++s +E+G +g  +  +l++++ alg 
  gi|121637905|ref|YP_978128.1| 34 RLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGG 85
                                   8*************************************************95 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.1e-10   2.9e-07       3      56 ..      34      87 ..      33      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.1e-10
                         HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56
                                   rL+e+R    ltq ++a  ++i++s+ s iEng +  +  ++l+k++ alg +l
  gi|121637905|ref|YP_978128.1| 34 RLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALGGEL 87
                                   9**********************************9999***********9765 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   1.9e-09     5e-06       1      52 [.      34      84 ..      34      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                                   HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTSS-HHHHHHHHHHHH CS
                         HTH_25  1 rLraaRearglsleevaketkIrkdylealEeddfdalpepvylrgylrnYA 52
                                   rLr+ R a++l+  +va+  +Ir++ +  +E++d+ +    + lr y+ ++ 
  gi|121637905|ref|YP_978128.1| 34 RLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNT-LRKYVSALG 84
                                   7*********************************99888775.677766655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.63   1.6e+03      33      49 ..      15      31 ..      11      32 .. 0.77
   2 ?   13.1   0.3     2e-05     0.051      15      42 ..      38      65 ..      26      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                                   -HHHHHHHHHHHHHHHH CS
                     Sigma70_r4 33 SrerVrqiekrAlrkLR 49
                                    re+V ++++r ++ +R
  gi|121637905|ref|YP_978128.1| 15 NREAVDRHKARMRDEVR 31
                                   68888888888877777 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2e-05
                                   HHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                     Sigma70_r4 15 lrfgeglTleEIgerlgiSrerVrqiek 42
                                   lr  + lT+ ++++  +i ++rV++ie+
  gi|121637905|ref|YP_978128.1| 38 LRAAQSLTQVQVAALAHIRQSRVSSIEN 65
                                   445899********************95 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.042       1      51 [.      34      84 ..      34      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                         HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                   +Lrel a+  +t+ ++a  + i ++ +s + +g + +   +tL k   aLg
  gi|121637905|ref|YP_978128.1| 34 RLRELRAAQSLTQVQVAALAHIRQSRVSSIENGDIGSAQVNTLRKYVSALG 84
                                   8********************************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 847.48
//
Query:       gi|121637906|ref|YP_978129.1|  [L=201]
Description: hypothetical protein BCG_2039c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-22   78.5   0.0    4.5e-22   78.0   0.0    1.2  1  Gp49      Phage derived protein Gp49-like (DUF891)


Domain annotation for each model (and alignments):
>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   2.5e-26   4.5e-22       1      89 [.      86     181 ..      86     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2.5e-26
                           Gp49   1 eeldalpkkarakilaaldlleeggpdlgkplvkkle....dglwElrpksag.giiRvlyafdpgrkvilLhafqKkt. 74 
                                    ++l+ l+ ++++ ++aa++ lee+gp lg plv++++    ++++Elrp s+g +++R+l+afdp+r++i+L a++K++ 
  gi|121637906|ref|YP_978129.1|  86 AWLNGLDRETYELVFAAIEVLEEEGPALGCPLVDTVRgsrhKNMKELRPGSQGrSEVRILFAFDPARQAIMLAAGNKAGr 165
                                    59***********************************************999999************************8 PP

                           Gp49  75 .qktpkkeielAekrl 89 
                                     +++++++i+ A++ +
  gi|121637906|ref|YP_978129.1| 166 wTQWYDEKIKAADEMF 181
                                    88**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1464.83
//
Query:       gi|121637907|ref|YP_978130.1|  [L=119]
Description: hypothetical protein BCG_2040c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 894.57
//
Query:       gi|121637908|ref|YP_978131.1|  [L=225]
Description: hypothetical protein BCG_2041c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1701.78
//
Query:       gi|121637909|ref|YP_978132.1|  [L=298]
Description: hypothetical protein BCG_2042c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2328.84
//
Query:       gi|121637910|ref|YP_978133.1|  [L=1606]
Description: hypothetical protein BCG_2043c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.4e-106  356.4   0.0     2e-106  355.9   0.0    1.2  1  Type_ISP_C  Type ISP C-terminal specificity domain
    3.3e-47  159.5   0.0    6.7e-47  158.5   0.0    1.5  1  Mrr_cat_2   Restriction endonuclease
    1.8e-28   99.7   0.0    3.5e-28   98.7   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
    2.6e-08   33.8   0.1    2.9e-07   30.4   0.0    2.5  2  DEAD        DEAD/DEAH box helicase
    2.2e-06   27.7   0.0    7.6e-06   25.9   0.0    2.0  1  Mrr_cat     Restriction endonuclease
    1.2e-05   25.6   0.0      5e-05   23.6   0.0    2.1  2  Helicase_C  Helicase conserved C-terminal domain
    0.00077   18.8   0.0     0.0016   17.8   0.0    1.5  1  N6_Mtase    N-6 DNA Methylase
      0.003   17.3   0.0     0.0081   15.9   0.0    1.7  1  SWI2_SNF2   SWI2/SNF2 ATPase
  ------ inclusion threshold ------
      0.048   14.2   0.0        0.9   10.1   0.0    2.8  3  Eco57I      Eco57I restriction-modification methylase


Domain annotation for each model (and alignments):
>> Type_ISP_C  Type ISP C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.9   0.0  9.9e-110    2e-106       2     343 .]    1199    1577 ..    1198    1577 .. 0.94

  Alignments for each domain:
  == domain 1  score: 355.9 bits;  conditional E-value: 9.9e-110
                     Type_ISP_C    2 lfplyslGvktnRDawvynfskeelekrikrlideyneevkrkk..............kktkdstkikwsralkkdlk 65  
                                     +f +ys G+kt+RDaw+ynfs+ +le++i r id+yn+ev+r +               +t ds k++w r  k++++
  gi|121637910|ref|YP_978133.1| 1199 VFANYSAGLKTSRDAWCYNFSRGALEANIGRTIDFYNSEVDRINeirgrdaktppvdaLITVDSAKFSWDRINKRQVA 1276
                                     89*****************************************9777777777777666666**************** PP

                     Type_ISP_C   66 knkklefdeekiveilYRPFdkqwlyydkr..lierprqlpelfphlskenlvivvsgsgsgkgfsvlvtdlipdlhl 141 
                                     +++++ef +  ++   YRPF+k++ y d++  l++  +qlp++fp+ ++ n++  v g gs+k+fs+l+ + ipdl +
  gi|121637910|ref|YP_978133.1| 1277 QGIRIEFAPAGMRLGTYRPFTKEHAYLDPNqqLNNCTYQLPSMFPTPEHGNVGYYVVGMGSDKPFSCLMLNAIPDLAF 1354
                                     ****************************9999********************************************** PP

                     Type_ISP_C  142 lskrggqvfPlylyeeee.snlaag.................erkdnitdellaefreayggatitkedifyYiYAvl 201 
                                       +++gq+fP+++ye++e ++   g                 +r dnit  +l+ +r+ + g ++tk+difyY+Y++l
  gi|121637910|ref|YP_978133.1| 1355 WGSSNGQFFPRWTYEKTEpRD---GeldfesttnaevddhgyRRVDNITGVILKLYRD-TIGDQVTKDDIFYYVYGLL 1428
                                     ******************532...2345779999**********************99.******************* PP

                     Type_ISP_C  202 hspeYrerYaedLkkdlpRiPltkdfelFkelvelGreLadLhlnyes.epleegietep.....eegdnrvekmkyk 273 
                                     h+p+Yr++Ya+dLkk+lp+iP+++ +e+F++l+ +Gr+LadLh++yes +p++ +++ +p     +++++rvekmk+k
  gi|121637910|ref|YP_978133.1| 1429 HDPAYRTKYAADLKKMLPHIPTPETRERFDQLASAGRKLADLHVGYESvKPYPLDVQLKPgadpeDRETWRVEKMKWK 1506
                                     ************************************************888888885555444458888********* PP

                     Type_ISP_C  274 kkkdkgtiiindeitlegvpeeaweYkvgGksaleWlkdrykrktdkasgilndpnewak.leeteellel 343 
                                     +k+d++tii+n+++t++g+p ea +Y +g +sal W++dry+++tdkasgi+ndpn+w+  + +++++++l
  gi|121637910|ref|YP_978133.1| 1507 SKQDHSTIIYNSRVTIAGIPDEAERYLLGSRSALGWIIDRYRVTTDKASGIVNDPNDWCDeHANPTYIVDL 1577
                                     ***********************************************************9999*****987 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   0.0   3.4e-50   6.7e-47       2     121 ..      34     151 ..      33     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 3.4e-50
                      Mrr_cat_2   2 tdpayaeefkeVwlwkewpeekrlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrlii 81 
                                     dp++a++++ Vw+w +wp  +r g++DtGIDlVa+er++g+y+AIQcKfY++++++ k+didsF++asgk+ ft+r+ii
  gi|121637910|ref|YP_978133.1|  34 LDPTMAQQYDAVWRWIDWP--ERRGRTDTGIDLVARERDTGNYTAIQCKFYEPTHTLAKGDIDSFFTASGKTGFTNRVII 111
                                    69*****************..5569******************************************************* PP

                      Mrr_cat_2  82 sTtdkwsknaeealknqkipvkridledLeeseidwskls 121
                                    sTtd+w++nae+al++q  pv+ri++++++es+idw+ ++
  gi|121637910|ref|YP_978133.1| 112 STTDRWGRNAEDALADQLVPVQRIGMAEIAESPIDWDIAW 151
                                    ************************************9776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   1.7e-31   3.5e-28       2     170 ..     166     363 ..     165     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.7e-31
                                    -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG CS
                         ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkflse 80 
                                    +elr++Q++ai+++   +   ++ rg + ma+GtGKT++a+k++er++  ++ + ++l+lvp++sll+qtl+e++  ++ 
  gi|121637910|ref|YP_978133.1| 166 HELRPHQQQAIDAVFRGFA-VGNDRGKLIMACGTGKTFTALKIAERIAADNGGSaRILLLVPSISLLSQTLREWTAQSEL 244
                                    68****************9.**************************987766556*******************777777 PP

                                    ........GEEEESSS-B--..............................-SEEEEEHHHHHHTH........HHHTTT- CS
                         ResIII  81 ayke....igkkvsgdkkka.......................kekdstnkkilvttiqsldadseeeeeeseellrdrf 133
                                    ++ +      +kvs     +                       +++ ++   +++ t+qsl         + ++l+ d+f
  gi|121637910|ref|YP_978133.1| 245 DVRAfavcSDTKVSRSA--EdyhvhdvpipvttdarvllhemaHRRCAQGLTVVFCTYQSLPTVA-----KAQRLGVDEF 317
                                    76656644222222222..233566777778888888899998999999************9999.....99******** PP

                                    SEEEEETGGGTTS........TTTHHH..HHT---SEEEEEESS-S CS
                         ResIII 134 dviiiDEaHrlgak.......kswrei..lekfkeavllglTATpe 170
                                    d++ +DEaHr+++        +++ ++   +++k+a +l++TATp+
  gi|121637910|ref|YP_978133.1| 318 DLVMCDEAHRTTGVtlagddeSNFVRVhdGQYLKAARRLYMTATPR 363
                                    *************9666555449999988899*************7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.6   7.1e+03      23      36 ..      98     111 ..      95     120 .. 0.80
   2 !   30.4   0.0   1.5e-10   2.9e-07       2     170 ..     170     363 ..     169     368 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                                    TTSSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxx RF
                           DEAD  23 TGsGKTlaflipvl 36 
                                    T+sGKT+     ++
  gi|121637910|ref|YP_978133.1|  98 TASGKTGFTNRVII 111
                                    99****98777766 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 1.5e-10
                                    HHHHHHHHHHHTTCEEE.....EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvl.....vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                    + Q++ai+++ +g  v      + ++ G+GKT  +l  + +i +  ++    ++l+++P+ +L  qtl++++   + +d+
  gi|121637910|ref|YP_978133.1| 170 PHQQQAIDAVFRGFAVGndrgkLIMACGTGKTFTALKIAERIAA--DNGGSARILLLVPSISLLSQTLREWTAQSE-LDV 246
                                    789999999997744444444577889******97766665554..588899*******************99888.788 PP

                                    EEEEEETTSSHHHHHHHHH.TTCSEEEEEHHHHHHHH........................HCTSSHCTTEEEEEEETHH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxx RF
                           DEAD  77 rvlliiggvaardqlskld.ngvdivvgtpgrlddll........................stgklnlsqvrflVlDEad 131
                                    r+ ++ ++++ ++  ++ + ++v i v+t  r++ +                         + ++l ++++ ++  DEa+
  gi|121637910|ref|YP_978133.1| 247 RAFAVCSDTKVSRSAEDYHvHDVPIPVTTDARVLLHEmahrrcaqgltvvfctyqslptvaKAQRLGVDEFDLVMCDEAH 326
                                    8888877655555555554255888888887776654567777777777777777777776888999************* PP

                                    HHHHTTTHHHHHHHHHHSHHHCTTST..TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                           DEAD 132 rlldqgfsdfinrilnqlpqitcdgk..lqrqvivlSATlp 170
                                    r        + ++ + ++    +dg+  +  + + ++AT+ 
  gi|121637910|ref|YP_978133.1| 327 RTTGVTLAGDDESNFVRV----HDGQylKAARRLYMTATPR 363
                                    *99884444434333333....1222213345888888875 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.8e-09   7.6e-06       6     106 ..      21     135 ..      17     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.8e-09
                                    TTCHHHHHHHHHHHHSSS...........EEE---B-TTSSB--EEEETTEEEEEEEEEEE--T..S-B-HHHHHHHHHH CS
                        Mrr_cat   6 pkeFeklvaellealGyk...........eveltgrsgDggiDliakkdplgserilvqaKryk..nkvgvkeVqeliga 72 
                                    +++Fe+l+ +++e +              +    +++ D giDl+a++++ g   +++q+K y+  ++  + ++ +++ a
  gi|121637910|ref|YP_978133.1|  21 GTKFEQLMVRYFELDPTMaqqydavwrwiDWPERRGRTDTGIDLVARERDTG-NYTAIQCKFYEptHTLAKGDIDSFFTA 99 
                                    66777777777776433333333555444333666788**********9988.999*******65599************ PP

                                    CTTS..SEEEEEE.SS-B-HHHHHHHHT.T--EEEE CS
                        Mrr_cat  73 lkkrgadkgifvt.tsdftkaAreeaee.lnkieLl 106
                                      k g+++ ++++ t++  ++A+++ ++ l +++ +
  gi|121637910|ref|YP_978133.1| 100 SGKTGFTNRVIIStTDRWGRNAEDALADqLVPVQRI 135
                                    *****8887777725669999987765514466555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.5e-08     5e-05      40     110 ..     505     579 ..     464     580 .. 0.73
   2 ?   -3.0   0.0       4.7   9.3e+03      39      70 ..    1009    1041 ..    1002    1047 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
                                    TSTEEEESTTSTHHHHHHHHHHHH....TTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  40 gikvavlhgelpqnereeileqfn....kgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    + +v  ++g+ ++  r+e l+  +    ++e+++L   + +++G+d+p ++ V ++++  ++ +++q++GR++R 
  gi|121637910|ref|YP_978133.1| 505 ACSVRHVDGTFNALVRNEQLAWLKgvvaEDECRILSNARCLSEGVDVPALDAVLFLNPRNSIVDVVQSVGRVMRK 579
                                    456667777777777777777777666789999****************************************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                                     TTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EE CS
                     Helicase_C   39 kgikvavlhgelpqnereeileqfnkgesd.vL 70  
                                      ++k+ +l+g+++q   +++ +q ++  +d ++
  gi|121637910|ref|YP_978133.1| 1009 ANVKYPTLDGRIEQTYAKRSTAQLKNSLYDsYI 1041
                                     4789999*******9999999999998888666 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.2e-07    0.0016       3     151 ..     822    1013 ..     820    1038 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.2e-07
                       N6_Mtase    3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivell...........epksgesvyDpacGsggll...vqaek 66  
                                     + ++ ++YE + r   +++++  G ++TP ev+ +iv+ +            + +g  ++D  +G+g ++   +q++ 
  gi|121637910|ref|YP_978133.1|  822 QQVIAELYEKFFRIGFKKQAEALGIVYTPVEVVDFIVRAAdfvsrkhfgrgLTDEGVHILDGFAGTGTFItrlLQSDL 899 
                                     568899*******9999**********************9999999999987778888***********722144444 PP

                       N6_Mtase   67 vlkeedgktkelsiyGqeknettyrLakmNl..llhgieykkvk.........irlgdtlekpkfe............ 121 
                                        ++   + + +++  e+   +y +a +N+    h  + k+++         ++l+dt++  +              
  gi|121637910|ref|YP_978133.1|  900 ITAADLTRKYSQELHANEIMLLAYYIAAVNIesTYHALAGKTADadayepfpgMALADTFQISEAGdsmdaimfpynn 977 
                                     334445566677788888888888888888644445554444333445566666667777665555788889999999 PP

                       N6_Mtase  122 ......kdkkfdvvvaNppfnqkewkektlekderf 151 
                                             + + v++ Npp++  + + ++l+ + ++
  gi|121637910|ref|YP_978133.1|  978 arilrqLATPISVIIGNPPYSVGQSSANDLNANVKY 1013
                                     998887778889999999998886666666666655 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.1e-06    0.0081       1     160 [.     171     365 ..     171     413 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
                      SWI2_SNF2   1 qQyravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakag....... 73 
                                    +Q  a+ ++ +    g+++ G +    G GK++t +++a+++++++  ++++++++    L +Q+ ++ ++ +       
  gi|121637910|ref|YP_978133.1| 171 HQQQAIDAVFRGFAVGNDR-GKLIMACGTGKTFTALKIAERIAADNGGSARILLLVPSISLLSQTLREWTAQSeldvraf 249
                                    5667777777777766444.4444678*****************899********************9998742333333 PP

                      SWI2_SNF2  74 ....eekpkqaesrk........................eLkellekesekiifttiqKfeeeek............... 110
                                        +         +                         L+e+                    +               
  gi|121637910|ref|YP_978133.1| 250 avcsD---------TkvsrsaedyhvhdvpipvttdarvLLHEMA-------------------Hrrcaqgltvvfctyq 301
                                    32221.........2112222233344444444443332222222...................1233334444444444 PP

                      SWI2_SNF2 111 .....eklevlsereniivlvDEaHRsqyg.........elakklrkalpnaafigFTGTPilk 160
                                         +k + l  +e  +v++DEaHR+             ++ +  + l+ a ++ +T TP   
  gi|121637910|ref|YP_978133.1| 302 slptvAKAQRLGVDEFDLVMCDEAHRTTGVtlagddesnFVRVHDGQYLKAARRLYMTATPRIF 365
                                    444444567777777789*********8776667766543444445778888888888888554 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.69   1.4e+03       5      59 ..     460     513 ..     458     526 .. 0.77
   2 ?   -2.1   0.0       2.7   5.3e+03      22      51 ..     819     848 ..     811     850 .. 0.78
   3 ?   10.1   0.0   0.00045       0.9       4      21 ..     989    1006 ..     986    1082 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.69
                         Eco57I   5 viiGNPPYqeseakkelkaleekakdiyqkFvekalkledkylaliiparflasg 59 
                                    ++ G PP +++ a  +  +++++ ++++ k ve   +l d   +l ++ r++  g
  gi|121637910|ref|YP_978133.1| 460 IVAGEPPMRRAVAFAKDIKTSKQVAELFPKVVEAYRELVDDGPGLACSVRHV-DG 513
                                    789*******998777666888899999999999888888877777777776.44 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                         Eco57I  22 kaleekakdiyqkFvekalkledkylalii 51 
                                    +++++  +++y+kF+  ++k + ++l++++
  gi|121637910|ref|YP_978133.1| 819 EGKQQVIAELYEKFFRIGFKKQAEALGIVY 848
                                    455677899*******99998888887776 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00045
                         Eco57I    4 dviiGNPPYqeseakkel 21  
                                      viiGNPPY   +++ + 
  gi|121637910|ref|YP_978133.1|  989 SVIIGNPPYSVGQSSAND 1006
                                     79*******998844433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.02u 0.27s 00:00:01.29 Elapsed: 00:00:00.46
# Mc/sec: 10563.44
//
Query:       gi|121637911|ref|YP_978134.1|  [L=332]
Description: hypothetical protein BCG_2044c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-43  146.6  12.9    9.4e-43  146.3  12.9    1.1  1  Cation_efflux  Cation efflux family
    5.6e-16   58.4   1.0    4.9e-15   55.4   0.3    2.3  2  ZT_dimer       Dimerisation domain of Zinc Transporter


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3  12.9     1e-46   9.4e-43       2     199 .]      45     237 ..      44     237 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 1e-46
                  Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgl 81 
                                     +sll+  + al++++ +++++S+al ad +h+++d+++ + l++a+ l  kp+++r+++G+gr+e l++ ++ +++ + 
  gi|121637911|ref|YP_978134.1|  45 KISLLVLGLTALIQIVIVVMSGSVALAADTIHNFADALTAVPLWIAFALGAKPATRRYTYGFGRVEDLAGSFVVAMITMS 124
                                    68999*************************************************************************** PP

                  Cation_efflux  82 avfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvil 161
                                    a+ + +eai +li ++++ +h g++++ +lv+++ n +++l+ +r+g++++saal a+ lh+++D++tsl+vl+sa ++ 
  gi|121637911|ref|YP_978134.1| 125 AIIAGYEAIARLI-HPQQIEHVGWVALAGLVGFIGNEWVALYRIRVGHRIGSAALIADGLHARTDGFTSLAVLCSAGGVA 203
                                    *************.****************************************************************** PP

                  Cation_efflux 162 lfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                    l+     plaDp+++lli + il   +  +++ ++ Ll
  gi|121637911|ref|YP_978134.1| 204 LG----FPLADPIVGLLITAAILAVLRTAARDVFRRLL 237
                                    *7....588*************************9997 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.054   4.8e+02      51      72 ..      23      44 ..      21      48 .. 0.84
   2 !   55.4   0.3   5.4e-19   4.9e-15       2      78 ..     241     317 ..     240     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.054
                                   HHHHHHHHHHHHHHH-TT--EE CS
                       ZT_dimer 51 aHeiadevekrikeefpgvadv 72
                                   +H+ ad v + +++   g++ v
  gi|121637911|ref|YP_978134.1| 23 SHDAADSVDDTLESTAAGIRTV 44
                                   8***********9988887766 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 5.4e-19
                                    ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                       ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                    d++++++ ++++++ pgv+ v ++r+r +G+++++d ++ vd+ l + +aH+ia++ e+++ + +p+++  liH  P
  gi|121637911|ref|YP_978134.1| 241 DPAMVDAAEQALAARPGVQAVRSVRMRWIGHRLHADAELDVDPALDLAQAHRIAHDAEHELTHTVPKLTTALIHAYP 317
                                    56788899999999************************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2314.77
//
Query:       gi|121637912|ref|YP_978135.1|  [L=294]
Description: hypothetical protein BCG_2045c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-55  185.3   4.1    1.4e-27   96.9   0.6    2.0  2  Usp        Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.1   1.2e-29   2.2e-25       5     141 .]      10     148 ..       9     148 .. 0.95
   2 !   96.9   0.6   7.7e-32   1.4e-27       5     141 .]     161     292 ..     159     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.2e-29
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHHHHCTTC CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaaaeaggv 80 
                                    IlV+vDgs +s +A+ wA+++a +r+ +++llh++ p   g+      +  +e++++ +++  ++a    ++ + e + +
  gi|121637912|ref|YP_978135.1|  10 ILVGVDGSAQSNAAVAWAAREAVMRQLPITLLHIVAPVVVGWPVGQLYANMTEWQKDNAQQVIEQArealTNSLGESKPP 89 
                                    9****************************************************************999888888899999 PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +v++++++ ++ ++++++  +++a l+VvGs g+++l rlllGS s ++l+ha cpV +++
  gi|121637912|ref|YP_978135.1|  90 QVHTELVFSNVVPTLIDA--SQQAWLMVVGSQGMGALGRLLLGSISTALLHHARCPVAIIH 148
                                    999999999999987775..677**********************************9985 PP

  == domain 2  score: 96.9 bits;  conditional E-value: 7.7e-32
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                    +lV++Dgs++s++A   A+++a +r  +l++lh++ +  + +v  +d+ ++e+++++ +ae+ a      ++++ ++v+v
  gi|121637912|ref|YP_978135.1| 161 VLVGIDGSPASEAATALAFDEASRRRVDLVALHAWTDLGMFPVLGMDWREREKREAEVLAERLA-----GWQEQYPDVRV 235
                                    8*************************************************************85.....68999999999 PP

                                    EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    ++     +++  +++ +e+a+l+VvGs+gr+g+s++llGSvs++v++++ +pV+vVr
  gi|121637912|ref|YP_978135.1| 236 HRSLVCDKPARWLLEHSEQAQLVVVGSHGRGGFSGMLLGSVSSAVAHSVRIPVIVVR 292
                                    9999999999999999999*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1887.01
//
Query:       gi|121637913|ref|YP_978136.1|  [L=573]
Description: histidine kinase response regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-25   89.8   9.4    1.1e-17   64.6   0.3    3.0  3  GAF_2        GAF domain
    4.6e-23   82.3   0.6    2.2e-14   54.2   0.0    2.6  2  GAF          GAF domain
    1.1e-18   67.9   0.1    2.6e-08   34.3   0.1    2.7  2  GAF_3        GAF domain
    3.4e-10   40.3   0.3    3.4e-10   40.3   0.3    3.1  3  HisKA_3      Histidine kinase
      1e-06   29.2   0.4    7.2e-06   26.5   0.4    2.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0024   17.8   1.3     0.0039   17.1   0.2    1.9  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0027   17.5   0.4     0.0049   16.7   0.4    1.3  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.3   4.2e-21   1.1e-17       4     138 .]      62     199 ..      59     199 .. 0.86
   2 !   29.6   1.3   2.7e-10     7e-07       3     137 ..     229     366 ..     227     367 .. 0.68
   3 ?   -2.2   0.0       1.8   4.7e+03       5      32 ..     491     520 ..     488     553 .. 0.68

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 4.2e-21
                                    HHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.---TTHHHHHHHHTS-EEES-GGG-S-HH CS
                          GAF_2   4 leelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldr.plgeglvgealrtgrpvilndleedpdkk 81 
                                    l+ +l++++ +++el +a++g +++   d++l+  ++ + +ee ++ + + p g+g++g  +++ +p+ l+d+ ++p++ 
  gi|121637913|ref|YP_978136.1|  62 LDATLRAIVHTAAELvDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSlPEGRGVLGALIEEPKPIRLDDISRHPASV 141
                                    7999**********889********5555775555777777777777755455***9*********************** PP

                                    HHHHHHHTT--EEEEEE-TTS---EEEEE.S......--HHHHHHHHHHHHHHHHHHH CS
                          GAF_2  82 glpaghaglrsflavPlisegrvvGvlnl.yankppafdeedlelLeelaeqiaiaie 138
                                    g p+ h+++r+fl+vP++ +++v+G l l   ++ ++f+++d  l+++la+ ++ia++
  gi|121637913|ref|YP_978136.1| 142 GFPLHHPPMRTFLGVPVRIRDEVFGNLYLtEKADGQPFSDDDEVLVQALAAAAGIAVD 199
                                    *****************99889******954555555*******************86 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.7e-10
                                    HHHHHHHHHHHHHHH.S.S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--......-TT.HHHHHHHHTS-EEES CS
                          GAF_2   3 dleelldlvldelve.l.g.aalgyillvdddgglrlaawgeaeeefgaaldrpl......geg.lvgealrtgrpviln 72 
                                    d+  +++l+ +e+++ + g a+l+ + l+d+++    ++      e+ +++++++       +g  +g +++++ p  + 
  gi|121637913|ref|YP_978136.1| 229 DPAMVFRLIAEEALTlMaGaATLVAVPLDDEAPA--CEVDDLVIVEVAGEISPAVkqmtvaVSGtSIGGVFHDRTPRRF- 305
                                    56668999*****995599777999999997777..3322222222222222211111123344345666666555554. PP

                                    -GGG-S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEE.S......--HHHHHHHHHHHHHHHHHH CS
                          GAF_2  73 dleedpdkkglp.aghaglrsflavPlisegrvvGvlnl.yankppafdeedlelLeelaeqiaiai 137
                                          d+  l+  g + +++ l++Pl++ + v Gvl+   ++++++f++ +l+++ ++a+q+a+a+
  gi|121637913|ref|YP_978136.1| 306 ------DRLDLAvDGPVEPGPALVLPLRAADTVAGVLVAlRSADEQPFSDKQLDMMAAFADQAALAW 366
                                    ......4444444799999999*******778*****9768999999******************96 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHS.S...EEEEEEE-TTS CS
                          GAF_2   5 eelldlvldelvel.gaa.lgyillvdddg 32 
                                    e +l+++++ +v+  +a+ l++ + v+dd 
  gi|121637913|ref|YP_978136.1| 491 EAVLREAVSNAVRHaNATsLAINVSVEDDV 520
                                    678888888888865744477766666543 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   8.5e-18   2.2e-14       2     133 .]      62     198 ..      61     198 .. 0.86
   2 !   25.8   0.2   5.3e-09   1.4e-05      21     132 ..     230     365 ..     222     366 .. 0.53

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 8.5e-18
                                    HHHHHHHHHHHHHHHHTESEEEE.EE........EEETTEEECEEEEECC..EEEETTSHHHHHHHHHSSSEEESTGGTS CS
                            GAF   2 leelldtvveelrellgadrval.yl........pdydGlhydipqasrw..lfmkngrgicgqvlatgqplvipdstpd 70 
                                    l+ +l+ +v +++el++a+++al  +          y+    +i+++ r      ++grg+ g+ +++++p++++d++++
  gi|121637913|ref|YP_978136.1|  62 LDATLRAIVHTAAELVDARYGALgVRgydhrlveFVYE----GIDEETRHliGSLPEGRGVLGALIEEPKPIRLDDISRH 137
                                    7899*******************522333444442244....599999998777777*******************9999 PP

                                    TTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHHH CS
                            GAF  71 prfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvaval 133
                                    p          l+++ +r++l+vP++ ++e++G l+l+ + +  pf+++++ l+q+la+ +++a+
  gi|121637913|ref|YP_978136.1| 138 PASVG----FPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADgqPFSDDDEVLVQALAAAAGIAV 198
                                    99888....68899*************************777789*****************996 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.3e-09
                                    EEEEEE.........................EEETTEEE.............CEEEEECC.EEEETTSHHHHHHHHHSSS CS
                            GAF  21 rvalyl.........................pdydGlhy.............dipqasrw.lfmkngrgicgqvlatgqp 61 
                                     +++++                         p      +             +i++a    +  + g++ +g v++ + p
  gi|121637913|ref|YP_978136.1| 230 PAMVFRliaeealtlmagaatlvavplddeaP------AcevddlvivevagEISPAVKQmTVAVSGTS-IGGVFHDRTP 302
                                    55554444433333332222222222222221......0223333222222222222222122222444.4445555555 PP

                                    EEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHH CS
                            GAF  62 lvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvava 132
                                     +++   + +         + ++ ++  +lv+Pl++ + + G+lv+ +  +  pf++ +l+++ ++adq+a+a
  gi|121637913|ref|YP_978136.1| 303 RRFD---RLDLA-------VDGPVEPGPALVLPLRAADTVAGVLVALRSADeqPFSDKQLDMMAAFADQAALA 365
                                    5555...33333.......3355666689*******************555668*****************98 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.2e-10   3.1e-07       2     129 .]      62     200 ..      61     200 .. 0.79
   2 !   34.3   0.1     1e-11   2.6e-08      80     126 ..     310     365 ..     269     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                          GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqva.agwdgkpalse..sldedsalarralssgevvsepsfaeedg. 77 
                                    ld +l ++++ +++l++a +gal+++  d + +  +  g+d++ +     sl+e+  +  +++++  ++   +  + ++ 
  gi|121637913|ref|YP_978136.1|  62 LDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVyEGIDEETRH-LigSLPEGRGVLGALIEEPKPIRLDDISRHPAs 140
                                    6889999****************99887777777774555444442.256**************9999866444443333 PP

                          GAF_3  78 .......lpdraalavPLvagrqviGvlal.astkprafdaedlelleslArqiataier 129
                                            p+r  l vP++++++v+G l+l +  ++++f+++d+ l+++lA+ +++a+++
  gi|121637913|ref|YP_978136.1| 141 vgfplhhPPMRTFLGVPVRIRDEVFGNLYLtEKADGQPFSDDDEVLVQALAAAAGIAVDN 200
                                    344444456799999*****99********55556667********************98 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1e-11
                          GAF_3  80 d........raalavPLvagrqviGvlal.astkprafdaedlelleslArqiata 126
                                    +        ++al++PL+a ++v Gvl++ +s ++++f++++l+++ ++A+q+a+a
  gi|121637913|ref|YP_978136.1| 310 LavdgpvepGPALVLPLRAADTVAGVLVAlRSADEQPFSDKQLDMMAAFADQAALA 365
                                    33333333399********99*******748888889*****************87 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.4   8.8e+03      56      65 ..      16      25 ..      15      38 .. 0.72
   2 ?   -2.0   0.1       2.1   5.4e+03      45      52 ..     355     362 ..     330     378 .. 0.51
   3 !   40.3   0.3   1.3e-13   3.4e-10       2      64 ..     384     444 ..     383     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.4
                                   HHHHHHHHTT CS
                        HisKA_3 56 vRrllhnLrp 65
                                   vR++l++Lr 
  gi|121637913|ref|YP_978136.1| 16 VRETLSQLRL 25
                                   6777777773 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                    HHHHHHHH CS
                        HisKA_3  45 ieelarea 52 
                                    +++ a++a
  gi|121637913|ref|YP_978136.1| 355 MAAFADQA 362
                                    33333333 PP

  == domain 3  score: 40.3 bits;  conditional E-value: 1.3e-13
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        HisKA_3   2 RariARELHDsvgqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRrllhnLr 64 
                                    R riAR+LHD v q+L+a+ l l+ a+ +++ +  +++e +    + ++e +qe+R ++ +L+
  gi|121637913|ref|YP_978136.1| 384 RDRIARDLHDHVIQRLFAVGLTLQGAAPRARVP--AVRESIYSSIDDLQEIIQEIRSAIFDLH 444
                                    9**************************888655..9***********************9998 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.4   2.8e-09   7.2e-06       8      55 ..     492     537 ..     487     573 .] 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.8e-09
                                    HHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT CS
                      HATPase_c   8 qiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlk 55 
                                     +++++v+Nav++ ++a+++ +++++++ d++++v D+G Gi+ ++ +
  gi|121637913|ref|YP_978136.1| 492 AVLREAVSNAVRH-ANATSLAINVSVED-DVRVEVVDDGVGISGDITE 537
                                    689**********.88999988888656.**************98877 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.7   9.5e+03      28      43 ..     230     245 ..     211     255 .. 0.66
   2 !   17.1   0.2   1.5e-06    0.0039      25      80 ..     483     533 ..     467     555 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.7
                    HATPase_c_2  28 lldeirlaveEactNa 43 
                                     +   rl +eEa+t  
  gi|121637913|ref|YP_978136.1| 230 PAMVFRLIAEEALTLM 245
                                    4445789999998865 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.5e-06
                    HATPase_c_2  25 seelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdp 80 
                                    ++ l+++ + ++ Ea++Nav+ha+       v+v+     + ++vev D+G g   
  gi|121637913|ref|YP_978136.1| 483 DTVLANHAEAVLREAVSNAVRHANATSLAINVSVE-----DDVRVEVVDDGVGISG 533
                                    56677788999*************97776666666.....789********98544 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.9e-06    0.0049       4      55 ..     491     541 ..     488     555 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                    HATPase_c_3   4 ekAlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalr 55 
                                    e +l e v N++  A+a++  i+v+ ++  + ++ + DdG G+s +  +++lr
  gi|121637913|ref|YP_978136.1| 491 EAVLREAVSNAVRhANATSLAINVSVED--DVRVEVVDDGVGISGDITESGLR 541
                                    67899******988*****999999865..69***********9887766775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4017.74
//
Query:       gi|121637914|ref|YP_978137.1|  [L=279]
Description: hypothetical protein BCG_2047c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-20   71.9  13.5    8.2e-18   65.3   4.2    2.9  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   4.2   4.6e-22   8.2e-18       5     141 .]      10     141 ..       8     141 .. 0.93
   2 !    9.6   1.8   6.7e-05       1.2     101     140 ..     236     274 ..     153     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 4.6e-22
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                    I+V++Dgs+ + +A+ wA+++a++r+ +l+ll++i+p+++g+++ ++ + + +++e + + +      +a ea++  v+v
  gi|121637914|ref|YP_978137.1|  10 IVVGIDGSKPAVQAALWAVDEAASRDIPLRLLYAIEPDDPGYAAHGAAARKLAAAENAVRYAF-----TAVEAADRPVKV 84 
                                    9**********************************************9999999999998776.....678888888888 PP

                                    EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +ve  + +++  ++  +  a l++vG+ g ++++   +GS++ +++ +a+cpV +Vr
  gi|121637914|ref|YP_978137.1|  85 EVEITQERPVTSLIRASAAAALVCVGAIGVHHFRPERVGSTAAALALSAQCPVAIVR 141
                                    8888888888899999999**********99999999*******************8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 6.7e-05
                                    HTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                            Usp 101 eedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                     +++ ++V+ ++++ ++++ l+G   ++vl++a c +lvV
  gi|121637914|ref|YP_978137.1| 236 GRSVHMVVLSASDQEHVEQ-LVGAPGNAVLQEAGCTLLVV 274
                                    57899*************9.89*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.91
# Mc/sec: 924.45
//
Query:       gi|121637915|ref|YP_978138.1|  [L=339]
Description: phosphofructokinase pfkB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-56  191.8   0.0      2e-56  191.6   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
     0.0083   15.5   0.0      0.012   15.0   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0   2.2e-60     2e-56       3     299 ..      19     305 ..      17     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 2.2e-60
                                    EEEEEEEEE.EEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETT CS
                           PfkB   3 kvvviGeal.idliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdy 81 
                                    ++++++++  +d+++ +ek     ++++  ++ +GG g+NvA++++ lg+ +++++  G+++ G+ l+++l ++gv+ + 
  gi|121637915|ref|YP_978138.1|  19 MNPALDITTsVDVVRPTEK-----MRCGAPRYDPGGGGINVARIVHVLGGCSTALFPAGGST-GSLLMALLGDAGVPFRV 92 
                                    6778888888999999998.....**************************************.***************** PP

                                    EEEESSSEEEEEEEEETTT.SEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE CS
                           PfkB  82 vkidedtrtglalivvded.gertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt 160
                                    + i + tr + ++ +   + + r ++  ++ + ++++++l+e + + ++a++++ sg+l++++  ++++++a++++ +  
  gi|121637915|ref|YP_978138.1|  93 IPIAASTRESFTVNESRTAkQYRFVLPGPSLTVAEQEQCLDELRGAAASAAFVVASGSLPPGVAADYYQRVADICRRSS- 171
                                    *****************999999999999999999999999**************************************. PP

                                    EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGGGEEEEEETTE CS
                           PfkB 161 fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGkeGalvvekdg 239
                                     +p +ld++g      l+++ +++ llk++ +El++++g++l ++ e laa+h+l+ +g  ++vvv+lG++Gal++++++
  gi|121637915|ref|YP_978138.1| 172 -TPLILDTSG----GGLQHISSGVFLLKASVRELRECVGSELLTEPEQLAAAHELIDRGRaEVVVVSLGSQGALLATRHA 246
                                    .*********....69**************************************************************** PP

                                    EEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCS CS
                           PfkB 240 elkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiasl 299
                                    +++++++p  ++v+ +GAGD++v++++++l++g+sl +++r++na++a+++ ++g++a++
  gi|121637915|ref|YP_978138.1| 247 SHRFSSIP-MTAVSGVGAGDAMVAAITVGLSRGWSLIKSVRLGNAAGAAMLLTPGTAACN 305
                                    ******65.99*********************************************9986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-06     0.012     122     224 ..     192     288 ..     166     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-06
                                    EEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHH CS
                   Phos_pyr_kin 122 vitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGC 201
                                    ++   + E+++ +g+++ te +  +aa++l++ g   V++        +     +l +++  +++++  ++  +  G+G+
  gi|121637915|ref|YP_978138.1| 192 LLKASVRELRECVGSELLTEPEQLAAAHELIDRGRAEVVVVSLGS---QG---ALLATRHASHRFSSIPMTAVSGVGAGD 265
                                    566678899999999999**************9988888766542...33...478899999999999999999****** PP

                                    HHHHHHHHHHHCTSSHHHHHHHH CS
                   Phos_pyr_kin 202 tlssaiaaelakgesleeAvkkA 224
                                    ++ +ai+  l++g sl ++v+ +
  gi|121637915|ref|YP_978138.1| 266 AMVAAITVGLSRGWSLIKSVRLG 288
                                    *******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2208.85
//
Query:       gi|121637916|ref|YP_978139.1|  [L=681]
Description: hypothetical protein BCG_2049c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-109  367.1   8.1   2.1e-109  366.5   8.1    1.3  1  Erythro_esteras  Erythromycin esterase
    2.4e-22   79.1   0.0      8e-22   77.5   0.0    1.9  1  Pribosyltran     Phosphoribosyl transferase domain
    4.9e-05   22.9   0.0      9e-05   22.0   0.0    1.4  1  UPRTase          Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.075   12.5   0.0       0.25   10.8   0.0    1.8  2  PRTase_2         Phosphoribosyl transferase
       0.08   12.8   9.0       0.46   10.4   0.1    3.6  4  ETF              Electron transfer flavoprotein domain
      0.086   12.8   0.0       0.22   11.4   0.0    1.7  1  PSCyt2           Protein of unknown function (DUF1549)


Domain annotation for each model (and alignments):
>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.5   8.1  6.9e-113  2.1e-109       1     344 []     294     656 ..     294     656 .. 0.93

  Alignments for each domain:
  == domain 1  score: 366.5 bits;  conditional E-value: 6.9e-113
                                    HHHC---EEEEEEEHHHHHHHHHHHHHS-S-GGGT.........S-CCC-CHHHHHHHHHHHHHHHSTT-SS-..-EEEE CS
                Erythro_esteras   1 veehGfrtvalEadwpdalrvdryvrggtgdaeea......krfptwmWrneevlelveWlReyNagrpkker..vrfyG 72 
                                    +ee+Gf +va Eadwpda+rv+ryvrg  +d  ++      +rfp wmWrn+ v+++veWlR+ N++ ++ +    +fyG
  gi|121637916|ref|YP_978139.1| 294 IEEKGFGAVAAEADWPDAYRVNRYVRGLGEDTNADealsgfERFPAWMWRNTVVRDFVEWLRTRNQRYESGALrqAGFYG 373
                                    89***********************9877666666789***************************6444433367***** PP

                                    EE-S---HHHHHHHHHHHHCHCCCCHHHHHHHCCHGGC.S...........TSSCCCCCHHHHHHHHHHHHCCHGGG... CS
                Erythro_esteras  73 lDlqslresldavldyLakvdpelagaareryaclapl.adp.....raarsaeaaelrscedevvallkellakreeya 146
                                    lDl+sl++s+++v++yL+kvdp++a++ar+ryac+++  ad           a      sce+e+v++l ++++++  ya
  gi|121637916|ref|YP_978139.1| 374 LDLYSLHRSIQEVISYLDKVDPRAAARARARYACFDHAcADDgqaygF---AAAFGAGPSCEREAVEQLVDVQRNALAYA 450
                                    **************************************9644444333...3445699********************** PP

                                    ..GG..TSHHHHHHHHHHHHHHHHHHHC.....CSSSSSCHHHHHHHHHHHHHHHHHHHH........HHSSEEEEEEHH CS
                Erythro_esteras 147 aedg..eaeeffsaeqnarlvknaeryyra...gdeeswnlrllalRDrhMaenleallehe......argkivvwAHNs 215
                                    ++dg  +++e f a+qna++v++ae yyra   g+ +swnl     RD+hMa++l  ll h       ++++ivvwAHNs
  gi|121637916|ref|YP_978139.1| 451 RQDGllAEDELFYAQQNAQTVRDAEVYYRAmfsGRVTSWNL-----RDQHMAQTLGSLLTHLdrhldaPPARIVVWAHNS 525
                                    ******9**********************************.....**************87999***99********** PP

                                    HHSSS-STTTT-S..S-HHHHHHHHHGGGEEEEEEEEEEEEEEEC-.......EEEE----TTSHHHHHHCSS-SEEEEE CS
                Erythro_esteras 216 HigdaratdmgkerglnaGqllrerlgdeyvaiGftfgtgtvaaasewgepmevmtvrppppgslEallhaagppdflld 295
                                    H+gdarat+   + +l++Gq++rer+gde ++iGf+++tgtv+aasewg+ +++++vrp+ +gs+E+l+h+++   fl+ 
  gi|121637916|ref|YP_978139.1| 526 HVGDARATEVWADGQLTLGQIVRERYGDESRSIGFSTYTGTVTAASEWGGIAQRKAVRPALHGSVEELFHQTAD-SFLVS 604
                                    **********86644*********************************************************85.89999 PP

                                    G-..CHHHHHHEE............EEE---SB-BTTSHHHH-SEEEEEEEE CS
                Erythro_esteras 296 lr.neelrewleeprleraiGv..rpeterqshyveaslaeqfDalifvdet 344
                                     r ++++++ l+  rl raiGv   p+terqshy + ++a+qfDa+i++d+t
  gi|121637916|ref|YP_978139.1| 605 ARlSRDAEAPLDVVRLGRAIGVvyLPATERQSHYLHVRPADQFDAMIHIDQT 656
                                    98889*********************************************97 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   2.7e-25     8e-22      14     150 ..      23     202 ..      15     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 2.7e-25
                                    EEEETTEEEEEE--GGGEE.EEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..................... CS
                   Pribosyltran  14 avarlaaeileeyngkpdv.vvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............. 79 
                                    ++ r +ae+l  y+ +pdv v+g argG+p+a ++a +L +pl+   ++k  ++g  e+a g+ ++              
  gi|121637916|ref|YP_978139.1|  23 EAGRVLAELLAAYRDQPDViVLGLARGGLPVAWEVAAALHAPLDAFVVRKLGAPGHDEFAVGALASGgrvvvnddvvrgl 102
                                    788999***********96267**************************************9998877************* PP

                                    ............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                   Pribosyltran  80 ............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpatee 131
                                                                r+++d+ gk+V++VDD+l+tG ++ aa+++L+++ p+++ iav++++ +t +
  gi|121637916|ref|YP_978139.1| 103 ritpqqlrdiaeregrellrresayrgeRPPTDITGKTVIVVDDGLATGASMFAAVQALRDAQPAQIVIAVPAAPESTCR 182
                                    ****************************************************************************9999 PP

                                    HHHHH-TTS......EEEEE CS
                   Pribosyltran 132 evdknakrvfsls.pdnfva 150
                                    e    ++ v++ + p+ f a
  gi|121637916|ref|YP_978139.1| 183 EFAGLVDDVVCATmPTPFLA 202
                                    99999999998887776665 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     3e-08     9e-05     114     160 ..     131     175 ..     117     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3e-08
                        UPRTase 114 kLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                    + P++i+ +tv+++D  +aTG+s+ aa+q L++  ++  +I+++   
  gi|121637916|ref|YP_978139.1| 131 RPPTDITGKTVIVVDDGLATGASMFAAVQALRD--AQPAQIVIAVPA 175
                                    569999***************************..888888765443 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   3.6e+03      33      75 ..      22      61 ..      19      67 .. 0.74
   2 ?   10.8   0.0   8.4e-05      0.25     122     154 ..     139     171 ..     130     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                       PRTase_2 33 reagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadal 75
                                   reag+ Laella+    + + +v+v+g+A     ++  va+al
  gi|121637916|ref|YP_978139.1| 22 REAGRVLAELLAA---YRDQPDVIVLGLARGGLPVAWEVAAAL 61
                                   6789999999994...345778899999987777776666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.4e-05
                       PRTase_2 122 kelvLvDDEistGktalnliralqeklprkryv 154
                                    k++++vDD ++tG ++ + ++al+++ p++ ++
  gi|121637916|ref|YP_978139.1| 139 KTVIVVDDGLATGASMFAAVQALRDAQPAQIVI 171
                                    789**********************99986554 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00015      0.46      78     121 ..      25      70 ..      14      88 .. 0.91
   2 ?    0.4   0.3      0.17   5.2e+02     100     151 ..     150     197 ..     138     224 .. 0.80
   3 ?    5.3   0.1    0.0053        16      48     114 ..     230     292 ..     211     294 .. 0.69
   4 ?   -1.8   0.1      0.81   2.4e+03      41      74 ..     428     467 ..     420     499 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHC..--SEEEEESSCCHHHHHHHHHHHCT-EEEEEES CS
                            ETF  78 akalaalikke..dpdlvlagataigkqvaprlAalLgvplitdvt 121
                                     ++la+l++++  +pd++++g    g  va  +Aa L++pl + v+
  gi|121637916|ref|YP_978139.1|  25 GRVLAELLAAYrdQPDVIVLGLARGGLPVAWEVAAALHAPLDAFVV 70 
                                    689********999***************************99887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                    CHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSS CS
                            ETF 100 igkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlp 151
                                    +g+ + + + al +++ +  v+++ ++ +     R+  g   +  vv+a++p
  gi|121637916|ref|YP_978139.1| 150 TGASMFAAVQALRDAQPAQIVIAVPAAPE--STCREFAG--LVDDVVCATMP 197
                                    47888899999999999999999999977..77788877..77799999666 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0053
                                    -CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCH.HHHHHHHHHHCT- CS
                            ETF  48 alrealaamGadkvilvddpalagydaeatakalaalikkedpdlvlagataig.kqvaprlAalLgv 114
                                    +lr+ +a   ad +  v  +a       +t ++la+l+ +  + +vl+g+++ g  ++ +  Aa+ ++
  gi|121637916|ref|YP_978139.1| 230 SLRRPAASTAADVLRRVAIDAPG---GVPTHEVLAELVGD--ARIVLIGESSHGtHEFYQARAAMTQW 292
                                    45665553444444444444443...46799*********..99*********769998888888776 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.81
                                    ES....S-.......CHHHHHHCT-SEEEEEE-GGGSS--C CS
                            ETF  41 Gppeaeea.......lrealaamGadkvilvddpalagyda 74 
                                    Gp+++ ea        r ala +   + +l++d+ + + + 
  gi|121637916|ref|YP_978139.1| 428 GPSCEREAveqlvdvQRNALA-YARQDGLLAEDELFYAQQN 467
                                    555555543333333555666.6666666666666554433 PP

>> PSCyt2  Protein of unknown function (DUF1549)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.4e-05      0.22      16     103 ..     232     344 ..     215     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.4e-05
                         PSCyt2  16 kpseeadrrtllRRvsldLtGlpPtpeeveaFladksad..............ayeklvdrlLaspaygerwar.hwldl 80 
                                    +  ++ + +++lRRv +d  G +Pt e +++ + d++                a++++ + l++++ +g+  a+  w d+
  gi|121637916|ref|YP_978139.1| 232 RRPAASTAADVLRRVAIDAPGGVPTHEVLAELVGDARIVligesshgthefyqARAAMTQWLIEEKGFGAVAAEaDWPDA 311
                                    5556677889***********************888753455566777888889999999999******9887537*999 PP

                         PSCyt2  81 aryads.kgyekde.........erkeawryrd 103
                                     r++   +g  +d+         er  aw +r+
  gi|121637916|ref|YP_978139.1| 312 YRVNRYvRGLGEDTnadealsgfERFPAWMWRN 344
                                    988743133333331222344444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4540.04
//
Query:       gi|121637917|ref|YP_978140.1|  [L=144]
Description: heat shock protein hspX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-24   84.4   0.1    6.4e-24   84.0   0.1    1.1  1  HSP20       Hsp20/alpha crystallin family
      9e-12   44.4   0.0    1.3e-11   43.9   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.1   7.2e-28   6.4e-24       5     101 ..      47     140 ..      44     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 7.2e-28
                                    SEEEEEEEEE-TT--CC.CEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEE CS
                          HSP20   5 eeeefevkldvpglkke.elkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtv 83 
                                    +e ++ev++++pg++++ +++++v+d+++++k+e++  e+++ + ++e ++++F+r+++LP ++d+d++ka++++G+Ltv
  gi|121637917|ref|YP_978140.1|  47 KEGRYEVRAELPGVDPDkDVDIMVRDGQLTIKAERT--EQKDFDGRSEFAYGSFVRTVSLPVGADEDDIKATYDKGILTV 124
                                    5789***********766******************..9999************************************** PP

                                    EEEBSS--..-------- CS
                          HSP20  84 tvpkkepekkkkerkiqi 101
                                    +v  +e +  ++e++iqi
  gi|121637917|ref|YP_978140.1| 125 SVAVSEGK--PTEKHIQI 140
                                    *****999..68****99 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.4e-15   1.3e-11       2      62 ..      49     125 ..      48     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.4e-15
                     ArsA_HSP20   2 deyvlkldLPfvdke.eidlsrsgdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                    ++y+++++LP+vd++ ++d+  ++ +LtIk++                +f R+++LP   +++++ +A++ +g L+++
  gi|121637917|ref|YP_978140.1|  49 GRYEVRAELPGVDPDkDVDIMVRDGQLTIKAErteqkdfdgrsefaygSFVRTVSLPVGADEDDI-KATYDKGILTVS 125
                                    89**********99868************************************************.**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 974.57
//
Query:       gi|121637918|ref|YP_978141.1|  [L=331]
Description: hypothetical protein BCG_2051 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-10   39.7   0.5    0.00023   21.3   0.0    2.9  3  Nitroreductase  Nitroreductase family
    9.6e-06   25.3   0.0     0.0019   17.8   0.0    2.1  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.9e-06     0.017      13      43 ..       4      34 ..       2      46 .. 0.90
   2 ?   -0.4   0.0      0.11     1e+03     107     136 ..      51      80 ..      37      91 .. 0.81
   3 !   21.3   0.0   2.5e-08   0.00023      96     169 ..     222     302 ..     139     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                   ----HHHHHHHHHHHHTS--GGG---EEEEE CS
                 Nitroreductase 13 epvpkeelekileaarraPsagnlqpwrfvv 43
                                   + v+ +++++ ++ a raPs +n+qpwr ++
  gi|121637918|ref|YP_978141.1|  4 TMVTTDVIKSAVQLACRAPSLHNSQPWRWIA 34
                                   5599************************986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTT-E CS
                 Nitroreductase 107 aaerayryalldagaaaqnllLaAtalGlg 136
                                    a + + r+all +ga++  + +a++a+G  
  gi|121637918|ref|YP_978141.1|  51 ATDHSGREALLGCGAVLDHFRVAMAAAGTT 80 
                                    56788999*********9999999999865 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.5e-08
                                    E......---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG...GGHHHHHHHHT-S..SEEEEEE CS
                 Nitroreductase  96 i......vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd...eaaeevrkllglpdeeeivvli 166
                                            ++ +k    +  +++r +ll +g ++  +lL At++Gl++c +++++   + ++ v++l+g p    +++l+
  gi|121637918|ref|YP_978141.1| 222 TdrrpefGHDRSKVLVLSTYDNERASLLRCGEMLSAVLLDATMAGLATCTLTHITelhASRDLVAALIGQP--ATPQALV 299
                                    3555555555666666689999*********************************655333389*****99..9999999 PP

                                    EEE CS
                 Nitroreductase 167 avG 169
                                    +vG
  gi|121637918|ref|YP_978141.1| 300 RVG 302
                                    998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.1e-07    0.0019     157     214 ..       8      73 ..       3      74 .. 0.83
   2 !    5.4   0.0    0.0014        12      70     105 ..     236     272 ..     225     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-07
                                    -HHHHHHHHHHHTS--GGG----EEE.E-SSEE..............EEE-S-HHHHHHHHHHHHHH CS
                 TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkdddeiki.........kasvlgklskiDlGIallHfela 214
                                     + +k+++++a  APs  N+qpwr   +d+ ++++           ++ g+   + +G +l Hf +a
  gi|121637918|ref|YP_978141.1|   8 TDVIKSAVQLACRAPSLHNSQPWRWIAEDH-TVALfldkdrvlyATDHSGREALLGCGAVLDHFRVA 73 
                                    56799*********************7775.666677777776455777999999********9986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0014
                                    EE----SS.HHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                 TM1586_NiRdase  70 ialvgekk.edleekaGYygeqlvLkltalGlgtcWv 105
                                    ++l   ++ ++++ ++G ++  ++L +t +Gl+tc +
  gi|121637918|ref|YP_978141.1| 236 LVLSTYDNeRASLLRCGEMLSAVLLDATMAGLATCTL 272
                                    555554443677889********************55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2497.01
//
Query:       gi|121637919|ref|YP_978142.1|  [L=280]
Description: hypothetical protein BCG_2052c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.8e-120  399.9   0.8   5.5e-120  399.7   0.8    1.0  1  DUF3097   Protein of unknown function (DUF3097)


Domain annotation for each model (and alignments):
>> DUF3097  Protein of unknown function (DUF3097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.7   0.8    3e-124  5.5e-120       1     271 []       4     275 ..       4     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 399.7 bits;  conditional E-value: 3e-124
                        DUF3097   1 rygsdvlaeearkkrkkvseveaelglvvedaasgfvGavvrvekeaekevveledrkgrrrlfplgpagflleGkpvtl 80 
                                    ryg+dvla+  r++  +  e+++elg+vveda++g+vGavvrve +     ++ledr g++r fplgp g+ll+G pv l
  gi|121637919|ref|YP_978142.1|   4 RYGTDVLAAGGRRRP-RSVEHPVELGMVVEDAETGYVGAVVRVEYG----RIDLEDRYGKTRGFPLGP-GYLLDGLPVIL 77 
                                    7*******9766444.45589*************************....9*****************.*********** PP

                        DUF3097  81 vrpkaaaaaapkrtasGsvaveeararvarasriyveGkhDaelvekvWGdDLrveGvvvelleGvDdlaeivaefepgp 160
                                    ++p+ aaaa p+rtasGsvav +ararvarasriyveG+hDael+  vWG DLr+eGvvve+l GvDdl eiva+f+pgp
  gi|121637919|ref|YP_978142.1|  78 TAPRCAAAAGPRRTASGSVAVPGARARVARASRIYVEGRHDAELIAAVWGADLRIEGVVVEHLGGVDDLVEIVAKFRPGP 157
                                    ******************************************************************************** PP

                        DUF3097 161 grrlGvlvDhLvegskesriaeevak...eehvlvvGhpyvDvWqavkpeavglkaWPevprgedwkeGvlaalGwp... 234
                                    +rrlGvlvDhLv+gske+riae v++    +++lvvGhpyvD+Wqavkp++vgl+aWP+vpr+ +wk+Gv++alGwp   
  gi|121637919|ref|YP_978142.1| 158 RRRLGVLVDHLVAGSKEARIAEVVRRgpgGSDTLVVGHPYVDIWQAVKPQRVGLAAWPRVPRHIEWKHGVCDALGWPhad 237
                                    **************************998899**********************************************99 PP

                        DUF3097 235 .advaeawkrilakvksyrdlepellgaveeliDfvte 271
                                     ad+a+aw+ri+++v++++dlep+l+g+veeliDfvt+
  gi|121637919|ref|YP_978142.1| 238 qADIAAAWRRIRSQVRDWTDLEPALIGRVEELIDFVTQ 275
                                    99**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2078.06
//
Query:       gi|121637920|ref|YP_978143.1|  [L=107]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-13   49.6   0.0    3.9e-13   49.0   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
    2.4e-10   40.3   0.3    3.7e-10   39.7   0.3    1.3  1  HTH_20          Helix-turn-helix domain
    6.2e-08   32.4   0.8      1e-07   31.7   0.8    1.5  1  MarR_2          MarR family
    0.00018   21.4   0.0    0.00028   20.8   0.0    1.3  1  HTH_11          HTH domain
      0.001   19.1   0.5     0.0015   18.6   0.5    1.3  1  DprA_WH         DprA winged helix domain
     0.0021   18.0   0.0     0.0029   17.5   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0038   17.1   0.0     0.0051   16.7   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0095   15.7   0.1      0.017   14.9   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.037   14.1   0.1    1.6  1  HTH_28          Helix-turn-helix domain
      0.048   13.5   0.0      0.063   13.1   0.0    1.2  1  HxlR            HxlR-like helix-turn-helix
       0.11   12.2   0.1       0.14   11.8   0.1    1.4  1  GntR            Bacterial regulatory proteins, gntR family
       0.11   12.5   0.0       0.26   11.2   0.0    1.6  2  MarR            MarR family
       0.12   11.9   0.0       0.18   11.4   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.18   12.0   0.0        0.3   11.3   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0     3e-16   3.9e-13       1      45 [.      16      60 ..      16      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3e-16
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   d tR+ I+  La g+l v+ela++l +s+++vS+HLk+L+ a+LV
  gi|121637920|ref|YP_978143.1| 16 DGTRRAIVERLAHGPLAVGELARDLPVSRPAVSQHLKVLKTARLV 60
                                   679*****************************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.3   2.9e-13   3.7e-10       5      54 ..      12      60 ..       8      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.9e-13
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                    ALa+ +Rr+i   L   ++l ++ela+ l +s+  +s+HL+vL  a Lv
  gi|121637920|ref|YP_978143.1| 12 QALADGTRRAIVERL-AHGPLAVGELARDLPVSRPAVSQHLKVLKTARLV 60
                                   79*************.****************************999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.8   8.2e-11     1e-07       7      56 ..      19      65 ..      12      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 8.2e-11
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                    + +   L+++p   l+vgelar l +s++avs++lk L  a Lv  rp+
  gi|121637920|ref|YP_978143.1| 19 RRAIVERLAHGP---LAVGELARDLPVSRPAVSQHLKVLKTARLVCDRPA 65
                                   555556677777...9*****************************88876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.2e-07   0.00028       2      42 ..      19      57 ..      18      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                   +++i+e+L  a+gp+   eLA+ L vSr +v +++k L+++
  gi|121637920|ref|YP_978143.1| 19 RRAIVERL--AHGPLAVGELARDLPVSRPAVSQHLKVLKTA 57
                                   68999999..8889************************986 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   1.1e-06    0.0015       6      51 ..      11      56 ..       6      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                        DprA_WH  6 aepplddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLEL 51
                                    ++ +d+++r+++++L++ P++v +L+r++ ++  +vs +L  L  
  gi|121637920|ref|YP_978143.1| 11 WQALADGTRRAIVERLAHGPLAVGELARDLPVSRPAVSQHLKVLKT 56
                                   566789********************************99977755 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0029      21      68 .]      30      81 ..      11      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..T.EEEEES-HHHHHHH CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.r..g.rririldleaLral 68
                                   pl   elA+ l ++r  vs+ l+ Lk + l+  r  g rr+  ld+ +L+al
  gi|121637920|ref|YP_978143.1| 30 PLAVGELARDLPVSRPAVSQHLKVLKTARLVCdRpaGtRRVYQLDPTGLAAL 81
                                   778889*************************985665445*********975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     4e-06    0.0051      18      63 ..      26      72 ..      21      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                                   HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                           TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63
                                   l++gp+ + e+a++l v+r+ v + L+ L+ + lV  ++ g++++Y+
  gi|121637920|ref|YP_978143.1| 26 LAHGPLAVGELARDLPVSRPAVSQHLKVLKTARLVCDRPaGTRRVYQ 72
                                   689********************************999945566775 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.3e-05     0.017      16      48 ..      28      60 ..      12      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                   BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                    ++l + elAr + +++++v+ +L+ L   ++v
  gi|121637920|ref|YP_978143.1| 28 HGPLAVGELARDLPVSRPAVSQHLKVLKTARLV 60
                                   35589**********************988876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.9e-05     0.037       2      38 ..      19      56 ..      18      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                         HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryee 38
                                   R+ i+++la+G  +v e+Ar l +sr  v++ +k + +
  gi|121637920|ref|YP_978143.1| 19 RRAIVERLAHGPlAVGELARDLPVSRPAVSQHLKVLKT 56
                                   899********88******************9986665 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.9e-05     0.063      10      52 ..      22      63 ..      14      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                                   HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE CS
                           HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdgliere 52
                                   i+  l +g+   +el+r lp +s+   +q+L+ L++ +l+  +
  gi|121637920|ref|YP_978143.1| 22 IVERLAHGPLAVGELARDLP-VSRPAVSQHLKVLKTARLVCDR 63
                                   8899***************7.9***************999544 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011      0.14      20      55 ..      27      61 ..      12      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                   ++ +L ++ eLa  + Vsr+ v + L+ L+++ lv 
  gi|121637920|ref|YP_978143.1| 27 AHGPL-AVGELARDLPVSRPAVSQHLKVLKTARLVC 61
                                   45689.9*************************9996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.26      15      41 ..      28      54 ..      26      60 .. 0.91
   2 ?   -2.0   0.0       2.8   3.6e+03      26      41 ..      58      73 ..      56      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                   STTEEHHHHHHHHTS-HHHHHHHHHHH CS
                           MarR 15 qgplsvseLakklgvskstvtrvldrL 41
                                   +gpl v eLa+ l vs+++v+  l+ L
  gi|121637920|ref|YP_978143.1| 28 HGPLAVGELARDLPVSRPAVSQHLKVL 54
                                   89********************99977 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                   HHTS-HHHHHHHHHHH CS
                           MarR 26 klgvskstvtrvldrL 41
                                   +l +++++ tr + +L
  gi|121637920|ref|YP_978143.1| 58 RLVCDRPAGTRRVYQL 73
                                   6778888888888766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.18      15      43 ..      28      56 ..      16      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                         HTH_24 15 nprisqreLAerlglSpstvnrrlkrLee 43
                                   ++ +   eLA+ l +S+++v+++lk L+ 
  gi|121637920|ref|YP_978143.1| 28 HGPLAVGELARDLPVSRPAVSQHLKVLKT 56
                                   4778889******************9975 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024       0.3      21      52 ..      29      60 ..      22      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                   SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                 Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                   ++  + +la+ L vs + Vs+ lk L+ + +v
  gi|121637920|ref|YP_978143.1| 29 GPLAVGELARDLPVSRPAVSQHLKVLKTARLV 60
                                   667789******************99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 734.02
//
Query:       gi|121637921|ref|YP_978144.1|  [L=162]
Description: hypothetical protein BCG_2054 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-08   33.0   0.1    8.2e-08   32.5   0.1    1.2  1  AHSA1     Activator of Hsp90 ATPase homolog 1-like protein


Domain annotation for each model (and alignments):
>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   4.6e-12   8.2e-08       1     119 [.      16     151 ..      16     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4.6e-12
                                    SS-HHHHHHHHH-HHHHHHH.........EEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEE.T CS
                          AHSA1   1 dapperVfraltdpellkrW.........ftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrle.d 70 
                                    +ap+er f+++t+   +  +         + +te  ++ ++Gg+++  ++ dg+ +++   +l  +pp r+ +tw+    
  gi|121637921|ref|YP_978144.1|  16 NAPIERAFAVFTTR--FGDFkprehnllaIPITETVFECHAGGHIYD-RGVDGSVCKWAR-VLVYEPPSRVLFTWDIGpT 91 
                                    68999******998..7778888889989999999999999**9998.668888888886.***************9974 PP

                                    SET....EEEEEEEEEEEE.ETTEEEEEEEE....EEEEHCHHHHHH..HHHHHHHHHHH CS
                          AHSA1  71 epe....eeestvtielee.egggTrltlth....tglprkqkeeeg..veeGweqsldq 119
                                    ++      + s+v++ +++   + Tr+ l+h    +  p  +  ++g   e+Gw+ +l++
  gi|121637921|ref|YP_978144.1|  92 WRPetdlAKTSEVEVRFTAqSAETTRVDLEHrhldRHGPGWESVADGvdSEAGWPLYLRR 151
                                    444799988**********66677*******66653333333333346789999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1277.78
//
Query:       gi|121637922|ref|YP_978145.1|  [L=213]
Description: hypothetical protein BCG_2055 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   45.3   5.0    1.1e-09   39.1   0.4    2.7  3  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
    8.2e-05   23.4   1.9    0.00016   22.5   1.9    1.5  1  MDMPI_C   MDMPI C-terminal domain
    0.00028   21.4   0.0    0.00046   20.7   0.0    1.4  1  DinB_2    DinB superfamily
  ------ inclusion threshold ------
      0.036   14.7   1.2        3.3    8.4   0.4    3.0  3  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.4   2.4e-13   1.1e-09       2      40 ..      17      55 ..      16      61 .. 0.93
   2 !    7.8   0.0    0.0011       5.1      99     141 .]      82     126 ..      70     126 .. 0.80
   3 ?   -1.9   0.1       1.1     5e+03     104     120 ..     164     180 ..     137     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.4e-13
                        MDMPI_N  2 reewaalaalvagLtdeqwaapspcpGWtvadlvaHlar 40
                                   r+e+a+laa++  Lt +qw +ps+c+GW+v+++vaH+++
  gi|121637922|ref|YP_978145.1| 17 RAERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMIS 55
                                   899*********************************986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                        MDMPI_N  99 aalaalppdaiadrlgipggpr..slgeflrtrlvEavvHglDla 141
                                    +++a l p++ +d +g +++pr  ++g+  ++ lv+ ++H++D++
  gi|121637922|ref|YP_978145.1|  82 DEFAGLSPQELVDYVGRHLQPRglTAGFGGMIALVDGMIHHQDIR 126
                                    6789999******995555554116667999************96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                        MDMPI_N 104 lppdaiadrlgipggpr 120
                                    l +++  +++g++++++
  gi|121637922|ref|YP_978145.1| 164 LRATDLDWTIGTGPEVT 180
                                    33444445555555444 PP

>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.9   3.6e-08   0.00016       5      90 ..     138     210 ..     134     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.6e-08
                        MDMPI_C   5 dgvdellatvvarraaapdsrvvlelegprtvhlhatdggrarlalwadgadatvrGtaadlllllwGRlspddtlevdG 84 
                                      +d++l+ +   ++         ++++ + ++l+atd       +w+ g + +v+G+ ++ll++++GR ++ ++l+  G
  gi|121637922|ref|YP_978145.1| 138 QRLDRVLRLMPKNPR-------LRARPRIKGLRLRATD------LDWTIGTGPEVTGPGEALLMAMAGRPAAVSDLSGPG 204
                                    555666665555554.......678899999******9......36888888********************99999999 PP

                        MDMPI_C  85 dralla 90 
                                     + l+ 
  gi|121637922|ref|YP_978145.1| 205 KPTLAG 210
                                    888775 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     1e-07   0.00046       4      74 ..      18      95 ..      15     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1e-07
                         DinB_2  4 rararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlr.....geeap...rpgldpltppsaaealay 74
                                   + ra l a+l++lt +++  +    +ws+ +++aH +++e+l +  l+     g +++   + g d+ + +s++e+++y
  gi|121637922|ref|YP_978145.1| 18 AERAELAAFLTTLTLQQWETPSLCAGWSVKEVVAHMISYEDLGVFGLLkrfakG-RIVranEVGVDEFAGLSPQELVDY 95
                                   679******************99999***************7776666244432.222233345555555777777666 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.023     1e+02      32      67 ..      18      57 ..       8      61 .. 0.65
   2 ?   -1.6   0.0      0.94   4.2e+03      47      56 ..      87      96 ..      65     103 .. 0.74
   3 ?    8.4   0.4   0.00073       3.3      18      49 ..     123     155 ..     110     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.023
                         HTH_32 32 evrariiallreep..rW.sprqlaarlaeregvk..vShs 67
                                   ++ra++ a l++    +W +p++ a++ +++      +S++
  gi|121637922|ref|YP_978145.1| 18 AERAELAAFLTTLTlqQWeTPSLCAGWSVKEVV-AhmISYE 57
                                   678888888843335688777777777744442.1236665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.94
                         HTH_32 47 Wsprqlaarl 56
                                   +sp++l++++
  gi|121637922|ref|YP_978145.1| 87 LSPQELVDYV 96
                                   5888888887 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00073
                         HTH_32  18 kdrprr.grprklsdevrariiallreeprWsp 49 
                                    +d +r+ g pr+++++  +r+++l  ++pr+ +
  gi|121637922|ref|YP_978145.1| 123 QDIRRPlGQPRTIPAQRLDRVLRLMPKNPRLRA 155
                                    45578889*****************88885533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1589.13
//
Query:       gi|121637923|ref|YP_978146.1|  [L=324]
Description: hypothetical protein BCG_2056c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-30  105.0   1.5    9.6e-30  104.3   1.5    1.4  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   1.5   5.4e-34   9.6e-30       1     204 []      11     210 ..      11     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 5.4e-34
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdl.lirelaanl 79 
                                    Lv +GGG+rg+  +ga+ aL  ++g+rf  ++G+SaGAi+a+l+a+ +++++ v  l ++ ++ +  ++l + +     l
  gi|121637923|ref|YP_978146.1|  11 LVCEGGGVRGIGLVGAVDAL-ADAGYRFPRVAGSSAGAIVASLVAALQTAGEPVTRLAEMMRSIDYPKFLdRNLIGHVPL 89 
                                    899*****************.********************999999888887776666666655555533225555566 PP

                        Patatin  80 aarlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglytedd 159
                                         +ll  +g + + +l++ll ++lad++++ +   + +          + + +a+  +++a+  ++ r      + d
  gi|121637923|ref|YP_978146.1|  90 IGGGLSLLLSDGVYRGAYLEQLLGGLLADLGVHTFGDLRTGE---------APEQFAWSLVVTASDLSRRRLVRIPWDLD 160
                                    777778899999999999999999999999999999999999.........45555555555555555554444333333 PP

                        Patatin 160 dd.....dvdladavraSsafPglfppvsldgelyvDGGilsNvPilaal 204
                                     +     d+++a+av aSsa+P++f+pv+++g ++vDGG+lsN+P+ +++
  gi|121637923|ref|YP_978146.1| 161 SYgihpdDFSVARAVHASSAIPFVFEPVRVRGATWVDGGLLSNFPVALFD 210
                                    3344444***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2387.44
//
Query:       gi|121637924|ref|YP_978147.1|  [L=357]
Description: sugar-transport ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-28   97.5   0.0    1.6e-27   96.7   0.0    1.4  1  ABC_tran         ABC transporter
    8.5e-08   32.9   0.0    2.6e-07   31.3   0.0    1.9  1  OB_MalK          MalK OB fold domain
    2.3e-07   30.9   0.6    1.7e-06   28.1   0.1    2.4  2  TOBE_2           TOBE domain
    4.4e-05   23.9   0.0    0.00026   21.5   0.0    2.3  2  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0015   18.8   0.3     0.0028   17.9   0.3    1.7  1  AAA_22           AAA domain
     0.0015   18.4   0.0        1.3    8.8   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0017   18.8   0.4     0.0028   18.1   0.4    1.5  1  AAA_16           AAA ATPase domain
      0.002   18.4   0.0     0.0077   16.5   0.0    2.0  2  TOBE             TOBE domain
     0.0029   18.0   0.0     0.0087   16.5   0.0    1.9  1  AAA              ATPase family associated with various cellul
     0.0049   16.5   0.0      0.064   12.8   0.0    2.2  2  AAA_25           AAA domain
      0.006   16.0   0.1      0.026   14.0   0.1    1.8  1  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.023   14.4   0.1    1.6  1  AAA_30           AAA domain
      0.028   14.3   0.0      0.039   13.9   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.034   14.0   0.0      0.079   12.9   0.0    1.5  2  RsgA_GTPase      RsgA GTPase
      0.079   13.2   0.2       0.18   12.0   0.0    1.6  2  AAA_28           AAA domain
      0.096   12.8   0.6       0.16   12.1   0.6    1.6  1  AAA_33           AAA domain
       0.19   10.5   0.0       0.31    9.8   0.0    1.3  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   1.5e-30   1.6e-27       1     136 [.      21     163 ..      21     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.5e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++++l +  ge v++vG++G+GK+t l+++agl++ + G+i++ ++d++e      ++ +++++q+  l p++tv++n 
  gi|121637924|ref|YP_978147.1|  21 LDRLDLIVGDGEFVVLVGPSGCGKTTSLRMVAGLETLDCGRIRIGERDVTE--VDPKDRDVAMVFQNYALYPHMTVAQNm 98 
                                    678899999******************************************..999999********************* PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e     e++l+  +l +  ++ ++++p+ LSgGq+qrva+ ra++++p+++l+DEp 
  gi|121637924|ref|YP_978147.1|  99 gfalkvakigkaEI---RERVLAAAKLLD-LQSYLDRKPKDLSGGQRQRVAMGRAIVRRPQVFLMDEPL 163
                                    ***99999854444...555555555555.445556666*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.5e-10   2.6e-07       1      53 []     237     282 ..     237     282 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.5e-10
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                    GSPaMN++   + ++  +v  g+ ++ lp++           evi+G+RPEh+
  gi|121637924|ref|YP_978147.1| 237 GSPAMNLFRLSIADS--TVSLGDWQILLPRAV-----VGTAAEVIIGVRPEHL 282
                                    9************55..699999*******99.....9999***********7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.81   8.6e+02      47      66 ..     188     208 ..     173     211 .. 0.70
   2 !   28.1   0.1   1.6e-09   1.7e-06       1      76 []     275     348 ..     275     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.81
                         TOBE_2  47 vrqpnadr.dsalapGdtVel 66 
                                    + + ++++  +a++ Gd+V++
  gi|121637924|ref|YP_978147.1| 188 TTVYVTHDqVEAMTMGDRVAV 208
                                    444555553489999**9987 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.6e-09
                         TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadr.d..salapGdtVelswdpddavvl 76 
                                    +++RPE+l+l   gg  g++  V+ ve lG++  ++ ++ +g   ++ q+  +r d   +++ G++V+l+ +p +++++
  gi|121637924|ref|YP_978147.1| 275 IGVRPEHLEL---GG-AGIEMDVDMVEELGADAYLYGRIVSGGC-EMDQSIVARvDgrGPPERGSRVRLCPTPGHLHFF 348
                                    58********...77.7*******************99887754.333333333333459*****************98 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.3   3.4e+03       9      17 ..      59      67 ..      56      79 .. 0.76
   2 !   21.5   0.0   2.5e-07   0.00026       1      43 []     242     284 ..     242     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.3
                CysA_C_terminal  9 dGklriGgl 17
                                    G++riG+ 
  gi|121637924|ref|YP_978147.1| 59 CGRIRIGER 67
                                   59****984 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.5e-07
                CysA_C_terminal   1 NlFhGrvedGklriGglalpvPelagadgqevvayVRPhDlei 43 
                                    NlF+  + d ++ +G+ ++ +P++     +ev+ +VRP++le+
  gi|121637924|ref|YP_978147.1| 242 NLFRLSIADSTVSLGDWQILLPRAVVGTAAEVIIGVRPEHLEL 284
                                    99999999**************7777788************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   2.7e-06    0.0028       6      27 ..      32      53 ..      28     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                         AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                    ++v++G+sG+GKTt+lr+++ 
  gi|121637924|ref|YP_978147.1| 32 EFVVLVGPSGCGKTTSLRMVAG 53
                                   689***************9875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0022       2.4       1      22 [.      33      54 ..      33      76 .. 0.77
   2 !    8.8   0.0    0.0012       1.3     155     299 ..      95     196 ..      60     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   + vl+Gp g+GK++ L+   +l
  gi|121637924|ref|YP_978147.1| 33 FVVLVGPSGCGKTTSLRMVAGL 54
                                   68***********988777666 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                         AAA_21 155 lllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelp 233
                                    ++++ + +k  +ig ++i  + +  ak+++l + l r++k+                                       
  gi|121637924|ref|YP_978147.1|  95 AQNMGFALKVaKIGKAEIRERVLAAAKLLDLQSYLDRKPKDL-------------------------------------- 136
                                    555555555555555555555555555555555555555555...................................... PP

                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                        S G+++  a+  a+ r++    ++l DEp ++L+ kl       + +l+r  g+  + +TH+ 
  gi|121637924|ref|YP_978147.1| 137 ----SGGQRQRVAMGRAIVRRP---QVFLMDEPLSNLDAKLRGQTRNQIAALQRqLGTTTVYVTHDQ 196
                                    ....999999999999***999...9**************999999877777776888889999985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   2.7e-06    0.0028      22      45 ..      29      52 ..      20     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                   g++e v+l+G+sG+GK++ +r+++
  gi|121637924|ref|YP_978147.1| 29 GDGEFVVLVGPSGCGKTTSLRMVA 52
                                   67799****************987 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.5     1e+04      36      53 ..     191     206 ..     186     209 .. 0.70
   2 !   16.5   0.0   7.3e-06    0.0077      10      64 .]     292     347 ..     286     347 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.5
                           TOBE  36 rvtrrsaeeLgLapGeeV 53 
                                     vt +++e+  ++ G++V
  gi|121637924|ref|YP_978147.1| 191 YVTHDQVEA--MTMGDRV 206
                                    477777777..7777776 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.3e-06
                           TOBE  10 tVvvveplgseveVrvdlggga.....tLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                     V+ ve+lg++++++ ++  g      +++Arv++r  +e    +G++V++ + ++ +h+
  gi|121637924|ref|YP_978147.1| 292 DVDMVEELGADAYLYGRIVSGGcemdqSIVARVDGRGPPE----RGSRVRLCPTPGHLHF 347
                                    6999*************988888*****************....*******999999885 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.2e-06    0.0087       1      51 [.      34      84 ..      34     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-06
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfk 51
                                   v+l+Gp G+GKT+  + va     ++ +i   e     v  + ++++++f+
  gi|121637924|ref|YP_978147.1| 34 VVLVGPSGCGKTTSLRMVAGLETLDCGRIRIGERDVTEVDPKDRDVAMVFQ 84
                                   689****************87544444444433333355566666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.1e-05     0.064      19      50 ..      17      48 ..       4      57 .. 0.80
   2 ?    1.0   0.0      0.25   2.6e+02     165     189 ..     170     195 ..     155     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                         AAA_25 19 ppprrwlvkgllpagelallaGapgtGKttla 50
                                    +p  + ++ ++  ge+++l+G++g+GKtt +
  gi|121637924|ref|YP_978147.1| 17 DRPALDRLDLIVGDGEFVVLVGPSGCGKTTSL 48
                                   55555666777889***************976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                         AAA_25 165 v.galvealeriarrtgaavllvhHv 189
                                      g+  ++++ ++r++g +++ v H 
  gi|121637924|ref|YP_978147.1| 170 LrGQTRNQIAALQRQLGTTTVYVTHD 195
                                    34888899***************995 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.4e-05     0.026      25     208 ..      32     203 ..      25     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisrrv 103
                                    +f ++vGp G+GK+    +++ v G ++    r +  ++ +++       k  +v+++f+n       + ++++    +v
  gi|121637924|ref|YP_978147.1|  32 EFVVLVGPSGCGKTT---SLRMVAGLETLDCGRIRIGERDVTE----VDPKDRDVAMVFQNYALYpHMTVAQNMGFALKV 104
                                    789999*******86...6777789777755565555555555....455556666677666665222344445555555 PP

                                    ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                     + g+   +i ++    +++ +l +  + +++ LSgG+++ va+    Ai  v++  ++l+De  ++LD+k + +  + +
  gi|121637924|ref|YP_978147.1| 105 AKIGK--AEIRERVLAAAKLLDLQSYLDRKPKDLSGGQRQRVAMG--RAI--VRRPQVFLMDEPLSNLDAKLRGQTRNQI 178
                                    55555..6799999999999999999999**********987765..344..45566899***********999999999 PP

                                    HHHCTTSEEEEE-SSHHHCCC-SCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 184 keksknaQfivislreemlekadkl 208
                                     + + +     + ++++++e +   
  gi|121637924|ref|YP_978147.1| 179 AALQRQLGTTTVYVTHDQVEAMTMG 203
                                    9988887666666666666666544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.2e-05     0.023      13      45 ..      27      58 ..      22     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                         AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaa 45
                                   ++++g+ ++vl+Gp G GKtt+l+ ++ + + +
  gi|121637924|ref|YP_978147.1| 27 IVGDGE-FVVLVGPSGCGKTTSLRMVAGLETLD 58
                                   555665.99***************998776655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.7e-05     0.039      48      66 ..      34      52 ..      23     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                          Rad17 48 LLisGPsGCgkstvvkvLs 66
                                   +++ GPsGCgk+t +++++
  gi|121637924|ref|YP_978147.1| 34 VVLVGPSGCGKTTSLRMVA 52
                                   6789***********9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.079      96     131 ..      27      63 ..      14      68 .. 0.79
   2 ?   -3.4   0.0       7.7   8.1e+03      64      83 ..     174     193 ..     163     201 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                    HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                     + d +++vlvG+SG GK+t + ++++ ++l  g ++
  gi|121637924|ref|YP_978147.1|  27 IVGDgEFVVLVGPSGCGKTTSLRMVAGLETLDCGRIR 63 
                                    5555599*************99999998888877775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.7
                                    HHHHHHHHHHHTTSEEEE-- CS
                    RsgA_GTPase  64 eleelkeelealgyevllvs 83 
                                    + +++++  ++lg+++++v 
  gi|121637924|ref|YP_978147.1| 174 TRNQIAALQRQLGTTTVYVT 193
                                    34555555666666665554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.18       2      20 ..      34      52 ..      33      73 .. 0.83
   2 ?   -2.8   0.0       6.1   6.4e+03     120     143 ..     165     187 ..     139     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   +v++G++++GKTt l+  a
  gi|121637924|ref|YP_978147.1| 34 VVLVGPSGCGKTTSLRMVA 52
                                   8**************9887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.1
                         AAA_28 120 eidddgeRredleereaiderlre 143
                                     + d + R ++ ++ +a++++l  
  gi|121637924|ref|YP_978147.1| 165 NL-DAKLRGQTRNQIAALQRQLGT 187
                                    44.555555555555555554443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   0.00015      0.16       2      21 ..      34      53 ..      33     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                         AAA_33  2 vllvGlpGsGKstlaerllk 21
                                   v+lvG++G+GK+t ++ ++ 
  gi|121637924|ref|YP_978147.1| 34 VVLVGPSGCGKTTSLRMVAG 53
                                   899**********9998863 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0003      0.31      28      63 ..      17      50 ..       2      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                T4SS-DNA_transf 28 dkkalyaggllntdGdfehvlvvAptrsgKgvgvvi 63
                                   d++al+  +l ++dG+f  v++v+p++ gK++++ +
  gi|121637924|ref|YP_978147.1| 17 DRPALDRLDLIVGDGEF--VVLVGPSGCGKTTSLRM 50
                                   44577777789999988..*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 1953.83
//
Query:       gi|121637925|ref|YP_978148.1|  [L=280]
Description: sugar-transport integral membrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-19   68.7  15.4    5.2e-19   68.7  15.4    1.5  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.16   2.9e+03      71      71 ..      36      36 ..       5      85 .. 0.55
   2 !   68.7  15.4   2.9e-23   5.2e-19       4     183 ..      96     273 ..      89     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.16
                   BPD_transp_1 71 i 71
                                    
  gi|121637925|ref|YP_978148.1| 36 A 36
                                   2 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 2.9e-23
                   BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslpkd 82 
                                    +G+  a +  +++++ l +l+  +l++P  v +i+ +   +++ i+g+  +p ++i+  l+  ++ ++++r+++r+lp+d
  gi|121637925|ref|YP_978148.1|  96 AGYAFA-RLQFRGRDTLFVLYLSTLMVPLTVTVIPQF---ILMRIVGWVDTPwAMIVPGLFGSAFGTYLMRQFFRTLPTD 171
                                    566666.99999*******************777754...3679********666666788899**************** PP

                   BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseisnggvlal 161
                                    l+eaa ++G+s+wqi+++++lP++ p ++ + +l+++++++++++++++++ +   +++l  + l   y +   ++++a 
  gi|121637925|ref|YP_978148.1| 172 LEEAAILDGCSPWQIYWRILLPHSRPAVLVLGVLTWVNVWNDFLWPLLMIQRNSlATLTLGLVRLRGEYVARWPVLMAAS 251
                                    **************************************************999965666667777777777777888888 PP

                   BPD_transp_1 162 viavlllnlvadilqrlldprv 183
                                     +++++l++++ + qr + + +
  gi|121637925|ref|YP_978148.1| 252 MLMLVPLVILYAVAQRSFVRGI 273
                                    8999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1549.78
//
Query:       gi|121637926|ref|YP_978149.1|  [L=300]
Description: sugar-transport integral membrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-16   59.7  23.7      3e-16   59.7  23.7    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.24   11.2   3.2        2.4    8.0   0.2    2.4  2  Pam17         Mitochondrial import protein Pam17


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   4.1         1   9.2e+03      43      68 ..      33      77 ..       5      89 .. 0.48
   2 !   59.7  23.7   3.4e-20     3e-16       5     181 ..      88     289 ..      84     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1
                   BPD_transp_1 43 f.................vilsilghlilp..viillllsaapyv 68
                                   f                 v l+ + +l+++  +++++++ +a y+
  gi|121637926|ref|YP_978149.1| 33 FslymsfqkwdlfthatfVRLDNFRNLFTSdpLFLIAVVNTAVYT 77
                                   133333354445555554333333333333323444444444444 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 3.4e-20
                   BPD_transp_1   5 Gilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviilllls 63 
                                    ++++a  lnr+ k+  l+r++++++l++ s+v+a+++++vf                    +l    +++ ++++++++ 
  gi|121637926|ref|YP_978149.1|  88 SLVVAafLNRKIKGISLFRTVVFLPLAISSVVMAVVWQFVFntdngllnimlgwlgigpiPWLIEPRWAMVSLCLVSVWR 167
                                    55666588899999999*************************************************************** PP

                   BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG....lgt 139
                                    ++p+++++  aa++ +p+  +eaar++Ga++++ f+ +++P++   +   +++++++++ ++ l++ l++ +G     ++
  gi|121637926|ref|YP_978149.1| 168 SVPFATVVLLAAMQGVPETVYEAARIDGAGEIRQFVSITVPLIRGALSFVVVISIIHAFQAFDLVYVLTGANGgpetATY 247
                                    *********************************************************************99998977444 PP

                   BPD_transp_1 140 llleailgydyseisnggvlalviavlllnlvadilqrlldp 181
                                    +l   + +  +s+  +g++ al+ ++++++lv+ +lq  +  
  gi|121637926|ref|YP_978149.1| 248 VLGIMLFQHAFSFLEFGYASALAWVMFAILLVLTVLQLRITH 289
                                    444444444444444788888888888888888888766655 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00027       2.4      57     104 ..      51      98 ..       5     111 .. 0.79
   2 ?    3.6   0.3    0.0062        55      62     106 ..     223     267 ..     198     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00027
                          Pam17  57 leidptqqilglDplvvlglatlasgalGwllGpvlgsavfkllnrkk 104
                                    +++d+ ++++  Dpl++++++ +a+ ++G ++  v+ s v +++ ++k
  gi|121637926|ref|YP_978149.1|  51 VRLDNFRNLFTSDPLFLIAVVNTAVYTVGTVVPTVIVSLVVAAFLNRK 98 
                                    678999*************************99999888776654444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0062
                          Pam17  62 tqqilglDplvvlglatlasgalGwllGpvlgsavfkllnrkklk 106
                                    ++ +  +D ++vl+ a  +  ++ ++lG +l++++f++l+  +++
  gi|121637926|ref|YP_978149.1| 223 IHAFQAFDLVYVLTGANGGPETATYVLGIMLFQHAFSFLEFGYAS 267
                                    5567789******************************99876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1943.41
//
Query:       gi|121637927|ref|YP_978150.1|  [L=439]
Description: sugar-binding lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-49  168.7   0.5    3.8e-49  168.3   0.5    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    3.4e-29  102.5   0.0    4.3e-29  102.2   0.0    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
     0.0016   18.2   2.7     0.0064   16.3   2.7    2.1  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.5   6.4e-53   3.8e-49      12     314 ..      54     350 ..      44     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 6.4e-53
                                    HHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEE CS
                      SBP_bac_1  12 alvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaad 91 
                                     +v ++f++++p+ikV+   +g g ++q l++ +a+G++p Dv + +  ++a+la+ g+ll+l+++++ +     + +a+
  gi|121637927|ref|YP_978150.1|  54 RVV-NEFQRRYPDIKVRALLSGPGVMQQ-LATFCAGGKCP-DVLMAWELTYAELADRGVLLDLNTLLARD-----QAFAA 125
                                    567.9************98876666665.*********99.****************************9.....89999 PP

                                    EEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGG.......SHBHHHHHHHHHHHHHHCTCTHCCHCC CS
                      SBP_bac_1  92 klsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldp.......pwtWdelveaakklkekgkkpiggarg 158
                                     l s+  ++ +++ ++   +y +P +   + l+YNk+lf++ag++p       pw++ e+++aa+ l+++g+++  +++g
  gi|121637927|ref|YP_978150.1| 126 ELKSDSIGALYETfTFnggQYaFPEQWsGNFLFYNKQLFDDAGVPPppgswerPWSFAEFLDAAQALTKQGRSGRDRQWG 205
                                    999*9*******9899**********55**************************************************** PP

                                    EEHHHHHHHHHHHHHHHHTGGGEECCCT....HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTS CS
                      SBP_bac_1 159 gsasgtayyfalalakslggkvfdkdgg....gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGe 234
                                    + +++  +y a  +a ++g+++   +++    ++d +++ +a++++ +l      +k +  ++a+++++++ ++lf+ G+
  gi|121637927|ref|YP_978150.1| 206 FVNAWVSFYAAGLFAMNNGVPWSVPRMNpthlNFDHDGFLEAVQFYADLT-----NKHKVAPSAAEQQSMSTADLFSVGK 280
                                    **************************************************.....9************************ PP

                                    CSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                      SBP_bac_1 235 aamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgsknpeaAkkFldfllspe 312
                                    a++a++g+w           +++ + ++++  +++vaplP g+ g  +   +g+ glai ++s  +++A++F++f+++p 
  gi|121637927|ref|YP_978150.1| 281 AGIALAGHWR----------YQTFDRADGL--DFDVAPLPIGPRGRAACsdIGVTGLAIAATSRRKDQAWEFVKFATGPV 348
                                    **********..........5555555555..7799******9999999*****************************99 PP

                                    HH CS
                      SBP_bac_1 313 aq 314
                                    +q
  gi|121637927|ref|YP_978150.1| 349 GQ 350
                                    88 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   7.2e-33   4.3e-29       2     276 ..      55     374 ..      54     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 7.2e-33
                                    HHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH.......... CS
                      SBP_bac_8   2 lakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd.......... 70 
                                    +++ef+ ++ ++kv++   ++++++q+l +  a g+ pd+   +a+e   a+la++g+l dl++l   d+          
  gi|121637927|ref|YP_978150.1|  55 VVNEFQRRYpDIKVRAL-LSGPGVMQQLATFCAGGKCPDVL--MAWELTYAELADRGVLLDLNTLLARDQafaaelksds 131
                                    6899*****99****94.4789****************855..555556789***********66555555566655444 PP

                                    -HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS..........---BHHHHHHHHHHHHHH-........SEGG-- CS
                      SBP_bac_8  71 ltdalaavgydgklygvPyasetpyvliynkdlleka.........edpktwdellaaakklkgkf........glpdpa 133
                                    + + +++++++g  y++P +++   +l+ynk l+++a         e p++++e+l+aa++l+++         g+ + +
  gi|121637927|ref|YP_978150.1| 132 IGALYETFTFNGGQYAFPEQWSG-NFLFYNKQLFDDAgvppppgswERPWSFAEFLDAAQALTKQGrsgrdrqwGFVNAW 210
                                    66689999**************6.9***********99999999******************633345666666777766 PP

                                    -GGGGGGTHH.ETTEE---H..........HHH.HHHHHHHHHHHHTT-EE....-S...--SSTTTTTSBSEEEE-TTH CS
                      SBP_bac_8 134 sgwlqaalla.kdgksldddg........gkdglkealellkklkdngkty....dtga.davsefanGevaftingswd 199
                                     +++ a+l+a ++g++++           + dg+ ea++++++l ++ k+     + ++ ++ ++f  G++ ++++g w+
  gi|121637927|ref|YP_978150.1| 211 VSFYAAGLFAmNNGVPWSVPRmnpthlnfDHDGFLEAVQFYADLTNKHKVApsaaEQQSmSTADLFSVGKAGIALAGHWR 290
                                    667777777787777776555667777788999************9988776666444425666**************** PP

                                    HHHHH-T.TTSEEEE--S--.......EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTH CS
                      SBP_bac_8 200 iaaaqka.gkklgaivpkqg.......sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaals 271
                                    +++++ a g ++ +++++ g       s +g++gla+ + +  +d+ A++F+k++t p +qa   e   ++pv+ sa +s
  gi|121637927|ref|YP_978150.1| 291 YQTFDRAdGLDFDVAPLPIGprgraacSDIGVTGLAIAATSRRKDQ-AWEFVKFATGPVGQALIGESRLFVPVLRSAINS 369
                                    *****77478*****6533333366668889999***********9.***************************999887 PP

                                    HHHHH CS
                      SBP_bac_8 272 pevkk 276
                                      +++
  gi|121637927|ref|YP_978150.1| 370 HGFAN 374
                                    66665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.7   1.1e-06    0.0064       3      26 .]       7      30 ..       5      30 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                     TAT_signal  3 SRRdFLKgsAAaaAAaalggcaaa 26
                                    RR++L+g++A++AA +++ +a++
  gi|121637927|ref|YP_978150.1|  7 ERRSLLRGAGALTAASLAPWAAGC 30
                                   5****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3029.52
//
Query:       gi|121637928|ref|YP_978151.1|  [L=265]
Description: hypothetical protein BCG_2061c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-13   49.8   0.0    7.3e-13   49.2   0.0    1.3  1  NTF2      Nuclear transport factor 2 (NTF2) domain
    1.1e-07   32.4   0.9    1.1e-07   32.4   0.9    2.4  2  SnoaL_2   SnoaL-like domain
  ------ inclusion threshold ------
      0.088   12.9   0.0       0.74    9.9   0.0    2.2  1  SnoaL_4   SnoaL-like domain


Domain annotation for each model (and alignments):
>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.2e-16   7.3e-13       3     118 ..      10     128 ..       8     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.2e-16
                                    HHHHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHHHSSCSC.E.EEEEEEEEEEETSEGGGCEEEE CS
                           NTF2   3 kafvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffrslpftr.i.elkittvdaqpdeaslstgvlv 80 
                                     a+v+++ +a  a+dr g++ l+++da++++p+gs+p +g+eaI +f+++++  r i  ++  ++ +    + + +++ +
  gi|121637928|ref|YP_978151.1|  10 LAAVERSPQAAAAHDRAGWVGLFTGDARVEDPVGSQPQVGHEAIGRFYDTFIGPRdItFHRDLDIVSG---TVVLRDLEL 86 
                                    689****************************************************97799999****9...99******* PP

                                    EEEEEEEETTSCCE.EEEEEEEEEEEET...TTEEEEEEEEE CS
                           NTF2  81 mvtGelkvddfkkr.rkfsqtfilapqs...nkgyfvlnDif 118
                                    +v+++  v+ f ++ +++  + +  +++    ++y+ l++++
  gi|121637928|ref|YP_978151.1|  87 EVAMDSAVTVFIPAfLRYDLRPVTGEWQiaaLRAYWELPAMM 128
                                    ************99**************99999999999987 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.9   1.9e-11   1.1e-07       1      86 [.      13      96 ..      13     116 .. 0.79
   2 ?    0.7   0.4      0.14   8.2e+02      71      86 ..     197     233 ..     148     260 .. 0.47

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.9e-11
                                   HHHHHHHHHTTCHHHHHHTEEEEEEEEETTSE..EESHHHHHHHHHHHHHHEEEEEEEEEEE..EEETTEEEEEEEEEEEEE CS
                        SnoaL_2  1 vraflaalnagdldalaalfapdvvwedpgge..lrGreairaffralfaafpdlrfeihdv..vadgdrvavewtvtgtip 78
                                   v++  +a +a+d ++++ lf+ d+++edp+g+  ++G+eai +f+ ++    + +++++h+   +++g  v+   ++++   
  gi|121637928|ref|YP_978151.1| 13 VERSPQAAAAHDRAGWVGLFTGDARVEDPVGSqpQVGHEAIGRFYDTFI---GPRDITFHRDldIVSGTVVLRDLELEV--- 88
                                   6788899**********************44446**************8...5555555555559***99998888774... PP

                                   TTSSEEEE CS
                        SnoaL_2 79 atgrgvtv 86
                                   a +++vtv
  gi|121637928|ref|YP_978151.1| 89 AMDSAVTV 96
                                   66666666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                    EEEEEE.....................EETTSSEEEE CS
                        SnoaL_2  71 wtvtgt.....................ipatgrgvtv 86 
                                     t+t+t                     ++ tg+g tv
  gi|121637928|ref|YP_978151.1| 197 RTATMTlgedelldivelfeqlrgaswTKVTGAGSTV 233
                                    3333334444444444444444444444444444444 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00012      0.74      11     126 ..      11     118 ..       5     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEETTEEEEEEEE CS
                        SnoaL_4  11 dlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldgdtAtgrayl 90 
                                      v r  +++ ++d + ++ lFt da+v+ +  g++   g +ai +++ + +++++ t H       +ld    t++ + 
  gi|121637928|ref|YP_978151.1|  11 AAVERSPQAAAAHDRAGWVGLFTGDARVEDPV-GSQPQVGHEAIGRFYDTFIGPRDITFHR------DLDIVSGTVVLRD 83 
                                    5666777777788999999********99995.5666779999999999999888888887......5555555555555 PP

                                    EEEEEETTEEEEEE..EEEEEEEEEEETTEEEEEEE CS
                        SnoaL_4  91 latlvrdgdggrqvlaggryedelvredggWrisrr 126
                                    l  +v + d + +v++ ++++ +l+ + g+W+i+ +
  gi|121637928|ref|YP_978151.1|  84 LELEV-AMDSAVTVFIPAFLRYDLRPVTGEWQIAAL 118
                                    55553.335667788888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1886.57
//
Query:       gi|121637929|ref|YP_978152.1|  [L=186]
Description: pyrazinamidase/nicotinamidas pncA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-32  112.7   0.1    2.3e-32  112.6   0.1    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
       0.17   10.0   0.0       0.22    9.6   0.0    1.1  1  Flavi_NS5        Flavivirus RNA-directed RNA polymerase


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.1   2.5e-36   2.3e-32       2     170 ..       3     182 ..       2     186 .] 0.93

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 2.5e-36
                Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe...leevkgdlderkaaphfkpgttgael 78 
                                    al+++D+qndf+e+g  ++ + +a+ ++i++ l++a +   +v++t+d h     +  + ++    ++ph++ gt+ga++
  gi|121637929|ref|YP_978152.1|   3 ALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYH-HVVATKDFHIdpgDDFSGTPDYSSSWPPHCVSGTPGADF 81 
                                    9***********************************9999.7*****999889777777788899*************** PP

                Isochorismatase  79 vpelaplegdvvvdKt....rfsaf.....agtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAva 149
                                    +p+l   + + v+ K      +s+f     +gt+l ++L+++g++++ ++Giatd CV++ta da+++G  + v+ D +a
  gi|121637929|ref|YP_978152.1|  82 HPSLDTSAIEAVFYKGaytgAYSGFegvdeNGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTA 161
                                    ***************9777777888******************************************************* PP

                Isochorismatase 150 alspelhdaalkrlkqafatv 170
                                    ++s+++  aal++++ a +++
  gi|121637929|ref|YP_978152.1| 162 GVSADTTVAALEEMRTASVEL 182
                                    **************9766655 PP

>> Flavi_NS5  Flavivirus RNA-directed RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   2.5e-05      0.22     391     435 ..     113     159 ..     103     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 2.5e-05
                                    THHHHHHHHHHHHHHHTTEEEETTEEEEXXSSG..GGGGXXHHHHHT CS
                      Flavi_NS5 391 aerveawlkehgtdrlkrmavsgddcvvkpidd..rfalalsalndm 435
                                     + +++wl+++g+d +  + ++ d cv +  +d  r +la ++l d+
  gi|121637929|ref|YP_978152.1| 113 GTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDavRNGLATRVLVDL 159
                                    47789*************************99944556676777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1369.84
//
Query:       gi|121637930|ref|YP_978153.1|  [L=105]
Description: hypothetical protein BCG_2063c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-31  108.0   8.4    2.9e-31  107.8   8.4    1.0  1  DUF2784   Protein of Unknown function (DUF2784)
  ------ inclusion threshold ------
          4    7.8   8.0       0.12   12.7   1.0    1.9  2  2TM       2TM domain


Domain annotation for each model (and alignments):
>> DUF2784  Protein of Unknown function (DUF2784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   8.4   3.2e-35   2.9e-31      10     110 ..       1      99 [.       1     101 [. 0.98

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 3.2e-35
                        DUF2784  10 lHllfvlFvvlGglliwrwvrtlwlHlaaialvaasellglaCplTdlenqlreaageaal.eegFiehylekllyldlp 88 
                                    +H++f+++v++Gg+l++rw+rt+wlH++a+++++++++  ++CplT++e ++r++a  ++l ++gF++hy+++++y   p
  gi|121637930|ref|YP_978153.1|   1 MHFAFIAYVLAGGFLALRWRRTMWLHVPAVIWGIGIAAKRVDCPLTWVERWARTKAAMTPLsPDGFVAHYITGVIY---P 77 
                                    6***************************************************************************...* PP

                        DUF2784  89 eelttavqlllallvlllwvlv 110
                                    +++++a+ql+++++v+++w l+
  gi|121637930|ref|YP_978153.1|  78 AGWVAAAQLVMFAIVAASWTLY 99 
                                    *******************986 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   1.4e-05      0.12      17      51 ..       5      39 ..       2      55 .. 0.83
   2 ?   -1.2   1.0      0.29   2.6e+03      19      36 ..      88      96 ..      65     102 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                            2TM 17 lvvYlivniflilinl.gsswflwpilfWgiglllh 51
                                   ++ Y+++  fl l  + +  w  +p+++Wgig++++
  gi|121637930|ref|YP_978153.1|  5 FIAYVLAGGFLALR-WrRTMWLHVPAVIWGIGIAAK 39
                                   67788888888886.459999999*********986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                            2TM 19 vYlivniflilinlgssw 36
                                   +++iv           sw
  gi|121637930|ref|YP_978153.1| 88 MFAIV---------AASW 96
                                   22222.........2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 772.35
//
Query:       gi|121637931|ref|YP_978154.1|  [L=511]
Description: carboxylesterase LipT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-95  319.2   0.0    3.2e-94  316.6   0.0    1.8  1  COesterase     Carboxylesterase family
    9.8e-13   48.4   3.6    2.6e-06   27.4   0.1    2.3  2  Abhydrolase_3  alpha/beta hydrolase fold
     0.0014   18.2   0.1     0.0033   16.9   0.1    1.6  1  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.054   12.8   0.1      0.096   11.9   0.1    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
      0.091   11.6   0.0       0.21   10.4   0.0    1.5  1  Say1_Mug180    Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.6   0.0     9e-98   3.2e-94       6     502 ..      19     494 ..      13     504 .. 0.86

  Alignments for each domain:
  == domain 1  score: 316.6 bits;  conditional E-value: 9e-98
                                    EETTEEEEEEEEEESTCSEEEEEEEEESSB---GGGTTS--BE----SSEEECBS---BESEECSSSSSCGHHCHHHBES CS
                     COesterase   6 etslGkvrGkrvklksekevdaFlGiPYAepPvgelRFkkPepaepwtgvrdAtkfspaCpqnaeksekeekeleawvsE 85 
                                    +t +G v+G + +      v+ ++ iPYA +Pvg+lRF++P+pa+pw gvr +++f++  pq+++ + ++     ++ sE
  gi|121637931|ref|YP_978154.1|  19 RTATGIVEGFTRD-----GVHRWRSIPYARAPVGSLRFRAPQPAQPWPGVRHCHTFANCAPQQRRYTVMGIGR-YQTRSE 92 
                                    6778999999999.....9**************************************9999999988888754.456*** PP

                                    ---EEEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-SS.....TTSB CS
                     COesterase  86 DCLyLnvytPkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlstgd.....eeap 158
                                    DCL+Lnv tP+e   a++ lPV+V+ihGgg+  gs+ +  ydg aLa++ +++ V++nYRlG+lG l +++       ++
  gi|121637931|ref|YP_978154.1|  93 DCLTLNVVTPEE--PATQPLPVMVFIHGGGYILGSSATpiYDGAALARR-GCVYVSVNYRLGALGCLDLSSlstpqITLD 169
                                    **********85..467777****************999**********.****************98855333335678 PP

                                    S-HHHHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSGGGTTSBSEEEEES--TTSTTTSBSHHHHHHHH CS
                     COesterase 159 GNvGllDqvlALrWVkenIasFGGdpervtlfGesAGaasvsllllsplsrglfkraIlqSGsalspwaiqkkarkrakk 238
                                     Nv l D+vlALrWV++nIa+FGGdp +vt+fGesAGa + + ll+ p ++glf raI++S +    +  ++ a + a +
  gi|121637931|ref|YP_978154.1| 170 SNVYLRDLVLALRWVHDNIAEFGGDPGNVTIFGESAGAHITATLLAVPAAKGLFARAISESPA-AGMVRSREVAAEFAAR 248
                                    9************************************************************74.4445556669999*** PP

                                    HHHHTTS-CSSHHHHHHHHHCS-HHHHHHCCGG...SSSSSSTTC-SSS-B--SSSSSS-HHHHHHCGC..CSEEEEEEE CS
                     COesterase 239 lakkvgckassskelveclrsksaeelldaqek...aleasssklvsfaPvvdgdflpekPeellkseg..kvplliGvn 313
                                    +a+ +g     +++ ++ l++ s  +l++aq     +   +    ++++Pv+++d+lp +P e+++s    +vpl++G+n
  gi|121637931|ref|YP_978154.1| 249 FANLIGA---RTQDAANALMQASPAQLVEAQHHlirQGMRKRLGAFPIGPVFGDDYLPMDPVEAMRSGRvhAVPLIVGTN 325
                                    ******9...777788***************99887777888899**********************66*********** PP

                                    TTTTHHHHCCHSTTTSSSSHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHSTTTSSTCHHHHHHHHHHHHHHHHTHHH CS
                     COesterase 314 kdegllflaylldkeksvkkkeeklsesllkdelyleaekkeelseaikeeytdeadrddaeksrkallelltdvlfkap 393
                                    ++eg lf ++l         ++e      +++el   +  k + +e i+  y        +    +a+++l +d  f   
  gi|121637931|ref|YP_978154.1| 326 AEEGRLFTRFLGMLP-----TNE-----PMVEELLSGM--KPADRERITAAYP-------NYPAPSACIQLGGDFAFSSA 386
                                    *******99654432.....122.....2222222222..5666777777776.......5556789************* PP

                                    HHHHHHHHHHTT-SEEEEEEE--STTSSSTTTGSSBTTTTHHHHTTGGGTSGCS......S-HHHHHHHHHHHHHHHHHH CS
                     COesterase 394 vlrtaklhasrgspvYlYsfdyrnssskkpkwmgvvhgdeleyvfglpllekee......ftkedeklsrkmmtywtnFa 467
                                    + ++a++h  +++p+YlY++dy  ++ ++   +g++h++el  vf+ +  +         ++ +   +s+++ + w+ F 
  gi|121637931|ref|YP_978154.1| 387 AWQIAEAH-GANAPTYLYRYDYAPRTLRWS-GFGATHATELFAVFDIYRTRFGAlltaaaDRRAALRVSNEVQRRWRCFS 464
                                    ********.***************999997.69*************99886665755543444456699*********** PP

                                    HHSSTTSTTSS----B.TTTBEEEEESSSSSEEEE CS
                     COesterase 468 ktgnPnkeeeekWpkytkeeekylkinlkpkrvkk 502
                                    + g P       Wp+yt++++ +l ++++  r++ 
  gi|121637931|ref|YP_978154.1| 465 QIGVPGD----DWPAYTQDDRAVLVFDRRC-RIEF 494
                                    *****99....*************999885.4555 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.5   4.6e-08   0.00016       1      40 [.     113     151 ..     113     153 .. 0.87
   2 !   27.4   0.1   7.3e-10   2.6e-06      50     112 ..     175     235 ..     170     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.6e-08
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---T CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlA 40 
                                    +v++HGGG++lgs++t+    + la+  g+v vsv+Yrl 
  gi|121637931|ref|YP_978154.1| 113 MVFIHGGGYILGSSATPIYDGAALAR-RGCVYVSVNYRLG 151
                                    79***************666666776.69*********95 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 7.3e-10
                                    HHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SST CS
                  Abhydrolase_3  50 edalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdl 112
                                     d + alrw++++ +e+g dp +++++G+SaG++++a ++   +++g    a  +  +P+  +
  gi|121637931|ref|YP_978154.1| 175 RDLVLALRWVHDNIAEFGGDPGNVTIFGESAGAHITATLLAVPAAKG--LFARAISESPAAGM 235
                                    68899********99*********************99885555543..56666666664433 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.2e-07    0.0033      42     143 ..     171     276 ..     132     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-07
                                    HHHHHHHHHHHHHH...HHTTS--GGGEEEEEETHHHHHHHHHHH..H-GGG-SEEEEESE---CCCHHCSTTSTHHHCC CS
                   Peptidase_S9  42 qnefdDfiaaaeal...akegyvdserlaitGgSyGGyltgaaln..qrpdlFkaavaevpvvdvlrydsdtdllteeym 116
                                    ++ ++D++ a++++   ++e+  d+ ++ i+G S+G   t+++l+   ++ lF+ a++e p + ++r+      +++++ 
  gi|121637931|ref|YP_978154.1| 171 NVYLRDLVLALRWVhdnIAEFGGDPGNVTIFGESAGAHITATLLAvpAAKGLFARAISESPAAGMVRSREVAAEFAARFA 250
                                    45578999998888666777789**************9999888877999******************999777888887 PP

                                    CC--TTTCHHHHHHHHHH-CGGG---- CS
                   Peptidase_S9 117 ewgnpeeneegykelspyspldnvkay 143
                                    +   + + ++  ++l ++sp++ v+a+
  gi|121637931|ref|YP_978154.1| 251 NLIGA-RTQDAANALMQASPAQLVEAQ 276
                                    75554.566667777788877766644 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05     0.096      70     133 ..     189     256 ..     169     290 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                    Hydrolase_4  70 keehpel..plfllGhSmGGliallyl..lrypdkvaglilsaPalkikaklk.appllklllkllgkl 133
                                    + e ++   +++++G+S G+ i++++l     +  +a++i  +Pa ++  + + a ++++ +++l+g  
  gi|121637931|ref|YP_978154.1| 189 A-EFGGDpgNVTIFGESAGAHITATLLavPAAKGLFARAISESPAAGMVRSREvAAEFAARFANLIGAR 256
                                    3.333334789**************995444445788********998766444444444444444433 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.8e-05      0.21     114     209 ..     102     210 ..      86     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.8e-05
                    Say1_Mug180 114 petfdPkvD..pvllylHGGgfalklipvtl...vfLsnlrklfpdm.....ailvsDYtvtaa...kdqskkYplqvle 180
                                    pe+  P +   pv++++HGGg++l+   + +     L   +  + ++     a+  +D + +++   + +s+ Y + +  
  gi|121637931|ref|YP_978154.1| 102 PEE--PATQplPVMVFIHGGGYILGSSATPIydgAALARRGCVYVSVnyrlgALGCLDLSSLSTpqiTLDSNVYLRDLVL 179
                                    555..7776569************97766551222444444445444555565555666555541113455555555443 PP

                    Say1_Mug180 181 sla.vydylvkskg.fknvvvlGdSaGGnlv 209
                                    +l  v+d + +  g   nv+++G+SaG  + 
  gi|121637931|ref|YP_978154.1| 180 ALRwVHDNIAEFGGdPGNVTIFGESAGAHIT 210
                                    3322566665555423577777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 3817.49
//
Query:       gi|121637932|ref|YP_978155.1|  [L=218]
Description: lipoprotein lppI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1541.92
//
Query:       gi|121637933|ref|YP_978156.1|  [L=854]
Description: hypothetical protein BCG_2066c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-20   70.4   0.1    1.9e-19   69.1   0.1    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
    1.1e-14   54.4   0.3    3.9e-14   52.7   0.1    1.9  2  Epimerase        NAD dependent epimerase/dehydratase family
    2.9e-14   53.4   0.8    1.2e-13   51.3   0.8    2.1  1  NAD_binding_10   NAD(P)H-binding
    4.5e-10   39.0   0.0    8.9e-10   38.0   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-06   27.6   0.2    2.2e-05   23.7   0.1    2.2  2  RmlD_sub_bind    RmlD substrate binding domain
    1.7e-05   24.4   0.4      0.022   14.2   0.1    2.3  2  adh_short        short chain dehydrogenase
    0.00021   20.9   0.2    0.00039   20.1   0.2    1.4  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.025   13.7   0.0        1.3    8.2   0.0    2.7  3  NAD_binding_4    Male sterility protein
      0.033   13.6   0.1       0.12   11.7   0.1    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.068   13.7   0.7        1.8    9.1   0.1    3.2  2  CoA_binding_2    CoA binding domain
       0.12   12.6   0.0       0.32   11.2   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.98    8.5   3.2         19    4.3   3.2    2.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.1   1.3e-22   1.9e-19       2      73 .]     761     832 ..     760     832 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.3e-22
                                    --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    l++g+ILvae t+  ++a++  aa++vte GG++SHaA+vAre+g P+Vv +++at+ l  g l+ vDg+tG
  gi|121637933|ref|YP_978156.1| 761 LQPGEILVAEVTDVGYTAAFCYAAAVVTELGGPMSHAAVVAREFGFPCVVDAQGATRFLPPGALVEVDGATG 832
                                    6899****************************************************888888*********9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   2.6e-17   3.9e-14       1     117 [.       3     105 ..       3     112 .. 0.88
   2 ?   -1.5   0.0      0.94   1.4e+03     157     180 ..     113     135 ..     107     175 .. 0.57

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2.6e-17
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHH CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaas 80 
                                    i VtGa+G +G+ l+ +ll++g+ev+g++r    ++ +    ++++ +d++d++a+e ++   ++d+v h+A v g ++ 
  gi|121637933|ref|YP_978156.1|   3 IAVTGASGVLGRGLTARLLSQGHEVVGIARH---RPDSWPSSADFIAADIRDATAVESAMT--GADVVAHCAWVRGRND- 76 
                                    78****************************9...3333444448*****************..9*******66555555. PP

                                    HHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGG CS
                      Epimerase  81 sedpadfieknlqgtlnlleaarkagvkrllflsSse 117
                                            ++n+ gt n+l+a+ ++g  r++f sS +
  gi|121637933|ref|YP_978156.1|  77 --------HINIDGTANVLKAMAETGTGRIVFTSSGH 105
                                    ........689************************65 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.94
                                    HHHHT-EEEEEEESEEESTTS-TT CS
                      Epimerase 157 aaqyglnaiilrlfnlyGprngeg 180
                                     a+ gl+ +++r+  ++G +  ++
  gi|121637933|ref|YP_978156.1| 113 LADCGLEWVAVRCALIFGRN-VDN 135
                                    56678888999999999988.222 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.8   8.4e-17   1.2e-13       1     100 [.       7     105 ..       7     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 8.4e-17
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC....HH CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk....de 75 
                                    GA+G  Gr l+++ll++ ghev+ ++R+ p++ +     + ++ + +d+ d+ ++++a++gad+V  ++  +g+    + 
  gi|121637933|ref|YP_978156.1|   7 GASGVLGRGLTARLLSQ-GHEVVGIARHrPDSWP-----SSADFIAADIRDATAVESAMTGADVVAHCAWVRGRndhiNI 80 
                                    9****************.5********9566666.....5789**********************888844444123545 PP

                                    HHHHHHHHHHHHCT--EEEEEEETT CS
                 NAD_binding_10  76 egaknivdaakeagvkRfvlvsaig 100
                                    +g++n+++a+ e+g+ R+v+ s+ +
  gi|121637933|ref|YP_978156.1|  81 DGTANVLKAMAETGTGRIVFTSSGH 105
                                    55******************99864 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   5.9e-13   8.9e-10       1     116 [.       4     103 ..       4     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.9e-13
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +vtG++G lGr l  +L++ ++ + v ++  r +++          +++i +D++d+  +e a+ g+dvv h a    v+
  gi|121637933|ref|YP_978156.1|   4 AVTGASGVLGRGLTARLLSQGH-EVVGIARHRPDSWP-------SSADFIAADIRDATAVESAMTGADVVAHCA---WVR 72 
                                    59*******************6.55555555555555.......334599**********************94...466 PP

                      3Beta_HSD  81 gkltedeimkvnvkGTrnvleacvkagvrvlvYtSs 116
                                    g  ++   +++n+ GT nvl+a  ++g  ++v+tSs
  gi|121637933|ref|YP_978156.1|  73 G--RN---DHINIDGTANVLKAMAETGTGRIVFTSS 103
                                    6..33...589************************9 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   2.2e-05       1      60 [.       1      70 [.       1     103 [. 0.88
   2 ?    1.4   0.0     0.093   1.4e+02     133     166 ..     110     143 ..     106     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE--- CS
                  RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAA 60
                                   m+i vtGa+G lG+ L+++l ++g+ev+++ r+            ++d++da+av++++     dvv ++A 
  gi|121637933|ref|YP_978156.1|  1 MRIAVTGASGVLGRGLTARLLSQGHEVVGIARHrpdswpssadfiAADIRDATAVESAMTG--ADVVAHCAW 70
                                   89****************************9999999999999999999999999999988..789999995 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.093
                                    HHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHH CS
                  RmlD_sub_bind 133 EqavlaagkkalivRtswvygekgknfvktmlrl 166
                                    Eq+ ++ g +++ vR + ++g++  n+v++++ l
  gi|121637933|ref|YP_978156.1| 110 EQMLADCGLEWVAVRCALIFGRNVDNWVQRLFAL 143
                                    8899999999******************998765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.5e-05     0.022       3      71 ..       3      62 ..       1      67 [. 0.86
   2 !    7.9   0.0    0.0012       1.9     115     137 ..      82     104 ..      77     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                   + vtGas+ +Gr +  +l+++G +vv ++r+  +   + ++       a +i++D++d+++ve ++  a
  gi|121637933|ref|YP_978156.1|  3 IAVTGASGVLGRGLTARLLSQGHEVVGIARHRPDS--WPSS-------ADFIAADIRDATAVESAMTGA 62
                                   78*************************99996544..4444.......889999999999999998765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHCTTEEEEEEEEG CS
                      adh_short 115 ltravlpamlkqssGrIvnvsSv 137
                                     t+ vl+am +   GrIv++sS 
  gi|121637933|ref|YP_978156.1|  82 GTANVLKAMAETGTGRIVFTSSG 104
                                    68899999**************7 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   2.6e-07   0.00039       1     106 [.       3     107 ..       3     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                                    EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG....S CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy....s 76 
                                    I+v+Ga+G +G+ +++ ll++gh+v  + R            + + ++++d+ d   +++a+ g+dvv     +     +
  gi|121637933|ref|YP_978156.1|   3 IAVTGASGVLGRGLTARLLSQGHEVVGIARHRPDSWP-----SSADFIAADIRDATAVESAMTGADVVAHCAWVRgrndH 77 
                                    89****************************9865543.....5689*********************9877666678455 PP

                                    -HHHHHHHHHHHHHHHS-SEEEEEE---GG CS
                           NmrA  77 keiedgkklvdAakeaGvkhfiySslgddn 106
                                     +i+   ++ +A +e G  ++++ s g + 
  gi|121637933|ref|YP_978156.1|  78 INIDGTANVLKAMAETGTGRIVFTSSGHQP 107
                                    5556668999*************9988776 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00084       1.3       1      24 [.       5      29 ..       5      68 .. 0.83
   2 ?   -1.4   0.0      0.72   1.1e+03     110     136 ..      78     103 ..      73     112 .. 0.80
   3 ?    2.3   0.0     0.053        79     187     244 ..     109     165 ..     106     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00084
                                   EE-TTSHHHHHHHHHHHHHS-.T.E CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.k 24
                                   +TGa+G LG+ L ++LL++  ev  
  gi|121637933|ref|YP_978156.1|  5 VTGASGVLGRGLTARLLSQGHEVvG 29
                                   7****************99986533 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.72
                                    HHHHHHHHHHHHHTSSS--.-EEEEEE CS
                  NAD_binding_4 110 vNveGtrevlelakklkklkvllhvST 136
                                    +N++Gt +vl+  +++     +++ S+
  gi|121637933|ref|YP_978156.1|  78 INIDGTANVLKAMAETGTG-RIVFTSS 103
                                    8*********987777776.6777776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.053
                                    HHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB---TT CS
                  NAD_binding_4 187 vrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgdkeav 244
                                    v+++   +gl +v vR+  i g+ +  w+++    + +l +++a +v++ ++ d+ ++
  gi|121637933|ref|YP_978156.1| 109 VEQMLADCGLEWVAVRCALIFGRNVDNWVQRLF-ALPVLPAGYADRVVQVVHSDDAQR 165
                                    566777899***********************9.999***********9999987766 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.1e-05      0.12       2      81 ..       5      67 ..       4     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.1e-05
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81
                                   +TG +G  G  l+ +Ll++g+ev+gi r+         +++ +        +  ++ +D++D++++e+++  +  d v +
  gi|121637933|ref|YP_978156.1|  5 VTGASGVLGRGLTARLLSQGHEVVGIARHRP-------DSWPS--------SADFIAADIRDATAVESAMTGA--DVVAH 67
                                   9************************987543.......44432........2458888888888888877766..45555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0012       1.8      66     114 ..      81     129 ..       1     131 [. 0.76
   2 ?   -0.1   0.0      0.83   1.2e+03      38      87 ..     599     656 ..     595     671 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                    HHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHH CS
                  CoA_binding_2  66 eatpeivkealalgakavwlqpgsedeeaaelaeeagirvvgdrCilve 114
                                    + t++++k++++ g+ ++++ ++  ++ + +++++ g++ v  rC l+ 
  gi|121637933|ref|YP_978156.1|  81 DGTANVLKAMAETGTGRIVFTSSGHQPRVEQMLADCGLEWVAVRCALIF 129
                                    4588999**************************************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.83
                                    SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH-......-SEEEE-T CS
                  CoA_binding_2  38 eeilgekvyaslae.d.pepvdlvdvftppeatpeivkealalg......akavwlqp 87 
                                    +e+l + v ++l + + p+p+  v  ++   +++  ++++ +++      ++a+w+  
  gi|121637933|ref|YP_978156.1| 599 PELLVRMVAKTLRAvPaPQPPTPVIPLRAKPVALLAARQLRDREvrrdrmVRAIWVLR 656
                                    5777778888888877899999999999999999999999988544556688888765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021      0.32       2      62 ..       3      68 ..       2     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                   EEEE--.SHHHHHHHHHHHHTT-EEEEE-SSH....HHHHHHHHTTEEE-SSHHHHHHHCSEEEE- CS
                  NAD_binding_2  2 igfiGl.GvMGsnmalnllkagykvavynrtk....ekveelvaegakaaesieelvasldvvitm 62
                                   i++ G  Gv+G+ +  +ll++g++v+++ r++     +  +++a+ ++ a+ +e++++++dvv  +
  gi|121637933|ref|YP_978156.1|  3 IAVTGAsGVLGRGLTARLLSQGHEVVGIARHRpdswPSSADFIAADIRDATAVESAMTGADVVAHC 68
                                   66677549*********************99855556778999999**************999876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.2     0.013        19       3     128 ..       5     103 ..       3     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                                    EETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEE CS
                Polysacc_synt_2   3 vtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvf 82 
                                    vtGa+G +G+ l+ ++l++  + + +  +   +  +                +   + +d+rd++ +e+a++  + dvv 
  gi|121637933|ref|YP_978156.1|   5 VTGASGVLGRGLTARLLSQGHEVVGIARHRPDSWPS----------------SADFIAADIRDATAVESAMT--GADVVA 66 
                                    677777777777777776666655555443322211................11134689999999999999..999999 PP

                                    E------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  83 haAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                    h+A ++             + N+ gt nv++a  e+g  ++v+ S+
  gi|121637933|ref|YP_978156.1|  67 HCAWVRG---------RNDHINIDGTANVLKAMAETGTGRIVFTSS 103
                                    9996553.........223458888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (854 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 5847.72
//
Query:       gi|121637934|ref|YP_978157.1|  [L=4151]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.3e-177  586.4   5.3    1.9e-91  306.1   0.7    5.0  6  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
   8.1e-152  505.3   4.2      1e-89  301.2   0.1    2.6  2  Acyl_transf_1    Acyl transferase domain
   6.4e-119  394.4  15.6    3.9e-59  199.6   3.2    3.5  3  KR               KR domain
     2e-104  349.0  11.4    4.9e-53  180.3   1.5    2.5  2  PS-DH            Polyketide synthase dehydratase
    2.1e-87  289.0   7.0    5.7e-43  145.7   0.8    3.0  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    4.7e-42  144.2   0.2    1.7e-19   71.2   0.0    3.9  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    1.7e-30  105.7  12.0    4.7e-15   55.7   0.1    4.3  4  ADH_zinc_N       Zinc-binding dehydrogenase
    1.5e-28   99.5   0.0    1.1e-12   48.3   0.0    2.8  2  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    2.1e-28   98.5   0.0    2.6e-13   50.1   0.0    2.8  2  PP-binding       Phosphopantetheine attachment site
    9.1e-17   61.1  18.8    3.2e-09   36.5   0.9    3.9  4  adh_short        short chain dehydrogenase
    1.7e-13   50.6   3.9    6.5e-06   25.8   0.3    2.4  2  Epimerase        NAD dependent epimerase/dehydratase family
      3e-11   43.2   5.7    5.5e-05   22.6   0.3    2.8  2  Thiolase_N       Thiolase, N-terminal domain
    4.1e-10   39.5   0.4    8.4e-05   22.4   0.1    2.8  2  ADH_N            Alcohol dehydrogenase GroES-like domain
    7.9e-08   32.1   0.0      0.013   14.9   0.0    2.3  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.8e-08   31.6   0.5      0.011   14.9   0.1    2.2  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.5e-06   26.3   5.5      0.028   13.9   0.5    2.7  2  Creatininase     Creatinine amidohydrolase
    7.2e-06   25.7   7.3      0.022   14.3   0.8    2.5  2  NmrA             NmrA-like family
    0.00031   20.6   2.8        1.1    8.9   0.0    4.3  4  SAT              Starter unit:ACP transacylase in aflatoxin b
     0.0014   18.8   4.7       0.98    9.5   0.2    3.3  3  MLTR_LBD         MmyB-like transcription regulator ligand bin
     0.0034   16.9   5.5     0.0086   15.6   5.5    1.7  1  PikAIV_N         Narbonolide/10-deoxymethynolide synthase Pik
  ------ inclusion threshold ------
      0.014   15.3  13.9       0.38   10.6   0.1    4.4  4  YjeF_N           YjeF-related protein N-terminus
      0.027   14.3   5.3        4.4    7.2   0.1    4.0  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
      0.036   13.7   0.4         20    4.8   0.0    3.6  2  MoCF_biosynth    Probable molybdopterin binding domain
      0.079   12.6   2.9        4.8    6.7   0.1    3.2  3  Amdase           Arylmalonate decarboxylase
       0.45   10.2   3.7        4.2    7.1   0.2    2.8  2  GBP_PSP          Paralytic/GBP/PSP peptide


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.8   0.3   1.6e-90   1.1e-87       2     253 .]      35     281 ..      34     281 .. 0.97
   2 ?   -0.2   0.1      0.82   5.9e+02      95     147 ..     317     371 ..     315     396 .. 0.62
   3 ?   -2.9   0.2       5.7   4.1e+03     166     202 ..    1301    1334 ..    1296    1348 .. 0.87
   4 !  306.1   0.7   2.7e-94   1.9e-91       2     253 .]    2057    2304 ..    2056    2304 .. 0.97
   5 ?   -0.2   0.1      0.82   5.9e+02      95     147 ..    2340    2394 ..    2338    2419 .. 0.62
   6 ?   -2.8   0.1       5.2   3.8e+03     183     233 ..    3418    3467 ..    3416    3480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 293.8 bits;  conditional E-value: 1.6e-90
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadklydpparaagkiktklggfld.vddfdpeffgis 78 
                                    ep+aivGm++rfPgg+d +e +w+++ + rd +se+p+dr wd  +l+dp++++  k++++ ggf+d v+dfdp+ffgis
  gi|121637934|ref|YP_978157.1|  35 EPIAIVGMSCRFPGGVDsPEGLWQMVADARDVMSEFPTDRgWDLAGLFDPDPDVRHKSYARTGGFVDgVADFDPAFFGIS 114
                                    89****************************************************************************** PP

                                    HHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHH CS
                  ketoacyl-synt  79 preaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagri 158
                                    p+ea amdpq+r+lle +weale+ag++p+ l+gs++gvf+G+  g y+   +l e   e ++++  +g+ +++v++gr+
  gi|121637934|ref|YP_978157.1| 115 PSEALAMDPQHRMLLELSWEALERAGIDPTGLRGSATGVFAGLIVGGYG---MLAE---EIEGYR-LTGM-TSSVASGRV 186
                                    **********************************************995...5653...357899.9997.********* PP

                                    HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-B CS
                  ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvl 238
                                    +y lgl+Gp+v+vdtACsSslva+h+av slrsge+d+alaGGv++  tp  ++ fs+ + l+pdgrck+++ +adG+ +
  gi|121637934|ref|YP_978157.1| 187 AYVLGLEGPAVSVDTACSSSLVALHMAVGSLRSGECDLALAGGVTVNATPTVFVEFSRHRGLAPDGRCKPYAGRADGVGW 266
                                    ******************************************************************************** PP

                                    B-EEEEEEEEECHHH CS
                  ketoacyl-synt 239 GEGvGavvLkrleda 253
                                    +EG G++vL+rl+da
  gi|121637934|ref|YP_978157.1| 267 SEGGGMLVLQRLSDA 281
                                    *************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.82
                                    HHHHHHHHHTS-HHTC...TTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHH CS
                  ketoacyl-synt  95 aawealedagltpeel...dgsrvgvfiGvgagdyaalaaldedgsevkaspkavg 147
                                    +++ al++agl+++e+   +g  +g ++G  ++ +a la++ +d + + + p ++g
  gi|121637934|ref|YP_978157.1| 317 VVRAALANAGLSAAEVdvvEGHGTGTTLGDPIEAQALLATYGQDRG-EPGEPLWLG 371
                                    6789*********999666666699999988886654444443333.222222222 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.7
                                     SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEE CS
                  ketoacyl-synt  166 GpsvtvdtACsSslvavhaavqslrsgeadvalaGGv 202 
                                     G+ v vd+  ++  +a+++a   l +ge +v+l GG 
  gi|121637934|ref|YP_978157.1| 1301 GRIVLVDSDAATDDAAIAMA---LATGEPQVVLRGGQ 1334
                                     7889999999999*****99...**********9995 PP

  == domain 4  score: 306.1 bits;  conditional E-value: 2.7e-94
                                     --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTH CS
                  ketoacyl-synt    2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadklydpparaagkiktklggfld.vddfdpeffg 76  
                                     +p+aivGm++r+Pgg++ ++++w++L++grd  se+padr wd  +ly+p+++aag ++t+ ggf+d v dfdp+ffg
  gi|121637934|ref|YP_978157.1| 2057 DPIAIVGMACRYPGGVNsPDDMWDMLIQGRDVLSEFPADRgWDLAGLYNPDPDAAGACYTRTGGFVDgVGDFDPAFFG 2134
                                     69***************9************************************************************ PP

                                     HHHHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHH CS
                  ketoacyl-synt   77 ispreaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanvi 154 
                                     + p+ea amdpqqr+lle +weale+ag++p+ l+gs++gvf+Gv+ + y+  aa      +v++++  +g  l++v+
  gi|121637934|ref|YP_978157.1| 2135 VGPSEALAMDPQQRMLLELSWEALERAGIDPTGLRGSATGVFAGVMTQGYGMFAAE-----PVEGFR-LTGQ-LSSVA 2205
                                     ************************************************99753333.....477889.9999.***** PP

                                     HHHHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTT CS
                  ketoacyl-synt  155 agrisyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpk 232 
                                     +gr++y lgl+Gp+v+vdtACsSslva+h+av slrsge+d+alaGGv++  tp  ++ fs+++ lspdgrckaf+++
  gi|121637934|ref|YP_978157.1| 2206 SGRVAYVLGLEGPAVSVDTACSSSLVALHMAVGSLRSGECDLALAGGVTVNATPDIFVEFSRWRGLSPDGRCKAFAAA 2283
                                     ****************************************************************************** PP

                                     B-SB-BB-EEEEEEEEECHHH CS
                  ketoacyl-synt  233 adGfvlGEGvGavvLkrleda 253 
                                     adG+ ++EG G++vL+rl+da
  gi|121637934|ref|YP_978157.1| 2284 ADGTGFSEGGGMLVLQRLSDA 2304
                                     *******************98 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.82
                                     HHHHHHHHHTS-HHTC...TTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHH CS
                  ketoacyl-synt   95 aawealedagltpeel...dgsrvgvfiGvgagdyaalaaldedgsevkaspkavg 147 
                                     +++ al++agl+++e+   +g  +g ++G  ++ +a la++ +d + + + p ++g
  gi|121637934|ref|YP_978157.1| 2340 VVRAALANAGLSAAEVdvvEGHGTGTTLGDPIEAQALLATYGQDRG-EPGEPLWLG 2394
                                     6789*********999666666699999988886654444443333.222222222 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 5.2
                                     HHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TTSGGGTTBTTB CS
                  ketoacyl-synt  183 haavqslrsgeadvalaGGvellltpeavagfsaag.llspdgrckafdpka 233 
                                      +av+++ ++  dv++a G      p av+g +a+g ++ ++ +  +f+ ++
  gi|121637934|ref|YP_978157.1| 3418 RVAVSAIAANFRDVMIALGLY--PDPDAVMGVEACGvVIETSLNKGSFAVGD 3467
                                     68999**************87..88999999999997777777777777777 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.2   0.1   1.4e-92     1e-89       1     318 [.     559     880 ..     559     881 .. 0.97
   2 !  204.4   1.3   4.3e-63   3.1e-60       1     317 [.    2582    2893 ..    2582    2895 .. 0.94

  Alignments for each domain:
  == domain 1  score: 301.2 bits;  conditional E-value: 1.4e-92
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--T.TGGGSHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpe.glldaiqfvqpaLaavqialaellks 79 
                                    vfvf+GqGsQw GMG eLl+t +afa+ i++++eaf++  ++s+ dvlr +p  + ld++++vqp+L+av+++lael+ks
  gi|121637934|ref|YP_978157.1| 559 VFVFPGQGSQWLGMGIELLDTAPAFAQQIDACAEAFAEFVDWSLVDVLRGAPGaPGLDRVDVVQPVLFAVMVSLAELWKS 638
                                    8**************************************************97689************************ PP

                                    TT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS...HHHHHHH...TT.EEEEEEECC CS
                  Acyl_transf_1  80 kGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel..aeeeeklr.cqddvvgavanspr 156
                                      v+p+av+GHS+GE+Aaa+vagals+ +a+++v lrs+l + lagpg+m +++   ++ +  l+   d+v+ av+n+p+
  gi|121637934|ref|YP_978157.1| 639 VAVHPDAVIGHSQGEIAAAYVAGALSLRDAARVVTLRSKLLAGLAGPGGMVSIACgaDQARDLLApFGDRVSIAVVNGPS 718
                                    *****************************************************998766777777899************ PP

                                    CCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHH CS
                  Acyl_transf_1 157 rvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaey 236
                                     vv+sg+ +al+el++ +s ++++ ++++v++a+hs  v+ai+  la+al  i pr  +  + s+++ +  ++  l+a+y
  gi|121637934|ref|YP_978157.1| 719 AVVVSGEVGALEELIAVCSTKELRTRRIEVDYASHSVEVEAIRGPLAEALSGIEPRSTRTVFFSTVTGNRLDTAGLDADY 798
                                    ******************************************************************************** PP

                                    HHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TC.CCCCCTEETTSS-HHHCHHHHHHHHHHC CS
                  Acyl_transf_1 237 wvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvks.atlvGklkrdltdflvtflyllakahlt 315
                                    w++n+r++v+f++av++a e+++++f+e spH+ l  ++e+t+    d+ s a +v++l r+ ++ l++fl ++a a+++
  gi|121637934|ref|YP_978157.1| 799 WYRNVRQTVLFDQAVRNACEQGYRTFIESSPHPALITGVEETFAACTDGDSeAIVVPTLGRGDGG-LHRFLLSAASAFVA 877
                                    *********************************************77776515678*********.************** PP

                                    T-H CS
                  Acyl_transf_1 316 gse 318
                                    g++
  gi|121637934|ref|YP_978157.1| 878 GVA 880
                                    997 PP

  == domain 2  score: 204.4 bits;  conditional E-value: 4.3e-63
                                     EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHH CS
                  Acyl_transf_1    1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellk 78  
                                     vfvf+GqGsQw GMGm L +  ++fa++ +     +  +    + +v+   +e+ll++++f+qpaL+av++al+ ll 
  gi|121637934|ref|YP_978157.1| 2582 VFVFPGQGSQWLGMGMGLHAGYPVFAEAFNTVVGELDRHLLRPLREVMWGHDENLLNSTEFAQPALFAVEVALFRLLG 2659
                                     8********************9999987775544444444448*********************************** PP

                                     HTT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECC CS
                  Acyl_transf_1   79 skGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavanspr 156 
                                     s Gvrp+ v+GHS+GEl+aa+vag ls+e+a++ v+ r+rlm+ l   g+m av+ aeee +     +v  a++n+p 
  gi|121637934|ref|YP_978157.1| 2660 SWGVRPDFVMGHSIGELSAAHVAGVLSLENAAVLVAARGRLMQALPAGGAMVAVQAAEEEVRPLLSAEVDIAAVNGPA 2737
                                     ********************************************************99999999************** PP

                                     CCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHH CS
                  Acyl_transf_1  157 rvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsa 234 
                                     + visg q+a++++  +++++g+++++ +v+ a+hsp +d++ d+ a+  a ia   p++  is ++ + +     sa
  gi|121637934|ref|YP_978157.1| 2738 SLVISGAQNAVAAVADQLRADGRRVHQLAVSHAFHSPLMDPMIDEFAAVAAGIAIGRPTIGVISNVTGQLAGDDFGSA 2815
                                     ****************************************************************************** PP

                                     HHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHH CS
                  Acyl_transf_1  235 eywvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllaka 312 
                                     +yw++ +r++vrfa+ v+ a + +   f+e+ p   l+a +e+ l    dv++ t+   l++d  +   t+  + a+ 
  gi|121637934|ref|YP_978157.1| 2816 AYWRRHIRQAVRFADSVRFAQAAGGSRFLEVGPSGGLVASIEESLP---DVAVTTMSA-LRKDRPE-PATLTNAVAQG 2888
                                     ********************999999******************99...787777665.8999988.88888888888 PP

                                     HHCT- CS
                  Acyl_transf_1  313 hltgs 317 
                                     ++tg+
  gi|121637934|ref|YP_978157.1| 2889 FVTGM 2893
                                     88876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   3.2   5.4e-62   3.9e-59       1     179 [.    1680    1858 ..    1680    1859 .. 0.97
   2 ?   -1.2   0.0       2.2   1.6e+03      15      34 ..    3281    3300 ..    3262    3316 .. 0.68
   3 !  199.6   3.2   5.4e-62   3.9e-59       1     179 [.    3710    3888 ..    3710    3889 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 5.4e-62
                                     SEEEEETTTSHHHHHHHHHHH.HHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwla.ekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77  
                                     gt+litGG+G  G ++ar+ + ++g r+lvl+sR+++  + +++l+ael+a ga+v+vva+D +d++a+++++++i  
  gi|121637934|ref|YP_978157.1| 1680 GTVLITGGTGMAGSAVARHVVaRHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQVVACDAADRAALAKVIADIPV 1757
                                     89****************9873688***************************************************96 PP

                                     HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR   78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaf 155 
                                     ++ p++Gvih+Ag+l+d+ ++++t ++++ vl++Kv++aw+Lhel++d ++  fv+fSS+agl+gs gqanYaaaN+f
  gi|121637934|ref|YP_978157.1| 1758 QH-PLSGVIHTAGALDDAVVMSLTPDRVDVVLRSKVDAAWHLHELTRDLDVSAFVMFSSMAGLVGSSGQANYAAANSF 1834
                                     65.*************************************************************************** PP

                                     HHHHHHHHHHHHHTEEEEEE--BT CS
                             KR  156 lDalaeyrrsqglpavsinwglwa 179 
                                     lDala++rr++glpa+s+ wglw+
  gi|121637934|ref|YP_978157.1| 1835 LDALAAHRRAHGLPAISLGWGLWD 1858
                                     ***********************7 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                     HHHHHHHHHHS-EEEEE-SS CS
                             KR   15 elarwlaekgarhlvllsRs 34  
                                     +l  wl ++ga  lv+++R 
  gi|121637934|ref|YP_978157.1| 3281 VLQSWLTRDGAGVLVVMTRG 3300
                                     34567777777777777765 PP

  == domain 3  score: 199.6 bits;  conditional E-value: 5.4e-62
                                     SEEEEETTTSHHHHHHHHHHH.HHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwla.ekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77  
                                     gt+litGG+G  G ++ar+ + ++g r+lvl+sR+++  + +++l+ael+a ga+v+vva+D +d++a+++++++i  
  gi|121637934|ref|YP_978157.1| 3710 GTVLITGGTGMAGSAVARHVVaRHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQVVACDAADRAALAKVIADIPV 3787
                                     89****************9873688***************************************************96 PP

                                     HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR   78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaf 155 
                                     ++ p++Gvih+Ag+l+d+ ++++t ++++ vl++Kv++aw+Lhel++d ++  fv+fSS+agl+gs gqanYaaaN+f
  gi|121637934|ref|YP_978157.1| 3788 QH-PLSGVIHTAGALDDAVVMSLTPDRVDVVLRSKVDAAWHLHELTRDLDVSAFVMFSSMAGLVGSSGQANYAAANSF 3864
                                     65.*************************************************************************** PP

                                     HHHHHHHHHHHHHTEEEEEE--BT CS
                             KR  156 lDalaeyrrsqglpavsinwglwa 179 
                                     lDala++rr++glpa+s+ wglw+
  gi|121637934|ref|YP_978157.1| 3865 LDALAAHRRAHGLPAISLGWGLWD 3888
                                     ***********************7 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   1.5   6.9e-56   4.9e-53       1     296 [.     926    1194 ..     926    1196 .. 0.91
   2 !  173.5   2.7   8.1e-54   5.8e-51       1     297 [.    2940    3215 ..    2940    3216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 6.9e-56
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlp 78  
                                     hpllG+ v+ +++  vv   rl+++ +pwL+DH+v + v++Pg+g++e+a+ A+ ++     + +l ++++ ++l lp
  gi|121637934|ref|YP_978157.1|  926 HPLLGAVVDLPASGGVVLTGRLSPNVQPWLADHAVSDVVLFPGTGFVELAIRAGDEVG----CSVLDELTLAAPLLLP 999 
                                     9********************************************************9....999************* PP

                                     -SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HHH CS
                          PS-DH   79 edepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrsvssae 156 
                                      +++v vq+++ + +d+++     ++ifSr++++++w +ha+G +r +  ++   +dl+ ++++ a +     v++a+
  gi|121637934|ref|YP_978157.1| 1000 ATGSVAVQVVVDAGRDSNS---RGVSIFSRADAQAGWLLHAEGILRPGSVEP--GADLSVWPPAGAVT-----VDVAD 1067
                                     **************77665...69**********99**********776655..88888885555555.....99999 PP

                                     HHHHHHHHSEEE-GGG--EEEEEEETTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEEE CS
                          PS-DH  157 fYerlaargleyGpsFqglralwrgdgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylPv 234 
                                      Yerla rg+ yGp+F+gl+a+w++  e +ae+rlpe++  g + + +hPallDa+l+++++a      + d+++lP+
  gi|121637934|ref|YP_978157.1| 1068 GYERLATRGYRYGPAFRGLTAMWARGEEIFAEVRLPEAAG-GVGGFGVHPALLDAVLHAVVIA-----GDPDELALPF 1139
                                     ************************************9987.6667*************88554.....579******* PP

                                     EEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XXXX CS
                          PS-DH  235 aierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrvereal 296 
                                     a++ ++++      ++   v+ar++ +g    +++++l d  G +v+++  +  r+v++++l
  gi|121637934|ref|YP_978157.1| 1140 AWQGVSLHA-----TGASAVRARIAPAGP--SAVSVELADGLGLPVLSVASMVARPVTERQL 1194
                                     ********6.....445678888877774..5899***********************9876 PP

  == domain 2  score: 173.5 bits;  conditional E-value: 8.1e-54
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlp 78  
                                     h llG+ ++ +++  vv   rl+++ + wL+DH+v g +++Pgag++e+a+ A+ ++     + ++ ++++ ++lvlp
  gi|121637934|ref|YP_978157.1| 2940 HALLGAVIDLPASGGVVLTGRLSPRVQGWLADHSVAGVTIFPGAGFVELAIRAGDEVG----CGVVDELTLAAPLVLP 3013
                                     99*******************************************************9....778************* PP

                                     -SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HHH CS
                          PS-DH   79 edepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrsvssae 156 
                                      +++v vq++++  +++ +     ++++Sr++ g++w++ha+G +r++ +++  ++dl+ ++++ a p     v++a+
  gi|121637934|ref|YP_978157.1| 3014 ASGSVAVQVVVNGPDESGV---RGVSVYSRGDVGTGWVLHAEGALRAGSAEP--TADLAMWPPAGAVP-----VEVAD 3081
                                     ***********98855444...69**********************998887..78888886666666.....88999 PP

                                     HHHHHHHHSEEE-GGG--EEEEEEETTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEEE CS
                          PS-DH  157 fYerlaargleyGpsFqglralwrgdgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylPv 234 
                                      Y++la+rg+ yG +F+gl+a+wr+ +e++ae++lp+++  +   + +hP+llDaal+++++ +++++++++++ +P+
  gi|121637934|ref|YP_978157.1| 3082 GYQQLAERGYGYGLAFRGLTAMWRRGDEVFAEVALPADAGVSVTGFGVHPVLLDAALHAVVLSAESAERGQGSVLVPF 3159
                                     ************************************999999999*************9888888899********** PP

                                     EEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XXXXX CS
                          PS-DH  235 aierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrvereals 297 
                                     +++ ++++       +   v+ar++  g    +++++l d  G +v+++  +  r+v++++l+
  gi|121637934|ref|YP_978157.1| 3160 SWQGVSLHA-----AGASAVRARIAPVGP--SAVSIELADGLGLPVLSVASMLARPVTDQQLR 3215
                                     ********6.....344788888888884..58999**********************99876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   0.8   7.9e-46   5.7e-43       1     117 [.     289     407 ..     289     408 .. 0.98
   2 !  145.7   0.8   7.9e-46   5.7e-43       1     117 [.    2312    2430 ..    2312    2431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 7.9e-46
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG..SCTS CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar..kqpl 78 
                                    +av++gsavn+dga+n+ltapng +q+r++++ala+ag+++++vd+ve hgtgt+lgDpiE++al +++g+++    +pl
  gi|121637934|ref|YP_978157.1| 289 LAVVVGSAVNQDGASNGLTAPNGPSQQRVVRAALANAGLSAAEVDVVEGHGTGTTLGDPIEAQALLATYGQDRGepGEPL 368
                                    69*********************************************************************9999999** PP

                                    EEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  79 avgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    ++gSvKsn+GH++aAaGva++ik+vla++h+ +p+tl++
  gi|121637934|ref|YP_978157.1| 369 WLGSVKSNMGHTQAAAGVAGVIKMVLAMRHELLPATLHV 407
                                    **************************************8 PP

  == domain 2  score: 145.7 bits;  conditional E-value: 7.9e-46
                                     SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG..SC CS
                Ketoacyl-synt_C    1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar..kq 76  
                                     +av++gsavn+dga+n+ltapng +q+r++++ala+ag+++++vd+ve hgtgt+lgDpiE++al +++g+++    +
  gi|121637934|ref|YP_978157.1| 2312 LAVVVGSAVNQDGASNGLTAPNGPSQQRVVRAALANAGLSAAEVDVVEGHGTGTTLGDPIEAQALLATYGQDRGepGE 2389
                                     69*********************************************************************9999999 PP

                                     TSEEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C   77 plavgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117 
                                     pl++gSvKsn+GH++aAaGva++ik+vla++h+ +p+tl++
  gi|121637934|ref|YP_978157.1| 2390 PLWLGSVKSNMGHTQAAAGVAGVIKMVLAMRHELLPATLHV 2430
                                     ****************************************8 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   1.5e-21   1.1e-18       4     132 ..    1540    1670 ..    1537    1671 .. 0.89
   2 !   71.2   0.0   2.3e-22   1.7e-19       4     132 ..    3570    3700 ..    3567    3701 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.5e-21
                                     SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE-- CS
                   ADH_zinc_N_2    4 devidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyef 77  
                                     d++ d+r+ +fe    aatgg+g+Dvvld+++ge +++asl+++++gG ++++g++   ++ +  a++  g + ++  
  gi|121637934|ref|YP_978157.1| 1540 DHISDSRSLEFEdkfrAATGGRGFDVVLDSLAGE-FVDASLRLVAPGGVFLEMGKT-DIRDPGVIAQQYPGVRYRAFD 1615
                                     8999999999999999****************99.66*******888*******54.455566666667788888888 PP

                                     GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEE CS
                   ADH_zinc_N_2   78 lfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiV 132 
                                     lf++ +++ a+il+ela+l+ +G lr  +  +f+  +a+ A+ryl ++r++GK+V
  gi|121637934|ref|YP_978157.1| 1616 LFEAGPDRIAQILAELATLFGDGVLRLLPVTTFDVRRAPAALRYLSQARHTGKVV 1670
                                     88776779**********************************************9 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 2.3e-22
                                     SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE-- CS
                   ADH_zinc_N_2    4 devidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyef 77  
                                     d++ d+r+ +fe    aatgg+g+Dvvld+++ge +++asl+++++gG ++++g++   ++ +  a++  g + ++  
  gi|121637934|ref|YP_978157.1| 3570 DHISDSRSLEFEdkfrAATGGRGFDVVLDSLAGE-FVDASLRLVAPGGVFLEMGKT-DIRDPGVIAQQYPGVRYRAFD 3645
                                     8999999999999999****************99.66*******888*******54.455566666667788888888 PP

                                     GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEE CS
                   ADH_zinc_N_2   78 lfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiV 132 
                                     lf++ +++ a+il+ela+l+ +G lrp +  +f+  +a+ A+ryl ++r++GK+V
  gi|121637934|ref|YP_978157.1| 3646 LFEAGPDRIAQILAELATLFGDGVLRPLPVTTFDVRRAPAALRYLSQARHTGKVV 3700
                                     88776779**********************************************9 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   6.5e-18   4.7e-15       1      90 [.    1504    1593 ..    1504    1614 .. 0.90
   2 ?   -1.9   0.5       4.3   3.1e+03      10      63 ..    1728    1788 ..    1724    1793 .. 0.53
   3 !   55.7   0.1   6.5e-18   4.7e-15       1      90 [.    3534    3623 ..    3534    3644 .. 0.90
   4 ?   -1.9   0.5       4.3   3.1e+03      10      63 ..    3758    3818 ..    3754    3823 .. 0.53

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 6.5e-18
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT.ESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklG.adevinykea.dlverikeltggegvdvvfecvGsgatleaal 76  
                                     gvG+aavqlA++lG ev+a++s+  k + ++ +G  d  i  ++  +++++ +++tgg+g+dvv++ ++ g+ ++a+l
  gi|121637934|ref|YP_978157.1| 1504 GVGMAAVQLARHLGLEVFATASKG-KWDTLRAMGfDDDHISDSRSlEFEDKFRAATGGRGFDVVLDSLA-GEFVDASL 1579
                                     9*******************9988.69*******756667666888***********************.******** PP

                                     HCEEEEEEEEECSC CS
                     ADH_zinc_N   77 kllkpgGrlvvvGg 90  
                                     +l++pgG +  +G 
  gi|121637934|ref|YP_978157.1| 1580 RLVAPGGVFLEMGK 1593
                                     *********99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                                     HHHTT-EEEEEESSHH.HHHHHHHTTESEEEET......TTC.HH.HHHHHHHTTTSSEEEEE CS
                     ADH_zinc_N   10 AkalGaeviavdssee.klelakklGadeviny......kea.dl.verikeltggegvdvvf 63  
                                     ++a+Ga+v +v+ ++  +++lak + ad  + +      ++a  l ++ + +lt ++ vdvv+
  gi|121637934|ref|YP_978157.1| 1728 LAAAGAQVQVVACDAAdRAALAKVI-ADIPVQHplsgviHTAgALdDAVVMSLT-PDRVDVVL 1788
                                     5689996666555555045555544.4444444344444223333044455555.77777776 PP

  == domain 3  score: 55.7 bits;  conditional E-value: 6.5e-18
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT.ESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklG.adevinykea.dlverikeltggegvdvvfecvGsgatleaal 76  
                                     gvG+aavqlA++lG ev+a++s+  k + ++ +G  d  i  ++  +++++ +++tgg+g+dvv++ ++ g+ ++a+l
  gi|121637934|ref|YP_978157.1| 3534 GVGMAAVQLARHLGLEVFATASKG-KWDTLRAMGfDDDHISDSRSlEFEDKFRAATGGRGFDVVLDSLA-GEFVDASL 3609
                                     9*******************9988.69*******756667666888***********************.******** PP

                                     HCEEEEEEEEECSC CS
                     ADH_zinc_N   77 kllkpgGrlvvvGg 90  
                                     +l++pgG +  +G 
  gi|121637934|ref|YP_978157.1| 3610 RLVAPGGVFLEMGK 3623
                                     *********99985 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.3
                                     HHHTT-EEEEEESSHH.HHHHHHHTTESEEEET......TTC.HH.HHHHHHHTTTSSEEEEE CS
                     ADH_zinc_N   10 AkalGaeviavdssee.klelakklGadeviny......kea.dl.verikeltggegvdvvf 63  
                                     ++a+Ga+v +v+ ++  +++lak + ad  + +      ++a  l ++ + +lt ++ vdvv+
  gi|121637934|ref|YP_978157.1| 3758 LAAAGAQVQVVACDAAdRAALAKVI-ADIPVQHplsgviHTAgALdDAVVMSLT-PDRVDVVL 3818
                                     5689996666555555045555544.4444444344444223333044455555.77777776 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.6e-15   1.1e-12       1     112 []     410     524 ..     410     524 .. 0.94
   2 !   48.3   0.0   1.6e-15   1.1e-12       1     112 []    2433    2547 ..    2433    2547 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.6e-15
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeeskeeslprLlvlsgrteeavea 76 
                                    P+p+++ ++ g +++ t p  wp g+    +gv+sfG++G+n+Hvi+++ +   r+e+   +     +v+s+++e+a++ 
  gi|121637934|ref|YP_978157.1| 410 PSPHVD-WSAGAVELLTAPRVWPAGArtrrAGVSSFGISGTNAHVIIEAVPVVPRREAGW-AGPVVPWVVSAKSESALRG 487
                                    99****.******************999***********************999999998.6777789************ PP

                 KAsynt_C_assoc  77 llekleehlldaellsllneilseeisr.lpyRGyav 112
                                    ++++l+++ + ++ l++++   s + ++ +++R+ +v
  gi|121637934|ref|YP_978157.1| 488 QAARLAAYVRGDDGLDVADVGWSLAGRSvFEHRAVVV 524
                                    *******************999998888899999876 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 1.6e-15
                 KAsynt_C_assoc    1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeeskeeslprLlvlsgrteeav 74  
                                     P+p+++ ++ g +++ t p  wp g+    +gv+sfG++G+n+Hvi+++ +   r+e+   +     +v+s+++e+a+
  gi|121637934|ref|YP_978157.1| 2433 PSPHVD-WSAGAVELLTAPRVWPAGArtrrAGVSSFGISGTNAHVIIEAVPVVPRREAGW-AGPVVPWVVSAKSESAL 2508
                                     99****.******************999***********************999999998.6777789********** PP

                 KAsynt_C_assoc   75 eallekleehlldaellsllneilseeisr.lpyRGyav 112 
                                     + ++++l+++ + ++ l++++   s + ++ +++R+ +v
  gi|121637934|ref|YP_978157.1| 2509 RGQAARLAAYVRGDDGLDVADVGWSLAGRSvFEHRAVVV 2547
                                     *********************999998888899999876 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   3.6e-16   2.6e-13       4      67 .]    1970    2034 ..    1968    2034 .. 0.94
   2 !   45.5   0.0     1e-14   7.3e-12       2      66 ..    4000    4065 ..    3999    4066 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3.6e-16
                     PP-binding    4 relvaevlg.vpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     r  +a+vlg + +e+idpd  + dlG+DSl+ave+ ++l+ + g++++++ +f++pt+++la y+
  gi|121637934|ref|YP_978157.1| 1970 RLHIATVLGnITPEAIDPDKAFQDLGFDSLTAVEMRNRLKSATGLSLSPTLIFDYPTPNRLASYI 2034
                                     567899999679999***********************************************997 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 1e-14
                     PP-binding    2 klrelvaevlgv.pleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaay 66  
                                      +r+ +a+vlg  ++e+idpd  + +lG+DSl+ave+ ++l+ + g++++++ +f++p+ a+la y
  gi|121637934|ref|YP_978157.1| 4000 LVRSHIATVLGSaSPEAIDPDRAFQELGFDSLTAVEMRNRLKSATGLSLSPTLIFDYPNSAALAGY 4065
                                     6899*******758888**********************************************998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       3.1   2.2e+03       2      32 ..    1495    1525 ..    1494    1529 .. 0.89
   2 !   36.5   0.9   4.5e-12   3.2e-09       2     161 ..    1681    1840 ..    1680    1849 .. 0.86
   3 ?   -2.1   0.3       3.1   2.2e+03       2      32 ..    3525    3555 ..    3524    3559 .. 0.89
   4 !   36.5   0.9   4.5e-12   3.2e-09       2     161 ..    3711    3870 ..    3710    3879 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.1
                                     EEEEESTTSHHHHHHHHHHHHTT-EEEEEES CS
                      adh_short    2 vvlvtGassGIGraiakelakeGakvvvvdr 32  
                                      vl+  +++G+G a ++     G +v+++++
  gi|121637934|ref|YP_978157.1| 1495 RVLIHAGTGGVGMAAVQLARHLGLEVFATAS 1525
                                     58999*********************99775 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 4.5e-12
                                     EEEEESTTSHHHHHHHHHH.HHTT-EEEE.EESCHHH...HHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                      adh_short    2 vvlvtGassGIGraiakel.akeGakvvv.vdrseek...leevakelkeegakalaiqvDvtdreevealvekavkk 74  
                                     +vl+tG+++  G a+a+++ a+ G++ +v v+r+  +   ++e+++el ++ga++ ++++D +dr+++ ++++++  +
  gi|121637934|ref|YP_978157.1| 1681 TVLITGGTGMAGSAVARHVvARHGVRNLVlVSRRGPDapgAAELVAELAAAGAQVQVVACDAADRAALAKVIADIPVQ 1758
                                     69**************99725789998887887754422268999999999************************887 PP

                                     HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short   75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152 
                                     + +l  +++ AG   ++ + +l+ ++++ v+   + ++ +l ++  + +      + v  sS+ag+v++ g+a Y+A+
  gi|121637934|ref|YP_978157.1| 1759 H-PLSGVIHTAGALDDAVVMSLTPDRVDVVLRSKVDAAWHLHELT-RDL---DVSAFVMFSSMAGLVGSSGQANYAAA 1831
                                     5.8**********99***********9999999999999887764.443...58999********************9 PP

                                     HHHHHHHHH CS
                      adh_short  153 Kaavagltr 161 
                                       ++++l+ 
  gi|121637934|ref|YP_978157.1| 1832 NSFLDALAA 1840
                                     888888765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.1
                                     EEEEESTTSHHHHHHHHHHHHTT-EEEEEES CS
                      adh_short    2 vvlvtGassGIGraiakelakeGakvvvvdr 32  
                                      vl+  +++G+G a ++     G +v+++++
  gi|121637934|ref|YP_978157.1| 3525 RVLIHAGTGGVGMAAVQLARHLGLEVFATAS 3555
                                     58999*********************99775 PP

  == domain 4  score: 36.5 bits;  conditional E-value: 4.5e-12
                                     EEEEESTTSHHHHHHHHHH.HHTT-EEEE.EESCHHH...HHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                      adh_short    2 vvlvtGassGIGraiakel.akeGakvvv.vdrseek...leevakelkeegakalaiqvDvtdreevealvekavkk 74  
                                     +vl+tG+++  G a+a+++ a+ G++ +v v+r+  +   ++e+++el ++ga++ ++++D +dr+++ ++++++  +
  gi|121637934|ref|YP_978157.1| 3711 TVLITGGTGMAGSAVARHVvARHGVRNLVlVSRRGPDapgAAELVAELAAAGAQVQVVACDAADRAALAKVIADIPVQ 3788
                                     69**************99725789998887887754422268999999999************************887 PP

                                     HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short   75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152 
                                     + +l  +++ AG   ++ + +l+ ++++ v+   + ++ +l ++  + +      + v  sS+ag+v++ g+a Y+A+
  gi|121637934|ref|YP_978157.1| 3789 H-PLSGVIHTAGALDDAVVMSLTPDRVDVVLRSKVDAAWHLHELT-RDL---DVSAFVMFSSMAGLVGSSGQANYAAA 3861
                                     5.8**********99***********9999999999999887764.443...58999********************9 PP

                                     HHHHHHHHH CS
                      adh_short  153 Kaavagltr 161 
                                       ++++l+ 
  gi|121637934|ref|YP_978157.1| 3862 NSFLDALAA 3870
                                     888888765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   9.1e-09   6.5e-06       1     116 [.    1682    1816 ..    1682    1837 .. 0.75
   2 !   25.8   0.3   9.1e-09   6.5e-06       1     116 [.    3712    3846 ..    3712    3867 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.1e-09
                                     EEEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHH....H CS
                      Epimerase    1 ilVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl.........elveldltdrsalerlfke....e 63  
                                     +l+tG+tG+ Gsa+++++ +++ ++ ++ ++r+  + + a++  +         ++v +d  dr+al++++++    +
  gi|121637934|ref|YP_978157.1| 1682 VLITGGTGMAGSAVARHVVARHgVRnLVLVSRRGPDAPGAAELVAelaaagaqvQVVACDAADRAALAKVIADipvqH 1759
                                     79**************9987776665777777755554444333379************************9822224 PP

                                     T-SEEEE--S.---HHHHHHSH...HHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEG CS
                      Epimerase   64 qpdavihlAa.vggvaassedp...adfieknlqgtlnlleaarkagvkrllflsSs 116 
                                         vih A+   +  + s +p     ++++ +  +++l e  r+ +v  ++ +sS 
  gi|121637934|ref|YP_978157.1| 1760 PLSGVIHTAGaLDDAVVMSLTPdrvDVVLRSKVDAAWHLHELTRDLDVSAFVMFSSM 1816
                                     5567****8855444333333311134678*************************93 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9.1e-09
                                     EEEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHH....H CS
                      Epimerase    1 ilVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl.........elveldltdrsalerlfke....e 63  
                                     +l+tG+tG+ Gsa+++++ +++ ++ ++ ++r+  + + a++  +         ++v +d  dr+al++++++    +
  gi|121637934|ref|YP_978157.1| 3712 VLITGGTGMAGSAVARHVVARHgVRnLVLVSRRGPDAPGAAELVAelaaagaqvQVVACDAADRAALAKVIADipvqH 3789
                                     79**************9987776665777777755554444333379************************9822224 PP

                                     T-SEEEE--S.---HHHHHHSH...HHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEG CS
                      Epimerase   64 qpdavihlAa.vggvaassedp...adfieknlqgtlnlleaarkagvkrllflsSs 116 
                                         vih A+   +  + s +p     ++++ +  +++l e  r+ +v  ++ +sS 
  gi|121637934|ref|YP_978157.1| 3790 PLSGVIHTAGaLDDAVVMSLTPdrvDVVLRSKVDAAWHLHELTRDLDVSAFVMFSSM 3846
                                     5567****8855444333333311134678*************************93 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   7.7e-08   5.5e-05      66     112 ..     186     230 ..     165     236 .. 0.87
   2 !   21.7   0.8   1.5e-07    0.0001      68     112 ..    2211    2253 ..    2197    2257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.7e-08
                                    HHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  66 aalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                    +a  +g+  e pav v+ +csS+l a+++a++s+++ge+d ++agGv
  gi|121637934|ref|YP_978157.1| 186 VAYVLGL--EGPAVSVDTACSSSLVALHMAVGSLRSGECDLALAGGV 230
                                    5666677..889**********************************8 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.5e-07
                                     HHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N   68 lkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112 
                                       +g+  e pav v+ +csS+l a+++a++s+++ge+d ++agGv
  gi|121637934|ref|YP_978157.1| 2211 YVLGL--EGPAVSVDTACSSSLVALHMAVGSLRSGECDLALAGGV 2253
                                     55566..789**********************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.2e-07   8.4e-05       1      60 [.    1385    1440 ..    1385    1448 .. 0.93
   2 !   14.3   0.0     4e-05     0.028       1      61 [.    3414    3471 ..    3414    3486 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60  
                                     pg+v++ ++a + +  D++i  g       ++  lG E +G+v+evgp+v++++vGd V+
  gi|121637934|ref|YP_978157.1| 1385 PGQVRVAMRAIAANFRDIMITLG----MFTHDALLGGEGAGVVVEVGPGVTEFSVGDSVF 1440
                                     57999***************999....699999*************************97 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4e-05
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvv 61  
                                     pg+v++ v+a + +  D++i+ g   l   ++ ++G E++G+v e+  +  +++vGdrV+ 
  gi|121637934|ref|YP_978157.1| 3414 PGQVRVAVSAIAANFRDVMIALG---LYPDPDAVMGVEACGVVIETSLNKGSFAVGDRVMG 3471
                                     589*******************9...788999***************99999*******96 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.9e-05     0.013       1      75 [.    1683    1756 ..    1683    1804 .. 0.85
   2 !   14.9   0.0   1.9e-05     0.013       1      75 [.    3713    3786 ..    3713    3834 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                     EEETTTSHHHHHHHHHHHHC.T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
                  GDP_Man_Dehyd    1 LiTGiaGfiGsylaelLlek.gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75  
                                     LiTG++G  Gs +a++ +++ g +  ++v r    + g  e +a+     +  +++++ +D  D+++l +++a++ 
  gi|121637934|ref|YP_978157.1| 1683 LITGGTGMAGSAVARHVVARhGVRNLVLVSRRGPDAPGAAELVAELA--AAGAQVQVVACDAADRAALAKVIADIP 1756
                                     9***************9987578888888888777777776666544..45679******************9984 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-05
                                     EEETTTSHHHHHHHHHHHHC.T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
                  GDP_Man_Dehyd    1 LiTGiaGfiGsylaelLlek.gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75  
                                     LiTG++G  Gs +a++ +++ g +  ++v r    + g  e +a+     +  +++++ +D  D+++l +++a++ 
  gi|121637934|ref|YP_978157.1| 3713 LITGGTGMAGSAVARHVVARhGVRNLVLVSRRGPDAPGAAELVAELA--AAGAQVQVVACDAADRAALAKVIADIP 3786
                                     9***************9987578888888888777777776666544..45679******************9984 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.5e-05     0.011       1     127 [.    1682    1814 ..    1682    1817 .. 0.75
   2 !   14.9   0.1   1.5e-05     0.011       1     127 [.    3712    3844 ..    3712    3847 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                     EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                Polysacc_synt_2    1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77  
                                     vl+tG++G  Gs++ r+++++  +++++l++r        ++ + +el++     ++ +v +d +d++ l+k++ ++ 
  gi|121637934|ref|YP_978157.1| 1682 VLITGGTGMAGSAVARHVVARhGVRNLVLVSRRGPDAPGAAELV-AELAAAGA--QVQVVACDAADRAALAKVIADIP 1756
                                     89***************998869*********999887776654.45555555..4458899***********99877 PP

                                     -SE....EEE--.----HHHHHHSH...HHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                Polysacc_synt_2   78 vdv....vfhaA.AlKhVPlveenp...leaiktNvlgtenvieaaieagvkkvvliS 127 
                                     v+     v+h+A Al    ++   p     +++  v ++ ++ e + + +v+++v+ S
  gi|121637934|ref|YP_978157.1| 1757 VQHplsgVIHTAgALDDAVVMSLTPdrvDVVLRSKVDAAWHLHELTRDLDVSAFVMFS 1814
                                     6643344888774666655555444111345788888888888888888888888887 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                                     EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                Polysacc_synt_2    1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77  
                                     vl+tG++G  Gs++ r+++++  +++++l++r        ++ + +el++     ++ +v +d +d++ l+k++ ++ 
  gi|121637934|ref|YP_978157.1| 3712 VLITGGTGMAGSAVARHVVARhGVRNLVLVSRRGPDAPGAAELV-AELAAAGA--QVQVVACDAADRAALAKVIADIP 3786
                                     89***************998869*********999887776654.45555555..4458899***********99877 PP

                                     -SE....EEE--.----HHHHHHSH...HHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                Polysacc_synt_2   78 vdv....vfhaA.AlKhVPlveenp...leaiktNvlgtenvieaaieagvkkvvliS 127 
                                     v+     v+h+A Al    ++   p     +++  v ++ ++ e + + +v+++v+ S
  gi|121637934|ref|YP_978157.1| 3787 VQHplsgVIHTAgALDDAVVMSLTPdrvDVVLRSKVDAAWHLHELTRDLDVSAFVMFS 3844
                                     6643344888774666655555444111345788888888888888888888888887 PP

>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   3.9e-05     0.028      94     235 ..    1699    1840 ..    1673    1844 .. 0.69
   2 !   13.9   0.5   3.9e-05     0.028      94     235 ..    3729    3870 ..    3703    3874 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                   Creatininase   94 slarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aaeeseeeegggH.Agel 169 
                                      +arhG+r++vlv+  g   +  +e+++el+a   +  v++++a +  a     +++   +  ++++ +g +H Ag l
  gi|121637934|ref|YP_978157.1| 1699 VVARHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQVVACDAADRAAL----AKV-IaDIPVQHPLSGVIHtAGAL 1771
                                     478***************99999999999*99995555554433333333....222.22455566666889989*** PP

                   Creatininase  170 EtSlmlalrpelVrmdraedpeeaklakeg.....vstaedaeelspsGvlGdpskataekGealleaave 235 
                                     + ++++ l+p+ V+     + ++a   +e      vs   ++++    G +G+  +a+ ++ + +l+a+++
  gi|121637934|ref|YP_978157.1| 1772 DDAVVMSLTPDRVDVVLRSKVDAAWHLHELtrdldVSAFVMFSS--MAGLVGSSGQANYAAANSFLDALAA 1840
                                     **************654333333322222256544433334433..8999999999999999999998876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
                   Creatininase   94 slarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aaeeseeeegggH.Agel 169 
                                      +arhG+r++vlv+  g   +  +e+++el+a   +  v++++a +  a     +++   +  ++++ +g +H Ag l
  gi|121637934|ref|YP_978157.1| 3729 VVARHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQVVACDAADRAAL----AKV-IaDIPVQHPLSGVIHtAGAL 3801
                                     478***************99999999999*99995555554433333333....222.22455566666889989*** PP

                   Creatininase  170 EtSlmlalrpelVrmdraedpeeaklakeg.....vstaedaeelspsGvlGdpskataekGealleaave 235 
                                     + ++++ l+p+ V+     + ++a   +e      vs   ++++    G +G+  +a+ ++ + +l+a+++
  gi|121637934|ref|YP_978157.1| 3802 DDAVVMSLTPDRVDVVLRSKVDAAWHLHELtrdldVSAFVMFSS--MAGLVGSSGQANYAAANSFLDALAA 3870
                                     **************654333333322222256544433334433..8999999999999999999998876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.8   3.1e-05     0.022       1      64 [.    1682    1754 ..    1682    1761 .. 0.82
   2 !   14.3   0.8   3.1e-05     0.022       1      64 [.    3712    3784 ..    3712    3791 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                     EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S......-SHHHHHHHHSTTE..EEES-TT-HHHHHHHHTT CS
                           NmrA    1 IlviGaTGrqGksvvrallk.aghkvralvRdt......kselakslkeaGve..lvkgdlddkeslvealkg 64  
                                     +l++G+TG  G++v+r++++ +g +  +lv           el+++l++aG++  +v+ d+ d++ l++++ +
  gi|121637934|ref|YP_978157.1| 1682 VLITGGTGMAGSAVARHVVArHGVRNLVLVSRRgpdapgAAELVAELAAAGAQvqVVACDAADRAALAKVIAD 1754
                                     79**************998755655555554447799999***********752168************9976 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.1e-05
                                     EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S......-SHHHHHHHHSTTE..EEES-TT-HHHHHHHHTT CS
                           NmrA    1 IlviGaTGrqGksvvrallk.aghkvralvRdt......kselakslkeaGve..lvkgdlddkeslvealkg 64  
                                     +l++G+TG  G++v+r++++ +g +  +lv           el+++l++aG++  +v+ d+ d++ l++++ +
  gi|121637934|ref|YP_978157.1| 3712 VLITGGTGMAGSAVARHVVArHGVRNLVLVSRRgpdapgAAELVAELAAAGAQvqVVACDAADRAALAKVIAD 3784
                                     79**************998755655555554447799999***********752168************9976 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.022        16     104     128 ..     643     667 ..     620     674 .. 0.79
   2 !    8.9   0.0    0.0015       1.1     194     240 .]     707     753 ..     694     753 .. 0.87
   3 ?   -0.3   0.1         1   7.4e+02     106     127 ..    2667    2688 ..    2659    2698 .. 0.85
   4 ?    2.3   0.0      0.16   1.1e+02     182     240 .]    2714    2772 ..    2698    2772 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                            SAT 104 stylvGlCtGllaAaavacskslse 128
                                    +  ++G+++G +aAa va + sl +
  gi|121637934|ref|YP_978157.1| 643 PDAVIGHSQGEIAAAYVAGALSLRD 667
                                    3489**************9998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                            SAT 194 srvyisavssss.vtisGpPstleallksskakkkkkksklpiyapyH 240
                                     rv i++v+++s v++sG   +le+l++ +++k+ +++ ++++  + H
  gi|121637934|ref|YP_978157.1| 707 DRVSIAVVNGPSaVVVSGEVGALEELIAVCSTKELRTR-RIEVDYASH 753
                                    799*******999*********************9998.888876655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                            SAT  106 ylvGlCtGllaAaavacsksls 127 
                                      ++G+++G l+Aa va   sl+
  gi|121637934|ref|YP_978157.1| 2667 FVMGHSIGELSAAHVAGVLSLE 2688
                                     799************9877765 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.16
                            SAT  182 aefneekglppasrvyisavssss.vtisGpPstleallksskakkkkkksklpiyapyH 240 
                                     ++  ee     ++ v i+av++++ ++isG  ++++a+ ++ +a+ ++ + +l ++ ++H
  gi|121637934|ref|YP_978157.1| 2714 QAAEEEVRPLLSAEVDIAAVNGPAsLVISGAQNAVAAVADQLRADGRRVH-QLAVSHAFH 2772
                                     555555554466999******9999****************999999865.999999998 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0014      0.98      59     106 ..    1689    1736 ..    1681    1778 .. 0.81
   2 ?   -2.7   0.0       8.1   5.8e+03      46      72 ..    2762    2788 ..    2724    2790 .. 0.59
   3 !    9.5   0.2    0.0014      0.98      59     106 ..    3719    3766 ..    3711    3808 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                       MLTR_LBD   59 glrpliedweevaralvarLraeaarrpddpalaalvaeLsaaspefa 106 
                                     g++   + ++ var+ v++L     r pd p +a+lvaeL+aa ++++
  gi|121637934|ref|YP_978157.1| 1689 GMAGSAVARHVVARHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQ 1736
                                     66777788999******************************9877654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.1
                       MLTR_LBD   46 perNllrlvfldpglrpliedweevar 72  
                                       + ++   f++p + p+i + ++va+
  gi|121637934|ref|YP_978157.1| 2762 VHQLAVSHAFHSPLMDPMIDEFAAVAA 2788
                                     333345677899999999988888886 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0014
                       MLTR_LBD   59 glrpliedweevaralvarLraeaarrpddpalaalvaeLsaaspefa 106 
                                     g++   + ++ var+ v++L     r pd p +a+lvaeL+aa ++++
  gi|121637934|ref|YP_978157.1| 3719 GMAGSAVARHVVARHGVRNLVLVSRRGPDAPGAAELVAELAAAGAQVQ 3766
                                     66777788999******************************9877654 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   5.5   1.2e-05    0.0086       8      28 ..      10      30 ..       7      32 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                       PikAIV_N  8 eALRaSLkEnERLRqqNrrLt 28
                                   eALR++L   ERL++ Nr+L 
  gi|121637934|ref|YP_978157.1| 10 EALRKALVQVERLKRTNRALL 30
                                   9******************97 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00054      0.38      12      58 ..    1473    1522 ..    1467    1581 .. 0.65
   2 ?    0.5   0.4      0.69     5e+02      36      87 ..    1686    1737 ..    1656    1756 .. 0.67
   3 ?    9.6   0.2    0.0011      0.81      21      58 ..    3513    3552 ..    3497    3611 .. 0.66
   4 ?    0.3   0.5      0.76   5.4e+02      36      87 ..    3716    3767 ..    3686    3785 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                         YjeF_N   12 vaevlrallg......nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv 58  
                                     +++v+++++       + +++++vl+ +G g  G  ++++ArhL   g++V +
  gi|121637934|ref|YP_978157.1| 1473 ISAVFTTAYYafihlaDVQPGQRVLIHAGTGGVGMAAVQLARHL---GLEVFA 1522
                                     33322222223577878999************************...766666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.69
                         YjeF_N   36 gnnGgdglaaArhL.aqegakVtvllleeeekldedaeralellkkaggkvve 87  
                                     g +G  g a+Arh  a++g++  vl+ ++ ++ ++ a + +++l +ag +v+ 
  gi|121637934|ref|YP_978157.1| 1686 GGTGMAGSAVARHVvARHGVRNLVLVSRRGPDAPGAA-ELVAELAAAGAQVQV 1737
                                     5567777888888877778877775555544444444.444444455555544 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0011
                         YjeF_N   21 g.....nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv 58  
                                            + ++++vl+ +G g  G  ++++ArhL   g++V +
  gi|121637934|ref|YP_978157.1| 3513 AlvdlaAARSGQRVLIHAGTGGVGMAAVQLARHL---GLEVFA 3552
                                     23455578899***********************...766666 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.76
                         YjeF_N   36 gnnGgdglaaArhL.aqegakVtvllleeeekldedaeralellkkaggkvve 87  
                                     g +G  g a+Arh  a++g++  vl+ ++ ++ ++ a + +++l +ag +v+ 
  gi|121637934|ref|YP_978157.1| 3716 GGTGMAGSAVARHVvARHGVRNLVLVSRRGPDAPGAA-ELVAELAAAGAQVQV 3767
                                     5567777888888877778877775555544444444.444444445555544 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0073       5.3       3      30 ..     199     226 ..     197     235 .. 0.88
   2 ?    7.2   0.1    0.0062       4.4       3      30 ..    2222    2249 ..    2220    2260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEE CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvL 30 
                                    + +aCs+ ++al++A + ++sg++  +L
  gi|121637934|ref|YP_978157.1| 199 VDTACSSSLVALHMAVGSLRSGECDLAL 226
                                    578*******************998877 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0062
                                     EE-GGGHHHHHHHHHHHHHHTTS-SEEE CS
                    ACP_syn_III    3 lnaaCsgfvyalsvAdaliesgaakrvL 30  
                                     + +aCs+ ++al++A + ++sg++  +L
  gi|121637934|ref|YP_978157.1| 2222 VDTACSSSLVALHMAVGSLRSGECDLAL 2249
                                     578*******************998877 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.029        21      59      88 ..    1681    1710 ..    1661    1736 .. 0.90
   2 ?    4.8   0.0     0.028        20      59      88 ..    3711    3740 ..    3646    3766 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                                     EEEEESS-SSSTT--HHHHHHHHHSEE-HH CS
                  MoCF_biosynth   59 viittGGtGptpdDvtpealaklfekeleg 88  
                                      +++tGGtG++   v + ++a+ + + l++
  gi|121637934|ref|YP_978157.1| 1681 TVLITGGTGMAGSAVARHVVARHGVRNLVL 1710
                                     69********************99987765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.028
                                     EEEEESS-SSSTT--HHHHHHHHHSEE-HH CS
                  MoCF_biosynth   59 viittGGtGptpdDvtpealaklfekeleg 88  
                                      +++tGGtG++   v + ++a+ + + l++
  gi|121637934|ref|YP_978157.1| 3711 TVLITGGTGMAGSAVARHVVARHGVRNLVL 3740
                                     69********************99987764 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1        10   7.1e+03     164     195 ..     688     719 ..     667     724 .. 0.76
   2 ?    4.7   0.0     0.028        20     163     213 ..    1494    1544 ..    1471    1548 .. 0.79
   3 ?    6.7   0.1    0.0066       4.8     156     213 ..    3517    3574 ..    3498    3578 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 10
                         Amdase 164 allisCGGLrtldvvreledelglpvvssalA 195
                                     + i+CG  +++d+ ++  d++ ++vv  + A
  gi|121637934|ref|YP_978157.1| 688 MVSIACGADQARDLLAPFGDRVSIAVVNGPSA 719
                                    45699*********************998777 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                         Amdase  163 dallisCGGLrtldvvreledelglpvvssalAGlwdavrlagldaraage 213 
                                     + +li  G      + ++l ++lgl v + a  G wd++r++g d    + 
  gi|121637934|ref|YP_978157.1| 1494 QRVLIHAGTGGVGMAAVQLARHLGLEVFATASKGKWDTLRAMGFDDDHISD 1544
                                     5567766655555567799************************99776555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0066
                         Amdase  156 vaaapeadallisCGGLrtldvvreledelglpvvssalAGlwdavrlagldaraage 213 
                                     +aaa++ + +li  G      + ++l ++lgl v + a  G wd++r++g d    + 
  gi|121637934|ref|YP_978157.1| 3517 LAAARSGQRVLIHAGTGGVGMAAVQLARHLGLEVFATASKGKWDTLRAMGFDDDHISD 3574
                                     4577888899998876666777789*************************99776555 PP

>> GBP_PSP  Paralytic/GBP/PSP peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0058       4.2      15      21 ..     250     256 ..     248     257 .. 0.92
   2 ?    2.8   0.4      0.13        91      15      20 ..    2273    2278 ..    2272    2279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0058
                                    TTS-EEE CS
                        GBP_PSP  15 aDGRCKP 21 
                                    +DGRCKP
  gi|121637934|ref|YP_978157.1| 250 PDGRCKP 256
                                    9****** PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                     TTS-EE CS
                        GBP_PSP   15 aDGRCK 20  
                                     +DGRCK
  gi|121637934|ref|YP_978157.1| 2273 PDGRCK 2278
                                     9****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (4151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 1.48u 0.33s 00:00:01.81 Elapsed: 00:00:00.52
# Mc/sec: 24097.17
//
Query:       gi|121637935|ref|YP_978158.1|  [L=74]
Description: hypothetical protein BCG_2068c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.4   0.2      0.048   14.1   0.2    1.0  1  NYN       NYN domain
        0.1   13.0   0.0       0.14   12.6   0.0    1.1  1  DciA      Dna[CI] antecedent, DciA


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   5.4e-06     0.048      97     144 ..      13      60 ..       6      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-06
                            NYN  97 dtivLvsgD.gDFaplveklrergkrVevllaeeastsseLisaadefi 144
                                    d +vL + D +D+++ v ++r     V+  l  e+++++eL++ +de i
  gi|121637935|ref|YP_978158.1|  13 DAVVLSADDaADLSDRVYQVRCAAEDVVTAL-DEGAAATELRDLCDELI 60 
                                    677777777************6666556666.889***********987 PP

>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05      0.14      36      82 ..      24      70 ..      22      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DciA 36 elaahcrpvklrdgtLvvevesgawateLryqkpqllerlneelgee 82
                                   +l+++++ v+   +  v + ++ga+ateLr + ++l+++++++ g++
  gi|121637935|ref|YP_978158.1| 24 DLSDRVYQVRCAAEDVVTALDEGAAATELRDLCDELIRAARAADGWR 70
                                   5777888888888889999**********************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 501.94
//
Query:       gi|121637936|ref|YP_978159.1|  [L=111]
Description: hypothetical protein BCG_2069 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-40  136.0   0.1      7e-40  135.9   0.1    1.0  1  RbpA      RNA polymerase-binding protein


Domain annotation for each model (and alignments):
>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9   0.1   3.9e-44     7e-40       1     104 []       4     106 ..       4     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 3.9e-44
                           RbpA   1 ralrGsrlGaksleedervelaprqevsYacakghetevtfaaeaevPetwecrrcGkeakl.dgeepeeekkekpyrtH 79 
                                    r+lrGsrlGa s+e+d++++laprq ++Y++++g+e+ev+fa++ae+P tw cr +G+e++l +g+ p e+kk kp+rtH
  gi|121637936|ref|YP_978159.1|   4 RVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCR-NGMEGTLiEGDLP-EPKKVKPPRTH 81 
                                    78****************************************************.*******666666.*********** PP

                           RbpA  80 ldmlkERRseeeleelLaerLellr 104
                                    +dml+ERRs+eeleelL+erLel+r
  gi|121637936|ref|YP_978159.1|  82 WDMLLERRSIEELEELLKERLELIR 106
                                    **********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 800.97
//
Query:       gi|121637937|ref|YP_978160.1|  [L=874]
Description: polyprenol-monophosphomannose synthase Ppm1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-29  100.5   0.0    1.5e-28   99.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-14   54.2   0.0    2.1e-14   53.5   0.0    1.3  1  CN_hydrolase     Carbon-nitrogen hydrolase
    7.9e-07   29.2   0.0    1.3e-06   28.5   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   2.5e-32   1.5e-28       2     168 ..     614     779 ..     613     781 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 2.5e-32
                                    EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraatg 80 
                                    v+ipt+Ne ++l+   ++l +    p ++++vvDD+S+D+t ++++ela+  ++r +v++r+ ++G+++a+ ag+++  +
  gi|121637937|ref|YP_978160.1| 614 VIIPTFNERENLPVIHRRLTQA--CPAVHVLVVDDSSPDGTGQLADELAQaDPGRTHVMHRTAKNGLGAAYLAGFAWGLS 691
                                    9*******99999888888887..99************************9999***********************999 PP

                                    S...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTC CS
                Glycos_transf_2  81 d...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigs 157
                                    +   +++ +DaD  ++p+ l++l++a ++ gad+++g+r++ +g  +++++++     ++  ++  +  l++++++++ +
  gi|121637937|ref|YP_978160.1| 692 ReysVLVEMDADGSHAPEQLQRLLDAVDA-GADLAIGSRYVAGGTVRNWPWRRL--VLSKTANTYSRLALGIGIHDITAG 768
                                    999**************************.***********************9..7*********************** PP

                                    CCEEEEHHHHH CS
                Glycos_transf_2 158 aallrrealee 168
                                    ++++rreale 
  gi|121637937|ref|YP_978160.1| 769 YRAYRREALEA 779
                                    *********86 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   3.4e-18   2.1e-14      32     242 ..     286     486 ..     242     500 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 3.4e-18
                                    TESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEE....EEEEECCTTEEEEEEEEEEEETTSEE CS
                   CN_hydrolase  32 gadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvig....liereltngklqayntavlldldgkl 107
                                    + + +++PE +       + f+           ++++a+a+  g  + ig    +++r ++n+     nta++ ++++  
  gi|121637937|ref|YP_978160.1| 286 QPQFVIWPENSSD----IDPFVN------PDAGQRISAAAEAIGAPILIGtlmdVPGRPRENPEW--TNTAIVWNPGTGP 353
                                    4455555555543....233333......2345899999999999999995544444444*****..************* PP

                                    EEEEE-SS--E.ECTTSCECCGHHTSCS.........-SSS-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH CS
                   CN_hydrolase 108 vgkyrKlhLfp.geprpptaverelfep.........gdgipvfdtpvgkiGaaiCyeigfpellralalkgaeilvnls 177
                                    + +++K    p ge+ p   + r+l +          g+g  v+  +++ +G+a C+e +f+++ r+  l ga++l+  s
  gi|121637937|ref|YP_978160.1| 354 ADRHDKAIVQPfGEYLPMPWLFRHLSGYadraghfvpGNGTGVVRIAGVPVGVATCWEVIFDRAPRKSILGGAQLLTVPS 433
                                    ********657777777777777777779******99776799999999*****************************99 PP

                                    .GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSS CS
                   CN_hydrolase 178 erapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglgee 242
                                    + a++ k m++ q ++ ++ ra+e + +v+ a  +g+           Sa+i+pdG  l + + +
  gi|121637937|ref|YP_978160.1| 434 NNATFNKTMSEQQ-LAFAKVRAVEHDRYVVVAGTTGI-----------SAVIAPDGGELIRTDFF 486
                                    99********999.9**********************...........*******9766666655 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.2e-10   1.3e-06       3     128 ..     611     733 ..     608     839 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.2e-10
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                    +++v++ptfne ++ + v++  l+q+ p+v+v vv+d s ++t + a+ela+a p+ r +v +++ + g      a+  +
  gi|121637937|ref|YP_978160.1| 611 RVLVIIPTFNE-RENLPVIHRRLTQACPAVHVLVVDDSSPDGTGQLADELAQADPG-RTHVMHRTAKNG---LGAAYLAG 685
                                    79*********.77778**************************************9.899999986445...44556788 PP

                Glyco_tranf_2_3  83 lravk...sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvflln 128
                                    +       + +++ +D+D    P+ l+rll ++ +++++ + +++++  
  gi|121637937|ref|YP_978160.1| 686 FAWGLsreYSVLVEMDADGSHAPEQLQRLLDAV-DAGADLAIGSRYVAG 733
                                    88644223669999*****************99.888888888777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6118.85
//
Query:       gi|121637938|ref|YP_978161.1|  [L=534]
Description: hypothetical protein BCG_2071c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.4e-106  357.9  18.4   1.6e-106  357.7  18.4    1.0  1  Amidohydro_3  Amidohydrolase family
      1e-07   31.7   0.1     0.0011   18.3   0.0    2.6  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.7  18.4  1.7e-110  1.6e-106       1     473 []      49     533 ..      49     533 .. 0.96

  Alignments for each domain:
  == domain 1  score: 357.7 bits;  conditional E-value: 1.7e-110
                   Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpyal 80 
                                    +v D++Gr+v+PGFvDsH+Hl+++g++l++l+l++  +ts +++l++v+d+a+  ++g+ ++g+Gwde++++e+++p + 
  gi|121637938|ref|YP_978161.1|  49 DVQDLDGRFVAPGFVDSHIHLTATGLMLSGLDLRP--ATSRAQCLRMVADYAAD-HPGQPLWGHGWDESAWPENAAP-ST 124
                                    589********************************..*****************.9*********************.** PP

                   Amidohydro_3  81 aeldevledapvllaaldtHaavrnsaaldl.agiteatpdpaggeilrdangegatgllregafhlvldla.pl.area 157
                                    a+ld+vl d+p +la++d+H+a+++s +++l +++++at +              a++ l+++a+hl++++a +l +  +
  gi|121637938|ref|YP_978161.1| 125 ADLDAVLGDCPAYLARIDSHSALVSSGLRRLvPELAAATGYT-------------AQRPLTGDAHHLARAAArYLlTDVQ 191
                                    *******************************99***999998.............*****************9555**** PP

                   Amidohydro_3 158 eaaavaaalaalasyGitsv.eagggnvsslddleplfeltaeeklplrvi.........ikelldaaerlglplspgse 227
                                    +a+a a al+a+a+ G+++v e++g++ ++ldd+ +l++l++      +vi         +++ +d + +          
  gi|121637938|ref|YP_978161.1| 192 LADARAVALQAIAAAGVVAVhECAGPEIGGLDDWLRLRALEHGV----EVIgywgeavatPAQARDLVTE---------T 258
                                    *******************************************5....9999975554444444444444.........4 PP

                   Amidohydro_3 228 eltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaek 302
                                    + +  a +lf+dg+lgsrta+l+epy+      g+++++ + ++++v+a++++++ +++h+igdaav+++++afe+++++
  gi|121637938|ref|YP_978161.1| 259 GARGLAGDLFVDGALGSRTAWLHEPYAdapdcIGTCHLDVDGIEAHVRACTKAEVTAGFHVIGDAAVSAAVAAFERVVAD 338
                                    55666*************************************************************************** PP

                   Amidohydro_3 303 ngnqdrr....rlehaegvtesqiervaalqvaagvqpvfnf....edelldsrlgperargstpvkellnagvkvalgs 374
                                    +g+  ++    rleh e+vt++q++++ a++v+a+vqp f+     +d+++++rlg++r++ ++p+++l ++gv++algs
  gi|121637938|ref|YP_978161.1| 339 LGVVAVArcghRLEHVEMVTADQAAKLGAWGVIASVQPNFDElwggGDGMYARRLGAQRGSELNPLALLASQGVPLALGS 418
                                    ***99999999**************************99999************************************** PP

                   Amidohydro_3 375 DapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrk.GtLevGadADlvvldadpldvd 453
                                    Dapv+ fdpw +++aav+++t        p+  +s ++a+a+ Trg+++a g +d + GtL +Ga+A+++++da  +dvd
  gi|121637938|ref|YP_978161.1| 419 DAPVTGFDPWASVRAAVNHRT--------PGSGVSARAAFAAATRGGWRAGGVRDGRiGTLVPGAPASYAIWDAGDFDVD 490
                                    *********************........8999**********************777********************** PP

                   Amidohydro_3 454 ppelaear.......................vrltvvdGrvvy 473
                                    +p++a +r                       +r+tv++G v+y
  gi|121637938|ref|YP_978161.1| 491 APRDAVQRwstdprsrvpalprlgptdalprCRQTVHRGAVIY 533
                                    *****************************************98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   2.9e-05      0.26       1      16 [.      57      72 ..      57      99 .. 0.78
   2 !   18.3   0.0   1.3e-07    0.0011     133     320 ..     300     488 ..     228     510 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.9e-05
                                   EEEE-EEEEEEECETT CS
                   Amidohydro_1  1 ivlPGlIDaHvHleqs 16
                                   +v PG++D+H+Hl  +
  gi|121637938|ref|YP_978161.1| 57 FVAPGFVDSHIHLTAT 72
                                   699**********754 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEE........EHCTCEEE..HHH CS
                   Amidohydro_1 133 elkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeikli........lahgvhlt..pte 202
                                    ++++ ++++ k+ +   +H+ ++ +  ++a+aaf + + + + + va +++ l+ + ++         a gv  +  p  
  gi|121637938|ref|YP_978161.1| 300 GIEAHVRACTKAEVTAGFHVIGDAAV-SAAVAAFERVVADLGVVAVARCGHRLEHVEMVtadqaaklGAWGVIASvqP-- 376
                                    56666666666666666666553333.366666665555555555555544444444443222211111111111111.. PP

                                    HHHHHHHHHHHCEEHHHHHHHH...................SEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHH CS
                   Amidohydro_1 203 aellkerlkeagvahcpfsnsi...................lrsgrealrkaldeGvkvglgtDgaasgnslnlleelrl 263
                                                         +                    +s++++l+ + ++Gv  +lg+D    g  +  + ++r 
  gi|121637938|ref|YP_978161.1| 377 ---------------------NfdelwgggdgmyarrlgaqRGSELNPLALLASQGVPLALGSDAPVTGFDP--WASVRA 433
                                    .....................0112222223333333333478999999999999*********77888888..889999 PP

                                    HHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TT.TSSSS-TTSB--EEEECC...C CS
                   Amidohydro_1 264 alklqrgllyedeegglslkealrmaTingAkalgldd.kvGsievGkdADlvvvdl...d 320
                                    a+      +++ +  g+s+  a+++aT +g +a g+ d ++G++ +G +A  +++d    d
  gi|121637938|ref|YP_978161.1| 434 AV------NHRTPGSGVSARAAFAAATRGGWRAGGVRDgRIGTLVPGAPASYAIWDAgdfD 488
                                    99......44467888*******************85549***************876442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3281.13
//
Query:       gi|121637939|ref|YP_978162.1|  [L=175]
Description: FxsA protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   63.5  14.2    2.5e-17   62.9  14.2    1.2  1  FxsA      FxsA cytoplasmic membrane protein
  ------ inclusion threshold ------
        1.1    9.3   7.1       0.24   11.4   1.3    2.3  2  DUF3927   Protein of unknown function (DUF3927)


Domain annotation for each model (and alignments):
>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9  14.2   2.8e-21   2.5e-17       2     106 ..       4     109 ..       3     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2.8e-21
                           FxsA   2 lllllpvlEilllvlvasaiGvlatllllvltallGallvrr.qgrralrrlqeklaqgelpaeelldglllllggvLLl 80 
                                    lll + v+E+++++++a +iG+++tll+l++t++lG+ l+    g+++ rrl    +    p+ +l dg+l+ +++vL+l
  gi|121637939|ref|YP_978162.1|   4 LLLSYAVVELAVVFALAATIGFGWTLLVLLATFVLGFGLLAPlGGWQLGRRLLWLRSGLAEPRSALSDGALVTVASVLVL 83 
                                    67899*******************************9877651445555555444444456******************* PP

                           FxsA  81 lPGfvtdvlGlllllPptRkllrrll 106
                                    +PG+vt+++Gllll+Pp+R+l+r  l
  gi|121637939|ref|YP_978162.1|  84 VPGLVTTTMGLLLLVPPIRALARPGL 109
                                    *********************98655 PP

>> DUF3927  Protein of unknown function (DUF3927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.5     0.056   5.1e+02       5      25 ..       3      23 ..       2      41 .. 0.62
   2 ?   11.4   1.3   2.7e-05      0.24      27      42 ..      67      82 ..      66      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.056
                        DUF3927  5 klIlAlvFlvlsvlvdfsSrI 25
                                   +l+l +  ++l v+  ++ +I
  gi|121637939|ref|YP_978162.1|  3 RLLLSYAVVELAVVFALAATI 23
                                   566666666666655554444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.7e-05
                        DUF3927 27 SVLsDGvLVAvvVvlv 42
                                   S LsDG+LV v+ vlv
  gi|121637939|ref|YP_978162.1| 67 SALSDGALVTVASVLV 82
                                   78********998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1178.48
//
Query:       gi|121637940|ref|YP_978163.1|  [L=237]
Description: hypothetical protein BCG_2073 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-60  203.5   0.0    3.3e-60  203.3   0.0    1.0  1  DLH             Dienelactone hydrolase family
      3e-06   27.3   0.6      0.015   15.2   0.2    2.8  2  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina
     0.0034   16.9   0.0       0.14   11.6   0.0    2.1  2  Peptidase_S9    Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.018   15.7   1.8      0.049   14.2   1.8    1.7  1  Abhydrolase_6   Alpha/beta hydrolase family
      0.076   12.8   0.0       0.12   12.2   0.0    1.2  1  Abhydrolase_2   Phospholipase/Carboxylesterase
       0.24   10.4   0.0       0.32   10.0   0.0    1.4  1  Chlorophyllase  Chlorophyllase


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   0.0   1.1e-63   3.3e-60       1     216 [.      13     228 ..      13     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 1.1e-63
                            DLH   1 idaylatpkna.kkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvl 79 
                                    ida+l +p  + ++p+vvv+++++G+  + k iser+a++GYv+l+P++Yar++    ++++++r+++el +k+   + l
  gi|121637940|ref|YP_978163.1|  13 IDALLGLPPGQgPWPGVVVVHDAVGYVPDNKLISERIARAGYVVLTPNMYARGG----RARCITRVFRELLTKR--GRAL 86 
                                    7999******99***************77789**********************....9***************..8999 PP

                            DLH  80 ddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefip 159
                                    dd+ aa ++l ++p +++++vg+vGfCmGG++al+l+ ++  + a+++fYG+ ++++l+e+ + ++pi+a+fg++D+   
  gi|121637940|ref|YP_978163.1|  87 DDILAARDHLLAMP-ECSGRVGIVGFCMGGQFALVLSPRG--FGATAPFYGTPLPRHLSETLNGACPIVASFGTRDPLGI 163
                                    9999**********.999**********************..9**********************************999 PP

                            DLH 160 adevekleealkaanvdlelkvYpgagHaFandsre.........syneeaaedawervlelfkqv 216
                                     + +++l++ ++a+n+++++k+YpgagH+Fan+ +          +yne+a+edaw+rv+e+f+q+
  gi|121637940|ref|YP_978163.1| 164 GA-ANRLRKVTAAKNIPADIKSYPGAGHSFANKLPGqplvriagfGYNEAATEDAWRRVFEFFGQH 228
                                    98.7*****************************99999*************************997 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00043       1.3      10      40 ..      93     122 ..      91     125 .. 0.89
   2 !   15.2   0.2   5.2e-06     0.015     141     212 ..     168     230 ..     162     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00043
                                    HHHHHCSTTB--SSEEEEEETHHHHHHHHHH CS
                         BAAT_C  10 inyllrhpkvkkdkigllGiSkGgelallla 40 
                                     + ll  p+++  ++g++G + Gg+ al+l+
  gi|121637940|ref|YP_978163.1|  93 RDHLLAMPECS-GRVGIVGFCMGGQFALVLS 122
                                    57789999999.89**************986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.2e-06
                                    HHHC..TT--.--EEEEETTB-S---..STT-----EEEETTTTEEEE--B-HHHHHHHHHHHHHHHHHHHHHH-X CS
                         BAAT_C 141 rLkk..agkkvevqlltYpkaGHlie..pPyfplceavlaklvgekvlyGGetkahakAqedsWkkilkFlkkhla 212
                                    rL+k  a k+    + +Yp+aGH ++   P +pl++++          +G    ++++A ed+W+++ +F+ +hl+
  gi|121637940|ref|YP_978163.1| 168 RLRKvtAAKNIPADIKSYPGAGHSFAnkLPGQPLVRIA---------GFG----YNEAATEDAWRRVFEFFGQHLR 230
                                    55542245666788999******995337999999994.........344....899*****************97 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.6e-05      0.14      11      80 ..      50     120 ..      43     129 .. 0.87
   2 ?    3.1   0.0     0.019        57     170     190 ..     170     194 ..     162     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                                    HCCT-EEEEE--TTSSTTHCHHHHTTSGGG..GHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHH CS
                   Peptidase_S9  11 adrGyvvvvanirGsggyGeafhdagkrkl..gqnefdDfiaaaealakegyvdserlaitGgSyGGyltga 80 
                                    a +Gyvv+ +n+   gg+ +  ++ +++ l    + +dD++aa ++l +   + s r++i G   GG+ +++
  gi|121637940|ref|YP_978163.1|  50 ARAGYVVLTPNMYARGGRARCITRVFRELLtkRGRALDDILAARDHLLAMPEC-SGRVGIVGFCMGGQFALV 120
                                    689*********9999999999999987651156789**************99.78***********98775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.019
                                    H....--S-SEEEEEETTS-SSTTS CS
                   Peptidase_S9 170 q....kkgknvlllifpdegHgvgk 190
                                    +     k+ +++++ +p++gH++++
  gi|121637940|ref|YP_978163.1| 170 RkvtaAKNIPADIKSYPGAGHSFAN 194
                                    44434677789**********6654 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.8   1.6e-05     0.049      25     139 ..      50     197 ..      18     233 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                    CT..CEEEEE--TTS.TS-GGCS--HHH........CHHHHHHHCCTT.....TTSEEEEEETCHHHHHHHHHHCC.... CS
                  Abhydrolase_6  25 ag..vhvlapDlpGh.Grsdpppldled........ladlaalldelaa...gggpvvlvGHSlGGalalaaapla.... 86 
                                    a+  + vl+p      Gr+ +    +++        l+d++a+ d+l a   + g+v +vG ++GG  al + p      
  gi|121637940|ref|YP_978163.1|  50 ARagYVVLTPNMYARgGRARCITRVFRElltkrgraLDDILAARDHLLAmpeCSGRVGIVGFCMGGQFALVLSPRGfgat 129
                                    333466688888888445544445554432223332466688888887789999*************9999777774444 PP

                                    ................EEEEES-........----TTTS----TTHHHHHHTT-C..CCCHCCHS-HSCCCCHHH CS
                  Abhydrolase_6  87 ..............lvvgvlldppp......talpagllaaalelllallallrl..lawlsreplprlfladed 139
                                                       l  ++p      t +p+g +aa +    ++ ++ ++    ++    ++++f ++++
  gi|121637940|ref|YP_978163.1| 130 apfygtplprhlseT----LNGACPivasfgTRDPLGIGAANRLRKVTAAKNIPAdiKSYPG---AGHSFANKLP 197
                                    444444444322221....2222224444335555555555554444555544443344443...3334444333 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.9e-05      0.12     104     203 ..     103     194 ..      85     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                    GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHH CS
                  Abhydrolase_2 104 ssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvplalgkaakevlk 183
                                    s r+ i+GF +G+  al l   +p   g +  f g+ pl++ l++  ++   + pi+ ++g+ Dp+  +  ++++ +v  
  gi|121637940|ref|YP_978163.1| 103 SGRVGIVGFCMGGQFALVL---SPRGFGATAPFYGT-PLPRHLSETLNG---ACPIVASFGTRDPL-GIGAANRLRKVTA 174
                                    67999*********99865...57777777778886.777788874554...55***********6.7899999999999 PP

                                    TTS-GEEEEEETT--SS--H CS
                  Abhydrolase_2 184 kllkkvelksyeglaHside 203
                                    + +   + ksy+g +Hs  +
  gi|121637940|ref|YP_978163.1| 175 AKNIPADIKSYPGAGHSFAN 194
                                    99999***********9866 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.32      25      83 ..       5      63 ..       1     130 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                 Chlorophyllase 25 srsspapPkpliivtPaeaGtypvvlflhGtllsnkfyskllnhiashGfivvaPqlyk 83
                                   + + pa P   ++  P  +G +p v+++h  + +  +   + + ia  G++v++P++y 
  gi|121637940|ref|YP_978163.1|  5 EIDAPAGPIDALLGLPPGQGPWPGVVVVHDAVGYVPDNKLISERIARAGYVVLTPNMYA 63
                                   56677888888899999************9999999999999**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1705.39
//
Query:       gi|121637941|ref|YP_978164.1|  [L=88]
Description: 30S ribosomal protein S18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-22   77.8   0.1    7.4e-22   77.3   0.1    1.3  1  Ribosomal_S18  Ribosomal protein S18
      0.007   16.3   0.4       0.12   12.3   0.0    2.1  2  Ribosomal_S5   Ribosomal protein S5, N-terminal domain
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.011   15.0   0.1    1.1  1  GSK-3_bind     Glycogen synthase kinase-3 binding


Domain annotation for each model (and alignments):
>> Ribosomal_S18  Ribosomal protein S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.1   1.2e-25   7.4e-22       3      52 .]      24      73 ..      22      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 1.2e-25
                  Ribosomal_S18  3 ekidYkdvelLsqFiterGkIlprriTGlcakhQrklakaIkrARhlaLL 52
                                   e +dYkd+ +L+ Fi++rGkI +r +TGl+ ++Qr++a+aIk+AR++aLL
  gi|121637941|ref|YP_978164.1| 24 ESVDYKDTATLRVFISDRGKIRSRGVTGLTVQQQRQVAQAIKNAREMALL 73
                                   789**********************************************8 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.031   1.9e+02      48      61 ..       4      17 ..       1      19 [. 0.83
   2 !   12.3   0.0   2.1e-05      0.12      33      58 ..      47      72 ..      46      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHTE CS
                   Ribosomal_S5 48 tAirkAiekAkknl 61
                                   ++ rk+  kAkknl
  gi|121637941|ref|YP_978164.1|  4 KSARKGPTKAKKNL 17
                                   6679999******8 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.1e-05
                                   TTEEEEEEEEESSHHHHHHHHHHHHH CS
                   Ribosomal_S5 33 nGlvGlGvgkakevatAirkAiekAk 58
                                   +G+ Gl v+  ++va+Ai++A e+A 
  gi|121637941|ref|YP_978164.1| 47 RGVTGLTVQQQRQVAQAIKNAREMAL 72
                                   6999*******************996 PP

>> GSK-3_bind  Glycogen synthase kinase-3 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.9e-06     0.011      78     138 ..       2      63 ..       1      84 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                     GSK-3_bind  78 aavradkarsparqlllraasaetvgpappgalrcalgdrgrvrgraaP.ycvaelaagpsa 138
                                    aa +a k  ++a++ ll +  +e+v+   + +lr  + drg++r+r      v +  +++ a
  gi|121637941|ref|YP_978164.1|   2 AAKSARKGPTKAKKNLLDSLGVESVDYKDTATLRVFISDRGKIRSRGVTgLTVQQQRQVAQA 63 
                                    7889999**************************************98651344444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 695.43
//
Query:       gi|121637942|ref|YP_978165.1|  [L=101]
Description: 30S ribosomal protein S14 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-23   82.1   0.3    3.8e-23   81.0   0.3    1.6  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.062   13.5   0.4       0.15   12.3   0.1    1.9  2  HTH_17         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.3   4.2e-27   3.8e-23       2      54 .]      48     100 ..      47     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 4.2e-27
                                    ------SS..CTTT---SSS--SSSEE-GGG-EHHHHHHHTTT...TT-EE-- CS
                  Ribosomal_S14   2 laklprnssptrirnrCrvtGrprGvirkfgLsRicfRelAlkgelpGvkKaS 54 
                                    la+ pr++sp+r+rnr++++GrprG +rkfgLsR++ R+lA++g lpGv+KaS
  gi|121637942|ref|YP_978165.1|  48 LARQPRDASPVRLRNRDAIDGRPRGHLRKFGLSRVRVRQLAHDGHLPGVRKAS 100
                                    899*************************************************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.3   1.2e+04      15      22 ..      41      49 ..      41      51 .. 0.61
   2 ?   12.3   0.1   1.6e-05      0.15      11      32 ..      77      98 ..      75     101 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                         HTH_17 15 rstvyr.li 22
                                   rst++r l+
  gi|121637942|ref|YP_978165.1| 41 RSTAQRaLA 49
                                   788887244 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                         HTH_17 11 Lgvsrstvyrlirrgelpaaki 32
                                   +g+sr  v++l+++g lp +++
  gi|121637942|ref|YP_978165.1| 77 FGLSRVRVRQLAHDGHLPGVRK 98
                                   79****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 786.04
//
Query:       gi|121637943|ref|YP_978166.1|  [L=54]
Description: 50S ribosomal protein L33 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-15   57.8   0.0    1.2e-15   57.6   0.0    1.0  1  Ribosomal_L33  Ribosomal protein L33


Domain annotation for each model (and alignments):
>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   6.8e-20   1.2e-15       2      46 ..       9      53 ..       8      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 6.8e-20
                                   EEEEEET......EEEEETT..--S--EEEEEETTTTEEEEEEEE CS
                  Ribosomal_L33  2 kvtLeCtecksrnYtttknkkntperLelkKYcprcrkhtlhkEt 46
                                   +v+L++t     +Ytt+kn++n p+rL l+KY+p +r+h+ ++E+
  gi|121637943|ref|YP_978166.1|  9 IVKLRSTAGTGYTYTTRKNRRNDPDRLILRKYDPILRRHVDFREE 53
                                   79*****777777*******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 447.27
//
Query:       gi|121637944|ref|YP_978167.1|  [L=78]
Description: 50S ribosomal protein L28 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-24   83.8   0.7    8.3e-24   83.6   0.7    1.1  1  Ribosomal_L28  Ribosomal L28 family
  ------ inclusion threshold ------
       0.11   12.6   0.2       0.11   12.6   0.2    1.6  2  Tat            Transactivating regulatory protein (Tat)
       0.19   11.9   0.0        0.2   11.8   0.0    1.1  1  AAA_lid_10     AAA lid domain


Domain annotation for each model (and alignments):
>> Ribosomal_L28  Ribosomal L28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.7   1.4e-27   8.3e-24       2      59 ..       4      61 ..       3      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.4e-27
                                   --TTT------------S-..-SSS-BTTEEEEEEEE.TTTEEEEEEEEHHHHHH--. CS
                  Ribosomal_L28  2 vCeltGkkpqfGnnvshsknkTkRtwkPNlqkvrlwseelgrkvrikvstkcLRtidk 59
                                    C++tG+kp fGn+vshs+++++R+w PN+q+++++++++gr +r++vstk+++ id+
  gi|121637944|ref|YP_978167.1|  4 HCQVTGRKPGFGNTVSHSHRRSRRRWSPNIQQRTYYLPSEGRRIRLRVSTKGIKVIDR 61
                                   6*******************************************************96 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.9e-05      0.11      30      60 ..       2      32 ..       1      35 [. 0.88
   2 ?   -3.0   0.1       1.4   8.7e+03      50      58 ..      44      52 ..      42      55 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                   HTSSHHHHHHCTT---S-XXXXXXXXXXXXX CS
                            Tat 30 sfhcqvcfikkalGisyerkkrrqrrrahrk 60
                                   s hcqv   k ++G +    +rr rrr   +
  gi|121637944|ref|YP_978167.1|  2 SAHCQVTGRKPGFGNTVSHSHRRSRRRWSPN 32
                                   67************************97655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                   XXXXXXXXX CS
                            Tat 50 krrqrrrah 58
                                   +rr r r  
  gi|121637944|ref|YP_978167.1| 44 GRRIRLRVS 52
                                   566666654 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05       0.2      26      56 ..      32      62 ..      11      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                                   -------------------------HHHHHH CS
                     AAA_lid_10 26 aeeekkqklPenvkkvrlkisddaieiasrk 56
                                   + ++++ +lP++ +++rl++s + i+++ r+
  gi|121637944|ref|YP_978167.1| 32 NIQQRTYYLPSEGRRIRLRVSTKGIKVIDRD 62
                                   34667889*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 609.86
//
Query:       gi|121637945|ref|YP_978168.1|  [L=511]
Description: hypothetical protein BCG_2078 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-40  136.8   0.1    1.1e-39  136.4   0.1    1.1  1  ZnuA      Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
       0.02   15.2   0.1      0.039   14.2   0.1    1.4  1  PucR      Purine catabolism regulatory protein-like family


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.1   1.2e-43   1.1e-39       7     229 ..     110     341 ..     108     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 1.2e-43
                                    HHHHHHHHHHGGGCEEE.ECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCE.EEEETTTTC CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                           ZnuA   7 plgdlvrqvaGdrvevt.vLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrv.evidlsegv 84 
                                    ++g+++r+v G +v v+ +L+ + adpHsy+++p+d++++ +A+l++yng ++++w+d++la  ++ + v + + l  g 
  gi|121637945|ref|YP_978168.1| 110 VWGSVARAVTGGHVPVKsILTGAHADPHSYQASPADAAAIVDAELVIYNGGGYDPWVDQVLAGHPGVQAVdAYS-LL-GA 187
                                    799**************889999**************************************9998655553333.33.33 PP

                                    CSEBCSSESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESSSTTH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA  85 eeeeeeeDpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrklvtthdafg 164
                                      ++++ ++H++++p+ a+a++ +iad+L+++dp n  +y+anaa++ +  +++    ++   + p +   ++ t+++++
  gi|121637945|ref|YP_978168.1| 188 VGDDDAPNEHVFYDPNVAKAVAATIADRLADLDPSNSGNYRANAAEFSRGADAIAISEHAIATTYPDAA--VIATEPVVH 265
                                    3566777***********************************************999999999999777..********* PP

                                    HHHHHTT-EEEEEE.SSSSS.......HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHH...HHT-EEEEE-S CS
                                    xxxxxxxxxxxxxx.xxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                           ZnuA 165 ylarayglevagia.giste.......aaqiaalieeikeagvkaifveplaspklaetlae...eagvkvatlys 229
                                    yl  a gl+  + a  i ++       +a++aa+ ++i  ++v a++v+p+++++++++l+    +agv + +l  
  gi|121637945|ref|YP_978168.1| 266 YLLAAAGLKNRTPAtFIAANengndptPADMAAVLDMIAGREVAALLVNPQTPTAATDELQVaarRAGVPITELTE 341
                                    *********9988843333366******************************999977665522266788777654 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.3e-06     0.039      55     105 ..     292     344 ..     279     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-06
                           PucR  55 dpealaelvrelaeagvaaLviklg.r.eipeelieaadelglPlielpeevp 105
                                    +p+++a++++ +a ++vaaL ++ + + +  +el  aa+++g+P+ el e++p
  gi|121637945|ref|YP_978168.1| 292 TPADMAAVLDMIAGREVAALLVNPQtPtAATDELQVAARRAGVPITELTETLP 344
                                    789999******************7546889****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3689.16
//
Query:       gi|121637946|ref|YP_978170.1|  [L=134]
Description: hypothetical protein BCG_2080c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-11   44.4   0.0    1.9e-11   44.0   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.024   14.2   0.0    1.2  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   2.2e-15   1.9e-11       8      87 ..       7      88 ..       1      89 [. 0.92

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.2e-15
                                   HHHHSSEEEEEEEETTSEEEEEEEEEEEETTT.TEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEEEEEESCH CS
                 Putative_PNPOx  8 flaeskavvlATvdedGrPnvspvllkagdgr.dgivfatnadsrklrnleenprvallfldde.lgrgvrieGtaelvsdg 87
                                    lae+++  l+T ++dGrP  +p++ + + +r d+++++t ++s k++++++ prv+l  +      ++  +e+ta+++++ 
  gi|121637946|ref|YP_978170.1|  7 DLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRgDRLLVITEKKSWKVKRIRNTPRVTLATCTLRgRPTSEAVEATAAILDES 88
                                   57889************************999******************************99888999999999999875 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-06     0.024      12      67 ..      10      66 ..       3     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                  Pyrid_ox_like 12 diktamLttteadgklksrPMatq.kveedgdlwfltkkdsdkvkeirkdsqvnlaf 67
                                   +++  +Ltt ++dg+ k  P  ++ +++  ++l  +t+k+s kvk ir+ ++v la 
  gi|121637946|ref|YP_978170.1| 10 EAQYLLLTTFTKDGRPKPVPIWAAlDTDRGDRLLVITEKKSWKVKRIRNTPRVTLAT 66
                                   4577899*************976615666678*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 955.51
//
Query:       gi|121637947|ref|YP_978171.1|  [L=1194]
Description: cobaltochelatase subunit CobN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1326.4   0.0          0 1326.2   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1326.2   0.0         0         0       3    1088 ..     104    1176 ..     102    1177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1326.2 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    3 YlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyrah 80  
                                     Yl++ggv+Nl++l+++l+d++l  +   + ppv +p++g+++                      ++ pt+++l+yra+
  gi|121637947|ref|YP_978171.1|  104 YLAHGGVDNLRELHAFLCDTVLM-TGFGFTPPVATPTWGVLERP-----------------DAGKTGPTIAVLYYRAQ 163 
                                     9*********************8.555688***********711.................245789*********** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   81 llagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpaeeeeeeaeeea 158 
                                     +lagnt +++al+ra+e++g ++lp++++sl++++ + le+l    +++ v +++   +++ ++ +a++++++ + e+
  gi|121637947|ref|YP_978171.1|  164 HLAGNTGYVEALCRAIEDAGGRPLPLYCASLRTAEPRLLERLG--GADAMVVTVLAAGGVKPAAASAGGDDDSWNVEH 239 
                                     ******************************8766666767665..333344444444444444444455555555566 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  159 lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekyepipervervad 236 
                                     l++l++P+lq++++++ r++W ++++Glspld+a +va+pE+dGri++v++sfke   +++++ +y+++per++rva+
  gi|121637947|ref|YP_978171.1|  240 LAALDIPILQGLCLTSPRDQWCANDDGLSPLDVASQVAVPEFDGRIITVPFSFKEI--DDDGLISYVADPERCARVAG 315 
                                     9****************************************************875..4789**************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx RF
                   CobN-Mg_chel  237 laarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpe....sgdeLiellle 310 
                                     la r+arLr+ ++a+k+va+++  yp++++r+gnavgLd+paS v+lL+a++++GY+v++lp     +gd+Li++l+e
  gi|121637947|ref|YP_978171.1|  316 LAVRHARLRQVAPADKRVALVFSAYPTKHARIGNAVGLDTPASAVALLQAMRQRGYRVGDLPGvesnDGDALIHALIE 393 
                                     **********************************************************755544455*********** PP

                                     xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  311 ggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppge.mveeeksgekklvipglqlGnvfvg 384 
                                      g +dp+w    +l+ g++ +++a+eY++wf++Lp+el++ v++ Wg+ppge +v+++++ ++++vi++l+ Gn +++
  gi|121637947|ref|YP_978171.1|  394 CGGHDPDWlteGQLA-GNPIRVSAKEYRDWFATLPAELTDVVTAYWGPPPGElFVDRSHDPDGEIVIAALRAGNLVLM 470 
                                     ********9866667.*************************************9************************ PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  385 vQPargyeedpsklyhdpdlpPthqYlAfYlWlr....eefgadavvHvGkHGtlEwlPGKqvglseecyPdillgdl 458 
                                     vQP+rg++e+p ++yhdpdlpP+h+YlA+Y+Wl+    + fga+avvH+GkHG+lEwlPGK++g+s++c Pd++lgdl
  gi|121637947|ref|YP_978171.1|  471 VQPPRGFGENPVAIYHDPDLPPSHHYLAAYRWLDtgfsNGFGAHAVVHLGKHGNLEWLPGKTLGMSASCGPDAALGDL 548 
                                     *********************************9333347************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  459 PhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqilelveeln 536 
                                     P +Yp+ vn+pgEGtqAKRR++Av++dHl+Ppm+rae+yg++a+Le+l+de++++++ldp +l+a+r+qi++l+++++
  gi|121637947|ref|YP_978171.1|  549 PLIYPFLVNDPGEGTQAKRRAHAVLVDHLIPPMARAETYGDIARLEQLLDEHASVAALDPGKLPAIRQQIWTLIRAAK 626 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                   CobN-Mg_chel  537 ldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrlene.....egeslte 609 
                                     +d+dlgl+e  + ee++f+++l ++dg+l+e+k+ qirdglhilG+ p+geq  dlv+ailr+ +      + ++l++
  gi|121637947|ref|YP_978171.1|  627 MDHDLGLTE--RPEEDSFDDMLLHVDGWLCEIKDVQIRDGLHILGQNPTGEQELDLVLAILRACQLfggahAIPGLRQ 702 
                                     *****9886..5579**********************************************99887877778888888 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                   CobN-Mg_chel  610 alaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee...........e 676 
                                     al  a             ++ + ++ ++++ e++a+elv++l ++++++++a++ + + ++++  +            
  gi|121637947|ref|YP_978171.1|  703 ALGLA-------------EDGTDERATVDQTEAKARELVAALQATGWDPSAADRLTGNADAAAVLRfaateviprlaG 767 
                                     88887.............4455677899*********************99988888888777777**********87 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  677 teeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekv 754 
                                     t  Ei+++lraLdG++ip+gpsG+p+rg  +vLPTGrNfysvDp+a+P++ Awe G +la++ll+ry++ehg++P++v
  gi|121637947|ref|YP_978171.1|  768 TATEIEQVLRALDGRFIPAGPSGSPLRGLVNVLPTGRNFYSVDPKAVPSRLAWEAGVALADSLLARYRDEHGRWPRSV 845 
                                     779*************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  755 glslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkav 831 
                                     gls+wgt++mrt G+diA++LallGvrPvwd+a +rv dl  +  +eLgRPRiDVtvriSGffRDafp+++ +ld+av
  gi|121637947|ref|YP_978171.1|  846 GLSVWGTSAMRTAGDDIAEVLALLGVRPVWDDAsRRVIDLAPMQPAELGRPRIDVTVRISGFFRDAFPHVVTMLDDAV 923 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  832 elvaeldEpeedNfvrkhvleeeaeleekeeaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssya 909 
                                     +lva+ldE +edN+vr+h++++ a++     +++rat+R+FgskpG+Ygag+ +li+s++W+d++dLa++Y+ w+++a
  gi|121637947|ref|YP_978171.1|  924 RLVADLDEAAEDNYVRAHAQADLAHHG----DQRRATTRIFGSKPGTYGAGLLQLIDSRSWRDDADLAQVYTAWGGFA 997 
                                     ***********************9997....679******************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  910 YgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtl 987 
                                     Yg++ +g+ea ++++++++r+ v+++n+d+rehd+ dsddy+q++GG+ a+vr+l+g++p+ay+gd+++p+++++rtl
  gi|121637947|ref|YP_978171.1|  998 YGRDLDGREAIDDMNRQYRRIAVAAKNTDTREHDIADSDDYFQYHGGMVATVRALTGQAPAAYIGDNTRPDAIRTRTL 1075
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  988 keeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwA 1065
                                     +ee++r++r+rv+NP+W+++m+rhGykGafe+aatvd+lfg+data+v++dw+ye+++++YvlD+++r f+ e+NpwA
  gi|121637947|ref|YP_978171.1| 1076 SEETTRVFRARVVNPRWMAAMRRHGYKGAFEMAATVDYLFGYDATAGVMADWMYEQLTQRYVLDAQNRTFMTESNPWA 1153
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1066 lreiaerLlEaarrglWeaseet 1088
                                     l+ +aerLlEaa rglW +++++
  gi|121637947|ref|YP_978171.1| 1154 LHGMAERLLEAAGRGLWAQPAPE 1176
                                     ******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.27s 00:00:01.04 Elapsed: 00:00:00.43
# Mc/sec: 8364.39
//
Query:       gi|121637948|ref|YP_978172.1|  [L=77]
Description: hypothetical protein BCG_2082 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.2   0.9      0.035   14.0   0.9    1.7  1  RHH_1     Ribbon-helix-helix protein, copG family
      0.029   14.2   2.0       0.04   13.8   2.0    1.3  1  RHH_4     Ribbon-helix-helix domain
      0.038   14.4   1.6       0.05   14.0   1.6    1.3  1  CcdA      Post-segregation antitoxin CcdA
       0.12   12.3   0.9       0.32   10.9   0.1    2.0  2  HicB      HicB family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9   7.9e-06     0.035       2      36 ..       5      39 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlrey 36
                                   ++ir++ ++ +rL + ar+rg S+S+l+ e+++++
  gi|121637948|ref|YP_978172.1|  5 TTIRVSTQTRDRLAAQARERGISMSALLTELAAQA 39
                                   79*************************98888876 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.0     9e-06      0.04      12      47 ..       4      39 ..       2      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaeidadr 47
                                   +T+ir   +  d L + Ar++g++++aL++e+ a+ 
  gi|121637948|ref|YP_978172.1|  4 STTIRVSTQTRDRLAAQARERGISMSALLTELAAQA 39
                                   79999999999*********************6433 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   1.1e-05      0.05      10      45 ..      15      55 ..       6      69 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                           CcdA 10 sdllaqAralgiNlSatleeaLaeevk.....eekaerwke 45
                                     l aqAr+ gi++Sa+l+e+ a++ +     +e++++++e
  gi|121637948|ref|YP_978172.1| 15 DRLAAQARERGISMSALLTELAAQAERqaifrAEREASHAE 55
                                   5799**************99888777766664344444444 PP

>> HicB  HicB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   7.2e-05      0.32      21      43 ..       6      28 ..       1      36 [. 0.87
   2 ?    0.0   0.3      0.17   7.8e+02      31      41 ..      34      44 ..      29      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.2e-05
                           HicB 21 nlRvspeLHarlalaAaeqgvSL 43
                                   ++Rvs +   rla++A e g+S+
  gi|121637948|ref|YP_978172.1|  6 TIRVSTQTRDRLAAQARERGISM 28
                                   89********************8 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                           HicB 31 rlalaAaeqgv 41
                                   +la++A+ q++
  gi|121637948|ref|YP_978172.1| 34 ELAAQAERQAI 44
                                   68999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 622.67
//
Query:       gi|121637949|ref|YP_978173.1|  [L=363]
Description: cobalamin biosynthesis protein CobG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-17   61.1   0.1    2.6e-12   46.4   0.1    2.6  2  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1   1.5e-16   2.6e-12       7      67 ..      21      78 ..      15      80 .. 0.84
   2 !   12.4   0.0   6.1e-06      0.11       3      67 ..     229     286 ..     227     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.5e-16
                   NIR_SIR_ferr  7 kgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLa 67
                                   +g    r+r+p+G ita+ql  la +a ++gs ++ lT+r n+ql+g+++  ++++ +++a
  gi|121637949|ref|YP_978173.1| 21 DGA-LARIRLPGGMITAAQLATLASVASDFGSATLELTARGNVQLRGIRD--VAAVADAVA 78
                                   444.89******************************************65..666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.1e-06
                   NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLa 67 
                                    q d  + +++++ vp G + a  ++ la+i        + +T++ ++++++++++ +++ l+ La
  gi|121637949|ref|YP_978173.1| 229 QDD--SRVTLGAAVPLGVLPARVAECLAAIE-----APLVITPWRSVLICDLDDATADAALRVLA 286
                                    445..4479*********************9.....9******************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2633.08
//
Query:       gi|121637950|ref|YP_978174.1|  [L=208]
Description: precorrin-8X methylmutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-67  226.9   1.5    1.9e-67  226.7   1.5    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.7   1.5   1.1e-71   1.9e-67       1     194 [.      10     204 ..      10     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.7 bits;  conditional E-value: 1.1e-71
                                    HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHH CS
                           CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrle 80 
                                    eI+++Sfa+i++e++  +++++ ++vv R+ih+++++++ae++ +++d+v+++ +al+agap+++D +mv+aGit +rl+
  gi|121637950|ref|YP_978174.1|  10 EIYRRSFAVIRAEADLARFPADVARVVVRLIHTCGQVDVAEHVAYTDDVVARAGAALAAGAPVLCDSSMVAAGITTSRLP 89 
                                    69****************************************************************************** PP

                                    TTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHH CS
                           CbiC  81 klgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaa 160
                                    + +n+++ l+adp+++ela+++++trsaa++e++ae+l+ga+++iGnAPtAL++llel++eg++ pa+v+g PvGFvg a
  gi|121637950|ref|YP_978174.1|  90 A-DNQIVSLVADPRATELAARRQTTRSAAGVELCAERLPGAVLAIGNAPTALFRLLELVDEGAPPPAAVLGGPVGFVGSA 168
                                    9.9***************************************************************************** PP

                                    HHHHHHHCSS..S-EEEESSS---HHHHHHHHHHHH CS
                           CbiC 161 esKealaese..vpyitveGrkGGsavAaaivnaLl 194
                                    ++Ke+l+e+   + y++v+Gr+GGsa+Aaa+vna++
  gi|121637950|ref|YP_978174.1| 169 QAKEELIERPrgMSYLVVRGRRGGSAMAAAAVNAIA 204
                                    *******85456**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1587.92
//
Query:       gi|121637951|ref|YP_978175.1|  [L=508]
Description: bifunctional protein, CobI-CobJ fusion protein: S-adenosyl-L-methionine-precorrin-2 methyl transferase + precorrin-3 methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-74  249.4  13.1    2.1e-42  145.5   2.7    2.0  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   2.7   1.2e-46   2.1e-42       1     205 [.       6     218 ..       6     223 .. 0.88
   2 !  109.7   2.9     1e-35   1.9e-31       2     212 ..     249     457 ..     248     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.2e-46
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr.....aleilldllaeel...........eleapmgkekepleea 64 
                                    +l++VG+GpGdpel+Tv+A+r++ +advv++  +      a  i++++l++ +           e+  + g  +  le  
  gi|121637951|ref|YP_978175.1|   6 TLWGVGLGPGDPELVTVKAARVIGEADVVAYHSAPhghsiARGIAEPYLRPGQleehlvypvttEATNHPGGYAGALEDF 85 
                                    589**************************777744555778888888888888999766555554444444448888888 PP

                   TP_methylase  65 yeeiaealaealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllp 144
                                    y+++ e++a++l+ag++V+ll  GDPl+y+++++l+++l++r    +  ++PGv+s++aa a++ +pl+ g++vlsvl p
  gi|121637951|ref|YP_978175.1|  86 YADATERIATHLDAGRNVALLAEGDPLFYSSYMHLHTRLTRRF---NAVIVPGVTSVSAASAAVATPLVAGDQVLSVL-P 161
                                    *****************************************65...6*******************************.8 PP

                   TP_methylase 145 glakeeereleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervv 205
                                    g+   +  el + la++d  v++k +r + +++e+L+++  + + ++++vera+t+++rv 
  gi|121637951|ref|YP_978175.1| 162 GTL--PVGELTRRLADADAAVVVKLGRSYHNVREALSAS--GLLGDAFYVERASTAGQRVL 218
                                    866..777788888889**********************..66779*************97 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 1e-35
                   TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aealragk 80 
                                    + +VG+GpGd + +T+  +r l++a  ++g++  +l++++  + +          ++ p++ + e + ++l   ++++g+
  gi|121637951|ref|YP_978175.1| 249 VAVVGLGPGDSDWMTPQSRRELAAATDLIGYR-GYLDRVEVRDGQ----------RRHPSDNTDEPARARLaCSLADQGR 317
                                    889********************887777888.8*****876655..........34444444443344446******** PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleall 158
                                     V++++sGDP v+ ++ +++e++++  +g++v+viP+++++qa+a+r+g+pl++++ v s++  l++++ +++r+ +a++
  gi|121637951|ref|YP_978175.1| 318 AVAVVSSGDPGVFAMATAVLEEAEQ-WPGVRVRVIPAMTAAQAVASRVGAPLGHDYAVISLSdrLKPWDVIAARLTAAAA 396
                                    ********************88887.9*************************************************9999 PP

                   TP_methylase 159 angdtlvllkaprk......laelaelLkealyddttpvavver....agtedervvrgtleel 212
                                    a  d ++++++p        +  ++elL+++ +d+  pv+++++    ++ ++e v++++l++l
  gi|121637951|ref|YP_978175.1| 397 A--DLVLAIYNPASvtrtwqVGAMRELLLAH-RDPGIPVVIGRNvsgpVSGPNEDVRVVKLADL 457
                                    9..99999999995556888999********.77788*******66666677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3451.36
//
Query:       gi|121637952|ref|YP_978176.1|  [L=407]
Description: hypothetical protein BCG_2086c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.5   0.0      2e-14   53.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.5e-13   51.3   0.1    3.8e-13   50.0   0.1    1.7  1  Methyltransf_12  Methyltransferase domain
    3.6e-13   50.0   0.1      3e-12   47.0   0.0    2.4  3  Methyltransf_11  Methyltransferase domain
      5e-13   49.6   0.0    2.2e-11   44.3   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
    2.2e-07   30.9   0.0    3.5e-07   30.2   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    7.7e-06   25.1   0.0    1.2e-05   24.4   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0036   16.7   0.0     0.0062   16.0   0.0    1.3  1  TehB             Tellurite resistance protein TehB
      0.005   16.2   0.0     0.0076   15.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.022   14.4   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.13   12.3   0.0       0.23   11.5   0.0    1.3  1  IL34             Interleukin 34


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   1.1e-17     2e-14       6     108 ..      58     156 ..      54     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.1e-17
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                     +l +GCGt + ++ ++   +  a+vv iDis  a+ + +   +k+gl n+e++  +ieel +l   + fDl++s +vl+
  gi|121637952|ref|YP_978176.1|  58 DILIAGCGTNQAAIFAF--TNRAAKVVAIDISRPALDHQQYLKDKHGLANLELHLLPIEELATL-G-RDFDLVVSTGVLH 133
                                    45558****99999999..7889*************************************9985.5.88*********** PP

                Methyltransf_31  86 aladpdkileeiervlkpggill 108
                                    +ladp + ++e+   l+ +g+++
  gi|121637952|ref|YP_978176.1| 134 HLADPRAGMKELAHCLRRDGVVA 156
                                    ******************99986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   2.1e-16   3.8e-13       3      98 ..      62     154 ..      60     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.1e-16
                Methyltransf_12   3 iGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdi 82 
                                     GcGt + +     + + ++++++Dis+ a+ d+++ l++++++ n +++l  ++ l + g+  fDlvv+ +vlhhl+d+
  gi|121637952|ref|YP_978176.1|  62 AGCGTNQAAIFAFTN-RAAKVVAIDISRPAL-DHQQYLKDKHGLANLELHLLPIEELATLGR-DFDLVVSTGVLHHLADP 138
                                    699999988888777.89*************.*********************999988887.***************** PP

                Methyltransf_12  83 revldnirklLkpgGr 98 
                                    r+ +++++++L+ +G+
  gi|121637952|ref|YP_978176.1| 139 RAGMKELAHCLRRDGV 154
                                    **************98 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   1.7e-15     3e-12       3      95 ..      62     156 ..      57     157 .. 0.89
   2 ?   -0.5   0.0       1.1   1.9e+03      29      70 ..     205     245 ..     177     255 .. 0.64
   3 ?   -3.7   0.0        10   1.8e+04      19      33 ..     313     327 ..     299     329 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.7e-15
                                    ET-TTSHHHHHHH.HTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   3 vGcGtGrlaeala.krgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    +GcGt + a     +r+a+vv++D+s  +l+  +  + + gl ++e++   +e+l      fDlvvs+ vlhh++dp++ 
  gi|121637952|ref|YP_978176.1|  62 AGCGTNQAAIFAFtNRAAKVVAIDISRPALDHQQYLKDKHGLaNLELHLLPIEELATLGRDFDLVVSTGVLHHLADPRAG 141
                                    6***8877766653777*************99988888888899***********98888******************** PP

                                    HHHHHHHEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllv 95 
                                    +ke+a +L+ +G+++
  gi|121637952|ref|YP_978176.1| 142 MKELAHCLRRDGVVA 156
                                    ************975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                                    HHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES- CS
                Methyltransf_11  29 emlklakekaseeglkvefvvadaeklpfednsfDlvvssev 70 
                                    + l+ a++  s++ l  +f++++ ++  +e+  +Dlv+s   
  gi|121637952|ref|YP_978176.1| 205 NYLTKARDLLSDSALVDTFLHGRQRSYTVEE-CVDLVTSAGL 245
                                    4556666666666665567777777766555.8888888764 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 10
                                    SEEEEEES-HHHHHH CS
                Methyltransf_11  19 arvvgvDlskemlkl 33 
                                    ++v ++D+ + m+++
  gi|121637952|ref|YP_978176.1| 313 STVAALDYVPLMRTR 327
                                    678888888877765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   1.2e-14   2.2e-11       1      97 []      59     153 ..      59     153 .. 0.91
   2 ?    2.7   0.0      0.12   2.2e+02       3      74 ..     177     247 ..     176     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.2e-14
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    +L +GcGt + ++ + ++  +akv+++Dis  +l++ +   +++gl n+e++   +e+l    + fDlvvs+g+lhhl  
  gi|121637952|ref|YP_978176.1|  59 ILIAGCGTNQAAIFAFTN-RAAKVVAIDISRPALDHQQYLKDKHGLaNLELHLLPIEELATLGRDFDLVVSTGVLHHLA- 136
                                    6789*****988777666.47***************9999999999*************************988***98. PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                     d ++ +ke+a +L+ +G
  gi|121637952|ref|YP_978176.1| 137 -DPRAGMKELAHCLRRDG 153
                                    .56699*********998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                                    EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.l 74 
                                    dlG G+ + +++lak+   + +    +  ++l +ar  ++++ l  +f++g  +++  e+  +Dlv+s+g  +
  gi|121637952|ref|YP_978176.1| 177 DLGLGQDDASIKLAKEA-ISLLPTYHPLRNYLTKARDLLSDSALVDTFLHGRQRSYTVEE-CVDLVTSAGLvF 247
                                    56666666666666664.44555566667889999999999999999*****99999886.*******87644 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.9e-10   3.5e-07      25     123 ..      58     163 ..      32     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.9e-10
                Methyltransf_23  25 rvLdiGcGtGillevlrengf.svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd 97 
                                     +L  GcGt   +  + +n++ +v+++D+s+ a +  +      +  + + +  + +e a   + fdl+v++ vl+h+ d
  gi|121637952|ref|YP_978176.1|  58 DILIAGCGTNQAAIFAFTNRAaKVVAIDISRPALDHQQylkdkhGLANLELHLLPIEELATLGRDFDLVVSTGVLHHLAD 137
                                    56668*****999988777666********8655543333333333333333333335555666**************** PP

                Methyltransf_23  98 ppellrqiatllkpgGylllseplas 123
                                    p + ++ +a +l+ +G++  + ++++
  gi|121637952|ref|YP_978176.1| 138 PRAGMKELAHCLRRDGVVAAMLYGKY 163
                                    ****************9988887765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   6.5e-09   1.2e-05     118     215 ..      58     155 ..      25     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.5e-09
                                    EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T-.--EEEEEEES-GGG-S CS
                 Methyltransf_9 118 tildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpel.eafdtvfsmGvlyhrr 196
                                     il  Gcg+        ++ a+ vv id s+  l   + ++   g  + + +l l ie+l +l   fd v s Gvl+h  
  gi|121637952|ref|YP_978176.1|  58 DILIAGCGTNQAAIFAFTNRAAKVVAIDISRPALDHQQYLKDKHGLANLELHL-LPIEELATLgRDFDLVVSTGVLHHLA 136
                                    466679*9999999999999******************************999.9******96379************** PP

                                    -HHHHHHHHHCTEEEEEEE CS
                 Methyltransf_9 197 sPldhllqlkdqlvkgGel 215
                                     P   + +l ++l+++G +
  gi|121637952|ref|YP_978176.1| 137 DPRAGMKELAHCLRRDGVV 155
                                    ****************965 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.5e-06    0.0062      35     110 ..      60     137 ..      52     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                                    EEES-TTSHHHHHH.HHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG.----S-EEEEEEESSGGGS-G CS
                           TehB  35 ldlgcgqgrnslyl.sllgydvtawdknensiafleeikekenlknistalydine.aklderydfilstvvlmflea 110
                                    l  gcg  + +++  +    +v a+d    ++ + + +k+k  l n++  l+ i+e a+l +++d+++st vl  l  
  gi|121637952|ref|YP_978176.1|  60 LIAGCGTNQAAIFAfTNRAAKVVAIDISRPALDHQQYLKDKHGLANLELHLLPIEElATLGRDFDLVVSTGVLHHLAD 137
                                    5679*****999961556789*********************************984689*************98865 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.2e-06    0.0076      66     163 ..      59     156 ..      52     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                    EEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES-GGGTSG CS
                           CMAS  66 lLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvgafehvgk 142
                                    +L  GcG  + ++ a  +  +kvv++ +S+    +++   d+ +l+ + e++ll  e+l+     +d vvs g++ h+  
  gi|121637952|ref|YP_978176.1|  59 ILIAGCGTNQAAIFAFTNRAAKVVAIDISRPALDHQQYLKDKHGLA-NLELHLLPIEELATlgrDFDLVVSTGVLHHLAD 137
                                    5667*****************************9999988888865.57788888888877777*************987 PP

                                    GGHHHHHHHHHHHS-TT-EEE CS
                           CMAS 143 enydtffkklkkllkedGlll 163
                                     +    +k+l + l++dG+++
  gi|121637952|ref|YP_978176.1| 138 PRA--GMKELAHCLRRDGVVA 156
                                    764..4688888888888875 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.022      29      74 ..      47      93 ..      28     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                   HHHT.T-S--EEEEEET-TT-HH.HHHH-BTTEEEEEE-S-HHHHHH CS
                           TPMT 29 fldalkakaglrvlvPlCGkald.lvwlAeqgrevvGvelselAvek 74
                                   ++++ +  + l +l+ +CG  +  + ++ ++  +vv++++s  A+ +
  gi|121637952|ref|YP_978176.1| 47 LWPDREYRPDLDILIAGCGTNQAaIFAFTNRAAKVVAIDISRPALDH 93
                                   67788889999********98752679****************9976 PP

>> IL34  Interleukin 34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.23      75     126 ..     190     244 ..     184     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                    HHHHHTT--TTSTTHHHHHHHHHHHHHH...HHTTTT----HHHHHHHHHHHST- CS
                           IL34  75 vekvlevLlekHPsrkYlqelerllkdv...qevlkdvevsekvedvldlltekg 126
                                     ++ ++ L++ HP r+Yl+  ++ll+d    ++ l+ +++s +ve+ +dl+t++g
  gi|121637952|ref|YP_978176.1| 190 AKEAISLLPTYHPLRNYLTKARDLLSDSalvDTFLHGRQRSYTVEECVDLVTSAG 244
                                    6777899******************985444788888************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2761.07
//
Query:       gi|121637953|ref|YP_978177.1|  [L=307]
Description: beta-lactamase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-39  134.6   0.0    4.2e-39  134.2   0.0    1.1  1  Beta-lactamase2  Beta-lactamase enzyme family
    1.7e-19   70.2   1.8    3.3e-18   66.0   1.8    2.1  1  Beta-lactamase   Beta-lactamase
  ------ inclusion threshold ------
      0.098   13.1   0.1       0.23   11.9   0.1    1.6  1  DUF4350          Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.0     7e-43   4.2e-39       3     202 .]      68     277 ..      66     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 7e-43
                                    TTSEEEESTTS-EE-GGGGHHHHHHHHHHHHHC..TSTGTT-EEEGGHHHHTSSSTSGGGSTTSEEEHHHHHHHHHHTT- CS
                Beta-lactamase2   3 tgeelgvnadeefpaaStiKvpillalleavle..gklslderltltaedivggsgilqklpgktlslrdlltlmiavSD 80 
                                    t + ++++ade+f  +St+K p++    +avl+      ld+ +t+t++di++ s++ q++ ++ +++ +l+ ++i +SD
  gi|121637953|ref|YP_978177.1|  68 TTAAIEYRADERFAFCSTFKAPLV----AAVLHqnPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSD 143
                                    667899******************....77764324567***************************************** PP

                                    HHHHHHHHHHH.....THHHHHHHHHHCTHTTSB--SHTTCCH.HHTTSSTTEE-HHHHHHHHHHHHHTTSSHHH...HH CS
                Beta-lactamase2  81 NtAtnlLidrl.....gleavnawlkelglretrlrrklpdle.aadkdkrntttardlarllealargellspe...el 151
                                     tA+nlL++ l     g  a+  +l++lg +  rl+  +p+l+ + + d+r+ttt+++ a  l++l+ g++l p+    l
  gi|121637953|ref|YP_978177.1| 144 GTAANLLLADLggpggGTAAFTGYLRSLGDTVSRLDAEEPELNrDPPGDERDTTTPHAIALVLQQLVLGNALPPDkraLL 223
                                    ***********99985599*********************99944556779*************************9999 PP

                                    HHHHH.T-STTTTTTTTTTTTSEEEEEEEE.ETTEEEEEEEEEE.TTEEEEEEE CS
                Beta-lactamase2 152 leils.nqqfrdrlaaglpegvrvahKtGe.ldgvrhdvGivya.dgrpyvvav 202
                                     +++  n++   r++ag+p +++v++KtG+ ++g+++d+++v+  +g pyvvav
  gi|121637953|ref|YP_978177.1| 224 TDWMArNTTGAKRIRAGFPADWKVIDKTGTgDYGRANDIAVVWSpTGVPYVVAV 277
                                    99*99899999*******************88********************98 PP

>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   1.8   5.5e-22   3.3e-18       4     329 ..      51     299 ..      48     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.5e-22
                                    HHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBG.... CS
                 Beta-lactamase   4 lvrelmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpV.... 79 
                                    l+r+++a   + Gv+v  + +   +               ++ad++f+ +S++K+   aavl +    +  Ld+ +    
  gi|121637953|ref|YP_978177.1|  51 LERRYDA---RLGVYVPATGTTAAI--------------EYRADERFAFCSTFKAPLVAAVLHQNPLTH--LDKLItyts 111
                                    5555555...666655555555555..............9*********************99999887..999998888 PP

                                    ..........GGTSTTCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHH CS
                 Beta-lactamase  80 ..........skylPefagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgy 149
                                              ++++      ++g +T+ +L+++   +                                     ++ t++
  gi|121637953|ref|YP_978177.1| 112 ddirsispvaQQHV------QTG-MTIGQLCDAAIRY-------------------------------------SDGTAA 147
                                    88877777777777......566.*************.....................................888999 PP

                                    H.HHHHHHHHHH.TSH....HHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEE CS
                 Beta-lactamase 150 g.llgellekvt.grs....leqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglis 223
                                    + ll+  l+++  g+     + ++l++++ r  +  ++el+ +++gd+rd++++                         +
  gi|121637953|ref|YP_978177.1| 148 NlLLAD-LGGPGgGTAaftgYLRSLGDTVSRL-DAEEPELNRDPPGDERDTTTP------------------------HA 201
                                    999999.9999951334455************.*********************........................** PP

                                    EHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE....STEEEEEEEEC CS
                 Beta-lactamase 224 tardlarflglalegglllsaetlaqltaklssgttrpagiraglglGwvladktgapgtfghtG....ggygtyvfvdp 299
                                     a  l  ++ l    g++l + ++a lt+++ ++tt+  +irag++ +w + dktg        G     +  ++v+   
  gi|121637953|ref|YP_978177.1| 202 IALVLQQLV-L----GNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGT-------GdygrANDIAVVWSPT 269
                                    *********.8....*****************************************8.......7554666667777777 PP

                                    GGTEEEEEEESBCSSHHHHHHHHHHHHHHH CS
                 Beta-lactamase 300 eanlvvavltnrdppnedaaedarlialaa 329
                                      ++vvav++ r ++  da+ + +l a+aa
  gi|121637953|ref|YP_978177.1| 270 GVPYVVAVMSDRAGGGYDAEPREALLAEAA 299
                                    77************9888888888888776 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.9e-05      0.23       5      60 ..     159     228 ..     158     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                        DUF4350   5 nGtralaelLeaqGvevrrvrkpfdaleg..........edgtllvvapdlrlte....eelaallewva 60 
                                    +Gt+a+  +L++ G +v+r +    +l +          +++ + +v ++l l +    +  a l +w+a
  gi|121637953|ref|YP_978177.1| 159 GGTAAFTGYLRSLGDTVSRLDAEEPELNRdppgderdttTPHAIALVLQQLVLGNalppDKRALLTDWMA 228
                                    6*****************9999988887667888755554555666666666665555455556667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2152.40
//
Query:       gi|121637954|ref|YP_978178.1|  [L=185]
Description: RNA polymerase sigma factor SigC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-15   56.1   0.1    3.3e-15   55.5   0.1    1.3  1  Sigma70_r4_2   Sigma-70, region 4
    6.9e-15   54.6   2.4    1.1e-14   53.9   1.2    2.0  2  Sigma70_r2     Sigma-70 region 2
    2.7e-06   26.8   0.0    5.4e-06   25.8   0.0    1.5  1  Sigma70_r4     Sigma-70, region 4
    5.6e-05   23.1   0.3    8.2e-05   22.6   0.3    1.3  1  Sigma70_ECF    ECF sigma factor
     0.0042   16.8   0.0       0.01   15.6   0.0    1.6  1  HTH_23         Homeodomain-like domain
      0.008   16.0   0.1       0.32   10.9   0.0    2.4  2  Dioxygenase_N  Catechol dioxygenase N terminus
  ------ inclusion threshold ------
      0.078   13.5   0.0       0.15   12.7   0.0    1.5  1  DUF134         Protein of unknown function  DUF134
       0.15   12.4   0.0        0.4   11.0   0.0    1.8  1  CHMI           5-carboxymethyl-2-hydroxymuconate isomerase


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   1.5e-18   3.3e-15       3      54 .]     123     174 ..     121     174 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.5e-18
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    ++ +++a L+++qre++ll +l glsy+++A+++g+++gt++sr++RAr +L
  gi|121637954|ref|YP_978178.1| 123 EVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
                                    7889*********************************************876 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   1.2   5.1e-18   1.1e-14       2      69 ..      30      94 ..      29      96 .. 0.92
   2 ?   -1.9   0.0       1.3   2.9e+03      23      32 ..     118     127 ..     113     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 5.1e-18
                                   HHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2  2 verylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69
                                   +++ ++ v+r++  +l++  +a+Dl+Qe+flr++ a++rf  +r+ s+++wll iar+ + d++R  r
  gi|121637954|ref|YP_978178.1| 30 IKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFS-ARS-SARTWLLAIARHVVADHIRHVR 94
                                   7788899999998.899999*********************.999.9******************855 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                    HHHHHHHHHH CS
                     Sigma70_r2  23 aeDlvQeafl 32 
                                    +eDlv  +++
  gi|121637954|ref|YP_978178.1| 118 FEDLVEVTTM 127
                                    79**999876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.4e-09   5.4e-06       2      48 ..     128     174 ..     127     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-09
                                    HHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   2 LasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    +a L+ ++re l l  + gl++++ +++ g + +++r++ +rA++ L
  gi|121637954|ref|YP_978178.1| 128 IADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
                                    689****************************************9987 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   3.7e-08   8.2e-05      52     178 ..      53     173 ..       9     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.7e-08
                    Sigma70_ECF  52 LvfeaflrlvdkekfpdlsgrdhlfalaaeamrrilidhaRrrkrqkRGGdvvraeldeeedsvdsdspdelleLdeale 131
                                    L  e flr+++  + p +s r    + ++ + r ++ dh R  +++ R     r e   +  ++d  ++   ++L e  +
  gi|121637954|ref|YP_978178.1|  53 LTQETFLRAIG--AIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRGARPE---HLIDGDR-HARGFEDLVEVTT 126
                                    77899999998..99********9999************99999999877777777...4434444.456789999999* PP

                    Sigma70_ECF 132 rllsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRaw 178
                                     +++l  +q++ + l +l Gls +++A++ g+   t++ r a aR  
  gi|121637954|ref|YP_978178.1| 127 MIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDA 173
                                    *****************************************999954 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.5e-06      0.01       8      40 ..     138     169 ..     132     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                         HTH_23   8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40 
                                    ++ l  l+ Gls++++A+ +g++  T++  + r
  gi|121637954|ref|YP_978178.1| 138 ALLLTQLL-GLSYADAAAVCGCPVGTIRSRVAR 169
                                    44444445.*******************65555 PP

>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00014      0.32      24      52 ..      32      59 ..      25      63 .. 0.90
   2 ?    2.6   0.0     0.055   1.2e+02      44      60 ..     132     148 ..     117     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                   --HHHHHHHHHHHHHHHH.....TT-HHH CS
                  Dioxygenase_N 24 lteeEwwaavdfLtrvGqisddkrqEfiL 52
                                    t+++ w  v++L +vG+  dd  qE  L
  gi|121637954|ref|YP_978178.1| 32 ATQQDVWRFVAYLSDVGS-ADDLTQETFL 59
                                   6999**************.9999999887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                                    ...TT-HHHHHHHTTHH CS
                  Dioxygenase_N  44 ddkrqEfiLlsdvLGle 60 
                                    ++++ E+ Ll+  LGl+
  gi|121637954|ref|YP_978178.1| 132 TTDQREALLLTQLLGLS 148
                                    44678**********98 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.5e-05      0.15       5      78 ..     100     174 ..      89     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                         DUF134   5 grprklrd.ileePkvrifkPeaveetg.kvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkki 78 
                                    +r+ ++ + i ++ + r f+   ve t     ++ d+ ea+ l     l++ +aa++ G    t+ + ++ ar  +
  gi|121637954|ref|YP_978178.1| 100 TRGARPEHlIDGDRHARGFEDL-VEVTTmIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
                                    4444443313344566666666.5555515789***************************************9864 PP

>> CHMI  5-carboxymethyl-2-hydroxymuconate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018       0.4      33      58 ..     157     182 ..     120     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                    TS-GGG-EEEEEEESSEEETTSS-T- CS
                           CHMI  33 vfplgGiRvrairlddyavADgkedd 58 
                                      p+g iR+r  r+ d ++AD ++dd
  gi|121637954|ref|YP_978178.1| 157 GCPVGTIRSRVARARDALLADAEPDD 182
                                    67********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1272.40
//
Query:       gi|121637955|ref|YP_978179.1|  [L=231]
Description: cobalt-precorrin-6x reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.5e-61  205.6   0.0    8.7e-61  205.4   0.0    1.0  1  CbiJ        Precorrin-6x reductase CbiJ/CobK
     0.0045   17.5   0.5        1.4    9.5   0.1    2.7  3  ATPgrasp_N  ATP-grasp N-terminal domain


Domain annotation for each model (and alignments):
>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   9.7e-65   8.7e-61      22     235 ..      10     225 ..       4     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 9.7e-65
                                    T--EEEEE---SSS----S..S-EEES--S.HHHHHHHHHHHT--EEEE-S-TT-HHHHHHHHHHHHHHT-EEEEE---- CS
                           CbiJ  22 gievvvsvateygaellpekklevrvgrlg.eeglaellreekidlvvDATHPfAaeisanaaeackelgipylrleRps 100
                                    ++e+v+s+a+++ +++lp   ++vr+g++g +egl+ +lree+id+vvDATHPfA++i+a+aa++c elg+pyl+l Rp+
  gi|121637955|ref|YP_978179.1|  10 HVEIVSSLAGRVPNPALPI--GPVRIGGFGgVEGLRGWLREERIDAVVDATHPFAVTITAHAAQVCGELGLPYLVLARPP 87 
                                    689****************..*********************************************************** PP

                                    ---..EEEEESSHHHHH..........EEEESTSTTGGGGSTT...SEEEEEESS--SS.--SSS....SEEEEE--SS- CS
                           CbiJ 101 wea..kiievdsleeaaella......vllttGskelaafaealkkerllaRvlptpeslekalplglkakeiiamrGpf 172
                                    w++   ii v+++e+a  ++a      v+lttG++ +aafa+   ++++l+Rv+ +p+   +alp    ++++++ rGp+
  gi|121637955|ref|YP_978179.1|  88 WDPgtAIIAVSDIEAAD-VVAeqgysrVFLTTGRSGIAAFANS--DAWFLIRVVTAPDG--TALPR---RHKLVLSRGPY 159
                                    **************995.44459*****************976..799***********..46885...9********** PP

                                    -HHHHHHHHHHTT--EEEEES--SS.TTTHHHHHHHHTT-EEEEE---....--EEE-SHHHHHHHH CS
                           CbiJ 173 skelerallreykidvlVtKeSGgaGgteeKleaArelgipvivikRp....eveevsdveellewl 235
                                     + +e allre +id+lVtK+SGg+ +t++Kl+aA++lgi v++i Rp     v +v++v+++  w+
  gi|121637955|ref|YP_978179.1| 160 GYHDEFALLREQRIDALVTKNSGGK-MTRAKLDAAAALGISVVMIARPllpaGVAAVDSVHRAAMWV 225
                                    *************************.**********************9996555599998888876 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0029        26      53      81 ..      47      79 ..      39      80 .. 0.65
   2 ?   -3.3   0.0       1.5   1.4e+04      51      62 ..     167     178 ..     166     180 .. 0.81
   3 !    9.5   0.1   0.00016       1.4       2      21 ..     191     210 ..     190     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0029
                                   HHS--SEEE---GGG....HHHHHHHHHHTT-S CS
                     ATPgrasp_N 53 rerpvdGivtftdla....vplvArlaeaLgLP 81
                                   re+++d++v +t ++    +  +A+++ +LgLP
  gi|121637955|ref|YP_978179.1| 47 REERIDAVVDATHPFavtiTAHAAQVCGELGLP 79
                                   67777877766665411114457888889**99 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                                    HHHHS--SEEE- CS
                     ATPgrasp_N  51 lsrerpvdGivt 62 
                                    l re+++d++vt
  gi|121637955|ref|YP_978179.1| 167 LLREQRIDALVT 178
                                    678999999998 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00016
                                    HHHHHTT-EEEEEEETTS-- CS
                     ATPgrasp_N   2 eaAkaLGikvvlvdeedewa 21 
                                    +aA+aLGi+vv++ ++   a
  gi|121637955|ref|YP_978179.1| 191 DAAAALGISVVMIARPLLPA 210
                                    79***********9995333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1849.81
//
Query:       gi|121637956|ref|YP_978180.1|  [L=251]
Description: precorrin-4 C11-methyltransferase CobM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-43  147.3   3.5      6e-43  147.3   3.5    1.4  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0021   18.5   0.0     0.0033   17.8   0.0    1.5  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   3.5   6.7e-47     6e-43       1     212 [.       2     209 ..       2     210 .. 0.92
   2 ?   -3.1   0.0      0.68   6.1e+03      81      94 ..     220     233 ..     215     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 6.7e-47
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    ++y++G+GpG+++l+Tvr+ r+l++++v l+++s  ++ ll+ +++        ++ +++   + e+i+++la+a ++g+
  gi|121637956|ref|YP_978180.1|   2 TVYFIGAGPGAADLITVRGQRLLQRCPVCLYAGSIMPDDLLAQCPP-------GATIVDTGPLTLEQIVRKLADADADGR 74 
                                    59*******************************7788888777754.......46666777778**************** PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeerele 155
                                    dV++l+sGDP++y++ +e +++l a   gi +e++PGv+++ aaaa+l+ +lt  g++++v+     + ++ +++ ++l+
  gi|121637956|ref|YP_978180.1|  75 DVARLHSGDPSLYSALAEQCRELDA--LGIGYEIVPGVPAFAAAAAALKRELTVPGVAQTVTltrvaTLSTPMPPGEDLA 152
                                    *************************..***************************************944455678899*9 PP

                   TP_methylase 156 allangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                    al+  + tlvl  a  +++ ++ +L++  ++++t pvavv+ a+++++r+ rgtl+++
  gi|121637956|ref|YP_978180.1| 153 ALARSRATLVLHLAAAQIDAIVPRLLDGgYRPET-PVAVVAFASWPQQRTLRGTLADI 209
                                    ****************************888855.********************987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.68
                   TP_methylase  81 dVvllvsGDPlvyg 94 
                                    + +++v GD l + 
  gi|121637956|ref|YP_978180.1| 220 RTAVIVVGDVLTAE 233
                                    57888999988873 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.7e-07    0.0033      21     127 ..      49     184 ..      25     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                    Radical_SAM  21 rregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.......................... 74 
                                    ++ ++   l++e+i++++  +   +g ++  l++g+p+ly+ ++e  ++l +l                           
  gi|121637956|ref|YP_978180.1|  49 ATIVDTGPLTLEQIVRKLADA-DADGRDVARLHSGDPSLYSALAEQCRELDALGigyeivpgvpafaaaaaalkreltvp 127
                                    46667777999*******999.6888**************8888888888888777777777777777766666666876 PP

                                    .....CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 .....vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtf 127
                                         v   r++  + ++ p  e l++l++ + + +++l +  +d   v +l+ +g+ +
  gi|121637956|ref|YP_978180.1| 128 gvaqtVTLTRVATLSTPMPP-GEDLAALARSRaTLVLHLAAAQIDAI-VPRLLDGGYRP 184
                                    55555444444444444444.78888888877455555555555555.66666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1864.98
//
Query:       gi|121637957|ref|YP_978181.1|  [L=294]
Description: precorrin-6y methyltransferase CobLb [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00012   22.1   0.1    0.00019   21.5   0.1    1.3  1  TP_methylase    Tetrapyrrole (Corrin/Porphyrin) Methylases
      0.003   16.9   0.0       0.05   12.9   0.0    2.5  3  Methyltransf_2  O-methyltransferase domain
  ------ inclusion threshold ------
       0.14   11.7   0.0       0.23   11.0   0.0    1.3  1  MTS             Methyltransferase small domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   3.1e-08   0.00019     116     210 ..       2      87 ..       1      90 [. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-08
                   TP_methylase 116 PGvsslqaaaarlgiplteggevlsvl.lpglakeeereleallangdtlvllkaprklaelaelLkealyddttpvavv 194
                                    P vs++++a+ar+g+ ++++++++ v+ +p+      + ++    +g++ ++l + r  ++++++L+++++  + +  v 
  gi|121637957|ref|YP_978181.1|   2 PHVSAVTLACARMGWNVYDTEVISLVTaQPH------TAVR----RGGRAIVLSGDRSTPQALAVLLTEHGRGDSKFSVL 71 
                                    99****************9999999992222......3333....346777776666555555555555477788***** PP

                   TP_methylase 195 eragtedervvrgtle 210
                                    e++g + er + gt +
  gi|121637957|ref|YP_978181.1|  72 EQLGGPAERRRDGTAR 87 
                                    *********9998875 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.27   1.6e+03     142     165 ..      20      44 ..       2      54 .. 0.71
   2 !   12.9   0.0   8.4e-06      0.05      63      92 ..     145     174 ..     118     178 .. 0.84
   3 ?    0.6   0.0     0.047   2.8e+02     148     169 ..     225     245 ..     196     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.27
                                    HHHHHHHH.HHHHHH--TT-EEEEE CS
                 Methyltransf_2 142 dekcvklL.krvkkalpagGkvivv 165
                                    d ++  l+ ++ + a++ gG+ iv 
  gi|121637957|ref|YP_978181.1|  20 DTEVISLVtAQPHTAVRRGGRAIVL 44 
                                    4444444315678899999999886 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.4e-06
                                    -SEEEEET-TTSHHHHHHHHH-TT-EEEEE CS
                 Methyltransf_2  63 lkslvDvGGGtGalakaivsayPtikvivf 92 
                                     ++l DvG G+Ga+a +  + +P+++++ f
  gi|121637957|ref|YP_978181.1| 145 GQRLWDVGAGSGAIAVQWCRSWPGCTAVAF 174
                                    479***********************9998 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.047
                                    HHHHHHHH--TT-EEEEEE--- CS
                 Methyltransf_2 148 lLkrvkkalpagGkvivveavl 169
                                    lL+ + ++lpagG+++ ++av 
  gi|121637957|ref|YP_978181.1| 225 LLEACLDSLPAGGNLV-ANAVT 245
                                    8999999999999864.55553 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.8e-05      0.23      24      67 ..     137     180 ..     133     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                                    HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHH CS
                            MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarA 67 
                                    l +l  +  +++ D+G+G G+++++  + +p  + ++++ d r 
  gi|121637957|ref|YP_978181.1| 137 LAALAPRPGQRLWDVGAGSGAIAVQWCRSWPGCTAVAFERDERR 180
                                    566777788999********************999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2544.78
//
Query:       gi|121637958|ref|YP_978182.1|  [L=62]
Description: precorrin-6y methyltransferase CobLa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 517.94
//
Query:       gi|121637959|ref|YP_978183.1|  [L=262]
Description: hypothetical protein BCG_2093c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0014   17.7   0.2     0.0096   15.0   0.1    2.0  2  PI-PLC-C1  Phosphoinositide phospholipase C, Ca2+-dependent


Domain annotation for each model (and alignments):
>> PI-PLC-C1  Phosphoinositide phospholipase C, Ca2+-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   5.3e-07    0.0096       2      61 ..     113     162 ..     112     170 .. 0.80
   2 ?    0.2   0.0     0.018   3.2e+02     110     144 ..     194     227 ..     170     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.3e-07
                      PI-PLC-C1   2 rlnqiqviGtHNSYkreispkllealkkknaksaealeYshasleeqldlgvrqlElDvy 61 
                                     l + q +GtHNS++   +  ++++       s      ++ sl++qld +vr lElD++
  gi|121637959|ref|YP_978183.1| 113 PLRETQWLGTHNSFNSLSDSFTVSHAD-----SN-----QQLSLAQQLDIDVRALELDLH 162
                                    57889*********9877665555554.....33.....4568***************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.018
                      PI-PLC-C1 110 etlvecLkevkkWsdahpkhvpifillelkdeesa 144
                                      l ++L ++ +W +a p h+  +ill l+d+ ++
  gi|121637959|ref|YP_978183.1| 194 PLLATVLPQIANWLNA-PGHTEEVILLYLEDQLKN 227
                                    4678899******987.555554444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1916.80
//
Query:       gi|121637960|ref|YP_978184.1|  [L=83]
Description: hypothetical protein BCG_2094c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0072   16.4   0.4       0.01   15.8   0.4    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   5.8e-07      0.01      40      89 ..      21      74 ..      16      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-07
                Phage_holin_3_6 40 lgaagvlallalllllval.alalaa...lwlaalivaavllvlagvlalvglk 89
                                   l ++ ++a+++++ +l+a+ a+a a+   lw+    +++++l+ a+v + + ++
  gi|121637960|ref|YP_978184.1| 21 LRGGCYFAFMGVAWVLLAIsAIANAVkgsLWWDIWSLGLLVLIPAVVYGKMRRS 74
                                   557889999999999999954333346889999999*********999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 457.28
//
Query:       gi|121637961|ref|YP_978185.1|  [L=323]
Description: hypothetical protein BCG_2095c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 2610.50
//
Query:       gi|121637962|ref|YP_978186.1|  [L=99]
Description: hypothetical protein BCG_2096c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.37
# Mc/sec: 807.26
//
Query:       gi|121637963|ref|YP_978187.1|  [L=104]
Description: hypothetical protein BCG_2097 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-58  195.9   8.3    1.6e-58  195.8   8.3    1.0  1  DUF2563        Protein of unknown function (DUF2563)
     0.0008   19.8   0.4    0.00088   19.7   0.4    1.2  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> DUF2563  Protein of unknown function (DUF2563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   8.3   1.7e-62   1.6e-58       1     104 []       1     104 []       1     104 [] 0.99

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 1.7e-62
                        DUF2563   1 mfvdtellhsGgneshraGghareGadqlarGpllsGmfGdfaaadafhdavvaahaqhvrnlqahrealiavGekarha 80 
                                    mfvd++llhsG+nesh+aG+ha++Gadql+rGpllsGmfG+f++a++fhdav+aahaq++rnl+ahr+ali+vGekarha
  gi|121637963|ref|YP_978187.1|   1 MFVDVGLLHSGANESHYAGEHAHGGADQLSRGPLLSGMFGTFPVAQTFHDAVGAAHAQQMRNLHAHRQALITVGEKARHA 80 
                                    9******************************************************************************* PP

                        DUF2563  81 akGftdmdeqnaeelkavrlsaat 104
                                    a+Gftdmd++na+elkav++s+at
  gi|121637963|ref|YP_978187.1|  81 ATGFTDMDDGNAAELKAVVCSCAT 104
                                    **********************97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   9.8e-08   0.00088      46      99 ..      43      96 ..       2      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.8e-08
                  T7SS_ESX_EspC 46 picaatndavaaaeaarraagealaaasteLadkLraAAaaYeatDeeaagald 99
                                   p+ + ++dav aa+a + + + a ++a+ ++ +k r AA+ + + D+ +a +l+
  gi|121637963|ref|YP_978187.1| 43 PVAQTFHDAVGAAHAQQMRNLHAHRQALITVGEKARHAATGFTDMDDGNAAELK 96
                                   467889********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.27u 0.25s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 857.01
//
Query:       gi|121637964|ref|YP_978188.1|  [L=656]
Description: hypothetical protein BCG_2098 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-31  107.3   2.7    6.6e-31  107.3   2.7    1.8  2  Abhydrolase_8  Alpha/beta hydrolase
     0.0013   18.5   0.1     0.0034   17.1   0.1    1.8  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.086   12.6   0.3       0.14   11.9   0.3    1.2  1  DUF2913        Protein of unknown function (DUF2913)
        1.6    9.7   0.0        1.6    9.7   0.0    4.5  3  TPR_14         Tetratricopeptide repeat
        5.7    7.3   5.9        2.2    8.6   0.2    3.1  3  TPR_2          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.3   4.6e+03      85     105 ..     110     131 ..      76     138 .. 0.64
   2 !  107.3   2.7   1.9e-34   6.6e-31       4     176 ..     348     520 ..     345     522 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                  Abhydrolase_8  85 drAa.agAaeLnallrdlrats 105
                                     +A+ a+A+++  l  +l+++ 
  gi|121637964|ref|YP_978188.1| 110 AEAQrAAAGRIATLESQLQRID 131
                                    3344145667777777777665 PP

  == domain 2  score: 107.3 bits;  conditional E-value: 1.9e-34
                  Abhydrolase_8   4 gkvlaavavGdldrAerVsVtvpGvdttlrrtlatmvaearglraeaaaaeeaagkpesvAviAWlgYeaPagas.keva 82 
                                    gk++aa a+G++d+A++ +V+vpG ++ ++   ++ ++ + + + ++ ++++aa + + +AviAW+gY+aP + +   +a
  gi|121637964|ref|YP_978188.1| 348 GKGRAAIAIGNPDTAKHTAVIVPGTSSSVK---GGWLHDNHDDALNLFNQAKAADPNNPTAVIAWMGYDAPNDFTdPRIA 424
                                    5899*********************99885...4566667777777888888899999*************665415789 PP

                  Abhydrolase_8  83 tddrAaagAaeLnallrdlrats.vpgqhlallgHSYGSlvaslAlddaaseVsdvvlyGSPGlea.esaakLgledarv 160
                                    t   A+ g a L   +++l  t  + gq++++lgHSYGS + + A    + + +d+vl G PG+++ +saa  +l+ +rv
  gi|121637964|ref|YP_978188.1| 425 TPMLARIGGAALAEDVNGLWVTHlGVGQNVTVLGHSYGSTTVADAFALGGMHANDAVLLGCPGTDLaHSAASFHLDGGRV 504
                                    99*******************999*******************9999999***************7256899******** PP

                  Abhydrolase_8 161 fvmrgadDlienvpel 176
                                    +v+ ++ D+i+ + +l
  gi|121637964|ref|YP_978188.1| 505 YVGAASTDPISMLGQL 520
                                    **********987766 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.4e-07    0.0034      44     106 ..     420     485 ..     388     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.4e-07
                                    SSTTTGB..CHHSHHHHHHHHHHH.HHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  44 spapacin.ddygtasvaddldri.ldalgddklt.lvGhSmGGmialayaaeyperVkalvllga 106
                                    +p++a+++  + g a++a+d++ + + +lg+++ + ++GhS+G+++++ ++a+   + +  vllg 
  gi|121637964|ref|YP_978188.1| 420 DPRIATPMlARIGGAALAEDVNGLwVTHLGVGQNVtVLGHSYGSTTVADAFALGGMHANDAVLLGC 485
                                    56666666666677889*****777*******9999***********9998887666666666665 PP

>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3     4e-05      0.14      54     111 ..     105     166 ..     103     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                        DUF2913  54 vakdLkrwqkqgrskGknaqLkalleriseqykevaeeekel......dskleallaeleekew 111
                                    +a dL + q+++   G+ a L+++l+ri +q  ++ e e++       +s+l al+  le++  
  gi|121637964|ref|YP_978188.1| 105 IAADLAEAQRAAA--GRIATLESQLQRIDDQLDQALELEHDPrlaaaeRSELDALITCLEQDAI 166
                                    899*********9..*********************99999899999999*******9999865 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.6     0.031   1.1e+02       4      34 ..      34      65 ..      31      68 .. 0.85
   2 ?   -1.7   3.3       2.1   7.5e+03       6      30 ..     108     133 ..     104     154 .. 0.60
   3 ?    9.7   0.0   0.00045       1.6      15      41 ..     383     409 ..     380     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.031
                         TPR_14  4 llalaeallalGd.pdeAiallrralalaPdd 34
                                    ++laea+ a+G+ ++eA a++++a +++ ++
  gi|121637964|ref|YP_978188.1| 34 IAELAEAFHAAGRcTAEANAAFEEARRRFEAS 65
                                   679**********8899*******99988765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                         TPR_14   6 alaeal.lalGdpdeAiallrralal 30 
                                    +laea  +a+G+ ++ +  l+r+ ++
  gi|121637964|ref|YP_978188.1| 108 DLAEAQrAAAGRIATLESQLQRIDDQ 133
                                    66666523456766666666665333 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00045
                         TPR_14  15 GdpdeAiallrralalaPddaeawlll 41 
                                    +++d+A++l+++a a++P++++a +++
  gi|121637964|ref|YP_978188.1| 383 DNHDDALNLFNQAKAADPNNPTAVIAW 409
                                    689*******************98876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.1      0.66   2.4e+03      18      29 ..      49      60 ..      36      64 .. 0.75
   2 ?   -3.1   0.0       3.5   1.3e+04       7      21 ..     349     363 ..     346     364 .. 0.84
   3 ?    8.6   0.2   0.00063       2.2      15      34 .]     383     402 ..     380     402 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.66
                          TPR_2 18 eeAleafekAle 29
                                   +eA +afe+A +
  gi|121637964|ref|YP_978188.1| 49 AEANAAFEEARR 60
                                   799999999965 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                          TPR_2   7 lGlayyklgdyeeAl 21 
                                     G+a+++ g+++ A+
  gi|121637964|ref|YP_978188.1| 349 KGRAAIAIGNPDTAK 363
                                    589999999999886 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00063
                          TPR_2  15 gdyeeAleafekAleldPnn 34 
                                    +++++Al++f++A + dPnn
  gi|121637964|ref|YP_978188.1| 383 DNHDDALNLFNQAKAADPNN 402
                                    799***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 3612.78
//
Query:       gi|121637965|ref|YP_978189.1|  [L=187]
Description: lipoprotein LppJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1070.38
//
Query:       gi|121637966|ref|YP_978190.1|  [L=203]
Description: hypothetical protein BCG_2100c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1135.16
//
Query:       gi|121637967|ref|YP_978191.1|  [L=695]
Description: hypothetical protein BCG_2101 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-38  128.7   1.7    7.9e-38  128.7   1.7    3.1  3  DUF5631   Family of unknown function (DUF5631)
    8.2e-36  121.9   1.6    2.8e-35  120.2   1.6    2.0  1  DUF5632   Family of unknown function (DUF5632)


Domain annotation for each model (and alignments):
>> DUF5631  Family of unknown function (DUF5631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.071   6.4e+02      13      84 ..      71     141 ..      61     148 .. 0.66
   2 ?   -0.8   0.1      0.24   2.1e+03      26      52 ..     473     499 ..     453     501 .. 0.69
   3 !  128.7   1.7   8.8e-42   7.9e-38       1      95 [.     593     687 ..     593     688 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.071
                        DUF5631  13 rrrdgLPrlvhtlakaaaagtgvldeEvdllrehldtirkqvlaaYPdvdaalvlnwlLLAaiealvagdev 84 
                                    r +++L  ++h+    + + + v+d  v+ lr++l++i+++  ++  ++ a +      +Aa++a+++ +++
  gi|121637967|ref|YP_978191.1|  71 RGEQRLATIAHQCEVKSDQSEQVAD-AVNYLRDRLTEIAQSGNQQINQILAGKGPIEAKVAAVNAVIEQSNA 141
                                    5567788888887777766666666.5999999999998876555555544444444455666666666555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                        DUF5631  26 akaaaagtgvldeEvdllrehldtirk 52 
                                    + aaa +t+   +E + lr  ldt+++
  gi|121637967|ref|YP_978191.1| 473 TGAAAGDTSRRAAEQQRLRRILDTVAR 499
                                    335556677778889999999998876 PP

  == domain 3  score: 128.7 bits;  conditional E-value: 8.8e-42
                        DUF5631   1 idelgvelseatrrrdgLPrlvhtlakaaaagtgvldeEvdllrehldtirkqvlaaYPdvdaalvlnwlLLAaiealva 80 
                                    idelg++l+e++rr+d+LPr++++++ aa++++gv d+E+dll++++++i+++vl++YP++d+a+v++w+LLAai+al+a
  gi|121637967|ref|YP_978191.1| 593 IDELGPTLVETVRRHDTLPRIAQAVVVAATRNYGVPDNETDLLHHKTTEIHQAVLTTYPNHDIATVVDWMLLAAINALIA 672
                                    8******************************************************************************* PP

                        DUF5631  81 gdevaAnYHlaWfra 95 
                                    gd++ AnYHlaW+ a
  gi|121637967|ref|YP_978191.1| 673 GDQSGANYHLAWAIA 687
                                    ************865 PP

>> DUF5632  Family of unknown function (DUF5632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   1.6   3.1e-39   2.8e-35       2      81 .]     485     567 ..     484     567 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.1e-39
                        DUF5632   2 seeqrLqRlldavaRqeprLaWavGeraDg.ttllvtDlasGWiPpgvelpagvtLlePa..rrsgeleallGevavaaa 78 
                                    +e+qrL+R+ld vaRqep+L+Wa+G r++g ttllvtDlasGWiPp+++lpa++tLlePa  rr++++++llG+++vaaa
  gi|121637967|ref|YP_978191.1| 485 AEQQRLRRILDTVARQEPGLSWAAGLRDNGqTTLLVTDLASGWIPPHIRLPAHITLLEPAprRRHATVTDLLGTTTVAAA 564
                                    689**************************999***************************998999*************** PP

                        DUF5632  79 yep 81 
                                    ++p
  gi|121637967|ref|YP_978191.1| 565 HHP 567
                                    *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.85u 0.38s 00:00:01.23 Elapsed: 00:00:00.56
# Mc/sec: 3731.52
//
Query:       gi|121637968|ref|YP_978192.1|  [L=314]
Description: hypothetical protein BCG_2102 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1851.55
//
Query:       gi|121637969|ref|YP_978193.1|  [L=331]
Description: hypothetical protein BCG_2103 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0052   17.4   0.8     0.0097   16.5   0.0    1.8  2  Adaptin_binding  Alpha and gamma adaptin binding protein p34
  ------ inclusion threshold ------
       0.22   12.3   1.2       0.41   11.4   0.5    1.9  2  DUF2203          Uncharacterized conserved protein (DUF2203)


Domain annotation for each model (and alignments):
>> Adaptin_binding  Alpha and gamma adaptin binding protein p34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.34     3e+03     109     120 ..     124     135 ..      97     136 .. 0.85
   2 !   16.5   0.0   1.1e-06    0.0097      87     120 ..     255     297 ..     188     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.34
                Adaptin_binding 109 eeRkkeAakval 120
                                    +eR+++Aa v+ 
  gi|121637969|ref|YP_978193.1| 124 AERRAMAAAVVA 135
                                    79******9985 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-06
                Adaptin_binding  87 e.........dlesllsklqqakdnvrnlpdeeRkkeAakval 120
                                    +         dl+s+l +++ a+   +  +++eR+++Aa v+ 
  gi|121637969|ref|YP_978193.1| 255 DlrdartlltDLDSILREMRTAATIQQAYTRAERRAMAAAVVA 297
                                    2334444555******************************985 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.55     5e+03      61      61 ..     104     104 ..      53     164 .. 0.62
   2 ?   11.4   0.5   4.6e-05      0.41       5      74 ..     256     329 ..     254     331 .] 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.55
                        DUF2203  61 e 61 
                                     
  gi|121637969|ref|YP_978193.1| 104 V 104
                                    3 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.6e-05
                        DUF2203   5 leeAnalLpllkelleelralrkeleelee.....eleeakaeaekseaaeleaeleeleaeieelveeieelGv 74 
                                    l +A++lL+ l+++l+e+r+++  ++++++     ++++a  ++ + +a+ l a+ +++   + ++++ ++++G+
  gi|121637969|ref|YP_978193.1| 256 LRDARTLLTDLDSILREMRTAA-TIQQAYTraerrAMAAAVVAKIRGDAMGLDAQRDAVHRAAADALHALQSVGI 329
                                    789***************9443.23333321112234444444444449************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2101.31
//
Query:       gi|121637970|ref|YP_978194.1|  [L=101]
Description: hypothetical protein BCG_2105 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.086   13.2   0.0       0.12   12.8   0.0    1.3  1  HTH_Tnp_1  Transposase


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.5e-06      0.12      32      66 ..      40      81 ..      27      89 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-06
                      HTH_Tnp_1 32 rhgvspnqLykWrrqyr.......egeeaspaefeltaleee 66
                                   ++g+s+++L++W  q++       + ++++  + +  +le++
  gi|121637970|ref|YP_978194.1| 40 SLGISAETLRRWAGQAEvdsgvvaGVSASRSGSVKTSELEQT 81
                                   69**************96554442222222333444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 702.71
//
Query:       gi|121637971|ref|YP_978195.1|  [L=201]
Description: hypothetical protein BCG_2106 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-09   36.9   0.9    6.2e-07   29.5   0.0    2.6  3  HTH_21    HTH-like domain


Domain annotation for each model (and alignments):
>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.001        18      15      36 ..      13      33 ..       5      39 .. 0.82
   2 !   29.5   0.0   3.5e-11   6.2e-07      20      55 ..      79     113 ..      51     117 .. 0.86
   3 ?   -3.7   0.9      0.77   1.4e+04      42      58 ..     170     186 ..     163     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.001
                         HTH_21 15 eeskgrYGyrriwaeLrreggv 36
                                   +++k +YG+  i+++L    gv
  gi|121637971|ref|YP_978195.1| 13 DKHKHTYGVTPICRALAVH-GV 33
                                   69*************9877.44 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 3.5e-11
                         HTH_21  20 rYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgv 55 
                                     YG++++wa+L+r+ g+r+   +V  +Mr +G+rgv
  gi|121637971|ref|YP_978195.1|  79 LYGSLKMWAHLQRQ-GFRWPSATVKTIMRANGWRGV 113
                                    8*************.67*****************98 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.77
                         HTH_21  42 rVrRlMrelGLrgvqrr 58 
                                    r rR  r lG+++ qrr
  gi|121637971|ref|YP_978195.1| 170 RLRRCDRGLGMLADQRR 186
                                    56677777788887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1522.12
//
Query:       gi|121637972|ref|YP_978196.1|  [L=76]
Description: hypothetical protein BCG_2107 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   21.1   0.0    0.00027   20.7   0.0    1.2  1  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-08   0.00027       2      52 ..       4      59 ..       3      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-08
                          rve_3  2 gielsyiapgkPqqNglvEsfngtlrdellneel.....frslaearekleawred 52
                                   g+++s++ +g++ +N+l+E   g  r+e+   ++      r+la+++ +  aw+e+
  gi|121637972|ref|YP_978196.1|  4 GLRPSIGIVGDALDNALCETTTGPHRTECSHGSPfrsgpIRTLADLEDIASAWVEH 59
                                   77899999**************************88888889************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 542.21
//
Query:       gi|121637973|ref|YP_978197.1|  [L=589]
Description: transmembrane serine/threonine-protein kinase j pknJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-45  153.4   0.0    9.8e-45  153.0   0.0    1.1  1  Pkinase         Protein kinase domain
    1.4e-38  132.7   1.6    2.7e-38  131.7   0.0    2.3  3  PknH_C          PknH-like extracellular domain
    1.4e-27   96.7   0.0    1.9e-27   96.2   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
    0.00062   19.8   2.9       0.67    9.8   0.0    3.2  3  APH             Phosphotransferase enzyme family
     0.0017   17.2   0.0     0.0041   16.0   0.0    1.5  2  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.047   13.1   0.0    1.9  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.0   3.3e-48   9.8e-45       1     256 [.      14     268 ..      14     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 3.3e-48
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    y+ ++ lG G++G+Vy a++ +  +  A+K+++ e  ++ +   +++rE  + + l+hpniv + +  + + +l++ +++
  gi|121637973|ref|YP_978197.1|  14 YRIERMLGAGGMGTVYLARNPDLPRSEALKVLAAELSRDLDFrARFVREADVAAGLDHPNIVAVHQRGQFEGRLWIAMQF 93 
                                    678899*****************************999988779************************************ PP

                                    -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEET.TTE....EEE-SGTTSEESSSSCS. CS
                        Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLide.kge....lKitDFGlakelesssk. 153
                                    v+gg+ +d+l+   +++ ++a  ++ +++++l+y H++g+iHrD+Kp+N+L+++        + ++DFG+a+ l  +   
  gi|121637973|ref|YP_978197.1|  94 VDGGNAEDALR-AATMTTARAVYVIGEVAKALDYAHQQGVIHRDIKPANFLLSRaA-GgderVLLSDFGIARALGDTGLt 171
                                    **********7.6889999999*******************************532.23566************998876 PP

                                    .BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTT CS
                        Pkinase 154 .ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpease 232
                                     + s+ +t  Y APEvl +++++  +D++slG+ l+ lltg+ pf++  g     + +       ++ ++    +++   
  gi|121637973|ref|YP_978197.1| 172 sTGSVLATLAYAAPEVLAGQGFDGRADLYSLGCALFRLLTGEAPFAAGAGAA--VAVVAG-----HLHQPPPTVSDRVPG 244
                                    68899*****************************************655554..222222.....222344445566777 PP

                                    S-HHHHHHHHHHT-SSGCCSTTHH CS
                        Pkinase 233 iseeakdllkkllkkdpkkRltae 256
                                    +s  +  ++   ++kdp++R+t +
  gi|121637973|ref|YP_978197.1| 245 LSAAMDAVIATAMAKDPMRRFTSA 268
                                    7*******************9954 PP

>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   5.6e+03       8      29 ..     153     173 ..     152     187 .. 0.72
   2 ?   -2.4   0.2       1.2   3.6e+03      13      38 ..     354     375 ..     337     383 .. 0.48
   3 !  131.7   0.0     9e-42   2.7e-38       1     189 []     394     586 ..     394     586 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                    GGS--HHHHHHHHT-S.--EE- CS
                         PknH_C   8 slLltpaelaailGtpeaasat 29 
                                    ++Ll++  +a++lG++  + +t
  gi|121637973|ref|YP_978197.1| 153 RVLLSDFGIARALGDT-GLTST 173
                                    8999999999***999.43333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHT-S.--EE-S-B-S-B-S CS
                         PknH_C  13 paelaailGtpeaasatesdttppdt 38 
                                    +a+  +++    ++ ++++ t+ p++
  gi|121637973|ref|YP_978197.1| 354 AAAAVTAV----TMTSHQPRTATPPS 375
                                    22222222....34455555555554 PP

  == domain 3  score: 131.7 bits;  conditional E-value: 9e-42
                                    --GGGGGGGS--HHHHHHHHT-S.--EE-S-B-S-B-S--EESSGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT-S CS
                         PknH_C   1 vpaaaldslLltpaelaailGtpeaasatesdttppdtaasvdppeClgvasageesvYggsgvtavagqtlrdsaddga 80 
                                    v++++l++lL++ +++++ +G + +++a+e+ ++p+  ++s++p+eC+++++ g +s+Y+   v +++g t++++++++a
  gi|121637973|ref|YP_978197.1| 394 VTRSRLPGLLPPLDDVKNFVGIQ-NLVAHEPMLQPQTPNGSINPAECWPAVGGGVPSAYDLGTVIGFYGLTIDEPPTGTA 472
                                    789********************.******************************************************** PP

                                    EE.EEEEEEE-SSHHHHHHHHHHHHHHHHTTTT-EEEEEETTEEEEEEE---B--..TT-EEEEEE.ESSTT--.EEEEE CS
                         PknH_C  81 sl.vsqavvafptadaAqaffaalaaqwrrCagvttttdsggatetwtvgdvsdd..dgvltatvtvtsggdga.rcqra 156
                                    +  v+q +vaf++a++Aq+ +a+la+ wrrC+g+t+t  + +++ +++++  +++  dg++t++ t ++g++ + r  +a
  gi|121637973|ref|YP_978197.1| 473 PNqVGQLIVAFRDAATAQRHLADLASIWRRCGGRTVTLFRSEWRRPVELSTSVPEvvDGITTMVLT-AQGPVLRvREDHA 551
                                    *9***********************************************99999999********9.55666666***** PP

                                    EEEETTEEEEEEEEE...SS-SSHHHHHHHHHHHH CS
                         PknH_C 157 lavranvvvdvevcgf..edggdaaaeiadaildk 189
                                    +a+++nv+vdv+++++  ++g++a++ i++ il+k
  gi|121637973|ref|YP_978197.1| 552 IAAKNNVLVDVDIMTPdtSRGQQAVIGITNYILAK 586
                                    ***************99888************997 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   6.2e-31   1.9e-27       3     213 ..      16     223 ..      14     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 6.2e-31
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE- CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivtey 82 
                                    +++ lG+G  G+V+ ++  +  +++ +kV    l+++ +   ++++++ea++   l+hpniv+++     e++l+i +++
  gi|121637973|ref|YP_978197.1|  16 IERMLGAGGMGTVYLARNPDLPRSEALKVLAAELSRDLDF--RARFVREADVAAGLDHPNIVAVHQRGQFEGRLWIAMQF 93 
                                    7899*************99666666666666666444443..69*************************99********* PP

                                    -TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE....TTEEEE-STTTHEETTTSSE CS
                    Pkinase_Tyr  83 vkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse....nkvvkisDfGLardiekdde 158
                                    v+gG+ ++ Lr+    ++t+ + + ++ +vAk+++y +++ ++Hrd+   N Lls+    ++ v +sDfG+ar++  d  
  gi|121637973|ref|YP_978197.1|  94 VDGGNAEDALRAA---TMTTARAVYVIGEVAKALDYAHQQGVIHRDIKPANFLLSRaaggDERVLLSDFGIARAL-GDTG 169
                                    ***********98...9**************************************9999899*************.8888 PP

                                    EEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHH CS
                    Pkinase_Tyr 159 yvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglknee 213
                                     +++++    + + apE+l  + f  ++D +s G  l+ ++t ge p++    + 
  gi|121637973|ref|YP_978197.1| 170 LTSTGSVLATLAYAAPEVLAGQGFDGRADLYSLGCALFRLLT-GEAPFAAGAGAA 223
                                    899999************************************.****98655444 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00035       1.1      14      86 ..      29     108 ..      18     129 .. 0.66
   2 !    9.8   0.0   0.00023      0.67     152     187 ..     116     154 ..     102     165 .. 0.74
   3 ?   -0.1   0.1      0.24   7.1e+02      49     110 ..     179     236 ..     159     282 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00035
                                    EEEEETT..--EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS..... CS
                            APH  14 ylvttpa..gryvlrrnppa..raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr..... 84 
                                    yl   p+  ++ +l++ +++  r   + +r+v++ ++ a++    P ++a  + ++++g+l+ ++++v+g  +++     
  gi|121637973|ref|YP_978197.1|  29 YLARNPDlpRSEALKVLAAElsRDLDFRARFVREADVAAGL--DHPNIVAVHQRGQFEGRLWIAMQFVDGGNAEDalraa 106
                                    55555555456677777777433444444566666665555..5589999999******************999966544 PP

                                    HH CS
                            APH  85 kl 86 
                                    ++
  gi|121637973|ref|YP_978197.1| 107 TM 108
                                    33 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00023
                                    HHHHHHHH--SSS-EEEE-SS-SGGGEEEC.....TTEE CS
                            APH 152 vlaalaallpgelptvllHgDlhpgNllvd...pddgrv 187
                                    v+ ++a+ l+ + +++++H+D++p N+l+     +d rv
  gi|121637973|ref|YP_978197.1| 116 VIGEVAKALDYAHQQGVIHRDIKPANFLLSraaGGDERV 154
                                    55666666666789***************9887555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.24
                                    HTT-B--B-CTTBS-EEETTE......EEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.- CS
                            APH  49 kagvpvPevlagdtddeeigl......lfalieyvpgrsllrklsaaqlpellealgeflaalhqvdp 110
                                     +   +Pevlag   +++ g+        al+  + g+ +           +++a++ + ++lhq +p
  gi|121637973|ref|YP_978197.1| 179 TLAYAAPEVLAG---QGFDGRadlyslGCALFRLLTGEAPFA-------AGAGAAVAVVAGHLHQPPP 236
                                    343368888884...333333444577566666666666666.......3456666777777777653 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0041     315     399 ..     120     201 ..     105     203 .. 0.85
   2 ?   -3.6   0.0       1.1   3.4e+03     305     323 ..     476     494 ..     474     500 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                 Pkinase_fungal 315 aIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgeeHsyr 394
                                    + k++   + ++g++HrDi   N l+   +  g+++ lL+D+ +a  l+d +   + +    Tl++ a evl g+    r
  gi|121637973|ref|YP_978197.1| 120 VAKALDYAH-QQGVIHRDIKPANFLLS-RAAGGDERVLLSDFGIARALGD-TGLTSTGSVLATLAYAAPEVLAGQGFDGR 196
                                    556666667.99**************9.77779****************7.66666799**************9989999 PP

                 Pkinase_fungal 395 hDLES 399
                                     DL S
  gi|121637973|ref|YP_978197.1| 197 ADLYS 201
                                    99876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                 Pkinase_fungal 305 pkellealrDaIkghrsLf 323
                                    + +l+ a+rDa ++ r L 
  gi|121637973|ref|YP_978197.1| 476 VGQLIVAFRDAATAQRHLA 494
                                    67999*********99997 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.047     115     166 ..     108     159 ..      45     164 .. 0.78
   2 ?   -1.0   0.0      0.31   9.2e+02      35      62 ..     499     528 ..     484     529 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                            Kdo 115 laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                    +  ++    + +v+++    h+ gv H+d+ + n+ll  ++++++++ l D+
  gi|121637973|ref|YP_978197.1| 108 MTTARAVYVIGEVAKALDYAHQQGVIHRDIKPANFLLSRAAGGDERVLLSDF 159
                                    44555556677899999999********************999999999999 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.31
                            Kdo  35 yyr..ggllgklskdlyrfklgrtravrEf 62 
                                    ++r  gg +  l+++++r++++  ++v E+
  gi|121637973|ref|YP_978197.1| 499 IWRrcGGRTVTLFRSEWRRPVELSTSVPEV 528
                                    44334899999**********999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4339.30
//
Query:       gi|121637974|ref|YP_978198.1|  [L=375]
Description: dipeptidase PepE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-61  208.2   0.7    1.4e-61  207.9   0.7    1.1  1  Peptidase_M24  Metallopeptidase family M24
    1.6e-11   45.0   0.1    4.3e-11   43.6   0.0    1.7  2  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.7   1.5e-65   1.4e-61       2     209 .]     154     356 ..     153     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1.5e-65
                                    HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEE CS
                  Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlida 81 
                                    ++rka+++ ++++++v e + pg te+++aa i ++ + ++g  ++af +iv+sg+++a +h+  +dr+l+egd+v++d+
  gi|121637974|ref|YP_978198.1| 154 ALRKAGAAIDRVHARVPEFLVPGRTEADVAADIAEA-IVAEGHSEVAF-VIVGSGPHGADPHHGYSDRELREGDIVVVDI 231
                                    68********************************98.8899*******.6*************999************** PP

                                    EEEET.TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSS CS
                  Peptidase_M24  82 gaeyd.gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGle 160
                                    g+ y  gy+sD+trT+++G+++ + ++ y  +++aq+aa++a++pGvt++++daaar+vl++agla++f h++GHg+Gl 
  gi|121637974|ref|YP_978198.1| 232 GGTYGpGYHSDSTRTYSIGEPDSDVAQSYSMLQRAQRAAFEAIRPGVTAEQVDAAARDVLAEAGLAEYFVHRTGHGIGLC 311
                                    *********************999999***************************************************** PP

                                    SSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                  Peptidase_M24 161 vhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                    vh+e p++   ++++ +l +Gm f+iEpgiyf+ ++ g+ried v+vte
  gi|121637974|ref|YP_978198.1| 312 VHEE-PYIV--AGNDLVLVPGMAFSIEPGIYFPGRW-GARIEDIVIVTE 356
                                    ***9.**87..577*****************98889.***********7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   4.8e-15   4.3e-11       1     132 []      14     146 ..      14     146 .. 0.87
   2 ?   -2.5   0.0      0.85   7.6e+03      78      90 ..     284     296 ..     257     304 .. 0.52

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4.8e-15
                                    HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH......TTSEEEEE CS
                   Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaees.....atveevvey 74 
                                    Rl+ ++a+ +++gl +l++t+ ++l+Yl G ++et++r++alv++a+ga   ++++l+ +  +++      ++v ++v+ 
  gi|121637974|ref|YP_978198.1|  14 RLALAAAATADAGLAGLVITPGYDLCYLIGSRAETFERLTALVLPAAGApAVVLPRLELAALKQSAaaelgLRVCDWVDG 93 
                                    78889999***********************************************8888888888899999999999999 PP

                                    STHSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                   Creatinase_N  75 ddpvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                    ddp+  + ++l+ +       +v ++ +++  +  l  al ++  v a+ ++++lR+v
  gi|121637974|ref|YP_978198.1|  94 DDPYGLVSAVLGGAPV---ATAVTDS-MPALHMLPLADAL-GVLPVLATDVLRRLRMV 146
                                    9988888888888822...2245554.8999999999999.78899999999999997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.85
                                    SSHHHHHHHHHHH CS
                   Creatinase_N  78 vealadllkelle 90 
                                    ++a  d+l+e+++
  gi|121637974|ref|YP_978198.1| 284 DAAARDVLAEAGL 296
                                    3444455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2501.73
//
Query:       gi|121637975|ref|YP_978199.1|  [L=355]
Description: 5'-3' exonuclease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-48  164.7   0.0    2.2e-48  164.1   0.0    1.3  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
    6.9e-19   68.3   0.0    1.1e-18   67.7   0.0    1.3  1  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
    0.00061   19.8   0.1     0.0019   18.3   0.0    1.7  2  HHH_2         Helix-hairpin-helix motif
      0.006   17.2   0.1      0.014   16.0   0.1    1.6  1  HHH_5         Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.043   13.7   0.2       0.13   12.2   0.2    1.8  1  HHH           Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   6.2e-52   2.2e-48       2     159 .]      42     222 ..      41     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 6.2e-52
                   5_3_exonuc_N   2 llLiDgsslifRayyal...lttsdgeptnavygflnmllklleeekpthlavvfDa.kkktfRhelypeYKanR..... 72 
                                    l+L+Dg+s++fR+++++   +t++dg+p+nav+gf++ ++ ++++++p++lav++D   +++fR +l+p+YKa+R     
  gi|121637975|ref|YP_978199.1|  42 LVLLDGASMWFRSFFGVpssITAPDGRPVNAVRGFIDSMAVVITQQRPNRLAVCLDLdWRPQFRVDLIPSYKAHRvaepe 121
                                    89**************999999**************************99******73699******************* PP

                   5_3_exonuc_N  73 .......eetpeelkeqlplikevlealgikvlevegyEADDvigtlakraeeegvvivsgDkDllQlvedn...vrvld 142
                                           ee+p+el++q+++i e+l+a+gi+++ ++g+EADDv+gtla+r +++ v++vsgD+DllQ+v d+   vrvl+
  gi|121637975|ref|YP_978199.1| 122 pngqpdvEEVPDELTPQVDMIMELLDAFGIAMAGAPGFEADDVLGTLATRERRDPVIVVSGDRDLLQVVADDpvpVRVLY 201
                                    **************************************************76655**************76667899999 PP

                   5_3_exonuc_N 143 ....vkkeelldeeevaekyg 159
                                         +k +l++++evae+yg
  gi|121637975|ref|YP_978199.1| 202 lgrgLAKATLFGPAEVAERYG 222
                                    9988666778*********98 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   2.9e-22   1.1e-18       5      86 ..     231     315 ..     228     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.9e-22
                     5_3_exonuc   5 qiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelke...kklkekLeenkeearlskkLatiktdvp 81 
                                     +++l+ L+GD+sD +pGvpg+GektAa+Ll+++gsl++i++++d+ k+   k l++kL ++  +++ + +++++ td+p
  gi|121637975|ref|YP_978199.1| 231 AYAELALLRGDPSDGLPGVPGVGEKTAATLLARHGSLDQIMAAADDRKTtmaKGLRTKLLAASAYIKAADRVVRVATDAP 310
                                    6789999*************************************9534434478************************** PP

                     5_3_exonuc  82 lelel 86 
                                    ++l++
  gi|121637975|ref|YP_978199.1| 311 VTLST 315
                                    98764 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.2e-07    0.0019       7      33 ..     248     274 ..     246     277 .. 0.94
   2 ?   -2.5   0.0       1.5   5.6e+03      18      32 ..     332     349 ..     328     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-07
                          HHH_2   7 GIrhVGektAklLakrFksldaLkkas 33 
                                    G++ VGektA +L  r +sld++++a 
  gi|121637975|ref|YP_978199.1| 248 GVPGVGEKTAATLLARHGSLDQIMAAA 274
                                    89*********************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                          HHH_2  18 lLakrFk...sldaLkka 32 
                                    +La+rF+   s+ +L+ka
  gi|121637975|ref|YP_978199.1| 332 ELATRFGvesSIARLQKA 349
                                    699999877788888877 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.9e-06     0.014       6      36 ..     248     277 ..     243     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                    TSTT--HHHHHHHHTTT--SHHHHHHS-HHH CS
                          HHH_5   6 svsGiGpktAlallsaGiesvedlaaadvee 36 
                                    +v+G+G+ktA +ll    +s+++++aa+ ++
  gi|121637975|ref|YP_978199.1| 248 GVPGVGEKTAATLLAR-HGSLDQIMAAADDR 277
                                    79**********9999.89*****9997765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.6e-05      0.13      16      28 ..     249     261 ..     244     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                                    STT-SHHHHHHHH CS
                            HHH  16 lPGVGpktAeaIl 28 
                                    +PGVG+ktA   l
  gi|121637975|ref|YP_978199.1| 249 VPGVGEKTAATLL 261
                                    9********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2686.55
//
Query:       gi|121637976|ref|YP_978200.1|  [L=244]
Description: hypothetical protein BCG_2111c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-26   91.7   2.4    3.9e-26   91.1   2.4    1.3  1  DUF4333   Domain of unknown function (DUF4333)
  ------ inclusion threshold ------
      0.014   15.1  16.7      0.014   15.1  16.7    1.8  2  Collagen  Collagen triple helix repeat (20 copies)


Domain annotation for each model (and alignments):
>> DUF4333  Domain of unknown function (DUF4333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   2.4   4.3e-30   3.9e-26       1      78 []     154     236 ..     154     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 4.3e-30
                        DUF4333   1 llvvgcslpgflgskvldkaaveagvaqvLtes...ygakkvsdVtCpsgl..kvevGatftCtltvdGetltVtvtvtd 75 
                                    +l++g+++pgf+++++ld  +++agv+qvLt++   ygak+v+dV+C++g   +v++Gatf+Ct+++dG++++Vtvt++d
  gi|121637976|ref|YP_978200.1| 154 VLILGFWAPGFFVTTKLDVIKAQAGVQQVLTDEttgYGAKNVKDVKCNNGSdpTVKKGATFECTVSIDGTSKRVTVTFQD 233
                                    6899***************************999**************65555*************************** PP

                        DUF4333  76 ddG 78 
                                    ++G
  gi|121637976|ref|YP_978200.1| 234 NKG 236
                                    998 PP

>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.55     5e+03      10      13 ..       3       6 ..       1      12 [. 0.46
   2 ?   15.1  16.7   1.6e-06     0.014      10      53 ..      86     130 ..      79     135 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.55
                                   XXXX CS
                       Collagen 10 GppG 13
                                   Gp+G
  gi|121637976|ref|YP_978200.1|  3 GPQG 6 
                                   1111 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-06
                                    XXXXXXXXX-----XXXXEEEE-TTSS-----.------------ CS
                       Collagen  10 GppGppGkrGepGeaGekGekGpaGekGppGa.aGkpGapGekGe 53 
                                    G pG+ G+  +pG+ G++G+ G++G+  ppG+ +G+ G+ G++G+
  gi|121637976|ref|YP_978200.1|  86 GVPGQYGQYQQPGQYGQPGQYGQPGQYAPPGQyPGQYGPYGQSGQ 130
                                    333444444444444444444444444444432333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2040.33
//
Query:       gi|121637977|ref|YP_978201.1|  [L=906]
Description: ATP-dependent DNA helicase helY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-40  139.0   0.0    1.2e-39  135.6   0.0    2.6  3  DSHCT           DSHCT (NUC185) domain
    3.8e-19   69.1   0.0      1e-18   67.8   0.0    1.8  2  DEAD            DEAD/DEAH box helicase
    2.1e-07   31.1   0.0    3.3e-07   30.4   0.0    1.3  1  ResIII          Type III restriction enzyme, res subunit
    8.4e-06   26.1   0.0    2.4e-05   24.7   0.0    1.8  1  Helicase_C      Helicase conserved C-terminal domain
    0.00029   20.9   0.0      0.054   13.4   0.0    2.2  2  rRNA_proc-arch  rRNA-processing arch domain
  ------ inclusion threshold ------
      0.043   14.1   0.0       0.21   11.9   0.0    2.2  1  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   8.8e+03      34      58 ..     431     455 ..     430     492 .. 0.55
   2 ?   -0.7   0.1      0.34     1e+03     128     159 ..     674     706 ..     671     708 .. 0.77
   3 !  135.6   0.0   3.9e-43   1.2e-39       3     162 ..     729     901 ..     727     903 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                          DSHCT  34 lepeelaAllsalvfeekredeeek 58 
                                    +ep+e+a+l s+ +f  +++   ++
  gi|121637977|ref|YP_978201.1| 431 IEPSEVAGLASTRTFPLRSSFAPSY 455
                                    5788999999988888775443332 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                          DSHCT 128 eellrqlakaakv.igneeLkkkaeeaielikR 159
                                    e+ +rq ++  ++   n++L++k+ +a + + R
  gi|121637977|ref|YP_978201.1| 674 EDQIRQAERYLRIeRDNAQLERKVAAATNSLAR 706
                                    566666666666557899**********99988 PP

  == domain 3  score: 135.6 bits;  conditional E-value: 3.9e-43
                          DSHCT   3 tvtlkGrvaaeirsedeLlltellfsgvlddlepeelaAllsalvfeekredeeeke...pkl.seeleeal.......e 71 
                                    +vt++Gr++a+i+se++Ll++e+l++g++++l+p+ela+++sa+v+e++  d + +    + + +++l++al       +
  gi|121637977|ref|YP_978201.1| 729 VVTDDGRLLARIYSESDLLVAECLRTGAWEGLKPAELAGVVSAVVYETRGGDGQGAPfgaD-VpTPRLRQALtqtsrlsT 807
                                    79***********************************************999888769953.447788887744445441 PP

                          DSHCT  72 el...keiaeriakvsvesrl.dlglvevvyaWakgasfaellektdld.......eGdiVRllrrleellrqlakaakv 140
                                         +e+a+ri+     sr+ d g+v v+y+W +  ++a+ l+++d+        +Gd+VR++r++ +ll+q+++aa+ 
  gi|121637977|ref|YP_978201.1| 808 -TlraDEQAHRIT-P---SREpDDGFVRVIYRWSRTGDLAAALAAADVNgsgspllAGDFVRWCRQVLDLLDQVRNAAP- 881
                                    .0466********.6...5666***********************87777777777***********************. PP

                          DSHCT 141 igneeLkkkaeeaielikRdiV 162
                                      n+eL+++a++ai  i+R++V
  gi|121637977|ref|YP_978201.1| 882 --NPELRATAKRAIGDIRRGVV 901
                                    ..9******************9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   3.4e-22     1e-18       2     170 ..      20     167 ..      19     172 .. 0.87
   2 ?   -4.0   0.0       3.6   1.1e+04      81     107 ..     538     563 ..     526     573 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 3.4e-22
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    d Q++a+ ++ +g+ vlv+a+TG+GKT +  ++v  ++       g k+++ +P+++L +q +++l+ +    d ++ l+
  gi|121637977|ref|YP_978201.1|  20 DFQQRACSALERGHGVLVCAPTGAGKTVVGEFAVHLAL-----AAGSKCFYTTPLKALSNQKHTDLTARYGR-D-QIGLL 92 
                                    68***************************999999666.....7899*******************999885.2.34344 PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                    +g      +ls+   ++ +vv+t++ l ++l   +  l+ ++++V+DE++ l d  +++ +++++ ql       + + +
  gi|121637977|ref|YP_978201.1|  93 TG------DLSVN-GNAPVVVMTTEVLRNMLYADSPALQGLSYVVMDEVHFLADRMRGPVWEEVILQL-------PDDVR 158
                                    44......34455.67*************99666778*******************************.......56678 PP

                                    EEEEESSBS CS
                                    xxxxxxxxx RF
                           DEAD 162 vivlSATlp 170
                                    v+ lSAT++
  gi|121637977|ref|YP_978201.1| 159 VVSLSATVS 167
                                    *******98 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.6
                                    EETTSSHHHHHHHHHTTCSEEEEEHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldngvdivvgtpgr 107
                                    +   +aa+d l++l ++ di+  t+gr
  gi|121637977|ref|YP_978201.1| 538 LQRRQAATDALAAL-RRGDIITITHGR 563
                                    45567888999999.788888888887 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.1e-10   3.3e-07       5     169 ..      19     166 ..      15     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.1e-10
                                    -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                         ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke 84 
                                     + Q++a+ +l      +r + +l+ ++TG+GKT+v   ++   l +g+  k++   p k+l +q  ++++  +  +   
  gi|121637977|ref|YP_978201.1|  19 DDFQQRACSAL------ERGHGVLVCAPTGAGKTVVGEFAVHLALAAGS--KCFYTTPLKALSNQKHTDLTARYGRD--- 87 
                                    55566666666......477889999**********9666666666656..9**********************998... PP

                                    GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHH.HHHT---S CS
                         ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswre.ilekfkea 160
                                    + + ++gd   +      n+ ++v+t++ l + +     + ++   +   ++++DE+H l++      w+e il+  ++ 
  gi|121637977|ref|YP_978201.1|  88 QIGLLTGDLSVN-----GNAPVVVMTTEVLRNML-----YADSPALQGLSYVVMDEVHFLADRmrgPVWEEvILQLPDDV 157
                                    799999999999.....9****************.....777777777889**********986555****447777889 PP

                                    EEEEEESS- CS
                         ResIII 161 vllglTATp 169
                                     ++ l+AT 
  gi|121637977|ref|YP_978201.1| 158 RVVSLSATV 166
                                    9*******7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   7.9e-09   2.4e-05      43     111 .]     340     416 ..     318     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.9e-09
                                    EEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE........ESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  43 vavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi........nfdlprnvtsyiqriGRtgRag 111
                                     a++h+ +    r  + e f +g ++ + at  ++ Gi++p  ++V           ++p ++ +y q  GR+gR g
  gi|121637977|ref|YP_978201.1| 340 LAAHHAGMLPAFRHTVEELFTAGLVKAVFATETLALGINMPARTVVLerlvkfngEQHMPLTPGEYTQLTGRAGRRG 416
                                    567899999999*****************************8887776666555555566779************75 PP

>> rRNA_proc-arch  rRNA-processing arch domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.8e-05     0.054       3      98 ..     473     574 ..     472     591 .. 0.74
   2 !    5.1   0.2    0.0063        19     227     268 ..     656     697 ..     654     699 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                    HHHHSHHHHHHHHHHHHHHHHHHHHHHHHHTC--TT...HHHHHHHHHHHHHHHHHHHHHH..HHHC...SHHHHGGG-- CS
                 rRNA_proc-arch   3 MlerSFsqfqnqkslpelekklkeleeelksitied...eedieeyyklrqqleelreeir..kilt...kpknilpfLq 74 
                                    +le+SF q+q+++s+  l + +++    l +i +e     + i ey  lr  ++el++     + l+   + + +l +L 
  gi|121637977|ref|YP_978201.1| 473 LLEQSFAQYQADRSVVGLVRGIERGNRILGEIAAELggsDAPILEYARLRARVSELERAQAraSRLQrrqAATDALAALR 552
                                    89*****************************99996677779*********99999764330033332213344555566 PP

                                    TTEEEEEEETTTEEEEEEEEEEEE CS
                 rRNA_proc-arch  75 pGRlvrvksnddldfgwGivlnfk 98 
                                     G ++ ++   + + g+++vl+  
  gi|121637977|ref|YP_978201.1| 553 RGDIITIT--HGRRGGLAVVLESA 574
                                    67777776..44667888888875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0063
                                    HHHHHHHHTSGG.GSSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 rRNA_proc-arch 227 ealesrlaknpllhspnleelyalyekkvalqeeikelkkei 268
                                    e+  ++l+++p+++sp le+++ + e++  ++++  +l++++
  gi|121637977|ref|YP_978201.1| 656 ESSREQLRRHPVHTSPGLEDQIRQAERYLRIERDNAQLERKV 697
                                    667799******77*******************999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.9e-05      0.21       8     112 ..      35     149 ..      29     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..............erl 73 
                                    ++v++++G+GKT++ +  ++ + ++        +  f+t p +  s +  ++l   +g+++ +                 
  gi|121637977|ref|YP_978201.1|  35 VLVCAPTGAGKTVVGEFAVHLALAA-------GSKCFYTTPLKALSNQKHTDLTARYGRDQIGlltgdlsvngnapvVVM 107
                                    579*****************99643.......333355555555455556677777777777777777888777787778 PP

                         AAA_22  74 sseellealeqalraravielliiDEaqhlr...seealeeL 112
                                    ++e l+++l+  + a +  + ++ DE+++l    +  ++ee+
  gi|121637977|ref|YP_978201.1| 108 TTEVLRNMLYADSPALQGLSYVVMDEVHFLAdrmRGPVWEEV 149
                                    888888888888888888999999999999664435555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.23s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 6516.08
//
Query:       gi|121637978|ref|YP_978202.1|  [L=308]
Description: Sec-independent protein translocase transmembrane protein tatC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-59  201.4  11.0    1.7e-59  201.1  11.0    1.1  1  TatC      Sec-independent protein translocase protein (TatC)
  ------ inclusion threshold ------
       0.27   10.6   2.2        9.2    5.6   0.0    3.0  3  GPI2      Phosphatidylinositol N-acetylglucosaminyltransferas


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1  11.0   1.9e-63   1.7e-59       1     204 [.      29     252 ..      29     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.9e-63
                                    -HHHHHHHHHHHHHHHHHHHHHHHHH.THHHHHH......HCCHHHHC..C.........TTS-EE--SSS-HHHHHHHH CS
                           TatC   1 ehLeeLrkrlirallavaiafiitfv.faeelia......fllepleea.e.........eevelivlspleafllklkv 63 
                                    +hL eLr+rl+++l+a+++++i++fv +++ ++       +l +p+ +  +          e++l++++p+++f+l+lkv
  gi|121637978|ref|YP_978202.1|  29 DHLTELRTRLLISLAAILVTTIFGFVwYSHSIFGldslgeWLRHPYCALpQsaradisadGECRLLATAPFDQFMLRLKV 108
                                    7************************934444444555556999999876436666665543499**************** PP

                                    HHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT..TTTSST.TEEHHHH CS
                           TatC  64 slvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll..seevep.llslsey 140
                                    ++ ag+vla+Pv++yqlwaf++pgLy++err+++ f+i + +lf++Ga++ay+ vl  +l fll  +++v+  +ls + y
  gi|121637978|ref|YP_978202.1| 109 GMAAGIVLACPVWFYQLWAFITPGLYQRERRFAVAFVIPAAVLFVAGAVLAYL-VLSKALGFLLtvGSDVQVtALSGDRY 187
                                    ****************************************************6.999*******7855565525****** PP

                                    HHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHH CS
                           TatC 141 lsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlll 204
                                    + f+l ll++fg++Fe+Pl++v+l+ +gl+++e l+++rr  i++++v+aa++tP +d++s+++l
  gi|121637978|ref|YP_978202.1| 188 FGFLLNLLVVFGVSFEFPLLIVMLNLAGLLTYERLKSWRRGLIFAMFVFAAIFTPgSDPFSMTAL 252
                                    **************************************************************987 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.023   2.1e+02     243     269 ..      85     126 ..      25     130 .. 0.59
   2 ?    1.3   0.4     0.021   1.8e+02     232     268 ..     154     211 ..     128     214 .. 0.61
   3 ?    5.6   0.0     0.001       9.2      53     101 ..     230     278 ..     227     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.023
                           GPI2 243 k...............lllavvlllllalimgvcpwwliglq 269
                                                      ++ + + ++a i++ cp+w+ +l 
  gi|121637978|ref|YP_978202.1|  85 IsadgecrllatapfdQFMLRLKVGMAAGIVLACPVWFYQLW 126
                                    055555555555555445555667788999999999998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.021
                           GPI2 232 llagagvgiilk.....................lllavvlllllalimgvcpwwligl 268
                                    ++a+++ ++++k                     + ++++ ll+++ +++ +p++++ l
  gi|121637978|ref|YP_978202.1| 154 AGAVLAYLVLSKalgflltvgsdvqvtalsgdrYFGFLLNLLVVFGVSFEFPLLIVML 211
                                    3333333333334455555555666666666888899999999999999888888766 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.001
                           GPI2  53 iifvlvFvgiyqervspvsvvllssiltvlgwllwelwaskeesrssra 101
                                    i+ ++vF++i++   +p s++ l+++ltvl+ l+++++  +++++ +r+
  gi|121637978|ref|YP_978202.1| 230 IFAMFVFAAIFTPGSDPFSMTALGAALTVLLELAIQIARVHDKRKAKRE 278
                                    77899*****************************999887766554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2454.43
//
Query:       gi|121637979|ref|YP_978203.1|  [L=83]
Description: twin arginine translocase A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-24   84.5   0.1    2.8e-24   84.2   0.1    1.1  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.18   12.0   0.0    1.2  1  HTH_17       Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.1   3.1e-28   2.8e-24       1      51 [.       4      54 ..       4      56 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 3.1e-28
                                   S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH---XXX CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeenekea 51
                                   l++++++i++vV+++lFG+kkLP++ar+LGk+Lr Fk++v+el++en+ ea
  gi|121637979|ref|YP_978203.1|  4 LSPWHWAILAVVVIVLFGAKKLPDAARSLGKSLRIFKSEVRELQNENKAEA 54
                                   69*********************************************9997 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.18      25      50 ..      23      50 ..      16      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                         HTH_17 25 gelpaa.k.iGrrwriprsdleewlekr 50
                                   ++lp a + +G+++ri +s++ e  +++
  gi|121637979|ref|YP_978203.1| 23 KKLPDAaRsLGKSLRIFKSEVRELQNEN 50
                                   788888668***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 651.12
//
Query:       gi|121637980|ref|YP_978204.1|  [L=316]
Description: hypothetical protein BCG_2115c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-31  109.5   0.0    3.4e-31  108.6   0.0    1.5  2  WYL       WYL domain
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.055   13.5   0.0    1.3  1  HTH_Mga   M protein trans-acting positive regulator (MGA) HTH


Domain annotation for each model (and alignments):
>> WYL  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.75   6.7e+03     153     170 ..     104     121 ..      83     122 .. 0.74
   2 !  108.6   0.0   3.8e-35   3.4e-31       4     171 ..     140     306 ..     137     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.75
                            WYL 153 eVlePaeLreevkeeaer 170
                                     V++P+  r +++++a++
  gi|121637980|ref|YP_978204.1| 104 GVVDPQAARSAIAKIAAA 121
                                    589999999999998875 PP

  == domain 2  score: 108.6 bits;  conditional E-value: 3.8e-35
                            WYL   4 etlaeAieerrrvefrYrsp.agege..ertvePyglvlkngrwYLvaydekrdeirtfrldRiselelldetfeppdf. 79 
                                    + ++ A+++ r ++++Y+ +  +  +  +r v+P+++ l  g+ YL a++++++ +r+fr+dRi ++  l+e++ pp+  
  gi|121637980|ref|YP_978204.1| 140 AAVRAAVRNSRALTIDYYAAsHD--TltTRIVDPIRVLLIGGHSYLEAWSREAEGVRLFRFDRIVDAAELGEPAVPPESa 217
                                    67999**************6444..456*********************************************9877442 PP

                            WYL  80 .dlakylsksfgvfkspvevkvrfspeaarrvrerrfpdqkieeedddgsvrvelpvesleellswllsfgdeveVlePa 158
                                     +     s + g+ +   ++++r++p+a++++++  +p  ++++  +dgs++v ++ +s++++ + ll+fg++v+Vl+P+
  gi|121637980|ref|YP_978204.1| 218 rQAPPDTSLFDGDLS-LPSATLRVAPSASWMLEY--YPIRELRQ-LPDGSCEVAMTYASEDWMTRLLLGFGSDVRVLAPE 293
                                    134444455666666.99**************66..66677777.99********************************* PP

                            WYL 159 eLreevkeeaerl 171
                                    +L ++v+++a ++
  gi|121637980|ref|YP_978204.1| 294 SLAQRVRDAATAA 306
                                    *********9887 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.2e-06     0.055      16      44 ..      19      47 ..       9      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-06
                        HTH_Mga 16 eneksltldelakeLglseltlqsdiseL 44
                                   + ++++t  e+a eLg + ++l +d+++L
  gi|121637980|ref|YP_978204.1| 19 QANPRITRAEAAAELGVTAKQLEEDLNQL 47
                                   5699***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1692.29
//
Query:       gi|121637981|ref|YP_978205.1|  [L=332]
Description: hypothetical protein BCG_2116c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-28  100.3   0.0    1.8e-28   99.8   0.0    1.2  1  WYL            WYL domain
  ------ inclusion threshold ------
      0.037   14.5   0.1       0.38   11.3   0.1    2.5  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> WYL  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0     2e-32   1.8e-28       2     170 ..     154     326 ..     153     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 2e-32
                            WYL   2 vletlaeAieerrrvefrYrspagege...ertvePyglvlkngrwYLvaydekrdeirtfrldRise.lellde..tfe 75 
                                    vl  l  Ai+++++v+f++rs+  ++e   +rtveP+g+v  +grwYLv++d++rd+ r+frl+Ri   +++++     +
  gi|121637981|ref|YP_978205.1| 154 VLGILLSAIDSGQVVQFSHRSS--RAEpytVRTVEPWGVVTEKGRWYLVGHDRDRDATRVFRLSRIGAqVTPIGPagATT 231
                                    677899***************5..444447************************************75599999844333 PP

                            WYL  76 pp.dfdlakylsksfgvfkspvevkvrfspeaarrvrerrfpdqkieeedddgsvrvelpvesleellswllsfgdeveV 154
                                     p + dl++ +++   + +  ++++v++++  a+ +r+   +++  ++  + +  ++el+++s++ l++ + ++g+++ V
  gi|121637981|ref|YP_978205.1| 232 VPaGVDLRSIVAQKVTEVPTGEQATVWVAEGRATALRRA-GRSAGPRQLGGRDGEVIELEIRSSDRLAREITGYGADAIV 310
                                    55378******976655555*********9999999764.4444444444444456888999****************** PP

                            WYL 155 lePaeLreevkeeaer 170
                                    l+P +Lr+ v +++++
  gi|121637981|ref|YP_978205.1| 311 LQPGSLRDDVLARLRA 326
                                    ************9986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.2e-05      0.38      57     101 ..     250     327 ..     196     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                                    -...................................EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHT CS
                  CoA_binding_2  57 d...................................lvdvftppeatpeivkealalgakavwlqpgsedeeaaelaeea 101
                                                                        ++ + ++++    +++e+   ga a++lqpgs  ++++++++++
  gi|121637981|ref|YP_978205.1| 250 PtgeqatvwvaegratalrragrsagprqlggrdgeVIELEIRSS--DRLAREITGYGADAIVLQPGSLRDDVLARLRAQ 327
                                    245555566666666666666666666666666666666555544..468899*99********************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1813.82
//
Query:       gi|121637982|ref|YP_978206.1|  [L=452]
Description: hypothetical protein BCG_2117c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     2e-159  531.3   0.5     4e-159  530.4   0.5    1.4  1  Pup_ligase  Pup-ligase protein


Domain annotation for each model (and alignments):
>> Pup_ligase  Pup-ligase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.4   0.5  2.2e-163    4e-159       1     439 [.       4     422 ..       4     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 530.4 bits;  conditional E-value: 2.2e-163
                                    --EEEEEE-EEEECT-TTEEEE-HHHHHHHHHHHHGGGEE--------------CHHHHHHHS-S--EEEETTS-EEEEE CS
                     Pup_ligase   1 rimGiEtEYgilvpaepeaeslspeelarelvaayaaaeawdyeeesplrdargfelerararssqlnvflanGarlYvd 80 
                                    rimGiEtE+g++++  +++++lsp+e+ar+l                       f+ ++++ rss  nvfl+nGarlY+d
  gi|121637982|ref|YP_978206.1|   4 RIMGIETEFGVTCTF-HGHRRLSPDEVARYL-----------------------FRRVVSWGRSS--NVFLRNGARLYLD 57 
                                    9************55.67779**********.......................9999999****..************* PP

                                    .TTEEEEE---BSSHHHHHHHHHHHHHHHHHHHHHHHHCCC.....-EEEEESSSB-TTS-B--EEEEEEEETTS-HHHH CS
                     Pup_ligase  81 .gahpEystpEvtspldlvaydrAgdeilreaaeeaeeelg.....gevklykNnvDskGasYGchENYlvrravpfeel 154
                                     g+hpEy+t+E++s+ +lv++drAg+ +l++++ +ae++l+     g+++l+kNn+Ds+G+sYGchENYl+ ra +f+++
  gi|121637982|ref|YP_978206.1|  58 vGSHPEYATAECDSLVQLVTHDRAGEWVLEDLLVDAEQRLAdegigGDIYLFKNNTDSAGNSYGCHENYLIVRAGEFSRI 137
                                    **************************************999999************************************ PP

                                    HHCHHHHHHHCHHHH---EEEETTTS-CEEEES-SSHHHCCCCCCSSSTTSEECEES-S--SS-TTTEEEEEE------S CS
                     Pup_ligase 155 akkLlpflvtRqiitGaGrvglgeegeeagFqlsqrAdfieeevslettleRpiintrdEphadaskyrRLhvivgDsnl 234
                                     + LlpflvtRq+i+GaG+v   ++ + a+++lsqrA++i+e vs++tt++RpiintrdEphada+kyrRLhvivgDsn+
  gi|121637982|ref|YP_978206.1| 138 SDVLLPFLVTRQLICGAGKV--LQTPKAATYCLSQRAEHIWEGVSSATTRSRPIINTRDEPHADAEKYRRLHVIVGDSNM 215
                                    *******************9..4579999*************************************************** PP

                                    SHHHHHHHHHHHHHHHHHHHCT---S---BSSCCCCHHHHHC-TTS--EEEBTTS-EEEHHHHHHHHHHHHHHHHHHHHG CS
                     Pup_ligase 235 sevatllkvgttalvLdlieagkelpdleladpvaalrevsrdltlkatveladgreltaleiqrayleavrkfleeeee 314
                                    se++t+lkvgt+alvL++ie+g++++d++l++p++a+revs+d+t +++v+la gr+++al+iqr+y++++ ++l+++e 
  gi|121637982|ref|YP_978206.1| 216 SETTTMLKVGTAALVLEMIESGVAFRDFSLDNPIRAIREVSHDVTGRRPVRLAGGRQASALDIQREYYTRAVEHLQTREP 295
                                    ****************************************************************************9986 PP

                                    GCSHHHHHHHHHHHHHHHH.HC-SCCCTTT-HHHHHHHHHHHHHHHHT--TT-HHHHHHHHHTTB-STTTSHHHHHHHCT CS
                     Pup_ligase 315 eeeetkevlelWeevldal.eedpqaladridWvaKlrLleelrereglswddpklkalDlqYhdirpekglfarLvarg 393
                                    + ++ ++v++lW++ lda+ ++d ++++++idWv+K++L++++++r ++++++pk+++lDl+Yhdi++++g+f+ L+++g
  gi|121637982|ref|YP_978206.1| 296 N-AQIEQVVDLWGRQLDAVeSQDFAKVDTEIDWVIKRKLFQRYQDRYDMELSHPKIAQLDLAYHDIKRGRGIFDLLQRKG 374
                                    4.5****************999********************************************************** PP

                                    SS--SS-HHHHHHHHHS--SSSTHHHHHHHHHHHHHH..EEEEESSEE CS
                     Pup_ligase 394 rverlvteeeieravtepPadtrAalRgelvrefaee..vvavdWdsv 439
                                     + r++t+eei++av++pP++trA+lRge++++++e+  +++vdW ++
  gi|121637982|ref|YP_978206.1| 375 LAARVTTDEEIAEAVDQPPQTTRARLRGEFISAAQEAgrDFTVDWVHL 422
                                    ************************************9999*****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2502.02
//
Query:       gi|121637983|ref|YP_978207.1|  [L=491]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-35  120.5  16.9    4.1e-35  120.0  16.9    1.2  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0  16.9   2.3e-39   4.1e-35       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 2.3e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Peal aaa+dla+i+s+++aanaaaa ptt+ la+aaDeVSa iAalf+a+aq+yqa+saqaaafh++fvq l+a
  gi|121637983|ref|YP_978207.1|  1 MSFVIASPEALLAAATDLAAIRSTIRAANAAAAVPTTGALAPAADEVSAGIAALFGAQAQSYQAVSAQAAAFHDRFVQLLNA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   ++gsYa+aE 
  gi|121637983|ref|YP_978207.1| 83 GGGSYASAEI 92
                                   ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.58
# Mc/sec: 2538.48
//
Query:       gi|121637984|ref|YP_978208.1|  [L=550]
Description: hypothetical protein BCG_2119 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-55  186.5  18.0    7.9e-55  186.5  18.0    1.9  2  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5  18.0   4.4e-59   7.9e-55       4     301 .]      66     408 ..      64     408 .. 0.97
   2 ?   -3.9   0.4       0.4   7.2e+03      97     128 ..     499     530 ..     492     538 .. 0.48

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 4.4e-59
                         DUF222   4 aleeleaaarrlaavevllvael..aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalraGdi 81 
                                    a+ e++a arrl a+++l  ++   ++r++++ d ++  aa+vaa+l is ++As +++l  al+  Lp+vaa + aG++
  gi|121637984|ref|YP_978208.1|  66 ARVEAAASARRLSAIAELTGRRTgaDQRADWACDFWDCAAAEVAAALTISHGKASGQMHLSLALNR-LPQVAALFLAGHL 144
                                    6889******************999***************************************97.************* PP

                         DUF222  82 dlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltk..ded 159
                                    ++r + +Ia rt l+ d ++l+ +d+a+a+ ++ +  l+  +L+k++d +++r+dp + rr++ +ar+r l +++  ++ 
  gi|121637984|ref|YP_978208.1| 145 GARLFSIIAWRTYLVRDPHALSLLDAALAEHAGAWGPLSAPKLEKAIDSWIDRYDPGALRRSRISARTRDLCIGDpdEDA 224
                                    **************************************************************************998888 PP

                         DUF222 160 GmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlall....rlalaagaldchagvp.....atv 230
                                    G +++ g l a++aa ld++L ++a  vc++    DpR+ aqrraDAL+al+    +la+++g++dc++g+      a v
  gi|121637984|ref|YP_978208.1| 225 GTAALWGRLYATDAAMLDRRLTEMAHGVCED----DPRTLAQRRADALGALAagadHLACGCGKPDCPSGAGnderaAGV 300
                                    *******************************....********************************************* PP

                         DUF222 231 vvhvtaeeltaaagg.......................................aaltgggglLpasdvrrLAkd.Atla 270
                                    v+hv+a+ +  +a++                                          t ggg++pa   ++L +  At++
  gi|121637984|ref|YP_978208.1| 301 VIHVVADASALDAQPdphlsgdeppsrpltpettlfealtpdpepdppathapaELITTGGGVVPAPLLAELIRGgATIS 380
                                    ****************************************************98566777*************9736688 PP

                         DUF222 271 ifdepagrpld.lgrtkrtasaalrralraRD 301
                                        ++ +p d +++  +++sa+l++++r+RD
  gi|121637984|ref|YP_978208.1| 381 ----QVRHPGDlAAEPHYRPSAKLAEFVRMRD 408
                                    ....89*****88899***************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.4
                         DUF222  97 pdavdlatvdkaeaallrraakldpaeLaklv 128
                                    p++ ++a   +a+   + r  + + aeLa ++
  gi|121637984|ref|YP_978208.1| 499 PQTSTAAVNVDARGLMMPRRRRTRAAELAHRI 530
                                    44444444444444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3507.49
//
Query:       gi|121637985|ref|YP_978209.1|  [L=1013]
Description: helicase helZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-58  198.4   0.0    1.9e-58  197.8   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
    1.4e-41  141.5   1.1    9.5e-41  138.9   0.4    2.6  2  DUF3670     SNF2 Helicase protein
    1.5e-15   57.5   0.0    2.6e-15   56.7   0.0    1.4  1  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   0.0   3.2e-62   1.9e-58      54     348 ..     550     819 ..     468     821 .. 0.89

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 3.2e-62
                                    TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqk 133
                                       G  LaD+mGLGKTvq+lal +     e  ++   ++d+  gptL+++P+sl+ +W++e +r++++   rv++++g+ 
  gi|121637985|ref|YP_978209.1| 550 LGLGSCLADDMGLGKTVQLLALET----LESVQR---HQDRGVGPTLLLCPMSLVGNWQQEAARFAPNL--RVYAHHGGA 620
                                    567899***************988....233333...457899***********************987..679999986 PP

                                    H-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 134 kmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltG 213
                                         + + +++ l+ +d v+ tY +  r+       ++l++ ew+rvvlDE++ +kns s+aa+av++L++ +r+ ltG
  gi|121637985|ref|YP_978209.1| 621 ---RLHGEALRDHLERTDLVVSTYTTATRDI------DELSEYEWNRVVLDEAQAVKNSLSRAAKAVRRLRAAHRVALTG 691
                                    ...67788999*****************999......9****************************************** PP

                                    --SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH.HHHHHHHHHHHTT-STTEE---GGGT..--S---EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                         SNF2_N 214 TPiqnsledlygLlkfLreepfgekqtfdkllqrpie.aqaekgrsrLlqllqrlmlrrakkdv..eknlPpkteeiifl 290
                                    TP+ n l++l+++++fL+++ +g+ + f++++  pie + +++ ++rL+   ++++lrr k+d     +lP+k+e   ++
  gi|121637985|ref|YP_978209.1| 692 TPMENRLAELWSIMDFLNPGLLGSSERFRTRYAIPIErHGHTEPAERLRASTRPYILRRLKTDPaiIDDLPEKIEIKQYC 771
                                    *************************************99999*********************954568*********** PP

                                    E--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH--- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 291 klskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpq 348
                                    +l+ +++++Y+ +  ++++k+ ++  ++           + ++l  + +l+q+cnhp 
  gi|121637985|ref|YP_978209.1| 772 QLTTEQASLYQAVVADMMEKIENTEGIE----------RRGNVLAAMAKLKQVCNHPA 819
                                    ***********44444444333333332..........3345899***********95 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9   0.4   1.6e-44   9.5e-41       2     136 ..     352     486 ..     351     487 .. 0.96
   2 ?   -0.5   0.0      0.17     1e+03      23      45 ..     920     942 ..     917     965 .. 0.73

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 1.6e-44
                        DUF3670   2 vpdalelddeeaaefLkeaaeaLeaaGvgVllPrwlkkrarprltlklavkgp..asaakesklgldalldfdwelalGd 79 
                                     p++leld++ a++fL+ +a+ L +aG+gVllP+w+  ++r++l+l l++ +p  +   k+sk+g ++l++f+wela+Gd
  gi|121637985|ref|YP_978209.1| 352 CPSGLELDADGAYRFLSGTAAVLDEAGFGVLLPSWW--DRRRKLGLVLSAYTPvdGVVGKASKFGREQLVEFRWELAVGD 429
                                    699*********************************..99999999999999998888899******************* PP

                        DUF3670  80 eeLseeEldrLaeakrpLvrlrgqWvevdpeelrraleflkrreekkltladaLraa 136
                                    ++LseeE+++L e+k+pL+rlrgqWv++d e+lrr lefl+r+++++ t+a++L++a
  gi|121637985|ref|YP_978209.1| 430 DPLSEEEIAALTETKSPLIRLRGQWVALDTEQLRRGLEFLERKPTGRKTTAEILALA 486
                                    *******************************************999********986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                        DUF3670  23 aLeaaGvgVllPrwlkkrarprl 45 
                                     L+aa   V+l rw++  ++++ 
  gi|121637985|ref|YP_978209.1| 920 NLTAANHVVHLDRWWNPAVENQA 942
                                    58899999*******43333333 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   4.4e-19   2.6e-15       5     111 .]     841     950 ..     834     950 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 4.4e-19
                                    HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSS..EEEESGGGTS CS
                     Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesd..vLiatdvaer 78 
                                    +l e+l   +eg+++l+f+++++ +e  v  l  ++   +  +a+lhg +p + r+e++++f++g+    +L++ +++++
  gi|121637985|ref|YP_978209.1| 841 ILEEIL---AEGDRVLCFTQFTEFAELlVPHLAARFgraARDIAYLHGGTPRKRRDEMVARFQSGDGPpiFLLSLKAGGT 917
                                    344445...99************88656555556666668***********************76655559********* PP

                                    SSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                    G++++ +n+V+++d ++n++  +q+ +R+ R+g
  gi|121637985|ref|YP_978209.1| 918 GLNLTAANHVVHLDRWWNPAVENQATDRAFRIG 950
                                    *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1013 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.27s 00:00:01.02 Elapsed: 00:00:00.43
# Mc/sec: 7040.93
//
Query:       gi|121637986|ref|YP_978210.1|  [L=238]
Description: hypothetical protein BCG_2121 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-07   28.6   0.2    1.4e-06   27.8   0.2    1.4  1  SWIM      SWIM zinc finger
  ------ inclusion threshold ------
       0.17   12.5   0.0       0.34   11.5   0.0    1.4  1  TipAS     TipAS antibiotic-recognition domain


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.2   1.6e-10   1.4e-06      10      38 ..     101     126 ..      86     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.6e-10
                           SWIM  10 vrlnkatCsCpefqkngipCkHalAvlla 38 
                                     r+   +CsCp+   +  pCkH++A ++ 
  gi|121637986|ref|YP_978210.1| 101 ARELSLDCSCPD---YAVPCKHLAATFYL 126
                                    6788899*****...***********986 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.34      36      74 ..     145     183 ..     142     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                    XXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TipAS  36 elkelfaklaaalaagkdpdseeaqelaeehralieefw 74 
                                    e ++l+a+laaa a+g +p+ + a ++a+ +++ + +++
  gi|121637986|ref|YP_978210.1| 145 EREDLLANLAAARADGAAPAADHAEQVAQPLTDCLDRYY 183
                                    6799****************************9999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1610.02
//
Query:       gi|121637987|ref|YP_978211.1|  [L=144]
Description: hypothetical protein BCG_2122c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-15   55.4   0.0    9.5e-15   55.2   0.0    1.0  1  PIN       PIN domain
     0.0027   17.4   0.0     0.0064   16.2   0.0    1.6  2  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.1e-18   9.5e-15       2     120 ..       3     133 ..       2     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.1e-18
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS.......SEEEEEHHHHHHHHHHHHS..SCHCHHHHHHHHHHHHHHHTSEEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel.......eelvtsalvlaEllyvlar..rkskrekaaelvelllllsalkil 71 
                                    ++D++vl++++   +e+++ ++++l+++       +  +++ l++  l+ ++    r++ re+a++ v+++l +++  ++
  gi|121637987|ref|YP_978211.1|   3 IVDANVLLYAVnTTSEHHKPSLRWLDGAlsgadrvGFAWVPLLAFVRLATKVGLfpRPLPREAAITQVADWLAAPSAVLV 82 
                                    79******************************9999999999999999999999************************** PP

                                    EBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  72 pidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                    + + ++a++ a+     g    l+nDa++aA+A eh+++++ ++D+df r +
  gi|121637987|ref|YP_978211.1|  83 NPTVRHADILARMLTYVGtgaNLVNDAHLAALAVEHRASIV-SYDSDFGRFE 133
                                    **************************************999.******9975 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.43   3.8e+03      37      46 ..       5      14 ..       2      28 .. 0.71
   2 !   16.2   0.0   7.1e-07    0.0064      30      69 ..     101     141 ..      86     144 .] 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.43
                        DUF5615 37 DeeileyAke 46
                                   D ++l yA +
  gi|121637987|ref|YP_978211.1|  5 DANVLLYAVN 14
                                   6666666654 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.1e-07
                        DUF5615  30 lglegasDeeileyAkeedriivTkDkDFgel.lllggppp 69 
                                    +g + ++D +  ++A e+ + iv+ D+DFg+    + ++pp
  gi|121637987|ref|YP_978211.1| 101 TGANLVNDAHLAALAVEHRASIVSYDSDFGRFeGVRWDQPP 141
                                    5555689***********************98766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1006.35
//
Query:       gi|121637988|ref|YP_978212.1|  [L=84]
Description: hypothetical protein BCG_2123c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 636.34
//
Query:       gi|121637989|ref|YP_978213.1|  [L=98]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-28   96.7   3.4    8.4e-28   96.5   3.4    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   3.4   4.7e-32   8.4e-28       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 4.7e-32
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+v+P  + aaaa l+++gs+++  naa+a++tt+v ++aaD VS + + +fs+h+q+yq  +a+++afh+++v++la+
  gi|121637989|ref|YP_978213.1|  1 MSFVNVDPFGMLAAAATLESLGSHMAVSNAAVASVTTKVPPPAADYVSKKLSLFFSSHGQQYQVQAARGTAFHRKLVRTLAN 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +a +Y++ E 
  gi|121637989|ref|YP_978213.1| 83 GALAYEEVEI 92
                                   *******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 762.15
//
Query:       gi|121637990|ref|YP_978214.1|  [L=243]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-57  192.8   9.8    5.1e-57  192.4   9.8    1.1  1  PPE       PPE family
     0.0098   16.1   2.8      0.027   14.7   2.8    1.7  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4   9.8   5.7e-61   5.1e-57       1     157 [.       6     161 ..       6     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 5.7e-61
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+ns+++y Gpgsgp+laAa+ W++La+el+++   l+s l++l  e+++G+ss+a++++++py++WL+++a++a+
  gi|121637990|ref|YP_978214.1|   6 ALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLL-ESYRGQSSQALIQQTLPYVQWLTTTAEHAH 84 
                                    79***********************************************.****************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    ++A q++aaa+aYe+A+aamvppa++ anr ++++l a n+fGq +++Ia+ ea+ye+mw qda +m++Y +a+++a
  gi|121637990|ref|YP_978214.1|  85 KTAIQLTAAANAYEQARAAMVPPAMVRANRVQTTVLKAINWFGQFSTRIADKEADYEQMWFQDALVMENYWEAVQEA 161
                                    **********************************************************************9999876 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.8     3e-06     0.027      10      84 ..      26     100 ..      23     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  10 rqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                     +aa+  ++ a+ele     l++ +d l ++++G++++a  ++   + q +++ ++  ++++ +l++aana+e+a
  gi|121637990|ref|YP_978214.1|  26 LAAAQGWNALASELEKTKVGLQSALDTLLESYRGQSSQALIQQTLPYVQWLTTTAEHAHKTAIQLTAAANAYEQA 100
                                    57888889999**************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1815.19
//
Query:       gi|121637991|ref|YP_978215.1|  [L=248]
Description: proteasome subunit alpha PrcA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-39  134.2   0.1    4.5e-39  133.9   0.1    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.1   2.5e-43   4.5e-39       2     189 ..      25     205 ..      24     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 2.5e-43
                                    HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                     Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                    +++++vv++++ +gv+++a+  ++      s+s ++Ki++++d++g+a+aG+++++++l+r   + a+++ + y+r+  +
  gi|121637991|ref|YP_978215.1|  25 ARAKSVVALAYAGGVLFVAE--NP------SRS-LQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVT 95 
                                    6899***************9..88......666.9********************************************* PP

                                    HHHHHHHHHHHHHHHHHCTTTTTSEEEEEE...EEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTB CS
                     Proteasome  82 erlvarvaaklqaytqrsgrrpfgvsllia...gvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedl 158
                                     r++a+v+a++++++++++ +p+ v+l++a   ++ e++ peLy+i+++Gs+++e ++v++G ++e++ +al+++y e+ 
  gi|121637991|ref|YP_978215.1|  96 GRQLANVYAQTLGTIFTEQAKPYEVELCVAevaHYGETKPPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENA 175
                                    ***********************99999885558889999**********************99**************** PP

                                    SHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                     Proteasome 159 tleeavelavkalkealerdklsgknievav 189
                                    +l++a+ +av al++++  d+++g++ +++v
  gi|121637991|ref|YP_978215.1| 176 SLTDALGIAVAALRAGSA-DTSGGDQPTLGV 205
                                    ****************99.889999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1831.02
//
Query:       gi|121637992|ref|YP_978216.1|  [L=291]
Description: proteasome subunit beta PrcB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-27   94.5   0.1      7e-27   94.1   0.1    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
      0.043   13.1   0.0      0.063   12.5   0.0    1.2  1  MCH         Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1   7.9e-31     7e-27       3     183 ..      56     240 ..      54     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 7.9e-31
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    +Gtt+v++k+ +gvv+a+d+r+t+g+++ s ++v+K++  dd+++ ++aG+aa a  ++r   +e+++y+  +g p++  
  gi|121637992|ref|YP_978216.1|  56 HGTTIVALKYPGGVVMAGDRRSTQGNMI-SGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFA 134
                                    8***************************.6666*********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTT.....EEEEEEEETTSEEEEES.SEEEESTTHHHHHHHHHHHHST CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeg.....gpeLyqidpsGsyieek.davaiGsgseaaktalekeyke 156
                                      ++r+a ++ ++++ + ++ +++  l+ag+d +      + ++ ++d +G    e+  + a+Gsgs +ak+ ++k+y++
  gi|121637992|ref|YP_978216.1| 135 GKINRLAIMVRGNLAAA-MQGLLALPLLAGYDIHAsdpqsAGRIVSFDAAGGWNIEEeGYQAVGSGSLFAKSSMKKLYSQ 213
                                    ****************9.7777788888999944334555889*******976444449********************* PP

                                    TBSHHHHHHHHHHHHHHHHHHBTTSCS CS
                     Proteasome 157 dltleeavelavkalkealerdklsgk 183
                                      + ++++++av+al+ a+++d+++g+
  gi|121637992|ref|YP_978216.1| 214 VTDGDSGLRVAVEALYDAADDDSATGG 240
                                    ********************9998875 PP

>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-06     0.063      93     128 ..     184     219 ..     146     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-06
                                    --EEEEETTEEEEEESTTHHHHTSHHHHHHHT---- CS
                            MCH  93 AgWelsaekffalgsGPaRalaakeelfeelgyede 128
                                     gW++++e+++a+gsG   a +  ++l+++++  d+
  gi|121637992|ref|YP_978216.1| 184 GGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDS 219
                                    48***************************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2160.85
//
Query:       gi|121637993|ref|YP_978217.1|  [L=64]
Description: hypothetical protein BCG_2128c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-22   79.8   4.0    2.2e-22   79.7   4.0    1.1  1  Pup       Pup-like protein
  ------ inclusion threshold ------
      0.011   16.2   0.2      0.015   15.9   0.2    1.2  1  YtxH      YtxH-like protein
      0.047   12.3   0.5      0.047   12.3   0.5    1.0  1  TH1       TH1 protein


Domain annotation for each model (and alignments):
>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   4.0   3.8e-26   2.2e-22       6      68 .]       3      64 .]       1      64 [] 0.83

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.8e-26
                            Pup  6 qeqasrskeeveeaeaeaeassevkerkeelsedvDdlLDeIDevLEeNAeeFVrsfvQKGGq 68
                                   qeq++r     ++ +  a ++++ +er+e+l+e++DdlLDeID+vLEeNAe+FVr++vQKGGq
  gi|121637993|ref|YP_978217.1|  3 QEQTKRGGGGGDDDDI-AGSTAAGQERREKLTEETDDLLDEIDDVLEENAEDFVRAYVQKGGQ 64
                                   5555555554445444.5578999**************************************9 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.2   2.4e-06     0.015      22      60 ..      24      55 ..      21      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                           YtxH 22 sGketRkdlkekaddlkekakelleeakekakekaedlk 60
                                    G e R++l e++ddl + ++++l       +e+aed++
  gi|121637993|ref|YP_978217.1| 24 AGQERREKLTEETDDLLDEIDDVL-------EENAEDFV 55
                                   69*********************9.......66666665 PP

>> TH1  TH1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   7.8e-06     0.047      15      67 ..      11      63 ..       1      64 [] 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-06
                            TH1 15 geetraeeseaaedllenkeevleeclekfsekDyimepgiidqlkryvqaGG 67
                                   g ++ ++ ++++++ +e +e+  ee  + + e D ++e ++ d +++yvq GG
  gi|121637993|ref|YP_978217.1| 11 GGGDDDDIAGSTAAGQERREKLTEETDDLLDEIDDVLEENAEDFVRAYVQKGG 63
                                   333334444555666778888888999999**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      891  (0.049696); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 450.09
//
Query:       gi|121637994|ref|YP_978218.1|  [L=535]
Description: hypothetical protein BCG_2129c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   7.3e-179  595.4   0.0   8.3e-179  595.2   0.0    1.0  1  Pup_ligase  Pup-ligase protein


Domain annotation for each model (and alignments):
>> Pup_ligase  Pup-ligase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.2   0.0  4.6e-183  8.3e-179       1     439 [.      33     488 ..      33     489 .. 0.98

  Alignments for each domain:
  == domain 1  score: 595.2 bits;  conditional E-value: 4.6e-183
                                    --EEEEEE-EEEECT-TTEEEE-HHHHHHHHHHHHGGGEE........--------------CHHHHHHHS-S--..... CS
                     Pup_ligase   1 rimGiEtEYgilvpaepeaeslspeelarelvaayaaaea........wdyeeesplrdargfelerararssql..... 67 
                                    ri+G+E EYgi+ p++p+a   +p  +++++v ayaaa+         wdye esplrdargf+l+r++  +  +     
  gi|121637994|ref|YP_978218.1|  33 RIIGTEVEYGISSPSDPTA---NPILTSTQAVLAYAAAAGiqrakrtrWDYEVESPLRDARGFDLSRSAGPPPVVdadev 109
                                    9************998888...*************9888899***********************99977777669**** PP

                                    ...EEEETTS-EEEEETTEEEEE---BSSHHHHHHHHHHHHHHHHHHHHHHHHCCC.-EEEEESSSB-TTS-B--EEEEE CS
                     Pup_ligase  68 ...nvflanGarlYvdgahpEystpEvtspldlvaydrAgdeilreaaeeaeeelg.gevklykNnvDskGasYGchENY 143
                                       n++l+nGarlYvd+ahpEys+pE+t+pld+v++d+Ag++++++aa+++++++g ++++lykNnvD+kGasYG+hENY
  gi|121637994|ref|YP_978218.1| 110 gaaNMILTNGARLYVDHAHPEYSAPECTDPLDAVIWDKAGERVMEAAARHVASVPGaAKLQLYKNNVDGKGASYGSHENY 189
                                    *****************************************************9999*********************** PP

                                    EEETTS-HHHHHHCHHHHHHHCHHHH---EEEETTTS-CEEEES-SSHHHCCCCCCSSSTTSEECEES-S--SS-TTTEE CS
                     Pup_ligase 144 lvrravpfeelakkLlpflvtRqiitGaGrvglgeegeeagFqlsqrAdfieeevslettleRpiintrdEphadaskyr 223
                                    l++r++pf+ + + L+pflv+Rq++tG+Grvg+g +g+e+gFqlsqr+d+ie ev+lettl+R+iintrdEphada++yr
  gi|121637994|ref|YP_978218.1| 190 LMSRQTPFSAIITGLTPFLVSRQVVTGSGRVGIGPSGDEPGFQLSQRSDYIEVEVGLETTLKRGIINTRDEPHADADRYR 269
                                    ******************************************************************************** PP

                                    EEEE------SSHHHHHHHHHHHHHHHHHHHC....T---S---BSSCCCCHHHHHC-TTS--EEEBTTS-EEEHHHHHH CS
                     Pup_ligase 224 RLhvivgDsnlsevatllkvgttalvLdliea....gkelpdleladpvaalrevsrdltlkatveladgreltaleiqr 299
                                    RLhvi+gD+nl+e++t+lk+gttalvLdlie+    + +l+dl+la+pv+a++++srd++l+atv+ladgrelt l +qr
  gi|121637994|ref|YP_978218.1| 270 RLHVIIGDANLAETSTYLKLGTTALVLDLIEEgpahAIDLTDLALARPVHAVHAISRDPSLRATVALADGRELTGLALQR 349
                                    ********************************9999999***************************************** PP

                                    HHHHHHHHHHHHHHGGCSHHHHHHHHHHHHHHHHHC-SCCCTTT-HHHHHHHHHHHHHHHHT--TT-HHHHHHHHHTTB- CS
                     Pup_ligase 300 ayleavrkfleeeeeeeeetkevlelWeevldaleedpqaladridWvaKlrLleelrereglswddpklkalDlqYhdi 379
                                     yl++v+k++++++ ++ ++++++e+W++vld+le+dp+ +a+ +dW aKlrLl+++r+re+lsw+ p+l+ +DlqY+d+
  gi|121637994|ref|YP_978218.1| 350 IYLDRVAKLVDSRDPDP-RAADIVETWAHVLDQLERDPMDCAELLDWPAKLRLLDGFRQRENLSWSAPRLHLVDLQYSDV 428
                                    ************98755.99************************************************************ PP

                                    STTTSHHHHHHHCTSS--SS-HHHHHHHHHS--SSSTHHHHHHHHHHHHHHEEEEESSEE CS
                     Pup_ligase 380 rpekglfarLvargrverlvteeeieravtepPadtrAalRgelvrefaeevvavdWdsv 439
                                    r +kgl++rLvarg+++rlvte+++ +av++pP+dtrA++Rge++r+f ++++a++Wdsv
  gi|121637994|ref|YP_978218.1| 429 RLDKGLYNRLVARGSMKRLVTEHQVLSAVENPPTDTRAYFRGECLRRFGADIAAASWDSV 488
                                    **********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3998.13
//
Query:       gi|121637995|ref|YP_978219.1|  [L=397]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   10.4   4.2       0.83    8.8   4.2    1.8  1  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.2   4.6e-05      0.83     233     287 ..      69     123 ..      61     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 4.6e-05
                            Zip 233 aiLlkaglsrkkavllnllfaltaplGiliGilvrsisessgaeivsgillalsa 287
                                    + ++ + ++    +++  l+a++ pl+ l+G+lv++is+++g+ +v+++  a++a
  gi|121637995|ref|YP_978219.1|  69 GEVFISATPTTAQWVILALLAVALPLASLVGWLVSQISSGRGQAAVATMAVAFAA 123
                                    55555555555566788899****************9999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3141.56
//
Query:       gi|121637996|ref|YP_978220.1|  [L=207]
Description: hypothetical protein BCG_2131 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1318.22
//
Query:       gi|121637997|ref|YP_978221.1|  [L=609]
Description: ATPase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-49  166.4   0.1    4.5e-48  163.0   0.0    2.5  2  AAA              ATPase family associated with various cellul
    2.6e-25   87.8   0.3    1.2e-24   85.7   0.1    2.3  2  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    1.2e-20   73.2   0.2    8.4e-19   67.3   0.0    2.9  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    4.9e-09   36.8   0.5      1e-06   29.2   0.0    3.5  2  AAA_16           AAA ATPase domain
    1.7e-05   25.0   0.0    3.7e-05   23.9   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    8.3e-05   22.0   0.0    0.00019   20.8   0.0    1.5  1  Zeta_toxin       Zeta toxin
    0.00011   22.4   0.0    0.00023   21.3   0.0    1.5  1  AAA_33           AAA domain
    0.00021   21.7   0.0    0.00054   20.3   0.0    1.7  1  RNA_helicase     RNA helicase
    0.00022   21.5   0.2     0.0016   18.7   0.0    2.7  1  AAA_22           AAA domain
     0.0003   20.6   0.0     0.0021   17.8   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00052   20.0   0.0     0.0017   18.4   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0023   17.3   0.0     0.0058   16.0   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0025   17.8   0.0      0.042   13.8   0.0    2.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0056   16.6   0.0      0.079   12.9   0.0    2.3  2  Rad17            Rad17 P-loop domain
     0.0093   16.0   0.0      0.026   14.6   0.0    1.7  1  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.042   14.4   0.0    2.1  1  AAA_18           AAA domain
      0.012   16.2   0.0      0.066   13.7   0.0    2.2  1  ABC_tran         ABC transporter
      0.013   14.8   0.0      0.021   14.0   0.0    1.4  1  TIP49            TIP49 P-loop domain
      0.022   14.5   0.3       0.72    9.7   0.0    2.8  2  AAA_lid_3        AAA+ lid domain
      0.023   14.5   0.0      0.054   13.2   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.026   14.0   0.0      0.055   13.0   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.039   14.4   1.5       0.66   10.5   0.2    2.7  2  ZapB             Cell division protein ZapB
       0.04   14.0   0.0       0.33   11.1   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.042   13.4   0.0       0.18   11.4   0.0    2.1  1  AAA_25           AAA domain
      0.043   14.3   0.4        0.3   11.5   0.0    2.3  2  AAA_23           AAA domain
      0.048   13.9   0.7        0.1   12.8   0.4    1.6  1  FliJ             Flagellar FliJ protein
      0.057   12.6   0.0       0.26   10.4   0.0    2.1  2  DUF815           Protein of unknown function (DUF815)
      0.063   13.2   0.0       0.24   11.3   0.0    2.1  1  NTPase_1         NTPase
      0.089   12.7   0.4       0.16   11.9   0.4    1.4  1  JAKMIP_CC3       JAKMIP CC3 domain
       0.11   12.8   0.2        1.7    9.0   0.0    2.6  2  AAA_19           AAA domain
       0.11   12.4   0.0       0.25   11.2   0.0    1.6  1  NACHT            NACHT domain
       0.13   12.8   3.6       0.29   11.7   3.6    1.6  1  APG6_N           Apg6 coiled-coil region
       0.14   11.8   0.0       0.47   10.1   0.0    1.9  1  AAA_24           AAA domain
       0.15   11.2   0.0        0.3   10.2   0.0    1.4  1  NB-ARC           NB-ARC domain
        0.2   10.7   0.0       0.37    9.8   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.21   10.7   0.0       0.33   10.0   0.0    1.2  1  FUSC-like        FUSC-like inner membrane protein yccS
       0.23   11.5   5.2        2.3    8.3   3.6    2.5  2  DUF465           Protein of unknown function (DUF465)
       0.75   10.0   3.5        1.2    9.4   2.0    1.8  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.3    9.2   5.2       0.34   11.0   0.6    2.2  2  bZIP_1           bZIP transcription factor
        3.2    8.2   7.8        6.2    7.2   5.9    2.4  2  Nnf1             Nnf1
        4.4    6.6   6.4        1.7    7.9   1.4    2.1  2  GAS              Growth-arrest specific micro-tubule binding
        7.3    7.2   7.5        2.6    8.6   3.1    2.7  2  HSCB_C           HSCB C-terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.9   1.2e+03      67     116 ..      63     114 ..      62     125 .. 0.64
   2 !  163.0   0.0   1.1e-50   4.5e-48       1     132 []     289     439 ..     289     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.9
                                    GGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                            AAA  67 idalaksr..sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                    id+la ++    ++ +e+++ + +L +e+d++ +  s   v++at++ d++d
  gi|121637997|ref|YP_978221.1|  63 IDSLAARNskLMETLKEARQQLLALREEVDRLGQPPSGYGVLLATHDDDTVD 114
                                    6777766632223334455555566666666666688899999999888877 PP

  == domain 2  score: 163.0 bits;  conditional E-value: 1.1e-50
                                    EEEESSTTSSHHHHHHHHHHHH...............THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEE CS
                            AAA   1 vllyGppGtGKTllakavakel...............gvefleisgsellskyvgesekkirelfkeakeka...kpsil 62 
                                    vllyGppG+GKTl+akava++l               +++fl+i+g+ell+k+vge+e++ir +f++a+eka   +p+i+
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLakkmaevrgddaheaKSYFLNIKGPELLNKFVGETERHIRLIFQRAREKAsegTPVIV 368
                                    79*******************7555555555555544688**********************************999*** PP

                                    EEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  63 fiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    f+DE+d+++++r +g +s++e++vv+qLl+e+dgv+  e+ viviga+nr+d++dpa+lr gR+d+ki+ie+
  gi|121637997|ref|YP_978221.1| 369 FFDEMDSIFRTRgTGVSSDVETTVVPQLLSEIDGVEGLEN-VIVIGASNREDMIDPAILRpGRLDVKIKIER 439
                                    ************9999*********************866.****************************986 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.1   2.8e-27   1.2e-24       2      62 .]     101     160 ..     100     160 .. 0.98
   2 ?   -1.9   0.0       6.4   2.7e+03      34      46 ..     211     223 ..     208     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 2.8e-27
                  Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvVealgyertGe 62 
                                    yG++la++ +d+t+dV+++gr+mr++ sP++da++L+ Gq+V+LnEal+vVea ++e++Ge
  gi|121637997|ref|YP_978221.1| 101 YGVLLATH-DDDTVDVFTSGRKMRLTCSPNIDAASLKKGQTVRLNEALTVVEAGTFEAVGE 160
                                    9*******.8**************************************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.4
                  Prot_ATP_OB_N  34 aeeLrpGqeVlLn 46 
                                    + +LrpG+ +l++
  gi|121637997|ref|YP_978221.1| 211 PRKLRPGDSLLVD 223
                                    679*****99875 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.29   1.2e+02      19      47 ..     117     145 ..     101     151 .. 0.87
   2 !   67.3   0.0     2e-21   8.4e-19       1      57 []     161     234 ..     161     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.29
                                    TTS-EEEEEE-GGGSSST--TTEEEEEET CS
                 Prot_ATP_ID_OB  19 ssdeevvvslagavpremLrpgDlVavdk 47 
                                    +s+ ++ + ++  ++++ L+ g +V+++ 
  gi|121637997|ref|YP_978221.1| 117 TSGRKMRLTCSPNIDAASLKKGQTVRLNE 145
                                    56677888899999*************96 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 2e-21
                                    EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST.................--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavprem.................LrpgDlVavdkdtgfifEkLP 57 
                                    + t++E+l d++ra+V++++dee+vv+la+++ +e+                 LrpgD+++vd+++g++fE++P
  gi|121637997|ref|YP_978221.1| 161 ISTLREILADGHRALVVGHADEERVVWLADPLIAEDlpdglpealnddtrprkLRPGDSLLVDTKAGYAFERIP 234
                                    689**********************************************************************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3         4   1.7e+03      94     114 ..      33      69 ..      17     107 .. 0.44
   2 !   29.2   0.0   2.4e-09     1e-06       7     145 ..     259     374 ..     256     412 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4
                         AAA_16  94 leawrekleeala................avpelaga 114
                                    ++  re+le a++                 +++la+ 
  gi|121637997|ref|YP_978221.1|  33 AAVLREQLENAVGshaptrsardihqleaRIDSLAAR 69 
                                    3333344444333222222111111111111122222 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.4e-09
                         AAA_16   7 eeleqLlsalervrsgrp..........elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                    +++eq+++a+e    + +            vll+G++G+GK+ ++++++++l k+    ++ + d+ ++a +y  ++++ 
  gi|121637997|ref|YP_978221.1| 259 RQIEQIRDAVELPFLHKElyreyslrppKGVLLYGPPGCGKTLIAKAVANSLAKK---MAEVRGDDAHEAKSY--FLNIK 333
                                    66666666666333333335555556679**************************...588888888777776..66666 PP

                         AAA_16  77 areellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                       ell++   e+e                          ++++  ++r+ +++s+ + p+++++D+++
  gi|121637997|ref|YP_978221.1| 334 GP-ELLNKFVGETE--------------------------RHIRLIFQRAREKASE-GTPVIVFFDEMD 374
                                    44.66666666633..........................4566666666666666.666666666666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.7e-08   3.7e-05       6      99 ..     289     397 ..     284     405 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.7e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---.......----THHHHHHHHHTTT-HHH.HTTS....... CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle.......eeevehlvsrligappgyvga.eegG....... 70 
                                    +ll gp g+Gkt++aka+a+ l  kk  ++   da e               +l+++++g+ +  ++   ++        
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLA-KKMAEVRGDDAHEAKSyflnikgP----ELLNKFVGETERHIRLiFQRArekaseg 363
                                    6899******************9.899999999999998888855553....4444444444333221011112223566 PP

                                    ...EEEEETGGG----..---------HHHHHHH CS
                          AAA_2  71 ...ivllDEidKihpk..essgadvSregVqrdL 99 
                                       iv++DE+d i ++  +  ++dv  + V ++L
  gi|121637997|ref|YP_978221.1| 364 tpvIVFFDEMDSIFRTrgTGVSSDVETTVVPQLL 397
                                    799************7766677777666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-07   0.00019      14      94 ..     284     363 ..     274     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilk.adpkkaseltqkdaselvekllqeai 92 
                                    + Pk +ll G pG+GK+ +a++++++l  ++++ ++ +Dd  e    + +i   +  +k++  t++ ++ + ++++++a 
  gi|121637997|ref|YP_978221.1| 284 RPPKGVLLYGPPGCGKTLIAKAVANSL--AKKMAEVRGDDAHEAKSYFLNIKGpELLNKFVGETERHIRLIFQRAREKAS 361
                                    56999**********************..9**********9998888888777457889999999999999999999998 PP

                     Zeta_toxin  93 en 94 
                                    e 
  gi|121637997|ref|YP_978221.1| 362 EG 363
                                    86 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   5.4e-07   0.00023       2      75 ..     289     368 ..     289     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.4e-07
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg....tdqqsktdytrvldrlyqilnelarkalsagrnvil 75 
                                    vll G+pG+GK+  a+ +++ l+  +  ++ d+++++  +    ++++ +++    ++r ++ ++++ar+++s+g +vi+
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAkkMAEVRGDDAHEAKSYflniKGPELLNKFVGETERHIRLIFQRAREKASEGTPVIV 368
                                    7899******************9*999*********9999766555555555555788899999**************98 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-06   0.00054       1      35 [.     289     328 ..     289     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-06
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvy 35 
                                    ++lyGp+g+GK+++ak +a++l+kk+      +  ++ + y
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKKMaevrgdD-AHEAKSY 328
                                    689**********************97777633.3333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.7e-06    0.0016       8     104 ..     289     377 ..     284     421 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                    ++++G++G+GKT+ ++ ++++l   +k +e      ++++ +f ++++++    ll++++ +++    +     + ++++
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLA--KKMAEvrgddaHEAKSYFLNIKGPE----LLNKFVGETE----R---HIRLIFQR 355
                                    689******************92..3333344555544444455554444....3333333333....1...22223344 PP

                         AAA_22  82 leqalraravielliiDEaqhlr 104
                                     ++ +++    +++  DE++ ++
  gi|121637997|ref|YP_978221.1| 356 AREKASEGTP-VIVFFDEMDSIF 377
                                    4444444444.777788888854 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     5e-06    0.0021      35      65 ..     288     318 ..     264     357 .. 0.89
   2 ?   -1.0   0.0       3.1   1.3e+03      27      56 ..     525     554 ..     515     567 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-06
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkits 65 
                                     vllyGpPG Gkt +ak +a+ l  k+    
  gi|121637997|ref|YP_978221.1| 288 GVLLYGPPGCGKTLIAKAVANSLAKKMAEVR 318
                                    69********************999887655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                         RuvB_N  27 kkreealdhvllyGpPGlGkttlakiiake 56 
                                    +++++a+  vl +G PGl    l   i +e
  gi|121637997|ref|YP_978221.1| 525 RAKKNAIKSVLETGQPGLRIQHLLDSIVDE 554
                                    567889999********9876665555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.9e-06    0.0017       1      39 [.     288     326 ..     288     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-06
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdttee 39 
                                    +vlL GppG+gK+ +a+ +a  l +++ +v + +  +++
  gi|121637997|ref|YP_978221.1| 288 GVLLYGPPGCGKTLIAKAVANSLAKKMAEVRGDDAHEAK 326
                                    59*********************9999888877766655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05    0.0058      25      48 ..     289     312 ..     286     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpp 48 
                                    +ll+GppG+GKt++ak++++ l++
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAK 312
                                    79**************99877765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   9.8e-05     0.042      19      58 ..     285     318 ..     275     384 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-05
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr 58 
                                    p + +++YGp g+GKt + k +++ l +k        ++r
  gi|121637997|ref|YP_978221.1| 285 PPKGVLLYGPPGCGKTLIAKAVANSLAKKMA------EVR 318
                                    5666899*********988888888855433......334 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00019     0.079      27      75 ..     260     316 ..     247     318 .. 0.74
   2 ?    1.9   0.0      0.43   1.8e+02     123     177 ..     316     375 ..     311     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                          Rad17  27 kieevkewlkadvLesrkkr........iLLisGPsGCgkstvvkvLskelgiklre 75 
                                    +ie+++++++  +L ++  r         +L+ GP+GCgk+ + k ++  l+ k+ e
  gi|121637997|ref|YP_978221.1| 260 QIEQIRDAVELPFLHKELYReyslrppkGVLLYGPPGCGKTLIAKAVANSLAKKMAE 316
                                    566666666666666655444554555567899*************99999988766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.43
                          Rad17 123 qklGddlrtdkklilvedlP...nkfyrdsdalrevirkylr..ssealplilviteies 177
                                    + +Gdd++  k+  l    P   nkf +++++   +i +  r   se  p+i+   e++s
  gi|121637997|ref|YP_978221.1| 316 EVRGDDAHEAKSYFLNIKGPellNKFVGETERHIRLIFQRARekASEGTPVIVFFDEMDS 375
                                    56899999999887754434444*******888888877665114555699998888876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.1e-05     0.026       5      76 ..     289     376 ..     286     421 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.1e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd.............kkladpe....kllelileklke..... 62 
                                    +++ G+  +GKT ++k ++++l    +++ ++  dd ++              ++        + ++li+++  +     
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLA---KKMAEVRGDDAHEaksyflnikgpelLNKF--VgeteRHIRLIFQR--Arekas 361
                                    7899**************98888...777777777777743333333222222222..02222334444444..023455 PP

                         AAA_14  63 .ekktylflDEiqev 76 
                                         ++f+DE+  +
  gi|121637997|ref|YP_978221.1| 362 eGTPVIVFFDEMDSI 376
                                    345566999998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.8e-05     0.042       1      44 [.     289     334 ..     289     375 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpe 44 
                                    +ll G+pG+GKt +ak+++++l +   ++ +d a e  +++ + + 
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLaKKmAEVRGDDAHEAKSYFLNIKG 334
                                    799***************8776322466666666666666665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00015     0.066       7      67 ..     282     355 ..     278     363 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.............EETTCEGGGB-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGei.............lldgkdlkeqeleslrkeigvlpqe 67 
                                    +l++ + v + G+ G+GK+ ++k++a+ l +++ e+             +++g +l ++   +++++i+ ++q 
  gi|121637997|ref|YP_978221.1| 282 SLRPPKGVLLYGPPGCGKTLIAKAVANSLAKKMAEVrgddaheaksyflNIKGPELLNKFVGETERHIRLIFQR 355
                                    566777799*********************99999944444444444444444444446666666666666665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-05     0.021      51      79 ..     287     315 ..     248     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvp 79 
                                    ++vLl Gp+g Gkt +a a++++l++++ 
  gi|121637997|ref|YP_978221.1| 287 KGVLLYGPPGCGKTLIAKAVANSLAKKMA 315
                                    89***********************9875 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.4      0.72   3.1e+02      17      28 ..      24      35 ..      23      44 .. 0.90
   2 ?    9.7   0.0    0.0017      0.72      15      36 ..     515     536 ..     514     548 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.72
                      AAA_lid_3 17 ADlaalcreAal 28
                                   A+l++l reAa 
  gi|121637997|ref|YP_978221.1| 24 AELEQLRREAAV 35
                                   9*********96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                      AAA_lid_3  15 SGADlaalcreAallAlrrgik 36 
                                    SGA +++++++A  +A++ +++
  gi|121637997|ref|YP_978221.1| 515 SGAMIQNVVDRAKKNAIKSVLE 536
                                    9****************98776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.054      48      78 ..     287     317 ..     273     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsv 78 
                                    ++++l Gp+G GK+ +a a++ + +++  +v
  gi|121637997|ref|YP_978221.1| 287 KGVLLYGPPGCGKTLIAKAVANSLAKKMAEV 317
                                    6899*****************9988776655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013     0.055      33      60 ..     286     313 ..     272     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                     k vll+Gp G+GKt+i+k + ++l k+
  gi|121637997|ref|YP_978221.1| 286 PKGVLLYGPPGCGKTLIAKAVANSLAKK 313
                                    5789******************999954 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.77   3.3e+02      46      65 ..      24      43 ..      14      46 .. 0.69
   2 ?   10.5   0.2    0.0015      0.66       7      43 ..      57      93 ..      53     100 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.77
                           ZapB 46 eeneqlkeereawqerlkkL 65
                                   +e+eql+ e + ++e l++ 
  gi|121637997|ref|YP_978221.1| 24 AELEQLRREAAVLREQLENA 43
                                   56666666666666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0015
                           ZapB  7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenre 43
                                   +qLE++i+++  + ++L + ++e +++  +l ee ++
  gi|121637997|ref|YP_978221.1| 57 HQLEARIDSLAARNSKLMETLKEARQQLLALREEVDR 93
                                   4566666666666666666666666666666555554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.3   1.9e+03      41      75 ..      56      87 ..      33      96 .. 0.59
   2 ?   11.1   0.0   0.00077      0.33      24      70 ..     289     334 ..     282     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                                   C--TTS-EE--SSTTHHHH-HHHHHHHTTTSEEEE CS
                Sigma54_activ_2 41 LhknsgpwleifvverlaklpldlleqakggtLyl 75
                                   +h+ +++ +++   +   +  +++l++a++++L l
  gi|121637997|ref|YP_978221.1| 56 IHQLEARIDSL---AARNSKLMETLKEARQQLLAL 87
                                   44444443333...222344566666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00077
                                    EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHHTTT CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklpldlleqakg 70 
                                    v+l G++G+gk+l+A++ +++ +++++ ++  ++a++ ++ + ++kg
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKKMAEVR-GDDAHEAKSYFLNIKG 334
                                    9*******************9999777644.4667766666655555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00042      0.18      36      60 ..     289     313 ..     280     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                         AAA_25  36 allaGapgtGKttlaldlalavatG 60 
                                    +ll+G+pg+GKt +a  +a ++a+ 
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKK 313
                                    69*************9999998843 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       3.3   1.4e+03     164     190 ..      58      89 ..      17      94 .. 0.44
   2 ?   11.5   0.0   0.00071       0.3      22      87 ..     289     367 ..     273     442 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.3
                         AAA_23 164 eledekkllekl.....eqekekekeleelee 190
                                    +le++++ l ++     e +ke +++l +l+e
  gi|121637997|ref|YP_978221.1|  58 QLEARIDSLAARnsklmETLKEARQQLLALRE 89 
                                    22222222222233333333444444444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00071
                         AAA_23  22 tlItGpNGaGKTTildAiklaLygetprlsrks.......grgfeksdveiesegkvkayveltfenkdgry......t 87 
                                    +l++Gp G+GKT i  A+   L  + ++ ++++         +++  +   ++ g++++ ++l f++ +++        
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKKMAEVRGDDaheaksyFLNIKGPELLNKFVGETERHIRLIFQRAREKAsegtpvI 367
                                    599*********************998877766666655444555555556666***********99877656666551 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   0.00024       0.1      19      82 ..      24      91 ..      22     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                           FliJ 19 ekleeleqyrqeyqkqlsgea.q...glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82
                                   ++le+l+++ + +++ql+++  +   + sa ++++++a i++l  + ++++++l+ a++q+ + ree 
  gi|121637997|ref|YP_978221.1| 24 AELEQLRREAAVLREQLENAVgShapTRSARDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEV 91
                                   6789999999999999998876433456899999**************************99999875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0006      0.26      51      81 ..     284     314 ..     227     336 .. 0.71
   2 ?   -2.2   0.0       4.2   1.8e+03     140     155 ..     406     421 ..     379     425 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg 81 
                                    +p + vLL+G  G+GK  + ka+ n++a++ 
  gi|121637997|ref|YP_978221.1| 284 RPPKGVLLYGPPGCGKTLIAKAVANSLAKKM 314
                                    57789********************999864 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                         DUF815 140 penvliyaTsNrRhLl 155
                                     env++   sNr +++
  gi|121637997|ref|YP_978221.1| 406 LENVIVIGASNREDMI 421
                                    4677777788877766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00057      0.24       2      36 ..     289     323 ..     288     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00057
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyte 36 
                                    v++ GppG GKt + k v++ l+++  +v+G  ++
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKKMAEVRGDDAH 323
                                    6788*********************9999996555 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00038      0.16      81     134 ..      24      80 ..      23     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                     JAKMIP_CC3  81 aeyqalqrayalLreklg...geldaerelkareqleselrktkskikdLeeaLaqk 134
                                    ae ++l+r+ a Lre+l    g+  + r ++   qle+ + +  ++ ++L e+L++ 
  gi|121637997|ref|YP_978221.1|  24 AELEQLRREAAVLREQLEnavGSHAPTRSARDIHQLEARIDSLAARNSKLMETLKEA 80 
                                    5789***********985222667889***************************986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.3   5.5e+02      69     138 ..      53     180 ..      28     223 .. 0.54
   2 ?    9.0   0.0     0.004       1.7      11      37 ..     287     313 ..     281     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                         AAA_19  69 atTiHrlal..............................................................ldfddllte 86 
                                    a+ iH+l                                                                l+  + +  
  gi|121637997|ref|YP_978221.1|  53 ARDIHQLEAridslaarnsklmetlkearqqllalreevdrlgqppsgygvllathdddtvdvftsgrkmrLTCSPNI-- 130
                                    444555522333333333333333333333444444444444444444444444444444333333333332222222.. PP

                         AAA_19  87 alelleeaeeekklqeeellivDEfqdvd.elqyrLlkallgekkklllvGDp 138
                                     ++   + ++ ++++ +e+l v E+   +   + + l+++l ++++ l+vG +
  gi|121637997|ref|YP_978221.1| 131 DAA---SLKKGQTVRLNEALTVVEAGTFEaVGEISTLREILADGHRALVVGHA 180
                                    111...22233444334566666666666666666666666666666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.004
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallvel 37 
                                    k +l+ ++pG+GKT + k++ + l + 
  gi|121637997|ref|YP_978221.1| 287 KGVLLYGPPGCGKTLIAKAVANSLAKK 313
                                    5689***********999998887664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00059      0.25       3      27 ..     289     313 ..     287     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00059
                                    EEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                    v+l G++G+GKT  ++ +a  +a++
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLAKK 313
                                    799*****************99986 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.6   0.00068      0.29      16      86 ..      24      93 ..      18      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00068
                         APG6_N 16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86
                                    +leq+++e   ++e l++   ++  ++ +  ++ +le +++ l +  ++l+e Lke+ ++  +l++e+  
  gi|121637997|ref|YP_978221.1| 24 AELEQLRREAAVLREQLENAVGSHAPTR-SARDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDR 93
                                   5789999999999988888775544433.589999999999999999999999999999999999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.47       5      22 ..     289     306 ..     286     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g GKT +ak  
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAV 306
                                    89************9987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00071       0.3      23      45 ..     289     311 ..     275     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    v l+G +G+GKt +ak + n+++
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSLA 311
                                    679***************99865 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00087      0.37     117     138 ..     289     310 ..     282     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00087
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    v++yGp+ +Gkt +a+a a+ +
  gi|121637997|ref|YP_978221.1| 289 VLLYGPPGCGKTLIAKAVANSL 310
                                    89***************99875 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00078      0.33     129     161 ..      57      89 ..      52     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00078
                      FUSC-like 129 ddleakrlaLaqqnakvvealnaareillsrlk 161
                                    ++lea+   La +n+k++e+l++ar++ll  ++
  gi|121637997|ref|YP_978221.1|  57 HQLEARIDSLAARNSKLMETLKEARQQLLALRE 89 
                                    68899999********************98865 PP

>> DUF465  Protein of unknown function (DUF465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.64   2.7e+02      24      44 ..      21      41 ..      15      42 .. 0.86
   2 ?    8.3   3.6    0.0055       2.3       9      46 ..      57      94 ..      56      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.64
                                   S-HHHHHHHHHHHHHHHHHHH CS
                         DUF465 24 tddleierLKkeKLeLKDeIy 44
                                    d+ e+e+L++e   L+++++
  gi|121637997|ref|YP_978221.1| 21 GDAAELEQLRREAAVLREQLE 41
                                   6999********999999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0055
                                   HHHHHHHHHHHTT-.S-HHHHHHHHHHHHHHHHHHHHH CS
                         DUF465  9 eeLdkeIhalearpvtddleierLKkeKLeLKDeIyrl 46
                                   ++L+++I+ l ar++   +++++ + + L+L++e+ rl
  gi|121637997|ref|YP_978221.1| 57 HQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL 94
                                   78********************************9987 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0    0.0028       1.2      15      59 ..      50      94 ..      37      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0028
                    TMF_TATA_bd 15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneel 59
                                   +r    i++lE+ + sl  ++++l +  +ear+++++l +e+++l
  gi|121637997|ref|YP_978221.1| 50 TRSARDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL 94
                                   555677899999999999999999999999999999998888876 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.4       3.5   1.5e+03      26      41 ..      24      39 ..      23      43 .. 0.66
   2 ?   11.0   0.6    0.0008      0.34      27      62 ..      55      90 ..      50      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.5
                                   HHHHHHHHHHHHHHHH CS
                         bZIP_1 26 aeieeLerrvkaLeke 41
                                   ae e+L r++++L ++
  gi|121637997|ref|YP_978221.1| 24 AELEQLRREAAVLREQ 39
                                   5667777777777665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0008
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLksk 62
                                    i +Le r + L + N++L ++l+e + +   L+++
  gi|121637997|ref|YP_978221.1| 55 DIHQLEARIDSLAARNSKLMETLKEARQQLLALREE 90
                                   689**************9999999998888777766 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.9     0.015       6.2      37     110 .]      25      82 ..      22      94 .. 0.84
   2 ?   -1.5   0.0       7.7   3.3e+03      77     109 ..     133     165 ..     130     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHCCHH-T..........TTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  37 eLDdlieeAkerreegeeeasrpevpphtLpPeeliaahlapakkeeqeeLearlqeleaenaelaeeveeqre 110
                                    eL++l +eA+  re+                 e+++ +h  +  ++  ++Lear++ l a n +l+e+++e r+
  gi|121637997|ref|YP_978221.1|  25 ELEQLRREAAVLREQ----------------LENAVGSHAPTRSARDIHQLEARIDSLAARNSKLMETLKEARQ 82 
                                    778888888877775................6888888999999999999999999999999999999998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.7
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  77 apakkeeqeeLearlqeleaenaelaeeveeqr 109
                                    a++kk ++ +L++ l  +ea + e   e++++r
  gi|121637997|ref|YP_978221.1| 133 ASLKKGQTVRLNEALTVVEAGTFEAVGEISTLR 165
                                    67899999**********999999999988877 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.68   2.9e+02      62      80 ..      25      43 ..      23      55 .. 0.84
   2 ?    7.9   1.4     0.004       1.7      44      78 ..      58      92 ..      50      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.68
                            GAS 62 pLkkaeeeveeLrkqlkny 80
                                   +L+++++e + Lr+ql+n 
  gi|121637997|ref|YP_978221.1| 25 ELEQLRREAAVLREQLENA 43
                                   7999999999999999986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.004
                            GAS 44 rnekelseisqenkrlkepLkkaeeeveeLrkqlk 78
                                   + e +++ ++++n++l+e+Lk+a++++  Lr+++ 
  gi|121637997|ref|YP_978221.1| 58 QLEARIDSLAARNSKLMETLKEARQQLLALREEVD 92
                                   67889999**********************99875 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.59   2.5e+02      22      47 ..      20      45 ..      18      48 .. 0.84
   2 ?    8.6   3.1     0.006       2.6      12      65 ..      36      94 ..      32      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.59
                                   SSSHHHHHHHHHHHHHHHHHHHHHHH CS
                         HSCB_C 22 aadkeeleelkaeveerieeleaele 47
                                   ++d++ele+l++e    +e+le+++ 
  gi|121637997|ref|YP_978221.1| 20 SGDAAELEQLRREAAVLREQLENAVG 45
                                   56899999999999999999998876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.006
                                   HHHHHHCG.......GGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         HSCB_C 12 lrEeleea.......eeaadkeeleelkaeveerieeleaeleeafekkdleaaadllrrl 65
                                   lrE+le+a       ++a+d  +le+  + + +r  +l++ l+ea   ++l a+++++ rl
  gi|121637997|ref|YP_978221.1| 36 LREQLENAvgshaptRSARDIHQLEARIDSLAARNSKLMETLKEAR--QQLLALREEVDRL 94
                                   79******99999887788889999999999999999999999994..5888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       196  (0.010932); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.89u 0.34s 00:00:01.23 Elapsed: 00:00:00.52
# Mc/sec: 3553.41
//
Query:       gi|121637998|ref|YP_978222.1|  [L=189]
Description: lipoprotein lppK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.1    9.8   2.8        2.7    8.6   2.8    1.7  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.8   0.00015       2.7       7      18 .]      13      24 ..       8      24 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00015
                         LPAM_1  7 algalllLsGCs 18
                                   +++a+l LsGCs
  gi|121637998|ref|YP_978222.1| 13 TIVAALGLSGCS 24
                                   69*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1310.02
//
Query:       gi|121637999|ref|YP_978223.1|  [L=97]
Description: hypothetical protein BCG_2134 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-30  105.4   0.0    1.1e-30  105.3   0.0    1.0  1  DUF503    Protein of unknown function (DUF503)
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.16   11.4   0.0    1.2  1  DUF604    Protein of unknown function, DUF604


Domain annotation for each model (and alignments):
>> DUF503  Protein of unknown function (DUF503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   1.3e-34   1.1e-30       1      87 [.       3      89 ..       3      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.3e-34
                         DUF503  1 vgvltlelrlpdvrSLKeKRsvvkslieklrnrfnvSvaEvdeqdlwqraeigvavvsnsrahveevldkvlrfieanpeae 82
                                   +g+l+++++l+dvrSLK+KRsv ++l+++l+++f vS+aE++ +dl++ra igvavvs +r+h+ +vld+++r+++a+pe+e
  gi|121637999|ref|YP_978223.1|  3 IGWLEFDVLLGDVRSLKQKRSVTRPLVAELQRKFSVSAAETGSHDLYRRAGIGVAVVSGDRSHAVDVLDNAERLVAAHPEFE 84
                                   89******************************************************************************** PP

                         DUF503 83 lldve 87
                                   ll+v+
  gi|121637999|ref|YP_978223.1| 85 LLSVR 89
                                   **997 PP

>> DUF604  Protein of unknown function, DUF604
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05      0.16      53      88 ..      53      88 ..      23      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                         DUF604 53 elGvpltkekGfHqvDlrgdllGlLaahplaplvsl 88
                                    +Gv ++     H vD+ +++  l+aahp   l+s+
  gi|121637999|ref|YP_978223.1| 53 GIGVAVVSGDRSHAVDVLDNAERLVAAHPEFELLSV 88
                                   68999999999*******************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 720.05
//
Query:       gi|121638000|ref|YP_978224.1|  [L=280]
Description: RNA methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-26   89.7   0.1    1.4e-25   88.9   0.1    1.5  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    5.8e-21   75.3   0.0    8.5e-20   71.5   0.0    2.1  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    6.2e-08   33.2   0.0      1e-07   32.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.2e-07   29.9   0.0      6e-07   29.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.4e-06   26.6   0.0    6.1e-06   26.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.9e-05   23.4   0.0    0.00013   22.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0003   19.9   0.0    0.00039   19.6   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00055   20.6   0.0    0.00096   19.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0048   17.9   0.0       0.01   16.9   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
     0.0048   16.8   0.0     0.0091   15.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.1   7.6e-29   1.4e-25       1      51 []       4      54 ..       4      54 .. 0.99

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 7.6e-29
                        GCD14_N  1 rGpfraGdrVqLtDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGsVV 51
                                   +Gpf  G+rVqLtDaKgr++t+ L+pG+efhthrG+i+HD +IG ++GsVV
  gi|121638000|ref|YP_978224.1|  4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVV 54
                                   6*************************************************9 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   4.7e-23   8.5e-20      14     179 ..      73     237 ..      62     243 .. 0.89
   2 ?    1.7   0.0     0.092   1.7e+02     228     244 ..     241     257 ..     238     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4.7e-23
                          GCD14  14 tlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel..s 91 
                                     +++p   q++y +D + i+++ ++ pG++v+e+G+Gsg+l+ +++r+v+P G++ ++e  ++ ae+ar +         
  gi|121638000|ref|YP_978224.1|  73 VMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGqpP 152
                                    56788889***************************************************999999999999886544335 PP

                          GCD14  92 qlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelg.fteietl 170
                                    ++  + + D+  + +    +g+vD   LD+ aPwe ++ +++ l   gg+l  +   + q+ r +eaLr+++ +te ++ 
  gi|121638000|ref|YP_978224.1| 153 DNWRLVVSDLADSELP---DGSVDRAVLDMLAPWEVLDAVSRLL-VAGGVLMVYVATVTQLSRIVEALRAKQcWTEPRAW 228
                                    6888888999988773...5679************999998888.9**********************97544******* PP

                          GCD14 171 evllrtyev 179
                                    e l+r ++v
  gi|121638000|ref|YP_978224.1| 229 ETLQRGWNV 237
                                    *******98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.092
                          GCD14 228 llkPvselkghtgyLtf 244
                                    +++P + ++ght++L+ 
  gi|121638000|ref|YP_978224.1| 241 AVRPQHSMRGHTAFLVA 257
                                    789***********975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   5.6e-11     1e-07       1      97 []     103     197 ..     103     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.6e-11
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHH...TTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraee...egl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                    vL++G+G+G ltl l++++g +++v+  +  ++  e+ar++++    + +  n+++v+ d+ d +++dgs+D  v+  +l
  gi|121638000|ref|YP_978224.1| 103 VLEAGAGSGALTLSLLRAVGpAGQVISYEQRADHAEHARRNVSGcygQ-PpdNWRLVVSDLADSELPDGSVDRAVLD-ML 180
                                    8******************66*********************777544.26**********************9993.32 PP

                                    GGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       +     ++l+ ++r+L  gG
  gi|121638000|ref|YP_978224.1| 181 A--P----WEVLDAVSRLLVAGG 197
                                    2..1....246777777776666 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.3e-10     6e-07      48     174 ..      74     204 ..      67     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.3e-10
                                    EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC... CS
                           PCMT  48 lsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle... 124
                                    +s+  +  +  p+  a ++   ++ +garvLe G+GsG lt  l r vg+ g+v+s e+ ++ +e+a+rn+     +   
  gi|121638000|ref|YP_978224.1|  74 MSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQppd 153
                                    5555555556666667777767799**********************************************865544455 PP

                                    SEEEEES-GGGTTGGG-SEEE.EEESSBBSS--HHHHHTEEEEEEEEEEES CS
                           PCMT 125 nvivvvgDGrkGyeekaPYda.ihvgaaapeiPealidQLkeGGrlvvPvg 174
                                    n  +vv+D      +    d+ ++   a+ e+ +a  + L  GG l+v v 
  gi|121638000|ref|YP_978224.1| 154 NWRLVVSDLADSELPDGSVDRaVLDMLAPWEVLDAVSRLLVAGGVLMVYVA 204
                                    666666665544444444443033334444666666666666666666555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.4e-09   6.1e-06       4     130 ..     100     220 ..      97     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.4e-09
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaq...klgldnveFeqgdieeleklledekfDlils 80 
                                    g rvl++G+G+G+lt+ l + +gp ++v++ +  ++  e+Ar n +    +  dn ++ ++d  + e  l d ++D  + 
  gi|121638000|ref|YP_978224.1| 100 GARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSgcyGQPPDNWRLVVSDLADSE--LPDGSVDRAVL 177
                                    679****************************************76511156777***********99..89999998666 PP

                Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelpakveeeskaye 130
                                         ++ +p ++l  ++r+l  gg+l+  ++ + ++l ++ve+ + + +
  gi|121638000|ref|YP_978224.1| 178 -----DMLAPWEVLDAVSRLLVAGGVLM-VYVATVTQLSRIVEALRAK-Q 220
                                    .....6899*************999888.5666688888777777663.3 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   7.2e-08   0.00013       1      96 []     104     201 ..     104     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.2e-08
                                    EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl....kvefvvadaeklpfednsfDlvvssevlhh 73 
                                    L++G+G+G+l+  l +++   ++v+  +  +   + a++++s+ +     + ++vv+d+ +  ++d+s+D  v+    + 
  gi|121638000|ref|YP_978224.1| 104 LEAGAGSGALTLSLLRAVgpaGQVISYEQRADHAEHARRNVSGCYGqppdNWRLVVSDLADSELPDGSVDRAVL----DM 179
                                    799************7777999******9999999999999988778889889*****************7755....55 PP

                                    -CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                    +  p ++l+ + R+L  gG+l++
  gi|121638000|ref|YP_978224.1| 180 L-APWEVLDAVSRLLVAGGVLMV 201
                                    6.47889***********99975 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.2e-07   0.00039      19      74 ..      88     149 ..      82     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.2e-07
                                    HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...T CS
                         RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...k 74 
                                    +++I+ + ++ +   vle g+G G+lT +L+  +    qv ++E++ + a++ + ++s    
  gi|121638000|ref|YP_978224.1|  88 AAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVgpaGQVISYEQRADHAEHARRNVSgcyG 149
                                    6899**************************99999999*************99998875551 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.3e-07   0.00096       1      99 []     104     199 ..     104     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.3e-07
                Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl 79 
                                    Le G+G+G+l+  ll++  p  +++ ++  ++  e+a++  +   ++  +n++l + dl+d++ +   D  v   vl  l
  gi|121638000|ref|YP_978224.1| 104 LEAGAGSGALTLSLLRAVgPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELP---DGSVDRAVLDML 180
                                    89****************9999999**********************************999865...888889999998 PP

                Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                      + evld + +lL+ gG+l
  gi|121638000|ref|YP_978224.1| 181 -APWEVLDAVSRLLVAGGVL 199
                                    .7889*************87 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.6e-06      0.01       1     102 [.     104     200 ..     104     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.6e-06
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare......aglddrvrlikadseealaslaagsiDllf 74 
                                    +E G+ sG  tl llra+  +g+  +++ +  +   ++a++ar+       +  d++rl+++d+ +   +l +gs+D ++
  gi|121638000|ref|YP_978224.1| 104 LEAGAGSGALTLSLLRAVGPAGQ--VISYEQRA---DHAEHARRnvsgcyGQPPDNWRLVVSDLADS--ELPDGSVDRAV 176
                                    799999**************995..9**99999...66777777777798899999********998..899999***** PP

                Methyltransf_24  75 iDgghaaeavledleallprlapggvvl 102
                                    +D+     a  e l+a+ ++l  ggv++
  gi|121638000|ref|YP_978224.1| 177 LDML----APWEVLDAVSRLLVAGGVLM 200
                                    **98....55666667777777777765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.1e-06    0.0091      21     120 ..      98     204 ..      86     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.1e-06
                Methyltransf_23  21 raggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae............kakkaqkdqfdeqeaaepqgkfdl 85 
                                    ++g+rvL+ G+G+G  +l++lr+ g   +v+ ++++    e a+            + +  ++d +       +++ +d 
  gi|121638000|ref|YP_978224.1|  98 FPGARVLEAGAGSGaLTLSLLRAVGPagQVISYEQRADHAEHARrnvsgcygqppdNWRLVVSDLA-------DSELPDG 170
                                    7899**********446666699999999******9877776655555555553332222222222.......3345566 PP

                Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllsep 120
                                     v r vl  + +++ +l+ + +ll  gG+l++ + 
  gi|121638000|ref|YP_978224.1| 171 SVDRAVLDMLAPWE-VLDAVSRLLVAGGVLMVYVA 204
                                    66666666666654.47777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1995.80
//
Query:       gi|121638001|ref|YP_978225.1|  [L=278]
Description: hypothetical protein BCG_2136 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-38  131.6   0.0    5.1e-38  131.4   0.0    1.0  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
    2.1e-06   27.3   0.0    4.4e-06   26.2   0.0    1.5  1  DUF2800   Protein of unknown function (DUF2800)


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.0   5.7e-42   5.1e-38       2     255 .]      14     260 ..      13     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 5.7e-42
                       PDDEXK_1   2 lSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefye..wkkldke.dleelleeaveelwpellleee 78 
                                    lS+sr  +f++Cpl +++r +++l+e ++ ++  +G++vHaale++y         + +  + ++ +v+++w++   +e+
  gi|121638001|ref|YP_978225.1|  14 LSPSRATDFKQCPLLYRFRAIDRLPEATSAAQ-LRGSVVHAALEQLYGlpA-----GlRSPDTARSLVQRAWDQMVAAEP 87 
                                    9***********************88777777.9**************432.....233333333556666666555555 PP

                       PDDEXK_1  79 ilessarl...rylaeklkevleklverlaeeleakrg..frpvalelefggekvrLkGriDrvd.dkegelriiDyKtg 152
                                     l  + +     +l e+++++++ +  rl+++++  ++   + v++el+ g     L+G iDr+d  + gelr++DyKtg
  gi|121638001|ref|YP_978225.1|  88 ELAGELDPgqpTQLLEDARALVSGY-YRLEDPTRFDPQccEQRVEVELADG---TLLRGYIDRIDvAATGELRVVDYKTG 163
                                    5443333322377777778888888.5677777777777878888887666...78*********999999********* PP

                       PDDEXK_1 153 sappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeei 232
                                    +app   +lae k  +Q+ +Y++al +   ++ +  p ++ ++ l        +++     +++el ++++ l  ++++i
  gi|121638001|ref|YP_978225.1| 164 KAPPAARALAEFKAMFQMKFYAVALFRS--RGVP--PTRLRLIYL------ADGQLLDYSPDRDELLRFEKTLMAIWRAI 233
                                    ****************************..6666..888888888......56677777799****99999999998888 PP

                       PDDEXK_1 233 l....agefparpskkCeyCpyksvCr 255
                                    +     g+f+++ps+ C++Cp +++C+
  gi|121638001|ref|YP_978225.1| 234 QsageTGDFRPNPSRLCDWCPHQQRCP 260
                                    8877666*******99**********7 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.9e-10   4.4e-06       4     228 ..      14     260 ..      12     263 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.9e-10
                        DUF2800   4 lSaSsahrWlkCppSar..leeeipdesSeyAeeGtlaHelaelklrkaldakekkgvkselkk.......keeevteem 74 
                                    lS+S a  + +Cp   r  + +++p+ +S +   G++ H+  e +     + ++ ++ +s +++       +e+e   e+
  gi|121638001|ref|YP_978225.1|  14 LSPSRATDFKQCPLLYRfrAIDRLPEATSAAQLRGSVVHAALEQLYGLPAGLRSPDTARSLVQRawdqmvaAEPELAGEL 93 
                                    9************9887225689********************9987777777777766666556666777444444444 PP

                        DUF2800  75 e.....eavdeyvdfvlekieeak..kdalvlvEqrvdfskyvpe.gfGtaDvviia.ddvLeviDlKyGkgvkVsa... 142
                                    +     +  +++ ++v   ++  +  + +    Eqrv+++   +   +G  D + +a +++L v+D+K Gk  ++     
  gi|121638001|ref|YP_978225.1|  94 DpgqptQLLEDARALVSGYYRLEDptRFDPQCCEQRVEVELADGTlLRGYIDRIDVAaTGELRVVDYKTGKAPPAARala 173
                                    322222556666666666655444544455679************99*******887689***********955544487 PP

                        DUF2800 143 ..ekNpQlalYAlGAleefdllydiktVrltIvQPrldnvseweisveeLlewaeevlkp.kaekaaegegefv..pgeh 217
                                      +   Q++ YA++ +++ +    +   rl  +    +++ +++ + +eLl++ +++++  +a + a ++g+f   p++ 
  gi|121638001|ref|YP_978225.1| 174 efKAMFQMKFYAVALFRSRG----VPPTRLRLIYLADGQLLDYSPDRDELLRFEKTLMAIwRAIQSAGETGDFRpnPSRL 249
                                    888999******99877765....44444444444556666666666666666655443212333333334443004445 PP

                        DUF2800 218 crFCkakatCr 228
                                    c +C  +++C+
  gi|121638001|ref|YP_978225.1| 250 CDWCPHQQRCP 260
                                    56666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1999.38
//
Query:       gi|121638002|ref|YP_978226.1|  [L=160]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-05   25.2  19.0    1.3e-05   24.9  19.0    1.1  1  DUF4126          Domain of unknown function (DUF4126)
    1.9e-05   24.5  15.0    1.9e-05   24.5  15.0    2.6  3  Rick_17kDa_Anti  Glycine zipper 2TM domain
    0.00099   19.1  13.8    0.00099   19.1  13.8    2.4  3  Gly-zipper_Omp   Glycine zipper


Domain annotation for each model (and alignments):
>> DUF4126  Domain of unknown function (DUF4126)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  19.0   2.2e-09   1.3e-05       1     154 [.       7     155 ..       7     160 .] 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-09
                        DUF4126   1 lllglglsaaaGlrvylplLllglaarfgliplpe.glewlgspvvlgalavltlvElvadkipvvdsvldtiqtfvrpv 79 
                                    lll+l ++  aGlr   +  ++++aa +g+i+l    ++w+g+ v++++++vl+++Elv dk p       t    vr++
  gi|121638002|ref|YP_978226.1|   7 LLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGtWASWMGNFVTVVIVSVLAVAELVNDKRPKTPPRTVTPVFAVRII 86 
                                    57899999************************9885789**************************99999999999**** PP

                        DUF4126  80 aGallaaaaagaveldpvlkavlavlaGgllAlvvhlvkaltRlasnastegfgnpvvstlEdvlavvlvllail 154
                                    +Ga+ +a + +a      +  + a+++G++l +++ + +a tRl++     g   + +++lEd++av++ ++ ++
  gi|121638002|ref|YP_978226.1|  87 LGAFAGAVIGTAW--GYRWGGLGAGVIGAVL-GTMGGYQARTRLVA---ARGGHDLPIALLEDSVAVLGGFAIVA 155
                                    ***9999998855..5567777777777777.68899999999999...56667777799****99988766554 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.9      0.28   1.7e+03      25      34 ..       9      18 ..       8      19 .. 0.78
   2 !   24.5  15.0   3.1e-09   1.9e-05       4      41 ..      86     123 ..      85     124 .. 0.96
   3 ?   -3.5   1.9       1.7     1e+04       8      11 ..     147     150 ..     146     158 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.28
                Rick_17kDa_Anti 25 lGavvGAaaG 34
                                   l+ ++G++aG
  gi|121638002|ref|YP_978226.1|  9 LALLIGVVAG 18
                                   5678999998 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.1e-09
                Rick_17kDa_Anti   4 liGAaaGgvaGaaigggggrvlGavvGAaaGavaGnai 41 
                                    ++GA aG+v+G a+g ++g++ ++v+GA++G++ G ++
  gi|121638002|ref|YP_978226.1|  86 ILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGGYQA 123
                                    79*********************************986 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.7
                Rick_17kDa_Anti   8 aaGg 11 
                                    ++Gg
  gi|121638002|ref|YP_978226.1| 147 VLGG 150
                                    3333 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.3       2.2   1.3e+04       5      10 ..      13      18 ..      12      19 .. 0.48
   2 !   19.1  13.8   1.7e-07   0.00099       5      41 ..      87     122 ..      85     126 .. 0.91
   3 ?   -3.8   2.7       2.2   1.3e+04       4       8 ..     152     156 ..     145     160 .] 0.43

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                 Gly-zipper_Omp  5 iGAaaG 10
                                   iG +aG
  gi|121638002|ref|YP_978226.1| 13 IGVVAG 18
                                   444444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.7e-07
                 Gly-zipper_Omp   5 iGAaaGaliGgavggrgtGaliGAavGaavGgliGaa 41 
                                    +GA+aGa+iG+a g r +G l+++++Ga++G + G++
  gi|121638002|ref|YP_978226.1|  87 LGAFAGAVIGTAWGYR-WGGLGAGVIGAVLGTMGGYQ 122
                                    8*************86.***************99987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.2
                 Gly-zipper_Omp   4 aiGAa 8  
                                    ai Aa
  gi|121638002|ref|YP_978226.1| 152 AIVAA 156
                                    22233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1307.64
//
Query:       gi|121638003|ref|YP_978227.1|  [L=284]
Description: ATP phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-39  134.7   0.0    3.6e-39  134.3   0.0    1.1  1  HisG      ATP phosphoribosyltransferase
    2.1e-24   85.4   0.0    5.1e-24   84.2   0.0    1.6  2  HisG_C    HisG, C-terminal domain
  ------ inclusion threshold ------
      0.059   13.4   0.0      0.088   12.9   0.0    1.3  1  DUF1990   Domain of unknown function (DUF1990)


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0     6e-43   3.6e-39       1     159 [.      49     204 ..      49     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 6e-43
                                    -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHHHHH CS
                           HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnlakk 80 
                                    r++di+ yV++g++d+GitG+D+v +s++  +v e l Lgfg++++ +a+p+  ++++++ l   +g+riaT ypnl++k
  gi|121638003|ref|YP_978227.1|  49 RPKDIAIYVGSGELDFGITGRDLVCDSGA--QVRERLALGFGSSSFRYAAPAGRNWTTAD-L---AGMRIATAYPNLVRK 122
                                    89************************865..6********************88777554.3...688************ PP

                                    HHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEE.EEEEEEEEEEEEEHHHHH.S..HHHHHHHHH CS
                           HisG  81 yfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkai.etilessavLiankkslk.k..kekieelle 156
                                     ++ kg+++++i+l+G+vE++++lg+aDaI+D+v +G+TL ++ L a+ e +++s+avLi  ++ ++ +   e  ++l++
  gi|121638003|ref|YP_978227.1| 123 DLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFgEPLCDSEAVLIE-RAGTDgQdqTEARDQLVA 201
                                    ************************************************889*********4.444443433447788888 PP

                                    HHH CS
                           HisG 157 rlr 159
                                    r++
  gi|121638003|ref|YP_978227.1| 202 RVQ 204
                                    876 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.9   1.1e+04      29      44 ..     131     146 ..     126     151 .. 0.69
   2 !   84.2   0.0   8.6e-28   5.1e-24       2      71 ..     210     279 ..     209     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                                    -EEEE-.SS-EEEEEE CS
                         HisG_C  29 PTvspladegwvaVsa 44 
                                    +Tv +l+    ++V+ 
  gi|121638003|ref|YP_978227.1| 131 ATVIRLDGAVEISVQL 146
                                    6888887766666665 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 8.6e-28
                                    TTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE- CS
                         HisG_C   2 rkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpi 71 
                                    ++y +l+y++p+++l+++++i+PGl+sPT++plad++wva++a+v++++v+ ++deL a+GA++Il ++i
  gi|121638003|ref|YP_978227.1| 210 QQYLMLDYDCPRSALKKATAITPGLESPTIAPLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDI 279
                                    799****************************************************************998 PP

>> DUF1990  Domain of unknown function (DUF1990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.088      15      54 ..      78     117 ..      65     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                        DUF1990  15 vdrarvrlGegeevFerAaeallswemhrlagvrvraeap 54 
                                    ++r+r  lG g  +F+ Aa a ++w+  +lag+r+ ++ p
  gi|121638003|ref|YP_978227.1|  78 QVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYP 117
                                    67899999**************************987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2173.97
//
Query:       gi|121638004|ref|YP_978228.1|  [L=93]
Description: phosphoribosyl-ATP pyrophosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-08   32.8   0.1    8.1e-08   32.6   0.1    1.1  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase
    6.7e-06   26.2   0.3    2.7e-05   24.2   0.2    1.8  2  MazG      MazG nucleotide pyrophosphohydrolase domain


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   9.1e-12   8.1e-08       2      78 ..       8      92 ..       7      93 .] 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 9.1e-12
                                   HHHHHHC...T----SS-----HHHHHH.....HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHH CS
                         PRA-PH  2 kefhrli...gerkpetPeastaelasl.....raaligEEavElleaasegdlaeladelaDllYvtygllvllGidldav 75
                                   k+f++l+   g+r  ++P  st   a +     + +++ EEa E+  aa+ ++   la+e+  llY t +l+   G++ld+v
  gi|121638004|ref|YP_978228.1|  8 KTFEDLFaelGDRARTRPADSTTVAALDggvhaLGKKLLEEAGEVWLAAEHESNDALAEEISQLLYWTQVLMISRGLSLDDV 89
                                   66666661115566666666644444447999999*********************************************** PP

                                   HHH CS
                         PRA-PH 76 fee 78
                                   +++
  gi|121638004|ref|YP_978228.1| 90 YRK 92
                                   987 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.13   1.2e+03      26      35 ..      10      19 ..       3      20 .. 0.80
   2 !   24.2   0.2   3.1e-09   2.7e-05       4      61 ..      39      92 ..      37      93 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.13
                                   HHHHHHHHHH CS
                           MazG 26 rdeleeELGD 35
                                   +++l  ELGD
  gi|121638004|ref|YP_978228.1| 10 FEDLFAELGD 19
                                   678899***9 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3.1e-09
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH CS
                           MazG  4 etllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaet 61
                                   ++l + lleE+gEv  a ++e  d+l+eE+  +L++   l+ +    +g++l+dv ++
  gi|121638004|ref|YP_978228.1| 39 HALGKKLLEEAGEVWLAAEHESNDALAEEISQLLYWTQVLMIS----RGLSLDDVYRK 92
                                   688999****************************998888886....99999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 622.07
//
Query:       gi|121638005|ref|YP_978229.1|  [L=464]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-45  155.7  18.4    3.2e-45  154.0  18.4    1.9  1  PPE       PPE family
  ------ inclusion threshold ------
      0.043   14.0   1.0      0.043   14.0   1.0    1.8  2  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0  18.4   3.6e-49   3.2e-45       1     156 [.       8     154 ..       8     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 3.6e-49
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv sa l++G g+gpllaA         ++++ a+el+svla+++a++WqGps+++++ a++p+  WL++aa+ a 
  gi|121638005|ref|YP_978229.1|   8 AVPPEVPSAWLSTGMGPGPLLAA---------QYTEIATELASVLAAVQASSWQGPSADRFVVAHQPFRYWLTHAATVAT 78 
                                    68******************765.........7999******************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaa 156
                                    +aAa +e+aaa Y++Al  m+++ae+aan+a++ alv+tnffG+nt++Ia +ea+y +mw+q+a++m++Y+a++++
  gi|121638005|ref|YP_978229.1|  79 AAAAAHETAAAGYTSALGGMPTLAELAANHAMHGALVTTNFFGVNTIPIALNEADYLRMWIQAATVMSHYQAVAHE 154
                                    ************************************************************************9875 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   4.8e-06     0.043      20      84 ..      29      94 ..      28      94 .. 0.91
   2 ?   -2.4   0.1      0.65   5.8e+03       6      34 ..     360     388 ..     358     391 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 20 aeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84
                                   a++ +++ ++l++ ++a+ +s+W+G +ad+f  + + ++  ++  ++  +  + a+++aa+ +++a
  gi|121638005|ref|YP_978229.1| 29 AAQYTEIATELASVLAAVqASSWQGPSADRFVVAHQPFRYWLTHAATVATAAAAAHETAAAGYTSA 94
                                   567889999*********999***************999999999999999999999999999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.65
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   6 peelrqaaarfqkqaeeledelqrlkaev 34 
                                    +++ + aa+  ++qa++  +  +rl++ +
  gi|121638005|ref|YP_978229.1| 360 TDAAAPAAKLPGDQAQSSASKATRLRRRL 388
                                    55566666666777777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 2358.87
//
Query:       gi|121638006|ref|YP_978230.1|  [L=1192]
Description: 5-methyltetrahydrofolate--homocystein methyltransferase MetH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-59  202.0   0.0    5.3e-59  200.2   0.0    1.9  2  S-methyl_trans  Homocysteine S-methyltransferase
    3.2e-48  164.5   0.4    5.6e-48  163.7   0.4    1.4  1  Pterin_bind     Pterin binding enzyme
    9.8e-33  113.8   0.0    1.8e-32  112.9   0.0    1.4  1  Met_synt_B12    Vitamin B12 dependent methionine synthase, ac
    1.3e-25   89.6   0.2    5.2e-25   87.7   0.2    2.2  1  B12-binding_2   B12 binding domain
    3.9e-20   72.1   1.3    5.5e-19   68.4   0.4    3.3  4  B12-binding     B12 binding domain
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.45   10.3   0.0    2.1  2  HTH_39          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> S-methyl_trans  Homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.0   1.8e-62   5.3e-59       2     268 .]      23     312 ..      22     312 .. 0.88
   2 ?   -1.5   0.0       0.6   1.8e+03     159     202 ..     511     565 ..     453     615 .. 0.68

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 1.8e-62
                                    EB---SHHHHHHT----ST.TH....HCCHH..H-HHHHHHHHHHHHHHT-SEEE-TTTT--..GG..T--HHHHH.HHH CS
                 S-methyl_trans   2 ilDGgmgteLerradlsee.lw....saell..trpelikeihrdyleaGadiieTnTyqas..kik.gleeeeeveeln 71 
                                    + DG+mgt+L++  dl+ + ++    ++e+l  trp++++ ihr+y+eaGad +eTnT++++  +   +++ ++++++l 
  gi|121638006|ref|YP_978230.1|  23 VGDGAMGTQLQAA-DLTLDdFRglegCNEILneTRPDVLETIHRNYFEAGADAVETNTFGCNlsN-LgDYDIADRIRDLS 100
                                    89*********95.777777667779*****888****************************643.2455666******* PP

                                    HHHHHHHHHHHHHH.......HEEEEE--HHHHCTS---.--HHHHHHHHHHHHHHHHHCT-SEEEEEEE--HHHHHHHH CS
                 S-methyl_trans  72 raavelareaadeaaa...plfvagsvGpygatlsdgydllsfeelveahreqiralleagvDlllietipdlleakaav 148
                                    +++ ++ar++ade  +   +++v gs+Gp +++ + g  +++++ +++a++e + ++l++g+D +l+et++dll++kaa 
  gi|121638006|ref|YP_978230.1| 101 QKGTAIARRVADELGSpdrKRYVLGSMGPGTKLPTLG--HTEYAVIRDAYTEAALGMLDGGADAILVETCQDLLQLKAA- 177
                                    **************88999999*******99998775..36899***********99**********************. PP

                                    HHHT......T....--EEEEE-ECCT.TETTS-BHHH.HHHHHCT-TE.EEEEEES--.GGGHHHHHHHHHTT--S-.E CS
                 S-methyl_trans 149 ellaa.....e....lpvwisftikdestlrsGetleeavaalaaatqp.lavgvNCak.peelepllkelksetalpav 217
                                     +l +     +    +pv++ +t++ + t+  G+++ +a++a++      +++g+NCa+ p e++++l++l+++ ++p v
  gi|121638006|ref|YP_978230.1| 178 -VLGSrramtRagrhIPVFAHVTVETTGTMLLGSEIGAALTAVEPL--GvDMIGLNCATgPAEMSEHLRHLSRHARIP-V 253
                                    .666544444156689********76546559*************9..6599*******************7777777.* PP

                                    EEE--.......-.S-----------....-HHHTT.EEEE---TT--HHHHHHHHH.. CS
                 S-methyl_trans 218 ivypn.......sagevydltpeewaesaeewleag.aniiGGCCgttpehIraiaeav 268
                                    +v pn       ++g +y l p+e+ae +++++++  ++++GGCCgttp+hIr++a+av
  gi|121638006|ref|YP_978230.1| 254 SVMPNaglpvlgAKGAEYPLLPDELAEALAGFIAEFgLSLVGGCCGTTPAHIREVAAAV 312
                                    *****999998537889**************997766******************9986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.6
                                    EEE-ECCT..T.ETTS-BHHH.HHHHHCT-.........TEEEEEEES--GGGHH CS
                 S-methyl_trans 159 isftikdes.t.lrsGetleeavaalaaat.........qplavgvNCakpeele 202
                                    ++fti  ++ +  r+G ++ ea+++l++ +         +++++g+N a  ++l+
  gi|121638006|ref|YP_978230.1| 511 LTFTIATGQeEsRRDGIETIEAIRELKKRHpdvqttlglSNISFGLNPAARQVLN 565
                                    5666654444347788877777888888877777776655566777766655554 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.4   1.9e-51   5.6e-48       1     244 []     347     583 ..     347     583 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 1.9e-51
                                    EEEEETTTTTCHCCHHC.THHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE CS
                    Pterin_bind   1 mgilNvtpdsfsdggkf.edldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiD 79 
                                    ++++N+++++ ++++++ ed++k+l+ a++++++GA++lD++++++      +d+ ++++ ++  l+     +++pi++D
  gi|121638006|ref|YP_978230.1| 347 GERTNANGSKGFREAMIaEDYQKCLDIAKDQTRDGAHLLDLCVDYV-----GRDGVADMKALASRLA---TSSTLPIMLD 418
                                    699*************99****************************.....****************...3349****** PP

                                    -S-HHHHHHHHHT..TSEEEEETTTTS......SSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHH CS
                    Pterin_bind  80 ttkaevaeaAlka..gadivNdvsgee......rdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveafle 151
                                    +t++ v++a+l++  g++ +N+v++e+      r++k++ lvae+gaavv+++++        eegq++++ ++ve++ +
  gi|121638006|ref|YP_978230.1| 419 STETAVLQAGLEHlgGRCAINSVNYEDgdgpesRFAKTMALVAEHGAAVVALTID--------EEGQARTAQKKVEIAER 490
                                    **************99***************************************........459************** PP

                                    HHHHHHHHTT--GGGEEEETTTTS..STTHHHHHHHHHTHHHHHHTTS....SEBEEEGTTGHHHHHHHCTTCHGHHHHH CS
                    Pterin_bind 152 arveaaeeaGvaperillDpgigf..gkteehnlellrrldelreale....vpvllGvSrksflgrllelgkaeeRdag 225
                                      ++ + ++Gv+++ il+D ++++  +++ee++ + +++++++re ++    v+++lG+S++sf +++       +R+++
  gi|121638006|ref|YP_978230.1| 491 LINDITGNWGVDESSILIDTLTFTiaTGQEESRRDGIETIEAIRELKKrhpdVQTTLGLSNISFGLNPA------ARQVL 564
                                    ***********************99******************99999*******************65......9**** PP

                                    HHHHHHHHHHTT-SEEEES CS
                    Pterin_bind 226 taaflalaaaaGadivrVh 244
                                    +++fl+++++aG+d ++Vh
  gi|121638006|ref|YP_978230.1| 565 NSVFLHECQEAGLDSAIVH 583
                                    ******************9 PP

>> Met_synt_B12  Vitamin B12 dependent methionine synthase, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0     6e-36   1.8e-32      48     257 ..     978    1192 .]     967    1192 .] 0.86

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 6e-36
                   Met_synt_B12   48 lkriieekll.kakavvglfpAnsegddievytdesrse.vlatlhtLRqqeekeeeepnlcLaDfvapk....esgi 119 
                                     l+r+ ++  l +a  v+g fpA seg+di+v t+ + ++ v  ++h+ Rqq+        lc+aDf++++    e+g 
  gi|121638006|ref|YP_978230.1|  978 LDRLSTDGILaHAAVVYGYFPAVSEGNDIVVLTEPKPDApVRYRFHFPRQQRG-----RFLCIADFIRSRelaaERGE 1050
                                     66666665441677899**************9988855537788*******54.....58********9644447899 PP

                   Met_synt_B12  120 kdyiGlFavtagigieelaekfeaekddYssilvkaladrLaeAfaellhekvrkelWgyakdeklsn......eeli 191 
                                      d++ +  vt+g  i + a+++ a++     + v+ +  +L+eA+ae+ h+++r+el +++ d ++ +      e+ +
  gi|121638006|ref|YP_978230.1| 1051 VDVLPFQLVTMGQPIADFANELFASNAYRDYLEVHGIGVQLTEALAEYWHRRIREEL-KFSGDRAMAAedpeakEDYF 1127
                                     9*******************9988844444466899******************986.6666666665555555899* PP

                   Met_synt_B12  192 kekyqgirpApGYpacpdhtekktlfelldaeekigieLteslamvPaasvsGlyfahpearYfav 257 
                                     k  y+g r A+GY acpd ++++++++ll+ e+ ig++L e+l + P+ s  ++++ hpea+Yf+v
  gi|121638006|ref|YP_978230.1| 1128 KLGYRGARFAFGYGACPDLEDRAKMMALLEPER-IGVTLSEELQLHPEQSTDAFVLHHPEAKYFNV 1192
                                     *******************************99.******************************97 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.2   1.7e-28   5.2e-25       2      75 .]     645     717 ..     644     717 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.7e-28
                  B12-binding_2   2 aerlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75 
                                     erl++ iv+g+++g+++++dea+  ++ +++++n+ ll++mk VG+lfg+g+++lp+vl+saevmk+ava+Le
  gi|121638006|ref|YP_978230.1| 645 FERLAQRIVDGERNGLDADLDEAM-TQKPPLQIINEHLLAGMKTVGELFGSGQMQLPFVLQSAEVMKAAVAYLE 717
                                    69**********************.4456*******************************************97 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.37   1.1e+03      45      78 ..     217     249 ..     201     256 .. 0.77
   2 ?   -3.0   0.0       2.5   7.3e+03      41      78 ..     280     315 ..     263     319 .. 0.66
   3 ?   -2.1   0.0       1.2   3.7e+03      40      59 ..     450     472 ..     421     495 .. 0.68
   4 !   68.4   0.4   1.8e-22   5.5e-19       2     119 ..     731     848 ..     730     850 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.37
                    B12-binding  45 aairaekpdvvglSalltsqleavkelvellkri 78 
                                     a++ + +d++gl +  t   e  ++l +l + +
  gi|121638006|ref|YP_978230.1| 217 TAVEPLGVDMIGLNC-ATGPAEMSEHLRHLSRHA 249
                                    56777899*******.888888888888776555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                    B12-binding  41 edivaairaekpdvvglSalltsqleavkelvellkri 78 
                                    e+++  i+++   +vg     +++ ++++e++ +++ i
  gi|121638006|ref|YP_978230.1| 280 EALAGFIAEFGLSLVGGC--CGTTPAHIREVAAAVANI 315
                                    666677777777778884..478888888888775544 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                    B12-binding  40 n...edivaairaekpdvvglSa 59 
                                        ++++a ++++ + vv+l++
  gi|121638006|ref|YP_978230.1| 450 EsrfAKTMALVAEHGAAVVALTI 472
                                    25678899999999999999986 PP

  == domain 4  score: 68.4 bits;  conditional E-value: 1.8e-22
                    B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrir 79 
                                    +++latv+gd+h++G++++  +l+++g+eV+++g++++ ++i++ +++  +dvvg+S ll ++   +ke +e+   +++ 
  gi|121638006|ref|YP_978230.1| 731 RIVLATVKGDVHDIGKNLVDIVLSNNGYEVVNIGIKQPIATILEVAEDKSADVVGMSGLLVKSTVVMKENLEEmnTRGVA 810
                                    79****************************************************************************** PP

                    B12-binding  80 prvkvvvGGahpsldpeetleak.lgiddvvvgegedalea 119
                                    ++++v++GGa+ +  + e   ++  +i+   v +++da+e 
  gi|121638006|ref|YP_978230.1| 811 EKFPVLLGGAALTRSYVE---NDlAEIYQGEVHYARDAFEG 848
                                    *********986655555...67777777777777777776 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.45      26      67 ..      88     124 ..      83     127 .. 0.81
   2 ?   -2.3   0.0       1.2   3.7e+03      13      25 ..     524     536 ..     522     539 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                         HTH_39  26 ditrlaaRIkeLrekGyeIktervteaterGrthrrVarYsL 67 
                                    + ++ a RI++L +kG +I ++    a+e G++    +rY+L
  gi|121638006|ref|YP_978230.1|  88 GDYDIADRIRDLSQKGTAIARRV---ADELGSPD--RKRYVL 124
                                    5578899**************99...88888887..367777 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                         HTH_39  13 hgsittleamrel 25 
                                    +  i t+ea+rel
  gi|121638006|ref|YP_978230.1| 524 RDGIETIEAIREL 536
                                    55699******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.96u 0.35s 00:00:01.31 Elapsed: 00:00:00.57
# Mc/sec: 6323.07
//
Query:       gi|121638007|ref|YP_978231.1|  [L=292]
Description: hypothetical protein BCG_2142 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-54  183.1   0.0    8.4e-54  182.8   0.0    1.1  1  PAC2      PAC2 family
  ------ inclusion threshold ------
       0.11   11.2   0.0       0.18   10.5   0.0    1.3  1  Ndr       Ndr family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.0   9.3e-58   8.4e-54       1     211 [.      21     238 ..      21     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 9.3e-58
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEE...EEE.TTT..SEEEEEE CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprl...yak.dsg.srdllvlq 73 
                                    +++G++++G +++ av +L++s++a ++ eid++ +++++++rpv+   +g  rel++p +   +++ + g +rd++++ 
  gi|121638007|ref|YP_978231.1|  21 AFEGWNDAGDAASDAVAHLAASWQALPIVEIDDEAYYDYQVNRPVIRQVDGvtRELQWPAMrisHCRpP-GsDRDVVLMC 99 
                                    589**********************************************************66655544.45******** PP

                                    EE-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH..HCT-CEEEEHHHHHHH CS
                           PAC2  74 grepilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel..eeseyggivgitglLl 151
                                    g+ep++++++f+++ll ++++l+v++vv+Lg+l     ad+phtrp++v+gaa + + ++++  +e++y+g++gi+g++ 
  gi|121638007|ref|YP_978231.1| 100 GVEPNMRWRTFCDELLAVIDKLNVDTVVILGALL----ADTPHTRPVPVSGAAYSAASARQFglQETRYEGPTGIAGVFQ 175
                                    **********************************....99*************99999988863488************* PP

                                    HHHHHTT-EEEEEEEEEECCC...--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                           PAC2 152 saakergipavgllaevphyl...pdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                    sa+  +gipav ++a vphy+   p+Pka++all++++++l++ev++ dL  +ae++e+++ e
  gi|121638007|ref|YP_978231.1| 176 SACVGAGIPAVTFWAAVPHYVshpPNPKATIALLRRVEDVLDVEVPLADLPAQAEAWEREITE 238
                                    **********************988***********************************988 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     2e-05      0.18      58     106 ..      83     131 ..      75     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2e-05
                                    EEEEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEE CS
                            Ndr  58 ilhvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGv 106
                                    i h  +PG + +   ++  ++       +d+llav+d++++++v+ lG+
  gi|121638007|ref|YP_978231.1|  83 ISHCRPPGSDRDVVLMCGVEPNMRWRTFCDELLAVIDKLNVDTVVILGA 131
                                    7899***************999999********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2101.52
//
Query:       gi|121638008|ref|YP_978232.1|  [L=256]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                       96  (0.00535445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 1632.03
//
Query:       gi|121638009|ref|YP_978233.1|  [L=489]
Description: L-asparagine permease ansP1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-103  347.1  39.8   1.7e-103  346.8  39.8    1.0  1  AA_permease    Amino acid permease
    1.4e-35  123.0  39.5    1.7e-35  122.7  39.5    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.8  39.8  1.9e-107  1.7e-103       2     448 ..      26     444 ..      25     464 .. 0.96

  Alignments for each domain:
  == domain 1  score: 346.8 bits;  conditional E-value: 1.9e-107
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                    +++i +gg+iGtglf+g +  l++aGp g++l+y ++gv++fl+ ++lge++ + p+sg+f  ya++f g+++++++G++
  gi|121638009|ref|YP_978233.1|  26 LQMIGIGGAIGTGLFLGASGRLAKAGP-GLFLVYGVCGVFVFLILRALGELVLHRPSSGSFVSYAREFFGEKAAYAVGWM 104
                                    79*************************.**************************************************** PP

                    AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiill 161
                                    y++ w+++ ++++ta++ ++q w  +t +p +w+ +++ l+v+l +nl++v+++ge ef++alik++a+ af++vg ++l
  gi|121638009|ref|YP_978233.1| 105 YFLHWAMTSIVDTTAIATYLQRWTIFTVVP-QWILALIALTVVLSMNLISVEWFGELEFWAALIKVLALMAFLVVGTVFL 183
                                    ***********************99*****.************************************************* PP

                    AA_permease 162 aggkpnkga..gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                    ag  p +g   g++ ++++g+     +p +         +  ++v + vvfa++  elv+++agE+++Pek +P+ai++v
  gi|121638009|ref|YP_978233.1| 184 AGRYPVDGHstGLSLWNNHGG----LFPTS--------WLPLLIVTSGVVFAYSAVELVGTAAGETAEPEKIMPRAINSV 251
                                    *********************....88888........9***************************************** PP

                    AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlysla 319
                                    v ri+ifYv+s++l+ ll+p+++ +  +      spfv+f+++ g  ++++l+n+v+ltaalss+n++lys+ Rv++s a
  gi|121638009|ref|YP_978233.1| 252 VARIAIFYVGSVALLALLLPYTAYKAGE------SPFVTFFSKIGFHGAGDLMNIVVLTAALSSLNAGLYSTGRVMHSIA 325
                                    **************************99......9********************************************* PP

                    AA_permease 320 kdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgr 399
                                    ++g aP++ +++sk+gvP+ +i+l+++i l+++ l++++++  ++f+++l++sal +++ w  i l++lr+ k   ++  
  gi|121638009|ref|YP_978233.1| 326 MSGSAPRFTARMSKSGVPYGGIVLTAVITLFGVALNAFKPG--EAFEIVLNMSALGIIAGWATIVLCQLRLHKL--ANAG 401
                                    *****************************************..**************************66666..8888 PP

                    AA_permease 400 sieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaas 448
                                     +++ +f++++ p+  +l+l++l+ +l+++a  +++       +w +a+
  gi|121638009|ref|YP_978233.1| 402 IMQRPRFRMPFSPYSGYLTLLFLLVVLVTMASDKPIG------TWTVAT 444
                                    899***************************9998877......444444 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7  39.5   1.9e-39   1.7e-35       4     422 ..      24     449 ..      21     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.9e-39
                  AA_permease_2   4 lsafalvigsvigsgifvkn..laasggpa.lilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafls 80 
                                    +++ ++ ig +ig+g f     ++a++gp  ++++++ +v+++    l ++ El  + p+sg  ++y++++fg+k+a+ +
  gi|121638009|ref|YP_978233.1|  24 RQLQMIGIGGAIGTGLFLGAsgRLAKAGPGlFLVYGVCGVFVF--LILRALGELVLHRPSSGSFVSYAREFFGEKAAYAV 101
                                    6777899**********99899899999972445555555554..5666999**877*********************** PP

                  AA_permease_2  81 awfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                    +w++++ ++ +  + ++++a yl+ ++      + +++ ++a + l++v  +n++++ + + + ++ +++k+l ++++l+
  gi|121638009|ref|YP_978233.1| 102 GWMYFLHWAMTSIVDTTAIATYLQRWTIF----TVVPQWILALIALTVVLSMNLISVEWFGELEFWAALIKVLALMAFLV 177
                                    **********8766667777777776533....345667778889999999*********************87777777 PP

                  AA_permease_2 161 ilglitvdgggfssl.stetdt......ffpngwpgvllgllivlwsfdGfesaanvsee.vkk..kdvpkaifiglliv 230
                                     +g +++ g++  +  st  +        fp+ w   l + ++v+++++++e +   + e + +  k +p+ai+++++ +
  gi|121638009|ref|YP_978233.1| 178 -VGTVFLAGRYPVDGhSTGLSLwnnhggLFPTSWLPLLIVTSGVVFAYSAVELVGTAAGEtA-EpeKIMPRAINSVVARI 255
                                    .777777777776554222222111222444444445666666*****************63.43488************ PP

                  AA_permease_2 231 lvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPr 310
                                    +++y++   +++  +p    +  ++  s++  ff + g   +  +++i++  ++l ++n+ ++++ rv++++a  g  Pr
  gi|121638009|ref|YP_978233.1| 256 AIFYVGSVALLALLLPYTAYKA-GE--SPFVTFFSKIGFHGAGDLMNIVVLTAALSSLNAGLYSTGRVMHSIAMSGSAPR 332
                                    ******9777777777766665.44..3699*******889999999********************************* PP

                  AA_permease_2 311 ffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrp.hl...krpgkil 386
                                    f a+++k g p+++i+lta+++l+ + l ++ +++a+ ++l++s+lg+i  ++ ++++ l l k  +      +r++++ 
  gi|121638009|ref|YP_978233.1| 333 FTARMSKSGVPYGGIVLTAVITLFGVALNAFKPGEAFEIVLNMSALGIIAGWATIVLCQLRLHKLANaGImqrPRFRMPF 412
                                    **********************77777777777**********************9999966666553335336677776 PP

                  AA_permease_2 387 vaiigalfllfllvalffp.pkgpatqssliytiilt 422
                                        g l+llfllv+l  + +++p  + +++++ii++
  gi|121638009|ref|YP_978233.1| 413 SPYSGYLTLLFLLVVLVTMaSDKPIGTWTVATLIIVI 449
                                    7777788888888887766245555666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3548.48
//
Query:       gi|121638010|ref|YP_978234.1|  [L=67]
Description: hypothetical protein BCG_2145 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.078   13.0   0.6      0.098   12.6   0.6    1.2  1  UL42             HCMV UL42
       0.14   11.8   4.4       0.14   11.8   4.4    1.1  1  DUF2244          Integral membrane protein (DUF2244)
       0.21   11.6   5.2       0.24   11.4   5.2    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.51   10.5   3.3       0.56   10.3   3.3    1.0  1  DUF4337          Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> UL42  HCMV UL42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   2.2e-05     0.098      62     105 ..      21      63 ..       7      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                           UL42  62 dmdmmempatmhpttgayfdngwkwtfallvvailgiiflavvf 105
                                     m m+ +  ++  +  ayf  gw   +     ai+g+i +a+ f
  gi|121638010|ref|YP_978234.1|  21 GMAMVFLAMAV-VAVTAYFRMGWWSIIGYAAAAIIGVIGFALAF 63 
                                    45555444433.45679******9999999********999988 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.4   3.2e-05      0.14      14      52 ..      21      59 ..       8      66 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                        DUF2244 14 llllalalvslvialafllaGawpvlpFaglevlalala 52
                                    + +++ ++ +v+ +a + +G w ++++a+ ++++++  
  gi|121638010|ref|YP_978234.1| 21 GMAMVFLAMAVVAVTAYFRMGWWSIIGYAAAAIIGVIGF 59
                                   4444444555555556669**********9999887543 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.2   5.4e-05      0.24      40      80 ..      20      62 ..      11      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                Phage_holin_3_6 40 lgaagvlallalllllval.alala.alwlaalivaavllvla 80
                                    g+a+v++++a++++++ + + + + +  +aa i++++ ++la
  gi|121638010|ref|YP_978234.1| 20 YGMAMVFLAMAVVAVTAYFrMGWWSiIGYAAAAIIGVIGFALA 62
                                   5788888888888888888544444345666666666666655 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3   0.00013      0.56     111     161 .]      14      63 ..       6      63 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                        DUF4337 111 neasdkfdlasalLqiaIvlaaialltkkklllylsl.vlglvGlvlflagf 161
                                      +   + +a+++L +a+v  a+++  ++ +  ++++ +++++G++ f+++f
  gi|121638010|ref|YP_978234.1|  14 ASKPPLYGMAMVFLAMAVV--AVTAYFRMGWWSIIGYaAAAIIGVIGFALAF 63 
                                    4444558999999977765..8999999655555555166788999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 559.96
//
Query:       gi|121638011|ref|YP_978235.1|  [L=293]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-45  154.8   0.1    2.6e-45  154.3   0.1    1.2  1  adh_short        short chain dehydrogenase
    3.6e-37  128.2   0.5      5e-37  127.7   0.5    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.8e-11   43.7   0.4    4.6e-11   43.0   0.4    1.3  1  KR               KR domain
  ------ inclusion threshold ------
      0.025   13.7   0.0      0.029   13.5   0.0    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.094   12.1   0.2       0.25   10.7   0.1    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.11   11.9   0.3       0.16   11.4   0.3    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.1   8.6e-49   2.6e-45       1     192 [.       7     196 ..       7     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 8.6e-49
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kvv++tGa++GIG ++a++l ++Gak+v++d s+++l+ + +el+ + +++l++ +Dv+d  +++a+ e+av+++g++dv
  gi|121638011|ref|YP_978235.1|   7 KVVFITGAARGIGAEVARRLHNKGAKLVLTDLSKSELAVMGAELGGD-DRLLTVVADVRDLPAMQAAAETAVERFGGIDV 85 
                                    89*******************************************95.99****************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    +v+NAGi+  g++ +++ ++++rv++vNl g f+++ra lpa++  ++G +  vsS a++ + +g+a+Y  sKa+ ++++
  gi|121638011|ref|YP_978235.1|  86 VVANAGIASYGSVLKVDPQAFRRVLDVNLLGNFHTVRATLPALI-DRRGYVLIVSSLAAFAAPPGMAPYNMSKAGNEHFA 164
                                    ******************************************99.899******************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmakelre 192
                                    ++l+ e+a  g++v + +   +dT++++++++
  gi|121638011|ref|YP_978235.1| 165 NALRLEVAHLGVSVGSAHMSWIDTALVRDTKA 196
                                    *************************9988766 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.5   1.7e-40     5e-37       1     210 [.      13     224 ..      13     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 1.7e-40
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..v..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                    Gaa+gIG+++A++l+++Ga++vltdl++++   ++ + +elg +  +  + +DV+d  +++a++e++ve+fg++D++v n
  gi|121638011|ref|YP_978235.1|  13 GAARGIGAEVARRLHNKGAKLVLTDLSKSE---LAVMGAELGGDdrLltVVADVRDLPAMQAAAETAVERFGGIDVVVAN 89 
                                    9****************************9...6667777764445347******************************* PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    agia    g++l+++ + f+r+ldvnl + f++++a lp l+ ++g ++ +ss++a  + p+ + y+++Ka+ e+++ +l
  gi|121638011|ref|YP_978235.1|  90 AGIASY--GSVLKVDPQAFRRVLDVNLLGNFHTVRATLPaLIDRRGYVLIVSSLAAFAAPPGMAPYNMSKAGNEHFANAL 167
                                    ******..*******************************888888*********************************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHST..TSS-B-HHHHHHH CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgikgfdelleelearap..lgrlgtpeevaea 210
                                      e+++ g+ v + + ++i+T ++++ k      +el ar p  l+++++++++a+a
  gi|121638011|ref|YP_978235.1| 168 RLEVAHLGVSVGSAHMSWIDTALVRDTKADLPAFAELLARLPwpLNKTTSVNKCAAA 224
                                    ************************999987777777766665226666666666665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.4   1.5e-14   4.6e-11       3     167 ..       9     171 ..       7     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.5e-14
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                    ++itG++ g+G e+ar l +kga+ lvl+  s++   + + + ael   + +  +v aDv d  a++a+ e++ ++++ i
  gi|121638011|ref|YP_978235.1|   9 VFITGAARGIGAEVARRLHNKGAK-LVLTDLSKS---ELAVMGAELGGDD-RLLTVVADVRDLPAMQAAAETAVERFGGI 83 
                                    68********************96.666666622...2233446666654.5666667********************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaaNaflDal 159
                                      v+  Ag++  + + +++ +++++vl   + G  +  +++ +   ++  +++++SS+a++   +g a Y    a  + +
  gi|121638011|ref|YP_978235.1|  84 DVVVANAGIASYGSVLKVDPQAFRRVLDVNLLGNFHTVRATLPaliDRRGYVLIVSSLAAFAAPPGMAPYNMSKAGNEHF 163
                                    *********************************999999998856666679*******************9888888888 PP

                                    HHHHHHHH CS
                             KR 160 aeyrrsqg 167
                                    a+  r + 
  gi|121638011|ref|YP_978235.1| 164 ANALRLEV 171
                                    87766554 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.8e-06     0.029       1      75 [.       9      75 ..       9     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT. CS
                Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekalee 75
                                   v++tGa+  iG e+ r++ +k  +k++l + +  +l  +  el     +++l    ++v++dvrd   ++ a e+
  gi|121638011|ref|YP_978235.1|  9 VFITGAARGIGAEVARRLHNK-GAKLVLTDLSKSELAVMGAELG---GDDRL----LTVVADVRDLPAMQAAAET 75
                                   79************9997665.67899**************993...45455....568******9999887764 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.3e-05      0.25      32      80 ..       2      48 ..       1      63 [. 0.83
   2 ?   -2.0   0.0      0.66     2e+03      49      70 ..     263     284 ..     257     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.3e-05
                                   S-GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                   2-Hacid_dh_C 32 kelsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeeelgv 80
                                   ++l+gk v i G+ r IG +va+rl+  g+k++ +d sk++    + +g+
  gi|121638011|ref|YP_978235.1|  2 TSLQGKVVFITGAARgIGAEVARRLHNKGAKLVLTDLSKSE---LAVMGA 48
                                   5799********9988********************99773...445554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.66
                                    HHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  49 qavakrlkafgmkviaydrskk 70 
                                    ++vak++ +++++v a  r+ +
  gi|121638011|ref|YP_978235.1| 263 NTVAKLMPQMDAEVAALGRFAS 284
                                    5799999999999999988866 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.3e-05      0.16       1      84 [.       9     103 ..       9     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SEEE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpdavi 69 
                                    +++tGa+  iG+ ++++l +kg +++  d   +++     ++l        v +d++d      a e +++++ ++d+v+
  gi|121638011|ref|YP_978235.1|   9 VFITGAARGIGAEVARRLHNKGAKLVLTDLS-KSELAVMGAELggddrlLTVVADVRDLPamqaAAETAVERFgGIDVVV 87 
                                    68********************998877766.333333344447888885556666665522223344445555788888 PP

                                    E--S.---HHHHHHSH CS
                      Epimerase  70 hlAa.vggvaassedp 84 
                                      A+  +  ++   dp
  gi|121638011|ref|YP_978235.1|  88 ANAGiASYGSVLKVDP 103
                                    8777454444444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2251.44
//
Query:       gi|121638012|ref|YP_978236.1|  [L=414]
Description: cysteinyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-82  276.9   0.0    2.5e-82  276.6   0.0    1.0  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
      6e-06   25.2   0.0      0.036   12.8   0.0    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.028   12.7   0.0      0.044   12.0   0.0    1.3  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.6   0.0   4.1e-86   2.5e-82       8     299 ..      36     338 ..      29     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 276.6 bits;  conditional E-value: 4.1e-86
                                    TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                   tRNA-synt_1e   8 kkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdl 87 
                                     k t+YvCG+t yda+hlGha ++v+fD+++r+  +lg+++++vqn+tDidD + +ra +++  +++la+  ++ f +d+
  gi|121638012|ref|YP_978236.1|  36 SKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDM 115
                                    5789**************************************************************************** PP

                                    HHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TT.....S-EEE-GGG-TTTTTTTT--HHHHHHT----S-... CS
                   tRNA-synt_1e  88 eaLnvlkptleprvsekvdeiielvekliekgyaYavsd.....gdvyfdvskkeeYgklskqnleelelgaegevs... 159
                                    +aL vl+p+    ++e ++e++el+ek+++ g aY+++      +d+yf   ++ ++g  s  + +++ +  e+++    
  gi|121638012|ref|YP_978236.1| 116 AALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDRemgeyQDIYFRADATLQFGYESGYDRDTMLRLCEERGGdpr 195
                                    *************************************99999999*******************9998777777666577 PP

                                    .-S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S-- CS
                   tRNA-synt_1e 160 .eekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafd.kql 237
                                      +k d+ D  LW+a+++gepsw+sP+g GRPGWh+eC+++a + +gs +di +GG+DL+fPhhe  +a +e++ + +++
  gi|121638012|ref|YP_978236.1| 196 rPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGeRRF 275
                                    789************************************************************************9899* PP

                                    EEEEEEE--EEETTBE--TTTT---BHHHH.HTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHH CS
                   tRNA-synt_1e 238 vkyflhnghlkiegekmsksLknfitikdv.lkkfdprqlRllllsahyrsqldfkeelleea 299
                                    +++++h+g++  +g+kmsks +n++++ ++  + ++p+++Rl ll  hyr    ++++ l+ea
  gi|121638012|ref|YP_978236.1| 276 ARHYVHAGMIGWDGHKMSKSRGNLVLVSALrAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEA 338
                                    ***************************99835789***************9998898888876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   3.3e-05       0.2      12      82 ..      49     119 ..      39     147 .. 0.86
   2 !   12.8   0.0     6e-06     0.036     307     356 ..     271     321 ..     251     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                                    S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT CS
                   tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkkln 82 
                                    +++HlGh+++++  D ++R     g+e ++v        p   +A++ gv+ ++l++   + + e+++ l 
  gi|121638012|ref|YP_978236.1|  49 DATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALR 119
                                    578****************************9998899999999999999999999988888777777665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6e-06
                                    TT----S-EEEE--EEE--------------HHHHHHH.H-HHHHHHHHHH CS
                   tRNA-synt_1g 307 aelklpkkvvaheyltvegkKlSkSrgvvvkakealer.ldadllRYylaa 356
                                     e ++ ++ v  +++  +g+K+SkSrg++v ++ +  + +++ ++R  l+a
  gi|121638012|ref|YP_978236.1| 271 GERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQdVEPSAVRLGLLA 321
                                    55566677777899******************9987777999999977765 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.3e-06     0.044     523     597 ..     251     326 ..     243     331 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-06
                    tRNA-synt_1 523 GlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvid.pldvikkygadalRltlilsdvgr 597
                                    G+D i+   +  +  +  + g++ f + +vh+ ++  +G+KmSKs gN +  +   ++ +   a+Rl l+  ++ +
  gi|121638012|ref|YP_978236.1| 251 GSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLvSALRAQDVEPSAVRLGLLAGHYRA 326
                                    56666666666666666778999999**********************7640444466667777777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2962.61
//
Query:       gi|121638013|ref|YP_978237.1|  [L=267]
Description: hypothetical protein BCG_2148c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-28   98.2   0.1    4.9e-27   95.1   0.1    1.9  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.1   2.8e-31   4.9e-27      42     253 ..      45     244 ..      12     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.8e-31
                                    HHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHH.HHT-SG-EEEEEEEETTEEEE CS
                     Inositol_P  42 lvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknF.vrgipqvaVsigllvegkpvl 120
                                    l +a d+++++l+l +l++++p++++l+ee+ ++ +  +l++d ++wi+DP+DGT++F + g + +aV+i+l  +     
  gi|121638013|ref|YP_978237.1|  45 LGEAGDRQANSLLLRRLQAERPGDAVLSEEAHDDLA--RLKSD-RVWIIDPLDGTREFsTPGRDDWAVHIALWRRSSN-- 119
                                    55677*******************************..99999.**************66799***********6555.. PP

                                    EEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHH CS
                     Inositol_P 121 GviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgssalkl 200
                                       +qP       a   +G+++      +s+a p+     + ++avs+++ +     l ++ + ++ +  +s+gs+++k 
  gi|121638013|ref|YP_978237.1| 120 ---GQPEITDAAVALPARGNVVYRTDTVTSGAAPAGVPGTL-RIAVSATRPPAV---LHRIRQTLAIQ-PVSIGSAGAKA 191
                                    ...66655555666666777777644444444422222221.233444444444...44444444444.588******** PP

                                    HHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEEEESSSCSSSTTSSEEEE CS
                     Inositol_P 201 aavaeGkadaylefgrekkWDhAAGeaileeaGGvvtdakgegrlllargiia 253
                                     av++G +dayl++g  ++WD AA++ +  +aG     ++g+++ +++ ++  
  gi|121638013|ref|YP_978237.1| 192 MAVIDGYVDAYLHAGGQWEWDSAAPAGVMLAAGMHASRLDGSPLRYNQLDPYL 244
                                    **************99*************************988887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1892.73
//
Query:       gi|121638014|ref|YP_978238.1|  [L=76]
Description: hypothetical protein BCG_2149 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-05   22.3   0.6    0.00013   21.8   0.6    1.3  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.6   7.2e-09   0.00013       1      38 [.       2      39 ..       2      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.2e-09
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                   r++++l +++++++++l+++r    Se++ e++r+ l+
  gi|121638014|ref|YP_978238.1|  2 RTTVSLADDVAAAVQRLRKERSIGLSEAVNELIRAGLT 39
                                   89********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 641.32
//
Query:       gi|121638015|ref|YP_978239.1|  [L=262]
Description: hypothetical protein BCG_2150c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-05   22.9   0.0      9e-05   22.4   0.0    1.2  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     5e-09     9e-05     143     185 ..     146     189 ..     144     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5e-09
                                    HHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCC..TCSHC CS
                 PI3_PI4_kinase 143 aklsvldyilgngDRhldNilvdktsgklihIDfGlil..pdewk 185
                                     +++v d++++n+DR  + il    +g++  +D+Gl+l  +++ +
  gi|121638015|ref|YP_978239.1| 146 RRMAVFDVLINNADRKGGHILC-GIDGQVYGVDHGLCLhvENKLR 189
                                    589*******************.***************4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1780.19
//
Query:       gi|121638016|ref|YP_978240.1|  [L=195]
Description: hypothetical protein BCG_2151c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-68  227.4   0.0      1e-67  227.2   0.0    1.0  1  DUF3090   Protein of unknown function (DUF3090)


Domain annotation for each model (and alignments):
>> DUF3090  Protein of unknown function (DUF3090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.0   5.8e-72     1e-67       1     171 []       6     175 ..       6     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 5.8e-72
                        DUF3090   1 hefdspdrfvagtvGepGeRtFyLqaregervvsvalekeqvaaLaerieelLdelarregasvPaeaeeelkdeepLee 80 
                                    h+f++pdrfvagtvG+pG+RtFyLqa++++rvvsv+lek+qva+Laeri +lL e++rr+g+ vP+e ++e +d +pL +
  gi|121638016|ref|YP_978240.1|   6 HVFRTPDRFVAGTVGQPGNRTFYLQAVHDSRVVSVVLEKQQVAVLAERIGALLFEVNRRFGTPVPPE-PTEIDDLSPLIM 84 
                                    89***************************************************************97.99********** PP

                        DUF3090  81 pveeeFrvgtlalawDeetervviealaleeeeedeeldeeeeeeeaealrvrltreqarafakrarevvaaGrpsCplC 160
                                    pv++eFrvgt++l+wD+e+++vv+e+la++++e d ++  +++ee ++a+rv+lt+e+ar+fa+r+ +v++aGrp+CplC
  gi|121638016|ref|YP_978240.1|  85 PVDAEFRVGTMGLGWDSEAQSVVVELLAVTDAEFDASVVLDDTEEGPDAVRVFLTPESARQFATRSYRVISAGRPPCPLC 164
                                    **********************************99996666666666******************************** PP

                        DUF3090 161 gqPldpegHlC 171
                                    ++PldpegH+C
  gi|121638016|ref|YP_978240.1| 165 DEPLDPEGHIC 175
                                    *********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1463.54
//
Query:       gi|121638017|ref|YP_978241.1|  [L=236]
Description: hypothetical protein BCG_2152c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-44  151.5   0.2    2.6e-44  151.2   0.2    1.1  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.2   0.2   1.5e-48   2.6e-44       1     193 [.       3     198 ..       3     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 1.5e-48
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS-- CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEi 80 
                                    ++L+RH++++ n++g+l gr+ v+L+e+GreqA  l +r+ + pi+a+ sSp+ R+++T+e++aeal l++ +d+++ E+
  gi|121638017|ref|YP_978241.1|   3 VILLRHARSTSNTAGVLAGRSGVDLDEKGREQATGLIDRIGDLPIRAVASSPMLRCQRTVEPLAEALCLEPLIDDRFSEV 82 
                                    68****************************************************************************** PP

                                    --GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSE.....EEEEE-HHHHHHHH CS
                     His_Phos_1  81 dfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarheget.....vlvVsHggvirall 155
                                    d+G+w g++  ++ +e    ++  +++p+ + +pggE l++v+ R++aa++e  +r ++++     +l ++Hg vi+a++
  gi|121638017|ref|YP_978241.1|  83 DYGEWTGRKIGDLVDE--PLWRVVQAHPSAAVFPGGEGLAQVQTRAVAAVREHDRRLADQHghdvlWLACTHGDVIKAVI 160
                                    ********99999999..889999999999*********************555554444444469************** PP

                                    HHHHT--GGGGGGB---TT-EEEEEE-SS-EEEEEEEE CS
                     His_Phos_1 156 arllglpleelrrleldnaslsvlefdeggwrlvrlnd 193
                                    a+++g++l+ ++r+  d+ s+sv+++++ ++ ++++n 
  gi|121638017|ref|YP_978241.1| 161 ADAFGMHLDSFQRITADPGSVSVVRYTQLRPFVLHVNH 198
                                    ****************************9999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1781.65
//
Query:       gi|121638018|ref|YP_978242.1|  [L=276]
Description: UDP pyrophosphate phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-76  257.0  14.0    2.5e-76  256.8  14.0    1.0  1  BacA            Bacitracin resistance protein BacA
  ------ inclusion threshold ------
      0.021   14.1   0.0      0.036   13.3   0.0    1.3  1  DNA_processg_A  DNA recombination-mediator protein A
       0.22   11.5   0.1       0.22   11.5   0.1    1.7  2  DUF3290         Protein of unknown function (DUF3290)
       0.25   11.2   6.0        1.1    9.2   2.9    3.1  2  DUF2474         Protein of unknown function (DUF2474)
       0.88   10.1   6.4       0.17   12.3   0.5    2.7  3  DUF4491         Domain of unknown function (DUF4491)
        2.5    8.0   5.7        1.5    8.7   0.1    3.3  4  PetG            Cytochrome B6-F complex subunit 5
          9    6.6  12.6         10    6.4   6.5    3.4  2  VirB3           Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> BacA  Bacitracin resistance protein BacA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.8  14.0   9.9e-80   2.5e-76       2     255 ..       7     262 ..       6     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 256.8 bits;  conditional E-value: 9.9e-80
                           BacA   2 iilGivqGltefLPvSSsGhlilveellglekedlllfdvvihlGtllAvlvlfrkdilrllkgllkslkkkkkekeelr 81 
                                    i+l+  qGltefLPvSSsGhl++v++++ ++ ++ + f++v +lGt +Av+++f +di+r+l ++l+ l  k+++++++r
  gi|121638018|ref|YP_978242.1|   7 IVLAAAQGLTEFLPVSSSGHLAIVSRIF-FSGDAGASFTAVSQLGTEAAVVIYFARDIVRILSAWLHGLVVKAHRNTDYR 85 
                                    89*************************9.55333467******************************************* PP

                           BacA  82 lllliivatipaailglllkdlieellrsplvvaialivtglllllaeklrkkkkksledltlkdalliGlaQalAllPG 161
                                    l +++i++tip++ilgl++kd i++ +r+++vv++al+v++ ++ lae +  ++++++e+lt++da+++G+aQ+lAl+PG
  gi|121638018|ref|YP_978242.1|  86 LGWYVIIGTIPICILGLFFKDDIRSGVRNLWVVVTALVVFSGVIALAEYVG-RQSRHIERLTWRDAVVVGIAQTLALVPG 164
                                    ************************************************664.5777778********************* PP

                           BacA 162 vSRSGaTivaglllglsreaaaefSFllaiPailgagllkllksa....ealtasellllvgfvvafvvallaikfllkl 237
                                    vSRSG+Ti+agl+lgl+re aa+f FllaiPa++++gl++l ++     e ++a+  +llv++++afv +l a+++ll++
  gi|121638018|ref|YP_978242.1| 165 VSRSGSTISAGLFLGLDRELAARFGFLLAIPAVFASGLFSLPDAFhpvtEGMSATGPQLLVATLIAFVLGLTAVAWLLRF 244
                                    ****************************************554443334444444444499******************* PP

                           BacA 238 lkkkklkvFaiYrivlGl 255
                                    l ++++++F+ Yr+++G 
  gi|121638018|ref|YP_978242.1| 245 LVRHNMYWFVGYRVLVGT 262
                                    ****************95 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.036     125     184 ..     127     186 ..     119     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                 DNA_processg_A 125 gglllseyppgtkpkkenFpeRnriiaglseavlvveaaekSGalitaelAlelgrevfa 184
                                    g + l+ey  ++  + e+++ R+ +++g+++++ +v   ++SG+ i+a l l l+re+ a
  gi|121638018|ref|YP_978242.1| 127 GVIALAEYVGRQSRHIERLTWRDAVVVGIAQTLALVPGVSRSGSTISAGLFLGLDRELAA 186
                                    557799**********************************************99999887 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.7e-05      0.22      15      75 ..      81     141 ..      72     161 .. 0.84
   2 ?   -2.5   0.5       1.8   4.6e+03      20      42 ..     228     250 ..     222     272 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                        DUF3290  15 ndllryililvlllllivvlilylrnrldtkyRdLsiilllllllllgiqysdyqqsqsas 75 
                                    n+  r++  +++  + i++l l++++ +++ +R+L +++  l+++   i + +y   qs++
  gi|121638018|ref|YP_978242.1|  81 NTDYRLGWYVIIGTIPICILGLFFKDDIRSGVRNLWVVVTALVVFSGVIALAEYVGRQSRH 141
                                    4445666777777888888999********************************9988876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                        DUF3290  20 yililvlllllivvlilylrnrl 42 
                                    +i +++ l +++++l + +r+++
  gi|121638018|ref|YP_978242.1| 228 LIAFVLGLTAVAWLLRFLVRHNM 250
                                    44444555555556666666654 PP

>> DUF2474  Protein of unknown function (DUF2474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.13   3.4e+02       6      15 ..      85      94 ..      82     103 .. 0.77
   2 ?    9.2   2.9   0.00042       1.1      17      32 ..     231     246 ..     224     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                        DUF2474  6 RlgWLvlIWa 15
                                   RlgW v+I +
  gi|121638018|ref|YP_978242.1| 85 RLGWYVIIGT 94
                                   9******965 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00042
                        DUF2474  17 SVlaLgvvAlllRllM 32 
                                     Vl L +vA+llR+l 
  gi|121638018|ref|YP_978242.1| 231 FVLGLTAVAWLLRFLV 246
                                    59***********996 PP

>> DUF4491  Domain of unknown function (DUF4491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   6.8e-05      0.17      16      61 ..      69     114 ..      60     147 .. 0.83
   2 ?   -0.6   0.2      0.74   1.9e+03       9      45 ..     122     158 ..     115     174 .. 0.60
   3 ?   -1.0   0.5      0.99   2.5e+03      12      30 ..     235     253 ..     219     275 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                        DUF4491  16 glfhpivikaeyylgkkiwwvflvagillivaslfvenvllsavlg 61 
                                     ++h +v+ka+  +  ++ w+ ++  i ++++ lf ++ + s v  
  gi|121638018|ref|YP_978242.1|  69 AWLHGLVVKAHRNTDYRLGWYVIIGTIPICILGLFFKDDIRSGVRN 114
                                    589***********************************99998754 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.74
                        DUF4491   9 iatfliiglfhpivikaeyylgkkiwwvflvagilli 45 
                                    +++f  +  +   v ++  ++ + +w+  +v+gi+ +
  gi|121638018|ref|YP_978242.1| 122 LVVFSGVIALAEYVGRQSRHIERLTWRDAVVVGIAQT 158
                                    4444444444444555555555556666777777655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.99
                        DUF4491  12 fliiglfhpivikaeyylg 30 
                                    +  + ++  ++++ ++y+ 
  gi|121638018|ref|YP_978242.1| 235 LTAVAWLLRFLVRHNMYWF 253
                                    3344444445567776662 PP

>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.71   1.8e+03      18      27 ..      71      80 ..      70      87 .. 0.82
   2 ?    8.7   0.1   0.00059       1.5      10      24 ..      91     105 ..      88     106 .. 0.90
   3 ?   -3.6   0.2       4.2   1.1e+04      19      23 ..     174     178 ..     173     180 .. 0.55
   4 ?   -0.5   0.1      0.45   1.2e+03       9      17 ..     231     239 ..     226     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.71
                           PetG 18 laGLFvaAYl 27
                                   l GL v+A +
  gi|121638018|ref|YP_978242.1| 71 LHGLVVKAHR 80
                                   6799999975 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00059
                           PetG  10 VLGLvpVTlaGLFva 24 
                                    ++G +p+ ++GLF++
  gi|121638018|ref|YP_978242.1|  91 IIGTIPICILGLFFK 105
                                    689**********96 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                           PetG  19 aGLFv 23 
                                    aGLF 
  gi|121638018|ref|YP_978242.1| 174 AGLFL 178
                                    46653 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.45
                           PetG   9 iVLGLvpVT 17 
                                     VLGL +V 
  gi|121638018|ref|YP_978242.1| 231 FVLGLTAVA 239
                                    699998885 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.13   3.5e+02      35      51 ..     102     126 ..      86     164 .. 0.72
   2 ?    6.4   6.5     0.004        10      14      64 ..     176     253 ..     173     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                          VirB3  35 l........vglslwillllvplhl 51 
                                    l         +++lw+++++++++ 
  gi|121638018|ref|YP_978242.1| 102 LffkddirsGVRNLWVVVTALVVFS 126
                                    1347777777788888877665544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.004
                          VirB3  14 mllGvplelvllnllvsvilfl...........................vglslwillllvplhlvlrliakrDpqmf 64 
                                    ++lG+++el++  +++ +i+++                           v+  ++++l l ++ ++lr+++++ +  f
  gi|121638018|ref|YP_978242.1| 176 LFLGLDRELAARFGFLLAIPAVfasglfslpdafhpvtegmsatgpqllVATLIAFVLGLTAVAWLLRFLVRHNMYWF 253
                                    79********************99999999999999999999999999888888888888899999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1990.56
//
Query:       gi|121638019|ref|YP_978243.1|  [L=137]
Description: hypothetical protein BCG_2154c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 943.35
//
Query:       gi|121638020|ref|YP_978244.1|  [L=358]
Description: lipoprotein LppL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.4   0.1       0.24   10.9   0.0    2.9  3  SGL       SMP-30/Gluconolactonase/LRE-like region
    0.00016   21.6   0.0       0.82    9.8   0.0    3.9  3  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0019        17      23     103 ..      94     171 ..      90     175 .. 0.79
   2 !    5.4   0.1    0.0013        12      34     112 ..     146     235 ..     137     260 .. 0.72
   3 !   10.9   0.0   2.7e-05      0.24     197     245 ..     294     343 ..     282     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0019
                            SGL  23 rihrldpatgketvldtpesvGaiaprkdgrlvvasksglalldlasgeletladeeedekpllrfNDgvvdpdGrlwfG 102
                                    +i+ +d++  + +v+ +p+++ a++  ++g+  +a+++g ++ dl+sg    +     d  + + f  ++  +dG+l+ G
  gi|121638020|ref|YP_978244.1|  94 SIMVFDDVHVAPRVIFLPGPAAALTSDDHGTAFLAARGGYFVADLSSGHTARVNVA--DA-AHTDFTAIARRSDGKLVLG 170
                                    57777888888888999999999999555999999999*9999*999865554443..45.7888888888888888888 PP

                            SGL 103 t 103
                                    +
  gi|121638020|ref|YP_978244.1| 171 S 171
                                    7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0013
                            SGL  34 etvldtpe.svGaiaprkdgrlvvasksglall.......dlasgeletladeee....dekpllrfNDgvvdpdGrlwf 101
                                     +v+d+     +aia+r dg+lv++s++g +++       d+asg+ ++  +  +     +   ++ N  vv ++G+  +
  gi|121638020|ref|YP_978244.1| 146 VNVADAAHtDFTAIARRSDGKLVLGSADGAVYTlaknpavDPASGAATVASRT-KifarVDALVTQGNTTVVLDRGQTSV 224
                                    4555655567899999999**********988877655555777755444443.22333444889999999999999999 PP

                            SGL 102 Gtmgdeeakge 112
                                    +t g + ++++
  gi|121638020|ref|YP_978244.1| 225 TTIGADGHAQQ 235
                                    98888877666 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 2.7e-05
                            SGL 197 vwvAvwgggkvvrfdpd.Gklieeiklp.akrvtscaFgGpdlrtLyitsa 245
                                     wv + ++++v+ +d   G  +e+++ p ++++ s+aF  +  +tLy++s 
  gi|121638020|ref|YP_978244.1| 294 AWVSQTASNTVIGYDLTtGIPVEKVRYPtVQQPNSLAF-DETSDTLYVVSG 343
                                    59**************99**********777*******.6888*****996 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0057        51       5      23 ..     122     142 ..     122     148 .. 0.86
   2 !    9.8   0.0   9.1e-05      0.82       7      28 .]     246     267 ..     241     267 .. 0.87
   3 ?    2.9   0.0     0.015   1.3e+02       2      17 ..     324     340 ..     323     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0057
                                    EEEEEE.TTTEEEEEE.CCCT CS
                            NHL   5 hGvavd.snGdiyVaD.senh 23 
                                    hG+a +   G  +VaD s  h
  gi|121638020|ref|YP_978244.1| 122 HGTAFLaARGGYFVADlSSGH 142
                                    8999999*********96555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.1e-05
                                    EEEETTTEEEEEECCCTEEEEE CS
                            NHL   7 vavdsnGdiyVaDsenhrvqvF 28 
                                     a+d+ G++++aD++  ++ v+
  gi|121638020|ref|YP_978244.1| 246 MAADPLGRVLIADTRGGQLLVY 267
                                    799**********999999887 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.015
                                    SSEEEEEEE.TTTEEEE CS
                            NHL   2 nyPhGvavd.snGdiyV 17 
                                    ++P+++a d +++ +yV
  gi|121638020|ref|YP_978244.1| 324 QQPNSLAFDeTSDTLYV 340
                                    69**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3026.84
//
Query:       gi|121638021|ref|YP_978245.1|  [L=357]
Description: dihydroorotate dehydrogenase 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-99  332.6   0.0    2.2e-99  332.4   0.0    1.0  1  DHO_dh    Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.4   0.0  1.2e-103   2.2e-99       2     295 .]      49     336 ..      48     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 332.4 bits;  conditional E-value: 1.2e-103
                                    G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHH CS
                         DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavl 81 
                                    la++v+g++f+ p+glAaGfdk+g++++++ ++gfg++eig+vt++pq+Gnp+Pr+frl+ dr++lN++G+nn+G+ a++
  gi|121638021|ref|YP_978245.1|  49 LASTVFGVRFPAPLGLAAGFDKDGTALSSWGAMGFGYAEIGTVTAHPQPGNPAPRLFRLADDRALLNRMGFNNHGARALA 128
                                    899***************************************************************************** PP

                                    HHHHHHHHHHHCC.CEEEEEEE-TTS..S.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHHHHHHHH CS
                         DHO_dh  82 ekllkrrkeqeekkelginlskakkt..enavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkaillkvvke 159
                                     +l+++r e    + +g+n++k+kkt  ++av+dy++++r +gp+a++l++NvSsPntpglrdlq+ e+l+ il++v +e
  gi|121638021|ref|YP_978245.1| 129 IRLARHRPE----IPIGVNIGKTKKTpaGDAVNDYRASARMVGPLASYLVVNVSSPNTPGLRDLQAVESLRPILSAVRAE 204
                                    *****9988....459**********999*******************************************99999999 PP

                                    HHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHH CS
                         DHO_dh 160 vskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelyk 239
                                    +s  pvlvK+aPdl+d++ +diad+++el l+gi++tNttv+r+   l + + v++ + GG+sG++l ++a++v+r+ly+
  gi|121638021|ref|YP_978245.1| 205 TS-TPVLVKIAPDLSDSDLDDIADLAVELDLAGIVATNTTVSRD--GLTT-PGVDRLGPGGISGPPLAQRAVQVLRRLYD 280
                                    88.9****************************************..5555.7788889********************** PP

                                    HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                         DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                    r+ +++ +I+vGGie+++Da+e+i+aGAsl+q yt++++ g  +ak+i+++++++L
  gi|121638021|ref|YP_978245.1| 281 RVGDRLALISVGGIETADDAWERITAGASLLQGYTGFIYGGERWAKDIHEGIARRL 336
                                    ****************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2989.28
//
Query:       gi|121638022|ref|YP_978246.1|  [L=176]
Description: hypothetical protein BCG_2157c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-34  117.8   0.0    4.7e-34  117.6   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0   2.6e-38   4.7e-34       7     132 .]      42     173 ..      25     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 2.6e-38
                                    CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC..........EE-B-TTSSCCCCS CS
                            PBP   7 egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega..........vqgknslgeesesg 76 
                                    +g + sP+l+ws++p++t+s+a++v+DpDap+ s+ f+Hw v+n+pa+vt+lpeg             + n++g      
  gi|121638022|ref|YP_978246.1|  42 GGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSG-FWHWAVANLPANVTELPEGVgdgrelpggaLTLVNDAGM---RR 117
                                    68899**************************9999.******************998899998888889999998...9* PP

                                    ---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                            PBP  77 YlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                    Y+g++Pp+g+g HrY++ ++a++ve+ldl+++++ a lg+++ +h++a+a++ g+Y
  gi|121638022|ref|YP_978246.1| 118 YVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTY 173
                                    *****************************************999**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1356.60
//
Query:       gi|121638023|ref|YP_978247.1|  [L=448]
Description: hypothetical protein BCG_2158c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-38  132.6   0.9    2.5e-36  125.3   0.2    2.9  2  Peptidase_M20  Peptidase family M20/M25/M40
    8.9e-16   57.8   0.0    1.6e-15   56.9   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
    2.5e-10   40.4   0.1    1.3e-08   34.7   0.1    2.7  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.032   1.9e+02     117     159 ..      23      66 ..       4      77 .. 0.80
   2 !  125.3   0.2   4.3e-40   2.5e-36       1     206 [.      85     446 ..      85     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.032
                                    EEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.SS CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                  Peptidase_M20 117 vevelleggapvtln.dsplvkalaeaaeelfgekvelivsg.pg 159
                                    ++++   +g+p t++ ++++++++ae + e+ g+++e + sg pg
  gi|121638023|ref|YP_978247.1|  23 IRFDTTNSGEPGTTKgEAECARWVAEQLAEV-GYQPEYVESGaPG 66 
                                    55666689999999999*************9.*999888888544 PP

  == domain 2  score: 125.3 bits;  conditional E-value: 4.3e-40
                                    EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                  Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGa 78 
                                    l+++HlDvVp+e+  +w+  pfs+ +edG+++GrGa+dmk +v +++ ++r+l+++ i p++++v++f++dEE g+  G+
  gi|121638023|ref|YP_978247.1|  85 LIHGHLDVVPAEPA-EWSVhPFSGAIEDGYVWGRGAVDMKDMVGMMIVVARHLRQAAIVPPRDLVFAFVADEEHGGkYGS 163
                                    689*******4444.7*********************************************************6556*** PP

                                    HHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE........................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                  Peptidase_M20  79 kallegleerekvdavfelhieepgileagklaigvv........................................... 115
                                     +l++      ++d + ++   e  i e g+++ +v                                            
  gi|121638023|ref|YP_978247.1| 164 HWLVD-----NRPDLFDGI--TEA-IGEVGGFSLTVPrhdggerrlylietaekgiqwmrltargraghgsmvhdqnavt 235
                                    *****.....466665543..333.3333666666667888999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Peptidase_M20 116 ................................................................................ 115
                                                                                                                    
  gi|121638023|ref|YP_978247.1| 236 avceavarlgrhqfplvctdtvaqflavvgeetglafdldspdlagtidklgpmarmlkavlhdtanptmlkagykanvv 315
                                    9999999999********************************************************************** PP

                                    ..............................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHH..TSCEEEEEESSSBHT CS
                                    ..............................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                  Peptidase_M20 116 ..............................kvevelleggapvtln.dsplvkalaeaaeelf..gekvelivsgpggtd 162
                                                                  +v+ e++++ +++++  d++lv+a+ +a+ ++   g ++ +++ + ggtd
  gi|121638023|ref|YP_978247.1| 316 pataeavvdcrvlpgrraafeaevdaligpDVTREWVSDLPSYETTfDGDLVAAMNAAVLAVDpdG-RTVPYMLS-GGTD 393
                                    *****************************88******99999999999*************98744.56777888.9*** PP

                                    HHHH..TTTEEEEE..EE.SSG....GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                    xxxx..xxxxxxxx..xx.xxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 163 arff..agiptvmi..fg.pgs....glaHspnEyvdledlekgikvlarlle 206
                                    a+ f  +gi ++ +  +  p +    +l H+++E+v ++ l+ g++vl++ll 
  gi|121638023|ref|YP_978247.1| 394 AKAFarLGIRCFGFspLRlPPDldftSLFHGVDERVPIDGLRFGTEVLTHLLT 446
                                    ****8888899966696666644599************************986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   2.7e-19   1.6e-15       1      90 [.     206     333 ..     206     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.7e-19
                                    SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.................................. CS
                      M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia................................ 48 
                                    +++kG+ ++++t++g+agH+++ ++  NA+++ ++++a+l  ++++                                  
  gi|121638023|ref|YP_978247.1| 206 TAEKGIQWMRLTARGRAGHGSMVHDQ-NAVTAVCEAVARLGRHQFPLVctdtvaqflavvgeetglafdldspdlagtid 284
                                    589******************99998.9******************99******************************** PP

                                    ..........TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHH CS
                      M20_dimer  49 .......eerslprttlnvtgiegGsaknvipdeaeakidiRllpgedp 90 
                                             + + + t n+t++++G+++nv+p++aea +d+R+lpg  +
  gi|121638023|ref|YP_978247.1| 285 klgpmarMLKAVLHDTANPTMLKAGYKANVVPATAEAVVDCRVLPGRRA 333
                                    *********************************************8654 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   2.3e-12   1.3e-08       1      85 [.      69     169 ..      69     180 .. 0.89
   2 ?    2.7   0.0     0.015        90     137     173 ..     378     423 ..     230     430 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.3e-12
                                    EEEEEESTTCE.SEEEEEEEE--B-TTT..............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEE CS
                  Peptidase_M28   1 Nviatlegkat.devlllgAHyDsvgvg..............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvr 64 
                                    Nv a+l g ++    ll+ +H+D v+ +              +g     GA D   +v++++ +ar l +    p r+++
  gi|121638023|ref|YP_978247.1|  69 NVFARLAGADSsRGALLIHGHLDVVPAEpaewsvhpfsgaieDGYvWGRGAVDMKDMVGMMIVVARHLRQAAIVPPRDLV 148
                                    9*****99999455************9999**99999888764446677*********************999******* PP

                                    EEEESSCSG.SSHHHHHHHHHH CS
                  Peptidase_M28  65 flffdaEEa.gllGSkafakak 85 
                                    f+f+  EE  g +GS+ ++ ++
  gi|121638023|ref|YP_978247.1| 149 FAFVADEEHgGKYGSHWLV-DN 169
                                    *********99*****999.44 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.015
                                    CEEEEES...STT-STTHHHHTTT--EEEE......CTSSS-TTTT CS
                  Peptidase_M28 137 dpfders...grgrsDhspflkagvpvldl......aetgfpevyH 173
                                    dp  +++     g +D+ +f++ g+ +  +      ++ +f++ +H
  gi|121638023|ref|YP_978247.1| 378 DPDGRTVpymLSGGTDAKAFARLGIRCFGFsplrlpPDLDFTSLFH 423
                                    3333333323566789999999999888886666665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3344.81
//
Query:       gi|121638024|ref|YP_978248.1|  [L=105]
Description: hypothetical protein BCG_2159c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-10   41.2   0.5    2.2e-10   41.0   0.5    1.1  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.5   1.3e-14   2.2e-10       1      90 []       5      92 ..       5      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.3e-14
                                   EEEEHHHHHHHHHHHHHHH.CC-H....HHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEEC..TEEEEEEEETST CS
                     ParE_toxin  1 vrltprAlkdlkkiadyia.rdgp....aakrfldaleealellaenpalgrprrelglkglrririg..dyriiYriddee 75
                                   +r+++ +++dl ++++y+a ++++      + f+da+++++ + ++++a+  +       ++r i ++  +y + Yr  ++ 
  gi|121638024|ref|YP_978248.1|  5 LRVHNGVEDDLFEAFSYYAdAAPDqidrLYNLFVDAVTKRIPQAPNAFAPLFK-------HYRHIYLRpfRYYVAYRT-TD- 77
                                   6899***************9999546633667777777777777777777666.......777777777799999995.45. PP

                                   TEEEEEEEEEHHHHC CS
                     ParE_toxin 76 lvvvilrvlhrsedy 90
                                   ++++il+v+h++e++
  gi|121638024|ref|YP_978248.1| 78 EAIDILAVRHGMENP 92
                                   5555*******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 834.43
//
Query:       gi|121638025|ref|YP_978249.1|  [L=352]
Description: hypothetical protein BCG_2160 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-23   81.8   0.0    3.7e-22   78.5   0.0    2.0  1  Pribosyltran  Phosphoribosyl transferase domain
    2.8e-05   23.7   0.1      4e-05   23.1   0.1    1.2  1  UPRTase       Uracil phosphoribosyltransferase
     0.0002   20.9   0.0     0.0055   16.2   0.0    2.3  2  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   6.2e-26   3.7e-22      14     158 ..     144     331 ..     138     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 6.2e-26
                                    EEEETTEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..................... CS
                   Pribosyltran  14 avarlaaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............. 79 
                                    ++ r +a+ l +  ++ + +v+g argGvp++ ++a++L+++l++ +++k   ++  e a g+ ++              
  gi|121638025|ref|YP_978249.1| 144 DAGRVLADELASyRGRDRLLVLGLARGGVPVGWEVASALGAELDVFLVRKLGVPQWRELAMGALASGggvvmnddvvssl 223
                                    34455555555515666779***********************************999999888777************* PP

                                    ............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                   Pribosyltran  80 ............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpatee 131
                                                                r+  dp+ ++V++VDD+++tG ++laa++ +++ gpe++ +av+v + +  +
  gi|121638025|ref|YP_978249.1| 224 ritdqqvraaidsetaelqrrelayrggRPVVDPRARIVILVDDGIATGASMLAAVRTIRATGPESIVVAVPVGPATACR 303
                                    ******************************************************************************** PP

                                    HHHHH-TTS......EEEEEEE-SEE-T CS
                   Pribosyltran 132 evdknakrvfsls.pdnfvavvgfelds 158
                                    e  ++a+ v++ + p +f+av +++ d+
  gi|121638025|ref|YP_978249.1| 304 ELAAEADDVVCATmPAAFEAVGQVYNDF 331
                                    ************************9887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   6.8e-09     4e-05     120     178 ..     258     314 ..     211     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.8e-09
                        UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkv 178
                                    ++r v+l+D  iaTG+s+ aa+++++    g e+I+v+  +  + ++++la+e  +v  
  gi|121638025|ref|YP_978249.1| 258 RARIVILVDDGIATGASMLAAVRTIRA--TGPESIVVAVPVGPATACRELAAEADDVVC 314
                                    6678***********************..67899****999999999999999998865 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.019   1.1e+02      32      77 ..     142     184 ..     132     193 .. 0.82
   2 !   16.2   0.0   9.2e-07    0.0055     121     156 ..     259     294 ..     245     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.019
                       PRTase_2  32 vreagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadalee 77 
                                     r+ag+ La++la   + + ++++lv+g+A   + +g  va+al +
  gi|121638025|ref|YP_978249.1| 142 RRDAGRVLADELA---SYRGRDRLLVLGLARGGVPVGWEVASALGA 184
                                    6789999999999...5567999*****************999843 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 9.2e-07
                       PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvv 156
                                    a+ ++LvDD i+tG ++l+ +r+++++ p++ +v v
  gi|121638025|ref|YP_978249.1| 259 ARIVILVDDGIATGASMLAAVRTIRATGPESIVVAV 294
                                    67899**********************999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2504.16
//
Query:       gi|121638026|ref|YP_978250.1|  [L=118]
Description: hypothetical protein BCG_2161c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.014   15.7   4.6      0.019   15.3   4.6    1.1  1  DUF308           Short repeat of unknown function (DUF308)
       0.39    9.4   1.6       0.47    9.2   1.6    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.44   10.6   9.9       0.59   10.2   9.9    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        7.9    6.6   5.7        4.3    7.5   0.2    2.3  2  CrgA             Cell division protein CrgA


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   4.6   4.2e-06     0.019       1      50 [.       3      53 ..       3      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                         DUF308  1 llGillivlGilalllPvaallalvllfGilllvsGivqii.aafaarkkn 50
                                   +++++l+++G+lal++ v+++  lv ++ i + v G++ +i  a++ r+++
  gi|121638026|ref|YP_978250.1|  3 IIALVLALIGLLALVFAVVTSNQLVAWVCIGASVLGVALLIvDALRERQQG 53
                                   57899*******************************999963777555544 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.6   0.00011      0.47     388     445 ..       3      58 ..       1      62 [. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                        DUF2207 388 lgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGaell 445
                                    +++++l+li++l++++++v+ + + ++++++  +++  v+ll+   l+ r + Ga+++
  gi|121638026|ref|YP_978250.1|   3 IIALVLALIGLLALVFAVVTSNQLVAWVCIGASVLG--VALLIVDALRERQQGGADEA 58 
                                    455555555555555555543444444444444443..33333467777788888776 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   9.9   0.00013      0.59      39      79 ..       1      44 [.       1      55 [. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                Phage_holin_3_6 39 llgaagvlallalllllvalalala.a..lwlaalivaavllvl 79
                                   +l++a+vlal++ll+l++a++   + +    ++a +++++ll++
  gi|121638026|ref|YP_978250.1|  1 MLIIALVLALIGLLALVFAVVTSNQlVawVCIGASVLGVALLIV 44
                                   7899****************944432211233444444444444 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.0     0.036   1.6e+02      36      58 ..       3      25 ..       1      27 [. 0.83
   2 ?    7.5   0.2   0.00095       4.3      29      57 ..      22      50 ..      19      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.036
                           CrgA 36 pvmlglmllGllwlvvyYlagee 58
                                   ++ l l l+Gll lv   +++++
  gi|121638026|ref|YP_978250.1|  3 IIALVLALIGLLALVFAVVTSNQ 25
                                   5778999*******999988876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00095
                           CrgA 29 psprwyvpvmlglmllGllwlvvyYlage 57
                                   +s++++++v +g  +lG++ l+v  l + 
  gi|121638026|ref|YP_978250.1| 22 TSNQLVAWVCIGASVLGVALLIVDALRER 50
                                   57899******************888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 838.59
//
Query:       gi|121638027|ref|YP_978251.1|  [L=260]
Description: hypothetical protein BCG_2162c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-20   73.3  22.0    3.3e-12   46.6   0.0    3.2  3  DivIVA          DivIVA protein
    0.00079   19.4  25.5     0.0009   19.2  21.8    2.1  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.025   15.2   8.5      0.025   15.2   8.5    3.4  5  DUF883          Bacterial protein of unknown function (DUF883
      0.041   13.8  21.1       0.76    9.6  10.9    3.2  3  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
      0.099   12.8   3.2       0.64   10.2   0.0    3.1  4  Cnn_1N          Centrosomin N-terminal motif 1
       0.17   11.8   2.8       0.41   10.6   2.8    1.6  1  Shugoshin_N     Shugoshin N-terminal coiled-coil region
       0.24   11.5  11.1          3    7.9   8.5    2.4  2  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.48   10.4   4.6       0.86    9.6   0.9    3.0  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
        1.2    8.4  15.6        1.9    7.7  15.6    1.4  1  DUF4407         Domain of unknown function (DUF4407)
        2.8    8.0   9.2        3.7    7.6   6.8    2.1  2  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
        3.8    7.6  28.0        0.5   10.5  18.4    2.4  2  ATP-synt_B      ATP synthase B/B' CF(0)


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0     2e-15   3.3e-12       1      56 [.       3      61 ..       3      63 .. 0.94
   2 !   17.3   7.3   2.3e-06    0.0037      62     116 ..      98     154 ..      89     161 .. 0.82
   3 !   12.6   9.3   6.5e-05      0.11      57     131 .]     153     224 ..     145     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2e-15
                                   --HHHHHH----EEE...EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXX CS
                         DivIVA  1 ltplDIknkeFkkkl...rGYdedeVdeFLdqvakdyeallkeneelkekvkeleeklk 56
                                   ltp D++n  F+k     rGY+edeVd+FLd v +++ +l++en++l+++++el+++l+
  gi|121638027|ref|YP_978251.1|  3 LTPADVHNVAFSKPPigkRGYNEDEVDAFLDLVENELTRLIEENSDLRQRINELDQELA 61
                                   79**********9776669*************************************997 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.3e-06
                                    XXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  62 eetLk..ktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeei 116
                                    e++Lk  + l +aq+ta++++++ak+e++ ++++A+++ae+i+ ea++ a+   +e 
  gi|121638027|ref|YP_978251.1|  98 EQALKaaRVLSLAQDTADRLTNTAKAESDKMLADARANAEQILGEARHTADATVAEA 154
                                    555551145779**********************************99998877665 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  57 eykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqarlfrqrlk 131
                                    e +++ ++   +l  aq+ +e   ++a+++a+ + ++Ae k ++i+ + +++ + ++ ++e+l+  +r +r+rlk
  gi|121638027|ref|YP_978251.1| 153 EARQRADA---MLADAQSRSEAQLRQAQEKADALQADAERKHSEIMGTINQQRAVLEGRLEQLRTFEREYRTRLK 224
                                    34444443...6777888888888888888888888888888888888888888888888888888888888875 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.14   2.2e+02      30     176 ..      41      55 ..      24      67 .. 0.44
   2 !   19.2  21.8   5.5e-07    0.0009      18     140 ..     104     237 ..      95     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHH CS
                 Apolipoprotein  30 rlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerle 109
                                    rl +e  +lr+r++                                                                  
  gi|121638027|ref|YP_978251.1|  41 RLIEENSDLRQRIN------------------------------------------------------------------ 54 
                                    22222222222221.................................................................. PP

                                    HHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHHS--X CS
                 Apolipoprotein 110 rhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqaeelrerlea 176
                                                                                                      +
  gi|121638027|ref|YP_978251.1|  55 ------------------------------------------------------------------E 55 
                                    ..................................................................1 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 5.5e-07
                                    HCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCH CS
                 Apolipoprotein  18 eqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeql 97 
                                    +++ +laq+++drl++ +++ ++++   l ++ra+ e+ + e++++  +++ e rqr ++ + + + r +a+++++qe+ 
  gi|121638027|ref|YP_978251.1| 104 ARVLSLAQDTADRLTNTAKAESDKM---LADARANAEQILGEARHTADATVAEARQRADAMLADAQSRSEAQLRQAQEKA 180
                                    4677789999999999999888888...***************************************************9 PP

                                    CCHCHH..............HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH- CS
                 Apolipoprotein  98 avyaee..............lrerlerhvealkarlapyveelrqklaerleelkes 140
                                    ++ +++               r  le ++e+l++   +y+ +l++ l+++leel+++
  gi|121638027|ref|YP_978251.1| 181 DALQADaerkhseimgtinqQRAVLEGRLEQLRTFEREYRTRLKTYLESQLEELGQR 237
                                    999999455555555554444444444466666666666666667777777777665 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.1   5.1e+03      28      37 ..      45      54 ..      28      67 .. 0.56
   2 ?   15.2   8.5   1.5e-05     0.025      11      66 ..     111     166 ..     101     168 .. 0.91
   3 ?   11.4  14.4   0.00023      0.37       7      67 ..     129     189 ..     122     194 .. 0.92
   4 ?    3.4   3.4     0.073   1.2e+02      31      63 ..     164     196 ..     161     205 .. 0.82
   5 ?    0.7   0.1      0.51   8.3e+02       7      46 ..     198     237 ..     192     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                         DUF883 28 eaeelRerle 37
                                   e ++lR+r++
  gi|121638027|ref|YP_978251.1| 45 ENSDLRQRIN 54
                                   2333333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                         DUF883  11 ladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                     ++++ l+++a++e+++ ++++R+++e+ l +ar++++++  ++++ra+++ ++a+
  gi|121638027|ref|YP_978251.1| 111 QDTADRLTNTAKAESDKMLADARANAEQILGEARHTADATVAEARQRADAMLADAQ 166
                                    578899********************************************999887 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00023
                         DUF883   7 leslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                    l++++a++e++l ea  +a+ +++e+R+r++++l++a++r +++ ++++e+a++  ++a++
  gi|121638027|ref|YP_978251.1| 129 LADARANAEQILGEARHTADATVAEARQRADAMLADAQSRSEAQLRQAQEKADALQADAER 189
                                    678999***********************************************99998875 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.073
                         DUF883  31 elRerleerlerarerlrdaeeavaerakeaae 63 
                                    ++ +r e++l++a+e++++++ +++++ +e++ 
  gi|121638027|ref|YP_978251.1| 164 DAQSRSEAQLRQAQEKADALQADAERKHSEIMG 196
                                    677888999999999999999999999888765 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.51
                         DUF883   7 leslladleellkeaadeageeaeelRerleerlerarer 46 
                                    +++ +a le  l++     +e+  +l+  le++le++ +r
  gi|121638027|ref|YP_978251.1| 198 INQQRAVLEGRLEQLRTFEREYRTRLKTYLESQLEELGQR 237
                                    5555555666666666666666666666666666665444 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.29   4.8e+02      87     126 ..      23      63 ..      19      74 .. 0.80
   2 ?    8.7   4.0   0.00091       1.5      29      60 ..     122     153 ..     100     156 .. 0.82
   3 ?    9.6  10.9   0.00047      0.76      32      89 ..     147     207 ..     145     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.29
                           HrpE  87 leeqlltaveqLLsdalarlLde.tplaeRasALlRqLlks 126
                                    ++e+ + a  +L+++ l+rl++e  +l +R++ L  +L+++
  gi|121638027|ref|YP_978251.1|  23 YNEDEVDAFLDLVENELTRLIEEnSDLRQRINELDQELAAG 63 
                                    5667777788899999***9986257899999999888765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00091
                           HrpE  29 slrarellaeArlqAeqllaqarekaeellev 60 
                                    +  ++++la+Ar  Aeq+l +ar+ a+  ++ 
  gi|121638027|ref|YP_978251.1| 122 KAESDKMLADARANAEQILGEARHTADATVAE 153
                                    456789*****************999988774 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00047
                           HrpE  32 arellaeArlqAeqllaqarekaeellevaveqAea...qFWeqAnalLrglqqeRealee 89 
                                    a++ +aeAr+ A+++la+a+ + e  l +a e+A a      ++  ++++ ++q+R+ le 
  gi|121638027|ref|YP_978251.1| 147 ADATVAEARQRADAMLADAQSRSEAQLRQAQEKADAlqaDAERKHSEIMGTINQQRAVLEG 207
                                    6778899999999999999999999999898887641113456677899999999998875 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00039      0.64       6      34 ..      36      64 ..      35      77 .. 0.82
   2 ?   -0.1   0.7      0.66   1.1e+03      35      57 ..     163     185 ..     114     197 .. 0.62
   3 ?   -0.8   1.1       1.1   1.8e+03      34      62 ..     181     208 ..     165     226 .. 0.48
   4 ?    0.4   0.1      0.46   7.6e+02      25      35 ..     226     236 ..     193     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                         Cnn_1N  6 eeqidkLkKENFdLKLriyfLeerlekls 34
                                   e+++ +L  EN dL+ ri++L+++l +++
  gi|121638027|ref|YP_978251.1| 36 ENELTRLIEENSDLRQRINELDQELAAGG 64
                                   78899999999999999999999998766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.66
                         Cnn_1N  35 eeqkeellkenielkveveslqk 57 
                                     + +   ++++ + +++   lq 
  gi|121638027|ref|YP_978251.1| 163 ADAQSRSEAQLRQAQEKADALQA 185
                                    33333333333444444444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                         Cnn_1N  34 seeqkeellkenielkveveslqkelkek 62 
                                    +   + +++++  e+  ++ + +  l+ +
  gi|121638027|ref|YP_978251.1| 181 DA-LQADAERKHSEIMGTINQQRAVLEGR 208
                                    33.33333333333333333333333333 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.46
                         Cnn_1N  25 fLeerleklse 35 
                                    +Le++le+l++
  gi|121638027|ref|YP_978251.1| 226 YLESQLEELGQ 236
                                    34444444444 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.8   0.00025      0.41      27      44 ..      36      53 ..      34      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                    Shugoshin_N 27 ekevseLlsENlnLReli 44
                                   e+e+++L+ EN +LR++i
  gi|121638027|ref|YP_978251.1| 36 ENELTRLIEENSDLRQRI 53
                                   9***************98 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.037        60      98     133 ..      25      60 ..       9      63 .. 0.77
   2 ?    7.9   8.5    0.0018         3      87     176 ..     125     216 ..      90     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.037
                        UPF0242  98 eeeLkeeldakeeelerlkeenqqLqekleaiaedf 133
                                    e+e    ld  e+el rl een  L+++ ++  ++ 
  gi|121638027|ref|YP_978251.1|  25 EDEVDAFLDLVENELTRLIEENSDLRQRINELDQEL 60 
                                    556666688889999999999999998888777665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                        UPF0242  87 keealeelqeeeee.LkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqL.aekqellqeyqetieeqrsv 164
                                     ++ l +++++ e+ L e     + ++++ +++   +   ++  +e   ++ +e  ++L a  + +++e   ti++qr+v
  gi|121638027|ref|YP_978251.1| 125 SDKMLADARANAEQiLGEARHTADATVAEARQRADAMLADAQSRSEAQLRQAQEKADALqADAERKHSEIMGTINQQRAV 204
                                    344566665554441444444555566666555555444555545444444455555551667899************** PP

                        UPF0242 165 lekrqdqieqLe 176
                                    le r +q    e
  gi|121638027|ref|YP_978251.1| 205 LEGRLEQLRTFE 216
                                    *****9987766 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9   0.00053      0.86       4      18 ..      47      61 ..      44      62 .. 0.88
   2 ?    0.6   0.1      0.35   5.8e+02      13      19 ..     227     233 ..     218     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00053
                 Pox_A_type_inc  4 srlRsRIsDLErqLs 18
                                   s lR RI +L+++L+
  gi|121638027|ref|YP_978251.1| 47 SDLRQRINELDQELA 61
                                   569***********8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                 Pox_A_type_inc  13 LErqLse 19 
                                    LE+qL+e
  gi|121638027|ref|YP_978251.1| 227 LESQLEE 233
                                    9****97 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  15.6    0.0012       1.9     108     245 ..      28     206 ..      24     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                        DUF4407 108 Idaelaeeqqeeakelkeqlaaaltaelaeleaqia........................................alqa 147
                                    +da l+   +e ++ ++e+  ++l+++++el++++a                                        ++ +
  gi|121638027|ref|YP_978251.1|  28 VDAFLDLVENELTRLIEEN--SDLRQRINELDQELAagggagvtpqatqaipayepepgkpapaavsagmneeqalKAAR 105
                                    5555555555555555444..44888899999988889999999999999999999999999999999877777666666 PP

                        DUF4407 148 eidaaearldalraeaqkeldgtk...gtgttgvaGkgpaakekkaqldaaqaelaelkakld..atarlaalraelael 222
                                     ++ a++++d+l+++a++e d          ++ +  g+a ++++a  ++a+++ +++ a+ +  ++a+l +++++++ l
  gi|121638027|ref|YP_978251.1| 106 VLSLAQDTADRLTNTAKAESDKMLadaR--ANAEQILGEARHTADATVAEARQRADAMLADAQsrSEAQLRQAQEKADAL 183
                                    6777788888888888888776556441..33333334444445555555555555554444444777888888888888 PP

                        DUF4407 223 eaerakeraasqaaaaaddGlla 245
                                    +a++++++++   ++++++ +l+
  gi|121638027|ref|YP_978251.1| 184 QADAERKHSEIMGTINQQRAVLE 206
                                    88777777777766666655554 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.52   8.5e+02      72      92 ..      40      60 ..      25      75 .. 0.69
   2 ?    7.6   6.8    0.0023       3.7      33     127 ..     105     200 ..      96     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.52
                      ApoLp-III 72 dklseenPevkkkaqelqekv 92
                                     l een+++ + ++el +++
  gi|121638027|ref|YP_978251.1| 40 TRLIEENSDLRQRINELDQEL 60
                                   344456777777777776654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0023
                      ApoLp-III  33 nlvdqlkqvikslqeelkkksde.leealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslk 111
                                     +++ ++++++ l++ +k +sd+ l+ a  ++ + + e++ +  +  +e+ + a+++ +  Qs+ ++ + ++q+ a +l+
  gi|121638027|ref|YP_978251.1| 105 RVLSLAQDTADRLTNTAKAESDKmLADARANAEQILGEARHTADATVAEARQRADAMLADAQSRSEAQLRQAQEKADALQ 184
                                    5666778888888888888776524666667777777777777779********************************** PP

                      ApoLp-III 112 ensqeakeklakaikq 127
                                    ++++    ++  +i q
  gi|121638027|ref|YP_978251.1| 185 ADAERKHSEIMGTINQ 200
                                    ****999999988876 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  18.4   0.00031       0.5      40     117 ..      98     175 ..      90     176 .. 0.93
   2 ?    2.8  13.6     0.071   1.2e+02      62     115 ..     153     209 ..     152     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                     ATP-synt_B  40 aeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLre 117
                                    ++A ++++ +  +++ a +  + A+ae++++ ++A+++ae++  e++  a a ++  ++ A a ++ +++r +a+Lr+
  gi|121638027|ref|YP_978251.1|  98 EQALKAARVLSLAQDTADRLTNTAKAESDKMLADARANAEQILGEARHTADATVAEARQRADAMLADAQSRSEAQLRQ 175
                                    567777778889999999999********************************************************8 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.071
                     ATP-synt_B  62 eAraeAaeiiknAkkeae...klkeeieaeaeaeaerlkesAaaeIeqekdralaeL 115
                                    eAr++A+ + ++A++++e   ++++e+ ++ +a+aer  ++   +I+q+++ ++  L
  gi|121638027|ref|YP_978251.1| 153 EARQRADAMLADAQSRSEaqlRQAQEKADALQADAERKHSEIMGTINQQRAVLEGRL 209
                                    788888888888888877223345666666778888888888888888776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2100  (0.117129); expected 358.6 (0.02)
Passed bias filter:                      800  (0.0446204); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 1414.07
//
Query:       gi|121638028|ref|YP_978252.1|  [L=96]
Description: hypothetical protein BCG_2163c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-11   43.6   8.5    3.7e-11   43.3   8.5    1.2  1  YGGT      YGGT family
  ------ inclusion threshold ------
       0.54   10.0   2.9       0.55   10.0   0.2    2.2  2  DUF4051   Protein of unknown function (DUF4051)


Domain annotation for each model (and alignments):
>> YGGT  YGGT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   8.5   4.1e-15   3.7e-11       2      65 ..      10      87 ..       9      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4.1e-15
                           YGGT  2 lllslyilllilrills........w.pnpfynpiaqflyklTePllapfRrlip..ggg...iDlSplvallvlqll 65
                                   ++l +++llli+r++ +        w p ++  +i ++++ +T+P+++ +Rrlip   +g   +DlS +v+llv  + 
  gi|121638028|ref|YP_978252.1| 10 FALFIFWLLLIARVVVEfirsfsrdWrPTGVTVVILEIIMSITDPPVKVLRRLIPqlTIGavrFDLSIMVLLLVAFIG 87
                                   5799************8555555556*99**************************98455688**********98775 PP

>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   6.1e-05      0.55       6      27 ..      15      36 ..      12      38 .. 0.89
   2 ?   -0.8   0.2      0.14   1.3e+03      10      19 ..      77      86 ..      74      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.1e-05
                        DUF4051  6 ywlllvvlvvvgyichlkRycr 27
                                   +wlll++ vvv +i  + R  r
  gi|121638028|ref|YP_978252.1| 15 FWLLLIARVVVEFIRSFSRDWR 36
                                   69************99999877 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.14
                        DUF4051 10 lvvlvvvgyi 19
                                   ++vl++v++i
  gi|121638028|ref|YP_978252.1| 77 IMVLLLVAFI 86
                                   5677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.38s 00:00:00.91 Elapsed: 00:00:00.57
# Mc/sec: 508.44
//
Query:       gi|121638029|ref|YP_978253.1|  [L=241]
Description: hypothetical protein BCG_2164c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-24   85.2   0.0    4.4e-24   84.5   0.0    1.4  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   2.5e-28   4.4e-24       1      72 []     153     224 ..     153     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 2.5e-28
                                    EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTCHHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                           SepF   1 vvvveprsfedaqeiadalkegkiVilnledldkeeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                    +++++p+++++a++i++++++g +Vi++l ++d+++akr+vdf++g+++al+G++ kv++kvfl++P++vd+
  gi|121638029|ref|YP_978253.1| 153 ITTLRPKDYSEARTIGERFRDGSPVIMDLVSMDNADAKRLVDFAAGLAFALRGSFDKVATKVFLLSPADVDV 224
                                    6789******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1294.42
//
Query:       gi|121638030|ref|YP_978254.1|  [L=258]
Description: hypothetical protein BCG_2165c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-14   54.4   0.8    1.6e-14   54.1   0.8    1.1  1  Ala_racemase_N  Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.8   9.1e-19   1.6e-14       3     218 ..      19     253 ..      18     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 9.1e-19
                                    HHHHHHHHHHHHHHS.CT..TSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHH.............HHHHTT CS
                 Ala_racemase_N   3 ldalrhNlrrlrala.gp..gaklmavvKanayghgavevaralaeggadgfgvatleEal.............elreag 66 
                                    l+a+r++l++++++a ++  + +l++++K       a  va  ++  g++ +g+++ +Ea              el  +g
  gi|121638030|ref|YP_978254.1|  19 LAAMRSRLAAAAEAAgRNvgEIELLPITKF----FPATDVAILFR-LGCRSVGESREQEASakmaelnrllaaaELGHSG 93 
                                    688999999999999544777789999999....77777888666.66*********************99777666666 PP

                                    SCSEEEEESCSTGGGHHHHHHT.TEEEEESSHHHHHHHHHHHHH......TTS-EEEEEEBESSSS..SSS...BSCHHH CS
                 Ala_racemase_N  67 itapilvlegfspeelaalaey.dltvtvdsleqlealaaaare......agkplrvhlkidtgmg..RlG...ftpeel 134
                                        + +++ ++++++ +la++ +  + vds   + al++a  +       g++lrv +++  +++  R+G    tp ++
  gi|121638030|ref|YP_978254.1|  94 -GVHWHMVGRIQRNKAGSLARWaHTAHSVDSSRLVTALDRAVVAalaehrRGERLRVYVQVSLDGDgsRGGvdsTTPGAV 172
                                    .6667778889**********88999******999999999999999999999999999998865567***88778899* PP

                                    HHHHHHHHHTTTEEEEEEE-S-SSTTSTSHHHHHHHHHHHHHHHHHHHTTGGGSEEEEESHHHHHHSGGG.TTEEEESGG CS
                 Ala_racemase_N 135 eellealaalpglrleglmtHfasadepdeeteaqlarfeealeelekaglrppvvslanSaaillaaah.fdmvRpGia 213
                                    +++++++++++gl+l+glm +++   +pde++++ ++  +++++ ++    +   +s+++S ++  a +h ++ vR+G+a
  gi|121638030|ref|YP_978254.1| 173 DRICAQVQESEGLELVGLMGIPPLDWDPDEAFDRLQSEHNRVRAMFP----HAIGLSAGMSNDLEVAVKHgSTCVRVGTA 248
                                    *************************9999666665556677777776....66779***********7688********* PP

                                    GGT-S CS
                 Ala_racemase_N 214 lyGls 218
                                    l G +
  gi|121638030|ref|YP_978254.1| 249 LLGPR 253
                                    *9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1397.98
//
Query:       gi|121638031|ref|YP_978255.1|  [L=250]
Description: hypothetical protein BCG_2166c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-71  238.4   0.4    8.7e-71  238.2   0.4    1.0  1  Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase


Domain annotation for each model (and alignments):
>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.2   0.4   4.8e-75   8.7e-71       1     231 []      25     248 ..      25     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 4.8e-75
                                    E-S-SS-B-GGG-B----SSSSS-HHHHHHHHHHHHHHTTS...GEEE-B--SS--EEE-EE--GGCSSSS..B...-SE CS
                   Cu-oxidase_4   1 ttregGvsegpyaslNlglhvgDdpeaVaenrrrlaaalgv...rlvlleqvHgtevvvvaeeaaakgsaeeeele.aDa 76 
                                    ttr+gGvs++p++++Nlg+hvgDdp+aVa+nr+rlaaa+g+   r+v+++qvHg++v  v++   + ++++    + +D+
  gi|121638031|ref|YP_978255.1|  25 TTRAGGVSAPPFDTFNLGDHVGDDPAAVAANRARLAAAIGLpgnRVVWMNQVHGDRVELVDQ---P-RNTAL---DdTDG 97 
                                    89**************************************99888************77775...2.22233...339** PP

                                    EEESSTTSEEEEEESSSEEEEEEETTSSEEEEEEE-HHHHHHTHHHHHHHHHCSTT--GGGEEEEE-SB--TTT-EEEHH CS
                   Cu-oxidase_4  77 lvtdepgvalavltADCvPvlladpkgkvvaaaHaGwrGlvagvlektveamkelgakpedilaaiGPsIgpecyeVgee 156
                                    lvt +p++alav+tADCvPvl+ad ++++ aa+HaG+ G+  gv+ +++e m +lga+ +di a++GP+++ ++yeV++ 
  gi|121638031|ref|YP_978255.1|  98 LVTATPRLALAVVTADCVPVLMADARAGIAAAVHAGRAGAQRGVVVRALEVMLSLGAQVRDISALLGPAVSGRNYEVPAA 177
                                    ****************************************************99************************** PP

                                    HHHHHHHHSGGGGEEEEETTEEEE-HHHHHHHHHHHTT-..SEEEE---BTTT-TTT---HHHHSH---EEEEEE CS
                   Cu-oxidase_4 157 vaeafeaadpeaaaaaeeegkaylDLaalarlqLeeaGvkeenieasglCTvceedrfFSyRrdggtGrmaaliw 231
                                    +a+++eaa p + ++++++g++ +DL+a +  qL+++Gv  e+i++ + CTv++++ +FS+Rrd+ tGr+a+l+w
  gi|121638031|ref|YP_978255.1| 178 MADEVEAALPGS-RTTTAAGTPGVDLRAGIACQLRDLGV--ESIDVDPRCTVADPT-LFSHRRDAPTGRFASLVW 248
                                    ******999998.899999999*****************..***********9886.*******66*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1387.93
//
Query:       gi|121638032|ref|YP_978256.1|  [L=379]
Description: cell division protein FtsZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-39  136.8   0.1    1.6e-39  136.2   0.1    1.3  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    3.7e-35  120.1   3.4      7e-35  119.2   1.7    2.3  2  FtsZ_C     FtsZ family, C-terminal domain
  ------ inclusion threshold ------
       0.18   11.0   4.2        2.1    7.4   0.4    2.3  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.1   2.7e-43   1.6e-39       2     195 ..      11     169 ..      10     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 2.7e-43
                                    EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                        Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                    i+v+g+G++G++++n+++e     +g+             +g ve+i    ai+td+q+l  ++a+       kl +g +
  gi|121638032|ref|YP_978256.1|  11 IKVVGIGGGGVNAVNRMIE-----QGL-------------KG-VEFI----AINTDAQALLMSDAD------VKLDVGRD 61 
                                    89*****************.....699.............88.****....***************......******** PP

                                    CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG. CS
                        Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefs 161
                                    +++++gag++pevg++aae+ ++ei++ ++++d+   +f+ta+ gGGTG+G +pv+++++++   +al+v+vv+ P++f 
  gi|121638032|ref|YP_978256.1|  62 STRGLGAGADPEVGRKAAEDAKDEIEELLRGADM---VFVTAGEGGGTGTGGAPVVASIARKL--GALTVGVVTRPFSF- 135
                                    **********************************...**************************..**************. PP

                                    G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                        Tubulin 162 evvvepynailalkelieesdavividNdaLlki 195
                                    e+++++++a+ ++ +l+e++d++ivi+Nd+Ll++
  gi|121638032|ref|YP_978256.1| 136 EGKRRSNQAENGIAALRESCDTLIVIPNDRLLQM 169
                                    *******************************997 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   1.7   1.2e-38     7e-35       1      95 []     219     313 ..     219     313 .. 0.99
   2 ?   -1.1   0.0      0.41   2.4e+03       7      33 ..     323     350 ..     322     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1.2e-38
                                    EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT CS
                         FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavidee 80 
                                    G+A+mg+G+a+ge+r+ +aae ai+spLL+++++gA+gvl++i+ggsdl+l+E++e+a+ ++++++++an+i+G+vid++
  gi|121638032|ref|YP_978256.1| 219 GTALMGIGSARGEGRSLKAAEIAINSPLLEASMEGAQGVLMSIAGGSDLGLFEINEAASLVQDAAHPDANIIFGTVIDDS 298
                                    89****************************************************************************** PP

                                    --SEEEEEEEEES-X CS
                         FtsZ_C  81 ledeirvtvvatglk 95 
                                    l de+rvtv+a+g++
  gi|121638032|ref|YP_978256.1| 299 LGDEVRVTVIAAGFD 313
                                    *************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                                    EEEEESTTHHHHHHHHHHTSGGGT.--G CS
                         FtsZ_C   7 vGeasgedraeeaaeaaisspLLd.vdl 33 
                                    +Ge+ g +r e+a    + s L + vd 
  gi|121638032|ref|YP_978256.1| 323 MGETGGAHRIESAKAGKLTSTLFEpVDA 350
                                    7999999999999999999999998875 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4    0.0028        16       2      46 ..      13      48 ..      13      65 .. 0.76
   2 ?    7.4   0.4   0.00036       2.1     155     223 ..      93     153 ..      55     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0028
                      Tubulin_2  2 viGLGGtGgkvlaelrrrlreelgslelpdkvqFlyiDtdenekn 46
                                   v+G+GG G +++    r++++ l      + v+F++i td +++ 
  gi|121638032|ref|YP_978256.1| 13 VVGIGGGGVNAV---NRMIEQGL------KGVEFIAINTDAQALL 48
                                   799999997665...67788888......789********99884 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00036
                      Tubulin_2 155 glnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkE 223
                                       vfV  +  GGTG G +  va + rk+         ++g+v+ P  f    + + +  +N+ aaL E
  gi|121638032|ref|YP_978256.1|  93 ADMVFVTAGEGGGTGTGGAPVVASIARKLGA------LTVGVVTRPFSFEG--KRRSNQAENGIAALRE 153
                                    246**************99988888877643......46678888888543..4688999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2121.93
//
Query:       gi|121638033|ref|YP_978257.1|  [L=314]
Description: cell division protein ftsQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-15   55.9   0.5    7.2e-15   55.1   0.5    1.4  1  POTRA_1   POTRA domain, FtsQ-type
    4.8e-08   33.8   0.0    1.5e-07   32.2   0.0    1.9  2  FtsQ      Cell division protein FtsQ
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.059   13.4   0.0    1.6  1  H2TH      Formamidopyrimidine-DNA glycosylase H2TH domain
      0.077   13.1   1.5       0.17   12.0   1.5    1.5  1  DUF3742   Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.5   1.6e-18   7.2e-15       2      69 .]     125     192 ..     124     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.6e-18
                                    XX-EEEEES-SS--HHHHHHHHHTTSTT-GGGS-HHHHHHHHHH-TTEEEEEEEEETTTEEEEEEEC- CS
                        POTRA_1   2 pikqvevsGnkhlsseeiikalgiekgtslfsldleaieqrleklpwvksasVrrqwPntleitveEr 69 
                                    + +++++ G   +s+ee+++a+++ + t+l+++d++++++r++ + +v+sa+V+rq+P+ l+it++Er
  gi|121638033|ref|YP_978257.1| 125 SAREIVIIGIGAVSREEVLDAARVRPATPLLQIDTQQVADRVATIRRVASARVQRQYPSALRITIVER 192
                                    5799***************************************************************9 PP

>> FtsQ  Cell division protein FtsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   9.6e+03      30      43 ..      38      58 ..      23      82 .. 0.56
   2 !   32.2   0.0   3.4e-11   1.5e-07      10     104 ..     205     298 ..     195     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                                   S-EEE......S.-......H CS
                           FtsQ 30 lPlltGpegsek.e......v 43
                                    P ++Gp  ++  e      +
  gi|121638033|ref|YP_978257.1| 38 HPEFEGPRRRARrEraerraA 58
                                   677777666666444333331 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 3.4e-11
                                    EEEETT--B-C.....CC.B.SS-EEE..........S.-HHHHHCCS-HHHHH.S-SEE-SS-TTEEEE-T.TS-EEEE CS
                           FtsQ  10 alidaeGevfeadeeaed.e.klPllt....Gpegsek.evlevlaelpeelkpleiseialserrrwqlvlddgvevkl 82 
                                    +l d++G+ f+     +    +lP +     Gp +  + ++l+vl +l +e+++ ++  ia  +  +++l+l+dg  v +
  gi|121638033|ref|YP_978257.1| 205 HLFDRDGVDFAT----DPpPpALPYFDvdnpGPSDPTTkAALQVLTALHPEVAS-QVGRIAAPSVASITLTLADGRVVIW 279
                                    799*******77....332334***997777787777756*************8.************************* PP

                                    ES....TTHHHHHHT-CCHHHC CS
                           FtsQ  83 greelaedleeklarlvkilpq 104
                                    g     ++ eek + l+++l q
  gi|121638033|ref|YP_978257.1| 280 GTT---DRCEEKAEKLAALLTQ 298
                                    **9...6677888888888877 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.059      35      82 ..     130     177 ..     127     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    TSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHHHH CS
                           H2TH  35 lvaGlGNiyadEvLfrakihPerlakslskeelellhqeikevlkeai 82 
                                    ++ G+G + ++EvL +a++ P+++  ++ +++++  +++i++v  + +
  gi|121638033|ref|YP_978257.1| 130 VIIGIGAVSREEVLDAARVRPATPLLQIDTQQVADRVATIRRVASARV 177
                                    799*****************************9999999988876655 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.5   3.7e-05      0.17       5      86 ..      60     139 ..      56     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                        DUF3742   5 trtslaerlgrllgrawRallrlerraaswlvakGvpaavatavlwvvklavlGvllyvafWlalllvvvvlvawaarsv 84 
                                    +r +  e++ r++ r  R+ +  e++ a+  +a+Gv+++  +a+l +v lav+G++l  a +++ ++ +  +v++ +++v
  gi|121638033|ref|YP_978257.1|  60 ARATAIEQARRAAKRRARGQIVSEQNPAK-PAARGVVRGL-KALLATVVLAVVGIGLGLALYFTPAMSAREIVIIGIGAV 137
                                    66777788999999999999999988766.5799*****9.9***************99999888888877777777666 PP

                        DUF3742  85 dt 86 
                                      
  gi|121638033|ref|YP_978257.1| 138 SR 139
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 1698.32
//
Query:       gi|121638034|ref|YP_978258.1|  [L=494]
Description: UDP-N-acetylmuramate--L-alanine ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-26   92.4   0.0    5.2e-26   91.8   0.0    1.3  1  Mur_ligase_M  Mur ligase middle domain
      8e-24   83.8   0.2    7.6e-23   80.7   0.2    2.5  2  Mur_ligase    Mur ligase family, catalytic domain
      1e-23   83.4   0.1    3.9e-23   81.5   0.0    2.0  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   8.7e-30   5.2e-26       1     192 []     120     309 ..     120     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 8.7e-30
                                    EESSS-HHHHHHHHHHHHHCT.EEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE-- CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaaileka.gkvigtvgttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitn 79 
                                    vTGt+GKTTtt+++  +l++      + vg      +l ++ +++++   + +v E+ ++   ++ l + + p+vavitn
  gi|121638034|ref|YP_978258.1| 120 VTGTHGKTTTTSMLIVALQHCgLDPSFAVGG-----ELGEAGTNAHHGSGDCFVAEADES---DGSLLQ-YTPHVAVITN 190
                                    9********************6446666665.....67777777788889**********...888888.9********* PP

                                    -TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEE CS
                   Mur_ligase_M  80 ispdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegte 159
                                    i++dHldf+g++e+y + + +++er+ ++g +v+  ddp +++l++++++ +++v+++g      +++a+ ++ +++g+ 
  gi|121638034|ref|YP_978258.1| 191 IESDHLDFYGSVEAYVAVFDSFVERIVPGGALVVCTDDPGGAALAQRATELGIRVLRYGSVPGE-TMAATLVSWQQQGVG 269
                                    ***********************************************************99998.466666777666666 PP

                                    E........EEEEETTEEEEEEESSCSCHHHHHHHHHHHHH CS
                   Mur_ligase_M 160 i........ellevkggeleieipllGkhnvyNalaaiaaa 192
                                             el  + +g   ++++++G+h + Nal a++aa
  gi|121638034|ref|YP_978258.1| 270 AvahirlasELA-TAQGPRVMRLSVPGRHMALNALGALLAA 309
                                    566665554444.4566666*****************9885 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.2   1.3e-26   7.6e-23       2      87 ..      13     115 ..      12     116 .. 0.94
   2 ?   -0.2   0.0      0.22   1.3e+03      39      85 ..     220     257 ..     211     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.3e-26
                                    EEEESTTSCCHHHHHHHHHHTTSEEEEEESSHC.....HHHTT-EEEES-HGGGG..........EE-T..S-TTCHHHH CS
                     Mur_ligase   2 ihfigidgrgmsagalflalkGykvdGsdfies.....lialGaaavvghdaani..........vvss..iskdnpele 64 
                                    +h++gi+g+gms++a++l+++G  v+Gsd++es     l+a+Ga + +ghda+ +          v++   i+k npel+
  gi|121638034|ref|YP_978258.1|  13 VHMVGIGGAGMSGIARILLDRGGLVSGSDAKESrgvhaLRARGALIRIGHDASSLdllpggatavVTTHaaIPKTNPELV 92 
                                    9***************************************************************74443689999***** PP

                                    HHHHTTEEEEEHHHHHHHHHHCC CS
                     Mur_ligase  65 aakepgipvesraeaLaelaarf 87 
                                    +a+++gipv+ r+++La+l+a +
  gi|121638034|ref|YP_978258.1|  93 EARRRGIPVVLRPAVLAKLMAGR 115
                                    ********************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                    T-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHHHHHHH CS
                     Mur_ligase  39 GaaavvghdaanivvssiskdnpeleaakepgipvesraeaLaelaa 85 
                                    Ga +v ++d++         +    ++a+e+gi+v ++  + +e +a
  gi|121638034|ref|YP_978258.1| 220 GALVVCTDDPG---------GAALAQRATELGIRVLRYGSVPGETMA 257
                                    66666666666.........455666999999999998888777776 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.83     5e+03      28      56 ..     131     158 ..     112     170 .. 0.67
   2 !   81.5   0.0   6.5e-27   3.9e-23       1      89 [.     329     421 ..     329     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.83
                                    HHHHHHHHHHSSSSEEEEEEEESTT.CCS CS
                   Mur_ligase_C  28 saalkalreiapdkrlilvfgpggelger 56 
                                    s ++ al++      +++v g++ge g++
  gi|121638034|ref|YP_978258.1| 131 SMLIVALQHC-GLDPSFAVGGELGEAGTN 158
                                    4455555444.556788888877775544 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 6.5e-27
                                    CTTSSEEEEE....TTTEEEEEET--SHHHHHHHHHHHHHHSS...SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSS CS
                   Mur_ligase_C   1 vkgRlevvge....adgvtvidDyahnpdslsaalkalreiap...dkrlilvfgpggelgertrtfhdefgrlasalad 73 
                                    v++R+e+vg+    + +v+v+dDyah+p+++sa+l+a+r++ +    +r+++vf+p  +l++rt++f +efgr+++a ad
  gi|121638034|ref|YP_978258.1| 329 VRRRFELVGTcgvgKASVRVFDDYAHHPTEISATLAAARMVLEqgdGGRCMVVFQP--HLYSRTKAFAAEFGRALNA-AD 405
                                    78************99*************************9999999********..******************9.** PP

                                    EEEEEESS-TTSTHHH CS
                   Mur_ligase_C  74 slvvlgdypraedsia 89 
                                    +++vl++y ++e++ a
  gi|121638034|ref|YP_978258.1| 406 EVFVLDVYGAREQPLA 421
                                    ***********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3457.76
//
Query:       gi|121638035|ref|YP_978259.1|  [L=410]
Description: UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-41  141.5   0.0    3.3e-41  141.1   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    4.2e-40  137.0   0.0      9e-40  135.9   0.0    1.6  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
    0.00051   20.1   5.0     0.0014   18.6   2.2    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   5.5e-45   3.3e-41       1     166 [.     231     392 ..     231     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 5.5e-45
                                    -EEEEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS CS
                Glyco_tran_28_C   1 tilVtGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRA 80 
                                    ++lV+GGSqga  Ln++v +++++l+  +  + vlh++G+++  e++   +++ +++ ++++ d+m+ a++aadLvI+RA
  gi|121638035|ref|YP_978259.1| 231 VLLVFGGSQGAVSLNRAVSGAAADLAAAG--VCVLHAHGPQNVLELRRRAQGD-PPYVAVPYLDRMELAYAAADLVICRA 307
                                    589*************************5..*********************9.9************************* PP

                                    -CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS---S---SSCH..CHH CS
                Glyco_tran_28_C  81 GagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaaeklrlaekskasaaskf 160
                                    Ga+t+aE++a+g+p+I+vplp ++ ++q+ Na  +++ag+++v+ ++ ltpe ++ ++  l++++ rla++++a+a+ ++
  gi|121638035|ref|YP_978259.1| 308 GAMTVAEVSAVGLPAIYVPLPIGN-GEQRLNALPVVNAGGGMVVADAALTPELVARQVAGLLTDPARLAAMTAAAARVGH 386
                                    **********************77.*************************************************999999 PP

                                    HHHHHH CS
                Glyco_tran_28_C 161 adlaer 166
                                    +d+a +
  gi|121638035|ref|YP_978259.1| 387 RDAAGQ 392
                                    998865 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9   0.0   1.5e-43     9e-40       1     138 [.      38     185 ..      38     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 1.5e-43
                                    EEEEE-SSHHHHHHHHHHHHHHHCTT-EEE..EEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHH CS
                Glyco_transf_28   1 ivllggGTgGhvfPalAlakeLkkegheVr..ylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavv 78 
                                    +vl+ggGT+Ghv+Pa+A+a++L + +++Vr  +lgt+rgle+rlv+++g+++e i++ +++rk   +  + +++v++av+
  gi|121638035|ref|YP_978259.1|  38 VVLAGGGTAGHVEPAMAVADALVALDPRVRitALGTPRGLETRLVPQRGYHLELITAVPMPRKPGGDLARLPSRVWRAVR 117
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHCCCCCCCCCCCHCCCCCHC........CCTTHCCCCCHCTS-ECCCCCCCCC-SCCC CS
                Glyco_transf_28  79 kakkilkeakpdavvgtggyvslpaviaap........laripviihEqnaipglanktlsrtatkva 138
                                    +a+ +l +  +d+vvg+ggyv+lpa++aa+        ++ripv+ihE+na++glan++ + ta++v+
  gi|121638035|ref|YP_978259.1| 118 EARDVLDDVDADVVVGFGGYVALPAYLAARglplpprrRRRIPVVIHEANARAGLANRVGAHTADRVL 185
                                    ******************************************************************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.2   2.4e-07    0.0014      11     102 ..      55     164 ..      52     232 .. 0.85
   2 ?    1.7   0.0     0.037   2.2e+02      98     139 ..     260     305 ..     238     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                 Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleeev..........elvvrvprvp.lpllkrllrslaflrrlrrllkrekpDvvHah 79 
                                    +a aL ++  +V++ + g+++ le +           ++ v +pr+p   l + + r ++++r +r +l+  + Dvv   
  gi|121638035|ref|YP_978259.1|  55 VADALVALDPRVRITALGTPRGLETRLvpqrgyhlelITAVPMPRKPgGDLARLPSRVWRAVREARDVLDDVDADVVVGF 134
                                    789999999******999999999999999998885533333333331345566778999999999************** PP

                 Glyco_transf_4  80 spaalgaallalrr.......rlgiplVlt 102
                                    + + ++ a+la+r        r++ip+V++
  gi|121638035|ref|YP_978259.1| 135 GGYVALPAYLAARGlplpprrRRRIPVVIH 164
                                    *************99999999999999875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.037
                 Glyco_transf_4  98 plVltvHglye....krllkarlkplsrllralerrllrradrvia 139
                                     +Vl++Hg+      +r+ ++        +   ++ ++ +ad vi+
  gi|121638035|ref|YP_978259.1| 260 VCVLHAHGPQNvlelRRRAQGDPPYVAVPYLDRMELAYAAADLVIC 305
                                    4566666666575543333333333333333334445888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2725.44
//
Query:       gi|121638036|ref|YP_978260.1|  [L=524]
Description: FtsW-like protein FtsW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.4e-126  419.9  17.1   8.6e-126  419.7  17.1    1.0  1  FTSW_RODA_SPOVE  Cell cycle protein
  ------ inclusion threshold ------
      0.033   13.3   0.0      0.067   12.3   0.0    1.4  1  TMEM192          TMEM192 family
        3.2    8.0   4.6        8.9    6.5   0.2    2.9  2  DUF872           Eukaryotic protein of unknown function (DUF8
        3.5    6.2   4.6        4.1    5.9   3.4    1.6  2  EMP70            Endomembrane protein 70


Domain annotation for each model (and alignments):
>> FTSW_RODA_SPOVE  Cell cycle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.7  17.1  1.9e-129  8.6e-126       2     357 ..      58     412 ..      57     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 419.7 bits;  conditional E-value: 1.9e-129
                FTSW_RODA_SPOVE   2 allllvllllvilGlvmiysaslveslvlfgdsfvlfirqlvylllglivfvlllriplkfleklakllliislllLvlv 81 
                                    +l+++v++ll++lGl+m++sas+v+s++  g+++v+f +q++++l+gli  +++lr++++f++++a+ ++ i++++Lvlv
  gi|121638036|ref|YP_978260.1|  58 HLIIAVAALLTTLGLIMVLSASAVRSYDDDGSAWVIFGKQVLWTLVGLIGGYVCLRMSVRFMRRIAFSGFAITIVMLVLV 137
                                    68999*************************************************************************** PP

                FTSW_RODA_SPOVE  82 kvp.lgssanGAkrWirlggisiqPsEfvkialilflAavlskkkkevksrlrellillv.ivllilvlillqpdlgtav 159
                                     vp +g++anG++ W+ ++g+s+qPsE++k+a++++ A++l++ +++++++lre+li+lv +++++l+li++qpdlg++v
  gi|121638036|ref|YP_978260.1| 138 LVPgIGKEANGSRGWFVVAGFSMQPSELAKMAFAIWGAHLLAA-RRMERASLREMLIPLVpAAVVALALIVAQPDLGQTV 216
                                    *******************************************.99********************************** PP

                FTSW_RODA_SPOVE 160 llliillvvlflsglslklilaivlalilviaivllilledyqvkrvtslldpfkdplgsgYqviqsliAigsGGllGkG 239
                                     ++iill++l+++gl+l+++l+ ++  ++v+++++l++++ y+++rv s+l+p++dp++sgYq  q+++A+++GG++G+G
  gi|121638036|ref|YP_978260.1| 217 SMGIILLGLLWYAGLPLRVFLSSLA--AVVVSAAILAVSAGYRSDRVRSWLNPENDPQDSGYQARQAKFALAQGGIFGDG 294
                                    *************************..89999999********************************************* PP

                FTSW_RODA_SPOVE 240 lgnsqqkleyLPeahtDfIfavigEelGlvGvllllllffllivrglriarkakdrfgsllavgivllivvqsfinigmv 319
                                    lg++++k++yLP+ah+DfIfa+igEelGlvG+l ll lf+l++++g+ria++++d+f +ll+++++l+++ q+finig+v
  gi|121638036|ref|YP_978260.1| 295 LGQGVAKWNYLPNAHNDFIFAIIGEELGLVGALGLLGLFGLFAYTGMRIASRSADPFLRLLTATTTLWVLGQAFINIGYV 374
                                    ******************************************************************************** PP

                FTSW_RODA_SPOVE 320 lGllPvtGltlPflSyGGsSllalliligillnisree 357
                                    +GllPvtGl+lP++S+GG+S+ a+l ligi++n++r+e
  gi|121638036|ref|YP_978260.1| 375 IGLLPVTGLQLPLISAGGTSTAATLSLIGIIANAARHE 412
                                    **********************************9986 PP

>> TMEM192  TMEM192 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05     0.067      22      80 ..      51     110 ..      34     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                        TMEM192  22 tvplaslllllsva..lvvlgivlavlcsdeenkedkcvyfvllylrvilWlltllidryv 80 
                                      p++s++l+++va  l++lg++++++ s  ++ +d      +++++ +lW l+ li  yv
  gi|121638036|ref|YP_978260.1|  51 GRPMTSFHLIIAVAalLTTLGLIMVLSASAVRSYDD-DGSAWVIFGKQVLWTLVGLIGGYV 110
                                    56899******9983345667777776666665544.499*************99987765 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.002       8.9      33      88 ..      49     106 ..      11     127 .. 0.75
   2 ?    2.1   0.1     0.047   2.1e+02      45      75 ..     354     384 ..     348     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                         DUF872  33 wlkhPkvkknrkvvlaallLlllGlvLlllgvvilvepseGvssavf...lvlGlllfi 88 
                                    wl  P   +    ++ a lL++lGl+++l + ++     +G+   +f   ++  l+ +i
  gi|121638036|ref|YP_978260.1|  49 WLGRPM-TSFHLIIAVAALLTTLGLIMVLSASAVRSYDDDGSAWVIFgkqVLWTLVGLI 106
                                    555554.34455789999*****************999999988888664344444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.047
                         DUF872  45 vvlaallLlllGlvLlllgvvilvepseGvs 75 
                                     + a++ L +lG + + +g+vi + p +G +
  gi|121638036|ref|YP_978260.1| 354 LLTATTTLWVLGQAFINIGYVIGLLPVTGLQ 384
                                    567788999***************9999976 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.4   0.00092       4.1     274     338 ..      66     137 ..      52     143 .. 0.69
   2 ?   -2.2   0.0      0.26   1.2e+03     298     325 ..     239     266 ..     212     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00092
                          EMP70 274 lllmalvtlllallgflspsnrgslltva..lllyvllgliaGYvsarlyktfggekwkkn......tlltal 338
                                    ll+++ ++++l++  + s+   gs   ++   +l++l+gli+GYv+ r+   f  +++  +      ++l+ +
  gi|121638036|ref|YP_978260.1|  66 LLTTLGLIMVLSASAVRSYDDDGSAWVIFgkQVLWTLVGLIGGYVCLRMSVRFM-RRIAFSgfaitiVMLVLV 137
                                    677888888999999999999998776653379****************98886.333333111111222222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.26
                          EMP70 298 lltvalllyvllgliaGYvsarlyktfg 325
                                     l ++++  ++l++ aGY s r+ + ++
  gi|121638036|ref|YP_978260.1| 239 SLAAVVVSAAILAVSAGYRSDRVRSWLN 266
                                    5678899999999999999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 2728.14
//
Query:       gi|121638037|ref|YP_978261.1|  [L=486]
Description: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-21   74.7   0.0    1.3e-20   74.2   0.0    1.2  1  Mur_ligase_M  Mur ligase middle domain
    1.9e-11   44.1   0.5    7.6e-11   42.1   0.2    2.2  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   1.5e-24   1.3e-20       1     191 [.     118     290 ..     118     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.5e-24
                                    EESSS-HHHHHHHHHHHHHCTEEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE-- CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvgttnneiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitn 79 
                                    vTGtnGKTTtt++++a+l + g  + + g+      + ++++++ ++ ae++++E+ss    + ++  + l+p++++++n
  gi|121638037|ref|YP_978261.1| 118 VTGTNGKTTTTSMLHAMLIAGGRRAVLCGN------IGSAVLDVLDEPAELLAVELSSF---QlHWAPS-LRPEAGAVLN 187
                                    9****************************9......55666777777************...5488888.9********* PP

                                    -TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTS...ECEEEEEEEEETT CS
                   Mur_ligase_M  80 ispdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekea...edlraknieekse 156
                                    i +dHld h t+ +y +aKa+ ++    +g+av  +dd  a++l + +  + v  v f l + a     +r + +   ++
  gi|121638037|ref|YP_978261.1| 188 IAEDHLDWHATMAEYTAAKARVLT----GGVAVAGLDDSRAAALLDGSPAQ-V-RVGFRLGEPAageLGVRDAHLVDRAF 261
                                    ********************9988....689********555555554443.2.34444444443232233333333344 PP

                                    EEEEEEEEETTEEEEEEESSCSCHHHHHHHHHHHH CS
                   Mur_ligase_M 157 gteiellevkggeleieipllGkhnvyNalaaiaa 191
                                    +++++ll v       +ip++G   v  alaa+a+
  gi|121638037|ref|YP_978261.1| 262 SDDLTLLPV------ASIPVPGPVGVLDALAAAAL 290
                                    444444423......67777777777777777776 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   8.4e-15   7.6e-11       2      81 ..     312     381 ..     311     389 .. 0.91
   2 ?   -2.6   0.0      0.77   6.9e+03      27      48 ..     438     459 ..     426     478 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 8.4e-15
                                    TTSSEEEEETTTEEEEEE.T--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEES CS
                   Mur_ligase_C   2 kgRlevvgeadgvtvidD.yahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvlgd 80 
                                    ++R+evv  adg+t++dD +a+np++++a + a+       r+++++g g     +++++h+e++++as+l+  +++ g 
  gi|121638037|ref|YP_978261.1| 312 RHRAEVVAVADGITYVDDsKATNPHAARASVLAY------PRVVWIAG-GLL---KGASLHAEVAAMASRLVGAVLI-GR 380
                                    69********************************......6*******.899...9**************9999888.44 PP

                                    S CS
                   Mur_ligase_C  81 y 81 
                                    +
  gi|121638037|ref|YP_978261.1| 381 D 381
                                    3 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.77
                                    HHHHHHHHHHHSSSSEEEEEEE CS
                   Mur_ligase_C  27 lsaalkalreiapdkrlilvfg 48 
                                    + aa++a+r +a+ +  +l++ 
  gi|121638037|ref|YP_978261.1| 438 MTAAVAAARRMAQPGDTVLLAP 459
                                    6788888888887777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2675.74
//
Query:       gi|121638038|ref|YP_978262.1|  [L=359]
Description: phospho-N-acetylmuramoyl-pentapeptide-transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-39  132.9  12.0    9.4e-39  132.9  12.0    2.0  3  Glycos_transf_4  Glycosyl transferase family 4
    3.5e-05   23.1   0.1    3.5e-05   23.1   0.1    2.2  2  MraY_sig1        Phospho-N-acetylmuramoyl-pentapeptide-transf


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       1.1     1e+04      36      45 ..       7      16 ..       3      32 .. 0.49
   2 !  132.9  12.0   1.1e-42   9.4e-39       3     159 ..      86     276 ..      84     277 .. 0.90
   3 ?   -2.2   0.4       0.4   3.6e+03      55      61 ..     308     322 ..     279     347 .. 0.38

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.1
                Glycos_transf_4 36 alililtldl 45
                                   a+ +++t+++
  gi|121638038|ref|YP_978262.1|  7 AVAVAVTVSI 16
                                   3333333332 PP

  == domain 2  score: 132.9 bits;  conditional E-value: 1.1e-42
                Glycos_transf_4   3 lllltillilllGflDDv........lglkarlKlilqilaalililtld.........lslttlglllt.........q 56 
                                    l+l ++++++ +Gf+DD+        lgl+++ K+++qi++a+++ +++                    +          
  gi|121638038|ref|YP_978262.1|  86 LVLGLATALGGVGFIDDLikirrsrnLGLNKTAKTVGQITSAVLFGVLVLqfrnaagltP---------GsadlsyvreI 156
                                    6788999**********9999999999*****************9998885555544443.........23333343336 PP

                Glycos_transf_4  57 vlielglilavlltllvivgvtNavNliDGldGlaagvsiiialalvvla.................avdgrsellllal 119
                                     +++l ++l+vl++++++ +++NavN++DGldGlaag+++++++a+v+++                  v++  +l+l+a+
  gi|121638038|ref|YP_978262.1| 157 ATVTLAPVLFVLFCVVIVSAWSNAVNFTDGLDGLAAGTMAMVTAAYVLITfwqyrnacvtapglgcyNVRDPLDLALIAA 236
                                    99***************************************************************99899********** PP

                Glycos_transf_4 120 allgallGfllfNrypAkvFmGDsgslflGlvlavlailg 159
                                    a +ga++Gfl++N+ pAk+FmGD+gsl+lG+v+a l++++
  gi|121638038|ref|YP_978262.1| 237 ATAGACIGFLWWNAAPAKIFMGDTGSLALGGVIAGLSVTS 276
                                    *************************************986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.4
                Glycos_transf_4  55 t........qvliel 61 
                                             ++ +el
  gi|121638038|ref|YP_978262.1| 308 RrmfrmapfHHHFEL 322
                                    122222222233332 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1     4e-09   3.5e-05       1      13 []      46      58 ..      46      58 .. 0.96
   2 ?   -3.0   0.5      0.76   6.8e+03       8      11 ..     266     269 ..     265     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-09
                      MraY_sig1  1 KkGTPTMGGvlIi 13
                                   K+GTP+MGGv I+
  gi|121638038|ref|YP_978262.1| 46 KRGTPSMGGVAIL 58
                                   9**********97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.76
                      MraY_sig1   8 GGvl 11 
                                    GGv+
  gi|121638038|ref|YP_978262.1| 266 GGVI 269
                                    9*97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1866.86
//
Query:       gi|121638039|ref|YP_978263.1|  [L=510]
Description: UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase MurF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-39  135.1   0.0    4.6e-39  134.4   0.0    1.3  1  Mur_ligase_M  Mur ligase middle domain
    5.7e-28   97.0   0.3    2.7e-27   94.8   0.1    2.2  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain
    8.1e-10   38.9   1.6    1.9e-09   37.7   0.4    2.3  2  Mur_ligase    Mur ligase family, catalytic domain
  ------ inclusion threshold ------
       0.17   12.3   0.2       0.17   12.3   0.2    2.4  2  DUF108        Domain of unknown function DUF108
       0.18   10.3   0.8       0.24    9.9   0.8    1.1  1  MFS_2         MFS/sugar transport protein
       0.59    9.6   6.4        4.9    6.6   0.1    3.6  4  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.0   1.5e-42   4.6e-39       1     192 []     134     321 ..     134     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 1.5e-42
                                    EESSS-HHHHHHHHHHHHHCTEEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE-- CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvgttnneiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitn 79 
                                    +TG++GKT+t++l+aa+l+  g+v++  g++nne+g p t++++++ +++y++lE+++++ g+ + l+++++p ++v++n
  gi|121638039|ref|YP_978263.1| 134 ITGSSGKTSTKDLMAAVLAPLGEVVAPPGSFNNELGHPWTVLRATR-RTDYLILEMAARHHGNiAALAEIAPPSIGVVLN 212
                                    8*********************************************.********************************* PP

                                    -TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEET.TEE CS
                   Mur_ligase_M  80 ispdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeks.egt 158
                                    ++++Hl+++g++e +a++Kael + ++  g +v+naddp   ++++++k + ++vv+++ ++   d++a+ ++ ++  + 
  gi|121638039|ref|YP_978263.1| 213 VGTAHLGEFGSREVIAQTKAELPQAVPHSGAVVLNADDP---AVAAMAKLTAARVVRVSRDNTG-DVWAGPVSLDElARP 288
                                    ***************************************...888888888899********98.799996666541555 PP

                                    EEEEEEETTEEEEEEESSCSCHHHHHHHHHHHHH CS
                   Mur_ligase_M 159 eiellevkggeleieipllGkhnvyNalaaiaaa 192
                                    +++l+   + ++e+++++ G+h+v Nal+a+a+a
  gi|121638039|ref|YP_978263.1| 289 RFTLH-AHDAQAEVRLGVCGDHQVTNALCAAAVA 321
                                    66666.6899999******************986 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   3.5e+03      33      69 ..     112     152 ..     102     160 .. 0.49
   2 !   94.8   0.1   9.2e-31   2.7e-27       2      82 ..     343     429 ..     341     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                    HHHHHSS.........SSEEEEEEEESTT.CCSCHCTHHHHHHHHC CS
                   Mur_ligase_C  33 alreiap.........dkrlilvfgpggelgertrtfhdefgrlas 69 
                                    al+++a+            +i + g+ g     +    d+++++++
  gi|121638039|ref|YP_978263.1| 112 ALAKLATavaaqlvagGLTIIGITGSSGK---TST--KDLMAAVLA 152
                                    44444333333344334556666665433...222..255555555 PP

  == domain 2  score: 94.8 bits;  conditional E-value: 9.2e-31
                                    TTSSEEEEETTTEEEEEE.T--SHHHHHHHHHHHHHHSS....SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSE.E CS
                   Mur_ligase_C   2 kgRlevvgeadgvtvidD.yahnpdslsaalkalreiap....dkrlilvfgpggelgertrtfhdefgrlasalads.l 75 
                                    ++R++v++++dgvtvidD y++npds++a+l+al++ia+    ++r+++v+g+++elge+++++hd++grla++l++s l
  gi|121638039|ref|YP_978263.1| 343 RHRMQVTTRGDGVTVIDDaYNANPDSMRAGLQALAWIAHqpeaTRRSWAVLGEMAELGEDAIAEHDRIGRLAVRLDVSrL 422
                                    5******************************************************************************* PP

                                    EEEESS- CS
                   Mur_ligase_C  76 vvlgdyp 82 
                                    vv+g ++
  gi|121638039|ref|YP_978263.1| 423 VVVGTGR 429
                                    **99876 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.4   6.3e-13   1.9e-09       5      52 ..      34      84 ..      32     117 .. 0.84
   2 ?   -2.8   0.0       2.7   8.1e+03      38      71 ..     241     267 ..     239     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6.3e-13
                                   ESTTSCCHHHHHHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGG...E CS
                     Mur_ligase  5 igidgrgmsagalflalkGykvdGsdfieslialGaaavvghdaani...v 52
                                   +  d+r +++g lflal+G++ dG+d+++s++a+Gaa+v++ ++  +   v
  gi|121638039|ref|YP_978263.1| 34 VEFDSRAIGPGGLFLALPGARADGHDHAASAVAAGAAVVLAARPVGVpaiV 84
                                   678**************************************9998555542 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                    TT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTE CS
                     Mur_ligase  38 lGaaavvghdaanivvssiskdnpeleaakepgi 71 
                                    +Ga+++ ++d+a        +    l aa+++++
  gi|121638039|ref|YP_978263.1| 241 SGAVVLNADDPA-------VAAMAKLTAARVVRV 267
                                    588888888888.......344556666666665 PP

>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.5       2.7   8.2e+03      28      53 ..      70      97 ..      64     128 .. 0.61
   2 ?   12.3   0.2   5.7e-05      0.17      25      63 ..     316     355 ..     311     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                                   HHHHHH..H.CCGEEEEEEEETT-SSEE CS
                         DUF108 28 alaLaa..lgfdrvkvelvadpnldkni 53
                                   a+ Laa  +g+ ++ v  va pn+   +
  gi|121638039|ref|YP_978263.1| 70 AVVLAArpVGVPAIVVPPVAAPNVLAGV 97
                                   5556666666666666666666654433 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.7e-05
                                    HHHHHHHHH.H.CCGEEEEEEEETT-SSEEEEEEEEETTE CS
                         DUF108  25 vaaalaLaa.lgfdrvkvelvadpnldkniheieveGsfg 63 
                                     aaa+aL + +++++v   l a p +++++++++ +G+  
  gi|121638039|ref|YP_978263.1| 316 CAAAVALECgASVEQVAAALTAAPPVSRHRMQVTTRGDGV 355
                                    58899998889**************************944 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   8.1e-05      0.24     352     394 ..     100     142 ..      41     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.1e-05
                          MFS_2 352 krregvffavlsfisklatgiglgvsgllLsafgyrakasvqs 394
                                      ++g+ +avl+++ klat++++ ++++ L+++g++  +++ s
  gi|121638039|ref|YP_978263.1| 100 HDNDGSGAAVLAALAKLATAVAAQLVAGGLTIIGITGSSGKTS 142
                                    5789999****************************44444333 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7     5e+03      27      38 ..       4      14 ..       2      14 .. 0.81
   2 ?    6.6   0.1    0.0016       4.9      11      36 ..     176     202 ..     176     204 .. 0.94
   3 ?   -3.1   0.3       1.8   5.3e+03      32      47 ..     252     267 ..     252     268 .. 0.73
   4 ?    4.6   0.1    0.0069        21      10      36 ..     309     334 ..     308     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                   HTH_Tnp_ISL3 27 srsvkavArqlg 38
                                     +v+++A+++g
  gi|121638039|ref|YP_978263.1|  4 L-TVAQIAEIVG 14
                                   4.9999**9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0016
                   HTH_Tnp_ISL3  11 riTlrleayilellles.rsvkavArq 36 
                                    r T+r ++ ile++ ++  +++a A++
  gi|121638039|ref|YP_978263.1| 176 RATRRTDYLILEMAARHhGNIAALAEI 202
                                    78**********************986 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.8
                   HTH_Tnp_ISL3  32 avArqlgvSwtTVwri 47 
                                    avA++  +++ +V r+
  gi|121638039|ref|YP_978263.1| 252 AVAAMAKLTAARVVRV 267
                                    6788888888888775 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0069
                   HTH_Tnp_ISL3  10 sriTlrleayilellles.rsvkavArq 36 
                                    ++ T++l a++++l  e+ +sv +vA+ 
  gi|121638039|ref|YP_978263.1| 309 HQVTNALCAAAVAL--ECgASVEQVAAA 334
                                    789***********..999*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2756.39
//
Query:       gi|121638040|ref|YP_978264.1|  [L=535]
Description: UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-46  158.1   0.0    3.5e-46  157.6   0.0    1.2  1  Mur_ligase_M  Mur ligase middle domain
    5.8e-25   87.4   0.1    5.1e-23   81.2   0.0    2.9  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain
    4.5e-10   39.7   0.1    1.9e-09   37.7   0.1    2.2  1  Mur_ligase    Mur ligase family, catalytic domain
  ------ inclusion threshold ------
      0.032   13.5   0.8       0.12   11.6   0.5    2.2  2  DUF1611       Domain of unknown function (DUF1611_C) P-loop d
      0.078   12.0   0.0       0.13   11.3   0.0    1.2  1  FUSC-like     FUSC-like inner membrane protein yccS


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.0   9.7e-50   3.5e-46       1     191 [.     151     354 ..     151     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 9.7e-50
                                    EESSS-HHHHHHHHHHHHHCT...EEEEETTC............SS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTT CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaaileka...gkvigtvg............ttnneiglpktlaemekkeaeyavlEvsshglgekr 65 
                                    +TGt+GKTTtt+l++a l++a   +++igt+g            tt+++ +l+++la m++ +++++v+Evssh+l+ +r
  gi|121638040|ref|YP_978264.1| 151 ITGTSGKTTTTYLVEAGLRAAgrvAGLIGTIGirvggadlpsalTTPEAPTLQAMLAAMVERGVDTVVMEVSSHALALGR 230
                                    8********************55445555555************************************************ PP

                                    TCCHCBESEEEE---TSTTHHHHSSHHHHHHHHHHHH..HTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTS CS
                   Mur_ligase_M  66 legllkpdvavitnispdHldfhgtlenyaeaKaelf..erlkeegiavinaddpyakelikklkkakvkvvtfglekea 143
                                    ++g ++++v+++tn+s+dHldfh ++ +y+eaKa+lf  ++     +av+ +dd+++++++++++    +++t++ +++ 
  gi|121638040|ref|YP_978264.1| 231 VDG-TRFAVGAFTNLSRDHLDFHPSMADYFEAKASLFdpDSALRARTAVVCIDDDAGRAMAARAA----DAITVSAADRP 305
                                    ***.9********************************542333344*********5555555544....56999999998 PP

                                    ECEEEEEEEEE.TTEEEEEEEEETTEEEEEEESSCSCHHHHHHHHHHHH CS
                   Mur_ligase_M 144 edlraknieek.segteiellevkggeleieipllGkhnvyNalaaiaa 191
                                    + +ra+++  + + g++++ +++ g  ++i i+l+G++nv+N l+a+a+
  gi|121638040|ref|YP_978264.1| 306 AHWRATDVAPTdAGGQQFTAIDPAGVGHHIGIRLPGRYNVANCLVALAI 354
                                    88899966665056677777777888888******************97 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   1.4e-26   5.1e-23       1      90 [.     374     458 ..     374     459 .. 0.97
   2 ?    2.9   0.0     0.037   1.3e+02      32      58 ..     487     512 ..     475     528 .. 0.77

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.4e-26
                                    CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEES CS
                   Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvlgd 80 
                                    v+gRle++++++g++ ++Dyah p++l+ +l++l++  pd+rl +vfg+gg+   r+  +++ +gr+a++lad +vv++d
  gi|121638040|ref|YP_978264.1| 374 VPGRLEQIDRGQGFLALVDYAHKPEALRSVLTTLAH--PDRRLAVVFGAGGD---RDPGKRAPMGRIAAQLADLVVVTDD 448
                                    79********************************77..89************...************************* PP

                                    S-TTSTHHHH CS
                   Mur_ligase_C  81 ypraedsiaa 90 
                                    +pr ed++a+
  gi|121638040|ref|YP_978264.1| 449 NPRDEDPTAI 458
                                    ******9875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.037
                                    HHHHHHSSSSEEEEEEEESTT.CCSCH CS
                   Mur_ligase_C  32 kalreiapdkrlilvfgpggelgertr 58 
                                    +a+++  p + ++l++g g e+g+r+ 
  gi|121638040|ref|YP_978264.1| 487 HAVAWARP-GDVVLIAGKGHETGQRGG 512
                                    44555545.9***********999975 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   5.3e-13   1.9e-09       1      87 [.      61     138 ..      61     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.3e-13
                                    EEEEESTTSCCHHHHHHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHH.HHHHTTEEEEEHHHH CS
                     Mur_ligase   1 eihfigidgrgmsagalflalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpele.aakepgipvesraea 79 
                                    +++++++  + +s+g+lf+al G +++G++++ ++ia+Ga+av+++ a+            e++ +a +p++ +  ++ +
  gi|121638040|ref|YP_978264.1|  61 TVTGVTLRAQDVSPGDLFAALTGSTTHGARHVGDAIARGAVAVLTDPAG----------VAEIAgRAAVPVLVHPAPRGV 130
                                    589**********************************************..........88888899999999999**** PP

                                    HHHHHHCC CS
                     Mur_ligase  80 Laelaarf 87 
                                    L+ laa  
  gi|121638040|ref|YP_978264.1| 131 LGGLAATV 138
                                    **999875 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.3   4.5e+03     151     176 ..      55      80 ..      47     102 .. 0.70
   2 ?   11.6   0.5   3.4e-05      0.12       9      49 ..     140     180 ..     122     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.3
                        DUF1611 151 alaakkkvvgislNtknlseeeakea 176
                                    a++++++v g++l  +++s  ++ +a
  gi|121638040|ref|YP_978264.1|  55 AVTEDRTVTGVTLRAQDVSPGDLFAA 80 
                                    55556679999999998887665554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.4e-05
                        DUF1611   9 evkakrvlvvGTdcavGKrttaleleealeerGlkaafvaT 49 
                                    +++ +r++v+G     GK tt++ +e+ l+++G  a++++T
  gi|121638040|ref|YP_978264.1| 140 GHPSERLTVIGITGTSGKTTTTYLVEAGLRAAGRVAGLIGT 180
                                    678999*****99**********************999998 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.13     111     131 ..     254     274 ..     251     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                      FUSC-like 111 alAdYleaKaslfepdreddl 131
                                    ++AdY eaKaslf+pd++ + 
  gi|121638040|ref|YP_978264.1| 254 SMADYFEAKASLFDPDSALRA 274
                                    59**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2910.40
//
Query:       gi|121638041|ref|YP_978265.1|  [L=344]
Description: hypothetical protein BCG_2176c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.5   8.0    7.1e-09   35.6   3.1    3.2  3  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   3.1     4e-13   7.1e-09       5      80 ..      49     121 ..      46     126 .. 0.90
   2 ?    0.3   0.0     0.041   7.3e+02       3      29 ..     220     245 ..     218     254 .. 0.85
   3 ?    1.4   0.3     0.018   3.3e+02      48      71 ..     298     321 ..     285     328 .. 0.55

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4e-13
                                    HHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHH CS
                            CMD   5 raltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAl 80 
                                    + ++ lre ll   g++++  +e +a av+a+++c +CvdaHt ++  aG t+   a +la  a++ag p+a +++
  gi|121638041|ref|YP_978265.1|  49 AGWATLRETLL--VGQVPRGRKEAVAAAVAASLRCPWCVDAHTTMLYAAGQTDTAAA-ILAGTAPAAGDPNAPYVA 121
                                    67899999999..788************************************88777.*************98654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.041
                                    HHHHHHHHHHHHCCGSSTS-HHHHHHH CS
                            CMD   3 llraltalreallareggLdpkereLi 29 
                                    ++ a++al ++l    ++L+p +r+++
  gi|121638041|ref|YP_978265.1| 220 IATAFAALSHHLDT-APHLPPPTRQVV 245
                                    57899999999998.999******987 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.018
                                    HHHHHTT--HHHHHHHHHHHHHHH CS
                            CMD  48 raAleaGvteeeiaevlaqaaaya 71 
                                    +aA+    t+  +  +la+aa++a
  gi|121638041|ref|YP_978265.1| 298 AAARSLLDTDAALVGALAWAAFTA 321
                                    334444444444445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2223.40
//
Query:       gi|121638042|ref|YP_978266.1|  [L=206]
Description: hypothetical protein BCG_2177c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-10   39.0   1.2    7.2e-10   38.5   0.1    1.9  2  TetR_N     Bacterial regulatory proteins, tetR family
     0.0058   17.0   0.2      0.019   15.3   0.2    1.9  1  HTH_31     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.4   0.5      0.033   14.3   0.5    1.6  1  TetR_C_21  Tetracyclin repressor-like, C-terminal domain
      0.028   14.4   0.0      0.045   13.7   0.0    1.3  1  TetR_C_13  Tetracyclin repressor-like, C-terminal domain
      0.049   13.9   6.7      0.074   13.4   6.1    1.8  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
       0.06   12.9   0.0       0.16   11.5   0.0    1.7  2  HTH_24     Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   2.4e-13   7.2e-10       1      46 [.      14      59 ..      14      60 .. 0.96
   2 ?   -3.4   0.1         3   8.9e+03       3      10 ..      62      69 ..      61      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.4e-13
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   Il aA+   + +G +++++ e+A r+G+sk+ l+r+F+ Ke+L +a
  gi|121638042|ref|YP_978266.1| 14 ILRAAMDIASVKGLSGLSIGELAGRLGMSKSGLFRHFGAKEQLQLA 59
                                   9*****************************************9665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3
                                   HHHHHHHH CS
                         TetR_N  3 daArelfa 10
                                   +aA+ +f+
  gi|121638042|ref|YP_978266.1| 62 EAAVSVFE 69
                                   79999986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   6.4e-06     0.019       9      57 ..      15      71 ..       7      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.4e-06
                         HTH_31  9 lRera.........GLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                   lR++          GLs  e+A+rlg+s+s l r   ++++  ++a++ea++ ++ ++
  gi|121638042|ref|YP_978266.1| 15 LRAAMdiasvkglsGLSIGELAGRLGMSKSGLFRHFGAKEQ-LQLATVEAAVSVFEAE 71
                                   44444666777777**************************6.********99998876 PP

>> TetR_C_21  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   1.1e-05     0.033      43     108 ..     132     193 ..     120     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                      TetR_C_21  43 esleekvaairaaQraGtvdaswkpedlltlvlalasawaaaparaaaaaadaeerarrraavvea 108
                                    + +++  a ++ aQr+G+++a++++ +l + + a a+    a        +d+   +r r+a+ +a
  gi|121638042|ref|YP_978266.1| 132 AGIAAITADVETAQRRGEIRADIEARQLAFELHAYAMEANWALL----LLDDDGAGERARTAIDAA 193
                                    556667789*******************9999887764432222....345555555555555555 PP

>> TetR_C_13  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.045       3      80 ..      83     160 ..      80     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHHHHHHTTTT----HHHHHHHTGGGS-TTHHHHHHHHHHHHHHHHHHHHHHHHCTTSS-TTS-HHHHH CS
                      TetR_C_13   3 lerlrafvedakagmeryefkrGCLvGnLgqEvaalpesfrerleevledwqkrvaacleeaqeageiaadadaeela 80 
                                    ++r+ra+++     +er  f  GC+      +v+++p  +r+r+ ++  +  + ++a +e aq++gei+ad +a++la
  gi|121638042|ref|YP_978266.1|  83 VDRVRALMHAWVGYLERDVFPGGCFFAAAAADVDSQPGPVRDRIAATGRAGIAAITADVETAQRRGEIRADIEARQLA 160
                                    578999999999999************************************************************998 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.1   2.5e-05     0.074      11      87 ..      86     165 ..      80     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                      TetR_C_11  11 Lrallralaealas..pragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadve.lvldlll 87 
                                    +ral++a +  l++   ++g  ++a +a++ + p   + + ++  +   aa+ a ++ A++rGe+rad+ ++ l+++l +
  gi|121638042|ref|YP_978266.1|  86 VRALMHAWVGYLERdvFPGGCFFAAAAADVDSQPGPVRDRIAATGRAGIAAITADVETAQRRGEIRADIEARqLAFELHA 165
                                    5677777777666655349999********9999765555555999999999999**************98614555544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.16      17      38 ..      29      50 ..      28      57 .. 0.87
   2 ?   -4.0   0.0       3.9   1.2e+04      31      38 ..     119     126 ..     118     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                         HTH_24 17 risqreLAerlglSpstvnrrl 38
                                   ++s+ eLA rlg+S+s + r+ 
  gi|121638042|ref|YP_978266.1| 29 GLSIGELAGRLGMSKSGLFRHF 50
                                   89**************998886 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.9
                         HTH_24  31 pstvnrrl 38 
                                    p++v+ r+
  gi|121638042|ref|YP_978266.1| 119 PGPVRDRI 126
                                    79999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1474.72
//
Query:       gi|121638043|ref|YP_978267.1|  [L=288]
Description: hypothetical protein BCG_2178c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-41  142.0   8.8    3.4e-41  141.7   8.8    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   8.8   1.9e-45   3.4e-41      28     245 ..      19     248 ..      17     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 1.9e-45
                 Bac_luciferase  28 laraaEelGfdavwvaehhggpgga................ldaftllaalaaaTerirlgtavtplytrhPavlAqqaa 91 
                                    +a+ aEe Gf ++ v+e+ ++p ++                 d+++ laa+aa+T+r+r+gt+++ + +++P++lA+q+a
  gi|121638043|ref|YP_978267.1|  19 VAVWAEERGFAGLYVPEKTHVPISRstpwpggelpdwyrrcYDPVVALAAAAAVTTRLRVGTGACLVAVHDPILLAKQIA 98 
                                    699******************9999******************************************************* PP

                 Bac_luciferase  92 tLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyv 171
                                    +L  +sg Rf+lg+g g++ +e + +Gv++++r a + + + ++r+lw+ e+v +eG + sv   + +p+p+   +Pv++
  gi|121638043|ref|YP_978267.1|  99 SLCAMSGERFVLGVGFGWNVEELADHGVPFADRIAVTVDKLAAMRALWAAEPVHYEGTHASVPPSWAWPKPAVA-PPVLF 177
                                    ************************************************99*********************888.99*** PP

                 Bac_luciferase 172 aaas.paglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearali 245
                                    +     ++ e+ arh+dg+ +      e+  +++ l+a+ ++agrdpa   ++  + ++ a +++  ++++ra +
  gi|121638043|ref|YP_978267.1| 178 GCRPsARAFEVIARHGDGWQPIE-GYGELLGALPMLHAAFERAGRDPA---TAQVCVYSSAGDPATLHEYRRAGV 248
                                    ***98***************998.555555678999999******555...555555566666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1872.10
//
Query:       gi|121638044|ref|YP_978268.1|  [L=490]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-35  121.0  16.7    2.8e-35  120.5  16.7    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5  16.7   1.6e-39   2.8e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 1.6e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe++aaaa+dla+igs++saa+aaaa+pt+++laa+aDeVS+ai+alf++haq yq+lsaq aa h+qfv+al+a
  gi|121638044|ref|YP_978268.1|  1 MSFVIAAPEVMAAAATDLANIGSSISAASAAAAGPTMGILAAGADEVSVAISALFGSHAQGYQTLSAQLAAYHNQFVRALNA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +agsYa+aEaa
  gi|121638044|ref|YP_978268.1| 83 GAGSYASAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 3250.42
//
Query:       gi|121638045|ref|YP_978269.1|  [L=679]
Description: penicillin-binding membrane protein pbpB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-89  299.5   0.0    3.5e-89  299.0   0.0    1.2  1  Transpeptidase   Penicillin binding protein transpeptidase do
    3.2e-11   43.9   0.2    2.5e-09   37.7   0.2    2.3  1  PBP_dimer        Penicillin-binding Protein dimerisation doma
    0.00029   20.5   0.0     0.0018   17.9   0.0    2.2  1  Beta-lactamase2  Beta-lactamase enzyme family
  ------ inclusion threshold ------
       0.12   12.2   2.9      0.085   12.8   0.5    2.0  2  CHASE3           CHASE3 domain


Domain annotation for each model (and alignments):
>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.0   0.0   7.8e-93   3.5e-89       2     304 ..     339     654 ..     338     656 .. 0.96

  Alignments for each domain:
  == domain 1  score: 299.0 bits;  conditional E-value: 7.8e-93
                                    EEEEEETTT-BEEEEEEESE-TTTHHCC..TCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTS CS
                 Transpeptidase   2 aavvldaktgevlamaskpsydpnakvg..kneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqgg 79 
                                    +avvldaktgevlama+++++dp++++g   +++l n av+s +ePGS+ K+v+a+a +e+g+ +pde+l+ +g  ++gg
  gi|121638045|ref|YP_978269.1| 339 SAVVLDAKTGEVLAMANDNTFDPSQDIGrqGDKQLGNPAVSSPFEPGSVNKIVAASAVIEHGLSSPDEVLQVPGSIQMGG 418
                                    89***************************99***********************************************99 PP

                                    S..ECTCCCC-SSSSEEEHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--B--S..SHHHHHHH CS
                 Transpeptidase  80 qs.ikdweqdnkgsegitlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaGvptr..kwlegati 156
                                     + +++we+      + t + ++ kSsn+++  l+q++g+++++++l+kfglG++tg++lpgesaG++++  +w+++ ++
  gi|121638045|ref|YP_978269.1| 419 VTvHDAWEHGV---MPYTTTGVFGKSSNVGTLMLSQRVGPERYYDMLRKFGLGQRTGVGLPGESAGLVPPidQWSGSTFA 495
                                    999999**997...678*************************************************555558*****999 PP

                                    HHTTT..SBB-HHHHHHHHHHHHTTTEEE--BSEEEEEECTTEEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCT..... CS
                 Transpeptidase 157 sfgiG..ltvtplqlaqayaaiangGklvkPhlvkaivdpdgvrkvkpkelnklpisketaekvkeglkgvvsrg..... 229
                                    ++ iG  l++t lq+  +y+aian+G++v+P+++ka+v+pdg+r+++p+++  +++s++ta++v+++l+ vv+r+     
  gi|121638045|ref|YP_978269.1| 496 NLPIGqgLSMTLLQMTGMYQAIANDGVRVPPRIIKATVAPDGSRTEEPRPDDIRVVSAQTAQTVRQMLRAVVQRDpmgyq 575
                                    9999999********************************************************************98877 PP

                                    TTTGCG.TCTTS--EEEEEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEEEECTCS...SSSSCCHHHHHHHHH CS
                 Transpeptidase 230 sgtata.avegykvagKTGTAevagkkgngkkegakiswfvgyapadnpkyavavlieqpk...eaaggkaaapiakki 304
                                    +gt+ +  v+gy++agKTGTA++++++++++ ++ ++++f+g+a+adnp+y++ +++++p+   + a g++aap++++i
  gi|121638045|ref|YP_978269.1| 576 QGTGPTaGVPGYQMAGKTGTAQQINPGCGCYFDDVYWITFAGIATADNPRYVIGIMLDNPArnsDGAPGHSAAPLFHNI 654
                                    66666689*****************************************************99999999********99 PP

>> PBP_dimer  Penicillin-binding Protein dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2   5.6e-13   2.5e-09       2     176 ..     131     294 ..     130     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.6e-13
                                    .EE----EE-TTS-EEEEEEEEEEEEEEESSS-HHHHHHH............HHHHHHHCHHHTTS-H..HHHHHHHCCC CS
                      PBP_dimer   2 ipapRGeIyDrngrlLAtnrpsytltitpsklkkkkalek............ikklaklleseenldd..erleelalkk 67 
                                    +pa+RG+I+Drn++ LA   ++ +lt++p+ + ++ ++ +            ++++a+ ++ + n ++  + + +     
  gi|121638045|ref|YP_978269.1| 131 QPAARGSIVDRNNDRLAFTIEARALTFQPKRIRRQLEEARkktsaapdpqqrLRDIAQEVAGKLNNKPdaAAVLK----- 205
                                    69****************************999887665456778888877755555555333333332222222..... PP

                                    CTSSTTSCECCCCCEECHHHCCCHHHHHCSTT-EEEEEEEEEETTTSTTHHHH-EEEEC-HHHHHCCCCHTCCTTCEEEE CS
                      PBP_dimer  68 nsykaykpvviaediseeevarikenakdlpGinievepkRyYpkgelaahvlGyvgkiteeelekykekgyssgdliGk 147
                                    + ++ +++v +a+ ++ + +++i ++   +p + +e +  R+Yp g+laa+v+G +                      G 
  gi|121638045|ref|YP_978269.1| 206 KLQSDETFVYLARAVDPAVASAICAK---YPEVGAERQDLRQYPGGSLAANVVGGIDWD-----------------GHGL 265
                                    45667777888888888888888765...566********************9988765.................78** PP

                                    SHHHHHTHHHHHECCCEEEEEEECTSSCC CS
                      PBP_dimer 148 sGlEkqyEeeLrGkkGkrqvkvdarGril 176
                                     GlE ++++ L G++G+ ++ + + G ++
  gi|121638045|ref|YP_978269.1| 266 LGLEDSLDAVLAGTDGSVTYDRGSDGVVI 294
                                    ********************999999876 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     4e-07    0.0018      13     181 ..     380     596 ..     377     630 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-07
                                    S-EE-GGGGHHHHHHHHHHHHHC.TSTGTT-EEEGGHHHHTSSSTSGGGSTTSEEEHHHHHHHHHHTT-HHHHHHHHHHH CS
                Beta-lactamase2  13 eefpaaStiKvpillalleavle.gklslderltltaedivggsgilqklpgktlslrdlltlmiavSDNtAtnlLidrl 91 
                                     +f+ +S+ K++ +     av e g  s+de l++  +   gg  + + ++ + +++ +  t +   S N+ t +L +r+
  gi|121638045|ref|YP_978269.1| 380 SPFEPGSVNKIVAA----SAVIEhGLSSPDEVLQVPGSIQMGGVTVHDAWEHGVMPYTT--TGVFGKSSNVGTLMLSQRV 453
                                    58999*******99....77766488889999999999888999999988888888754..789999************* PP

                                    THHHHHHHHHHCTHTTSB--SHTT................CCHHHTTSSTTEE-HHHHHHHHHHHHHTTSSHHHHHHHH. CS
                Beta-lactamase2  92 gleavnawlkelglretrlrrklp................dleaadkdkrntttardlarllealargellspeellei. 154
                                    g+e+  ++l++ gl + + +  lp                 + + + ++  + t  +++ + +a+a++ +  p +++++ 
  gi|121638045|ref|YP_978269.1| 454 GPERYYDMLRKFGLGQRT-GVGLPgesaglvppidqwsgsTFANLPIGQGLSMTLLQMTGMYQAIANDGVRVPPRIIKAt 532
                                    *************97554.445677999999*******997788888888899999999999999998655554233333 PP

                                    .....................HHT-STTTTTTTTTT................TTSEEEEEEEEE CS
                Beta-lactamase2 155 .....................lsnqqfrdrlaaglp................egvrvahKtGel 181
                                                           +q+ r++l+a ++                +g++ a KtG+ 
  gi|121638045|ref|YP_978269.1| 533 vapdgsrteeprpddirvvsaQTAQTVRQMLRAVVQrdpmgyqqgtgptagvPGYQMAGKTGTA 596
                                    3334444444444444443323356666666666666666666666666666677777777773 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   1.9e-05     0.085      49      84 ..     160     196 ..     110     229 .. 0.79
   2 ?   -3.8   0.1       2.5   1.1e+04     116     133 ..     547     564 ..     544     568 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                         CHASE3  49 aeiqealeelreltadnpeqqerldrlealieqkl.a 84 
                                    ++i+++lee+r+ t+  p+ q+rl ++ + ++ kl +
  gi|121638045|ref|YP_978269.1| 160 KRIRRQLEEARKKTSAAPDPQQRLRDIAQEVAGKLnN 196
                                    589*****************************99944 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.5
                         CHASE3 116 eiraliaemrdeerrlla 133
                                    +ir  +a+  ++ r+ l+
  gi|121638045|ref|YP_978269.1| 547 DIRVVSAQTAQTVRQMLR 564
                                    556666666555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 4587.93
//
Query:       gi|121638046|ref|YP_978270.1|  [L=384]
Description: proline rich membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   11.3   0.0       0.42   10.5   0.0    1.4  1  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.3e-05      0.42      16      62 ..     121     173 ..     110     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.3e-05
                       LapA_dom  16 elpLsllllvafgiGallgwllsl.....wsyl.rlrrelrrlkkkikkleke 62 
                                    ++p ++l+++++g+G+ l++ ls+     + +l   r + r l++  ++le++
  gi|121638046|ref|YP_978270.1| 121 KVPFVVLVIGSLGVGLGLTLWLSTdaaerSYQLsNARERTRMLQQHKEALERD 173
                                    89**************8888888867666444413444444445555556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2980.89
//
Query:       gi|121638047|ref|YP_978271.1|  [L=396]
Description: S-adenosyl-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.1e-119  396.7   0.0   9.5e-119  396.5   0.0    1.0  1  Methyltransf_5   MraW methylase family
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.027   15.2   0.0    1.7  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.5   0.0  1.1e-122  9.5e-119       2     308 ..      63     379 ..      62     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.5 bits;  conditional E-value: 1.1e-122
                                    XXX--TTTHHHHHHT--........-TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EEE CS
                 Methyltransf_5   2 leHvpVLlqevvellep........kedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrltl 73 
                                    + HvpVL+q+++ell+p        ++++v++DaT+GaggH+e++Le l+ lrlig+drD++al++a++rL +f++rltl
  gi|121638047|ref|YP_978271.1|  63 FGHVPVLAQRCFELLTPaltryypdGSQAVLLDATIGAGGHAERFLEGLPGLRLIGLDRDPTALDVARSRLVRFADRLTL 142
                                    67****************************************************************************** PP

                                    EES-GGGHHHHHHHTT...TT-EEEEEEE-S--HHHHH-GGG---SSS--BS---S-TTSS--HHHHHHH--HHHHHHHH CS
                 Methyltransf_5  74 vkgnfkelkealaean...vtkvdgillDLGvSslqldkaerGFsfaedapLDmRmdqsaeltAaevlnrlseeeLakil 150
                                    v++++++l +alae++   v++vdgil+DLGvSs+qld+aerGF++a+dapLDmRmd+++ ltAa+++n+++e++La+il
  gi|121638047|ref|YP_978271.1| 143 VHTRYDCLGAALAESGyaaVGSVDGILFDLGVSSMQLDRAERGFAYATDAPLDMRMDPTTPLTAADIVNTYDEAALADIL 222
                                    ***************999999*********************************************************** PP

                                    HHHH--TTHHHHHHHHHHHHHHS---BHHHHHHHHHHHS-------..-TTHHHHHHHHHHHHTHHHHHHHHHHHHHHHE CS
                 Methyltransf_5 151 keygeekfakriakaivekrkkkpiettkelaevikkvvpakekrkkihpatrvFQAlRIavNdEleeleelleaalell 230
                                    ++ygee+fa+ria+ iv++r+k+p+++t+el+ ++++++pa+++r ++hpa+r+FQAlRIavNdEle+l+++++aal++l
  gi|121638047|ref|YP_978271.1| 223 RRYGEERFARRIAAGIVRRRAKTPFTSTAELVALLYQAIPAPARRVGGHPAKRTFQALRIAVNDELESLRTAVPAALDAL 302
                                    ******************************************************************************** PP

                                    EEEEEEEEEESSHHHHHHHHHHHHHTT-------------------EEEEE.E.E---HHHHHH-GGGTT-EEEEEEE CS
                 Methyltransf_5 231 akggrlavisFhSledrivkkvfkeaskkeevPaglpvaseelkaklklitkkpilpseeeikeNprsrsakLrviek 308
                                    a ggr+av++++Sledrivk+vf ea + +++Paglpv+  +++++++ +t+ +  +s +ei++Nprs++++Lr++++
  gi|121638047|ref|YP_978271.1| 303 AIGGRIAVLAYQSLEDRIVKRVFAEAVA-SATPAGLPVELPGHEPRFRSLTHGAERASVAEIERNPRSTPVRLRALQR 379
                                    ***************************9.79*******************************************9987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     3e-06     0.027       2      56 ..      94     148 ..      93     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCC CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdae 56 
                                    Ld+  G G +++++++ l+  +++g+D ++++l+ ar+r+ +   ++++v+   +
  gi|121638047|ref|YP_978271.1|  94 LDATIGAGGHAERFLEGLPGLRLIGLDRDPTALDVARSRLVRFADRLTLVHTRYD 148
                                    8999*************955*******************9764336666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2903.56
//
Query:       gi|121638048|ref|YP_978272.1|  [L=143]
Description: cell division protein MraZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-45  152.0   0.0    5.7e-22   77.5   0.0    2.0  2  MraZ      MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   8.1e-25   1.5e-20       1      72 []       1      71 [.       1      71 [. 0.99
   2 !   77.5   0.0   3.2e-26   5.7e-22       2      70 ..      73     140 ..      72     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 8.1e-25
                                   CCTTEEEEEB-TTSEEE--CHHHHHTTSCSEEEEEECCSEEEEEEHHHHHHHHHCHHTS-CCCHHHCHHHHH CS
                           MraZ  1 mfagatevelDakGRlllPaklreeaklekevvviGvsncLeiwpraeWekyeeelaeeslsekaerallrl 72
                                   mf+g+++ +lD+kGRl+lPak+r+++++  ++v+++++++L ++pra +e++ ++++++++s++++ra+lr+
  gi|121638048|ref|YP_978272.1|  1 MFLGTYTPKLDDKGRLTLPAKFRDALAGG-LMVTKSQDHSLAVYPRAAFEQLARRASKAPRSNPEARAFLRN 71
                                   9****************************.***************************************996 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 3.2e-26
                                    CTTEEEEEB-TTSEEE--CHHHHHTTSCSEEEEEECCSEEEEEEHHHHHHHHHCHHTS-CCCHHHCHHH CS
                           MraZ   2 fagatevelDakGRlllPaklreeaklekevvviGvsncLeiwpraeWekyeeelaeeslsekaerall 70 
                                     ag++e++ D++GR++l+a++r++a+l+k++vviG  ++Leiw+ + W+ y++  +ee++s+++++al 
  gi|121638048|ref|YP_978272.1|  73 AAGTDEQHPDSQGRITLSADHRRYASLSKDCVVIGAVDYLEIWDAQAWQNYQQI-HEENFSAASDEALG 140
                                    689************************************************999.9******9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1017.06
//
Query:       gi|121638049|ref|YP_978273.1|  [L=134]
Description: hypothetical protein BCG_2184c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28   99.2   1.5    2.2e-28   98.4   0.2    1.8  2  DUF3040   Protein of unknown function (DUF3040)
  ------ inclusion threshold ------
      0.084   13.1   1.6       0.13   12.5   1.6    1.2  1  DUF3784   Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.2   2.4e-32   2.2e-28       1      83 [.       1      86 [.       1      87 [. 0.94
   2 ?   -0.4   0.1      0.16   1.4e+03      23      43 ..      92     112 ..      89     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.4e-32
                        DUF3040  1 MpLsehEqrvLeeiEraLaaeDPklaaalrggaararrrslrrlavlavllfvaGllllvlGvaaaa......vvlgvvGfv 76
                                   MpLs+hEqr+L++iE+aL+aeDPk+a+++rgg  ra+    rr ++++++lf++Gl +lv Gva +       ++l+v+Gfv
  gi|121638049|ref|YP_978273.1|  1 MPLSDHEQRMLDQIESALYAEDPKFASSVRGGGFRAPTA--RR-RLQGAALFIIGLGMLVSGVAFKEtmigsfPILSVFGFV 79
                                   9*******************************9996665..56.8*****************999999************** PP

                        DUF3040 77 vmlagvv 83
                                   vm++gvv
  gi|121638049|ref|YP_978273.1| 80 VMFGGVV 86
                                   *****98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.16
                        DUF3040  23 Pklaaalrggaar.arrrslrr 43 
                                    P+l  ++  g +   ++r +rr
  gi|121638049|ref|YP_978273.1|  92 PRLSGRMDRGGSAaGASR-QRR 112
                                    888888855544424443.343 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.6   1.4e-05      0.13      44      87 ..      42      89 ..      39      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                        DUF3784 44 rfmgivllligilflllgll....saiesealliialiviiiiviyli 87
                                   r  g +l++ig+ +l++g+     ++     l++++++v++++v+y+i
  gi|121638049|ref|YP_978273.1| 42 RLQGAALFIIGLGMLVSGVAfketMIGSFPILSVFGFVVMFGGVVYAI 89
                                   67899***************7764444555555557777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 977.51
//
Query:       gi|121638050|ref|YP_978274.1|  [L=206]
Description: hypothetical protein BCG_2185 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-07   31.8   0.1    5.7e-07   29.4   0.0    2.0  2  FR47             FR47-like protein
    1.5e-05   25.3   0.0    2.5e-05   24.6   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      4e-05   23.6   0.0    6.4e-05   22.9   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.8e-05   23.1   0.0    0.00011   22.5   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.21   9.4e+02      30      47 ..      43      60 ..      28      82 .. 0.69
   2 !   29.4   0.0   1.3e-10   5.7e-07       1      80 [.     104     184 ..     104     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                                   -GGG-SSSHHHHHHHHHH CS
                           FR47 30 lpehrrrGlgsrlvkala 47
                                   l+  rrrG+  + + +++
  gi|121638050|ref|YP_978274.1| 43 LEHIRRRGWQAVAAVEVT 60
                                   456666666555555554 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.3e-10
                                    EEEEEETTT--EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE...EETT-HHHHHHHHHHT- CS
                           FR47   1 vlGlyrkelgelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllv...vvasNtpsirlyeklGf 77 
                                    vlGl r+   +la  +l   + el  l +lp +++rGlg  l++ l ++  + +++vll    ++ +++++ rly +lGf
  gi|121638050|ref|YP_978274.1| 104 VLGLQRSGFPRLAIARLMTSYFELTELHILPRAQGRGLGEALARRLLAG--RDEDNVLLStpeTNGEDNRAWRLYRRLGF 181
                                    5899999999999999999999*********************998765..3445555551124456799********** PP

                                    EEE CS
                           FR47  78 eki 80 
                                    + i
  gi|121638050|ref|YP_978274.1| 182 TDI 184
                                    987 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.5e-09   2.5e-05      23      75 ..     118     182 ..      95     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.5e-09
                                    ES.....TCTEEEEE-GGGTTSSHHHHHHH.HTTSEEEEE.EEEE....THH....HHHHHHHHTTEE CS
                 Acetyltransf_7  23 ld.....aeitrlaVdpeyrgkGiGraLle.aaekgiile.qlel....nae....kaikfYeklGFe 75 
                                           +e+t+l ++p ++g+G+G aL + +   g + e ++ l    + +    +a ++Y++lGF+
  gi|121638050|ref|YP_978274.1| 118 ARlmtsyFELTELHILPRAQGRGLGEALARrL-LAG-RDEdNVLLstpeT-NgednRAWRLYRRLGFT 182
                                    33444446777799***************943.223.2122223322221.133459999*******7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.4e-08   6.4e-05      45     110 ..     117     185 ..      99     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.4e-08
                Acetyltransf_10  45 viel.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                                    +++l ++  +++ l + p ++g+G+g+aL  ++++  ++d+  l + + n  +  a ++Y++lGF+++ 
  gi|121638050|ref|YP_978274.1| 117 IARLmTSYFELTELHILPRAQGRGLGEALARRLLAGRDEDNVLLsTPETNGEDnRAWRLYRRLGFTDII 185
                                    556657777999*************************99999999888887666***********9875 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.4e-08   0.00011      60     117 .]     124     181 ..      95     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.4e-08
                                    EEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEE...EEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  60 vayieslaVspeyrgkGlGsaLlealeeraree.gikkivl...aveedndaairlYeklGF 117
                                    + ++ +l++ p ++g+GlG aL + l+   r+e +   + l   ++   +++a rlY++lGF
  gi|121638050|ref|YP_978274.1| 124 YFELTELHILPRAQGRGLGEALARRLLA-GRDEdN---VLLstpETNGEDNRAWRLYRRLGF 181
                                    557889*********************9.888833...3444478877789******88**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1414.02
//
Query:       gi|121638051|ref|YP_978275.1|  [L=227]
Description: lipoprotein lppM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.5   0.1       0.14   12.2   0.1    2.3  1  DUF834    Domain of unknown function (DUF834)


Domain annotation for each model (and alignments):
>> DUF834  Domain of unknown function (DUF834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     8e-06      0.14      26      47 ..     132     153 ..     130     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-06
                         DUF834  26 epaAGllLglAePtvaaAqsGD 47 
                                    +p+A+++L++A P+ ++ + GD
  gi|121638051|ref|YP_978275.1| 132 DPDADVELTVAFPAAVTSTNGD 153
                                    699*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1560.93
//
Query:       gi|121638052|ref|YP_978276.1|  [L=301]
Description: hypothetical protein BCG_2187c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2169.13
//
Query:       gi|121638053|ref|YP_978277.1|  [L=352]
Description: geranylgeranyl pyrophosphate synthetase idsA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-47  161.4   0.0    2.5e-47  161.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.0   1.4e-51   2.5e-47      10     242 ..      36     290 ..      29     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 1.4e-51
                                    HHHHSSS--HHHHHHHHHHHHHS.CGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HH............. CS
                polyprenyl_synt  10 ylveagGKrlRpllvllaaealk.eeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcah............. 75 
                                     +v  gGKrlRpl+     +a++ +e     +++ l  ++ellha  LvhDD++D s tRRG+p+a+             
  gi|121638053|ref|YP_978277.1|  36 DFVLGGGKRLRPLFAYWGWHAVAsRE--PDPDVLLLFSALELLHAWALVHDDLIDRSATRRGRPTAQlryaalhrdrdwr 113
                                    45569******************433..4589***********************************8888887777777 PP

                                    ...HCTCHHHHHHHHHHHHHHHHHHHHHHH......STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHH CS
                polyprenyl_synt  76 ...rlvGnklAindgdfllarafellaklf......ekslellelfsevllqtveGqlldleeekdddlskfsleeylei 146
                                        ++G+++Ai+ gd+ +++a  +++k++      + + ++ ++ +++  ++  Gq+ld+ +e +     +s+e  +++
  gi|121638053|ref|YP_978277.1| 114 gspDQFGMSAAILLGDLAQVWADDIVSKVCqsalapDAQRRVHRVWADIRNEVLGGQYLDIVAEASAA---ESIESAMNV 190
                                    76666***********************9999887555599********************7774344...46******* PP

                                    HHHHTH.HHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHH CS
                polyprenyl_synt 147 vkyKTa.ylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkale 225
                                     + KTa y+++ p++l+ ++a   +++++ ++++g  lG+aFQ++DD+l +fgdp+v+gKp g+D++ gk t+++ +a+e
  gi|121638053|ref|YP_978277.1| 191 ATLKTAcYTVSRPLQLGTAAAADRSDVAAIFEHFGADLGVAFQLRDDVLGVFGDPAVTGKPSGDDLKSGKRTVLVAEAVE 270
                                    *********************9878999**************************************************** PP

                                    CT-HH...HHHHHHHHTTSS CS
                polyprenyl_synt 226 laspe...qrkvlkeilgkk 242
                                    la+++    +k l++ +g +
  gi|121638053|ref|YP_978277.1| 271 LADRSdplAAKLLRTSIGTR 290
                                    87754111456677766644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2605.77
//
Query:       gi|121638054|ref|YP_978278.1|  [L=567]
Description: hypothetical protein BCG_2189 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.9   5.0       0.05   12.9   4.8    1.9  1  EpsG      EpsG family


Domain annotation for each model (and alignments):
>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.8   2.8e-06      0.05      45     191 ..     178     339 ..     163     434 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-06
                           EpsG  45 nfEpgyvllnllvkslgfd....yqfflfilalitllllfvfikkyskn.....lflslllfllslffllsmnqiRq.gl 114
                                    ++ p ++l++++v  + ++     +++l +++l  l ll++++ ++        +  ++++ l +l  ++ m+++ + +l
  gi|121638054|ref|YP_978278.1| 178 PYGPAFILVAKFVTVIVGNnvvaGTMLLRLCMLPGLALLVWATPRLASHlgthgPTALWICVLNPLVLIHLMGGVHNeML 257
                                    6778999999999996666688889999999999************9999***955555555566666666777765388 PP

                           EpsG 115 AiailllaliflikkkkikflllillAslfHsSaiiflpl...yfllklklk.......lkllllllafillllllldli 184
                                    +++++  ++++ ++++ ++ ++li +A+ +  +a i lp+   ++l+   l+       +     +la+  + ll+++ +
  gi|121638054|ref|YP_978278.1| 258 MVGLMTAGIALTVQGRNVAGIILITVAIAVKATAGIALPFlvwVWLRH--LRerrgyrpV---QAFLAAAAISLLIFVAV 332
                                    999************************************996633333..3333664442...33333333333333333 PP

                           EpsG 185 lsllsll 191
                                    +++ls +
  gi|121638054|ref|YP_978278.1| 333 FAVLSAV 339
                                    3333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4139.29
//
Query:       gi|121638055|ref|YP_978279.1|  [L=146]
Description: regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-29  101.5   0.4    3.2e-29  100.8   0.1    1.5  2  Rv2175c_C  Rv2175c C-terminal domain of unknown function
     0.0018   18.4   0.0     0.0032   17.6   0.0    1.4  1  HTH_17     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.67     6e+03      38      48 ..      48      58 ..      32      61 .. 0.59
   2 !  100.8   0.1   3.6e-33   3.2e-29       1      56 []      78     145 ..      78     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.67
                      Rv2175c_C 38 dALregrkrEV 48
                                   + Lreg+   V
  gi|121638055|ref|YP_978279.1| 48 QQLREGHLVAV 58
                                   34555555555 PP

  == domain 2  score: 100.8 bits;  conditional E-value: 3.6e-33
                      Rv2175c_C   1 VkgLpGtltvLrDgGfddeeilrWLFteDesLp............grPidALregrkrEVkRrAqAlA 56 
                                    Vk+LpG+lt+L+DgG++d+ei+rWLFt+D+sL+            +rP+dAL+++++rEV+RrAqA+A
  gi|121638055|ref|YP_978279.1|  78 VKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTitrdgsrdavsnARPVDALHAHQAREVVRRAQAMA 145
                                    9*******************************************99*********************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.6e-07    0.0032       3      39 ..      31      67 ..      29      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-07
                         HTH_17  3 tveEaAelLgvsrstvyrlirrgelpaak.iGrrwrip 39
                                   +   +AelLgv +s+v + +r+g l a++  G+ + ip
  gi|121638055|ref|YP_978279.1| 31 DLPRVAELLGVPVSKVAQQLREGHLVAVRrAGG-VVIP 67
                                   56679********************88874666.8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 972.00
//
Query:       gi|121638056|ref|YP_978280.1|  [L=399]
Description: transmembrane serine/threonine-protein kinase L pknL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-47  159.6   0.0    1.2e-46  159.3   0.0    1.1  1  Pkinase         Protein kinase domain
    2.6e-29  102.3   0.0    3.5e-29  101.9   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    0.00031   20.7   6.6      0.012   15.5   0.1    3.0  3  APH             Phosphotransferase enzyme family
      0.001   17.9   0.0     0.0017   17.2   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0041   16.5   0.0     0.0086   15.4   0.0    1.5  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.015   14.6   0.0      0.026   13.9   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.085   12.4   0.0       0.14   11.7   0.0    1.3  1  RIO1            RIO1 family
      0.098   11.6   0.0       0.13   11.1   0.0    1.1  1  Haspin_kinase   Haspin like kinase domain
       0.23   11.1   0.0        5.4    6.6   0.0    2.1  2  FTA2            Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0   5.9e-50   1.2e-46       3     253 ..      21     265 ..      19     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 5.9e-50
                                    EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--T CS
                        Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyve 81 
                                    ++ k+ +G++++Vy++++ + ++ vA+K+++ + a +++  ++++ E + +++l+ + +v +y+  ++ ++ +lv+e++e
  gi|121638056|ref|YP_978280.1|  21 VQAKIASGGTSTVYRGLDVRLDRPVALKVMDARYAGDEQFlTRFRLEARAVARLNNRALVAVYDQGKDGRHPFLVMELIE 100
                                    567999*****************************999989*************************************** PP

                                    TEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS..BCTTTS CS
                        Pkinase  82 ggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk..ltsfvg 159
                                    gg+l +ll ++g ++++ +  +++ +l gl+  H++g++HrD+KpeNiLi+++g++K++DFGl++ +   s   +  + g
  gi|121638056|ref|YP_978280.1| 101 GGTLRELLIERGPMPPHAVVAVLRPVLGGLAAAHRAGLVHRDVKPENILISDDGDVKLADFGLVRAVAAASItsTGVILG 180
                                    ******************************************************************9998875577789* PP

                                    CGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHH CS
                        Pkinase 160 tseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakd 239
                                    t  Yl+PE +++ + ++ +Dv+s+Gv++yelltg++pf g++  + +++ ld          ++  +++  + +++++ +
  gi|121638056|ref|YP_978280.1| 181 TAAYLSPEQVRDGNADPRSDVYSVGVLVYELLTGHTPFTGDSALSIAYQRLDA---------DVPRASAVIDGVPPQFDE 251
                                    ***************************************77777666666655.........444555666666888888 PP

                                    HHHHHT-SSGCCST CS
                        Pkinase 240 llkkllkkdpkkRl 253
                                    l+    +++p +R+
  gi|121638056|ref|YP_978280.1| 252 LVACATARNPADRY 265
                                    88888888888886 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   1.7e-32   3.5e-29       4     218 ..      22     231 ..      20     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 1.7e-32
                                    EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE CS
                    Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee..keelleeakimkklkhpnivkllgvctkeepllivte 81 
                                    + k+++G  ++V++g       + +  Va+K++++++  +e   +++  ea+   +l+++ +v+++    ++++ ++v+e
  gi|121638056|ref|YP_978280.1|  22 QAKIASGGTSTVYRGLDV----RLDRPVALKVMDARYAGDEqfLTRFRLEARAVARLNNRALVAVYDQGKDGRHPFLVME 97 
                                    568899999999999887....7899*******8877666545799999******************************* PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEE CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvk 161
                                    +++gG+L++ L ++   ++  + ++ +   v  G++  ++  lvHrd+   N+L+s++  vk++DfGL r++    + ++
  gi|121638056|ref|YP_978280.1|  98 LIEGGTLRELLIER--GPMPPHAVVAVLRPVLGGLAAAHRAGLVHRDVKPENILISDDGDVKLADFGLVRAV-AAASITS 174
                                    ************98..9*******************************************************.7777788 PP

                                    TTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHH.HHHHH CS
                    Pkinase_Tyr 162 keeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglknee.vlekl 218
                                    ++       +++pE +++++   +sDv+s Gvl++E++t g++p++g ++ + ++++l
  gi|121638056|ref|YP_978280.1| 175 TGVILGTAAYLSPEQVRDGNADPRSDVYSVGVLVYELLT-GHTPFTGDSALSiAYQRL 231
                                    8899999********************************.****99875544145555 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0012       2.3       7     107 ..      28     135 ..      22     136 .. 0.66
   2 !   15.5   0.1   6.2e-06     0.012     161     197 ..     131     165 ..     118     170 .. 0.76
   3 ?    0.7   0.2      0.21   4.2e+02      60     134 ..     228     303 ..     208     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                                    -.SSCEEEEEEETT..--EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTE.EEEEEE----EE CS
                            APH   7 ggasnrtylvttpa..gryvlrrnppa..raaeeirrevallrlLakagvpvPevlagdtddeeigl.lfalieyvpgrs 81 
                                    gg+s  +y+  + +  ++++l++  ++    ++++ r+  + r++a+++ ++ ++++   d++  g+ +f+++e ++g +
  gi|121638056|ref|YP_978280.1|  28 GGTST-VYRGLDVRldRPVALKVMDARyaGDEQFLTRFRLEARAVARLNNRALVAVY---DQGKDGRhPFLVMELIEGGT 103
                                    44444.666666665458888887777656777777888888888888887767776...45555555999999999999 PP

                                    -SS......HHHHHHHHHHHHHHHHHHCCHHC CS
                            APH  82 llr......klsaaqlpellealgeflaalhq 107
                                    l++      ++ +    ++l+ +   laa h+
  gi|121638056|ref|YP_978280.1| 104 LRElliergPMPPHAVVAVLRPVLGGLAAAHR 135
                                    98877777766665566666655555555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.2e-06
                                    -SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 161 pgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                    +++ +++l+H+D +p N+l+ +d++    + Df++++
  gi|121638056|ref|YP_978280.1| 131 AAAHRAGLVHRDVKPENILISDDGDVK--LADFGLVR 165
                                    33789****************666666..88888775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.21
                                    TBS-EEETTEEEEEEE----EE-SS..HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHH CS
                            APH  60 gdtddeeigllfalieyvpgrsllr..klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesata 134
                                    ++  d++ ++ +a+i +vp++  +     +a+   + +++++++ a+l ++ +++l l+ f+ + +++ +q  sa+ 
  gi|121638056|ref|YP_978280.1| 228 YQRLDADVPRASAVIDGVPPQFDELvaCATARNPADRYADAIAMGADLEAI-AEELALPEFRVPAPRNSAQHRSAAL 303
                                    555555555566666666665433345445677777888888888888888.7777777777776666666666644 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.3e-07    0.0017     306     399 ..     117     203 ..     114     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-07
                 Pkinase_fungal 306 kellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaiev 385
                                     +++++lr ++ g+   +  ag++HrD+  +Nili      ++    L+D+ l   ++  s + + +   GT+++++ e 
  gi|121638056|ref|YP_978280.1| 117 HAVVAVLRPVLGGLAAAH-RAGLVHRDVKPENILIS-----DDGDVKLADFGLVRAVAAASIT-STGVILGTAAYLSPEQ 189
                                    567888999999999999.9****************.....677889*******999975555.55999********999 PP

                 Pkinase_fungal 386 lkgeeHsyrhDLES 399
                                    +++++  +r D+ S
  gi|121638056|ref|YP_978280.1| 190 VRDGNADPRSDVYS 203
                                    99988888888766 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.3e-06    0.0086     161     254 ..     134     222 ..     127     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-06
                    Kinase-like 161 qakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve.....kgfaPpEllgsrggytrknktkmthkldaWq 235
                                    +  glvh +++++n+l   +g ++l +f+ Lvra + + + ++      +++  pE +            +     d++ 
  gi|121638056|ref|YP_978280.1| 134 HRAGLVHRDVKPENILISDDGDVKLADFG-LVRAVAAASITSTGvilgtAAYLSPEQVRD---------GNADPRSDVYS 203
                                    789*************************7.888888888777764555555555554433.........34455667788 PP

                    Kinase-like 236 lGlviyriwclklPltlat 254
                                    +G+ +y +   + P+t + 
  gi|121638056|ref|YP_978280.1| 204 VGVLVYELLTGHTPFTGDS 222
                                    8888887777777777765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.026      77     162 ..      77     157 ..      34     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                            Kdo  77 kpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeee 156
                                    +++ a + + + +++ +l++e +eg   L +ll +   ++ +   a l+ v    a  hrag+ H+d+ + nil+  ++ 
  gi|121638056|ref|YP_978280.1|  77 RALVAVYDQGKDGRHPFLVMELIEGGT-LRELLIERGPMPPHAVVAVLRPVLGGLAAAHRAGLVHRDVKPENILISDDG- 154
                                    3455555666667999*****999975.777777644456666667777777777888*****************9998. PP

                            Kdo 157 eeaeiw 162
                                        + 
  gi|121638056|ref|YP_978280.1| 155 ---DVK 157
                                    ...444 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.14      80     150 ..      91     162 ..      47     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                                    TTEEEEE--EETTEEGGBHHHCG-.HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                           RIO1  80 rhvlvmefigedgvaapklkdvee.eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                    +  lvme+i+   ++   ++  ++  +    +++ vl  ++++  +aglvH D+   N+l+++d +v + D++
  gi|121638056|ref|YP_978280.1|  91 HPFLVMELIEGGTLRELLIERGPMpPHAVVAVLRPVLGGLAAAH-RAGLVHRDVKPENILISDDgDVKLADFG 162
                                    4579******4444444445555667788888899999877776.******************9899998875 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.7e-05      0.13     229     258 ..     139     173 ..     120     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.7e-05
                  Haspin_kinase 229 EHRdLhldniLvdknlnvtlidlklsRle.....s 258
                                     HRd + +niL+ + + v l d+ l R+      +
  gi|121638056|ref|YP_978280.1| 139 VHRDVKPENILISDDGDVKLADFGLVRAVaaasiT 173
                                    5**************************97443333 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.058   1.2e+02      79      97 ..      58      76 ..      45      83 .. 0.82
   2 ?    6.6   0.0    0.0027       5.4     174     212 ..     119     162 ..     109     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.058
                           FTA2 79 asysdpfasECRAfgRLke 97
                                   +++++ f  E+RA +RL++
  gi|121638056|ref|YP_978280.1| 58 EQFLTRFRLEARAVARLNN 76
                                   6899*************54 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                           FTA2 174 evsqlpkllrdlkklhklgIvvrDlkeenyi.....dgkLvDls 212
                                     v+ l+ +l  l  +h++g+v+rD+k+en++     d kL D++
  gi|121638056|ref|YP_978280.1| 119 VVAVLRPVLGGLAAAHRAGLVHRDVKPENILisddgDVKLADFG 162
                                    56778889999******************975553344666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2856.27
//
Query:       gi|121638057|ref|YP_978281.1|  [L=221]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-23   82.2   0.0    3.8e-23   81.6   0.0    1.3  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   2.1e-27   3.8e-23       2      87 .]      57     143 ..      56     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 2.1e-27
                 Transposase_20   2 elLesipGiGpvtaaallaei.gdlrr.fksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                    el+ sipGiG   +a++++ei  d+   f+sa++la+++ l+p +++S++k++ ++ +++Gn++l+ +L+e+A+aa+r++
  gi|121638057|ref|YP_978281.1|  57 ELIASIPGIGVGASATVISEIgADPAAwFPSAEHLASWVRLCPGNHESAGKRH-HGARRKGNQHLQPVLVECAWAAVRTD 135
                                    799******************8888556***********************98.667777******************** PP

                 Transposase_20  80 pelrayye 87 
                                      lr+yy+
  gi|121638057|ref|YP_978281.1| 136 GYLREYYR 143
                                    ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1448.14
//
Query:       gi|121638058|ref|YP_978282.1|  [L=462]
Description: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.4e-186  620.3   0.0   1.7e-186  620.0   0.0    1.0  1  DAHP_synth_2  Class-II DAHP synthetase family


Domain annotation for each model (and alignments):
>> DAHP_synth_2  Class-II DAHP synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.0   0.0  9.6e-191  1.7e-186       8     437 .]      31     457 ..      25     457 .. 0.97

  Alignments for each domain:
  == domain 1  score: 620.0 bits;  conditional E-value: 9.6e-191
                   DAHP_synth_2   8 skpaaqqpeyedeealekvlkklkklpplvtaeeieklkeqLaevaegkaflLqgGdCaEsfeectaekieeklkvllqm 87 
                                    +kpaaqqp+++ ++al ++++ l+++pp+ +++ei +l+eqLa+va+g+aflLqgGdCaE+f + t+ +i+ +++ llqm
  gi|121638058|ref|YP_978282.1|  31 AKPAAQQPTWPADQAL-AMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQM 109
                                    799*******987777.57899********************************************************** PP

                   DAHP_synth_2  88 slvltlgaslpvvkigRiAGqyaKPRSsetetvdgkelpsyrGdivnglelteeeRepdPerllkaYfhsaatlnlvral 167
                                    ++vlt+gas+pvvk++RiAGqyaKPRS++ + ++   l syrGd++ng+++++++Re+dP+rl++aY++++a++nlvral
  gi|121638058|ref|YP_978282.1| 110 AVVLTYGASMPVVKVARIAGQYAKPRSADIDALG---LRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRAL 186
                                    *****************************99988...9****************************************** PP

                   DAHP_synth_2 168 lssgladlekveewnlefvksselkekyeelaeeleealefmkaigvdeeeeeeleevdlytsHeaLlleyeealtr... 244
                                    +ssgla+l+ v++wn+efv++s+++++ye+la+e+++ l+fm+a+gv    +++l+++++y+sHeaL+l+ye+a+ r   
  gi|121638058|ref|YP_978282.1| 187 TSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVA---DRNLQTAEIYASHEALVLDYERAMLRlsd 263
                                    ***********************************************4...4789**********************554 PP

                   DAHP_synth_2 245 .kdsetklydtsahflWiGdRTrqldgahveflrgieNpigvKvgpslkpeelvelldilnPekepGrltlitRlgadkv 323
                                     +d e +l+d+sah++WiG+RTrq+dgah+ f++ i+Np+gvK+gp+++pe +ve++++l+P+++pGrltl++R+g++kv
  gi|121638058|ref|YP_978282.1| 264 gEDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKV 343
                                    4466667************************************************************************* PP

                   DAHP_synth_2 324 eelLpklieavkksgakvvwvcDpmHGNtltsssglKtRefedilkEvksfleihkeegsvlgGvhlEltgedVtEclgg 403
                                    ++lLp+++e+v+++g++v+w+cDpmHGNt++ss+g+KtR+f++i++Ev+ f+e+h++ g+++gG+h+E+tge+VtEclgg
  gi|121638058|ref|YP_978282.1| 344 RDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGG 423
                                    ******************************************************************************** PP

                   DAHP_synth_2 404 seelseedlserYetlcDPRLnaeqslelaflia 437
                                    ++++se+dl+ rYet+cDPRLn++qslelafl+a
  gi|121638058|ref|YP_978282.1| 424 AQDISETDLAGRYETACDPRLNTQQSLELAFLVA 457
                                    ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3432.76
//
Query:       gi|121638059|ref|YP_978283.1|  [L=168]
Description: hypothetical protein BCG_2194c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-19   70.2   0.0    3.3e-19   69.5   0.0    1.4  1  DUF5051         3' exoribonuclease, RNase T-like
  ------ inclusion threshold ------
      0.026   14.7   0.7       0.17   12.0   0.2    2.1  2  Acetyltransf_6  Acetyltransferase (GNAT) domain
      0.076   13.4   0.0       0.24   11.8   0.0    1.9  2  DUF3046         Protein of unknown function (DUF3046)


Domain annotation for each model (and alignments):
>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   5.5e-23   3.3e-19       1     164 [.       1     155 [.       1     157 [. 0.78

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 5.5e-23
                        DUF5051   1 nklmiDiEtlgneetaelvsIGaVffpetG.eFyaeidlesd.eeagidaetieWWlkqskearaell.kdtqeakslkd 77 
                                    +++++D+E+++  +t+el+sIG+V   e+G e+ya+++  +d e+ag      + W +++   +       +q + s ++
  gi|121638059|ref|YP_978283.1|   1 MRYFYDTEFIEDGHTIELISIGVV--AEDGrEYYAVSTE-FDpERAG------S-WVRTHVLPKL--PpPASQLWRSRQQ 68 
                                    689*******888***********..*********9887.4413344......3.4444332222..22334579***** PP

                        DUF5051  78 alqaleeFl....ekslkvwangasfDlviLraafel.......lipwkywndrdvrtlvalapelekgeekkreipfeg 146
                                    ++++leeFl     +s+++wa+++++D+v L+++  +                r+ r l++l ++  +g+   r  p+  
  gi|121638059|ref|YP_978283.1|  69 IRLDLEEFLridgTDSIELWAWVGAYDHVALCQL--WgpmtalpP-----TVPRFTRELRQLWED--RGC--PRMPPRPR 137
                                    *************999******************..766765431.....556888889998866..443..56777789 PP

                        DUF5051 147 vkHnALaDAkhqakavsa 164
                                    + H+AL+DA+ q + ++ 
  gi|121638059|ref|YP_978283.1| 138 DVHDALVDARDQLRRFRL 155
                                    9*********99887765 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.096   5.8e+02      82     107 ..      18      43 ..      12      50 .. 0.84
   2 ?   12.0   0.2   2.9e-05      0.17      31      79 ..     113     161 ..     106     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.096
                 Acetyltransf_6  82 pvAvalglrsgdrlyywlggydpela 107
                                    ++++ ++ ++g+ +y+  + +dpe a
  gi|121638059|ref|YP_978283.1|  18 LISIGVVAEDGREYYAVSTEFDPERA 43 
                                    677778899999**********9965 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.9e-05
                 Acetyltransf_6  31 leallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrld 79 
                                    + ++ + +r++w+ r +   +p++r+ + +l++a ++  + rl +   d
  gi|121638059|ref|YP_978283.1| 113 VPRFTRELRQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDD 161
                                    67899999*******999999*************998888888887765 PP

>> DUF3046  Protein of unknown function (DUF3046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.24      10      31 ..      34      55 ..      31      62 .. 0.92
   2 ?   -2.9   0.0       1.5   9.1e+03      46      56 ..     136     146 ..     135     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                        DUF3046 10 veeeFGsayarslardhvlsel 31
                                   v++eF +++a s++r+hvl++l
  gi|121638059|ref|YP_978283.1| 34 VSTEFDPERAGSWVRTHVLPKL 55
                                   789****************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                        DUF3046  46 prdVWralcda 56 
                                    prdV  al+da
  gi|121638059|ref|YP_978283.1| 136 PRDVHDALVDA 146
                                    78998898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1294.33
//
Query:       gi|121638060|ref|YP_978284.1|  [L=295]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.9   1.9      0.026   14.9   1.9    1.8  2  DUF4396   Domain of unknown function (DUF4396)


Domain annotation for each model (and alignments):
>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.9   1.5e-06     0.026      41     139 ..      94     188 ..      59     189 .. 0.74
   2 ?   -3.1   0.0      0.51   9.1e+03      89     104 ..     195     210 ..     194     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-06
                        DUF4396  41 tmilsvvlalllgllletalllre.kglslaealktAlkadtlSmlamevgmnlvmllllgamdaeleltsplfWfslql 119
                                      i + ++++   l+l  ++l  + + + + e  +t++ a ++ +++  +  +++  l++  + +   + + + W++lq 
  gi|121638060|ref|YP_978284.1|  94 FTIAASIFGVGAALVLDEYALILHlSDVYWEEDGRTSVDAVFAAVAVAGLLIMGLHPLIF--FLT---VRQGANWVVLQT 168
                                    34555667777777887666666669*******************999999999998886..444...7899******** PP

                        DUF4396 120 sllaGflvalPvNywllkkg 139
                                     l+aG +++lP  ++ l kg
  gi|121638060|ref|YP_978284.1| 169 TLIAGLVLTLPLAVVVLLKG 188
                                    ***********999888776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.51
                        DUF4396  89 vgmnlvmllllgamda 104
                                    +gm++v+ll++ga+  
  gi|121638060|ref|YP_978284.1| 195 LGMFVVVLLVVGAVRL 210
                                    5788888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1828.31
//
Query:       gi|121638061|ref|YP_978285.1|  [L=427]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-60  204.5  38.4      2e-60  204.5  38.4    3.6  4  GT87       Glycosyltransferase family 87
  ------ inclusion threshold ------
      0.012   15.5   0.7        1.4    8.9   0.1    2.8  3  DUF2678    Protein of unknown function (DUF2678)


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   1.3    0.0012        11     186     219 ..       7      41 ..       1      48 [. 0.76
   2 !  204.5  38.4   2.2e-64     2e-60       1     239 []      80     324 ..      80     324 .. 0.94
   3 ?   -7.2  14.1         2   1.8e+04       6      63 ..     336     402 ..     331     411 .. 0.67
   4 ?   -0.5   3.4     0.094   8.4e+02     193     215 ..     389     411 ..     369     422 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
                           GT87 186 lalgls.avtllwlvlvllvvalaavaawrlrrre 219
                                     ++g + ++ +lw +l+ll+ ++++++awrl+ + 
  gi|121638061|ref|YP_978285.1|   7 PEVGSRlGRRVLWCLLWLLAGVALGYVAWRLFGHT 41 
                                    44555445789*********999999999997554 PP

  == domain 2  score: 204.5 bits;  conditional E-value: 2.2e-64
                           GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgral..............asavalalllaalalep 66 
                                    FtYPP+aa+lf+p+a+l +++a++++++l+l++l+++++++l+ l+ +               + av+ ++++a+++lep
  gi|121638061|ref|YP_978285.1|  80 FTYPPLAAVLFSPFAWLQMPAASVAITVLTLVLLIASTAIVLTGLDAWPtsrlvpaparlrrlWLAVL-IVAPATIWLEP 158
                                    9********************************************9999**********998544444.45689****** PP

                           GT87  67 vlstlgfGqinllllllvlldllllrrrrpllaGlliGlaaaiKltPalfllylllrrrwralaaaaatalvltalplll 146
                                    + s+++fGqin++l++lv++d++++r  +p+++Gl++Gl++a+KltPa+flly+llrr+ ra+++a a+++v+t+l+++l
  gi|121638061|ref|YP_978285.1| 159 ISSNFAFGQINVVLMTLVIVDCFPRR--TPWPRGLMLGLGIALKLTPAVFLLYFLLRRDGRAALTALASFAVATLLGFVL 236
                                    ***********************988..9*************************************************** PP

                           GT87 147 lppssleyfletlfdtseri..aedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlr.rrerlla 223
                                    ++++s+ey+++tl+ t +ri  a++++ q+   +ag+lar++ +g++++ +lw++  llv+a++ +a++r++ ++e++la
  gi|121638061|ref|YP_978285.1| 237 AWRDSWEYWTHTLHHT-DRIgaAALNTDQN---IAGALARLT-IGDDERFALWVAGSLLVLAATIWAMRRVLrAGEPTLA 311
                                    ****************.***9999999999...*******54.44437999*******************9967788888 PP

                           GT87 224 laaallvallalLvsP 239
                                    +    +val++l+vsP
  gi|121638061|ref|YP_978285.1| 312 VI---CVALFGLVVSP 324
                                    88...**********9 PP

  == domain 3  score: -7.2 bits;  conditional E-value: 2
                           GT87   6 faallfaplallpyglalalwallnlaallla.lrlllrrlgral........asavalalllaala 63 
                                     a+l++  l++    +ala++ l+ ++++ ++ + ll ++ ++++         s v++al+++++a
  gi|121638061|ref|YP_978285.1| 336 PAVLVIGLLGWRRRNVALAMLSLAGVVLMRWTpIDLLPQHRETTAvwwrqlagMSYVWWALAVIVVA 402
                                    5778888888888888888888888888888877777776555557777776655555555444444 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.094
                           GT87 193 vtllwlvlvllvvalaavaawrl 215
                                     +++w +l+++vva + v a+  
  gi|121638061|ref|YP_978285.1| 389 MSYVWWALAVIVVAGLTVTARMT 411
                                    23444444555555555555544 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0056        50      14      78 ..      58     121 ..      49     129 .. 0.78
   2 ?    8.9   0.1   0.00015       1.4      31      98 ..     162     227 ..     157     237 .. 0.75
   3 ?   -3.3   0.0      0.95   8.5e+03      67      91 ..     352     375 ..     350     379 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0056
                        DUF2678  14 ldnrplfgetsardriinlvvggltsllvlvtvvssfvfpslppkplniffavcillisssvivl 78 
                                    ld rpl+g     ++ i l +  +t   +   + s f + ++p  ++ i     +lli+s++ivl
  gi|121638061|ref|YP_978285.1|  58 LDGRPLYGGGVLFHTPIGLNLP-FTYPPLAAVLFSPFAWLQMPAASVAITVLTLVLLIASTAIVL 121
                                    6666666666666666666653.45555556788999**************************98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                        DUF2678  31 nlvvggltsllvlvtvvssfvfpslppkplniffavcillisssvivlifwyrqgdlepkfrnliyyi 98 
                                    n+++g +  +l  +t+v    fp+  p p  +++ + i l  + ++ l+++  + d    +  l  + 
  gi|121638061|ref|YP_978285.1| 162 NFAFGQINVVL--MTLVIVDCFPRRTPWPRGLMLGLGIALKLTPAVFLLYFLLRRDGRAALTALASFA 227
                                    77788887655..5666666799999999999999999999999999999876666666666655555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.95
                        DUF2678  67 cillisssvivlifwyrqgdlepkf 91 
                                     + + s + +vl+ w    dl p+ 
  gi|121638061|ref|YP_978285.1| 352 ALAMLSLAGVVLMRWTP-IDLLPQH 375
                                    66788889999998853.4555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3044.53
//
Query:       gi|121638062|ref|YP_978286.1|  [L=247]
Description: 1-acylglycerol-3-phosphate O-acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-29  101.0   0.0    5.1e-29  100.6   0.0    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   2.8e-33   5.1e-29       2     134 ..      21     151 ..      20     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.8e-33
                Acyltransferase   2 vrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsi.pllgflmr....llgfifidRksna 76 
                                     +v+gle++p++gpail++NH   +D ++l l++     +r+++++ak e+++   l g++ r     +g ++idR++++
  gi|121638062|ref|YP_978286.1|  21 PKVEGLEYIPSSGPAILASNHLAVADSFYLPLVV-----RRRIWFLAKSEYFTGtGLKGWINRwfysVSGQVPIDRTNAD 95 
                                    689*******************************.....8************988888877777776************* PP

                Acyltransferase  77 raagsleniselleegklvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                    +a+g+l++++ ll +gkl++++PEGtrs +g+l++ k+Gl+rla+++  gvp++Pva+
  gi|121638062|ref|YP_978286.1|  96 SAQGALQTAVVLLGQGKLLGMYPEGTRSPDGRLYKGKTGLARLALHT--GVPVIPVAM 151
                                    ***********************************************..*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1612.71
//
Query:       gi|121638063|ref|YP_978287.1|  [L=131]
Description: hypothetical protein BCG_2198c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 966.35
//
Query:       gi|121638064|ref|YP_978288.1|  [L=379]
Description: hypothetical protein BCG_2199c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-25   90.3   0.0      2e-25   89.6   0.0    1.3  1  ArsA_ATPase     Anion-transporting ATPase
    1.2e-13   50.3   0.0    2.9e-13   49.1   0.0    1.7  1  ArsA_HSP20      HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.058   13.5   1.7       0.17   12.1   1.7    1.8  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.0   3.3e-29     2e-25      33     296 ..       1     276 [.       1     282 [. 0.84

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.3e-29
                                    EEEE-STTTHHHHHHTS....--BSS-EEET........SSEEEEE--HHHHHHHHHCCHHGGGSCCHHHHHHHHHHHHH CS
                    ArsA_ATPase  33 llistDPAhslsDsfdq....klgkeptkvk........eNLsavEidpeveleeakqevqkeeeallgleeledvlaee 100
                                    +++stD Ahsl D++        + +p +v           L a  +d+   le  + +v ++ ++ +  +el+ +  ee
  gi|121638064|ref|YP_978288.1|   1 MVVSTDQAHSLGDVLGIavppTGQGDPVRVLaydpeaggGFLDALALDTLALLEGRWLHVVETLDRRFPGSELSSIAPEE 80 
                                    69**************9666633445555544555444467999999999******************99********** PP

                                    HTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHH CS
                    ArsA_ATPase 101 laslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglggvsi 180
                                    l +lPGi+e+l ++++ ++  ++ +d +v+D a T ++lr+l lp +++ ++e++   ++ ls         +g+ +   
  gi|121638064|ref|YP_978288.1|  81 LCALPGIQEVLGLHAVGELAAARRWDRIVVDCASTADALRMLTLPATFGLYVERAWPRHRRLS---------IGADDGRS 151
                                    *****************************************************9988888443.........23334444 PP

                                    HHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-.TTCSSS....... CS
                    ArsA_ATPase 181 eealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNkll.peeeqe....... 252
                                       +e le   +++++++  ltd    s  lV++pE+++  E  R + +L+++g++v+ ++vN+ll ++e+ e       
  gi|121638064|ref|YP_978288.1| 152 AVLAELLERIRASVERLSTLLTDGALVSAHLVLTPERVVAAEAVRTLGSLALMGVRVEELLVNQLLvQDENYEyrslpdh 231
                                    445566667777788888**********************************************6614444446767654 PP

                                    .TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHH CS
                    ArsA_ATPase 253 .nCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekl 296
                                       +  ++r   q+++l++++ +  d+++v +p l++E  G ++l
  gi|121638064|ref|YP_978288.1| 232 pAFHWYAERIGEQRAVLDDLDATIGDVALVLVPHLAGEPIGPKAL 276
                                    445667899999**************************9998887 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   4.9e-17   2.9e-13       4      63 .]     311     370 ..     308     370 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.9e-17
                     ArsA_HSP20   4 yvlkldLPfvdkeeidlsrsgdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                    y+l+l+LP +d++ + l r++d+L++++g  rR++ L svl+r++v +A ++ g+L++rF
  gi|121638064|ref|YP_978288.1| 311 YRLRLALPQLDPGTLTLGRADDDLIVSAGGMRRRVRLASVLRRCTVLDAHLRGGELTVRF 370
                                    9**********************************************************9 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   2.8e-05      0.17      25      95 ..     122     190 ..      97     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                 Acetyltransf_6  25 atdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrl 95 
                                     t p+++   +e+ + +++r  ++ ad+ + a l++ll++   +   rl++l  dg +v+++l+l  ++++
  gi|121638064|ref|YP_978288.1| 122 LTLPATFGLYVERAWPRHRR-LSIGADDGRSAVLAELLERIR-ASVERLSTLLTDGALVSAHLVLTPERVV 190
                                    22233333344444445555.5*******************4.44448****************9877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2801.68
//
Query:       gi|121638065|ref|YP_978289.1|  [L=144]
Description: hypothetical protein BCG_2200c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-16   59.6   0.0    4.6e-16   59.4   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.1e-14   53.8   0.0      4e-14   52.9   0.0    1.5  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    1.8e-05   24.9   0.0    4.6e-05   23.6   0.0    1.6  2  DUF2505          Protein of unknown function (DUF2505)


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   7.7e-20   4.6e-16       3     143 .]       4     143 ..       2     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.7e-20
                                    EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.SEEEEEEEE.EE.T.TTTEEEEE CS
                Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.gtvreelve.vd.p.egrllsyr 78 
                                    k+t+++ i+a+p +V ++++d e++p+W++e+++ve+ + ++   g   + r+    +  +++l++ ++ p ++ +ls++
  gi|121638065|ref|YP_978289.1|   4 KTTQTIYIDADPGEVMKAIADIEAYPQWISEYKEVEILEADDE--GYPKRARMLMDaAIFKDTLIMsYEwPeDRQSLSWT 81 
                                    689********************************98874444..4444444433234488888875667778******* PP

                                    EE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  79 ivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                    +++   +++ ++t++++p g gt+vt++ ++d   l+ p+ + + +ka ++ ++ +L+ Lk+r+e
  gi|121638065|ref|YP_978289.1|  82 LESSSLLKSLEGTYRLAPKGSGTEVTYELAVD---LAVPMIGMLKRKAERRLIDGALKDLKKRVE 143
                                    *878888999*******************999...45666556677778888***********98 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   6.7e-18     4e-14       1     129 [.      11     138 ..      11     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 6.7e-18
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE.........EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes......glsadlevgfggltesftarvtldppeeitfklvegdf 74 
                                    ++a++ +v++++ad+e yp++++++++ve+le +++      ++ +d  + +  l +s++    ++     t +    + 
  gi|121638065|ref|YP_978289.1|  11 IDADPGEVMKAIADIEAYPQWISEYKEVEILEADDEgypkraRMLMDAAIFKDTLIMSYEWPEDRQSLSW-TLE-SSSLL 88 
                                    789********************************87776655555777777777777644443333333.222.44589 PP

                                    CEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  75 kslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldellaal 129
                                    ksleg+ ++++ ++   gt  +v++e+ ++ a+p++g+l +++++r +d  l +l
  gi|121638065|ref|YP_978289.1|  89 KSLEGTYRLAPKGS---GT--EVTYELAVDLAVPMIGMLKRKAERRLIDGALKDL 138
                                    99999999988876...55..55555556669**************999888776 PP

>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.21   1.3e+03       6      31 ..      11      36 ..       6      65 .. 0.68
   2 !   23.6   0.0   7.7e-09   4.6e-05      77     132 ..      68     120 ..      38     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                        DUF2505  6 ypapvdrvyaaltdeeywearleevg 31
                                   ++a++ +v++a++d e + + + e++
  gi|121638065|ref|YP_978289.1| 11 IDADPGEVMKAIADIEAYPQWISEYK 36
                                   68889999999999877766666543 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 7.7e-09
                        DUF2505  77 teswgplsdgratgtvsasvkgapvelsGtltLepegegtrlevegevkvkiPlvG 132
                                    + +w    ++r + +++ +++    +l+Gt++L p+g+gt++++e  v+  +P++G
  gi|121638065|ref|YP_978289.1|  68 SYEW---PEDRQSLSWTLESSSLLKSLEGTYRLAPKGSGTEVTYELAVDLAVPMIG 120
                                    4455...358889999999****9*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1067.73
//
Query:       gi|121638066|ref|YP_978290.1|  [L=129]
Description: hypothetical protein BCG_2201c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00045   20.5   3.7    0.00063   20.0   3.7    1.5  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.7   3.5e-08   0.00063       4      64 ..       6      63 ..       3     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-08
                                   EEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSE.STSSSTTTEEEEECCCSSEEEEE CS
                Polyketide_cyc2  4 vtvsvviaappekVwalvsdfenwprWhpevarveleg.gggpargvegtvrvggrgtvree 64
                                   + +++ +aa++++V a+v+d ++w+rW p ++  ++++ + +  +g+++tv+ + +g + e 
  gi|121638066|ref|YP_978290.1|  6 IADETYVAADAARVSAAVADRCSWRRWWPDLR-LQVTEdRAD--KGIRWTVTGALTG-TMEI 63
                                   667889***********************998.555542344..4888888866533.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1018.18
//
Query:       gi|121638067|ref|YP_978291.1|  [L=170]
Description: hypothetical protein BCG_2202 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-10   40.7   0.0    1.4e-10   40.3   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   8.1e-15   1.4e-10       5      67 ..      26      90 ..      22      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8.1e-15
                                   HHHSTTSEEEEE..CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHH CS
                    AMP-binding  5 aaktpdkvalvd..sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallai 67
                                    +  pd v + +  +g ++ +T++e  ++++++A gL slGv+ gdrV+i++ +++ew ++++ai
  gi|121638067|ref|YP_978291.1| 26 ERDDPDYVIYQRliDGVWTDVTCAEAANQIRAAALGLISLGVQAGDRVVIFSATRYEWAILDFAI 90
                                   55677888775588899***********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1236.81
//
Query:       gi|121638068|ref|YP_978292.1|  [L=508]
Description: long-chain-fatty-acid-CoA ligase fadD15 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-76  256.6   0.0    3.9e-76  256.3   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.3   0.0   2.2e-80   3.9e-76      70     422 ..       1     375 [.       1     376 [. 0.88

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 2.2e-80
                                    TT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                    AMP-binding  70 aGavvvplnptltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                    +Gav+vp++ t++ae+++++l+dsea vl+   +++  + +++e  ++++a ++v+++   +++  ++l e+  s + ae
  gi|121638068|ref|YP_978292.1|   1 MGAVTVPIYETSSAEQVRWVLQDSEAVVLF--AETDShATMVAELSGSVPALREVLQIAGSGPNALDRLTEAGASVDPAE 78 
                                    69****************************..677777899*************************99999998887774 PP

                                    -TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT CS
                    AMP-binding 149 kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsG 228
                                       + ++l++ d+a++iYTSGTTG+PKG++l++ nlv+ ++ +  ++   l++++++l++lplah+++  +  ++a++s 
  gi|121638068|ref|YP_978292.1|  79 LTARLAALRSTDPATLIYTSGTTGRPKGCQLTQSNLVHEIKGARAYHPTLLRKGERLLVFLPLAHVLAR-AISMAAFHSK 157
                                    34466789*******************************999763322446789**************6.********** PP

                                    -EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHC........................... CS
                    AMP-binding 229 atvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkak........................... 280
                                     tv++ +  +      ll +++ +k+tv+++vPrv+e++ + + + +aa + k                           
  gi|121638068|ref|YP_978292.1| 158 VTVGFTSDIKN-----LLPMLAVFKPTVVVSVPRVFEKVYNtA-EQNAANAGKgrifaiaaqtavdwseacdrggpglll 231
                                    *****886665.....4569999****************7744.333333333557777778999999999999999999 PP

                                    .................CGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE CS
                    AMP-binding 281 .................dlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkp 342
                                                      l++  r +++gg+pl + l +f+r  + + ++egYGl+Et+g v++ + ++   k+g+vGkp
  gi|121638068|ref|YP_978292.1| 232 rakhavfdrlvyrklraALGGnCRAAVSGGAPLGARLGHFYRGAGLT-IYEGYGLSETSGGVAISQFND--LKIGTVGKP 308
                                    999999999999999988888899999*****************887.**************9544333..489****** PP

                                    -TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 343 lpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +pg+ ++i+D+           Gellvrg  v++gY+++++at eaf+  ++w++TGDlg +dedG l i+gRkk++i++
  gi|121638068|ref|YP_978292.1| 309 VPGNSLRIADD-----------GELLVRGGVVFSGYWRNEQATTEAFT--DGWFKTGDLGAVDEDGFLTITGRKKEIIVT 375
                                    **********8...........9************************9..57**************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3639.71
//
Query:       gi|121638069|ref|YP_978293.1|  [L=385]
Description: hypothetical protein BCG_2204c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-44  151.8   0.0    2.5e-44  150.8   0.0    1.5  2  Glycos_transf_1  Glycosyl transferases group 1
    7.6e-30  104.1   0.1    1.4e-29  103.3   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.4e-13   49.6   1.8    9.1e-13   48.6   1.2    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-10   41.8   0.0    2.1e-10   40.9   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.13   11.0   0.0       0.19   10.4   0.0    1.1  1  Coprogen_oxidas  Coproporphyrinogen III oxidase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.8   0.0     7e-48   2.5e-44       4     172 .]     187     360 ..     184     360 .. 0.97
   2 ?   -1.9   0.0      0.58   2.1e+03     139     159 ..     361     381 ..     359     384 .. 0.78

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 7e-48
                                    HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsr 83 
                                    + rk++++ ++++++++++rl+++Kg+d+l++a+++++++  + + lvi+G+g+++++l+kla+ +++ d+v+f+g v  
  gi|121638069|ref|YP_978293.1| 187 ELRKRYRL-GERPTVVCLSRLVPRKGQDTLVTALPSIRRR-VDGAALVIVGGGPYLETLRKLAHDCGVADHVTFTGGVAT 264
                                    55666666.7999************************998.*************************************** PP

                                    SSHHHHHHCESEEEEEESS.......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                Glycos_transf_1  84 edleellknadifvlpsis.......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                    ++l++ +  ad+f++p+++       Eg+Giv lEA aag+pvia n+gg++e+v++++tGl+v+  +++  a+a+++ll
  gi|121638069|ref|YP_978293.1| 265 DELPAHHALADVFAMPCRTrgagmdvEGLGIVFLEASAAGVPVIAGNSGGAPETVQHNKTGLVVDGRSVDRVADAVAELL 344
                                    ******************************************************************************** PP

                                    HSHHHHHHHHHHHHHH CS
                Glycos_transf_1 157 edeelrerlgenarkr 172
                                     d+++++++g ++r++
  gi|121638069|ref|YP_978293.1| 345 IDRDRAVAMGAAGREW 360
                                    *************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.58
                                    EE-TT-HHHHHHHHHHHHHSH CS
                Glycos_transf_1 139 lvkpnnaealaeairkllede 159
                                    + ++  +++la++++++l+ +
  gi|121638069|ref|YP_978293.1| 361 VTAQWRWDTLAAKLADFLRGD 381
                                    455559**********99865 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.1   3.8e-33   1.4e-29       1     133 [.     197     345 ..     197     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 3.8e-33
                                    SEEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH- CS
                Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaa 73 
                                    rp++++++rl+ ++kg+d l+ a+p +r++ d + lvivG+gp  +  l++la+  g++++v+ftG v  ++l+++ a a
  gi|121638069|ref|YP_978293.1| 197 RPTVVCLSRLV-PRKGQDTLVTALPSIRRRvDgAALVIVGGGPyLE-TLRKLAHdcGVADHVTFTGGVatDELPAHHALA 274
                                    689*******6.56**************88768*********9875.999888679************9677******** PP

                                    SEEEE--.........---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  74 dvfvaPs.........egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                    dvf +P          eg+g++ lEa aag+pv+a + gg++e+v  +++gl+v+ ++++  a+a+++Ll 
  gi|121638069|ref|YP_978293.1| 275 DVFAMPCrtrgagmdvEGLGIVFLEASAAGVPVIAGNSGGAPETVqhNKTGLVVDGRSVDRVADAVAELLI 345
                                    *******9988887777****************************988*******999***********96 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   1.2   2.5e-16   9.1e-13       2     170 .]      16     177 ..      15     177 .. 0.87
   2 ?   -1.8   0.0      0.76   2.7e+03     142     162 ..     182     201 ..     180     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.5e-16
                 Glyco_transf_4   2 GGverhvleLaraLar.rGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                    GG++ ++ e++ +L   r h  tv++p+++g+ +  +    ++ rv + ++   l  ++   r+rrl+ ++++  v    
  gi|121638069|ref|YP_978293.1|  16 GGIQSYLGEFVGRLVGsRAHAMTVYAPQWKGADAFDDAARAAGYRVVRHPSTVMLPGPTVDVRMRRLIAEHDIETVWFGA 95 
                                    99************99899************9999974444444444555777788899999**************6666 PP

                 Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                    +a+l + + ++r++   ++ ++ Hg++         +   +++r ++rr+ + +d v+ vS +t+ ++++ +g p++ ++
  gi|121638069|ref|YP_978293.1|  96 AAPLALLAPRARLAGASRVLASTHGHE-------VGWSMLPVARSVLRRIGDGTDVVTFVSSYTRSRFASAFG-PAASLE 167
                                    66666666666668999**********.......8999999********************************.99**** PP

                 Glyco_transf_4 161 VipnGvDler 170
                                     +p+GvD++r
  gi|121638069|ref|YP_978293.1| 168 YLPPGVDTDR 177
                                    ********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.76
                 Glyco_transf_4 142 eatadelrerygvppekitVi 162
                                    +a+++elr+ry++  e+ tV+
  gi|121638069|ref|YP_978293.1| 182 PAARAELRKRYRLG-ERPTVV 201
                                    68999999999998.565554 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   5.7e-14   2.1e-10       9      90 ..     291     374 ..     270     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 5.7e-14
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                    e++  +++Ea a+G+++++  + g +e ++ +k++++++  +++ +a+++++ll +++++ a+++a+re+v a+ ++d  
  gi|121638069|ref|YP_978293.1| 291 EGLGIVFLEASAAGVPVIAGNSGGAPETVQHNKTGLVVDgrSVDRVADAVAELLIDRDRAVAMGAAGREWVTAQWRWDTL 370
                                    677889************************************************************************99 PP

                Glyco_trans_1_2  87 aeql 90 
                                    a++l
  gi|121638069|ref|YP_978293.1| 371 AAKL 374
                                    9887 PP

>> Coprogen_oxidas  Coproporphyrinogen III oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.2e-05      0.19      83     128 ..      52      99 ..      22     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.2e-05
                Coprogen_oxidas  83 leffaagvslvihprnPlvP..tvhlnyryfeaeekkkawWFgGgaDL 128
                                        aag  +v hp+  ++P  tv + +r + ae++ +++WFg  a L
  gi|121638069|ref|YP_978293.1|  52 DAARAAGYRVVRHPSTVMLPgpTVDVRMRRLIAEHDIETVWFGAAAPL 99 
                                    556899************97225666666666666789*****87755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2595.79
//
Query:       gi|121638070|ref|YP_978294.1|  [L=257]
Description: hypothetical protein BCG_2205c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   17.5   0.0     0.0075   16.5   0.0    1.6  1  DUF4157   Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
      0.061   13.1   0.0       0.11   12.3   0.0    1.6  1  BSP       Peptidase of plants and bacteria


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.4e-07    0.0075      42      74 ..     111     143 ..      95     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-07
                        DUF4157  42 TlgndivfaageyqpesaagrellaHELtHvvq 74 
                                     +g+ ivfa+g+  ++ aa r +l+HEL H + 
  gi|121638070|ref|YP_978294.1| 111 VVGQRIVFAPGAAHMSPAALRIVLGHELFHYAA 143
                                    58****************************775 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05      0.11      96     131 ..     128     164 ..      28     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                            BSP  96 aevtgvLthelvhvyqweaeg.rapggliEGiAdyvR 131
                                    a+++ vL hel h     ++  +ap +l EG+Ad+v+
  gi|121638070|ref|YP_978294.1| 128 AALRIVLGHELFHYAARADTAlDAPRWLAEGVADFVA 164
                                    677889*******776666555**************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1684.33
//
Query:       gi|121638071|ref|YP_978295.1|  [L=385]
Description: hypothetical protein BCG_2206c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-23   81.0   0.0    1.3e-22   79.8   0.0    1.6  1  NLPC_P60         NlpC/P60 family
    0.00016   21.5   4.8    0.00032   20.5   4.6    1.6  1  DUF4254          Protein of unknown function (DUF4254)
     0.0015   18.7   0.2       0.63   10.1   0.0    3.3  3  Peptidase_C92    Permuted papain-like amidase enzyme, YaeF/Yi
  ------ inclusion threshold ------
        0.1   13.0   6.1       0.22   11.9   6.1    1.6  1  Dsh_C            Segment polarity protein dishevelled (Dsh) C
       0.15   12.4   0.5       0.51   10.7   0.0    2.0  2  LRAT             Lecithin retinol acyltransferase
       0.17   11.9  14.0        1.8    8.6   2.5    2.4  2  DHR10            Designed helical repeat protein 10 domain
        3.1    8.3  13.5        4.6    7.8   2.5    2.1  2  APG6_N           Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   5.2e-26   1.3e-22       1      90 [.     285     370 ..     285     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 5.2e-26
                                    T-BB-TT--BTTEB-HHHHHHHHHHTTT----SSHHHHCCCSEE..EEGGG--TTEEEEESGTGGESEEEEEEETTEEEE CS
                       NLPC_P60   1 gkpYrwGGkspsgfDCsglvryafakagielprssgeqeaagkkkeiskselkrGDLvffktkkgisHvgiYlgngkmlh 80 
                                    g pY+wGG  p gfDCsglv++af++agi lp+ss++ ++ g+   +  s+l++GD++ f +   +sH+giY+g+g m+h
  gi|121638071|ref|YP_978295.1| 285 GAPYAWGGAAPGGFDCSGLVMWAFQQAGIALPHSSQALAHGGQP--VALSDLQPGDVLTFYS--DASHAGIYIGDGLMVH 360
                                    78************************************999999..************9988..9*************** PP

                                    EETTEEEEEE CS
                       NLPC_P60  81 assekvsvss 90 
                                    +s+ +v v+ 
  gi|121638071|ref|YP_978295.1| 361 SSTYGVPVRV 370
                                    **77776654 PP

>> DUF4254  Protein of unknown function (DUF4254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.6   1.2e-07   0.00032       9     112 ..      60     164 ..      51     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                        DUF4254   9 rintvlwhlediardpdvddaeiaklkreIDklnqeRndlveriDslllekl.kevkpkadarlntEtpgaaiDRlSila 87 
                                    + +  + +l+++  ++ + d+++a+ + ++D+   + + +  ++ ++ ++++    ++  da l  E+p ++iDRlS++ 
  gi|121638071|ref|YP_978295.1|  60 ALHSAQLDLNEKLAAQRAADQKLADNRTALDAARARLATFQTAVNKVAAATYmGGRTHGMDAILTAESPQLLIDRLSVQR 139
                                    567788888888889999999999999999999888888889999999988855566999******************** PP

                        DUF4254  88 Lkiyhmeeeaertdaseehrekcke 112
                                    + +++m+ +++r +a  e+  k ++
  gi|121638071|ref|YP_978295.1| 140 VMAHQMSTQMARFKAAGEQAVKAEQ 164
                                    ************9977666555544 PP

>> Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.7      0.44   1.1e+03      58      88 ..     137     165 ..     100     193 .. 0.58
   2 !   10.1   0.0   0.00025      0.63      82     128 ..     273     317 ..     267     324 .. 0.88
   3 ?    3.6   0.0     0.024        62      26      58 ..     344     373 ..     333     375 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                  Peptidase_C92  58 Lseflarrssiavyrlkealtaeqrqkaaea 88 
                                    +++ +a++ s++ +r k+a   eq  ka +a
  gi|121638071|ref|YP_978295.1| 137 VQRVMAHQMSTQMARFKAA--GEQAVKAEQA 165
                                    4444444444444444444..2222222222 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                  Peptidase_C92  82 rqkaaeaalrrlgkpYdfgFeleddrlYCsklVakaykealgikvkt 128
                                    r  +++aal ++g pY +g   +     Cs lV+ a+ +++gi +++
  gi|121638071|ref|YP_978295.1| 273 RTAVVQAALTQVGAPYAWG-GAAPGGFDCSGLVMWAF-QQAGIALPH 317
                                    66789**************.88899999*********.888998876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.024
                  Peptidase_C92  26 sefkHvgivvgeegderlvveaaakegvrvtpL 58 
                                    s+ +H+gi++g++    +v  +++  +vrv+p+
  gi|121638071|ref|YP_978295.1| 344 SDASHAGIYIGDGL---MVHSSTYGVPVRVVPM 373
                                    788*******9764...4666666667777776 PP

>> Dsh_C  Segment polarity protein dishevelled (Dsh) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.1   8.4e-05      0.22      93     186 ..     154     244 ..     134     262 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                          Dsh_C  93 skeekerkaggsgsesesstrssvsrrerekaqserssaaaserskrssklrsks.slsshaerssalsygppglppl.s 170
                                    +  e++ ka  ++++s   +rs++++    +a + + ++   ++s+ ++++   + +  + +++  +   +p ++p+  +
  gi|121638071|ref|YP_978295.1| 154 AAGEQAVKAEQAAAKSAADARSAAEQA---AAVRANLQH---KQSQLQVQIAVVKsQYVALTPEERTALADPGPVPAVaA 227
                                    222223333333333333333333222...122222222...22222222211111222223333344445544554433 PP

                          Dsh_C 171 lp.psstsagpPGaPPv 186
                                    ++  ++ +a pPGaPP+
  gi|121638071|ref|YP_978295.1| 228 IApGAPPAALPPGAPPG 244
                                    33256667789999997 PP

>> LRAT  Lecithin retinol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.89   2.3e+03      61      98 ..     143     180 ..     109     206 .. 0.63
   2 ?   10.7   0.0    0.0002      0.51       3      32 ..     334     362 ..     332     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.89
                                    EEEEEEHHHHHTTSEEEE--HHHHCT----HHHHHHHH CS
                           LRAT  61 gVrkssleefaagdklrvneksdskaeslpneeviqrA 98 
                                    +  ++++  f+a +++ v++ +   +++ ++ + +++A
  gi|121638071|ref|YP_978295.1| 143 HQMSTQMARFKAAGEQAVKAEQAAAKSAADARSAAEQA 180
                                    44455566666666666666555444433333333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                                    --TT-EEEEE-SSSEEEEEEEETTEEEEEE CS
                           LRAT   3 lkrGdllevsRtlyeHhgiyvGdgkVvHlt 32 
                                    l++Gd+l +    ++H giy+Gdg  vH +
  gi|121638071|ref|YP_978295.1| 334 LQPGDVLTF-YSDASHAGIYIGDGLMVHSS 362
                                    688999984.46789*************75 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5   0.00072       1.8      46      99 ..      41      94 ..      29     107 .. 0.73
   2 ?    8.4   3.9   0.00085       2.2      46      95 ..     157     206 ..     147     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00072
                          DHR10 46 eaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlre 99
                                    + lakl+e +++++++ +al++ + +l+e  + ++   ++l+  +  l+ +r 
  gi|121638071|ref|YP_978295.1| 41 DDALAKLNELSRQAEQTTEALHSAQLDLNEKLAAQRAADQKLADNRTALDAARA 94
                                   566778888888888888888888888888888877777777777776666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00085
                          DHR10  46 eaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeekle 95 
                                    e+ +++++ a k ++++r a e+  + ++ l++k+++lq q++  + ++ 
  gi|121638071|ref|YP_978295.1| 157 EQAVKAEQAAAKSAADARSAAEQAAAVRANLQHKQSQLQVQIAVVKSQYV 206
                                    567889999*********************************99887765 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.5    0.0063        16      53      98 ..      41      86 ..      34     109 .. 0.76
   2 ?    7.8   2.5    0.0018       4.6      31     100 ..     152     214 ..     128     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0063
                         APG6_N 53 eeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98
                                   ++ l+kl++  +++++  ++l +++ +l+++laa+++  ++l ++ 
  gi|121638071|ref|YP_978295.1| 41 DDALAKLNELSRQAEQTTEALHSAQLDLNEKLAAQRAADQKLADNR 86
                                   5677888888888888888888888888888888888777776654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                         APG6_N  31 flkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                    f +  ++         + ++++ ++ ++ +++ e++ +  ++l++++++l+ ++a  +++  al  ee+ 
  gi|121638071|ref|YP_978295.1| 152 FKAAGEQA-------VKAEQAAAKSAADARSAAEQAAAVRANLQHKQSQLQVQIAVVKSQYVALTPEERT 214
                                    33333322.......3456788889999999999999999999999999999999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1758  (0.0980534); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 2702.18
//
Query:       gi|121638072|ref|YP_978296.1|  [L=645]
Description: hypothetical protein BCG_2207 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-36  124.3   0.0      1e-35  123.8   0.0    1.3  1  RNase_T   Exonuclease
    1.5e-06   28.3   0.0    3.1e-06   27.3   0.0    1.6  1  DUF5051   3' exoribonuclease, RNase T-like
    2.3e-05   24.6   0.0    3.8e-05   23.9   0.0    1.4  1  GIY-YIG   GIY-YIG catalytic domain
  ------ inclusion threshold ------
       0.19   11.5   0.5       0.49   10.2   0.5    1.7  1  UVR       UvrB/uvrC motif


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   2.2e-39     1e-35       1     165 []      44     207 ..      44     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 2.2e-39
                                    EEEEEEESSSTT.....CTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHH CS
                        RNase_T   1 vviDlEttglda.....kekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevle 75 
                                    vv+DlEttg  +     +++d+i+ei+a++++gg   +  +f ++v+p+++  ++++++++tgit +m+ +ap++++vl+
  gi|121638072|ref|YP_978296.1|  44 VVVDLETTGGRTtgndaTPPDAITEIGAVKVCGGA--VLGEFATLVNPQHS--IPPQIVRLTGITTAMVGNAPTIDAVLP 119
                                    89*******9999999999***************9..7888**********..*************************** PP

                                    HHHHHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHC..HHHHHHHHHTTCHSSSSTSS CS
                        RNase_T  76 efkellrklallvahnaafdvgflraadkrilkkevpkrnqfldtlildkatlkelar..tsldklaeklgleedgraHr 153
                                     f+e+ + +++lvahna fd+gflraa +r+  +++p ++q+l+t++l++++l++      +l++la+ + +  + + Hr
  gi|121638072|ref|YP_978296.1| 120 MFFEFAG-DSVLVAHNAGFDIGFLRAAARRC-DITWP-QPQVLCTMRLARRVLSRDEApsVRLAALARLFAVASNPT-HR 195
                                    *******.***********************.999**.***************9999999****************8.** PP

                                    HHHHHHHHHHHH CS
                        RNase_T 154 AldDaeataklf 165
                                    AldDa+at+ ++
  gi|121638072|ref|YP_978296.1| 196 ALDDARATVDVL 207
                                    ********9875 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   6.8e-10   3.1e-06       3     164 ..      44     209 ..      42     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.8e-10
                        DUF5051   3 lmiDiEtlgne.......etaelvsIGaVffpetG.....eFyaeidlesdeeag.idaetieWWlkqskearaellkdt 69 
                                    +++D+Et+g +       +  ++++IGaV ++  G     eF + ++++ + +++ +              +  +++   
  gi|121638072|ref|YP_978296.1|  44 VVVDLETTGGRttgndatPPDAITEIGAVKVC--GgavlgEFATLVNPQHSIPPQiVRLT----------GITTAMV--- 108
                                    6789998875544433445568*******994..225667*********99877732222..........2223333... PP

                        DUF5051  70 qeakslkdalqaleeFlekslkvwangasfDlviLraafellipwkywndrdvrtlvalapelekgeekkreipfe.... 145
                                     +a++++ +l  ++eF   +  ++a++a fD+  Lraa ++ +++++ + + + t++  ++ l++ e ++ ++       
  gi|121638072|ref|YP_978296.1| 109 GNAPTIDAVLPMFFEFA-GDSVLVAHNAGFDIGFLRAAARR-CDITWPQPQVLCTMRLARRVLSRDEAPSVRLAALarlf 186
                                    469**************.5788****************554.67888888888888888855555554444443334455 PP

                        DUF5051 146 ....gvkHnALaDAkhqakavsa 164
                                        +  H AL+DA++ + +++a
  gi|121638072|ref|YP_978296.1| 187 avasNPTHRALDDARATVDVLHA 209
                                    5777899********99988776 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.5e-09   3.8e-05       3      53 ..     251     295 ..     249     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.5e-09
                                    EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEE CS
                        GIY-YIG   3 gvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliile 53 
                                    gvY++r   ++++YvG++ +l++R +q+++g++++      k+  e+++l 
  gi|121638072|ref|YP_978296.1| 251 GVYLFRGPSGEVLYVGTAADLRRRVSQYFNGTDRR------KRMTEMVMLA 295
                                    9*****************************99544......4444444444 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00011      0.49      13      29 ..     445     461 ..     444     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                            UVR  13 eAaenedFEkAAklRDq 29 
                                    e+ae+ ++E AA+lRD 
  gi|121638072|ref|YP_978296.1| 445 ELAERRRYESAARLRDH 461
                                    789999**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 5160.98
//
Query:       gi|121638073|ref|YP_978297.1|  [L=370]
Description: anthranilate phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-93  312.6   1.2    2.8e-93  312.2   1.2    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    6.8e-15   54.7   0.4    1.6e-14   53.5   0.4    1.7  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.2   1.2   3.1e-97   2.8e-93       3     252 ..     101     356 ..      99     357 .. 0.99

  Alignments for each domain:
  == domain 1  score: 312.2 bits;  conditional E-value: 3.1e-97
                                    TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHH CS
                Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfap 82 
                                    d+vD+vgTGGdg nt+N+St+aaivvAaaGv+v+khgnr++ss sG+aD+Lealgv+++l p+ v+++l+evg+gf+fap
  gi|121638073|ref|YP_978297.1| 101 DAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAP 180
                                    79****************************************************************************** PP

                                    SSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHH CS
                Glycos_transf_3  83 eyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakt 161
                                    ++h++++h+a+vrre+g++TvfnlLGPL+npar+++ l+g++ ++lae +a v+++ +++++lvvhg dGlde+++++++
  gi|121638073|ref|YP_978297.1| 181 RFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAA-RRSSVLVVHGdDGLDELTTTTTS 259
                                    *******************************************************9.*********************** PP

                                    HHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSS...... CS
                Glycos_transf_3 162 tvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkads...... 235
                                    t++++++g+++++t++p+ fg++ra+l++l+gg++++na++++avl g+++ + rd+v+lna+ a+v+++ ++s      
  gi|121638073|ref|YP_978297.1| 260 TIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPV-RDAVVLNAAGAIVAHAGLSSraewlp 338
                                    ****************************************************9.*******************9****** PP

                                    .HHHHHHHHHHHHHTSHH CS
                Glycos_transf_3 236 .lkegvakaeevidsGkA 252
                                     ++eg+++a+++id+G+A
  gi|121638073|ref|YP_978297.1| 339 aWEEGLRRASAAIDTGAA 356
                                    ****************99 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.4   1.8e-18   1.6e-14       2      63 .]      29      90 ..      28      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.8e-18
                                   HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                   +i+ +l d+ +L + ++++a+++i++g++ +aqiaAf++A+ +k  ta+E+ +la +m+ ++
  gi|121638073|ref|YP_978297.1| 29 QILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHA 90
                                   68999******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2616.27
//
Query:       gi|121638074|ref|YP_978298.1|  [L=203]
Description: cytochrome C oxidase (subunit III) ctaE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-26   94.3  12.3    1.2e-26   94.1  12.3    1.1  1  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1  12.3   6.9e-31   1.2e-26      73     255 ..      22     201 ..       6     203 .] 0.89

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 6.9e-31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTB CS
                           COX3  73 qkGlklGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegn 152
                                     + + +G i+++ se+++f++lf  +f sa     + G  wpP   +      vP+  t +l++s  t     ++  +g+
  gi|121638074|ref|YP_978298.1|  22 PNMVSVGTIVWLSSELMFFAGLFAFYF-SA---RAQAGGNWPPPPTELNLYQAVPV--TLVLIASSFTCQMGVFAAERGD 95 
                                    556789****************97666.44...5688*****98877665666776..99******************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH...-SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSSB- CS
                           COX3 153 rkkalkgllltillavlftllqaveyle...asftisdgvyGsvfylatGlhglhviigtillavallrllkyhltknhh 229
                                         +  ++t+l++++f+l qa+ey +      +i  ++yGsvfylatG+hglhv  g i +++ l r+    +t    
  gi|121638074|ref|YP_978298.1|  96 IFGLRRWYVITFLMGLFFVLGQAYEYRNlmsHGTSIPSSAYGSVFYLATGFHGLHVTGGLIAFIFLLVRTGMSKFTPAQA 175
                                    **************************763225679************************9999***************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTTT CS
                           COX3 230 lGfeaailywhfvdvvwlflyvsvyw 255
                                    +   +  +ywhfvd+vw+ l+ ++y+
  gi|121638074|ref|YP_978298.1| 176 TASIVVSYYWHFVDIVWIALFTVIYF 201
                                    *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1358.22
//
Query:       gi|121638075|ref|YP_978299.1|  [L=280]
Description: ubiquinol-cytochrome C reductase QcrC (cytochrome C subunit) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-19   69.8   0.0    1.5e-09   38.1   0.0    2.4  2  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
    8.4e-15   55.7   3.8    3.6e-07   31.2   0.1    4.0  2  Cytochrom_C      Cytochrome c
    5.5e-05   22.9   0.0       0.25   11.0   0.0    2.3  2  Cytochrom_C550   Cytochrome c-550 domain
     0.0018   18.6   0.0          3    8.3   0.1    2.4  2  DUF1924          Domain of unknown function (DUF1924)
     0.0023   18.6   0.0        1.8    9.2   0.0    2.2  2  CCP_MauG         Di-haem cytochrome c peroxidase
  ------ inclusion threshold ------
      0.044   13.8   0.0        9.2    6.3   0.0    2.2  2  Cytochrome_C7    Cytochrome c7 and related cytochrome c
       0.15   11.8   0.1         11    5.7   0.0    2.4  2  Cytochrom_C1     Cytochrome C1 family
       0.16   11.7   0.8         15    5.4   0.1    2.3  2  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
        1.9    8.1   4.6        0.9    9.2   0.1    2.2  2  MCR              Magnetochrome domain


Domain annotation for each model (and alignments):
>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.6e-10   7.2e-07       2      67 .]      61     136 ..      60     136 .. 0.71
   2 !   38.1   0.0   7.3e-13   1.5e-09       3      67 .]     163     235 ..     161     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.6e-10
                Cytochrome_CBB3   2 aaaaGaalykknCasCHgkggag.....pslagrdwepdalvdiiknGkg.aMp.....afgg.qlsdeelwalvaYl 67 
                                     +++G++l++ +C+sCHg++ +g     psl g +  ++a++  +  G++ aM      ++++  +++++++a+ aY+
  gi|121638075|ref|YP_978299.1|  61 LLRTGKQLFDTSCVSCHGANLQGvpdhgPSLIGVG--EAAVYFQVSTGRMpAMRgeaqaPRKDpIFDEAQIDAIGAYV 136
                                    5799**************55444545559999986..67888888888632333333334444699999999999997 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 7.3e-13
                Cytochrome_CBB3   3 aaaGaalykknCasCHg.kggag........pslagrdwep...dalvdiiknGkgaMpafgg.qlsdeelwalvaYl 67 
                                    + +G  l++ nCasCH  +g++g        p     d++p   +++ ++   G + Mp f + qls e +++++aY+
  gi|121638075|ref|YP_978299.1| 163 LGRGGDLFRLNCASCHNfTGKGGalssgkyaP-----DLAPaneQQILTAMLTGPQNMPKFSNrQLSFEAKKDIIAYV 235
                                    568999***********766666443322222.....33335569999*****************************7 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.8e-10   3.6e-07       3      89 ..      64     137 ..      62     140 .. 0.78
   2 !   18.6   0.6   1.5e-06    0.0031       3      88 ..     165     235 ..     163     239 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-10
                                    -HHHHHHTTGGGTB-SSSBSSS....--HHHHHHHTTT-HHHHHHHHTTSS--SSSHHHHHHHGGGGGGG.TT--HHHHH CS
                    Cytochrom_C   3 rGkelftanCaaCHgvegggakqgggptlsgaaerasaasigasvanpaavsaprddfekkkltaemparkerlteqeia 82 
                                     Gk+lf++ C++CHg++ +g++ + gp l g++e+a +++    ++  +        +  +++  ++p      +e++i+
  gi|121638075|ref|YP_978299.1|  64 TGKQLFDTSCVSCHGANLQGVPDH-GPSLIGVGEAAVYFQVSTGRMPAM--------RGEAQAPRKDP----IFDEAQID 130
                                    6*****99**************99.*********999998877777552........22222222333....57888888 PP

                                    HHHHHHH CS
                    Cytochrom_C  83 dlaaYLk 89 
                                    ++ aY++
  gi|121638075|ref|YP_978299.1| 131 AIGAYVQ 137
                                    8888886 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.5e-06
                                    -HHHHHHTTGGGTB-SSSBSSS.......--HHHHHHHTTT-HHHHHHHHTTSS--SSSHHHHHHHGGGGGGG.TT--HH CS
                    Cytochrom_C   3 rGkelftanCaaCHgvegggakqgg...gptlsgaaerasaasigasvanpaavsaprddfekkkltaemparkerlteq 79 
                                    rG  lf  nCa+CH  +g+g +  +   +p+l+ a        +++++        +  ++++ +++++   r  +l+ +
  gi|121638075|ref|YP_978299.1| 165 RGGDLFRLNCASCHNFTGKGGALSSgkyAPDLAPA--------NEQQILTA-----MLTGPQNMPKFSN---R--QLSFE 226
                                    7889**99***********9864333343333333........33333333.....3444444443333...2..46666 PP

                                    HHHHHHHHH CS
                    Cytochrom_C  80 eiadlaaYL 88 
                                    + +d++aY+
  gi|121638075|ref|YP_978299.1| 227 AKKDIIAYV 235
                                    666666666 PP

>> Cytochrom_C550  Cytochrome c-550 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00013      0.25      22      41 ..      58      77 ..      46      89 .. 0.84
   2 !    9.5   0.0   0.00038      0.77      17      42 ..     154     179 ..     137     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                   EHHHHHHHHHHHHHHTHHHH CS
                 Cytochrom_C550 22 seeqlkkgkklFeaeCaqCH 41
                                   s++ l++gk+lF+++C +CH
  gi|121638075|ref|YP_978299.1| 58 SSALLRTGKQLFDTSCVSCH 77
                                   4556789************* PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00038
                                    -EEEEEHHHHHHHHHHHHHHTHHHHG CS
                 Cytochrom_C550  17 etvtlseeqlkkgkklFeaeCaqCHv 42 
                                     t+ l  ++l +g  lF+ +Ca+CH 
  gi|121638075|ref|YP_978299.1| 154 ATQSLRGNDLGRGGDLFRLNCASCHN 179
                                    467788899****************6 PP

>> DUF1924  Domain of unknown function (DUF1924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0015         3      25      38 ..      69      82 ..      56      90 .. 0.79
   2 !    7.9   0.0    0.0019       3.9      27      64 ..     172     207 ..     161     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                                   T-SSTHHHH-SSTT CS
                        DUF1924 25 kelsCasCHgedpt 38
                                    ++sC sCHg++++
  gi|121638075|ref|YP_978299.1| 69 FDTSCVSCHGANLQ 82
                                   568********987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0019
                                    SSTHHHH-SSTTS-EE.-TTS-EE--SSTTTSTTTT-- CS
                        DUF1924  27 lsCasCHgedptkegkhaktgkaieplapsvnpkrftd 64 
                                    l+CasCH  + t +g   ++gk    lap+  ++ +t 
  gi|121638075|ref|YP_978299.1| 172 LNCASCH--NFTGKGGALSSGKYAPDLAPANEQQILTA 207
                                    68*****..688899999*****999**9988877765 PP

>> CCP_MauG  Di-haem cytochrome c peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0035       6.9      21      44 ..      70      94 ..      64     139 .. 0.68
   2 !    9.2   0.0   0.00089       1.8      21      61 ..     171     223 ..     163     255 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0035
                                   S--HHHHSGCCCTT.S-SSSSBBEG CS
                       CCP_MauG 21 kisCasCHdpaagf.tdglkvslgv 44
                                   ++sC sCH  + ++ +d+ +  +gv
  gi|121638075|ref|YP_978299.1| 70 DTSCVSCHGANLQGvPDHGPSLIGV 94
                                   68******76654425544444443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00089
                                    S--HHHHSGCCCTT............S-SSSSBBEGGGEBSSS----STTGGG CS
                       CCP_MauG  21 kisCasCHdpaagf............tdglkvslgvegrlgarnaptllnaaf 61 
                                    + +CasCH+ + ++            +  +++++ +   +g++n p+  n ++
  gi|121638075|ref|YP_978299.1| 171 RLNCASCHNFTGKGgalssgkyapdlAPANEQQILTAMLTGPQNMPKFSNRQL 223
                                    579*****753333233333333222111223333345677788888887766 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.01        20      47      56 ..      70      79 ..      48      98 .. 0.71
   2 ?    6.3   0.0    0.0046       9.2      14      23 ..     172     181 ..     157     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.01
                  Cytochrome_C7 47 sltCgaCHdg 56
                                   +++C +CH  
  gi|121638075|ref|YP_978299.1| 70 DTSCVSCHGA 79
                                   2335555543 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0046
                  Cytochrome_C7  14 ykCtdCHskl 23 
                                     +C++CH+ +
  gi|121638075|ref|YP_978299.1| 172 LNCASCHNFT 181
                                    4677777766 PP

>> Cytochrom_C1  Cytochrome C1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0055        11      13      33 ..      60      80 ..      52      84 .. 0.86
   2 ?    3.5   0.0     0.026        51      13      31 ..     161     179 ..     152     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                   Cytochrom_C1 13 aqlqRGlqvykevcsaCHslk 33
                                   a l+ G q++   c +CH+ +
  gi|121638075|ref|YP_978299.1| 60 ALLRTGKQLFDTSCVSCHGAN 80
                                   56899*************976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                   Cytochrom_C1  13 aqlqRGlqvykevcsaCHs 31 
                                    + l RG  +++  c++CH 
  gi|121638075|ref|YP_978299.1| 161 NDLGRGGDLFRLNCASCHN 179
                                    6789**************7 PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.015        30       8      14 ..      72      78 ..      62      88 .. 0.76
   2 ?    5.4   0.1    0.0076        15       8      17 ..     173     182 ..     168     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.015
                 Paired_CXXCH_1  8 eClsCHn 14
                                   +C sCH 
  gi|121638075|ref|YP_978299.1| 72 SCVSCHG 78
                                   4667763 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0076
                 Paired_CXXCH_1   8 eClsCHnphg 17 
                                    +C sCHn  g
  gi|121638075|ref|YP_978299.1| 173 NCASCHNFTG 182
                                    5999998655 PP

>> MCR  Magnetochrome domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.9      0.41   8.2e+02      20      24 ..      73      77 ..      71      78 .. 0.90
   2 ?    9.2   0.1   0.00045       0.9      18      29 ..     172     183 ..     171     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.41
                                   GGGT- CS
                            MCR 20 CtkCH 24
                                   C +CH
  gi|121638075|ref|YP_978299.1| 73 CVSCH 77
                                   ***** PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00045
                                    S-GGGT--BSST CS
                            MCR  18 mnCtkCHqIiga 29 
                                     nC++CH  +g+
  gi|121638075|ref|YP_978299.1| 172 LNCASCHNFTGK 183
                                    69******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2082.78
//
Query:       gi|121638076|ref|YP_978300.1|  [L=429]
Description: Rieske iron-sulfur protein QcrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-09   36.4   0.1    7.4e-09   35.4   0.1    1.5  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
      0.096   12.3   1.9       0.13   11.9   0.8    1.7  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   8.2e-13   7.4e-09      33      89 .]     343     400 ..     304     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8.2e-13
                                    TS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE..TTSBEEE-TTHHHEEEET CS
                         Rieske  33 dgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd..adGkvikgPaprplatyp 89 
                                     ge++A+ +vC+H+g+p s  +  +  ++ CpcH++++d  + +k i gPa r+la++p
  gi|121638076|ref|YP_978300.1| 343 FGEFFAFTKVCSHLGCPSSLYEQ-QSYRILCPCHQSQFDalHFAKPIFGPAARALAQLP 400
                                    6899*************444333.678************9999999999**99999875 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   1.4e-05      0.13       5      63 ..      98     170 ..      93     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                        DUF4131   5 lalvllalllllllllllllrr...............rprrrvllllllllllallgfalrapqpnandlsqll 63 
                                    ++l+l ++++l+lll++l++                  +++ + l+++l +l +++g++l++ +   +++s + 
  gi|121638076|ref|YP_978300.1|  98 VWLLLGGVFGLALLLIFLFW-PwefkaadgesdfiysLTTPLYGLTFGLSILSIAIGAVLYQKRFIPEEISIQE 170
                                    34444444444444444444.369*************999999*************999999998888877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2901.60
//
Query:       gi|121638077|ref|YP_978301.1|  [L=549]
Description: ubiquinol-cytochrome C reductase QcrB (cytochrome B subunit) [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-60  203.7   8.5      2e-60  203.7   8.5    2.2  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    2.7e-23   82.8  12.8    2.7e-23   82.8  12.8    2.7  3  Cytochrome_B     Cytochrome b/b6/petB
    0.00013   22.5   5.8    0.00013   22.5   5.8    3.4  2  DUF4405          Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
        1.4    8.6  14.9          5    6.7   1.4    3.5  3  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7   8.5   4.4e-64     2e-60       2     169 .]     120     294 ..     119     294 .. 0.94
   2 ?   -1.6   1.2      0.52   2.3e+03      93     125 ..     325     358 ..     323     411 .. 0.40

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 4.4e-64
                Cytochrom_B_N_2   2 imiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrv.gagiissvPvvgtwlvellf 80 
                                    ++ ++i+vH++r+fftGa+++pRe+nW+iG lll+l+++eg++GysLpddlls+ +lr  +++i+ ++Pv+gtwl+++lf
  gi|121638077|ref|YP_978301.1| 120 MFAAAIMVHLARIFFTGAFRRPRETNWVIGSLLLILAMFEGYFGYSLPDDLLSGLGLRAaLSSITLGMPVIGTWLHWALF 199
                                    7999******************************************************84569***************** PP

                Cytochrom_B_N_2  81 GgelpgeallsrlyalHilllpalllalivahlllv..ekkgqtpsr.rkeknvvgeplvpvnavkmlllflvl...val 154
                                    Gg++pg+ l++rlyalHilllp+++lali++hl+lv  +k++q+p++ r+e+nvvg++++pv+a+k++++f+++   + l
  gi|121638077|ref|YP_978301.1| 200 GGDFPGTILIPRLYALHILLLPGIILALIGLHLALVwfQKHTQFPGPgRTEHNVVGVRVMPVFAFKSGAFFAAIvgvLGL 279
                                    ***********************************556********99********************999987344555 PP

                Cytochrom_B_N_2 155 lialalinPvpllgp 169
                                    + +l++inP+++lgp
  gi|121638077|ref|YP_978301.1| 280 MGGLLQINPIWNLGP 294
                                    55**********987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                Cytochrom_B_N_2  93 lyalHilllpallla.livahlllvekkgqtpsr 125
                                    +y +H  + + + +a ++++ ++l+ ++   ++r
  gi|121638077|ref|YP_978301.1| 325 FYFWHHTIPAPVWVAvIMGLVFVLLPAYPFLEKR 358
                                    6777774433333330333444444555444444 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8  12.8     6e-27   2.7e-23      14     185 ..      45     235 ..      34     239 .. 0.86
   2 ?   -4.6   1.2       3.6   1.6e+04     163     184 ..     325     346 ..     324     348 .. 0.75
   3 ?   -4.3   0.9       3.1   1.4e+04      73     103 ..     388     421 ..     381     434 .. 0.51

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 6e-27
                   Cytochrome_B  14 ynlGsllllvlvlqiltGvalafyytptv.................tlaflsvqyilrdvnfGwlirsvhangasllfll 76 
                                    + lG ++l  +v+ ++tGv l++++ p++                 + a+ s   i  +v  G ++r++h ++a ++   
  gi|121638077|ref|YP_978301.1|  45 FLLGEIALYSFVVLLITGVYLTLFFDPSMvdvtyngvyqplrgvemSRAYQSALDISFEVRGGLFVRQIHHWAALMFAAA 124
                                    668999999999999999999999987541111111111111111156788888999*********************** PP

                   Cytochrome_B  77 lylhifrglllgglkktrelvWviGvillllvivtafiGyvLpwdqmsyWavt.vitnllsaiPviGstlvellwgsvsv 155
                                    +++h++r +++g++ ++re  WviG +ll+l + +++ Gy+Lp d +s  +++  ++++   +PviG++l   l+g+ + 
  gi|121638077|ref|YP_978301.1| 125 IMVHLARIFFTGAFRRPRETNWVIGSLLLILAMFEGYFGYSLPDDLLSGLGLRaALSSITLGMPVIGTWLHWALFGGDFP 204
                                    ************************************************999862689*********************** PP

                   Cytochrome_B 156 ddatLtrffslh.fllPflllillllhllll 185
                                    +   + r+++lh +llP ++l+l+ lhl l+
  gi|121638077|ref|YP_978301.1| 205 GTILIPRLYALHiLLLPGIILALIGLHLALV 235
                                    ************8899***********9875 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 3.6
                   Cytochrome_B 163 ffslhfllPflllillllhlll 184
                                    f+  h  +P  + + +++ l++
  gi|121638077|ref|YP_978301.1| 325 FYFWHHTIPAPVWVAVIMGLVF 346
                                    7888888888888888887776 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 3.1
                   Cytochrome_B  73 lflllylhifrglllgglk.ktrelvWv..iGvi 103
                                    ++++l l  +  ++   ++ +    +W+  iG++
  gi|121638077|ref|YP_978301.1| 388 FYMVLTLAAMNDIIALKFHiSLNATTWIgrIGMV 421
                                    5666666555555554444134445564223333 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   5.8   2.8e-08   0.00013       6      63 ..      51     130 ..      49     133 .. 0.88
   2 ?   -2.3   6.1       1.5   6.8e+03      53      66 .]     223     236 ..     178     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                        DUF4405   6 lllsflvlaiSGillsfavlpsgrgaywa..................flgl.....skhqwrdiHeilgllflilvvlHl 62 
                                    +l sf+vl+i+G+ l    + ++ +  ++                  +l++     +  ++r+iH++++l f +++++Hl
  gi|121638077|ref|YP_978301.1|  51 ALYSFVVLLITGVYLTLF-FDPSMVDVTYngvyqplrgvemsrayqsALDIsfevrGGLFVRQIHHWAALMFAAAIMVHL 129
                                    5789************99.777777777789****************5555555589999*******************9 PP

                        DUF4405  63 g 63 
                                    +
  gi|121638077|ref|YP_978301.1| 130 A 130
                                    7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                        DUF4405  53 lflilvvlHlglhw 66 
                                    + l+l++lHl+l w
  gi|121638077|ref|YP_978301.1| 223 IILALIGLHLALVW 236
                                    5789********99 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.4    0.0011         5       5      45 ..     116     158 ..     112     177 .. 0.68
   2 ?    3.3   0.6     0.013        58       9      50 ..     223     287 ..     212     306 .. 0.54
   3 ?    6.7   0.6    0.0012       5.3       3      48 ..     334     395 ..     332     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0011
                        DUF4131   5 lalvllalllllllllllllrr..rprrrvllllllllllall 45 
                                    +a++++a+++++ l+++++     rpr + +++ +lll+la++
  gi|121638077|ref|YP_978301.1| 116 WAALMFAAAIMVHLARIFFTGAfrRPRETNWVIGSLLLILAMF 158
                                    5566666666666666666544888888888887777777764 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.013
                        DUF4131   9 llalllllllllllllrr.......................rprrrvllllllllllallgfalr 50 
                                    ++++l+ l l+l+++++                         ++  +++++  +l l+++ +++ 
  gi|121638077|ref|YP_978301.1| 223 IILALIGLHLALVWFQKHtqfpgpgrtehnvvgvrvmpvfaFKSGAFFAAIVGVLGLMGGLLQIN 287
                                    45555555555555554478888888777777774444444333333333333333333333333 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0012
                        DUF4131   3 lplalvllalllllllllllllrr.............rprrrv...llllllllllallgfa 48 
                                     p+++ +++ l+++ll ++ +l +             rpr      +++++++++ ++l +a
  gi|121638077|ref|YP_978301.1| 334 APVWVAVIMGLVFVLLPAYPFLEKrftgdyahhnllqRPRDVPvrtAIGAMAIAFYMVLTLA 395
                                    68999999999999999998877789999999999764444334446677777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3632.34
//
Query:       gi|121638078|ref|YP_978302.1|  [L=214]
Description: hypothetical protein BCG_2213c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-102  341.3  14.5   2.8e-102  341.1  14.5    1.0  1  DUF2561          Protein of unknown function (DUF2561)
  ------ inclusion threshold ------
      0.024   14.7  13.4       0.05   13.7   4.9    2.1  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.17   11.8   2.0       0.64   10.0   0.2    2.3  2  Flavi_NS4A       Flavivirus non-structural protein NS4A
       0.23   11.6   0.2       0.23   11.6   0.2    3.5  4  CcmD             Heme exporter protein D (CcmD)


Domain annotation for each model (and alignments):
>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.1  14.5  6.3e-106  2.8e-102       1     208 []       1     206 [.       1     206 [. 0.99

  Alignments for each domain:
  == domain 1  score: 341.1 bits;  conditional E-value: 6.3e-106
                        DUF2561   1 mvsrysayrrGsdvvaldvidriLlGacaavwLvllGvsvaatvaLvdLgrGfaksaedshttwvLyavivvsalvivga 80 
                                    mvsrysayrrG+dv+++dvidriL+GacaavwLv++Gvsvaa+vaL+dLgrGf+++a+++httwvLyavivvsalvivga
  gi|121638078|ref|YP_978302.1|   1 MVSRYSAYRRGPDVISPDVIDRILVGACAAVWLVFTGVSVAAAVALMDLGRGFHEMAGNPHTTWVLYAVIVVSALVIVGA 80 
                                    9******************************************************************************* PP

                        DUF2561  81 vPlLLrarrvaeaePaarargaperaaaapargadapaeraeaeeasaekaealreaaewssaavdrvwLrgtvvlasal 160
                                    +P+LLrarr+aeaePa+r++ga+ r++++  +g+++pa+ra+ae+a +++a+a++ aaewss+avdr+wLrgtvvl+sa+
  gi|121638078|ref|YP_978302.1|  81 IPVLLRARRMAEAEPATRPTGASVRGGRS--IGSGHPAKRAVAESAPVQHADAFEVAAEWSSEAVDRIWLRGTVVLTSAI 158
                                    ***************************98..99*********************************************** PP

                        DUF2561 161 GvalvavaaatyLmavgkdgasWvlyglaGvvtagmpvieWlylrqLr 208
                                    G+al+avaaatyLmavg+dg+sW++yglaGvvtagmpvieWly rqLr
  gi|121638078|ref|YP_978302.1| 159 GIALIAVAAATYLMAVGHDGPSWISYGLAGVVTAGMPVIEWLYSRQLR 206
                                    ***********************************************8 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.9   1.1e-05      0.05      39     106 ..      25     105 ..      19     110 .. 0.57
   2 ?    6.4   1.3     0.002       8.9      36      93 ..     150     207 ..     129     214 .] 0.47

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                Phage_holin_3_6  39 llgaagvlallalllllvala..........lalaa....lwlaalivaavllvlagvlalvglkklkkakplpertiee 104
                                    + + a+v ++++ +++ +a+a          +a         l a+iv  +l++++++ +l+  +++++a+p+ + t ++
  gi|121638078|ref|YP_978302.1|  25 VGACAAVWLVFTGVSVAAAVAlmdlgrgfheMAG-NphttWVLYAVIVVSALVIVGAIPVLLRARRMAEAEPATRPTGAS 103
                                    3334444444444444444433455555555333.134644445555777777777777777777788888888888887 PP

                Phage_holin_3_6 105 lk 106
                                    ++
  gi|121638078|ref|YP_978302.1| 104 VR 105
                                    76 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.002
                Phage_holin_3_6  36 gagllgaagvlallalllllvalalalaa.....lwlaalivaavllvlagvlalvglkklkk 93 
                                    g ++l  a  +al+a+++++ ++a    +     +w+++ + ++v + + ++  l  + +l++
  gi|121638078|ref|YP_978302.1| 150 GTVVLTSAIGIALIAVAAATYLMA----VghdgpSWISYGLAGVVTAGMPVIEWLYSR-QLRR 207
                                    233333333333333333333333....233456888888866655554444433333.3555 PP

>> Flavi_NS4A  Flavivirus non-structural protein NS4A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.095   4.2e+02      87     117 ..      51      82 ..       8      94 .. 0.60
   2 ?   10.0   0.2   0.00014      0.64      75     105 ..     156     186 ..     146     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.095
                     Flavi_NS4A  87 ssallflasvkpthiaavillefvlmvl.lip 117
                                     ++  + ++ + t++ +++++   l+++  ip
  gi|121638078|ref|YP_978302.1|  51 RGFHEMAGNPHTTWVLYAVIVVSALVIVgAIP 82 
                                    44444444555677777666555444331555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                     Flavi_NS4A  75 sktsialltviassallflasvkpthiaavi 105
                                    s + ial +v+a+++l+ ++   p +i++ +
  gi|121638078|ref|YP_978302.1| 156 SAIGIALIAVAAATYLMAVGHDGPSWISYGL 186
                                    557899**********************975 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   2.0       0.8   3.6e+03      12      27 ..      26      41 ..      25      47 .. 0.75
   2 ?    2.0   0.5     0.051   2.3e+02      13      34 ..      72      93 ..      61      97 .. 0.81
   3 ?   -3.5   0.8       2.6   1.1e+04      12      20 ..     159     167 ..     156     171 .. 0.72
   4 ?   11.6   0.2   5.1e-05      0.23       8      37 ..     181     210 ..     181     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.8
                           CcmD 12 gitllvlagLilwslr 27
                                   g++++v+++    s++
  gi|121638078|ref|YP_978302.1| 26 GACAAVWLVFTGVSVA 41
                                   8888888888877775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.051
                           CcmD 13 itllvlagLilwslrdrrrllr 34
                                   +++lv++g i   lr rr + +
  gi|121638078|ref|YP_978302.1| 72 VSALVIVGAIPVLLRARRMAEA 93
                                   7899999988888888886665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.6
                           CcmD  12 gitllvlag 20 
                                    gi+l+++a+
  gi|121638078|ref|YP_978302.1| 159 GIALIAVAA 167
                                    677777765 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 5.1e-05
                           CcmD   8 WlsYgitllvlagLilwslrdrrrllrelr 37 
                                    W sYg++ +v ag  +  ++  r+l+r ++
  gi|121638078|ref|YP_978302.1| 181 WISYGLAGVVTAGMPVIEWLYSRQLRRVVA 210
                                    **************************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1638.76
//
Query:       gi|121638079|ref|YP_978303.1|  [L=299]
Description: membrane protein mmpS3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-07   30.3   0.7    7.5e-07   29.2   0.2    1.8  2  Mycobact_memb  Mycobacterium membrane protein
  ------ inclusion threshold ------
      0.036   13.0   0.0      0.046   12.7   0.0    1.2  1  MFS_1          Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.2   1.8e+03      83      97 ..      98     112 ..      65     142 .. 0.72
   2 !   29.2   0.2   8.3e-11   7.5e-07      43     119 ..     205     286 ..     193     299 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.2
                                    S--B--EE-SSS--- CS
                  Mycobact_memb  83 lPWsltikttlaavv 97 
                                     PW + + + +aav+
  gi|121638079|ref|YP_978303.1|  98 WPWVVGVAAIIAAVA 112
                                    566666655555554 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 8.3e-11
                                    XXXXXXXXEEB-B----..TT-----B---TTS------S-SS--B--EE-SSS------B--S..S-S------BB.TT CS
                  Mycobact_memb  43 dskpfnPkkvkyevfGp..agtvadisyldadaepqridgaalPWsltikttlaavvgnvvaqg..nsdsigCriiv.dg 117
                                     ++p  P++v+y v G+  +g +++++y+da ++ +  +++ +PWs+t++    + vg v a +    + + C i+  dg
  gi|121638079|ref|YP_978303.1| 205 TTTPTGPRQVTYSVTGTkaPGDIISVTYVDAAGRRRTQHNVYIPWSMTVTPISQSDVGSVEASSlfRVSKLNCSITTsDG 284
                                    567889**********644899*******************************999999999883346678999875256 PP

                                    B- CS
                  Mycobact_memb 118 vv 119
                                    +v
  gi|121638079|ref|YP_978303.1| 285 TV 286
                                    65 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.1e-06     0.046     149     188 ..      97     136 ..      89     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-06
                          MFS_1 149 gWravfyilaivsllafvlfllllpeepperkrkspkeee 188
                                     W++v  ++ai++++a+v+ + ll+++p+++k  ++ + +
  gi|121638079|ref|YP_978303.1|  97 RWPWVVGVAAIIAAVALVVSVSLLVTRPHTSKLATGDTTS 136
                                    5*****************9999999999999888877763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2261.87
//
Query:       gi|121638080|ref|YP_978304.1|  [L=139]
Description: hypothetical protein BCG_2215c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-50  170.3   8.0    2.4e-50  170.1   8.0    1.0  1  Cyt_c_ox_IV      Cytochrome c oxidase subunit IV
  ------ inclusion threshold ------
      0.096   12.2   0.1      0.096   12.2   0.1    1.4  2  UNC-50           UNC-50 family
       0.41   10.7  16.2       0.11   12.5   2.2    2.1  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Cyt_c_ox_IV  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   8.0     4e-54   2.4e-50       1     131 [.       1     137 [.       1     138 [. 0.98

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 4e-54
                    Cyt_c_ox_IV   1 mkveaklflllavffllvavvYgvltkie.....elvGttalvltgglallvgtylafvarridarpedredaeiadgaG 75 
                                    m++ea+lf+++a+ff++ av+Ygvlt++      e++Gttal+ltgg+al+v+t+++fvarr+d rped+e aei+dgaG
  gi|121638080|ref|YP_978304.1|   1 MHIEARLFEFVAAFFVVTAVLYGVLTSMFatggvEWAGTTALALTGGMALIVATFFRFVARRLDSRPEDYEGAEISDGAG 80 
                                    99*************************8899************************************************* PP

                    Cyt_c_ox_IV  76 elGffsPhSwwPlvlalaaalaalglal.gwWllligvvlvlialvGlvfeyyrgee 131
                                    elGffsPhSwwP+++al+ ++aa+g+al   Wl+++gv+++l++++Glvfeyy g+e
  gi|121638080|ref|YP_978304.1|  81 ELGFFSPHSWWPIMVALSGSVAAVGIALwLPWLIAAGVAFILASAAGLVFEYYVGPE 137
                                    ****************************99************************987 PP

>> UNC-50  UNC-50 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05     0.096      54     109 ..      10      65 ..       5      84 .. 0.89
   2 ?   -2.7   0.2      0.58   3.5e+03      55      69 ..     109     123 ..      91     132 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                         UNC-50  54 Llvlllllsaiawglayssslleilklilvmvlvdfllvglliatvlwllvnrlll 109
                                    +++++++++a+++g++ s  +++ ++ +  + l+   +++l++at++ ++++rl +
  gi|121638080|ref|YP_978304.1|  10 FVAAFFVVTAVLYGVLTSMFATGGVEWAGTTALALTGGMALIVATFFRFVARRLDS 65 
                                    57899**********99999999****************************99865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.58
                         UNC-50  55 lvlllllsaiawgla 69 
                                     + +l+ +++a+ la
  gi|121638080|ref|YP_978304.1| 109 WLPWLIAAGVAFILA 123
                                    344445555555444 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.2   1.9e-05      0.11      42      93 ..      11      65 ..       4      71 .. 0.57
   2 ?    4.0   6.4    0.0081        49      57      86 ..     100     129 ..      78     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                Phage_holin_3_6 42 aagvlallalllllvalalala.a..lwlaalivaavllvlagvlalvglkklkk 93
                                   +a++++++a+l+ +++ ++a + +  +   al +++ ++++ + + +   ++l +
  gi|121638080|ref|YP_978304.1| 11 VAAFFVVTAVLYGVLTSMFATGgVewAGTTALALTGGMALIVATFFRFVARRLDS 65
                                   3344444444444443344444453355667777777777777777777777766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0081
                Phage_holin_3_6  57 alalala.alwlaalivaavllvlagvlalv 86 
                                      ++a++ alwl  li a+v ++la +++lv
  gi|121638080|ref|YP_978304.1| 100 S-VAAVGiALWLPWLIAAGVAFILASAAGLV 129
                                    2.23333246888888888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1071.95
//
Query:       gi|121638081|ref|YP_978305.1|  [L=363]
Description: transmembrane cytochrome C oxidase (subunit II) ctaC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-15   55.0   0.4    1.3e-13   50.9   0.0    2.3  2  COX2             Cytochrome C oxidase subunit II, periplasmic
  ------ inclusion threshold ------
      0.046   12.8   0.4      0.073   12.2   0.4    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
      0.048   13.8   0.4        0.1   12.8   0.4    1.5  1  COX2_TM          Cytochrome C oxidase subunit II, transmembra
        0.2   10.1   0.1       0.27    9.7   0.1    1.1  1  DUF4486          Domain of unknown function (DUF4486)
       0.42   10.5   4.1        1.3    8.9   0.6    2.2  2  DUF2062          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.049   1.7e+02       3      19 ..     153     169 ..     151     184 .. 0.68
   2 !   50.9   0.0   3.7e-17   1.3e-13      48     119 ..     235     312 ..     214     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.049
                           COX2   3 ikaiGhqwywsyeytdf 19 
                                    i     qw w++ y+  
  gi|121638081|ref|YP_978305.1| 153 IDITSFQWNWKFGYQRV 169
                                    666789****9888643 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 3.7e-17
                           COX2  48 vvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsll......idreGvfyGqcselcGvnhssmpivvea 119
                                    +vlp  ++i ++++++dv+h+f vp +  k d++p  +++ s+       i+++G f G c+e+cG+ hs+m   v+ 
  gi|121638081|ref|YP_978305.1| 235 LVLPSGKRIEFQMASADVIHAFWVPEFLFKRDVMPNPVANNSVNvfqieeITKTGAFVGHCAEMCGTYHSMMNFEVRV 312
                                    699********************************998765543113333689*******************988875 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4     2e-05     0.073     204     252 ..      70     136 ..      68     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                ABC2_membrane_3 204 qywlskilgdflvyllqlllill.lafgl..............gipfg...nlglllllfllfglay 252
                                    ++w++ ++++++v+++++ li++  +f++              ++p +    ++ +l+ ++lf++++
  gi|121638081|ref|YP_978305.1|  70 ELWIGAVIASLAVGVIVWGLIFWsAVFHRkkntdtelprqfgyNMPLElvlTVIPFLIISVLFYFTV 136
                                    68*********************669*99******99776655444443333344445555555544 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.8e-05       0.1      28      82 ..      76     131 ..      50     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                        COX2_TM  28 lliltlililVlyilvlilvefrrrknkita..kylvhgqeiEiiWTiiPalilili 82 
                                    ++   l + ++++ l+     f+r+kn  t+  +++  +  +E++ T+iP li+ ++
  gi|121638081|ref|YP_978305.1|  76 VIA-SLAVGVIVWGLIFWSAVFHRKKNTDTElpRQFGYNMPLELVLTVIPFLIISVL 131
                                    333.3334455678888888899999988873355666777***********98665 PP

>> DUF4486  Domain of unknown function (DUF4486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   7.4e-05      0.27     493     532 ..     134     172 ..      99     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.4e-05
                        DUF4486 493 lysivvvsakevqpdkeivvDvvlfLWqkcklglqriqis 532
                                    +  +v +++ ++  d e+v+D++ f W+  k+g qr++ +
  gi|121638081|ref|YP_978305.1| 134 FTVVVQEKMLQIAKDPEVVIDITSFQWN-WKFGYQRVNFK 172
                                    22334445556789*************6.79999999875 PP

>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.6   0.00035       1.3      77     145 ..      34     100 ..      27     103 .. 0.79
   2 ?    2.7   0.2     0.029   1.1e+02      53     102 ..     112     160 ..     108     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                        DUF2062  77 ayklGalllgeeaeal.....slseleelglewlleslleiglplllGslilglilallgYflvlllwrlyrrr 145
                                    a +lGal        +     s+se   +g+ + ++  +++   l++G++i +l++++++  l+ +   ++r++
  gi|121638081|ref|YP_978305.1|  34 AAMLGALA-------VtvsgcSWSEALGIGWPEGITPEAHLNRELWIGAVIASLAVGVIVWGLIFWSAVFHRKK 100
                                    45555555.......2335568899999999777777779999********************99999888887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                        DUF2062  53 vnlpaavagtwisnPlt.lppiyylayklGalllgeeaealslseleelgl 102
                                     n+p+ +++t+i  P+  + +++y+++ + + +l+  ++   + +++++++
  gi|121638081|ref|YP_978305.1| 112 YNMPLELVLTVI--PFLiISVLFYFTVVVQEKMLQIAKDPEVVIDITSFQW 160
                                    689999999999..6551557788999999999876666554555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2389.95
//
Query:       gi|121638082|ref|YP_978306.1|  [L=652]
Description: asparagine synthetase AsnB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   7.3e-105  351.5   0.0   9.2e-105  351.2   0.0    1.1  1  Asn_synthase  Asparagine synthase
    1.9e-38  131.1   0.0    3.1e-38  130.4   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    6.1e-34  117.1   0.0    1.1e-33  116.3   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
      8e-05   22.2   0.0    0.00016   21.2   0.0    1.4  1  DUF3700       Aluminium induced protein
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.023   14.2   0.0    1.3  1  QueC          Queuosine biosynthesis protein QueC
      0.014   14.5   0.0      0.027   13.6   0.0    1.4  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.2   0.0  3.1e-108  9.2e-105       2     354 ..     262     631 ..     261     632 .. 0.90

  Alignments for each domain:
  == domain 1  score: 351.2 bits;  conditional E-value: 3.1e-108
                   Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlte 81 
                                    + ++Led+V++++radv vGa+LSGG+DS++iaala r+++ +l tF+ gfe +g++e+++a + ae++g +h+  v+++
  gi|121638082|ref|YP_978306.1| 262 ITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAIRHNP-RLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSA 340
                                    7789***********************************98.9********99*************************** PP

                   Asn_synthase  82 eelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp....lars 157
                                    +e+++alp+++++l+ep+ad++ +pl++++r+a rk+vkvvLsGeGaDElfgGY+ +y+++ls  r f++lp        
  gi|121638082|ref|YP_978306.1| 341 DEFVAALPEIVWYLDEPVADPALVPLFFVAREA-RKHVKVVLSGEGADELFGGYT-IYREPLSL-RPFDYLPkplrR--- 414
                                    *********************************.677*****************9.*****888.666799956551... PP

                   Asn_synthase 158 lrasllarklrklaellelaeardleelaelyrlkasdsae........................aelegedelhrelyl 213
                                     + + +++ l +  +  +l ++ +l +l+e+y+++a+++                          ae++g+d++ r++++
  gi|121638082|ref|YP_978306.1| 415 -SMGKVSKPLPEGMRGKSLLHRGSL-TLEERYYGNARSFSGaqlrevlpgfrpdwthtdvtapvyAESAGWDPVARMQHI 492
                                    .444444444444444444444444.446677777777666777777777888888899999****************** PP

                   Asn_synthase 214 dlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpKegfsapv 292
                                    dl t+l+gd+l+k D+++ma++lE+RvPflD +++ va rlp+  k+++ ++Ky LR+ale ++P+++l+RpK gf++p+
  gi|121638082|ref|YP_978306.1| 493 DLFTWLRGDILVKaDKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPI 572
                                    ******************************************************************************** PP

                   Asn_synthase 293 gewklk.gelrelaeellsdsrlakeglldreaveelleeheagkrnesrqlwslllsleawl 354
                                    ++w l+ gel e+a++++ +s  ++  l+d +av ++l+eh+ g +++sr+lw++l  +++w+
  gi|121638082|ref|YP_978306.1| 573 RHW-LRaGELLEWAYATVGSS--QAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTML-IFMLWH 631
                                    ***.999***********999..4545*****************************.*****9 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.0     1e-41   3.1e-38       2     122 ..      59     181 ..      58     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1e-41
                       GATase_7   2 rrlsiidseagaQPmvs...sedgrlvivfnGeiyNykelreeLeak.ghrfrtksDtevllalleaewgeealerlnGm 77 
                                    +rlsiid ++++QP+     ++ +r+v+vfnGeiyNy elr+eL+++ g  f+t++D e +la +++ wg+e+l+rl+Gm
  gi|121638082|ref|YP_978306.1|  59 NRLSIIDIAHSHQPLRWgppEAPDRYVLVFNGEIYNYLELRDELRTQhGAVFATDGDGEAILAGYHH-WGTEVLQRLRGM 137
                                    69*************9654457899*******************965389***************97.************ PP

                       GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    fAfa+wd+ +++l++aRD++GikPL++++ +g + ++aSe k+ll
  gi|121638082|ref|YP_978306.1| 138 FAFALWDTVTRELFCARDPFGIKPLFIATGAG-GTAVASEKKCLL 181
                                    ******************************86.9*********97 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   3.5e-37   1.1e-33       1     134 []      38     176 ..      38     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 3.5e-37
                       GATase_6   1 pdasglaslvede...valaHvRlaivglaeeegaqPf....psedgrlllvhNGeiynykelreelpalkglafrsrsD 73 
                                    pd sg+ ++v++    v+++ +Rl+i++ a  +++qP+    p++ +r++lv+NGeiyny elr+el+ ++g+ f+++ D
  gi|121638082|ref|YP_978306.1|  38 PDESGTWHAVDGAsggVVFGFNRLSIIDIA--HSHQPLrwgpPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGD 115
                                    5667775556442334*************9..999***9998899999******************************** PP

                       GATase_6  74 tevllalleelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                     e +la ++++G+evl+rlrGmfafa+wd  +++l++ard +g+kpl++a+  +g+a+ase
  gi|121638082|ref|YP_978306.1| 116 GEAILAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASE 176
                                    ************************************************************8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.5e-08   0.00016     124     173 ..     129     178 ..     124     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.5e-08
                        DUF3700 124 qvvkdleGkfafvlydskaktvfvaldadgsvplyWGiaadgsvvisddl 173
                                    +v++ l+G faf l+d+ ++++f a+d  g  pl+  + a g+ v s+++
  gi|121638082|ref|YP_978306.1| 129 EVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKK 178
                                    799******************************************99976 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.5e-06     0.023       5      56 ..     283     333 ..     280     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                                    E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-E CS
                           QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveeh 56 
                                     lSGG+DSt+++ala ++  ++++ t  +++   +e+++a + a+++g  +h
  gi|121638082|ref|YP_978306.1| 283 FLSGGIDSTAIAALAIRHNPRLITFTTGFEREGFSEIDVAVASAEAIGA-RH 333
                                    59*************************************9999999887.33 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     9e-06     0.027       3      39 ..     260     298 ..     258     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-06
                                    HHHHHHHHHHHHHCTTSEEEEE..E-SSHHHHHHHHHHH CS
                   NAD_synthase   3 eelvdflkeyvkkagakgvvlG..lSGGvDSslvaalav 39 
                                    +e++++l++ v+k+    v +G  lSGG+DS+ +aala 
  gi|121638082|ref|YP_978306.1| 260 DEITAVLEDSVAKHMRADVTVGafLSGGIDSTAIAALAI 298
                                    678999****************999************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3695.56
//
Query:       gi|121638083|ref|YP_978307.1|  [L=324]
Description: adenosine kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-54  183.5   0.0    6.9e-54  183.2   0.0    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   3.8e-58   6.9e-54      11     297 ..      15     295 ..       6     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 3.8e-58
                                    EEEEEEECSSH......TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEE CS
                           PfkB  11 lidliavsekl......egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvk 83 
                                    ++   ++se+l      + +l+  v +++++ GG++ N+A+a+  lg++va++ga G D+  ++++++lk++gv++d+v 
  gi|121638083|ref|YP_978307.1|  15 MRFPGRFSEQLlpehlhKVSLSfLVDDLVMHRGGVAGNMAFAIGVLGGEVALVGAAGADF--ADYRDWLKARGVNCDHVL 92 
                                    55555555555556667899999*************************************..****************** PP

                                    EESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE..E CS
                           PfkB  84 idedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt..f 161
                                    i+e+++t+  ++++d d+ +   f++ga++++++ +l ++++++++ +l+ i++    ++pea++ +++e++k g +  +
  gi|121638083|ref|YP_978307.1|  93 ISETAHTARFTCTTDVDMAQIASFYPGAMSEARNIKLADVVSAIGKPELVIIGA----NDPEAMFLHTEECRKLGLAfaA 168
                                    *****************99**********************************9....*******************999 PP

                                    EEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE.TTEE CS
                           PfkB 162 dpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve.kdge 240
                                    dp +  +  +   e++++l+++a +l++n++E++ l++++++++++++a+        +++ v tlG +G+ +ve  +++
  gi|121638083|ref|YP_978307.1| 169 DPSQQLARLS--GEEIRRLVNGAAYLFTNDYEWDLLLSKTGWSEADVMAQ--------IDLRVTTLGPKGVDLVEpDGTT 238
                                    ***9999998..5************************************9........578**************77777 PP

                                    EEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                           PfkB 241 lkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                    ++v  vp++ + D+tG GD+f +gfl + ++g  le+++++++ vA lv++++g+++
  gi|121638083|ref|YP_978307.1| 239 IHVGVVPETSQTDPTGVGDAFRAGFLTGRSAGLGLERSAQLGSLVAVLVLESTGTQE 295
                                    777777*************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2128.95
//
Query:       gi|121638084|ref|YP_978308.1|  [L=230]
Description: hypothetical protein BCG_2219 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.045   13.9   0.0    1.2  1  PUFD      BCORL-PCGF1-binding domain


Domain annotation for each model (and alignments):
>> PUFD  BCORL-PCGF1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-06     0.045      41      77 ..     155     191 ..     151     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-06
                           PUFD  41 klssrifrarfPhlevvslaeaefyrqvslsqllsse 77 
                                    klss  fr++f ++ev s+ +  ++ q ++  l++ +
  gi|121638084|ref|YP_978308.1| 155 KLSSDAFRKQFSQVEVTSIDKIVYWSQYQAQVLFTMQ 191
                                    89*************************9876666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1671.35
//
Query:       gi|121638085|ref|YP_978309.1|  [L=118]
Description: hypothetical protein BCG_2220c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-19   69.5   0.0    3.1e-19   69.2   0.0    1.0  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   1.7e-23   3.1e-19       4     111 .]      15     115 ..      13     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.7e-23
                                    EE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS. CS
                    Fe-S_biosyn   4 tlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfld 80 
                                     lteaAa+k k+ll++++++   lr++v+ gg       C+ g +y+l + d+   + d++ e +g++++v+++s+++  
  gi|121638085|ref|YP_978309.1|  15 ILTEAAAAKAKSLLDQEGRDdlaLRIAVQPGG-------CA-GLRYNLFFDDRT-LDGDQTAEFGGVRLIVDRMSAPYV- 84 
                                    58*****************9************.......**.************.************************. PP

                                    TTEEEEEEEETTEEEEEEETCCEEEEEEEEE CS
                    Fe-S_biosyn  81 eglvldfvedlgtlgLksdngilddnvglgk 111
                                    eg ++dfv++ +  g++ dn+++++++ +g+
  gi|121638085|ref|YP_978309.1|  85 EGASIDFVDTIEKQGFTIDNPNATGSCACGD 115
                                    9****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 914.97
//
Query:       gi|121638086|ref|YP_978310.1|  [L=358]
Description: hypothetical protein BCG_2221c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-93  313.4  15.7    2.8e-52  177.9   6.8    2.0  2  Gly_kinase  Glycerate kinase family


Domain annotation for each model (and alignments):
>> Gly_kinase  Glycerate kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   1.7   2.6e-45   4.7e-41       1     148 [.       3     151 ..       3     153 .. 0.97
   2 !  177.9   6.8   1.6e-56   2.8e-52     176     364 ..     155     348 ..     152     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 2.6e-45
                     Gly_kinase   1 iviapdsFkgslsaaevaeaiaegikkaapeaevvklplaDGGeGtvealvaalggelvevevtgplgrpveakyglled 80 
                                    +++apd + +slsa e+a+aia+g+++ +p  ++++ p +DGG G+ve+l + lg + ++++v gpl + v+a++++   
  gi|121638086|ref|YP_978310.1|   3 VLVAPDCYGDSLSAVEAAAAIATGWTRSRPGDSFIVAPQSDGGPGFVEVLGSRLGET-RRLRVCGPLNTVVNAAWVFDPG 81 
                                    79***************************************************9888.6*******************99 PP

                     Gly_kinase  81 ektAviEmAeasGlklv..peeernplktttyGvGelikaaldkgarkiiigiGGSatnDgGaGmlqaLG 148
                                    ++tA++E+A+a+Gl l+  p++ +++l +++ GvG+li+aal++ga +i++g+GGSa++DgG Gm+++LG
  gi|121638086|ref|YP_978310.1|  82 SATAYLECAQACGLGLLggPPTPETALAAHSKGVGQLIAAALRAGAARIVVGLGGSACTDGGKGMIAELG 151
                                    99**************977788899999*****************************************9 PP

  == domain 2  score: 177.9 bits;  conditional E-value: 1.6e-56
                     Gly_kinase 176 kldprlkdveitvacDvtnpLlGeeGaaavFgpQKGatpeqveeldaalehlaevlkkdlg......pGaGAAGGlgaal 249
                                    +++++l+dve+++a+Dv+ pLlG+ G+a+vF+pQKGa+ ++v+ l+ +l+ +a  l+++ g      pGaGAAGG+ga+l
  gi|121638086|ref|YP_978310.1| 155 AARRQLADVEVIAASDVEYPLLGPWGTARVFAPQKGADMATVAVLEGRLAAWAIELDAAAGrgvsaePGAGAAGGIGAGL 234
                                    567899***********************************************99999775678889************* PP

                     Gly_kinase 250 laflgaelksGielvlelvgleeklkeadlviTGEGrlDsqtlsGKvpvgvaklakkagvpvialaGsveedaeeleeag 329
                                    la +g++ +sG+++++e++++++ l++a+l++TGEGr+D+q+l+GKv+ ++a++a+   +pvi+laG+v+ d+++l++ag
  gi|121638086|ref|YP_978310.1| 235 LA-VGGRYQSGAAIIAEHTHFADDLADAELIVTGEGRFDEQSLHGKVVGAIAAAARPLAIPVIVLAGQVSLDKSALRSAG 313
                                    85.9**************************************************************************** PP

                     Gly_kinase 330 idavfsildgpesleealeeaaelleeaaeqvarl 364
                                    i+a++si++ + s++ al++aa++l  +a+qva+ 
  gi|121638086|ref|YP_978310.1| 314 IMAALSIAEYAGSVRLALADAANQLMGLASQVAAR 348
                                    *******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2662.72
//
Query:       gi|121638087|ref|YP_978311.1|  [L=236]
Description: hypothetical protein BCG_2222 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-58  196.3  15.4    7.1e-58  195.4  15.4    1.4  1  DUF3043   Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4  15.4     4e-62   7.1e-58       1     170 [.      48     232 ..      48     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 4e-62
                        DUF3043   1 kKGrpTPkRkeaeaarrrplv..apktrkearkra................reaarerrerareamraGderylpardrg 62 
                                    +KGrpTPkR+++++++++++v  ap+t ++ar+r+                ++a+r+r ++ re+m+aG+e+yl++rdrg
  gi|121638087|ref|YP_978311.1|  48 PKGRPTPKRNQSRRHTKKGPVapAPMTAAQARARRkslagpklsreerraeKAANRARMTERRERMMAGEEAYLLPRDRG 127
                                    6************9999999989999*99999999*************88877777777778888*************** PP

                        DUF3043  63 pvRryvRDlVDsrrnlgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgillgrkvkkkvrekFp.ete 141
                                    pvRryvRD+VDsrrnl +lf+p al +l+++++    vp+vq ++s ++l+ll+l+ id+i+lgrkv + v++kFp +te
  gi|121638087|ref|YP_978311.1| 128 PVRRYVRDVVDSRRNLLGLFMPSALTLLFVMFA----VPQVQFYLSPAMLILLALMTIDAIILGRKVGRLVDTKFPsNTE 203
                                    ******************************998....9****************************************** PP

                        DUF3043 142 sekglglYavsRalqiRrlRlPkPqvkrg 170
                                    s+++lglYa+ Ra+qiRrlR+P+Pqv+rg
  gi|121638087|ref|YP_978311.1| 204 SRWRLGLYAAGRASQIRRLRAPRPQVERG 232
                                    ***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1450.23
//
Query:       gi|121638088|ref|YP_978312.1|  [L=361]
Description: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-129  431.4  20.7   2.6e-129  431.2  20.7    1.0  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.2  20.7  1.4e-133  2.6e-129       2     329 .]       8     343 ..       7     343 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.2 bits;  conditional E-value: 1.4e-133
                                    ...XHHHHHHHHHHHCTBSSSTTTTHHHHHHHHHHHCHHCGTTS.---EEEEEEEEE-BGGGGGT--SS-TTHHHHHHHH CS
                        DBI_PRT   2 epldeeameaararldsltkPlgsLGrLeelavqlagiqgtlkp.elekkavlvfagDhGvaaegvsaypqevTaqmven 80 
                                    + +d++a++aarar+dsltkP+g+LG Le+l+v++a +q++++p ++e+++v+vfagDhGva+ gvsayp+evTaqmv+n
  gi|121638088|ref|YP_978312.1|   8 STPDAAAEAAARARQDSLTKPRGALGSLEDLSVWVASCQQRCPPrQFERARVVVFAGDHGVARSGVSAYPPEVTAQMVAN 87 
                                    679***************************************************************************** PP

                                    HHCT-SHHHHHHHHCTEEEEEEEEE-S..--T..EE-.-SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEE CS
                        DBI_PRT  81 flaggaavnvlarqagaelrvvDvgva..dle..vdr.kvrrgtaniakepAmtreeaeaaleaGieladeladagadll 155
                                    + aggaa+n+la  aga++rv D++v+  +l+  + + kvrrg++nia+e+A+t++e++aa++aG ++ade++dagadll
  gi|121638088|ref|YP_978312.1|  88 IDAGGAAINALADVAGATVRVADLAVDadPLSerIGAhKVRRGSGNIATEDALTNDETAAAITAGQQIADEEVDAGADLL 167
                                    *************************8876666885555****************************************** PP

                                    EEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH-T.T..HHHHHHHHS-HHHHHHHHHH CS
                        DBI_PRT 156 alGemGigNttaaaallaallglepeevvGrGtglddeglarKiavieqalarhae.k.dplevLakvGGleiaalaGai 233
                                    ++G+mGigNttaaa+l+aal+++ep +vvG Gtg+dd+g+arK+a++++al r+++   dp+ +L++ GG+++aa+aG++
  gi|121638088|ref|YP_978312.1| 168 IAGDMGIGNTTAAAVLVAALTDAEPVAVVGFGTGIDDAGWARKTAAVRDALFRVRPvLpDPVGLLRCAGGADLAAIAGFC 247
                                    ******************************************************74245********************* PP

                                    HHHHHTT--EEE-SHHHHHHHHHHHHHSGGGGGGEEE-B--SSTCHHHHHHHHT---SB-S---S-TTHHHHHHHHHHHH CS
                        DBI_PRT 234 lgAaarripvvlDGfistaAalvAvrlapevkdyliashrsaepghkllleaLgleplldlglrlGEGtGAalalpllea 313
                                     +Aa+rr+p +lDG+ +taAalvA+rlap++++++ a+hrs epgh l+l+aLgl+p++dl +rlGEGtGAa+al +l+a
  gi|121638088|ref|YP_978312.1| 248 AQAAVRRTPLLLDGVAVTAAALVAERLAPGAHRWWQAGHRSSEPGHGLALAALGLDPIVDLHMRLGEGTGAAVALMVLRA 327
                                    ******************************************************************************** PP

                                    HHHHCCHS-BHHHHT- CS
                        DBI_PRT 314 AaallnematfeeagV 329
                                    A+a l++matf+eagV
  gi|121638088|ref|YP_978312.1| 328 AVAALSSMATFTEAGV 343
                                    **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2676.31
//
Query:       gi|121638089|ref|YP_978313.1|  [L=249]
Description: cobalamin synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-43  149.7  22.5    1.4e-43  149.5  22.5    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5  22.5   7.7e-48   1.4e-43       1     202 [.       8     239 ..       8     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 7.7e-48
                           CobS   1 alsflTrlPvp.....elar.alaffPlvGlllGlll.llallllllll...llaallavaalvlltgglHlDGlaDtaD 70 
                                    a++f T++P p      ++r  + ++P+vG+ lG+l+ ++a++ ++++    +l+++l+va+l+++t+glH+DG+aDtaD
  gi|121638089|ref|YP_978313.1|   8 AFAFATVIPTPgsattPMGRgPMTALPVVGAALGALAaAIAWAGAQVFGpssPLSGMLTVAVLLVVTRGLHIDGVADTAD 87 
                                    799*******976655445569**************86666665555558*9889999999999**************** PP

                           CobS  71 glgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala......lllapvlsRlaallaiallpya..eeglgal 142
                                    glg++++++r+l++m+D ++G+fGv+a+vlv++l+ +a+a+l+      + la + +R++a+l+++++ +a   + lg+ 
  gi|121638089|ref|YP_978313.1|  88 GLGCYGPPQRALAVMRDGSTGPFGVAAVVLVIALQGLAFATLTtvgiagITLAVLSGRVTAVLVCRRSVPAahGSTLGSR 167
                                    **************************************877767788888899****************9974489**** PP

                           CobS 143 faeaqkk.lvllal........avlllllall............laallvalllrrlarrklggvtGDvlGavieltell 201
                                    +a++q++ +v+++l                 +            +a+++ a+l++++++r +ggvtGDvlG +iel++++
  gi|121638089|ref|YP_978313.1| 168 VAGTQPApVVAAWLavllavsvP--------AgprpwqgpiavlVAVTAGAALAAHCVHR-FGGVTGDVLGSAIELSTTV 238
                                    **998885222222112222330........1455555555443444446668899****.****************998 PP

                           CobS 202 v 202
                                     
  gi|121638089|ref|YP_978313.1| 239 S 239
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1691.80
//
Query:       gi|121638090|ref|YP_978314.1|  [L=512]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.035   13.0  55.4      0.021   13.8  23.0    3.0  3  MFS_1       Major Facilitator Superfamily
       0.98    8.2  18.2      0.072   11.9  11.4    2.1  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  15.9   4.8e-05      0.43     216     335 ..      26     146 ..       3     163 .. 0.72
   2 ?    0.5   2.6     0.024   2.2e+02       9      59 ..     158     215 ..     150     231 .. 0.53
   3 ?   13.8  23.0   2.3e-06     0.021      16     170 ..     242     404 ..     234     468 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.8e-05
                          MFS_1 216 lllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglalla 295
                                    ++++++ + +  + lp++   + gl+  + agll+++++++++ +  l+  +++r g  r ll+a +++++aal ++ +a
  gi|121638090|ref|YP_978314.1|  26 FYTAGLQLGSGAVVLPVI-CAHQGLT--WAAGLLYPAFCIGAILGNSLSPLILQRAGQLRHLLMAAISATAAALVVCNAA 102
                                    444444445577889997.*******..99*************************9998888888888888888888888 PP

                          MFS_1 296 vtssavllllvlvl...iGf.glgfvfpsllalasdlappeeag 335
                                    v+++ v +++v++    +G    g+ +++++ ++s+++p+ ++g
  gi|121638090|ref|YP_978314.1| 103 VPWTGVGVAAVFLAttgAGGvVTGVSSVAYTDMISSMLPAVRRG 146
                                    88777777664444333222233444677777777777776666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.024
                          MFS_1   9 alarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrl.......sdrf 59 
                                     la +++++++p+ a +++     + + +l ++  + +++a+l++G++       ++r+
  gi|121638090|ref|YP_978314.1| 158 VLATGVTLVIVPMlAHGNEMA-RYHDLLWLGAAGLVCSGIAALFVGPMrsvsvttATRM 215
                                    445555555555434444433.5556666666666666666666666633333333355 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.3e-06
                          MFS_1  16 gpalplalaedlg.....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa......ss 84 
                                    ++++p+ l++++       s  +++ l+ l ++g +v+s+++  +   fG r +ll ++ll a+++ll+++a       +
  gi|121638090|ref|YP_978314.1| 242 LLFVPISLGTTFFslraaQSNGSLHVLVILSSIGLVVGSMLWRQINRLFGVRGLLLGSALLNAAAALLCMVAescgqwVH 321
                                    45555555555443333356667888999************************************666665455656655 PP

                          MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslg.Wravfyilaivsl 162
                                     w+   + +l+ ++a ++++a++++i+ ++p++ r+  i + s+ +++ a +lg +lgg+   ++  W++v  ++  +++
  gi|121638090|ref|YP_978314.1| 322 AWAYGTAFLLATVAAQTVVAASISWISVLAPERYRATLICVGSTLAAVEAtVLGVALGGIAQKHATiWPVV--VVLTLAV 399
                                    6767777778888889************************9999999977477777777666444335555..5555555 PP

                          MFS_1 163 lafvlfll 170
                                    +a+v   +
  gi|121638090|ref|YP_978314.1| 400 IAAV---A 404
                                    5544...2 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.5     0.033   2.9e+02     278     314 ..      69     106 ..      50     148 .. 0.67
   2 ?   11.9  11.4   8.1e-06     0.072     256     376 ..     259     385 ..     221     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.033
                     MFS_1_like 278 ffaeklleklG.hvklliiallayilrfllyaiienaw 314
                                     ++  +l++ G ++ ll++a++a+++ +++ ++   + 
  gi|121638090|ref|YP_978314.1|  69 SLSPLILQRAGqLRHLLMAAISATAAALVVCNAAVPWT 106
                                    5566788888844789999******9999999873332 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.1e-06
                     MFS_1_like 256 gasntllGslvalgvvaeiplfffaeklleklGhvklliiall..ayilrfllyaii....enawlvlpievLhgisfgl 329
                                      sn  l +lv+l  ++ ++  ++  ++ + +G++ ll+ + l  a ++ ++++a        aw    + +L  ++  +
  gi|121638090|ref|YP_978314.1| 259 AQSNGSLHVLVILSSIGLVVGSMLWRQINRLFGVRGLLLGSALlnAAAALLCMVAEScgqwVHAWAYGTAFLLATVAAQT 338
                                    5578888899999999999999999**********999887661244566777776578867777777888888899999 PP

                     MFS_1_like 330 lwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdl 376
                                    + aa ++++s +ap++++at++ + s+l     + lG  +GG+  ++
  gi|121638090|ref|YP_978314.1| 339 VVAASISWISVLAPERYRATLICVGSTLAAVEATVLGVALGGIAQKH 385
                                    *****************************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3780.23
//
Query:       gi|121638091|ref|YP_978315.1|  [L=368]
Description: branched-chain amino acid aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-32  113.8   0.0    1.3e-32  113.5   0.0    1.1  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0     7e-37   1.3e-32       2     222 ..      76     323 ..      75     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 7e-37
                    Aminotran_4   2 lfEtmrvy...ngei..ffldeHleRLrksaellglelpfdeeelrkileelleannsen........grlrllvsrggg 68 
                                    +fE++++y   +g+i  f+ d++++RLr sa++l + ++++   + + l++l++ ++ ++        ++lr+++++++ 
  gi|121638091|ref|YP_978315.1|  76 VFEGLKAYrwaDGSIvsFRADANAARLRSSARRL-AIPELPDAVFIESLRQLIAVDKAWVpgaggeeaLYLRPFIFATEP 154
                                    9*****99999****9999************999.89999999999******************999999********** PP

                    Aminotran_4  69 glgaatsepsvavyvsalppgpeseke...lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvd.. 142
                                    glg   ++ ++  +++a+p g++ +     +++++s+++ r  p  +  aK    y+ ++la++ea+e+g+d+v+++d  
  gi|121638091|ref|YP_978315.1| 155 GLG-VRPATQYRYLLIASPAGAYFKGGiapVSVWVSTEYVRACPGGTGAAKFGGnYAASLLAQAEAAENGCDQVVWLDav 233
                                    ***.6666666666667777777777788*99*******************7766**********************955 PP

                    Aminotran_4 143 edgnvtEgstsNvfivk....ggelitPplssgiLpGitrrallelakalgleveereitlkdle......eadeafltn 212
                                    e++++ E + +N+f+v       +l+tP+ls+++LpGitr++ll+la ++g+ veer+i +++ +      e+ e+f ++
  gi|121638091|ref|YP_978315.1| 234 ERRYIEEMGGMNIFFVLgsggSARLVTPELSGSLLPGITRDSLLQLAIDAGFAVEERRIDIDEWQkkaaagEITEVFACG 313
                                    5677*************7877789******************************************************** PP

                    Aminotran_4 213 tlrgvlpvrs 222
                                    t++ ++pv +
  gi|121638091|ref|YP_978315.1| 314 TAAVITPVAR 323
                                    ********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2872.97
//
Query:       gi|121638092|ref|YP_978316.1|  [L=379]
Description: glycine cleavage system aminomethyltransferase T [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-82  274.3   0.0    1.1e-81  274.0   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    1.3e-15   57.1   0.1    2.8e-15   56.0   0.1    1.5  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.0   0.0   1.2e-85   1.1e-81       1     257 []      24     272 ..      24     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 274.0 bits;  conditional E-value: 1.2e-85
                          GCV_T   1 lydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkaty 80 
                                    l+drh++lga+f ef+gw mPv+Y   ++  eh+a+r+a+glfDvSh+gk  v+Gp+aa++++++ltnd+ ++ pgka+y
  gi|121638092|ref|YP_978316.1|  24 LEDRHRELGASFAEFGGWLMPVSY--AGTVSEHNATRTAVGLFDVSHLGKALVRGPGAAQFVNSALTNDLGRIGPGKAQY 101
                                    689*********************..****************************************************** PP

                          GCV_T  81 tlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlskllga 160
                                    tl+++e+GgvidDli + +++de++lv naan++ ++  l++ a+     +++++++ ++a+la+qGP +++vl +l   
  gi|121638092|ref|YP_978316.1| 102 TLCCTESGGVIDDLIAYYVSDDEIFLVPNAANTAAVVGALQA-AA--PGGLSITNLHRSYAVLAVQGPCSTDVLTALG-- 176
                                    ******************************************.77..8999***************************.. PP

                          GCV_T 161 dlselkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRlEaglrlyg 240
                                      +e++++ +a+  +  g++v+v+RtgytGe+G+e++ p+e a  +++aLl+a++++g +paGlgArdtlR E+g++l g
  gi|121638092|ref|YP_978316.1| 177 LPTEMDYMGYADASYS-GVPVRVCRTGYTGEHGYELLPPWESAGVVFDALLAAVSAAGGEPAGLGARDTLRTEMGYPLHG 255
                                    46899**********9.*************************************************************** PP

                          GCV_T 241 hdldeettPleaglgwa 257
                                    h+l+ +++Pl+a++gwa
  gi|121638092|ref|YP_978316.1| 256 HELSLDISPLQARCGWA 272
                                    ****************6 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   3.2e-19   2.8e-15       2      79 ..     297     374 ..     296     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 3.2e-19
                        GCV_T_C   2 rlvgleld.dgapllrggepilrdgevvGhvTSgaysptlgksialAyvkael.aklgtevevevrgkrvpaevvkkpfy 79 
                                     l gl++  +g  +lr g ++l ++e+vG +TSg++sptl+  i+lA++++++  + g++++v+vrg+ v+++vv +pf+
  gi|121638092|ref|YP_978316.1| 297 LLRGLRMVgRG--VLRPGLAVLVGDETVGVTTSGTFSPTLQVGIGLALIDSDAgIEDGQQINVDVRGRAVECQVVCPPFV 374
                                    58899996555..88***********************************55535559********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2722.26
//
Query:       gi|121638093|ref|YP_978317.1|  [L=378]
Description: hypothetical protein BCG_2228 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-16   58.2   0.0    1.8e-15   57.1   0.0    1.5  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    5.1e-09   36.1   0.7    8.2e-09   35.5   0.7    1.3  1  Ad_Cy_reg      Adenylate cyclase regulatory domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0     2e-19   1.8e-15       9     172 ..     207     350 ..     201     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2e-19
                  Guanylate_cyc   9 vtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdmlea 88 
                                    ++i Fad+ +ftal +a +p ++ +lL e  a + ++++++++  vk+iGda m vs +p       ++l++ a d++++
  gi|121638093|ref|YP_978317.1| 207 CGIGFADLSSFTALTQALTPAQLQDLLTEFDAAVTDVVHADGGRLVKFIGDAVMWVSSSP-------ERLVRAAVDLVDH 279
                                    6899********************************************************.......899999******* PP

                  Guanylate_cyc  89 leevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellkeeqfeltergev 168
                                     +  a+e    l+vr G+ +G+v+a          d++Gn vnlA+r+ + + +g+i   ++ +++l   ++   + g+ 
  gi|121638093|ref|YP_978317.1| 280 PGARAAE----LQVRAGLAYGTVLALNG-------DYFGNPVNLAARLVAAAAPGQILAAAQLRDMLP--DWPALAHGPL 346
                                    9887766....8************9777.......**********************99999888887..5555555666 PP

                  Guanylate_cyc 169 evkG 172
                                     +kG
  gi|121638093|ref|YP_978317.1| 347 TLKG 350
                                    6666 PP

>> Ad_Cy_reg  Adenylate cyclase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.7   9.2e-13   8.2e-09      18     180 ..      19     185 ..       7     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 9.2e-13
                      Ad_Cy_reg  18 aeRaeliewLlerGvsieeiraa.aepmL..LaaervlgddgtyvsareisektGidlellqrlqrAvGLprvddpDaav 94 
                                    +eRa+l+  L e G+++ee+ +a ++ +L  La   +l       +    +++ G+  +++ r    +GL+ v+ pD   
  gi|121638093|ref|YP_978317.1|  19 RERAGLLTYLDELGFTVEEMVQAeRRGRLfgLAGDVLLWSGPPIYTLATAADELGLSADDVARAWSLLGLT-VAGPDVPT 97 
                                    79*****************999989999988888888877666669999********************86.6******* PP

                      Ad_Cy_reg  95 llraDaeaaarakrfldlGldedqivavarvLaegLsraae....vlReaalkallepgaselelakaaealvaeiapll 170
                                    l +aD++a a+  ++ +l + ed+++   rvL+  ++r ae    ++R+   +  ++ + +el  a+a+  ++ae  p +
  gi|121638093|ref|YP_978317.1|  98 LSQADVDALATWVALKAL-VGEDGAFGLLRVLGTAMARLAEaestMIRAGSPNIQMTHTHDELATARAYR-AAAEFVPRI 175
                                    *******99988777665.89*****************99833324555555666666666666666665.466788999 PP

                      Ad_Cy_reg 171 gpmiqellal 180
                                    g +i+ + + 
  gi|121638093|ref|YP_978317.1| 176 GALIDTVHRH 185
                                    9998877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2902.04
//
Query:       gi|121638094|ref|YP_978318.1|  [L=515]
Description: leucyl aminopeptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.8e-115  383.3   0.1   1.1e-114  382.9   0.1    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    5.8e-28   97.3   0.3    7.4e-27   93.7   0.0    2.5  2  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.9   0.1  1.2e-118  1.1e-114       2     310 ..     193     504 ..     192     505 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.9 bits;  conditional E-value: 1.2e-118
                                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SS.....TT CS
                  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgak.....ek 76 
                                    +ardlvntp+++l p++la++a++l+++ g ++vev+de++l++ g+g++++Vg+gS ++pprlv+l ++g++     +k
  gi|121638094|ref|YP_978318.1| 193 TARDLVNTPPSHLFPAELAKRAKTLSESVG-LDVEVIDEKALKKAGYGGVIGVGQGS-SRPPRLVRLIHRGSRlaknpQK 270
                                    69*********************9999998.9*************************.56*********99999999999 PP

                                    SEEEEEEEEEEEEEE-TTSS--HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-T CS
                  Peptidase_M17  77 ekklalVGKGitfDtGGlslKpsasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitam 156
                                    +kk+alVGKGitfDtGG+s+Kp+asm++m++DmgGAAav+++++++a+l+lp++v+a++p+aeNm+s +a++pgdv+t++
  gi|121638094|ref|YP_978318.1| 271 AKKVALVGKGITFDTGGISIKPAASMHHMTSDMGGAAAVIATVTLAARLRLPIDVIATVPMAENMPSATAQRPGDVLTQY 350
                                    ******************************************************************************** PP

                                    TS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEEE---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE- CS
                  Peptidase_M17 157 nGktvevlnTDaEGRLvLADalayaeekekpdlivdvATLTgavvvalGkkaaglfsnddelaeelekageeagervwrl 236
                                     G+tvevlnTDaEGRL+LADa++ a+ ++kpd++++++TLTga+ valG+++ g+++ +de+++++++ ++++ge+ w++
  gi|121638094|ref|YP_978318.1| 351 GGTTVEVLNTDAEGRLILADAIVRAC-EDKPDYLIETSTLTGAQTVALGTRIPGVMG-SDEFRDRVAAISQRVGENGWPM 428
                                    *************************7.67****************************.778******************* PP

                                    ---HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSE.CGEEEEE-TTTTES.BTTB.S...EE--TTHHHH CS
                  Peptidase_M17 237 pleeeykkqlkskvaDlknvgkkrragaitAalFLkefvke.tpWaHlDiagtalkekealkke.kgatGvgvrtL 310
                                    pl +++k++lks+vaDl+nv+++r ag+++A++FL+efv+e ++WaH+D+ag+a+++ +a+ ++ kgatGv++rt+
  gi|121638094|ref|YP_978318.1| 429 PLPDDLKDDLKSTVADLANVSGQRFAGMLVAGVFLREFVAEsVDWAHIDVAGPAYNTGSAWGYTpKGATGVPTRTM 504
                                    **********************9999*************88899***********9888888889*********97 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   8.2e-31   7.4e-27       2     126 .]      30     157 ..      29     157 .. 0.92
   2 ?    0.6   0.1     0.055   4.9e+02      47      61 ..     267     280 ..     233     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 8.2e-31
                Peptidase_M17_N   2 vgvf......eggklspaa.ekldealagllsellkegdftGkagevlvlralsgekakrvllVGLGkeee.ltaealrk 73 
                                    v+v+      ++g++ ++a  +l +++ +++++ l+++d+tG++++v++l  +s   + +vl+VGLGk++  ++a+++r+
  gi|121638094|ref|YP_978318.1|  30 VPVVstgeedRPGAVVASAePFLRADTVAEIEAGLRALDATGASDQVHRLAVPSLP-VGSVLTVGLGKPRReWPADTIRC 108
                                    666666666655666666679*********************************99.***********9988******** PP

                Peptidase_M17_N  74 aagaaaralkg.akvttiavalplegknsdekaeaaaegallglYrfdrykskk 126
                                    aag+aaral++ + v t++++lp      d++++a +eg+ lg+Yrf +++s+k
  gi|121638094|ref|YP_978318.1| 109 AAGVAARALNSsEAVITTLAELP-----GDGICSATVEGLILGSYRFSAFRSDK 157
                                    ***********9***********.....99**********************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.055
                Peptidase_M17_N  47 lsgekakrvllVGLG 61 
                                     + +kak+v+lVG G
  gi|121638094|ref|YP_978318.1| 267 NP-QKAKKVALVGKG 280
                                    23.347777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3551.63
//
Query:       gi|121638095|ref|YP_978319.1|  [L=592]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-49  167.6   1.1    3.1e-49  167.1   1.1    1.2  1  adh_short        short chain dehydrogenase
      4e-42  144.4   1.7    5.9e-42  143.8   1.7    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      3e-36  125.4   0.1    4.2e-36  124.9   0.1    1.2  1  Abhydrolase_1    alpha/beta hydrolase fold
    8.9e-13   49.4  11.7    2.1e-12   48.1  11.7    1.6  1  Abhydrolase_6    Alpha/beta hydrolase family
    3.7e-09   36.7   0.4    6.3e-09   36.0   0.4    1.3  1  KR               KR domain
    7.3e-09   35.2   0.1    1.5e-08   34.2   0.1    1.6  1  Hydrolase_4      Serine aminopeptidase, S33
     0.0014   18.2   0.1     0.0022   17.5   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0046   16.9   0.4     0.0074   16.2   0.4    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.044   13.3   0.1      0.074   12.6   0.1    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
        0.2   10.7   0.0       0.29   10.2   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   1.1   1.8e-52   3.1e-49       3     189 ..     327     514 ..     325     518 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 1.8e-52
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    v vtGa+sGIGr++a ++a+eGa++v+ d+ e++++ +a+e+ + g  a+++ +Dv+d+e+vea+ e++ +++g  d++v
  gi|121638095|ref|YP_978319.1| 327 VSVTGAGSGIGRETALAFAREGAEIVISDIDEATVKDTAAEIAARGGIAYPYVLDVSDAEAVEAFAERVSAEHGVPDIVV 406
                                    78****************************************************************************** PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                    nNAGi + g f ++ +e+++rv++vNl gv++ +ra+ + ++ ++ +G+IvnvsS+a+  p+ +++aY++sKaa  ++++
  gi|121638095|ref|YP_978319.1| 407 NNAGIGQAGRFLDTPAEQFDRVLAVNLGGVVNGCRAFGQRLVeRGTGGHIVNVSSMAAYAPLQSLSAYCTSKAATYMFSD 486
                                    ****************************************9988999********************************* PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmake 189
                                    +l+ el   g+  ++++PG++dT+++++
  gi|121638095|ref|YP_978319.1| 487 CLRAELDAAGVGLTTICPGVIDTNIVAT 514
                                    ***********************99865 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   1.7   3.3e-45   5.9e-42       1     183 [.     331     516 ..     331     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 3.3e-45
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIGr++A a+a+eGae+v++d++e+  k++++e+a+++g ++ + +DV+d e+vea++e+v +++g  Di+vnnag
  gi|121638095|ref|YP_978319.1| 331 GAGSGIGRETALAFAREGAEIVISDIDEATvKDTAAEIAARGGIAYpYVLDVSDAEAVEAFAERVSAEHGVPDIVVNNAG 410
                                    889****************************************8877********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    i ++  g+fl+t+ e+fdr+l+vnl ++++ ++a+ + l+++g  g ivn+ss++a   +++ +ay+++Kaa   ++ +l
  gi|121638095|ref|YP_978319.1| 411 IGQA--GRFLDTPAEQFDRVLAVNLGGVVNGCRAFGQrLVERGtgGHIVNVSSMAAYAPLQSLSAYCTSKAATYMFSDCL 488
                                    ****..*******************************88887799*********************************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGST CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgik 183
                                     +el + g+   +++pg+i+T++++   
  gi|121638095|ref|YP_978319.1| 489 RAELDAAGVGLTTICPGVIDTNIVATTG 516
                                    *********************9976554 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.1   2.3e-39   4.2e-36       1     256 [.      30     286 ..      30     287 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 2.3e-39
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH.HHHHHCTTSSEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld.rildalgddkltlvG 79 
                                    p++v++hG+p+s+ +w +  ++p La+ +f+++ +D rGvg+Ss ++    + y++a++add+d  i +  + +++++++
  gi|121638095|ref|YP_978319.1|  30 PTVVLVHGFPDSHVLWDG--VVPLLAE-RFRIVRYDNRGVGRSSVPKPI--SAYTMAHFADDFDaVIGELSPGEPVHVLA 104
                                    78****************..*******.********************9..9************5559999999999*** PP

                                    ETHHHHHHHHHHHHH..GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHH CS
                  Abhydrolase_1  80 hSmGGmialayaaey..perVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrl 157
                                    h++G+  +++y+ +    +rV++++++++  p+ ++     +   + p+  +++  +  ++    ++a  +  +  ++ l
  gi|121638095|ref|YP_978319.1| 105 HDWGSVGVWEYLRRPgaSDRVASFTSVSG--PSQDHLVNYVYGGLRRPWRPRTFLRAISQTLRLSYMALFSVPVVAPLLL 182
                                    *****************************..************************************************* PP

                                    HHHHHH....HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC..THHHHSEEEEEEETTCSSSCHHHHH CS
                  Abhydrolase_1 158 vdalkf....pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre..lknvlaptlvisgtsDplvppkale 231
                                      al +    +++++++p + +  + +la+ a+ s++++p+++++++  ++r+  +  v +p+ +i  ++Dp+v p  ++
  gi|121638095|ref|YP_978319.1| 183 RVALSSaavrRNMVGDIPVDQIHHSETLARDAAHSVKTYPANYFRSFSSSRRGraIPIVDVPVQLIVNSQDPYVRPYGYD 262
                                    ****99********************************************99955333444******************* PP

                                    HHHHCHTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 232 dlaqllpkkrlvvisdagHlafleg 256
                                    + a++ p+ +++++ +agH++ + +
  gi|121638095|ref|YP_978319.1| 263 QTARWVPR-LWRRDIKAGHFSPMSH 286
                                    ********.**********987765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1  11.7   1.2e-15   2.1e-12       1     220 []      32     293 ..      32     293 .. 0.56

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.2e-15
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH......CHHHHHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled......ladlaalldelaagggpvvlvGHSl 74 
                                    v+l+HG++ s+  W    +++lla++++++ +D +G G +++ p   ++      ++d++a++ el   g pv++++H++
  gi|121638095|ref|YP_978319.1|  32 VVLVHGFPDSHVLWD--GVVPLLAERFRIVRYDNRGVG-RSSVPKPISAytmahfADDFDAVIGELS-PGEPVHVLAHDW 107
                                    8*****999888887..99999****999*********.5555555544111222344466666664.77777******* PP

                                    HHHHHHHHHHCC......EE.EEES-...........----TTTS----TTHHHHHHTT-C............CCCHCCH CS
                  Abhydrolase_6  75 GGalalaaapla....lvvg.vlldppp.........talpagllaaalelllallallrl............lawlsre 128
                                    G + ++++++ +    +v++   +++p+         +  +++ + +++++l+a  + lrl            +      
  gi|121638095|ref|YP_978319.1| 108 GSVGVWEYLRRPgasdRVASfTSVSGPSqdhlvnyvyG--GLRRPWRPRTFLRAISQTLRLsymalfsvpvvaP-----L 180
                                    ***99994444478866666888888667776655331..2222333333333333333332221112222221.....0 PP

                                    .........S-HSCCCCHHH....CCCCHCHCCCGHH.........HHCCHHCHTTCCHHTT-TTGCEEECTT-CHHHHC CS
                  Abhydrolase_6 129 .........plprlfladed....adaawrarlarla.........allaglgllpaaawadlpvpllvlggeDplvprl 186
                                             +++r +++d +     + +  ar+a+++         +++++    +a ++ d+pv+l ++ ++Dp v+++
  gi|121638095|ref|YP_978319.1| 181 llrvalssaAVRRNMVGDIPvdqiHHSETLARDAAHSvktypanyfRSFSSSRRGRAIPIVDVPVQL-IVNSQDPYVRPY 259
                                    2222333433333555544433332355555555555554444322333333355577888888887.779****88866 PP

                                    ....HHCCCH.STTEEETCE...SSS-HHHHSHHHHHHH CS
                  Abhydrolase_6 187 ....lerlla.qagarlpvvlpgaGHlphleepdevaea 220
                                         +r+   + ++++      aGH+  +++p+  a+a
  gi|121638095|ref|YP_978319.1| 260 gydqTARWVPrLWRRDI-----KAGHFSPMSHPQVMAAA 293
                                    42223344443333444.....59**66666**998875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.4   3.5e-12   6.3e-09       5     154 ..     329     479 ..     325     502 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.5e-12
                                    EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---E CS
                             KR   5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikG 84 
                                    +tG+  g+G+e+a   a++ga+ +  +s     +++ k++ ae++a+g     + +Dvsd++avea  e+++ae++    
  gi|121638095|ref|YP_978319.1| 329 VTGAGSGIGRETALAFAREGAEIV--ISDI--DEATVKDTAAEIAARGGIAYPYVLDVSDAEAVEAFAERVSAEHGVPDI 404
                                    9********************854..4555..5788888999******999999*********************88888 PP

                                    EEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHHHH CS
                             KR  85 vihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaaNa 154
                                    v++ Ag+ + + + ++ ae++++vla  + G+ n  +++ +      +  ++v +SS+a+    +  ++Y +  a
  gi|121638095|ref|YP_978319.1| 405 VVNNAGIGQAGRFLDTPAEQFDRVLAVNLGGVVNGCRAFGQrlverGTGGHIVNVSSMAAYAPLQSLSAYCTSKA 479
                                    9**************************99888888777777444446777999*****99988888888866544 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   8.5e-12   1.5e-08       6      99 ..      31     121 ..      26     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.5e-12
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhS 84 
                                    +vvlvHG+ ++    + ++  La++ f ++ +D+rG Grs  +k      + ++ dD++a++ ++    p++p+ +l+h 
  gi|121638095|ref|YP_978319.1|  31 TVVLVHGFPDSHVLWDGVVPLLAER-FRIVRYDNRGVGRSSvPKPISAYTMAHFADDFDAVIGELS---PGEPVHVLAHD 106
                                    8******************988876.***************99******************87666...*********** PP

                    Hydrolase_4  85 mGGliallyllrypd 99 
                                    +G++ + +yl r  +
  gi|121638095|ref|YP_978319.1| 107 WGSVGVWEYLRRPGA 121
                                    *********988766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.2e-06    0.0022       2     149 ..     328     481 ..     327     500 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                                    EEETTTSHHHHHHHHHHHHCTSEEEE..EES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHH....HH.T-SEEEE CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevig..ldrlssasntarledl....elveldltdrsalerlfk....ee.qpdavih 70 
                                     VtGa   iG+ ++ a++++g e++   +d  + ++  a+++        + ld+ d++a+e++ +    e+  pd+v++
  gi|121638095|ref|YP_978319.1| 328 SVTGAGSGIGRETALAFAREGAEIVIsdIDEATVKDTAAEIAARggiaYPYVLDVSDAEAVEAFAErvsaEHgVPDIVVN 407
                                    59*******************995551245555555555555449*99999********9988766111145569***** PP

                                    --S---HHHHHHSHHHHHHHHTHHHH.HHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHH CS
                      Epimerase  71 lAavggvaassedpadfieknlqgtl.nlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlag 149
                                     A++g  ++  ++pa+ +++ l+++l  +++ +r+ g  rl+  ++     ++ +     ++ + pl++ s+Y  +K+a 
  gi|121638095|ref|YP_978319.1| 408 NAGIGQAGRFLDTPAEQFDRVLAVNLgGVVNGCRAFGQ-RLVERGTGGHIVNVSS-----MAAYAPLQSLSAYCTSKAAT 481
                                    ****************9998877777347888887777.7777777444444444.....34444777777777777765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   4.1e-06    0.0074       2      70 ..     327     398 ..     326     410 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-06
                                    EEEE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH..HHHCCTTTTSS-HHHHCCCHHCEEEE CS
                        3HCDH_N   2 vaviGaGt.mGagiaavfasagleVvlvdiseealekalekiek..sleklvekgklkeeeveaalarisft 70 
                                    v v GaG  +G++ a +fa++g e+v+ di+e+++++ +++i++   ++        ++e vea ++r+s++
  gi|121638095|ref|YP_978319.1| 327 VSVTGAGSgIGRETALAFAREGAEIVISDIDEATVKDTAAEIAArgGIAYPYVLDVSDAEAVEAFAERVSAE 398
                                    789999977*****************************9999874433333333444455566666666655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.1e-05     0.074       3      39 ..     327     364 ..     325     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                                    EEEE--ST.THHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                 UDPG_MGDP_dh_N   3 isviGlGY.vGlvtaavlaeighevigvDideekvdkl 39 
                                    +sv G+G  +G  ta+++a+ g e+++ Dide++v+  
  gi|121638095|ref|YP_978319.1| 327 VSVTGAGSgIGRETALAFAREGAEIVISDIDEATVKDT 364
                                    789999965**************************976 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00016      0.29       1      76 [.     327     395 ..     327     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                    v vtGag  iG+e    ++++  ++i++ + dE ++ + + e+    ++  +    +p + dv d+e +e   e++
  gi|121638095|ref|YP_978319.1| 327 VSVTGAGSGIGRETALAFARE-GAEIVISDIDEATVKDTAAEIA---ARGGI---AYPYVLDVSDAEAVEAFAERV 395
                                    679**********99888765.578************9999984...33345...468999*****9999887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4187.05
//
Query:       gi|121638096|ref|YP_978320.1|  [L=553]
Description: dihydrolipoamide acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-71  239.5   0.0    4.9e-71  238.9   0.0    1.1  1  2-oxoacid_dh   2-oxoacid dehydrogenases acyltransferase (cata
    3.1e-42  142.3  11.8    1.1e-21   76.4   1.4    2.7  3  Biotin_lipoyl  Biotin-requiring enzyme
    4.3e-15   55.8   0.2    1.2e-14   54.3   0.2    1.9  1  E3_binding     e3 binding domain
     0.0024   17.7   5.9          1    9.2   0.1    3.8  4  GCV_H          Glycine cleavage H-protein
     0.0059   16.4   0.1        3.7    7.3   0.0    2.7  2  PTS_EIIA_1     phosphoenolpyruvate-dependent sugar phosphotra
  ------ inclusion threshold ------
      0.042   13.5   3.0        0.9    9.2   0.0    3.5  4  PYNP_C         Pyrimidine nucleoside phosphorylase C-terminal
      0.064   14.0  12.1        5.8    7.7   0.2    4.7  5  HlyD_3         HlyD family secretion protein
       0.14   10.9   0.0       0.47    9.2   0.0    1.8  2  DUF2254        Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   0.0   2.2e-74   4.9e-71       5     227 ..     317     544 ..     314     547 .. 0.97

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 2.2e-74
                                    XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE CS
                   2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasv 84 
                                    ++++ s+ir+++a++  es+q ++++t ++evd+t+++ lr++ k+++a++e ++lt+l+f++kav+ Alk +P++nas+
  gi|121638096|ref|YP_978320.1| 317 TTQKASRIRQITANKTRESLQATAQLTQTHEVDMTKIVGLRARAKAAFAEREGVNLTFLPFFAKAVIDALKIHPNINASY 396
                                    67899********************************************9999*************************** PP

                                    .EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---------- CS
                   2-oxoacid_dh  85 deeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvtsf 164
                                    +e++kei+++++ ++G+Av+t++GLl Pvi++a ++sl+ +a++++++a +ar+g+lkp++l+ggtfti+N+G+ G  + 
  gi|121638096|ref|YP_978320.1| 397 NEDTKEITYYDAEHLGFAVDTEQGLLSPVIHDAGDLSLAGLARAIADIAARARSGNLKPDELSGGTFTITNIGSQGALFD 476
                                    ******************************************************************************** PP

                                    -----TT-SEEEEE---.B--TT.STT-....HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-H CS
                   2-oxoacid_dh 165 tPiinppqvaIlgvgrikerpvv.kege....lvvrkvmtlslsaDHRvidGaeaarFlntlkkllen 227
                                    tPi+ ppq+a+lg g+i +rp v ++ +    + vr+v+++ l++DHR+idGa+a rFl+t+k+ le+
  gi|121638096|ref|YP_978320.1| 477 TPILVPPQAAMLGTGAIVKRPRVvVDASgnesIGVRSVCYVPLTYDHRLIDGADAGRFLTTIKHRLEE 544
                                    *****************999977455557899**********************************97 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   1.4     5e-25   1.1e-21       3      73 .]       5      76 ..       4      76 .. 0.98
   2 !   72.0   1.3   1.2e-23   2.7e-20       3      73 .]     124     195 ..     122     195 .. 0.97
   3 ?   -2.4   0.0         2   4.5e+03      23      40 ..     267     284 ..     266     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 5e-25
                                   EEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl  3 iksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                   +++P++Gesv+eg v+++l+++Gd+V+ +++l+ev+++K+ +ei++p+aGv+++i ++e+dtvevg  la+i
  gi|121638096|ref|YP_978320.1|  5 VQMPALGESVTEGtVTRWLKQEGDTVELDEPLVEVSTDKVDTEIPSPAAGVLTKIIAQEDDTVEVGGELAVI 76
                                   89******************************************************************9987 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 1.2e-23
                                    EEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl   3 iksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                    + +P++Gesv+eg v+++l+k Gd+V+ +++l+ev+++K+ +ei++p+aGv+++i ++e++tv vg  la+i
  gi|121638096|ref|YP_978320.1| 124 VLMPELGESVTEGtVIRWLKKIGDSVQVDEPLVEVSTDKVDTEIPSPVAGVLVSISADEDATVPVGGELARI 195
                                    779*****************************************************************9987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2
                                    TTCEE-TTSEEEEEECTT CS
                  Biotin_lipoyl  23 vGdkVkagqvlaeveamK 40 
                                    vG+ + + +vla  e  K
  gi|121638096|ref|YP_978320.1| 267 VGGRIRKQDVLAAAEQKK 284
                                    7999*******9888766 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.2   5.4e-18   1.2e-14       2      36 .]     243     277 ..     242     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 5.4e-18
                                    BE-HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
                     E3_binding   2 lAsPaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                                    + +P++RklA e++idL+ v+GtG gGRI+k+DVl
  gi|121638096|ref|YP_978320.1| 243 YVTPLVRKLASENNIDLAGVTGTGVGGRIRKQDVL 277
                                    689*******************************7 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0014         3      35      73 ..      20      58 ..       3      66 .. 0.86
   2 ?   -0.7   0.1      0.56   1.2e+03      40      67 ..      62      89 ..      58     102 .. 0.85
   3 !    9.2   0.1   0.00046         1      37      74 ..     141     178 ..     125     184 .. 0.88
   4 ?    0.4   0.0      0.25   5.6e+02      26      60 ..     252     286 ..     247     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                                   EEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                          GCV_H 35 fvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                      l+++g++v+ +e+l  v + K  +e+++p  G +++
  gi|121638096|ref|YP_978320.1| 20 TRWLKQEGDTVELDEPLVEVSTDKVDTEIPSPAAGVLTK 58
                                   55699*****************************98765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.56
                                   -TT-EE-TT-EEEEEEESS-EEEEE-SS CS
                          GCV_H 40 evgtkvkkgeslaavEsvKaasevyapv 67
                                   ++ ++v+ g +la++   K a+e  ap 
  gi|121638096|ref|YP_978320.1| 62 QEDDTVEVGGELAVIGDAKDAGEAAAPA 89
                                   56789999*************9999986 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00046
                                    E---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                          GCV_H  37 elpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                     l++ g++v+ +e+l  v + K  +e+++pv G +v +
  gi|121638096|ref|YP_978320.1| 141 WLKKIGDSVQVDEPLVEVSTDKVDTEIPSPVAGVLVSI 178
                                    5899*****************************99876 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.25
                                    HHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-E CS
                          GCV_H  26 aqeelgdvvfvelpevgtkvkkgeslaavEsvKaa 60 
                                    a e+  d+  v+   vg ++ k++ laa E  K+a
  gi|121638096|ref|YP_978320.1| 252 ASENNIDLAGVTGTGVGGRIRKQDVLAAAEQKKRA 286
                                    6666677777888889**************99987 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0037       8.3      81     116 ..      17      52 ..       9      65 .. 0.83
   2 !    7.3   0.0    0.0016       3.7      80     122 ..     135     177 ..     129     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0037
                                    TTTEEES----SEE-SEEEEEEE-HHHHGGGSS--- CS
                     PTS_EIIA_1  81 gegFellvkegdkVkagdklvevdleaikkagystt 116
                                    g++ + l +egd+V+  ++lvev+ ++++ +  s++
  gi|121638096|ref|YP_978320.1|  17 GTVTRWLKQEGDTVELDEPLVEVSTDKVDTEIPSPA 52 
                                    666677889******************998876665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                    TTTTEEES----SEE-SEEEEEEE-HHHHGGGSS---EEEEES CS
                     PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleaikkagystttpvvvt 122
                                    +g++ + l k gd+V+  ++lvev+ ++++ +  s++  v+v+
  gi|121638096|ref|YP_978320.1| 135 EGTVIRWLKKIGDSVQVDEPLVEVSTDKVDTEIPSPVAGVLVS 177
                                    6778888999********************9999998877775 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.049   1.1e+02      38      57 ..      24      43 ..      21      59 .. 0.85
   2 ?   -2.3   0.0       1.7   3.7e+03      37      53 ..      60      76 ..      41      89 .. 0.68
   3 ?    9.2   0.0    0.0004       0.9      34      57 ..     139     162 ..     129     167 .. 0.84
   4 ?   -2.7   0.1       2.2     5e+03      19      28 ..     268     277 ..     261     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.049
                                   --TT-EEBTTSEEEEEEESS CS
                         PYNP_C 38 kklGdkVkkGeplatiYank 57
                                   k+ Gd V+ +epl+ + ++k
  gi|121638096|ref|YP_978320.1| 24 KQEGDTVELDEPLVEVSTDK 43
                                   889***********986665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                   S--TT-EEBTTSEEEEE CS
                         PYNP_C 37 hkklGdkVkkGeplati 53
                                     +  d V+ G  la+i
  gi|121638096|ref|YP_978320.1| 60 IAQEDDTVEVGGELAVI 76
                                   45667899999988888 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0004
                                    EEES--TT-EEBTTSEEEEEEESS CS
                         PYNP_C  34 ielhkklGdkVkkGeplatiYank 57 
                                    i+  kk+Gd+V+ +epl+ + ++k
  gi|121638096|ref|YP_978320.1| 139 IRWLKKIGDSVQVDEPLVEVSTDK 162
                                    7789*************9986655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.2
                                    TSBSSTTS-- CS
                         PYNP_C  19 AGRakkeDpi 28 
                                    +GR +k+D +
  gi|121638096|ref|YP_978320.1| 268 GGRIRKQDVL 277
                                    5688887765 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.045     1e+02       6      33 ..      15      42 ..      12      49 .. 0.86
   2 ?    7.7   0.2    0.0026       5.8       2      35 ..      48      81 ..      47      95 .. 0.82
   3 ?    1.8   0.1      0.18     4e+02       7      33 ..     135     161 ..     131     168 .. 0.83
   4 ?    6.1   0.2    0.0078        17       2      30 ..     167     195 ..     166     203 .. 0.92
   5 ?   -2.3   0.0       3.3   7.4e+03      17      46 ..     267     296 ..     264     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.045
                         HlyD_3  6 vdGvvvelnveegevvqagdelleiipp 33
                                     G+v+ +  +eg+ v+  ++l+e+  +
  gi|121638096|ref|YP_978320.1| 15 TEGTVTRWLKQEGDTVELDEPLVEVSTD 42
                                   579*********************9853 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdelleiippdt 35
                                   + +p +Gv++++ ++e + v+ g el+ i + ++
  gi|121638096|ref|YP_978320.1| 48 IPSPAAGVLTKIIAQEDDTVEVGGELAVIGDAKD 81
                                   569**************************99643 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.18
                         HlyD_3   7 dGvvvelnveegevvqagdelleiipp 33 
                                     G+v  +  + g+ vq  ++l+e+  +
  gi|121638096|ref|YP_978320.1| 135 EGTVIRWLKKIGDSVQVDEPLVEVSTD 161
                                    6999999999************99843 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0078
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                    + +pv+Gv+v++++ e   v+ g el++i
  gi|121638096|ref|YP_978320.1| 167 IPSPVAGVLVSISADEDATVPVGGELARI 195
                                    569************************98 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.3
                         HlyD_3  17 egevvqagdelleiippdtllveakvpaad 46 
                                    +g  ++++d+l+    ++++++ a  ++a+
  gi|121638096|ref|YP_978320.1| 267 VGGRIRKQDVLAAAEQKKRAKAPAPAAQAA 296
                                    677899999999999889988888877776 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.49   1.1e+03     218     247 ..      16      45 ..       4      78 .. 0.69
   2 ?    9.2   0.0   0.00021      0.47     160     255 ..      81     172 ..      65     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.49
                        DUF2254 218 hdlvielevrpGdfvvkgeplakvwgeedd 247
                                    +++v +  ++ Gd v  +epl++v+ ++ d
  gi|121638096|ref|YP_978320.1|  16 EGTVTRWLKQEGDTVELDEPLVEVSTDKVD 45 
                                    455666667778888888888888766633 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00021
                        DUF2254 160 eelrkailearedeeeeeeeeakdeeeseeeeatpiraersGylqaidveaLvklaeehdlvielevrpGdfvvkgepla 239
                                    ++ ++a     + e+ +++++++++++++++ + +  a++ G  + + + +L + + ++++vi+  +++Gd v  +epl+
  gi|121638096|ref|YP_978320.1|  81 DAGEAAA---PAPEKVPAAQPESKPAPEPPPVQPTSGAPAGGDAKPVLMPELGE-SVTEGTVIRWLKKIGDSVQVDEPLV 156
                                    4444444...334455666667777777788888888999999999******99.566799******************* PP

                        DUF2254 240 kvwgeeddeelaeklr 255
                                    +v+ ++ d e+   ++
  gi|121638096|ref|YP_978320.1| 157 EVSTDKVDTEIPSPVA 172
                                    **99886666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 3753.14
//
Query:       gi|121638097|ref|YP_978321.1|  [L=301]
Description: hypothetical protein BCG_2232 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-14   52.5   0.1      7e-14   51.4   0.1    1.6  1  DUF1731         Domain of unknown function (DUF1731)
    1.8e-10   40.7   0.0    3.5e-10   39.7   0.0    1.5  1  Epimerase       NAD dependent epimerase/dehydratase family
    6.4e-05   22.9   0.4    0.00012   22.0   0.4    1.5  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.018   14.9   1.0       0.38   10.6   0.3    2.5  2  Rossmann-like   Rossmann-like domain
      0.063   12.7   0.0          1    8.7   0.0    2.6  2  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> DUF1731  Domain of unknown function (DUF1731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1     2e-17     7e-14       2      44 ..     250     293 ..     249     294 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2e-17
                        DUF1731   2 PafalklllGemae.llLegqrVlPkrLleaGFqFrypdleeAL 44 
                                    P+ a+++++Ge+a+  lL gqr++P  L++aGFqF+++++ eAL
  gi|121638097|ref|YP_978321.1| 250 PSVAVRAAFGEFADeGLLIGQRAIPSALERAGFQFHHNTIGEAL 293
                                    9******************************************9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   9.9e-14   3.5e-10       2     230 ..       7     215 ..       6     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.9e-14
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE-.-S.---HHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl.Aa.vggvaa 79 
                                     ++G +G+iGsal+ al +++++v+ + r+  a+           el +  +s   +  + +++dav++l +  ++  ++
  gi|121638097|ref|YP_978321.1|   7 AIAGSSGLIGSALTAALRAADHTVLRIVRRAPANS---------EELHWNPESGEFDPHALTDVDAVVNLcGVnIAQRRW 77 
                                    69****************************44433.........35666655544444455589******5447788888 PP

                                    HHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHH CS
                      Epimerase  80 ssedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaq 159
                                    s   ++ + ++ +  t  l  a+ +agv  l+++s +  YG+ ++   +e+         + +  a l++++ +    aq
  gi|121638097|ref|YP_978321.1|  78 SGAFKQSLRDSRITPTEVLSAAVADAGVATLINASAVGYYGNTKDRVVDEND-----SAGTGFL-AQLCVDWETATRPAQ 151
                                    88888888888888888888888999***************99994333333.....4556665.999999998888777 PP

                                    H.T-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                      Epimerase 160 y.glnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                    + g +++  r   + +p        +++ ++   +  g      lg+g++ + ++  eD ++a+ +++++++
  gi|121638097|ref|YP_978321.1| 152 QsGARVVLARTGVVLSPA------GGMLRRMRPLFSVGL--GARLGSGRQYMSWISLEDEVRALQFAIAQPN 215
                                    77***************9......555555555555555..4568***********************9975 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   3.4e-08   0.00012       1     145 [.      10     164 ..      10     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.4e-08
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-..........- CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsal..........g 69 
                                    G +G +G++l++ l a+ +h+v  +vR+ p+  +el  + + e  e d +       al+++daVv             g
  gi|121638097|ref|YP_978321.1|  10 GSSGLIGSALTAALRAA-DHTVLRIVRRaPANSEEL--HWNPESGEFDPH-------ALTDVDAVVNLCgvniaqrrwsG 79 
                                    899**************.588766655527888877..688888888887.......77777776655533433234432 PP

                                    -TCC......HHHH..HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH....CCHHHHHHHHHHHHHHHHSSSE CS
                 NAD_binding_10  70 gggk......deeg..aknivdaakeagvkRfvlvsaigvgdevpgefgewnke....llkaylaakraaeellrasgld 137
                                              d+++  ++ + +a+  agv  ++  sa+g + ++++++ + n++    +l++   + + a +  ++sg  
  gi|121638097|ref|YP_978321.1|  80 ---AfkqslrDSRItpTEVLSAAVADAGVATLINASAVGYYGNTKDRVVDENDSagtgFLAQLCVDWETATRPAQQSGAR 156
                                    ...13335555555889999999*****************9876665433333222336666666666676666777766 PP

                                    EEEEEE-C CS
                 NAD_binding_10 138 wTivrpgg 145
                                     +  r g 
  gi|121638097|ref|YP_978321.1| 157 VVLARTGV 164
                                    66666665 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00011      0.38      17      43 ..      11      37 ..       2      47 .. 0.80
   2 ?    2.1   0.0     0.047   1.7e+02      34     112 ..      56     136 ..      49     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                  Rossmann-like 17 saGrvGtalgaaleraghvvvgisais 43
                                   s+G +G+al+aal  a+h+v  i   +
  gi|121638097|ref|YP_978321.1| 11 SSGLIGSALTAALRAADHTVLRIVRRA 37
                                   7899****************9887655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.047
                  Rossmann-like  34 hvvvgisaisa.asreraerrlPdvpvlevedv.aaraellllavPdaelpglvkglaatgavraGtivahtsganGvei 111
                                    h+++ + a+ + +  + a+rr  +    +++d+ ++ +e+l  av da ++ l++  a     ++   v+    + G + 
  gi|121638097|ref|YP_978321.1|  56 HALTDVDAVVNlCGVNIAQRRWSGAFKQSLRDSrITPTEVLSAAVADAGVATLINASAVGYYGNTKDRVVDENDSAGTGF 135
                                    66777776544277788888888888888887635678999999*******99998776655555555555555555555 PP

                  Rossmann-like 112 l 112
                                    l
  gi|121638097|ref|YP_978321.1| 136 L 136
                                    5 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00029         1       2      42 ..       8      44 ..       7     132 .. 0.82
   2 ?   -0.3   0.0      0.16   5.6e+02     213     250 ..     187     224 ..     182     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00029
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHC CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehl 42
                                   i G +G iGs l+  L + +++v  ivrr+ + n +   +l
  gi|121638097|ref|YP_978321.1|  8 IAGSSGLIGSALTAALRAADHTVLRIVRRAPA-NSE---EL 44
                                   7899***********************99876.333...33 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                                    ECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT CS
                  GDP_Man_Dehyd 213 ylGnldakRdwghvkDyveamwlmlqqdkpedyviatg 250
                                    +lG +++  +w   +D v+a++ ++ q + +  v  tg
  gi|121638097|ref|YP_978321.1| 187 RLGSGRQYMSWISLEDEVRALQFAIAQPNLSGPVNLTG 224
                                    58999***************999998877666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2160.18
//
Query:       gi|121638098|ref|YP_978322.1|  [L=230]
Description: lipoate-protein ligase B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-07   30.4   0.0    5.8e-07   29.5   0.0    1.5  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
      0.032   13.8   0.0       0.05   13.2   0.0    1.3  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.5e-11   5.8e-07      25     131 .]      68     166 ..      58     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.5e-11
                                    -EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH......HHTT-TTEEEETTTEEE CS
                  BPL_LplA_LipB  25 glvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealgyrdskpgiegipvfikwpnDly 102
                                    g+ vv + +gG+ +wh+p++ + y ++ ++e    + +v+  +    ++ ++v+  l       g +   v   +++ + 
  gi|121638098|ref|YP_978322.1|  68 GTPVVGTDRGGKITWHGPGQLVGYPIIGLAE----PLDVVNYVrrLEESLIQVCADL-------GLHAGRVD--GRSGVW 134
                                    55688899*********************98....4556666688888999999999.......55555555..555555 PP

                                    E...TTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                  BPL_LplA_LipB 103 v...ngrKlaGiavtstrgktlhhivigvgvn 131
                                    +     rK+a+i+v++ r  tlh+++++++ +
  gi|121638098|ref|YP_978322.1| 135 LpgrPARKVAAIGVRVSRATTLHGFALNCDCD 166
                                    555599***********************976 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.6e-06      0.05      72     119 ..     167     216 ..     142     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-06
                                    EEEEEEEES..SSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEE CS
                        Gp_dh_C  72 ldglAvrVP..tpnvsvvdlvvelekevtveevnaalkeaaegalkgils 119
                                    l +   +VP  + +  v++l+ el ++vtv+ev a++ +a   al+g+l 
  gi|121638098|ref|YP_978322.1| 167 LAAFTAIVPcgISDAAVTSLSAELGRTVTVDEVRATVAAAVCAALDGVLP 216
                                    6666677774457899*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1510.38
//
Query:       gi|121638099|ref|YP_978323.1|  [L=311]
Description: lipoyl synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-12   48.0   0.0    3.6e-12   47.0   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    7.1e-09   36.1   0.2    1.2e-08   35.3   0.2    1.4  1  LIAS_N       N-terminal domain of lipoyl synthase of Radical_


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0     4e-16   3.6e-12       7     163 ..      81     232 ..      78     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 4e-16
                                    ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                    Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpgiritv 82 
                                    C++rC fC++      +g++++l+ +e  + +++++  +g ++ +++g   ++ pd   +l ++  +a    +p   + +
  gi|121638099|ref|YP_978323.1|  81 CTRRCDFCQID-----TGKPAELDRDEPRRVADSVR-TMGLRYATVTGVARDDLPDGGAWLYAATVRAikelNPSTGVEL 154
                                    ***********.....6******************6.999***************************9666666666666 PP

                                    EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                     ++ +  ++  l++  e g+ ++++++e++    ++++  +  t+ + l +l ++r+ag+  ++++++++ Ge+ +e++ 
  gi|121638099|ref|YP_978323.1| 155 LIPDFNGEPTRLAEVFESGPEVLAHNVETVPRI-FKRIR-PAFTYRRSLGVLTAARDAGLV-TKSNLILGLGETSDEVRT 231
                                    66666666************************9.99999.******************999.**************9876 PP

                                    H CS
                                    x RF
                    Radical_SAM 163 l 163
                                     
  gi|121638099|ref|YP_978323.1| 232 A 232
                                    5 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.2   1.4e-12   1.2e-08      72     108 .]      24      60 ..       8      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.4e-12
                         LIAS_N  72 rLPswlktkiPlGknynkikndlreLnLhtvCeeaRC 108
                                    r P+w+kt+  +G +y+ +kn +r   LhtvCeea C
  gi|121638099|ref|YP_978323.1|  24 RKPPWIKTRARIGPEYTELKNLVRREGLHTVCEEAGC 60 
                                    78*********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1958.48
//
Query:       gi|121638100|ref|YP_978324.1|  [L=250]
Description: hypothetical protein BCG_2235 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-83  277.4   2.1    7.5e-83  277.2   2.1    1.0  1  DUF4191   Domain of unknown function (DUF4191)
     0.0081   15.0   0.2       0.01   14.7   0.2    1.1  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.2   2.1   8.3e-87   7.5e-83       2     217 ..      23     241 ..      22     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 277.2 bits;  conditional E-value: 8.3e-87
                        DUF4191   2 akkkgrlkqiaqvfkltrkedkkllwlllaaflvvvvvfvvlglllg..slilllilgillgllvalivltrraekaaya 79 
                                    a+ ++r++q++q+f+l+rkedk+ll+++++afl++v + v +g+++g  +++++++lg+llg+lva+++++rra++++y+
  gi|121638100|ref|YP_978324.1|  23 AAARQRRAQLWQAFTLQRKEDKRLLPYMIGAFLLIVGASVGVGVWAGgfTMLTMIPLGVLLGALVAFVIFGRRAQRTVYR 102
                                    67899****************************************97556999*************************** PP

                        DUF4191  80 qiegqpGaaaavlenlrrgwrvepavavtrqqDvvhrvvGrpGvvLvgEGnkkrvkkllaqekkrikrvvadvpvyeivv 159
                                    ++egq+Gaaa++l+nlr++wrv+p+va+t + D+vhrv+GrpGv++vgEG+  rvk+llaqekkr++r+v+dvp+y+i+v
  gi|121638100|ref|YP_978324.1| 103 KAEGQTGAAAWALDNLRGKWRVTPGVAATGNLDAVHRVIGRPGVIFVGEGSAARVKPLLAQEKKRTARLVGDVPIYDIIV 182
                                    ******************************************************************************** PP

                        DUF4191 160 GngegqvplkkLqktlkklprnltkaeveevekRLkald.kksklpiPkGpdPkrarvs 217
                                    Gng+g+vpl+kL+++l++lp n+t +++++ve+RL+al+ ++ +  +PkGp+P+ a+++
  gi|121638100|ref|YP_978324.1| 183 GNGDGEVPLAKLERHLTRLPANITVKQMDTVESRLAALGsRAGAGVMPKGPLPTTAKMR 241
                                    ***************************************66666669*********997 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.1e-06      0.01     373     442 ..      37     107 ..       4     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-06
                        DUF2207 373 dkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgr...rteeGa 442
                                    + + +k+ k+l  + +g+++l++ +++++ + +++ +++l ++ l++ll a++++++f r+ +r   r++eG+
  gi|121638100|ref|YP_978324.1|  37 TLQ-RKEDKRLLPYMIGAFLLIVGASVGVGVWAGG-FTMLTMIPLGVLLGALVAFVIFGRRAQRtvyRKAEGQ 107
                                    333.8889999999999999999999999999888.8888888888888888888888888887444466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1863.82
//
Query:       gi|121638101|ref|YP_978325.1|  [L=140]
Description: hypothetical protein BCG_2236c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-09   36.2  13.5    3.3e-08   33.9  13.5    1.9  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9  13.5   1.8e-12   3.3e-08       2     107 ..      25     116 ..      24     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.8e-12
                            RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllgl 81 
                                    a +grRl+A+liD+++ + + ll + ++v+               + ++l++v+l+++l+  +  +  +g T+G+l+lgl
  gi|121638101|ref|YP_978325.1|  25 APMGRRLAALLIDWLIAYGLALLGVEFGVW---------------STPMLSTVVLVIWLLLGVAAVRLFGFTPGQLMLGL 89 
                                    899*****************9999999999...............99********************************* PP

                            RDD  82 kvvd.edgrklglaqaliRalllllll 107
                                     vv     r++g++++++R ll+ l++
  gi|121638101|ref|YP_978325.1|  90 VVVAvGGRRPVGIGRLVVRGLLIGLVV 116
                                    ****6666788999******9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1031.47
//
Query:       gi|121638102|ref|YP_978326.1|  [L=478]
Description: glutamine synthetase glnA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.1e-134  446.4   0.0   7.1e-134  446.1   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
      5e-28   96.6   0.1    1.2e-27   95.5   0.1    1.7  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.1   0.0    8e-138  7.1e-134       2     345 .]     106     475 ..     105     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.1 bits;  conditional E-value: 8e-138
                                    T-HHHHHHHHHHHHHHTTC..EEEEEEEEEEEEESEECCCE.SSEEEEEEE.T.................B...B.TSS- CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGl..tvvvgpElEFflfdkeedke.asksllevdse.................ekgrpaekgg 61 
                                    rdPR+++++a+++l ++G+  t+++g+E+EF++fd++++++ a++s++evd+                  ++++ ++kgg
  gi|121638102|ref|YP_978326.1| 106 RDPRNIARKAENYLISTGIadTAYFGAEAEFYIFDSVSFDSrANGSFYEVDAIsgwwntgaateadgspnRGYKVRHKGG 185
                                    7***************************************99**********9*****************9********* PP

                                    TTBHCCCCCTCCHHHHHHHHHHHTT--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSS CS
                     Gln-synt_C  62 yfsvapvdeaedlrreivealealgieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpK 140
                                    yf+vap+d+  dlr+++++ l + g+ +e+ hhEv+ g Q Ein++f+++l+aaD+++++K+++k++A ++g+t+tFmpK
  gi|121638102|ref|YP_978326.1| 186 YFPVAPNDQYVDLRDKMLTNLINSGFILEKGHHEVGSGgQAEINYQFNSLLHAADDMQLYKYIIKNTAWQNGKTVTFMPK 265
                                    ******************************************************************************** PP

                                    SSTTS---BEEEEEEEEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEES CS
                     Gln-synt_C 141 plegdnGsgmHvhlSlwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawga 220
                                    pl+gdnGsgmH+h+Slw kdg +l++de++  +ls++arh+igGll+ha++l+a+t+ptvnSYkRlvpgyeaP++l++++
  gi|121638102|ref|YP_978326.1| 266 PLFGDNGSGMHCHQSLW-KDGAPLMYDETGYAGLSDTARHYIGGLLHHAPSLLAFTNPTVNSYKRLVPGYEAPINLVYSQ 344
                                    *****************.***********9999*********************************************** PP

                                    S-TTCSEEEE-..TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHH CS
                     Gln-synt_C 221 rNRsallRipa..skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasle 298
                                    rNRsa++Rip   s++kakr+E+R+pd+s NPYLa++a+l+AgldGi+nk+ep++pv+kdlyel+pee+++i++ P++l+
  gi|121638102|ref|YP_978326.1| 345 RNRSACVRIPItgSNPKAKRLEFRSPDSSGNPYLAFSAMLMAGLDGIKNKIEPQAPVDKDLYELPPEEAASIPQTPTQLS 424
                                    ***********999****************************************************************** PP

                                    HHHHHHHCS.HHHCC..SS-HHHHHHHHHHHHH.CHHHHHCT--HHHHHHH CS
                     Gln-synt_C 299 eAlealeed.ellke..vlgeevieaylalkra.Eleeleeevsdwelery 345
                                    + +++le+d e+l+e  v+++++ie+++++kr+ E+e ++ +++++e+  y
  gi|121638102|ref|YP_978326.1| 425 DVIDRLEADhEYLTEggVFTNDLIETWISFKREnEIEPVNIRPHPYEFALY 475
                                    ********************************99*************9877 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.1   1.3e-31   1.2e-27       1      83 []      17      98 ..      17      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 1.3e-31
                                   T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE- CS
                     Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicdvyd 82
                                   +v++vd++F+D+ g ++h+tipa++++++++++g++FDGSsi+gf++i+eSDmlL Pd++ta idPfr++k t+++   v+d
  gi|121638102|ref|YP_978326.1| 17 KVEYVDVRFCDLPGIMQHFTIPASAFDKSVFDDGLAFDGSSIRGFQSIHESDMLLLPDPETARIDPFRAAK-TLNINFFVHD 97
                                   589*******************************************************************9.9999998887 PP

                                   T CS
                     Gln-synt_N 83 p 83
                                   p
  gi|121638102|ref|YP_978326.1| 98 P 98
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3619.33
//
Query:       gi|121638103|ref|YP_978327.1|  [L=994]
Description: bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     1e-106  356.0   7.6    5.2e-72  242.3   0.1    3.4  3  GlnE           Glutamate-ammonia ligase adenylyltransferase
    1.3e-57  194.1   5.5    1.1e-33  116.4   2.6    2.5  2  GlnD_UR_UTase  GlnD PII-uridylyltransferase
    9.4e-06   25.5   0.0        0.2   11.4   0.0    2.6  2  DUF294         Putative nucleotidyltransferase DUF294
    0.00035   20.4   1.3     0.0066   16.2   0.2    2.6  2  DUF294_C       Putative nucleotidyltransferase substrate bind


Domain annotation for each model (and alignments):
>> GlnE  Glutamate-ammonia ligase adenylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.7   7.2e-37   3.2e-33       3     249 ..      90     315 ..      88     317 .. 0.83
   2 ?   -3.9   0.2       1.6     7e+03      25      76 ..     425     476 ..     420     478 .. 0.76
   3 !  242.3   0.1   1.2e-75   5.2e-72       2     250 ..     589     828 ..     588     829 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 7.2e-37
                                    HHHHHHHH-HHHHHHHHH-CHHHHHHCHCHHHTSGGGCCCHHHHHHHHTTTS-TC.HHHHHHHHHHHHHHHHHHHHHHHT CS
                           GlnE   3 qlaevlaaSpfvaellarrprlldelldkellaepkeleaaaaelaealaavede.eqliealRqfkreellriavadll 81 
                                    +l +vl+ S  + + l  +p+  + l  k    +++  ++++    e ++++e    +l+++lR+  r+ +l +a+ dl+
  gi|121638103|ref|YP_978327.1|  90 RLFSVLGSSLALGDHLVAHPQSWKLLRGK---VTLPSHDQLQRSFVECVEESEGMpGSLVHRLRTQYRDYVLMLAALDLA 166
                                    67889999999999999999999666666...56666677777777777777777899********************** PP

                                    TSS-HHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHCTSCCCCTTCC-SEEEEE-HHHHTT---TT--EEEEEEE- CS
                           GlnE  82 glltvee......vsraLseLaeavieaaldlllrqvvaelgtpvdekgepqqllvlGmGklGgaELnysSDiDliflyd 155
                                    ++++ e       v  +L++ a+a + aal ++ + v+ e+         p +l+v++mGk G++ELny SD+D+if+ +
  gi|121638103|ref|YP_978327.1| 167 ATVEDEPvlpftvVAARLADAADAALAAALRVAEASVCGEH--------PPPRLAVIAMGKCGARELNYVSDVDVIFVAE 238
                                    99876651111115678888888888888888888888884........4569*************************99 PP

                                    --TT-BSSSS-SBHHHHHHHHHHHHHHHHH--BTTB-S--EE-TTSTTGGGS-SEEEHHHHHHHHHHC--HHHHHHHCT- CS
                           GlnE 156 edaeteggkksidaakfftrlaqrlisiLsartadGvlYevDlrLRPsGesGplvlsvaAfekYyeeeartWErqAlirA 235
                                      +++             +r+a  ++++ s        +evD+ LRP+G++G lv+++++  +Yy+++a+tWE qAl++A
  gi|121638103|ref|YP_978327.1| 239 RSDPR------------NARVASEMMRVAS-----AAFFEVDAALRPEGRNGELVRTLESHIAYYQRWAKTWEFQALLKA 301
                                    99988............5688888887755.....4689***************************************** PP

                                    EECCE-HCHHHHHH CS
                           GlnE 236 rvvagdaelkaafl 249
                                    r v+gdael++++l
  gi|121638103|ref|YP_978327.1| 302 RPVVGDAELGERYL 315
                                    *********99876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.6
                                    HHHHCHCHHHTSGGGCCCHHHHHHHHTTTS-TCHHHHHHHHHHHHHHHHHHH CS
                           GlnE  25 ldelldkellaepkeleaaaaelaealaavedeeqliealRqfkreellria 76 
                                    l+ l  ++ll++p++ ea+++ +++a ++   ++ +  +lR+  +++ +r++
  gi|121638103|ref|YP_978327.1| 425 LQRLKRTHLLPDPEDEEAVRWLARAAHIRPDGRNDAAGVLREELKKQNVRVS 476
                                    5667777788888888888888888877777778888888887777777775 PP

  == domain 3  score: 242.3 bits;  conditional E-value: 1.2e-75
                                    HHHHHHHHH-HHHHHHHHH-CHHHHHHCHCHHHTSGGGCCCHHHHHHHHTTTS-TC....HHHHHHHHHHHHHHHHHHHH CS
                           GlnE   2 kqlaevlaaSpfvaellarrprlldelldkellaepkeleaaaaelaealaavede....eqliealRqfkreellriav 77 
                                    k+l++vl++S++v +ll+r+pr+++++ d    a pk le+ +a++a+al+a++++    e++i+ +R+++r+el+ri++
  gi|121638103|ref|YP_978327.1| 589 KRLMHVLGTSAYVPDLLMRAPRVIQQYEDG--PAGPKLLETEPAAVARALIASASRypdpERAIAGARTLRRRELARIGS 666
                                    79****************************..*********************9999999******************** PP

                                    HHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSCCCCTTCC-SEEEEE-HHHHTT---TT--EEEEEEE--- CS
                           GlnE  78 adllglltveevsraLseLaeavieaaldlllrqvvaelgtpvdekgepqqllvlGmGklGgaELnysSDiDliflyded 157
                                    adllgll+v+ev+raL++++ av++aald+++r+ + +      ++++p++++v+GmG+lGgaEL+y+SD+D++f+++++
  gi|121638103|ref|YP_978327.1| 667 ADLLGLLEVTEVCRALTSVWVAVLQAALDVMIRASLPD------DDRAPAAIAVIGMGRLGGAELGYGSDADVMFVCEPA 740
                                    **********************************9998......789999****************************** PP

                                    TT-BSSSS-SBHHHHHHHHHHHHHHHHH--BTTB-S--EE-TTSTTGGGS-SEEEHHHHHHHHHHC--HHHHHHHCT-EE CS
                           GlnE 158 aeteggkksidaakfftrlaqrlisiLsartadGvlYevDlrLRPsGesGplvlsvaAfekYyeeeartWErqAlirArv 237
                                    + +    ++++a k++t++a+r++++L ++++d++l e+D++LRP+G++Gplv+++ ++++Yye++a+ WE+qAl+rA++
  gi|121638103|ref|YP_978327.1| 741 TGV----DDARAVKWSTSIAERVRALLGTPSVDPPL-ELDANLRPEGRNGPLVRTLGSYAAYYEQWAQPWEIQALLRAHA 815
                                    988....9999*************************.******************************************* PP

                                    CCE-HCHHHHHHH CS
                           GlnE 238 vagdaelkaafle 250
                                    vagdael+++fl+
  gi|121638103|ref|YP_978327.1| 816 VAGDAELGQRFLR 828
                                    ***********97 PP

>> GlnD_UR_UTase  GlnD PII-uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   2.6   2.4e-37   1.1e-33       1     146 []     336     483 ..     336     483 .. 0.94
   2 !   78.0   0.1   1.7e-25   7.4e-22       1     146 []     849     992 ..     849     992 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 2.4e-37
                  GlnD_UR_UTase   1 rfmkakieeekarrgrsdtllepniKlGpGGlRdiefivqvlqlirGgrdpelrerstlealeelvergllteeeakelr 80 
                                    ++m++++e+ + ++ r +     ++KlG GGlRd+ef vq+lql++ ++d++lr+ st++al++l e g++ +e+a+++ 
  gi|121638103|ref|YP_978327.1| 336 QAMRRRVEQLVPADVRGR-----ELKLGSGGLRDVEFAVQLLQLVHARSDESLRVASTVDALAALGEGGYIGREDAANMT 410
                                    5799********999999.....********************************************************* PP

                  GlnD_UR_UTase  81 eayrflrrlehrLqlladrqthrLp..fdeeeqrrlaealgy..redkaa...fmkelfqhaerVrrlfekll 146
                                    ++y+flr lehrLql++ ++th Lp  +dee+ r+la+a  +  +++++a   +++el+++  rV++l++kl+
  gi|121638103|ref|YP_978327.1| 411 ASYEFLRLLEHRLQLQRLKRTHLLPdpEDEEAVRWLARAAHIrpDGRNDAagvLREELKKQNVRVSKLHTKLF 483
                                    ************************9667789***********8744444478******************997 PP

  == domain 2  score: 78.0 bits;  conditional E-value: 1.7e-25
                  GlnD_UR_UTase   1 rfmkakieeekarrgrsdtllepniKlGpGGlRdiefivqvlqlirGgrdpelrerstlealeelvergllteeeakelr 80 
                                    r +ka+ie+e+  rg      +   KlG+GGl die  vq+lql +  + p+l+++stl++l+ +++++l+++++++ lr
  gi|121638103|ref|YP_978327.1| 849 RRIKARIESERLPRGADP---NTHTKLGRGGLADIEWTVQLLQLQHAHQVPALHNTSTLQSLDVIAAADLVPAADVELLR 925
                                    578999999999888887...6799******************************************************* PP

                  GlnD_UR_UTase  81 eayrflrrlehrLqlladrqthrLpfdeeeqrrlaealgy.redkaafmkelfqhaerVrrlfekll 146
                                    +a+    r +++L l++++ t++Lp   ++ +++a a g+ ++d  +f++++ ++++r +++ +k++
  gi|121638103|ref|YP_978327.1| 926 QAWLTATRARNALVLVRGKPTDQLPGPGRQLNAVAVAAGWrNDDGGEFLDNYLRVTRRAKAVVRKVF 992
                                    ****************************************6666666**********9999998876 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   4.5e-05       0.2      20     102 ..     180     263 ..     165     294 .. 0.76
   2 !   11.1   0.0   5.9e-05      0.27      18      98 ..     680     763 ..     670     766 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                         DUF294  20 larlvselndallrrlielaeeelgk..ppvpfallvmGSeGReEqtlktDqDnalvledeeeeaareyfaelaervnea 97 
                                    +a+ +++  da+l  ++++ae+ +    pp + a+++mG  G +E  + +D D  +v e+ ++ ++++   e+++  ++a
  gi|121638103|ref|YP_978327.1| 180 VAARLADAADAALAAALRVAEASVCGehPPPRLAVIAMGKCGARELNYVSDVDVIFVAER-SDPRNARVASEMMRVASAA 258
                                    56667888899999999999988744448******************************9.7777777777777666666 PP

                         DUF294  98 LaalG 102
                                      ++ 
  gi|121638103|ref|YP_978327.1| 259 FFEVD 263
                                    55555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.9e-05
                         DUF294  18 ealarlvselndallrrlielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvled...eeeeaareyfaelaerv 94 
                                    +al++++ ++ +a+l+ +i+  +++ +++p+++a++ mG  G  E  + +D D  +v e     ++++a ++  ++aerv
  gi|121638103|ref|YP_978327.1| 680 RALTSVWVAVLQAALDVMIRASLPDDDRAPAAIAVIGMGRLGGAELGYGSDADVMFVCEPatgVDDARAVKWSTSIAERV 759
                                    45666666667777777777777777779*******************************998889999999*******9 PP

                         DUF294  95 neaL 98 
                                     + L
  gi|121638103|ref|YP_978327.1| 760 RALL 763
                                    8877 PP

>> DUF294_C  Putative nucleotidyltransferase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.5e-06    0.0066      58     106 ..     382     430 ..     341     436 .. 0.79
   2 ?    2.1   0.1     0.034   1.5e+02      41      96 ..     875     935 ..     861     948 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                       DUF294_C  58 gieatnTleRlkalaeagvlsaelaedlleayefllrlrlrhqleaiea 106
                                    +++ ++T++ l al e g + +e+a++++ +yefl  l  r ql+++++
  gi|121638103|ref|YP_978327.1| 382 SLRVASTVDALAALGEGGYIGREDAANMTASYEFLRLLEHRLQLQRLKR 430
                                    366789**************************************99875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.034
                       DUF294_C  41 agifplvdlvRllALeag.....ieatnTleRlkalaeagvlsaelaedlleayefllrlr 96 
                                    +g++ +   v+ll L++      +++t+Tl+ l+ +a+a  + a+++e l +a+ + +r r
  gi|121638103|ref|YP_978327.1| 875 GGLADIEWTVQLLQLQHAhqvpaLHNTSTLQSLDVIAAADLVPAADVELLRQAWLTATRAR 935
                                    556666666666666654221125689**************************97776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (994 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 6528.28
//
Query:       gi|121638104|ref|YP_978328.1|  [L=446]
Description: glutamine synthetase glnA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.6e-126  422.0   0.0   1.9e-126  421.7   0.0    1.0  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    7.9e-27   92.8   0.0    3.4e-26   90.8   0.0    2.0  2  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
     0.0084   15.9   0.0      0.054   13.3   0.0    2.1  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.7   0.0  3.2e-130  1.9e-126       2     345 .]     107     443 ..     106     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 421.7 bits;  conditional E-value: 3.2e-130
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                    +dPR+vl+r+l+++ e G++++v+pE+EFfl++  +++            +   p +++gyf+ a  d+a ++rr+ ++a
  gi|121638104|ref|YP_978328.1| 107 ADPRHVLRRQLTKAGELGFSCYVHPEIEFFLLKPGPEDG-----------SVPVPVDNAGYFDQAVHDSALNFRRHAIDA 175
                                    69*******************************999977...........445677889********************* PP

                                    HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT CS
                     Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg 161
                                    le +gi+ve shhE a+gQ+Ei+l+fadal++aDnv+tf++v+kevA ++g +a+FmpKp+ +++Gs+mH+h+Sl+ + +
  gi|121638104|ref|YP_978328.1| 176 LEFMGISVEFSHHEGAPGQQEIDLRFADALSMADNVMTFRYVIKEVALEEGARASFMPKPFGQHPGSAMHTHMSLF-EGD 254
                                    ****************************************************************************.888 PP

                                    EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-...TSGGCST CS
                     Gln-synt_C 162 knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa...skekakr 238
                                     n+f+++dd+ +lse++++fi+G+l+ha +++a+t+++vnSYkRlv+g eaP+a++wga NRsal+R+p+   +k++++r
  gi|121638104|ref|YP_978328.1| 255 VNAFHSADDPLQLSEVGKSFIAGILEHACEISAVTNQWVNSYKRLVQGGEAPTAASWGAANRSALVRVPMytpHKTSSRR 334
                                    ***********************************************************************999****** PP

                                    EEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-H CS
                     Gln-synt_C 239 vElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlge 316
                                    vE+R+pd+++NPYL++A+llaAgl+G+e+++ +g+++e+++++l+peer  +g++elP+sl++Al+a+e++el++e+lge
  gi|121638104|ref|YP_978328.1| 335 VEVRSPDSACNPYLTFAVLLAAGLRGVEKGYVLGPQAEDNVWDLTPEERraMGYRELPSSLDSALRAMEASELVAEALGE 414
                                    *************************************************99***************************** PP

                                    HHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                     Gln-synt_C 317 evieaylalkraEleeleeevsdwelery 345
                                    +v++ +l+ kr+E+++++++v+++el++y
  gi|121638104|ref|YP_978328.1| 415 HVFDFFLRNKRTEWANYRSHVTPYELRTY 443
                                    **************************987 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   5.7e-30   3.4e-26       1      83 []      16     100 ..      16     100 .. 0.96
   2 ?   -1.2   0.0       0.3   1.8e+03       5      34 ..     197     226 ..     194     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 5.7e-30
                                    T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-....EEEEE CS
                     Gln-synt_N   1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek...ktarvi 77 
                                    +++fv+l+FtD+ g lk+v+i+  el e a+eeg++FDGSsiegfa+++eSD + +Pd+st+ ++P+  ++   + ar++
  gi|121638104|ref|YP_978328.1|  16 DIRFVRLWFTDVLGFLKSVAIAPAEL-EGAFEEGIGFDGSSIEGFARVSESDTVAHPDPSTFQVLPWATSSghhHSARMF 94 
                                    589***********************.*****************************************98888899**** PP

                                    EEEE-T CS
                     Gln-synt_N  78 cdvydp 83 
                                    cd+  p
  gi|121638104|ref|YP_978328.1|  95 CDITMP 100
                                    ***876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
                                    EEEEEE-SSS-EEEEEEEHHHHHHHTTTT- CS
                     Gln-synt_N   5 vdlqFtDikgklkhvtipadelsedaleeg 34 
                                    +dl+F+D      +v      ++e aleeg
  gi|121638104|ref|YP_978328.1| 197 IDLRFADALSMADNVMTFRYVIKEVALEEG 226
                                    899****99888887666566666666665 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     9e-06     0.054       4     106 ..       6     104 ..       3     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-06
                                    .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-GGG- CS
                   Gln-synt_N_2   4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdPasa 83 
                                    e v+  lee++++++++ ++d  G  +  a++ a+Le  + +GiG+  +  +++    + e++ ++        pdP+++
  gi|121638104|ref|YP_978328.1|   6 EFVLRTLEERDIRFVRLWFTDVLGFLKSVAIAPAELEGAFEEGIGFDGS--SIEGFARVSESDTVA-------HPDPSTF 76 
                                    5688999**************************************9754..455555555555443.......4888888 PP

                                    EEE---SSTTS.....EEEEEE-TTS-B CS
                   Gln-synt_N_2  84 valpyaPdaaa.....llgdlvevdgtP 106
                                     +lp a          ++ d++  dg+P
  gi|121638104|ref|YP_978328.1|  77 QVLPWATSSGHhhsarMFCDITMPDGSP 104
                                    8888876543333444777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3282.87
//
Query:       gi|121638105|ref|YP_978329.1|  [L=520]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-72  244.0   0.4    1.3e-64  218.4   0.3    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    6.1e-22   77.7   0.0      6e-21   74.5   0.1    2.6  2  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.24   11.2   0.0    1.5  1  Ser_hydrolase  Serine hydrolase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.4   0.3   2.1e-68   1.3e-64       1     254 [.     105     403 ..     105     406 .. 0.95
   2 !   23.9   0.0   4.5e-09   2.7e-05     199     256 ..     444     494 ..     411     495 .. 0.86

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 2.1e-68
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHT....TSEEEEEEETTSTTSSSTTTGB.....CHH.................. CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakd....gfdvillDlrGvgySspapacin....ddy.................. 54 
                                    ++l++++G+pg s v + +++apa+a++    +fd++++D+rGvg+S+pa++c++    d y                  
  gi|121638105|ref|YP_978329.1| 105 GALLVNPGGPGASAVDMVAAMAPAIADTdilrHFDLVGFDPRGVGHSTPALRCRTdaefDAYrrdpmadyspagvthveq 184
                                    589****************************************************9777333666667779999999999 PP

                                    .....................SHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHH CS
                  Abhydrolase_1  55 .....................gtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaasl 113
                                                         gtasva+d+d++++algdd+++++G+S+G+ +++ay++++  +V+a+vl+gaidpa s+
  gi|121638105|ref|YP_978329.1| 185 vyrqlaqdcvdrmgfsflaniGTASVARDMDMVRQALGDDQINYLGYSYGTELGTAYLERFGTHVRAMVLDGAIDPAVSP 264
                                    99****************************************************************************** PP

                                    HHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH.HCHHHCCHHHHHHHCHHHHHHHHHHHHHH CS
                  Abhydrolase_1 114 ieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdalkf.pdkskrfpssgsdnasslatgalksieqw 192
                                    ie+   q+++f+++f+ yaadcar pa+pl++d++++++ +h+lvd+l++ p k+++++  ++++a++++ +al+s ++w
  gi|121638105|ref|YP_978329.1| 265 IEESISQMAGFQTAFNDYAADCARSPACPLGTDSAQWVNRYHSLVDPLVQkPGKTSDPRGLSYADATTGTINALYSPQRW 344
                                    ******************************************************************************** PP

                                    HHCCHHHHHHHHHCTHHHHS.EEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHH CS
                  Abhydrolase_1 193 pttdsaklllrlrelknvla.ptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafl 254
                                    +++ s+ l l++++     a + lv++ ++D+ + ++++++ +++++ +r+v  ++    a +
  gi|121638105|ref|YP_978329.1| 345 KYLTSGLLGLQRGS----DAgDLLVLADDYDGRDADGHYSNDQDAFNAVRCVDAPTPADPAAW 403
                                    ***********999....446*******************************99988777766 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.5e-09
                                    HHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 199 klllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                    +      +      +++v+s+t+Dp++p+++++dla++l    l+++++++H+a+++g
  gi|121638105|ref|YP_978329.1| 444 PAAPAGAG------KVVVVSTTHDPATPYQSGVDLARQLGA-PLITFDGTQHTAVFDG 494
                                    45555556......99************************9.**************97 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.26   1.5e+03      35      50 ..     249     264 ..     240     276 .. 0.81
   2 !   74.5   0.1     1e-24     6e-21       6     103 .]     421     518 ..     414     518 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                  Abhydrolase_4  35 apvLllqnerDpaTPy 50 
                                    +++++l++  Dpa+ +
  gi|121638105|ref|YP_978329.1| 249 VRAMVLDGAIDPAVSP 264
                                    7899********9976 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 1e-24
                  Abhydrolase_4   6 aalaeslls.CagwpvspqrprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvd 84 
                                    +++ +++   Ca wpv+ +  ++ +  +ga +v ++++++DpaTPy+++  la++lg a l+t +g+ H+a+ +gn+Cvd
  gi|121638105|ref|YP_978329.1| 421 QFTGSAPRDlCALWPVPATSTPHPAAPAGAGKVVVVSTTHDPATPYQSGVDLARQLG-APLITFDGTQHTAVFDGNQCVD 499
                                    5555555556**************9999*****************************.9********************* PP

                  Abhydrolase_4  85 kavdaYLltGelpaddtvC 103
                                    +av +Y+l+G+lp +   C
  gi|121638105|ref|YP_978329.1| 500 SAVMHYFLDGTLPPTSLRC 518
                                    *************987776 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.24     104     155 ..     439     491 ..     402     503 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                                    GCTTS-SSHHCCHC.EEEEETTBTTC-HHHHHHHHHHCT-EEEEETT-TTSSG CS
                  Ser_hydrolase 104 efaplpreklpfps.lvvaSenDpyvsfeeaeelaeawgaelvdlgeaGHina 155
                                    + +p p+ ++   + +vv+ + Dp+ +++   +la+++ga+l+    + H  +
  gi|121638105|ref|YP_978329.1| 439 TSTPHPAAPAGAGKvVVVSTTHDPATPYQSGVDLARQLGAPLITFDGTQHTAV 491
                                    3344444444444446667789*********************9999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3637.52
//
Query:       gi|121638106|ref|YP_978330.1|  [L=520]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-91  304.2   0.0    1.1e-90  303.7   0.0    1.2  1  Abhydrolase_1  alpha/beta hydrolase fold
    8.3e-22   77.3   0.1    2.6e-21   75.7   0.0    1.9  2  Abhydrolase_4  TAP-like protein
     0.0055   16.0   0.0       0.29   10.4   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.7   0.0   1.9e-94   1.1e-90       1     257 []     102     497 ..     102     497 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.7 bits;  conditional E-value: 1.9e-94
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHT...TSEEEEEEETTSTTSSSTTTGB.............CHH........... CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakd...gfdvillDlrGvgySspapacin............ddy........... 54 
                                    ++lvi++G+pg+s+++a++g++++L+k+   +fd++++D+rGv++S+pa++c++            +dy           
  gi|121638106|ref|YP_978330.1| 102 GSLVINPGGPGESGIEAALGVFQTLPKRvheRFDLVGFDPRGVASSRPAIWCNSdadndrlraepqVDYsregvahiene 181
                                    589****************************************************9998888888866688888888999 PP

                                    ....................SHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHH CS
                  Abhydrolase_1  55 ....................gtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaasli 114
                                                        gt++va+dld+i++algddklt++G+S+G++i++aya+e+p+rV+a++l+ga+dp+a++i
  gi|121638106|ref|YP_978330.1| 182 tkqfvgrcvdkmgknflahvGTVNVAKDLDAIRAALGDDKLTYLGYSYGTRIGSAYAEEFPQRVRAMILDGAVDPNADPI 261
                                    99999999999999999999************************************************************ PP

                                    HHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH............................... CS
                  Abhydrolase_1 115 eaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdalkf............................... 163
                                    ea+++qak+f+d+f++yaadca+n+++pl+ad+++a+e++h+lvd+l++                               
  gi|121638106|ref|YP_978330.1| 262 EAELRQAKGFQDAFNNYAADCAKNAGCPLGADPAKAVEVYHSLVDPLVDpdnprisrpartkdprglsysdaivgtimal 341
                                    ******************************************************************************** PP

                                    ...........................HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC.......... CS
                  Abhydrolase_1 164 ...........................pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre.......... 206
                                                               +d+++r++s+g++n+s++a++a+++++q+p+td++k+++++r+          
  gi|121638106|ref|YP_978330.1| 342 yspnlwqhltdglselvdnrgdtllalADMYMRRDSHGRYNNSGDARVAINCVDQPPVTDRDKVIDEDRRareiapfmsy 421
                                    ******************************************************************************** PP

                                    ......................THHHHS....EEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 207 ......................lknvla....ptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                                          +++v+a    pt+v+s+t+Dp++p+ka++dla++l++ +l+++++++H+++++g+
  gi|121638106|ref|YP_978330.1| 422 gkftgdaplgtcafwpvpptsqPHAVSApglvPTVVVSTTHDPATPYKAGVDLANQLRG-SLLTFDGTQHTVVFQGD 497
                                    ***********************************************************.**************986 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   9.3e+03      34      60 ..     244     271 ..     238     275 .. 0.65
   2 !   75.7   0.0   4.4e-25   2.6e-21       4     103 .]     421     520 .]     416     520 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                  Abhydrolase_4  34 aapvLllqnerDpaT.Pyegakklakal 60 
                                     +++++l++  Dp   P e   + ak +
  gi|121638106|ref|YP_978330.1| 244 RVRAMILDGAVDPNAdPIEAELRQAKGF 271
                                    4678899999999762555555555555 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 4.4e-25
                  Abhydrolase_4   4 fgaalaeslls.CagwpvspqrprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntC 82 
                                    +g+++  ++l  Ca+wpv+p+ +++ ++a+g +p+ ++++++DpaTPy+ +  la++l+ ++l+t +g+ H+++ +g++C
  gi|121638106|ref|YP_978330.1| 421 YGKFTGDAPLGtCAFWPVPPTSQPHAVSAPGLVPTVVVSTTHDPATPYKAGVDLANQLR-GSLLTFDGTQHTVVFQGDSC 499
                                    667777777777***********************************************.79****************** PP

                  Abhydrolase_4  83 vdkavdaYLltGelpaddtvC 103
                                    +d+ v+aYL  G++p  +++C
  gi|121638106|ref|YP_978330.1| 500 IDEYVTAYLIGGTTPPSGAKC 520
                                    ******************999 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   4.8e-05      0.29      66     110 ..     210     254 ..     199     303 .. 0.83
   2 !    3.2   0.0    0.0073        44     192     235 ..     453     493 ..     441     497 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.8e-05
                    Hydrolase_4  66 vekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPa 110
                                    ++++++  ++ +l+ lG S G  i  +y+++ p++v+++il +++
  gi|121638106|ref|YP_978330.1| 210 LDAIRAALGDDKLTYLGYSYGTRIGSAYAEEFPQRVRAMILDGAV 254
                                    467788888999*****************************8865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0073
                    Hydrolase_4 192 lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHell 235
                                    +P+ +++ ++D+ ++++a  +l+++l+    +l +++g  H ++
  gi|121638106|ref|YP_978330.1| 453 VPTVVVSTTHDPATPYKAGVDLANQLR---GSLLTFDGTQHTVV 493
                                    8*********************99999...58999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3475.62
//
Query:       gi|121638107|ref|YP_978331.1|  [L=281]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.1e-106  353.8   1.1   5.9e-106  353.6   1.1    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    0.00011   21.8   4.2    0.00021   20.8   4.2    1.7  1  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.6   1.1  6.6e-110  5.9e-106       1     258 [.      20     276 ..      20     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 353.6 bits;  conditional E-value: 6.6e-110
                Pantoate_transf   1 kvtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvv 80 
                                    k+++++l+++k++g+k+amlTayd++tA+++deag+ v+LVGDs+++vv+gy++t+p++++e+i  ++ V+rga++alvv
  gi|121638107|ref|YP_978331.1|  20 KIRTHHLQRWKADGHKWAMLTAYDYSTARIFDEAGIPVLLVGDSAANVVYGYDTTVPISIDELIPLVRGVVRGAPHALVV 99 
                                    57899*************************************************************************** PP

                Pantoate_transf  81 adlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeea 160
                                    adlPfgsyea +++al++A+r+lk gga+avKlegg++vae+++ l++agipVm+HiG+tPqsvn+lgg++vqg+  ++a
  gi|121638107|ref|YP_978331.1| 100 ADLPFGSYEAGPTAALAAATRFLKDGGAHAVKLEGGERVAEQIACLTAAGIPVMAHIGFTPQSVNTLGGFRVQGRG-DAA 178
                                    ***************************************************************************6.667 PP

                Pantoate_transf 161 eklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesi 240
                                    e+ ++da a++eaGafa+v+E+vpaela++it kl+ipt+GIGAG++cdGqvlv++D+ g++ +++++fvk+ya+++ ++
  gi|121638107|ref|YP_978331.1| 179 EQTIADAIAVAEAGAFAVVMEMVPAELATQITGKLTIPTVGIGAGPNCDGQVLVWQDMAGFSGAKTARFVKRYADVGGEL 258
                                    89999*************************************************************************** PP

                Pantoate_transf 241 eeavkaYaeevkegsFPa 258
                                    ++a+ +Ya+ev  g FPa
  gi|121638107|ref|YP_978331.1| 259 RRAAMQYAQEVAGGVFPA 276
                                    *****************8 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   4.2   2.4e-08   0.00021       6     178 ..      31     201 ..      26     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-08
                     PEP_mutase   6 akgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevv.slPlivDledG.yges 83 
                                    a g+   ++ a+D  +a+i+ eag++ l ++  a   ++G++ +  ++++el+ +vr +++   +  + +Dl  G y++ 
  gi|121638107|ref|YP_978331.1|  31 ADGHKWAMLTAYDYSTARIFDEAGIPVLLVGDSAANVVYGYDTTVPISIDELIPLVRGVVRGApHALVVADLPFGsYEAG 110
                                    566677899***************************************************9884577799**98845444 PP

                     PEP_mutase  84 p.eevaetvrrliaaGvvgvniEDkkkndaerqlldie..efaekiaaaraaaeeag.fvinARtdalllsagagleeai 159
                                    p + +a++ r l + G+ +v +E  ++ +++  +l+++    ++ i    ++ ++ g f +  R da    a++++++ai
  gi|121638107|ref|YP_978331.1| 111 PtAALAAATRFLKDGGAHAVKLEGGERVAEQIACLTAAgiPVMAHIGFTPQSVNTLGgFRVQGRGDA----AEQTIADAI 186
                                    4156667777777889*********433455555544311356778888888888889999999999....555555555 PP

                     PEP_mutase 160 eRaraYaeAGAdgvfvpgl 178
                                        a aeAGA +v++ ++
  gi|121638107|ref|YP_978331.1| 187 ----AVAEAGAFAVVMEMV 201
                                    ....788999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2113.87
//
Query:       gi|121638108|ref|YP_978332.1|  [L=513]
Description: hypothetical protein BCG_2243 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-45  153.5  22.4    8.1e-45  153.5  22.4    2.2  2  CHAD      CHAD domain
    2.2e-13   50.5   0.0    4.5e-13   49.5   0.0    1.5  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5  22.4   9.1e-49   8.1e-45       2     226 ..     239     462 ..     238     463 .. 0.91
   2 ?    0.2   0.2     0.067     6e+02     141     164 ..     488     511 ..     466     513 .] 0.55

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 9.1e-49
                                    HHHHHHHHHHCHHHHHTT--THHHHHHHHHHHHHHHHHHHTTTSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                           CHAD   2 laklldkllanepgvradedpeavHqmRvalRRlRsalrlfapvldkeeaaalekelrwlaraLGeaRDldVllerllsr 81 
                                    + +++++ll ++ +vrad+  +avHqmRv +R++Rs+l+  ++ ++ +e a + +elr+la++LG aRD++Vl +r++ +
  gi|121638108|ref|YP_978332.1| 239 VSEQVEQLLLWDRAVRADA-YDAVHQMRVTTRKIRSLLTDSQESFGLKESAWVIDELRELANVLGVARDAEVLGDRYQRE 317
                                    6799*************98.9*************************9********************************* PP

                                    H.......HTS-TTTCGGGHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHT--S--TSBHHHHHHHHHHHHHH CS
                           CHAD  82 le......erlpaaeqealerllkrlekerkrararvlaaLdsaryqalldaldallaaerleaepaaaalekrlrkayr 155
                                    l+             +   erl + +++++++  +r l aL+s+ry++lldaldal++ er++a++ ++ ++  +++ayr
  gi|121638108|ref|YP_978332.1| 318 LDalapelV-----RGRVRERLVDGARRRYQTGLRRSLIALRSQRYFRLLDALDALVS-ERAHATSGEESAPVTIDAAYR 391
                                    *95533222.....235667*************************************5.555678999999999999999 PP

                                    HH.HHHH--......------THHHHHHHHHHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           CHAD 156 klekraaka......eadesdeealHelRkaaKrlRYaaeafaplypaalkallkalkklqevLGdlqDlvvarell 226
                                    +++k+a++a      + d+ ++ealH +Rk+aKrlRY+a a       ++++  +++k +q++LGd+qD+vv+re+l
  gi|121638108|ref|YP_978332.1| 392 RVRKAAKAAktagdqAGDHHRDEALHLIRKRAKRLRYTAAAT------GADNVSQEAKVIQTLLGDHQDSVVSREHL 462
                                    996655555999999899**********************99......89*************************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.067
                                    BHHHHHHHHHHHHHHHH.HHHH-- CS
                           CHAD 141 paaaalekrlrkayrklekraaka 164
                                    ++a+  +++l++a rkl+k+ +ka
  gi|121638108|ref|YP_978332.1| 488 DLAERCREQLEAALRKLDKAVRKA 511
                                    444444444444444444443333 PP

>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0     5e-17   4.5e-13       2     124 ..      12     138 ..      11     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5e-17
                                    EEEEEEEEE-.HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSSTEEE CS
                           CYTH   2 iEvEvKflvs.aaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdgeree 79 
                                     EvE+Kf v  ++  ++ e  +a +r+++  t++++ +Y+dtp +dlar++ +LR R  +g+    ++lK p+       
  gi|121638108|ref|YP_978332.1|  12 LEVERKFDVIeSTVSPSFEGIAAVVRVEQSPTQQLDAVYFDTPSHDLARNQITLRRR--TGGADAgWHLKLPA------- 82 
                                    69*******977777776555************************************..7888888******9....... PP

                                    EEEEECCCEEECCCC.........HHHHHHHHHHHTT-EEEEEEEEEEEEEEE....T CS
                           CYTH  80 vegevsreEyeepls.........daaeaaelldglglepvasvkklRrkykl....e 124
                                      g+ +r E+ +pls           + ++++++ +  +pva++ + R++  l    +
  gi|121638108|ref|YP_978332.1|  83 --GPDKRTEMRAPLSasgdavpaeLLDVVLAIVRDQPVQPVARISTHRESQILygagG 138
                                    ..77778888899998899977755555889999999************988855431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3497.15
//
Query:       gi|121638109|ref|YP_978333.1|  [L=106]
Description: hypothetical protein BCG_2244 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 704.59
//
Query:       gi|121638110|ref|YP_978334.1|  [L=124]
Description: hypothetical protein BCG_2245 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-58  196.1   0.0    3.3e-58  196.0   0.0    1.0  1  Oxygenase-NA    Oxygenase, catalysing oxidative methylation o
     0.0068   17.3   0.0      0.009   16.9   0.0    1.2  1  2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> Oxygenase-NA  Oxygenase, catalysing oxidative methylation of damaged DNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.0   3.7e-62   3.3e-58      51     172 .]       2     123 ..       1     123 [. 0.99

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 3.7e-62
                   Oxygenase-NA  51 aechaagqerptplllkyeegdynaLHqdlyGelvFPlqvvilLsepgedftGGefvlveqrpraqsraevvkleqGdal 130
                                    a+chaagq+r+t+l+lky+++d+naLHqdlyGelvFPlqvvi Ls+p++d+tGGef+lveqrpraqsr+++++l qG++ 
  gi|121638110|ref|YP_978334.1|   2 ASCHAAGQTRSTALMLKYGTNDWNALHQDLYGELVFPLQVVINLSDPETDYTGGEFLLVEQRPRAQSRGTAMQLPQGHGY 81 
                                    78****************************************************************************** PP

                   Oxygenase-NA 131 ifatreRpvkgkrgvyrvnlrhgvsrvrsGeRltlglifHda 172
                                    +++tr+Rpv+++rg+++ ++rhg+s++rsGeR+++glifHda
  gi|121638110|ref|YP_978334.1|  82 VLTTRDRPVRTSRGWSASPVRHGLSTIRSGERYAMGLIFHDA 123
                                    *****************************************8 PP

>> 2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-06     0.009       4      96 .]      17     121 ..      14     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                                    EEE-TT-EEEEE-SS----TT.-.EEEEEEEEE.....ET-B--EEE................---TT-EEEEE-..B-T CS
                 2OG-FeII_Oxy_3   4 lrygegqeykpHvDnfekeegsgqrrltvllyLne.keseeGGelelyekdk......eavkikpkkgrlvlFesdellp 76 
                                    l+yg+++    H+D      g+    l v++ L++ +++++GGe+ l+e+++       a+++ p+    vl   d + p
  gi|121638110|ref|YP_978334.1|  17 LKYGTNDWNALHQDL----YGELVFPLQVVINLSDpETDYTGGEFLLVEQRPraqsrgTAMQL-PQGHGYVLTTRD-R-P 89 
                                    678888888899997....4668899********97777*****9998888888885533333.333333333332.2.2 PP

                                    .............EEE--B.-SS-EEEEEEEEE CS
                 2OG-FeII_Oxy_3  77 .............HevlpvtkggeRlsltgwir 96 
                                                 H+ + +++ geR+++ + ++
  gi|121638110|ref|YP_978334.1|  90 vrtsrgwsaspvrHGLSTIRS-GERYAMGLIFH 121
                                    346888888888899999966.5***9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 828.35
//
Query:       gi|121638111|ref|YP_978335.1|  [L=364]
Description: bifunctional RNase H/acid phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-54  183.2   0.9    4.6e-54  183.1   0.2    1.4  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)
    2.2e-24   85.6   0.3    4.2e-24   84.7   0.0    1.7  2  RVT_3       Reverse transcriptase-like
    1.2e-09   38.5   0.1    3.2e-09   37.1   0.0    1.7  2  RNase_H     RNase H


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.4   8.3e+03      31      44 ..      97     110 ..      96     114 .. 0.79
   2 !  183.1   0.2   7.7e-58   4.6e-54       1     193 [.     167     359 ..     167     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHTTS- CS
                     His_Phos_1  31 eqAealaerlagep 44 
                                     qA+ala  +++++
  gi|121638111|ref|YP_978335.1|  97 VQAQALASQFRRIN 110
                                    59999999998865 PP

  == domain 2  score: 183.1 bits;  conditional E-value: 7.7e-58
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTT.S---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS- CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlag.epidaiysSplkRarqTaeliaealglpveldegLrE 79 
                                    l+L+RHG+te ++++r++gr+++ L+e G +q+ a+a +la+  +i+a++sSpl+Ra++Ta  +a+al l+v +d++L E
  gi|121638111|ref|YP_978335.1| 167 LLLLRHGQTELSEQRRYSGRGNPGLNEVGWRQVGAAAGYLARrGGIAAVVSSPLQRAYDTAVTAARALALDVVVDDDLVE 246
                                    68****************************************889999******************************** PP

                                    ---GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHH CS
                     His_Phos_1  80 idfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarll 159
                                    +dfG+weglt+ae+ae+ pe +++wl+d++  +ppggEs++dv +Rv++  ++++  +eg tvlvVsH ++i++ll+ +l
  gi|121638111|ref|YP_978335.1| 247 TDFGAWEGLTFAEAAERDPELHRRWLQDTS-ITPPGGESFDDVLRRVRRGRDRIIVGYEGATVLVVSHVTPIKMLLRLAL 325
                                    ***************************998.89*********************************************** PP

                                    T--GGGGGGB---TT-EEEEEE-SS-EEEEEEEE CS
                     His_Phos_1 160 glpleelrrleldnaslsvlefdeggwrlvrlnd 193
                                    +     l rl+ld asls+ ef+++g + vrl +
  gi|121638111|ref|YP_978335.1| 326 DAGSGVLYRLHLDLASLSIAEFYADGASSVRLVN 359
                                    **************************99988765 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   7.1e-28   4.2e-24       2     124 .]       7     129 ..       6     129 .. 0.97
   2 ?   -3.4   0.1       1.3   7.9e+03      23      47 ..     209     233 ..     199     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 7.1e-28
                          RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrek 81 
                                     dg  + + g +g g+v+ +++   +la ++++ g+a++ +AE+++L+ GL  a+klg ++  v  Dsk vv++++gr+k
  gi|121638111|ref|YP_978335.1|   7 ADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWK 86 
                                    5888899***********************99************************************************ PP

                          RVT_3  82 vksselanlldeirkllksfesvsvehipReqNrvAdalAkra 124
                                    vk+++l +l+ ++++l+++f+++  e++pR  N++Ad lA+ a
  gi|121638111|ref|YP_978335.1|  87 VKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDA 129
                                    ****************************************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                          RVT_3  23 nGevllagaeklqgkasveeAElqA 47 
                                    +G + ++++++lq+ ++  +  ++A
  gi|121638111|ref|YP_978335.1| 209 RGGIAAVVSSPLQRAYDTAVTAARA 233
                                    5555555665666655555555555 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   5.4e-13   3.2e-09       4     142 ..       3     130 ..       1     131 [. 0.73
   2 ?   -3.1   0.0       1.4   8.3e+03       6      14 ..     347     355 ..     345     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.4e-13
                                    EEEEEEEEEECTTTCEEEEEEECTT..E....EEEEEEC..CCCHHHHHHHHHHHHHHH.TT.SC.SEEEEEES-HHHHH CS
                        RNase_H   4 vvvYtDGsclgnpgeggagavlykegar....nisaple..eaqtnnraELsAvieaLk.alksd.ekvniytDSkYvvk 75 
                                    vv+ +DG ++gnpg++g+gav+++ + +       ++ +  ++ tnn aE + +i+ L  a+k + ++  +  DSk vv+
  gi|121638111|ref|YP_978335.1|   3 VVIEADGGSRGNPGPAGYGAVVWTAD-HstvlA--ESKQaiGRATNNVAEYRGLIAGLDdAVKLGaTEAAVLMDSKLVVE 79 
                                    67789***************997664.333332..2222468*****************77776667788********** PP

                                    HHHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHHH CS
                        RNase_H  76 gitqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkeaa 142
                                       q+  rwk ++ +   +   v +   ++l+    + ++++ +wv+        N+ aDrlA++a+
  gi|121638111|ref|YP_978335.1|  80 ---QMSGRWKVKHPDL-LKLY-VQA---QALA---SQFRRINYEWVP----R-ARNTYADRLANDAM 130
                                    ...6667887755533.3331.333...3333...33467******9....4.48999*****9985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                                    EEEEEEEEC CS
                        RNase_H   6 vYtDGsclg 14 
                                    +Y+DG+++ 
  gi|121638111|ref|YP_978335.1| 347 FYADGASSV 355
                                    79***9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2667.34
//
Query:       gi|121638112|ref|YP_978336.1|  [L=245]
Description: hypothetical protein BCG_2247c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-11   42.9   2.8    1.4e-10   41.2   2.8    2.0  1  zf-RING_7        C4-type zinc ribbon domain
    5.7e-05   23.4  22.5    8.9e-05   22.8  22.5    1.4  1  ATG16            Autophagy protein 16 (ATG16)
     0.0028   17.7   4.9     0.0067   16.5   4.9    1.5  1  SYCE1            Synaptonemal complex central element protein
  ------ inclusion threshold ------
      0.043   13.1  12.2      0.062   12.6  12.2    1.3  1  CorA             CorA-like Mg2+ transporter protein
      0.058   12.9  29.5      0.028   14.0  26.5    1.8  2  MscS_porin       Mechanosensitive ion channel porin domain
      0.088   12.5   0.8       0.27   10.9   0.0    2.0  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        0.1   12.7   0.5       0.26   11.4   0.5    1.7  1  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.3   1.8       0.24   11.4   1.8    1.5  1  Prok-RING_1      Prokaryotic RING finger family 1
       0.13   11.7   0.1       0.13   11.7   0.1    1.6  1  zf-ribbon_3      zinc-ribbon domain
       0.16   11.5   6.2       0.26   10.8   6.1    1.3  1  CENP-K           Centromere-associated protein K
       0.17   11.2  16.7       0.29   10.5   0.3    2.2  2  GAS              Growth-arrest specific micro-tubule binding
       0.19    9.9   8.6       0.27    9.4   8.6    1.2  1  EzrA             Septation ring formation regulator, EzrA
        0.2   12.2  24.6        1.3    9.5   0.5    2.9  2  APG6_N           Apg6 coiled-coil region
       0.23   12.0   2.0          1   10.0   0.1    2.6  2  Scaffolding_pro  Phi29 scaffolding protein
       0.25   11.5   7.1        5.5    7.1   0.1    2.5  3  COG2             COG (conserved oligomeric Golgi) complex com
       0.33   11.1   6.1        1.9    8.6   2.8    2.1  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.34   11.0  25.1        4.8    7.2   8.0    3.2  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.43    9.9  21.4        7.4    5.8  21.4    2.1  1  DUF4407          Domain of unknown function (DUF4407)
       0.44   10.3  21.7       0.33   10.7   0.6    3.6  3  DivIC            Septum formation initiator
       0.56   10.4   5.2        4.4    7.4   0.2    2.4  2  RasGAP_C         RasGAP C-terminus
       0.62    8.9  19.1        2.1    7.2  12.7    2.1  2  Spc7             Spc7 kinetochore protein
        0.8    7.5   4.4       0.97    7.3   4.4    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.92   10.0  22.3         13    6.3  12.7    3.3  3  ZapB             Cell division protein ZapB
       0.99    9.7  12.7        2.4    8.4   7.8    2.6  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
          1    7.9   8.2        1.4    7.4   7.4    1.3  1  AAA_13           AAA domain
        1.2    9.2  18.9        3.8    7.6   2.4    2.1  2  DivIVA           DivIVA protein
        1.3    9.3  15.2        1.6    9.0   3.7    3.2  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.4    8.6  14.0        1.9    8.1   2.0    2.6  2  GrpE             GrpE
        1.7    8.8   5.0        5.2    7.2   0.1    3.0  2  DUF2730          Protein of unknown function (DUF2730)
        1.8    8.6   7.5        1.1    9.3   4.3    2.1  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        2.4    7.8  13.4         18    5.0   7.9    2.8  3  DUF4201          Domain of unknown function (DUF4201)
        2.9    8.0  16.5       0.86    9.7  13.0    1.7  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        3.8    7.9  13.7        9.9    6.6  13.8    1.7  1  Fez1             Fez1
        3.9    4.9  22.1        9.5    3.6  22.1    1.4  1  DUF3584          Protein of unknown function (DUF3584)
        4.2    5.9   6.7         16    3.9   6.7    1.8  1  FapA             Flagellar Assembly Protein A
        4.4    7.9  17.7       0.23   12.0   8.6    3.1  3  HSCB_C           HSCB C-terminal oligomerisation domain
        4.7    6.0   6.1          7    5.4   6.1    1.2  1  Apt1             Golgi-body localisation protein domain
        4.8    6.3   6.1        3.7    6.7   3.8    1.7  2  TMPIT            TMPIT-like protein
        4.9    6.1  15.0        1.8    7.5  11.5    1.8  2  Atg14            Vacuolar sorting 38 and autophagy-related su
        6.1    6.9  18.1        2.6    8.1  11.4    2.1  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
        6.2    6.6  10.2         13    5.6   0.2    2.1  2  DUF724           Protein of unknown function (DUF724)
        6.8    6.8  18.4        7.8    6.6   0.8    2.4  2  ADIP             Afadin- and alpha -actinin-Binding
          8    5.6   8.4        2.1    7.5   4.2    1.8  2  ISG65-75         Invariant surface glycoprotein
        8.2    6.7  14.9         44    4.4  10.2    3.2  2  Spc24            Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   2.8   3.4e-13   1.4e-10       1      33 []     203     237 ..     203     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.4e-13
                                    EETTT--B--CCHHHHHCCS..TB-EE-TTT--EE CS
                      zf-RING_7   1 tCgGChmelppqvlselrag..devvtCpeCGRIL 33 
                                    +Cg+C++e+  ++l+++ a+  devv+CpeCG+IL
  gi|121638112|ref|YP_978336.1| 203 RCGACRIEIGRGELAQISAAaeDEVVRCPECGAIL 237
                                    7****************88889************9 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  22.5   2.2e-07   8.9e-05      13     162 ..      33     175 ..       7     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.2e-07
                          ATG16  13 qekafaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelae 92 
                                    q++a++++ + +n   dr++al+  ++ l  + ++ +s    ++++k+  + +s       ++ ++++++la l++el  
  gi|121638112|ref|YP_978336.1|  33 QRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFES--EIDAVRKRGDRDRS-----LLTSGATDAKQLADLQHELDS 105
                                    56888999999999***************777777666..22233333333333.....478999*************** PP

                          ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsa 162
                                    l+++++ l++ lle+ e  ++l+++ ++++++l++l+a+ aa +++l++  +e+ + ++ +  ++D l+a
  gi|121638112|ref|YP_978336.1| 106 LQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRDMLTA 175
                                    *************************************************************999997765 PP

>> SYCE1  Synaptonemal complex central element protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.9   1.6e-05    0.0067      36     116 ..      97     177 ..      89     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                          SYCE1  36 ealkrElDsLnaEkvhLeevlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltskiqeeklkrrklrlefeeq 115
                                      l++ElDsL+  +++Le+ l +  e  + Lq +   + +  q  ++     +q + e  ++i++++ +++++r  +   
  gi|121638112|ref|YP_978336.1|  97 ADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRDMLTAT 176
                                    469*******************************99999999998899999**********************9887776 PP

                          SYCE1 116 l 116
                                    l
  gi|121638112|ref|YP_978336.1| 177 L 177
                                    6 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  12.2   0.00015     0.062      99     227 ..      41     171 ..       9     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                           CorA  99 k...deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlk 175
                                    +   ++ +++  + ++ ++ ld  v r++ +++++ ++ d+  + l   + + ++++la+l+++l  l+r  a ++++l 
  gi|121638112|ref|YP_978336.1|  41 QaehNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLL--TSGATDAKQLADLQHELDSLQRRQASLEDALL 118
                                    444456667777778888889*******************988888..8888999************************* PP

                           CorA 176 rlla.kaddkllddedkeylrdlldelerllemlealrerleslqdtysslls 227
                                    ++l+ +++      ++++ l+ l+ +l+ +++ l+     +++ + ++ss+ +
  gi|121638112|ref|YP_978336.1| 119 EVLErREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRD 171
                                    ****544444444445566*****************************99865 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       1.4   5.7e+02     100     127 ..      13      40 ..       5      46 .. 0.58
   2 ?   14.0  26.5   6.8e-05     0.028      30     155 ..      42     165 ..      34     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                     MscS_porin 100 qlaqlnsqlvelqtrperaqqqltearq 127
                                    +la+l+++l+ + +r + ++q+ +  + 
  gi|121638112|ref|YP_978336.1|  13 ELAKLDAELTRIAHRATHLPQRAAYQQV 40 
                                    5666677777777666666665443333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.8e-05
                     MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlv 109
                                    +++++ ++++++l+ a +d   ++   + e++a     +  ++++   +s ++  ++l++ + +l +lq+++a+l++ l 
  gi|121638112|ref|YP_978336.1|  42 AEHNAANDRMAALRIAAEDLDGQVSRFESEIDAV---RKRGDRDRSLLTSGATDAKQLADLQHELDSLQRRQASLEDALL 118
                                    688999****************************...555555555555556667999********************** PP

                     MscS_porin 110 elqtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrtalq 155
                                    e   r e++q+q+t+ +++lq++r++L++ ++a   al++  ++  q
  gi|121638112|ref|YP_978336.1| 119 EVLERREELQAQQTAESRALQALRADLAAAQQALDeALAEIDQARHQ 165
                                    ***************************66644444466665555555 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       2.9   1.2e+03       3       8 ..     204     209 ..     202     216 .. 0.76
   2 ?   10.9   0.0   0.00067      0.27      15      25 ..     225     235 ..     217     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.9
                                    -SSS-- CS
                 DNA_RNApol_7kD   3 CgeCga 8  
                                    Cg C  
  gi|121638112|ref|YP_978336.1| 204 CGACRI 209
                                    888865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00067
                                    SS----SSS-- CS
                 DNA_RNApol_7kD  15 gdpiRCkeCGh 25 
                                     +++RC eCG 
  gi|121638112|ref|YP_978336.1| 225 DEVVRCPECGA 235
                                    699*******6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00064      0.26       7      34 ..     203     235 ..     202     239 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                    Zn-ribbon_8   7 rCeeCghefe..vlqsis..daplta.CPeCgs 34 
                                    rC +C  e    +l++is   +++++ CPeCg+
  gi|121638112|ref|YP_978336.1| 203 RCGACRIEIGrgELAQISaaAEDEVVrCPECGA 235
                                    677777444477444444334446667*****8 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.8   0.00059      0.24       4      28 ..     201     235 ..     198     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                    Prok-RING_1   4 gkkCpvCgkelkee..........dDiVvCpeCgt 28 
                                    g++C +C+ e+  +          d +V CpeCg+
  gi|121638112|ref|YP_978336.1| 201 GHRCGACRIEIGRGelaqisaaaeDEVVRCPECGA 235
                                    67788888888877788888888799********8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00032      0.13       3      11 ..     228     237 ..     226     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00032
                    zf-ribbon_3   3 vrCPnCGa.p 11 
                                    vrCP+CGa +
  gi|121638112|ref|YP_978336.1| 228 VRCPECGAiL 237
                                    8*******55 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.1   0.00063      0.26      83     176 ..      91     181 ..      38     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00063
                         CENP-K  83 lgkeelqklksqLelvlsiiqsknkklkedLkrEqewleeqqeilesLkektkelkkqvvafsektrksaelkekirkik 162
                                       ++l+ l+++L+ ++    s ++ l e+L+r  e + +q    ++L+   ++l   ++a+ e    +ae+++  ++  
  gi|121638112|ref|YP_978336.1|  91 TDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEA---LAEIDQARHQHS 167
                                    3456788899999999999999999******************************9999999988...999999999999 PP

                         CENP-K 163 eykeeLltaLgefL 176
                                    ++++ L  +L+  L
  gi|121638112|ref|YP_978336.1| 168 SQRDMLTATLDPEL 181
                                    99999999998665 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00071      0.29      62     128 ..      13      78 ..       5      89 .. 0.84
   2 ?    4.6  10.6     0.046        19      40     111 ..      94     169 ..      84     190 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                            GAS  62 pLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykk 128
                                    +L k+++e+ +  +++  +  +++++++++a+ + +++ + +l+  +e l  ++++ e+e+d+++k+
  gi|121638112|ref|YP_978336.1|  13 ELAKLDAELTRIAHRAT-HLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKR 78 
                                    56677777777766654.555699**************************************99987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.046
                            GAS  40 kkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekd....kqslknlkarlkelekelkdlkwehevl 111
                                    k+ +  + el+ ++ +  +l++ L ++ e +eeL++q    ++     +++l+++++ l e+  e+ + +++h + 
  gi|121638112|ref|YP_978336.1|  94 KQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRAlqalRADLAAAQQALDEALAEIDQARHQHSSQ 169
                                    4555666677777777777777777777777777765554444200003333344444444444444444444443 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.6   0.00066      0.27     299     429 ..      35     165 ..       8     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00066
                                    HHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTG CS
                           EzrA 299 eAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelq 378
                                    +A+++v+ + +  ++++  l+   ++l  +++r + + +   +  ++ r+l +   +  k++ +l+++l++ +    +l+
  gi|121638112|ref|YP_978336.1|  35 AAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGATDAKQLADLQHELDSLQRRQASLE 114
                                    57888888888888888888888888888888888888888888888888888888889999999999999999999*** PP

                                    GGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 379 eeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrk 429
                                    + l e+ e+ ee++ +q   +++l++lr d + A++ lde   e+ +++++
  gi|121638112|ref|YP_978336.1| 115 DALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQ 165
                                    ****************************************99999888776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5    0.0033       1.3      45      99 ..      26      80 ..       7      84 .. 0.79
   2 ?    5.1  17.9     0.075        31      62     132 ..      95     165 ..      81     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0033
                         APG6_N 45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeee 99
                                   ++  +   +  ++++++e +++   +++l  + e+l+ +++  e+e +a+ +  +
  gi|121638112|ref|YP_978336.1| 26 HRATHLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGD 80
                                   555666667779***********************************99887665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.075
                         APG6_N  62 eeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqnq 132
                                    + ++l+ eL+ l++ +++le++l +  e  e+l+++++++ r  ++l+ +l+  ++ ld   a++++a++q
  gi|121638112|ref|YP_978336.1|  95 QLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQ 165
                                    44556666666666666666666666666666666666666666666666666666666666666665554 PP

>> Scaffolding_pro  Phi29 scaffolding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0025         1      15      65 ..      17      67 ..       8     103 .. 0.85
   2 ?    1.0   0.2       1.6   6.3e+02      44      64 ..     130     150 ..      95     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0025
                                   TSTTS-.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                Scaffolding_pro 15 ldPela.ieertealqtlrvdyvevvveysdltksieklkvekddlivsnsk 65
                                   ld el+ i +r+ +l + r  y +v++e++    ++ +l++  +dl    s+
  gi|121638112|ref|YP_978336.1| 17 LDAELTrIAHRATHLPQ-RAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSR 67
                                   45665427889999987.99*******************9999999766665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHHHHHHH CS
                Scaffolding_pro  44 dltksieklkvekddlivsns 64 
                                    ++t +  +l++ ++dl ++  
  gi|121638112|ref|YP_978336.1| 130 QQTAESRALQALRADLAAAQQ 150
                                    344444444444444444443 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.6   3.5e+03      76      97 ..      31      52 ..      12      60 .. 0.54
   2 ?    7.1   0.1     0.014       5.5      70     126 ..      57     113 ..      49     120 .. 0.88
   3 ?    6.6   2.9     0.019       7.9      61     121 ..     114     174 ..     110     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.6
                           COG2 76 splaaarkkvesvreklseree 97
                                    p  aa ++v++ +++ ++r++
  gi|121638112|ref|YP_978336.1| 31 LPQRAAYQQVQAEHNAANDRMA 52
                                   3444455555555555555554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                           COG2  70 eleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevv 126
                                    + e ++ +++++ +++++vr+  ++ ++ ++s   +ak+l++ +  l++l++ ++ +
  gi|121638112|ref|YP_978336.1|  57 AAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGATDAKQLADLQHELDSLQRRQASL 113
                                    5678999*************************************9999998877666 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.019
                           COG2  61 SghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllk 121
                                     ++L  + e+ ee++ + +a  + ++++r+ l+++++++++ l+e  +++ +  + +++l 
  gi|121638112|ref|YP_978336.1| 114 EDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRDMLT 174
                                    5677778888999999999999999999999999999999999999999999988888775 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.17        68      36      99 ..      13      74 ..       6      80 .. 0.67
   2 ?    8.6   2.8    0.0048       1.9      34     115 ..      93     170 ..      81     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                      Fib_alpha 36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99
                                   +l+kl  el++i+++ ++  +   +  ++++++ + ++d   +++  +++l+ +++r++ +ida
  gi|121638112|ref|YP_978336.1| 13 ELAKLDAELTRIAHRATHLPQRAAY--QQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDA 74
                                   5667777777777666666665444..3334444444445788888899999999999999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0048
                                    CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                      Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                     k+l++l++el+++++++ + e+   e+ +  +e q++++ ++++++ ++ +l       ++ +d+   +i + +  ++s
  gi|121638112|ref|YP_978336.1|  93 AKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLA----AAQQALDEALAEIDQARHQHSS 168
                                    689********************9999999988888888877777777777666....5666666666666666666666 PP

                                    HH CS
                      Fib_alpha 114 ne 115
                                    ++
  gi|121638112|ref|YP_978336.1| 169 QR 170
                                    65 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2  13.6       2.4   9.9e+02      63     118 ..      76     130 ..       5     133 .. 0.48
   2 ?    7.2   8.0     0.012       4.8      51      92 ..     130     171 ..     125     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.4
                     TPR_MLP1_2  63 reelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneq 118
                                    r++ ++ ++ +++  ++a+++ a+l+ +  s+++++ +le+ l e+ +r+e+l++q
  gi|121638112|ref|YP_978336.1|  76 RKRGDRDRSLLTSGATDAKQL-ADLQHELDSLQRRQASLEDALLEVLERREELQAQ 130
                                    333333333333322332222.3455555555566666666666666666666555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                     TPR_MLP1_2  51 khaedvkelqalreelnelkaeiaelkaeaesakaeleesee 92 
                                    ++ +++++lqalr++l+ +++ + e+ ae ++a+++++ ++ 
  gi|121638112|ref|YP_978336.1| 130 QQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRD 171
                                    567889999999999999999999999999999999988776 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  21.4     0.018       7.4     130     231 ..      54     182 ..       6     198 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                        DUF4407 130 a......ltaelaeleaqia........................alqaeidaaearldalraeaqkeldgtk..gtgttg 177
                                           l+ ++++ e++i+                        +lq e+d++++r + l++++ + l+     +++   
  gi|121638112|ref|YP_978336.1|  54 LriaaedLDGQVSRFESEIDavrkrgdrdrslltsgatdakqlaDLQHELDSLQRRQASLEDALLEVLERREelQAQ--- 130
                                    03333443333333333333333333344444444444444444777777777777777777777766665444333... PP

                        DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakera 231
                                       +  a ++ +a+l+aaq++l+e+ a+   ++++ ++ ++++ l+a ++ e a
  gi|121638112|ref|YP_978336.1| 131 QTAESRALQALRADLAAAQQALDEALAE--IDQARHQHSSQRDMLTATLDPELA 182
                                    3446666777777777777777777777..667777777777766666665555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00082      0.33      14      60 ..      32      78 ..      24      86 .. 0.92
   2 ?    6.3   3.6      0.02       8.1      24      45 ..      94     115 ..      90     130 .. 0.89
   3 ?    0.5   6.3       1.3   5.4e+02      27      59 ..     129     158 ..     117     173 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00082
                                   XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                          DivIC 14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60
                                    +  ay+q+++e +a ++ +a+l+   e+L+ +v++ +s+ d++++r
  gi|121638112|ref|YP_978336.1| 32 PQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKR 78
                                   57789********************************9999999887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  24 qeiaalqaelaklkaeneeLea 45 
                                    +++a+lq+el++l+ ++++Le+
  gi|121638112|ref|YP_978336.1|  94 KQLADLQHELDSLQRRQASLED 115
                                    799*****************97 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  27 aalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                    a+++ae  +l+a +++L+a  + L    ++++e
  gi|121638112|ref|YP_978336.1| 129 AQQTAESRALQALRADLAAAQQALD---EALAE 158
                                    4555666666666666666666662...22222 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.011       4.4      41      87 ..      33      79 ..      21     111 .. 0.82
   2 ?    3.2   2.8      0.22        89      48     106 ..     106     168 ..      90     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                       RasGAP_C 41 kgrlrekrkeElesleetlktLseknnylesqlesYkayienvleql 87
                                   ++ + +++++E +++++ +++L+   + l  q++ +++ i+ v++  
  gi|121638112|ref|YP_978336.1| 33 QRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRG 79
                                   577899*************************************9976 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
                       RasGAP_C  48 rkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgk....lpfskqyfkkrel 106
                                     ++   sle++l ++ e+++ l+ q    ++ ++  +++l++++++    l    q+ ++ ++
  gi|121638112|ref|YP_978336.1| 106 LQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQAldeaLAEIDQARHQHSS 168
                                    455555667777777777777777777777777777777766654454443333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.012       5.1     169     228 ..      21      78 ..       5      93 .. 0.55
   2 ?    7.2  12.7    0.0051       2.1     146     233 ..      94     170 ..      86     179 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                           Spc7 169 lpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                    l ++ ++ + l ++++ +q +ae   +  ++++++lr + ++l+ ++++++ e++ ++++
  gi|121638112|ref|YP_978336.1|  21 LTRIAHRATHLPQRAAYQQVQAE--HNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKR 78 
                                    33333333333333333333222..34556666666666666666666666666666555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0051
                           Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael 225
                                    ++l++l+++ + L+++++ l+++l e+ e+++el+++ +            ++  L++lr +la++++ ++e  +e+++ 
  gi|121638112|ref|YP_978336.1|  94 KQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQT-----------AESRALQALRADLAAAQQALDEALAEIDQA 162
                                    223333333333333333333333333333333333333...........445556666666666666666555555555 PP

                           Spc7 226 qeqleele 233
                                    + q  +++
  gi|121638112|ref|YP_978336.1| 163 RHQHSSQR 170
                                    55555444 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.4    0.0024      0.97      32     143 ..      58     168 ..      33     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                     V_ATPase_I  32 cdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlek 111
                                     ++++ +++ +e+ei+  +k   ++++   ++ a+++k+l +l++el++l+++  +l++ l ++ ++++el+ ++   ++
  gi|121638112|ref|YP_978336.1|  58 AEDLDGQVSRFESEIDAVRKRGDRDRS-LLTSGATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESR 136
                                    578888889999999996666666555.6666777777777777777777777777777777777777777777777766 PP

                     V_ATPase_I 112 akefleeeeeeeeeeeseeeeeekeeeeeees 143
                                    a + l+++ + ++++ +e+ +e ++++++++s
  gi|121638112|ref|YP_978336.1| 137 ALQALRADLAAAQQALDEALAEIDQARHQHSS 168
                                    66666655333333222222222222222221 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.8     0.051        21      28      65 ..      15      54 ..       6      56 .. 0.70
   2 ?    6.3  12.7     0.032        13      20      70 ..      96     160 ..      92     161 .. 0.74
   3 ?    5.7   1.2     0.048        20      28      64 ..     139     175 ..     134     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.051
                           ZapB 28 eeLkeeneelkeenrele..eeneqlkeereawqerlkkL 65
                                   ++L +e    + ++  l   +  +q ++e++a ++r+ +L
  gi|121638112|ref|YP_978336.1| 15 AKLDAELTRIAHRATHLPqrAAYQQVQAEHNAANDRMAAL 54
                                   44444444444444444477999*************9876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.032
                           ZapB  20 itlLqmeieeLkeeneelkeenrele..............eeneqlkeereawqerlkkLLgkle 70 
                                    ++ Lq e++ L++++++l++   e+               + +++l+++ +a q+ l+  L++++
  gi|121638112|ref|YP_978336.1|  96 LADLQHELDSLQRRQASLEDALLEVLerreelqaqqtaesRALQALRADLAAAQQALDEALAEID 160
                                    67899999999999999999998888666555566666666666666777777777777777776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.048
                           ZapB  28 eeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                    ++L+++ ++ ++  +e  +e++q +++++++++ l +
  gi|121638112|ref|YP_978336.1| 139 QALRADLAAAQQALDEALAEIDQARHQHSSQRDMLTA 175
                                    4566666666666777778888888888888776665 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3      0.13        51      44      85 ..      36      74 ..      13      81 .. 0.76
   2 ?    8.4   7.8    0.0059       2.4      18     104 ..      75     159 ..      67     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHH CS
                   Seryl_tRNA_N 44 eleelqaerNelskeIgkakkkkedaeeliaevkelkeelka 85
                                   + +++qae+N+++  ++ +  +   ae+l  +v+    e++a
  gi|121638112|ref|YP_978336.1| 36 AYQQVQAEHNAANDRMAALRIA---AEDLDGQVSRFESEIDA 74
                                   5689999999999999998876...45566666666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0059
                                    HCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  18 lkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                    ++kRg +d +++ +     ++   lq+el++lq+++ +l  +  +  ++   +eel a+  + +  l+al a+l++++++
  gi|121638112|ref|YP_978336.1|  75 VRKRGdRDRSLLTSGATDAKQLADLQHELDSLQRRQASLEDALLEVLER---REELQAQQTAESRALQALRADLAAAQQA 151
                                    455554567777777777888999*****************99999965...5677777777777777777777777777 PP

                                    HHHHHCTS CS
                   Seryl_tRNA_N  97 leklllai 104
                                    l+++l++i
  gi|121638112|ref|YP_978336.1| 152 LDEALAEI 159
                                    77777665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.4    0.0035       1.4     336     469 ..      16     147 ..       3     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0035
                         AAA_13 336 qLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk 415
                                    +L++   ++  + + + +++ +++v+a+ +++++ +a++    ++   +v+++e+e  +++k   +++      + d   
  gi|121638112|ref|YP_978336.1|  16 KLDAELTRIAHRATHLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGATD--A 93 
                                    57888888999999999999999999999999999999999999999999999999999999988877654444433..5 PP

                         AAA_13 416 kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                    k++++l++++ +l+++++  e++l ++ e+ +eL++q + e +a + +   L+a
  gi|121638112|ref|YP_978336.1|  94 KQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAA 147
                                    678888888888888888888888888888888888888888888888777776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4    0.0094       3.8      66     129 ..       8      71 ..       5      73 .. 0.93
   2 ?    7.2   8.9     0.012         5      42     117 ..      90     167 ..      81     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0094
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  66 kktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqarlfrqr 129
                                    +++l+   +   e+++ a++   l  ++A ++ ++  + a+++++ +++  e+l  q   f+++
  gi|121638112|ref|YP_978336.1|   8 QRSLLELAKLDAELTRIAHRATHLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESE 71 
                                    57888888999999***********************************************986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                    HHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  42 eelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeli..ikeAekkaekiveeaeeeakkiaeeie 117
                                    ++  +++++l+++l++ + ++ +L+++l+   e  ee++a++++e++ +  +++  ++a++ ++ea  e+++++ ++ 
  gi|121638112|ref|YP_978336.1|  90 ATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALqaLRADLAAAQQALDEALAEIDQARHQHS 167
                                    566789**********************99999999998887777665411566677888889999999888887765 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.077        31      32      81 ..      34      80 ..       4      90 .. 0.64
   2 ?    9.0   3.7    0.0039       1.6      63      99 ..      93     129 ..      86     132 .. 0.87
   3 ?    1.9   0.3      0.63   2.6e+02      28      59 ..     138     169 ..     132     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.077
                    TMF_TATA_bd 32 keelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81
                                   +  +++++ae ++a++ +++l    e+l   +++++  e+e++++++r +
  gi|121638112|ref|YP_978336.1| 34 RAAYQQVQAEHNAANDRMAALRIAAEDL---DGQVSRFESEIDAVRKRGD 80
                                   4457788888888888888887766655...4556666667666666654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0039
                    TMF_TATA_bd  63 kkeleelekeleelqeryetlLellGeksEeveELra 99 
                                    +k+l++l+ el++lq+r+ +l   l e  E+ eEL+a
  gi|121638112|ref|YP_978336.1|  93 AKQLADLQHELDSLQRRQASLEDALLEVLERREELQA 129
                                    6889999999999999999999999999999999987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.63
                    TMF_TATA_bd  28 laslkeelerleaerdeareeivklmkeneel 59 
                                    l++l+ +l+  ++  dea +ei +  ++  ++
  gi|121638112|ref|YP_978336.1| 138 LQALRADLAAAQQALDEALAEIDQARHQHSSQ 169
                                    45556666666666666666665544444333 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0    0.0048       1.9      10      80 ..      40     111 ..      16     120 .. 0.84
   2 ?    1.3   9.2      0.59   2.4e+02       5      55 ..     122     172 ..      87     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0048
                                    THHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                           GrpE  10 eedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaie.kfakdLLpvlDnleralk 80 
                                     ++e ++ + ++++l+  +++l  ++ r + e++ +rkr +++++ + + a   k + dL   lD+l+r  +
  gi|121638112|ref|YP_978336.1|  40 VQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGATDaKQLADLQHELDSLQRRQA 111
                                    45666777788999999****************************998887742788888888888888655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.59
                                    ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHH CS
                           GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekee 55 
                                    e+ ee+++++++  + l++l++ +++++++l+++lae++++r ++  +++ 
  gi|121638112|ref|YP_978336.1| 122 ERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRDM 172
                                    345566666666666677788888888888888888888887777777665 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.013       5.2      36      92 ..      22      78 ..      12      80 .. 0.78
   2 ?    1.0   2.0       1.1   4.5e+02      60      87 ..     133     160 ..      83     173 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                        DUF2730 36 eklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshq 92
                                   +++a+ +++  +r +  +++ e+   ++ +++L++  +dl+g+++  e e+++++++
  gi|121638112|ref|YP_978336.1| 22 TRIAHRATHLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKR 78
                                   55555566666666666667777777889***********************99875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                        DUF2730  60 PtakdlekLkllladlrgelkaleaevr 87 
                                       + l++L+ +la  +  l+++ ae++
  gi|121638112|ref|YP_978336.1| 133 AESRALQALRADLAAAQQALDEALAEID 160
                                    2233344444444444444444444555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.9   7.9e+02      71      80 ..      46      55 ..       7      80 .. 0.45
   2 ?    9.3   4.3    0.0028       1.1      10      82 ..      91     162 ..      83     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.9
                   Baculo_PEP_C 71 nLtdalnalq 80
                                   + +d ++al 
  gi|121638112|ref|YP_978336.1| 46 AANDRMAALR 55
                                   3333333332 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0028
                   Baculo_PEP_C  10 gggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdt 82 
                                    + + q  dL   L++++  ++++  +l + l+  e+ L+a +++ +++l++l+++l+++ ++L++al+++ ++
  gi|121638112|ref|YP_978336.1|  91 TDAKQLADLQHELDSLQRRQASLEDALLEVLERREE-LQAQQTAESRALQALRADLAAAQQALDEALAEIDQA 162
                                    5678999****************9999999997666.99999999999********************99854 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.096        39      64     127 ..      13      78 ..       9      87 .. 0.77
   2 ?    5.0   7.9     0.045        18      90     139 ..      93     142 ..      83     167 .. 0.85
   3 ?    2.2   0.3      0.32   1.3e+02      92     122 ..     137     167 ..     132     181 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.096
                        DUF4201  64 eLkrlkkkttktvhalthlkeklh..mleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                    eL +l    t+  h+ thl +++    +++e +++++++  +    ++l+ ++++ + e d +rk+
  gi|121638112|ref|YP_978336.1|  13 ELAKLDAELTRIAHRATHLPQRAAyqQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKR 78 
                                    788888999999999999877665447788888888888888888888888888888887777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.045
                        DUF4201  90 eselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr 139
                                    +++l++l+ el+++++r+a+l++ l +v ++r+ l++q++  ++ ++ lr
  gi|121638112|ref|YP_978336.1|  93 AKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALR 142
                                    679999*******************************9988777776655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.32
                        DUF4201  92 elselkkelkekeerlaklrkelykvklerd 122
                                     l++l+ +l   ++ l++  +e+ +++++++
  gi|121638112|ref|YP_978336.1| 137 ALQALRADLAAAQQALDEALAEIDQARHQHS 167
                                    3333344444333333333333333333333 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.9   1.2e+03     104     138 ..      34      70 ..       5      81 .. 0.42
   2 ?    9.7  13.0    0.0021      0.86      85     165 ..      90     173 ..      57     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.9
                        UPF0242 104 e..ldakeeelerlkeenqqLqekleaiaedfeelkl 138
                                    +  +++ + e +  + + + L++ +e+   +++++  
  gi|121638112|ref|YP_978336.1|  34 RaaYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFES 70 
                                    1223333333333333333444444444444444433 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                        UPF0242  85 ktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel...eeqLaekqellqeyqetieeq 161
                                    +t +++l +lq+e + L++++++ e +l +  e+ ++Lq +  a ++  ++l+ +l   +++L+e    +++ +++ ++q
  gi|121638112|ref|YP_978336.1|  90 ATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLaaaQQALDEALAEIDQARHQHSSQ 169
                                    577899*********************************99999888555554432111455555555666666666677 PP

                        UPF0242 162 rsvl 165
                                    r +l
  gi|121638112|ref|YP_978336.1| 170 RDML 173
                                    7666 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  13.8     0.024       9.9      36     169 ..      33     170 ..       6     175 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.024
                           Fez1  36 lkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekle...eelkelreelselsleeee 112
                                     +a  ++++a+ ++ ++++  l+ ++e+ + ++ + e+e++  +++ +  r  +++     ++l++l++el +l++++++
  gi|121638112|ref|YP_978336.1|  33 QRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGAtdaKQLADLQHELDSLQRRQAS 112
                                    36666677777777777777777777777777777777766553333333333332220003355556666666655555 PP

                           Fez1 113 aalesdeakaqrqe.aeeleelkreverlraeLkeerqkkeeqassFeqERrtWqeeK 169
                                     + +  e+ ++r+e + + ++++r ++ lra L+  +q+ +e  ++ +q R++ ++++
  gi|121638112|ref|YP_978336.1| 113 LEDALLEVLERREElQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQR 170
                                    5544444444444433455667778899999999999999999999999888876665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  22.1     0.023       9.5     288     427 ..      32     169 ..       3     180 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.023
                        DUF3584 288 akaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeel 367
                                     +++  qq+++++++ +++ ++l+ + ++++++++++ese++a+ ++ ++ + + + + + d+ ql  +++el  l+++ 
  gi|121638112|ref|YP_978336.1|  32 PQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDR-DRSLLTSGATDAKQLADLQHELDSLQRRQ 110
                                    34445566777777777777777777777777777777777777655443.66667777777777777777777777777 PP

                        DUF3584 368 daltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesq 427
                                    + l+++  +v e+ ++++++      ++l+ l+++l+a +++ d+ +a+i++a ++  sq
  gi|121638112|ref|YP_978336.1| 111 ASLEDALLEVLERREELQAQQT-AESRALQALRADLAAAQQALDEALAEIDQARHQHSSQ 169
                                    7777777777666665554433.3345555566666666666666666666665554443 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   6.7      0.04        16     298     403 ..      59     165 ..       4     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                           FapA 298 gkivggnikalkevkak.klGselgtkteievgldepelkeklkeleeeleeleeeleklkkk.ikklpklkaekqlese 375
                                    +++ g   +++ e++a+ k     g + +  ++    +  ++l++l+ el +l++++  l+++ ++ l+  ++ ++++  
  gi|121638112|ref|YP_978336.1|  59 EDLDGQVSRFESEIDAVrKR----GDRDRSLLTSG-ATDAKQLADLQHELDSLQRRQASLEDAlLEVLERREELQAQQTA 133
                                    56777777777777777333....33333333333.33355668888888888888888888854444443233333333 PP

                           FapA 376 kkeqlkklletk....eklkeeleeleeelke 403
                                     +  l+ l+ ++    ++l e l+e+++ +++
  gi|121638112|ref|YP_978336.1| 134 ESRALQALRADLaaaqQALDEALAEIDQARHQ 165
                                    33333333333311114444444444444444 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5       3.6   1.5e+03      26      26 ..      52      52 ..       9      97 .. 0.61
   2 ?   -0.1   0.1       3.3   1.3e+03      24      40 ..      92     108 ..      71     116 .. 0.74
   3 ?   12.0   8.6   0.00055      0.23       4      49 ..     115     159 ..     113     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.6
                                   H CS
                         HSCB_C 26 e 26
                                   +
  gi|121638112|ref|YP_978336.1| 52 A 52
                                   2 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.3
                                    SHHHHHHHHHHHHHHHH CS
                         HSCB_C  24 dkeeleelkaeveerie 40 
                                    d+ +l++l++e+++ ++
  gi|121638112|ref|YP_978336.1|  92 DAKQLADLQHELDSLQR 108
                                    66777777777776554 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00055
                                    HHHHHHHHHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         HSCB_C   4 efLmevMelrEeleeaeeaadkeeleelkaeveerieeleaeleea 49 
                                    + L ev+e rEel+  + a +  +l++l+a++ + +++l ++l+e 
  gi|121638112|ref|YP_978336.1| 115 DALLEVLERREELQAQQTA-ESRALQALRADLAAAQQALDEALAEI 159
                                    5699**********99655.77999999999999998888888764 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.1     0.017         7      87     165 ..      90     169 ..      71     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                           Apt1  87 asdfsdleglpemvkklqerirqleeikehfqieskyl...dkegwedrlklekelaeceeeLfllmkaittsqlrkkek 163
                                    a d ++l++l+ ++ +lq+r  +le+   ++  +++ l   ++ + + +++l+ +la++++ L  ++  i ++  ++  +
  gi|121638112|ref|YP_978336.1|  90 ATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELqaqQTAESRALQALRADLAAAQQALDEALAEIDQARHQH--S 167
                                    368888******************996666666666552323333377899*******************6666333..2 PP

                           Apt1 164 sk 165
                                    s+
  gi|121638112|ref|YP_978336.1| 168 SQ 169
                                    33 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.082        33      10      84 ..      36     112 ..      13     117 .. 0.74
   2 ?    6.7   3.8    0.0091       3.7       5      78 ..      97     169 ..      93     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.082
                          TMPIT  10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvlke 84 
                                     +++++++++  + +++ l    +++  ++++ + ++ +++++ ++ ++ ++  + +++++++l++el++ ++  ++
  gi|121638112|ref|YP_978336.1|  36 AYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTsgATDAKQLADLQHELDSLQRRQAS 112
                                    57888888888888888888888888888888888888888777766655334478888888888888776665544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0091
                          TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                    ++l++e+++l+ ++ +++  l e+ +  ++++ + + +++ l++l+++l   +++++ e   e+++ +++ +++
  gi|121638112|ref|YP_978336.1|  97 ADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALD-EALAEIDQARHQHSSQ 169
                                    556666666666666666666666666666666666666666666666666665543.3333333333333333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.62   2.5e+02      37      86 ..      20      75 ..       5      89 .. 0.37
   2 ?    7.5  11.5    0.0045       1.8      21     101 ..      93     170 ..      49     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.62
                          Atg14 37 ekeslkkkiekalegke......eaeqledkiknkkakleelksliadlrerlqel 86
                                   e   +  + + + ++        e + ++d+   ++ ++e+l  ++++ ++++  +
  gi|121638112|ref|YP_978336.1| 20 ELTRIAHRATHLPQRAAyqqvqaEHNAANDRMAALRIAAEDLDGQVSRFESEIDAV 75
                                   33333333332111111111111112333333333333333333333333333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                          Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                     ++l +l+++l +l+ +++sl+  + + le++e   +l+++   ++ +l+ l+++ a  ++ l e  + ++q + ++  +
  gi|121638112|ref|YP_978336.1|  93 AKQLADLQHELDSLQRRQASLEDALLEVLERRE---ELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQ 169
                                    335555666666666666666666666666665...55555555555555555555555555555555555555555555 PP

                          Atg14 101 k 101
                                    +
  gi|121638112|ref|YP_978336.1| 170 R 170
                                    5 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5      0.24        99       8      54 ..      11      60 ..       7      81 .. 0.64
   2 ?    8.1  11.4    0.0064       2.6      20      94 ..      95     169 ..      82     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                          Mod_r  8 Lqelledeeklealvk...tlpevkqlkeekeellaeneslaeknlslep 54
                                   L el + +  l ++++    lp+  ++++ + e  a+n ++a   ++ e+
  gi|121638112|ref|YP_978336.1| 11 LLELAKLDAELTRIAHratHLPQRAAYQQVQAEHNAANDRMAALRIAAED 60
                                   44555555555555555537799999999999999999999976665554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0064
                          Mod_r  20 alvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd 94 
                                    +l+ +l +e+++l+ ++ +l+++  +++e+  +l+ + + ++  lq+ +  l++++++++e  +e d++  + s++
  gi|121638112|ref|YP_978336.1|  95 QLA-DLqHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQ 169
                                    444.444889999999999999999999999999999999999999999999999999999999999999777765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.032        13     124     184 ..      13      75 ..       5      79 .. 0.87
   2 ?    4.6   6.3     0.062        25      87     181 ..      65     159 ..      64     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.032
                         DUF724 124 ekrkleeeidelekkilelerqlallk..ekkeaadkeiarlkseaekleeeledveqeFeav 184
                                    e +kl++e+  + ++  +l +++a  +  ++++aa+ ++a+l+  ae+l+ ++++ e+e +av
  gi|121638112|ref|YP_978336.1|  13 ELAKLDAELTRIAHRATHLPQRAAYQQvqAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAV 75 
                                    67899999*********999999887776778888999*****************99998877 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.062
                         DUF724  87 VkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkse 166
                                    V  ++s ++ + +  d+ ++ll+      k++++ ++e  +l+   + le + le+ ++++ l++++ a+++ + +l+++
  gi|121638112|ref|YP_978336.1|  65 VSRFESEIDAVRKRGDRDRSLLTSGATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRAD 144
                                    66777888888888888888888888889999999999999999999999999999999999999999************ PP

                         DUF724 167 aekleeeledveqeF 181
                                     ++++++l+++  e 
  gi|121638112|ref|YP_978336.1| 145 LAAAQQALDEALAEI 159
                                    *99999999887665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.8     0.019       7.8      68     130 ..      13      77 ..       6      83 .. 0.78
   2 ?    4.4  11.1     0.091        37      63     126 ..      90     153 ..      77     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                           ADIP  68 eierlqskierlktqleqlerela..lvqakerqlekklktleqklknekeelqrlknalqqikt 130
                                    e+++l ++  r   + + l +++a  +vqa+++ ++ ++++l  ++  +  +++r ++ ++++++
  gi|121638112|ref|YP_978336.1|  13 ELAKLDAELTRIAHRATHLPQRAAyqQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRK 77 
                                    5566666666666666665555544689999***************************9999986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                           ADIP  63 rkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalq 126
                                     +    ++ lq + ++l+++ ++le  l  v ++  +l++++++++++l+ ++ +l+  ++al+
  gi|121638112|ref|YP_978336.1|  90 ATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALD 153
                                    4555667788899999999999999999999999999999999999999999999998877765 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.5   6.1e+02      66      96 ..      17      47 ..       9      81 .. 0.54
   2 ?    7.5   4.2    0.0052       2.1      51     128 ..      91     168 ..      83     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                       ISG65-75 66 ienakekvdyyvekleslleeakekgtltes 96
                                   ++ ++ ++ ++ ++l+++ + ++ +++ +++
  gi|121638112|ref|YP_978336.1| 17 LDAELTRIAHRATHLPQRAAYQQVQAEHNAA 47
                                   4455555666666665555554333332222 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0052
                       ISG65-75  51 tadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaek 128
                                    t+ + l++ +++l++++  +++++  + ++ ++ ee ++++t+++ + + l+  +++A+++ ++a ++ ++a+ ++ +
  gi|121638112|ref|YP_978336.1|  91 TDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSS 168
                                    555556666666666777777766666666666666666677777666677666666666666666666666665543 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.59   2.4e+02      21      37 ..      38      54 ..       8      88 .. 0.49
   2 ?    4.4  10.2      0.11        44      10      51 ..      93     134 ..      85     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.59
                          Spc24 21 esleselaelkeeleel 37
                                   +++++e +  +++++ l
  gi|121638112|ref|YP_978336.1| 38 QQVQAEHNAANDRMAAL 54
                                   23333333333333333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                          Spc24  10 akelsdleselesleselaelkeeleeleeesee.keserved 51 
                                    ak+l dl+ el+sl+ ++a+l++ l e+ e +ee + ++++++
  gi|121638112|ref|YP_978336.1|  93 AKQLADLQHELDSLQRRQASLEDALLEVLERREElQ-AQQTAE 134
                                    89**************************99999952.333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2009  (0.112053); expected 358.6 (0.02)
Passed bias filter:                      908  (0.0506442); expected 358.6 (0.02)
Passed Vit filter:                       173  (0.00964917); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.98u 0.35s 00:00:01.33 Elapsed: 00:00:00.52
# Mc/sec: 1420.81
//
Query:       gi|121638113|ref|YP_978337.1|  [L=379]
Description: hypothetical protein BCG_2248c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-60  202.3   0.0    1.3e-59  201.9   0.0    1.1  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.9   0.0     7e-64   1.3e-59       1     242 [.       7     352 ..       7     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 7e-64
                           NIF3   1 eivevleelaplelaeswDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykkrl 80 
                                    ++++vl++ +p++la+swD vGl +gdp++ v +v +a+d+t++v++++ +  a l+++hHPl+++++++++++++k+ l
  gi|121638113|ref|YP_978337.1|   7 DVIDVLDQAYPPRLAQSWDSVGLVCGDPDDVVDSVTVAVDATPAVVDQVPQ--AGLLLVHHPLLLRGVDTVAANTPKGVL 84 
                                    699***********************************************9..99************************* PP

                           NIF3  81 lkkliknnislysaHtnlDaapgGvndwlakalglekieplepskeek................................ 128
                                    +++li+ + sl++aHtn D+a  Gv+d la+a+gl+   +l+p   +                                 
  gi|121638113|ref|YP_978337.1|  85 VHRLIRTGRSLFTAHTNADSASPGVSDALAHAVGLTVDAVLDPVPGAAdldkwviyvprenseavraavfeagaghigdy 164
                                    ************************************9999999887769999**************************** PP

                           NIF3 129 .......................................................................keeeeglgr 137
                                                                                                              + glgr
  gi|121638113|ref|YP_978337.1| 165 shcswsvagtgqflahdgaspaigsvgtvervaedrvevvapararaevlaamraahpyeepafdifalvpPPVGSGLGR 244
                                    ***********************************************************************99999**** PP

                           NIF3 138 igeleepvsleelakklkkkl..glekvrvagdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealda.kek 214
                                    ig+l++p  l++++ +l+++l   +++vr+agd+d  v++va+c+G+G+sl+ +++a+++ +++T++l+hh a +  +++
  gi|121638113|ref|YP_978337.1| 245 IGRLPKPEPLRTFVARLEAALppTATGVRAAGDPDLLVSRVAVCGGAGDSLLATVAAADVQAYVTADLRHHPADEHcRAS 324
                                    *********************533466***********************************************997999 PP

                           NIF3 215 giavidvgHyatErvflealaelLkekl 242
                                    ++a+idv H+a+E ++  + ae L++++
  gi|121638113|ref|YP_978337.1| 325 QVALIDVAHWASEFPWCGQAAEVLRSHF 352
                                    9***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2501.45
//
Query:       gi|121638114|ref|YP_978338.1|  [L=364]
Description: hypothetical protein BCG_2249c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-23   83.0   0.0      3e-23   82.6   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   1.7e-27     3e-23       5     339 ..      42     332 ..      38     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.7e-27
                                    ESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHH CS
                  Aminotran_1_2   5 nLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalieal 84 
                                    ++++n   +d     +pe++ ++   a+  ++l++y+ +d  + ++ a+a+ +g       +r+ +v+ + Ga ++ ++l
  gi|121638114|ref|YP_978338.1|  42 DFAVNVR-HD----RPPEWLVRQL--AALLPELARYPSTDDVHRAQDAVAERHG------RTRD-EVLPLVGAAEGFALL 107
                                    5555554.33....5777877775..59999***********************......6777.*************** PP

                                    HHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B CS
                  Aminotran_1_2  85 ifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtv 164
                                      l       +i+vp+  +++   +l ++g++ + + l+  + f ld  ++ +             +++v +p NPt ++
  gi|121638114|ref|YP_978338.1| 108 HNLSP--VRAAIVVPA--FTEPAIALSAAGITAHHVVLK--PPFVLDTAHVPD----------DADLVVVGNPTNPTSVL 171
                                    99995..555566655..666666777788887777777..99*********9..........4459************* PP

                                    --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                  Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsql 243
                                      +e+l +l    ++ + +l+vDea+a+ v g++      +++++    +l+++sl K ++laG+RvGy+lg+++v+  l
  gi|121638114|ref|YP_978338.1| 172 HLREQLLEL----RRPGRILVVDEAFADWVPGEP-----QSLADDSLPdVLVLRSLTKTWSLAGLRVGYALGSPDVLARL 242
                                    *********....888****************76.....4555555556******************************* PP

                                    HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHH CS
                  Aminotran_1_2 244 rklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskk 323
                                    +   +++     lq  + aa  ++  ++    + + rl ++r e++++L++ g +v++  + ++l+   +a     l   
  gi|121638114|ref|YP_978338.1| 243 TVQRAHWPL-GTLQLTAIAACCAPRAVA-AAAADAVRLTALRAEMVAGLRSVGAEVVDGAAPFVLFNIADAD---GLRNY 317
                                    988777665.556777777777777665.9999999******************************999999...89999 PP

                                    HHHTCTEEEEEGGGGT CS
                  Aminotran_1_2 324 Lleevgvyvtpgtsft 339
                                    L+ + g++v++g  f 
  gi|121638114|ref|YP_978338.1| 318 LQSK-GIAVRRGDTFV 332
                                    9999.*****998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2767.23
//
Query:       gi|121638115|ref|YP_978339.1|  [L=291]
Description: hypothetical protein BCG_2250 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-31  109.3   0.0    2.9e-31  108.9   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    2.3e-16   60.8   0.3    2.9e-15   57.1   0.3    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    7.8e-12   46.0   0.2    1.3e-11   45.2   0.2    1.4  1  HAD             haloacid dehalogenase-like hydrolase
    2.6e-08   33.8   0.6    5.7e-08   32.7   0.6    1.6  1  Hydrolase_like  HAD-hyrolase-like
      0.001   19.0   0.0      0.023   14.6   0.0    2.1  1  Acid_PPase      Acid Phosphatase
     0.0062   16.3   0.0        1.5    8.5   0.0    2.3  2  Hydrolase_3     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0   9.6e-35   2.9e-31       1     178 []      82     258 ..      82     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 9.6e-35
                          HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkp 80 
                                    +iFDlDgTl d+   i+++f+++l++ g + ++ +   +++g++++e+lr +g  e  ee i  ++ +y ++    + ++
  gi|121638115|ref|YP_978339.1|  82 VIFDLDGTLTDSARGIVSSFRHALNHIGAPVPEGDLATHIVGPPMHETLRAMGLGESAEEAIVAYRADYSARGWA-MNSL 160
                                    7****************************9999999999****************999*****************.**** PP

                          HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGD 160
                                    +dg+  lL +L+ ag++l+++Tsk + ++++ l+++gie++F+vi ++++ + +  + +v++ al +l   +e+ ++vGD
  gi|121638115|ref|YP_978339.1| 161 FDGIGPLLADLRTAGVRLAVATSKAEPTARRILRHFGIEQHFEVIAGASTDGSRGSKVDVLAHALAQLRPLPERLVMVGD 240
                                    ***********************************************9999988667*********************** PP

                          HAD_2 161 sptDieaakkagikviav 178
                                     ++D+ +a + gi++++v
  gi|121638115|ref|YP_978339.1| 241 RSHDVDGAAAHGIDTVVV 258
                                    ***************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.3   9.7e-19   2.9e-15       3     210 .]      81     252 ..      79     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 9.7e-19
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..HHHHHETTTEHHHHTHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal..tgfatfigrgayaigkpewltal 80 
                                    +v+fD+dGTLt++ + ++  ++ a                        ++++ ++   + at      +     e l+a+
  gi|121638115|ref|YP_978339.1|  81 LVIFDLDGTLTDSARGIVSSFRHA-----------------------LNHIGAPVpeGDLAT----HIVGPPMHETLRAM 133
                                    79*********9996666666666.......................555544442144444....14444455556666 PP

                                    HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddy 159
                                              g  +s+ +  +    ra+        +++++++  ++a L+ ag++++++t+  + ta+r+++++G +++
  gi|121638115|ref|YP_978339.1| 134 ----------GLGESAEEAIVAY--RADYSARGWAMNSLFDGIGPLLADLRTAGVRLAVATSKAEPTARRILRHFGiEQH 201
                                    ..........6666666666666..6666666666666****************************************** PP

                                    ESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 160 fdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    f+++ ++++++  + + + + +a+ +L+  pe+ +mVGD+  D+ ++aa g
  gi|121638115|ref|YP_978339.1| 202 FEVIAGASTDGSRGSKVDVLAHALAQLRPLPERLVMVGDRSHDVDGAAAHG 252
                                    ****************************99******************987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   4.4e-15   1.3e-11       1     185 [.      82     246 ..      82     249 .. 0.66

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.4e-15
                            HAD   1 alfDfDgTLldgdsle.....lllrfllrrgaprlwralrek.....lllalfrellrldraglaelleallaglseela 70 
                                    ++fD+DgTL+d+  ++     +     l + + +  +  +++     ++   +r ++    ++++e++ a+ a++s    
  gi|121638115|ref|YP_978339.1|  82 VIFDLDGTLTDSARGIvssfrH----ALNHIGAPVPEGDLAThivgpPMHETLRAMGLG--ESAEEAIVAYRADYS---- 151
                                    79**********7777654432....444443333333333321222333334444444..344444444444444.... PP

                            HAD  71 aelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvr 150
                                    a+  ++        l+  g+  lla  r aG+r++v ++  +p ++++l+++g    +        ++   +g + + +r
  gi|121638115|ref|YP_978339.1| 152 ARGWAMN------SLF-DGIGPLLADLRTAGVRLAVATSKAEPTARRILRHFG----IEQ------HFEVIAGASTDGSR 214
                                    3333333......245.8***********************************....***......55555556888899 PP

                            HAD 151 gegkvaalrewlaaegegidleevvayGDspsDlp 185
                                    g  kv++l+   a +   + +e++v +GD  +D+ 
  gi|121638115|ref|YP_978339.1| 215 G-SKVDVLAH--ALAQLRPLPERLVMVGDRSHDVD 246
                                    9.99999999..444455556779*********96 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.6   1.9e-11   5.7e-08      10      59 ..     221     269 ..     217     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.9e-11
                                    HHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHH CS
                 Hydrolase_like  10 ydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedle 59 
                                    +  al++l   pe+ +m+GDr  +D+ gA ++G+++v V  G  r++   
  gi|121638115|ref|YP_978339.1| 221 LAHALAQLRPLPERLVMVGDR-SHDVDGAAAHGIDTVVVGWGYGRADFID 269
                                    66799999999**********.********************98875433 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.5e-06     0.023       2      87 ..      78     200 ..      77     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.5e-06
                                    --SEEEE-STTTSSSS-TTTS.......................S-S-EEE-TTS..........-EE......ETT--E CS
                     Acid_PPase   2 lpklivFDLDyTLWpfevdtl.......................vsaplkkeskks.........evv......Drrgee 43 
                                     p+l++FDLD TL +    ++                       v++p++++ + +           v       +rg  
  gi|121638115|ref|YP_978339.1|  78 SPQLVIFDLDGTLTDSARGIVssfrhalnhigapvpegdlathiVGPPMHETLRAMglgesaeeaI-VayradySARGWA 156
                                    599**********98888777899999999999999999999998888888888876676666641.2344433344444 PP

                                    E.---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G. CS
                     Acid_PPase  44 l.klypdveeileelkskevklavaSrtdepdlarelLklleind 87 
                                    + +l++    +l++l++++v+lava + +ep  ar++L+++ i++
  gi|121638115|ref|YP_978339.1| 157 MnSLFDGIGPLLADLRTAGVRLAVATSKAEP-TARRILRHFGIEQ 200
                                    42689999999999999********998888.5999*****9991 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0005       1.5       1      26 [.      82     107 ..      82     110 .. 0.89
   2 !    5.5   0.0    0.0041        12      24      67 ..     168     211 ..     165     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0005
                                    EEEEIIIIIS-TTS---HHHHHHHHH CS
                    Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikk 26 
                                    +++DlDGTL +s   i  + ++a++ 
  gi|121638115|ref|YP_978339.1|  82 VIFDLDGTLTDSARGIVSSFRHALNH 107
                                    69***********9999999999875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0041
                                    HHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEE CS
                    Hydrolase_3  24 ikklkekgikvviATGRslravlpvleelgldlpvialNGalid 67 
                                    ++ l+ +g+ +++AT     +++++l+++g+++++    Ga +d
  gi|121638115|ref|YP_978339.1| 168 LADLRTAGVRLAVATSKAEPTARRILRHFGIEQHFEVIAGASTD 211
                                    6778999*************************999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2077.61
//
Query:       gi|121638116|ref|YP_978340.1|  [L=163]
Description: phosphotyrosine protein phosphatase ptpA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-46  158.0   0.0    2.2e-46  157.8   0.0    1.0  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0   1.2e-50   2.2e-46       1     140 [.       7     148 ..       7     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 1.2e-50
                                    EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTST.TT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSS CS
                          LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgal.vgkradpravevlkekgislsghvarqlskeelaelD 79 
                                    v+fvC+gNicRSpmAe++f ++l+++gl+++v+v+SaGtg++ vg++ad+ra+ vl+ +g++++ h+a q+ +e+la +D
  gi|121638116|ref|YP_978340.1|   7 VTFVCTGNICRSPMAEKMFAQQLRHRGLGDAVRVTSAGTGNWhVGSCADERAAGVLRAHGYPTD-HRAAQVGTEHLA-AD 84 
                                    79**************************************************************.***********9.** PP

                                    EEEESSHHHHHHHHHHCCTTGGGGEEEGGGG.....SSTSS---HTTSSHHHHHHHHHHHHHHHHH CS
                          LMWPc  80 lilamdeenkreleslapekekakvkllgey.....teqldieDPyygeieafeevldeieeavkk 140
                                    l++a+d++++r l++l +e  +a+v++l+++     t+ ld+eDPyyg++++feev++ ie+a+  
  gi|121638116|ref|YP_978340.1|  85 LLVALDRNHARLLRQLGVE--AARVRMLRSFdprsgTHALDVEDPYYGDHSDFEEVFAVIESALPG 148
                                    *******************..79*************9************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1063.91
//
Query:       gi|121638117|ref|YP_978341.1|  [L=271]
Description: hypothetical protein BCG_2252 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-24   87.1   0.0    2.2e-24   86.7   0.0    1.1  1  SURF1     SURF1 family
  ------ inclusion threshold ------
      0.088   13.0   1.2        6.1    7.1   1.0    2.7  3  DUF4381   Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> SURF1  SURF1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   2.5e-28   2.2e-24       4     175 ..      24     225 ..      21     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 2.5e-28
                          SURF1   4 vvvlfgLGtWQlqRlkwkealiaeleerlaaeplplleka...leale.efeyrrvtvtGrfdhdkevlvgngqprv... 76 
                                    ++++++L+ WQl + ++  + +++++  l+ +p+pl +     +++ + ++++rrvt+tG++  d +vl +    rv   
  gi|121638117|ref|YP_978341.1|  24 YLCFTVLAPWQLGKNAKTSRENQQIRYSLDTPPVPLKT-LlpqQDSSApDAQWRRVTATGQYLPDVQVLARL---RVveg 99 
                                    57899****************************99833.35654444569************9998888773...43444 PP

                          SURF1  77 ..GylvltplrleddgeavlVnrGWvpaea.eklpka.apegeevrevtGllr..ksstp....ape..eesgewqvqsi 144
                                      +++vl p+++ d g++vlV+rG+v  +  +++p   + + ++v+ +t++lr  +   p    +++  ++  + qv+si
  gi|121638117|ref|YP_978341.1| 100 dqAFEVLAPFVV-DGGPTVLVDRGYVRPQVgSHVPPIpRLPVQTVT-ITARLRdsE---PsvagKDPfvRDGFQ-QVYSI 173
                                    55**********.88***********88666666554755556788.******431...222342224333333.89*** PP

                          SURF1 145 dvaalaealgaq..............kvlpvvl............hlgYaltWfgla 175
                                    ++ ++a+ +g q                    l             l+Y ++W++++
  gi|121638117|ref|YP_978341.1| 174 NTGQVAALTGVQlagsylqliedqpgG-----LgvlgvphldpgpFLSYGIQWISFG 225
                                    ********8655555555555444440.....14444555555559*********98 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.0   0.00068       6.1      16      47 ..       7      41 ..       2      63 .. 0.70
   2 ?   -2.2   0.0      0.51   4.6e+03     101     125 ..      63      87 ..      59      98 .. 0.75
   3 ?    3.1   0.0     0.011     1e+02      20      47 ..     218     246 ..     207     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00068
                        DUF4381 16 PpapGwwlllaalll...llllvlalwllrrrkrn 47
                                    + pGw +l++++++   l++ vla w+l ++ + 
  gi|121638117|ref|YP_978341.1|  7 LLRPGWLALALVVVAftyLCFTVLAPWQLGKNAKT 41
                                   5789*999997777776666666666666544443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.51
                        DUF4381 101 LdatlpakgfasgaralleaaYrpe 125
                                    L ++  ++ +a+++r+ +++ Y p+
  gi|121638117|ref|YP_978341.1|  63 LPQQDSSAPDAQWRRVTATGQYLPD 87 
                                    6677777888888888888888877 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.011
                        DUF4381  20 Gwwlllaalll.llllvlalwllrrrkrn 47 
                                    G   + +++l+ ++l ++a+  +r r+r+
  gi|121638117|ref|YP_978341.1| 218 GIQWISFGILApIGLGYFAYAEIRARRRE 246
                                    444444478888***********977763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2225.66
//
Query:       gi|121638118|ref|YP_978342.1|  [L=313]
Description: cobalamin biosynthesis protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-88  294.5   1.3      8e-88  294.2   1.3    1.0  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   1.3   4.4e-92     8e-88       2     275 ..      14     292 ..      13     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 4.4e-92
                      CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvallllllalaallglvlealll 81 
                                    l+++llD+++gdp+r  hPv+l+g+++++le+++++  + r+aG++++ llv++++l++++l++l    +  ++++a ++
  gi|121638118|ref|YP_978342.1|  14 LIGCLLDVVFGDPKR-GHPVALFGRAAAKLEQITYR--DGRVAGAVHVGLLVGAVGLLGAALQRLPGRCW-PVAATATAT 89 
                                    789**********98.6***************9875..5799*********************9653223.36899**** PP

                      CobD_Cbib  82 kltlalrsLleevrkvakalk.gdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflllglpgal 160
                                    +++l+++sL++++r++ + l+ +d+eaaR+ +  ++gRd+++l  ++++rAa+EsvaEN++D+ v Pl++++  g+p++l
  gi|121638118|ref|YP_978342.1|  90 WAALGGTSLARTGRQISDLLErDDVEAARRLLPSLCGRDPAQLGGPGLTRAALESVAENTADAQVVPLLWAASSGVPAVL 169
                                    ********************6599******************************************************** PP

                      CobD_Cbib 161 aykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.........aalriarrdarkhpSpNsgwpea 231
                                     y+a+nTlDsm+GY+++ry +fGwaaArlDD++ny+ AR ta+l+++           a+r++rrda++hpSpN+g++ea
  gi|121638118|ref|YP_978342.1| 170 GYRAINTLDSMIGYRSPRYLRFGWAAARLDDWANYVGARATAVLVVICapvvggsprGAVRAWRRDAARHPSPNAGVVEA 249
                                    **********************************************9555666666677********************* PP

                      CobD_Cbib 232 alAgalgvrLggpnvYlgkleekptlgdkkrpleaedieralrl 275
                                    a+Agal+vrLggp++Y+++l+ +ptlgd++  ++++d++ra+ l
  gi|121638118|ref|YP_978342.1| 250 AFAGALDVRLGGPTRYHHELQIRPTLGDGRS-PKVADLRRAVVL 292
                                    ***************************9855.5********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2257.76
//
Query:       gi|121638119|ref|YP_978343.1|  [L=255]
Description: hypothetical protein BCG_2254 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-43  147.1   5.0    1.1e-42  146.8   5.0    1.0  1  DUF2236   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   5.0   6.1e-47   1.1e-42      15     226 ..       5     222 ..       1     224 [. 0.91

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 6.1e-47
                        DUF2236  15 laalllqaahplvltgvldh...s.tf.adplrRllrTaqfiltvvygsgeeaeaaaarVrllHaavrgtdasgerygai 89 
                                     a++++q+a p+v+ gvl++   s ++  +p++R ++T+++++ ++ g+++++  +   V  +H++vr+t +s+  y+a+
  gi|121638119|ref|YP_978343.1|   5 AANVIMQLAVPGVGYGVLESpvdSgNVyKHPFKRARTTGTYLAVATIGTESDRALIRGAVDVAHRQVRSTASSPVSYNAF 84 
                                    4789**************777665466466*****************************************99******* PP

                        DUF2236  90 npedllwvhatfsasflraygrtvgpltaeeeeayyhewrrvgrllGvpdrllpatraafdayldemvlaelevdeeare 169
                                    +p+++lwv+a+++  f++ ++ ++gpl ++ ++a+y++++r+g++l+vp++++p +r afd+y+ +  l+ l++d+++re
  gi|121638119|ref|YP_978343.1|  85 DPKLQLWVAACLYRYFVDQHEFLYGPLEDATADAVYQDAKRLGTTLQVPEGMWPPDRVAFDEYWKRS-LDGLQIDAPVRE 163
                                    *********************99******************************99************.6*********** PP

                        DUF2236 170 l....gdarll.......parpalpllrvitrgllppalrellglpvpwssrdellvvalralvrlar 226
                                         +            ++ +a+p+  ++t+g+l p++r +++l+  ws +++++   + +l  ++r
  gi|121638119|ref|YP_978343.1| 164 HlrgvA----SvaflpwpLRAVAGPFNLFATTGFLAPEFRAMMQLE--WSQAQQRR---FEWLLSVLR 222
                                    955552....0445567678999***********************..********...888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1920.91
//
Query:       gi|121638120|ref|YP_978344.1|  [L=153]
Description: peroxiredoxin AhpE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-33  112.9   0.0    9.9e-33  112.7   0.0    1.0  1  AhpC-TSA  AhpC/TSA family
    2.8e-18   66.1   0.0    3.3e-18   65.8   0.0    1.0  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   1.1e-36   9.9e-33       1     123 [.       4     129 ..       4     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.1e-36
                                    TTSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH CS
                       AhpC-TSA   1 vgdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiek 79 
                                    vg  apdf+l +++++ v+l  y+g k v+l+f+p +++  C+ el +l+++++ef++ +   +++sv +p +hk ++ +
  gi|121638120|ref|YP_978344.1|   4 VGATAPDFTLRDQNQQLVTLRGYRGaKNVLLVFFPLAFTGICQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWATQ 83 
                                    7999*********************9****************************************************** PP

                                    -H.SSEEEE-..TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  80 eslnfpllsD..eegkvakaygvlkeekglalratfvidkegkiry 123
                                     +++fpllsD  ++g+v++aygv++e++g+a r+tfv+d+ g+ir+
  gi|121638120|ref|YP_978344.1|  84 SGFTFPLLSDfwPHGAVSQAYGVFNEQAGIANRGTFVVDRSGIIRF 129
                                    ********************************************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   3.6e-22   3.3e-18       2     133 ..       4     133 ..       3     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.6e-22
                                    TTSBB---ECCEETTCEEEEEHHHHTTSE.EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                        Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkk.vvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefw 80 
                                    +g++aPdftl +  ++++ v+l+ ++g k v+++f+p af++ C+ e+ +l++  +++++ +   +a+++   +  k ++
  gi|121638120|ref|YP_978344.1|   4 VGATAPDFTLRD--QNQQLVTLRGYRGAKnVLLVFFPLAFTGICQGELDQLRDHLPEFENDDSAALAISVGPPPTHKIWA 81 
                                    799******988..**********999887999****************9999988879999999888888888888888 PP

                                    HHTT-TSEEEE-..TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEES CS
                        Redoxin  81 gkeglkfpvlsD..gsaaftkalGlrleedaseglrtpryavidedgkvvyleve 133
                                    ++ g +fp+lsD  + +a+++a+G+      ++g++ + ++v+d+ g ++  e  
  gi|121638120|ref|YP_978344.1|  82 TQSGFTFPLLSDfwPHGAVSQAYGVF---NEQAGIANRGTFVVDRSGIIRFAEMK 133
                                    88************9*********44...334569**************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1151.45
//
Query:       gi|121638121|ref|YP_978345.1|  [L=158]
Description: hypothetical protein BCG_2256c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-55  186.3   3.0    1.9e-55  186.1   3.0    1.1  1  DUF3052   Protein of unknown function (DUF3052)


Domain annotation for each model (and alignments):
>> DUF3052  Protein of unknown function (DUF3052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.1   3.0   1.1e-59   1.9e-55       1     125 []      29     152 ..      29     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.1 bits;  conditional E-value: 1.1e-59
                        DUF3052   1 aeklglkagqvvqelgwDdDvdedlreaiedligeelvdedadevvDvvllWwrddDgdLvdalvdaltsLadegviwll 80 
                                    a+klg++++q++qe+gwD+D+d+d+r+aie+++g el+ded+dev+DvvllWwrd+DgdLvd+l+da+++La++gviw++
  gi|121638121|ref|YP_978345.1|  29 ARKLGIQRDQLIQEWGWDEDTDDDIRAAIEEACGGELLDEDTDEVIDVVLLWWRDGDGDLVDTLMDAIGPLAEDGVIWVV 108
                                    789***************************************************************************** PP

                        DUF3052  81 tpkagreghvepseiaeaaktaGLvqtssvsvskdwsgtrlvark 125
                                    tpk+g++ghv p+eiaeaa+taGL  tssv+++ +ws++rlv++k
  gi|121638121|ref|YP_978345.1| 109 TPKTGQPGHVLPAEIAEAAPTAGLMPTSSVNLG-NWSASRLVQPK 152
                                    *********************************.********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1188.68
//
Query:       gi|121638122|ref|YP_978346.1|  [L=265]
Description: hypothetical protein BCG_2257c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1952.65
//
Query:       gi|121638123|ref|YP_978347.1|  [L=901]
Description: pyruvate dehydrogenase subunit E1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.6e-111  369.2   0.1   1.2e-110  368.5   0.1    1.3  1  PDH_E1_M         Pyruvate dehydrogenase E1 component middle d
      4e-14   52.3   0.0    4.4e-10   39.0   0.0    2.3  2  Transketolase_N  Transketolase, thiamine diphosphate binding 
     0.0096   15.8   0.4      0.029   14.2   0.1    1.9  2  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> PDH_E1_M  Pyruvate dehydrogenase E1 component middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.5   0.1    2e-114  1.2e-110       1     229 []     477     704 ..     477     704 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.5 bits;  conditional E-value: 2e-114
                       PDH_E1_M   1 lelpdeddktyeiqrkgsktrevattmafvrvlkdlvkdkkigkrvvpiipdeartfgmealfrtlkiytsegqkyesvd 80 
                                    l+lp  d   y+  +kgs+ +evattma vr +k++++dk+ig r+vpiipdeartfgm++ f++lkiy+ +gq y +vd
  gi|121638123|ref|YP_978347.1| 477 LTLPGRDI--YAPLKKGSGHQEVATTMATVRTFKEVLRDKQIGPRIVPIIPDEARTFGMDSWFPSLKIYNRNGQLYTAVD 554
                                    57777776..999******************************************************************* PP

                       PDH_E1_M  81 knlilsykedkegqileegiteagavaafiaaassydthdltllpvyvyysmfgfqrvgdliwaaadqlargflvgatag 160
                                    ++l+l yke++ gqil+egi+eag+v +fiaa++sy th+ +++p+y++ysmfgfqr+gd+ waaadq+argf++gatag
  gi|121638123|ref|YP_978347.1| 555 ADLMLAYKESEVGQILHEGINEAGSVGSFIAAGTSYATHNEPMIPIYIFYSMFGFQRTGDSFWAAADQMARGFVLGATAG 634
                                    ******************************************************************************** PP

                       PDH_E1_M 161 kttlageglqhqdghshllaasipavvsydpayayevavlvaeglkrmyae.kenviyyltvlnenlvqp 229
                                    +ttl+geglqh dghs llaa++pavv+ydpa+aye+a++v+ gl rm +e  en+++y+tv+ne++vqp
  gi|121638123|ref|YP_978347.1| 635 RTTLTGEGLQHADGHSLLLAATNPAVVAYDPAFAYEIAYIVESGLARMCGEnPENIFFYITVYNEPYVQP 704
                                    ***************************************************89***************98 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   7.4e-14   4.4e-10      59     222 ..     136     302 ..      79     310 .. 0.85
   2 !   10.9   0.0   2.6e-05      0.16     214     260 ..     362     409 ..     351     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 7.4e-14
                                    EESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-S......S--TTTSTT--S---STTHHHHHHHHHHHHHHHHH CS
                Transketolase_N  59 vLsnGhaslllYsllhLtGydlsledlksfrqlgsktpG......hPelghtagvevttGPLGqGianavglalaektla 132
                                    v  +Ghas  +Y+  +L G  l+ e+l  frq +s+  G      hP l   +  e  t  +G G  na+  a+ ++ l 
  gi|121638123|ref|YP_978347.1| 136 VFIQGHASPGIYARAFLEG-RLTAEQLDGFRQEHSHVGGglpsypHPRLMP-DFWEFPTVSMGLGPLNAIYQARFNHYLH 213
                                    6779***************.69*************9876544444444333.345999************9999999998 PP

                                    HHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGG..GT--S-HHHHHHHTT-EE CS
                Transketolase_N 133 atynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGete..isftedvakrfeaygWhv 210
                                    ++     +d +d++++++lgDg + e  s   + + +  +L++L  + + n   +dG +     + ++ ++ f+  gW+v
  gi|121638123|ref|YP_978347.1| 214 DRGI---KDTSDQHVWCFLGDGEMDEPESRGLAHVGALEGLDNLTFVINCNLQRLDGPVRgnGKIIQELESFFRGAGWNV 290
                                    7665...6789**********************************************9962256889************* PP

                                    EEETTTT-HHHH CS
                Transketolase_N 211 ievedgedveai 222
                                    i+v  g +  a+
  gi|121638123|ref|YP_978347.1| 291 IKVVWGREWDAL 302
                                    **9888776665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 2.6e-05
                                    TTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTST.TTTTSGGGTS CS
                Transketolase_N 214 edgedveaikaaieeakaekdkPsliklrtviGygsp.akagtedvhG 260
                                    ++g+d +++ aa ++a  +k +P++i  +t+ Gy+     +g +++h 
  gi|121638123|ref|YP_978347.1| 362 RGGHDYRKVYAAYRAAVDHKGQPTVILAKTIKGYALGkHFEGRNATHQ 409
                                    599******************************986415577777775 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.7e+03      69      86 ..      95     112 ..      87     118 .. 0.73
   2 !   14.2   0.1   4.9e-06     0.029       3      54 ..     724     776 ..     723     784 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                    EEESTTSHHHHHHHHHHH CS
                Transketolase_C  69 eavkrgGigsevaaalae 86 
                                     +++ +G+g +++++ + 
  gi|121638123|ref|YP_978347.1|  95 AQRPGVGVGGHISTYASS 112
                                    5567789******99887 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.9e-06
                                    EEEEETTSSEEEEEETTHHHHHHHHHHHHHTT.TTCEEEEE-SEEESHHHHHH CS
                Transketolase_C   3 aeilregkdvtlvayGsmveealeAaeeLeke.gisaeVvdlrtvkplDketi 54 
                                    a +++  ++  ++a G  ++ al+Aa++L++e  + a+V+++ +   l ++ +
  gi|121638123|ref|YP_978347.1| 724 AATEQRTNKAQILASGVAMPAALRAAQMLAAEwDVAADVWSVTSWGELNRDGV 776
                                    5677889999******************************9998777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (901 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 6540.27
//
Query:       gi|121638124|ref|YP_978348.1|  [L=414]
Description: hypothetical protein BCG_2259 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   76.1   0.0    3.9e-21   74.6   0.0    1.9  1  HTH_30    PucR C-terminal helix-turn-helix domain
    1.1e-15   57.9   0.5    6.5e-15   55.4   0.1    2.3  2  GGDEF_2   GGDEF-like domain
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.52   10.1   0.0    2.1  2  HTH_8     Bacterial regulatory protein, Fis family


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   6.5e-25   3.9e-21       1      57 [.     347     403 ..     347     405 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 6.5e-25
                                    ...HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSHHHHHHHHHHH CS
                         HTH_30   1 LleTLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddpddrlaLylAl 57 
                                    L+eTL+ayl++gg i+ +A++L+vH+nT+ryRL+ri + +g+d+++p+d++ L +A 
  gi|121638124|ref|YP_978348.1| 347 LIETLDAYLDCGGAIETCARKLFVHPNTVRYRLKRITDFTGRDPTQPRDAYVLRVAA 403
                                    79***************************************************9995 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.23   1.4e+03      34      58 ..      23      47 ..       6      79 .. 0.79
   2 !   55.4   0.1   1.1e-18   6.5e-15       2     111 ..     180     295 ..     179     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                        GGDEF_2 34 aerllraleealralgpdalvavrg 58
                                   +++llr+l+++  +l+ +a+ a+++
  gi|121638124|ref|YP_978348.1| 23 PDSLLRRLKQYSGRLATEAVSAMQE 47
                                   5678888888888888888877754 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 1.1e-18
                        GGDEF_2   2 grsdeellerarrlgldldgpyvvvviel.........eedaerllraleealralgpdalvavrgdrlvlllpaedeed 72 
                                    g++ +ell+ra++l++d ++p +v+v ++         ++d+er+ + +++ ++++g+ al+ v+g  lv++++++ ++ 
  gi|121638124|ref|YP_978348.1| 180 GDTGPELLSRAAALNWDTTAPATVLVGTPapgpngsnsDGDSERASQDVRDTAARHGRAALTDVHGTWLVAIVSGQLSP- 258
                                    667789**********************9888877765559999*********************************85. PP

                        GGDEF_2  73 aeallerlarrlgglsvriGiGspveglaglrrSyreAr 111
                                     e++l++l++++++  + + iG++++ l+ ++rS  eA 
  gi|121638124|ref|YP_978348.1| 259 TEKFLKDLLAAFAD--APVVIGPTAPMLTAAHRSASEAI 295
                                    69**********99..*********************96 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   1.7e+03      34      42 .]      25      33 ..      17      33 .. 0.81
   2 ?   10.1   0.0   8.7e-05      0.52      17      41 ..     357     381 ..     351     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                                   HHHHHHHHT CS
                          HTH_8 34 tLyrKLkkY 42
                                   +L r+Lk+Y
  gi|121638124|ref|YP_978348.1| 25 SLLRRLKQY 33
                                   788*****9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.7e-05
                                    TTT-HHHHHHHHTS-HHHHHHHHHH CS
                          HTH_8  17 tgGnkskAArlLGisRrtLyrKLkk 41 
                                    +gG +  +Ar L ++++t++++Lk+
  gi|121638124|ref|YP_978348.1| 357 CGGAIETCARKLFVHPNTVRYRLKR 381
                                    78999999****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3420.36
//
Query:       gi|121638125|ref|YP_978349.1|  [L=302]
Description: malonyl CoA-ACP transacylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-22   79.7   3.8    3.5e-22   79.3   3.8    1.0  1  Acyl_transf_1  Acyl transferase domain
  ------ inclusion threshold ------
        4.8    7.4   9.3         17    5.6   0.9    3.4  3  Attacin_N      Attacin, N-terminal region


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   3.8   3.9e-26   3.5e-22       5     280 ..       7     283 ..       4     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 3.9e-26
                                    --TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHH..HHTT. CS
                  Acyl_transf_1   5 sGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaell..kskG. 81 
                                    +GqGsQ  GM    l+  + +a+ ia+  +a    +++ ++ + + + + +++++ ++qp ++a  + + + l  ++   
  gi|121638125|ref|YP_978349.1|   7 PGQGSQTEGMLSPWLQL-PGAADQIAAWSKA----ADLDLARLGTTASTEEITDTAVAQPLIVAATLLAHQELarRCVLa 81 
                                    8****************.9999999987654....788888888888888**********98777665555553544435 PP

                                    -TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHT..S-EECCEECS..HHHHHHH...TT.EEEEEEECCC CS
                  Acyl_transf_1  82 vrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqla..gpgdmaavel.aeeeeklr.cqddvvgavansprr 157
                                     ++ +v+GHS+GE+Aa + ag + + +a+  +++r+  m+++    p +m av   +e+e   r  q d+v+a  n  ++
  gi|121638125|ref|YP_978349.1|  82 GKDVIVAGHSVGEIAAYAIAGVIAADDAVALAATRGAEMAKACatEPTGMSAVLGgDETEVLSRlEQLDLVPANRNAAGQ 161
                                    78999********************************9998754589999999887899999999999************ PP

                                    CECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHH CS
                  Acyl_transf_1 158 vvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeyw 237
                                    +v++g   al++l e+  ++  +++   v  a+h ++++++ d  a+a a+ia   p+ +  s +  ++ +      +  
  gi|121638125|ref|YP_978349.1| 162 IVAAGRLTALEKLAEDPPAKA-RVRALGVAGAFHTEFMAPALDGFAAAAANIATADPTATLLSNRDGKPVTSAAAAMDTL 240
                                    ********************9.99999***************************************************** PP

                                    HHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCH CS
                  Acyl_transf_1 238 vanlrspvrfaeavlsaaetiplvfveispHslllaalektlk 280
                                    v  l +pvr +   + ++e    ++ve +p  +l  + ++ l+
  gi|121638125|ref|YP_978349.1| 241 VSQLTQPVRWDLCTATLREHTVTAIVEFPPAGTLSGIAKRELR 283
                                    ***************99*************9999888877776 PP

>> Attacin_N  Attacin, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.9    0.0019        17      21      50 ..      92     121 ..      81     127 .. 0.85
   2 ?    0.9   0.0     0.058   5.2e+02      25      39 ..     155     169 ..     147     191 .. 0.80
   3 ?    4.0   0.6    0.0059        53      10      50 ..     203     237 ..     197     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0019
                      Attacin_N  21 lgtpdhnvlaqvFAagntqagpvtsGgtla 50 
                                    +g+  + ++a+v Aa ++ a+ +t G+  a
  gi|121638125|ref|YP_978349.1|  92 VGEIAAYAIAGVIAADDAVALAATRGAEMA 121
                                    67777889******************9766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.058
                      Attacin_N  25 dhnvlaqvFAagntq 39 
                                    + n+ +q+ Aag  +
  gi|121638125|ref|YP_978349.1| 155 NRNAAGQIVAAGRLT 169
                                    6899******99755 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0059
                      Attacin_N  10 tGgAdarlkltlgtpdhnvlaqvFAagntqagpvtsGgtla 50 
                                    +G A a++++ +++p + +l+      n +++pvts++ + 
  gi|121638125|ref|YP_978349.1| 203 DGFAAAAANIATADPTATLLS------NRDGKPVTSAAAAM 237
                                    789999999999999999999......999******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2032.22
//
Query:       gi|121638126|ref|YP_978350.1|  [L=115]
Description: acyl carrier protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-17   62.6   0.1    5.4e-17   61.9   0.1    1.3  1  PP-binding     Phosphopantetheine attachment site
    0.00036   20.6   0.0    0.00044   20.3   0.0    1.2  1  Ribosomal_L50  Ribosomal subunit 39S
  ------ inclusion threshold ------
      0.052   13.8   1.8       0.49   10.7   0.2    2.1  2  HalOD1         Halobacterial output domain 1
       0.11   13.3   0.0       0.15   12.8   0.0    1.3  1  Herpes_US12    Herpesvirus US12 family


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   1.2e-20   5.4e-17       3      67 .]      12      77 ..      10      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.2e-20
                     PP-binding  3 lrelvaevlgvpleeidpdtdlf.dlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                   + e+++ev+g++++ei+p+ ++  dl +DSl++ve++++ e+++gv+ip++dl  ++t+++++ay+
  gi|121638126|ref|YP_978350.1| 12 IAEIIEEVTGIEPSEITPEKSFVdDLDIDSLSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYI 77
                                   889********************77****************************99*********98 PP

>> Ribosomal_L50  Ribosomal subunit 39S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.9e-08   0.00044      37     104 ..      40      99 ..       3     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.9e-08
                  Ribosomal_L50  37 DlelKFaflkrlqqllgheipDykltklhtvkdlveyleevvnpkpkklaerlpnaielrsedfklpN 104
                                    D     +++ +   + g  ipD  l+ l tv d+v y+        +kl e++p+a +  + + +++N
  gi|121638126|ref|YP_978350.1|  40 DSLSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYI--------QKLEEENPEAAQALRAKIESEN 99 
                                    5555667777788999**********************........9999999999887777777766 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00011      0.49       2      36 ..       5      42 ..       4      55 .. 0.83
   2 ?    2.9   0.1     0.031   1.4e+02       8      39 ..      72     103 ..      68     115 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                         HalOD1  2 eespstaVveavaavegvdptelep...LydaiDpdAL 36
                                   +e++   ++e + +v+g +p e+ p     d  D d L
  gi|121638126|ref|YP_978350.1|  5 QEEIIAGIAEIIEEVTGIEPSEITPeksFVDDLDIDSL 42
                                   6788999****************996666666666666 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.031
                         HalOD1   8 aVveavaavegvdptelepLydaiDpdALdaL 39 
                                     Vv+ + ++e+++p++ + L   i  +  da+
  gi|121638126|ref|YP_978350.1|  72 DVVAYIQKLEEENPEAAQALRAKIESENPDAV 103
                                    69999999999999999999998865444433 PP

>> Herpes_US12  Herpesvirus US12 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05      0.15      17      42 ..      65      90 ..      48     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                   SS---HHHHHHHHHHT--XXXXXXXX CS
                    Herpes_US12 17 vthrtyadvrdeinkreredreaart 42
                                    + rt +dv + i+k e e+ eaa++
  gi|121638126|ref|YP_978350.1| 65 AGLRTVGDVVAYIQKLEEENPEAAQA 90
                                   688********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 941.25
//
Query:       gi|121638127|ref|YP_978351.1|  [L=416]
Description: 3-oxoacyl-ACP synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-49  168.4   1.4    2.2e-49  168.4   1.4    1.7  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.7e-30  105.5   0.6    3.1e-30  104.6   0.6    1.5  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    4.8e-07   29.4   1.5    7.4e-07   28.8   0.6    1.7  2  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   1.4   3.6e-53   2.2e-49       3     252 ..      13     253 ..      12     254 .. 0.91
   2 ?   -1.6   0.0      0.26   1.6e+03      96     124 ..     291     322 ..     287     358 .. 0.60

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 3.6e-53
                                    -EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTSTHHHHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfldvddfdpeffgisprea 82 
                                    +v+++++ a+++ ++d e++w+ Ll+g+++i+ l++   +  +  d++ +++g+ k+          +d ++ +   r  
  gi|121638127|ref|YP_978351.1|  13 SVVVTAVTATTSISPDIESTWKGLLAGESGIHALED---EFVTKWDLAVKIGGHLKD---------PVDSHMGRLDMR-- 78 
                                    69*********************************6...556666889********9.........7***********.. PP

                                    CTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH....HHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHH CS
                  ketoacyl-synt  83 eamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdy....aalaaldedgsevkaspkavgavlanviagri 158
                                     +m+ +qr+      + +e+ag ++  +d +r++v++G+g g      +    l ++g+++k+sp av+++++n +a+ i
  gi|121638127|ref|YP_978351.1|  79 -RMSYVQRMGKLLGGQLWESAGSPE--VDPDRFAVVVGTGLGGAerivES-YDLMNAGGPRKVSPLAVQMIMPNGAAAVI 154
                                    .*********************999..9999***********66456443.34444666********************* PP

                                    HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TT.SGGGTTBTTB... CS
                  ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag.llspd.grckafdpka... 233
                                     ++lg+r+ ++t+++ACsS+  a+++a+++++ g+adva++GGve ++++  +a+fs+++ +++++ ++++a++p++   
  gi|121638127|ref|YP_978351.1| 155 GLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRaMSTRNdEPERASRPFDkdr 234
                                    ************************************************************99999999999999999999 PP

                                    -SB-BB-EEEEEEEEECHH CS
                  ketoacyl-synt 234 dGfvlGEGvGavvLkrled 252
                                    dGfv+GE  ++++++++e+
  gi|121638127|ref|YP_978351.1| 235 DGFVFGEAGALMLIETEEH 253
                                    ********55555555554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.26
                                    HHHHHHHHTS-HHTCTTGG...EEEEEEESST CS
                  ketoacyl-synt  96 awealedagltpeeldgsr...vgvfiGvgag 124
                                    + + le agl+p+++d+ +   ++  iG +a+
  gi|121638127|ref|YP_978351.1| 291 MTRSLELAGLSPADIDHVNahgTATPIGDAAE 322
                                    56667777777777766665444444443333 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.6   5.2e-34   3.1e-30       1     117 [.     262     373 ..     262     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 5.2e-34
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a + g++++sd+ h+ ++a +g  + ra+++ l+ ag++p+d+d+v+ahgt+tp+gD++E++a++ + +++a     av
  gi|121638127|ref|YP_978351.1| 262 LARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQA-----AV 336
                                    58899*************************************************************9999977.....9* PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                     + Ks +GH+ +A G++e + +vl+l++gvipptln+
  gi|121638127|ref|YP_978351.1| 337 YAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNY 373
                                    ************************************8 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.6   1.2e-10   7.4e-07      66     113 ..     152     199 ..     136     224 .. 0.81
   2 ?   -1.9   0.0      0.29   1.8e+03      30      60 ..     290     320 ..     287     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-10
                                    HHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEE CS
                     Thiolase_N  66 aalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvE 113
                                    a++ +++   + ++t   +csSg +a+a+a+++i +g+adv+v+gGvE
  gi|121638127|ref|YP_978351.1| 152 AVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVE 199
                                    3444555556666677789****************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.29
                                    HHHHHHHHHTS-GGGCCEEEEEHSSCTTSTS CS
                     Thiolase_N  30 alkallekagvdpeevdevivGnvlqagegq 60 
                                    a+++ le ag++p+++d+v     ++   ++
  gi|121638127|ref|YP_978351.1| 290 AMTRSLELAGLSPADIDHVNAHGTATPIGDA 320
                                    7888999999999999999765555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2847.67
//
Query:       gi|121638128|ref|YP_978352.1|  [L=438]
Description: 3-oxoacyl-ACP synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-54  185.7   0.9    1.3e-54  185.4   0.3    1.5  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    3.1e-33  114.3   0.4    5.6e-33  113.5   0.4    1.4  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      2e-08   33.9   1.2    9.1e-08   31.8   0.7    1.9  2  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.3   2.3e-58   1.3e-54       4     252 ..      34     274 ..      32     275 .. 0.92
   2 ?   -3.5   0.0         1   6.2e+03      96     125 ..     312     340 ..     310     359 .. 0.67

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 2.3e-58
                                    EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTSTHHHHHHHC CS
                  ketoacyl-synt   4 vaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfldvddfdpeffgispreae 83 
                                    v+++G++++++ ++d+e++w+lLl+ +++i++l++      + +d+p r++g+  +         +fd+++ +i+ r   
  gi|121638128|ref|YP_978352.1|  34 VVVTGIAMTTALATDAETTWKLLLDRQSGIRTLDD---PFVEEFDLPVRIGGHLLE---------EFDHQLTRIELR--- 98 
                                    9*********************************5...77777899*******998.........9***********... PP

                                    TS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTT...GGGSCTTHHHHHSTTHHHHHHHH CS
                  ketoacyl-synt  84 amdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgs...evkaspkavgavlanviagrisy 160
                                    +m   qr++ + +++ +e+ag ++  +d++r +v iG+g g+ ++l+ +++d +   ++ +sp +v+++++n +a+ + +
  gi|121638128|ref|YP_978352.1|  99 RMGYLQRMSTVLSRRLWENAGSPE--VDTNRLMVSIGTGLGSAEELVFSYDDMRargMKAVSPLTVQKYMPNGAAAAVGL 176
                                    *********************999..99*************9999999998888999999******************** PP

                                    HHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TT..SG...GGTTBTTB- CS
                  ketoacyl-synt 161 alglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag.llspd..gr...ckafdpkad 234
                                    + ++++ ++t+++AC+S++ a++ a+q+++ gead+a++GGve+ +++  +agf++++ ++s++  ++   c++fd + d
  gi|121638128|ref|YP_978352.1| 177 ERHAKAGVMTPVSACASGAEAIARAWQQIVLGEADAAICGGVETRIEAVPIAGFAQMRiVMSTNndDPagaCRPFDRDRD 256
                                    **********************************************************977766574444488888888* PP

                                    SB-BB-EEEEEEEEECHH CS
                  ketoacyl-synt 235 GfvlGEGvGavvLkrled 252
                                    Gfv+GEG ++++++++e+
  gi|121638128|ref|YP_978352.1| 257 GFVFGEGGALLLIETEEH 274
                                    *******55555555554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1
                                    HHHHHHHHTS-HHTCTTGGEEEEEEESSTH CS
                  ketoacyl-synt  96 awealedagltpeeldgsrvgvfiGvgagd 125
                                      +a++ agl p ++d+ + +  +G+  gd
  gi|121638128|ref|YP_978352.1| 312 ITRAIQLAGLAPGDIDHVN-AHATGTQVGD 340
                                    5678888999999988877.3444444444 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.4   9.3e-37   5.6e-33       1     117 [.     283     395 ..     283     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 9.3e-37
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a i g++++sdg h+ +++pnge + +ai++a++ ag++p d+d+v+ah+tgt++gD +E +a+++++g ++     av
  gi|121638128|ref|YP_978352.1| 283 LARIMGASITSDGFHMVAPDPNGERAGHAITRAIQLAGLAPGDIDHVNAHATGTQVGDLAEGRAINNALGGNR----PAV 358
                                    689********************************************************************98....89* PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                     + Ks +GH+ +A G++e i +vlal+++vipptlnl
  gi|121638128|ref|YP_978352.1| 359 YAPKSALGHSVGAVGAVESILTVLALRDQVIPPTLNL 395
                                    ***********************************97 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.7   1.5e-11   9.1e-08      62     114 ..     166     220 ..     155     244 .. 0.84
   2 ?   -0.0   0.0     0.076   4.6e+02      29      51 ..     310     332 ..     305     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.5e-11
                                    HHHHHHHHTTS-TTSEEEEEE..HGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEE CS
                     Thiolase_N  62 iarqaalkagipeevpavtvn..kvcsSglkavalaaqsiaageadvvvagGvEs 114
                                    + + aa ++g+++++ a  ++   +c+Sg++a+a+a+q+i  gead++++gGvE+
  gi|121638128|ref|YP_978352.1| 166 MPNGAAAAVGLERHAKAGVMTpvSACASGAEAIARAWQQIVLGEADAAICGGVET 220
                                    6788999999999888876662267*****************************6 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.076
                                    HHHHHHHHHHTS-GGGCCEEEEE CS
                     Thiolase_N  29 ealkallekagvdpeevdevivG 51 
                                    +a++++++ ag++p ++d+v   
  gi|121638128|ref|YP_978352.1| 310 HAITRAIQLAGLAPGDIDHVNAH 332
                                    7999***************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2877.10
//
Query:       gi|121638129|ref|YP_978353.1|  [L=473]
Description: acetyl/propionyl CoA carboxylase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.7e-124  416.2   0.3   2.2e-124  415.8   0.3    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    2.3e-06   27.3   6.8    3.9e-05   23.2   0.2    2.4  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.8   0.3  2.5e-128  2.2e-124      44     478 ..      38     460 ..      20     470 .. 0.95

  Alignments for each domain:
  == domain 1  score: 415.8 bits;  conditional E-value: 2.5e-128
                                    .EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHH CS
                 Carboxyl_trans  44 prdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeaikagepligindsgGaegriqegveslrgsGkif 123
                                     r gv +  G+v+G+++  +  d tv+gg++g +  + +++a ++ai+ + p++gi  sgGa  r++egv +l+ +G++f
  gi|121638129|ref|YP_978353.1|  38 DRSGVLAAAGTVNGVRTIAFCTDGTVMGGAMGVEGCTHIVNAYDTAIEDQSPIVGIWHSGGA--RLAEGVRALHAVGQVF 115
                                    5789**********************************************************..99************** PP

                                    HHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSE CS
                 Carboxyl_trans 124 genskasgeIpqislvtgrcaGggaYlpalgdrvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahl 203
                                     +  +asg Ipqis+v+g +aGg+aY pal+d+v+m  e s +f+tGpdv+ +v+g e+v++ +lgG ++h +ksGv+h+
  gi|121638129|ref|YP_978353.1| 116 EAMIRASGYIPQISVVVGFAAGGAAYGPALTDVVVMAPE-SRVFVTGPDVVRSVTG-EDVDMASLGGPETHHKKSGVCHI 193
                                    ***************************************.****************.*********************** PP

                                    EESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSSSH..HCS-CTTTS---HHHHHHCEEC.TTC-EEESTTSST CS
                 Carboxyl_trans 204 taeddeealelirkllsylPkkasnnresaPivetadepdrdlieivPdnakkpyDvreviarlvd.egeFlEikegyAk 282
                                    +a+d+++a +  r+l++ +    +++  +  ++e+ d++ +    + P++++++yDvr +++++ d +  F+E+++++A+
  gi|121638129|ref|YP_978353.1| 194 VADDELDAYDRGRRLVGLFC---QQGHFDRSKAEAGDTDIH---ALLPESSRRAYDVRPIVTAILDaDTPFDEFQANWAP 267
                                    ********************...666679999999888777...8*********************7788********** PP

                                    TEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHH CS
                 Carboxyl_trans 283 tvVvGfArlgGipvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvd 362
                                    ++VvG++rl G++vGv+An++   +G +l ++sa+Kaarf+rlcda+ +Plv+++dv+G+l+G +qe+gg++++Gakl+ 
  gi|121638129|ref|YP_978353.1| 268 SMVVGLGRLSGRTVGVLANNPLRLGG-CLNSESAEKAARFVRLCDAFGIPLVVVVDVPGYLPGVDQEWGGVVRRGAKLLH 346
                                    *********************99999.***************************************************** PP

                                    HHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Carboxyl_trans 363 alaeakvPkitvilrkayGGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklke 442
                                    a+ e++vP +t+++rk yGGay++m+s+ ++a  v+awp+a++aV+g++ av+il +k++aaa ++  +++a   +  +e
  gi|121638129|ref|YP_978353.1| 347 AFGECTVPRVTLVTRKTYGGAYIAMNSRSLNATKVFAWPDAEVAVMGAKAAVGILHKKKLAAAPEH--EREALHDQLAAE 424
                                    ********************************9*****************************9955..456666777777 PP

                                    HHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEE CS
                 Carboxyl_trans 443 yeeellnpyvaaargfaDavidpsetraklvialel 478
                                     e+    +  a  +g++D+ idp++tr kl+ al+ 
  gi|121638129|ref|YP_978353.1| 425 HERIAGGVDSALDIGVVDEKIDPAHTRSKLTEALAQ 460
                                    888888899999******************999864 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   2.2   0.00082       7.4      18     127 ..      41     146 ..      26     176 .. 0.78
   2 !   23.2   0.2   4.4e-09   3.9e-05      66     202 ..     316     459 ..     273     470 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00082
                                    EEEEEEETTEEEEEEEE---TT..SS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHH CS
                           MdcE  18 kvldgsltlesvrfvaVigdan..kgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrrdEllGihealahla 95 
                                     vl++  t + vr++a  +d    +g++Gv+    + +a + ai  +++ pi+ +  + + rl+ +  +l   +a+  + 
  gi|121638129|ref|YP_978353.1|  41 GVLAAAGTVNGVRTIAFCTDGTvmGGAMGVEGCTHIVNAYDTAI--EDQSPIVGIWHSGGARLAEGVRAL---HAVGQVF 115
                                    57777777788999999988878899*****************9..899**************9988887...5677788 PP

                                    HHHHHHHHHT--EEEEEEEEEEHHHHHHTTTT CS
                           MdcE  96 kalarArlaGhpvigllvGkavsGaflahglq 127
                                    +a++rA     p i+++vG a+ Ga    +l 
  gi|121638129|ref|YP_978353.1| 116 EAMIRASG-YIPQISVVVGFAAGGAAYGPALT 146
                                    88888753.3699***********97665553 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.4e-09
                                    EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHT...TTT-SEEEEEET-EEESS CS
                           MdcE  66 pilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflah...glqanrlialpgvqvavm 142
                                    p++v+vDv++   g  +E  G+    a l +a+    +   p ++l+  k+  Ga++a+   +l+a ++ a p+++vavm
  gi|121638129|ref|YP_978353.1| 316 PLVVVVDVPGYLPGVDQEWGGVVRRGAKLLHAFGECTV---PRVTLVTRKTYGGAYIAMnsrSLNATKVFAWPDAEVAVM 392
                                    99********************9999999999988875...99**************96333799*************** PP

                                    -HHHHHHHHT-.-H........HHHH.HHGGCSGGG--SHHHHHTTT--SEEEE-S-SSS--HHHHHHHH CS
                           MdcE 143 dkasaArvTkr.sv........eaLe.alaksipvfAydvdnyarlGlleelldveeaealaeallalva 202
                                    + ++a  + ++  +        eaL+ +la++   +A +vd+   +G + e +d  ++ +  ++    +a
  gi|121638129|ref|YP_978353.1| 393 GAKAAVGILHKkKLaaapeherEALHdQLAAEHERIAGGVDSALDIGVVDEKIDPAHTRSKLTE---ALA 459
                                    *988876643312222333323777536899999***************999995444443333...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3494.88
//
Query:       gi|121638130|ref|YP_978354.1|  [L=134]
Description: hypothetical protein BCG_2265 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 864.77
//
Query:       gi|121638131|ref|YP_978355.1|  [L=234]
Description: hypothetical protein BCG_2266 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-05   23.8   0.0    8.7e-05   22.6   0.0    1.6  1  MTES_1575  REase_MTES_1575
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.052   13.4   0.0    1.5  1  DUF559     Protein of unknown function (DUF559)


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   9.7e-09   8.7e-05      24      93 ..     159     225 ..     138     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.7e-09
                      MTES_1575  24 gfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwssdwyrnpeeeleklve 93 
                                      r+D+++ d    +la e ++ ++h  + ++ rd +r + L++lGW+i+ i   d  r+p +  +++ +
  gi|121638131|ref|YP_978355.1| 159 MWRVDFAWPDM---RLAAEYESIEWHAGPAEMLRDKTRWAKLQELGWTIVPIVVDDVRREPGRLAARIAR 225
                                    56899999998...**********************************************9999888876 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.8e-06     0.052      46     108 ..     162     227 ..     155     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-06
                                    EEEEETTTTEEEEEE---.----..----HHHHHHHHHTT-EEEEEEHHHHHH-HHHHHHHHHHHH CS
                         DUF559  46 vDfvclkaklivelDGaq.hdee..eeyDaeRtelLeslGftvlRfkndevlknieevleeilkal 108
                                    vDf+   ++l  e + ++ h++     +D++R + L++lG+t++    d+v++++++ +++i ++l
  gi|121638131|ref|YP_978355.1| 162 VDFAWPDMRLAAEYESIEwHAGPaeMLRDKTRWAKLQELGWTIVPIVVDDVRREPGRLAARIARHL 227
                                    8999999999999998763777643568******************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1540.50
//
Query:       gi|121638132|ref|YP_978356.1|  [L=516]
Description: glycerol-3-phosphate dehydrogenase glpd1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-48  166.7   4.6    1.3e-48  166.4   4.6    1.1  1  DAO            FAD dependent oxidoreductase
    3.8e-14   52.6   1.1    6.8e-14   51.8   0.0    2.0  3  DAO_C          C-terminal domain of alpha-glycerophosphate ox
    1.8e-06   27.3   8.3    3.4e-05   23.1   8.3    2.3  1  FAD_binding_2  FAD binding domain
    5.5e-05   22.7   0.8    0.00011   21.8   0.8    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00068   19.0   2.1     0.0011   18.2   0.6    2.0  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0015   17.7   0.4     0.0022   17.1   0.4    1.2  1  GIDA           Glucose inhibited division protein A
     0.0023   17.0   0.3      0.071   12.1   0.3    2.2  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.013   14.7   1.1      0.023   13.9   1.1    1.3  1  Thi4           Thi4 family
      0.014   15.3   0.3      0.026   14.4   0.3    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.017   13.9   0.9      0.024   13.4   0.9    1.2  1  HI0933_like    HI0933-like protein
      0.053   12.8   0.1      0.092   12.0   0.1    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.064   13.8   0.5       0.25   11.9   0.5    2.0  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.071   13.3   4.9      0.051   13.8   1.5    2.6  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.076   12.2   1.1       0.18   11.0   1.1    1.6  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.4   4.6     1e-51   1.3e-48       1     323 [.      28     363 ..      28     390 .. 0.77

  Alignments for each domain:
  == domain 1  score: 166.4 bits;  conditional E-value: 1e-51
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    dv++iGGGi+G+++A+++a+rg  V+l+ek+ +++ g+S  +s+l+h+glryl+++   +  ++++  e+  l  +++++
  gi|121638132|ref|YP_978356.1|  28 DVIVIGGGITGVGIALDAATRGltVALVEKH-DLAFGTSRWSSKLVHGGLRYLASG--NVGIARRSAVERGILMTRNAPH 104
                                    8******************************.8888******************88..56******************** PP

                                    TSEEEEEEEEEES..SH..........HHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEE CS
                            DAO  79 idyrrtGllslaa..de..........eelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvd 144
                                    + + ++ l++l    ++             +al+ l++ +++  ++++ + a++v e++p    +gl g+l+ +d+  +d
  gi|121638132|ref|YP_978356.1| 105 LVHAMPQLVPLLPsmGHtkralvragfLAGDALRVLAGTPAATLPRSRRIPASRVVEIAPTvrRDGLDGGLLAYDGQLID 184
                                    ***********84222122222222221134455555555645556689***99******96444999*******5555* PP

                                    HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECT.EEEE..EEEEEEE--GGGHHHHHTTCTTTSEEE CS
                            DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgve...rttp.gend..aadavVnaaGawsdllgllkeldlpis 218
                                    +a+l+ a+ar+a+++G++il++  + ++      ++ ve   r t+    +  +a+av+naaG+w++++  ++   l+++
  gi|121638132|ref|YP_978356.1| 185 DARLVMAVARTAAQHGARILTYVGASNV-----TGTSVEltdRRTRqS--FalSARAVINAAGVWAGEI--DPS--LRLR 253
                                    **********************777776.....256665545444323..14567**********9877..133..489* PP

                                    EEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE..EETTCSSTSCSHHHHHHHHHHHHHHS CS
                            DAO 219 pvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad..eesgdddpevdeedidellealrklf 296
                                    p rg++lv++ +s     p a l++p++ + +r v+++p   gr+++G t++  +   +d+p++++e+i  ll+ +++ +
  gi|121638132|ref|YP_978356.1| 254 PSRGTHLVFDAKSF--ANPTAALTIPIPGELNRFVFAMPEQLGRIYLGLTDEdaPGPIPDVPQPSSEEITFLLDTVNTAL 331
                                    *********77666..345677888889999********999********97665556666******************* PP

                                    GGG...CGEEEEEEEEEEE..TTSSEEEEEEE CS
                            DAO 297 Pql...gdvlrkwaGlrpl..pdglpligetp 323
                                     +    +dv  ++aGlrpl  + g  + g+t 
  gi|121638132|ref|YP_978356.1| 332 GTAvgtKDVIGAYAGLRPLidTGGAGVQGRTA 363
                                    88435599**********74345577777754 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       9.7   1.2e+04      92     103 ..     222     233 ..     211     241 .. 0.69
   2 ?   -3.8   0.2       8.8   1.1e+04      81      99 ..     388     406 ..     387     409 .. 0.75
   3 !   51.8   0.0   5.3e-17   6.8e-14       1     104 [.     411     504 ..     411     515 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9.7
                                    TTS-HHHH-HHH CS
                          DAO_C  92 RRtrlafldada 103
                                    RRtr +f    +
  gi|121638132|ref|YP_978356.1| 222 RRTRQSFALSAR 233
                                    999988864443 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.8
                                    S---SHHHHHHTTS-HHHH CS
                          DAO_C  81 EmartlvDvlaRRtrlafl 99 
                                    E+   ++Dvl R ++l  l
  gi|121638132|ref|YP_978356.1| 388 EYRYMAEDVLNRAITLRHL 406
                                    7777889999998877665 PP

  == domain 3  score: 51.8 bits;  conditional E-value: 5.3e-17
                                    --TTS---TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHHHHHH CS
                          DAO_C   1 crTkklpLvGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvYavrh 80 
                                    crT++lpL+Ga        a+     g  +   e L+ rYG++a +v++ a  +   + +e++++  ++++ae +Yav+h
  gi|121638132|ref|YP_978356.1| 411 CRTRNLPLIGAP-------ANPGPAPGSGAGLPESLVARYGAEAANVAAAATCE---RPTEPVADGIDVTRAEFEYAVTH 480
                                    99*********9.......5566667777888899************9555544...59********************* PP

                                    S---SHHHHHHTTS-HHHH-HHHH CS
                          DAO_C  81 EmartlvDvlaRRtrlafldadaa 104
                                    E a+ ++D+l RRtr+ ++ +d+ 
  gi|121638132|ref|YP_978356.1| 481 EGALDVDDILDRRTRIGLVPRDRE 504
                                    *****************9955543 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   8.3   2.7e-08   3.4e-05       1     204 [.      28     244 ..      28     269 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.7e-08
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--....S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT- CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq....Ggidavlspeqkkagikdspelhrtdtlkaldel 76 
                                    DviViG+G+ G   Al aa +Gl+va+vek +   g++ ws+    Gg+  ++s++   a+    +e  +  t++a +  
  gi|121638132|ref|YP_978356.1|  28 DVIVIGGGITGVGIALDAATRGLTVALVEKHDLAFGTSRWSSklvhGGLRYLASGNVGIARR-SAVERGILMTRNAPHLV 106
                                    9****************************************744447777777665522222.22222222222222222 PP

                                    S.-HHHHHHHHHTHHHHHHHHHHTT----BCCTS.SB-EEE-TT-SST...............EEEE-.STT-....... CS
                  FAD_binding_2  77 a.dqplveafveaapeavdeLeelgvpfsrtedg.pvdvrelGglsat...............artlhdaadarr.etlv 138
                                    +  ++lv ++ + ++ +++  ++ ++  +      ++++++  +l +                +r + d +      +l+
  gi|121638132|ref|YP_978356.1| 107 HaMPQLVPLLPSMGHTKRALVRAGFLAGDA---LrVLAGTPAATLPRSrripasrvveiaptvRRDGLDGGLLAYdGQLI 183
                                    222222222222222222222222222222...02333333333333334444444444444522222222222234777 PP

                                    HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                    +  +l+ +++++a ++g ++++   a +++      t ++++++++ + +++ a+av+ a+g + +
  gi|121638132|ref|YP_978356.1| 184 DDARLVMAVARTAAQHGARILTYVGASNVTG-----TSVELTDRRTRQSFALSARAVINAAGVWAG 244
                                    7777777777777777777777777777733.....555566668888888888888888887776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.8   8.2e-08   0.00011       1      32 [.      28      59 ..      28      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.2e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                   Dv+V+GGg+ Gv  A+ Aa +G +v+Lve+++
  gi|121638132|ref|YP_978356.1| 28 DVIVIGGGITGVGIALDAATRGLTVALVEKHD 59
                                   9****************************987 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6     9e-07    0.0011       2      35 ..      28      60 ..      27      96 .. 0.81
   2 ?   -0.7   0.0      0.53   6.8e+02      14     213 ..     191     216 ..     183     246 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                   dv+viGgG+ G+  al++a+ g+ v+lve+ + +
  gi|121638132|ref|YP_978356.1| 28 DVIVIGGGITGVGIALDAATRGLTVALVEKHD-L 60
                                   89**************************6433.3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.53
                                    HHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  14 aaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvklekkkeg 93 
                                    a+a+t+aq+ga+++ +                                                                
  gi|121638132|ref|YP_978356.1| 191 AVARTAAQHGARILTY---------------------------------------------------------------- 206
                                    4455555555555544................................................................ PP

                                    CEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  94 deekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlvea 173
                                                                                                                    
  gi|121638132|ref|YP_978356.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                                    SSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 174 rdrllraldkelsaaleealekeGvevklgtsvkeidgng 213
                                                                    + +++g +
  gi|121638132|ref|YP_978356.1| 207 ------------------------------VGASNVTGTS 216
                                    ..............................4444444333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   1.7e-06    0.0022       1      31 [.      28      58 ..      28      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                   dviViGgG  G+  Al aa +G+ v+L+ ++
  gi|121638132|ref|YP_978356.1| 28 DVIVIGGGITGVGIALDAATRGLTVALVEKH 58
                                   8**************************9554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.3   5.6e-05     0.071       1      36 [.      28      61 ..      28      74 .. 0.86
   2 ?    2.6   0.0     0.044        57     114     200 ..     209     297 ..     172     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   Dv+viG+G  g+ +A     a  gl v l+e  +  
  gi|121638132|ref|YP_978356.1| 28 DVIVIGGGITGVGIALDA--ATRGLTVALVEKHDLA 61
                                   9****************9..**********876654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.044
                  Lycopene_cycl 114 eeeageslvvleggr.....kirarlvvdarglaslkkarrlglQtfyGvevevdnppfdldkmvlMDfrveqklkgltF 188
                                    +++++ ++v l + r      + ar+v+ a g+ +++  + l l   +G  +  d++ f   ++ l   +++ + +  +F
  gi|121638132|ref|YP_978356.1| 209 ASNVTGTSVELTDRRtrqsfALSARAVINAAGVWAGEIDPSLRLRPSRGTHLVFDAKSFANPTAAL---TIPIPGELNRF 285
                                    33334444555555544555899*********9999999999999999999999999998777765...45555567889 PP

                  Lycopene_cycl 189 lYalPldsdrll 200
                                    ++a+P +  r++
  gi|121638132|ref|YP_978356.1| 286 VFAMPEQLGRIY 297
                                    999987777766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.1   1.8e-05     0.023      14      59 ..      23      68 ..      11      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                   HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS.SS--TTTTT CS
                           Thi4 14 kyaesDvvivGaGssGLtaayylakkpdlkvailers.vspGGGawl 59
                                   +    Dv+++G+G +G+  a   a++ +l va++e++ +++G   w 
  gi|121638132|ref|YP_978356.1| 23 DGGALDVIVIGGGITGVGIALDAATR-GLTVALVEKHdLAFGTSRWS 68
                                   44567*********************.********8659***99996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3     2e-05     0.026       2      34 ..      29      61 ..      28      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v viG G+ G gia  +a +gl+V lv+ ++ a
  gi|121638132|ref|YP_978356.1| 29 VIVIGGGITGVGIALDAATRGLTVALVEKHDLA 61
                                   78*************************987755 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   1.9e-05     0.024       2      32 ..      28      58 ..      27      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                   dviviGgG  G+  A+ aa+rg  V+l+ek 
  gi|121638132|ref|YP_978356.1| 28 DVIVIGGGITGVGIALDAATRGLTVALVEKH 58
                                   8****************************97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.1e-05     0.092       1      39 [.      30      67 ..      28      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyry 39
                                   i+iG+G  G+++a+ +   gl ++  +Ek+ +    +r+
  gi|121638132|ref|YP_978356.1| 30 IVIGGGITGVGIALDAATRGL-TVALVEKHDLAFGTSRW 67
                                   899**************9999.69999999877666666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00019      0.25       2      32 ..      29      59 ..      28      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                   v+v+GgG +g+  A  +a  g  V +ve +d
  gi|121638132|ref|YP_978356.1| 29 VIVIGGGITGVGIALDAATRGLTVALVEKHD 59
                                   89**************************988 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5     4e-05     0.051       1      34 [.      31      64 ..      31      82 .. 0.88
   2 ?   -1.8   0.0       2.9   3.7e+03      10      25 ..     191     206 ..     190     233 .. 0.68
   3 ?   -3.4   0.0       9.6   1.2e+04      24      32 ..     489     497 ..     488     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                   ++G+G++G  +A  +a +g+ v l+ek+d   G 
  gi|121638132|ref|YP_978356.1| 31 VIGGGITGVGIALDAATRGLTVALVEKHDLAFGT 64
                                   8***************************976665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
                                    HHHHHHHCCTEEEEEE CS
                  NAD_binding_8  10 vaAylLakagfdvlll 25 
                                    + A+++a++g+++l +
  gi|121638132|ref|YP_978356.1| 191 AVARTAAQHGARILTY 206
                                    5566666666666544 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.6
                                    EE-SSSSSS CS
                  NAD_binding_8  24 llekrdrlG 32 
                                    +l++r+r+G
  gi|121638132|ref|YP_978356.1| 489 ILDRRTRIG 497
                                    89******9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   0.00014      0.18       2      41 ..      27      66 ..      26      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr 41
                                    dV+++G+G +G+  al  +++G  v lvek++ +  ++r
  gi|121638132|ref|YP_978356.1| 27 LDVIVIGGGITGVGIALDAATRGLTVALVEKHDLAFGTSR 66
                                   59******************************98877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3363.93
//
Query:       gi|121638133|ref|YP_978357.1|  [L=189]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-12   47.4   0.0    4.5e-12   45.6   0.0    2.0  2  TetR_N         Bacterial regulatory proteins, tetR family
    0.00011   21.9   0.8    0.00037   20.3   0.4    2.1  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00013   21.7   0.3    0.00037   20.2   0.3    1.8  1  HTH_23         Homeodomain-like domain
    0.00017   21.3   0.0     0.0005   19.8   0.0    1.8  1  HTH_IclR       IclR helix-turn-helix domain
     0.0011   19.0   0.1     0.0029   17.6   0.0    1.8  1  HTH_7          Helix-turn-helix domain of resolvase
     0.0018   18.3   0.3     0.0055   16.8   0.3    1.8  1  HTH_28         Helix-turn-helix domain
     0.0028   17.4   0.0     0.0091   15.8   0.0    2.0  2  LacI           Bacterial regulatory proteins, lacI family
     0.0092   16.7   3.7      0.013   16.3   2.2    1.9  2  TetR_C_15      Tetracyclin repressor-like, C-terminal domain
     0.0097   15.9   0.2      0.029   14.4   0.2    1.8  1  HTH_29         Winged helix-turn helix
     0.0098   16.0   0.0       0.02   15.0   0.0    1.5  1  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos
  ------ inclusion threshold ------
       0.01   15.4   0.0       0.03   13.9   0.0    1.8  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.016   14.7   0.0      0.046   13.2   0.0    1.8  1  Sigma70_r4     Sigma-70, region 4
       0.02   14.7   1.4       0.14   12.1   0.1    2.7  2  MarR_2         MarR family
      0.021   14.8   0.3      0.069   13.1   0.1    1.9  2  HTH_11         HTH domain
       0.03   14.1   0.2       0.09   12.6   0.2    1.9  1  HTH_38         Helix-turn-helix domain
      0.033   14.2   0.1       0.21   11.7   0.0    2.3  3  HTH_22         HTH domain
      0.056   13.4   1.6       0.65   10.0   0.0    3.0  3  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.072   13.4   2.5      0.077   13.4   0.4    2.2  2  HTH_31         Helix-turn-helix domain
      0.073   13.3   0.0       0.14   12.4   0.0    1.5  1  HTH_17         Helix-turn-helix domain
       0.16   11.8   0.1       0.36   10.7   0.1    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.17   11.7   0.0       0.23   11.2   0.0    1.3  1  BSP            Peptidase of plants and bacteria


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   5.3e-15   4.5e-12       1      44 [.      15      58 ..      15      61 .. 0.93
   2 ?   -1.9   0.0       3.6   3.1e+03      22      33 ..     113     124 ..     113     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.3e-15
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLl 44
                                   Il aA+ +  ++G d++t++eIA+rAGvs++++Yr++p+ + ++
  gi|121638133|ref|YP_978357.1| 15 ILRAAASCVVDYGVDRVTLAEIARRAGVSRPTVYRRWPDTRSIM 58
                                   9*************************************987766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                    HHHHHTSSHHHH CS
                         TetR_N  22 IAkrAGvskgal 33 
                                    I +r+G+s+  l
  gi|121638133|ref|YP_978357.1| 113 ITERLGTSQQVL 124
                                    567777776554 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   4.3e-07   0.00037      17      38 ..      30      51 ..      29      52 .. 0.94
   2 ?   -3.0   0.0         8   6.8e+03      25      31 ..     115     121 ..     106     122 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                  HTH_AsnC-type 17 RisyaeLAervGlSestvlrRv 38
                                   R + ae+A+r G+S++tv rR+
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYRRW 51
                                   7899*****************6 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                  HTH_AsnC-type  25 ervGlSe 31 
                                    er+G S+
  gi|121638133|ref|YP_978357.1| 115 ERLGTSQ 121
                                    5788776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   4.4e-07   0.00037      10      37 ..      15      51 ..      13      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.4e-07
                         HTH_23 10 illllae........GlsvreIAreLgvsrrTvy.rw 37
                                   il+++a         + + +eIAr+ gvsr Tvy rw
  gi|121638133|ref|YP_978357.1| 15 ILRAAAScvvdygvdRVTLAEIARRAGVSRPTVYrRW 51
                                   66666633344555699*****************555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.9e-07    0.0005      18      37 ..      30      49 ..      12      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-07
                                   S-BHHHHHHHHTS-HHHHHH CS
                       HTH_IclR 18 eltlselArrtglpkStvhR 37
                                   ++tl+e+Arr+g++++tv+R
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYR 49
                                   489****************9 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.4e-06    0.0029      25      44 ..      34      53 ..      31      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                                   TTTSSSS---SSSS--SS-- CS
                          HTH_7 25 skIAkevnisRsTvYRylad 44
                                   ++IA++ ++sR TvYR ++d
  gi|121638133|ref|YP_978357.1| 34 AEIARRAGVSRPTVYRRWPD 53
                                   68**************9987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   6.5e-06    0.0055      12      32 ..      30      50 ..      14      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-06
                         HTH_28 12 GhsvreaArelgisrrtvyrW 32
                                    ++ +e+Ar+ g+sr tvyr 
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYRR 50
                                   35999*************874 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.2   6.2e+03      28      39 ..       9      20 ..       8      21 .. 0.78
   2 !   15.8   0.0   1.1e-05    0.0091       1      17 [.      32      48 ..      32      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.2
                                   HHHHHHHHHHHH CS
                           LacI 28 eetrerVeaame 39
                                   ++t  r+++a++
  gi|121638133|ref|YP_978357.1|  9 ADTGGRILRAAA 20
                                   578999999985 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                                   -HHHHHHHCTS-HHHHH CS
                           LacI  1 tikDVArlAGVSkaTVS 17
                                   t+ ++Ar+AGVS  TV 
  gi|121638133|ref|YP_978357.1| 32 TLAEIARRAGVSRPTVY 48
                                   899************95 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.73   6.3e+02      73     103 ..      58      90 ..      27      92 .. 0.60
   2 !   16.3   2.2   1.5e-05     0.013       4     108 .]      81     188 ..      79     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.73
                      TetR_C_15  73 vaveaveallhlaleedp...adrealiaelkrl 103
                                    +a  ++++ +  +l+e p   +dreal+++++++
  gi|121638133|ref|YP_978357.1|  58 MASMLTSH-IADVLREVPldgDDREALVKQIVAV 90 
                                    33333333.3333444444668899999998875 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                      TetR_C_15   4 ealdalvdallaahrenpalrrvlleeapslgelelvealeqriaealaalL..arrrpelppedlelaafvaveaveal 81 
                                    eal + + a+++  r +  +  v+++e +++   e+    +q ++e laa L  a+r   +++ d++++a++++ +++++
  gi|121638133|ref|YP_978357.1|  81 EALVKQIVAVADRLRGDDLIMSVMHSELARVYITERLGTSQQVLIEGLAARLtvAQRSGSVRSGDARRLATMVLLIAQST 160
                                    555555667777777778888999999999999999999*******999988445788888899**************** PP

                      TetR_C_15  82 lhlaleedp.adrealiaelkrlllaYL 108
                                    +  a   d   d +al +el+++l +YL
  gi|121638133|ref|YP_978357.1| 161 IQSADIVDSiLDSAALATELTHALNGYL 188
                                    ***************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   3.4e-05     0.029      13      31 ..      29      49 ..      17      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-05
                         HTH_29 13 s..tvsqiAkllglsrrtvyr 31
                                   +  t ++iA++ g+sr+tvyr
  gi|121638133|ref|YP_978357.1| 29 DrvTLAEIARRAGVSRPTVYR 49
                                   45589***************9 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05      0.02      15      50 ..      19      55 ..       8      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHH.HHH-H CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlyk.Wkkkk 50
                                   aa  +v+   +++tl+eia+  gvsr T y+ W + +
  gi|121638133|ref|YP_978357.1| 19 AASCVVDYGVDRVTLAEIARRAGVSRPTVYRrWPDTR 55
                                   3344466666********************6376655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05      0.03      17      37 ..      30      50 ..      29      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                         HTH_24 17 risqreLAerlglSpstvnrr 37
                                   r + +e+A+r g+S++tv rr
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYRR 50
                                   899***************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.4e-05     0.046      18      37 ..      28      47 ..      18      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                                   TTT--HHHHHHHHTS-HHHH CS
                     Sigma70_r4 18 geglTleEIgerlgiSrerV 37
                                   ++  Tl+EI++r g+Sr +V
  gi|121638133|ref|YP_978357.1| 28 VDRVTLAEIARRAGVSRPTV 47
                                   6778*************999 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00016      0.14      21      40 ..      30      49 ..       8      50 .. 0.79
   2 ?    0.9   0.1       0.5   4.3e+02      22      36 ..     108     122 ..      61     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                   EEEHHHHHHHHTSSHHHHHH CS
                         MarR_2 21 dltvgelarrlglsksavsr 40
                                   ++t +e+arr g+s+++v r
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYR 49
                                   69***************966 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.5
                                    EEHHHHHHHHTSSHH CS
                         MarR_2  22 ltvgelarrlglsks 36 
                                    l+   +++rlg s++
  gi|121638133|ref|YP_978357.1| 108 LARVYITERLGTSQQ 122
                                    444456666666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.1e-05     0.069      16      34 ..      31      49 ..      27      50 .. 0.91
   2 ?   -2.7   0.0       6.9   5.9e+03      22      31 ..     114     123 ..     112     134 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                         HTH_11 16 isgeeLAeeLnvSrrtvrr 34
                                   ++ +e+A++ +vSr tv+r
  gi|121638133|ref|YP_978357.1| 31 VTLAEIARRAGVSRPTVYR 49
                                   9*****************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.9
                         HTH_11  22 AeeLnvSrrt 31 
                                     e+L+ S ++
  gi|121638133|ref|YP_978357.1| 114 TERLGTSQQV 123
                                    5566655543 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00011      0.09      22      39 ..      32      49 ..      29      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                         HTH_38 22 slreIArrLgrspsTIsR 39
                                   +l+eIArr g+s+ T++R
  gi|121638133|ref|YP_978357.1| 32 TLAEIARRAGVSRPTVYR 49
                                   89***************9 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.21      45      60 ..      34      49 ..      30      50 .. 0.88
   2 ?   -2.2   0.0       5.5   4.7e+03       3      31 ..      63      86 ..      59      87 .. 0.62
   3 ?   -2.6   0.0       6.9   5.9e+03      45      55 ..     111     121 ..     109     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                         HTH_22 45 ekvAekLgiSraTvYr 60
                                    ++A++ g+Sr+TvYr
  gi|121638133|ref|YP_978357.1| 34 AEIARRAGVSRPTVYR 49
                                   689************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.5
                         HTH_22  3 esiieevladlgkpverltkeekieivra 31
                                    s i++vl  + +p   l+ +++ ++v++
  gi|121638133|ref|YP_978357.1| 63 TSHIADVL--REVP---LDGDDREALVKQ 86
                                   45555555..3466...667778777775 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.9
                         HTH_22  45 ekvAekLgiSr 55 
                                     ++ e+Lg S+
  gi|121638133|ref|YP_978357.1| 111 VYITERLGTSQ 121
                                    57899999996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00076      0.65      21      40 ..      30      49 ..      13      51 .. 0.85
   2 ?   -0.7   0.0       1.6   1.4e+03      23      40 ..      54      71 ..      49      73 .. 0.79
   3 ?    0.5   0.1      0.69   5.9e+02       3      30 ..      83     111 ..      81     130 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                                   EHHHHHHHHHTTSSHHHHHH CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsr 40
                                   ++t +e+A++ G++r tv r
  gi|121638133|ref|YP_978357.1| 30 RVTLAEIARRAGVSRPTVYR 49
                                   68999*************88 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                   HHHHHHHHTTSSHHHHHH CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsr 40
                                   t+  +Asml ++   v r
  gi|121638133|ref|YP_978357.1| 54 TRSIMASMLTSHIADVLR 71
                                   78889***9998877766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.69
                                    HHHHHHHHHCTTTC.EEEEEHHHHHHHHH CS
                      HTH_Crp_2   3 lArfLlrlaeragg.eielpltqeelAsm 30 
                                    l + ++  a+r +g  + +++ + elA+ 
  gi|121638133|ref|YP_978357.1|  83 LVKQIVAVADRLRGdDLIMSVMHSELARV 111
                                    55566666666554434466677777653 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4     9e-05     0.077       7      33 ..      14      49 ..      14      58 .. 0.93
   2 ?   -2.8   0.1       9.9   8.4e+03      23      40 ..     137     139 ..     128     152 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-05
                         HTH_31  7 ralRera.........GLsqeevAerlgvsestlsr 33
                                   r lR++a         +++++e A+r+gvs+ t+ r
  gi|121638133|ref|YP_978357.1| 14 RILRAAAscvvdygvdRVTLAEIARRAGVSRPTVYR 49
                                   6799999999999999****************9977 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.9
                         HTH_31  23 rlgvsestlsrlEqGrrg 40 
                                    r+               g
  gi|121638133|ref|YP_978357.1| 137 RS---------------G 139
                                    22...............2 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.14       3      21 ..      32      51 ..      30      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                         HTH_17  3 tveEaAelLgvsrstvy.rl 21
                                   t +E+A+  gvsr tvy r+
  gi|121638133|ref|YP_978357.1| 32 TLAEIARRAGVSRPTVYrRW 51
                                   899**************446 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00043      0.36      23      41 ..      31      49 ..      28      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                                   CHHCHHCCCTTSSCHCHHH CS
                           TrmB 23 atadeiaeelgvprskvYe 41
                                    t  eia+++gv+r++vY+
  gi|121638133|ref|YP_978357.1| 31 VTLAEIARRAGVSRPTVYR 49
                                   6889**************7 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00027      0.23      92     130 ..      92     132 ..      50     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            BSP  92 kdak..aevtgvLthelvhvyqweaegrapggliEGiAdyv 130
                                    ++ +  + +++v+  el++vy  e  g+ ++ liEG+A  +
  gi|121638133|ref|YP_978357.1|  92 DRLRgdDLIMSVMHSELARVYITERLGTSQQVLIEGLAARL 132
                                    444455789****************************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1461.13
//
Query:       gi|121638134|ref|YP_978358.1|  [L=529]
Description: flavoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-45  154.7   0.0    4.5e-45  154.2   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    7.9e-32  109.9   0.1    1.2e-30  106.1   0.0    2.4  2  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.0   5.1e-49   4.5e-45       1     250 []     277     527 ..     277     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 5.1e-49
                                    --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHH CS
                  FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeel 80 
                                    +pe++++ +++fp+f+ +v+a+r+i+q g +p+ ++l d+ ++ + +at +a    +   ++l +  feg++e + e+++
  gi|121638134|ref|YP_978358.1| 277 IPESTRYEAWSFPDFATGVAALRTITQTGTGPTVVRLSDEAETGVNLATTEAIGETQITGGCLGITVFEGTQE-HTESRH 355
                                    599*************************************************888899999999********5.555555 PP

                                    HHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH... CS
                  FAD-oxidase_C  81 ealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyg... 157
                                    + +  a+l a g+++       +  +++w+  ++a pylrd ll+ag  +++ +t+  +s+ + l +++ ++l  +    
  gi|121638134|ref|YP_978358.1| 356 A-ETRALLAARGGTS-----LGEGPARAWERGRFAAPYLRDSLLAAGALCETLETATVWSNTPVLKAAVTEALTTSLaas 429
                                    5.5555555555555.....2224469*********************************************99999999 PP

                                    ....EEEEEEEEEETTEEEEEEEEEEE...--TT--THHHHHHHHHHHHTT-----------------------THHHHH CS
                  FAD-oxidase_C 158 ....levvlfgHagdgnlhlyilfdlade.aeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalm 232
                                        l++++++H+++ ++ ly+++ + ++ +  e++ ++ +   d++++ gG+i+++H+vG d++++++ e+g+ g++l+
  gi|121638134|ref|YP_978358.1| 430 gtpaLVMCHVSHVYPTGASLYFTVVAGQRgDPIEQWLAAKKAASDAIMATGGTITHHHAVGSDHRPWMRAEVGDLGVTLL 509
                                    9***********************9997753334444444445777********************************** PP

                                    HHHHHHH-TT--BSTT-- CS
                  FAD-oxidase_C 233 rriKaalDPkgiLNPgkv 250
                                    r iKa+lDP+giLNPgk+
  gi|121638134|ref|YP_978358.1| 510 RTIKATLDPAGILNPGKL 527
                                    ****************96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.0   1.3e-34   1.2e-30       7     133 ..     106     237 ..      97     242 .. 0.93
   2 ?    1.1   0.0     0.034   3.1e+02      62      90 ..     447     475 ..     423     485 .. 0.79

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.3e-34
                                    ESSHHHHHHHHHHHHHCTSCEEEESSSTTEE.STTC....SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                  FAD_binding_4   7 peseeevaaalrlaneaglpvlvrGgGssll.gqav....atggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                    p  e+ va++l++++++g+ v+++GgG+s++ g +      +  + ld++r++r++ ide +g a++eaGvt++++++ l
  gi|121638134|ref|YP_978358.1| 106 PNGEDAVADILHYCSDHGIAVVPFGGGTSVVgGLDPvrndFRAVISLDMRRFDRLHRIDEVSGEAELEAGVTGPEAERLL 185
                                    66799**************************76664677666679****99***************************** PP

                                    HHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTS CS
                  FAD_binding_4  82 aakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladG 133
                                     ++g+ lg+ p+s++ +t+GG+ at+++G+ s  yG + d++lgl+++++ G
  gi|121638134|ref|YP_978358.1| 186 GEHGFSLGHFPQSFEFATIGGFAATRSSGQDSAGYGRFNDMILGLRMITPVG 237
                                    **************************************************99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.034
                                    TTTEEEEETTSBHHHHHHHHHHHTTECSS CS
                  FAD_binding_4  62 eegtatveaGvtlgdlvealaakglllgl 90 
                                    ++ + tv aG +++ ++++laak+ +   
  gi|121638134|ref|YP_978358.1| 447 ASLYFTVVAGQRGDPIEQWLAAKKAASDA 475
                                    478999**************999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3951.16
//
Query:       gi|121638135|ref|YP_978359.1|  [L=309]
Description: diacylglycerol kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-27   96.2   1.6      1e-27   96.2   1.6    1.6  2  DAGK_cat      Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.019   14.7   0.5      0.024   14.3   0.5    1.1  1  Peripla_BP_6  Periplasmic binding protein
      0.026   13.7   4.1      0.068   12.4   4.1    1.7  1  NAD_kinase    ATP-NAD kinase


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   1.6   1.7e-31     1e-27       2     126 .]      14     136 ..      13     136 .. 0.97
   2 ?   -2.7   0.0      0.69   4.1e+03      16      42 ..     243     269 ..     238     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.7e-31
                                    EEEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCT CS
                       DAGK_cat   2 llvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelat 81 
                                    ++ + Np sG+g++ k+++ +   l+++gv++  i    ++da++l++ a ++g+d+++v GGDG+vs++l++l++   t
  gi|121638135|ref|YP_978359.1|  14 VTALTNPLSGHGAAVKAAHGAIARLKHRGVDVVEIVGGDAHDARHLLAAAVAKGTDAVMVTGGDGVVSNALQVLAG---T 90 
                                    77899**************************9999999**************************************...* PP

                                    TSEEEEEE-SS--HHHHHCT--S.SHHHHHHCHHCTBEEEEEEEEE CS
                       DAGK_cat  82 kpplgiiPlGtgNdlaralgigk.dieealesiikgetrkvdvgkv 126
                                    ++plgiiP+GtgNd ar +g+++ ++++a++ +++g t+++d+g++
  gi|121638135|ref|YP_978359.1|  91 DIPLGIIPAGTGNDHAREFGLPTkNPKAAADIVVDGWTETIDLGRI 136
                                    ***********************9*******************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.69
                                    HHHHHHCHHHHHHCTCEEEEEE--STT CS
                       DAGK_cat  16 ekllrkvrelleeagvelelieteepg 42 
                                     kllr +  +++ a+vel+ + t++++
  gi|121638135|ref|YP_978359.1| 243 TKLLRLFPTIFKGAHVELDEVSTTRAK 269
                                    466788889999999999988888765 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   3.9e-06     0.024     136     227 ..      12     103 ..       2     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-06
                                    CEEEEEEES.SHHHHHHHH..HHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHH CS
                   Peripla_BP_6 136 kkvalvyad.yafgregia..alkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaae 212
                                     kv  +++  +  g+++ a  ++ a +k  G++vv  e v  ++ d   +++++ a+g dav+++g+ + + ++l+ +a 
  gi|121638135|ref|YP_978359.1|  12 GKVTALTNPlSGHGAAVKAahGAIARLKHRGVDVV--EIVGGDAHDARHLLAAAVAKGTDAVMVTGGDGVVSNALQVLAG 89 
                                    444444444366666665533778889999****9..4577799************************************ PP

                                    TT-SSSCEEEECCC- CS
                   Peripla_BP_6 213 aGldakrillvswsg 227
                                    ++++ + i+ ++++ 
  gi|121638135|ref|YP_978359.1|  90 TDIPLG-IIPAGTGN 103
                                    ****85.44444443 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.1   1.1e-05     0.068      65     113 ..      52     102 ..       5     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                    ...EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS- CS
                     NAD_kinase  65 d..dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvk 113
                                    d  d r+ l a + +g d++ v GGDG +  + ++l+  +iP+  ++aG+ 
  gi|121638135|ref|YP_978359.1|  52 DahDARHLLAAAVAKGTDAVMVTGGDGVVSNALQVLAGTDIPLGIIPAGTG 102
                                    05588888999999****************************999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2444.93
//
Query:       gi|121638136|ref|YP_978360.1|  [L=167]
Description: hypothetical protein BCG_2271 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.6   0.2        0.2   11.6   0.2    2.1  2  MVL       Mannan-binding protein


Domain annotation for each model (and alignments):
>> MVL  Mannan-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   1.1e-05       0.2       2      24 ..      16      38 ..      15      48 .. 0.87
   2 ?   -2.4   1.0      0.25   4.5e+03      18      23 ..      97     103 ..      96     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                            MVL  2 peAqasCPsvCaalggeWnGqWt 24
                                   + A + +P+  aa+  +WnGq+ 
  gi|121638136|ref|YP_978360.1| 16 SLAATLAPNAVAAAEPSWNGQYL 38
                                   579999***99999999*****5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.25
                            MVL  18 eWnG.qW 23 
                                    +WnG qW
  gi|121638136|ref|YP_978360.1|  97 TWNGtQW 103
                                    5999555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1354.95
//
Query:       gi|121638137|ref|YP_978361.1|  [L=151]
Description: hypothetical protein BCG_2272c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-08   31.7   6.6    1.1e-07   31.5   6.6    1.0  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   6.6   6.2e-12   1.1e-07      64     191 ..      23     147 ..      12     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.2e-12
                           LysE  64 llGgayLlwlgvlalrdakekkveaeksveaslvkpflkgll..lslsNPkailfwlsvisallakaeqygdagrlilaa 141
                                    ++G+++Ll ++ + +   ++++ e   +++ +    ++ +l+  l++ NP +++++ +v  +l+    +   +  ++ ++
  gi|121638137|ref|YP_978361.1|  23 IVGAIVLLVIAAMGIGHGLRPSPEPVPAPQ-KQLGCVRFALIfgLTVINPATFVYFTAVAVTLAR---ALRATTAIAVVV 98 
                                    7899*************9999999999998.44444444544349999****************9...89999999999* PP

                           LysE 142 glvvasliwfsllaflaarlsrrlsskkvlriinvvvg.vlligfavklll 191
                                    g+ +asl+w  ll   +a+l++r  ++  +  ++v++g +++ +f++ l++
  gi|121638137|ref|YP_978361.1|  99 GVALASLLWQLLLVSAGAFLRSRATARV-R-RMTVLAGnAVIAAFGAVLVV 147
                                    *************999999998888885.4.567777658999****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1165.90
//
Query:       gi|121638138|ref|YP_978362.1|  [L=64]
Description: hypothetical protein BCG_2273c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.096   13.2   0.0       0.12   12.9   0.0    1.1  1  MerR-DNA-bind  MerR, DNA binding


Domain annotation for each model (and alignments):
>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.9e-06      0.12      30      55 ..      10      35 ..       3      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                                   TTTBHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 30 rappcqdvrallarklaeleeriaeL 55
                                   ra+pcq+v a+l+r   ++++r+++ 
  gi|121638138|ref|YP_978362.1| 10 RARPCQKVVAVLRRSKSHIDKRLDAA 35
                                   89********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 487.36
//
Query:       gi|121638139|ref|YP_978363.1|  [L=177]
Description: hypothetical protein BCG_2274c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-69  230.9   0.4    5.8e-69  230.6   0.4    1.0  1  DUF3145   Protein of unknown function (DUF3145)


Domain annotation for each model (and alignments):
>> DUF3145  Protein of unknown function (DUF3145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.6   0.4   3.2e-73   5.8e-69       1     157 []      21     174 ..      21     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 3.2e-73
                        DUF3145   1 vvyvhsapaalcpHvewavssvlgarvslkWtaqpaapgslraelsWegevgtaarlasaLraweelrfevtedpsegvd 80 
                                    vvy+h +paa+cpHvewa+ss+l+a+++l Wt+qpa p +lra ++W+g+vgt+arla+aLr+w+ lrfevtedps+gvd
  gi|121638139|ref|YP_978363.1|  21 VVYIHGSPAAVCPHVEWALSSTLQAKANLVWTPQPALPPQLRAVTNWVGPVGTGARLANALRSWSVLRFEVTEDPSPGVD 100
                                    89****************************************************************************** PP

                        DUF3145  81 geRysvtPelGlfsaatsanGdvvvsEdrlrallekaaedeeelaeeldkllGtawDeeLepfRsagegaevrwLhr 157
                                    g+R+s+tP+lGl+s+a+sanGd++v+E+rlra++++   ++++la+eld++lGtawD++Le++R +g+  ev+wL+r
  gi|121638139|ref|YP_978363.1| 101 GQRFSHTPQLGLWSGAMSANGDIMVGEMRLRAMMAQ---GADTLAAELDSVLGTAWDQALEVYRDGGDAGEVTWLSR 174
                                    **********************************95...5899********************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1374.17
//
Query:       gi|121638140|ref|YP_978364.1|  [L=272]
Description: hypothetical protein BCG_2275c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-34  119.0   4.2    5.1e-34  118.0   4.2    1.4  1  Beta-lactamase   Beta-lactamase
  ------ inclusion threshold ------
      0.072   12.7   0.0          1    8.9   0.0    2.1  2  Beta-lactamase2  Beta-lactamase enzyme family


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   4.2   5.7e-38   5.1e-34      15     318 ..      13     255 ..      10     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 5.7e-38
                                    SEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTCTTGGGTTE CS
                 Beta-lactamase  15 pGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPefagpgkgki 94 
                                    p +a+av+    v++++g            ++  +f++aSvtK+++a a+   veeG ++Ld+p           g  + 
  gi|121638140|ref|YP_978364.1|  13 PAAAAAVIGPAGVLATHG------------DTARVFALASVTKPLVARAAQVAVEEGVVNLDTPA----------GPPGS 70 
                                    566666666666665444............67789******************************..........77779 PP

                                    BHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHHHHHHHHHHHHTSHHHHHHHHHTTT CS
                 Beta-lactamase  95 TlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgygllgellekvtgrsleqllreeilr 174
                                    T+r+Ll HtsGl+ +                     + +    pGt+++Ysn+g+++l+e + + +g  ++++l+e +++
  gi|121638140|ref|YP_978364.1|  71 TVRHLLAHTSGLAMH---------------------SDQALARPGTRRMYSNYGFTVLAESVQRESGIEFGRYLTEAVCE 129
                                    ************555.....................3334556************************************* PP

                                    TTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEEEHHHHHHHHHHHHHCCSSSSHHHHHHHHHHH CS
                 Beta-lactamase 175 pLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglistardlarflglalegglllsaetlaqltakl 254
                                    pLgm  t l   +++     ag                       g  st++dla f+ + l++++++sa+ +a +t+ +
  gi|121638140|ref|YP_978364.1| 130 PLGMVTTRLDGGPAA-----AGF----------------------GATSTVADLAVFA-GDLLRPSTVSAQMHADATTVQ 181
                                    *********997777.....555......................669**********.444444444444444444444 PP

                                    TSEEEECTTEEEEC........ECSSEEEEECCH........TEEEEEEESTEEEEEEEECGGTEEEEEEESBCSSHHHH CS
                 Beta-lactamase 255 ssgttrpagiragl........glGwvladktga........pgtfghtGggygtyvfvdpeanlvvavltnrdppneda 318
                                      g +++ ++   +        glG+ + +++++         +tfgh G   g +++vdp+a+l+++vlt rd +  d 
  gi|121638140|ref|YP_978364.1| 182 FPGLDGVLPG---YgvqrpndwGLGFEIRNSKSPhwtgecnsTRTFGHFG-QSGGFIWVDPKADLALVVLTARDFG--DW 255
                                    4444443332...223345555666666666666****************.**********************996..33 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00011         1      11      43 ..      32      64 ..      25      68 .. 0.91
   2 ?    1.4   0.0     0.023   2.1e+02      98     153 ..     126     175 ..     119     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00011
                                   TTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-E CS
                Beta-lactamase2 11 adeefpaaStiKvpillalleavlegklslder 43
                                     ++f +aS+ K +++ a++ av+eg ++ld++
  gi|121638140|ref|YP_978364.1| 32 TARVFALASVTKPLVARAAQVAVEEGVVNLDTP 64
                                   5689**************************986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.023
                                    HHHHHCTHTTSB--SHTTCCHHHTTSSTTEE-HHHHHHHHHHHHHTTSSHHHHHHH CS
                Beta-lactamase2  98 awlkelglretrlrrklpdleaadkdkrntttardlarllealargellspeelle 153
                                    a+++ lg+ +trl++   +     ++   t+t++dla +   l r + +s++ +++
  gi|121638140|ref|YP_978364.1| 126 AVCEPLGMVTTRLDGGPAA-----AGFGATSTVADLAVFAGDLLRPSTVSAQ-MHA 175
                                    7788899999999987443.....578999**************99999995.554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1992.43
//
Query:       gi|121638141|ref|YP_978365.1|  [L=353]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-26   91.8   0.0    6.1e-26   91.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    7.2e-18   65.1   0.4    1.5e-17   64.1   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
      5e-17   62.5   0.0    8.3e-17   61.8   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.5e-16   60.6   0.0    2.3e-16   60.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-15   57.1   0.1    5.5e-15   55.8   0.1    1.7  1  Methyltransf_11  Methyltransferase domain
    1.4e-08   34.3   0.0    3.8e-08   33.0   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-07   31.3   0.0    2.2e-07   30.6   0.0    1.3  1  MTS              Methyltransferase small domain
    6.7e-06   25.5   0.1    1.2e-05   24.7   0.1    1.4  1  Methyltransf_2   O-methyltransferase domain
    8.2e-06   25.7   0.0    1.2e-05   25.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    8.4e-06   25.3   0.0    1.3e-05   24.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    1.1e-05   25.0   0.0    1.7e-05   24.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00037   21.5   0.1     0.0012   19.9   0.1    1.9  1  Methyltransf_24  Methyltransferase domain
    0.00039   19.9   0.0     0.0021   17.5   0.0    1.9  2  Methyltransf_4   Putative methyltransferase
     0.0031   17.1   0.0      0.005   16.5   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
     0.0061   16.6   0.0      0.009   16.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0078   16.2   0.2      0.016   15.2   0.2    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0084   15.5   0.0      0.013   14.9   0.0    1.2  1  TehB             Tellurite resistance protein TehB
     0.0095   14.9   0.0      0.015   14.3   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.041   13.3   0.0      0.072   12.5   0.0    1.4  1  Zn_peptidase_2   Putative neutral zinc metallopeptidase
      0.066   12.4   0.0       0.13   11.4   0.0    1.4  1  Methyltransf_20  Putative methyltransferase
        0.1   11.6   0.0       0.16   11.0   0.0    1.2  1  DREV             DREV methyltransferase
       0.21   11.9   0.0       0.36   11.1   0.0    1.3  1  DRE2_N           Fe-S cluster assembly protein DRE2 N-terminu


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   7.5e-29   6.1e-26       2     151 ..     170     330 ..     169     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 7.5e-29
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                    ++g  v D GCG+G+ ++ +a +++  ++++GiD+s ea+   +e+a++lgl n++Fe+ d  el+k      +D+i+ +
  gi|121638141|ref|YP_978365.1| 170 RSGADVADFGCGSGRAVKLMA-QAFGASRFTGIDFSDEAVAAGTEEAARLGLANATFERHDLAELDKV---GAYDVITVF 245
                                    57889****************.777789**************************************87...89******* PP

                Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelpakveeeskay..evvegak...........igt..qkdelye 146
                                    ++++++a p+ +l++i r+l+pgg+ll+ d+++ ++l ++v      y  +++ +++            gt  + + +++
  gi|121638141|ref|YP_978365.1| 246 DAIHDQAQPARVLQNIYRALRPGGVLLMVDIKASSQLEDNVGVPLSTYlyTTSLMHCmtvslaldgagLGTvwGRQLATS 325
                                    ********************************777777555332222246666666666677776666566656666666 PP

                Methyltransf_31 147 lleea 151
                                    +l+ a
  gi|121638141|ref|YP_978365.1| 326 MLADA 330
                                    66655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.1   1.9e-20   1.5e-17       1      97 []     175     269 ..     175     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.9e-20
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    v d+GcG+Gr ++ +a+++g++++tg+D+s+e+++a  e+a++ gl n++f+++d+ +l+   g +D+++++ a+h   +
  gi|121638141|ref|YP_978365.1| 175 VADFGCGSGRAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLaNATFERHDLAELDK-VGAYDVITVFDAIHD--Q 251
                                    78*****************************************999*************95.57*******877774..5 PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                    ++ +++l++i+r+L+pgG
  gi|121638141|ref|YP_978365.1| 252 AQPARVLQNIYRALRPGG 269
                                    67889************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0     1e-19   8.3e-17       2      99 .]     177     271 ..     176     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1e-19
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                    ++GcG+G+ ++ +++++  +++tg+D+s +a+++  e+ a+ +    +n ++e  dl++ld+ +++D++++++++h  ++
  gi|121638141|ref|YP_978365.1| 177 DFGCGSGRAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGL---ANATFERHDLAELDKVGAYDVITVFDAIHDQAQ 253
                                    8*******************************666666666664...67778888888888889**************** PP

                Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                    +++vl+ni+++L+pgG+l
  gi|121638141|ref|YP_978365.1| 254 PARVLQNIYRALRPGGVL 271
                                    ****************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   2.8e-19   2.3e-16      13     164 ..     162     336 ..     150     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.8e-19
                Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg 81 
                                    ++ l+++lr+g+ v d+GcG+G+  +++ +++g+  +tg+D s+eav+            +a + ++d +    + ++ g
  gi|121638141|ref|YP_978365.1| 162 VDGLPDRLRSGADVADFGCGSGRAVKLMaQAFGAsRFTGIDFSDEAVAAGTeeaarlglaNATFERHDLA----ELDKVG 237
                                    55577889********************55568889********99887768998885554444444444....555667 PP

                Methyltransf_23  82 kfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl..............kedrllldwly.lvpag.rhisf 145
                                     +d+I+ ++ ++    p+++l++i++ l+pgG+ll  ++ as+              + ++l++ ++  l+ +g +++ +
  gi|121638141|ref|YP_978365.1| 238 AYDVITVFDAIHDQAQPARVLQNIYRALRPGGVLLMVDIKASSqlednvgvplstylYTTSLMHCMTVsLALDGaGLGTV 317
                                    ***************************************998889999999888876555554444321344444999** PP

                Methyltransf_23 146 fsarslkelleeaGlevve 164
                                    + ++    +l +aG+++v+
  gi|121638141|ref|YP_978365.1| 318 WGRQLATSMLADAGFTDVT 336
                                    **777788889****9997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.1   6.7e-18   5.5e-15       2      95 ..     177     272 ..     176     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 6.7e-18
                                    EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                    d+GcG+Gr ++ +a+++  +r +g+D+s+e++++  e+a + gl + +f + d+ +l  + + +D+++++ ++h  ++p+
  gi|121638141|ref|YP_978365.1| 177 DFGCGSGRAVKLMAQAFgaSRFTGIDFSDEAVAAGTEEAARLGLaNATFERHDLAELD-KVGAYDVITVFDAIHDQAQPA 255
                                    89************7777*********************9999999999999999985.4478***************** PP

                                    HHHHHHHHHEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                    ++l++i+R L+pgG+l+
  gi|121638141|ref|YP_978365.1| 256 RVLQNIYRALRPGGVLL 272
                                    **************997 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   4.7e-11   3.8e-08      46     154 ..     170     276 ..     166     312 .. 0.85
   2 ?   -2.1   0.0       2.4     2e+03     205     220 ..     324     339 ..     317     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.7e-11
                                    --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                    ++ga+v D  +G+g  a+kl+ ++    + +++D++++ +  g + + + g  n  f   +  eL+   +++Dv+tv   
  gi|121638141|ref|YP_978365.1| 170 RSGADVADFGCGSGR-AVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLANATFERHDLAELDK-VGAYDVITVFDA 247
                                    679999*******97.6777777777789****************************9999998874.59********** PP

                                    GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                Ubie_methyltran 126 lrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                    + + +   ++L+++yr l+pGG l+++++
  gi|121638141|ref|YP_978365.1| 248 IHDQAQPARVLQNIYRALRPGGVLLMVDI 276
                                    ***********************999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                    HHHHHHTTEEEEEEEE CS
                Ubie_methyltran 205 keliedaGfksveyes 220
                                     +++ daGf+ v+  +
  gi|121638141|ref|YP_978365.1| 324 TSMLADAGFTDVTVAE 339
                                    58999****9997655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.7e-10   2.2e-07      23     139 ..     161     275 ..     144     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.7e-10
                                    HHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EE CS
                            MTS  23 Lletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfd 99 
                                    L++ lp++     +v+D+GcG G     +a++    + t +d + +A+++ +e +++ +l+ +++  +d+ e  + + +d
  gi|121638141|ref|YP_978365.1| 161 LVDGLPDRlrSGADVADFGCGSGRAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLAnATFERHDLAELDKVGAYD 240
                                    67778888756678***********99*****************************99999899999999999899**** PP

                                    EEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEE CS
                            MTS 100 livsNPPfhagkatelavaeeliaeAkeaLkegGeLliVa 139
                                    +i     +h++ +       +++++  +aL++gG Ll+V 
  gi|121638141|ref|YP_978365.1| 241 VITVFDAIHDQAQ-----PARVLQNIYRALRPGGVLLMVD 275
                                    *********9999.....56777777899*********95 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.5e-08   1.2e-05      63     176 ..     172     285 ..     132     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.5e-08
                                    -SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS---.--TTEEEEES-TTT.S-----SEEEEESSGGGS CS
                 Methyltransf_2  63 lkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsag.eeervefvgGdffk.dslPeaDaillkrvlhDw 140
                                       + D G G+G ++k +++a+   + +  D+++ + aA +   a     + +f   d+ + d++   D+i +   +hD 
  gi|121638141|ref|YP_978365.1| 172 GADVADFGCGSGRAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARlGLANATFERHDLAElDKVGAYDVITVFDAIHDQ 251
                                    4568899*************************998888877732221235567777777644778888888888888886 PP

                                    -HHHHHHHHHHHHHH--TT-EEEEEE----TTS--- CS
                 Methyltransf_2 141 sdekcvklLkrvkkalpagGkvivveavlgadpsge 176
                                    +  + +++L+++++al++gG +++v+   + + +++
  gi|121638141|ref|YP_978365.1| 252 A--QPARVLQNIYRALRPGGVLLMVDIKASSQLEDN 285
                                    5..6689******************98766655554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.5e-08   1.2e-05      71     179 ..     169     281 ..     136     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-08
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-.....GGGTTGGG-SEEE CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD.....GrkGyeekaPYda 145
                                    l+ ga v + G+GsG    ++a+ +g++    +i+ + e v++ +++  +l+l+n ++   D         y+  + +da
  gi|121638141|ref|YP_978365.1| 169 LRSGADVADFGCGSGRAVKLMAQAFGASR-FTGIDFSDEAVAAGTEEAARLGLANATFERHDlaeldKVGAYDVITVFDA 247
                                    899***********************986.99***********99999999999666655442111066679999***** PP

                                    EEESSBBSS--HHHHHTEEEEEEEEE.EESBSSSE CS
                           PCMT 146 ihvgaaapeiPealidQLkeGGrlvv.PvgeeeeQ 179
                                    ih  a +  + +++ + L +GG l++  ++  ++Q
  gi|121638141|ref|YP_978365.1| 248 IHDQAQPARVLQNIYRALRPGGVLLMvDIK-ASSQ 281
                                    **********************97651455.5555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.6e-08   1.3e-05      59     171 ..     168     280 ..     158     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                                    T--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEEEEES CS
                           CMAS  59 elkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrvvsvg 135
                                    +l+ G  + d GcG G  v+ +++ ++++   g+ +S+e  +   ++ ++l+l+ +++ +  d  +ld+   +d +  ++
  gi|121638141|ref|YP_978365.1| 168 RLRSGADVADFGCGSGRAVKLMAQAFGASrFTGIDFSDEAVAAGTEEAARLGLA-NATFERHDLAELDKvgAYDVITVFD 246
                                    6899***********************96278********************76.578999999*999887888776665 PP

                                    -GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                           CMAS 136 afehvgkenydtffkklkkllkedGllllhtitslh 171
                                    a+    +++ ++  ++++++l+++G+ll+  i + +
  gi|121638141|ref|YP_978365.1| 247 AIH--DQAQPARVLQNIYRALRPGGVLLMVDIKASS 280
                                    554..355667899**************98887665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.1e-08   1.7e-05     156     258 ..     166     273 ..     159     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.1e-08
                           PrmA 156 eklvkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvi.va 232
                                     + +++g+ v D+G+GSG    + a+ +ga++ +++D  + Av +  e a++ ++++  +e +  +el k + +dvi v 
  gi|121638141|ref|YP_978365.1| 166 PDRLRSGADVADFGCGSGrAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLANaTFERHDLAELDKVGAYDVItVF 245
                                    56689999**********66899**********************99988887777758888888888888999998444 PP

                           PrmA 233 NILaevl..ielaedikklvkeggllil 258
                                      + +     + +++i++++++gg+l++
  gi|121638141|ref|YP_978365.1| 246 DAIHDQAqpARVLQNIYRALRPGGVLLM 273
                                    4444333124666777777777777665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.4e-06    0.0012       4     105 ..     179     275 ..     176     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-06
                Methyltransf_24   4 GvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikads.eealasla.agsiDll.fiDggha 80 
                                    G+ sG+   ++++a+ +   +r + +d     e++aa  +e   ++r+ l +a++ ++ la+l+  g +D++ ++D+ h+
  gi|121638141|ref|YP_978365.1| 179 GCGSGRAVKLMAQAFGA---SRFTGIDFSD--EAVAAGTEE---AARLGLANATFeRHDLAELDkVGAYDVItVFDAIHD 250
                                    66699999999887765...5689***988..455555555...7777777777744478888877899*87367***** PP

                Methyltransf_24  81 aeavledleallprlapggvvlfdD 105
                                    +++ ++ l+++ + l+pggv+l+ D
  gi|121638141|ref|YP_978365.1| 251 QAQPARVLQNIYRALRPGGVLLMVD 275
                                    *********************9866 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-06    0.0021       4      59 ..     174     229 ..     171     238 .. 0.92
   2 ?   -0.4   0.0      0.82   6.7e+02      99     115 ..     257     273 ..     252     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES- CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgd 59 
                                     v++ GcG+G+++  +A+++    f Gi+ + + va+  +++++l+l N    r+d
  gi|121638141|ref|YP_978365.1| 174 DVADFGCGSGRAVKLMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLANATFERHD 229
                                    5899*********************************************9888887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.82
                                    HHHHHHHHEEEEEEEEE CS
                 Methyltransf_4  99 llkelarvLkkgGvlel 115
                                    +l+++ r+L++gGvl +
  gi|121638141|ref|YP_978365.1| 257 VLQNIYRALRPGGVLLM 273
                                    68999*********987 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.1e-06     0.005      11     101 ..     169     264 ..     164     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-06
                           MetW  11 ikpgsrvldlGcGdGellellkeekqv.dgrGleldeegvaecvakGlsv..iqgdld.kdlenfed.ksfdyvvlsqtl 85 
                                    +++g+ v d GcG G  ++l+++  +  +  G++ ++e+va+ ++    +   +   + +dl++ +   ++d++ +  ++
  gi|121638141|ref|YP_978365.1| 169 LRSGADVADFGCGSGRAVKLMAQAFGAsRFTGIDFSDEAVAAGTEEAARLglANATFErHDLAELDKvGAYDVITVFDAI 248
                                    577899***************9987762568*********998876544400333333257776654268********** PP

                           MetW  86 qatrnpkevldellri 101
                                        +p++vl+++ r 
  gi|121638141|ref|YP_978365.1| 249 HDQAQPARVLQNIYRA 264
                                    ************9885 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05     0.009      24      90 ..     170     231 ..     152     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90 
                                    ++  +v+D+G+G g     +a+        +++gid ++e v++  + a++lg  + ++  f+ ++ +
  gi|121638141|ref|YP_978365.1| 170 RSGADVADFGCGSGRAVKLMAQ---AfGASRFTGIDFSDEAVAAGTEEAARLG--L-ANATFERHDLA 231
                                    55679*********98888777...44799***********************..4.45555544444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2     2e-05     0.016       5      93 ..     185     281 ..     181     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                                    HHHHHHHHTT-.EEEEEESSHHHH....HHHHHTT.ESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC....SHHHHHH CS
                     ADH_zinc_N   5 aavqlAkalGa.eviavdsseekl....elakklG.adevinykeadlverikeltggegvdvvfecvG....sgatlea 74 
                                    a+  +A a+Ga + +++d s+e +    e a++lG a++++ +++    +++ +     +v  vf+++       ++l++
  gi|121638141|ref|YP_978365.1| 185 AVKLMAQAFGAsRFTGIDFSDEAVaagtEEAARLGlANATFERHD---LAELDKVG-AYDVITVFDAIHdqaqPARVLQN 260
                                    5556899***************8788889**************44...44444444.344444555555211166799** PP

                                    HHHCEEEEEEEEECSC..TSS CS
                     ADH_zinc_N  75 alkllkpgGrlvvvGg..gkg 93 
                                     +++l+pgG l +v +  +++
  gi|121638141|ref|YP_978365.1| 261 IYRALRPGGVLLMVDIkaSSQ 281
                                    ************998765444 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05     0.013      32     142 ..     173     283 ..     167     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                    -EEEEES-TTSHHH.HHHHHTT-.EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS- CS
                           TehB  32 gkvldlgcgqgrns.lylsllgy.dvtawdknensiafleeikekenlknistalydineaklderydfilstvvlmfle 109
                                    + v d+gcg+gr   l  ++ g    t +d  ++++a   e + +  l n + +  d+ e++    yd i  tv   + +
  gi|121638141|ref|YP_978365.1| 173 ADVADFGCGSGRAVkLMAQAFGAsRFTGIDFSDEAVAAGTEEAARLGLANATFERHDLAELDKVGAYDVI--TVFDAIHD 250
                                    6789********8624555666525799*********9999999999999999999*9999999999987..66666666 PP

                                    GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS- CS
                           TehB 110 aeripsiienmqectkvggynlivaamstddvp 142
                                    + + +++++n+ +  ++gg  l+v    + ++ 
  gi|121638141|ref|YP_978365.1| 251 QAQPARVLQNIYRALRPGGVLLMVDIKASSQLE 283
                                    6677799*************9999765555444 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.8e-05     0.015     116     236 ..     172     293 ..     158     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                    T-EEEEET-TTSHHHHHHHHC.T-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvge.gaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyh 194
                                    g  ++d Gcg+G  +  m+ + ga+   Gid s   +         lg  + +++    + +l+++ a+d++     ++ 
  gi|121638141|ref|YP_978365.1| 172 GADVADFGCGSGRAVKLMAQAfGASRFTGIDFSDEAVAAGTEEAARLGLANATFER-HDLAELDKVGAYDVITVFDAIHD 250
                                    55799********99888754499*******9998877654333344444444443.5679******************* PP

                                    -S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-.TT-EE--SS-B CS
                 Methyltransf_9 195 rrsPldhllqlkdqlvkgGelvletlvieGd.enavlvPedry 236
                                    +  P   l+++  +l+ gG l++  +    + e++v vP  +y
  gi|121638141|ref|YP_978365.1| 251 QAQPARVLQNIYRALRPGGVLLMVDIKASSQlEDNVGVPLSTY 293
                                    ********************99866555544255666776666 PP

>> Zn_peptidase_2  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.9e-05     0.072      37      68 ..     319     350 ..     314     353 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                 Zn_peptidase_2  37 GaevArkiLdknglkdVkveeveGeltDhYdp 68 
                                    G+++A+++L+++g +dV+v e+e+++ ++Y  
  gi|121638141|ref|YP_978365.1| 319 GRQLATSMLADAGFTDVTVAEIESDVLNNYYI 350
                                    99**********************99999965 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.13     136     246 ..     174     274 ..     166     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                Methyltransf_20 136 rildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgdafdeeslaalePrptlaivsG 215
                                     + d  +G Gr v   l +++  ++  +  d+s+  v++G++ +a+ gl++  +fe+ d  + +++ a        ++  
  gi|121638141|ref|YP_978365.1| 174 DVADFGCGSGRAVK--LMAQAFGASRFTGIDFSDEAVAAGTEEAARLGLANA-TFERHDLAELDKVGA------YDVI-T 243
                                    57899999999884..44444446778888*******************997.676666555555444......4444.4 PP

                Methyltransf_20 216 lyelfpdndlvkrslaGlaeavepgglliyt 246
                                    +++   d ++ +r l+ + +a++pgg+l+  
  gi|121638141|ref|YP_978365.1| 244 VFDAIHDQAQPARVLQNIYRALRPGGVLLMV 274
                                    6888899999999999999999999999865 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.16      97     185 ..     174     272 ..     165     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                           DREV  97 klldlGaGdGeitkrvaptfee...........vyatelsetmrdrlkkkkynvlsalelqetdvkldlilclnlldrcf 165
                                     + d+G G G   k +a+ f               a+   e  r  l    ++     el++ +  +d+i++++ +    
  gi|121638141|ref|YP_978365.1| 174 DVADFGCGSGRAVKLMAQAFGAsrftgidfsdeAVAAGTEEAARLGLANATFERHDLAELDKVG-AYDVITVFDAIHDQA 252
                                    5779999999999999999988888998777775566666677777888888877777777555.7************** PP

                           DREV 166 dplklledirsalepngrvi 185
                                    +p ++l++i+ al+p g  +
  gi|121638141|ref|YP_978365.1| 253 QPARVLQNIYRALRPGGVLL 272
                                    **************977543 PP

>> DRE2_N  Fe-S cluster assembly protein DRE2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00044      0.36      49      91 ..     237     275 ..     227     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                    SS--SEEEE---..SS-S----HHHHHHHHTT--TT--EE--- CS
                         DRE2_N  49 stYdlvllltdeeeeeeelliprkliqkivkaLkpgGklkgqd 91 
                                     +Yd++ ++     +  +  +p +++q i++aL+pgG l   d
  gi|121638141|ref|YP_978365.1| 237 GAYDVITVFDAI--H--DQAQPARVLQNIYRALRPGGVLLMVD 275
                                    589999998766..4..667889**************996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.50u 0.19s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2818.86
//
Query:       gi|121638142|ref|YP_978366.1|  [L=361]
Description: zinc-dependent alcohol dehydrogenase AdhE2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-27   93.3   0.9    1.5e-26   92.4   0.9    1.5  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    2.2e-26   92.3   0.1    4.1e-26   91.5   0.1    1.4  1  ADH_zinc_N       Zinc-binding dehydrogenase
      5e-09   37.3   0.0    9.9e-09   36.4   0.0    1.4  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    1.1e-06   28.2   0.6    6.7e-05   22.5   1.1    2.2  2  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.005   16.2   0.7       0.01   15.2   0.7    1.4  1  ThiF             ThiF family
     0.0098   15.2   3.9      0.016   14.5   3.9    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.07   13.4   0.4       0.13   12.6   0.4    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.14   12.7   0.6       0.49   11.0   0.6    2.1  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.15   11.4   0.3       0.27   10.6   0.3    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.16   11.5   1.5       0.26   10.8   0.7    1.7  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.16   11.3   4.0       0.22   10.9   4.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.9   9.2e-30   1.5e-26       1     109 []      29     148 ..      29     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 9.2e-30
                                    TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG CS
                          ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenl 80 
                                    pge++++v+a+g+C++Dl + +gg  ++ ++p+ lGHE++G++e+vgp+v+ ++ Gd V++++   cg+C+aCk+g++++
  gi|121638142|ref|YP_978366.1|  29 PGEAVVDVTACGVCHTDLTYREGG--INDEYPFLLGHEAAGIIEAVGPGVTAVEPGDFVILNWRAVCGQCRACKRGRPRY 106
                                    5899******************95..****************************************************** PP

                                    -............TTBEETTTS......S-SSSBSEEEECGGGEEEE CS
                          ADH_N  81 C............eeakllgvs......ldGgfaeyvvvpekklvkl 109
                                    C            +++     +        G+fa++++v++ ++ k+
  gi|121638142|ref|YP_978366.1| 107 CfdtfnaeqkmtlTDG-----TeltaalGIGAFADKTLVHSGQCTKV 148
                                    ***9998766665222.....1333445789*******999999875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.1   2.5e-29   4.1e-26       1     128 [.     190     322 ..     190     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.5e-29
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    gvG aa++ A+  Ga ++iavd ++ kl+ a+ +Ga++++n++e d+v++i  lt+g g+dvv+++vG ++t+++a+ + 
  gi|121638142|ref|YP_978366.1| 190 GVGDAAIAGAALVGAkRIIAVDTDDTKLDWARTFGATHTVNAREVDVVQAIGGLTDGFGADVVIDAVGRPETYQQAFYAR 269
                                    8*****************************************666*********************************** PP

                                    EEEEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSC..HHHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGg..gkgeeefdlrnlllkeksilGsllgs..lreefkealdll 128
                                    +  G++v+vG+  + +  +++l +++ +   ++ s++g+  + ++f++++dl 
  gi|121638142|ref|YP_978366.1| 270 DLAGTVVLVGVptPDMRLDMPLVDFFSHGGALKSSWYGDclPESDFPTLIDLY 322
                                    ***********99889999********************99999***999985 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   6.1e-12   9.9e-09       2     126 ..     224     353 ..     223     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 6.1e-12
                                    T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--...S-EEE-CHHHCTTT-EEE CS
                   ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp..lsaallkpakkrkgrsvk 74 
                                    GA++ ++ r+ d++      t+g g Dvv+d+vg ++++++++ + +  G++v +g      ++ +++ + ++  g+++k
  gi|121638142|ref|YP_978366.1| 224 GATHTVNAREVDVVqaigGLTDGFGADVVIDAVGRPETYQQAFYARDLAGTVVLVGvP-TpdMRLDMPLVDFFSHGGALK 302
                                    9********999998999899999**********7777799985556679*9888843.34799999999********** PP

                                    E--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS- CS
                   ADH_zinc_N_2  75 yeflfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesgr 126
                                     +++ +  +    d + +l +l+ +G+  l+  v+++ +le++ eA+ +++ g+
  gi|121638142|ref|YP_978366.1| 303 SSWYGDCLPE--SD-FPTLIDLYLQGRlpLQRFVSERIGLEDVEEAFHKMHGGK 353
                                    ****986665..77.************777899*****************9987 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.1   4.1e-08   6.7e-05      31     136 ..     180     284 ..     168     295 .. 0.78
   2 ?    3.0   0.0     0.038        61     182     203 ..     329     350 ..     319     361 .] 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.1e-08
                    Glu_dehyd_C  31 pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatY.vdsretp.vdeipease..emdlvvE 106
                                     +++ v+G G +G  a+a  ++   g +r+  ++   ++d ++d  +  Gat  v+ re + v+ i   +     d+v++
  gi|121638142|ref|YP_978366.1| 180 DDTVAVIGCGGVGDAAIAGAAL--VGAKRIIAVD---TDDTKLDWARTFGATHtVNAREVDvVQAIGGLTDgfGADVVID 254
                                    678999*******988776665..5788887777...5888***********83556655414455555442257***** PP

                    Glu_dehyd_C 107 aTGsakhafeaiealapnGvaaLlGvpeds 136
                                    a G ++   +a  a + +G ++L+Gvp++ 
  gi|121638142|ref|YP_978366.1| 255 AVGRPETYQQAFYARDLAGTVVLVGVPTPD 284
                                    ***************************975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                    Glu_dehyd_C 182 ldelvtkvvdldeleeAfeddd 203
                                    l+++v+++++l+++eeAf++ +
  gi|121638142|ref|YP_978366.1| 329 LQRFVSERIGLEDVEEAFHKMH 350
                                    7899**************9766 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.7   6.1e-06      0.01      18      52 ..     180     214 ..     177     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.1e-06
                                    TSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  18 dskvllvGaGglGsellknLalsGvgkltlvDnDk 52 
                                    d +v+++G+Gg+G  ++   al+G +++  vD D 
  gi|121638142|ref|YP_978366.1| 180 DDTVAVIGCGGVGDAAIAGAALVGAKRIIAVDTDD 214
                                    6689*****************************97 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   3.9   9.7e-06     0.016      16      87 ..     170     238 ..     156     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.7e-06
                                    EEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHH CS
                    AlaDh_PNT_C  16 kgtlaGgvpgvepakvlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvevlksqeellae 87 
                                      +  Ggv+  +  +v viG G +G +Aia a+ +gak + ++D++ ++l   +++ga+  +++++ e  + +
  gi|121638142|ref|YP_978366.1| 170 AAINTGGVT--RDDTVAVIGCGGVGDAAIAGAALVGAKrIIAVDTDDTKLDWARTFGAT--HTVNAREVDVVQ 238
                                    556678888..9999*********************9658999********99999998..443333333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   7.7e-05      0.13       1      80 [.     183     259 ..     183     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SS CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnlsp 78 
                                    v +iG+G+vG a++   a  +    +i+ +d +++kl+ +     g +++  a  ++ ++a +  l  +   d+v+++++
  gi|121638142|ref|YP_978366.1| 183 VAVIGCGGVGDAAIAGAALVGAK--RIIAVDTDDTKLDWART--FGATHTVNAREVDVVQA-IGGLTDGFgaDVVIDAVG 257
                                    689*****************998..***********887764..45555555555555666.666555557899999987 PP

                                    GG CS
                Sacchrp_dh_NADP  79 pi 80 
                                      
  gi|121638142|ref|YP_978366.1| 258 RP 259
                                    65 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6    0.0003      0.49       1      60 [.     182     241 ..     182     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaae 60 
                                    ++++iG+G +g a + g++  g  ++ i+ a   + ++   +a+++g    v++ +vd  +a+ 
  gi|121638142|ref|YP_978366.1| 182 TVAVIGCGGVGDAAIAGAALVG--AKRII-A-VDTDDTKLDWARTFGathtVNAREVDVVQAIG 241
                                    58********************..77777.7.56666666999999977776666666666654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00016      0.27      34      73 ..     178     218 ..     170     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                    GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH CS
                   2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee 73 
                                     ++ tv++iG+G +G a++  ++ +g+ ++ia+d+  +k +
  gi|121638142|ref|YP_978366.1| 178 TRDDTVAVIGCGGVGDAAIAGAALVGAkRIIAVDTDDTKLD 218
                                    5789***********************67888888766554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00016      0.26       2      37 ..     182     218 ..     181     240 .. 0.91
   2 ?   -1.9   0.0       1.3   2.1e+03      78      88 ..     274     284 ..     249     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                    EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHH CS
                 UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeig.hevigvDideekvd 37 
                                    +++viG G vG    a  a +g + +i vD d++k d
  gi|121638142|ref|YP_978366.1| 182 TVAVIGCGGVGDAAIAGAALVGaKRIIAVDTDDTKLD 218
                                    699*******************889*********987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                    SEEEE-----B CS
                 UDPG_MGDP_dh_N  78 dvifiaVgTPs 88 
                                     v+++ V+TP 
  gi|121638142|ref|YP_978366.1| 274 TVVLVGVPTPD 284
                                    58899999996 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.0   0.00014      0.22     160     231 ..     178     253 ..     170     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                           PrmA 160 kegeevlDvGtG.SGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkvea.klevals.eellkeekadviv 231
                                     ++++v  +G+G  G  aia aa++gak+++avD+D+  ++ a+   +   v+a +++v ++ + l++   adv++
  gi|121638142|ref|YP_978366.1| 178 TRDDTVAVIGCGgVGDAAIAgAALVGAKRIIAVDTDDTKLDWARTFGATHTVNArEVDVVQAiGGLTDGFGADVVI 253
                                    567899999*972588999857788******************999888888886666643314444455566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2469.57
//
Query:       gi|121638143|ref|YP_978367.1|  [L=211]
Description: hypothetical protein BCG_2278 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-19   70.1  11.3    3.6e-19   69.5  11.3    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
      0.001   18.6   1.5     0.0035   16.9   1.5    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0041   17.0   0.3       0.02   14.8   0.1    2.2  3  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
        1.7    9.2   9.9        6.7    7.3   1.6    4.0  4  PQQ_3          PQQ-like domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5  11.3   8.1e-23   3.6e-19       6     197 .]      24     190 ..      20     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 8.1e-23
                                    SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                    Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                     n++l+ +d +v+++D+  +++            +++++v avi TH+H DH+  +++l  a d+pv +++ +a  ++m 
  gi|121638143|ref|YP_978367.1|  24 NNIWLVGDDSEVVVFDAAHHAAPIID-------AVGGRKVVAVICTHGHNDHVTVAPELGTALDAPVLMHPGDAVLWRMT 96 
                                    69***********************8.......5********************************************** PP

                                    HHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE....TTCCEEEECTTTSSHHCCCCC CS
                    Lactamase_B  86 eaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey....gggkvlftGDallagetgrid 161
                                    ++d+                + +   ++d  + g+ +l + ++pgh++g+++ ++    +g +++f+GD+l+ag  g ++
  gi|121638143|ref|YP_978367.1|  97 HPDK----------------SFRAVSDGDAVRVGGTELRALHTPGHSPGSVCWYApelgPGTGTVFSGDTLFAGGPGATG 160
                                    **55................6699******************************933334679***************** PP

                                    C.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                    Lactamase_B 162 ltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                    + + +++++ +s+ + +        +l+ +++v  gH
  gi|121638143|ref|YP_978367.1| 161 RSYSDFPTILRSISGRLG-------ALPGDTVVHtGH 190
                                    966666666666655555.......888888887777 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.5   7.8e-07    0.0035      21     144 ..      46     151 ..      31     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-07
                                    --S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEEC CS
                  Lactamase_B_2  21 Pve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelg 99 
                                    P   ++   +++ aV+ th+H DH++ ++ l +    ++p++ ++g +   +          +p  +++ +  g+ +++g
  gi|121638143|ref|YP_978367.1|  46 PIIdAVGG-RKVVAVICTHGHNDHVTVAPELGTAL--DAPVLMHPGDAVLWRMT--------HPDKSFRAVSDGDAVRVG 114
                                    44433443.7999************9888888833..36777776644433333........234577889999999998 PP

                                    STTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                  Lactamase_B_2 100 dggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                      g e++a   ++ s+         +++  ++ +g   +++gDt 
  gi|121638143|ref|YP_978367.1| 115 --GTELRALHTPGHSPG-----SVCWYAPELG-PGTGTVFSGDTL 151
                                    ..557788877777777.....3345555555.888888888885 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.12   5.5e+02      88     110 ..      16      38 ..       6      50 .. 0.78
   2 !   14.8   0.1   4.4e-06      0.02       7      85 ..      24     125 ..      19     152 .. 0.73
   3 ?   -1.4   0.0      0.41   1.8e+03     105     116 ..     182     193 ..     176     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                  Lactamase_B_3  88 vggsergenngflleqdgltiyh 110
                                     ggs++  nn++l+ +d   +++
  gi|121638143|ref|YP_978367.1|  16 DGGSWEVDNNIWLVGDDSEVVVF 38 
                                    47899999*****9998666654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.4e-06
                  Lactamase_B_3   7 hnsflletagarilvDPfka..nlgyeppa....eeaDlvlisqaledHahletlkql.....................a 59 
                                     n +l+ ++  +++ D  +    +          +++ +v+ +++++dH ++++  +                      +
  gi|121638143|ref|YP_978367.1|  24 NNIWLVGDDSEVVVFDAAHHaaPII----DavggRKVVAVICTHGHNDHVTVAPELGTaldapvlmhpgdavlwrmthpD 99 
                                    5667777777777777654322222....1234489999************99888877788888888888888888888 PP

                  Lactamase_B_3  60 envkvleegeslevggleiravatsh 85 
                                    + ++ +++g++++vgg+e+ra +t  
  gi|121638143|ref|YP_978367.1| 100 KSFRAVSDGDAVRVGGTELRALHTPG 125
                                    88888888999999999999998865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.41
                  Lactamase_B_3 105 gltiyhlGhlah 116
                                    g t++h Gh++ 
  gi|121638143|ref|YP_978367.1| 182 GDTVVHTGHGDS 193
                                    67899***9986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.052   2.3e+02      21      39 ..      23      41 ..      15      41 .. 0.87
   2 ?   -1.6   0.0      0.95   4.3e+03      17      27 ..      46      59 ..      43      65 .. 0.74
   3 ?    2.2   0.0     0.061   2.8e+02       3      29 ..      91     115 ..      90     123 .. 0.64
   4 ?    7.3   1.6    0.0015       6.7       1      29 [.     129     156 ..     129     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.052
                          PQQ_3 21 gglvyvgtgdGtlyAlDae 39
                                   ++ +  +++d  ++ +Da+
  gi|121638143|ref|YP_978367.1| 23 DNNIWLVGDDSEVVVFDAA 41
                                   678899999********95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.95
                          PQQ_3 17 p...avdgglvyvg 27
                                   p   av+g++v+++
  gi|121638143|ref|YP_978367.1| 46 PiidAVGGRKVVAV 59
                                   44558899988764 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.061
                          PQQ_3   3 vlWsvqlpgpvnsspavdgglvyvgtg 29 
                                    vlW+ + p++  +  av++g  + ++g
  gi|121638143|ref|YP_978367.1|  91 VLWRMTHPDKSFR--AVSDGDAVRVGG 115
                                    89**999998543..666665554444 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0015
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg 29 
                                    G v+W  +  gp+ ++++++g+++++g++
  gi|121638143|ref|YP_978367.1| 129 GSVCWYAPELGPG-TGTVFSGDTLFAGGP 156
                                    5667777666787.789**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1334.04
//
Query:       gi|121638144|ref|YP_978368.1|  [L=502]
Description: hypothetical protein BCG_2279c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-17   63.6   0.4    3.7e-17   62.5   0.1    1.6  2  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0     0.099   1.8e+03      30      44 ..     115     129 ..      97     185 .. 0.68
   2 !   62.5   0.1   2.1e-21   3.7e-17       1     254 [.     222     460 ..     222     464 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.099
                                    HTTESEEEEETTTTT CS
                   CN_hydrolase  30 rkgadLivlPElfit 44 
                                    r ga L+v+P +++ 
  gi|121638144|ref|YP_978368.1| 115 RVGAALVVVPSAWVA 129
                                    448888888888876 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 2.1e-21
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvi 80 
                                    rvA+vQ+    ad++a l+  +e+ a++a++  dL+v+ E ++   ++  +           +la+la+l+++ g  + +
  gi|121638144|ref|YP_978368.1| 222 RVALVQAGD-IADAAARLAAGEEFTAAVADQRPDLVVWGESSVG--QDLTRHP--------DVLARLAELSQRVGADLLV 290
                                    79*******.69*******************************8..6666655........5****************** PP

                                    EEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--E.ECTTSCECCGHHTSCS..........-SSS-EEEETTEEEE CS
                   CN_hydrolase  81 gliereltngklqayntavlldldgklvgkyrKlhLfp.geprpptaverelfep..........gdgipvfdtpvgkiG 149
                                     +   +  +g +  y +avl+ +    vg+yrK++L+p ge+ p + +   +             g g  v++++   i 
  gi|121638144|ref|YP_978368.1| 291 NVDAPA-PDGGI--YKSAVLVGAHEA-VGSYRKTRLVPfGEYVPLRPLFGWITRYskaaakdrqrGAGPVVLAVNSLHIA 366
                                    999987.89999..*******99998.8**********999999887754443336689*99975443677799999*** PP

                                    EEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE CS
                   CN_hydrolase 150 aaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaii 229
                                     +i ye++f  l+r  a+ ga +lv+ s+++++ +s ++pq+ +    ra+e+g++++ a+  g            S+++
  gi|121638144|ref|YP_978368.1| 367 PLISYEMTFSDLTRHAARLGAALLVYQSSTSTFQGSWAQPQLAAQPAVRAVEAGIPAVHASLSGD-----------SSAF 435
                                    **************************9999**************************999999999...........**** PP

                                    -TTS-EEEECCSSSTEEEEEEEEHH CS
                   CN_hydrolase 230 dpdGrilaglgeeeegvliaeidla 254
                                    d +Gr la ++ e  g +++ ++la
  gi|121638144|ref|YP_978368.1| 436 DTRGRRLAWCSAEFNGAIVVNVPLA 460
                                    **********999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3191.38
//
Query:       gi|121638145|ref|YP_978369.1|  [L=317]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-32  110.3   0.0    5.2e-31  107.6   0.0    1.9  1  adh_short     short chain dehydrogenase
    1.8e-21   76.8   0.2    6.7e-21   74.9   0.2    1.7  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      1e-06   28.8   0.3    1.5e-06   28.2   0.3    1.3  1  KR            KR domain
    8.4e-06   25.4   0.0    1.3e-05   24.8   0.0    1.3  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   1.2e-34   5.2e-31       1     187 [.      15     216 ..      15     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 1.2e-34
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkl 78 
                                    k +++tGa sG+G  +a++l ++Ga+v+++ r+ +k e++++e++ +   ak+++ ++D+++ ++v al e+ +++  ++
  gi|121638145|ref|YP_978369.1|  15 KLAIITGANSGLGFGLARRLSAAGADVIMAIRNRAKGEAAVEEIRTAvpDAKLTIKALDLSSLASVAALGEQLMADGRPI 94 
                                    679********************************************99999**************************** PP

                                    SEEEE---SS--SSGGGCSHHH.HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TT............ CS
                      adh_short  79 dvLvnNAGitgsgpfselseee.wervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvag............ 145
                                    d+L+nNAG+  ++p ++++ ++ +e  +  N  g f lt+++lp + +++++r+v  sS a++ + ++            
  gi|121638145|ref|YP_978369.1|  95 DLLINNAGV--MTPPERVTTADgFELQFGSNHLGHFALTAHLLPLLRAAQRARVVSLSSLAARRGRIHfddlqfersyap 172
                                    *********..677888888888***************************************988665222333333333 PP

                                    BHHHHHHHHHHHHHHHHHHHHHGGGT..EEEEEEEESSBSSHHH CS
                      adh_short 146 vaaYsAsKaavagltrslakelaptg..irvnavaPGlvdTdma 187
                                    ++aY+ sK av +++r+l +  +  g  i  na +PGl++T+++
  gi|121638145|ref|YP_978369.1| 173 MTAYGQSKLAVLMFARELDRRSRAAGwgIISNAAHPGLTKTNLQ 216
                                    79****************8876555444*************987 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.2   1.5e-24   6.7e-21       1     179 [.      21     216 ..      21     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.5e-24
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE...EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae...vlecDVtdeeqvealveevvekfgklDilvnn 76 
                                    Ga sg+G+++A++l ++Ga+v+++ +n+++ +++vee+ ++++ +   + ++D ++ ++v+al e+++++   +D l+nn
  gi|121638145|ref|YP_978369.1|  21 GANSGLGFGLARRLSAAGADVIMAIRNRAKgEAAVEEIRTAVPDAkltIKALDLSSLASVAALGEQLMADGRPIDLLINN 100
                                    899***************************************955454499***************************** PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBS.........TTTT...HHH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervv.........pnyn...ayg 142
                                    ag++++   p   t+ ++f+  +  n  + f+l+ ++lpl+++   +++v lss++a+r+           +y+   ayg
  gi|121638145|ref|YP_978369.1| 101 AGVMTP---PERVTTADGFELQFGSNHLGHFALTAHLLPLLRAAqrARVVSLSSLAARRGRihfddlqfeRSYApmtAYG 177
                                    ******...6567899***********************7765557**********9987412222222234445669** PP

                                    HHHHHHHHHHHHHHHHHGG..GTEEEEEEEE--BHCTGG CS
                   adh_short_C2 143 aaKaalealtrylAvelgp..kgiRvNavspgpikTlaa 179
                                     +K a+  ++r l +   +   gi  Na +pg++kT+++
  gi|121638145|ref|YP_978369.1| 178 QSKLAVLMFARELDRRSRAagWGIISNAAHPGLTKTNLQ 216
                                    *************7754442279*************984 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.3   3.4e-10   1.5e-06       4      93 ..      18     105 ..      16     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.4e-10
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT..T-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal..gaevevvaaDvsdkdavealleeikaeepp 81 
                                    +itG+  gLG  lar l + ga  ++ +  +a +    +a ++e++    +a+ ++ a+D+s+ ++v+al e++ a+++p
  gi|121638145|ref|YP_978369.1|  18 IITGANSGLGFGLARRLSAAGADVIMAIRNRA-KG---EAAVEEIRTAvpDAKLTIKALDLSSLASVAALGEQLMADGRP 93 
                                    8*********************9998887773.33...344555555445899999************************ PP

                                    --EEEE------ CS
                             KR  82 ikGvihaAgvlr 93 
                                    i   i+ Agv+ 
  gi|121638145|ref|YP_978369.1|  94 IDLLINNAGVMT 105
                                    *********986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.9e-09   1.3e-05       2     160 ..      18     194 ..      17     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.9e-09
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHH....HHHH.T-SEE CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerl....fkee.qpdav 68 
                                    ++tGa+  +G  l+++l ++g +vi   r++ +++ a +e          ++  ldl   +++++l    +++   +d  
  gi|121638145|ref|YP_978369.1|  18 IITGANSGLGFGLARRLSAAGADVIMAIRNRAKGEAAVEEIRtavpdaklTIKALDLSSLASVAALgeqlMADGrPIDLL 97 
                                    89*********************888888766666665555589******9999999999988665111155555689** PP

                                    EE--S---HHHHHHSHHHH...HHHH....THHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SS CS
                      Epimerase  69 ihlAavggvaassedpadf...iekn....lqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgplkpns 140
                                    i+ A+v +++++++++  f   + +n    +++t +ll  +r+a+  r++ lsS  +  +  ++  ++ +  + +++p +
  gi|121638145|ref|YP_978369.1|  98 INNAGVMTPPERVTTADGFelqFGSNhlghFALTAHLLPLLRAAQRARVVSLSS--LAARRGRIHfDDLQF-ERSYAPMT 174
                                    ***************98774333355122256788888899999999*******..455555543144444.5678**** PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                      Epimerase 141 pYaaaKlageklveayaaqy 160
                                    +Y+ +Kla+   ++++ +  
  gi|121638145|ref|YP_978369.1| 175 AYGQSKLAVLMFARELDRRS 194
                                    *********99988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1979.25
//
Query:       gi|121638146|ref|YP_978370.1|  [L=592]
Description: hypothetical protein BCG_2281c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-18   63.8   0.0    1.2e-17   63.3   0.0    1.1  1  HSP70     Hsp70 protein
    0.00054   18.9   0.0    0.00097   18.0   0.0    1.3  1  MreB_Mbl  MreB/Mbl protein
  ------ inclusion threshold ------
       0.13   10.5   0.0       0.19   10.0   0.0    1.1  1  Gp58      gp58-like protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   2.1e-21   1.2e-17     172     390 ..     150     363 ..     147     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 2.1e-21
                                    HHHHHHHTCCSS...SCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGG CS
                          HSP70 172 AaalaYGldkkd...kernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlsk 248
                                    Aaa  Y +  +       +v+v D+Gg+ + + +++  +    v aT   +++ G+  D+ l+ ++++e+  +   d + 
  gi|121638146|ref|YP_978370.1| 150 AAAALYAIRADPgipARGIVAVCDFGGSGTGITLVDAADEYRPVAATVRHQAFSGDLIDQSLLSYVMSELPGTGAFDPAG 229
                                    6666677776667767889********************************************************99765 PP

                                    SH..HHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGG CS
                          HSP70 249 dk..kalqrlkeaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelvedllertlepvekalkdaklkkee 326
                                     +    l +l+ ++ kaK  LSss  t       t+  d    +++l+R+++e+ ++d l+ + +++e+ l+ +++++ e
  gi|121638146|ref|YP_978370.1| 230 TSaiGSLTKLRIECRKAKERLSSS--TV------TTLTDALGGDIRLTRNELEDTIRDSLDSVGRALEQTLARSGIRTAE 301
                                    5411679****************3..32......333324566899********************************** PP

                                    CSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBE CS
                          HSP70 327 idevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvt 390
                                    + ++v vGG + iP+v+++++  f  +  +t  p    a G A+ a+   g  +++  +l+ vt
  gi|121638146|ref|YP_978370.1| 302 LVAIVSVGGGANIPAVTTTLSGRFCVPVVRTPRPQLTAAFGGALWAARRPG--DTSATVLTAVT 363
                                    ********************************************9998888..77777777766 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-07   0.00097     134     316 ..     156     344 ..     127     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-07
                                    HHHTT--TTSSS-EEEEEE-SS-EEEEEEETTE.....EEEEEEES-SHHHHHHHHHHHHHHHHSEE......--HHHHH CS
                       MreB_Mbl 134 AiGaglpveepsgnmvvdiGggttevavislgg.....ivtsksvrvaGdeldeaiikyirkkynll......iGertae 202
                                    Ai a+  + +     v+d Gg  t ++++ +++       t +    +Gd +d+++++y+ ++   +        ++   
  gi|121638146|ref|YP_978370.1| 156 AIRADPGIPARGIVAVCDFGGSGTGITLVDAADeyrpvAATVRHQAFSGDLIDQSLLSYVMSELPGTgafdpaGTSAIGS 235
                                    66666666666666799999999999999988733221223334447899999999999999864331111102222333 PP

                                    HHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESG CS
                       MreB_Mbl 203 kikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGG 282
                                      k++i + + +e+ ++ ++  + l+  l   ++++ +e+++++++++ ++  a++++L +     a  +v  +iv +GG
  gi|121638146|ref|YP_978370.1| 236 LTKLRIECRKAKERLSSSTV--TTLTDALGGDIRLTRNELEDTIRDSLDSVGRALEQTLARSGIRTAE-LV--AIVSVGG 310
                                    44666666655555555555..467889999****************************998765443.33..59999** PP

                                    GGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
                       MreB_Mbl 283 gallkgldkllseetglpvkvaedpltcvakGtg 316
                                    ga +  + ++ls ++ +pv  + +p  ++a G +
  gi|121638146|ref|YP_978370.1| 311 GANIPAVTTTLSGRFCVPVVRTPRPQLTAAFGGA 344
                                    *************************999888865 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   3.1e-05      0.19     314     389 ..     247     323 ..     234     329 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.1e-05
                           Gp58 314 pnsklesrvtqLadli..eqkvtrgdvesiirqsgdsiklaikaklpqskmsakeiisainLngyGvrisGeriaLdG 389
                                    +++  +s vt L+d +  + ++tr+++e +ir s ds+  a+++ l  s + + e+++ + + g G +i     +L G
  gi|121638146|ref|YP_978370.1| 247 KERLSSSTVTTLTDALggDIRLTRNELEDTIRDSLDSVGRALEQTLARSGIRTAELVAIVSV-GGGANIPAVTTTLSG 323
                                    3444568899999988556899*********************************9976665.446666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 3942.56
//
Query:       gi|121638147|ref|YP_978371.1|  [L=409]
Description: hypothetical protein BCG_2282 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-16   58.5  53.1    1.9e-08   33.6  26.0    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6  26.0   1.1e-12   1.9e-08      23     251 ..      49     272 ..      28     277 .. 0.67
   2 !   27.9  24.2     6e-11   1.1e-06      35     174 ..     268     403 ..     259     409 .] 0.81

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-12
                          MFS_1  23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslwlllvlrvlqGlgaga 101
                                    l  +lg+++ ++g ++++  ++a+ + l+ G+l+dr  r + + ++g++l+++++ ll +a  lw+ ++l +   +g ++
  gi|121638147|ref|YP_978371.1|  49 LLASLGATGLVVGVVTGVGEAAALGLRLVSGPLADRSRRFWaWTIAGYTLTVVTVPLLGIAGALWVACALVIAERVGKAV 128
                                    345799999***************************76666666666666666633333558899*************** PP

                          MFS_1 102 lfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllll..peep 176
                                      pa  +l+++ ++ + rgr++++  a  ++Ga++gpl  + +++  g    +a+ ++  + ++ +++l  l+l  ++++
  gi|121638147|ref|YP_978371.1| 129 RGPAKDTLLSHAASVTGRGRGFAVHEALDQVGAMIGPLTVAGMLAITGnayAPALGVLTLPGGAALALL--LWLqrRVPR 206
                                    ************************************887777776777663444444444444444444..444234444 PP

                          MFS_1 177 perkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllagllla 251
                                    pe+  + p+ +++  +p+p++        + ++w l +++  +++  +g++ ll +  +  +g  ++ ++ +++a
  gi|121638147|ref|YP_978371.1| 207 PESYEDCPVVLGNPSAPRPWAL-------PAQFW-LYCGFTAITMLGFGTFGLLSFH-MVSHGVLAAAMVPVVYA 272
                                    4444444444423334444444.......77888.5555555555555555555553.44444442233333333 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 6e-11
                          MFS_1  35 gllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwf 114
                                      ++++ +++ a+++l  G+  dr+G++ + +l +l+ ++  l+++ + ++++++++ ++ G++ g+  ++   ++ad++
  gi|121638147|ref|YP_978371.1| 268 PVVYAAAMAADALTALASGFSYDRYGAKTLAVLPILSILVV-LFAF-TDNVTMVVIGTLVWGAAVGIQESTLRGVVADLV 345
                                    44566666777*******************99999999999.4444.58888**************************** PP

                          MFS_1 115 pkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpe 174
                                    + ++r++a+g+++ag +++++ g +l g+l+  s+g  +v +i+  +++l+++   + ++ 
  gi|121638147|ref|YP_978371.1| 346 ASPRRASAYGVFAAGLGAATAGGGALIGWLYdISIGTLVVVVIALELMALVMM---FAIRL 403
                                    *******************************6666665555555555555544...33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2983.86
//
Query:       gi|121638148|ref|YP_978372.1|  [L=428]
Description: cytochrome P450 124 CYP124 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-22   79.3   0.0    2.6e-12   46.3   0.0    3.1  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.7e-10     3e-06      86     297 ..     109     291 ..      64     298 .. 0.74
   2 !   46.3   0.0   1.4e-16   2.6e-12     327     426 ..     304     393 ..     300     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.7e-10
                                    SSTTCGHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHT CS
                           p450  86 gvlfangekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdl 164
                                    ++++ + +++++lR+++ +++t +    ++e+ v + a++lv  +  ++  ++  d++  l+      i   ++g++   
  gi|121638148|ref|YP_978372.1| 109 SMIVLDDPRHQRLRSIVSRAFTPK-VVaRIEAAVRDRAHRLVSSMIANNPDRQ-ADLVSELAGPLPLQIICDMMGIP--- 183
                                    466777799999999999999999.5558999999999999999988888884.77777777776666666788887... PP

                                    TTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHH CS
                           p450 165 ledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdflda 244
                                      d+  +++ ++++             +l f   ++ +  ++ ++ ++  ++  ++ +l e+rr +  ++      +++ 
  gi|121638148|ref|YP_978372.1| 184 KADH--QRIFHWTNV------------ILGFG--DPDLATDFDEFMQVSADIGAYATALAEDRRVNHHDD------LTSS 241
                                    2233..234444444............44444..556778889999999999999999999998765555......8999 PP

                                    HHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHH CS
                           p450 245 lllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqe 297
                                    l++a+   +ge  ls +e+a   + l +aG +Tt ++++ + + L ++Pe  +
  gi|121638148|ref|YP_978372.1| 242 LVEAE--VDGE-RLSSREIASFFILLVVAGNETTRNAITHGVLALSRYPEQRD 291
                                    99995..8887.9************************************9765 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 1.4e-16
                                    HHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTE CS
                           p450 327 vikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFG 406
                                    +++E+ R  ++v+  + R +t+d+++rg ++ +G++v+++ ++ +rd++ f +P +Fd  R          ++  +l+FG
  gi|121638148|ref|YP_978372.1| 304 AVEEIVRWASPVV-YMRRTLTQDIELRGTKMAAGDKVSLWYCSANRDESKFADPWTFDLAR----------NPNPHLGFG 372
                                    799**********.999*****************************************976..........46679***8 PP

                                    E.GGGS-TTHHHHHHHHHHHH CS
                           p450 407 a.GpRnCiGerlArmelklfl 426
                                      G++ C+G +lAr e+++++
  gi|121638148|ref|YP_978372.1| 373 GgGAHFCLGANLARREIRVAF 393
                                    5279*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3131.75
//
Query:       gi|121638149|ref|YP_978373.1|  [L=388]
Description: hypothetical protein BCG_2284c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-41  141.5   0.2    8.4e-41  140.7   0.2    1.4  1  Sulfotransfer_3  Sulfotransferase family
    1.1e-13   51.4   0.0    3.6e-13   49.6   0.0    1.8  2  Sulfotransfer_1  Sulfotransferase domain
  ------ inclusion threshold ------
      0.025   14.4   1.4       0.16   11.7   0.0    2.6  3  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   0.2   1.4e-44   8.4e-41       1     214 [.      82     325 ..      81     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 1.4e-44
                                    -EEEE--TTSSHHHHHHHHHTSTT..EE--S--.--TT.-SBHH.HHHHHHTT-S...TTTHHHHHHHHHHT--HHHHHH CS
                Sulfotransfer_3   1 PifivGlpRSGTTlLhrlLaahpd..vripeetlfvaprllall.eawskdgrelrrlldagltqeeaelphledaeepe 77 
                                    PifivG++R+GTTlLh+lL  + +   + ++e+l  ++ ll ++ + + ++ +++ r +d+          + ++ ++p+
  gi|121638149|ref|YP_978373.1|  82 PIFIVGHWRTGTTLLHELLVVDDRhtGPTGYECLAPHHFLLTEWfAPYVEFLVSKHRAMDN----------MDLSLHHPQ 151
                                    7********************7775544445554444444433302233444444444443..........222233333 PP

                                    HHHHH.HHTT-BHHHHHHHHHH..HTTTSEEEE.................................EESSGGG-HHHHHH CS
                Sulfotransfer_3  78 edlql.lraalasvilealarv..psyarwlvd.................................KsPshlfrldllle 121
                                    ed ++   + l s +l+ +++   p+y+++l d                                 K+P+h fr++ lle
  gi|121638149|ref|YP_978373.1| 152 EDEFVwCMQGLPSPYLTIAFPNrpPQYEEYL-DleqvapreleiwkrtlfrfvqqvyfrrrktvilKNPTHSFRIKVLLE 230
                                    3333323444555444443332113444433.3456666666666667777777777777777777************** PP

                                    HBSSEEEEEEE--H.HHHHHHHHHTT---..-------..-HHH.HHHHHHHHHHHHHHHHHHHS-TTSEEEEEHHHHHH CS
                Sulfotransfer_3 122 lfPdAkfihlvRdpvdtvlssyvslfgkk..resysedsldele.daleewarayerllaararlppdrfldvrYedLva 198
                                    +fP+Akfih+vRdp + v++s+++l+++    + +++  +d l+ ++++++ + y++l + r+ ++p rf+++rYedL+ 
  gi|121638149|ref|YP_978373.1| 231 VFPQAKFIHIVRDP-YVVYPSTIHLHKALyrIHGLQQPTFDGLDdKVVSTYVDLYRKLDEGRELVDPTRFYELRYEDLIG 309
                                    **************.**********65421145555999999998899999999********99**************** PP

                                    -HHHHHHHHHHHHT-- CS
                Sulfotransfer_3 199 dpegtlrriyeflglp 214
                                    dpeg+lrr+y++lgl 
  gi|121638149|ref|YP_978373.1| 310 DPEGQLRRLYQHLGLG 325
                                    **************95 PP

>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.34     2e+03     110     135 ..      33      58 ..      32      68 .. 0.81
   2 !   49.6   0.0     6e-17   3.6e-13       1     197 [.      80     325 ..      80     338 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.34
                                    EE--HHHHHHHHHHHHHHBTTSTTT- CS
                Sulfotransfer_1 110 lvRnpkdvavSryhfsrslkklkepe 135
                                    l+Rn  +v  Sr+hf    + l++ +
  gi|121638149|ref|YP_978373.1|  33 LIRNRFAVHHSRWHFAVLYTFLSMVN 58 
                                    789999********987766666555 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 6e-17
                                    TTSEEEEESTTSSHHHHHHHHHH..............................................HHTTTCC.... CS
                Sulfotransfer_1   1 dddvlivtypKSGTtwlqellsl..............................................itsegdf.... 30 
                                    d+ ++iv+  ++GTt l+ell                                                +++e +f    
  gi|121638149|ref|YP_978373.1|  80 DPPIFIVGHWRTGTTLLHELLVVddrhtgptgyeclaphhflltewfapyveflvskhramdnmdlslhHPQEDEFvwcm 159
                                    5789*******************888888888888888888877777777777666666555555555555555554444 PP

                                    ....HHHTSSGHCT-.HHHSCBTTHECCTSGCCGTTECCC....................HHHTTTEEHHHHHHHSTSS. CS
                Sulfotransfer_1  31 ....ekaeepalfna.rdrspfLelydlyfpnslkppdhl....................rsyshvaekvvrlralespr 85 
                                        ++   +a++n+  +                     +                      ++ v++++ r r+     
  gi|121638149|ref|YP_978373.1| 160 qglpSPYLTIAFPNRpPQ---------------------YeeyldleqvapreleiwkrtL-FRFVQQVYFRRRKT---V 214
                                    444444444444444444.....................0444555555555556666532.33333333333333...3 PP

                                    EEE..E....GGGS.CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S.-HHHHHHHHHTTHSTTC-HHHHHHH CS
                Sulfotransfer_1  86 llk..tHlp.lkllpkslldsnlKiiylvRnpkdvavSryhfsrslkklkepet.pfeeffdlflegrvvcgsyfdhvks 161
                                    +lk  tH + +k+l +    +++K i++vR+p  v+ S +h +++l+  +  ++ +f+ + d++     ++ + ++ + +
  gi|121638149|ref|YP_978373.1| 215 ILKnpTHSFrIKVLLEV--FPQAKFIHIVRDPYVVYPSTIHLHKALYRIHGLQQpTFDGLDDKVV---STYVDLYRKLDE 289
                                    66655554314455444..699*************************999999989998877777...89999******* PP

                                    HHHHTTTTTEEEEEHHHHHHHHHHHHHHHHHHTT-- CS
                Sulfotransfer_1 162 wlklrkkgnvlflrYEdlkkdpakeikkiaeFlGip 197
                                    + +l ++ +++ lrYEdl+ dp+++++++++ lG+ 
  gi|121638149|ref|YP_978373.1| 290 GRELVDPTRFYELRYEDLIGDPEGQLRRLYQHLGLG 325
                                    *********************************985 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4      0.41   2.5e+03     114     144 ..      38      68 ..      13      76 .. 0.75
   2 ?    0.5   0.0     0.075   4.5e+02       2      17 ..      83      98 ..      82     102 .. 0.82
   3 ?   11.7   0.0   2.8e-05      0.16      80     117 ..     224     261 ..     180     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.41
                Sulfotransfer_4 114 lrsetlsrllalldpllellaklvellralv 144
                                    +  ++ ++++a l ++l++++++  l++++v
  gi|121638149|ref|YP_978373.1|  38 FAVHHSRWHFAVLYTFLSMVNSCLGLWQKIV 68 
                                    3345567788888888999999999998885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.075
                Sulfotransfer_4  2 ViglGlpRtGTkSlka 17
                                   ++++G +RtGT+ l++
  gi|121638149|ref|YP_978373.1| 83 IFIVGHWRTGTTLLHE 98
                                   7899*******96665 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 2.8e-05
                Sulfotransfer_4  80 faeelleayPdakvIlteRdpekWlksmkktllalrse 117
                                     ++ lle++P+ak+I ++Rdp   + s+ ++ +al++ 
  gi|121638149|ref|YP_978373.1| 224 RIKVLLEVFPQAKFIHIVRDPYVVYPSTIHLHKALYRI 261
                                    46789****************99999998888877754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2372.58
//
Query:       gi|121638150|ref|YP_978374.1|  [L=489]
Description: cytochrome P450 128 cyp128 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   82.6   0.0    6.9e-17   61.3   0.0    3.1  3  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0   0.00074        13      45     155 ..     133     234 ..     127     239 .. 0.71
   2 !   13.1   0.1   1.6e-06     0.029     251     294 ..     304     346 ..     284     354 .. 0.84
   3 !   61.3   0.0   3.8e-21   6.9e-17     324     432 ..     358     455 ..     351     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.00074
                                    EEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHH CS
                           p450  45 pvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltptltsfgkl.sleelveeeae 123
                                    +v +ls++ +v+e+  +++  +s+r   ++++     ++   + +++++ ++++R+ l p +  + +l +++++v++ a+
  gi|121638150|ref|YP_978374.1| 133 DVYILSRYADVREAARNHDTLSSAR--GVTFSR---GWLP-FLPTSDPPAHTRMRKQLAPGMARG-ALeTWRPMVDQFAR 205
                                    5666666777777766665444443..334443...3443.45568889**************99.999*********** PP

                                    HHHHHHHCCCCHCSEEETHHHHHHHHHHHHHH CS
                           p450 124 dlveklrkkagesselditellskaaldvigs 155
                                    +lv  l +++ +     ++++ + +++ +i+s
  gi|121638150|ref|YP_978374.1| 206 ELVGGLLTQTPAD---VVSTVAAPMPMRAITS 234
                                    **99888887777...5555555555555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.6e-06
                                    TCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHH CS
                           p450 251 ekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPe 294
                                    + ++   lsd+el   +  ll+aG++ t++ +s  ++ La++P+
  gi|121638150|ref|YP_978374.1| 304 HAEQ-GRLSDDELFFFAVLLLVAGYESTAHMISTLFLTLADYPD 346
                                    3333.37************************************8 PP

  == domain 3  score: 61.3 bits;  conditional E-value: 3.8e-21
                                    HHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT-- CS
                           p450 324 ldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfafl 403
                                       +i+E LR+++++  ++ R +  d++++  +ip+G+ v++  +a +rdp ++++P++F+ +          r+++ +l
  gi|121638150|ref|YP_978374.1| 358 IPSAIEEHLRFISPIQ-NICRTTRVDYSVGQAVIPAGSLVLLAWGAANRDPRQYEDPDVFRAD----------RNPVGHL 426
                                    5679************.*******************************************865..........57899** PP

                                    TTEEGGGS-TTHHHHHHHHHHHHHHHHHH CS
                           p450 404 PFGaGpRnCiGerlArmelklflatlLqn 432
                                    +FG G + C+G +lArme + +l  ++ n
  gi|121638150|ref|YP_978374.1| 427 AFGSGIHLCPGTQLARMEGQAILREIVAN 455
                                    **********************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3132.45
//
Query:       gi|121638151|ref|YP_978375.1|  [L=110]
Description: hypothetical protein BCG_2286c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 609.53
//
Query:       gi|121638152|ref|YP_978376.1|  [L=175]
Description: lipoprotein lppN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.024   15.1   0.2      0.059   13.9   0.2    1.7  1  LPAM_1       Prokaryotic membrane lipoprotein lipid attachmen
      0.043   13.3   0.0       0.19   11.2   0.0    1.9  1  Septum_form  Septum formation


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.5e-06     0.059       5      18 .]       9      22 ..       6      22 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                         LPAM_1  5 llalgalllLsGCs 18
                                   l+al+a+ +L++Cs
  gi|121638152|ref|YP_978376.1|  9 LYALSAVTMLAACS 22
                                   89***********9 PP

>> Septum_form  Septum formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.1e-05      0.19       2      88 ..      69     142 ..      68     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                    Septum_form   2 GdCltwdesa..dasdlekVdCaeehrfevvaredlsaypgsefgagapppseeraaelaeelCeqavaeylggkldpag 79 
                                    GdCl     a  ++ +++ VdCa+ h +ev  r              ap++ +++   +a+++C++  a y g+ +d ++
  gi|121638152|ref|YP_978376.1|  69 GDCLADLPPAdlSRITVTIVDCATAHSAEVYLR--------------APVAVDAAVVSMANRDCAAGFAPYTGQSVD-TS 133
                                    788877766656666778899999999888874..............455555566666666666666666666666.66 PP

                    Septum_form  80 rfsigvilP 88 
                                     +s++ +  
  gi|121638152|ref|YP_978376.1| 134 PYSVAYLID 142
                                    666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1234.46
//
Query:       gi|121638153|ref|YP_978377.1|  [L=99]
Description: hypothetical protein BCG_2288 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-24   86.3   1.0    1.9e-24   85.6   0.3    1.6  2  DUF2695   Protein of unknown function (DUF2695)
     0.0069   15.3   2.4     0.0088   15.0   2.4    1.0  1  DUF2397   Protein of unknown function (DUF2397)
  ------ inclusion threshold ------
       0.04   14.3   0.0       0.05   14.0   0.0    1.2  1  Ret2_MD   RNA editing 3' terminal uridylyl transferase 2 midd


Domain annotation for each model (and alignments):
>> DUF2695  Protein of unknown function (DUF2695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.47   2.8e+03      22      37 ..      10      25 ..       7      27 .. 0.80
   2 !   85.6   0.3   3.2e-28   1.9e-24       1      53 []      39      91 ..      39      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                        DUF2695 22 refldqrqlaaedlld 37
                                   r+fl+    +ae++++
  gi|121638153|ref|YP_978377.1| 10 RRFLRDAYKNAERVAR 25
                                   7899999899998876 PP

  == domain 2  score: 85.6 bits;  conditional E-value: 3.2e-28
                        DUF2695  1 LfdyldeklkaegCDhtlrftrefldqrqlaaedlldvlkenGGyCDCEvllN 53
                                   L+dy+de+l++++CDht+r+++++++++++++e+l+++l+e+GGyCDCE+++N
  gi|121638153|ref|YP_978377.1| 39 LLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLAEGLQEFGGYCDCEIVMN 91
                                   89**************************************************9 PP

>> DUF2397  Protein of unknown function (DUF2397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.4   1.5e-06    0.0088     194     256 ..      11      74 ..      10      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-06
                        DUF2397 194 efvadLqrrsarIa.tlLreleeagverllaraaereariprleeertveellerwrarWegLr 256
                                    +f +d  ++++r+a t+L +++++++e+ll+ ++er  ++p ++++r+++++++ +r +We L+
  gi|121638153|ref|YP_978377.1|  11 RFLRDAYKNAERVArTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLA 74 
                                    67777778888886368999*****************************************997 PP

>> Ret2_MD  RNA editing 3' terminal uridylyl transferase 2 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.3e-06      0.05       5      54 ..      20      70 ..      17      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-06
                        Ret2_MD  5 edrkartalldvrnkkitekeleyiaeklgrenvegi..yverttyGcriai 54
                                    +r artall + + ++ e+ l+y+ e+lg++  +++  + +r +   ri+ 
  gi|121638153|ref|YP_978377.1| 20 AERVARTALLTIDQDQL-EQLLDYVDERLGEQPCDHTarHAQRWAQSHRIEW 70
                                   69**********99887.567***********99998555666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 745.31
//
Query:       gi|121638154|ref|YP_978378.1|  [L=122]
Description: hypothetical protein BCG_2289 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-18   64.4   8.8    3.1e-17   62.8   5.4    2.0  2  DUF202           Domain of unknown function (DUF202)
  ------ inclusion threshold ------
      0.049   13.8   0.1       0.08   13.2   0.1    1.3  1  zf-HC3           zinc-finger
        7.3    6.8   6.4         35    4.6   6.4    2.0  1  SdpI             SdpI/YhfL protein family
        9.7    6.2   8.3       0.41   10.6   1.5    1.9  2  SLATT_1          SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   5.4   6.9e-21   3.1e-17       1      67 [.      17      83 ..      17      84 .. 0.93
   2 ?    3.2   0.1     0.028   1.3e+02      36      58 ..      95     115 ..      86     120 .. 0.54

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.9e-21
                         DUF202  1 rdglAnERTfLaWlRtslalialglallrffltgepsalgkilglilivlgiltllvglvrylrrqr 67
                                   r  lAnERTfLaW Rt+l+l+a+++al+++  +     ++++lg++l++l+ilt ++gl r+++  r
  gi|121638154|ref|YP_978378.1| 17 RFTLANERTFLAWQRTALGLLAAAVALVQLVPELTIPGARQVLGVVLAILAILTSGMGLLRWQQADR 83
                                   789***************************8877777789***********************9866 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                         DUF202  36 psalgkilglilivlgiltllvg 58 
                                    p+++   l+++l v+g+++l+++
  gi|121638154|ref|YP_978378.1|  95 PTPG--YLAVGLCVVGVVALALV 115
                                    5553..34444555555554443 PP

>> zf-HC3  zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05      0.08       2      34 ..      77     109 ..      76     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                    EEEEET..TEEEEEETTT---BTTB-EE-TTS-EE CS
                         zf-HC3   2 rWqqad..grRHavdternrpepGeaftaLCgvev 34 
                                    rWqqad   rRH+ +  r+ p+pG  +  LC v v
  gi|121638154|ref|YP_978378.1|  77 RWQQADraMRRHL-PLPRH-PTPGYLAVGLCVVGV 109
                                    8*****8778886.77888.9**********8866 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.4    0.0078        35      13      62 ..      17      69 ..      16     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0078
                           SdpI 13 pwtlkseetWrkahrfagklw.iiaGlilllla.....lgavvlvllvlvlllviv 62
                                   ++tl++e+t+ + +r a  l+  ++ l+ l++            vl v++++l+i+
  gi|121638154|ref|YP_978378.1| 17 RFTLANERTFLAWQRTALGLLaAAVALVQLVPEltipgA---RQVLGVVLAILAIL 69
                                   579************887544244455555555775441...23333333333322 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.5   9.2e-05      0.41      22      76 ..      22      80 ..      18      88 .. 0.82
   2 ?   -0.8   0.7       0.3   1.3e+03      29      46 ..     102     119 ..      98     122 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.2e-05
                        SLATT_1 22 raakrwrlllillellalllaalrafgelsv....dlvgvlaavaaallaWlelkqyee 76
                                   ++++++ +   +l+lla+++a+++ ++el++    +++gv+ a+ a l++ + l ++++
  gi|121638154|ref|YP_978378.1| 22 NERTFLAWQRTALGLLAAAVALVQLVPELTIpgarQVLGVVLAILAILTSGMGLLRWQQ 80
                                   677889999999*****************999888899999999988887766666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                        SLATT_1  29 lllillellalllaalra 46 
                                    + l +++++al+l++++a
  gi|121638154|ref|YP_978378.1| 102 VGLCVVGVVALALVVAKA 119
                                    566778888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 898.85
//
Query:       gi|121638155|ref|YP_978379.1|  [L=109]
Description: hypothetical protein BCG_2290 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.5   2.8    2.3e-12   47.2   0.3    1.9  2  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.3   1.3e-16   2.3e-12       1      67 [.      10      72 ..      10      73 .. 0.91
   2 ?    0.8   0.1     0.037   6.7e+02      41      56 ..      90     105 ..      78     109 .] 0.62

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.3e-16
                         DUF202  1 rdglAnERTfLaWlRtslalialglallrffltgepsalgkilglilivlgiltllvglvrylrrqr 67
                                   + gl++ERT+LaW+Rt+ al++ g++l+     ++ + +  ++gli ++l+ +++++ +v  l+rqr
  gi|121638155|ref|YP_978379.1| 10 DRGLQAERTTLAWTRTAFALLVNGVLLTL----KDTQGADGPAGLIPAGLAGAAASCCYVIALQRQR 72
                                   579*************************6....55555568***********************998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.037
                         DUF202  41 kilglilivlgiltll 56 
                                    +il+++ +vl ++t++
  gi|121638155|ref|YP_978379.1|  90 HILATAVLVLMVVTAF 105
                                    4555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 801.27
//
Query:       gi|121638156|ref|YP_978380.1|  [L=105]
Description: hypothetical protein BCG_2291c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   11.2   2.2        0.5   10.7   2.2    1.2  1  MamL-1    MamL-1 domain


Domain annotation for each model (and alignments):
>> MamL-1  MamL-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   2.8e-05       0.5       2      14 ..      51      63 ..      50      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.8e-05
                         MamL-1  2 krsavvdRLRrRi 14
                                    rs+v +RLRrRi
  gi|121638156|ref|YP_978380.1| 51 VRSVVTERLRRRI 63
                                   69**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 561.62
//
Query:       gi|121638157|ref|YP_978381.1|  [L=289]
Description: hypothetical protein BCG_2292 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-87  291.4   0.0    5.2e-87  291.1   0.0    1.1  1  CDPS      Cyclodipeptide synthase
  ------ inclusion threshold ------
       0.26   11.2   0.6       0.53   10.2   0.6    1.5  1  Spo12     Spo12 family


Domain annotation for each model (and alignments):
>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.1   0.0   5.8e-91   5.2e-87       1     220 []      64     283 ..      64     283 .. 1.00

  Alignments for each domain:
  == domain 1  score: 291.1 bits;  conditional E-value: 5.8e-91
                                    EEEEESSHHHHHHHHHTSEEEEEE-TTBTTS-HHHHHHHHHHHHHHSSEEEEEE--TTHHHHHHHTT--HHHHHHHHHHH CS
                           CDPS   1 FevepltenceeilergehvvvgvSpgnsyfsedrlaalirwaareFaqvdvvvadtevaellealGyspeeArrkaare 80 
                                    F v+p+t++c+ i+++g+h+v+gvSpgnsyfs++rl++l  w  ++F++vd+v++d +vae +ealG s+ eArrka+++
  gi|121638157|ref|YP_978381.1|  64 FLVRPFTQQCQIIHTEGDHAVIGVSPGNSYFSRQRLRDLGLWGLTNFDRVDFVYTDVHVAESYEALGDSAIEARRKAVKN 143
                                    889***************************************************************************** PP

                                    HHHHHHHHHHHHHHHTTTTTCEEEEECCCCCC-HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCHHHS----HHHH CS
                           CDPS  81 lravrarieraleeagpepervrvrrlseflanpaYrelraeveralaedeelreacdemvrqvlerrlkdeeapseaql 160
                                    +r+vra+i+++++e++p+++r++vr++sef++n+aYrel+a++ ++l++de+lr++c+++vr++l++++ +++ ++++q 
  gi|121638157|ref|YP_978381.1| 144 IRGVRAKITTTVNELDPAGARLCVRPMSEFQSNEAYRELHADLLTRLKDDEDLRAVCQDLVRRFLSTKVGPRQGATATQE 223
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHT-S-EEEEESS--CCHHHHCTTSSSS---TTEEEEEEEE CS
                           CDPS 161 eaaleYllaElPffldtpailgvessvlayhrtlplaelLygrelllrparkqGyaivrp 220
                                    +++++Y++aE P+fldtpailgv+ss+++yh++lpla +Ly+r+++lr++r+qG+aiv+p
  gi|121638157|ref|YP_978381.1| 224 QVCMDYICAEAPLFLDTPAILGVPSSLNCYHQSLPLAAMLYARGSGLRASRNQGHAIVTP 283
                                    **********************************************************98 PP

>> Spo12  Spo12 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   5.9e-05      0.53       2      12 ..      13      23 ..      12      24 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.9e-05
                          Spo12  2 SPTDnllSPCs 12
                                   SPTD+l+SP s
  gi|121638157|ref|YP_978381.1| 13 SPTDDLQSPRS 23
                                   *********66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1622.60
//
Query:       gi|121638158|ref|YP_978382.1|  [L=396]
Description: cytochrome P450 121 CYP121 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   60.8   0.0    1.8e-14   53.3   0.0    2.5  2  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0     0.077   1.4e+03      98     132 ..      94     127 ..      43     154 .. 0.77
   2 !   53.3   0.0     1e-18   1.8e-14     256     431 ..     216     364 ..     196     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.077
                                    HHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCC CS
                           p450  98 lRrfltptltsfgklsleelveeeaedlveklrkk 132
                                    lR+ +++++t + +  le+++ + a+ l+++l ++
  gi|121638158|ref|YP_978382.1|  94 LRKAVMKAITPK-APGLEQFLRDTANSLLDNLITE 127
                                    688899999966.4489999999999999888655 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 1e-18
                                    SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHS CS
                           p450 256 sklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikEtLRlh 335
                                    s++sde  a+   ++++aGv  t s l+ aL+ L+++P++ + l+e                    ++  a ++E LR+ 
  gi|121638158|ref|YP_978382.1| 216 SHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEK------------------PELIPAGVEELLRIN 277
                                    55666666666677777777777777777777777777777766665..................2578889*******9 PP

                                    CSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTH CS
                           p450 336 pvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGe 415
                                         +lpR +t d++++++l++kG  v+v l + + dpe+fpnP +   +R ++++         +l+FG G + C+G 
  gi|121638158|ref|YP_978382.1| 278 LSFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTS---------HLAFGRGQHFCPGS 348
                                    88777**************************************************94.........7************* PP

                                    HHHHHHHHHHHHHHHH CS
                           p450 416 rlArmelklflatlLq 431
                                     l+r + ++ +  lL+
  gi|121638158|ref|YP_978382.1| 349 ALGRRHAQIGIEALLK 364
                                    *********9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2176.64
//
Query:       gi|121638159|ref|YP_978383.1|  [L=299]
Description: glycerolphosphodiesterase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   73.1   0.0    2.4e-19   70.1   0.0    2.0  1  GDPD      Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   1.4e-23   2.4e-19       1     258 [.      34     292 ..      34     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.4e-23
                                    TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCC CS
                           GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaq 80 
                                    HR+   ++pEnT++++ +A+++G+d   + vq+++DgvpV++  ++l+ +td+ag  +v++ t+++l++l+ + +  +  
  gi|121638159|ref|YP_978383.1|  34 HRAGTRDFPENTVLAITNAVAAGVDGMWLTVQVSSDGVPVLYRPSDLATLTDGAG--PVNSKTVQQLQQLNAGWNFTTPG 111
                                    *******************************************************..**************333334445 PP

                                    SCCCSSGCC.B...BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTH CS
                           GDPD  81 lsenrvrle.fpfptleevlkk.pqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnp 158
                                    + ++++r+  +p+ptle+++   p+  ++ +   +++++ +           +++++ +++        + + i+ s+n+
  gi|121638159|ref|YP_978383.1| 112 VEGHPYRQRaTPIPTLEQAIGAtPP--DMTLFLDLKQTPPQPLVSA------VAQVLTRTG-------AAGRSIVYSTNA 176
                                    67777766689*********99544..4444555555554444444......334444444.......222333335555 PP

                                    HHHHHHHHTCT.......CTEEEEEEHHHHHHC-E...........EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHH CS
                           GDPD 159 dilkllrekqp.......klpllflteggteaead..........ssleraakfakadallgevsavaeglgdpdlVkra 221
                                    di  + ++ +        ++  + l++++ + + d            l r++ +  +  l + +sav+  l d   V+ +
  gi|121638159|ref|YP_978383.1| 177 DITAAASRQEGlqvaesrDVTRQRLFNMALNHHCDpqpdpgkwagFELHRDVTVTEEFTLGSGISAVNAELWDEASVDCF 256
                                    5555555555544444444444445544444444455666999887788999999************************9 PP

                                    HHT.T-EEEEBSB-THSHHHHHHHHCCC-SEEEES-HH CS
                           GDPD 222 ksr.glvvhvytvnnedeeemkrlleagvdgvitDfpd 258
                                    +s+ g++v+ + v +   ++ ++++++g d+v++D+p 
  gi|121638159|ref|YP_978383.1| 257 RSQsGMKVMGFAVKTV--DDYRLAHKIGLDAVLVDSPL 292
                                    97626***********..******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1625.02
//
Query:       gi|121638160|ref|YP_978384.1|  [L=459]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-58  198.6   0.1      2e-58  198.0   0.1    1.2  1  FAD-oxidase_C   FAD linked oxidases, C-terminal domain
    3.4e-38  130.5   2.3    7.2e-38  129.5   2.3    1.6  1  FAD_binding_4   FAD binding domain
  ------ inclusion threshold ------
        9.7    6.6   6.5          7    7.1   0.1    3.2  3  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   0.1   3.4e-62     2e-58       4     249 ..     217     454 ..     215     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 3.4e-62
                                    EEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS....TTS-TTT-EEEEEEEEE-HHHHHHHH CS
                  FAD-oxidase_C   4 aravalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak....kglpdeeealllvefegddeeeaeee 79 
                                    + a++l++f++f+++++av++i ++g+ p  le +d++++ +  +t++ +    ++++d++ea+llv +e + +++++e+
  gi|121638160|ref|YP_978384.1| 217 HNASVLAPFADFDQVMAAVPKILASGLAPDILEYIDNTSMAALISTQNLElgipDQIRDSCEAYLLVALENRIADRLFED 296
                                    67899*************************************************************************** PP

                                    HHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEE CS
                  FAD-oxidase_C  80 lealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkygle 159
                                    ++ +v ++l++ ga d + + +  +a++l++aR++a++     ++ka +a ++ Dt+vP++ ++++++ ++ l+++ + +
  gi|121638160|ref|YP_978384.1| 297 IQ-TVGEMLMELGAVD-AYVLEGGSARKLIEAREKAFW-----AAKALGADDIIDTVVPRASMPKFLSTARGLAAAADGA 369
                                    **.*************.5555566669***********.....899********************************** PP

                                    EEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH CS
                  FAD-oxidase_C 160 vvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaal 239
                                    +v +gHagdgn+h+ i++     ++ e+ +kl++++++la+elgG isgEHGvG++k  y  +  +++++ lmrriK+ +
  gi|121638160|ref|YP_978384.1| 370 AVGCGHAGDGNVHMAIAC-----KDPEKKKKLMTDIFALAMELGGAISGEHGVGRAKTGYFLELEDPVKISLMRRIKQSF 444
                                    ******************.....889999999************************************************ PP

                                    -TT--BSTT- CS
                  FAD-oxidase_C 240 DPkgiLNPgk 249
                                    DP+giLNPg 
  gi|121638160|ref|YP_978384.1| 445 DPAGILNPGV 454
                                    *********6 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   2.3   1.2e-41   7.2e-38       1     139 []      40     178 ..      40     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.2e-41
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlve 79 
                                    pa+ ++p+++eeva +l++a+e+g+pv++rG+G +l+g+a   +gg++++++r+n++le+d ++++a+v++Gv l dl++
  gi|121638160|ref|YP_978384.1|  40 PAYAAKPATPEEVAQLLKAASENGVPVTARGSGCGLSGAARpVEGGLLISFDRMNKVLEVDTANQVAVVQPGVALTDLDA 119
                                    78999********************************999889************************************* PP

                                    HHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                  FAD_binding_4  80 alaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                    a+a +gl + ++pg +++ +vGG++ tnagG+++ kyG  r+nvlgl++vl++Ge++r++
  gi|121638160|ref|YP_978384.1| 120 ATADTGLRYTVYPGELSS-SVGGNVGTNAGGMRAVKYGVARHNVLGLQAVLPTGEIIRTG 178
                                    ***************965.9*************************************985 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0012         7      31      59 ..      47      74 ..      43      80 .. 0.76
   2 ?    1.3   0.1     0.075   4.5e+02       7      55 ..     287     338 ..     281     339 .. 0.67
   3 ?   -1.0   0.1       0.4   2.4e+03      36      58 ..     397     416 ..     391     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                 GHMP_kinases_C 31 ilppeleellealselGalgaklsGaGgG 59
                                     p+e+ +ll+a+se+G   +   G+G+G
  gi|121638160|ref|YP_978384.1| 47 ATPEEVAQLLKAASENG-VPVTARGSGCG 74
                                   5799*************.55555555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.075
                 GHMP_kinases_C   7 r.......gdlellgellnlsqrselkavvgilppeleellealselGalgaklsG 55 
                                    +       +d++++ge+l ++ +   ++ +  +  + ++l+ea +++  ++ak  G
  gi|121638160|ref|YP_978384.1| 287 NriadrlfEDIQTVGEMLMELGA---VDAYVLEGGSARKLIEAREKAF-WAAKALG 338
                                    45555566899999999999999...7777777777777777765554.5555555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.4
                 GHMP_kinases_C  36 leellealselGalgaklsGaGg 58 
                                    ++++  +++elG   + +sG +g
  gi|121638160|ref|YP_978384.1| 397 MTDIFALAMELG---GAISGEHG 416
                                    577888899999...99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2510.22
//
Query:       gi|121638161|ref|YP_978385.1|  [L=552]
Description: phosphate-transport permease PitB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-109  366.6  34.4   8.7e-109  363.6  34.4    2.0  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.6  34.4  4.8e-113  8.7e-109       1     337 []      84     541 ..      84     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: 363.6 bits;  conditional E-value: 4.8e-113
                           PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdve.lf.dpselmlgmlaallgaavwll 78 
                                    +G nDvan+f+tsvg+++lt++qA+++aaife++Gav++G++V+etir+givd++ +  dp+++m +ml+al +aa+wll
  gi|121638161|ref|YP_978385.1|  84 VGGNDVANSFGTSVGAGTLTMKQALLVAAIFEVSGAVIAGGDVTETIRSGIVDLSgVSvDPRDFMNIMLSALSAAALWLL 163
                                    699***************************************************95448********************* PP

                           PHO4  79 latvlglPvStthslvGaliGaalaa........egg.eavkwkklvkivlswvlsPllggiiaallfllvkrl...... 143
                                    +a+ +g+PvStths++G+++Gaa+a+        + + ++v+w+++++iv+swvlsP+lgg++++ll+ ++kr+      
  gi|121638161|ref|YP_978385.1| 164 FANRMGYPVSTTHSIIGGIVGAAIALgmvsgqggA-AlRMVQWDQIGQIVVSWVLSPVLGGLVSYLLYGVIKRHillyne 242
                                    ******************************98633.459**********************************9666666 PP

                           PHO4 144 .....................................ilvk...................................eklk 151
                                                                                                                ++++
  gi|121638161|ref|YP_978385.1| 243 qaerrlteikkeriahrerhkaafdrlteiqqiaytgA--LardavaanrkdfdpdelesdyyrelheidaktssvDAFR 320
                                    66666666666665555555555555555555555550..0555555555666666666666677777788888899999 PP

                           PHO4 152 nalralpvlvlvtiailalsilfkge.................................sk..kddeeteklfkflqvvs 196
                                    +  +++p+++++  +i+++++lfkg                                   +  + +++t  +f+++qv++
  gi|121638161|ref|YP_978385.1| 321 ALQNWVPLVAAAGSMIIVAMLLFKGFkhmhlglttmnnyfiiamvgaavwmatfifaktLRgeSLSRSTFLMFSWMQVFT 400
                                    99999999999999999999999966666666677777777777777777777776655225588999************ PP

                           PHO4 197 aalvsfahGanDvanaiGpllaalisiyk...a.sk.evplwvlllgglaialGlllgGkrviktvGekitkkltpsrGf 271
                                    a+ ++f+hG+nD+anaiGp+ aa++++++   +  + +vp   ++++g+a+++Gl+++G+rvi tvG+++t +++p++Gf
  gi|121638161|ref|YP_978385.1| 401 ASGFAFSHGSNDIANAIGPF-AAILDVLRtgaIeGNaAVPAAAMVTFGVALCAGLWFIGRRVIATVGHNLT-TMHPASGF 478
                                    ********************.9999***99853666799********************************.5******* PP

                           PHO4 272 aaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsalls 337
                                    aael+aa +v+ a+ lglPvS+Th+l+gav+GvG+++ r  + nw+l++ ivlaWv+Tlp +a+l+
  gi|121638161|ref|YP_978385.1| 479 AAELSAAGVVMGATVLGLPVSSTHILIGAVLGVGIVN-R--STNWGLMKPIVLAWVITLPSAAILA 541
                                    *************************************.5..9*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3224.90
//
Query:       gi|121638162|ref|YP_978386.1|  [L=312]
Description: LysR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-44  151.0   8.8    4.7e-44  150.2   8.8    1.3  1  LysR_substrate  LysR substrate binding domain
    1.3e-19   69.9   3.1    2.9e-19   68.8   1.6    2.3  2  HTH_1           Bacterial regulatory helix-turn-helix protein
      7e-08   31.8   0.0    1.8e-07   30.5   0.0    1.6  1  PBP_like        PBP superfamily domain
    0.00038   20.3   0.2     0.0018   18.1   0.0    2.2  2  MarR_2          MarR family
     0.0057   16.7   2.6       0.12   12.5   0.1    2.9  2  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.05   13.5   0.6       0.17   11.7   0.6    2.0  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   8.8   1.6e-47   4.7e-44       3     206 ..      95     309 ..      93     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 1.6e-47
                                    TSCEEEEEEEECCCHHHHHHHHHHHHHHHSTT.....EEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTTEEEEEEEE CS
                 LysR_substrate   3 glrgrLrigapptlaryllppllarfraryPe.....velelvegdseelldllaegelDlairagppedsglearpLae 77 
                                    + r+r+r+ a++t+a++l+p+++ ++ra+  +      e+ l++++se+ ++++++g +Dl+++ +p++++gl ++++a+
  gi|121638162|ref|YP_978386.1|  95 EGRQRIRVVASQTIAEQLMPHWMLSLRAADMRrggtvPEVILTATNSEHAIAAVRDGIADLGFIENPCPPTGLGSVVVAR 174
                                    6799**************************************************************************** PP

                                    EEEEEEEETTSGGGGSSSE.CGGGGCTSEEEEESTTSTHHHHHHHHHHCT....TEECEEEEEESSHHHHHHHHHTTS-B CS
                 LysR_substrate  78 eplvlvaspdhpLargepv.sledLadeplilleegsglrdlledalrea....glkprvalevnsleallalvaaGlGi 152
                                    ++lv+v++p+h++ar+ +v s+++La+ pl+++e++sg+rd+l +alr++     +++ ++le++s++a++a+v+aG G 
  gi|121638162|ref|YP_978386.1| 175 DELVVVVPPGHKWARRSRVvSARELAQTPLVTREPNSGIRDSLTAALRDTlgedMQQAPPVLELSSAAAVRAAVLAGAGP 254
                                    ***************88888************************99999999888999********************** PP

                                    EEEEGGGHHCCCHTTTEEEEEESSTTCEEEEEEEEETTCCCHH.HHHHHHHHHHH CS
                 LysR_substrate 153 allprsavrdeladgrlvalplpepplprelylvyrkgrelsp.avrafidflre 206
                                    a ++r+a++d+la grl a+++p+++l+r+l +++  gr +++ a+r+++ ++++
  gi|121638162|ref|YP_978386.1| 255 AAMSRLAIADDLAFGRLLAVDIPALNLRRQLRAIWVGGRTPPAgAIRDLLSHITS 309
                                    ***************************************8888999999998865 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   1.6   9.8e-23   2.9e-19       4      59 ..      13      68 ..      10      69 .. 0.97
   2 ?   -0.7   0.0      0.46   1.4e+03      36      52 ..     195     212 ..     191     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 9.8e-23
                                   HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                          HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                   +++f+a+ae+gs+ +AA+eLgl+q avsr+++++E+++gv+L +Rt+rg +LT+aG
  gi|121638162|ref|YP_978386.1| 13 FEIFLAIAEAGSLGGAARELGLTQQAVSRRLASMEAQIGVRLAIRTTRGSQLTPAG 68
                                   689****************************************************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                                    HHHHHHTS-SEEESSS.E CS
                          HTH_1  36 rLEeelgvpLfeRtgr.g 52 
                                    + +e+ ++pL++R  + g
  gi|121638162|ref|YP_978386.1| 195 SARELAQTPLVTREPNsG 212
                                    56788999****966533 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0     6e-11   1.8e-07      47     160 ..     153     265 ..     137     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6e-11
                                    HCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHH....S--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-C.EECTE CS
                       PBP_like  47 ynapalrkaldgievvlvnlarreqglvvakgnpk....kitnwkdladaplrlvnRetGSGtrdlfdellkke.gisks 121
                                    +++ ++++  + + +  v +ar+e  +vv +g ++    ++ ++++l  a+  lv+Re  SG rd ++ +l+++ g + +
  gi|121638162|ref|YP_978386.1| 153 ADLGFIENPCPPTGLGSVVVARDELVVVVPPGHKWarrsRVVSAREL--AQTPLVTREPNSGIRDSLTAALRDTlGEDMQ 230
                                    5677788888888888899*************999555559999999..556689*****************99777778 PP

                                    -SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCC CS
                       PBP_like 122 sikgyaqearshlavaaaVaagradvgvgieavaeelkg 160
                                    + + +  e  s  av aaV ag + ++++  a+a+   +
  gi|121638162|ref|YP_978386.1| 231 QAPPV-LELSSAAAVRAAVLAGAGPAAMSRLAIAD---D 265
                                    88886.8********************99888884...3 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     6e-07    0.0018      13      48 ..      18      49 ..       6      51 .. 0.81
   2 ?   -3.1   0.0       2.5   7.5e+03      44      55 ..     198     209 ..     190     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6e-07
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                         MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48
                                   a++ ++    + g  ar+lgl+++avsr+l+ ++a+
  gi|121638162|ref|YP_978386.1| 18 AIAEAG----SLGGAARELGLTQQAVSRRLASMEAQ 49
                                   555554....77889******************996 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                    HHHHTTSEEEEE CS
                         MarR_2  44 rLvaaGLverrp 55 
                                    +L +  Lv+r+p
  gi|121638162|ref|YP_978386.1| 198 ELAQTPLVTREP 209
                                    344444566665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   3.9e-05      0.12      14      50 ..      14      48 ..      11      60 .. 0.86
   2 ?    3.2   0.3     0.032        96      10      47 ..     243     287 ..     235     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLee 50
                                   +i+ a+  ae+ +++  a++l+l+++ +s++L+ +e 
  gi|121638162|ref|YP_978386.1| 14 EIFLAI--AEAGSLGGAARELGLTQQAVSRRLASMEA 48
                                   677777..99**********************99964 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.032
                                    HHHHHHHHHHSTCTTB-HHHHHHHH........TS-HHHHHHHHHH CS
                         HTH_20  10 PvRrrilraLaraegltaselaerl........dlskntlsyHLrv 47 
                                     vR+++l+   ++++++  ++a+ l        d++  +l+++Lr+
  gi|121638162|ref|YP_978386.1| 243 AVRAAVLAGA-GPAAMSRLAIADDLafgrllavDIPALNLRRQLRA 287
                                    5788888887.99************888777777999999999986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   5.7e-05      0.17      24      42 .]      29      47 ..      28      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                  HTH_AsnC-type 24 AervGlSestvlrRvrrLe 42
                                   A+++Gl++++v rR++ +e
  gi|121638162|ref|YP_978386.1| 29 ARELGLTQQAVSRRLASME 47
                                   99*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2043.62
//
Query:       gi|121638163|ref|YP_978387.1|  [L=64]
Description: hypothetical protein BCG_2298 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.028   14.4   0.0    1.0  1  Med19     Mediator of RNA pol II transcription subunit 19


Domain annotation for each model (and alignments):
>> Med19  Mediator of RNA pol II transcription subunit 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-06     0.028      51      93 ..      17      59 ..      14      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-06
                          Med19 51 pGvidl.kgtkenssLrsliekPPiggkellpltssalaGfrLh 93
                                   +G+ d+ ++t  n  L s i kPPi ++   pl s++ aG r  
  gi|121638163|ref|YP_978387.1| 17 IGITDNdPATATNRRLASTIRKPPI-EHAAGPLGSTSRAGHRSY 59
                                   5777751577899************.77889******9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 421.16
//
Query:       gi|121638164|ref|YP_978388.1|  [L=431]
Description: esterase LipM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-20   71.9   0.1    9.6e-20   71.3   0.1    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
    1.7e-13   50.5   0.1    8.3e-13   48.3   0.1    2.0  1  Peptidase_S9   Prolyl oligopeptidase family
    3.7e-12   45.9   0.0    3.5e-11   42.7   0.0    1.9  1  COesterase     Carboxylesterase family
    0.00055   19.6   0.2       0.74    9.4   0.1    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0021   17.4   0.6      0.013   14.8   0.0    2.3  3  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.099   12.0   0.0    2.0  2  LIP            Secretory lipase
       0.16   11.6   0.0       0.28   10.8   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.1   3.7e-23   9.6e-20       3     209 ..     185     392 ..     183     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.7e-23
                                    EE--STTTS--TTTT.HHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                  Abhydrolase_3   3 yfHGGGfvlgsldth.dalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                    ++ GG++++g+ + + ++l+++la+ lg ++v+++Yr +P + +P  + d+ +al w++++ +e+g dp+ i++ G SaG
  gi|121638164|ref|YP_978388.1| 185 QIPGGAWTTGNKRGQaHPLMSHLAE-LGWICVAINYRHSPRNTWPDHIIDVKRALAWVKAHISEYGGDPDFIAITGGSAG 263
                                    566********98776999999986.***********************************99***************** PP

                                    HHHHHHHHHHHHHTT.---.......EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS...GGGG CS
                  Abhydrolase_3  82 Gnlaaavalrardeg.epk.......vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp...eadr 150
                                    G+l+  +al   d   +p+       v++ v +y v d++r  ++++            ++ +l l+ r++++    a++
  gi|121638164|ref|YP_978388.1| 264 GHLSSLAALTPNDPRfQPGfeeadtrVQAAVPFYGVYDFTRL-QDAM------------HPMMLPLLERMVVKqprTANM 330
                                    ********999997544449999999**********988333.3333............233455666666632222333 PP

                                    GST.TTSGGGCS-SST---EEEEEETT-TTH..HHHHHHHHHHHH.TT--EEEEEETTEETTG CS
                  Abhydrolase_3 151 ddp.laspllaedlsglpptlvvvaefDplr..degeayaerlra.agvevelieyegmvHgf 209
                                    ++   asp+ +   +++pp +v+ + +D l   ++++ + ++lr+  +++v + e + + H+f
  gi|121638164|ref|YP_978388.1| 331 QSYlDASPVTH-ISADAPPFFVLHGRNDSLVpvQQARGFVDQLRQvSKQPVVYAELPFTQHAF 392
                                    32235667655.4667************9973368888******96788999*****999999 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   3.2e-16   8.3e-13      44     188 ..     233     392 ..     202     417 .. 0.72

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.2e-16
                                    HHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH.HHHHH-GGG-S...........EEEEESE---CCCHHCSTTS. CS
                   Peptidase_S9  44 efdDfiaaaealakegyvdserlaitGgSyGGyltg.aalnqrpdlFk...........aavaevpvvdvlrydsdtdl. 110
                                    +++  +a+++a ++e+  d++ +aitGgS+GG l+  aal+ ++ +F+           aav  ++v+d +r     +  
  gi|121638164|ref|YP_978388.1| 233 DVKRALAWVKAHISEYGGDPDFIAITGGSAGGHLSSlAALTPNDPRFQpgfeeadtrvqAAVPFYGVYDFTRLQDAMHPm 312
                                    5566799*************************987515666888888533333333333777888888888877775557 PP

                                    .THH.HCCCC--TTT.CHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-S CS
                   Peptidase_S9 111 .lte.eymewgnpee.neegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegH 186
                                     l   e m   +p+  n + y ++sp+++  +    pp++++hG +D+ vp+++a  +v++L++  k+ v +   p  +H
  gi|121638164|ref|YP_978388.1| 313 mLPLlERMVVKQPRTaNMQSYLDASPVTHISA--DAPPFFVLHGRNDSLVPVQQARGFVDQLRQVSKQpVVYAELPFTQH 390
                                    84444445445554348899999999999999..*****************************98888899988888888 PP

                                    ST CS
                   Peptidase_S9 187 gv 188
                                     +
  gi|121638164|ref|YP_978388.1| 391 AF 392
                                    43 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.4e-14   3.5e-11      90     206 ..     166     274 ..     165     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.4e-14
                                    EEEEE.ESSSSSTTSSEEEEEEE--STTTS-BGCGS-THHHHHHH...TSEEEEE----HHHHH-B-SSTTSBS-HHHHH CS
                     COesterase  90 Lnvyt.PkekkeakkklPVlVwihGggfqtgsaseydgsaLaaeg...nvivVtinYRlGvlGFlstgdeeapGNvGllD 165
                                    L+++  P+   + + + PVl+ i Gg+ +tg ++  +++ L+++    + i V+inYR  +   +            + D
  gi|121638164|ref|YP_978388.1| 166 LDIWRrPD--LDLTGTAPVLFQIPGGAWTTGNKRG-QAHPLMSHLaelGWICVAINYRHSPRNTWPD---------HIID 233
                                    77888564..4567777***********9998754.444444444444**********988543332.........379* PP

                                    HHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSG CS
                     COesterase 166 qvlALrWVkenIasFGGdpervtlfGesAGaasvsllllsp 206
                                    +  AL WVk +I+++GGdp+ + + G sAG+ + sl  l+p
  gi|121638164|ref|YP_978388.1| 234 VKRALAWVKAHISEYGGDPDFIAITGGSAGGHLSSLAALTP 274
                                    ********************************999998887 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00029      0.74      16      93 ..     200     273 ..     181     278 .. 0.74
   2 !    8.1   0.0   0.00073       1.9     193     239 ..     325     374 ..     311     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                                    GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH....HHHCTTSSEE.EEEETHHHHHHHHH CS
                  Abhydrolase_1  16 waerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri....ldalgddklt.lvGhSmGGmialay 90 
                                     +   l+++La+ g+ +++++ r +++ + +        ++++v + l ++     +  gd  ++ + G+S GG +++ +
  gi|121638164|ref|YP_978388.1| 200 AHP--LMSHLAELGWICVAINYRHSPRNTWPD-------HIIDVKRALAWVkahiSEYGGDPDFIaITGGSAGGHLSSLA 270
                                    344..78899999********99777774333.......688899999988445566779999999************99 PP

                                    HHH CS
                  Abhydrolase_1  91 aae 93 
                                    a+ 
  gi|121638164|ref|YP_978388.1| 271 ALT 273
                                    986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00073
                                    HHCCHHHHHHHHHCTHHHHS...EEEEEEETTCSSSCHHHHHHHHHCHTS CS
                  Abhydrolase_1 193 pttdsaklllrlrelknvla...ptlvisgtsDplvppkaledlaqllpk 239
                                    p t++++++l+   ++ ++a   p +v++g++D lvp ++ + + ++l++
  gi|121638164|ref|YP_978388.1| 325 PRTANMQSYLDASPVTHISAdapPFFVLHGRNDSLVPVQQARGFVDQLRQ 374
                                    56777888888888999999999***************666666666666 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.85   2.2e+03      95     139 ..      11      55 ..       1     104 [. 0.66
   2 ?    0.2   0.0      0.15   3.7e+02      68      99 ..     243     276 ..     198     337 .. 0.70
   3 !   14.8   0.0   5.1e-06     0.013     192     229 ..     347     384 ..     318     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.85
                    Hydrolase_4  95 lrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv 139
                                     +  + v +++ +a+ ++   +l  + ++ l+++++g ++ ++++
  gi|121638164|ref|YP_978388.1|  11 RQIGALVVAAVTAAATINAYRPLARNGFASLWSWFIGLVVTEFPL 55 
                                    555555556677777766666655666777777877777777666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                    Hydrolase_4  68 kvkeehpel..plfllGhSmGGliallyllrypd 99 
                                    ++ +e+++    + + G S GG ++ l++l+  d
  gi|121638164|ref|YP_978388.1| 243 AHISEYGGDpdFIAITGGSAGGHLSSLAALTPND 276
                                    3334444442346678999999999988855444 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 5.1e-06
                    Hydrolase_4 192 lPllllhGeaDkvvdpeasrelyerlgskdktlklypg 229
                                     P+++lhG +D +v+ +++r ++++l++  k+  +y++
  gi|121638164|ref|YP_978388.1| 347 PPFFVLHGRNDSLVPVQQARGFVDQLRQVSKQPVVYAE 384
                                    59*********************************987 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.24   6.1e+02      22      89 ..     207     271 ..     198     284 .. 0.65
   2 ?   12.0   0.0   3.9e-05     0.099     212     272 ..     343     403 ..     322     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.24
                            LIP  22 lLkeGyyVvvpDye.GpkstftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGslAsawAa 89 
                                    l + G+  v   y   p+ t++    + k+ L  ++a +   +  g  +   +a+ G S G+  s+ Aa
  gi|121638164|ref|YP_978388.1| 207 LAELGWICVAINYRhSPRNTWPDHIIDVKRALAWVKAHI--SEYGG--DPDFIAITGGSAGGHLSSLAA 271
                                    555677777777742677777777777777777777777..33434..444566777776666666555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.9e-05
                            LIP 212 avPqiPvlvyhgvidelipikdakklaknwcdkgiaslefaedlssgHlaetlvgapaalt 272
                                     +  +P +v+hg  d+l+p+++a+   ++  +   + + +ae  +++H  ++l +a aa t
  gi|121638164|ref|YP_978388.1| 343 SADAPPFFVLHGRNDSLVPVQQARGFVDQLRQVSKQPVVYAELPFTQHAFDLLGSARAAHT 403
                                    55678*******************************************9999988888755 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.28      80     189 ..     228     374 ..     205     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                           FSH1  80 kneyegleesldavkdyikengp...fdGiiGFSqGaalaallaslleellkea....shpslkfai.lvsGfkleepk. 150
                                    ++++++++ +l+ vk +i+e g    f  i G S G++l++l a + +  + +      +++++ a+ ++  +++++++ 
  gi|121638164|ref|YP_978388.1| 228 PDHIIDVKRALAWVKAHISEYGGdpdFIAITGGSAGGHLSSLAALTPNDPRFQPgfeeADTRVQAAVpFYGVYDFTRLQd 307
                                    677889999***********987779*************99998877666654466656777788884555567777778 PP

                           FSH1 151 ......................yeeyyeedki......qtptLhvlGelDtvvdeerseaLaeafkn 189
                                                          +++y + +++      + p++ ++G++D++v+ ++++ ++++ ++
  gi|121638164|ref|YP_978388.1| 308 amhpmmlpllermvvkqprtanMQSYLDASPVthisadAPPFFVLHGRNDSLVPVQQARGFVDQLRQ 374
                                    889999999999999999888644444444445557767899999****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3248.04
//
Query:       gi|121638165|ref|YP_978389.1|  [L=445]
Description: hypothetical protein BCG_2300 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-83  279.6   0.0    4.1e-83  279.2   0.0    1.2  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
      1e-27   96.9   0.0    1.6e-27   96.2   0.0    1.3  1  DUF1298         Protein of unknown function (DUF1298)
  ------ inclusion threshold ------
      0.065   11.8   0.0      0.089   11.3   0.0    1.1  1  AATase          Alcohol acetyltransferase


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.2   0.0   6.9e-87   4.1e-83       1     264 []       4     256 ..       4     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 279.2 bits;  conditional E-value: 6.9e-87
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    LsplD++f ++e+++tpmh+ga+av++ p kga+++++r+l+eai+q +   +++++   +  +g+++++W++++ +D++
  gi|121638165|ref|YP_978389.1|   4 LSPLDQMFARMEAPRTPMHIGAFAVFDLP-KGAPRRFIRDLYEAISQLAFLPFPFDS---VIAGGASMAYWRQVQ-PDPS 78 
                                    89***************************.***************************...9*************9.**** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yHvR +alp+PGt r+l++lv+rL+s+pLD+ +PlWe+h+iEGl+g+++A+++k HH+ +DG+gg++l++++l++dp++p
  gi|121638165|ref|YP_978389.1|  79 YHVRLSALPYPGTGRDLGALVERLHSTPLDMAKPLWELHLIEGLTGRQFAMYFKAHHCAVDGLGGVNLIKSWLTTDPEAP 158
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaal.earslvlpfaaprtplntplsraRrf 239
                                    p + +p+ p +d  +++l++    v+++a++++++++v++v++ agrl++++l +++s+ +++++prtp+nt+++r+Rr+
  gi|121638165|ref|YP_978389.1| 159 PGSGKPE-PFGD--DYDLAS----VLAAATTKRAVEGVSAVSELAGRLSSMVLgANSSVRAALTTPRTPFNTRVNRHRRL 231
                                    *******.8888..799987....799************************9999999********************** PP

                 WES_acyltransf 240 aaaslpLadvkavakalgvtiNDvv 264
                                    a++ l+L ++kava+a+++t+NDv+
  gi|121638165|ref|YP_978389.1| 232 AVQVLKLPRLKAVAHATDCTVNDVI 256
                                    ***********************96 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   2.8e-31   1.6e-27       3     144 ..     295     439 ..     294     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.8e-31
                        DUF1298   3 NqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllel.llkllpakvaaal..ikrllsnttlviSNvpGP 79 
                                    N  +  ++pL++ ++dP+ rl ++ ++++r K +l a+++++l+++ ++ llp +v+++   +  +++ +++++SNv+ +
  gi|121638165|ref|YP_978389.1| 295 NAASGFVAPLGTSIEDPVARLTTISASTTRGKAELLAMSPNALQHYsVFGLLPIAVGQKTgaLGVIPPLFNFTVSNVVLS 374
                                    788999**************************************9945789999999998756666************** PP

                        DUF1298  80 qeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    +++lyl Ga+l+ i+p++++ +g +ln+t++ y++k+ +g+++++d++p++q+l+++   a+eel
  gi|121638165|ref|YP_978389.1| 375 KDPLYLSGAKLDVIVPMSFLCDGYGLNVTLVGYTDKVVLGFLGCRDTLPHLQRLAQYTGAAFEEL 439
                                    ***************************************************************98 PP

>> AATase  Alcohol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.5e-05     0.089     128     178 ..     100     148 ..      91     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                         AATase 128 selvipvgdpkkPlwrlivlpsaddkkkwkkfvfitdHllfDGisgvnffk 178
                                    + l +   d  kPlw l +++    +++ + + f   H+  DG+ gvn+ k
  gi|121638165|ref|YP_978389.1| 100 ERLHSTPLDMAKPLWELHLIEGL--TGRQFAMYFKAHHCAVDGLGGVNLIK 148
                                    555555566778*********96..66788889***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3139.97
//
Query:       gi|121638166|ref|YP_978390.1|  [L=87]
Description: hypothetical protein BCG_2301c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 698.30
//
Query:       gi|121638167|ref|YP_978391.1|  [L=133]
Description: hypothetical protein BCG_2302c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-08   35.0   0.0    1.3e-06   28.3   0.0    2.0  1  DSBA      DSBA-like thioredoxin domain


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   7.5e-11   1.3e-06       1     156 [.       3     132 ..       3     133 .] 0.81

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.5e-11
                                    EEEEEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGS CS
                           DSBA   1 tvdeffDvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpk 80 
                                    tvd+ fD lCP+ y+ +  ++ ++a+  ++++ +r f+l++    +g +                  +          ++
  gi|121638167|ref|YP_978391.1|   3 TVDFHFDPLCPFAYQTSVWIRDVRAQL-GITINWRFFSLEEINLVAGKKH----------------PW----------ER 55 
                                    79*************************.**************33222222................22..........22 PP

                                    S.HHH.HHHHHHHHHHHHHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHH CS
                           DSBA  81 d.klk.nstraarlllaagaeglaekvvrelfealwsegqaitddqellevaekaGldaeeldealeseavkeavren 156
                                    d   + ++ r  +ll  ++++ l ++ + ++ + l++ g ++ d+++ ++++ ++G++a+ ld+al+++   ++vr +
  gi|121638167|ref|YP_978391.1|  56 DwSYGwSLMRIGALLRRTNMS-LLDRWYAAIGHELHTLGGKPHDPAVARRLLCDVGVNAAILDAALDDPTTHDDVRAD 132
                                    222233455555555555554.899***********************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 921.03
//
Query:       gi|121638168|ref|YP_978392.1|  [L=542]
Description: integral membrane transport protein YjcE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-74  251.2  37.0    1.8e-74  250.9  37.0    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.9  37.0   9.9e-79   1.8e-74       3     381 .]      19     417 ..      17     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: 250.9 bits;  conditional E-value: 9.9e-79
                                    HHHHH.HHHHHHH.HHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                 Na_H_Exchanger   3 llill.allvgll.arrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlks 78 
                                    +++l+ a++vg++  +r++++++v+li+ G llG++ +     +  ++d ev++ l+l+ +l++ ++++++re+r+nl+ 
  gi|121638168|ref|YP_978392.1|  19 IVALVaAVVVGTVlGHRYRVGPPVLLILSGSLLGLIPRF----GdvQIDGEVVLLLFLPAILYWESMNTSFREIRWNLRV 94 
                                    33333277777755***********************99....3368********************************* PP

                                    HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCC CS
                 Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvl 158
                                    i+++++++v++t+v++++++++   lg++ ++a ++ga+ls+td+++v+ +    +r+p+r  t+l ges++nD++a+vl
  gi|121638168|ref|YP_978392.1|  95 IVMFSIGLVIATAVAVSWTARA---LGMESHAAAVLGAVLSPTDAAAVAGLA---KRLPRRALTVLRGESLINDGTALVL 168
                                    *********************8...79*************************...************************* PP

                                    CHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHH CS
                 Na_H_Exchanger 159 lavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgi 238
                                    +av +a+a  e +++++ ++l+++f+v ++gg+++gl++g l+ l++r++ d +  e +l+ll++++a+lla++l++sg+
  gi|121638168|ref|YP_978392.1| 169 FAVTVAVA--EGAAGIGPAALVGRFVVSYLGGIMAGLLVGGLVTLLRRRI-DAPLEEGALSLLTPFAAFLLAQSLKCSGV 245
                                    ********..9**************************************8.***************************** PP

                                    HHHHHHHHHHHHHHHHTTHHHH....HHHHHH...HHHHHHHHHHHHHHSX...............HHHHHXXHHHHHHH CS
                 Na_H_Exchanger 239 lgaflaGlvlseyefsnklsek....lesfre...glfnplfFvlvGlsld...............lkvlnnhlsvlilv 296
                                    +++++  lvl+ +++   ++++     ++f++   +l+n+ ++v+vG++++                +vl   l v+ +v
  gi|121638168|ref|YP_978392.1| 246 VAVLVSALVLTYVGPTV-IRARsrlqAHAFWDiatFLINGSLWVFVGVQIPgaidhiagedgglprATVL--ALAVTGVV 322
                                    ***********999988.88888899*************************9999999999888777777..5******* PP

                                    HHHHHHHHTHHHHHHHHHTTTX.....SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH.....XHHHHTT.SSTTTCSTS CS
                 Na_H_Exchanger 297 llilvaillgrilavflllrll.....glslrealiigfgglqrgavalalaalgpal.....gllarel.yallivvvl 365
                                    +++ +a++ + ++ ++++ r+l     ++++r++++ +++g+ rgav+la+a+++p++     ++++r+l ++++ vv+l
  gi|121638168|ref|YP_978392.1| 323 IATRIAWVQATTVLGHTVDRVLkkptrHVGFRQRCVTSWAGF-RGAVSLAAALAVPMTtnsgaPFPDRNLiIFVVSVVIL 401
                                    ******************************************.************************************* PP

                                    XHHHHHHHHHHHHHHC CS
                 Na_H_Exchanger 366 ftvlvqGlslkpllkk 381
                                    +tvlvqG+sl++++++
  gi|121638168|ref|YP_978392.1| 402 VTVLVQGTSLPTVVRW 417
                                    ************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3768.39
//
Query:       gi|121638169|ref|YP_978393.1|  [L=125]
Description: hypothetical protein BCG_2304 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 858.37
//
Query:       gi|121638170|ref|YP_978394.1|  [L=260]
Description: CDP-diacylglycerol pyrophosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-70  235.5   0.0    6.2e-70  235.3   0.0    1.0  1  CDH       CDP-diacylglycerol pyrophosphatase


Domain annotation for each model (and alignments):
>> CDH  CDP-diacylglycerol pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.3   0.0   3.5e-74   6.2e-70       1     223 [.      41     257 ..      41     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 3.5e-74
                            CDH   1 rdaLWkivseqCvpaqqakgepapCaevdlakgyavlkdrngplqyLliPtarisGiespallepetpnyfaaAwaarkl 80 
                                    r+aLWkiv+++C   ++++g++apC+ vd+++g+a++k++ +p+q+LliP+ari+Gie+pal e++++ny+++Awaar l
  gi|121638170|ref|YP_978394.1|  41 REALWKIVHDRCEFGYRRTGAYAPCTFVDEQSGTALYKADFDPYQFLLIPLARITGIEDPALRESAGRNYLYDAWAARFL 120
                                    589***************************************************************************** PP

                            CDH  81 vseklgkalpdealsLaiNsasgRsQdqLhiHidClrpdvraaLkkaaakigekWkslpekLegheylarrveaeelaqk 160
                                    v+++l+++lp++++ L+iN +++R+QdqLhiHi+C +p+++aaL+++ ++    Wk+lp +L g++++ ++v++++++++
  gi|121638170|ref|YP_978394.1| 121 VTARLNNSLPESDVVLTINPKNARTQDQLHIHISCSSPTTSAALRNVDTSEYVGWKQLPIDLGGRRFQGLAVDTKAFESR 200
                                    ******************************************************************************** PP

                            CDH 161 npfrllaeelpeareemaeaslalvgasekdgkkgfvlLaseadllkgnrasaeelqDheCki 223
                                    n fr +  +++++ ++m++as+a++++++++    f+lL  e ++++    +ae+lqDh+C+i
  gi|121638170|ref|YP_978394.1| 201 NLFRDIYLKVTADGKKMENASIAVANVAQDQ----FLLLLAEGTEDQ--PVAAETLQDHDCSI 257
                                    ************************7777776....999999998875..59**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1972.05
//
Query:       gi|121638171|ref|YP_978395.1|  [L=51]
Description: lipoprotein lppOa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      116  (0.00646996); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.24s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 426.54
//
Query:       gi|121638172|ref|YP_978396.1|  [L=121]
Description: lipoprotein lppOb [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-12   46.2   0.6    1.3e-11   44.8   0.6    1.6  1  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen


Domain annotation for each model (and alignments):
>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.6   7.4e-16   1.3e-11      12     116 .]       2     120 ..       1     120 [. 0.82

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7.4e-16
                    Myco_19_kDa  12 vdGqdlqt.tgsvtCtqaggaltiaig............dgasgvsavltdgdeptvesvgigdvdGf...tltyaegtg 75 
                                    v+G ++ t +g+v+C ++    t + +            d++ +v++ l+d+ +p v+ +gi+   G+   ++ y+  ++
  gi|121638172|ref|YP_978396.1|   2 VEGHTH-TiSGAVECRTSPAVRTATPSesgtqttrvnahDDSASVTLSLSDSTPPDVNGFGISLKIGSvdyQMPYQPVQS 80 
                                    788884.55888999766666666664466666666554579999999999***********998676688999999998 PP

                    Myco_19_kDa  76 ggsaevtkdgntYtitGtaegadsanpaqpvtktFeievtC 116
                                      ++e+t++g++Yt+tGt++++  ++  ++++ +F ++vtC
  gi|121638172|ref|YP_978396.1|  81 PTQVEATRQGKSYTLTGTGHAVIPGQT-GMRELPFGVHVTC 120
                                    899******************999885.89*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 936.96
//
Query:       gi|121638173|ref|YP_978397.1|  [L=284]
Description: thiosulfate sulfurtransferase SseB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-31  109.2   0.0    5.5e-18   65.4   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   3.1e-22   5.5e-18       1     106 [.      10     131 ..      10     132 .. 0.90
   2 !   42.0   0.0   6.2e-15   1.1e-10       7     106 ..     166     273 ..     161     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3.1e-22
                      Rhodanese   1 sakelkellekgkva.llDvR.....ppee....YekghIpgAvnv......skdtlsrakkseapllelpeellel.gi 63 
                                    +a+el+ ++++g+++ +lDvR     p  +    Y +gh+pgAv v      s  t+ +  +++ p+ + +++  ++ gi
  gi|121638173|ref|YP_978397.1|  10 TAAELAGMIQAGDPVsILDVRwrldeP--DghaaYLQGHLPGAVFVsledelSDHTIAGRGRHPLPSGASLQATVRRcGI 87 
                                    68899****8888888*****988541..35667******************999999999******************* PP

                      Rhodanese  64 dnkktvvvycdgggr.aaaaaallkklGyknvsvldGGfkawke 106
                                    +++ +vvvy+d +   +a+a++ l+++G  nv++ldGG+ aw +
  gi|121638173|ref|YP_978397.1|  88 RHDVPVVVYDDWNRAgSARAWWVLTAAGIANVRILDGGLPAWRS 131
                                    **********8777778888**********************87 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 6.2e-15
                      Rhodanese   7 ellekgkvallDvRppeeY.........ekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdggg 77 
                                    +  ++g+v llD+R pe++          +ghIpgA+nv++ +    + +     +l++ l+++gid++ +v vyc +g 
  gi|121638173|ref|YP_978397.1| 166 QQAGAGGVTLLDARVPERFrgdvepvdaVAGHIPGAINVPSGSVLADDGTFLGNGALNALLSDHGIDHGGRVGVYCGSGV 245
                                    556778888**********99999999888*********6666666666666666666666666**************** PP

                      Rhodanese  78 raaaaaallkklGyknvsvldGGfkawke 106
                                    +aa   a+l   G ++  +  G++++w++
  gi|121638173|ref|YP_978397.1| 246 SAAVIVAALAVIG-QDAALFPGSWSEWSS 273
                                    95555666666**.9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2103.33
//
Query:       gi|121638174|ref|YP_978398.1|  [L=334]
Description: hypothetical protein BCG_2309c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-23   81.5   0.2    1.2e-13   50.9   0.3    2.1  2  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.3   6.7e-18   1.2e-13       3     108 ..      40     148 ..      38     195 .. 0.85
   2 !   28.7   0.0   3.9e-11     7e-07     169     233 ..     264     328 ..     235     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 6.7e-18
                                    EEEESSHHHHHHHHHH.EEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC......--SEEEE CS
                      PNP_UDP_1   3 aiivgspgevellaes.pleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkef......gvkaiir 75 
                                     ++ ++p e+++++++  l+  p+      +++++G++ gk+v++++tGiG +na   ++  + ++f       + a+++
  gi|121638174|ref|YP_978398.1|  40 LVLSAFPAEADAVLAHtALDANPVVVA-DRRRYYLGSISGKKVIVAMTGIGLVNAT-NTTETAFARFtcassiAIAAVMF 117
                                    6899************66666666666.****************************.8888888889999999******* PP

                                    EEEEEESSTTT-TT-EEEEEEEEESSSCCGCCT CS
                      PNP_UDP_1  76 iGtaGglnpdlkvGDvvipddainfdgrsplyg 108
                                    +G+aGg    + +GDv+ip + + +d++++ +g
  gi|121638174|ref|YP_978398.1| 118 SGVAGGA-GRTSIGDVAIPAR-WTLDNGATFRG 148
                                    *******.9999*********.55555555444 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.9e-11
                                    C-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.....HCCCHHHHHHHHHHHHHHHHHH CS
                      PNP_UDP_1 169 gadaveMEtaavaqlArelgipfaairvvsdlaaggadaeath....eeveefaqeaaknaaalllall 233
                                    g dav+ Etaa  ++A  +g+pf++ir+ sd    g +++         +    q+aa+naa++++a+l
  gi|121638174|ref|YP_978398.1| 264 GFDAVDQETAAAQAVADAHGVPFLGIRGMSD----GPGDPLHLpgfpVQFFVYKQIAANNAARVTEAFL 328
                                    69*****************************....5555554467779999999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1768.43
//
Query:       gi|121638175|ref|YP_978399.1|  [L=407]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-28   99.3   0.0    2.9e-28   99.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.09   11.5   0.0       0.12   11.1   0.0    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
       0.16   11.3   0.0       0.25   10.6   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
       0.19   11.6   0.0       0.29   11.0   0.0    1.2  1  SPOC             SPOC domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   6.5e-32   2.9e-28      62     360 ..      81     396 ..      29     399 .. 0.80

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 6.5e-32
                                    TCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTT CS
                  Aminotran_1_2  62 klklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealke 141
                                     ++l+ + +    ++   +i+ + +l+  ++gd ++v +p+ya++   + + g  v++ pl+   d ++dl+al+ea ++
  gi|121638175|ref|YP_978399.1|  81 WHDLEVS-RTAIVPDVMLGIVEVLRLI-TDRGDPVIVNSPVYAPFYAFVSHDGRRVIPAPLR--GDGRIDLDALQEAFSS 156
                                    4446666.4444555555566666777.58******************************99..***************9 PP

                                    HHCTTE..TEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEES CS
                  Aminotran_1_2 142 apegnk..ktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgsl 219
                                    a + +    +   l+++phNPtG+v t +el+ +++ a++ ++++++De++a +     ++++ ++ v  + n + + s 
  gi|121638175|ref|YP_978399.1| 157 ARASSGssGNVAYLLCNPHNPTGSVHTADELRGIAERAQRFGVRVVSDEIHAPLIPSGARFTP-YLSVPGAENAFALMSA 235
                                    87766666888999*******************************************999999.**************** PP

                                    SSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..T CS
                  Aminotran_1_2 220 sKafGlaGeRvGyilg.naavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..g 296
                                    sKa++l G+  + +++  +a ++ +r     +  +s+l  ++ +a+  +    ++l++  + l ++r+ l +  +e   g
  gi|121638175|ref|YP_978399.1| 236 SKAWNLGGLKAALAIAgREAAADLARMPEEVGHGPSHLGVIAHTAAFRTGG--NWLDALLRGLDHNRTLLGALVDEHlpG 313
                                    ************999956666666666666666699998888888877775..4********************999*** PP

                                    EEEECCSCSSEEEEEETHH........CHHHHHHH................HHHTCTEEEEEGGGGTS..TTEEEEECTT CS
                  Aminotran_1_2 297 lkvlasqsgmflltdlsae........takelskk................Lleevgvyvtpgtsftv..pgrlRitvAg 350
                                    +++  +q++++ + d++++        +      +                 l++  v+++ g  f++   g++Ri++ +
  gi|121638175|ref|YP_978399.1| 314 VQYRWPQGTYLAWLDCRELgfddaasdE------MteglavvsdlsgparwFLDHARVALSSGHVFGIggAGHVRINF-A 386
                                    *******************977765552......0334555788999999*99999**********************.7 PP

                                    S-HHHHHHHH CS
                  Aminotran_1_2 351 lteeeleelv 360
                                    ++++ l e+v
  gi|121638175|ref|YP_978399.1| 387 TSRAILIEAV 396
                                    7766666665 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.8e-05      0.12      96     199 ..      83     191 ..      70     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHHHHHC--TT-SS-GGGG.--EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE.-HHHHHHHHHC-TTEE CS
                 Aminotran_MocR  96 slelqglvltlallhGvrdsegpwvkeekvkllvtvpGydrhfllleelGielltvdlqddGp.dvdaveklvaedasvk 174
                                     le+  ++++  ++ G+++  +  +++    ++v +p y   ++++ + G +++  +l+ dG  d+da+++  ++  +  
  gi|121638175|ref|YP_978399.1|  83 DLEVSRTAIVPDVMLGIVEVLRLITDR-GDPVIVNSPVYAPFYAFVSHDGRRVIPAPLRGDGRiDLDALQEAFSSARASS 161
                                    677777777778888888877766655.66689*****************************65*****99766555444 PP

                                    E.....EEE-SSS-TTT-----HHHHHHHH CS
                 Aminotran_MocR 175 G.....ilavpkysnptGetiseevarrla 199
                                    G      + + +  nptG++ +++  r +a
  gi|121638175|ref|YP_978399.1| 162 GssgnvAYLLCNPHNPTGSVHTADELRGIA 191
                                    411111344455568888888877777655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.6e-05      0.25      94     167 ..     130     204 ..     103     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                                    C--EEEEE-EBTTTBE-HHHHHHHS--S-T...TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase  94 agvklrdlknkeaGkmdlekleaaikevga...heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                     g ++++++ + +G +dl++l++a     a    + +++++ l + +n   G v + +elr +a+ a++ g++++ D
  gi|121638175|ref|YP_978399.1| 130 DGRRVIPAPLRGDGRIDLDALQEAFSSARAssgSSGNVAYL-LCNPHN-PTGSVHTADELRGIAERAQRFGVRVVSD 204
                                    6677788888888**********999877775444455554.445555.47***********************998 PP

>> SPOC  SPOC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.29      29     118 ..     126     213 ..     104     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                                    E----------SEEEE-EEEEHHHHHHHHHH-S......EEEEEEEE.ESSGGGHHHHHH.HHHHHHTTTEEEE.....E CS
                           SPOC  29 llsgdrslvspslLritqRlrldqvkkyldevsrri.tadllavalf.psdesdesgfae.lvdYLksKqraGvvnlnks 105
                                    ++s d   v p  Lr  +R++ld++++ + + + +  ++  +a+ l+ p++ + +++ a+ l +  +  qr+Gv      
  gi|121638175|ref|YP_978399.1| 126 FVSHDGRRVIPAPLRGDGRIDLDALQEAFSSARASSgSSGNVAYLLCnPHNPTGSVHTADeLRGIAERAQRFGV-----R 200
                                    45555556667779************9999999999888999999**9*6666666555549999999999999.....4 PP

                                    E-TTS-EEEEE-S CS
                           SPOC 106 glnqngvlyifPp 118
                                       ++ +  ++P 
  gi|121638175|ref|YP_978399.1| 201 VVSDEIHAPLIPS 213
                                    4555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 2117.40
//
Query:       gi|121638176|ref|YP_978400.1|  [L=212]
Description: hypothetical protein BCG_2311 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-61  205.9   0.0    4.2e-61  205.7   0.0    1.0  1  UPF0167   Uncharacterised protein family (UPF0167)


Domain annotation for each model (and alignments):
>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   0.0   2.3e-65   4.2e-61       1     173 []      37     211 ..      37     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 2.3e-65
                        UPF0167   1 lpeFkYhpdpletgaiekeeekCqcCgkereliyespfysvedv.ealCpwCiadGsaakkfegefqddaslveeeldee 79 
                                    lp+F+Yhpdp+ tg+i+++e++C +C+++r ++y++p+y++e++ ea+CpwCiadGsaa++f+++f+d++++v ++++e+
  gi|121638176|ref|YP_978400.1|  37 LPQFRYHPDPVGTGSIVADEVSCVSCEQRRPYTYTGPVYAEEELnEAICPWCIADGSAASRFDATFTDAMWAVPDDVPED 116
                                    79******************************************99********************************** PP

                        UPF0167  80 lleellkrtpgyiswqqeqWlahCddacaflgevgaeelealkiklekeelaaikddle.skieellellekdgeltgyl 158
                                    ++ee+l+rtpg+++w qe+Wl+hC+da+aflg vga+e+++l+++l++ + +    d+  +kiee++ +l+++g +t+yl
  gi|121638176|ref|YP_978400.1| 117 VTEEVLCRTPGFTGWLQEEWLHHCGDAAAFLGPVGASEVADLPDALDALRNEYRGYDWPaDKIEEFILTLDRNGLATAYL 196
                                    ************************************************9999999999967******************* PP

                        UPF0167 159 FrClhcgkhrlyiDa 173
                                    FrCl+cg h +y+D+
  gi|121638176|ref|YP_978400.1| 197 FRCLSCGVHLAYADF 211
                                    *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1433.92
//
Query:       gi|121638177|ref|YP_978401.1|  [L=300]
Description: haloalkane dehalogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-19   71.0   0.1    2.1e-19   70.2   0.1    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
      3e-13   50.9  13.0    3.7e-13   50.6  13.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.3e-08   32.4   0.0    2.3e-07   30.3   0.0    1.9  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   3.5e-23   2.1e-19       1     135 [.      47     171 ..      47     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3.5e-23
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p++v+lhG p +s++++   ++p L+ +g++v+++Dl G+g+S+++ +   +dy+   + +++    + l+++ +tl  +
  gi|121638177|ref|YP_978401.1|  47 PPIVLLHGEPTWSYLYRT--MIPPLSAAGHRVLAPDLIGFGRSDKPTRI--EDYTYLRHVEWVTSWFENLDLHDVTLFVQ 122
                                    89****************..****************************9..9************88899*********** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHH CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadc 135
                                    ++G++i+l  aae+ +r+++lv  ++      +  a++   + + + ++ +a   
  gi|121638177|ref|YP_978401.1| 123 DWGSLIGLRIAAEHGDRIARLVVANG------FLPAAQGRTPLPFYVWRAFARYS 171
                                    **************************......44444444444444444444444 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  13.0   6.2e-17   3.7e-13       1     219 [.      49     291 ..      49     292 .. 0.60

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 6.2e-17
                                    EEEE--GC.....G..CHHHH.HHHHCCTCEEEEE--TTSTS-GGCS..--HHHCHHHHHHHCCTT...TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassW..lvapL.aallaagvhvlapDlpGhGrsdppp..ldledladlaalldelaa.gggpvvlvGHSl 74 
                                    ++llHG ++    W  l++ +  +l+aag++vlapDl G+Grsd p    d++ l++++ +   + + + ++v l+  ++
  gi|121638177|ref|YP_978401.1|  49 IVLLHGEPT----WsyLYRTMiPPLSAAGHRVLAPDLIGFGRSDKPTriEDYTYLRHVEWVTSWFENlDLHDVTLFVQDW 124
                                    8*****998....6535777779999999999*********6633334433333788877777777789*********** PP

                                    HHHHHHH.HHHCC...EE.EEES-....----TTTS----TTHHHHHHTT-CCCCHCCH........S-HSCCCCHHH.. CS
                  Abhydrolase_6  75 GGalala.aapla.lvvg.vlldp..pptalpagllaaalelllallallrllawlsre........plprlfladed.. 139
                                    G +++l+ aa +  ++++ v+ ++  p  +++++l+  +++ ++++ ++l++ ++++ +          + ++ a+ +  
  gi|121638177|ref|YP_978401.1| 125 GSLIGLRiAAEHGdRIARlVVANGflPAAQGRTPLPFYVWRAFARYSPVLPAGRLVNFGtvhrvpagV-RAGYDAPFPdk 203
                                    *******7555554555566666632223555555777777777777777775555444444443321.21333333332 PP

                                    ...CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC...EEE.CTT-C........HHHHCHHCCCHSTTEEETCE... CS
                  Abhydrolase_6 140 ...adaawrarlarlaallaglgllpaaawadlpvpl...lvl.ggeDp........lvprllerllaqagarlpvvlpg 204
                                       a a+  +rl + ++ ++++ ++ +aaw++l  +    l + g +Dp        l+++   ++++ ++ar++     
  gi|121638177|ref|YP_978401.1| 204 tyqAGARAFPRLVPTSPDDPAVPAN-RAAWEALGRWDkpfLAIfGYRDPilgqadgpLIKHIPGAAGQ-PHARIK----- 276
                                    2122333333333333444433333.445555555555544333433333333222488888888888.999*98..... PP

                                    SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 205 aGHlphleepdevae 219
                                    a+H++++++ +e+ae
  gi|121638177|ref|YP_978401.1| 277 ASHFIQEDSGTELAE 291
                                    9******888**998 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.9e-11   2.3e-07       7     162 ..      49     199 ..      47     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.9e-11
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                    +vl+HG    s  y  ++  L a+G  v+a D  G+Grs+ + r +   + ++v+ + + +e++        ++l+ + +
  gi|121638177|ref|YP_978401.1|  49 IVLLHGEPTWSYLYRTMIPPLSAAGHRVLAPDLIGFGRSDkPTRIEDYTYLRHVEWVTSWFENLD----LHDVTLFVQDW 124
                                    89*************************************87777766666666777777766666....447999***** PP

                    Hydrolase_4  86 GGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaayeadp 162
                                    G+li l++++++ d++a+l++++ +l  ++  + + p++    + +++  p l+  + +++  + r p+ v+a  + p
  gi|121638177|ref|YP_978401.1| 125 GSLIGLRIAAEHGDRIARLVVANGFLPAAQG-RtPLPFYV--WRAFARYSPVLPAGRLVNFGTVHRVPAGVRAGYDAP 199
                                    ***********************99977766.33444444..467777777777766688888888888877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2320.26
//
Query:       gi|121638178|ref|YP_978402.1|  [L=150]
Description: hypothetical protein BCG_2313 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1112.24
//
Query:       gi|121638179|ref|YP_978403.1|  [L=323]
Description: hypothetical protein BCG_2314 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-55  188.8   0.0    1.4e-55  188.6   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.0   7.9e-60   1.4e-55       1     290 [.      14     297 ..      14     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 7.9e-60
                                    .EEEE-SSS-ST......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSS CS
                   Aldo_ket_red   1 elglGtwqlgsk.....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrda 75 
                                    ++glGtwq+gs+     ++++   a ++++ra   G+++fDtAe+Yg g+se++lGeal +   +r+ev++a+Kv     
  gi|121638179|ref|YP_978403.1|  14 RIGLGTWQFGSRewgygDRYATGAARDIVKRARALGVTLFDTAEIYGLGKSERILGEALGD---DRTEVVVASKV----- 85 
                                    59**********9888888888889999*********************************...***********..... PP

                                    TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                   Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                      ++   ++ i ++ ++s +rL+++++ l+++H+p+p +p    ++  + +l ++G i a GvSn+s ++ +ka +  + 
  gi|121638179|ref|YP_978403.1|  86 -FPVAPFPAVIKNRERASARRLQLNRIPLYQIHQPNPVVP-DSVIMPGMRDLLDSGDIGAAGVSNYSLARWRKADAALGR 163
                                    .***************************************.9************************************** PP

                                    -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHH CS
                   Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelsel 235
                                    ++v++qv+++l  +++ e l+++++ ++  +iayspl++Gll gky  e++++   +   l  +e++++   ++ +l+++
  gi|121638179|ref|YP_978403.1| 164 PVVSNQVHFSLAHPDALEDLVPFAELENRIVIAYSPLAQGLLGGKYGLENRPGGVRALNPLFGTENLRRIEPLLATLRAI 243
                                    ***************************************************9976666666555**************** PP

                                    HHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHH CS
                   Aldo_ket_red 236 akehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeld 290
                                    a + + ++aq+al++++s  +++++ipgas++eqle n++a +++ls+++ ++l 
  gi|121638179|ref|YP_978403.1| 244 AVDVDAKPAQVALAWLIS-LPGVVAIPGASSVEQLEFNVAAADIELSAQSRDALT 297
                                    *****************5.778899**********************99877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2329.30
//
Query:       gi|121638180|ref|YP_978404.1|  [L=647]
Description: heat shock protein 90 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-141  472.7   0.0   6.4e-135  451.0   0.0    2.1  2  HSP90          Hsp90 protein
    6.4e-13   48.7   0.1    1.3e-12   47.7   0.1    1.5  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
      1e-10   42.1   0.0    1.9e-10   41.3   0.0    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.083   12.3   1.0        8.1    5.8   0.1    2.5  2  Flagellar_rod  Paraflagellar rod protein


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.1e-08   0.00018       1      36 [.     192     227 ..     192     236 .. 0.84
   2 !  451.0   0.0  1.4e-138  6.4e-135      72     487 ..     235     645 ..     224     647 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.1e-08
                                    GGGSHHHHHHHHHHCCTTSSS-EEEEEEEEXXXXXX CS
                          HSP90   1 eyleekklkelvkkySeFinfpiyllkekeeekeve 36 
                                    +y++e k+++lvkkyS+Fi +pi++ +e+ +   +e
  gi|121638180|ref|YP_978404.1| 192 DYTSEWKIRNLVKKYSDFIAWPIRMDVERRTPASQE 227
                                    799**********************99988776554 PP

  == domain 2  score: 451.0 bits;  conditional E-value: 1.4e-138
                                    XXXEEEEEEESXXSXGGGSXGGGSXHHHHHHHHHHTTTTTSXXSEEEEEEEXSSSXEEEEEEEXSSXXTTTTTTTTTSXX CS
                          HSP90  72 ketvkewellNkqkpiWlrkpkevteeeYkeFYkslskdsedplavkhfsaegevefkaiLfvPkrapsdlfekykkkkk 151
                                    + ++ e+e+lN+ k++W r+++ev+e+eYkeFYk +++ ++dpl ++  +aeg  e++a+Lf+P++ap+dlf++   + +
  gi|121638180|ref|YP_978404.1| 235 ETVTIETETLNSMKALWARPKEEVSEQEYKEFYKHVAHAWDDPLEIIAMKAEGTFEYQALLFIPSHAPFDLFDR---DAH 311
                                    5567899******************************************************************6...679 PP

                                    TTEEEEETTEEEESXXTTSSXGGGTTXEEEEEESSSXSSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTSXHH.H..HHTH CS
                          HSP90 152 nnikLYvrrVfitdefedllPkyLsFvkGvvdsddLPLNvsREtlqqnkilkvikkklvrKvlemlkklaee.keeykkf 230
                                      i+LYv+rVfi+ ++++l+P+yL+FvkGvvd++d+ LNvsRE+lqq++ +k i+++l +Kvl ++k+++++  e+y++f
  gi|121638180|ref|YP_978404.1| 312 VGIQLYVKRVFIMGDCDQLMPEYLRFVKGVVDAQDMSLNVSREILQQDRQIKAIRRRLTKKVLSTIKDVQSSrPEDYRTF 391
                                    99*******************************************************************7651578**** PP

                                    HHHHHHHHHHHHHHXGGGHHHHHTTXEEEETTEEEEEEEHHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHHTTXX CS
                          HSP90 231 ykefsknlklGiiedsanrkklakLlrfksskseeeltsLedYvermkekqksiYyiageskeevekspflerlkkkgye 310
                                    + +f++ lk G++ d  nr+ l  +  f s+ seee t+L++Yvermk++q++i+y +ge+++++ ksp le++k+kgye
  gi|121638180|ref|YP_978404.1| 392 WTQFGRVLKEGLLSDIDNRETLLGISSFVSTYSEEEPTTLAEYVERMKDGQQQIFYATGETRQQLLKSPHLEAFKAKGYE 471
                                    ******************************************************************************** PP

                                    EEEEXSTTHHHHHHTXSEETTEEEEETTBSTXXXX.XXHHHHHHHHHHHHHHHHHHHHHHHTTTTTESEEEEXSSXSSXS CS
                          HSP90 311 vlylvdpiDeyvvqqlkeyegkklvnvakeglele.eeeeekkkkeelkkkfeeltkllkevlkdkvekvkvserlvdsP 389
                                    vl+l+dp+De+ v  ++e++gk l++vak +++l+ ee+++++++ee +k+f +l+++l+e+l+d+v++v++s+rl++sP
  gi|121638180|ref|YP_978404.1| 472 VLLLTDPVDEVWVGMVPEFDGKPLQSVAKGEVDLSsEEDTSEAEREERQKEFADLLTWLQETLSDHVKEVRLSTRLTESP 551
                                    **********************************758888899999********************************** PP

                                    EEEEBXTTSXXHHHHHHHHHHHHHHHSSTSSSSSXEEEEEXTTSHHHHHHHHHHHHTTTX..HHHHHHHHHHHHHHHHHT CS
                          HSP90 390 cvlvtseygwsanmerimkaqalrdkskssymsskktleinprhpiikeLkkkveedked..eeakdlaellyetalles 467
                                    ++l+t+ +g+++ + ri +a         ++  +k++le+np+hp+++ L++  ++ ++d  +++ ++aelly tall+ 
  gi|121638180|ref|YP_978404.1| 552 ACLITDAFGMTPALARIYRASGQ------EVPVGKRILELNPSHPLVTGLRQAHQDRADDaeKSLAETAELLYGTALLAE 625
                                    ******************99654......56678*****************998875554338999************** PP

                                    TXXXSXHHHHHHHHHHHHTT CS
                          HSP90 468 Gfsledpasfakrierllkl 487
                                    G  ledpa+fa+ + + l  
  gi|121638180|ref|YP_978404.1| 626 GGALEDPARFAELLAERLAR 645
                                    ************99887766 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   2.9e-16   1.3e-12       6     117 ..      32     166 ..      26     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.9e-16
                    HATPase_c_3   6 AlaelvdNsldAdaen................vkievnknrgktgeivieDdGkGmseeelkn.alrlatsskeakr... 65 
                                     l el+ N+ dA  +                  +ie++ ++ ++ +++++D+G Gm +ee+ +   +la+s + + r   
  gi|121638180|ref|YP_978404.1|  32 FLRELISNASDALDKLriealrnkdlevdtsdLHIEIDADK-AARTLTVRDNGIGMAREEVVDlIGTLAKSGTAELRaql 110
                                    377********987778999999*********777777765.689******************55589999988775555 PP

                    HATPase_c_3  66 ........kstslGkkGiGlklAslslgkkltvitkkegesstltldvdkidkenekvle 117
                                            +++ +G++GiG + +s+++++k+++ t+k ges +++++ +    e+++++e
  gi|121638180|ref|YP_978404.1| 111 reaknaaaSEELIGQFGIG-FYSSFMVADKVQLLTRKAGESAATRWESS---GEGTYTIE 166
                                    555444445666*******.**********************9999764...44555555 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   4.2e-14   1.9e-10       2     111 ..      29     184 ..      28     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.2e-14
                                    HHHHHHHHHHHHHHHHHHH..........HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.......GTCSTTCH. CS
                      HATPase_c   2 dekrLrqiisnlvdNavkf..........atkageieveikaseddlvisveDnGiGipkedlk.......klfekfsq. 63 
                                    +  +Lr++isn++d+++k           + +++++++ei+a++   +++v+DnGiG+ +e++        k++    + 
  gi|121638180|ref|YP_978404.1|  29 KDAFLRELISNASDALDKLriealrnkdlEVDTSDLHIEIDADKAARTLTVRDNGIGMAREEVVdligtlaKSG----Ta 104
                                    5679***************99987766543366677888888789******************97666666333....24 PP

                                    .............HCSTCHTSTSSSH..HHHHH.............HHHHHH.....TT.TEEEEEEET..TTEEEEEEE CS
                      HATPase_c  64 .............ddstkrggggtGl..Glsiv.............kklvel.....mg.Geiwvesep..grGttftft 107
                                                 ++++ +g++g G+  +++++                         g G+ ++es +   +Gt++t++
  gi|121638180|ref|YP_978404.1| 105 elraqlreaknaaASEELIGQFGIGFysSFMVAdkvqlltrkagesA----AtrwesSGeGTYTIESVEdaPQGTSVTLH 180
                                    44456777766555666666666665544444455444444333331....0333323345666665556689******* PP

                                    EESS CS
                      HATPase_c 108 lple 111
                                    l+ e
  gi|121638180|ref|YP_978404.1| 181 LKPE 184
                                    *976 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0018       8.1      52     157 ..     337     444 ..     331     467 .. 0.71
   2 ?    4.6   0.1    0.0042        19      84     132 ..     502     550 ..     493     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0018
                  Flagellar_rod  52 flqeneeqqeklvreieelereLqklaeerrelvedriea.eerEekRetdyeeFl.kvaeqhkqkLrktlenldkaldl 129
                                    f++ ++++q+  ++  +e  ++ +++++ rr l++++++  ++    R +dy +F  +++   k+ L   ++n ++ l +
  gi|121638180|ref|YP_978404.1| 337 FVKGVVDAQDMSLNVSREILQQDRQIKAIRRRLTKKVLSTiKDVQSSRPEDYRTFWtQFGRVLKEGLLSDIDNRETLLGI 416
                                    56667777776666555555555666666666666666651334578********63688999999***********999 PP

                  Flagellar_rod 130 arsleelVkegvkklkakqdklqnalse 157
                                       ++ + +e  ++l+++ + +++  ++
  gi|121638180|ref|YP_978404.1| 417 SSFVSTYSEEEPTTLAEYVERMKDGQQQ 444
                                    9999999999999998877766554444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0042
                  Flagellar_rod  84 lvedrieaeerEekRetdyeeFlkvaeqhkqkLrktlenldkaldlars 132
                                    +v+   e+ + E++Re+  +eF+++ +  ++ L + ++ +  + +l++s
  gi|121638180|ref|YP_978404.1| 502 EVDLSSEEDTSEAEREERQKEFADLLTWLQETLSDHVKEVRLSTRLTES 550
                                    6777779999*************************99999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4134.84
//
Query:       gi|121638181|ref|YP_978405.1|  [L=310]
Description: hypothetical protein BCG_2316c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-18   65.1  10.6      2e-17   63.8  10.5    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.8e-05   24.3   1.0      3e-05   23.6   1.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8  10.5   2.3e-21     2e-17       6     178 ..      70     268 ..      66     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.3e-21
                                    SEEEEEEETTCEEEES--SCHHHHHHHH.....................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGC CS
                    Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal.....................elaalglkpkdvdavilTHlHlDHiGglggl 64 
                                    + + l+e+d+g++L+DtG++ +  +                        ++ +lg+   dv++++lTH+++DHiGg +++
  gi|121638181|ref|YP_978405.1|  70 CHVLLVETDDGLVLVDTGFGIQDCLDPGrvglfrhvlrpaflqaetaarQIEQLGYRTSDVRHIVLTHFDFDHIGGIADF 149
                                    6789****************999998889999************************************************ PP

                                    TTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH.......TTCHCGCCEEEEETTTE.ECCCTEEEEEHECTTSTSCCEE CS
                    Lactamase_B  65 veatdvpvgavaeeapalfmeeaddaasrkgll.......lagvsadkpdvdeeeld.gnaggrralyvtggpghghghg 136
                                    +ea+  +++a+a  a + +   +   + r+++          g++  ++  +    + +  g ++ l++++g++ gh  +
  gi|121638181|ref|YP_978405.1| 150 PEAHLHVTAAEARGAIHAPSLRERLRYRRGQWAhgpklveH-GPDGEPWRGFASAKPlDSIGTGVVLVPMPGHTRGHAAV 228
                                    ***************999999999999999988**988852.333333333333333144567888999*********** PP

                                    EEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHH CS
                    Lactamase_B 137 vveygggkvlftGDallagetgridltlrgaevrdpsdaeky 178
                                     v++g + vl +GDa++ + t+++++  r+++v+ + ++  +
  gi|121638181|ref|YP_978405.1| 229 AVDAGHRWVLHCGDAFYHRGTLDGRF--RVPFVMRAEEKLLS 268
                                    **************************..66666665555444 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.0   3.3e-09     3e-05       3     150 ..      82     250 ..      81     263 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.3e-09
                                    EEES--TT....................HHHH..HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC....C-- CS
                  Lactamase_B_2   3 iLiDagpd....................lrqq..alralqPve.lrdelppidaVllthaHyDHlaglltlre....lrp 55 
                                    +L+D+g++                    ++q   a+r+    e l  + +++  ++lth ++DH+ g+ ++ e       
  gi|121638181|ref|YP_978405.1|  82 VLVDTGFGiqdcldpgrvglfrhvlrpaFLQAetAARQI---EqLGYRTSDVRHIVLTHFDFDHIGGIADFPEahlhV-- 156
                                    688888888888888888998888888766663334443...44666667***********************55331.. PP

                                    EE..EE.EEEEHHHHHHCCTTCGHHHCHTT......TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSE CS
                  Lactamase_B_2  56 kk..lp.lyapkgvlavleanfvylaleee......pavnvheldwgesfelgdggleitatparhksgrrldrnagdtl 126
                                    +   ++  +  +++++ l+ +  + a +++      ++++++ ++  ++++  ++g  + ++p ++ +           +
  gi|121638181|ref|YP_978405.1| 157 TAaeARgAIHAPSLRERLRYRRGQWAHGPKlvehgpDGEPWRGFASAKPLDSIGTG--VVLVPMPGHTRG--------HA 226
                                    22112212223455555555544444444455666667778888777777664344..888888877777........78 PP

                                    EEEEECTTEEEEEESS-S---HHH CS
                  Lactamase_B_2 127 GlriegggkrvyyigDtgyipeei 150
                                    +++++ g++ v+++gD  y  + +
  gi|121638181|ref|YP_978405.1| 227 AVAVDAGHRWVLHCGDAFYHRGTL 250
                                    888888788888888877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2125.39
//
Query:       gi|121638182|ref|YP_978406.1|  [L=230]
Description: cutinase cut2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-53  179.5   0.0    6.9e-53  179.2   0.0    1.1  1  Cutinase  Cutinase
  ------ inclusion threshold ------
      0.019   14.8   0.9       0.25   11.2   0.0    2.2  2  Lipase_3  Lipase (class 3)


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.2   0.0   7.7e-57   6.9e-53       1     178 []      44     229 ..      44     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 7.7e-57
                                    ---SEEEEEE--TT--TTTSSHHHHHHHHHHHH.TTT-EEEEE------CGGSTTSS-HHHHHHHHHHHHHHHHH-TT-E CS
                       Cutinase   1 sckdvevifArgttepgglgsvGeavvsalesavgsksvavqgvnYpAdleqlyegseeagakeaaalvqslaskCPdtk 80 
                                    +c+d+ev+fArg+ ep+g+g+vG+a+vsal+s+v+ k+v+v++v+YpAd++       + ga++++a++qs+a++CP+t+
  gi|121638182|ref|YP_978406.1|  44 ACPDAEVVFARGRFEPPGIGTVGNAFVSALRSKVN-KNVGVYAVKYPADNQI------DVGANDMSAHIQSMANSCPNTR 116
                                    6*********************************9.9************995......9********************* PP

                                    EEEEEETHHHHHHHHHHTT..........S-HHHHHHEEEEEEES-TTC.CCCTTS-TTS-GGGEEEE--TT-GGG..TS CS
                       Cutinase  81 ivlgGYSqGaqvidnaiegga...tat..lpaavadkvaavvlfGdpsn.vaglpevsklyaskikslCdagDpiC..gs 152
                                    +v gGYS Ga+v+d ++++++   ++t  lp+ +++++aav+lfG++s+ v++++++s++y++++++lC+ +Dp+C  ++
  gi|121638182|ref|YP_978406.1| 117 LVPGGYSLGAAVTDVVLAVPTqmwGFTnpLPPGSDEHIAAVALFGNGSQwVGPITNFSPAYNDRTIELCHGDDPVChpAD 196
                                    ********************988856678********************99*************************9988 PP

                                    ----GG....GG..-GGGG..HHHHHHHHHHH- CS
                       Cutinase 153 gnelea....Hl..sYvsey.ttqaakFvvskl 178
                                     n++ea    Hl  +Yvs++ ++qaa+Fv+ kl
  gi|121638182|ref|YP_978406.1| 197 PNTWEAnwpqHLagAYVSSGmVNQAADFVAGKL 229
                                    888887777799889****99********9875 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.5     0.047   4.2e+02      74      88 ..      12      26 ..      11      51 .. 0.77
   2 ?   11.2   0.0   2.8e-05      0.25      33      79 ..      63     129 ..      41     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.047
                                   HHHHHHHHHHHHHHH CS
                       Lipase_3 74 LGgalAlLaaldlve 88
                                   +G+a A+Laa+ l +
  gi|121638182|ref|YP_978406.1| 12 MGAAAAMLAAVLLLT 26
                                   7*********99876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.8e-05
                                    -EEEHHHHHHHH....................S-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHH CS
                       Lipase_3  33 gkvhsgfleaye....................eslreqvlkelkrllekypeysivvtGHSLGgalA 79 
                                    g+v + f++a++                       ++++ + ++++ ++ p++++v  G SLG+a+ 
  gi|121638182|ref|YP_978406.1|  63 GTVGNAFVSALRskvnknvgvyavkypadnqiDVGANDMSAHIQSMANSCPNTRLVPGGYSLGAAVT 129
                                    56666666666666666666666667777676777899***************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1663.16
//
Query:       gi|121638183|ref|YP_978407.1|  [L=80]
Description: hypothetical protein BCG_2318 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-28   96.4   1.2    7.9e-28   95.9   1.2    1.2  1  DUF1918   Domain of unknown function (DUF1918)


Domain annotation for each model (and alignments):
>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   1.2   4.4e-32   7.9e-28       1      58 []       1      58 [.       1      58 [. 0.99

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 4.4e-32
                                   ----TTEEEEES-TTTS--EEEEEEEE-S-SSS-S-EEEEETTTTEEEEE---SS-EE CS
                        DUF1918  1 MkAkvGDrlvvegrtvgepereGeiveVrgedGaPPYlVRweddgheslvfPGpDaeV 58
                                   M+AkvGD lvv+g+t++++++++ei+eVr++dG+PPY+VRw  +ghe++v+PG+Da+V
  gi|121638183|ref|YP_978407.1|  1 MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVV 58
                                   9*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 604.01
//
Query:       gi|121638184|ref|YP_978408.1|  [L=307]
Description: antibiotic-resistance protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-47  160.4   0.7    8.8e-47  160.3   0.7    1.0  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.7   4.9e-51   8.8e-47       1     291 []      11     305 ..      11     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 4.9e-51
                                    EEEEEEE..SHHH................CCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHH CS
                   Amidohydro_2   1 iDvHaHllppeaa................irddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaa 64 
                                    iD++a ++p  +                     +  ++ ++ + +a++ r+  d  l+s++++ ++++ +  +++  +++
  gi|121638184|ref|YP_978408.1|  11 IDMWAPFVPSAEViddlregfpvellsyfEVFTKTTISAEQFGAYAESLRRTDDQILDSLDDAGITRSLITGFDERSTCG 90 
                                    67777777666667777888888888888777788888888899************************************ PP

                                    HHHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-E CS
                   Amidohydro_2  65 lcrgannrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglp 144
                                    +++  n++v+a aa++pdrf+++a  + l +++a++e+er+v e gf+G+ l p + g ++++++++ p++++++elg+p
  gi|121638184|ref|YP_978408.1|  91 VTFVHNASVAAVAARYPDRFLPFAGADILAGDSAVDEFERWVVEHGFRGLSLRPFMIGRPASDPAYF-PCYAKCVELGVP 169
                                    *******************************************************************.************ PP

                                    EEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEE CS
                   Amidohydro_2 145 vdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfd 224
                                    v iht+       + ++  ++  +p ++++va +fP+l+i ++HgG+p  ++ +a  +++++pnvy++l ++ +  +yf 
  gi|121638184|ref|YP_978408.1| 170 VSIHTS-----ADWTRTRLSDLGHPRHIDDVACRFPELTILMSHGGYP--WVLQACLIAWKHPNVYLELAAHRP--KYFA 240
                                    ****88.....555666678999*************************..*********************988..9*** PP

                                    CCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCTB CS
                   Amidohydro_2 225 spladppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarlygl 291
                                    sp a +++l r  +++  ++i++G+  + +++        +++l+   + e++e+ l+ NA r+++l
  gi|121638184|ref|YP_978408.1| 241 SPGAGWEPLMRFGQTTIRNKIVYGTGGFLINRPYLQLCDEMRALPV--PREVLEDWLWRNATRVLRL 305
                                    ********************************77777777777766..*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1981.95
//
Query:       gi|121638185|ref|YP_978409.1|  [L=69]
Description: hypothetical protein BCG_2320c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 512.40
//
Query:       gi|121638186|ref|YP_978410.1|  [L=429]
Description: hypothetical protein BCG_2321 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-08   33.2   0.0    7.3e-05   21.6   0.0    2.1  2  Condensation    Condensation domain
  ------ inclusion threshold ------
      0.016   15.0   0.2      0.074   12.8   0.2    1.9  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
       0.05   12.7   0.0      0.087   11.9   0.0    1.3  1  Herpes_U59      Herpesvirus U59 protein


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-08   7.3e-05      29     158 ..      25     146 ..      23     157 .. 0.79
   2 !    9.4   0.0   6.4e-05      0.38     245     312 ..     227     298 ..     207     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-08
                                    EEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-.TT-----EEEE-T..TSSSHHHHHHHHHHHHH CS
                   Condensation  29 mqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvil.eerevelevleisdleeseeeeaieefaqkdl 107
                                    +q+  +++g++dl+rl  al++ + +h   R ++ +   +   ++ + ++r  +l ++ei+d   +     + e+ ++ +
  gi|121638186|ref|YP_978410.1|  25 VQIEARVSGRFDLDRLAAALRAAVAKHALARARLGRASLTARTLYWEvPDRADHL-AVEITD---E----PVGEVRSRFY 96 
                                    56778999**************************998666666666644444444.455552...2....2444444455 PP

                                    TC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHH CS
                   Condensation 108 qepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklY 158
                                    ++  +L ++p f +a+++ ++ ++ lll++HH  +DG+    ll +la++Y
  gi|121638186|ref|YP_978410.1|  97 ARAPELHRSPVFAVAVVR-ETVGDRLLLNFHHAAFDGMGGLRLLLSLARAY 146
                                    56999*************.******************98888888888888 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 6.4e-05
                                    HSTSS-HHHHHHHHHHHHHHHHHT-SE......EEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHH CS
                   Condensation 245 keqgvtlndvllaalgllLskytgqdd......ivvgteisgReseikdiermvGlFvntlPlridvkeaktfs 312
                                    + +g+t+nd+ +aal+l++ +++++ d      + v++++  R+ +     +++  F + l+++++v+e +++ 
  gi|121638186|ref|YP_978410.1| 227 RPEGATVNDLAMAALALTILQWNRTHDvpaadsVSVNMPVNFRPTA--WSTEVISNFASYLAIVLRVDEVTDLE 298
                                    5689*******************9876222222689*********9..89999**************9988876 PP

>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.2e-05     0.074     131     161 ..     121     151 ..      28     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                 WES_acyltransf 131 illkvHHAliDGvgglkllarlldldpddpp 161
                                    +ll +HHA  DG+ggl+ll +l+ +  d+p 
  gi|121638186|ref|YP_978410.1| 121 LLLNFHHAAFDGMGGLRLLLSLARAYADEPD 151
                                    5899**************8665554444433 PP

>> Herpes_U59  Herpesvirus U59 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05     0.087     125     243 ..     246     363 ..     233     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                     Herpes_U59 125 vvWsktsvlWakd.veiktvkrraaaaralvsvlPeveeklapllrlaergdseiFdervasvykrlereledisrsere 203
                                    ++W +t  + a d v++++  + +++a   ++v+ + ++ la++lr++e +d+e  +  va +   l  +++  ++   +
  gi|121638186|ref|YP_978410.1| 246 LQWNRTHDVPAADsVSVNMPVNFRPTA-WSTEVISNFASYLAIVLRVDEVTDLEKATAIVAGITGPL--KQSGAAGWVVD 322
                                    678777666544326665533344444.4466777999*****************************..99********* PP

                     Herpes_U59 204 llekCvel.AaakklllldgprlenfflaqvCLyeLgedel 243
                                    lle  + l A +k+ l l +p +e+ f+  vCL +Lg  ++
  gi|121638186|ref|YP_978410.1| 323 LLEGGKVLpAMLKRQLQLLLPLVEDRFVESVCLSNLGRVDV 363
                                    *****99977899999999******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3050.19
//
Query:       gi|121638187|ref|YP_978411.1|  [L=197]
Description: hypothetical protein BCG_2322 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1410.31
//
Query:       gi|121638188|ref|YP_978412.1|  [L=144]
Description: hypothetical protein BCG_2323 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-10   40.0   4.7    8.4e-10   39.2   2.5    2.0  2  SNARE_assoc      SNARE associated Golgi protein
  ------ inclusion threshold ------
      0.023   14.9   0.8       0.04   14.1   0.8    1.4  1  HemY_N           HemY protein N-terminus
      0.047   13.9   0.4       0.07   13.4   0.4    1.2  1  DUF4381          Domain of unknown function (DUF4381)
       0.15   12.2   3.0        0.3   11.3   3.0    1.6  1  Phage_holin_3_5  Bacteriophage holin Hol, superfamily III
       0.17   11.1   1.4       0.22   10.8   1.4    1.1  1  Peptidase_U4     Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   2.5   2.3e-13   8.4e-10      69     119 ..       2      52 ..       1      53 [. 0.96
   2 ?    0.9   0.0      0.17   5.9e+02      34      55 ..      72      92 ..      58     114 .. 0.55

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.3e-13
                    SNARE_assoc  69 lallllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                    +a++  r++p++ ++l++y++G+++v++++ ++++fiGs+p+++vy+ lG+
  gi|121638188|ref|YP_978412.1|   2 WAVVGQRFVPGISDALASYTFGAFGVPLWQMVVGSFIGSAPRVFVYTALGA 52 
                                    789999******************************************997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                    SNARE_assoc 34 ayllgrylgrkalrrkllsekr 55
                                   + ++g++++ ++ +rk++ + r
  gi|121638188|ref|YP_978412.1| 72 TAIIGAFAA-RRWYRKWRARPR 92
                                   223333333.444444444444 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8   1.1e-05      0.04      15      66 ..      53     103 ..      43     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                         HemY_N  15 slvvavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseG 66 
                                    s++ +   lv  +++++++ ++++++ ++ +  r+wr+r r+r + ++l++G
  gi|121638188|ref|YP_978412.1|  53 SITNLSSPLVYSAIAVWCVTAIIGAF-AARRWYRKWRARPRRRCGLAQLTTG 103
                                    55666666778888888888877765.55799*****************998 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4     2e-05      0.07      15      64 ..      62     109 ..      53     118 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                        DUF4381  15 wPpapGwwlllaalllllllvlalwllrrrkrn...rreAlreLaalradead 64 
                                    ++ a+  w++      +++ ++a++++ r++r+   rr  l++L++ ++++++
  gi|121638188|ref|YP_978412.1|  62 VYSAIAVWCVT-----AIIGAFAARRWYRKWRArprRRCGLAQLTTGSQQRHT 109
                                    44555555555.....4555555555555555522355566666655533333 PP

>> Phage_holin_3_5  Bacteriophage holin Hol, superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.0   8.3e-05       0.3      70     107 ..      61     101 ..       2     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                Phage_holin_3_5  70 allsaaalgsltaaagaevavglykrwvak...rlgvcelt 107
                                     ++sa a+ ++ta  ga  a   y++w a+   r g+ +lt
  gi|121638188|ref|YP_978412.1|  61 LVYSAIAVWCVTAIIGAFAARRWYRKWRARprrRCGLAQLT 101
                                    368999**********************9722255555555 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   6.1e-05      0.22      31      84 ..      28      85 ..      19      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.1e-05
                   Peptidase_U4 31 kklrlllaAllGalyvvlvlflpklesillsillkilvsllmvli......afgpkslke 84
                                     +++++++++G++  v+v ++ +l + ++++ + +++s++ v++      af  +++ +
  gi|121638188|ref|YP_978412.1| 28 PLWQMVVGSFIGSAPRVFV-YT-ALGASITNLSSPLVYSAIAVWCvtaiigAFAARRWYR 85
                                   579************7774.44.3566666666666666666654222234577777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1084.15
//
Query:       gi|121638189|ref|YP_978413.1|  [L=281]
Description: hypothetical protein BCG_2324c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-14   52.6   0.1    7.6e-09   35.2   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    1.1e-09   38.3   0.1    6.3e-05   22.8   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      3e-07   31.3  12.6     0.0011   19.6   1.3    2.4  2  Abhydrolase_6  Alpha/beta hydrolase family
    1.9e-05   24.4   0.1     0.0012   18.5   0.1    2.1  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    0.00016   20.5   0.1       0.07   11.8   0.1    2.6  3  AXE1           Acetyl xylan esterase (AXE1)
    0.00021   20.9   0.0    0.00078   19.0   0.0    1.9  1  Peptidase_S9   Prolyl oligopeptidase family
    0.00056   19.5   0.0     0.0019   17.8   0.0    1.7  1  DLH            Dienelactone hydrolase family
     0.0015   18.5   0.1     0.0025   17.7   0.1    1.4  1  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.19   11.6   0.0        2.2    8.1   0.0    2.1  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   3.8e-12   7.6e-09       6     115 ..      80     185 ..      77     208 .. 0.85
   2 !   15.5   0.0   4.1e-06    0.0081     186     232 ..     209     254 ..     200     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.8e-12
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel..plfllGh 83 
                                    +v++++G a   +  aela aL   G +v+ +D+rG+G ++g+       + + +D++a+ e +  ++     ++  +G+
  gi|121638189|ref|YP_978413.1|  80 AVLVCNGNAGDRSMRAELAVALHGLGLSVLLFDYRGYGGNPGRPS----EQGLAADARAAQEWLSGQSDVDpaRIAYFGE 155
                                    689999999999999*************************88865....999********9988855544446999**** PP

                    Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkika 115
                                    S+G+++a+ ++ ++p+  a+l+l +P+ ++++
  gi|121638189|ref|YP_978413.1| 156 SLGAAVAVGLAVQRPP--AALVLRSPFTSLAE 185
                                    ***********99999..9*******998774 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.1e-06
                    Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                    r a++++P+l++ G++D +v+   s+ l+++++   k++ + pg  H
  gi|121638189|ref|YP_978413.1| 209 RIASVHAPVLVIAGGSDDIVPATLSEWLVAAAAE-PKRYVVVPGVGH 254
                                    556788************************9996.9********999 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   3.1e-08   6.3e-05       1     106 [.      79     179 ..      79     197 .. 0.84
   2 !   13.7   0.0   1.8e-05     0.036     204     252 ..     207     256 ..     189     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.1e-08
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH..HHHCTTSSEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri..ldalgddkltlv 78 
                                    p+++++ G +g   + ae  la aL   g  v+l+D rG+g  + +p++   +   a+ ++  +++  +   +  ++++ 
  gi|121638189|ref|YP_978413.1|  79 PAVLVCNGNAGDRSMRAE--LAVALHGLGLSVLLFDYRGYGGNPGRPSE---QGLAADARAAQEWLsgQSDVDPARIAYF 153
                                    79****************..**99*999*******************96...334445666666999999999999**** PP

                                    EETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga 106
                                    G S+G ++a  +a + p   +alvl ++
  gi|121638189|ref|YP_978413.1| 154 GESLGAAVAVGLAVQRPP--AALVLRSP 179
                                    ********9999988876..56666666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.8e-05
                                    HHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSSH CS
                  Abhydrolase_1 204 lrelknvlaptlvisgtsDplvppkaledlaqllpk.krlvvisdagHla 252
                                    ++++  v ap+lvi+g sD +vp   +e l ++  + kr+vv+++ gH++
  gi|121638189|ref|YP_978413.1| 207 IERIASVHAPVLVIAGGSDDIVPATLSEWLVAAAAEpKRYVVVPGVGHND 256
                                    333677999***************55555555533346**********85 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   7.7   1.5e-05     0.031      18      95 ..      96     178 ..      81     206 .. 0.59
   2 !   19.6   1.3   5.7e-07    0.0011     141     208 ..     190     256 ..     168     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                    HH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT......TTSEEEEEETCHHHHHHHHHHCC..EEEE CS
                  Abhydrolase_6  18 pL.aallaagvhvlapDlpGhGrsdpppldledladlaalldelaa....gggpvvlvGHSlGGalalaaaplalvvgvl 92 
                                    +L +al + g  vl +D++G+G+++++p +   +ad +a+ + l +    ++ ++  +G SlG+a+a  +a + + ++++
  gi|121638189|ref|YP_978413.1|  96 ELaVALHGLGLSVLLFDYRGYGGNPGRPSEQGLAADARAAQEWLSGqsdvDPARIAYFGESLGAAVAVGLAVQRPPAALV 175
                                    44233333345669*******867666644444888888888887778888899999********999944444434422 PP

                                    ES- CS
                  Abhydrolase_6  93 ldp 95 
                                    l +
  gi|121638189|ref|YP_978413.1| 176 LRS 178
                                    222 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.7e-07
                                    CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH...STTEEETCE...SSS.- CS
                  Abhydrolase_6 141 daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla...qagarlpvvlpgaGH.l 208
                                    +++w +  + l++  ++      +++a + +p+lv+ gg+D++vp++l ++l+   ++ +r+ vv+pg GH  
  gi|121638189|ref|YP_978413.1| 190 HYPWLPLRRLLLDHYPS-----IERIASVHAPVLVIaGGSDDIVPATLSEWLVaaaAEPKRY-VVVPGVGHnD 256
                                    34444444444444443.....4488999999999977*******99999999777788888.********52 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     6e-07    0.0012      57     126 ..     105     173 ..      37     191 .. 0.86
   2 ?    4.1   0.0     0.015        30     222     264 ..     208     250 ..     200     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-07
                                    T-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTE CS
                  Peptidase_S15  57 GYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpal 126
                                    G  v++ d rG gg  G      +  a+d+ ++ +Wl +q +    +++ +G S ++ +++ +a++++pa 
  gi|121638189|ref|YP_978413.1| 105 GLSVLLFDYRGYGGNPGRPSE--QGLAADARAAQEWLSGQsDVDPARIAYFGESLGAAVAVGLAVQRPPAA 173
                                    677888999999999998877..9999**************************************999975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                                    HHHCT--S-EEEEEECCSSTTCCHHHHHHHHHCCTT-EEEEEC CS
                  Peptidase_S15 222 edadkvkapvllvgGwnDwnvkngaiklyealkapgvklilgp 264
                                    e+++ v+apvl++ G  D++v  + +++  a+ a++++ ++ p
  gi|121638189|ref|YP_978413.1| 208 ERIASVHAPVLVIAGGSDDIVPATLSEWLVAAAAEPKRYVVVP 250
                                    57799*************9999999999988888877555555 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0028       5.6      59     123 ..      55     119 ..      51     129 .. 0.76
   2 !   11.8   0.1   3.5e-05      0.07     156     208 ..     130     181 ..     125     185 .. 0.84
   3 ?   -1.2   0.0      0.31   6.3e+02     257     300 ..     212     255 ..     203     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                                    EEEEEGGGEEEEEEEEEES.SSSSEEEEEEEE-TT--GGGHHH.HHHHHHTT-EEEEEE-TTTS.. CS
                           AXE1  59 ltfegvrgarikaklvlPkekeeklPavvefhGYegsrgeihd.llnyaaaGyavvvmdvRGqgge 123
                                    +  e+  g r+ +++  P+++ +  Pav+   G  g+r   ++  +     G +v+  d RG gg+
  gi|121638189|ref|YP_978413.1|  55 VVVETQDGMRLGGWYF-PHTSGGSGPAVLVCNGNAGDRSMRAElAVALHGLGLSVLLFDYRGYGGN 119
                                    5667778999999996.8879************8877554444145555667789999****9975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES-SS CS
                           AXE1 156 lDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvadyPfL 208
                                     Da  + e +++ + vD+ R+a +G+s G a+a+  a +++ ++a+v   Pf 
  gi|121638189|ref|YP_978413.1| 130 ADARAAQEWLSGQSDVDPARIAYFGESLGAAVAVGLA-VQRPPAALVLRSPFT 181
                                    5788888999999*******************99875.667777777788885 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.31
                                    C--S-EEEEEETT-SSS-HHHHHHHHHH--SSEEEEEETT-STT CS
                           AXE1 257 rvkaevllsvgLeDevcpPstvfaaynkletekeikvyeefahe 300
                                     v+a+vl+++g  D++ p +    +  + +  k + v +  +h+
  gi|121638189|ref|YP_978413.1| 212 SVHAPVLVIAGGSDDIVPATLSEWLVAAAAEPKRYVVVPGVGHN 255
                                    578999*********99987776677777777888888877776 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.9e-07   0.00078      43     186 ..     127     254 ..      98     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.9e-07
                                    HHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTSTHHHCCCC--TT CS
                   Peptidase_S9  43 nefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdllteeymewgnpe 122
                                      ++D  aa e+l  ++ vd+ r+a +G S G  ++  ++ qrp   +a+v   p++ +             y   +  +
  gi|121638189|ref|YP_978413.1| 127 GLAADARAAQEWLSGQSDVDPARIAYFGESLGAAVAVGLAVQRPP--AALVLRSPFTSLAEVGAVH------YPWLPLRR 198
                                    567899999************************999999998998..6**********99999983......44455554 PP

                                    TCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                   Peptidase_S9 123 eneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH 186
                                       ++y  +  ++ +++     p+L+i G  Dd vp   ++ lvaa  +   + ++++ p+ gH
  gi|121638189|ref|YP_978413.1| 199 LLLDHYPSIERIASVHA-----PVLVIAGGSDDIVPATLSEWLVAAAAE---PKRYVVVPGVGH 254
                                    57788866666666666.....*************99999888888665...456777777777 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.6e-07    0.0019      78     170 ..     128     240 ..     121     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.6e-07
                            DLH  78 vlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG.....................lspeke 136
                                    + +d++aa ++l  +++v++ +++  G  +G+a+a+ la + p  +a v   +                     l   + 
  gi|121638189|ref|YP_978413.1| 128 LAADARAAQEWLSGQSDVDPARIAYFGESLGAAVAVGLAVQRP-PAALVLRSPftslaevgavhypwlplrrllLDHYPS 206
                                    567899**********************************996.3344433335567777777777******99899999 PP

                            DLH 137 leeaakikapilalfgeeDefipadevekleeal 170
                                    +e++a + ap+l+++g+ D ++pa   e l  a 
  gi|121638189|ref|YP_978413.1| 207 IERIASVHAPVLVIAGGSDDIVPATLSEWLVAAA 240
                                    ***********************99655554443 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0025      49     112 ..     129     183 ..      90     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                    HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SST CS
                  Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdl 112
                                      da aa +wl  q     +dp+ri+ +G+S G+  a  +a    ++   ++a++vl +P t l
  gi|121638189|ref|YP_978413.1| 129 AADARAAQEWLSGQ---SDVDPARIAYFGESLGAAVAVGLA---VQR---PPAALVLRSPFTSL 183
                                    46999*******99...68***************9998888...455...78889998887755 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       2.2       9      42 ..     135     168 ..     133     188 .. 0.89
   2 ?    1.2   0.0      0.15   2.9e+02     109     134 ..     208     233 ..     198     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                    HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHH CS
                         BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasf 42 
                                    a ++l+ ++ v   +i+  G S G+ +a+ la+ 
  gi|121638189|ref|YP_978413.1| 135 AQEWLSGQSDVDPARIAYFGESLGAAVAVGLAVQ 168
                                    779*************************999975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                                    --GGG--SEEEEEEETT-SSS-HHHH CS
                         BAAT_C 109 ipvekakgpillvvgedDknwpSkes 134
                                     ++   ++p+l+++g  D ++p+  s
  gi|121638189|ref|YP_978413.1| 208 ERIASVHAPVLVIAGGSDDIVPATLS 233
                                    3455559*************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1834.61
//
Query:       gi|121638190|ref|YP_978414.1|  [L=63]
Description: hypothetical protein BCG_2325c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 451.27
//
Query:       gi|121638191|ref|YP_978415.1|  [L=143]
Description: hypothetical protein BCG_2326c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1017.75
//
Query:       gi|121638192|ref|YP_978416.1|  [L=60]
Description: hypothetical protein BCG_2327c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 460.67
//
Query:       gi|121638193|ref|YP_978417.1|  [L=238]
Description: hypothetical protein BCG_2328 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-12   47.3   0.0    2.4e-12   46.5   0.0    1.4  1  DUF433    Protein of unknown function (DUF433)
  ------ inclusion threshold ------
      0.025   14.7   0.0        5.1    7.3   0.0    2.5  2  HTH_28    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.7e-16   2.4e-12       1      55 [.     173     226 ..     173     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.7e-16
                                    EEE-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHHT. CS
                         DUF433   1 ItidpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaalaY 55 
                                    I+i+p   +G+P++ g+R++  ti+++++ Ge  e++++dy +L+l++iq+a++Y
  gi|121638193|ref|YP_978417.1| 173 IVINPSRYSGQPTFVGRRVSPVTIAQMVDGGEEREDLAADY-GLSLKQIQDAIDY 226
                                    9****************************************.************9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0037        33      21      38 ..      24      41 ..      18      46 .. 0.84
   2 ?    7.3   0.0   0.00057       5.1       5      33 ..     196     224 ..     194     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0037
                         HTH_28 21 elgisrrtvyrWikryee 38
                                   + g+   t +rWi+ ye 
  gi|121638193|ref|YP_978417.1| 24 LIGLPAGTAKRWINGYER 41
                                   5688889*********98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00057
                         HTH_28   5 iikllaaGhsvreaArelgisrrtvyrWi 33 
                                    i + +  G+ + ++A+ +g+s  ++++ i
  gi|121638193|ref|YP_978417.1| 196 IAQMVDGGEEREDLAADYGLSLKQIQDAI 224
                                    555566677****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1578.15
//
Query:       gi|121638194|ref|YP_978418.1|  [L=151]
Description: integrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   58.0   0.0    1.3e-15   57.6   0.0    1.1  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   7.2e-20   1.3e-15      57     164 ..       7     106 ..       2     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.2e-20
                                    EEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHH CS
                Phage_integrase  57 vheregKgskeravplseealellkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhs 136
                                    v   e+++++ r vp++e + e l++ l ++     ++ l+f+s rg +l  +++r+af + +++ gi  +l pH lRh+
  gi|121638194|ref|YP_978418.1|   7 V---ETTTNRVRHVPVPEPVSERLRDELPTE-----PNALVFPSYRGGHLPIEEYRRAFDKGCKAVGIA-DLVPHGLRHT 77 
                                    5...78999*********************9.....9********************************.********** PP

                                    HHHHHHHHCTSHHHHHHHHT-SSCCHH.H CS
                Phage_integrase 137 fataLleagvdlrvvqkllGHssistt.q 164
                                     a+  + ag++++vvq+llGH+  ++t  
  gi|121638194|ref|YP_978418.1|  78 TASLAISAGANVKVVQRLLGHATAAMTlD 106
                                    **************************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1024.11
//
Query:       gi|121638195|ref|YP_978419.1|  [L=95]
Description: hypothetical protein BCG_2330 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 706.39
//
Query:       gi|121638196|ref|YP_978420.1|  [L=114]
Description: excisionase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-13   50.1   0.1    3.6e-13   49.5   0.1    1.3  1  HTH_17     Helix-turn-helix domain
    0.00017   21.7   0.0    0.00046   20.3   0.0    1.7  1  AbiEi_4    Transcriptional regulator, AbiEi antitoxin
    0.00021   21.2   0.2    0.00065   19.7   0.0    2.0  2  HTH_29     Winged helix-turn helix
    0.00033   20.3   0.0     0.0013   18.5   0.0    1.9  1  HTH_23     Homeodomain-like domain
    0.00091   19.2   0.1     0.0016   18.3   0.1    1.5  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.003   17.3   0.1     0.0063   16.3   0.1    1.6  1  MerR       MerR family regulatory protein
  ------ inclusion threshold ------
      0.011   15.5   0.2       0.03   14.1   0.0    1.9  2  HTH_8      Bacterial regulatory protein, Fis family
      0.011   15.6   0.0      0.021   14.8   0.0    1.5  1  HTH_37     Helix-turn-helix domain
      0.024   14.8   0.0      0.033   14.3   0.0    1.3  1  DUF3853    Protein of unknown function (DUF3853)
      0.038   14.5   0.0       0.11   13.0   0.0    1.8  2  DUF134     Protein of unknown function  DUF134
      0.061   13.3   0.0       0.11   12.5   0.0    1.4  1  HTH_6      Helix-turn-helix domain, rpiR family
       0.11   12.6   0.0       0.26   11.4   0.0    1.7  1  HTH_22     HTH domain
       0.11   12.6   0.8       0.15   12.2   0.0    1.7  2  HTH_3      Helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   2.6e-16   3.6e-13       2      51 .]      20      69 ..      19      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.6e-16
                         HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdleewlekrr 51
                                   lt+++aA+lLgvsr tv rli++gel a +iG+r r   +d+ ++ e+rr
  gi|121638196|ref|YP_978420.1| 20 LTTQQAADLLGVSRPTVVRLIKSGELAAERIGNRHRLVLDDVLAYREARR 69
                                   9*************************5559***************99985 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.3e-07   0.00046       4      38 ..      11      45 ..       9      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-07
                        AbiEi_4  4 pelasrqvGlfttrelea.aGispsalrrLvrkGwL 38
                                   +++a +++ ++tt++++  +G+s+ ++ rL+++G+L
  gi|121638196|ref|YP_978420.1| 11 VTIAPQSM-TLTTQQAADlLGVSRPTVVRLIKSGEL 45
                                   56777777.99************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.7e-07   0.00065      14      35 ..      21      42 ..       4      60 .. 0.81
   2 ?   -1.5   0.0       1.9   2.6e+03      15      29 ..      89     103 ..      81     112 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.7e-07
                         HTH_29 14 tvsqiAkllglsrrtvyrwlkr 35
                                   t++q+A llg+sr+tv r +k 
  gi|121638196|ref|YP_978420.1| 21 TTQQAADLLGVSRPTVVRLIKS 42
                                   899*****************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                         HTH_29  15 vsqiAkllglsrrtv 29 
                                    +  i+++l+  rr v
  gi|121638196|ref|YP_978420.1|  89 PEVICEQLREARRVV 103
                                    666777766555544 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.4e-07    0.0013      19      39 ..      21      41 ..      15      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.4e-07
                         HTH_23 19 svreIAreLgvsrrTvyrwlk 39
                                   +++++A++Lgvsr Tv r +k
  gi|121638196|ref|YP_978420.1| 21 TTQQAADLLGVSRPTVVRLIK 41
                                   899***************998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.2e-06    0.0016      20      43 ..      18      41 ..       3      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                   EEHHHHHHHHHTTSSHHHHHHHHH CS
                      HTH_Crp_2 20 lpltqeelAsmlGltretvsrils 43
                                   + lt ++ A++lG++r tv r+++
  gi|121638196|ref|YP_978420.1| 18 MTLTTQQAADLLGVSRPTVVRLIK 41
                                   789******************997 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.6e-06    0.0063       1      37 [.      21      56 ..      21      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                                   EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEE CS
                           MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyRl 37
                                   t+ ++A+l+Gvs  t+ ++ + G + ++eR  +++Rl
  gi|121638196|ref|YP_978420.1| 21 TTQQAADLLGVSRPTVVRLIKSGEL-AAERIGNRHRL 56
                                   6789*********************.*********97 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.2e-05      0.03      22      37 ..      23      38 ..      21      41 .. 0.89
   2 ?   -2.8   0.1         4   5.6e+03       9      18 ..      91     100 ..      90     107 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHTS-HHHHHH CS
                          HTH_8 22 skAArlLGisRrtLyr 37
                                   ++AA+lLG+sR t+ r
  gi|121638196|ref|YP_978420.1| 23 QQAADLLGVSRPTVVR 38
                                   79***********976 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                    HHHHHHHHTT CS
                          HTH_8   9 lIeaALertg 18 
                                    +I + L++++
  gi|121638196|ref|YP_978420.1|  91 VICEQLREAR 100
                                    5666666665 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.021      28      52 ..      16      40 ..       6      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                   HHCT--HHHHHHHHT--HHHHHHHH CS
                         HTH_37 28 ekrelsqseaaqllgiaqPkvsrll 52
                                   +++ l++++aa llg+++P v+rl 
  gi|121638196|ref|YP_978420.1| 16 QSMTLTTQQAADLLGVSRPTVVRLI 40
                                   6789******************996 PP

>> DUF3853  Protein of unknown function (DUF3853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.033      47      89 ..      21      63 ..       4      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                        DUF3853 47 GikglarllGislptanrikksGkiDkaitqiGrkiivDadla 89
                                     ++ a llG+s pt+ r+ ksG +    + + +++++D  la
  gi|121638196|ref|YP_978420.1| 21 TTQQAADLLGVSRPTVVRLIKSGELAAERIGNRHRLVLDDVLA 63
                                   5577899*****************9887777777888887766 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.2e-05      0.11      51      74 ..      20      43 ..       9      60 .. 0.85
   2 ?   -0.9   0.0       1.8   2.4e+03      52      52 ..      77      77 ..      46     107 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                         DUF134 51 lkqeeaaklmGiskatlwrlltea 74
                                   l+ ++aa+l+G+s++t+ rl++++
  gi|121638196|ref|YP_978420.1| 20 LTTQQAADLLGVSRPTVVRLIKSG 43
                                   67899****************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                         DUF134 52 k 52
                                    
  gi|121638196|ref|YP_978420.1| 77 A 77
                                   2 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.8e-05      0.11      32      57 ..      17      42 ..      13      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                                   -TT--HHHHHHHTT--HHHHHHHH-- CS
                          HTH_6 32 aielsikalAkaaavSeativrfakk 57
                                   ++ l+ ++ A  ++vS++t+vr+ k+
  gi|121638196|ref|YP_978420.1| 17 SMTLTTQQAADLLGVSRPTVVRLIKS 42
                                   5678999***************9886 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.26      44      62 ..      22      40 ..      17      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                         HTH_22 44 vekvAekLgiSraTvYryL 62
                                    ++ A+ Lg+Sr+Tv r +
  gi|121638196|ref|YP_978420.1| 22 TQQAADLLGVSRPTVVRLI 40
                                   6899***********7765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.15      11      31 ..      21      41 ..      15      51 .. 0.82
   2 ?   -3.3   0.2       7.2     1e+04       2      11 ..      65      74 ..      65      80 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHTSSHHHHHHHHT CS
                          HTH_3 11 sqeeLAeklGvsrstisriEn 31
                                   + +++A++lGvsr t+ r+++
  gi|121638196|ref|YP_978420.1| 21 TTQQAADLLGVSRPTVVRLIK 41
                                   4479************99987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.2
                                   HHHHHHTTHH CS
                          HTH_3  2 kelRkqlgls 11
                                   +e+R q+ ++
  gi|121638196|ref|YP_978420.1| 65 REARRQRQYD 74
                                   5777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 726.69
//
Query:       gi|121638197|ref|YP_978421.1|  [L=174]
Description: hypothetical protein BCG_2332 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00017   21.3   1.7    0.00056   19.7   1.7    1.9  1  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.022   14.5   0.2      0.027   14.2   0.2    1.1  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.7   6.2e-08   0.00056       1      47 [.      76     115 ..      76     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.2e-08
                       UvrD_C_2   1 hayaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAre 47 
                                    h+ya+t+h +QG  +  +  +  d ++       r  LY+a+T Are
  gi|121638197|ref|YP_978421.1|  76 HGYAITVHASQGTTAHSTHAVLGDNTS-------RATLYVAMTPARE 115
                                    89******************7777777.......568******8886 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     3e-06     0.027     172     229 ..      65     116 ..      35     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-06
                Viral_helicase1 172 ftqalkealgvr.evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrks 229
                                    f+ + ++++  +  + tvh  qG+t+ ++  vl ++t       sr++l+vA+T +r+s
  gi|121638197|ref|YP_978421.1|  65 FSGDYLHEHITHgYAITVHASQGTTAHSTHAVLGDNT-------SRATLYVAMTPARES 116
                                    556666777777878*******************776.......589*******88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1331.25
//
Query:       gi|121638198|ref|YP_978422.1|  [L=89]
Description: hypothetical protein BCG_2333 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.9   0.5       0.68   10.3   0.1    2.0  2  Styelin   Styelin


Domain annotation for each model (and alignments):
>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.26   4.7e+03      42      49 ..      53      60 ..      51      62 .. 0.79
   2 ?   10.3   0.1   3.8e-05      0.68      34      45 ..      74      85 ..      70      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.26
                        Styelin 42 efmkeveq 49
                                   +fm+e+ q
  gi|121638198|ref|YP_978422.1| 53 QFMEELSQ 60
                                   79999887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.8e-05
                        Styelin 34 DmtDeefqefmk 45
                                   D+tD+efq f++
  gi|121638198|ref|YP_978422.1| 74 DLTDDEFQAFLQ 85
                                   9*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 648.68
//
Query:       gi|121638199|ref|YP_978423.1|  [L=284]
Description: hypothetical protein BCG_2334c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.4   0.4     0.0069   16.4   0.4    2.0  2  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.13   2.4e+03      65      83 ..      93     111 ..      86     111 .. 0.78
   2 !   16.4   0.4   3.8e-07    0.0069       7      84 ..     138     214 ..     133     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.13
                                    HHHHHHHSHHHHHHHHHHH CS
                            CMD  65 aqaaayagwpaaraAlaaa 83 
                                      + +++++p++ra l+a+
  gi|121638199|ref|YP_978423.1|  93 VAMYIADFVPRVRAGLEAL 111
                                    557788999****999885 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.8e-07
                                    HHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHHH CS
                            CMD   7 ltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaae 84 
                                    ++ +  a+     +Ldp + eL+ l+ +a ++c  C +     Al+aG +e    e+ +   +     +a+aAl++a+
  gi|121638199|ref|YP_978423.1| 138 FNGFLPAVAR-MRALDPVTSELVRLRGAAQHNCRVCKSLREVSALDAGGSETLYGEIERFDTSVLLDVRAKAALRYAD 214
                                    5556666665.668***************************************************9999*9**99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2264.39
//
Query:       gi|121638200|ref|YP_978424.1|  [L=457]
Description: hypothetical protein BCG_2335c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-26   93.9   0.0      2e-26   93.5   0.0    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   1.1e-30     2e-26       4     277 ..      26     320 ..      23     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.1e-30
                                    EEEEEEEEEEEEEETTEEEEEEEEEEEEEEEE.EEETTEEEE....EE....ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                      PmbA_TldD   4 vrleesestsvrfengevetnsssedsglgvr.vikggrlgf....astl.dtsdealeeaveraveiaklapedpea.. 75 
                                    v ++e+ ++++r++ ++++tn+ s+++ ++v  +++ g ++f    +s+  d+s   l  +v  + ++a++ape+ +a  
  gi|121638200|ref|YP_978424.1|  26 VLVTEKVEATLRWAGNSMTTNGVSHSRNVTVIsIVRRGDSAFvgsvVSAEvDPS--VLPGLVVSSQDAARSAPEAGDAap 103
                                    778899999***********************9999998888665544444555..999999999999999999988777 PP

                                    ...............GGS-HHHHHH........HHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEE CS
                      PmbA_TldD  76 ...............eevsaeekie........lleelekalrsadpkienskgarisgvsaslsaskeeklianSeGld 132
                                                   +                 ++ +l++  r            +++   +  + s++++++a+S+Gl+
  gi|121638200|ref|YP_978424.1| 104 lladtgepddwdapvP--------GtgagvftgIAGSLSRGFR------------GADRLYGYAHRSVSTTFLASSTGLR 163
                                    6666544444222110........0111222222333333322............33334455688889*********** PP

                                    EEEEEEEEEEEEEEEE.STCSETEEEEEEEE.....SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHH CS
                      PmbA_TldD 133 veqtrtrvslslsviaddggsgdgmgggsgy.....edleeedleeiaeeaaekalasleakplppgkypVvlspeavgs 207
                                     ++t+++  ++++++          g  s++      d+ e  ++ ++e++  +++++ + ++lp+g+y +++ p+ v++
  gi|121638200|ref|YP_978424.1| 164 RRYTQPTGAIEINAKR---------GDASAWvgigtPDFVEVPIDLMLERLSTRLRWAQRTVELPAGRYQTIMPPSTVAD 234
                                    ********99999999.........335566677776666677788********************************** PP

                                    HHHGHHHHHTBHHHHHTT--TT.....TT-TTSB-S-TT--EEEETT...........-......-SB-TTSBB---EEE CS
                      PmbA_TldD 208 llheavghaleadavlegrSfl.....kdklGekvaselltivddpt...........s.gglgsypfDdEGvptqrtvl 270
                                    ++  ++g+++ ++ ++egr+++     ++++Ge++    lt++ dp              ++  + +++d+G+  + +++
  gi|121638200|ref|YP_978424.1| 235 MMI-YLGWSMAGRGAQEGRTAFsapggGTRVGERLTELPLTLFTDPAapglactpfvaVsNSSETQSVFDNGMEISQVDW 313
                                    **9.799***************99995558****************9666666666653355555666************ PP

                                    EETTEE- CS
                      PmbA_TldD 271 IenGvLk 277
                                    I+ Gv +
  gi|121638200|ref|YP_978424.1| 314 IRSGVIN 320
                                    *****75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 2437.14
//
Query:       gi|121638201|ref|YP_978425.1|  [L=505]
Description: hypothetical protein BCG_2336c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-49  169.2   0.0    2.1e-49  168.9   0.0    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   0.0   1.2e-53   2.1e-49       1     279 []      34     345 ..      34     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.2e-53
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    +a++r+++ +++ +++++ge+et+  s++ gl+vrvi+ g +gfas  +++ +  +++++ av+ a + +  + +     
  gi|121638201|ref|YP_978425.1|  34 HADLRVHRISTEIIQLRDGELETAVISRELGLAVRVIVAGTWGFASHAELAPDVAAATARHAVHVATVLAALNTErvrla 113
                                    599*****************************************998888878888999999999977777777688999 PP

                                    ..................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEE CS
                      PmbA_TldD  76 ..................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtr 137
                                                        v+a+eki++l++ + +l +ad         +i++vsasl+a+ke++++a++ G++++q+r
  gi|121638201|ref|YP_978425.1| 114 pepvytdaewvsnyridpFGVPASEKIAVLRDYSGRLLDAD---------GIDHVSASLNAVKEQTFYADTFGSSITQQR 184
                                    99999999999999999999999999999999998877777.........69**************************** PP

                                    EEEEEEEEEEE...S...TCS..ET.EEEEEEEE........SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE- CS
                      PmbA_TldD 138 trvslslsvia.d.d...ggs..gd.gmgggsgy........edleeedleeiaeeaaekalasleakplppgkypVvls 201
                                     r  ++l ++a d +   + +   +   ++  g+        +++ + +l ++ + +aek++a      + pg +++v++
  gi|121638201|ref|YP_978425.1| 185 VRLLPCLDAVAvDsAagnF-EsmRTlAPPTARGWevvagdeiWNWTD-ELAQLPSLLAEKVRAPS----VMPGPTDLVID 258
                                    ***********99667632.268555556666665566665555555.77778888899988888....*********** PP

                                    HHHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTS.B-S-TT--EEEETT-......-SB-TTSBB---EEEEE CS
                      PmbA_TldD 202 peavgsllheavghaleadavl......egrSflkd.klGe.kvaselltivddpts.gglgsypfDdEGvptqrtvlIe 272
                                    p  +++++he++gha+e+d++       +g+Sf ++ klG+ +++s+ ++++ d t   gl++ ++DdEGv++q ++l++
  gi|121638201|ref|YP_978425.1| 259 PTNLWLTIHESIGHATEYDRAIgyeaayAGTSFATPdKLGTlRYGSPVMNVTADRTAeFGLATVGYDDEGVAAQSWDLVR 338
                                    ************************99999*****9999******************99********************** PP

                                    TTEE--- CS
                      PmbA_TldD 273 nGvLkny 279
                                    +Gv+++y
  gi|121638201|ref|YP_978425.1| 339 DGVFVGY 345
                                    *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2720.31
//
Query:       gi|121638202|ref|YP_978426.1|  [L=290]
Description: sugar-transport integral membrane protein ABC transporter uspA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-19   69.7  15.9    2.6e-19   69.7  15.9    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.8     0.033   5.9e+02      33      44 ..      26      58 ..       8      82 .. 0.48
   2 !   69.7  15.9   1.4e-23   2.6e-19       2     179 ..      84     280 ..      83     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.033
                   BPD_transp_1 33 fvlaillvlvf.....................v 44
                                   f+l+++lv+v                      +
  gi|121638202|ref|YP_978426.1| 26 FLLLPILVVVWlslhrwdllgplryvgltnwrS 58
                                   224444443335555556666666655663333 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 1.4e-23
                   BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...............vilsilghlilpviillllsa 64 
                                    ++lG+laa  l+r+ +++ l+r+l+ +++   ++++a+++ +++                +l++ g +   v +++++++
  gi|121638202|ref|YP_978426.1|  84 TVLGLLAAslLARRLPGTGLFRTLYVLPWICAPLAIAVMWRWILaptdgaistvlghriEWLTDPGLALPVVSAVVVWTN 163
                                    6899****9999*****************************999**********************88888********* PP

                   BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                    ++yv l++ a+l ++p+d  +aar++Gas wq+f++++lP++ p+++  l+  ++++   +  ++ l+++++ g++ l a
  gi|121638202|ref|YP_978426.1| 164 VGYVSLFFLAGLMAIPQDIHNAARTDGASAWQRFWRITLPMLRPTMFFVLVTGIISAAQVFDTVYALTGGGPQGSTDLVA 243
                                    *********************************************************99999888888887766666666 PP

                   BPD_transp_1 145 ilgydyseis..nggvlalviavlllnlvadilqrll 179
                                      +y  ++++  +g + +++++++++++ a ++q l 
  gi|121638202|ref|YP_978426.1| 244 HRIYAEAFGAaaIGRASVMAVVLFVILVGATVVQHLY 280
                                    6666666666554444444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1511.05
//
Query:       gi|121638203|ref|YP_978427.1|  [L=274]
Description: sugar-transport integral membrane protein ABC transporter uspB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-20   71.8  15.9    5.8e-20   71.8  15.9    1.9  2  BPD_transp_1     Binding-protein-dependent transport system i


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.1     0.047   8.4e+02     107     167 ..      18      82 ..       8      93 .. 0.52
   2 !   71.8  15.9   3.2e-24   5.8e-20       2     182 ..      85     267 ..      84     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.047
                   BPD_transp_1 107 lppiitglilafggllggavlleflgswpGlgtllleailgydyseis.....nggvlalviavll 167
                                    +  +it+ ++ +g+l   +++  f ++ p l++++  ++ +y   + +     +++++ +++++ll
  gi|121638203|ref|YP_978427.1|  18 IGAVITLSPFLLGLLTSFTSAHQFATGTP-LQLPRPPTLANYADIADAgfrraAVVTALMTAVILL 82 
                                    45566666666666666666666666444.555554444444433333677743333333333333 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 3.2e-24
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalr 77 
                                    +++++laa    +  ++++++l +++ ++l++P  v +++l+l+   +  lg  ++  +++l +++  py++++ r+ +r
  gi|121638203|ref|YP_978427.1|  85 LTFSVLAAyafARLQFRGRDALFWVYVATLMVPGTVTVVPLYLM---MAQLGLRNTFwALVLPFMFGSPYAIFLLREHFR 161
                                    56778888888899**********************88888864...5667755555466666777889*********** PP

                   BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyseis 154
                                     +p+dl++aar++Ga++  ++++vv+P++ p++++++++++++ ++++++++ ++s++    l+  + + ++ ++ +++ 
  gi|121638203|ref|YP_978427.1| 162 LIPDDLINAARLDGANTLDVIVHVVIPSSRPVLAALAMITVVSQWNNFMWPLVITSGHKwrvLTVATADLQSRFNDQWT- 240
                                    *******************************************************998895555555555555555555. PP

                   BPD_transp_1 155 nggvlalviavlllnlvadilqrlldpr 182
                                      +++a+++a+++l++++  +qr++   
  gi|121638203|ref|YP_978427.1| 241 -LVMAATTVAIVPLIALFVTFQRHIVAS 267
                                    .5**********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1631.10
//
Query:       gi|121638204|ref|YP_978428.1|  [L=440]
Description: periplasmic sugar-binding lipoprotein uspC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.9e-45  153.8   5.8    1.4e-44  153.3   5.8    1.2  1  SBP_bac_1  Bacterial extracellular solute-binding protein
    2.1e-19   70.4   1.3    2.9e-19   69.9   1.3    1.1  1  SBP_bac_8  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   5.8   1.6e-48   1.4e-44       7     314 ..      51     351 ..      46     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 1.6e-48
                                    HHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTT CS
                      SBP_bac_1   7 gaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgv 86 
                                     aa+++ + +af++ hp+i+V+ + v ++++ + l++++a+G+++ D+++ +n+++a +a++g l+ ++++++++ + +v
  gi|121638204|ref|YP_978428.1|  51 AAAYRQSF-AAFTRSHPDIEVRTNLVAYSTYFETLRTDVAGGSAD-DIFWLSNAYFAAYADSGRLMKIQTDAADWEPAVV 128
                                    56999999.99********************************77.*******************************999 PP

                                    CCTEEEEHHHHTHHHHCEEEES.EEEE.E.EEEEEEETTTHHCTTGGG.........SHBHHHHHHHHHHHHHHCTCT.. CS
                      SBP_bac_1  87 kdaadklsssvlpkildskvly.vPly.a.argliYNkdlfekagldp.........pwtWdelveaakklkekgkkp.. 152
                                    ++++ +            +vl+ vP+      +++YN dl++ ag+dp             d+l   + +l+        
  gi|121638204|ref|YP_978428.1| 129 DQFTRS------------GVLWgVPQLtDaGIAVFYNADLLAAAGVDPtqvdnlrwsRGDDDTLRPMLARLT-----Vda 191
                                    998888............55999****99***********************66555333333333333333.....334 PP

                                    .............HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEE CS
                      SBP_bac_1 153 .............iggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgae 219
                                                  ++++g+ a+++ ++ +l++++s+gg + ++   ++dnp++ +a+ ylv l+   n+++  ++++ +
  gi|121638204|ref|YP_978428.1| 192 dgrtantpgfdarRVRQWGYNAANDPQAIYLNYIGSAGGVFQRDGKFAFDNPGAIEAFRYLVGLI---NDDHVAPPASDT 268
                                    4558888999999*************************766666555999999999999999999...************ PP

                                    CSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHH CS
                      SBP_bac_1 220 nkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpe 299
                                    n +g++ +++f aG++a++ +g+++            +a+ ++++ +++gva+lPag+ g  + +++   a +++sk+p+
  gi|121638204|ref|YP_978428.1| 269 NDNGDFSRNQFLAGKMALFQSGTYS------------LAPVARDALFHWGVAMLPAGPAGRVSVTNGIAAAGNSASKHPD 336
                                    *********************9988............*************************99**************** PP

                                    HHHHHHHHHTSHHHH CS
                      SBP_bac_1 300 aAkkFldfllspeaq 314
                                    a++++l+++ s e++
  gi|121638204|ref|YP_978428.1| 337 AVRQVLAWMGSTEGN 351
                                    ************986 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.3   3.3e-23   2.9e-19       4     269 ..      59     368 ..      56     378 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.3e-23
                                    HHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HH.HHHTT--T CS
                      SBP_bac_8   4 kefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltd.alaavgyd 81 
                                    ++f+ ++ +++v+   +a+ ++ ++l++++a g+a+  d++w +++++a++a++g l  + +  +++d+++ ++++++  
  gi|121638204|ref|YP_978428.1|  59 AAFTRSHpDIEVRTNLVAYSTYFETLRTDVAGGSAD--DIFWLSNAYFAAYADSGRLMKIQT--DAADWEPaVVDQFTRS 134
                                    79***********9889*****************97..578*****************9996..678885548888899* PP

                                    S.----EEEEEEE-EEEEEHHHHHHS..---BHHHH.H.....HHHHHH...........HHH-............SE.G CS
                      SBP_bac_8  82 gklygvPyasetpyvliynkdlleka.edpktwdel.l.....aaakkl...........kgkf............gl.p 130
                                    g l gvP  +  + +++yn+dll +a  dp+ +d l +     ++   l            g++            ++ +
  gi|121638204|ref|YP_978428.1| 135 GVLWGVPQLTDAGIAVFYNADLLAAAgVDPTQVDNLrWsrgddDT---LrpmlarltvdaDGRTantpgfdarrvrQWgY 211
                                    ************************989999999999643333222...12223334444345556667555555663332 PP

                                    G---GGGGGGTHH........ETTEE---H......HHH.HHHHHHHHHHHHTT-EE.......-S..--SSTTTTTSBS CS
                      SBP_bac_8 131 dpasgwlqaalla........kdgksldddg....gkdglkealellkklkdngkty.......dtgadavsefanGeva 191
                                    + a++       +        ++g  +  dg    +++g  ea+++l  l ++  +        d+g+   + f  G++a
  gi|121638204|ref|YP_978428.1| 212 NAANDP------QaiylnyigSAGGVFQRDGkfafDNPGAIEAFRYLVGLINDDHVAppasdtnDNGDFSRNQFLAGKMA 285
                                    223332......0222222455788888888889999**************888766788877566678888******** PP

                                    EEEE-TTHHHHHH.-TTTSEEEE.--..S--..EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS- CS
                      SBP_bac_8 192 ftingswdiaaaq.kagkklgai.vp..kqg..sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvn 265
                                     +++g+ ++a ++ +a + +g++ +p  + g  s+++g   a ++ +k++d a  + l w+ s e++      +  ip+ 
  gi|121638204|ref|YP_978428.1| 286 LFQSGTYSLAPVArDALFHWGVAmLPagPAGrvSVTNGIAAAGNSASKHPD-AVRQVLAWMGSTEGNSYVGRHGAAIPAV 364
                                    ******998887747789*****555532234477777667779999999*.6************998776666667776 PP

                                    S-TT CS
                      SBP_bac_8 266 ksaa 269
                                     sa+
  gi|121638204|ref|YP_978428.1| 365 LSAQ 368
                                    6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3150.78
//
Query:       gi|121638205|ref|YP_978429.1|  [L=292]
Description: hypothetical protein BCG_2340c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-30  104.2   2.3    5.6e-18   65.8   1.2    2.0  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   1.2   3.1e-22   5.6e-18       4     141 .]       2     141 ..       1     141 [. 0.96
   2 !   37.7   0.0   1.5e-13   2.6e-09      12     141 .]     161     291 ..     152     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.1e-22
                                    EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTCE CS
                            Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggvk 81 
                                    +I+V++   +    Al+ A++ a+++++ l++++++  + ++++ +  ++++e ++e+ +a+++++a    +++++g+++
  gi|121638205|ref|YP_978429.1|   2 TIVVGYLAGKVGPSALHLAVRVARMHKTSLTVATIVRRHWPTPSLARVDAEYELWSEQLAAASAREAqrYLRRLADGIEV 81 
                                    68888888888999*************************************************9999999********** PP

                                    EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                      +++ + +++ ++l+v+ee++a  +V+Gs   ++ +r+l+GS+++++l+++p+pV +++
  gi|121638205|ref|YP_978429.1|  82 SYHHRAHRSVSAGLLDVVEELEAGVLVLGSFPSGRRARVLIGSTADRLLHSSPVPVAITP 141
                                    ********************************************************9975 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 1.5e-13
                                    SHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHCTTCEEEEEEEESS CS
                            Usp  12 seeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaeaggvkvevvveegd 90 
                                    ++ s  ++++  +la ++g + +++++    +  + ++    ae + le  +a+++++  + +      ++v+++v+ g+
  gi|121638205|ref|YP_978429.1| 161 TSGSVDVVRRCGHLASRYGVPMRVITFAVRGRTMYPPEVGLHAEASVLEAWAAQARELLeKLRINGVVSEDVVLQVVTGN 240
                                    566778999999***********99998887777777777776666666666666555525566666667889999**** PP

                                    HHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  91 paeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +    l++a+ +d +++ +G++  + ++r++lGS s +++r +p+pVlv +
  gi|121638205|ref|YP_978429.1| 241 GWAQALDAADWQDGEILALGTSPFGDVARVFLGSWSGKIIRYSPVPVLVLP 291
                                    *************************************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2211.76
//
Query:       gi|121638206|ref|YP_978430.1|  [L=476]
Description: cationic amino acid transport integral membrane protein rocE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-51  176.1  42.1    1.5e-51  175.6  42.1    1.2  1  AA_permease_2   Amino acid permease
    3.7e-36  124.7  38.5    5.1e-36  124.3  38.5    1.1  1  AA_permease     Amino acid permease
    2.8e-11   43.3   5.4    2.8e-11   43.3   5.4    4.3  5  AA_permease_C   C-terminus of AA_permease
    0.00024   20.0  11.3    0.00085   18.2   0.2    2.8  3  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.16   12.6   0.0       0.32   11.6   0.0    1.5  1  ThiS            ThiS family
       0.21   11.6   1.8       0.35   10.9   1.8    1.2  1  RP-C_C          Replication protein C C-terminal region


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6  42.1   5.1e-55   1.5e-51       1     402 [.      35     442 ..      35     465 .. 0.86

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 5.1e-55
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                    +++++++++ +g++ig+gif++   ++  +gp +i++++ia ++     +++yaEl+sa p sg +y+y++ + g+ va 
  gi|121638206|ref|YP_978430.1|  35 FGTFQLTMFGVGATIGTGIFFVLaqAVPEAGPGVIVSFIIAGIAA-GLAAICYAELASAVPISGSAYSYAYTTLGEAVAM 113
                                    799******************96555555***************9.78999*****999********************* PP

                  AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgp..........dlqgn...twltyliaiaililvalinirgikesakiqn 145
                                    ++a ++++ y +++a++++   +y   +l+           +  ++   +  + l a++++ l+al+ irg +esa+++ 
  gi|121638206|ref|YP_978430.1| 114 VVAACLLLEYGVATAAVAVGWSGYVNKLLSNlfgfqmphvlSAAPWdthPGWVNLPAVILIGLCALLLIRGASESARVNA 193
                                    **************99999999998666543444567777733344333445667789********************** PP

                  AA_permease_2 146 ilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkai 223
                                    i++++k+ ++l ++ i+++ + ++++          f+p g  g+ ++ +++++s++G ++++   +evk   k++p+a+
  gi|121638206|ref|YP_978430.1| 194 IMVLIKL-GVLGMFMIIAFSAYSADHLK-------DFVPFGVAGIGSAAGTIFFSYIGLDAVSTAGDEVKDpqKTMPRAL 265
                                    *******.79999998888887666664.......7********************************775559****** PP

                  AA_permease_2 224 figllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavg.gkvvaiivvilialsllgaintavigssrvleal 302
                                    + +l++v+++y+lv++a+lg  p+  +a+ ++ g  +a+ +++v  g ++++i+++++++s++   +  ++g++r+l+a+
  gi|121638206|ref|YP_978430.1| 266 IAALVVVTGVYVLVALAALGTQPWQDFAEQETAG--LAIILDNVThGEWASTILAAGAVVSIFTVTLVTMYGQTRILFAM 343
                                    ***************************9988876..556666665166******************************** PP

                  AA_permease_2 303 ardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr 381
                                    +rdg lP +fakvn ++ +p+  ++++ai+++ l+   ++++   ++ l+++ s+g +  + ++++g+++lr+++p+l+r
  gi|121638206|ref|YP_978430.1| 344 GRDGLLPARFAKVNpRTMTPVHNTVIVAIFASTLA---AFIP---LDSLADMVSIGTLTAFSVVAVGVIVLRVREPDLPR 417
                                    **************99***************6554...4444...69*******************************99 PP

                  AA_permease_2 382 ....pgkilvaiigalfllfllval 402
                                        pg++++  +++l + ++l+ l
  gi|121638206|ref|YP_978430.1| 418 gfkvPGYPVTPVLSVLACGYILASL 442
                                    9777666656666666666666544 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3  38.5   1.7e-39   5.1e-36       2     436 ..      40     449 ..      39     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 1.7e-39
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                    ++++ +g  iGtg+f+ l+ ++ +aGp g+++++++ag+   l++++ +e+a+++p sg++y ya  +lg++++ v+++ 
  gi|121638206|ref|YP_978430.1|  40 LTMFGVGATIGTGIFFVLAQAVPEAGP-GVIVSFIIAGIAAGLAAICYAELASAVPISGSAYSYAYTTLGEAVAMVVAAC 118
                                    689************************.*************************************************999 PP

                    AA_permease  82 .ylfswitvlaleltaasiliqfwelvtdlpkawvt.....................gavflvvlliinlvgvkvygeae 139
                                     +l ++++++a++++ ++++ +++++      ++++                     +++++++  ++ + g+  ++++ 
  gi|121638206|ref|YP_978430.1| 119 lLLEYGVATAAVAVGWSGYVNKLLSN------LFGFqmphvlsaapwdthpgwvnlpAVILIGLCALLLIRGASESARVN 192
                                    44556666666666655555444422......222234455566667****99999988888888888888999999999 PP

                    AA_permease 140 filalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielva 219
                                     i+ lik+  +  f+i+ ++  + +                ++k+++p g        ++++ s++ +++f++ G  +v 
  gi|121638206|ref|YP_978430.1| 193 AIMVLIKLGVLGMFMIIAFSAYSAD----------------HLKDFVPFG--------VAGIGSAAGTIFFSYIGLDAVS 248
                                    9999999999999999996444444................456668888........********************** PP

                    AA_permease 220 iiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavilta 299
                                    ++++EvkdP+k++P+a + +++ +t +Yvl++l++  + p++d    +   +a ++ +i  + +    ++++++a+  ++
  gi|121638206|ref|YP_978430.1| 249 TAGDEVKDPQKTMPRALIAALVVVTGVYVLVALAALGTQPWQDFAEQE---TA-GLAIILDNVTHGEWASTILAAGAVVS 324
                                    *******************************************44333...45.999*********************** PP

                    AA_permease 300 alssansslysasRvlyslakdglaP.kvlkkvskrgvPl.raillsmiisllalllaslnlaapivfnfllaisaligl 377
                                    ++ + +  +y  +R+l+++ +dgl+P +++k+  + + P+ + +++ +++s la ++             l  ++ + +l
  gi|121638206|ref|YP_978430.1| 325 IFTVTLVTMYGQTRILFAMGRDGLLPaRFAKVNPRTMTPVhNTVIVAIFASTLAAFIPLD---------SLADMVSIGTL 395
                                    **************************99999999*****736677777777776655555.........5559******* PP

                    AA_permease 378 ivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyaylt 436
                                      + ++++  +++R      + ++   gfk +++p +++l ++a+  il  l +y  l+
  gi|121638206|ref|YP_978430.1| 396 TAFSVVAVGVIVLRVR----EPDL-PRGFKVPGYPVTPVLSVLACGYILASLHWYTWLA 449
                                    ***********77766....4434.459************************9998777 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.094   2.8e+02      26      45 ..      37      56 ..      34      60 .. 0.84
   2 ?   -3.1   0.1       2.9   8.6e+03      12      30 ..     111     129 ..     110     135 .. 0.68
   3 ?   -1.4   0.3      0.88   2.6e+03      30      50 ..     198     218 ..     193     219 .. 0.69
   4 ?   -3.0   0.2       2.7   7.9e+03      12      25 ..     269     282 ..     265     284 .. 0.65
   5 !   43.3   5.4   9.2e-15   2.8e-11       1      51 []     419     469 ..     419     469 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.094
                  AA_permease_C 26 sltwirfgvwmliglliYfl 45
                                   + ++ +fgv   ig+ i+f+
  gi|121638206|ref|YP_978430.1| 37 TFQLTMFGVGATIGTGIFFV 56
                                   567899************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                  AA_permease_C  12 lsIlvNiyLmlqLdsltwi 30 
                                    ++++v  +L+l+ +++t +
  gi|121638206|ref|YP_978430.1| 111 VAMVVAACLLLEYGVATAA 129
                                    6778888888877777755 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.88
                  AA_permease_C  30 irfgvwmliglliYflYgirh 50 
                                    i  gv  +++++ + +Y+  h
  gi|121638206|ref|YP_978430.1| 198 IKLGVLGMFMIIAFSAYSADH 218
                                    666677777788888887766 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.7
                  AA_permease_C  12 lsIlvNiyLmlqLd 25 
                                    l +++++y+++ L 
  gi|121638206|ref|YP_978430.1| 269 LVVVTGVYVLVALA 282
                                    45667777777765 PP

  == domain 5  score: 43.3 bits;  conditional E-value: 9.2e-15
                  AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYgirhs 51 
                                    FkvP +P+ P+ls+l+  y++++L++ tw+ f+ w+++ +++Y++ g++hs
  gi|121638206|ref|YP_978430.1| 419 FKVPGYPVTPVLSVLACGYILASLHWYTWLAFSGWVAVAVIFYLMWGRHHS 469
                                    9*************************************************8 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   2.3   0.00067         2       4      82 ..      37     116 ..      35     133 .. 0.85
   2 !   18.2   0.2   2.8e-07   0.00085     119     231 ..     171     284 ..     150     290 .. 0.89
   3 ?   -2.2   0.1      0.47   1.4e+03     161     186 ..     355     380 ..     348     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00067
                 Spore_permease   4 tkqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfp.ektliellkkilgkwLGslls 82 
                                    t+ql++  v + +G+gi ++++ ++ +a+p   +s ++agi++ ++++ + +l +  p + + +++   +lg  ++++  
  gi|121638206|ref|YP_978430.1|  37 TFQLTMFGVGATIGTGIFFVLAQAVPEAGPGVIVSFIIAGIAAGLAAICYAELASAVPiSGSAYSYAYTTLGEAVAMVVA 116
                                    6788899999*********************************************9985568888988888888777665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.8e-07
                 Spore_permease 119 lllllvilYlvvkGieslareflfiivilliilllillfslklaeiknlrPvlgngikpvlkslkttslsflgveillll 198
                                    ++l+ ++++l++ G ++ ar+++++++i l +l +++++ ++ +  ++l+  +  g+  + +++ t+ +s++g   +   
  gi|121638206|ref|YP_978430.1| 171 VILIGLCALLLIRGASESARVNAIMVLIKLGVLGMFMIIAFSAYSADHLKDFVPFGVAGIGSAAGTIFFSYIGLDAVSTA 250
                                    5788899999********************************************************************** PP

                 Spore_permease 199 vpflkdkkkvk.kaallgvlistllyllttlivi 231
                                       +kd++k+  +a++ +++++t +y+l+ l ++
  gi|121638206|ref|YP_978430.1| 251 GDEVKDPQKTMpRALIAALVVVTGVYVLVALAAL 284
                                    *****98877626667777778889999887766 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.47
                 Spore_permease 161 laeiknlrPvlgngikpvlkslktts 186
                                     ++++ ++Pv ++ i+ ++ s+  + 
  gi|121638206|ref|YP_978430.1| 355 KVNPRTMTPVHNTVIVAIFASTLAAF 380
                                    56677777777777777776654444 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.32      27      73 ..     280     328 ..     264     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                    HHHHHHHHTCHHG...TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEES CS
                           ThiS  27 lleaLgerypela...lerrvavavNgeivpr.lwldtelkdgDevailpp 73 
                                    +l+aLg++   ++   + +   +a+  ++v++ +w++t+l++g +v+i+++
  gi|121638206|ref|YP_978430.1| 280 ALAALGTQP--WQdfaEQETAGLAIILDNVTHgEWASTILAAGAVVSIFTV 328
                                    566677666..44447444444444456788888***************85 PP

>> RP-C_C  Replication protein C C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.8   0.00012      0.35     137     167 ..      90     120 ..      84     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                         RP-C_C 137 rsmlgvspsaweeAcevmGreqAavalacil 167
                                     s++ +s sa++ A +++G++ A v+ ac+l
  gi|121638206|ref|YP_978430.1|  90 ASAVPISGSAYSYAYTTLGEAVAMVVAACLL 120
                                    57788************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3386.49
//
Query:       gi|121638207|ref|YP_978431.1|  [L=181]
Description: ornithine aminotransferase (C-terminus part) rocD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-39  135.5   0.0    2.1e-39  135.4   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0   1.2e-43   2.1e-39     229     406 .]       1     176 [.       1     176 [. 0.97

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 1.2e-43
                                    EEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHH CS
                    Aminotran_3 229 livDEvqtGfGrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgshgsTfgGnplacavalavlei 307
                                    +i+DE+q+G+++TG  fA++h gv pD+++l+K l+gG  plsa++a++e+  +++pg+hgsTfgGnpla+a+   v+ +
  gi|121638207|ref|YP_978431.1|   1 MIADEIQSGLACTGYPFACDHGGVLPDIYLLGKTLGGGaVPLSAMVADREIFGVVHPGEHGSTFGGNPLAAAIGTPVVSM 80 
                                    69****************************************************************************** PP

                                    HHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE--- CS
                    Aminotran_3 308 ieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllpp 387
                                    +   + + + ++lga l ++L +l  +      +Rg+G    ++++ +     +++  ++ + Gvl++ +   ++r++pp
  gi|121638207|ref|YP_978431.1|  81 VVWGECQARSAKLGAHLHQRLADLIGD--GAVALRGLGWWADVDIERALAIG-TDMSMRLADRGVLLKDTYGAALRFAPP 157
                                    *************************66..5889**************99966.89*************9988******** PP

                                    TT--HHHHHHHHHHHHHHH CS
                    Aminotran_3 388 liitdeeidelleilkkal 406
                                    l+it++eid ++ ++ +al
  gi|121638207|ref|YP_978431.1| 158 LVITAQEIDCAVRRFADAL 176
                                    ***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1440.17
//
Query:       gi|121638208|ref|YP_978432.1|  [L=221]
Description: ornithine aminotransferase (N-terminus part) rocD1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-34  119.4   0.0    2.1e-34  118.9   0.0    1.3  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   1.2e-38   2.1e-34       3     219 ..      20     217 ..      18     221 .] 0.95

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.2e-38
                                    -TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHH CS
                    Aminotran_3   3 areednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkl 82 
                                    a+++ +l++v+  aeG++++d dg rylD ++++++vnlGh++P+ ++ +++q++++++++ +al+ + +  l   l++l
  gi|121638208|ref|YP_978432.1|  20 AHNYSPLPVVAASAEGAWIADIDGLRYLDWLAAYSAVNLGHRNPASTATAHAQVDTVTLLN-RALHADRLGPLGAALAQL 98 
                                    67888889*****************************************************.****************** PP

                                    CT-..SEEEEESSHHHHHHHHHHHHHHHHHHTS..HCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE CS
                    Aminotran_3  83 apkgldkvflansGseAvetAlKlarkyarekk..atektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrl 160
                                     +k  d v+ +ns +eAve+ l++ark+   ++     ++ ii  +++fHG+t   +s +++ +   ++++p++p+  ++
  gi|121638208|ref|YP_978432.1|  99 CGK--DVVLPMNSDAEAVESGLRVARKWGADVNglPAGRHDIILANNNFHGHTSSVVSFSSD-PAAGSGVEPSTPGLRSV 175
                                    ***..*************************9998999*************************.***************** PP

                                    -TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHH CS
                    Aminotran_3 161 kypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklr 219
                                    ++ d                 + a  ++++d++ A ++Epi+g++G++v+++++l ++ 
  gi|121638208|ref|YP_978432.1| 176 PFGD-----------------AAAPAQTIDDNTVADLLEPIPGQAGIIVPADDYLPAAS 217
                                    ***9.................445557889999999******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1644.13
//
Query:       gi|121638209|ref|YP_978433.1|  [L=302]
Description: hypothetical protein BCG_2344c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-18   64.6   0.0    1.1e-17   64.2   0.0    1.2  1  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0     6e-22   1.1e-17     108     339 ..      96     301 ..      22     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 6e-22
                                    EE---GGGG-TTTTEEEEBSEEEE---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----G.GGEEEEETTE CS
                  Amidinotransf 108 lipplpnlvFtrdwfstigggvvlnpmaapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEG.Gdfvvlskgv 186
                                     i  lp++v+t +  + +   +v+ ++  p+R  E++++  ++           ++++    ++   EG Gd+++++++v
  gi|121638209|ref|YP_978433.1|  96 PISGLPDMVYTANGGFITHDIAVVARFRFPERAGESRAYASWMSS---------VGYRP-VTTRHVNEGqGDLLMVGERV 165
                                    47889****************************************.........88884.6778899***********99 PP

                                    EEEEESSSS-HHHHHHHHHHHHHTTS-SEEEEEE--GGSSTS-GGGTEEEEETTEEEE-HHHH.TT-ESS-HHHHHHHHT CS
                  Amidinotransf 187 vaigvssRtdeegieelakklfyktvafkviaieipkgraimHldtvftvvdddavvclpsildaegvkakereavaqaL 266
                                    +a g + Rtd+ +  e+a+ l+  +      +     +  ++Hldt ++v+dd+++ ++p   +++          ++ L
  gi|121638209|ref|YP_978433.1| 166 LA-GYGFRTDQRAHAEIAAVLGLPV------VSLELVDPRFYHLDTALAVLDDHTIAYYPPAFSTA---------AQEQL 229
                                    99.*********************4......444447899********************999888.........77777 PP

                                    T-SS-EEEE-CS-SS-B---S-EEEETTEE..EEETTGHHHHHHHHHTT-EEEEE-HTTTGGGS--TTTT-EEEE CS
                  Amidinotransf 267 kekgleiIeigeeeqwnfggNvLelkpgvv..vaydrntvtnekleeagievievpiselerGgGgarCmsaplf 339
                                    ++   + I +g ++   fg N+++ + +vv  va + +    ++l++ag+e + v++sel +GgG+++C++ +++
  gi|121638209|ref|YP_978433.1| 230 SALFPDAIVVGSADAFVFGLNAVSDGLNVVlpVAAMGF---AAQLRAAGFEPVGVDLSELLKGGGSVKCCTLEIH 301
                                    7777788*****************99889866666666...579***************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2465.65
//
Query:       gi|121638210|ref|YP_978434.1|  [L=148]
Description: AsnC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-15   56.4   1.1    9.9e-15   54.1   0.4    2.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.2e-14   53.2   0.1    3.7e-14   52.4   0.1    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.4e-14   51.5   0.0    8.6e-14   50.8   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.9e-05   23.5   0.1    0.00024   21.0   0.0    2.2  2  MarR            MarR family
    8.7e-05   22.3   0.6    0.00017   21.4   0.1    1.7  2  MarR_2          MarR family
      0.004   17.0   0.0      0.095   12.6   0.0    2.3  3  TrmB            Sugar-specific transcriptional regulator TrmB
      0.007   16.4   0.5      0.025   14.6   0.0    1.9  2  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.063   13.5   0.0    1.8  2  DUF4777         Domain of unknown function (DUF4777)
      0.032   13.8   0.7       0.05   13.1   0.1    1.7  2  Sigma70_r4      Sigma-70, region 4
       0.11   12.0   0.0       0.18   11.3   0.0    1.2  1  LPD37           Large polyvalent protein associated domain 37


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.4   5.5e-18   9.9e-15       1      41 [.       4      44 ..       4      45 .. 0.98
   2 ?   -0.3   0.0      0.55   9.9e+02       7      17 ..     105     115 ..     103     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 5.5e-18
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                   LD++D +IL++L e aR+++ae++ +v lS+++v rRv+r+
  gi|121638210|ref|YP_978434.1|  4 LDDTDERILAELAEHARATFAEIGHKVSLSAPAVKRRVDRM 44
                                   8***************************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.55
                  HTH_AsnC-type   7 kILeaLqedaR 17 
                                    +IL+ L +d R
  gi|121638210|ref|YP_978434.1| 105 AILHVLAHDMR 115
                                    69****99966 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   2.1e-17   3.7e-14      12      74 ..      79     140 ..      70     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.1e-17
                                    HHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg  12 qleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                    + +++++a  ++peVv++ +vtG  d +l+v ++d+++le+ l++ ++s  +v+r+e+++vl+
  gi|121638210|ref|YP_978434.1|  79 APDQLRAAWVNIPEVVSAATVTGTSDAILHVLAHDMRHLEAALER-IRSSADVERSESTVVLS 140
                                    5688999999*********************************99.****************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   4.8e-17   8.6e-14       1      48 []       4      51 ..       4      51 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.8e-17
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ld+td +IL +L +++r + +e+  ++ lS ++v+rr++r+ e+G+Ik
  gi|121638210|ref|YP_978434.1|  4 LDDTDERILAELAEHARATFAEIGHKVSLSAPAVKRRVDRMLESGVIK 51
                                   79*********************************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07   0.00024       7      48 ..      10      51 ..       4      59 .. 0.92
   2 ?   -0.6   0.0      0.71   1.3e+03      29      40 ..      94     105 ..      92     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                   +iL+ l+e+  ++ +e++ k+++s ++v r +dr+ + G i+
  gi|121638210|ref|YP_978434.1| 10 RILAELAEHARATFAEIGHKVSLSAPAVKRRVDRMLESGVIK 51
                                   79*************************************985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                                    S-HHHHHHHHHH CS
                           MarR  29 vskstvtrvldr 40 
                                    vs +tvt ++d+
  gi|121638210|ref|YP_978434.1|  94 VSAATVTGTSDA 105
                                    799****99986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   9.5e-08   0.00017       6      51 ..       7      50 ..       3      62 .. 0.90
   2 ?   -1.9   0.0       1.8   3.2e+03      23      23 ..     120     120 ..     100     145 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.5e-08
                                   HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                         MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                   ++ r+La+L+ + +   t +e+  +  ls +av r+++r+ + G +
  gi|121638210|ref|YP_978434.1|  7 TDERILAELAEHAR--ATFAEIGHKVSLSAPAVKRRVDRMLESGVI 50
                                   5669*********9..9***************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                    E CS
                         MarR_2  23 t 23 
                                    +
  gi|121638210|ref|YP_978434.1| 120 A 120
                                    3 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   5.3e-05     0.095       7      53 ..       5      51 ..       4      55 .. 0.94
   2 ?   -3.6   0.0       5.9   1.1e+04      12      26 ..      67      81 ..      66      85 .. 0.73
   3 ?    1.7   0.1      0.13   2.4e+02      22      49 ..     118     145 ..     110     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                   HHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                           TrmB  7 seyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                    +++ ++ + L ++ +at  ei +++ ++ + v + + ++++ G+++
  gi|121638210|ref|YP_978434.1|  5 DDTDERILAELAEHARATFAEIGHKVSLSAPAVKRRVDRMLESGVIK 51
                                   6789999*************************************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.9
                                   CHCHHHHHHCCCHHC CS
                           TrmB 12 kvYlaLlklgpatad 26
                                   ++Y+ + ++g+   d
  gi|121638210|ref|YP_978434.1| 67 EAYVQIFCHGRIAPD 81
                                   689998888876655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.13
                                    CCHHCHHCCCTTSSCHCHHHHHHHHHHC CS
                           TrmB  22 patadeiaeelgvprskvYevLrsLedk 49 
                                    +a  + i + ++v+rs    vL++L+d+
  gi|121638210|ref|YP_978434.1| 118 EAALERIRSSADVERSESTVVLSNLIDR 145
                                    5667889999999999999999999875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.025      14      55 ..      10      51 ..       5      54 .. 0.95
   2 ?   -0.8   0.1      0.89   1.6e+03       3      12 ..     106     115 ..     104     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   ril++La+ + +t++e+ + ++ls   + ++++ + e g ++
  gi|121638210|ref|YP_978434.1| 10 RILAELAEHARATFAEIGHKVSLSAPAVKRRVDRMLESGVIK 51
                                   8**************************************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.89
                                    HHHHHS-HHH CS
                         HTH_20   3 iaeALahPvR 12 
                                    i+++Lah +R
  gi|121638210|ref|YP_978434.1| 106 ILHVLAHDMR 115
                                    5555665554 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.063      29      58 ..      26      55 ..      11      60 .. 0.82
   2 ?   -3.5   0.0       7.5   1.3e+04       6      14 ..     103     111 ..     102     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                        DUF4777 29 vaerydlseeelkkvVkntLeaAvrhGFlk 58
                                   ++ +  ls   +k+ V+++Le +v++GF +
  gi|121638210|ref|YP_978434.1| 26 IGHKVSLSAPAVKRRVDRMLESGVIKGFTT 55
                                   45555688889*****************66 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.5
                        DUF4777   6 galvlealk 14 
                                    ++ +l++l+
  gi|121638210|ref|YP_978434.1| 103 SDAILHVLA 111
                                    688999985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.8e-05      0.05       2      46 ..       1      46 [.       1      47 [. 0.87
   2 ?   -2.5   0.1       2.2   3.9e+03      43      49 ..     119     125 ..     115     126 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                   HHHS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                     Sigma70_r4  2 LasLpererevlelrf.geglTleEIgerlgiSrerVrqiekrAlr 46
                                   +++L++ + ++l         T++EIg +  +S  +V+++  r l+
  gi|121638210|ref|YP_978434.1|  1 MDRLDDTDERILAELAeHARATFAEIGHKVSLSAPAVKRRVDRMLE 46
                                   678888888888777768889*******************999876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                                    HHHHHHH CS
                     Sigma70_r4  43 rAlrkLR 49 
                                     Al+++R
  gi|121638210|ref|YP_978434.1| 119 AALERIR 125
                                    4555554 PP

>> LPD37  Large polyvalent protein associated domain 37
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05      0.18      97     138 ..      12      55 ..      10      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                          LPD37  97 vatyAhnngkvF..iGDpaGlsdkAliRRtenMlSsALrhGttk 138
                                    +a++A+ +  +F  iG    ls  A++RR++ Ml s +  G t 
  gi|121638210|ref|YP_978434.1|  12 LAELAEHARATFaeIGHKVSLSAPAVKRRVDRMLESGVIKGFTT 55 
                                    688888888888779*********************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1208.62
//
Query:       gi|121638211|ref|YP_978435.1|  [L=282]
Description: hypothetical protein BCG_2346c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-50  169.5   7.9      1e-49  169.1   7.9    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   7.9   5.6e-54     1e-49       2     211 ..      28     245 ..      27     251 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 5.6e-54
                                    SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE....... CS
                           CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlitteg 80 
                                    +sv+h+l++++kl+++f ++++l+++p++vt+++++al+l+++ ++++p  +l +++++ +++l +g+l++++    + g
  gi|121638211|ref|YP_978435.1|  28 SSVIHDLWAGTKLLVVFGISVLLTFYPGWVTIGMMAALVLAAARIAHIPrGALPSVPRWLWIVLAIGFLTAAL----AGG 103
                                    79***********************************************99**********************....89* PP

                                    EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHH....HHHHS-HHHHHHHCCCSS--H........HHHHHHHHHHH CS
                           CbiQ  81 efvfagggqisitseGllrglllalRiltllsllll....lalTTppeeltsslerlgvPl........elalillLayR 148
                                    + v+a+gg    ++ G l g+l++lRi++l+++ll+    +++TT+++e+ +++ +lg+P         e+a++l+La+R
  gi|121638211|ref|YP_978435.1| 104 TPVVAVGG----VQLG-LGGALHFLRITALSVVLLAlgamVSWTTNVAEISPAVATLGRPFrvlripvdEWAVALALALR 178
                                    ********....****.9**********9999999899999*************************************** PP

                                    HHHHHHHHHHHHHHHHHHTTTTS......SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 149 fiflLleevqrikqAqklRlgds....klgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                    ++++L++e+q+++ A++lR  ++    k++++r++r+l++l+aa+++ +l+ra+++  A++aRG tg
  gi|121638211|ref|YP_978435.1| 179 AFPMLIDEFQVLYAARRLRPKRMppsrKARRQRHARELIDLLAAAITVTLRRADEMGDAITARGGTG 245
                                    ******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2145.27
//
Query:       gi|121638212|ref|YP_978436.1|  [L=697]
Description: transmembrane ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-44  149.7   0.0    8.4e-21   74.9   0.0    2.4  2  ABC_tran         ABC transporter
    2.7e-11   43.8  10.2    4.8e-06   26.6   0.0    3.7  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.5e-08   33.6   3.0       0.11   11.9   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    5.4e-08   32.5   0.5       0.01   15.6   0.1    2.6  2  AAA_29           P-loop containing region of AAA domain
    9.9e-07   29.5   0.3      0.027   15.0   0.1    2.1  2  AAA_23           AAA domain
    4.6e-06   27.1   9.2     0.0024   18.3   1.7    2.5  2  AAA_16           AAA ATPase domain
      5e-05   23.1   1.0        2.9    7.6   0.2    4.0  4  IstB_IS21        IstB-like ATP binding protein
    0.00012   21.5   0.1      0.071   12.5   0.0    2.4  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
    0.00013   22.3   5.0     0.0069   16.7   0.1    3.5  3  AAA_22           AAA domain
    0.00043   20.5   2.9       0.58   10.4   0.1    3.5  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0011   19.2   3.3       0.27   11.5   0.9    2.6  2  AAA_28           AAA domain
     0.0044   15.7   3.0       0.17   10.5   0.2    2.1  2  AAA_13           AAA domain
     0.0076   16.7   2.6        1.1    9.6   0.5    3.3  2  AAA              ATPase family associated with various cellul
     0.0087   15.8   0.5        3.8    7.2   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0098   15.8   5.5        1.3    8.9   0.1    3.1  3  NACHT            NACHT domain
  ------ inclusion threshold ------
       0.01   15.9   1.7      0.041   14.0   0.1    2.1  2  DUF87            Helicase HerA, central domain
      0.012   15.4   1.6        2.7    7.7   0.0    2.6  3  AAA_24           AAA domain
      0.015   15.5   6.4       0.58   10.3   0.3    3.4  2  AAA_33           AAA domain
      0.016   15.0   0.0       0.41   10.3   0.0    2.3  3  AAA_15           AAA ATPase domain
      0.021   14.2   0.4          6    6.2   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.03   13.4   0.1        3.5    6.6   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
      0.031   13.7   0.1          6    6.2   0.0    3.3  4  TniB             Bacterial TniB protein
      0.038   11.5   0.9        0.1   10.1   0.1    1.8  2  DUF3584          Protein of unknown function (DUF3584)
      0.052   13.2   0.2        1.7    8.3   0.0    2.9  3  Sigma54_activat  Sigma-54 interaction domain
      0.058   13.2   0.3         17    5.1   0.0    3.1  3  DEAD             DEAD/DEAH box helicase
      0.078   12.6  11.3       0.84    9.2   1.7    3.4  2  AAA_25           AAA domain
       0.12   12.7   1.7         30    4.9   0.3    3.0  3  AAA_19           AAA domain
       0.18   11.3   0.0         11    5.5   0.0    2.2  2  Ploopntkinase1   P-loop Nucleotide Kinase1
       0.19   10.6   1.4        1.3    7.8   0.1    2.5  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
        0.2   12.1   1.0         12    6.3   0.1    2.3  2  RNA_helicase     RNA helicase
       0.26   10.5   1.0         17    4.5   0.1    2.2  2  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   8.1e-23   4.7e-20       1     136 [.     268     401 ..     268     402 .. 0.85
   2 !   74.9   0.0   1.5e-23   8.4e-21       1     136 [.     497     634 ..     497     635 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 8.1e-23
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vsl++++ge +ai+G nG+GK+tL+ +lag   pt+G++   g+      l +l     vl++ ++   +++v++  
  gi|121638212|ref|YP_978436.1| 268 LREVSLDVRAGEHLAIIGANGSGKTTLMLILAGRA-PTSGTVDRPGTV----GLGKLGGTAVVLQHPESQVLGTRVADDv 342
                                    679******************************96.8*****433333....4456665555555445555566688889 PP

                                    ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                            ++++ ++ls++gl+ l+++       sLSgG+ qr+ala+al+++p +l++DE t
  gi|121638212|ref|YP_978436.1| 343 vwglplGTTADVGRLLSEVGLEALAERDT----GSLSGGELQRLALAAALAREPAMLIADEVT 401
                                    *****999999************999999....****************************98 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 1.5e-23
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren 79 
                                    l+++++ +++g  v i G nG+GKStL+ ++agl+ pt G  lldg++++e         ++  +q ++l+   + v   
  gi|121638212|ref|YP_978436.1| 497 LRDINFVVEQGDGVLIHGGNGSGKSTLAWIMAGLTIPTTGACLLDGRPTHE-----QVGAVALSFQAARLQLMRSrVD-L 570
                                    689********************************************9999.....4444555555544443332122.1 PP

                                    ..........HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ..........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               +++++++al+ +gl+  l ++++     +LSgGq +rv+la +l+++p+ l+lDEp 
  gi|121638212|ref|YP_978436.1| 571 evasaagfsaSEQDRVAAALTVVGLDPaLGARRI----DQLSGGQMRRVVLAGLLARAPRALILDEPL 634
                                    3555677777888889999999999883445555....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.7   8.8e-06    0.0051       3      21 ..     282     300 ..     281     321 .. 0.81
   2 ?   -1.3   0.1       2.6   1.5e+03     235     265 ..     372     399 ..     361     403 .. 0.82
   3 ?    4.7   0.3     0.039        23       4      16 ..     512     524 ..     510     537 .. 0.81
   4 !   26.6   0.0   8.4e-09   4.8e-06     229     298 ..     599     666 ..     559     668 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.8e-06
                         AAA_21   3 vliGpNgsGKSnLLdaldl 21 
                                    ++iG+NgsGK++L+ +l +
  gi|121638212|ref|YP_978436.1| 282 AIIGANGSGKTTLMLILAG 300
                                    79**************953 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDE 265
                                     +lS G ++ lal++al+r +   + l+ DE
  gi|121638212|ref|YP_978436.1| 372 GSLSGGELQRLALAAALAREP---AMLIADE 399
                                    67999999999*******988...7776666 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.039
                         AAA_21   4 liGpNgsGKSnLL 16 
                                    + G NgsGKS+L 
  gi|121638212|ref|YP_978436.1| 512 IHGGNGSGKSTLA 524
                                    5699*******96 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 8.4e-09
                         AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                     + + +++lS G+ r   l+ +l+ra+   + l++DEp +gL+ + +r ll+ll++l+r +g  v++++H+
  gi|121638212|ref|YP_978436.1| 599 LGARRIDQLSGGQMRRVVLAGLLARAP---RALILDEPLAGLDAASQRGLLRLLEDLRRaRGLTVVVVSHD 666
                                    566778999***999989999999999...89**************************************7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0012      0.71      26      41 ..     280     295 ..     269     298 .. 0.85
   2 !   11.9   0.0   0.00019      0.11     121     212 ..     352     447 ..     348     454 .. 0.74
   3 ?    4.4   0.1     0.039        22      28      40 ..     511     523 ..     501     528 .. 0.87
   4 ?    5.2   0.0     0.021        12     135     199 ..     605     667 ..     553     680 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                    EEEEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnll 41 
                                    + ai+G+NGSGK+ l+
  gi|121638212|ref|YP_978436.1| 280 HLAIIGANGSGKTTLM 295
                                    679**********986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                                    HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEE CS
                                    xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          SMC_N 121 kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQf 192
                                    ++v +ll+++g++        +LSgGe + +ala  +A    +  ++ + De+    D++ + ++  +l   ++++++ +
  gi|121638212|ref|YP_978436.1| 352 ADVGRLLSEVGLEALaerdtgSLSGGELQRLALAAALA----REPAMLIADEVTTMVDQQGRDALLAVLSglTQRHRTAL 427
                                    5666666666665544555558*****87666665544....44567889*******************95555556788 PP

                                    EEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 193 ivislreemlekadklvgvt 212
                                    + i++ ++    ad+++ ++
  gi|121638212|ref|YP_978436.1| 428 VHITHYDNEADSADRTLSLS 447
                                    88999999999999988766 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.039
                                    EEEESTTSSHHHH CS
                                    xxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnl 40 
                                     i G NGSGKs l
  gi|121638212|ref|YP_978436.1| 511 LIHGGNGSGKSTL 523
                                    699********87 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.021
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre 199
                                    ++LSgG+   v la l+A     p++l +lDe  a LD++  + + +ll+  +      ++v+s++ 
  gi|121638212|ref|YP_978436.1| 605 DQLSGGQMRRVVLAGLLA---RAPRAL-ILDEPLAGLDAASQRGLLRLLEDLRRArgLTVVVVSHDF 667
                                    49*****99988888876...456665.89*******************977655336677777764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     4e-05     0.023      17      39 ..     273     295 ..     266     301 .. 0.79
   2 !   15.6   0.1   1.8e-05      0.01      22      38 ..     506     523 ..     492     536 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                         AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                    ++++  +   ++G++GsGK+Tl+
  gi|121638212|ref|YP_978436.1| 273 LDVRAGEHLAIIGANGSGKTTLM 295
                                    5555444899***********97 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                         AAA_29  22 kg.atlltGpsGsGKSTl 38 
                                    +g  +l+ G +GsGKSTl
  gi|121638212|ref|YP_978436.1| 506 QGdGVLIHGGNGSGKSTL 523
                                    3347*************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00029      0.17      23      36 ..     282     295 ..     268     300 .. 0.87
   2 !   15.0   0.1   4.6e-05     0.027      15      36 ..     500     524 ..     496     533 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                         AAA_23  23 lItGpNGaGKTTil 36 
                                    +I+G NG+GKTT++
  gi|121638212|ref|YP_978436.1| 282 AIIGANGSGKTTLM 295
                                    79**********98 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.6e-05
                         AAA_23  15 idF....skgltlItGpNGaGKTTil 36 
                                    i+F    ++g+ lI+G NG+GK+T+ 
  gi|121638212|ref|YP_978436.1| 500 INFvveqGDGV-LIHGGNGSGKSTLA 524
                                    66666645555.************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.0   0.00022      0.13      13     139 ..     269     428 ..     262     457 .. 0.53
   2 !   18.3   1.7   4.1e-06    0.0024      21     169 ..     506     660 ..     495     663 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                         AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekd...............ggiflrgkcdqlesaipy..sa.laq 74 
                                    +++  +vr+g  e + ++G+ G+GK++l+  l+ ++ ++               g  ++ ++ ++   +++   ++ +  
  gi|121638212|ref|YP_978436.1| 269 REVSLDVRAG--EHLAIIGANGSGKTTLMLILAGRAPTSgtvdrpgtvglgklgGTAVVLQHPESQVLGTRVadDVvWGL 346
                                    4444467777..79***************999999999888888888777777544444444444422222222111333 PP

                         AAA_16  75 alareellrqlldeaesaeleawrekleeala....................avpelagaea......srllellkrlla 128
                                     l +   +  ll+e     lea +e+ +++l+                    +++      +      ++ +++l + l+
  gi|121638212|ref|YP_978436.1| 347 PLGTTADVGRLLSE---VGLEALAERDTGSLSggelqrlalaaalarepamlIAD------EvttmvdQQGRDALLAVLS 417
                                    33333333333333...33333333333333333332332222233333333333......0344444777777777775 PP

                         AAA_16 129 llsrderplvl 139
                                     l++++r+ ++
  gi|121638212|ref|YP_978436.1| 418 GLTQRHRTALV 428
                                    55554554444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.1e-06
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellr.alekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                    +g    vl++G  G+GKs+l++  +   + ++g+ +l g+ ++ + +   +al  ++ar +l+r   d + ++++  +++
  gi|121638212|ref|YP_978436.1| 506 QG--DGVLIHGGNGSGKSTLAWIMAGlTIPTTGACLLDGRPTHEQVG--AVALSFQAARLQLMRSRVDLEVASAA-GFSA 580
                                    33..57***************98885356666666688888888444..24455555588999999988555333.3333 PP

                         AAA_16 100 kleeala...avpelagaea.....srllellkrll.allsrderplvlvlDd.lqwadeaslqllaaLlrlles.kpll 168
                                      ++++a    v  l++a+      +    +++r + a l   + p  l+lD+ l  +d+as+  l  Ll++l + + l+
  gi|121638212|ref|YP_978436.1| 581 SEQDRVAaalTVVGLDPALGarridQLSGGQMRRVVlAGLLA-RAPRALILDEpLAGLDAASQRGLLRLLEDLRRaRGLT 659
                                    334434436634444444444444422233445555444444.3457888884366777777777555554444424665 PP

                         AAA_16 169 v 169
                                    v
  gi|121638212|ref|YP_978436.1| 660 V 660
                                    4 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.019        11      44      73 ..     275     304 ..     254     308 .. 0.80
   2 ?    4.3   0.0     0.052        30     104     145 ..     387     427 ..     375     443 .. 0.79
   3 !    7.6   0.2     0.005       2.9      37      68 ..     496     528 ..     487     537 .. 0.83
   4 ?   -0.0   0.0       1.1   6.2e+02     109     152 ..     625     668 ..     601     679 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavr 73 
                                    +++ e ++++G  G GK+ l   l+ +a +
  gi|121638212|ref|YP_978436.1| 275 VRAGEHLAIIGANGSGKTTLMLILAGRAPT 304
                                    788999**************9988877755 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.052
                      IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                                    +   ++++li D++ +  +dq+ +  l+ v++   +r+ +++
  gi|121638212|ref|YP_978436.1| 387 ALAREPAMLIADEVTT-MVDQQGRDALLAVLSGLTQRHRTAL 427
                                    344556999****975.69*************9999877655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.005
                      IstB_IS21  37 eLatlsfi.ekkenivllGpsGvGKshlaialg 68 
                                    +L+  +f+ e+ +++++ G+ G GKs la  ++
  gi|121638212|ref|YP_978436.1| 496 ALRDINFVvEQGDGVLIHGGNGSGKSTLAWIMA 528
                                    6777788527889****************8776 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.1
                      IstB_IS21 109 vdllilDdlgllpldqaeaellfeviekrye.rrsiiitsnlpfa 152
                                    ++ lilD+  l  ld a+++ l++++e+    r  +++     fa
  gi|121638212|ref|YP_978436.1| 625 PRALILDE-PLAGLDAASQRGLLRLLEDLRRaRGLTVVVVSHDFA 668
                                    47799999.58899999999****999854404445555555555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00012     0.071      31      56 ..     271     295 ..     250     304 .. 0.84
   2 !    6.3   0.1    0.0091       5.3      42      55 ..     510     523 ..     481     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                    EEEEGGGS-.SEEEE--TTSSHHHHH CS
                   FtsK_SpoIIIE  31 lvldlkkmashllvaGatgsGKStal 56 
                                    + ld +  + hl ++Ga gsGK+t +
  gi|121638212|ref|YP_978436.1| 271 VSLDVRAGE-HLAIIGANGSGKTTLM 295
                                    566777788.*************964 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0091
                                    EEEE--TTSSHHHH CS
                   FtsK_SpoIIIE  42 llvaGatgsGKSta 55 
                                    +l++G+ gsGKSt 
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTL 523
                                    7***********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.2e-05    0.0069       5     125 ..     278     427 ..     275     436 .. 0.76
   2 ?    4.0   0.2     0.096        56       8      22 ..     510     524 ..     504     531 .. 0.88
   3 ?    1.5   0.1      0.57   3.3e+02      72     127 ..     606     662 ..     553     673 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..................erpevvfvtlpsst......sskdllrel 60 
                                      +l+++G  G+GKTtl+  l+ +++     ++                  ++++v+   ++ +       + +    +l
  gi|121638212|ref|YP_978436.1| 278 GEHLAIIGANGSGKTTLMLILAGRAPTSGTVDRpgtvglgklggtavvlqhPESQVLGTRVADDVvwglplGTTADVGRL 357
                                    5689*********************98888888****************9644444444444444555666778888999 PP

                         AAA_22  61 lralglelkaerlsseell.ealeqalrarav...ielliiDEaqhlr....seealeeLrsllnlsrkgvql 125
                                    l+++gle+ a + ++  l    l++ + a+a    +++li DE+  +     ++++l  L+ l    r+ ++l
  gi|121638212|ref|YP_978436.1| 358 LSEVGLEALA-ERDTGSLSgGELQRLALAAALarePAMLIADEVTTMVdqqgRDALLAVLSGLTQ--RHRTAL 427
                                    9999999999.6666666669999999999999999*******9996555433666666655555..555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.096
                         AAA_22   8 lvvtGesGtGKTtll 22 
                                    ++++G  G+GK+tl+
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLA 524
                                    689**********97 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.57
                         AAA_22  72 rlsseellealeqalraravielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                     ls  ++++ +   l ara  ++li+DE    l+   +  +l+ L +l      g+++++
  gi|121638212|ref|YP_978436.1| 606 QLSGGQMRRVVLAGLLARAP-RALILDEPLAgLDaasQRGLLRLLEDLRR--ARGLTVVV 662
                                    55666777777777888888.99999997777877643555555555555..55555544 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.5     0.007         4      26      51 ..     367     389 ..     354     417 .. 0.74
   2 !   10.4   0.1     0.001      0.58      62      89 ..     623     650 ..     598     651 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaala 51 
                                     +r++g+lSGGe q l   alaaala
  gi|121638212|ref|YP_978436.1| 367 AERDTGSLSGGELQRL---ALAAALA 389
                                    6899*********765...5555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                        SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                    +a+r ++LDE  ++lD+ s++ ll+lle
  gi|121638212|ref|YP_978436.1| 623 RAPRALILDEPLAGLDAASQRGLLRLLE 650
                                    5799*********************997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.9   0.00046      0.27       3      22 ..     282     301 ..     280     322 .. 0.81
   2 !    7.2   0.1    0.0093       5.4       2      20 ..     510     528 ..     509     592 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00046
                         AAA_28   3 vitGgestGKTtlleaLaar 22 
                                    +i+G+ ++GKTtl+  La r
  gi|121638212|ref|YP_978436.1| 282 AIIGANGSGKTTLMLILAGR 301
                                    89***************976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0093
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    + i Gg ++GK+tl+  +a
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLAWIMA 528
                                    6899**********97777 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.2    0.0088       5.1      21      37 ..     283     299 ..     281     307 .. 0.85
   2 !   10.5   0.2    0.0003      0.17      20      40 ..     511     531 ..     509     538 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0088
                         AAA_13  21 iYGwNGaGKTtLSrllr 37 
                                    i G+NG+GKTtL  +l+
  gi|121638212|ref|YP_978436.1| 283 IIGANGSGKTTLMLILA 299
                                    67**********87776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0003
                         AAA_13  20 liYGwNGaGKTtLSrllrsle 40 
                                    li G NG+GK+tL+++++ l+
  gi|121638212|ref|YP_978436.1| 511 LIHGGNGSGKSTLAWIMAGLT 531
                                    79**************99885 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.5     0.002       1.1       3     120 ..     283     442 ..     281     449 .. 0.62
   2 ?    4.3   0.1      0.09        52       1      19 [.     510     528 ..     510     560 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                                    EESSTTSSHHHHHHHHHHHHTHE..........................................EEEEETTTCSSS... CS
                            AAA   3 lyGppGtGKTllakavakelgve..........................................fleisgsellsk... 37 
                                    ++G  G GKT+l+  +a  + ++                                          +              
  gi|121638212|ref|YP_978436.1| 283 IIGANGSGKTTLMLILAGRAPTSgtvdrpgtvglgklggtavvlqhpesqvlgtrvaddvvwglpL----------Gtta 352
                                    68999************9973222333445555445555555444444444444444444444440..........0444 PP

                                    .....................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                            AAA  38 .....................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                                         + g   ++++   + a+   +p  l+ DE+  ++ ++            ++Ll++l+g+
  gi|121638212|ref|YP_978436.1| 353 dvgrllsevglealaerdtgsLSGGELQRLALAAALAR---EPAMLIADEVTTMVDQQ----------GRDALLAVLSGL 419
                                    44444445555555556653333333333333333333...4789999******9988..........7899******** PP

                                    TTSSSTEEEEEEESSGGGSTHHHH CS
                            AAA  97 kkkeskvivigatnrpdkldpall 120
                                    +++ +++ ++ +t++ ++ d+a +
  gi|121638212|ref|YP_978436.1| 420 TQR-HRTALVHITHYDNEADSADR 442
                                    996.66999999999888888766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.09
                                    EEEESSTTSSHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakava 19 
                                    vl++G  G GK++la  +a
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLAWIMA 528
                                    799***********98776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.014         8      32      55 ..     277     300 ..     268     320 .. 0.89
   2 !    7.2   0.0    0.0066       3.8      31      54 ..     505     528 ..     496     543 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                         RuvB_N  32 aldhvllyGpPGlGkttlakiiak 55 
                                    a +h+ ++G+ G Gkttl  i+a 
  gi|121638212|ref|YP_978436.1| 277 AGEHLAIIGANGSGKTTLMLILAG 300
                                    5589*****************985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0066
                         RuvB_N  31 ealdhvllyGpPGlGkttlakiia 54 
                                    e+ d vl++G  G Gk+tla i+a
  gi|121638212|ref|YP_978436.1| 505 EQGDGVLIHGGNGSGKSTLAWIMA 528
                                    56799*****************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0023       1.3       3      19 ..     281     297 ..     279     306 .. 0.85
   2 ?   -1.0   0.0       2.5   1.4e+03      85     130 ..     395     435 ..     354     461 .. 0.70
   3 !    8.0   0.4    0.0044       2.6       3      20 ..     510     526 ..     508     538 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                                    EEEEC-TTTCHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqk 19 
                                    +++ G++GsGKTtL+  
  gi|121638212|ref|YP_978436.1| 281 LAIIGANGSGKTTLMLI 297
                                    689***********965 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                                    EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECC CS
                          NACHT  85 lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpr 130
                                    li D +  +v+   q+++ ++  +Ls+l ++   ++a + +t   +
  gi|121638212|ref|YP_978436.1| 395 LIADEVTTMVD---QQGRDALLAVLSGLTQR--HRTALVHITHYDN 435
                                    55555555554...44668888888888888..5555555554444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0044
                                    EEEEC-TTTCHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                    v+++G +GsGK+tL+ ++
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLA-WI 526
                                    89***********96.45 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     7e-05     0.041      13      43 ..     270     298 ..     263     307 .. 0.85
   2 ?    0.6   0.2      0.89   5.2e+02      27      41 ..     511     525 ..     508     533 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-05
                          DUF87  13 pvyldlnklvtrHlAilgsTGsGKSntvavL 43 
                                    +v+ld+ ++  +HlAi+g  GsGK++++ +L
  gi|121638212|ref|YP_978436.1| 270 EVSLDV-RA-GEHLAIIGANGSGKTTLMLIL 298
                                    488888.55.8****************9877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.89
                          DUF87  27 AilgsTGsGKSntva 41 
                                    +i g  GsGKS+++ 
  gi|121638212|ref|YP_978436.1| 511 LIHGGNGSGKSTLAW 525
                                    678889******985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0047       2.7       5      22 ..     281     298 ..     277     311 .. 0.85
   2 ?    5.9   0.2     0.016       9.4       5      22 ..     510     527 ..     507     542 .. 0.86
   3 ?   -2.3   0.0       5.3   3.1e+03     112     130 ..     646     665 ..     640     666 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0047
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    ++i+G +g+GKTtl++ l
  gi|121638212|ref|YP_978436.1| 281 LAIIGANGSGKTTLMLIL 298
                                    79************9876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +li G +g+GK+tla+ +
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLAWIM 527
                                    799************987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.3
                         AAA_24 112 rrllkklqelrk.nvifiah 130
                                     rll++l+ +r+ +v++++h
  gi|121638212|ref|YP_978436.1| 646 LRLLEDLRRARGlTVVVVSH 665
                                    566777777777******99 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.1     0.023        13       4      22 ..     283     301 ..     281     442 .. 0.77
   2 ?   10.3   0.3     0.001      0.58       2      20 ..     510     528 ..     510     667 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                         AAA_33   4 lvGlpGsGKstlaerllkk 22 
                                    ++G++GsGK+tl   l+ +
  gi|121638212|ref|YP_978436.1| 283 IIGANGSGKTTLMLILAGR 301
                                    69*********98666555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                         AAA_33   2 vllvGlpGsGKstlaerll 20 
                                    vl++G +GsGKstla+ ++
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLAWIMA 528
                                    789************9765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00071      0.41      25      43 ..     280     298 ..     267     299 .. 0.75
   2 ?    1.8   0.1      0.28   1.6e+02      27      40 ..     511     524 ..     501     529 .. 0.85
   3 ?   -3.1   0.0       8.6     5e+03     294     351 ..     604     652 ..     603     665 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00071
                         AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +iG+N+sGK++++ +l
  gi|121638212|ref|YP_978436.1| 280 HLAIIGANGSGKTTLMLIL 298
                                    678************9876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                         AAA_15  27 vliGkNnsGKSsil 40 
                                    ++ G N+sGKS+++
  gi|121638212|ref|YP_978436.1| 511 LIHGGNGSGKSTLA 524
                                    5669********97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.6
                         AAA_15 294 lnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                                    +++ + G++r ++l+ l+++a +          l+++EP a L    q+ l +ll +l
  gi|121638212|ref|YP_978436.1| 604 IDQLSGGQMRRVVLAGLLARAPRA---------LILDEPLAGLDAASQRGLLRLLEDL 652
                                    68889999******9999999999.........8899998888888888888888776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1      0.01         6      19      43 ..     276     299 ..     262     309 .. 0.70
   2 ?    5.9   0.0     0.013       7.5      22      52 ..     507     537 ..     489     563 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                   Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlp 43 
                                     aG+ +l ++G+ GsGKt l   l+
  gi|121638212|ref|YP_978436.1| 276 RAGE-HLAIIGANGSGKTTLMLILA 299
                                    3555.5899*********9876665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                   Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplsee 52 
                                    g  +l+ G  GsGK+ la  +++l  p + +
  gi|121638212|ref|YP_978436.1| 507 GDGVLIHGGNGSGKSTLAWIMAGLTIPTTGA 537
                                    556899**************99998777665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.028        16     123     153 ..     272     302 ..     249     308 .. 0.75
   2 ?    6.6   0.0     0.006       3.5     122     149 ..     500     527 ..     470     540 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.028
                          T2SSE 123 rkavrerglilvsGgTgsGKttllyallkei 153
                                    +  vr+   + + G+ gsGKttl+ +l    
  gi|121638212|ref|YP_978436.1| 272 SLDVRAGEHLAIIGANGSGKTTLMLILAGRA 302
                                    5556777778889*********998776655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.006
                          T2SSE 122 lrkavrerglilvsGgTgsGKttllyal 149
                                    ++  v++   +l+ Gg gsGK+tl+ ++
  gi|121638212|ref|YP_978436.1| 500 INFVVEQGDGVLIHGGNGSGKSTLAWIM 527
                                    55556666789************98665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.71   4.1e+02      36      52 ..     279     295 ..     266     307 .. 0.86
   2 ?    6.2   0.0      0.01         6      75     159 ..     346     429 ..     321     435 .. 0.83
   3 ?   -2.9   0.0       6.5   3.7e+03      37      51 ..     509     523 ..     505     525 .. 0.88
   4 ?    2.0   0.0       0.2   1.1e+02     104     160 ..     609     663 ..     597     669 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.71
                           TniB  36 pnlllvGdsnnGKtmiv 52 
                                    ++l ++G    GKt+++
  gi|121638212|ref|YP_978436.1| 279 EHLAIIGANGSGKTTLM 295
                                    6899**********986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                           TniB  75 vqappkpdekrlyaai.LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnel 153
                                    + + +++d  rl +++ Leal ++   + +  +l++ +l+   + ++ +Li DE+  ++   ++ + ++l++l  L+++ 
  gi|121638212|ref|YP_978436.1| 346 LPLGTTADVGRLLSEVgLEALAERDTGSLSGGELQRLALAAALAREPAMLIADEVTTMV--DQQGRDALLAVLSGLTQRH 423
                                    556678888888888889999999888888899999999999999*************9..6777889999999998888 PP

                           TniB 154 kipivl 159
                                    + ++v 
  gi|121638212|ref|YP_978436.1| 424 RTALVH 429
                                    888775 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.5
                           TniB  37 nlllvGdsnnGKtmi 51 
                                     +l++G    GK+++
  gi|121638212|ref|YP_978436.1| 509 GVLIHGGNGSGKSTL 523
                                    689**********98 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.2
                           TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                      ++++ vl+ l +  +r Li+DE    l   a +qr +l +l  L +   +++v+v
  gi|121638212|ref|YP_978436.1| 609 GGQMRRVVLAGLLARAPRALILDEPLAGL--DAASQRGLLRLLEDLRRARGLTVVVV 663
                                    5678889999999999********87777..78999999999999999999999887 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00018       0.1      14      35 ..     275     296 ..     270     299 .. 0.83
   2 ?   -0.5   0.1      0.27   1.6e+02      18      33 ..     508     523 ..     503     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                        DUF3584  14 ldldghtnieGtNaaGKTtLlr 35 
                                    ++  +h  i G+N++GKTtL+ 
  gi|121638212|ref|YP_978436.1| 275 VRAGEHLAIIGANGSGKTTLML 296
                                    4556999*************95 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.27
                        DUF3584  18 ghtnieGtNaaGKTtL 33 
                                    +++ i G N++GK tL
  gi|121638212|ref|YP_978436.1| 508 DGVLIHGGNGSGKSTL 523
                                    7899***********9 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.1   6.1e+02      13      38 ..     269     294 ..     261     303 .. 0.77
   2 ?    8.3   0.0    0.0029       1.7       9      42 ..     494     527 ..     488     537 .. 0.87
   3 ?   -0.4   0.0       1.4   8.1e+02      88     119 ..     620     651 ..     613     656 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                                    HHHHHHCTSSS-EEEECSTTSSHHHH CS
                Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKell 38 
                                    ++++  ++   ++ i G +G+GK++l
  gi|121638212|ref|YP_978436.1| 269 REVSLDVRAGEHLAIIGANGSGKTTL 294
                                    55555566677899*********976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0029
                                    HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                Sigma54_activat   9 kelleqikkvaktdlsvlitGesGtGKellarai 42 
                                    k++l+ i+ v+++   vli+G +G+GK++la  +
  gi|121638212|ref|YP_978436.1| 494 KTALRDINFVVEQGDGVLIHGGNGSGKSTLAWIM 527
                                    677889999999999***************9766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                                    HHHHTTTSEEEEET.GGGS-HHHHHHHHHHHHH CS
                Sigma54_activat  88 lfekadgGtlfLDe.igelplelQekLlrvlqe 119
                                    l+ +a    l LDe ++ l+++ Q  Llr+l++
  gi|121638212|ref|YP_978436.1| 620 LLARAPRA-LILDEpLAGLDAASQRGLLRLLED 651
                                    55555554.667776899*************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.093        54      13      35 ..     277     299 ..     265     325 .. 0.85
   2 ?    0.5   0.0      0.76   4.4e+02     123     151 ..     393     421 ..     374     431 .. 0.83
   3 ?    5.1   0.0      0.03        17      13      39 ..     506     532 ..     490     663 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.093
                                    TTCEEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlaflipv 35 
                                     g+++ + ++ GsGKT+ +li +
  gi|121638212|ref|YP_978436.1| 277 AGEHLAIIGANGSGKTTLMLILA 299
                                    688999999********999865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.76
                                    EEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldqgfsdfinrilnqlpq 151
                                     +l+ DE+ ++ dq+ +d + ++l+ l q
  gi|121638212|ref|YP_978436.1| 393 AMLIADEVTTMVDQQGRDALLAVLSGLTQ 421
                                    689***********999999998888855 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.03
                                    TTCEEEEEESTTSSHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlaflipvlqiv 39 
                                    +g+ vl+++  GsGK++ ++i +  ++
  gi|121638212|ref|YP_978436.1| 506 QGDGVLIHGGNGSGKSTLAWIMAGLTI 532
                                    7889***********999998875444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7    0.0015      0.84      29      87 ..     275     327 ..     250     437 .. 0.56
   2 ?    6.3   2.2     0.011       6.3      32     188 ..     506     665 ..     500     666 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                         AAA_25  29 llpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                    + +age  +++Ga g+GKttl l la    t        + ++g+V +  + +++  l+
  gi|121638212|ref|YP_978436.1| 275 V-RAGEHLAIIGANGSGKTTLMLILAGRAPTSGT-----VDRPGTVGLGKLGGTAVVLQ 327
                                    4.6899999**************99977653221.....22444444444444444333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                         AAA_25  32 agelallaGapgtGKttlaldlalava..tGkpwlg..pvapeqgkVlyvsaEdsedelr.rRlravgeal......... 97 
                                     g+ +l+ G  g+GK+tla  +a  +   tG  +l+  p  +eq+  + +s+  ++ +l   R+     ++         
  gi|121638212|ref|YP_978436.1| 506 QGDGVLIHGGNGSGKSTLAWIMAGLTIptTGACLLDgrP-THEQVGAVALSFQAARLQLMrSRVD---LEVasaagfsas 581
                                    66778999***********99987777889998888644.3599999999988886333313333...222334577765 PP

                         AAA_25  98 ...rddarllvldlagveslpLfakdrggtlltadvda.leaaieevegvrlvviDplsralggdensnsdvgalveale 173
                                       r  a l+v+ l    +  L  ++r ++l  +++++ + a + +   +r +++D    + g d  s++   +l+   e
  gi|121638212|ref|YP_978436.1| 582 eqdRVAAALTVVGL----DPAL-GARRIDQLSGGQMRRvVLAGLLA-RAPRALILDE--PLAGLDAASQRGLLRLL---E 650
                                    33333333333333....3333.33344444333333303444444.3478888885..33444444444444444...4 PP

                         AAA_25 174 riarrtgaavllvhH 188
                                    +++r+ g +v++v H
  gi|121638212|ref|YP_978436.1| 651 DLRRARGLTVVVVSH 665
                                    444456888888888 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.051        30      10      28 ..     278     296 ..     270     318 .. 0.83
   2 ?    0.1   0.0       1.6   9.5e+02      97     126 ..     385     417 ..     320     428 .. 0.76
   3 ?    4.7   0.0     0.061        35      11      55 ..     508     559 ..     500     661 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.051
                         AAA_19  10 ekvllvtaGpGtGKTrvlk 28 
                                     ++l++++  G+GKT+++ 
  gi|121638212|ref|YP_978436.1| 278 GEHLAIIGANGSGKTTLML 296
                                    57899**********9865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                         AAA_19  97 ekklqeee.llivDEf.qdvd.elqyrLlkall 126
                                       l +e  +li DE+  +vd +   +Ll  l 
  gi|121638212|ref|YP_978436.1| 385 AAALAREPaMLIADEVtTMVDqQGRDALLAVLS 417
                                    4455455559999**735888777777776665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.061
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkp.......eeillvaftgrAa 55 
                                    + +l+ +G G+GK+++   +  l + ++g  +       e++ +va+  +Aa
  gi|121638212|ref|YP_978436.1| 508 DGVLIHGGNGSGKSTLAWIMAGLTIPTTGACLldgrpthEQVGAVALSFQAA 559
                                    5689*********987555554444444443355555556666666666666 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.018        11      16      53 ..     277     314 ..     269     325 .. 0.85
   2 ?    3.3   0.0      0.09        52      16      38 ..     506     528 ..     501     546 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                 Ploopntkinase1  16 rgelyyvkgsngsgkstvpsylaekdpeayvvtldgkv 53 
                                     ge   + g+ngsgk+t+   la + p + +v + g v
  gi|121638212|ref|YP_978436.1| 277 AGEHLAIIGANGSGKTTLMLILAGRAPTSGTVDRPGTV 314
                                    47888899*******************99999887776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                 Ploopntkinase1  16 rgelyyvkgsngsgkstvpsyla 38 
                                    +g+   ++g ngsgkst+   +a
  gi|121638212|ref|YP_978436.1| 506 QGDGVLIHGGNGSGKSTLAWIMA 528
                                    56777899*********987776 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0023       1.3      16      34 ..     279     297 ..     268     306 .. 0.85
   2 ?    0.5   0.2      0.38   2.2e+02      17      31 ..     509     523 ..     502     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalek 34 
                                    +h++i+G+ GsGKt+ +  
  gi|121638212|ref|YP_978436.1| 279 EHLAIIGANGSGKTTLMLI 297
                                    7*************99865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.38
                  TrwB_AAD_bind  17 hilivGttGsGKtqa 31 
                                     +li G+ GsGK++ 
  gi|121638212|ref|YP_978436.1| 509 GVLIHGGNGSGKSTL 523
                                    589*********985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.097        56       3      19 ..     283     299 ..     281     317 .. 0.85
   2 ?    6.3   0.1     0.021        12       1      18 [.     510     527 ..     510     538 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.097
                   RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                    + G++g GK+tl+  La
  gi|121638212|ref|YP_978436.1| 283 IIGANGSGKTTLMLILA 299
                                    88**********98876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                   RNA_helicase   1 iwlyGpsgeGKStlakeL 18 
                                    ++++G +g GKStla  +
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLAWIM 527
                                    689***********9875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.029        17      23      37 ..     281     295 ..     270     302 .. 0.89
   2 ?    4.4   0.1     0.032        19      23      37 ..     510     524 ..     500     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                                    EEEEESTTSSHHHHH CS
                         NB-ARC  23 valvGmgGvGKttla 37 
                                    +a+ G  G+GKttl+
  gi|121638212|ref|YP_978436.1| 281 LAIIGANGSGKTTLM 295
                                    89***********98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.032
                                    EEEEESTTSSHHHHH CS
                         NB-ARC  23 valvGmgGvGKttla 37 
                                    v ++G  G+GK+tla
  gi|121638212|ref|YP_978436.1| 510 VLIHGGNGSGKSTLA 524
                                    78************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 4506.55
//
Query:       gi|121638213|ref|YP_978437.1|  [L=163]
Description: hypothetical protein BCG_2348 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-16   59.6   0.0    4.6e-16   58.5   0.0    1.6  1  MarR      MarR family
    2.4e-12   46.5   0.8    2.4e-12   46.5   0.8    2.5  3  MarR_2    MarR family
    7.8e-09   35.9   0.1    1.5e-08   35.0   0.1    1.5  1  HTH_27    Winged helix DNA-binding domain
    0.00021   21.1   0.0    0.00056   19.7   0.0    1.7  2  HxlR      HxlR-like helix-turn-helix
    0.00076   19.5   1.0     0.0017   18.4   0.2    2.1  2  HTH_20    Helix-turn-helix domain
     0.0038   17.1   0.0     0.0058   16.5   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.035   13.7   0.0    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   1.8e-19   4.6e-16       2      59 .]      44     101 ..      43     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.8e-19
                                    -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                           MarR   2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59 
                                     ++q ++L++++ qg++++ +La   ++s++t+t++++rLe++Gl++R+ +p+D R+v
  gi|121638213|ref|YP_978437.1|  44 PAAQARLLATIEAQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAV 101
                                    57899***************************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.6   6.7e+03      12      45 ..      26      34 ..      22      38 .. 0.50
   2 !   46.5   0.8   9.4e-16   2.4e-12       3      62 .]      43     100 ..      41     100 .. 0.97
   3 ?   -0.5   0.1      0.45   1.1e+03       4      12 ..     132     140 ..     128     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                   HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                         MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrL 45
                                   a+++                         +l+rL
  gi|121638213|ref|YP_978437.1| 26 AVVA-------------------------RLNRL 34
                                   4444.........................44444 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 9.4e-16
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62 
                                    l+ aqar+La + + ++   ++g+la+  + s+++++  ++rL++aGLv+r+++p+D+Ra
  gi|121638213|ref|YP_978437.1|  43 LPAAQARLLATIEAQGE--ARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARA 100
                                    789*************9..9***************************************7 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.45
                                    -HHHHHHHH CS
                         MarR_2   4 tpaqarvLa 12 
                                    +pa++rvLa
  gi|121638213|ref|YP_978437.1| 132 PPADRRVLA 140
                                    677777775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1     6e-12   1.5e-08       4      68 .]      46     109 ..      43     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 6e-12
                         HTH_27   4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                     qa +L +i+  ++++++ dl+ +  +++ ++   +++L+ +GLv+rt+d+ d r++r+r+T++G
  gi|121638213|ref|YP_978437.1|  46 AQARLLATIE-AQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEG 109
                                    6788999999.99***************************************************9 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6   4.1e+03      69      86 ..      21      38 ..      16      41 .. 0.67
   2 !   19.7   0.0   2.2e-07   0.00056      15      70 ..      56     111 ..      47     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                   GGGGHHHHHHHHHHHHHH CS
                           HxlR 69 Grslepvlqelkkwgeey 86
                                   G +l +v++ l+ ++++ 
  gi|121638213|ref|YP_978437.1| 21 GADLLAVVARLNRLATQR 38
                                   677777777777766654 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.2e-07
                                    TTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCG.G CS
                           HxlR  15 lkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekG.r 70 
                                     +g+ R ++l++ + ++sq +++++ r+Le  gl+ r++ p     v  ++t++G r
  gi|121638213|ref|YP_978437.1|  56 AQGEARIGDLAA-VDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEGiR 111
                                    35999****975.67***********************************9999934 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   6.7e-07    0.0017      23      57 ..      47      92 ..      23      95 .. 0.72
   2 ?   -1.4   0.0      0.96   2.5e+03      14      24 ..     144     154 ..     133     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.7e-07
                                   TTB-HHHHHHHHT...........S-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 23 egltaselaerld...........lskntlsyHLrvLeeagLvevv 57
                                   +++ ++ + ++++           +s+ t+  ++r Le+agLv+++
  gi|121638213|ref|YP_978437.1| 47 QARLLATIEAQGEarigdlaavdhCSQPTMTTQVRRLEDAGLVTRT 92
                                   444444444444222333444445*******************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.96
                                    HHHHHHSTCTT CS
                         HTH_20  14 rilraLaraeg 24 
                                    ++lr L + ++
  gi|121638213|ref|YP_978437.1| 144 DVLRRLLDHAA 154
                                    56666644444 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.3e-06    0.0058      12      46 ..      56      90 ..      49      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                                   TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   a+ge+ +++la+  + sq+t   + ++L++aGLV+
  gi|121638213|ref|YP_978437.1| 56 AQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVT 90
                                   469*******************************7 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.035       7      48 .]      49      90 ..      46      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                         HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++L ++++++   + +LA   + S++t +++++rLe++Gl++
  gi|121638213|ref|YP_978437.1| 49 RLLATIEAQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVT 90
                                   67889999999999999999999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1142.39
//
Query:       gi|121638214|ref|YP_978438.1|  [L=382]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-31  107.7   8.4    2.8e-31  107.7   8.4    4.1  4  PE             PE family
  ------ inclusion threshold ------
      0.027   14.9   3.7      0.027   14.9   3.7    3.5  3  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
       0.29   11.1   1.6         12    5.9   0.0    2.7  2  CRPA           Chlamydia 15 kDa cysteine-rich outer membrane 
        0.6   11.1   4.0          2    9.4   0.8    2.6  2  DUF1484        Protein of unknown function (DUF1484)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   8.4   6.3e-35   2.8e-31       1      92 [.       1      92 [.       1      93 [. 0.99
   2 ?   -2.8   8.0       1.9   8.5e+03      50      71 ..     134     155 ..      97     172 .. 0.62
   3 ?   -6.7  13.2         4   1.8e+04      14      77 ..     135     193 ..     115     207 .. 0.57
   4 ?   -1.7   2.4      0.86   3.8e+03      47      70 ..     320     343 ..     281     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 6.3e-35
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   M+f++v Pe++++aa+dlagi+salsa  aaaa+pttav++aa+DeVS+aiA+ f+a+++++q lsaqa+afh++fv+ l++
  gi|121638214|ref|YP_978438.1|  1 MQFLSVIPEQVESAAQDLAGIRSALSASYAAAAGPTTAVVSAAEDEVSTAIASIFGAYGRQCQVLSAQASAFHDEFVNLLKT 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +a++Y ++E 
  gi|121638214|ref|YP_978438.1| 83 GATAYRNTEF 92
                                   *******996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                             PE  50 aiAalfsahaqeyqalsaqaaa 71 
                                     +A l ++ ++++ ++ +qaaa
  gi|121638214|ref|YP_978438.1| 134 VTAGLAAQAGRAVATVEQQAAA 155
                                    3333333333333333333333 PP

  == domain 3  score: -6.7 bits;  conditional E-value: 4
                                    HHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  14 aaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfv 77 
                                    +a+  a+ g+a+++  ++aaa+++ + +a+a       A++++   ++ q  +a+ a+ ++ ++
  gi|121638214|ref|YP_978438.1| 135 TAGLAAQAGRAVATVEQQAAAAVAPLPSAGA-----GLAQVVNGVVTAGQGSAAKLATALQSAA 193
                                    3444455555566655555555554444443.....3455555555555555555555555555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.86
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  47 VSaaiAalfsahaqeyqalsaqaa 70 
                                    V a iAal +a aq  q +++++ 
  gi|121638214|ref|YP_978438.1| 320 VVAGIAALQTAGAQFAQGVNHTML 343
                                    556667777777776666665543 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.7     6e-06     0.027       3      96 ..       2      96 ..       1      97 [. 0.87
   2 ?    1.2   7.9      0.12   5.2e+02      22      84 ..     138     193 ..     115     199 .. 0.68
   3 ?    0.0   0.9      0.27   1.2e+03      12      56 ..     310     352 ..     306     377 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                  T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavld.shGpicaatndavaaaeaarraagealaaasteLadkLraA 83
                                   + LsV p+++ ++a+++ ++ + ++++ aaaag ++av++     ++ a ++ + a+ +  +   ++  a ++e+ + L++ 
  gi|121638214|ref|YP_978438.1|  2 QFLSVIPEQVESAAQDLAGIRSALSASYAAAAGPTTAVVSaAEDEVSTAIASIFGAYGRQCQVLSAQASAFHDEFVNLLKTG 83
                                   579*************************999877776655156788889999999999999999999999999********* PP

                  T7SS_ESX_EspC 84 AaaYeatDeeaag 96
                                   A+aY +t+ ++a+
  gi|121638214|ref|YP_978438.1| 84 ATAYRNTEFANAQ 96
                                   ********99986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                  T7SS_ESX_EspC  22 vaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAA 84 
                                     aa++        +a+a v ++  +  a++ +a a + +  ++ ++a ++++++La+ L++AA
  gi|121638214|ref|YP_978438.1| 138 LAAQAG-------RAVATVEQQAAAAVAPLPSAGAGLAQVVNGVVTAGQGSAAKLATALQSAA 193
                                    222222.......44566777777777778888888888888888888888888888888777 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.27
                  T7SS_ESX_EspC  12 lrelaakhdevaaeiasavaaaagasaavldshGpicaatndava 56 
                                    ++ l+  + +v+a+ia++++a   a+ a   +h+++ a++ +   
  gi|121638214|ref|YP_978438.1| 310 VQHLSLVVPNVVAGIAALQTAG--AQFAQGVNHTMLAAQLGAPGI 352
                                    5566666667777777666555..444445555566666555444 PP

>> CRPA  Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0027        12      84     109 ..     203     228 ..     197     240 .. 0.87
   2 ?    3.5   0.2     0.015        68      88     109 ..     278     299 ..     266     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                           CRPA  84 filqaqlganafylliPaviGlvkll 109
                                    fi+ +q++   + ll Pav+G+v+  
  gi|121638214|ref|YP_978438.1| 203 FIVAGQSALTGVALLQPAVVGVVQAG 228
                                    9**********************865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
                           CRPA  88 aqlganafylliPaviGlvkll 109
                                     ql++ af+l++P ++G v  l
  gi|121638214|ref|YP_978438.1| 278 VQLFSPAFLLAVPTALGGVGSL 299
                                    589999**********988543 PP

>> DUF1484  Protein of unknown function (DUF1484)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.11   5.2e+02      20      60 ..      14      54 ..       5      59 .. 0.87
   2 ?    9.4   0.8   0.00045         2      15      54 ..     133     172 ..     121     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                        DUF1484 20 LaeqlakkdkaaaresAatvaqletvsediedaveeaiaqL 60
                                    a++la++  a  +  Aa++ +  +v    ed v  aia +
  gi|121638214|ref|YP_978438.1| 14 AAQDLAGIRSALSASYAAAAGPTTAVVSAAEDEVSTAIASI 54
                                   5789999999999999**99999999999999999999987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
                        DUF1484  15 eliaqLaeqlakkdkaaaresAatvaqletvsediedave 54 
                                     ++a La+q++++   ++++ Aa+va+l++ ++ + + v 
  gi|121638214|ref|YP_978438.1| 133 TVTAGLAAQAGRAVATVEQQAAAAVAPLPSAGAGLAQVVN 172
                                    46899*************************9999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2896.93
//
Query:       gi|121638215|ref|YP_978439.1|  [L=515]
Description: nitrite extrusion protein 1 narK1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-16   59.3  43.5    2.9e-16   59.3  43.5    1.9  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        3.2    7.9   3.9        5.9    7.0   0.0    2.9  3  ETRAMP    Malarial early transcribed membrane protein (ETRAMP
        4.9    7.4   7.3         17    5.7   0.8    3.3  3  DUF2304   Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3  43.5   4.9e-20   2.9e-16       8     329 ..      62     403 ..      55     434 .. 0.74
   2 ?   -1.9   3.8       0.2   1.2e+03     120     167 ..     419     467 ..     410     480 .. 0.50

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 4.9e-20
                          MFS_1   8 salarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll...fa. 82 
                                     +++ ++l+p+l l + ++ +g+s s   ll t+ +l+ a++ +p++  s  fG r +  ++++++++  ++++   ++ 
  gi|121638215|ref|YP_978439.1|  62 LGYSVWTLWPVLELlMPQDVYGFSTSDKFLLGTIATLFGAFLRMPYALASAIFGGRNWATFSAIVLLIP-AIGTtvlLTh 140
                                    5678899******9888999*************************************999999999999.5555452335 PP

                          MFS_1  83 ..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                       +lw+ lv+ +l+Glg g+ f+++++ + + +p++ +g+a+g++++  +lG+    l+g l ++ +g r +++++a+ 
  gi|121638215|ref|YP_978439.1| 141 pgLPLWPYLVCAALTGLG-GGNFASSMSNANAFYPHRLKGSALGIAGGVGNLGVPAIQLVGLLAIATVGERKPYLVCALY 219
                                    4455889***********.79999999999************************************************99 PP

                          MFS_1 161 sllafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevl 238
                                     +l+++  +++ l++ +  +++ +  + +       p   + +a+l+ +  w  l++ll+ +  f ++  +++++  +vl
  gi|121638215|ref|YP_978439.1| 220 VVLVAIavIGVSLFMNNVEQHRVQVNRLR-------P---IVSAVLSTRDTW--LLSLLYLG-TFGSFIGFSFVF-GQVL 285
                                    99997775666777777777777655444.......4...455888888886..33333333.444455555555.6666 PP

                          MFS_1 239 gls..............glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt....... 297
                                      +              + ++++    ++ l++a++++ +grl+dr+g   rl+l++++++++a+gl++ a t       
  gi|121638215|ref|YP_978439.1| 286 QTNflacgqsparatlhA-VELA---FVGPLLAAVARIYGGRLADRVGG-SRLTLIVFVAMTLAAGLLISASTlegrhvg 360
                                    666667778899965533.5555...5555555555**********996.777777777777777777777777****** PP

                          MFS_1 298 ........ssavllllvlvliGfglgfv...fpsllalasdla 329
                                               v++++++vl G+g g v    p+++ ++s+++
  gi|121638215|ref|YP_978439.1| 361 qhrgatmvGYFVCFVALFVLSGLGNGSVykmIPTIFEACSRSL 403
                                    9997665333333333666688899999777777777777777 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.2
                          MFS_1 120 graigllsagfslGa.ilgpllggllasslgWravfyilaivsllafvl 167
                                    g +ig+++a+ +lG   + ++l    +s ++ + +f+i+   ++ a+vl
  gi|121638215|ref|YP_978439.1| 419 GVVIGFVAAFGALGGvGINMALRESYLSTGSGTDAFWIFMMCYAAAAVL 467
                                    4455555555555554444555444444444444555555555555443 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.098   5.9e+02       6      30 ..     215     239 ..     211     260 .. 0.84
   2 ?   -3.6   0.5         2   1.2e+04       9      20 ..     338     349 ..     333     356 .. 0.50
   3 ?    7.0   0.0   0.00098       5.9      57      79 ..     416     438 ..     404     441 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.098
                         ETRAMP   6 vllffafLlavnlltpeslcdevnk 30 
                                    v+ + ++L+a+ ++ ++++ ++v++
  gi|121638215|ref|YP_978439.1| 215 VCALYVVLVAIAVIGVSLFMNNVEQ 239
                                    6899999999999999998888765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                         ETRAMP   9 ffafLlavnllt 20 
                                    f+a+ la  ll+
  gi|121638215|ref|YP_978439.1| 338 FVAMTLAAGLLI 349
                                    333334443433 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00098
                         ETRAMP  57 iistiatalallvasalGlgiyk 79 
                                    iis ++++ +++++++ G+gi++
  gi|121638215|ref|YP_978439.1| 416 IISGVVIGFVAAFGALGGVGINM 438
                                    9************99999***97 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.01        60       2      30 ..     218     246 ..     199     256 .. 0.85
   2 ?    5.7   0.8    0.0029        17      31      79 ..     332     380 ..     308     384 .. 0.89
   3 ?   -2.5   0.0         1     6e+03      61      77 ..     448     464 ..     442     473 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                        DUF2304   2 lqiiliivsvllllliirlvrkkklkley 30 
                                    l ++l++++v+ + l++++v + ++++++
  gi|121638215|ref|YP_978439.1| 218 LYVVLVAIAVIGVSLFMNNVEQHRVQVNR 246
                                    56789999999999999999998888765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0029
                        DUF2304  31 sllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvil 79 
                                    +l+ ++++++ + + l  ++ t   + +G +rg++++ +++ ++ l++l
  gi|121638215|ref|YP_978439.1| 332 RLTLIVFVAMTLAAGLLISASTLEGRHVGQHRGATMVGYFVCFVALFVL 380
                                    7889999******************************999988888875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1
                        DUF2304  61 grgtnllfllgivfllv 77 
                                    g+gt+++ +++++    
  gi|121638215|ref|YP_978439.1| 448 GSGTDAFWIFMMCYAAA 464
                                    56666666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3396.33
//
Query:       gi|121638216|ref|YP_978440.1|  [L=175]
Description: lipoprotein lppP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-24   85.4   0.0    3.5e-24   84.7   0.0    1.3  1  Lipoprotein_21  LppP/LprE lipoprotein


Domain annotation for each model (and alignments):
>> Lipoprotein_21  LppP/LprE lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   1.9e-28   3.5e-24       2      86 ..      79     162 ..      78     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.9e-28
                 Lipoprotein_21   2 gydpcaaLswvvistegatasspqqallFhdgeflGtatpepyasiprvlrsdddtVtVeYrwykpddplccpsgtatvt 81 
                                    g++++++L+wv i  + a++s+pqq+l+F+++ +lG +t +p ++i +vl ++ddtVtV+Y+w  ++d+ ccp+g++tv+
  gi|121638216|ref|YP_978440.1|  79 GHTRNCRLHWVQIIPTIAAQSTPQQLLFFDRNIPLGSPTRNPKPYI-TVLPAGDDTVTVQYQWQIGSDQECCPTGIGTVR 157
                                    79999*****************************************.********************************* PP

                 Lipoprotein_21  82 Frwdg 86 
                                    F++ +
  gi|121638216|ref|YP_978440.1| 158 FHIGS 162
                                    **976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1293.36
//
Query:       gi|121638217|ref|YP_978441.1|  [L=128]
Description: hypothetical protein BCG_2352 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 825.62
//
Query:       gi|121638218|ref|YP_978442.1|  [L=112]
Description: hypothetical protein BCG_2353 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 808.79
//
Query:       gi|121638219|ref|YP_978443.1|  [L=548]
Description: malate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-98  328.6   0.2    2.8e-98  328.3   0.2    1.1  1  Malic_M         Malic enzyme, NAD binding domain
    7.4e-67  224.7   0.0    1.2e-66  224.0   0.0    1.3  1  malic           Malic enzyme, N-terminal domain
  ------ inclusion threshold ------
       0.18   12.4   0.0       0.44   11.1   0.0    1.7  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
       0.26   10.1   0.1       0.65    8.8   0.0    1.5  2  DUF4551         Protein of unknown function (DUF4551)


Domain annotation for each model (and alignments):
>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.3   0.2  6.1e-102   2.8e-98       1     257 [.     265     521 ..     265     522 .. 0.99

  Alignments for each domain:
  == domain 1  score: 328.3 bits;  conditional E-value: 6.1e-102
                                    THHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---T CS
                        Malic_M   1 iqgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedreklee 80 
                                    +qgT+av+la+++++lk+tg +l++q+ivv+GaG+ag+Gia+qi++a+v++G++ e+a ++i+ +Dr GLl++d+++l++
  gi|121638219|ref|YP_978443.1| 265 MQGTGAVVLAAVYSGLKVTGIPLRDQTIVVFGAGTAGMGIADQIRDAMVADGATLEQAVSQIWPLDRPGLLFDDMDDLRD 344
                                    6******************************************************************************* PP

                                    TTGGGSBS--SS--S.....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHH CS
                        Malic_M  81 ekkpfakkkeelkeak.dkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataedvlk 159
                                    ++ p+ak++++l  a  d++ L++++k + pt+l+G+s+v gaft+e+v++m++s+++P+i+plSNPts++Ea ++dvl+
  gi|121638219|ref|YP_978443.1| 345 FQVPYAKNRHQLGVAVgDRVGLSDAIKIASPTILLGCSTVYGAFTKEVVEAMTASCKHPMIFPLSNPTSRMEAIPADVLA 424
                                    ************97768*************************************************************** PP

                                    HTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT-SS--G CS
                        Malic_M 160 wtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkegsllPel 239
                                    w++g+al+a+GsP++pve++++ty igQaNN+++fPg+glgviva+a+ it +ml+aaa+a+a+++++++++ +sllP++
  gi|121638219|ref|YP_978443.1| 425 WSNGRALLATGSPVAPVEFDETTYVIGQANNVLAFPGIGLGVIVAGARLITRRMLHAAAKAIAHQANPTNPG-DSLLPDV 503
                                    ***********************************************************************9.9****** PP

                                    GGHHHHHHHHHHHHHHHH CS
                        Malic_M 240 seirevslkvavavakaa 257
                                    +++r +s++va av++aa
  gi|121638219|ref|YP_978443.1| 504 QNLRAISTTVAEAVYRAA 521
                                    ***************998 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.0   0.0   2.7e-70   1.2e-66       2     181 ..      74     254 ..      73     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 224.0 bits;  conditional E-value: 2.7e-70
                                    TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS...SS..EEEEE-SSSBT CS
                          malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlp..eedvkvivvtdgeriL 79 
                                     ++e+l++k+l+++l el+p+vYtPtvgea+q++s+eyr +rgl+lsi++ ++i+e++++l    edv++iv+td+e+iL
  gi|121638219|ref|YP_978443.1|  74 YRHEVLYFKVLADHLPELMPVVYTPTVGEAIQRFSDEYRGQRGLFLSIDEPDEIEEAFNTLGlgPEDVDLIVCTDAEAIL 153
                                    589*********************************************************98889*************** PP

                                    TTBS-GHHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHHHHG CS
                          malic  80 GlGdlGvagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavkelfp 159
                                    G+Gd+Gv+g++i+vGKlaLyta +g+dP+++l+v ldvgt+ne+ll+dp+YlG+r+ R +g+eydefv +++e++++lf 
  gi|121638219|ref|YP_978443.1| 154 GIGDWGVGGIQIAVGKLALYTAGGGVDPRRCLAVSLDVGTDNEQLLADPFYLGNRHARRRGREYDEFVSRYIETAQRLF- 232
                                    *******************************************************************************. PP

                                    CTSEEEE-S--CCHHHHHHHHH CS
                          malic 160 pkaliqfEDfkaknafeilery 181
                                    p+a+++fEDf+ +na +il+ y
  gi|121638219|ref|YP_978443.1| 233 PRAILHFEDFGPANARKILDTY 254
                                    9******************998 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.8e-05      0.44       4      37 ..     111     144 ..     109     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                 FGAR-AT_linker   4 ankelglaLsdeEidylqeafeklgrnPtdvEle 37 
                                    ++ ++gl Ls +E d ++eaf++lg  P dv l 
  gi|121638219|ref|YP_978443.1| 111 YRGQRGLFLSIDEPDEIEEAFNTLGLGPEDVDLI 144
                                    66789*************************9775 PP

>> DUF4551  Protein of unknown function (DUF4551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00014      0.65     317     373 ..      28      83 ..      13     106 .. 0.84
   2 ?   -2.2   0.0      0.31   1.4e+03     589     609 ..     394     414 ..     391     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00014
                        DUF4551 317 sertaklFaqLkselLqedisleklylllqeLrtAaqrnvtLkrLFWkssdlfnFlv 373
                                    + r++ l ++L s +L+ d++ e+++++lq L t   rn+ L +L ++  ++++F v
  gi|121638219|ref|YP_978443.1|  28 QRRRLGLTGRLPSAVLTLDQQAERVWHQLQSLATDLGRNLLLEQLHYRH-EVLYFKV 83 
                                    567888999*************************************996.5555532 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.31
                        DUF4551 589 klsalekkLppkYPisqptlk 609
                                    +  ++  k p+ +P+s+pt +
  gi|121638219|ref|YP_978443.1| 394 EAMTASCKHPMIFPLSNPTSR 414
                                    556677899**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4125.88
//
Query:       gi|121638220|ref|YP_978444.1|  [L=523]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-57  195.3  49.3    2.6e-57  194.3  46.4    2.1  2  MFS_1     Major Facilitator Superfamily
    5.1e-07   28.9  12.7    5.1e-07   28.9  12.7    3.3  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.01   14.4  37.0       0.44    9.0   6.7    3.2  2  MFS_2     MFS/sugar transport protein
       0.43   10.5   7.9      0.062   13.2   1.4    3.0  3  YrhK      YrhK-like protein
        1.2    7.3  22.9        0.9    7.7   0.4    4.2  5  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3  46.4   7.4e-61   2.6e-57       3     352 ..      14     403 ..      12     404 .. 0.92
   2 ?    1.5   0.0     0.031   1.1e+02     149     187 ..     475     513 ..     472     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 7.4e-61
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                    l++f+++l++ i+++alp  +++++ + ++ ++++++ y+lg+av+++ ++ l+d +Grrr++l+g+ lf lg++++ +a
  gi|121638220|ref|YP_978444.1|  14 LGLFMIFLDALIVNVALP-DIQRSFAVGEDGLQWVVASYSLGMAVFIMSAATLADLYGRRRWYLIGVSLFTLGSIACGLA 92 
                                    899***************.******************************************************5555567 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    +s+ +l  +r  qGlga+a+  +++al+++ fp+ +e++raig+++a +s+G+  gp lggll++++gWr++fy++ +++
  gi|121638220|ref|YP_978444.1|  93 PSIAVLTTARGAQGLGAAAVSVTSLALVSAAFPEaKEKARAIGIWTAIASIGTTTGPTLGGLLVDQWGWRSIFYVNLPMG 172
                                    8888**************************************************************************** PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeee..............................................kgtgpap 195
                                    +l+  lfl l ++e++ ++r +  +++                                              +++   p
  gi|121638220|ref|YP_978444.1| 173 ALV--LFLTLCYVEESCNERARRFDLSgqllfivavgalvyaviegpqigwtsvqtivmlwtaavgcalfvwlERRSSNP 250
                                    ***..66699999999999999999999999***************9999999888888776666666666666666666 PP

                          MFS_1 196 lvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275
                                    + + +++++   +  +++++++++ff+++g+l l++ +lq v+g++    +gl++  +++++ai+++l+g l+ r+g+r 
  gi|121638220|ref|YP_978444.1| 251 MMD-LTLFRDTSYA-LAIATICTVFFAVYGMLLLTTQFLQNVRGYT-PSVTGLMILPFSAAVAIVSPLVGHLVGRIGARV 327
                                    666.6666666655.59999**************************.7899988999999999999************** PP

                          MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                    ++l +l  l+l++l+l++  +  s++l+l++l l+G g++++ ++++++a+  +p+e+ag+asg+++  +++g+ +g
  gi|121638220|ref|YP_978444.1| 328 PILAGLCMLMLGLLMLIFSEHR-SSALVLVGLGLCGSGVALCLTPITTVAMTAVPAERAGMASGIMSAQRAIGSTIG 403
                                    **********************.9999999********************************************998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.031
                          MFS_1 149 gWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                    g r++ +++++ ++++f+ ++ ++p++  + + ++++e 
  gi|121638220|ref|YP_978444.1| 475 GIRVALLVATATLAVVFLAGWRWFPRDVQTAGSDAKREA 513
                                    6899999999*********99***999988888877765 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9  12.7   1.4e-10   5.1e-07      49     194 ..      45     186 ..       7     194 .. 0.83
   2 ?    0.9  14.0     0.045   1.6e+02      45     154 ..     295     403 ..     260     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-10
                                    HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                     ++v+++++G ++  + a +l+d +GR+  +li++ lf  g++ +++a+   s+ vl+++R   G+g+ ++sv++  ++s
  gi|121638220|ref|YP_978444.1|  45 QWVVASYSLGMAVFIMSAATLADLYGRRRWYLIGVSLFTLGSIACGLAP---SIAVLTTARGAQGLGAAAVSVTSLALVS 121
                                    69***********************************************...**************************** PP

                                    TTS-SCCHHH.HHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHH.HHHHHHHGGGS--- CS
                       Sugar_tr 129 EiApkklRga.lvslyqlaitfGilvaaifglglnktsnadgwrillglqlvp.allllilllflPES 194
                                       p+++ +a  ++++    ++G   + ++g     +++ +gwr  ++++l + al+l++ l+ ++ES
  gi|121638220|ref|YP_978444.1| 122 AAFPEAKEKArAIGIWTAIASIGTTTGPTLG--GLLVDQ-WGWRSIFYVNLPMgALVLFLTLCYVEES 186
                                    9999888755145555556667766555554..444555.99*********88245566667999998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.045
                                    ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                       Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                     + +gl+   f++  +i s ++g l+ r+G +  +l++  +++ g ++ ++++  +s  +++vg  l+G gv l+ + ++
  gi|121638220|ref|YP_978444.1| 295 PSVTGLMILPFSAAVAIVSPLVGHLVGRIGARVPILAGLCMLMLGLLMLIFSE-HRSSALVLVGLGLCGSGVALCLTPIT 373
                                    3578999999999999999**********************************.5599999*******987766655555 PP

                                    HHHHTTS-SCCHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilva 154
                                    + +    p++ +g+  ++     ++G  ++
  gi|121638220|ref|YP_978444.1| 374 TVAMTAVPAERAGMASGIMSAQRAIGSTIG 403
                                    555444477777887777777766666665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.7   0.00012      0.44     259     376 ..      42     155 ..      35     163 .. 0.86
   2 ?    7.8  22.3    0.0003       1.1     216     383 ..     252     413 ..     161     427 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00012
                          MFS_2 259 saasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsm 338
                                    +  +++ +   ++++++i+ ++ la  +g+++ yl+g +l  ++++ + l+   ++++++++  + g+g+++  ++  ++
  gi|121638220|ref|YP_978444.1|  42 DGLQWVVASYSLGMAVFIMSAATLADLYGRRRWYLIGVSLFTLGSIACGLA--PSIAVLTTARGAQGLGAAAVSVTSLAL 119
                                    5679999999**************************************999..7899999999******99999999999 PP

                          MFS_2 339 ladvvDygelktGkrregvffavlsfisklatgiglgv 376
                                    ++ ++ +   k + r+ g+ +a+ s+ +  + ++g+++
  gi|121638220|ref|YP_978444.1| 120 VSAAFPE--AKEKARAIGIWTAIASIGTTTGPTLGGLL 155
                                    9999865..55777888887777777777776666554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0003
                          MFS_2 216 qlkevfrnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyll 294
                                    +   +fr+  + + ++++ ++++a++ +  l+  +l+ v g + s   ++ l + +++++++pl+  l+ r+g +  +l+
  gi|121638220|ref|YP_978444.1| 252 MDLTLFRDTSYALAIATICTVFFAVYGMLLLTTQFLQNVRGyTPSVTGLMILPFSAAVAIVSPLVGHLVGRIGARVPILA 331
                                    3344667777767777777777777777788888999****777777777777788888********************* PP

                          MFS_2 295 galltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgigl 374
                                    g+++++++l+++++ + ++ +l+lv l + g gv+++ + ++   +++v +        r+g++ ++ s+   ++++ig 
  gi|121638220|ref|YP_978444.1| 332 GLCMLMLGLLMLIFSEHRSSALVLVGLGLCGSGVALCLTPITTVAMTAVPA-------ERAGMASGIMSAQRAIGSTIGF 404
                                    ****99999999999999*************99887776666666666644.......4699999999999999999999 PP

                          MFS_2 375 gvsgllLsa 383
                                    +v+g +L+a
  gi|121638220|ref|YP_978444.1| 405 AVLGSVLAA 413
                                    999998875 PP

>> YrhK  YrhK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   1.7e-05     0.062      20      58 ..      59      98 ..      45     100 .. 0.84
   2 ?   -1.9   0.1      0.91   3.3e+03      14      21 ..     198     205 ..     192     241 .. 0.55
   3 ?   -2.2   0.0       1.1     4e+03      23      29 ..     489     495 ..     480     507 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                           YrhK 20 vGSilflpnse.fwkwqiagvwlFliGSilflirpvirlv 58
                                   + S   l++ + +  w  +gv lF +GSi+ ++ p i+++
  gi|121638220|ref|YP_978444.1| 59 IMSAATLADLYgRRRWYLIGVSLFTLGSIACGLAPSIAVL 98
                                   44788899999999**********************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.91
                           YrhK  14 gsllFlvG 21 
                                    g llF+v+
  gi|121638220|ref|YP_978444.1| 198 GQLLFIVA 205
                                    55555554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                           YrhK  23 ilflpns 29 
                                    ++fl+ +
  gi|121638220|ref|YP_978444.1| 489 VVFLAGW 495
                                    4455555 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4   0.00025       0.9      11      85 ..      17      91 ..       7     106 .. 0.87
   2 ?    0.9   0.0     0.031   1.1e+02     490     523 ..     126     158 ..     108     162 .. 0.72
   3 ?    1.0   0.1     0.027        98     494     523 ..     130     158 ..     123     195 .. 0.54
   4 ?    2.5   5.3      0.01        36     288     379 ..     254     344 ..     243     348 .. 0.64
   5 ?    6.6   0.5   0.00055         2     133     198 ..     352     417 ..     345     432 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00025
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 11 lvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslllal 85
                                   ++  +   ++++++  i++ F        ++++s+ +g +++i+  + +++   r rw  ig+ l++lgs+ + l
  gi|121638220|ref|YP_978444.1| 17 FMIFLDALIVNVALPDIQRSFAVGEDGLQWVVASYSLGMAVFIMSAATLADLYGRRRWYLIGVSLFTLGSIACGL 91
                                   44466667899**********************************************************998866 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.031
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 490 kkedksfalGlqlllirllgliPgPiifGaiiDs 523
                                    + ++k+ a+G+++++ ++ g+  gP + G ++D+
  gi|121638220|ref|YP_978444.1| 126 EAKEKARAIGIWTAIASI-GTTTGPTLGGLLVDQ 158
                                    456777788887777777.888888887777775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.027
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 494 ksfalGlqlllirllgliPgPiifGaiiDs 523
                                    k+ a+G+++++ ++ g+  gP + G ++D+
  gi|121638220|ref|YP_978444.1| 130 KARAIGIWTAIASI-GTTTGPTLGGLLVDQ 158
                                    44444444444433.444444444444432 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.01
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 288 krllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklak 367
                                    + l+++  + l i + ++ +++v G+   ++++l++  + ++s   l++ +++  +a++   l G lv ++  ++  la 
  gi|121638220|ref|YP_978444.1| 254 LTLFRDTSYALAIATICTVFFAVYGMLLLTTQFLQNVRGYTPSVTGLMILPFSAAVAIVSP-LVGHLVGRIGARVPILAG 332
                                    5677777788888888888888888888888888888777777555554444443333333.335667777777777777 PP

                                    xxxxxxxxxxxx RF
                           OATP 368 lvlvvsllslll 379
                                    l++++  l +l+
  gi|121638220|ref|YP_978444.1| 333 LCMLMLGLLMLI 344
                                    776665444443 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.00055
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 133 llfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdi 198
                                     l++++  l+G G ++  t  ++     v  +++ +  gi++a r++G  +Gf++ + +l  +   
  gi|121638220|ref|YP_978444.1| 352 ALVLVGLGLCGSGVALCLTPITTVAMTAVPAERAGMASGIMSAQRAIGSTIGFAVLGSVLAAWLSA 417
                                    46677777777777777777777777789999*********************9777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 3367.55
//
Query:       gi|121638221|ref|YP_978445.1|  [L=310]
Description: cysteine synthase A cysK1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-70  237.6   2.2    2.1e-70  237.5   2.2    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.5   2.2   1.2e-74   2.1e-70       1     294 []       7     294 ..       7     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 237.5 bits;  conditional E-value: 1.2e-74
                                    GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHH CS
                           PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaall 77 
                                    +t+ ig+TPlvrl+r+++   +++ +KlE++np  S+KdR  + +l++++++   ++ + ++e +sGN+g+alA+++a+ 
  gi|121638221|ref|YP_978445.1|   7 ITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAgliKPDTIILEPTSGNTGIALAMVCAAR 86 
                                    6889********************************************99999*************************** PP

                                    T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHT CS
                           PALP  78 GlkvtivvpadaspekvallrllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileql 154
                                    G+++++ +p+++s e++ llr++Gae+++++g      a a+a+ela+ ++ +++ +qf+np++ +    t++ E+++++
  gi|121638221|ref|YP_978445.1|  87 GYRCVLTMPETMSLERRMLLRAYGAELILTPGAdgMSGAIAKAEELAKTDQRYFVPQQFENPANPAIhRVTTAEEVWRDT 166
                                    ******************************65534777888899*****99999999999******************** PP

                                    TTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHHH CS
                           PALP 155 ggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafell 233
                                    +gk+d vv++vG+Gg+i+G+a+ +ker+p+ r+++vep+ s+ l ++          ++++ ++g+++g +p +l     
  gi|121638221|ref|YP_978445.1| 167 DGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPAASPVLSGGQ---------KGPHPIQGIGAGfVPPVL----D 233
                                    ***********************************************9.........7799********444443....4 PP

                                    SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-H.HHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                           PALP 234 drlvdeivtvsdeealeamrllarregivvep.ssaaalaalklreagelkegdrvvviltg 294
                                    ++lvdei+tv +e+al  +r+lar+eg++v+  s+aa +aal+ +++ e +++  +vv+l++
  gi|121638221|ref|YP_978445.1| 234 QDLVDEIITVGNEDALNVARRLAREEGLLVGIsSGAATVAALQVARRPENAGK-LIVVVLPD 294
                                    677899999***********************777777777755555555555.99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2452.79
//
Query:       gi|121638222|ref|YP_978446.1|  [L=229]
Description: serine acetyltransferase cysE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-16   57.5  13.4    7.4e-09   35.0   2.0    3.1  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
    4.3e-07   29.6  12.3    2.8e-05   23.7   2.6    3.5  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase
    0.00032   21.0   0.0    0.00046   20.5   0.0    1.2  1  SATase_N   Serine acetyltransferase, N-terminal


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   6.6e-05      0.39      13      34 ..      59      80 ..      55      82 .. 0.72
   2 !   26.8   2.9   4.8e-10   2.9e-06       1      36 []      71     108 ..      71     108 .. 0.97
   3 !   35.0   2.0   1.2e-12   7.4e-09       1      34 [.     117     150 ..     117     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                                   TEEEETTEEE-TTEEEETTEEE CS
                        Hexapep 13 faviggnVkIGdnvkIgagvvi 34
                                   f+ i+ +V I+++++Iga v i
  gi|121638222|ref|YP_978446.1| 59 FTRILTGVDIHPGAVIGARVFI 80
                                   5667777777777777777766 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 4.8e-10
                                    TEEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   1 stvIGsnvlIgp..faviggnVkIGdnvkIgagvvigg 36 
                                    ++vIG  v+I++  ++vig+ +++Gd+v+I +gv++gg
  gi|121638222|ref|YP_978446.1|  71 GAVIGARVFIDHatGVVIGETAEVGDDVTIYHGVTLGG 108
                                    689********************************997 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 1.2e-12
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    ++++G+ v+Ig++a+++g++kIG++++Iga++v+
  gi|121638222|ref|YP_978446.1| 117 HPTVGDRVIIGAGAKVLGPIKIGEDSRIGANAVV 150
                                    5799*****************************9 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.018   1.1e+02      17      32 ..      65      80 ..      62      82 .. 0.70
   2 !    9.4   1.7   0.00014      0.85       3      32 ..      73     106 ..      68     107 .. 0.81
   3 !   23.7   2.6   4.8e-09   2.8e-05       3      32 ..     119     150 ..     119     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                                   SEEE-TT-EE-TT-EE CS
                      Hexapep_2 17 GvslGdncvvgaGvvi 32
                                   Gv++  ++v+ga v+i
  gi|121638222|ref|YP_978446.1| 65 GVDIHPGAVIGARVFI 80
                                   7777777777776666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00014
                                    EE-TT-EE.-TT-E.ES..EEE-TT-EE-TT-EE CS
                      Hexapep_2   3 iIGdnCli.Ganag.iG..vslGdncvvgaGvvi 32 
                                     IG++++i +a  + iG   ++Gd+++++ Gv++
  gi|121638222|ref|YP_978446.1|  73 VIGARVFIdHATGVvIGetAEVGDDVTIYHGVTL 106
                                    699999996666444799899*******999987 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 4.8e-09
                                    EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                      Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                    ++Gd+++iGa a +  ++++G+++ +ga+ v+
  gi|121638222|ref|YP_978446.1| 119 TVGDRVIIGAGAKVlgPIKIGEDSRIGANAVV 150
                                    59***********9955************998 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.7e-08   0.00046      71     103 ..       3      35 ..       1      36 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.7e-08
                                    HHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                       SATase_N  71 eaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                    +a+r D++A +erDpA++++le++  + G hA+
  gi|121638222|ref|YP_978446.1|   3 TAMRGDIRAARERDPAAPTALEVIFCYPGVHAV 35 
                                    7899***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1799.21
//
Query:       gi|121638223|ref|YP_978447.1|  [L=322]
Description: hypothetical protein BCG_2358 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2687.11
//
Query:       gi|121638224|ref|YP_978448.1|  [L=372]
Description: hypothetical protein BCG_2359c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.7   0.5        1.3    9.1   0.1    3.9  4  Nitroreductase  Nitroreductase family
     0.0059   16.2   0.0      0.018   14.7   0.0    1.8  2  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.028   14.4   0.1      0.064   13.2   0.1    1.6  1  CobW_C          Cobalamin synthesis protein cobW C-terminal d


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00021       1.3      15      40 ..      13      38 ..      10      48 .. 0.88
   2 !    6.1   0.0    0.0017        10     102     139 ..      52      89 ..      49     109 .. 0.84
   3 ?   -1.3   0.0      0.33     2e+03     128     147 ..     145     164 ..     121     182 .. 0.64
   4 ?    1.5   0.0     0.046   2.7e+02     116     144 ..     272     300 ..     263     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00021
                                   --HHHHHHHHHHHHTS--GGG---EE CS
                 Nitroreductase 15 vpkeelekileaarraPsagnlqpwr 40
                                   ++++e+ +++eaa+ aPsa n+++++
  gi|121638224|ref|YP_978448.1| 13 LDPAEFLSLVEAAALAPSADNRREVQ 38
                                   6889999**************99886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0017
                                    S---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                 Nitroreductase 102 kserkaaerayryalldagaaaqnllLaAtalGlgscp 139
                                    + +r a+e ++  +l+ +gaa++n+ L A +lG+++ +
  gi|121638224|ref|YP_978448.1|  52 QTWRSAPEHRRIMSLVAIGAAVENVKLRAGRLGFETKV 89 
                                    567889999999*********************99855 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.33
                                    HHHHHTT-EEEEE-GGGGGH CS
                 Nitroreductase 128 LaAtalGlgscpiggfdeaa 147
                                    L+A+a G++ + ++ fd  +
  gi|121638224|ref|YP_978448.1| 145 LSAEATGIDGIQLHWFDSPE 164
                                    56666677776666666443 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.046
                                    HHHHHHHHHHHHHHHHHTT-EEEEE-GGG CS
                 Nitroreductase 116 lldagaaaqnllLaAtalGlgscpiggfd 144
                                    +l+aga+ ++++L  t lG + +p  +  
  gi|121638224|ref|YP_978448.1| 272 ALTAGAVFERIWLRTTLLGAELQPFAASA 300
                                    67899999999999999998887765555 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.9e-06     0.018     157     191 ..      15      48 ..      10      80 .. 0.77
   2 ?   -2.7   0.0      0.58   3.5e+03     154     170 ..     160     176 ..     149     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-06
                                    -HHHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
                 TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                                    p++f +++eaa lAPsA N++ +++e  +  ++++
  gi|121638224|ref|YP_978448.1|  15 PAEFLSLVEAAALAPSADNRREVQLEHAG-RRVRL 48 
                                    788999********************555.58876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.58
                                    GGS-HHHHHHHHHHHTS CS
                 TM1586_NiRdase 154 eelpewfkeileaarlA 170
                                     + pe  k+il+++rlA
  gi|121638224|ref|YP_978448.1| 160 FDSPETRKQILRLVRLA 176
                                    467999999***99998 PP

>> CobW_C  Cobalamin synthesis protein cobW C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.064      39      88 ..      31      80 ..      26      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                         CobW_C 39 agkpdalvlqgvggrlrlepagawwaaededrrseLVfIGrdldkealee 88
                                   a++++ ++l+ +g+r+rl+  ++w +a++ +r   LV IG  ++  +l++
  gi|121638224|ref|YP_978448.1| 31 ADNRREVQLEHAGRRVRLWGDQTWRSAPEHRRIMSLVAIGAAVENVKLRA 80
                                   5667799************98999888999999********999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2940.11
//
Query:       gi|121638225|ref|YP_978449.1|  [L=318]
Description: hypothetical protein BCG_2360c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-54  184.0   0.0      4e-54  183.5   0.0    1.1  1  ThiF            ThiF family
  ------ inclusion threshold ------
       0.15   11.6   0.2        2.1    7.9   0.1    2.1  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.5   0.0   4.5e-58     4e-54       3     238 ..      27     282 ..      25     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.5 bits;  conditional E-value: 4.5e-58
                                    HHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   3 rqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealq 82 
                                    r+l l+++  q++Lr+s+v++ G+Gg+G + +++La++G+gk+t++D D+ e+ N nRq+ ++++  G++Kaev+++ ++
  gi|121638225|ref|YP_978449.1|  27 RNLGLISPTEQQRLRNSRVAIAGMGGVGGIDMVALARMGIGKFTIADPDVFEIRNSNRQYGAMRSTNGQAKAEVMRNIVH 106
                                    78889999************************************************************************ PP

                                    HT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSS..HHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE..CCS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                           ThiF  83 einpdveveavteritdetvleellesvDlVvdalDn..iearrlvnracvkkgiplieagtlgfegqvvviip..gktg 158
                                    +inp++e++a++e+i++e+ +  +le++D+ vd++D   i+ rrl+ r ++++gi  + ag+lgf++++vv++p  ++ +
  gi|121638225|ref|YP_978449.1| 107 DINPEAEIRAFCEPIGKEN-AATFLEGADVLVDGIDAfeIDLRRLLYREAQQRGIYALGAGPLGFSTAWVVFDPkgMTFD 185
                                    *****************99.56***************88899******************************98667777 PP

                                    ECTSS-TGGS.EECCCCEEHHHHHHCT.....................E-B-HHHHHHHHHHHHHHHHHHH..TTBCGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                           ThiF 159 cyeCldpsstedptekkvplctsiagn.....................ipaiatttavvaglaalellkll..sgkekle 215
                                     y++l   s++++t +k+ ++  iag                       p+++ ++++++g++a+e+lk+l  +g+   +
  gi|121638225|ref|YP_978449.1| 186 RYFDL---SDAMNTVDKFVAF--IAGIapsathrrsidlsyvdienrtGPSVGLACHLASGVVAAEVLKILlgHGRV-YA 259
                                    77777...6799999999999..5555444444444444444444457899********************976666.99 PP

                                    CCEEEECCTTTTEEEEECCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 216 nslltqvdllesrfenvelerak 238
                                    + +++q+d+++s++ + +l++++
  gi|121638225|ref|YP_978449.1| 260 APYFHQFDAYRSIYVRKRLRCGN 282
                                    9*************999998766 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00024       2.1       2      41 ..      44      84 ..      43     110 .. 0.86
   2 ?    1.6   0.0      0.02   1.8e+02      73     101 ..     193     223 ..     180     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00024
                                   EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCT CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklns 41
                                   ++++ G+G vG++ +++la++g  + ++ D d   +++ n+
  gi|121638225|ref|YP_978449.1| 44 RVAIAGMGGVGGIDMVALARMGiGKFTIADPDVFEIRNSNR 84
                                   89********************6578888888877777665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.02
                                    HHHC-S..EEEE-----B-TTTTCB-THHHH CS
                 UDPG_MGDP_dh_N  73 aveead..vifiaVgTPskkkgkaaDlkyve 101
                                    a++  d  v fia   Ps ++ +++Dl+yv 
  gi|121638225|ref|YP_978449.1| 193 AMNTVDkfVAFIAGIAPSATHRRSIDLSYVD 223
                                    444444338899999**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2489.85
//
Query:       gi|121638226|ref|YP_978450.1|  [L=826]
Description: transmembrane transport protein mmpL9a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.5e-166  552.6  25.2   3.7e-114  381.1   9.1    2.8  3  MMPL            MMPL family
     0.0034   17.9   0.2       0.03   14.9   0.1    2.1  2  Syntaxin-6_N    Syntaxin 6, N-terminal
     0.0035   15.4   0.3     0.0035   15.4   0.3    1.5  2  Prominin        Prominin
  ------ inclusion threshold ------
      0.035   14.1   1.6        1.8    8.6   0.3    2.5  2  DUF1664         Protein of unknown function (DUF1664)
      0.043   13.9   1.0       0.37   10.8   0.6    2.1  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.046   14.3   1.1         22    5.7   0.3    3.3  3  SlyX            SlyX
      0.055   11.1  15.7        0.8    7.3   0.2    3.0  2  ACR_tran        AcrB/AcrD/AcrF family
       0.15   11.2   1.8       0.23   10.5   1.8    1.2  1  APG17           Autophagy protein Apg17
       0.23   11.7   0.1       0.23   11.7   0.1    5.6  4  DUF948          Bacterial protein of unknown function (DUF948
       0.39   11.4   9.6      0.044   14.4   1.7    2.9  3  Cytochrom_B562  Cytochrome b562
       0.54   10.3   6.8       0.81    9.7   0.5    2.6  2  Spidroin_N      Major ampullate spidroin 1, spider silk prote


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.1   9.1  2.3e-117  3.7e-114       2     333 .]      59     387 ..      58     387 .. 0.99
   2 ?   -1.1   0.3      0.44   7.2e+02      19      67 ..     512     550 ..     492     577 .. 0.51
   3 !  181.4   2.7   1.3e-56   2.1e-53       2     200 ..     607     826 .]     606     826 .] 0.97

  Alignments for each domain:
  == domain 1  score: 381.1 bits;  conditional E-value: 2.3e-117
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    + p+da+s++am+r+++ f+e  ds++i++vvl e+d+ lg+ +a++++d+lvd l  d++h+++++df++dp +aa++v
  gi|121638226|ref|YP_978450.1|  59 VAPDDAQSMRAMRRAGKVFNE-FDSNSIAMVVL-ESDQPLGE-KAHRYYDHLVDTLVLDQSHIQHIQDFWRDPLTAAGAV 135
                                    5799*****************.***********.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    S+Dgkaa+++++l+g+ g+ +a+esv+a+r++v++ +p+eg++ +vtGpaa++ad+  a+dr++kli+ +t++vi v+Ll
  gi|121638226|ref|YP_978450.1| 136 SADGKAAYVQLYLAGNMGEALANESVEAVRKIVANSTPPEGIRTYVTGPAALFADQIAAGDRSMKLITGLTFAVITVLLL 215
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                    +vyrS+++ ll+l +v ++l+a++g++++l ++ +++lstfv+++l++l+ia+GtDYa++Lv+Ry+e+++ g++re++++
  gi|121638226|ref|YP_978450.1| 216 LVYRSIATTLLILPMVFIGLGATRGTIAFLGYHGMVGLSTFVVNILTALAIAAGTDYAIFLVGRYQEARHIGQNREASFY 295
                                    ******************************************************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrr 321
                                    +++++t++v++++Glt+a+a+++L++arl+ ++++G+++a+G+lv+v+++lTl PA+++++Gr++l +p+r++k+r Wrr
  gi|121638226|ref|YP_978450.1| 296 TMYRGTANVILGSGLTIAGATYCLSFARLTLFHTMGPPLAIGMLVSVAAALTLAPAIIAIAGRFGLLDPKRRLKTRGWRR 375
                                    ******************************************************************************** PP

                           MMPL 322 lgrlvvrrPlpv 333
                                    +g++vvr+P p+
  gi|121638226|ref|YP_978450.1| 376 VGTAVVRWPGPI 387
                                    *********985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.44
                           MMPL  19 afpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgev 67 
                                    ++ + ++           ++de+l + ++++++ +lv++l++ t +++++
  gi|121638226|ref|YP_978450.1| 512 RMADmLT-----------MSDEMLVAINSMEQMLDLVQQLNDVTHEMAAT 550
                                    3333333...........44444444444444444444444444443332 PP

  == domain 3  score: 181.4 bits;  conditional E-value: 1.3e-56
                           MMPL   2 lspadaesvkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf.......... 70 
                                    l++++ +++++m+++ea  p+ +a  +++i++++++++++l+++++ ++v++++++++++++++g+++d+          
  gi|121638226|ref|YP_978450.1| 607 LTDQLRALTDDMNKMEALTPQfLALLPPMITTMKTMRTMMLTMRSTISGVQDQMADMQDHATAMGQAFDTaksgdsfylp 686
                                    67889999**************************************************************9999999999 PP

                           MMPL  71 ...lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdas 141
                                       +++ +   ++++f+S++gka+r+++++e dp+ste++++++airaa ++a    pl+g+k++++G+aat++d+rd++
  gi|121638226|ref|YP_978450.1| 687 peaFDNAEfqqGMKLFLSPNGKAVRFVISHESDPASTEGIDRIEAIRAATKDAIkatPLQGAKIYIGGTAATYQDIRDGT 766
                                    99877887888*****************************************99999*********************** PP

                           MMPL 142 drdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglels 200
                                    ++d+ ++++++++++++++l++++Sl+a l++++tv++sl++a+gl vli++++ gl+++
  gi|121638226|ref|YP_978450.1| 767 KYDILIVGIAAVCLVFIVMLMITQSLIASLVIVGTVLLSLGTAFGLsVLIWQHFVGLQVH 826
                                    *********************************************************997 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.8e-05      0.03       7      65 ..     520     573 ..     517     584 .. 0.74
   2 ?    0.3   0.0      0.64     1e+03      12      63 ..     616     666 ..     597     682 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                   Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvr 65 
                                     +e   ++n++e++++  ++l ++     ++e+  t++e++++ ++++  l d+++ vr
  gi|121638226|ref|YP_978450.1| 520 SDEMLVAINSMEQMLDLVQQLNDV-----THEMAATTREIKATTSELRDHLADIDDFVR 573
                                    677888999999999999998888.....566777777777777777777777776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.64
                   Syntaxin-6_N  12 kslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeet 63 
                                    + +nk+e+l  ++  ll   ++ t + ++  +  +r++++ ++ ++ d+++ 
  gi|121638226|ref|YP_978450.1| 616 DDMNKMEALTPQFLALLPPMIT-TMKTMRTMMLTMRSTISGVQDQMADMQDH 666
                                    5677777777777776666665.48888888888999999999999888875 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   2.2e-06    0.0035     231     375 ..     520     667 ..     511     682 .. 0.72
   2 ?   -4.1   0.9       1.7   2.7e+03     417     437 ..     772     792 ..     757     801 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                       Prominin 231 esnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdln...qa.lsn.lCqs.eeCskilssle 304
                                    ++++l a++++e++l+ +++ ++  +++ +++ e++ ++s+Lrd l ++ + ++   +    +  C +   Cs ++s  +
  gi|121638226|ref|YP_978450.1| 520 SDEMLVAINSMEQMLDLVQQLNDVTHEMAATTREIKATTSELRDHLADIDDFVRplrSYfYWEhHCFDiPLCSATRSLFD 599
                                    56678889999999999999999999999999999999999999998876555411132122347887789999999998 PP

                       Prominin 305 iekldtskcl.dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqi 375
                                    +  ld   +l dql  +++ ++++e ++ + l+ ++   ++++++++ ++  +++++++ ++ ++a+ +++ 
  gi|121638226|ref|YP_978450.1| 600 T--LDGVDTLtDQLRALTDDMNKMEALTPQFLALLP-PMITTMKTMR-TMMLTMRSTISGVQDQMADMQDHA 667
                                    8..99988889**************99888888777.4555665554.344455555555555555555444 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.7
                       Prominin 417 liglivcsllllivvililgL 437
                                    ++g+ + +l+++++++   +L
  gi|121638226|ref|YP_978450.1| 772 IVGIAAVCLVFIVMLMITQSL 792
                                    555555555555555555444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3    0.0011       1.8      27      78 ..     518     568 ..     497     580 .. 0.77
   2 ?    4.1   0.0     0.028        45      44     105 ..     605     669 ..     588     679 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                        DUF1664  27 klsdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeq 78 
                                    ++sd m v   s+++ ++ v +ql++v +++aat r++++   ++ ++l + 
  gi|121638226|ref|YP_978450.1| 518 TMSDEMLVAINSMEQMLDLV-QQLNDVTHEMAATTREIKATTSELRDHLADI 568
                                    67888888888888888766.6888888888888888887777777666554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                        DUF1664  44 esvskqleqvseslaatkr...hLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                    ++++ ql  + +++++      ++ + +  + ++++ +  +   +++ ++ v+++++++++  ++
  gi|121638226|ref|YP_978450.1| 605 DTLTDQLRALTDDMNKMEAltpQFLALLPPMITTMKTMRTMMLTMRSTISGVQDQMADMQDHATA 669
                                    44444444444433333221113333333344444444444444555555555555555544444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   0.00023      0.37       8     116 ..     526     640 ..     519     648 .. 0.76
   2 ?    4.5   0.2      0.02        33      40     104 ..     604     670 ..     590     675 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                   Baculo_PEP_C   8 nggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt.......rldtlltnLtdalnalq 80 
                                     +++  q ldL ++Ln++    + ++ +++++  ++   L ++++ ++ l + +          l +++  L d+l  + 
  gi|121638226|ref|YP_978450.1| 526 AINSMEQMLDLVQQLNDVTHEMAATTREIKATTSELRDHLADIDDFVRPLRSYFYWehhcfdiPLCSATRSLFDTLDGV- 604
                                    678899************9999999999999999999999999998888777766556666665666666666666655. PP

                   Baculo_PEP_C  81 dtlrneLtnlnsiltnLlssvtNinstLnnllqaln 116
                                    dtl+ +L +l+ +++ + +  +   + L  ++++++
  gi|121638226|ref|YP_978450.1| 605 DTLTDQLRALTDDMNKMEALTPQFLALLPPMITTMK 640
                                    588888888888888888777777776666666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                   Baculo_PEP_C  40 ldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNi 104
                                    +d++  qL al++d+++ +++l+ ++ +ll  + ++++++     t+r+ + +++ ++++++   t +
  gi|121638226|ref|YP_978450.1| 604 VDTLTDQLRALTDDMNK-MEALTPQFLALLPPMITTMKTMRtmmLTMRSTISGVQDQMADMQDHATAM 670
                                    67788888888888888.66677788888888888887777666788999999999998888776665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.014        22      17      51 ..     535     569 ..     529     574 .. 0.90
   2 ?    3.6   0.0     0.064     1e+02      33      54 ..     604     625 ..     597     634 .. 0.86
   3 ?    1.3   0.0      0.34   5.6e+02      21      56 ..     641     676 ..     637     687 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                           SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                    d++++Lndv  e + +  ++++   +l+++l++++
  gi|121638226|ref|YP_978450.1| 535 DLVQQLNDVTHEMAATTREIKATTSELRDHLADID 569
                                    799**************************999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                                    HHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX  33 idrlqrqlrllaerlkeleess 54 
                                    +d l+ qlr+l++ ++++e+ +
  gi|121638226|ref|YP_978450.1| 604 VDTLTDQLRALTDDMNKMEALT 625
                                    799************9998765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.34
                                    HHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                           SlyX  21 eLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                    ++  ++   + +i+  q q++ ++++  ++ ++  +
  gi|121638226|ref|YP_978450.1| 641 TMRTMMLTMRSTISGVQDQMADMQDHATAMGQAFDT 676
                                    556666677777777778888777777777666554 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  10.0    0.0049       7.9     311     488 ..     174     355 ..     151     383 .. 0.65
   2 ?    7.3   0.2   0.00049       0.8     860     903 ..     766     809 ..     717     821 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0049
                                    STTEEEEEEEESHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHH..SSHHHHHHHHHHHHHHHH......HHHHHHH...H CS
                       ACR_tran 311 Pegveivvvydrtefvra.sieeVvktLleaivLvvlvvflFL..qnlratlipaiavPlsll......gtfavlk...a 378
                                    Peg+ + v+   + f ++ +  + + +L+ ++  +v++v+l L  +++ +tl   +++P++ +      gt+a+l    +
  gi|121638226|ref|YP_978450.1| 174 PEGIRTYVTGPAALFADQiAAGDRSMKLITGLTFAVITVLLLLvyRSIATTL---LILPMVFIglgatrGTIAFLGyhgM 250
                                    5555555555555554321445667788999888888888877334555554...4444444322222268888862223 PP

                                    TT--...BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHH CS
                       ACR_tran 379 lgfs...lNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGv 455
                                    +g+s   +N l   +L++A G   D Ai  v   ++  +    +++ea++++m   +  ++ ++   +a     l++  +
  gi|121638226|ref|YP_978450.1| 251 VGLStfvVNIL--TALAIAAGT--DYAIFLVGRYQEARHI--GQNREASFYTMYRGTANVILGSGLTIAGATYCLSFARL 324
                                    44442215554..488888885..9999999876543333..44677777777777777777777666666555555555 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH CS
                       ACR_tran 456 eGklfrqfaltivlaillsvlvaltltPalcal 488
                                       lf+ ++  +++ +l+sv  altl Pa+ a+
  gi|121638226|ref|YP_978450.1| 325 --TLFHTMGPPLAIGMLVSVAAALTLAPAIIAI 355
                                    ..5999999999999999999999999999886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00049
                                    HHCHHHHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHHHHHHHH CS
                       ACR_tran 860 asnsllilvalalllvflvLaalyeslsepllilltvPlalvGa 903
                                    ++  +li+ ++a+ lvf+v+ +  +sl++ l+i+ tv l+l  a
  gi|121638226|ref|YP_978450.1| 766 TKYDILIVGIAAVCLVFIVMLMITQSLIASLVIVGTVLLSLGTA 809
                                    33445667778888999999999999999999988887766544 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.8   0.00014      0.23      40     189 ..     522     672 ..     500     676 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHT..SS-TTS............... CS
                          APG17  40 kteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrk..tkvepsfrpegee........ 109
                                    ++   +++++q l+l++               +++d+ +e+ a ++++++t ++Lr+   +++ ++rp  +         
  gi|121638226|ref|YP_978450.1| 522 EMLVAINSMEQMLDLVQ---------------QLNDVTHEMAATTREIKATTSELRDhlADIDDFVRPLRSYfywehhcf 586
                                    33333333344444433...............444445555555555555555554422234444444442255555677 PP

                                    ........STGGGCS--TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH-------STCCHHHHHHHHHH CS
                          APG17 110 ........ktLlDFvdedsveelkealkesidelqaaqkkldssllefdtdlrelkkelsksksksessslipellkele 181
                                            ++L+D    d+v+ l ++l++++d+++++++ + + l  +   ++++k+    + + +++ s +++ +++++
  gi|121638226|ref|YP_978450.1| 587 diplcsatRSLFD--TLDGVDTLTDQLRALTDDMNKMEALTPQFLALLPPMITTMKTMRTMMLTMRSTISGVQDQMADMQ 664
                                    88899999***99..6779*****************99999999998888888887766433344599************ PP

                                    HHHHHHHH CS
                          APG17 182 sleeemAs 189
                                    +++++m +
  gi|121638226|ref|YP_978450.1| 665 DHATAMGQ 672
                                    *****976 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.8       1.2   1.9e+03       4      28 ..     201     225 ..     200     227 .. 0.92
   2 ?   11.7   0.1   0.00014      0.23      24      66 ..     530     571 ..     518     580 .. 0.64
   3 ?    2.0   0.1      0.15   2.5e+02      31      52 ..     600     621 ..     586     630 .. 0.53
   4 ?    6.2   0.3    0.0077        13      10      52 ..     628     670 ..     625     679 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                         DUF948   4 lIaAiAFvvLviflivvllklkktl 28 
                                    lI  ++F+v++++l  v ++++ tl
  gi|121638226|ref|YP_978450.1| 201 LITGLTFAVITVLLLLVYRSIATTL 225
                                    8999**************9999886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                         DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvnek 66 
                                    ++++ld + ++++++++++ ++++e+++++++ ++ l+d+ + 
  gi|121638226|ref|YP_978450.1| 530 MEQMLD-LVQQLNDVTHEMAATTREIKATTSELRDHLADIDDF 571
                                    344443.345677777777777777777777777777666554 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.15
                         DUF948  31 aaatieelekqvdpilkevedl 52 
                                    + + +++l++q+++++++++++
  gi|121638226|ref|YP_978450.1| 600 TLDGVDTLTDQLRALTDDMNKM 621
                                    3333444555555555554444 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0077
                         DUF948  10 FvvLviflivvllklkktldeaaatieelekqvdpilkevedl 52 
                                    F++L   +i +++ ++ ++  +++ti ++++q+  + + ++++
  gi|121638226|ref|YP_978450.1| 628 FLALLPPMITTMKTMRTMMLTMRSTISGVQDQMADMQDHATAM 670
                                    6777777899999999999999**********99999998877 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.8      0.86   1.4e+03      21      55 ..     529     562 ..     509     576 .. 0.47
   2 ?   14.4   1.7   2.7e-05     0.044       4      66 ..     640     704 ..     637     736 .. 0.82
   3 ?   -1.8   0.0         3   4.9e+03      28      48 ..     728     746 ..     706     761 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.86
                 Cytochrom_B562  21 daeelkkalkelraaaedakeatpsklekdseeqk 55 
                                    ++e++ + +++l+ + ++  ++t  +++   +e +
  gi|121638226|ref|YP_978450.1| 529 SMEQMLDLVQQLNDVTHEMAATTR-EIKATTSELR 562
                                    444444444444443333332222.3333333333 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.7e-05
                 Cytochrom_B562   4 eeMkqmkkalkqva..kaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklid 66 
                                    ++M +m   +++     +d++++++++++++ +a++ ak++  + l  ++ + +++q+G++ +++
  gi|121638226|ref|YP_978450.1| 640 KTMRTMMLTMRSTIsgVQDQMADMQDHATAMGQAFDTAKSGDSFYLPPEAFDNAEFQQGMKLFLS 704
                                    678888888877666668999**********************99999999*********98876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                 Cytochrom_B562  28 alkelraaaedakeatpskle 48 
                                     ++++raa +da +atp  l+
  gi|121638226|ref|YP_978450.1| 728 RIEAIRAATKDAIKATP--LQ 746
                                    57889999999999999..44 PP

>> Spidroin_N  Major ampullate spidroin 1, spider silk protein 1, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5    0.0005      0.81      26      93 ..     509     575 ..     493     586 .. 0.79
   2 ?    2.8   1.0     0.068   1.1e+02      20      47 ..     650     677 ..     635     689 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                                    -HHHHHHHHHHHHHHHHHHHHHHHTTS--HHHHHHHHHHHHHHHHHHHHHSSSSSHHHHHHHHHHHHH CS
                     Spidroin_N  26 saqqmdDlesiadtilsavdkmarsgksskaklqAlnmafAssiAeiavaesggkslsakinaianal 93 
                                     ++ m+D+ +++d++l a+++m+ +     ++l  ++  +A+   ei ++ s  ++  a+i+  +  l
  gi|121638226|ref|YP_978450.1| 509 MRERMADMLTMSDEMLVAINSME-QMLDLVQQLNDVTHEMAATTREIKATTSELRDHLADIDDFVRPL 575
                                    4789******************8.77778889999999999999999998876666666666555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.068
                                    HTCSSS-HHHHHHHHHHHHHHHHHHHHH CS
                     Spidroin_N  20 sqsgvfsaqqmdDlesiadtilsavdkm 47 
                                     ++    ++qm+D+++ a ++ +a+d  
  gi|121638226|ref|YP_978450.1| 650 RSTISGVQDQMADMQDHATAMGQAFDTA 677
                                    3333334677777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (826 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.86u 0.29s 00:00:01.14 Elapsed: 00:00:00.42
# Mc/sec: 5967.06
//
Query:       gi|121638227|ref|YP_978451.1|  [L=131]
Description: transmembrane transport protein mmpL9b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-44  150.4   9.0    6.2e-44  150.3   9.0    1.0  1  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   9.0   3.5e-48   6.2e-44     206     331 ..       1     111 [.       1     116 [. 0.95

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 3.5e-48
                           MMPL 206 llvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvl 285
                                    ++v++l+avG+DY+llLvsR++ee++ag ++  ++ira+a+tg vvt aGl++a++m++++v++l+v++qvG++i+lG+l
  gi|121638227|ref|YP_978451.1|   1 MSVIVLLAVGSDYNLLLVSRFKEEVGAGLKT--GIIRAMAGTGAVVTSAGLVFAFTMASMAVSELRVIGQVGTTIGLGLL 78 
                                    789****************************..*********************************************** PP

                           MMPL 286 vdvlivlTll.PAllvllGraalakprrkrkkrwWrrlgrlvvrrPl 331
                                    +d+l+v++++ P++++llGr+           +wW+++   +++rP+
  gi|121638227|ref|YP_978451.1|  79 FDTLVVRSFMtPSIAALLGRW-----------FWWPNM---IHSRPT 111
                                    *********************...........***999...555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.51
# Mc/sec: 769.18
//
Query:       gi|121638228|ref|YP_978452.1|  [L=413]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-31  108.5  21.0    1.5e-31  108.5  21.0    2.5  2  PE              PE family
  ------ inclusion threshold ------
        1.4    7.3   6.3      0.074   11.5   0.5    1.6  2  DUF1631         Protein of unknown function (DUF1631)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5  21.0   1.7e-35   1.5e-31       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -2.8   6.0      0.91   8.2e+03      33      71 ..     292     330 ..     278     337 .. 0.49

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 1.7e-35
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+v++aP++laa a++la+igs+++aanaaaaapt++vlaa+ D+VSa iAalf+a aq+yqa+saqaa fh++fvq l++
  gi|121638228|ref|YP_978452.1|  1 MSHVTAAPNVLAASAGELAAIGSTMRAANAAAAAPTAGVLAAGGDDVSAGIAALFGARAQAYQAISAQAALFHDRFVQILQE 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a++Ya aEaa
  gi|121638228|ref|YP_978452.1| 83 GAAAYAMAEAA 93
                                   *********97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.91
                                    HHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  33 aapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaa 71 
                                     a+  av +a    V a   ++ ++ aq+++a +  ++a
  gi|121638228|ref|YP_978452.1| 292 VATAPAVSPATTSAVAAESGSTPATKAQAMHATTNPGNA 330
                                    333333444444444444444444444444444444444 PP

>> DUF1631  Protein of unknown function (DUF1631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7      0.11   9.9e+02      53      89 ..      59      95 ..      10     120 .. 0.49
   2 ?   11.5   0.5   8.3e-06     0.074     206     310 ..     288     406 ..     255     411 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.11
                        DUF1631 53 fdamrelrrkrkaierrflqalekafaelaaakaaaa 89
                                    +a + +  +++ + +rf q l++  a+ a+a+aa+a
  gi|121638228|ref|YP_978452.1| 59 AQAYQAISAQAALFHDRFVQILQEGAAAYAMAEAANA 95
                                   2333333333333333333333333333333333222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.3e-06
                        DUF1631 206 vlPelkaapr...arqsrrasasaagaaeekeeeqkaPaaaaaaaag.....aaeaqasaaaaaegaae........... 266
                                    v P + +ap    a           + ++   e+ ++Pa++a+a++      +a  q+++a+                  
  gi|121638228|ref|YP_978452.1| 288 VAPAVATAPAvspA-----------TTSAVAAESGSTPATKAQAMHAttnpgNAAHQGNPAD------Pgnsarradggr 350
                                    55555555552221...........2222222233333333322222000001111111111......112222344556 PP

                        DUF1631 267 ..........lfsaLqqLLsqareaaaaaaqaassasg..aearalssaeLlqaLs 310
                                               +  L++ L++ ++ +a +   ++s+++   ++r+++ ++Ll+aL+
  gi|121638228|ref|YP_978452.1| 351 deqllllpltSLRGLRHTLKKLSGLRARNGLLTASGDNasGSGRPWDRDQLLRALG 406
                                    678899*99999999999999999999998888888888899************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2785.48
//
Query:       gi|121638229|ref|YP_978453.1|  [L=139]
Description: lipoprotein lppQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1076.20
//
Query:       gi|121638230|ref|YP_978454.1|  [L=85]
Description: hypothetical protein BCG_2365 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 640.59
//
Query:       gi|121638231|ref|YP_978455.1|  [L=639]
Description: DNA primase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-36  122.9   0.0    1.3e-35  122.2   0.0    1.3  1  Toprim_N        DNA primase catalytic core, N-terminal domain
    1.1e-34  118.2   0.0      2e-34  117.3   0.0    1.4  1  zf-CHC2         CHC2 zinc finger
    3.4e-31  108.4   0.1    9.1e-31  107.0   0.1    1.8  1  DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
    1.4e-18   66.8   0.3    4.3e-18   65.2   0.0    2.1  2  DnaB_bind       DnaB-helicase binding domain of primase
    3.6e-13   49.8   0.1    8.6e-13   48.6   0.1    1.6  1  Toprim_4        Toprim domain
    2.1e-08   34.5   0.0    4.7e-08   33.3   0.0    1.7  1  Toprim_2        Toprim-like
    7.5e-07   29.3   0.0    1.7e-06   28.2   0.0    1.6  1  Toprim          Toprim domain
    0.00019   21.7   0.1    0.00079   19.7   0.0    2.1  2  Toprim_3        Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_N  DNA primase catalytic core, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.0   5.9e-39   1.3e-35       1     127 [.     127     254 ..     127     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 5.9e-39
                                    HHHHHHHCSCHHHHHHHHHCTT--HHHHHHCT-EEE-SHSCHHHHHHHHCT-HHHHHCCTTCEECSTTT-EEETTTTEEE CS
                       Toprim_N   1 fykeelkseegekaleYLkkRglseetiekFqlGyapkswdnllkllkkkkvseeelleagllskkekgklydrFrnRim 80 
                                    fy + l+s+e + a++YL++R ++ + ++kF++G+ap++wd+l+k+l++k+++ eel++agl ++ + ++ +drF++R++
  gi|121638231|ref|YP_978455.1| 127 FYAQALQSDEAAPARQYLTERSFDAAAARKFGCGFAPSGWDSLTKHLQRKGFEFEELEAAGLSRQGR-HGPMDRFHRRLL 205
                                    7999**********************************************************99886.8*********** PP

                                    EEEE-TTS-EEEEEEEES..SS-SS.SEEE--SBTTB-CCC-EETHHHH CS
                       Toprim_N  81 fPikdakgkvvgFgGRal..eeeekaKYlNspetelFkKselLYgldea 127
                                    +Pi+ + g+vvgFg+R+l  ++  +aKY+N+pet l+kKs++++g+d a
  gi|121638231|ref|YP_978455.1| 206 WPIRTSAGEVVGFGARRLfdDDAMEAKYVNTPETLLYKKSSVMFGIDLA 254
                                    ******************98777899*******************9987 PP

>> zf-CHC2  CHC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.0   8.7e-38     2e-34       2      95 ..       6     100 ..       5     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 8.7e-38
                        zf-CHC2   2 seevidelkeridivdvveeyvkLkkkgkd.yvalCPFHeektpsftvspekqfyyCfgCgagGdaikFlmeieklsfve 80 
                                    s++ i++++e ++i dvv++yv+L+++g+d  ++lCPFH+ek+psf+v+p++++++CfgCg+gGd+++F+++ie++sfve
  gi|121638231|ref|YP_978455.1|   6 SDRDIAAIREGARIEDVVGDYVQLRRAGADsLKGLCPFHNEKSPSFHVRPNHGHFHCFGCGEGGDVYAFIQKIEHVSFVE 85 
                                    567899**********************9879************************************************ PP

                        zf-CHC2  81 aveklakklglelea 95 
                                    ave la+++g+++++
  gi|121638231|ref|YP_978455.1|  86 AVELLADRIGHTISY 100
                                    **********99987 PP

>> DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.1   4.1e-34   9.1e-31       1     124 []     487     614 ..     487     614 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 4.1e-34
                 DnaG_DnaB_bind   1 vrealallLqhPelagelpdalaleafedpglallrelieal.aaepelntaaLlerlrg.tp...eeallaeLaveelq 75 
                                    +real+ +Lq+P+lag+++dal+ e f++p++a++r++i+++ +++ +l++a++l+ +r+ t     +al++eL ve +q
  gi|121638231|ref|YP_978455.1| 487 QREALKSALQYPALAGPVFDALTVEGFTHPEYAAVRAAIDTAgGTSAGLSGAQWLDMVRQqTTstvTSALISELGVEAIQ 566
                                    7*****************************************8777999**********8666999************** PP

                 DnaG_DnaB_bind  76 veeeeelerefadalarLqeqlverriaeLkaklrqgL.seeEkeelreL 124
                                    v+++ +l r++a++larLqe +++r+iae+k+kl q++ + e+ +e+++L
  gi|121638231|ref|YP_978455.1| 567 VDDD-KLPRYIAGVLARLQEVWLRRQIAEVKSKL-QRMsPIEQGDEYHAL 614
                                    ****.7****************************.***999999999987 PP

>> DnaB_bind  DnaB-helicase binding domain of primase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.3   1.4e+04      16      26 ..     321     331 ..     320     331 .. 0.81
   2 !   65.2   0.0   1.9e-21   4.3e-18       1      54 [.     376     429 ..     376     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.3
                                    SHHHHHHHHHH CS
                      DnaB_bind  16 tpegkaravre 26 
                                    ++ g+a+a+++
  gi|121638231|ref|YP_978455.1| 321 DEAGRAAALKA 331
                                    5789****985 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 1.9e-21
                                    HHHHHHHTTTT--TTSHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHHT-- CS
                      DnaB_bind   1 seFlierllegydlstpegkaravrealpllaripdpieRdlYirrlAerlgid 54 
                                    +eF+i+ ++++ dl+++eg+++a+r+++p++ +i+dp +Rd+Y+r+lA+++g+ 
  gi|121638231|ref|YP_978455.1| 376 FEFAIRAAIAEMDLDSAEGRVAALRRCVPMVGQIKDPTLRDEYARQLAGWVGWA 429
                                    7***************************************************95 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   3.8e-16   8.6e-13       2      77 ..     263     336 ..     262     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.8e-16
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlveaekkvkevilaldgDaeGeataerlae..l 77 
                                    ++++VEgy+Dv+a++ ag++++va++g+a+   ++++++++   +   +      e+i ++dgD++G a+a+++ +  +
  gi|121638231|ref|YP_978455.1| 263 QAVVVEGYTDVMAMHLAGVTTAVASCGTAF-GGEHLAMLRRLMmD---D-SFFRGELIYVFDGDEAGRAAALKAFDgeQ 336
                                    689***************************.99999966655522...2.223489*****************988541 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.1e-11   4.7e-08       1      88 [.     265     355 ..     265     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.1e-11
                       Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllery......pekkvvlalDnDkaGrkaakrlaellreagvr 74 
                                    vv+Eg+ D+++++ +g +    +va+ Gta+  ++l +l+r          +++  +D D+aGr+aa ++ +  ++   +
  gi|121638231|ref|YP_978455.1| 265 VVVEGYTDVMAMHLAGVT---TAVASCGTAFGGEHLAMLRRLmmddsfFRGELIYVFDGDEAGRAAALKAFDGEQKLAGQ 341
                                    79***************7...********99999999998884433332236***************9998777777778 PP

                       Toprim_2  75 ekirelpegkDwne 88 
                                      ++  p+g D+ +
  gi|121638231|ref|YP_978455.1| 342 SFVAVAPDGMDPCD 355
                                    88888889999877 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   7.4e-10   1.7e-06       2      91 ..     264     335 ..     263     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.4e-10
                                    EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHS....EEEEECSSSHHHH CS
                         Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakrad....eiilatDpDreGe 77 
                                     v+vEg++d+++++ a   g ++++as+G+++  e+               l++l++l  + +    e+i+ +D+D++G+
  gi|121638231|ref|YP_978455.1| 264 AVVVEGYTDVMAMHLA---GVTTAVASCGTAFGGEH---------------LAMLRRLMMDDSffrgELIYVFDGDEAGR 325
                                    69**************...9****************...............777888887777999************** PP

                                    HHHHHHHHHHTHHH CS
                         Toprim  78 aiawellevlkell 91 
                                    a+a++++    ++ 
  gi|121638231|ref|YP_978455.1| 326 AAALKAF----DGE 335
                                    *****99....444 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.5e-07   0.00079       2      94 ..     264     362 ..     263     363 .. 0.77
   2 ?   -2.5   0.0       3.1     7e+03      16      39 ..     546     569 ..     541     600 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                       Toprim_3   2 liivEGietaLsileartgaaviAllsa.......anlkaiawp..ergkrvviaaDnDaandGreaaeklaerleaagi 72 
                                    +++vEG+ ++++  +    ++++A  ++       a l+++ ++  + + +++ ++D+D a  Gr+aa k+ +  ++   
  gi|121638231|ref|YP_978455.1| 264 AVVVEGYTDVMAM-HLAGVTTAVASCGTafggehlAMLRRLMMDdsFFRGELIYVFDGDEA--GRAAALKAFDGEQKLAG 340
                                    589**********.444444455544444444366777888888755888888899*****..*************9666 PP

                       Toprim_3  73 eavllepaegeDwndvlqkeGa 94 
                                    + +++++++g D +d+  k+G 
  gi|121638231|ref|YP_978455.1| 341 QSFVAVAPDGMDPCDLRLKCGD 362
                                    666667779********99996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.1
                       Toprim_3  16 eartgaaviAllsaanlkaiawpe 39 
                                    ++ t + + Al+s  +++ai++++
  gi|121638231|ref|YP_978455.1| 546 QQTTSTVTSALISELGVEAIQVDD 569
                                    566667777888888888888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4406.74
//
Query:       gi|121638232|ref|YP_978456.1|  [L=431]
Description: deoxyguanosinetriphosphate triphosphohydrolase-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   74.0   0.0    2.2e-20   73.1   0.0    1.5  1  HD        HD domain
      1e-15   58.0   0.5      2e-15   57.1   0.5    1.5  1  HD_assoc  Phosphohydrolase-associated domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   2.5e-24   2.2e-20       1     120 [.      72     220 ..      72     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.5e-24
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHH....CTCCHHHHHHHHHHHHHHHHHHHH CS
                             HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeee....fekflaHekvgaeilrevekrlgl 76 
                                    rl+HsleVa+++r +a+ lg  +d +l++la+L HDiG++p g+++e++ +e    +++f+++++ ++ +++ ++k+ + 
  gi|121638232|ref|YP_978456.1|  72 RLTHSLEVAQIGRGMAIGLG--CDLDLVELAGLAHDIGHPPYGHNGERALDEvaasHGGFEGNAQNFRILTSLEPKVVDA 149
                                    789*****************..***************************6666778******************999966 PP

                                    H.HHHHHHHHHTTCCHHHHHHHH.........................H...HHHCCTSCHHHHHHHHHHHHH CS
                             HD  77 d.ledvaklirehheswegkkrp.........................r...glaerqlslearivklaDrla 120
                                      l++ ++l r+ ++     k+p                         +   g +++  +lea+++++aD +a
  gi|121638232|ref|YP_978456.1| 150 QgLSAGLNLTRASLDAVT--KYPwmrgdglgsqrrkfgfydddresavWvrqGAPPERACLEAQVMDWADDVA 220
                                    6**************995..88899999999999999998887766551668******************987 PP

>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.5   2.3e-19     2e-15       2      88 ..     330     417 ..     329     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.3e-19
                       HD_assoc   2 avseevaaeiaeLkkflfenvyrhpevqreeekarriireLfealledperllpeefrarleaaedd.araRvVcDyiAg 80 
                                    +v++ v+ae+a+Lk ++++ ++++p++ ++++++r+ i+++ + l++ +++ l++ ++a++++a+dd ar RvV+D+iA+
  gi|121638232|ref|YP_978456.1| 330 QVPDLVRAEVAVLKILALQFIMSDPRHLETQARQRERIHRVAHRLYSGAPQTLDPVYAAAFNTAADDaARLRVVVDQIAS 409
                                    78999******************************************9999***************9************* PP

                       HD_assoc  81 mTDryalr 88 
                                     T+    r
  gi|121638232|ref|YP_978456.1| 410 YTEGRLER 417
                                    **998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3019.24
//
Query:       gi|121638233|ref|YP_978457.1|  [L=660]
Description: hypothetical protein BCG_2368 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-17   63.6   0.0    4.1e-17   62.5   0.0    1.6  1  TPM_phosphatase  TPM domain
  ------ inclusion threshold ------
      0.032   14.1   0.1        5.9    6.7   0.0    2.8  2  CK2S             Casein Kinase 2 substrate
      0.048   13.5   0.1       0.14   12.0   0.1    1.8  1  TMEM51           Transmembrane protein 51
      0.074   12.9   0.0         15    5.4   0.0    2.3  2  EssA             WXG100 protein secretion system (Wss), prote
      0.094   12.8   1.9         10    6.2   0.1    3.2  3  DUF1664          Protein of unknown function (DUF1664)
       0.16   12.4   2.0       0.69   10.3   2.0    2.1  1  HHH_8            Helix-hairpin-helix domain
        0.2   11.6   0.0       0.54   10.2   0.0    1.7  1  TMEM154          TMEM154 protein family
        4.4    8.0  13.5        4.6    7.9   0.5    4.0  4  SlyX             SlyX
        7.5    5.8   8.1        1.7    8.0   0.4    2.9  4  Rab5-bind        Rabaptin-like protein


Domain annotation for each model (and alignments):
>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   2.1e-20   4.1e-17       1     123 [.      36     153 ..      36     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.1e-20
                                    EEE-SS-S-HHHHHHHHHHHHHHHHTT--EEEEEEESB-TT--HHHHHHHHHHHHSTTTTS-SSEEEEEEETTTTEEEEE CS
                TPM_phosphatase   1 vvDeaglLsdeeeaeleeklaalekktgvqivvvtvdsldgediedyadelfdkwglgkkkkdngvllliavddrkvrie 80 
                                    v+D+ag+L+++ +++++++ ++l++++ ++++vv+v+++ g+++ ++a+++ ++  lg+      +ll++a+  r++++ 
  gi|121638233|ref|YP_978457.1|  36 VTDNAGVLTSSGRTAVTAAVDRLYADRRIRLWVVYVENFSGQSALNWAQRTTRTSELGN----YDALLAVATTGREYAFL 111
                                    89*****************************************99**************....569*****999****** PP

                                    E-STTTTT--HHHHHHHHHHTHHHHHHHT-HHHHHHHHHHHHH CS
                TPM_phosphatase  81 tgyglegaltdaraesildetilpalkdgdyaggilaavdaie 123
                                    + +++ g +++++++++++ +i+pal dgdy+g+++aa+++++
  gi|121638233|ref|YP_978457.1| 112 VPSAMPG-VSEGQVDNVRRYQIEPALHDGDYSGAAVAAANGLN 153
                                    *****98.******************************99876 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.02        39      62     107 ..     411     456 ..     362     466 .. 0.77
   2 ?    6.7   0.0     0.003       5.9      62     105 ..     491     534 ..     471     545 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                           CK2S  62 ekqlealeevlakLrekleelqkvrdsleklvrdalqlyeekadkl 107
                                    +++l a+++  +++r  +++l  v+ +++   + a+q++++ ++++
  gi|121638233|ref|YP_978457.1| 411 RALLDAVDSAATDIRHAVASLPAVVADIQTGIKRANQHLQQAQQPQ 456
                                    46899***********************************988844 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                           CK2S  62 ekqlealeevlakLrekleelqkvrdsleklvrdalqlyeekad 105
                                     k  + l+++la+L e+ ++ + +++sle+++ +a + ++  ++
  gi|121638233|ref|YP_978457.1| 491 TKVDADLDRLLATLAEEQATADRLNRSLEQALFTAESRVRAVSE 534
                                    688999*************************9888777766555 PP

>> TMEM51  Transmembrane protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     7e-05      0.14      56      99 ..     154     197 ..     130     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                         TMEM51  56 kksktssvAyVLvGaGvalLlLsicLgirdkkrarqeeeelara 99 
                                    ++  +ss  + Lv +G++++++++ L +  ++ +r++ +ela+a
  gi|121638233|ref|YP_978457.1| 154 RSPSSSSRVVLLVTVGIIVIVVAVLLVVMRHRNRRRRADELAAA 197
                                    334456666779***********999875554444455554443 PP

>> EssA  WXG100 protein secretion system (Wss), protein EssA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0074        15      94     145 ..     139     184 ..     121     187 .. 0.67
   2 ?    5.1   0.0    0.0095        19      62     107 ..     493     538 ..     488     550 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0074
                           EssA  94 seYevrasasevassetaeEesisktkskiiilliaggvvalaiGlyvvlrk 145
                                    ++Y   a    va ++  +  + s+  s++++l+ +g++v+++  l vv+r+
  gi|121638233|ref|YP_978457.1| 139 GDYSGAA----VAAANGLNRSPSSS--SRVVLLVTVGIIVIVVAVLLVVMRH 184
                                    5555555....33344444444333..5788888888888888889999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0095
                           EssA  62 EkkeieelkdsLFeeekesneavkdtkesLFsseYevrasasevas 107
                                     ++++++l   L ee+ + +   +   + LF+ e  vra+++ +++
  gi|121638233|ref|YP_978457.1| 493 VDADLDRLLATLAEEQATADRLNRSLEQALFTAESRVRAVSEYIDT 538
                                    5689999*************999999*************9988765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0051        10      37     120 ..     262     348 ..     253     351 .. 0.86
   2 ?    4.3   0.0     0.019        38      37      82 ..     411     456 ..     362     476 .. 0.67
   3 ?   -1.1   0.0      0.94   1.9e+03      92      98 ..     514     520 ..     486     571 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0051
                        DUF1664  37 rslsdavesvskqleqvseslaatkrhLssri....drvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                      ls+a  +v +ql++   +  a++r+L  r+    ++ d++l +q+e+ +++++ v ++   l+ + ++  ++ + +  
  gi|121638233|ref|YP_978457.1| 262 AALSQAF-TVRQQLDDNTPETPAQRRELLTRVivsaAHADRELASQTEAFEKLRDLVINAPARLDLLTQQYVELTTRIGP 340
                                    5566665.699*****************99986666799*************************9999999999999988 PP

                        DUF1664 113 leskleri 120
                                     +++l+++
  gi|121638233|ref|YP_978457.1| 341 TQQRLAEL 348
                                    88888877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                        DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeis 82 
                                    r l dav+s ++++ +  +sl a+  +++  i+r +++l++ ++ +
  gi|121638233|ref|YP_978457.1| 411 RALLDAVDSAATDIRHAVASLPAVVADIQTGIKRANQHLQQAQQPQ 456
                                    4555666666666666666666666666666666666666555544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.94
                        DUF1664  92 vredlse 98 
                                    +++ l++
  gi|121638233|ref|YP_978457.1| 514 LNRSLEQ 520
                                    2222222 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0   0.00035      0.69      10      45 ..     557     592 ..     549     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                    HHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH CS
                          HHH_8  10 eladllelkgedpfrvraYrrAaraiealpeeitsl 45 
                                    +l   +++k  +p  + aY++Aa++++a+ + ++++
  gi|121638233|ref|YP_978457.1| 557 QLEAAHDRKSSNPTEAIAYANAASTLAAHAQSLANA 592
                                    566677888899*******************99985 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00027      0.54      55      94 ..     159     195 ..     141     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                        TMEM154  55 qlelvlmiiiPlvllillllvviiliqkkkrkrsKddeks 94 
                                    +  +vl++    v +i+++++v++++++++ +r++ de  
  gi|121638233|ref|YP_978457.1| 159 SSRVVLLVT---VGIIVIVVAVLLVVMRHRNRRRRADELA 195
                                    444555554...5567777788888899999999888654 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5    0.0023       4.6      12      52 ..     303     343 ..     300     354 .. 0.87
   2 ?    2.7   0.1     0.097   1.9e+02      16      45 ..     425     454 ..     412     471 .. 0.80
   3 ?    4.3   0.5     0.031        61      13      42 ..     491     520 ..     489     534 .. 0.85
   4 ?   -3.5   0.1       8.8   1.7e+04      33      46 ..     551     564 ..     547     572 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                           SlyX  12 lafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    la q ++ e+L d v++   ++d l++q  +l+ r+   ++
  gi|121638233|ref|YP_978457.1| 303 LASQTEAFEKLRDLVINAPARLDLLTQQYVELTTRIGPTQQ 343
                                    899******************************99955554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.097
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllae 45 
                                     +++ +L +vva+ q  i+r  ++l++ ++
  gi|121638233|ref|YP_978457.1| 425 RHAVASLPAVVADIQTGIKRANQHLQQAQQ 454
                                    678889999999999999999999998776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.031
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrl 42 
                                    +  +  +++L +++ae q + drl r l++
  gi|121638233|ref|YP_978457.1| 491 TKVDADLDRLLATLAEEQATADRLNRSLEQ 520
                                    556788999****************99987 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.8
                                    HHHHHHHHHHHHHT CS
                           SlyX  33 idrlqrqlrllaer 46 
                                    +++ +rql++ ++r
  gi|121638233|ref|YP_978457.1| 551 LAEAKRQLEAAHDR 564
                                    33344444444433 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4   0.00084       1.7      47     151 ..     214     319 ..     206     328 .. 0.87
   2 ?    5.9   0.1    0.0035       7.1     216     282 ..     289     355 ..     282     360 .. 0.90
   3 ?   -1.3   0.3      0.55   1.1e+03     228     280 ..     465     519 ..     427     530 .. 0.60
   4 ?   -0.6   0.2      0.35     7e+02     177     208 ..     500     531 ..     478     587 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00084
                      Rab5-bind  47 keLedslkelseetskqvselakrvk.ksEllleeLqqafskakrniqeqlavlvksreqvedelvrLqkdyesLlGkhr 125
                                    + L+d  + +  ++ + v + ++  + + E   e   + f++a +n +  l+ + + r+q++d+      +  +Ll +  
  gi|121638233|ref|YP_978457.1| 214 QALDDLSRSMVVDVDNAVRTSTNELAlAIEEFGERRTAPFTQAVNNAKAALSQAFTVRQQLDDNTPETPAQRRELLTRVI 293
                                    567888888888888888777665442678888888999***************************************** PP

                      Rab5-bind 126 khvslleeEkidlPddveeLqelvlk 151
                                     ++ +   E  +  +  e+L+ lv +
  gi|121638233|ref|YP_978457.1| 294 VSAAHADRELASQTEAFEKLRDLVIN 319
                                    **********9999******999975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0035
                      Rab5-bind 216 leeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqtELDvs 282
                                    l +++v     +  la +t++++kl+ ++ +  ++l  l+++ +++ + +   +++   L tE D +
  gi|121638233|ref|YP_978457.1| 289 LTRVIVSAAHADRELASQTEAFEKLRDLVINAPARLDLLTQQYVELTTRIGPTQQRLAELHTEFDAA 355
                                    66777777778888999************************************************86 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.55
                      Rab5-bind 228 kslaektrqldklqtikselE..eqlkelekekaaveqlvleeknkaqrLqtELD 280
                                    +++  + r+ld  +   + l   +ql +++++   +  ++ ee+  a rL + L+
  gi|121638233|ref|YP_978457.1| 465 AARDAAARALDRARGAADPLTafDQLTKVDADLDRLLATLAEEQATADRLNRSLE 519
                                    4555555555555555555542246666666666666666666666666665554 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.35
                      Rab5-bind 177 LkeqiqaEkalkEnlEetlqleierlkeelas 208
                                    L + +++E+a+ + l+ +l++ +    + + +
  gi|121638233|ref|YP_978457.1| 500 LLATLAEEQATADRLNRSLEQALFTAESRVRA 531
                                    33444445555555555555554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1644  (0.091695); expected 358.6 (0.02)
Passed bias filter:                      964  (0.0537676); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.87u 0.34s 00:00:01.21 Elapsed: 00:00:00.49
# Mc/sec: 4035.96
//
Query:       gi|121638234|ref|YP_978458.1|  [L=60]
Description: ESAT-6 like protein 6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-08   34.6   0.9    1.8e-08   34.5   0.9    1.1  1  WXG100     Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.063   13.8   1.3      0.067   13.7   0.3    1.5  2  Nup214_FG  Nucleoporin Nup214 phenylalanine-glycine (FG) doma


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.9     2e-12   1.8e-08      38      86 .]       5      53 ..       1      53 [. 0.95

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2e-12
                                   GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         WXG100 38 qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaDe 86
                                   ++ W Ga ++a+q++++++ +++q ++++ + +++++++a+n+++++D+
  gi|121638234|ref|YP_978458.1|  5 GDFWGGAGSVACQEFITQLGRNFQVIYEQANAHGQKVQAAGNNMAQTDS 53
                                   789********************************************95 PP

>> Nup214_FG  Nucleoporin Nup214 phenylalanine-glycine (FG) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   7.5e-06     0.067      28      44 ..       3      19 ..       2      24 .. 0.92
   2 ?   -2.0   0.0      0.61   5.5e+03      11      11 ..      47      47 ..      33      58 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-06
                      Nup214_FG 28 psGtfsaGgGsvasqGf 44
                                   ++G f  G+Gsva+q f
  gi|121638234|ref|YP_978458.1|  3 AAGDFWGGAGSVACQEF 19
                                   689************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.61
                      Nup214_FG 11 s 11
                                    
  gi|121638234|ref|YP_978458.1| 47 N 47
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 423.04
//
Query:       gi|121638235|ref|YP_978459.1|  [L=468]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-56  188.5  27.1    1.4e-55  187.7  27.1    1.4  1  PPE             PPE family
    2.7e-52  174.4 232.7      3e-10   39.8  27.4    8.3  9  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.7  27.1   1.6e-59   1.4e-55       1     158 []       6     166 ..       6     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.7 bits;  conditional E-value: 1.6e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT....TTS-SHHHHHHHHHTHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaela...aeaWqGpssaamaaaaapylaWLsaaaa 77 
                                    +lpPE+ns +++ G+gsgp+laAaaaWdgLaael  aa+++  v+++la   ++aWqG+++aam+ aaapy+ WL+aaaa
  gi|121638235|ref|YP_978459.1|   6 VLPPEINSGRMFFGAGSGPMLAAAAAWDGLAAELGLAAESFGLVTSGLAggsGQAWQGAAAAAMVVAAAPYAGWLAAAAA 85 
                                    59*********************************************98555678************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  78 qaeeaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a  aA qa+a+a a+eaA+aamv+p ++aanr ++++lv +n+fGqn+paIaa+ea ye+mwa+d+aam +Y+  ++aa
  gi|121638235|ref|YP_978459.1|  86 RAGGAAVQAKAVAGAFEAARAAMVDPVVVAANRSAFVQLVLSNVFGQNAPAIAAAEATYEQMWAADVAAMVGYHGGASAA 165
                                    ****************************************************************************9998 PP

                                    H CS
                            PPE 158 a 158
                                    a
  gi|121638235|ref|YP_978459.1| 166 A 166
                                    5 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3  24.0   1.6e-11   1.4e-07       6      39 ..     208     241 ..     207     242 .. 0.92
   2 !   32.8  27.6   5.1e-12   4.6e-08       1      40 []     233     272 ..     233     272 .. 0.98
   3 !   39.8  27.4   3.4e-14     3e-10       1      40 []     263     302 ..     263     302 .. 0.98
   4 !   33.4  34.4   3.4e-12     3e-08       1      40 []     293     332 ..     293     332 .. 0.98
   5 !   30.7  37.1   2.4e-11   2.2e-07       1      39 [.     303     341 ..     303     342 .. 0.98
   6 !   22.6  46.3   7.9e-09   7.1e-05       1      39 [.     323     361 ..     323     371 .. 0.95
   7 !   31.5  31.1   1.4e-11   1.2e-07       3      39 ..     372     408 ..     370     409 .. 0.97
   8 !   37.9  27.1   1.4e-13   1.2e-09       1      40 []     410     449 ..     410     449 .. 0.97
   9 !   25.8  18.3   8.2e-10   7.4e-06       1      33 [.     430     462 ..     430     468 .] 0.94

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.6e-11
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                     N+G gN+G++NlGsgNtG++N+GsgN+G++n+G
  gi|121638235|ref|YP_978459.1| 208 INFGFGNIGSLNLGSGNTGDTNVGSGNIGNTNLG 241
                                    5999999999999999999999999999999998 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 5.1e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+G gN+G+fNlGsgN G+ NlG gN+G++n+Gs
  gi|121638235|ref|YP_978459.1| 233 GNIGNTNLGGGNIGSFNLGSGNQGDINLGIGNVGNLNLGS 272
                                    8*************************************96 PP

  == domain 3  score: 39.8 bits;  conditional E-value: 3.4e-14
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G+lN+GsgN+G+ NlGsgN+Gs+N+GsgN+Gs+n+Gs
  gi|121638235|ref|YP_978459.1| 263 GNVGNLNLGSGNFGSQNLGSGNIGSTNVGSGNIGSTNVGS 302
                                    8*************************************96 PP

  == domain 4  score: 33.4 bits;  conditional E-value: 3.4e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+Gs+N+GsgN+G+ N+GsgN+G++N+G+gN G++n+Gs
  gi|121638235|ref|YP_978459.1| 293 GNIGSTNVGSGNIGSTNVGSGNIGDTNFGNGNNGNFNFGS 332
                                    8**************************************6 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 2.4e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+Gs+N+GsgN+G+ N G+gN G+fN+GsgNtGs+n+G
  gi|121638235|ref|YP_978459.1| 303 GNIGSTNVGSGNIGDTNFGNGNNGNFNFGSGNTGSNNIG 341
                                    8*************************************9 PP

  == domain 6  score: 22.6 bits;  conditional E-value: 7.9e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN G++N+GsgNtG+ N+G+gNtGs+N+G+gNtG++n+G
  gi|121638235|ref|YP_978459.1| 323 GNNGNFNFGSGNTGSNNIGFGNTGSGNFGFGNTGNNNIG 361
                                    799**********************************98 PP

  == domain 7  score: 31.5 bits;  conditional E-value: 1.4e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G lNsGsgN+Gf+N+G+gN+G fN+G+gN+G+gn+G
  gi|121638235|ref|YP_978459.1| 372 IGGLNSGSGNIGFGNSGTGNVGLFNSGTGNVGFGNSG 408
                                    89**********************************9 PP

  == domain 8  score: 37.9 bits;  conditional E-value: 1.4e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG++N+G++NtGf+N Gs+NtG +N+G gNtG++ +G+
  gi|121638235|ref|YP_978459.1| 410 ANTGFGNAGNVNTGFWNGGSTNTGLANAGAGNTGFFDAGN 449
                                    6************************************996 PP

  == domain 9  score: 25.8 bits;  conditional E-value: 8.2e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNt 33 
                                    +NtG +N+G gNtGff+ G+ N+Gs N+G++N+
  gi|121638235|ref|YP_978459.1| 430 TNTGLANAGAGNTGFFDAGNYNFGSLNAGNINS 462
                                    6******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2882.20
//
Query:       gi|121638236|ref|YP_978460.1|  [L=463]
Description: glycyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-19   68.8   0.0      6e-19   68.0   0.0    1.4  1  HGTP_anticodon  Anticodon binding domain
    1.7e-07   31.4   0.0    2.5e-07   30.9   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   6.7e-23     6e-19       1      91 [.     369     456 ..     369     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 6.7e-23
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    +++v+pl+++a+ l + a++l +eLr+  +++++d +++ ig+++r+ d++g+pf+v+v++++l+++ vtvr+rd + q 
  gi|121638236|ref|YP_978460.1| 369 KAAVLPLSRHAD-LSPKARDLGAELRKC-WNIDFD-DAGAIGRRYRRQDEVGTPFCVTVDFDSLQDNAVTVRERDAMTQD 445
                                    689******888.***************.9****8.79****************************************** PP

                                    EEETTHHHHHH CS
                 HGTP_anticodon  81 rvsldelvekl 91 
                                    rv++++++++l
  gi|121638236|ref|YP_978460.1| 446 RVAMSSVADYL 456
                                    ********998 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.8e-11   2.5e-07      11     110 ..     160     277 ..     153     415 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.8e-11
                                    EEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  11 yiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisr 89 
                                     +L+P+  +++   + + v    k+ P+ + qi+  +R+E      ++R reF+q + + f+ +a++++  +  i    +
  gi|121638236|ref|YP_978460.1| 160 HYLRPETAQGIFVNFANVVTTArKKPPFGIGQIGKSFRNEITPGNFIFRTREFEQMEMEFFVEPATAKEWHQYWIDNRLQ 239
                                    58*********999999977555779**************985779***********************99999****** PP

                                    HHHHTT.SCEEEEEEGTTSC.................B CS
                                    xxxxxxxxxxxxxxxxxxxx.................x RF
                   tRNA-synt_2b  90 iferlglefraiielmsaks.................a 110
                                    ++ +lg+    +++  + k+                 +
  gi|121638236|ref|YP_978460.1| 240 WYIDLGIRRENLRLWEHPKDklshysdrtvdieykfgF 277
                                    *******9877776644333444444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2674.56
//
Query:       gi|121638237|ref|YP_978461.1|  [L=135]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   54.7   0.3    6.9e-15   54.7   0.3    1.6  2  HTH_5     Bacterial regulatory protein, arsR family
    2.1e-11   43.7   0.9    3.7e-11   42.9   0.9    1.4  1  HTH_20    Helix-turn-helix domain
    0.00024   20.9   0.3    0.00062   19.6   0.3    1.8  1  MarR_2    MarR family
     0.0017   18.6   0.0     0.0029   17.8   0.0    1.4  1  PaaX      PaaX-like protein
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.013   15.8   0.1    1.2  1  Rrf2      Transcriptional regulator
      0.032   14.1   0.0      0.044   13.7   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.079   12.5   0.0       0.13   11.8   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.091   12.6   0.0       0.13   12.1   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.3   3.1e-18   6.9e-15       2      46 ..      58     102 ..      57     102 .. 0.97
   2 ?   -3.6   0.6       4.9   1.1e+04      33      37 ..     116     120 ..     115     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3.1e-18
                                    HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                    p R+ I+ +L+e+++cv+el+++l+++q+ vS+HLk+L+ aG+V+
  gi|121638237|ref|YP_978461.1|  58 PVRIAIVLQLRESQRCVHELVDALHVPQPLVSQHLKILKAAGVVT 102
                                    89*****************************************95 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.9
                                    HHHHH CS
                          HTH_5  33 ShHLk 37 
                                    +hHL+
  gi|121638237|ref|YP_978461.1| 116 DHHLA 120
                                    69*96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.9   1.6e-14   3.7e-11       2      61 .]      50     108 ..      49     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.6e-14
                                    HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20   2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                    ++++ALa PvR +i   L r+  +++ el ++l +++  +s+HL++L  ag v+++r+gr
  gi|121638237|ref|YP_978461.1|  50 ELLRALAAPVRIAIVLQL-RESQRCVHELVDALHVPQPLVSQHLKILKAAGVVTGERSGR 108
                                    689***************.***************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3   2.8e-07   0.00062      23      56 ..      73     106 ..      42     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                    EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  23 tvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                     v el+++l+++++ vs++lk L aaG v+ +++
  gi|121638237|ref|YP_978461.1|  73 CVHELVDALHVPQPLVSQHLKILKAAGVVTGERS 106
                                    589**************************87765 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.3e-06    0.0029      29      69 ..      77     117 ..      72     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                           PaaX  29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69 
                                    l+ +l + + lv   l  l++aG +++e+ gr+++YrL+d+
  gi|121638237|ref|YP_978461.1|  77 LVDALHVPQPLVSQHLKILKAAGVVTGERSGREVLYRLADH 117
                                    677777888888888999*********************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   5.9e-06     0.013      11      70 ..      59     117 ..      51     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                                    HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET.TT-TCEEESSH CS
                           Rrf2  11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr.GkgGGyrLakp 70 
                                    +++ ++L+++e+++   ++e+ +   ++++ +++ l+ L+ ag+v+ +r G++  yrLa +
  gi|121638237|ref|YP_978461.1|  59 VRIAIVLQLRESQR--CVHELVDALHVPQPLVSQHLKILKAAGVVTGERsGREVLYRLADH 117
                                    67788888888887..899**************************9865488888888864 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.044      19      66 ..      68     116 ..      61     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                    HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
                           TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravd 66 
                                    ++ +  + e+  +l vp++ v + L+ L+ +G+V+ e++    lYr +d
  gi|121638237|ref|YP_978461.1|  68 RESQRCVHELVDALHVPQPLVSQHLKILKAAGVVTGERSGrEVLYRLAD 116
                                    556667899**************************99955267999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.8e-05      0.13      21      48 .]      75     102 ..      64     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                         HTH_24  21 reLAerlglSpstvnrrlkrLeeeGlIk 48 
                                     eL ++l+++++ v+++lk L+ +G+++
  gi|121638237|ref|YP_978461.1|  75 HELVDALHVPQPLVSQHLKILKAAGVVT 102
                                    58999*********************96 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.9e-05      0.13       8      53 ..      61     105 ..      59     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                                    HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE CS
                           HxlR   8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev 53 
                                    + i+ +l + ++  +el +al +++q + +q+L+ L++ g++  e 
  gi|121638237|ref|YP_978461.1|  61 IAIVLQLRESQRCVHELVDAL-HVPQPLVSQHLKILKAAGVVTGER 105
                                    56999****************.*******************97653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 899.71
//
Query:       gi|121638238|ref|YP_978462.1|  [L=130]
Description: ferric uptake regulation protein furB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-39  133.1   0.3      6e-39  132.9   0.3    1.0  1  FUR            Ferric uptake regulator family
    4.5e-05   23.3   0.0    6.5e-05   22.8   0.0    1.3  1  HTH_12         Ribonuclease R winged-helix domain
     0.0052   16.7   0.0     0.0077   16.2   0.0    1.3  1  PadR           Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.018   15.7   0.2      0.048   14.3   0.1    1.7  2  HTH_32         Homeodomain-like domain
      0.023   14.6   0.0      0.049   13.5   0.0    1.6  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.023   14.8   0.4      0.036   14.1   0.4    1.3  1  HTH_20         Helix-turn-helix domain
      0.044   13.6   0.0      0.056   13.2   0.0    1.2  1  Arg_repressor  Arginine repressor, DNA binding domain
       0.17   12.1   2.2        1.4    9.1   0.1    2.5  3  SR1P           SR1 protein


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.3   2.7e-42     6e-39       2     119 ..       4     121 ..       3     122 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 2.7e-42
                                    TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEE CS
                            FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhdhl 81 
                                    ag++ T+qR +i ++le+ +++ sa+e+++el++++++i+l+TVYrtL+ ++++glv++l +++ges+y+ ++++hh+hl
  gi|121638238|ref|YP_978462.1|   4 AGVRSTRQRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLRTDTGESVYRRCSEHHHHHL 83 
                                    79****************************************************************************** PP

                                    EETTT--EEEE--HHHHHHHHHHHHHTT-EEEEEEEEE CS
                            FUR  82 icekCgkviefkddeiekiqeeiaekegfklvshrlel 119
                                    +c++Cg++ie+ d+e+e++++e+a+k+gf+ vsh++e+
  gi|121638238|ref|YP_978462.1|  84 VCRSCGSTIEVGDHEVEAWAAEVATKHGFSDVSHTIEI 121
                                    ************************************98 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-08   6.5e-05       6      49 ..      18      61 ..      13      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                         HTH_12  6 ilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                   +l+  d+  +a+e+ +eL+ rg++ig  +v + L+++   gl+ 
  gi|121638238|ref|YP_978462.1| 18 LLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVD 61
                                   6777788889*******************************986 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.4e-06    0.0077      13      60 ..      29      73 ..      18      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                                   HHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-E CS
                           PadR 13 yeiikeleelsegllelseGslYpaLkrLekeglveseweesgegppr 60
                                    e+ +el+++  g +++  +++Y++L+++  +glv++ ++++ge+  r
  gi|121638238|ref|YP_978462.1| 29 QELHDELRRR--G-ENIGLTTVYRTLQSMASSGLVDTLRTDTGESVYR 73
                                   6899999999..8.89*********************99998766555 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.1e-05     0.048      31      73 .]       9      51 ..       5      51 .. 0.83
   2 ?   -2.6   0.0       3.9   8.8e+03      32      42 ..      98     108 ..      95     118 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                         HTH_32 31 devrariiallre.eprWsprqlaarlaeregvkvShstvyriL 73
                                    ++ra+i  ll++ +   s+++l+++l +r+g+ +   tvyr L
  gi|121638238|ref|YP_978462.1|  9 TRQRAAISTLLETlDDFRSAQELHDEL-RRRGENIGLTTVYRTL 51
                                   578999999995523366*********.888899********97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.9
                         HTH_32  32 evrariiallr 42 
                                    ev+a+  ++++
  gi|121638238|ref|YP_978462.1|  98 EVEAWAAEVAT 108
                                    55555555553 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05     0.049      34      57 ..      42      65 ..      27      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                   SSCHCHHHHHHHHHHCTSEEEESS CS
                           TrmB 34 vprskvYevLrsLedkGlVerekg 57
                                   +  ++vY++L+s+ + GlV++ + 
  gi|121638238|ref|YP_978462.1| 42 IGLTTVYRTLQSMASSGLVDTLRT 65
                                   6669***************98764 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.6e-05     0.036      16      58 ..      16      64 ..       8      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                   HHHH.STCTTB-HHHHHHHHT.....S-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 16 lraL.araegltaselaerld.....lskntlsyHLrvLeeagLvevvr 58
                                     +L + ++ ++a el+++l+     +  +t+++ L+ +++ gLv++ r
  gi|121638238|ref|YP_978462.1| 16 STLLeTLDDFRSAQELHDELRrrgenIGLTTVYRTLQSMASSGLVDTLR 64
                                   55555569999*********556677*******************9876 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.056       6      62 ..      11      72 ..       6      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHHHH.S---SHHHHHHHHHTTT----HHHHHHHHHHH...T-EEE.ETTSTSEEE CS
                  Arg_repressor  6 rqklikkiike.ekissQkelvelLkeeGidvtQatvSRdLkel...glvkv.raengeyvY 62
                                     ++i  +++   +++s +el ++L+  G ++  +tv R L+ +   glv + r++ ge vY
  gi|121638238|ref|YP_978462.1| 11 QRAAISTLLETlDDFRSAQELHDELRRRGENIGLTTVYRTLQSMassGLVDTlRTDTGESVY 72
                                   44678888876478***************************999444444331455555555 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   8.2e+03      13      28 ..      60      75 ..      59      78 .. 0.56
   2 ?    9.1   0.1   0.00063       1.4       5      15 ..      84      94 ..      82      99 .. 0.84
   3 ?    2.2   0.1     0.091     2e+02      24      34 ..     121     129 ..     117     130 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                           SR1P 13 IdhfedekVttLYgtC 28
                                   +d++ ++     Y  C
  gi|121638238|ref|YP_978462.1| 60 VDTLRTDTGESVYRRC 75
                                   5666555555556555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00063
                           SR1P  5 vCqtCnatIdh 15
                                   vC++C+ tI+ 
  gi|121638238|ref|YP_978462.1| 84 VCRSCGSTIEV 94
                                   9********85 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.091
                           SR1P  24 LYgtCnqceCk 34 
                                    ++gtC   +C+
  gi|121638238|ref|YP_978462.1| 121 IFGTCS--DCR 129
                                    789997..887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 957.66
//
Query:       gi|121638239|ref|YP_978463.1|  [L=142]
Description: hypothetical protein BCG_2374c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1081.72
//
Query:       gi|121638240|ref|YP_978464.1|  [L=296]
Description: UDP pyrophosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-72  242.0   0.1      6e-72  241.8   0.1    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8   0.1   3.4e-76     6e-72       1     224 []      74     294 ..      74     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 3.4e-76
                                    EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkeelkell 80 
                                    +mDGN+RwA++rg + r+eGhk+G   + +i   ++elg+k +++YafSteN+kRs+eev++lm +  +++++++ ++l+
  gi|121638240|ref|YP_978464.1|  74 VMDGNGRWATQRG-LARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFN-RDVVRRRRDTLK 151
                                    8************.66667**********************************************98.559999877777 PP

                                    HTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCT CS
                   Prenyltransf  81 kegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekh 159
                                    k gvr+r++G++ +l ++v ++l+ aee+tk +n+ +++n +vnYg+r+ei+ea+re+++e+++ + + e+i+e+t+++h
  gi|121638240|ref|YP_978464.1| 152 KLGVRIRWVGSRPRLWRSVINELAVAEEMTK-SNDVITINYCVNYGGRTEITEATREIAREVAAGRLNpERITESTIARH 230
                                    77*****************************.5556**********************999987666657889******* PP

                                    STT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                   Prenyltransf 160 lytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                    l+   ++pd+Dl++RtsGe+R SnF+lwq+ay+e++f d+lWPd++++dl++a +ey++r+rrfg
  gi|121638240|ref|YP_978464.1| 231 LQR-PDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFG 294
                                    **7.557********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2240.87
//
Query:       gi|121638241|ref|YP_978465.1|  [L=265]
Description: DNA repair protein RecO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-31  107.7   0.3    5.7e-31  107.4   0.3    1.1  1  RecO_C    Recombination protein O C terminal
      4e-28   97.2   0.1    2.7e-27   94.5   0.1    2.1  2  RecO_N    Recombination protein O N terminal
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.021   14.5   0.0    1.4  1  RecO_N_2  RecO N terminal


Domain annotation for each model (and alignments):
>> RecO_C  Recombination protein O C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.3   9.6e-35   5.7e-31       3     156 ..      86     237 ..      84     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 9.6e-35
                                    SHHHHHHHHHHHHHHHHHS.-SSS--HHHHHHHHHHHHHHHHSS.-HHHHHHHHHHHHHHHTTS----SB-TTT--BS-- CS
                         RecO_C   3 dlerlaaasylaElldrll.peeepnpeLFdlllatLdaLdeas.daalallvfelrlLallGyapdldsCaacgekial 80 
                                    d+ r++++ +++E+++rl  +e+ p+p+L +l++ +L+a ++++ +  l+l++++lr +  +G+ap l++Ca+c ++ ++
  gi|121638241|ref|YP_978465.1|  86 DYGRYTCGCAILETAERLAgEERAPAPALHRLTVGALRAVADGQrPRDLLLDAYLLRAMGIAGWAPALTECARCATPGPH 165
                                    899*************************************8888577888888*************************** PP

                                    EE-TTT.....SSEE-TTT-SS----HHHHHHHHHTTTS-HHHHHHS---GGGHHHHHHHHHHHHHHHSS.S-SGG CS
                         RecO_C  81 aafspswggllcsecaakapagrplspetlallrlllrgdleklgelkvspeelrellrllrayleehlerplksr 156
                                     af++  g  ++++  ++++++   +   ++l+ +l++gd+e+++   ++++ ++  + l+ a+l++hler+lk++
  gi|121638241|ref|YP_978465.1| 166 RAFHIATG--GSVCAHCRPAGSTTPPLGVVDLMSALYDGDWEAAE--AAPQSARSHVSGLVAAHLQWHLERQLKTL 237
                                    ******98..***********************************..99*************************97 PP

>> RecO_N  Recombination protein O N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.1   4.6e-31   2.7e-27       1      80 []       1      79 [.       1      79 [. 0.97
   2 ?   -0.1   0.0      0.15     9e+02      54      71 ..     221     237 ..     207     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 4.6e-31
                                   X-EEEEEEEEEEEEEETTSEEEEEEEETT.EEEEEEEET-..TTSTTTTTS-TT-EEEEEEESSS-SSEEEEEEEEEE-X CS
                         RecO_N  1 MslvkteaiVLksrkygEsdlivtlfTrehGkvsalargarksksrlrallqpftllevqlrkkgrgLktlkqaeliksf 80
                                   M+l++++a+VL+++k+gE+d+ivtl+Tr+hG+v+a+a+g+r+++s+++a+l+pf+++evql+  gr+L+ ++q+ ++++f
  gi|121638241|ref|YP_978465.1|  1 MRLYRDRAVVLRQHKLGEADRIVTLLTRDHGLVRAVAKGVRRTRSKFGARLEPFAHIEVQLH-PGRNLDIVTQVVSVDAF 79
                                   999***********************************************************.**********9998865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                                    T-EEEEEEESSS-SSEEE CS
                         RecO_N  54 ftllevqlrkkgrgLktl 71 
                                    ++  ++q++  +r+Lktl
  gi|121638241|ref|YP_978465.1| 221 LVAAHLQWH-LERQLKTL 237
                                    667789999.99**9998 PP

>> RecO_N_2  RecO N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.5e-06     0.021       5      45 ..      10      50 ..       7      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                       RecO_N_2  5 ilriqkvkdedlivtiltkeklktlyrfyGarhsliqlgtk 45
                                   +lr  k ++ d ivt+lt++++ +     G+r+   + g +
  gi|121638241|ref|YP_978465.1| 10 VLRQHKLGEADRIVTLLTRDHGLVRAVAKGVRRTRSKFGAR 50
                                   999********************999999999966655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2106.24
//
Query:       gi|121638242|ref|YP_978466.1|  [L=484]
Description: amidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-120  403.3   0.0   1.7e-120  403.0   0.0    1.1  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.0   0.0  9.6e-125  1.7e-120       1     450 [.      39     460 ..      39     461 .. 0.97

  Alignments for each domain:
  == domain 1  score: 403.0 bits;  conditional E-value: 9.6e-125
                                    HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS CS
                        Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaek 80 
                                    elv+ +l+ i+  +++lna+  v+ e+ala+Aa++dk+ra   ++ pL G+Pi+vKD +dv+gvpt++G++ +   pa++
  gi|121638242|ref|YP_978466.1|  39 ELVRRSLRAIDVSQPTLNAFRVVLTESALADAAAADKRRA-AGDTAPLLGIPIAVKDDVDVAGVPTAFGTQGYVA-PATD 116
                                    799************************************8.999*****************************99.**** PP

                                    --HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHH CS
                        Amidase  81 DatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPA 160
                                    D++vv+rLk+aGavi+gkTn++e++++  t+ + fg+trNPw++++tpGGSSGGsAAavAaglv +aiG+D++GSiRiPA
  gi|121638242|ref|YP_978466.1| 117 DCEVVRRLKAAGAVIVGKTNTCELGQWPFTSGPGFGHTRNPWSRRHTPGGSSGGSAAAVAAGLVTAAIGSDGAGSIRIPA 196
                                    ******************************************************************************** PP

                                    HHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EE CS
                        Amidase 161 sfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglri 240
                                    ++++lvG+KP++gr+S +++ +  ++  v+G+lar+ved+al+l++++g+ + d++++++     +++  ++ ++ +l+i
  gi|121638242|ref|YP_978466.1| 197 AWTHLVGIKPQRGRISTWPLPEAFNGVTVNGVLARTVEDAALVLDAASGNVEGDRHQPPP----VTVSDFVGIAPGPLKI 272
                                    **********************************************************94....599************* PP

                                    EEEGGGC....SS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SC CS
                        Amidase 241 Gvvkedg....vasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkv 316
                                    ++ ++++     a+l+pe+ +a++++ ++Le +Gh+vv+    ++++ l+l++++l+   +                   
  gi|121638242|ref|YP_978466.1| 273 ALSTHFPytgfRAKLHPEILAATQRVGDQLELLGHTVVK---GNPDYGLRLSWNFLARSTA------------------G 331
                                    ******97777789*************************...999*****99999887766..................6 PP

                                    CCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHH CS
                        Amidase 317 lsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdkti 396
                                    l+e+ ++  +e  ++  +++  +++++ls+      ++ a++++++ +r++  +f  +Dv+l+Pt+++p+p+ +++d+++
  gi|121638242|ref|YP_978466.1| 332 LWEWAERLGDEVTLDRRTVSNLRMGHVLSQAI----LRSARRHEAADQRRVGSIFDIVDVVLAPTTAQPPPMARAFDRLG 407
                                    89***************************985....*****************************************997 PP

                                    CSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                        Amidase 397 dsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                     s  + +++++ +++++p+nl g+p+++vpag++ dglP+Gvq++g+a +e +l
  gi|121638242|ref|YP_978466.1| 408 -SFGTDRAIIAACPSTWPWNLLGWPSINVPAGFTSDGLPIGVQLMGPANSEGML 460
                                    .999***********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3258.86
//
Query:       gi|121638243|ref|YP_978467.1|  [L=300]
Description: GTP-binding protein Era [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-20   71.8   0.1    6.3e-20   70.8   0.1    1.6  1  KH_2         KH domain
    5.3e-20   71.6   0.0    9.8e-20   70.7   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    3.7e-09   36.3   0.4    2.6e-07   30.3   0.0    2.1  2  FeoB_N       Ferrous iron transport protein B
    5.3e-08   32.9   0.4    0.00057   19.8   0.1    2.2  2  RsgA_GTPase  RsgA GTPase
    1.2e-07   31.9   0.2    0.00013   22.0   0.1    2.3  2  Dynamin_N    Dynamin family
    2.2e-07   30.6   0.9    7.7e-05   22.3   0.9    2.6  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.1e-06   25.8   0.0    2.5e-05   24.1   0.0    1.8  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
    1.6e-05   24.4   0.0    2.4e-05   23.8   0.0    1.3  1  AIG1         AIG1 family
     0.0017   18.6   0.0     0.0079   16.5   0.0    1.9  2  AAA_22       AAA domain
     0.0052   16.2   0.0     0.0095   15.4   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
  ------ inclusion threshold ------
      0.055   13.0   0.6       0.31   10.6   0.1    2.3  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.15   12.2   0.0       0.54   10.5   0.0    1.9  1  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.17   12.3   0.7          1    9.8   0.4    2.4  2  AAA          ATPase family associated with various cellular a
       0.17   11.5   0.0       0.67    9.5   0.0    1.8  1  Ras          Ras family


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.1   4.9e-23   6.3e-20       1      78 []     210     289 ..     210     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 4.9e-23
                                    HHHHHHHHHTECET...EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE.EETTT CS
                           KH_2   1 eipeslaveikkag...vskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv.kVkkp 76 
                                    e+p+slav+i +      ++  I+   +++ +v+r+sq+givIGkgG++++++g+++r +ie+l+g+kV+l++  kV k+
  gi|121638243|ref|YP_978467.1| 210 ELPHSLAVVIDEVSpreGRDDLIDV--HAALYVERDSQKGIVIGKGGARLREVGTAARSQIENLLGTKVYLDLRvKVAKN 287
                                    79********544447755555655..***************************************************** PP

                                    GG CS
                           KH_2  77 el 78 
                                    ++
  gi|121638243|ref|YP_978467.1| 288 WQ 289
                                    *6 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   7.7e-23   9.8e-20       2     113 ..       9     125 ..       8     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 7.7e-23
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC.TS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee.ad 77 
                                    v++vGrpN+GKStL nal+g+ +ai+s +p+tTr+ ++g v+ ++ +i+lvDtpG ++  +   +k+l++ +++    +d
  gi|121638243|ref|YP_978467.1|   9 VCLVGRPNTGKSTLTNALVGAkVAITSTRPQTTRHAIRGIVHSDDFQIILVDTPG-LHrpRTLLGKRLNDLVRETYAaVD 87 
                                    89******************9679******************999**********.552322222222222222222369 PP

                                    EEEEEEETTTTCSHHHHHHHHHHHHH...TTSEEEEEEE CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleellee...akkplilvln 113
                                    +i l++ a  e + p d+ + e l++   a+  l+++++
  gi|121638243|ref|YP_978467.1|  88 VIGLCIPAD-EAIGPGDRWIVEQLRStgpANTTLVVIVT 125
                                    999999977.66888888888877666666666666666 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     2e-10   2.6e-07       3      58 ..       9      65 ..       8      91 .. 0.90
   2 ?    4.1   0.2     0.024        30     105     154 ..     117     168 ..     104     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2e-10
                                   EEEEESTTSSHHHHHHHHHTTSEEEEE.STTSSSEEEEEEEEETTEEEEEEE----S CS
                         FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgN.wpGvtvekkegklklkgkeveivDlPGiY 58
                                   v+lvG pn+Gk+tl nal gak  +    p +t    +g ++ ++ ++ +vD PG +
  gi|121638243|ref|YP_978467.1|  9 VCLVGRPNTGKSTLTNALVGAKVAITStRPQTTRHAIRGIVHSDDFQIILVDTPGLH 65
                                   78********************99976167888888999999999**********86 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                                    TSSEEEEEETHHHHHHTTEEE-HHHHHHHHT..S-EEEEBTTTTBTHHHHHH CS
                         FeoB_N 105 gvpvvlalnmideaekkgieidlkkLsekLg..vpvvktsakkkegieellk 154
                                    ++ +v+++ +id++ k+++  +l ++se +    ++v++sa +++ ++ l++
  gi|121638243|ref|YP_978467.1| 117 NTTLVVIVTKIDKVPKEKVVAQLVAVSELVTnaAEIVPVSAMTGDRVDLLID 168
                                    57899******************999999864479*********99998865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   4.5e-07   0.00057      98     163 ..       5      66 ..       1      69 [. 0.77
   2 !   11.3   0.0   0.00018      0.23       3      98 ..      73     171 ..      71     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.5e-07
                                    TTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETT.TEEEESS-SSSS CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelae.gglliDtPGfre 163
                                    ++ +++lvG    GKStL nal++    k++ +s++ ++ +h  +     + ++ + +l+DtPG+++
  gi|121638243|ref|YP_978467.1|   5 HSGFVCLVGRPNTGKSTLTNALVGA---KVAITSTRPQTTRHAIRGIV--HSDDfQIILVDTPGLHR 66 
                                    567899******************9...67777888788888777543..33322799******986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                                    --S-EETTTTEES--EEEEEEESTTT.T--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSE CS
                    RsgA_GTPase   3 eRknelvrpkvaNvdqllivvslkep.elslnlldrfLvlaeekgiepvivlnKiDlleeee...eleelkeelealgye 78 
                                    +R n lvr++ a vd + +++ ++e      + +   L     ++ ++v++++KiD + +e+   +l +  +el +   e
  gi|121638243|ref|YP_978467.1|  73 KRLNDLVRETYAAVDVIGLCIPADEAiGPGDRWIVEQLRSTGPANTTLVVIVTKIDKVPKEKvvaQLVA-VSELVTNAAE 151
                                    68899999999999999998888843134567788889999999******************5433333.3444455589 PP

                                    EEE--TTTHTTHHHHHHHCT CS
                    RsgA_GTPase  79 vllvsaktkegleelkellk 98 
                                    ++ vsa t++ ++ l ++l+
  gi|121638243|ref|YP_978467.1| 152 IVPVSAMTGDRVDLLIDVLA 171
                                    99999999999999988876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.1e-07   0.00013       1      34 [.       9      42 ..       9      46 .. 0.91
   2 !    8.0   0.0    0.0022       2.8     102     148 ..      55     105 ..      45     127 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                   +++vG  + GKS++ naL+g+++  +++ p T r
  gi|121638243|ref|YP_978467.1|  9 VCLVGRPNTGKSTLTNALVGAKVAITSTRPQTTR 42
                                   689**************************98866 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                                    SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS-CCC-CHH CS
                      Dynamin_N 102 gltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhdlsnseal 148
                                    ++ lvD+PGl++  +       +lv+e+    d+i +  +a+ ++   ++ 
  gi|121638243|ref|YP_978467.1|  55 QIILVDTPGLHRPRTLLGkrlnDLVRETYAAVDVIGLCIPADEAIGPGDRW 105
                                    688********9776554556688888888888887777777776655554 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.9     6e-08   7.7e-05       7     193 ..      10     175 ..       7     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6e-08
                                    EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESS.S..... CS
                       GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPG.H..... 80 
                                    +++g  ++GK+TLt +L+ ++ ai++                   r  T   a   +  ++++++i l+DtPG H     
  gi|121638243|ref|YP_978467.1|  10 CLVGRPNTGKSTLTNALVGAKVAITS------------------TRPQTTRHAIRGIV-HSDDFQIILVDTPGlHrprtl 70 
                                    66777777777777777744444444..................22233333333333.5899**********6522222 PP

                                    ..GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE...EEEEEESCGST.HHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  81 ..vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp...iivfiNKmDrl.kaelkeiveevkqklsrke 154
                                      +  ++ v ++++++D+  l + a+e + p  + +++++++ g     ++v+++K+D++ k+++  +  +v+ +l    
  gi|121638243|ref|YP_978467.1|  71 lgKRLNDLVRETYAAVDVIGLCIPADEAIGPGDRWIVEQLRSTGPAnttLVVIVTKIDKVpKEKVVAQLVAVS-EL---- 145
                                    223566788899**********************999999998766677***********6555555555555.33.... PP

                                    HHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 155 eklekygekgekevpvvfgSalkgegvktllealvellp 193
                                          +++     ++v++Sa++g+ v+ l+++l   lp
  gi|121638243|ref|YP_978467.1| 146 ------VTN---AAEIVPVSAMTGDRVDLLIDVLAAALP 175
                                    ......233...468*****************9998877 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.9e-08   2.5e-05       4     141 ..       9     170 ..       6     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                      PduV-EutP   4 illiGkvgsGKttLtqalkgeelkYkkt..qa.......iefsdev....iDtPGey....lenrklysalivtsaeadv 66 
                                    + l+G+ ++GK tLt+al g ++  ++t  q+       i +sd++    +DtPG +    l  ++l   ++ t a +dv
  gi|121638243|ref|YP_978467.1|   9 VCLVGRPNTGKSTLTNALVGAKVAITSTrpQTtrhairgIVHSDDFqiilVDTPGLHrprtLLGKRLNDLVRETYAAVDV 88 
                                    789*****************8877776633441112222344444333348****87333355666777777888899** PP

                      PduV-EutP  67 ialvqdatee......esvfppgfasvfnkeviGiitkidlaedeenieaveelLk.saGaekifevsavekegieellk 139
                                    i+l+  a+e       + v     +   n  ++ i+tkid++ +e+ + +     +    a++i  vsa++ + ++ l++
  gi|121638243|ref|YP_978467.1|  89 IGLCIPADEAigpgdrWIVEQLRSTGPANTTLVVIVTKIDKVPKEKVVAQLVAVSElVTNAAEIVPVSAMTGDRVDLLID 168
                                    *****99986222211333344556778999**********9888777653333221345789*********99999988 PP

                      PduV-EutP 140 yl 141
                                    +l
  gi|121638243|ref|YP_978467.1| 169 VL 170
                                    77 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.8e-08   2.4e-05       3     108 ..       9     111 ..       8     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                                    EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT CS
                           AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllsee 82 
                                    + lvG+  +GkS+  N+++g k+  +++   + t++  +     d+++i  +DTPgl    +   k  ++ vr    +  
  gi|121638243|ref|YP_978467.1|   9 VCLVGRPNTGKSTLTNALVGAKVAITST-RPQTTRHAIRGIVHSDDFQIILVDTPGLHRPRTLLGKRLNDLVR---ETYA 84 
                                    579********************99886.455688888888899*************8777665555555555...2233 PP

                                    -ESEEEEEEETT.B-SHHHHHHHHHHH CS
                           AIG1  83 gihalllvlslg.rfteedekalktlk 108
                                     ++++ l + ++  +   d+ ++++l+
  gi|121638243|ref|YP_978467.1|  85 AVDVIGLCIPADeAIGPGDRWIVEQLR 111
                                    345555555555555555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.2e-06    0.0079       4      71 ..       5      94 ..       2     152 .. 0.74
   2 ?   -0.4   0.0         1   1.3e+03      70     100 ..     180     222 ..     132     224 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka. 70
                                   + g+++++G + tGK+tl + l+  +++ +  ++               + ++++v+ p++  +++ll + l++l +e+ a 
  gi|121638243|ref|YP_978467.1|  5 HSGFVCLVGRPNTGKSTLTNALVGAKVA-ITSTRpqttrhairgivhsDDFQIILVDTPGLHRPRTLLGKRLNDLVRETYAa 85
                                   789*********************9864.444446999********97777777*************999999999888876 PP

                         AAA_22 71 ........e 71
                                           +
  gi|121638243|ref|YP_978467.1| 86 vdviglciP 94
                                   666666653 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                         AAA_22  70 a......erlsseell.ealeqalrarav.....ielliiDEa 100
                                    +          +e l+ e++++a+ +  +       +++iDE+
  gi|121638243|ref|YP_978467.1| 180 YypdgelTDEPEEVLMaELIREAALQGVRdelphSLAVVIDEV 222
                                    3555554223333444233333333333356667788999996 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.4e-06    0.0095       6      69 ..       9      74 ..       5      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-06
                                   EEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG...GGTT-SEEEETT-GCCSHHHHHH CS
                          SRPRB  6 vllvGlsdsGKTslftrLttdsvkktvtSq..essaalkvksekgskltliDfPGheklrqkllek 69
                                   v lvG  ++GK +l + L   +v  t t      +a   +  ++++++ l+D PG ++ r+ l ++
  gi|121638243|ref|YP_978467.1|  9 VCLVGRPNTGKSTLTNALVGAKVAITSTRPqtTRHAIRGIVHSDDFQIILVDTPGLHRPRTLLGKR 74
                                   789****************9987766654322333444458999***********99988877665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.48   6.1e+02       4      21 ..      10      27 ..       8      45 .. 0.80
   2 ?   10.6   0.1   0.00024      0.31      76     176 ..      48     153 ..      30     154 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.48
                                   EEEESTTCCHHHHHHHHH CS
                           cobW  4 vltGflGsGKTtLlnhll 21
                                    l+G + +GK+tL n+l+
  gi|121638243|ref|YP_978467.1| 10 CLVGRPNTGKSTLTNALV 27
                                   68899999*****99998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                                    HHHHHTT-SEEEEEECTTTTHHHHHTT..SHHHHH.CCCECEEEEEEETTTH....CCHCCHHHHHHH..HHHTSSEEEE CS
                           cobW  76 leereerldviliEttGlaePapvaft..eeelks.dltldavvavvDaknl...eaeeekieekaed..qlaaadllvl 147
                                    +++   ++++il+ t Gl  P +++ +  ++ +++  + +d++  ++ a+++      ++ i e++++    +++ ++++
  gi|121638243|ref|YP_978467.1|  48 IVHSD-DFQIILVDTPGLHRPRTLLGKrlNDLVREtYAAVDVIGLCIPADEAigpG--DRWIVEQLRStgPANTTLVVIV 124
                                    44444.89999999999999999933334333333256666666777776666542..2223222222002344557899 PP

                                    E-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                           cobW 148 nKtDlldeeallekleerlrqlnpeakvl 176
                                    +K+D +++e+ +++l ++ + ++++a+++
  gi|121638243|ref|YP_978467.1| 125 TKIDKVPKEKVVAQLVAVSELVTNAAEIV 153
                                    ***************99999999888876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00042      0.54       2      29 ..       9      36 ..       9     129 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsekek 29
                                   v+lvG  ++GK++l + +v  k+  +++
  gi|121638243|ref|YP_978467.1|  9 VCLVGRPNTGKSTLTNALVGAKVAITST 36
                                   79*****************988854432 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4    0.0008         1       1      21 [.       9      29 ..       9     172 .. 0.70
   2 ?   -2.0   0.0       3.5   4.5e+03      79      98 ..     228     247 ..     196     269 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0008
                                   EEEESSTTSSHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavake 21
                                   v+l+G p tGK++l +a++  
  gi|121638243|ref|YP_978467.1|  9 VCLVGRPNTGKSTLTNALVGA 29
                                   79***************9877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                    CHHHHHHHHHHHHHHHHTTT CS
                            AAA  79 seeeervvnqLlteldgvkk 98 
                                    +++  +v ++L+ e d +k 
  gi|121638243|ref|YP_978467.1| 228 RDDLIDVHAALYVERDSQKG 247
                                    33555555555555555444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00052      0.67       3     157 ..      10     171 ..       9     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00052
                                    EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHH....HHTTESEE..E CS
                            Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrel....yyrdaegi..l 76 
                                     lvG  ++GK++l++  v  k   +++       +  +  v++ + ++ + DT G  + ++l  +     +r++ ++  +
  gi|121638243|ref|YP_978467.1|  10 CLVGRPNTGKSTLTNALVGAKVAITSTRPQ-TTRHAIRGIVHSDDFQIILVDTPGLHRPRTLLGKrlndLVRETYAAvdV 88 
                                    689*************99988765554444.22444444577889999999****9887766433111123333333114 PP

                                    EEEETTBHHHHHTHHHHH.HHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHH.HHHHHHTSEEEEEBTTTTCTHHHHHH CS
                            Ras  77 lvyditsresfenvkkwv.eeikrvaeenvpivLvGnKvDleekravsteege.elakelglkfletSAktnenveeafe 154
                                    +   i   e+    ++w+ e+++++ + n+++v++ +K+D   k++v ++ +  +    + ++ + +SA t  +v+ +++
  gi|121638243|ref|YP_978467.1|  89 IGLCIPADEAIGPGDRWIvEQLRSTGPANTTLVVIVTKIDKVPKEKVVAQLVAvSELVTNAAEIVPVSAMTGDRVDLLID 168
                                    55668888999999988625555566699999999999998777666665544033344558888999999988887776 PP

                                    HHH CS
                            Ras 155 ell 157
                                     l+
  gi|121638243|ref|YP_978467.1| 169 VLA 171
                                    665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2037.37
//
Query:       gi|121638244|ref|YP_978468.1|  [L=113]
Description: hypothetical protein BCG_2379c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 781.62
//
Query:       gi|121638245|ref|YP_978469.1|  [L=435]
Description: hypothetical protein BCG_2380c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-33  114.5   0.2    5.7e-33  114.1   0.2    1.2  1  DUF21      Cyclin M transmembrane N-terminal domain
    1.6e-13   50.9   4.4    1.1e-05   25.7   0.2    3.3  3  CBS        CBS domain
    2.1e-12   46.9   0.7    7.4e-12   45.1   0.1    2.2  2  CorC_HlyC  Transporter associated domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.2   9.6e-37   5.7e-33       3     176 .]      10     185 ..       8     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 9.6e-37
                          DUF21   3 ivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellaeg 82 
                                     ++l++l ++f++  +A++++s++r++el+++++++a  l+k+++++ r+++ ++++ t ++i ++al+ +++   ++  
  gi|121638245|ref|YP_978469.1|  10 SIVLIGLGGLFAAIDAAISTVSPARVDELVRDQRPGAGSLRKVMADRPRYVNLVVLLRTSCEITATALLVVFIRYHFS-M 88 
                                    689******************************************************************999999998.7 PP

                          DUF21  83 alavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil...esesepavseeel 159
                                     +++++a  i++l+ +v+  + P++l++++a +i+la+a plr++++ll+P+++ll +l n+++   + +++p+ se el
  gi|121638245|ref|YP_978469.1|  89 VWGLYLAAGIMVLASFVVVGVGPRTLGRQNAYSISLATALPLRLISWLLMPISRLLVLLGNALTpgrGFRNGPFASEIEL 168
                                    99*****************************************************************99*********** PP

                          DUF21 160 kklveeseeegvieeee 176
                                    +++v++++++gv+ ++e
  gi|121638245|ref|YP_978469.1| 169 REVVDLAQQRGVVAADE 185
                                    ************98876 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1     9e-09   5.4e-05       3      53 ..     202     255 ..     200     256 .. 0.84
   2 !   25.7   0.2   1.9e-09   1.1e-05       1      56 [.     269     323 ..     269     324 .. 0.79
   3 ?    1.6   0.0     0.065   3.9e+02      14      45 ..     334     363 ..     333     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9e-09
                                    HH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                            CBS   3 di..mtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                    ++  ++++++ +  d t ++a+ l +++g+sr+PV+  + d  +vG+v l+Dl++
  gi|121638245|ref|YP_978469.1| 202 EVmvPRTEMIWIESDKTAGQAMTLAVRSGHSRIPVIgeNVD-DIVGVVYLKDLVE 255
                                    554478899***************669*********84444.5*********985 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.9e-09
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllrall 56 
                                    V+ +m++  v+vp + +l  +l++m + + +++ + Vde+g + G+v+ +D+l+ ++
  gi|121638245|ref|YP_978469.1| 269 VARVMRP-AVFVPDSKPLDALLREMQRDR-NHMaLLVDEYGAIAGLVSIEDVLEEIV 323
                                    5678855.459999999********6333.4552379****************9986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.065
                                    TTSBHHHHHHH.HHHHTSS.EEEEEETTTBEEEE CS
                            CBS  14 pdttleealel.mrekgvs.rlPVVdedgklvGi 45 
                                    +++++e++ ++ + +  vs rlP+ ++ g+l G+
  gi|121638245|ref|YP_978469.1| 334 ETAPVEDLGDKrF-R--VSaRLPI-EDVGELYGV 363
                                    7899999999999.6..66699*9.689999996 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.45   2.7e+03      10      29 ..     309     328 ..     298     335 .. 0.69
   2 !   45.1   0.1   1.2e-15   7.4e-12       3      69 ..     341     406 ..     339     421 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.45
                                    EETT-BHHHHHHHHTSTTHH CS
                      CorC_HlyC  10 vdGslpldeleeelglelpe 29 
                                    + G ++++++ ee+  e+ +
  gi|121638245|ref|YP_978469.1| 309 IAGLVSIEDVLEEIVGEIAD 328
                                    56788888887777666555 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.2e-15
                                    ECTTEEEEETT-BHHHHHHHHTSTTHHC.T-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEET CS
                      CorC_HlyC   3 ldegsylvdGslpldeleeelglelpee.dyeTlgGlllellgriPkegesvevdleglrftVlemdg 69 
                                    l++++++v+++lp++++ e++g+e++++ d++T+gGll  +lgr+P +g   ev  +glr+  +   +
  gi|121638245|ref|YP_978469.1| 341 LGDKRFRVSARLPIEDVGELYGVEFDDDlDVDTVGGLLALELGRVPLPGA--EVISHGLRLHAEGGTD 406
                                    67999**********************77*********************..6665588887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3032.21
//
Query:       gi|121638246|ref|YP_978470.1|  [L=182]
Description: metalloprotease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-37  126.2   0.0    1.1e-36  125.5   0.0    1.4  2  UPF0054   Uncharacterized protein family UPF0054


Domain annotation for each model (and alignments):
>> UPF0054  Uncharacterized protein family UPF0054
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.0   6.1e-41   1.1e-36      14     127 ..      26     152 ..      14     153 .. 0.90
   2 ?   -3.9   0.1      0.65   1.2e+04     105     114 ..     160     169 ..     157     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 6.1e-41
                        UPF0054  14 vleealkkekle...evsvllvdneeirelnkeyrgkdkpTDVLSFpleeeeee.ee.........lGDivisvekakeq 80 
                                    v++ ++ k++++   e+s+ll+d++++++l+ ++++   pTDV+SFp++e e   +          lGDiv+++e a+eq
  gi|121638246|ref|YP_978470.1|  26 VARFVIAKMDVNpcaELSMLLLDTAAMADLHMRWMDLPGPTDVMSFPMDELEPGgRPdapepgpsmLGDIVLCPEFAAEQ 105
                                    346677667777778***********************************99995337899******************* PP

                        UPF0054  81 aeeyghslerelafllvHgllHllGYDHeeeeeekeMeekeeeilee 127
                                    a  +ghsl +ela+l++Hg+lHllGYDH e++eekeM+++++++lee
  gi|121638246|ref|YP_978470.1| 106 AAAAGHSLGHELALLTIHGVLHLLGYDHAEPDEEKEMFALQDRLLEE 152
                                    ********************************************986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.65
                        UPF0054 105 GYDHeeeeee 114
                                     Y H +++e+
  gi|121638246|ref|YP_978470.1| 160 AYQHDRQDEK 169
                                    5777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1373.12
//
Query:       gi|121638247|ref|YP_978471.1|  [L=352]
Description: phoH-like protein phoH1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-94  315.0   0.0    2.4e-94  314.5   0.0    1.2  1  PhoH           PhoH-like protein
    6.3e-11   42.4   0.0    9.7e-11   41.7   0.0    1.3  1  AAA_30         AAA domain
    1.2e-05   25.7   0.9    1.2e-05   25.7   0.9    2.9  3  AAA_19         AAA domain
    0.00068   19.4   0.0     0.0012   18.6   0.0    1.3  1  IstB_IS21      IstB-like ATP binding protein
     0.0013   18.5   0.0     0.0034   17.2   0.0    1.7  1  KH_1           KH domain
     0.0043   17.3   0.4      0.081   13.2   0.4    2.5  1  AAA_22         AAA domain
     0.0087   15.8   0.1       0.28   10.9   0.1    2.3  2  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.02   14.5   0.6      0.071   12.7   0.1    2.1  2  AAA_25         AAA domain
       0.02   14.4   1.2        4.1    6.8   0.1    2.2  2  UvrD-helicase  UvrD/REP helicase N-terminal domain
      0.028   14.1   0.0        7.7    6.1   0.0    2.1  2  Zot            Zonular occludens toxin (Zot)
       0.16   11.1   0.1       0.99    8.5   0.0    2.1  2  PIF1           PIF1-like helicase


Domain annotation for each model (and alignments):
>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.5   0.0   1.5e-97   2.4e-94       2     204 ..     126     328 ..     125     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 314.5 bits;  conditional E-value: 1.5e-97
                                    ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTH CS
                           PhoH   2 ikpktkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylr 81 
                                    i+pkt +Qk+y++a+++n+ivf+iGpaGtGKtyla+a av+al+ k+v+riiltrpaveage+lGflpg+l+ek+dpylr
  gi|121638247|ref|YP_978471.1| 126 IRPKTLNQKRYVDAIDANTIVFGIGPAGTGKTYLAMAKAVHALQTKQVTRIILTRPAVEAGERLGFLPGTLSEKIDPYLR 205
                                    99****************************************************************************** PP

                                    HHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE-------- CS
                           PhoH  82 plydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqidlp 161
                                    plydaL+d+++ e + kl+++g+ievaplaymRGrTlndaf++lDEAQntt eqmkmfltRlG++skvvvtGdvtqidlp
  gi|121638247|ref|YP_978471.1| 206 PLYDALYDMMDPELIPKLMSAGVIEVAPLAYMRGRTLNDAFIVLDEAQNTTAEQMKMFLTRLGFGSKVVVTGDVTQIDLP 285
                                    ******************************************************************************** PP

                                    ------THHHHHHTTT-TTEEEEE--GGG----HHHHHHHHHH CS
                           PhoH 162 kgkksGlaealevlknvegieivelkkkdvvRhplvkkivkay 204
                                     g +sGl+ a+++l+++++i+i+el++ dvvRh+lv++iv+ay
  gi|121638247|ref|YP_978471.1| 286 GGARSGLRAAVDILEDIDDIHIAELTSVDVVRHRLVSEIVDAY 328
                                    *****************************************99 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   5.9e-14   9.7e-11       6     129 ..     133     283 ..     130     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.9e-14
                         AAA_30   6 QaaavealltsgdrvavltGpAGtGKtt.alkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlk.. 81 
                                    Q++ v+a+ +++  +++  GpAGtGKt+ a++++++a++++   r+i+  p  +a ++L+   g+ ++ i+ +l+ l   
  gi|121638247|ref|YP_978471.1| 133 QKRYVDAIDANT--IVFGIGPAGTGKTYlAMAKAVHALQTKqVTRIILTRPAVEAGERLGFLPGTLSEKIDPYLRPLYda 210
                                    888887775555..9************84588888888888569999999************************88889* PP

                         AAA_30  82 ..........................grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQla 129
                                                               r r  ++  ++ DEa  + ++q++ +l+++   g kv++ GD  Q +
  gi|121638247|ref|YP_978471.1| 211 lydmmdpelipklmsagvievaplayMRGRTLNDAFIVLDEAQNTTAEQMKMFLTRLGF-GSKVVVTGDVTQID 283
                                    ************************983345556699*********************99.***********975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.58   9.5e+02      25      62 ..      93     130 ..      75     146 .. 0.78
   2 !   25.7   0.9   7.3e-09   1.2e-05       9     141 ..     142     282 ..     133     286 .. 0.67
   3 ?   -3.2   0.2         6   9.7e+03     105     126 ..     304     325 ..     295     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.58
                         AAA_19  25 rvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                    +v++h va+lv +g+++p+e+l +   +r  k +r ++
  gi|121638247|ref|YP_978471.1|  93 EVVRHSVAMLVGTGNESPAEVLTLDILSRRGKTIRPKT 130
                                    589999********999999999887777777777666 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 7.3e-09
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.................atT 71 
                                    ++++++ ++++GtGKT++ +++  +++++++v   +i+l  ++  A ++l     +l ++                  + 
  gi|121638247|ref|YP_978471.1| 142 ANTIVFGIGPAGTGKTYLAMAKAVHALQTKQV--TRIILTRPAVEAGERLGFLPGTLSEKidpylrplydalydmmdPEL 219
                                    3455566999********************88..89*9999999999999876655555544444334333333322222 PP

                         AAA_19  72 iHrlalldfddlltealelle.........eaeeekklqeeellivDEfqdvd.elqyrLlkallgekkklllvGDpdQl 141
                                    i +l  +                          + ++l + + ++ DE+q+++ e+++ +l +l   + k+++ GD  Q 
  gi|121638247|ref|YP_978471.1| 220 IPKL--M-------------SagvievaplAYMRGRTL-NDAFIVLDEAQNTTaEQMKMFLTRLG-FGSKVVVTGDVTQI 282
                                    2222..2.............133444555533556778.7889**********666666666666.8877*******995 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6
                         AAA_19 105 llivDEfqdvdelqyrLlkall 126
                                     + + E   vd +  rL+++++
  gi|121638247|ref|YP_978471.1| 304 DIHIAELTSVDVVRHRLVSEIV 325
                                    5677888899999999998886 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.4e-07    0.0012      34      75 ..     130     171 ..     114     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.4e-07
                      IstB_IS21  34 kvkeLatlsfiekkenivllGpsGvGKshlaialgveavrag 75 
                                    ++++ +  + i+++  +  +Gp+G+GK++la+a +v+a ++ 
  gi|121638247|ref|YP_978471.1| 130 TLNQKRYVDAIDANTIVFGIGPAGTGKTYLAMAKAVHALQTK 171
                                    334444444555555566689**************9998754 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0034       3      66 .]      24      79 ..      22      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                   EEEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHHH CS
                           KH_1  3 rilvPsslvgriIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspeavekAkeliee 66
                                   +i vP +lv  ++G   +n++ +++ t  a  +v  ++        vt+ G+p++v+ A++ i+e
  gi|121638247|ref|YP_978471.1| 24 SIDVPPDLVVGLLGSADENLRALER-TlSADLHVR-GN-------AVTLCGEPADVALAERVISE 79
                                   689**********************.88*****87.54.......6*****8888*****99975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   4.9e-05     0.081       9     116 ..     147     267 ..     140     282 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsst..sskdllrellralglelkaerlss 75 
                                    + +G++GtGKT+l+   +  + + ++ ++           er +++  tl+++    ++ l+ +l   ++ el    l s
  gi|121638247|ref|YP_978471.1| 147 FGIGPAGTGKTYLAMAKAVHALQTKQVTRiiltrpaveagERLGFLPGTLSEKIdpYLRPLYDALYDMMDPELIP-KLMS 225
                                    558********9986665555555544445665555554444444433333333333444444444444444444.3333 PP

                         AAA_22  76 eell.ealeqalrarav.ielliiDEaqhlrseealeeLrsll 116
                                      ++  a   ++r r    +++++DEaq+  ++e+++ + ++l
  gi|121638247|ref|YP_978471.1| 226 AGVIeVAPLAYMRGRTLnDAFIVLDEAQNT-TAEQMKMFLTRL 267
                                    3333333333333333377**********9.877777765554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00017      0.28       3      55 ..     132     181 ..     130     188 .. 0.84
   2 ?    2.2   0.0      0.08   1.3e+02     123     144 ..     245     266 ..     231     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkaliveP 55 
                                     Q++ +++i  +  v++ ++ G+GKT  ++  +++++   ++k+ +++++  P
  gi|121638247|ref|YP_978471.1| 132 NQKRYVDAIDANTIVFGIGPAGTGKTYLAMAKAVHAL---QTKQVTRIILTRP 181
                                    59999999999999********************999...4566667777666 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                                    EEEEEETHHHHHHTTTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldqgfsdfinr 144
                                     f+VlDEa++   ++++ f+ r
  gi|121638247|ref|YP_978471.1| 245 AFIVLDEAQNTTAEQMKMFLTR 266
                                    59*******9999988887766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.4e-05     0.071      28      65 ..     138     175 ..     115     189 .. 0.81
   2 ?   -1.8   0.0       1.2     2e+03      78     116 ..     248     284 ..     224     335 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                         AAA_25  28 gllpagelallaGapgtGKttlaldlalavatGkpwlg 65 
                                    + + a++++  +G+ gtGKt la+  a++ ++ k+++ 
  gi|121638247|ref|YP_978471.1| 138 DAIDANTIVFGIGPAGTGKTYLAMAKAVHALQTKQVTR 175
                                    456888899999*****************998887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                         AAA_25  78 saEdsedelrrRlravgealrddarllvldlagveslpL 116
                                    +++++++++++ ++  ++ l + +++ v+    v++++L
  gi|121638247|ref|YP_978471.1| 248 VLDEAQNTTAEQMKMFLTRLGFGSKVVVTGD--VTQIDL 284
                                    4455555555555544444433333322221..122333 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0025       4.1      20      47 ..     150     175 ..     131     179 .. 0.78
   2 ?    6.3   0.1    0.0037       6.1     259     294 ..     246     281 ..     243     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                                    E-TTSSHHHHHHHHHHHHHHTSSSTGGG CS
                  UvrD-helicase  20 AsAGsGKTfvlaerilrlikeeeiepdr 47 
                                      AG+GKT+  +++ ++ ++++  +++r
  gi|121638247|ref|YP_978471.1| 150 GPAGTGKTYLAMAKAVHALQTK--QVTR 175
                                    56******************99..4455 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0037
                                    EEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                  UvrD-helicase 259 eiliDEyQDTnkiQyrilkllasgheelfmvGDpkQ 294
                                    +i  DE+Q T   Q++++ +     +++++ GD+ Q
  gi|121638247|ref|YP_978471.1| 246 FIVLDEAQNTTAEQMKMFLTRLGFGSKVVVTGDVTQ 281
                                    6899************997777777799999*9999 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0048       7.8       2      34 ..     145     179 ..     144     192 .. 0.78
   2 ?    6.1   0.0    0.0047       7.7      79      92 ..     242     255 ..     212     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0048
                            Zot   2 islvtGapGsgKtsgavkkdllp..alkegRkiit 34 
                                    i++  G+ G+gKt+ a+ k +     ++  R+i t
  gi|121638247|ref|YP_978471.1| 145 IVFGIGPAGTGKTYLAMAKAVHAlqTKQVTRIILT 179
                                    78999***********9985544213334888877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0047
                            Zot  79 dkgallviDEcqei 92 
                                     ++a++v+DE+q++
  gi|121638247|ref|YP_978471.1| 242 LNDAFIVLDEAQNT 255
                                    38**********87 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00061      0.99       6      40 ..     133     161 ..     130     179 .. 0.71
   2 ?   -0.6   0.0      0.36   5.8e+02     137     153 ..     267     282 ..     236     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00061
                                    HHHHHHHH......HCTS-EEEEESTTSSCHHHHH CS
                           PIF1   6 QkkvfdaiieavlnekgklfFvtGsgGtgKtflwk 40 
                                    Qk+ +dai      +   ++F  G +GtgKt+l  
  gi|121638247|ref|YP_978471.1| 133 QKRYVDAI------DANTIVFGIGPAGTGKTYLAM 161
                                    66666666......667899************954 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.36
                                    SCCCC-EEEEE--TTS- CS
                           PIF1 137 kpFGGktvvlgGDfrQi 153
                                      FG   vv+ GD  Qi
  gi|121638247|ref|YP_978471.1| 267 LGFG-SKVVVTGDVTQI 282
                                    4455.456678999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2260.40
//
Query:       gi|121638248|ref|YP_978472.1|  [L=100]
Description: hypothetical protein BCG_2383c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 720.14
//
Query:       gi|121638249|ref|YP_978473.1|  [L=437]
Description: hypothetical protein BCG_2384c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-15   55.7   2.3    1.5e-14   54.3   0.9    2.4  2  GGDEF_2   GGDEF-like domain
    1.3e-10   40.9   3.8    1.3e-10   40.9   3.8    2.3  2  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.9   1.7e-18   1.5e-14      11     115 ..     188     294 ..     180     295 .. 0.81
   2 ?    0.6   0.0     0.073   6.6e+02      43      75 ..     294     341 ..     291     399 .. 0.60

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.7e-18
                        GGDEF_2  11 rarrlgldldgpyvvvvielee..daerllraleealral..gpdalvavrgd.rlvlllpaedeedaeallerlarrlg 85 
                                    + + lg++ld+++++++i+ ++  d+++ l++ ++a+ ++   p++l+av +  + +++++ ++  d  + +++++++ +
  gi|121638249|ref|YP_978473.1| 188 AEAKLGYPLDRSHTAAIIWYDDpdDNQNHLDHTARAFGRAlgCPQPLIAVASAaTRWVWVSDAATLDT-DRIHQVLDHAP 266
                                    4578****************88778888*********5555879999988777466777766666554.55666666766 PP

                        GGDEF_2  86 glsvriGiGspveglaglrrSyreArrAlr 115
                                    +  +ri++G++++g++g+rrS+r+A+++ r
  gi|121638249|ref|YP_978473.1| 267 H--ARIAVGTTARGIDGFRRSHRDALATQR 294
                                    6..8**********************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.073
                        GGDEF_2  43 ealral.gpdalvavrgdrlvlllpaedeedae..............a 75 
                                    ++l++l +++ l++  + + +++l+ +++++a+              +
  gi|121638249|ref|YP_978473.1| 294 RMLARLrSQQRLAFFADIHMIAVLTENPDSAADfitstlgdlesaspQ 341
                                    566666555556666666777777766666666444333333333332 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.43   3.8e+03      36      56 ..     129     149 ..     127     151 .. 0.84
   2 !   40.9   3.8   1.5e-14   1.3e-10       1      47 [.     342     388 ..     342     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.43
                                    HHHHHS--TTSHHHHHHHHHH CS
                         HTH_30  36 ieellgldlddpddrlaLylA 56 
                                    ++ell l+++++++  +  lA
  gi|121638249|ref|YP_978473.1| 129 LHELLTLPFRSASEFIDATLA 149
                                    689*******99998887776 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.5e-14
                                    ...HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSH CS
                         HTH_30   1 LleTLraylenggnisatAkaLhvHrnTlryRLrrieellgldlddp 47 
                                    Ll T+ +y+++++n+s++A  Lh HrnTl  RL+ +++ll ++ld +
  gi|121638249|ref|YP_978473.1| 342 LLTTVLTYINEQCNASRAAHVLHTHRNTLLRRLETAQRLLPRPLDHT 388
                                    799*****************************************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3015.73
//
Query:       gi|121638250|ref|YP_978474.1|  [L=61]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-16   58.5   4.7    6.8e-16   58.4   4.7    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   4.7   3.8e-20   6.8e-16       1      59 [.       1      60 [.       1      61 [] 0.95

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3.8e-20
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH----SSSSHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsa.anaaaaapttavlaaaaDeVSaaiAalfsaha 59
                                   Ms v+vaPe++ +a  d+a+igs++ a  +aaaa ptt+vlaa+aDeVSa + alf+  a
  gi|121638250|ref|YP_978474.1|  1 MSLVSVAPELVVTAVPDVARIGSSIGApDTAAAARPTTSVLAAGADEVSADVVALFGWVA 60
                                   9**************************78889999*********************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 466.91
//
Query:       gi|121638251|ref|YP_978475.1|  [L=262]
Description: 16S ribosomal RNA methyltransferase RsmE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-60  202.0   0.0    9.2e-60  201.8   0.0    1.0  1  Methyltrans_RNA  RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8   0.0   5.1e-64   9.2e-60       3     224 ..      20     240 ..      18     242 .. 0.97

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 5.1e-64
                                    EEHHHHHHHHTTTT--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SSSSEEEEEEE--SSHHHHHHHHHH CS
                Methyltrans_RNA   3 ltdeeahHlvkVlRlkegdeiklfdgdgkeyeaeieeiskkkvtvkilekeeenkespekitlaqalpkgdklelilqka 82 
                                    ++++e  H+++V+R+++g++++l+dg g+++++ +e++ +  +++++l+++++++ +p+ +t++qalpk+++ el+++ a
  gi|121638251|ref|YP_978475.1|  20 VDGDEGFHAATVRRIRPGEQLVLGDGVGRLARCVVEQAGRGGLRARVLRRWSVPPVRPP-VTVVQALPKSERSELAIELA 98 
                                    6889******************************************************9.******************** PP

                                    HHTT-SEEEEEE-TTSSS...HHHHHHHHHHHHHHHHHHHHHHT-SS--EEEEEEEHHHHHHHCSCCEE....EEEEETT CS
                Methyltrans_RNA  83 tElGvseivplisersvvkldekkkdkklerwqkilieAaeQsgrtrlpevkepislkelleelkeadl....klildee 158
                                    tE G++++ +++++r+v+++d+ + dk l+rw++++++Aa+Qs+r+r+p v+ + s+  l+++++e+ +    +l+l+ee
  gi|121638251|ref|YP_978475.1|  99 TEAGADAFLAWQAARCVANWDGARVDKGLRRWRAVVRSAARQSRRARIPPVDGVLSTPMLVQRVREEVAagaaVLVLHEE 178
                                    ******************************************************9999999999998778888******* PP

                                    SSEBGGGSSHCCHTHHCSEEEEEE--TT---HHHHHHHHHTTCEEEB-SSS---HHHHHHHHHHHH CS
                Methyltrans_RNA 159 ekksleelsekkkelkevkvlliiGPEGGfsekEiellkeagfkpvsLgpriLRteTAalaalsal 224
                                    +++++ + ++++++    +++l++GPEGG+ ++E+++l++ag+ +v+Lgp++LRt+TAa +al+a+
  gi|121638251|ref|YP_978475.1| 179 ATERIVDIAAAQAG----SLMLVVGPEGGIAPDELAALTDAGAVAVRLGPTVLRTSTAAAVALGAV 240
                                    **********9998....9********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1809.95
//
Query:       gi|121638252|ref|YP_978476.1|  [L=382]
Description: chaperone protein DnaJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-37  128.5   0.0    2.9e-37  128.0   0.0    1.2  1  DnaJ_C           DnaJ C terminal domain
    9.6e-25   86.5   0.4    1.4e-24   86.0   0.4    1.2  1  DnaJ             DnaJ domain
      2e-12   47.3  10.8    3.3e-12   46.6  10.8    1.4  1  DnaJ_CXXCXGXG    DnaJ central domain
    4.9e-05   23.2  11.1      0.023   14.7   3.0    3.4  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
  ------ inclusion threshold ------
       0.54   10.7   8.2        1.8    9.0   0.1    3.3  3  Lar_restr_allev  Restriction alleviation protein Lar
        4.7    7.3   5.1          5    7.2   1.0    2.2  2  HypA             Hydrogenase/urease nickel incorporation, met


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.0   9.8e-41   2.9e-37       4     148 .]     121     336 ..     119     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 9.8e-41
                                    EEEE-HHHHHH-.EEE.EEEE........................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx........................................................ RF
                         DnaJ_C   4 eleisleelykGktkkikikrnvi........................................................ 27 
                                    +++++lee+++G+tk+++++  v                                                         
  gi|121638252|ref|YP_978476.1| 121 RMRLDLEECATGVTKQVTVDTAVLcdrcqgkgtngdsvpipcdtcggrgevqtvqrsllgqmltsrpcptcrgvgvvipd 200
                                    6899***************99888******************************************************** PP

                                    ..............TEEEEEE-TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHH CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  28 ..........kkekktlevkipaGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyveveislaeal 95 
                                              ++ +++++vkipaG+ dg+++rl+ +G+  ++gg++GDl+v+++++ h+vF r+g++l+++v++++++a+
  gi|121638252|ref|YP_978476.1| 201 pcqqcmgdgrIRARREISVKIPAGVGDGMRVRLAAQGEvgPGGGPAGDLYVEVHEQAHDVFVREGDHLHCTVSVPMVDAA 280
                                    *********8666668**********************65555************************************* PP

                                    HTEEEEEE-S.S-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                    xxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  96 lGgklevptl.dgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                    lG +++v+ + dg  +++i   tqpg+v++++g+Gmp+l+ +++rGdl+v+v+v++P
  gi|121638252|ref|YP_978476.1| 281 LGVTVTVDAIlDGLSEITIppgTQPGSVITLRGRGMPHLR-SNTRGDLHVHVEVVVP 336
                                    *****99988899999999********************8.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.4   4.7e-28   1.4e-24       1      63 []       4      65 ..       4      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 4.7e-28
                                   HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   dyY +Lgvsk+as+++Ik+aYrkla+++HPD n  d+ a+ kFkei+ AyevLsdp+kR++ D
  gi|121638252|ref|YP_978476.1|  4 DYYGLLGVSKNASDADIKRAYRKLARELHPDVN-PDEAAQAKFKEISVAYEVLSDPDKRRIVD 65
                                   8********************************.6777**********************987 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6  10.8   1.1e-15   3.3e-12       1      67 []     145     209 ..     145     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.1e-15
                  DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                    C++C+G+g++ ++ +  C+tC+G+G+v++ q++ lg++   ++++Cp+C+G G vi   d+C++C G+g
  gi|121638252|ref|YP_978476.1| 145 CDRCQGKGTNGDSvPIPCDTCGGRGEVQTVQRSlLGQML--TSRPCPTCRGVGVVI--PDPCQQCMGDG 209
                                    ********976556889********88888876688877..679************..899*****986 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.1   5.9e-05      0.18      10      46 ..     142     175 ..     133     183 .. 0.84
   2 !   14.7   3.0   7.6e-06     0.023      11      42 ..     160     197 ..     155     200 .. 0.86
   3 !    7.9   0.1   0.00097       2.9      12      47 ..     201     237 ..     198     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                                    EEE-TTTTTTSEETTE......E-TTTTTSSEEE-HH CS
                      Anti-TRAP  10 EtkCdaCngsGkiepeeprasleCPkCsGkglipTaq 46 
                                     + Cd C+g G          ++C  C+G+g + T q
  gi|121638252|ref|YP_978476.1| 142 AVLCDRCQGKGTNGDS---VPIPCDTCGGRGEVQTVQ 175
                                    567********98777...899*********999987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.6e-06
                                    EE-TTTTTTSEETTE............E-TTTTTSSEE CS
                      Anti-TRAP  11 tkCdaCngsGkiepe......eprasleCPkCsGkgli 42 
                                     +Cd+C g G++++       +  +s +CP C G+g++
  gi|121638252|ref|YP_978476.1| 160 IPCDTCGGRGEVQTVqrsllgQMLTSRPCPTCRGVGVV 197
                                    58**********998777777778999*********97 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00097
                                    E-TTTTTTSEETTE......E-TTTTTSS..EEE-HHH CS
                      Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkg..lipTaqG 47 
                                    +C++C g G+i +     s++ P+  G g  + + aqG
  gi|121638252|ref|YP_978476.1| 201 PCQQCMGDGRIRAR-REISVKIPAGVGDGmrVRLAAQG 237
                                    8***********99.77788888876655115667776 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.63   1.9e+03       6      14 ..     145     153 ..     131     157 .. 0.78
   2 ?    9.0   0.1   0.00059       1.8       5      20 ..     161     176 ..     159     181 .. 0.90
   3 ?    2.7   2.6     0.058   1.7e+02       4      16 ..     186     198 ..     184     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.63
                Lar_restr_allev   6 CPfCggrav 14 
                                    C+ C g+++
  gi|121638252|ref|YP_978476.1| 145 CDRCQGKGT 153
                                    888887766 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00059
                Lar_restr_allev   5 pCPfCggravlersqr 20 
                                    pC+ Cggr+++++ qr
  gi|121638252|ref|YP_978476.1| 161 PCDTCGGRGEVQTVQR 176
                                    9**********99887 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.058
                Lar_restr_allev   4 kpCPfCggravle 16 
                                     pCP C g +v++
  gi|121638252|ref|YP_978476.1| 186 RPCPTCRGVGVVI 198
                                    6*******99987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.0    0.0017         5      65      96 ..     137     170 ..     120     178 .. 0.78
   2 ?    7.0   0.7     0.002       5.8      69      98 ..     158     197 ..     153     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                                    EEE--EEEETTTS-EEECHHH.HHS-TTTSSS.- CS
                           HypA  65 eevpvkvrCreCgkefeleek.alrCpkCgsa.d 96 
                                     +v+  v C++C+ +++  ++  + C +Cg++ +
  gi|121638252|ref|YP_978476.1| 137 VTVDTAVLCDRCQGKGTNGDSvPIPCDTCGGRgE 170
                                    46788999*****999977655789****99734 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                                    -EEEETTTS-EEECHH.HHH..........S-TTTSSS-EE CS
                           HypA  69 vkvrCreCgkefelee.kal..........rCpkCgsadve 98 
                                    v + C++Cg ++e+++ +             Cp+C + +v 
  gi|121638252|ref|YP_978476.1| 158 VPIPCDTCGGRGEVQTvQ-RsllgqmltsrPCPTCRGVGVV 197
                                    5678*********88743.2358999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2669.50
//
Query:       gi|121638253|ref|YP_978477.1|  [L=343]
Description: heat-inducible transcription repressor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-60  203.7   1.8    4.6e-60  203.3   1.8    1.2  1  HrcA          HrcA protein C terminal domain
    8.2e-05   22.3   0.2    0.00073   19.2   0.0    2.7  3  HTH_DeoR      DeoR-like helix-turn-helix domain
     0.0013   18.6   0.0     0.0042   17.0   0.0    1.9  1  HTH_11        HTH domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.034   13.8   0.0    1.6  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor


Domain annotation for each model (and alignments):
>> HrcA  HrcA protein C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   1.8     1e-63   4.6e-60       1     220 []     105     326 ..     105     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 1e-63
                           HrcA   1 edllqraarlLseltgyvavvlapslskaklkhielvplsssrllvvlvtdsgrvenrllelpeevseeelaklsnllne 80 
                                    +d+l+ra+rlL++lt++vavv++p+ls+++++h+e++ l++ rll+v++tdsgrv++r++el + +++ +la+l+++l +
  gi|121638253|ref|YP_978477.1| 105 DDVLRRAVRLLAQLTRQVAVVQYPTLSTSTVRHLEVIALTPARLLMVVITDSGRVDQRIVELGDVIDDHQLAQLREILGQ 184
                                    79****************************************************************************** PP

                           HrcA  81 klagltlseiaerlreeklkeels..eye.elleqllealeeale..rseelyvsGtsnllrqpefsdd.eklrellell 154
                                    +l+g++ls ++ ++++++ ++         + + +++++l e l   ++e+l + Gt+nl+r++   d+  +lr++le+l
  gi|121638253|ref|YP_978477.1| 185 ALEGKKLSAASVAVADLA-SQLGGagG-LgDAVGRAATVLLESLVehTEERLLLGGTANLTRNAA--DFgGSLRSILEAL 260
                                    *************99995.54444343.15999999999966665588899***********996..999********** PP

                           HrcA 155 eekvvllkllselsdaegvsvrIGsEneleelkdcSvVtatYglggepvgtigviGPtrMdYakvi 220
                                    ee+vv+l+ll++ ++a++v+vrIG+E+  e++ ++S+V++ Yg+++++ g +gv+GPtrMdY+ +i
  gi|121638253|ref|YP_978477.1| 261 EEQVVVLRLLAAQQEAGKVTVRIGHETASEQMVGTSMVSTAYGTAHTVYGGMGVVGPTRMDYPGTI 326
                                    **********77667778**************************99*****************998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-07   0.00073      23      48 ..      36      61 ..      15      65 .. 0.84
   2 ?   -2.3   0.1      0.88     4e+03      20      32 ..     124     136 ..     122     137 .. 0.79
   3 ?   -2.2   0.0      0.79   3.5e+03      35      47 ..     257     269 ..     255     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                       HTH_DeoR 23 llgvSeaTiRRDLneLeeqglltRth 48
                                    lgvS aT+R+D++ Le++g +t  h
  gi|121638253|ref|YP_978477.1| 36 NLGVSSATVRNDMAVLEAEGYITQPH 61
                                   49*******************99877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.88
                       HTH_DeoR  20 lvellgvSeaTiR 32 
                                    +v++   S+ T+R
  gi|121638253|ref|YP_978477.1| 124 VVQYPTLSTSTVR 136
                                    566777899***9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.79
                       HTH_DeoR  35 LneLeeqglltRt 47 
                                    L+ Leeq+++ R 
  gi|121638253|ref|YP_978477.1| 257 LEALEEQVVVLRL 269
                                    6789999999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.4e-07    0.0042      24      44 ..      36      56 ..      12      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.4e-07
                         HTH_11 24 eLnvSrrtvrrdIkaLeelgv 44
                                    L+vS +tvr+d++ Le+ g+
  gi|121638253|ref|YP_978477.1| 36 NLGVSSATVRNDMAVLEAEGY 56
                                   399****************96 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.6e-06     0.034       8      73 ..      10      76 ..       5      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-06
                   HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAe..vlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayeal 73
                                   e+l+a++  +   ++++ ++++ e   l+  + tvRN + +L a g +  +p  + G +Pt k y+++
  gi|121638253|ref|YP_978477.1| 10 EVLRAIVADFVATQEPIGSKSLVErhNLGVSSATVRNDMAVLEAEGYIT-QPHTSSGRVPTEKGYREF 76
                                   89999999999999***99999873358899***************985.7899999*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2466.45
//
Query:       gi|121638254|ref|YP_978478.1|  [L=105]
Description: hypothetical protein BCG_2389 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 758.31
//
Query:       gi|121638255|ref|YP_978479.1|  [L=168]
Description: low molecular weight antigen cfp2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1140.68
//
Query:       gi|121638256|ref|YP_978480.1|  [L=71]
Description: protein mbtH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-30  102.6   0.1    6.7e-30  102.3   0.1    1.1  1  MbtH      MbtH-like protein


Domain annotation for each model (and alignments):
>> MbtH  MbtH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.1   3.7e-34   6.7e-30       1      52 [.       2      53 ..       2      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 3.7e-34
                                   --SCGG-SSSEEEEEEETT--EEEEETTS---TTEEEEEEEEEHHHHHHHHH CS
                           MbtH  1 msnpfddedgtflVLvNdeeqySlWPafaavPaGWrvvggpgsreeClayie 52
                                   ++npfdd++g f+VLvNde+q+SlWP+fa++PaGWrvv+g++sr++Cl+y+e
  gi|121638256|ref|YP_978480.1|  2 STNPFDDDNGAFFVLVNDEDQHSLWPVFADIPAGWRVVHGEASRAACLDYVE 53
                                   59*************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 535.01
//
Query:       gi|121638257|ref|YP_978481.1|  [L=431]
Description: lysine-N-oxygenase mbtG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-12   45.1   0.0    1.3e-11   44.3   0.0    1.4  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      5e-05   22.7   0.0     0.0036   16.6   0.0    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.1e-05   22.7   0.0    7.5e-05   22.1   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0005   20.5   0.0     0.0013   19.1   0.0    1.7  2  NAD_binding_7  Putative NAD(P)-binding
     0.0072   16.3   8.0        1.4    8.9   1.7    3.8  3  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.03   14.4   0.0    1.7  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   4.4e-15   1.3e-11      68     278 ..      88     284 ..      81     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.4e-15
                    K_oxygenase  68 spfsFlnYlkekgrLykFlnletflpsRkefedYlrWvasqleeqvrfgeeveevepdeeeeeelltveskdaegeeeel 147
                                     ++s+ +Yl ++  + +++ + + +p+ + +++Yl+Wva+++  +  +  eve++ +  ++   +l  +       e+++
  gi|121638257|ref|YP_978481.1|  88 TRYSWQSYLIATASFAEWIDRGRPAPTHRRWSQYLAWVADHIGLK-VIHGEVERLAVTGDR--WALCTH-------ETTV 157
                                    69*****************************************84.56678*****99975..345544.......6899 PP

                    K_oxygenase 148 earnlvlgvG...tepkiPevleklegkervvHsseylerkee..llakkriaVvGsGqSaaeifedllrrqkkvelklv 222
                                    +a +l+++      +  +P         +rv+  +++  r +   + +++r+aV+G+G +aa ++++l r++  ++++++
  gi|121638257|ref|YP_978481.1| 158 QADALMITGPgqaEKSLLPGN-------PRVLSIAQFWDRAAGhdRINAERVAVIGGGETAASMLNELFRHRV-STITVI 229
                                    ****99954302133344444.......556666666555544345699********************9876.79**** PP

                    K_oxygenase 223 trsealeplddspfvneifsPeyvdyfyslpeekreallkeqkatnykgvdaelie 278
                                    + +  l+   +  f n++fs + +d+ +   +e+r+al ++++   ++ v+++l++
  gi|121638257|ref|YP_978481.1| 230 SPQVTLFTRGEGFFENSLFS-DPTDWAALTFDERRDALARTDRGVFSATVQEALLA 284
                                    **************999997.67788777778888889999988888888888775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.011        33     144     177 ..       4      40 ..       1      49 [. 0.83
   2 !   16.6   0.0   1.2e-06    0.0036      64     225 ..     119     316 ..      83     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                    EEEEES-SHHHHHHHHH...HHHHT-EEEEEESSSSS CS
                                    xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaa...laklgkevtlveardrl 177
                                     ++v G+G+ +v +Aa    l+++g++v+ v a +r+
  gi|121638257|ref|YP_978481.1|   4 TLAVLGAGAKAVAVAAKasvLRDMGVDVPDVIAVERI 40 
                                    589************9966679999999877777776 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-06
                                    HHHCCCCHCCTCEEEEESC.EEEEETEEEC...TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCS CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  64 nqgielllgeevvkidpgk.kkvklekkke...gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklk 139
                                    +q + +++++ ++k+++g+ +++ ++ ++     +e+++++d+l++   +++ +  +pG  + v    + +d a +  + 
  gi|121638257|ref|YP_978481.1| 119 SQYLAWVADHIGLKVIHGEvERLAVTGDRWalcTHETTVQADALMITGPGQAEKSLLPGN-PRVLSIAQFWDRAAGHDRI 197
                                    5556666675577787777777777766646779999*********7668999999****.9998886666666665555 PP

                                    S-TSEEEEES-SHHHHHHHHHHHHHT-................................EEEEEESSSSSSTTS-HHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgk................................evtlveardrllraldkelsa 187
                                    +  +r++v+GgG ++  +  +l +  +                                  t  e+rd l r+    +sa
  gi|121638257|ref|YP_978481.1| 198 NA-ERVAVIGGGETAASMLNELFRHRVstitvispqvtlftrgegffenslfsdptdwaALTFDERRDALARTDRGVFSA 276
                                    55.5***********99999987777766666777555555555555555555555443344555555555666666666 PP

                                    HHHHHHHHT.TEEEEESCEEEEEEETTE.EEEEEETTSCE CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                    Pyr_redox_2 188 aleealeke.Gvevklgtsvkeidgnge.klevvledgee 225
                                    +++eal ++  ++   g +++++ ++g+ +l++ ++ g+e
  gi|121638257|ref|YP_978481.1| 277 TVQEALLADdRIHHLRGRVAHAVGRQGQiRLTLSTNRGSE 316
                                    6666666554555555555555555555544455555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.5e-08   7.5e-05      75     195 ..     110     231 ..      87     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.5e-08
                    Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhy 153
                                    ++ ++ +   +Yl+ va++  l++    eVe+++ +++   + t + t++A+ ++i tG  ++ +k   pG  + l++ +
  gi|121638257|ref|YP_978481.1| 110 RPAPTHRRWSQYLAWVADHIGLKVIH-GEVERLAVTGDRWALCTHETTVQADALMI-TGP-GQAEKSLLPGNPRvLSIAQ 186
                                    667899999**************975.68************************999.666.6778888888885333333 PP

                    Pyr_redox_3 154 skv..kefhkyagqkvvViGgknSavDaAlelvrk.gaeVtvvtr 195
                                      +     + ++ ++v+ViGg+++a+ +  el+r+  +++tv+ +
  gi|121638257|ref|YP_978481.1| 187 FWDraAGHDRINAERVAVIGGGETAASMLNELFRHrVSTITVISP 231
                                    222114556799*********************994345666554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.3e-07    0.0013       5      51 ..     197     255 ..     195     327 .. 0.73
   2 ?   -3.6   0.0       5.3   1.6e+04      15      39 ..     355     379 ..     355     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.3e-07
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele..............elvkla 51 
                                    ++ ++v v+GgGe Aa+ ++ l +    ++tv++p+v+ ++               +   +a
  gi|121638257|ref|YP_978481.1| 197 INAERVAVIGGGETAASMLNELFRHRvSTITVISPQVTLFTRgegffenslfsdptD---WA 255
                                    67799*******************98789*******965555444444555553332...33 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                  NAD_binding_7  15 gGevAarkvrklleagakvtvvape 39 
                                    gG++ a +++  + ++  vt v+p+
  gi|121638257|ref|YP_978481.1| 355 GGPLTADRLQEAIGYDLAVTDVTPK 379
                                    7888999999999999999988887 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   1.7   0.00046       1.4      92     151 ..     114     164 ..       6     167 .. 0.68
   2 !    7.0   0.0    0.0017       5.2       1      33 [.     203     231 ..     203     252 .. 0.81
   3 ?    1.6   0.1      0.08   2.4e+02      96     146 ..     271     318 ..     228     322 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00046
                  NAD_binding_9  92 pRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvL 151
                                    + + +++Yl++++++        + ++v+++ev++l+ ++d++a+  +++++++ada+++
  gi|121638257|ref|YP_978481.1| 114 THRRWSQYLAWVADH--------IGLKVIHGEVERLAVTGDRWAL-CTHETTVQADALMI 164
                                    555566666666655........55889*************9876.56778889998876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp 33 
                                    a++G+G +++++l++L +++      +it++ p
  gi|121638257|ref|YP_978481.1| 203 AVIGGGETAASMLNELFRHR----VSTITVISP 231
                                    89*****************6....555555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.08
                  NAD_binding_9  96 yGrYlrdlfeellarlpegvtvevhraevvdleeradgqavll.adgaslaa 146
                                     G + + + e+ll    ++ +++++r++v     r+++ +++l ++  s  +
  gi|121638257|ref|YP_978481.1| 271 RGVFSATVQEALL----ADDRIHHLRGRVAHAVGRQGQIRLTLsTNRGSENF 318
                                    5555554444444....45589*******99999998887777234445555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05      0.03       8      45 ..     195     232 ..     190     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                    S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45 
                                    ++++ ++v +iG Ge+a  +++ L +++v  ++v+  +
  gi|121638257|ref|YP_978481.1| 195 DRINAERVAVIGGGETAASMLNELFRHRVSTITVISPQ 232
                                    468899****************************8755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2951.70
//
Query:       gi|121638258|ref|YP_978482.1|  [L=1461]
Description: peptide synthetase mbtF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-85  285.2   0.6    1.4e-83  280.9   0.6    2.2  1  AMP-binding    AMP-binding enzyme
    4.9e-78  262.8   0.0    2.5e-60  204.4   0.0    2.1  2  Condensation   Condensation domain
    4.4e-10   40.4   0.6      4e-09   37.3   0.1    3.0  3  AMP-binding_C  AMP-binding enzyme C-terminal domain
    5.7e-09   36.2   0.3    1.9e-08   34.5   0.3    1.9  1  PP-binding     Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.9   0.6   3.1e-87   1.4e-83       1     423 []     477     862 ..     477     862 .. 0.87

  Alignments for each domain:
  == domain 1  score: 280.9 bits;  conditional E-value: 3.1e-87
                                    HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                    ++e aa +pd va+ +   + +lTYreld+ ++rlA gLr+++v +++ Va++l ++p++v+a+la+lkaG+++vpl+p+
  gi|121638258|ref|YP_978482.1| 477 FAEIAAAQPDSVAVSW--ADGQLTYRELDALADRLATGLRRADVSRETPVAVALSRGPRYVAAMLAVLKAGGMIVPLDPA 554
                                    5688999*******99..8999******************99************************************** PP

                                    S-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTS CS
                    AMP-binding  81 ltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpdd 160
                                    ++ e++a il+++ a v+i +         + + a+  +v + i                e++++         ++  d+
  gi|121638258|ref|YP_978482.1| 555 MPGERVAEILRQTSAPVVI-D---------EGVFAA--SVGADI---------------LEDDRAI--------TVPVDQ 599
                                    *******************.2.........122221..111211...............1211111........234599 PP

                                    EEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TT CS
                    AMP-binding 161 layiiYTSGTTGkPKGVmlshrnlvanvaslk...letr.fklkeddvvlsilplahifglilelllallsGatvvllpk 236
                                     ay+i+TSGTTG+PKGV+ +hr+l+a + ++    l++  ++l++  ++ +  ++ +++++    l+all G++v++++ 
  gi|121638258|ref|YP_978482.1| 600 AAYVIFTSGTTGTPKGVIGTHRALSAYADDHIervLRPAaQRLGRPLRIAHAWSFTFDAAW--QPLVALLDGHAVHIVDD 677
                                    ***************************9997565544444556668899999999999996..****************9 PP

                                    CGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEE CS
                    AMP-binding 237 daaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge...evle 313
                                      ++d+++l+e+i++++  +i ++P+++ +l ++g l       d   l ++ lgge+l ++++r +++ + +   + ++
  gi|121638258|ref|YP_978482.1| 678 HRQRDAGALVEAIDRFGLDMIDTTPSMFAQLHNAGLL-------DRAPLAVLALGGEALGAATWRMIQQNCARtamTAFN 750
                                    988****************************998755.......4556999999*************99998899999** PP

                                    EEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.. CS
                    AMP-binding 314 gYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds.. 391
                                    +YG+TEtt+ ++v+   e+   ++ +G+p + ++++++D   ++pvpdg+ Gel++ g+++++gYl++p++ta +f++  
  gi|121638258|ref|YP_978482.1| 751 CYGPTETTVEAVVAAVAEH--ARPVIGRPTCTTRAYVMDSW-LRPVPDGVAGELYLAGAQLTRGYLGRPAETAARFVAep 827
                                    ***********85443444..4567***************9.***********************************778 PP

                                    ...TCCEEEEEEEEEEETTSEEEEEEECCCEEEET CS
                    AMP-binding 392 ...egrwlrTGDlgrldedGyleivgRkkdliklr 423
                                       + r++rTGD++r+ +dG le++gR++d++k+r
  gi|121638258|ref|YP_978482.1| 828 ngrGSRMYRTGDVVRRLPDGGLEFLGRSDDQVKIR 862
                                    764256***************************96 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.4   0.0   5.7e-64   2.5e-60       3     452 ..      17     455 ..      15     458 .. 0.89
   2 !   56.4   0.0   4.7e-19   2.1e-15      29     313 ..    1068    1345 ..    1060    1349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 5.7e-64
                                    EEEEXXCCHHHHHHHHHHSSSSST........TEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE CS
                   Condensation   3 deyplspaQkrmwflekleeessa........ynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvi 74 
                                    d+++lsp+Q++++  + l  ++s         y+++++  + g ld+ +l++   ++++rh+ LR +fl+ +  +pvQvi
  gi|121638258|ref|YP_978482.1|  17 DVMALSPLQQGLFSRATLVAAESGseaaeadpYVIAMAADAAGPLDIALLRDCAAAMLTRHPNLRASFLHGNLSRPVQVI 96 
                                    56778888888766555544333222233444999********************************************* PP

                                    -TT-----EEEE-T..TSSSHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHH CS
                   Condensation  75 leerevelevleisdleeseeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdl 154
                                     +++ev +     +++ +    + + ++a ++ ++ fd+ +gpL+r+ l+++ ++ ++l++  HHi++DG+Sl++++ +l
  gi|121638258|ref|YP_978482.1|  97 PSSAEVLW-----RHVRAHP--SEVGALAAEERRRRFDVGRGPLIRFLLIELPDECWHLVIVAHHIVIDGWSLPLFVSEL 169
                                    ********.....4434443..4477777778899********************************************* PP

                                    HHHHHHHHTT-------S--HHHHHHHHHHHHCSHHHHHHHHHHHHHHH......S---BSS---SS---S-EEEEEEEE CS
                   Condensation 155 aklYqqlekgeelplpqktpYkdyaeweqqyleskdlekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsiklde 234
                                     +lY +  +   lp+ + + Y+dy+ w    l+ +d+  ++a W++ l+g    + L +  a+++++     r++++ld 
  gi|121638258|ref|YP_978482.1| 170 LALYRAGGHVAALPAAPRP-YRDYIGW----LAGRDQTASRAMWADHLNGLDGPTLLSPALADTPVQPGIPGRTEVRLDR 244
                                    ****888888888888888.*******....88899999***********777777777778888888888********* PP

                                    -S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHHH CS
                   Condensation 235 eteeklrklakeqgvtlndvllaalgllLskytgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfsel 314
                                    e +++l ++a+  gvt+ ++ + a++ +Ls  tg+ d+ +g+++sgR+se +++e+m+GlF+nt+Plr+++++  t    
  gi|121638258|ref|YP_978482.1| 245 EATAELADAARTRGVTISTLVQMAWATTLSAFTGRGDVTFGVTVSGRPSELSGVETMIGLFINTVPLRVRLDARATVGGQ 324
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHCCTTS-HHHHHHCSS.SS-SSSS-S-SEEEEESSS-HH.CCCEEECCCCSEEECEE...E.....SSE CS
                   Condensation 315 ikrvkedllkaephqgypleeLvkdlelqrkesrspLfdpvfsfenylgq.eseeeesqlselklsvssveaeeeskydl 393
                                       ++++    ++h++ +++e +    + +      +fd+ +++en++    + + e+  ++ +++  +v  e+ s + +
  gi|121638258|ref|YP_978482.1| 325 CAVLQRQFAMLRDHSYLGFNEFRAIAGIGE------MFDTLLVYENFPPGeVVGTAEFVANGVTFR--PVALESLSHFPV 396
                                    **********************99999887......7*********98773455556666666666..77789******* PP

                                    EEEEEETTSSEEEEEEEETTTS-HHHHHHHHHHHHHHHHHHHHSTTSBCCC-----HHH CS
                   Condensation 394 sleasetngkltikieYntslFdeetierflerlkelleqviehpeqklselkllsdae 452
                                    ++ a  ++g+lt+ +e    +      e + +r++ +l+++++  + +l+++++l d e
  gi|121638258|ref|YP_978482.1| 397 TVAAHRSTGELTLLVEVLDGALGTMAPESLGRRVLAVLQRLVSRWDRPLRDVDILLDGE 455
                                    ***************99999999999999999999999999999999999999999887 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 4.7e-19
                                     EEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSSSHHHHHHHHHHHH CS
                   Condensation   29 mqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdleeseeeeaieefaqkd 106 
                                     ++ v++l  ++  erl  +l ++++ h++LR +f +++   + Q  ++  +  +   e+   ++ + e+++       
  gi|121638258|ref|YP_978482.1| 1068 QTEVIRLPDRITRERLDAVLAAVVDGHEVLRCRFDRDAMALVAQPKTDILSEVWVSGELV--TAVA-EQTLGV----- 1137
                                     67789999**************************98877777776666666666444444..4443.343443..... PP

                                     HTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT-------S--.HHHHHHHHH CS
                   Condensation  107 lqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekgeelplpqktp.Ykdyaeweq 183 
                                        ++d ++g L+ a  ++  +   +l+l+ H + +D  S++i+l +l +   +l+ g+ ++  +++  Y+++     
  gi|121638258|ref|YP_978482.1| 1138 -LASLDPQAGRLLSAVWLREPDGPGVLVLTAHVLAMDPASWRIVLGELDAGLHALAAGRAPSPARENTsYRQWSRL-- 1212
                                     .4469**************999************************************987666555337755555.. PP

                                     HHHCSHHHHHHHHHHHHHHH......S---BSS---SS---S-EEEEEEEE-S-HHHHHHHHSTSS-HHHHHHHHHHH CS
                   Condensation  184 qyleskdlekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsikldeeteeklrklakeqgvtlndvllaalgl 261 
                                       ++ ++  ++ ++W   leg  p   L    +r a ++ +  +l+i+++ + ++++ +l  ++g +++d+l +a + 
  gi|121638258|ref|YP_978482.1| 1213 -LAQRAKALDSVDFWVAELEGADP--PLG--ARRVAPQTDRVGELAITMSISDADLTARLL-STGRSMTDLLATAAAR 1284
                                     .77788889************555..444..556666666667888888666655555554.6899************ PP

                                     HHHHHHT-SEEEE.....EEEEESSTT....CSTCHHC--SS-EEEEEEEEE--TT-BHHH CS
                   Condensation  262 lLskytgqddivv.....gteisgRes....eikdiermvGlFvntlPlridvkeaktfse 313 
                                     +   + +q+   +      +e++gR +    ++ d +++vGl   ++Plri+ ++a++f+ 
  gi|121638258|ref|YP_978482.1| 1285 MVTAWRRQRGQQTpapllALETHGRADvhvdKTADTSDTVGLLSAIYPLRIHCDGATDFAR 1345
                                     *****9988765422222799*****99999899***********************9985 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8   1.3e+04      31      61 ..     601     638 ..     596     641 .. 0.70
   2 ?   -2.1   0.0       1.8   8.2e+03      24      50 ..     757     770 ..     748     788 .. 0.55
   3 !   37.3   0.1   8.8e-13     4e-09       1      76 []     870     943 ..     870     943 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                    EEEEE---.-.--.....HHHHHHHHHHHHT-TTTS-S CS
                  AMP-binding_C  31 afVvlkdg.s.ea.....leeeLkahvrkelgpyavpk 61 
                                    a+V+  +g + ++     + ++L a++ ++++ + +p 
  gi|121638258|ref|YP_978482.1| 601 AYVIFTSGtTgTPkgvigTHRALSAYADDHIERVLRPA 638
                                    66665444312224667788999999999999998886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                    TTS---EEEEEE------HHHHHHHHH CS
                  AMP-binding_C  24 vkGealvafVvlkdgsealeeeLkahv 50 
                                    ++ ea+va V              +h+
  gi|121638258|ref|YP_978482.1| 757 TTVEAVVAAVA-------------EHA 770
                                    44445554443.............333 PP

  == domain 3  score: 37.3 bits;  conditional E-value: 8.8e-13
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEE..E------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVv..lkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+ ++l+ h aV  + V +  ++  G +l a+V   +++   +  +eL+a + ++l+ y vp+++v++delp+t +GK
  gi|121638258|ref|YP_978482.1| 870 EIAAVLNGHHAVHGCHVTARGHA-SGPRLTAYVAggPQP---PPVAELRAMLLERLPRYLVPHHIVVLDELPLTPHGK 943
                                    7899**************99999.**********44322...236********************************9 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.3   4.3e-12   1.9e-08       3      67 .]     970    1031 ..     969    1031 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.3e-12
                     PP-binding    3 lrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     l e++a+v++++    d+++ +  +GlDS++a++++ a +++ g+++  + + e++t++elaa++
  gi|121638258|ref|YP_978482.1|  970 LAEAFADVMETSNV--DVTAGFLQMGLDSIVALSVVQAARRR-GIALRARLMVECDTIRELAAAI 1031
                                     78999999998865..59************************.*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.83u 0.28s 00:00:01.10 Elapsed: 00:00:00.46
# Mc/sec: 9557.61
//
Query:       gi|121638259|ref|YP_978483.1|  [L=1682]
Description: peptide synthetase mbtE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.7e-127  425.2   0.0    4.1e-72  243.3   0.0    2.1  2  Condensation   Condensation domain
   1.1e-101  340.6   0.0    3.4e-94  315.8   0.0    2.9  2  AMP-binding    AMP-binding enzyme
    4.9e-28   97.3   0.3    3.1e-15   56.3   0.1    2.8  2  PP-binding     Phosphopantetheine attachment site
    5.3e-10   40.1   0.8    2.6e-09   37.9   0.5    2.4  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.0   0.0   1.5e-56   6.7e-53      14     456 ..       1     425 [.       1     426 [. 0.94
   2 !  243.3   0.0   9.1e-76   4.1e-72       5     456 ..    1028    1471 ..    1025    1472 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 1.5e-56
                                    HHHHHHHSSSSSTTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSS CS
                   Condensation  14 mwflekleeessaynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdlees 93 
                                    mwf+++ +++    n+ ++ +++g +dl rl++a++++ +rh +LRt++   ++g    +++ +    +   +++dl+++
  gi|121638259|ref|YP_978483.1|   1 MWFVQMADPSGALLNICVSYRITGDIDLARLRDAVNAVARRHRILRTTYPVGDDGVAQPTVHADLRPGWTQYDLTDLSQR 80 
                                    8************************************************998788888899999999************* PP

                                    SHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT-------S- CS
                   Condensation  94 eeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekgeelplpqkt 173
                                    ++   +e +aq++   pf+L+++ ++r+ +++ a+++++lll  HHi  D  S+++++ dl+++Y  +  g +l    ++
  gi|121638259|ref|YP_978483.1|  81 AQRLRLEVLAQREFCAPFELSRDAPLRITVVRTAADEHVLLLVAHHIAWDDGSWRVFFTDLTQAYSRADLGADLGP--EH 158
                                    *9888************************************************************99999999655..55 PP

                                    -HHHHHHHHHHHHCSHHHHHHHHHHHHHHH......S---BSS---SS---S-EEEEEEEE-S-HHHHHHHHSTSS-HHH CS
                   Condensation 174 pYkdyaeweqqyleskdlekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsikldeeteeklrklakeqgvtlnd 253
                                           + +  ++ +  e + +YW+ +++   + l+Lp    +    s++a r +++l+++t++++ ++ak++g t ++
  gi|121638259|ref|YP_978483.1| 159 -------RPSAASGPDTTEADLNYWRAIMADPPEPLELPGPAGTCVPTSWRAARATLRLPADTAARVATMAKNTGCTPYM 231
                                    .......3456689999************************9************************************** PP

                                    HHHHHHHHHHHHHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHHHHHHHHHHHCCTTS-H CS
                   Condensation 254 vllaalgllLskytgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfselikrvkedllkaephqgypl 333
                                    vllaa+g+l ++yt++dd+ v  ++ +R       e+++G F nt+++r++++ a +f el++++++ +  a+ hq++ l
  gi|121638259|ref|YP_978483.1| 232 VLLAAFGALVHRYTHSDDFLVAAPVLNRGAG---TEDAIGYFGNTVAMRLRPQSAMSFRELLTATRDIASGAFAHQRINL 308
                                    ****************************986...9********************************************* PP

                                    HHHHHCSS.SS-SSSS-S-SEEEEESSS-HHCCCEEECCCCSEEECEE....E.....SSEEEEEEETTSSEEEEEEEET CS
                   Condensation 334 eeLvkdlelqrkesrspLfdpvfsfenylgqeseeeesqlselklsvssve.aeeeskydlsleasetngkltikieYnt 412
                                     ++v++l+ +r  + + +  ++f f          +   ++  +++ + +   +++++  l +++  +  +  ++ e   
  gi|121638259|ref|YP_978483.1| 309 DRVVRELNPDRRHGAERMTRVSFGFRE-------PDGGGFNPPGIECERYDlRSNITQLPLGFMVEFDRAGVLVEAEHLV 381
                                    *************************66.......566666666666666666688999********************** PP

                                    TTS-HHHHHHHHHHHHHHHHHHHHSTTSBCCC-----HHHHHHH CS
                   Condensation 413 slFdeetierflerlkelleqviehpeqklselkllsdaekekL 456
                                    +  + +  +++l+++  ll+++++ p+++ls l l+++++++ L
  gi|121638259|ref|YP_978483.1| 382 EILEPALAKQMLRHFGVLLDNALAAPDNTLSGLALMDERDAARL 425
                                    *************************************9998876 PP

  == domain 2  score: 243.3 bits;  conditional E-value: 9.1e-76
                                     EEXXCCHHHHHHHHHHSSSSSTTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT----- CS
                   Condensation    5 yplspaQkrmwflekleeessaynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevel 82  
                                     + ls+ Q r wf   +++ +   n++++  l+g  d +++  a++ ++ rh++LRtv++ e  g p Q+i++ +ev++
  gi|121638259|ref|YP_978483.1| 1028 VRLSSSQMRSWFNYRFDGPNAVNNIPFAAALHGPCDTNAFAAAITDVVARHEILRTVYR-EIGGVPHQIIQPPAEVPV 1104
                                     579*******************************************************5.66**************** PP

                                     EEEE-T..TSSSHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHH CS
                   Condensation   83 evleisdleeseeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqq 160 
                                     +    sd++       + + ++++    fdLe++ ++raal++ + ++ +l l vHHi  D +S g+l+ dl ++Y +
  gi|121638259|ref|YP_978483.1| 1105 RCAAGSDAAW------LRAELNNERGYVFDLETDWPIRAALLS-TPEQTVLSLVVHHIAGDHWSAGVLFTDLLTAYRA 1175
                                     8888884333......455566667889***************.********************************** PP

                                     HHTT-------S--.HHHHHHHHHHHHCSHH..HHHHHHHHHHHHH......S---BSS---SS---S-EEEEEEEE- CS
                   Condensation  161 lekgeelplpqktp.Ykdyaeweqqyleskd..lekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsikldee 235 
                                        g+ ++  + +  Y+dy +w++  l   +  +  +++YW  ql g + ++ L +d +rpa  s  +d ++++l ++
  gi|121638259|ref|YP_978483.1| 1176 RSTGQRPSWAPLPVqYADYSVWQSALLDDGAgiVGPQRDYWIRQLGGLAGETGLRPDFPRPALLSGAGDAVEFRLGAA 1253
                                     ******999888878*******99988766533679****************************************** PP

                                     S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHH CS
                   Condensation  236 teeklrklakeqgvtlndvllaalgllLskytgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfse 313 
                                     + +kl  + ++ gvt  ++l+aa++++L+k  g+ d+ +g +++gR ++  ++++ +G+F+n++ lr d++++ t+ e
  gi|121638259|ref|YP_978483.1| 1254 IRDKLAAVSRDLGVTEFMLLQAAVAVVLHKAGGGVDVPIGAPVAGRSEA--NLDQLIGFFINIVVLRNDLRGNPTLRE 1329
                                     *************************************************..*************************** PP

                                     HHHHHHHHHHHHHCCTTS-HHHHHHCSS.SS-SSSS-S-SEEEEESSS-HHCCCEEECCCCSEEECEE....E..... CS
                   Condensation  314 likrvkedllkaephqgypleeLvkdlelqrkesrspLfdpvfsfenylgqeseeeesqlselklsvssve.aeeesk 390 
                                     +++r+++++l a+ hq+ p+ ++v+ ++ qr+ sr+pLfd v+     + q+   ++    + +l+  + e  ++ ++
  gi|121638259|ref|YP_978483.1| 1330 VLQRTRQMALAAYAHQDLPFDQVVEAVNPQRSLSRNPLFDIVVHVREQMPQDHVIDTGPDGDTTLR--VLEpTFDAAQ 1405
                                     *********************************************997778777777777777777..77889***** PP

                                     SSEEEEEEETTSSEEEEEEEETTTS-HHHHHHHHHHHHHHHHHHHHSTTSBCCC-----HHHHHHH CS
                   Condensation  391 ydlsleasetngkltikieYntslFdeetierflerlkelleqviehpeqklselkllsdaekekL 456 
                                      dls++ +  +++ + ++ Y+t+l++++t +rf++ l++++e++++ p+q+l+e++++s + ++ +
  gi|121638259|ref|YP_978483.1| 1406 ADLSVNFFACGDEYRGHVIYRTELYERATAQRFADWLVRVVEAFADRPDQPLREVEMVSAQARRRI 1471
                                     ***********************************************************9988776 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.8   0.0   7.6e-98   3.4e-94       3     423 .]     447     828 ..     445     828 .. 0.89
   2 !   20.5   0.0   3.4e-08   0.00015     346     412 ..    1482    1554 ..    1465    1556 .. 0.87

  Alignments for each domain:
  == domain 1  score: 315.8 bits;  conditional E-value: 7.6e-98
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                    eq  +tpd++a+v+  egq++TY++l+e++nrl+++L + G++++drVa+ll++sp+++v++l+++k Gav+vp++p+++
  gi|121638259|ref|YP_978483.1| 447 EQTTRTPDATAVVY--EGQHFTYHDLNEASNRLGHWLIEQGIGSEDRVAVLLDKSPDLIVTALGVVKSGAVYVPVDPSYP 524
                                    7889**********..**********************99**************************************** PP

                                    HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEE CS
                    AMP-binding  83 aeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddla 162
                                    +++l +il+d++ak+++          ++e a++         +d  +       ++++         ++ ++l+pd++a
  gi|121638259|ref|YP_978483.1| 525 QDRLDFILADCDAKLVL-R------TPVRELAGY--------RSD--D-------PTDA---------DRIRPLRPDNTA 571
                                    *****************.2......123333332........122..1.......1111.........1345699***** PP

                                    EEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHH CS
                    AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldp 242
                                    y+iYTSGTTG PKGV + hr ++    ++k   + +++++d++l++++ ++++++ +e++++l++Ga++v++++   +d 
  gi|121638259|ref|YP_978483.1| 572 YLIYTSGTTGLPKGVAVPHRPVAEYFVWFK--GEYDVDDTDRLLQVASPSFDVSI-AEIFGTLACGARMVIPRPGGLTDI 648
                                    **********************99988875..44456789**************7.***********************9 PP

                                    HHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSS CS
                    AMP-binding 243 klllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttg 322
                                    + l +l++++++t ++ vP++l  +l+ +  +      +   l+ v +ggepl+ e++++f+a+f   +++ YG+TEt +
  gi|121638259|ref|YP_978483.1| 649 GYLTALLRDEGITAMHFVPSLLGLFLSLPGVS------QWRTLQRVPIGGEPLPGEVADKFHATFDALLHNFYGPTETVI 722
                                    9**************************98887......6777999889*****************99************* PP

                                    ECEE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE....T.CC CS
                    AMP-binding 323 vvtv...lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds....e.gr 394
                                     ++    +  ++  +++  +G+p  ++ ++++D++ ++pvp+g+ Ge++++g +v+ gY+++  +tae+f++    +  r
  gi|121638259|ref|YP_978483.1| 723 NASRfkvVG-PQG-TRIVPIGRPKINTTMHLLDDS-LQPVPTGVIGEIYIGGTHVAYGYHRRAGLTAERFVAdpfnPgSR 799
                                    **5555333.333.34556***************9.***********************************788974456 PP

                                    EEEEEEEEEEETTSEEEEEEECCCEEEET CS
                    AMP-binding 395 wlrTGDlgrldedGyleivgRkkdliklr 423
                                    ++r+GDl+r+++dG +e+vgR+++++k+r
  gi|121638259|ref|YP_978483.1| 800 MYRSGDLARRNADGDIEFVGRADEQVKIR 828
                                    ***************************96 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.4e-08
                                     EEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE......T.CCEEEEEEEEEEETTSEEEE CS
                    AMP-binding  346 vevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds......e.grwlrTGDlgrldedGylei 412 
                                     ++v+++D++ ++pvp g++G ++ +g       l +p++ta +f++      +  r++r G  g++ +dG+le+
  gi|121638259|ref|YP_978483.1| 1482 ARVYLLDDA-LKPVPVGVVGDVYYGGGPAVGARLARPSETATRFVAdpfaaqPgSRLYRNGERGVWKADGQLEL 1554
                                     699*****9.*************9976666666779*********77999964456***************997 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1   6.9e-19   3.1e-15       2      67 .]     944    1007 ..     943    1007 .. 0.96
   2 !   38.3   0.0   2.9e-13   1.3e-09       2      67 .]    1581    1643 ..    1580    1643 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.9e-19
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +l +l+ e+lg++  ++++d+++fdlG++Slla++l+aa++ +fgv++ ++++fe+ t+ +la ++
  gi|121638259|ref|YP_978483.1|  944 RLAQLFGELLGRD--RVGADDSFFDLGGHSLLATKLVAAVRNAFGVDVGVREIFEFATVTALAGHI 1007
                                     799********99..577**********************************************98 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.9e-13
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +l +++a+vl+v   e++  +d+f+lG+DS+la++++a+ ++  g++++ +++fehp l elaa++
  gi|121638259|ref|YP_978483.1| 1581 ALAAILADVLEVG--EVGRYDDFFNLGGDSILATQVAARARDG-GIPLTARMVFEHPVLCELAAAV 1643
                                     799********96..46789**********************9.***************9999875 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.5   5.9e-13   2.6e-09       3      76 .]     838     917 ..     836     917 .. 0.87
   2 ?   -2.4   0.0       2.2   9.9e+03      32      61 ..    1314    1346 ..    1299    1357 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 5.9e-13
                                    HHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   3 EsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                     +a++  p V +a+Vv  + ++ G+ lv++V++++g   +++     + ++a+v+++l++y+ p + v++de+p t++GK
  gi|121638259|ref|YP_978483.1| 838 AAAIAVDPTVGQAVVVVSDLPRLGKSLVGYVTPAAGgdgPADvgvDLDRIRARVAAALPEYMLPAAYVVLDEIPITAHGK 917
                                    578888899*******78888************76644333378889********************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                     EEEE---.-.--HHHHHHHHHHH.HT-TTTS-S CS
                  AMP-binding_C   32 fVvlkdg.s.ealeeeLkahvrk.elgpyavpk 61  
                                     +Vvl+++   +++ +e+ ++ r+ +l++ya  +
  gi|121638259|ref|YP_978483.1| 1314 IVVLRNDlRgNPTLREVLQRTRQmALAAYAHQD 1346
                                     688976552344455555555554999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.08u 0.37s 00:00:01.45 Elapsed: 00:00:00.59
# Mc/sec: 8593.05
//
Query:       gi|121638260|ref|YP_978484.1|  [L=1004]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-48  165.1   0.1    4.9e-48  164.3   0.1    1.4  1  Acyl_transf_1    Acyl transferase domain
    2.5e-34  118.8   1.6    4.8e-34  117.8   1.6    1.5  1  KR               KR domain
    1.9e-10   40.5   0.4    4.1e-10   39.5   0.4    1.5  1  adh_short        short chain dehydrogenase
      1e-09   38.6   0.9    5.1e-09   36.4   0.3    2.6  2  PP-binding       Phosphopantetheine attachment site
      5e-06   26.2   0.0    1.5e-05   24.6   0.1    1.8  2  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-05   25.2   1.1    1.1e-05   25.2   1.1    2.4  3  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    0.00018   20.7   0.1    0.00031   20.0   0.1    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00043   19.8   0.0    0.00068   19.1   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0048   17.2   0.4      0.015   15.6   0.1    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.04   13.6   0.0      0.088   12.5   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.3   0.1   2.7e-51   4.9e-48       2     299 ..      99     404 ..      98     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 2.7e-51
                                    EEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT-.-HHHHHHS--T....TGGGSHHHHHHHHHHHHHHHHHH CS
                  Acyl_transf_1   2 fvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygf.svldvlrnnpe....glldaiqfvqpaLaavqialael 76 
                                    fvf+GqG  w GMG+  +++ + ++ + + ++ af++ +g  s l  l++ p     + + +i+ +  a ++  +alae+
  gi|121638260|ref|YP_978484.1|  99 FVFPGQGGHWPGMGAVAYRELPTYRTATDTCAAAFAA-AGVdSPLPYLIAPPGtderQAFCEIE-IEGAQFVHAVALAEV 176
                                    9***********************************9.66536677788887434444444444.455778999****** PP

                                    HHHTT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS....HHHHHHH....TT.EEEE CS
                  Acyl_transf_1  77 lkskGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel...aeeeeklr..cqddvvgav 151
                                    ++s Gv p++ vGHSlGE+Aaa+ ag++++ +a+ +v+ r  ++ +l g  + aa++    +    +l+  +   + ++v
  gi|121638260|ref|YP_978484.1| 177 WRSCGVLPDLTVGHSLGEVAAAYLAGSITLSDAVAVVAARANVVGRLPGRYAVAALGIgeqD--ASALIatTGGWLELSV 254
                                    ************************************************99999999887433..3333323667799*** PP

                                    EEECCCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHC CS
                  Acyl_transf_1 152 ansprrvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldessere 231
                                    +n  ++v++sg+ +a++++v  v+  g +a+ ++v++ vh   +++++d+l ++l d   +++ v++i  t+ d   +++
  gi|121638260|ref|YP_978484.1| 255 VNASSTVAVSGERQAVAAIVDTVRSSGHFARGITVGFPVHTSVLESLRDELCEQLPDSEFMEAPVQFIGGTTGDVVAPGT 334
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-T..CCCCCCTEETTSS CS
                  Acyl_transf_1 232 lsaeywvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvk..satlvGklkrdlt 299
                                     +++yw+anlr +vrf+ av sa+ ++ ++f+eis+H+ ll a+ +  + a++ +  +a lvG+ +r+ +
  gi|121638260|ref|YP_978484.1| 335 TFGDYWYANLRHTVRFDRAVESAIRCGARAFIEISAHPALLFAIGQNCEGAANLPdgPAVLVGSARRGER 404
                                    *************************************************988887336999999998766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   1.6   2.7e-37   4.8e-34       4     179 ..     670     840 ..     668     841 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 2.7e-37
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppi 82 
                                    ++tGG+G++G++ ar lae+gar++vllsR+a    +++a++a l+++ g+ +   ++D++d+++++a+ +e+   ++++
  gi|121638260|ref|YP_978484.1| 670 VVTGGAGAIGMHYARYLAEHGARRIVLLSRRA----ADQATVAMLRKQhGTVIVSPPCDITDPTQLSAIAAEYGGVGASL 745
                                    8******************************3....3455677777665************************9777655 PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaflDalaey 162
                                      ++haAg +  ++   +t++++   +a+Kv G+ ++ el + ++    +l+SS+ g++g  g ++Y+aaN  lD +a++
  gi|121638260|ref|YP_978484.1| 746 --IVHAAGSVISGTAPGVTSAAVVDNFAAKVLGLAQMIELWPLRPDVRTLLCSSVMGVWGGHGVVAYSAANRLLDVMAAQ 823
                                    ..9***************************************98888899****************************** PP

                                    HHHHHHTEEEEEE--BT CS
                             KR 163 rrsqglpavsinwglwa 179
                                     r+qg + v+++wglw+
  gi|121638260|ref|YP_978484.1| 824 LRAQGRHCVAVKWGLWQ 840
                                    ****************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.4   2.3e-13   4.1e-10       3     166 ..     669     827 ..     667     837 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.3e-13
                                    EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE.. CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkl.. 78 
                                    v+vtG+++ IG  +a+ la+ Ga+ +v ++r++++  ++++ l+++ g+ ++  ++D+td ++++a+ ++    +g++  
  gi|121638260|ref|YP_978484.1| 669 VVVTGGAGAIGMHYARYLAEHGARRIVlLSRRAADQ-ATVAMLRKQhGTVIVSPPCDITDPTQLSAIAAE----YGGVga 743
                                    89**********************999566666666.55555555549999999*********9987665....566622 PP

                                    SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHH CS
                      adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavag 158
                                     ++v+ AG   sg++  +++    + +  N+ + +l  +++++ +  +   r    sSv g  +  gv+aYsA+   ++ 
  gi|121638260|ref|YP_978484.1| 744 SLIVHAAGSVISGTAPGVTS----AAVVDNFAAKVLGLAQMIELWPLRPDVRTLLCSSVMGVWGGHGVVAYSAANRLLDV 819
                                    46899999965555555555....55555888888888888888888**************************9877777 PP

                                    HHHHHHHH CS
                      adh_short 159 ltrslake 166
                                    ++ +l+ +
  gi|121638260|ref|YP_978484.1| 820 MAAQLRAQ 827
                                    77777665 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7     3e+03      36      58 ..     296     318 ..     295     319 .. 0.84
   2 !   36.4   0.3   2.8e-12   5.1e-09       1      58 [.     919     977 ..     919     986 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                     PP-binding  36 ellaaleeefgveiplsdlfehp 58 
                                    ++l +l++e+  ++p+s+++e p
  gi|121638260|ref|YP_978484.1| 296 SVLESLRDELCEQLPDSEFMEAP 318
                                    57888999999999999999976 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 2.8e-12
                     PP-binding   1 eklrelvaevlgv.pleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehp 58 
                                    +++r+ +a vlg+  + e++++++lfdlG+DS+la++l ++l++  g +++l++l+   
  gi|121638260|ref|YP_978484.1| 919 DAVRTQLAAVLGIpQAGEVNLQESLFDLGVDSMLALDLRNRLKRSIGATVSLATLMGDI 977
                                    57999********545559************************************9755 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2     4e+03      74     114 ..     326     369 ..     296     371 .. 0.69
   2 !   24.6   0.1   8.5e-09   1.5e-05       1      90 [.     669     769 ..     669     806 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                                    ---HHHHHHSHHHHHHHHTHHHHH...HHHHHHHHTCTEEEEEE CS
                      Epimerase  74 vggvaassedpadfieknlqgtln...lleaarkagvkrllfls 114
                                     g+v a  ++  d++++nl+ t++    +e a ++g++ ++ +s
  gi|121638260|ref|YP_978484.1| 326 TGDVVAPGTTFGDYWYANLRHTVRfdrAVESAIRCGARAFIEIS 369
                                    55556666667899999999998622246666688888888777 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 8.5e-09
                                    EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHH...T-SEEEE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl......elveldltdrsalerlfkee...qpdavih 70 
                                    ++VtG++G iG + +++l+e+g + ++ l+r+  +++t +  ++          +d+td+++l ++ +e+   ++  ++h
  gi|121638260|ref|YP_978484.1| 669 VVVTGGAGAIGMHYARYLAEHGARrIVLLSRRAADQATVAMLRKqhgtviVSPPCDITDPTQLSAIAAEYggvGASLIVH 748
                                    68********************776999999966666554444479987766689******99999999764578999** PP

                                    --S.---HHHHHHSHHHHHHH CS
                      Epimerase  71 lAa.vggvaassedpadfiek 90 
                                    +A+ v +  a   + a+++++
  gi|121638260|ref|YP_978484.1| 749 AAGsVISGTAPGVTSAAVVDN 769
                                    *99865544444444444443 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.82   1.5e+03      60     110 ..     213     264 ..     190     272 .. 0.70
   2 ?   -1.9   0.0       1.1     2e+03     123     159 ..     564     600 ..     555     604 .. 0.84
   3 !   25.2   1.1   5.9e-09   1.1e-05       3     176 ..     675     841 ..     673     876 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.82
                                    HHHHHHHHSSEEE..EEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHH CS
                   adh_short_C2  60 veevvekfgklDi..lvnnagiapklkgpfletsreefdraldvnlyslflla 110
                                    v++ ++ +g+l +  +v + gi ++ ++++l ++  ++ +   vn+ s+++++
  gi|121638260|ref|YP_978484.1| 213 VAARANVVGRLPGryAVAALGIGEQ-DASALIATTGGWLELSVVNASSTVAVS 264
                                    4444445566654115666666666.888888999999999999999999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    EEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2 123 ivnlssvgaervvpnynaygaaKaalealtrylAvel 159
                                     v+l  vgae+v +  ++ +a  aal a+ r++  e 
  gi|121638260|ref|YP_978484.1| 564 SVCLVTVGAEQVDAADAVPSAGQAALAAMHRSIGFEH 600
                                    68888999999999999999**********9998775 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 5.9e-09
                                    TTSHHHHHHHHHHHTT-E.EEEEESSGGHHHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   3 asgIGraiAkalaeeGae.vvltdlneeakkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                    a  IG + A+ lae+Ga+ +vl  ++ +++++v+ l +++g+  v  +cD+td++q+ a+++e      +   +v++ag 
  gi|121638260|ref|YP_978484.1| 675 AGAIGMHYARYLAEHGARrIVLLSRRAADQATVAMLRKQHGTViVsPPCDITDPTQLSAIAAEYGGV--GASLIVHAAGS 752
                                    668**************8567777777779***********995589************99997765..56779****** PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvel 159
                                    + +  g +  ++ + + + ++ ++ +l+++++   pl     + + +ssv +  +  +  ay+aa      l   +A++l
  gi|121638260|ref|YP_978484.1| 753 VIS--GTAPGVTSAAVVDNFAAKVLGLAQMIEL-WPLRP-DVRTLLCSSVMGVWGGHGVVAYSAAN----RLLDVMAAQL 824
                                    999..9999999999999999999999999875.45544.45555556665666666666777664....4445567777 PP

                                    GGGTEEEEEEEE--BHC CS
                   adh_short_C2 160 gpkgiRvNavspgpikT 176
                                     ++g  + av  g+ + 
  gi|121638260|ref|YP_978484.1| 825 RAQGRHCVAVKWGLWQA 841
                                    77777777766666555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.8e-07   0.00031       1      85 [.     669     750 ..     669     778 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.....T CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel...k 77 
                                    v+vtG++G+iG +  r ++++ +++i+ll+r    + ++++  +   ++ +    iv+  +d++d ++l+ +  e+   +
  gi|121638260|ref|YP_978484.1| 669 VVVTGGAGAIGMHYARYLAEHGARRIVLLSRRAADQATVAMLRK---QHGT---VIVSPPCDITDPTQLSAIAAEYggvG 742
                                    79***********************************9999652...2222...35667899999999999988873335 PP

                                    -SEEEE-- CS
                Polysacc_synt_2  78 vdvvfhaA 85 
                                      +++haA
  gi|121638260|ref|YP_978484.1| 743 ASLIVHAA 750
                                    78999998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.8e-07   0.00068       2      74 ..     671     738 ..     670     757 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.8e-07
                                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74 
                                    +TG+aG iG + a++L e g + +++  r ++ + ++++ l+k+ +    + +    +D+tD ++l  + ae+
  gi|121638260|ref|YP_978484.1| 671 VTGGAGAIGMHYARYLAEHGARRIVLLSRRAADQ-ATVAMLRKQ-H---GTVIVSPPCDITDPTQLSAIAAEY 738
                                    9*******************99998887777644.567777653.2...34577889*********9998875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.6   1.4e+04      61      89 ..     514     540 ..     501     541 .. 0.73
   2 !   15.6   0.1   8.4e-06     0.015       5      80 ..     674     753 ..     669     766 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.6
                                    HHHHHHHTTSSEEEE-SSGGGHHHHHHHH CS
                Sacchrp_dh_NADP  61 avLaallkegdlvvnlsppissldvlkaC 89 
                                    + L+a  ++++l++  +p++++ d ++a+
  gi|121638260|ref|YP_978484.1| 514 E-LSA-ARDAELILVIAPDFEHTDAVRAA 540
                                    4.555.47888899999999999999886 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.4e-06
                                    --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS.....SEEEE- CS
                Sacchrp_dh_NADP   5 GaGsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg.....dlvvnl 76 
                                    GaG++G   a++la+h+    +i++ +r  +   a++a +   +g+ + +  +d+ ++++ L+a+ +e+      l+v++
  gi|121638260|ref|YP_978484.1| 674 GAGAIGMHYARYLAEHGAR--RIVLLSRRAADQ-ATVAMLrkqHGTVIVSPPCDITDPTQ-LSAIAAEYggvgaSLIVHA 749
                                    66***************98..********9994.444444567999999***********.***9999888888888888 PP

                                    SSGG CS
                Sacchrp_dh_NADP  77 sppi 80 
                                    ++++
  gi|121638260|ref|YP_978484.1| 750 AGSV 753
                                    8877 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.9e-05     0.088       5      58 ..     674     725 ..     670     737 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                                    S-SHHHHHHHHHHHHHTHC.EEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEE CS
                           ApbA   5 GaGaiGsllaakLakagad.vtlilrsrrlealkknGlrltseggeeilrppeal 58 
                                    GaGaiG  +a +La++ga  ++l+ r++ +++   +   l++ +g +i++pp  +
  gi|121638260|ref|YP_978484.1| 674 GAGAIGMHYARYLAEHGARrIVLLSRRA-ADQ--ATVAMLRKQHGTVIVSPPCDI 725
                                    9**************7777577777777.332..222222223345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1004 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.87u 0.37s 00:00:01.24 Elapsed: 00:00:00.56
# Mc/sec: 5361.56
//
Query:       gi|121638261|ref|YP_978485.1|  [L=444]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-77  261.0   0.2      2e-77  260.2   0.0    1.5  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    4.1e-36  123.6   0.6    1.7e-35  121.5   0.5    2.0  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    2.8e-08   33.4   0.1    5.7e-08   32.4   0.1    1.5  1  Thiolase_N       Thiolase, N-terminal domain
    6.3e-08   33.1   0.0    1.1e-07   32.3   0.0    1.3  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.2   0.0   4.5e-81     2e-77       2     253 .]       5     254 ..       4     254 .. 0.93
   2 ?   -3.0   0.0      0.99   4.4e+03     217     243 ..     288     314 ..     284     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 260.2 bits;  conditional E-value: 4.5e-81
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSB.TSSTTEEE-BSS.EEE..S.TTEGGTTSTHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadkly.dpparaagkiktklggfld.vddfdpeffgi 77 
                                    +pv+ivG+++ +Pgg++ ++++w lL e+r++ +++p+dr w  ++l+  ++++  + i+ +lggfl  + +fdpeff+i
  gi|121638261|ref|YP_978485.1|   5 DPVVIVGLAIEAPGGVEtADDYWTLLSEQREGLGPFPTDRgWALRELFdGSRRNGFKPIH-NLGGFLSsATTFDPEFFRI 83 
                                    69*************999******************************455555555666.5****************** PP

                                    HHHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHH CS
                  ketoacyl-synt  78 spreaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagr 157
                                    sprea+amdpqqr+ l++aw++le++g++p++l g +vg+++G++a +y+   +  ++    +++  ++g+ +  vi+gr
  gi|121638261|ref|YP_978485.1|  84 SPREATAMDPQQRVGLRVAWRTLENSGINPDDLAGHDVGCYVGASALEYGPALTEFSH---HSGHL-ITGT-SLGVISGR 158
                                    *************************************************764444433...46777.8998.******** PP

                                    HHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB- CS
                  ketoacyl-synt 158 isyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfv 237
                                    i+y+l+l Gp++tvdt CsS+l+a h avq++r+g++d+alaGGv ++ tp+ ++ fs++++ls+dg+c+++++ a+G+ 
  gi|121638261|ref|YP_978485.1| 159 IAYTLDLAGPALTVDTSCSSALAAFHTAVQAIRAGDCDLALAGGVCVMGTPGYFVEFSKQHALSDDGHCRPYSAHASGTA 238
                                    ******************************************************************************** PP

                                    BB-EEEEEEEEECHHH CS
                  ketoacyl-synt 238 lGEGvGavvLkrleda 253
                                    ++EG+++++L+r++ a
  gi|121638261|ref|YP_978485.1| 239 WAEGAAMFLLQRRSRA 254
                                    ************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.99
                                    TTBB-TTSGGGTTBTTB-SB-BB-EEE CS
                  ketoacyl-synt 217 agllspdgrckafdpkadGfvlGEGvG 243
                                    ++ll +   + a  p++ G+v G G +
  gi|121638261|ref|YP_978485.1| 288 TRLLRRAIAQAAVVPADVGMVEGHGTA 314
                                    456777777788888999999999976 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.45     2e+03      15      43 ..      87     115 ..      83     120 .. 0.86
   2 !  121.5   0.5   3.9e-39   1.7e-35       1     117 [.     262     378 ..     262     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.45
                                    TSSSTSTTHHHHHHHHHHHHHHHT--GGG CS
                Ketoacyl-synt_C  15 hnsltapngeaqaraiekalaeagvdped 43 
                                    ++++++p+++   r+  + l+++g++p+d
  gi|121638261|ref|YP_978485.1|  87 EATAMDPQQRVGLRVAWRTLENSGINPDD 115
                                    5678888888889999**********998 PP

  == domain 2  score: 121.5 bits;  conditional E-value: 3.9e-39
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +a++++s +nsdg + +ltap+g+aq r++++a+a+a v p+dv++ve hgt+t+lgD++El++l++ +g+    +   +
  gi|121638261|ref|YP_978485.1| 262 LAEVRASCLNSDGLSDGLTAPSGDAQTRLLRRAIAQAAVVPADVGMVEGHGTATRLGDRTELRSLAASYGTAPAGRGPLL 341
                                    69**********************************************************************9965667* PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    gSvKsniGH++aAaG ++l+kv+la +h +ipptl++
  gi|121638261|ref|YP_978485.1| 342 GSVKSNIGHAQAAAGGLGLVKVILAAQHAAIPPTLHV 378
                                    ************************************8 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   1.3e-11   5.7e-08      75     118 ..     166     209 ..     144     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.3e-11
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsna 118
                                      pa tv+  csS+l+a ++a+q+i+ag++d ++agGv  m++ 
  gi|121638261|ref|YP_978485.1| 166 AGPALTVDTSCSSALAAFHTAVQAIRAGDCDLALAGGVCVMGTP 209
                                    5699**********************************999875 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   2.4e-11   1.1e-07       1      54 [.     381     437 ..     381     442 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.4e-11
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkee 54 
                                    P+ ei+ +e+  l++ ++ tpw+       ++v++fG++G+n+Hvi+  +++ +++e+
  gi|121638261|ref|YP_978485.1| 381 PSREID-WEKQGLRLADKLTPWRAVDgwrtAAVSAFGMSGTNSHVIVSMPDTVSAPER 437
                                    899***.***************99888999*****************99887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2517.88
//
Query:       gi|121638262|ref|YP_978486.1|  [L=1414]
Description: phenyloxazoline synthase mbtB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-91  306.7   0.0      3e-91  306.1   0.0    1.3  1  AMP-binding    AMP-binding enzyme
    1.1e-57  195.8   0.0    2.3e-57  194.8   0.0    1.5  1  Thioesterase   Thioesterase domain
    1.1e-26   93.5   0.0    1.6e-26   93.0   0.0    1.1  1  Condensation   Condensation domain
    5.7e-25   87.5   0.4    5.6e-13   49.1   0.2    2.7  2  PP-binding     Phosphopantetheine attachment site
      4e-07   30.9   0.1    1.3e-06   29.3   0.1    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.1   0.0   8.4e-95     3e-91       1     422 [.     558     950 ..     558     951 .. 0.91

  Alignments for each domain:
  == domain 1  score: 306.1 bits;  conditional E-value: 8.4e-95
                                    HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                    + +qa+++pd++a+    +   l+Y++l+++++++Aa+Lr++G++ gd+Va+l p++ e v+a+l+il aG+v+ p+  +
  gi|121638262|ref|YP_978486.1| 558 FFRQAQQQPDAPAVFA--SSGDLSYAQLRDQASAVAAALRAAGLRVGDTVAVLGPKTGEQVAAVLGILAAGGVYLPIGVD 635
                                    689***********77..999*******************99************************************** PP

                                    S-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTS CS
                    AMP-binding  81 ltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpdd 160
                                     ++++ + il+   + + +  v         +++ ++  +  +++l         ++ +++++e        + + +p  
  gi|121638262|ref|YP_978486.1| 636 QPRDRAERILATGSVNLAL--VC------GPPCQVRV--PVPTLLLA--------DVLAAAPAEF------VPGPSDPTA 691
                                    *******************..42......22334332..22233333........2223333343......334689*** PP

                                    EEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCC CS
                    AMP-binding 161 layiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaal 240
                                    lay+++TSG+TG+PKGV + h++++++v ++   ++f+l++ d++l+ + l +++++ l++++al sG+++v++++ +++
  gi|121638262|ref|YP_978486.1| 692 LAYVLFTSGSTGEPKGVEVAHDAAMNTVETF--IRHFELGAADRWLALATLECDMSV-LDIFAALRSGGAIVVVDEAQRR 768
                                    ******************************6..6689999****************8.*******************99* PP

                                    HHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGG CS
                    AMP-binding 241 dpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlTE 319
                                    dp+++++li++++vt ++  P  l++lle g         +lsslr v +gg++++p+l+r+++   +  ++  + G TE
  gi|121638262|ref|YP_978486.1| 769 DPDAWARLIDTYEVTALNFMPGWLDMLLEVGGG-------RLSSLRAVAVGGDWVRPDLARRLQVQAPSaRFAGLGGATE 841
                                    *****************************6544.......79************************99999********* PP

                                    GSSECEE......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEET. CS
                    AMP-binding 320 ttgvvtv......lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdse. 392
                                    t++++t+      ++l+ d+++++ +G p+p++ +++v ++ g  +pd + Gel+v+g g+++gY ++pe+tae+f+++ 
  gi|121638262|ref|YP_978486.1| 842 TAVHATIfevqdaANLPPDWASVP-YGVPFPNNACRVVADS-GDDCPDWVAGELWVSGRGIARGYRGRPELTAERFVEHd 919
                                    *****8889999999999999998.*************998.9**********************************757 PP

                                    CC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 393 gr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                    gr w+rTGDl+r+ +dG+le+vgR+++ +k+
  gi|121638262|ref|YP_978486.1| 920 GRtWYRTGDLARYWHDGTLEFVGRADHRVKI 950
                                    888*********988**************98 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.8   0.0   6.3e-61   2.3e-57       3     229 ..    1190    1411 ..    1189    1413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 194.8 bits;  conditional E-value: 6.3e-61
                                     EEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHH CS
                   Thioesterase    3 LflfppagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGgl 78  
                                     + +fp+agG+a+++r+la++l ++ v++++vq+p+r   r++p+++sie+la e++ea  ++ p  P++lfGh++G++
  gi|121638262|ref|YP_978486.1| 1190 VLVFPHAGGAAAAYRWLAKSLVANDVDTFVVQYPQRAdrRSHPAADSIEALALELFEAGDWHLPA-PLTLFGHCMGAI 1266
                                     578**************************************************************.************ PP

                                     HHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHHTHHHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHH CS
                   Thioesterase   79 lAfevArqLesqGlavkslflidssapseteaqeasrraedeefveeltdlggtepeelledeellsellpalradyr 156 
                                     +Afe+Ar  e++G +v++l+ + ++aps+ +a   +  ++d+++++++ dlggt ++ lledee+++ l+pa++adyr
  gi|121638262|ref|YP_978486.1| 1267 VAFEFARLAERNGVPVRALWASSGQAPST-VAASGPLPTADRDVLADMVDLGGT-DPVLLEDEEFVELLVPAVKADYR 1342
                                     ***************************99.9999999999999***********.*********************** PP

                                     HHTCCS-TTSCSEHHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCCHHHSHHHHHHHHHHHH CS
                   Thioesterase  157 aleqyslrpeaaqklratlfngsddklkdldtlelaerweqktsgevsvhvlegdhfylledrleavleiiek 229 
                                     al  ys++p+ +   ra++++   ++ ++++ ++l++ we++tsg++++++++g+hfyl+ d+l+av++++++
  gi|121638262|ref|YP_978486.1| 1343 ALSGYSCPPDVRI--RANIHAVGGNRDHRISREMLTS-WETHTSGRFTLSHFDGGHFYLN-DHLDAVARMVSA 1411
                                     *************..**********************.**********************.7******99876 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   4.5e-30   1.6e-26       5     357 ..     100     442 ..      97     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 4.5e-30
                                    EEXXCCHHHHHHHHHHSSSSSTTEEEEEEEEES.---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----E CS
                   Condensation   5 yplspaQkrmwflekleeessaynmqavlkleg.eldlerlekalqelierhdaLRtvfleeengepvQvileerevele 83 
                                     pl p+Q  mw+    +++       ++++++g ++d++rl+ a + l  rh+ LR++fl +  ++ +     +r++++ 
  gi|121638262|ref|YP_978486.1| 100 FPLAPMQHAMWVGRHDHQQLGGVAGHLYVEFDGaRVDPDRLRAAATRLALRHPMLRVQFLPD-GTQRIPPAAGSRDFPIS 178
                                    599*****************************9459***********************766.4444455559******* PP

                                    EEE-T..TSSSHHHHHHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHT CS
                   Condensation  84 vleisdleeseeeeaieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlek 163
                                    v ++++++ +  ++ +   ++ d++++ +L+ g  f  al  +  +r  l +++    +D++S +ill dla+lY    +
  gi|121638262|ref|YP_978486.1| 179 VADLRHVAPDVVDQRLAG-IR-DAKSHQQLD-GAVFELALTLLPGERTRLHVDLDMQAADAMSYRILLADLAALY----D 251
                                    ******999986665444.44.366666665.45566666666666666666666689*****************....* PP

                                    T-------S--HHHH...HHHHHHHHCSHHHHHHHHHHHHHHH......S---BSS---SS---S-EEEEEE.EE-S-HH CS
                   Condensation 164 geelplpqktpYkdy...aeweqqyleskdlekeeaYWseqlegelpvlqLpkdkarpakrsfkadrlsikl.deeteek 239
                                    g+e+p++  t Y++y   +e+ ++ l +  +  ++++W++++ +  +  +Lp++ a  + ++ + ++ +  + d++t ++
  gi|121638262|ref|YP_978486.1| 252 GREPPALGYT-YQEYrqaIEA-EETLPQPVRDADRDWWAQRIPQLPDPPALPTR-AGGERDRRR-STRRWHWlDPQTRDA 327
                                    *******999.7777331444.67799999*************97777779988.333333333.33344436******* PP

                                    HHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTT..CSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHH CS
                   Condensation 240 lrklakeqgvtlndvllaalgllLskytgqddivvgteisgRes..eikdiermvGlFvntlPlridvkeaktfselikr 317
                                    l   a++ g+t  + l aa++ +L +++ ++++  +++   R+   +  d++  vG F++ l l +d+ +a t +   ++
  gi|121638262|ref|YP_978486.1| 328 LFARARARGITPAMTLAAAFANVLARWSASSRFLLNLPLFSRQAlhP--DVDLLVGDFTSSLLLDVDLTGARTAAARAQA 405
                                    *******************************************9555..******************************* PP

                                    HHHHHHHHHCCTTS-.HHHHHHCSS.SS-SSSS-S-SEEEE CS
                   Condensation 318 vkedllkaephqgyp.leeLvkdlelqrkesrspLfdpvfs 357
                                    v+e+l++a  h+ yp l  L++ ++++ +    +++ pv+ 
  gi|121638262|ref|YP_978486.1| 406 VQEALRSAAGHSAYPgLSVLRDLSRHRGT----QVLAPVVF 442
                                    **************935555555555444....45555444 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.8e-12   6.6e-09       3      67 .]      11      74 ..       9      74 .. 0.96
   2 !   49.1   0.2   1.5e-16   5.6e-13       2      67 .]    1065    1131 ..    1064    1131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.8e-12
                     PP-binding  3 lrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                   +r+ vae+lgv +++++p ++l   GlDS+ +++l+++ +++ g++++ ++l + pt++++++++
  gi|121638262|ref|YP_978486.1| 11 IRAEVAELLGVRADALHPGANLVGQGLDSIRMMSLVGRWRRK-GIAVDFATLAATPTIEAWSQLV 74
                                   89****************************************.*********99******99976 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.5e-16
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeef.gveiplsdlfehptlaelaayl 67  
                                     +lr++va++lg++ +++++++d+f lG+DS+la++++a +++ +   ++ ++d+f+ +t+a+la++l
  gi|121638262|ref|YP_978486.1| 1065 ALRRIVADILGRANDAVGVHDDFFALGGDSVLATQVVAGIRRWLdSPSLMVADMFAARTIAALAQLL 1131
                                     79******************************************555*****************986 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   3.6e-10   1.3e-06       1      76 []     959    1031 ..     959    1031 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.6e-10
                                     HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE-.-----HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C    1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlk.dgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76  
                                     e+E+al + p+V  aa+   p      +l+a V  + +g+  ++e +++++++ +++++ p++v ++d++p t sGK
  gi|121638262|ref|YP_978486.1|  959 EIEAALQRLPGVHAAAATVLPGG--SDVLAAAVCVDdAGV--TAESIRQQLADLVPAHMIPRHVTLLDRIPFTDSGK 1031
                                     8***************8844444..255777777741233..68********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.48
# Mc/sec: 8843.19
//
Query:       gi|121638263|ref|YP_978487.1|  [L=565]
Description: bifunctional salicyl-AMP ligase/salicyl-S-arcp synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-82  277.1   0.0    2.4e-82  276.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.1e-10   41.4   0.0    7.1e-10   39.7   0.0    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.8   0.0   2.7e-86   2.4e-82       3     421 ..      48     457 ..      46     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 276.8 bits;  conditional E-value: 2.7e-86
                                    HHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                    AMP-binding   3 eqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                    ++a+++pd+ a+ d   + ++  l+Y+eld+r++r+Aa+L  lG+++gdrV++ lpn++++ val+a+l+aGa++v++ p
  gi|121638263|ref|YP_978487.1|  48 DAARRWPDRLAVADagdRPGHGGLSYAELDQRADRAAAALHGLGITPGDRVLLQLPNGCQFAVALFALLRAGAIPVMCLP 127
                                    7899********98999667889********************************************************* PP

                                    TS-HHHHHHHHHHHTESEEE..ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS- CS
                    AMP-binding  80 tltaeelayiledseakvli..atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeel 156
                                    + +a+el +  + s a+ l+  +  +  +  ++++e  a+ ++ ++ +++d d+ ++ ++++ ++++        +++++
  gi|121638263|ref|YP_978487.1| 128 GHRAAELGHFAAVSAATGLVvaDVASGFDyRPMARELVADHPTLRH-VIVDGDPGPFVSWAQLCAQAGTG----SPAPPA 202
                                    ********************76233445556666666666555655.679*9999999998888855533....35668* PP

                                    BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS-TTSCHH.HHHHHHHHHHTT-EEEE CS
                    AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsilplahifg.lilelllallsGatvvl 233
                                    +p ++a+++ ++GTTG+PK +  +h+ +v+n+++ +  +    +l++ddv+l++l   h f   + +ll+a+++Gat v+
  gi|121638263|ref|YP_978487.1| 203 DPGSPALLLVSGGTTGMPKLIPRTHDDYVFNATASAalC----RLSADDVYLVVLAAGHNFPlACPGLLGAMTVGATAVF 278
                                    *************************88888877743322....3678**************9434689************ PP

                                    -TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEE CS
                    AMP-binding 234 lpkdaaldpklllelieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfgeevl 312
                                    +p  +   p++ +++ie+++vtv+a+vP++++ +++s + +         +slrl+ +gg++l+pe +r++r  + + + 
  gi|121638263|ref|YP_978487.1| 279 APDPS---PEAAFAAIERHGVTVTALVPALAKLWAQSCEWEpV-----TPKSLRLLQVGGSKLEPEDARRVRTALTPGLQ 350
                                    99554...456689********************996444422.....4567***********************999** PP

                                    EEEEEGGGSSECEECHCTTTCTSTTS-BEE-T.TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE CS
                    AMP-binding 313 egYGlTEttgvvtvlpleedkkklgsvGkplp.gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds 391
                                    +++G++E +  +t    + ++++  ++G+pl+   e++iv+ + gepv++geeGellvrgp +  gY+  +  +++ fd 
  gi|121638263|ref|YP_978487.1| 351 QVFGMAEGLLNFT-RIGDPPEVVEHTQGRPLCpADELRIVNAD-GEPVGPGEEGELLVRGPYTLNGYFAAERDNERCFD- 427
                                    ************9.77788889999*****9779********9.************************99777777787. PP

                                    TCCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 392 egrwlrTGDlgrldedGyleivgRkkdlik 421
                                    +++++r+GDl+r+++dG+l ++gR kd+i 
  gi|121638263|ref|YP_978487.1| 428 PDGFYRSGDLVRRRDDGNLVVTGRVKDVIC 457
                                    767**********99*************96 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         2   1.8e+04       6      23 ..     165     182 ..     162     187 .. 0.83
   2 !   39.7   0.0     8e-14   7.1e-10       2      76 .]     468     542 ..     467     542 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                    HHSSTTEEEEEEE----- CS
                  AMP-binding_C   6 lvshpaVaeaaVvGvpde 23 
                                    ++ hp  + + V G+p +
  gi|121638263|ref|YP_978487.1| 165 VADHPTLRHVIVDGDPGP 182
                                    678999999999999866 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 8e-14
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHH.HHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahv.rkelgpyavpkkvvfvdelpktrsGK 76 
                                    +E+ l+shpa+  aa+vG pd+  Ge ++a Vv + g + + +eL+ ++ r+ ++++ +p+++v+ ++lp t  GK
  gi|121638263|ref|YP_978487.1| 468 LEEQLLSHPAIFSAAAVGLPDQYLGEKICAAVVFA-GAPITLAELNGYLdRRGVAAHTRPDQLVAMPALPTTPIGK 542
                                    79*******************************95.743478*******88899*******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4294.70
//
Query:       gi|121638264|ref|YP_978488.1|  [L=306]
Description: acetyl hydrolase mbtJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-38  132.9   0.8    1.6e-38  132.7   0.8    1.1  1  Abhydrolase_3  alpha/beta hydrolase fold
    0.00019   20.4   0.0    0.00026   20.0   0.0    1.1  1  Say1_Mug180    Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.8   1.8e-42   1.6e-38       2     210 ..      77     277 ..      76     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 1.8e-42
                                    EEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                  Abhydrolase_3   2 vyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                     y+HG G++++s++th++l + l++ +g  v+svdYrlAP ++fP+a  d+ aa+ wla      g+ ++++v+a dSaG
  gi|121638264|ref|YP_978488.1|  77 YYVHGSGYTMCSPRTHRRLTSWLSSLTGLPVFSVDYRLAPRYRFPTAATDVRAAWDWLAHV---CGLAAEHMVIAADSAG 153
                                    69*********************************************************99...79************** PP

                                    HHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTT.SHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                  Abhydrolase_3  82 GnlaaavalrardegepkvagqvliyPvtdlerte.sesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                    G+l+  ++l+   +   ++a++vl++P+ dl +++ ++s+   e ++ +p++ +++ +  + ly  + d ++ +++  +a
  gi|121638264|ref|YP_978488.1| 154 GHLTVDMLLQPEVA-ARPPAAVVLFSPLIDL-TFRlGASR---ELQRPDPVVRADRAARSVALYYTGVDPAHHRLALDVA 228
                                    *******9887776.568*********9999.44404444...333788****************999999999996666 PP

                                    S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                         lpptl++v++ ++l  +++++ + +raag  +el+++++++H+f+
  gi|121638264|ref|YP_978488.1| 229 -GGPPLPPTLIQVGGAEILEADARQLDADIRAAGGICELQVWPDQMHVFQ 277
                                    .55569******************************************96 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.9e-08   0.00026     125     243 ..      76     189 ..      60     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-08
                    Say1_Mug180 125 llylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvkskgf..knvvvlGd 202
                                    + y+HG g+ +   p t   L+     +  +++  +DY +       + +p    ++ a +d+l +  g+   ++v+  d
  gi|121638264|ref|YP_978488.1|  76 IYYVHGSGYTM-CSPRTHRRLTSWLSSLTGLPVFSVDYRLAP----RYRFPTAATDVRAAWDWLAHVCGLaaEHMVIAAD 150
                                    679******98.57999999*******************988....99*****************9988632689999** PP

                    Say1_Mug180 203 SaGGnlvLslllklsklnkvvlPkkaiaiSPWlnltildek 243
                                    SaGG l + +ll+ +   +   P  +++ SP ++lt++   
  gi|121638264|ref|YP_978488.1| 151 SAGGHLTVDMLLQPEVAAR--PPAAVVLFSPLIDLTFRLGA 189
                                    *************999999..79*************87555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2150.51
//
Query:       gi|121638265|ref|YP_978489.1|  [L=450]
Description: salicylate synthase MbtI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-61  207.6   0.0    3.4e-61  207.1   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.1   0.0   1.9e-65   3.4e-61       4     258 .]     186     438 ..     183     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.1 bits;  conditional E-value: 1.9e-65
                                    HHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEE CS
                Chorismate_bind   4 dYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrri 83 
                                     ++++v+ +++ei+ag+++kv+lsr ++++   a+d   +yr  r++n+   sfll+l++++ lg SPEl+  v++++ +
  gi|121638265|ref|YP_978489.1| 186 GFRRRVAVAVDEIAAGRYHKVILSRCVEVP--FAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVV 263
                                    7999**************************..889999****************************************** PP

                                    EEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEE CS
                Chorismate_bind  84 etepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegel 163
                                     tep+aGTra g+ p+ d+ ++++l +++Ke+ Eh++ v++  ++++ +a+pgs  v ++++v++ ++v+hl sti+++l
  gi|121638265|ref|YP_978489.1| 264 ITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARL 343
                                    ******************************************************************************** PP

                                    STT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEE CS
                Chorismate_bind 164 kedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIv 243
                                    +++ + + +l+alfP+ + +G+Pk + +e+i +l+e +Rg+Y+Gav +l+adg +++a+++R a +  ++ +l+aGaGI+
  gi|121638265|ref|YP_978489.1| 344 DPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGII 423
                                    ******************************************************************9999********** PP

                                    TT--HHHHHHHHHHH CS
                Chorismate_bind 244 adSdpeaEyeEtlaK 258
                                     +S+pe+E+eEt++K
  gi|121638265|ref|YP_978489.1| 424 EESEPEREFEETCEK 438
                                    *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3396.40
//
Query:       gi|121638266|ref|YP_978490.1|  [L=417]
Description: hypothetical protein BCG_2401 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.4e-110  367.7  10.4   5.1e-110  367.6  10.4    1.0  1  Sbt_1     Na+-dependent bicarbonate transporter superfamily
  ------ inclusion threshold ------
       0.34   11.2   1.5        9.1    6.6   0.0    3.3  4  DUF2811   Protein of unknown function (DUF2811)
        3.1    7.7   5.1       0.56   10.1   0.2    2.2  2  Beta-APP  Beta-amyloid peptide (beta-APP)


Domain annotation for each model (and alignments):
>> Sbt_1  Na+-dependent bicarbonate transporter superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.6  10.4  8.5e-114  5.1e-110       1     307 [.      16     402 ..      16     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: 367.6 bits;  conditional E-value: 8.5e-114
                          Sbt_1   1 PvvlffilGllaallksdLeiPealykllslyLLlaiGlkGGvelaeselsaelllallaavvlgll....ipllaflil 76 
                                    P++lff++G+l+ ++k+++e+P+ ly+ l+lyLLlaiG++GG ela+  ++ + + a++ ++v+g++    i++la+++l
  gi|121638266|ref|YP_978490.1|  16 PLLLFFYFGFLIPIFKVRFEFPYVLYQGLTLYLLLAIGWHGGEELAK--IKPSNVGAIVGFMVVGFAlnfvIGTLAYFLL 93 
                                    99********************************************9..6778888888888888766666999****** PP

                          Sbt_1  77 rkltkldkvdaaaiAalYGsvSavtfaaalavlesqgiayegymvallalmeipaivvalllakllkkkkkkese..... 151
                                    +klt +++vd+a++A++YGs Sa+tfa+++avl+s g+a+++ym+++la+meip+++val+l+++l+++ ++e+      
  gi|121638266|ref|YP_978490.1|  94 SKLTAMRRVDRATVAGYYGSDSAGTFATCVAVLTSVGMAFDAYMPVMLAVMEIPGCLVALYLVARLRHRGMNEAGymade 173
                                    ***********************************************************************87779**** PP

                          Sbt_1 152 ................................................................lkevlkeallnksvvl 167
                                                                                                    ++e+l+e++ln ++vl
  gi|121638266|ref|YP_978490.1| 174 pgyttaamigagpgtparpahsdsltaqaergieeelelslekrehpnwdedgvkdsgtnasifSRELLQEVFLNPGLVL 253
                                    ******************************************************************************** PP

                          Sbt_1 168 LlggliiGlltge...kgleklepffedlFkgvLalfLLemGlvaarrlkelrkvglflilfailaplvnallgillak. 243
                                    L+gg++iGl++g    k+l++ ++ff+++F+gvL+lfLLemG++a+r+lk+l+++g  +++f++lap+++a+lgi++a+ 
  gi|121638266|ref|YP_978490.1| 254 LFGGIVIGLISGLqgqKVLHDDDNFFVAAFQGVLCLFLLEMGMTASRKLKDLASAGSGFVFFGLLAPNLFATLGIIVAHg 333
                                    **********9953447788899*******************************************************87 PP

                          Sbt_1 244 llgls.....aGgavllavLaaSaSyIavPaalrlaiPeAnpslyltaslgitfpfniligiPlYlala 307
                                    ++ ++     +G++vl+avL+++aSyIavPa++rlaiPeA+p+l l+aslg+tf++n++igiPlY+++a
  gi|121638266|ref|YP_978490.1| 334 YAYVTnndfaPGTYVLFAVLCGAASYIAVPAVQRLAIPEASPTLPLAASLGLTFSYNVTIGIPLYIEIA 402
                                    7766666777********************************************************998 PP

>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.63   3.8e+03       5      18 ..      35      48 ..      32      54 .. 0.81
   2 ?   -0.9   0.0      0.34     2e+03      34      50 ..      88     104 ..      83     108 .. 0.84
   3 ?    6.6   0.0    0.0015       9.1       6      29 ..     206     227 ..     199     231 .. 0.79
   4 ?    0.7   0.1      0.11   6.6e+02      30      45 ..     279     298 ..     272     305 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.63
                        DUF2811  5 eipeeLheslkkfl 18
                                   e p  L++ l+ +l
  gi|121638266|ref|YP_978490.1| 35 EFPYVLYQGLTLYL 48
                                   7899999*999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                        DUF2811  34 LslFLlqngssdravar 50 
                                    L+ FLl + +  r+v r
  gi|121638266|ref|YP_978490.1|  88 LAYFLLSKLTAMRRVDR 104
                                    99****99988888877 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0015
                        DUF2811   6 ipeeLheslkkflethpnWDqdrl 29 
                                    i eeL  sl+k  ++hpnWD+d +
  gi|121638266|ref|YP_978490.1| 206 IEEELELSLEK--REHPNWDEDGV 227
                                    66677777776..79******987 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.11
                        DUF2811  30 lqaA....LslFLlqngssd 45 
                                    + aA    L lFLl+ g + 
  gi|121638266|ref|YP_978490.1| 279 FVAAfqgvLCLFLLEMGMTA 298
                                    55554444899***999765 PP

>> Beta-APP  Beta-amyloid peptide (beta-APP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   9.4e-05      0.56      23      35 ..      66      78 ..      60      81 .. 0.89
   2 ?   -2.0   0.8      0.55   3.3e+03      31      38 ..     253     260 ..     251     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.4e-05
                       Beta-APP 23 SNKGAIIGLMVGG 35
                                   SN GAI+G MV G
  gi|121638266|ref|YP_978490.1| 66 SNVGAIVGFMVVG 78
                                   9**********77 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.55
                       Beta-APP  31 LMVGGVVI 38 
                                    L+ GG+VI
  gi|121638266|ref|YP_978490.1| 253 LLFGGIVI 260
                                    67799998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2790.62
//
Query:       gi|121638267|ref|YP_978491.1|  [L=375]
Description: coproporphyrinogen III oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-16   58.8   0.0    1.3e-15   58.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.012   15.6   1.3      0.037   14.1   1.3    1.8  1  HemN_C       HemN C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.5e-19   1.3e-15       3     164 ..      11     181 ..       9     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.5e-19
                                    EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH..HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk..aekg.vkevilgggepllypdfvellerlakla... 74 
                                    ++++C  rC +C++++    + +g++ ++ +  + +e++ ++   +   v++v +ggg+p+l   +  +++  + ++   
  gi|121638267|ref|YP_978491.1|  11 HVPFCLTRCGYCDFNTYtpAQLGGVSPDRWLLALRAELELAAakLDAPtVHTVYVGGGTPSLLGGERLATLLDMVRDhfv 90 
                                    789************99**777777777777777777766664345667*************944444444444444557 PP

                                    .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEB CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                    Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivgl 152
                                      p+ +++ e+n+    +e+ ++++ +g +rvslg +++ ++ vl  + r h++ +  +a   + + g+   + d i+g 
  gi|121638267|ref|YP_978491.1|  91 lAPDAEVSTEANPESTWPEFFATIRAAGYTRVSLGMQSVAPR-VLATLDRVHSPGRAAAAATEAIAEGFTHvNLDLIYGT 169
                                    767889999999988779************************.************************************* PP

                                    TTTSHHHHHHHH CS
                                    xxxxxxxxxxxx RF
                    Radical_SAM 153 pGendeeleell 164
                                    pGe+d++l+  +
  gi|121638267|ref|YP_978491.1| 170 PGESDDDLVRSV 181
                                    *******98766 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.3   4.1e-06     0.037      11      66 .]     317     364 ..     310     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-06
                         HemN_C  11 iilgLRlreGldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprGrl 66 
                                    ++l  Rlr+Gl+la++ +        + +   e   ++GLL  +g+rl+lt rGrl
  gi|121638267|ref|YP_978491.1| 317 VLLKVRLRQGLPLARLGA--------AERERAEAVLADGLLDYHGDRLVLTGRGRL 364
                                    78899**********544........4466689999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2709.97
//
Query:       gi|121638268|ref|YP_978492.1|  [L=154]
Description: resuscitation-promoting factor rpfD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-32  112.4   7.6    1.6e-32  112.0   7.6    1.2  1  Transglycosylas  Transglycosylase-like domain
  ------ inclusion threshold ------
      0.027   14.1   0.0       0.04   13.6   0.0    1.1  1  SLT              Transglycosylase SLT domain


Domain annotation for each model (and alignments):
>> Transglycosylas  Transglycosylase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   7.6   1.8e-36   1.6e-32       2      77 .]      49     121 ..      48     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1.8e-36
                                    XTHHHHHHHHHHHHSS-TT-TTSSSEBTTTTBEHHHHHHTTCCST.SCGGGS-HHHHHHHHHHHHHHHCGGGSTTC CS
                Transglycosylas   2 adesnwdaiAqcEsggnwaintgnGyyGglqfsqstWeavggekyapsaaqAsreqQiavAekvlatqGagaWptc 77 
                                    ad+ +wdaiAqcEsggnwa+ntgnG+yGglq+sq+tW+++gg++   s+a+As +qQi+vA+++++tqG gaWp+c
  gi|121638268|ref|YP_978492.1|  49 ADDIDWDAIAQCESGGNWAANTGNGLYGGLQISQATWDSNGGVG---SPAAASPQQQIEVADNIMKTQGPGAWPKC 121
                                    7899****************************************...****************************9 PP

>> SLT  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-06      0.04      19      77 ..      56     111 ..      53     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-06
                                    HHHHHHHTT-TT-B-TTSEBTTTTBETTTHHHHHHHHT-SHHHHCSHHHHHHHHHHHHH CS
                            SLT  19 aiaqvESgfnpkAvsksgavGLmQimpstakrlglrvklsedelldPeknisagakyLk 77 
                                    aiaq ESg+n  A  ++g +G  Qi ++t  + g     +   +  P++ i+++ +++k
  gi|121638268|ref|YP_978492.1|  56 AIAQCESGGNWAANTGNGLYGGLQISQATWDSNGG---VGSPAAASPQQQIEVADNIMK 111
                                    8*****************************99664...788899999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1074.99
//
Query:       gi|121638269|ref|YP_978493.1|  [L=185]
Description: hypothetical protein BCG_2404c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.5   0.2      0.059   13.1   0.2    1.1  1  TPR_21    Tetratricopeptide repeat-like domain
       0.15   12.0   5.6       0.26   11.2   5.6    1.4  1  Fer4_5    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   6.6e-06     0.059      10      94 ..      38     130 ..      34     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-06
                         TPR_21  10 lilvgvvlalvglaGwqgwqdyqee....qaeeAsalYqqlqeave.....akdaakakeaaeeladeyggtaYaalaaL 80 
                                    +++v+v la  g+ Gw  ++++q++    qa +A+  Y   +++++     ++ ++ ++ +++e++d+yg++  a+l +L
  gi|121638269|ref|YP_978493.1|  38 AVAVVVSLAGSGWCGWVLFEKHQTDvaagQALQAARSYVVKLATMDceridHNMRDILEGSTGEFKDKYGKS-SAHLRQL 116
                                    677788888888999999999997533337778888887777655555554666667778899999999999.6888888 PP

                         TPR_21  81 llAkaaveagdlaa 94 
                                    l+ ++ + +g + a
  gi|121638269|ref|YP_978493.1| 117 LADNRVATHGTVVA 130
                                    77666555555555 PP

>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.6   2.9e-05      0.26       5      27 ..      31      54 ..      28      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.9e-05
                         Fer4_5  5 llilfl.aivlvtllfGRafCgWi 27
                                   ++i+++ a+ +v  l G  +CgW+
  gi|121638269|ref|YP_978493.1| 31 SVIGWVgAVAVVVSLAGSGWCGWV 54
                                   578888566677777********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1332.04
//
Query:       gi|121638270|ref|YP_978494.1|  [L=563]
Description: ferredoxin-dependent nitrite reductase NirA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-48  162.5   0.0    4.9e-35  120.4   0.0    2.3  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    6.8e-27   93.1   0.2    2.7e-13   49.6   0.0    3.2  3  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   5.5e-39   4.9e-35       2     156 ..     170     321 ..     169     324 .. 0.96
   2 !   40.0   0.0   2.9e-14   2.6e-10       6     142 ..     420     557 ..     417     563 .] 0.86

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 5.5e-39
                                    SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigf 81 
                                    g++ r v ++p ag   +++lD t+++++i +++ +++++ +lPrK K+a+sg   ++va+e+nD++++gv+++e+  g+
  gi|121638270|ref|YP_978494.1| 170 GDCPRVVLGSPLAGESLDEVLDPTWAIEEIVRRYIGKPDFADLPRKYKTAISGL--QDVAHEINDVAFIGVNHPEHGPGL 247
                                    899**************************************************9..78********************** PP

                                    EEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH.HHCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                        NIR_SIR  82 nilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv.eeelg 156
                                     ++vGGgl+++++ ++     ++vp  ev ev+ a++ v+rd+g+r  r+k+Rlk l++++G++kFre++  e+l+
  gi|121638270|ref|YP_978494.1| 248 DLWVGGGLSTNPMLAQRVG--AWVPLGEVPEVWAAVTSVFRDYGYRRLRAKARLKFLIKDWGIAKFREVLeTEYLK 321
                                    ****************999..8************************************************555554 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.9e-14
                                    CCCCCSTCCCTBSS-SS-T....HHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE.. CS
                                    xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                        NIR_SIR   6 rnvtlcpgaglceeallDt....telakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei.. 79 
                                    rn ++c g ++c+    +t    + l+ ++e++le++ ++ ++P    +++ gcpn c++ ++ Dig+ g   d++    
  gi|121638270|ref|YP_978494.1| 420 RNLMACSGIEFCKLSFAETrvraQHLVPELERRLEDINSQLDVP--ITVNINGCPNSCARIQIADIGFKGQMIDDGHGgs 497
                                    78889999999988888885555666667777777777666666..667889*****************99888887778 PP

                                    ..EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHH CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR  80 ..gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverl 142
                                      gf++ +GG+lg + g ++++++   v+ +e+ ++++ +v+ +     ++  + eR++ +v r 
  gi|121638270|ref|YP_978494.1| 498 veGFQVHLGGHLGLDAGFGRKLRQ-HKVTSDELGDYIDRVVRNFV----KHRSEGERFAQWVIRA 557
                                    99**********************.8999999*************....99**********9875 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0     3e-17   2.7e-13       7      68 ..     100     160 ..      94     161 .. 0.93
   2 ?    0.4   0.0     0.068   6.1e+02      53      67 ..     268     282 ..     267     284 .. 0.87
   3 !   39.1   0.0   5.6e-14   5.1e-10       4      68 ..     346     408 ..     343     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3e-17
                   NIR_SIR_ferr   7 kgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                    k y+m+r+r  +G ++a+ lr l +i+ ++++ +++++ rQn+q h+++ e+++ei+++L++
  gi|121638270|ref|YP_978494.1| 100 K-YFMMRVRCDGGALSAAALRTLGQISTEFARDTADISDRQNVQYHWIEVENVPEIWRRLDD 160
                                    4.56*******************************************************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.068
                   NIR_SIR_ferr  53 gvpeedleeileeLa 67 
                                    +vp  +++e+++++ 
  gi|121638270|ref|YP_978494.1| 268 WVPLGEVPEVWAAVT 282
                                    9**********9975 PP

  == domain 3  score: 39.1 bits;  conditional E-value: 5.6e-14
                   NIR_SIR_ferr   4 kdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                    k+  g+++v++ + +Gr++   l+a+ad+  + gs +ir+T+ Q l++ ++p++ l+++++ L++
  gi|121638270|ref|YP_978494.1| 346 KN--GLNAVGVAPIAGRVSGTILTAVADLMARAGSDRIRFTPYQKLVILDIPDALLDDLIAGLDA 408
                                    45..459******************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 4042.61
//
Query:       gi|121638271|ref|YP_978495.1|  [L=254]
Description: phosphoadenosine phosphosulfate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-46  156.3   0.0    9.4e-46  156.0   0.0    1.1  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.0   5.2e-50   9.4e-46       4     173 ..      61     228 ..      58     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 5.2e-50
                                    EE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC... CS
                    PAPS_reduct   4 vsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee... 80 
                                    + v+  + ++Vl++La k+ + vpv+f+dtg++f eti ++d++e+ y++r+  ++pe++vae+ +  +  ++l+ +   
  gi|121638271|ref|YP_978495.1|  61 YVVASNMADAVLVDLAAKVRPGVPVIFLDTGYHFVETIGTRDAIESVYDVRVLNVTPEHTVAEQDELLG--KDLFARnph 138
                                    556668999*******************************************************99998..588887889 PP

                                    HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCC CS
                    PAPS_reduct  81 aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLyd 160
                                    +++r++Kv+pl k+L++++  a++tG+Rr + ++ra+ p+v++de+f+  ++v+Pl+ Wt +dv++yi  +++ +npL +
  gi|121638271|ref|YP_978495.1| 139 ECCRLRKVVPLGKTLRGYS--AWVTGLRRVDAPTRANAPLVSFDETFK-LVKVNPLAAWTDQDVQEYIADNDVLVNPLVR 215
                                    *******************..*************************99.******************************* PP

                                    TT-SS--BCTTB- CS
                    PAPS_reduct 161 qgfrsiGcvpctg 173
                                    +g+ siGc pct+
  gi|121638271|ref|YP_978495.1| 216 EGYPSIGCAPCTA 228
                                    ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1701.95
//
Query:       gi|121638272|ref|YP_978496.1|  [L=299]
Description: hypothetical protein BCG_2407 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-31  106.3   0.0    1.2e-16   61.0   0.0    2.2  2  CbiX           CbiX
  ------ inclusion threshold ------
      0.024   15.1   0.1      0.076   13.5   0.0    1.8  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   1.3e-20   1.2e-16       1     106 [.      71     168 ..      71     169 .. 0.97
   2 !   43.4   0.0     4e-15   3.6e-11       2     104 ..     191     284 ..     190     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.3e-20
                                    -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--S CS
                           CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeae 80 
                                    HGS+dp+s ++++++a +l +++p   v+++f+el++p+l ++l+++        vv Pl+l++++h++ DIp +++ ++
  gi|121638272|ref|YP_978496.1|  71 HGSKDPRSAANARAIAGRLARMRPGLDVRVAFCELNSPNLVDVLNRC----RGAAVVTPLLLADAYHARVDIPAQIASCR 146
                                    **********************************************9....56789************************ PP

                                    SSS-TTEEEEE---CCCSCCHHHHHH CS
                           CbiX  81 eahpkdveieytepLGthplvaevlk 106
                                      h     ++ +++LG++ +++ +l+
  gi|121638272|ref|YP_978496.1| 147 VGHR----VRQASVLGEDIRLVSALH 168
                                    ****....*************99987 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 4e-15
                                    STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SS CS
                           CbiX   2 GSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaee 81 
                                    GS++p +n++  ++a++l e  +   v ++f++  e sl +a ++l++ g++r+v+ P +l++G++ ++     ++ +++
  gi|121638272|ref|YP_978496.1| 191 GSSHPAANARTSTVASRLAEGTQWAAVTTAFITRPEASLADATDRLRRHGARRMVIAPWLLAPGILSDR-----VRGYAR 265
                                    9********************************************************************.....999999 PP

                                    SS-TTEEEEE---CCCSCCHHHH CS
                           CbiX  82 ahpkdveieytepLGthplvaev 104
                                    + +    i +++pLG+hp va+ 
  gi|121638272|ref|YP_978496.1| 266 EAG----IAMAQPLGAHPMVAAT 284
                                    999....************9976 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.99   8.9e+03      72     100 ..      56      84 ..      53      98 .. 0.69
   2 ?   13.5   0.0   8.5e-06     0.076      44     108 ..     203     274 ..     180     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.99
                                    HHHHHHH--SEEEE-TT---HHHHHHHHH CS
                  CoA_binding_2  72 vkealalgakavwlqpgsedeeaaelaee 100
                                    ++e +++ ++ v    gs d+  a+ a++
  gi|121638272|ref|YP_978496.1|  56 AEESGTIAPQLVLTAHGSKDPRSAANARA 84 
                                    55666667777788888888887777776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.5e-06
                                    ES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT.....---HHHHHHHHHTT-EEE.E CS
                  CoA_binding_2  44 kvyaslae.d.pepvdlvdvftppeatpeivkealalgakavwlqpg.....sedeeaaelaeeagirvvgd 108
                                    +v  +lae     +v ++++ +p + +++  + + + ga+++++ p      + ++ +  +a+eagi + ++
  gi|121638272|ref|YP_978496.1| 203 TVASRLAEgTqWAAVTTAFITRPEASLADATDRLRRHGARRMVIAPWllapgILSDRVRGYAREAGIAMAQP 274
                                    4666777654577899**********************99999988888888***************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2371.22
//
Query:       gi|121638273|ref|YP_978497.1|  [L=643]
Description: gamma-glutamyltranspeptidase precursor ggtB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.3e-154  513.5   0.0   7.3e-154  513.3   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.3   0.0  4.1e-158  7.3e-154       2     512 .]      95     636 ..      94     636 .. 0.93

  Alignments for each domain:
  == domain 1  score: 513.3 bits;  conditional E-value: 4.1e-158
                                    HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTT......TSCBCCHHHH CS
                G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmf......dkegdsklsk 75 
                                    +vLr+GG+A+DA+vAa+++lg+vepqssGiGGGg+l+++da+t++v+a+d+re+APaaat++++      d+++ + +++
  gi|121638273|ref|YP_978497.1|  95 RVLRDGGTAADAVVAAQAVLGLVEPQSSGIGGGGYLVYFDARTGSVQAYDGREVAPAAATENYLrwvsdvDRSAPRPNAR 174
                                    79******************************************************************9999999999** PP

                                    SSGGG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEE.TTSE--TT CS
                G_glu_transpept  76 tgalavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlp.egevlkag 154
                                    ++++++gVPG++++le++h+++G+ pw+dl+ pa++la  Gf +s ++ +a+++a+++l+ dpe++k+Fl+ +g++  ag
  gi|121638273|ref|YP_978497.1| 175 ASGRSIGVPGILRMLEMVHNEHGRTPWRDLFGPAVTLADGGFDISARMGAAISDAAPQLRDDPEARKYFLNpDGSPKPAG 254
                                    ***********************************************************************56666899* PP

                                    SEE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHH.....TT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTC CS
                G_glu_transpept 155 ellkqpalAktLerlaeeGaeaFYkGelAeklvaelqk.....agGiltaeDLanykvevreplsadyrggytvyeppps 229
                                    ++l++pa++ktL+ +a+ Ga+aFY+G++A+++va + +     ++G+lt eDLa y ++ r+pl+++y +g++++  +ps
  gi|121638273|ref|YP_978497.1| 255 TRLTNPAYSKTLSAIASAGANAFYSGDIAHDIVAAASDtsngrTPGLLTIEDLAGYLAKRRQPLCTTY-RGREIC-GMPS 332
                                    ***********************************8885554459***********************.556665.5689 PP

                                    SHHHHHHHHHHHHCTTTGGGCTTTC.........HHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHH CS
                G_glu_transpept 230 sggivllqiLnilegfdlkslssns.........aetlhllvEamklayadRsrylgDpdfvknptelveellskeyake 300
                                    sgg++++++L ile+f+++++++ +         + ++hl++Ea++layadR++y++D dfv+ p  ++  l+++ y++ 
  gi|121638273|ref|YP_978497.1| 333 SGGVAVAATLGILEHFPMSDYAPSKvdlnggrptVMGVHLIAEAERLAYADRDQYIADVDFVQLPGGSLTTLVDPGYLAA 412
                                    9****************9999998899***************************************************** PP

                                    HHTT.BTTB..SG...GGCSCGGCSCG...TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBST CS
                G_glu_transpept 301 raklIkdkaatps...seyykaaeaaee..sggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstg 375
                                    ra+lI++++++ s    +++++++ a++  ++gT+hlsvvD++gna  lt+t++++FGs ++v+  G++Lnn+++dfs  
  gi|121638273|ref|YP_978497.1| 413 RAALISPQHSMGSarpGDFGAPTAVAPPvpEHGTSHLSVVDSYGNAATLTTTVESSFGSYHLVD--GFILNNQLSDFS-- 488
                                    ************999967778887777778**********************************..************.. PP

                                    S..TTSCSTTSTTB--TT----B----EEEEE.....TTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--E CS
                G_glu_transpept 376 venafgldpspanaiePgkRplssmaPtivlk.....dgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdapri 450
                                    +e +++  +  an++ePgkRp+ssmaPt+v++      g  ++vlG++GGs+ii+ v+++lv +ld+gl++q+av+   +
  gi|121638273|ref|YP_978497.1| 489 AEPHATDGSPVANRVEPGKRPRSSMAPTLVFDhssagRGALYAVLGSPGGSMIIQFVVKTLVAMLDWGLNPQQAVSLVDF 568
                                    89999999999*********************98877788999***********************************99 PP

                                    EESSSST.........EEEESTTS.HHHHHHHHHTTSEEEESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
                G_glu_transpept 451 hhqllpd.........kvevEegfseevveeLearGhkvkevedsssvvaavavakekgvleaasDprkdg 512
                                         p+             ++g ++ +v++L+a+Gh+v+  e+ss+++a++++   ++ + +++Dpr++g
  gi|121638273|ref|YP_978497.1| 569 GAANSPHtnlggenpeINTSDDGDHDPLVQGLRALGHRVNLAEQSSGLSAITRS---EAGWAGGADPRREG 636
                                    9944554433334332444455999***************************99...7***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 5044.73
//
Query:       gi|121638274|ref|YP_978498.1|  [L=146]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-06   26.1   1.5    3.7e-06   25.9   1.5    1.0  1  OPT       OPT oligopeptide transporter protein


Domain annotation for each model (and alignments):
>> OPT  OPT oligopeptide transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.5     2e-10   3.7e-06       1      35 [.      10      44 ..      10      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2e-10
                            OPT  1 elTlRavvlGillgvlgsavnmyfglrtglvsiss 35
                                   e+T+R vvlG l++ +++a+n+y+glr+gl++++s
  gi|121638274|ref|YP_978498.1| 10 EITIRGVVLGALITLVFTAANVYLGLRVGLTFATS 44
                                   69******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1005.47
//
Query:       gi|121638275|ref|YP_978499.1|  [L=516]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-72  243.4  32.0    7.3e-72  242.9  32.0    1.2  1  OPT       OPT oligopeptide transporter protein
    0.00057   19.8   0.1    0.00057   19.8   0.1    4.7  5  DUF418    Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> OPT  OPT oligopeptide transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.9  32.0   8.1e-76   7.3e-72     163     615 ..       8     453 ..       2     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 8.1e-76
                            OPT 163 flivflgsfvwglfplylfpalssfswltwiapknvvlanlfglgllpltfdwnviaayiGsglivplwvavnmliGavl 242
                                    ++++ lg+++ +   +  +++l+s+++++++++        f +g  ++++ +++++a+iG+g +v++ v+v m++G+++
  gi|121638275|ref|YP_978499.1|   8 IGVIALGAAAAA---G--YALLASLRVINNSLSA------TFRVGSGATMIGASLSLALIGVGHLVGVTVGVAMIVGLAI 76 
                                    555555555544...2..667999****999987......67999999******************************** PP

                            OPT 243 swgiliPllyysngwypaylpydvteild.edgvldyekyigyglmllaalvallylvqfaaitllivhtilkhgkdika 321
                                    ++g+++P+       ++++lp d +  +    +++ ++++ig+g++++aa++++          l+i  +il+++ d + 
  gi|121638275|ref|YP_978499.1|  77 AFGVMLPI------RTAGQLPPDGDYAVAvARIFSTDVRFIGAGAIAVAAAWTF----------LKILGPILRGIADAAV 140
                                    ********......56666666666667779***********************..........**************** PP

                            OPT 322 alksarsprteeddrhrrlmrkykdvpmwwylallvlslvigiivvealftqlpvw..........glllalllafllai 391
                                    ++++          r +++ ++++d+p   ++a++vl+++i i ++ a ft+ + +          g+ll+l++++++a+
  gi|121638275|ref|YP_978499.1| 141 SARTR--------RRGQAVGQTERDIPI-HIVAMVVLLSLIPIGWLLADFTDGTPLddrrpgaiaaGVLLVLVIGLMVAA 211
                                    ****9........99************9.566666888************9999999*********************** PP

                            OPT 392 vsaiiaGltgl..npvsgigkltqlifgallpg...........r.pvanlvfgavvyaaaaqagdfmqDLKtGhllkas 457
                                    v++++aGl+g+  +p+sg+g+l+ +++g+l++            + ++++++++a+v+++a  ++d++qDLKtG+l++a+
  gi|121638275|ref|YP_978499.1| 212 VCGYMAGLIGSsnSPISGVGILVVVLAGLLIKTaygpatgsqipAlVAYTVFTAALVFGVATISNDNLQDLKTGQLVGAT 291
                                    ********************************98877776655525888999999************************* PP

                            OPT 458 PraqfvaqliGtlvgavvniavlkllvkaygdict.adasnaftaPqakvfaavavllvggkkglpwafllgavapfill 536
                                    P++q+va +iG+lvg+vv++++l+l+   +g+ ++   ++na++aPqa+++ a+a+ +v+g+ +l+w ++ +++++++++
  gi|121638275|ref|YP_978499.1| 292 PWKQQVALIIGVLVGSVVMAPILQLMQAGFGFQGApGATANALAAPQAALMSALAK-GVFGG-SLNWSLVGVGALTGVIA 369
                                    **********************************989999****************.*****.***************** PP

                            OPT 537 lllkkfpkkstarklplplafavgfylppslsialligglianlwlk.....rrdaewakkynyvlaaGLiaGealmgvi 611
                                    ++l++  +k+t +   +pla+++g+ylp++l++ + ig+++  +++       +d+e+ k+++++la GLi+Ge+l+gv+
  gi|121638275|ref|YP_978499.1| 370 VALDETLAKTTTNLRLPPLAVGMGMYLPAALTLMIPIGAFLGRIYDSwarwsGDDDERKKRLGVMLATGLIVGESLYGVL 449
                                    *****88788888778***************8866666655555544444999*************************** PP

                            OPT 612 iafl 615
                                     a++
  gi|121638275|ref|YP_978499.1| 450 FAVI 453
                                    9987 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   2.8       0.4   3.6e+03     101     111 ..      49      59 ..       3      87 .. 0.46
   2 ?   -1.2   1.1      0.19   1.7e+03     120     133 ..      68      81 ..      47     132 .. 0.54
   3 ?    0.1   0.6     0.076   6.9e+02      24      64 ..     206     243 ..     187     252 .. 0.53
   4 ?    0.1   0.8     0.078     7e+02      17      36 ..     295     314 ..     283     365 .. 0.60
   5 !   19.8   0.1   6.4e-08   0.00057       6      91 ..     420     506 ..     417     507 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.4
                         DUF418 101 qslictllfyg 111
                                     sl ++l+  g
  gi|121638275|ref|YP_978499.1|  49 ASLSLALIGVG 59 
                                    22222222222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                         DUF418 120 lgraallllallif 133
                                    + ++ +l++a++++
  gi|121638275|ref|YP_978499.1|  68 VAMIVGLAIAFGVM 81 
                                    22222222222222 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.076
                         DUF418  24 gllvglplnllla.vlaeaaeesallelllsvlrylagllla 64 
                                    gl+v++++      ++  +++++++ + +  ++  lagll+ 
  gi|121638275|ref|YP_978499.1| 206 GLMVAAVC----GyMAGLIGSSNSPISGVGILVVVLAGLLIK 243
                                    22222222....223335555555556665555555555555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.078
                         DUF418  17 lrrllligllvglplnllla 36 
                                     ++ l+ig+lvg ++ +++ 
  gi|121638275|ref|YP_978499.1| 295 QQVALIIGVLVGSVVMAPIL 314
                                    34455555555555555555 PP

  == domain 5  score: 19.8 bits;  conditional E-value: 6.4e-08
                         DUF418   6 lledpeehkrllrrllligllvglplnllla.vlaeaaeesallelllsvlrylaglllalgyvalillllakekrrrll 84 
                                    +  d++e+k++l ++l+ gl+vg  l+ +l+ v ++++ ++ +l+++   +r ++++l a+++++l+++l+++++     
  gi|121638275|ref|YP_978499.1| 420 WSGDDDERKKRLGVMLATGLIVGESLYGVLFaVIVATTGKEEPLAMVGDGFRFASQPLGAIVFAGLLAWLYQRTRVTASY 499
                                    556788999**************9999998889999999**********************************9998777 PP

                         DUF418  85 ralaavG 91 
                                    r+ a++G
  gi|121638275|ref|YP_978499.1| 500 RLAAPAG 506
                                    7777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3724.72
//
Query:       gi|121638276|ref|YP_978500.1|  [L=360]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-35  119.8  17.4    6.5e-35  119.3  17.4    1.2  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3  17.4   3.6e-39   6.5e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 3.6e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msf++++Pealaa+a+ l+gigsa++aana aaaptt++laa+ DeVS+ai+alf+ahaq+yqalsa++aafh+qfv++l+a
  gi|121638276|ref|YP_978500.1|  1 MSFLIASPEALAATATYLTGIGSAINAANAVAAAPTTEILAAGTDEVSTAISALFGAHAQAYQALSAHVAAFHDQFVHTLTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +agsY+aaEaa
  gi|121638276|ref|YP_978500.1| 83 GAGSYMAAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2658.36
//
Query:       gi|121638277|ref|YP_978501.1|  [L=351]
Description: sulfate-transport ATP-binding protein ABC transporter cysA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-36  124.9   0.0    4.4e-36  124.4   0.0    1.2  1  ABC_tran     ABC transporter
      4e-11   42.6   0.8    1.1e-10   41.3   0.8    1.7  1  TOBE_3       TOBE-like domain
    1.6e-08   34.7   0.6    0.00044   20.2   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.8e-07   31.3   1.9    1.8e-07   31.3   1.9    2.0  2  TOBE         TOBE domain
    5.3e-06   26.5   3.7    8.6e-06   25.8   1.8    2.3  2  TOBE_2       TOBE domain
    8.1e-06   25.4   0.0      0.021   14.3   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    5.6e-05   23.4   0.3    0.00035   20.8   0.3    2.0  1  AAA_22       AAA domain
     0.0002   21.8   0.6    0.00047   20.6   0.6    1.7  1  AAA_16       AAA ATPase domain
    0.00022   20.9   0.2    0.00042   20.0   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00023   21.1   0.0    0.00045   20.2   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
    0.00046   19.6   0.0      0.015   14.7   0.0    2.1  2  TniB         Bacterial TniB protein
     0.0035   17.0   1.1      0.035   13.7   0.1    2.4  2  AAA_25       AAA domain
     0.0053   17.3   0.0     0.0085   16.6   0.0    1.2  1  AAA_23       AAA domain
     0.0069   15.2   0.6        2.5    6.8   0.0    2.7  2  ABC_ATPase   Predicted ATPase of the ABC class
  ------ inclusion threshold ------
       0.01   16.0   0.2       0.12   12.6   0.2    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.013   15.5   0.1       0.08   12.9   0.0    2.0  2  NACHT        NACHT domain
      0.013   15.9   0.0      0.093   13.2   0.0    2.1  1  AAA          ATPase family associated with various cellular a
      0.026   14.7   0.2      0.072   13.2   0.2    1.8  1  AAA_33       AAA domain
      0.033   13.9   0.0        0.1   12.3   0.0    1.8  1  AAA_30       AAA domain
      0.074   13.1   0.1       0.15   12.2   0.1    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
       0.08   12.7   0.7       0.53   10.0   0.1    2.3  2  AAA_24       AAA domain
        0.1   12.2   0.0       0.18   11.3   0.0    1.4  1  AAA_27       AAA domain
       0.17   11.2   0.0         16    4.7   0.0    2.2  2  ATPase       KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.0   5.7e-39   4.4e-36       1     136 [.      20     162 ..      20     163 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 5.7e-39
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++v++ +  g+++a++G++G+GKStLl+++agl +p+ G+i+++g+d+++   +  r+ ig+++q+   f++ltvr+n 
  gi|121638277|ref|YP_978501.1|  20 LDHVDFVVPTGSLTALLGPSGSGKSTLLRTIAGLDQPDTGTITINGRDVTR--VPPQRRGIGFVFQHYAAFKHLTVRDNv 97 
                                    7899***********************************************..9************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e +++++++l+ +gl++++ +      ++LSgGq+qr+alaral+ +p++lllDEp+
  gi|121638277|ref|YP_978501.1|  98 afglkirkrpkaEIKAKVDNLLQVVGLSGFQSRYP----NQLSGGQRQRMALARALAVDPEVLLLDEPF 162
                                    ********999999999************999998....*****************************6 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.8   1.4e-13   1.1e-10       3      59 ..     270     325 ..     268     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.4e-13
                         TOBE_3   3 aegglpatvrrirpvGpivRlELerlgdtgeliEvelprdrfeelglaeGetvylrP 59 
                                      g l a+v r+ ++G +vR+EL  + +tg  ++++++r  +e l+l+eG+tvy+r+
  gi|121638277|ref|YP_978501.1| 270 STGVLRAVVDRVVVLGFEVRVELTSA-ATGGAFTAQITRGDAEALALREGDTVYVRA 325
                                    568899********************.****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.6e-07   0.00044       1      24 [.      32      55 ..      32      85 .. 0.79
   2 !   13.1   0.0   7.8e-05     0.061     231     298 ..     129     194 ..      92     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.6e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                   l++l Gp gsGKS+LL+++ +l +
  gi|121638277|ref|YP_978501.1| 32 LTALLGPSGSGKSTLLRTIAGLDQ 55
                                   69*****************99932 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.8e-05
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                     + +++lS G+++  al+ al+ ++    +ll+DEp   L+ k+ ++l  +l++l++   +  +l+TH+
  gi|121638277|ref|YP_978501.1| 129 SRYPNQLSGGQRQRMALARALAVDP---EVLLLDEPFGALDAKVREELRAWLRRLHDeVHVTTVLVTHD 194
                                    5678999*****9999999999999...9********************99988888566666999998 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.3   6.5e+03      34      47 ..     188     201 ..     185     202 .. 0.82
   2 !   31.3   1.9   2.3e-10   1.8e-07       5      56 ..     272     324 ..     270     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.3
                           TOBE  34 tArvtrrsaeeLgL 47 
                                    t+ vt ++ae+L++
  gi|121638277|ref|YP_978501.1| 188 TVLVTHDQAEALDV 201
                                    57899999999876 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2.3e-10
                           TOBE   5 NqlpgtVvvveplg..seveVrvdlgggatLtArvtrrsaeeLgLapGeeVfal 56 
                                    ++l++ V++v+ lg  ++ve++ ++ gga  tA +tr  ae+L+L+ G++V+++
  gi|121638277|ref|YP_978501.1| 272 GVLRAVVDRVVVLGfeVRVELTSAATGGA-FTAQITRGDAEALALREGDTVYVR 324
                                    68************888888888888888.**********************86 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.4   2.7e+03      30      53 ..     126     149 ..     119     155 .. 0.77
   2 !   25.8   1.8   1.1e-08   8.6e-06       3      68 ..     246     325 ..     244     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                         TOBE_2  30 Gsstryvvelaggqlvvvrqpnad 53 
                                    G ++ry  +l ggq+++++ + a 
  gi|121638277|ref|YP_978501.1| 126 GFQSRYPNQLSGGQRQRMALARAL 149
                                    778889999999999998877665 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.1e-08
                         TOBE_2   3 iRPEklrla...........aagga..n.glsGtVedveylGsstryvvelag.gqlvvvrqpnadr.dsalapGdtVel 66 
                                    +RP ++r+            +   a  +  l+++V++v+ lG ++r+ ++ a+ g  ++++   +d+ + al++GdtV +
  gi|121638277|ref|YP_978501.1| 246 VRPHDIRVGrtpnmavaaadGT--AgsTgVLRAVVDRVVVLGFEVRVELTSAAtGGAFTAQITRGDAeALALREGDTVYV 323
                                    9**********99999864322..2344588*****************7777725665555555665559*********9 PP

                         TOBE_2  67 sw 68 
                                    + 
  gi|121638277|ref|YP_978501.1| 324 RA 325
                                    85 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0     0.001      0.81      25      44 ..      31      50 ..      17      53 .. 0.87
   2 !   14.3   0.0   2.7e-05     0.021     133     212 ..     131     206 ..      85     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                   s+ta++Gp GSGKs ll  i
  gi|121638277|ref|YP_978501.1| 31 SLTALLGPSGSGKSTLLRTI 50
                                   689************99877 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                    ++++LSgG+++ +ala  +A+   +p+   llDe   aLD+k ++++   l++ ++++ +  + +++++ e  d   ++ 
  gi|121638277|ref|YP_978501.1| 131 YPNQLSGGQRQRMALARALAV---DPEV-LLLDEPFGALDAKVREELRAWLRRLHDEVHVTTVLVTHDQAEALDVADRIA 206
                                    4679************99886...5665.689********************9999987776666666666665555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   4.5e-07   0.00035       5     132 ..      30     195 ..      28     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.5e-07
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..........................erpevvfvtlpsstsskdllr 58 
                                     +++++ G+sG+GK+tllr+++  ++ +    +                          +                +++ 
  gi|121638277|ref|YP_978501.1|  30 GSLTALLGPSGSGKSTLLRTIAGLDQPDTGTITingrdvtrvppqrrgigfvfqhyaafK--------------HLTVRD 95 
                                    57899*****************99865444444888888888855533333333333330..............333344 PP

                         AAA_22  59 ellralglelka.......................erlsseellealeqalrarav.ielliiDEaqh.lr...seeale 110
                                    +++  l+ ++                         ++++++   ++    +ra av +e+l++DE    l+   +ee+  
  gi|121638277|ref|YP_978501.1|  96 NVAFGLKIRKRPkaeikakvdnllqvvglsgfqsrYPNQLSGGQRQRMALARALAVdPEVLLLDEPFGaLDakvREELRA 175
                                    4444444333335556666666666666667777766666666666666777777799*******555587755699999 PP

                         AAA_22 111 eLrsllnlsrkgvqliLvGtpe 132
                                    +Lr+l++  + +v+ +Lv + +
  gi|121638277|ref|YP_978501.1| 176 WLRRLHD--EVHVTTVLVTHDQ 195
                                    9999999..9999999997665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.6     6e-07   0.00047      24     132 ..      30     182 ..      20     210 .. 0.50

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6e-07
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekle 102
                                    ++l+ l G+sG+GKs+l+r+++  l + +  +++ + ++ ++  p    +  ++     ++ l  +++ a     r++ +
  gi|121638277|ref|YP_978501.1|  30 GSLTALLGPSGSGKSTLLRTIA-GLDQPDTGTITINGRDVTRVPPQRRgIGFVFQHYAAFKHLTVRDNVAFGLKIRKRPK 108
                                    47899*****************.677776666666666664453332223333322333443333322222222222222 PP

                         AAA_16 103 eala............................avpelagaea................srllellkrllallsr 132
                                    ++++                            +  +la+a+a                  ++e+l++ l++l+ 
  gi|121638277|ref|YP_978501.1| 109 AEIKakvdnllqvvglsgfqsrypnqlsggqrQRMALARALAvdpevllldepfgaldAKVREELRAWLRRLHD 182
                                    22223333444355555555554444444444333333333344444444444444444444444444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   5.4e-07   0.00042      19      43 ..      27      51 ..      17      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.4e-07
                         AAA_29 19 idlkg.atlltGpsGsGKSTllDAiq 43
                                   +   g  t l GpsGsGKSTll  i+
  gi|121638277|ref|YP_978501.1| 27 VP-TGsLTALLGPSGSGKSTLLRTIA 51
                                   44.4559**************96665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.7e-07   0.00045      95     132 ..      25      63 ..       3      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.7e-07
                                    HHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                    RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                     ++   ++++l+G+SG GKStL+ ++++ ++  tg +  
  gi|121638277|ref|YP_978501.1|  25 FVVPTgSLTALLGPSGSGKSTLLRTIAGLDQPDTGTITI 63 
                                    55544489********************99999998865 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.097        75      39      63 ..      34      58 ..      29      72 .. 0.82
   2 !   14.7   0.0   1.9e-05     0.015      91     165 ..     124     196 ..      98     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.097
                           TniB 39 llvGdsnnGKtmivekFarlhppek 63
                                    l+G+s  GK+++++  a l++p++
  gi|121638277|ref|YP_978501.1| 34 ALLGPSGSGKSTLLRTIAGLDQPDT 58
                                   689***********99887776654 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                           TniB  91 LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteea 165
                                    L  ++ ++ ++ +  + ++++l+   +++++vL++DE   +l   a+ ++e+ + l++L++e++++ vlv  ++a
  gi|121638277|ref|YP_978501.1| 124 LSGFQSRYPNQLSGGQRQRMALARALAVDPEVLLLDEPFGAL--DAKVREELRAWLRRLHDEVHVTTVLVTHDQA 196
                                    455666666666667777777888888999*******99999..6777899******************976665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   4.5e-05     0.035      29      50 ..      26      47 ..      21      52 .. 0.88
   2 ?    1.3   0.1      0.29   2.3e+02     166     188 ..     171     193 ..     156     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                         AAA_25 29 llpagelallaGapgtGKttla 50
                                   ++p g+l++l G++g+GK+tl+
  gi|121638277|ref|YP_978501.1| 26 VVPTGSLTALLGPSGSGKSTLL 47
                                   789*****************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                         AAA_25 166 galvealeriarrtgaavllvhH 188
                                    ++l ++l+r+ ++ +++++lv H
  gi|121638277|ref|YP_978501.1| 171 EELRAWLRRLHDEVHVTTVLVTH 193
                                    56667899999999999999999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0085      15      39 ..      23      50 ..      13      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                         AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                   +dF      lt++ Gp G+GK+T+l+ i
  gi|121638277|ref|YP_978501.1| 23 VDFvvpTGSLTALLGPSGSGKSTLLRTI 50
                                   677777788****************987 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0083       6.4     242     265 ..      27      51 ..      25      55 .. 0.91
   2 !    6.8   0.0    0.0032       2.5     379     419 ..     176     216 ..     129     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0083
                                    E-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                    +p+G +t++ G+   GKsTLL+ ++
  gi|121638277|ref|YP_978501.1|  27 VPTGsLTALLGPSGSGKSTLLRTIA 51 
                                    78999*****************985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0032
                                    CHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE- CS
                     ABC_ATPase 379 rvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdv 419
                                     +r+l++++ v+t+lv+    + ldvAd++ ++++ ++++v
  gi|121638277|ref|YP_978501.1| 176 WLRRLHDEVHVTTVLVTHDQAEALDVADRIAVLHKGRIEQV 216
                                    46889999***********************9998777766 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00016      0.12      32      88 ..     134     177 ..      90     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                        SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    +lSGG++q        +ala ++        ++++++LDE F+ lD++ +++l + l
  gi|121638277|ref|YP_978501.1| 134 QLSGGQRQR-------MALARALAV------DPEVLLLDEPFGALDAKVREELRAWL 177
                                    555555532.......233333333......5899*************999886655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001      0.08       2      21 ..      32      51 ..      31      57 .. 0.90
   2 ?    0.1   0.0      0.88   6.9e+02      90     120 ..     158     188 ..     145     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   l +l G++GsGK+tLl+ +a
  gi|121638277|ref|YP_978501.1| 32 LTALLGPSGSGKSTLLRTIA 51
                                   57899*************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.88
                                    STT-SS-TCH.........HHHHHCTTTTT- CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpe 120
                                    lDe    l++k ++++r +L++l  + ++++
  gi|121638277|ref|YP_978501.1| 158 LDEPFGALDAKVREELRAWLRRLHDEVHVTT 188
                                    5677777777666666677766666644443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.093       3      98 ..      35     182 ..      33     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                    EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................... CS
                            AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................... 37 
                                    l Gp G GK++l + +a   +  +  ++i+g +++                                             
  gi|121638277|ref|YP_978501.1|  35 LLGPSGSGKSTLLRTIAGLDQpdTGTITINGRDVTRVppqrrgigfvfqhyaafkhltvrdnvafglkirkrpkaeikak 114
                                    89***************984323556777777777446777777777777777777777777777777777777777777 PP

                                    ................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                            AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                                    y  + +   r+ ++ a++ a +p +l++DE      ++          v ++L + l ++ +
  gi|121638277|ref|YP_978501.1| 115 vdnllqvvglsgfqsrYPNQLSGGQRQRMALARALAvDPEVLLLDEPFGALDAK----------VREELRAWLRRLHD 182
                                    777888888888777888888888888888898888889999999944444444..........44444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   9.3e-05     0.072       3      33 ..      34      93 ..      32     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.3e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklg....avllssdt.........................l 33
                                    l G++GsGKstl++ ++   +    +++++  +                         +
  gi|121638277|ref|YP_978501.1| 34 ALLGPSGSGKSTLLRTIAGLDQpdtgTITINGRDvtrvppqrrgigfvfqhyaafkhltV 93
                                   678************986332233444444443355555555665555555555555551 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1      19      45 ..      31      57 ..      21      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                    +++l Gp G+GK+t+l++++ + + +
  gi|121638277|ref|YP_978501.1| 31 SLTALLGPSGSGKSTLLRTIAGLDQPD 57
                                   48999***************9887766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019      0.15       3      34 ..      34      70 ..      32     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   EEEESTTSSHHHHHHHHHT.....STEEESSSTTSSS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg.....ekaivsdkpgtTr 34
                                   a++G + +GKStL++++ g     +  i+ +   +Tr
  gi|121638277|ref|YP_978501.1| 34 ALLGPSGSGKSTLLRTIAGldqpdTGTITINGRDVTR 70
                                   899**************98432211234444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00068      0.53       6      23 ..      34      55 ..      30     122 .. 0.77
   2 ?    0.2   0.1      0.66   5.2e+02     106     134 ..     168     197 ..     163     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                         AAA_24  6 liyGpsgiGKTtlakel....g 23
                                   ++ Gpsg+GK+tl++++    +
  gi|121638277|ref|YP_978501.1| 34 ALLGPSGSGKSTLLRTIagldQ 55
                                   789************9954443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.66
                         AAA_24 106 elaeefrrllkklqelrk.nvifiahektr 134
                                    +++ee+r +l++l++  + + +++ h + +
  gi|121638277|ref|YP_978501.1| 168 KVREELRAWLRRLHDEVHvTTVLVTHDQAE 197
                                    78999*******877666688888887765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.18       9      48 ..      12      52 ..      10      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                         AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisd 48
                                   +ryG f    ++df   + +l+ ++Gp  +GKst+lr i  
  gi|121638277|ref|YP_978501.1| 12 KRYGDFVAlDHVDFVVPTGSLTALLGPSGSGKSTLLRTIAG 52
                                   79***976259**************************9975 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.021        16      16      37 ..      27      48 ..      20     123 .. 0.66
   2 ?    4.2   0.0      0.03        23     137     166 ..     166     196 ..     156     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                         ATPase 16 ipegrvvlitGepGtGKtifal 37
                                   +p g+ + + G +G+GK+++  
  gi|121638277|ref|YP_978501.1| 27 VPTGSLTALLGPSGSGKSTLLR 48
                                   58999*************9865 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.03
                         ATPase 137 eavaReilrqlvrvl.kklgvTailvsekss 166
                                    +a++Re+lr  +r+l  +  vT++lv+  + 
  gi|121638277|ref|YP_978501.1| 166 DAKVREELRAWLRRLhDEVHVTTVLVTHDQA 196
                                    5789***********99*********98554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2392.11
//
Query:       gi|121638278|ref|YP_978502.1|  [L=272]
Description: sulfate-transport integral membrane protein ABC transporter cysW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-15   58.0   9.9      1e-15   58.0   9.9    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   5.6      0.04   7.2e+02     114     171 ..      16      71 ..       4      73 .. 0.66
   2 !   58.0   9.9   5.6e-20     1e-15       5     183 ..      73     265 ..      69     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.04
                   BPD_transp_1 114 lilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                                    l+++f++l+   +l+++ +  pG+g++   ++    +s+ +  ++l +v++v++ln++
  gi|121638278|ref|YP_978502.1|  16 LGYVFVLLIVPVALILWRTFEPGFGQFYAWISTPAAISALN--LSLLVVAIVVPLNVI 71 
                                    45555666666666666666666776666666666666666..778888888888876 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 5.6e-20
                   BPD_transp_1   5 Gilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.............vilsilghlilpviillllsaapyv 68 
                                    G+ +a    + +++++ +l+ +i++++++ ++++++ l+l+               ++  + ++  ++++++++ + p+v
  gi|121638278|ref|YP_978502.1|  73 GVTTAlvlARNRFRGKGVLQAIIDLPFAVSPVIVGVSLILLWgsagalgfveqdlGFK--IIFGLPGIVLASMFVTCPFV 150
                                    5555555549999****************999988888866689*****887754333..44455569999********* PP

                   BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                    ++ ++ +l +l +d+++aa +lG + wq+f++++lP++   +  g++l++++ lg++ ++ ++ s+ + ++++l+ + + 
  gi|121638278|ref|YP_978502.1| 151 VREVEPVLHELGTDQEQAAATLGSGWWQTFWRITLPSIRWGLTYGIVLTVARTLGEYGAVIIVSSNLPGTSQTLTLLVSD 230
                                    ****************************************************************9877444444444444 PP

                   BPD_transp_1 149 dyseisnggvlalviavlllnlvadilqrlldprv 183
                                     y+ ++  g++al  +++++++v+ i+q +ld r 
  gi|121638278|ref|YP_978502.1| 231 RYHRGAEYGAYALSTLLMAVSVVVLIVQMVLDARR 265
                                    44444434788888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1900.67
//
Query:       gi|121638279|ref|YP_978503.1|  [L=283]
Description: sulfate-transport integral membrane protein ABC transporter cysT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-22   78.1  11.7    6.6e-22   78.1  11.7    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.6      0.13   2.3e+03      37      61 ..      31      51 ..      22      86 .. 0.53
   2 !   78.1  11.7   3.7e-26   6.6e-22       2     182 ..      87     274 ..      86     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.13
                   BPD_transp_1 37 illvlvfvilsilghlilpviilll 61
                                   + +v    +ls++  l l++i+  +
  gi|121638279|ref|YP_978503.1| 31 MAVV----WLSVIVLLPLAAIVWQA 51
                                   4444....33333333333333333 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 3.7e-26
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf....vilsilghlilpviillllsaapyvrlirra 74 
                                    +++G+l+a   ++  + ++++++ +i+++++lP++v  ++++++      +   ++h++++v ++l++ ++p+v++ ++ 
  gi|121638279|ref|YP_978503.1|  87 LVFGLLIAwvlVRDDFAGKRIVDAIIDLPFALPTIVASLVMLALYgnnsPVGLHFQHTATGVGVALAFVTLPFVVRAVQP 166
                                    6899*****99999**********************555555444789966679************************** PP

                   BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG....lgtllleailgydy 150
                                    +l +++++ +eaa  lGa+  +if  vvlP++ p +++g++laf +++g++  + ++g+  +    ++++++++++++d 
  gi|121638279|ref|YP_978503.1| 167 VLLEIDRETEEAAASLGANGAKIFTSVVLPSLTPALLSGAGLAFSRAIGEFGSVVLIGGAVPgkteVSSQWIRTLIENDD 246
                                    **********************************************************7776899999999999999998 PP

                   BPD_transp_1 151 seisnggvlalviavlllnlvadilqrlldpr 182
                                         +g++a+ +++l +++++ ++ r++  r
  gi|121638279|ref|YP_978503.1| 247 R----TGAAAISVVLLSISFIVLLILRVVGAR 274
                                    8....677888888888888888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2122.08
//
Query:       gi|121638280|ref|YP_978504.1|  [L=356]
Description: sulfate-binding lipoprotein subI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-33  116.0   1.8    2.5e-33  115.7   1.8    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    8.4e-11   42.2   0.1    2.8e-10   40.5   0.1    1.6  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    5.1e-06   26.1   0.0    7.8e-06   25.5   0.0    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
     0.0025   17.0   0.0     0.0057   15.8   0.0    1.5  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   1.8   5.6e-37   2.5e-33       2     230 .]      59     303 ..      58     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 5.6e-37
                                    EEEE-SSTHHHHHHHHHHH.HHHH-..--EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGG.....GG- CS
                     SBP_bac_11   2 tvaaagslaaalrelaaaF.eahtg..vkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqa.....esa 73 
                                    t++a++  ++  +++++aF +++ g  v+v  s+g s+++ r +adg+++D++    +  +++l++ag+v++     ++ 
  gi|121638280|ref|YP_978504.1|  59 TLVAYAVPEPGWSAVIPAFnASEQGrgVQVITSYGASADQSRGVADGKPADLVNFSVEPDIARLVKAGKVDKdwdadATK 138
                                    666666677888999****66676666***************************99999****************99888 PP

                                    EEEEEEEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTH...H.HHHHGGG...--......HHHHHHHHHTEE CS
                     SBP_bac_11  74 vplassplviavpkgnpkkikgwadLlkpglklavadPttspsGl...aalalleaa...ga......qellkalekkvv 141
                                        +s + ++v++gnpk+i++w+dLl+pg+++++++P +s+s++       +  aa   g+       +++++l +  v
  gi|121638280|ref|YP_978504.1| 139 GIPFGSVVTFVVRAGNPKNIRDWDDLLRPGIEVITPSPLSSGSAKwnlL---APYAAksdGGrnnqagIDFVNTLVNEHV 215
                                    88999*********************************99999995332...333332332256677799********99 PP

                                    EEESSHHH.HHHHHHTTT-SEEEEEHHHHH..H.STTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHH CS
                     SBP_bac_11 142 klgessrq.lltaveageadagivyeseakaae.ngdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspe 219
                                    kl+++s++ +++ + +g+ d++i+ye+ea+a+e +g++++ v++p++     ++ p+av++++++  aA aF +f ++ +
  gi|121638280|ref|YP_978504.1| 216 KLRPGSGReATDVFVQGSGDVLISYENEAIATErAGKPVQHVTPPQTFK---IENPLAVVATSTHLGAATAFRNFQYTVQ 292
                                    9*9999661555599**************99965899**********99...578999999999999************* PP

                                    HHHHHHHTT-B CS
                     SBP_bac_11 220 aqailrkyGfr 230
                                    aq++++++Gfr
  gi|121638280|ref|YP_978504.1| 293 AQKLWAQAGFR 303
                                    **********8 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   6.2e-14   2.8e-10      42     270 ..      90     311 ..      69     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.2e-14
                                    .EEE-HHHHHHHHHTTSB--GG..GS.TTHHH-HHHHHTT--TS....----EEEEEEE-EEEEEHHHHHHS.---BHHH CS
                      SBP_bac_8  42 vvwanedalatlaeeglladls..dl.dnlddltdalaavgydgk...lygvPyasetpyvliynkdllekaedpktwde 115
                                    + ++++++ ++ ++ g+ adl   ++ ++++ l + + +v+ d++   ++g+P+ s    ++++++   +    + +wd+
  gi|121638280|ref|YP_978504.1|  90 TSYGASADQSRGVADGKPADLVnfSVePDIARLVK-AGKVDKDWDadaTKGIPFGSV--VTFVVRAGNPK---NIRDWDD 163
                                    44444444555555666665554433355555533.2223334444459******76..49999977755...8****** PP

                                    HHHHHHHHHHH-SEGG--.-GGGGGGTHHETTEE---H..HHH.HHHHHHHHHHH.HTT-.EE-S..--SSTTTTTSBSE CS
                      SBP_bac_8 116 llaaakklkgkfglpdpa.sgwlqaallakdgksldddggkdglkealellkklk.dngk.tydtgadavsefanGevaf 192
                                    ll   + +   +++p p  sg++ + lla  ++ ++d     +  + ++++++l+ +++k  +++g +a++ f +G+   
  gi|121638280|ref|YP_978504.1| 164 LLR--PGI--EVITPSPLsSGSAKWNLLA-PYAAKSDG--GRNNQAGIDFVNTLVnEHVKlRPGSGREATDVFVQGSGDV 236
                                    ***..666..3455666524788888888.55555554..3444899******9954455577999************** PP

                                    EEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT CS
                      SBP_bac_8 193 tingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaal 270
                                     i+++ +++a + agk+++ + p+q +f   ++lav + +++   aA +F ++ ++ ++q+ +a+  g+ pv +++a+
  gi|121638280|ref|YP_978504.1| 237 LISYENEAIATERAGKPVQHVTPPQ-TFKIENPLAVVATSTHLG-AATAFRNFQYTVQAQKLWAQ-AGFRPVDPAVAA 311
                                    *********************8876.6666667***********.6*******************.999999999885 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-09   7.8e-06      75     227 ..     159     312 ..     141     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-09
                      SBP_bac_6  75 ksWaDLldPeykgkvalpgnng...sdlfealllalykdfg..edgvkkllrnlkanlhpaq...mvkaagslesgepav 146
                                    ++W+DLl+P    +v  p++       ++ ++  a + d g   +++ ++++ l + + + +   + +a +   +g+   
  gi|121638280|ref|YP_978504.1| 159 RDWDDLLRPGI--EVITPSPLSsgsAKWNLLAPYAAKSDGGrnNQAGIDFVNTLVNEHVKLRpgsGREATDVFVQGS--G 234
                                    89*********..77777777655555666666666666665578999**********9999986666667777777..* PP

                      SBP_bac_6 147 svvpyffadilpekkkgknlkvvwPed.GalvspifmlvkkgkkkelakafidfllspevqailakaggvfPvvtnpavl 225
                                    +v++ + + +++    gk+++ v+P +   + +p +++  +  +   a af +f +  ++q+ +a ag+  Pv+  pav+
  gi|121638280|ref|YP_978504.1| 235 DVLISYENEAIATERAGKPVQHVTPPQtFKIENPLAVVATST-HLGAATAFRNFQYTVQAQKLWAQAGF-RPVD--PAVA 310
                                    ***************************889999999999999.**************************.9985..3333 PP

                      SBP_bac_6 226 ne 227
                                     +
  gi|121638280|ref|YP_978504.1| 311 AD 312
                                    33 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06    0.0057      72     100 ..     147     175 ..     142     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    CCCCHCCHHHS--BGGGC-S-B-EEEEE- CS
                       PBP_like  72 glvvakgnpkkitnwkdladaplrlvnRe 100
                                     +vv++gnpk+i++w dl ++++ ++++ 
  gi|121638280|ref|YP_978504.1| 147 TFVVRAGNPKNIRDWDDLLRPGIEVITPS 175
                                    589**********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2679.50
//
Query:       gi|121638281|ref|YP_978505.1|  [L=109]
Description: hypothetical protein BCG_2416 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.084   12.9   0.0      0.095   12.7   0.0    1.2  1  Flavin_Reduct    Flavin reductase like domain
      0.095   11.6   0.0        0.1   11.4   0.0    1.2  1  Chondroitinas_B  Chondroitinase B


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.095      45      80 ..      45      83 ..      18     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                   TSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS......S CS
                  Flavin_Reduct 45 psstadalkeagefvinllsesqealadafsqksg...p 80
                                   +++ ad  +++ ++++++ +++   lad++++ s+   p
  gi|121638281|ref|YP_978505.1| 45 ANERADIAPRKTRCCVHVAKPNRIRLADQLARSSMgekP 83
                                   5667888999999*******************9885551 PP

>> Chondroitinas_B  Chondroitinase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.2e-05       0.1     152     189 ..      11      46 ..       6      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                                    ...EE-S--EEES-EE.EE---SSS---SEEE-..SST CS
                Chondroitinas_B 152 gneninnyHkiknnfFGsrPrkgGpagetiqlGdsyts 189
                                    g + i ++ + ++ +   rPr gG+++ t+q+G s  +
  gi|121638281|ref|YP_978505.1|  11 GGKAIAEHCRTHELHI--RPRTGGESATTVQVGRSAAN 46 
                                    5677888999999999..***************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 922.00
//
Query:       gi|121638282|ref|YP_978506.1|  [L=67]
Description: hypothetical protein BCG_2417c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 463.93
//
Query:       gi|121638283|ref|YP_978507.1|  [L=642]
Description: hypothetical protein BCG_2418 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-53  182.2   0.0    6.9e-50  170.1   0.0    2.1  2  Glyco_hydro_15   Glycosyl hydrolases family 15
  ------ inclusion threshold ------
       0.14   11.0   0.1       0.32    9.8   0.0    1.5  2  Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.0   7.6e-54   6.9e-50       5     349 ..     255     566 ..     252     584 .. 0.94
   2 !   10.3   0.0   2.3e-05      0.21     414     447 ..     586     619 ..     570     620 .. 0.87

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 7.6e-54
                                    HHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH........HHHHHTTT-HCCHH CS
                 Glyco_hydro_15   5 dlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglg.yrdedrakayeleqslvk 74 
                                     +++r++ tl+ l+++p tG+l A+++ts+p         DYry+W+RDs + +  + +lg +r+ d+ +a   + s ++
  gi|121638283|ref|YP_978507.1| 255 AYLQRSALTLKGLTYSP-TGALLAASTTSLPetprgernwDYRYAWIRDSTFALWGLYTLGlDREADDFFAFIADVSGAN 333
                                    689**************.**********************************9999999999997888788777887777 PP

                                    HHHH.HHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCCHHHH CS
                 Glyco_hydro_15  75 lmrg.lleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiistldeva 153
                                     ++   l+ m+   g+ +++ e ++    h++++ +  ++++G+ ++++ Q D+ + +l  ++   +s  q+ ++l++v 
  gi|121638283|ref|YP_978507.1| 334 NNERhPLQVMYGVGGE-RSLVEAELH---HLSGYDHARPVRIGNGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPV- 408
                                    665538999**99998.999999***...**************************************************. PP

                                    THHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GG CS
                 Glyco_hydro_15 154 fvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrg 233
                                      +  v+   +++++pd g+WE++++ ++++ s+v+ ++Al++++++a++ g+k+ aq ++  +dei  ++      ++g
  gi|121638283|ref|YP_978507.1| 409 -LKRQVEEAIKHWREPDRGIWEVRGEPQHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKADI-----LEHG 482
                                    .**********************************************************************.....8888 PP

                                    GEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT- CS
                 Glyco_hydro_15 234 fwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavge 313
                                     +  ++ +++ +g+            ealdaslll++   f p+dd          pr+ +++l+i d+l+++g+     
  gi|121638283|ref|YP_978507.1| 483 VDS-RGVFTQRYGD------------EALDASLLLVVLTRFLPPDD----------PRVRNTVLAIADELTEDGL----- 534
                                    765.999*******............********************..........*******************..... PP

                                    STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHHH CS
                 Glyco_hydro_15 314 ldplvrRysedvkpdklglsGrpyylctlwtvetll 349
                                        v Ry     +d+l+++++ + +c++w v  l+
  gi|121638283|ref|YP_978507.1| 535 ----VLRYRVHETDDGLSGEEGTFTICSFWLVSALV 566
                                    ....9*************************666554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.3e-05
                                    -TTS---SEE-TTT--EESSTT-HHHHHHHHHHH CS
                 Glyco_hydro_15 414 nslgvLteevdvylgeliraqpllfsealllrig 447
                                      l +++ee+  ++g+ ++++p++f +++l++++
  gi|121638283|ref|YP_978507.1| 586 SPLLLYAEEIEPRSGRHLGNFPQAFTHLALINAV 619
                                    566789*************************985 PP

>> Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.29   2.6e+03      38      50 ..     297     309 ..     294     317 .. 0.79
   2 ?    9.8   0.0   3.6e-05      0.32     223     278 ..     435     490 ..     433     497 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.29
                                    SEEHHHHHHHHGG CS
                Glyco_hydro_125  38 amWlRDsanqlas 50 
                                      W+RDs+  l+ 
  gi|121638283|ref|YP_978507.1| 297 YAWIRDSTFALWG 309
                                    58******98875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 3.6e-05
                                    SEEHHHHHHHHHHHHHHHHHHHHTS--.HHHHHHHHHHHHHHHHHHHSEEEETTTE CS
                Glyco_hydro_125 223 qflipaNmmlaveLeklaeileklaekelakearklakeiregiekhavvehkkfg 278
                                    q+++ + +m+ v+L++ a+++e+  ek+ a++ r++a+ei++ i +h+v +   f 
  gi|121638283|ref|YP_978507.1| 435 QHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKADILEHGVDSRGVFT 490
                                    689999******************************************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4210.47
//
Query:       gi|121638284|ref|YP_978508.1|  [L=251]
Description: lipoprotein lppR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-42  145.1   3.9    2.6e-42  144.8   3.9    1.1  1  PknH_C    PknH-like extracellular domain


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   3.9   1.5e-46   2.6e-42       4     189 .]      42     246 ..      39     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.5e-46
                                    GGGGGGS--HHHHHHHHT-S......--EE-S-B-S-B-S--EESSGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT CS
                         PknH_C   4 aaldslLltpaelaailGtp.....eaasatesdttppdtaasvdppeClgvasageesvYggsgvtavagqtlrdsadd 78 
                                    + ++++ l+ a+l+++l++p     +   +   +++  d+++s+ p++C+gv++ +++ vY++ +v++va+ ++r+++++
  gi|121638284|ref|YP_978508.1|  42 SLIQRVPLDGAALSTLLNQPfqalpPFPPVFGGSDSLGDSDVSARPADCVGVGYLTQRNVYRSVEVKSVARVSWRHDGSS 121
                                    6789*********************77777777777778889999*********************************** PP

                                    -SEE.EEEEEEE-SSHHHHHHHHHHHHHHHHTTTT-EEEEEETTEEEEEEE---B--TT-EEEEEE....ESSTT--.EE CS
                         PknH_C  79 gasl.vsqavvafptadaAqaffaalaaqwrrCagvttttdsggatetwtvgdvsdddgvltatvtv...tsggdga.rc 153
                                     ++   +++vva+p+a+aA+++fa+++aqw++C+g tt t+++ a  +  ++dv+++d+v++atv++   t+++ +  + 
  gi|121638284|ref|YP_978508.1| 122 VKVDdLDEGVVALPSAAAADDLFARFSAQWKECDG-TTLTVPASAFGQRSITDVRVADSVVAATVSLrrgTHSILASvPQ 200
                                    **99*******************************.8*********************************99999999** PP

                                    EEEEEEETTEEEEEEEEE...........SS-SSHHHHHHHHHHHH CS
                         PknH_C 154 qralavranvvvdvevcgf..........edggdaaaeiadaildk 189
                                    +ra++vr+n+vv+v+v+ f          +d++++a++ia+a++d+
  gi|121638284|ref|YP_978508.1| 201 ARAVGVRGNCVVEVAVTFFgithpsdqgsADISTSAVDIAHAMMDR 246
                                    *****************************9**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1767.52
//
Query:       gi|121638285|ref|YP_978509.1|  [L=653]
Description: GTP-binding protein LepA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-51  175.2   0.0    1.6e-51  174.6   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    6.1e-49  164.6   1.2      1e-48  164.0   1.2    1.3  1  LepA_C       GTP-binding protein LepA C-terminus
    1.7e-21   76.1   0.1    5.1e-21   74.5   0.0    1.9  2  EFG_C        Elongation factor G C-terminus
      8e-07   29.4   4.6    9.3e-07   29.1   1.7    2.2  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.3e-05   23.0   0.0    0.00011   22.2   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0005   20.1   0.0     0.0023   18.0   0.0    2.0  1  EFG_II       Elongation Factor G, domain II
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.043   13.4   0.0    1.4  1  Ras          Ras family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.0   6.4e-55   1.6e-51       2     193 ..      51     228 ..      50     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 6.4e-55
                                    CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEEESS CS
                       GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliDtPG 79 
                                    +irn++ii+h+DhGK+TL dr+l+ tg +++++++a+   +lD+++ ErergiTik++++ l  + ++++y ++liDtPG
  gi|121638285|ref|YP_978509.1|  51 QIRNFCIIAHIDHGKSTLADRMLQLTGVVDERSMRAQ---YLDRMDIERERGITIKAQNVRLPwRvDKTDYVLHLIDTPG 127
                                    79*****************************999986...8**********************84699************ PP

                                    SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  80 HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklek 159
                                    HvdF+ ev+r+l++++gavl+vda++G+e+qt  +l+lal+++++ii ++NK+D + a+ ++ + e+ + +         
  gi|121638285|ref|YP_978509.1| 128 HVDFTYEVSRALEACEGAVLLVDAAQGIEAQTLANLYLALDRDLHIIPVLNKIDLPAADPDRYAAEMAHII--------- 198
                                    ********************************************************************666......... PP

                                    HHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 160 ygekgekevpvvfgSalkgegvktllealvellp 193
                                     g +     +v+++S+++gegv++ll+ +v+ +p
  gi|121638285|ref|YP_978509.1| 199 -GCE---PAEVLRVSGKTGEGVSDLLDEVVRQVP 228
                                    .333...457********************9987 PP

>> LepA_C  GTP-binding protein LepA C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   1.2   3.9e-52     1e-48       2     106 ..     538     642 ..     537     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 3.9e-52
                                    SSCB-GGG-EEEETTTHHHHHHHHHHHHHHHS---SS-EEEEEEETTEEEEEEEE----XXXXXXXXXXXXXXXXXXXXX CS
                         LepA_C   2 ngekvdaLslivhrskaeergrklvekLkeliprqlfevaiqaaigskviaretikalrkdvlaklyggditrkkKllek 81 
                                    +ge vda+s ivh+++a+  g+k+++kLkeliprq+fev++qaaigsk+iare+i+a+rkdvl+k+yggditrk+Kllek
  gi|121638285|ref|YP_978509.1| 538 QGEAVDAFSAIVHKDTAYAYGNKMTTKLKELIPRQQFEVPVQAAIGSKIIARENIRAIRKDVLSKCYGGDITRKRKLLEK 617
                                    799***************************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXX CS
                         LepA_C  82 qkegkkrlkkignveipqeaflavl 106
                                    qkegkkr+k+ig+ve+pqeaf+a l
  gi|121638285|ref|YP_978509.1| 618 QKEGKKRMKTIGRVEVPQEAFVAAL 642
                                    **********************988 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.4   8.6e+03      13      31 ..     312     330 ..     311     336 .. 0.80
   2 !   74.5   0.0     2e-24   5.1e-21       2      87 ..     448     534 ..     447     536 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.4
                                    EECCCCCCHHHHHHHCT-E CS
                          EFG_C  13 vpeeyvgkvisdlssrrGe 31 
                                    v ++ vg+ +++ls+ rG 
  gi|121638285|ref|YP_978509.1| 312 VRQSKVGDTVTSLSRARGA 330
                                    6677789999999999996 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 2e-24
                                    EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-T.THHHCHHHCTTTS-EEEEEEEEEEE CS
                          EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeli.gfateLrslTkGegsfsmefsgYee 80 
                                    ++EP+vk +i++p+e++g+++++++srrGe+ +m++ + +rv +++++Pl e+i +f+++L+s T+G++s+++e +g +e
  gi|121638285|ref|YP_978509.1| 448 VYEPVVKTTIIAPSEFIGTIMELCQSRRGELGGMDYLSPERVELRYTMPLGEIIfDFFDALKSRTRGYASLDYEEAGEQE 527
                                    79************************************************************************999888 PP

                                    --HHHHH CS
                          EFG_C  81 vpgdkld 87 
                                    +  +k+d
  gi|121638285|ref|YP_978509.1| 528 AALVKVD 534
                                    8777766 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.7   3.6e-10   9.3e-07       1      74 []     252     322 ..     252     322 .. 0.96
   2 ?    0.3   0.1      0.37   9.5e+02      26      57 ..     619     650 ..     603     653 .] 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.6e-10
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                    G+v+++rv++G++ + +++++  ++t+ ++++ +++ +  + ++++ + +g+++++i+++k++ ++ +vGdt+t
  gi|121638285|ref|YP_978509.1| 252 GVVTYVRVVDGKISPRERIMM--MSTGATHELLEVGIVSPEPKPCEGLGVGEVGYLITGVKDVRQS-KVGDTVT 322
                                    89*******************..8888889***********************************6.*****96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                    TTSEEEEEEEEEEEEETEEESEEETTSEEEEE CS
                    GTP_EFTU_D2  26 tskkeivtrissletfhededeavaganaGvi 57 
                                    +++k+   +i+++e+++e    a   ++aG++
  gi|121638285|ref|YP_978509.1| 619 KEGKKRMKTIGRVEVPQEAFVAALSTDAAGDK 650
                                    44455889********9999999999999987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-08   0.00011       4     114 .]      57     179 ..      54     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                                    EEESTTSSHHHHHHHHHT...............STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHHHH CS
                       MMR_HSR1   4 ivGrpNvGKStLinaltg...............ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegaseek 64 
                                    i+ +   GKStL  ++++               ++  ++++ g T++ +  r+     + +  ++l+DtpG ++      
  gi|121638285|ref|YP_978509.1|  57 IIAHIDHGKSTLADRMLQltgvvdersmraqylDRMDIERERGITIKAQNVRLPwrvdKTDYVLHLIDTPGHVD------ 130
                                    5556678*********9777777777777765559999**********9999873322334669*******655...... PP

                                    HHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                       MMR_HSR1  65 glgkaflalee.adlillvvdaseeklkpldeeleellee..akkplilvlnk 114
                                     ++ ++ +  e ++ ++l+vda+++ ++   ++l++l     ++  +i vlnk
  gi|121638285|ref|YP_978509.1| 131 -FTYEVSRALEaCEGAVLLVDAAQG-IE--AQTLANLYLAldRDLHIIPVLNK 179
                                    .555555544438********8844.63..34555554332244456778776 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.2e-07    0.0023       2      71 ..     341     413 ..     340     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.2e-07
                         EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsG.....mGelHleivverlkreykvev 71 
                                    P+P++   + p + +d  +l +aL++l+  D  l++  ++eT   +  G     +G lH+ei+ erl+re+++++
  gi|121638285|ref|YP_978509.1| 341 PKPMVYSGLYPVDGSDYPNLRDALDKLQLNDAALTY--EPETSVALGFGfrcgfLGLLHMEITRERLEREFGLDL 413
                                    99******************************9986..57888777655333457*****************986 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.043      27     160 ..      97     227 ..      82     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                    SCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSE CS
                            Ras  27 eyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvp 106
                                    e   Ti +++ +   +vd++++ l++ DT G  +f+   +  ++ +eg++l+ d  +    +++++++  + r     ++
  gi|121638285|ref|YP_978509.1|  97 ERGITIKAQNVRLPWRVDKTDYVLHLIDTPGHVDFTYEVSRALEACEGAVLLVDAAQGIEAQTLANLYLALDRD----LH 172
                                    566799999999999*************************************9998888877777777777664....56 PP

                                    EEEEEETTTGGGG-SS-HHHHHHHHHHHT...SEEEEEBTTTTCTHHHHHHHHHHHH CS
                            Ras 107 ivLvGnKvDleekravsteegeelakelg...lkfletSAktnenveeafeellrei 160
                                    i+ v nK+Dl        + + e+a+ +g   ++ l +S kt e+v+++++e++r++
  gi|121638285|ref|YP_978509.1| 173 IIPVLNKIDLPAAD--PDRYAAEMAHIIGcepAEVLRVSGKTGEGVSDLLDEVVRQV 227
                                    89999*****9855..4555667887777223566778***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4757.93
//
Query:       gi|121638286|ref|YP_978510.1|  [L=189]
Description: hypothetical protein BCG_2421 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-09   37.0   0.0    7.1e-09   36.1   0.0    1.4  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   3.9e-13   7.1e-09       2     108 ..      84     183 ..      83     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.9e-13
                                    TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HH.HCSSSSSSSSEEEECCCE CS
                     PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvelese.ildlngldkdswvkldqi 80 
                                     GeIv+ ++  ++ +  gk Rpv+Vv +d+    ++++ + ++s+++++++   +v + s+ ++ +    ++swv+ld +
  gi|121638286|ref|YP_978510.1|  84 PGEIVWTWVAYEQDPTRGKDRPVLVVGRDR----SVLLGLLVSSQERHAAD-RDWVGIGSGaWDYE---GRESWVRLDRV 155
                                    69*******66778889***********93....59**********99999.77*****9955444...368******** PP

                                    EEEEGGGEEEEEEE--HHHHHHHHHHHH CS
                     PemK_toxin  81 rtvdkarlrkkigklsredlaevqrala 108
                                      v+++ +r+    l+re+++ v+++l+
  gi|121638286|ref|YP_978510.1| 156 LDVPEESIRREGAILEREVFDVVAARLR 183
                                    *********99999*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1379.10
//
Query:       gi|121638287|ref|YP_978511.1|  [L=142]
Description: hypothetical protein BCG_2422c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-21   75.4   5.4    2.2e-10   40.8   1.0    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.2   1.9e-13   3.3e-09       9      55 ..      14      59 ..       3      61 .. 0.90
   2 !   40.8   1.0   1.2e-14   2.2e-10       1      54 [.      71     123 ..      71     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.9e-13
                                   CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   vvt++pd+t++e+l  ++e +++++ VV  +g +vGiv++rD++r l
  gi|121638287|ref|YP_978511.1| 14 VVTINPDATVGELLAGLAEQNIGAMVVVGAEG-VVGIVSERDVVRQL 59
                                   79***********************7888788.**********9977 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.2e-14
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                    V+ im++ v t++ ++t+ ++  lm+e++v+++PV+d  +kl+Giv+  D+++ 
  gi|121638287|ref|YP_978511.1|  71 VAKIMSTTVATCTKSDTVDKISVLMTENRVRHVPVLD-GKKLIGIVSIGDVVKS 123
                                    6789**********************999*******5.557**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1074.56
//
Query:       gi|121638288|ref|YP_978512.1|  [L=280]
Description: ribonuclease Z [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-22   77.4   3.2    1.2e-21   77.1   3.2    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.5e-12   46.7   6.7    1.2e-11   45.0   6.6    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0051   16.7   0.1      0.013   15.4   0.1    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   3.2   2.1e-25   1.2e-21       3     201 .]      32     241 ..      30     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.1e-25
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC........C--EE..EEEEEEHHHHHHCCT CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre........lrpkk..lplyapkgvlavlea 72 
                                    +L+D+g +++q  + a          + + aVllth H DH+a l ++                 lp+++p+g+++v+ea
  gi|121638288|ref|YP_978512.1|  32 FLVDCGRGVLQR-AAAV-----GVGAAGLSAVLLTHLHSDHIAELGDVLItswvtnfaAD--PapLPIIGPPGTAEVVEA 103
                                    79******9988.4444.....33567******************999999777764333..2569************** PP

                                    TCGHHHCHTT............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEE CS
                  Lactamase_B_2  73 nfvylaleee............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyi 140
                                     ++++  +              p+++vhe ++g   + +  g++i++ p  h   +       +t+G+rie++g +v+ +
  gi|121638288|ref|YP_978512.1| 104 TLKAFGHDIGyriahhadlttpPPIEVHEYTAGPAWDRD--GVTIRVAPTDHRPVT-------PTIGFRIESDGASVVLA 174
                                    *98888777787777777777777777777777777776..788888888887766.......***************** PP

                                    SS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.........HHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 141 gDtgyipeeigerlggadllllditayeddemir.........hmgHltpeeaveaaadlgakrlvliHi 201
                                    gDt  ++ +++++ +gad l+   t+ ++d   +          ++H++++ea++ a+++g+++lv++H+
  gi|121638288|ref|YP_978512.1| 175 GDTVPCD-SLDQLAAGADALV--HTVIRKDIVTQipqqrvkdiCDYHSSVREAAATANRAGVGTLVMTHY 241
                                    ****999.7799*********..5566666655567999999***************************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   6.6     2e-15   1.2e-11       4     153 ..      18     179 ..      15     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2e-15
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    + + s+l++ +  ++L+D+G +  +  aa     +g++   ++av+lTHlH+DHi+ lg++  + +v  +a   +    +
  gi|121638288|ref|YP_978512.1|  18 RAGPSTLVRAGAQAFLVDCGRGVLQRAAA-----VGVGAAGLSAVLLTHLHSDHIAELGDVLITSWVTNFAADPAPLPII 92 
                                    56789**********************98.....**************************99999999988877777777 PP

                                    CHHHHHHHHHCCHH.................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEE CS
                    Lactamase_B  84 meeaddaasrkgll.................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvl 146
                                    ++ +  + +   l+                  +++ + + ++     d ++  +r  ++ + p++  +++++e++g++v+
  gi|121638288|ref|YP_978512.1|  93 GPPGTAEVVEATLKafghdigyriahhadltTPPPIEVHEYTAGPAWDRDGVTIRVAPTDHRPVTPTIGFRIESDGASVV 172
                                    6666333333333377778*******9999755555555555555566666666666666777888899*********** PP

                                    EECTTTS CS
                    Lactamase_B 147 ftGDall 153
                                    ++GD+++
  gi|121638288|ref|YP_978512.1| 173 LAGDTVP 179
                                    ****985 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.1e-06     0.013      31     135 ..      48     196 ..      21     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                  Lactamase_B_3  31 eppaeeaDlvlisqaledHahletlkql......................................aenvkvlee..... 67 
                                    +  a    +vl+++ ++dH +   +  +                                      +       +     
  gi|121638288|ref|YP_978512.1|  48 GVGAAGLSAVLLTHLHSDHIAELGDVLItswvtnfaadpaplpiigppgtaevveatlkafghdigY-------Riahha 120
                                    3334666778888888888777666665889999999877777777755555555555555443331.......033334 PP

                  Lactamase_B_3  68 .........geslevg.gleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltP 135
                                              +++++g + +  +v+    ++  ++  + +gf++e+dg +++  G+++   s ++l++   +D ++  
  gi|121638288|ref|YP_978512.1| 121 dlttpppieVHEYTAGpAWDRDGVTIRVAPTDHRPVTPTIGFRIESDGASVVLAGDTVPCDSLDQLAAG--ADALVHT 196
                                    444444444344555433344444444455555788999*******************86666666544..5555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1947.08
//
Query:       gi|121638289|ref|YP_978513.1|  [L=239]
Description: PE family-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.3   7.5    1.1e-13   51.3   7.5    2.3  2  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   7.5     6e-18   1.1e-13      20      92 ..      16      87 ..       2      88 .. 0.88
   2 ?   -0.1   3.4     0.065   1.2e+03      29      61 ..     125     138 ..     114     151 .. 0.42

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 6e-18
                                   HHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--X CS
                             PE 20 gigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaagsYaaaEa 92
                                   +++++ +  + aaaa t +v + aaD+V aaiAa + +haq yq +s+q+aafh+q+v+  +a ++sYa+aEa
  gi|121638289|ref|YP_978513.1| 16 AMRAKAADLDLAAAAKTVGVQP-AADQVAAAIAAILLSHAQIYQDISTQMAAFHDQLVENRTADSTSYASAEA 87
                                   5566666677888888997766.68***********************************************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.065
                                    HHHHHHHHH----SSSSHHHHHHHHHHHHHHHH CS
                             PE  29 naaaaapttavlaaaaDeVSaaiAalfsahaqe 61 
                                    +aa+aa+tt                   a a +
  gi|121638289|ref|YP_978513.1| 125 TAAVAAATT-------------------ARAGS 138
                                    222222222...................22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1673.42
//
Query:       gi|121638290|ref|YP_978514.1|  [L=279]
Description: hypothetical protein BCG_2425c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-25   89.0   0.4    4.5e-25   88.3   0.4    1.3  1  Transglut_core   Transglutaminase-like superfamily
    2.7e-18   66.6   3.2    2.7e-18   66.6   3.2    1.8  2  Bact_transglu_N  Bacterial transglutaminase-like N-terminal r
  ------ inclusion threshold ------
      0.057   12.9   0.0       0.13   11.7   0.0    1.6  1  DUF553           Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.4   7.5e-29   4.5e-25       3     112 .]     126     232 ..     124     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 7.5e-29
                 Transglut_core   3 laeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsge 82 
                                    + +++ ++ ++p+e+++a ++w r++ +y  p++t+ + +  ++le+gkG+c+df +l  ++lR++Gip+R+v+gyl+ +
  gi|121638290|ref|YP_978514.1| 126 VGRRI-RKCHEPSEAVVAAARWARSELDYI-PGTTSVHSSGLDALEQGKGVCQDFVHLSLMVLRSMGIPCRYVSGYLHPK 203
                                    66788.9***********************.**********************************************965 PP

                 Transglut_core  83 eekeq.svasedaHawvevylegygWvplDp 112
                                    ++++  +   + +Hawv++++  +gW+++Dp
  gi|121638290|ref|YP_978514.1| 204 RDAVVgKTVDGRSHAWVQAWT--GGWWHYDP 232
                                    4444377777788********..*******9 PP

>> Bact_transglu_N  Bacterial transglutaminase-like N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   3.2   4.5e-22   2.7e-18       2      80 .]       5      82 ..       4      82 .. 0.96
   2 ?   -2.9   0.0       2.3   1.4e+04      24      30 ..     111     117 ..     106     134 .. 0.57

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 4.5e-22
                Bact_transglu_N  2 rvrHrtrYtYdrpvslapqvlrLrPrsharqrvlsyslkvePepaevnwqqDafgnkvarvvvdephteleveaeseve 80
                                   rv H+t Y Y++pv+ +++++rL+Prs++rq++   +++  P+ +   ++ D++g  v+ +++++phtel+v+++s+ve
  gi|121638290|ref|YP_978514.1|  5 RVVHTTGYVYQSPVTASYNEARLTPRSSSRQNLVLNRVETIPATR-SYRYIDYWGTAVTAFDLHAPHTELTVTSSSVVE 82
                                   89***************************************9755.4******************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                Bact_transglu_N  24 LrPrsha 30 
                                    LrP +h 
  gi|121638290|ref|YP_978514.1| 111 LRPTPHT 117
                                    4444442 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05      0.13      64      98 ..     161     195 ..     123     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                         DUF553  64 ietpkeilktkkgiCrDYaiLTaalLlnlniskvy 98 
                                      +  + l++ kg+C+D+  L + +L  ++i   y
  gi|121638290|ref|YP_978514.1| 161 HSSGLDALEQGKGVCQDFVHLSLMVLRSMGIPCRY 195
                                    44677899*******************99986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1921.00
//
Query:       gi|121638291|ref|YP_978515.1|  [L=325]
Description: hypothetical protein BCG_2426c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-76  255.5   4.8    9.7e-76  255.3   4.8    1.0  1  Alpha-E   A predicted alpha-helical domain with a conserved E


Domain annotation for each model (and alignments):
>> Alpha-E  A predicted alpha-helical domain with a conserved ER motif.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.3   4.8   5.4e-80   9.7e-76       1     293 []       1     301 [.       1     301 [. 0.91

  Alignments for each domain:
  == domain 1  score: 255.3 bits;  conditional E-value: 5.4e-80
                        Alpha-E   1 mlSRvAenLfWlgRYlERaentaRllrvtlqlllde.....eeewrallaalgaeegfeeryeeae..leevlkflllde 73 
                                    ml+R Ae L+W+gRY+ERa++taR+l+v++++ll++     +++ r ll++lg e   +    e +    + l ++ +++
  gi|121638291|ref|YP_978515.1|   1 MLARNAEALYWIGRYVERADDTARILDVAVHQLLEDssvdpDQASRLLLRVLGIEPPDH----ELDvwSLTDLVAFSTNS 76 
                                    9**********************************545565899999999999997553....33423333345555566 PP

                        Alpha-E  74 enpgSiasclraarenaravRerlssemWevlnelylelke..kl.sel...eflervkerlaafsGlaeetmlrdegwr 147
                                    +  +Si+ +++aarena++ Re  sse+We+ln++y++l e  ++ ++l   efl+ +  r+a+f+Gla++t+lrd+g+r
  gi|121638291|ref|YP_978515.1|  77 QGGSSIVDAISAARENAKSAREVTSSETWECLNTTYNALPEreRAaKRLgphEFLSFIEGRAAMFAGLADSTLLRDDGYR 156
                                    6779************************************876445555789**************************** PP

                        Alpha-E 148 FlrlGrrlERadntarlldvklaelevedslqlealLrsvssletYrrryrsriepervlelLlldednPrSlafqleel 227
                                    F+ lGr +ER+d+t+rll +++ + +  +s ++ +lLrs+++++tY r+yr+ +++ rv+e+++ld+ +PrS+ ++l+ +
  gi|121638291|ref|YP_978515.1| 157 FMLLGRAIERVDMTVRLLLSRVGDSA--SSPAWVTLLRSAGAHDTYLRTYRGVLDAGRVVEFMMLDRLFPRSVFHSLKLA 234
                                    *********************99873..578************************************************* PP

                        Alpha-E 228 eealaalsp.aeseegrsseaerllgellaelrladieelleglhelldelqeelaelsdaiserYf 293
                                    e++la+l +  +s+ g+++ea+rllg++++el++ ++  lle+l++ l+ lq+++++++da++ +Yf
  gi|121638291|ref|YP_978515.1| 235 EHNLAELMHnPHSRIGATTEAQRLLGQARSELEFVQPGVLLETLESRLAGLQTTCRDVGDALALQYF 301
                                    *******88767788999********************999*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2642.66
//
Query:       gi|121638292|ref|YP_978516.1|  [L=551]
Description: hypothetical protein BCG_2427c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.5e-164  545.6   0.2   4.6e-164  545.3   0.2    1.1  1  CP_ATPgrasp_1   A circularly permuted ATPgrasp
   6.9e-159  528.8   0.1   8.7e-159  528.4   0.1    1.1  1  CP_ATPgrasp_2   Circularly permuted ATP-grasp type 2
    0.00029   20.2   0.0       0.19   11.0   0.0    2.8  3  ATPgrasp_YheCD  YheC/D like ATP-grasp
  ------ inclusion threshold ------
      0.017   14.5   0.0       0.18   11.2   0.0    2.1  2  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
       0.18   11.8   0.0       0.52   10.3   0.0    1.7  1  ATP-grasp_3     ATP-grasp domain


Domain annotation for each model (and alignments):
>> CP_ATPgrasp_1  A circularly permuted ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.3   0.2  1.3e-167  4.6e-164       1     332 []     100     431 ..     100     431 .. 1.00

  Alignments for each domain:
  == domain 1  score: 545.3 bits;  conditional E-value: 1.3e-167
                  CP_ATPgrasp_1   1 PrivsaeewerlerGlkqRvraLnafLaDiYgdqeilkdGlvPeelvlgnaaylramnGvevPgdvylhvagiDlvraed 80 
                                    Pr++sa ew+rlerG++qRv+aL+++L+DiYgdqeil+dG++P++lv+++++++r++ G+ +P++v++hvagiDl+r+++
  gi|121638292|ref|YP_978516.1| 100 PRVISAPEWTRLERGITQRVKALECYLDDIYGDQEILRDGVIPRRLVTSCEHFHRQAVGIVPPNGVRIHVAGIDLIRDHR 179
                                    9******************************************************************************* PP

                  CP_ATPgrasp_1  81 gefrvlednlrvpsGvsYllenRkivarlfPelfaelrvrpvadyaqaLlealrevapaeaadptvvvltPGvynsayfe 160
                                    g+frvlednlr+psGvsY++enR+++ar+fP+lfa++rvr+v+dya++Ll+alr++a++++adptvvvltPGvynsayfe
  gi|121638292|ref|YP_978516.1| 180 GDFRVLEDNLRSPSGVSYVMENRRTMARVFPNLFATHRVRAVDDYASHLLRALRNSAATNEADPTVVVLTPGVYNSAYFE 259
                                    ******************************************************************************** PP

                  CP_ATPgrasp_1 161 hayLarklGveLvegrDLvvrdnkvylrtteglkrvdviyRRvdddflDPlefrpdsvlGvpGlleayraGnvtlanavG 240
                                    h++Lar++GveLvegrDL++rdn+vy+rtteg+++vdviyRR+dd+flDPl+fr+dsvlGv+Gl++a+raGnv+l++a+G
  gi|121638292|ref|YP_978516.1| 260 HSLLARQMGVELVEGRDLFCRDNQVYMRTTEGERQVDVIYRRIDDAFLDPLQFRADSVLGVAGLVNAARAGNVVLSSAIG 339
                                    ******************************************************************************** PP

                  CP_ATPgrasp_1 241 sGvaddkavyafvPelieyyLgeepilknvetyrceeaddlkevLdrlselvvkevegsggygiviGptaskaelaelar 320
                                    +Gv ddk vy++vP++ieyyL+e+p+l+nvet rc+ +d+++evLdr++elv+k+vegsggygiv+Gp+as+aela++++
  gi|121638292|ref|YP_978516.1| 340 NGVGDDKLVYTYVPTMIEYYLHEKPLLANVETLRCWLDDEREEVLDRIRELVLKPVEGSGGYGIVFGPEASQAELAAVSQ 419
                                    ******************************************************************************** PP

                  CP_ATPgrasp_1 321 rilaepeqyiaq 332
                                    +i+++p+++iaq
  gi|121638292|ref|YP_978516.1| 420 KIRDDPRSWIAQ 431
                                    ***********9 PP

>> CP_ATPgrasp_2  Circularly permuted ATP-grasp type 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.4   0.1  2.4e-162  8.7e-159       1     375 []     100     476 ..     100     476 .. 0.99

  Alignments for each domain:
  == domain 1  score: 528.4 bits;  conditional E-value: 2.4e-162
                                    -EEE-HHHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHTTSS-GG.GGG-TT--GGGTT---GGG-S-SEEEEEEEE.SS CS
                  CP_ATPgrasp_2   1 PriisaeeWaeleaGlaqRarllnaflaDiYgeqkllkegvlPaelvegspgflrelkgvkppggvrlhiaavDLvrded 80 
                                    Pr+isa eW++le+G++qR+++l++ l+DiYg+q++l++gv+P++lv+++++f r++ g+ pp+gvr+h+a++DL+rd+ 
  gi|121638292|ref|YP_978516.1| 100 PRVISAPEWTRLERGITQRVKALECYLDDIYGDQEILRDGVIPRRLVTSCEHFHRQAVGIVPPNGVRIHVAGIDLIRDHR 179
                                    9******************************************************************************* PP

                                    S-EEEEEEE-SS---HHHHHHHHHHHHHH-HHHHHHS-B---TTHHHHHHHHHHHTS-.-S...S-EEEE---SSSTTHH CS
                  CP_ATPgrasp_2  81 grwlVlednlraPsGvgYalenRevlsrvlpelfrelrvrrlaeffealreaLaalapakaeeprtivlLtpGpynsayf 160
                                    g+++Vlednlr+PsGv+Y++enR++++rv+p+lf+++rvr ++++ ++l++aL++ a +++ +p+ +v+LtpG ynsayf
  gi|121638292|ref|YP_978516.1| 180 GDFRVLEDNLRSPSGVSYVMENRRTMARVFPNLFATHRVRAVDDYASHLLRALRNSAATNEADPT-VVVLTPGVYNSAYF 258
                                    **********************************************************8888998.************** PP

                                    HHHHHHHHHT-EEE-GGGEEE-SS-EEE--TT--EEE-EEEE-S-GGGS-TTTS-TT-SSS-TTHHHHHHTTS-EEES-T CS
                  CP_ATPgrasp_2 161 EhafLArylgveLvegsDLtvrdgrvylktleglkrVdviyrrvdddfldplelradsllGvpgLleavragnvavaNal 240
                                    Eh++LAr++gveLveg+DL++rd++vy++t+eg+++Vdviyrr+dd+fldpl++rads+lGv+gL++a+ragnv++  a+
  gi|121638292|ref|YP_978516.1| 259 EHSLLARQMGVELVEGRDLFCRDNQVYMRTTEGERQVDVIYRRIDDAFLDPLQFRADSVLGVAGLVNAARAGNVVLSSAI 338
                                    ******************************************************************************** PP

                                    TTHHHHSTTTGGGHHHHHHHHH-S--SSEE---EETTSHHHHHHHHHSGGGEEEEE--------EEEGGG--HHHHHHHH CS
                  CP_ATPgrasp_2 241 GsgvaddkalyaflpaliryllgeellLpnvptwwcgeeealeevlenldelvvkpvdesggegvligpelsaaeleelr 320
                                    G+gv ddk +y+++p +i+y+l+e++lL+nv+t  c  ++++eevl++++elv+kpv++sgg+g+++gpe+s+ael+++ 
  gi|121638292|ref|YP_978516.1| 339 GNGVGDDKLVYTYVPTMIEYYLHEKPLLANVETLRCWLDDEREEVLDRIRELVLKPVEGSGGYGIVFGPEASQAELAAVS 418
                                    ******************************************************************************** PP

                                    HHHHHSGGGEEEEE-----EEEEE...EEEEEEEEEE-EEE.ES.SEEE-S--EEEEE CS
                  CP_ATPgrasp_2 321 arikanperyvaqevvelstaptl...kleprhvdlRvFvlateegirvmpggLtRvA 375
                                    ++i+++p++++aq+++elst+pt    +l+pr vdlR+F+++++++++v+pggLtRvA
  gi|121638292|ref|YP_978516.1| 419 QKIRDDPRSWIAQPMMELSTVPTRiegTLAPRYVDLRPFAVNDGNEVWVLPGGLTRVA 476
                                    ***********************97666**************999************8 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   7.5e+02     208     244 ..     171     207 ..     143     214 .. 0.77
   2 !   11.0   0.0   5.2e-05      0.19      41      67 ..     380     406 ..     369     446 .. 0.76
   3 !    5.9   0.0    0.0018       6.6     119     165 ..     447     494 ..     409     517 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                 ATPgrasp_YheCD 208 GlDlgidkegkvWllEvNskpgrsifkeagdkeaark 244
                                    G+Dl  d++g + +lE N +    +   ++++++  +
  gi|121638292|ref|YP_978516.1| 171 GIDLIRDHRGDFRVLEDNLRSPSGVSYVMENRRTMAR 207
                                    9***************998877766666666555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.2e-05
                 ATPgrasp_YheCD  41 leemlekyksvylKpanGskGkgilri 67 
                                     ee+l++ ++++lKp++Gs+G gi+  
  gi|121638292|ref|YP_978516.1| 380 REEVLDRIRELVLKPVEGSGGYGIVFG 406
                                    5789********************974 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0018
                 ATPgrasp_YheCD 119 idgrpfDfRvlvqKngkgkWevtgiaaRia.gkgsittnlsrGGtalp 165
                                    +  r +D+R +   +g++ W++ g   R+a  +gs + n s+GG  ++
  gi|121638292|ref|YP_978516.1| 447 LAPRYVDLRPFAVNDGNEVWVLPGGLTRVAlVEGSRVVNSSQGGGSKD 494
                                    34578*************************558999999999997765 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.09   3.2e+02     146     172 ..     169     200 ..     163     203 .. 0.76
   2 ?   11.2   0.0     5e-05      0.18      25      75 ..     381     431 ..     367     438 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.09
                                    EEEEEEETT.....EEEEEE-SS---HHHHHH CS
                      GSH-S_ATP 146 fvGlDvigd.....kltEinvtsPtgireiee 172
                                    ++G+D+i d     ++ E n+ sP+g++ + e
  gi|121638292|ref|YP_978516.1| 169 VAGIDLIRDhrgdfRVLEDNLRSPSGVSYVME 200
                                    6899999873333458999*******998876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5e-05
                                    HHHHHHHSSEEEEESS--TTTT-EEE-TT.-TTHHHHHHHHTTTTTS-EEEE CS
                      GSH-S_ATP  25 rafleeqgdvilKPldgkgGegvfrvkks.dpnlksilellteegkepviaq 75 
                                    +++l++ ++++lKP++g+gG g++   ++ +++l ++ + + +   + +iaq
  gi|121638292|ref|YP_978516.1| 381 EEVLDRIRELVLKPVEGSGGYGIVFGPEAsQAELAAVSQKIRDD-PRSWIAQ 431
                                    678899999*************9876555377777776665544.4466666 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.52      25      65 ..     381     429 ..     372     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                                    EESS--SSSEEEEESS-------B--SS--TTE...............E CS
                    ATP-grasp_3  25 eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........l 65 
                                    ee+     +lv+Kp++G+gg ++++  e  +ae a  +++        +
  gi|121638292|ref|YP_978516.1| 381 EEVLDRIRELVLKPVEGSGGYGIVFGPEASQAELAAVSQKirddprswI 429
                                    666777889*****************99999998777766455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3791.29
//
Query:       gi|121638293|ref|YP_978517.1|  [L=86]
Description: 30S ribosomal protein S20 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-26   93.3  19.5    1.2e-26   93.2  19.5    1.0  1  Ribosomal_S20p  Ribosomal protein S20
  ------ inclusion threshold ------
      0.023   15.0   1.1       0.03   14.6   0.9    1.3  1  DUF4878         Domain of unknown function (DUF4878)
       0.24   11.1   2.2       0.27   10.9   2.2    1.1  1  DUF2937         Protein of unknown function (DUF2937)


Domain annotation for each model (and alignments):
>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2  19.5     2e-30   1.2e-26       1      82 []       2      84 ..       2      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2e-30
                                   ..SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.-HHHHHHHHHHHHHHHHHHHCTTSSTCCHHHHHHHHHHHHH CS
                 Ribosomal_S20p  1 ANikSakKrirqnekrrlrNrsyksavrtaiKkvraaiea.dkekaqealkkaiskidkaakkgvihkNtAaRkkSrlakki 81
                                   ANikS++Kr r+ne++rlrN+++ks++rta++ +r+a++a dk+ka e+l+++ +k+dkaa+kgvihkN+Aa+kkS la+++
  gi|121638293|ref|YP_978517.1|  2 ANIKSQQKRNRTNERARLRNKAVKSSLRTAVRAFREAAHAgDKAKAAELLASTNRKLDKAASKGVIHKNQAANKKSALAQAL 83
                                   9*************************************888***************************************98 PP

                                   H CS
                 Ribosomal_S20p 82 n 82
                                   n
  gi|121638293|ref|YP_978517.1| 84 N 84
                                   7 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   5.1e-06      0.03      10      56 ..      29      75 ..      21      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-06
                        DUF4878 10 eeavknFleavkeGdvedaikyltestreedalaeklkgkfkelkak 56
                                    +av +F ea+  Gd ++a+++l+   r+ d+ a+k    ++++++k
  gi|121638293|ref|YP_978517.1| 29 RTAVRAFREAAHAGDKAKAAELLASTNRKLDKAASKGVIHKNQAANK 75
                                   689**************************999999966666665554 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.2   4.5e-05      0.27      35      96 ..      25      86 .]      18      86 .] 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.5e-05
                        DUF2937 35 ldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeqelqal 96
                                     +l++++ +f++ A + +k+   +l+a + ++ d++ ++    ++++ ++ ++L q+l++l
  gi|121638293|ref|YP_978517.1| 25 KSSLRTAVRAFREAAHAGDKAKAAELLASTNRKLDKAASKGVIHKNQAANKKSALAQALNKL 86
                                   56899****************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1341  (0.074795); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 630.73
//
Query:       gi|121638294|ref|YP_978518.1|  [L=316]
Description: hypothetical protein BCG_2429c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-07   31.8   0.0    1.5e-07   31.4   0.0    1.1  1  DNA_pol3_delta  DNA polymerase III, delta subunit
  ------ inclusion threshold ------
      0.018   14.7   0.6      0.018   14.7   0.6    1.9  2  AA_kinase       Amino acid kinase family


Domain annotation for each model (and alignments):
>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.7e-11   1.5e-07       1     168 [.       2     164 ..       2     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.7e-11
                                    EEEEES-HHHHHHHHHHHHHHH.HTTTEEEEEEEE-STTS-HHH.HTTTSTTTTSSSSEEEEEEE--.....TT-S-TTH CS
                 DNA_pol3_delta   1 YllyGedellleeskdqilkqa.lkqgfedlnyikfdlnedwiddvleecetlpffsdkrivvlknpklltkesklnekl 79 
                                    +l++G++ell+e ++ ++l  a  + g+ d  ++++ + ++ +   l e+ ++++f+++rivvl  +          ++ 
  gi|121638294|ref|YP_978518.1|   2 HLVLGDEELLVERAVADVLRSArQRAGTADVPVSRMRAGDVGAY-ELAELLSPSLFAEERIVVLGAA------AEAGKDA 74 
                                    6899**********9887655427899**********9998887.899******************9......4578899 PP

                                    HHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTT.TEEEEEE---.-TTTHHHHHHHHHHHTT-EE-HHHHHHHHHH CS
                 DNA_pol3_delta  80 lkeLeeylsnlpedtlLiliapkklderkklvklLkk.katvveaktl.keeelkkwiqkraqelglkiekealelLlel 157
                                    ++ +e+   +lp+ t+L+++ +    ++k+l  +L +  a v  + +  k +e  ++i + +++l +k ++e+++ Ll++
  gi|121638294|ref|YP_978518.1|  75 AAVIESAAADLPAGTVLVVVHS-GGGRAKSLANQLRSmGAQVHPCARItKVSERADFIRSEFASLRVKVDDETVTALLDA 153
                                    999*******************.5556888999999956777789999899***************************** PP

                                    HTT-HHHHHHH CS
                 DNA_pol3_delta 158 vennlsaikqe 168
                                    v+++ + ++++
  gi|121638294|ref|YP_978518.1| 154 VGSDVRELASA 164
                                    *****999876 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6     2e-06     0.018      16     107 ..      73     160 ..      58     187 .. 0.65
   2 ?   -3.1   0.1      0.52   4.7e+03      14      30 ..     295     310 ..     261     313 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-06
                                    CCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHH CS
                      AA_kinase  16 eeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrdalaslgerlvaal 93 
                                    ++    +++e  aa   +g  lvvVh+gg+++  l+++   +g + ++ a   r t + +     r + asl  ++ ++ 
  gi|121638294|ref|YP_978518.1|  73 DA---AAVIESAAADLPAGTVLVVVHSGGGRAKSLANQlrSMGAQVHPCA---RITKVSERADFIRSEFASLRVKVDDET 146
                                    33...3344444444455699*****************996666666665...445555555555566666666666666 PP

                                    HHTTHGEEEE-GGG CS
                      AA_kinase  94 laaglpavglsaaa 107
                                    ++a+l+avg +++ 
  gi|121638294|ref|YP_978518.1| 147 VTALLDAVGSDVRE 160
                                    66666666655544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.52
                                    CTCCHHHHHHHHHHHHH CS
                      AA_kinase  14 dkeeaslrrlaeqiaal 30 
                                    d++  +l+++++q+a+l
  gi|121638294|ref|YP_978518.1| 295 DADY-ALESAVRQVAEL 310
                                    2222.345555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2275.61
//
Query:       gi|121638295|ref|YP_978519.1|  [L=514]
Description: hypothetical protein BCG_2430c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-44  151.2  37.3    3.3e-44  151.2  37.3    2.3  3  Competence  Competence protein
    0.00014   21.6   1.1    0.00014   21.6   1.1    4.3  4  DUF4131     Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Competence  Competence protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.7     0.089     8e+02     191     221 ..      22      52 ..       9      87 .. 0.54
   2 !  151.2  37.3   3.6e-48   3.3e-44       1     270 [.     221     485 ..     221     487 .. 0.97
   3 ?   -3.7   0.2      0.65   5.8e+03     129     140 ..     495     506 ..     488     511 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.089
                     Competence 191 vPlvsllvlplallallllllpslaalllql 221
                                    v  +++++  + ++al+++++++ +  l+++
  gi|121638295|ref|YP_978519.1|  22 VTAAGIVWPIGNVCALCCVVVALGGGALWWC 52 
                                    2333334344444444444443333333332 PP

  == domain 2  score: 151.2 bits;  conditional E-value: 3.6e-48
                     Competence   1 LllGdrselseevweafqktGlaHllAiSGlHvglvagllllllrrlllrlplrklaallallflllYallaGfspsvlR 80 
                                    L+lGd+s +++ ++++f+++Gl+Hl A+SG +v++v++++l+ +r++     ++++a+++a+++l+++++l   + svlR
  gi|121638295|ref|YP_978519.1| 221 LVLGDTSTVTALTSREFRAAGLTHLTAVSGANVTIVCAAALVSARLI-----GPRAAVVCAAVALVAFVILVQPTASVLR 295
                                    89*********************************************.....999************************* PP

                     Competence  81 AllmlllvllalllkrkaspldalalaallvllvdPlallsaGfqLSflavagilllaprlekalkrlskkvrellllav 160
                                    A++m +++l++ l  r+ +++ al+ ++l++l+  P+ ++++Gf LS++a+ +++++ap ++++l  +  +   + +lav
  gi|121638295|ref|YP_978519.1| 296 AAVMGAIALVGMLSARRRQAIPALSGSVLVLLAAAPHLAVDIGFALSVAATGALVVIAPVWSRRLVDRGCPKVLADALAV 375
                                    *************************************************************************99***** PP

                     Competence 161 slaaqlallplllylfgqislvsllaNllavPlvsllvlplallallllllpslaalllqladlllelllellellaslp 240
                                      aaql+++pl++ + g++slv+++aNl++  +++ +++ ++++a+l++++p+ a++l+++++  ++++l+++++++ +p
  gi|121638295|ref|YP_978519.1| 376 AAAAQLVTAPLVAAISGRVSLVAVVANLAVAAVIAPITVLGSVAAVLVVPWPAGAQVLIRFTGPEVWWVLRVAHWASGVP 455
                                    ******************************************************************************** PP

                     Competence 241 laslvlgkpslllllllyllllllllller 270
                                     a+++++   + +ll+  + +++++ +++r
  gi|121638295|ref|YP_978519.1| 456 AATVPVAAGLPGVLLVGGATVFTVAQWRWR 485
                                    ******888888888888887777777665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.65
                     Competence 129 lavagilllapr 140
                                    +ava+i+lla++
  gi|121638295|ref|YP_978519.1| 495 MAVAVICLLAWS 506
                                    344444444444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.1   1.5e-08   0.00014      11     136 ..      38     168 ..      28     170 .. 0.77
   2 ?   -4.1  10.2       1.2   1.1e+04       7      52 ..     271     313 ..     249     363 .. 0.71
   3 ?   -1.7   0.7      0.22   1.9e+03      28      28 ..     383     383 ..     335     432 .. 0.51
   4 ?   -0.9   6.6      0.12   1.1e+03       4      52 ..     460     505 ..     457     512 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-08
                        DUF4131  11 alllllllllllllrr.rprrrv........llllllllllallgfalrapqpnandlsqlles.gqeviveGvvaslpe 80 
                                    + ++++l   +l++   r  r +         ++l ++ ++++++ ++ a++ +a d ++++   g++ +v+ + ++ p 
  gi|121638295|ref|YP_978519.1|  38 CCVVVALGGGALWWCVaR--RSWhaprlgsiSAGLVAVGMVGAGYGLAVALRSEAVDRHPITVAfGTSALVTVTPSESPV 115
                                    333333333333322221..222224445558899999999999999999999999999999889999**9999999999 PP

                        DUF4131  81 ltgsgt.rfvlevervlsagktkpvsgrvlvtvpkspaeglrpGdrlrltgrlkrpr 136
                                      g+g+  f ++v+r+    +   +sgrv v+ ++ +  +l  G+ +++++r++rp 
  gi|121638295|ref|YP_978519.1| 116 SLGRGRlMFRATVQRL----RDDETSGRVVVFARALDFGELMVGQPVQFRARISRPA 168
                                    9999998888888776....88899***********9999***************97 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.2
                        DUF4131   7 lvllalllllllllllllrrrprrrvllllllllllallgfalrap 52 
                                    + +++++++l ++ +l+   +p+  vl ++ + ++++++++ +r +
  gi|121638295|ref|YP_978519.1| 271 AAVVCAAVALVAFVILV---QPTASVLRAAVMGAIALVGMLSARRR 313
                                    44444555555555555...45555544444444444444444433 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.22
                        DUF4131  28 p 28 
                                    +
  gi|121638295|ref|YP_978519.1| 383 T 383
                                    2 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.12
                        DUF4131   4 plalvllalllllllllllllrrrprrrvllllllllllallgfalrap 52 
                                    p+a+ l ++ll+  ++ + +   +++r +++ ++++  +a+++++l a+
  gi|121638295|ref|YP_978519.1| 460 PVAAGLPGVLLVGGATVFTV---AQWRWRWFRAAMCKTMAVAVICLLAW 505
                                    66666666666666666666...55555566666665555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3552.55
//
Query:       gi|121638296|ref|YP_978520.1|  [L=297]
Description: hypothetical protein BCG_2431c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-21   74.6   0.0    8.4e-21   74.0   0.0    1.3  1  HHH_3           Helix-hairpin-helix motif
    6.4e-13   47.8   2.2      3e-08   33.1   0.1    3.1  3  HHH             Helix-hairpin-helix motif
      2e-08   34.0   1.4    3.3e-08   33.2   1.4    1.4  1  SLBB            SLBB domain
    4.1e-05   24.1   0.0      0.048   14.3   0.0    2.6  2  HHH_5           Helix-hairpin-helix domain
    6.4e-05   23.0   0.0     0.0027   17.8   0.0    2.5  2  HHH_2           Helix-hairpin-helix motif
    0.00012   22.3   0.0    0.00026   21.2   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family
     0.0024   18.2   0.0       0.37   11.2   0.0    2.7  2  HHH_8           Helix-hairpin-helix domain
     0.0057   16.6   0.0      0.009   16.0   0.0    1.2  1  PsbU            Photosystem II 12 kDa extrinsic protein (PsbU
     0.0073   16.5   0.0      0.015   15.5   0.0    1.5  1  HHH_6           Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.048   13.0   0.1       0.31   10.4   0.0    1.8  1  T2SSK           Type II secretion system (T2SS), protein K
       0.17   12.3   0.0        5.4    7.6   0.0    2.8  3  IMS_HHH         IMS family HHH motif
       0.97    9.2   3.9       0.49   10.2   1.1    2.0  2  Cecropin        Cecropin family


Domain annotation for each model (and alignments):
>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   5.6e-24   8.4e-21       3      65 .]     234     296 ..     232     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 5.6e-24
                          HHH_3   3 avgvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpktfeqlagflr 65 
                                    a+  d+NtA++e+L+ lpG+gp++A +Iva+R+ nG+f+s+++L +v g+gp+ +++l+  +r
  gi|121638296|ref|YP_978520.1| 234 AEVLDLNTATVEQLDALPGIGPVTAAAIVAWRQRNGRFTSVDQLADVDGIGPARLDKLRNLVR 296
                                    5779******************************************************98775 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2         4   5.9e+03      20      24 ..     226     230 ..     226     230 .. 0.95
   2 !   33.1   0.1     2e-11     3e-08       4      29 ..     238     263 ..     235     264 .. 0.92
   3 !   13.2   0.0   4.1e-05     0.061       4      25 ..     268     289 ..     267     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                                    SHHHH CS
                            HHH  20 GpktA 24 
                                    GpktA
  gi|121638296|ref|YP_978520.1| 226 GPKTA 230
                                    9***9 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2e-11
                                    HHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   4 glipasreeLlalPGVGpktAeaIls 29 
                                     l++a++e+L alPG+Gp tA aI +
  gi|121638296|ref|YP_978520.1| 238 DLNTATVEQLDALPGIGPVTAAAIVA 263
                                    689*********************86 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 4.1e-05
                                    HHHTSSHHHHHTSTT-SHHHHH CS
                            HHH   4 glipasreeLlalPGVGpktAe 25 
                                    + +  s+++L+++ G+Gp++ +
  gi|121638296|ref|YP_978520.1| 268 NGRFTSVDQLADVDGIGPARLD 289
                                    56778*************9866 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   1.4   2.2e-11   3.3e-08       1      56 [.     139     192 ..     139     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.2e-11
                                    EEEEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.........-E.EEE-SSSSS- CS
                           SLBB   1 vVtVtGeVkrPgnyevpigttlsdlieqaGGltddadlksvnLarl.avipgGpmmg 56 
                                    vV V+G V +Pg +++ +g++++d++++aGG  d ad    n ar+     +G+ + 
  gi|121638296|ref|YP_978520.1| 139 VVSVVGLVHTPGLVTLAPGARIADALQAAGGAVDGADTVGLNMARQlG---DGEQIV 192
                                    79***********************************99999999888...888776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.2e-05     0.048      27      52 ..     237     262 ..     224     267 .. 0.78
   2 !    6.9   0.0    0.0063       9.4      34      51 ..     274     291 ..     268     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHS-HHHHHTSTTS-HHHHHHHH CS
                          HHH_5  27 edlaaadveeLakipGiGkktAerii 52 
                                     dl  a+ve+L ++pGiG+ tA  i+
  gi|121638296|ref|YP_978520.1| 237 LDLNTATVEQLDALPGIGPVTAAAIV 262
                                    47777899999999999999999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0063
                                    HHHHHTSTTS-HHHHHHH CS
                          HHH_5  34 veeLakipGiGkktAeri 51 
                                    v++La++ GiG+ + +++
  gi|121638296|ref|YP_978520.1| 274 VDQLADVDGIGPARLDKL 291
                                    667777777777666654 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0027      28      54 ..     238     264 ..     226     272 .. 0.90
   2 ?    2.4   0.0      0.11   1.7e+02      32      45 ..     272     285 ..     270     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                          HHH_2  28 aLkkasleeLlevddiGeeiAqsivef 54 
                                     L +a++e+L ++++iG+++A++iv +
  gi|121638296|ref|YP_978520.1| 238 DLNTATVEQLDALPGIGPVTAAAIVAW 264
                                    699**********************99 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                          HHH_2  32 asleeLlevddiGe 45 
                                    +s+++L+ vd+iG+
  gi|121638296|ref|YP_978520.1| 272 TSVDQLADVDGIGP 285
                                    58999*******98 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.7e-07   0.00026       2      42 ..     245     285 ..     244     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-07
                 Transposase_20   2 elLesipGiGpvtaaallaeigdlrrfksakqlaayaGlap 42 
                                    e L+ +pGiGpvtaaa++a  +   rf s +qla   G+ p
  gi|121638296|ref|YP_978520.1| 245 EQLDALPGIGPVTAAAIVAWRQRNGRFTSVDQLADVDGIGP 285
                                    67999****************9999*********9888776 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00025      0.37      38      65 ..     237     263 ..     228     266 .. 0.80
   2 ?    4.3   0.0     0.036        53      42      66 ..     271     294 ..     265     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                    -SS-HHHHTTHCTTSTT--HHHHHHHHH CS
                          HHH_8  38 lpeeitsleeeltklpgiGkkiaakiee 65 
                                    l+  ++++e+ l +lpgiG+ +aa i  
  gi|121638296|ref|YP_978520.1| 237 LDLNTATVEQ-LDALPGIGPVTAAAIVA 263
                                    5666677799.*************9975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.036
                                    HHHHTTHCTTSTT--HHHHHHHHHH CS
                          HHH_8  42 itsleeeltklpgiGkkiaakieei 66 
                                     ts+++ l +++giG++  +k++ +
  gi|121638296|ref|YP_978520.1| 271 FTSVDQ-LADVDGIGPARLDKLRNL 294
                                    689999.********9988888766 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-06     0.009       7      59 ..     229     285 ..     224     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                                    TTSGGGTSEETTTS-GGGGGGSTTTTTHHHHHHH....HS---SSGGGGGG-TT--H CS
                           PsbU   7 latelgekvDlnnanvrafrqlrGlyPtlakkiv....knaPYdsvedvlniPgLse 59 
                                    +a +++e +Dln a v +   l+G+ P  a+ iv    +n+ + sv+++ ++ g+  
  gi|121638296|ref|YP_978520.1| 229 TAPKTAEVLDLNTATVEQLDALPGIGPVTAAAIVawrqRNGRFTSVDQLADVDGIGP 285
                                    5567899**************************955445999*****9999988765 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.015      29      62 ..     247     280 ..     238     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                          HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarr 62 
                                    L+a+ g+g  +a++iva R+++g f+s+++la+ 
  gi|121638296|ref|YP_978520.1| 247 LDALPGIGPVTAAAIVAWRQRNGRFTSVDQLADV 280
                                    78999************************99874 PP

>> T2SSK  Type II secretion system (T2SS), protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.31     144     176 ..     263     295 ..     255     297 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                          T2SSK 144 pylpanqpladvseLrlvkgvtpelyarLrPyv 176
                                    + + +n ++++v++L++v+g+ p+ +++Lr +v
  gi|121638296|ref|YP_978520.1| 263 AWRQRNGRFTSVDQLADVDGIGPARLDKLRNLV 295
                                    56789*************************988 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.4   3.7e+03      20      31 ..     226     238 ..     226     239 .. 0.82
   2 ?    7.6   0.0    0.0036       5.4      14      26 ..     248     260 ..     246     264 .. 0.83
   3 ?    0.8   0.0      0.49   7.3e+02      18      30 ..     282     294 ..     277     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.4
                        IMS_HHH  20 Ggklgek.LeklG 31 
                                    G+k++ k  e+l+
  gi|121638296|ref|YP_978520.1| 226 GPKTAPKtAEVLD 238
                                    8999999888886 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                        IMS_HHH  14 tkipGiGgklgek 26 
                                      +pGiG+++++ 
  gi|121638296|ref|YP_978520.1| 248 DALPGIGPVTAAA 260
                                    679********97 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.49
                        IMS_HHH  18 GiGgklgekLekl 30 
                                    GiG+   +kL++l
  gi|121638296|ref|YP_978520.1| 282 GIGPARLDKLRNL 294
                                    9********9876 PP

>> Cecropin  Cecropin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.5   3.7e+03      19      29 ..     134     144 ..     134     145 .. 0.78
   2 ?   10.2   1.1   0.00033      0.49      10      26 ..     157     173 ..     157     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                       Cecropin  19 kggPavrrvaa 29 
                                    +g+P+v  v++
  gi|121638296|ref|YP_978520.1| 134 SGLPVVVSVVG 144
                                    599**987776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00033
                       Cecropin  10 GkrirdAaIkggPavrr 26 
                                    G ri+dA + +g+av +
  gi|121638296|ref|YP_978520.1| 157 GARIADALQAAGGAVDG 173
                                    88*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2093.74
//
Query:       gi|121638297|ref|YP_978521.1|  [L=408]
Description: hypothetical protein BCG_2432c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-24   86.6   0.0    4.1e-24   85.1   0.0    1.8  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    6.9e-17   62.3   0.3    1.6e-16   61.1   0.3    1.7  1  Acetyltransf_17  Acetyltransferase (GNAT) domain
    1.4e-12   47.9   0.1    2.5e-12   47.1   0.1    1.4  1  SCP2_2           Sterol carrier protein domain
    0.00066   19.6   0.1      0.002   18.0   0.0    1.8  2  FR47             FR47-like protein
     0.0049   17.1   0.0     0.0089   16.2   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.029   14.8   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   1.4e-27   4.1e-24       4     127 ..      13     139 ..      10     140 .. 0.96
   2 ?   -1.7   0.0      0.99     3e+03     105     121 ..     217     233 ..     201     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.4e-27
                                    EE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE....TTEEEEEEEEEEEEEEETT.EEEEEEEEEE CS
                 Acetyltransf_9   4 elteedldevlellkyaFqdeespleeireyfrklleesrvlgaed....ngelvgqlallplelnvpG.ktlkaagvtg 78 
                                    + te+d+++++ l +++F d   p  e   ++r l+  + +++++d    + e+vg++ +++l+l+vpG   l++ag++ 
  gi|121638297|ref|YP_978521.1|  13 SPTEDDWPGMFLLAAASFTDFIGP--ESATAWRTLVPTDGAVVVRDgagpGSEVVGMALYMDLRLTVPGeVVLPTAGLSF 90 
                                    569*********************..577899**************99999******************999******** PP

                                    EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-EE CS
                 Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGyei 127
                                    Vavap+hr+rg+l+++ a++++++++ g+p++ l++s+ +iY+rfGy++
  gi|121638297|ref|YP_978521.1|  91 VAVAPTHRRRGLLRAMCAELHRRIADSGYPVAALHASEGGIYGRFGYGP 139
                                    ***********************************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.99
                                    TT--EEEE--SSHHHHH CS
                 Acetyltransf_9 105 egqplsllfPssipiYr 121
                                    ++++++ll+P  +++Yr
  gi|121638297|ref|YP_978521.1| 217 DRESFALLHPDGYALYR 233
                                    5789******9999998 PP

>> Acetyltransf_17  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.3   5.4e-20   1.6e-16       1     116 []     194     304 ..     194     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 5.4e-20
                                    TEBE--HHHHHHHHHTTTTS.T.GCSEEEEEE.TTSEETEEEEEEEETTE.TTC..EEEEEEEEESSHHHHHHHHHHHHC CS
                Acetyltransf_17   1 GaleRseawWrrrllkrrea.r.egalayvvyrdddgpeGyllYrvkeesgaeg..tleVrelvaltpeayraLlrflas 76 
                                    G l R++  W++ l + ++a   +++ +++++     p+Gy+lYrv    ++ +    +V+el a t++a+ aL+r l +
  gi|121638297|ref|YP_978521.1| 194 GGLLRPQVLWDELLAECKAApGgDRESFALLH-----PDGYALYRV----DRTDlkLARVSELRAVTADAHCALWRALIG 264
                                    7899********98888876533444677776.....89*******....333444677********************* PP

                                    GTGTESEEEEEEESTT-SCGGGCSSGG.EECEEEEEE.....EEE CS
                Acetyltransf_17  77 hdslveeveawkappddplpllledprikeaarpgam.....lRi 116
                                    +d  +e+++ + ++p+dplp+ll+d r    ar+++      lRi
  gi|121638297|ref|YP_978521.1| 265 LD-SMERIS-IITHPQDPLPHLLTDTR---LARTTWRqdglwLRI 304
                                    **.******.88899************...888777666666665 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   8.3e-16   2.5e-12       1      99 [.     307     399 ..     307     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 8.3e-16
                                    HHHHHHHS--SS-S.SEEEEEEEE-TTSGGGSEEEEEEEETTSEEEECSCE-SCE..EEEEHHHHHHHHTTSS-HHHHHH CS
                         SCP2_2   1 veaalearpyekee.kgeltleveDpllpwnngrfrltiedgkgeevgkeeeada.dltldiqtLaqlllGyrsaseLar 78 
                                    v+aalear+y+ e  + + +lev+D       grf l+i dg++ +++ ++  +a ++++d + L++l+lG+ +as+La+
  gi|121638297|ref|YP_978521.1| 307 VPAALEARGYAHEVgEFSTVLEVSD------GGRFALKIGDGRA-RCTPTD--AAaEIEMDRDVLGSLYLGAHRASTLAA 377
                                    79********655569********8......56*********99.787776..3336*********************** PP

                                    TTSSB.SSHHHHHHHHHHS-SS CS
                         SCP2_2  79 lgrie.gaeealatldalfpke 99 
                                    ++r++ ++++ l++lda+f + 
  gi|121638297|ref|YP_978521.1| 378 ANRLRtKDSQLLRRLDAAFASD 399
                                    *****555599********665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.7e-07     0.002      19      60 ..      83     124 ..      65     130 .. 0.88
   2 ?   -3.6   0.0       3.8   1.1e+04      18      41 ..     296     319 ..     289     321 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.7e-07
                                    -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE CS
                           FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllv 60 
                                    ++   l+ + v p+hrrrGl + + ++l ++ia  g+ v ++
  gi|121638297|ref|YP_978521.1|  83 LPTAGLSFVAVAPTHRRRGLLRAMCAELHRRIADSGYPVAAL 124
                                    567889******************************988776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.8
                                    E-TTSSEEEEEE-GGG-SSSHHHH CS
                           FR47  18 rkdggelgalqvlpehrrrGlgsr 41 
                                    r+dg  l  + v    + rG++  
  gi|121638297|ref|YP_978521.1| 296 RQDGLWLRIMNVPAALEARGYAHE 319
                                    555556667777777888888876 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-06    0.0089      25      96 ..      41     121 ..      20     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                    HHHHHSTTCEEEEEEET....TEEEEEEEEEEEET.......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                 Acetyltransf_1  25 eesfsleaegllvaeed....geliGfisllkipd.......ekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                    +++   +++g +v++++     e++G++ +            +  ++a + ++aV+p++r++Gl +a+  +l +r  + g
  gi|121638297|ref|YP_978521.1|  41 AWRTLVPTDGAVVVRDGagpgSEVVGMALYMDLRLtvpgevvL--PTAGLSFVAVAPTHRRRGLLRAMCAELHRRIADSG 118
                                    45555667777776666666688*****888877777777552..789999*************9999999988877777 PP

                                    ESE CS
                 Acetyltransf_1  94 ikk 96 
                                    +  
  gi|121638297|ref|YP_978521.1| 119 YPV 121
                                    654 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   9.6e-06     0.029      11      74 ..      57     137 ..      42     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.6e-06
                                    T....TEEEEEEEEEEES...........TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEEEEEETHHHHHHHHH CS
                 Acetyltransf_7  11 d....gkivGfialslld...........aeitrlaVdpeyrgkGiGraLlea...ae..kgiileqlelnaekaikfYe 70 
                                    +     ++vG++ ++ l            a + ++aV+p +r++G+ ra+ +    ++  +g+   ++ l+a    + Y 
  gi|121638297|ref|YP_978521.1|  57 GagpgSEVVGMALYMDLRltvpgevvlptAGLSFVAVAPTHRRRGLLRAMCAElhrRIadSGYP--VAALHA-SEGGIYG 133
                                    3555556667655555547777666666556666*****************8533411456633..223322.2255999 PP

                                    HTTE CS
                 Acetyltransf_7  71 klGF 74 
                                    ++G+
  gi|121638297|ref|YP_978521.1| 134 RFGY 137
                                    9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3013.37
//
Query:       gi|121638298|ref|YP_978522.1|  [L=280]
Description: hypothetical protein BCG_2433c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-72  241.8   0.0      1e-71  241.6   0.0    1.0  1  DegV      Uncharacterised protein, DegV family COG1307


Domain annotation for each model (and alignments):
>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.6   0.0   5.6e-76     1e-71       2     277 ..       3     272 ..       2     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.6 bits;  conditional E-value: 5.6e-76
                                    EEEEEEGGG---HHHHHHCTEEEE--EEEETTEEEECCTCCCHHHHHHHHHHTSS--EEE---HHHHHHHHHH.HHHTTT CS
                           DegV   2 iaIvtDStadlppelieklditvlplsviidgesyedgvdlspeelyeklakegelpkTsqpsvgeleelfek.llkegy 80 
                                    + +vtD+++ lp +l e++ i+++pl++ +dg +++dgvd  p++++++       ++T+  ++ el  ++++ l+ +g 
  gi|121638298|ref|YP_978522.1|   3 VVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRH------ATTAGATPVELSAAYQRaLADSGG 76 
                                    689***********************************999999988888......89**************999***** PP

                                    SEEEEEES-TTT-THHHHHHHHHHTSSTTCEEEEE-SS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTEEEEEEE CS
                           DegV  81 devlsltissklSgtfqsaklaaeeleekkvrvvDsksvsaglgllvleaarlakqGksfeeilkkleeikektklyfvv 160
                                    d v++++iss+lSgtf +a+l a el +  vrv+Ds+s+++g+g+++l+a r+a++G++++++++++++  ++++++++v
  gi|121638298|ref|YP_978522.1|  77 DGVVAVHISSALSGTFRAAELTAAEL-GPAVRVIDSRSAAMGVGFAALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAV 155
                                    **************************.***************************************************** PP

                                    S-THHHHHHTCCHHHHHHHCCCCTSEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHTTTSEEEEEEEECS-HHHHH CS
                           DegV 161 ddLdyLvkgGRiskaaallgslLkikpilkvedgeleplakvrgqkkaleklielikkdeeekkaervavlhagaeeeae 240
                                    ++Ld+L+++GRis+a+a+lg++L +kp+l+v+dg+l+++++vr+ ++a++ +i+ +  +  ++ ++ +av+h  ++ +a+
  gi|121638298|ref|YP_978522.1| 156 ARLDNLRRSGRISGAKAWLGTALALKPLLSVDDGKLVLVQRVRTVSNATAVMIDRV-CQLVGDRPAALAVHHVADPAAAN 234
                                    ******************************************************99.9********************** PP

                                    HHHHHHCCCSCTE.EEEEEE--HHHHHHH-TTEEEEEE CS
                           DegV 241 elkellkakveke.disiseigpvigvhvGpgalgvav 277
                                    ++++ l+++ +   +++++ +gpv++ hvG+ga+gv+v
  gi|121638298|ref|YP_978522.1| 235 DVAAALAERLPACePAMVTAMGPVLALHVGAGAVGVCV 272
                                    *************9**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1860.61
//
Query:       gi|121638299|ref|YP_978523.1|  [L=247]
Description: hypothetical protein BCG_2434c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-08   33.9   0.1    9.2e-08   32.7   0.1    1.5  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.015   15.3   0.0    1.2  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1     1e-11   9.2e-08       4     179 .]      16     226 ..      16     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1e-11
                                    SHHHHTCTTB.CCHCHHCCCCCCCHHHTT-EEEEE.EEHCCH-H.......HHHHHHHHCTGGG-TSEEEEE--CCC... CS
                  Lipase_GDSL_2   4 DSiTaGygad.gggrsypaylarllaarlgldvvnnlgvsGatt.....allrllerlrdllrlkpdlvtiliGtND... 74 
                                    DS+++ yg++ g +  +p+ +++ +a++l++d +   g  G+t      a+++ ++ + +l+r+ +  v++  G+ D   
  gi|121638299|ref|YP_978523.1|  16 DSLAY-YGPTgGLPADDPRIWPNIVASQLDWDLEL-IGRIGWTCrdvwwAATQDPRAWAALPRAGA--VIFATGGMDslp 91 
                                    89999.666667788888888**************.9*****998999988999999999999888..*********555 PP

                                    ............CCTT--HHHHHHH.....................................HHHHHHHHCCC...GEEE CS
                  Lipase_GDSL_2  75 ............lgrgvpaaaaaand...................................nleelidalraaapgaril 107
                                                +                                                 le+   a+    pg++i+
  gi|121638299|ref|YP_978523.1|  92 svlptalrelirY------------VrpswlrrwvrdgyawvqprlspvaraalpphltaeYLEKTRGAIDFNRPGIPII 159
                                    5555555555552............0444555555555777788888888888888844444444444555559999999 PP

                                    CEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-HHHHHHHCCCCCGGBBTTS.SSB-HHHHHH CS
                  Lipase_GDSL_2 108 vlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDlhdaladsgerladlladdglHPnaaGyrl 179
                                      + lp+++ a ++ +  +  +a   +a+ e+a+++++p+vDl  a+a++   l+ + ++dg+H n + +++
  gi|121638299|ref|YP_978523.1| 160 --ASLPSVHIAETYGKA-HHGRAGTVAAITEWAQHHDIPLVDLKAAVAEQI--LSGYGNRDGIHWNFEAHQA 226
                                    ..667777777766665.7799999******************88888877..677888999****999986 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.7e-06     0.015     149     199 ..     181     230 ..      72     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                    HHHHHHHHHHHHCTEEEECHHHHHHHTHCCGCHCHTSSSB-HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL 149 eynqrlndlaekdgfavvDlydelqglsgieqlkaDglHpsekgyeklael 199
                                      +  + + a+  ++++vDl     +    ++++ Dg+H++ ++++++ael
  gi|121638299|ref|YP_978523.1| 181 TVAA-ITEWAQHHDIPLVDLKAAVAEQILSGYGNRDGIHWNFEAHQAVAEL 230
                                    4444.778889*************99955555555**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1804.28
//
Query:       gi|121638300|ref|YP_978524.1|  [L=223]
Description: phosphoglycerate mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-49  168.5   1.1    1.5e-49  168.3   1.1    1.1  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.092   12.1   0.0       0.25   10.7   0.0    1.5  2  PALP        Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   1.1   1.7e-53   1.5e-49       1     192 [.       6     213 ..       6     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 1.7e-53
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS-- CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEi 80 
                                    l+++RHG+t++n+  r+qg+ d++L+e+Gr+qA a+ae l ++++  i+sS+l+Ra++Ta  ++e++gl v++d +LrE+
  gi|121638300|ref|YP_978524.1|   6 LVMLRHGQTDYNVGSRMQGQLDTELSELGRTQAVAAAEVLGKRQPLLIVSSDLRRAYDTAVKLGERTGLVVRVDTRLRET 85 
                                    689***************************************************************************** PP

                                    --GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSE........EEEEE-HHHHH CS
                     His_Phos_1  81 dfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarheget........vlvVsHggvir 152
                                    ++Gdw+glt+a+i+++ p +  aw++d    +p+ggEs  dvaaR ++ + el+a++++          v++V+Hgg+i 
  gi|121638300|ref|YP_978524.1|  86 HLGDWQGLTHAQIDADAPGARLAWREDAT-WAPHGGESRVDVAARSRPLVAELVASEPEWGgadepdrpVVLVAHGGLIA 164
                                    **********************9999988.58999********************99987777889999*********** PP

                                    HHHHHHHT--GGGGGGB--.-TT-EEEE........EE-SS-EEEEEEE CS
                     His_Phos_1 153 allarllglpleelrrlel.dnaslsvl........efdeggwrlvrln 192
                                    al a+ll+lp+++++ l    nas++ l        +f++ +wrl  +n
  gi|121638300|ref|YP_978524.1| 165 ALSAALLKLPVANWPALGGmGNASWTQLsghwapgsDFESIRWRLDVWN 213
                                    ***************99888********777777777777777777777 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.16   1.5e+03     239     263 ..      52      76 ..      19      89 .. 0.71
   2 ?   10.7   0.0   2.8e-05      0.25     118     180 ..     104     172 ..      91     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.16
                                    EEEEEEHHHHHHHHHHHHHHHSB-B CS
                           PALP 239 eivtvsdeealeamrllarregivv 263
                                     iv+ +   a++++++l +r+g+vv
  gi|121638300|ref|YP_978524.1|  52 LIVSSDLRRAYDTAVKLGERTGLVV 76 
                                    4666667777777777777777776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHSTTCEE--TTT..SHHHHHHHHTHHHHHH...HHTT..TTEEEEEEE-SSSHHHHHHHHHHHH CS
                           PALP 118 aaelaaegegaylvsqfd..nptviegygtiglEil...eqlg..gkpdavvvpvGgGgliaGiaaglke 180
                                     a+la + e+a+++++++   ++v +    +++E++    ++g  ++pd  vv v  Gglia+++a+l +
  gi|121638300|ref|YP_978524.1| 104 GARLAWR-EDATWAPHGGesRVDVAARSRPLVAELVasePEWGgaDEPDRPVVLVAHGGLIAALSAALLK 172
                                    4577777.888888888874455555599******98899999***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1437.69
//
Query:       gi|121638301|ref|YP_978525.1|  [L=127]
Description: hypothetical protein BCG_2436c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   86.3   0.1    1.8e-24   86.1   0.1    1.1  1  RsfS      Ribosomal silencing factor during starvation
  ------ inclusion threshold ------
      0.036   13.8   0.1      0.062   13.0   0.1    1.3  1  NETI      NETI protein


Domain annotation for each model (and alignments):
>> RsfS  Ribosomal silencing factor during starvation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.1     2e-28   1.8e-24       6      99 .]      17     108 ..      12     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2e-28
                                    HHHHTT-EEEEEEE-TTTTBSS-SEEEEEEESSHHHHHHHHHHHHHHHHHC.C-.--EEECBTTS.SEEEEE-SSEEEEE CS
                           RsfS   6 aledkkaedivvidlrekkssladymviatakserhlkalaeelekklkeeaae.alsveGlnegddWvlvdlgdvvVhl 84 
                                    a+ +k a d+vvid++  +  ++d++via++++er+++a+++e+e+k++++ ++ + + eG +eg +W+l+d+ d+vVh+
  gi|121638301|ref|YP_978525.1|  17 AAAAKLADDVVVIDVSG-QLVITDCFVIASGSNERQVNAIVDEVEEKMRQA-GYrPARREGAREG-RWTLLDYRDIVVHI 93 
                                    67789999*********.8******************************87.5568999***655.************** PP

                                    EECCCHHHHHHHHHC CS
                           RsfS  85 lteeaReeydLEelW 99 
                                     +++ R++y L++lW
  gi|121638301|ref|YP_978525.1|  94 QHQDDRNFYALDRLW 108
                                    *************** PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.9e-06     0.062      10      27 ..      56      73 ..      50      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                           NETI 10 IedcLeRmkkeGYmPvrR 27
                                   ++++ e+m+++GY+P rR
  gi|121638301|ref|YP_978525.1| 56 VDEVEEKMRQAGYRPARR 73
                                   788889***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 889.35
//
Query:       gi|121638302|ref|YP_978526.1|  [L=211]
Description: nicotinic acid mononucleotide adenylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-31  109.9   0.0    1.4e-31  109.6   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.18   11.0   0.0    1.3  1  HIGH_NTase1      HIGH Nucleotidyl Transferase
       0.14   12.0   0.0       0.21   11.4   0.0    1.3  1  DUF4863          Domain of unknown function (DUF4863)


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   2.3e-35   1.4e-31       3     143 .]       2     166 ..       1     166 [. 0.98

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 2.3e-35
                                    EE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH........ CS
                CTP_transf_like   3 gGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr........ 74 
                                    gGtFDpiH+GHl  + ++++l+++d +v+vps +p +k  + + +ae+R+ m+  a+ +++ +sv+  +++r        
  gi|121638302|ref|YP_978526.1|   2 GGTFDPIHYGHLVAASEVADLFDLDEVVFVPSGQPWQKG-RQVSAAEHRYLMTVIATASNPRFSVSRVDIDRggptytkd 80 
                                    9************************************86.***************************************9 PP

                                    ..HHHHHTTTT.EEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE..............HTTCEEEEEEECCTTTCSH CS
                CTP_transf_like  75 ..evlkklkpd.klylvigadvledfsewkeleeilgnvklvvvsrp..............ekqanvllkaekrtngiSs 137
                                        l+ l+pd +ly+  gad+l+++ +w+ +ee+++  ++v+vsrp              +  +  l++ e +   iSs
  gi|121638302|ref|YP_978526.1|  81 tlADLHALHPDsELYFTTGADALASIMSWQGWEELFELARFVGVSRPgyelrnehitsllgQLAKDALTLVEIPALAISS 160
                                    9999999999***************************************************9999999************ PP

                                    HHHHHH CS
                CTP_transf_like 138 tkirer 143
                                    t++r+r
  gi|121638302|ref|YP_978526.1| 161 TDCRQR 166
                                    ****97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.1e-05      0.18      10      46 ..       5      41 ..       4      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                    HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviavmSGnFvqRGe 46
                                   + P H GHl   +++  l++ d v+ v SG+  q+G 
  gi|121638302|ref|YP_978526.1|  5 FDPIHYGHLVAASEVADLFDLDEVVFVPSGQPWQKGR 41
                                   78*****************************999996 PP

>> DUF4863  Domain of unknown function (DUF4863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.21      48     118 ..      36     113 ..       8     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                        DUF4863  48 gWvaereidGakyrrgriikpseetkgfsvdvvemd.......eedlagqyHaHPyGEinlvvpldesaelkglegwq 118
                                     W   r++  a+ r+   + +++++  fsv  v++d       ++ la  +  HP  E+ +    d+ a++ + +gw+
  gi|121638302|ref|YP_978526.1|  36 PWQKGRQVSAAEHRYLMTVIATASNPRFSVSRVDIDrggptytKDTLADLHALHPDSELYFTTGADALASIMSWQGWE 113
                                    5777888888999999999999********************77788888889**************99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1499.93
//
Query:       gi|121638303|ref|YP_978527.1|  [L=90]
Description: hypothetical protein BCG_2438 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 654.09
//
Query:       gi|121638304|ref|YP_978528.1|  [L=348]
Description: hypothetical protein BCG_2439 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-10   39.7   0.1    2.2e-09   37.9   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    1.2e-08   34.9   0.0    1.8e-08   34.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-05   25.6   0.0    3.7e-05   24.3   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    1.8e-05   24.2   0.0    2.8e-05   23.6   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00015   21.4   0.0    0.00025   20.7   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00021   21.0   0.0    0.00032   20.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0007   19.4   0.1      0.011   15.6   0.0    2.5  2  DUF938           Protein of unknown function (DUF938)
     0.0035   17.2   0.0     0.0056   16.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.021   15.6   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      0.021   14.3   0.1      0.054   12.9   0.1    1.6  2  SAM_MT           Putative SAM-dependent methyltransferase
      0.022   13.8   0.0      0.032   13.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.13   11.7   0.0       0.22   11.0   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.5e-12   2.2e-09       1      96 [.     150     245 ..     150     245 .. 0.94
   2 ?   -3.1   0.0       9.2   1.4e+04      22      44 ..     271     287 ..     260     298 .. 0.51

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.5e-12
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEEST.GGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssga.lhhls 78 
                                    vL++G+GtGr++lala+r+  + v  v++++++ +++r+ ae+++l+v+++  d+ ++++   + + l+v+s +   + +
  gi|121638304|ref|YP_978528.1| 150 VLEIGAGTGRNALALARRG--HPVDVVEMTPKFADIIRSDAERDSLDVRVIMRDVfSTMDDLRQDYQLMVLSEVvPDFRT 227
                                    9*****************5..9********************************9777999999*******999777789 PP

                                    HHHHHHHHHHHHHHEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpg 96 
                                     ++l+++++ +a++L pg
  gi|121638304|ref|YP_978528.1| 228 TQQLRNLFELAAQCLAPG 245
                                    99**************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.2
                                    SEEEEEESSHHHHHHHHHHHHHT CS
                Methyltransf_25  22 akvtgvDiseemleaareraeee 44 
                                    + +tg+        +a+  a+++
  gi|121638304|ref|YP_978528.1| 271 QMYTGMC------TRAEMSAAAA 287
                                    4444444......4444444444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.2e-11   1.8e-08      19     124 ..     143     257 ..     107     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                     +++  rvL+iG+GtG+++  l+++g+ v++v++ p+  +i++                  d f  +  ++  + ++l+v
  gi|121638304|ref|YP_978528.1| 143 ADPTTHRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRsdaerdsldvrV---IMRDVF--STMDDLRQDYQLMV 217
                                    267778******************************9999999666666553331...222222..23355777****** PP

                Methyltransf_23  88 lrevlehvp...dppellrqiatllkpgGylllseplasl 124
                                    l+ev   ++    +  l+  +a++l+pg++l++  +la+ 
  gi|121638304|ref|YP_978528.1| 218 LSEVVPDFRttqQLRNLFELAAQCLAPGARLVFNAFLANG 257
                                    ****9888855468999999*************9998876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.5e-08   3.7e-05       1      96 []     151     250 ..     151     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.5e-08
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.T.SS-TT-EEEEEEES-CCC-...C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek.l.pfednsfDlvvssevlhhv...e 75 
                                    L++G+GtGr+a ala+rg+ v  v++++++ ++ ++ a+++ l v+++  d+ + +  ++   + l v+sev+  +   +
  gi|121638304|ref|YP_978528.1| 151 LEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAERDSLDVRVIMRDVFStMdDLRQ-DYQLMVLSEVVPDFrttQ 229
                                    89*****************************************999999999973434555.677777778877777889 PP

                                    CHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                    +++ +++ +a++L pg +lv+
  gi|121638304|ref|YP_978528.1| 230 QLRNLFELAAQCLAPGARLVF 250
                                    *****************9997 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   2.8e-05      32     130 ..     148     248 ..     137     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG-..---S-EEE.EEEESSGGGS CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydinea..klderydf.ilstvvlmfl 108
                                     +vl++g g grn+l l+  g+ v+ ++   +    +++ +e+++l+ ++  + d+ ++  +l ++y++ +ls vv  f 
  gi|121638304|ref|YP_978528.1| 148 HRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAERDSLD-VRVIMRDVFSTmdDLRQDYQLmVLSEVVPDFR 226
                                    479*******************************************9.999999998762256667764378******** PP

                                    -GGGHHHHHHHHHHTEEEEEEE CS
                           TehB 109 eaeripsiienmqectkvggyn 130
                                     ++++ ++ e   +c  +g   
  gi|121638304|ref|YP_978528.1| 227 TTQQLRNLFELAAQCLAPGARL 248
                                    *********9999999988643 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.7e-07   0.00025      28     136 ..     143     249 ..     128     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                                    HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTT..S-EEEEEE-. CS
                            MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleevee..kkfdlivsN. 104
                                     + ++++vl +G+G+G  ++ala++     v++v+   +  ++ +  +e+  l+v+v+ +dv++++++  ++++l+v   
  gi|121638304|ref|YP_978528.1| 143 ADPTTHRVLEIGAGTGRNALALARRGHP--VDVVEMTPKFADIIRSDAERDSLDVRVIMRDVFSTMDDlrQDYQLMVLSe 220
                                    4448899*****************8877..99999999999************************996225566666433 PP

                                    ..--STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 105 ..PPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                      P f++ ++      ++l++ A+++L++g +L+
  gi|121638304|ref|YP_978528.1| 221 vvPDFRTTQQ-----LRNLFELAAQCLAPGARLV 249
                                    5599999888.....999**********998875 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.1e-07   0.00032      41     145 ..     144     251 ..     130     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                           NodS  41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararerv.kesshiswivsdvqqf..stdekfdlivvaevly 117
                                    + +   +le+G  +G  +  la   + + vv++ ++  +  r    ++s ++  i+ dv     ++ + + l+v +ev+ 
  gi|121638304|ref|YP_978528.1| 144 DPTTHRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAeRDSLDVRVIMRDVFSTmdDLRQDYQLMVLSEVVP 223
                                    5566789***************************99766555544156679********7542357899*********** PP

                           NodS 118 yiedvaelraavrnlvsllapdgqlvfG 145
                                      +  ++lr   +   + lap+ +lvf 
  gi|121638304|ref|YP_978528.1| 224 DFRTTQQLRNLFELAAQCLAPGARLVFN 251
                                    ***************************6 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.4   5.1e+03     118     131 ..      47      60 ..      46      65 .. 0.81
   2 !   15.6   0.0   7.1e-06     0.011      20      50 ..     141     171 ..     133     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                         DUF938 118 saveglfagagell 131
                                     ++ glfag+g+ +
  gi|121638304|ref|YP_978528.1|  47 TMCAGLFAGVGRKF 60 
                                    589******99865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.1e-06
                         DUF938  20 sylakttervLEiasGtGqHAvffApalpnl 50 
                                    ++ + tt+rvLEi++GtG+ A  +A +  ++
  gi|121638304|ref|YP_978528.1| 141 EAADPTTHRVLEIGAGTGRNALALARRGHPV 171
                                    66788999*************9999875554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-06    0.0056       6     113 ..     149     254 ..     145     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevl 84 
                                    rvl++G+GtG+ +++la++  p   v  ++++++     r+ a++  ld v++   d+++ ++ l  ++ + l++  ev+
  gi|121638304|ref|YP_978528.1| 149 RVLEIGAGTGRNALALARRGHP---VDVVEMTPKFADIIRSDAERDSLD-VRVIMRDVFStMDDL--RQDYQLMVLSEVV 222
                                    89***************55333...666788888888888888888887.**********99975..478********** PP

                Methyltransf_31  85 ...naladpdkileeiervlkpggilliedpr 113
                                        ++  + + +e + + l pg +l+ + + 
  gi|121638304|ref|YP_978528.1| 223 pdfRTTQQLRNLFELAAQCLAPGARLVFNAFL 254
                                    99888888888899999999999999987665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.4e-05     0.021       1      99 []     151     248 ..     151     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    LeiG+GtG+++ al+++  +  + +v+  p++  d  +  a+r+ +++ ++  ++ +  d+   + + l v+s+v+  + 
  gi|121638304|ref|YP_978528.1| 151 LEIGAGTGRNALALARR--GHPVDVVEMTPKFA-DIIRSDAERDSLDVRVIMRDVFSTMDDLR-QDYQLMVLSEVVPDFr 226
                                    8****************..99999999999999.66666666666676666666666555444.59*********99998 PP

                Methyltransf_12  80 ..kdirevldnirklLkpgGrl 99 
                                      +++r +++ ++++L+pg+rl
  gi|121638304|ref|YP_978528.1| 227 ttQQLRNLFELAAQCLAPGARL 248
                                    8899999999*********986 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   2.1e+03      98     159 ..      41      98 ..      38     104 .. 0.60
   2 ?   12.9   0.1   3.6e-05     0.054      68     122 ..     143     197 ..     127     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                         SAM_MT  98 liErhpvvaaLLedglkRakqdaeigellaerlkLlaasslealakleeekpdvvYlDPmyP 159
                                    +i+    + a L  g+ R+ +d+e+++ l++ l+ + a+   a a+ ++++  + Y  Pm P
  gi|121638304|ref|YP_978528.1|  41 MIDEYVTMCAGLFAGVGRKFSDEELAH-LRAVLQGQLAE---AYAASQRSTIVISYNAPMGP 98 
                                    555566677777888999999998887.55544433333...33333333445556666655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                         SAM_MT  68 kkgvlptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRakqdaei 122
                                    ++ ++ +vl+  aG Gr a  la  G  v+++E  p  a +++   +R + d ++
  gi|121638304|ref|YP_978528.1| 143 ADPTTHRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAERDSLDVRV 197
                                    5556789********************************9999999998888764 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.032      32      87 ..     148     204 ..     136     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                                    SEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCG CS
                         RrnaAD  32 ltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflk 87 
                                      vleig+G+G     La r   v v+E+ +++a + +   + ++  + v+ +D+  
  gi|121638304|ref|YP_978528.1| 148 HRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAErDSLDVRVIMRDVFS 204
                                    68************************************9999777899999999854 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.22      54     160 ..     145     251 ..     134     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                Methyltransf_PK  54 revkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWiqWcvg 133
                                     +++++l++GaG Gr +   L +  + vD+ve + kf + ++++  +++  v+ ++   + +    ++ Y+l+    +v 
  gi|121638304|ref|YP_978528.1| 145 PTTHRVLEIGAGTGRNALA-LARRGHPVDVVEMTPKFADIIRSDAERDSLDVRVIMRDVFSTMDDLRQDYQLMVLSEVVP 223
                                    567899*********7765.6777899************99988888887777777777777777788888887777776 PP

                Methyltransf_PK 134 hL.tDedlvaflkrckkalkpnGlivvk 160
                                     + t ++l + ++ +++ l+p+  +v  
  gi|121638304|ref|YP_978528.1| 224 DFrTTQQLRNLFELAAQCLAPGARLVFN 251
                                    6536788888888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2423.59
//
Query:       gi|121638305|ref|YP_978529.1|  [L=230]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-23   81.1   0.0    8.5e-23   80.5   0.0    1.3  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   4.8e-27   8.5e-23       2      87 .]      66     152 ..      65     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 4.8e-27
                 Transposase_20   2 elLesipGiGpvtaaallaei.gdlrr.fksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                    el+ sipGiG   +a++++ei  d+   f+sa++la+++ l+p +++S++k++ ++ ++ Gn++l+ +L+e+A+aa+r++
  gi|121638305|ref|YP_978529.1|  66 ELIASIPGIGVGASATVISEIgADPAAwFPSAEHLASWVRLCPGNHESAGKRH-HGARRTGNQHLQPVLVECAWAAVRTD 144
                                    799******************8888556***********************98.889999******************** PP

                 Transposase_20  80 pelrayye 87 
                                      lr+yy+
  gi|121638305|ref|YP_978529.1| 145 GYLREYYR 152
                                    ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1552.61
//
Query:       gi|121638306|ref|YP_978530.1|  [L=97]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-06   28.3   0.0    1.6e-06   28.1   0.0    1.1  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   8.7e-11   1.6e-06      85     146 ..       5      65 ..       1      68 [. 0.91

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.7e-11
                 DEDD_Tnp_IS110  85 rklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrl 146
                                    ++ ++ ++KtD +DA+++ +ll   g lr    +++++ + r + r+r++lv+ rt+  +rl
  gi|121638306|ref|YP_978530.1|   5 AREERPGRKTDLLDAEWLVHLLE-CGLLRGWLIPPADIKAARDVIRYRRKLVEHRTSKLQRL 65 
                                    3567789***************9.********************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 742.30
//
Query:       gi|121638307|ref|YP_978531.1|  [L=480]
Description: hypothetical protein BCG_2442c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-65  218.2   1.5    1.5e-64  217.4   1.5    1.4  1  VWA_CoxE   VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.087   12.8   1.6       0.46   10.5   0.0    2.3  2  Trigger_C  Bacterial trigger factor protein (TF) C-terminus


Domain annotation for each model (and alignments):
>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.4   1.5   1.7e-68   1.5e-64       2     223 .]     253     473 ..     252     473 .. 0.97

  Alignments for each domain:
  == domain 1  score: 217.4 bits;  conditional E-value: 1.7e-68
                       VWA_CoxE   2 akklaalllglarrrrrrkrrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflall 81 
                                    ++ +a+l++ la+r   r+rr+r+++iDlr+tlr+++++gg +++lv++kpr ++p elv+l+DvSgS+a +s+++l l+
  gi|121638307|ref|YP_978531.1| 253 RRVVAPLARTLATRLAARRRRARAGSIDLRKTLRKSMSTGGVPIDLVLHKPRPARP-ELVVLCDVSGSVAGFSHFTLLLV 331
                                    6788887777777778888*************************************.*********************** PP

                       VWA_CoxE  82 hAllqqlprtevfaFdtrlvdlTral.rerDpaeaLarv..saavedlgGgTrigaalaeflelvtrpaLsrravvvlvs 158
                                    hAl+qq++r++vfaF +++ ++T+++  e+D+a a++r+  +a v++++G++++g+a+ +f++++  ++Ls+r+++++++
  gi|121638307|ref|YP_978531.1| 332 HALRQQFSRVRVFAFIDSTDEVTHMFgPESDLAIAIQRItrEAGVYARDGHSDYGNAFVSFMQGFP-NVLSPRSSLLVLG 410
                                    ***************************9***********99999**********************.************* PP

                       VWA_CoxE 159 Dglergdreellaelarlvrrarrlvwlnplsdagtpgydpe.aralrailphvdelrpleqlasl 223
                                    Dg ++++r+ +++ la++v+++r+++wlnp++++ ++++d++ +r++++i++h  e+r+++qla++
  gi|121638307|ref|YP_978531.1| 411 DG-RTNYRNPATDVLADMVTASRHAHWLNPEPKHLWGSGDSAvPRYQEVITMH--ECRSAKQLATV 473
                                    **.**************************************************..********986 PP

>> Trigger_C  Bacterial trigger factor protein (TF) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.1e-05      0.46      96     157 ..     115     176 ..     112     181 .. 0.77
   2 ?    0.7   0.6     0.052   4.6e+02      43     131 ..     207     235 ..     187     261 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.1e-05
                                    HHHHHHHHHHHTT----HHHHHHHHHHHCCCTTSXHHHHHHHHHHXHHHHHHHHHHHHHHHH CS
                      Trigger_C  96 lgLvleeiakeekievteeelkeeleelasqygmepeevkeflkkneqlsalkedileekvv 157
                                    ++L+l+ +a+++ +  ++e+l e++++++++yg+  +     +++ + l+a+  d le k++
  gi|121638307|ref|YP_978531.1| 115 RQLLLDLLANNQDLAGKDERLVEMIARIVEAYGKYSSSRGPSFSSYQALKAMALDELEGKLL 176
                                    79*******************************74444444444555666666666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.052
                                    HHHHHHHHHHHHHHHHHCT...TSSHHCHHHHHCTHCCCHCHHCHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                      Trigger_C  43 eslveeeidrllrqakqqleqqGldleeylelsgsseeelreelkeeAekrVklgLvleeiakeekievteeelkeelee 122
                                     ++v++e++r+ ++++ +                                                             e
  gi|121638307|ref|YP_978531.1| 207 RRMVDAETKRRTAEQLGR-------------------------------------------------------------E 225
                                    455555555555544432.............................................................2 PP

                                    HCCCTTS.XH CS
                      Trigger_C 123 lasqygm.ep 131
                                     +++yg+ + 
  gi|121638307|ref|YP_978531.1| 226 HVQMYGIpQL 235
                                    2233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2743.66
//
Query:       gi|121638308|ref|YP_978532.1|  [L=291]
Description: hypothetical protein BCG_2443c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-11   44.5   0.2      7e-11   42.3   0.2    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    3.1e-10   40.6   0.0    5.8e-10   39.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    5.6e-06   26.8   1.4    2.3e-05   24.9   0.7    2.2  2  AAA_16           AAA ATPase domain
    4.6e-05   23.6   0.0      8e-05   22.8   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    6.2e-05   23.3   0.0    0.00012   22.3   0.0    1.6  1  AAA_22           AAA domain
    0.00015   21.6   0.1       0.15   11.9   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
     0.0013   18.5   0.1       0.68    9.7   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0016   19.0   0.0     0.0034   17.9   0.0    1.6  1  AAA_18           AAA domain
     0.0028   16.7   0.0     0.0043   16.1   0.0    1.2  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.007   16.1   0.1       0.84    9.3   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0076   16.3   0.0      0.017   15.2   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0078   15.9   0.5      0.022   14.5   0.5    1.7  1  AAA_30           AAA domain
     0.0097   16.1   0.1      0.015   15.4   0.1    1.5  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.011   15.7   1.2      0.025   14.5   0.0    2.0  2  NACHT            NACHT domain
      0.021   14.2   0.1      0.047   13.1   0.0    1.5  2  IPT              Isopentenyl transferase
      0.039   13.9   0.0       0.25   11.3   0.0    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
       0.04   13.1   0.4       0.23   10.6   0.0    2.0  2  TIP49            TIP49 P-loop domain
      0.079   13.3   2.7       0.73   10.2   1.1    2.8  2  AAA_19           AAA domain
       0.13   12.0   0.3       0.26   11.0   0.0    1.6  2  IstB_IS21        IstB-like ATP binding protein
        0.2   11.7   0.0       0.85    9.7   0.0    2.0  1  AAA_14           AAA domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2   7.8e-14     7e-11       2     138 .]      46     194 ..      45     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 7.8e-14
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.......................--------... CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..............ngttslvdsplvraar... 64 
                                    +l+ Gp G+gK+ela+ +a+a+++ ++  q++++  e+  +++++ +                             +   
  gi|121638308|ref|YP_978532.1|  46 LLVEGPAGVGKTELARAVAQATGSGLVRLQCYEGVDEARALYEWNHAkqilriqagsgdweA--------------Tktd 111
                                    7999*****************************************98666666655444440..............3444 PP

                                    ...................G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--. CS
                          AAA_5  65 ...................egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldr 125
                                                       e+ +l++DE ++a+ e+ + Ll +l++  + ++e+g+l+  +++       v+ t+n  + 
  gi|121638308|ref|YP_978532.1| 112 vlseefllqrplltairrtEPTVLLIDETDKADIEIEGLLLEVLSDFAVTVPELGTLTATRAP------FVLLTSNATR- 184
                                    44445556666666666*****************************************99996......4778888888. PP

                                    -TT-TTHHHHTT- CS
                          AAA_5 126 slnelspalrsRf 138
                                       els+al++R+
  gi|121638308|ref|YP_978532.1| 185 ---ELSEALKRRC 194
                                    ...8999****96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   6.4e-13   5.8e-10       1     124 [.      46     194 ..      46     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 6.4e-13
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.............................STTHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.............................yvgesekkirelfk 51 
                                    +l+ Gp G+GKT la+ava+ +g+ ++++++ e +++                             +++e     r l++
  gi|121638308|ref|YP_978532.1|  46 LLVEGPAGVGKTELARAVAQATGSGLVRLQCYEGVDEaralyewnhakqilriqagsgdweatktdVLSEEFLLQRPLLT 125
                                    5899*******************************889*************************99999999999999999 PP

                                    HHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.........SSTEEEEEEESSGGGSTHHHHST CS
                            AAA  52 eakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.........eskvivigatnrpdkldpallrg 122
                                    ++++ + p++l+iDE d+              ++   Ll++l+++            ++  +v++++n  ++l++al r 
  gi|121638308|ref|YP_978532.1| 126 AIRRTE-PTVLLIDETDKAD-----------IEIEGLLLEVLSDFAVTvpelgtltaTRAPFVLLTSNATRELSEALKR- 192
                                    999998.***********93...........347999999999999999999999995557999999**********95. PP

                                    TS CS
                            AAA 123 Rf 124
                                    R+
  gi|121638308|ref|YP_978532.1| 193 RC 194
                                    65 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.7   2.5e-08   2.3e-05      25     150 ..      44     146 ..      31     161 .. 0.69
   2 ?   -1.1   0.0       2.4   2.1e+03     108     127 ..     203     230 ..     159     265 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.5e-08
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                      +l+ G++GvGK+ l+r+++ +++++   ++r +c +       +  a+al +    +q+l+   +a  ++w ++ +++
  gi|121638308|ref|YP_978532.1|  44 KPLLVEGPAGVGKTELARAVA-QATGS--GLVRLQCYEG------VDEARALYEWNHAKQILRI--QAGSGDWEATKTDV 112
                                    569******************.78877..3555555555......2233444444555555543..34678899988888 PP

                         AAA_16 105 laavpelagaeasrllellkrll.allsrderplvlvlDdlqwadea 150
                                    l+          + +l +  r l   ++r  +p+vl++D+ ++ad +
  gi|121638308|ref|YP_978532.1| 113 LS----------EEFLLQ--RPLlTAIRR-TEPTVLLIDETDKADIE 146
                                    88..........555444..444356666.567**********9965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                         AAA_16 108 vpelagaea........srllellkrll 127
                                    +pel++ +         ++++e+l r++
  gi|121638308|ref|YP_978532.1| 203 TPELERRILlsrvpelpEHFAEELVRII 230
                                    3333333333333333366666666666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     9e-08     8e-05       7     136 ..      47     189 ..      44     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9e-08
                                    EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS................ CS
                          AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG................ 70 
                                    l+ gp gvGktela+a+a+         l+r+ + e       ++ + +  +a++    ++ +G                
  gi|121638308|ref|YP_978532.1|  47 LVEGPAGVGKTELARAVAQATGS----GLVRLQCYEGVD---EARALYEWNHAKQILRIQAGSGdweatktdvlseefll 119
                                    789******************96....666666665555...34455555555555555555555666666666777777 PP

                                    ..............EEEEETGGG-------------HHHHHHHHHHHH--EE-.------EE-TT-EEEEEE--TTHHHH CS
                          AAA_2  71 ..............ivllDEidKihpkessgadvSregVqrdLLqileggtlt.dkqgrkvdtknilfImtgafgsskis 135
                                                  ++l+DE dK+             ++  +LL +l +  +t ++ g    t+   +++t++   +  +
  gi|121638308|ref|YP_978532.1| 120 qrplltairrteptVLLIDETDKADI-----------EIEGLLLEVLSDFAVTvPELGTLTATRAPFVLLTSNATRELSE 188
                                    77777777777888************...........**********999999778888899999999999998776655 PP

                                    T CS
                          AAA_2 136 d 136
                                     
  gi|121638308|ref|YP_978532.1| 189 A 189
                                    5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.4e-07   0.00012       7     113 ..      45     156 ..      40     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.4e-07
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka..........erlss 75 
                                     l+v G++G+GKT l+r +++           ++++v+ ++ ++  + + l+++   +  l+  a            ls+
  gi|121638308|ref|YP_978532.1|  45 PLLVEGPAGVGKTELARAVAQAT---------GSGLVRLQCYEGVdEARALYEWNHAKQILRIQAgsgdweatktDVLSE 115
                                    6899******************9.........***********9998888876654444444444459999998888888 PP

                         AAA_22  76 eell.ealeqalraravielliiDEaqhlr...seealeeLr 113
                                    e ll + l  a+r++    +l+iDE ++ +   +  +le L+
  gi|121638308|ref|YP_978532.1| 116 EFLLqRPLLTAIRRTEP-TVLLIDETDKADieiEGLLLEVLS 156
                                    88888888888888888.*********986543333444333 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00017      0.15       2      32 ..      46      76 ..      45      83 .. 0.93
   2 !    7.4   0.1    0.0043       3.8      64     111 ..     133     181 ..     110     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                          AAA_3  2 vllegvPGlaktllvkalakaldlefkriqf 32
                                   +l+eg  G++kt l++a+a+a +  + r+q+
  gi|121638308|ref|YP_978532.1| 46 LLVEGPAGVGKTELARAVAQATGSGLVRLQC 76
                                   699**************************97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0043
                          AAA_3  64 nllladeinrappktqsalleameerqvtvege.thklpepflvlatqn 111
                                     +ll de ++a   ++  lle++ +  vtv +  t +  +  +vl t n
  gi|121638308|ref|YP_978532.1| 133 TVLLIDETDKADIEIEGLLLEVLSDFAVTVPELgTLTATRAPFVLLTSN 181
                                    589**************************97641444444455566666 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00076      0.68      36      59 ..      46      69 ..      35      82 .. 0.88
   2 !    6.4   0.0    0.0077       6.9      79     115 ..     124     162 ..     105     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00076
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                   +l+ Gp G+Gkt la+ +a+  g+
  gi|121638308|ref|YP_978532.1| 46 LLVEGPAGVGKTELARAVAQATGS 69
                                   6899***************98876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0077
                         RuvB_N  79 ltnleekd..vlfideihrlsraveevlysamedfrldi 115
                                    lt +++++  vl+ide  + + ++e +l   + df++ +
  gi|121638308|ref|YP_978532.1| 124 LTAIRRTEptVLLIDETDKADIEIEGLLLEVLSDFAVTV 162
                                    5555544333*************************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.8e-06    0.0034       2      56 ..      47     102 ..      46     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedk 56 
                                    l+ G++GvGKt+la+++++ +g+     ++ + + e + l+e++++  ++ +r++ + 
  gi|121638308|ref|YP_978532.1|  47 LVEGPAGVGKTELARAVAQATGSglvRLQCYEGVDEARALYEWNHA--KQILRIQAGS 102
                                    699****************998887777777777888888888887..6666665554 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.8e-06    0.0043      37      71 ..      48      82 ..      20      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                          AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncsdqldy 71
                                   ++Gpag GKtE  + +a+a +  +v ++c +++d 
  gi|121638308|ref|YP_978532.1| 48 VEGPAGVGKTELARAVAQATGSGLVRLQCYEGVDE 82
                                   68*****************************9986 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00093      0.84      23      46 ..      44      67 ..      29      82 .. 0.80
   2 ?    4.4   0.0      0.03        27      90     152 ..     128     193 ..     124     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00093
                                   S-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat 23 lsvlitGesGtGKellaraiheas 46
                                    ++l++G  G+GK+ lara+ +a+
  gi|121638308|ref|YP_978532.1| 44 KPLLVEGPAGVGKTELARAVAQAT 67
                                   789****************98754 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
                                    HHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE..SBTSSS.EEE--EEEEEEESS-HHHHHHTT CS
                Sigma54_activat  90 ekadgGtlfLDeigelplelQekLlrvlqegeve..rvGssk.eikvdvriiaatnedleeaveeg 152
                                    ++++  +l++De  + ++e+   Ll+vl +  v+   +G+ + ++   v + + ++++l+ea++++
  gi|121638308|ref|YP_978532.1| 128 RRTEPTVLLIDETDKADIEIEGLLLEVLSDFAVTvpELGTLTaTRAPFVLLTSNATRELSEALKRR 193
                                    5667789*********************98654422899855156666777778888998888764 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.017       9      45 ..      33      69 ..      26      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  9 algkklakalgdvilLeGdLGaGKTtlvrglakalgv 45
                                   a +  la+ lg+ +l eG+ G+GKT l+r++a+a g 
  gi|121638308|ref|YP_978532.1| 33 ATAVFLADRLGKPLLVEGPAGVGKTELARAVAQATGS 69
                                   4556677777889********************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.5   2.5e-05     0.022      22     111 ..      47     154 ..      35     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                         AAA_30  22 vltGpAGtGKttalkalreaweaag.........grviglAptgkaAkvLaeelgi...eastiakllkrlk......gr 83 
                                    +++GpAG GKt + +a+++a  +            +  +l   + a + L+ ++g    ea  ++ l ++         +
  gi|121638308|ref|YP_978532.1|  47 LVEGPAGVGKTELARAVAQATGSGLvrlqcyegvDEARALYEWNHAKQILRIQAGSgdwEATKTDVLSEEFLlqrpllTA 126
                                    79***************999886535666666554455555555555556655553334444444444333366688855 PP

                         AAA_30  84 arlepgtllivDEagmvdtkqlaallka 111
                                     r ++ t+l++DE+  +d++    ll+ 
  gi|121638308|ref|YP_978532.1| 127 IRRTEPTVLLIDETDKADIEIEGLLLEV 154
                                    6666779999999998887765555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-05     0.015       3      32 ..      47      78 ..      46     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklg..avllssdt 32
                                   l+ G++G+GK+ la+ +++++g   v+l   +
  gi|121638308|ref|YP_978532.1| 47 LVEGPAGVGKTELARAVAQATGsgLVRLQCYE 78
                                   789******************98766665444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.8e-05     0.025       2      27 ..      45      70 ..      44      79 .. 0.88
   2 ?   -0.8   0.2       1.4   1.2e+03      78      94 ..     128     144 ..     103     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                   +++++G+aG+GKT L++ +a+a  +g
  gi|121638308|ref|YP_978532.1| 45 PLLVEGPAGVGKTELARAVAQATGSG 70
                                   689*****************987665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                    CSCCCEEEEEE-STT-S CS
                          NACHT  78 elperlLlilDglDelv 94 
                                    ++ e ++l++D  D++ 
  gi|121638308|ref|YP_978532.1| 128 RRTEPTVLLIDETDKAD 144
                                    45566667777777654 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.047       5      40 ..      47      79 ..      44      85 .. 0.89
   2 ?   -2.9   0.0       4.1   3.7e+03      41      84 ..      98     140 ..      94     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                            IPT  5 lifGatttGKtaeaiklaketgapvivlDRvqcyse 40
                                   l+ G+ ++GKt+ a ++a++tg  ++   R+qcy+ 
  gi|121638308|ref|YP_978532.1| 47 LVEGPAGVGKTELARAVAQATGSGLV---RLQCYEG 79
                                   678*******************9977...8999975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.1
                            IPT  41 lavgsGrpleeelegtrRiylddrslseGvidaeeanerLikev 84 
                                    +  gsG   + + + +   +l +r+l   +    e   +Li+e 
  gi|121638308|ref|YP_978532.1|  98 IQAGSGDWEATKTDVLSEEFLLQRPLLTAIRR-TEPTVLLIDET 140
                                    66788888888888888888888888765433.33444555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.25      21     189 ..      44     199 ..      37     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksk 100
                                    +++++ Gp g+GKt L + +++   + +   + +   ++++++++       +e + +++ l i+ ++   e+   +   
  gi|121638308|ref|YP_978532.1|  44 KPLLVEGPAGVGKTELARAVAQATGS-G--LVRLQCYEGVDEARAL------YEWNHAKQILRIQAGSGDWEATKTDVLS 114
                                    688999************99999833.2..2333333333322222......2344445555555555555333223334 PP

                       ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvv....iclsSeglfiervyn 176
                                    + f     ll +i+++    +++iDe  k+  + ++  +ll++ L ++ +  ++   l+      ++l+S+         
  gi|121638308|ref|YP_978532.1| 115 EEFLLQRPLLTAIRRT-EPTVLLIDETDKAD-IEIE--GLLLEVLSDFAVTVPELGTLTATrapfVLLTSNATREL---- 186
                                    4344444444555444.55889999999988.6666..88888888888887776666655555455566543333.... PP

                       ATPase_2 177 eselegrhkyilv 189
                                    +  l+ r+ y+++
  gi|121638308|ref|YP_978532.1| 187 SEALKRRCLYLHI 199
                                    3345556666555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00026      0.23      50      76 ..      43      69 ..      33      78 .. 0.89
   2 ?    0.1   0.0      0.41   3.7e+02     279     299 ..     132     152 ..     127     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 50 GravLlaGpsgtGktalaiaiskelge 76
                                   G+ +L+ Gp+g Gkt la a++++ g+
  gi|121638308|ref|YP_978532.1| 43 GKPLLVEGPAGVGKTELARAVAQATGS 69
                                   79********************99886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.41
                                    XXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 279 pGvlfiDevhmlDiecfsyln 299
                                    p vl iDe+   Die+   l 
  gi|121638308|ref|YP_978532.1| 132 PTVLLIDETDKADIEIEGLLL 152
                                    78*************876665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00082      0.73      10     126 ..      43     155 ..      33     166 .. 0.64
   2 ?   -0.8   0.0         2   1.8e+03      43      63 ..     171     191 ..     158     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00082
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllteale 89 
                                     k+llv +++G GKT++ +++ +   +   +   +++      rA  e + + + l  +a         + +d l    e
  gi|121638308|ref|YP_978532.1|  43 GKPLLVEGPAGVGKTELARAVAQATGSGLVR--LQCYEGVDEARALYEWNHAKQILRIQAGSGDWE--ATKTDVL--SEE 116
                                    6899************999888877776644..788888888888888888776666664443322..2222222..222 PP

                         AAA_19  90 lleeaeeekklqeee..llivDEfqdvdelqyrLlkall 126
                                    +l ++   + ++++e  +l++DE+   d  +  Ll ++l
  gi|121638308|ref|YP_978532.1| 117 FLLQRPLLTAIRRTEptVLLIDETDKADIEIEGLLLEVL 155
                                    333333333333333348889999999866666666655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                         AAA_19  43 eeillvaftgrAakelrerla 63 
                                     +   v +t+ A++el+e+l+
  gi|121638308|ref|YP_978532.1| 171 TRAPFVLLTSNATRELSEALK 191
                                    55667788999******9984 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.26      49      70 ..      45      66 ..      28      82 .. 0.87
   2 ?   -3.4   0.1       7.4   6.6e+03     107     134 ..     130     155 ..     124     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                      IstB_IS21 49 nivllGpsGvGKshlaialgve 70
                                    +++ Gp+GvGK+ la a++++
  gi|121638308|ref|YP_978532.1| 45 PLLVEGPAGVGKTELARAVAQA 66
                                   57889**************987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfevi 134
                                    +++++l++D+    +++   + ll+ev+
  gi|121638308|ref|YP_978532.1| 130 TEPTVLLIDETDKADIEI--EGLLLEVL 155
                                    567899999986655543..34555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00095      0.85       3      76 ..      44     143 ..      42     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00095
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell.....................vkkesilyinldderdkkladpekllelilek.. 59 
                                    k+l+++G+  vGKT l++ +++                         ++++il i+  + + ++ ++    +e++l++  
  gi|121638308|ref|YP_978532.1|  44 KPLLVEGPAGVGKTELARAVAQATGsglvrlqcyegvdearalyewNHAKQILRIQAGSGDWEATKTDVLSEEFLLQRpl 123
                                    899****************9988876666666666644444444444444444444444333332211111223333232 PP

                         AAA_14  60 lke....ekktylflDEiqev 76 
                                    l +     + t+l++DE  ++
  gi|121638308|ref|YP_978532.1| 124 L-TairrTEPTVLLIDETDKA 143
                                    1.1355567777788877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.65u 0.40s 00:00:01.05 Elapsed: 00:00:00.57
# Mc/sec: 1540.80
//
Query:       gi|121638309|ref|YP_978533.1|  [L=415]
Description: gamma-glutamyl phosphate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-21   75.1  10.5    1.6e-13   50.0   6.2    2.4  2  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.05   13.6   6.4      0.022   14.7   2.5    2.0  2  CHAD      CHAD domain


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   6.2   1.8e-17   1.6e-13      28     304 ..      12     301 ..       5     306 .. 0.81
   2 !   26.9   0.1   1.9e-10   1.7e-06     376     461 ..     316     404 ..     314     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.8e-17
                                    HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH......HHHHHHHHHHHHH CS
                         Aldedh  28 aedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara......eveeaidvlryya 101
                                    +++v++a ++A+ a ++ a+lp + + + L++aad l ++++++ ++ + +     + a++       ++   + ++ +a
  gi|121638309|ref|YP_978533.1|  12 RQEVHDAARRARVAARRLASLPTTVKDRALHAAADELLAHRDQILAANAEDLNAARE-ADTpaamldRLSLNPQRVDGIA 90 
                                    5799****************************************9998888764332.2221110012222233334444 PP

                                    HHHHHHSEEE...EEEC........TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHH CS
                         Aldedh 102 elaeklegev...lpss........egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsal 170
                                    + +++++g        +        +g +   +r PlGvvg+I  ++   ++++ ++   l  GN+ +l+ ++ ++ s  
  gi|121638309|ref|YP_978533.1|  91 AGLRQVAGLRdpvG--EvlrgytlpNGLQLRQQRVPLGVVGMI--YEGRPNVTVDAFGLTLKSGNAALLRGSSSAAKSNE 166
                                    44444444222331..1333444657889999999********..89********************************* PP

                                    HHHHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TT.ESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-.--EEEEE CS
                         Aldedh 171 llaelfeea....glPkgvlnvvtgsgsevgealvehpe.vdkvsftGstevgrkiakaaaknlkrvtlElG.Gknpliv 244
                                    +l+ +++ a    +lP++++++++  ++ +  +l+++++ vd+v   G+    + +++ a+      t+E+G G+ ++ v
  gi|121638309|ref|YP_978533.1| 167 ALVAVLRTAlvglELPADAVQLLSAADRATVTHLIQARGlVDVVIPRGGAGLIEAVVRDAQ----VPTIETGvGNCHVYV 242
                                    *********99999************99999999988764899999************999....45788885777888* PP

                                    -TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTST CS
                         Aldedh 245 ledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplde 304
                                    ++ aDld a + ++++ ++    vC aa+ llv   i++  + +l++a++   v  +ld+
  gi|121638309|ref|YP_978533.1| 243 HQAADLDVAERILLNSKTR-RPSVCNAAETLLVDAAIAETALPRLLAALQHAGVTVHLDP 301
                                    ******9988888887776.568**************************99888777776 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.9e-10
                                    EEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB-.-..CGGGEES.-BSHHH CS
                         Aldedh 376 svikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfg.G..vkqSglG.reggke 451
                                    +v  ++ ++ ai+  N+   G + +++t++l+ a+r++e+++a  v++N st+++  +  fg G  ++ S    + +g+ 
  gi|121638309|ref|YP_978533.1| 316 AVAVVDGVDAAIAHINEYGTGHTEAIVTTNLDAAQRFTEQIDAAAVMVNASTAFTDGE-QFGfGaeIGISTQKlHARGPM 394
                                    6888999********************************************9999888.554121122333335556666 PP

                                    HHHHTEEEEE CS
                         Aldedh 452 gleeytevkt 461
                                    gl e t +k+
  gi|121638309|ref|YP_978533.1| 395 GLPELTSTKW 404
                                    6666666665 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.5   2.5e-06     0.022      20      79 ..      14      80 ..       6     203 .. 0.77
   2 ?    0.6   0.1     0.053   4.7e+02      50     121 ..     227     295 ..     215     368 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-06
                                   --THHHHHHHHHHHHHHHHHHHTTTSS....-HHHHHHHHHHHHHHHHHHHHHHHHHH...HHHTHH CS
                           CHAD 20 edpeavHqmRvalRRlRsalrlfapvl....dkeeaaalekelrwlaraLGeaRDldV...llerll 79
                                   e  +a +++Rva RRl s+ +++++       +e  a+ ++ l+  a+ L++aR +d    +l+rl 
  gi|121638309|ref|YP_978533.1| 14 EVHDAARRARVAARRLASLPTTVKDRAlhaaADELLAHRDQILAANAEDLNAAREADTpaaMLDRLS 80
                                   44699*****************987776764555556666889999***********9776666654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.053
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH.HTS-TTTCGGGHHHHHHHHHHHHHHHHHHHHHHTSHHH CS
                           CHAD  50 eaaalekelrwlaraLGeaRDldVllerllsrleerlpaaeqealerllkrlekerkrararvlaaLdsary 121
                                    ++ ++e+ +++      +a DldV +  ll+    +   +  +a e ll +++ + ++a +r+laaL++a  
  gi|121638309|ref|YP_978533.1| 227 QVPTIETGVGNCHVYVHQAADLDVAERILLNSK--TRRPSVCNAAETLLVDAAIA-ETALPRLLAALQHAGV 295
                                    444444444444444445556666544444443..33333334444554444444.3445555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.60
# Mc/sec: 2077.98
//
Query:       gi|121638310|ref|YP_978534.1|  [L=195]
Description: alkyl hydroperoxide reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-32  111.2   0.0    4.3e-32  110.6   0.0    1.3  1  AhpC-TSA   AhpC/TSA family
    7.6e-14   51.7   0.0    8.8e-14   51.4   0.0    1.1  1  Redoxin    Redoxin
     0.0016   18.3   0.0     0.0031   17.4   0.0    1.4  1  SCO1-SenC  SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   7.2e-36   4.3e-32       1     123 [.       6     146 ..       6     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 7.2e-36
                                    TTSB----EEE...............STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEE CS
                       AhpC-TSA   1 vgdkapdfelk...............nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigv 65 
                                    +gd++p  +l+                  ++t++ ++  gk+ v+ff+pkd+++vC+te+ a++kl++ef++r+++++gv
  gi|121638310|ref|YP_978534.1|   6 IGDQFPAYQLTaliggdlskvdakqpGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGV 85 
                                    5667777776666666666665444355689***9999****************************************** PP

                                    ESSSCHHHHHHHHH-H.....SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  66 svdspeshkkfiekes....lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                    s+ds+++h ++ ++++    l+fp+lsD ++++++a gvl+ + g+a r tf++d++  i++
  gi|121638310|ref|YP_978534.1|  86 SIDSEFAHFQWRAQHNdlktLPFPMLSDIKRELSQAAGVLNAD-GVADRVTFIVDPNNEIQF 146
                                    ****************************************998.***************996 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.5e-17   8.8e-14      10     138 ..      14     155 ..       5     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.5e-17
                                    E.............CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH. CS
                        Redoxin  10 t.............lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf. 75 
                                    +              ++  +  ++++ +e +gk  vv+f+p  f+ +C +e+ ++ kl++++++++ ++++v++d++   
  gi|121638310|ref|YP_978534.1|  14 QltaliggdlskvdAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAh 93 
                                    55555555555555333447889999999**********************************************98765 PP

                                    .HHHHHHH..TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                        Redoxin  76 .vkefwgk..eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                     + ++  +  + l+fp+lsD + ++++a G+     +++g++ + ++++d ++ +  +   + +++
  gi|121638310|ref|YP_978534.1|  94 fQWRAQHNdlKTLPFPMLSDIKRELSQAAGVL----NADGVADRVTFIVDPNNEIQFVSATAGSVG 155
                                    5555555599999*****************66....677889999999999999999988877765 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.2e-07    0.0031      13      68 ..      37      90 ..      32      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-07
                      SCO1-SenC 13 avteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPe 68
                                   ++t+++  gk+ +vff     + vCpt++a  +++ d+++++  + q+l +++D e
  gi|121638310|ref|YP_978534.1| 37 TITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDR--DAQILGVSIDSE 90
                                   6899999**********9999*******************99..999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1079.96
//
Query:       gi|121638311|ref|YP_978535.1|  [L=177]
Description: alkyl hydroperoxide reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-14   51.6   0.2    7.2e-14   51.6   0.2    1.9  2  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6      0.11     2e+03      68      81 ..      59      73 ..      40      79 .. 0.59
   2 !   51.6   0.2     4e-18   7.2e-14       9      83 ..     101     174 ..      95     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.11
                                   HHHHSHHHHH.HHHH CS
                            CMD 68 aayagwpaar.aAla 81
                                   a ++ ++aar aAl 
  gi|121638311|ref|YP_978535.1| 59 ATDHLSAAARhAALG 73
                                   344444555534443 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 4e-18
                                    HHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHH CS
                            CMD   9 alreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaa 83 
                                     lr++++a ++g++++  eL ++avsa+ngc +C+ aH   ++  Gv++e i e+l  aa+ +g+++a+a  +a+
  gi|121638311|ref|YP_978535.1| 101 GLRMNIIA-NPGIPKANFELWSFAVSAINGCSHCLVAHEHTLRTVGVDREAIFEALKAAAIVSGVAQALATIEAL 174
                                    57899999.788********************************************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1005.88
//
Query:       gi|121638312|ref|YP_978536.1|  [L=194]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-50  170.8   0.1    2.8e-50  170.5   0.1    1.1  1  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   0.1   1.6e-54   2.8e-50       1     156 [.       5     159 ..       5     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 1.6e-54
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEvnsa++yaGpg++++laAa+aW++L  e+++++++++++l +l+ +aW Gp  +++++aa p+++WL+  + q +
  gi|121638312|ref|YP_978536.1|   5 AYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLM-DAWAGPVVMQLMEAAKPFVRWLTDLCVQLS 83 
                                    68***********************************************.****************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaa 156
                                    e+ +q++ ++ aYe A++ mvp+a+i +nrae++ l+ +n +Gq t++Ia++++ey+++w +d ++m++Y+  ++ 
  gi|121638312|ref|YP_978536.1|  84 EVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNALGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSD 159
                                    **********************************************************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1074.86
//
Query:       gi|121638313|ref|YP_978537.1|  [L=99]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-24   84.8   8.8    4.3e-24   84.6   8.8    1.0  1  PE             PE family
  ------ inclusion threshold ------
      0.033   14.7   5.6       0.03   14.8   4.7    1.4  1  EspB_PE        ESX-1 secreted protein B PE domain
      0.036   14.5   3.0      0.046   14.2   3.0    1.2  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   8.8   7.2e-28   4.3e-24       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 7.2e-28
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Peal+ aa+++ +i+++  + +a++a++ttav ++aaD VS ++A+++ ++a++y++  a aa ++e+f++al++
  gi|121638313|ref|YP_978537.1|  1 MSFVITNPEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTT 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +a++Ya+aEa
  gi|121638313|ref|YP_978537.1| 83 GADKYATAEA 92
                                   *********8 PP

>> EspB_PE  ESX-1 secreted protein B PE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.7   5.1e-06      0.03       3      74 ..      21      91 ..      19      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                                   HHHHHHHCTS----------.-SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        EspB_PE  3 LrarAaeleaplpeppsavpqaPdgLelakaaveqLnasAealrkylaageaErerLAesLrnaAkaYeevD 74
                                   +r rA + +a+++++++av+ +P +  ++++a++ L  +A++ r+++aa++   e  A++L   A+ Y  ++
  gi|121638313|ref|YP_978537.1| 21 IRDRAIQSDAQVAPMTTAVR-PPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTGADKYATAE 91
                                   789999****9998888888.777777899999***********************************8765 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.0   7.7e-06     0.046       8      94 ..       7      94 ..       1      98 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaaagasaavldshG.picaatndavaaaeaarraagealaaasteLadkLraAAaaYe 88
                                   +p++l  +a++++++ +++ ++ a +a+ ++av +     ++ + ++ + ++ +  r++++a a +++e+a+ L++ A+ Y 
  gi|121638313|ref|YP_978537.1|  7 NPEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAAdLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTGADKYA 88
                                   79999999999999999999999999999999998766145555666678999****************************9 PP

                  T7SS_ESX_EspC 89 atDeea 94
                                    ++ ++
  gi|121638313|ref|YP_978537.1| 89 TAEADN 94
                                   998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 575.96
//
Query:       gi|121638314|ref|YP_978538.1|  [L=136]
Description: hypothetical protein BCG_2451c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 757.70
//
Query:       gi|121638315|ref|YP_978539.1|  [L=96]
Description: hypothetical protein BCG_2452c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 526.14
//
Query:       gi|121638316|ref|YP_978540.1|  [L=481]
Description: hypothetical protein BCG_2453c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-41  140.4   0.0    9.5e-41  139.6   0.0    1.4  1  MS_channel    Mechanosensitive ion channel
    9.5e-14   51.2   0.1    1.6e-13   50.5   0.1    1.4  1  cNMP_binding  Cyclic nucleotide-binding domain
  ------ inclusion threshold ------
        1.5    9.3   6.7          3    8.3   5.0    2.2  2  DUF4491       Domain of unknown function (DUF4491)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.0   1.6e-44   9.5e-41       3     205 ..     117     310 ..     115     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.6e-44
                                    HHHHHHHHHHHHHHHHTTT--.SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                     MS_channel   3 ilkiliivvgilivlsllgvn.vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                    + ++ +i +g+ ++ls+++   v+ l+a+lG++++++gl+l++++ ++v+G+++lfe+pf+i+D++e+++++G+V+++++
  gi|121638316|ref|YP_978540.1| 117 VARFALIGIGLAVILSYIWGVrVGGLFAALGVTSVVIGLMLQNSVGQIVSGLFMLFEQPFRIDDWLETPTARGRVVEVNW 196
                                    6799*************97665********************************************************** PP

                                    SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEE CS
                     MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvld 161
                                    r+++i t +g + ++Pns+l+t++++Nlsr  ++  +++si+ t+s++ + ++kv+ +l++a++  p+v+    + vv  
  gi|121638316|ref|YP_978540.1| 197 RAVHIDTGSG-LQIMPNSMLATTAFTNLSR--PAGAHECSITTTFSTS-DPPDKVCAMLNRAASALPHVK----PGVVPA 268
                                    **********.9******************..****************.99******************9....8***** PP

                                    EE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT-- CS
                     MS_channel 162 efgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegie 205
                                    +++  + +++ +v +++  p++   +q+ + ++++++ ++eg++
  gi|121638316|ref|YP_978540.1| 269 TIARGAAEYRTTVRLTS--PADEGPTQATFLRWVWYAARREGLH 310
                                    *****************..***********************98 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.1   2.7e-17   1.6e-13       2      88 ..     353     438 ..     352     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.7e-17
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    +++  +e++ ++G  + ++ +v+ G+vr++ +++dg  v +a+l++G ++G  al + +p +a +vAl++++ l++ r++
  gi|121638316|ref|YP_978540.1| 353 VRYGTDEIVQHAGVVPMGITFVIAGSVRLTVTTDDGSVVAIATLKKGTFLGLTALTR-QPDPAGAVALEEVTALQIGREH 431
                                    689999*********99***********************************99999.********************** PP

                                    HHHHHHH CS
                   cNMP_binding  82 flellqq 88 
                                    +++++++
  gi|121638316|ref|YP_978540.1| 432 LEQVVMN 438
                                    ***9986 PP

>> DUF4491  Domain of unknown function (DUF4491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.45   2.7e+03       4      33 ..      14      44 ..      12      69 .. 0.71
   2 ?    8.3   5.0   0.00051         3       5      62 ..     113     168 ..     110     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.45
                        DUF4491  4 Gliigiat.fliiglfhpivikaeyylgkki 33
                                   G++ig+ + ++++  +h i+++ + +l+++ 
  gi|121638316|ref|YP_978540.1| 14 GIAIGLPAgLIVLTELHNILVRRNSHLARQA 44
                                   8899986515566779999999998887664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                        DUF4491   5 liigiatfliiglfhpivikaeyylgkkiwwvflvagillivaslfvenvllsavlgv 62 
                                    +++ +a f +ig++  +++   y +g ++  +f  +g++ +v+ l+++n +   v g+
  gi|121638316|ref|YP_978540.1| 113 IFVDVARFALIGIGLAVIL--SYIWGVRVGGLFAALGVTSVVIGLMLQNSVGQIVSGL 168
                                    6788999******987765..7***************************997776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2655.41
//
Query:       gi|121638317|ref|YP_978541.1|  [L=730]
Description: cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-36  126.1   0.0      5e-35  120.8   0.0    2.2  2  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    3.2e-18   65.9   0.1    1.4e-17   63.8   0.1    2.2  1  HAMP           HAMP domain
     0.0031   17.0   0.3     0.0052   16.3   0.3    1.3  1  HNOBA          Heme NO binding associated
  ------ inclusion threshold ------
       0.27   11.1   1.8        6.6    6.6   0.1    2.4  2  DUF4307        Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        64       4      48 ..      81     123 ..      78     132 .. 0.88
   2 !  120.8   0.0   1.1e-38     5e-35       3     173 ..     550     719 ..     548     727 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                  Guanylate_cyc   4 esydevtilFadIvgftalssahspievvklLnelyarfdellde 48 
                                     +++ v  lF+d+ ++  ++++  +  vv+++    a fd+l+d+
  gi|121638317|ref|YP_978541.1|  81 SQKRAVETLFSDLTNSLVIYER--GLTVVDAVVRFTAGFDQLADA 123
                                    56788999*******9999995..6****************9986 PP

  == domain 2  score: 120.8 bits;  conditional E-value: 1.1e-38
                  Guanylate_cyc   3 aesydevtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaela 82 
                                    a+++++vt+lFadI g  ++ss  s+ e+vk++ el+ +fd+ +++ +v++++t+ + y++ +g+++++ +++ + +++a
  gi|121638317|ref|YP_978541.1| 550 AQEHQDVTVLFADILGVDEISSGLSGNELVKIVDELVRQFDSAAEHLGVERIRTLHNGYLAGCGVTTPRLDNIPRTVDFA 629
                                    699***************************************************************************** PP

                  Guanylate_cyc  83 LdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellkeeqfel 162
                                    L+m   ++ ++ ++ ++l++rvGi+tG v++g++G++   yd+wG +v lA +m s + +  i v++++ye  + + +++
  gi|121638317|ref|YP_978541.1| 630 LEMRRIVDRFNCQTGNDLHLRVGINTGDVISGLVGRSSVVYDMWGAAVSLAYQMHSGSPQPGIYVTSQVYEAMR-DVWQF 708
                                    *************************************************************************9.9**** PP

                  Guanylate_cyc 163 tergevevkGk 173
                                    t+ g ++v G 
  gi|121638317|ref|YP_978541.1| 709 TAAGTISVGGL 719
                                    ********993 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1     3e-21   1.4e-17       1      52 [.     462     513 ..     462     514 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3e-21
                                    HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    l+a++++rP+rrL+  +++i+aGd+++ +pv++rDEiG+L +afN+M+++L+
  gi|121638317|ref|YP_978541.1| 462 LIAHAMVRPIRRLEVGTQKISAGDYEVNIPVKSRDEIGDLTAAFNEMSRNLQ 513
                                    69*************************************************8 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.2e-06    0.0052     185     220 ..     506     541 ..     495     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                          HNOBA 185 eeksaeLeesmkeleeekkrtdeLLysmiPkevAer 220
                                    +e s++L+++ + l+e++k  d+LL sm+P+ v er
  gi|121638317|ref|YP_978541.1| 506 NEMSRNLQTKEELLNEQRKENDRLLLSMMPEPVVER 541
                                    67899****************************987 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.017        76       4      34 ..      39      69 ..      37      81 .. 0.80
   2 ?    6.6   0.1    0.0015       6.6       6      57 ..     445     496 ..     442     500 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.017
                        DUF4307  4 llvillvvlvvvalalvawigysqgsadvsa 34
                                    l++ll++  +v +a++a i+y++g+++ +a
  gi|121638317|ref|YP_978541.1| 39 KLMVLLLLTSIVSVAAIAAIVYQSGRTSLRA 69
                                   5788899999999999999999997766655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                        DUF4307   6 villvvlvvvalalvawigysqgsadvsaevvgfevvddstvevtfeVtrdd 57 
                                    ++l++v ++v+++++ +++ +    +++  +vg + +++   ev++ V+++d
  gi|121638317|ref|YP_978541.1| 445 LVLVTVGIIVVICVASMLIAHAMVRPIRRLEVGTQKISAGDYEVNIPVKSRD 496
                                    455555555555655566666699*********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4636.09
//
Query:       gi|121638318|ref|YP_978542.1|  [L=304]
Description: ribokinase rbsK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-54  185.6   5.4    1.7e-53  181.9   5.4    1.9  1  PfkB             pfkB family carbohydrate kinase
  ------ inclusion threshold ------
       0.45   10.4   5.0       0.74    9.7   0.6    2.5  2  Transglut_core3  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   5.4   1.9e-57   1.7e-53       3     301 ..      15     288 ..      13     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 1.9e-57
                                    EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEET CS
                           PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtd 80 
                                    +v+v+G++++dl  v+++l  +ge+v ++++++++GG+gaN+Ava+ar ga+v+f ga GdD+++++l+++l+++ v  d
  gi|121638318|ref|YP_978542.1|  15 RVCVVGSVNMDLTFVVDALprPGETVLAASLTRTPGGKGANQAVAAARAGAQVQFSGAFGDDPAAAQLRAHLRANAVGLD 94 
                                    79****************************************************************************** PP

                                    TEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE CS
                           PfkB  81 yvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt 160
                                    +++ +++ + g+a+ivvd+ +e+t+++ +ga+a+lt+ +     +++++ d+l        e+p+a+  ++a aa+++++
  gi|121638318|ref|YP_978542.1|  95 RTVTVPG-PSGTAIIVVDASAENTVLVAPGANAHLTPVP-----SAVANCDVLLTQL----EIPVATALAAARAAQSADA 164
                                    ***9999.**********99*****************76.....5999999998876....******************* PP

                                    EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEE CS
                           PfkB 161 fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdge 240
                                    ++++  +p+g++ ++ l++l a ad++++ne+E+  + + +                   +++v+tlG++Ga +v  dg+
  gi|121638318|ref|YP_978542.1| 165 VVMVNASPAGQD-RSSLQDLAAIADVVIANEHEANDWPSPP-------------------THFVITLGVRGARYVGADGV 224
                                    **********98.***************************9...................58****************** PP

                                    EEEEE.SSSS-SBGTTHHHHHHHHHHHHHHT....THHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                           PfkB 241 lkvpavpkvkvvDttGAGDsfvggflaalle....gksleealrfanavAalvvqkkgaiaslpt 301
                                    ++vpa p v++vDt GAGD f+g ++a++ +     ++  +alr+a+a++ l++  +ga++++p+
  gi|121638318|ref|YP_978542.1| 225 FEVPA-PTVTPVDTAGAGDVFAGVLAANWPRnpgsPAERLRALRRACAAGVLATLVSGAGDCAPA 288
                                    *****.*************************99665666689*******************9986 PP

>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3     0.021   1.9e+02       9      45 ..     154     190 ..     147     198 .. 0.72
   2 ?    9.7   0.6   8.3e-05      0.74      24      75 ..     249     302 ..     234     304 .] 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.021
                Transglut_core3   9 lrlarlglarlrarlreaprgarpasaeearrlgrav 45 
                                    ++++  + a +   ++++p+g++++s +++++++++v
  gi|121638318|ref|YP_978542.1| 154 AAARAAQSADAVVMVNASPAGQDRSSLQDLAAIADVV 190
                                    3444455555666777888888********9999887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 8.3e-05
                Transglut_core3  24 reaprgarpasaeearrlgravra..aarllpgrskCLpralalalllrrrgip 75 
                                    +++ ++++ ++ae++r+l+ra++a  +a l+ g+ +C p a a+ + lr+++++
  gi|121638318|ref|YP_978542.1| 249 AANWPRNPGSPAERLRALRRACAAgvLATLVSGAGDCAPAAAAIDAALRANRHN 302
                                    44445556777777777777776533778999999***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2283.52
//
Query:       gi|121638319|ref|YP_978543.1|  [L=139]
Description: hypothetical protein BCG_2456 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-11   44.7   0.4    1.7e-11   44.4   0.4    1.1  1  PEMT      Phospholipid methyltransferase
    4.4e-11   43.0   0.1      6e-11   42.6   0.1    1.2  1  ICMT      Isoprenylcysteine carboxyl methyltransferase (ICMT)
     0.0013   18.3   0.1     0.0014   18.2   0.1    1.1  1  DUF1295   Protein of unknown function (DUF1295)
  ------ inclusion threshold ------
      0.014   14.9   0.8      0.016   14.7   0.8    1.2  1  NnrU      NnrU protein
      0.056   14.0   1.1       0.13   12.9   0.2    1.8  2  DUF2627   Protein of unknown function (DUF2627)


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.4   4.8e-15   1.7e-11       5     101 ..      22     116 ..      18     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.8e-15
                           PEMT   5 lGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvll 84 
                                    +G++   +g++ ++ +  a+g+      d   +++++lv++G+++++++P y+++++  lGl L+t ++++l+  +l+++
  gi|121638319|ref|YP_978543.1|  22 AGIIPATAGIAATVYAQLAMGDSWRIGVDE--QENTTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFILLVA 99 
                                    466667777777777777777776666665..7777******************************************** PP

                           PEMT  85 vylialkfvEephlaki 101
                                    +  + +++vEep+l + 
  gi|121638319|ref|YP_978543.1| 100 TLEVHVRRVEEPYLLRT 116
                                    *************9876 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   1.7e-14     6e-11       8      92 ..      30     113 ..      21     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.7e-14
                           ICMT   8 aqalrlvvmatlGeiwttrvailpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvalllfvRik. 86 
                                    + a  +++   +G++w   v  +++++lv++g++k++rHP Y++  +++ +  lLl+ + l+al  ++l ++ l v ++ 
  gi|121638319|ref|YP_978543.1|  30 GIAATVYAQLAMGDSWRIGVDEQENTTLVRTGPFKWVRHPIYTA--MMAFGLGLLLVTPNLVALAGFILLVATLEVHVRr 107
                                    667778888999********************************..6777777888999999999999999999855541 PP

                           ICMT  87 eEekaL 92 
                                     Ee +L
  gi|121638319|ref|YP_978543.1| 108 VEEPYL 113
                                    466555 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.8e-07    0.0014     117     199 ..      16     101 ..       3     128 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-07
                        DUF1295 117 lkaldviglalwlvgivlealaDq...QlsafkkdpankgkvldsGLwrysRHPNYfgealiWwglflialealegleal 193
                                    + +++v+g++ +  gi++ ++a       ++   d + ++ ++++G +++ RHP Y + + + +gl+l++ + ++ + ++
  gi|121638319|ref|YP_978543.1|  16 MVWIQVAGIIPATAGIAATVYAQLamgDSWRIGVDEQENTTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFI 95 
                                    55666666666655555555554411144555667788889****************************99987776666 PP

                        DUF1295 194 aiagpl 199
                                    ++++ l
  gi|121638319|ref|YP_978543.1|  96 LLVATL 101
                                    666533 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.8   4.6e-06     0.016      84     150 ..      35     103 ..       5     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                           NnrU  84 laaallpgnplsvglka....dlaetgivritrHPmllgvaiWAlaHllanGdlasvllfgglllwalvgv 150
                                    ++a l+ g    +g ++    +l +tg ++++rHP+ ++++   l+ ll+ ++l ++   g +ll a ++v
  gi|121638319|ref|YP_978543.1|  35 VYAQLAMGDSWRIGVDEqentTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVAL--AGFILLVATLEV 103
                                    233333333333333335577899**************************9998654..555555555554 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.83     3e+03      37      53 ..      16      31 ..       5      35 .. 0.66
   2 ?   12.9   0.2   3.6e-05      0.13      22      61 ..      57      96 ..      54      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.83
                        DUF2627 37 slwlqflaGlllfaigl 53
                                    +w+q +aG++ + +g+
  gi|121638319|ref|YP_978543.1| 16 MVWIQ-VAGIIPATAGI 31
                                   44665.46777777776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                        DUF2627 22 lmrdalfgilsspfsslwlqflaGlllfaiglgfiaGfil 61
                                   l+r   f+ + +p+ ++++ f +Glll+   l  +aGfil
  gi|121638319|ref|YP_978543.1| 57 LVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFIL 96
                                   677888999999999************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1063.72
//
Query:       gi|121638320|ref|YP_978544.1|  [L=679]
Description: NAD synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-23   82.0   0.0    4.9e-23   81.5   0.0    1.2  1  NAD_synthase  NAD synthase
    2.1e-16   60.1   0.0    3.1e-16   59.5   0.0    1.2  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   5.4e-27   4.9e-23       5     166 ..     347     520 ..     343     554 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.4e-27
                                    HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHH.....TCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                   NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkal.....gkenvlalllPssvsseedvedalalaenlgievkti 79 
                                     v  l++ ++  +  +vv+G+SGG+DS+ +  +a +a+      +  +la  lP+  + e+ +++a++la  lg+ + +i
  gi|121638320|ref|YP_978544.1| 347 QVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMdregrPRSDILAFALPGFATGEHTKNNAIKLARALGVTFSEI 426
                                    5778999*******************************7776556789******************************** PP

                                    --HHHHHHHHHHHHHHH......-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-T.TTTT--SBETTT CS
                   NAD_synthase  80 dikpivrafeqelkeak......edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTk.yGDgaadlapia 152
                                    di ++ r + +++ +         d++ +N++a +R   l+ ian+ + +vlgTg+ sEl++G+ T   GD     +  a
  gi|121638320|ref|YP_978544.1| 427 DIGDTARLMLHTIGHPYsvgekvYDVTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYgVGDQMSHYNVNA 506
                                    *********99665544455555999***************************************964799999999999 PP

                                    TS-HHHHHHHHHHT CS
                   NAD_synthase 153 ellKtevkeLakel 166
                                    ++ Kt +++L +++
  gi|121638320|ref|YP_978544.1| 507 GVPKTLIQHLIRWV 520
                                    99999999999875 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   3.4e-20   3.1e-16       1     257 [.      13     280 ..      13     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.4e-20
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHB..HSSSHHHHHHHHHHHHHTEEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAe..aglgetlallaalarkngiav 78 
                                    rvA++  +++  d +an + +l+++++  + ga L v+PEl + gy+ e+  l+ +   a++ ++l+l+ + a +  +++
  gi|121638320|ref|YP_978544.1|  13 RVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLldAVEDALLDLVTESA-DLLPVL 91 
                                    79****99999***********************************555555554447666667777666665.566888 PP

                                    EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS..................-SS.S- CS
                   CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfep..................gdg.ip 139
                                    v+g + r  +  ++  yntav++ ++   +g   K+ L    p+  +++er  + p                   d  ++
  gi|121638320|ref|YP_978544.1|  92 VVGAPLR--HRHRI--YNTAVVIHRGAV-LGVVPKSYL----PTYREFYERRQMAPgdgergtiriggadvafgTDLlFA 162
                                    8999999..99***..*******66555.7*******8....56677777777777888888888888888884444888 PP

                                    EEEETTEEEEEEEGGGGGSHHHHHH.HHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCET CS
                   CN_hydrolase 140 vfdtpvgkiGaaiCyeigfpellra.lalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeql 218
                                      d+p+  + ++iC++++ p    a  al ga +l nls ++p +  ++++ ++l+  a a ++  +v aa+  g     
  gi|121638320|ref|YP_978544.1| 163 ASDLPGFVLHVEICEDMFVPMPPSAeAALAGATVLANLS-GSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGE-STT 240
                                    8888888****************999***********44.89**********************************.888 PP

                                    TEEEE--EEEE-TTS-EEEECCSSSTEE..EEEEEEHHHHH CS
                   CN_hydrolase 219 ilwpvghSaiidpdGrilaglgeeeegv..liaeidladvr 257
                                    +l   g+++i+  +G +la+  ++ +gv  ++a++d +++r
  gi|121638320|ref|YP_978544.1| 241 DLAWDGQTMIW-ENGALLAESERFPKGVrrSVADVDTELLR 280
                                    88888999998.59*************64488999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 5156.56
//
Query:       gi|121638321|ref|YP_978545.1|  [L=92]
Description: hypothetical protein BCG_2458 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 651.08
//
Query:       gi|121638322|ref|YP_978546.1|  [L=376]
Description: gamma-glutamyl kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-37  127.7   3.5    9.5e-37  126.9   3.5    1.4  1  AA_kinase  Amino acid kinase family
      4e-16   58.7   3.2      8e-16   57.8   0.3    2.7  3  PUA        PUA domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   3.5   1.1e-40   9.5e-37       3     238 ..      15     239 ..      13     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 1.1e-40
                                    EEEEE-TTCCCCTCC....HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                      AA_kinase   3 vVvKlGGssltdkee....aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                    +VvK+G ++lt++++     +l  lae +++ +++g ++v+V++g ++++g+  l  gls+++++            +at
  gi|121638322|ref|YP_978546.1|  15 LVVKVGTTALTTPSGmfdaGRLAGLAEAVERRMKAGSDVVIVSSG-AIAAGIEPL--GLSRRPKD------------LAT 79 
                                    6**********99999*****************************.*********..*******9............89* PP

                                    HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE CS
                      AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrg 158
                                    ++a+as+g+  + + ++a+++ +g ++ ++++t+ ++   s ++   + ++++ +l +   v ++++++++ +++   +g
  gi|121638322|ref|YP_978546.1|  80 KQAAASVGQVALVNSWSAAFARYGRTVGQVLLTAHDI---SMRVQHTNAQRTLDRLRALHAVAIVNENDTVATNEIR-FG 155
                                    *************************************...777777777777777777799******9988877775.9* PP

                                    -HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.....CSSS.TTTHHHHCHHHHHHHHHCT CS
                      AA_kinase 159 ssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.....saselatgGmkvkhpaalaaarrg 233
                                    ++D+++al+A+++gAd l++l+d+dG+yd+dp+k  da+ +pe+s    ++      +s+l+tgGm +k+ aal aa  g
  gi|121638322|ref|YP_978546.1| 156 DNDRLSALVAHLVGADALVLLSDIDGLYDCDPRKTADATFIPEVSGPADLDgvvagRSSHLGTGGMASKVSAALLAADAG 235
                                    ********************************************88777777***************************9 PP

                                    T-EEE CS
                      AA_kinase 234 gipvv 238
                                     +pv 
  gi|121638322|ref|YP_978546.1| 236 -VPVL 239
                                    .9986 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.29   2.6e+03      27      48 ..      43      62 ..      39      66 .. 0.70
   2 ?   -0.5   0.0      0.13   1.2e+03      30      45 ..     131     146 ..     126     154 .. 0.80
   3 !   57.8   0.3   8.9e-20     8e-16       1      70 [.     281     351 ..     281     355 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.29
                                   EETT--TTSEEEEEETTSCEEE CS
                            PUA 27 vegdfeegdvVaivdedgelva 48
                                   ve   ++g  V+iv+    ++a
  gi|121638322|ref|YP_978546.1| 43 VERRMKAGSDVVIVSS--GAIA 62
                                   6677788888888887..4444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.13
                                    T--TTSEEEEEETTSC CS
                            PUA  30 dfeegdvVaivdedge 45 
                                     +++   Vaiv+e+++
  gi|121638322|ref|YP_978546.1| 131 RLRALHAVAIVNENDT 146
                                    5788899*****9764 PP

  == domain 3  score: 57.8 bits;  conditional E-value: 8.9e-20
                                    CEEEE-HHHHHHHHT.T-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEE CS
                            PUA   1 grvvvddgAvkalls.gasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksvei 70 
                                    g++++d+gAv+a+++ ++sLla+G++ v g f  gdvV++ ++d   va+G++ y+++ela++ g+ + e+
  gi|121638322|ref|YP_978546.1| 281 GALTLDAGAVRAVVRqRRSLLAAGITAVSGRFCGGDVVELRAPDAAMVARGVVAYDASELATMVGRSTSEL 351
                                    6899***********999*********************************************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2667.14
//
Query:       gi|121638323|ref|YP_978547.1|  [L=479]
Description: GTPase ObgE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-51  173.7   5.7    2.7e-51  173.2   5.7    1.2  1  GTP1_OBG     GTP1/OBG
    6.7e-25   86.8   0.0      1e-24   86.2   0.0    1.3  1  DUF1967      Domain of unknown function (DUF1967)
    1.4e-21   76.7   0.0    2.6e-21   75.8   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    1.6e-07   31.0   0.0    4.6e-07   29.5   0.0    1.7  2  FeoB_N       Ferrous iron transport protein B
     0.0027   17.6   0.0       0.11   12.5   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.035   13.6   0.0       0.17   11.3   0.0    2.0  1  Arf          ADP-ribosylation factor family


Domain annotation for each model (and alignments):
>> GTP1_OBG  GTP1/OBG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   5.7     9e-55   2.7e-51       1     155 []       5     158 ..       5     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 9e-55
                                    EEEEEEEEE----------BEEETTCCCEEB-S--------EEEEE-TT--SSGCCCTSSEEE-------BTTTB----- CS
                       GTP1_OBG   1 vdevkikvkaGkGGdGcvsfrrekyvpkggpdGGdGGkGGdvileadeklntlldlkykkkikAenGenGkgknksGkkg 80 
                                    vd+v i+ +aG+GG+Gc+s++rek++p+ggpdGG+GG+GG++++++d++++tlld++++++++A +G++G+g+n++G+ g
  gi|121638323|ref|YP_978547.1|   5 VDRVVIHTRAGSGGNGCASVHREKFKPLGGPDGGNGGRGGSIVFVVDPQVHTLLDFHFRPHLTAASGKHGMGNNRDGAAG 84 
                                    79****************************************************************************** PP

                                    --EEEEESTTEEEEETTTTEEEEEE-STT-EEEEE-----EE-GGGC-CSSCSS--EEEE-----EEEEEEEECS CS
                       GTP1_OBG  81 kdlvikvPvgtvvkdeetgevladltedgeevlvakGGkgGkGnaafksstnraprfaekGeegeereleLelkl 155
                                    +dl +kvP gtvv d e+g++ladl  +g+++ +a+GG+gG+Gnaa++s+ ++ap fa  Ge+g++r+l+Lelk+
  gi|121638323|ref|YP_978547.1|  85 ADLEVKVPEGTVVLD-ENGRLLADLVGAGTRFEAAAGGRGGLGNAALASRVRKAPGFALLGEKGQSRDLTLELKT 158
                                    **************7.8899*****************************************************95 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   3.5e-28     1e-24       1      70 []     366     434 ..     366     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.5e-28
                                    ..EE.EEETTEEEEE-HHHHHHHTTEEE-TGGGHHHHHHHHHHTTHHHHHHTTT--TT-EEEETTEEEE- CS
                        DUF1967   1 ftiekkdeegvfvVeGekierlvkqtnfeneeavrrfarrLkklGvedaLrkaGakeGdtVrIgdveFey 70 
                                    ft+e  d +g fvV+G+++er++ qtnf+n+eav+++a+rL++lGve++L ++Ga+ G  V+Ig+++F++
  gi|121638323|ref|YP_978547.1| 366 FTVE-PDGHGGFVVSGARPERWIDQTNFDNDEAVGYLADRLARLGVEEELLRLGARSGCAVTIGEMTFDW 434
                                    8999.9999************************************************************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   8.7e-25   2.6e-21       1      95 [.     161     264 ..     161     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 8.7e-25
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adli 79 
                                    +v++vG p +GKS+L++a++ +k +++d+p+tT+ +n g v+ +++ ++++D+pGli gas+++glg +fl+++e + ++
  gi|121638323|ref|YP_978547.1| 161 DVGLVGFPSAGKSSLVSAISAAKPKIADYPFTTLVPNLGVVSAGEHAFTVADVPGLIPGASRGRGLGLDFLRHIErCAVL 240
                                    599***************************************888***************************9998**** PP

                                    EEEEETT.........TTCSHHHHH CS
                       MMR_HSR1  80 llvvdas.........eeklkplde 95 
                                    ++vvd++         + ++++l+ 
  gi|121638323|ref|YP_978547.1| 241 VHVVDCAtaepgrdpiS-DIDALET 264
                                    *****996555433321.2333333 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.5e-10   4.6e-07       3      89 ..     162     247 ..     160     252 .. 0.88
   2 ?   -2.0   0.0      0.78   2.3e+03     107     150 ..     286     329 ..     282     332 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.5e-10
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHC.TSSSE CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflle.eepdv 81 
                                    v lvG p +Gk++l+ a++ ak k++ +p +t   + g ++  ++ +++ D+PG   +   s+   +  dfl + e+  v
  gi|121638323|ref|YP_978547.1| 162 VGLVGFPSAGKSSLVSAISAAKPKIADYPFTTLVPNLGVVSAGEHAFTVADVPGL--IPGASRGRGLGLDFLRHiERCAV 239
                                    789**************************************999**********7..67788888888888875367888 PP

                                    EEEEEEGG CS
                         FeoB_N  82 vvnvvdat 89 
                                    +v+vvd +
  gi|121638323|ref|YP_978547.1| 240 LVHVVDCA 247
                                    88888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.78
                                    SEEEEEETHHHHHHTTEE.E-HHHHHHHHTS-EEEEBTTTTBTHH CS
                         FeoB_N 107 pvvlalnmideaekkgie.idlkkLsekLgvpvvktsakkkegie 150
                                    p  ++ln+id+ e++++     + ++ + g pv  +s++++e+++
  gi|121638323|ref|YP_978547.1| 286 PRAVVLNKIDVPEARELAeFVRDDIA-QRGWPVFCVSTATRENLQ 329
                                    56789999999887775403334443.346777777666666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.041   1.2e+02      92     121 ..     151     181 ..     138     189 .. 0.74
   2 !   12.5   0.0   3.5e-05      0.11      50      99 ..     288     337 ..     282     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.041
                                    HHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +l+ +lk    + lvG   +GKS+L+ a+  
  gi|121638323|ref|YP_978547.1| 151 DLTLELKTvADVGLVGFPSAGKSSLVSAISA 181
                                    5555555544456899999*******99876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.5e-05
                                    EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                     +vlnKiD+ e +e +e +++++++ g +v++vs+ t+e+l+ l   l++
  gi|121638323|ref|YP_978547.1| 288 AVVLNKIDVPEARELAEFVRDDIAQRGWPVFCVSTATRENLQPLIFGLSQ 337
                                    69************999999*********************999877765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.8e-05      0.17      19     174 ..     164     338 ..     151     339 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                    EEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-....SSGGGGGGGGGGCTTES...EEEEE CS
                            Arf  19 llGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvG....GqeklRplWknYfektd...avifv 88 
                                    l+G  +aGK+ ++  ++  + +       T+ +n   ++  +  ftv Dv     G ++ R l  +++++++   ++++v
  gi|121638323|ref|YP_978547.1| 164 LVGFPSAGKSSLVSAISAAKPKIadyPFTTLVPNLGVVSAGEHAFTVADVPglipGASRGRGLGLDFLRHIErcaVLVHV 243
                                    7899999999999988765543322256699999999999999999999852333678889988887766542228999* PP

                                    EETT-CT.......THHHHHHHHH....HHCTSG...CCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEE CS
                            Arf  89 vDsadre.......RleeakeeLk....alleee...elkevallvlaNKqDlpealseeelrellgleelkgkrkleiq 154
                                    vD+a  e        ++  ++eL+    +l  +    +l+  +  v+ NK+D+pea + +e       +++  +r + ++
  gi|121638323|ref|YP_978547.1| 244 VDCATAEpgrdpisDIDALETELAcytpTLQGDAalgDLAARPRAVVLNKIDVPEARELAEF----VRDDIA-QRGWPVF 318
                                    **99877453333346667777762221222233111344667899********99877765....456788.99***** PP

                                    EEBTTTTBTHHHHHHHHHHH CS
                            Arf 155 kcsavkgeglkeglewlses 174
                                     +s+ ++e+l+  +  ls++
  gi|121638323|ref|YP_978547.1| 319 CVSTATRENLQPLIFGLSQM 338
                                    *******9999887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3632.23
//
Query:       gi|121638324|ref|YP_978548.1|  [L=86]
Description: 50S ribosomal protein L27 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-35  120.6   4.7    2.3e-35  120.5   4.7    1.0  1  Ribosomal_L27  Ribosomal L27 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L27  Ribosomal L27 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   4.7   1.3e-39   2.3e-35       1      79 []       2      80 ..       2      80 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 1.3e-39
                  Ribosomal_L27  1 AhkkagGstkngrdskgkrlGvKkfggqlvkagnIivrQrgtkfhpGenvgiGkdhtlfAlvdGvVkfekkkkrkyvsv 79
                                   Ahkk+++s++ngrds+++rlGvK++ggq+vkag+I+vrQrgtkfhpG nvg+G d+tlfA+++G V+f  k+ rk+vs+
  gi|121638324|ref|YP_978548.1|  2 AHKKGASSSRNGRDSAAQRLGVKRYGGQVVKAGEILVRQRGTKFHPGVNVGRGGDDTLFAKTAGAVEFGIKRGRKTVSI 80
                                   9********************************************************************999****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.54
# Mc/sec: 481.25
//
Query:       gi|121638325|ref|YP_978549.1|  [L=104]
Description: 50S ribosomal protein L21 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-33  113.3   6.2    6.3e-33  113.0   6.2    1.0  1  Ribosomal_L21p  Ribosomal prokaryotic L21 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L21p  Ribosomal prokaryotic L21 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   6.2   3.5e-37   6.3e-33       2     101 .]       5     103 ..       4     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.5e-37
                                    EEEEECSTEEEEESSSEEEEEESSSSSTTCEEEESSEEE....EE.ECTSSSESSTCEEEEEEEEEE---EEEEEEETTT CS
                 Ribosomal_L21p   2 yAiietgGkqykVeegdvlkvekleaevgdkveldkVllvgskddvkvGaplvegakVeaevvehgkgkkiivfkkkrrk 81 
                                    yAi++tgGkqykV+ gdv+kvekle e+g+kv+l  V lv +  +v+++a++++++ V++ev+ h+kg+ki+++k+k+++
  gi|121638325|ref|YP_978549.1|   5 YAIVKTGGKQYKVAVGDVVKVEKLESEQGEKVSL-PVALVVDGATVTTDAKALAKVAVTGEVLGHTKGPKIRIHKFKNKT 83 
                                    9*********************************.566667778899********************************* PP

                                    TEEEEEEE--EEEEEEEEEE CS
                 Ribosomal_L21p  82 nyrrkqghRqkytklrItkI 101
                                    +y+++qghRq++t+l++t+I
  gi|121638325|ref|YP_978549.1|  84 GYHKRQGHRQQLTVLKVTGI 103
                                    ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 710.07
//
Query:       gi|121638326|ref|YP_978550.1|  [L=491]
Description: C4-dicarboxylate-transport transmembrane protein dctA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-96  321.4  36.8    8.9e-96  321.3  36.8    1.0  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.3  36.8    5e-100   8.9e-96       1     390 []      26     418 ..      26     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 321.3 bits;  conditional E-value: 5e-100
                            SDF   1 LllqiliglvlGlviGllelvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglktllyfllttl 80 
                                    L+l +++++++G+++Gl  +++++++ + +lg++f+nl+km+i+P++f++i++gi s+++a+++gk+g+ +l+yfl+++ 
  gi|121638326|ref|YP_978550.1|  26 LYLAVIFAVIAGVIVGL--TAPSTGKSLTVLGTVFVNLIKMMIAPVIFCTIVLGIGSVRKAAAVGKVGGLALAYFLTMSS 103
                                    67899************..************************************************************* PP

                            SDF  81 iAaiiglilalllkpg.....selaleassakeaekketdslldlilslipsnifealaegnvlavivfailfGialaal 155
                                    +A+ igli+++ll pg     + +a  + +a + +++e++ ++ +i+++ip+ + +al+egnvl+v+++a+l+G+a++ l
  gi|121638326|ref|YP_978550.1| 104 VALGIGLIVGNLLSPGrdlhlRPGAVGSGAALAGQAAESHGIAGFIQQIIPRSLPSALTEGNVLQVLLVALLVGFAVQGL 183
                                    ****************9988844555556666666778999*************************************** PP

                            SDF 156 gekgepllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihllivlpllllvltk 235
                                    g  ge++l+ +e+l+++v+kv+ +v++laPig f++ia++va++g++a+ +l+ +++ +yl++++++++vl +ll+++++
  gi|121638326|ref|YP_978550.1| 184 GPAGESILRAVENLQKLVFKVLVMVLWLAPIGAFGAIANIVATTGFNAVTNLLLLMAGFYLTCVVFVFGVLGVLLRIVSG 263
                                    ******************************************************************************** PP

                            SDF 236 knplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalyeavaaifiaqlfgvels 315
                                    ++++++l+++++ +l+ f+T+SS+ +LP  ++++++ lgv++s++++v+P+G+++n+dGta+y+++a +fia ++g  l+
  gi|121638326|ref|YP_978550.1| 264 LSIFRLLRYLAREYLLIFATSSSEVVLPRLITKMKH-LGVQSSTVGVVVPTGYSFNLDGTAIYLTMASLFIADAMGHRLT 342
                                    ************************************.9****************************************** PP

                            SDF 316 lgqllllvlvatlasiGaagvPgaglvalllvlsalglp.vegialilaidrllDmfrTavNvtGdavaalivakl 390
                                    +g+++ l++ +++as Gaagv gagl +l+  l+a +   ++g++li++idr++  +r+++N +G+ava+++va +
  gi|121638326|ref|YP_978550.1| 343 WGEQIALLAFMIIASKGAAGVSGAGLATLAGGLQAHRPElLDGVGLIVGIDRFMSEARSLTNFSGNAVATILVASW 418
                                    **********************************999664599******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3504.73
//
Query:       gi|121638327|ref|YP_978551.1|  [L=953]
Description: ribonuclease E rne [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.9e-101  337.2   0.3     9e-101  336.8   0.3    1.1  1  RNase_E_G  Ribonuclease E/G family
    0.00027   20.7   0.0    0.00077   19.2   0.0    1.8  1  IF2_N      Translation initiation factor IF-2, N-terminal reg
    0.00052   20.3   0.0     0.0011   19.2   0.0    1.6  1  S1         S1 RNA binding domain
     0.0084   16.9   0.1      0.032   15.0   0.1    2.0  1  PCB_OB     Penicillin-binding protein OB-like domain
  ------ inclusion threshold ------
       0.17   11.8   0.0        0.5   10.4   0.0    1.8  1  Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibito


Domain annotation for each model (and alignments):
>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.8   0.3  2.5e-104    9e-101       1     269 [.     455     736 ..     455     737 .. 0.95

  Alignments for each domain:
  == domain 1  score: 336.8 bits;  conditional E-value: 2.5e-104
                      RNase_E_G   1 slaGrylVllpegkkvgvSkkiedeeererlkelleelkpeevGlIvRtaaegaseeelekdleelkkkweeileka... 77 
                                    slaGr+lV++p ++++g+S+k++d +er+rlke+l+e++p+++G+I+Rta+eg++e+++++d+++l+++we+i++ka   
  gi|121638327|ref|YP_978551.1| 455 SLAGRFLVYVPGASSTGISRKLPD-TERQRLKEILREVVPSDAGVIIRTASEGVKEDDIRADVARLRERWEQIEAKAqet 533
                                    89*********99999********.88**************************************************554 PP

                      RNase_E_G  78 ..kkrkapsllyeeedlllrvlrdllnedieeivvddkelyeeikeyleevapeleekvelyeeee........plfely 147
                                      k + a   lyee+d+l++v+rdl+ned+  ++v+ +e++++i+ey+++vapel +k++ ye+ +        ++f+ +
  gi|121638327|ref|YP_978551.1| 534 keKAAGAAVALYEEPDVLVKVIRDLFNEDFVGLIVSGDEAWNTINEYVNSVAPELVSKLTKYESADgpdgqsapDVFTVH 613
                                    332244588*****************************************************8554556667778***** PP

                      RNase_E_G 148 siekqiekalsrkvwlksGgylvIeqTEAltvIDVNsGkftgkk.nleetvlktNleAaeeiarqlrLRnlgGiIviDFI 226
                                    +i++q++ka++rkvwl+sGg+lvI++TEA+tvIDVN+Gkftg   nle+tv+k+NleAaeei+rqlrLR++gGi+viDFI
  gi|121638327|ref|YP_978551.1| 614 RIDEQLAKAMDRKVWLPSGGTLVIDRTEAMTVIDVNTGKFTGAGgNLEQTVTKNNLEAAEEIVRQLRLRDIGGIVVIDFI 693
                                    ****************************************99887*********************************** PP

                      RNase_E_G 227 dmkeeenreevleelkealkkDraktqvleitklgLveitRkr 269
                                    dm  e+nr+ vl++l+e+l++Dr+++qv+e+t+lgLv++tRkr
  gi|121638327|ref|YP_978551.1| 694 DMVLESNRDLVLRRLTESLARDRTRHQVSEVTSLGLVQLTRKR 736
                                    ******************************************9 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.1e-07   0.00077       2      47 ..      21      65 ..      20      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-07
                          IF2_N  2 skirVyeLAkeLgvkskevikkLfkelGievkshsssLDeetaeli 47
                                   + +rV+ LA+ Lg++s +v++ L + l   v s+ s++D  +a  +
  gi|121638327|ref|YP_978551.1| 21 DRLRVHSLARTLGTTSRRVLDALTA-LDGRVRSAHSTVDRVDAVRV 65
                                   689********************99.*9999********9877665 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.1e-07    0.0011       4      62 ..     375     440 ..     374     453 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
                                    TTCEEEEEEEEEET..TEEEEEETTTEEEEEEGGGSSSS.....CEESCHHHCEETTEEEEEEEEE CS
                             S1   4 kgevveGeVtsvtk..gGafVelgngvegfvpaselsrd.....arvedpdevlkvGdevkvkvlk 62 
                                    +g+++ G+V++v +  ++afV++g g  g + a e+ +d       ++++++ lk+Gd v v+v k
  gi|121638327|ref|YP_978551.1| 375 VGNIYLGIVQNVLPsmEAAFVDIGRGRNGVLYAGEVNWDaaglgGADRKIEQALKPGDYVVVQVSK 440
                                    69************99****************************8899***************987 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   8.9e-06     0.032      26     101 ..     370     445 ..     357     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
                                    CTSSTCTTEEEEEEEEEETT..EEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEEEEEE-TT... CS
                         PCB_OB  26 kklpdsgelrpAvVlsvsek..sarvglrdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdvvlvrkeed... 100
                                    ++++ +g++++++V +v ++  +a v +  g++g++ + +++w +        g a ++++++lkpGd v+v+  +d   
  gi|121638327|ref|YP_978551.1| 370 ASASLVGNIYLGIVQNVLPSmeAAFVDIGRGRNGVLYAGEVNWDAA-----GLGGADRKIEQALKPGDYVVVQVSKDpvg 444
                                    56778899********98876589999999*************999.....5677889***************9998655 PP

                                    . CS
                         PCB_OB 101 e 101
                                    +
  gi|121638327|ref|YP_978551.1| 445 H 445
                                    3 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014       0.5      18      46 ..     738     762 ..     734     764 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                    TTSEETTE......E-TTTTTSSEEE-HH CS
                      Anti-TRAP  18 gsGkiepeeprasleCPkCsGkglipTaq 46 
                                    g+G ie+     s  CP+CsG+g+++ a+
  gi|121638327|ref|YP_978551.1| 738 GTGLIEAF----STSCPNCSGRGILLHAD 762
                                    56666666....889*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (953 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.05u 0.37s 00:00:01.42 Elapsed: 00:00:00.53
# Mc/sec: 5462.16
//
Query:       gi|121638328|ref|YP_978552.1|  [L=136]
Description: nucleoside diphosphate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-54  181.2   0.0    9.6e-54  181.1   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
     0.0073   16.1   0.5      0.014   15.1   0.5    1.5  1  TruB_C    tRNA Pseudouridine synthase II, C terminal


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.0   1.1e-57   9.6e-54       1     131 [.       3     134 ..       3     136 .] 0.99

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 1.1e-57
                                    EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHH CS
                            NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedai 80 
                                    ertlvliKPd+++r+ligeiisr+e+kgl+i+al++ +++ e+a++hYaeh+gkpff +l+ef+tsgpvva ++eg++ai
  gi|121638328|ref|YP_978552.1|   3 ERTLVLIKPDGIERQLIGEIISRIERKGLTIAALQLRTVSAELASQHYAEHEGKPFFGSLLEFITSGPVVAAIVEGTRAI 82 
                                    89****************************************************************************** PP

                                    HHHHHHH--SSTTTS.STTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHST CS
                            NDK  81 ekvreliGatnpaea.apgtiRadfgvslgeNlvHgSdseesaereiklfFk 131
                                    ++vr+l+G t+p +a apgtiR+df+++++ NlvHgSds esa+rei+l+F+
  gi|121638328|ref|YP_978552.1|  83 AAVRQLAGGTDPVQAaAPGTIRGDFALETQFNLVHGSDSAESAQREIALWFP 134
                                    ************9987***********************************7 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.5   1.6e-06     0.014      16      52 ..      59      95 ..      58      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-06
                                   TT---B-----S-EEEE-TTS-EEEEEEEETTEEEEE CS
                         TruB_C 16 hGrrLeaagikgvvAaiaPdGrliALleerggrarsv 52
                                   +G  Le+ +  +vvAai + +r+iA +++ +g + +v
  gi|121638328|ref|YP_978552.1| 59 FGSLLEFITSGPVVAAIVEGTRAIAAVRQLAGGTDPV 95
                                   58889999*********************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 984.73
//
Query:       gi|121638329|ref|YP_978553.1|  [L=123]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-27   94.6  10.5      5e-27   94.3  10.5    1.0  1  DUF4233   Protein of unknown function (DUF4233)


Domain annotation for each model (and alignments):
>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3  10.5   2.8e-31     5e-27       3     102 ..      18     117 ..      17     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.8e-31
                        DUF4233   3 vmagtLvlEaivvlLallv.....aiglrdtepatvlsvggvlavallllagllrrpwglalglvlQvlliaagfvvp.a 76 
                                    vma+tL+lEaivvlLa++v     + glr +     l++ ++lav+l+ll+gl+rrpw+++++l++Q +l+ agf+v   
  gi|121638329|ref|YP_978553.1|  18 VMAATLILEAIVVLLAIPVvdavgG-GLRPA----SLGYLVGLAVLLILLTGLQRRPWAIWVNLGAQPVLV-AGFAVYpG 91 
                                    8******************876633.66555....777777******************************.8888888* PP

                        DUF4233  77 mfvvgvvFaavWvyalvlgrridrek 102
                                    ++++gv+Faa+Wv++ +l+++++r++
  gi|121638329|ref|YP_978553.1|  92 VGFIGVLFAALWVLIAYLRAEVRRRR 117
                                    ***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 901.12
//
Query:       gi|121638330|ref|YP_978554.1|  [L=487]
Description: folylpolyglutamate synthase folC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-16   59.4   0.0      1e-15   58.3   0.0    1.6  1  Mur_ligase_M  Mur ligase middle domain
    1.5e-11   44.4   0.4    3.9e-11   43.1   0.0    1.8  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.1e-19     1e-15       1     191 [.      69     308 ..      69     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.1e-19
                                    EESSS-HHHHHHHHHHHHHCT...EEEEETTC................................................ CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaaileka...gkvigtvg................................................ 29 
                                    ++GtnGKT++++++ a++++    ++ +++                                                  
  gi|121638330|ref|YP_978554.1|  69 IAGTNGKTSVARMVDALVTALhrrTGRTTSPHlqspverisidgkpispaqyvatyreieplvalidqqsqasagkggpa 148
                                    89****************9996555555555599********************************************99 PP

                                    SS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETT CS
                   Mur_ligase_M  30 ttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkee 108
                                      + e+ +  ++a ++++ +++av+Ev++   g     ++++  vavit is dH+d++  ++  +a +Ka +++r +++
  gi|121638330|ref|YP_978554.1| 149 MSKFEVLTAMAFAAFADAPVDVAVVEVGMG--GRWDATNVINAPVAVITPISIDHVDYLgADIAGIAGEKAGIITRAPDG 226
                                    556667777788888888************..55333444899****************789****************98 PP

                                    C...EEEEETTSC...CHHHHHCTCCTC.EEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHH CS
                   Mur_ligase_M 109 g...iavinaddpyakelikklkkakvk.vvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyN 184
                                    +   +avi ++ p   ++++ l  ++v+   ++  e+    + +++i +   g+ ++l  + g   +i +pl G+h++ N
  gi|121638330|ref|YP_978554.1| 227 SpdtVAVIGRQVP---KVMEVLLAESVRaDASVAREDSEFAVLRRQIAV--GGQVLQLQGLGGVYSDIYLPLHGEHQAHN 301
                                    8999*******99...999998888888666666666653444456666..7888888877666666************* PP

                                    HHHHHHH CS
                   Mur_ligase_M 185 alaaiaa 191
                                    a++a+a 
  gi|121638330|ref|YP_978554.1| 302 AVLALAS 308
                                    ****996 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   4.4e-15   3.9e-11       2      86 ..     336     413 ..     335     418 .. 0.92
   2 ?   -3.5   0.1       1.4   1.3e+04      15      25 ..     445     455 ..     437     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 4.4e-15
                                    TTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEESS CS
                   Mur_ligase_C   2 kgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvlgdy 81 
                                    +gRle++++  ++tv++D ahnp+++sa+ ++l++ ++ + l+ v+  +g+   ++ +    +++l+  ++ ++v+++++
  gi|121638330|ref|YP_978554.1| 336 PGRLERMRS--APTVFIDAAHNPAGASALAQTLAHEFDFRFLVGVLSVLGD---KDVD--GILAALEPVFDSVVVTHNGS 408
                                    8*******9..99**********************************9777...9999..********988779999999 PP

                                    -TTST CS
                   Mur_ligase_C  82 praed 86 
                                    pra d
  gi|121638330|ref|YP_978554.1| 409 PRALD 413
                                    99876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                                    EEEEET--SHH CS
                   Mur_ligase_C  15 tvidDyahnpd 25 
                                     ++dD a+ pd
  gi|121638330|ref|YP_978554.1| 445 SLVDDAAADPD 455
                                    67889999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3229.89
//
Query:       gi|121638331|ref|YP_978555.1|  [L=876]
Description: valyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-198  661.1   0.1   6.6e-149  496.9   0.0    2.9  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    1.5e-36  125.7   0.0    2.6e-36  124.9   0.0    1.4  1  Anticodon_1      Anticodon-binding domain of tRNA
    2.6e-19   69.3   0.0    1.2e-06   27.6   0.0    4.1  4  tRNA-synt_1g     tRNA synthetases class I (M)
    1.7e-16   60.3   5.0    3.4e-16   59.3   5.0    1.6  1  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
      2e-07   30.7   0.1    8.5e-06   25.4   0.0    2.3  2  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
    5.7e-05   22.2   0.0     0.0001   21.4   0.0    1.3  1  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0003   20.2   0.0       0.33   10.3   0.0    2.2  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
  ------ inclusion threshold ------
      0.028   13.8   0.0      0.047   13.0   0.0    1.3  1  EXS              EXS family
      0.077   13.2   2.6       0.32   11.3   2.6    2.0  2  ABC_tran_CTD     ABC transporter C-terminal domain
       0.19   11.9   0.7       0.34   11.1   0.7    1.4  1  Tropomyosin_1    Tropomyosin like


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.9   0.0  3.7e-152  6.6e-149       2     444 ..      15     426 ..      14     435 .. 0.97
   2 !  159.2   0.0   6.7e-50   1.2e-46     480     601 ..     436     569 ..     430     570 .. 0.96

  Alignments for each domain:
  == domain 1  score: 496.9 bits;  conditional E-value: 3.7e-152
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                    +y+kW ++++f +    + +k+ +++v +PP+vtGslH+Ghal++t++d ++r krm+G+evl++pG+DhaG+a++++ve
  gi|121638331|ref|YP_978555.1|  15 IYQKWLDAGYFTAD--PTSTKPAYSIVLPPPNVTGSLHMGHALEHTMMDALTRRKRMQGYEVLWQPGTDHAGIATQSVVE 92 
                                    8***********99..88889*********************************************************** PP

                    tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkk 161
                                    ++l+ ++ k++++lgre f++kv++wk e+   i  q++rlG  vD++r+++T+d++l+ av+ +f+rl+d gliyr+++
  gi|121638331|ref|YP_978555.1|  93 QQLAVDG-KTKEDLGRELFVDKVWDWKRESGGAIGGQMRRLGDGVDWSRDRFTMDEGLSRAVRTIFKRLYDAGLIYRAER 171
                                    ***8887.5*********************************************************************** PP

                    tRNA-synt_1 162 lvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallk 241
                                    lvnws+ l+ta+s+lEv+y+d+++ l+++++   d+++ ++v+aTT+ eT+lgdta+av+p+                  
  gi|121638331|ref|YP_978555.1| 172 LVNWSPVLQTAISDLEVNYRDVEGELVSFRYGSLDDSQPHIVVATTRVETMLGDTAIAVHPD------------------ 233
                                    *******************************99999999***********************.................. PP

                    tRNA-synt_1 242 slvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedg 321
                                                 der+++L+g  + +p+v+r++ i+ad++vd e+GtG+Vk++Pahd++D+e+g +++l++++ild++g
  gi|121638331|ref|YP_978555.1| 234 -------------DERYRHLVGTSLAHPFVDRELAIVADEHVDPEFGTGAVKVTPAHDPNDFEIGVRHQLPMPSILDTKG 300
                                    .............9****************************************************************** PP

                    tRNA-synt_1 322 tlteeaaefeglkvfdarkkvveelkekglllka.ekiehsvpfcerskkpiiyrateqWfvrvkeladaalkave..kv 398
                                    ++ ++ + f+g+++f+ar +v ++l ++g+ +++  +  hsv+++ers++pi++r++ qW+vrv++la+aa +av+  ++
  gi|121638331|ref|YP_978555.1| 301 RIVDTGTRFDGMDRFEARVAVRQALAAQGRVVEEkRPYLHSVGHSERSGEPIEPRLSLQWWVRVESLAKAAGDAVRngDT 380
                                    *****************************9886516799*************************************9999 PP

                    tRNA-synt_1 399 qfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvv 444
                                     + p s e r++sw+ +++dWciSRq+wWGhrip+++  + e+v v
  gi|121638331|ref|YP_978555.1| 381 VIHPASMEPRWFSWVDDMHDWCISRQLWWGHRIPIWYGPDGEQVCV 426
                                    9**************************************9988766 PP

  == domain 2  score: 159.2 bits;  conditional E-value: 6.7e-50
                    tRNA-synt_1 480 lekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse............Pf 547
                                    +e+d+dvlD+WFsS++wpfstlg+p++ t el+kf+p+++l++G+Di+++Wvar++++++ + +++            Pf
  gi|121638331|ref|YP_978555.1| 436 WEQDPDVLDTWFSSALWPFSTLGWPDK-TAELEKFYPTSVLVTGYDILFFWVARMMMFGTFVGDDAaitldgrrgpqvPF 514
                                    79*************************.9*******************************9988889************* PP

                    tRNA-synt_1 548 kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                    ++v++hgl+rde GrKmSKs+gNvidpld ++  gadalR+tl+  ++ g d+++
  gi|121638331|ref|YP_978555.1| 515 TDVFLHGLIRDESGRKMSKSKGNVIDPLDWVEMFGADALRFTLArGASPGGDLAV 569
                                    ********************************************99999999876 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   1.4e-39   2.6e-36       1     148 [.     611     750 ..     611     754 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 1.4e-39
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    drwil +l+++ +ev+ a++ y+f++a+ +ly+f w+++cdwylel+k +l++   +    + +vl+  l+tllrll+P+
  gi|121638331|ref|YP_978555.1| 611 DRWILGRLEEVRAEVDSAFDGYEFSRACESLYHFAWDEFCDWYLELAKTQLAQGLTH----TTAVLAAGLDTLLRLLHPV 686
                                    9**************************************************775543....55***************** PP

                    Anticodon_1  81 mPfitEelwqreeeelgkkesimlaewpekaeel...ekeleeeevellkeivkairklrselkikpssel 148
                                    +Pf+tE lw      l + es++ a+wpe +         +  + ++ ++++v+ +r++rs+++++ ++++
  gi|121638331|ref|YP_978555.1| 687 IPFLTEALW----LALTGRESLVSADWPEPSGISvdlV--A-AQRINDMQKLVTEVRRFRSDQGLADRQKV 750
                                    *********....9999999********7443335422..3.579999999*************9998875 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.7e-09   8.4e-06       8      55 ..      43      90 ..      36     109 .. 0.88
   2 ?    2.0   0.0     0.038        68      91     135 ..     144     188 ..     125     194 .. 0.83
   3 !    9.2   0.0   0.00026      0.46     178     239 ..     354     418 ..     336     427 .. 0.73
   4 !   27.6   0.0   6.5e-10   1.2e-06     315     376 ..     517     579 ..     501     588 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.7e-09
                                   B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHH CS
                   tRNA-synt_1g  8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielk 55
                                   p ++g+lH+Gh+le+   D+++R kr++g+evl+  gtD+ G++++  
  gi|121638331|ref|YP_978555.1| 43 PNVTGSLHMGHALEHTMMDALTRRKRMQGYEVLWQPGTDHAGIATQSV 90
                                   66899*************************************998765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.038
                                    TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                   tRNA-synt_1g  91 ttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                    t +e  +++v+ ifk+l++ gliy+ e  + ++p  ++ ++d +v
  gi|121638331|ref|YP_978555.1| 144 TMDEGLSRAVRTIFKRLYDAGLIYRAERLVNWSPVLQTAISDLEV 188
                                    566677899******************999999988888887666 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00026
                                    EE.EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-ESS-SSS-EET...T CS
                   tRNA-synt_1g 178 vketehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlaisrdldwGipvP...g 239
                                     + + +++ ++++++k+  + +++ ++   + +++    +w+++ ++d++isr+l wG ++P   g
  gi|121638331|ref|YP_978555.1| 354 PRLSLQWWVRVESLAKAAGDAVRNGDTViHPASMEPRWFSWVDD-MHDWCISRQLWWGHRIPiwyG 418
                                    55566677777777777777775555556667777777789988.***************996553 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 6.5e-10
                                    EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHH CS
                   tRNA-synt_1g 315 vvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervN 376
                                    v+ h+ +   +g+K+SkS+g+v+++ +++e + ad+lR+ la+ a+   Dl  s++ + +  N
  gi|121638331|ref|YP_978555.1| 517 VFLHGLIRdESGRKMSKSKGNVIDPLDWVEMFGADALRFTLARGASPGGDLAVSEDAVRASRN 579
                                    6666666513599******************************99999999999988776655 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   5.0   1.9e-19   3.4e-16       1      65 [.     811     875 ..     811     876 .] 0.98

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.9e-19
                Val_tRNA-synt_C   1 DvekeraRLeKeLaklekeiervqkKLanpgFveKAPaeVVeeekaklaeleeqaeklkerLskL 65 
                                    Dv++er+RLeKeLa ++ke+++ + KLan +F++KAP++V+ + +++   ++++ e++++rL+ L
  gi|121638331|ref|YP_978555.1| 811 DVAAERRRLEKELAGAQKELASTAAKLANADFLAKAPDAVIAKIRDRQRVAQQETERITTRLAAL 875
                                    9*************************************************************988 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.039        71      16      46 ..     205     235 ..     193     243 .. 0.81
   2 !   25.4   0.0   4.7e-09   8.5e-06      86     144 ..     242     300 ..     238     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.039
                  tRNA-synt_1_2  16 veeseeklevfttrpdtlfGvtfvalapehp 46 
                                    +++s+ ++ v ttr +t+ G t +a+ p+ +
  gi|121638331|ref|YP_978555.1| 205 LDDSQPHIVVATTRVETMLGDTAIAVHPDDE 235
                                    55667799*****************999865 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 4.7e-09
                  tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikped 144
                                    g+   hP+ ++++ i   ++v  e+gtgav   Pahd +Dfe   +++lp+  ++ +++
  gi|121638331|ref|YP_978555.1| 242 GTSLAHPFVDRELAIVADEHVDPEFGTGAVKVTPAHDPNDFEIGVRHQLPMPSILDTKG 300
                                    67789**********************************************99988765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.7e-08    0.0001     272     311 ..     521     560 ..     512     578 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.7e-08
                   tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflilrr 311
                                     li ++ g+kms+SkGnv+ + dw+e+   + lrf ++r 
  gi|121638331|ref|YP_978555.1| 521 GLIRDESGRKMSKSKGNVIDPLDWVEMFGADALRFTLARG 560
                                    68999******************************99984 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0012       2.2      17      50 ..      43      76 ..      32      82 .. 0.90
   2 !   10.3   0.0   0.00018      0.33     236     282 ..     513     559 ..     506     577 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                   EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                   tRNA-synt_1e 17 ptvydashlGhaRslvafDilrrilqalgYdvqf 50
                                   p v    h+Gha +  ++D l r  +++gY+v +
  gi|121638331|ref|YP_978555.1| 43 PNVTGSLHMGHALEHTMMDALTRRKRMQGYEVLW 76
                                   6788999************************965 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                                    --EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                   tRNA-synt_1e 236 qlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                    +++  flh  +    g+kmsks +n+i   d ++ f + +lR+ l+ 
  gi|121638331|ref|YP_978555.1| 513 PFTDVFLHGLIRDESGRKMSKSKGNVIDPLDWVEMFGADALRFTLAR 559
                                    5778899977777789***************************9975 PP

>> EXS  EXS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.047     220     287 ..     611     682 ..     572     710 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                            EXS 220 d...........esestlrvlwllaalvnslysfiWDvtmDWgLlkllksknwflRdellypkkwvYylaivldlvlRf 287
                                    d            + ++ +  + ++ ++ sly f+WD + DW L  l k+    l + l+ +     +la +ld +lR+
  gi|121638331|ref|YP_978555.1| 611 DrwilgrleevrAEVDSAFDGYEFSRACESLYHFAWDEFCDWYLE-LAKT---QLAQGLTHT---TAVLAAGLDTLLRL 682
                                    2555555555555555666677788899****************9.6664...355555222...34677777777776 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.6   4.7e+03      49      64 ..     617     632 ..     614     633 .. 0.82
   2 ?   11.3   2.6   0.00018      0.32      10      67 ..     816     875 ..     811     876 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                   ABC_tran_CTD  49 eleeleaeLeelyerW 64 
                                    +lee++ae + +++ +
  gi|121638331|ref|YP_978555.1| 617 RLEEVRAEVDSAFDGY 632
                                    899*****99999765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyerWeeL 67 
                                      +le+e++  ++e+a+  a+la++++ ++   + +a++  ++  +++e e+ + r   L
  gi|121638331|ref|YP_978555.1| 816 RRRLEKELAGAQKELASTAAKLANADFLAKApdAVIAKIRDRQRVAQQETERITTRLAAL 875
                                    4579************************5554788*****************99986665 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00019      0.34      84     140 ..     818     874 ..     808     876 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                  Tropomyosin_1  84 lLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleekyke 140
                                     LE el  ++k+L++t  kL ++d  a   +  ++++ +++    +  e +++++++
  gi|121638331|ref|YP_978555.1| 818 RLEKELAGAQKELASTAAKLANADFLAKAPDAVIAKIRDRQRVAQQETERITTRLAA 874
                                    69*************************999999999999988888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 5252.83
//
Query:       gi|121638332|ref|YP_978556.1|  [L=419]
Description: hypothetical protein BCG_2469c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-13   49.9   0.1    6.7e-13   49.0   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0039   17.1   0.5      0.012   15.5   0.3    1.8  2  KR               KR domain
     0.0048   16.8   0.2     0.0078   16.1   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.13   11.7   0.0        0.2   11.1   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   1.5e-16   6.7e-13       1     129 [.      10     136 ..      10     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.5e-16
                                    EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                    +++ Ga G+vG+ +ae+lar +   a+i++a+rs +++ a+ +++  + ++  + + da+ ++  L+a+ + +++vv  +
  gi|121638332|ref|YP_978556.1|  10 IVLYGAtGFVGKLTAEYLARAGGD-ARIALAGRSTQRVLAVREALgeSAQTWPILTADASLPST-LQAMAARAQVVVTTV 87 
                                    7999*****************986.6***********999998765444444555566665555.*************** PP

                                    SGG..GHHHHHHHHHHHT-EEEE.SS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                Sacchrp_dh_NADP  78 ppi..ssldvlkaCietgvhyvd.tsiskeertnyalreavlklkekakeagvta 129
                                    +p+  ++l++++aC+++g++y d t       ++ ++r+ +  ++++a++ g+ +
  gi|121638332|ref|YP_978556.1|  88 GPYtrYGLPLVAACAAAGTDYADlT-G-----EPMFMRNSIDLYHKQAADTGARI 136
                                    ***9*******************54.4.....47889999999999999999866 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   2.7e-06     0.012       4      75 ..      11      80 ..      10      87 .. 0.83
   2 ?   -2.0   0.0      0.64   2.9e+03      78     100 ..     382     405 ..     376     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                                   EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHH CS
                             KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleei 75
                                   ++ G++G +G+ +a+ la+ g  ++++l +Rs   +++  a  ++l ++  +  ++ aD s ++ ++a+ +++
  gi|121638332|ref|YP_978556.1| 11 VLYGATGFVGKLTAEYLARAGgDARIALAGRS---TQRVLAVREALGESAQTWPILTADASLPSTLQAMAARA 80
                                   578****************9989*********...34555567788888888889999999999998887766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                                    HS.S---EEEE---------TTT- CS
                             KR  78 ee.ppikGvihaAgvlrdklleem 100
                                    ++ + ++Gv+  A ++ d+lle++
  gi|121638332|ref|YP_978556.1| 382 DKlSDMRGVLTPAAAMGDALLERL 405
                                    444789999999999999999876 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.7e-06    0.0078       1      87 [.      14     103 ..      14     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                                    TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCH CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaele.....aeeglevvegdvtdvedlaealkgadaVvsalggggkd 74 
                                    GAtG vG+l ++ l+++g + ++ +  R+++++ +++     +++   ++++d++ +++l++  + a++Vv+++g+  + 
  gi|121638332|ref|YP_978556.1|  14 GATGFVGKLTAEYLARAGgDARIALAGRSTQRVLAVRealgeSAQTWPILTADASLPSTLQAMAARAQVVVTTVGPYTR- 92 
                                    9*****************7777777789999997666232223345568999**9999*999999*******9997543. PP

                                    HHHHHHHHHHHHH CS
                 NAD_binding_10  75 eegaknivdaake 87 
                                          +v+a+ +
  gi|121638332|ref|YP_978556.1|  93 --YGLPLVAACAA 103
                                    ..33444444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05       0.2       1      61 [.      10      78 ..      10      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                                   EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHH CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl.......elveldltdrsalerlfk 61
                                   i++ GatGf+G+ ++++l+++g +  i+l+ +s+++  a +e l        + ++d   +s l+++ +
  gi|121638332|ref|YP_978556.1| 10 IVLYGATGFVGKLTAEYLARAGGDaRIALAGRSTQRVLAVREALgesaqtwPILTADASLPSTLQAMAA 78
                                   6788******************88788888887877777776667777666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2944.65
//
Query:       gi|121638333|ref|YP_978557.1|  [L=172]
Description: resuscitation-promoting factor rpfE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-35  119.3   6.3    1.2e-34  118.8   6.3    1.3  1  Transglycosylas  Transglycosylase-like domain


Domain annotation for each model (and alignments):
>> Transglycosylas  Transglycosylase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   6.3   6.7e-39   1.2e-34       2      77 .]      96     168 ..      95     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 6.7e-39
                                    XTHHHHHHHHHHHHSS-TT-TTSSSEBTTTTBEHHHHHHTTCCST.SCGGGS-HHHHHHHHHHHHHHHCGGGSTTC CS
                Transglycosylas   2 adesnwdaiAqcEsggnwaintgnGyyGglqfsqstWeavggekyapsaaqAsreqQiavAekvlatqGagaWptc 77 
                                    a + nwdaiAqcEsggnw+intgnGyyGglqf++ tW+a+gg++   saa+Asre+Qi+vAe+vl++qG++aWp+c
  gi|121638333|ref|YP_978557.1|  96 AYSVNWDAIAQCESGGNWSINTGNGYYGGLQFTAGTWRANGGSG---SAANASREEQIRVAENVLRSQGIRAWPVC 168
                                    6789****************************************...****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1333.32
//
Query:       gi|121638334|ref|YP_978558.1|  [L=132]
Description: hypothetical protein BCG_2471 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1094.72
//
Query:       gi|121638335|ref|YP_978559.1|  [L=48]
Description: hypothetical protein BCG_2472c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 373.19
//
Query:       gi|121638336|ref|YP_978560.1|  [L=201]
Description: molybdopterin-guanine dinucleotide biosynthesis protein A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-28   99.9   4.0    2.3e-28   99.6   4.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   4.0   1.3e-32   2.3e-28       1     155 [.      13     166 ..      13     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.3e-32
                                    EEEEEESS-TTTTTTHHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmggdKallpl..ggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaa 78 
                                    +v+LAGG+S+Rmg+dKa lpl  g ++l+e+++  l +  +++v+v + + +    l+ l+v+v++de pg gpl +   
  gi|121638336|ref|YP_978560.1|  13 GVVLAGGESRRMGRDKATLPLpgGTTTLVEHMVGILGQR-CAPVFVMAAPGQP---LPTLPVPVLRDELPGLGPLPATGR 88 
                                    79*******************966679**********98.9******998654...5789******************** PP

                                    HHHHH...SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHCHH CS
                   NTP_transf_3  79 alraaa..dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrllr 155
                                    +lraaa  +   ++v+a+DmP+lt el+e l+++a +++a+vv p +  ++   +++r++l++++ +l g +g+r++ +
  gi|121638336|ref|YP_978560.1|  89 GLRAAAeaGVRLAFVCAVDMPYLTVELIEDLARRAVQTDAEVVLPWDGRNHYLAAVYRTDLADRVDTLVG-AGERKMSA 166
                                    **9976568888****************************99999766555445599***********77.56666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1524.70
//
Query:       gi|121638337|ref|YP_978561.1|  [L=373]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-30  105.8   0.0    2.8e-30  105.1   0.0    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   1.5e-34   2.8e-30       2     153 .]      88     235 ..      87     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.5e-34
                                    SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEE CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvv 79 
                                    iGc+++    +     p+ yl   g+++ +G++ ++A+G++la++d  v++++GDG+ l i +++l++a rrn+++t+++
  gi|121638337|ref|YP_978561.1|  88 IGCSSR----F-----PY-YLEtYGFHSIHGRAPAIATGLALAREDLSVWVVTGDGDALSIgGNHLIHALRRNINVTILL 157
                                    677776....2.....44.444499*******************9*********************************** PP

                                    EE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  80 lnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                    +nN++yg+t+gq   ++  g+ +ks+p g+ ++p++++ la +++a+ + r  ++d + l e+l++a +++g al+e+
  gi|121638337|ref|YP_978561.1| 158 FNNRIYGLTKGQyspTSEVGKVTKSTPMGSLDHPFNPVSLALGAEATfVGRALDSDRNGLTEVLRAAAQHRGAALVEI 235
                                    **************99999999*******9*****************666999999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2964.59
//
Query:       gi|121638338|ref|YP_978562.1|  [L=653]
Description: oxidoreductase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-60  203.9   0.0      4e-60  203.5   0.0    1.2  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    2.2e-25   89.7   0.1    3.4e-25   89.1   0.1    1.3  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    2.5e-08   34.2   0.0    4.8e-08   33.2   0.0    1.5  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
    0.00035   20.2   0.0    0.00074   19.2   0.0    1.5  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   0.0   8.8e-64     4e-60       3     220 ..     269     486 ..     267     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 8.8e-64
                                    HHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                          POR_N   3 aiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                    ++a+ + v+ +YPITP+s+i++el+++  +++v   +++q+e+Eig i+a++GAa++Ga+++T TSg+G++L++e+lgl 
  gi|121638338|ref|YP_978562.1| 269 QLAGLPVVLGSYPITPASDILHELSKHK-NFNV---VTFQAEDEIGGICAALGAAYGGALGVTSTSGPGISLKSEALGLG 344
                                    5677788999****************98.8886...9******************************************* PP

                                    HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHH CS
                          POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfl 157
                                    +++elP+++++v+R++pstgl+++t+q Dl++a+     +++++vla+++ +++f++al+A+++A+++++Pvi+l+Dg +
  gi|121638338|ref|YP_978562.1| 345 VMTELPLLVIDVQRGGPSTGLPTKTEQADLLQALygrngESPVAVLAPRSPADCFETALEAVRIAVSYHTPVILLSDGAI 424
                                    ******************************************************************************** PP

                                    H.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXX CS
                          POR_N 158 lshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaed 220
                                    + +  e++++pd++++  ++++++++ e+++++++ ++++ar+ a + + glehr  g ea++
  gi|121638338|ref|YP_978562.1| 425 A-NGSEPWRIPDVNALPPIKHTFAKPGEPFQPYARDRETLARQFAIPGTPGLEHRIGGLEAAN 486
                                    *.******************************************************9999876 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.1   7.6e-29   3.4e-25       1     175 [.      37     225 ..      35     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 7.6e-29
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSS......SSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGG CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseir......Gghsyshvrisdepivpsievgeadllvaldaetlsehld 74 
                                    +G+G++++g  ++  aa  G +  + + y++eir       g+s +++ i+d   + + + +++d+lva+++++l+ ++ 
  gi|121638338|ref|YP_978562.1|  37 SGDGMQLTGDRFTSEAALFGNDLATQPNYPAEIRapagtlPGVSSFQIQIADY-DILTAG-DRPDVLVAMNPAALKANIG 114
                                    5*********************************9999999***********8.789999.9****************** PP

                                    GEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHH..T-EEEEE-HHHHHH.........HCCC.CCHHHHHHHHHHHHHH CS
                            POR  75 glkpggiiiynseelkpdelkkakeeerelkerl..gvrvygvdatkiak.........eiggneraaNtvmlGalaall 143
                                    +l  gg +i+ns+e+ +++l+k  +  ++l++ +  ++ v +v +t +           ++ g +ra+N+++lG l+++ 
  gi|121638338|ref|YP_978562.1| 115 DLPLGGMVIVNSDEFTKRNLTKVGYVTNPLESGElsDYVVHTVAMTTLTLgaveaigasKKDG-QRAKNMFALGLLSWMY 193
                                    ***************************999887788666666666666666676555544444.**************** PP

                                    TS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHH CS
                            POR 144 glplealeeaikkrfpkkkeviekNlkafrag 175
                                    g +le+ e+ i+++f++k e++e+N+ a++ag
  gi|121638338|ref|YP_978562.1| 194 GRELEHSEAFIREKFARKPEIAEANVLALKAG 225
                                    ******************************99 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.1e-11   4.8e-08       1      96 [.     526     620 ..     526     625 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.1e-11
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G...-HHHHHHHHH CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse...Gqlveevkaa 77 
                                    Ae ++++ Gs+ g + +a +++R++g kv    lr+l PFP+ +l e+l+++ kvv  ++n    ++   G ++ +v++ 
  gi|121638338|ref|YP_978562.1| 526 AELLLIGWGSSYGPIGEACRRARRRGTKVAHAHLRYLNPFPA-NLGEVLRRYPKVVAPELNLGQLAQvlrGKYLVDVQSV 604
                                    899**************************************6.799****************655557788888898888 PP

                                    TGGGTSEEEEEE--GGG-- CS
                        PFOR_II  78 lkkskvkvvnfvaglgGrd 96 
                                    +k    k v+f+a   Gr 
  gi|121638338|ref|YP_978562.1| 605 TKV---KGVSFLADEIGRF 620
                                    753...4667666666665 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.7e-07   0.00074      23     157 ..     281     418 ..     272     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-07
                                    --CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--C CS
                   TPP_enzyme_N  23 pGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrpt 102
                                    p +   ++l +ls++++++vv++  E   +++  ++  a g    v  tsgpG+     al     + +Pllv+  +r+ 
  gi|121638338|ref|YP_978562.1| 281 PITPASDILHELSKHKNFNVVTFQAEDEIGGICAALGAAYGGALGVTSTSGPGISLKSEALGLGVMTELPLLVIDVQRGG 360
                                    556677899***************************9999888888889******************************* PP

                                    CCHH..S..TC--T-CCHHHC...CCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                   TPP_enzyme_N 103 slrg..qgvlqqeldqlalfr...pvtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                     ++g  +++ q +   +al+    +   ++  ++sp++  e+  +A+r+a  + ++Pv l
  gi|121638338|ref|YP_978562.1| 361 PSTGlpTKTEQ-ADLLQALYGrngESPVAVLAPRSPADCFETALEAVRIA-VSYHTPVIL 418
                                    *9994333333.22233333323344444777778888777777888888.666667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 4149.89
//
Query:       gi|121638339|ref|YP_978563.1|  [L=418]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-33  115.7  42.4    3.6e-21   75.5  21.2    2.0  2  MFS_1       Major Facilitator Superfamily
    4.8e-11   42.1  11.0    5.6e-10   38.6  11.0    2.0  1  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5  21.2     4e-25   3.6e-21      11     265 ..      26     279 ..      16     280 .. 0.84
   2 !   48.6  16.3     6e-17   5.3e-13      38     185 ..     264     412 ..     250     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 4e-25
                          MFS_1  11 arsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllllfasslwll 88 
                                     r+ lgp l+++l   + ++ ++ig+++++ +++a+va+ p+G+l+dr  ++r ++++g++l  ++ ++++lf ++l+ +
  gi|121638339|ref|YP_978563.1|  26 VRDGLGPYLSIYLLLIHDWDQASIGFVMAVGGIAAIVAQTPIGALVDRTTAKRaLVVAGAVLVTAAaVAMPLF-AGLYSI 104
                                    567799999999999999******************************9899978888888888885666669.99999* PP

                          MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                     vl +++G+++++++pa aa++   + ++  +r ig   a++ +G + ++++ g+la  +g  +vf++la+++l++ vl+
  gi|121638339|ref|YP_978563.1| 105 SVLQAVTGIASSVFAPALAAITLGAVGPQFFARRIGRNEAFNHAGNASAAGATGALAYFFGPVVVFWVLAGMALIS-VLA 183
                                    ***************************************************************************9.667 PP

                          MFS_1 169 llllpeepperkrkspkeeekgtgpaplvp...awkallkdpvlwillialllfffgfsglltllplylqevlgls.... 241
                                     l +p +++++   ++ +     +p +  p    ++ l +++ l  +++++++++ ++++  ++lpl   e l l     
  gi|121638339|ref|YP_978563.1| 184 TLRIPPDAVDHDLARGMDH----APGEPHPqpsRFTVLAHNREL--VIFGAAVVA-FHFANAAMLPLV-GELLALHnrde 255
                                    8888999999999998888....3333333445699******99..666666665.888888999996.88888887777 PP

                          MFS_1 242 glllaglllallalvgailallag 265
                                    g  l++  + ++++v++++a ++g
  gi|121638339|ref|YP_978563.1| 256 GTALMSSCIVAAQVVMVPVAYVVG 279
                                    434444448888888888877776 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 6e-17
                          MFS_1  38 ltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpk. 116
                                    +++  ++++  ++++G  +d +Gr++++l+g++++ + ++l +++ ++++l+ + +l G+gag++ ++   ++ d++++ 
  gi|121638339|ref|YP_978563.1| 264 IVAAQVVMVPVAYVVGTRADAWGRKPIFLVGFAVLTARGFLYTLSDNSYWLVGVQLLDGIGAGIFGALFPLVVQDVTHGt 343
                                    2334445566666667779999****888888777777455555655557*****************************9 PP

                          MFS_1 117 eergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspk 185
                                     + +  +g +++++++Ga+l  l++g+++  +g+ a+f+ l++++  +f+l l+ +pe+  +  r++++
  gi|121638339|ref|YP_978563.1| 344 GHFNISLGAVTTATGIGAALSNLVAGWIVVVAGYDAAFMSLGALAGAGFLLYLVAMPETVDSDVRVRSR 412
                                    9*************************************************8777777777666666655 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6  11.0   6.3e-14   5.6e-10      18     374 ..      30     372 ..      26     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.3e-14
                     MFS_1_like  18 llPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesk 96 
                                    l PYl+iyl    + + + ig+++++  + +i+++  +g+l+Dr+ ++ ++v+++++l +++ +++              
  gi|121638339|ref|YP_978563.1|  30 LGPYLSIYLLlIHDWDQASIGFVMAVGGIAAIVAQTPIGALVDRTTAKRALVVAGAVLVTAAAVAMP------------- 96 
                                    67******994579************************************99999999888887555............. PP

                     MFS_1_like  97 levsvaqdvdaektfwilfllvvlasfflaailvlldaatlkel..gedrkdyGrqrlfGsvGyaifafitGilidhysv 174
                                                  + ++ +l ++  + ++   + l a+tl ++  + ++++ Gr   f   G a +a +tG+l  ++  
  gi|121638339|ref|YP_978563.1|  97 ----------LFAGLYSISVLQAVTGIASSVFAPALAAITLGAVgpQFFARRIGRNEAFNHAGNASAAGATGALAYFFGP 166
                                    ..........455788888888888888888888999*******77778999********************99766555 PP

                     MFS_1_like 175 nllpysallyvlaallvisllvvlilnetekesklkvtksl.........qvllnilknpeviifllvalilgmswgiie 245
                                         ++++ vla++ +is+l  l ++ +   ++l+    +         + ++ + +n+e++if ++++  +++++++ 
  gi|121638339|ref|YP_978563.1| 167 -----VVVFWVLAGMALISVLATLRIPPDAVDHDLARGMDHapgephpqpSRFTVLAHNRELVIFGAAVVAFHFANAAML 241
                                    .....46999*********999999888777777665544467******988999999***************9999998 PP

                     MFS_1_like 246 nFlflYL..kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLh 323
                                      +   L  ++ +  + l++s ++   v  +p+ ++     +  G   + ++++ + ++r +ly + +n  +++ +++L 
  gi|121638339|ref|YP_978563.1| 242 PLVGELLalHNRDEGTALMSSCIVAAQVVMVPVAYVVGTRADAWGRKPIFLVGFAVLTARGFLYTLSDNSYWLVGVQLLD 321
                                    8877776546677778899999999999999999999999**************************************** PP

                     MFS_1_like 324 gisfgllwaaaveyvskiapksleatgqgl.lsglyfglGralGsliGGllw 374
                                    gi  g++ +a+   v + +++++  + ++l  +++  g+G al +l++G + 
  gi|121638339|ref|YP_978563.1| 322 GIGAGIF-GALFPLVVQDVTHGTGHFNISLgAVTTATGIGAALSNLVAGWIV 372
                                    ***9987.88888888888888888888883345678999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2713.85
//
Query:       gi|121638340|ref|YP_978564.1|  [L=426]
Description: ATP-dependent protease ATP-binding subunit ClpX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-50  169.6   0.0      1e-49  168.9   0.0    1.3  1  AAA_2            AAA domain (Cdc48 subfamily)
    9.1e-21   73.5   6.0    1.9e-20   72.4   6.0    1.6  1  zf-C4_ClpX       ClpX C4-type zinc finger
    1.5e-17   64.3   0.1      5e-17   62.6   0.0    1.9  2  AAA              ATPase family associated with various cellul
    2.4e-17   62.8   0.1    6.6e-17   61.3   0.1    1.8  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    3.6e-07   30.3   0.0    3.3e-06   27.2   0.1    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    8.8e-06   25.2   0.0     0.0026   17.2   0.0    3.1  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.8e-05   23.9   0.2    0.00018   21.3   0.2    2.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.7e-05   23.0   0.1    0.00063   20.0   0.1    2.4  1  AAA_22           AAA domain
    0.00052   19.8   0.0      0.041   13.6   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    0.00052   20.0   0.1     0.0015   18.6   0.0    1.8  1  AAA_14           AAA domain
    0.00055   19.1   0.0    0.00094   18.3   0.0    1.3  1  MCM              MCM P-loop domain
     0.0014   18.4   0.0     0.0027   17.5   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0039   17.7   0.0     0.0083   16.7   0.0    1.6  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.022   14.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.014   15.8   0.0       0.03   14.7   0.0    1.7  1  RNA_helicase     RNA helicase
      0.015   15.4   0.0      0.037   14.1   0.0    1.6  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.016   15.4   0.0      0.045   13.9   0.0    1.8  1  AAA_33           AAA domain
      0.018   15.4   1.5      0.042   14.3   0.0    2.4  1  B12-binding_2    B12 binding domain
       0.02   14.8   0.0      0.042   13.8   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.021   14.3   0.0      0.044   13.2   0.0    1.5  1  PhoH             PhoH-like protein
      0.028   14.4   0.0      0.079   12.9   0.0    1.8  1  NACHT            NACHT domain
      0.029   14.7   0.1       0.15   12.4   0.1    2.2  1  AAA_16           AAA ATPase domain
       0.03   14.1   0.0      0.069   12.9   0.0    1.6  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.04   13.9   0.0      0.074   13.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.045   13.5   0.0      0.075   12.8   0.0    1.4  1  AAA_24           AAA domain
      0.055   14.0   0.0       0.11   13.0   0.0    1.6  1  ABC_tran         ABC transporter
      0.057   12.5   0.0      0.092   11.8   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.058   12.6   0.1       0.13   11.5   0.1    1.5  1  TIP49            TIP49 P-loop domain
       0.11   12.4   0.5        1.5    8.7   0.1    3.0  2  AAA_3            ATPase family associated with various cellul
       0.16   12.1   0.0       0.28   11.3   0.0    1.4  1  SKI              Shikimate kinase
       0.16   11.7   0.0       0.27   10.9   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   0.0   1.8e-52     1e-49       3     170 ..     114     310 ..     112     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.8e-52
                                    ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---....----THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                          AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselle....eeevehlvsrligappgyvgaeegGivllDEid 78 
                                    +++il+lgptg+Gkt+la++la++l+v    ++++ada++l+e    +e+ve+++ +li+a++++v+++e Gi+++DE+d
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTLAKMLNV----PFAIADATALTEagyvGEDVENILLKLIQAADYDVKRAETGIIYIDEVD 189
                                    799***********************8....************************************************* PP

                                    G----...---------HHHHHHHHHHHH--EE-.........----.--EE-TT-EEEEEE--TTHHHHTTTS-S.... CS
                          AAA_2  79 Kihpk...essgadvSregVqrdLLqileggtlt.........dkqg.rkvdtknilfImtgafgsskisdesrsk.... 141
                                    Ki++k   +s+++dvS+egVq++LL+ileg++++         ++q+  ++dt+n+lfI++gaf++ +++  +r +    
  gi|121638340|ref|YP_978564.1| 190 KIARKsenPSITRDVSGEGVQQALLKILEGTQASvppqgarkhPHQEfIQIDTTNVLFIVAGAFAGLEKIIYERVGkrgl 269
                                    ******999**********************************99999*******************9999999889*** PP

                                    ............TTTTSGGG--HHHHHHTT--HHHHTT--E CS
                          AAA_2 142 ............eeeeekkkeeveeelkkglipEllgRlpe 170
                                                +++++ ++ ++e+++k+glipE++gRlp+
  gi|121638340|ref|YP_978564.1| 270 gfgaevrskaeiDTTDHFADVMPEDLIKFGLIPEFIGRLPV 310
                                    **********99999999*********************97 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   6.0   3.3e-23   1.9e-20       2      39 .]      12      48 ..      11      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3.3e-23
                     zf-C4_ClpX  2 rCSFCgksesevkklIagpngvyICdeCvelcneiiee 39
                                   +CSFCgks+++vkklIagp gvyICdeC++lcneiiee
  gi|121638340|ref|YP_978564.1| 12 KCSFCGKSQKQVKKLIAGP-GVYICDECIDLCNEIIEE 48
                                   8******************.6***************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   8.6e-20     5e-17       1     111 [.     117     245 ..     117     261 .. 0.82
   2 ?   -2.3   0.0       9.3   5.4e+03      80     110 ..     371     400 ..     332     421 .. 0.58

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 8.6e-20
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SSSTTHHHHHHH.HHHHHHHHTS....TSEEEEEETGGGHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.skyvgesekkir.elfkeakeka....kpsilfiDEidalaksr 74 
                                    +l+ Gp G+GKT+la+ +ak l+v+f   +++ l+   yvge  ++i  +l+++a        ++ i+ iDE+d++a+++
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLNVPFAIADATALTeAGYVGEDVENILlKLIQAA-DYDvkraETGIIYIDEVDKIARKS 195
                                    6899*******************************667****9999861555555.333355567*************** PP

                                    ...TTCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEESS CS
                            AAA  75 ...sgseseeeervvnqLlteldgvkkk..........eskvivigatnr 111
                                       s + + ++e v+++Ll+ l+g + +          ++++i i +tn 
  gi|121638340|ref|YP_978564.1| 196 enpSITRDVSGEGVQQALLKILEGTQASvppqgarkhpHQEFIQIDTTNV 245
                                    98877899999****************99999999999444555555553 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.3
                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatn 110
                                    + +  + ++Ll+++ +  ++++ v  +++t+
  gi|121638340|ref|YP_978564.1| 371 GLRAIMEEVLLPVMYDIPSRDD-VAKVVVTK 400
                                    3333344556666666665433.54444444 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.1   1.1e-19   6.6e-17       1      75 [.     317     395 ..     317     401 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.1e-19
                                    SCHHHHHHHHHH...HHHHHHHHSCT.TTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSST CS
                  ClpB_D2-small   1 LtkeelkkIvdl...alkklekrlke.rgvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelke 75 
                                    L+ke l+kI+ +   al k++ rl e +gvele+td+al+a+a++++ + +GAR+Lr i+++ +++++++ ++++++++
  gi|121638340|ref|YP_978564.1| 317 LDKESLVKILSEpknALVKQYIRLFEmDGVELEFTDDALEAIADQAIHRGTGARGLRAIMEEVLLPVMYDIPSRDDVAK 395
                                    89***********9**********99899******************************************99999875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   5.7e-09   3.3e-06       1      79 [.     116     193 ..     116     197 .. 0.82
   2 ?   -0.7   0.0       2.2   1.3e+03      81     117 ..     209     246 ..     203     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.7e-09
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------......G-SEEEEESG CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar......egeilvlDEv 74 
                                    ++l++Gp+G+gK+ la+ la++ln ++ +   t+ t++  +   +e           +l +aa       e  i+++DEv
  gi|121638340|ref|YP_978564.1| 116 NILMLGPTGCGKTYLAQTLAKMLNVPFAIADATALTEAGYVGEDVEN-------ILLKLIQAADydvkraETGIIYIDEV 188
                                    689*******************************9888888888873.......3344444444666678999******* PP

                                    GG--H CS
                          AAA_5  75 eraes 79 
                                    +++ +
  gi|121638340|ref|YP_978564.1| 189 DKIAR 193
                                    *9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHSSEEE..-SSSEEE---.......-EEE CS
                          AAA_5  81 vlnsLlslleerrllleeggelvkakndd.llerfrvi 117
                                    v+++Ll++le  + ++++ g + +  +++ ++ +++v+
  gi|121638340|ref|YP_978564.1| 209 VQQALLKILEGTQASVPPQGARKHPHQEFiQIDTTNVL 246
                                    8999***********99999999888876555554444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43   2.5e+02       5      30 ..      75     100 ..      73     105 .. 0.81
   2 !   17.2   0.0   4.4e-06    0.0026      23      47 ..     115     139 ..     110     159 .. 0.88
   3 ?    2.8   0.0      0.11        64     101     121 ..     174     194 ..     167     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                   Mg_chelatase   5 vkGqeeakraleiaaaGgHnlllvGp 30 
                                    v+Gq++akr+l +a+  + + + +G 
  gi|121638340|ref|YP_978564.1|  75 VIGQDTAKRTLAVAVYNHYKRIQAGE 100
                                    89************987776666665 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.4e-06
                   Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllp 47 
                                     n+l++Gp G+GKt la+ l+++l 
  gi|121638340|ref|YP_978564.1| 115 SNILMLGPTGCGKTYLAQTLAKMLN 139
                                    59******************99985 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                   Mg_chelatase 101 eislahnGvLfLDElpefkrk 121
                                    ++ +a++G++++DE+ ++ rk
  gi|121638340|ref|YP_978564.1| 174 DVKRAETGIIYIDEVDKIARK 194
                                    7999***********999886 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   3.1e-07   0.00018      33     101 ..     114     196 ..      64     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.1e-07
                         RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekag....dlaalltnl..........eekdvlfideihrlsr 98 
                                       +l+ Gp G Gkt la+ +ak l+v + i+ + +l +ag    d+  +l +l           e+ +++ide+ +++r
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTLAKMLNVPFAIADATALTEAGyvgeDVENILLKLiqaadydvkrAETGIIYIDEVDKIAR 193
                                    3579*********************************9997555577888877632222222212345899999999988 PP

                         RuvB_N  99 ave 101
                                    + e
  gi|121638340|ref|YP_978564.1| 194 KSE 196
                                    776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.1e-06   0.00063       4     104 ..     113     192 ..     110     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                    t++ ++  G++G+GKT+l+++l++ l         +++++  +++++t+   + +++ ++l             l++a  
  gi|121638340|ref|YP_978564.1| 113 TKSNILMLGPTGCGKTYLAQTLAKML---------NVPFAIADATALTEAGYVGEDVENILL-----------KLIQAAD 172
                                    57789999******************.........999999999999988888888877777...........4888888 PP

                         AAA_22  84 qalraravielliiDEaqhlr 104
                                      ++++ + +++ iDE++++ 
  gi|121638340|ref|YP_978564.1| 173 YDVKRAET-GIIYIDEVDKIA 192
                                    88888888.888888888874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   7.1e-05     0.041      17      45 ..     109     137 ..     101     154 .. 0.81
   2 ?    3.3   0.0      0.11        62      89     106 ..     175     192 ..     169     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                                    HHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                Sigma54_activat  17 kvaktdlsvlitGesGtGKellaraihea 45 
                                     v  t++++l++G +G+GK++la+++ + 
  gi|121638340|ref|YP_978564.1| 109 PVELTKSNILMLGPTGCGKTYLAQTLAKM 137
                                    5677899*****************98764 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                                    HHHTTTSEEEEETGGGS- CS
                Sigma54_activat  89 fekadgGtlfLDeigelp 106
                                    +++a+ G++++De+ ++ 
  gi|121638340|ref|YP_978564.1| 175 VKRAETGIIYIDEVDKIA 192
                                    789***********9986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-06    0.0015       5      77 ..     117     192 ..     113     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.......ekktylflDEiqevp 77 
                                    +++ G+  +GKT+l+++l+k l      +   +    +++ +   e++++++l+++++        ++ ++++DE+ ++ 
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLN---VPFAIADATALTEAGYVG-EDVENILLKLIQAadydvkrAETGIIYIDEVDKIA 192
                                    6789**************98887...223333333333322222.2344444444333344577788999******9983 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.6e-06   0.00094      26     137 ..      75     195 ..      63     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                                    SSS-HHHHHHHHHHHH---EBBBSSSSB........BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE.ESSSSSSSH CS
                            MCM  26 iyghedvkkaillqlfggvkkkledktk........lrgdinvllvgdpgtaKsqlLkyveklapravyt.sgkgssaag 96 
                                    ++g+++ k+++++++   +k+ +  ++           ++ n+l++g  g++K+ l ++++k+++    +  +++ ++ag
  gi|121638340|ref|YP_978564.1|  75 VIGQDTAKRTLAVAVYNHYKRIQAGEKGrdsrcepvELTKSNILMLGPTGCGKTYLAQTLAKMLNVPFAIaDATALTEAG 154
                                    66677777777777666666543321111211222234689********************9988776541577889999 PP

                                    SSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHH CS
                            MCM  97 LtaavvrdeetgefvleaGalvladkGvcciDefdkmkeed 137
                                     +   v +   + +      +  a++G+++iDe+dk+ ++ 
  gi|121638340|ref|YP_978564.1| 155 YVGEDVENILLKLIQAADYDVKRAETGIIYIDEVDKIARKS 195
                                    99999877766666666667889*************98765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.6e-06    0.0027      47      69 ..     114     136 ..     109     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
                      IstB_IS21  47 kenivllGpsGvGKshlaialgv 69 
                                    k ni++lGp+G GK++la +l++
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTLAK 136
                                    78*****************9986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-05    0.0083       1      48 [.     117     179 ..     117     221 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf................gvnlrdvakenglllevdpealde 48 
                                    Il  G+ G+GKt la+ L+k+l++                g+ +  ++ +     ++d +   e
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLNVpfaiadatalteagyvGEDVENILLKLIQAADYDVK-RAE 179
                                    7889*****************998986666666665555544444444444443333333.444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-05     0.022      33     108 ..     114     187 ..     110     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr.rkgvygPpggkklvvFvDD 108
                                    k ++l+ GptG+GKt ++++l k l+   + +++   +a t+a  + + +e+ l k  +   y  +  ++ ++++D+
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTLAKMLN---VPFAIADATALTEAGYVGEDVENILLKLiQAADYDVKRAETGIIYIDE 187
                                    6799****************999998...555555666666666666666665555313355666666666666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.2e-05      0.03       1      23 [.     117     139 ..     117     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                    i++ Gp+g+GK++la++Lak l 
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLN 139
                                    6789***************9987 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.5e-05     0.037      15      83 ..     108     193 ..     104     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-05
                                    HHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHH.......TTTSEE CS
                Sigma54_activ_2  15 eqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleq.......akggtL 73 
                                    e ++  k++++++G+ G+gk++ A++L+k      +i++   l ++               +            a+ g++
  gi|121638340|ref|YP_978564.1| 108 EPVELTKSNILMLGPTGCGKTYLAQTLAKMLNVPFAIADATALTEAGyvgedvenillkliQ----AadydvkrAETGII 183
                                    66677899********************9988766666665555433555555555543330....33333333688888 PP

                                    EEEE-TT--H CS
                Sigma54_activ_2  74 ylkdiadlsk 83 
                                    y+ +++++ +
  gi|121638340|ref|YP_978564.1| 184 YIDEVDKIAR 193
                                    8888887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.8e-05     0.045       2      30 ..     117     146 ..     117     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.avllss 30 
                                    +l+ G+ G+GK++la+ l+k l   + ++ 
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLNvPFAIAD 146
                                    689****************99986444444 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.3e-05     0.042      11      46 ..     349     387 ..     348     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.3e-05
                  B12-binding_2  11 hgdkegieelidealaqgsa...avdvlndvllpamkeV 46 
                                    ++ ++++e+++d+a+ +g     + +++++vllp+m+++
  gi|121638340|ref|YP_978564.1| 349 EFTDDALEAIADQAIHRGTGargLRAIMEEVLLPVMYDI 387
                                    677899*********99966689*************987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.2e-05     0.042      43      71 ..     113     140 ..      82     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.2e-05
                          Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgi 71 
                                     k + +L+ GP+GCgk+   + L+k l +
  gi|121638340|ref|YP_978564.1| 113 TKSN-ILMLGPTGCGKTYLAQTLAKMLNV 140
                                    4344.5667****************9865 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.7e-05     0.044      20      40 ..     115     135 ..      96     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                                    SEEEEE--TTSSTTHHHHHHH CS
                           PhoH  20 divfaiGpaGtGKtylavala 40 
                                    + + ++Gp+G+GKtyla +la
  gi|121638340|ref|YP_978564.1| 115 SNILMLGPTGCGKTYLAQTLA 135
                                    456789***********9887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.079       3      24 ..     117     138 ..     115     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    +++ G+ G+GKT+L+q la  +
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKML 138
                                    7899**************9866 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00026      0.15      25      49 ..     115     139 ..     100     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                         AAA_16  25 elvllsGesGvGKsslvrellrale 49 
                                    +++l  G+ G+GK+ l+++l++ l+
  gi|121638340|ref|YP_978564.1| 115 SNILMLGPTGCGKTYLAQTLAKMLN 139
                                    7899****************98554 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.069       2      23 ..     115     136 ..     114     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkg 23 
                                    ++il++G++g+GKt L+q+l +
  gi|121638340|ref|YP_978564.1| 115 SNILMLGPTGCGKTYLAQTLAK 136
                                    579***************9975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013     0.074      19      48 ..     114     144 ..      91     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--.-- CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve.ev 48 
                                    ++ il+ G+ G+GKT l++ lak l+v  ++
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTLAKMLNVPfAI 144
                                    45699*******************9986655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.075       2      37 ..     114     157 ..     113     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                         AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfi.........dtekGlks 37 
                                    k +il+ Gp g GKT+la +l  k l +          te+G+  
  gi|121638340|ref|YP_978564.1| 114 KSNILMLGPTGCGKTYLAQTL-AKMLNVpfaiadataLTEAGYVG 157
                                    6789*****************.77766644446666655555533 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0002      0.11      13      36 ..     116     139 ..     111     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0002
                                    EEEEEESTTSSHHHHHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllk 36 
                                     + ++G++G+GK+ L+++la++l+
  gi|121638340|ref|YP_978564.1| 116 NILMLGPTGCGKTYLAQTLAKMLN 139
                                    6789***************99876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016     0.092     128     154 ..     113     139 ..      50     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                          T2SSE 128 erglilvsGgTgsGKttllyallkein 154
                                    ++ +il+ G+Tg GKt l+ +l k++n
  gi|121638340|ref|YP_978564.1| 113 TKSNILMLGPTGCGKTYLAQTLAKMLN 139
                                    4789***************99999887 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00022      0.13      51      89 ..     115     151 ..     107     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                      +L+ Gp+g Gkt la +++k l+  vpf++  ++ + 
  gi|121638340|ref|YP_978564.1| 115 SNILMLGPTGCGKTYLAQTLAKMLN--VPFAIADATALT 151
                                    579*********************8..9**998887765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.6   1.5e+03      11      32 ..      77      98 ..      72     100 .. 0.86
   2 ?    8.7   0.1    0.0026       1.5       2      43 ..     117     157 ..     116     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                          AAA_3 11 aktllvkalakaldlefkriqf 32
                                   ++ ++ ++la a+  ++kriq 
  gi|121638340|ref|YP_978564.1| 77 GQDTAKRTLAVAVYNHYKRIQA 98
                                   56678899************95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilG 43 
                                    +l+ g  G +kt l+++lak+l++ f     t+ l  +  +G
  gi|121638340|ref|YP_978564.1| 117 ILMLGPTGCGKTYLAQTLAKMLNVPFAIADATA-LTEAGYVG 157
                                    6888999*****************998666554.44444455 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00048      0.28       2      25 ..     124     147 ..     123     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00048
                                    TSSHHHHHHHHHHHHTSEEEEHHH CS
                            SKI   2 GaGKstvGkllAkklglefiDlDe 25 
                                    G+GK+ +++ lAk+l+++f  +D 
  gi|121638340|ref|YP_978564.1| 124 GCGKTYLAQTLAKMLNVPFAIADA 147
                                    9******************87776 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00047      0.27       2      70 ..     118     187 ..     117     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDE 70 
                                    ++ G  GcGK+ l ++l+++  + + +    a +lte+    ++++n   + ++++    ++  +  i+ +DE
  gi|121638340|ref|YP_978564.1| 118 LMLGPTGCGKTYLAQTLAKMLnVPFAIAD--ATALTEAGyvgEDVENILLKLIQAADYDVKR-AETGIIYIDE 187
                                    667889**************433332222..2333333356767777666666655554444.3566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 2869.86
//
Query:       gi|121638341|ref|YP_978565.1|  [L=302]
Description: homocysteine methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-74  251.8   0.0    1.1e-74  251.6   0.0    1.0  1  S-methyl_trans  Homocysteine S-methyltransferase
  ------ inclusion threshold ------
       0.18   12.1   0.1        2.8    8.2   0.0    2.4  3  AlaDh_PNT_N     Alanine dehydrogenase/PNT, N-terminal domain


Domain annotation for each model (and alignments):
>> S-methyl_trans  Homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.6   0.0   1.3e-78   1.1e-74       1     267 [.       9     294 ..       9     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 1.3e-78
                                    EEB---SHHHHHHT.----STTHHCCHH.H-HHHHHHHHHHHHHHT-SEEE-TTTT--....GG.T--HHHHH.HHHHHH CS
                 S-methyl_trans   1 lilDGgmgteLerr.adlseelwsaell.trpelikeihrdyleaGadiieTnTyqas....kikgleeeeeveelnraa 74 
                                    li DGg++teLe+r +dls++lwsa+ll   p++i ++h++y++aGa+i++T++yqas    +++g+  ++++  l+r++
  gi|121638341|ref|YP_978565.1|   9 LISDGGLATELEARgHDLSDPLWSARLLvDAPHAITAVHTAYFRAGAQIATTASYQASfegfAARGIG-HDDATVLLRRS 87 
                                    699*************************77****************************8866444886.455559***** PP

                                    HHHHHHHHHHH.....HEEEEE--HHHHCTS.-.--....--HHHHHHHHHHHHHHHHHCT-SEEEEEEE--HHHHHHHH CS
                 S-methyl_trans  75 velareaadeaaa.plfvagsvGpygatlsd.g.yd..l.lsfeelveahreqiralleagvDlllietipdlleakaav 148
                                    vela++a+de+    l va+svGpyga+l+d + y   + ls+++l+++h +++++l++ag+D+l++etipd++ea+a+v
  gi|121638341|ref|YP_978565.1|  88 VELAQAARDEVGVgGLSVAASVGPYGAALADgSeYRgcYgLSVAALMKWHLPRLEVLVDAGADMLALETIPDIDEAEALV 167
                                    **********9668777**************734434435***************99*********************** PP

                                    HHHT.T.--EEEEE-ECCT.T.ETTS-BHHH.HHHHHCT-TEEEEEEES--GGGHHHHHHHHHTT--S-.EEEE---.S- CS
                 S-methyl_trans 149 ellaae.lpvwisftikdest.lrsGetleeavaalaaatqplavgvNCakpeelepllkelksetalpavivypnsage 226
                                    +l++ + +p+w+s ti+ + t +r G++l++a a +a   +++avgvNC+ p+++ p+++ + ++t +p vivypns ge
  gi|121638341|ref|YP_978565.1| 168 NLVRRLaTPAWLSYTIN-G-TrTRAGQPLTDAFAVAAGVPEIVAVGVNCCAPDDVLPAIAFAVAHTGKP-VIVYPNS-GE 243
                                    *9998789********5.4.4499*******77777776477******************998999999.99****8.** PP

                                    ----------....-...........HHHTTEEEE---TT--HHHHHHHHH. CS
                 S-methyl_trans 227 vydltpeewaesaee...........wleaganiiGGCCgttpehIraiaea 267
                                     +d   + w     +           w++aga+i+GGCC+++p +I++i +a
  gi|121638341|ref|YP_978565.1| 244 GWDGRRRAWVGPR-RfsgssgqlareWVAAGARIVGGCCRVRPIDIAEIGRA 294
                                    ***9999998764.358889999999**********************9776 PP

>> AlaDh_PNT_N  Alanine dehydrogenase/PNT, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.054   4.8e+02      44      58 ..      47      61 ..      34      68 .. 0.78
   2 ?    8.2   0.0   0.00032       2.8      97     127 ..     137     167 ..     122     172 .. 0.80
   3 ?   -4.0   0.0       1.9   1.7e+04      46      55 ..     268     277 ..     265     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.054
                                   HHHHHHTTEEEESCH CS
                    AlaDh_PNT_N 44 deeYeeaGaeivesa 58
                                     +Y +aGa+i+++a
  gi|121638341|ref|YP_978565.1| 47 HTAYFRAGAQIATTA 61
                                   57899******9877 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00032
                                    HHHHHHHHHHCTEEEEEGGG-BSSGCCGGGT CS
                    AlaDh_PNT_N  97 npellealaekgvtaialElvprisraqsld 127
                                    + + le l ++g+ ++alE++p+i++a++l 
  gi|121638341|ref|YP_978565.1| 137 HLPRLEVLVDAGADMLALETIPDIDEAEALV 167
                                    5578999*****************9997765 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.9
                                    HHHHTTEEEE CS
                    AlaDh_PNT_N  46 eYeeaGaeiv 55 
                                    e+ +aGa+iv
  gi|121638341|ref|YP_978565.1| 268 EWVAAGARIV 277
                                    6789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2279.99
//
Query:       gi|121638342|ref|YP_978566.1|  [L=508]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-48  166.1  40.3      1e-48  166.1  40.3    2.0  2  MFS_1     Major Facilitator Superfamily
    9.8e-08   31.3  28.5    1.9e-06   27.1  14.0    3.1  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
      0.063   13.5   0.2      0.063   13.5   0.2    3.4  3  DUF3007   Protein of unknown function (DUF3007)
        8.8    4.5  21.1      0.017   13.5   1.3    3.5  4  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1  40.3   2.3e-52     1e-48       3     352 ..      14     404 ..      12     405 .. 0.87
   2 ?   -3.8   0.4       1.1   4.7e+03     281     296 ..     484     499 ..     475     506 .. 0.46

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 2.3e-52
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                    l++f+++ + +i+++alp  +++ ++  ++ +++++++y+lg+a+  +  + l+dr+Grrr +++g++lf++++++++++
  gi|121638342|ref|YP_978566.1|  14 LGIFMVFVDVNIVNVALP-SIQKVFHTGEQGLQWAVAGYSLGMAAVLMSCALLGDRYGRRRSFVFGVTLFVVSSIVCVLP 92 
                                    899***************.9*****************************************************6666664 PP

                          MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                     sl ++ v+rv+qGlga+++  +++al+++ fp  + ++rai+ ++a   +Ga+ +p+lggl+++ lgWr+vf+++ +++
  gi|121638342|ref|YP_978566.1|  93 VSLAVFTVARVIQGLGAAFISVLSLALLSHSFPNpRMKARAISNWMAIGMVGAASAPALGGLMVDGLGWRSVFLVNVPLG 172
                                    5555******************************99******************************************** PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeee............................................kgtgpaplv 197
                                    +++ +l   l+ +++++ + +++ +                                              +++++++++
  gi|121638342|ref|YP_978566.1| 173 AIVWLL--TLVGVDESQDPEPTQLDWVgqltlipavaliaytiieaprfdrqsagfvaalllaagvllwlfVRHEHRAAF 250
                                    ***888..66666666666665444437799**********************999999999999999999555555555 PP

                          MFS_1 198 p.awkallkdpvlw.illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275
                                    p +  +l++ p  + ++li+ ++++ +f+g+l+ ++  +q v++ls  l agl++  + +++ +++llagr ++++g+  
  gi|121638342|ref|YP_978566.1| 251 PlVDLKLFAEPL-YrSVLIVYFVVMSCFFGTLMVITQHFQNVRDLS-PLHAGLMMLPVPAGFGVASLLAGRAVNKWGP-Q 327
                                    532244444442.35677888888789999888888888*******.799999999999999999*************.6 PP

                          MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                      +l++l+++++ l+++ +++ +  +++l++l ++G g+g + ++ll l +  +   +ag+a+g  n+ +slgg++g
  gi|121638342|ref|YP_978566.1| 328 LPVLTCLAAMFIGLAIFAISMDHAHPVALVGLTIFGAGAGGCATPLLHLGMTKVDDGRAGMAAGMLNLQRSLGGIFG 404
                                    666666666666777777777889999999*******99999*********************************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.1
                          MFS_1 281 llllllaalglallav 296
                                    l+++++++ g ++l++
  gi|121638342|ref|YP_978566.1| 484 LGGAAVLLTGAFVLGW 499
                                    3333333333333333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1  14.0   4.1e-10   1.9e-06      49     184 ..      45     175 ..       8     187 .. 0.75
   2 !    8.6   6.6   0.00016      0.72      48     120 ..     299     370 ..     263     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.1e-10
                                    HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                     + v+ +++G ++  +   llgdr+GR+ s++++++lfv++++++++     s+ v++v+Rv+ G+g+ ++svl+  ++s
  gi|121638342|ref|YP_978566.1|  45 QWAVAGYSLGMAAVLMSCALLGDRYGRRRSFVFGVTLFVVSSIVCVLPV---SLAVFTVARVIQGLGAAFISVLSLALLS 121
                                    588999999*9999999********************************...9*********************998888 PP

                                    TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH CS
                       Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll 184
                                       p + R +   + ++ +++G++ aa   +    + +  gwr  + +++ +  ++
  gi|121638342|ref|YP_978566.1| 122 HSFP-NPRMKARAISNW-MAIGMVGAASAPALGGLMVDGLGWRSVFLVNVPLGAIV 175
                                    7554.444444444444.35565555555544455555577777777777765444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00016
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                     gl++  + +G  + sl+ag +++++G +   l++ + ++ig ++ a++  + ++ v +vg  + G g+G++ 
  gi|121638342|ref|YP_978566.1| 299 AGLMMLPVPAGFGVASLLAGRAVNKWGPQLPVLTCLAAMFIGLAIFAISM-DHAHPVALVGLTIFGAGAGGCA 370
                                    57777778889999***********************************9.559***************9975 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.3   5.9e+03      18      28 ..     172     182 ..     146     188 .. 0.63
   2 ?   13.5   0.2   1.4e-05     0.063      13      51 ..     203     241 ..     192     245 .. 0.90
   3 ?    0.1   0.3      0.22   9.7e+02       6      36 ..     336     366 ..     332     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                        DUF3007  18 glaylvlqalG 28 
                                    g++ ++l+++G
  gi|121638342|ref|YP_978566.1| 172 GAIVWLLTLVG 182
                                    22334444455 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                        DUF3007  13 vlllgglaylvlqalGldslsagiwsqavlvlglvgWvl 51 
                                    + +++ +ay++++a  +d +sag+++ ++l +g++ W++
  gi|121638342|ref|YP_978566.1| 203 IPAVALIAYTIIEAPRFDRQSAGFVAALLLAAGVLLWLF 241
                                    567899*******************************86 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.22
                        DUF3007   6 vlaiglgvlllgglaylvlqalGldslsagi 36 
                                    +++igl+++++++     + ++Gl  + ag 
  gi|121638342|ref|YP_978566.1| 336 AMFIGLAIFAISMDHAHPVALVGLTIFGAGA 366
                                    6778888888887777777777777766664 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   3.7e-06     0.017       5      87 ..      11      93 ..       7      97 .. 0.90
   2 ?    4.9   0.6    0.0014       6.5     133     192 ..      96     156 ..      93     217 .. 0.90
   3 ?   -0.9   0.6     0.082   3.7e+02     283     369 ..     250     335 ..     242     351 .. 0.57
   4 ?   -0.7   0.6     0.072   3.2e+02     137     191 ..     357     420 ..     345     427 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP  5 llsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslllalP 86
                                   + +l +++  +   ++++++ +i+k F+   +   + ++++ +g +++++  + +g+r  r r   +g+ l+ ++s++++lP
  gi|121638342|ref|YP_978566.1| 11 ATGLGIFMVFVDVNIVNVALPSIQKVFHTGEQGLQWAVAGYSLGMAAVLMSCALLGDRYGRRRSFVFGVTLFVVSSIVCVLP 92
                                   5555566667777889****************************************************************** PP

                                   x RF
                           OATP 87 h 87
                                    
  gi|121638342|ref|YP_978566.1| 93 V 93
                                   6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0014
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 133 llfflaqlllGiGatpiytlGisYidDnvk.kknsplylgilyalrilGpalGfllGslll 192
                                     +f +a +++G+Ga+ i  l ++ +  +   ++  +  ++ ++a+ ++G a + +lG+l++
  gi|121638342|ref|YP_978566.1|  96 AVFTVARVIQGLGAAFISVLSLALLSHSFPnPRMKARAISNWMAIGMVGAASAPALGGLMV 156
                                    4899*********************9876615666799*******************9986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.082
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                           OATP 283 fpkalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipg...aalGillgGllvkklk 359
                                    fp + ++l+ +p++  v++   + ++++ G  +     + ++F+  +  + l +G++++p+   +++  ll+G  v+k+ 
  gi|121638342|ref|YP_978566.1| 250 FPLVDLKLFAEPLYRSVLIVYFVVMSCFFGTLM----VITQHFQNVRDLSPLHAGLMMLPVpagFGVASLLAGRAVNKWG 325
                                    555556666666666666654444444444433....4667777777777777777777642114455688888888887 PP

                                    xxxxxxxxxx RF
                           OATP 360 lsakklaklv 369
                                    ++   l  l+
  gi|121638342|ref|YP_978566.1| 326 PQLPVLTCLA 335
                                    7765443333 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.072
                                    xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                           OATP 137 laqlllGiG....atpiytlGisYidDnvkkknsplyl.....gilyalrilGpalGfllGsll 191
                                    ++ ++ G+G    atp+  lG++ +dD      + ++      g ++ +++lG +++  lG++l
  gi|121638342|ref|YP_978566.1| 357 VGLTIFGAGaggcATPLLHLGMTKVDDGRAGMAAGMLNlqrslGGIFGVAFLGTIVAAWLGAAL 420
                                    4444444442233699999999999997665555543223333666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3134.47
//
Query:       gi|121638343|ref|YP_978567.1|  [L=214]
Description: ATP-dependent Clp protease proteolytic subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-74  248.7   0.1    4.1e-74  248.4   0.1    1.1  1  CLP_protease  Clp protease


Domain annotation for each model (and alignments):
>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.4   0.1   2.3e-78   4.1e-74       7     181 ..      30     206 ..      24     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 2.3e-78
                                    HHHHHHHHTTTEEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEE CS
                   CLP_protease   7 ydiysrllkeriiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaa 86 
                                     + y++l++eriiflg ++dd++an+i+aqLl+Le+ dpd+di++yinspGG +t+ +aIydtmqy+++d++t+clG+aa
  gi|121638343|ref|YP_978567.1|  30 SNPYNKLFEERIIFLGVQVDDASANDIMAQLLVLESLDPDRDITMYINSPGGGFTSLMAIYDTMQYVRADIQTVCLGQAA 109
                                    6789**************************************************************************** PP

                                    THHHHHHHTS-TTGEEEETTEEEEES-T..EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEE CS
                   CLP_protease  87 SmgslllaagekgkRfalpnarimihqP..lggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtfl 164
                                    S++++llaag++gkR+alpnar++ihqP  +g +qgq sd+ei+a e++++++ ++++la+htg+++  i+kd+drd++l
  gi|121638343|ref|YP_978567.1| 110 SAAAVLLAAGTPGKRMALPNARVLIHQPslSGVIQGQFSDLEIQAAEIERMRTLMETTLARHTGKDAGVIRKDTDRDKIL 189
                                    ****************************766999********************************************** PP

                                    EHHHHHHHTSSSEE-SS CS
                   CLP_protease 165 saeeAveyGLideviek 181
                                    +aeeA++yG+id+v+e 
  gi|121638343|ref|YP_978567.1| 190 TAEEAKDYGIIDTVLEY 206
                                    **************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1407.28
//
Query:       gi|121638344|ref|YP_978568.1|  [L=200]
Description: ATP-dependent Clp protease proteolytic subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-74  248.6   0.1    4.2e-74  248.4   0.1    1.0  1  CLP_protease  Clp protease


Domain annotation for each model (and alignments):
>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.4   0.1   2.3e-78   4.2e-74       7     181 ..      18     192 ..      11     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 2.3e-78
                                    HHHHHHHHTTTEEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEE CS
                   CLP_protease   7 ydiysrllkeriiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaa 86 
                                     ++y+rll+eriiflgse++de+an+++aq+llL aed +kdi+lyinspGGs++ag+aIydtm +  +d++t+++G+aa
  gi|121638344|ref|YP_978568.1|  18 DSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAA 97 
                                    679***************************************************************************** PP

                                    THHHHHHHTS-TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEH CS
                   CLP_protease  87 SmgslllaagekgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsa 166
                                    Smg +llaag+kgkR+alp+ari++hqPlgg++g+a di+i+ae++  ik+++ ++ a+ tgq++e+ie+d drd++++a
  gi|121638344|ref|YP_978568.1|  98 SMGEFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTA 177
                                    ******************************************************************************** PP

                                    HHHHHHTSSSEE-SS CS
                   CLP_protease 167 eeAveyGLideviek 181
                                    +eA+eyG++d++i++
  gi|121638344|ref|YP_978568.1| 178 AEALEYGFVDHIITR 192
                                    ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1653.10
//
Query:       gi|121638345|ref|YP_978569.1|  [L=466]
Description: trigger factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-40  136.6   5.9    1.8e-39  135.3   4.7    2.2  3  Trigger_C  Bacterial trigger factor protein (TF) C-terminus
    7.4e-39  133.3   0.0    2.7e-38  131.5   0.0    2.0  1  Trigger_N  Bacterial trigger factor protein (TF)
    0.00011   22.5   0.0     0.0003   21.0   0.0    1.7  1  FKBP_C     FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
      0.024   15.0   0.1       0.11   12.9   0.1    2.1  1  CM_2       Chorismate mutase type II


Domain annotation for each model (and alignments):
>> Trigger_C  Bacterial trigger factor protein (TF) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.37   1.6e+03      38      69 ..      16      47 ..      13      68 .. 0.81
   2 ?   -3.5   0.0       2.1   9.3e+03     107     128 ..     129     150 ..     126     152 .. 0.79
   3 !  135.3   4.7   4.1e-43   1.8e-39       1     161 [.     258     418 ..     258     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.37
                                   EEEE-HHHHHHHHHHHHHHHHHCT...TSSHH CS
                      Trigger_C 38 eidiPeslveeeidrllrqakqqleqqGldle 69
                                   ++++P + +e  ++r+++++++q++  G+++ 
  gi|121638345|ref|YP_978569.1| 16 NVEVPFAELEPDFQRAYKELAKQVRLPGFRPG 47
                                   68888889999999999999999987777665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                                    TT----HHHHHHHHHHHCCCTT CS
                      Trigger_C 107 ekievteeelkeeleelasqyg 128
                                      ie+ e+++++el  l  ++g
  gi|121638345|ref|YP_978569.1| 129 DPIEIGEDDVDAELQSLRTRFG 150
                                    5689999999999998887776 PP

  == domain 3  score: 135.3 bits;  conditional E-value: 4.1e-43
                                    CHHHHHHHHCCCCHHHHHHHHHHHHHCCCHCCCGCGEEEEE-HHHHHHHHHHHHHHHHHCT...TSSHHCHHHHHCTHCC CS
                      Trigger_C   1 tLeeLkedlrkqleeekeeatkeelkealldkLvekaeidiPeslveeeidrllrqakqqleqqGldleeylelsgssee 80 
                                    +++eL+++l +q++++k+++++e++++a +d+L+e++++++Pes v++++d++l+ a++ l++++++++e+l ++gss++
  gi|121638345|ref|YP_978569.1| 258 SIDELRASLSDQVRQAKRAQQAEQIRNATIDALLEQVDVPLPESYVQAQFDSVLHSALSGLNHDEARFNELLVEQGSSRA 337
                                    69****************************************************************************** PP

                                    CHCHHCHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHCCCTTSXHHHHHHHHHHXHHHHHHHHHHHHHHHHHHH CS
                      Trigger_C  81 elreelkeeAekrVklgLvleeiakeekievteeelkeeleelasqygmepeevkeflkkneqlsalkedileekvvdll 160
                                    ++++e++++ ek+Vk++L+l+++a+e +++v +++l+e+l  +++qyg+ep++++ +l++++ql+++ +d+++e ++ + 
  gi|121638345|ref|YP_978569.1| 338 AFDAEARTASEKDVKRQLLLDALADELQVQVGQDDLTERLVTTSRQYGIEPQQLFGYLQERNQLPTMFADVRRELAIRAA 417
                                    ****************************************************************************9987 PP

                                    C CS
                      Trigger_C 161 l 161
                                    +
  gi|121638345|ref|YP_978569.1| 418 V 418
                                    6 PP

>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   6.1e-42   2.7e-38       1     140 [.       1     144 [.       1     145 [. 0.96

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 6.1e-42
                                    -EEEEEEEETTEEEEEEEE-HHHCHHHHHHHHHHHHTTS-BTTC-TT---CCCHHHHCTCC.CHHHHHHHHHHCCCCCCC CS
                      Trigger_N   1 mkvtvekleglkvkltvevpaeevekavekalkklakkvkipGFRkGkvPrsiiekrygke.vleealeellnealeeai 79 
                                    mk tve+l++++v+++vevp +e+e+ +++a+k+lak+v++pGFR+Gk+P++++e r+g+e +l+++++++l++ + +a+
  gi|121638345|ref|YP_978569.1|   1 MKSTVEQLSPTRVRINVEVPFAELEPDFQRAYKELAKQVRLPGFRPGKAPAKLLEARIGREaMLDQIVNDALPSRYGQAV 80 
                                    99****************************************************************************** PP

                                    CCS..-EE.EE.E..E.EETTC.EEEEEEEEE--EEEE.XCCCSEEEEEXHHHHHHHHHHHHHH CS
                      Trigger_N  80 eeeklepvgqpei..e.leegkdleftvevevkPevelgdykglevekeevevtdeevdeelee 140
                                     e++++p+g+p+i  + +e g+dl+ft+ev+++P++ l+d++ l+v+++ +e+ +++vd+el++
  gi|121638345|ref|YP_978569.1|  81 AESDVQPLGRPNIevTkKEYGQDLQFTAEVDIRPKISLPDLSALTVSVDPIEIGEDDVDAELQS 144
                                    *************753366699***************************************986 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.8e-08    0.0003       6      66 ..     160     217 ..     156     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.8e-08
                                    -TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEE CS
                         FKBP_C   6 kegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltip 66 
                                    + gd+V+++  +++ dg+ + +    a+ l+ +vGsg++i G+++a++g++++e r +t +
  gi|121638345|ref|YP_978569.1| 160 AVGDVVSIDLSATV-DGEDIPNA--AAEGLSHEVGSGRLIAGLDDAVVGLSADESRVFTAK 217
                                    5699**********.99999999..9******************************99876 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.4e-05      0.11      18      68 ..     263     312 ..     259     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHHS-HHHHHHHHHHHHH CS
                           CM_2  18 RaelakevgeyKkeeglpvydpeReaevlerleegaldeeaierifreiis 68 
                                    Ra l+++v+++K++++++  + +  +++le++   +l+e+++++ f  ++ 
  gi|121638345|ref|YP_978569.1| 263 RASLSDQVRQAKRAQQAEQIRNATIDALLEQVDV-PLPESYVQAQFDSVLH 312
                                    9************9999*****************.*********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3232.33
//
Query:       gi|121638346|ref|YP_978570.1|  [L=394]
Description: esterase/lipase lipP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-72  243.9   2.6    3.1e-72  243.6   2.6    1.0  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.6   2.6   1.7e-76   3.1e-72      13     324 ..      29     378 ..      18     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: 243.6 bits;  conditional E-value: 1.7e-76
                                    TESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTSTTCTTGGGT CS
                 Beta-lactamase  13 gipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylPefagpgkg 92 
                                    +  G+avav++dg +v++ +gG ad++g+rp++ dtl  + S tK++ta++v+qlv++G+ldL +pV++y+Pef+++gk+
  gi|121638346|ref|YP_978570.1|  29 NEVGAAVAVWVDGDLVVNLWGGSADAGGTRPWQHDTLATVLSGTKALTATCVHQLVDRGELDLHAPVARYWPEFGQAGKQ 108
                                    458***************************************************************************** PP

                                    TEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHH.HHHHHHHHHHTSHHHHHHHHH CS
                 Beta-lactamase  93 kiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgyg.llgellekvtgrsleqllree 171
                                    +iTl+++++H+sG  +    +l +e+ ad++ ++++la+++p+++pG ++gY+ t++g +lge+ ++vtgr+++q+lr+e
  gi|121638346|ref|YP_978570.1| 109 AITLAMVMSHRSGAIGP-RGRLGWEQVADWDFVCEQLAAAEPWWQPGAAQGYHMTTFGfILGEVFRRVTGRTVGQYLRTE 187
                                    **************777.************************************************************** PP

                                    TTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC................................... CS
                 Beta-lactamase 172 ilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae................................... 216
                                    i++p    d ++g+ + ++ r a + ++++  + ++++++p +++                                   
  gi|121638346|ref|YP_978570.1| 188 IAEP-LGADVHIGLHPGEQLRCADLVDKPHIRQLLADVQAPGYPTslnehpkaalsvsmgfapddelgsndlqlwrqief 266
                                    ****.899******************9999999999999999999*********************************** PP

                                    TTTBEEEEHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEEC....ECSSEEEEECCH...TEEEEEEES CS
                 Beta-lactamase 217 gagglistardlarflglalegglllsaetlaqltaklssgttrpagiragl....glGwvladktga...pgtfghtGg 289
                                    ++ ++  +a  la f+   l++++lls+e+++  + ++ +  t   ++++      glG++l++++ +   p++fgh+G 
  gi|121638346|ref|YP_978570.1| 267 PGTNGQVSALGLATFY-NGLAQEKLLSREHMELVRVSQGGFDTDLVLGPRVAdhgwGLGYMLNQRGVNgpnPRIFGHGG- 344
                                    ****************.889999999999999998888888887666666556666*******99999***********. PP

                                    TEEEEEEEECGGTEEEEEEESBCSSHHHHHHHHHH CS
                 Beta-lactamase 290 gygtyvfvdpeanlvvavltnrdppnedaaedarl 324
                                     +g++ fvd e++++ a+++nr+     a +d+r 
  gi|121638346|ref|YP_978570.1| 345 LGGSFGFVDLEHRIGYAYVMNRFDA-TKANADPRS 378
                                    ***********************96.666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2612.38
//
Query:       gi|121638347|ref|YP_978571.1|  [L=268]
Description: DNA glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-27   94.4   0.0    4.8e-27   93.8   0.0    1.3  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
    2.8e-07   30.3   2.9    5.9e-07   29.2   2.9    1.6  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
    4.8e-06   27.2   0.0    1.3e-05   25.8   0.0    1.7  2  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.15   11.8   0.0    1.3  1  DUF3328         Domain of unknown function (DUF3328)


Domain annotation for each model (and alignments):
>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   1.1e-30   4.8e-27       1      89 [.     126     214 ..     126     217 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.1e-30
                                    ---BTTSTTS-HHHHHHHHHT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHH CS
                           H2TH   1 LgpeplseaftvdalaerlkkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqeikevlke 80 
                                    Lgp+pl+++++ +++++r++k++r+i++lL+Dq+++aG+GN+y++E+Lfr++i+P+r+++ + + e+++ ++++++++k 
  gi|121638347|ref|YP_978571.1| 126 LGPDPLRSDANPSSAWSRITKSRRPIGALLMDQTVIAGVGNVYRNELLFRHRIDPQRPGRGIGEPEFDAAWNDLVSLMKV 205
                                    8******************************************************************************* PP

                                    HHHTTTTGC CS
                           H2TH  81 aielgksgi 89 
                                    ++++gk ++
  gi|121638347|ref|YP_978571.1| 206 GLRRGKIIV 214
                                    ***988765 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   2.9   1.3e-10   5.9e-07       1      28 [.     240     267 ..     240     268 .] 0.98

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.3e-10
                                    TSB-TTT--BBEEEECTTEEEEE-TTTT CS
                   zf-FPG_IleRS   1 GepCpRCwryiervgqagrstyfCprCq 28 
                                    GepC++C+++i++  + gr+ ++Cp+Cq
  gi|121638347|ref|YP_978571.1| 240 GEPCRVCGGVIRTALLEGRNVFWCPVCQ 267
                                    9*************************** PP

>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.8e-09   1.3e-05       1      90 [.       1      86 [.       1     111 [. 0.79
   2 ?   -2.2   0.0       1.4   6.2e+03      55      64 ..     208     217 ..     176     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.8e-09
                                   X--HHHHHHHHHHHHHHHTT-EEEEEEE-SSHHHTSTHHHHHTT-.SEEEEEEEEETTEEEEEE..EEEEEEE-TTTEEE.. CS
                 Fapy_DNA_glyco  1 MPElpEVetvrrglrrhllgkkiakvevlkdktlrgspaafakalkgrkiasvgrrGKyllleldggevlvvhlgmtGrl.. 80
                                   MPE   +++++r  +r+  g+ +   +v ++++ r+  a+ a+al+gr++++++  GK+l+ +  gg+v+ vhlg+ G +  
  gi|121638347|ref|YP_978571.1|  1 MPEGHTLHRLARLHQRRFAGAPV---SV-SSPQGRF--ADSASALNGRVLRRASAWGKHLFHHYVGGPVVHVHLGLYGTFte 76
                                   99**9999999999999999887...44.3355555..77899************************************963 PP

                                   SS........ CS
                 Fapy_DNA_glyco 81 likeaeeepp 90
                                   + + ++ + p
  gi|121638347|ref|YP_978571.1| 77 WARPTDGWLP 86
                                   3335555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                    EETTEEEEEE CS
                 Fapy_DNA_glyco  55 rrGKylllel 64 
                                    rrGK ++++ 
  gi|121638347|ref|YP_978571.1| 208 RRGKIIVVRP 217
                                    8899888875 PP

>> DUF3328  Domain of unknown function (DUF3328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.15      59     109 ..     168     220 ..     124     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                        DUF3328  59 yelkqfk.....lgskeapsiyrgepspevdaaWddllkleailipree..lrrlgkd 109
                                    y           +++ +++++ rg  +pe daaW+dl++l  + + r +  + r ++d
  gi|121638347|ref|YP_978571.1| 168 Y-----RnellfRHRIDPQRPGRGIGEPEFDAAWNDLVSLMKVGLRRGKiiVVRPEHD 220
                                    3.....1444458999**********************99999999888654444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1984.17
//
Query:       gi|121638348|ref|YP_978572.1|  [L=162]
Description: ribose-5-phosphate isomerase B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-43  147.0   0.0    3.6e-43  146.9   0.0    1.0  1  LacAB_rpiB  Ribose/Galactose Isomerase
  ------ inclusion threshold ------
      0.023   14.6   0.2      0.035   14.1   0.2    1.3  1  PhnG        Phosphonate metabolism protein PhnG


Domain annotation for each model (and alignments):
>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0     4e-47   3.6e-43       1     137 [.       6     143 ..       6     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 4e-47
                                    EEEEE-GCGHHHHHHHHHHHHHTTTEEEEECESS.SS---HHHHHHHHHHHHHTTSSSEEEEEESSSHHHHHHHHTSTT- CS
                     LacAB_rpiB   1 iaigsDhagfelkekikeyLkekghevidvgtes.eesvdYpdfakkvaeavasgeadlgiliCgtGiGmsiaaNkvkgi 79 
                                    +++g+Dhag+elk++i+e+Lk+ ghe id+g+   ++++dYp f++++a++  +   +lgi++ g+G+G +iaaNkv+g 
  gi|121638348|ref|YP_978572.1|   6 VYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRyDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGA 85 
                                    79******************999********8887889************999999************************ PP

                                    -EEE-SSHHHHHHHHHTT--SEEEEETTTS-HHHHHHHHHHHHHS---.HTHHHHHHH CS
                     LacAB_rpiB  80 raalchdeesAklarehnnanvlalGarvigeelakeivkaFletefeeggrharrvd 137
                                    r+al+++ ++A larehnna+ + +G+r+++  +a +iv+aF++t+ ++++rh+rr+d
  gi|121638348|ref|YP_978572.1|  86 RCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRID 143
                                    ***********************************************99*******98 PP

>> PhnG  Phosphonate metabolism protein PhnG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.9e-06     0.035      79     120 ..     110     151 ..      71     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                                    EESS-HHHHHHHHHHHHHCTSHHHHHHHHHHTHHHHHHHHHH CS
                           PhnG  79 vlgrdkrkAelaAllDAllqtpereeeleaelieplearlae 120
                                    + gr ++ Ae++A++DA ++tp  +++ +++ i  l++  ++
  gi|121638348|ref|YP_978572.1| 110 IGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERT 151
                                    5699*********************99999999888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1066.96
//
Query:       gi|121638349|ref|YP_978573.1|  [L=207]
Description: hypothetical protein BCG_2486c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-13   49.0   2.8    8.8e-12   45.2   2.8    2.0  1  DSBA      DSBA-like thioredoxin domain


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   2.8   4.9e-16   8.8e-12       3     181 ..      12     165 ..      10     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.9e-16
                                    EEEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSH CS
                           DSBA   3 deffDvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdk 82 
                                    d++fD lCP+C++ ++ + ++a+ + d++v ++ ++la       n  + +lpe++++ ++                   
  gi|121638349|ref|YP_978573.1|  12 DFWFDPLCPWCWITSRWILEVAKVR-DIEVNFHVMSLAIL-----NENRDDLPEQYREGMA------------------- 66 
                                    8************************.********999999.....5555667777665333................... PP

                                    HHHHHHHHHHHHHHHHHHGHHHHHHHHHHHH...HTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHH CS
                           DSBA  83 lknstraarlllaagaeglaekvvrelfeal...wsegqaitddqellevaekaGldaeeldealeseavkeavrentaa 159
                                      ++    r+++aa++++  +kv+ +l+ a+   + ++ ++  d+++ + + +aGl  +el++a  s+a+ +a+r++++a
  gi|121638349|ref|YP_978573.1|  67 --RAWGPVRVAIAAEQAH-GAKVLDPLYTAMgnrIHNQGNHELDEVITQSLADAGL-PAELAKAATSDAYDNALRKSHHA 142
                                    ..4445557777777776.55666666666522234589999999***********.78999****************** PP

                                    HHHT..T-SSSSEEEETTCEEEES CS
                           DSBA 160 aqsl..gvtGvPtvvvdgkrmvfG 181
                                    + +      G+Pt++v+g  ++fG
  gi|121638349|ref|YP_978573.1| 143 GMDAvgEDVGTPTIHVNGV-AFFG 165
                                    988622457*********9.9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1420.23
//
Query:       gi|121638350|ref|YP_978574.1|  [L=861]
Description: aminopeptidase N pepN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-58  197.9   0.7    2.2e-58  197.4   0.7    1.2  1  Peptidase_M1    Peptidase family M1 domain
    1.5e-56  192.2   0.0    2.4e-56  191.6   0.0    1.3  1  ERAP1_C         ERAP1-like C-terminal domain
    8.6e-18   65.2   0.0    1.6e-17   64.3   0.0    1.5  1  Peptidase_M1_N  Peptidase M1 N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.4   0.7   3.8e-62   2.2e-58       6     218 .]     234     444 ..     230     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.4 bits;  conditional E-value: 3.8e-62
                                    HHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTTTEE CS
                   Peptidase_M1   6 tkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGnlVt 85 
                                    tk+ + f++++f++pY++ k+d++++p+f+agAMEn g++t+ e ++     + + +++++ ae++ HE+aH+WfG+lVt
  gi|121638350|ref|YP_978574.1| 234 TKQGFGFYHKHFGLPYAFGKYDQLFVPEFNAGAMENAGAVTFLEDYVFRS--KVTRASYERRAETVLHEMAHMWFGDLVT 311
                                    678899****************************************9998..56666778889999************** PP

                                    ESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHHHHH CS
                   Peptidase_M1  86 mkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKGasl 165
                                    m wWddlwLnE+fat++++l+ +++ + +e ++++ + e + a  +d+l ++hpi   + + + ++  Fd i+Y+KGas+
  gi|121638350|ref|YP_978574.1| 312 MTWWDDLWLNESFATFASVLCQSEATEFTEAWTTFATVEKSWAYRQDQLPSTHPIAADIPDLAAVEVNFDGITYAKGASV 391
                                    ***************************999************************************************** PP

                                    HHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                   Peptidase_M1 166 lrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                    l+ l +++g e F  gl+ Y+++++++na+ +dl+ ale+a++ d+s+  ++w
  gi|121638350|ref|YP_978574.1| 392 LKQLVAYVGLERFLAGLRDYFRTHAFGNASFDDLLAALEKASGRDLSNWGEQW 444
                                    ************************************************99999 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0   4.1e-60   2.4e-56       1     315 []     531     850 ..     531     850 .. 0.90

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 4.1e-60
                                    -EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG..GGGG--SHHHHHHH CS
                        ERAP1_C   1 lvllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlll.gylanEtdylvwsqa 79 
                                    l+l+Nddd++y+  ++de+sl+++l+  + ++ +pl+R++++s+a++++r +el+a+d+++l++ g+  +Et+  v +++
  gi|121638350|ref|YP_978574.1| 531 LILVNDDDLTYCSLRLDERSLQTALD-RIADIAEPLPRTLVWSAAWEMTREAELRARDFVSLVSgGV-HAETEVGVAQRL 608
                                    69************************.99***********************************999.7*********** PP

                                    HHHHHHHHHHHTTST...THHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHH CS
                        ERAP1_C  80 lsqlatlksllsadp...lyaalkaflrklleplaeklgwepgeshldaqlrslllsaac.aagdpevveearklfkawl 155
                                    l q++t+   + a+p    ++++ +f+++lle + e  + epg   +d+ql    ++ +c +  +p++v+ + +l+++  
  gi|121638350|ref|YP_978574.1| 609 LLQAQTALGCY-AEPgwaRERGWPQFADRLLELARE--A-EPG---SDHQLA--YINSLCsSVLSPRHVQTLGALLEGEP 679
                                    ***********.8785655569**********9999..3.699...888888..88888845559**************5 PP

                                    C..STT.-.S-HHHHHHHHHHHHHHS..-HHH.....HHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT CS
                        ERAP1_C 156 e..gdd.l.ippdlrwavycalaang..geae.....wdallerykdtsapsekeaalralaatpdpellerllnfvles 224
                                    +  g + l +++dlrw++++ala +g  ++++     +da+ +r  d++a ++k++a++a+aa+p+  ++ +++  v+e+
  gi|121638350|ref|YP_978574.1| 680 AacGLAgLaVDTDLRWRIVTALATAGaiDADGpetprIDAEVQR--DPTA-AGKRHAAQARAARPQFVVKDEAFTTVVED 756
                                    433322556*************999988555334455*******..****.**************************99* PP

                                    ..S-GGGHHHHHHHH.HSTTHHHHHH.HHHHHCHCCHHHHTS..STSCHHHHHHHHHTT--.SHHHHHHHHHHHCHT.T- CS
                        ERAP1_C 225 devrnqdlrallaglannpegrellw.efvkenwdalakrws..ggeildrivkgllpgft.seeelaeieaffadk.dt 299
                                    d++ n+  ra++ag+   ++g+ +l+ +f +++++a+  +w+  ++e+++++v gl+p+++ se+ + ++e+f++d   +
  gi|121638350|ref|YP_978574.1| 757 DTLANATGRAMIAGI--AAPGQGELLkPFARRYFQAIPGVWArrSSEVAQSVVIGLYPHWDiSEQGITAAEEFLSDPeVP 834
                                    ***************..7889998888**************754678***************************88845* PP

                                    -GGGHHHHHHHHHHHH CS
                        ERAP1_C 300 pglrrtlkqaletvrr 315
                                    p+lrr + ++ ++v+r
  gi|121638350|ref|YP_978574.1| 835 PALRRLVLEGQAAVQR 850
                                    **********999987 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.6e-21   1.6e-17      97     186 .]     107     189 ..      22     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.6e-21
                                    BSSSSEEEEEEEEE..TSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCEEEETTCEEEE CS
                 Peptidase_M1_N  97 ndklaGlykstYtd..kgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeeeseklengqkit 174
                                    +++ +Gl +  ++d  +ge+  ++ +qfe +dA+++f CfD+P+ KAtf+++++ap++  ++Sn+   + ++      ++
  gi|121638350|ref|YP_978574.1| 107 SNTGEGLHR--FVDpvDGET--YLYSQFETADAKRMFACFDQPDLKATFDVRVTAPAHWKVISNGAPLAAANG-----VH 177
                                    566777777..666545555..99*****************************************98844333.....79 PP

                                    EEEEEESBEGGG CS
                 Peptidase_M1_N 175 eFeqtpkmstYL 186
                                    +F++tp+mstYL
  gi|121638350|ref|YP_978574.1| 178 TFATTPRMSTYL 189
                                    ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 6337.96
//
Query:       gi|121638351|ref|YP_978575.1|  [L=167]
Description: hypothetical protein BCG_2488c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-65  217.2   0.1      9e-65  217.0   0.1    1.0  1  DUF5130          Domain of unknown function (DUF5130)
  ------ inclusion threshold ------
       0.21   11.8   0.0       0.31   11.2   0.0    1.2  1  TPM_phosphatase  TPM domain


Domain annotation for each model (and alignments):
>> DUF5130  Domain of unknown function (DUF5130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.0   0.1     1e-68     9e-65       1     136 []      26     161 ..      26     161 .. 1.00

  Alignments for each domain:
  == domain 1  score: 217.0 bits;  conditional E-value: 1e-68
                        DUF5130   1 LPlGavltssGrisavrelgelsvelPfskddlvalDdaLkeasrkakvrfavyiGdlgedtaaaareilakvpepenav 80 
                                    LP G+vlt+sGris+v+e+gelsv++Pf+ +dlvalDdaL+++sr+++vrfa+y+Gdlg+dtaa+areil kvp+p+nav
  gi|121638351|ref|YP_978575.1|  26 LPPGWVLTTSGRISGVTEPGELSVHYPFPIADLVALDDALTYSSRACQVRFAIYLGDLGRDTAARAREILGKVPTPDNAV 105
                                    8******************************************************************************* PP

                        DUF5130  81 LiavsPnqraievvsGaevadrvadrvaqlGvtaavssfreGdLidglvsavrvls 136
                                    L+avsPnq+aievv+G++v++r+a+++a+lGv+aa s+f++G+L+dgl+sa+rvls
  gi|121638351|ref|YP_978575.1| 106 LLAVSPNQCAIEVVYGSQVRGRGAESAAPLGVAAASSAFEQGELVDGLISAIRVLS 161
                                    ******************************************************97 PP

>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05      0.31      15     120 ..      60     158 ..      56     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHHHHHTT--EEEEEEESB-TT--HHHHHHHHHHHHSTTT.TS-SSEEEEEEETTTTEEEEEE-STTTTT--HHH CS
                TPM_phosphatase  15 eleeklaalekktgvqivvvtvdsldgediedyadelfdkwglgk.kkkdngvllliavddrkvrietgyglegaltdar 93 
                                    +l+++l+  ++ ++v+++++  d l g d+  +a e++     gk    dn vll++++++  + + +g++++g   ++ 
  gi|121638351|ref|YP_978575.1|  60 ALDDALTYSSRACQVRFAIYLGD-L-GRDTAARAREIL-----GKvPTPDNAVLLAVSPNQCAIEVVYGSQVRGRGAESA 132
                                    57788888888888888888776.7.566668888884.....4433345*******98777777778888888665555 PP

                                    HHHHHHHTHHHHHHHT-HHHHHHHHHH CS
                TPM_phosphatase  94 aesildetilpalkdgdyaggilaavd 120
                                    a   + +   +a+ +g+  +g+ +a++
  gi|121638351|ref|YP_978575.1| 133 APLGVAA-ASSAFEQGELVDGLISAIR 158
                                    5544444.7888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1271.85
//
Query:       gi|121638352|ref|YP_978576.1|  [L=222]
Description: hypothetical protein BCG_2489c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-13   50.3   1.4    2.8e-13   49.5   1.4    1.3  1  HNH_5          HNH endonuclease
    1.1e-11   44.7   3.9      2e-11   43.9   3.9    1.4  1  HNH            HNH endonuclease
      6e-07   29.3   0.1      2e-06   27.6   0.1    1.9  1  HNH_4          HNH endonuclease
  ------ inclusion threshold ------
      0.082   12.8   6.3       0.15   12.0   6.3    1.4  1  Cys_rich_CPXG  Cysteine-rich CPXCG


Domain annotation for each model (and alignments):
>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   1.4   6.2e-17   2.8e-13       1      51 [.     138     184 ..     138     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.2e-17
                          HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkgqkvdaal 51 
                                    C+yCg + ++     +H++P+s+GG ++++n+v++C+ CN++kg+++  +l
  gi|121638352|ref|YP_978576.1| 138 CAYCGGKADT----VDHVVPRSRGGAHSWENCVACCSPCNHRKGDRLLTEL 184
                                    *****99655....*******************************987766 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   3.9   4.5e-15     2e-11       1      47 []     138     179 ..     138     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.5e-15
                            HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhdr 47 
                                    C yCg k     a +vdH++p+s+gga+++eN+++ C+ C+ +k+dr
  gi|121638352|ref|YP_978576.1| 138 CAYCGGK-----ADTVDHVVPRSRGGAHSWENCVACCSPCNHRKGDR 179
                                    99***99.....479*****************************986 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   4.5e-10     2e-06      21      53 ..     148     180 ..     138     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.5e-10
                                    EEESSTTTT---BSGGGEEEES-GGGGTSSSSS CS
                          HNH_4  21 iDHilPrsrskdDsvsNkVLvlrdaNqeKsnrt 53 
                                    +DH++Prsr+   s+ N V +++ +N  K++r+
  gi|121638352|ref|YP_978576.1| 148 VDHVVPRSRGGAHSWENCVACCSPCNHRKGDRL 180
                                    9*****************************986 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   6.3   3.3e-05      0.15       2      34 ..     137     172 ..     136     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                  Cys_rich_CPXG   2 qCPyCgeeiev...lvDlsagdqeYieDCqvCCrPi 34 
                                    +C+yCg + ++   +v  s g  +  e C +CC+P 
  gi|121638352|ref|YP_978576.1| 137 CCAYCGGKADTvdhVVPRSRGGAHSWENCVACCSPC 172
                                    7*****87766222688999*99************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1676.80
//
Query:       gi|121638353|ref|YP_978577.1|  [L=128]
Description: globin (oxygen-binding protein) glbO [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-42  143.6   0.0    3.3e-42  143.4   0.0    1.0  1  Bac_globin   Bacterial-like globin
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.097   12.6   0.0    1.6  2  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Bac_globin  Bacterial-like globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   3.7e-46   3.3e-42       1     120 [.       4     121 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 3.7e-46
                                    -HHHHHTHHHHHHHHHHHHHHHHHT-CCCCCCGGGTTSSHHHHHHHHHHHHHHHTTSSSHHHHHHSS-.HHHHHTTS--B CS
                     Bac_globin   1 tlydaiGgeatveelvdrfYervdedeeealseifsgtdlegsreklveFlvqalgGPelYverrGhPrlrkrHapfeit 80 
                                    ++yda+Gg++t+ ++v+rfY++v+ede   l+++++ +dl+g++e+l++Fl+q++gGP++Y+e+rGhPrlr+rHapf+i 
  gi|121638353|ref|YP_978577.1|   4 SFYDAVGGAKTFDAIVSRFYAQVAEDEV--LRRVYPEDDLAGAEERLRMFLEQYWGGPRTYSEQRGHPRLRMRHAPFRIS 81 
                                    58**************************..************************************************** PP

                                    HHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHC CS
                     Bac_globin  81 aaerdawlkhlaeAleetgvssedreeklellealahaaq 120
                                      erdawl+++++A++++++++ d+e++ ell++l++aa+
  gi|121638353|ref|YP_978577.1|  82 LIERDAWLRCMHTAVASIDSETLDDEHRRELLDYLEMAAH 121
                                    ************************************9987 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.097      32      71 ..      14      56 ..      11      59 .. 0.91
   2 ?   -2.4   0.0      0.42   3.8e+03     132     153 ..      72      93 ..      61      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                   CHHHHHHHHHHHHCTSHHHHHHHCH...HCHHHHHHHHHHHHH CS
                    Protoglobin 32 lipavvdafYekllsfpetarifet...ssqierlkdflksyl 71
                                     +a+v +fY+++++ + ++r+  +       erl++fl++y+
  gi|121638353|ref|YP_978577.1| 14 TFDAIVSRFYAQVAEDEVLRRVYPEddlAGAEERLRMFLEQYW 56
                                   579********************9988888889*********9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.42
                                    HHHHHHHHHHHHHHHHHCGGGB CS
                    Protoglobin 132 alvkalnKliwldndlaleaYv 153
                                    ++  a +++ +++ d +l++++
  gi|121638353|ref|YP_978577.1|  72 RMRHAPFRISLIERDAWLRCMH 93 
                                    5566667777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1036.25
//
Query:       gi|121638354|ref|YP_978578.1|  [L=546]
Description: alpha-glucosidase aglA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-80  269.5   0.0    8.4e-80  268.8   0.0    1.2  1  Alpha-amylase  Alpha amylase, catalytic domain
  ------ inclusion threshold ------
       0.12   11.5   0.0       0.22   10.6   0.0    1.3  1  hDGE_amylase   Glycogen debranching enzyme, glucanotransferas


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.8   0.0   9.4e-84   8.4e-80       1     335 [.      54     399 ..      54     403 .. 0.94

  Alignments for each domain:
  == domain 1  score: 268.8 bits;  conditional E-value: 9.4e-84
                                    --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TT CS
                  Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsde 80 
                                    GDL+G+ ++Ld l++LGv+aiw++P++ sp+adhgYd+ad + idp fG + ++++L+++ah +gikv +D+V+NHts++
  gi|121638354|ref|YP_978578.1|  54 GDLDGLASRLDHLQQLGVDAIWINPVTVSPMADHGYDVADPRDIDPLFGGMPAFERLVAAAHRQGIKVTMDVVPNHTSSA 133
                                    9******************************************************************************* PP

                                    SCCCHCCHHS.TTSGGGCCC-E........ESS-STTC-TTTTCSCEE....CTTTTCEEESSS-TTS-BB-TTTCCCCC CS
                  Alpha-amylase  81 hewfkeslkk.kgepkrdyyiwkegk..eekeppnnwkslfdgsawey....dekaqeyylhlflkklpdLnteneevrk 153
                                    h wf+ +l+  +g+p rd y++++g+      ppnnw+s+f+g+aw+     d + +++ylhlf  ++pdLn++n+e+  
  gi|121638354|ref|YP_978578.1| 134 HPWFQAALADlPGSPARDRYFFRDGRgpDGSLPPNNWESVFGGPAWTRvrepDGNPGQWYLHLFDTEQPDLNSDNPEILD 213
                                    ******998637899*********99888899***************9998899999*********************** PP

                                    CCCCCCCCCCTTT-SEEEETTCCCTTTCCCC..................HCCHCCHHHHHHHHHHHTCCGTT-EEEEE-T CS
                  Alpha-amylase 154 elkdvvkfwlekgidGfRlDvvkhvskveal..................esngeflheftqalnetvasrkevmtvgEvs 215
                                    + ++ ++fwl++g+dGfR+Dv++ ++k ++l                  + n + +h ++ ++ ++++++  ++tvgEv+
  gi|121638354|ref|YP_978578.1| 214 DFEKTLRFWLDRGVDGFRIDVAHGMAKPPGLpdspdlgievlhhrdddpRFNHPNVHAIHRDIRTVIDEYPGAVTVGEVW 293
                                    ***************************9999*****************999***************************** PP

                                    T-SCCCHCCCC-CGG-SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHH CS
                  Alpha-amylase 216 sdasedlrvyttearlelemvldfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsr 295
                                     +++ + + y   ++l l   ++f   ++           +++a+++ ++++++l+a   ++ + ++ l nHD  R +sr
  gi|121638354|ref|YP_978578.1| 294 VHDNARWAEYLRPDELHLG--FNFRLART-----------EFDAAEIRDAVANSLAAAALQNATPTWTLANHDVGREVSR 360
                                    ****999999999988888..66554333...........34688899999999999999999***************** PP

                                    TTSSTTTTHHHHHHHHHCCCTSSSEEEEETTCCCT----S CS
                  Alpha-amylase 296 lgddsaeaekklklaaillltlrGvpviYyGeEigmtggk 335
                                    +g  +   ++++k++a+++l l+Gv + Y+G+E+g+ +++
  gi|121638354|ref|YP_978578.1| 361 YGGGE-IGLRRAKAMAVVMLALPGVVFLYNGQELGLPDVD 399
                                    **998.469**************************99876 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.4e-05      0.22      19     111 ..      54     138 ..      50     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.4e-05
                                    -SHHHHHHHHHHHHHTT--EEEES--EEE-TT--TTSEEEEEEE-TTT-.....SSC.HHHHHHHHHHHHHH--EEEEEE CS
                   hDGE_amylase  19 GpleeWekvlkeikekgYnmiHftPlqelGesnSpYSiadqleldkelfeekdkeekeedveklvkklekeygllsltDv 98 
                                    G l+   ++l++ ++ g + i   P++     +  Y +ad  ++d+ +        ++  +e+lv  +++  g+  ++Dv
  gi|121638354|ref|YP_978578.1|  54 GDLDGLASRLDHLQQLGVDAIWINPVTVSPMADHGYDVADPRDIDPLF-------GGMPAFERLVAAAHR-QGIKVTMDV 125
                                    777888899999999******************************976.......456678999987765.699****** PP

                                    --SEEETT-CCCC CS
                   hDGE_amylase  99 VlnHtannskwle 111
                                    V nHt++  +w +
  gi|121638354|ref|YP_978578.1| 126 VPNHTSSAHPWFQ 138
                                    ***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4066.82
//
Query:       gi|121638355|ref|YP_978579.1|  [L=97]
Description: hypothetical protein BCG_2492 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 661.28
//
Query:       gi|121638356|ref|YP_978580.1|  [L=238]
Description: hypothetical protein BCG_2493 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0023   18.2   0.3     0.0074   16.5   0.0    1.9  2  DUF4381       Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-07    0.0074      11      86 ..      71     149 ..      68     157 .. 0.71
   2 ?   -1.7   0.1      0.18   3.1e+03      47      57 ..     185     201 ..     161     215 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-07
                        DUF4381  11 pvswwPpapGwwlllaalll.llllvlalwllrrrkrnrre..AlreLaalradeadakellaalselLkrvalayypr 86 
                                    ++s  P  pG w l+aal+l ++ l+++++ + +r+ + +   A ++ + ++++ +dake ++a++++++++a+   ++
  gi|121638356|ref|YP_978580.1|  71 APSTTPRSPGRWSLVAALALaVVSLGVGIVGWFHRQPHDKPspAPSAPTFTSQQISDAKENVCAAHRIVRQAAVLNTNQ 149
                                    68999*****9999988888866666666666555555333224444333335679*****************987774 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.18
                        DUF4381  47 n......rreAlreLaa 57 
                                    +       r+A r La+
  gi|121638356|ref|YP_978580.1| 185 EpatpaeLRDAVRSLAN 201
                                    22222222333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1861.84
//
Query:       gi|121638357|ref|YP_978581.1|  [L=217]
Description: hypothetical protein BCG_2494c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1686.81
//
Query:       gi|121638358|ref|YP_978582.1|  [L=138]
Description: hypothetical protein BCG_2495c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-09   37.8   0.1    2.4e-09   37.7   0.1    1.1  1  4HBT_2       Thioesterase-like superfamily
    0.00017   21.0   0.0    0.00024   20.5   0.0    1.2  1  Acyl-ACP_TE  Acyl-ACP thioesterase
    0.00084   19.6   0.1     0.0013   19.0   0.1    1.3  1  4HBT         Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1     4e-13   2.4e-09       1     109 [.      11     119 ..      11     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4e-13
                         4HBT_2   1 vrpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdr.ltvefrvididaktl 79 
                                    vr+ d+D++ h+n+a+ + +leearv fl ++ +    i+  + gl +++ +v+y+ +l+++d  l+v+    +  a  +
  gi|121638358|ref|YP_978582.1|  11 VRWSDIDMYQHVNHATMVTILEEARVPFL-KDAF-GADIT--STGLLIADVRVTYKGQLRLSDSpLQVTIWTKRLRAVDF 86 
                                    89***************************.3555.44444..88********************9*99988877666666 PP

                         4HBT_2  80 iiehrfls.na..dgkkaarveerivvmdygkr 109
                                     + ++++s na  d + a ++e +++ +  +++
  gi|121638358|ref|YP_978582.1|  87 TLGYEVRSvNAepDSRPAVIAESQLAAFHIEEQ 119
                                    666666664333355557777666666655554 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     4e-08   0.00024     158     185 ..       8      34 ..       2      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4e-08
                    Acyl-ACP_TE 158 elkvrysDlDlnqHvNNvkYlewilevl 185
                                       vr+sD+D++qHvN ++ +  ++e +
  gi|121638358|ref|YP_978582.1|   8 PVGVRWSDIDMYQHVNHATMVTILEE-A 34 
                                    667**************998875554.3 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.2e-07    0.0013       2      72 ..      20      94 ..      19      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                                   SSB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTC.EEEEEEEEEEEESSEEEEEEEEEE CS
                           4HBT  2 GvvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgd.eltvearvlrlgrtsavvevevrd 72
                                    +v++++++++l+ea+  +l+   g+    +++ +++ +++++ + rl d +l v+ +  rl    +++ +evr+
  gi|121638358|ref|YP_978582.1| 20 QHVNHATMVTILEEARVPFLKDAFGAditSTGLLIADVRVTYKGQLRLSDsPLQVTIWTKRLRAVDFTLGYEVRS 94
                                   79************************99999******************99*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1048.92
//
Query:       gi|121638359|ref|YP_978583.1|  [L=1623]
Description: NAD-dependent glutamate dehydrogenase gdh [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1775.9   0.0          0 1775.5   0.0    1.0  1  Bac_GDH        Bacterial NAD-glutamate dehydrogenase
  ------ inclusion threshold ------
      0.066   12.9   0.3       0.58    9.8   0.3    2.1  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
        0.1   13.4   0.1         22    5.8   0.1    3.0  2  PIN_3          PIN domain


Domain annotation for each model (and alignments):
>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1775.5   0.0         0         0      20    1530 ..      96    1611 ..      92    1612 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1775.5 bits;  conditional E-value: 0
                        Bac_GDH   20 veivtddmpFlvdsvtaelnrqgltvhlvvhpvleverdkegklleveeekeeaekaekeslilieidrqsdaeelee 97  
                                     +++v +    l+dsvt+ l+r g++  +++ pv++v+r+ +g+ll++e+++e ++ +  e+++++ ++   d++ l+e
  gi|121638359|ref|YP_978583.1|   96 LQVVAEHGGMLMDSVTVLLHRLGIAYAAILTPVFDVHRSPTGELLRIEPKAEGTSPHLGEAWMHVALSPAVDHKGLAE 173 
                                     6899999999***********************************************9******************** PP

                        Bac_GDH   98 leeelekvledvraaveDwkkmreklkelaeelekekak.vekeeleeaaefLewladdhftfLgyreyeleeeeeee 174 
                                     +e+ l kvl+dv+++ +D +++ ++l+ela e+e+++    ++ ++++  e+L+wl d +f++Lgy++ ++++     
  gi|121638359|ref|YP_978583.1|  174 VERLLPKVLADVQRVATDATALIATLSELAGEVESNAGGrFSAPDRQDVGELLRWLGDGNFLLLGYQRCRVADG---- 247 
                                     **********************************8776647779**************************9987.... PP

                        Bac_GDH  175 eleaveesglGilrkeeekeksrelaelpeearkelkekellvltkansrstvhrpayldyvgvkkfdekgkvvgerr 252 
                                      +  + +sg+G+lr ++             +  + +++++llvl++a+  s +   ay+ +++v+++  +g+vv e+r
  gi|121638359|ref|YP_978583.1|  248 MVYGEGSSGMGVLRGRT------------GSRPRLTDDDKLLVLAQARVGSYLRYGAYPYAIAVREY-VDGSVV-EHR 311 
                                     688999*********99............12223345799**************************9.567775.7** PP

                        Bac_GDH  253 flGlftsaaykesvkeiPllrrkveevleragleeeshsgkalleiletyprdeLfqiseeeLleialgilklqerkr 330 
                                     f+Glf+ aa++++v eiP ++r+v+e l++a+ ++ sh g+ ll++++t pr eLf+ s+++Ll++a ++++l ++++
  gi|121638359|ref|YP_978583.1|  312 FVGLFSVAAMNADVLEIPTISRRVREALAMAESDP-SHPGQLLLDVIQTVPRPELFTLSAQRLLTMARAVVDLGSQRQ 388 
                                     ******************************99876.9***************************************** PP

                        Bac_GDH  331 vrlflrrdkfgrfvsvlvyvprdryntelrekiqelleealegesvefttllsesvlarlhfvvrvekkea.pe.... 403 
                                       lflr+d+ + fvs+lvy+prdry+t++r++++++l ++++g+++eft+++ses+ a +hf+vr+ +  +  e    
  gi|121638359|ref|YP_978583.1|  389 ALLFLRADRLQYFVSCLVYMPRDRYTTAVRMQFEDILVREFGGTRLEFTARVSESPWALMHFMVRLPEVGVaGEgaaa 466 
                                     *****************************************************************9865432113334 PP

                        Bac_GDH  404 .......vdveelearlaeaarsWedelaealleelgeekakellkryaeafpeaYkedfsaeeavaDierlekleee 474 
                                             +  +++  l+eaar+W+d+l  a ++    + +++ + +ya+af+eaYk+++++++a+ Di+ +++l++ 
  gi|121638359|ref|YP_978583.1|  467 ppvdvseANRIRIQGLLTEAARTWADRLIGAAAAG---SVGQADAMHYAAAFSEAYKQAVTPADAIGDIAVITELTD- 540 
                                     4533322455568999***********97765544...567778899****************************54. PP

                        Bac_GDH  475 eelalslyrpleaeeeelrlklyraeeplsLsdvlpvlenlGlrvlderpyeieaedekevwihdfeleleke..... 547 
                                     ++  ++l+ ++++e++ ++l  +  +++ sLs++lp+l+++G+ vl+erp+++++ d+ +vwi++f+++ + +     
  gi|121638359|ref|YP_978583.1|  541 DS--VKLVFSERDEQGVAQLTWFLGGRTASLSQLLPMLQSMGVVVLEERPFSVTRPDGLPVWIYQFKISPHPTiplap 616 
                                     44..55555666899999999************************************************999877765 PP

                        Bac_GDH  548 eeldldevkerfeeafaavwrgeaenDgfnrLvleagltwrevavlrayakYlrQigltfsqeyieetllkhpeiarl 625 
                                     + ++ +++++rf ea++a+w+g++e D+fn+Lv++agltw++v++lrayakYlrQ+g+++sq+yie++l++hp+ +r+
  gi|121638359|ref|YP_978583.1|  617 TVAERAATAHRFAEAVTAIWHGRVEIDRFNELVMRAGLTWQQVVLLRAYAKYLRQAGFPYSQSYIESVLNEHPATVRS 694 
                                     566688888********************************************************************* PP

                        Bac_GDH  626 lvelFearfdpaleeeeeeeeeekleeeieeaLdevasldedrilrrllelieatlRtnfyqkde.dgeakeyislKl 702 
                                     lv+lFea f p  + +++++ +++  +++++ +d++ sld drilr++++l++atlRtn++ +++ + + +++++lKl
  gi|121638359|ref|YP_978583.1|  695 LVDLFEALFVPVPSGSASNRDAQAAAAAVAADIDALVSLDTDRILRAFASLVQATLRTNYFVTRQgSARCRDVLALKL 772 
                                     *****************99999***************************************98662556799****** PP

                        Bac_GDH  703 dpskipelPePrPlfEifVysprvegvHLRggkvARGGlRWSDRreDfRtEvLGLvKaQqvKNavIVPvGaKGGFvvk 780 
                                     +++ i+elP PrP +EifVysprvegvHLR+g vARGGlRWSDRr+DfRtE+LGLvKaQ vKNavIVPvGaKGGFvvk
  gi|121638359|ref|YP_978583.1|  773 NAQLIDELPLPRPRYEIFVYSPRVEGVHLRFGPVARGGLRWSDRRDDFRTEILGLVKAQAVKNAVIVPVGAKGGFVVK 850 
                                     ****************************************************************************** PP

                        Bac_GDH  781 rlp.....kaadreallaegiacYktfirgLLditDnl..vdgevvppedvvrhDedDpYLVVAADKGTAtFSDiANe 851 
                                     r+p     +aadr+a+ aeg+acY+ fi+gLLd+tDn+  +  +v pp +vvr D+dD+YLVVAADKGTAtFSDiAN+
  gi|121638359|ref|YP_978583.1|  851 RPPlptgdPAADRDATRAEGVACYQLFISGLLDVTDNVdhATASVNPPPEVVRRDGDDAYLVVAADKGTATFSDIAND 928 
                                     **99999999***************************9434558999******************************* PP

                        Bac_GDH  852 vsaeygFWLgDAFASGGsvGYDHKkmGITArGAWesvkrhFrelgvdiqtedftvvGiGDmsGDVFGNGmLlsehirL 929 
                                     v+++ygFWLgDAFASGGsvGYDHK+mGITArGAWe+vkrhFre+g+d+qt+dftvvGiGDmsGDVFGNGmLls+hirL
  gi|121638359|ref|YP_978583.1|  929 VAKSYGFWLGDAFASGGSVGYDHKAMGITARGAWEAVKRHFREIGIDTQTQDFTVVGIGDMSGDVFGNGMLLSKHIRL 1006
                                     ****************************************************************************** PP

                        Bac_GDH  930 vaAFdHrhiFiDPnPdaaasfaErkRLFelprssWadYdksliSkGGgvfsRsaKsiklspevrellgieeee..... 1002
                                     +aAFdHrhiF+DPnPdaa s+aEr+R+FelprssW dYd+sliS+GGgv+sR++K+i+ls++vr++lgi+ ++     
  gi|121638359|ref|YP_978583.1| 1007 IAAFDHRHIFLDPNPDAAVSWAERRRMFELPRSSWGDYDRSLISEGGGVYSREQKAIPLSAQVRAVLGIDGSVdggaa 1084
                                     *********************************************************************988777778 PP

                        Bac_GDH 1003 .ltPneLikaiLkapvdLlwnGGiGTYvkaseeshadvgDkandalRvngkelrakvvgEGgNLGltQlgRiEyalkg 1079
                                      ++P +Li+aiL+apvdLl+nGGiGTY+ka++es+advgD+and +Rvn++++rakv+gEGgNLG+t lgR+E+ l+g
  gi|121638359|ref|YP_978583.1| 1085 eMAPPNLIRAILRAPVDLLFNGGIGTYIKAESESDADVGDRANDPVRVNANQVRAKVIGEGGNLGVTALGRVEFDLSG 1162
                                     8***************************************************************************** PP

                        Bac_GDH 1080 grintDaiDNsaGVdcSDhEVNiKilLnklvaegeltlkqRnklLaemtdeVaelVLrdnyrqtqalslaeaqaaeel 1157
                                     grintDa+DNsaGVdcSDhEVNiKil+++lv++g++++++R +lL++mtdeVa+lVL+dn +q+  + +++a+aa+ l
  gi|121638359|ref|YP_978583.1| 1163 GRINTDALDNSAGVDCSDHEVNIKILIDSLVSAGTVKADERTQLLESMTDEVAQLVLADNEDQNDLMGTSRANAASLL 1240
                                     ****************************************************************************** PP

                        Bac_GDH 1158 eeqarliraLekegkLdralefLPsdeelaerkaagkgltrPelavLlaYakivlkeellasdlpddpylakelaeyF 1235
                                      ++a  i++L +e  ++r+le+LPs++e+a+r++ag glt+Pela+L+a++k+ lkee+la++lpd++++a++l +yF
  gi|121638359|ref|YP_978583.1| 1241 PVHAMQIKYLVAERGVNRELEALPSEKEIARRSEAGIGLTSPELATLMAHVKLGLKEEVLATELPDQDVFASRLPRYF 1318
                                     ****************************************************************************** PP

                        Bac_GDH 1236 PkalrerfaeeiekHrLrreiiatalaNelvnrlGitfvlrlaeetgasvaevvrayvvarevfdleelweeiealdn 1313
                                     P+alrerf+ ei++H+Lrrei++t+l N+lv+++Git+++r+ae++g+++ + vr+yv++ ++f++ ++w++i+a + 
  gi|121638359|ref|YP_978583.1| 1319 PTALRERFTPEIRSHQLRREIVTTMLINDLVDTAGITYAFRIAEDVGVTPIDAVRTYVATDAIFGVGHIWRRIRAAN- 1395
                                     **************************************************************************986. PP

                        Bac_GDH 1314 kvsaevqlelllevrrlleratrWllrnrrkeldiaaeverfkekvealkakleelleeeelealearaeelveagvp 1391
                                      ++ ++  +l+l++rrl++ra rWll+ r+++l++ ae++rf++ v+al+++++e+l++++++ +e++a+e++++gvp
  gi|121638359|ref|YP_978583.1| 1396 -LPIALSDRLTLDTRRLIDRAGRWLLNYRPQPLAVGAEINRFAAMVKALTPRMSEWLRGDDKAIVEKTAAEFASQGVP 1472
                                     .67778899999****************************************************************** PP

                        Bac_GDH 1392 eelakrvaslealasaldivevaeetkrdveevaevyfalgerlelkwlleqiselevedrwqalarealrddlaaaq 1469
                                     e+la rv++  + +s+ldi+++a+ ++ d +eva++yfal +rl+ + ll+++s+l+++drw++lar a+rdd++ a 
  gi|121638359|ref|YP_978583.1| 1473 EDLAYRVSTGLYRYSLLDIIDIADIADIDAAEVADTYFALMDRLGTDGLLTAVSQLPRHDRWHSLARLAIRDDIYGAL 1550
                                     ****************************************************************************** PP

                        Bac_GDH 1470 raltaevlkkseeeesaeeaveawlekneealerakallaelkasekldlaklsvalrelr 1530
                                     r+l  +vl+  e  es e+++++w++ ++++++ra+++l++++as++ dla+lsva+r++r
  gi|121638359|ref|YP_978583.1| 1551 RSLCFDVLAVGEPGESSEQKIAEWEHLSASRVARARRTLDDIRASGQKDLATLSVAARQIR 1611
                                     ***********************************************************97 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   9.7e-05      0.58       7     189 ..     954    1189 ..     944    1246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.7e-05
                                     TTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHH....HHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHH CS
                  ELFV_dehydrog    7 peaTglGvvyyveemlkklkldslegkrvaisGsGnvgs....yaallltelgakvvavsDssGviydpeGldieell 80  
                                      + T++G+  +v++ ++++++d ++ + +++ G G++      + +ll+  +  + +a  D++ +  dp+    ++ +
  gi|121638359|ref|YP_978583.1|  954 MGITARGAWEAVKRHFREIGID-TQTQDFTVVGIGDMSGdvfgNGMLLS--KHIRLIAAFDHRHIFLDPNP---DAAV 1025
                                     5567777777777777776666.55556666665554430100333333..45666777777777776653...3333 PP

                                     HHHHCSSSSTTHSHH...............STSTSEEESHHSHH................................HH CS
                  ELFV_dehydrog   81 elkeerksvkeykks...............sekkaeyieneeel................................le 111 
                                     +++e+r++++   +s                        +++ +                                l+
  gi|121638359|ref|YP_978583.1| 1026 SWAERRRMFELPRSSwgdydrslisegggvY------SREQKAIplsaqvravlgidgsvdggaaemappnliraiLR 1097
                                     3333333322222222222222443333221......22222223444446666666666666666666666655555 PP

                                     SS-SEEEE-SSTTSB-HHHH.THTH.............HTT-SEEE-SSSS-B-HHHHHHHHHTT-EEE-HHHHTTHH CS
                  ELFV_dehydrog  112 lkvdilvPcAtqneideena.kali.............kngvklvvEgANlpttqeAkeileeagvlvvpdkaaNaGG 175 
                                      +vd+l+  ++   i++e+  +a +             + ++k++ Eg Nl++t   +  +  +g  +  d++ N+ G
  gi|121638359|ref|YP_978583.1| 1098 APVDLLFNGGIGTYIKAESEsDADVgdrandpvrvnanQVRAKVIGEGGNLGVTALGRVEFDLSGGRINTDALDNSAG 1175
                                     677777777777777655430333466656555655544479************************************ PP

                                     HHHHHHHHHHHHCT CS
                  ELFV_dehydrog  176 VtvSslEmlqnlar 189 
                                     V +S  E+  ++  
  gi|121638359|ref|YP_978583.1| 1176 VDCSDHEVNIKILI 1189
                                     *******9766443 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.014        81      23      70 ..     153     198 ..     137     239 .. 0.75
   2 ?    5.8   0.1    0.0037        22      91     115 ..     711     735 ..     621     736 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                          PIN_3  23 ildaletgaitlvvsprlldElervlarelaypqfklraadkaallak 70 
                                    + +a+ + a+ + v+ + l E+er l ++la+ q  +++a ++ +  +
  gi|121638359|ref|YP_978583.1| 153 LGEAWMHVALSPAVDHKGLAEVERLLPKVLADVQRVATDATALIA--T 198
                                    556788889999*******************99999998888433..3 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0037
                          PIN_3  91 rDpdDqkvlelAlaaradvlVTkdr 115
                                    +   D+  +++A+aa+ d+lV+ d+
  gi|121638359|ref|YP_978583.1| 711 ASNRDAQAAAAAVAADIDALVSLDT 735
                                    4789*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.94u 0.32s 00:00:01.26 Elapsed: 00:00:00.43
# Mc/sec: 11316.95
//
Query:       gi|121638360|ref|YP_978584.1|  [L=558]
Description: ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-51  172.5   0.0    3.7e-27   95.5   0.0    2.5  2  ABC_tran      ABC transporter
    4.1e-17   62.9   6.4    0.00018   21.4   0.0    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.1e-15   54.5   8.3    1.1e-13   51.0   6.6    2.3  2  ABC_tran_Xtn  ABC transporter
    5.9e-09   35.7   2.3        0.3   10.5   0.0    4.2  4  SMC_N         RecF/RecN/SMC N terminal domain
    2.4e-05   24.9   6.3       0.01   16.3   0.2    2.9  3  AAA_23        AAA domain
    4.8e-05   23.0   0.4       0.16   11.7   0.1    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00011   22.3   0.8       0.14   12.3   0.1    2.5  2  MMR_HSR1      50S ribosome-binding GTPase
    0.00027   21.0   0.0      0.018   15.1   0.0    2.4  2  Dynamin_N     Dynamin family
    0.00059   20.1   0.6        0.3   11.4   0.0    3.0  2  AAA_22        AAA domain
      0.001   18.8   0.5       0.85    9.3   0.2    2.4  2  AAA_24        AAA domain
     0.0013   18.7   0.3       0.24   11.3   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
     0.0017   18.2   0.1          1    9.0   0.0    2.6  2  AAA_15        AAA ATPase domain
     0.0022   18.2   0.1        8.8    6.6   0.0    4.0  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0046   17.5   1.3        2.4    8.7   0.1    3.2  2  AAA_18        AAA domain
     0.0053   17.0   1.0       0.89    9.8   0.0    2.9  3  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0061   16.2   2.6       0.89    9.1   0.0    2.6  2  AAA_27        AAA domain
     0.0064   15.7   1.2      0.061   12.5   0.0    2.8  3  NB-ARC        NB-ARC domain
     0.0073   16.7   1.0       0.45   10.9   0.1    2.7  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.019   14.9   0.2        0.4   10.5   0.0    2.6  3  ATPase_2      ATPase domain predominantly from Archaea
      0.047   12.5   0.2       0.27   10.0   0.1    2.0  2  DLIC          Dynein light intermediate chain (DLIC)
      0.048   13.3   0.7        2.1    7.9   0.1    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.051   13.7   2.2        2.2    8.4   0.0    2.8  2  AAA_33        AAA domain
      0.052   13.3   1.6        5.6    6.6   0.1    2.5  2  AAA_30        AAA domain
      0.062   13.3   0.1       0.84    9.7   0.1    2.8  3  AAA_14        AAA domain
      0.097   12.6   0.6        1.4    8.8   0.1    2.3  2  NACHT         NACHT domain
        0.1   12.5   1.6          2    8.3   0.5    3.3  4  NTPase_1      NTPase
       0.13   12.0   0.2         13    5.4   0.0    2.5  2  PRK           Phosphoribulokinase / Uridine kinase family
       0.15   10.7   0.1         25    3.3   0.0    3.2  4  AAA_13        AAA domain
       0.16   12.4  11.8       0.89    9.9   0.1    3.6  3  AAA_16        AAA ATPase domain
       0.18   12.2   0.1         11    6.4   0.0    2.3  2  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   6.2e-30   3.7e-27       1     137 []      21     188 ..      21     188 .. 0.95
   2 !   74.6   0.0   1.8e-23   1.1e-20       2     137 .]     338     471 ..     337     471 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 6.2e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++v+l++++g k+++vG+nGaGKS++l+++agl kp++G+               + + +g+l+qep l++++tvr n 
  gi|121638360|ref|YP_978584.1|  21 LDDVTLSFYPGAKIGVVGPNGAGKSSVLRIMAGLDKPNNGDA-----------FLATGATVGILQQEPPLNEDKTVRGNv 89 
                                    799**************************************9...........45699********************** PP

                                    ..............................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                    ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..............................................esdeeiekalsklglkelkdtvvksspssLSgGq 113
                                                                                  + d+++e+a++ l+ +  +d++v    ++LSgG+
  gi|121638360|ref|YP_978584.1|  90 eegmgdikikldrfnevaelmatdytdelmeemgrlqeeldhadawDLDAQLEQAMDALRCPP-ADEPV----TNLSGGE 164
                                    *******************************99999999999998888888999999999999.88888....9****** PP

                                    HHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 114 kqrvalarallkkpkllllDEpta 137
                                    ++rval+++ll+kp+llllDEpt+
  gi|121638360|ref|YP_978584.1| 165 RRRVALCKLLLSKPDLLLLDEPTN 188
                                    ***********************8 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.8e-23
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren. 79 
                                    k++s++l ++ +v+++G+nG GK+tL+k++ gl+kp++G++++               +++++ q  + ++p++tv e  
  gi|121638360|ref|YP_978584.1| 338 KDLSFSLPRNGIVGVIGPNGVGKTTLFKTIVGLEKPDSGSVKV-----------GETVKLSYVDQArAGIDPRKTVWEVv 406
                                    89***************************************44...........468899******99***********9 PP

                                    ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              + ++   +++s +g k+ ++++    +  LSgG++ r+ la +l +  +l+llDEpt+
  gi|121638360|ref|YP_978584.1| 407 sdgldyiqvgQTEVPSRAYVSAFGFKGPDQQKP---AGVLSGGERNRLNLALTLKQGGNLILLDEPTN 471
                                    99*999988877777899999999999666655...7******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.9e-06    0.0017       3      22 ..      35      54 ..      34      88 .. 0.85
   2 !   21.4   0.0     3e-07   0.00018     232     303 .]     155     220 ..     127     220 .. 0.86
   3 !   19.1   0.3   1.5e-06   0.00091       2      22 ..     350     370 ..     349     392 .. 0.84
   4 ?    4.6   0.0      0.04        24     233     275 ..     439     478 ..     419     487 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +++GpNg+GKS++L+++ +l
  gi|121638360|ref|YP_978584.1| 35 GVVGPNGAGKSSVLRIMAGL 54
                                   68***************998 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3e-07
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpllld 303
                                     p+++lS G +r  al  +ll+ +   +lll+DEp n+L+     + +++l+++ +   + ++++TH+ ++ld
  gi|121638360|ref|YP_978584.1| 155 EPVTNLSGGERRRVALCKLLLSKP---DLLLLDEPTNHLDA----ESVQWLEQHLAsYPGAILAVTHDRYFLD 220
                                    588999*******99999999988...*************9....6666664444447788999999988776 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.5e-06
                         AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                     ++iGpNg+GK++L++++ +l
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTIVGL 370
                                    689***************988 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.04
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkll 275
                                    pa  lS G +  l l++ l +      l+l+DEp n L+ + l
  gi|121638360|ref|YP_978584.1| 439 PAGVLSGGERNRLNLALTLKQGG---NLILLDEPTNDLDVETL 478
                                    67777777777777777777644...89**********98665 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   6.6   1.8e-16   1.1e-13       1      84 [.     227     305 ..     227     307 .. 0.84
   2 ?    2.7   0.0      0.21   1.3e+02       7      26 ..     521     540 ..     518     549 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.8e-16
                   ABC_tran_Xtn   1 velengklteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLeklekiekpeekk 80 
                                    +el++g+++ Y+GnYs+yle+k+erl+ q ++ +k qk++ ++ ++++  ++    a+qa+s+  +L++ e+++++ ek+
  gi|121638360|ref|YP_978584.1| 227 LELDRGRAYPYEGNYSTYLEKKAERLAVQGRKDAKLQKRLTEELAWVRSGAK----ARQAKSK-ARLQRYEEMAAEAEKT 301
                                    69*********************************************98655....7777776.5677777777775666 PP

                   ABC_tran_Xtn  81 pklr 84 
                                    +kl 
  gi|121638360|ref|YP_978584.1| 302 RKLD 305
                                    6655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                   ABC_tran_Xtn   7 klteYkGnYseyleekeerl 26 
                                    k   ++Gn+ +y e k erl
  gi|121638360|ref|YP_978584.1| 521 KWFWFEGNFGAYEENKVERL 540
                                    55689************997 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0005       0.3      28      41 ..      35      48 ..      16      52 .. 0.76
   2 !    8.9   0.0    0.0016      0.95     119     202 ..      85     219 ..      70     228 .. 0.71
   3 !    8.2   0.3    0.0025       1.5      24      44 ..     347     367 ..     337     393 .. 0.87
   4 ?    4.0   0.0     0.047        28     136     186 ..     442     488 ..     436     509 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                   EEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnll 41
                                    +vGpNG+GKs++l
  gi|121638360|ref|YP_978584.1| 35 GVVGPNGAGKSSVL 48
                                   59**********98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                                    -HHHHHHHHHCTT-STT.........................................................CS-HHH CS
                                    xxxxxxxxxxxxxxxxx.........................................................xxxxxx RF
                          SMC_N 119 tkkevsellesagiske.........................................................lLSgGe 141
                                     + +v+e + + +i+ +                                                         +LSgGe
  gi|121638360|ref|YP_978584.1|  85 VRGNVEEGMGDIKIKLDrfnevaelmatdytdelmeemgrlqeeldhadawdldaqleqamdalrcppadepvtNLSGGE 164
                                    555555555556666556666666666666666677777777778888888888888888888888888888889***** PP

                                    HHHHHHH.HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                    xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 142 ktLvala.LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                    +  val  Ll+     ++  l llDe   +LD++ v+ + + l +      ++ +++++ +l
  gi|121638360|ref|YP_978584.1| 165 RRRVALCkLLL-----SKPDLLLLDEPTNHLDAESVQWLEQHLASYP--GAILAVTHDRYFL 219
                                    98777651554.....344589***************9999988765..5566666666555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                                    SSEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAi 44 
                                    +++  ++GpNG GK+ l+  i
  gi|121638360|ref|YP_978584.1| 347 NGIVGVIGPNGVGKTTLFKTI 367
                                    567889***********9988 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.047
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                    +LSgGe+  + laL       +   l llDe    LD +    + + l + 
  gi|121638360|ref|YP_978584.1| 442 VLSGGERNRLNLALT----LKQGGNLILLDEPTNDLDVETLGSLENALLNF 488
                                    69*****97777776....5788899***********99998888777655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00084       0.5      22      37 ..      34      49 ..      19      53 .. 0.73
   2 ?   -2.3   0.7       8.9   5.3e+03     149     160 ..     282     293 ..     226     310 .. 0.46
   3 !   16.3   0.2   1.7e-05      0.01      11      39 ..     338     367 ..     333     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00084
                         AAA_23 22 tlItGpNGaGKTTild 37
                                     ++GpNGaGK+++l+
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVLR 49
                                   4689*********997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.9
                         AAA_23 149 kdkkerleelek 160
                                    ++ k rl+ +e+
  gi|121638360|ref|YP_978584.1| 282 AKSKARLQRYEE 293
                                    111112222222 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.7e-05
                         AAA_23  11 rdqeidF.skgltlItGpNGaGKTTildAi 39 
                                    +d ++ +  +g++ ++GpNG GKTT++  i
  gi|121638360|ref|YP_978584.1| 338 KDLSFSLpRNGIVGVIGPNGVGKTTLFKTI 367
                                    5556666889****************9765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0021       1.2      18      39 ..      27      48 ..      20      61 .. 0.78
   2 !   11.7   0.1   0.00027      0.16      16      39 ..     341     364 ..     336     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                         AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                   ++ +   + ++Gp+G+GKS++l
  gi|121638360|ref|YP_978584.1| 27 SFYPGAKIGVVGPNGAGKSSVL 48
                                   55544466799********987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00027
                         AAA_29  16 tieidlkgatlltGpsGsGKSTll 39 
                                    ++++ ++g++ ++Gp+G+GK+Tl+
  gi|121638360|ref|YP_978584.1| 341 SFSLPRNGIVGVIGPNGVGKTTLF 364
                                    56777888999************8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0044       2.6       1      21 [.      33      53 ..      33      77 .. 0.83
   2 !   12.3   0.1   0.00023      0.14       2      26 ..     350     375 ..     349     402 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                                   EEEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltg 21
                                   ++++vG   +GKS++++ + g
  gi|121638360|ref|YP_978584.1| 33 KIGVVGPNGAGKSSVLRIMAG 53
                                   699*************99876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                                    EEEEESTTSSHHHHHHHHHTS.TEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaiv 26 
                                    v+++G   vGK+tL+++++g  k   
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTIVGLeKPDS 375
                                    89****************99423332 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.1e-05     0.018       1     136 [.      34     213 ..      34     223 .. 0.68
   2 ?    3.5   0.0      0.11        68       1      45 [.     350     393 ..     350     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                                    EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S-EEEEECCT---CCS...SSEEEE....T-EB--CHHHHHHHH.H CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrrplelqlgeeeeaseravkeelkek....ekkledfsevreeie.k 74 
                                    i vvG   +GKSSvl  + g d   +g   + T +++ +  +e +  ++++v+ +++e+    + kl+ f+ev+e +  +
  gi|121638360|ref|YP_978584.1|  34 IGVVGPNGAGKSSVLRIMAGLDKPNNGDAfLATGATVGILQQEPPLNEDKTVRGNVEEGmgdiKIKLDRFNEVAELMAtD 113
                                    79********************6666666677888777777555555544444444444444499999999998865413 PP

                                    HHHHHHTSSSS--SS......................................-EEEEEEETTS-SEEEEE---B-SSSG CS
                      Dynamin_N  75 etekiagankgiskk......................................villkilsllvkgltlvDlPGldsvnk 116
                                     t+++ +++ + +++                                       + l++l l +++l l+D P  ++ ++
  gi|121638360|ref|YP_978584.1| 114 YTDELMEEMGRLQEEldhadawdldaqleqamdalrcppadepvtnlsggerrRVALCKLLLSKPDLLLLDEP-TNHLDA 192
                                    3445554555555546667788888888888888888888888888888887777777777777777777777.444444 PP

                                    TTSHHHHHHH.STTEEEEEEE CS
                      Dynamin_N 117 rdqelvkeyi.kkadiilavt 136
                                    +  +++++++     +ilavt
  gi|121638360|ref|YP_978584.1| 193 ESVQWLEQHLaSYPGAILAVT 213
                                    444666666656666666666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT-- CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeee 45 
                                    + v+G    GK+++   ++g +  p +  +    +++l++ ++ +
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTIVGLE-KPDSGSVKVGETVKLSYVDQAR 393
                                    689*****************99.7777666667777777776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.022        13      10      27 ..      36      53 ..      31     205 .. 0.85
   2 !   11.4   0.0    0.0005       0.3       6      28 ..     348     370 ..     345     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                         AAA_22 10 vtGesGtGKTtllrrlle 27
                                   v+G+ G+GK+ +lr ++ 
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIMAG 53
                                   89**********997765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0005
                         AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                    gi+ v+G+ G+GKTtl ++++  
  gi|121638360|ref|YP_978584.1| 348 GIVGVIGPNGVGKTTLFKTIVGL 370
                                    78889************998765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0052       3.1       3      22 ..      32      51 ..      30     110 .. 0.90
   2 !    9.3   0.2    0.0014      0.85       5      22 ..     350     367 ..     346     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0052
                         AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                   +ki ++Gp+g+GK+++++ +
  gi|121638360|ref|YP_978584.1| 32 AKIGVVGPNGAGKSSVLRIM 51
                                   79*************99887 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    + ++Gp+g+GKTtl k++
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTI 367
                                    679************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.034        20     104     121 ..      36      53 ..      16      65 .. 0.85
   2 !   11.3   0.1    0.0004      0.24      90     125 ..     337     373 ..     319     385 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                                    EECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 104 lvGqSGvGKStLinallp 121
                                    +vG+ G+GKS+++  +++
  gi|121638360|ref|YP_978584.1|  36 VVGPNGAGKSSVLRIMAG 53 
                                    79**********998776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                    +++l+  l    ++ ++G+ GvGK+tL +++++ ++ 
  gi|121638360|ref|YP_978584.1| 337 IKDLSFSLPRnGIVGVIGPNGVGKTTLFKTIVGLEKP 373
                                    5677777766478889**************9986554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0017         1      28      44 ..      36      52 ..      21     124 .. 0.85
   2 !    6.6   0.1    0.0092       5.5      25      43 ..     349     367 ..     336     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                         AAA_15 28 liGkNnsGKSsileald 44
                                   ++G+N++GKSs+l+++ 
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIMA 52
                                   8************9985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0092
                         AAA_15  25 ltvliGkNnsGKSsileal 43 
                                    +  +iG+N++GK+++ + +
  gi|121638360|ref|YP_978584.1| 349 IVGVIGPNGVGKTTLFKTI 367
                                    6669**********99877 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.015       8.8      62      82 ..     176     196 ..     136     202 .. 0.74
   2 ?    4.9   0.1     0.052        31      29      84 ..     439     481 ..     425     486 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                        SbcCD_C  62 palrlvfLDEAFsklDeesia 82 
                                    ++++l++LDE  + lD+es++
  gi|121638360|ref|YP_978584.1| 176 SKPDLLLLDEPTNHLDAESVQ 196
                                    358999999999999999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.052
                        SbcCD_C  29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                     +g lSGGe+ + + lal       +      ++   l++LDE  + lD e++ +l
  gi|121638360|ref|YP_978584.1| 439 PAGVLSGGER-NRLNLALT------L------KQGGNLILLDEPTNDLDVETLGSL 481
                                    5566666666.33333333......1......234578999999999999988776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.021        12       1      19 [.      34      52 ..      34     152 .. 0.83
   2 !    8.7   0.1     0.004       2.4       1      18 [.     350     367 ..     350     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.021
                         AAA_18  1 IlltGtpGvGKttlakeLs 19
                                   I++ G+ G+GK+++ +  +
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVLRIMA 52
                                   89************99764 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                         AAA_18   1 IlltGtpGvGKttlakeL 18 
                                    +++ G+ GvGKttl k +
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTI 367
                                    6899**********9877 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.071        43       1      17 [.      33      49 ..      33      73 .. 0.87
   2 ?   -1.3   0.0       4.2   2.5e+03      74     103 ..     200     230 ..     192     234 .. 0.69
   3 !    9.8   0.0    0.0015      0.89       4      40 ..     352     388 ..     350     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.071
                                   EEEEESSTTSSHHHHHH CS
                            Roc  1 KvvlvGdsgvGKtsllk 17
                                   K+ +vG +g+GK+s l+
  gi|121638360|ref|YP_978584.1| 33 KIGVVGPNGAGKSSVLR 49
                                   8999**********986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                                    HHHHCTSCEEEEEEEGHHH.HCHHHHHHHHH CS
                            Roc  74 plylreaalailvydsrss.enlkeWlkelk 103
                                    ++  +   ++++v+ +r + +n+ eW+ el+
  gi|121638360|ref|YP_978584.1| 200 QHLASYPGAILAVTHDRYFlDNVAEWILELD 230
                                    5555555667777777765599****99986 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0015
                                    EESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEE CS
                            Roc   4 lvGdsgvGKtsllkrfvedkfsekekstigvdfltke 40 
                                    ++G +gvGKt+l+k +v  +  ++ +  +g +++ + 
  gi|121638360|ref|YP_978584.1| 352 VIGPNGVGKTTLFKTIVGLEKPDSGSVKVGETVKLSY 388
                                    89*************9988887777777777665554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0015      0.89      31      46 ..      36      51 ..      21      54 .. 0.75
   2 !    6.6   0.0    0.0089       5.3      18      47 ..     339     368 ..     333     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                         AAA_27 31 iyGpNEAGKstalrAi 46
                                   ++GpN AGKs++lr +
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIM 51
                                   79**********9966 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0089
                         AAA_27  18 sldfsaeeadlhliyGpNEAGKstalrAis 47 
                                     l+fs  ++++  ++GpN  GK+t+++ i 
  gi|121638360|ref|YP_978584.1| 339 DLSFSLPRNGIVGVIGPNGVGKTTLFKTIV 368
                                    5778878999999************99886 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.3   7.5e+02      23      37 ..      34      48 ..      26      52 .. 0.86
   2 ?   -0.2   0.0      0.75   4.5e+02      88     111 ..     162     185 ..     107     197 .. 0.82
   3 !   12.5   0.0    0.0001     0.061       9      41 ..     337     368 ..     331     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                   EEEEESTTSSHHHHH CS
                         NB-ARC 23 valvGmgGvGKttla 37
                                   +++vG  G GK+ ++
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVL 48
                                   89*********9765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.75
                                    STTSHHHHHHHHCCCTTEEEEEEE CS
                         NB-ARC  88 eveslkrklvrlLltkrfllvlDD 111
                                     +e +   l++lLl+k  ll+lD 
  gi|121638360|ref|YP_978584.1| 162 GGERRRVALCKLLLSKPDLLLLDE 185
                                    444478899999999999999995 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0001
                                    HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                         NB-ARC   9 iekLlekdelqslvvalvGmgGvGKttlakqil 41 
                                    i+ L+    +   +v++ G  GvGKttl+k i+
  gi|121638360|ref|YP_978584.1| 337 IKDLS-FSLPRNGIVGVIGPNGVGKTTLFKTIV 368
                                    55555.33344469****************997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.15        90       3      19 ..      36      52 ..      34      59 .. 0.89
   2 !   10.9   0.1   0.00075      0.45       3      22 ..     352     371 ..     350     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                                   EESSTTSSHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakava 19
                                   ++Gp G GK+++ + +a
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIMA 52
                                   79**********99887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00075
                                    EESSTTSSHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakel 22 
                                    ++Gp G+GKT+l k ++   
  gi|121638360|ref|YP_978584.1| 352 VIGPNGVGKTTLFKTIVGLE 371
                                    79************998765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.43   2.6e+02      25      41 ..      36      52 ..      30     130 .. 0.73
   2 ?   -2.6   0.0       6.8     4e+03      98      98 ..     283     283 ..     226     325 .. 0.49
   3 ?   10.5   0.0   0.00068       0.4      20      44 ..     347     371 ..     335     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.43
                       ATPase_2 25 iYGpegsGKtaLlkeii 41
                                   + Gp g GK+++l+ ++
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIMA 52
                                   67*********998655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.8
                       ATPase_2  98 k 98 
                                    k
  gi|121638360|ref|YP_978584.1| 283 K 283
                                    1 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00068
                       ATPase_2  20 neiyfiYGpegsGKtaLlkeiienl 44 
                                    n i+ + Gp g+GKt+L+k i+   
  gi|121638360|ref|YP_978584.1| 347 NGIVGVIGPNGVGKTTLFKTIVGLE 371
                                    5678899*************99765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.56   3.3e+02      27      55 ..      33      61 ..      25     116 .. 0.91
   2 ?   10.0   0.1   0.00046      0.27      21      55 ..     343     377 ..     338     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.56
                           DLIC 27 svlvlGedgsGkttliaklqGveeekkGr 55
                                   ++ v+G +g+Gk++++  + G+++++ G 
  gi|121638360|ref|YP_978584.1| 33 KIGVVGPNGAGKSSVLRIMAGLDKPNNGD 61
                                   57799************999999998886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00046
                           DLIC  21 klPsgksvlvlGedgsGkttliaklqGveeekkGr 55 
                                     lP +  v v+G +g Gkttl   + G+e++  G+
  gi|121638360|ref|YP_978584.1| 343 SLPRNGIVGVIGPNGVGKTTLFKTIVGLEKPDSGS 377
                                    5899999**********************998876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.089        53       3      21 ..      34      52 ..      32      68 .. 0.82
   2 ?    7.9   0.1    0.0035       2.1       3      30 ..     350     377 ..     348     401 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.089
                                   EEEEESTTCCHHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhll 21
                                   ++++G+ G+GK+++l+ + 
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVLRIMA 52
                                   6799**********98765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                                    EEEEESTTCCHHHHHHHHHCT--SS-EE CS
                           cobW   3 tvltGflGsGKTtLlnhllenraglkla 30 
                                    +++ G+ G GKTtL ++++  ++  +  
  gi|121638360|ref|YP_978584.1| 350 VGVIGPNGVGKTTLFKTIVGLEKPDSGS 377
                                    6789**************9444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.063        38       4      17 ..      36      49 ..      34      64 .. 0.88
   2 ?    8.4   0.0    0.0037       2.2       3      20 ..     351     368 ..     349     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.063
                         AAA_33  4 lvGlpGsGKstlae 17
                                   +vG++G+GKs +++
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLR 49
                                   79********9987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0037
                         AAA_33   3 llvGlpGsGKstlaerll 20 
                                     ++G++G+GK+tl + ++
  gi|121638360|ref|YP_978584.1| 351 GVIGPNGVGKTTLFKTIV 368
                                    589**********99875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.027        16      23      45 ..      36      58 ..      31      73 .. 0.81
   2 ?    6.6   0.1    0.0094       5.6      20      42 ..     349     371 ..     342     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.027
                         AAA_30 23 ltGpAGtGKttalkalreaweaa 45
                                   ++Gp G+GK+ +l+ ++ + + +
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIMAGLDKPN 58
                                   79************988776655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0094
                         AAA_30  20 vavltGpAGtGKttalkalreaw 42 
                                    ++ + Gp G GKtt+ k+++ + 
  gi|121638360|ref|YP_978584.1| 349 IVGVIGPNGVGKTTLFKTIVGLE 371
                                    77899************998765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.4   1.5e+03       6      22 ..      35      51 ..      32      65 .. 0.83
   2 ?    9.7   0.1    0.0014      0.84       2      24 ..     347     369 ..     346     402 .. 0.84
   3 ?   -2.5   0.0       7.9   4.7e+03      61      75 ..     458     471 ..     446     478 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.4
                         AAA_14  6 vitGaRrvGKTtllkql 22
                                    ++G+  +GK+ +l+ +
  gi|121638360|ref|YP_978584.1| 35 GVVGPNGAGKSSVLRIM 51
                                   689********998755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                         AAA_14   2 rkilvitGaRrvGKTtllkqlik 24 
                                    + i+ + G+  vGKTtl k+++ 
  gi|121638360|ref|YP_978584.1| 347 NGIVGVIGPNGVGKTTLFKTIVG 369
                                    67999************999874 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.9
                         AAA_14  61 keekktylflDEiqe 75 
                                    k ++ ++++lDE  +
  gi|121638360|ref|YP_978584.1| 458 K-QGGNLILLDEPTN 471
                                    3.48899****9765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.44   2.7e+02       5      19 ..      36      50 ..      33      64 .. 0.80
   2 ?    8.8   0.1    0.0024       1.4       4      21 ..     351     368 ..     349     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.44
                                   EEC-TTTCHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqk 19
                                   + G++G GK+  l+ 
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRI 50
                                   79********99864 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                                    EEEC-TTTCHHHHHHHHH CS
                          NACHT   4 ilqGeaGsGKTtLlqkla 21 
                                     + G++G+GKTtL + ++
  gi|121638360|ref|YP_978584.1| 351 GVIGPNGVGKTTLFKTIV 368
                                    589***********9997 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.9   1.1e+03       2      17 ..      34      49 ..      33      58 .. 0.80
   2 ?   -0.4   0.0       1.5   9.2e+02      65     103 ..     147     185 ..     136     235 .. 0.70
   3 ?   -2.3   0.0         6   3.6e+03      48      88 ..     258     298 ..     223     313 .. 0.63
   4 ?    8.3   0.5    0.0033         2       3      21 ..     351     369 ..     349     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                                   EEEE--TTSSHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvk 17
                                   + + Gp G GK+ +++
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVLR 49
                                   7899********9875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                                    ---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE-- CS
                       NTPase_1  65 akreprvgkyvvdvesfeelalealrkalseadviviDE 103
                                    a r+p  ++ v ++   e+  ++  +  ls++d++++DE
  gi|121638360|ref|YP_978584.1| 147 ALRCPPADEPVTNLSGGERRRVALCKLLLSKPDLLLLDE 185
                                    457777888888999989998888888889*******99 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6
                                    EEEET.T--EEEEEETT---SSEETTEEE-HHHHHHHHHHH CS
                       NTPase_1  48 kivdlasgeegiLarveakreprvgkyvvdvesfeelalea 88 
                                    k  +l++  +++La v++  ++r  k + ++++ ee+a+ea
  gi|121638360|ref|YP_978584.1| 258 KDAKLQKRLTEELAWVRSGAKARQAKSKARLQRYEEMAAEA 298
                                    44455555556666666666666666666666666666655 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0033
                                    EEE--TTSSHHHHHHHHHH CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvle 21 
                                     + Gp GvGKtTl+k ++ 
  gi|121638360|ref|YP_978584.1| 351 GVIGPNGVGKTTLFKTIVG 369
                                    578************9986 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.022        13       2      19 ..      34      51 ..      33      62 .. 0.91
   2 ?    4.0   0.0     0.061        36       1      22 [.     349     370 ..     349     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                            PRK  2 IgvagsSGaGkttvarkl 19
                                   Igv g+ GaGk++v r +
  gi|121638360|ref|YP_978584.1| 34 IGVVGPNGAGKSSVLRIM 51
                                   9*************9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.061
                            PRK   1 vIgvagsSGaGkttvarkleki 22 
                                    ++gv g+ G Gktt+ ++++ +
  gi|121638360|ref|YP_978584.1| 349 IVGVIGPNGVGKTTLFKTIVGL 370
                                    79*************9999864 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.058        35      23      47 ..      38      62 ..      36      80 .. 0.82
   2 ?   -1.9   0.0       1.6   9.5e+02     493     511 ..     153     171 ..     112     179 .. 0.79
   3 ?   -1.7   0.1       1.4   8.3e+02     161     161 ..     261     261 ..     206     310 .. 0.50
   4 ?    3.3   0.0     0.042        25      23      41 ..     354     372 ..     350     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.058
                         AAA_13 23 GwNGaGKTtLSrllrslelgetepk 47
                                   G NGaGK+++ r+++ l + +  ++
  gi|121638360|ref|YP_978584.1| 38 GPNGAGKSSVLRIMAGLDKPNNGDA 62
                                   99*************9977655555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                         AAA_13 493 gsqaaetLSeGEktaIafl 511
                                     +++ ++LS GE+  +a++
  gi|121638360|ref|YP_978584.1| 153 ADEPVTNLSGGERRRVALC 171
                                    567899*******999998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.4
                         AAA_13 161 k 161
                                    k
  gi|121638360|ref|YP_978584.1| 261 K 261
                                    1 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.042
                         AAA_13  23 GwNGaGKTtLSrllrslel 41 
                                    G NG GKTtL + +  le+
  gi|121638360|ref|YP_978584.1| 354 GPNGVGKTTLFKTIVGLEK 372
                                    99*********99999975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.5     0.019        11      29     156 ..      36     199 ..      32     212 .. 0.46
   2 ?   -0.1   0.2       1.8   1.1e+03      67     145 ..     235     328 ..     212     341 .. 0.61
   3 ?    9.9   0.1    0.0015      0.89      25      45 ..     348     368 ..     334     457 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                         AAA_16  29 lsGesGvGKsslvrellralekd..................................ggiflrgkcdqlesaipysalaq 74 
                                    ++G+ G GKss++r  +  l k                                   g+  ++ k d++ + +++     
  gi|121638360|ref|YP_978584.1|  36 VVGPNGAGKSSVLRIMA-GLDKPnngdaflatgatvgilqqepplnedktvrgnveeGMGDIKIKLDRFNEVAEL---MA 111
                                    89***********8777.566665666666665444444444444444444333332222244444444222111...11 PP

                         AAA_16  75 alareellrqllde......aesaeleawrekleealaavpelagaea....srllellkrllallsrderplvlvlD.d 143
                                    +  ++el++++++       a++ +l+a  e+  +al++ p++++       +r + +l +ll  ls+   p +l+lD  
  gi|121638360|ref|YP_978584.1| 112 TDYTDELMEEMGRLqeeldhADAWDLDAQLEQAMDALRCPPADEPVTNlsggERRRVALCKLL--LSK---PDLLLLDeP 186
                                    111222222222221111113333333333333333333333333333444466666666666..333...434444414 PP

                         AAA_16 144 lqwadeaslqlla 156
                                       +d++s q+l+
  gi|121638360|ref|YP_978584.1| 187 TNHLDAESVQWLE 199
                                    5577777777766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                         AAA_16  67 ipysa.laqalareellrqlldeaesaeleawrekleeala...avpelagaeasrllellkrllallsrder....... 135
                                     py   + ++l++ +  r   +    ++ +  +++l+e+la   ++++++ a++++ l+   +++a ++++++       
  gi|121638360|ref|YP_978584.1| 235 YPYEGnYSTYLEK-KAERLAVQG---RKDAKLQKRLTEELAwvrSGAKARQAKSKARLQRYEEMAAEAEKTRKldfeeiq 310
                                    4554445555533.333333333...233444444444444444777777777777777777777777765557777777 PP

                         AAA_16 136 ........plvlvlDdlq 145
                                             +v+ +D+l+
  gi|121638360|ref|YP_978584.1| 311 ipvgprlgNVVVEVDHLD 328
                                    777766655777777777 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0015
                         AAA_16  25 elvllsGesGvGKsslvrell 45 
                                    ++v ++G+ GvGK++l +++ 
  gi|121638360|ref|YP_978584.1| 348 GIVGVIGPNGVGKTTLFKTIV 368
                                    7899************98876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.16        94       3      18 ..      36      51 ..      34      63 .. 0.85
   2 ?    6.4   0.0     0.019        11       3      18 ..     352     367 ..     350     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.16
                   RNA_helicase  3 lyGpsgeGKStlakeL 18
                                   ++Gp+g GKS++ + +
  gi|121638360|ref|YP_978584.1| 36 VVGPNGAGKSSVLRIM 51
                                   79********998874 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                   RNA_helicase   3 lyGpsgeGKStlakeL 18 
                                    + Gp+g+GK+tl k++
  gi|121638360|ref|YP_978584.1| 352 VIGPNGVGKTTLFKTI 367
                                    78**********9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.40
# Mc/sec: 4173.13
//
Query:       gi|121638361|ref|YP_978585.1|  [L=161]
Description: hypothetical protein BCG_2498 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-15   55.6   0.0    5.5e-15   55.3   0.0    1.1  1  SSB       Single-strand binding protein family


Domain annotation for each model (and alignments):
>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0     3e-19   5.5e-15       6     101 ..       1      96 [.       1      99 [. 0.95

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 3e-19
                                    EEEEESSS-EEEEETTSEEEEEEEEEEEEEEEE.TTCCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEEEEEEE CS
                            SSB   6 lvGrlgkdpelrqtesGnavarftlatnrrfkd.qegekdeetewhrvvvfgklaevvaeylkkGslvyveGrlqtrkye 84 
                                    +vG++++d + r++  +++v++f++a+n+r++  + g++ +++ +++v  +g+l++ v  +l kG+ v+v G + t++ye
  gi|121638361|ref|YP_978585.1|   1 MVGHIVNDLQRRKVG-DQEVVKFRVASNSRRRTsDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYE 79 
                                    59************9.89999********9888899******************************************** PP

                                    CTTSCEEEEEEEEEEEE CS
                            SSB  85 dqegqkrysteivaeev 101
                                    d++g +r+s+e  a +v
  gi|121638361|ref|YP_978585.1|  80 DRDGIRRSSLEMRATSV 96 
                                    ************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1354.58
//
Query:       gi|121638362|ref|YP_978586.1|  [L=107]
Description: hypothetical protein BCG_2499c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 771.72
//
Query:       gi|121638363|ref|YP_978587.1|  [L=789]
Description: glycerol-3-phosphate acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-14   53.4   0.0    4.1e-14   52.3   0.0    1.5  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   2.3e-18   4.1e-14      12     124 ..     266     379 ..     253     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.3e-18
                Acyltransferase  12 ekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidR..ksnaraagslenisell 89 
                                    e++pa+l+  H+sy+D ++  ++++++++ ++v++ ++ +l  + l+g+lmr++g+ifi+R  +++  ++ +l++++  +
  gi|121638363|ref|YP_978587.1| 266 EAHPAVLLFSHRSYIDGVVVPVAMQDNRL-PPVHMFGGINLS-FGLMGPLMRRSGMIFIRRniGNDPLYKYVLKEYVGYV 343
                                    479*********************88887.899999999965.5*****************9988888999999999988 PP

                Acyltransferase  90 eegkl.vviFPEGtrsregellpfkkGlvrlaakak 124
                                     e++  +    EGtrsr+g++lp+k Gl++ +a+a 
  gi|121638363|ref|YP_978587.1| 344 VEKRFnLSWSIEGTRSRTGKMLPPKLGLMSYVADAY 379
                                    888998*************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (789 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 5427.12
//
Query:       gi|121638364|ref|YP_978588.1|  [L=580]
Description: transmembrane phospholipid biosynthesis bifunctionnal l-3-phosphoserine phosphatase/1-acyl-SN-glycerol-3-phosphate acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-31  109.5   0.2    6.5e-31  108.2   0.2    1.7  1  HAD              haloacid dehalogenase-like hydrolase
    6.3e-28   97.1   0.0      1e-27   96.4   0.0    1.3  1  Acyltransferase  Acyltransferase
  ------ inclusion threshold ------
      0.061   13.0   0.6         15    5.2   0.0    3.2  3  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.2   1.1e-34   6.5e-31       1     187 [.      40     223 ..      40     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 1.1e-34
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerfvae 79 
                                    a+fD+DgTL++g ++  l++ +lrr++     +l+    + l+ +l+r + ++l    +a+lag    +l++  er++a+
  gi|121638364|ref|YP_978588.1|  40 AFFDLDGTLVAGFTAVILTQERLRRRDMG-VGELLGMVQAGLNHTLGRIEFEDLIGKAAAALAGRLlTDLEEIGERLFAQ 118
                                    8***********************99988.788888889999999999999999999999999999899999999999** PP

                            HAD  80 virpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvrgegkvaa 157
                                     i+ +++ p+++el++ah a+G++vv+ S++l + v p++++lg+ + l +++e+++   ltg+  +  ++ +g gk++a
  gi|121638364|ref|YP_978588.1| 119 RIESRIY-PEMRELVRAHVARGHTVVLSSSALTIQVGPVARFLGINNMLTNKFETNEdgILTGG--VLKPILWGPGKATA 195
                                    *****66.********************************************************..************** PP

                            HAD 158 lrewlaaegegidleevvayGDspsDlpll 187
                                    +++  +a++++idl+++++y+D+  D++l+
  gi|121638364|ref|YP_978588.1| 196 VQR--FAAEHDIDLKDSYFYADGDEDVALM 223
                                    ***..**********************997 PP

>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   1.7e-31     1e-27       1     134 [.     312     438 ..     312     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 1.7e-31
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraag 80 
                                    +++v g+enl +++pa+++ NH+  +D+++  +l+     + n+v ++kkel+s p++g+l +ll+ +fidR++   a +
  gi|121638364|ref|YP_978588.1| 312 HLNVIGKENLTAQRPAVFIFNHRNQVDPVIAGALV-----RDNWVGVGKKELASDPIMGTLGKLLDGVFIDRDDPVAAVE 386
                                    68999*****************************9.....7999************************************ PP

                Acyltransferase  81 sleniselleegklvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                    +l++++e+ ++g  +vi PEGtr+ ++e+  fkkG +r+a+ a  ++pivP++i
  gi|121638364|ref|YP_978588.1| 387 TLHTVEERARNGLSIVIAPEGTRLDTTEVGSFKKGPFRIAMAA--KIPIVPIVI 438
                                    *******************************************..*******97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.039   2.3e+02       2      10 ..      41      49 ..      40      56 .. 0.89
   2 ?    2.4   0.0     0.018   1.1e+02      15      58 ..     123     166 ..     119     173 .. 0.88
   3 ?    5.2   0.0    0.0025        15     188     224 ..     192     228 ..     189     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.039
                                   EEEIIIIIS CS
                    Hydrolase_3  2 alDlDGTLl 10
                                   ++DlDGTL+
  gi|121638364|ref|YP_978588.1| 41 FFDLDGTLV 49
                                   89******8 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                                    ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                    +i ++ +e ++   ++g++vv+++   + +v pv++ lg+++++
  gi|121638364|ref|YP_978588.1| 123 RIYPEMRELVRAHVARGHTVVLSSSALTIQVGPVARFLGINNML 166
                                    57788999999999**********************99999654 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSE CS
                    Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDieMLeaagl 224
                                    K+ta++++a e +i+l++ +   Dg+ D++++  +g+
  gi|121638364|ref|YP_978588.1| 192 KATAVQRFAAEHDIDLKDSYFYADGDEDVALMYLVGN 228
                                    9*******************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.38s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 3011.30
//
Query:       gi|121638365|ref|YP_978589.1|  [L=491]
Description: hypothetical protein BCG_2502c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-85  285.6   0.4    6.5e-85  285.1   0.4    1.2  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    3.7e-12   46.4   0.0    5.6e-12   45.8   0.0    1.3  1  DUF1298         Protein of unknown function (DUF1298)


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   0.4   7.3e-89   6.5e-85       5     264 .]       8     282 ..       5     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 7.3e-89
                 WES_acyltransf   5 Dalflelesaetpmhvgalavleppskgagel.....llrrlreaieqreeraprlrqkvveeplglaapvWvededfDl 79 
                                    ++l +el+ ++++mh+g+++++++++ +a el     +++r+r+++e++++r++rlrqkvv+++l++aap+Wv+d+df+l
  gi|121638365|ref|YP_978589.1|   8 PRLSDELGPVDYLMHRGEANPRTRSGIMALELldgtpDWDRFRTRFENASRRVLRLRQKVVVPTLPTAAPRWVVDPDFNL 87 
                                    6788999************************99*********************************************** PP

                 WES_acyltransf  80 dyHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpdd 159
                                    d+HvRrv+++ P+t re+l+l++++ +spLD+srPlW+++++EG+++gr+A+ll+v+HA++DGvgg++++a+++dl++d+
  gi|121638365|ref|YP_978589.1|  88 DFHVRRVRVSGPATLREVLDLAEVILQSPLDISRPLWTATLVEGMADGRAAMLLHVSHAVTDGVGGVEMFAQIYDLERDP 167
                                    ******************************************************************************** PP

                 WES_acyltransf 160 pprpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaap......rtplntpl 233
                                    ppr++ppq++p+d s ++l+++g++++++a +g+vl++++g+vs+agr++ ++++++s++l++a++      r+++++pl
  gi|121638365|ref|YP_978589.1| 168 PPRSTPPQPIPEDLSPNDLMRRGINHLPIAVVGGVLDALSGAVSMAGRAVLEPVSTVSGILGYARSgirvlnRAAEPSPL 247
                                    ******************************************************************************** PP

                 WES_acyltransf 234 sraR....rfaaaslpLadvkavakalgvtiNDvv 264
                                     r+R    r++a++++Lad++++aka g++iND++
  gi|121638365|ref|YP_978589.1| 248 LRRRslttRTEAIDIRLADLHKAAKAGGGSINDAY 282
                                    *********************************86 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   6.2e-16   5.6e-12       2     144 ..     321     460 ..     320     461 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.2e-16
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrllsnttlviSNvpGPqe 81 
                                    GNq++ v l  p+++ dP+ r++k++++m++ + +++  +  +++ + l++lp++v++ + ++    + +  SNvp    
  gi|121638365|ref|YP_978589.1| 321 GNQFTGVNLAAPVGTIDPVARMKKIRAQMTQRRDEPAMNIIGSIAPV-LSVLPTAVLEGI-TGSVIGSDVQASNVPVYPG 398
                                    9*********************************************9.*********998.66678899********888 PP

                        DUF1298  82 elylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                      ylaGa++   y++ p+   +a+++ ++S  g  ++++  d++ v + + ++++l+  ++e+
  gi|121638365|ref|YP_978589.1| 399 DTYLAGAKILRQYGIGPLPG-VAMMVVLISRGGWCTVTVRYDRASVRNDELFAQCLQAGFDEI 460
                                    8****************988.****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3303.73
//
Query:       gi|121638366|ref|YP_978590.1|  [L=421]
Description: carboxylesterase lipQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-21   77.1   0.6    2.4e-21   76.6   0.6    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
    1.1e-13   51.2   0.7    8.1e-13   48.3   0.7    2.0  1  Peptidase_S9   Prolyl oligopeptidase family
    2.4e-12   46.5   0.0    1.2e-11   44.2   0.0    1.9  1  COesterase     Carboxylesterase family
    0.00012   21.7   0.3    0.00059   19.5   0.3    2.0  1  DLH            Dienelactone hydrolase family
     0.0026   17.1   0.1      0.051   12.8   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0086   15.7   0.0      0.029   14.1   0.0    1.8  2  FSH1           Serine hydrolase (FSH1)
  ------ inclusion threshold ------
      0.033   14.3   0.0      0.083   13.0   0.0    1.7  1  Abhydrolase_4  TAP-like protein
      0.033   14.1   0.0       0.09   12.7   0.0    1.6  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.036   13.9   0.0       0.13   12.1   0.0    1.7  2  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.042   13.2   0.0       0.14   11.5   0.0    1.9  2  LIP            Secretory lipase
      0.043   13.5   0.0        4.4    6.9   0.0    2.5  3  Abhydrolase_1  alpha/beta hydrolase fold
      0.074   11.9   0.0       0.12   11.3   0.0    1.2  1  Alliinase_C    Allinase


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.6   1.6e-24   2.4e-21       3     209 ..     173     379 ..     171     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.6e-24
                                    EE--STTTS--TTTT.HHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                  Abhydrolase_3   3 yfHGGGfvlgsldth.dalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                    ++ GG++++ + + +  +l+++++ elg ++vs++Y  +P   +Pa + d+ +a+ w++e+ +++g dp+ i++ G SaG
  gi|121638366|ref|YP_978590.1| 173 QVPGGAWTINGKRPQaYPLMSRMV-ELGWICVSINYSKSPRCTWPAHIVDVKRAIAWVRENIADYGGDPDFITITGGSAG 251
                                    5669***98777666377777776.5***********************************99***************** PP

                                    HHHHHHHHHHHHHTT---.........EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHS.SGGGGG CS
                  Abhydrolase_3  82 Gnlaaavalrardegepk.........vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlyl.peadrd 151
                                    ++laa +al a d   ++         v++ + +y v dl  t+ e++              +++  f+++++     +d
  gi|121638366|ref|YP_978590.1| 252 AHLAALAALSANDPA-LQpgfesadtaVQAAAPYYGVYDL--TNAENM-------------HEMMMPFLEHFVmRSRYVD 315
                                    *************85.332477777777777777777766..222333.............2334445555553477778 PP

                                    ST....TTSGGGCS-SST---EEEEEETT-TTH..HHHHHHHHHHHHTT-.-EEEEEETTEETTG CS
                  Abhydrolase_3 152 dp....laspllaedlsglpptlvvvaefDplr..degeayaerlraagv.evelieyegmvHgf 209
                                    +p    +asp+     s++pp +v+ +e+Dp+    +++a++++lr+ag   v++ e +++ H+f
  gi|121638366|ref|YP_978590.1| 316 NPglfkAASPISY-VHSEAPPFFVLHGEKDPMVpsAQSRAFSAALRDAGAaTVSYAELPNAHHAF 379
                                    8876668888855.6999**************72257789******9886258999*******99 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.7   5.4e-16   8.1e-13      46     189 ..     223     380 ..     218     400 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 5.4e-16
                                    HHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG.....-.......SEEEEESE---CCCHHCSTTS... CS
                   Peptidase_S9  46 dDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdl.....F.......kaavaevpvvdvlrydsdtdl... 110
                                    +  ia++++ ++ +  d++ + itGgS+G  l++ a+ +++d      F       +aa+  ++v+d+++     ++   
  gi|121638366|ref|YP_978590.1| 223 KRAIAWVRENIADYGGDPDFITITGGSAGAHLAALAALSANDPalqpgFesadtavQAAAPYYGVYDLTNAENMHEMmmp 302
                                    5579999999**********************9999886655323444433332227899999********999998999 PP

                                    THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-SSTT CS
                   Peptidase_S9 111 lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegHgvg 189
                                    + e++       +n+  +k++sp+s+++   + pp++++hG++D  vp a++  + aaL+++g   v +   p++ H + 
  gi|121638366|ref|YP_978590.1| 303 FLEHFVMRSRYVDNPGLFKAASPISYVHS--EAPPFFVLHGEKDPMVPSAQSRAFSAALRDAGAAtVSYAELPNAHHAFD 380
                                    7785555577789****************..**********************************9***********654 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   8.1e-15   1.2e-11      90     206 ..     154     262 ..     149     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.1e-15
                                    EEEEE.ESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHH CS
                     COesterase  90 Lnvyt.PkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDq 166
                                    L+++  P+      ++ PVl+ + Gg+ +++ ++   y+  + + e + i V+inY          ++  ++  + ++D+
  gi|121638366|ref|YP_978590.1| 154 LDIWRrPD--LAPGRRAPVLIQVPGGAWTINGKRPqaYPLMSRMVELGWICVSINY---------SKSPRCTWPAHIVDV 222
                                    78888564..3456667**********9987765434555555555599******9.........46788899999**** PP

                                    HHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSG CS
                     COesterase 167 vlALrWVkenIasFGGdpervtlfGesAGaasvsllllsp 206
                                      A+ WV+enIa +GGdp+ +t+ G sAGa +++l  ls 
  gi|121638366|ref|YP_978590.1| 223 KRAIAWVRENIADYGGDPDFITITGGSAGAHLAALAALSA 262
                                    *********************************9999985 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   3.9e-07   0.00059     120     191 ..     276     381 ..     221     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.9e-07
                            DLH 120 pevdaavafYG.................................lspekeleeaakikapilalfgeeDefipadevekl 166
                                     +v+aa+++YG                                  ++ +++++++  + p ++l+ge+D+++p ++   +
  gi|121638366|ref|YP_978590.1| 276 TAVQAAAPYYGvydltnaenmhemmmpflehfvmrsryvdnpglFKAASPISYVHSEAPPFFVLHGEKDPMVPSAQSRAF 355
                                    4699999999999999999999999999999999999999999989999******************************* PP

                            DLH 167 eealkaanv.dlelkvYpgagHaFan 191
                                      al++a++ ++     p+a HaF  
  gi|121638366|ref|YP_978590.1| 356 SAALRDAGAaTVSYAELPNAHHAFDL 381
                                    *****998725677889*******53 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.071   1.1e+02      77     138 ..     242     312 ..     214     329 .. 0.62
   2 !   12.8   0.0   3.4e-05     0.051     193     232 ..     335     377 ..     323     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.071
                    Hydrolase_4  77 plfllGhSmGGliallyl..lrypd........kva.glilsaPalkikaklkappllklllkllgkllpklq 138
                                     +++ G S G+ +a+l++  +   d        + + ++  +aP +++   ++a  + ++++ +l +++ + +
  gi|121638366|ref|YP_978590.1| 242 FITITGGSAGAHLAALAAlsA--NDpalqpgfeSADtAVQAAAPYYGVYDLTNAENMHEMMMPFLEHFVMRSR 312
                                    46789**********999543..33324444544443444555555555544577777778888877766554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.4e-05
                    Hydrolase_4 193 PllllhGeaDkvvdpeasrelyerlgsk...dktlklypglyH 232
                                    P+++lhGe+D+ v+ ++sr++ ++l+ +    ++++  p++ H
  gi|121638366|ref|YP_978590.1| 335 PFFVLHGEKDPMVPSAQSRAFSAALRDAgaaTVSYAELPNAHH 377
                                    9*****************7776665544111666666666666 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7     4e+03     180     199 ..      92     112 ..      87     112 .. 0.85
   2 !   14.1   0.0   1.9e-05     0.029      81     191 ..     217     364 ..     196     378 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                           FSH1 180 seaLaeafkns.skvlkHpgg 199
                                    + aL++af  + +++++Hp g
  gi|121638366|ref|YP_978590.1|  92 HAALVDAFGPDfRDLVWHPTG 112
                                    67999***9999******986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.9e-05
                           FSH1  81 neyegleesldavkdyikengp...fdGiiGFSqGaalaallaslleellkea.......................shps 134
                                     ++ +++ +++ v++ i + g    f  i G S Ga+laal a   +    +                            
  gi|121638366|ref|YP_978590.1| 217 AHIVDVKRAIAWVRENIADYGGdpdFITITGGSAGAHLAALAALSANDPALQPgfesadtavqaaapyygvydltnA--- 293
                                    566778888999999999987667899*************9998888777655455544444444444444444440... PP

                           FSH1 135 lkfailvsGfkleepk.........................yee....yyeedkiqtptLhvlGelDtvvdeerseaLae 185
                                                   +                         +++     y  ++ + p++ ++Ge+D +v++++s+a++ 
  gi|121638366|ref|YP_978590.1| 294 ---------------EnmhemmmpflehfvmrsryvdnpglFKAaspiSY-VHSEAPPFFVLHGEKDPMVPSAQSRAFSA 357
                                    ...............25555555555555544444333334333444433.22226799999****************99 PP

                           FSH1 186 afkns.s 191
                                    a ++  +
  gi|121638366|ref|YP_978590.1| 358 ALRDAgA 364
                                    9988662 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.6e-05     0.083      32      68 ..     331     369 ..     320     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                  Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalgg..avlvtv 68 
                                     +a+p  +l +e Dp++P ++ ++++ al++  a+ v++
  gi|121638366|ref|YP_978590.1| 331 SEAPPFFVLHGEKDPMVPSAQSRAFSAALRDagAATVSY 369
                                    3469**************************943355544 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     6e-05      0.09      20     186 ..     239     403 ..     222     410 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                    --SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT-B--T CS
                         BAAT_C  20 kkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkvnknglldivdvlall 99 
                                      d i++ G S G+ la l a   +++        + + v++++ y      l++ ++  e +    ++ +++ ++++++
  gi|121638366|ref|YP_978590.1| 239 DPDFITITGGSAGAHLAALAALSANDPALQPGFESADTAVQAAAPYYGV-YDLTNAENMHEMMMPFLEHFVMRSRYVDNP 317
                                    4688999999999999999999999999888888887777777766644.344444444444433666666666666666 PP

                                    TTGGGCCCB--GGG-.-SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---STT-----EEEETT CS
                         BAAT_C 100 keklaekalipveka.kgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliepPyfplceavlakl 178
                                       +a    i    +   p+ ++ ge+D ++pS++s    s+ L+ ag    v +   p+a H+++   ++ +++v +++
  gi|121638366|ref|YP_978590.1| 318 GLFKAAS-PISYVHSeAPPFFVLHGEKDPMVPSAQSR-AFSAALRDAGAA-TVSYAELPNAHHAFDLAATVRSRMVAEAV 394
                                    5443333.355555527789999***********997.99**********.9*************999999999888777 PP

                                    TTEE.EE-- CS
                         BAAT_C 179 vgek.vlyG 186
                                     +   v+yG
  gi|121638366|ref|YP_978590.1| 395 SDFLgVIYG 403
                                    665566666 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   1.8e+03     100     127 ..     236     263 ..     224     267 .. 0.79
   2 ?   12.1   0.0   8.6e-05      0.13     158     200 ..     335     378 ..     321     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                    TT--GGGEEEEEETHHHHHHHHHHHT-S CS
                  Abhydrolase_2 100 kgipssriiigGFSqGaalalylaltlp 127
                                    +g + + i i G S Ga la  +al+ +
  gi|121638366|ref|YP_978590.1| 236 YGGDPDFITITGGSAGAHLAALAALSAN 263
                                    566778899**********998888765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.6e-05
                                    EEEEEEETT-SSS-HHHHHHHHHHHHTTS-.GEEEEEETT--SS CS
                  Abhydrolase_2 158 pilqiHgeeDpvvplalgkaakevlkkllk.kvelksyeglaHs 200
                                    p + +Hge+Dp+vp+a + a++ +l+++    v+   +++  H+
  gi|121638366|ref|YP_978590.1| 335 PFFVLHGEKDPMVPSAQSRAFSAALRDAGAaTVSYAELPNAHHA 378
                                    8899***********************99988999999977665 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.7   1.1e+03      23      82 ..     196     252 ..     190     283 .. 0.54
   2 ?   11.5   0.0   9.2e-05      0.14     215     260 ..     333     378 ..     249     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.7
                            LIP  23 LkeGyyVvvpDy.eGpkstftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGs 82 
                                     + G+  v+  y + p+ t++   ++ k+ +  +r  +   +  g  +   +++ G S G+
  gi|121638366|ref|YP_978590.1| 196 VELGWICVSINYsKSPRCTWPAHIVDVKRAIAWVRENI--ADYGG--DPDFITITGGSAGA 252
                                    55566655555523456666665555555555555544..33333..22234444444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.2e-05
                            LIP 215 qiPvlvyhgvidelipikdakklaknwcdkgiaslefaedlssgHl 260
                                     +P +v+hg  d ++p  ++++      d+g a + +ae   + H 
  gi|121638366|ref|YP_978590.1| 333 APPFFVLHGEKDPMVPSAQSRAFSAALRDAGAATVSYAELPNAHHA 378
                                    579***********************************98777775 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.9   5.9e+03      84     106 ..      76      98 ..      76     115 .. 0.81
   2 ?    4.0   0.0     0.022        32      54      95 ..     206     263 ..     146     267 .. 0.68
   3 ?    6.9   0.0    0.0029       4.4     207     240 ..     329     367 ..     277     382 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.9
                                    HHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  84 GmialayaaeyperVkalvllga 106
                                    G++++ +aa+  + + + +l++a
  gi|121638366|ref|YP_978590.1|  76 GRFGTSWAAQRADQILHAALVDA 98 
                                    78899999999999999999988 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                                    H...........SHHHHHHHHHHH....HHHCTTSSEE.EEEETHHHHHHHHHHHHHG CS
                  Abhydrolase_1  54 y...........gtasvaddldri....ldalgddklt.lvGhSmGGmialayaaeyp 95 
                                                ++++v + + ++     d  gd  ++ + G+S G  +a+ +a+ ++
  gi|121638366|ref|YP_978590.1| 206 NysksprctwpaHIVDVKRAIAWVreniADYGGDPDFItITGGSAGAHLAALAALSAN 263
                                    045555555555788888888865444488899999999************9998765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0029
                                    THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.....E CS
                  Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaqllpk.....k 240
                                    ++    p +v++g++Dp+vp  +++ + ++l++     +
  gi|121638366|ref|YP_978590.1| 329 VHSEAPPFFVLHGEKDPMVPSAQSRAFSAALRDagaatV 367
                                    555556***************666655555555454433 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.8e-05      0.12      24     111 ..     195     290 ..     189     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.8e-05
                                    EEE-TTTT-SS-S-TTSS.TT..S-HHHHHHHHHHHHHH-SB--TTSEEEEECHHHHHHHHHHHHHHHH.......SSSS CS
                    Alliinase_C  24 vvisgwhrlsYfsdeknl.ef..lsaeLekeikelhevvGnaatddryivvGtGstqLlqalvyalspe.....assesk 95 
                                    +v  gw  +s  ++++   ++    ++++++i  + e + +   d  +i +  Gs+    a++ als++        es 
  gi|121638366|ref|YP_978590.1| 195 MVELGWICVSINYSKSPRcTWpaHIVDVKRAIAWVRENIADYGGDPDFITITGGSAGAHLAALAALSANdpalqPGFESA 274
                                    6666777777554444333331133578999999999999999*************************955432234677 PP

                                    SEEEEE-SS--THHHH CS
                    Alliinase_C  96 pvkvvaavPyysvyke 111
                                     + v aa+Pyy vy  
  gi|121638366|ref|YP_978590.1| 275 DTAVQAAAPYYGVYDL 290
                                    8899**********74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2846.10
//
Query:       gi|121638367|ref|YP_978591.1|  [L=256]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-47  160.6   0.3    4.9e-47  160.4   0.3    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.3e-26   93.9   0.2    1.5e-26   93.7   0.2    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.3   5.4e-51   4.9e-47       4     211 ..      13     219 ..      10     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 5.4e-51
                                    TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                          ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                    + va+i+ n+P+  Na+++e+++ l +a++++e d+ v avv+tG +kaF+aGadl ++ ++    ++     +++ +++
  gi|121638367|ref|YP_978591.1|  13 KHVALITVNDPDRRNAVTDEMSAQLRAAIQRAEGDPDVHAVVVTGAGKAFCAGADLSALGAGVGDPAEPRLLRLYDGFMA 92 
                                    679**********************************************************875666666789******* PP

                                    HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHH CS
                          ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqe 163
                                    ++++++p+iaavnGaa+g+Gl+lala+D++ia+  a f + + klGl pg g+t++l+r+vG + A+ +ll+g  + a+ 
  gi|121638367|ref|YP_978591.1|  93 VSSCNLPTIAAVNGAAVGAGLNLALAADVRIAGPAALFDARFQKLGLHPGGGATWMLQRAVGPQVARAALLFGMCFDAES 172
                                    ******************************************************************************** PP

                                    HHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.H CS
                          ECH_1 164 alkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.d 211
                                    a ++Gl   v + ++ +  alela+  a ++++++ + k+ ++a+++  
  gi|121638367|ref|YP_978591.1| 173 AVRHGLALMV-A-DDPVTAALELAAGPAAAPREVVLASKATMRATASpG 219
                                    ******7654.4.555678999**9999999999999999999988742 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.2   1.6e-30   1.5e-26       2     186 ..      16     197 ..      15     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.6e-30
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    ++it n p+  Na++ em  +l++a+++ e d++v++vv++gag kafCAG D+ al     + ++       + Y+   
  gi|121638367|ref|YP_978591.1|  16 ALITVNDPDRRNAVTDEMSAQLRAAIQRAEGDPDVHAVVVTGAG-KAFCAGADLSALGAGVGDPAEP---RLLRLYDGFM 91 
                                    689***************************************99.*************999997766...58889***** PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkga 160
                                    ++++++ p++a ++G ++G G+ l++ + +r++   ++f     ++Gl+P  G++++L+r+ g ++++   l G  ++++
  gi|121638367|ref|YP_978591.1|  92 AVSSCNLPTIAAVNGAAVGAGLNLALAADVRIAGPAALFDARFQKLGLHPGGGATWMLQRAVGpQVARAALLFGMCFDAE 171
                                    ************************************************************98879*************** PP

                                    HHHHTTS--EE--GGGHHHHHHHHHT CS
                          ECH_2 161 dalaaglathyvpseklealeeaLae 186
                                     a+  gla  + ++   +ale a   
  gi|121638367|ref|YP_978591.1| 172 SAVRHGLALMVADDPVTAALELAAGP 197
                                    ********999999888888644433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1798.75
//
Query:       gi|121638368|ref|YP_978592.1|  [L=527]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-34  116.2  21.3    6.4e-34  116.2  21.3    2.6  2  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2  21.3   3.6e-38   6.4e-34       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?   -7.6  12.6         1   1.8e+04      19      43 ..     449     473 ..     439     498 .. 0.45

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 3.6e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms v+++P++la+aa dla+igs++saanaaaa ptt+v+aaaaDeVSaaiA lf+aha++yqals q+aafheqfvqal+a
  gi|121638368|ref|YP_978592.1|  1 MSLVIATPQLLATAALDLASIGSQVSAANAAAAMPTTEVVAAAADEVSAAIAGLFGAHARQYQALSVQVAAFHEQFVQALTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aag Ya++Eaa
  gi|121638368|ref|YP_978592.1| 83 AAGRYASTEAA 93
                                   *********97 PP

  == domain 2  score: -7.6 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHH----SS CS
                             PE  19 agigsalsaanaaaaapttavlaaa 43 
                                    ++ ++a + a+aa a+p +  + aa
  gi|121638368|ref|YP_978592.1| 449 MAARAAAALASAAPAGPAARAATAA 473
                                    3333333333333333332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3403.10
//
Query:       gi|121638369|ref|YP_978593.1|  [L=1137]
Description: LuxR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-16   57.3   0.0    1.6e-15   56.4   0.0    1.5  1  GerE           Bacterial regulatory proteins, luxR family
    6.3e-07   28.8   0.0    1.4e-06   27.7   0.0    1.5  1  NB-ARC         NB-ARC domain
    0.00016   22.1   0.8    0.00016   22.1   0.8    3.8  3  AAA_16         AAA ATPase domain
    0.00033   20.6   0.0     0.0044   16.9   0.0    2.2  2  NACHT          NACHT domain
     0.0017   18.0   0.0     0.0042   16.7   0.0    1.7  1  Sigma70_r4_2   Sigma-70, region 4
     0.0023   17.6   6.0     0.0088   15.6   0.5    3.2  3  AAA_25         AAA domain
      0.008   15.8   0.0      0.066   12.8   0.0    2.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.032   14.5   0.0    1.7  1  AAA_22         AAA domain
      0.059   12.9   0.0       0.27   10.8   0.0    2.2  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.28   10.3   0.0       0.44    9.7   0.0    1.2  1  ArsA_ATPase    Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   8.6e-19   1.6e-15       3      55 ..    1070    1122 ..    1068    1124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 8.6e-19
                                     S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHH CS
                           GerE    3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvr 55  
                                     L++ E+ev  l+ eG+snkeI+ +l+iS++TV++h++++++KL++ sr +l++
  gi|121638369|ref|YP_978593.1| 1070 LTPTELEVALLVGEGLSNKEIGVRLFISPRTVHSHLTHVYTKLGLSSRLQLAQ 1122
                                     9**************************************************97 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   7.7e-10   1.4e-06      18     206 ..     258     436 ..     245     456 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.7e-10
                                    SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHH CS
                         NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleekeeveslkrkl 96 
                                    ++  +v+l G gGvGKt la+q+ +    v   ++ +v +v ++   +   +  + +++L+l       ++ +    + +
  gi|121638369|ref|YP_978593.1| 258 VK-RWVTLTGVGGVGKTRLATQVASA---VADGYPdGVWYVNLAPITDPALVPIAAARVLGLP-----DQPGRS-TVDTI 327
                                    44.69******************999...7777763777788888888888888889999887.....222223.5789* PP

                                    HHHCCCTTEEEEEEEE-SHHH.H.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS- CS
                         NB-ARC  97 vrlLltkrfllvlDDVweeed.wdkigvvlparenrlrvllTTRdeevanavsatsekievelLekdeawellenkvfek 175
                                    vr + ++r+l+vlD   +  d   ++ v+l      lrvl T+R+  +  av++ ++  +v  L + ea el+   + e+
  gi|121638369|ref|YP_978593.1| 328 VRRIGDRRMLVVLDNCEHLLDgCAALIVALLGACPALRVLATSREP-I--AVAG-EQIWRVPPLGHGEAIELFTDRAREA 403
                                    ***************98877776677888888999*********75.4..2444.6789******************999 PP

                                    GGCHH....CHHHHHHHHHHCTT-HHHHHHHHH CS
                         NB-ARC 176 kleekes..leevakeivekckGlPlalkvlgg 206
                                    + e + +    ++  ei ++  G Pla+ + ++
  gi|121638369|ref|YP_978593.1| 404 RPELEITadNLALVTEICHRLDGIPLAIELAAS 436
                                    8776655335566789999999******98765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.8   8.7e-08   0.00016       1      52 [.     241     290 ..     241     434 .. 0.86
   2 ?   -3.2   2.4       5.3   9.5e+03      57      57 ..     633     633 ..     518     782 .. 0.64
   3 ?   -0.9   0.2         1   1.9e+03      75     111 ..     821     880 ..     798     965 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.7e-08
                         AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd....g 52 
                                    rlvGR +e++q++ +l+ v+    + v l+G  GvGK++l+++++  + +d    g
  gi|121638369|ref|YP_978593.1| 241 RLVGRVDEVAQVRGLLD-VK----RWVTLTGVGGVGKTRLATQVAS-AVADgypdG 290
                                    69**************9.54....89*******************5.555536654 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.3
                         AAA_16  57 r 57 
                                    r
  gi|121638369|ref|YP_978593.1| 633 R 633
                                    1 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1
                         AAA_16  75 alareellrqlldeaesaeleawrekleeala.......................avpel 111
                                    ++ +  l  +l+ + ++ +++a+++ +++a++                       a++e 
  gi|121638369|ref|YP_978593.1| 821 CAGQACLAHALAHRGDTEAAAAAQASIDTAVGlspvlsgsacsalvfatlaagdvAAAEH 880
                                    554444555666666677778888888888886666666666666666554444422222 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06    0.0044       2     129 ..     261     372 ..     260     395 .. 0.80
   2 ?    1.0   0.0      0.19   3.5e+02      76     165 ..     481     572 ..     464     573 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCCSC CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavllelp 80 
                                     v l+G  G+GKT L+ ++a+a a+g++++     v +++l+ ++++  +    a++l  + ++  ++v++  +v+    
  gi|121638369|ref|YP_978593.1| 261 WVTLTGVGGVGKTRLATQVASAVADGYPDG-----VWYVNLAPITDPALVpIAAARVLGLPDQPGRSTVDT--IVRRIGD 333
                                    6889***********************999.....899999999999888444455554444444455555..4444457 PP

                                    CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                          NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                    +r+L +lD  + l +   +        l+  l+ +  +p  ++l+t+r 
  gi|121638369|ref|YP_978593.1| 334 RRMLVVLDNCEHLLDGCAA--------LIVALLGA--CPALRVLATSRE 372
                                    8999999999999986655........99999999..999999999985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                    HCCSCCCEE..........EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..E CS
                          NACHT  76 llelperlL..........lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivl 145
                                    ll+ pe++L          + lDg+  +++  +  ++ +v +lLs      ll   sl++t  ++++    ++le+ + +
  gi|121638369|ref|YP_978593.1| 481 LLTGPEQVLfrrlavfpsgFDLDGAQAAAAGGDV-QRYEVVDLLS------LLADKSLVVTEDSDGR-TRYRLLETVRQY 552
                                    6666777777777777777778888887776665.7777777773......3444588888888888.667788888999 PP

                                    EEE--TCCHHHHHHHHCTTT CS
                          NACHT 146 evegfsesrrkqlvrkyfsd 165
                                    ++e + es  +  vr  ++d
  gi|121638369|ref|YP_978593.1| 553 ALEKLRESGDADAVRARHRD 572
                                    99999999999999888776 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.3e-06    0.0042      23      53 ..    1081    1111 ..    1069    1112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                     HTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                   Sigma70_r4_2   23 yleglsykEIAellgisegtVksrlsRArkk 53  
                                       egls kEI  +l is++tV s+l     k
  gi|121638369|ref|YP_978593.1| 1081 VGEGLSNKEIGVRLFISPRTVHSHLTHVYTK 1111
                                     579**********************877666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   4.9e-06    0.0088      26      62 ..     252     288 ..     248     297 .. 0.86
   2 ?   -2.5   0.0       1.8   3.2e+03     131     157 ..     325     349 ..     302     351 .. 0.74
   3 ?    2.8   0.3     0.041        74      77     164 ..     532     617 ..     530     635 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                         AAA_25  26 vkgllpagelallaGapgtGKttlaldlalavatGkp 62 
                                    v+gll  +  + l+G +g+GKt la+++a ava G p
  gi|121638369|ref|YP_978593.1| 252 VRGLLDVKRWVTLTGVGGVGKTRLATQVASAVADGYP 288
                                    67888899999**********************9975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                         AAA_25 131 daleaaieevegvrlvviDplsralgg 157
                                    d + ++i ++    lvv+D++ ++l+g
  gi|121638369|ref|YP_978593.1| 325 DTIVRRIGDR--RMLVVLDNCEHLLDG 349
                                    4444455443..4799****9998765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.041
                         AAA_25  77 vsaEdsedelrrRlravgeal.....rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDpl 151
                                    v++Eds  ++r Rl ++ +++     r+ ++ +++ +  +   + +a+     l ++ v+  e++++++e    + iD+l
  gi|121638369|ref|YP_978593.1| 532 VVTEDSDGRTRYRLLETVRQYaleklRESGDADAVRARHR---DHYAA-VAAGLDAPSVAGHERRLNQAE----LEIDNL 603
                                    899***************9996766644444444432221...11222.222234677788888888866....779999 PP

                         AAA_25 152 sralgg.densnsd 164
                                     +a++   en ++ 
  gi|121638369|ref|YP_978593.1| 604 RAAFAFsRENGDTG 617
                                    99888856666655 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.7e-05     0.066       5     155 ..      53     182 ..      50     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                  Guanylate_cyc   5 sydevtilFadIvgftalssahspievvklLnelyarfdelldekk.vykvk.tiGdaymvvsglpeekaahaaklaela 82 
                                    ++ +vt+l adI+g t+l   +      +++++l   + el++e++ v  v+   Gd+++v++          ++++ +a
  gi|121638369|ref|YP_978593.1|  53 PTGTVTLLLADIEGATHLPGSQ---LDTTAIAKLDRTLTELVREHRgVCPVEqGEGDSFLVAFARA-------SDAVACA 122
                                    578899*********9998855...567788888999999999998855555169****9998666.......6667777 PP

                  Guanylate_cyc  83 LdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyell 155
                                    L +  a           +++r+G+htG+v +   G         G t+  ++r+  ++++g+  +s +t +l 
  gi|121638369|ref|YP_978593.1| 123 LGLQRA-------PLAPIRLRIGMHTGEVSSPDEG------NCVGPTIDRTARLRELAHGGQTVLSGTTSDLV 182
                                    776443.......34689**********9765543......45688888888888888888888888887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.032       7     103 ..     261     346 ..     256     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqal 86 
                                     +++tG  G+GKT+l+ ++++       a+  +++v +v+l+  t+++ +  + +r lgl+        +  ++++ + +
  gi|121638369|ref|YP_978593.1| 261 WVTLTGVGGVGKTRLATQVASAV-----ADGYPDGVWYVNLAPITDPALVPIAAARVLGLPDQP----GRSTVDTIVRRI 331
                                    6789*****************98.....455799999*************99999999975555....666668888888 PP

                         AAA_22  87 raravielliiDEaqhl 103
                                     +r++  l+++D+ +hl
  gi|121638369|ref|YP_978593.1| 332 GDRRM--LVVLDNCEHL 346
                                    88888..9********7 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.27      17      38 ..    1084    1105 ..    1078    1106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                         HTH_24   17 risqreLAerlglSpstvnrrl 38  
                                     ++s++e+  rl +Sp tv+ +l
  gi|121638369|ref|YP_978593.1| 1084 GLSNKEIGVRLFISPRTVHSHL 1105
                                     89******************97 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00025      0.44       2      27 ..     260     285 ..     259     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                                    EEEEEEESTTSSHHHHHHHHHHHHHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklse 27 
                                    ++++++G GGVGKt +++ +a  +++
  gi|121638369|ref|YP_978593.1| 260 RWVTLTGVGGVGKTRLATQVASAVAD 285
                                    8**************99999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.82u 0.25s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 7635.21
//
Query:       gi|121638370|ref|YP_978594.1|  [L=99]
Description: hypothetical protein BCG_2508c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 804.11
//
Query:       gi|121638371|ref|YP_978595.1|  [L=1150]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                       67  (0.00373696); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.53u 0.36s 00:00:01.89 Elapsed: 00:00:00.62
# Mc/sec: 5552.34
//
Query:       gi|121638372|ref|YP_978596.1|  [L=475]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-35  118.9  18.6    1.5e-34  118.2  18.6    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2  18.6   8.2e-39   1.5e-34       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 8.2e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms+v+++Pe++a+aa dla+igs++saa+a aa ptt+v+aa+aDeVSa iAalfsahaqeyqalsaqaaafh+qfv++l+a
  gi|121638372|ref|YP_978596.1|  1 MSYVIATPEMMATAAFDLARIGSQVSAASAVAAMPTTEVVAAGADEVSAGIAALFSAHAQEYQALSAQAAAFHDQFVHTLTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   aa+ Y+a+E 
  gi|121638372|ref|YP_978596.1| 83 AARWYTATEI 92
                                   ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 2985.41
//
Query:       gi|121638373|ref|YP_978597.1|  [L=207]
Description: hypothetical protein BCG_2511 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-37  127.8   0.3    2.9e-37  127.7   0.3    1.1  1  LDcluster4      SLOG cluster4 family
    0.00042   19.6   1.2    0.00096   18.5   0.3    1.8  2  DNA_processg_A  DNA recombination-mediator protein A
  ------ inclusion threshold ------
      0.073   12.3   0.3       0.32   10.2   0.0    1.8  2  LSDAT_prok      SLOG in TRPM, prokaryote


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.3   4.9e-41   2.9e-37       2     130 ..      27     154 ..      26     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 4.9e-41
                     LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiy 81 
                                    ++igV+Gs++  ++++++ela+++G +iAk+g++l++Gg+tG+mea+s+Ga++a+Gl+vG+lp+ ++ ++ n+y +i i+
  gi|121638373|ref|YP_978597.1|  27 YQIGVFGSGT--IGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPG-DKFTDGNAYSTIKIL 103
                                    79********..9***************************************************.999999999****** PP

                     LDcluster4  82 TGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt...d 130
                                    +G+++a Rn+i  ls++  i++gg+sG+++E    +e + pv+vl ++   +
  gi|121638373|ref|YP_978597.1| 104 SGMQFA-RNYITGLSCHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSgspT 154
                                    ******.***************************************876552 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   1.6e-07   0.00096      43     104 ..      27      88 ..      19     101 .. 0.93
   2 ?   -1.2   0.0      0.17     1e+03      59      81 ..     107     128 ..     102     150 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-07
                 DNA_processg_A  43 ravaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                                     ++++ G+ ++ ++  e+a ++ +e+a++g++ +SG+  G  +a+ r+a +a+g  v+vl++
  gi|121638373|ref|YP_978597.1|  27 YQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPG 88 
                                    579999******************************************************86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.17
                 DNA_processg_A  59 evakklakelaeagitivSGlAl 81 
                                    ++a++ +  l+ +g ++v G   
  gi|121638373|ref|YP_978597.1| 107 QFARNYITGLSCHGAIVVGG-SS 128
                                    56666666666666555543.33 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.092   5.5e+02      26      74 ..      46      90 ..      39      99 .. 0.66
   2 ?   10.2   0.0   5.3e-05      0.32     124     158 ..     118     152 ..     105     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.092
                     LSDAT_prok 26 ravlaplaealgavvidgGtdtGvmkllgraraaveatfpLiGVApegt 74
                                   ++v a++a++ g + i+gG  tG m+++ r  +   a   ++GV p ++
  gi|121638373|ref|YP_978597.1| 46 YQVGAEIAKQ-GHILISGGM-TGTMEASSRGASD--ADGLVVGVLPGDK 90
                                   5555666666.778888887.5777776554444..5556788888765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.3e-05
                     LSDAT_prok 124 psvtvlvnGgeitlkdiresvkagrpilvvaGsgr 158
                                    +  +++v+G++ +++++r   + + p++v+a sg 
  gi|121638373|ref|YP_978597.1| 118 CHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSGS 152
                                    66689***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1279.79
//
Query:       gi|121638374|ref|YP_978598.1|  [L=250]
Description: hypothetical protein BCG_2512 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   21.3   0.0    0.00023   20.4   0.0    1.3  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-08   0.00023     107     224 ..     106     236 ..      63     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-08
                                    SSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGG.S.....SS--SEEEEEEEE...SEETEEEEEEEEEEEETTTHHHH CS
                Thymidylat_synt 107 kkidqlakvidqlkenpdsRriivsawnpaeldk.m.....aLppChvlfqfyvk.dkkegkLslqlyqRSaDvflGvpF 179
                                    k+  +++ vi++l+  p+s++ +v   + ++  + m        pC v++qf    d+k+  ++ ++y RS+D       
  gi|121638374|ref|YP_978598.1| 106 KEGRMIEFVIERLSLIPESKKAVVVFPTYEDYAAvMrnhrdDYLPCLVSIQFRLLpDGKDYVFHTTFYSRSMDAWQKGHG 185
                                    455678999************99998877776533322222578**********98999899*************99999 PP

                                    HHHHHHHHHHHHHHHHT-EEEE......EEEEEEEEEEEGGGHHHHHHHHT CS
                Thymidylat_synt 180 NiasyalLthmlaqvtglkpge......lihtigdaHiYsnhveqvkeqle 224
                                    N+ s a L   + + +  + g+      l  +i d+HiY++ + ++ ++l+
  gi|121638374|ref|YP_978598.1| 186 NLLSIAKLSDWVRENVSARIGRkimlgpLDGMICDVHIYKETYAEACKRLA 236
                                    ********9999888876655411111177899*******99887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1683.03
//
Query:       gi|121638375|ref|YP_978599.1|  [L=73]
Description: hypothetical protein BCG_2513 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00056   19.8   0.6     0.0016   18.4   0.3    1.8  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
      0.079   12.9   0.1       0.13   12.2   0.1    1.3  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
       0.13   12.3   2.8          2    8.5   1.9    2.3  2  RHH_1           Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   2.6e-07    0.0016       1      19 [.       1      19 [.       1      24 [. 0.92
   2 ?   -1.1   0.0      0.31   1.9e+03      26      34 ..      64      72 ..      63      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-07
                                   XXXXXXXXXXXXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirlt 19
                                   Mrt++++DD+ +a A +l+
  gi|121638375|ref|YP_978599.1|  1 MRTTLDLDDDVIAAARELA 19
                                   9**************9876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.31
                                   XXXXXXXXX CS
                 VapB_antitoxin 26 EaVnlALre 34
                                   E V+ AL e
  gi|121638375|ref|YP_978599.1| 64 EMVRRALDE 72
                                   789999975 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.1e-05      0.13      10      39 ..       9      38 ..       2      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                          RHH_5 10 eelleeLeewAdeegRsvSnlaafLvekal 39
                                   +++  + +e+A++++Rs+ ++++ L+ ++l
  gi|121638375|ref|YP_978599.1|  9 DDVIAAARELASSQRRSLGSVISELARRGL 38
                                   566666689****************99997 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.9   0.00034         2       1      35 [.       2      36 ..       2      38 .. 0.90
   2 ?    2.5   0.0     0.026   1.6e+02      27      34 ..      64      71 ..      62      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                   r+++ ld++++++ +ela  ++rS + +I e++r+
  gi|121638375|ref|YP_978599.1|  2 RTTLDLDDDVIAAARELASSQRRSLGSVISELARR 36
                                   8999********************99999888776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                                   HHHHHHHH CS
                          RHH_1 27 elIReAlr 34
                                   e++R+Al 
  gi|121638375|ref|YP_978599.1| 64 EMVRRALD 71
                                   99****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 513.43
//
Query:       gi|121638376|ref|YP_978600.1|  [L=141]
Description: hypothetical protein BCG_2514 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   29.0   0.1    1.6e-06   28.6   0.1    1.2  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.057   13.2   0.0    1.5  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   1.8e-10   1.6e-06       2     115 ..       3     122 ..       2     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.8e-10
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEEB CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel..eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkilpi 73 
                                    +lD ++l+al  +++ +++++r+++ +     ++t++l+ a +++v ++        ++  a++++ +l    ++++l  
  gi|121638376|ref|YP_978600.1|   3 LLDVNALVALAwDSHIHHARIREWFTANatLGWATCPLTEAGFVRVSTNpkvlpSAIGIADARRVLVALRAVGGHRFLAD 82 
                                    79********9**************99999*******************8877444444444444444444888888888 PP

                                    CHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH CS
                            PIN  74 daeiaeeaaeialkygllpnDaliaAtAkehgikliatfDed 115
                                    d ++++    ++  y + + Da+++ +A+++g +l+ tfD  
  gi|121638376|ref|YP_978600.1|  83 DVSLVDDDVPLIVGY-RQVTDAHLLTLARRRGVRLV-TFDAG 122
                                    888888888888888.********************.***75 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.4e-06     0.057      31      69 ..      96     134 ..      91     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-06
                        DUF5615  31 glegasDeeileyAkeedriivTkDkDFgellllggppp 69 
                                    g ++++D + l +A+++++ +vT+D+    l+++++++p
  gi|121638376|ref|YP_978600.1|  96 GYRQVTDAHLLTLARRRGVRLVTFDAGVFTLAQQRPKTP 134
                                    56789********************99889977776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 942.99
//
Query:       gi|121638377|ref|YP_978601.1|  [L=393]
Description: branched-chain alpha-keto acid dehydrogenase subunit E2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-66  223.7   0.0    3.1e-66  223.2   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    7.8e-18   64.1   0.1    1.6e-17   63.1   0.1    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.2e-11   44.7   1.1    2.9e-11   43.5   1.1    1.7  1  E3_binding       e3 binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.1       0.02   14.8   0.1    1.3  1  GCV_H            Glycine cleavage H-protein
      0.071   13.0   0.1       0.33   10.8   0.0    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
        0.2   11.9   0.0       0.37   11.1   0.0    1.3  1  Ribosomal_L13    Ribosomal protein L13


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.2   0.0     1e-69   3.1e-66       6     232 ..     167     390 ..     163     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 1e-69
                                    XXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE. CS
                   2-oxoacid_dh   6 rvplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasv. 84 
                                      p+ g+ +++a+++t s++eip++  s+ev + +ll+lr+ + +++      ++t +++ ++ +++Alk+  +ln+++ 
  gi|121638377|ref|YP_978601.1| 167 VRPVHGVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDWFVSAAP-----EITPFALTLRLLVIALKHNVILNSTWv 241
                                    56999************************************9999886.....8*************************9 PP

                                    ..EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE--------- CS
                   2-oxoacid_dh  85 .deeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvts 163
                                     ++e ++++v++ v++G+  at+rGLlvPv+ +a++k++ e+a++++el++ areg+l+p++l+g+tft+sN+G+lGv+ 
  gi|121638377|ref|YP_978601.1| 242 dSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAELITGAREGTLTPAELRGSTFTVSNFGALGVDD 321
                                    77888*************************************************************************** PP

                                    ------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXX CS
                   2-oxoacid_dh 164 ftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpeell 232
                                    + P+in+p++aIlg+g+ik rpvv+ ge+v+r++mtl+  +DHRv+dGa++a+F+++l++l+e+pe+ l
  gi|121638377|ref|YP_978601.1| 322 GVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPETAL 390
                                    ******************************************************************987 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   5.3e-21   1.6e-17       3      73 .]      10      81 ..       8      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.3e-21
                                   EEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl  3 iksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                   + +P++Ge  +e  v+ + v+vGd V+ +q+l+ ve+ K+e+ei++p aG+++e+   eGd ++vg  l++i
  gi|121638377|ref|YP_978601.1| 10 FPVPDLGEGLQEVtVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGAEGDVLKVGAELVRI 81
                                   789*****************************************************************9987 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   1.1   9.7e-15   2.9e-11       1      36 []     118     154 ..     118     154 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.7e-15
                                    SBE-HHHHHHHHHCT--TTTS-.--CTTTBE-HHHHC CS
                     E3_binding   1 vlAsPaaRklAkelGidLsdvk.GtGpgGRItkeDVl 36 
                                    +lA P +RklAkel +dL++++ G+G gG It++DVl
  gi|121638377|ref|YP_978601.1| 118 PLAAPVVRKLAKELAVDLAALQrGSGAGGVITRADVL 154
                                    5899*****************99*************7 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.7e-06      0.02      40      74 ..      30      64 ..      17      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.7e-06
                                   -TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                          GCV_H 40 evgtkvkkgeslaavEsvKaasevyapvsGevvev 74
                                    vg+ v+ +++l +vE+ Ka  e+++p  G +ve 
  gi|121638377|ref|YP_978601.1| 30 AVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVEL 64
                                   689******************************96 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.57   1.7e+03      13      35 ..      24      46 ..      23      53 .. 0.76
   2 ?   10.8   0.0   0.00011      0.33       3      42 ..      51      90 ..      43      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.57
                Biotin_lipoyl_2 13 VaqlnVkdGqrVkaGdvLaelDs 35
                                   V+ + V  G+ V+  ++L   ++
  gi|121638377|ref|YP_978601.1| 24 VTCWSVAVGDDVEINQTLCSVET 46
                                   88899999**9998777766655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlal 42
                                   v+I +p +Gr+++l   +G++ k G  L+++D+  +++a+
  gi|121638377|ref|YP_978601.1| 51 VEIPSPYAGRIVELGGAEGDVLKVGAELVRIDTGPTAVAQ 90
                                   8899****************************99998775 PP

>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.37       4      46 ..     272     314 ..     271     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                    EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEG CS
                  Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvina 46 
                                    v DA++++  +las++a++++G    t tp+   G    v n 
  gi|121638377|ref|YP_978601.1| 272 VTDAQDKNTRELASRVAELITGAREGTLTPAELRGSTFTVSNF 314
                                    78****************************9999999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2813.46
//
Query:       gi|121638378|ref|YP_978602.1|  [L=348]
Description: pyruvate dehydrogenase E1 component subunit beta pdhB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-40  138.1   0.0    3.7e-40  137.5   0.0    1.3  1  Transket_pyr     Transketolase, pyrimidine binding domain
    6.4e-36  123.0   0.0    8.7e-35  119.3   0.0    2.1  2  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.5   0.0   4.2e-44   3.7e-40       2     176 ..      25     200 ..      24     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 4.2e-44
                                    EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEE CS
                   Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvivea 79 
                                    ++++ +a++ al   +++d++v+++g+Dva  gg+f v++gl + +g++r++d++++E+a++g+avG+al+g   ++ e+
  gi|121638378|ref|YP_978602.1|  25 SLTMVQAINRALYDAMAADERVLVFGEDVAveGGVFRVTEGLADTFGADRCFDTPLAESAIIGIAVGLALRG-FVPVPEI 103
                                    67999************************999****************************************.5****** PP

                                    EEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHH CS
                   Transket_pyr  80 qFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrra 157
                                    qF  F+ +A  q++ + a+ + +++g++ ++v++r p   g  ++eh+s ++e+++ +++glkvv+Ps+p +++ llr a
  gi|121638378|ref|YP_978602.1| 104 QFDGFSYPAfdQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHA 183
                                    ******************************************************************************** PP

                                    HHSSS.SEEEEEE-SSEEC CS
                   Transket_pyr 158 irredrkPvvlrlpksllr 176
                                    i+++  +Pv+ ++pk+ + 
  gi|121638378|ref|YP_978602.1| 184 IACP--DPVMYLEPKRRYH 200
                                    **76..5********9885 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.032   2.9e+02      44      76 ..      27      59 ..      23      81 .. 0.82
   2 !  119.3   0.0   9.7e-39   8.7e-35       1     123 [.     215     336 ..     215     337 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.032
                                   SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSH CS
                Transketolase_C 44 rtvkplDketilesvkktgrlvvveeavkrgGi 76
                                     v+ + +++ +++++  + lv+ e+ +++gG+
  gi|121638378|ref|YP_978602.1| 27 TMVQAINRALYDAMAADERVLVFGEDVAVEGGV 59
                                   567778888999999999*************98 PP

  == domain 2  score: 119.3 bits;  conditional E-value: 9.7e-39
                                    TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTT.TTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHH CS
                Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLeke.gisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigse 79 
                                    g+a ++r+g+dvt+v+yG+ v++al  a+++e++  +s eV+dlr++ plD++ti++s+++tgr+vv++e+ ++ G g+ 
  gi|121638378|ref|YP_978602.1| 215 GHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQhDWSLEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAG 294
                                    78999***************************999********************************************* PP

                                    HHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHH CS
                Transketolase_C  80 vaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaek 123
                                    +aa+++ee+f +l+apv+r +g+d+  p++++ lek++++ +++
  gi|121638378|ref|YP_978602.1| 295 LAARIQEEMFYQLEAPVLRACGFDT--PYPPARLEKLWLPGPDR 336
                                    *************************..9************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2638.29
//
Query:       gi|121638379|ref|YP_978603.1|  [L=367]
Description: pyruvate dehydrogenase E1 component subunit alpha pdhA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-85  284.5   0.0    9.2e-85  284.2   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    4.6e-06   26.0   0.0    1.6e-05   24.3   0.0    1.6  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
      2e-05   24.4   0.7    0.00022   21.0   0.7    2.1  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
      0.004   16.2   0.0     0.0059   15.6   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   0.0   2.1e-88   9.2e-85       1     291 [.      48     332 ..      48     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 2.1e-88
                                    HHHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTS CS
                          E1_dh   1 eklvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgk 80 
                                    +++++++r +d   ++++r++ + +y ++ gqea++vg+aa l k+D+++++YRe gv l+rg++  ++   ++g    +
  gi|121638379|ref|YP_978603.1|  48 YEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTW--H 125
                                    689*************************************************************************9..3 PP

                                    SGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEE CS
                          E1_dh  81 ggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveN 160
                                    g + +   + +k     + + ++g+q  ++ G+a+aa+  ++++v++++ GDgA+++Gdv+ealn+aa++  p++f v+N
  gi|121638379|ref|YP_978603.1| 126 G-GLQ---FTTKC--CAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQN 199
                                    3.334...33455..889********99999************************************************* PP

                                    ESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSS CS
                          E1_dh 161 NkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyr 240
                                    N+++is ++++++a++++a +a g+g+pg+rVdgnD+la+y++  +Aa rar+g+gp+lie+vtYR+g+H++ Ddp++yr
  gi|121638379|ref|YP_978603.1| 200 NQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYR 279
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHH...HHHHHHHHHHHHHH CS
                          E1_dh 241 treeveevrkkkdpiqrlkelLvkkgvvseeelkeie...kevrkeveeavkka 291
                                    ++eev+ +    dpi r++++L+++g++s+  +++++   k+vr e  +av  a
  gi|121638379|ref|YP_978603.1| 280 SQEEVDRWATL-DPIPRYRTYLQDQGLWSQRLEEQVTaraKHVRSELRDAVFDA 332
                                    99999998777.*****************8666666511166777777777666 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.6e-09   1.6e-05     119     179 ..     148     208 ..     142     212 .. 0.94
   2 ?   -1.1   0.0       0.2   8.8e+02     229     273 .]     214     263 ..     206     263 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.6e-09
                 DXP_synthase_N 119 aalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknv 179
                                     a+G a+a++  +e++ +va +GDga + G  +ealn ++  ++  +  + +N+++is +v
  gi|121638379|ref|YP_978603.1| 148 HAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPV 208
                                    689******************************************************9987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                 DXP_synthase_N 229 vpgtlfeelgfkYlG.pidGhdleelikvleevkkl....kgpvllhvvt 273
                                    +p+  ++++g+   G  +dG+d+ +   v+ e+ +     +gp+l+  vt
  gi|121638379|ref|YP_978603.1| 214 APSIAHKAIGYGMPGiRVDGNDVLACYAVMAEAAARaragDGPTLIEAVT 263
                                    566677777777777459****9998888876543212227788887765 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.7     5e-08   0.00022      33     152 ..     149     260 ..     139     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5e-08
                                    HHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS-- CS
                   TPP_enzyme_C  33 glpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnl.pitvvvlnNegygmtggqqepfggkrksgpagkdlkp 110
                                    +++aA++a+++++d+  va+ GDG++    ++e  +++     p ++ v nN++       ++p   +         +  
  gi|121638379|ref|YP_978603.1| 149 AVGAAMAAQRLDEDSVTVAFLGDGATSEGdVHEALNFAAVFTtPCVFYVQNNQWA-I----SMPVSRQ---------TAA 214
                                    78999999999999***********998887666665555551666666666554.2....3333322.........234 PP

                                    --HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
                   TPP_enzyme_C 111 vdfaklaealGakgarvekadveeleealkeal....ekkgpalie 152
                                    +++a  a ++G++g+rv+ +dv    ++++ea     + +gp+lie
  gi|121638379|ref|YP_978603.1| 215 PSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAararAGDGPTLIE 260
                                    689999**************99998877777776777********8 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-06    0.0059     144     243 ..     162     263 ..     134     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-06
                                    ---EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEE.EESSEETTEEGGGT--.S-HHHHHHHTT-EEEEETTTT-HHH CS
                Transketolase_N 144 dhytyvilgDgclmeGvsseasslagtlkLgkLivly.DdnkisidGeteisft.edvakrfeaygWhvievedgedvea 221
                                    d+ t ++lgDg   eG  +ea ++a++       v+y  +n+ +i   ++ +++  ++a++   yg   i+  dg+dv a
  gi|121638379|ref|YP_978603.1| 162 DSVTVAFLGDGATSEGDVHEALNFAAVFTTP--CVFYvQNNQWAISMPVSRQTAaPSIAHKAIGYGMPGIR-VDGNDVLA 238
                                    78899*********************98754..55662678899999888665515666666667766677.56666655 PP

                                    ....HHHHHHHHHH-TTS-EEEEEE- CS
                Transketolase_N 222 ....ikaaieeakaekdkPsliklrt 243
                                        +++a ++a+a  d P+li+  t
  gi|121638379|ref|YP_978603.1| 239 cyavMAEAAARARAG-DGPTLIEAVT 263
                                    111145555556655.89****8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2715.90
//
Query:       gi|121638380|ref|YP_978604.1|  [L=273]
Description: citrate (pro-3s)-lyase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-30  104.5   6.3    2.3e-28   98.9   6.3    2.2  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    4.5e-10   39.2   0.0    3.9e-07   29.6   0.0    2.2  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
  ------ inclusion threshold ------
      0.063   13.0   0.0       0.16   11.8   0.0    1.6  2  Zds_C           Activator of mitotic machinery Cdc14 phosphat


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   6.3   3.8e-32   2.3e-28       4     221 .]      11     211 ..       9     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 3.8e-32
                                    EEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG.HHH CS
                      HpcH_HpaI   4 lflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle.vld 82 
                                    lf p+++++   kaa a aD+v++DlEd+va a+K aAR+ ++++  +++        +vVR+n+  +   ++dle ++ 
  gi|121638380|ref|YP_978604.1|  11 LFCPADRPERFAKAA-AAADVVILDLEDGVAEAQKPAARNALRDTPLDPER-------TVVRINAGGTADQARDLEaLAG 82 
                                    899999999999987.679********************988876555554.......89****************8888 PP

                                    TTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHHHTT-TT CS
                      HpcH_HpaI  83 lgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsadlgtkr 162
                                       ++v++Pk e+a++++e+       +           ++a +E+a+g   a eIaa++   g + GaeDl a+lg ++
  gi|121638380|ref|YP_978604.1|  83 TAYTTVMLPKAESAAQVIELA------P---------RDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSS 147
                                    9999*********99998764......3.........369**************************************** PP

                                    STTSHHHH.....HHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHHHH CS
                      HpcH_HpaI 163 spegtevl.....dareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgkllinp 221
                                    s   +  +     ++r+ il+aa a+g  ald v++di d+eg+++e++ + a+Gfd++++i+p
  gi|121638380|ref|YP_978604.1| 148 SRRADGAYrdvarHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHP 211
                                    999999889999***************************************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00033         2      11      57 ..      11      53 ..       6      62 .. 0.82
   2 !   29.6   0.0   6.5e-11   3.9e-07     249     330 ..     187     267 ..     154     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00033
                 C-C_Bond_Lyase 11 LYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlke 57
                                   L++Pa+r++       ++++ +  ++l+lED v+e++ +aA + l++
  gi|121638380|ref|YP_978604.1| 11 LFCPADRPER----FAKAAAAADVVILDLEDGVAEAQKPAARNALRD 53
                                   7888888544....34566778899****************999876 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 6.5e-11
                 C-C_Bond_Lyase 249 dldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldilesakg..gvfkseyankmnEvkphraWAeki 326
                                    d++gl++E     a G+    +IhPsqi++v+++++ s+e++  A+++l+++++  g f+ e  ++m++ +p  + Ae++
  gi|121638380|ref|YP_978604.1| 187 DVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRPSHEKLAWARRVLAASRSerGAFAFE--GQMVD-SPVLTHAETM 263
                                    6789****99999*************************************976534777666..99*95.6888888888 PP

                 C-C_Bond_Lyase 327 lkra 330
                                    l+ra
  gi|121638380|ref|YP_978604.1| 264 LRRA 267
                                    8887 PP

>> Zds_C  Activator of mitotic machinery Cdc14 phosphatase activation C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   8.4e+03      12      24 ..      55      67 ..      53      78 .. 0.66
   2 ?   11.8   0.0   2.6e-05      0.16      13      35 ..     214     236 ..     204     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                          Zds_C 12 pihvERaiYRlsH 24
                                   p+  ER + R+  
  gi|121638380|ref|YP_978604.1| 55 PLDPERTVVRINA 67
                                   6778999988765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.6e-05
                          Zds_C  13 ihvERaiYRlsHlKLanprRpLr 35 
                                    i v R  YR sH KLa +rR L 
  gi|121638380|ref|YP_978604.1| 214 IPVVRKAYRPSHEKLAWARRVLA 236
                                    667799**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2228.98
//
Query:       gi|121638381|ref|YP_978605.1|  [L=185]
Description: oxidase regulatory-related protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-28   99.0   0.0    1.9e-28   98.5   0.0    1.2  1  MaoC_dehydratas  MaoC like domain
     0.0028   17.8   0.0     0.0048   17.0   0.0    1.4  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   2.2e-32   1.9e-28       3     121 ..      39     159 ..      36     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 2.2e-32
                                    CCCTTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HH.HHHHTTTS.SSB--HHHHHHHHHHHHHHHHSTT.EGGGEE CS
                MaoC_dehydratas   3 qnaigekvetekeitvteadialyalvsgDlnpiHvdpe.fAkkagfg.gpIahGmltlaivaklveeelgdn.vvarvg 79 
                                    q  ig+++ +++ +tvtead++l+++++++++ +H+d++ + ++ gf+ ++ +++m+tl+++ +l +++l+ + +va++g
  gi|121638381|ref|YP_978605.1|  39 Q--IGTTYLHRPGRTVTEADNVLFTTLTMNTQSLHLDAAwAGQQPGFRgERLVNSMFTLSTMVGLSVAQLTLGtIVANLG 116
                                    4..9***********************************999*****989****************************** PP

                                    EEEEEE-S--BTTCEEEEEEEEEEEEEEE.EEEEEEEEEEEEE CS
                MaoC_dehydratas  80 eikvrFtkpVlpgdtlkvelevvgkrdvr.ktkkvevtkevte 121
                                    +++v+F+kpV++gdtl++e++++gkr+ + +  ++ vt e+++
  gi|121638381|ref|YP_978605.1| 117 FSEVSFPKPVFHGDTLYAETVCTGKRESKsRPGEGIVTLEHIA 159
                                    **************************99989999999998876 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.4e-07    0.0048      12     131 ..      50     169 ..      39     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-07
                MaoC_dehydrat_N  12 aevereavrefakavgetnpayldeeaaraa.gyrsliaPptflivlatkapellealgidlsrll.hge.qefeyhepi 88 
                                     +v++ +   f   + +t+ ++ld ++a ++ g+r+     + ++   +     l+  ++ l  ++ +++  e+ + +p+
  gi|121638381|ref|YP_978605.1|  50 RTVTEADNVLFTTLTMNTQSLHLDAAWAGQQpGFRGERLVNSMFTLSTMVG---LSVAQLTLGTIVaNLGfSEVSFPKPV 126
                                    445555555799999999999999999988889999998888877777766...4555555555552333489999**** PP

                MaoC_dehydrat_N  89 raGDelttesriadvydkkg.vGalefivvettvtnqrGepvat 131
                                      GD+l+ e+  +  ++ k+  G++ +++ e+   nq+Ge+va+
  gi|121638381|ref|YP_978605.1| 127 FHGDTLYAETVCTGKRESKSrPGEG-IVTLEHIARNQHGEVVAR 169
                                    *****************99977775.89999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1379.00
//
Query:       gi|121638382|ref|YP_978606.1|  [L=394]
Description: acyl-CoA dehydrogenase fadE19 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-47  161.1   2.7    2.9e-47  160.6   2.7    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      3e-36  124.5   0.0    6.1e-36  123.5   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    5.4e-22   77.8   0.4      1e-21   76.9   0.4    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.4e-18   67.4   2.7    2.6e-18   66.6   2.7    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   2.7   6.5e-51   2.9e-47       1     149 [.     243     391 ..     243     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 6.5e-51
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G + +++ l+ +R+a+aa a g+a+ +++e+++ya++r++fg+p++++q++ +k+a+m+a++++ar + y+aa+++ a
  gi|121638382|ref|YP_978606.1| 243 GSGYANFLSILDEGRIAIAALATGAAQGCVDESVKYANQRQSFGQPIGAYQAIGFKIARMEARAHVARTAYYDAAAKMLA 322
                                    578999999*********************************************************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    gkp ++ea++aK+  se+a++  ++a q++Gg+G+++eypv+r+yrd++vl+igeGt+e+q+++iar+l
  gi|121638382|ref|YP_978606.1| 323 GKPFKKEAAIAKMISSEAAMDNSRDATQIHGGYGFMNEYPVARHYRDSKVLEIGEGTTEVQLMLIARSL 391
                                    *******************************************************************86 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   1.4e-39   6.1e-36       2     112 ..      15     125 ..      14     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.4e-39
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                    +e ++lrdtv++fa++ +ap+ a++d+e+ fp+e++ k++e+Gl+g+++peeygG+g+dy++  +v+eel+++d ++a++
  gi|121638382|ref|YP_978606.1|  15 KEYQDLRDTVADFARTVVAPVSAKHDAEHSFPYEIVAKMGEMGLFGLPFPEEYGGMGGDYFALSLVLEELGKVDQSVAIT 94 
                                    57899*************************************************************************** PP

                                    HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasg 112
                                    l +  +l+a +i+rfGteeqk+++Lp+l sg
  gi|121638382|ref|YP_978606.1|  95 LEAAVGLGAMPIYRFGTEEQKQKWLPDLTSG 125
                                    *****************************99 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.4   2.2e-25     1e-21       1      96 [.     130     230 ..     130     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.2e-25
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT..-SEEEEEEE...TS---..----EEEEEEE..GGGE CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaai..atlalvlar...tekpd..rarglslflvprdapgv 73 
                                    +f+lTEp+aGsd+ s +t +a+ +g+e+++nG+K++itn+++   +l++v a    t +++  +++++s+++vp+++pg+
  gi|121638382|ref|YP_978606.1| 130 GFGLTEPGAGSDAGSTRT-TARLEGDEWIINGSKQFITNSGTdiTSLVTVTAVtgtT-GTAadAKKEISTIIVPSGTPGF 207
                                    69****************.77777777*************99988899999997743.333578**************** PP

                                    EE-----BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  74 svrrieeklGlrglptgelvfed 96 
                                    +v+++ +k+G +  +t+ l+f d
  gi|121638382|ref|YP_978606.1| 208 TVEPVYNKVGWNASDTHPLTFAD 230
                                    *******************9987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   2.7   5.8e-22   2.6e-18       2     127 ..     259     374 ..     258     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 5.8e-22
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                     iaa a+GaA+++++e v++a++r++  +g+++   +a+ +++a+++ar + Ar+  ++aaa+      agk++    ++
  gi|121638382|ref|YP_978606.1| 259 AIAALATGAAQGCVDESVKYANQRQS--FGQPIGAYQAIGFKIARMEARAHVARTAYYDAAAK----MLAGKPF----KK 328
                                    79************************..***********************************....999***9....** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                    ea++a++  +e a +  +++ +++Gg++  +e+p+ R++RD ++++
  gi|121638382|ref|YP_978606.1| 329 EAAIAKMISSEAAMDNSRDATQIHGGYGFMNEYPVARHYRDSKVLE 374
                                    *****************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2957.89
//
Query:       gi|121638383|ref|YP_978607.1|  [L=654]
Description: acetyl-/propionyl-coenzyme A carboxylase alpha chain subunit alpha accA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-82  275.0   0.0    5.8e-82  274.3   0.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    6.9e-43  145.7   0.1      2e-42  144.2   0.1    1.8  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    2.2e-33  114.6   0.0    6.3e-33  113.1   0.0    1.8  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    2.1e-15   56.3   5.9    5.6e-15   54.9   5.9    1.8  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.4e-08   34.5   0.0    4.5e-08   32.9   0.0    1.8  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    7.3e-06   25.7   0.0    1.8e-05   24.4   0.0    1.6  2  ATP-grasp        ATP-grasp domain
    0.00011   21.9   8.1      0.026   14.4   1.6    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0069   16.4   0.0      0.012   15.7   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.034   13.1   0.0        1.6    7.6   0.0    2.2  2  DUF3182          Protein of unknown function (DUF3182)
      0.074   13.2   2.9       0.35   11.0   0.3    3.2  3  LAL_C2           L-amino acid ligase C-terminal domain 2
      0.077   12.9   0.1       0.43   10.5   0.1    2.2  2  PASTA            PASTA domain
      0.096   12.6   0.8       0.19   11.6   0.8    1.5  1  GCV_H            Glycine cleavage H-protein
      0.098   12.9   1.5       0.47   10.7   0.9    2.4  3  Peptidase_M23    Peptidase family M23
          5    7.1   7.9         14    5.7   0.4    3.3  3  RnfC_N           RnfC Barrel sandwich hybrid domain
        6.5    7.5   6.3         57    4.5   5.7    2.4  2  HlyD_3           HlyD family secretion protein


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.3   0.0   4.9e-85   5.8e-82       1     208 [.     115     323 ..     115     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 274.3 bits;  conditional E-value: 4.9e-85
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    Dk +ak+a+++++vpvvp++a+++ t +  +++a+e+gyPv+ik+++g+GGkGmr++++ ++l e++ +a++ea+++fg+
  gi|121638383|ref|YP_978607.1| 115 DKIAAKNAVAAFDVPVVPGVARAGLTDDALVTAAAEVGYPVLIKPSAGGGGKGMRLVQDPARLPEALVSARREAMSSFGD 194
                                    99****************************************************************************** PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                    +++++e+++ +p++iEv+vl+Da+gnv++++ere+slq+r+qkvie+APs+ L++++r++++ aa++++r+v++vgagtv
  gi|121638383|ref|YP_978607.1| 195 DTLFLERFVLRPRHIEVQVLADAHGNVVHLGERECSLQRRHQKVIEEAPSPLLDPQTRERIGVAACNTARCVDYVGAGTV 274
                                    ******************************************************************************** PP

                                    EEEEET.TTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--G CS
                    CPSase_L_D2 161 eflldp.kskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekL 208
                                    ef++++ + +e++++E+NtRl+ve++++e++TGldlv++++++++gekL
  gi|121638383|ref|YP_978607.1| 275 EFIVSAqRPDEFFFMEMNTRLQVEHPVTEAITGLDLVEWQLRVGAGEKL 323
                                    ****985789*************************************99 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2   0.1   1.6e-45     2e-42       1     110 []       1     110 [.       1     110 [. 0.98

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 1.6e-45
                                    ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE- CS
                  Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhp 80 
                                    ++++vl+anrGeiAvr+ir++r+lgi++vavys++d +++hv ead+av+lgpa+a+esYl+i k+++aa ++ga+a+hp
  gi|121638383|ref|YP_978607.1|   1 MFDTVLVANRGEIAVRVIRTLRRLGIRSVAVYSDPDVDARHVLEADAAVRLGPAPARESYLDIGKVLDAAARTGAQAIHP 80 
                                    6899**************************************************************************** PP

                                    -SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                  Biotin_carb_N  81 GyGflsEnaefaeaveeagivfiGPsaeal 110
                                    GyGfl+Ena+fa+a+e+a +vf+GP+a+a+
  gi|121638383|ref|YP_978607.1|  81 GYGFLAENADFAAACERARVVFLGPPARAI 110
                                    **************************9886 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.0   5.2e-36   6.3e-33       1     108 []     338     445 ..     338     445 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 5.2e-36
                                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGv 80 
                                    eaR++aEdp+++flp+ G+v ++ +p+gpgvRvds++  g+ v ++yD+ll K+i+hg++reeal+rl++aLa++ + Gv
  gi|121638383|ref|YP_978607.1| 338 EARVYAEDPAREFLPTGGRVLAVFEPAGPGVRVDSSLLGGTVVGSDYDPLLTKVIAHGADREEALDRLDQALARTAVLGV 417
                                    89****************************************************************************** PP

                                    -BSHHHHHHHHH-HHHHHT---TTTCCC CS
                  Biotin_carb_C  81 ktnieflrailedeefakgeldtkflee 108
                                    +tn+eflr +l+de+++ g+ldt++l+e
  gi|121638383|ref|YP_978607.1| 418 QTNVEFLRFLLADERVRVGDLDTAVLDE 445
                                    ************************9985 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   5.9   4.7e-18   5.6e-15       2      73 .]     587     652 ..     586     652 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4.7e-18
                                    EEEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl   2 eiksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                    e+ sPm+G++++     v v+ G++++ag+v+++veamKme+ +eap++G+v+ +lv++Gd+v+v ++la+i
  gi|121638383|ref|YP_978607.1| 587 EVVSPMPGSVIA-----VQVESGSQISAGDVVVVVEAMKMEHSLEAPVSGRVQ-VLVSVGDQVKVEQVLARI 652
                                    7899********.....**********************************96.88899**********997 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.7e-11   4.5e-08      27     174 ..     143     293 ..     124     294 .. 0.85
   2 ?   -3.6   0.4       5.6   6.7e+03      72     106 ..     611     645 ..     607     649 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.7e-11
                                    HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevs 99 
                                     l    +e+gypv++Kp+  G   G+  v+  + l ea+ +a +       d + + E+++ + r iev vl + + +v 
  gi|121638383|ref|YP_978607.1| 143 ALVTAAAEVGYPVLIKPSAGGGGKGMRLVQDPARLPEALVSARREamssfgDDTLFLERFVlRPRHIEVQVLADAHGNVV 222
                                    45667899****************************99988876434445699********9****************** PP

                                    EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE..ETTTEEEEEEEES CS
                Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl..teegeivlnEvNt 174
                                    ++ge+  +    + ++k +    +      l+++++e+i  +a ++ + +d  G + v f++  ++ +e+++ E+Nt
  gi|121638383|ref|YP_978607.1| 223 HLGERECSL--QRRHQKVI----EEAPSPLLDPQTRERIGVAACNTARCVDYVGAGTVEFIVsaQRPDEFFFMEMNT 293
                                    ***998764..45666665....3333456899*****************************666779********9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.6
                                    -SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE- CS
                Dala_Dala_lig_C  72 dekvlvEeaiegreievavlgneklevsevgeivv 106
                                    d  v+vE++   + +e  v g  ++ vs+ +++ v
  gi|121638383|ref|YP_978607.1| 611 DVVVVVEAMKMEHSLEAPVSGRVQVLVSVGDQVKV 645
                                    66788898888899999999977666666665555 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       8.8   1.1e+04     124     144 ..      12      32 ..       9      38 .. 0.77
   2 !   24.4   0.0   1.5e-08   1.8e-05      18     156 ..     142     291 ..     131     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 8.8
                                    HHHHHHHHHHTSSEEEEEEEE CS
                      ATP-grasp 124 eiakkiveeLggvGvfavElF 144
                                    eia +++++L  +G+ +v ++
  gi|121638383|ref|YP_978607.1|  12 EIAVRVIRTLRRLGIRSVAVY 32 
                                    678888888888888877665 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.5e-08
                                    HHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEETTC- CS
                      ATP-grasp  18 eeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsaeGe 89 
                                    ++l  aa+e+g+pv++K +  g  GkG  +v+++++l++al  +        ++ ++ +E fv   + + v v  +a+G+
  gi|121638383|ref|YP_978607.1| 142 DALVTAAAEVGYPVLIK-PSAGGGGKGMRLVQDPARLPEALVSArreamssfGDDTLFLERFVLRPRHIEVQVLADAHGN 220
                                    5677899**********.99999****************999888999999999***********9*9999999*****9 PP

                                    EEE-.-EEEEEEETTEEEEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT..EEEEEE CS
                      ATP-grasp  90 tafy.pvvetvqedgilrlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledge..llvnEl 156
                                    ++ + +    +q++   ++  ap+++ +    +++   a + ++ +++vG  +vE+ v ++     ++ E+
  gi|121638383|ref|YP_978607.1| 221 VVHLgERECSLQRRHQKVIEEAPSPLLDPqTRERIGVAACNTARCVDYVGAGTVEFIVSAQRPdeFFFMEM 291
                                    77661444567777777777788877665155666666679**************9988443234555555 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.4   0.00022      0.26       5      35 ..     588     618 ..     584     626 .. 0.84
   2 !   14.4   1.6   2.1e-05     0.026       5      34 ..     625     653 ..     622     654 .] 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDs 35 
                                    + +p +G V ++ V+ G ++ aGdv ++ + 
  gi|121638383|ref|YP_978607.1| 588 VVSPMPGSVIAVQVESGSQISAGDVVVVVEA 618
                                    66899********************877665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.1e-05
                Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                    + apvsGrV q++V  G++Vk  +vLa++ 
  gi|121638383|ref|YP_978607.1| 625 LEAPVSGRV-QVLVSVGDQVKVEQVLARIK 653
                                    689*****8.9*****************96 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.8e-06     0.012      25     159 ..     146     296 ..     114     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-06
                                    EESS--SSSEEEEESS-------B--SS--TTE....................EEEE---SEEEEEEEEE.SSSEEEEEE CS
                    ATP-grasp_3  25 eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkplSvsllsdgekvlvlav 91 
                                    + ++e+ +++ +Kp+ G+gg+++r+v++   + +a+ +               l +  ++ +++ v++l+d++ ++v   
  gi|121638383|ref|YP_978607.1| 146 TAAAEVGYPVLIKPSAGGGGKGMRLVQDPARLPEALVSARreamssfgddtlfLERFVLRPRHIEVQVLADAHGNVVHLG 225
                                    45567799*********************999999988878999*******977777789***********998888777 PP

                                    EEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS....SEEEEEEESS-- CS
                    ATP-grasp_3  92 nrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkd...eepyviEvNPRlt 159
                                     r+   +++++ v     +p    + +e++  +a ++ +++ + +G   v+++++    +e  ++E N Rl+
  gi|121638383|ref|YP_978607.1| 226 ERECSLQRRHQKVIEEAPSPLLDPQtRERIGVAACNTARCV-DYVGAGTVEFIVSAqrpDEFFFMEMNTRLQ 296
                                    77777777777889889999888874666666777778888.***********999888899********97 PP

>> DUF3182  Protein of unknown function (DUF3182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0013       1.6     134     176 ..     151     193 ..     119     213 .. 0.80
   2 ?    3.1   0.0      0.03        36      60      95 ..     363     401 ..     326     414 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                        DUF3182 134 kegkvRlKeveatgGrgQrvvedaaeldaaLaaldeeelaaeG 176
                                       +v +K+ ++ gG+g r v+d a l +aL +   e++++ G
  gi|121638383|ref|YP_978607.1| 151 VGYPVLIKPSAGGGGKGMRLVQDPARLPEALVSARREAMSSFG 193
                                    456899**************************99999988777 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                        DUF3182  60 aaelGiegeedlfGGvv...phafvatKaithplveeaa 95 
                                     a  G++ ++ l+GG+v   +++ + tK+i+h+  +e+a
  gi|121638383|ref|YP_978607.1| 363 PAGPGVRVDSSLLGGTVvgsDYDPLLTKVIAHGADREEA 401
                                    55569**********9856668899*******9877665 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.86     1e+03      25      53 ..     309     337 ..     299     340 .. 0.85
   2 ?   11.0   0.3   0.00029      0.35      52      73 ..     391     412 ..     388     414 .. 0.92
   3 ?   -2.8   0.1       6.2   7.4e+03      28      40 ..     632     644 ..     628     646 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.86
                         LAL_C2  25 gvveveltvkpGdevrpprssgdrlGyvi 53 
                                    + ve++l+v +G++++ +++  +  G+ i
  gi|121638383|ref|YP_978607.1| 309 DLVEWQLRVGAGEKLGFAQNDIELRGHAI 337
                                    5799************9999988888866 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00029
                         LAL_C2  52 viatgdtaeeaeaaaeeaaaei 73 
                                    via+g+++eea++++++a+a+ 
  gi|121638383|ref|YP_978607.1| 391 VIAHGADREEALDRLDQALART 412
                                    9******************985 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.2
                         LAL_C2  28 eveltvkpGdevr 40 
                                    +v++ v++Gd+v+
  gi|121638383|ref|YP_978607.1| 632 RVQVLVSVGDQVK 644
                                    6899999***997 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.4   2.9e+03      14      32 ..      17      35 ..      15      39 .. 0.73
   2 ?   10.5   0.1   0.00036      0.43      31      60 ..     587     616 ..     570     617 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                                   HHHHHHHTT--CCCEEEEC CS
                          PASTA 14 AkatLkalGlkiktveets 32
                                   +++tL+ lG++   v++++
  gi|121638383|ref|YP_978607.1| 17 VIRTLRRLGIRSVAVYSDP 35
                                   6899******666666544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00036
                                    ECTCCGTTBEEEECS-TTSEECTTS-EEEE CS
                          PASTA  31 tsddvpeGtVisQsPeaGtevskgskvtlt 60 
                                    ++++  +G+Vi++ +e+G+++s+g+ v+++
  gi|121638383|ref|YP_978607.1| 587 EVVSPMPGSVIAVQVESGSQISAGDVVVVV 616
                                    5667779******************99885 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   0.00016      0.19      30      71 ..     593     633 ..     573     646 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                    H-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEE CS
                          GCV_H  30 lgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGev 71 
                                     g v++v++ e g ++++g+ + +vE+ K+   + apvsG v
  gi|121638383|ref|YP_978607.1| 593 PGSVIAVQV-ESGSQISAGDVVVVVEAMKMEHSLEAPVSGRV 633
                                    578888887.78****************************98 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.2   3.8e+03      15      30 ..     212     227 ..     208     239 .. 0.81
   2 ?   -3.0   0.0       7.4   8.8e+03      57      73 ..     311     327 ..     269     335 .. 0.66
   3 ?   10.7   0.9    0.0004      0.47      14      72 ..     586     652 ..     576     654 .] 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.2
                                    EEEESSSEEEEEEEEE CS
                  Peptidase_M23  15 pVlAaadGtVvfagkk 30 
                                    +VlA a+G Vv+ g++
  gi|121638383|ref|YP_978607.1| 212 QVLADAHGNVVHLGER 227
                                    79999*****998875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.4
                                    S-TTEEE-TTCEEEEEB CS
                  Peptidase_M23  57 vkegqkVkaGqvIGtvg 73 
                                    v+ + +V aG+++G + 
  gi|121638383|ref|YP_978607.1| 311 VEWQLRVGAGEKLGFAQ 327
                                    66666788888888766 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0004
                                    -EEEESSSEEEEEEEEET....TTEEEEEEEECTC.EEEEEEEESE.ES..S-TTEEE-TTCEEEEE CS
                  Peptidase_M23  14 tpVlAaadGtVvfagkke....gyGnvviidhgdg.ystlyahlsk.is..vkegqkVkaGqvIGtv 72 
                                    ++V++++ G V+ ++ ++    ++G vv++  + +  ++l a +s  ++  v++g++Vk  qv++++
  gi|121638383|ref|YP_978607.1| 586 AEVVSPMPGSVIAVQVESgsqiSAGDVVVVVEAMKmEHSLEAPVSGrVQvlVSVGDQVKVEQVLARI 652
                                    57*********555553234448888887777666244555555543335599***********987 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.8   4.6e+03      65      94 ..     209     238 ..     204     241 .. 0.79
   2 ?    4.7   1.9     0.024        29      27      78 ..     585     634 ..     570     636 .. 0.73
   3 ?    5.7   0.4     0.011        14      41      60 ..     632     651 ..     621     654 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                         RnfC_N  65 vsapvhasvsGtVkaiekrlvahgsgveav 94 
                                    + ++v a   G+V+++ +r+ + +++ + v
  gi|121638383|ref|YP_978607.1| 209 IEVQVLADAHGNVVHLGERECSLQRRHQKV 238
                                    467899999999999999988877766655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                         RnfC_N  27 pkelvlplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVk 78 
                                    p+e+v p+    G+   + v+ g ++  G+++   e+  +     a+vsG+V+
  gi|121638383|ref|YP_978607.1| 585 PAEVVSPMP---GSVIAVQVESGSQISAGDVVVVVEAmKMEHSLEAPVSGRVQ 634
                                    556666664...56677889999999999998887775568999999999996 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                         RnfC_N  41 pakplvkvgdkVlkGqkiae 60 
                                    + ++lv+vgd+V+  q++a+
  gi|121638383|ref|YP_978607.1| 632 RVQVLVSVGDQVKVEQVLAR 651
                                    5689*************997 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.7     0.048        57       2      59 ..     588     645 ..     587     647 .. 0.76
   2 ?    3.0   0.5      0.14   1.7e+02       2      31 ..     625     653 ..     624     654 .] 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.048
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdelleiippd.tllveakvpaadlgsikkkgqkvtl 59 
                                    + +p  G v +++ve g+ ++agd+++ +   + +  +ea v+ +   ++ ++g++v++
  gi|121638383|ref|YP_978607.1| 588 VVSPMPGSVIAVQVESGSQISAGDVVVVVEAMKmEHSLEAPVSGRVQVLV-SVGDQVKV 645
                                    789************************99975325556666665555555.46666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdelleii 31 
                                    l Apv+G+v ++ v++g+ v   ++l++i 
  gi|121638383|ref|YP_978607.1| 625 LEAPVSGRV-QVLVSVGDQVKVEQVLARIK 653
                                    679*****9.588999***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4186.50
//
Query:       gi|121638384|ref|YP_978608.1|  [L=529]
Description: acetyl-/propionyl-coa carboxylase subunit beta accD1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     3e-149  497.9   0.0   3.9e-149  497.5   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    2.9e-05   23.7   0.4      0.022   14.2   0.0    2.3  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.5   0.0  4.3e-153  3.9e-149       2     483 ..      42     518 ..      41     524 .. 0.95

  Alignments for each domain:
  == domain 1  score: 497.5 bits;  conditional E-value: 4.3e-153
                                    SCTTCEEEEEEEEHTTSGGGE.BEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCE CS
                 Carboxyl_trans   2 ehprGkltareridllldpgs.FgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakge 80 
                                    + +rGkl+ rer d lldpgs F+el+ l++  +++ +     p+ g++tg+G+v Gr++++va+d tv+gg+++p++++
  gi|121638384|ref|YP_978608.1|  42 HVSRGKLLPRERVDRLLDPGSpFLELAPLAAGGMYSDE----SPGAGIITGIGRVSGRQCVIVANDATVKGGTYYPMTVK 117
                                    568*****************************999988....6************************************* PP

                                    EECHHHHHHHHHTEEEEEEEEE-ESSS.GHHSSHHHHHHHHHHHHHHHHHHH.CS-EEEEESSEEETHHHHHHHHTSEEE CS
                 Carboxyl_trans  81 kllkaqeeaikagepligindsgGaeg.riqegveslrgsGkifgenskasg.eIpqislvtgrcaGggaYlpalgdrvi 158
                                    k+l+aqe a+++ +p+i+++dsgGa++ r+ e++++++++G+if++++++s  +Ipq++ v+g+c++ggaY+pa++d+++
  gi|121638384|ref|YP_978608.1| 118 KHLRAQEVALQNMLPCIYLVDSGGAFLpRQDEVFPDREHFGRIFYNQATMSAkGIPQVAAVLGSCTAGGAYVPAMSDEAV 197
                                    *************************767**************************************************** PP

                                    EETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGG.SS----E CS
                 Carboxyl_trans 159 mveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnr.esaPive 237
                                     v+e+++ifl Gp+++k+++g e v++eelgG++ h ++sGv++ +a+dde+al+++r +   +   ++ +  +   + +
  gi|121638384|ref|YP_978608.1| 198 IVREQGTIFLGGPPLVKAATG-EIVSAEELGGGDLHSRTSGVTDHLADDDEDALRIVRAIADTFGPCEPAQWdVRRSVEP 276
                                    *********************.*************************************998775333333325555555 PP

                                    CSSGSSSH..HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHH CS
                 Carboxyl_trans 238 tadepdrdlieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsav 317
                                    + ++ +  l+++vP++++ pyDv+ev+ r+vd +eF+E+k++y+kt+V++fAr++G pvG+vAn+     G vl ++sa+
  gi|121638384|ref|YP_978608.1| 277 KYPQAE--LYDVVPPDPRVPYDVHEVVVRIVDGSEFSEFKAKYGKTLVTAFARVHGHPVGIVANN-----G-VLLSESAL 348
                                    544444..58*******************************************************.....8.******** PP

                                    HHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTE CS
                 Carboxyl_trans 318 KaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlv 397
                                    K a+fi+lcd++++Pl++l++++Gf+vG++ e+ggi+khGak+v+a+a+a+vPk+tv+++ +yG++++ m++++++++++
  gi|121638384|ref|YP_978608.1| 349 KGAHFIELCDKRKIPLLFLQNIAGFMVGRDYEAGGIAKHGAKMVTAVACARVPKLTVVIGGSYGAGNYSMCGRAYSPRFL 428
                                    ******************************************************************************** PP

                                    EETTT-EEESS-HHHHHHHHSHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTT CS
                 Carboxyl_trans 398 aawptariaVlgpegaveilfrkekaaaemer.....kdlaaerkkklkeyeeellnpyvaaargfaDavidpsetrakl 472
                                     +wp+ari+V+g+e+a+++l + + ++ ++++      +++a+++   ++ye++  npy+ +ar ++D +idp++tr+++
  gi|121638384|ref|YP_978608.1| 429 WMWPNARISVMGGEQAASVLATVRGEQLSAAGtpwspDEEEAFKAPIRAQYEDQ-GNPYYSTARLWDDGIIDPADTRTVV 507
                                    ***********************9999999999**9877888899999999999.************************* PP

                                    SSSEEEHGGGH CS
                 Carboxyl_trans 473 vialelewkka 483
                                      al+l ++++
  gi|121638384|ref|YP_978608.1| 508 GLALSLCAHAP 518
                                    ****9998876 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1   0.00031       2.7      60     120 ..     126     186 ..      68     199 .. 0.81
   2 !   14.2   0.0   2.5e-06     0.022      56     151 ..     354     448 ..     314     469 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00031
                                    TSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHH CS
                           MdcE  60 eraekrpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGa 120
                                      ++  p + lvD+ +  l r+dE++   e +  +    a   ++G p ++ + G   +G+
  gi|121638384|ref|YP_978608.1| 126 ALQNMLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFYNQATMSAKGIPQVAAVLGSCTAGG 186
                                    55667799****************************9999999*************99986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.5e-06
                                    HHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE.HHH..HHHTTTT-SEEE CS
                           MdcE  56 leaieraekrpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkav.sGa..flahglqanrli 132
                                    +e    ++k p+l l   a+  +gr  E+ Gi +  a ++ a a Ar+   p +++++G +  +G   +   ++  + l 
  gi|121638384|ref|YP_978608.1| 354 IEL-CDKRKIPLLFLQNIAGFMVGRDYEAGGIAKHGAKMVTAVACARV---PKLTVVIGGSYgAGNysMCGRAYSPRFLW 429
                                    333.367899************************************98...7788888888635652246678999**** PP

                                    EEET-EEESS-HHHHHHHH CS
                           MdcE 133 alpgvqvavmdkasaArvT 151
                                      p++ + vm+   aA v 
  gi|121638384|ref|YP_978608.1| 430 MWPNARISVMGGEQAASVL 448
                                    ***********99999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3670.81
//
Query:       gi|121638385|ref|YP_978609.1|  [L=218]
Description: succinyl-CoA:3-ketoacid-coenzyme A transferase subunit beta scoB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-49  166.7   0.7    5.5e-49  166.5   0.7    1.0  1  CoA_trans        Coenzyme A transferase
    1.4e-06   28.3   0.1      2e-06   27.8   0.1    1.2  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.7   6.1e-53   5.5e-49       3     216 ..      10     204 ..       8     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 6.1e-53
                                    HHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBCEHHHH CS
                      CoA_trans   3 taaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetvnprfg 82 
                                    ++a++va e++dG++v++G    ig+P +li + +++    ++v++se+g+lg+gp+++ + v+++++++g+etv++  g
  gi|121638385|ref|YP_978609.1|  10 EMAARVAAEFEDGQYVNLG----IGMP-TLIPNHIPD--GVHVVLHSENGILGVGPYPRREDVDADLINAGKETVTTLPG 82 
                                    68888999***********....****.*********..999************************************** PP

                                    HHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTTESEEEEETTEEEEEEESSSEEEEEEECCEEETT CS
                      CoA_trans  83 kqflsgelefellpqgtlaerlraGgaglpelgfltntgigtlvapklkkvpgfgGaeyilepalkadvalikaskadee 162
                                    ++f+s++ +f  +++g++++++++G+++++ +g+l+n++i+    +k  +v+g+gGa++++++a  +++++++++ +d+ 
  gi|121638385|ref|YP_978609.1|  83 AAFFSSSTSFG-IIRGGHLDVAVLGAMQVSVTGDLANWMIP----GK--MVKGMGGAMDLVHGAR-KVIVMMEHTAKDGS 154
                                    ***********.*****************************....66..****************.6************* PP

                                    CSEESSGGGHTTHSHHHHHHEEEEEEEEEEEECTTSSECCCESBTGGGHSEEEE CS
                      CoA_trans 163 gnlvfeksagnfnkpaiaeaakvtileveeivekgkldpekvliPgvlvdavve 216
                                    +++  +++++ ++ ++++  ++vt l+v+++  +++ +++ ++ Pgv+vd+vv+
  gi|121638385|ref|YP_978609.1| 155 PKILERCTLPLTGVGCVD--RIVTELAVIDV--CADGLHLVQTAPGVSVDEVVA 204
                                    ****************99..***********..*******************97 PP

>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.3e-10     2e-06      36     126 ..     102     183 ..      86     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-10
                                    EEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHSTT-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-S CS
                AcetylCoA_hyd_C  36 vsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalskggksiialpStakkgeiSrIvpslkegahvtttrhdvd 115
                                    v++  a++v +tG  +  ++ g++v G+Gg +d v+ga +      i++++ tak+g+  +I+ +++      t    vd
  gi|121638385|ref|YP_978609.1| 102 VAVLGAMQVSVTGDLANWMIPGKMVKGMGGAMDLVHGARK-----VIVMMEHTAKDGS-PKILERCT---LPLTGVGCVD 172
                                    78999**********************************9.....9***********8.99999999...7777888999 PP

                                    EEEETTEEEE- CS
                AcetylCoA_hyd_C 116 yvvTEyGiadL 126
                                     +vTE  ++d+
  gi|121638385|ref|YP_978609.1| 173 RIVTELAVIDV 183
                                    99999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1566.43
//
Query:       gi|121638386|ref|YP_978610.1|  [L=248]
Description: succinyl-CoA:3-ketoacid-coenzyme A transferase subunit alpha scoA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-78  263.5   0.1    1.3e-78  263.3   0.1    1.0  1  CoA_trans  Coenzyme A transferase


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.3   0.1   7.3e-83   1.3e-78       2     216 ..       6     233 ..       5     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 263.3 bits;  conditional E-value: 7.3e-83
                                    CHHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTE..ECCHHHHHTTTEEEEEESCTTBBCEH CS
                      CoA_trans   2 etaaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagv..lglgplllngsvkkviasyggetvnp 79 
                                     taaeava +i +G+ +avGGFgl+giPealiaal++sgv+dl ++++++g+  +glg+ll+++++++ ++sy+ge  n+
  gi|121638386|ref|YP_978610.1|   6 ATAAEAVA-DIANGSSLAVGGFGLCGIPEALIAALVDSGVTDLETVSNNCGIdgVGLGLLLQHKRIRRTVSSYVGE--NK 82 
                                    699*****.*******************************************************************..** PP

                                    HHHHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTT.................ESEEEEETTEEEE CS
                      CoA_trans  80 rfgkqflsgelefellpqgtlaerlraGgaglpelgfltntgigtlvapk.................lkkvpgfgGaeyi 142
                                    +f++qfl+gele+el+pqgtlaerlraGg+g+p  +f+t+ g+gt+va++                  k++++f+G +y+
  gi|121638386|ref|YP_978610.1|  83 EFARQFLAGELEVELTPQGTLAERLRAGGMGIP--AFYTPAGVGTQVADGglpwrydasggvavvspAKETREFDGVTYV 160
                                    *********************************..********************************99*********** PP

                                    EEESSSEEEEEEECCEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEEEEEECTTSSECCCESBTGGGHSEEEE CS
                      CoA_trans 143 lepalkadvalikaskadeegnlvfeksagnfnkpaiaeaakvtileveeivekgkldpekvliPgvlvdavve 216
                                    le+ +++d+al++a+++d++gnl+++++a+nfn p +a a+++ti+eve++ve g++dp +v++Pgv+v++vv+
  gi|121638386|ref|YP_978610.1| 161 LERGIRTDFALVHAWQGDRHGNLMYRHAAANFN-PECASAGRITIAEVEHLVEPGEIDPATVHTPGVFVHRVVH 233
                                    *********************************.99999*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1789.66
//
Query:       gi|121638387|ref|YP_978611.1|  [L=547]
Description: AMP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.7e-111  372.8   0.3     2e-111  372.6   0.3    1.0  1  AMP-binding    AMP-binding enzyme
    2.6e-16   60.4   0.0    3.2e-15   56.9   0.0    2.6  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.6   0.3  2.3e-115    2e-111       3     422 ..      34     444 ..      32     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 372.6 bits;  conditional E-value: 2.3e-115
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                    ++aa++  + alvd    +++ Y+el   v+rlA gL ++G+++gdrV+i++pn++ewv++ +a++++Ga++v++np+++
  gi|121638387|ref|YP_978611.1|  34 ATAARYGHREALVDMVARRRFNYSELLTDVHRLATGLVRAGIGPGDRVGIWAPNRWEWVLVQYATAEIGAILVTINPAYR 113
                                    68999*********8889********************99**************************************** PP

                                    HHHHHHHHHHHTESEEEE..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTT CS
                    AMP-binding  83 aeelayiledseakvlia..tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpd 159
                                     +e++y+l++s++ ++ia    ++++ +++l+e+ ++ ++ + vi+l++d+++  + +   e++  +   ++++++l+ +
  gi|121638387|ref|YP_978611.1| 114 VREVEYALRQSGVAMVIAvaSFKDADyAAMLAEVGPRCPDLADVILLESDRWDALAGA---EPDLPAL--QQTAARLDGS 188
                                    *****************44667788889********************9998866444...4333333..447789**** PP

                                    SEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC CS
                    AMP-binding 160 dlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa 239
                                    d+++i+YTSGTT  PKGV lshrn+++n + +   +  + +++d+++  +p++h+fg++++ l+a ++Ga++v++ +   
  gi|121638387|ref|YP_978611.1| 189 DPVNIQYTSGTTAYPKGVTLSHRNILNNGYLV--GELLGYTAQDRICIPVPFYHCFGMVMGNLAATSHGAAMVIPAPG-- 264
                                    ****************************7775..55677789********************************7744.. PP

                                    CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEG CS
                    AMP-binding 240 ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlT 318
                                    +dp++ l++++++++t ++gvP+++ a l  ++++    +++l+slr+ +++g++++ e++r++ +++    v+ +YG+T
  gi|121638387|ref|YP_978611.1| 265 FDPAATLRAVQDERCTSLYGVPTMFIAELGLPDFT----DYELGSLRTGIMAGAACPVEVMRKVISRMHMpGVSICYGMT 340
                                    789999**********************9987777....569*************************99877******** PP

                                    GGSSECEE..CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEE CS
                    AMP-binding 319 Ettgvvtv..lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwl 396
                                    Et++v t   ++ +  ++++g+vG++ p+ e+k+vD++tge vp+g++Ge + rg +vm gY+++p++tae++d  ++w+
  gi|121638387|ref|YP_978611.1| 341 ETSPVSTQtrAD-DSVDRRVGTVGRVGPHLEIKVVDPATGEAVPRGVVGEFCTRGYSVMAGYWNDPQKTAEVID-ADGWM 418
                                    ******766544.4555799*****************************************************9.657** PP

                                    EEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 397 rTGDlgrldedGyleivgRkkdlikl 422
                                    +TGDl+++d+ Gy++i gR+kdl+++
  gi|121638387|ref|YP_978611.1| 419 HTGDLAEMDPSGYVRIAGRIKDLVVR 444
                                    ***********************986 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.18   1.6e+03      42      66 ..      89     114 ..      70     125 .. 0.75
   2 !   56.9   0.0   3.6e-19   3.2e-15       1      76 []     453     529 ..     453     529 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHT-TTT.S-SEEEE- CS
                  AMP-binding_C  42 leeeLkahvrkelgpya.vpkkvvfv 66 
                                     e  L++++++e+g++  + + ++ v
  gi|121638387|ref|YP_978611.1|  89 WEWVLVQYATAEIGAILvTINPAYRV 114
                                    57899**********95366655555 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 3.6e-19
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E+ l +hp++ +  V+Gvpd++ Ge l+a+V l+++ +e++ e L++++  +++ ++ p+++ +vde+p+t +GK
  gi|121638387|ref|YP_978611.1| 453 EIEELLHTHPDIVDGHVIGVPDAKYGEELMAVVKLRNDaPELTIERLREYCMGRIARFKIPRYLWIVDEFPMTVTGK 529
                                    8**********************************8663466**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3977.26
//
Query:       gi|121638388|ref|YP_978612.1|  [L=215]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-18   66.5   0.2    2.9e-18   65.4   0.2    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
    1.5e-08   34.9   0.1    2.8e-08   34.0   0.1    1.5  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.2   3.3e-22   2.9e-18       1      47 []      30      76 ..      30      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3.3e-22
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+aA++lfaerG+ a+ +++I ++AGvs +a+Yr+Fp+Ke Ll +l
  gi|121638388|ref|YP_978612.1| 30 LLAAAERLFAERGFLAVRLEDIGAAAGVSGPAIYRHFPNKESLLVEL 76
                                   79******************************************985 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   3.1e-12   2.8e-08       6      88 ..     100     180 ..      95     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.1e-12
                                    HHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHH CS
                      TetR_C_24   6 erLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmln 85 
                                    + L  l++ h+++ + e + +++  r+l +L++ + +++r+ +r+y +++  +++e      ++++d++l+a a++g+ln
  gi|121638388|ref|YP_978612.1| 100 AALDGLIEFHLDFALGEADLIRIQDRDLAHLPAVAERQVRKAQRQYVEVWVGVLRELNPG--LAEADARLMAHAVFGLLN 177
                                    668899**************************************************7654..5799************** PP

                                    CHH CS
                      TetR_C_24  86 wvy 88 
                                    +++
  gi|121638388|ref|YP_978612.1| 178 STP 180
                                    997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1585.35
//
Query:       gi|121638389|ref|YP_978613.1|  [L=273]
Description: proline rich membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-05   24.1   0.2    2.6e-05   24.1   0.2    1.5  2  Mycobact_memb  Mycobacterium membrane protein
  ------ inclusion threshold ------
      0.066   13.6   0.4      0.066   13.6   0.4    2.0  2  DUF1180        Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.7      0.99   8.9e+03      13      21 ..     123     131 ..     118     139 .. 0.45
   2 !   24.1   0.2   2.9e-09   2.6e-05      49     124 ..     187     262 ..     169     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.99
                                    XXXXXXXXX CS
                  Mycobact_memb  13 vvvvggltv 21 
                                    v++v +l++
  gi|121638389|ref|YP_978613.1| 123 VALVIALVI 131
                                    333333322 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.9e-09
                                    XXEEB-B----TT-----B---TTS------S-SS--B--EE-SSS------B--SS.-S------BBTTB------ CS
                  Mycobact_memb  49 PkkvkyevfGpagtvadisyldadaepqridgaalPWsltikttlaavvgnvvaqgn.sdsigCriivdgvvkderv 124
                                     ++v+y+v G  g  ++i+y+d     q   ++alPW  +++ + +++ +  v+  n +  ++C ++v gv   +r+
  gi|121638389|ref|YP_978613.1| 187 MQTVVYDVTGE-GRAISITYMDSGNVIQTEFNVALPWRKEVSLSKSSLHPASVTIVNiGHNVTCSVTVAGVQVRQRT 262
                                    5789******9.5559*****************************9999877776664899********98666665 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -9.9   9.1         2   1.8e+04      53      53 ..      44      44 ..      12      81 .. 0.56
   2 ?   13.6   0.4   7.4e-06     0.066       4      65 ..     120     188 ..     117     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: -9.9 bits;  conditional E-value: 2
                        DUF1180 53 t 53
                                   t
  gi|121638389|ref|YP_978613.1| 44 T 44
                                   1 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.4e-06
                        DUF1180   4 lLalvlLLlllLaa.......saadasralspaasspeaepPlppgataaespgkataieaksaqaaeg 65 
                                    lL ++l+++l++a+       + +   +   p++++p+++ P+pp+++aa +p  +t + +++ ++a +
  gi|121638389|ref|YP_978613.1| 120 LLVVALVIALVIANgsvkkqtAIEPLPPMPGPSPTRPTTTTPTPPSPSAAPAPTTTTGTPSETVAGAMQ 188
                                    688889998888875443332222222333455566666699999999997788777776666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2271.04
//
Query:       gi|121638390|ref|YP_978614.1|  [L=445]
Description: integral membrane leucine and alanine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-26   91.7  11.5    4.1e-26   91.7  11.5    2.1  2  ATG22     Vacuole effluxer Atg22 like
    7.1e-18   64.7  42.3      1e-17   64.1  42.3    1.2  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
          9    6.3  11.7      0.054   13.4   1.0    2.9  3  DUF485    Protein of unknown function, DUF485


Domain annotation for each model (and alignments):
>> ATG22  Vacuole effluxer Atg22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.018   1.1e+02      80     155 ..      67     144 ..      57     151 .. 0.65
   2 !   91.7  11.5   6.9e-30   4.1e-26     190     472 ..     150     434 ..     141     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.018
                          ATG22  80 svllqavvvislsglADygnyrknlLlafa.ligslstilfllvtpkkYllga.vlyivsntcfgaslvllnsfLPll 155
                                    + l+ +v++++++  +   + r+  L +++ ++ +l++ +fl  +  +Yl +  vl     ++   s v +n++L +l
  gi|121638390|ref|YP_978614.1|  67 AGLTIGVLAPVVGVWVESPHRRRVALSVLTgTAVALTCAMFLIRDDPRYLWAGlVLLAATAASSDLSSVPYNAMLRQL 144
                                    556667788888888888877777776655055555555555557888855440444444555668899999998655 PP

  == domain 2  score: 91.7 bits;  conditional E-value: 6.9e-30
                          ATG22 190 striSslGlaigylgailvqi.isilivialgsta.........tfslrlalllvGlwWliftipaalllkkrp..gppl 257
                                      riS+ G+a+gy+g++ +++ i + ++ ++gs++           ++r+a+l+++ w +++ +p++l+  + p  g  +
  gi|121638390|ref|YP_978614.1| 150 AGRISGFGWASGYVGSVALLLvIYLGFMSGSGSQRgllqlpvanGLNVRMAMLVAAAWLALLGLPLLLVAHRLPdsGAAS 229
                                    569*************9766515666777777777********99*****************************766666 PP

                          ATG22 258 pkglsyliygwkslgrtl.kqarklkdvllfLvawfllsdgiatvsstavlfaktelkmstaklillsivaviaavlGaf 336
                                    +   + l  g ++l++ +  + r+ ++++ fLva  ++ dg+a +    ++++ +  ++++a++ + +  a+++a +Ga+
  gi|121638390|ref|YP_978614.1| 230 HPS-TGLLGGYRKLWTEIsAEWRRDRNLVYFLVASAIFRDGLAAIFAFGAVLGVNAYGLTQADVLIFGAAASVVAAVGAV 308
                                    655.45556777766555389999******************************************************** PP

                          ATG22 337 lwplvsrrlnlktkktllaiivlfeliplyGllGiilgkiGlkqpwEfyvlavvyglvlgglssysRslfseLiPrGkEa 416
                                    l  +v +r++ k   +++   ++++++ + +l       + l  p  f++ +++ ++++g+ +s +R+l   +   GkE 
  gi|121638390|ref|YP_978614.1| 309 LGGFVDHRIGSK--PVIV-GSLAAIIAAALTL-------LTLSGPTAFWACGLLLCVFIGPAQSSARALLLHMAQHGKEG 378
                                    ********9888..3333.3333444444444.......46889************************************ PP

                          ATG22 417 aFFsLyaitdkgssvigplivglItDrtgnirsafvflavLlvvplpllllvdver 472
                                      F+Ly +t+++ s++gp ++++ +D  + +r+++  ++++l+++l l+l+v+v+r
  gi|121638390|ref|YP_978614.1| 379 VAFGLYTMTGRAVSFLGPWLFSVFVDVFHTVRAGLGGVCLVLTTGLLLMLRVQVSR 434
                                    *****************************************************998 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1  42.3   1.7e-21     1e-17      16     353 .]      35     396 ..      23     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.7e-21
                          MFS_1  16 gpalplalaedlg....ispseigl...lltlyalgaavaslplGrlsdr.fGrrrvlllglllfalglllllfa....s 83 
                                    +++++ +l+++ g       s +++   + ++ +l+ +v+++++G++++  + rrrv l  l+++a++l++++f     +
  gi|121638390|ref|YP_978614.1|  35 TFVFSVYLTSAVGqglpGGTSPASWlgrAGAVAGLTIGVLAPVVGVWVESpH-RRRVALSVLTGTAVALTCAMFLirddP 113
                                    33333344444443333444446676668999999***************55.999************888887445654 PP

                          MFS_1  84 slw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg..llasslg........... 149
                                     +  + lvl + +++ + ++    +a+++++++++  gr  g+  a+  +G++   l+    +++ s++           
  gi|121638390|ref|YP_978614.1| 114 RYLwAGLVLLAATAASSDLSSVPYNAMLRQLSTPSTAGRISGFGWASGYVGSVALLLVIYlgFMSGSGSqrgllqlpvan 193
                                    4444888888888888888999999*********99999999988888888855533333114444544*********** PP

                          MFS_1 150 ...Wravfyilaivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                        r +++++a+ ++l+++ l  l+  + p + + + p + + g  ++ ++++  + ++d+ l ++l+a+++f  g+++
  gi|121638390|ref|YP_978614.1| 194 glnVRMAMLVAAAWLALLGLpLL-LVAHRLPDSGAASHPSTGLLGGYRKLWTEISAEWRRDRNLVYFLVASAIFRDGLAA 272
                                    ******************99643.44444444444444444448899999999666677777665566666666668888 PP

                          MFS_1 226 lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll 305
                                    ++++  ++ +  +gl+    ++++ a++++v+a++a+l+g++ +r+g+++ ++ +l+++++aal l+ l+ + +a+++  
  gi|121638390|ref|YP_978614.1| 273 IFAFGAVLGVNAYGLT-QADVLIFGAAASVVAAVGAVLGGFVDHRIGSKPVIVGSLAAIIAAALTLLTLSGP-TAFWACG 350
                                    99999999********.799999999999999999*9999999***************************99.5555544 PP

                          MFS_1 306 vlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                    +l++  ++ g +++s+ al+ ++a   + g a+gl++++g ++++lgp
  gi|121638390|ref|YP_978614.1| 351 LLLC--VFIGPAQSSARALLLHMAQHGKEGVAFGLYTMTGRAVSFLGP 396
                                    4444..678889***********************************8 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       1.6   9.6e+03      57      67 ..      31      41 ..      26      45 .. 0.44
   2 ?   13.4   1.0   9.1e-06     0.054      21      62 ..     166     208 ..     160     215 .. 0.86
   3 ?   -2.9   0.4       1.2   7.1e+03      43      49 ..     271     277 ..     253     309 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                         DUF485 57 lgllqivltfl 67
                                   + +  +v+++ 
  gi|121638390|ref|YP_978614.1| 31 AIVTTFVFSVY 41
                                   33333444433 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.1e-06
                         DUF485  21 taiflvvYfgfvllvafapdllatkvgeg.nitvglllgllqi 62 
                                    +a+ lv+Y+gf+  ++ +++ll+ +v++g n+ +++l++++ +
  gi|121638390|ref|YP_978614.1| 166 VALLLVIYLGFMSGSGSQRGLLQLPVANGlNVRMAMLVAAAWL 208
                                    6899***********************9988888888877655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                         DUF485  43 atkvgeg 49 
                                    a+ ++ g
  gi|121638390|ref|YP_978614.1| 271 AAIFAFG 277
                                    3333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3260.79
//
Query:       gi|121638391|ref|YP_978615.1|  [L=268]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-38  130.9   0.0      5e-38  130.5   0.0    1.1  1  adh_short        short chain dehydrogenase
    6.5e-24   84.8   0.1    8.7e-24   84.4   0.1    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      2e-10   40.9   0.2      3e-10   40.3   0.2    1.3  1  KR               KR domain
    9.3e-05   22.0   0.5    0.00071   19.1   0.6    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0013   18.7   0.7       0.25   11.3   0.2    2.4  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0015   18.4   1.5     0.0037   17.2   1.5    1.7  1  NAD_binding_10   NAD(P)H-binding
     0.0015   19.0   4.3      0.032   14.7   1.3    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0049   17.4   0.0      0.012   16.2   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.014   14.9   0.3        3.1    7.3   0.3    2.3  2  NmrA             NmrA-like family
      0.045   13.1   0.0      0.097   12.0   0.0    1.6  2  DUF1776          Fungal family of unknown function (DUF1776)
       0.16   11.9   0.0       0.71    9.8   0.0    1.9  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.0   3.1e-41     5e-38       3     188 ..      12     196 ..      10     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 3.1e-41
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    ++vtGas+ IG a+a ela++G +++v++r+e+ l e+a+ l ++ + ++ + ++D++d +e ++l ++      ++ +L
  gi|121638391|ref|YP_978615.1|  12 AVVTGASQNIGAALATELAARGHHLIVTARREDVLTELAARLADKyRVTVDVRPADLADPQERSKLADEL--AARPISIL 89 
                                    89********************************************************************..5579**** PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                     +NAG + +gp+++l+ +  +  +++N ++v  lt avlp m+++++G I   +S ag+ p +  a Y+A+Ka+v+ +++
  gi|121638391|ref|YP_978615.1|  90 CANAGTATFGPIASLDLAGEKTQVQLNAVAVHDLTLAVLPGMIERKAGGILISGSAAGNSPIPYNATYAATKAFVNTFSE 169
                                    ******************************************************************************** PP

                                    HHHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 162 slakelaptgirvnavaPGlvdTdmak 188
                                    sl+ el+ +g+ v+++aPG+v+T++  
  gi|121638391|ref|YP_978615.1| 170 SLRGELRGSGVHVTVLAPGPVRTELPD 196
                                    ***********************9865 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.1   5.3e-27   8.7e-24       1     181 [.      16     197 ..      16     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 5.3e-27
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                    Ga + IG+a+A +la++G ++++t ++e+   + +++la+++  +v   ++D +d+++  +l++e++++   + il+ na
  gi|121638391|ref|YP_978615.1|  16 GASQNIGAALATELAARGHHLIVTARREDVlTELAARLADKYRVTVdvRPADLADPQERSKLADELAAR--PISILCANA 93 
                                    899***************************99**********988555******************998..7******** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtryl 155
                                    g a+   gp+++++ ++ ++ ++ n+ +++ l+ a+lp +++++ g i+   s +++  +p ++ y+a+Ka ++ ++ +l
  gi|121638391|ref|YP_978615.1|  94 GTATF--GPIASLDLAGEKTQVQLNAVAVHDLTLAVLPgMIERKaGGILISGSAAGNSPIPYNATYAATKAFVNTFSESL 171
                                    *****..*******************************8777767999999***************************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGG CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasg 181
                                      el   g+ v + +pgp++T++ ++
  gi|121638391|ref|YP_978615.1| 172 RGELRGSGVHVTVLAPGPVRTELPDA 197
                                    *********************98544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.2   1.8e-13     3e-10       4     165 ..      13     173 ..      10     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.8e-13
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppi 82 
                                    ++tG+  ++G +la+ la++g  hl++++R++   +  ++l a+l+++  ++v+v++aD++d+++ ++l +e+   ++pi
  gi|121638391|ref|YP_978615.1|  13 VVTGASQNIGAALATELAARGH-HLIVTARRE---DVLTELAARLADKyRVTVDVRPADLADPQERSKLADELA--ARPI 86 
                                    8*******************95.899999993...444456666766559***********************8..678* PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDa 158
                                    +     Ag++  +++++++ +  ++ ++    +++ L  ++ +    ++   +++  S+ag    +  a+Yaa+ af+++
  gi|121638391|ref|YP_978615.1|  87 SILCANAGTATFGPIASLDLAGEKTQVQLNAVAVHDLTLAVLPgmieRKAGGILISGSAAGNSPIPYNATYAATKAFVNT 166
                                    *******************99998888888888888888777666668888999999*****************999999 PP

                                    HHHHHHH CS
                             KR 159 laeyrrs 165
                                    + e+ r 
  gi|121638391|ref|YP_978615.1| 167 FSESLRG 173
                                    9987664 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   4.4e-07   0.00071       2      99 ..      13     118 ..      12     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.4e-07
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqpdavihlAa 73 
                                    +VtGa+  iG+al+ +l+++g+++i+ +r+++   t++ ++l        ++  +dl d+++  +l +e ++  +  l a
  gi|121638391|ref|YP_978615.1|  13 VVTGASQNIGAALATELAARGHHLIVTARRED-VLTELAARLadkyrvtvDVRPADLADPQERSKLADELAARPISILCA 91 
                                    8**********************999999944.44444444468899999999*************99997777766655 PP

                                    .---HHHHHHSHHHHHHHHTHHHHHHH CS
                      Epimerase  74 .vggvaassedpadfieknlqgtlnll 99 
                                      g+     +   d++ + +q++ln +
  gi|121638391|ref|YP_978615.1|  92 nAGTATFGPIASLDLAGEKTQVQLNAV 118
                                    477766666666676666666666655 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00015      0.25      10      87 ..      24      99 ..      20     121 .. 0.81
   2 !    5.5   0.0    0.0095        15       5      36 ..     165     196 ..     164     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                 Glyco_transf_4 10 eLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaa 87
                                    La +La+rGh+  v +++ d  +e +  ++ +  rv    ++  l +++ +++l+  l +  + ++ + +++++ ++
  gi|121638391|ref|YP_978615.1| 24 ALATELAARGHHLIVTARREDVLTELA-ARLADKYRVTVDVRPADLADPQERSKLADELAARPISIL-CANAGTATFG 99
                                   69*****************99999999.888888888888889999999999999999999999888.4444444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0095
                 Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleee 36 
                                    +++ + L  +L+  G++Vtv++pg+ + +   
  gi|121638391|ref|YP_978615.1| 165 NTFSESLRGELRGSGVHVTVLAPGPVRTELPD 196
                                    6777889999************9986665554 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.5   2.3e-06    0.0037       1     181 [.      16     226 ..      16     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH....CTT..TCEEEE--TT-C...CHHHHHHTT-SEEEES-.-- CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele....aee..glevvegdvtdv...edlaealkgadaVvsal.gg 70 
                                    GA+ ++G +l++el+arg h++ + +R+++ l+el+    ++    ++v  +d+ d+   ++la+ l+   + + ++ +g
  gi|121638391|ref|YP_978615.1|  16 GASQNIGAALATELAARG-HHLIVTARREDVLTELAarlaDKYrvTVDVRPADLADPqerSKLADELAARPISILCAnAG 94 
                                    99***************5.9********9999877633334442244566688888622256888888777645555244 PP

                                    TCC...........HHHH.............HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHH CS
                 NAD_binding_10  71 ggk...........deeg.............aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakra 126
                                    +++           +                + +++  + e +   +++ +++  +  +p +    ++   ka +    +
  gi|121638391|ref|YP_978615.1|  95 TATfgpiasldlagE--KtqvqlnavavhdlTLAVLPGMIERKAGGILISGSAAGNSPIPYNATYAAT---KAFVNTFSE 169
                                    444666665544441..034566666777778888888887777666555554444334433333333...444444333 PP

                                    HHH.HHHHSSSEEEEEEE-CEE-S.T.--SEEEEETTSS----EEEHHHHHHHHHHHC CS
                 NAD_binding_10 127 aee.llrasgldwTivrpggLtde.p.ttkyrvvekgepfkggsisradVAdvlvavl 181
                                    + + +lr sg+  T++ pg    e p +++  +vek  p +   is +  A+v +++l
  gi|121638391|ref|YP_978615.1| 170 SLRgELRGSGVHVTVLAPGPVRTElPdASEASLVEKLVP-DFLWISTEHTARVSLNAL 226
                                    333268889999999999888655444556555554433.223567777777666666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.3   1.9e-05     0.032       8      91 ..      23     105 ..      16     137 .. 0.74
   2 ?    5.0   0.1     0.018        29       8      34 ..     169     195 ..     164     259 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                Glyco_trans_4_4   8 aelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahspt..ag 85 
                                    a+la +LaarGh++ v +++++   + l ++ +  +r+ v  rp+ lad++    l++ l  +++++ ++ a+  t   g
  gi|121638391|ref|YP_978615.1|  23 AALATELAARGHHLIVTARREDVLTE-LAARLADKYRVTVDVRPADLADPQERSKLADEL--AARPISILCANAGTatFG 99 
                                    789*************9998877766.6666666666666666667999999999*9999..999999999998552345 PP

                Glyco_trans_4_4  86 laarla 91 
                                    ++a l 
  gi|121638391|ref|YP_978615.1| 100 PIASLD 105
                                    555444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                Glyco_trans_4_4   8 aelaraLaarGheVtvltpapapgape 34 
                                    + l  +L+  G++Vtvl+p+p + + +
  gi|121638391|ref|YP_978615.1| 169 ESLRGELRGSGVHVTVLAPGPVRTELP 195
                                    5667789999********987665442 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.2e-06     0.012       9      48 ..      20      59 ..      13      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                                   HHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....- CS
                  F420_oxidored  9 nmgealasgllaagaqpheivvansrnpekaeelaeelg....v 48
                                   n+g+ala  l+a+g   h+++v+  r ++ ++ela++l     v
  gi|121638391|ref|YP_978615.1| 20 NIGAALATELAARG---HHLIVT-ARREDVLTELAARLAdkyrV 59
                                   89************...***966.99999999998887644443 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0019       3.1       2      48 ..      13      61 ..      12      97 .. 0.71
   2 ?    5.4   0.0    0.0074        12     135     180 ..     154     195 ..     146     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0019
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE CS
                           NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv 48
                                   +v+Ga+ ++G++++  l+++gh+  +  R +   +ela+ l+++  ++v
  gi|121638391|ref|YP_978615.1| 13 VVTGASQNIGAALATELAARGHHLIVTARREdvLTELAARLADKYRVTV 61
                                   699********************99999877665666666665544444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0074
                                    -EEEEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE CS
                           NmrA 135 pytfvyagffmenflsllaqlkvgdtappedkvtllgpgnpkavll 180
                                    ++t++++++f + f+ +l      +++ ++  vt+l+pg +   l+
  gi|121638391|ref|YP_978615.1| 154 NATYAATKAFVNTFSESLRG----ELRGSGVHVTVLAPGPVRTELP 195
                                    57**************8888....89999999******99988888 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     6e-05     0.097     104     195 ..      97     185 ..      78     207 .. 0.91
   2 ?   -3.2   0.0       2.6   4.2e+03     277     295 ..     236     254 ..     217     265 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                        DUF1776 104 ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkr 183
                                    ++gpi+ + l+  + +++ + ++   ++ a lp + +   +ka  i+++ s   +  +p+ a+ a +   ++++ e+L+ 
  gi|121638391|ref|YP_978615.1|  97 TFGPIASLDLAGEKTQVQLNAVAVHDLTLAVLPGMIE---RKAGGILISGSAAGNSPIPYNATYAATKAFVNTFSESLRG 173
                                    789************9**9999999889999999987...89************************************** PP

                        DUF1776 184 elrphnidvtqi 195
                                    elr  +++vt +
  gi|121638391|ref|YP_978615.1| 174 ELRGSGVHVTVL 185
                                    ***999999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                        DUF1776 277 Gkgarlyslvgkllpeglv 295
                                    G+ ++++s+ ++++p+ +v
  gi|121638391|ref|YP_978615.1| 236 GLTSKAMSVASQYAPRAIV 254
                                    6666666666666666555 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00043      0.71      34     105 ..      23      94 ..       9      97 .. 0.77
   2 ?   -0.7   0.0      0.74   1.2e+03      52     102 ..     159     213 ..     110     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                Glyco_tran_WecB  34 eelleraeeeglrvfllGgkpevlekaaerlrekypglriagthdgy.keeeeeaiieainaskpdlllvglG 105
                                     +l ++++++g+ + +   +++vl ++a+rl++ky ++++  + +   +++e  +++++++a   ++l    G
  gi|121638391|ref|YP_978615.1|  23 AALATELAARGHHLIVTARREDVLTELAARLADKY-RVTVDVRPADLaDPQERSKLADELAARPISILCANAG 94 
                                    5677777778899999999****************.4444333333245799999999999999988887766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                Glyco_tran_WecB  52 gkpevlekaaerlreky..pglriagthdgy.k.eeeeeaiieainaskpdlllv 102
                                    +++  ++++ e lr ++   g+++    +g  + e  +++ ++ +++  pd+l++
  gi|121638391|ref|YP_978615.1| 159 ATKAFVNTFSESLRGELrgSGVHVTVLAPGPvRtELPDASEASLVEKLVPDFLWI 213
                                    4444555555555555422466666666664423555666667777888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1777.10
//
Query:       gi|121638392|ref|YP_978616.1|  [L=533]
Description: hypothetical protein BCG_2530c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.1e-213  708.5   0.0   5.2e-213  708.2   0.0    1.0  1  DUF853         Bacterial protein of unknown function (DUF853)
    3.8e-07   30.4   0.0    9.6e-07   29.1   0.0    1.4  1  DUF87          Helicase HerA, central domain
    2.9e-05   23.2   0.3    8.3e-05   21.7   0.1    1.8  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00011   22.5   0.1       0.03   14.6   0.1    2.5  2  AAA_22         AAA domain
    0.00013   22.0   0.0      0.011   15.7   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
    0.00075   19.9   8.1     0.0027   18.1   0.5    3.4  3  AAA_16         AAA ATPase domain
    0.00082   19.1   1.6     0.0057   16.4   1.6    2.2  2  AAA_30         AAA domain
     0.0015   17.9   0.0     0.0042   16.5   0.0    1.7  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0018   18.7   0.3       0.62   10.5   0.2    2.3  2  AAA            ATPase family associated with various cellular
     0.0099   14.8   0.0       0.47    9.3   0.0    2.1  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.037   14.1   0.0      0.057   13.5   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.045   14.1   0.1      0.094   13.0   0.1    1.5  1  AAA_19         AAA domain
      0.063   12.5   0.3        2.7    7.1   0.0    2.1  2  DUF2075        Uncharacterized conserved protein (DUF2075)
      0.066   12.5   0.4       0.12   11.7   0.4    1.3  1  Zeta_toxin     Zeta toxin
      0.086   12.6   0.2          2    8.1   0.1    2.2  2  DEAD           DEAD/DEAH box helicase
      0.095   11.7   0.1       0.16   11.0   0.1    1.3  1  T2SSE          Type II/IV secretion system protein
       0.16   12.0   0.0       0.34   10.9   0.0    1.5  1  DUF1815        Domain of unknown function (DUF1815)
       0.21   11.1   0.1       0.36   10.3   0.1    1.3  1  AAA_7          P-loop containing dynein motor region
       0.27   10.1   0.2       0.43    9.5   0.2    1.2  1  AAA_6          Hydrolytic ATP binding site of dynein motor re


Domain annotation for each model (and alignments):
>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.2   0.0  5.5e-216  5.2e-213       7     504 .]      39     532 ..      34     532 .. 0.99

  Alignments for each domain:
  == domain 1  score: 708.2 bits;  conditional E-value: 5.5e-216
                         DUF853   7 keaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevkdklaarleeiglddy 86 
                                     ++++++++ l+++nrhGl+aGatGtGkt+tLq++ae+ls+aGv+v++advkGdLsg+a++Ge++dk+aar++++g dd+
  gi|121638392|ref|YP_978616.1|  39 PDPSAQIRIPLATVNRHGLVAGATGTGKTKTLQLIAEQLSAAGVAVLMADVKGDLSGLARPGEAADKTAARAKDTG-DDW 117
                                    577899**********************************************************************.99* PP

                         DUF853  87 qlkalPvtlwdvfge.kGhpvratiselGPllLarllelndvqegvLnivfriadeeGllLldlkdLrallkev.adnak 164
                                     ++a+Pv+++++ ++  G+pvratis++GP+lLa++l ln++qe++L ++f++ad++Gl+LldlkdLra+++++ +d++k
  gi|121638392|ref|YP_978616.1| 118 VPTAFPVEFLSLGASgVGVPVRATISSFGPILLAKVLGLNATQESTLGLIFHWADQRGLPLLDLKDLRAVITHLtSDEGK 197
                                    ************99989*********************************************************89**** PP

                         DUF853 165 elskqygnvskasvgaiqreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllqsPklyatfLlWllseL 244
                                       k++g+vs++++g+i+r+L++Le++Ga++ffGeP+L+ edllr+d++GrG+islL++ +++ +P++++tfL+W+l++L
  gi|121638392|ref|YP_978616.1| 198 VELKSLGAVSPTTAGVILRALVNLEAEGADTFFGEPELRPEDLLRVDSQGRGIISLLEFGSQALRPAMFSTFLMWVLADL 277
                                    ******************************************************************************** PP

                         DUF853 245 feeLPevGdldkPklvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraf 324
                                    f+ LPevGdldkPklvfffdeahLLf+da+ka+le+veq+v+LirskGvGv+f+tq P+dlP++vL+qLG+r+qhalraf
  gi|121638392|ref|YP_978616.1| 278 FTFLPEVGDLDKPKLVFFFDEAHLLFTDASKAFLEQVEQTVKLIRSKGVGVFFCTQLPTDLPNDVLSQLGARIQHALRAF 357
                                    ******************************************************************************** PP

                         DUF853 325 tpkdqkavkaaadtfranpefdveeaiteLgvGealvsvLdekGaPsiveralvvpPasrlgplseeeraalvqespvag 404
                                    tp+d+ka++++++t+++++ +d+e+a+t+Lg+Gea+v+vL+ekGaP++v+++ +++P+s ++++++e++ a++q+s++++
  gi|121638392|ref|YP_978616.1| 358 TPDDHKALRKTVRTYPKTDVYDLESALTSLGTGEAVVTVLSEKGAPTPVAWTRMRAPRSLMAAIGAEAIGAAAQASSLQA 437
                                    ******************************************************************************** PP

                         DUF853 405 kydeeidresayevLakkvaeaaeaaeqaaaeeekeeesgllgalkdtalgaaakkaeergskketvvealaksvvrsva 484
                                    +y ++idr+sa+e+L++k+a a+ea++q+a++ +  ++++ l++ +d++++++++ +e++g +  +++e+l++++v+sv 
  gi|121638392|ref|YP_978616.1| 438 VYGQTIDRPSAHEILSAKLAPAQEAPAQEAPAPR--GQYDPLPWPDDFEVPPMPAPVEPQGPA--VWEEILKNPTVKSVL 513
                                    ****************************999887..79**********************999..9************** PP

                         DUF853 485 sqvgrelvrgllGslggkkr 504
                                    ++++re++r+++G+ g+++r
  gi|121638392|ref|YP_978616.1| 514 NTTAREITRSIFGT-GRRRR 532
                                    **************.88886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     1e-09   9.6e-07      12      68 ..      43      97 ..      28     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1e-09
                          DUF87 12 vpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal 68
                                    ++++ l   v+rH ++ g TG+GK+ t  ++ e+l    g+ +l+ D+ G+ + + 
  gi|121638392|ref|YP_978616.1| 43 AQIRIPL-ATVNRHGLVAGATGTGKTKTLQLIAEQLS-AAGVAVLMADVKGDLSGLA 97
                                   4445555.569**************************.9************977766 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   8.8e-08   8.3e-05       6      55 ..      44      93 ..      41     101 .. 0.92
   2 ?   -2.1   0.0       1.4   1.4e+03     240     277 ..     287     330 ..     259     338 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.8e-08
                  TrwB_AAD_bind  6 gvplpkeretqhilivGttGsGKtqalekllrairargdraivlDltGaf 55
                                   ++ +p  + ++h l++G+tG+GKt++l+ + +++ a g  ++ +D +G++
  gi|121638392|ref|YP_978616.1| 44 QIRIPLATVNRHGLVAGATGTGKTKTLQLIAEQLSAAGVAVLMADVKGDL 93
                                   6778888999**************************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                  TrwB_AAD_bind 240 srerrlWfflDElpaLgr......leelksllaegRkfGgavvl 277
                                     ++ +l ff+DE + L        le++++ ++ +R++G+ v  
  gi|121638392|ref|YP_978616.1| 287 LDKPKLVFFFDEAHLLFTdaskafLEQVEQTVKLIRSKGVGVFF 330
                                    56778889999988774322334478888888888888877665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.2e-05      0.03       6      31 ..      54      79 ..      50      99 .. 0.84
   2 ?    5.3   0.0     0.024        22      92     128 ..     291     331 ..     277     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                   ++++v G +GtGKT +l+ ++eql +
  gi|121638392|ref|YP_978616.1| 54 RHGLVAGATGTGKTKTLQLIAEQLSA 79
                                   799********************963 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                         AAA_22  92 ielliiDEaqhlr...seealeeLrsllnl.srkgvqliLv 128
                                    + ++  DEa+ l+   s++ le++ + ++l ++kgv ++++
  gi|121638392|ref|YP_978616.1| 291 KLVFFFDEAHLLFtdaSKAFLEQVEQTVKLiRSKGVGVFFC 331
                                    36999******998876777777766666666999998876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05     0.011      23      51 ..      52      80 ..      28      90 .. 0.87
   2 ?    4.0   0.0     0.048        46     131     153 ..     289     310 ..     282     324 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                   TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                         ResIII 23 rdkrglikmaTGtGKTlvaaklierllkk 51
                                    +++gl++ aTGtGKT ++  ++e+l+ +
  gi|121638392|ref|YP_978616.1| 52 VNRHGLVAGATGTGKTKTLQLIAEQLSAA 80
                                   5789******************9999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.048
                                    TT-SEEEEETGGGTTS.TTTHHH CS
                         ResIII 131 drfdviiiDEaHrlgakkswrei 153
                                    + ++v+++DEaH l  + + ++ 
  gi|121638392|ref|YP_978616.1| 289 KPKLVFFFDEAHLLFTD-ASKAF 310
                                    45679*******99884.33333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   2.9e-06    0.0027      25     155 ..      54     179 ..      43     187 .. 0.62
   2 ?    4.8   0.1     0.036        34     134     157 ..     288     313 ..     184     329 .. 0.74
   3 ?   -0.4   0.1       1.4   1.3e+03      66     105 ..     401     439 ..     331     472 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                    +  l+ G+ G+GK++ ++ ++++l+++g+ +  +  k d ++ a+p     +a+++ +  r+ ++  ++  + a++ +++
  gi|121638392|ref|YP_978616.1|  54 RHGLVAGATGTGKTKTLQLIAEQLSAAGVAVlmADVKGDLSGLARP----GEAADK-TAARAKDTG-DDWVPTAFPVEFL 127
                                    4569***********************9888454444444433333....233322.222222222.2234444444444 PP

                         AAA_16 103 eala..avpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqll 155
                                    +  a   + ++++ ++s    ll++ l l +++e++l l+   ++wad+  l ll
  gi|121638392|ref|YP_978616.1| 128 SLGAsgVGVPVRATISSFGPILLAKVLGLNATQESTLGLI---FHWADQRGLPLL 179
                                    4444444555555555777777777777777767767777...477777777776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.036
                         AAA_16 134 erp.lvlvlDdlq.wadeaslqllaa 157
                                    ++p lv+++D+++  + +as ++l++
  gi|121638392|ref|YP_978616.1| 288 DKPkLVFFFDEAHlLFTDASKAFLEQ 313
                                    3455*********5455566666775 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                         AAA_16  66 aipysa.laqalareellrqlldeaesaeleawrekleeal 105
                                    ++p  + ++++ a ++l++++++ea    ++a +  l++++
  gi|121638392|ref|YP_978616.1| 401 GAPTPVaWTRMRAPRSLMAAIGAEAIG--AAAQASSLQAVY 439
                                    334433377777777777777777333..222222233333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.6     6e-06    0.0057      19      63 ..      54     107 ..      43     121 .. 0.83
   2 ?   -1.0   0.0       1.3   1.3e+03      90     119 ..     292     320 ..     266     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaag.........grviglAptgkaAkvLa 63 
                                    r  ++ G+ GtGKt +l+ ++e + aag         g++ glA  g+aA++ a
  gi|121638392|ref|YP_978616.1|  54 RHGLVAGATGTGKTKTLQLIAEQLSAAGvavlmadvkGDLSGLARPGEAADKTA 107
                                    567899**********************88888888888889999999888755 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                         AAA_30  90 tllivDEagmvdtkqlaallkaaekagakv 119
                                     ++  DEa ++ t+  +a+l+++e+  +k+
  gi|121638392|ref|YP_978616.1| 292 LVFFFDEAHLLFTDASKAFLEQVEQ-TVKL 320
                                    56778******************99.5555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.4e-06    0.0042      39      60 ..      48      73 ..      27     111 .. 0.72
   2 ?   -2.3   0.0       2.4   2.3e+03     151     211 ..     302     361 ..     295     371 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.4e-06
                                   -......SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE 39 a.....shllvaGatgsGKStalntLi 60
                                   +      h+lvaGatg+GK+ +l+  i
  gi|121638392|ref|YP_978616.1| 48 PlatvnRHGLVAGATGTGKTKTLQL-I 73
                                   3334448****************84.3 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                    TT-......................-----------B-----EEEEEEC-HHH..HHHHHHHH CS
                   FtsK_SpoIIIE 151 lvlDnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslvvivderie..Lrlaapkd 211
                                    l+ D  +++ ++ e+ ++L+    s+gv v   ++     +  +++++++ri+  Lr + p+d
  gi|121638392|ref|YP_978616.1| 302 LFTDASKAFLEQVEQTVKLIR---SKGVGVFFCTQLPTDLPNDVLSQLGARIQhaLRAFTPDD 361
                                    566666666666665555553...344555544455555677788888999873355555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   0.00065      0.62       2      30 ..      57      85 ..      56     114 .. 0.75
   2 ?    6.2   0.0     0.014        13      58     120 ..     289     343 ..     273     354 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                            AAA  2 llyGppGtGKTllakavakelgvefleis 30
                                   l+ G  GtGKT + + +a++l++  + + 
  gi|121638392|ref|YP_978616.1| 57 LVAGATGTGKTKTLQLIAEQLSAAGVAVL 85
                                   789*****************975444333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                                    TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTHHHH CS
                            AAA  58 kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkk..eskvivigatnrpdkldpall 120
                                    kp  ++f+DE++ l+++             +++l+++++  k   ++ v v   t+ p +l++ +l
  gi|121638392|ref|YP_978616.1| 289 KPkLVFFFDEAHLLFTDA-----------SKAFLEQVEQTVKLirSKGVGVFFCTQLPTDLPNDVL 343
                                    56689************9...........5666666665555554334666666666666666666 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0005      0.47      19      60 ..      51      92 ..      46     106 .. 0.91
   2 ?    3.3   0.0     0.034        32     241     313 ..     291     369 ..     264     392 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0005
                         AAA_10 19 tnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60
                                   t + + l+ G +G GK  + +l+  ++s++g  +l+ D k +
  gi|121638392|ref|YP_978616.1| 51 TVNRHGLVAGATGTGKTKTLQLIAEQLSAAGVAVLMADVKGD 92
                                   567899********************************9976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                         AAA_10 241 fkvvifDEawiftssaeGkkll..kelvRiGRsynaavylvtqsadDvlkee...lknniglkl.aFretdkeeikkvL 313
                                      v +fDEa  + + a  ++l+  ++ v+  Rs    v++ tq + D+ ++    l+  i ++l aF + d+++ +k++
  gi|121638392|ref|YP_978616.1| 291 KLVFFFDEAHLLFTDASKAFLEqvEQTVKLIRSKGVGVFFCTQLPTDLPNDVlsqLGARIQHALrAFTPDDHKALRKTV 369
                                    34689****9987777766664226889999****************96654233666677777678777776666554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.057       4      43 ..      58      97 ..      57     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannla 43
                                   +++  G+GKT ++  +a  l+ +g  Vl+ D+  + + la
  gi|121638392|ref|YP_978616.1| 58 VAGATGTGKTKTLQLIAEQLSAAGVAVLMADVKGDLSGLA 97
                                   57899**************************877755444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1    0.0001     0.094       7      38 ..      50      81 ..      44     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelg 38
                                   a+ +++ lv +  GtGKT++l+ i + l ++g
  gi|121638392|ref|YP_978616.1| 50 ATVNRHGLVAGATGTGKTKTLQLIAEQLSAAG 81
                                   56788999****************99998876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.048        45       5      25 ..      57      77 ..      54      96 .. 0.83
   2 ?    7.1   0.0    0.0029       2.7      91     129 ..     293     330 ..     280     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.048
                        DUF2075  5 lVtGvaGtGKtvvllnllael 25
                                   lV G++GtGKt  l  ++ +l
  gi|121638392|ref|YP_978616.1| 57 LVAGATGTGKTKTLQLIAEQL 77
                                   79*********9888777776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0029
                        DUF2075  91 vvivDEAhrlltksdqaekqseenqlkelmkrakvvval 129
                                    v  +DEAh+l t +++a   ++ +q  +l++ + v v++
  gi|121638392|ref|YP_978616.1| 293 VFFFDEAHLLFTDASKA-FLEQVEQTVKLIRSKGVGVFF 330
                                    789*********44443.334688899999999999998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00013      0.12      20      52 ..      57      88 ..      54      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                     Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpD 52
                                   l++G++G GK+++++l++++l  + +v +l +D
  gi|121638392|ref|YP_978616.1| 57 LVAGATGTGKTKTLQLIAEQLS-AAGVAVLMAD 88
                                   89*******************6.6666666665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0021         2       8      35 ..      47      74 ..      41      95 .. 0.85
   2 ?    2.1   0.0      0.15   1.4e+02     125     151 ..     294     320 ..     273     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                                   HHHHHTTCEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  8 iplilgggdvlvaaeTGsGKTlaflipv 35
                                   ipl+  +++ lva++TG+GKT   ++ +
  gi|121638392|ref|YP_978616.1| 47 IPLATVNRHGLVAGATGTGKTKTLQLIA 74
                                   7888899999***********9987765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                                    EEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 125 lVlDEadrlldqgfsdfinrilnqlpq 151
                                    + +DEa+ l  +  + f++++ ++++ 
  gi|121638392|ref|YP_978616.1| 294 FFFDEAHLLFTDASKAFLEQVEQTVKL 320
                                    458*******99888888886666644 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.16     130     156 ..      54      80 ..      22      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                          T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                       lv+G+Tg+GKt +l  + +++ + 
  gi|121638392|ref|YP_978616.1|  54 RHGLVAGATGTGKTKTLQLIAEQLSAA 80 
                                    4459*************9998888776 PP

>> DUF1815  Domain of unknown function (DUF1815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.34      39      88 ..     375     428 ..     362     438 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                        DUF1815  39 gdeaesasfvvdlgdghlvrflvsdlg....iswvesrddrelvkleGaeaiqe 88 
                                     d  +  s +++lg g++v  ++s+ g    ++w+ +r  r l+   Gaeai  
  gi|121638392|ref|YP_978616.1| 375 TDVYDLESALTSLGTGEAVVTVLSEKGaptpVAWTRMRAPRSLMAAIGAEAIGA 428
                                    555666788999999999999999987555589******************965 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00038      0.36      30      63 ..      50      83 ..      45      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                    + +++ l+ G tGtGKt +++ + ++l+   + 
  gi|121638392|ref|YP_978616.1| 50 ATVNRHGLVAGATGTGKTKTLQLIAEQLSAAGVA 83
                                   5678999***************999999876655 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00045      0.43      31      60 ..      52      81 ..      49      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00045
                          AAA_6 31 lklggapaGpagtGKtEtvkdLakalakqv 60
                                   ++  g +aG +gtGKt t + +a++l+   
  gi|121638392|ref|YP_978616.1| 52 VNRHGLVAGATGTGKTKTLQLIAEQLSAAG 81
                                   678899*****************9997653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3788.79
//
Query:       gi|121638393|ref|YP_978617.1|  [L=215]
Description: oligoribonuclease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-32  111.3   0.0    8.8e-32  110.9   0.0    1.2  1  RNase_T      Exonuclease
  ------ inclusion threshold ------
        5.8    7.7   5.9       0.81   10.4   0.9    2.1  2  ACC_epsilon  Acyl-CoA carboxylase epsilon subunit


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   9.8e-36   8.8e-32       1     164 [.       6     169 ..       6     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 9.8e-36
                                    EEEEEEESSSTTCTTS-EEEEEEEEEETTCC..EEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHH CS
                        RNase_T   1 vviDlEttgldakekdeiieiaaisidggen..eigetfhfyvkptelakltdecteftgitqemldeapsfkevleefk 78 
                                    v+iD+E+tgld    d++ieiaa ++d+++n    g +++++ ++  l+ + d + e++  +++  ++++s+ + +++++
  gi|121638393|ref|YP_978617.1|   6 VWIDCEMTGLDL-GSDKLIEIAALVTDADLNilGDGVDVVMHADDAALSGMIDVVAEMHSRSGLIDEVKASTVDLATAEA 84 
                                    9***********.8*******************89999****************************************** PP

                                    HHHHHHTCCCETT.TCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHCHHHHHHHHHTTCHSSSSTSSHHHH CS
                        RNase_T  79 ellrklallvahn.aafdvgflraadkrilkkevpkrnqfldtlildkatlkelartsldklaeklgleedgraHrAldD 157
                                     +l++++++v++  +a+++g++ a+d+ ++ +++p  ++fl+++++d++++kel+r++++ +  + + ++ +  HrAl+D
  gi|121638393|ref|YP_978617.1|  85 MVLDYINEHVKQPkTAPLAGNSIATDRAFIARDMPTLDSFLHYRMIDVSSIKELCRRWYPRIYFGQPPKGLT--HRALAD 162
                                    **********************************************************************99..****** PP

                                    HHHHHHH CS
                        RNase_T 158 aeatakl 164
                                    +++++++
  gi|121638393|ref|YP_978617.1| 163 IHESIRE 169
                                    ***9986 PP

>> ACC_epsilon  Acyl-CoA carboxylase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3      0.53   4.7e+03      14      20 ..      24      30 ..      23      30 .. 0.88
   2 ?   10.4   0.9   9.1e-05      0.81      10      39 ..     184     213 ..     183     215 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.53
                    ACC_epsilon 14 ELAALta 20
                                   E+AAL++
  gi|121638393|ref|YP_978617.1| 24 EIAALVT 30
                                   9****95 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.1e-05
                    ACC_epsilon  10 PtdeELAALtaVLaaraaaaaaaaaepapa 39 
                                    P+  E+AA++a L+  a+a++++++++ap+
  gi|121638393|ref|YP_978617.1| 184 PSTSEIAAVVAELSDGAGAQEETDSAEAPQ 213
                                    7889********************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1437.78
//
Query:       gi|121638394|ref|YP_978618.1|  [L=415]
Description: transposase IS1081 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-154  514.0   0.0   2.4e-154  513.8   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      2e-05   24.9   0.0    5.2e-05   23.6   0.0    1.7  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.8   0.0  2.7e-158  2.4e-154       1     380 [.       1     379 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 513.8 bits;  conditional E-value: 2.7e-158
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l++ e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121638394|ref|YP_978618.1|   1 MTSSH-LIDAEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.88999999****************************************************************** PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121638394|ref|YP_978618.1|  80 PKLRQGSYFPdWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **********9***************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121638394|ref|YP_978618.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    v+ai+a++p+aa+QrCr+H+++nl+a++pk ++ +v++ l+siy+++dae+++++++++l++l++k+p+vae+ld+a++d
  gi|121638394|ref|YP_978618.1| 239 VAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTD 318
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    +laf+afp+qi+r+i+s+N++ErLN+e+rRrt+vvgiFP+++si+rlvgavlae+hdew+e
  gi|121638394|ref|YP_978618.1| 319 LLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIE 379
                                    ***********************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.8e-09   5.2e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.8e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121638394|ref|YP_978618.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2964.51
//
Query:       gi|121638395|ref|YP_978619.1|  [L=45]
Description: hypothetical protein BCG_2533 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        98  (0.005466); expected 358.6 (0.02)
Passed bias filter:                       84  (0.00468515); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 359.79
//
Query:       gi|121638396|ref|YP_978620.1|  [L=140]
Description: hypothetical protein BCG_2534 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                      103  (0.00574488); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 999.04
//
Query:       gi|121638397|ref|YP_978621.1|  [L=153]
Description: hypothetical protein BCG_2535c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-39  133.8   0.0    5.6e-39  133.6   0.0    1.0  1  DUF4411         Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.025   15.1   0.0    1.2  1  PIN             PIN domain
       0.16   12.1   0.1       0.24   11.5   0.1    1.3  1  Suppressor_APC  Adenomatous polyposis coli tumour suppressor 


Domain annotation for each model (and alignments):
>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   9.4e-43   5.6e-39       1     162 []       3     153 .]       3     153 .] 0.98

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 9.4e-43
                        DUF4411   1 YllDtnvfieakrryYsfdifpsfWewleeeveegkllsikeVkrElergedelskWakenesieklesaedlavveevg 80 
                                    Y +Dt+++ +  r+ +++ +f+s+W  +e+ +++g++ s++eV+rEl+r++d++++Wa+ ++    l++  d++++++ +
  gi|121638397|ref|YP_978621.1|   3 YSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWADGQTG---LFCPLDEQIQQAAR 79 
                                    99*************************************************************...9************* PP

                        DUF4411  81 kvakwv.ivesekyskaakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkIPdvcealgikcidlfellrelg 159
                                    ++ + + ++ +++ ++       s aDpf+iA+A+++natvVT+E+++ n++k  ++IPdvc+alg+++++l+ +++++g
  gi|121638397|ref|YP_978621.1|  80 HILRLHpNMVRQGGRR-------SAADPFVIALAMVNNATVVTQETASGNIEK--PRIPDVCDALGVPWLTLMGYIEAQG 150
                                    *********9999999.......77**********************777777..************************* PP

                        DUF4411 160 ltf 162
                                    +tf
  gi|121638397|ref|YP_978621.1| 151 WTF 153
                                    *98 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.1e-06     0.025       3     113 ..       5     117 ..       3     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-06
                                    E-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHH..HHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   3 lDTsvliallrgeekaeaarklleeleelvtsalvl..aEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    +DTs++++  r+  + + +r l+ ++e+ ++   +    E+ + lar       +++  +++ +     + p+d++i+  
  gi|121638397|ref|YP_978621.1|   5 FDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRsvDEVQRELAR-------RDDDAKRWADGQTGLFCPLDEQIQQA 77 
                                    7*************************7777665444349********.......56666666665555566777777777 PP

                                    HHHHHHHHH........SBHHHHHHHHHHHHHT-EEE.ESS CS
                            PIN  81 aaeialkyg........llpnDaliaAtAkehgikliatfD 113
                                    a+ i + +         ++++D +++A+A  ++++++ t  
  gi|121638397|ref|YP_978621.1|  78 ARHILRLHPnmvrqggrRSAADPFVIALAMVNNATVV-TQE 117
                                    7777777777889*********************999.875 PP

>> Suppressor_APC  Adenomatous polyposis coli tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     4e-05      0.24      35      80 ..      38      83 ..      29      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                 Suppressor_APC 35 qlrevqerqkslgkvetqfdlqtdliqerlefelariqevnrelfe 80
                                   q+r+v e q++l++ +  ++ ++d++   +  + ++iq+  r+   
  gi|121638397|ref|YP_978621.1| 38 QIRSVDEVQRELARRDDDAKRWADGQTGLFCPLDEQIQQAARHILR 83
                                   9****************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1214.00
//
Query:       gi|121638398|ref|YP_978622.1|  [L=415]
Description: hypothetical protein BCG_2536c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-21   75.4   0.0    6.9e-21   74.4   0.0    1.5  1  Peptidase_M78  IrrE N-terminal-like domain
    4.9e-08   32.9   0.0    1.2e-07   31.7   0.0    1.7  1  HTH_3          Helix-turn-helix
      2e-07   31.3   3.4      3e-07   30.7   1.7    2.2  2  HTH_31         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.045   13.4   0.0       0.11   12.1   0.0    1.7  1  HTH_50         Helix-turn-helix domain
      0.053   14.0   0.0        4.1    7.9   0.0    2.5  2  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.9e-24   6.9e-21       2     123 .]     190     325 ..     189     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.9e-24
                  Peptidase_M78   2 erlgidvlaldlgakdldgfrfdns...etkvivlnsnhsptrqrftlaHElgHlllhherdkf..reegdskaqerler 76 
                                    e  g+ vla++ g+ ++d  r  ++   e +vivln +++p  + f+l+HE+ H++lh+e+ +    + + s++++ le 
  gi|121638398|ref|YP_978622.1| 190 ETSGVLVLATRGGKVAIDEMRGMCLyfdELPVIVLNGSDHPRPRLFSLLHEFVHVVLHTEGLCDviADAHPSTQDRSLEA 269
                                    6789******************999************************************999**************** PP

                  Peptidase_M78  77 eanafAaelllPeeaflalaatqrkdlee.........rlaeyfgVSkeavavrls 123
                                     +na+Aa++l+P + ++a+ +   + ++           +a++fgVS ea+ +rls
  gi|121638398|ref|YP_978622.1| 270 RCNAIAAAVLMPADVVRARPEVIVRSETPsswdyeslrPVAAHFGVSAEAFLRRLS 325
                                    ******************************************************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.3e-11   1.2e-07       1      54 [.      29      82 ..      29      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.3e-11
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                   l+ +R+  gl+   +A+klG++   ++++E Ge  P++  l k a++++ sl+ 
  gi|121638398|ref|YP_978622.1| 29 LRWARESCGLTEVAAARKLGLPDDRVAAWEVGEVVPTIAQLRKAAEVYKRSLAV 82
                                   799**********************************************99975 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.7   8.3e-11     3e-07       5      55 ..      28      77 ..      26      82 .. 0.95
   2 ?   -2.8   0.0       2.3   8.3e+03      20      28 ..     309     317 ..     305     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.3e-11
                         HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                    Lr++Re +GL+  ++A+ lg+  +++  +E G+  +p+ a+l+++a+++ 
  gi|121638398|ref|YP_978622.1| 28 VLRWARESCGLTEVAAARKLGLPDDRVAAWEVGEV-VPTIAQLRKAAEVYK 77
                                   7**********************************.7************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                         HTH_31  20 vAerlgvse 28 
                                    vA++ gvs+
  gi|121638398|ref|YP_978622.1| 309 VAAHFGVSA 317
                                    788888875 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.2e-05      0.11      23      49 ..     303     329 ..     301     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                         HTH_50  23 YpStRklAkrLGvShtaianklrkYgI 49 
                                    Y S R +A++ GvS  a +++l   gI
  gi|121638398|ref|YP_978622.1| 303 YESLRPVAAHFGVSAEAFLRRLSTLGI 329
                                    9*********************98888 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0011       4.1      17      39 ..      57      79 ..      51      88 .. 0.84
   2 ?    3.3   0.0     0.032   1.1e+02      11      68 ..     318     376 ..     315     396 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                    GlutR_dimer 17 lkslevvptIkalrekaeeiree 39
                                   ++  evvptI++lr+ ae ++++
  gi|121638398|ref|YP_978622.1| 57 WEVGEVVPTIAQLRKAAEVYKRS 79
                                   56679*************98875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHS-S..--------TTHHHHHHHH CS
                    GlutR_dimer  11 eefeawlkslevvptIkalrekaeeir..eeeleralkklaldgedreelekltrslvnk 68 
                                    e+f++ l +l++vp+ +  +++ae i+  e+e era++  +  +  r+++++l ++ v+ 
  gi|121638398|ref|YP_978622.1| 318 EAFLRRLSTLGIVPVEVYRQRRAEFIAahEDEAERARSAGG-GNWYRNTVRDLGKGYVRA 376
                                    789999****9988766666666655511677888887766.555555566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2937.12
//
Query:       gi|121638399|ref|YP_978623.1|  [L=267]
Description: hypothetical protein BCG_2537c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00019   20.9   0.0    0.00044   19.7   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
    0.00082   19.1   0.0      0.002   17.9   0.0    1.6  1  HTH_23          Homeodomain-like domain
     0.0034   17.5   0.0     0.0069   16.5   0.0    1.5  1  HTH_17          Helix-turn-helix domain
      0.007   16.2   0.0      0.016   15.0   0.0    1.7  1  MarR_2          MarR family
     0.0071   16.3   0.0      0.015   15.2   0.0    1.5  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.061   13.2   0.0    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.073   12.9   0.0       0.16   11.9   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.091   13.1   0.3       0.86    9.9   0.0    2.3  2  KORA            TrfB plasmid transcriptional repressor
      0.094   12.8   0.0        1.7    8.8   0.0    2.2  2  Sigma70_r3      Sigma-70 region 3
       0.11   12.3   0.0       0.27   11.1   0.0    1.6  2  HTH_10          HTH DNA binding domain
       0.13   12.0   0.0       0.23   11.2   0.0    1.4  1  Sigma70_r4_2    Sigma-70, region 4
       0.13   11.9   0.0       0.31   10.6   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     3e-07   0.00044      21      43 ..      98     120 ..      92     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
                                    --HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4  21 lTleEIgerlgiSrerVrqiekr 43 
                                    ++ +EI+++lg+Sr rV+q+ + 
  gi|121638399|ref|YP_978623.1|  98 MSAAEIADELGVSRQRVHQLRST 120
                                    7889***************9765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06     0.002       6      40 ..      87     120 ..      83     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                         HTH_23   6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkr 40 
                                     R+++       +s +eIA+eLgvsr+ v + +++
  gi|121638399|ref|YP_978623.1|  87 LRAEAFTTPE-LMSAAEIADELGVSRQRVHQLRST 120
                                    5555555555.899****************99987 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.6e-06    0.0069       1      34 [.      97     133 ..      97     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                         HTH_17   1 lltveEaAelLgvsrstvyrlirrgelpaa..k.iGr 34 
                                    l++ +E+A+ Lgvsr+ v++l+++  +pa     +G+
  gi|121638399|ref|YP_978623.1|  97 LMSAAEIADELGVSRQRVHQLRSTAGFPAPlaDlRGG 133
                                    799*********************9996545424444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.016      22      41 ..      97     117 ..      47     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                    E.EHHHHHHHHTSSHHHHHHH CS
                         MarR_2  22 l.tvgelarrlglsksavsri 41 
                                    l +++e+a++lg+s+++v+++
  gi|121638399|ref|YP_978623.1|  97 LmSAAEIADELGVSRQRVHQL 117
                                    449***************985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     1e-05     0.015      15      33 ..      96     115 ..      90     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                         HTH_11  15 p.isgeeLAeeLnvSrrtvr 33 
                                      +s++e+A+eL+vSr+ v+
  gi|121638399|ref|YP_978623.1|  96 ElMSAAEIADELGVSRQRVH 115
                                    449*************9887 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.1e-05     0.061      18      35 ..      98     115 ..      97     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                  HTH_AsnC-type  18 isyaeLAervGlSestvl 35 
                                    +s ae+A+++G+S+++v+
  gi|121638399|ref|YP_978623.1|  98 MSAAEIADELGVSRQRVH 115
                                    699**************8 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      10      37 ..      99     125 ..      95     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                 YdaS_antitoxin  10 gqkaLAealgvsqqaVsqWlkgkkqvpa 37 
                                    ++++ A++lgvs+q V+q+ + + ++pa
  gi|121638399|ref|YP_978623.1|  99 SAAEIADELGVSRQRVHQLRS-TAGFPA 125
                                    78999**************75.455665 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00058      0.86      34      51 ..     100     117 ..      96     121 .. 0.88
   2 ?    0.4   0.1      0.53   7.9e+02      55      70 ..     135     150 ..     132     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00058
                           KORA  34 qadvatelgltkqavsqa 51 
                                     a++a+elg+++q+v q+
  gi|121638399|ref|YP_978623.1| 100 AAEIADELGVSRQRVHQL 117
                                    589************997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.53
                           KORA  55 vwaahaereepagler 70 
                                    vw+a+a r +++ +er
  gi|121638399|ref|YP_978623.1| 135 VWDAAAVRRFAETWER 150
                                    9*************97 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.7      22      41 ..      99     118 ..      96     124 .. 0.89
   2 ?    1.5   0.0      0.22   3.3e+02      25      44 ..     201     220 ..     199     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                    XHHHHHHHHTXXHHHHHHHH CS
                     Sigma70_r3  22 tpeEiAeeLglseekVrevl 41 
                                    +++EiA+eLg+s ++V+++ 
  gi|121638399|ref|YP_978623.1|  99 SAAEIADELGVSRQRVHQLR 118
                                    579**************986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                                    HHHHHHTXXHHHHHHHHHHH CS
                     Sigma70_r3  25 EiAeeLglseekVrevleaa 44 
                                    +iAe ++++++++  +++ +
  gi|121638399|ref|YP_978623.1| 201 DIAEDVEIDLSRIDAITRNV 220
                                    7************9998765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.27      20      42 ..      94     116 ..      92     121 .. 0.86
   2 ?   -2.7   0.0       3.7   5.6e+03      27      50 ..     200     223 ..     199     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                         HTH_10  20 yPRrvtlkeLAkelGIskstlse 42 
                                    +P  ++++e+A+elG+s++ +++
  gi|121638399|ref|YP_978623.1|  94 TPELMSAAEIADELGVSRQRVHQ 116
                                    6777899************9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                         HTH_10  27 keLAkelGIskstlsehLrkaesk 50 
                                    +++A++  I  s +  + r++ +k
  gi|121638399|ref|YP_978623.1| 200 DDIAEDVEIDLSRIDAITRNVPKK 223
                                    689999888777776666666555 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.23      27      46 ..      98     117 ..      96     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                    --HHHHHHHHT--HHHHHHH CS
                   Sigma70_r4_2  27 lsykEIAellgisegtVksr 46 
                                    +s +EIA +lg+s + V + 
  gi|121638399|ref|YP_978623.1|  98 MSAAEIADELGVSRQRVHQL 117
                                    899************99886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.31      18      36 ..      98     116 ..      94     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                         HTH_24  18 isqreLAerlglSpstvnr 36 
                                    +s +e+A++lg+S++ v++
  gi|121638399|ref|YP_978623.1|  98 MSAAEIADELGVSRQRVHQ 116
                                    7899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1981.24
//
Query:       gi|121638400|ref|YP_978624.1|  [L=83]
Description: hypothetical protein BCG_2538c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.054   13.4   0.0       0.06   13.3   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-06      0.06      46     112 ..       3      76 ..       1      79 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                                    HHHHHHHHHHHHTS-EEEEEEEEEEGGGTTTBGGGTTTTTHTTCHHHHHHHHHHHHCTH........TTS--EEE CS
                     Ham1p_like  46 nalkKaraaaeaglpvladDsgLevdaLnglPGvysarfagegaedeenlaklleelee........eeedrsAr 112
                                     a++K  ++a+++++++ dD + +   +n   Gvy+arf  + +++ ++++ ll +l++        ++++r+A+
  gi|121638400|ref|YP_978624.1|   3 SAIIKIAKWAQSQQWTVEDDASGYTRFYN-PQGVYIARFPATPSNEYRRMRDLLGALKKagltwpppSKKERRAQ 76 
                                    58899999998777677777777777665.88*******888888899********9988777776433556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 666.53
//
Query:       gi|121638401|ref|YP_978625.1|  [L=408]
Description: lipoprotein lppS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-67  225.6   0.1    6.5e-67  225.0   0.1    1.3  1  Big_10    Bacterial Ig domain
    3.1e-16   60.1   0.7    6.6e-16   59.0   0.7    1.5  1  YkuD      L,D-transpeptidase catalytic domain
    1.2e-05   26.0   0.0     0.0047   17.6   0.0    2.7  2  Big_5     Bacterial Ig-like domain


Domain annotation for each model (and alignments):
>> Big_10  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.1   1.1e-70   6.5e-67       2     182 .]      71     250 ..      70     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 1.1e-70
                         Big_10   2 kdvkpeepvtvtvedgkLtevsltdeeGkevegelsadktsWtsteklgygttYtltakakdadgkavektssftTvapa 81 
                                     +v++++pv+vt++dg L +v++++++G++v+g+ls+d+  W++te+lgy+++Ytl+a+a + +g a +++ +f+T +pa
  gi|121638401|ref|YP_978625.1|  71 VGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAA-TRQLTFQTSSPA 149
                                    6899**********************************************************99998.69********** PP

                         Big_10  82 ktvsatltpedgstvGvgqpisikFdkpvedkaavekalkvttspavegafaWlsdsevdwRpkeYwkpgtkVtvkakly 161
                                    + ++ +++p+dg++vGvg+p++i+Fd++++d+ a+eka+k+tt+p+vegaf+Wl+++ev+wRp+++wkpgt V+v +++y
  gi|121638401|ref|YP_978625.1| 150 HLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTY 229
                                    ******************************************************************************** PP

                         Big_10 162 gvelgdgvygkedksvsftiG 182
                                    gv+lg+g++g+++++++ftiG
  gi|121638401|ref|YP_978625.1| 230 GVDLGEGMFGEDNVQTHFTIG 250
                                    ********************9 PP

>> YkuD  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.7   1.1e-19   6.6e-16       9     146 .]     260     377 ..     252     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.1e-19
                                    TTTEEEEEEETTEEEEEEE-BEBTTS.TTSE---EEEEECEEEEEEE..EEGGGGT--TTSTT.EEEEEEEECCCTTCEC CS
                           YkuD   9 aeqrllvlyengklvlsfpvsvGgkkegdreTPlGtfrikskvrnptwnvppsiarkeiypklrkdpeyldkknskvalg 88 
                                    ++ ++l++  ng++v+s+p+s+G k+  +++T +G + ++   ++ +  +++s  ++ + +  ++ ++ +d         
  gi|121638401|ref|YP_978625.1| 260 NT-KILTVRVNGEVVKSMPTSMG-KD--STPTANGIYIVG---SRYKHIIMDSSTYGVPVNSPNGYRTDVD--------- 323
                                    44.7788888*************.55..9***********...3333335666666666666666777777......... PP

                                    CCCEEE-STTS-EEEE.ETCSS...CT..HHC.BSSSEEE-HHHHHHHHHHHHTTEEEEE CS
                           YkuD  89 kvkfvfpngsgiyiHgtgapdlfergk..garrShGCirlseedakelyelvlvgtpvvi 146
                                      ++ + + sg+++H  +ap+  +     +++ ShGC ++s+++a+++y+ v++g+ v++
  gi|121638401|ref|YP_978625.1| 324 --WATQISYSGVFVH--SAPWSVG--AqgHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEV 377
                                    ..578889999****..6665432..1347888***********************9987 PP

>> Big_5  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0044        26      12      85 ..      66     130 ..      59     145 .. 0.73
   2 !   17.6   0.0   7.9e-07    0.0047      10     107 ..     156     248 ..     137     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0044
                          Big_5  12 PadgatgvavnaeitvtFseavdastvtaatvialsdsettavtgsydasgktvtitpsaeLaanttYtvtita 85 
                                     +dga+gv+v+a+++vt    v a+     t++   +  + +v+g    s + +    +++L +n++Yt++ ta
  gi|121638401|ref|YP_978625.1|  66 VTDGAVGVTVDAPVSVTAADGVLAA----VTMV---NDNGRPVAGR--LSPDGLRWSTTEQLGYNRRYTLNATA 130
                                    4688888888888887766555222....2344...5568899999..88889999999999999999998765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.9e-07
                          Big_5  10 tsPadgatgvavnaeitvtFseav.dastvtaatvialsdsettavtgs.ydasgktvtitpsaeLaanttYtvtitagi 87 
                                    + P dg++ v v +++ ++F+e++ d +  ++a++i+    ++ +v+g  y  ++++v  +p+  ++++t   v +++  
  gi|121638401|ref|YP_978625.1| 156 VMPGDGEV-VGVGEPVAIRFDENIaDRGAAEKAIKIT----TNPPVEGAfYWLNNREVRWRPEHFWKPGTAVDVAVNTYG 230
                                    45666665.78889**********7677777777773....355566666789***********************8877 PP

                          Big_5  88 kDlagnalaapytniewsFt 107
                                    +Dl + ++ +++ n++ +Ft
  gi|121638401|ref|YP_978625.1| 231 VDLGE-GMFGED-NVQTHFT 248
                                    78874.244433.3556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2992.95
//
Query:       gi|121638402|ref|YP_978626.1|  [L=492]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-29  100.6  19.0    6.6e-29  100.1  19.0    1.3  1  PE              PE family
  ------ inclusion threshold ------
      0.014   15.8  12.1      0.022   15.2  12.1    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 
      0.022   15.4   0.4       0.12   13.0   0.1    2.6  2  Asp_protease_2  Aspartyl protease


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1  19.0   1.1e-32   6.6e-29       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.1e-32
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Ms ++vaP++la+aaa++++igsalsaanaaaaaptt ++aaa+DeVSaa+Aalf+++++eyq+ls ++a   +qf+qal++
  gi|121638402|ref|YP_978626.1|  1 MSRLIVAPDWLASAAAEVQSIGSALSAANAAAAAPTTLLVAAAEDEVSAAAAALFANYGREYQTLSVRFASLDQQFAQALNS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aa+sY++aEa+
  gi|121638402|ref|YP_978626.1| 83 AAASYQTAEAT 93
                                   *********95 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2  12.1   3.6e-06     0.022       3      97 ..       2      97 ..       1     100 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.6e-06
                  T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraA 83
                                    +L V pd l ++aa+++++ + +++a+aaa a+++  v+     ++aa ++ +a++ +  ++   + a   +++a+ L++A
  gi|121638402|ref|YP_978626.1|  2 SRLIVAPDWLASAAAEVQSIGSALSAANAAAaAPTTLLVAAAEDEVSAAAAALFANYGREYQTLSVRFASLDQQFAQALNSA 83
                                   389**************************9977788888999999************************************* PP

                  T7SS_ESX_EspC 84 AaaYeatDeeaaga 97
                                   Aa Y+ ++ + a+ 
  gi|121638402|ref|YP_978626.1| 84 AASYQTAEATGASL 97
                                   ********999875 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   8.8e+03      23      55 ..      72     103 ..      68     110 .. 0.57
   2 ?   13.0   0.1     2e-05      0.12       4      77 ..     222     297 ..     219     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                 Asp_protease_2  23 ispelaeklglkvreseltvrvsgaggevkarl 55 
                                    +++++a++l+    + + t  ++ga+  ++a  
  gi|121638402|ref|YP_978626.1|  72 LDQQFAQALNSAAASYQ-TAEATGASLVQTATQ 103
                                    56677777766555553.555555555554444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2e-05
                 Asp_protease_2   4 tin.GkpvrfllDTGasttlispela..eklglkvreseltvrvsgaggevkarlvrldslklgg...ltlknvpalvld 77 
                                     +n G +v  llDTG+s+++i+ + +  + lgl++  +    +v   +g + +   +  ++ +gg    t ++v + +l+
  gi|121638402|ref|YP_978626.1| 222 LVNrGPTVPILLDTGSSSLVIPFWKIgwQNLGLPTGFD----VVHYGNGVSIVYADVPTTVDFGGgaaTTPTSVHVGILP 297
                                    577799***************95544449999999886....44554554444333333566666665566666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3897.32
//
Query:       gi|121638403|ref|YP_978627.1|  [L=75]
Description: hypothetical protein BCG_2541c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-18   65.7   5.8    3.8e-18   65.5   5.8    1.1  1  DUF3618        Protein of unknown function (DUF3618)
  ------ inclusion threshold ------
       0.58   10.0   0.1       0.58   10.0   0.1    2.0  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   5.8   4.3e-22   3.8e-18       1      46 [.       3      48 ..       3      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 4.3e-22
                        DUF3618  1 ardpeeIerdIertRaeLaeTvdeLaaradPkrladrakarvkarv 46
                                   +rdp +I+++I++tR++La+T+d+La+ra+P+rlad+ak+rv a++
  gi|121638403|ref|YP_978627.1|  3 DRDPNTIKQEIDQTRDQLAATIDSLAERANPRRLADDAKTRVIAFL 48
                                   69****************************************9987 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   6.4e-05      0.58       6      30 ..       7      31 ..       3      41 .. 0.91
   2 ?   -0.0   1.5     0.086   7.7e+02      71      80 ..      59      68 ..      34      72 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.4e-05
                                   HHHHHHHHCCCCHHCCHHHHCHCCC CS
                  Synaptobrevin  6 akikaevdevkdimkeNidkvlerg 30
                                   ++ik+e+d+++d +   id++ er 
  gi|121638403|ref|YP_978627.1|  7 NTIKQEIDQTRDQLAATIDSLAERA 31
                                   789********************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.086
                                   XXXXXXXXXX CS
                  Synaptobrevin 71 ililvvlili 80
                                    ++ vv++++
  gi|121638403|ref|YP_978627.1| 59 GIGSVVVVVV 68
                                   2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 517.73
//
Query:       gi|121638404|ref|YP_978628.1|  [L=157]
Description: bacterioferritin comigratory protein bcp [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-41  139.5   0.0      6e-41  139.2   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    2.7e-29  101.8   0.0      3e-29  101.6   0.0    1.0  1  Redoxin     Redoxin
    0.00011   21.9   0.0    0.00012   21.7   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
    0.00029   20.9   0.0      0.001   19.2   0.0    1.7  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.031   14.2   0.0    1.5  1  SCO1-SenC   SCO1/SenC
       0.03   13.9   0.0      0.044   13.4   0.0    1.3  1  GSHPx       Glutathione peroxidase


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0     2e-44     6e-41       2     122 ..      10     136 ..       9     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 2e-44
                                    TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                       AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                    gdkap f+l++adg++vsl+dy+g+ v+++fyp++++p+Ct++++++++++ +f+ +g++v+g+s+d+pe+++ f ++++
  gi|121638404|ref|YP_978628.1|  10 GDKAPAFTLPDADGNNVSLADYRGRRVIVYFYPAASTPGCTKQACDFRDNLGDFTTAGLNVVGISPDKPEKLATFRDAQG 89 
                                    9******************************************************************************* PP

                                    .SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEE CS
                       AhpC-TSA  82 lnfpllsDeegkvakaygvlkee......kglalratfvidkegkir 122
                                    l+fpllsD++++v +a+g++ e+       ++ +r+tfv+d++gki+
  gi|121638404|ref|YP_978628.1|  90 LTFPLLSDPDREVLTAWGAYGEKqmygktVQGVIRSTFVVDEDGKIV 136
                                    ***************************99999*************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0     1e-32     3e-29       2     141 ..       9     149 ..       8     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1e-32
                                    TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                        Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefw 80 
                                    +gdkaP+ftlp+   dgn+vsl++++g++v+v+f+p+a +P C+++++ + ++l ++  + g +vv+++ d+ +    f 
  gi|121638404|ref|YP_978628.1|   9 PGDKAPAFTLPD--ADGNNVSLADYRGRRVIVYFYPAASTPGCTKQACdFRDNLGDF-TTAGLNVVGISPDKPEKLATFR 85 
                                    7*********99..**********************************999999999.********************** PP

                                    HHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHTSTT CS
                        Redoxin  81 gkeglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvylevepepetees 141
                                    +++gl+fp+lsD++ ++  a+G++ e++   g      +++++v+dedgk+v  ++ +  ++ ++
  gi|121638404|ref|YP_978628.1|  86 DAQGLTFPLLSDPDREVLTAWGAYGEKQM-YGktvqGVIRSTFVVDEDGKIVVAQYNVKATGHVA 149
                                    **********************9965443.3358889**************99999887643555 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.1e-08   0.00012      83     172 ..      44     136 ..      21     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.1e-08
                         DUF899  83 egCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl. 161
                                    +  pgC+  a ++  +l ++++++++++ +s    ekl+++++  G t+p+ s+ + ++ +  ++  e++ + + ++g+ 
  gi|121638404|ref|YP_978628.1|  44 ASTPGCTKQACDFRDNLGDFTTAGLNVVGISPDKPEKLATFRDAQGLTFPLLSDPDREVLTAWGAYGEKQMYGKTVQGVi 123
                                    4569************************************************************9999999999998887 PP

                         DUF899 162 .svflrdd.grvf 172
                                     s+f+ d+ g++ 
  gi|121638404|ref|YP_978628.1| 124 rSTFVVDEdGKIV 136
                                    7899988866653 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.4e-07     0.001       7      55 ..      61     110 ..      55     128 .. 0.85
   2 ?   -0.6   0.0      0.48   1.4e+03      96     107 ..     126     137 ..     118     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.4e-07
                     AhpC-TSA_2   7 peldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkr 55 
                                     ++  ag ++v+i+ ++p ++ +F++  g  f+l+ Dp++++  a+g + 
  gi|121638404|ref|YP_978628.1|  61 GDFTTAGLNVVGISPDKPeKLATFRDAQGLTFPLLSDPDREVLTAWGAYG 110
                                    567789************55**************************9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.48
                     AhpC-TSA_2  96 tflfdkqgelvy 107
                                    tf++d++g++v 
  gi|121638404|ref|YP_978628.1| 126 TFVVDEDGKIVV 137
                                    899999998875 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.031       3     103 ..      15     109 ..      13     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                      SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleaf 82 
                                     F+l d dg++v+ +d++g+ ++v+f  +  +  C+++  + ++ l ++  ++ +v    + + P  D pe+l+++ +a 
  gi|121638404|ref|YP_978628.1|  15 AFTLPDADGNNVSLADYRGRRVIVYFYPAASTPGCTKQACDFRDNLGDFTTAGLNV----VGISP--DKPEKLATFRDAQ 88 
                                    7*************************988888888888777777777776663333....23333..6677777777776 PP

                      SCO1-SenC  83 dpriigltGskeeiakaakef 103
                                    +  +  l+++  e+ +a  ++
  gi|121638404|ref|YP_978628.1|  89 GLTFPLLSDPDREVLTAWGAY 109
                                    666666666666665555555 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.044       4      59 ..      16      73 ..      14      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                   BEEEBTTSSEEEGGGGTTSEEEEE..EEESSSTTHHHHHHHHHHHHHHGGGTEEEEEE CS
                          GSHPx  4 lsakdidgekvkleklrgkvvliv..nvaskCglteqykeleelqkrykdkglvilgf 59
                                   ++  d dg++v+l  +rg+ v++     as+ g t+q  ++++    ++  gl ++g 
  gi|121638404|ref|YP_978628.1| 16 FTLPDADGNNVSLADYRGRRVIVYfyPAASTPGCTKQACDFRDNLGDFTTAGLNVVGI 73
                                   566789*************988752278**************9999********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1039.48
//
Query:       gi|121638405|ref|YP_978629.1|  [L=470]
Description: hypothetical protein BCG_2543c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-33  114.8   0.8    6.1e-33  114.3   0.8    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    4.2e-19   68.5   0.0    7.9e-19   67.6   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.8   6.8e-37   6.1e-33       1     205 [.     102     457 ..     102     459 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 6.8e-37
                                    EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGak 79 
                                    ll++H Dv+pe++  +w + pf++te+ G+lyGrG++d+k+g++++++a+ a   +g++p+  +++ ++++EE+g+ + +
  gi|121638405|ref|YP_978629.1| 102 LLYAHHDVQPEGDRGQWVSpPFEPTERGGRLYGRGTADDKAGIATHVAAFWA---HGGRPPVGVTVFVEGEEESGSPSLG 178
                                    79********999999*********************************977...78899*************6555555 PP

                                    HHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                  Peptidase_M20  80 allegleerekvdavfelhieepgileagklaigvv............................................ 115
                                     ll+   +r+++ a + ++i ++++++ +  a +v+                                            
  gi|121638405|ref|YP_978629.1| 179 RLLAA--HRDALAADV-IVIADSDNWSTDIPALTVSlrgmadcvvevatldhglhsglwggvvpdaltvlvrllaslhdd 255
                                    55552..456666655.779*******777677777******************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Peptidase_M20 116 ................................................................................ 115
                                                                                                                    
  gi|121638405|ref|YP_978629.1| 256 dgnvavagmhestaarvdypagrvraesglldgvseigtgsvpqrlwakpaitvigidttsvaaasntliprarakisir 335
                                    ******************************************************************************** PP

                                    ..........................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH.. CS
                                    ..........................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                  Peptidase_M20 116 ..........................kvevelleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff.. 166
                                                              +v+v++ e g+p++++ ++p+++a+++a ++++g ++ ++  g  g  ++f+  
  gi|121638405|ref|YP_978629.1| 336 vapggdatahldaveahlrrhapwgaQVTVTRGEVGQPYAIEaSGPVYDAARSAFRQAWGADPIDM--G-MGGSIPFIae 412
                                    *************************87****99***************************555555..5.5556666644 PP

                                    ..TTTE..EEEEEESSG..GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                    ..xxxx..xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 167 ..agip..tvmifgpgs..glaHspnEyvdledlekgikvlarll 205
                                      a+ p  t+++ g ++   +aHs+nE ++l  le+++ + a ll
  gi|121638405|ref|YP_978629.1| 413 faAAFPqaTILVTGVEDpgTQAHSVNESLHLGVLERAATAEALLL 457
                                    4344473244445555456*****************998877666 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   8.8e-23   7.9e-19       2     108 ..     211     360 ..     210     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 8.8e-23
                                    EB-EEEEEEEE..EE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC................................ CS
                      M20_dimer   2 ghkGlaggkit..vkgkagHsg.apgagaNAieklarllaeledeegdia.............................. 48 
                                    +++G+a++ ++  + ++++Hsg  +g +++A++ l+rlla+l+d++g++a                              
  gi|121638405|ref|YP_978629.1| 211 SLRGMADCVVEvaTLDHGLHSGlWGGVVPDALTVLVRLLASLHDDDGNVAvagmhestaarvdypagrvraesglldgvs 290
                                    789********99******************************************************************* PP

                                    ..........TCCTCCCCCEECCE-C...CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
                      M20_dimer  49 .......eerslprttlnvtgiegGs...aknvipdeaeakidiRllpgedpeevleeieeilekeaped 108
                                           ++r +++++++v gi+  s   a+n++ ++a+aki+iR+ pg d+ + l+++e++l+++ap++
  gi|121638405|ref|YP_978629.1| 291 eigtgsvPQRLWAKPAITVIGIDTTSvaaASNTLIPRARAKISIRVAPGGDATAHLDAVEAHLRRHAPWG 360
                                    ************************99*****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2619.70
//
Query:       gi|121638406|ref|YP_978630.1|  [L=130]
Description: 4'-phosphopantetheinyl transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-18   67.1   0.0    1.6e-18   66.9   0.0    1.1  1  ACPS      4'-phosphopantetheinyl transferase superfamily
  ------ inclusion threshold ------
       0.21   11.7   2.9        9.2    6.5   0.1    2.4  2  4PPT_N    4'-phosphopantetheinyl transferase N-terminal domai


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   1.8e-22   1.6e-18       1      96 [.       5     104 ..       5     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.8e-22
                                    EEEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHT.TS-SSS....S--GGG. CS
                           ACPS   1 gvGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKal.gpglrk....lldfks. 74 
                                    gvGiD+++++++ ++v ++g+ ++++ ft+ Er+  + ++++a+ +++a++WaaKEA++Ka+ g  + +    + d+++ 
  gi|121638406|ref|YP_978630.1|   5 GVGIDLVSIPDFAEQVDQPGT-VFAETFTPGERRDASDKSSSAA-RHLAARWAAKEAVIKAWsGSRFAQrpvlPEDIHRd 82 
                                    7********************.77789********998777776.9****************866665545566666669 PP

                                    -EEEE-TTS-EEEE-S-SSEEE CS
                           ACPS  75 ievledstgrptlellseakkk 96 
                                    iev++d +grp+++l +  + +
  gi|121638406|ref|YP_978630.1|  83 IEVVTDMWGRPRVRLTGAIAEY 104
                                    **************76655543 PP

>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6    0.0024        21      15      30 ..      47      62 ..      37      81 .. 0.71
   2 ?    6.5   0.1     0.001       9.2      52      67 ..     110     125 ..      92     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0024
                         4PPT_N 15 aeFlaGRicAraalar 30
                                   a +la+R++A++a  +
  gi|121638406|ref|YP_978630.1| 47 ARHLAARWAAKEAVIK 62
                                   5678999999998754 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.001
                         4PPT_N  52 lvgSIsHtdglaaAav 67 
                                    + +S++H+ ++aaA++
  gi|121638406|ref|YP_978630.1| 110 IHVSLTHEGDTAAAVA 125
                                    678***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 937.56
//
Query:       gi|121638407|ref|YP_978631.1|  [L=3069]
Description: fatty acid synthase fas [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     8e-113  376.9   0.0   1.2e-112  376.3   0.0    1.3  1  DUF1729          Domain of unknown function (DUF1729)
    2.9e-41  142.0   1.1    3.4e-35  122.1   0.6    3.7  3  Acyl_transf_1    Acyl transferase domain
    8.7e-39  133.6   0.1    2.8e-38  131.9   0.1    1.9  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    3.3e-31  107.4   0.1    7.7e-31  106.2   0.1    1.7  1  MaoC_dehydratas  MaoC like domain
    2.7e-29  101.6   0.0    7.4e-29  100.2   0.0    1.8  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      4e-24   85.2   2.7    1.1e-23   83.8   2.7    1.8  1  DNA_pol_B_N      DNA polymerase beta N-terminal domain
      2e-05   25.0   0.0    4.8e-05   23.8   0.0    1.6  1  Fas_alpha_ACP    Fatty acid synthase subunit alpha Acyl carri
    2.9e-05   23.8   0.0    5.4e-05   22.9   0.0    1.3  1  FAS_I_H          Fatty acid synthase type I helical domain
    0.00042   19.8   0.4      0.003   17.0   0.1    2.5  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
       0.12   12.6   0.3       0.78    9.9   0.0    2.4  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> DUF1729  Domain of unknown function (DUF1729)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.3   0.0  6.9e-116  1.2e-112       1     353 []     561     898 ..     561     898 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.3 bits;  conditional E-value: 6.9e-116
                        DUF1729   1 piilqwtggraGGHHSledleaplletYakiRkqkNvvlvvGsGlgdaedsieyltGeWskelglppmPvdgillgsavm 80 
                                    p+i+ ++ggraGGHHS+edl+++ll+tY+++R ++N+ ++vG+G+g++ +++eyl+G W++++g p mP+dgil+g+a+m
  gi|121638407|ref|YP_978631.1| 561 PVIMHVEGGRAGGHHSWEDLDDLLLATYSELRSRANITVCVGGGIGTPRRAAEYLSGRWAQAYGFPLMPIDGILVGTAAM 640
                                    69****************************************************************************** PP

                        DUF1729  81 vakEaktseevkqlivetpGvkdeeWeatykkpaGgvvsvrSelgepihkianraaklwkeldetifsleavekrkaale 160
                                    ++kE++ts +vk+++v+t+G   ++W ++ +k +Gg+ s rS+lg++ih+i+n+a+++ ++lde+++++eav++r     
  gi|121638407|ref|YP_978631.1| 641 ATKESTTSPSVKRMLVDTQGT--DQWISA-GKAQGGMASSRSQLGADIHEIDNSASRCGRLLDEVAGDAEAVAER----- 712
                                    ********************9..99**99.9**************************************999999..... PP

                        DUF1729 161 kkrdeiierlnkdyakpwfavdeegelveleemtYsevvrRlveLaflksr.........kewidpswkklfqdllqrve 231
                                      rdeii+++ k+ akp+f     g+   +++mtY +++rR+veLa  + +         + w+  +w+ +f+++lqr+e
  gi|121638407|ref|YP_978631.1| 713 --RDEIIAAMAKT-AKPYF-----GD---VADMTYLQWLRRYVELAIGEGNstadtasvgSPWLADTWRDRFEQMLQRAE 781
                                    ..***********.*****.....88...9***************97543211112222268****************** PP

                        DUF1729 232 eRltaeehgeaesllesvealedPaeavetllaaypsaeaqlltaeDvawflqlvqrrgiKPvpFvPvldedfeaffkkd 311
                                    +Rl++++ g++++l+++   l++P++a+++lla yp+ae+ +l++ Dv +f++l++  g KPv+FvPv+d+d++++++ d
  gi|121638407|ref|YP_978631.1| 782 ARLHPQDFGPIQTLFTDAGLLDNPQQAIAALLARYPDAETVQLHPADVPFFVTLCKTLG-KPVNFVPVIDQDVRRWWRSD 860
                                    ***********************************************************.******************** PP

                        DUF1729 312 slwqsedldavvdqdaqrviilqgpvavryitkvdepvkeil 353
                                    slwq++d ++    da+ v+i++g+++v++it++depv+e+l
  gi|121638407|ref|YP_978631.1| 861 SLWQAHDARY----DADAVCIIPGTASVAGITRMDEPVGELL 898
                                    **********....**************************97 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2   0.00012      0.21      54     172 ..     107     250 ..      45     267 .. 0.75
   2 !  122.1   0.6   1.9e-38   3.4e-35       1     205 [.    1333    1536 ..    1333    1549 .. 0.92
   3 ?    4.6   0.0     0.011        19     262     299 ..    1560    1603 ..    1542    1620 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                    TGGGSHHHHHHHHHHHHHHHHHHHHHTT.....-TTSEEEE-TTHHHH..HHHHCCS........SSHHHHHHHHHHHHH CS
                  Acyl_transf_1  54 glldaiqfvqpaLaavqialaellkskG.....vrpaavvGHSlGElA..aavvaga........lsseeallavvlrsr 118
                                      l++  ++ p++ + qia++  l  +G       p a++GHS+G lA  a+ + ga          ++ a+  +v r+r
  gi|121638407|ref|YP_978631.1| 107 KHLTSAAVSVPGVLLTQIAATRALARQGmdlvaTPPVAMAGHSQGVLAveALKAGGArdvelfalAQLIGAAGTLVARRR 186
                                    5788889999******************9998667899*******99855555555433332222456778888899999 PP

                                    HHHHHTS-EECCEECS...........HHHHHHH..TT....EEEEEEECCCCECCEEHHHHHHHHH CS
                  Acyl_transf_1 119 lmmqlagpgdmaavel..........aeeeeklrcqddv...vgavansprrvvisgsqealrelve 172
                                     +  l     m +v++          +e  + +r+   v   v+++ n+ r vvi+g++e+l+++  
  gi|121638407|ref|YP_978631.1| 187 GISVLGDRPPMVSVTNadperigrllDEFAQDVRT---VlppVLSIRNGRRAVVITGTPEQLSRFEL 250
                                    88888777789999996554443333333333332...23447899****************99855 PP

  == domain 2  score: 122.1 bits;  conditional E-value: 1.9e-38
                                     EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--T.............TGGGSHHHHHHH CS
                  Acyl_transf_1    1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpe.............glldaiqfvqpa 65  
                                     v+ f+GqG Q +GMGme  + ska+++v++ ad+  +++ gfsvl+v+r+np+             g l  +qf+q+a
  gi|121638407|ref|YP_978631.1| 1333 VYAFPGQGIQHKGMGMEVRARSKAARKVWDTADKFTRDTLGFSVLHVVRDNPTsiiasgvhyhhpdGVLYLTQFTQVA 1410
                                     799*************************************************************************** PP

                                     HHHHHHHHHHHHHHTT..-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHH CS
                  Acyl_transf_1   66 LaavqialaellkskG..vrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeekl 141 
                                     +a v  a+++ ++ +G  v+ a+  GHS+GE+ a++  + + + eall++v+ ++ +m+  +p+d++++++       
  gi|121638407|ref|YP_978631.1| 1411 MATVAAAQVAEMREQGafVEGAIACGHSVGEYTALACVTGIYQLEALLEMVFHRGSKMHDIVPRDELGRSN------- 1481
                                     ***********************************************************************....... PP

                                     H..TT.EEEEEEECCCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHH CS
                  Acyl_transf_1  142 rcqddvvgavansprrvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasa 205 
                                           +  +a+ p+++ +    + + ++v+ +++ + g   e+vn++    q++ ++ ++ ++
  gi|121638407|ref|YP_978631.1| 1482 ------YRLAAIRPSQIDL--DDADVPAFVAGIAEST-GEFLEIVNFNLRGSQYAIAGTVRGLE 1536
                                     ......8888888888655..4677888888888888.88888888888888888887777655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.011
                                     CEECSSSSCCHCCCCCCCHH......GGG-TCCCCCCTEETTSS CS
                  Acyl_transf_1  262 fveispHslllaalektlks......aedvksatlvGklkrdlt 299 
                                     ++++++Hs +l++++  ++         d+ +  ++G+++++l 
  gi|121638407|ref|YP_978631.1| 1560 GIDVPFHSRVLRVGVAEFRRsldrvmPRDADPDLIIGRYIPNLV 1603
                                     8****************9999999998999***********975 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.1   1.6e-41   2.8e-38      19     251 ..    2575    2806 ..    2563    2808 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 1.6e-41
                                     HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTSTHHHHHHHCTS-HHHHHHHHHH CS
                  ketoacyl-synt   19 veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfldvddfdpeffgispreaeamdpqqrllleaa 96  
                                      ++ w+++++ +++i+ +p+    ++kl   ++ ++g+i+t          fdp+++gis+++a ++d+ + ++++a+
  gi|121638407|ref|YP_978631.1| 2575 DSTDWQVIRKAGTEIR-VPR----KTKL---SRVVGGQIPT---------GFDPTVWGISADMAGSIDRLAVWNMVAT 2635
                                     5789************.9*4....7777...8*********.........8*************************** PP

                                     HHHHHHHTS-HHTC...TTGG.EEEEEEESSTHHHHHHHHHHHTT..GGGSCT.THHHHHSTTHHHHHHHHH.HT--S CS
                  ketoacyl-synt   97 wealedagltpeel...dgsr.vgvfiGvgagdyaalaaldedgs..evkasp.kavgavlanviagrisya.lglrG 166 
                                      +a+ ++g++p+e+    +++ v++++G+g+g  +++++++++++    +  p ++ + vl+n+ia+++ ++ +g +G
  gi|121638407|ref|YP_978631.1| 2636 VDAFLSSGFSPAEVmryVHPSlVANTQGTGMG--GGTSMQTMYHGnlLGRNKPnDIFQEVLPNIIAAHVVQSyVGSYG 2711
                                     *************998844457**********..77888999998563444444466669**********999***** PP

                                     SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TT..SG....GGTTBTTB...- CS
                  ketoacyl-synt  167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag.llspd..gr....ckafdpka...d 234 
                                     +++++++AC++++v v+  v+++r g+a++++aGG + l+ ++ +++ ++a+ + +++  gr    +k+++p++    
  gi|121638407|ref|YP_978631.1| 2712 AMIHPVAACATAAVSVEEGVDKIRLGKAQLVVAGGLDDLTLEGIIGFGDMAAtADTSMmrGRgihdSKFSRPNDrrrL 2789
                                     *************************************88888888888888888888866559999**********9* PP

                                     SB-BB-EEEEEEEEECH CS
                  ketoacyl-synt  235 GfvlGEGvGavvLkrle 251 
                                     Gfv ++G G+++L r +
  gi|121638407|ref|YP_978631.1| 2790 GFVEAQGGGTILLARGD 2806
                                     *************9986 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.1   4.3e-34   7.7e-31       3     119 ..    1199    1317 ..    1197    1321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 4.3e-34
                                     CCCTTSEEEEEEEEEEE.HHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHH.HHHHSTTEGGGE CS
                MaoC_dehydratas    3 qnaigekvetekeitvt.eadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklv.eeelgdnvvarv 78  
                                     +na+++++++++++t+t + d++++a+vsgD+npiH+d+++A +ag++ pI+hGm  +a++  +v +++++ + +ar+
  gi|121638407|ref|YP_978631.1| 1199 ANATDTPRRRRRDVTITaPVDMRPFAVVSGDHNPIHTDRAAALLAGLESPIVHGMWLSAAAQHAVtATDGQARPPARL 1276
                                     578999***********9*************************************877776666505566666***** PP

                                     EEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                MaoC_dehydratas   79 geikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtkev 119 
                                      ++++rF ++V+pgd++++++e+vg +++ ++++v++++++
  gi|121638407|ref|YP_978631.1| 1277 VGWTARFLGMVRPGDEVDFRVERVGIDQGAEIVDVAARVGS 1317
                                     ************************************99876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   4.1e-32   7.4e-29       1     117 [.    2816    2941 ..    2816    2942 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 4.1e-32
                                     SEEEEEEEEEE--STSSSTSTTHHHHHHH.......HHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGG CS
                Ketoacyl-synt_C    1 yavikgsavnsdgahnsltapngeaqara.......iekalaeagvdpedvdyveahgtgtplgDpiElealkkvfge 71  
                                     +av++ +++ +dg h+s++ap   a+ +        +++ala++gv+++dv ++++h+t+t ++Dp+E+e+++++ ++
  gi|121638407|ref|YP_978631.1| 2816 LAVVAFAQSFGDGVHTSIPAPGLGALGAGrggkdspLARALAKLGVAADDVAVISKHDTSTLANDPNETELHERLADA 2893
                                     69************************99999*********************************************** PP

                                     GGG..SCTSEEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C   72 kar..kqplavgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117 
                                      +r   +pl+v S+Ks++GH++++a+v++++ ++++l++gvipp+ +l
  gi|121638407|ref|YP_978631.1| 2894 LGRseGAPLFVVSQKSLTGHAKGGAAVFQMMGLCQILRDGVIPPNRSL 2941
                                     9999999**************************************987 PP

>> DNA_pol_B_N  DNA polymerase beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   2.7   5.9e-27   1.1e-23       1     104 []     935    1037 ..     935    1037 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 5.9e-27
                    DNA_pol_B_N    1 ivlaapdisWaGrlvdnpvarlgdpsewevta...desaeaaatgadldidtdtgedgeglsvplavrsisIpLtvda 75  
                                     +vl+apd+ WaGr+v+npv+r+ dp ew+v +   + +a+++ tga+l    +t+ d+++lsvp+++++++I++t++a
  gi|121638407|ref|YP_978631.1|  935 VVLDAPDVRWAGRTVTNPVHRIADPAEWQVHDgpeNPRATHSSTGARL----QTHGDDVALSVPVSGTWVDIRFTLPA 1008
                                     599***************************995556678999999998....8888888******************* PP

                    DNA_pol_B_N   76 saatgavPvVdrerleaamreLlagaAGv 104 
                                     ++++g++Pv+ +e++  amr +la+aAGv
  gi|121638407|ref|YP_978631.1| 1009 NTVDGGTPVIATEDATSAMRTVLAIAAGV 1037
                                     ****************************8 PP

>> Fas_alpha_ACP  Fatty acid synthase subunit alpha Acyl carrier domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.7e-08   4.8e-05       2     124 ..    1770    1896 ..    1769    1906 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.7e-08
                  Fas_alpha_ACP    2 DepvkavdivraivaqklkkkldevplsksikdlvgGkStlqNEilgdLqaEfg.slpekaedlpleelaea...lqe 75  
                                     D   +a+d   a++a + k ++d+++   si ++++G S  +N +l dL++E++  + ++a +  l+ l ++   l +
  gi|121638407|ref|YP_978631.1| 1770 DLVFDAADATLALIALSAKMRIDQIEELDSIESITDGASSRRNQLLVDLGSELNlGAIDGAAESDLAGLRSQvtkLAR 1847
                                     66778999********************************************98347899999999999776111566 PP

                  Fas_alpha_ACP   76 sfsGklGkqssslis.rlvsskmpggfnlaairkyLekrwglgpgrqdsv 124 
                                     +++   G + s  i+ +l +   p+g    ai ++++k+w lg+g ++ v
  gi|121638407|ref|YP_978631.1| 1848 TYKP-YGPVLSDAINdQLRTVLGPSGKRPGAIAERVKKTWELGEGWAKHV 1896
                                     8876.566666666516777778********************9977665 PP

>> FAS_I_H  Fatty acid synthase type I helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     3e-08   5.4e-05      41      88 ..    2006    2053 ..    1998    2070 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3e-08
                        FAS_I_H   41 qaeLdlweaEhgdeylkgikpiFdakKaRrydSaWNwarqdilklyyd 88  
                                     ++ +dl++aE g ++ + + p+Fd+kKa ++d  W  ar+d++kl+  
  gi|121638407|ref|YP_978631.1| 2006 SELIDLVTAELGADWPRLVAPVFDPKKAVVFDDRWASAREDLVKLWLT 2053
                                     4668*****************************************984 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.57     1e+03      65      93 ..     494     522 ..     492     535 .. 0.81
   2 !   17.0   0.1   1.7e-06     0.003       2      73 ..    2118    2195 ..    2117    2200 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.57
                                    HHHHHHHHHHHSSESEEEE---SS--SSG CS
                      adh_short  65 ealvekavkklgkldvLvnNAGitgsgpf 93 
                                    ++lv+ka++    +d +v  AGi    ++
  gi|121638407|ref|YP_978631.1| 494 KRLVQKARQSGAAIDGVVISAGIPDLDEA 522
                                    6899*******************554444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.7e-06
                                     EEEEESTTSH.HHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT....TSEEEEEE-TTTSHHHHHHHHHHHHH CS
                      adh_short    2 vvlvtGassG.IGraiakelakeGakvvv.vdrseekleevakelkee....gakalaiqvDvtdreevealvekavk 73  
                                     v++vtGas+G I   ++ +l+  Ga+v++ +++ +e+  + +  l ++    ga ++ ++++++++++v+alve++  
  gi|121638407|ref|YP_978631.1| 2118 VAVVTGASKGsIAASVVARLLDGGATVIAtTSKLDEERLAFYRTLYRDharyGAALWLVAANMASYSDVDALVEWIGT 2195
                                     89*******99******************866666666677777666556778899******************9965 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   1.9e+03      72     131 ..    1114    1171 ..    1089    1172 .. 0.72
   2 ?    9.9   0.0   0.00043      0.78      17      98 ..    1218    1297 ..    1206    1313 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                MaoC_dehydrat_N   72 lsrllhgeqefey.hepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131 
                                     l  l+h++   ++  +   +  +lt++++ a   d   ++++ ++ v  +vt ++G ++at
  gi|121638407|ref|YP_978631.1| 1114 LLSLVHLDHAARVvGQLPTVPAQLTVTATAANATD---TDMGRVVPVSVVVTGADGAVIAT 1171
                                     66677777666663444456667777777777777...48999999999999999999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00043
                MaoC_dehydrat_N   17 eavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhepiraGDel 94  
                                      + r fa   g+ np+++d++aa  ag +s+i+  + l+++a +a  ++     + +rl+  + + ++  ++r+GDe+
  gi|121638407|ref|YP_978631.1| 1218 VDMRPFAVVSGDHNPIHTDRAAALLAGLESPIVHGMWLSAAAQHAVTATDGQARPPARLV--GWTARFLGMVRPGDEV 1293
                                     57899*********************************9999999444455556677777..4556778999999999 PP

                MaoC_dehydrat_N   95 ttes 98  
                                      ++ 
  gi|121638407|ref|YP_978631.1| 1294 DFRV 1297
                                     8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3069 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.31u 0.27s 00:00:01.58 Elapsed: 00:00:00.48
# Mc/sec: 19333.04
//
Query:       gi|121638408|ref|YP_978632.1|  [L=240]
Description: hypothetical protein BCG_2546c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-42  146.0   2.4    1.9e-42  145.7   2.4    1.1  1  DUF1906     Domain of unknown function (DUF1906)
     0.0004   20.1   0.7     0.0004   20.1   0.7    3.3  4  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> DUF1906  Domain of unknown function (DUF1906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   2.4   2.1e-46   1.9e-42       2     197 ..      53     230 ..      52     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 2.1e-46
                        DUF1906   2 alkasgyravgrYlsgaersnrack.qknltaeevqdilaaGlrlvpiyqggqdeaadftaaaaqGvadAkdAvaaasal 80 
                                    +++a+g  +++rY+s++ r+  a++ +k+++ +e++d+  +Gl++v++yq+g+ ++ad+  +a++Gv++A+++ + ++a+
  gi|121638408|ref|YP_978632.1|  53 QIRAAGAVGAIRYVSDR-RPGGAWMlGKPIQLSEARDLSGNGLKIVSCYQYGKGSTADWLGGASAGVQHARRGSELHAAA 131
                                    6899************5.77789********************************************************* PP

                        DUF1906  81 GfpagttIYfaVDldaydseikaavlpYfkgwkealnakgykvGvYgsrnvckfvsdmstgfsgnlydlpdnwageaatt 160
                                    G+p++++IY+++D++++ +++k++++pY+++w++++++  +++GvY+++++++                   wa +++++
  gi|121638408|ref|YP_978632.1| 132 GGPTSAPIYASIDDNPSYEQYKNQIVPYLRSWESVIGH--QRTGVYANSKTID-------------------WAVNDGLG 190
                                    *************************************9..***********99...................******** PP

                        DUF1906 161 edlpatdw.......aphqrihQyeedvtetsggvtiigiDrda 197
                                    +++++++w       +p++++hQ+e+d+++  gg   +g+D + 
  gi|121638408|ref|YP_978632.1| 191 SYFWQHNWgspkgytHPAAHLHQVEIDKRK-VGG---VGVDVNQ 230
                                    **************************8765.455...4888875 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   4.5e-08    0.0004       2      25 ..       3      26 ..       2      27 .. 0.90
   2 ?   -4.0   1.2       1.8   1.6e+04      18      22 ..      33      37 ..      30      41 .. 0.39
   3 ?    0.2   0.4     0.087   7.8e+02      10      16 ..      56      62 ..      54      63 .. 0.65
   4 ?   -3.0   1.2      0.89     8e+03      18      24 ..     129     135 ..     129     137 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-08
                     TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                   +SRRd LK +AA+   ++lg +a+
  gi|121638408|ref|YP_978632.1|  3 VSRRDVLKFAAATPGVLGLGVVAS 26
                                   8******************98776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.8
                     TAT_signal 18 aalgg 22
                                   a +g+
  gi|121638408|ref|YP_978632.1| 33 ASAGS 37
                                   22333 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.087
                     TAT_signal 10 gsAAaaA 16
                                   +++A++A
  gi|121638408|ref|YP_978632.1| 56 AAGAVGA 62
                                   6666666 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 0.89
                     TAT_signal  18 aalggca 24 
                                    aa+gg++
  gi|121638408|ref|YP_978632.1| 129 AAAGGPT 135
                                    5566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 1275.74
//
Query:       gi|121638409|ref|YP_978633.1|  [L=75]
Description: hypothetical protein BCG_2547 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-08   33.3   5.3    4.8e-08   32.8   5.3    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
    0.00068   20.0   1.2    0.00087   19.7   1.2    1.2  1  CcdA            Post-segregation antitoxin CcdA
     0.0033   18.2   7.9     0.0041   17.9   7.9    1.1  1  PSK_trans_fac   Rv0623-like transcription factor
  ------ inclusion threshold ------
        0.2   12.2   2.7       0.21   12.1   0.2    2.0  2  BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   5.3   1.1e-11   4.8e-08       1      42 [.       4      44 ..       4      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-11
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------H CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkre 42
                                   +rt+Ie+D++L++ A+++tg  t r++V+ AL+ L++ ++ +
  gi|121638409|ref|YP_978633.1|  4 KRTTIELDEDLVRAAQAVTG-ETLRATVERALQQLVAAAAEQ 44
                                   8*****************98.89**************99844 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.2   1.9e-07   0.00087       2      48 ..       4      53 ..       4      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.9e-07
                           CcdA  2 kavnlsldsdllaqAralgiN.lSatleeaLaeevk..eekaerwkeenr 48
                                   k++++ ld+dl++ A+a++   l at+e+aL++ v+  +e+a+++++   
  gi|121638409|ref|YP_978633.1|  4 KRTTIELDEDLVRAAQAVTGEtLRATVERALQQLVAaaAEQAAARRRRIV 53
                                   799**************9875499***********854344444444333 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   7.9   9.1e-07    0.0041      11      58 ..      12      58 ..      11      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.1e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHH CS
                  PSK_trans_fac 11 erlareLarltgeskteAvrrAleerlerlrreraepllerllallrr 58
                                   e+l+r  +++tge++ ++v+rAl++  +   + +a+++++r+ + l+ 
  gi|121638409|ref|YP_978633.1| 12 EDLVRAAQAVTGETLRATVERALQQLVAAAAE-QAAARRRRIVDHLAH 58
                                   689************************99765.444444444443333 PP

>> BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.7e-05      0.21      37      69 ..       4      37 ..       1      38 [. 0.91
   2 ?    0.4   0.2      0.21   9.5e+02       8      23 ..      43      58 ..      39      73 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                 BrnA_antitoxin 37 kkvtlRLDadVleaFka.tGkgwQtriNeaLrky 69
                                   k++t+ LD+d + a +a tG+   + + +aL++ 
  gi|121638409|ref|YP_978633.1|  4 KRTTIELDEDLVRAAQAvTGETLRATVERALQQL 37
                                   799**************99************985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                 BrnA_antitoxin  8 esdlararrakevlpe 23
                                   e+ +ar rr+ + l++
  gi|121638409|ref|YP_978633.1| 43 EQAAARRRRIVDHLAH 58
                                   4445555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1340  (0.0747392); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 418.91
//
Query:       gi|121638410|ref|YP_978634.1|  [L=133]
Description: hypothetical protein BCG_2548 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   25.6   0.1    1.6e-05   25.4   0.1    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     9e-10   1.6e-05      29     121 ..      27     119 ..       5     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9e-10
                                    SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHH........SBHHHHHHHH CS
                            PIN  29 eelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaeeaaeialkyg........llpnDaliaA 99 
                                     +l+++++   E ly +++        a+  ++++  l+a +il   ++i+++++ + + +           + D++ia 
  gi|121638410|ref|YP_978634.1|  27 TDLAICDIGELEWLYSARS--------ATDYDSQQTsLRAYQILRAPSDIFDRVRHLQRDLAhhrgmwhrTPLPDLFIAE 98 
                                    7889999999999999999........6666666666************************9*******99999****** PP

                                    HHHHHT-EEE.ESSTHHHHHHH CS
                            PIN 100 tAkehgikliatfDedfrrvak 121
                                    tA++h++ ++ + D+d +r+a 
  gi|121638410|ref|YP_978634.1|  99 TALHHRAGVL-HHDRDYKRIAV 119
                                    **********.********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 739.78
//
Query:       gi|121638411|ref|YP_978635.1|  [L=306]
Description: restriction system protein mrr [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-37  127.3   0.0    5.6e-37  126.3   0.0    1.5  1  Mrr_cat    Restriction endonuclease
    1.3e-28   99.0   0.0    3.1e-28   97.7   0.0    1.6  1  Mrr_N      Mrr N-terminal domain
    7.7e-11   42.0   0.0    1.3e-10   41.3   0.0    1.3  1  Mrr_cat_2  Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   9.4e-41   5.6e-37       3     115 .]     162     280 ..     160     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 9.4e-41
                                    TT-TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--..TS-B-HHHHHHHHHHCTTS. CS
                        Mrr_cat   3 kmspkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKry..knkvgvkeVqeligalkkrg 77 
                                    ++sp+ Fe+lv +llea+Gy+    ve+t  sgD giD+i+++dplg +ri+vqaKry  ++++g+++++e++gal +++
  gi|121638411|ref|YP_978635.1| 162 TLSPTGFEDLVIRLLEAMGYGragAVERTSASGDAGIDGIISQDPLGLDRIYVQAKRYavDQTIGRPKIHEFAGALLGKQ 241
                                    689*******************************************************7669****************** PP

                                    .SEEEEEESS-B-HHHHHHHHTT-.-EEEE-HHHHHHHH CS
                        Mrr_cat  78 adkgifvttsdftkaAreeaeeln.kieLldgdeLaell 115
                                     d+g+++tts+f++ Areeae++n +ieL+dg +Laell
  gi|121638411|ref|YP_978635.1| 242 GDRGVYITTSSFSRGAREEAERINaRIELIDGARLAELL 280
                                    **********************7669**********997 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.0   5.2e-32   3.1e-28       2      86 ..       7      91 ..       7      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 5.2e-32
                          Mrr_N  2 qelmlplLealadgsehrlkeirervaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGre 83
                                   q+lm+p+L +ladg++++ k+++++++++fgls++era++lpsg+q+++ +rv+W +t++++agll++p+rg++++T++Gr+
  gi|121638411|ref|YP_978635.1|  7 QTLMRPILAYLADGQAKSAKDVIAAMSDEFGLSDDERAQMLPSGRQRTMYDRVHWSLTHMSQAGLLDRPTRGHVQVTDTGRQ 88
                                   789******************************************************************************* PP

                          Mrr_N 84 vlk 86
                                   vlk
  gi|121638411|ref|YP_978635.1| 89 VLK 91
                                   *97 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   2.1e-14   1.3e-10      24     118 ..     190     284 ..     183     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.1e-14
                      Mrr_cat_2  24 rlgkkDtGIDlVake..rkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqkip 101
                                    ++++ D+GID ++++   + ++++ +Q+K+Ya d++i +++i +F +a   k+ ++++ i Tt+++s+ a e  +  ++ 
  gi|121638411|ref|YP_978635.1| 190 TSASGDAGIDGIISQdpLGLDRIY-VQAKRYAVDQTIGRPKIHEFAGALLGKQGDRGVYI-TTSSFSRGAREEAERINAR 267
                                    46789********99766667777.**********************************9.7777*************** PP

                      Mrr_cat_2 102 vkridledLeeseidws 118
                                    +++id ++L+e+ + ++
  gi|121638411|ref|YP_978635.1| 268 IELIDGARLAELLVRYR 284
                                    **********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1744.55
//
Query:       gi|121638412|ref|YP_978636.1|  [L=463]
Description: hypothetical protein BCG_2550 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-09   36.3   0.0      1e-08   35.5   0.0    1.4  1  ERCC4     ERCC4 domain
    2.7e-07   30.7   0.5    6.3e-06   26.3   0.1    2.4  2  Lsr2      Lsr2


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   1.2e-12     1e-08      10     154 ..     283     398 ..     277     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.2e-12
                                    HHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHHHHH.H-S CS
                          ERCC4  10 ieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsrlkrngyk 89 
                                    +++  ++++ ++++ e+lp+gdy  +  kv+   +l            +verk + dl++ + +g l  q+ +l  ++++
  gi|121638412|ref|YP_978636.1| 283 YPYT-FADKPAKTTREALPCGDY-GL--KVAG--QLV----------AAVERKALADLTSGVLNGNLKYQLTEL--AALP 344
                                    5666.8889999***********.55..4554..222..........89*************************..57** PP

                                    EEEEEEES..-GGGTT................THHH.HHHHHHHHHHHH.S-EEEEESSHHHHHHHHH CS
                          ERCC4  90 kpillveg..ldqykrknknsrnkqykakvrqinrktiesaLvqlqldf.gvsilttesanetaewla 154
                                    +  ++ve+  ++ + ++                ++ +i + L++lq+ f +v+i+++++++   e+++
  gi|121638412|ref|YP_978636.1| 345 RAAVVVEDrySEIFAHSF--------------ARPTAIADGLAELQIGFpNVPIVFCQTRKLAQEYTY 398
                                    *******99888888876..............78889***********************99998876 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.025   2.2e+02      32      69 ..     219     257 ..     213     271 .. 0.71
   2 !   26.3   0.1     7e-10   6.3e-06      65     110 .]     415     460 ..     389     460 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.025
                           Lsr2  32 eiDLseenaeklrdaLapyieaarrvggrkk.krrarrk 69 
                                     iD+ ++ a++ r++L + ++ +r+v   ++ k+r++++
  gi|121638412|ref|YP_978636.1| 219 AIDVVAARARENRSQLVHTMARGRQVVFWQSpKTRKQSR 257
                                    5999*********************99554323222222 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7e-10
                           Lsr2  65 rarrkaaaaasreqaaaiReWakengievserGripaevieaYeaA 110
                                    ++  + aaa+++ ++a+ R+Wak+ g++vs+rGr+  ++++a++aA
  gi|121638412|ref|YP_978636.1| 415 TTVFEPAAAEPEPSSAELRAWAKSVGLPVSDRGRLRPQILQAWRAA 460
                                    45556678889999*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3072.58
//
Query:       gi|121638413|ref|YP_978637.1|  [L=139]
Description: hypothetical protein BCG_2551c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   32.4   0.0    1.3e-07   32.1   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   7.5e-12   1.3e-07       2     117 ..       4     128 ..       3     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.5e-12
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEEB CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel..eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkilpi 73 
                                    +lD +vlial   ++++++aa +++ +   + ++t++++ a  +++ ++     ++++   a++ ++++  l+++ ++p 
  gi|121638413|ref|YP_978637.1|   4 LLDVNVLIALGwPNHVHHAAAQRWFTQFssNGWATTPITEAGYVRISSNrsvmqVSTTPAIAIAQLAAMTSLAGHTFWPD 83 
                                    79******9999**************99************9999999999*****************************6 PP

                                    CHHHHHHHHHHHHHHH..SBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                            PIN  74 daeiaeeaaeialkyg..llpnDaliaAtAkehgikliatfDedfr 117
                                    d ++    a  ++  +  +++ D++++A+A ++g +l+ tfD  ++
  gi|121638413|ref|YP_978637.1|  84 DVPLIVGSAGDRDAVSnhRRVTDCHLIALAARYGGRLV-TFDAALA 128
                                    666666666666666699********************.***8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1074.02
//
Query:       gi|121638414|ref|YP_978638.1|  [L=74]
Description: hypothetical protein BCG_2552c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00015   21.6   0.1    0.00025   20.9   0.1    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
       0.07   13.1   1.3       0.07   13.1   1.3    1.7  2  RHH_1           Ribbon-helix-helix protein, copG family
      0.073   13.0   0.0      0.087   12.7   0.0    1.2  1  RHH_4           Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   4.2e-08   0.00025       1      24 [.       1      24 [.       1      26 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.2e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeAirltglktK 24
                                   Mrt++ iDD+ l++A  +++  +K
  gi|121638414|ref|YP_978638.1|  1 MRTTLQIDDDVLEDARSIARSEGK 24
                                   9*****************999888 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   1.2e-05      0.07       1      35 [.       2      36 ..       2      39 .. 0.93
   2 ?   -2.8   0.1       1.2   7.1e+03       8      15 ..      64      71 ..      63      72 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                   r+++ +d+++le  + +ar +g+S++++I e++r+
  gi|121638414|ref|YP_978638.1|  2 RTTLQIDDDVLEDARSIARSEGKSVGAVISELARR 36
                                   89***************************998886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                   HHHHHHHH CS
                          RHH_1  8 eellerLd 15
                                   e+++++L+
  gi|121638414|ref|YP_978638.1| 64 EDVVRALE 71
                                   66777665 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.087      12      47 ..       2      36 ..       1      47 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaeidadr 47
                                   rT++++ + + +  + iAr+eg +v a+i+e+ a+r
  gi|121638414|ref|YP_978638.1|  2 RTTLQIDDDVLEDARSIARSEGKSVGAVISEL-ARR 36
                                   6777777777777789****************.777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 545.88
//
Query:       gi|121638415|ref|YP_978639.1|  [L=947]
Description: amino acid decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-75  252.5   0.0      2e-49  168.5   0.0    2.1  2  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
    5.2e-05   23.6   0.1    0.00024   21.4   0.0    2.1  2  OKR_DC_1_C       Orn/Lys/Arg decarboxylase, C-terminal domain
     0.0098   15.2   0.0      0.017   14.4   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.021   14.0   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
      0.041   14.1   0.3       0.11   12.6   0.3    1.7  1  DUF1380          Protein of unknown function (DUF1380)


Domain annotation for each model (and alignments):
>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0   5.6e-53     2e-49       1     225 [.     290     515 ..     290     526 .. 0.87
   2 !   82.0   0.0   9.7e-27   3.5e-23     226     414 ..     556     747 ..     547     750 .. 0.84

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 5.6e-53
                                    -HHHHHHHHHHHH---SSSS.STTTTTCGGGGSHHHHHHHHHH-HHHHHT---TTTGGGBBTTTTBTHHHHHHHHHHHHC CS
                       OKR_DC_1   1 pPlykaLvkyveegkvsfav.PGHqgGavfkkePagrlfydffGenllraDlsievveLgdLldheGaikeaqkyaarvf 79 
                                    +P+++aL  y+     +f++ P  +g ++f+ +   +   +f+G n++ a+ s+    L++Lld++G ik a + aa ++
  gi|121638415|ref|YP_978639.1| 290 TPFFDALRAYAAAPVGQFHAlPVARGASIFNSK-SLHDMGEFYGRNIFMAETSTTSGGLDSLLDPHGNIKTAMDKAAVTW 368
                                    7*****************972555555555555.666778**************************************** PP

                                    T-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHHHHHH CS
                       OKR_DC_1  80 gadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeeetlke 158
                                    +a+++yfv+nGTs++nk+v++a+  pgd+vl+dRNcHKS + +lvl+ga P+yl +    ++ i g ++l+ ++++ l  
  gi|121638415|ref|YP_978639.1| 369 NANQTYFVTNGTSTANKIVVQALTRPGDIVLIDRNCHKSHHYGLVLAGAYPMYLDAYpLPQYAIYGAVPLRTIKQALLD- 447
                                    ********************************************************9899**********666655553. PP

                                    HHHHSTTTGSESEEEEESS-TTSEEE-HHHHHHHHTTS..ESEEEEE-TT-TTGGGSGGGTTSSSSSSS CS
                       OKR_DC_1 159 kikevpdakaprlavitnsTYdGvlynakeivdklekl..sdrilfDeAwvgyeqfiplyadaskllae 225
                                     +++  + +  r++++tn+T+dGv+yn + +++++  +  ++  l DeAw++++   p   + +++ a 
  gi|121638415|ref|YP_978639.1| 448 -LEAAGQLHRVRMLLLTNCTFDGVVYNPRRVMEEVLAIkpDICFLWDEAWYAFATAVPWARQRTAMIAA 515
                                    .55555666699*********************9875511566788**********9999999998776 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 9.7e-27
                                    -BTTBEEEEEEEHCCCCS--TT-EEEEEES-BT..--HHHHHHHHHHTS-SS--HHHHHHHHHHHHHHSHHHHHHHHHHH CS
                       OKR_DC_1 226 nendpgilvtqSvHKllaalsqaSlihvkeeli..vneerlneafmmhattSpsYpllAsldvaakmlegesgrrlleev 303
                                    n++   +++t+S+HK l+al qaS+ihv+++    + ++++ eaf  h++tSp   llAsld a++ +  ++g +l+++v
  gi|121638415|ref|YP_978639.1| 556 NRARVRVYATHSTHKSLSALRQASMIHVRDQDFkaLTRDAFGEAFLTHTSTSPNQQLLASLDLARRQV-DIEGFELVRHV 634
                                    5666789***********************977789*****************************999.899******** PP

                                    HHHHHHHHHHHHH..........HSSS---.EESS-SEEESTSGEEE-TT-TTT--TT--TTSEEE-TTEEEEE-SSB-T CS
                       OKR_DC_1 304 veraielrkeikr..........ldnaeli.kpvnpevvdekeffklepgekWhgfediadeqyflDPiKlliltPGide 372
                                     + a+ +r+++++          ld++ l+ + + +++v + +  +++ g+     e    +q++lDP++l++ +     
  gi|121638415|ref|YP_978639.1| 635 YNMALVFRHRVRKdrliskwfriLDESDLVpDAFRSSTVSSYR--QVRQGALADWNEAWRSDQFVLDPTRLTLFI----- 707
                                    **********977766666666655555553455555565444..7777766666688999*************5..... PP

                                    TSSB-SS---HHHH.HHHHHHT.T---SEEESSEEEEE--TTS- CS
                       OKR_DC_1 373 dGeleelGvpaaiv.akyLren.givvektdlynilflltlged 414
                                         ++G+ +++  +k+L e+ gi  +kt  +++l+++t+g++
  gi|121638415|ref|YP_978639.1| 708 ----GATGMNGYDFrEKILMERfGIQINKTSINSVLLIFTIGVT 747
                                    ....7899999987368998888******************986 PP

>> OKR_DC_1_C  Orn/Lys/Arg decarboxylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   4.7e+03      15      55 ..     570     612 ..     560     631 .. 0.71
   2 !   21.4   0.0   6.7e-08   0.00024      53     110 ..     825     879 ..     814     892 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                                    -BHHHHHHHHHHHHHHHTHHHHHHHHCCS..--EESS-HHHHH CS
                     OKR_DC_1_C  15 mtlrdLcqemhdlykeakvaelqkeafsk..lpepamtpaeay 55 
                                     +l  L q+ +  ++++++++l+++af +  l +++ +p++  
  gi|121638415|ref|YP_978639.1| 570 KSLSALRQASMIHVRDQDFKALTRDAFGEafLTHTSTSPNQQL 612
                                    5677777777778899999999999999887778888887744 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6.7e-08
                                    HHHHHHHTT-EEEEEGGG-TTSBBSS-BEECTT-S-SB-TTEE--CCCHHHHHHHHHH CS
                     OKR_DC_1_C  53 eayeelvrgevelvpldelegriaaelvlpyPpGipllvpGErlgeeskaildYlkal 110
                                    ea +e+v+      +l+e +  ++++ v+pyPpG p+lvpG  +   sk+i+ +l  l
  gi|121638415|ref|YP_978639.1| 825 EADREYVQIGLAGRRLAEGKTLVSTTFVVPYPPGFPVLVPGQLV---SKEIIYFLAQL 879
                                    566666666666667778888899********************...88888887765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.8e-06     0.017      38     175 ..     361     501 ..     287     542 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-06
                                    HHHHHHHTT-SEEEEES-HH.HHHHHHHHHH--TTEEEEEETT-HHHHSST....THHHHCC--EEEEE-EBTTTBE-HH CS
                Beta_elim_lyase  38 edavaelfgkeaalfvpqGt.aAnsillkillqrgeevivtepahihfdet....gaiaelagvklrdlknkeaGkmdle 112
                                     d++a    ++++ fv++Gt  An+i +++l+++g+ v++++++h   +      ga+  + ++ + + +    G + l 
  gi|121638415|ref|YP_978639.1| 361 MDKAAVTWNANQTYFVTNGTsTANKIVVQALTRPGDIVLIDRNCHKSHHYGlvlaGAYPMYLDAYPLPQYAIY-GAVPLR 439
                                    56666777888999*****9569****************9999664433220112444444555455444444.****** PP

                                    HHHHHS--S-T..TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH CS
                Beta_elim_lyase 113 kleaaikevga..heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa 175
                                     +++a+ + +a     ++++++lt+ +    G v+ +  + e   +a k +i ++ D A +a a 
  gi|121638415|ref|YP_978639.1| 440 TIKQALLDLEAagQLHRVRMLLLTNCTFD--GVVYNPRRVME-EVLAIKPDICFLWDEAWYAFAT 501
                                    **996655444476888999999998877..99998876655.3356677777777777665555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-06     0.021      63     194 ..     366     500 ..     350     519 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                    CHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET....TTTEE-HHHHHHH CS
                  Aminotran_1_2  63 lklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse....edfhldlealeea 138
                                    ++ +++++  v++G++ ++ ++ ++l   pgd +l+++  + s++ +l l+g+  ++   y+         + l  +++a
  gi|121638415|ref|YP_978639.1| 366 VTWNANQTYFVTNGTSTANKIVVQAL-TRPGDIVLIDRNCHKSHHYGLVLAGAYPMYLDAYPLpqyaIYGAVPLRTIKQA 444
                                    55566778889999998888888888.68*************************99999887744442223334444444 PP

                                    HTTHHCTTE..TEEEEEEESS-TTT--B--HHHH.HHHHHHHHHTTEEEEEEETTTTCB CS
                  Aminotran_1_2 139 lkeapegnk..ktkvilvesphNPtGtvatleel.eklldlakkynlllfvDeaYagfv 194
                                    l ++ +  +  +++++l++++   +G+v+++  + e++l+++    +  + Dea  +f+
  gi|121638415|ref|YP_978639.1| 445 LLDLEAAGQlhRVRMLLLTNCT-FDGVVYNPRRVmEEVLAIKP--DICFLWDEAWYAFA 500
                                    4444444445556666666664.36666655543145544444..56666666666666 PP

>> DUF1380  Protein of unknown function (DUF1380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   3.2e-05      0.11      84     134 ..     508     559 ..     502     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                        DUF1380  84 rktvtvpadllatllrtaeqalwkrewaardaglavPesvtrrl.advakvr 134
                                    ++t ++ a+ l+++l tae a   r+w+a   g+   e v +rl  d +++r
  gi|121638415|ref|YP_978639.1| 508 QRTAMIAAERLEQMLSTAEYAEEYRNWCASMDGVDRSEWVDHRLlPDPNRAR 559
                                    57889*************************9999999999888625666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (947 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.25s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 6578.72
//
Query:       gi|121638416|ref|YP_978640.1|  [L=133]
Description: hypothetical protein BCG_2554c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.7    8.7  10.8       0.49   10.4   8.2    1.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   8.2   2.7e-05      0.49      40     108 ..       8      67 ..       2      72 .. 0.86
   2 ?   -2.9   0.0      0.39   7.1e+03      85      85 ..      84      84 ..      75     101 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.7e-05
                Phage_holin_3_6  40 lgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkklkkakplpertieelked 108
                                    +++a+vla++ +l ++v++a++l       +iva ++ + a+ ++++ ++++ +    ++r i++++  
  gi|121638416|ref|YP_978640.1|   8 VVVAAVLAATVVLGAVVCAAYGL-------TIVASAMSIYALGVGAWLYHAIER--LILARRISTVRTA 67 
                                    68999999999999999999999.......99*****************99999..6778888888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.39
                Phage_holin_3_6 85 l 85
                                   l
  gi|121638416|ref|YP_978640.1| 84 L 84
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1002.84
//
Query:       gi|121638417|ref|YP_978641.1|  [L=156]
Description: transcription antitermination protein NusB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-34  116.9   0.0    8.9e-34  116.6   0.0    1.1  1  NusB      NusB family


Domain annotation for each model (and alignments):
>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0     5e-38   8.9e-34       1     132 [.      11     138 ..      11     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5e-38
                                    HHHHHHHHHHHHHHHHH-S-...HHHHHHHHHHHT-.......--HHHHHHHHHHHHHHHHTHHHHHHHHHHTTTT--GG CS
                           NusB   1 skaRelalqalyqveinked...eeekeailqealnklleeedldeedkafltelvkgvlrnleelDeliekllknwple 77 
                                    ++aR+ a+++l++ e+++ +     +++a+l ea       ++   + + ++ ++++gv ++  ++D+li+ +l++w+l+
  gi|121638417|ref|YP_978641.1|  11 HQARKRAVDLLFEAEVRGISaaeVVDTRAALAEA-------KPDIARLHPYTAAVARGVSEHAAHIDDLITAHLRGWTLD 83 
                                    589***********88887753333333333333.......445677899****************************** PP

                                    GS-HHHHHHHHHHHHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHHHHHHHHHH CS
                           NusB  78 rlskvdraiLrlavyellylddvPakvaineavelakkygdeksakFvNgVLrkv 132
                                    rl+ vdraiLr++v+ell+ +dvP+ v+++eav+lak++++++s++FvNgVL++v
  gi|121638417|ref|YP_978641.1|  84 RLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQV 138
                                    *****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1205.43
//
Query:       gi|121638418|ref|YP_978642.1|  [L=187]
Description: elongation factor P [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-26   91.4   0.8    6.3e-26   90.2   0.4    1.9  2  EFP_N           Elongation factor P (EF-P) KOW-like domain
    6.5e-26   89.9   0.1    5.3e-25   86.9   0.0    2.5  3  Elong-fact-P_C  Elongation factor P, C-terminal
    8.1e-22   77.0   0.0    1.4e-21   76.3   0.0    1.4  1  EFP             Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.4   1.1e-29   6.3e-26       2      58 .]       4      60 ..       3      60 .. 0.97
   2 ?   -2.1   0.0      0.67     4e+03      22      30 ..     132     142 ..     131     162 .. 0.55

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.1e-29
                                   GGG--TT-EEEETTEEEEEEEEEEEEETTS--EEEEEEEETTTS-EEEEEEETT-EE CS
                          EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqafvrvklknlrtGakvektfkagdkv 58
                                   + ++k+Glv+ idg+l+++ ef+hvkpGkG afvr+klkn+++G++v+ktf+ag kv
  gi|121638418|ref|YP_978642.1|  4 TADFKNGLVLVIDGQLWTITEFQHVKPGKGPAFVRTKLKNVLSGKVVDKTFNAGVKV 60
                                   89****************************************************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.67
                                    EEEEEEET..T CS
                          EFP_N  22 efehvkpG..k 30 
                                    e+ h+ pG  +
  gi|121638418|ref|YP_978642.1| 132 EVTHTEPGlqG 142
                                    66777777332 PP

>> Elong-fact-P_C  Elongation factor P, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.18   1.1e+03      46      50 ..      60      64 ..      52      75 .. 0.56
   2 ?   -2.9   0.0         1   6.2e+03      34      39 ..     119     124 ..     118     124 .. 0.88
   3 !   86.9   0.0   8.9e-29   5.3e-25       1      56 []     129     184 ..     129     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                                   EETTT CS
                 Elong-fact-P_C 46 vdTrt 50
                                   vdT t
  gi|121638418|ref|YP_978642.1| 60 VDTAT 64
                                   33333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                                    EETT-- CS
                 Elong-fact-P_C  34 VPlFIn 39 
                                    VPl+I+
  gi|121638418|ref|YP_978642.1| 119 VPLYIE 124
                                    9***97 PP

  == domain 3  score: 86.9 bits;  conditional E-value: 8.9e-29
                                    EEEEEEE--SSS--SSSSTTEEEEEETTS-EEEEETT--TT-EEEEETTTTEEEEE CS
                 Elong-fact-P_C   1 VeleVvetepgvkGdtasggtKpatletGaevqVPlFIneGdkIkvdTrtgeYvsR 56 
                                    VeleV++tepg++Gd +s gtKpatl+tGa+++VPlFIn+Gdk+kvd r+g+Y++R
  gi|121638418|ref|YP_978642.1| 129 VELEVTHTEPGLQGDRSSAGTKPATLQTGAQINVPLFINTGDKLKVDSRDGSYLGR 184
                                    89***************99**********************************998 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   2.3e-25   1.4e-21       1      54 []      68     121 ..      68     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.3e-25
                                    EEEEEEEEETTEEEEEETTT--EEEEEHHHHTTGCGG--TT-EEEEEEETTEEE CS
                            EFP   1 remqylYkdgdeyvFMdnetYeqielpkeqlgdaakfLkEgmevtvllyegepi 54 
                                    r+ +ylY+dg+++vFMd+++Yeq+ lp++ +gdaa+fL Egm v+v +++g p+
  gi|121638418|ref|YP_978642.1|  68 RDTTYLYRDGSDFVFMDSQDYEQHPLPEALVGDAARFLLEGMPVQVAFHNGVPL 121
                                    6889***********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1347.98
//
Query:       gi|121638419|ref|YP_978643.1|  [L=372]
Description: cytoplasmic peptidase pepQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-60  204.9   0.3    1.5e-60  204.5   0.3    1.1  1  Peptidase_M24  Metallopeptidase family M24
      5e-24   85.4   0.1    1.1e-23   84.3   0.1    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.5   0.3   1.7e-64   1.5e-60       2     207 ..     142     344 ..     141     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 1.7e-64
                                    HHHHHHHHHHHHHHHHHHH..HHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEE CS
                  Peptidase_M24   2 lirkaariasaaleavlea..ikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvli 79 
                                    l+r a+++a+aal+ ++++  ++pg ter++ +e+ea  + +hga+ ++f++iva+g+n+a++h++p+d vl+ gd+v+i
  gi|121638419|ref|YP_978643.1| 142 LLRLACEAADAALTDLVARggLRPGRTERQVSRELEAL-MLDHGADAVSFETIVAAGANSAIPHHRPTDAVLQVGDFVKI 220
                                    6899***********988889***************77.89*************************************** PP

                                    EEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS CS
                  Peptidase_M24  80 dagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl 159
                                    d+ga + gy+sD+trT+++Gk  + q e+y++v eaq+a+ +a+ pG++l+ +daaar+++++ag++++f hglGHgvGl
  gi|121638419|ref|YP_978643.1| 221 DFGALVAGYHSDMTRTFVLGKAADWQLEIYQLVAEAQQAGRQALLPGAELRGVDAAARQLIADAGYGEHFGHGLGHGVGL 300
                                    ******************************************************************************** PP

                                    SSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEE CS
                  Peptidase_M24 160 evhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlv 207
                                    ++h+  p +     +  +l +G v+t+Epg+y  pg ggvriedt++v
  gi|121638419|ref|YP_978643.1| 301 QIHEA-PGIG--VTSAGTLLAGSVVTVEPGVY-LPGRGGVRIEDTLVV 344
                                    ***98.*998..5679****************.99***********99 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   1.3e-27   1.1e-23       1     132 []       6     134 ..       6     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.3e-27
                                    HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEESTHSS CS
                   Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveyddpve 79 
                                    R+++l+a +++ glda+l+++  n+rYl+Gf   +gs+g++lv++ +++ +l +d +ry ++a+++a++ ev   +    
  gi|121638419|ref|YP_978643.1|   6 RRDKLKAQIAASGLDAMLISDLINVRYLSGF---SGSNGALLVFADERDaVLATD-GRYRTQAASQAPDLEVAIER---- 77 
                                    99*****************************...********8888888899999.**********9999998777.... PP

                                    HHHHHHHHHHHHT..-EEEE-TTSSBHHHHHHHHHHCTTS..EEEETHHHHHHHHSC CS
                   Creatinase_N  80 aladllkellese..krvgveldaltvafyealkealpda..elvdaselieelRvv 132
                                    a+  +l+ ++ ++  +++g+e++++tv+ ++al  al+++  elv as+ +e lR+v
  gi|121638419|ref|YP_978643.1|  78 AVGRYLAGRAGEAgvGKLGFESHVVTVDGLDALAGALEGKntELVRASGTVESLREV 134
                                    677777766555567**********************55556*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2800.58
//
Query:       gi|121638420|ref|YP_978644.1|  [L=230]
Description: hypothetical protein BCG_2558 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0017   18.2   3.3     0.0019   18.0   2.5    1.4  1  DUF1282       Protein of unknown function (DUF1282)
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.055   13.1   0.0    1.5  1  DUF3341       Protein of unknown function (DUF3341)
       0.17   11.9   0.6        8.7    6.3   0.1    2.3  2  DUF3043       Protein of unknown function (DUF3043)
       0.31   11.2   8.2        2.7    8.2   1.9    2.8  2  Metal_resist  Heavy-metal resistance
       0.42   10.3   1.4        1.3    8.6   0.0    2.1  2  Tetraspanin   Tetraspanin family
       0.46    8.7   3.6          1    7.6   1.5    1.9  2  Silic_transp  Silicon transporter
        1.5    8.3  14.1       0.16   11.5   5.6    2.1  2  5TM-5TMR_LYT  5TMR of 5TMR-LYT
        1.6    9.0   0.0        1.6    9.0   0.0    3.1  3  DUF2749       Protein of unknown function (DUF2749)
        3.8    7.6   7.2       0.46   10.5   0.2    2.9  3  DUF5316       Family of unknown function (DUF5316)


Domain annotation for each model (and alignments):
>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.5   9.4e-07    0.0019      24     123 ..      38     135 ..      24     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.4e-07
                        DUF1282  24 ivlillllliglvvfiystfqvlseiltkq.......ankltlassliisvvfylal.gvlvlayliklmgrtydsqhsy 95 
                                    +vl+ll++++g+v  +          ++++       + +  +  ++ + +++ +a+ +  ++a+li l+ + +      
  gi|121638420|ref|YP_978644.1|  38 LVLLLLFAIGGVVWGV----------MDGRadakaspDPDRRQDLAMTWLLAGLVAGaLSGAVAWLISLFYKAIYTGGPI 107
                                    3333333333333333..........333344555545566666799999999999988899*******99998888888 PP

                        DUF1282  96 skifafaayalvplflgglalglsllll 123
                                    ++   faa+++ ++fl+g++ ++   +l
  gi|121638420|ref|YP_978644.1| 108 NELTTFAAFTALIVFLVGIVGVAVGRWL 135
                                    9*******************99888777 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.055      46     151 ..      68     173 ..      63     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                                    -SS-STHHHHHHHHHHHHHHHHHHHIIIIISS---STT--SS-HHHHHHHHTHHHHHHHHHHHHHTTT....TTT-S--- CS
                        DUF3341  46 kksrlpliallgGllGlalalllqvytsvvdyplnigGkPlfslpafipitFEltvLfaalatvlgll....llnglprl 121
                                    +++ l+++ ll+Gl++ al  ++++++s++ y+ +  G P++ l +f   t  +  L++ +++ +g +     l++ p  
  gi|121638420|ref|YP_978644.1|  68 RRQDLAMTWLLAGLVAGALSGAVAWLISLF-YKAIYTGGPINELTTFAAFTALIVFLVGIVGVAVGRWlvdrQLAKAPVR 146
                                    577899999*********999999999987.***********99887765555555555555555544100044444444 PP

                                    --TTTT-TTGGG.TTTS---EE--S-SS-- CS
                        DUF3341 122 yhpvfkaenfdrratdDkffllieatdpkf 151
                                    +h +      ++ra d   f +++a+d+ +
  gi|121638420|ref|YP_978644.1| 147 HHGL---AAEHERAADTDVFSAVRADDSPT 173
                                    4433...33356788888888888888755 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0044       8.7      77     128 ..       5      54 ..       2      76 .. 0.69
   2 ?    3.9   0.0     0.025        50      99     139 ..     109     151 ..      85     169 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0044
                        DUF3043  77 nlgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgillgrk 128
                                    +l +l + +a+vvl l +   + +++ q++  l+ lvllll++i g++ g +
  gi|121638420|ref|YP_978644.1|   5 MLRGLAFAAAMVVLRL-FQ-GALINAWQMLSGLISLVLLLLFAIGGVVWGVM 54 
                                    5556666666666666.43.56677788888888889999999988887765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.025
                        DUF3043  99 kvpevqavvsl.lllvllllvvidgillgrkvkkkvrekFp.e 139
                                    + ++++a+++l ++lv ++ v++  +l+ r++ k+  ++++  
  gi|121638420|ref|YP_978644.1| 109 ELTTFAAFTALiVFLVGIVGVAVGRWLVDRQLAKAPVRHHGlA 151
                                    3333444444423344667777777888888888777777763 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.006        12       2      32 ..      38      68 ..      37      81 .. 0.75
   2 ?    8.2   1.9    0.0013       2.7       3      54 ..     117     166 ..     115     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.006
                                   ..XXXXXXXXXXXXXXXXXXXXXXXTTHHBH CS
                   Metal_resist  2 sLalNlfllGalvgaalrgpggpppggparg 32
                                   +++l lf++G++v++  +g+++ +  +++ +
  gi|121638420|ref|YP_978644.1| 38 LVLLLLFAIGGVVWGVMDGRADAKASPDPDR 68
                                   5788889999999999888888888887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                    .XXXXXXXXXXXXXXXXXXXXXXXTTHHBH.HHHHHHHS-TTHHHHHHHHHH CS
                   Metal_resist   3 LalNlfllGalvgaalrgpggpppggpargraellraalgLpaeqraelraa 54 
                                     al +fl+G++++a  r+  +++ ++++ +  ++  aa++  a++ + + a 
  gi|121638420|ref|YP_978644.1| 117 TALIVFLVGIVGVAVGRWLVDRQLAKAPVR--HHGLAAEHERAADTDVFSAV 166
                                    5899*********************99865..55555555555555555555 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.19   3.8e+02      88      99 ..      38      49 ..       7      97 .. 0.62
   2 ?    8.6   0.0   0.00068       1.3       4      29 ..     113     143 ..     110     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.19
                                   XXXXXXXXXXXX CS
                                   xxxxxxxxxxxx RF
                    Tetraspanin 88 vlfllelaagil 99
                                   +++ll++a+g +
  gi|121638420|ref|YP_978644.1| 38 LVLLLLFAIGGV 49
                                   222222222221 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00068
                                    XXXXXXXXXXXXXXXXXXXXXXXXX.....X CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                    Tetraspanin   4 llfffnllfwligivllavGvwlrl.....k 29 
                                    +  f++l+++l+giv +avG wl        
  gi|121638420|ref|YP_978644.1| 113 FAAFTALIVFLVGIVGVAVGRWLVDrqlakA 143
                                    567999**************99943444440 PP

>> Silic_transp  Silicon transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.5    0.0005         1     233     277 ..       8      52 ..       4      61 .. 0.79
   2 ?    1.4   0.0     0.038        76     372     418 ..      93     138 ..      69     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0005
                   Silic_transp 233 vlcfalavtlkalfnGkt.tmwesipegvavvlfflllsvvGlleG 277
                                     l+fa a+ +  lf+G     w++++  +++vl++l+ ++ G++ G
  gi|121638420|ref|YP_978644.1|   8 GLAFAAAMVVLRLFQGALiNAWQMLSGLISLVLLLLF-AIGGVVWG 52 
                                    589*************86256**********998765.56555544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.038
                   Silic_transp 372 lasiawqlvasafpiaflsnplvyillviallleatGivaGawvlas 418
                                    l s  ++ + +  pi+ l+  +++  l i++l+  +G++ G w++ +
  gi|121638420|ref|YP_978644.1|  93 LISLFYKAIYTGGPINELTTFAAFTAL-IVFLVGIVGVAVGRWLVDR 138
                                    555556666666677777776666665.4455677777777776543 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.3     0.068   1.4e+02      63      92 ..       8      37 ..       5      64 .. 0.60
   2 ?   11.5   5.6   7.9e-05      0.16      50     103 ..      75     131 ..      72     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.068
                   5TM-5TMR_LYT 63 GliagliaglhRyllgGftalacgistila 92
                                   Gl+ ++ ++++R+++g     + ++s ++ 
  gi|121638420|ref|YP_978644.1|  8 GLAFAAAMVVLRLFQGALINAWQMLSGLIS 37
                                   777788888889998885444444443332 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.9e-05
                   5TM-5TMR_LYT  50 gvvvaGllgGplvGliagliaglhRyl.lgG....ftalacgistilagllaGlihrkl 103
                                    + ++aGl+ G l G++a li++++  +  gG     t +a+   t l+ +l+G+++  +
  gi|121638420|ref|YP_978644.1|  75 TWLLAGLVAGALSGAVAWLISLFYKAIyTGGpineLTTFAA--FTALIVFLVGIVGVAV 131
                                    5689*********************9955558766333333..3333333333333222 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00079       1.6       6      41 ..      35      70 ..      32      73 .. 0.90
   2 ?   -3.1   0.9       4.6   9.2e+03      14      24 ..      84      94 ..      76      95 .. 0.66
   3 ?    0.7   0.9      0.31   6.2e+02       9      49 ..     119     166 ..     114     182 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00079
                        DUF2749  6 lIvlviavaagagtilwlvvqpragtsgsgeaqReh 41
                                   lI lv+++ ++ g+++w v++ ra + +s++  R +
  gi|121638420|ref|YP_978644.1| 35 LISLVLLLLFAIGGVVWGVMDGRADAKASPDPDRRQ 70
                                   7999999999999****************9988876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.6
                        DUF2749 14 aagagtilwlv 24
                                   +a +g + wl+
  gi|121638420|ref|YP_978644.1| 84 GALSGAVAWLI 94
                                   46677888886 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.31
                        DUF2749   9 lvia.vaagagti.lwlvvqpr.agtsg.....sgeaqRehrerFfgad 49 
                                    l++  v++++  +  wlv + + a ++      + e +R++  + f a 
  gi|121638420|ref|YP_978644.1| 119 LIVFlVGIVGVAVgRWLV-DRQlAKAPVrhhglAAEHERAADTDVFSAV 166
                                    555446766544425774.433444442111124555666666666555 PP

>> DUF5316  Family of unknown function (DUF5316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.36   7.1e+02       7      30 ..       5      28 ..       3      32 .. 0.83
   2 ?   10.5   0.2   0.00023      0.46       6      60 ..      30      81 ..      26      95 .. 0.75
   3 ?   -2.6   0.4       2.9   5.8e+03       4      13 ..     119     128 ..     113     131 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.36
                        DUF5316  7 kisGfvglvfiliagllsGafvsg 30
                                   ++ G + ++++++  l+ Ga+++ 
  gi|121638420|ref|YP_978644.1|  5 MLRGLAFAAAMVVLRLFQGALINA 28
                                   677888889999999*****9986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                        DUF5316  6 ykisGfvglvfiliagllsGafvsgdriranytseskedrrkrfklsknllligl 60
                                    ++sG ++lv++l+ ++  G+  + +  ra+ +++ + d  +r+ l+++ ll gl
  gi|121638420|ref|YP_978644.1| 30 QMLSGLISLVLLLLFAI-GGVVWGVMDGRADAKASPDPD--RRQDLAMTWLLAGL 81
                                   57899999998888888.788888888899997766655..56777788888877 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.9
                        DUF5316   4 ltykisGfvg 13 
                                    l++++ G+vg
  gi|121638420|ref|YP_978644.1| 119 LIVFLVGIVG 128
                                    4455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1423.06
//
Query:       gi|121638421|ref|YP_978645.1|  [L=147]
Description: 3-dehydroquinate dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-54  181.3   0.0    7.9e-54  181.1   0.0    1.0  1  DHquinase_II  Dehydroquinase class II
  ------ inclusion threshold ------
      0.046   14.0   0.0       0.08   13.2   0.0    1.4  1  BtrH_N        Butirosin biosynthesis protein H, N-terminal


Domain annotation for each model (and alignments):
>> DHquinase_II  Dehydroquinase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.0   8.8e-58   7.9e-54       2     137 ..       6     141 ..       5     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 8.8e-58
                                    EEEEE-TTGGGTTTSTCCCC-SS-HHHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHHCTTT.TEEEEE-GGGGGT-H CS
                   DHquinase_II   2 ilvlnGpNlnllgkrepeiygsetledieeelkekaeelgvelevfqsnhEgelidriqeakekvdgiviNpgaythtSv 81 
                                    + v+nGpNl  lg+rep +yg +t +++ + ++++a+elg++  v+qs++E +l+d+i++a+++++ +++N+g++thtSv
  gi|121638421|ref|YP_978645.1|   6 VNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSV 85 
                                    579***************************************************************************** PP

                                    HHHHHHHTSSS-EEEEESS-GGGS-GGGG--SSGGGSSEEEESSTTHHHHHHHHHH CS
                   DHquinase_II  82 alrdalaaveipvvEvhlsnvhaReefrhksvlsdvakgviaGlglegYelaleal 137
                                    alrda+a++++p++Evh+snvhaReefr++s+ls++a+gvi+Glg++gY lal++l
  gi|121638421|ref|YP_978645.1|  86 ALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYL 141
                                    *****************************************************997 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-06      0.08      49      96 ..      28      77 ..      16      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-06
                         BtrH_N 49 rtkpg..dlekrlakrlglkvevketkdpeeawkalkeeLdaGrpvivqv 96
                                    t++    l +r a  lglk  v++ ++++++ +++ ++ da +pvi+ +
  gi|121638421|ref|YP_978645.1| 28 TTHDElvALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNA 77
                                   44422258899999*********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1018.22
//
Query:       gi|121638422|ref|YP_978646.1|  [L=362]
Description: 3-dehydroquinate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-92  309.7   0.0    1.6e-92  309.4   0.0    1.1  1  DHQ_synthase  3-dehydroquinate synthase
    5.4e-09   36.1   1.8    2.5e-08   34.0   0.2    2.0  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.2e-07   30.9   4.2    3.9e-07   29.2   4.2    1.9  1  Fe-ADH        Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.4   0.0   2.7e-96   1.6e-92       2     261 ..      69     325 ..      68     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 309.4 bits;  conditional E-value: 2.7e-96
                                    EEE-SSGGGCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEE CS
                   DHQ_synthase   2 lvvpdgeksKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtain 81 
                                    + +pd+e+ K+l  +  i+++l + ++ Rk++l++lGGG+ +D+aGf+Aat+lRGv++v++Pttll++vD++vGgKt+in
  gi|121638422|ref|YP_978646.1|  69 IEIPDAEAGKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSIVHLPTTLLGMVDAAVGGKTGIN 148
                                    679***************************************************************************** PP

                                    ETTEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHH CS
                   DHQ_synthase  82 lplgKNliGafaqPkavlidlevLktLperelraGlaEviKyalikdeelfelleenaeallkeeeeealeeliarsiev 161
                                    ++ gKNl+Gaf+qP avl+dl++L+tLp++e++ G+aEv+K ++i+d  +++l+e++ +a l+    ++l eli+r+i+v
  gi|121638422|ref|YP_978646.1| 149 TDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAEVVKAGFIADPVILDLIEADPQAALDP-AGDVLPELIRRAITV 227
                                    *************************************************************995.9************** PP

                                    HHHHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---S CS
                   DHQ_synthase 162 kaevveeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvs 241
                                    kaevv++Deke++lr++Ln+GHt+gHaiE+  +y +++HG aV++G+v+aael++ +g l++++++r++++l++lglpvs
  gi|121638422|ref|YP_978646.1| 228 KAEVVAADEKESELREILNYGHTLGHAIERRERY-RWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVS 306
                                    **********************************.********************************************* PP

                                    TTTT.-HHHHHHHHTTCTTX CS
                   DHQ_synthase 242 lkelleveellealkkDkkv 261
                                    ++ + ++ +lle+++ Dkk+
  gi|121638422|ref|YP_978646.1| 307 YDPD-ALPQLLEIMAGDKKT 325
                                    ****.**************7 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.2   4.1e-12   2.5e-08       1     162 [.      21     188 ..      21     245 .. 0.83
   2 ?    1.7   0.1     0.029   1.7e+02     229     249 ..     249     269 ..     247     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.1e-12
                       Fe-ADH_2   1 vigegaleklgellkelelkkvllvadentkkaagekveeslkeagikve..vveeveeeadleeveklveal...reke 75 
                                    vig g l++l++ll+++  +kv++v+  +  ++a e++++ l+ +g++++   + ++e+ +dl  v  + e+l      +
  gi|121638422|ref|YP_978646.1|  21 VIGTGLLDELEDLLADR--HKVAVVHQPGLAETA-EEIRKRLAGKGVDAHriEIPDAEAGKDLPVVGFIWEVLgriGIGR 97 
                                    58999999999999875..79*******999876.689*********999332334444556555555555542226789 PP

                       Fe-ADH_2  76 tdlvvavGgGtiiDiakyvsak..lnvpyvsvpTaa..SvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPr 151
                                     d++v++GgG + D+a +++a+  ++v++v +pT++   vD        + +d  k  v   + Plav++Dl  l++ Pr
  gi|121638422|ref|YP_978646.1|  98 KDALVSLGGGAATDVAGFAAATwlRGVSIVHLPTTLlgMVDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPR 177
                                    9*****************9986448999******98445899999999*****7787787899***************** PP

                       Fe-ADH_2 152 rllasGvGDll 162
                                      +  G+++++
  gi|121638422|ref|YP_978646.1| 178 DEMICGMAEVV 188
                                    *999***9987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.029
                       Fe-ADH_2 229 HliSHaldmlalkqalHGeqV 249
                                    H + Ha+++++  ++ HG+ V
  gi|121638422|ref|YP_978646.1| 249 HTLGHAIERRERYRWRHGAAV 269
                                    9**********99*****998 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   4.2   6.6e-11   3.9e-07       3     263 ..      19     272 ..      17     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.6e-11
                                    EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE..E.EEE-S-...--HHHHHHHHTTS CS
                         Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievt..vfdgvepn...ptleeveeaaala 77 
                                     +v+g+g l+el++ll++    ++ +v+ +g++   ++++++++ l+ +g++ +   + + e     p +  + e++ ++
  gi|121638422|ref|YP_978646.1|  19 PVVIGTGLLDELEDLLADRH--KVAVVHQPGLA---ETAEEIRKRLAGKGVDAHriEIPDAEAGkdlPVVGFIWEVLGRI 93 
                                    589***************96..*********99...889*******9999999854445555541115555566666666 PP

                                    -TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-.S.-S-TT-SEEEEE.-TTSEEEE CS
                         Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTta.G.tGsevtplavitdeeegekls 155
                                       + d+++++GGG + D+A  +a++  +                ++ ++  PTt  G  ++ v +   i  ++ g+ l+
  gi|121638422|ref|YP_978646.1|  94 GIGRKDALVSLGGGAATDVAGFAAATWLR----------------GVSIVHLPTTLlGmVDAAVGGKTGIN-TDAGKNLV 156
                                    77778***********************5................59*******97332478888888888.66655554 PP

                                    E-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH..........T---TTSSB--HHHHHHHHHHHHHHH CS
                         Fe-ADH 156 ifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvsk..........kanplsdalaleairliaknlerava 225
                                     +  +  P +++vD + + tlP++ ++++++ ++   + a                +p+ d+l + + r i    e + a
  gi|121638422|ref|YP_978646.1| 157 GA--FHQPLAVLVDLATLQTLPRDEMICGMAEVVKAGFIADPVIldlieadpqaALDPAGDVLPELIRRAITVKAEVVAA 234
                                    44..77899******************99998765543332221233333333366667777777777777777777777 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHH CS
                         Fe-ADH 226 dgedleareqmllastlaglafsnaglgavHalahalg 263
                                    d +  e re + ++ tl+       +  + H+ a ++g
  gi|121638422|ref|YP_978646.1| 235 DEKESELREILNYGHTLGHAIERRERYRWRHGAAVSVG 272
                                    77777777777777777776666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1903.18
//
Query:       gi|121638423|ref|YP_978647.1|  [L=176]
Description: shikimate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-45  154.6   0.0    2.5e-45  154.4   0.0    1.0  1  SKI              Shikimate kinase
      6e-08   33.0   0.0    1.3e-07   31.9   0.0    1.6  1  AAA_33           AAA domain
    2.6e-07   31.3   0.0      3e-07   31.0   0.0    1.3  1  AAA_18           AAA domain
     0.0016   18.6   0.1     0.0038   17.4   0.1    1.7  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0019   18.6   0.1     0.0047   17.4   0.1    1.8  1  AAA_17           AAA domain
     0.0033   17.4   0.2     0.0058   16.6   0.2    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0036   16.7   0.0     0.0057   16.1   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0078   15.7   0.0       0.01   15.3   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
     0.0083   15.9   0.4      0.026   14.3   0.1    1.8  2  Cytidylate_kin   Cytidylate kinase
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.018   15.5   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.013   15.8   0.0      0.046   14.0   0.0    1.8  2  AAA_22           AAA domain
      0.025   14.0   0.1      0.034   13.6   0.1    1.1  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.026   13.8   0.0      0.034   13.4   0.0    1.2  1  6PF2K            6-phosphofructo-2-kinase
      0.039   14.0   0.0      0.051   13.6   0.0    1.3  1  MMR_HSR1         50S ribosome-binding GTPase
      0.041   13.5   0.1      0.065   12.9   0.1    1.4  1  CoaE             Dephospho-CoA kinase
      0.043   12.8   0.2      0.063   12.3   0.2    1.2  1  Gly_kinase       Glycerate kinase family
      0.055   13.7   0.0       0.09   13.0   0.0    1.4  1  AAA_28           AAA domain
      0.065   13.6   0.5      0.066   13.6   0.5    1.3  1  AAA_16           AAA ATPase domain
       0.17   11.5   0.0       0.22   11.2   0.0    1.2  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   2.7e-48   2.5e-45       1     157 [.      11     166 ..      11     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 2.7e-48
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlseenre 80 
                                    +G+GKst+G++lAk+lg+ ++D+D  ie+rtg+sia+if+ +ge++Fr+ E++v+++ l+ ++ V+++GGGav+s+  r+
  gi|121638423|ref|YP_978647.1|  11 PGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRA 90 
                                    69****************************************************************************** PP

                                    HHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                            SKI  81 llkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeileal 157
                                    +l+ +++v+yL++s  e ++r+  ++ RPll +++++e+++  +a+r ply+++a++ vd++++++ +v+++il++l
  gi|121638423|ref|YP_978647.1|  91 ALA-GHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166
                                    ***.********************************999999999*****************************987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.4e-10   1.3e-07       3      41 ..       6      44 ..       5      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.4e-10
                         AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtd 41
                                   +lvGlpGsGKst  +rl+k+lg+ ll++d+++++ +g+ 
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRS 44
                                   68****************************999998843 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.2e-10     3e-07       3      70 ..       7      83 ..       6     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.2e-10
                         AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss........a 70
                                   l G pG+GK+t++++L+k lg+g   +dva e ++  +  +  a+d ++++++   d++  al  ++          
  gi|121638423|ref|YP_978647.1|  7 LVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIfATDGEQEFRRIEEDVVRAALADHDGvlslgggaV 83
                                   89*************************************99997776666666666667777777665544555552 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.1e-06    0.0038       8      33 ..      11      36 ..       7      73 .. 0.79
   2 ?   -1.2   0.0       2.1     2e+03      74     100 ..      50      76 ..      36      85 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-06
                Cytidylate_kin2  8 yGsgGetigeaLAekLglpfydreii 33
                                    Gsg++tig++LA+ Lg+ ++d ++ 
  gi|121638423|ref|YP_978647.1| 11 PGSGKSTIGRRLAKALGVGLLDTDVA 36
                                   6*********************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                Cytidylate_kin2  74 deklddelfeaqervirelaaeesvVi 100
                                      + ++e+++++e+v+r++ a++++V+
  gi|121638423|ref|YP_978647.1|  50 ATDGEQEFRRIEEDVVRAALADHDGVL 76 
                                    455566677777888887774444443 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     5e-06    0.0047       1      34 [.       8      40 ..       8     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreea 34
                                   +G+PGsGK+t+ ++l++ +g+  l + d+ +e  
  gi|121638423|ref|YP_978647.1|  8 VGLPGSGKSTIGRRLAKALGVGLLDT-DVAIEQR 40
                                   7*******************999884.5555554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.1e-06    0.0058       3      25 ..       6      28 ..       4     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.1e-06
                                   EEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnr 25
                                   +LvG pG+gKs++ +rla+al+ 
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGV 28
                                   7*******************953 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.1e-06    0.0057      26     112 ..       6     100 ..       3     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-06
                   Mg_chelatase  26 llvGppGsGKtmlakrlpsllpp..lseeealevakiasvagkkeeekl.....lkrrpfraphhsaskaalvGggskpk 98 
                                    +lvG pGsGK+ + +rl++ l    l+++ a+e ++ +s+a+  ++++      +++   ra       +  +Ggg+ + 
  gi|121638423|ref|YP_978647.1|   6 VLVGLPGSGKSTIGRRLAKALGVglLDTDVAIEQRTGRSIADIFATDGEqefrrIEEDVVRAALADHDGVLSLGGGAVTS 85 
                                    799**************999864337888899999999999854444330000033333333333333344479999999 PP

                   Mg_chelatase  99 pG.eislahnGvLfL 112
                                    pG   +la + v++L
  gi|121638423|ref|YP_978647.1|  86 PGvRAALAGHTVVYL 100
                                    984467888888877 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05      0.01       5      70 ..       6      71 ..       2      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                   EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT CS
                          KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLsk 70
                                   vl GlP sGKst+ ++Lakal     +  v  ++  g +  +   +  e++ R      v+ +L  
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALAD 71
                                   89******************9887777766666666666666666666666666666666666655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.7e-05     0.026       7      30 ..      11      34 ..       6      41 .. 0.90
   2 ?   -2.2   0.0       2.9   2.7e+03     180     207 ..     137     164 ..     126     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                   TTSSHHHHHHHHHHHHT-EEEEHH CS
                 Cytidylate_kin  7 agsGKssvaralaeklglkyldtg 30
                                    gsGKs+++r+la+ lg+ +ldt 
  gi|121638423|ref|YP_978647.1| 11 PGSGKSTIGRRLAKALGVGLLDTD 34
                                   69********************95 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                    S-S---TT-EEEETTTS-HHHHHHHHHH CS
                 Cytidylate_kin 180 gpLklaedaliidtskltieevvekile 207
                                    +pL      + +dt++     vv +il+
  gi|121638423|ref|YP_978647.1| 137 APLYRRVATMRVDTNRRNPGAVVRHILS 164
                                    4555555666677777666666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.9e-05     0.018       2      32 ..       6      36 ..       5      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETT CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgs 32
                                   +l+G pG GK+++ + +ak lgv +l ++++
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGVGLLDTDVA 36
                                   699*****************98776665543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.9e-05     0.046       9      29 ..       6      26 ..       3      73 .. 0.85
   2 ?   -0.9   0.0       1.9   1.8e+03      38      69 ..     141     171 ..     118     175 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                         AAA_22  9 vvtGesGtGKTtllrrlleql 29
                                   v++G +G+GK+t  rrl++ l
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKAL 26
                                   89***************9988 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                         AAA_22  38 erpevvfvtlpsstsskdllrellralglelk 69 
                                    +r+ +++v+ +   ++  + r++l+ l+++  
  gi|121638423|ref|YP_978647.1| 141 RRVATMRVDTNRR-NPGAVVRHILSRLQVPSP 171
                                    3344444444444.588889999999988765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.6e-05     0.034       8      59 ..       6      57 ..       4      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                           ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDi.....yGpsiprllgveeekpe 59
                                   vl g  G GKSt+   lA aL      vgllD+D+     +G si++++ +++e+  
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKAL-----GVGLLDTDVaieqrTGRSIADIFATDGEQEF 57
                                   6777889***********998.....6*******9666666******9999987554 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-05     0.034      17      46 ..       6      35 ..       4      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                          6PF2K 17 vlvGLpargKtyiskkltrylkwlgvrtkv 46
                                   vlvGLp  gK++i ++l + l    ++t v
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGVGLLDTDV 35
                                   9*****************999887777765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.4e-05     0.051       2      22 ..       5      31 ..       4     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                   EEEEESTTSSHHHHHHHHHT......S CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg......e 22
                                   +++vG p +GKSt+ ++l +       
  gi|121638423|ref|YP_978647.1|  5 AVLVGLPGSGKSTIGRRLAKalgvglL 31
                                   689***************973333330 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.9e-05     0.065       7      36 ..       9      39 ..       6      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                                   ESTTSSHHHHHHHHHH.TT-EEEEHHHHHHH CS
                           CoaE  7 GgiasGKstvanlfad.lgvpivDaDlvArq 36
                                   G  +sGKst+ +++a+ lgv ++D+D++  q
  gi|121638423|ref|YP_978647.1|  9 GLPGSGKSTIGRRLAKaLGVGLLDTDVAIEQ 39
                                   4458**********999*********97655 PP

>> Gly_kinase  Glycerate kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.7e-05     0.063     125     191 ..       4      71 ..       2      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                     Gly_kinase 125 rkiiigiGGSatnDgGaGmlqaLGvrfldadgkelepggaaLaklasidlskldprlk.dveitvacD 191
                                    + +++g+ GS+ +  G  +++aLGv +ld+d +  +++g+++a++   d ++  +r++ dv   +++D
  gi|121638423|ref|YP_978647.1|   4 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEeDVVRAALAD 71 
                                    6799*****************************************99998877777752444445555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.5e-05      0.09       2      44 ..       5      55 ..       4      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.5e-05
                         AAA_28  2 ivitGgestGKTtlleaLaar......gypvv..pEaareileeklakged 44
                                    v++G +++GK+t+ ++La+       ++ v   ++++r i +  + +ge+
  gi|121638423|ref|YP_978647.1|  5 AVLVGLPGSGKSTIGRRLAKAlgvgllDTDVAieQRTGRSIADIFATDGEQ 55
                                   699****************87755555444444466666666544444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     7e-05     0.066      28      51 ..       6      29 ..       2     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                         AAA_16 28 llsGesGvGKsslvrellralekd 51
                                   +l+G +G+GKs++ r+l++al   
  gi|121638423|ref|YP_978647.1|  6 VLVGLPGSGKSTIGRRLAKALGVG 29
                                   699***************977643 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.22       2      40 ..       2      42 ..       1      75 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                         AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfi...dtekGlkslda 40
                                   + k +++G +g+GK+t+ ++l  k+l +   dt+    +  +
  gi|121638423|ref|YP_978647.1|  2 APKAVLVGLPGSGKSTIGRRL-AKALGVgllDTDVAIEQRTG 42
                                   7899*****************.77775522366554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1022.51
//
Query:       gi|121638424|ref|YP_978648.1|  [L=401]
Description: chorismate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.7e-118  393.6   1.1   5.4e-118  393.4   1.1    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.4   1.1    3e-122  5.4e-118       1     327 []       2     367 ..       2     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 393.4 bits;  conditional E-value: 3e-122
                                    SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TT CS
                Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkd 80 
                                    lr++t+GeShg+al+av++g+ ag++++++di ++L+rRr g  + +++  E+D+v++lsG+ +g tlG pia+ i N++
  gi|121638424|ref|YP_978648.1|   2 LRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVLSGIRHGSTLGGPIAIEIGNTE 81 
                                    799***************************************889*****************98**************** PP

                                    S-..SSSSSTS...................BE-TTSTCHHHHHHC-S.STHCC.CCCTHHCHHHHHHHHHHHHHHHHT.T CS
                Chorismate_synt  81 qrskdyeeike...................vpRpgHADltyalkYgirdlrgg.grsSaReTaarvaaGavakklLke.l 139
                                    +   ++e++++                   +pRpgHAD++++lkYg+ d+r + +r+SaReTaarvaaG+va+++L++ l
  gi|121638424|ref|YP_978648.1|  82 WP--KWETVMAadpvdpaeladvarnapltRPRPGHADYAGMLKYGFDDARPVlERASARETAARVAAGTVARAFLRQaL 159
                                    **..**************************************************************************78 PP

                                    TEEEEEEEEEETTE.............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTT CS
                Chorismate_synt 140 gieivayvssigei.............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvf 206
                                    g+e+ ++v+sig+               +  ++pvr+ d++a+++m ++ie+akk+gd+lGgvve v+ g+p+GlG+ + 
  gi|121638424|ref|YP_978648.1| 160 GVEVLSHVISIGASapyegpppraedlPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTS 239
                                    ************656666666666543222566**********************************************9 PP

                                    ..B-HHHHHHHHHHTSTTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS- CS
                Chorismate_synt 207 ..dkldakLakalmsipAvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpips 278
                                      ++ld++La+a+m+i+A+kgveiG+Gf++a+++Gs+a+De++      +r+tn+aGG+eGG++nG+p+ vr+a+Kpi++
  gi|121638424|ref|YP_978648.1| 240 gdHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYpgpdgvVRSTNRAGGLEGGMTNGQPLRVRAAMKPIST 319
                                    999****************************************99998888***************************** PP

                                    -SSEEEEEBTTS-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                Chorismate_synt 279 iakeqktvdletkeevelevkgrhDpcvvpravvvveamvalvladall 327
                                    + ++++tvdl+t +e+ + +  r+D+c+vp+a vvve+mvalvla+a+l
  gi|121638424|ref|YP_978648.1| 320 VPRALATVDLATGDEAVAIH-QRSDVCAVPAAGVVVETMVALVLARAAL 367
                                    **************555555.5***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2798.02
//
Query:       gi|121638425|ref|YP_978649.1|  [L=135]
Description: hypothetical protein BCG_2563 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00013   22.3  17.6    0.00044   20.7  17.6    1.7  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  17.6   2.4e-08   0.00044       3      99 ..      40     127 ..      38     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-08
                  T7SS_ESX_EspC   3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLra 82 
                                    ++L+V++d l++la +  + a+e+++ava + ga+ +         +a + av+aa+a   aa++a+ a ++  a+ L +
  gi|121638425|ref|YP_978649.1|  40 ARLRVTADGLQALAGRCATLAGELSAAVAPS-GAVLSW--------QANAVAVNAAHARAGAAAAAVSARMRATAAALGQ 110
                                    589************************9999.333333........35688999999999999***************** PP

                  T7SS_ESX_EspC  83 AAaaYeatDeeaagald 99 
                                    AA +Y   D +aa al+
  gi|121638425|ref|YP_978649.1| 111 AARRYAGQDTAAAAALG 127
                                    **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 898.28
//
Query:       gi|121638426|ref|YP_978650.1|  [L=403]
Description: hypothetical protein BCG_2564 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-77  257.6   0.9    1.2e-76  256.3   0.9    1.7  1  Abhydrolase_8  Alpha/beta hydrolase
  ------ inclusion threshold ------
       0.09   12.6   0.0        5.7    6.8   0.0    2.3  2  Ser_hydrolase  Serine hydrolase


Domain annotation for each model (and alignments):
>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.3   0.9   1.3e-80   1.2e-76       1     178 []     169     349 ..     169     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 1.3e-80
                  Abhydrolase_8   1 DpagkvlaavavGdldrAerVsVtvpGvdttlrrtlatmvaearglraeaaaaeeaagkpesvAviAWlgYeaP.agask 79 
                                    Dpa++++a++avGd+++A++VsVtvpGv++t+r+t+atm++earglr+ea+++++++g++e+vA+iAW+gY++P + as+
  gi|121638426|ref|YP_978650.1| 169 DPADMIPAVTAVGDPFTADHVSVTVPGVSGTTRQTIATMTQEARGLREEARVIAHSVGESENVATIAWVGYQPPpVLASW 248
                                    9***********************************************************************9989**** PP

                  Abhydrolase_8  80 evatddrAaagAaeLnallrdlrats.vpgqhlallgHSYGSlvaslAldd.aaseVsdvvlyGSPGleaesaakLgled 157
                                    ++++dd A+agA++L+a+lrdl+a s +pg+++al+gHSYGSl++++Al+d a+s V+++vlyGSPG++a+s+akLg++d
  gi|121638426|ref|YP_978650.1| 249 NTVDDDLAQAGAPKLEAFLRDLQAGShNPGHTTALFGHSYGSLLSGIALKDgASSLVDNAVLYGSPGFDATSPAKLGMND 328
                                    ***************************************************999************************** PP

                  Abhydrolase_8 158 arvfvmrgadDlienvpelaa 178
                                    +++fvm+++dD+i+++++la+
  gi|121638426|ref|YP_978650.1| 329 HNFFVMTTPDDPIRYPARLAP 349
                                    ******************986 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0059        53      43      67 ..     204     228 ..     186     246 .. 0.82
   2 ?    6.8   0.0   0.00064       5.7      33      93 ..     257     317 ..     243     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0059
                                    HHHHHHHHHC-STTEEEEEETCHHH CS
                  Ser_hydrolase  43 vaaleaaveaaeekvvlvAHSlgcl 67 
                                    +a++ ++++ ++e++ ++AHS+g  
  gi|121638426|ref|YP_978650.1| 204 IATMTQEARGLREEARVIAHSVGES 228
                                    67889999999***********954 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00064
                                    --TS--HHHHHHHHHHHHHC-STTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGG CS
                  Ser_hydrolase  33 dwlkPdledWvaaleaaveaaeekvvlvAHSlgclavlhaaelqlakkvagalLVapadve 93 
                                    +   P+le  +  l+a  ++  + + l  HS g l++  a++  + + v+ a+L   +  +
  gi|121638426|ref|YP_978650.1| 257 QAGAPKLEAFLRDLQAGSHNPGHTTALFGHSYGSLLSGIALKDGASSLVDNAVLYGSPGFD 317
                                    34689********************************999998899999999998777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2933.73
//
Query:       gi|121638427|ref|YP_978651.1|  [L=219]
Description: lipoprotein lppA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-43  147.7   0.0    3.1e-43  147.3   0.0    1.1  1  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.0   1.7e-47   3.1e-43       3     152 ..      41     194 ..      39     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 1.7e-47
                                    HHHHHH.HHHHHHHHHHHGGG--HHHHHHHHHHHHHHHHHHHHHHSTT--EEE---HH.....HH-EE.SSS-TTTEEE- CS
                           LppA   3 epealtskeevaeaedelrqkPslEeaeeqleallariadaisalvpgltWktdedrs.....rngCe.dpyeetdgrrv 76 
                                    ++++lt +e++ ++ d++r+k+s+E+a+e+l+a+++ iad++sa++pg+tWk+d+d++     rng+  d+++++++rr 
  gi|121638427|ref|YP_978651.1|  41 TSRRLT-GEQKIQLIDSMRNKGSYEAARERLTATARIIADRVSAAIPGQTWKFDDDPNiqqsdRNGALcDKLTADIARRP 119
                                    677888.9***********************************************88888899***************** PP

                                    B---EEESS---HHHHHHHHHHHHHHHHTTT--EEE-S-BSSS-EEEEEEET.TEEEEEEESSSEEEEEE---EE- CS
                           LppA  77 alesvvsagpipddqWpqaleiVrelAakygatevevfkDepgdhdvrftgpeGgeiklgtakaavltittgCrLp 152
                                    +++sv++ +++++++++ a++iVre+Aakygat+ +++++e++++d++++g+ G+e++l++ k+a+l+it++C+L 
  gi|121638427|ref|YP_978651.1| 120 IANSVMFGATFSAEDFKIAANIVREEAAKYGATTESSLFNESAKRDYDVQGN-GYEFRLLQIKFATLNITGDCFLL 194
                                    ****************************************************.9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1614.73
//
Query:       gi|121638428|ref|YP_978652.1|  [L=219]
Description: lipoprotein lprR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-40  138.1   0.0    2.8e-40  137.7   0.0    1.1  1  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   1.6e-44   2.8e-40       3     152 ..      41     194 ..      39     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.6e-44
                                    HHHHHH.HHHHHHHHHHHGGG--HHHHHHHHHHHHHHHHHHHHHHSTT--EEE---HH.......HH-EESSS-TTTEEE CS
                           LppA   3 epealtskeevaeaedelrqkPslEeaeeqleallariadaisalvpgltWktdedrs.......rngCedpyeetdgrr 75 
                                    ++++lt +e++ ++ d++r+k+s+E+a+e+l+a+++ iad++sa++pg+tWk+ ed++       + +C+ +++ +++rr
  gi|121638428|ref|YP_978652.1|  41 TSRRLT-DEQKIQLIDSMRNKGSYEAARERLTATARIIADRVSAAIPGQTWKFTEDPAgrkadreGLSCK-ELTGDIARR 118
                                    677888.9***********************************************555555553367777.********* PP

                                    -B---EEESS---HHHHHHHHHHHHHHHHTTT--EEE-S-BSSS-EEEEEEET.TEEEEEEESSSEEEEEE---EE- CS
                           LppA  76 valesvvsagpipddqWpqaleiVrelAakygatevevfkDepgdhdvrftgpeGgeiklgtakaavltittgCrLp 152
                                     +++ v++  ++++++++ + +iVre+Aakygat+ +++++e++++d++++g+ G+e++l++ k+a+l+it++C+L 
  gi|121638428|ref|YP_978652.1| 119 PIADAVIFGTAFSAEDFKVVTNIVREEAAKYGATTESSLFNESAKRDYDVQGN-GYEFRLLQIKFATLNITGDCFLL 194
                                    *****************************************************.9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1689.56
//
Query:       gi|121638429|ref|YP_978653.1|  [L=220]
Description: lipoprotein lppB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-39  133.2   0.0    9.2e-39  132.8   0.0    1.1  1  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   0.0   5.2e-43   9.2e-39       4     152 ..      42     194 ..      39     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 5.2e-43
                                    HHHHH.HHHHHHHHHHHGGG--HHHHHHHHHHHHHHHHHHHHHHSTT--EEE---HH.....HH-EE.SSS-TTTEEE-B CS
                           LppA   4 pealtskeevaeaedelrqkPslEeaeeqleallariadaisalvpgltWktdedrs.....rngCe.dpyeetdgrrva 77 
                                    + +lt +e++ ++ d++r k+s+E+a+e+l+a+++ iad++sa++pg+tWk+++d +     rng   ++++++++rr +
  gi|121638429|ref|YP_978653.1|  42 SPHLT-GEQKIQLIDSMRHKGSYEAARERLTATAQIIADRVSAAIPGQTWKFNDDSYgqdfyRNGSLcKELSADIARRPM 120
                                    55788.9***********************************************666666669999999*********** PP

                                    ---EEESS---HHHHHHHHHHHHHHHHTTT--EEE-S-BSSS-EEEEEEET.TEEEEEEESSSEEEEEE---EE- CS
                           LppA  78 lesvvsagpipddqWpqaleiVrelAakygatevevfkDepgdhdvrftgpeGgeiklgtakaavltittgCrLp 152
                                    ++ v +  ++++++++ a++iVre+Aakyg+t+ +++++e++++d++++g+ G+e++lg+ k+a+l+it++C+L 
  gi|121638429|ref|YP_978653.1| 121 AKPVDFGSTFSAEDFKIAANIVREEAAKYGVTTESSLFNESAKRDYDVQGN-GYEFNLGQIKFATLNITGDCFLL 194
                                    ***************************************************.9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1607.25
//
Query:       gi|121638430|ref|YP_978654.1|  [L=92]
Description: hypothetical protein BCG_2568 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-06   25.9   2.4    1.1e-05   25.3   2.4    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   2.4     6e-10   1.1e-05       2      34 ..      57      89 ..      56      92 .] 0.95

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6e-10
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 VapB_antitoxin  2 rtnIeiDDeLlaeAirltglktKrEaVnlALre 34
                                   rt+I+iDD Lla+A++  g ++ +  V+ ALr+
  gi|121638430|ref|YP_978654.1| 57 RTTIDIDDILLARAQAALGTTGLKDRVDAALRA 89
                                   9*******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 731.97
//
Query:       gi|121638431|ref|YP_978655.1|  [L=137]
Description: hypothetical protein BCG_2569 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   55.0   1.3    1.3e-14   54.8   1.3    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   1.3     7e-19   1.3e-14       2     121 ..       4     122 ..       3     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 7e-19
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                    ++DTs++ ++ r+e+ ++++++l +  + + ++++v  E+ly +++       a++  +l ++l++l  +p++ae + +a
  gi|121638431|ref|YP_978655.1|   4 CVDTSAWHHAARPEVARRWLAALSA--DQIGICDHVRLEILYSANS-------ATDYDALADELDGLARIPVGAETFTRA 74 
                                    8**********99997755444444..9******************.......8888888888***************** PP

                                    HHHHHHHH.........SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  82 aeialkyg.........llpnDaliaAtAkehgikliatfDedfrrvak 121
                                     ++ +++          ++++D++iaA A+ +g  +++++De+ +rva+
  gi|121638431|ref|YP_978655.1|  75 CQVQRELAhvaglhhrsVKIADLVIAAAAELSGT-IVWHYDENYDRVAA 122
                                    **********************************.777********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1020.49
//
Query:       gi|121638432|ref|YP_978656.1|  [L=85]
Description: hypothetical protein BCG_2570 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-12   45.2   0.5    1.4e-11   43.9   0.5    1.7  1  RHH_1            Ribbon-helix-helix protein, copG family
      0.007   16.2   0.2      0.026   14.4   0.1    1.8  2  RHH_5            CopG-like RHH_1 or ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.018   15.8   0.9        1.8    9.4   0.5    2.1  2  PSK_trans_fac    Rv0623-like transcription factor
      0.032   14.1   0.1      0.042   13.7   0.1    1.3  1  RHH_4            Ribbon-helix-helix domain
      0.049   13.6   0.1      0.062   13.2   0.1    1.3  1  DUF1778          Protein of unknown function (DUF1778)
      0.087   12.8   0.1      0.092   12.7   0.1    1.1  1  Lipase_chap      Proteobacterial lipase chaperone protein
       0.16   12.1   0.0       0.21   11.7   0.0    1.2  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.5   5.5e-15   1.4e-11       1      37 [.       2      38 ..       2      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.5e-15
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   r++++l +e+le+Ld+ a+++g SrSelIR+A+++++
  gi|121638432|ref|YP_978656.1|  2 RTQVTLGKEELELLDRAAKASGASRSELIRRAIHRAY 38
                                   89*******************************9876 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1     1e-05     0.026       3      37 ..       2      36 ..       1      37 [. 0.91
   2 ?   -0.9   0.0      0.62   1.6e+03      11      19 ..      74      82 ..      73      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                          RHH_5  3 RvnvtLPeelleeLeewAdeegRsvSnlaafLvek 37
                                   R++vtL  e le L++ A++ g s+S l+   + +
  gi|121638432|ref|YP_978656.1|  2 RTQVTLGKEELELLDRAAKASGASRSELIRRAIHR 36
                                   99**************************9766665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
                          RHH_5 11 elleeLeew 19
                                   +l+e+L+++
  gi|121638432|ref|YP_978656.1| 74 DLNERLARL 82
                                   899***985 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5    0.0007       1.8      13      52 ..      14      50 ..      10      61 .. 0.77
   2 ?    5.3   0.0     0.014        35      20      41 ..      62      83 ..      60      85 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0007
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHH CS
                  PSK_trans_fac 13 lareLarltgeskteAvrrAleerlerlrreraepllerl 52
                                   l ++ a++ g+s  e +rrA+ +++      +++++l+ l
  gi|121638432|ref|YP_978656.1| 14 LLDRAAKASGASRSELIRRAIHRAYGTG---SKQERLAAL 50
                                   77889****************9998765...455555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                                   XXXXXXXXXXXXXXXXXXXXXX CS
                  PSK_trans_fac 20 ltgeskteAvrrAleerlerlr 41
                                    tg+   +A+r  l erl+rl 
  gi|121638432|ref|YP_978656.1| 62 FTGTEYVDAIRGDLNERLARLG 83
                                   589999**************85 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.6e-05     0.042      12      47 ..       2      37 ..       1      57 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaeidadr 47
                                   rT ++L ++  + L++ A++ g + ++Li +  ++ 
  gi|121638432|ref|YP_978656.1|  2 RTQVTLGKEELELLDRAAKASGASRSELIRRAIHRA 37
                                   9****************************9874444 PP

>> DUF1778  Protein of unknown function (DUF1778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.4e-05     0.062       8      33 ..       9      34 ..       2      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                        DUF1778  8 peakeliqrAAalsgktltdFvleaa 33
                                   +e+ el++rAA++sg ++++ + +a+
  gi|121638432|ref|YP_978656.1|  9 KEELELLDRAAKASGASRSELIRRAI 34
                                   7889***************9765544 PP

>> Lipase_chap  Proteobacterial lipase chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.6e-05     0.092     106     154 ..      10      60 ..       2      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                    Lipase_chap 106 eelaarlaelkkqg.aseqqrrqaraalvgp.eaaqRlaaldqqraqwqqr 154
                                    eel+   ++ k++g  +++ +r+a+ +++g     +Rlaald +r  w+ r
  gi|121638432|ref|YP_978656.1|  10 EELELLDRAAKASGaSRSELIRRAIHRAYGTgSKQERLAALDHSRGSWRGR 60 
                                    566666677788994445557789977777626789************988 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.2e-05      0.21      91     122 ..       2      33 ..       1      34 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.2e-05
                HicB_lk_antitox  91 riNitlpervlkriDaavkaagesRSgflaka 122
                                    r  +tl ++ l+ +D+a+ka+g sRS ++ +a
  gi|121638432|ref|YP_978656.1|   2 RTQVTLGKEELELLDRAAKASGASRSELIRRA 33 
                                    6789***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 665.82
//
Query:       gi|121638433|ref|YP_978657.1|  [L=125]
Description: hypothetical protein BCG_2571 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-11   44.7   1.2    2.1e-11   44.4   1.2    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   1.2   1.2e-15   2.1e-11       2     113 ..       3     111 ..       2     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.2e-15
                                    EE-HHHHHHHHTTSHHHHHHH.HHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaar.klleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    ++DT + +++lrge+ a+ ++ +l+++ ee++ s+lv  Ell++++          el +l+   sa+    ++++ia++
  gi|121638433|ref|YP_978657.1|   3 LIDTTIAVDHLRGEPAAAVLLaELINNGEEIAASELVRFELLAGVRE--------SELAALEAFFSAVVWTLVTEDIARI 74 
                                    79*********99999987651555555*******************........88888888899999999******** PP

                                    HHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESS CS
                            PIN  81 aaeialkyg.....llpnDaliaAtAkehgikliatfD 113
                                     +++a++y+     ++  D liaAtA+  +++l+ t +
  gi|121638433|ref|YP_978657.1|  75 GGRLARRYRsshrgIDDVDYLIAATAIVVDADLL-TTN 111
                                    **********************************.654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 975.86
//
Query:       gi|121638434|ref|YP_978658.1|  [L=131]
Description: hypothetical protein BCG_2572c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-17   62.4   0.0    6.4e-17   62.2   0.0    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   3.6e-21   6.4e-17       1     121 [.       2     125 ..       2     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 3.6e-21
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCHHH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp.idaei 77 
                                    i++DTs++ al   g+ ++ +a++l+++    ++ts++vl E++  l+r   +++++a++ ++ ++ls +  ++ ++a++
  gi|121638434|ref|YP_978658.1|   2 IFVDTSFWAALGnAGDARHGTAKRLWASKpPVVMTSNHVLGETWTLLNR---RCGHRAAVAAAAIRLSTVVRVEhVTADL 78 
                                    79*******999*************************************...**************555555555***** PP

                                    HHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  78 aeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvak 121
                                     e+a+e+  +++    +  Da   A++++ gi+  + fD df+ +++
  gi|121638434|ref|YP_978658.1|  79 EEQAWEWLVRHDereYSFVDATSFAVMRKKGIQNAYAFDGDFSAAGF 125
                                    ******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 960.35
//
Query:       gi|121638435|ref|YP_978659.1|  [L=81]
Description: hypothetical protein BCG_2573c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-07   30.5   4.6    3.5e-07   29.9   4.6    1.3  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   4.6   1.9e-11   3.5e-07       1      39 []      11      49 ..      11      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-11
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyler 39
                                   r++i++de+++++L   arrr+ S+ +lIRe+++e+l +
  gi|121638435|ref|YP_978659.1| 11 RLQIYIDEDVDRALAVEARRRRTSKAALIREYVAEHLRQ 49
                                   89**********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 579.93
//
Query:       gi|121638436|ref|YP_978660.1|  [L=139]
Description: hypothetical protein BCG_2574c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-17   62.3  12.7    7.4e-17   61.7  12.7    1.3  1  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7  12.7   4.1e-21   7.4e-17       3     106 ..       6     108 ..       4     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.1e-21
                  Peptidase_A24   3 lltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvlllislvdeqamGgGDvklaavl 82 
                                    +l+++ vl+v D+++r+lp++ltlp++ +++lfa      +     a++ga+++a+v+ll+ l    amG+GDvkla++l
  gi|121638436|ref|YP_978660.1|   6 VLAWMGVLCVCDVRQRRLPNWLTLPGAGVILLFAG----LAGRGVPALAGAAALAGVYLLVHLALPAAMGAGDVKLAIGL 81 
                                    6899*****************************93....5777788999999999999999999**************** PP

                  Peptidase_A24  83 gaflgwerl...llavlvaillgavlg 106
                                    g + g++ +   +la l+a ll+av+g
  gi|121638436|ref|YP_978660.1|  82 GGLTGCFGVevwFLAALAAPLLTAVCG 108
                                    ***995555444999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1008.62
//
Query:       gi|229576791|ref|YP_978661.2|  [L=275]
Description: shikimate 5-dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-18   65.1   0.0    9.9e-18   64.2   0.0    1.5  1  Shikimate_dh_N  Shikimate dehydrogenase substrate binding dom
    3.3e-10   39.5   0.7    6.1e-10   38.7   0.7    1.4  1  SDH_C           Shikimate 5'-dehydrogenase C-terminal domain
     0.0002   21.5   0.1    0.00031   20.8   0.1    1.2  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
       0.12   13.0   0.5       0.27   11.8   0.5    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   2.2e-21   9.9e-18       1      83 []      16      98 ..      16      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.2e-21
                                   EEESS-TT-SHHHHHHHHHHHCTS.SEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--S CS
                 Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalgl.ngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvN 81
                                   v+G+pi+hS+SP++h aa++algl +++ye +e  + el+ +v ++  +++ G++vT+P K a+++++de +++A+ +g++N
  gi|229576791|ref|YP_978661.2| 16 VLGSPIAHSRSPQLHLAAYRALGLhDWTYERIECGAAELPVVVGGFG-PEWVGVSVTMPGKFAALRFADERTARADLVGSAN 96
                                   79*********************989********************9.8********************************* PP

                                   EE CS
                 Shikimate_dh_N 82 ti 83
                                   t+
  gi|229576791|ref|YP_978661.2| 97 TL 98
                                   *7 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.7   1.4e-13   6.1e-10       1      26 [.     242     267 ..     242     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.4e-13
                                    HHHHHHHHHHHHHHHHHS----HHHH CS
                          SDH_C   1 GLgMLveQgaeqFelWTGrepPvevM 26 
                                    GL+ML++Q+++q e +TG ++P+e+M
  gi|229576791|ref|YP_978661.2| 242 GLQMLLHQAFAQVEQFTGLPAPREAM 267
                                    9************************* PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     7e-08   0.00031      14      85 ..     125     200 ..     117     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-08
                                    EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCG..HHHHHHT-SEEEE-SSS CS
                   Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealklee..lkellaeadvvisatas 85 
                                    ++l++G G +a  ++  L++ gv++++v+ R+ ++a++l++     g+ ++++++++  l +++a+a+v++s + +
  gi|229576791|ref|YP_978661.2| 125 HALVLGSGGTAPAAVVGLAELGVTDITVVARNSDKAARLVDLGtrVGVATRFCAFDSggLADAVAAAEVLVSTIPA 200
                                    789**********************************999754223556777777755588999999999887765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5     6e-05      0.27       4      81 ..     128     210 ..     126     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneeaaeeadvvvlavkpedve 75 
                                    ++G+G  + a + gl++ g   ++i+v+  rn +ka+ l +               ++  ++a++ a+v+v +++ e+++
  gi|229576791|ref|YP_978661.2| 128 VLGSGGTAPAAVVGLAELG--VTDITVV-ARNSDKAARLVDLGTrvgvatrfCAFDSGGLADAVAAAEVLVSTIPAEVAA 204
                                    68*****************..8888877.899999999987666777987775566667899999*********999998 PP

                                    HHHHHC CS
                  F420_oxidored  76 evlsel 81 
                                      +  l
  gi|229576791|ref|YP_978661.2| 205 GYAGTL 210
                                    877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1966.77
//
Query:       gi|121638438|ref|YP_978662.1|  [L=417]
Description: hypothetical protein BCG_2576c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-64  216.6   0.0    5.6e-64  216.4   0.0    1.1  1  YceG      YceG-like family
  ------ inclusion threshold ------
       0.15   11.5   1.4       0.33   10.3   1.4    1.5  1  Vac7      Vacuolar segregation subunit 7


Domain annotation for each model (and alignments):
>> YceG  YceG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.4   0.0   6.2e-68   5.6e-64       1     274 [.      86     405 ..      86     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 6.2e-68
                                    EEE-TT--HHHHHHHHHHTTSSS-HHHHHHHHHHHT.------EEEEE-TT--HHHHHHHHHCTSBS....SEEE-TT-- CS
                           YceG   1 vtipegsslseiaekLeeagviksaeafkllaklkk.kkalkaGeyelkkgmsleeilekLtkgkqekr..kvtipeglt 77 
                                    ++i++g+s+++++e+L ++gv+++ +af  +a+ ++  +++++G y++++++s+++++++Lt++++  r  k++ipeg++
  gi|121638438|ref|YP_978662.1|  86 IQIRAGDSTTAVGETLLKHGVVATVRAFVDAAHGNTaISSIQPGFYRMRTEISAASAVARLTDPHN--RvgKLVIPEGRQ 163
                                    689********************99999444444444566***********************966..3368******** PP

                                    HHHHH............HHHHHSTTS-HHHHH..............S-GGGG-TT-.....................STT CS
                           YceG  78 leqia............eklekkaelskeell..............kaskeeklkv.....................ekl 110
                                    l++++            + ++++++++ + ++              +        +                     +++
  gi|121638438|ref|YP_978662.1| 164 LDDTTdmktnvvnpgifALISRATCVDLDGTQrcvsvadlraaasrS--------TptmlsvprwavgpvmelgtdhRRI 235
                                    *****888888888887777766666665555887777654433220........1233445666667777777777889 PP

                                    TT-S-SCEE--SSS--HHHHHHHHHHHHHHHT...HHH.......HCT--HHHHHHHHHHHHHH--SSS-HHHHHHHHHH CS
                           YceG 111 eGylfPdtYefkkgtsaeeilkrmlaefekvl...kraek...akasgltpyevltlASivekEaakaeerpkvAsVfln 184
                                    eG+++P t+++++++sae+il++++++   ++           ak+ gl+py++l++AS+v++Ea+ ++++pkvA+V++n
  gi|121638438|ref|YP_978662.1| 236 EGLIAPGTFNIDPSASAETILATLISAGAVEYmksG---LvdtAKSLGLSPYDILVVASLVQQEAN-TQDFPKVARVIYN 311
                                    **************************9977554443...144589********************8.899********** PP

                                    HHHTT-----HHHHHHH.T-S---CCHH..C---TT-TTTSSSS-SS-SS---HHHHHHHHS-------EEEE-....-E CS
                           YceG 185 RLkkgmrLqsDpTviYg.gkgrltkkdl..etdspYNTYkikGLPpgPIanPgkaaieAalnpaktdylYFvakk.dgth 260
                                    RL+++ +L++D+Tv+Y  +++++  +d+  ++++p+NTY+ +GLP+++I++Pg +a++Aa +p   d+lYFv+ + +gt+
  gi|121638438|ref|YP_978662.1| 312 RLHEHRTLEFDSTVNYPlDRREVATSDTdrAQRTPWNTYMAQGLPATAICSPGVDALRAAEHPVPGDWLYFVTIDsQGTT 391
                                    *****************76665666555324779******************************999*****764389** PP

                                    EEESSHHHHHCT-X CS
                           YceG 261 aFaktleeHnknva 274
                                     F++++++H +n++
  gi|121638438|ref|YP_978662.1| 392 LFTRDYQQHLANIE 405
                                    ***********985 PP

>> Vac7  Vacuolar segregation subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.4   3.7e-05      0.33     263     316 ..      14      64 ..       8      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.7e-05
                           Vac7 263 svRsarsrrsrrrpnsaslrqleelqqrrrsllsrfaaClvltvllllvvsgai 316
                                    svR +r+rr +r   s + r++ ++ +rrr +   fa  l+++v+++ vv+ga 
  gi|121638438|ref|YP_978662.1|  14 SVRPNRHRR-TRV--SRAQRRHAQQIRRRRRVAGGFALSLLVVVVVVAVVVGAK 64 
                                    567777666.444..4555555554699999*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3200.14
//
Query:       gi|121638439|ref|YP_978663.1|  [L=170]
Description: Holliday junction resolvase-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-41  142.0   0.6    1.6e-41  141.8   0.6    1.0  1  RuvX      Holliday junction resolvase


Domain annotation for each model (and alignments):
>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.6   9.2e-46   1.6e-41       2     135 .]      23     156 ..      22     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 9.2e-46
                                    -EEEEEESSSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHH CS
                           RuvX   2 rilglDvGtkriGvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeL 81 
                                    r+lg+DvG++riGvA+sdp+ ila+p+et++r+++ k+l++l++l++e e+ e++vGlP++l ++ g+sa+ + ++ae+L
  gi|121638439|ref|YP_978663.1|  23 RRLGIDVGAARIGVACSDPDAILATPVETVRRDRSGKHLRRLAALAAELEAVEVIVGLPRTLADRIGRSAQDAIELAEAL 102
                                    79*******************************999******************************************** PP

                                    HHT..T-EEEEE--S----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                           RuvX  82 akrlkklpvelvDErlttveaerilresglsrkkrkkvvDklaAviiLqsyLds 135
                                    a+r+++ pv+l DErlttv+a+r+lr++g++++++++v+D++aAv iLqs+Ld+
  gi|121638439|ref|YP_978663.1| 103 ARRVSPTPVRLADERLTTVSAQRSLRQAGVRASEQRAVIDQAAAVAILQSWLDE 156
                                    ****************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1381.15
//
Query:       gi|121638440|ref|YP_978664.1|  [L=904]
Description: alanyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.1e-206  686.7   0.0   2.6e-206  686.4   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.8e-19   70.6   6.0    4.1e-19   69.4   4.5    2.3  2  DHHA1         DHHA1 domain
    8.6e-17   61.0   0.2    1.8e-16   59.9   0.2    1.6  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
      0.001   16.8   0.0     0.0024   15.6   0.0    1.5  2  ACR_tran      AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
        3.8    7.6   6.0         14    5.9   6.0    1.9  1  DUF1192       Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.4   0.0  7.2e-210  2.6e-206       1     550 [.       5     574 ..       5     576 .. 0.97

  Alignments for each domain:
  == domain 1  score: 686.4 bits;  conditional E-value: 7.2e-210
                                    HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSS CS
                   tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGkta 80 
                                    eir++Fld+F k gHt+v+s+sv+  +dp+llfvnAgm+qf p+flg++ +p++++a+++QkciR+     D+++VG+t+
  gi|121638440|ref|YP_978664.1|   5 EIRKRFLDHFVKAGHTEVPSASVIL-DDPNLLFVNAGMVQFVPFFLGQR-TPPYPTATSIQKCIRTP----DIDEVGITT 78 
                                    8************************.***********************.*****************....********* PP

                                    S--SEEEEEEEEESSSS-HHHHHHHHHHHHHTT.....TT--GGGEEEEEETTEHHHHHHHHHTTTTEGGGEEEE-HHHH CS
                   tRNA-synt_2c  81 rHhTfFeMlGnfsfgdYfkeeaiefawelltke.....lgldkerlyvtvfeeddeaveiweklvgvpeerilrfgekdn 155
                                    rH+TfF+M+GnfsfgdYfk+ aie+aw llt++     +gld+er+++tv+ +ddeav++w++++g+p+eri+r g++dn
  gi|121638440|ref|YP_978664.1|  79 RHNTFFQMAGNFSFGDYFKRGAIELAWALLTNSlaaggYGLDPERIWTTVYFDDDEAVRLWQEVAGLPAERIQRRGMADN 158
                                    *******************************9989999****************************************** PP

                                    EEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST......TSHEEEEEEEEEEEEEEHH CS
                   tRNA-synt_2c 156 fwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree......dgtlkpLpkksidtGmgle 229
                                    +w+mg  gpcgp+seiyydrg+e+g   a+++   ++dr+le+wnlvfmq++r e       ++l pLp+++idtGmg+e
  gi|121638440|ref|YP_978664.1| 159 YWSMGIPGPCGPSSEIYYDRGPEFGP--AGGPIV-SEDRYLEVWNLVFMQNERGEgttkedYQILGPLPRNNIDTGMGVE 235
                                    *************************9..677666.9*****************9999988889999************** PP

                                    HHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--T.CSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHH CS
                   tRNA-synt_2c 230 rlvavLqevrsnydtdlfvpvieaieeisgaty.edkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRra 308
                                    r++ vLq+v++ y+tdl++pvi++++++++++y   ++e d+++r+iaDH r++a++++dGv+p+n+grgYvlRrllRr+
  gi|121638440|ref|YP_978664.1| 236 RIALVLQDVHNVYETDLLRPVIDTVARVAARAYdVGNHEDDVRYRIIADHSRTAAILIGDGVSPGNDGRGYVLRRLLRRV 315
                                    *********************************88999****************************************** PP

                                    HHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC..CSEEXHHH CS
                   tRNA-synt_2c 309 vrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkk..kkelsged 386
                                    +r ak Lg++++++ +l+a+v +++g+ ypel ++ e++++i  +Ee++F++Tl++G++l+ee+++++kk  +++lsg+d
  gi|121638440|ref|YP_978664.1| 316 IRSAKLLGIDAAIVGDLMATVRNAMGPSYPELVADFERISRIAVAEETAFNRTLASGSRLFEEVASSTKKsgATVLSGSD 395
                                    *********************************************************************99999****** PP

                                    HHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHH..CCTSTTTXXXXXX CS
                   tRNA-synt_2c 387 afkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkt..eeflgyeeleaea 464
                                    af+L+dtyGfP++lt e+a+e+gl+vd+ gf+++m+eqr+r+k++++++k++++d++a++el ++  +ef+g++el+++a
  gi|121638440|ref|YP_978664.1| 396 AFTLHDTYGFPIELTLEMAAETGLQVDEIGFRELMAEQRRRAKADAAARKHAHADLSAYRELVDAgaTEFTGFDELRSQA 475
                                    ***************************************************************9999************* PP

                                    TSXXXXXXSEEEEEEEEEETTE........EEESEEXXXXSSSSCSXXXEEEEESS....EEEEESEEEEET.TEEEEEX CS
                   tRNA-synt_2c 465 kvlallkdkefveeveegeevg........vvLdrTpfYaesGGqigDeGliekeg....aefrvkdvqkak.gvvlhkg 531
                                    ++l+++ d++ v  v++g ++g        +vLdrTp+YaesGGqi+DeG+i+++g    a+++v+dvqk++ ++++h++
  gi|121638440|ref|YP_978664.1| 476 RILGIFVDGKRVPVVAHGVAGGagegqrveLVLDRTPLYAESGGQIADEGTISGTGsseaARAAVTDVQKIAkTLWVHRV 555
                                    ***************999888888888888**********************9877666699*********999****** PP

                                    SS.XSXXXTTSEEEEEEXH CS
                   tRNA-synt_2c 532 kleegklkvgdkvkaevde 550
                                    ++e+g++ +gd+v+a+vd 
  gi|121638440|ref|YP_978664.1| 556 NVESGEFVEGDTVIAAVDP 574
                                    *****************95 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.61   2.2e+03      33      57 ..     559     582 ..     534     585 .. 0.65
   2 !   69.4   4.5   1.1e-22   4.1e-19       2     137 ..     754     896 ..     753     897 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.61
                                    TCEEECTCEEEEEECHCCHHHHHHH CS
                          DHHA1  33 kaeevkgvkvlvaevgeewdagalg 57 
                                    + e v+g++v++a + ++w++ga++
  gi|121638440|ref|YP_978664.1| 559 SGEFVEGDTVIAAVD-PGWRRGATQ 582
                                    233344777777777.***999876 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 1.1e-22
                                    HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEEC CS
                          DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeeg 80 
                                     +l e+++++ekele+ + a a+++a ++ + a+++ +v +++++++ ++ a +l++++++++ kl++ p +v++++e++
  gi|121638440|ref|YP_978664.1| 754 ANLVERLRAAEKELERVRMASARAAATNAAAGAQRIGNVRLVAQRMSGGMTAADLRSLIGDIRGKLGSePAVVALIAEGE 833
                                    67889*************************************************************88899999999999 PP

                                    T.EEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHH CS
                          DHHA1  81 d.kvkvsarskkd....gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeea 137
                                    + +v   ++++++    g+ a++l+k++a ++ g+GGG+ dlA+G+g+++  +++al+a+++ 
  gi|121638440|ref|YP_978664.1| 834 SqTVPYAVAANPAaqdlGIRANDLVKQLAVAVEGRGGGKaDLAQGSGKNPTGIDAALDAVRSE 896
                                    998888888887788********************************************9976 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.2   5.2e-20   1.8e-16       1      44 []     673     717 ..     673     717 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.2e-20
                                    EEEEEETT..EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGd.isvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    vrvv++G  +s elCgGtHv+nT +Ig + il e+si++g+rR++
  gi|121638440|ref|YP_978664.1| 673 VRVVEMGGpFSLELCGGTHVSNTAQIGPVTILGESSIGSGVRRVE 717
                                    9*****866**********************************96 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.27   9.6e+02     725     770 ..     319     367 ..     317     373 .. 0.79
   2 !   15.6   0.0   6.6e-07    0.0024     594     747 ..     714     869 ..     708     882 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.27
                                    HHHCTCSHH...HHHHHHHHHHTTEEEEEEEETTEEEEEEEEE-GGGSS CS
                       ACR_tran 725 aarlGvsis...dindtletalggsyvndfieegrrvkvvvrleedlrs 770
                                    a+ lG++++   d  +t+ +a+g sy + + + +r  ++ v  e+++  
  gi|121638440|ref|YP_978664.1| 319 AKLLGIDAAivgDLMATVRNAMGPSYPELVADFERISRIAVAEETAFNR 367
                                    66677776511166678999*********************99998865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.6e-07
                                    EEEEEEECECS..SE..ECCCEEEEEEEES.-GCGS-SGGGSHHHHHHHHHHHCTTSTSSEEEEEETTSSCCCSSSSCEE CS
                       ACR_tran 594 esvfavtGfae..sgdtagpnsakvfisLk.pekerkeeeksvealierlrkelkkipganvellapiqlreletlsgvr 670
                                    ++v a +G++   +  ++++ +a +  sLk p +e ++   +  + +++++kel+ ++ a  ++ a+ +  + + ++ vr
  gi|121638440|ref|YP_978664.1| 714 RRVEAYVGLDSfrHLAKERALMAGLASSLKvPSEEVPARVANLVERLRAAEKELERVRMASARAAATNAAAGAQRIGNVR 793
                                    56666666654455556677777777888756777766666666666777788899999999999999999********* PP

                                    EEEEE.SSSSHHHHHHHHHHHHHHHHCCSTTEEEEEESS-S-EEEEEEEE-HHHHHHCTCSHHHHHHHHHHHHTTEE CS
                       ACR_tran 671 selqvklfgddleaLseaaeqllaalkelpelsdvrseqqedqpqlqveidrekaarlGvsisdindtletalggsy 747
                                    +  q +  g  +  L+ +  +++ +l   p++  +  e+++++  + v  +  +a++lG++++d  + l++a++g+ 
  gi|121638440|ref|YP_978664.1| 794 LVAQRMSGGMTAADLRSLIGDIRGKLGSEPAVVALIAEGESQTVPYAVAAN-PAAQDLGIRANDLVKQLAVAVEGRG 869
                                    ***************************************999999999887.579******************9985 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.0    0.0038        14      22      55 ..     753     786 ..     752     786 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0038
                        DUF1192  22 veELeerIalLeaEIaRleaaiakkkasraAAea 55 
                                    v+ L er  + e+E +R++ a a++ a++aAA a
  gi|121638440|ref|YP_978664.1| 753 VANLVERLRAAEKELERVRMASARAAATNAAAGA 786
                                    78899***************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (904 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.40
# Mc/sec: 6830.78
//
Query:       gi|121638441|ref|YP_978665.1|  [L=129]
Description: hypothetical protein BCG_2579c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-25   87.1   0.0    1.2e-24   86.7   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   6.5e-29   1.2e-24       1     113 [.      13     124 ..      13     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 6.5e-29
                                    E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHHH-S CS
                        UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssllgs 79 
                                    d+t+ v+++   +  ++Gl++vf++h+ta+++i E+  ++  eDl ++l +l+p++ +Yrh++    +++ Hl  +++ +
  gi|121638441|ref|YP_978665.1|  13 DLTDAVRAF--CTAHDDGLCNVFVPHATAGVAIIET-GAGSDEDLVDTLVRLLPRDdRYRHAHGSYGHGADHLLPAFVAP 89 
                                    689999999..66789*******************9.9999*********************5555699*********** PP

                                    EEEEEEETTEE---TTEEEEEEESS.-SSEEEEEE CS
                        UPF0047  80 sltipvedgklalGtwqsiylveld.gpreRkvvv 113
                                    s+t+pv+ g+  lGtwqsi+lv+l+ ++ +R+v +
  gi|121638441|ref|YP_978665.1|  90 SVTVPVSGGQPLLGTWQSIVLVDLNqDNPRRSVRL 124
                                    ************************95556687765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 945.83
//
Query:       gi|121638442|ref|YP_978666.1|  [L=224]
Description: hypothetical protein BCG_2580 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.3   0.7    0.00018   21.6   0.0    3.1  3  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   9.9e-09   0.00018       7      67 ..      25      84 ..      19      88 .. 0.89
   2 ?    0.9   0.6     0.029   5.1e+02      54      70 ..     104     120 ..     103     122 .. 0.88
   3 !    5.1   0.0    0.0013        24       9      67 ..     130     187 ..     122     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.9e-09
                                   EEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHH CS
                            ABM  7 eirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahl 67
                                   +i+++++  +  ++ ++++v + l+ ++Gc+g++ll  +++ ++ + ++ We+++a+ a +
  gi|121638442|ref|YP_978666.1| 25 TIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLLV-DRQSGRCIATSAWETAEAMHASR 84
                                   788888888999999******999*************.888888************98865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.029
                                    EEEESSHHHHHHHHTSH CS
                            ABM  54 ieeWeseaaleahlksp 70 
                                    +eeWe +a +++h++++
  gi|121638442|ref|YP_978666.1| 104 VEEWEIAAMHRDHRSAE 120
                                    79***********9876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0013
                                    EESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHH CS
                            ABM   9 rvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahl 67 
                                    +v+ +q ++ ++ +++ v + ++  +G+ +++ll  ++  ++ v+ + ++s +a+e+ +
  gi|121638442|ref|YP_978666.1| 130 KVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLV-DRTSGRAVSSATFDSFDAMERNR 187
                                    577777777777777766666699**********9.77777799999999999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1763.14
//
Query:       gi|121638443|ref|YP_978667.1|  [L=236]
Description: hypothetical protein BCG_2581 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.5   0.0     0.0069   16.5   0.0    2.3  2  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.8e-07    0.0069      19      67 ..      48      95 ..      31      99 .. 0.84
   2 !    9.8   0.0   4.6e-05      0.83       9      65 ..     141     197 ..     134     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-07
                                   HHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHH CS
                            ABM 19 ldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahl 67
                                   ++ ++++v + l+e +Gc g++ll  +++ ++ + ++ We+ +a++a +
  gi|121638443|ref|YP_978667.1| 48 IAHVRDVVMPALQEIDGCVGVSLLV-DRQSGRCIATSAWETLEAMRASV 95
                                   6778888888889************.888888*************9976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4.6e-05
                                    EESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHH CS
                            ABM   9 rvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaalea 65 
                                    +v p+q    l+ ++  v ++l++ +G+ +++l+ +  + ++ v+ + ++s++a+ +
  gi|121638443|ref|YP_978667.1| 141 KVVPDQLGRSLEFYRTSVLPELESLDGFCSASLMVDHPACRRAVSCSTFDSMDAMAR 197
                                    56666666666666666667889*******************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1621.01
//
Query:       gi|121638444|ref|YP_978668.1|  [L=452]
Description: recombination factor protein RarA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-69  231.0   0.3    1.3e-68  230.1   0.3    1.4  1  MgsA_C           MgsA AAA+ ATPase C terminal
    1.2e-26   92.8   2.9    1.5e-26   92.5   0.8    2.2  2  AAA_assoc_2      AAA C-terminal domain
    5.2e-14   52.8   0.1    1.6e-13   51.2   0.0    1.8  2  AAA              ATPase family associated with various cellul
    3.4e-13   49.7   0.0    1.1e-12   48.0   0.0    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.8e-10   38.9   0.3    3.4e-08   33.6   0.2    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
      2e-06   27.6   0.1      0.012   15.3   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    4.8e-06   26.7   0.0    9.5e-06   25.8   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
    7.3e-06   26.5   9.4     0.0003   21.2   0.2    3.2  3  AAA_16           AAA ATPase domain
    3.1e-05   24.3   0.8      0.047   13.9   0.1    2.7  2  AAA_22           AAA domain
    5.5e-05   22.6   7.5      0.013   14.9   0.1    3.2  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00013   21.9   1.4      0.039   13.9   0.0    2.3  2  NACHT            NACHT domain
    0.00022   21.8   0.0    0.00038   21.0   0.0    1.4  1  AAA_18           AAA domain
    0.00038   19.8   0.1     0.0011   18.2   0.1    1.7  1  TIP49            TIP49 P-loop domain
    0.00052   20.1   0.0    0.00098   19.2   0.0    1.4  1  AAA_14           AAA domain
    0.00053   20.0   0.5      0.015   15.3   0.1    2.2  2  ResIII           Type III restriction enzyme, res subunit
    0.00064   19.3   3.9    0.00087   18.9   0.1    2.9  3  AAA_25           AAA domain
     0.0011   18.8   1.2       0.01   15.7   0.1    2.7  2  AAA_3            ATPase family associated with various cellul
     0.0016   18.2   4.4     0.0025   17.6   1.1    2.7  2  AAA_30           AAA domain
     0.0025   17.5   0.0      0.005   16.6   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0043   17.2   0.0      0.011   16.0   0.0    1.7  1  AAA_33           AAA domain
     0.0045   16.2   0.0     0.0074   15.5   0.0    1.4  1  NB-ARC           NB-ARC domain
     0.0054   16.5   0.1      0.044   13.6   0.1    2.0  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0082   15.9   0.0      0.014   15.1   0.0    1.4  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.053   13.9   0.0    1.9  1  AAA_17           AAA domain
      0.021   14.1   0.1      0.057   12.7   0.0    1.8  2  Zeta_toxin       Zeta toxin
      0.021   15.2   0.0      0.038   14.4   0.0    1.4  1  RNA_helicase     RNA helicase
      0.024   15.2   0.0      0.036   14.6   0.0    1.2  1  AAA_23           AAA domain
      0.026   14.4   0.3        1.3    8.9   0.0    2.3  2  ATPase_2         ATPase domain predominantly from Archaea
      0.033   14.7   0.1       0.14   12.7   0.1    1.8  1  ABC_tran         ABC transporter
      0.034   13.2   0.0      0.082   12.0   0.0    1.6  1  MCM              MCM P-loop domain
      0.051   13.8   0.0       0.11   12.8   0.0    1.6  1  AAA_28           AAA domain
      0.074   11.7   0.0        0.1   11.2   0.0    1.1  1  AAA_13           AAA domain
      0.075   13.1   0.0       0.15   12.1   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.092   13.1   6.2        2.6    8.4   0.2    2.8  3  AAA_19           AAA domain
       0.12   12.4   0.0       0.45   10.5   0.0    1.9  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.2   0.2        0.6   10.0   0.0    1.9  2  NTPase_1         NTPase
       0.14   12.8   0.2       0.51   11.0   0.2    2.1  1  HTH_32           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> MgsA_C  MgsA AAA+ ATPase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   0.3   2.8e-71   1.3e-68       1     166 [.     278     443 ..     278     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 2.8e-71
                                    TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHTTGGGSTTHHHHHHHHHHHHHHH-TTTTHHHHHHHHHHHHCS---- CS
                         MgsA_C   1 GSdpdAAlyylarmleaGedprfiaRRlviiAseDiGlAdpqalqlavaaaeaveriGlpEariaLaqavvylalapKSn 80 
                                    GSd+dAAl+ylarml aGedprfiaRRl+i+AseDiG+Adp+alq+avaaa++v  iG+pEa+++La+a+++la+apKSn
  gi|121638444|ref|YP_978668.1| 278 GSDVDAALHYLARMLVAGEDPRFIARRLMILASEDIGMADPSALQVAVAAAQTVALIGMPEAQLTLAHATIHLATAPKSN 357
                                    9******************************************************************************* PP

                                    GG.GHHHHHHHHH---------GGGST...........T-T---GGG--SS------S-CCG--..--------HHHHHH CS
                         MgsA_C  81 aaykAikkaledvkekkslevPlhLrnaptklakklgygkgYkyphdypegvvkqqylpdelkkkkfYepterglekkik 160
                                    a+++A+ +a++d+k++k++ vP+hLr+ ++++a++lg+ +gYky+hd+p+gvv+qqy pdel + ++Y+pt rg e++i+
  gi|121638444|ref|YP_978668.1| 358 AVTTALAAAMNDIKAGKAGLVPAHLRDGHYSGAAALGNAQGYKYSHDDPDGVVAQQYPPDELVDVDYYRPTGRGGEREIA 437
                                    **************************************************************999*************** PP

                                    H-XXX. CS
                         MgsA_C 161 erlekl 166
                                     rl++l
  gi|121638444|ref|YP_978668.1| 438 GRLDRL 443
                                    *99987 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       8.7   4.2e+03      12      40 ..      81     109 ..      78     152 .. 0.64
   2 !   92.5   0.8   3.1e-29   1.5e-26       4      81 .]     202     277 ..     200     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.7
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                    AAA_assoc_2  12 lealaeladGDaRkaLnlLElaaeaaeak 40 
                                    l+al++ a G    aL +L + ++  +a 
  gi|121638444|ref|YP_978668.1|  81 LAALISQATGRRFEALSALSAGVKEVRAV 109
                                    56666777776667777777666665543 PP

  == domain 2  score: 92.5 bits;  conditional E-value: 3.1e-29
                                    .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHH CS
                    AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryDkagdehYdliSAlhKSiR 81 
                                    +++++++a+++l++la GDaR+aL++LE+aaeaa+a    + ++ +++e++++++a+ryD++gd+hYd++SA++KS+R
  gi|121638444|ref|YP_978668.1| 202 AVAVAPEAVDLLVQLAAGDARRALTALEVAAEAAQA--AGELVSVQTIERSVDKAAVRYDRDGDQHYDVVSAFIKSVR 277
                                    68899*****************************97..999************************************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   3.4e-16   1.6e-13       1     112 [.      68     161 ..      68     178 .. 0.81
   2 ?   -1.9   0.0       8.5   4.1e+03      76     114 ..     259     315 ..     214     324 .. 0.57

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 3.4e-16
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgs 77 
                                    v+lyGppG GKT+la  + + +g++f  +s+ +          k++r+++++ ++     ++++lfiDE++++ k++   
  gi|121638444|ref|YP_978668.1|  68 VILYGPPGSGKTTLAALISQATGRRFEALSALSAG-------VKEVRAVIENSRKALlhgEQTVLFIDEVHRFSKTQ--- 137
                                    79***************************999998.......88888888887776688777***************... PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..G CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnr..p 112
                                            +++Ll++++         ++++at++   
  gi|121638444|ref|YP_978668.1| 138 --------QDALLSAVEHRVV-----LLVAATTEnpS 161
                                    ........9999999998755.....55666655343 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.5
                                    TCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESSGGG CS
                            AAA  76 gseseeeervvnqLlteldgvkkk..................eskvivigatnrpdk 114
                                    +++ +++ +vv+++++ + g + +                   ++ ++i+a+ ++ +
  gi|121638444|ref|YP_978668.1| 259 DRDGDQHYDVVSAFIKSVRGSDVDaalhylarmlvagedprfIARRLMILASEDIGM 315
                                    445555556666666655555555444444444444444444333455555555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.2e-15   1.1e-12       1     116 [.      35     153 ..      35     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.2e-15
                         RuvB_N   1 lrPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt 80 
                                    +rP sl+e +gq+++ +  + + +     ++ +  v+lyGpPG Gkttla++i++  g ++++ s+      +++ a++ 
  gi|121638444|ref|YP_978668.1|  35 MRPASLDEVVGQDHLLAPGSPLRRL--VEGSGVASVILYGPPGSGKTTLAALISQATGRRFEALSALSA-GVKEVRAVIE 111
                                    6899999999999887654333222..23456788************************9998887543.3445555555 PP

                         RuvB_N  81 n....le..ekdvlfideihrlsraveevlysamedfrldiv 116
                                    n    l   e+ vlfide+hr+s++ ++ l sa+e   + +v
  gi|121638444|ref|YP_978668.1| 112 NsrkaLLhgEQTVLFIDEVHRFSKTQQDALLSAVEHRVVLLV 153
                                    412223222678***********************8776555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   7.1e-11   3.4e-08       1     102 [.      67     158 ..      67     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 7.1e-11
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE.--TT--HHHHH--B--.........--------G-SEEEEESGGG--H CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvq.ltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraes 79 
                                    +v+L GppG+gK++la  +++a++r++e    l+++   ++++  +e  n++     ++l     e  +l++DEv+r ++
  gi|121638444|ref|YP_978668.1|  67 SVILYGPPGSGKTTLAALISQATGRRFEALSaLSAGV--KEVRAVIE--NSR-----KALL--HGEQTVLFIDEVHRFSK 135
                                    59*********************99999875145544..34444444..333.....3344..34777************ PP

                                    HHHHHHHHHHHSSEEE..-SSSE CS
                          AAA_5  80 evlnsLlslleerrllleeggel 102
                                      +++Lls  e+r +ll   +++
  gi|121638444|ref|YP_978668.1| 136 TQQDALLSAVEHRVVLLVAATTE 158
                                    ***************99888776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0014      0.67      23      56 ..      66      99 ..      53     112 .. 0.83
   2 !   15.3   0.0   2.5e-05     0.012      92     130 ..     120     158 ..     111     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                Sigma54_activat 23 lsvlitGesGtGKellaraiheaskrkekpfvav 56
                                   +sv++ G  G+GK++la +i +a+ r+ + + a+
  gi|121638444|ref|YP_978668.1| 66 ASVILYGPPGSGKTTLAALISQATGRRFEALSAL 99
                                   789******************9998887766655 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.5e-05
                                    TTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                     ++ +lf+De+++++ + Q  Ll +++++ v  v +++e
  gi|121638444|ref|YP_978668.1| 120 GEQTVLFIDEVHRFSKTQQDALLSAVEHRVVLLVAATTE 158
                                    67899***********************99988876655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     2e-08   9.5e-06      22     131 ..      66     180 ..      58     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2e-08
                                    S-EEEEEETT--HHHHHHCC--TTS-EE.--SSTTHHHH-HHHHHHHT.......TTSEEEEEE-TT--HHHHHHHHHHH CS
                Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgpwl.eifvverlaklpldlleqa.......kggtLylkdiadlskaeqkeLlell 93 
                                    + v l G++Gsgk++ A l+++  g+   ++  +  ++k+   ++e++       ++ +L++ +++ +sk +q  Ll ++
  gi|121638444|ref|YP_978668.1|  66 ASVILYGPPGSGKTTLAALISQATGRRFeALSALSAGVKEVRAVIENSrkallhgEQTVLFIDEVHRFSKTQQDALLSAV 145
                                    57999****************99988651566677777777777776444466669999*****************9999 PP

                                    HHHTTTT-EEEEEEEE-TTT..----HHHHHHHHSSSE CS
                Sigma54_activ_2  94 akaeksslrlVstsskdleqlleagafdekLlkeLsel 131
                                    ++     + lV+++ ++    + a+ + ++L+ +L +l
  gi|121638444|ref|YP_978668.1| 146 EHR---VVLLVAATTENPSFSVVAPLLSRSLILQLRPL 180
                                    888...999********999999999999999998665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   6.1e-07    0.0003      16      50 ..      56      91 ..      53     106 .. 0.83
   2 !    9.8   0.1    0.0019      0.94     119     158 ..     106     144 ..      92     165 .. 0.74
   3 ?    0.0   0.7         2   9.7e+02      80      88 ..     211     219 ..     145     339 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.1e-07
                         AAA_16 16 lervrsgrp.elvllsGesGvGKsslvrellralek 50
                                   l+r+ +g++  +v+l+G++G+GK++l+  + +a  +
  gi|121638444|ref|YP_978668.1| 56 LRRLVEGSGvASVILYGPPGSGKTTLAALISQATGR 91
                                   7888999999*****************999954443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                         AAA_16 119 llellkrllallsrderplvlvlDdlqwadeaslqllaaL 158
                                    +++++ +  + l ++e+ +vl++D+++++  +++++l + 
  gi|121638444|ref|YP_978668.1| 106 VRAVIENSRKALLHGEQ-TVLFIDEVHRFSKTQQDALLSA 144
                                    55566666644555466.*****************95433 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2
                         AAA_16  80 ellrqllde 88 
                                    +ll ql++ 
  gi|121638444|ref|YP_978668.1| 211 DLLVQLAAG 219
                                    222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   9.8e-05     0.047       7      29 ..      67      89 ..      61     110 .. 0.83
   2 !    8.2   0.1    0.0059       2.9      83     116 ..     114     145 ..      94     159 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                   +++++G++G+GKTtl++ + +  
  gi|121638444|ref|YP_978668.1| 67 SVILYGPPGSGKTTLAALISQAT 89
                                   689************99877655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0059
                         AAA_22  83 eqalraravielliiDEaqhlrseealeeLrsll 116
                                    ++al +     +l iDE++++ s+++   L s +
  gi|121638444|ref|YP_978668.1| 114 RKALLHGEQ-TVLFIDEVHRF-SKTQQDALLSAV 145
                                    344444444.8**********.766655554444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.7e-05     0.013      20      43 ..      63      86 ..      40     120 .. 0.86
   2 !    9.8   0.1   0.00099      0.48     106     141 ..     121     156 ..     113     169 .. 0.85
   3 ?    0.3   1.2      0.79   3.8e+02      13      65 ..     319     369 ..     314     396 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                   Mg_chelatase 20 aGgHnlllvGppGsGKtmlakrlp 43
                                   +G  +++l+GppGsGKt la+ ++
  gi|121638444|ref|YP_978668.1| 63 SGVASVILYGPPGSGKTTLAALIS 86
                                   78899***************8776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00099
                   Mg_chelatase 106 hnGvLfLDElpefkrkvlevLRePledgevtisrak 141
                                    ++ vLf+DE+  f+++  ++L + +e++ v +  a+
  gi|121638444|ref|YP_978668.1| 121 EQTVLFIDEVHRFSKTQQDALLSAVEHRVVLLVAAT 156
                                    577************************999876655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.79
                   Mg_chelatase  13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                     al++a+a    + l+G p +  t+  + ++   +   +++a+ +a  a++++
  gi|121638444|ref|YP_978668.1| 319 SALQVAVAAAQTVALIGMPEAQLTLAHATIHL--ATAPKSNAVTTALAAAMND 369
                                    69999999999999**9998877765555543..3333444444444444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.1e-05     0.039       3      24 ..      68      89 ..      66      96 .. 0.88
   2 ?    7.0   0.5      0.01       5.1      64     163 ..      98     193 ..      92     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                   vil G++GsGKTtL++ + +a 
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQAT 89
                                   89*************9998875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                                    S--SSS-CCHHHHCCSCCCEE......EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH..H CS
                          NACHT  64 epaapvsevwavllelperlL......lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd..l 135
                                    +++a v+ev+av+   ++ lL      l +D + ++++  +          L + ++     ++ ll+++++++ +   +
  gi|121638444|ref|YP_978668.1|  98 ALSAGVKEVRAVIENSRKALLhgeqtvLFIDEVHRFSKTQQD--------ALLSAVEH----RVVLLVAATTENPSFsvV 165
                                    566667777777777777777888888889999999985444........44455555....788888888888866789 PP

                                    CTTSSCE..EEEE--TCCHHHHHHHHCT CS
                          NACHT 136 eeqleeaivlevegfsesrrkqlvrkyf 163
                                    + +l+++ +l+++++++++++++v + +
  gi|121638444|ref|YP_978668.1| 166 APLLSRSLILQLRPLTAEDTRAVVQRAI 193
                                    9**********************98865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.9e-07   0.00038       1      65 [.      68     146 ..      68     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.9e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf..............gvnlrdvakenglllevdpealdeskrldedkldklldale 65 
                                    ++l G+pG+GKttla  +s+ +g               ++ ++++ ++  l  e++   +de +r+ + ++d+ll+a+e
  gi|121638444|ref|YP_978668.1|  68 VILYGPPGSGKTTLAALISQATGRrfealsalsagvkeVRAVIENSRKALLHGEQTVLFIDEVHRFSKTQQDALLSAVE 146
                                    79****************9998666888899999988877777777888888888777888888888888888888766 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.3e-06    0.0011      27     150 ..      44     157 ..      34     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  27 vGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrks 106
                                    vGq +     + + +l++   +a  +v+l Gp+g+Gkt la  is++ g+   f als+    s+ vk   +++++ rk+
  gi|121638444|ref|YP_978668.1|  44 VGQDHLLAPGSPLRRLVEGSGVA--SVILYGPPGSGKTTLAALISQATGR--RFEALSA---LSAGVKEVRAVIENSRKA 116
                                    66666655556666777777777..899*******************995..5777766...79999999*********9 PP

                                    XXXXXXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-S CS
                          TIP49 107 igvrikeekevleGevveleveeaenplskekkikevkitlkta 150
                                    +     e++ ++  ev  ++ ++++  ls + +++ v ++  t+
  gi|121638444|ref|YP_978668.1| 117 LL--HGEQTVLFIDEVHRFSKTQQDALLS-AVEHRVVLLVAATT 157
                                    85..3577777888888888888888777.44444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     2e-06   0.00098       5     126 ..      68     181 ..      66     185 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpe.weka 82 
                                    +++ G+  +GKTtl+  + +      +++  ++  +   k+ +     +e  ++  l++ ++t+lf+DE+++ ++  ++a
  gi|121638444|ref|YP_978668.1|  68 VILYGPPGSGKTTLAALISQATG---RRFEALSALSAGVKEVRAV---IENSRKAlLHG-EQTVLFIDEVHRFSKtQQDA 140
                                    7999**********877766665...6666666665555555533...34444442445.899********986515678 PP

                         AAA_14  83 lkslvdegknldvivtGSnskllskeiatslagrvaeielypls 126
                                    l s v+++    v++      + s  +   l  r   ++l pl+
  gi|121638444|ref|YP_978668.1| 141 LLSAVEHRV---VLLVAATTENPSFSVVAPLLSRSLILQLRPLT 181
                                    888888772...22222222233333555666666666666665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.17        82      27      47 ..      68      88 ..      56      99 .. 0.81
   2 !   15.3   0.1   3.1e-05     0.015     122     170 ..     111     158 ..      91     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                                   EEEEESTTSTHHHHHHHHHHH CS
                         ResIII 27 glikmaTGtGKTlvaaklier 47
                                   +++  + G+GKT +aa + ++
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQA 88
                                   5667789*****999887654 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.1e-05
                                    .....HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEEEEESS-S CS
                         ResIII 122 eeeseellrdrfdviiiDEaHrlgakkswreilekfkeavllglTATpe 170
                                    e+ ++ ll++++ v++iDE+Hr+++ ++  ++l ++++ v+l + AT e
  gi|121638444|ref|YP_978668.1| 111 ENSRKALLHGEQTVLFIDEVHRFSK-TQQDALLSAVEHRVVLLVAATTE 158
                                    67788899999**************.88888999999999999999975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.8e-06   0.00087       6      54 ..      39      86 ..      34     146 .. 0.82
   2 ?   -2.3   0.0       5.9   2.8e+03     162     186 ..     218     242 ..     213     244 .. 0.83
   3 ?   -0.0   0.1       1.2   5.7e+02      75     107 ..     291     325 ..     277     379 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                         AAA_25  6 elsavsvad.laapppprrwlvkgllpagelallaGapgtGKttlaldla 54
                                    l +v+  d l ap  p+r lv+g     + ++l+G+pg+GKttla  ++
  gi|121638444|ref|YP_978668.1| 39 SLDEVVGQDhLLAPGSPLRRLVEGS--GVASVILYGPPGSGKTTLAALIS 86
                                   555555555599999********99..5699**************97543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                         AAA_25 162 nsdvgalvealeriarrtgaavllv 186
                                    + d++++++ale  a++ +aa  lv
  gi|121638444|ref|YP_978668.1| 218 AGDARRALTALEVAAEAAQAAGELV 242
                                    6789999999999999999987766 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.2
                         AAA_25  75 lyvsaEdsedelrrRlravg.eal..rddarllvld 107
                                    ++v++Ed++  ++rRl  +  e++  +d++ l+v  
  gi|121638444|ref|YP_978668.1| 291 MLVAGEDPR-FIARRLMILAsEDIgmADPSALQVAV 325
                                    678888888.66666665443555554444444433 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.1e-05      0.01       2     108 ..      68     166 ..      67     168 .. 0.79
   2 ?    0.1   0.1       1.4   6.9e+02      74     101 ..     324     351 ..     309     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsa 81 
                                    v+l g PG +kt+l+  +++a + +f+ +      l + +  ++ + e++++  ++ G   + +l+ de+ r +   q a
  gi|121638444|ref|YP_978668.1|  68 VILYGPPGSGKTTLAALISQATGRRFEALS----ALSAGVKEVRAVIENSRKALLH-GE--QTVLFIDEVHRFSKTQQDA 140
                                    78999****************999999875....4677888777666666555444.43..67899************** PP

                          AAA_3  82 lleameerqvtvegethklpepflvla 108
                                    ll a+e r v +  +t++ p  f v+a
  gi|121638444|ref|YP_978668.1| 141 LLSAVEHRVVLLVAATTENP-SFSVVA 166
                                    *****999888877776644.566665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                          AAA_3  74 appktqsalleameerqvtvegethklp 101
                                    a + +q+  l  m e q+t++++t +l 
  gi|121638444|ref|YP_978668.1| 324 AVAAAQTVALIGMPEAQLTLAHATIHLA 351
                                    667788888999********99999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   5.1e-06    0.0025      16     119 ..      63     150 ..      56     161 .. 0.74
   2 ?   -1.6   0.1       3.7   1.8e+03      37     154 ..     230     244 ..     206     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.1e-06
                         AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivD 95 
                                    sg   ++l Gp+G+GKtt+ + + +a    g+r  +l+  ++  k++++ ++   ++ + ll  ++      ++t+l +D
  gi|121638444|ref|YP_978668.1|  63 SGVASVILYGPPGSGKTTLAALISQAT---GRRFEALSALSAGVKEVRAVIE---NSRKALL--HG------EQTVLFID 128
                                    555568999*********988777655...6778888888888888884433...2333444..22......469***** PP

                         AAA_30  96 Eagmvdtkqlaallkaaekagakv 119
                                    E+   + +q +all+a+e+    v
  gi|121638444|ref|YP_978668.1| 129 EVHRFSKTQQDALLSAVEH--RVV 150
                                    *****************98..233 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                         AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekag 116
                                    +++e                                                                            
  gi|121638444|ref|YP_978668.1| 230 VAAE---------------------------------------------------------------------------- 233
                                    1122............................................................................ PP

                         AAA_30 117 akvilvGDerQlasVeaGgvlrdlveaagigtaeLtev 154
                                                               a++ + eL +v
  gi|121638444|ref|YP_978668.1| 234 ---------------------------AAQAAGELVSV 244
                                    ...........................22233333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-05     0.005      49     139 ..      67     150 ..      62     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                      IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeae 128
                                    +++l Gp+G GK+ la+ +++++ r     +f  +++L + +k  r+  + +r++    + ++l +D++  + +++ ++ 
  gi|121638444|ref|YP_978668.1|  67 SVILYGPPGSGKTTLAALISQATGR-----RFEALSALSAGVKEVRAVIENSRKALLHGEQTVLFIDEV--HRFSKTQQD 139
                                    799*************877776554.....6999999*****9999999999999999999******97..788888899 PP

                      IstB_IS21 129 llfeviekrye 139
                                     l+  +e+r+ 
  gi|121638444|ref|YP_978668.1| 140 ALLSAVEHRVV 150
                                    99999988865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-05     0.011       2      29 ..      68      97 ..      68     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg..avlls 29
                                   v+l G+pGsGK+tla  + +++g  ++ ls
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQATGrrFEALS 97
                                   7899************99998887776666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05    0.0074      11      55 ..      58      97 ..      55     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                   HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEE CS
                         NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFdsva 55
                                   +L+e  ++    v l+G +G+GKttla+ i +    + +rF+ + 
  gi|121638444|ref|YP_978668.1| 58 RLVEGSGVA--SVILYGPPGSGKTTLAALISQA---TGRRFEALS 97
                                   677666666..899**************99877...777888765 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.96   4.7e+02      21      42 ..      67      88 ..      57      95 .. 0.86
   2 !   13.6   0.1   9.1e-05     0.044      84     162 ..     102     180 ..      90     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.96
                DNA_pol3_delta2 21 ayLfeGdegigkkelalnlaka 42
                                   + +++G+ g+gk +la  +++a
  gi|121638444|ref|YP_978668.1| 67 SVILYGPPGSGKTTLAALISQA 88
                                   6899************998876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.1e-05
                DNA_pol3_delta2  84 kldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtn....klLktirSRcqelkf 159
                                     + ++r +ie+  +    +++ ++ i+++ + +k  + alL  +E      +++L++  t+    ++  ++ SR  +l++
  gi|121638444|ref|YP_978668.1| 102 GVKEVRAVIENSRKALLHGEQTVLFIDEVHRFSKTQQDALLSAVEHR----VVLLVAATTEnpsfSVVAPLLSRSLILQL 177
                                    5789****************************************965....4444433333122356************* PP

                DNA_pol3_delta2 160 spl 162
                                    +pl
  gi|121638444|ref|YP_978668.1| 178 RPL 180
                                    997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.9e-05     0.014       4      22 ..      67      85 ..      65     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   ++++yGp+g+GKTtla+ +
  gi|121638444|ref|YP_978668.1| 67 SVILYGPPGSGKTTLAALI 85
                                   789*************977 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00011     0.053       1      24 [.      71      96 ..      71     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                                   EE-TTSSHHHHHHHHHHHH..TEEEE CS
                         AAA_17  1 lGgPGsGKgtqceklveky..gfthl 24
                                   +G+PGsGK+t+++ + +     f+ l
  gi|121638444|ref|YP_978668.1| 71 YGPPGSGKTTLAALISQATgrRFEAL 96
                                   7***********99999873323333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.057      18     108 ..      67     161 ..      60     167 .. 0.67
   2 ?   -3.1   0.0       8.2     4e+03     167     194 ..     241     266 ..     224     268 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                     Zeta_toxin  18 lillgGqpGAGKselaellkdele...rqgnvvrldpDdlRelhPeyeeilka..dpkkaseltqkdaselvekllqeai 92 
                                    +++l G pG+GK++la+l+ ++++   ++ +++     ++R+ + + +++l +  +   + + +++++++ ++ +l  a+
  gi|121638444|ref|YP_978668.1|  67 SVILYGPPGSGKTTLAALISQATGrrfEALSALSAGVKEVRAVIENSRKALLHgeQTVLFIDEVHRFSKT-QQDALLSAV 145
                                    68999****************9985555666666666777777766666554311333345556665544.445555677 PP

                     Zeta_toxin  93 engyniivegtlrspd 108
                                    e+++ ++v  t ++p+
  gi|121638444|ref|YP_978668.1| 146 EHRVVLLVAATTENPS 161
                                    7777777777766665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.2
                     Zeta_toxin 167 resvealeeekqldrvkikdrdgktvly 194
                                      sv+++e++ +   v++ drdg  ++y
  gi|121638444|ref|YP_978668.1| 241 LVSVQTIERSVDKAAVRY-DRDG-DQHY 266
                                    345566666554444444.5555.4555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.8e-05     0.038       1      27 [.      68     102 ..      68     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl........k 27 
                                    ++lyGp+g GK+tla  +++a  +++        +
  gi|121638444|ref|YP_978668.1|  68 VILYGPPGSGKTTLAALISQATGRRFealsalsaG 102
                                    689**************999988877555554432 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.4e-05     0.036      23      54 ..      69     100 ..      66     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.4e-05
                         AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrks 54 
                                    +++Gp G+GKTT+   i  a++ +++ ls  s
  gi|121638444|ref|YP_978668.1|  69 ILYGPPGSGKTTLAALISQATGRRFEALSALS 100
                                    79********************9998888765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0026       1.3      13      37 ..      58      82 ..      54      89 .. 0.78
   2 ?    3.5   0.0      0.11        56      95     141 ..      99     142 ..      84     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0026
                       ATPase_2 13 eilerepneiyfiYGpegsGKtaLl 37
                                   +++e +    + +YGp gsGKt+L 
  gi|121638444|ref|YP_978668.1| 58 RLVEGSGVASVILYGPPGSGKTTLA 82
                                   5666666667889**********96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                       ATPase_2  95 lkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaell 141
                                    l+   k+v + ie+  +++   g + +++iDe+ +    + ++++ll
  gi|121638444|ref|YP_978668.1|  99 LSAGVKEVRAVIENSRKALLH-GEQTVLFIDEVHRFS--KTQQDALL 142
                                    446677777788877777764.5789********999..55533333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00028      0.14      14      34 ..      68      88 ..      63     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                                   EEEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagl 34
                                   v + G+ G+GK+tL++l+++ 
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQA 88
                                   7899**************976 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017     0.082      59     152 ..      67     152 ..      56     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                    EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHH CS
                            MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedr 138
                                     v+l g pg +K++l   +++ + r   +  + s ++  + av  ++          al+  ++ v+ iDe+ + +++++
  gi|121638444|ref|YP_978668.1|  67 SVILYGPPGSGKTTLAALISQATGRRFEALSALSAGVKEVRAVIENS--------RKALLHGEQTVLFIDEVHRFSKTQQ 138
                                    67888888888888877777555554444333333333333333222........2389999****************** PP

                                    HHHHHHHHHSEEEE CS
                            MCM 139 salhEamEqqtisi 152
                                    +al+ a+E+  + +
  gi|121638444|ref|YP_978668.1| 139 DALLSAVEHRVVLL 152
                                    ********998865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00022      0.11       2      23 ..      68      90 ..      67     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                         AAA_28  2 ivitGgestGKTtlleaLaar.g 23
                                   +++ G++++GKTtl++ +++  g
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQAtG 90
                                   899************99986434 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021       0.1      20      43 ..      69      92 ..      68     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                         AAA_13 20 liYGwNGaGKTtLSrllrslelge 43
                                   ++YG  G+GKTtL+ l+++ + ++
  gi|121638444|ref|YP_978668.1| 69 ILYGPPGSGKTTLAALISQATGRR 92
                                   58*****************86544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00032      0.15       4      82 ..      66     135 ..      63     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                    --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                          AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                    +s++l gp g+Gkt la  +++           r++a + l   +  + v   i ++     + e+ ++++DE+ + ++
  gi|121638444|ref|YP_978668.1|  66 ASVILYGPPGSGKTTLAALISQATG-------RRFEALSALS--AGVKEVRAVIENSRKALLHGEQTVLFIDEVHRFSK 135
                                    78999*********99999998887.......5777777766..55688999999999999*************99888 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0053       2.6      12      30 ..      67      85 ..      57     100 .. 0.79
   2 ?    7.5   0.1      0.01       4.9      90     127 ..     109     147 ..      86     155 .. 0.70
   3 ?   -2.1   0.2         9   4.4e+03      45      75 ..     323     351 ..     305     383 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0053
                         AAA_19 12 vllvtaGpGtGKTrvlkhi 30
                                    +++ ++pG+GKT++   i
  gi|121638444|ref|YP_978668.1| 67 SVILYGPPGSGKTTLAALI 85
                                   6899*********976555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.01
                         AAA_19  90 lleeaeeekklqeee.llivDEfqdvd.elqyrLlkallg 127
                                    ++ e++++  l+ e+ +l++DE+   +  +q +Ll+a+ +
  gi|121638444|ref|YP_978668.1| 109 VI-ENSRKALLHGEQtVLFIDEVHRFSkTQQDALLSAVEH 147
                                    33.3455566655557***********999999***9983 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9
                         AAA_19  45 illvaftgrAakelrerlaalgaeatTiHrl 75 
                                    ++++a    A   + e+   l+++  TiH  
  gi|121638444|ref|YP_978668.1| 323 VAVAAAQTVALIGMPEAQ--LTLAHATIHLA 351
                                    444444555555555555..55556666633 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00092      0.45      20      45 ..      66      91 ..      46     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00092
                                   EEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE 20 dvilLeGdLGaGKTtlvrglakalgv 45
                                   + ++L+G+ G+GKTtl+  + +a g 
  gi|121638444|ref|YP_978668.1| 66 ASVILYGPPGSGKTTLAALISQATGR 91
                                   349**************999998875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012       0.6       2      22 ..      68      88 ..      67      95 .. 0.87
   2 ?   -0.7   0.0       2.4   1.2e+03      86     123 ..     110     146 ..      90     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                                   EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                   v++ GppG+GKtTl   ++++
  gi|121638444|ref|YP_978668.1| 68 VILYGPPGSGKTTLAALISQA 88
                                   7899**********9998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                                    HHHHHHHH..HHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                       NTPase_1  86 lealrkal..seadviviDEiGkmElkskkfkeaveevLk 123
                                    +e+ rkal   e+ v+ iDE+ +   +sk+ ++a+  +++
  gi|121638444|ref|YP_978668.1| 110 IENSRKALlhGEQTVLFIDEVHR---FSKTQQDALLSAVE 146
                                    45555555434445888999854...34444455555554 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2    0.0011      0.51      19      72 ..     194     250 ..     181     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                         HTH_32  19 drprr.grprklsdevrariiallreep..rWsprqlaarlaeregvkvShstvyri 72 
                                    d pr+ gr   + +e ++ +++l+  +   ++++ ++aa+ a+  g+ vS  t+ r 
  gi|121638444|ref|YP_978668.1| 194 DDPRGlGRAVAVAPEAVDLLVQLAAGDArrALTALEVAAEAAQAAGELVSVQTIERS 250
                                    5677779999**************63334599999****997888999******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 2804.46
//
Query:       gi|121638445|ref|YP_978669.1|  [L=325]
Description: proline and glycine rich transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.6   3.2      0.013   15.3   2.9    1.4  1  UPF0259       Uncharacterised protein family (UPF0259)
        1.2    8.9  18.4          2    8.1   7.6    2.1  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
        3.5    5.8  15.0          5    5.3  15.0    1.2  1  DUF2070       Predicted membrane protein (DUF2070)
        3.5    7.3   8.7       0.53   10.0   4.2    2.0  2  Claudin_2     PMP-22/EMP/MP20/Claudin tight junction


Domain annotation for each model (and alignments):
>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.9     3e-06     0.013     123     208 ..     186     272 ..     107     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                        UPF0259 123 iglsllllPklliLiflttlli....qlGllllliPGiivaillslsPiillkekksildsikasvnitfknikliaPav 198
                                    +++ +++ P+ l L+ +t lli     +G ll +iPG+i   +  ++  + +   +s +ds+kas++   +n   i+ +v
  gi|121638445|ref|YP_978669.1| 186 VTIATFFRPRNLGLVLVTGLLIvaltFIGGLLCVIPGLIFGFVAQFAVAFAVDRSTSPIDSVKASIETVGSN---IGGSV 262
                                    566788889999999988876422226999*************************************99998...58999 PP

                        UPF0259 199 llWllvklll 208
                                    l+Wl+  + +
  gi|121638445|ref|YP_978669.1| 263 LSWLAQLTAV 272
                                    9999865544 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.6   0.00046         2      63     138 ..      94     170 ..      91     176 .. 0.72
   2 ?    6.4   3.0    0.0016       7.1      47     135 ..     198     284 ..     189     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00046
                   Trp_oprn_chp  63 rglgrrvvgvllalagagaavaalslltdpadaaraaa.aaatgvasaaaaveltawpvlalaggvllllagvllll 138
                                    ++++  vv vl+ +++++a++ a ++l+ + +  +++a ++++gv+s++ ++++t+++ +++  g ++l+a vl + 
  gi|121638445|ref|YP_978669.1|  94 QNAVTLVVPVLAYAVALAAVIGATAGLVVALSDRATTAyTNTSGVSSESVDITMTPAAGIVMFLGYIALFALVLYMH 170
                                    56667788889888888888888888777666666666688899999999999999777776666666666555543 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0016
                   Trp_oprn_chp  47 alAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaave.ltawpvlalag 125
                                     l lv+   +vA++  +gl+ ++ g++   ++  a++ a+   t+p d+++a+ ++++    + +  + l  + + a++ 
  gi|121638445|ref|YP_978669.1| 198 GLVLVTGLLIVALTFIGGLLCVIPGLIFGFVAQFAVAFAVDRSTSPIDSVKASIETVGSN-IGGSVLSwL--AQLTAVLV 274
                                    455666667899**************************************9999663332.233333312..33444444 PP

                   Trp_oprn_chp 126 gvllllagvl 135
                                    g ll++ g+l
  gi|121638445|ref|YP_978669.1| 275 GELLCFVGML 284
                                    4444444444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  15.0    0.0011         5      12     169 ..     102     287 ..      92     308 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0011
                        DUF2070  12 Pswkvsllliillalligllaflssk.............................lfgillfglpalvaflltlpvlril 62 
                                    P + ++++l++++++ +gl++ ls                               l  i lf l + + + +++ +l+i+
  gi|121638445|ref|YP_978669.1| 102 PVLAYAVALAAVIGATAGLVVALSDRattaytntsgvssesvditmtpaagivmfLGYIALFALVLYMHAGILTGCLDIA 181
                                    66678888888888888888888888999999999999999999999998888853334444455556666666999999 PP

                        DUF2070  63 ggr......ltykrslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpali 136
                                     g+      +   r+l l l+t l++v++++++ ll           ++ +l++ f+ ++ v +av++++ +  ++ a+i
  gi|121638445|ref|YP_978669.1| 182 DGKpvtiatFFRPRNLGLVLVTGLLIVALTFIGGLLC----------VIPGLIFGFVAQFAVAFAVDRSTSPIDSVKASI 251
                                    9999999999999*********************987..........455788888888888888888888888888888 PP

                        DUF2070 137 qpllailllvly...fspesfllllllslifalavy 169
                                     ++ + +   ++    + + +l+  ll+++ +l+ +
  gi|121638445|ref|YP_978669.1| 252 ETVGSNIGGSVLswlAQLTAVLVGELLCFVGMLIGI 287
                                    887777766666443233334444444444444443 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.23     1e+03      97     113 ..     106     123 ..      72     139 .. 0.52
   2 ?   10.0   4.2   0.00012      0.53      70     149 ..     135     231 ..     116     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.23
                      Claudin_2  97 iLslvlivlavvlgl.la 113
                                        +++v+++++gl +a
  gi|121638445|ref|YP_978669.1| 106 YAVALAAVIGATAGLvVA 123
                                    222233445555554223 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                      Claudin_2  70 fekkeeeivsisatsllalarfvqvlliLslvlivlavvlgllallkqsv.............lllkaagilfl....la 132
                                        ++e+v i +t++ ++ +f   +++++lvl + a +l+ +  +   +             +l++++g l++    ++
  gi|121638445|ref|YP_978669.1| 135 TSGVSSESVDITMTPAAGIVMFLGYIALFALVLYMHAGILTGCLDIADGKpvtiatffrprnlGLVLVTGLLIValtfIG 214
                                    455678999999**********************999988887777776679***********9999999999999999* PP

                      Claudin_2 133 gvlgllavvvfiesvkk 149
                                    g+l++++ ++f++  + 
  gi|121638445|ref|YP_978669.1| 215 GLLCVIPGLIFGFVAQF 231
                                    *******9999988773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2186.93
//
Query:       gi|121638446|ref|YP_978670.1|  [L=245]
Description: hypothetical protein BCG_2584 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-45  152.6   0.0    5.8e-45  152.2   0.0    1.2  1  DUF2652   Protein of unknown function (DUF2652)


Domain annotation for each model (and alignments):
>> DUF2652  Protein of unknown function (DUF2652)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.2   0.0   3.2e-49   5.8e-45       1     118 []      34     149 ..      34     149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.2 bits;  conditional E-value: 3.2e-49
                        DUF2652   1 iaeLleviidanklglklseieGDAvlfyklgealtleelleqveamrkaFhkklkllekdrickckacaqaekLslKlv 80 
                                    +a+Lle++ida+k g+kl+++eGDA++f++ g ++++  ++++  +mr++F++++++++kd+ c+ck+c+q+++Ls+K+v
  gi|121638446|ref|YP_978670.1|  34 VAQLLESVIDAAK-GMKLAKLEGDAAFFWAPGGNTSV-LVCDRPPQMRQRFRTRREQIKKDHPCDCKSCEQRDNLSIKFV 111
                                    79***********.***********************.9***************************************** PP

                        DUF2652  81 aHsGevatqkvkrfkkllGkdvilvHrlLKnevavseY 118
                                    aH+Geva+qkvkr+ +l+G+dvilvHr+LKnev+vseY
  gi|121638446|ref|YP_978670.1| 112 AHEGEVAEQKVKRNVELAGVDVILVHRMLKNEVPVSEY 149
                                    *************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1931.91
//
Query:       gi|121638447|ref|YP_978671.1|  [L=349]
Description: glutamine-transport transmembrane protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-05   23.6  10.8    5.4e-05   23.6  10.8    3.2  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
      0.051   12.7  12.7      0.011   14.8   9.4    1.5  2  EIIC-GAT  PTS system sugar-specific permease component


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.053   4.8e+02      12      41 ..      11      40 ..       3      99 .. 0.79
   2 ?    0.1   1.9      0.13   1.2e+03      67      85 ..     231     249 ..     211     259 .. 0.53
   3 !   23.6  10.8   6.1e-09   5.4e-05       2      96 .]     259     342 ..     258     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                           FtsX 12 mkkkqvlllllteillitlvalviGlglgl 41
                                   ++k++++  +++ +l++++   + Gl++g+
  gi|121638447|ref|YP_978671.1| 11 WRKRRLVIAIVSTGLVFAMTLVLTGLVNGF 40
                                   567777777778888888888888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                           FtsX  67 itvliiivlllllallagl 85 
                                    itv+++++ ++  +++ ++
  gi|121638447|ref|YP_978671.1| 231 ITVVAVLLWIVAALIVGSV 249
                                    3333332222222222222 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 6.1e-09
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                    r +++++a+G+ ++++l +l +++++++l+a+v+G +l+ll+a l           + +++ ++l++++++ ++++++ l
  gi|121638447|ref|YP_978671.1| 259 RDFAVFKAIGVPTRSILAGLALQAVVVALLAAVVGGILSLLLAPL-----------FPMTVVVPLSAFVALPAIATVIGL 327
                                    6799***************************************99...........9*********************** PP

                           FtsX  82 lagllsiskilkkep 96 
                                    la+++ ++++  ++p
  gi|121638447|ref|YP_978671.1| 328 LASVAGLRRVVAIDP 342
                                    ********9987776 PP

>> EIIC-GAT  PTS system sugar-specific permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.32   2.9e+03     248     264 ..      17      33 ..       9      45 .. 0.61
   2 ?   14.8   9.4   1.3e-06     0.011     252     366 ..     224     343 ..     173     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.32
                       EIIC-GAT 248 vvqiltqaltfaaglvi 264
                                    v+ i++++l fa+ lv+
  gi|121638447|ref|YP_978671.1|  17 VIAIVSTGLVFAMTLVL 33 
                                    45555555555554443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.3e-06
                       EIIC-GAT 252 ltqaltfaaglviilkgvr.mfveelvpaf..kgiseklvpgavpAlDvavvfgfapnavtiGfllsfigqllallilil 328
                                    l++a+   ++++++l +v  ++v+ +v ++  +  +++ v +a+      ++ g a +av++++l +++g++l+ll+ +l
  gi|121638447|ref|YP_978671.1| 224 LKVAVDAITVVAVLLWIVAaLIVGSVVYLSalERLRDFAVFKAIGVPTRSILAGLALQAVVVALLAAVVGGILSLLLAPL 303
                                    67777777788887777751555666543322666667666644444455899*************************** PP

                       EIIC-GAT 329 lgaaiilPg..vlplfflgatagvfanavggikgaiigsf 366
                                    + +++++P+  +++l  +++++g  a   g ++   i ++
  gi|121638447|ref|YP_978671.1| 304 FPMTVVVPLsaFVALPAIATVIGLLASVAGLRRVVAIDPA 343
                                    *******************************999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2662.03
//
Query:       gi|121638448|ref|YP_978672.1|  [L=330]
Description: glutamine-transport ATP-binding protein ABC transporter glnQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-31  108.9   0.0    4.7e-31  108.1   0.0    1.4  1  ABC_tran      ABC transporter
    2.5e-19   69.1   0.3      6e-19   67.9   0.2    1.7  1  cNMP_binding  Cyclic nucleotide-binding domain
      1e-09   38.7   0.4     0.0001   22.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.1e-06   26.8   0.1    5.2e-05   22.8   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00012   22.5   0.1     0.0003   21.2   0.1    1.6  1  AAA_16        AAA ATPase domain
      0.002   18.7   0.0     0.0029   18.1   0.0    1.2  1  AAA_23        AAA domain
     0.0034   17.0   1.6     0.0083   15.7   0.1    2.3  3  AAA_25        AAA domain
     0.0035   17.1   0.1      0.011   15.5   0.1    1.7  1  AAA_30        AAA domain
     0.0036   17.3   0.2     0.0059   16.5   0.2    1.3  1  Rad17         Rad17 P-loop domain
     0.0046   16.4   0.0     0.0081   15.6   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0046   16.7   0.1       0.01   15.5   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0046   17.4   0.1       0.03   14.7   0.1    2.2  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.028   14.4   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
      0.026   14.3   0.2       0.18   11.5   0.2    2.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.033   14.5   2.5       0.45   10.8   2.5    2.2  1  AAA_22        AAA domain
      0.033   13.9   0.0        2.5    7.7   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.037   13.9   1.0      0.096   12.6   0.3    1.9  2  NACHT         NACHT domain
      0.085   13.2   0.1       0.17   12.2   0.1    1.6  1  AAA_19        AAA domain
      0.097   12.7   0.0       0.22   11.5   0.0    1.5  1  Urease_beta   Urease beta subunit
       0.11   12.4   0.4       0.25   11.3   0.4    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.14   12.5   0.0       0.24   11.8   0.0    1.3  1  RNA_helicase  RNA helicase
       0.21   11.8   1.1       0.43   10.8   0.5    1.8  2  AAA_28        AAA domain
       0.21   10.4   0.0       0.37    9.6   0.0    1.3  1  DLIC          Dynein light intermediate chain (DLIC)
       0.29   11.3   1.8       0.34   11.1   0.4    1.9  2  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   6.3e-34   4.7e-31       2     137 .]      24     172 ..      23     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 6.3e-34
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                    + +sl++ +g++v ++G++G+GK+tLl++l g l+p++G+i++d+ d+++       +  r ++g+++q  +l + lt+ 
  gi|121638448|ref|YP_978672.1|  24 DGLSLDVAPGSLVILLGPSGCGKTTLLSCLGGILRPKSGSIKFDDVDITTlegaALAKYRRDKVGIVFQAFNLVSSLTAL 103
                                    789***********************************************999888899999****************** PP

                                    HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    en             ++++++e++l +++l e  +++    p  +SgGq+qrva+ara++ +p+l+l+DEpta
  gi|121638448|ref|YP_978672.1| 104 ENvmvplraagvsraAARKRAEDLLIRVNLGERMKHR----PGDMSGGQQQRVAVARAIALDPQLILADEPTA 172
                                    ***********99988888999999999999955555....5*****************************97 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.2   8.1e-22     6e-19       2      84 ..     229     311 ..     228     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 8.1e-22
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    +++kagev+f+q + +d +y+v +Ge++++r  +dg e ++++  pGd+fGe+++l + pr+atv+A++d++ +  ++++
  gi|121638448|ref|YP_978672.1| 229 VHVKAGEVLFEQSTMGDLIYVVSEGEFEIVRELADGGEELVKTAAPGDYFGEIGVLFHLPRSATVRARSDATAVGYTAQA 308
                                    689*****************************************************99****************999999 PP

                                    HHH CS
                   cNMP_binding  82 fle 84 
                                    f+e
  gi|121638448|ref|YP_978672.1| 309 FRE 311
                                    997 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.6e-05      0.02       2      25 ..      36      59 ..      35      92 .. 0.77
   2 !   22.2   0.0   1.4e-07    0.0001     195     299 ..     120     203 ..      94     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                    +l Gp g+GK++LL +l ++ r 
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSCLGGILRP 59
                                   689***************999764 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.4e-07
                         AAA_21 195 veielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                    ++ +++dl+++++l ++ ++r                  + ++S G+++  a++ a++ ++    l+l DEp ++L+   
  gi|121638448|ref|YP_978672.1| 120 ARKRAEDLLIRVNLGERMKHR------------------PGDMSGGQQQRVAVARAIALDP---QLILADEPTAHLDFIQ 178
                                    566778888888888888888..................577*******999999999999...99************** PP

                         AAA_21 275 lrrllellkelsrngaQviltTHSp 299
                                    ++++l+l+++l++++  v+++TH+ 
  gi|121638448|ref|YP_978672.1| 179 VEEVLRLIRSLAQGDRVVVVATHDS 203
                                    ***********************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   6.9e-08   5.2e-05      29     213 ..      38     217 ..      26     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.9e-08
                                    EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkge 108
                                    ++Gp G+GK+ ll  +  +L  +s  +++ ++++    + ++ a+  + +v i+f+  +  ++ ++   ++++ +   g 
  gi|121638448|ref|YP_978672.1|  38 LLGPSGCGKTTLLSCLGGILRPKSG-SIKFDDVDITTLEGAALAKYRRDKVGIVFQAFNLVSSLTAL-ENVMVPLRAAGV 115
                                    5566666666666666666665444.55555555444444555556666666666555544222221.222333333333 PP

                                    EEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 109 seykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    s+ +  ++        +l e+++  +  +SgG+++ va+a  +A+    p  l l De  a+LD+ +v++v +l+++  +
  gi|121638448|ref|YP_978672.1| 116 SRAAARKRAEDLLIRVNLGERMKHRPGDMSGGQQQRVAVARAIALD---P-QLILADEPTAHLDFIQVEEVLRLIRSLAQ 191
                                    3333322222222223344455555669************999875...4.48899********************9998 PP

                                    TSE.EEEE-SSHHHCCC-SCEEEEEE CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 189 naQ.fivislreemlekadklvgvtk 213
                                        ++v +++++ml  ad+++ ++ 
  gi|121638448|ref|YP_978672.1| 192 GDRvVVVATHDSRMLPLADRVLELMP 217
                                    755156678999*******9988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1     4e-07    0.0003      25     107 ..      34     150 ..      26     199 .. 0.48

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4e-07
                         AAA_16  25 elvllsGesGvGKsslvrellralekd...............ggiflrgkcdqlesaipy.....salaqalareellrq 84 
                                    +lv+l G+sG+GK++l+ +l   l+ +               g+ +           + y      ++ qa+   + l++
  gi|121638448|ref|YP_978672.1|  34 SLVILLGPSGCGKTTLLSCLGGILRPKsgsikfddvdittleGAAL-----------AKYrrdkvGIVFQAFNLVSSLTA 102
                                    79******************98888885444444443333321111...........11233331235555544444444 PP

                         AAA_16  85 llde.....aesaeleawrekleeala....................a 107
                                    l++      a+  +++a+r++ e+ l                     +
  gi|121638448|ref|YP_978672.1| 103 LENVmvplrAAGVSRAAARKRAEDLLIrvnlgermkhrpgdmsggqqQ 150
                                    444454443222222222222222222444555555555555555441 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.9e-06    0.0029       7      43 ..      20      57 ..      19      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-06
                         AAA_23  7 frsfrdqeidFsk.gltlItGpNGaGKTTildAiklaL 43
                                   +r++++ ++d  +  l+++ Gp G+GKTT+l ++  +L
  gi|121638448|ref|YP_978672.1| 20 VRPIDGLSLDVAPgSLVILLGPSGCGKTTLLSCLGGIL 57
                                   5777888888867359999**************98776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.1e-05    0.0083      29      53 ..      30      53 ..      17      57 .. 0.85
   2 ?   -2.3   0.0       3.6   2.7e+03     120     120 ..     192     192 ..     146     224 .. 0.59
   3 ?   -1.3   0.0       1.8   1.3e+03     156     156 ..     290     290 ..     225     325 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                         AAA_25 29 llpagelallaGapgtGKttlaldl 53
                                   + + g+l++l G++g+GKttl++ l
  gi|121638448|ref|YP_978672.1| 30 V-APGSLVILLGPSGCGKTTLLSCL 53
                                   4.459****************9987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                         AAA_25 120 d 120
                                    +
  gi|121638448|ref|YP_978672.1| 192 G 192
                                    1 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                         AAA_25 156 g 156
                                    +
  gi|121638448|ref|YP_978672.1| 290 S 290
                                    0 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.5e-05     0.011      19     122 ..      34     198 ..      29     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g....grviglAptgkaAkv.Laeelgi..eastiakllkrlk......... 81 
                                     +++l Gp G GKtt+l+ l  +++ + g     +v + + +g+a ++  ++++gi  +a ++ + l++l+         
  gi|121638448|ref|YP_978672.1|  34 SLVILLGPSGCGKTTLLSCLGGILRPKsGsikfDDVDITTLEGAALAKyRRDKVGIvfQAFNLVSSLTALEnvmvplraa 113
                                    5899*******************999967999977778888877766624456665557777777777777788888888 PP

                         AAA_30  82 ........................................grarlepg.tllivDE.agmvdtkqlaallkaaek..aga 117
                                                                             + +++ + +l++ DE ++ +d+ q++++l+ +++  +g 
  gi|121638448|ref|YP_978672.1| 114 gvsraaarkraedllirvnlgermkhrpgdmsggqqqrvaVARAIALDpQLILADEpTAHLDFIQVEEVLRLIRSlaQGD 193
                                    88888888889999999999999999999*******99994456777779******556779999999999999864578 PP

                         AAA_30 118 kvilv 122
                                    +v++v
  gi|121638448|ref|YP_978672.1| 194 RVVVV 198
                                    88887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.9e-06    0.0059      38      71 ..      26      59 ..      20      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.9e-06
                          Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLskelgi 71
                                    +L+ ++  ++++ GPsGCgk+t +  L  +l +
  gi|121638448|ref|YP_978672.1| 26 LSLDVAPGSLVILLGPSGCGKTTLLSCLGGILRP 59
                                   57888889999**************999887765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05    0.0081      20      65 ..      31      76 ..      23     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                   Mg_chelatase 20 aGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                   a g  ++l+Gp+G+GKt l ++l ++l p s +  ++   i+++ g
  gi|121638448|ref|YP_978672.1| 31 APGSLVILLGPSGCGKTTLLSCLGGILRPKSGSIKFDDVDITTLEG 76
                                   5566789********************9988777776666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.4e-05      0.01      14      54 ..      25      66 ..      22      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrf 54
                                   g ++++ + + ++l GpsG GK+Tll  +  +L p++ +++f
  gi|121638448|ref|YP_978672.1| 25 GLSLDVAPGSLVILLGPSGCGKTTLLSCLGGILRPKSgSIKF 66
                                   5567777777999*************9999999998766655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.1e-05      0.03       1      35 [.      36      80 ..      36     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                                   EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS CS
                            AAA  1 vllyGppGtGKTllakavakel..........gvefleisgsell 35
                                   v+l Gp G+GKT+l + +   l          +v++ +++g+ l 
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSCLGGILrpksgsikfdDVDITTLEGAALA 80
                                   689************999999855444222222334444444443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.7e-05     0.028      99     126 ..      33      60 ..      18      70 .. 0.79
   2 ?   -3.2   0.0       9.1   6.8e+03      47      80 ..      85     118 ..      78     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                                    TSEEEEECSTTSSHHHHHHHHCTT---- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelk 126
                                    +++++l+G+SG GK+tL+  l + l+ k
  gi|121638448|ref|YP_978672.1|  33 GSLVILLGPSGCGKTTLLSCLGGILRPK 60 
                                    4889**************9997765555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.1
                                    -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEE CS
                    RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevl 80 
                                     ++ iv+   +l+++ ++le+++  l+a+g++  
  gi|121638448|ref|YP_978672.1|  85 DKVGIVFQAFNLVSSLTALENVMVPLRAAGVSRA 118
                                    4666777777777777777777777777776655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00024      0.18       4      22 ..      36      54 ..      34      77 .. 0.84
   2 ?   -0.1   0.0      0.92   6.8e+02      88     122 ..      82     117 ..      63     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                      PduV-EutP  4 illiGkvgsGKttLtqalk 22
                                   ++l+G++g+GKttL   l 
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSCLG 54
                                   89************88775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                      PduV-EutP  88 fnkeviGiitk.idlaedeenieaveelLksaGaek 122
                                     +++ +Gi+ +  +l+++  ++e+v   L++aG+++
  gi|121638448|ref|YP_978672.1|  82 YRRDKVGIVFQaFNLVSSLTALENVMVPLRAAGVSR 117
                                    5788999998735999999999999999****9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.5    0.0006      0.45       6      29 ..      34      57 ..      31     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                         AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                   +++++ G+sG+GKTtll  l   l
  gi|121638448|ref|YP_978672.1| 34 SLVILLGPSGCGKTTLLSCLGGIL 57
                                   67899***********99887666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0033       2.5      24      64 ..      33      70 ..      21      94 .. 0.74
   2 ?    4.3   0.0     0.037        28     323     368 ..     161     205 ..     148     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                         AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnkekknkkvikieked 64
                                     l +l G+ ++GK+++l  l  +l  k    +  ik+++ d
  gi|121638448|ref|YP_978672.1| 33 GsLVILLGPSGCGKTTLLSCLGGILRPK----SGSIKFDDVD 70
                                   4599****************99999888....3444444444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.037
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    ++ ++l +EP ahL   + +++ +l+++la+ ++  v++ TH + +
  gi|121638448|ref|YP_978672.1| 161 DPQLILADEPTAHLDFIQVEEVLRLIRSLAQGDR-VVVVATHDSRM 205
                                    78899*********7777777889*********9.9******9877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00013     0.096       2      18 ..      35      51 ..      34      58 .. 0.90
   2 ?   -1.1   0.0       2.1   1.6e+03      90     130 ..     167     204 ..     105     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                   CEEEEC-TTTCHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlq 18
                                   lvil G++G+GKTtLl 
  gi|121638448|ref|YP_978672.1| 35 LVILLGPSGCGKTTLLS 51
                                   79*************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                                    STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECC CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpr 130
                                    +De  ++l++ + ++v +l+++l ++    ++ +++t  +r
  gi|121638448|ref|YP_978672.1| 167 ADEPTAHLDFIQVEEVLRLIRSLAQG---DRVVVVATHDSR 204
                                    67777777777777777777777776...555555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00023      0.17       9      59 ..      32      83 ..      27     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallv.elggvkpeeillvaftgrAakelr 59
                                   + ++++++++ G+GKT++l +   +l  + g++k +++ + ++ g A  + r
  gi|121638448|ref|YP_978672.1| 32 PGSLVILLGPSGCGKTTLLSCLGGILRpKSGSIKFDDVDITTLEGAALAKYR 83
                                   67899***************99988762556677788888888888866554 PP

>> Urease_beta  Urease beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0003      0.22      36      81 ..     172     217 ..     169     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                                    TTS-GGGS-TTEES-HHHHTTEEE-SSTT-EEEE-TT-EEEEEEEE CS
                    Urease_beta  36 shyhflevnkaLefdRekalGlrldipagtavrfepgeekevelve 81 
                                    +h+ f++v + L++ R+ a+G r+ + a+   r+ p + + +el++
  gi|121638448|ref|YP_978672.1| 172 AHLDFIQVEEVLRLIRSLAQGDRVVVVATHDSRMLPLADRVLELMP 217
                                    7***********************************9999999987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00033      0.25       2      18 ..      36      52 ..      35      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                   EEEE--SSSSHHHHHHH CS
                          AAA_5  2 vlLvGppGtgKselaer 18
                                   v+L+Gp+G+gK++l   
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSC 52
                                   89***********9865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00032      0.24       1      59 [.      36      94 ..      36     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfg 59
                                   ++l Gpsg+GK+tl   L   l  k++++k d+v + + e   + +Y++ +v +++   
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSCLGGILRPKSGSIKFDDVDITTLEGAALAKYRRDKVGIVFQAF 94
                                   6799************9999998888888888888888888888888888887777655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   0.00058      0.43       2      19 ..      36      53 ..      35      61 .. 0.91
   2 ?   -2.0   0.0       5.2   3.9e+03      27      62 ..     179     215 ..     166     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                         AAA_28  2 ivitGgestGKTtlleaL 19
                                   ++++G++++GKTtll+ L
  gi|121638448|ref|YP_978672.1| 36 VILLGPSGCGKTTLLSCL 53
                                   899***********9866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                         AAA_28  27 vpEaareileeklakgedalpwv.edllafaervlee 62 
                                    v+E+ r i +  + ++    + +  ++l +a+rvle 
  gi|121638448|ref|YP_978672.1| 179 VEEVLRLIRSLAQGDRVVVVATHdSRMLPLADRVLEL 215
                                    5677777766666666655555556777777777765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0005      0.37      26      55 ..      34      63 ..      27      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0005
                           DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGr 55
                                     v++lG +g+Gkttl++ l G+  +k G+
  gi|121638448|ref|YP_978672.1| 34 SLVILLGPSGCGKTTLLSCLGGILRPKSGS 63
                                   5699*******************9999986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00046      0.34       1      16 [.      35      50 ..      35      58 .. 0.91
   2 ?   -1.8   0.0       4.3   3.2e+03      73      73 ..     165     165 ..     100     206 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                         AAA_33  1 lvllvGlpGsGKstla 16
                                   lv+l G++G+GK+tl+
  gi|121638448|ref|YP_978672.1| 35 LVILLGPSGCGKTTLL 50
                                   79************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                         AAA_33  73 v 73 
                                    +
  gi|121638448|ref|YP_978672.1| 165 I 165
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2178.20
//
Query:       gi|121638449|ref|YP_978673.1|  [L=583]
Description: hypothetical protein BCG_2587 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-21   76.4  12.1    1.9e-20   73.9   8.6    2.9  2  Patatin       Patatin-like phospholipase
    4.6e-17   61.9   0.0    1.3e-16   60.4   0.0    1.8  2  cNMP_binding  Cyclic nucleotide-binding domain


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.1     9e+02     126     173 ..      99     177 ..      15     202 .. 0.70
   2 !   73.9   8.6   2.2e-24   1.9e-20       1     202 [.     309     467 ..     309     469 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                        Patatin 126 s...............................lftanqavpaittataatastanranglytedddddvdladavraSs 173
                                    +                               ++  + ++    + ++a +++++r  g  +  d+ +++++da++ S+
  gi|121638449|ref|YP_978673.1|  99 RsagvralrdgvvwriaaetftdmleatpllqSAMLRAMARMLRQSRPAKTARRPRVIGVVSNGDTAAAPMVDAIATSL 177
                                    4444444444455555555555555555555556666677777777888888888888888888888999999888886 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 2.2e-24
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanla 80 
                                    Lv++GGG+rg++++g+ ++L  e+g  +d ++GtS GAi+++++alg+d+++  ++ r++ +  +   d           
  gi|121638449|ref|YP_978673.1| 309 LVMAGGGARGLAHFGVYQEL-TEAGVVIDRFGGTSSGAIASAAFALGMDAGDAIAAAREFIAGSDPLGD----------- 376
                                    8*******************.*******************************99999999999999999........... PP

                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglyteddd 160
                                         ++  ++l  ++   +l+++++++  +++l + ++ +                             + ++  +   
  gi|121638449|ref|YP_978673.1| 377 ----YTIPISALTRGGRVDRLVQGFFGNTLIEHLPRGFFSV---------------------------SADMITGDQIIH 425
                                    ....9999999999999**********************99...........................89********** PP

                        Patatin 161 ddvdladavraSsafPglfppvsldgelyvDGGilsNvPila 202
                                    + ++++ avraS ++Pgl+ppv+ +  l+vDGG+l+N+P+ +
  gi|121638449|ref|YP_978673.1| 426 RRGSVSGAVRASISIPGLIPPVHNGEQLLVDGGLLNNLPANV 467
                                    ***************************************987 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   1.5e-20   1.3e-16       1      87 [.      42     124 ..      42     126 .. 0.97
   2 ?   -3.2   0.0      0.99   8.9e+03      56      78 ..     459     480 ..     447     483 .. 0.63

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.5e-20
                                    EEEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHH CS
                   cNMP_binding   1 rrsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprd 80 
                                    rr+++a++ +f++G+pads+yiv sG++    ++++g  +v+a++ +Gd +G+l+++ g+ r+a v+Al d +++++ ++
  gi|121638449|ref|YP_978673.1|  42 RRHVPANQWLFHAGEPADSIYIVDSGRFVA--VAPEG--HVFAEMASGDSIGDLGVIAGAARSAGVRALRDGVVWRIAAE 117
                                    689************************999..8****..89****************99********************* PP

                                    HHHHHHH CS
                   cNMP_binding  81 dflellq 87 
                                    +f ++l+
  gi|121638449|ref|YP_978673.1| 118 TFTDMLE 124
                                    ***9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.99
                                    HHHTS--SSE.EEESSTEEEEEEE CS
                   cNMP_binding  56 lltgeprtat.vvAltdsellalp 78 
                                    ll+  + +a+ + A td e+++++
  gi|121638449|ref|YP_978673.1| 459 LLN--NLPANvMCADTDGEVICVD 480
                                    444..3445514567889998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4313.80
//
Query:       gi|121638450|ref|YP_978674.1|  [L=533]
Description: hypothetical protein BCG_2588 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-72  243.4   0.0    5.8e-72  243.0   0.0    1.1  1  DUF2126          Putative amidoligase enzyme (DUF2126)
      1e-24   87.2   0.2    2.6e-24   85.9   0.2    1.8  1  Bact_transglu_N  Bacterial transglutaminase-like N-terminal r
    2.6e-18   66.5   0.0      5e-18   65.6   0.0    1.5  1  Transglut_core   Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> DUF2126  Putative amidoligase enzyme (DUF2126)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.0   0.0   9.6e-76   5.8e-72       2     194 ..     315     509 ..     314     523 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 9.6e-76
                        DUF2126   2 kaevefefemkvtRvaedpRvtkPyteeqWeaiealgekvdeelaaedvrltmGGePtfvsiddlesaeWntaalgptkr 81 
                                     +++ +ef+++vtRv+edpRvt Pyt+e+W++i+++g++vde+laa+dvrlt+GGePtfvs+d++ ++eW+taa+gp+kr
  gi|121638450|ref|YP_978674.1| 315 LCDTVLEFSNTVTRVHEDPRVTLPYTDESWKTICEVGQRVDERLAAADVRLTVGGEPTFVSVDNQVAEEWRTAADGPHKR 394
                                    69999*************************************************************************** PP

                        DUF2126  82 elaeellkrlrerfapggllhlgqGkwYPGeslPRWalalywrkDgepvWkdeellade...kkekkataeeaekfleal 158
                                    e+a++l++rl++ +ap+gl+h+gqG+wYPGe+lPRW++alywr+Dg+p+W++++llad+     ++ ++ ++a ++l+ +
  gi|121638450|ref|YP_978674.1| 395 ERASDLAARLKAVWAPQGLIHRGQGRWYPGEPLPRWQIALYWRTDGRPLWTNDALLADPwgaPPADPVDDDAAYRVLAGI 474
                                    **********************************************************966544567788899******* PP

                        DUF2126 159 aeklgldeklvlpayeDalayllkeaklpanvdpld 194
                                    a+ lgl+ ++v+payeD+l+ l++  ++pa+ dp++
  gi|121638450|ref|YP_978674.1| 475 ADGLGLPISQVRPAYEDPLSRLAAAVRMPAG-DPVE 509
                                    *****************************98.6654 PP

>> Bact_transglu_N  Bacterial transglutaminase-like N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.2   4.4e-28   2.6e-24       2      78 ..      33     109 ..      32     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 4.4e-28
                Bact_transglu_N   2 rvrHrtrYtYdrpvslapqvlrLrPrsharqrvlsyslkvePepaevnwqqDafgnkvarvvvdephteleveaese 78 
                                    +++Hrt+Yt+dr v+  p+ +rLrP++h+r+ +++ysl++eP+ +++nwqqDa gn +ar+v+++p ++l++++ ++
  gi|121638450|ref|YP_978674.1|  33 ALEHRTSYTFDRLVRVYPHIVRLRPAPHSRTSIEAYSLRIEPADHFINWQQDALGNFLARLVFPNPMRQLRITVGLI 109
                                    679**********************************************************************9886 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   8.4e-22     5e-18       3     112 .]     167     284 ..     165     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 8.4e-22
                 Transglut_core   3 laeeltagakdpl.ekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsg 81 
                                    +++++t  + +++ + ++a++++++  v+y   r +pg ++++ +l+tg G c+d a l+v++lR  G+ aR+v+gyl +
  gi|121638450|ref|YP_978674.1| 167 WVRNFTVPDGTRTiDFLVALNRAINADVGYC-VRMEPGVQTPDFTLRTGVGSCRDSAWLLVSILRQFGLAARFVSGYLVQ 245
                                    666666666677779999*************.9**********************************************6 PP

                 Transglut_core  82 eeekeq........svasedaHawvevylegygWvplDp 112
                                       + +         ++  d Haw e+y++g gW+ lDp
  gi|121638450|ref|YP_978674.1| 246 LASDIEaldgpsgpAADFTDLHAWSEAYIPGAGWIGLDP 284
                                    544444788888888899999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3483.85
//
Query:       gi|121638451|ref|YP_978675.1|  [L=597]
Description: hypothetical protein BCG_2589 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.2e-270  897.8   0.0   1.5e-269  896.6   0.0    1.5  1  DUF2126   Putative amidoligase enzyme (DUF2126)


Domain annotation for each model (and alignments):
>> DUF2126  Putative amidoligase enzyme (DUF2126)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  896.6   0.0  8.5e-274  1.5e-269     221     822 .]       1     590 [.       1     590 [. 0.96

  Alignments for each domain:
  == domain 1  score: 896.6 bits;  conditional E-value: 8.5e-274
                        DUF2126 221 vlPlkreeekeakwksekwklrrerlvlvpGdsplGlRlPldslplveeeeleaeveedpleereelpeeaaeaeeeeek 300
                                    +lPl+r+++ +  w+s++w+lrr+r+vl++Gdsp+GlRlPlds+++ ++   +a++++dp++ r++lp+           
  gi|121638451|ref|YP_978675.1|   1 MLPLHRRDDGQ-GWASANWRLRRGRIVLLEGDSPAGLRLPLDSISWRPP---RASFDADPVAVRSTLPA----------- 65 
                                    59***999986.9***********************************9...5789************9........... PP

                        DUF2126 301 eekekakeeeeekekekeeaeevvrtalcvevrdgkllvFlPPleeledylelvaaveataeelklpvvieGyepPsdpr 380
                                            e +++++  e+ e++ +tal++evr+g +++FlPP+++le++++lva+vea+a+++++pvvieGy pP dpr
  gi|121638451|ref|YP_978675.1|  66 --------EPHTDRAVVEDPETAPTTALVAEVRGGLVHIFLPPTDALEHFIDLVARVEAAATTANCPVVIEGYGPPPDPR 137
                                    ........3344556677788999******************************************************** PP

                        DUF2126 381 leklkvtPDPGvievnihpaaswkelvektealyeearearLgtekfmldGrhtgtGGGnhvvlGgatpadsPllrrpdl 460
                                    l++ ++tPDPGvievni+p+as++e+ +++e+ly++ar arL+te f++dG+h gtGGGnh++lGg tpadsPllrrpdl
  gi|121638451|ref|YP_978675.1| 138 LTSTTITPDPGVIEVNIAPTASFAEQRQQLETLYQQARLARLTTEAFDVDGTHGGTGGGNHITLGGVTPADSPLLRRPDL 217
                                    ******************************************************************************** PP

                        DUF2126 461 lkslitywqrhPsLsylFsglfiGptsqaPRvDeaRedslyeleialaqi....peeeeeeappWlvDrllRnllvDvtG 536
                                    l sl+tywqrhPsLsylF+g+f+G+tsqaPRvDe+R ++lyeleia+a+i    p++ + +++pW++Dr+lR+ll+D+tG
  gi|121638451|ref|YP_978675.1| 218 LVSLLTYWQRHPSLSYLFAGRFVGTTSQAPRVDEGRAEALYELEIAFAEIlrlsPSSGGGRPQPWVTDRALRHLLTDITG 297
                                    **************************************************7655448999******************** PP

                        DUF2126 537 nthRaelciDklyspdsatGRlGllelRafempPharmslvqqlllralvarfwkePykkklvrwgtelhdrfllphfvk 616
                                    nthRae+ciDklyspdsa+GRlGllelR fempPh +m++vq+ll+r+lva+fw++P++++l+r+g++lh r+llphf+ 
  gi|121638451|ref|YP_978675.1| 298 NTHRAEFCIDKLYSPDSARGRLGLLELREFEMPPHLHMAMVQSLLVRSLVAWFWDQPLRAPLIRHGANLHGRYLLPHFLI 377
                                    ******************************************************************************** PP

                        DUF2126 617 eDlkdvvadlkeagyafeaewfepflefRfpllGevevegvelelraalepWhvlgeeaaaggtaRyvDssverlqvkve 696
                                    +D++dv+adl+++g+afe++w++pf+efRfp++G++  +g+e+elr a+epWh+lgeea+a+gtaRyvDssver+qv++ 
  gi|121638451|ref|YP_978675.1| 378 HDIADVAADLRAHGIAFETSWLDPFTEFRFPRIGTAVFDGIEIELRGAIEPWHTLGEEATAAGTARYVDSSVERIQVRII 457
                                    ******************************************************************************** PP

                        DUF2126 697 gleeeryvvacngrrvplkktgtkgeavagvryraWqpasalhptievdaplvfdlvdtwskrslggctyhvahPgGrsy 776
                                    g++++ryvv+cng+++pl +t++ + +v+gvr++aWqp+salhpti+vd pl+f+l+d ++  s+ggctyhvahPgGr+y
  gi|121638451|ref|YP_978675.1| 458 GADRHRYVVTCNGYPMPLLATDNPDIHVGGVRFKAWQPPSALHPTITVDGPLRFELIDIATATSCGGCTYHVAHPGGRAY 537
                                    ******************************************************************************** PP

                        DUF2126 777 dtfpvnaleaesRrlarfeelghtpgklkveee.......eankefPltlDlR 822
                                    d+ pvna+eae+Rr++rfe++g+tpgkl+++         +++  +P +lDlR
  gi|121638451|ref|YP_978675.1| 538 DEPPVNAVEAEARRARRFEATGFTPGKLDLSDIrekqariSTDIGAPGILDLR 590
                                    **************************665333222233345666789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3898.57
//
Query:       gi|121638452|ref|YP_978676.1|  [L=884]
Description: hypothetical protein BCG_2590 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.1e-126  420.3   0.0   8.8e-126  419.8   0.0    1.2  1  CP_ATPgrasp_2  Circularly permuted ATP-grasp type 2
   2.2e-125  418.1   0.0   3.1e-125  417.6   0.0    1.2  1  CP_ATPgrasp_1  A circularly permuted ATPgrasp
    3.7e-67  227.2   5.0    6.9e-67  226.3   5.0    1.4  1  Alpha-E        A predicted alpha-helical domain with a conser


Domain annotation for each model (and alignments):
>> CP_ATPgrasp_2  Circularly permuted ATP-grasp type 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.8   0.0  1.5e-129  8.8e-126       1     374 [.     115     487 ..     115     488 .. 0.99

  Alignments for each domain:
  == domain 1  score: 419.8 bits;  conditional E-value: 1.5e-129
                                    -EEE-HHHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHTTSS-GG.GGG-TT--GGGTT---GGG-S-SEEEEEEEE.SS CS
                  CP_ATPgrasp_2   1 PriisaeeWaeleaGlaqRarllnaflaDiYgeqkllkegvlPaelvegspgflrelkgvkppggvrlhiaavDLvrded 80 
                                    P++isa++W+ leaGl+qR rll+a+laD+Yg++++l+egvlP+e+++++pg++r+++g+++pg+++l ++a+DL r +d
  gi|121638452|ref|YP_978676.1| 115 PLVISAADWEVLEAGLVQRSRLLDAILADLYGPRSMLTEGVLPPEMLFAHPGYVRAANGIQMPGRHQLFMHACDLSRLPD 194
                                    9******************************************************************************* PP

                                    S-EEEEEEE-SS---HHHHHHHHHHHHHH-HHHHHHS-B---TTHHHHHHHHHHHTS-.-S...S-EEEE---SSSTTHH CS
                  CP_ATPgrasp_2  81 grwlVlednlraPsGvgYalenRevlsrvlpelfrelrvrrlaeffealreaLaalapakaeeprtivlLtpGpynsayf 160
                                    g+++V +d ++aPsG gYa+++R+v+++++p+l++el  r+ ++f +alr aL ++ap+ a++p  +v+L+pG+y+++ f
  gi|121638452|ref|YP_978676.1| 195 GTFQVNADWTQAPSGSGYAMADRRVVAHAVPDLYEELAPRPTTPFAQALRLALIDAAPDVAQDPV-VVVLSPGIYSETAF 273
                                    **********************************************************9999998.************** PP

                                    HHHHHHHHHT-EEE-GGGEEE-SS-EEE--TT--EEE-EEEE-S-GGGS-TTTS-TT-SSS-TTHHHHHHTTS-EEES-T CS
                  CP_ATPgrasp_2 161 EhafLArylgveLvegsDLtvrdgrvylktleglkrVdviyrrvdddfldplelradsllGvpgLleavragnvavaNal 240
                                    ++a+LA  lg++Lve++DL+vrdg++++++l+ lkrVdv++rrvd ++ dpl+lrads+lGv gL+ea ++g+v+v+N+l
  gi|121638452|ref|YP_978676.1| 274 DQAYLATLLGFPLVESADLVVRDGKLWMRSLGTLKRVDVVLRRVDAHYADPLDLRADSRLGVVGLVEAQHRGTVTVVNTL 353
                                    ******************************************************************************** PP

                                    TTHHHHSTTTGGGHHHHHHHHH-S--SSEE---EETTSHHHHHHHHHSGGGEEEEE--------EEEGGG--HHHHHHHH CS
                  CP_ATPgrasp_2 241 GsgvaddkalyaflpaliryllgeellLpnvptwwcgeeealeevlenldelvvkpvdesggegvligpelsaaeleelr 320
                                    Gsg++++++l++flp+l+++ll+e++lL+++p +w g ++++++ l+n+++l++k++ + +   +l+gp+ls+a+l++l+
  gi|121638452|ref|YP_978676.1| 354 GSGILENPGLLRFLPQLSERLLDESPLLHTAPVYWGGIASERSHLLANVSSLLIKSTVSGE---TLVGPTLSSAQLADLA 430
                                    ********************************************************99985...8*************** PP

                                    HHHHHSGGGEEEEE-----EEEEE...EEEEEEEEEE-EEE.ES.SEEE-S--EEEE CS
                  CP_ATPgrasp_2 321 arikanperyvaqevvelstaptl...kleprhvdlRvFvlateegirvmpggLtRv 374
                                     ri+a p+++v+qe+ ++s+apt    +l++  v +R+F++a+++g+  m ggL  v
  gi|121638452|ref|YP_978676.1| 431 VRIEAMPWQWVGQELPQFSSAPTNhagVLSSAGVGMRLFTVAQRSGYAPMIGGLGYV 487
                                    ************************6555***************99*********876 PP

>> CP_ATPgrasp_1  A circularly permuted ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.6   0.0  5.3e-129  3.1e-125       1     332 []     115     443 ..     115     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 417.6 bits;  conditional E-value: 5.3e-129
                  CP_ATPgrasp_1   1 PrivsaeewerlerGlkqRvraLnafLaDiYgdqeilkdGlvPeelvlgnaaylramnGvevPgdvylhvagiDlvraed 80 
                                    P+++sa++we+le+Gl+qR+r+L+a+LaD+Yg++++l++G++P+e+++ ++ y+ra+nG+++Pg ++l+++++Dl+r +d
  gi|121638452|ref|YP_978676.1| 115 PLVISAADWEVLEAGLVQRSRLLDAILADLYGPRSMLTEGVLPPEMLFAHPGYVRAANGIQMPGRHQLFMHACDLSRLPD 194
                                    99****************************************************************************** PP

                  CP_ATPgrasp_1  81 gefrvlednlrvpsGvsYllenRkivarlfPelfaelrvrpvadyaqaLlealrevapaeaadptvvvltPGvynsayfe 160
                                    g+f+v++d++++psG +Y++++R++va+++P+l++el+ rp++ +aqaL+ al ++ap+ a+dp+vvvl+PG+y++++f+
  gi|121638452|ref|YP_978676.1| 195 GTFQVNADWTQAPSGSGYAMADRRVVAHAVPDLYEELAPRPTTPFAQALRLALIDAAPDVAQDPVVVVLSPGIYSETAFD 274
                                    ******************************************************************************** PP

                  CP_ATPgrasp_1 161 hayLarklGveLvegrDLvvrdnkvylrtteglkrvdviyRRvdddflDPlefrpdsvlGvpGlleayraGnvtlanavG 240
                                    +ayLa+ lG++Lve++DLvvrd+k+++r++ +lkrvdv++RRvd++++DPl++r+ds+lGv+Gl+ea+++G vt++n++G
  gi|121638452|ref|YP_978676.1| 275 QAYLATLLGFPLVESADLVVRDGKLWMRSLGTLKRVDVVLRRVDAHYADPLDLRADSRLGVVGLVEAQHRGTVTVVNTLG 354
                                    ******************************************************************************** PP

                  CP_ATPgrasp_1 241 sGvaddkavyafvPelieyyLgeepilknvetyrceeaddlkevLdrlselvvkevegsggygiviGptaskaelaelar 320
                                    sG+++++++++f+P+l e++L+e p+l++++ y+ + a++++++L+++s+l++k++    + ++++Gpt+s+a+la+la 
  gi|121638452|ref|YP_978676.1| 355 SGILENPGLLRFLPQLSERLLDESPLLHTAPVYWGGIASERSHLLANVSSLLIKSTV---SGETLVGPTLSSAQLADLAV 431
                                    ********************************************************9...6799**************** PP

                  CP_ATPgrasp_1 321 rilaepeqyiaq 332
                                    ri+a+p+q+++q
  gi|121638452|ref|YP_978676.1| 432 RIEAMPWQWVGQ 443
                                    **********98 PP

>> Alpha-E  A predicted alpha-helical domain with a conserved ER motif.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   5.0   1.2e-70   6.9e-67       3     290 ..     539     861 ..     538     863 .. 0.87

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.2e-70
                        Alpha-E   3 SRvAenLfWlgRYlERaentaRllrvtlqllld........eeeewrallaalgaeegf......eeryeeae....... 61 
                                     Rv ++LfW+gRY ERaen+aRll vt ++++         e+e++  l+aalg+ +g+       + y   +       
  gi|121638452|ref|YP_978676.1| 539 PRVLSDLFWMGRYGERAENMARLLIVTRERYHVfrhqqdtdESECVPVLMAALGKITGYdtatgaGSAY---Dradmiav 615
                                    69******************************98887655449999*************6555542222...13346779 PP

                        Alpha-E  62 leevlkfllldeenpgSiasclraarenaravRerlssemWevlnelylelke......kl..sel...eflervkerla 130
                                    + + l +l++d+++pgS++++++ +  +aravR++ls+++W+vl +   ++++      +l  +++   ++  +++  ++
  gi|121638452|ref|YP_978676.1| 616 APSTLWSLTVDPDRPGSLVQSVEGLALAARAVRDQLSNDTWMVLANVERAVEHksdppqSLaeADAvlaSAQAETLAGML 695
                                    9999*****************************************6555555445555422332225789999******* PP

                        Alpha-E 131 afsGlaeetmlrdegwrFlrlGrrlERadntarlldvklael.e.vedslqlealLrsvssletYrrryrsriepervle 208
                                    ++sG+a e+m++d gw ++++G+r+ER+  +++ll+++l++  + + ++  +ea L +++s  +Yrrr  +++++++v e
  gi|121638452|ref|YP_978676.1| 696 TLSGVAGESMVHDVGWTMMDIGKRIERGLWLTALLQATLSTVrHpAAEQAIIEATLVACESSVIYRRRTVGKFSVAAVTE 775
                                    ****************************************9963233889****************************** PP

                        Alpha-E 209 lLlldednPrSlafqleeleealaalspaeseegrsseaerllgellaelrladieelle........glhelldelqee 280
                                    l+l+d++nPrSl++qle+l+++l++l++    ++ ss++er++ e++++lr +++eel e        +l+ell+ ++++
  gi|121638452|ref|YP_978676.1| 776 LMLFDAQNPRSLVYQLERLRADLKDLPG----SSGSSRPERMVDEMNTRLRRSHPEELEEvsadglraELAELLAGIHAS 851
                                    **************************44....3457899*************9999999445788999999999999999 PP

                        Alpha-E 281 laelsdaise 290
                                    l++++d +++
  gi|121638452|ref|YP_978676.1| 852 LRDVADVLTA 861
                                    9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6206.10
//
Query:       gi|121638453|ref|YP_978677.1|  [L=341]
Description: hypothetical protein BCG_2591c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.9e-100  334.1   0.0   4.7e-100  333.8   0.0    1.0  1  Peptidase_Mx    Putative zinc-binding metallo-peptidase
    5.1e-18   65.5   3.2      4e-17   62.7   3.2    2.1  1  zinc-ribbon_6   zinc-ribbon domain
      0.001   18.4   1.4      0.001   18.4   1.4    2.6  3  zf-ribbon_3     zinc-ribbon domain
     0.0015   18.0   0.0     0.0019   17.6   0.0    1.2  1  Peptidase_Mx1   Putative zinc-binding metallo-peptidase
  ------ inclusion threshold ------
       0.14   12.2   5.2       0.83    9.7   5.3    2.0  1  DZR             Double zinc ribbon
       0.16   12.1   0.6        5.1    7.2   0.1    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> Peptidase_Mx  Putative zinc-binding metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.8   0.0  1.6e-103  4.7e-100       3     234 ..      88     323 ..      86     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 333.8 bits;  conditional E-value: 1.6e-103
                   Peptidase_Mx   3 erwarieaakrrllysllrlglplesreedpeeglafdfladeeekekvltGhanGvitlnlaEaddaereklreelgEp 82 
                                    +++ar+e akrrl+++l++l+lp+  r++dp++glaf++l++++  e+v+tGh+nGvitl+laE+dd++re+lr+e++Ep
  gi|121638453|ref|YP_978677.1|  88 AEFARAEGAKRRLIAELHELKLPIVGRDQDPDHGLAFRLLSSAH--ENVTTGHQNGVITLDLAEGDDVHREQLRVEMDEP 165
                                    6899**************************************99..9********************************* PP

                   Peptidase_Mx  83 yRtllGHlRHEvgHyywdrlvede.erleefralFGderadYaaalqahYaegppadweeefvsaYAtaHpwEDwAEtwa 161
                                    yRtllGH+RHE+gHyy+ rl++++ + l++f++lFGd +adY++al++hY+ gpp+ w+++fvs+YAt+H+ EDwAEt+a
  gi|121638453|ref|YP_978677.1| 166 YRTLLGHFRHEIGHYYFYRLIASSsDYLSRFNELFGDPDADYSQALDRHYRGGPPEGWQDSFVSSYATMHASEDWAETFA 245
                                    **********************77589***************************************************** PP

                   Peptidase_Mx 162 hylhivdtletaaafgleleldpyeaa.....dfeelleawlpltlalnslnrslGqedlypfvlseavleKlefvhe 234
                                    hylhi d+l+taa +gl+ +  +++ +     +f++++++wlpl+++ln++nrs+G++dlypfvl++avleK++f+h+
  gi|121638453|ref|YP_978677.1| 246 HYLHIRDALDTAAWCGLAPASATFDRPalgpsAFNTIIDKWLPLSWSLNMVNRSMGHDDLYPFVLPAAVLEKMRFIHT 323
                                    ******************955555444555669********************************************7 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   3.2   1.3e-20     4e-17       2      90 ..       4      80 ..       3      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.3e-20
                  zinc-ribbon_6  2 feCeqCgqllffenssClkCgaalgfapeelellaleeaeeeewrslaekeskyklCanaaeaaCnwlvpaedaealCeaCr 83
                                   f+C +Cgq+l fens Cl+Cg+algf+  +++ll+++++ +            ++lCan + a+Cnwlvp+++   lC++C 
  gi|121638453|ref|YP_978677.1|  4 FHCPNCGQRLAFENSACLSCGSALGFSLGRMALLVIADDAD------------VQLCANLHLAQCNWLVPSDQLGGLCSSCV 73
                                   9*********************************9998877............78*************************** PP

                  zinc-ribbon_6 84 lnrtiPd 90
                                   l+   P 
  gi|121638453|ref|YP_978677.1| 74 LTIERPS 80
                                   *998886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.4   3.5e-07     0.001       4      24 ..       5      25 ..       3      27 .. 0.90
   2 ?   -1.0   0.0      0.43   1.3e+03       7      16 ..      55      64 ..      55      65 .. 0.76
   3 ?   -3.4   0.6       2.5   7.4e+03       5       8 ..      69      72 ..      68      72 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.5e-07
                    zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGt 24
                                   +CPnCG+ + + + ++C +CG+
  gi|121638453|ref|YP_978677.1|  5 HCPNCGQrL-AFENSACLSCGS 25
                                   8******66.***********7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.43
                    zf-ribbon_3  7 nCGaplssdd 16
                                   +C++++ sd+
  gi|121638453|ref|YP_978677.1| 55 QCNWLVPSDQ 64
                                   7***767775 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.5
                    zf-ribbon_3  5 CPnC 8 
                                   C++C
  gi|121638453|ref|YP_978677.1| 69 CSSC 72
                                   7777 PP

>> Peptidase_Mx1  Putative zinc-binding metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.5e-07    0.0019      94     195 ..     134     250 ..     127     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.5e-07
                  Peptidase_Mx1  94 ivlgtaegglkitLykvneldekek....dl.....vnellrtvhh.efahiLhqtkeydteFkkise...gkYtsstw. 159
                                    ++ g ++g + + L + +++++++     d      + ++ +++ h  f + +    +y ++F+++     ++Y++ +  
  gi|121638453|ref|YP_978677.1| 134 VTTGHQNGVITLDLAEGDDVHREQLrvemDEpyrtlLGHFRHEIGHyYFYRLIASSSDYLSRFNELFGdpdADYSQ-ALd 212
                                    5566666666666666666665511232321334434444466644156677778888888899986411156763.223 PP

                  Peptidase_Mx1 160 ..inkteaeankrGfvtayassspeeDfaEvislylte 195
                                      ++    e +++ fv++ya+ +++eD aE+ + yl  
  gi|121638453|ref|YP_978677.1| 213 rhYRGGPPEGWQDSFVSSYATMHASEDWAETFAHYLHI 250
                                    4455557789*************************965 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.3   0.00028      0.83       1      22 [.       6      27 ..       6      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                            DZR  1 CpqCgeelppdarfCseCgtkl 22
                                   Cp+Cg+ l  ++  C  Cg++l
  gi|121638453|ref|YP_978677.1|  6 CPNCGQRLAFENSACLSCGSAL 27
                                   9999999999999999999887 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0017       5.1       1       9 [.       5      13 ..       5      17 .. 0.88
   2 ?    2.7   0.0     0.044   1.3e+02       2       9 ..      20      27 ..      19      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                 DNA_ligase_ZBD  1 hCPvCGsav 9 
                                   hCP CG+ +
  gi|121638453|ref|YP_978677.1|  5 HCPNCGQRL 13
                                   9*****987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                 DNA_ligase_ZBD  2 CPvCGsav 9 
                                   C +CGsa+
  gi|121638453|ref|YP_978677.1| 20 CLSCGSAL 27
                                   899***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2820.34
//
Query:       gi|121638454|ref|YP_978678.1|  [L=314]
Description: hypothetical protein BCG_2592c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-23   81.6   1.0    1.3e-22   80.5   1.0    1.6  1  Bact_transglu_N  Bacterial transglutaminase-like N-terminal r
    7.2e-16   58.6   0.0    1.2e-15   57.9   0.0    1.4  1  Transglut_core   Transglutaminase-like superfamily
     0.0023   17.5   0.0     0.0039   16.7   0.0    1.3  1  DUF553           Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> Bact_transglu_N  Bacterial transglutaminase-like N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   1.0   2.1e-26   1.3e-22       1      80 []      17      96 ..      17      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 2.1e-26
                Bact_transglu_N  1 lrvrHrtrYtYdrpvslapqvlrLrPrsharqrvlsyslkvePepaevnwqqDafgnkvarvvvdephteleveaeseve 80
                                   +rv+Hrt+Y+Y++ v+ ++ +  L+Pr++ rqr+ +++l+++P+pa +++ +D +gn   +++v+eph++l+++++s+v+
  gi|121638454|ref|YP_978678.1| 17 YRVTHRTEYRYSDVVTSSYGRGFLTPRNSLRQRCVAHRLTIDPAPADRSTSRDGYGNISSYFHVTEPHRTLTITSDSIVD 96
                                   89***************************************************************************996 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   2.1e-19   1.2e-15      15     112 .]     158     260 ..     144     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.1e-19
                 Transglut_core  15 lekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsgeeekeq..svase 92 
                                     e ++ +++ + + ++y+ +++t+ s  +++vl ++ G+c+dfa l++a lRa+G+ a +v+gyl ++  + +   +  +
  gi|121638454|ref|YP_978678.1| 158 VEVLRDLASRIYTDFTYR-SGSTTISTGVNEVLLAREGVCQDFARLAIACLRANGLAACYVSGYLATDPPPGKdrMIGID 236
                                    4788999999999*****.999999999**************************************87766667889999 PP

                 Transglut_core  93 daHawvevyl....egygWvplDp 112
                                     +Haw+ v++        W+ lDp
  gi|121638454|ref|YP_978678.1| 237 ATHAWASVWTpqqpGRFEWLGLDP 260
                                    99********77555556999998 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.6e-07    0.0039      66      99 ..     184     217 ..     159     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-07
                         DUF553  66 tpkeilktkkgiCrDYaiLTaalLlnlniskvyl 99 
                                      +e+l  ++g+C+D+a L  a L ++++   y+
  gi|121638454|ref|YP_978678.1| 184 GVNEVLLAREGVCQDFARLAIACLRANGLAACYV 217
                                    5789*********************999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2300.89
//
Query:       gi|121638455|ref|YP_978679.1|  [L=129]
Description: hypothetical protein BCG_2593 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-06   27.5   0.0    4.2e-06   27.2   0.0    1.1  1  YjbR      YjbR


Domain annotation for each model (and alignments):
>> YjbR  YjbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.4e-10   4.2e-06       3      85 ..      14     113 ..      12     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.4e-10
                                    STTEEEEECTTS-EEEECCCEEEEEEECCCCG.................EEEES.-HHHHHHHHHSSTT.EEE-TS..TT CS
                           YjbR   3 lpgatedfpfgpelvfkvggKmFallgleees.................lnlkc.dpeeaeaLreqypa.iapgyh..kk 61 
                                    lp + e+ p++    ++vg+K  a+ ++ ++s                 + +++ d+  + aL++++p  ++   h    
  gi|121638455|ref|YP_978679.1|  14 LPLTAEQAPHD----WRVGRKLLAWERPLRKSdrealtragseppsgdiVGVRVsDEGVKFALIADEPGvYFTTPHfdGY 89 
                                    8899999**96....*************88867788999999************9999999********77777797644 PP

                                    TEEEEETTSS-HHHHHHHHHHHHH CS
                           YjbR  62 hWitvlldgvpddeleelideSYr 85 
                                      + v l +++  +leeli+e++ 
  gi|121638455|ref|YP_978679.1|  90 PAVLVRLAEIEVRDLEELITEAWL 113
                                    577778888**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1021.70
//
Query:       gi|121638456|ref|YP_978680.1|  [L=355]
Description: transmembrane alanine and valine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-13   49.7  17.8    6.8e-13   48.9  17.8    1.4  1  FUSC_2    Fusaric acid resistance protein-like
    9.4e-05   22.3  14.7    0.00016   21.5  14.7    1.4  1  DUF2955   Protein of unknown function (DUF2955)
    0.00015   21.9  11.4    0.00015   21.9  11.4    2.2  2  ArAE_1    Aromatic acid exporter family member 1
  ------ inclusion threshold ------
       0.12   12.1   2.1        1.5    8.7   0.3    2.5  2  Rz1       Lipoprotein Rz1 precursor


Domain annotation for each model (and alignments):
>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9  17.8   1.5e-16   6.8e-13       3     127 .]      38     163 ..      32     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.5e-16
                         FUSC_2   3 v.liaellglwrgeWalitaaivlsptlgasltravqRilGtvlGavlallllyllpgn.lalallvfll....vfliaf 76 
                                    + l   +++++++++a+i+a++++s t    ++ra q+i+G++lG+vl++ + +ll ++ +a+ ++vf++    v++++ 
  gi|121638456|ref|YP_978680.1|  38 WyLTHDVFNHPQAFFAPISAVVCMSATNVLCARRAQQMIVGVALGIVLGAGVHALLGSGpIAMGVVVFIAlsvaVLCARG 117
                                    42444589*********************************************988886699999999994444555566 PP

                         FUSC_2  77 flkrnyal.afifltllalllyslaagsgnpieialhRlldvliGiliallv 127
                                    +++++ ++ ++++++++++l+++    +g   +++++Rl+d+l+G+ +a+++
  gi|121638456|ref|YP_978680.1| 118 LVAQGLMFiNQAAVSAVLVLVFAS---NG---SVVFERLFDALVGGGLAIVF 163
                                    666666442556666666666653...34...579**************986 PP

>> DUF2955  Protein of unknown function (DUF2955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  14.7   3.6e-08   0.00016      16     137 ..      42     164 ..      29     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.6e-08
                        DUF2955  16 skllgwplgvfapvlpvllLtlvpklslkallqlllsvvltalevlllvellqhyPvlmtllvflll..llkfrlmsrgs 93 
                                      +++ p ++fap+ +v+ ++ +++l ++ + q+++ v+l ++ ++ +  ll++ P+ m ++vf+ l   +++++ +  +
  gi|121638456|ref|YP_978680.1|  42 HDVFNHPQAFFAPISAVVCMSATNVLCARRAQQMIVGVALGIVLGAGVHALLGSGPIAMGVVVFIALsvAVLCARGLVAQ 121
                                    458********************************************************999998872245688888999 PP

                        DUF2955  94 kflfgamlvislsillvfasydttdvedlilsllaalllavvia 137
                                      +f     +s +++lvfas  +++ e l  +l+ +  la+v  
  gi|121638456|ref|YP_978680.1| 122 GLMFINQAAVSAVLVLVFASNGSVVFERLFDALVGG-GLAIVFS 164
                                    9999999************98777666666665555.4555444 PP

>> ArAE_1  Aromatic acid exporter family member 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9  11.4   3.4e-08   0.00015       7     136 ..      27     162 ..      25     167 .. 0.72
   2 ?   -2.0   0.1      0.83   3.7e+03      13      29 ..     254     270 ..     253     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.4e-08
                         ArAE_1   7 tlKtaiavalailiae.llgleyavsAgIiailsiqptkkrslrtalerllasvlaliiavvffellGykpiviglvlll 85 
                                    ++ t + + la ++ + +++ ++a +A I a+++++ t+    r a + +++++l++++++ + +llG  pi++g+v+++
  gi|121638456|ref|YP_978680.1|  27 ITQTSVVAGLAWYLTHdVFNHPQAFFAPISAVVCMSATNVLCARRAQQMIVGVALGIVLGAGVHALLGSGPIAMGVVVFI 106
                                    5678889999999986489********************************************************99877 PP

                         ArAE_1  86 fipltvklk...leegivv..ssVlvlhllesksislalllnelllilvGigvall 136
                                     + ++v      + +g++      +   l+   +++ ++++++l+  lvG g+a++
  gi|121638456|ref|YP_978680.1| 107 ALSVAVLCArglVAQGLMFinQAAVSAVLVLVFASNGSVVFERLFDALVGGGLAIV 162
                                    66655433211144444321111222223333444555666777777777777666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.83
                         ArAE_1  13 avalailiaellgleya 29 
                                    av la+l++++l+l  +
  gi|121638456|ref|YP_978680.1| 254 AVYLALLVSSVLHLART 270
                                    78899999999999754 PP

>> Rz1  Lipoprotein Rz1 precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.029   1.3e+02       1      12 [.      60      70 ..      60      73 .. 0.85
   2 ?    8.7   0.3   0.00033       1.5      15      37 ..     204     226 ..     199     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.029
                            Rz1  1 CsSkPpvqCQvk 12
                                   C+S  +v+C  +
  gi|121638456|ref|YP_978680.1| 60 CMSATNVLC-AR 70
                                   *********.44 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00033
                            Rz1  15 aPPAWamqpppdwqqlLneiisv 37 
                                    aPP W m  +  + q Ln+ i v
  gi|121638456|ref|YP_978680.1| 204 APPDWPMAAADRLHQQLNGLIEV 226
                                    8******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2664.15
//
Query:       gi|121638457|ref|YP_978681.1|  [L=611]
Description: aspartyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-99  331.0   0.0    7.6e-99  330.7   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    4.8e-16   58.5   0.0      1e-15   57.5   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.5e-12   47.5   0.0      3e-12   46.6   0.0    1.4  1  GAD              GAD domain
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.31   11.0   0.0    1.2  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.7   0.0  1.7e-102   7.6e-99       2     313 ..     122     562 ..     121     563 .. 0.99

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 1.7e-102
                                    CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspql 81 
                                    eelrlk+ryldlr+++  + +rlrs+v +a r +l +++f+eietP++++s t+egar+F+v+ r ++++f+aL+qspql
  gi|121638457|ref|YP_978681.1| 122 EELRLKYRYLDLRRDDPAAAIRLRSRVNAAARAVLARHDFVEIETPTITRS-TPEGARDFLVPARLHPGSFYALPQSPQL 200
                                    799************************************************.**************************** PP

                                    HHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  82 ylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrns 161
                                    +++ll+vag++r++qiar++R+Ed+r+dr++ EFtq+++emsf++ edi+ + ee++++l+  +  +             
  gi|121638457|ref|YP_978681.1| 201 FKQLLMVAGMERYYQIARCYRDEDFRADRQP-EFTQLDMEMSFVDAEDIIAISEEVLTELWALI--GY------------ 265
                                    *******************************.******************************99..55............ PP

                                    EE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH............................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                    tRNA-synt_2 162 kdlkkpfkrltykeaieklneigkdldkaderalvk............................................ 197
                                      +++p++r+ y+ea+++      ++dk+d+r+ ++                                            
  gi|121638457|ref|YP_978681.1| 266 -RIPTPIPRIGYAEAMRR-----FGTDKPDLRFGLElvectdffsdttfrvfqapyvgavvmpggasqprrtldgwqdwa 339
                                    .7899*************.....9******************************************************** PP

                                    ............................................................................HS-- CS
                                    ............................................................................xxxx RF
                    tRNA-synt_2 198 ............................................................................kekn 201
                                                                                                                 + +
  gi|121638457|ref|YP_978681.1| 340 kqrghrglayvlvaedgtlggpvaknlteaertgladhvgakpgdciffsagpvkssrallgaarveianrlglidPDAW 419
                                    ******************************************************************************** PP

                                    SEEEEEEEB......................GGGSTTCBBBSTTS........TTBBSEEEEEETTEEEEEEEEB--SHH CS
                                    xxxxxxxxx......................xxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 202 epvfvtdfP......................aelkpFyarkeedd........kkltesyDllingvElvgGslRiedpe 251
                                     +v+v+d P                      a ++ F+a+k e +        + l+++yD+++ng E++gGs+Ri++++
  gi|121638457|ref|YP_978681.1| 420 AFVWVVDPPlfepadeataagevavgsgawtAVHHAFTAPKPEWEdriesdtgSVLADAYDIVCNGHEIGGGSVRIHRRD 499
                                    *****************************************999899********************************* PP

                                    HHHHHHHHCCHH.SSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 252 eleeklkskgld.eeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                    ++e+++   gld  e eekf+++lea+ +GapphgG+++G+dR+++ll+g++sIr+viaFPk+
  gi|121638457|ref|YP_978681.1| 500 IQERVFAVMGLDkAEVEEKFGFLLEAFMFGAPPHGGIAFGWDRTTALLAGMDSIREVIAFPKT 562
                                    ************99***********************************************97 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   2.2e-19     1e-15       1      76 []      21     106 ..      21     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.2e-19
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET...HHHHHHHTTS-TTSEEEEEEEEEECTTS.........SEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr...eeatklaenlkeGdvvrvtGrvkrrpgg.........elel 68 
                                    Vt+aG+v ++  r++g+vifidlrD +g+ qvv+ +   +e+ ++a +l+ + +v v G v+ rp+g         e+e+
  gi|121638457|ref|YP_978681.1|  21 VTLAGWVARR--RDHGGVIFIDLRDASGIAQVVFRDpqdTEVLAQAHRLRAEFCVSVAGVVEIRPEGnanpeiatgEIEV 98 
                                    89********..****************************************************99999999******** PP

                                    EEEEEEEE CS
                tRNA_anti-codon  69 kveeiell 76 
                                    +++++++l
  gi|121638457|ref|YP_978681.1|  99 NATSLTVL 106
                                    ****9986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   6.6e-16     3e-12      10      90 ..     315     395 ..     310     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 6.6e-16
                                    EEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESS.GGEETTTCCCS-HHHHHHHHHHCT--TTEEEEEEEEEH CS
                            GAD  10 svkalrvpggaaklsrkeideleefakelgakglawikveg.egltgpiakflteeevkklleavgaeegDillfvAdkk 88 
                                     v a+++pgg a+ +r+ +d  ++ ak+ g +gla++ v + + l gp+ak lte+e   l++ vga++gD ++f A++ 
  gi|121638457|ref|YP_978681.1| 315 YVGAVVMPGG-ASQPRRTLDGWQDWAKQRGHRGLAYVLVAEdGTLGGPVAKNLTEAERTGLADHVGAKPGDCIFFSAGPV 393
                                    5889*****8.999***********************99884668899******************************97 PP

                                    HH CS
                            GAD  89 kt 90 
                                    k+
  gi|121638457|ref|YP_978681.1| 394 KS 395
                                    65 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.8e-05      0.31      38      94 ..     212     263 ..     211     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.8e-05
                                    EEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  38 klyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlikaisriferl 94 
                                    ++yqi ++yRdE        R+ eF+q d ++    ++   d+++  +++  +++  +
  gi|121638457|ref|YP_978681.1| 212 RYYQIARCYRDEDF-RAD--RQPEFTQLDMEMSFVdAE---DIIAISEEVLTELWALI 263
                                    79**********97.335..999******987555255...55555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4570.99
//
Query:       gi|121638458|ref|YP_978682.1|  [L=246]
Description: 2-dehydropantoate 2-reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-23   81.7   0.1    1.1e-22   80.5   0.0    1.6  2  ApbA_C       Ketopantoate reductase PanE/ApbA C terminal
    7.1e-17   61.5   0.0    1.1e-16   60.9   0.0    1.3  1  ApbA         Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.062   13.4   0.1       0.17   12.0   0.1    1.7  1  Phage_lysis  Bacteriophage Rz lysis protein


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.71   4.2e+03      33      54 ..      29      50 ..      23      73 .. 0.66
   2 !   80.5   0.0   1.9e-26   1.1e-22       1     123 [.     120     240 ..     120     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.71
                         ApbA_C 33 spelralvrallkEalavaeae 54
                                   + ++r  +++l++E   va  +
  gi|121638458|ref|YP_978682.1| 29 NDAARPWLTRLCDERTVVAVLQ 50
                                   6677777888888865555332 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 1.9e-26
                         ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan.rs 79 
                                    d+++a+w+Kll+n a+ +  +l + +  ++++  +++al r++++E+lava+aeg++l+++ + ++v ++++ +++   +
  gi|121638458|ref|YP_978682.1| 120 DFTTAAWRKLLVN-ALAGFMVLSGRRS-AMFRRDDVAALSRRYVAECLAVARAEGARLDDD-VVDEVVRLVRSAPQDmGT 196
                                    67899********.8888888888776.5556888********************99****.6666666666666644** PP

                         ApbA_C  80 SMlqDveagrktEidyinGavvklAeklgvetPvnellyellka 123
                                    SMl D +a+r++E+d  nG +v+ A+++g+ tP  ++l+ ll a
  gi|121638458|ref|YP_978682.1| 197 SMLADRAAHRPLEWDLRNGVIVRKARAHGLATPISDVLVPLLAA 240
                                    **************************************999875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   1.8e-20   1.1e-16      58     148 ..       8      96 ..       1     100 [. 0.91

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.8e-20
                                    ECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEE CS
                           ApbA  58 lsaeekselepidlvivtvKayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgev 137
                                    +s  +++ ++p+d++i++vKa+q+++a  ++ +l+d++tvv +lqNG+++ e+++ ++p + v++++++ +a+ +++g v
  gi|121638458|ref|YP_978682.1|   8 TS--PREVAGPVDVLILAVKATQNDAARPWLTRLCDERTVVAVLQNGVEQVEQVQPHCPSSAVVPAIVWCSAETQPQGWV 85 
                                    33..34889*********************************************************************** PP

                                    EECS--EEEEE CS
                           ApbA 138 hhagkgeikig 148
                                    +++g++++++ 
  gi|121638458|ref|YP_978682.1|  86 RLRGEAALVVP 96 
                                    ****9999876 PP

>> Phage_lysis  Bacteriophage Rz lysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.9e-05      0.17      29      66 ..     149     187 ..     141     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                    Phage_lysis  29 rqravaeldakhtke.LadaksendrlradvaaGrrrLr 66 
                                    r+ +va+l++++  e La a++e +rl +dv +  +rL 
  gi|121638458|ref|YP_978682.1| 149 RRDDVAALSRRYVAEcLAVARAEGARLDDDVVDEVVRLV 187
                                    5669********87779**************99999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1848.75
//
Query:       gi|121638459|ref|YP_978683.1|  [L=167]
Description: hypothetical protein BCG_2597 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-21   76.2   0.5    3.6e-21   75.9   0.5    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    9.5e-05   22.6   0.1    0.00013   22.1   0.1    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    0.00028   21.1   0.1    0.00034   20.9   0.1    1.1  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.5     6e-25   3.6e-21       5     140 ..      20     155 ..      17     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 6e-25
                                    EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS...SEEEEEEEEEETTTTEEEEEEE. CS
                Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr...gtvreelvevdpegrllsyriv. 80 
                                    + +v+ a +pe+ +++++d+++wprW   +++v++++ ++p  + +gt+r + +       ee++ ++p  +++++r++ 
  gi|121638459|ref|YP_978683.1|  20 RNTVDLAITPEQLFEVLADPQAWPRWATVITKVTWTS-PEP--FGAGTTRIVEMrggIVGDEEFISWEP-FTRMAFRFNe 95 
                                    57999*******************************9.999..88899997777777569*********.********88 PP

                                    ..SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  81 .kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLka 140
                                     +++ v+ +   ++v++ +gg+r+twt++ + +++++p+   +++ ++  +l++ L++L++
  gi|121638459|ref|YP_978683.1|  96 cSTRAVGAFAEDYRVQAIPGGCRLTWTMAQKLAGPARPA-LFVFRPLLNLALRRFLRNLRR 155
                                    99**************************88877777776.577999999999999999987 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.2e-08   0.00013       3     130 .]      27     154 ..      25     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.2e-08
                                    S-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E...............EEECSTTSSCEEEEEEEEEEETTTEEE CS
                 Polyketide_cyc   3 apadqvyalvadvesypeflphcssvevleeaesglsa...............dlevgfggltesftarvtldppeeitf 67 
                                      ++q+++++ad + +p++   +++v++++ ++    a               +  +++ ++t+  +  +++   +    
  gi|121638459|ref|YP_978683.1|  27 ITPEQLFEVLADPQAWPRWATVITKVTWTSPEPF--GAgttrivemrggivgdEEFISWEPFTRMAFRFNECSTRAV--- 101
                                    679******************************6..44445579999999999999999999999999999998888... PP

                                    CTTCCCCCEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  68 klvegdfkslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldellaale 130
                                             +    +++  p    g+r+++++  ++ +  ++  ++ +++++ +l+++l++l+
  gi|121638459|ref|YP_978683.1| 102 -------GAFAEDYRVQAIPG---GCRLTWTMAQKLAGPARPALFVFRPLLNLALRRFLRNLR 154
                                    .......7899999******8...*********************************999986 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   5.6e-08   0.00034       3      98 ..      28     126 ..      26     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.6e-08
                                    -HHHHHHHHH-HHHHHHH.EEEEEEEE--.ST.TE.EEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEEEE CS
                          AHSA1   3 pperVfraltdpellkrW.ftlteaemdl.rp.Gg.kfrlrdspdgkefgnegeylevvpperlvytwrledepeeeest 78 
                                    +pe++f++l dp++  rW   +t++++   +p G  + r+   +  +   +  e++ ++p +r+ ++++  ++++ +++ 
  gi|121638459|ref|YP_978683.1|  28 TPEQLFEVLADPQAWPRWaTVITKVTWTSpEPfGAgTTRI--VEMRGGIVGDEEFISWEPFTRMAFRFNECSTRAVGAFA 105
                                    8*****************8777777777766685448888..455677777778*************9999999977999 PP

                                    EEEEEEEETTEEEEEEEE.EE CS
                          AHSA1  79 vtieleeegggTrltlth.tg 98 
                                      +  ++ +gg rlt t+ ++
  gi|121638459|ref|YP_978683.1| 106 EDYRVQAIPGGCRLTWTMaQK 126
                                    999999999999999998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1311.71
//
Query:       gi|121638460|ref|YP_978684.1|  [L=293]
Description: membrane glycine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-75  252.2   0.8    8.2e-75  251.9   0.8    1.0  1  Zn_peptidase  Putative neutral zinc metallopeptidase


Domain annotation for each model (and alignments):
>> Zn_peptidase  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.9   0.8   4.6e-79   8.2e-75      19     290 .]      14     287 ..       4     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 251.9 bits;  conditional E-value: 4.6e-79
                   Zn_peptidase  19 sggegaGGggkgrslggktgllvlilvlvgllfGvdlsallglgqesstaeaaaqssegtaeeaedeqkefvsvvladte 98 
                                     +++g GGg ++ + g  +gl+ l++v+v++l+Gvd+ ++l+ +q+  t++  a   + ++  +  ++++fv+  +  t 
  gi|121638460|ref|YP_978684.1|  14 TSTSGSGGG-RRLAIG--GGLGGLLVVVVAMLLGVDPGGVLS-QQPLDTRDHVAPGFDLSQCRTGADANRFVQCRVVATG 89 
                                    333344443.344444..49**********************.555555555555444555555888999*999888899 PP

                   Zn_peptidase  99 dtWtqifkekgktyqkpklvlfsrvvrsaCGtassatGPfyCPadrkvyldlsffdelkqklgaa.GdfaaayviahevG 177
                                    +    ++k     y++p + lfs++v ++CG ass +GPfyCP d++ y+d+ ff+ l +++g++ G fa  yv+ahe G
  gi|121638460|ref|YP_978684.1|  90 NSVDAVWKPLLPGYTRPHMRLFSGQVGTGCGPASSEVGPFYCPVDKTAYFDTDFFQVLVTQFGSSgGPFAEEYVVAHEYG 169
                                    99999*********************************************************987257************ PP

                   Zn_peptidase 178 hhvqnllGilekveqarqgaseaeanqlsvrleLqadcfaGvWansvq...qkg..l.....lekgdieealnaakaiGd 247
                                    hhvqnllG+l + +q  qg     a    vr eLqadc+aGvWa++++   q+   +     l + di++al+aa+a+Gd
  gi|121638460|ref|YP_978684.1| 170 HHVQNLLGVLGRAQQGAQG-----AAGSGVRTELQADCYAGVWAYYAStvkQEStgVpylepLSDKDIQDALAAAAAVGD 244
                                    *********9876554444.....45668***************9875221332222453446689************** PP

                   Zn_peptidase 248 dtLqkqsqgrvvPdsfthGtsqqrqrWfkrGfesGdlaqcdtf 290
                                    d++q+q++gr+ P+++thG+++qrq+Wf+ G+++Gd++ cdtf
  gi|121638460|ref|YP_978684.1| 245 DRIQQQTTGRTNPETWTHGSAAQRQKWFTVGYQTGDPNICDTF 287
                                    ******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2142.36
//
Query:       gi|121638461|ref|YP_978685.1|  [L=154]
Description: hypothetical protein BCG_2599c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1197.12
//
Query:       gi|121638462|ref|YP_978686.1|  [L=529]
Description: hypothetical protein BCG_2600 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-16   59.6   0.7    7.1e-16   58.6   0.7    1.5  1  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
    2.9e-13   50.8   0.3    4.9e-13   50.0   0.3    1.3  1  Metallophos      Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.011   15.1   2.8      0.011   15.1   2.8    2.0  2  UCR_Fe-S_N       Ubiquitinol-cytochrome C reductase Fe-S subu
       0.02   15.8   3.5       0.28   12.1   0.8    3.1  2  Metallophos_C    Iron/zinc purple acid phosphatase-like prote
      0.048   13.5   7.5      0.094   12.6   7.5    1.5  1  TAT_signal       TAT (twin-arginine translocation) pathway si


Domain annotation for each model (and alignments):
>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.7     2e-19   7.1e-16       3      83 ..      67     148 ..      65     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2e-19
                Pur_ac_phosph_N   3 qvhlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyet.tnyksgyshkatltgLepgttYyYrvgd 81 
                                    ++hl+++ + st+m+vsW+t+++++++ v  gt ++   s + a++++y + +++++  +++a+lt+L+p+t Y+Y    
  gi|121638462|ref|YP_978686.1|  67 GLHLQFGRNASTEMVVSWHTTDTVGNPRVMLGTPTSGFGSVVVAETRSYRDaKSNTEVRVNHAHLTNLTPDTDYVYAAVH 146
                                    58***********************************************9966777899*****************9988 PP

                Pur_ac_phosph_N  82 de 83 
                                    d+
  gi|121638462|ref|YP_978686.1| 147 DG 148
                                    87 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.3   1.4e-16   4.9e-13      38     204 .]     213     389 ..     197     389 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.4e-16
                                    EEESTSSSSS.......HHHHHHHHHHHHHHHHTSEEEEEC-TTS.....CHHHHHHHHHHHHHHH.HHHHEHHHCEEET CS
                    Metallophos  38 llaGDlvdrg.......dlekellellaalvkypipvylllGNHe.....gfeeellnkygylgif.sepwrsdaevfnn 104
                                    l++GDl + +        ++ ++ ++ +       p+++++GNHe     g         +y+++f  ++  s  +  + 
  gi|121638462|ref|YP_978686.1| 213 LINGDLCYANlaqdrirTWSDWFDNNTRSAR--YRPWMPAAGNHEnevgnG----PIGYDAYQTYFaVPDSGSSPQLRGL 286
                                    556**99999777777777774444433333..48**********666431....2222222222232222222233344 PP

                                    SEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC..HHHHHH....HHHHTTCSEEEEEESSESS.....C CS
                    Metallophos 105 lplaslgsgslkvlllhGgspellvsldklgslnleleapepg..dewlkd....lekrekadwvivlgHsply.....r 173
                                    ++++  gs   +v+ lh++     +   + g+ ++ + ++  g    wl+      ++ ++ dwv+v  H         +
  gi|121638462|ref|YP_978686.1| 287 WYSFTAGSV--RVISLHND-----DVCYQDGGNSYVRGYSG-GeqRRWLQAelanARRDSEIDWVVVCMHQTAIstaddN 358
                                    455554555..77777777.....22223333333333333.34799999999999999***************888888 PP

                                    SSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                    Metallophos 174 gsgylfgdealedllkkygvdlvisGHtHvy 204
                                    ++ +l  ++++ +l+++y+vdlv++GH+H+y
  gi|121638462|ref|YP_978686.1| 359 NGADLGIRQEWLPLFDQYQVDLVVCGHEHHY 389
                                    888888888888*****************97 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.8     3e-06     0.011       4      29 ..      13      36 ..      11      43 .. 0.77
   2 ?   -3.0   0.1       1.4   4.9e+03      19      28 ..     101     110 ..      97     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-06
                     UCR_Fe-S_N  4 aesdeptRRDFLyiATgavgaVGaaa 29
                                   + +++ +RR+FL  +Tga+++VG++ 
  gi|121638462|ref|YP_978686.1| 13 SPPKGVSRRRFL--TTGAAAVVGTGV 36
                                   567899******..777777777764 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                     UCR_Fe-S_N  19 TgavgaVGaa 28 
                                    T+++g V++a
  gi|121638462|ref|YP_978686.1| 101 TSGFGSVVVA 110
                                    9999**9998 PP

>> Metallophos_C  Iron/zinc purple acid phosphatase-like protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.1   1.5e+04       9      16 ..     250     257 ..     250     271 .. 0.64
   2 ?   12.1   0.8   7.8e-05      0.28       1      42 [.     421     490 ..     421     492 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.1
                  Metallophos_C   9 aAGndegd 16 
                                    aAGn+e++
  gi|121638462|ref|YP_978686.1| 250 AAGNHENE 257
                                    69999992 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.8e-05
                  Metallophos_C   1 ApvhiviGaAGndeg....................dafkg.........eppqpewsafrstd..yGygrltv 42 
                                    ++vh+viG++G +                      d   +           + ++wsafr+ d  yG++ + v
  gi|121638462|ref|YP_978686.1| 421 GTVHLVIGGGGTSKPtnallfpqprcqvitgvgdfD---PairrkpsifVLEDAPWSAFRDRDnpYGFVAFDV 490
                                    79*********7766999999999999999885551...3444556666667889*****6666699988766 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.5   2.6e-05     0.094       2      25 ..      18      41 ..      17      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                     TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                   +SRR FL ++AAa  ++++g+ ++
  gi|121638462|ref|YP_978686.1| 18 VSRRRFLTTGAAAVVGTGVGAGGT 41
                                   8*******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4039.51
//
Query:       gi|121638463|ref|YP_978687.1|  [L=340]
Description: hypothetical protein BCG_2601c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-11   43.5   0.0    7.3e-11   42.7   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
     0.0094   16.2   0.0      0.017   15.4   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   8.1e-15   7.3e-11       4     158 ..      69     237 ..      66     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 8.1e-15
                                    ESEESS--TTTSCCTT...........HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   4 trgCnlrCsfCarpet...........vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlak 72 
                                    +rgC+++C++C  + t             + +++++     + +e+++ +  ++ ++v lg  +  +++ + +++++   
  gi|121638463|ref|YP_978687.1|  69 YRGCSHACRYCFARPTheyldfnpgtdFDTQVVVKTNVAAVLRHELRRPS--WRRETVALGTNTDPYQRAEGRYALMPGI 146
                                    79********************9877655555666666666666666665..5488999998888888888888887777 PP

                                    TC...CCTEEEEEEECSSCHGHHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETE CS
                                    xx...xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  73 la...vpgiritvetngtlpdeeklerllelg...vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrv 145
                                    +     +g  +++ t gtl+ ++ l +++e+    +  v+++l  +d+e  ++ ++ +++t++++l+++ ++r+ag++  
  gi|121638463|ref|YP_978687.1| 147 IGalaASGTPLSILTKGTLL-RRDLPLIAEAAqqvPVSVAVSLAVGDPE-LHRDVEsGTPTPQARLALITAIRAAGLDCH 224
                                    778899**************.9********99999**************.9999999********************988 PP

                                    EEEEEEBTTTSHH CS
                                    xxxxxxxxxxxxx RF
                    Radical_SAM 146 vdrivglpGende 158
                                    v + ++lp  +d+
  gi|121638463|ref|YP_978687.1| 225 VMVAPVLPQLTDS 237
                                    9999999999995 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-06     0.017      12      42 ..      69     102 ..      61     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                        Fer4_12  12 vsgCnlsCkgCfnketw...sfksgkeftkelle 42 
                                      gC+++C++Cf++ t+   +f+ g++f++++  
  gi|121638463|ref|YP_978687.1|  69 YRGCSHACRYCFARPTHeylDFNPGTDFDTQVVV 102
                                    67**********9988766699999999877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2972.36
//
Query:       gi|121638464|ref|YP_978688.1|  [L=300]
Description: haloalkane dehalogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-16   60.2   0.4    1.5e-15   57.5   0.6    1.8  2  Abhydrolase_1   alpha/beta hydrolase fold
      5e-09   37.1   4.1      6e-09   36.8   4.1    1.1  1  Abhydrolase_6   Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.041   14.0   0.7         13    5.9   0.3    3.3  4  Acetyltransf_6  Acetyltransferase (GNAT) domain
       0.18   11.0   0.0       0.27   10.4   0.0    1.2  1  Hydrolase_4     Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.6   3.4e-19   1.5e-15       2     127 ..      32     155 ..      31     160 .. 0.90
   2 ?    0.2   0.0       0.1   4.6e+02     196     256 ..     227     279 ..     197     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 3.4e-19
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEE.EEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddklt.lvGh 80 
                                    ++v+ hG p ss++w++  ++p+L+    ++++ Dl G g S++ + + +d+y+    +d+l ++ dal+++  + lv h
  gi|121638464|ref|YP_978688.1|  32 AIVFQHGNPTSSYLWRN--IMPHLEG-LGRLVACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVvLVLH 108
                                    79***************..******9.779999*************9999********************976666**** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCH CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdf 127
                                    ++G+++++ +a ++ +rV+++++++ai +++ + ++ +  +  f++f
  gi|121638464|ref|YP_978688.1| 109 DWGSALGFDWANQHRDRVQGIAFMEAIVTPMTWADWPPAVRGVFQGF 155
                                    **************************777777777777666666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                                    CHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 196 dsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                     ++++l + ++      p l+i ++   +++ + ++d+ + +p+ + ++ +++ H+++ + 
  gi|121638464|ref|YP_978688.1| 227 EYRSWLEETDM------PKLFINAEPGAIIT-GRIRDYVRSWPN-QTEITVPGVHFVQEDS 279
                                    55566666666......88888775555555.778888889999.9999999999999876 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   4.1   1.3e-12     6e-09       1     217 [.      33     283 ..      33     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.3e-12
                                    EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTST......S-GGCS--HHHCHHH.HHHHCCTT..TTSEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGhG......rsdpppldledladl.aalldelaagggpvvlvG 71 
                                    +++ HG ++s++ W+  +++L   + ++   +a Dl G+G      +s p+ +++ + +d+  al d+l+  g+ vvlv 
  gi|121638464|ref|YP_978688.1|  33 IVFQHGNPTSSYLWRniMPHL--EGLGRL--VACDLIGMGasdklsPSGPDRYSYGEQRDFlFALWDALD-LGDHVVLVL 107
                                    5677**********6345555..555557..8********777775557777***999999755555555.78889**** PP

                                    ETCHHHHHHHHHHCC....EE.EEES-..----TTT...S----TTHHHHHHTT-C.....CCCHCCHS-HSCCCCHHH. CS
                  Abhydrolase_6  72 HSlGGalalaaapla..lvvg.vlldppptalpagl...laaalelllallallrl.....lawlsreplprlfladed. 139
                                    H++G al+  +a +   +v g  ++++   ++p+++   ++a++ ++++++++           ++++ lp  +l++++ 
  gi|121638464|ref|YP_978688.1| 108 HDWGSALGFDWANQHrdRVQGiAFMEA--IVTPMTWadwPPAVRGVFQGFRSPQGEpmaleHNIFVERVLPGAILRQLSd 185
                                    **********666667777779*****..888888877766666666655553333222222222333455566665554 PP

                                    ..CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC..EEE.....C..TT-C...........HHHHCHHCCCH.STTE CS
                  Abhydrolase_6 140 ..adaawrarlarlaallaglgllpaaawadlpvpl..lvl.....g..geDp...........lvprllerlla.qaga 196
                                      +  + r+ + ++ + ++ l + +  ++ + p+ +  l +     +  ++D+           ++   ++++ + ++  
  gi|121638464|ref|YP_978688.1| 186 eeMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVvaL-VneyrsWleETDMpklfinaepgaIITGRIRDYVRsWPNQ 264
                                    334577777777777777777777766666666666431.2443333556666777777666773334488888877777 PP

                                    EETCE...SSS-HHHHSHHHH CS
                  Abhydrolase_6 197 rlpvvlpgaGHlphleepdev 217
                                    +  +++pg  H++++++p+e+
  gi|121638464|ref|YP_978688.1| 265 TE-ITVPGV-HFVQEDSPEEI 283
                                    77.999999.8****999987 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   5.5e+03      52      75 ..      40      61 ..      36      66 .. 0.73
   2 ?    5.9   0.3    0.0029        13      51      95 ..      83     126 ..      68     132 .. 0.88
   3 ?    0.2   0.0      0.17   7.6e+02      25      56 ..     215     248 ..     207     267 .. 0.83
   4 ?    3.4   0.0     0.017        77      18      43 ..     270     295 ..     252     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                 Acetyltransf_6 52 pltraflrdllaalaargalrlyv 75
                                   p +  ++r+++++l  +g +rl++
  gi|121638464|ref|YP_978688.1| 40 PTSSYLWRNIMPHL--EGLGRLVA 61
                                   55566889999999..77777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                 Acetyltransf_6  51 dpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrl 95 
                                      ++r+fl +l++al + g+ +++vl+  g  +++ ++ +++dr+
  gi|121638464|ref|YP_978688.1|  83 YGEQRDFLFALWDAL-DLGDHVVLVLHDWGSALGFDWANQHRDRV 126
                                    56789**********.6899999********************97 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.17
                 Acetyltransf_6  25 atdpedleallelfraqwarr..pdvfadpltra 56 
                                    + +p+++ al+  +r++ +++  p++f ++++ a
  gi|121638464|ref|YP_978688.1| 215 DGEPAEVVALVNEYRSWLEETdmPKLFINAEPGA 248
                                    6789999**********99998888877776665 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.017
                 Acetyltransf_6  18 gevrfrvatdpedleallelfraqwa 43 
                                     +v f+ +++pe++ a++++f++q +
  gi|121638464|ref|YP_978688.1| 270 PGVHFVQEDSPEEIGAAIAQFVRQLR 295
                                    57899999*************99976 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.1e-05      0.27       6     114 ..      32     139 ..      29     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.1e-05
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                    ++v+ HG   +s    +++ +L   G  v a D  G G s+      p+  +y +  + ++    +   +  ++l+ h +
  gi|121638464|ref|YP_978688.1|  32 AIVFQHGNPTSSYLWRNIMPHLEGLGRLV-ACDLIGMGASDKLSPSGPDRYSYGEQRDFLFALWDALDLGDHVVLVLHDW 110
                                    68899999999999999999999999766.78********966666677777777777777777777889999******* PP

                    Hydrolase_4  86 GGliallyllrypdkvaglilsaPalkik 114
                                    G+++ + ++ +++d+v+g+ ++ + + + 
  gi|121638464|ref|YP_978688.1| 111 GSALGFDWANQHRDRVQGIAFMEAIVTPM 139
                                    *******************9887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.99
# Mc/sec: 915.80
//
Query:       gi|121638465|ref|YP_978689.1|  [L=423]
Description: histidyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-43  148.1   0.1    1.1e-42  146.4   0.1    1.8  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.3e-17   64.3   0.0    2.3e-17   63.5   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    9.5e-15   54.5   0.0    3.3e-14   52.8   0.0    1.9  2  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.013   15.0   0.1        2.5    7.5   0.0    2.2  2  tRNA-synt_2d    tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.1   2.5e-46   1.1e-42       1     309 [.      12     311 ..      12     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 2.5e-46
                                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH....HS-EEE-TTSSEEEE-SSSHHHHH CS
                  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld....qtfklvDqsgrllglRaDiTpqva 76 
                                    g+ d  p+++++  ++r  ll +++++GY+ + +P++E +  + +g+ge++d    +++ + D  +r++ lR++ T+ v+
  gi|121638465|ref|YP_978689.1|  12 GVPDYVPPDSAQFVAVRDGLLAAARQAGYSHIELPIFEDTALFARGVGESTDvvskEMYTFADRGDRSVTLRPEGTAGVV 91 
                                    67899******************************************9999888878*********************** PP

                                    HHHHH.HHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEET CS
                  tRNA-synt_His  77 Riaah.rln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghv 154
                                    R++ +  l  +  p +lcYaG+ +r ++ ++gr r+  QvG+E iG+++++ d+Ev+ ++ + + +++g++++rl++++ 
  gi|121638465|ref|YP_978689.1|  92 RAVIEhGLDrGALPVKLCYAGPFFRYERPQAGRYRQLQQVGVEAIGVDDPALDAEVIAIADAGF-RSLGLDGFRLEITSL 170
                                    *98661577899****************************************************.6*********99987 PP

                                    CHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHCTHHHHHHHHHH CS
                  tRNA-synt_His 155 glvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkalelygdaevleealealaaapalqaalde 234
                                    g          ++++ +e l ++l   dl e  +  ++ag+  + +++l+  + + + +++++ +  l + +    a+++
  gi|121638465|ref|YP_978689.1| 171 GDE-------SCRPQYRELLQEFLFGLDLDE--DTRRRAGI--NPLRVLD--DKRPELRAMTASAPVLLD-HLSDVAKQH 236
                                    644.......589***************999..44444344..3444444..445555666665554433.44466889* PP

                                    HHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---EEEEEEEEHHH CS
                  tRNA-synt_His 235 leelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarpAtGfsldlea 309
                                    ++ + a+l+al+   v++ +++  +rg++Yyt++ F+++ +g g+   i++GGrYd+l++++ g+  +++Gf l +++
  gi|121638465|ref|YP_978689.1| 237 FDTVLAHLDALG---VPYVINPRMVRGLDYYTKTAFEFVHDGLGAqsGIGGGGRYDGLMHQLgGQDLSGIGFGLGVDR 311
                                    **********96...***************************886559**************99*********99986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   5.1e-21   2.3e-17       1     175 [.      70     316 ..      70     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5.1e-21
                                    EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                    Y++ dr dr+ +L+P++++++v+++++++l    LP+kl + ++ +R+E++ + G  R+r+++q + + ++ ++  +  +
  gi|121638465|ref|YP_978689.1|  70 YTFADRGDRSVTLRPEGTAGVVRAVIEHGLDRGALPVKLCYAGPFFRYERP-QAG--RYRQLQQVGVEAIGVDD--PALD 144
                                    9*****************************9988*****************.99*..***************99..9999 PP

                                    HHHHHHHHHHHHHTT.SCEEEEEE.GTTSC.................................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.................................................. RF
                   tRNA-synt_2b  81 rdlikaisriferlglefraiiel.msaks.................................................. 109
                                    +++i  ++  f++lgl  + ++    +++s                                                  
  gi|121638465|ref|YP_978689.1| 145 AEVIAIADAGFRSLGLDGFRLEITsLGDEScrpqyrellqeflfgldldedtrrraginplrvlddkrpelramtasapv 224
                                    ****************7755443337777799************************************************ PP

                                    ....................................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTT CS
                                    ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 110 ....................................adykdkkefeavsesltkgieigtiqklgtrlserlgatvlden 153
                                                                        +dy+ k+ fe v   l+++  ig  + ++++l  +lg++     
  gi|121638465|ref|YP_978689.1| 225 lldhlsdvakqhfdtvlahldalgvpyvinprmvrgLDYYTKTAFEFVHDGLGAQSGIGGGG-RYDGLMHQLGGQD---- 299
                                    ********************************************************999865.559*****99976.... PP

                                    SSEEEEEEEEEEEEHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 154 nreksvimicaaigveRllsai 175
                                            i++++gv R+++a+
  gi|121638465|ref|YP_978689.1| 300 -----LSGIGFGLGVDRTVLAL 316
                                    .....23577888888887775 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.89     4e+03      37      57 ..     233     253 ..     227     254 .. 0.78
   2 !   52.8   0.0   7.4e-18   3.3e-14       2      93 ..     331     419 ..     330     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.89
                                    SSSTHHHHHHHHHHTT-SEEE CS
                 HGTP_anticodon  37 snesigkkireadllgipfav 57 
                                     ++++   +++ d lg+p+++
  gi|121638465|ref|YP_978689.1| 233 AKQHFDTVLAHLDALGVPYVI 253
                                    56677777889999****987 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 7.4e-18
                                    EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                 HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                    v+ +pl+e   +++     la +Lraag+rv+l + ++ ++ ++r a + g ++a+v G++++e gtv+v+d++t+eq++
  gi|121638465|ref|YP_978689.1| 331 VFGVPLGE---AAKLRLAVLAGRLRAAGVRVDLAYGDRGLKGAMRAAARSGARVALVAGDRDIEAGTVAVKDLTTGEQVS 407
                                    77889999...78888899************************************************************* PP

                                    EETTHHHHHHHH CS
                 HGTP_anticodon  82 vsldelveklke 93 
                                    vs+d++v+++++
  gi|121638465|ref|YP_978689.1| 408 VSMDSVVAEVIS 419
                                    *******99975 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00056       2.5      73     137 ..      74     143 ..      33     168 .. 0.77
   2 ?    5.0   0.3    0.0032        14     202     223 ..     294     314 ..     281     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00056
                                    SSS-ECESEEE-SSTHHHHHHHH.....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEE..EEEEEETT-- CS
                   tRNA-synt_2d  73 pekaveekllLRthttavqirtl.....ekkkppikiisigrvfRrdavDathlaeFhqv..eglvvdenvs 137
                                    ++   +++++LR   ta  +r++     ++  +p+k+   g  fR +   a +  + +qv  e + vd+   
  gi|121638465|ref|YP_978689.1|  74 DRG--DRSVTLRPEGTAGVVRAViehglDRGALPVKLCYAGPFFRYERPQAGRYRQLQQVgvEAIGVDDPAL 143
                                    333..7889************99999989999****************999988888885226677776555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0032
                                    HTT-.TTSEEEEEEEEHHHHHH CS
                   tRNA-synt_2d 202 avgideevsgfafGlGveRlam 223
                                    ++g  ++ sg++fGlGv+R+ +
  gi|121638465|ref|YP_978689.1| 294 QLGG-QDLSGIGFGLGVDRTVL 314
                                    4454.799***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2689.27
//
Query:       gi|121638466|ref|YP_978690.1|  [L=224]
Description: glyoxalase II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-28   97.6   3.9    2.2e-27   96.3   3.9    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.7e-06   26.0   0.2      1e-05   25.2   0.2    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0003   20.7   0.0    0.00047   20.1   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   3.9   3.7e-31   2.2e-27       2     197 .]       9     203 ..       8     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 3.7e-31
                                    CCCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                    Lactamase_B   2 gpdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                    g++ +n+y++    +++++++D+G ++  ++ +     l+++ + + av+lTH+H+DHi+ + ++ +++++p+++++++ 
  gi|121638466|ref|YP_978690.1|   9 GLLACNCYVLAerPGTDAVIVDPGQGAMGTLRRI----LDKNRLTPAAVLLTHGHIDHIWSAQKVSDTFGCPTYVHPADR 84 
                                    6789********999*****************97....****************************************** PP

                                    HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE.......EETTCCEEEECTTT CS
                    Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv.......eygggkvlftGDal 152
                                    ++l+++  + ++   +l + ++ + +++v+e+++dg+  + ++  v   +++gh+ g+v       ++ +++++ftGD+l
  gi|121638466|ref|YP_978690.1|  85 FMLTDPIYGLGPRIAQLVAGAFFREPKQVVELDRDGDKIDLGGISVNIDHTPGHTRGSVvfrvlqaTNNDKDIVFTGDTL 164
                                    ********99999999999999999999999999999999999999999999999998833444445779********** PP

                                    SSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                    Lactamase_B 153 lagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                    +++ +gr+dl ++ + ++ +s+++k+l        l+++++v+ gH
  gi|121638466|ref|YP_978690.1| 165 FERAIGRTDLAGGSGRDLLRSIVDKLL-------VLDDSTVVLpGH 203
                                    **********88888888888888888.......677777777699 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   1.7e-09     1e-05       3     144 ..      27     164 ..      26     176 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.7e-09
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEE....HHHHHHCCTTCGH CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre..lrpkklplyap....kgvlavleanfvy 76 
                                    +++D+g + ++ ++r l     +++l   +aVllth+H+DH+  +  +    ++p     y++     ++ + +   +++
  gi|121638466|ref|YP_978690.1|  27 VIVDPGQGAMGTLRRIL----DKNRLT-PAAVLLTHGHIDHIWSAQKVSDtfGCP----TYVHpadrFMLTDPIYGLGPR 97 
                                    789*****999955555....233344.567***********8888888866444....344422221222333333333 PP

                                    HHCHTT.....TTEEEEEE-.TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE..CTTEEEEEESS-S CS
                  Lactamase_B_2  77 laleee.....pavnvheld.wgesfelgdggleitatparhksgrrldrnagdtlGlrie..gggkrvyyigDtg 144
                                    +a+ ++      + +v+eld  g++++lg+  ++i  tp +  +           +  +++  +++k ++++gDt 
  gi|121638466|ref|YP_978690.1|  98 IAQLVAgaffrEPKQVVELDrDGDKIDLGGISVNIDHTPGHTRGSV---------VFRVLQatNNDKDIVFTGDTL 164
                                    3333333333334688888867788888866666666664444444.........444444568888899999985 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.8e-08   0.00047       7     116 ..      13     165 ..      10     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.8e-08
                  Lactamase_B_3   7 hnsflleta.g.arilvDPfkanlgyeppa.....eeaDlvlisqaledH.ahletlkqlaenvkvlee........... 67 
                                     n+++l  + g   ++vDP+++ +g+ +        ++ +vl+++++ dH + ++++   +  ++++++           
  gi|121638466|ref|YP_978690.1|  13 CNCYVLAERpGtDAVIVDPGQGAMGTLRRIldknrLTPAAVLLTHGHIDHiWSAQKVSDTFGCPTYVHPadrfmltdpiy 92 
                                    589999884487899*****8744444333445559**************446778888877777777766666666666 PP

                  Lactamase_B_3  68 ..................geslev....ggleiravatshdavggsergenngflleq...dgltiyhlGhlah 116
                                                      ++ +e+    +++++ +++ ++d ++g++rg  ++f++ q   ++  i++ G++  
  gi|121638466|ref|YP_978690.1|  93 glgpriaqlvagaffrepKQVVELdrdgDKIDLGGISVNIDHTPGHTRGS-VVFRVLQatnNDKDIVFTGDTLF 165
                                    66666666666677776634444433325888899999999999999995.88887774444889999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1470.84
//
Query:       gi|121638467|ref|YP_978691.1|  [L=308]
Description: peptidyl-prolyl cis-trans isomerase B ppiB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-28   97.9   0.0    1.1e-27   97.3   0.0    1.2  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.036   14.3   0.0    1.4  1  DUF4064        Protein of unknown function (DUF4064)
      0.054   13.8   4.6       0.09   13.1   4.6    1.4  1  RskA           Anti-sigma-K factor rskA
      0.054   13.7   0.5        0.1   12.8   0.5    1.4  1  CnrY           Anti-sigma factor CnrY
      0.078   13.3   0.1       0.19   12.0   0.0    1.6  2  Sigma_reg_N    Sigma factor regulator N-terminal
       0.08   12.6   0.4       0.12   12.1   0.4    1.2  1  DUF1345        Protein of unknown function (DUF1345)
      0.099   13.1   0.4       0.21   12.0   0.4    1.5  1  DUF3357        Domain of unknown function (DUF3357)
       0.13   12.4   2.0       0.23   11.7   2.0    1.3  1  DUF4519        Domain of unknown function (DUF4519)
       0.17   11.8   0.0       0.27   11.2   0.0    1.2  1  Wzy_C_2        Virulence factor membrane-bound polymerase, C-


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   5.5e-31   1.1e-27       2     156 ..     143     305 ..     142     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 5.5e-31
                  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikg...fmvqgGdptgktsageqe.kkgge.sirai 76 
                                    v++ t+ +G+i + L++++ P tv+ F+ l+++gf++gtt hR+       ++q Gdp+g+++ g++  ++++  + ++ 
  gi|121638467|ref|YP_978691.1| 143 VSMVTN-QGNIGLMLANNESPCTVNSFVSLAQQGFFKGTTCHRLTTSpmlAVLQCGDPKGDGTGGPGYqFANEYpTDQYS 221
                                    678997.*************************************988555677*******99955544334443322444 PP

                  Pro_isomerase  77 pdEit.s.klkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVv.eGmdvvekiekvetde....erpkk 149
                                    +++ + +  +   rG+lama++g  pn+++sqFf++  + + l  +ytvFG++  +G+++++ki+k+ + +     +p +
  gi|121638467|ref|YP_978691.1| 222 ANDPKlNePVIYPRGTLAMANAG--PNTNSSQFFMVYRD-SKLPPQYTVFGTIQaDGLTTLDKIAKAGVAGggedGKPAT 298
                                    4555444245559********98..8***********95.567888*******99***********55554567779999 PP

                  Pro_isomerase 150 nvkivsa 156
                                    +v+i+s+
  gi|121638467|ref|YP_978691.1| 299 EVTITSV 305
                                    9***986 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.8e-05     0.036       6      49 ..      46      86 ..      42     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                        DUF4064  6 iiLglIGgilgillglllllflfllssgefsqeltee..qalsged 49
                                    iL+++Gg+l +++++++++f++++++++ + + +++  +      
  gi|121638467|ref|YP_978691.1| 46 RILTIVGGSLAAVAVIVAVVFTVVVNKDDHQSTTSATptD-----S 86
                                   69***********************887765555443432.....3 PP

>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.6   4.5e-05      0.09      16      86 ..      20     126 ..      11     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                    .....................................XXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXX CS
                           RskA  16 tpqaaaaaaaaaaapppaaapaararr..........laaaaAaalllvlgqlavasaaldplrqsaaqaeavvavlaap 85 
                                     +q++a+a+++ +++ +++a++a++rr          ++a+++a++  v+ ++   +++  + +++ a+++   a  a p
  gi|121638467|ref|YP_978691.1|  20 NAQRRATAKRKLERQLERRAKQAKRRRiltivggslaAVAVIVAVVFTVVVNKDDHQSTTSATPTDSASTSPPQAATAPP 99 
                                    4556666666666666666666666669***9876433333333333444466777777777777777777777766666 PP

                                    ..........................X CS
                           RskA  86 ..........................d 86 
                                                              +
  gi|121638467|ref|YP_978691.1| 100 lppfkpsanlgancqyppspdkavkpV 126
                                    667764444444444444444444440 PP

>> CnrY  Anti-sigma factor CnrY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   5.1e-05       0.1      25      86 ..      25      86 ..      18      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                                   HHHHT-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX CS
                           CnrY 25 asleeqldkemaqivlvarrdaqraivcaalaalvafvainrvatlmlekaa..ptwlaspsaa 86
                                   a+ +++l+++  +++  a+r    +iv ++laa+   va+  v t++++k     t  a+p+ +
  gi|121638467|ref|YP_978691.1| 25 ATAKRKLERQLERRAKQAKRRRILTIVGGSLAAVAVIVAV--VFTVVVNKDDhqSTTSATPTDS 86
                                   67899999999***********************999995..5555555544338888888655 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.5e-05      0.19       4      41 ..      39      77 ..      36      91 .. 0.77
   2 ?   -3.5   0.0       6.8   1.3e+04      66      77 ..     170     181 ..     166     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.5e-05
                    Sigma_reg_N  4 lkkakrksilrivlislivlllifvil.vvtllylaeke 41
                                    k akr+ il+iv  sl+++ +i+++   v  +++++++
  gi|121638467|ref|YP_978691.1| 39 AKQAKRRRILTIVGGSLAAVAVIVAVVfTVVVNKDDHQS 77
                                   689***************999999888666666654433 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.8
                    Sigma_reg_N  66 svsqsgffggei 77 
                                    s++q+gff+g++
  gi|121638467|ref|YP_978691.1| 170 SLAQQGFFKGTT 181
                                    678999*99975 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4     6e-05      0.12      28      75 ..      31      78 ..      12      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                        DUF1345 28 daeelrkraeredesrvlilllvllaalaslvaivlllasakaekpae 75
                                    +++l++ra++ +++r+l+ +   laa+a +va+v+++  +k++++++
  gi|121638467|ref|YP_978691.1| 31 LERQLERRAKQAKRRRILTIVGGSLAAVAVIVAVVFTVVVNKDDHQST 78
                                   47899999999999************************8888877766 PP

>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00011      0.21      12      65 ..      37      92 ..      26     101 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                        DUF3357 12 aaaaaararr..pllaavliasalvvlvvlvalagvrlagqaslvapgevavseta 65
                                   ++a +a++rr  ++    l+a+a++v vv++++++  ++++   ++p+  a+ + +
  gi|121638467|ref|YP_978691.1| 37 RRAKQAKRRRilTIVGGSLAAVAVIVAVVFTVVVNKDDHQSTTSATPTDSASTSPP 92
                                   46677777777766666777777777777777776766665555555555444433 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.0   0.00011      0.23       8      49 ..      22      66 ..      19      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                        DUF4519  8 ktKEtrkdKkeRrke...nkeaqekvttvVlPvlavlillivvfv 49
                                   + + t+k K eR  e    ++ + +++t+V   la+++++++v++
  gi|121638467|ref|YP_978691.1| 22 QRRATAKRKLERQLErraKQAKRRRILTIVGGSLAAVAVIVAVVF 66
                                   5689********7661115566788*****999999998887765 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.27      39     127 ..      38     123 ..      31     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                        Wzy_C_2  39 ksrsrrlrlrpklvlrvvalvlallglalllsilhdyqrleqlyltsepneaalrevtnpkvwkdrflfrayadllelgl 118
                                    ++++ + r++ + v   +a+v++++++++++++  d ++ +   +++++++ + ++     ++   + f++ a+l++   
  gi|121638467|ref|YP_978691.1|  38 RAKQAKRRRILTIVGGSLAAVAVIVAVVFTVVVNKDDHQSTTSATPTDSASTSPPQAA---TAPPLPPFKPSANLGANCQ 114
                                    45566666678889999*********************************99999886...3334477888888888888 PP

                        Wzy_C_2 119 lplspenla 127
                                    +p+sp+++ 
  gi|121638467|ref|YP_978691.1| 115 YPPSPDKAV 123
                                    888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2074.45
//
Query:       gi|121638468|ref|YP_978692.1|  [L=790]
Description: GTP pyrophosphokinase relA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.5e-47  158.6   1.6    2.9e-46  157.1   1.6    1.9  1  HD_4       HD domain
    2.3e-37  127.9   0.0    4.5e-37  126.9   0.0    1.5  1  RelA_SpoT  Region found in RelA / SpoT proteins
    1.9e-23   82.2   0.0    4.7e-23   81.0   0.0    1.7  1  TGS        TGS domain
    5.6e-17   62.1   0.0    1.2e-16   61.0   0.0    1.6  1  ACT_4      ACT domain
    8.1e-14   51.9   0.4    2.6e-13   50.3   0.4    1.9  1  HD         HD domain
    2.2e-12   46.5   0.2    2.2e-12   46.5   0.2    2.9  4  ACT        ACT domain
  ------ inclusion threshold ------
        0.4   10.6   2.2       0.59   10.0   0.1    2.5  3  Ub-Mut7C   Mut7-C ubiquitin
        4.2    7.6   6.8         21    5.3   0.4    3.7  3  DprA_WH    DprA winged helix domain


Domain annotation for each model (and alignments):
>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   1.6   1.3e-49   2.9e-46       1     155 [.      86     233 ..      86     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 1.3e-49
                           HD_4   1 AlelaaelhagqrkltgepllahalevAailaelgldaetviAalLhdvveda.lsleeirerfGeevarLvegvsklkr 79 
                                    A+e+a++ ha+q +++g p+++h+l+vA+ilaelg+d  t++AalLhd+ved+  +le+++e+fGeev +Lv+gv+kl+r
  gi|121638468|ref|YP_978692.1|  86 AYEVADQRHASQLRQSGDPYITHPLAVANILAELGMDTTTLVAALLHDTVEDTgYTLEALTEEFGEEVGHLVDGVTKLDR 165
                                    899*************************************************97788*********************** PP

                           HD_4  80 lqkvaaadeaeekaeqvenlRkmLlAmveDirvvliklAdrlqtlrslaaakeekrrdvaretldiyaplAnrlGi 155
                                    +  +        +a++ e++Rkm+ Am++D+rv++ik+Adrl+++r+++  ++ek+ ++aretl++ aplA+rlG+
  gi|121638468|ref|YP_978692.1| 166 VVLG--------SAAEGETIRKMITAMARDPRVLVIKVADRLHNMRTMRFLPPEKQARKARETLEVIAPLAHRLGM 233
                                    ****........99**********************************999************************8 PP

>> RelA_SpoT  Region found in RelA / SpoT proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0     2e-40   4.5e-37       1     115 [.     293     402 ..     293     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 2e-40
                                    EEE--HHHHHHHHHHCT--CCCCCCCSSTSEEEEEEESSHHHHHHHHHHHHT-SSSEEEEEEETSTSHCTTCCSEEEEEE CS
                      RelA_SpoT   1 gRvKslysiieKlerkgikveekfeeitDligiRvivefkddvyevlelikklwdvkpkrfkdyiaepkengYrslHtvv 80 
                                    gR+K+++si++K++ kg +   +f++i+Dl+g+R+++++++d+y++++++++lw+++ +rfkdyia+p+   Y+slHt+v
  gi|121638468|ref|YP_978692.1| 293 GRPKHYWSIYQKMIVKG-R---DFDDIHDLVGVRILCDEIRDCYAAVGVVHSLWQPMAGRFKDYIAQPRYGVYQSLHTTV 368
                                    6****************.7...9********************************************************* PP

                                    EETTEEEEEEEEEEEEEHHHHHHHH..HHHHHHHHCT CS
                      RelA_SpoT  81 ssekgeekvlvEiQiRtiamdawae..iehhlrYkek 115
                                        g+e++++E+QiRt++m+++ae  i++h+rYke 
  gi|121638468|ref|YP_978692.1| 369 ---VGPEGKPLEVQIRTRDMHRTAEygIAAHWRYKEA 402
                                    ...********************************96 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   2.1e-26   4.7e-23       1      60 []     452     511 ..     452     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 2.1e-26
                                    EEEEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECSEEEETTSBB-SSEEEEEEE CS
                            TGS   1 irvytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnGqrvgldhvLedgdvveIvt 60 
                                    i+v+tP+G+v++lp+g+t++DfAy++h+++++++i+A+VnG++v l+++Le+g vve++t
  gi|121638468|ref|YP_978692.1| 452 IFVFTPKGDVITLPTGSTPVDFAYAVHTEVGHRCIGARVNGRLVALERKLENGEVVEVFT 511
                                    78*******************************************************997 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.5e-20   1.2e-16       3      80 .]     709     785 ..     707     785 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.5e-20
                          ACT_4   3 esytvrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVeR 80 
                                    + + v ++vea dr++lL+d+t+++++ek+ni s +++t   d +a  ++t+e  d +hL ++++++r+++gV++V+R
  gi|121638468|ref|YP_978692.1| 709 SVFLVAIQVEALDRHRLLSDVTRALADEKVNILSASVTTSG-DRVAISRFTFEMGDPKHLGHLLNAVRNVEGVYDVYR 785
                                    5799***********************************75.99*********************************9 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.4   1.1e-16   2.6e-13       1     122 []     105     202 ..     105     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.1e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH.HHHCTCCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk.eeefekflaHekvgaeilrevekrlgldle 79 
                                    +++H+l+Va+++++l++d         +l+aaLlHD+++++ + + +++ +eef+++++H ++g+++l +v         
  gi|121638468|ref|YP_978692.1| 105 YITHPLAVANILAELGMDTT-------TLVAALLHDTVEDTGY-T-LEAlTEEFGEEVGHLVDGVTKLDRV--------- 166
                                    689*****************.......**************66.4.5454888************999999......... PP

                                    HHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHHH CS
                             HD  80 dvaklirehheswegkkrprglaerqlslearivklaDrlaam 122
                                     +  +++  + +++++       +++ +++++++k+aDrl++m
  gi|121638468|ref|YP_978692.1| 167 VLGSAAEGETIRKMIT-------AMARDPRVLVIKVADRLHNM 202
                                    5566666666666654.......6666677***********98 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         5   1.1e+04      16      25 ..     111     120 ..     111     121 .. 0.86
   2 ?   -3.7   0.0       4.9   1.1e+04      45      63 ..     204     222 ..     201     224 .. 0.83
   3 ?   -0.5   0.1       0.5   1.1e+03       3      18 ..     642     657 ..     641     658 .. 0.85
   4 !   46.5   0.2   9.8e-16   2.2e-12       3      66 ..     715     778 ..     713     779 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                                    HHHHHHHHTT CS
                            ACT  16 rvfgaladrg 25 
                                    +v+++la++g
  gi|121638468|ref|YP_978692.1| 111 AVANILAELG 120
                                    5999***998 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.9
                                    EEEEEEEHHHHHHHHHHHH CS
                            ACT  45 fvvivvdeedleevlealk 63 
                                    ++ +++ e+++ ++ e+l+
  gi|121638468|ref|YP_978692.1| 204 TMRFLPPEKQARKARETLE 222
                                    6889999999999999987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.5
                                    EEEEEESSTTHHHHHH CS
                            ACT   3 lrvgvpDrPGlLarvf 18 
                                    + v+vp+ PG+L +++
  gi|121638468|ref|YP_978692.1| 642 VGVSVPGAPGVLTKLA 657
                                    5699********8876 PP

  == domain 4  score: 46.5 bits;  conditional E-value: 9.8e-16
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                    + v++ Dr+ lL++v++alad  +Ni s+++++s+d+va   f+++ +d+++l ++l+a++++e
  gi|121638468|ref|YP_978692.1| 715 IQVEALDRHRLLSDVTRALADEKVNILSASVTTSGDRVAISRFTFEMGDPKHLGHLLNAVRNVE 778
                                    889*********************************************************9987 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.8   1.1e+04      20      43 ..      45      68 ..      42      74 .. 0.72
   2 ?   -3.3   0.0       3.8   8.4e+03      14      37 ..     206     229 ..     204     231 .. 0.80
   3 ?   10.0   0.1   0.00026      0.59      46      79 ..     478     515 ..     477     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.8
                       Ub-Mut7C 20 rreralavafdeaatvkhviEalG 43
                                    r r +++ +++ +t   v+E l 
  gi|121638468|ref|YP_978692.1| 45 VRARLARRMTAQRSTTNPVLEPLV 68
                                   577788888889999988888775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                       Ub-Mut7C  14 dflprarreralavafdeaatvkh 37 
                                     flp++++ r+++   +  a + h
  gi|121638468|ref|YP_978692.1| 206 RFLPPEKQARKARETLEVIAPLAH 229
                                    599999999999888887777776 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00026
                       Ub-Mut7C  46 htEVel....ilvnGesvgfshiledGdrvavypvfea 79 
                                    htEV+      +vnG+ v +++ le+G+ v+v + +++
  gi|121638468|ref|YP_978692.1| 478 HTEVGHrcigARVNGRLVALERKLENGEVVEVFTSKAP 515
                                    778775333358********************998765 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.093   2.1e+02      27      46 ..       2      21 ..       1      22 [. 0.94
   2 ?    5.3   0.4    0.0092        21      24      48 ..     108     132 ..     107     132 .. 0.93
   3 ?    1.1   0.1       0.2   4.5e+02      15      35 ..     607     627 ..     601     631 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.093
                        DprA_WH 27 hvDqLvrrtglpaaevsaaL 46
                                   ++DqL +++ +p+ e saaL
  gi|121638468|ref|YP_978692.1|  2 AEDQLTAQAVAPPTEASAAL 21
                                   89****************99 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0092
                        DprA_WH  24 ePvhvDqLvrrtglpaaevsaaLle 48 
                                     P++v  + +++g+++ ++ aaLl+
  gi|121638468|ref|YP_978692.1| 108 HPLAVANILAELGMDTTTLVAALLH 132
                                    599999*****************96 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.2
                        DprA_WH  15 rrvLaaLgpePvhvDqLvrrt 35 
                                    +r+La Lg    ++++L++r+
  gi|121638468|ref|YP_978692.1| 607 QRLLAELGGIDQAEEELAERS 627
                                    89*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 5689.26
//
Query:       gi|121638469|ref|YP_978693.1|  [L=223]
Description: adenine phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-17   61.0   1.7    1.9e-16   60.0   1.7    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.044   13.2   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   1.7   2.1e-20   1.9e-16       6     125 ..      81     202 ..      77     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.1e-20
                                    TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............. CS
                   Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...... 79 
                                    ++ +  l+av +++a++ +      d+v+g++ +G+ +a ++a +Lev +  vrk  + p +  +               
  gi|121638469|ref|YP_978693.1|  81 FADRRGLAAVTEALADRASG----ADLVAGVDARGFLVAAAVATRLEVGVLAVRKGGKLPRPVLSEEY-----Yreygaa 151
                                    66788899999999999999....9*********************8777777777777776666642.....1233567 PP

                                    .....EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE CS
                   Pribosyltran  80 .....rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvd 125
                                            +++ag++V+i+DD+l+tGgT+ a+ +lL++ g+ + ++av+v+
  gi|121638469|ref|YP_978693.1| 152 tleilAEGIEVAGRRVVIIDDVLATGGTIGATRRLLERGGANVAGAAVVVE 202
                                    7888789*****************************************994 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.9e-06     0.044     120     165 ..     163     205 ..     134     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-06
                        UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseeg 165
                                    a r+v+++D v+aTGg++ a  +lL + g++   +  ++v++  +g
  gi|121638469|ref|YP_978693.1| 163 AGRRVVIIDDVLATGGTIGATRRLLERGGAN---VAGAAVVVELAG 205
                                    6788*************98887777775655...444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1545.21
//
Query:       gi|121638470|ref|YP_978694.1|  [L=557]
Description: lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-16   58.8   0.0    1.1e-15   57.6   0.0    1.6  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   5.9e-20   1.1e-15      19     364 ..     100     459 ..      92     474 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 5.9e-20
                                    EEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC..........TCTEEEEEEEETTEEEEEESSETTT CS
                      SBP_bac_5  19 tytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee..........dqdikkveavddytvrftlkkpnal 88 
                                    ++ + + +++ +sDG p+t +D v ++    +  ++  +a  + +          +q+ ++v  + d+ v+ +       
  gi|121638470|ref|YP_978694.1| 100 ILDYQISDDAVYSDGRPVTCDDLVLAWAAQSGRFPGFDAATQAGYvdianiectaGQKKARVSFIPDRSVVDH------- 172
                                    5678899******************888777777777776666657655555555444444444444444444....... PP

                                    TTTHCHHHHHHHGC...............................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEE CS
                      SBP_bac_5  89 fltllaavpasiak...............................kaaekeddkdkdtnekpvgtGPYklkefkpgqkiv 137
                                     ++l++a++  + +                                ++ k + + ++ +  + ++GPYk++++  +  +v
  gi|121638470|ref|YP_978694.1| 173 -SQLFTATSLMPSHviadqlhidvtaallsnnvsaveqiarlwnsTWDLKPGRSHDEVRSRFPSSGPYKIESVLDDGAVV 251
                                    .2222222222222333466688889999999999999999999866677777889999999****************** PP

                                    EEE-TTSTTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTG CS
                      SBP_bac_5 138 lernpdYwgggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkpp 217
                                    l++n+ +w g k+  +ri+++  p+ ++  + +++  + dv+++ +++  +l + ++++   + p++g++ l f  +   
  gi|121638470|ref|YP_978694.1| 252 LVANDRWW-GTKAITKRITVW--PQGADIQDRVNNRSV-DVVDVAAGSSGSLVTPDSYQR-TDYPSAGIEQLIFAPQ-GS 325
                                    ********.************..5788888888*****.777899999999877777887.999************9.57 PP

                                    GGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.....SHHHHHHHHHHHTT-BCSSTSCE CS
                      SBP_bac_5 218 fddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka.....ydpekAkklLkeaGykdgdgggl 292
                                    ++  r R+Al++ ++r++i++ +   +   ans l+p  + a  + + a +a      dp++A+  L   G + +     
  gi|121638470|ref|YP_978694.1| 326 LAQSRTRRALALCVPRDAIARDA---GVPIANSRLSPATDDALTDADGAAEArqfgrVDPAAARDALG--GTPLT----- 395
                                    999********************...555555557776666655555544345556666666666653..22222..... PP

                                    ETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHH CS
                      SBP_bac_5 293 rekklkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdn 364
                                          +++ +   ++   a+   i+++ + +Gi+v+  tvd+     ++ +dg+ d+ l + g+ ++++++
  gi|121638470|ref|YP_978694.1| 396 ------VRIGYGRPNARLAATIGTIADACAPAGITVSDVTVDT--PGPQALRDGKIDVLLASTGGATGSGSS 459
                                    ......4444555555555666679999999999999999987..444588999999999988887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 3036.80
//
Query:       gi|121638471|ref|YP_978695.1|  [L=442]
Description: preprotein translocase subunit SecF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-64  214.5   9.9    1.2e-63  213.9   9.9    1.2  1  SecD_SecF  Protein export membrane protein
    2.2e-06   27.0   0.9    4.8e-06   25.9   0.9    1.6  1  Sec_GG     SecD/SecF GG Motif


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.9   9.9   1.4e-67   1.2e-63       9     188 ..     167     354 ..     160     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: 213.9 bits;  conditional E-value: 1.4e-67
                                    SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                      SecD_SecF   9 vdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievdlatva 88 
                                     ++++++is+++v+++++ ++++kav+al+++lvl+++y+++r+e+++ ++ai+a+++D+++t+gv+sl+g+ev++atv+
  gi|121638471|ref|YP_978695.1| 167 GQPSKQAISDSAVSETWGGQITKKAVIALVVFLVLVALYITVRYERYMTISAITAMLFDLTVTAGVYSLVGFEVTPATVI 246
                                    456899************************************************************************** PP

                                    HHHHHTTSSSHHHHHHHHHHHHH...HHH--SS-HHHHHHHHHHHHHHHHHHTTHH.....HHHHHHHHHHHHTTTTHHH CS
                      SecD_SecF  89 alLtiiGYSvndtvvvfdrvren...lrkkkratlkeiinlslnqtLtrtiltslt.....tllvvvallllggdslkdf 160
                                    +lLti+G+S++dtv+vfd+v+en   +++++r+t++e++nl++nqt++r+i+tsl+     + l+vva++llg ++lkd+
  gi|121638471|ref|YP_978695.1| 247 GLLTILGFSLYDTVIVFDKVEENthgFQHTTRRTFAEQANLAINQTFMRSINTSLIgvlpvLTLMVVAVWLLGVGTLKDL 326
                                    ********************************************************888877889999999********* PP

                                    HHHHHHHTSTTTTTHHHHHHHHHHHHH- CS
                      SecD_SecF 161 alallvGlivgtyssifiasplllllke 188
                                    al++l+G+i+gtyssif+a+pll++l+e
  gi|121638471|ref|YP_978695.1| 327 ALVQLIGIIIGTYSSIFFATPLLVTLRE 354
                                    ************************9987 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.9   5.3e-10   4.8e-06       2      20 ..      81      99 ..      80     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.3e-10
                                   HHHHC--EE-TTTS-EEEE CS
                         Sec_GG  2 slftkGlNLGlDFtGGthi 20
                                   s++++G+++G+DF+GGt++
  gi|121638471|ref|YP_978695.1| 81 SIVFRGFTFGIDFKGGTTV 99
                                   89***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3047.46
//
Query:       gi|121638472|ref|YP_978696.1|  [L=573]
Description: preprotein translocase subunit SecD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-08   33.2   7.3    3.1e-08   33.2   7.3    1.4  2  SecD_SecF  Protein export membrane protein
    0.00014   21.2   0.0    0.00044   19.6   0.0    1.8  1  Sec_GG     SecD/SecF GG Motif
    0.00036   19.6  18.7    0.00036   19.6  18.7    1.7  2  MMPL       MMPL family
  ------ inclusion threshold ------
      0.044   11.4   7.7      0.073   10.7   7.7    1.2  1  ACR_tran   AcrB/AcrD/AcrF family
        1.2    9.5   3.4        1.9    8.8   3.4    1.2  1  DUF737     Protein of unknown function (DUF737)
        9.2    6.2  10.0         29    4.6  10.0    1.8  1  Reticulon  Reticulon


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.2   1.2         6   1.8e+04      39      52 ..      17      30 ..      12      31 .. 0.61
   2 !   33.2   7.3     1e-11   3.1e-08      13     185 ..     366     539 ..     358     543 .. 0.82

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 6
                                   HHHHHHHHHHHHHT CS
                      SecD_SecF 39 ialvliliyvalrF 52
                                   + ++li iy+ + F
  gi|121638472|ref|YP_978696.1| 17 FLVMLIGIYLLVFF 30
                                   44566666766665 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1e-11
                                    EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT....----HHHHH CS
                      SecD_SecF  13 aekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllg....ievdlatva 88 
                                    +e  +++tv+++++    + +++a +i l+l+l+y  l+++   +l   ++lv    ++ ++l+llg      +dla +a
  gi|121638472|ref|YP_978696.1| 366 FEPSEAQTVSATLGLSSLRAGMIAGAIGLLLVLVYSLLYYRVL-GLLTALSLVASGSMVFAILVLLGryinYTLDLAGIA 444
                                    5667899****************************99999964.33333344444444555555555444488999**** PP

                                    HHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHT CS
                      SecD_SecF  89 alLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGl 168
                                    +l+  iG   ++ vv f+r+++++r+   ++++ ++ ++     +  +   ++t+l+++ l++l+ + +k+fa++l +  
  gi|121638472|ref|YP_978696.1| 445 GLIIGIGTTADSFVVFFERIKDEIRE--GRSFRSAVPRGWARARKTIVSGNAVTFLAAAVLYFLAIGQVKGFAFTLGLTT 522
                                    ***********************999..7889999999999987755666788**************************9 PP

                                    STTTTTHHHHHHHHHHH CS
                      SecD_SecF 169 ivgtyssifiaspllll 185
                                    i++ +   ++  pl++l
  gi|121638472|ref|YP_978696.1| 523 ILDLVVVFLVTWPLVYL 539
                                    99999888888777765 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-07   0.00044       9      27 ..      39      57 ..      37      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                                   EE-TTTS-EEEEEEEE-TT CS
                         Sec_GG  9 NLGlDFtGGthielqfdqp 27
                                   +LG+D++GGt+++l + +p
  gi|121638472|ref|YP_978696.1| 39 KLGIDLQGGTRVTLTARTP 57
                                   7*************98876 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.45   1.3e+03      41      91 ..     214     263 ..     203     276 .. 0.70
   2 !   19.6  18.7   1.2e-07   0.00036     154     309 ..     389     548 ..     372     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.45
                           MMPL  41 lgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafvSkDgkaaral 91 
                                    l++ +++++++ ++ ++++   + + + +  +dp++  ++ S D+k+a++l
  gi|121638472|ref|YP_978696.1| 214 LRQ-STNQYMQMVALQFQATRCESDDILAGNDDPKLPLVTCSTDHKTAYLL 263
                                    444.55555555555665555555555555667889999999999999986 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.2e-07
                           MMPL 154 vvilviLlivyrSlvaallplltvvvsllaalgl.vli.lalllglelstfvlgl.lvvlliavGtDYallLvsRyreel 230
                                    + ++ +Ll++  Sl+   ++ l  ++sl+a+ ++  +i + l   ++ +   +g+   +++i++ +D  + ++ R+++e+
  gi|121638472|ref|YP_978696.1| 389 AGAIGLLLVLVYSLLYYRVLGLLTALSLVASGSMvFAIlVLLGRYINYTLDLAGIaGLIIGIGTTADSFVVFFERIKDEI 468
                                    334445555555655555555555567777777732330333344555555555534678899999999999******** PP

                           MMPL 231 aagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraa.la 308
                                    ++g++ ++av r  a++ k+++   ++  +a + L ++ ++ +++++++++l+ ++d+ +v+ ++ P l+ l++++  la
  gi|121638472|ref|YP_978696.1| 469 REGRSFRSAVPRGWARARKTIVSGNAVTFLAAAVLYFLAIGQVKGFAFTLGLTTILDLVVVFLVTwP-LVYLASKSSlLA 547
                                    *************************************************************999966.666777776455 PP

                           MMPL 309 k 309
                                    k
  gi|121638472|ref|YP_978696.1| 548 K 548
                                    4 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   7.7   2.4e-05     0.073     342     479 ..     395     534 ..     374     553 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT....--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                       ACR_tran 342 vLvvlvvflFLqnlratlipaiavPlsllgtfavlkalg....fslNlltLfgLvlAiGlvvDdAiVvvEnierkleeeg 417
                                    +Lv+  v+  L      l +a+++  s  + fa+l++lg    ++l l  + gL ++iG   D+ +V  E i+ +++e g
  gi|121638472|ref|YP_978696.1| 395 LLVL--VYSLLYYRVLGLLTALSLVASGSMVFAILVLLGryinYTLDLAGIAGLIIGIGTTADSFVVFFERIKDEIRE-G 471
                                    3333..33334444445666666666666666777666511116666667889*************************.* PP

                                    S-HHHHHHHHHHHHHHHHHHHHHH..HHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ACR_tran 418 ekpleaalksmkeiqgalvaialv..llavflPilflgGveGklfrqfaltivlaillsvlval 479
                                     + + a+ ++    + ++v++ +v  l a++l +l++g v+G  f  ++lt +l +++  lv  
  gi|121638472|ref|YP_978696.1| 472 RSFRSAVPRGWARARKTIVSGNAVtfLAAAVLYFLAIGQVKGFAFT-LGLTTILDLVVVFLVTW 534
                                    ********************97663377899999999999998884.78888887777777765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.4   0.00064       1.9      19     112 ..     121     226 ..     115     240 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00064
                         DUF737  19 VinRmkesskaakkkqakeplpaspspeelappqess...........skaaestsaps............sasssssqa 75 
                                    V+n m + ++a++ +q  ++++++p+ ++ app+ +s           +                      ++ +s+++a
  gi|121638472|ref|YP_978696.1| 121 VLNSMPAQPAAEE-PQPAPSAEPQPPGQPAAPPPAQSgapaspqpgaqP---------RpypqdpapspnpTSPASPPPA 190
                                    5666666555554.55555555555554555533333443333333341.........2333333343443233344444 PP

                         DUF737  76 kveeeelrkkikeelqkrleeeqakaeavqeelakll 112
                                    +  +e+  ++ +++l +r+++e++++++ ++ ++ ++
  gi|121638472|ref|YP_978696.1| 191 PP-AEAPATDPRKDLAERIAQEKKLRQSTNQYMQMVA 226
                                    44.4788888899999999999999888444333333 PP

>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  10.0    0.0097        29      16     146 ..     394     541 ..     387     545 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0097
                      Reticulon  16 vlgglllllllfell.gysllslvsklllllllvlflwa..........eyagllnkskp.........pe....pelel 71 
                                    +l++l+ +ll  ++l   ++lslv+  ++++ ++++l +                              +       +e 
  gi|121638472|ref|YP_978696.1| 394 LLLVLVYSLLYYRVLgLLTALSLVASGSMVFAILVLL-GryinytldlaG---------IagliigigtTAdsfvVFFER 463
                                    5566666666666662235555555555544444444.335555555552.........122233222233222255555 PP

                      Reticulon  72 seesvreladsllellnkalselrrlalgedlklflkvalllyilsilgslfs....lltllyigvvlaftvPllYeky 146
                                     ++++re  +s+++ + ++ +++r+ +   + ++fl +a+l +++   ++ f     l+t+l ++vv+++t Pl+Y   
  gi|121638472|ref|YP_978696.1| 464 IKDEIRE-GRSFRSAVPRGWARARKTIVSGNAVTFLAAAVLYFLAIGQVKGFAftlgLTTILDLVVVFLVTWPLVYLAS 541
                                    5555553.6799**************9999****999988766654333333311115799999************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 3806.06
//
Query:       gi|121638473|ref|YP_978697.1|  [L=115]
Description: preprotein translocase subunit YajC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-16   57.4   0.0    1.2e-15   57.1   0.0    1.1  1  YajC      Preprotein translocase subunit
  ------ inclusion threshold ------
      0.053   13.8   0.1      0.083   13.2   0.1    1.3  1  Tad       Putative Flp pilus-assembly TadE/G-like
      0.059   13.0   0.8       0.15   11.7   0.8    1.6  1  BRD4_CDT  C-terminal domain of bromodomain protein 4


Domain annotation for each model (and alignments):
>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   2.1e-19   1.2e-15       2      79 ..       6      81 ..       5      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.1e-19
                           YajC  2 sllplvlifvifyfllirpqqkkqkehkemlasLkkGdeVvtigGivGkvvkvdddevtveigesagvkikversaia 79
                                    +lp++li++ f+++  r+q++ ++++ ++++sL++G +V t++G+ +++v++ dd++ +ei+  +gv++++ + ai+
  gi|121638473|ref|YP_978697.1|  6 LFLPFLLIMGGFMYFASRRQRRAMQATIDLHDSLQPGERVHTTSGLEATIVAIADDTIDLEIA--PGVVTTWMKLAIR 81
                                   57899999999999999*************************************999999994..58********996 PP

>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.4e-05     0.083       8      39 ..       4      34 ..       1      35 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                            Tad  8 alallpllllvglavDvgravlartrlQnAAD 39
                                   ++++lp+ll++g+ + + + +++r+ +Q++ D
  gi|121638473|ref|YP_978697.1|  4 FVLFLPFLLIMGGFM-YFASRRQRRAMQATID 34
                                   57889***9999999.9************999 PP

>> BRD4_CDT  C-terminal domain of bromodomain protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8   2.5e-05      0.15      17      29 ..      23      35 ..      21      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
                       BRD4_CDT 17 RRrreamagtIDm 29
                                   RR r+am++tID+
  gi|121638473|ref|YP_978697.1| 23 RRQRRAMQATIDL 35
                                   9***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 811.62
//
Query:       gi|121638474|ref|YP_978698.1|  [L=449]
Description: 4-aminobutyrate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.8e-132  441.9   0.0   2.2e-132  441.6   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.6   0.0  1.2e-136  2.2e-132       9     405 ..      38     445 ..      30     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 441.6 bits;  conditional E-value: 1.2e-136
                                    SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S CS
                    Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld 88 
                                    l++++ +a G +++dvdg+r++Dl s+iav+++G+++P+vv+av++q+a+++h++f ++ +e ++++ae+l++++p++  
  gi|121638474|ref|YP_978698.1|  38 LPVFVARAGGGIVEDVDGNRLIDLGSGIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGP 117
                                    459*************************************************************************9543 PP

                                    .EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGG CS
                    Aminotran_3  89 .kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeev 167
                                     + +l+nsG+eAve+A+K+ar+      +t k++++af++a+HGrt++++++t+++++yk++fgpf+pe++r++++++++
  gi|121638474|ref|YP_978698.1| 118 kRSVLFNSGAEAVENAVKIARS------YTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPLSYPYR 191
                                    69********************......9**************************************************9 PP

                                    TB-HH.....HHHHHHHHHHHHHH.CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTT CS
                    Aminotran_3 168 lkene.....eeeaalleeleale.kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrT 241
                                        +     + e a+++++  +  ++ ++++aA+++EpiqgegG++v++++fl +l ++c+k+ v++i+DEvqtGf+rT
  gi|121638474|ref|YP_978698.1| 192 DGLLDkqlatNGELAAARAIGVIDkQVGANNLAALVIEPIQGEGGFIVPAEGFLPALLDWCRKNHVVFIADEVQTGFART 271
                                    988886666566777777777777999***************************************************** PP

                                    SSSSGGGGC...TS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHH CS
                    Aminotran_3 242 GklfAleha...gvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaq 318
                                    G++fA+eh    g++pDl+++aK++++Glplsav+++ae+m+a ++g+ g+TfgGnp+aca+ala++++ie + l+e+a+
  gi|121638474|ref|YP_978698.1| 272 GAMFACEHEgpdGLEPDLICTAKGIADGLPLSAVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERAR 351
                                    ********99999******************************************************************* PP

                                    HHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC.....HHHHHHHHHCTEE-EEETT..TEEEE---TT-- CS
                    Aminotran_3 319 elgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke.....keilkkakekGvlilsaGd..nvirllppliit 391
                                    ++++ ++++L+ lq+ ++ i++vRg+G+mia+el+++ ++++     ++++++a+++Gv+il++G+  n+irllppl+i 
  gi|121638474|ref|YP_978698.1| 352 QIERLVTDRLTTLQAVDDRIGDVRGRGAMIAVELVKSGTTEPdagltERLATAAHAAGVIILTCGMfgNIIRLLPPLTIG 431
                                    ***************************************998*****99******************************* PP

                                    HHHHHHHHHHHHHH CS
                    Aminotran_3 392 deeidelleilkka 405
                                    de + e+l+i+ ++
  gi|121638474|ref|YP_978698.1| 432 DELLSEGLDIVCAI 445
                                    *********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2915.88
//
Query:       gi|121638475|ref|YP_978699.1|  [L=1168]
Description: fatty-acid-CoA ligase fadD9 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-66  225.0   0.0    1.9e-66  224.4   0.0    1.2  1  AMP-binding    AMP-binding enzyme
    3.7e-57  193.4   0.0    5.7e-57  192.8   0.0    1.3  1  NAD_binding_4  Male sterility protein
    4.2e-12   46.3   0.0    1.7e-11   44.3   0.1    2.1  2  PP-binding     Phosphopantetheine attachment site
    7.3e-09   35.4   0.0    1.3e-08   34.6   0.0    1.4  1  Epimerase      NAD dependent epimerase/dehydratase family
     0.0028   18.6   0.0      0.012   16.5   0.0    2.2  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.082   12.3   0.0        5.4    6.3   0.0    2.1  2  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   0.0   6.4e-70   1.9e-66      19     422 ..      82     507 ..      65     508 .. 0.78

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 6.4e-70
                                    STEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESE CS
                    AMP-binding  19 egqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakv 97 
                                    + +t+TYrel++r+  lA +L  +  +++gdrV +l  ns++++ +++a+ ++Gav vpl ++ +   l+ i++++e+++
  gi|121638475|ref|YP_978699.1|  82 RFETITYRELWARAGTLATALSaEPAIRPGDRVCVLGFNSVDYTTIDIALIRLGAVSVPLQTSAPVTGLRPIVTETEPTM 161
                                    5789******************88899***************************************************** PP

                                    EEETCTCCCHHHHHHHHSCC-EECEEEEESCC.S-HCCHCCCHCCCCSCTTS.....................-TSCCCS CS
                    AMP-binding  98 liatvdselleklleaaakleavklvivldad.ellkeeelkeeeeseekae.....................kpeeeee 155
                                    +   ++ ++l  + e+ a  +a++  +v d   ++++++e+ e++ ++                         +  + + 
  gi|121638475|ref|YP_978699.1| 162 IA--TSIDNLGDAVEVLAG-HAPARLVVFDYHgKVDTHREAVEAARAR---LagsvtidtlaeliergralpaT--PIAD 233
                                    **..554454444444443.3333334444330333333332222222...13456677788888888887432..4556 PP

                                    -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsilplahifglilelllallsGatvvl 233
                                       d la++iYTSG+TG PKG+m++  +++++ ++ +  +e+    +  +  l ++p++h+ g    l+++l++G+t ++
  gi|121638475|ref|YP_978699.1| 234 SADDALALLIYTSGSTGAPKGAMYRESQVMSFWRKSSgwFEPS---GYPSITLNFMPMSHVGGR-QVLYGTLSNGGTAYY 309
                                    77799***************************99965433332...235788***********6.*************** PP

                                    -TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH..............HHCCCHHCHHHHC................CGT CS
                    AMP-binding 234 lpkdaaldpklllelieklkvtviagvPrvleal..............lesgalkaakkak................dls 283
                                    + k++     +l+e+++  ++t ++ vPr+++++                                            l+
  gi|121638475|ref|YP_978699.1| 310 VAKSDL---STLFEDLALVRPTELCFVPRIWDMVfaefhsevdrrlvdG-----------AdraaleaqvkaelrenVLG 375
                                    **9988...3589*********************644444444333220...........12222333233333333455 PP

                                    T.-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEET CS
                    AMP-binding 284 s.lrlvllggeplspellrffralfge.evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpd 361
                                    +   ++l+g +p+s+e++ ++++l+ + +++egYG TE+++v+  +  + +        +p + +++k+vD  +++++++
  gi|121638475|ref|YP_978699.1| 376 GrFVMALTGSAPISAEMTAWVESLLADvHLVEGYGSTEAGMVLN-DG-MVR--------RP-AVIDYKLVDVPELGYFGT 444
                                    54555789********************************9977.33.444........45.6789*************9 PP

                                    TSE...EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEE.EETTSEEEEEEECCCEEEE CS
                    AMP-binding 362 gee...GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgr.ldedGyleivgRkkdlikl 422
                                    +++   Gellv+ +++++gY+++p+ tae+fd +++++rTGD+   + +d ++ +++R  +++kl
  gi|121638475|ref|YP_978699.1| 445 DQPyprGELLVKTQTMFPGYYQRPDVTAEVFD-PDGFYRTGDIMAkVGPD-QFVYLDRRNNVLKL 507
                                    999999*************************9.867*******9945665.99**********98 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.8   0.0   1.9e-60   5.7e-57       1     257 []     773    1035 ..     773    1035 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 1.9e-60
                                     EE-TTSHHHHHHHHHHHHHS-.T..EEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHH..HHTTTEEEEE--TTSGGG CS
                  NAD_binding_4    1 lTGaTGFLGkvLlekLLrttpev..kiyllvRaksgesaeeRleeelekkelfsallk..elaerikvveGDlseprl 74  
                                     lTGaTGFLG++L  ++L++ + v  k+++lvRa+s+e+a++Rl++++++ + + + +     a r++v++GD  e +l
  gi|121638475|ref|YP_978699.1|  773 LTGATGFLGRYLALEWLDRMDLVngKLICLVRARSDEEAQARLDATFDSGDPYLVRHYreLGAGRLEVLAGDKGEADL 850 
                                     8*******************999***********************999998877754668899************** PP

                                     G--HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS CS
                  NAD_binding_4   75 GLseedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekv 151 
                                     GL+  ++q+la++vd+i++ aA vn++ py++l+ +N  Gt e+l+la ++k++ ++++ ST a+ ++   ++++e+ 
  gi|121638475|ref|YP_978699.1|  851 GLDRVTWQRLADTVDLIVDPAALVNHVLPYSQLFGPNAAGTAELLRLALTGKRK-PYIYTSTiAVGEQIPPEAFTED- 926 
                                     *****************************************************9.*******999999999888777. PP

                                     -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST---TTSHHHHHHHHH CS
                  NAD_binding_4  152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwingsdlgirgllgl 228 
                                           + ++ + +r+ +++++n+Y +sK+++E l+rea++++glpv+++R+ +i++  s tG++n  d+ +r++l+l
  gi|121638475|ref|YP_978699.1|  927 -----ADIRAISPTRRIDDSYANGYANSKWAGEVLLREAHEQCGLPVTVFRCDMILAdTSYTGQLNLPDMFTRLMLSL 999 
                                     .....5569************************************************77889**************** PP

                                     HHH-EEES-SB---TT.......--EEEHHHHHHHH CS
                  NAD_binding_4  229 iakgvlpeilgdkeav.......ldlvpvDyvanai 257 
                                     +a+g+ p  +++ +a+       +d +pv++va+ai
  gi|121638475|ref|YP_978699.1| 1000 AATGIAPGSFYELDAHgnrqrahYDGLPVEFVAEAI 1035
                                     ************9999999**************997 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.9   1.5e+04      17      36 ..     107     126 ..      98     127 .. 0.71
   2 !   44.3   0.1   5.5e-15   1.7e-11       2      67 .]     650     716 ..     649     716 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.9
                     PP-binding  17 eidpdtdlfdlGlDSllave 36 
                                    +i p +  + lG++S++ ++
  gi|121638475|ref|YP_978699.1| 107 AIRPGDRVCVLGFNSVDYTT 126
                                    45677888889****98765 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 5.5e-15
                     PP-binding   2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfe.hptlaelaayl 67 
                                    +l++++a +lg  + ++ pd+++ dlG+DSl+a++l++ l e fgv++p+ ++    + l++la+++
  gi|121638475|ref|YP_978699.1| 650 TLCRAAAALLGSTAADVRPDAHFADLGGDSLSALSLANLLHEIFGVDVPVGVIVSpASDLRALADHI 716
                                    589999******999*99************************************************8 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.4e-12   1.3e-08       1     171 [.     771     975 ..     771    1024 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.4e-12
                                    EEEETTTSHHHHHHHHHHHHCT....SEEEEEES-STTTTCHHCHHC..........................EEEE--T CS
                      Epimerase   1 ilVtGatGfiGsalvkallekg....yevigldrlssasntarledl..........................elveldl 50 
                                    +l+tGatGf+G++l+ ++l++      ++i+l r +s+++ +++ d+                          +  e+dl
  gi|121638475|ref|YP_978699.1| 771 VLLTGATGFLGRYLALEWLDRMdlvnGKLICLVRARSDEEAQARLDAtfdsgdpylvrhyrelgagrlevlagDKGEADL 850
                                    699*****************9999877777777776666555555556********************999987778888 PP

                                    .T-HHHHHHHHHHHT-SEEEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGT........ CS
                      Epimerase  51 .tdrsalerlfkeeqpdavihlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYG........ 120
                                     +dr+ ++rl +   +d ++  Aa v +v  +s+     +  n++gt +ll  a + + k +++ s+ +v          
  gi|121638475|ref|YP_978699.1| 851 gLDRVTWQRLAD--TVDLIVDPAAlVNHVLPYSQL----FGPNAAGTAELLRLALTGKRKPYIYTSTIAVGEqippeaft 924
                                    67999****999..89********99999997765....778*************9999999999995443322233222 PP

                                    SCSSSSBSTCSTTS--..--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESE CS
                      Epimerase 121 kdaeqpkeettltgpl..kpnspYaaaKlageklveayaaqyglnaiilrlfn 171
                                    +da++   + t    +     + Ya +K age l++++++q gl+++++r+  
  gi|121638475|ref|YP_978699.1| 925 EDADIRAISPTRR--IddSYANGYANSKWAGEVLLREAHEQCGLPVTVFRCDM 975
                                    2222224444433..3558899****************************965 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-06     0.012       1      64 [.     517     588 ..     517     595 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-06
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---.........HHHHHHHHHHH.HT-TTTS-SEEE CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea.........leeeLkahvrk.elgpyavpkkvv 64 
                                    ++E++   +p V++++++G +      +++a+Vv++ g   s           + e L++ +r+  l +y  p++++
  gi|121638475|ref|YP_978699.1| 517 KLEAVFGDSPLVRQIFIYGNSAR---AYPLAVVVPS-GdalS-RhgienlkpvISESLQEVARAaGLQSYEIPRDFI 588
                                    58*********************...*********6.42341.1344445667777777777555788888888665 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0018       5.4       1      25 [.     772     796 ..     772     831 .. 0.73
   2 ?    3.8   0.0     0.011        32     103     180 ..     888     973 ..     882    1001 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0018
                                    EEETTTSHHHHHHHHHHHHCT-CCE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevh 25 
                                    L TG +Gf G yla  +l++   v 
  gi|121638475|ref|YP_978699.1| 772 LLTGATGFLGRYLALEWLDRMDLVN 796
                                    78***************99855443 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                                    THHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS----...........-SHHHHHHHHHHHHHHHHHHHH CS
                  GDP_Man_Dehyd 103 vlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyP...........rsPYaaaKlyadwivvnyreay 171
                                    + Gt++LL ++ + +   ++ ++ +St  v  +     +tE+  +++            + Ya +K + + + ++ +e+ 
  gi|121638475|ref|YP_978699.1| 888 AAGTAELLRLALTGK---RKPYIYTSTIAVGEQIPPEAFTEDADIRAisptrriddsyANGYANSKWAGEVLLREAHEQC 964
                                    566666666664422...2344555555553333455566665555422222233333456******************* PP

                                    ---EEEEEE CS
                  GDP_Man_Dehyd 172 glfavngil 180
                                    gl++++ ++
  gi|121638475|ref|YP_978699.1| 965 GLPVTVFRC 973
                                    ****98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.78u 0.26s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 7574.77
//
Query:       gi|121638476|ref|YP_978700.1|  [L=546]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-33  113.2  20.2    8.5e-33  112.6  20.2    1.3  1  PE              PE family
  ------ inclusion threshold ------
       0.21   11.7   0.1       0.36   11.0   0.1    1.3  1  T3SS_needle_E   Type III secretion system, cytoplasmic E comp


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6  20.2   9.5e-37   8.5e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 9.5e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPe+la+aa+++a+ig++lsaana aaa+tt+vlaa+aDeVS+aiA+lfs++a++yq+l+aqaaafh+ fvq+l+a
  gi|121638476|ref|YP_978700.1|  1 MSFVTAAPEMLATAAQNVANIGTSLSAANATAAASTTSVLAAGADEVSQAIARLFSDYATHYQSLNAQAAAFHHSFVQTLNA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a+g+Y++aEaa
  gi|121638476|ref|YP_978700.1| 83 AGGAYSSAEAA 93
                                   *********97 PP

>> T3SS_needle_E  Type III secretion system, cytoplasmic E component of needle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   4.1e-05      0.36       6      53 ..      23      72 ..      20      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                                   HHHCCCCTHHHHHHHHHHHHHHHHHHHHHCCTSS..HHHHHHHHHHHHHH CS
                  T3SS_needle_E  6 drLrhapgeqakelqdrLeaArarLkqalsspqs..peeYqqlqllaeAl 53
                                   ++L+ a +++a++ ++ L+a++ ++ qa +++ s  + +Yq+l+ +a A 
  gi|121638476|ref|YP_978700.1| 23 TSLSAANATAAASTTSVLAAGADEVSQAIARLFSdyATHYQSLNAQAAAF 72
                                   6899999************************9765599********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.24s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 3733.23
//
Query:       gi|121638477|ref|YP_978701.1|  [L=344]
Description: Holliday junction DNA helicase RuvB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-74  247.8   0.1    7.2e-74  246.8   0.0    1.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.1e-31  106.2   1.6      1e-30  105.3   1.6    1.6  1  AAA_lid_4        RuvB AAA lid domain
    9.2e-23   79.9   0.0    1.5e-22   79.2   0.0    1.4  1  RuvB_C           RuvB C-terminal winged helix domain
    8.9e-17   61.8   0.0    1.8e-16   60.8   0.0    1.6  1  AAA              ATPase family associated with various cellul
    2.7e-06   26.9   0.4    1.3e-05   24.6   0.0    1.9  2  TIP49            TIP49 P-loop domain
    8.1e-06   25.9   0.5     0.0003   20.8   0.1    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    1.8e-05   25.2   1.8    0.00021   21.7   0.1    2.7  3  AAA_16           AAA ATPase domain
    2.9e-05   23.6   0.4      0.034   13.5   0.0    2.7  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0011   18.7   0.0        1.6    8.4   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0028   18.0   0.5        1.3    9.3   0.0    2.5  2  AAA_22           AAA domain
      0.004   17.5   0.0     0.0069   16.8   0.0    1.3  1  RNA_helicase     RNA helicase
     0.0045   16.8   0.1       0.12   12.3   0.1    2.3  1  AAA_3            ATPase family associated with various cellul
     0.0073   16.3   0.0      0.026   14.5   0.0    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.024   13.9   0.1    1.2  1  Zeta_toxin       Zeta toxin
      0.023   14.4   4.5      0.089   12.5   0.2    3.3  3  IstB_IS21        IstB-like ATP binding protein
      0.026   14.6   0.0      0.055   13.5   0.0    1.5  1  AAA_14           AAA domain
       0.03   14.2   0.2       0.41   10.5   0.0    2.5  3  NTPase_1         NTPase
      0.031   14.3   0.0        8.5    6.3   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
      0.061   13.2   0.2       0.36   10.7   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.069   13.7   0.0       0.18   12.3   0.0    1.8  1  AAA_18           AAA domain
      0.073   13.2   0.2       0.25   11.4   0.0    2.0  2  Resolvase        Resolvase, N terminal domain
      0.089   12.7   0.0       0.13   12.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
       0.12   12.2   0.0       0.31   10.9   0.0    1.7  1  NACHT            NACHT domain
       0.14   12.4   0.5          2    8.7   0.1    2.2  2  AAA_19           AAA domain
       0.19   10.8   0.0       0.35   10.0   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)


Domain annotation for each model (and alignments):
>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   0.0     1e-76   7.2e-74       1     159 []      24     182 ..      24     182 .. 0.99
   2 ?   -3.0   0.0       7.4   5.3e+03      44      74 ..     282     311 ..     276     314 .. 0.67

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 1e-76
                         RuvB_N   1 lrPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt 80 
                                    lrP+sl+e+igq +v+e+l+++ie ak+r+ + dh+ll+GpPGlGkt+la+iia+elg++l++tsgP+le+agdlaa+l+
  gi|121638477|ref|YP_978701.1|  24 LRPRSLREFIGQPRVREQLQLVIEGAKNRGGTPDHILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPALERAGDLAAMLS 103
                                    8******************************************************************************* PP

                         RuvB_N  81 nleekdvlfideihrlsraveevlysamedfrldivigkGpsarsikldlpkftlvgattragllssPlrdrfgivarl 159
                                    nl e+dvlfideihr++r +ee+ly amedfr+d+v+gkGp+a+si l++++ftlvgattr+g+l+ Plrdrfg++a++
  gi|121638477|ref|YP_978701.1| 104 NLVEHDVLFIDEIHRIARPAEEMLYLAMEDFRVDVVVGKGPGATSIPLEVAPFTLVGATTRSGALTGPLRDRFGFTAHM 182
                                    ***************************************************************************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.4
                         RuvB_N  44 lGkttlakiiakelgvklkitsgPvlekagd 74 
                                    +G +tla  + +e  ++++  + P l +ag 
  gi|121638477|ref|YP_978701.1| 282 VGVSTLAVAVGEEA-ATVEEVCEPFLVRAGM 311
                                    67788888887775.5567777777777765 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   1.6   1.5e-33     1e-30       1      74 []     185     258 ..     185     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.5e-33
                      AAA_lid_4   1 YeeeeLeeivkrsakilgveieeegaaeiarRsRGTPRianrLLrRvrDfaqvkgdgkitkevakkaLellevd 74 
                                    Ye++eLe+++ rsa ilg+e+ +++ aeiarRsRGTPRianrLLrRvrDfa+v++dg it++vak+aLe+++vd
  gi|121638477|ref|YP_978701.1| 185 YEPAELERVLARSAGILGIELGADAGAEIARRSRGTPRIANRLLRRVRDFAEVRADGVITRDVAKAALEVYDVD 258
                                    999**********************************************************************9 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.0   2.1e-25   1.5e-22       1      71 [.     259     329 ..     259     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 2.1e-25
                                    TT---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHHH CS
                         RuvB_C   1 elGLdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglkyl 71 
                                    elGLd+ld+ +L++l+++f ggpvg++tla ++gee  t+e+v+EP+L++ g++ rt+rGR +T  ++++l
  gi|121638477|ref|YP_978701.1| 259 ELGLDRLDRAVLSALTRSFGGGPVGVSTLAVAVGEEAATVEEVCEPFLVRAGMVARTPRGRVATALAWTHL 329
                                    68********************************************************************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   2.5e-19   1.8e-16       1     127 [.      59     179 ..      59     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.5e-19
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +ll+GppG GKT+la  +a elg+++  +sg+ l       ++ +++++++++ e+    +lfiDEi+++a+        
  gi|121638477|ref|YP_978701.1|  59 ILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPALE------RAGDLAAMLSNLVEH---DVLFIDEIHRIARPA------ 123
                                    69*********************************......999999999998766...6**********9999...... PP

                                    HHHHHHHHHHHHHHHTTTS...............SSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                            AAA  81 eeervvnqLlteldgvkkk...............eskvivigatnrpdkldpallrgRfdrk 127
                                          + L+ ++++++ +                ++++++gat+r   l+ +l+ +Rf   
  gi|121638477|ref|YP_978701.1| 124 -----EEMLYLAMEDFRVDvvvgkgpgatsipleVAPFTLVGATTRSGALTGPLR-DRFGFT 179
                                    .....9****************************788******************.**9765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.8e-08   1.3e-05      25      79 ..      31      85 ..      15      92 .. 0.90
   2 ?   -0.2   0.1      0.63   4.5e+02     280     291 ..     109     120 ..     102     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 25 glvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvp 79
                                    ++Gq + re   +++e  k++  +   +Ll+Gp+g Gkt+la+ i+ elg+++ 
  gi|121638477|ref|YP_978701.1| 31 EFIGQPRVREQLQLVIEGAKNRGGTPDHILLSGPPGLGKTSLAMIIAAELGSSLR 85
                                   58*******************999999************************9876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.63
                                    XXXXXXXXXXXX CS
                          TIP49 280 GvlfiDevhmlD 291
                                     vlfiDe+h + 
  gi|121638477|ref|YP_978701.1| 109 DVLFIDEIHRIA 120
                                    59*******765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.2e-07    0.0003       1     137 [.      58     175 ..      58     176 .. 0.75
   2 ?   -2.8   0.0       8.3   5.9e+03      49      84 ..     233     272 ..     225     275 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.2e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    ++lL GppG gK++la+ +aa l++++ +  +++  ++ dl   ++            lv    e ++l++DE++r+ + 
  gi|121638477|ref|YP_978701.1|  58 HILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPALERAGDLAAMLS-----------NLV----EHDVLFIDEIHRIARP 122
                                    789**************************99999777777776666...........677....8999999999999988 PP

                                    HHHHHHHHHHSSEEE..-SSSEEE---.......-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  81 vlnsLlslleerrllleeggelvkakndd.llerfrviatanpldrslnelspalrsR 137
                                    + + L   +e+ r+++  g++    + +   ++ f++++++ +       l+ +lr+R
  gi|121638477|ref|YP_978701.1| 123 AEEMLYLAMEDFRVDVVVGKGPGATSIPLeVAP-FTLVGATTRSG----ALTGPLRDR 175
                                    888888888888887777776665555432222.77776666655....555555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.3
                                    ........--------G-SEEEEE....SGGG--HHHHHH CS
                          AAA_5  49 ngttslvdsplvraaregeilvlD....Everaesevlns 84 
                                    +  +++ d++++r + ++++ v D    +++r++++vl++
  gi|121638477|ref|YP_978701.1| 233 DFAEVRADGVITRDVAKAALEVYDvdelGLDRLDRAVLSA 272
                                    5566677777777777555443332223345555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     3e-07   0.00021       2      51 ..      32      83 ..      31     108 .. 0.78
   2 ?    1.8   0.1      0.39   2.8e+02     134     159 ..     107     131 ..      91     140 .. 0.72
   3 ?   -1.0   0.0       2.7     2e+03     116     128 ..     218     237 ..     178     280 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3e-07
                         AAA_16  2 lvGReeeleqLlsale..rvrsgrpelvllsGesGvGKsslvrellralekd 51
                                   ++G  + +eqL+ ++e  + r g+p  +llsG++G GK+sl+  ++ +l  +
  gi|121638477|ref|YP_978701.1| 32 FIGQPRVREQLQLVIEgaKNRGGTPDHILLSGPPGLGKTSLAMIIAAELGSS 83
                                   6777778899999999745555555*****************9999888766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                         AAA_16 134 erplvlvlDdlqwadeaslqllaaLl 159
                                    e+  vl++D+++++     ++l++ +
  gi|121638477|ref|YP_978701.1| 107 EH-DVLFIDEIHRIARPAEEMLYLAM 131
                                    33.59*******99888877777766 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.7
                         AAA_16 116 a......srllellkrll.a 128
                                    +      +rll+ +++++ +
  gi|121638477|ref|YP_978701.1| 218 RgtpriaNRLLRRVRDFAeV 237
                                    14432225555555555422 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.7e-05     0.034       2      44 ..      29      78 ..      28      93 .. 0.77
   2 !    7.2   0.1    0.0042         3     105     138 ..     106     139 ..     101     165 .. 0.85
   3 ?   -1.8   0.0       2.4   1.7e+03     184     199 ..     167     182 ..     159     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                   Mg_chelatase  2 lkdvkGqeeakraleiaaaGgH.......nlllvGppGsGKtmlakrlps 44
                                   l++ +Gq + ++ l++ + G         ++ll GppG GKt la  +++
  gi|121638477|ref|YP_978701.1| 29 LREFIGQPRVREQLQLVIEGAKnrggtpdHILLSGPPGLGKTSLAMIIAA 78
                                   567788999999888888886522222237**************987765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0042
                   Mg_chelatase 105 ahnGvLfLDElpefkrkvlevLRePledgevtis 138
                                     ++ vLf+DE+  + r + e+L   +ed +v + 
  gi|121638477|ref|YP_978701.1| 106 VEHDVLFIDEIHRIARPAEEMLYLAMEDFRVDVV 139
                                    5688************************998775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.4
                   Mg_chelatase 184 klsgplldRidlqvev 199
                                     l gpl dR+  + ++
  gi|121638477|ref|YP_978701.1| 167 ALTGPLRDRFGFTAHM 182
                                    689******9888776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0023       1.6       6      44 ..      40      78 ..      36      88 .. 0.86
   2 !    7.9   0.0    0.0033       2.3      93     125 ..     107     139 ..      89     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                                   HHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  6 ealkelleqikkvaktdlsvlitGesGtGKellaraihe 44
                                   e+l+ ++e +k+   t+ ++l+ G  G GK+ la  i +
  gi|121638477|ref|YP_978701.1| 40 EQLQLVIEGAKNRGGTPDHILLSGPPGLGKTSLAMIIAA 78
                                   67788889999999999*****************98865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                                    TTSEEEEETGGGS-HHHHHHHHHHHHHSEEESB CS
                Sigma54_activat  93 dgGtlfLDeigelplelQekLlrvlqegeverv 125
                                    ++ +lf+Dei+++   + e+L  ++++ +v  v
  gi|121638477|ref|YP_978701.1| 107 EHDVLFIDEIHRIARPAEEMLYLAMEDFRVDVV 139
                                    6789******************99999877654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0018       1.3       5      24 ..      56      75 ..      51      84 .. 0.82
   2 ?    6.6   0.1     0.012       8.7      81     110 ..     100     128 ..      75     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                         AAA_22  5 agilvvtGesGtGKTtllrr 24
                                     ++++ G++G GKT l+  
  gi|121638477|ref|YP_978701.1| 56 PDHILLSGPPGLGKTSLAMI 75
                                   6799***********99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                         AAA_22  81 aleqalrarav...ielliiDEaqhlr.s.eeale 110
                                    a+            + +l iDE++++  + ee+l 
  gi|121638477|ref|YP_978701.1| 100 AMLS------NlveHDVLFIDEIHRIArPaEEMLY 128
                                    3333......2444568********9642355553 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.7e-06    0.0069       1      64 [.      59     122 ..      59     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.7e-06
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                    i+l+Gp+g GK++la  +a++l ++l  ++ + +   +    ++++  +++v+ id++ ++   
  gi|121638477|ref|YP_978701.1|  59 ILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPALERAGDLAAMLSNLVEHDVLFIDEIHRIARP 122
                                    689***********************999988887788899999*************9998744 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00016      0.12       1      27 [.      58      84 ..      58     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                          AAA_3  1 hvllegvPGlaktllvkalakaldlef 27
                                   h+ll g PGl+kt l+  +a  l+ ++
  gi|121638477|ref|YP_978701.1| 58 HILLSGPPGLGKTSLAMIIAAELGSSL 84
                                   9********************999876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.6e-05     0.026      19      50 ..      56      88 ..      36     113 .. 0.86
   2 ?   -1.6   0.0       3.7   2.6e+03      67      76 ..     180     189 ..     171     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--.---- CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve.evkS 50
                                    d ilL+G+ G GKT l+  +a++lg + +v+S
  gi|121638477|ref|YP_978701.1| 56 PDHILLSGPPGLGKTSLAMIIAAELGSSlRVTS 88
                                   456************************999999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                                    EEEE-TT-SS CS
                           TsaE  67 yHfDlYRled 76 
                                     H+D+Y  ++
  gi|121638477|ref|YP_978701.1| 180 AHMDFYEPAE 189
                                    7****97543 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.4e-05     0.024      11      41 ..      51      81 ..      43      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                     Zeta_toxin 11 psqerPklillgGqpGAGKselaellkdele 41
                                    ++ +P+ ill+G pG GK++la  +++el+
  gi|121638477|ref|YP_978701.1| 51 NRGGTPDHILLSGPPGLGKTSLAMIIAAELG 81
                                   36699**********************9995 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00012     0.089      48     117 ..      57     116 ..      54     133 .. 0.73
   2 ?   -0.5   0.1       1.2   8.5e+02      90     127 ..     234     270 ..     224     278 .. 0.73
   3 ?    0.4   0.1      0.67   4.8e+02      54      73 ..     278     297 ..     276     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl 117
                                    + i+l Gp+G GK+ la+ ++ e    g s + ++ ++L       +r g la +l++l++ d+l +D++
  gi|121638477|ref|YP_978701.1|  57 DHILLSGPPGLGKTSLAMIIAAE---LGSSLRVTSGPAL-------ERAGDLAAMLSNLVEHDVLFIDEI 116
                                    5799*************998754...5666666666655.......345667777777777777777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                      IstB_IS21  90 lkrarrdgklaralkrllkvdllilDdlgllpldqaea 127
                                     +  r+dg ++r +++  + ++  +D+lgl  ld+a  
  gi|121638477|ref|YP_978701.1| 234 FAEVRADGVITRDVAKA-ALEVYDVDELGLDRLDRAVL 270
                                    55667777777777664.5788889*****99998765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.67
                      IstB_IS21  54 GpsGvGKshlaialgveavr 73 
                                    G+  vG s la+a+g ea++
  gi|121638477|ref|YP_978701.1| 278 GGGPVGVSTLAVAVGEEAAT 297
                                    6666899*********9986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.7e-05     0.055       5      97 ..      59     140 ..      56     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekalk 84 
                                    ++++G+   GKT l+  ++ el     s l ++     +  +a   +l  ++ +++   ++ +lf+DEi+++ +  + + 
  gi|121638477|ref|YP_978701.1|  59 ILLSGPPGLGKTSLAMIIAAELG----SSLRVTSGPALE--RAG--DLAAMLSNLV---EHDVLFIDEIHRIARPAEEML 127
                                    6899999*******988887777....555555444333..232..2456666655...5689*********98776666 PP

                         AAA_14  85 slvdegknldviv 97 
                                    +l  e+ ++dv+v
  gi|121638477|ref|YP_978701.1| 128 YLAMEDFRVDVVV 140
                                    6666655777775 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00058      0.41       1      26 [.      58      83 ..      58      95 .. 0.86
   2 ?    0.8   0.1      0.56     4e+02      89     104 ..     102     116 ..      89     125 .. 0.78
   3 ?   -2.4   0.0       5.2   3.8e+03      27      40 ..     236     249 ..     222     272 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                                   EEEEE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkss 26
                                   +++++GppG GKt l   ++ +l ss
  gi|121638477|ref|YP_978701.1| 58 HILLSGPPGLGKTSLAMIIAAELGSS 83
                                   799**************999999655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                                    HHHHHHHH-EEEE--- CS
                       NTPase_1  89 lrkalseadviviDEi 104
                                    l+  l e dv+ iDEi
  gi|121638477|ref|YP_978701.1| 102 LS-NLVEHDVLFIDEI 116
                                    44.35799*******9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                                    GGGEEEEEEEEE-- CS
                       NTPase_1  27 gvkvgGfyteevre 40 
                                    +v+ +G++t++v +
  gi|121638477|ref|YP_978701.1| 236 EVRADGVITRDVAK 249
                                    56666666666543 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017        12      22      50 ..      54      82 ..      32      88 .. 0.75
   2 ?    6.3   0.0     0.012       8.5     132     147 ..     107     122 ..      93     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                         ResIII 22 krdkrglikmaTGtGKTlvaaklierllk 50
                                       ++l+  + G GKT +a+ ++++l +
  gi|121638477|ref|YP_978701.1| 54 GTPDHILLSGPPGLGKTSLAMIIAAELGS 82
                                   345599**************999998865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                                    T-SEEEEETGGGTTS. CS
                         ResIII 132 rfdviiiDEaHrlgak 147
                                    ++dv++iDE Hr+++ 
  gi|121638477|ref|YP_978701.1| 107 EHDVLFIDEIHRIARP 122
                                    689*********9874 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.4   1.7e+03      21      37 ..      78      94 ..      75      98 .. 0.85
   2 ?   10.7   0.0   0.00051      0.36       1      34 [.     262     298 ..     262     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.4
                  HTH_AsnC-type 21 aeLAervGlSestvlrR 37
                                   aeL+  + ++  ++l+R
  gi|121638477|ref|YP_978701.1| 78 AELGSSLRVTSGPALER 94
                                   79999999999999999 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00051
                  HTH_AsnC-type   1 LDeiDrkILeaLqed...aRisyaeLAervGlSestv 34 
                                    LD++Dr+ L+aL +    +   ++ LA +vG  ++tv
  gi|121638477|ref|YP_978701.1| 262 LDRLDRAVLSALTRSfggGPVGVSTLAVAVGEEAATV 298
                                    8******************************999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026      0.18       1      25 [.      59      88 ..      59     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....g 25
                                   Ill+G+pG GKt+la  ++ +lg+     +
  gi|121638477|ref|YP_978701.1| 59 ILLSGPPGLGKTSLAMIIAAELGSslrvtS 88
                                   99****************999965454440 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.25      44     101 ..      88     142 ..      85     164 .. 0.78
   2 ?   -2.2   0.1       5.6     4e+03      57      57 ..     252     252 ..     224     276 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                    -TT-TT-.HHHHHHHHHHTT-EE.EEEESSCCCC-S...S-HHHHHHHHHTT-EEEESS CS
                      Resolvase  44 SGakleR.pglkrllaalregkgdvlvvekldRLaRsvrdlltlleelrekgvslvsld 101
                                    SG  leR  +l ++l+ l e  +dvl++ +++R+aR + ++l l   +++ +v++v+ +
  gi|121638477|ref|YP_978701.1|  88 SGPALERaGDLAAMLSNLVE--HDVLFIDEIHRIARPAEEMLYL--AMEDFRVDVVVGK 142
                                    6666675367999***9999..**************99999977..6666666666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                                    H CS
                      Resolvase  57 l 57 
                                    l
  gi|121638477|ref|YP_978701.1| 252 L 252
                                    1 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.13      47      81 ..      58      92 ..      38     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                          Rad17 47 iLLisGPsGCgkstvvkvLskelgiklrewlnpvs 81
                                    +L+sGP+G gk+    +++ elg +lr  + p +
  gi|121638477|ref|YP_978701.1| 58 HILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPAL 92
                                   4789***********************98888776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00044      0.31       3      25 ..      59      81 ..      57      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                   ++l G++G GKT L+  +a ++ 
  gi|121638477|ref|YP_978701.1| 59 ILLSGPPGLGKTSLAMIIAAELG 81
                                   899***************99886 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0028         2      11      38 ..      57      84 ..      49      95 .. 0.83
   2 ?    1.6   0.1      0.44   3.2e+02      98     121 ..     103     127 ..      90     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                         AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelg 38
                                   +++l+ ++pG GKT + + i a+l +  
  gi|121638477|ref|YP_978701.1| 57 DHILLSGPPGLGKTSLAMIIAAELGSSL 84
                                   6799***********9999988887665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.44
                         AAA_19  98 kklqeeellivDEfqdvd.elqyrL 121
                                    ++l e+++l++DE+  +  + +  L
  gi|121638477|ref|YP_978701.1| 103 SNLVEHDVLFIDEIHRIArPAEEML 127
                                    4565899*******99984444443 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00049      0.35      48     115 ..      51     115 ..      23     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                         DUF815  48 leglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDD 115
                                     +g +  ++LL G  G GK sl   + +e+  ++Lr+   +   l+   +l ++l++  e+ +lf+D 
  gi|121638477|ref|YP_978701.1|  51 NRGGTPDHILLSGPPGLGKTSLAMIIAAELG-SSLRVT--SGPALERAGDLAAMLSNLVEHDVLFIDE 115
                                    4677889***************988877765.568985..6788999999999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 2725.73
//
Query:       gi|121638478|ref|YP_978702.1|  [L=196]
Description: Holliday junction DNA helicase RuvA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   73.1   0.0    4.1e-20   71.6   0.1    1.7  2  RuvA_N    RuvA N terminal domain
    2.2e-15   57.0   0.0    6.1e-15   55.6   0.0    1.8  1  HHH_5     Helix-hairpin-helix domain
    9.5e-11   42.0   0.8    2.4e-10   40.7   0.8    1.8  1  RuvA_C    RuvA, C-terminal domain
  ------ inclusion threshold ------
      0.021   14.7   0.1         16    5.6   0.0    3.1  3  HHH       Helix-hairpin-helix motif
      0.064   13.5   0.0        2.4    8.5   0.0    2.4  2  HHH_3     Helix-hairpin-helix motif
       0.11   12.3   0.1       0.21   11.5   0.1    1.4  1  DUF2642   Protein of unknown function (DUF2642)


Domain annotation for each model (and alignments):
>> RuvA_N  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.1   1.4e-23   4.1e-20       1      60 []       1      61 [.       1      61 [. 0.99
   2 ?   -2.3   0.0       1.7   5.1e+03      18      30 ..      74      86 ..      69      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.4e-23
                                   -EEEEEEEEEEESSCEEEEEETTEEEEEEE-HHHHCC.-TTSEEEEEEEEEEETTEEEEEE CS
                         RuvA_N  1 MIaylkGkvvekepdsivvevggvGYevfvplstlss.kegeevklythlivrEdalsLYG 60
                                   MIa+++G+v+e+  d++v+e+ gvGY+v++++ tl++ ++g e++l t +ivrEd+++LYG
  gi|121638478|ref|YP_978702.1|  1 MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATlRQGTEARLITAMIVREDSMTLYG 61
                                   ***********************************99*99********************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                   EEEETTEEEEEEE CS
                         RuvA_N 18 vvevggvGYevfv 30
                                   ++ v+gvG ++ +
  gi|121638478|ref|YP_978702.1| 74 LLSVSGVGPRLAM 86
                                   5789999977766 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0     2e-18   6.1e-15       1      57 []      71     129 ..      71     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2e-18
                                    -HHHHTSTT--HHHHHHHHTT.T--SHH.HHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                          HHH_5   1 feeLlsvsGiGpktAlallsa.Giesve.dlaaadveeLakipGiGkktAeriilelkd 57 
                                    f  LlsvsG+Gp++A+a l       +   la+ +v++L+++pGiGk+ Aer++lel+d
  gi|121638478|ref|YP_978702.1|  71 FLTLLSVSGVGPRLAMAALAVhDAPALRqVLADGNVAALTRVPGIGKRGAERMVLELRD 129
                                    789**************99993345554257999************************8 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.8   8.1e-14   2.4e-10       6      46 ..     151     192 ..     146     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 8.1e-14
                                    HHHHHHHCTS-HHHHHHHHHHHHC.-TTS-HHHHHHHHHCCT CS
                         RuvA_C   6 aveALlaLGYkekeaekAvakvla.npgasveelIraALklL 46 
                                    +veAL++LG+ +k+ae+A + vla n +a+++ ++r AL lL
  gi|121638478|ref|YP_978702.1| 151 VVEALVGLGFAAKQAEEATDTVLAaNHDATTSSALRSALSLL 192
                                    8**************************************998 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.6   1.8e+03       6      16 ..      28      38 ..      24      39 .. 0.72
   2 ?    5.6   0.0    0.0053        16      13      21 ..      74      82 ..      73      90 .. 0.85
   3 ?    5.0   0.0     0.008        24      10      21 ..     106     117 ..     101     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.6
                                   HTSSHHHHHTS CS
                            HHH  6 ipasreeLlal 16
                                   ++a+++ L++l
  gi|121638478|ref|YP_978702.1| 28 VNATPATLATL 38
                                   57888887765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0053
                                   HHTSTT-SH CS
                            HHH 13 LlalPGVGp 21
                                   Ll+++GVGp
  gi|121638478|ref|YP_978702.1| 74 LLSVSGVGP 82
                                   99******9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.008
                                    HHHHHTSTT-SH CS
                            HHH  10 reeLlalPGVGp 21 
                                    ++ L+ +PG+G+
  gi|121638478|ref|YP_978702.1| 106 VAALTRVPGIGK 117
                                    67799******6 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.064   1.9e+02      16      31 ..      74      89 ..      72      94 .. 0.78
   2 ?    8.5   0.0    0.0008       2.4      13      38 ..     106     132 ..     104     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.064
                          HHH_3 16 LqklpGlgpklAknIv 31
                                   L  ++G+gp+lA + +
  gi|121638478|ref|YP_978702.1| 74 LLSVSGVGPRLAMAAL 89
                                   6789999999997765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0008
                          HHH_3  13 aeeLqklpGlgpklAknIv.ayReknG 38 
                                    ++ L+++pG+g++ A+++v + R+k G
  gi|121638478|ref|YP_978702.1| 106 VAALTRVPGIGKRGAERMVlELRDKVG 132
                                    6789***********998746676665 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.1e-05      0.21      30      49 ..       4      23 ..       2      29 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                        DUF2642 30 svrGiLkdvkPDHivveign 49
                                   svrG + +v  DH+v+e+++
  gi|121638478|ref|YP_978702.1|  4 SVRGEVLEVALDHVVIEAAG 23
                                   79**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1360.76
//
Query:       gi|121638479|ref|YP_978703.1|  [L=188]
Description: Holliday junction resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-62  208.9   1.2    3.7e-62  208.6   1.2    1.1  1  RuvC      Crossover junction endodeoxyribonuclease RuvC
  ------ inclusion threshold ------
      0.068   13.3   3.1       0.22   11.7   0.7    2.2  2  DUF4253   Domain of unknown function (DUF4253)


Domain annotation for each model (and alignments):
>> RuvC  Crossover junction endodeoxyribonuclease RuvC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6   1.2   4.1e-66   3.7e-62       1     148 []       3     152 ..       3     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 4.1e-66
                                    EEEEE--SSEEEEEEEEE.ETTEEEEEEEEEEE---S.-HHHHHHHHHHHHHHHHHHH--SEEEEEE-S----HHHHHHH CS
                           RuvC   1 ilGiDPGsrktGygviee.agrklslltsgvirtksd.plserlkavfdaveelldayepdalaieqvffaknvdsvlkl 78 
                                    ++G+DPG++++G+++ie+ +gr+l++l+++v+rt+sd  l++rl+a++dave++ld+++p+++aie+vf++ nv++v+++
  gi|121638479|ref|YP_978703.1|   3 VMGVDPGLTRCGLSLIESgRGRQLTALDVDVVRTPSDaALAQRLLAISDAVEHWLDTHHPEVVAIERVFSQLNVTTVMGT 82 
                                    79***************999*****************99***************************************** PP

                                    HHHHHHHHHHHHTTT--EEEEEHHHHHHHHTSSTT--HHHHHHHHHHHTT----SS.S-THHHHHHHHHH CS
                           RuvC  79 aqarGvvilaalereisvaeytpsqvkkavtGigkaekeqvqalvkrlLklkakpkpadaaDalavaith 148
                                    aqa+Gv++laa++r+++v+++tps+vk+avtG+g+a+k+qv+a+v+++L+l+akp+padaaDala+ai+h
  gi|121638479|ref|YP_978703.1|  83 AQAGGVIALAAAKRGVDVHFHTPSEVKAAVTGNGSADKAQVTAMVTKILALQAKPTPADAADALALAICH 152
                                    *********************************************************************9 PP

>> DUF4253  Domain of unknown function (DUF4253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.032   2.9e+02      32      66 ..      49      83 ..      40     112 .. 0.84
   2 ?   11.7   0.7   2.4e-05      0.22      43     101 ..     119     177 ..     100     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.032
                        DUF4253 32 lvavlrsWeerygaelvgigfdtlelsvakppkte 66
                                   ++  +++W + ++ e+v+i+    +l+v++   t 
  gi|121638479|ref|YP_978703.1| 49 ISDAVEHWLDTHHPEVVAIERVFSQLNVTTVMGTA 83
                                   56778999999999**9999999999998876555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.4e-05
                        DUF4253  43 ygaelvgigfdtlelsvakppkteeealalAaEhyafCpdlvdqgvgtledlaealkks 101
                                     +a+++++ + +l l+++  p++ ++alalA  h+  +p ++     t ++ a+a +++
  gi|121638479|ref|YP_978703.1| 119 DKAQVTAMVTKILALQAKPTPADAADALALAICHCWRAPTIARMAEATSRAEARAAQQR 177
                                    6899********************************99999997766665555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1397.46
//
Query:       gi|121638480|ref|YP_978704.1|  [L=81]
Description: hypothetical protein BCG_2618 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.2   3.1      2e-05   24.4   1.6    2.1  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.027   14.4   0.1    1.3  1  MraZ             MraZ protein, putative antitoxin-like
       0.14   12.2   0.0       0.15   12.1   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.6   3.3e-09     2e-05       7      41 ..       9      43 ..       8      48 .. 0.92
   2 ?    2.6   0.0     0.023   1.4e+02      21      33 ..      50      62 ..      46      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-09
                                   EEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCC CS
                 MazE_antitoxin  7 gavriPkevrfelgireGdevelevdgdkiilrpl 41
                                   g+ +iPk +r+ lg+r +d ve+++ +++i ++p 
  gi|121638480|ref|YP_978704.1|  9 GRLVIPKRIRERLGLRGNDQVEITERDGRIEIEPA 43
                                   689************************99999985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.023
                                   EECTCEEEEEECT CS
                 MazE_antitoxin 21 ireGdevelevdg 33
                                   +reG+ ++ +++ 
  gi|121638480|ref|YP_978704.1| 50 VREGSVLVARPER 62
                                   6788888888765 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.5e-06     0.027       9      29 ..       4      24 ..       1      44 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-06
                                   EB-TTSEEE--CHHHHHTTSC CS
                           MraZ  9 elDakGRlllPaklreeakle 29
                                   ++D +GRl +P++ re ++l 
  gi|121638480|ref|YP_978704.1|  4 TIDVAGRLVIPKRIRERLGLR 24
                                   79***************9986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.5e-05      0.15      40      76 ..      19      57 ..       8      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                                   HHHT--TT-EEEEEETTEEEEEEEEEESS..B-TTEEEE CS
                Molydop_binding 40 aalGikdGdlVevesrrGsvevrakvter..vrpGvvfm 76
                                   ++lG++ +d+Ve++ r G++e + + t    vr+G+v +
  gi|121638480|ref|YP_978704.1| 19 ERLGLRGNDQVEITERDGRIEIEPAPTGVelVREGSVLV 57
                                   79*****************99876555333488887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 640.91
//
Query:       gi|121638481|ref|YP_978705.1|  [L=134]
Description: hypothetical protein BCG_2619 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-12   46.5   0.1    5.6e-12   46.2   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   3.1e-16   5.6e-12       3     119 ..       4     122 ..       2     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.1e-16
                                    E-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   3 lDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaeiaee 80 
                                     DTsvl+a +   +e++eaa+++l+    +++ a+++ E++ vl+r  ++ r +  ++++ l +  + ++l +da+ ++ 
  gi|121638481|ref|YP_978705.1|   4 PDTSVLVAGFaTWHEGHEAAVRALN--RGVHLIAHAAVETYSVLTRlPPPHRIAPVAVHAYLADITSSNYLALDARSYRG 81 
                                    6************************..6******************988899999999999999**************** PP

                                    HHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  81 aaeialkyg...llpnDaliaAtAkehgikliatfDedfrrv 119
                                      +  ++++     ++Dal+  tAk+ g+kl+ t+D +  ++
  gi|121638481|ref|YP_978705.1|  82 LTDHLAEHDvtgGATYDALVGFTAKAAGAKLL-TRDLRAVET 122
                                    ********************************.***987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 959.75
//
Query:       gi|121638482|ref|YP_978706.1|  [L=206]
Description: hypothetical protein BCG_2620 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-30  104.7   1.0    5.3e-30  104.4   1.0    1.1  1  DUF4178   Domain of unknown function (DUF4178)


Domain annotation for each model (and alignments):
>> DUF4178  Domain of unknown function (DUF4178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   1.0   2.9e-34   5.3e-30       2     140 ..      55     191 ..      54     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 2.9e-34
                        DUF4178   2 lGdivtldgedyvVvGrlrydeggyrwtEylledgsegrwLsvee....lelalletvpgrelepgewpeapedppetlt 77 
                                    +G+iv++ g dyvV+G ++++eg + w+E+lle+g++  wLsv e    lela++ ++ +  l+pg+          +  
  gi|121638482|ref|YP_978706.1|  55 PGAIVSHGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEddgrLELAMWVKRTDLGLQPGG----------QHV 124
                                    8***********************************99****************************5..........889 PP

                        DUF4178  78 ldgkrYrleergtarvtavegegptgvrageevrywdyes....ddgrl.LsiErwg.ge.pevslGryv 140
                                    +dg++++ +erg+a    +++eg+tg++ag+e++y+d++s    +d+ + Ls+Erw+ +  +e+ +G+ v
  gi|121638482|ref|YP_978706.1| 125 IDGVTFQETERGHAG---YTTEGTTGLPAGGEMDYVDCASagqgADESMlLSFERWApDMgWEIATGKSV 191
                                    ***************...***********************999666666*******9778******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1431.33
//
Query:       gi|121638483|ref|YP_978707.1|  [L=164]
Description: hypothetical protein BCG_2621 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-54  182.3   0.5    7.5e-54  182.1   0.5    1.0  1  DUF2617   Protein of unknown function DUF2617


Domain annotation for each model (and alignments):
>> DUF2617  Protein of unknown function DUF2617
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1   0.5   4.2e-58   7.5e-54       2     161 .]       4     162 ..       3     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 4.2e-58
                        DUF2617   2 aeldvayaDvsaadLglslkapeleaLaelelevggl.tvelrvlGaSHqVtveaeegelsEtvaClagaa.spLPasae 79 
                                    ++l++a++Dvs+a Lgl l+ap++++La+++l+++++ +++l+vlGaSH+Vtve   g+++E+v+C a+++ ++LP+s++
  gi|121638483|ref|YP_978707.1|   4 HQLAIAPVDVSGALLGLVLNAPAPRPLATHRLAHTDGsALQLGVLGASHVVTVE---GRFCEEVSCVARSRgGDLPESTH 80 
                                    89********************************7776**************76...89***********99******** PP

                        DUF2617  80 eedeeYefasrvealdeeefaaraeelraraadeeeallgvFPgdpaalTalvaevdggglswrTwHlYPqe..geiVaT 157
                                    ++  +Y+++s++e++de++f++ a++lr+r+++++++l gvFPgd+aalTal+ae+dg+g++wrTwHlYP++  g++V+T
  gi|121638483|ref|YP_978707.1|  81 AP--GYHLQSHTETHDEAAFRRLARHLRERCTRATGWLGGVFPGDDAALTALAAEPDGTGWRWRTWHLYPSAsgGTVVHT 158
                                    **..*******************************************************************999****** PP

                        DUF2617 158 rsrl 161
                                    +sr+
  gi|121638483|ref|YP_978707.1| 159 TSRW 162
                                    **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1321.26
//
Query:       gi|121638484|ref|YP_978708.1|  [L=143]
Description: hypothetical protein BCG_2622 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-32  112.8   0.1    1.9e-32  112.6   0.1    1.0  1  DUF4247   Domain of unknown function (DUF4247)


Domain annotation for each model (and alignments):
>> DUF4247  Domain of unknown function (DUF4247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.1   1.1e-36   1.9e-32       2     125 .]      19     135 ..      18     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.1e-36
                        DUF4247   2 iallagcg..sasvrdyiaknYqlessadegktdstvYraanksvpeVakeiaaqeePedkspeddetmyLvYeddivtv 79 
                                    ++l++g++  +++v +yia++Y++es++     + t+Y +++ s+++Va++++++++P++++ ++++t+yL+Y+++ivtv
  gi|121638484|ref|YP_978708.1|  19 VSLISGITllNRDVGSYIASHYRQESRDV----NGTRYLCTG-SPKQVATTLVKYQTPAARA-SHTDTEYLRYRNNIVTV 92 
                                    789999999*************9999988....679******.*******************.***************** PP

                        DUF4247  80 qkddtkgsdvlveidskggYrgYsGsiirrgkgftssgpsvgsgGs 125
                                     +d+t+++ ++ve + ++gY++  G++++ g+gft+++ps+gsgGs
  gi|121638484|ref|YP_978708.1|  93 GPDGTYPCIIRVE-NLSAGYNH--GAYVFLGPGFTPGSPSGGSGGS 135
                                    *************.********..*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1103.89
//
Query:       gi|121638485|ref|YP_978709.1|  [L=68]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-12   45.0   6.0    1.1e-11   44.7   6.0    1.1  1  DUF350    Domain of Unknown Function (DUF350)
  ------ inclusion threshold ------
      0.056   13.0   1.0      0.056   13.0   1.0    1.8  2  PGPGW     Putative transmembrane protein (PGPGW)
       0.24   11.9   4.7       0.39   11.2   4.7    1.4  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   6.0   1.8e-15   1.1e-11       1      54 []       7      61 ..       7      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.8e-15
                         DUF350  1 YgvvGivllllgffvfdllTpgklgelIkqgnn.AaaivlagviiglaiivaaAi 54
                                   Y++vG ++l++gf+++ llTpg+l++l+  ++  +a ++ a ++++lai+  aAi
  gi|121638485|ref|YP_978709.1|  7 YFLVGAAVLVAGFLMVNLLTPGDLRRLVFIDRRpNAVVLAATMYVALAIVTIAAI 61
                                   9******************************99899999999************9 PP

>> PGPGW  Putative transmembrane protein (PGPGW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   9.4e-06     0.056       2      25 ..       5      28 ..       4      36 .. 0.80
   2 ?   -1.3   0.2      0.26   1.5e+03      31      32 ..      53      54 ..      42      65 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-06
                          PGPGW  2 vlvlvlGwvvvvvGiiliplPGPG 25
                                   vl  ++G++v+v+G++++ l  PG
  gi|121638485|ref|YP_978709.1|  5 VLYFLVGAAVLVAGFLMVNLLTPG 28
                                   56789************9775555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                          PGPGW 31 lG 32
                                   l+
  gi|121638485|ref|YP_978709.1| 53 LA 54
                                   22 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.7   6.5e-05      0.39      19      62 ..       7      65 ..       2      68 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.5e-05
                         DUF202 19 alialglallrffl................tgepsalgkilglilivlgiltllvglvry 62
                                   ++++ +++l++ fl                +  p+a  +++++++++l+i+t++  + ++
  gi|121638485|ref|YP_978709.1|  7 YFLVGAAVLVAGFLmvnlltpgdlrrlvfiDRRPNA-VVLAATMYVALAIVTIAAIYASW 65
                                   555555555554444555568888888875444444.5888999********99877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 477.31
//
Query:       gi|121638486|ref|YP_978710.1|  [L=59]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-11   42.3   7.0    6.5e-11   42.2   7.0    1.0  1  DUF350    Domain of Unknown Function (DUF350)


Domain annotation for each model (and alignments):
>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   7.0   3.7e-15   6.5e-11       1      54 []       4      58 ..       4      58 .. 0.99

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.7e-15
                         DUF350  1 YgvvGivllllgffvfdllTpgklgelIkqgnn.AaaivlagviiglaiivaaAi 54
                                   Yg+vG++l+ ++++++++ +pg+++e+I +  + +a +++a++++++a ++aaA+
  gi|121638486|ref|YP_978710.1|  4 YGIVGVALQGVALVILEIAVPGRFREHIDAPALhPAVFATAVMLLAVAGVIAAAL 58
                                   9******************************99********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 431.32
//
Query:       gi|121638487|ref|YP_978711.1|  [L=523]
Description: spermidine synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-31  109.4   0.0      2e-31  108.9   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    2.4e-05   24.9   0.0    5.4e-05   23.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0022   18.6   0.0     0.0051   17.4   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
       0.09   13.5   0.0       0.19   12.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0   4.4e-35     2e-31      16     173 ..     301     460 ..     287     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 4.4e-35
                                    SSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS...- CS
                 Spermine_synth  16 hknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgdgfkflkayek...k 92 
                                    + + + vL++GGgDG ++re+++ + +e+i+ v++D  vi++ +  l+++++++++++rv++v++d++  l+  ++    
  gi|121638487|ref|YP_978711.1| 301 D-GARSVLVLGGGDGLAARELLRQPGIEQIVQVELDPAVIELARTTLRDVNAGSLDNPRVHVVIDDAMSWLRGAAVppaG 379
                                    3.589*************************************************************************9* PP

                                    EEEEEEECCSTTCSSCG.CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEEEEEEEETTTSCSC CS
                 Spermine_synth  93 fdvvivdsldpvgpaen.lFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqvepsavlvPtylsg 171
                                    fd+vivd+ dp +p    l+s ef+ l +++l ++G++++qa +p  +   +  +  +++++    v p+ v vPt+  +
  gi|121638487|ref|YP_978711.1| 380 FDAVIVDLRDPDTPVLGrLYSTEFYALAARALAPGGLMVVQAGSPYSTPTAFWRIISTIRSAGY-AVTPYHVHVPTFGDW 458
                                    **************9999********************************************99.9**********9887 PP

                                    EE CS
                 Spermine_synth 172 mi 173
                                    + 
  gi|121638487|ref|YP_978711.1| 459 GF 460
                                    65 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.2e-08   5.4e-05       1      97 []     306     415 ..     306     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH......TTTTEEEEESBCCGBS....SSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee......eglnvefvqgdaedlp....fedgsfDlvvs 70 
                                    vL lG G G  +++l+++ g ++++ v+++++ +e ar+ +++      ++++v++v  da ++      + + fD+v++
  gi|121638487|ref|YP_978711.1| 306 VLVLGGGDGLAARELLRQPGIEQIVQVELDPAVIELARTTLRDvnagslDNPRVHVVIDDAMSWLrgaaVPPAGFDAVIV 385
                                    899***************88******************99999766555556*********886424447999******9 PP

                                    ..EST.GGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  71 ..sga.lhhlsdedlekalkeiarvLkpgG 97 
                                      +     +l +    ++++ +ar+L pgG
  gi|121638487|ref|YP_978711.1| 386 dlRDPdTPVLGRLYSTEFYALAARALAPGG 415
                                    221112223444445667788888888887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0051       1      96 []     307     419 ..     307     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCC....TSS-TT-EEEEEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......kvefvvadaek....lpfednsfDlvvss 68 
                                    L +G G G+ a++l ++   +++v v+l++++++la++  ++ +       +v +v  da +      ++ + fD+v++ 
  gi|121638487|ref|YP_978711.1| 307 LVLGGGDGLAARELLRQPgiEQIVQVELDPAVIELARTTLRDVNAgsldnpRVHVVIDDAMSwlrgAAVPPAGFDAVIVD 386
                                    5689***********7767*******************999999999999999999999997744456999*******99 PP

                                    S......-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  69 e......vlhhvedpekalkeiaRvLkpgGllvi 96 
                                           vl  +    ++ + +aR L pgGl+v+
  gi|121638487|ref|YP_978711.1| 387 LrdpdtpVLGRL-YSTEFYALAARALAPGGLMVV 419
                                    988888888888.589999999999999999885 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05      0.19       1      71 [.     307     384 ..     307     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.......ssfDlvv 71 
                                    L +G+G+G  +r+ll++    +++ v+++p++ie a++ l++ ++ + +n ++ +  ++  +         + fD+v+
  gi|121638487|ref|YP_978711.1| 307 LVLGGGDGLAARELLRQPGIEQIVQVELDPAVIELARTTLRDVNAGSLDNPRVHVVIDDAMSWLrgaavppAGFDAVI 384
                                    569**************5555566****************99999888887776655443333355777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3921.03
//
Query:       gi|121638488|ref|YP_978712.1|  [L=95]
Description: hypothetical protein BCG_2626 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.033   14.1   0.0    1.4  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
      0.068   13.7   1.1      0.087   13.4   0.0    1.7  2  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.6e-06     0.033       8      36 ..       7      35 ..       2      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-06
                          RHH_5  8 LPeelleeLeewAdeegRsvSnlaafLve 36
                                   LP+el+ ++++ A+++gR +  +++ L+ 
  gi|121638488|ref|YP_978712.1|  7 LPDELMRAIKVRAAQQGRKMKDVVTELLR 35
                                   9*****************87666655555 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.7e-06     0.087      46      77 ..       4      35 ..       1      37 [. 0.89
   2 ?   -1.8   0.2      0.52   4.6e+03      11      20 ..      82      91 ..      80      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.7e-06
                 CopG_antitoxin 46 slrlpedlLealkekAnkrdvpyqslikelle 77
                                   +l lp +l+ a+k++A +++  ++  + ell+
  gi|121638488|ref|YP_978712.1|  4 TLDLPDELMRAIKVRAAQQGRKMKDVVTELLR 35
                                   699*****************999999988887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.52
                 CopG_antitoxin 11 eeeeFwekhD 20
                                   +e+++w+ hD
  gi|121638488|ref|YP_978712.1| 82 QEAQWWSGHD 91
                                   6789999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 728.12
//
Query:       gi|121638489|ref|YP_978713.1|  [L=146]
Description: hypothetical protein BCG_2627 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-12   48.4   0.0    1.4e-12   48.2   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   7.9e-17   1.4e-12       2     120 ..       3     137 ..       2     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 7.9e-17
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHS..............SCHCHHHHHHHHHHHH CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel...eelvtsalvlaEllyvlar..............rkskrekaaelvelll 63 
                                    + DT++++al  +g+++++a+r++l+ +   + ++++ ++ + ll+ l++              r+ +  +aa l ++++
  gi|121638489|ref|YP_978713.1|   3 LCDTNIWLALAlSGHVHHRASRAWLDTInapGVIHFCRATQQSLLRLLTNrtvlgaygsppltnREAWAAYAAFLDDDRI 82 
                                    68********9*********************************************966666544444455555555555 PP

                                    HHHTSEEEEBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  64 llsalkilpidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                     l++ +     +++ ++++++a + +   + + Da++aA A+  g++l+ t D+ f +++
  gi|121638489|ref|YP_978713.1|  83 VLAGAEP----DGLEAQWRAFAVRQSpapKVWMDAYLAAFALTGGFELV-TTDTAFTQYG 137
                                    5555554....444455555555555559********************.******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1005.92
//
Query:       gi|121638490|ref|YP_978714.1|  [L=251]
Description: hypothetical protein BCG_2628c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-88  294.9   0.0    4.6e-88  294.7   0.0    1.0  1  Transcrip_reg  Transcriptional regulator


Domain annotation for each model (and alignments):
>> Transcrip_reg  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.7   0.0   2.6e-92   4.6e-88       1     240 []       5     238 ..       5     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 294.7 bits;  conditional E-value: 2.6e-92
                                    .XCHHCCCCCCHCCCCHHHHHHHHHHHHHHHHHTHH-S-GGG-HHHHHHHHHHHHTT--HHHHHHHHHHCCSTS.TS.-- CS
                  Transcrip_reg   1 skWsnikhkKaandakkgklftklakeItvaakeeggpDpesNprLraaiekakkanvpkdnIeraIkkgageksegany 80 
                                    skW+++khkKa  da++gk+f++l+k+I+vaa+  gg+Dp++Np+L +ai+kakk++vp++nIera k+gage+++ga+ 
  gi|121638490|ref|YP_978714.1|   5 SKWATTKHKKAVVDARRGKMFARLIKNIEVAARV-GGGDPAGNPTLYDAIQKAKKSSVPNENIERARKRGAGEEAGGADW 83 
                                    8********************************6.999**********************************98888*** PP

                                    EEEEEEEEETTTEEEEEEEEES-HHHHHHHHHHHHHHTT-EEE-TTSSGGGEEEEEEEEEECCHCT-HHHHHHHHHHHHT CS
                  Transcrip_reg  81 eevtyegygpggvavivealTdnknrtaaevrsifsknggnlgesgsvsflFerkgvivveekeeevdedelleaaieaG 160
                                    ++++yegy+p+gvav++e+lTdn+nr+a+evr ++++ngg+++++gsvs+lF+rkgv+++e++  + +ed++l a++eaG
  gi|121638490|ref|YP_978714.1|  84 QTIMYEGYAPNGVAVLIECLTDNRNRAASEVRVAMTRNGGTMADPGSVSYLFSRKGVVTLEKN--GLTEDDVLAAVLEAG 161
                                    ************************************************************554..9************** PP

                                    ESEEEEETTTC.EEEEEEGGGHHHHHHHHHHTTT---SEEEEEEEESS-EE--HHHHHHHHHHHHHHHTSTTEEEEEESE CS
                  Transcrip_reg 161 aeDveedeeeevievitepedlaavkkaLeeagglevesaeleyipkeeveldeeeaekleklidaLeeldDVqnvytNi 240
                                    aeDv++    +++evi ep++l av++aL++a g+++esae ++ p+  v +d + a+k+ kl+daLe+ dDVqnv+tN+
  gi|121638490|ref|YP_978714.1| 162 AEDVND--LGDSFEVISEPAELVAVRSALQDA-GIDYESAEASFQPSVSVPVDLDGARKVFKLVDALEDSDDVQNVWTNV 238
                                    *****6..3689********************.578*******************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1887.62
//
Query:       gi|121638491|ref|YP_978715.1|  [L=198]
Description: glutamine amidotransferase subunit PdxT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-58  197.6   0.0    1.9e-58  197.4   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    2.6e-08   33.7   0.0    5.9e-08   32.5   0.0    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    8.5e-05   22.3   0.0    0.00012   21.8   0.0    1.2  1  Peptidase_S51  Peptidase family S51


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.4   0.0   3.2e-62   1.9e-58       1     186 [.       8     194 ..       8     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.4 bits;  conditional E-value: 3.2e-62
                                    EESSSSSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHH CS
                            SNO   1 vlalqGaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlil 80 
                                    vlalqG+ +eh  a+++c+ae +tv+r+++l+ vdal+iPGGest+ms+l+   +l+ +l++ ++++ ++ +G CaG+il
  gi|121638491|ref|YP_978715.1|   8 VLALQGDTREHLAALRECGAEPMTVRRRDELDAVDALVIPGGESTTMSHLLLDLDLLGPLRARLADG-LPAYGSCAGMIL 86 
                                    8******************************************************************.************ PP

                                    HCCEETTB.....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEE CS
                            SNO  81 lskelene.....lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldgeiv 155
                                    l+ e+        +   l  ++++v+rnafG qvdsfe +++f +l++++ avfiraP +e+++  + v+vl    g+iv
  gi|121638491|ref|YP_978715.1|  87 LASEILDAgaagrQALPLRAMNMTVRRNAFGSQVDSFEGDIEFAGLDDPVRAVFIRAPWVERVG--DGVQVLARAAGHIV 164
                                    **9986555566688889**********************************************..889*********** PP

                                    EEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                            SNO 156 vakqkkilatsfhPelaeddirvhdyfveev 186
                                    +++q+ +lat+fhPe++ d  r+h++fv+ v
  gi|121638491|ref|YP_978715.1| 165 AVRQGAVLATAFHPEMTGD-RRIHQLFVDIV 194
                                    *****************99.9*******865 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   9.8e-12   5.9e-08      17      98 ..      20      97 ..      13     118 .. 0.84
   2 ?   -2.3   0.0      0.48   2.9e+03     169     188 ..     158     177 ..     145     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 9.8e-12
                       GATase_3 17 dpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegv 98
                                    +L++ +++ +  v+ ++++l++ +d++++pGg++t+ +  ll+  +l   +++ +++g p +g C+G+++L +ei d+   
  gi|121638491|ref|YP_978715.1| 20 AALRECGAEPM-TVR-RRDELDA-VDALVIPGGESTTMSHLLLDL-DLLGPLRARLADGLPAYGSCAGMILLASEILDAGAA 97
                                   67777665554.455.6889976.********************9.9999**************************998644 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.48
                       GATase_3 169 ekdGavkksedgnvlGtYlH 188
                                    ++ G +   ++g vl+t +H
  gi|121638491|ref|YP_978715.1| 158 RAAGHIVAVRQGAVLATAFH 177
                                    66777777788899999888 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.1e-08   0.00012      78     134 ..      36      92 ..      17     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-08
                                    HHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-G CS
                  Peptidase_S51  78 eklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesie 134
                                    + l + d++++ GG+   + +ll + +l  +lr ++++gl+  G+ AG i  +++i 
  gi|121638491|ref|YP_978715.1|  36 DELDAVDALVIPGGESTTMSHLLLDLDLLGPLRARLADGLPAYGSCAGMILLASEIL 92 
                                    34667*******************************************999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1433.52
//
Query:       gi|121638492|ref|YP_978716.1|  [L=281]
Description: acyl-CoA thioesterase II tesB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-55  184.9   0.0    9.3e-48  161.4   0.0    3.0  2  Acyl_CoA_thio  Acyl-CoA thioesterase
    2.7e-53  181.8   1.3    3.3e-53  181.5   1.3    1.0  1  4HBT_3         Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> Acyl_CoA_thio  Acyl-CoA thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-07    0.0031      48     131 ..      56     112 ..      16     113 .. 0.79
   2 !  161.4   0.0     1e-51   9.3e-48       3     132 .]     141     269 ..     139     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-07
                                    CCCHHHHHTTSSSGGGGGGGGTTTSTTEEEEEEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEEEEE. CS
                  Acyl_CoA_thio  48 hsvllaYlSDltllltalttHelledslqvsldHsvyFlrpgdlnewilydvespsasggrgLrqGriFstqdgklias. 126
                                    hs+                              H  yFlrpgd++e  ++ ve+    +g  L   r+ ++q+g++i+s 
  gi|121638492|ref|YP_978716.1|  56 HSL------------------------------HG-YFLRPGDAKERTVFLVER--IRDGGSLCTRRVNAVQHGETIFSm 102
                                    333..............................88.******************..77888899999999*********8 PP

                                    .....EEEEE CS
                  Acyl_CoA_thio 127 .....vqqeG 131
                                         + qeG
  gi|121638492|ref|YP_978716.1| 103 aasfqTEQEG 112
                                    8888888887 PP

  == domain 2  score: 161.4 bits;  conditional E-value: 1e-51
                                    CTCCEC-.SEEEECSSSSBTTCHHHHHEECCCCCCCCTS-TTHCCCCCHHHHHTTSSSGGGGGGGGTTTSTTEEE.EEEE CS
                  Acyl_CoA_thio   3 kelfeleypvevrpkelkrefgGqvvaekqsllrakktvPddallhsvllaYlSDltllltalttHelledslqv.sldH 81 
                                      ++++e++v++ p+e+ r ++G+ + ++q++lr+++ +Pdd++lh+++laY+SDltll +a+++H +++d+lqv sldH
  gi|121638492|ref|YP_978716.1| 141 GFRQFDEWDVCIVPRERLRLLPGKAS-QQQVWLRHRDPLPDDPVLHICALAYMSDLTLLGSAQVNHLDVRDQLQVaSLDH 219
                                    56899*******************55.5**************************************************** PP

                                    EEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEEECTTEEEEEEEEEEE CS
                  Acyl_CoA_thio  82 svyFlrpgdlnewilydvespsasggrgLrqGriFstqdgkliasvqqeGl 132
                                    +++F+rp++++ew+lyd++spsasggr+L++G+iF t++g+++a+v+qeGl
  gi|121638492|ref|YP_978716.1| 220 AMWFMRPFRADEWLLYDQSSPSASGGRALTRGEIF-TRSGEMVAAVMQEGL 269
                                    ***********************************.*************96 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   1.3   3.7e-57   3.3e-53      11     247 ..      32     269 ..      24     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 3.7e-57
                                    .-HHHHHHHHHHHHHHT.-S.SS..EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETTEEEEEEEEEEE--- CS
                         4HBT_3  11 gyGGyvlAlalraaqrtvpdprl..hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqggrpiftatasfgrae 87 
                                     +GG v+++ l  a rtv dpr+  hslh+yFlrpgda+ + ++ ver+rdG s +tr+v + q+g++if++ asf++++
  gi|121638492|ref|YP_978716.1|  32 TFGGHVAGQSLVSAVRTV-DPRYmvHSLHGYFLRPGDAKeRTVFLVERIRDGGSLCTRRVNAVQHGETIFSMAASFQTEQ 110
                                    4****************9.454457******************************************************* PP

                                    T....---EE-------.GGGE---.--SSGGGSGG..TEEEE-HHT-.--S.........S-EEEEEEEET...TTS-S CS
                         4HBT_3  88 stgwelepaaapppvpppdeaalaadeaplplfrrvpgflepfeprpa.egg..kpdspagpkrvrqWvrlr...eggep 161
                                    + g   ++++ +p+ pppd  +      +++ f+ + gf ++ e+  +  ++   +  p + +++++W+r r   ++++ 
  gi|121638492|ref|YP_978716.1| 111 E-G--ITHQDVMPAAPPPDGLPG---LNSIKVFDDA-GFRQFDEWDVCiVPRerLRLLPGKASQQQVWLRHRdplPDDPV 183
                                    8.6..556678999999999966...2334444422.344444444332111212225556778889*****99877899 PP

                                    SHHHHHHHHTT-....-GGGGTSS-......SB--EEEEEEEE-S--.S-...EEEEEE-SEEETTEEEEEEEEE-TTS- CS
                         4HBT_3 162 ahlaaLaylsDs.f..pvprvhglrldaeasgwmpsldltiyfhrep.aedeWllleaetpwagdgrglvearlwdedGr 237
                                    +h +aLay+sD  +    + v++l  + ++   ++sld++++f r p ++deWll++ ++p+a++gr+l+++++++++G+
  gi|121638492|ref|YP_978716.1| 184 LHICALAYMSDLtLlgS-AQVNHLDVR-DQ-LQVASLDHAMWFMR-PfRADEWLLYDQSSPSASGGRALTRGEIFTRSGE 259
                                    ************77753.555555543.44.899***********.63569***************************** PP

                                    EEEEEEEEEE CS
                         4HBT_3 238 lvAtstQegl 247
                                    +vA + Qegl
  gi|121638492|ref|YP_978716.1| 260 MVAAVMQEGL 269
                                    ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2089.34
//
Query:       gi|121638493|ref|YP_978717.1|  [L=299]
Description: pyridoxal biosynthesis lyase PdxS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.5e-106  354.8   3.3   1.9e-106  354.5   3.3    1.1  1  SOR_SNZ       SOR/SNZ family
    4.6e-05   22.8   8.9    0.00018   20.9   1.1    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    6.6e-05   22.2   0.0      0.029   13.5   0.0    2.2  2  Dus           Dihydrouridine synthase (Dus)
     0.0001   21.9   0.5     0.0045   16.5   0.1    2.8  2  His_biosynth  Histidine biosynthesis protein
     0.0017   17.8   1.6     0.0017   17.8   1.6    1.8  2  NMO           Nitronate monooxygenase
     0.0049   16.1   1.5      0.023   13.9   0.1    2.5  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0051   15.9   0.4      0.011   14.8   0.4    1.5  1  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.029   13.5   0.4      0.048   12.8   0.4    1.3  1  Glu_synthase  Conserved region in glutamate synthase
      0.032   13.4   0.0       0.27   10.3   0.0    2.1  2  IGPS          Indole-3-glycerol phosphate synthase
       0.12   12.4   0.0       0.29   11.2   0.0    1.6  1  TetR_C_27     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.5   3.3  1.1e-109  1.9e-106       2     207 .]      12     217 ..      11     217 .. 0.99

  Alignments for each domain:
  == domain 1  score: 354.5 bits;  conditional E-value: 1.1e-109
                                    THHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT- CS
                        SOR_SNZ   2 lkvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGh 81 
                                    ++vk+g+aemlkgGvimdvv++eqa+iae aGavavmalervpadir++ggv+rmsdp++i+ i++av+ipvmakvriGh
  gi|121638493|ref|YP_978717.1|  12 ARVKRGMAEMLKGGVIMDVVTPEQARIAEGAGAVAVMALERVPADIRAQGGVSRMSDPDMIEGIIAAVTIPVMAKVRIGH 91 
                                    689***************************************************************************** PP

                                    HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHH CS
                        SOR_SNZ  82 fveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrk 161
                                    fveaqil++lgvdyiDesevltpad ++hidk++f+vpfvcGa+nlgealrri+eGaamir+kGeagtGdv++a +h+r+
  gi|121638493|ref|YP_978717.1|  92 FVEAQILQTLGVDYIDESEVLTPADYAHHIDKWNFTVPFVCGATNLGEALRRISEGAAMIRSKGEAGTGDVSNATTHMRA 171
                                    ******************************************************************************** PP

                                    HHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                        SOR_SNZ 162 ikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                    i  eir+l+s+se+el+ +akel+ap+elv+eva++g+lpv  f+a
  gi|121638493|ref|YP_978717.1| 172 IGGEIRRLTSMSEDELFVAAKELQAPYELVAEVARAGKLPVTLFTA 217
                                    *******************************************987 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   1.4    0.0035       6.3     137     200 ..      36     105 ..      21     119 .. 0.81
   2 !   20.9   1.1     1e-07   0.00018     165     224 ..     198     260 ..     189     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0035
                                    HHHHHHTT-SEBEEB...SSSTTS----...S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SE CS
                           ThiG 137 arrleevGcaavmPl...aapiGsglGl...lnkealkiiieeakvPvivDAGigspsdaaqamelGada 200
                                    ar  e +G+ avm l    a i +  G+   +++ +++ ii+ +++Pv+    ig+  +a     lG+d 
  gi|121638493|ref|YP_978717.1|  36 ARIAEGAGAVAVMALervPADIRAQGGVsrmSDPDMIEGIIAAVTIPVMAKVRIGHFVEAQILQTLGVDY 105
                                    666788999999987333588887777611156889**********************999999999985 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1e-07
                                    HHHHHHHHH-.SS-BEE..ES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                           ThiG 165 ealkiiieea.kvPviv..DAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                    + l   +++a k+Pv +    Gi +p daa+ m+lGa++v++ + + ++  p + A+a+ +a+
  gi|121638493|ref|YP_978717.1| 198 YELVAEVARAgKLPVTLftAGGIATPADAAMMMQLGAEGVFVGSGIFKSGAPEHRAAAIVKAT 260
                                    5555545555578875522569************************************99886 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0021       3.7      95     133 ..      57      91 ..      53     102 .. 0.82
   2 !   13.5   0.0   1.6e-05     0.029     169     217 ..     195     244 ..     180     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0021
                                    TTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESES CS
                            Dus  95 trggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigi 133
                                    +r ++G + + +pd+++ i++    av iPv +k+rig 
  gi|121638493|ref|YP_978717.1|  57 IRAQGGVSRMSDPDMIEGIIA----AVTIPVMAKVRIGH 91 
                                    567788889999999999887....578*********95 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                                    G--CHHHHHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                            Dus 169 tadweaIkevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                    +a +e ++ev +a +  ++++  G+I ++ da  +++  Ga+gv +g g  
  gi|121638493|ref|YP_978717.1| 195 QAPYELVAEVARAGKlpVTLFTAGGIATPADAAMMMQL-GAEGVFVGSGIF 244
                                    78899999999976655999************998888.********9964 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.54   9.6e+02      59      78 ..      66      85 ..      47     106 .. 0.54
   2 !   16.5   0.1   2.5e-06    0.0045      59     108 ..     195     246 ..     187     299 .] 0.60

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.54
                                   HHHHHHHHHHHHH-SSEEEE CS
                   His_biosynth 59 eanldlveeiaeevfipvqv 78
                                     + d++e i+ +v+ipv+ 
  gi|121638493|ref|YP_978717.1| 66 MSDPDMIEGIIAAVTIPVMA 85
                                   23334555555555555544 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.5e-06
                                    HHHHHHHHHHHHH-SSEEEE..ESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                   His_biosynth  59 eanldlveeiaeevfipvqv..GGGIrsledveelleagadkviigtaavkn 108
                                    +a ++lv+e+a++ ++pv++   GGI +  d++ ++++ga+ v +g+  +k+
  gi|121638493|ref|YP_978717.1| 195 QAPYELVAEVARAGKLPVTLftAGGIATPADAAMMMQLGAEGVFVGSGIFKS 246
                                    55678999999998876664339****************8877777664433 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4      0.57     1e+03     183     198 ..      70      85 ..      26      90 .. 0.78
   2 !   17.8   1.6   9.3e-07    0.0017     182     226 ..     198     244 ..     188     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.57
                            NMO 183 aLvpqvldavdiPviA 198
                                     +++ +  av iPv+A
  gi|121638493|ref|YP_978717.1|  70 DMIEGIIAAVTIPVMA 85 
                                    5677888999999998 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.3e-07
                            NMO 182 faLvpqvldavdiPv..iAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                     +Lv++v+ a ++Pv    aGGi +  + a ++ lGA+gv +g+   
  gi|121638493|ref|YP_978717.1| 198 YELVAEVARAGKLPVtlFTAGGIATPADAAMMMQLGAEGVFVGSGIF 244
                                    6899********9974469************************9876 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.14   2.4e+02     134     168 ..      69     104 ..      23     125 .. 0.55
   2 !   13.9   0.1   1.3e-05     0.023     133     178 ..     197     245 ..     141     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                    HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--S CS
                           NanE 134 falvkalsea.glkviaeGrintPekakkaieiGvd 168
                                     ++++ + +a  + v+a  ri    +a+    +Gvd
  gi|121638493|ref|YP_978717.1|  69 PDMIEGIIAAvTIPVMAKVRIGHFVEAQILQTLGVD 104
                                    223333332213334444444444444444444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                                    -HHHHHHHHHTT...--EEEES---SHHHHHHHHTT--SEEEE-HHHH- CS
                           NanE 133 Dfalvkalseag...lkviaeGrintPekakkaieiGvdavvvGsaitr 178
                                     ++lv ++  ag   +++ + G i tP+ a+ ++++G++ v vGs i +
  gi|121638493|ref|YP_978717.1| 197 PYELVAEVARAGklpVTLFTAGGIATPADAAMMMQLGAEGVFVGSGIFK 245
                                    577888888776333458899************************9865 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   6.3e-06     0.011     255     302 ..     195     242 ..     190     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-06
                                    --HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                         FMN_dh 255 patidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                    +a+ +   e+++a +  ++++  gGi + +D++  + lGA++v++G  
  gi|121638493|ref|YP_978717.1| 195 QAPYELVAEVARAGKLPVTLFTAGGIATPADAAMMMQLGAEGVFVGSG 242
                                    67888899999999999*****************************76 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.7e-05     0.048     275     305 ..     212     242 ..     200     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                    -EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                   Glu_synthase 275 vsliadGglktgadvvkalalGAdavgigta 305
                                    v+l+++Gg+ t+ad ++ + lGA+ v +g++
  gi|121638493|ref|YP_978717.1| 212 VTLFTAGGIATPADAAMMMQLGAEGVFVGSG 242
                                    89************************99986 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.16   2.8e+02      61      86 ..      23      48 ..      14      53 .. 0.88
   2 ?   10.3   0.0   0.00015      0.27     208     246 ..     210     248 ..     191     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                                   TEESBSS--HHHHHHHHTTT.-SEEE CS
                           IGPS 61 kgliredfdpaeiAkkyeeagAsaiS 86
                                   kg + +d++ +e+A+  e agA a+ 
  gi|121638493|ref|YP_978717.1| 23 KGGVIMDVVTPEQARIAEGAGAVAVM 48
                                   788999************99999875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                                    TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TT CS
                           IGPS 208 kdvllvaeSGiktredveklkeegvnafLvGeslmrqed 246
                                      v+l +  Gi+t++d+ ++ + g++++ vG+ + ++  
  gi|121638493|ref|YP_978717.1| 210 LPVTLFTAGGIATPADAAMMMQLGAEGVFVGSGIFKSGA 248
                                    347889999***********************9988755 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.29      61      95 ..     240     274 ..     231     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                    HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                      TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                     +G Fk+  pe  a a+++at+ f +P ++a+ s+
  gi|121638493|ref|YP_978717.1| 240 GSGIFKSGAPEHRAAAIVKATTFFDDPDVLAKVSR 274
                                    689**************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2034.92
//
Query:       gi|121638494|ref|YP_978718.1|  [L=224]
Description: pyridoxamine 5'-phosphate oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-16   59.1   0.0      6e-16   58.4   0.0    1.4  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    9.8e-14   51.2   1.0      2e-13   50.1   1.0    1.6  1  PNP_phzG_C      Pyridoxine 5'-phosphate oxidase C-terminal di


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   6.7e-20     6e-16       2      88 .]      50     134 ..      49     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 6.7e-20
                                    HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEE CS
                 Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGta 81 
                                     ++ r+ ++e++a+vlATv +dG+P  + vl k +d+  g  f+t++ s+k+++l+  p+++ +f +++lgr+ +++G +
  gi|121638494|ref|YP_978718.1|  50 NDAQRAGVSEPNAMVLATV-ADGKPVTRSVLCKILDES-GVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPV 127
                                    57789999***********.******************.***************************************** PP

                                    EEESCHH CS
                 Putative_PNPOx  82 elvsdge 88 
                                     +vs +e
  gi|121638494|ref|YP_978718.1| 128 SKVSTEE 134
                                    ***9876 PP

>> PNP_phzG_C  Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   1.0   2.3e-17     2e-13       1      43 []     188     224 .]     188     224 .] 0.86

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.3e-17
                     PNP_phzG_C   1 WgGyrvvPeeiEFWqgrpsRlHdRfrYereeedgkWkierLsP 43 
                                    WgGyr+ Pe +EFWqgr++R+H+R+r  + +     ++erL+P
  gi|121638494|ref|YP_978718.1| 188 WGGYRIAPEIVEFWQGRENRMHNRIRVAN-G-----RLERLQP 224
                                    **************************863.3.....4666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1462.52
//
Query:       gi|121638495|ref|YP_978719.1|  [L=580]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-77  260.1   0.6    1.7e-77  260.1   0.6    1.8  2  PE-PPE          PE-PPE domain
    2.6e-59  199.8  28.9    2.7e-59  199.8  26.9    1.9  2  PPE             PPE family
    7.7e-11   41.7  45.4    8.8e-06   25.5  22.7    2.6  2  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4      0.36   2.2e+03      45      68 ..     138     167 ..      77     191 .. 0.70
   2 !  260.1   0.6   2.8e-81   1.7e-77       1     227 []     300     525 ..     300     525 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.36
                         PE-PPE  45 a......agekvvvfGySqgalvasnekar 68 
                                    a      a + ++ fGy + a  +++++a 
  gi|121638495|ref|YP_978719.1| 138 AeyeqiwAQDVAAMFGYHSAASAVATQLAP 167
                                    123334466777788887777777666554 PP

  == domain 2  score: 260.1 bits;  conditional E-value: 2.8e-81
                         PE-PPE   1 PgadaelvsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa..p 78 
                                    Pg++a+++++P++f+p+tgl+slt+d+Sva+G++nL++ai+a+laag++vvvfG Sq+a++a+ e+++l++l  + +   
  gi|121638495|ref|YP_978719.1| 300 PGYTATFLETPSQFFPFTGLNSLTYDVSVAQGVTNLHTAIMAQLAAGNEVVVFGTSQSATIATFEMRYLQSLPAHLRpgL 379
                                    899********************************************************************999999899 PP

                         PE-PPE  79 dqlsfvlvgnpnrpnggllarfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGialv 158
                                    d+lsf+l+gnpnrp+gg+l+rf  g+ ip lg+t +gatp+d  y+Tvd+++qYDgv dfP+yplN++A++Nai+Gi ++
  gi|121638495|ref|YP_978719.1| 380 DELSFTLTGNPNRPDGGILTRF--GFSIPQLGFTLSGATPADA-YPTVDYAFQYDGVNDFPKYPLNVFATANAIAGILFL 456
                                    **********************..56*****************.************************************ PP

                         PE-PPE 159 HtnyetevaeqlpanirttvnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgYd 227
                                    H++    ++++l++++ ++v+s +  tty+l+p+++lPLl plr ++ +++pl+d+++++Lrvlv+lgYd
  gi|121638495|ref|YP_978719.1| 457 HSGL-IALPPDLASGVVQPVSSPDVLTTYILLPSQDLPLLVPLRAIPlLGNPLADLIQPDLRVLVELGYD 525
                                    **99.88889***********************************************************7 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.8  26.9   4.5e-63   2.7e-59       1     158 []       5     162 ..       5     162 .. 0.99
   2 ?   -1.3   0.0      0.35   2.1e+03     111     137 ..     341     368 ..     293     374 .. 0.68

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 4.5e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPEvnsa+++aG+g gp+laAa+aWdgLa+el++aa +++sv+++la++aW+Gp+s am++aa py+ WL++aa qa+
  gi|121638495|ref|YP_978719.1|   5 VLPPEVNSARIFAGAGLGPMLAAASAWDGLAEELHAAAGSFASVTTGLAGDAWHGPASLAMTRAASPYVGWLNTAAGQAA 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                    +aA qa+ aa+a+ea+laa+v+pa++aanr++la+lva+n++Gqn+paIaa+eaeye++waqd+aam +Y++a++a+a
  gi|121638495|ref|YP_978719.1|  85 QAAGQARLAASAFEATLAATVSPAMVAANRTRLASLVAANLLGQNAPAIAAAEAEYEQIWAQDVAAMFGYHSAASAVA 162
                                    **************************************************************************9975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                                    HHHHHHHHT-TTSTTHHH.HHHHHHHHH CS
                            PPE 111 aelaalvatnffGqntpa.Iaateaeye 137
                                    a+laa  +  +fG  ++a Ia+ e+ y 
  gi|121638495|ref|YP_978719.1| 341 AQLAAGNEVVVFGTSQSAtIATFEMRYL 368
                                    2333333334677655434888888884 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  22.7   1.5e-09   8.8e-06       6      39 ..     186     219 ..     181     219 .. 0.62
   2 !   24.5  20.6   3.1e-09   1.9e-05       1      39 [.     211     249 ..     211     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.5e-09
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+GsgN+G +N+G+ N+G++N+G+gN G+ n+G
  gi|121638495|ref|YP_978719.1| 186 GNLGSGNVGVGNIGNDNIGNANIGFGNRGDANIG 219
                                    5666666666666666666666666666666665 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.1e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN G++N+G gN+G+ NlG gNtG+ N+G g tG+g +G
  gi|121638495|ref|YP_978719.1| 211 GNRGDANIGIGNIGDRNLGIGNTGNWNIGIGITGNGQIG 249
                                    799999999999999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3972.60
//
Query:       gi|121638496|ref|YP_978720.1|  [L=351]
Description: hypothetical protein BCG_2634c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-22   78.3   0.4    4.6e-21   75.2   0.2    2.1  2  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.051   13.3   2.6      0.082   12.6   2.6    1.3  1  TPR_21    Tetratricopeptide repeat-like domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.051   4.5e+02       4      23 ..     106     126 ..      70     138 .. 0.82
   2 !   75.2   0.2   5.1e-25   4.6e-21       2     129 ..     177     318 ..     176     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.051
                                    EEEEEE.EEETTSEEEEEEES CS
                          NUDIX   4 ravgvv.llnekgevLlvrrs 23 
                                    +a+ +  l + + +vLl+rr+
  gi|121638496|ref|YP_978720.1| 106 PAALIAeLADAEARVLLARRF 126
                                    567777778888889999888 PP

  == domain 2  score: 75.2 bits;  conditional E-value: 5.1e-25
                                    EEEEEEEEEEETTSEEEEEEES.......SSSTTT......EESSEEECBTTSHHHHHHHHHHHHHHS..EEE.EEEEEE CS
                          NUDIX   2 lrravgvvllnekgevLlvrrs.......kkpfpg......WelPgGkvepgEtpeeAArREleEEtG..lea.ellell 65 
                                    +r ++ vvll++ g+vLl++ s       +    +      W ++gG v+pgE +++AA+REl+EEtG  + + +++  +
  gi|121638496|ref|YP_978720.1| 177 RRTSARVVLLDDSGAVLLLCGSdpanpafR----DgaapkwWFTVGGQVRPGERLAQAAARELAEETGlrVAPaDMIGPI 252
                                    7899****************9989955540....345556589**********999************554555****** PP

                                    EEEEEEEEEEEEEEEEEEEEEEEE.....EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                          NUDIX  66 grlhylapydgpygdeheilyvfl.....eevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                    +r ++++ ++g+  d +e+++v++      +v+g+ e++ +  ++++rw++ +++  ++l+a+ ++++p
  gi|121638496|ref|YP_978720.1| 253 WRRDEVFEFNGSLIDSEEFYLVHRtrrfePAVQGRTELE-RRYIRDARWCDANDI--AQLVAAGERVYP 318
                                    ***************888887777734335555555555.999************..777777666666 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.6   9.1e-06     0.082      10     119 ..       3     113 ..       1     134 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.1e-06
                         TPR_21  10 lilvgvvlalvglaGwqgwqdyqeeqaeeAsalYqqlqeaveakdaakakeaaeeladeyggtaYa.alaaLllAkaave 88 
                                    +++++ ++ lv l+++ +w + + ++ ++    Y+   +++++  a +a  a +  +d+ygg + +  laaL+ A + + 
  gi|121638496|ref|YP_978720.1|   3 WLVLAGAVLLVVLVAFGAWGYQTANRLNRLNVRYDLSWQSLDSALARRAVVARAVAIDAYGGAPQGsRLAALADAAEGAP 82 
                                    5677778889999*****************************999999999999999999998776268*********** PP

                         TPR_21  89 agdlaaAkaqLewvlekakdeelkalarlRL 119
                                    +   ++A+++L+++l+  + ++l a     L
  gi|121638496|ref|YP_978720.1|  83 RHARENAENELSAALAMVNPASLPAALIAEL 113
                                    **************99887777766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2518.48
//
Query:       gi|121638497|ref|YP_978721.1|  [L=378]
Description: Alpha-mannosyltransferase pimA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-31  108.1   0.4      1e-30  106.9   0.2    1.8  3  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-28   99.0   0.0    3.2e-28   98.4   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.6e-24   86.1   0.4    5.6e-24   85.1   0.4    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    3.4e-12   47.1   3.1    3.4e-12   47.1   3.1    2.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    7.8e-06   26.2   0.0      2e-05   24.9   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00013   22.0   0.0    0.00024   21.2   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   1.3e+04      66     100 ..      79     116 ..      72     149 .. 0.62
   2 ?   -2.3   0.0       1.9   5.6e+03      36      73 ..     141     179 ..     114     181 .. 0.58
   3 !  106.9   0.2   3.5e-34     1e-30       2     134 .]     189     333 ..     188     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                                    HHHHHHH-SEEEE--.-..--SHHHHHHHHTT-EEEE- CS
                Glyco_trans_1_4  66 laellaaadvfvaPs.e..gfglkllEamaaglpvVat 100
                                    ++++la+ d  v+ + e    +l++l    a+ p+Vat
  gi|121638497|ref|YP_978721.1|  79 VKKWLAHGDFDVLHLhEpnAPSLSMLALNIAEGPIVAT 116
                                    55666666655555553223445555555555566666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                                    EES---..HHHHHHHT....T-T.TEEEE---THHHHHHHH- CS
                Glyco_trans_1_4  36 ivGdgprpeeleelaa....gleerveftGfvedlaellaaa 73 
                                    ivG+    ++l ++ +    g ++ ve+   v d++++ +aa
  gi|121638497|ref|YP_978721.1| 141 IVGRIAV-SDLARRWQmealG-SDAVEIPNGV-DVDSFASAA 179
                                    5663321.2333322222223.2567777777.666666666 PP

  == domain 3  score: 106.9 bits;  conditional E-value: 3.5e-34
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---TH..HHHHHHH-SEEE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfved..laellaaadvfv 77 
                                    +++lf+Gr++e++kg+ +ll+a+p++ ++  dv+l+ivG g+ +++l+ +a +l+++ +f+G+v+d  +a+++++adv++
  gi|121638497|ref|YP_978721.1| 189 KTVLFLGRYDEPRKGMAVLLDALPKVVQRfpDVQLLIVGHGD-ADQLRGQAGRLAAHLRFLGQVDDagKASAMRSADVYC 267
                                    789******8899**************99855*******995.469*988878999********7788************ PP

                                    E--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT..-..HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  78 aPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppg..d..pealaeailrLled 134
                                    aP+   e+fg++l+Eamaag++vVa+d+ ++++v+  ge g lvp +  d  ++ala+ ++++le+
  gi|121638497|ref|YP_978721.1| 268 APNtggESFGIVLVEAMAAGTAVVASDLDAFRRVLrdGEVGHLVPVDppDlqAAALADGLIAVLEN 333
                                    ***9999**************************99**9***9998664433477888888888875 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   1.1e-31   3.2e-28      15     169 ..     188     344 ..     183     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.1e-31
                                    -EEEEEESS-.TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
                Glycos_transf_1  15 kkiilsvgrl.ekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                     k++l++gr  e++Kg ++l++a++++ ++  p+v+l+i+G   + ++l+ +a    l ++++flg+v++  + + +++a
  gi|121638497|ref|YP_978721.1| 188 GKTVLFLGRYdEPRKGMAVLLDALPKVVQR-FPDVQLLIVG-HGDADQLRGQAGR--LAAHLRFLGQVDDAGKASAMRSA 263
                                    57899****84578*************987.**********.5666999999665..566******************** PP

                                    SEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT....-HHHHHHHHHHHHHSHHHHHHHHHH CS
                Glycos_transf_1  94 difvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn....naealaeairklledeelrerlgen 168
                                    d++++p +  E+fGivl+EAmaag++v+as+   ++ v++dge G lv+      +a+ala++++ +le++ lrer+  +
  gi|121638497|ref|YP_978721.1| 264 DVYCAPNTGgESFGIVLVEAMAAGTAVVASDLDAFRRVLRDGEVGHLVPVDppdlQAAALADGLIAVLENDVLRERYVAA 343
                                    ******777************************************999766668*****************999988776 PP

                                    H CS
                Glycos_transf_1 169 a 169
                                    +
  gi|121638497|ref|YP_978721.1| 344 G 344
                                    6 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.4   1.9e-27   5.6e-24       1     169 [.      14     173 ..      14     174 .. 0.94
   2 ?   -3.6   0.0       3.1   9.4e+03     104     139 ..     228     268 ..     216     269 .. 0.64

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.9e-27
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                    +GGv+ hvl+La+ ++ rGh V+v++p++++++        +++vp ++  + +rl++ +a +r+++++l ++++Dv+H 
  gi|121638497|ref|YP_978721.1|  14 PGGVQSHVLQLAEVMRTRGHLVSVLAPASPHAALPDYfvSGGRAVPIPYNGSVARLRFGPATHRKVKKWLAHGDFDVLHL 93 
                                    59****************************99999977888888888888999999************************ PP

                 Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppek 158
                                    h p a  +++lal      p+V+t+H++         +++   +++ ++r ++ +    iavS+ ++++ +e +g +   
  gi|121638497|ref|YP_978721.1|  94 HEPNAPSLSMLALNI-AEGPIVATFHTST-------TKSLTLTVFQGILRPMHEKIVGRIAVSDLARRWQMEALGSD--- 162
                                    **************9.888**********.......7999999********************************55... PP

                 Glyco_transf_4 159 itVipnGvDle 169
                                     + ipnGvD++
  gi|121638497|ref|YP_978721.1| 163 AVEIPNGVDVD 173
                                    599******98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.1
                 Glyco_transf_4 104 Hglye.....krllkarlkplsrllralerrllrradrvia 139
                                    Hg ++      ++l a+l++l ++  a  + ++r+ad   a
  gi|121638497|ref|YP_978721.1| 228 HGDADqlrgqAGRLAAHLRFLGQVDDAGKASAMRSADVYCA 268
                                    55555555555566667777777777777777777777665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   3.1   1.1e-15   3.4e-12       1     142 [.      15     153 ..      15     169 .. 0.69
   2 ?   -0.9   2.4      0.66     2e+03      81      81 ..     270     270 ..     167     362 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.1e-15
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape.leedgvrvhrlpvprrpspladlaal....ralrrllrqrrerpd 75 
                                    gG++ +v +la+ ++ rGh V vl+pa + +a + +   g r   +p+p+++s +a+l++     r ++ +l  ++  +d
  gi|121638497|ref|YP_978721.1|  15 GGVQSHVLQLAEVMRTRGHLVSVLAPASPHAALPdYFVSGGRA--VPIPYNGS-VARLRFGpathRKVKKWL--AHGDFD 89 
                                    8************************988777554344445554..67777764.566664422226778888..****** PP

                Glyco_trans_4_4  76 vvhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeae 142
                                    v+h+h+p a+++ +la   +  p+v t+h+ ++ +       +++ + r +     + ++vs+  ++
  gi|121638497|ref|YP_978721.1|  90 VLHLHEPNAPSLSMLALNIAEGPIVATFHTSTTKSL---TLTVFQGILRPMHEKIVGRIAVSDLARR 153
                                    *****************899*********7654433...3334444444444444444444444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                Glyco_trans_4_4  81 s 81 
                                    +
  gi|121638497|ref|YP_978721.1| 270 N 270
                                    2 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   6.6e-09     2e-05       9      91 ..     274     361 ..     251     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.6e-09
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe......dleelaekiryllanpeerraiaeaarervlaeht 82 
                                    es+  +l+Ea+a+G+ ++++d +++++ +++g+ + l+         + la+ + ++l+n+ +r++  +a+ + v ++++
  gi|121638497|ref|YP_978721.1| 274 ESFGIVLVEAMAAGTAVVASDLDAFRRVLRDGEVGHLVPvdppdlQAAALADGLIAVLENDVLRERYVAAGNAAV-RRYD 352
                                    78999****************************66666562665555667888999************9999995.799* PP

                Glyco_trans_1_2  83 ydhraeqll 91 
                                    +   a q++
  gi|121638497|ref|YP_978721.1| 353 WSVVASQIM 361
                                    ****99997 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     8e-08   0.00024      11     111 ..      19     122 ..      12     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8e-08
                Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkga..kdeleaegihvhrlkvdrkg...pleylkafklkklikkikPDvvhahyakp 85 
                                     h+l+la+ ++ rg+ V+v+ p  ++    + +  g +  +++ + ++    ++ ++ +k+kk ++   +Dv+h+h+++ 
  gi|121638497|ref|YP_978721.1|  19 SHVLQLAEVMRTRGHLVSVLAPASPHaaLPDYFVSGGRAVPIPYNGSVarlRFGPATHRKVKKWLAHGDFDVLHLHEPNA 98 
                                    599999****************6666577788899*******98866643466666789*******************99 PP

                Glyco_trans_4_2  86 ygllgslaar.lsgvipvvlsvwGldv 111
                                    + l  s++a+ ++   p+v++++ + +
  gi|121638497|ref|YP_978721.1|  99 PSL--SMLALnIAE-GPIVATFHTSTT 122
                                    876..445562555.9*******7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2460.53
//
Query:       gi|121638498|ref|YP_978722.1|  [L=316]
Description: lipid A biosynthesis lauroyl acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-101  339.6   0.0   1.7e-101  339.3   0.0    1.0  1  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera
  ------ inclusion threshold ------
      0.045   13.8   0.2      0.087   12.9   0.2    1.4  1  SUKH-4           SUKH-4 immunity protein


Domain annotation for each model (and alignments):
>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.3   0.0  1.9e-105  1.7e-101       4     294 ..      12     302 ..      10     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.3 bits;  conditional E-value: 1.9e-105
                Lip_A_acyltrans   4 fkkellhlrywlvwlgiavllllallPesvlrkilkglgrlaakflkrrrkiarkNLalvfpekseaerekiidksfesv 83 
                                    ++++++++r++++w+++a+++++++lPe ++r+++++++r++a ++ ++++++rkNLa+v+++ ++a+++ ++++s+es+
  gi|121638498|ref|YP_978722.1|  12 KDPRSSVTRTATDWAYAAGWMAVRALPEFAVRNAFDTGARYFA-RH-GGPEQLRKNLARVLGVPPAAVPDPLMCASLESY 89 
                                    678999*************************************.66.8******************************** PP

                Lip_A_acyltrans  84 graivetirvafisdeeiakrve..viglehikealaeeegvilllpHfanwelaglvlakqypglavvaenkknpllnq 161
                                    gr+++e++r+++++++++a++++  + gl+h+++ala++ g++l+lpH++nw++ag++l+++++++++vae+ k+++l+q
  gi|121638498|ref|YP_978722.1|  90 GRYWREVFRLPTMNHRKLARQLDrvIGGLDHLDAALAAGLGAVLALPHSGNWDMAGMWLVQRHGTFTTVAERLKPESLYQ 169
                                    ************************999***************************************************** PP

                Lip_A_acyltrans 162 liislRerfggkllprkna....ikelikalrkgevvvllpDqdlgrkdsvfvpfFgepaatttspaklalktkaavipv 237
                                    ++i++Re++g+++lp +++    ++ l+++lr+++vv+l++++dl+r+ +v+v+fFgep++++++pakla++t+aa++p+
  gi|121638498|ref|YP_978722.1| 170 RFIDYRESLGFEVLPLSGGerppFEVLCERLRNNRVVCLMAERDLTRT-GVEVDFFGEPTRMPVGPAKLAVETGAALLPT 248
                                    ************************************************.******************************* PP

                Lip_A_acyltrans 238 aiirkkdgskytvsvhPaldlssteDveqiaqalneilekeitaaPeqylwlhrrfk 294
                                    +++++++g  ++++v+Pald++s+ Dv++i+qal+++++++i+a+P+++++l+++++
  gi|121638498|ref|YP_978722.1| 249 HCWFEGRG--WGFQVYPALDCTSG-DVAAITQALADRFAQNIAAHPADWHMLQPQWL 302
                                    ********..**************.*******************************7 PP

>> SUKH-4  SUKH-4 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   9.8e-06     0.087       9     102 ..      39     138 ..      33     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                         SUKH-4   9 lfGpggvvrlpaeavaawllpeparrfLve.vGlPd.....lqllae.eeeaavadlelvaaerseelpaeaggllvLGa 81 
                                    +f+ ++ ++  a+ +a+++ pe+ r+ L++  G+P+     + l+ +  e+  + ++e+++ +++ +   + +   v+G 
  gi|121638498|ref|YP_978722.1|  39 EFAVRNAFDTGARYFARHGGPEQLRKNLARvLGVPPaavpdP-LMCAsLESYGRYWREVFRLPTMNHRKLARQLDRVIGG 117
                                    6777888899999***************77369999888742.333356677777888888888888888888889**** PP

                         SUKH-4  82 lesaslvldpgtGaVlavdle 102
                                    l+  + +l +g GaVla++ +
  gi|121638498|ref|YP_978722.1| 118 LDHLDAALAAGLGAVLALPHS 138
                                    *****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2378.78
//
Query:       gi|121638499|ref|YP_978723.1|  [L=217]
Description: phosphatidylinositol synthase pgsA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   40.4   2.1    3.7e-10   40.4   2.1    2.0  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.28   11.3   0.0       0.28   11.3   0.0    2.7  3  DUF4229          Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   2.1   4.1e-14   3.7e-10       2      66 .]      29      93 ..      28      93 .. 0.92
   2 ?   -0.4   0.1      0.23     2e+03      26      27 ..     136     160 ..     100     199 .. 0.51

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.1e-14
                                   -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   +P+++T+l+  +sv+ +l+l+ +  l+++++++ + +l+D+lDG +AR+++  +++G++lD  +D
  gi|121638499|ref|YP_978723.1| 29 TPDVVTILGTTASVAGALTLFPMGKLFAGACVVWFFVLFDMLDGAMARERGGGTRFGAVLDATCD 93
                                   8****************9888888888888888899***************9899*********9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                                    ......................... CS
                CDP-OH_P_transf  26 p.......................l 27 
                                                            l
  gi|121638499|ref|YP_978723.1| 136 AraeasglrgdggfierperliivL 160
                                    2334444444444444443333330 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.55     5e+03      10      22 ..      54      66 ..      53      71 .. 0.61
   2 ?   11.3   0.0   3.1e-05      0.28      12      48 ..      99     134 ..      93     140 .. 0.86
   3 ?   -1.0   0.3      0.22     2e+03      31      40 ..     180     189 ..     156     197 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.55
                        DUF4229 10 Lfvvltavillva 22
                                   Lf+++++v ++v 
  gi|121638499|ref|YP_978723.1| 54 LFAGACVVWFFVL 66
                                   6666666655543 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.1e-05
                        DUF4229  12 vvltavillvarliglp.vpllvaallAlvvalplSmv 48 
                                    +v++++++++a  + ++  pl++a l+ lv + ++S++
  gi|121638499|ref|YP_978723.1|  99 AVFCGLLWWIA--FHMRdRPLVIATLICLVTSQVISYI 134
                                    78899999999..444447*****************97 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.22
                        DUF4229  31 llvaallAlv 40 
                                     ++++ +A v
  gi|121638499|ref|YP_978723.1| 180 GMWLLAVASV 189
                                    2344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1521.44
//
Query:       gi|121638500|ref|YP_978724.1|  [L=195]
Description: hypothetical protein BCG_2638c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-15   55.8   0.0    8.7e-15   55.3   0.0    1.2  1  HIT            HIT domain
    1.4e-06   28.7   0.0    2.1e-06   28.2   0.0    1.2  1  DcpS_C         Scavenger mRNA decapping enzyme C-term binding
     0.0017   18.2   0.0     0.0033   17.3   0.0    1.4  1  CwfJ_C_1       Protein similar to CwfJ C-terminus 1
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.14   11.9   0.0    1.2  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   1.9e-18   8.7e-15       8      95 ..      71     159 ..      65     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.9e-18
                                    EEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSS. CS
                            HIT   8 vvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsva. 86 
                                    vv + +lv+a+l+  p  pghl v+p +++sel+dlt+ e a+l++ ++k  ++++++ +  g++v  n g +ag s a 
  gi|121638500|ref|YP_978724.1|  71 VVARGKLVYAVLNLYPYNPGHLMVVPYRRVSELEDLTDLESAELMAFTQKAIRVIKNVSRPHGFNVGLNLGTSAGGSLAe 150
                                    788889******************************************************************99988744 PP

                                    S-EEEEEEC CS
                            HIT  87 hlHiHvipr 95 
                                    hlH+Hv+pr
  gi|121638500|ref|YP_978724.1| 151 HLHVHVVPR 159
                                    *******98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.6e-10   2.1e-06      16     100 ..      71     157 ..      57     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.6e-10
                                    EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T..-EEEEE--SCCCT-.-S CS
                         DcpS_C  16 vvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne..vdaeelrvgvhyqP.sv 92 
                                    vv + + + ++  ++p ++ hl+v+p+r +++l+dLt+ +   l ++ +ka  vi++   +  +    l++g  +     
  gi|121638500|ref|YP_978724.1|  71 VVARGKLVYAVLNLYPYNPGHLMVVPYRRVSELEDLTDLESAELMAFTQKAIRVIKNVS-RphGFNVGLNLGTSAGGsLA 149
                                    44455778889999*****************************************8877.33455556666666666345 PP

                                    -S--EEEE CS
                         DcpS_C  93 yhlHlHvi 100
                                    +hlH+Hv+
  gi|121638500|ref|YP_978724.1| 150 EHLHVHVV 157
                                    8******8 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.3e-07    0.0033      24      83 ..      67     126 ..      61     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.3e-07
                                    -SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHH CS
                       CwfJ_C_1  24 ekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkmyk 83 
                                    e+ l+v+ g+ vY+ l   p + gH++++p   +s+l  l + +  e+ +f +  +++ k
  gi|121638500|ref|YP_978724.1|  67 EEGLVVARGKLVYAVLNLYPYNPGHLMVVPYRRVSELEDLTDLESAELMAFTQKAIRVIK 126
                                    6789**************************************999999999776665554 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.1e-05      0.14      49     145 ..      88     183 ..      60     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                                    STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS---EEEEEE---SCCCTT.TT--EEEEE--BCSSTT CS
                  GalP_UDP_tr_C  49 WPfevlllrkaevkslaeladeekedlaailkklarkydnlfetsfeysmGlhqaplnaeed.nswlHaHfevpllrsat 127
                                     P + ++++ ++v +l +l+d e+++l+a  +k  r   n  +    + +Gl   + ++  + ++ lH+H+ ++    a+
  gi|121638500|ref|YP_978724.1|  88 NPGHLMVVPYRRVSELEDLTDLESAELMAFTQKAIRVIKN-VSRPHGFNVGLNLGTSAGG-SlAEHLHVHVVPRWGGDAN 165
                                    36678999*******************9977665555555.4667778888833333333.24777*********999*9 PP

                                    EB----THHHHT-EEESS CS
                  GalP_UDP_tr_C 128 vrkieVGlelLperlrdl 145
                                       i  G +++p+ lrd 
  gi|121638500|ref|YP_978724.1| 166 FITIIGGSKVIPQLLRDT 183
                                    999999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1535.54
//
Query:       gi|121638501|ref|YP_978725.1|  [L=692]
Description: threonyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-38  132.2   0.0    3.2e-38  131.5   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.6e-15   56.4   0.1    5.8e-15   55.2   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    1.2e-12   47.7   0.0    2.3e-12   46.8   0.0    1.4  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
  ------ inclusion threshold ------
      0.079   12.1   0.0       0.16   11.2   0.0    1.4  1  DUF1839         Domain of unknown function (DUF1839)


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   7.2e-42   3.2e-38       8     179 .]     364     570 ..     356     570 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 7.2e-42
                                    SEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrdlik 85 
                                    +++y+LkP+n++ ++ ++r +  rs+r LPl+l++++t+yR+Eks   +GL+Rvr+++++d+++f++ ++++d+lr l++
  gi|121638501|ref|YP_978725.1| 364 GQDYYLKPMNCPMHCLIFRAR-GRSYReLPLRLFEFGTVYRYEKSgVVHGLTRVRGLTMDDAHIFCTRDQMRDELRSLLR 442
                                    689****************99.899777****************98899******************************* PP

                                    HHHHHHHHTT.SCEEEEEEGTTSC..................................BTTSEEEEEEEEETTTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx..................................xxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  86 aisriferlglefraiielmsaks..................................adykdkkefeavsesltkgiei 131
                                     + +++ + gl  + +++++++ +                                  a+y++k  +++ +  l++++++
  gi|121638501|ref|YP_978725.1| 443 FVLDLLADYGLTDFYLELSTKDPEkfvgaeevweeattvlaevgaesglelvpdpggaAFYGPKISVQVKDA-LGRTWQM 521
                                    ***********98888888665557999999**************************************999.******* PP

                                    EEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                   tRNA-synt_2b 132 gtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                    +tiq + ++++er+g+++   ++ +++++mi++a +g +eR+ ++++e++
  gi|121638501|ref|YP_978725.1| 522 STIQLD-FNFPERFGLEYTAADGTRHRPVMIHRAlFGsIERFFGILTEHY 570
                                    ******.***************************************9986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   1.3e-18   5.8e-15       1      92 [.     582     670 ..     582     672 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.3e-18
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    qvv ip+++   e+  y +++a +L+ +g+r+e+d s++++ kki ++ + ++pf+v  G++++  g v+ r  d ++ +
  gi|121638501|ref|YP_978725.1| 582 QVVGIPVAD---EHVAYLEEVATQLKSHGVRAEVDASDDRMAKKIVHHTNHKVPFMVLAGDRDVAAGAVSFRFGDRTQIN 658
                                    89*******...9******************************************************************* PP

                                    EEETTHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklk 92 
                                     v++d++v+++ 
  gi|121638501|ref|YP_978725.1| 659 GVARDDAVAAIV 670
                                    *******99886 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   5.1e-16   2.3e-12       9      44 .]     203     245 ..     180     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.1e-16
                                    .EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                       tRNA_SAD   9 isvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                    ++ +lC+G+H+p T++I afk++       +++++++ l+RIy
  gi|121638501|ref|YP_978725.1| 203 VWGDLCRGPHIPTTKHIPAFKLTrssaaywRGDQKNASLQRIY 245
                                    677***************************************9 PP

>> DUF1839  Domain of unknown function (DUF1839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05      0.16      61     129 ..     237     306 ..     223     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                        DUF1839  61 pledleaLYGlevqelavydsleehveeqvargklvl.vEvDayyLPdtrgtsYrrehtkttiaidaidr 129
                                    +++ l+++YG+  +  +  d+  e +ee+ +r +  l vE+D + +Pd  g++    h k  i+   ++ 
  gi|121638501|ref|YP_978725.1| 237 KNASLQRIYGTAWESQEALDRHLEFIEEAQRRDHRKLgVELDLFSFPDEIGSGLAVFHPKGGIVRRELED 306
                                    56789**********************99999876555**********************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4528.38
//
Query:       gi|121638502|ref|YP_978726.1|  [L=75]
Description: hypothetical protein BCG_2640 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0008   18.8   0.0    0.00094   18.6   0.0    1.1  1  TIM       Triosephosphate isomerase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.3e-08   0.00094     203     225 ..      10      32 ..       2      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-08
                                    EEEEESS--TTTHHHHHTSTT-- CS
                            TIM 203 rilYGGsvnkenakellkqkdid 225
                                    r+lYGGs++++++++l +q+d+d
  gi|121638502|ref|YP_978726.1|  10 RVLYGGSMSPKDVDDLATQQDVD 32 
                                    89********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 581.79
//
Query:       gi|121638503|ref|YP_978727.1|  [L=389]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                       87  (0.00485247); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 2306.29
//
Query:       gi|121638504|ref|YP_978728.1|  [L=76]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-14   52.0  11.0    9.2e-14   51.5  11.0    1.3  1  PE        PE family
  ------ inclusion threshold ------
       0.58    8.2   5.4       0.62    8.1   5.4    1.0  1  FSA_C     Fragile site-associated protein C-terminus


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5  11.0     1e-17   9.2e-14       1      53 [.       1      52 [.       1      67 [. 0.86

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1e-17
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAa 53
                                   Msfv+vaP+++++aaad a+igsa+++an+aaaa+t+ vl aa+DeVS++  +
  gi|121638504|ref|YP_978728.1|  1 MSFVNVAPQLVSTAAADAARIGSAINTANTAAAATTQ-VLVAAQDEVSTRRCS 52
                                   9******************************998666.**********87443 PP

>> FSA_C  Fragile site-associated protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.4   6.9e-05      0.62     537     592 ..       3      61 ..       1      71 [. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 6.9e-05
                          FSA_C 537 stsltpklmsaakssleslqgsqdsi....aiattasavelndatsstiasaatasslss 592
                                      +++p+l+s+a++    + gs  ++    a att   v ++d  s+  +saatas+++ 
  gi|121638504|ref|YP_978728.1|   3 FVNVAPQLVSTAAADAARI-GSAINTantaAAATTQVLVAAQDEVSTRRCSAATASTIKR 61 
                                    57899*****999999999.8888882222334444456778888999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 428.30
//
Query:       gi|121638505|ref|YP_978729.1|  [L=166]
Description: hypothetical protein BCG_2643 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-53  180.2   0.9    2.8e-53  180.1   0.9    1.0  1  DUF1990   Domain of unknown function (DUF1990)


Domain annotation for each model (and alignments):
>> DUF1990  Domain of unknown function (DUF1990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   0.9   1.6e-57   2.8e-53       1     153 []      12     165 ..      12     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 1.6e-57
                        DUF1990   1 tyaevgat....lPagyrvdrarvrlGegeevFerAaeallswemhrlagvrvraeapraaegatvvvevrflglgvl.a 75 
                                    ty+evgat    lPagy+++++++++G+g+++Fe+Aa+a+++w m+r+ag+rvra++++a + a+v+v +      +l a
  gi|121638505|ref|YP_978729.1|  12 TYPEVGATatgrLPAGYNHLDVSTQIGTGRQRFEQAADAVMHWGMQRNAGLRVRASSETAIVSAVVLVGIA-----FLrA 86 
                                    79*******************************************************99999999444444.....344* PP

                        DUF1990  76 pcrvvyvvdepdrfGFaYgTLpgHperGeerFlvelde.dgeVwfevtAfsrpaswlsrlggPvvrllQrrfarrylra 153
                                    pcrvvyv+depd++GF+YgTLpgHp++GeerF+v+ d+ +  V++ev +fsrpa+w s+++gP+  ++Qr +a+rylra
  gi|121638505|ref|YP_978729.1|  87 PCRVVYVIDEPDVRGFGYGTLPGHPVSGEERFAVRCDPmTSVVFAEVLSFSRPATWASKAAGPLGAVTQRFIAQRYLRA 165
                                    ****************************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 915.30
//
Query:       gi|121638506|ref|YP_978730.1|  [L=146]
Description: hypothetical protein BCG_2644c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-06   26.7   4.1    6.3e-06   26.7   4.1    1.6  1  DoxX      DoxX


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   4.1   3.5e-10   6.3e-06       3      81 ..      24     106 ..      22     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.5e-10
                           DoxX   3 lllRlllgvlfiahGlqkltg......fglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtl 76 
                                     llR l+ v  i+ Gl+k+++       +  + a+++++l + ++++  yl++++E+v+g+l+++  ++R++A ++a+ l
  gi|121638506|ref|YP_978730.1|  24 VLLRTLFTVAPILFGLDKFFNllthpqHWNMYLAGWINDLVPGTADQCMYLVGAIEIVAGVLVAV--APRIGAWVVAAWL 101
                                    689******************997777556679****************************9995..9999999999999 PP

                           DoxX  77 lvatl 81 
                                    ++++l
  gi|121638506|ref|YP_978730.1| 102 AGIIL 106
                                    98885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 834.16
//
Query:       gi|121638507|ref|YP_978731.1|  [L=225]
Description: hypothetical protein BCG_2645 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-05   23.4   0.0    0.00012   22.0   0.0    1.7  1  HTH_20     Helix-turn-helix domain
  ------ inclusion threshold ------
       0.05   14.0   0.0       0.12   12.7   0.0    1.6  1  FaeA       FaeA-like protein
       0.13   12.3   0.1       0.42   10.6   0.0    1.9  2  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     2e-08   0.00012       9      57 ..       2      51 ..       1      52 [. 0.97

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2e-08
                                   -HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  9 hPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   +PvRr +++   ++ ++++  + a+++++++ ++ +HL+ L   gL++++
  gi|121638507|ref|YP_978731.1|  2 DPVRRQLYQFVcSQSMPVSRDQAADAVGIPRHQAKFHLDRLTAEGLLDTE 51
                                   8*********************************************9975 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05      0.12       8      46 ..      11      49 ..       5      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                   HHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                           FaeA  8 ylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                   ++ s   p+   + Ada+g+   Qa++ L  L +eg + 
  gi|121638507|ref|YP_978731.1| 11 FVCSQSMPVSRDQAADAVGIPRHQAKFHLDRLTAEGLLD 49
                                   66666778888999**********************876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     7e-05      0.42      19      54 ..      16      51 ..       4      59 .. 0.83
   2 ?   -2.1   0.0      0.66     4e+03      12      31 ..      71      92 ..      67     102 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7e-05
                                   EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                      HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrg 54
                                    +p+++++ A+ +G+ r +    l +L  egl++++
  gi|121638507|ref|YP_978731.1| 16 SMPVSRDQAADAVGIPRHQAKFHLDRLTAEGLLDTE 51
                                   48*******************************965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.66
                                   CTTTC..EEEEEHHHHHHHHHT CS
                      HTH_Crp_2 12 eragg..eielpltqeelAsml 31
                                   +rag    + lp    elA +l
  gi|121638507|ref|YP_978731.1| 71 RRAGRdiALSLPQREYELAGRL 92
                                   4433224455666666777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1249.76
//
Query:       gi|121638508|ref|YP_978732.1|  [L=117]
Description: hypothetical protein BCG_2646c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-05   23.2   1.2    9.2e-05   22.1   0.1    1.9  2  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.055   13.2   0.0    1.7  2  Cupin_3   Protein of unknown function (DUF861)


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.12     1e+03      27      42 ..      22      38 ..      19      39 .. 0.68
   2 !   22.1   0.1     1e-08   9.2e-05       5      65 ..      44     102 ..      40     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                   ESEEEEE.ECTEEEEEE CS
                        Cupin_2 27 eGegelt.vdgeevele 42
                                   +G+++ t  +g+++el+
  gi|121638508|ref|YP_978732.1| 22 SGRAAHTiHGGHTHELR 38
                                   67766676677777765 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1e-08
                                    EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-E CS
                        Cupin_2   5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdepa 65 
                                    l  G++  +h  pge +++ Vl+G++ lt ++  +  +aGd+v +p+ t+H+++  +d   
  gi|121638508|ref|YP_978732.1|  44 LLAGHDLSEHDSPGE-ATLQVLQGHVCLTAGEDAWNGRAGDYVAIPP-TRHALHAVEDSVI 102
                                    667788889999**9.*******************************.8999998887644 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.17   1.5e+03      33      50 ..      22      39 ..      17      45 .. 0.82
   2 ?   13.2   0.0   6.1e-06     0.055      28      60 ..      60      91 ..      52     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.17
                                   ECEEEEEETTTEEEEEET CS
                        Cupin_3 33 eGevkvtpeggetvelra 50
                                   +G+   t  gg t+elr+
  gi|121638508|ref|YP_978732.1| 22 SGRAAHTIHGGHTHELRQ 39
                                   577777888999999985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.1e-06
                                   EEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                        Cupin_3 28 fcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                   +  +l+G+v +t+ g+ +   raGD+v +p+  
  gi|121638508|ref|YP_978732.1| 60 TLQVLQGHVCLTA-GEDAWNGRAGDYVAIPPTR 91
                                   5679*********.9999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 785.27
//
Query:       gi|121638509|ref|YP_978733.1|  [L=141]
Description: hypothetical protein BCG_2647c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.8    8.3  11.2       0.11   12.8   5.7    1.6  2  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.7   6.4e-06      0.11       3      79 ..      12      91 ..      10     105 .. 0.70
   2 ?   -3.3   0.2      0.65   1.2e+04      45      49 ..     130     134 ..     119     139 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-06
                        DUF4149  3 lglllGsqlwvtfvvapvlfrsL..prhqfgelqskl.Fplyfglglalsvlllltevavg.seklaseellqlllllvvl 79
                                   + ++lG++++++f  ap  fr+   + +  g   ++l F +++++ +++++++l   v+ +  ++ a++ +++l +l+v l
  gi|121638509|ref|YP_978733.1| 12 AFVWLGMVVAISFLEAPLKFRAAgvTLQ-IGLGIGRLvFRALNTVEVGFALVILAIVVVGStPARIAAAFSVALAALAVQL 91
                                   579*******************642555.666555545******************9986633333333333333333332 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.65
                        DUF4149  45 glals 49 
                                     l+++
  gi|121638509|ref|YP_978733.1| 130 ALLVA 134
                                    22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1032.41
//
Query:       gi|121638510|ref|YP_978734.1|  [L=223]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-09   35.3   0.1    2.4e-08   33.9   0.1    1.8  1  HTH_20         Helix-turn-helix domain
    0.00018   21.2   0.0    0.00049   19.8   0.0    1.8  1  HTH_IclR       IclR helix-turn-helix domain
    0.00034   20.1   0.0    0.00079   18.9   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.002   17.9   0.0      0.042   13.6   0.0    2.3  2  LexA_DNA_bind  LexA DNA binding domain
     0.0025   17.9   0.6      0.006   16.7   0.1    1.9  2  HTH_28         Helix-turn-helix domain
     0.0029   17.4   0.3     0.0059   16.4   0.0    1.7  1  HTH_30         PucR C-terminal helix-turn-helix domain
      0.003   17.5   0.0     0.0051   16.7   0.0    1.4  1  HTH_11         HTH domain
     0.0037   17.1   1.1      0.021   14.7   0.1    2.4  2  MarR_2         MarR family
     0.0074   16.6   0.0      0.014   15.8   0.0    1.4  1  FaeA           FaeA-like protein
     0.0087   15.7   0.0      0.017   14.7   0.0    1.5  1  GntR           Bacterial regulatory proteins, gntR family
     0.0087   15.9   0.0      0.017   15.0   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.027   14.0   0.0    1.5  1  GerE           Bacterial regulatory proteins, luxR family
      0.016   15.0   0.0      0.033   14.0   0.0    1.5  1  HTH_38         Helix-turn-helix domain
      0.019   14.7   0.1        0.1   12.4   0.0    2.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.024   14.4   0.0      0.045   13.6   0.0    1.6  1  DUF742         Protein of unknown function (DUF742)
       0.03   14.0   0.0      0.073   12.8   0.0    1.5  1  Sigma70_r4_2   Sigma-70, region 4
      0.031   14.1   0.0      0.084   12.7   0.0    1.7  1  HTH_23         Homeodomain-like domain
      0.043   13.8   0.1       0.11   12.6   0.1    1.7  1  HTH_29         Winged helix-turn helix
      0.045   13.2   0.0        0.1   12.0   0.0    1.6  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
      0.066   13.3   0.0       0.11   12.5   0.0    1.3  1  FeoC           FeoC like transcriptional regulator
      0.078   12.9   0.0       0.16   11.9   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.093   12.7   0.0        0.2   11.6   0.0    1.5  1  MarR           MarR family
       0.12   12.1   0.0       0.23   11.2   0.0    1.4  1  HTH_DeoR       DeoR-like helix-turn-helix domain
       0.17   12.3   0.0       0.32   11.5   0.0    1.3  1  HTH_40         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   3.3e-11   2.4e-08      12      61 .]      17      67 ..       8      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.3e-11
                                   HHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20 12 RrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                   Rr++lraL a++ +++ +++a  l++++nt+++HL+ L+  g ve+v++gr
  gi|121638510|ref|YP_978734.1| 17 RRAVLRALcASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEPGR 67
                                   9***********************************************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.6e-07   0.00049       7      51 ..      19      63 ..      14      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.6e-07
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                   a+L+al + + +++++ +A ++g+++ tv+ +L  Lv  G ve+ 
  gi|121638510|ref|YP_978734.1| 19 AVLRALCASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERV 63
                                   79****************************************985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06   0.00079       6      48 .]      18      61 ..      16      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         HTH_24  6 rkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   r++L++L +    +s++ +A +lg+ p+tv+ +l++L+ +G ++
  gi|121638510|ref|YP_978734.1| 18 RAVLRALCASRVpMSIAAIAGKLGVHPNTVRFHLDNLVADGQVE 61
                                   67778888844449***************************986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.6e-05     0.042      24      64 ..      29      69 ..      18      70 .. 0.86
   2 ?    1.6   0.0      0.31   2.3e+02      10      30 ..     134     154 ..     131     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                                   S---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G.GG-CC CS
                  LexA_DNA_bind 24 ypPsireiaralglkSpsaveehLkaLerKGyierd.pgkpR 64
                                    p si+ ia +lg++ p++v  hL  L   G +er  pg+ R
  gi|121638510|ref|YP_978734.1| 29 VPMSIAAIAGKLGVH-PNTVRFHLDNLVADGQVERVePGRGR 69
                                   6889***********.*****************985266665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHSS---HHH CS
                  LexA_DNA_bind  10 evldlikasieetgypPsire 30 
                                    e +d ++a +++ g++P +r 
  gi|121638510|ref|YP_978734.1| 134 ETIDHLVAVLDDLGFAPERRA 154
                                    6688999**********9985 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     8e-06     0.006       2      51 ..      16      70 ..      16      73 .. 0.85
   2 ?   -2.2   0.0       6.5   4.9e+03       5      21 ..      79      97 ..      77     106 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8e-06
                         HTH_28  2 Rleiiklla..aGh..svreaArelgisrrtvyrWikryeegG.iagLvprrrrp 51
                                   R++++++++  + +  s++++A +lg+++ tv+  +  + + G ++  +p r+rp
  gi|121638510|ref|YP_978734.1| 16 RRRAVLRALcaSRVpmSIAAIAGKLGVHPNTVRFHLDNLVADGqVERVEPGRGRP 70
                                   6677777775456677*************************99669999999988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                         HTH_28  5 iikllaaGh..svreaAre 21
                                   ++++  + +  ++r +A++
  gi|121638510|ref|YP_978734.1| 79 AVRRTDSTGtrRYRLLAEI 97
                                   5555554331455556665 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.9e-06    0.0059      13      34 ..      31      52 ..      18      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.9e-06
                                   T-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_30 13 gnisatAkaLhvHrnTlryRLr 34
                                   ++i+a A +L+vH+nT+r  L+
  gi|121638510|ref|YP_978734.1| 31 MSIAAIAGKLGVHPNTVRFHLD 52
                                   89***************97776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.8e-06    0.0051       1      45 [.      16      62 ..      16      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.8e-06
                         HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..vp 45
                                   R++++l+ L ++r p+s++ +A +L+v   tvr +++ L + g   +
  gi|121638510|ref|YP_978734.1| 16 RRRAVLRALCASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGqvER 62
                                   8999*********************************9999885444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.9e-05     0.021       8      56 ..      18      65 ..      15      72 .. 0.85
   2 ?   -0.1   0.1       1.2   8.7e+02       9      54 ..      92     106 ..      86     117 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   + vL aL ++   +++++++a +lg+ + +v  +l+ Lva G ver++ 
  gi|121638510|ref|YP_978734.1| 18 RAVLRALCASR-VPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEP 65
                                   67899987775.459*******************************943 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                    HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    r                               +l++  a GL  +r
  gi|121638510|ref|YP_978734.1|  92 R-------------------------------LLAEILASGLAAER 106
                                    4...............................55555555555555 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-05     0.014      13      56 ..      28      71 ..      16      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                   S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS- CS
                           FaeA 13 kapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvst 56
                                   + p   + iA  lg+    +R+ L +L + g+++r+  +rG ++
  gi|121638510|ref|YP_978734.1| 28 RVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEPGRGRPG 71
                                   56777889*********************************875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.3e-05     0.017      26      57 ..      32      63 ..      18      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           GntR 26 sereLaaefgVsrttvReALrrLeaeglverr 57
                                   s  ++a ++gV  +tvR  L++L+a+g ver 
  gi|121638510|ref|YP_978734.1| 32 SIAAIAGKLGVHPNTVRFHLDNLVADGQVERV 63
                                   6789*************************985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.017       4      45 ..      17      60 ..      15      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  4 RlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   R+ +L++L+    ++++  +a +lg+ + tv+ HL  L   G V
  gi|121638510|ref|YP_978734.1| 17 RRAVLRALCAsrVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQV 60
                                   9999****998788************************988865 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.027      19      41 ..      32      54 ..      16      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                   -HHHHHHHHTS-HHHHHHHHHHH CS
                           GerE 19 snkeIAeelniSekTVkvhksni 41
                                   s   IA +l++ ++TV++h+ n+
  gi|121638510|ref|YP_978734.1| 32 SIAAIAGKLGVHPNTVRFHLDNL 54
                                   6678****************998 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.4e-05     0.033      21      37 ..      31      47 ..      18      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                         HTH_38 21 lslreIArrLgrspsTI 37
                                   +s+++IA +Lg++p+T+
  gi|121638510|ref|YP_978734.1| 31 MSIAAIAGKLGVHPNTV 47
                                   9***************9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014       0.1       6      35 ..      18      48 ..      18      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                  HTH_AsnC-type  6 rkILeaLqed.aRisyaeLAervGlSestvl 35
                                   r+ L+aL +    +s a++A ++G+ ++tv+
  gi|121638510|ref|YP_978734.1| 18 RAVLRALCASrVPMSIAAIAGKLGVHPNTVR 48
                                   678999999999******************7 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     6e-05     0.045      46      93 ..      18      68 ..       4     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                         DUF742 46 rail.rLcre..plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtd 93
                                   ra+l +Lc++  p+s+a +a++l +   +vr  l +L++ g+++  +p   
  gi|121638510|ref|YP_978734.1| 18 RAVLrALCASrvPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEPGRG 68
                                   444416999989*******************************99888766 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-05     0.073      27      47 ..      31      51 ..      31      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                                   --HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2 27 lsykEIAellgisegtVksrl 47
                                   +s++ IA +lg++++tV+ +l
  gi|121638510|ref|YP_978734.1| 31 MSIAAIAGKLGVHPNTVRFHL 51
                                   89****************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.084      10      35 ..      20      48 ..      13      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                         HTH_23 10 illllae...GlsvreIAreLgvsrrTvy 35
                                   +l++l      +s+++IA +Lgv+++Tv+
  gi|121638510|ref|YP_978734.1| 20 VLRALCAsrvPMSIAAIAGKLGVHPNTVR 48
                                   4444444445689***************7 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014      0.11       7      53 ..      24      73 ..      16      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         HTH_29  7 llaeGvs.tvsqiAkllglsrrtvyrwlkrfeegG.laalld.rrrsgrp 53
                                   l+a  v+ +++ iA  lg+++ tv+ +l+  +++G ++   + r r+grp
  gi|121638510|ref|YP_978734.1| 24 LCASRVPmSIAAIAGKLGVHPNTVRFHLDNLVADGqVERVEPgRGRPGRP 73
                                   455555578**************************777788877778887 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014       0.1      23      45 ..      24      48 ..      17      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                   HTH_Tnp_ISL3 23 llles..rsvkavArqlgvSwtTVw 45
                                   l+ ++  +s++a+A  lgv+++TV+
  gi|121638510|ref|YP_978734.1| 24 LCASRvpMSIAAIAGKLGVHPNTVR 48
                                   44555778****************6 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11       5      50 ..      21      66 ..      19      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                           FeoC  5 lkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                   l+++ + r   s+  ++ ++ + p++++  L+ +v+ G+ve+v+ +
  gi|121638510|ref|YP_978734.1| 21 LRALCASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEPG 66
                                   7888899999*******************************99865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.16      17      65 ..      24      80 ..      19      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                   HH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.ST......TTEEEE- CS
                           TrmB 17 Ll.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.gr......pklYrav 65
                                   L  ++ p+++  ia +lgv  ++v   L +L+  G Ver++ gr      p ++rav
  gi|121638510|ref|YP_978734.1| 24 LCaSRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEpGRgrpgrpPLMFRAV 80
                                   5557789999*****************************985558999988899998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026       0.2      12      49 ..      25      62 ..      20      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                                   HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                   ++++ p+s++ +a klgv++ tv   ld L+ +G +eR
  gi|121638510|ref|YP_978734.1| 25 CASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVER 62
                                   677789******************************99 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.23      14      47 ..      30      63 ..      17      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                       HTH_DeoR 14 klsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                    +s+  ++  lgv ++T+R  L++L+++g ++R+
  gi|121638510|ref|YP_978734.1| 30 PMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERV 63
                                   58999**************************997 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00043      0.32      13      41 ..      31      59 ..      26      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                         HTH_40 13 lsieeIAkerglkesTIegHLaelieege 41
                                   +si++IA + g+ ++T+  HL +l+ +g+
  gi|121638510|ref|YP_978734.1| 31 MSIAAIAGKLGVHPNTVRFHLDNLVADGQ 59
                                   89************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1622.65
//
Query:       gi|121638511|ref|YP_978735.1|  [L=273]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-11   43.8   0.8    6.3e-10   39.6   0.0    2.7  3  Methyltransf_11  Methyltransferase domain
      2e-09   38.0   0.6    7.2e-09   36.2   0.1    2.1  2  Methyltransf_25  Methyltransferase domain
    1.1e-05   25.4   0.0    1.7e-05   24.7   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    0.00099   19.0   0.1     0.0018   18.1   0.0    1.4  2  Methyltransf_8   Hypothetical methyltransferase
      0.001   18.7   0.0     0.0016   18.0   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0018   19.0   0.2     0.0055   17.4   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
     0.0096   15.7   0.0      0.014   15.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   14.9   0.0      0.017   14.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.21   4.7e+02      85      93 ..      33      41 ..      21      43 .. 0.86
   2 !   39.6   0.0   2.8e-13   6.3e-10       1      95 [.      59     153 ..      59     154 .. 0.92
   3 ?   -1.5   0.0       1.8     4e+03      69      92 ..     201     224 ..     164     226 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                                   HHHEEEEEE CS
                Methyltransf_11 85 aRvLkpgGl 93
                                   +RvL+pgG+
  gi|121638511|ref|YP_978735.1| 33 KRVLRPGGV 41
                                   8*******6 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 2.8e-13
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edp 77 
                                    L+++ G Gr a+++  r  +++vg + ++++ +l+++   ++g   +++v da ++ + d+s D+v+   +l+    +  
  gi|121638511|ref|YP_978735.1|  59 LELAPGLGRTAAEILARNpRSYVGAESDPNAANLVRHVLAGRG---DVRVTDAADTGLSDASADVVIGEAMLTMQgnAAK 135
                                    7889999999988885556***********************9...78************************99999999 PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                    + +++e+aRvL+pgG+ +
  gi|121638511|ref|YP_978735.1| 136 HTIVAEAARVLRPGGRYA 153
                                    9**************987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                                    S-CCC-CCHHHHHHHHHHHEEEEE CS
                Methyltransf_11  69 evlhhvedpekalkeiaRvLkpgG 92 
                                     v++hv   + al + +Rv   +G
  gi|121638511|ref|YP_978735.1| 201 LVVEHVVTASMALLQPRRVIADEG 224
                                    355666555556666666666555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.4   3.2e+03      90      97 .]      33      40 ..      25      40 .. 0.87
   2 !   36.2   0.1   3.2e-12   7.2e-09       1      97 []      58     150 ..      58     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                   HHHEEEEE CS
                Methyltransf_25 90 arvLkpgG 97
                                   +rvL+pgG
  gi|121638511|ref|YP_978735.1| 33 KRVLRPGG 40
                                   79*****9 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3.2e-12
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vL+l+ G Gr+++++++r    +++g + ++++ + +r+ ++    + ++++ da d  + d+s D+v+   +l +  ++
  gi|121638511|ref|YP_978735.1|  58 VLELAPGLGRTAAEILARN-PRSYVGAESDPNAANLVRHVLAG---RGDVRVTDAADTGLSDASADVVIGEAMLTMQGNA 133
                                    8**************9995.7******************9953...77**********************6559999999 PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                      +++++e+arvL+pgG
  gi|121638511|ref|YP_978735.1| 134 AKHTIVAEAARVLRPGG 150
                                    99**************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   7.5e-09   1.7e-05      16     124 ..      47     162 ..      33     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.5e-09
                Methyltransf_23  16 llpk.lraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae...pqg 81 
                                    ll++ + +++ vL++++G G+++ ++ ++n+ s++g + +p+a ++++                      +aa+   +++
  gi|121638511|ref|YP_978735.1|  47 LLARaEVTDADVLELAPGLGRTAAEIlARNPRSYVGAESDPNAANLVRhvlagrgdvR----------VTDAADtglSDA 116
                                    444437899***********765555499999**************986554433321..........233333344788 PP

                Methyltransf_23  82 kfdlIvlrevlehvpd..ppellrqiatllkpgGylllse.plasl 124
                                    + d+++   +l    +   +  ++ +a+ l+pgG+  ++e  l+++
  gi|121638511|ref|YP_978735.1| 117 SADVVIGEAMLTMQGNaaKHTIVAEAARVLRPGGRYAIHElALVPD 162
                                    ***************9778899***********8777766245555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         4   8.9e+03     145     153 ..      33      41 ..      30      54 .. 0.79
   2 !   18.1   0.0   8.2e-07    0.0018     106     159 ..     101     157 ..      88     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4
                                    HHHEEEEEE CS
                 Methyltransf_8 145 nrvlkvGGl 153
                                    +rvl++GG+
  gi|121638511|ref|YP_978735.1|  33 KRVLRPGGV 41 
                                    799***997 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.2e-07
                                    TTEEES-TTS-S--TT-EEEEE..EES---SS-HH.HHHHHHHHHEEEEEEEEEEEE CS
                 Methyltransf_8 106 ervvacdlakvPledesvdvav..fclslmgtnla.dflkeanrvlkvGGllkvaev 159
                                     +v + d a   l d s+dv++    l++ g+  + + + ea rvl++GG + + e+
  gi|121638511|ref|YP_978735.1| 101 GDVRVTDAADTGLSDASADVVIgeAMLTMQGNAAKhTIVAEAARVLRPGGRYAIHEL 157
                                    579999***************9545677777766514679*************9997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.4e-07    0.0016      22     136 ..      46     153 ..      33     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.4e-07
                                    HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEE CS
                            MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdl 100
                                     Ll   +  ++ +vl l+ G G  +a++++++p+ + +  + d +A ++ ++ l+  +   +v+ +d+ +  +++++ d+
  gi|121638511|ref|YP_978735.1|  46 TLLARAEV-TDADVLELAPGLGRTAAEILARNPR-SYVGAESDPNAANLVRHVLAGRG---DVRVTDAADtGLSDASADV 120
                                    44444444.6778*********************.79999**********99998766...5666665541577999*** PP

                                    EEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 101 ivsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                    ++    +  + +   a+ ++++aeA+++L++gG+  
  gi|121638511|ref|YP_978735.1| 121 VIGEAMLTMQGN---AAKHTIVAEAARVLRPGGRYA 153
                                    ***998888777...899***************865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       6.2   1.4e+04      91      98 ..      34      41 ..      28      41 .. 0.83
   2 !   17.4   0.0   2.5e-06    0.0055       1      98 [.      59     151 ..      59     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.2
                Methyltransf_12 91 klLkpgGr 98
                                   ++L+pgG+
  gi|121638511|ref|YP_978735.1| 34 RVLRPGGV 41
                                   89****95 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.5e-06
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    Le+  G G++++++l++  + +y+g + +p+a +  +  la r++ +++    + l++      +s D+v+    l    
  gi|121638511|ref|YP_978735.1|  59 LELAPGLGRTAAEILAR-NPRSYVGAESDPNAANLVRHVLAGRGDVRVTDAADTGLSD------ASADVVIGEAMLTMQg 131
                                    89999************.778899*********8899999998864444444444443......3******777777777 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     + ++ ++++++++L+pgGr
  gi|121638511|ref|YP_978735.1| 132 nAAKHTIVAEAARVLRPGGR 151
                                    69999**************8 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.4e-06     0.014      61     124 ..     106     170 ..      53     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.4e-06
                Methyltransf_31  61 gdieelekl.ledekfDlilsnevl..naladpdkileeiervlkpggilliedpr.llaelpakvee 124
                                     d+ +   + l+d++ D+++  + l  +  a++  i  e+ rvl+pgg+++i +   + ++++++v+ 
  gi|121638511|ref|YP_978735.1| 106 TDAAD---TgLSDASADVVIGEAMLtmQGNAAKHTIVAEAARVLRPGGRYAIHELAlVPDDVAEQVRT 170
                                    34444...44899*********9999899999999******************999633333344443 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.4e-06     0.017      31      79 ..      55     104 ..      42     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-06
                                    TSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTTTCCCEE CS
                         RrnaAD  31 kltvleigpGkGilTeeLakra.kqvvvlElderLakllqkklskdeklk 79 
                                    +  vle++pG G + +e++ r  +++v  E+d++ a+l+++ l   + + 
  gi|121638511|ref|YP_978735.1|  55 DADVLELAPGLGRTAAEILARNpRSYVGAESDPNAANLVRHVLAGRGDVR 104
                                    457***************99999*************99999766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1863.36
//
Query:       gi|121638512|ref|YP_978736.1|  [L=297]
Description: hypothetical protein BCG_2650 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-47  161.4   8.0    9.7e-25   87.7   1.6    2.0  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.6   6.7e-26   1.2e-21       5     141 .]      10     148 ..       9     148 .. 0.91
   2 !   87.7   1.6   5.4e-29   9.7e-25       5     141 .]     162     293 ..     160     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 6.7e-26
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTCEE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggvkv 82 
                                    I+V++D+s++++ A++wA++ a+ r+ +l+l+h+++p+  ++   + ++    ++++ ++ l  da    ++a  +    
  gi|121638512|ref|YP_978736.1|  10 IIVGIDDSPAAQVAVRWAARDAELRKIPLTLVHAVSPEVATWLEVPLPPGVLRWQQDHGRHLIDDAlkVVEQASLRAGPP 89 
                                    89*************************************************************99999566666666666 PP

                                    EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +v+ e  ++a + ++v  ++da l+VvG  g ++  ++llGSvs+ +lrha+cpV++++
  gi|121638512|ref|YP_978736.1|  90 TVHSEIVPAAAVPTLVDMSKDAVLMVVGCLGSGRWPGRLLGSVSSGLLRHAHCPVVIIH 148
                                    667777777777777788888***********************************985 PP

  == domain 2  score: 87.7 bits;  conditional E-value: 5.4e-29
                                    EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                            Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                    +lV+vDgs++s+ A   A+++a +r+ +l++lh++++ + ++++  d++a ++ +e+ +ae+ a      ++++ ++v +
  gi|121638512|ref|YP_978736.1| 162 VLVGVDGSSASELATAIAFDEASRRNVDLVALHAWSDVDVSEWPGIDWPATQSMAEQVLAERLA-----GWQERYPNVAI 236
                                    8*************************************************************85.....67999999999 PP

                                    EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    ++++    ++  +v ++e+a+l+VvGsrgr+g +++l+GSv e v++ a  pV+v r
  gi|121638512|ref|YP_978736.1| 237 TRVVVRDQPARQLVQRSEEAQLVVVGSRGRGGYAGMLVGSVGETVAQLARTPVIVAR 293
                                    9999999999999*****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2063.65
//
Query:       gi|121638513|ref|YP_978737.1|  [L=272]
Description: hypothetical protein BCG_2651c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-25   89.4   8.8    8.7e-20   71.7   1.0    3.0  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.13   11.9   0.4        2.5    7.7   0.0    2.6  3  DUF374    Domain of unknown function (DUF374)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   1.0   9.7e-24   8.7e-20       1     141 []       9     140 ..       8     140 .. 0.87
   2 !   16.3   1.4   1.2e-06      0.01      19     141 .]     167     271 ..     151     271 .. 0.58

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 9.7e-24
                                    S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                            Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                    m k+I+V++Dgs ++  A+ w++++a +r  +l+l+ vi+p  +++ ++ ++ a  e++  e++ ++++      +++ v
  gi|121638513|ref|YP_978737.1|   9 M-KTIIVGIDGSHAAITAALWGVDEAISRAVPLRLVSVIKPTHPSPDDYDRDLAHAERSLREAQSAVEA------AGKLV 81 
                                    4.99***************************************99999999999999999999888743......45555 PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    k e+++  g++++  ++v+ ++da++i+vGs g ++ +  +lGS++  ++++a+cpV v r
  gi|121638513|ref|YP_978737.1|  82 KIETDIPRGPAGP--VLVEASRDAEMICVGSVGIGRYASSILGSTATELAEKAHCPVAVMR 140
                                    5556666665555..66667888**********************************9976 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.2e-06
                                    HHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...................HHHHHHCTT CS
                            Usp  19 lewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...................akaaaeagg 79 
                                    le+A+++ak r+a                                      +                   +++ ++ ++
  gi|121638513|ref|YP_978737.1| 167 LEYAAREAKLRQA--------------------------------------PilalggrpeelreipdgefERRVQDWHH 208
                                    3333333333333......................................12223333333334444444444444444 PP

                                    CEEEEEEEESSHHHHHH..HHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  80 vkvevvveegdpaeeil..evaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                     + +v v      ++i+  ++  +e ++l V+G    + l+r l+G   + v rha+c+VlvVr
  gi|121638513|ref|YP_978737.1| 209 RHPDVRVYPITTHTGIArfLADHDERVQLAVIGGGEAGQLAR-LVGPSGHPVFRHAECSVLVVR 271
                                    4444444444444444411456788899********999998.89******************8 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.57   5.1e+03      17      29 ..      17      29 ..      16      33 .. 0.62
   2 ?    7.7   0.0   0.00028       2.5      41      69 .]      63      92 ..      47      92 .. 0.91
   3 ?    1.1   0.0     0.033   2.9e+02      10      21 ..      95     106 ..      94     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.57
                         DUF374 17 DGeliarvlerlG 29
                                   DG+ +a +++ +G
  gi|121638513|ref|YP_978737.1| 17 DGSHAAITAALWG 29
                                   5666666666665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00028
                         DUF374 41 gaealremlral.kegesvaitpDgPrGPr 69
                                   + + lre+ +a+  +g+ v i  D+PrGP+
  gi|121638513|ref|YP_978737.1| 63 AERSLREAQSAVeAAGKLVKIETDIPRGPA 92
                                   57899*******888999***********6 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.033
                         DUF374  10 aliSrsrDGeli 21 
                                    +l+ +srD+e+i
  gi|121638513|ref|YP_978737.1|  95 VLVEASRDAEMI 106
                                    7999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1873.97
//
Query:       gi|121638514|ref|YP_978738.1|  [L=393]
Description: transmembrane alanine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-16   58.5   6.7    8.3e-09   35.1   0.1    3.2  3  Peptidase_M50  Peptidase family M50
    1.5e-12   47.8   0.0    5.4e-07   30.0   0.1    2.4  2  CBS            CBS domain
  ------ inclusion threshold ------
      0.023   15.0   0.5      0.023   15.0   0.5    2.4  3  DUF3267        Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   3.1   9.4e-09   5.6e-05       3     104 ..      56     122 ..      54     127 .. 0.90
   2 !   35.1   0.1   1.4e-12   8.3e-09     185     248 ..     136     197 ..     124     201 .. 0.79
   3 ?   -2.5   0.0      0.42   2.5e+03      97     129 ..     214     249 ..     206     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.4e-09
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                    +++l+ +++ HEl+H++vA+++gv ve+                    ++l+ +GG+  + ge                k
  gi|121638514|ref|YP_978738.1|  56 AVMLLASLLAHELAHAVVARRAGVSVES--------------------VTLWLFGGVTALGGEA---------------K 100
                                    689***********************99....................888999**99999988...............8 PP

                                    XXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  83 spwqrllivlAGplanfilail 104
                                    +p + ++i++AGp++ + l+  
  gi|121638514|ref|YP_978738.1| 101 TPKAAFRIAFAGPATSLALSAT 122
                                    89999********999998765 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.4e-12
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 185 eaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalll 248
                                     a ++s+ ++la +++ Lg++NLlP  +LDGg+l++a l++      s+r+   a ++g ++ l
  gi|121638514|ref|YP_978738.1| 136 PAIVISVAWWLATVNLLLGLFNLLPGAPLDGGRLVRAYLWRRH--GDSVRAGIGAARAGRVVAL 197
                                    55677999******************************98655..6666666666666666555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.42
                                    XXXXXXXXXXXX...-EEECE...CTTTSCEE-SEEEC- CS
                                    xxxxxxxxxxxx...xxxxxx...xxxxxxxxxxxxxxx RF
                  Peptidase_M50  97 anfilailvfvv...pkkske...seeekrgviGvspkp 129
                                     +++la++ +++       +e     ++++ + Gv+ + 
  gi|121638514|ref|YP_978738.1| 214 GGVWLAFIGWFIfaaA---REeetRISTQQLFAGVRVAD 249
                                    3555666555553321...22223444444555554443 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.1e-06     0.018       1      53 [.     247     300 ..     247     303 .. 0.83
   2 !   30.0   0.1   9.1e-11   5.4e-07       1      55 [.     311     367 ..     311     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
                                    HHHHSBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDllr 53 
                                    V+d mt +++t+p   ++e+ +++++  +++s++PV d dg + G+v lr l +
  gi|121638514|ref|YP_978738.1| 247 VADAMTAQPHTAPGWINVEDFIQRYVlGERHSAYPVADRDGSITGLVALRQLRD 300
                                    67889999955555566*******6557789*******************9976 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 9.1e-11
                                    HHHH..SBSSCEEEETTSBHHHHHHHHH..HHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 Vgdi..mtrdvvtvppdttleealelmr..ekgvsrlPVVdedgklvGivtlrDllral 55 
                                    Vgdi  + + v+t++p+++l  +le+m+    + sr +V++++  +vGivt +D++r++
  gi|121638514|ref|YP_978738.1| 311 VGDIalPLHSVPTARPQEPLTALLERMAplGPR-SRALVTEGSA-VVGIVTPSDVARLI 367
                                    7887778999*****************665333.5555997777.***********998 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.38   2.3e+03      53      61 ..      33      41 ..      10      65 .. 0.46
   2 ?   15.0   0.5   3.8e-06     0.023       2      90 ..      60     154 ..      59     162 .. 0.75
   3 ?   -2.1   0.5      0.76   4.6e+03      60      89 ..     201     228 ..     192     231 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.38
                        DUF3267 53 illaPfvll 61
                                   ++++P  + 
  gi|121638514|ref|YP_978738.1| 33 ATMLPGTVG 41
                                   222333332 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.8e-06
                        DUF3267   2 lvlvilHEllHglffklfgkkpkkkvkfgiklliayatsseallskkqfiiillaPfvllgilllllalllpsstl.... 77 
                                    l+ ++ HEl+H+++ ++ g+++++ + +   ++ + a   ea  +k  f i+   P+  l +   + al++  +      
  gi|121638514|ref|YP_978738.1|  60 LASLLAHELAHAVVARRAGVSVESVTLW--LFGGVTALGGEAKTPKAAFRIAFAGPATSLALSATFGALAITLAGVrtpa 137
                                    567899************9998877777..578889999999999***********988765555555554443334567 PP

                        DUF3267  78 ....llllllalnaags 90 
                                        ++++l+ +n++++
  gi|121638514|ref|YP_978738.1| 138 ivisVAWWLATVNLLLG 154
                                    77777777777776655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.76
                        DUF3267  60 llgilllllalllpsstlllllllalnaag 89 
                                     lg++ ++++ l+     +l++++++ +a+
  gi|121638514|ref|YP_978738.1| 201 ALGLAEFVAGGLVGGV--WLAFIGWFIFAA 228
                                    3333334444444443..677777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2766.44
//
Query:       gi|121638515|ref|YP_978739.1|  [L=143]
Description: hypothetical protein BCG_2653c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-26   90.0   0.7    1.3e-11   44.7   0.1    2.1  2  CBS       CBS domain
  ------ inclusion threshold ------
       0.11   11.4   0.0       0.24   10.3   0.0    1.5  2  TraI_2    Putative helicase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   2.5e-15   2.2e-11       1      52 [.       4      55 ..       4      57 .. 0.96
   2 !   44.7   0.1   1.5e-15   1.3e-11       2      56 ..      71     124 ..      70     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.5e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                   ++dim+  v +v + +tl  a++ mre+++++lP+  +d++l+G++t+rD++
  gi|121638515|ref|YP_978739.1|  4 ARDIMNAGVTCVGEHETLTAAAQYMREHDIGALPICGDDDRLHGMLTDRDIV 55
                                   589*********************************99999*********97 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.5e-15
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    g++ ++ + +v+ ++++ e l+ m+e+ v+r+PV+ ++++lvGivt+ D++r l+
  gi|121638515|ref|YP_978739.1|  71 GELARDSIYYVDANASIQEMLNVMEEHQVRRVPVI-SEHRLVGIVTEADIARHLP 124
                                    788888999***************9999*******.8999************986 PP

>> TraI_2  Putative helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.13   1.2e+03     291     318 ..      26      55 ..      19      61 .. 0.75
   2 ?   10.3   0.0   2.7e-05      0.24     264     324 ..      65     126 ..      59     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.13
                         TraI_2 291 alLlsdgisgiP..ksnetlfdllqeagii 318
                                    +++ +++i + P   + ++l ++l +++i+
  gi|121638515|ref|YP_978739.1|  26 QYMREHDIGALPicGDDDRLHGMLTDRDIV 55 
                                    566677777666335799999999999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.7e-05
                         TraI_2 264 vnkkgarvWltedglwlV.sktaadevralLlsdgisgiPks.netlfdllqeagiieaapdg 324
                                     n++  ++ l+ d ++ V +++  +e++++++++++  +P   +++l+++  ea+i+ + p+ 
  gi|121638515|ref|YP_978739.1|  65 PNTA-TAGELARDSIYYVdANASIQEMLNVMEEHQVRRVPVIsEHRLVGIVTEADIARHLPEH 126
                                    4444.6788899999888356678****************85499***********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1053.79
//
Query:       gi|121638516|ref|YP_978740.1|  [L=413]
Description: hypothetical protein BCG_2654c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-05   23.2   0.0      0.041   13.0   0.1    2.1  2  DUF2048      Abhydrolase domain containing 18
  ------ inclusion threshold ------
      0.015   14.6   0.0      0.084   12.1   0.0    1.9  2  Hydrolase_4  Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   4.6e-06     0.041     160     196 ..     246     283 ..     235     295 .. 0.84
   2 !    8.2   0.0   0.00013       1.2     303     346 ..     350     392 ..     326     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-06
                        DUF2048 160 ilEslvllhwlere.GyGplgltGlSmGGhmaslaasn 196
                                    + + + ll w+  +     +gl GlS+GG  asl+as+
  gi|121638516|ref|YP_978740.1| 246 VWDIRRLLSWIRSQeEESLIGLNGLSLGGYIASLVASL 283
                                    56788999999988567789****************97 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00013
                        DUF2048 303 dDayv.presvaslqeiwpgsevryldgGHvsayllkkklfrkai 346
                                     D+ v pre+v+ l e w   e+ +  gGH  ++ ++    r+ +
  gi|121638516|ref|YP_978740.1| 350 ADRLVhPREQVTRLWEHWGKPEIVWYPGGHTGFFQSR--PVRRFV 392
                                    689999************************9987554..345555 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-06     0.084      51     110 ..     238     296 ..     216     330 .. 0.82
   2 ?   -0.4   0.0     0.062   5.6e+02     195     229 ..     344     377 ..     321     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-06
                    Hydrolase_4  51 hvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPa 110
                                    +v+ + + v D++ +++ ++++++e+ + l G S+GG+ia l++  ++  +a +il  P+
  gi|121638516|ref|YP_978740.1| 238 DVHGTAQAVWDIRRLLSWIRSQEEESLIGLNGLSLGGYIASLVASLEEG-LACAILGVPV 296
                                    799999*************************************988888.7777776665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.062
                    Hydrolase_4 195 lllhGeaDkvvdpeas.relyerlgskdktlklypg 229
                                    +++ G aD++v+p+++  +l e+ g  + ++ +ypg
  gi|121638516|ref|YP_978740.1| 344 FIYAGIADRLVHPREQvTRLWEHWG--KPEIVWYPG 377
                                    688999********99888888887..467777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2582.52
//
Query:       gi|121638517|ref|YP_978741.1|  [L=120]
Description: hypothetical protein BCG_2655 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 910.79
//
Query:       gi|121638518|ref|YP_978742.1|  [L=374]
Description: hypothetical protein BCG_2656 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-43  148.7   0.8    1.2e-43  148.7   0.8    2.0  3  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
    3.7e-12   46.7   0.1    1.2e-11   45.1   0.1    1.9  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    4.2e-06   27.1   0.1    4.2e-06   27.1   0.1    2.9  3  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    4.2e-05   24.0   0.0      0.001   19.5   0.0    2.7  3  eRF1_3          eRF1 domain 3
    0.00011   22.5   0.3    0.00061   20.1   0.0    1.9  2  baeRF_family3   Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.025   14.8   0.2       0.19   12.0   0.1    2.3  2  RisS_PPD        Periplasmic domain of Sensor histidine kinase
      0.076   12.5   0.0       0.14   11.6   0.0    1.3  1  ROK             ROK family


Domain annotation for each model (and alignments):
>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.6   4.2e+03      89      99 ..      52      62 ..      25      76 .. 0.56
   2 !  148.7   0.8   4.8e-47   1.2e-43       1     149 []     118     266 ..     118     266 .. 0.99
   3 ?   -2.9   0.1       2.4   6.2e+03     106     134 ..     301     329 ..     290     332 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                  baeRF_family2 89 sllrdeLperv 99
                                   + l d+L+e+v
  gi|121638518|ref|YP_978742.1| 52 QELIDSLEEAV 62
                                   22333333333 PP

  == domain 2  score: 148.7 bits;  conditional E-value: 4.8e-47
                  baeRF_family2   1 pylvvevDrtGadltlvdaggeeeeetveGghdpvhkvraggw.shrryqrraeeswerNaeavAeevdrlvresgaelV 79 
                                    +y++++vD+tGad++l++++ + ++++++G ++pvhk+ ++gw +++++q+++ee++++N++avA++++rlv+  ++e+V
  gi|121638518|ref|YP_978742.1| 118 TYVFAAVDHTGADVKLYQGA-TISSTKIDGVGYPVHKPVTAGWnGYGDFQHTTEEAIRMNCRAVADHLTRLVDAADPEVV 196
                                    59****************77.*********************99************************************ PP

                  baeRF_family2  80 vlaGDvrarsllrdeLpervrelvvevegggraagadrealaeevaealaerrarrreevlerfraergr 149
                                    +++G+vr+r++l + Lp+rv+ +v+++++g r++  d+e++ + + +++++rr +++++v+++f+ae gr
  gi|121638518|ref|YP_978742.1| 197 FVSGEVRSRTDLLSTLPQRVAVRVSQLHAGPRKSALDEEEIWDLTSAEFTRRRYAEITNVAQQFEAEIGR 266
                                    *******************************************************************998 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                  baeRF_family2 106 vegggraagadrealaeevaealaerrar 134
                                    v g++r+  a ++++  e+ e +++++++
  gi|121638518|ref|YP_978742.1| 301 VTGKARTTVARDADMLSELGEPVDRVARA 329
                                    55566666666666666666666665554 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   4.6e-15   1.2e-11       1     119 [.     104     223 ..     104     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.6e-15
                 baeRF_family10   1 PylapLlealdeyerygvvlvdreraRlfevylgelee..veevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                    Py+ pL+++  + + y+ + vd+++a +  +++  +     ++v  +v+ ++ t+gw +   fq+  ee ++ + ++vA+
  gi|121638518|ref|YP_978742.1| 104 PYVVPLIDLEMRRPTYVFAAVDHTGADVKLYQGATISStkIDGVGYPVH-KPVTAGWNGYGDFQHTTEEAIRMNCRAVAD 182
                                    9*************************88888888887754778888888.799*************************** PP

                 baeRF_family10  79 llaklleergverlvlgGdeeetaalldrlpkalrarvvgt 119
                                    +l++l++  + e ++++G  + +  ll+ lp++++ rv + 
  gi|121638518|ref|YP_978742.1| 183 HLTRLVDAADPEVVFVSGEVRSRTDLLSTLPQRVAVRVSQL 223
                                    ***********************************999875 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.64   1.6e+03      59      86 ..      58      85 ..      24      99 .. 0.54
   2 !   27.1   0.1   1.6e-09   4.2e-06       3     119 ..     120     234 ..     117     238 .. 0.81
   3 ?    0.6   0.9      0.25   6.4e+02      49     115 ..     247     325 ..     241     333 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.64
                        acVLRF1 59 leavaeaaarllaeesaevvlgGdrslv 86
                                   le+++ + +  ++++ ++++ +G++ lv
  gi|121638518|ref|YP_978742.1| 58 LEEAVRDSRPAVGQRGRALIATGEQVLV 85
                                   1222222222222222226666665555 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.6e-09
                        acVLRF1   3 lgvllvrrggfavgvveggelvask.vgtrdvqgrtaaGGw.SqqRfaRrrenqadalleavaeaaarllaeesae.vvl 79 
                                    + ++++++g+ +v +++g ++ ++k  g  ++ ++    Gw     f+   e+ ++ + +ava+++ rl++++++e v++
  gi|121638518|ref|YP_978742.1| 120 VFAAVDHTGA-DVKLYQGATISSTKiDGVGYPVHKPVTAGWnGYGDFQHTTEEAIRMNCRAVADHLTRLVDAADPEvVFV 198
                                    4556777777.******99988887357789999999999967789******************************999* PP

                        acVLRF1  80 gGdrslvaevledarlaplatlareelldvpdprravLed 119
                                     G+ + + ++l+    +++a ++++     + pr+++L++
  gi|121638518|ref|YP_978742.1| 199 SGEVRSRTDLLSTLP-QRVAVRVSQ---LHAGPRKSALDE 234
                                    ************955.344444444...345677788876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.25
                        acVLRF1  49 Rrrenqadalleavaeaaarll.......aeesae...........vvlgGdrslvaevledarlaplatlare.ell.d 108
                                    Rrr  ++ + +++ ++++ r         a    e            +++G+   +  v  +ar    +t ar+ ++l +
  gi|121638518|ref|YP_978742.1| 247 RRRYAEITNVAQQFEAEIGRGSglaaqglA----EvcaalrdgdvdTLIVGELGEATVVTGKAR----TTVARDaDMLsE 318
                                    555555555555554444444433322221....122223334566777777777777776655....222222223337 PP

                        acVLRF1 109 vpdprra 115
                                    +++p+ +
  gi|121638518|ref|YP_978742.1| 319 LGEPVDR 325
                                    7777555 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3   8.5e+03      53      75 ..      40      62 ..      26      70 .. 0.54
   2 ?    1.2   0.0       0.2   5.1e+02      64     100 ..     171     210 ..     123     213 .. 0.80
   3 !   19.5   0.0     4e-07     0.001       5     112 ..     254     364 ..     250     365 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                                   HHHHHS-HHH-HHHHHHHHHHHH CS
                         eRF1_3 53 tlkekvketgeelelvelieelv 75
                                   +++++ ++  +++el++ +ee v
  gi|121638518|ref|YP_978742.1| 40 DVRKHLESRDAKQELIDSLEEAV 62
                                   24444455555666666555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                                    HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHH CS
                         eRF1_3  64 elelve...lieelvenveesgakveiisseseeGeqlvk 100
                                    e+ +++   ++++l++ v+    +v+++s e  + + l++
  gi|121638518|ref|YP_978742.1| 171 EAIRMNcraVADHLTRLVDAADPEVVFVSGEVRSRTDLLS 210
                                    3333335568999****************99988877765 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 4e-07
                                    HHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS..-HHH-HHHHHH.HHHHHHHHHHHT CS
                         eRF1_3   5 kklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv..ketgeelelve.lieelvenvees 81 
                                    +++ ++f  e+ +++g+a+ G  ev +al+ g v+tL+v e  e + +t k ++   ++ + l+++   ++++++  e  
  gi|121638518|ref|YP_978742.1| 254 TNVAQQFEAEIGRGSGLAAQGLAEVCAALRDGDVDTLIVGELGEATVVTGKARTtvARDADMLSELGePVDRVARADEAL 333
                                    577899**********************************9999988774444322444444444446777777777777 PP

                                    T-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                         eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRyk 112
                                        + +        + ++ + G++a+LRy 
  gi|121638518|ref|YP_978742.1| 334 PFAAIAVGAALVRDDNRIAPLDGVGALLRYA 364
                                    666666665555554444999********95 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.42   1.1e+03     113     149 ..      25      63 ..      18      70 .. 0.70
   2 !   20.1   0.0   2.4e-07   0.00061      12     167 ..     131     285 ..     127     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.42
                  baeRF_family3 113 paelsaeeLreaawplveayaeee..raealeeldearg 149
                                    ++ l+a e rea w  v++++e +  ++e+++ l+ea+ 
  gi|121638518|ref|YP_978742.1|  25 HDTLDAVERREATWRDVRKHLESRdaKQELIDSLEEAVR 63 
                                    566666677788888888877654226788888888876 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.4e-07
                  baeRF_family3  12 vrLfegtrdsleeveadgfPltleealgeedperqeghgdkkseyrdedtrrFlreVdkalqevls.esplplvlaGvee 90 
                                    v+L++g   s ++++  g P        ++ +    g+gd + +  +e +r   r+V ++l++++  ++p  +++ G+ +
  gi|121638518|ref|YP_978742.1| 131 VKLYQGATISSTKIDGVGYPVH------KPVTAGWNGYGDFQHT-TEEAIRMNCRAVADHLTRLVDaADPEVVFVSGEVR 203
                                    7788888888888876666732......3566667788998888.9********************999999*****866 PP

                  baeRF_family3  91 .nlslfrevsknpsliegglegnp..aelsaeeLreaawplveayaeeeraealeeldea..rgrgkfaagldevwqaar 165
                                      + l+  + ++  +    l+  p  ++l++ee+++        ++ +e +++++++++   rg+g++a+gl+ev +a r
  gi|121638518|ref|YP_978742.1| 204 sRTDLLSTLPQRVAVRVSQLHAGPrkSALDEEEIWDLTSAEFTRRRYAEITNVAQQFEAEigRGSGLAAQGLAEVCAALR 283
                                    15667777777777777777777766889*****************************98224557899*********99 PP

                  baeRF_family3 166 eG 167
                                    +G
  gi|121638518|ref|YP_978742.1| 284 DG 285
                                    98 PP

>> RisS_PPD  Periplasmic domain of Sensor histidine kinase RisS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.45   1.2e+03      42      77 ..      19      55 ..       6      62 .. 0.81
   2 ?   12.0   0.1   7.6e-05      0.19      23      83 ..     201     262 ..     178     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.45
                       RisS_PPD 42 ilprepsDkiepleddr.ltrliaeevrerlgektiv 77
                                   ++  +++D+++++e ++ ++r + +++++r  ++  +
  gi|121638518|ref|YP_978742.1| 19 VYFDDSHDTLDAVERREaTWRDVRKHLESRDAKQELI 55
                                   6777888999999887769999999999988777655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.6e-05
                       RisS_PPD  23 dpelrvaLlkeLaekegirilprepsDkiepleddrltrliaeev.rerlgektivassvng 83 
                                    +   r++Ll++L ++ ++r+++ ++  + ++l+++++++l ++e  r+r  e t va++++ 
  gi|121638518|ref|YP_978742.1| 201 EVRSRTDLLSTLPQRVAVRVSQLHAGPRKSALDEEEIWDLTSAEFtRRRYAEITNVAQQFEA 262
                                    56789***********************************9888626678888899998766 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.14     210     264 ..     168     222 ..     162     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTT CS
                            ROK 210 vaeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairklvkkylnk 264
                                    ++ee+++   +++a  ++ l+ + dp+++ + G+v    +ll ++ + v+ ++ +
  gi|121638518|ref|YP_978742.1| 168 TTEEAIRMNCRAVADHLTRLVDAADPEVVFVSGEVRSRTDLLSTLPQRVAVRVSQ 222
                                    68999****************************************9999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2654.40
//
Query:       gi|121638519|ref|YP_978743.1|  [L=179]
Description: hypothetical protein BCG_2657 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-19   71.0   0.0    1.7e-19   70.4   0.0    1.3  1  Archease       Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
       0.16   12.3   0.1       0.23   11.7   0.1    1.2  1  baeRF_family3  Bacterial archaeo-eukaryotic release factor fa


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   1.9e-23   1.7e-19       3     138 .]      49     179 .]      47     179 .] 0.83

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.9e-23
                                    E---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EE CS
                       Archease   3 yldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkv 82 
                                     ++htAD++ieaw+++ + ++ +a+l+++e++ dl++ ++ +++  +++a+  +dlL+++L+e++yl+dt      ++++
  gi|121638519|ref|YP_978743.1|  49 SVPHTADLRIEAWAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPVDLRL 128
                                    589*******************************************************************9666666622 PP

                                    EE.E-SSSEEEEEEEE----.-TT-.-------B--S---EEEEETTEEEEEEEEE- CS
                       Archease  83 deeeeeeeleleaeargekfdkekh.evqtevKAvTyhelrieeeddgweayvvvDi 138
                                        ++ +  +++++       +   +v++  KAv+++elr+++ ++gw++ v++D+
  gi|121638519|ref|YP_978743.1| 129 ----RDVDGGVDVTFATTDA--STLvQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV 179
                                    ....2233444444444444..3331456777************************8 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.6e-05      0.23      67     123 ..      88     149 ..      80     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                  baeRF_family3  67 eVdkalqevlsesplplvlaGveenlslfrevsknp.....sliegglegnpaelsaeeLre 123
                                    +V++ l+++ ++++  l++a +ee++ l++ v++ p     + ++gg++  +a ++a++L++
  gi|121638519|ref|YP_978743.1|  88 AVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPvdlrlRDVDGGVDVTFATTDASTLVQ 149
                                    7999*************************************99*************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1351.64
//
Query:       gi|121638520|ref|YP_978744.1|  [L=432]
Description: hypothetical protein BCG_2658 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-147  492.4   0.0   1.4e-147  492.2   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.2   0.0  7.6e-152  1.4e-147       1     412 []       2     432 .]       2     432 .] 0.98

  Alignments for each domain:
  == domain 1  score: 492.2 bits;  conditional E-value: 7.6e-152
                                    HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-....-EE-HHHC-SST.-EEEEEEEE.EEHHHHGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                           RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk....gviiPaaVGvDI.CGvrllktn.ltaeeleeklkelvkel 74 
                                    q+ nva+lpgiv++++amPDvH+G+g+piG+V+at+    gv++P++VG+DI CGvrll  + l++eel+++l +++++l
  gi|121638520|ref|YP_978744.1|   2 QVVNVATLPGIVRASYAMPDVHWGYGFPIGGVAATDvdndGVVSPGGVGFDIsCGVRLLVGEgLDREELQPRLPAVMDRL 81 
                                    899******************************************************987655***************** PP

                                    HHHS-------------.HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB  75 ekavpvglgskkkvkls.kkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGN 153
                                     +a+p g+g+++  +l  +++l+evl+ ga++ave+g g   dle++e+ g +++ad++k+s++a +r+  q+G+lGsGN
  gi|121638520|ref|YP_978744.1|  82 DRAIPRGVGTAGVWRLPdRNTLQEVLTGGARFAVEQGHGVALDLERCEDGGVMTGADAAKISDRALQRGLGQIGSLGSGN 161
                                    *********999999985699*********************************************************** PP

                                    -EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 154 HFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYl 233
                                    HF+Evq v++++d  aa+ +gl eg+v+vm+H+GSRglGhqi++d+++++++a+ ++gi +pdr+La++p++s++gqaYl
  gi|121638520|ref|YP_978744.1| 162 HFLEVQAVDRVYDPVAAAPMGLAEGTVCVMIHTGSRGLGHQICTDHVRQMEQAMGRYGIAVPDRQLACVPVHSPDGQAYL 241
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-....... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx....... RF
                           RtcB 234 kamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA....... 302
                                    +am+aaany++aNRq++te +r+++++ +++      l+l++dv+HN+ak E+h  d   ++v+VhRKGAtr+       
  gi|121638520|ref|YP_978744.1| 242 AAMAAAANYGRANRQLLTEATRRVFADATGT-----PLDLLYDVSHNLAKIETHPiDgqlRSVCVHRKGATRSlpphhhe 316
                                    *************************999963.....3589***************96799******************** PP

                                    ......TT--EEEE--STTS-EEEEE--HHHHSSSEE---S-----------------TTTTTCCCT-EEEE-------- CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 303 ......kvgqpviipGsmgtkSyivkGkgnaesfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvle 376
                                          +vgqpv+ipG mgt+Sy+++G   + +f St+HGAGR++sR++a ++ ++e ++++l+++gi+v+ ++++g++e
  gi|121638520|ref|YP_978744.1| 317 lpaelaAVGQPVLIPGTMGTASYVLAGVTGNPAFFSTAHGAGRVLSRHQAARHTSGEAIRASLAKRGIIVRGTSRRGIAE 396
                                    ******************************************************************************** PP

                                    ----------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 377 EapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                    E peaYKd+deV+ea +++gl+++varl p+++vkg
  gi|121638520|ref|YP_978744.1| 397 EKPEAYKDVDEVIEASHQSGLARKVARLVPLGCVKG 432
                                    ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3061.97
//
Query:       gi|121638521|ref|YP_978745.1|  [L=93]
Description: hypothetical protein BCG_2659c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-30  103.4   0.4    5.2e-30  103.2   0.4    1.0  1  DUF1876    Domain of unknown function (DUF1876)
  ------ inclusion threshold ------
      0.014   15.7   0.2      0.018   15.3   0.2    1.3  1  TetR_C_16  Tetracyclin repressor-like, C-terminal domain
        0.2   12.0   0.0       0.24   11.7   0.0    1.2  1  LPP20      LPP20 lipoprotein


Domain annotation for each model (and alignments):
>> DUF1876  Domain of unknown function (DUF1876)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.4   8.7e-34   5.2e-30       1      81 [.       9      88 ..       9      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 8.7e-34
                                   ----EEEEEEEETTEEEEEEEEE.ETTEEEEEEEEEES-SSS---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-XXX CS
                        DUF1876  1 kewtveleldEddgrTrAearlrltdetelrgvGlArrnpaDedvpeiGdElAaaRALsdLaeqLleaaaedieavthrpa 81
                                   k++++++ ++E+d+rTrA+arl+ +++++++gvGlAr +paDe v++iGdElA aRALsdLa+qL++ +++diea+th+p+
  gi|121638521|ref|YP_978745.1|  9 KTCQIDVLIEEHDERTRAKARLS-WAGRQMVGVGLARLDPADEPVAQIGDELAIARALSDLANQLFALTSSDIEASTHQPV 88
                                   689********************.*******************************************************97 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.9e-06     0.018      57      97 ..      22      62 ..      12      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                                   -STTHHHHHHHHHHHHHHHHHHHHTS--TTCCCS-HHHHHH CS
                      TetR_C_16 57 ggpdaelRaalvasqllGlalaRyvlrleplasasreelva 97
                                   + ++a+ R + ++ q++G++laR     ep+a+   e  +a
  gi|121638521|ref|YP_978745.1| 22 ERTRAKARLSWAGRQMVGVGLARLDPADEPVAQIGDELAIA 62
                                   345999*************************9988775555 PP

>> LPP20  LPP20 lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.24      14      50 ..      36      83 ..      23      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                          LPP20 14 yllgvGeaesl...........raAkqnAlrdiaeqiqvqvksssstq 50
                                   ++ gvG a+             + A++ Al+d+a q++   +s+ + +
  gi|121638521|ref|YP_978745.1| 36 QMVGVGLARLDpadepvaqigdELAIARALSDLANQLFALTSSDIEAS 83
                                   577777777667888888888899*****************9998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 699.61
//
Query:       gi|121638522|ref|YP_978746.1|  [L=161]
Description: hypothetical protein BCG_2660c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-15   55.7   1.6    7.5e-15   55.7   1.6    1.4  2  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.6   4.2e-19   7.5e-15       2     130 ..       3     116 ..       2     116 .. 0.90
   2 ?   -3.0   0.0      0.59   1.1e+04     115     118 ..     133     136 ..     123     150 .. 0.47

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.2e-19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHH CS
                    Hemerythrin   2 ivealdeeHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHd 81 
                                    ++++l+++H  l+ l + + ++  +        ++ + l+de+  el++H+++E++l++P+l    ++  ++ + ++eH+
  gi|121638522|ref|YP_978746.1|   3 AYDVLKRHHTVLKGLGRKVGEAPVN-------SEERHVLFDEMLIELDIHFRIEDDLYYPALS---AAGKPITGTHAEHR 72 
                                    5799*************99999998.......78999**************************...88888888888888 PP

                                    HHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                    Hemerythrin  82 eirelleelrellkgleepsaaafaelleeladllreHiakEesilfpl 130
                                    ++ ++l +l ++ ++++       +e+  +++++l+ H ++Ee+ ++p+
  gi|121638522|ref|YP_978746.1|  73 QVVDQLATLLRTPQRAP-----GYEEEWNVFRTVLEAHADVEERDMIPA 116
                                    88888888888888877.....899999******************995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.59
                                    HHHH CS
                    Hemerythrin 115 llre 118
                                     ++ 
  gi|121638522|ref|YP_978746.1| 133 KMAA 136
                                    1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1167.30
//
Query:       gi|121638523|ref|YP_978747.1|  [L=800]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-34  117.2  16.8    4.6e-34  116.6  16.8    1.3  1  PE              PE family
  ------ inclusion threshold ------
        1.4    9.5   7.8        2.2    8.8   7.8    1.3  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6  16.8   5.2e-38   4.6e-34       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.2e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Peal+ aa+dla+igs+++aanaaaa ptt+v+aaaaDeVSaa+Aalf+++aq+yqa++aq +afh+qfvq+l++
  gi|121638523|ref|YP_978747.1|  1 MSFVIAVPEALTMAASDLANIGSTINAANAAAALPTTGVVAAAADEVSAAVAALFGSYAQSYQAFGAQLSAFHAQFVQSLTN 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +a+sY  aEa
  gi|121638523|ref|YP_978747.1| 83 GARSYVVAEA 92
                                   *********9 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.8   0.00024       2.2       6      98 ..       5      98 ..       1     100 [. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00024
                  T7SS_ESX_EspC  6 sVdpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaa 86
                                     +p++l  +a+++ ++ ++i++a+aaa ++++  v+     ++aa+++ + ++ ++ +a g++l a ++++ + L+  A  
  gi|121638523|ref|YP_978747.1|  5 IAVPEALTMAASDLANIGSTINAANAAAaLPTTGVVAAAADEVSAAVAALFGSYAQSYQAFGAQLSAFHAQFVQSLTNGARS 86
                                   578***********************9988899999999999**************************************** PP

                  T7SS_ESX_EspC 87 YeatDeeaagal 98
                                   Y  ++ ++a  l
  gi|121638523|ref|YP_978747.1| 87 YVVAEATSAAPL 98
                                   **9999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.07u 0.35s 00:00:01.42 Elapsed: 00:00:00.57
# Mc/sec: 4207.11
//
Query:       gi|121638524|ref|YP_978748.1|  [L=80]
Description: hypothetical protein BCG_2662 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 558.11
//
Query:       gi|121638525|ref|YP_978749.1|  [L=225]
Description: hypothetical protein BCG_2663 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-70  235.4   0.0    3.9e-70  235.2   0.0    1.0  1  CPT         Chloramphenicol phosphotransferase-like protein
     0.0031   17.7   0.0     0.0099   16.0   0.0    1.9  1  AAA_33      AAA domain
  ------ inclusion threshold ------
      0.033   13.5   0.0      0.047   13.0   0.0    1.2  1  DnaB_C      DnaB-like helicase C terminal domain
      0.036   13.3   0.0       0.57    9.4   0.0    2.1  2  Zeta_toxin  Zeta toxin
      0.097   12.0   0.0       0.17   11.2   0.0    1.3  1  ATPase      KaiC
       0.13   12.6   0.0       0.45   10.9   0.0    1.8  3  AAA_16      AAA ATPase domain
       0.17   11.3   0.0       0.25   10.8   0.0    1.1  1  RecA        recA bacterial DNA recombination protein
       0.19   10.9   0.0       0.28   10.4   0.0    1.2  1  TIP49       TIP49 P-loop domain


Domain annotation for each model (and alignments):
>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.2   0.0   1.7e-73   3.9e-70       1     174 []      23     208 ..      23     208 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 1.7e-73
                                    --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGT...............STTSEEEETTSEEE-HHH CS
                            CPT   1 ariilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqd...............eadglefeteleeigpel 65 
                                    +++ilLnGgss+GK+sla a+q++++e+w+h+g+D f++alpp+++d               eadgle++t+++  gp+l
  gi|121638525|ref|YP_978749.1|  23 GKLILLNGGSSAGKTSLALAFQDLAAECWMHIGIDLFWFALPPEQLDlarvrpeyytwdsavEADGLEWFTVHP--GPIL 100
                                    799***********************************************************************..**** PP

                                    HHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTSSSTTHHHHHTTGG CS
                            CPT  66 dlllaalyeavaamaraGnnvivDdvilekewlvdllrrllsgldvllVGvrcplevlerRelergdRepGlaalqaeav 145
                                    dl+++++y+a++a++++G+nvi+Ddvi+++ewlvd+l r+++g++v++VGv++++e+ +rRelergdR+pG+++ +a+a+
  gi|121638525|ref|YP_978749.1| 101 DLAMHSRYRAIRAYLDNGMNVIADDVIWTREWLVDAL-RVFEGCRVWMVGVHVSDEEGARRELERGDRHPGWNRGSARAA 179
                                    *************************************.****************************************** PP

                                    GTT---SEEEETTSS-HHHHHHHHHTT-- CS
                            CPT 146 HagaeyDlevDtsaktpeecArairerle 174
                                    Ha+aeyD+e+Dt+a++++e+Ar+++e+++
  gi|121638525|ref|YP_978749.1| 180 HADAEYDFELDTTATPVHELARELHESYQ 208
                                    **************************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.4e-06    0.0099       1     121 [.      25     167 ..      25     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                         AAA_33   1 lvllvGlpGsGKstlaerl..lkklgavllssdtlrrrlfgtdqqskt......................dytrvldrly 56 
                                    l+ll G + +GK+ la     l+++ + ++  d + ++l +++ +  +                       +  +ld + 
  gi|121638525|ref|YP_978749.1|  25 LILLNGGSSAGKTSLALAFqdLAAECWMHIGIDLFWFALPPEQLDLARvrpeyytwdsaveadglewftvHPGPILDLAM 104
                                    68899999999999998754455555999999998888887555533355556777777777777766553334666666 PP

                         AAA_33  57 qilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                        + +r +l  g nvi+d   ++r+   + l++++  g++v +v v++++e+ ++R  +R ++
  gi|121638525|ref|YP_978749.1| 105 HSRYRAIRAYLDNGMNVIADDVIWTREWLVDALRVFE--GCRVWMVGVHVSDEEGARRELERGDR 167
                                    66678999*****************************..*******************9999986 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.047      12      45 ..      16      49 ..      13      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                                   HCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 12 ltsGlqkgdliiiAarpsmGktalalniaenaav 45
                                   ++ G+ +g+li++ + +s Gkt+lal +   aa+
  gi|121638525|ref|YP_978749.1| 16 AMAGMPEGKLILLNGGSSAGKTSLALAFQDLAAE 49
                                   5789**********************98877663 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00026      0.57      17      45 ..      24      50 ..      14      78 .. 0.84
   2 ?    1.9   0.0      0.05   1.1e+02      87     147 ..     110     168 ..     104     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                     Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgn 45
                                   klill G++ AGK++la +++d    ++ 
  gi|121638525|ref|YP_978749.1| 24 KLILLNGGSSAGKTSLALAFQDLA--AEC 50
                                   79****************999865..455 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.05
                     Zeta_toxin  87 llqeaiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeee 147
                                    ++ + ++ng+n+i +  + + +++ ++ + ++  G +v  v v v+ e+ + + l+R    
  gi|121638525|ref|YP_978749.1| 110 AIRAYLDNGMNVIADDVIWTREWLVDALRVFE--GCRVWMVGVHVSDEEGARRELERGDRH 168
                                    56677899********9999999998888885..688888888888877777766666555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.6e-05      0.17      14      39 ..      18      43 ..      13      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                         ATPase 14 gGipegrvvlitGepGtGKtifalqF 39
                                    G+peg+ +l+ G++ +GKt +al F
  gi|121638525|ref|YP_978749.1| 18 AGMPEGKLILLNGGSSAGKTSLALAF 43
                                   69*********************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.45      18      50 ..      17      48 ..       8      72 .. 0.80
   2 ?   -3.1   0.0       3.9   8.8e+03     142     160 ..      87     105 ..      83     110 .. 0.83
   3 ?   -2.4   0.0       2.5   5.5e+03      96     117 ..     184     209 ..     172     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralek 50
                                   ++ ++++ l+ll G s  GK+sl+ ++++ l +
  gi|121638525|ref|YP_978749.1| 17 MAGMPEGKLILLNGGSSAGKTSLALAFQD-LAA 48
                                   44455669****************99884.444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                         AAA_16 142 DdlqwadeaslqllaaLlr 160
                                    D l+w+  ++  +l++ ++
  gi|121638525|ref|YP_978749.1|  87 DGLEWFTVHPGPILDLAMH 105
                                    9999999999999888776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                         AAA_16  96 awrekleealaavpelagaea....s 117
                                    +++ +l++++++v ela++++     
  gi|121638525|ref|YP_978749.1| 184 EYDFELDTTATPVHELARELHesyqA 209
                                    44444666666666766666644440 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.25      47      72 ..      17      42 ..      10      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                   SSSEETTSEEEEEESTTSSHHHHHHH CS
                           RecA 47 iGGlpkGriieiyGpessGkttlalh 72
                                   + G+p+G++i + G  s+Gkt+lal 
  gi|121638525|ref|YP_978749.1| 17 MAGMPEGKLILLNGGSSAGKTSLALA 42
                                   679********************996 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.28      50      70 ..      23      43 ..       3      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                                   XXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 50 GravLlaGpsgtGktalaiai 70
                                   G+ +Ll G s++Gkt+la+a 
  gi|121638525|ref|YP_978749.1| 23 GKLILLNGGSSAGKTSLALAF 43
                                   99*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1574.20
//
Query:       gi|121638526|ref|YP_978750.1|  [L=218]
Description: transmembrane protein dedA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-18   67.5   5.1    1.4e-18   67.5   5.1    2.7  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
      0.069   13.3   0.2      0.069   13.3   0.2    2.1  2  DUF2178      Predicted membrane protein (DUF2178)
       0.25   11.8   0.0        0.4   11.1   0.0    1.2  1  ACP_PD       Acyl carrier protein phosphodiesterase
       0.33   11.4   5.4        2.3    8.7   0.0    3.1  3  DUF5455      Family of unknown function (DUF5455)


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.51   2.3e+03      18      30 ..      12      24 ..       5      25 .. 0.59
   2 !   67.5   5.1   3.1e-22   1.4e-18       1     118 [.      32     161 ..      32     163 .. 0.92
   3 ?    2.0   0.3     0.064   2.9e+02      59      77 ..     168     186 ..     157     195 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.51
                    SNARE_assoc 18 lgtlvtslgallG 30
                                     ++++++ga++G
  gi|121638526|ref|YP_978750.1| 12 PLMVYLVVGAVVG 24
                                   3566666666665 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 3.1e-22
                    SNARE_assoc   1 lPsevllvaaGvlf.......glllgtlvtslgallGaslayllgrylgr...kalrrkllsekrvka...lerlveryg 67 
                                    lP+e++lv a+vl        +++ +  ++++ga++G+s++y +gr++g    ++l+r++ ++   +    +erl++r g
  gi|121638526|ref|YP_978750.1|  32 LPGEIVLVSAAVLSshpelavNPIGVGGAAVIGAVVGDSIGYSIGRRFGLplfDRLGRRFPKHFGPGHvalAERLFNRWG 111
                                    79************99999999999************************9999888888866666666777********* PP

                    SNARE_assoc  68 flallllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylG 118
                                    ++a++l+r+++ + r +++ +aG++++++ rF++a++ G i wa  ++ l 
  gi|121638526|ref|YP_978750.1| 112 VRAVFLGRFIALL-RIFAGPLAGALKMPYPRFLAANVTGGICWAGGTTALV 161
                                    ***********99.*****************************98777665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.064
                    SNARE_assoc  59 lerlverygflallllrll 77 
                                    +++++er+ ++al+++ + 
  gi|121638526|ref|YP_978750.1| 168 AQHWLERFSWIALVIAVIA 186
                                    4556666666555544333 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.6      0.67     3e+03       9      14 ..      37      42 ..      13      67 .. 0.53
   2 ?   13.3   0.2   1.5e-05     0.069       7      47 ..     160     202 ..     157     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.67
                        DUF2178  9 alvglg 14
                                   +lv+ +
  gi|121638526|ref|YP_978750.1| 37 VLVSAA 42
                                   223333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.5e-05
                        DUF2178   7 vialvglgi..waaignvllaviavaaGvllaillkkkveevv 47 
                                    ++ + g+++  w +  ++ ++viav+aG+ +aill++++   +
  gi|121638526|ref|YP_978750.1| 160 LVYFAGMAAqhWLERFSWIALVIAVIAGITAAILLRERTSRAI 202
                                    55667777777779999********************998443 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.9e-05       0.4      43      88 ..     163     208 ..     158     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                         ACP_PD  43 lprmieedwLesYaelegieralqrmarrlkrasklaeaieeleen 88 
                                    ++ m++++wLe+++ ++ +  +++++   +  +++ ++ai+ele++
  gi|121638526|ref|YP_978750.1| 163 FAGMAAQHWLERFSWIALVIAVIAGITAAILLRERTSRAIAELEAE 208
                                    578************************99999999********986 PP

>> DUF5455  Family of unknown function (DUF5455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.17   7.7e+02      45      75 ..      16      46 ..       6      52 .. 0.85
   2 ?    8.7   0.0    0.0005       2.3      17      42 ..     101     126 ..      88     137 .. 0.86
   3 ?    2.3   0.9     0.049   2.2e+02      17      47 ..     162     192 ..     157     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                        DUF5455 45 vvllaalsglssiaetlpselsqgislvvPs 75
                                    ++++a+ g++s+  +lp e++ + ++v++s
  gi|121638526|ref|YP_978750.1| 16 YLVVGAVVGIESLGIPLPGEIVLVSAAVLSS 46
                                   5678999999999999999999999999886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0005
                        DUF5455  17 ylatfltkklAvaivalgliialivg 42 
                                    +la++l ++++v++v+lg +ial+  
  gi|121638526|ref|YP_978750.1| 101 ALAERLFNRWGVRAVFLGRFIALLRI 126
                                    5899******************9855 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.049
                        DUF5455  17 ylatfltkklAvaivalgliialivgllvvl 47 
                                    y+a + ++ +  +  +++l+ia i+g+  ++
  gi|121638526|ref|YP_978750.1| 162 YFAGMAAQHWLERFSWIALVIAVIAGITAAI 192
                                    5566666677777778888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1815.22
//
Query:       gi|121638527|ref|YP_978751.1|  [L=148]
Description: hypothetical protein BCG_2665 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-14   51.3   0.0    8.8e-14   51.1   0.0    1.1  1  STAS      STAS domain
    3.8e-07   30.3   0.7      6e-07   29.7   0.4    1.5  1  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   9.8e-18   8.8e-14       9     117 .]      39     137 ..      31     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 9.8e-18
                                    TEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES- CS
                           STAS   9 gililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlvni 88 
                                      l ++  g+id  n + +++ +++a++  +       ++ +li+d ++++f+ +++ +aL +  ++++ +g+++ lv+ 
  gi|121638527|ref|YP_978751.1|  39 AALLIHAGGEIDGRNEHLWRQLVTEAAAGVT-------APGPLIVDVTGLDFMGCCAFAALADEAQRCRCRGIDLRLVSH 111
                                    45889999********************996.......99**************************************** PP

                                    -HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  89 kpevreklektgffdeveeeklfltvhdA 117
                                    +p v++ +e+ g+++++   ++++tv++A
  gi|121638527|ref|YP_978751.1| 112 QPIVARIAEAGGLSRVL---PIYPTVDTA 137
                                    *****************...******987 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.4   6.7e-11     6e-07       2      80 .]      44     125 ..      43     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.7e-11
                         STAS_2   2 sLsGeldldtaaelreqlleal....aagaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlldly 77 
                                    +  Ge+d ++ + +r+ + ea+    a+g ++ vD++g+ ++ + a+a+L++ a ++r rg  l+l+ + p ++r+++  
  gi|121638527|ref|YP_978751.1|  44 HAGGEIDGRNEHLWRQLVTEAAagvtAPG-PLIVDVTGLDFMGCCAFAALADEAQRCRCRGIDLRLVSHQPIVARIAEAG 122
                                    66799999999999999988888887777.************************************************99 PP

                         STAS_2  78 Gld 80 
                                    Gl+
  gi|121638527|ref|YP_978751.1| 123 GLS 125
                                    985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 974.96
//
Query:       gi|121638528|ref|YP_978752.1|  [L=110]
Description: hypothetical protein BCG_2666c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-48  163.9   9.4    1.2e-48  163.8   9.4    1.0  1  UPF0060          Uncharacterised BCR, YnfA/UPF0060 family
  ------ inclusion threshold ------
       0.02   14.9   0.5       0.02   14.9   0.5    2.2  2  Phage_holin_2_1  Bacteriophage P21 holin S
       0.57    9.8   8.3        4.1    7.0   4.4    2.0  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> UPF0060  Uncharacterised BCR, YnfA/UPF0060 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   9.4     2e-52   1.2e-48       1     107 []       2     109 ..       2     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2e-52
                        UPF0060   1 vlksillfllaalaeigGaylvwlwlreaksvllalvaaillavygflatlqp.aafGrvyaayGGvfvvlallwglvvd 79 
                                    v++sillf+laa+aeigGa+lvw+++re++++l+a +++i+l+vygf+atlqp a+fGrv+aayGGvfv+++l+wg+++d
  gi|121638528|ref|YP_978752.1|   2 VVRSILLFVLAAVAEIGGAWLVWQGVREQRGWLWAGLGVIALGVYGFFATLQPdAHFGRVLAAYGGVFVAGSLAWGMALD 81 
                                    69****************************************************************************** PP

                        UPF0060  80 gvkldlydwiGalialvGvlvilyaprg 107
                                    g+++d++d+iGal++++Gv+vi+yaprg
  gi|121638528|ref|YP_978752.1|  82 GFRPDRWDVIGALGCMAGVAVIMYAPRG 109
                                    **************************96 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.0      0.14   8.4e+02      22      47 ..      25      51 ..       8      60 .. 0.65
   2 ?   14.9   0.5   3.4e-06      0.02       8      42 ..      64      98 ..      60     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                Phage_holin_2_1 22 qlldklspeeWsaigvlg.glvigllT 47
                                   q + +  +  W+ +gv++ g+   ++T
  gi|121638528|ref|YP_978752.1| 25 QGVREQRGWLWAGLGVIAlGVYGFFAT 51
                                   555555566699999998444444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-06
                Phage_holin_2_1  8 sYg..aSggsigywlkqlldklspeeWsaigvlgglv 42
                                   +Yg  + +gs +++    ld++ p+ W +ig lg ++
  gi|121638528|ref|YP_978752.1| 64 AYGgvFVAGSLAWG--MALDGFRPDRWDVIGALGCMA 98
                                   56533458888898..78*************999765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.4   0.00069       4.1       7      54 ..       7      54 ..       3      64 .. 0.60
   2 ?    5.1   0.1    0.0028        16      10      53 ..      65     108 ..      57     110 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00069
                        DUF4131  7 lvllalllllllllllllrrrprrrvllllllllllallgfalrapqp 54
                                   l++++++++ +  ++l+++  + +r +l ++l  ++++++ ++ ++qp
  gi|121638528|ref|YP_978752.1|  7 LLFVLAAVAEIGGAWLVWQGVREQRGWLWAGLGVIALGVYGFFATLQP 54
                                   455666666666667777665555555555555555555555555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0028
                        DUF4131  10 lalllllllllllllrrrprrrvllllllllllallgfalrapq 53 
                                     + ++++  l++   ++  r+ ++ ++++l ++a++ +  +ap+
  gi|121638528|ref|YP_978752.1|  65 YGGVFVAGSLAWGMALDGFRPDRWDVIGALGCMAGVAVIMYAPR 108
                                    4555555556655555699999**9***9999999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 818.05
//
Query:       gi|121638529|ref|YP_978753.1|  [L=119]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-17   62.4   0.0    4.3e-17   61.7   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    3.3e-14   52.7   1.3    5.2e-14   52.0   0.2    1.7  2  HTH_20          Helix-turn-helix domain
    0.00015   21.2   0.0    0.00023   20.6   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00018   21.3   0.1    0.00027   20.8   0.1    1.3  1  MarR_2          MarR family
     0.0002   21.5   0.0    0.00029   21.0   0.0    1.2  1  HTH_34          Winged helix DNA-binding domain
    0.00025   21.3   0.0    0.00036   20.8   0.0    1.2  1  Rrf2            Transcriptional regulator
     0.0015   18.4   0.0     0.0023   17.9   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0033   17.3   0.0     0.0049   16.8   0.0    1.3  1  MarR            MarR family
     0.0039   17.1   0.0     0.0057   16.6   0.0    1.3  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.014   15.0   0.1      0.023   14.3   0.1    1.3  1  RP-C            Replication protein C N-terminal domain
       0.03   14.5   0.0      0.044   14.0   0.0    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.043   14.3   0.0       0.15   12.6   0.0    1.8  2  HTH_27          Winged helix DNA-binding domain
      0.065   13.1   0.0      0.091   12.7   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.068   13.1   0.0       0.11   12.4   0.0    1.3  1  HTH_36          Helix-turn-helix domain
      0.078   13.4   0.0        0.1   13.1   0.0    1.2  1  HTH_40          Helix-turn-helix domain
       0.21   12.0   0.0       0.35   11.3   0.0    1.3  1  FaeA            FaeA-like protein
       0.22   12.0   0.0       0.29   11.6   0.0    1.2  1  Phage_X         Phage X family


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   4.1e-20   4.3e-17       1      47 []      41      90 ..      41      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.1e-20
                                   SHHHHHHHHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  1 dptRlkILklLae...gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   dp+R+kI+++L +   ge+ +++la++l ls +tvShHL++Lr+aGLV +
  gi|121638529|ref|YP_978753.1| 41 DPARVKIMSYLFSspaGEQVSGQLAAALSLSDGTVSHHLAQLRKAGLVIS 90
                                   8***********************************************75 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.9   3.1e+03      23      32 ..      12      21 ..      10      25 .. 0.82
   2 !   52.0   0.2     5e-17   5.2e-14       3      59 ..      35      93 ..      33      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.9
                                   TTB-HHHHHH CS
                         HTH_20 23 egltaselae 32
                                   ++++++++a+
  gi|121638529|ref|YP_978753.1| 12 APVCCAPVAA 21
                                   6899999987 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 5e-17
                                   HHHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  3 iaeALahPvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                    ++ALa+P R +i+++L  ++a+++  ++la++l+ls+ t+s+HL++L++agLv + r 
  gi|121638529|ref|YP_978753.1| 35 RLKALADPARVKIMSYLfsSPAGEQVSGQLAAALSLSDGTVSHHLAQLRKAGLVISDRR 93
                                   689**************************************************977765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.2e-07   0.00023      21      47 ..      62      88 ..      41      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                    +LA +l lS +tv+ +l +L ++Gl+
  gi|121638529|ref|YP_978753.1| 62 GQLAAALSLSDGTVSHHLAQLRKAGLV 88
                                   58***********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.6e-07   0.00027       5      52 ..      42      89 ..      37      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-07
                                   HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   pa   ++ +L  +p ++   g+la++l ls ++vs +l+ L +aGLv 
  gi|121638529|ref|YP_978753.1| 42 PARVKIMSYLFSSPAGEQVSGQLAAALSLSDGTVSHHLAQLRKAGLVI 89
                                   566666777777777777889**************************4 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-07   0.00029       2      46 ..      44      90 ..      43      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                         HTH_34  2 RlavlsyLas..vdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                   R +++syL s  + e    +l +al+++dg  s hl  L kag +  
  gi|121638529|ref|YP_978753.1| 44 RVKIMSYLFSspAGEQVSGQLAAALSLSDGTVSHHLAQLRKAGLVIS 90
                                   899******9888888899************************8865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.4e-07   0.00036      11      59 ..      45      92 ..      39      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-07
                                   HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   ++++ yL + + +e   s ++a+  ++s+  +++ la+Lrkaglv s r
  gi|121638529|ref|YP_978753.1| 45 VKIMSYLFSSPAGE-QVSGQLAAALSLSDGTVSHHLAQLRKAGLVISDR 92
                                   789****9999999.7789**************************9965 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.2e-06    0.0023      26      66 ..      63     107 ..      61     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                                    HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE...EEES-HHHHH CS
                      HTH_Crp_2  26 elAsmlGltretvsrilseLkreglis.rgrr...irildleaLr 66 
                                    +lA+ l l+  tvs  l++L+++gl+   +r+   ++   +eaL+
  gi|121638529|ref|YP_978753.1|  63 QLAAALSLSDGTVSHHLAQLRKAGLVIsDRRGmhvFHRVHPEALQ 107
                                    89***********************77544332245555566665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.7e-06    0.0049      17      48 ..      56      89 ..      41      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                                   TEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR 17 plsvs..eLakklgvskstvtrvldrLekkGlie 48
                                   +  +   +La +l++s +tv+  l +L k+Gl+ 
  gi|121638529|ref|YP_978753.1| 56 AGEQVsgQLAAALSLSDGTVSHHLAQLRKAGLVI 89
                                   5333345*************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.4e-06    0.0057      19      51 ..      62      94 ..      46      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.4e-06
                         HTH_11 19 eeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                    +LA  L++S  tv  ++++L+++g+ I  ++g
  gi|121638529|ref|YP_978753.1| 62 GQLAAALSLSDGTVSHHLAQLRKAGLVISDRRG 94
                                   57***********************77765555 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.2e-05     0.023      76     102 ..      63      89 ..      59      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                           RP-C  76 qLsralglsestlrrhlaaLveaGlii 102
                                    qL+ al+ls+ t+++hla+L +aGl+i
  gi|121638529|ref|YP_978753.1|  63 QLAAALSLSDGTVSHHLAQLRKAGLVI 89 
                                    899**********************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.2e-05     0.044      26      54 ..      62      90 ..      58      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                 Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyvey 54
                                    +la +L  s  +Vs  l  L+k+G+v+ 
  gi|121638529|ref|YP_978753.1| 62 GQLAAALSLSDGTVSHHLAQLRKAGLVIS 90
                                   589************************86 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.15      20      62 ..      60      97 ..      50     104 .. 0.83
   2 ?    0.9   0.0      0.62   6.6e+02      11      29 ..      96     114 ..      95     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                      +l+ +l ++d ++s  l +L ++GLv       drr ++v
  gi|121638529|ref|YP_978753.1| 60 VSGQLAAALSLSDGTVSHHLAQLRKAGLV-----ISDRRGMHV 97
                                   5568999**********************.....466777554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.62
                         HTH_27  11 lirhrrrrkkladlcgrln 29 
                                    ++ hr+++ +l +lc +ln
  gi|121638529|ref|YP_978753.1|  96 HVFHRVHPEALQALCTVLN 114
                                    78899**********9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.6e-05     0.091      27      68 .]      63     104 ..      56     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                                    HHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                           TrmB  27 eiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68 
                                    ++a +l ++  +v   L +L ++GlV   ++  ++++ v+pe
  gi|121638529|ref|YP_978753.1|  63 QLAAALSLSDGTVSHHLAQLRKAGLVISDRRGMHVFHRVHPE 104
                                    68889999*****************************99997 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.11      31      55 .]      64      88 ..      62      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                         HTH_36 31 lakrlglsknTvsraikeLeqlGyi 55
                                   la++l ls+ Tvs +++ L+++G++
  gi|121638529|ref|YP_978753.1| 64 LAAALSLSDGTVSHHLAQLRKAGLV 88
                                   99*********************85 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.6e-05       0.1      17      41 ..      63      87 ..      58     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-05
                         HTH_40 17 eIAkerglkesTIegHLaelieege 41
                                   + A+  +l+ +T+  HLa+l ++g 
  gi|121638529|ref|YP_978753.1| 63 QLAAALSLSDGTVSHHLAQLRKAGL 87
                                   679999****************994 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.35       5      55 ..      47      96 ..      44     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                   HHHHHHH.S----.HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS CS
                           FaeA  5 Ileylnsikapck.TreiAdalglsaYQaRyYLeqLekegkikrspvrrGvs 55
                                   I++yl s  a+ +   ++A al+ls+  + + L qL+k+g +     rrG+ 
  gi|121638529|ref|YP_978753.1| 47 IMSYLFSSPAGEQvSGQLAAALSLSDGTVSHHLAQLRKAGLVI--SDRRGMH 96
                                   777777755554414579**********************984..4466665 PP

>> Phage_X  Phage X family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.29      26      67 ..      62     104 ..      50     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                        Phage_X  26 Gydlvel.lskatfyrhraeLlkiGidiaqlcnlsefenvvpl 67 
                                    G+ + +l ls  t++ h+a+L+k G+ i+++  ++ f++v p+
  gi|121638529|ref|YP_978753.1|  62 GQLAAALsLSDGTVSHHLAQLRKAGLVISDRRGMHVFHRVHPE 104
                                    55556667999********************999999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 991.28
//
Query:       gi|121638530|ref|YP_978754.1|  [L=152]
Description: cadmium inducible protein cadI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-10   38.8   0.0    1.2e-09   38.4   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    0.00014   22.1   0.0      0.014   15.7   0.0    2.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    0.00014   22.6   0.0    0.00018   22.2   0.0    1.3  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.17   11.5   0.0    1.2  1  FAM124        FAM124 family


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.7e-13   1.2e-09       5     128 .]       6     114 ..       3     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.7e-13
                                    EEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEH CS
                     Glyoxalase   5 vallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdv 84 
                                    +al+v+dle+++ FY + ++++  k+++        ++a f + +  ++lvl e+p+++ +          h+++ + + 
  gi|121638530|ref|YP_978754.1|   6 LALNVDDLEAAITFYSRLFNAEPAKRKP--------GYANFAIADPPLKLVLLENPGTGGTLN--------HLGVEVGSS 69 
                                    689*************************........**************************9........9******** PP

                                    CHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE.EEEETTSEEEEE CS
                     Glyoxalase  85 edvgkaldrlkeagvkvvaepgrhyfgalysf.yfrDpdGillei 128
                                    + v + + rl eag+   +e+g+++  a ++  +++ p+G ++e+
  gi|121638530|ref|YP_978754.1|  70 NTVHAEIARLTEAGLVTEKEIGTTCCFATQDKvWVTGPGGERWEV 114
                                    ************************988888766999999999995 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     3e-06     0.014       2      91 ..       5      84 ..       4      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                                   EEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEE...S-HH CS
                   Glyoxalase_4  2 QigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywv...ddld 80
                                   Q+++ V+Dleaa+ ++s+l++ +p +r    p  ++ a+a+    ++++ L e+  +       g+ l+hl+++v   + ++
  gi|121638530|ref|YP_978754.1|  5 QLALNVDDLEAAITFYSRLFNAEPAKRK---PGYANFAIADP---PLKLVLLENPGT-------GGTLNHLGVEVgssNTVH 73
                                   89999****************9888774...33344444444...456777776665.......788888888883333688 PP

                                   HHHHHHCTTTE CS
                   Glyoxalase_4 81 aavarleeqGf 91
                                   a +arl+e+G+
  gi|121638530|ref|YP_978754.1| 74 AEIARLTEAGL 84
                                   88888888887 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     4e-08   0.00018       1      80 [.       5      83 ..       5     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4e-08
                   Glyoxalase_6  1 svvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpepaknrvHldlav...edldaevarlval 79
                                   +++l+++d +a+++F+++++  e ++++    +  +  ++a+   +l++ + p ++ +  Hl ++v   + ++ae+arl ++
  gi|121638530|ref|YP_978754.1|  5 QLALNVDDLEAAITFYSRLFNAEPAKRK----PGYANFAIADPPLKLVLLENPGTGGTLNHLGVEVgssNTVHAEIARLTEA 82
                                   57999*****************999999....333444456668899999****999999****998778889********9 PP

                   Glyoxalase_6 80 G 80
                                   G
  gi|121638530|ref|YP_978754.1| 83 G 83
                                   9 PP

>> FAM124  FAM124 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.17     130     168 ..       3      41 ..       1      49 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                         FAM124 130 RvtlyvseenyedavrlYelilrkeaaqkkedfCffvly 168
                                    Rv+l  + +++e a+ +Y+ + + e+a++k +++ f + 
  gi|121638530|ref|YP_978754.1|   3 RVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIA 41 
                                    99********************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1203.53
//
Query:       gi|121638531|ref|YP_978755.1|  [L=126]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-19   68.9   0.1    3.5e-19   68.4   0.1    1.2  1  HTH_5      Bacterial regulatory protein, arsR family
    2.1e-13   50.1   0.5    4.3e-13   49.1   0.5    1.5  1  HTH_20     Helix-turn-helix domain
    0.00076   19.3   0.5     0.0017   18.2   0.2    1.7  2  MarR_2     MarR family
      0.002   18.0   0.0      0.003   17.4   0.0    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0049   17.2   0.0      0.009   16.3   0.0    1.4  1  Rrf2       Transcriptional regulator
     0.0058   16.8   0.0      0.015   15.5   0.0    1.6  2  HTH_34     Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.024   14.2   0.0    1.3  1  HTH_24     Winged helix-turn-helix DNA-binding
      0.088   12.8   0.0       0.16   12.0   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.1   1.6e-22   3.5e-19       1      47 []      40      89 ..      40      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.6e-22
                                   SHHHHHHHHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  1 dptRlkILklLae...gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   dp Rl++L+++a+   ge+cvc++++ +++sq+t+ShHLk+Lr+aGL+++
  gi|121638531|ref|YP_978755.1| 40 DPVRLQLLSSVASragGEACVCDISAGVEVSQPTISHHLKVLRDAGLLTS 89
                                   8**********************************************975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.5   1.9e-16   4.3e-13       2      58 ..      33      91 ..      32      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.9e-16
                                   HHHHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20  2 qiaeALahPvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                     ++ALa+PvR+ +l+    + ++++++ ++ + +++s+ t+s+HL+vL++agL++++r
  gi|121638531|ref|YP_978755.1| 33 ARFKALADPVRLQLLSSVasRAGGEACVCDISAGVEVSQPTISHHLKVLRDAGLLTSRR 91
                                   579*****************99***********************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   2.8e+03      21      31 ..      25      35 ..      16      38 .. 0.66
   2 !   18.2   0.2   7.6e-07    0.0017       5      55 ..      41      91 ..      36      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                   EEEHHHHHHHH CS
                         MarR_2 21 dltvgelarrl 31
                                   + +++e a+r+
  gi|121638531|ref|YP_978755.1| 25 PPAAAEMAARF 35
                                   34777777775 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.6e-07
                                   HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   p  +++L  ++ r g++  v ++ +   +s++++s +lk L +aGL++ r+
  gi|121638531|ref|YP_978755.1| 41 PVRLQLLSSVASRAGGEACVCDISAGVEVSQPTISHHLKVLRDAGLLTSRR 91
                                   667899999999999999999**************************8774 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06     0.003      21      68 .]      56     103 ..      50     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                    CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                           TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68 
                                    g+a + +i+  ++v+++++   L+ L d+Gl + +++   +Y av pe
  gi|121638531|ref|YP_978755.1|  56 GEACVCDISAGVEVSQPTISHHLKVLRDAGLLTSRRRASWVYYAVVPE 103
                                    6677889*****************************999999999886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     4e-06     0.009      11      59 ..      44      91 ..      40      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4e-06
                                   HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   l++l   a+++++e + + +i++ +++s++ +++ l+ Lr agl++s+r
  gi|121638531|ref|YP_978755.1| 44 LQLLSSVASRAGGE-ACVCDISAGVEVSQPTISHHLKVLRDAGLLTSRR 91
                                   67788889999988.9999****************************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.5e-06     0.015       1      46 [.      42      89 ..      42      95 .. 0.92
   2 ?   -1.6   0.0       1.4   3.2e+03      14      36 ..      95     117 ..      91     119 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                         HTH_34  1 vRlavlsyLas..vdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                   vRl++ls+ as    ea+  ++++ +e+++  +s hlk+L +ag ++ 
  gi|121638531|ref|YP_978755.1| 42 VRLQLLSSVASraGGEACVCDISAGVEVSQPTISHHLKVLRDAGLLTS 89
                                   8*********98789****************************98875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                         HTH_34  14 eadfvelkealeatdgnLsvhlk 36 
                                    ++ ++ + eal + +  Lsvh++
  gi|121638531|ref|YP_978755.1|  95 WVYYAVVPEALTVLSNLLSVHAD 117
                                    55566666666666677777765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.024      22      47 ..      62      87 ..      44      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                         HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlI 47
                                   +++  + +S++t++ +lk L ++Gl+
  gi|121638531|ref|YP_978755.1| 62 DISAGVEVSQPTISHHLKVLRDAGLL 87
                                   79999*******************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05      0.16      26      55 ..      62      92 ..      61      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                   HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                      HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rgr 55
                                   ++++ + +++ t+s  l+ L+++gl++ r+r
  gi|121638531|ref|YP_978755.1| 62 DISAGVEVSQPTISHHLKVLRDAGLLTsRRR 92
                                   56777889*******************5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 938.76
//
Query:       gi|121638532|ref|YP_978756.1|  [L=498]
Description: arsenic-transport integral membrane protein arsC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-66  222.0   4.2    5.3e-66  222.0   4.2    2.0  2  SBF       Sodium Bile acid symporter family
    4.1e-20   72.6   0.0      6e-20   72.1   0.0    1.3  1  LMWPc     Low molecular weight phosphotyrosine protein phosph
      7e-10   38.7   2.3    1.1e-09   38.0   2.3    1.2  1  SBF_like  SBF-like CPA transporter family (DUF4137)


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.0   4.2   8.8e-70   5.3e-66       1     194 [.      62     258 ..      62     259 .. 0.99
   2 ?   -1.2   0.2      0.23   1.4e+03     123     149 ..     319     345 ..     265     359 .. 0.61

  Alignments for each domain:
  == domain 1  score: 222.0 bits;  conditional E-value: 8.8e-70
                            SBF   1 ailLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggamsnv 80 
                                    a++L++mm+p+++kv++++l++++ ++k+ll +l+l+wv++P lmf+la++ll+dl   pe+++Gli+vgla+++am+++
  gi|121638532|ref|YP_978756.1|  62 ALGLLIMMYPVLAKVRYDRLDTVTGDRKLLLSSLLLNWVLGPALMFALAWLLLADL---PEYRTGLIIVGLARCIAMVII 138
                                    589*****************************************************...********************* PP

                            SBF  81 wtylakGdlelsvvlvalstllailltPlllyllaksl......eqttlkvpieeivksvlivviiPliaGillryillk 154
                                    w++la+Gd+e ++vlval++++++ +++ l +++++ l      eqtt++ + ++i+ksvli+++iPl+aG+l+r+i  k
  gi|121638532|ref|YP_978756.1| 139 WNDLACGDREAAAVLVALNSIFQVAMFAALGWFYLSVLpgwlglEQTTIATSPWQIAKSVLIFLGIPLLAGYLSRRIGEK 218
                                    ******************************************************************************** PP

                            SBF 155 hkGrewfeskllpavspisligllltivvifalkgelive 194
                                    +kGr+w+es++lp+v p++l+gll+tiv++fal+g++i+ 
  gi|121638532|ref|YP_978756.1| 219 TKGRNWYESRFLPKVGPWALYGLLFTIVILFALQGDQITG 258
                                    *************************************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                            SBF 123 lkvpieeivksvlivviiPliaGillr 149
                                     + + + +++ v  ++ +P+++G++  
  gi|121638532|ref|YP_978756.1| 319 GATSGQALAGVVGPLIEVPVLVGLVYV 345
                                    344445555556666666666666654 PP

>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0     1e-23     6e-20       1     141 [.     367     487 ..     367     488 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1e-23
                                    EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSSE CS
                          LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelaelDl 80 
                                    vlfvC+ N++RS+mA  l+ ++     +++++ev+SaGt+  ++ +++p+av++++e gi++ + ++  l+  ++++ D+
  gi|121638532|ref|YP_978756.1| 367 VLFVCVHNAGRSQMAAGLLTHL-----AGDRIEVRSAGTE--PAGQVNPTAVAAMAEMGIDITANAPTLLTGGQVQSSDV 439
                                    89********************.....4668*********..************************************** PP

                                    EEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHH CS
                          LMWPc  81 ilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeieeavkkl 141
                                    +++m      ++++  p+          +y ++++++DP+++  + ++ ++d+i ++v++l
  gi|121638532|ref|YP_978756.1| 440 VITMGCG---DACPYFPG---------ASY-RNWKLPDPAGQPLDVVRMIRDDIADRVQAL 487
                                    ****654...459****9.........245.79*************************998 PP

>> SBF_like  SBF-like CPA transporter family (DUF4137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   2.3   1.9e-13   1.1e-09      58     289 ..      86     327 ..      74     339 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                       SBF_like  58 rnwrlhllvllisflltplivlalvsllkaaldpelliGllllaalPtTvssnvvmtsqAgGnealalceavignllGvf 137
                                     + +l l  ll++ +l p++++al+ ll a + pe  +Gl+++  +   +++ ++    A G+  +a + +++ +++ v 
  gi|121638532|ref|YP_978756.1|  86 GDRKLLLSSLLLNWVLGPALMFALAWLLLA-DLPEYRTGLIIVGLA-RCIAMVIIWNDLACGDREAAAVLVALNSIFQVA 163
                                    56688899999*****************87.999********9977.67******************************* PP

                       SBF_like 138 ltPalvqlll.........sgssvsvdyaevlkklllsvllPlvvGqvlqkifp..klvkrl.kkllkkvdslvlllivy 205
                                    + +al  ++l         ++++++ +  ++ k++l+ + +Pl++G + ++i +  k  +++ +++l kv+  +l  + +
  gi|121638532|ref|YP_978756.1| 164 MFAALGWFYLsvlpgwlglEQTTIATSPWQIAKSVLIFLGIPLLAGYLSRRIGEktKGRNWYeSRFLPKVGPWALYGLLF 243
                                    ****99999977777777766699999999999*******************88335566776889************** PP

                       SBF_like 206 tsfstafaqgaftsvshiillvifnvallLllvvlvillllarllklskedeiavlfcgsaKslalgvplisvlfgsnpq 285
                                    t +  +  qg   + +  +++ i +  l+ +++++v  +ll  +l+l  +++ ++ f ++     l++ ++  ++g+++ 
  gi|121638532|ref|YP_978756.1| 244 TIVILFALQGDQITGRPLDVARIALPLLAYFAIMWVGGYLLGAALRLGYRRTTTLAFTAASNNFELAIAVAIATYGATSG 323
                                    *****999999999999**********************************************************99885 PP

                       SBF_like 286 lgll 289
                                    ++l+
  gi|121638532|ref|YP_978756.1| 324 QALA 327
                                    5543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3403.76
//
Query:       gi|121638533|ref|YP_978757.1|  [L=105]
Description: hypothetical protein BCG_2671c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 776.50
//
Query:       gi|121638534|ref|YP_978758.1|  [L=73]
Description: hypothetical protein BCG_2672c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 508.02
//
Query:       gi|121638535|ref|YP_978759.1|  [L=129]
Description: hypothetical protein BCG_2673c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 960.64
//
Query:       gi|121638536|ref|YP_978760.1|  [L=90]
Description: hypothetical protein BCG_2674 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 710.89
//
Query:       gi|121638537|ref|YP_978761.1|  [L=77]
Description: hypothetical protein BCG_2675 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 555.51
//
Query:       gi|121638538|ref|YP_978762.1|  [L=84]
Description: hypothetical protein BCG_2676 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 618.86
//
Query:       gi|121638539|ref|YP_978763.1|  [L=163]
Description: hypothetical protein BCG_2677c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1154.39
//
Query:       gi|121638540|ref|YP_978764.1|  [L=93]
Description: hypothetical protein BCG_2678 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 668.94
//
Query:       gi|121638541|ref|YP_978765.1|  [L=267]
Description: transposase for insertion sequence element IS1081 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.2e-103  344.0   0.0   1.1e-102  343.8   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
    1.1e-05   25.7   0.0    2.4e-05   24.7   0.0    1.5  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.8   0.0  1.2e-106  1.1e-102       1     263 [.       1     262 [.       1     266 [. 0.98

  Alignments for each domain:
  == domain 1  score: 343.8 bits;  conditional E-value: 1.2e-106
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l+++e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121638541|ref|YP_978765.1|   1 MTSSH-LIDTEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.89999********************************************************************* PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121638541|ref|YP_978765.1|  80 PKLRQGSYFPdWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **********9***************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121638541|ref|YP_978765.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnl 263
                                    v+ai+a++p+aa+QrCr+H+++n 
  gi|121638541|ref|YP_978765.1| 239 VAAIGATLPAAAWQRCRTHYAANH 262
                                    *********************996 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.7e-09   2.4e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.7e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121638541|ref|YP_978765.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1809.95
//
Query:       gi|121638542|ref|YP_978766.1|  [L=252]
Description: ATP-dependent protease ATP-binding subunit clpX' [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-19   69.9   6.5    8.4e-10   38.6   0.3    3.1  3  Clp_N     Clp amino terminal domain, pathogenicity island com
  ------ inclusion threshold ------
       0.14   12.7   0.0       0.28   11.8   0.0    1.4  1  PAS_10    PAS domain


Domain annotation for each model (and alignments):
>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.5   4.4e+03      35      46 ..      68      79 ..      66      81 .. 0.82
   2 !   33.3   0.7   4.5e-12     4e-08       1      48 [.     110     157 ..     110     159 .. 0.96
   3 !   38.6   0.3   9.3e-14   8.4e-10       2      43 ..     184     223 ..     183     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.5
                                   HHTTSSHHHHHH CS
                          Clp_N 35 kkaGvdldalrk 46
                                   k +Gv+++a++k
  gi|121638542|ref|YP_978766.1| 68 KSMGVTKQAAQK 79
                                   679999999886 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 4.5e-12
                                    HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHH CS
                          Clp_N   1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkai 48 
                                    Aq  A  +  ++i+++HLLl++l ++  la  lL+++ +d+++lr a+
  gi|121638542|ref|YP_978766.1| 110 AQNAAHGATSSEITPDHLLLGVLTDPAALATALLQQQEIDIATLRTAV 157
                                    8999999***************************************98 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 9.3e-14
                                    HHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHH CS
                          Clp_N   2 qelAkslghqyistEHLLlALleeddGlaarlLkkaGvdlda 43 
                                    +++A++lgh+yi+tEHLLlALle +dG++   L + Gvd+ +
  gi|121638542|ref|YP_978766.1| 184 FREALRLGHNYIGTEHLLLALLELEDGDG--PLHRSGVDKSR 223
                                    579************************99..66666666655 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.1e-05      0.28      11      71 ..      86     147 ..      84     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                         PAS_10  11 eltflDdnlqirrFtpaa.kklfklipadvGrpladihpkkavknveeviealrtgekdeve 71 
                                    e t lD+n  +rrFtp+a + ++  ++a  G + ++i+p++ +  v  +  al t   +++e
  gi|121638542|ref|YP_978766.1|  86 EATTLDSNQGFRRFTPRArNAVVAAQNAAHGATSSEITPDHLLLGVLTDPAALATALLQQQE 147
                                    6799************7626899999999999999999998777776666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1322.98
//
Query:       gi|121638543|ref|YP_978767.1|  [L=173]
Description: hypothetical protein BCG_2681 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 946.34
//
Query:       gi|121638544|ref|YP_978768.1|  [L=156]
Description: hypothetical protein BCG_2682 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-17   61.7   0.0    8.5e-17   61.5   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.3e-15   57.5   0.0    1.6e-15   57.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      9e-10   38.9   0.0    1.4e-09   38.3   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.6e-05   24.9   0.0    2.9e-05   24.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0012   18.8   0.0     0.0016   18.4   0.0    1.2  1  FR47             FR47-like protein
      0.002   17.8   0.0       0.02   14.6   0.0    2.0  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0091   16.2   1.2      0.012   15.7   1.2    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0093   15.8   0.0          3    7.7   0.0    2.1  2  Acetyltransf_18  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.054   13.6   0.0      0.074   13.2   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.11   12.6   0.0        1.1    9.4   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   4.7e-20   8.5e-17      19     117 .]      36     131 ..      12     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.7e-20
                                    HHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEE CS
                 Acetyltransf_1  19 aseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkiv 98 
                                     s ++f+e++ ++   +l a++dg+++G+++l   +d   + +++  l+  p y+g G++ aL+ +++  a ++g+ +++
  gi|121638544|ref|YP_978768.1|  36 LSSARFAEYLTDPRRAILTARHDGRIVGYAMLIRGDD---RDVELSKLYLLPGYHGTGAAAALMHKVLATAADWGALRVW 112
                                    3445588888888889999******************...9***********************************999* PP

                                    EEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  99 laveedndaairlYeklGF 117
                                    l v + n++a+r+Y k GF
  gi|121638544|ref|YP_978768.1| 113 LGVNQKNQRAQRFYAKTGF 131
                                    **************99**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   8.9e-19   1.6e-15       6     113 ..      24     138 ..      19     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 8.9e-19
                Acetyltransf_10   6 seegietf.kefispealrerieegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeea 80 
                                     +e i+ f +  +s ++++e++++++  +l a  +g+ivG++ l r ++   ++s l+  p y+g+G ++aL+++v++ a
  gi|121638544|ref|YP_978768.1|  24 APEHIASFvDANLSSARFAEYLTDPRRAILTARHDGRIVGYAMLiRGDDrdvELSKLYLLPGYHGTGAAAALMHKVLATA 103
                                    678999999999999***************************8855555899**************************** PP

                Acetyltransf_10  81 ekdgikl.eltvnasp.yavpfYeklGFkavgeeq 113
                                     ++g     l vn+++  a++fY k GFk  g  +
  gi|121638544|ref|YP_978768.1| 104 ADWGALRvWLGVNQKNqRAQRFYAKTGFKINGTRT 138
                                    9**99999********************9876655 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   7.7e-13   1.4e-09       4      75 ..      51     132 ..      48     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.7e-13
                                    EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEEEEEEEE....THHHHHHHHHH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....ae.kgiileqlel....naekaikfYek 71 
                                     ++ a++dg+ivG++ l + d    e+ +l+ +p y+g G + aL+      a+ +g    +++l    ++++a++fY+k
  gi|121638544|ref|YP_978768.1|  51 AILTARHDGRIVGYAMLIRGDdrdVELSKLYLLPGYHGTGAAAALMHKvlatAAdWGAL--RVWLgvnqKNQRAQRFYAK 128
                                    57789*********999999898777777*****************8544442266622..245554323349******* PP

                                    TTEE CS
                 Acetyltransf_7  72 lGFe 75 
                                     GF+
  gi|121638544|ref|YP_978768.1| 129 TGFK 132
                                    ***8 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.6e-08   2.9e-05      56     138 .]      51     132 ..       2     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-08
                 Acetyltransf_3  56 waivlkdtgv.iGsvglrdleeedeeaelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvle 133
                                     +++ +++g  +G+++l + +++d  +el+ ++l p ++g G a   ++ +l  a ++ g+ r++  ++++N++ +r + 
  gi|121638544|ref|YP_978768.1|  51 AILTARHDGRiVGYAMLIRGDDRD--VELSkLYLLPGYHGTGAAAALMHKVLATA-ADWGALRVWLGVNQKNQRAQRFYA 127
                                    33334888866*******888876..99997888899******************.6777889***************** PP

                 Acetyltransf_3 134 klGfe 138
                                    k Gf+
  gi|121638544|ref|YP_978768.1| 128 KTGFK 132
                                    ****7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     9e-07    0.0016      22      80 ..      75     134 ..      57     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9e-07
                                    SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                     el+ l++lp   + G +  l +++ +  a  g   v l v+++N++++r+y k Gf+  
  gi|121638544|ref|YP_978768.1|  75 VELSKLYLLPGYHGTGAAAALMHKVLATAADWGAlRVWLGVNQKNQRAQRFYAKTGFKIN 134
                                    699****************************665289999*****************876 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05      0.02      90     144 ..      85     138 ..      23     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                    HHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEEE CS
                 Acetyltransf_8  90 eargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekevd 144
                                     ++g g ++al+ ++++ + ad ++ rv +    +N+ra r+++k Gf+  ++ +
  gi|121638544|ref|YP_978768.1|  85 GYHGTGAAAALMHKVLATA-ADWGALRVWLGVNQKNQRAQRFYAKTGFKINGTRT 138
                                    5566666666666666654.466*************************9988765 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   6.8e-06     0.012      31     135 ..       7     115 ..       1     126 [. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.8e-06
                 Acetyltransf_6  31 leallelfraqwarrpdvfadpltraflrdllaalaa.....rgalrlyvlrldgrpvAvalglrsgdrly.ywlggydp 104
                                    l+a+ ++ + +     +v+ +++  +f+ + l++        + +  ++++r+dgr+v++a+++r +dr   + +    p
  gi|121638544|ref|YP_978768.1|   7 LAAVAARTFPLACPP-AVA-PEHIASFVDANLSSARFaeyltDPRRAILTARHDGRIVGYAMLIRGDDRDVeLSKLYLLP 84 
                                    444444444444444.444.6666666666665432222444445669*******************9755155555599 PP

                 Acetyltransf_6 105 elaklspgllllweliedaaeeGlrrfdlgg 135
                                     +++ ++   l++++++ aa+ G  r+ lg 
  gi|121638544|ref|YP_978768.1|  85 GYHGTGAAAALMHKVLATAADWGALRVWLGV 115
                                    999999999**********999988887776 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0017         3      20      47 ..      44      71 ..      38      78 .. 0.83
   2 !    6.2   0.0    0.0047       8.5      62     103 ..      91     135 ..      86     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                Acetyltransf_18 20 rlkqaeqklvvveedgeivGyglarktr 47
                                    l+ ++  ++    dg+ivGy++++++ 
  gi|121638544|ref|YP_978768.1| 44 YLTDPRRAILTARHDGRIVGYAMLIRGD 71
                                   56677888899999**********9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0047
                Acetyltransf_18  62 iAeaLlkalvanaeg...kkvridvpeenkalielleklgfkevf 103
                                    +A+aL+++++a a       v + v ++n++++++ +k gfk + 
  gi|121638544|ref|YP_978768.1|  91 AAAALMHKVLATAADwgaLRVWLGVNQKNQRAQRFYAKTGFKING 135
                                    688888888877765433458899*****************9665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.1e-05     0.074      39     139 ..      40     136 ..      26     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                 Acetyltransf_4  39 kflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaels.vylaerdnnkeglgrelidaleqvlkeqnienllae 117
                                    +f e+l  + + ++ +  ++rivGya l     r+ d  +els  yl       +g + +l+  +   ++  + ++    
  gi|121638544|ref|YP_978768.1|  40 RFAEYLTDPRRAILTARHDGRIVGYAMLI----RGDDRDVELSkLYLL-PGYHGTGAAAALMHKVLATAADWGALRVWLG 114
                                    444454567788888888*********99....557788888636776.457888888888888889999999******* PP

                 Acetyltransf_4 118 iaspnensiqfhkalGFelvgi 139
                                    +  +n+ ++ f+++ GF++ g 
  gi|121638544|ref|YP_978768.1| 115 VNQKNQRAQRFYAKTGFKINGT 136
                                    ******************9875 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0006       1.1      78     126 ..      79     132 ..       3     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0006
                                    EEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                 Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                         p + g g + +L++++l+ ++++g+  ++l       ++ ++Y + G++
  gi|121638544|ref|YP_978768.1|  79 KLYLLPGYHGTGAAAALMHKVLATAADWGALRVWLGVnqknqRAQRFYAKTGFK 132
                                    4456799*******************9998777776655555455777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 857.77
//
Query:       gi|121638545|ref|YP_978769.1|  [L=369]
Description: hypothetical protein BCG_2683c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.4e-107  357.8   0.0    2.8e-72  243.6   0.0    2.0  2  AFG1_ATPase  AFG1-like ATPase
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.56   10.1   0.0    1.8  2  MobB         Molybdopterin guanine dinucleotide synthesis pro


Domain annotation for each model (and alignments):
>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.6   0.0   3.2e-76   2.8e-72       1     214 [.      33     247 ..      33     251 .. 0.97
   2 !  115.5   0.0   2.8e-37   2.5e-33     237     362 .]     244     368 ..     242     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 243.6 bits;  conditional E-value: 3.2e-76
                    AFG1_ATPase   1 ttprqryekelqrgeivadaaqaeavealdrlte...elaaqdlarks...salgklfgrkrksvepvrglYlwGgvGrG 74 
                                    t++++r+ ++l++++++a++++a+++++++++t+   ++a+qd++r++   +a++k++++kr +v p++glYl+Gg+G+G
  gi|121638545|ref|YP_978769.1|  33 TVSPVRLIAQLRPPPTFAEVSFATYRPDPVEPTQaaaVVACQDFCRQAverRAGRKKWFGKR-DVLPGVGLYLDGGFGVG 111
                                    57899*****************************9999*********99999*********9.999************** PP

                    AFG1_ATPase  75 KtylmdlffeslpvekkrrvhfhafmarvhdeltklrkekdplaivadrlaeearvlCfDEfevsDiadamllsrLleaL 154
                                    Kt+l+++++++lp+ ++++++++++++++++elt+l+ +++++a+++d la+++ +lC+DEfe++D+++++l+srLl+aL
  gi|121638545|ref|YP_978769.1| 112 KTHLLASAYYQLPG-TGPDAPTCPKAFATFGELTQLA-GVFGFADCIDLLANYT-ALCIDEFELDDPGNTTLISRLLSAL 188
                                    **************.9*********************.9***************.************************* PP

                    AFG1_ATPase 155 fargvtlvaTSNiaPedLykdglqrqrFLpaIdlleshlevlevdggvDYRlrklrqaev 214
                                    ++rgv+++aTSN++Pe+L+++++++q+FL++I++l+s++++++++g+ DYR+r+l++a++
  gi|121638545|ref|YP_978769.1| 189 VERGVSVAATSNTLPEQLGEGRFAAQDFLREINTLASIFTTVRIEGP-DYRHRDLPPAPA 247
                                    ***********************************************.********9984 PP

  == domain 2  score: 115.5 bits;  conditional E-value: 2.8e-37
                    AFG1_ATPase 237 gepeaestlevkaRklrvraaagdlvrfsfaelceaarsqsdYlalaerfhtvlledVpvltkakedaarRfiaLvDelY 316
                                    ++p++ s++ev+aR++r  +++++l++f++++++ a++++s+Yl+l+e +++v+l++V++++  ++++a R++aLvD+lY
  gi|121638545|ref|YP_978769.1| 244 PAPAPLSDEEVAARAAR--VEGATLDDFDALCAHLATMHPSRYLTLIEGVTAVFLTGVHGID--DQNVALRLVALVDRLY 319
                                    689999*********99..8999***************************************..**************** PP

                    AFG1_ATPase 317 dadvklvvs...aevaleelyeagrlefefeRtaSRLlelqsedylare 362
                                    da++++v+s   ++++++e++ ag +++++ R++SRLl+l++++++are
  gi|121638545|ref|YP_978769.1| 320 DAGIPVVASgakLDTIFSEEMLAGGYRKKYLRATSRLLALTAGVIQARE 368
                                    **********999********************************9996 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.37   3.3e+03       8      18 ..     108     118 ..     102     127 .. 0.76
   2 ?   10.1   0.0   6.2e-05      0.56       9      32 ..     174     197 ..     169     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.37
                           MobB   8 sgsGKTtLlek 18 
                                     g GKT Ll  
  gi|121638545|ref|YP_978769.1| 108 FGVGKTHLLAS 118
                                    589*****976 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.2e-05
                           MobB   9 gsGKTtLleklipelkarglrvgt 32 
                                    + G TtL+++l+++l +rg++v++
  gi|121638545|ref|YP_978769.1| 174 DPGNTTLISRLLSALVERGVSVAA 197
                                    679******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2013.71
//
Query:       gi|121638546|ref|YP_978770.1|  [L=258]
Description: hypothetical protein BCG_2684 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-48  164.0   0.2    4.3e-48  163.8   0.2    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.2   2.4e-52   4.3e-48       2     199 ..      40     251 ..      39     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2.4e-52
                                    EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS-EEE CS
                         RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearqpvrv 80 
                                    ++ ++++ SlDG ++ +g++++ ++g+++r +++ lr+ ad+i+vG+gtv+++ +s   + v +r+++ a+++++ p+  
  gi|121638546|ref|YP_978770.1|  40 WLRANFISSLDGGATVDGTSGA-MAGPGDRFVFNLLRELADVIVVGVGTVRIEGYSGVRMGVVQRQHRqARGQSEVPQLA 118
                                    899***********99998777.********************************************************* PP

                                    EEETTS-S-TTSHHHHSS.S-EEEEESSCSCHHHHHHCC....E.........SE-HHHHHHHHHHTT--EEEEEETHHH CS
                         RibD_C  81 Vvdstlrvpldakvltdd.aptlvatteeadkekveklk....v.........rvdlkelleeLkergirsllveGGatL 146
                                    +v+++ r+++d++v+t++ +++lv+tt++++++++++l+    v         +vd + l+++L++rg+r++l+eGG+tL
  gi|121638546|ref|YP_978770.1| 119 IVTRSGRLDRDMAVFTRTeMAPLVLTTTAVADDTRQRLAglaeViacsgddpgTVDEAVLVSQLAARGLRRILTEGGPTL 198
                                    ***************************************9988367889999**************************** PP

                                    HHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SSEEEEEEEEEEETTEEE CS
                         RibD_C 147 agsllraglvDelrlyiaPkllGg.agktlfdgegfkalklklvksealgegvv 199
                                    +g++++++++Del+l+iaP+++Gg a++++++ ++++ ++++++++ ++++g++
  gi|121638546|ref|YP_978770.1| 199 LGTFVERDVLDELCLTIAPYVVGGlARRIVTGPGQVL-TRMRCAHVLTDDSGYL 251
                                    ************************8888888888888.8**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1433.03
//
Query:       gi|121638547|ref|YP_978771.1|  [L=528]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-21   74.4   0.1    1.5e-20   73.2   0.1    1.6  1  Abhydrolase_4  TAP-like protein
    5.7e-15   55.6   0.0    1.2e-14   54.6   0.0    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.15   11.3   0.3        2.5    7.3   0.0    2.8  3  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.1   2.5e-24   1.5e-20       2     103 .]     425     526 ..     424     526 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 2.5e-24
                  Abhydrolase_4   2 pvfgaalaesllsCagwpvspqrprdestakgaapvLllqnerDpaTPyegakklakalgga....vlvtvegeGHgala 77 
                                    p fga++a +l++C +wp s+ ++++++ +   ++vLll+ ++Dp+++ eg +++a +  +a    + v+++g GHga++
  gi|121638547|ref|YP_978771.1| 425 PQFGAVAALNLVKCVHWPSSSPPQPPKDLK---VDVLLLGVQNDPIVGNEGVAATAATAINAnaasKRVMWQGIGHGASI 501
                                    789************************999...99****************999999988855567************97 PP

                  Abhydrolase_4  78 agntCvdkavdaYLltGelpaddtvC 103
                                     +++C+  ++ aYL+tG+lp++dt+C
  gi|121638547|ref|YP_978771.1| 502 -YSSCAVPPLVAYLDTGKLPDTDTYC 526
                                    .9***********************9 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.9e-18   1.2e-14      29     239 ..     160     483 ..     136     502 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.9e-18
                                    TSEEEEEEETTSTTSSSTTTGB.CHH...........................................SHHHHHHHHHH CS
                  Abhydrolase_1  29 gfdvillDlrGvgySspapacinddy...........................................gtasvaddldr 65 
                                     + ++++D rG g Ssp  +   d++                                            + + a d++r
  gi|121638547|ref|YP_978771.1| 160 SHPIVAVDRRGMGMSSPIDCR--DHFdrdemrdqaqfqagddpvanlsdisntattdctdaiapgesayDNTHAASDIER 237
                                    7889***********998877..666666667777778888888888888888888888888888888855569****** PP

                                    HHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHH CS
                  Abhydrolase_1  66 ildalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplla 145
                                    ++   ++  l+ vG   G+++alayaa  p++V++l+l+++i+   s + a++qq+++ + ++d +aa c   + + l++
  gi|121638547|ref|YP_978771.1| 238 LRKLWDVPALAFVGIGNGTQVALAYAASRPDNVARLILDSPIALGVSAEAAAEQQVQGQQAALDAFAAQCVA-VNCALGS 316
                                    **********************************************************************75.67999** PP

                                    CCSCHHHHHHHHHHHHHH......................................HCHHHCCHHHHHHHCHHHHHHHHH CS
                  Abhydrolase_1 146 delaaleqrhrlvdalkf......................................pdkskrfpssgsdnasslatgalk 187
                                    d+ +a+   +++  + ++                                      ++ ++++ s  +++a ++  ++ +
  gi|121638547|ref|YP_978771.1| 317 DPKGAVSALLSAARSGDGpggasvaavanavatalgfpdsgrvdsttkladalaaaRSGDMNLLSALINRADTTRDTDGQ 396
                                    *********99855444488888888888877777777777777777777777777444444444444444444444444 PP

                                    HHHHHHHCCHHHHHHHHHC..................................THHHHSEEEEEEETTCSSSCH.HHHHH CS
                  Abhydrolase_1 188 sieqwpttdsaklllrlre..................................lknvlaptlvisgtsDplvpp.kaled 232
                                    +i++ ++  +++  +r re                                  +k+ ++++l+++ ++Dp+v + ++   
  gi|121638547|ref|YP_978771.1| 397 FISSCSDAVNRPTPDRVRElvvawgklypqfgavaalnlvkcvhwpsssppqpPKDLKVDVLLLGVQNDPIVGNeGVAAT 476
                                    4444444444444444443777777777777778888***********************************99444444 PP

                                    HHHCHTS CS
                  Abhydrolase_1 233 laqllpk 239
                                     a +++ 
  gi|121638547|ref|YP_978771.1| 477 AATAINA 483
                                    4444554 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.085   5.1e+02      34      47 ..     163     176 ..     143     200 .. 0.68
   2 ?    7.3   0.0   0.00042       2.5      67     111 ..     236     280 ..     223     307 .. 0.81
   3 ?   -0.9   0.0      0.13   7.9e+02     188     217 ..     451     480 ..     447     497 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.085
                    Hydrolase_4  34 vyalDhrGhGrseg 47 
                                    ++a+D rG G s +
  gi|121638547|ref|YP_978771.1| 163 IVAVDRRGMGMSSP 176
                                    36899999999975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00042
                    Hydrolase_4  67 ekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPal 111
                                    e++++ +    l  +G   G  +al+y++ +pd+va+lil +P  
  gi|121638547|ref|YP_978771.1| 236 ERLRKLWDVPALAFVGIGNGTQVALAYAASRPDNVARLILDSPIA 280
                                    5556666666788899999***********************964 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.13
                    Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerl 217
                                    +++++ +lll  ++D++v +e+ +++++++
  gi|121638547|ref|YP_978771.1| 451 KDLKVDVLLLGVQNDPIVGNEGVAATAATA 480
                                    578899999999******999986665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.37s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2832.84
//
Query:       gi|121638548|ref|YP_978772.1|  [L=433]
Description: hypothetical protein BCG_2686 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-39  136.7  36.2      1e-39  136.7  36.2    1.9  2  GT87      Glycosyltransferase family 87


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7  36.2   5.7e-44     1e-39       1     238 [.      94     328 ..      94     329 .. 0.94
   2 ?   -2.8   1.1      0.23   4.1e+03     152     164 ..     356     369 ..     336     414 .. 0.49

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 5.7e-44
                           GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqinlll 80 
                                    ++YPP+++ll+ap+++lp+++++ l++ +n+aa+l+a++lllr+++++l s++a al+la++a+e v +tl+f++in+++
  gi|121638548|ref|YP_978772.1|  94 YLYPPGGTLLMAPFGYLPFAPSRYLFISINTAAILVAAYLLLRMFNFTLTSVAAPALILAMFATETVTNTLVFTNINGCI 173
                                    89****************************************************************************** PP

                           GT87  81 lllvlldllllrrr...rpllaGlliGlaaaiKltPalfll..ylllrrrwralaaaaatalvltalpllllppssleyf 155
                                    lll +l+l +l+ +   r+++ Gl+iGl  ++K  P+l +l  ++ll+r+wral+aa+++ +v+ +++l l+  +++++f
  gi|121638548|ref|YP_978772.1| 174 LLLEVLFLRWLLDGrasRQWCGGLAIGLTLVLK--PLLGPLllLPLLNRQWRALVAAVVVPVVVNVAALPLVS-DPMSFF 250
                                    ************554448999************..888877668899*******************9888888.99**** PP

                           GT87 156 letlfdtseriaedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlrrrerllalaaallvall.. 233
                                    ++tl++  +  ++d++n+s+l+   ++  +++l l        +l  ++   a+++++r++r+ ++l++ +++ ++ll  
  gi|121638548|ref|YP_978772.1| 251 TRTLPYILG--TRDYFNSSILGNGVYFGLPTWLIL-----FLRILFTAITFGALWLLYRYYRTGDPLFWFTTSSGVLLlw 323
                                    *******99..******************999999.....778889999*********************9999999768 PP

                           GT87 234 alLvs 238
                                    ++Lv+
  gi|121638548|ref|YP_978772.1| 324 SWLVM 328
                                    88875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.23
                           GT87 152 leyfle.tlfdtse 164
                                    + ++l+   f t +
  gi|121638548|ref|YP_978772.1| 356 WPAWLGvYGFMTLD 369
                                    33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2408.57
//
Query:       gi|121638549|ref|YP_978773.1|  [L=136]
Description: hypothetical protein BCG_2687 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-52  176.9   0.0    1.6e-52  176.7   0.0    1.0  1  SelR            SelR domain
     0.0024   18.0   0.0     0.0035   17.5   0.0    1.3  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
  ------ inclusion threshold ------
      0.025   14.5   1.4      0.079   12.9   1.4    1.8  1  Endonuclease_7  Recombination endonuclease VII
      0.033   14.9   1.0       0.69   10.6   1.0    2.2  2  zinc-ribbon_6   zinc-ribbon domain
      0.039   14.3   1.5        1.6    9.2   0.2    2.4  2  GFA             Glutathione-dependent formaldehyde-activating
       0.08   12.7   0.2        2.9    7.7   0.0    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.099   12.8   4.0       0.27   11.4   0.4    2.4  2  Ribosomal_L37e  Ribosomal protein L37e
       0.11   12.7   0.7        0.5   10.6   0.0    2.1  2  Jas             TPL-binding domain in jasmonate signalling
       0.38   10.8   3.9        1.3    9.1   2.2    2.4  3  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.7   0.0   7.9e-56   1.6e-52       1     120 [.      12     132 ..      12     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 7.9e-56
                                    HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECTTS CS
                           SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtslgm 80 
                                    e+++kLtp++++vlr++gterpftgey++++++G+y+c++cg++Lf+s++kf+s+cGwpsF+++ +++av+ ++d+slgm
  gi|121638549|ref|YP_978773.1|  12 EWRQKLTPQEFHVLRRAGTERPFTGEYTDTTTAGIYQCRACGAELFRSTEKFESHCGWPSFFDPKSSDAVTLRPDHSLGM 91 
                                    7******************************************************************************* PP

                                    EEEEEEETTCECEEEEEEC.TSSSSS.SEEEEE-CCCEEEE CS
                           SelR  81 ertevvcakcdahlGhvFe.dgpkpttgkrycinsvslkfk 120
                                    +rtev ca+cd+hlGhvF  +g++++t+krycins+sl+++
  gi|121638549|ref|YP_978773.1|  92 TRTEVLCANCDSHLGHVFAgEGYPTPTDKRYCINSISLRLV 132
                                    *******************9******************986 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0035       2      70 ..      46     110 ..      45     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                    EEEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEE CS
                   Yippee-Mis18   2 vfqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYk 70 
                                    ++qC+ C ++l  s++ ++++  +  ++  k +++v+++  ++       t +++ C++C+s+lG ++ 
  gi|121638549|ref|YP_978773.1|  46 IYQCRACGAELFRSTEKFESHCGWPSFFDPKSSDAVTLRPDHSLG----MTRTEVLCANCDSHLGHVFA 110
                                    589****************99999999999999999999999998....7889************9986 PP

>> Endonuclease_7  Recombination endonuclease VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4     4e-05     0.079      38      73 ..      79     124 ..      29     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                    --EEEEE-TTT--.E.EEEEHHHHH.HHHT.........TT-HHHH CS
                 Endonuclease_7  38 kalavDHdHktgkvR.gllCgsCNtalGkl.........kdspeal 73 
                                     a+ +  dH+ g +R ++lC++C + lG++         +d++ ++
  gi|121638549|ref|YP_978773.1|  79 DAVTLRPDHSLGMTRtEVLCANCDSHLGHVfagegyptpTDKRYCI 124
                                    55667779******9669***********87777777777776665 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.0   0.00034      0.69       1      42 [.      46      88 ..      46     104 .. 0.80
   2 ?    2.8   0.1     0.094   1.9e+02      15      28 ..      95     108 ..      90     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                  zinc-ribbon_6  1 lfeCeqCgqllffenssC.lkCgaalgfapeelellaleeaee 42
                                   +++C++Cg +lf  +++   +Cg    f+p++ + ++l+++++
  gi|121638549|ref|YP_978773.1| 46 IYQCRACGAELFRSTEKFeSHCGWPSFFDPKSSDAVTLRPDHS 88
                                   59*********9887665269*****************99887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.094
                  zinc-ribbon_6  15 nssClkCgaalgfa 28 
                                    ++ C++C+++lg++
  gi|121638549|ref|YP_978773.1|  95 EVLCANCDSHLGHV 108
                                    57899999999975 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00078       1.6      35      66 ..      32      63 ..      12      84 .. 0.73
   2 ?    4.1   0.0     0.029        57      41      60 ..      87     106 ..      73     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00078
                            GFA 35 keykktadsgnkvtrsfCpeCgsplyseesaa 66
                                   + ++ +   ++++  + C++Cg++l+ ++++ 
  gi|121638549|ref|YP_978773.1| 32 RPFTGEYTDTTTAGIYQCRACGAELFRSTEKF 63
                                   44555445566667799*********765554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.029
                            GFA  41 adsgnkvtrsfCpeCgsply 60 
                                    +  g + t+  C +C s+l 
  gi|121638549|ref|YP_978773.1|  87 HSLGMTRTEVLCANCDSHLG 106
                                    5567778889******9986 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.044        87      42      52 ..      44      54 ..      35      56 .. 0.74
   2 ?    7.7   0.0    0.0014       2.9      16      35 ..      89     108 ..      81     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.044
                 zinc_ribbon_10 42 evkyrCpkCga 52
                                      y+C  Cga
  gi|121638549|ref|YP_978773.1| 44 AGIYQCRACGA 54
                                   458******97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                 zinc_ribbon_10  16 saknryalICskChshnGla 35 
                                    + ++r  + C +C sh G +
  gi|121638549|ref|YP_978773.1|  89 LGMTRTEVLCANCDSHLGHV 108
                                    557889999*******9987 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00013      0.27      18      41 ..      48      71 ..      39      72 .. 0.93
   2 ?    2.2   0.2       0.1   2.1e+02      14      28 ..      93     107 ..      87     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                 Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascGyps 41
                                    Cr Cg + +   +k  ++cG+ps
  gi|121638549|ref|YP_978773.1| 48 QCRACGAELFRSTEKFESHCGWPS 71
                                   6*********************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                 Ribosomal_L37e  14 ktHilCrrCgkrsyh 28 
                                    +t +lC  C+++  h
  gi|121638549|ref|YP_978773.1|  93 RTEVLCANCDSHLGH 107
                                    577999999987555 PP

>> Jas  TPL-binding domain in jasmonate signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025       0.5      41      65 ..      41      68 ..      14      82 .. 0.78
   2 ?    0.3   0.1      0.41   8.2e+02      41      55 ..      91     105 ..      86     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                            Jas 41 ikrdgIv.CsCCgkvl..spseFeaHAG 65
                                   ++ +gI+ C+ Cg++l  s ++Fe H G
  gi|121638549|ref|YP_978773.1| 41 TTTAGIYqCRACGAELfrSTEKFESHCG 68
                                   56778855******9999*********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.41
                            Jas  41 ikrdgIvCsCCgkvl 55 
                                    ++r+ ++C  C+++l
  gi|121638549|ref|YP_978773.1|  91 MTRTEVLCANCDSHL 105
                                    58999******9987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0031       6.2      28      49 .]      46      68 ..      27      68 .. 0.73
   2 ?    9.1   2.2   0.00063       1.3      13      37 ..      47     104 ..      39     110 .. 0.80
   3 ?    1.1   0.9      0.21   4.1e+02       1      15 [.      98     123 ..      98     125 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                            DZR 28 edrCpsCgek.vdpearfCpeCG 49
                                    ++C +Cg++   ++++f  +CG
  gi|121638549|ref|YP_978773.1| 46 IYQCRACGAElFRSTEKFESHCG 68
                                   46677777776777777777776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00063
                            DZR  13 rfCseCgtklkavaa.................................edrCpsCgek 37 
                                      C +Cg++l + ++                                 e  C +C++ 
  gi|121638549|ref|YP_978773.1|  47 YQCRACGAELFRSTEkfeshcgwpsffdpkssdavtlrpdhslgmtrtEVLCANCDSH 104
                                    5788888888765557888888888888888899999999999999999999999875 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.21
                            DZR   1 CpqCgee...........lppdarfC 15 
                                    C++C +            +p d+r+C
  gi|121638549|ref|YP_978773.1|  98 CANCDSHlghvfagegypTPTDKRYC 123
                                    66666665555555555566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 943.63
//
Query:       gi|121638550|ref|YP_978774.1|  [L=250]
Description: hypothetical protein BCG_2688c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-15   56.9   0.0    5.8e-15   55.8   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    2.2e-14   53.9   0.0    2.8e-13   50.3   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    7.9e-14   51.7   0.0    9.9e-14   51.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.9e-09   35.8   0.0    8.7e-09   35.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.1e-07   29.9   0.0    1.2e-06   29.2   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.9e-05   24.4   0.0    4.3e-05   23.3   0.0    1.5  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00025   20.7   0.0    0.00036   20.1   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00073   19.3   0.0      0.001   18.8   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0031   16.9   0.0     0.0053   16.1   0.0    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.016   14.6   0.3      0.023   14.1   0.3    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.025   14.0   0.0      0.034   13.6   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.18   11.5   0.0       0.57    9.9   0.0    1.8  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   3.9e-18   5.8e-15       1      96 [.      54     149 ..      54     149 .. 0.87
   2 ?   -2.9   0.0       7.7   1.1e+04      29      43 ..     199     213 ..     191     229 .. 0.48

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.9e-18
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG.SS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh.ls 78 
                                    vLd G+G+G+++++ a+++  +  tg+D s +++e+ar +a+++g++v+f++gda++l+  dg+fD vv + a +h   +
  gi|121638550|ref|YP_978774.1|  54 VLDPGTGPGHHAIYYAAKG--YAATGIDGSVAAIERARDNARKAGVSVNFQVGDATTLDGLDGRFDTVVDC-AfYHTfST 130
                                    9*****************5..************************************************94.63555334 PP

                                    HHHHHH.HHHHHHHHEEEE CS
                Methyltransf_25  79 dedlek.alkeiarvLkpg 96 
                                     ++l++ +++ ++r+ kpg
  gi|121638550|ref|YP_978774.1| 131 APELQRcYVRALRRASKPG 149
                                    4555542678888888887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                                    SSHHHHHHHHHHHHH CS
                Methyltransf_25  29 iseemleaareraee 43 
                                    +s e+le +++r+ +
  gi|121638550|ref|YP_978774.1| 199 LSVEALELMAARNPD 213
                                    444444444444422 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   1.9e-16   2.8e-13       1      95 [.      55     153 ..      55     154 .. 0.93
   2 ?    1.4   0.0      0.33     5e+02      18      54 ..     191     227 ..     182     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.9e-16
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-....CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv....ed 76 
                                    Ld G+G G +a ++a +g+  +g+D s +++++a+++a+++g++v+f+v+da++l   d+ fD vv   + h++    e 
  gi|121638550|ref|YP_978774.1|  55 LDPGTGPGHHAIYYAAKGYAATGIDGSVAAIERARDNARKAGVSVNFQVGDATTLDGLDGRFDTVVDCAFYHTFstapEL 134
                                    89************************************************************************988444 PP

                                    HHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                    ++ +++ ++R  kpg +l+
  gi|121638550|ref|YP_978774.1| 135 QRCYVRALRRASKPGARLY 153
                                    4556899999999999887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.33
                                    TSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC CS
                Methyltransf_11  18 garvvgvDlskemlklakekaseeglkvefvvadaek 54 
                                    g++++ v+ls e+l+l  +++++   +v++v ++++ 
  gi|121638550|ref|YP_978774.1| 191 GTTTYQVNLSVEALELMAARNPDMADQVRCVLERFRA 227
                                    4889999999999999988888777788888877665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   6.6e-17   9.9e-14       6     113 ..      53     158 ..      51     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 6.6e-17
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl. 84 
                                    +vlD+G+G G+ ++  a +   +   +GiD s  aie+Ar na+k g++ v+F++gd+++l+ l  d +fD +++ +++ 
  gi|121638550|ref|YP_978774.1|  53 EVLDPGTGPGHHAIYYAAK---GYAATGIDGSVAAIERARDNARKAGVS-VNFQVGDATTLDGL--DGRFDTVVD-CAFy 125
                                    69***********999955...34489*********************8.************76..9*****999.6663 PP

                Methyltransf_31  85 ...naladpdkile.eiervlkpggilliedpr 113
                                        + ++++ ++   + r+ kpg +l + ++ 
  gi|121638550|ref|YP_978774.1| 126 htfSTAPELQRCYVrALRRASKPGARLYMFEFG 158
                                    555555555555553667888888899888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   5.8e-12   8.7e-09      21     121 ..      49     158 ..      36     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.8e-12
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                      +g+vLd G+G G+ + +++++g+  tg+D s +a+e+a+        +    +++  d+   +  +g+fd++v   + 
  gi|121638550|ref|YP_978774.1|  49 AIRGEVLDPGTGPGHHAIYYAAKGYAATGIDGSVAAIERARdnarkagvS---VNFQVGDATTLDGLDGRFDTVVDCAFY 125
                                    5589************************************9976543221...1122222334444777*********99 PP

                Methyltransf_23  93 ehvpdpp....ellrqiatllkpgGylllsepl 121
                                    +++   p     ++r +++  kpg++l+  e++
  gi|121638550|ref|YP_978774.1| 126 HTFSTAPelqrCYVRALRRASKPGARLYMFEFG 158
                                    999974425557899999999999998877754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   7.9e-10   1.2e-06       1      99 []      55     152 ..      55     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.9e-10
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhl 79 
                                    L+ G+G G+ + + ++k  +   tg+D s +aie+a+   +k        v++++ d+  ldg  + fD+vv + + h +
  gi|121638550|ref|YP_978774.1|  55 LDPGTGPGHHAIYYAAK--GYAATGIDGSVAAIERARDNARK----AGVSVNFQVGDATTLDGLdGRFDTVVDCAFYHTF 128
                                    6779*************..**************555555444....44567777777766666667******99999999 PP

                Methyltransf_12  80 ...kdir.evldnirklLkpgGrl 99 
                                       ++++  +++ +r++ kpg+rl
  gi|121638550|ref|YP_978774.1| 129 staPELQrCYVRALRRASKPGARL 152
                                    888666547888999999999886 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.9e-08   4.3e-05      14     190 ..      29     192 ..      26     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-08
                                    --TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE-- CS
                           TPMT  14 qipfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvke 93 
                                     +p++ ++ +p +++++        + vl P+ G ++ ++  A++g+   G++ s +A+e++ ++a     +        
  gi|121638550|ref|YP_978774.1|  29 ATPWDIGGPQPVVQQLVAL--GAIRGEVLDPGTGPGHHAIYYAAKGYAATGIDGSVAAIERARDNARK---AGVSV---- 99 
                                    59****9998888888877..555559**********************************6333333...22222.... PP

                                    ...........-TTT---SS-..EEEEEEESSTTTS..-GGGHHHHHHHHHHHEEEEEE..EEEEE---S----SS---- CS
                           TPMT  94 ysageiellcgdvFtlraeelgkfdliydraalvAl..ppelreryakslaelLkpdgeglLvtldypqaeheGPPfsvp 171
                                          +   gd+ tl+  +  +fd++ d a+       pel  +y+++l++  kp+++ ++    +++ +    P s++
  gi|121638550|ref|YP_978774.1| 100 ------NFQVGDATTLDGLDG-RFDTVVDCAFYHTFstAPELQRCYVRALRRASKPGARLYMFEFGEHNVNGFSMPRSLS 172
                                    ......333589999888875.9999999999865422699******************555555555555555788888 PP

                                    HHHHHHHHG.GTEEEEEEEE CS
                           TPMT 172 eaelealls.agfkvaelee 190
                                    e+ ++++l  +g++++ l +
  gi|121638550|ref|YP_978774.1| 173 EDDFRQVLPvGGWEITYLGT 192
                                    89999998768899887765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.4e-07   0.00036      28     102 ..      45     120 ..      31     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.4e-07
                                    HCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STT..TTSTTS-EEEEE CS
                            MTS  28 pke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvl..eeveekkfdliv 102
                                     +   ++g+vlD G+G G  ++  a++      t +d + +A+e a+ n+++ +++v++   d++  + + +++fd++v
  gi|121638550|ref|YP_978774.1|  45 VALgaIRGEVLDPGTGPGHHAIYYAAKGYA--ATGIDGSVAAIERARDNARKAGVSVNFQVGDATtlDGL-DGRFDTVV 120
                                    444458999**************9997776..89**********************88888886511445.59999998 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   6.8e-07     0.001      77     154 ..      73     147 ..      58     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.8e-07
                                    --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHH CS
                        UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkr 154
                                    +   g+D   +++++ar+Na+kagv+  ++f++ da+ L   +g +d++v +  +    +++++l++ Y   lr++++
  gi|121638550|ref|YP_978774.1|  73 YAATGIDGSVAAIERARDNARKAGVS--VNFQVGDATTLDGLDGRFDTVV-DCAFYHTFSTAPELQRCYVRALRRASK 147
                                    55789******************996..7899999*****9999***998.777778888888888888777777665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.5e-06    0.0053      76     176 ..      76     182 ..      46     196 .. 0.74
   2 ?   -3.6   0.0       3.6   5.4e+03     129     150 ..     214     238 ..     211     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                                    EEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE.EES..-GGG-S-HHHH.HHHHHHHEEEEEEEEE CS
                Ubie_methyltran  76 vvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt.vsf..GlrnvtDklka.LkeayrvlkpGGrlvv 151
                                    +++D +   ++ +++ +++ g+ +++f +++a  L+  d+ fD+v   +f   +   ++ ++  ++ ++r  kpG rl++
  gi|121638550|ref|YP_978774.1|  76 TGIDGSVAAIERARDNARKAGV-SVNFQVGDATTLDGLDGRFDTVVdCAFyhTFSTAPELQRCyVRALRRASKPGARLYM 154
                                    5667777777888888877775.7*******************875244422456667777653789999********** PP

                                    EEE----SHHHHHHHHHH...HH.HHHH CS
                Ubie_methyltran 152 lefskvelpllsqayely...skevlPv 176
                                    +ef + +++ +s++ +l    + +vlPv
  gi|121638550|ref|YP_978774.1| 155 FEFGEHNVNGFSMPRSLSeddFRQVLPV 182
                                    *****99999988755431114556665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                    -S-HHHHHHHHHHHEEE...EEEEE CS
                Ubie_methyltran 129 vtDklkaLkeayrvlkp...GGrlv 150
                                    ++D+ + + e +r +kp   GGr++
  gi|121638550|ref|YP_978774.1| 214 MADQVRCVLERFRAIKPwlvGGRVH 238
                                    5678888889999999755588876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   1.5e-05     0.023     163     231 ..      52     120 ..      40     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev..alseellkeekadviv 231
                                     evlD GtG G  ai  a  g   ++++D    A++ a++Na++ +v+ +++v  a++ + l+ +++d +v
  gi|121638550|ref|YP_978774.1|  52 GEVLDPGTGPGHHAIYYAAKGY-AATGIDGSVAAIERARDNARKAGVSVNFQVgdATTLDGLD-GRFDTVV 120
                                    58*************9888776.478*************************994434556666.8899887 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.034      32     101 ..      52     121 ..      41     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--.--S-EEEEEE CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineak.lderydfils 101
                                    g vld g g g  ++y +++gy  t +d    +i+  ++ + k  ++ ++ ++ d  +++ ld r+d ++ 
  gi|121638550|ref|YP_978774.1|  52 GEVLDPGTGPGHHAIYYAAKGYAATGIDGSVAAIERARDNARKAGVS-VNFQVGDATTLDgLDGRFDTVVD 121
                                    789*************************9888888887777777666.66666665554336666666655 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00038      0.57      18      58 ..      44      79 ..      37     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                         DUF938 18 LksylakttervLEiasGtGqHAvffApalpnlkwqpsdqd 58
                                   L    a ++e vL+ ++G G+HA+++A++     + ++  d
  gi|121638550|ref|YP_978774.1| 44 LVALGAIRGE-VLDPGTGPGHHAIYYAAK----GYAATGID 79
                                   4444445565.****************85....44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1835.28
//
Query:       gi|121638551|ref|YP_978775.1|  [L=231]
Description: hypothetical protein BCG_2689c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-73  243.9   0.0    1.2e-72  243.7   0.0    1.0  1  Chlor_dismutase  Chlorite dismutase
  ------ inclusion threshold ------
      0.086   12.1   0.0       0.12   11.6   0.0    1.1  1  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.7   0.0   1.3e-76   1.2e-72       1     194 []      32     221 ..      32     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 1.3e-76
                                    HHHHHHHHHHHHHHTTSC..EEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHH.STGGGGEEEEEEEEEEEEEES CS
                Chlor_dismutase   1 reeaveelealleeaeeg..vlralysvlGlradaDlmlwllretleelqeaerelrr.talgkvlepaysyvsvtelse 77 
                                    r++++++++++++++ee+  v+r+ly+v+GlradaD+m+w+++e +e+lq++++++rr t+lg++++p++s v++++++e
  gi|121638551|ref|YP_978775.1|  32 RDAIIDDASTFFKQQEERgvVVRGLYDVAGLRADADFMVWTHAERVEALQATYADFRRtTTLGRACTPVWSGVGLHRPAE 111
                                    7899**********888889*************************************9889******************* PP

                                    SSSS-GGGHHHCHHHHS----SSSEEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTTEEEEEEE-TTTSSSSEEEE CS
                Chlor_dismutase  78 YkeedeenkshvearlapelpkkkyvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgkVrqiitgsfGldDyEwgva 157
                                    +      nksh++a+la+e+ + +y+cvYP+++s+eWYllp+eeRr+++aeHg+++r Y++Vr++++ +f+l+DyEw++a
  gi|121638551|ref|YP_978775.1| 112 F------NKSHIPAFLAGEE-PGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYEWILA 184
                                    *......*************.99********************************************************* PP

                                    EEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEEE CS
                Chlor_dismutase 158 leaddleefkdlvyelRfdeasakvaeegpfyvGrrl 194
                                    +ea++l++++dl++elR+++a+++++ e+pf++G r+
  gi|121638551|ref|YP_978775.1| 185 FEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRV 221
                                    **********************************986 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.4e-05      0.12     229     289 ..      30      85 ..      20      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                                    ----THHHHHHHHHHHHHHHHBS-SSSSB-S-B-TTS-BSS--EEHHHHHHHHHHHHHHHH CS
                  GlcNAc_2-epim 229 eraakllekArkLfetalakgwdkdrgglvytldaagkpvddakllWpqtEalkaaaalae 289
                                    ++++ ++++A   f++++++g+ +++      +d ag  +d + ++W+++E+++a+ a ++
  gi|121638551|ref|YP_978775.1|  30 DQRDAIIDDASTFFKQQEERGVVVRGL-----YDVAGLRADADFMVWTHAERVEALQATYA 85 
                                    5666677**************877655.....8**********************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1587.78
//
Query:       gi|121638552|ref|YP_978776.1|  [L=452]
Description: protoporphyrinogen oxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-31  109.0   1.5    4.2e-31  108.7   1.5    1.1  1  Amino_oxidase  Flavin containing amine oxidoreductase
    1.1e-13   51.2   0.0      3e-13   49.8   0.0    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      1e-08   35.3   0.4     0.0007   19.6   0.1    2.7  3  NAD_binding_9  FAD-NAD(P)-binding
    1.2e-07   31.7   0.8    2.3e-07   30.7   0.8    1.6  1  DAO            FAD dependent oxidoreductase
     0.0019   17.5   0.0      0.033   13.4   0.0    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.003   17.4   1.3     0.0061   16.4   0.2    2.0  2  Rossmann-like  Rossmann-like domain
  ------ inclusion threshold ------
        4.1    7.8   5.8        3.6    8.0   0.4    3.2  3  HOASN          Haem-oxygenase-associated N-terminal helices


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   1.5   1.6e-34   4.2e-31       1     452 []      13     443 ..      13     443 .. 0.84

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 1.6e-34
                                    HHHHHHHHHHHHTT...EEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEE CS
                  Amino_oxidase   1 laGLaaArqLlsaG...fdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpgapkr 77 
                                    ++GL+ A++L +a      +t++E  dr+GG +rt++ +G++++lGa  f    +++ +ll elgl+d++  +  +  + 
  gi|121638552|ref|YP_978776.1|  13 ISGLTSAYRLRQAVgddATITLFEPADRLGGVLRTEHIGGQPMDLGAEAFVLRRPEMPALLAELGLSDRQLASTGA--RP 90 
                                    8*********888669999*************************************************99755545..77 PP

                                    EEETTEECC...TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHH CS
                  Amino_oxidase  78 vlskggref...pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdv 154
                                    +++ + r +   p+++  +p+   +++               +  +  a ++++ +  +  +  ++ ++++l ++++gd 
  gi|121638552|ref|YP_978776.1|  91 LIYSQQRLHplpPQTVVGIPSSAGSMAG-------------LVDDATLARIDAEAARPFTWQVGSDPAVADLVADRFGD- 156
                                    7787666665555555555555444444.............444444444455556788888899999***********. PP

                                    HHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE..................TTHTHHHHHHH CS
                  Amino_oxidase 155 evwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp..................rgGlsqlpeal 216
                                     v+ r ++p       ++sg++ag      +++a p++ +  + g+  ++                   +gG++ l + l
  gi|121638552|ref|YP_978776.1| 157 QVVARSVDP-------LLSGVYAGSAATIGLRAAAPSVAAALDRGATSVTDavrqalppgsggpvfgalDGGYQVLLDGL 229
                                    99*******.......********99888888889999999988888888899999************************ PP

                                    HHTTTTEEEE.TSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEE CS
                  Amino_oxidase 217 aeelrgldir.lntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvil 295
                                     +   + +++ +++rV +++r   g  ++ e+g   +aDaV+++vp + l+   ++ +  +   +a+r++ ++s+++v l
  gi|121638552|ref|YP_978776.1| 230 VR---RSRVHwVRARVVQLER---GWVLRDETGGRWQADAVILAVPAPRLA--RLVDGIAPRTHAAARQIVSASSAVVAL 301
                                    **...6666646899999999...888888888888***************..99999966888889************* PP

                                    EESSGG.SGCSTSECE..CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEEC.HHHHHHHTTS-HHHHHHHHHHHHHH CS
                  Amino_oxidase 296 efdrkf.wednalgqg..vlvseltttlgeafissdfpsrappgkglvllvyvg.gdaaneleslsdeelvqavlrdLrk 371
                                    ++++   +++ +   g  v  +e++   + + +s ++  r +    l+ l++   gd+     ++sd++l++ + +dL +
  gi|121638552|ref|YP_978776.1| 302 AVPGGTaFPHCS---GvlVAGDESPHAKAITLSSRKWGQRGDV--ALLRLSFGRfGDEPA--LTASDDQLLAWAADDLVT 374
                                    ***999777765...4567888999999999999999999666..553333333333222..345*************** PP

                                    HHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHH CS
                  Amino_oxidase 372 lfgeevpepkatlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgt.vegAilSGlraAar 450
                                    +fg  + +p+++ v+rW  ++++       ++gpgh d  +  +    p+l +AG++      g  v+ ++ ++ ra++ 
  gi|121638552|ref|YP_978776.1| 375 VFG-VAVDPVDVRVRRWI-EAMP-------QYGPGHADVVAELRAGLPPTLAVAGSYLD----GIgVPACVGAAGRAVTS 441
                                    ***.*************8.****.......***************7777********66....999*******9999987 PP

                                    HH CS
                  Amino_oxidase 451 il 452
                                    ++
  gi|121638552|ref|YP_978776.1| 442 VI 443
                                    75 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   1.2e-16     3e-13       1      67 [.       8      75 ..       8      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.2e-16
                                   EE--SHHHHHHHHHHHCC...TEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                   +vG+G+sGl+ Ay+L++a   ++ ++l+e +drlGG +++++++g++ d+ga +f    + p++ +ll+e
  gi|121638552|ref|YP_978776.1|  8 VVGGGISGLTSAYRLRQAvgdDATITLFEPADRLGGVLRTEHIGGQPMDLGAEAFVL--RRPEMPALLAE 75
                                   8****************777799*******************************976..34666666655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.7e-07    0.0007       2      45 ..       8      48 ..       7      61 .. 0.92
   2 !   12.7   0.0   3.7e-05     0.094     107     153 ..     225     268 ..     219     270 .. 0.88
   3 ?   -2.3   0.0       1.6     4e+03      69     101 ..     387     424 ..     355     440 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtd 45
                                   +vG+G++Gl+ + rL +    +++ +itlf+p+    g+v rt+
  gi|121638552|ref|YP_978776.1|  8 VVGGGISGLTSAYRLRQAV--GDDATITLFEPADRL-GGVLRTE 48
                                   9*****************8..***********9998.8999887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                  NAD_binding_9 107 llarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAl 153
                                    ll+ l ++ +v+ +ra+vv+le   +g+ ++ ++g +++adaV+LA+
  gi|121638552|ref|YP_978776.1| 225 LLDGLVRRSRVHWVRARVVQLE---RGWVLRDETGGRWQADAVILAV 268
                                    6677778899***********9...57999***************97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                  NAD_binding_9  69 faeWlrerga....lee.aeeldpddfvpRalyGrYlr 101
                                     ++W+++ ++    + + ++el+ +  ++ a+ G Yl+
  gi|121638552|ref|YP_978776.1| 387 VRRWIEAMPQygpgHADvVAELRAGLPPTLAVAGSYLD 424
                                    46777777766554222577777777777788888875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.8     9e-11   2.3e-07       2     203 ..       6     270 ..       5     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 9e-11
                                    EEEECTSHHHHHHHHHHHHT.T....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHH....HHHHHHH CS
                            DAO   2 vviiGGGiiGlstAyeLarr.g....VtllekgdiagsgaSgrnsgllhsglrylpeaselarlsleal....eelrele 72 
                                     +++GGGi Gl+ Ay L ++ g    +tl+e +d++g        g+l+  +   ++     +l +ea+     e+ +l 
  gi|121638552|ref|YP_978776.1|   6 YCVVGGGISGLTSAYRLRQAvGddatITLFEPADRLG--------GVLRTEHIGGQPM----DLGAEAFvlrrPEMPALL 73 
                                    59***************7768789*********9999........6776666433333....666666533335556666 PP

                                    HHHSST.TSEEEEEEEEEESS...........................HHHHHHHHHHHHHH.......HHTTTTEE.EE CS
                            DAO  73 eelgid.idyrrtGllslaad...........................eeelealdkllall.......leagldae.ll 116
                                    +elg+   ++  tG  +l ++                           ++ l+++d+++a++             a  + 
  gi|121638552|ref|YP_978776.1|  74 AELGLSdRQLASTGARPLIYSqqrlhplppqtvvgipssagsmaglvdDATLARIDAEAARPftwqvgsD-PA-VADlVA 151
                                    6667643556667777777765566666666666666666666666665668888888888877654321.11.112134 PP

                                    EH..HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEES............................ CS
                            DAO 117 da..eevrelepalpgllgalfypdtgqvdpakltaalaraaealGveileg............................ 166
                                    d+  ++v +++   ++ll +++  +++++  +++++++a+a+ ++G++ ++                             
  gi|121638552|ref|YP_978776.1| 152 DRfgDQVVARSV--DPLLSGVYAGSAATIGLRAAAPSVAAAL-DRGATSVTDavrqalppgsggpvfgaldggyqvlldg 228
                                    444445666553..589999*****99999999999988776.6889999998999************************ PP

                                    ...........ECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGG CS
                            DAO 167 ...........tevtgleeedgkvwgverttpgen.daadavVnaaGaw 203
                                               ++v+ le+    +w + r++ g + + adav++a  + 
  gi|121638552|ref|YP_978776.1| 229 lvrrsrvhwvrARVVQLER----GWVL-RDETGGRwQ-ADAVILAV-PA 270
                                    *999999999888888865....8999.444455645.599***98.33 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.3e-05     0.033       2      34 ..       5      48 ..       4      82 .. 0.80
   2 ?    1.9   0.0     0.041   1.1e+02      67     133 ..     222     294 ..     165     302 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                   SEEEE--SHHHHHHHHHHHH...HTS-EEEEE........TTHC CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxx........xxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq...agakvtlve........legt 34
                                   +++v+GgG+ Gl+ a +l+q     a +tl+e        l+++
  gi|121638552|ref|YP_978776.1|  5 SYCVVGGGISGLTSAYRLRQavgDDATITLFEpadrlggvLRTE 48
                                   689*****************777799999997665555544444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.041
                                    CCCCHC............CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHH CS
                                    xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  67 ielllg............eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsa 133
                                    +++ll+            + vv++++g+  + +     + + + ++d+++lA  +      ++G a+ ++   r + sa
  gi|121638552|ref|YP_978776.1| 222 YQVLLDglvrrsrvhwvrARVVQLERGW-VLRD-----ETGGRWQADAVILAVPAPRLARLVDGIAPRTHAAARQIVSA 294
                                    4444444443333333323677777777.3333.....455689********997555557888888877777766655 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   6.7e+03      77      96 ..     163     182 ..     150     194 .. 0.70
   2 !   16.4   0.2   2.4e-06    0.0061      68     107 ..     260     299 ..     251     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                  Rossmann-like  77 Pdaelpglvkglaatgavra 96 
                                     d+ l+g+ +g aat  +ra
  gi|121638552|ref|YP_978776.1| 163 VDPLLSGVYAGSAATIGLRA 182
                                    46667777777777665554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.4e-06
                  Rossmann-like  68 raellllavPdaelpglvkglaatgavraGtivahtsgan 107
                                    +a+ ++lavP ++l+ lv+g+a  +   a +iv   s+  
  gi|121638552|ref|YP_978776.1| 260 QADAVILAVPAPRLARLVDGIAPRTHAAARQIVSASSAVV 299
                                    6889*****************************9988765 PP

>> HOASN  Haem-oxygenase-associated N-terminal helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.1     8e+03      19      31 ..     184     196 ..     146     204 .. 0.64
   2 ?    8.0   0.4    0.0014       3.6      25      49 ..     281     305 ..     260     308 .. 0.81
   3 ?    0.8   0.0      0.25   6.4e+02      61      82 ..     370     391 ..     357     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                    HHHHHHHTSTT-- CS
                          HOASN  19 aalladalkvgas 31 
                                    a  +a al  ga+
  gi|121638552|ref|YP_978776.1| 184 APSVAAALDRGAT 196
                                    2335555555555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0014
                                    HTSTT--HHHHHHHHHHHHHHHHHH CS
                          HOASN  25 alkvgasldqidlalekllalaekG 49 
                                    a +++a+ +qi +a ++++ala  G
  gi|121638552|ref|YP_978776.1| 281 APRTHAAARQIVSASSAVVALAVPG 305
                                    44679****************9765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.25
                                    HHHHHHHHH---GGGHHHHHHH CS
                          HOASN  61 qalllvlslsddvateqtrrWl 82 
                                      l+ v+ ++ d+   + rrW+
  gi|121638552|ref|YP_978776.1| 370 DDLVTVFGVAVDPVDVRVRRWI 391
                                    57889999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3129.51
//
Query:       gi|121638553|ref|YP_978777.1|  [L=357]
Description: uroporphyrinogen decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.3e-119  397.7   0.0   4.8e-119  397.6   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  2.7e-123  4.8e-119       3     345 ..       9     356 ..       7     357 .] 0.96

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 2.7e-123
                                    --HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT CS
                          URO-D   3 nerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealG 82 
                                    ++++l+a++g+k++rvPvw+mRqaGr+lpeyra r+ +s+l +c  p+ a+e+tlqp+rr+++Daailfsdi+v++ a+G
  gi|121638553|ref|YP_978777.1|   9 QSPYLAAVTGRKPSRVPVWFMRQAGRSLPEYRALRERYSMLAACFEPDVACEITLQPIRRYDVDAAILFSDIVVPLRAAG 88 
                                    6789**************************************************************************** PP

                                    -EEEEETTTEEEEE--S-....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT.-SS- CS
                          URO-D  83 levefeegegPvvekpvrtaedveklevpddveegrlpyvleaikllkkelggevpligfvgaPftlasylveGg.skgf 161
                                    ++++++++ gPv+++pvrta+dv+++++ d+ +   ++ vl a +ll +elg +vpligf+gaPftlasylveGg s+++
  gi|121638553|ref|YP_978777.1|  89 VDLDIVADVGPVIADPVRTAADVAAMKPLDPQA---IQPVLVAASLLVAELG-DVPLIGFAGAPFTLASYLVEGGpSRHH 164
                                    *****************************9954...***************6.*************************** PP

                                    HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EE CS
                          URO-D 162 ekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifDswagllspedfeefvlpylkrivdevkaegpkvpvi 241
                                    ++++++++++p+++h+l+ kltd++i++l  qi+ag+daiq+fDswag+lsp d++++vlp+++r+++++ ++  +vp++
  gi|121638553|ref|YP_978777.1| 165 AHVKAMMLAEPASWHALMAKLTDLTIAFLVGQIDAGVDAIQVFDSWAGALSPIDYRQYVLPHSARVFAALGEH--GVPMT 242
                                    ***********************************************************************97..58*** PP

                                    EEESSHH.HHHHHHTT.......S-.-SEEE--TTS-HHHHHHSS....EEE--B-G.GGGGS-HHHHHHHHHHHHT... CS
                          URO-D 242 lfikgagaeiledlae.......lg.advlsldwtvdlkeaarevgdkvalqGnldPialLlgspeeiekevkeile... 310
                                    +f+ g++ e+l ++ e        g   v+++dw+++l++aa++v  ++alqGnldP a+ l+++ ++e++++++++   
  gi|121638553|ref|YP_978777.1| 243 HFGVGTA-ELLGAMSEavtagerPGrGAVVGVDWRTPLTDAAARVVPGTALQGNLDP-AVVLAGWPAVERAARAVVDdgr 320
                                    ******8.9******8777777744488*****************************.9******************998 PP

                                    ..T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT CS
                          URO-D 311 .kgaggkkgyilnlGhgippetppenvkalveavke 345
                                     +  +g+ g+i+nlGhg++pe++p+ ++ lv +v++
  gi|121638553|ref|YP_978777.1| 321 rAVDAGAAGHIFNLGHGVLPESDPAVLADLVSLVHS 356
                                    85567899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2487.39
//
Query:       gi|121638554|ref|YP_978778.1|  [L=276]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-40  137.0   0.0    8.9e-40  136.6   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    8.3e-16   58.4   0.0      1e-15   58.1   0.0    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.0   9.9e-44   8.9e-40       4     249 ..      22     267 ..      20     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 9.9e-44
                                    TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC..HHHHHHHCCHHHHH CS
                          ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek..akqallkeevlelw 81 
                                    +gv+++ l+ P  +N++ +++  +l++    ++ d++vr+v + G +kaF++G+ +  +ae     +    +  e  +l 
  gi|121638554|ref|YP_978778.1|  22 EGVLELVLDSP-GLNSVGPHMHRDLADIWPVIDRDPAVRVVLVRGEGKAFSSGGSFDLIAETIGdyQGRLRIMREARDLV 100
                                    799********.******************************************99988886542244445668999*** PP

                                    HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEH CS
                          ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisa 161
                                     +l + +kpv++a++G a+g+Gl++al +Di +a++ a++    +klG+ +g  +   ++  vG++kA++ ll+++++s+
  gi|121638554|ref|YP_978778.1| 101 LNLVNFDKPVVSAIRGPAVGAGLVVALLADISVAGRAAKIIDGHTKLGVAAGDHAAICWPLLVGMAKAKYYLLTCEPLSG 180
                                    ******************************************************************************** PP

                                    HHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHH CS
                          ECH_1 162 qealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqafl 241
                                    +ea+++Glv+  v ++++l +a  lae+la  +++a+r  k +ln+ +++  ++ +e    l    f   d++eGl a+ 
  gi|121638554|ref|YP_978778.1| 181 EEAERIGLVSICVDDDDVLPTATRLAERLAAGAQNAIRWTKRSLNHWYRMFGPA-FETSLGLEFIGFGGPDVREGLAAHR 259
                                    *************************************************99886.55566665556666799******** PP

                                    TCSH---- CS
                          ECH_1 242 Ekrkpefe 249
                                    Ekr+++f+
  gi|121638554|ref|YP_978778.1| 260 EKRPARFG 267
                                    ****9986 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.1e-19     1e-15      11     190 ..      33     211 ..      24     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.1e-19
                                    GTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHHHC-SS-E CS
                          ECH_2  11 alNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyliatypkpv 90 
                                     lN++  +m r+l+++   +++d++v++v+++g+g kaf++Gg +  ++e++ + + +  +++re  +l   + ++ kpv
  gi|121638554|ref|YP_978778.1|  33 GLNSVGPHMHRDLADIWPVIDRDPAVRVVLVRGEG-KAFSSGGSFDLIAETIGDYQGR-LRIMREARDLVLNLVNFDKPV 110
                                    49*******************************88.*****************99877.79******************* PP

                                    EEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHHHHTTS-- CS
                          ECH_2  91 valmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgadalaaglat 169
                                    v+ + G ++G G+ +++ + + v+   +++    t++G+     +    + l g + ++y  lT + l+g++a  +gl +
  gi|121638554|ref|YP_978778.1| 111 VSAIRGPAVGAGLVVALLADISVAGRAAKIIDGHTKLGVAAGDHAAICWPLLVGmAKAKYYLLTCEPLSGEEAERIGLVS 190
                                    ***************************************9877777777777664889********************** PP

                                    EE--GGGHHHHHHHHHTT... CS
                          ECH_2 170 hyvpseklealeeaLaeless 190
                                     +v+++++   +++Lae   +
  gi|121638554|ref|YP_978778.1| 191 ICVDDDDVLPTATRLAERLAA 211
                                    ******996666666654332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1887.66
//
Query:       gi|121638555|ref|YP_978779.1|  [L=210]
Description: hypothetical protein BCG_2693 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-73  245.2   0.1    3.3e-73  245.0   0.1    1.0  1  DUF3000   Protein of unknown function (DUF3000)


Domain annotation for each model (and alignments):
>> DUF3000  Protein of unknown function (DUF3000)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.1   1.8e-77   3.3e-73       2     176 .]      23     202 ..      22     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 1.8e-77
                        DUF3000   2 paeFreaveslraarlrpeieleeipapqrlapysvAlgaev......teeeeeeelatGrlilLhdpageeaWegtfrl 75 
                                    pa Freav++++a+++rpeiel +i++pqrlapys+Algae+        +e++e++a+Grli+L+dp+g++aW+gt+rl
  gi|121638555|ref|YP_978779.1|  23 PALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIkhpeldVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRL 102
                                    899***************************************88888777778888************************ PP

                        DUF3000  76 vayiraeldaelaaDpllpevawsWlteaLeeagaeytalgGtvtrvlserfgelaeeeeaaelElRaSWtpaeedlaah 155
                                    vay++a+ld++ a DpllpevawsWl++aL++++ +++algGtvt+++s+r+g+++++++a++lElRaSWt+++ dl ah
  gi|121638555|ref|YP_978779.1| 103 VAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAH 182
                                    ******************************************************************************** PP

                        DUF3000 156 leafadllaaaaGlppeegvt 176
                                    ++af+d+l +aaGlpp+ gvt
  gi|121638555|ref|YP_978779.1| 183 VQAFCDVLEHAAGLPPA-GVT 202
                                    ****************9.875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1447.23
//
Query:       gi|121638556|ref|YP_978780.1|  [L=438]
Description: hypothetical protein BCG_2694 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-31  108.2   0.0    4.7e-31  107.9   0.0    1.1  1  DNA_pol_A_exo1  3'-5' exonuclease
    3.2e-25   88.2   4.0    3.2e-25   88.2   4.0    2.3  3  DNA_pol_A_exoN  3' to 5' exonuclease C-terminal domain
    2.2e-13   50.0   0.1    4.7e-13   48.9   0.1    1.6  1  HRDC            HRDC domain


Domain annotation for each model (and alignments):
>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   7.8e-35   4.7e-31      10     175 ..      43     201 ..      34     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 7.8e-35
                                    HHHHHHHHTTSSEEEEEEEEE-SSSTTSSEEEEEEEEECS.SEEEEEECTTTTTT-..HGHHHHHHHT-TTSEEEESSHH CS
                 DNA_pol_A_exo1  10 leelieelknlkvvavDtEttsldlisatlvliliqlgek.eeayiidplelgddv..alealkrlledenitkvghnak 86 
                                    ++el+ + +   ++avD E  s     ++++ +liq+++   ++++idp+++g d+  +l +++++l+ +  ++++h+a+
  gi|121638556|ref|YP_978780.1|  43 AAELLDRGRG--PFAVDAERASGFR--YSGRAYLIQIRRAeAGTVLIDPVSHGGDPltVLAPVAEVLSTN--EWILHSAD 116
                                    4444444444..9************..************999*************99***********77..7******* PP

                                    HHHHHHHHHHTS--SSEEEHHHHHHHTTHSTTSSHHHHHHHHHSB---GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHH CS
                 DNA_pol_A_exo1  87 fDlevlardfgielenlfdtmlaayvldyershsLdsLaekylgdleldkeeqiakwqkarplleeqllYAaeDadvllr 166
                                    +Dl +la+ +g+ ++ l+dt+la ++ +++r ++L+ ++e++lg l l+k + +a+w+ +rpl+  +l+YAa+D+++l++
  gi|121638556|ref|YP_978780.1| 117 QDLPCLAE-VGMRPPALYDTELAGRLAGFDR-VNLAAMVERLLG-LGLTKGHGAADWS-KRPLPSAWLNYAALDVELLIE 192
                                    ********.**********************.************.*************.********************* PP

                                    HHHHHHHHH CS
                 DNA_pol_A_exo1 167 lfkkLtkel 175
                                    l+  + + l
  gi|121638556|ref|YP_978780.1| 193 LRAVISRVL 201
                                    *99888765 PP

>> DNA_pol_A_exoN  3' to 5' exonuclease C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.58   3.5e+03       5      29 ..     176     200 ..     173     212 .. 0.69
   2 ?   -3.0   0.3       1.5   9.1e+03       5      23 ..     217     235 ..     214     238 .. 0.77
   3 !   88.2   4.0   5.4e-29   3.2e-25       1      87 []     333     424 ..     333     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.58
                                    HHHHHHH-HHHHHHHHHHHHHHHHH CS
                 DNA_pol_A_exoN   5 praWaekdPeaaerlkavraaleel 29 
                                    p+aW +     +e+l + ra+++ +
  gi|121638556|ref|YP_978780.1| 176 PSAWLNYAALDVELLIELRAVISRV 200
                                    6677777777788888888888764 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                    HHHHHHH-HHHHHHHHHHH CS
                 DNA_pol_A_exoN   5 praWaekdPeaaerlkavr 23 
                                     r+ +++ P aa+r  + r
  gi|121638556|ref|YP_978780.1| 217 LRSFESRPPPAAARQDRWR 235
                                    5778889999999888777 PP

  == domain 3  score: 88.2 bits;  conditional E-value: 5.4e-29
                                    --S-HHHHHHH-HHHHHHHHHHHHHHHHHHHHHT--HHHHS-HHHHHHHH-SS-G.......GG--HHHHHHHHT--HHH CS
                 DNA_pol_A_exoN   1 GlPppraWaekdPeaaerlkavraaleelaeeleipvenlltpdllrrlvWeppet.....lteeavsaaLaelgaReWQ 75 
                                    G+Ppp +W +++P+aa+rl a+raal+e+++ +++p+enl++pdl+rrl+We+++          av+a L++++aR WQ
  gi|121638556|ref|YP_978780.1| 333 GPPPPGRWVRRKPAAAARLDAARAALTEVSQRVRVPTENLVSPDLVRRLCWEWEDIsqsspDPIAAVEAYLRTGQARAWQ 412
                                    8*****************************************************98665544456899************ PP

                                    HHHHHHHHHHHH CS
                 DNA_pol_A_exoN  76 velvapllaeaL 87 
                                     elv+p+l+ aL
  gi|121638556|ref|YP_978780.1| 413 LELVVPILTAAL 424
                                    *********998 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   7.8e-17   4.7e-13       2      67 ..     249     314 ..     248     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.8e-17
                                    HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHHH CS
                           HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeilea 67 
                                    la +++L+ +R+++A+++d++p++++pd+++++ A ++P+++++L +++ +g r  ++ ++ + +a
  gi|121638556|ref|YP_978780.1| 249 LAAVRELWTARDRIAQRRDIAPRRILPDSAIIDAAIADPKSVDDLVALPVFGGRNQRRSAAVWWAA 314
                                    67899*****************************************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3340.90
//
Query:       gi|121638557|ref|YP_978781.1|  [L=638]
Description: 1-deoxy-D-xylulose-5-phosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.8e-107  356.4   0.0   1.5e-106  355.6   0.0    1.4  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    4.5e-38  130.7   0.1    2.3e-37  128.4   0.0    2.1  2  Transket_pyr     Transketolase, pyrimidine binding domain
    1.1e-26   93.1   0.2    3.7e-26   91.4   0.0    2.0  2  Transketolase_C  Transketolase, C-terminal domain
    2.8e-06   27.2   0.0    3.2e-05   23.8   0.0    2.7  3  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
     0.0028   16.7   0.1      0.013   14.4   0.0    1.9  2  E1_dh            Dehydrogenase E1 component
     0.0074   16.6   0.0      0.021   15.1   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
      0.041   14.4   0.6       0.58   10.7   0.0    2.9  3  Usp              Universal stress protein family
       0.15   12.3   0.0       0.27   11.5   0.0    1.3  1  Beta-Casp        Beta-Casp domain


Domain annotation for each model (and alignments):
>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.6   0.0  6.7e-110  1.5e-106       1     273 []       2     278 ..       2     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 355.6 bits;  conditional E-value: 6.7e-110
                 DXP_synthase_N   1 LekinspedlkklskeeleelaeelrefliesvsktggHlasnLgvveLtlalhyvfdtpkDklvwDvgHqaYvhKiltg 80 
                                    L++i+ p+dl++ls+++l+ela+e+refli++v++tggHl++nLgvveLtlalh+vfd+p+D +++D+gHqaYvhK+ltg
  gi|121638557|ref|YP_978781.1|   2 LQQIRGPADLQHLSQAQLRELAAEIREFLIHKVAATGGHLGPNLGVVELTLALHRVFDSPHDPIIFDTGHQAYVHKMLTG 81 
                                    789***************************************************************************** PP

                 DXP_synthase_N  81 RkdkfktlrqkgGlsgfpkrsEseyDafeagHsstsisaalGlavardlkg.ekkkvvaviGDgaltgGmafealnnige 159
                                    R ++f+tlr+kgGlsg+p+r+Ese+D++e++H+s+++s+a Gla+a +l+g ++++vvav+GDgaltgGm++ealnni++
  gi|121638557|ref|YP_978781.1|  82 RSQDFATLRKKGGLSGYPSRAESEHDWVESSHASAALSYADGLAKAFELTGhRNRHVVAVVGDGALTGGMCWEALNNIAA 161
                                    **************************************************96789************************* PP

                 DXP_synthase_N 160 lkkkllvilNdNemsisknvGalskylskllsskayeklkkevkkllk...kigkklaelakklkeslkellvpgtlfee 236
                                    +++ +++++NdN +s+++++G+++++l++l+ ++aye++ +++++l++    +g  + ++++ +k  +k+ l+p+ lf++
  gi|121638557|ref|YP_978781.1| 162 SRRPVIIVVNDNGRSYAPTIGGVADHLATLRLQPAYEQALETGRDLVRavpLVGGLWFRFLHSVKAGIKDSLSPQLLFTD 241
                                    ***********************************************8555559999*********************** PP

                 DXP_synthase_N 237 lgfkYlGpidGhdleelikvleevkklkgpvllhvvt 273
                                    lg+kY+Gp+dGhd ++++ +l++++++  pv++hvvt
  gi|121638557|ref|YP_978781.1| 242 LGLKYVGPVDGHDERAVEVALRSARRFGAPVIVHVVT 278
                                    ***********************************98 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.53   1.2e+03       3      29 ..     118     144 ..     116     176 .. 0.79
   2 !  128.4   0.0     1e-40   2.3e-37       4     175 ..     315     476 ..     312     478 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.53
                                    EEHHHHHHHHHHHHHCTTTTEEEEESS CS
                   Transket_pyr   3 iawrkaeaealaellkedpevvligaD 29 
                                    +++++++a+a++  ++++ +vv++  D
  gi|121638557|ref|YP_978781.1| 118 LSYADGLAKAFELTGHRNRHVVAVVGD 144
                                    678889999999999999999877655 PP

  == domain 2  score: 128.4 bits;  conditional E-value: 1e-40
                                    EHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHH CS
                   Transket_pyr   4 awrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgd 83 
                                     w++ + +al  ++++  ++v+i+a++ g t+++ +g+++++   r++d+gi+Eq++++ a+G+a+ g  l++v+a++++
  gi|121638557|ref|YP_978781.1| 315 GWTATFSDALIGYAQKRRDIVAITAAMPGPTGLTAFGQRFPD---RLFDVGIAEQHAMTSAAGLAMGG--LHPVVAIYST 389
                                    69999*************************************...***********************..********** PP

                                    HHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS CS
                   Transket_pyr  84 FangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairred 162
                                    F+n    +a+++i++++a++kl+v+ v++r++i +g dG++h++++++++l  +pg++v++P d+  +++ l +a+  + 
  gi|121638557|ref|YP_978781.1| 390 FLN----RAFDQIMMDVALHKLPVTmVLDRAGI-TGSDGASHNGMWDLSMLGIVPGIRVAAPRDATRLREELGEALDVD- 463
                                    ***....**************************.*******************************************86. PP

                                    .SEEEEEE-SSEE CS
                   Transket_pyr 163 rkPvvlrlpksll 175
                                    ++P++lr+pk+ +
  gi|121638557|ref|YP_978781.1| 464 DGPTALRFPKGDV 476
                                    6*********976 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   4.3e+03      62      86 ..     137     161 ..     133     190 .. 0.68
   2 !   91.4   0.0   1.7e-29   3.7e-26       9     124 .]     500     612 ..     494     612 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                    SEEEEEEEEESTTSHHHHHHHHHHH CS
                Transketolase_C  62 grlvvveeavkrgGigsevaaalae 86 
                                    + + vv +++ +gG+  e ++ +a 
  gi|121638557|ref|YP_978781.1| 137 HVVAVVGDGALTGGMCWEALNNIAA 161
                                    5677788888888877666665554 PP

  == domain 2  score: 91.4 bits;  conditional E-value: 1.7e-29
                                    TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCC CS
                Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeea 88 
                                    ++dv+lva G+  ++al++a++L+++gi+++V+d+r+v p+  + ++e++ +++ lv++e++ ++gG gs+v+aal +  
  gi|121638557|ref|YP_978781.1| 500 NHDVLLVAIGAFAPMALAVAKRLHNQGIGVTVIDPRWVLPVS-DGVRELAVQHKLLVTLEDNGVNGGAGSAVSAALRR-- 576
                                    68***************************************9.99*********************************.. PP

                                    CTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
                Transketolase_C  89 fdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                     +++d+p+++vg+p++ +e++s+ e+++ +gl+ +++
  gi|121638557|ref|YP_978781.1| 577 -AEIDVPCRDVGLPQEfYEHASRSEVLADLGLTDQDV 612
                                    .*******************************99876 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.4e-08   3.2e-05      20      83 ..     107     174 ..      94     210 .. 0.81
   2 ?   -1.9   0.0       1.1   2.5e+03     116     153 .]     238     276 ..     220     276 .. 0.79
   3 ?   -1.7   0.0      0.95   2.1e+03     121     149 ..     440     467 ..     425     470 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.4e-08
                                    EEEC.ETTTS-TTTHHHHHHHHHH.HSTTSEEEEEEEHHH..HHHTGGGHHHHHHTT-SEEEEEEE-S CS
                   TPP_enzyme_C  20 sylt.sgglgtmGyglpaAiGakl.akpdrevvaivGDGg..flmilqelatavrrnlpitvvvlnNe 83 
                                     ++  s   +++ y+ + A + +l  +++r+vva+vGDG+    m+ ++l +++  + p+++vv +N+
  gi|121638557|ref|YP_978781.1| 107 DWVEsSHASAALSYADGLAKAFELtGHRNRHVVAVVGDGAltGGMCWEALNNIAASRRPVIIVVNDNG 174
                                    566655566777777777777777446799*********96557889********************6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    HHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C 116 laealGak.garvekadveeleealkealekkgpaliev 153
                                    l   lG k +  v+ +d   +e al+ a++ + p++++v
  gi|121638557|ref|YP_978781.1| 238 LFTDLGLKyVGPVDGHDERAVEVALRSARRFGAPVIVHV 276
                                    556677885557888889999999****99999999997 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.95
                                    TSEEEEESSH.HHHHHHHHHHHH.CSSSEE CS
                   TPP_enzyme_C 121 Gakgarvekadveeleealkeal.ekkgpa 149
                                    G+++a   ++d   l+e l eal   +gp+
  gi|121638557|ref|YP_978781.1| 440 GIRVAA--PRDATRLREELGEALdVDDGPT 467
                                    444444..667799********96566776 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.9e-06     0.013     103     162 ..     114     174 ..      67     181 .. 0.78
   2 ?   -0.7   0.0      0.23   5.2e+02     192     214 ..     250     268 ..     249     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                                    TTTHHHHHHHHHHHHHHHT.S---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEES CS
                          E1_dh 103 vgaqvplvaGialaakieg.kkevailliGDgAanqGdvyealnlaalwklpvifvveNNk 162
                                     +a  + + G+a a    g  ++ +++++GDgA   G  +ealn  a+ + pvi vv+ N+
  gi|121638557|ref|YP_978781.1| 114 ASAALSYADGLAKAFELTGhRNRHVVAVVGDGALTGGMCWEALNNIAASRRPVIIVVNDNG 174
                                    344447778999999966515778999******999********99999********9996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.23
                                    EETTSHHHHHHHHHHHHHHHHTT CS
                          E1_dh 192 VdgnDplavyeAvkfAaerareg 214
                                    Vdg D  av  A + A++    +
  gi|121638557|ref|YP_978781.1| 250 VDGHDERAVEVALRSARR----F 268
                                    889998888887777765....4 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.2e-06     0.021       2      77 ..     502     573 ..     501     585 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.2e-06
                                    SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                        PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                    +v++va+G+ a  a +++++l ++gi v ++ +r++ P  ++ ++el+ + k +v+l+ n   g     ++ v+aa
  gi|121638557|ref|YP_978781.1| 502 DVLLVAIGAFAPMALAVAKRLHNQGIGVTVIDPRWVLPV-SDGVRELAVQHKLLVTLEDNGVNG---GAGSAVSAA 573
                                    899***********************************8.789**************9998544...444444444 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.99   2.2e+03      86     128 ..     147     187 ..     100     190 .. 0.67
   2 ?   10.7   0.0   0.00026      0.58      15      56 ..     254     294 ..     248     314 .. 0.87
   3 ?   -0.8   0.0      0.91     2e+03      22      59 ..     515     552 ..     512     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.99
                                    EEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHH CS
                            Usp  86 veegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvsey 128
                                    +++g   e+++ +a ++ + +iVv   grs      +G v++ 
  gi|121638557|ref|YP_978781.1| 147 LTGGMCWEALNNIAASRRPVIIVVNDNGRSYAPT--IGGVADH 187
                                    4555556777888888888888887777766665..6666665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHH CS
                            Usp  15 skkAlewAlelakargaelillhvidprasgavsdadeeaee 56 
                                     ++A+e Al+ a+++ga+ +++hv+  + +g+ ++++++ae+
  gi|121638557|ref|YP_978781.1| 254 DERAVEVALRSARRFGAP-VIVHVVTRKGMGYPPAEADQAEQ 294
                                    579**************9.88999999999999988888776 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.91
                                    HHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHH CS
                            Usp  22 Alelakargaelillhvidprasgavsdadeeaeeeel 59 
                                    Al+ ak+ + + i ++vidpr   +vsd+ +e + + +
  gi|121638557|ref|YP_978781.1| 515 ALAVAKRLHNQGIGVTVIDPRWVLPVSDGVRELAVQHK 552
                                    78889998888899999999999999998888776655 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.27       3      99 ..      49     171 ..      47     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                    HHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG..................E-SHH.....HHH.H..HH.. CS
                      Beta-Casp   3 ellylLeelwkekkledlklpiyldsplaskatevYkeyae..................veaks.lewmesk.keeln.. 60 
                                    el + L+++ ++  + +   pi++d      + ++ +                      ++a+s  +w+es+ ++ ++  
  gi|121638557|ref|YP_978781.1|  49 ELTLALHRVFDS--P-HD--PIIFDTGHQAYVHKMLT---GrsqdfatlrkkgglsgypSRAESeHDWVESShAS-AAls 119
                                    666666666655..3.23..56666633333333322...12235555666888888886666667899999532.2256 PP

                                    .............HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS CS
                      Beta-Casp  61 .............sskgpkvilassgmlegGrsrellkklledprntvilvg 99 
                                                 ++++  v ++++g l+gG+  e+l++++  +r ++i v 
  gi|121638557|ref|YP_978781.1| 120 yadglakafeltgHRNRHVVAVVGDGALTGGMCWEALNNIAASRRPVIIVVN 171
                                    8899999999998667889*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 4143.07
//
Query:       gi|121638558|ref|YP_978782.1|  [L=165]
Description: hypothetical protein BCG_2696 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-09   37.7   0.8    0.00015   22.2   0.3    2.5  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.5e-06     0.062       5      54 ..      24      73 ..      17      76 .. 0.80
   2 !   22.2   0.3   8.2e-09   0.00015       8      55 ..     116     162 ..     106     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                                   SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                            CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                   m +d+++v+ d++  +a+++++e+++ +l+V+ + gk   ++  + ++r+
  gi|121638558|ref|YP_978782.1| 24 MAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGKQYAVLPASQVVRF 73
                                   89999******************999999998788876666666666665 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 8.2e-09
                                    SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    +v+ ++ d+t+ e++  m++ +   l VV +dg l+G+vt + ll a 
  gi|121638558|ref|YP_978782.1| 116 EVPPANADDTIIEVAAVMARLRSPLLAVV-KDGSLLGVVTASRLLAAA 162
                                    67899*************66443355799.8*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1126.12
//
Query:       gi|121638559|ref|YP_978783.1|  [L=429]
Description: arsenic-transport integral membrane protein arsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-53  180.3  42.1    4.8e-53  180.3  42.1    2.0  2  CitMHS         Citrate transporter
    1.7e-19   70.5  33.5    2.1e-19   70.2  33.5    1.0  1  ArsB           Arsenical pump membrane protein
    4.7e-15   55.6  39.7    4.4e-08   32.6  17.6    2.0  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    3.7e-06   26.1  23.9    1.5e-05   24.1  10.6    2.6  2  NhaB           Bacterial Na+/H+ antiporter B (NhaB)
  ------ inclusion threshold ------
        8.8    5.7  11.7         95    2.3  10.6    3.3  2  GPI2           Phosphatidylinositol N-acetylglucosaminyltrans


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3  42.1   1.3e-56   4.8e-53       1     300 []      13     367 ..      13     367 .. 0.76
   2 !    3.6   0.9    0.0086        31     119     165 ..     363     419 ..     356     428 .. 0.62

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 1.3e-56
                                    xxxxxxxxxxxxxxxxxxxxxx....xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS   1 lvllileklrldvvallvlvll....vltiee....alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkr 72 
                                    +vl++ +++++++val +++++    v+t  +      +gi++++i+ll+g+mii+++l +tG+f++ a + +++a+g++
  gi|121638559|ref|YP_978783.1|  13 YVLIASDRVNKTMVALTGAAAVvvlpVITSHDifysHDTGIDWDVIFLLVGMMIIVGVLRQTGVFEYTAIWAAKRARGSP 92 
                                    89**************99999998775555556666668***************************************** PP

                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  73 d.llvllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnl 151
                                      +++llvl++al sa+++n+++vl+++p++l ++ rl+ + +++l++ ++a+nigga+t++G+p            pn+
  gi|121638559|ref|YP_978783.1|  93 LrIMILLVLVSALASALLDNVTTVLLIAPVTLLVCDRLNINTTSFLMAEVFASNIGGAATLVGDP------------PNI 160
                                    *************************************9999999*********************............888 PP

                                    xx....................xxxxxxxx.............................................xxxxx RF
                         CitMHS 152 ll....................lalllvgl.............................................lplvl 166
                                    ++                    ++l    +                                             + ++ 
  gi|121638559|ref|YP_978783.1| 161 IVasragltfndfmlhltplvvIVL----IaliavlprlfgsitveadriadvmaldegeairdrgllvkcgavlVLVFA 236
                                    8888877776666555543321111....111223333333333333333333333333333333333333333244444 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 167 lfmfgvalalpvnapkvkkqkaiieaiarsllpvatillla........ykkveWsvlllfaGvfllvgaleqtGileal 238
                                    +f+++ +l++ +                 +ll  a++l+++        + +veW++ll+faG+f++vgal +tG+++ l
  gi|121638559|ref|YP_978783.1| 237 AFVAHPVLHIQPSL--------------VALL-GAGMLIVVsgltrseyLSSVEWDTLLFFAGLFIMVGALVKTGVVNDL 301
                                    44444444444443..............3333.355554448999*********************************** PP

                                    xxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                         CitMHS 239 adllga..ggplval.alvlgliallsafisnvavaalmapialgmapalgl.lspsplalalavg 300
                                    a ++++  gg++va  +l+lg++a +s +i+n++++a+m+p+++++ +++g   s +  ++ala+g
  gi|121638559|ref|YP_978783.1| 302 ARAATQltGGNIVATaFLILGVSAPISGIIDNIPYVATMTPLVAELVAVMGGqPSTDTPWWALALG 367
                                    *999778755555552666777777***********************988888888889999987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0086
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxx RF
                         CitMHS 119 plalaaniggaltpiGtpttraaarpglslpnllllal......................llvgllplv 165
                                    +lal+a  gg lt iG +             n+++l++                      + ++l++++
  gi|121638559|ref|YP_978783.1| 363 ALALGADFGGNLTAIGAS------------ANVVMLGIarragapisfweftrkgavvtaVSIALAAIY 419
                                    599***************............888885555555555555555555533322222222222 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2  33.5   5.7e-23   2.1e-19       2     423 .]       5     422 ..       4     422 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 5.7e-23
                           ArsB   2 avfiflltlvlviwqpknlsigwsacggavlaliagvvnfhdvltv..tgivwnatlafvaiilislildnigffewaal 79 
                                    av if+ + vl+  +  n +    a  ga   ++  v+  hd++    tgi w+  + +v +++i  +l + g+fe++a+
  gi|121638559|ref|YP_978783.1|   5 AVTIFVAAYVLIASDRVNKT--MVALTGAAAVVVLPVITSHDIFYShdTGIDWDVIFLLVGMMIIVGVLRQTGVFEYTAI 82 
                                    89999999999988777765..56888888889999******9864349******************************* PP

                           ArsB  80 hmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsnlvn 159
                                      ak a+g  +r+++ + l+ a+ +al+ n  + l+++p+ l +   l +n      f++a  f ++      +v +  n
  gi|121638559|ref|YP_978783.1|  83 WAAKRARGSPLRIMILLVLVSALASALLDNVTTVLLIAPVTLLVCDRLNINT---TSFLMAEVFASNIGGAATLVGDPPN 159
                                    ************************************************9997...5799********************* PP

                           ArsB 160 ivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkrydltevk..kpveaikdqnmfrlswyilgllligyf 237
                                    i+ a    +tf d+  ++    ++ l+a i vl  +f     +   +++v      eai+d+ ++     +l l++  ++
  gi|121638559|ref|YP_978783.1| 160 IIVASRAGLTFNDFMLHLTPLVVIVLIALIAVLPRLFGSITVEADRIADVMalDEGEAIRDRGLLVKCGAVLVLVFAAFV 239
                                    **************9998877788888888888877765444444455554115689*********************** PP

                           ArsB 238 aseffsipvsvvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdviqaaadqglfa 317
                                    a  ++ i  s+va   a ++++ +         + +    w  ++f  g++++v  + ++g+ + l+      +   ++a
  gi|121638559|ref|YP_978783.1| 240 AHPVLHIQPSLVALLGAGMLIVVSGL----TRSEYLSSVEWDTLLFFAGLFIMVGALVKTGVVNDLARAATQLTGGNIVA 315
                                    ************98777766665443....3445667789**99999*******99999887776666655555566777 PP

                           ArsB 318 gtigmgfiaailssimnnlptvmidalaiag.tdthg.m.mrealiyanvigsdlgpkitpigslatllwlhvlshkgmk 394
                                     +  +  ++a +s i++n+p v   +  +a      g     ++  +a  +g+d+g ++t ig+ a ++ l +  + g  
  gi|121638559|ref|YP_978783.1| 316 TAFLILGVSAPISGIIDNIPYVATMTPLVAElVAVMGgQpSTDTPWWALALGADFGGNLTAIGASANVVMLGIARRAGAP 395
                                    776666688899********986544433331222231214678899********************************* PP

                           ArsB 395 iswgtyfktgiiltiptllitlvglyiwl 423
                                    is+  + + g ++t   + i+l  +y+wl
  gi|121638559|ref|YP_978783.1| 396 ISFWEFTRKGAVVTA--VSIALAAIYLWL 422
                                    **********99885..67899999**97 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6  17.6   1.2e-11   4.4e-08     278     465 ..       8     196 ..       1     202 [. 0.80
   2 !   29.2  14.2   1.3e-10   4.8e-07     275     465 ..     230     421 ..     218     428 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-11
                  Na_sulph_symp 278 lllllWifgeslnidattvaivvlvillllrvldWkDivkqk...taWntllllgglialakllersgliewlgnkltts 354
                                    + +  ++   s  +++t+va+ + + +++l+v++ +Di  ++     W++++ll g++ +  +l ++g++e+ +   ++ 
  gi|121638559|ref|YP_978783.1|   8 IFVAAYVLIASDRVNKTMVALTGAAAVVVLPVITSHDIFYSHdtgIDWDVIFLLVGMMIIVGVLRQTGVFEYTAIWAAKR 87 
                                    44445555556669************************876522246*************************99877776 PP

                  Na_sulph_symp 355 lsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfg 434
                                        sp + i+i+l+l+ ++      ++ t+  ++p+ l v   +  +++  + ++ ++a++++g  + ++ +pn iv +
  gi|121638559|ref|YP_978783.1|  88 AR-GSP-LRIMILLVLVSALASALLDNVTTVLLIAPVTLLVCDRL-NINTTSFLMAEVFASNIGGAATLVGDPPNIIVAS 164
                                    66.455.5566666666777777889999****************.9********************************* PP

                  Na_sulph_symp 435 agylkvkdywrlGfils.iigllillllgalw 465
                                       l  +d+     +l  i+ ++++++l  l+
  gi|121638559|ref|YP_978783.1| 165 RAGLTFNDFMLHLTPLVvIVLIALIAVLPRLF 196
                                    *******9987666555055555666665555 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.3e-10
                  Na_sulph_symp 275 lfvlllllWifgeslnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnkltts 354
                                    ++vl+    + +  l+i+ + va+++  +l++++ l+  +   +   W+tll+++gl  +   l ++g+++ l+ + t++
  gi|121638559|ref|YP_978783.1| 230 VLVLVFAAFVAHPVLHIQPSLVALLGAGMLIVVSGLTRSE-YLSSVEWDTLLFFAGLFIMVGALVKTGVVNDLARAATQL 308
                                    4455555556666788******************999995.556789*****************************9999 PP

                  Na_sulph_symp 355 lsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllv.alllalatslagfllpyatgpnpivf 433
                                      g   a a++i+  ++ +    +  +  ++a++ p+++ ++ ++ g p   +   +lal   ++g l+ +++++n++++
  gi|121638559|ref|YP_978783.1| 309 TGGNIVATAFLIL-GVS-APISGIIDNIPYVATMTPLVAELVAVMGGQPSTDTpWWALALGADFGGNLTAIGASANVVML 386
                                    9855555554443.333.344567789999999999999999999887765442678889999***************** PP

                  Na_sulph_symp 434 gagy.....lkvkdywrlGfilsiigllillllgalw 465
                                    g+       ++  ++ r G++++ +++++ ++   lw
  gi|121638559|ref|YP_978783.1| 387 GIARragapISFWEFTRKGAVVTAVSIALAAIY--LW 421
                                    *97622223566788899***999887766554..44 PP

>> NhaB  Bacterial Na+/H+ antiporter B (NhaB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   5.4   0.00046       1.7      86     159 ..      47     123 ..       2     131 .. 0.77
   2 !   24.1  10.6   4.1e-09   1.5e-05     204     449 ..     136     377 ..     126     421 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00046
                           NhaB  86 vkeeivanlevllllvfmvagiyfmkqlllfiftklllkirsk...illslafclaaaflsafldaltvvavvisva 159
                                      ++   + +v++llv m+  +  ++q  +f +t +    r++   + + ++++l +a+ sa+ld +t v ++  v+
  gi|121638559|ref|YP_978783.1|  47 YSHDTGIDWDVIFLLVGMMIIVGVLRQTGVFEYTAIWAAKRARgspLRIMILLVLVSALASALLDNVTTVLLIAPVT 123
                                    4577778899**********9***************99888553337899999***************999987775 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 4.1e-09
                           NhaB 204 sllmhagvgtalggvvtlvgepqnliiaeqakwkfgefllrmspvtvpvlicglltcllveklklfgygeklpdevrkil 283
                                    s+lm     + +gg +tlvg+p n+i+a++a+ +f +f+l ++p+ v vli+ + +       +lfg      d++ +++
  gi|121638559|ref|YP_978783.1| 136 SFLMAEVFASNIGGAATLVGDPPNIIVASRAGLTFNDFMLHLTPLVVIVLIALI-A----VLPRLFGSITVEADRIADVM 210
                                    67888888999************************************9999743.2....23588998888888888887 PP

                           NhaB 284 vdfdreerkkrtkqdkikl.ivqaliavwlivalalhl..aavgliglsviilatsltgvtdehalgkafeealpftall 360
                                    + +d+ e  +  +   +k   v  l+   +++   lh+  + v l+g  ++i+ +   g+t    l     ++l f a l
  gi|121638559|ref|YP_978783.1| 211 A-LDEGEAIR-DRGLLVKCgAVLVLVFAAFVAHPVLHIqpSLVALLGAGMLIVVS---GLTRSEYLSSVEWDTLLFFAGL 285
                                    5.55544332.23333332123333434445555566522568888888888765...4454445555444444444332 PP

                           NhaB 361 avffsvvaviidqklfspviqfvlaaeektqlalfyiangl...lssvsdnv.fvgtv..yinevkaalleglitreqfe 434
                                       f +v  ++   + + + +++ +  +   +a  +++ g+   +s + dn+ +v+t+   + e  a +     t   + 
  gi|121638559|ref|YP_978783.1| 286 ---FIMVGALVKTGVVNDLARAATQLTGGNIVATAFLILGVsapISGIIDNIpYVATMtpLVAELVAVMGGQPSTDTPWW 362
                                    ...33344444444444555555444444444444443333112455556665677662235555554444445555666 PP

                           NhaB 435 llavaintgtnlpsv 449
                                     la+  + g nl ++
  gi|121638559|ref|YP_978783.1| 363 ALALGADFGGNLTAI 377
                                    677777777777665 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  10.6     0.026        95      49      96 ..       3      86 ..       1     331 [. 0.74
   2 ?   -0.8   0.2      0.24   8.5e+02     218     260 ..     307     353 ..     277     366 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.026
                           GPI2 49 vcsviifvlvFvgiyqervspvsvvllssiltvlgwllwelwaskee................................... 95
                                   v  v+ifv+++v i+++rv++++v+l++++++v++ ++ ++    ++                                   
  gi|121638559|ref|YP_978783.1|  3 VVAVTIFVAAYVLIASDRVNKTMVALTGAAAVVVLPVITSHDIFYSHdtgidwdvifllvgmmiivgvlrqtgvfeytaiwa 84
                                   789*************************999999988876655444455666666666666666666666666666555444 PP

                           GPI2 96 .s 96
                                    +
  gi|121638559|ref|YP_978783.1| 85 aK 86
                                   40 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                           GPI2 218 rswrlhvvltvllvllagagvgiilk....lllavvlllllalimgv 260
                                    + +  ++v t++l+l+++a +  i+     ++ +  l++ l+ +mg+
  gi|121638559|ref|YP_978783.1| 307 QLTGGNIVATAFLILGVSAPISGIIDnipyVATMTPLVAELVAVMGG 353
                                    23334788888888888887777777566544444444444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2884.78
//
Query:       gi|121638560|ref|YP_978784.1|  [L=428]
Description: arsenic-transport integral membrane protein arsB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-55  187.4  30.4    3.4e-55  187.4  30.4    1.6  2  CitMHS         Citrate transporter
      2e-16   60.4  26.8    2.5e-16   60.0  26.8    1.0  1  ArsB           Arsenical pump membrane protein
    7.3e-09   35.0   6.5    7.3e-09   35.0   6.5    2.1  2  NhaB           Bacterial Na+/H+ antiporter B (NhaB)
  ------ inclusion threshold ------
       0.12   12.2   0.1        0.2   11.4   0.1    1.3  1  Kinase-PPPase  Kinase/pyrophosphorylase


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4  30.4   7.5e-59   3.4e-55       1     299 [.      13     366 ..      13     367 .. 0.89
   2 ?    2.1   0.8     0.021        93     119     166 ..     363     422 ..     359     426 .. 0.61

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 7.5e-59
                                    xxxxxxxxxxxxxxxxxxxxxx....xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS   1 lvllileklrldvvallvlvll....vltiee....alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkr 72 
                                    ++l++ ++++++ val +++++    +++ ++      +gi++++i+lllg+mii+++l +tG+f+++a + +++a   +
  gi|121638560|ref|YP_978784.1|  13 YALIASDRVSKTRVALTCAAIMvgagIVGSDDvfysHEAGIDWDVIFLLLGMMIIVSVLRHTGVFEYVAIWAVKRANAAP 92 
                                    799*************99999999997777777888889***************************************** PP

                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  73 d.llvllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnl 151
                                      +++llvl+tal sa+++n+++vl+++p++l ++ rl+ +++ +l++ ++a+n+gga+t++G+p            pn+
  gi|121638560|ref|YP_978784.1|  93 LrIMILLVLVTALGSALLDNVTTVLLIAPVTLLVCDRLGVNSTPFLVAEVFASNVGGAATLVGDP------------PNI 160
                                    *************************************9999999*********************............999 PP

                                    xx...................xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         CitMHS 152 ll...................lalllvgl....lplvllfmfgvalalpvnapkvkkqkaiieaiarsllpvatillla. 207
                                    ++                   l   +v++    l  +ll   g + a p  + +v + +++ + + r+ll +++++l++ 
  gi|121638560|ref|YP_978784.1| 161 IIasragltfndflihmapavL---VVMIaligLLPWLL---GSVTAEPDRVADVLSLNEREAIHDRGLLIKCGVVLVLv 234
                                    9999988888888888885532...33332233333333...46888888888999**************9999997779 PP

                                    ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xx RF
                         CitMHS 208 ....................................ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gp 247
                                                                        + +veW++ll+faG+f++vgal +tG++e+la ++++   g  +
  gi|121638560|ref|YP_978784.1| 235 faafiahpvlhiqpslvallgagvlvrfsglersdyLSSVEWDTLLFFAGLFVMVGALVKTGVVEQLARAATEltgGnEL 314
                                    99******************************************************************999668854455 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                         CitMHS 248 lvalalvlgliallsafisnvavaalmapialgmapalgl.lspsplalalav 299
                                     +++ l+lg++a +s +i+n++++a+m+pi+ ++ +a+   ++p+ +++ala+
  gi|121638560|ref|YP_978784.1| 315 -LTVGLILGISAPVSGIIDNIPYVATMTPIVTELVAAMPGhVHPDTFWWALAL 366
                                    .556888888888**********************998889**********96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxx RF
                         CitMHS 119 plalaaniggaltpiGtpttraaarpglslpnllllal........................llvgllplvl 166
                                    +lal+a  gg lt +G +             n+++l++                        l+  +++l+l
  gi|121638560|ref|YP_978784.1| 363 ALALSADFGGNLTAVGAS------------ANVVMLGIarrsgtpisfwkftrkgavvtavsLVLSAVYLWL 422
                                    6999**************............888885554555555555555555543322222222355554 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0  26.8   5.6e-20   2.5e-16      19     423 .]      20     422 ..       4     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 5.6e-20
                           ArsB  19 nlsigwsacggavlaliagvvnfhdvltv..tgivwnatlafvaiilislildnigffewaalhmakaakgygvrmfvyv 96 
                                     +s    a   a + + ag+v   dv+    +gi w+  + ++ +++i  +l   g+fe+ a+   k a+   +r+++ +
  gi|121638560|ref|YP_978784.1|  20 RVSKTRVALTCAAIMVGAGIVGSDDVFYSheAGIDWDVIFLLLGMMIIVSVLRHTGVFEYVAIWAVKRANAAPLRIMILL 99 
                                    45666677788899999*********964338************************************************ PP

                           ArsB  97 sllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsnlvnivsadyfhitfidyasr 176
                                     l+ a+ +al+ n  + l+++p+ l +   l +n     pf++a  f ++      +v +  ni+ a    +tf d+  +
  gi|121638560|ref|YP_978784.1| 100 VLVTALGSALLDNVTTVLLIAPVTLLVCDRLGVNS---TPFLVAEVFASNVGGAATLVGDPPNIIIASRAGLTFNDFLIH 176
                                    *********************************97...6***************************************** PP

                           ArsB 177 mvvpylfsllasiivlylffr..ksipkrydltevkkpveaikdqnmfrlswyilgllligyfaseffsipvsvvagsia 254
                                    m    l+ ++a i +l  ++    + p r       +  eai+d+ ++     +l l++  ++a  ++ i  s+va   a
  gi|121638560|ref|YP_978784.1| 177 MAPAVLVVMIALIGLLPWLLGsvTAEPDRVADVLSLNEREAIHDRGLLIKCGVVLVLVFAAFIAHPVLHIQPSLVALLGA 256
                                    *988887777776666444430134466655445567789********99999999999999999999999999886655 PP

                           ArsB 255 iifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdviqa.aadqglfagtigmgfiaailssim 333
                                     +++    +   +     +    w  ++f  g++v+v  + ++g+ + l+      +  + l++  + +g i+a +s i+
  gi|121638560|ref|YP_978784.1| 257 GVLV----RFSGLERSDYLSSVEWDTLLFFAGLFVMVGALVKTGVVEQLARAATElTGGNELLTVGLILG-ISAPVSGII 331
                                    5543....344566677788899***************99999998888765433033344444334344.67889**** PP

                           ArsB 334 nnlptvmida..la..iagtdthgmmrealiyanvigsdlgpkitpigslatllwlhvlshkgmkiswgtyfktgiilti 409
                                    +n+p v   +  ++  +a    h +  +++ +a  + +d+g ++t +g+ a ++ l +  + g  is+  + + g ++t 
  gi|121638560|ref|YP_978784.1| 332 DNIPYVATMTpiVTelVAAMPGH-VHPDTFWWALALSADFGGNLTAVGASANVVMLGIARRSGTPISFWKFTRKGAVVTA 410
                                    ****8854330032113333333.45689999**********************************************99 PP

                           ArsB 410 ptllitlvglyiwl 423
                                     +l+++   +y+wl
  gi|121638560|ref|YP_978784.1| 411 VSLVLSA--VYLWL 422
                                    8887665..56775 PP

>> NhaB  Bacterial Na+/H+ antiporter B (NhaB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   8.6     0.049   2.2e+02      38     159 ..       5     123 ..       1     128 [. 0.75
   2 !   35.0   6.5   1.6e-12   7.3e-09     212     453 ..     144     381 ..     134     425 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.049
                           NhaB  38 lispfvagwllva.efiftlamalkcyplqpggllaieaviigmtsaeqvkeeivanlevllllvfmvagiyfmkqlllf 116
                                     i+ fvag+ l+a + +    +al c  ++ g      a i+g        +e   + +v++ll+ m+  +  ++   +f
  gi|121638560|ref|YP_978784.1|   5 AITVFVAGYALIAsDRVSKTRVALTCAAIMVG------AGIVGSD-DVFYSHEAGIDWDVIFLLLGMMIIVSVLRHTGVF 77 
                                    47778888887762456667788888776655......3334433.2344688889999********99999****9999 PP

                           NhaB 117 iftklllkirsk...illslafclaaaflsafldaltvvavvisva 159
                                     +  +    r++   + + ++++l +a+ sa+ld +t v ++  v+
  gi|121638560|ref|YP_978784.1|  78 EYVAIWAVKRANaapLRIMILLVLVTALGSALLDNVTTVLLIAPVT 123
                                    999998877776222457889999*************999887775 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.6e-12
                           NhaB 212 gtalggvvtlvgepqnliiaeqakwkfgefllrmspvtvpvlic..glltcllveklklfgygeklpdevrkilvdfdre 289
                                     + +gg +tlvg+p n+iia++a+ +f +fl+ m+p  + v+i+  gll         l+g     pd+v ++l+  +re
  gi|121638560|ref|YP_978784.1| 144 ASNVGGAATLVGDPPNIIIASRAGLTFNDFLIHMAPAVLVVMIAliGLLP-------WLLGSVTAEPDRVADVLSLNERE 216
                                    4679*********************************9999986113332.......357899999*********99999 PP

                           NhaB 290 erkkrtkqdkiklivqaliavwlivalalhl..aavgliglsviilatsltgvtdehalgkafeealpftall.avffsv 366
                                      + r    k  +++  + a  +i+   lh+  + v l+g  v++    ++g+     l     ++l f a l ++  ++
  gi|121638560|ref|YP_978784.1| 217 AIHDRGLLIKCGVVLVLVFAA-FIAHPVLHIqpSLVALLGAGVLV---RFSGLERSDYLSSVEWDTLLFFAGLfVMVGAL 292
                                    888888776666555444444.45666667622578999998876...69999998888887777776665540444455 PP

                           NhaB 367 vaviidqklfspviqfvlaaeektqlalfyiangllssvsdnv.fvgtv..yinevkaalleglitreqf.ellavaint 442
                                    v   + ++l +   ++   +e  t + l+  +   +s + dn+ +v+t+   + e  aa+  g + ++ f   la++ + 
  gi|121638560|ref|YP_978784.1| 293 VKTGVVEQLARAATELTGGNELLT-VGLILGISAPVSGIIDNIpYVATMtpIVTELVAAM-PGHVHPDTFwWALALSADF 370
                                    655555666665555544433333.33333344557788888778998833467777776.5777777662579999999 PP

                           NhaB 443 gtnlpsvatpn 453
                                    g nl +v +  
  gi|121638560|ref|YP_978784.1| 371 GGNLTAVGASA 381
                                    ****9996543 PP

>> Kinase-PPPase  Kinase/pyrophosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.4e-05       0.2     136     170 ..     379     414 ..     364     419 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                  Kinase-PPPase 136 keADivLvGvSRtsKTPlSlyLaq.kglkvaNvPLv 170
                                    ++A++v++G+ R s TP+S++  + kg  v  v Lv
  gi|121638560|ref|YP_978784.1| 379 ASANVVMLGIARRSGTPISFWKFTrKGAVVTAVSLV 414
                                    68*****************98544488877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3146.60
//
Query:       gi|121638561|ref|YP_978785.1|  [L=252]
Description: antibiotic ABC transporter integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1645.83
//
Query:       gi|121638562|ref|YP_978786.1|  [L=237]
Description: antibiotic ABC transporter integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00028   20.1  15.5    0.00041   19.6  15.5    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0026   17.7   9.2     0.0026   17.7   9.2    1.6  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
        1.7    7.9  17.6       0.35   10.1  13.5    1.8  2  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  15.5   6.9e-08   0.00041     172     334 ..      56     213 ..      49     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.9e-08
                ABC2_membrane_3 172 ifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfgnlglllllfllfgla 251
                                    ++i+++f+   + +Ek+ r++  +++++++ ++y+ +k++ +++++l++++++  ++ g  + + +l+ l+  ++l+ l+
  gi|121638562|ref|YP_978786.1|  56 AIIGFFFVGGTVFFEKQERTIGAIVSTPLRFWEYLAAKLTVLLAISLFVAVVVATIVHG--LGY-HLLPLVAGIVLGTLL 132
                                    68899999999***************************************999999777..433.777777777777777 PP

                ABC2_membrane_3 252 yialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli.tgd.plweillsl 329
                                    ++ +g+  s  f + ++ +++++i + ++++  ++ ++      + + ++++iP++ p l+l     +    +w++++++
  gi|121638562|ref|YP_978786.1| 133 MLLVGFSSSLPFASVTDWFLAAVIPLAIMLAPPVVHYS----GLWPNPVLYLIPTQGPLLLLGAAFdQVSlAPWQVGYAV 208
                                    77777776666666666444433333334444444442....12445688888888888888777752224677777777 PP

                ABC2_membrane_3 330 iilal 334
                                    ++ ++
  gi|121638562|ref|YP_978786.1| 209 VYPIV 213
                                    76665 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   9.2   4.3e-07    0.0026      63     171 ..      57     160 ..      45     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-07
                ABC2_membrane_4  63 ilgi.iasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkc 141
                                    i+g  + +  +f E+q+ t+  ++  P    ++l+aKl+vll +s+++ +v  ++t++++l  +  ++ ++ vl +l ++
  gi|121638562|ref|YP_978786.1|  57 IIGFfFVGGTVFFEKQERTIGAIVSTPLRFWEYLAAKLTVLLAISLFVAVV--VATIVHGLGYHLLPLVAGIVLGTLLML 134
                                    5555345666777****************************9999888876..778888888888877666666555544 PP

                ABC2_membrane_4 142 lelgllvffavlpiialvllkksyvlplil 171
                                    l    + f  +lp   ++ ++   v+pl++
  gi|121638562|ref|YP_978786.1| 135 L----VGFSSSLPFASVTDWFLAAVIPLAI 160
                                    4....4445555655555566666666665 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.35   2.1e+03     264     276 ..      24      36 ..      17      43 .. 0.79
   2 ?   10.1  13.5   5.9e-05      0.35      87     173 ..      57     159 ..      50     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.35
                ABC2_membrane_2 264 nllilllllavll 276
                                     +++ l++lavll
  gi|121638562|ref|YP_978786.1|  24 AVFSGLIWLAVLL 36 
                                    5678888888886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.9e-05
                ABC2_membrane_2  87 viaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvll...............alaiil 150
                                    +i+  f    ++ Ek ++T+ +  s+P   +e+l++K+   lai+l+  +v ++++  l                l++ +
  gi|121638562|ref|YP_978786.1|  57 IIGFFFVGGTVFFEKQERTIGAIVSTPLRFWEYLAAKLTVLLAISLFvAVVVATIVHGLgyhllplvagivlgtLLMLLV 136
                                    5555566667888*******************************998533333333333666666666666665555555 PP

                ABC2_membrane_2 151 algivlaledllllvvasvllll 173
                                    +++ +l++++++  ++a+v+ l+
  gi|121638562|ref|YP_978786.1| 137 GFSSSLPFASVTDWFLAAVIPLA 159
                                    56666666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1619.78
//
Query:       gi|121638563|ref|YP_978787.1|  [L=301]
Description: antibiotic-transport ATP-binding protein ABC transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-24   84.8   0.0    1.2e-23   84.2   0.0    1.3  1  ABC_tran  ABC transporter
    9.3e-10   38.8   0.1    2.1e-07   31.0   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0088   15.1   0.0      0.015   14.3   0.0    1.3  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.13   11.7   0.0    1.4  1  RecA      recA bacterial DNA recombination protein
       0.16   12.7   0.0       0.58   10.9   0.0    1.9  1  DUF4162   Domain of unknown function (DUF4162)
       0.17   11.6   0.2       0.35   10.6   0.2    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   3.9e-27   1.2e-23       2     137 .]      36     175 ..      35     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 3.9e-27
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + +++++ +ge+ +++G++GaGKSt  kll+gll++  G+ ++ +k+  e   + + ++igv ++ p++ ++lt +en  
  gi|121638563|ref|YP_978787.1|  36 RGMEFTVGRGEIFGLLGPSGAGKSTTQKLLIGLLRDHGGQATVWDKEPAE-WGPDYYERIGVSFELPNHYQKLTGYENlr 114
                                    5789*************************************999888888.89999************************ PP

                                    .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            +++++ ++l+ +gl ++++t v     ++S+G++ r+  ar+l+++p+ll+lDEpt+
  gi|121638563|ref|YP_978787.1| 115 ffaslyaGATADPMQLLAAVGLADDAHTLV----GKYSKGMQMRLTFARSLINDPELLFLDEPTS 175
                                    *****9988999******************....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1     0.003       9.1       2      24 ..      48      70 ..      47     106 .. 0.75
   2 !   31.0   0.0   7.2e-11   2.1e-07     237     299 ..     147     206 ..     107     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.003
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    +l Gp g+GKS+  ++l +l r
  gi|121638563|ref|YP_978787.1| 48 FGLLGPSGAGKSTTQKLLIGLLR 70
                                   689**********9999988874 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 7.2e-11
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                     S G++  l ++ +l+ ++    ll++DEp +gL+P   r++ +++ +l+++g  ++ltTH+ 
  gi|121638563|ref|YP_978787.1| 147 YSKGMQMRLTFARSLINDP---ELLFLDEPTSGLDPVNARKIKDIIVDLKARGRTIFLTTHDM 206
                                    5777776667888888877...9***********************888888*********96 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     5e-06     0.015      16      63 ..      32      79 ..      22      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                                   HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                           MeaB 16 kellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                   +  ++ +  + Gr +  Gl G  GaGkst+ + l+  lr++G + +v 
  gi|121638563|ref|YP_978787.1| 32 EPAVRGMEFTVGRGEIFGLLGPSGAGKSTTQKLLIGLLRDHGGQATVW 79
                                   45566666789*******************************988775 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.5e-05      0.13      50     126 ..      42     119 ..      35     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                                    EETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--.--HHHHHHTT--GGG-EEE--SSHHHHHHHHHHH CS
                           RecA  50 lpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeha.ldpkyakklGvdidellvsqpdtGeqaleiadal 126
                                    + +G i  + Gp  +Gk+t    +i   + +gg+a+  d e a   p+y +++Gv  +     q  tG + l    +l
  gi|121638563|ref|YP_978787.1|  42 VGRGEIFGLLGPSGAGKSTTQKLLIGLLRDHGGQATVWDKEPAeWGPDYYERIGVSFELPNHYQKLTGYENLRFFASL 119
                                    56899************************************98468*********98866666666666666655555 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.58      53      81 .]     269     296 ..     243     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                    ---------EEEEEEEE---HHHHHHHHH CS
                        DUF4162  53 llkaltsgveirsFeeeePsLndIFiekv 81 
                                      + l ++  ++++  +e+sL+d+F+e++
  gi|121638563|ref|YP_978787.1| 269 FHSVL-RNHHVETIHSREASLDDVFVEVT 296
                                    55555.78899***************986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00012      0.35      18      37 ..      41      60 ..      34      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                         AAA_29 18 eidlkgatlltGpsGsGKST 37
                                   ++ + +++ l GpsG+GKST
  gi|121638563|ref|YP_978787.1| 41 TVGRGEIFGLLGPSGAGKST 60
                                   5554448889*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1837.78
//
Query:       gi|121638564|ref|YP_978788.1|  [L=405]
Description: hypothetical protein BCG_2702c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-08   31.7   0.0    1.4e-07   30.8   0.0    1.4  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    5.7e-06   26.2   0.0    1.3e-05   25.1   0.0    1.5  1  TRAM             TRAM domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.018   14.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.029   13.7   0.0      0.048   13.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
        0.1   12.2   0.0       0.19   11.4   0.0    1.3  1  CmcI             Cephalosporin hydroxylase
       0.22   11.0   0.2        1.1    8.8   0.0    2.1  3  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.4   4.3e+03     207     234 ..     265     295 ..     244     307 .. 0.71
   2 !   30.8   0.0   4.8e-11   1.4e-07     288     357 .]     332     404 ..     325     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                tRNA_U5-meth_tr 207 elycGnGnfslalarnf...ekvlateiaks 234
                                    +ly G G f+  l + +    +vl+ + ++ 
  gi|121638564|ref|YP_978788.1| 265 DLYGGAGVFAAVLGEAVgesGRVLTVDTSRL 295
                                    6899999999998876622246776666655 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 4.8e-11
                tRNA_U5-meth_tr 288 fvdPPraGldketvklvk..kyerilyiscnPetlkenleels.ethrverlalfdqfpythhlesGvllekk 357
                                    ++dPPr+G  +e+v+l+     +r+++i c+  +++ ++   + + + ve++ +fd fp th++e+  ll++k
  gi|121638564|ref|YP_978788.1| 332 VLDPPRSGAGREVVDLLAgaGVPRLIHIGCEAASFARDIGLYRgHGYAVEKIKVFDAFPLTHYVECVALLTRK 404
                                    67**************9722579***************9755425668*********************9986 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.2e-09   1.3e-05      13      61 ..      15      60 ..      11      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.2e-09
                                   EEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                           TRAM 13 eglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                   +g  ++ g ++++++ g+vvfv+++lp  G++V +++t  +  y ++e+
  gi|121638564|ref|YP_978788.1| 15 TGAPANGGSCVAHHE-GRVVFVRYALP--GERVRARVTAQRGSYWHAEA 60
                                   5555699********.***********..*********99998888886 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     6e-06     0.018      65     117 ..     251     303 ..     225     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-06
                                    HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
                           PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                                    + ++ +  +g+ + ++ +G+G  +avl + vge+grv++++ ++    +a++ 
  gi|121638564|ref|YP_978788.1| 251 IADWAQPAPGMTAWDLYGGAGVFAAVLGEAVGESGRVLTVDTSRLASGAARAA 303
                                    567777889********************************987655555554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.048      35     106 ..     247     316 ..     238     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                Ubie_methyltran  35 WkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                    + + + +   + +g ++ D+ gG+g +a+ l ++vge+g+v  +D +   L  g +++      ++e ++++
  gi|121638564|ref|YP_978788.1| 247 YSDLIADWAQPAPGMTAWDLYGGAGVFAAVLGEAVGESGRVLTVDTSR--LASGAARAALVDLPQVEVVTGS 316
                                    5677888899999******************************99875..7788888877777777777766 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.2e-05      0.19      43      99 ..     267     322 ..     255     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                           CmcI  43 hGGsalfsasllallkskrkvlaididireknrqaieahplasrieliegssvdpei 99 
                                    +GG+ +f a l + ++++++vl++d   r    +a+ a    +++e+++gs   + +
  gi|121638564|ref|YP_978788.1| 267 YGGAGVFAAVLGEAVGESGRVLTVDT-SRLASGAARAALVDLPQVEVVTGSVRRVLA 322
                                    9*************************.555556666666778889998888766555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         2   5.9e+03      35      57 ..     156     182 ..     151     214 .. 0.61
   2 ?    8.8   0.0   0.00036       1.1      31     106 ..     259     336 ..     235     347 .. 0.76
   3 ?   -0.7   0.0       0.3   9.1e+02      32      44 ..     341     353 ..     336     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                    EEEET-T...TSHH.HHHHHHHTTC.E CS
                            MTS  35 vlDlGcG...aGvl.gaalakespeae 57 
                                    v Dl cG   +G+l g+++a+  pea+
  gi|121638564|ref|YP_978788.1| 156 VTDLDCGqlpVGMLdGLVAADWPPEAQ 182
                                    678888833335553344444445555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00036
                                    TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT..TSTTS-EEEEEE--- CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvle..eveekkfdlivsNPP 106
                                       ++ Dl  GaGv +a+l ++  e   v  vd +  A  +a++ l +   +vevv+ +v    +v+++  dl v  PP
  gi|121638564|ref|YP_978788.1| 259 PGMTAWDLYGGAGVFAAVLGEAVGESGrVLTVDTSRLASGAARAALVDLP-QVEVVTGSVRRvlAVQPAGADLAVLDPP 336
                                    566788**************9998876699********999999886643.4555555554311666789999999998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.3
                                    CSEEEEET-TTSH CS
                            MTS  32 sgkvlDlGcGaGv 44 
                                     ++v+Dl +GaGv
  gi|121638564|ref|YP_978788.1| 341 GREVVDLLAGAGV 353
                                    578*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2759.86
//
Query:       gi|121638565|ref|YP_978789.1|  [L=663]
Description: integral membrane alanine and valine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-21   76.6  38.4    2.4e-21   76.1  38.4    1.1  1  AA_permease_2   Amino acid permease
    0.00092   17.8  21.0      0.015   13.9   1.1    2.8  2  K_trans         K+ potassium transporter


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1  38.4   2.6e-25   2.4e-21      24     403 ..      59     458 ..      36     480 .. 0.70

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 2.6e-25
                  AA_permease_2  24 laasggpalilwvwiavligslavllvy.aEl.ssalprsgGiyvytkaafgkkvaflsawfnwfayvpvlasilsvaas 101
                                    ++a+  +a ++ + +a++++   v+  y   + +   p+ gG+y ++    g   + ++a +++++yv+++a+++s+aas
  gi|121638565|ref|YP_978789.1|  59 GLAAYSMAPLIGLAVAAVLL--VVVSSYrQNVhA--YPSGGGDYEVVTTNLGATGGLVVASALMVDYVLTVAVSISSAAS 134
                                    23444444455555555554..456666255544..6******************************************* PP

                  AA_permease_2 102 yllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkil..lpliiliilglitvdgggfssl.... 175
                                    ++ + ++p++++   + +l+a++ ++l++++n+rg++es+ +  i +++ i   +++++  ++ ++++++    ++    
  gi|121638565|ref|YP_978789.1| 135 NIGS-VSPFVYE---HKVLFAVGAIVLIMAMNLRGVRESGLAFAIPTYAFIAgiGTMLVWGLFRIFVLGNPVRAESaafe 210
                                    ****.5799877...56999********************9998866665541156666666666666555444446555 PP

                  AA_permease_2 176 .stetdtffpngwpg.vllgllivlwsfdGfesaanvsee..vkk.kdvpkaifigllivlvlyllvniaflgvvpddei 250
                                     + e++++++    + v+++++  + +++G+e+++n +     +k +++  ++ + ++i++ +++++   +l+v +  ++
  gi|121638565|ref|YP_978789.1| 211 mHAEHGQIVGFALVFlVARSFSSGCAALTGVEAISNGVPAfqKPKsRNAATTLLMLGIIAVSMFMGM--IVLAVETGVQV 288
                                    4444444444432234688*********************633345555555544444444444444..44444444444 PP

                  AA_permease_2 251 ......anlsnlgsv........aalffeavggk..vvaiivvilialsllgaintavigssrvlealardgvlPrffak 314
                                          + ++    +        +a +++av+g+   ++ ++++++al+l++a+nta+ g + +   la++ +lPr ++ 
  gi|121638565|ref|YP_978789.1| 289 vddpdtQLTGA---PpgyqqktlVAQLAQAVFGGfyLGFLLIAAVTALILVLAANTAFNGFPVLGSVLAQHSYLPRQLHT 365
                                    33333243333...12446666677777777776689999999************************************* PP

                  AA_permease_2 315 vnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl...kr.....pgk.i 385
                                       + + +++i + a  + i   ++++  +a +++l  ++ +g++is+++  +g++ ++ +       +r       +  
  gi|121638565|ref|YP_978789.1| 366 RGDRLAFSNGILFLAAAA-IG-AVVAF--RAELTALIQLYIVGVFISFTMSQVGMVRHWTRLLSAetdPRarramL-RsR 440
                                    *****************9.54.56666..89****************************99664423333444541.132 PP

                  AA_permease_2 386 lvaiigalfllfllvalf 403
                                     v+++g++++  +l +  
  gi|121638565|ref|YP_978789.1| 441 AVNTVGFVSTGTVLLIVL 458
                                    455555444444433322 PP

>> K_trans  K+ potassium transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5  11.8     7e-05      0.62      94     213 ..     109     227 ..      73     276 .. 0.77
   2 !   13.9   1.1   1.6e-06     0.015     334     451 ..     378     505 ..     370     562 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 7e-05
                        K_trans  94 laliGaalllgDgvltPaisvlsAveGlevaspsleklvvpislvilvlLFliQkfGtekigklfgpimliWflllavlG 173
                                     +l+ a++l+ D vlt a+s+ sA + +  +sp + ++ v+ ++  +vl+ ++  +G ++ g +f+  +    +++a +G
  gi|121638565|ref|YP_978789.1| 109 GGLVVASALMVDYVLTVAVSISSAASNIGSVSPFVYEHKVLFAVGAIVLIMAMNLRGVRESGLAFAIPTY---AFIAGIG 185
                                    5788899****************************9888888888899999**************97775...5577788 PP

                        K_trans 174 ilnivkkpsvlkAlnPlyaie..fllrnklagflvLgavlLa 213
                                     + ++  + ++   nP+ a +  f ++ ++  ++ ++ v+L+
  gi|121638565|ref|YP_978789.1| 186 TMLVWGLFRIFVLGNPVRAESaaFEMHAEHGQIVGFALVFLV 227
                                    888888888888888887754114444555556666667664 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.6e-06
                        K_trans 334 llliavilvvlvFk.sssnlaaAYGlavtltmlittlllllvlvlvw.........klklilvllvlllfllidllflsa 403
                                    +l++a+i  v++F+ + ++l + Y ++v ++++++ + ++   ++           +  l   ++ ++ f+   +++l+ 
  gi|121638565|ref|YP_978789.1| 378 FLAAAAIGAVVAFRaELTALIQLYIVGVFISFTMSQVGMVRHWTRLLsaetdprarRAMLRSRAVNTVGFVSTGTVLLIV 457
                                    577788999999983568999999777777777766544333222221111111002333344566788999999***** PP

                        K_trans 404 nlkKipeGgwvplllavvlllimltWkygrkkllekeaeeevpleell 451
                                     ++K+  G+w++++ +  ++++m + ++  + + ++ ae++ + e +l
  gi|121638565|ref|YP_978789.1| 458 LVTKFLAGAWIAIVAMGGFFMMMKLIHRHYDAVNRELAEQAEEAEITL 505
                                    **************9999999998877776666666555544443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 4151.27
//
Query:       gi|121638566|ref|YP_978790.1|  [L=227]
Description: TRK system potassium uptake protein ceoB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-25   89.3   0.3    3.5e-25   88.5   0.1    1.5  1  TrkA_N           TrkA-N domain
    6.5e-07   29.1   0.0    1.2e-06   28.2   0.0    1.4  1  TrkA_C           TrkA-C domain
    0.00019   21.1   0.0    0.00032   20.3   0.0    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00061   20.3   0.1     0.0013   19.3   0.1    1.6  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0027   17.6   0.1     0.0051   16.7   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0031   17.8   0.1     0.0056   16.9   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0067   17.0   0.2      0.021   15.4   0.1    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0088   15.4   0.3      0.012   14.9   0.3    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.028   13.8   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.016   14.6   0.2      0.024   14.0   0.2    1.3  1  ThiF             ThiF family
      0.021   14.7   0.5       0.06   13.2   0.2    1.9  2  Rossmann-like    Rossmann-like domain
       0.03   13.9   0.1      0.052   13.2   0.1    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.034   13.4   0.1      0.044   13.0   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.038   14.4   0.1      0.074   13.5   0.1    1.6  1  NAD_binding_7    Putative NAD(P)-binding
      0.043   14.3   0.2       0.12   12.9   0.0    1.9  1  XdhC_C           XdhC Rossmann domain
      0.066   12.5   0.2       0.12   11.6   0.1    1.4  2  FAD_binding_3    FAD binding domain
      0.075   13.1   0.0       0.11   12.6   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.16   11.5   2.8        0.4   10.2   2.7    1.9  1  DAO              FAD dependent oxidoreductase
       0.17   11.4   0.2       0.25   10.9   0.2    1.2  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.1   3.7e-28   3.5e-25       1     113 [.       3     116 ..       3     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 3.7e-28
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                    ++++G+GrvG s+a+ Ls+ g++ v +id+d +++++l+ ++  e v g++ d++vL +agi+ ada+ a+ + d +ni+
  gi|121638566|ref|YP_978790.1|   3 VVVMGCGRVGASVADGLSRiGHE-VAIIDRDSAAFNRLSPQFaGERVLGQGFDRDVLLRAGIQGADAFAAVSSGDNSNII 81 
                                    79*****************9995.******************788*********************************** PP

                                    HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEE CS
                         TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvv 113
                                     + la+e ++ ++++ar+ d+++ae++++lg+ ++
  gi|121638566|ref|YP_978790.1|  82 SARLARETFGVPRVVARIYDAKRAEVYERLGIPTI 116
                                    *******************************9876 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.3e-09   1.2e-06       2      67 ..     149     211 ..     147     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                    EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                         TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                    +ev+++++  +vG++  +  l++  g++++ + R g  ++p + tvL++GD++++++ +   ae+++
  gi|121638566|ref|YP_978790.1| 149 AEVVLHED--WVGHRATD--LEQAtGARIAFLIRFGTGVLPEPKTVLQAGDKVYIAAISGRAAEAAA 211
                                    56666655..8*******..88888*******************************99988888766 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.3e-07   0.00032       1      38 [.       1      38 [.       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-07
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdk 38
                                   m+++v+G G vG+  a  l++ighev ++D d+++ + 
  gi|121638566|ref|YP_978790.1|  1 MRVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNR 38
                                   89******************************987665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.4e-06    0.0013       1      37 [.       2      39 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TT CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rl 37
                                   +vvv+G G +g  +A  l+++g++V +++r +    rl
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFnRL 39
                                   79****************************98777554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.4e-06    0.0051       2      38 ..       3      39 ..       2      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                   v v+G+G +Ga++a  + + g+eV ++d++++a ++ 
  gi|121638566|ref|YP_978790.1|  3 VVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNRL 39
                                   89****************************9998876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     6e-06    0.0056       1      55 [.       3      54 ..       3      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE-- CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaiald 55
                                   v++ G+G+vG +va+ l+r ++   e++++dr+ +  ++l  + +g+r+  + +d
  gi|121638566|ref|YP_978790.1|  3 VVVMGCGRVGASVADGLSRIGH---EVAIIDRDSAAFNRLSPQFAGERVLGQGFD 54
                                   79*****************987...6**********9999988888887655555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.3e-05     0.021       1      47 [.       2      44 ..       2      90 .. 0.84
   2 ?   -1.9   0.0       5.4   5.1e+03      40      59 ..     191     210 ..     179     216 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47
                                   ++ + G+G++g+++a gl++ g   he+ ++ +r+    + l  ++ 
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIG---HEVAII-DRDSAAFNRLSPQFA 44
                                   57899*****************...****99.999998888887765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                                    HHHHHHHC-EEECECHHHHH CS
                  F420_oxidored  40 eelaeelgvkvtavdneeaa 59 
                                     ++ +++++ ++++ ++eaa
  gi|121638566|ref|YP_978790.1| 191 LQAGDKVYIAAISGRAAEAA 210
                                    34444444445554555554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   1.3e-05     0.012      30      71 ..       2      44 ..       1      83 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TT CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lg 71
                                   +v+v+G G +G + +   +++g +V ++D ++a+ ++l+  + 
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNRLSPqFA 44
                                   79*******************************9998876643 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.9e-05     0.028      38      69 ..       2      33 ..       1      46 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrsk 69
                                   +v ++G+Gr+G +va+ l+ +g +v ++dr  
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDS 33
                                   799*************************9975 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.5e-05     0.024      19      63 ..       1      44 [.       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                   SEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 19 skvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqfl 63
                                   ++v+++G+G +G  ++  L ++G  ++ ++D D   +  l+ qf 
  gi|121638566|ref|YP_978790.1|  1 MRVVVMGCGRVGASVADGLSRIG-HEVAIIDRDSAAFNRLSPQFA 44
                                   59*********************.58********99999999986 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   6.3e-05      0.06      12      48 ..       2      38 ..       1      50 [. 0.85
   2 ?   -1.9   0.0       2.9   2.7e+03      16      54 ..      72     111 ..      65     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                  Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgisaisaasre 48
                                    v +++ GrvG++++  l r+gh v  i   saa ++
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNR 38
                                   577899********************99988888655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                  Rossmann-like  16 isaGrvGtalgaaleraghvvvgisa.isaasreraerrl 54 
                                    +s+G    +++a l+r    v  + a i +a r    +rl
  gi|121638566|ref|YP_978790.1|  72 VSSGDNSNIISARLARETFGVPRVVArIYDAKRAEVYERL 111
                                    5666666666677777666665554424555555555554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.5e-05     0.052       1      35 [.       3      38 ..       3      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea 35
                                   ++++G+G +G  +a  L++ g++v +i+r+   +++
  gi|121638566|ref|YP_978790.1|  3 VVVMGCGRVGASVADGLSRIGHEVAIIDRDSaAFNR 38
                                   689**************************9955554 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.6e-05     0.044     144     184 ..       2      42 ..       1     102 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldke 184
                                    r+vv G G +G  +A  l+++g+ev ++++ +   + l ++
  gi|121638566|ref|YP_978790.1|   2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNRLSPQ 42 
                                    46666666666666666666666666666665555333333 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.8e-05     0.074       9      46 ..       2      44 ..       1     108 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.....e 46
                                   +v+v G G+v+a+ +  l + g +v +++ +++++        
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNRlspqfA 44
                                   79***************************99644333333331 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.12       1      88 [.       3      85 ..       3     102 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-HHHH CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpre.efatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGSrkka 81
                                   +v++G g v++++a+ ++++g +v ++d ++ +f+  +  p    +++     ++ +D+++l +a  + a  ++++ S  ++
  gi|121638566|ref|YP_978790.1|  3 VVVMGCGRVGASVADGLSRIGHEVAIIDRDSaAFN--RLSP----QFAGERVLGQGFDRDVLLRAGIQGADAFAAVSSGDNS 78
                                   689**************************993332..2222....2333333333344444444443445555555555555 PP

                                   HHHCTTS CS
                         XdhC_C 82 arrlerl 88
                                   + + +rl
  gi|121638566|ref|YP_978790.1| 79 NIISARL 85
                                   5555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.12       3      36 ..       2      35 ..       1      42 [. 0.92
   2 ?   -3.4   0.0       4.5   4.2e+03     168     202 ..     107     142 ..     100     157 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                    V++ G G +G++ a  Ls+ G +v ++++ s +
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHEVAIIDRDSAA 35
                                   699***************************9875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.5
                                    HHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC CS
                  FAD_binding_3 168 vrktlgiefegeetvyeagvldvlfda.dlsdivep 202
                                    v ++lgi+ +++   ++ ++l++l+++ +++++++p
  gi|121638566|ref|YP_978790.1| 107 VYERLGIPTIATVPWTTDRLLNALMQDtETAKWRDP 142
                                    555666665555555556666666555555555555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.11      14      62 ..       2      49 ..       1      89 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                   EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-E CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeie 62
                                   +v+++G G+++  va  L++ g + v+++ R+ +  ++l  ++ ge++ 
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGHE-VAIIDRDSAAFNRLSPQFAGERVL 49
                                   79*****************99998.*****************9988665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.7   0.00043       0.4       1      33 [.       2      35 ..       2     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   +vv+ G G +G+s+A  L+r g  V+++++++  +
  gi|121638566|ref|YP_978790.1|  2 RVVVMGCGRVGASVADGLSRIGheVAIIDRDSA-A 35
                                   59****************988999*******44.3 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00026      0.25       3      73 ..       4      74 ..       3      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                                   ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                           NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                   v+ + Gr G+sv++ l + gh+v ++ Rd+   +  s + aG  ++ +  d + +l++ ++g+d++ +v +
  gi|121638566|ref|YP_978790.1|  4 VVMGCGRVGASVADGLSRIGHEVAIIDRDSAAFNRLSPQFAGERVLGQGFDRDVLLRAGIQGADAFAAVSS 74
                                   77789*************************99999999999*99998889999999999999998766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1514.93
//
Query:       gi|121638567|ref|YP_978791.1|  [L=220]
Description: TRK system potassium uptake protein ceoC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-27   96.3   0.1    1.9e-27   95.8   0.1    1.2  1  TrkA_N           TrkA-N domain
    3.8e-11   42.7   0.8    2.3e-10   40.1   0.1    2.4  2  TrkA_C           TrkA-C domain
    7.5e-07   29.2   0.2    1.2e-06   28.5   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
      1e-05   25.9   0.1    1.9e-05   25.0   0.1    1.5  1  NAD_binding_7    Putative NAD(P)-binding
    1.8e-05   25.2   0.1    3.5e-05   24.3   0.1    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.4e-05   24.0   0.0    3.4e-05   23.5   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
    3.3e-05   24.0   0.0    6.8e-05   23.0   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00025   21.0   0.0    0.00035   20.5   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00039   20.7   0.1    0.00087   19.6   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0012   18.4   0.1     0.0016   17.9   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0036   16.9   0.2     0.0045   16.6   0.2    1.3  1  DAO              FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.016   15.2   0.0    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.012   15.8   0.0      0.017   15.3   0.0    1.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.012   16.1   0.1      0.022   15.3   0.1    1.6  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.014   15.5   0.1      0.023   14.8   0.1    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.02   14.1   0.0      0.025   13.8   0.0    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.036   14.6   0.1       0.06   13.9   0.1    1.4  1  XdhC_C           XdhC Rossmann domain
      0.039   13.2   0.1      0.056   12.7   0.1    1.2  1  FAD_binding_3    FAD binding domain
      0.041   14.2   0.2       0.17   12.2   0.1    2.0  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
      0.053   13.8   0.0        0.1   12.8   0.0    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.12   12.0   0.0       0.21   11.1   0.0    1.4  1  NmrA             NmrA-like family
       0.14   11.8   0.0       0.22   11.1   0.0    1.3  1  DAGK_cat         Diacylglycerol kinase catalytic domain
       0.16   11.5   0.0        0.3   10.6   0.0    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.1   2.4e-30   1.9e-27       1     115 [.       3     118 ..       3     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 2.4e-30
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                    ++++G+G vGrs+++eL e+g+d+++i++++++++ ++  ++++  gda + ++Le++++e++d+v+aatgdd++n++++
  gi|121638567|ref|YP_978791.1|   3 VAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAAAIPEAHWRLGDACELSLLESIHLEEFDVVVAATGDDKVNVVLS 82 
                                    689****************6669********************************************************* PP

                                    HHHHHHTSSSEEEEEESSGGGHHHHHH.HTTSEEEE CS
                         TrkA_N  81 llakelnpkkkiiaraqdpehaellkk.lgadvvis 115
                                    llak+ +  ++++ar++dp ++ l+++  g+dv++s
  gi|121638567|ref|YP_978791.1|  83 LLAKTEFAVPRVVARVNDPRNEWLFNDaWGVDVAVS 118
                                    *************************7769*****98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.9     7e+02      44      69 ..      59      84 ..      53      85 .. 0.77
   2 !   40.1   0.1     3e-13   2.3e-10       1      69 [.     149     216 ..     149     217 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.9
                                   T-B--TT-EEEEEEEHHHHHHHHHHH CS
                         TrkA_C 44 dtvLeeGDvllvvgspsdlaelrell 69
                                   +  Lee Dv++ ++ ++ ++ + +ll
  gi|121638567|ref|YP_978791.1| 59 SIHLEEFDVVVAATGDDKVNVVLSLL 84
                                   56799999999999988888777765 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 3e-13
                                    CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                         TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                    lve+t+p + p+ Gk+++ l+l++ ++ +v i Rg ++i+p  d  Le GD+ll+v+  ++ +el +ll
  gi|121638567|ref|YP_978791.1| 149 LVEITLPDNTPWGGKPVRKLQLPR-DAALVTILRGPRVIVPEADEPLEGGDELLFVAVTEAEEELSRLL 216
                                    79**********************.************************************99999986 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   1.6e-09   1.2e-06       3      73 ..       8      77 ..       7     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.6e-09
                                   TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHH.HHTT-SEEEES---TCC CS
                 NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlae.alkgadaVvsalggggk 73
                                    G vGr +++el+++ gh++t++ Rnp++l++  a ++++   gd+ + + l++ +l+  d+Vv+a+g ++ 
  gi|121638567|ref|YP_978791.1|  8 AGAVGRSVTRELVEN-GHDITLIERNPDHLDAA-AIPEAHWRLGDACELSLLESiHLEEFDVVVAATGDDKV 77
                                   79*************.5*************965.57***********99988873579*********98765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   2.4e-08   1.9e-05       9      83 ..       2      86 ..       1     104 [. 0.70

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.4e-08
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeelekd...........legadlviaatddrel 74
                                   kv v+G+G v+ +  r l+e+g ++t++  +              +++      d           le++d+v+aat d+++
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAaaipeA--HWRLG----DacelsllesihLEEFDVVVAATGDDKV 77
                                   799*************************999422222333221..22211....12222233333499************** PP

                  NAD_binding_7 75 neriaeaak 83
                                   n  +  +ak
  gi|121638567|ref|YP_978791.1| 78 NVVLSLLAK 86
                                   *88777776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   4.5e-08   3.5e-05       1      85 [.       2      88 ..       2      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.5e-08
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHH.HHHC...-EEECECHHHHHH..H-SEEEE-S-HHHHHH CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeela.eelg...vkvtavdneeaae..eadvvvlavkpedvee 76
                                   k+++ GaG +g+++++ l+++g   h+i+++ +rnp+ ++++a  e+     ++++ +  e +   e dvvv a    +v  
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENG---HDITLI-ERNPDHLDAAAiPEAHwrlGDACELSLLESIHleEFDVVVAATGDDKVNV 79
                                   68999*****************...****99.*******9998666667777788878887766558899999998888888 PP

                                   HHHHCGHHH CS
                  F420_oxidored 77 vlselakda 85
                                   vls lak +
  gi|121638567|ref|YP_978791.1| 80 VLSLLAKTE 88
                                   888886655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.4e-08   3.4e-05       1      35 [.       3      38 ..       3      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.4e-08
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea 35
                                   +a++GaGa+G+ +  +L ++g+d+tli r++ +l+a
  gi|121638567|ref|YP_978791.1|  3 VAVAGAGAVGRSVTRELVENGHDITLIERNPdHLDA 38
                                   69*****************************99987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.7e-08   6.8e-05      14      88 ..       2      77 ..       1     105 [. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.7e-08
                                   EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHH..HHHT.ET-EEEEGCGHHH.HHHT-SEEEE-SSSSS- CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakela..eelkgeeiealkleelke.llaeadvvisataseep 88
                                   kv + GaG +++ v++ L+++g + ++ + R+ ++ ++ a  e +      a++l+ l++ +l+e+dvv++at+  ++
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHD-ITLIERNPDHLDAAAipEAH-WRLGDACELSLLESiHLEEFDVVVAATGDDKV 77
                                   799****************99998.*********97765521444.3335677887777635***********98765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.4e-07   0.00035       1      38 [.       2      39 ..       2      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.4e-07
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                   kvav GaG +G++++  ++++g++++l++++++ l++a
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAA 39
                                   79*******************************99876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.1e-06   0.00087       1      80 [.       3      75 ..       3     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnlsppi 80
                                   v + GaG+vG++v+++l+++++    it+++r+ ++l+a+a     ++++ +  da + +  L+++ l+e d+vv ++++ 
  gi|121638567|ref|YP_978791.1|  3 VAVAGAGAVGRSVTRELVENGHD---ITLIERNPDHLDAAAI----PEAHWRLGDACELSL-LESIhLEEFDVVVAATGDD 75
                                   5678****************985...**********999974....344444444444444.4444466666666666655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.1e-06    0.0016       3      71 ..       5      71 ..       3      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                                   EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                      Epimerase  3 VtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl 71
                                   V+Ga G +G+ ++++l e+g++++ + r+++    a+++++++  +d ++ s le +  e ++d+v+ +
  gi|121638567|ref|YP_978791.1|  5 VAGA-GAVGRSVTRELVENGHDITLIERNPDHLDAAAIPEAHWRLGDACELSLLESIHLE-EFDVVVAA 71
                                   6666.**************************9999999999*********9999998885.89999977 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   5.8e-06    0.0045       1      31 [.       2      34 ..       2     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                   +v++ G+G +G s+ +eL + g  +tl+e++++
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGhdITLIERNPD 34
                                   599******************99*******954 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.1e-05     0.016       1      37 [.       2      38 ..       2     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHH CS
                 NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeeliee 37
                                   k+av GaG+ G ++ + l engh+++l+ r+++++++
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDA 38
                                   79******************************88764 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.1e-05     0.017       1      41 [.       2      42 ..       2      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvae 41
                                   k+++ G G  G++  ++l+++g+++++++r+++++++++  
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAAAIP 42
                                   689******************************99987654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   2.9e-05     0.022       1      35 [.       2      36 ..       2      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-05
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   kv+v G+G +g  +  +l e g+++t++er++  l
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHL 36
                                   79*****************************9888 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     3e-05     0.023       1      91 [.       1      88 [.       1      96 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEB.SSHHHH.HHH-SEEEE-S-HHH CS
                         DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavt.ddleev.lekadvliDFTtpea 79
                                   +kvav+Ga G +G++v++ + e +++ ++  ++r++ +    da  + + + +lg a + + le++ le++dv++  T  + 
  gi|121638567|ref|YP_978791.1|  1 MKVAVAGA-GAVGRSVTRELVE-NGHDITL-IERNPDH---LDAAAIPEAHwRLGDACElSLLESIhLEEFDVVVAATGDDK 76
                                   89*****9.********99888.6666665.5777734...45555555555666666623444441455********9999 PP

                                   HHHHHHHHHHTT CS
                         DapB_N 80 vlenlklalekg 91
                                   v  +l+l+++++
  gi|121638567|ref|YP_978791.1| 77 VNVVLSLLAKTE 88
                                   999998888775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.2e-05     0.025     144     179 ..       2      42 ..       1     115 [. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.....T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll.....r 179
                                    +++v G+G++G  ++ +l + g+++tl+e+++  l     +
  gi|121638567|ref|YP_978791.1|   2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLdaaaiP 42 
                                    56777777777777777777777777777777766543333 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   7.6e-05      0.06       1      57 [.       3      78 ..       3      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-05
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE...................-EEEE--S-HHHH CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade...................tavvvlthdhklD 57
                                   +++ Gag v++++ r + + g ++t+++ ++++ +++ +pea+                    ++vv++t d k  
  gi|121638567|ref|YP_978791.1|  3 VAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAAAIPEAHWrlgdacelsllesihleefDVVVAATGDDKVN 78
                                   5799***************************999******887699999999999999999888888888777665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.2e-05     0.056       3      36 ..       2      35 ..       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-05
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                   +V++ GaG +G + +++L e G + +l+e+  + 
  gi|121638567|ref|YP_978791.1|  2 KVAVAGAGAVGRSVTRELVENGHDITLIERNPDH 35
                                   79****************************8765 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00022      0.17       1      29 [.       1      30 [.       1      43 [. 0.79
   2 ?   -1.9   0.0       5.5   4.3e+03      87      96 ..      64      73 ..      40      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                   CEEEEESTSHHHHHHHHHHHHHT.TCEEEE CS
                        Gp_dh_N  1 vkvainGfGRIGrlvlralleek.elevva 29
                                   +kva+ G G +Gr v r l+e+  ++++++
  gi|121638567|ref|YP_978791.1|  1 MKVAVAGAGAVGRSVTRELVENGhDITLIE 30
                                   79******************7754666554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.5
                                   TSSEEEE-SS CS
                        Gp_dh_N 87 gvdlVvestG 96
                                   + d+Vv +tG
  gi|121638567|ref|YP_978791.1| 64 EFDVVVAATG 73
                                   5688888888 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013       0.1       1      30 [.       5      34 ..       5      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                   + GaG+ G +  ++L ++g+d++l+e++++
  gi|121638567|ref|YP_978791.1|  5 VAGAGAVGRSVTRELVENGHDITLIERNPD 34
                                   56************************9875 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.21       4      39 ..       5      40 ..       3      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                   SSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHH CS
                           NmrA  4 iGaTGrqGksvvrallkaghkvralvRdtkselaks 39
                                   + ++G+ G+sv+r l+++gh++  + R++++  a++
  gi|121638567|ref|YP_978791.1|  5 VAGAGAVGRSVTRELVENGHDITLIERNPDHLDAAA 40
                                   4567*************************8766655 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.22      20      77 ..      13      86 ..       5      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                   HHCHHHHHHCTCEEEEEE--STTH.................HHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT CS
                       DAGK_cat 20 rkvrelleeagvelelieteepgd.................akelakeakeegvdlivvaGGDGtvsevlnglle 77
                                   r+v++ l e+g++++lie + p++                 + +l++++  e++d++v+a GD  v+ vl+ l++
  gi|121638567|ref|YP_978791.1| 13 RSVTRELVENGHDITLIERN-PDHldaaaipeahwrlgdacELSLLESIHLEEFDVVVAATGDDKVNVVLSLLAK 86
                                   56666777777777777776.66667777888888887777788899************************9999 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039       0.3       1      37 [.       1      37 [.       1      45 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHH CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvd 37
                                   mk++v G+G vG      l e gh+++++  +  + d
  gi|121638567|ref|YP_978791.1|  1 MKVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLD 37
                                   89***************************99988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1686.09
//
Query:       gi|121638568|ref|YP_978792.1|  [L=223]
Description: integral membrane alanine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-66  222.1  18.9    5.7e-66  221.9  18.9    1.0  1  DUF3159   Protein of unknown function (DUF3159)


Domain annotation for each model (and alignments):
>> DUF3159  Protein of unknown function (DUF3159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9  18.9   3.2e-70   5.7e-66       2     186 ..      16     199 ..      15     201 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 3.2e-70
                        DUF3159   2 GGvrGlvesavPvvvFvvlflitkeLrlaiiaavavavlllvvRlvqresvqqalsgllgvaisavialrtgeakdffll 81 
                                    GGv+Glv+s++Pvv Fvv+++ +++L +ai++a+ +a l+l++Rl++res +++++g++gva++a+ia+ +g++k++fll
  gi|121638568|ref|YP_978792.1|  16 GGVSGLVYSSLPVVTFVVASS-AAGLLPAIGFALSMAGLILLWRLLRRESARPVVAGFCGVAVCALIAYLVGQSKGYFLL 94 
                                    *********************.********************************************************** PP

                        DUF3159  82 giltnlvyavvllvsilvrwPlvGlvvgavtgegtaWrkdralvrayslltlllvlvfalrlvVqvpLyladktgaLgva 161
                                    gi+++l++avv+++sil+r+P+vG+++++++g+++aWr+ +++v a++++tl ++lvfa+r++Vq +Ly+adktg+Lgva
  gi|121638568|ref|YP_978792.1|  95 GIWMSLLWAVVFTLSILIRRPIVGYLWSWLSGRDRAWRDVSRAVFAFDVATLGWTLVFAARFIVQRHLYDADKTGWLGVA 174
                                    ******************************************************************************** PP

                        DUF3159 162 rilmgwPllvlallvtvlvvrrakk 186
                                    ri mgwPl++la+l+t++++++a++
  gi|121638568|ref|YP_978792.1| 175 RIGMGWPLTALAALATYAAIKAAQR 199
                                    *********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1626.88
//
Query:       gi|121638569|ref|YP_978793.1|  [L=122]
Description: hypothetical protein BCG_2707c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-05   22.2   0.0    0.00012   21.8   0.0    1.2  1  RecG_wedge       RecG wedge domain
     0.0015   18.5   0.2     0.0021   18.0   0.2    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> RecG_wedge  RecG wedge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.3e-08   0.00012      44     129 ..      38     120 ..      32     122 .] 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-08
                     RecG_wedge  44 iseikedekvtvkgklvnvekkkissltiisavlsdgisqvlLkWfnqeyikkklktlkekevlvtGlvkkgefGaleik 123
                                     ++++++++vtv+g+l +ve+  ++    +sa l dg   v L W+ q  i   +   +++++ v G   k e G++ i 
  gi|121638569|ref|YP_978793.1|  38 AIDCQRGQEVTVVGTLRSVETNGKGCSGGVSAELFDGSDTVTLVWLGQRRIP-GID--TGRTLRVRGRLGKLENGTKAIY 114
                                    57899*******************************************9886.566..79******************** PP

                     RecG_wedge 124 nPeiee 129
                                    nP  e+
  gi|121638569|ref|YP_978793.1| 115 NPHYEI 120
                                    **9874 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.4e-07    0.0021       1      65 [.      47     117 ..      47     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-07
                                    EEEEEEEEEEE..EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS.......S CS
                tRNA_anti-codon   1 VtvaGrvtsis..drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg.......e 65 
                                    Vtv+G ++s++   ++ ++ ++++l Dg++++++v+     ++    ++ G  +rv+Gr+++ ++g        
  gi|121638569|ref|YP_978793.1|  47 VTVVGTLRSVEtnGKGCSGGVSAELFDGSDTVTLVWLG---QRRIPGIDTGRTLRVRGRLGKLENGtkaiynpH 117
                                    89*********87666688899****************...********************9988844444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 915.68
//
Query:       gi|121638570|ref|YP_978794.1|  [L=235]
Description: hypothetical protein BCG_2708 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-06   27.7  17.9    5.3e-06   27.2  17.9    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.8e-05   23.5   0.3    4.3e-05   22.9   0.3    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00032   20.6   1.4    0.00044   20.2   1.4    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold
    0.00038   20.6   0.4    0.00064   19.9   0.4    1.4  1  Thioesterase   Thioesterase domain
    0.00041   20.1   0.3     0.0015   18.3   0.1    1.9  2  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.098   12.8   2.6       0.15   12.2   2.6    1.3  1  Patatin        Patatin-like phospholipase
       0.11   12.7   0.1       0.19   12.0   0.1    1.3  1  DUF1823        Domain of unknown function (DUF1823)


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  17.9   2.1e-09   5.3e-06      32     192 ..      11     196 ..       3     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.1e-09
                                    E--TTSTS-......................GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC... CS
                  Abhydrolase_6  32 pDlpGhGrs......................dpppldledladlaalldelaagggpvvlvGHSlGGalalaaapla... 86 
                                    + lpG+G++                       p+p  l  ++ ++a+ld+ a ++gpvv+ G SlG+a+a+a    a   
  gi|121638570|ref|YP_978794.1|  11 VLLPGTGSDndyvrrafsaplrragavlvtpVPHPGRL--IDGYRAALDDAA-RDGPVVVGGVSLGAAVAAA---WAleh 84 
                                    55788884422222222222222222221001111222..334455555544.88999**************...44444 PP

                                    ..EE.EEES-..----TTTS----TTHHHHHHTT-CCCCH...CCH...S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHC CS
                  Abhydrolase_6  87 lvvg.vlldppptalpagllaaalelllallallrllawl...sre...plprlfladedadaawrarlarlaallaglg 159
                                    ++++  +l++ p  ++ ++la+a++ ++   a+lr +++    + +   + p  + ++++  ++wr+ + +l++ +    
  gi|121638570|ref|YP_978794.1|  85 PDRAvAVLAALPAWTGEPELAPAAQAARYTAARLRCDGLAattT-RmraSSPVWLAEELT--RSWRVQWPELPDAMEEAA 161
                                    44553666665545555555555555555555444444442221.123334435555666..888888888887777555 PP

                                    HT...TCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH CS
                  Abhydrolase_6 160 ll...paaawadlpvpllvl.ggeDplvprllerlla 192
                                    ++   ++a++a+l +pl v  + +Dp++p  l+ ++ 
  gi|121638570|ref|YP_978794.1| 162 AYvapSRAELARLVAPLAVAaAVDDPIHP--LQVAAD 196
                                    33222488999999999665448899777..443333 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.3   1.7e-08   4.3e-05      72     139 ..      59     124 ..      42     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-08
                    Hydrolase_4  72 ehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv 139
                                      ++ p+++ G S+G+++a++++l++pd+  ++  + Pa   +++l   p++++++ ++++l  +   
  gi|121638570|ref|YP_978794.1|  59 AARDGPVVVGGVSLGAAVAAAWALEHPDRAVAVLAALPAWTGEPEL--APAAQAARYTAARLRCDGLA 124
                                    34566***********************777777777888888774..55555555555555444443 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.4   1.7e-07   0.00044      65     182 ..      57     191 ..      30     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                                    HHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---...............EEEEEEESE-SSTSSTTSHHHHHCHHTTTS CS
                  Abhydrolase_3  65 elgadpsrivlaGdSaGGnlaaavalrardegepk...............vagqvliyPvtdlertesesikkaeeladg 129
                                    + +a    +v++G S G+  aaa al+  d+  ++               +a+q+  y +  l r ++ + ++++  a+ 
  gi|121638570|ref|YP_978794.1|  57 DDAARDGPVVVGGVSLGAAVAAAWALEHPDRA-VAvlaalpawtgepelaPAAQAARYTAARL-RCDGLAATTTRMRASS 134
                                    44577889**********************95.335789999999*99**********98878.6666666555555899 PP

                                    SSSCHHHHHHHHHHHSS..GGGGGST...TTSGGGCS-SST---EEEEEETT-TTHHH CS
                  Abhydrolase_3 130 plltraaldlfwrlylp..eadrddp...laspllaedlsglpptlvvvaefDplrde 182
                                    p++ +++l   wr+  p    d+++    +++p +ae  + ++p  v+ a  Dp++  
  gi|121638570|ref|YP_978794.1| 135 PVWLAEELTRSWRVQWPelP-DAMEEaaaYVAPSRAELARLVAPLAVAAAVDDPIHPL 191
                                    ***9*********9997643.4443323477777775577799**********99865 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   2.5e-07   0.00064      44     202 ..      41     204 ..      14     211 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                                    CTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCC..CCCHHCHHCCCHTTHHT CS
                   Thioesterase  44 plesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslflidssa..pseteaqeasrraedee 121
                                    p++  + l++ y +al     +gP++++G SlG+++A   A++Le   +av+ l    ++   p+   a +a r+++ + 
  gi|121638570|ref|YP_978794.1|  41 PVPHPGRLIDGYRAALDDAARDGPVVVGGVSLGAAVAA--AWALEHPDRAVAVLAALPAWTgePELAPAAQAARYTAARL 118
                                    4444466*****************************95..6666666666666655554431122222222222222222 PP

                                    ....HHHHHCCTTHH.HCCTTTHCCHHHHHHHHHHHHHHHHHTCCS-TTSCSE...HHCEEEEEEGSS-CTCCCCCCCHC CS
                   Thioesterase 122 ....fveeltdlggt.epeelledeellsellpalradyraleqyslrpeaaq...klratlfngsddklkdldtlelae 193
                                        + +  t+++ +  +  ++e ++ ++   p l +++     y ++++a     ++++++ +  dd+++ l+    a+
  gi|121638570|ref|YP_978794.1| 119 rcdgLAATTTRMRASsPVWLAEELTRSWRVQWPELPDAMEEAAAYVAPSRAELarlVAPLAVAAAVDDPIHPLQ---VAA 195
                                    44446666677776632222334444455555555555555555533333322555667777777777777777...455 PP

                                    HCHCTCESC CS
                   Thioesterase 194 rweqktsge 202
                                     w ++ +++
  gi|121638570|ref|YP_978794.1| 196 DWVSVAPHA 204
                                    566666665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   5.7e-07    0.0015      67     124 ..      57     113 ..      47     128 .. 0.84
   2 ?    0.2   0.0      0.18   4.7e+02     117     138 ..     146     167 ..     107     218 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.7e-07
                                    HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHHHHHHHHH CS
                  Abhydrolase_1  67 ldalgddkltlvGhSmGGmialayaaeyperVkalvllga.idpaaslieaqrqqaksf 124
                                     da  d+++++ G S+G ++a+a+a+e+p+  +a++ l+a +++  +++ a   qa+++
  gi|121638570|ref|YP_978794.1|  57 DDAARDGPVVVGGVSLGAAVAAAWALEHPD--RAVAVLAAlPAWTGEPELAPAAQAARY 113
                                    57888999**********************..777777777789988888888877776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                                    HHHHHHHHHCHHCHHHHHHHHH CS
                  Abhydrolase_1 117 qrqqaksfpdffdgyaadcarn 138
                                    +r q++ +pd+++  aa  a+ 
  gi|121638570|ref|YP_978794.1| 146 WRVQWPELPDAMEEAAAYVAPS 167
                                    3333333333333333333333 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.6   5.8e-05      0.15      19      87 ..      55     146 ..      48     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                        Patatin  19 aLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdl.........................lir 73 
                                    aL++++ + + +++G+S GA +a++ al+ ++ a   ++ ++l +++    l                         +  
  gi|121638570|ref|YP_978794.1|  55 ALDDAARDGPVVVGGVSLGAAVAAAWALEHPDRA--VAVLAALPAWTGEPELapaaqaarytaarlrcdglaatttrMRA 132
                                    47778889999******************88888..77777777777777777777777777555555555555544333 PP

                        Patatin  74 elaanlaarlsgll 87 
                                    +++ +la++l++ +
  gi|121638570|ref|YP_978794.1| 133 SSPVWLAEELTRSW 146
                                    34444444444433 PP

>> DUF1823  Domain of unknown function (DUF1823)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.2e-05      0.19      31      70 ..     129     168 ..     123     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                                    -EETTTTEE--TTS-HHHHTT-SS---TTT--HHHHHHHH CS
                        DUF1823  31 rydeaeekwdasevapeWreeypeppdliesrpatvkltR 70 
                                    r+++++  w a+e + +Wr ++pe pd +e+ +a v+  R
  gi|121638570|ref|YP_978794.1| 129 RMRASSPVWLAEELTRSWRVQWPELPDAMEEAAAYVAPSR 168
                                    56778889***********************988776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1639.28
//
Query:       gi|121638571|ref|YP_978795.1|  [L=259]
Description: hypothetical protein BCG_2709c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-54  184.2   0.6    2.4e-54  183.7   0.6    1.3  1  DUF3710   Protein of unknown function (DUF3710)
  ------ inclusion threshold ------
      0.051   13.5   0.1        1.2    9.2   0.0    2.7  3  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> DUF3710  Protein of unknown function (DUF3710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.6   2.7e-58   2.4e-54       1     176 []      52     221 ..      52     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 2.7e-58
                        DUF3710   1 GPfDaaeapeed....erlDLGsllvpvleglelqvevdektgrvvavtvvtgesalqlqafAAPkssglwdevraelae 76 
                                    GPfD+++ ++ +    +rlDLGs+l+p+++  ++qve++e +g ++av+v t++++  ++a+AAPk++glw+ev+ ela+
  gi|121638571|ref|YP_978795.1|  52 GPFDIDDFDDPSvavlARLDLGSVLIPMPAAGQVQVELTE-SGVPSAVWVITPNGRYSIAAYAAPKTGGLWREVAGELAD 130
                                    9****7777776779*************************.9************************************** PP

                        DUF3710  77 slekaggeveeeeGpfGtElvaevpaksedgeaaqlvRfigvdGpRWlLrgvvtgpaasdeeaaelleevlrevvVvRgd 156
                                    sl+k+ ++v+ ++Gp+G+E+++ +           +vRfigv+G+RW++r+vv+gp+++ ++ +e+++e+l+++vV+Rgd
  gi|121638571|ref|YP_978795.1| 131 SLRKDSAKVSIKDGPWGREVIGIAAG---------VVRFIGVNGYRWMIRCVVNGPQETVDALTEEAREALADTVVRRGD 201
                                    *********************98776.........7***********************777****************** PP

                        DUF3710 157 epmpprelLplrlPkelaeq 176
                                    +p+p+r++Lp++lP+ +a+q
  gi|121638571|ref|YP_978795.1| 202 TPLPVRTPLPVHLPEPMAAQ 221
                                    ***************99875 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       0.9   8.1e+03      27      33 ..     168     174 ..     168     175 .. 0.82
   2 ?    0.9   0.1     0.055     5e+02       7      20 ..     177     190 ..     177     191 .. 0.88
   3 ?    9.2   0.0   0.00013       1.2       2      20 ..     210     228 ..     209     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.9
                                    HHHHHHH CS
                          RHH_1  27 elIReAl 33 
                                    ++IR+ +
  gi|121638571|ref|YP_978795.1| 168 WMIRCVV 174
                                    99**975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.055
                                    EHHHHHHHHHHHHH CS
                          RHH_1   7 deellerLdelarr 20 
                                    ++e++++L e ar+
  gi|121638571|ref|YP_978795.1| 177 PQETVDALTEEARE 190
                                    6899*******996 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00013
                                    EEEEEEHHHHHHHHHHHHH CS
                          RHH_1   2 vsirldeellerLdelarr 20 
                                    + ++l+e ++++L+e a++
  gi|121638571|ref|YP_978795.1| 210 LPVHLPEPMAAQLREAAAA 228
                                    679*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1771.59
//
Query:       gi|121638572|ref|YP_978796.1|  [L=154]
Description: deoxyuridine 5'-triphosphate nucleotidohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-28   96.7   0.0      1e-27   96.4   0.0    1.1  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   5.6e-32     1e-27       4     129 .]      15     149 ..      14     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 5.6e-32
                                    TBEBESSTT-SSEEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE...EEEETTBTSEEEEEE CS
                        dUTPase   4 eiptrkspesAgyDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvp...gvidsdyrGevkvvl 80 
                                    ++p r+ +++Ag Dl++a+d+ + pg + lv t++++++p g+ +l+ pRSgla + +++ +   g id+ yrGe+kv l
  gi|121638572|ref|YP_978796.1|  15 PLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVnspGTIDAGYRGEIKVAL 94 
                                    57999*************************************************99777665567*************** PP

                                    EE-SSS.-EEE-TT-EEEEEEEEEBECGEEEEESSTT.....TESSBTTXTTTTX CS
                        dUTPase  81 fnltkk.dvkikkgdRiAqLifariltaeleevetlk.....atergeggfgssg 129
                                    +nl  + ++ +++gdRiAqL+++r++  el ev++++     +t rg+gg gssg
  gi|121638572|ref|YP_978796.1|  95 INLDPAaPIVVHRGDRIAQLLVQRVELVELVEVSSFDeaglaSTSRGDGGHGSSG 149
                                    ***9988******************99777766665312222799*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1207.92
//
Query:       gi|121638573|ref|YP_978797.1|  [L=161]
Description: alanine rich transmembrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-51  172.0  10.1      9e-51  171.8  10.1    1.0  1  DUF3093   Protein of unknown function (DUF3093)
  ------ inclusion threshold ------
        5.4    4.8   7.9        6.1    4.6   7.9    1.0  1  DUF4175   Domain of unknown function (DUF4175)


Domain annotation for each model (and alignments):
>> DUF3093  Protein of unknown function (DUF3093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8  10.1     1e-54     9e-51       1     140 []      12     159 ..      12     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 1e-54
                        DUF3093   1 rYrErlwvplwwWllaalvalaaalvaaevglavavlv....aavlvalavvallalsrtrieVtd.......geLrvgr 69 
                                    rYrErlwvp+wwW+la+++   aal+a+ev+l+va+l     +a l+++a+  ll+l+r++i+Vt+        +L++g 
  gi|121638573|ref|YP_978797.1|  12 RYRERLWVPWWWWPLAFAL---AALIAFEVNLGVAALPdwvpFATLFTVAAGTLLWLGRVEIRVTAgsadgagVKLWAGP 88 
                                    6******************...*************9999999***********************999999999****** PP

                        DUF3093  70 arlplavvgrvealdaeakraalgrqldpaAfvvlrgwiktavrveltDpeDptPywlvStrrPeeLaaal 140
                                    a+lp+av++r+++++a+ak+aalgrqldpaA+v++r+w++++v v+l+Dp+DptPywlvS+r+Pe++++al
  gi|121638573|ref|YP_978797.1|  89 AHLPVAVIARSAEIPATAKSAALGRQLDPAAYVLHRAWVGPMVLVVLDDPNDPTPYWLVSCRHPERVLSAL 159
                                    ********************************************************************997 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.9   0.00068       6.1       1      83 [.      15      97 ..      15     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.00068
                        DUF4175  1 Erlw.palwpllsvlalflalsllgl.wqllpdllrlalllafalallaalvlplrrfrwPtraealrrlerasglphrPlt 80
                                   Erlw p  w++l+ ++++l++  ++l   +lpd++ +a l+ +a+++l++l +  +r+++ + + a  +l +    +h P++
  gi|121638573|ref|YP_978797.1| 15 ERLWvPWWWWPLAFALAALIAFEVNLgVAALPDWVPFATLFTVAAGTLLWLGRVEIRVTAGSADGAGVKLWAG--PAHLPVA 94
                                   888845667788888888888877774569*********************9888999988888887777655..7777777 PP

                        DUF4175 81 ale 83
                                   +++
  gi|121638573|ref|YP_978797.1| 95 VIA 97
                                   765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1159.76
//
Query:       gi|121638574|ref|YP_978798.1|  [L=100]
Description: hypothetical protein BCG_2712c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-44  150.4   2.6    1.7e-44  150.3   2.6    1.0  1  DUF4193   Domain of unknown function (DUF4193)
     0.0026   17.8   0.4      0.073   13.1   0.4    2.0  2  ArfGap    Putative GTPase activating protein for Arf


Domain annotation for each model (and alignments):
>> DUF4193  Domain of unknown function (DUF4193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   2.6   1.9e-48   1.7e-44       1      98 []       1      99 [.       1      99 [. 0.98

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 1.9e-48
                        DUF4193  1 matDydapRkt.ddeleedsleelkarraekasavvdedetdaaesfelPgadlsgeelsvrvipkqadEFtCtscFlvkhr 81
                                   m tDydapR+t +d+++edsleelkarr+e+asavvd+de++ aesfelPgadlsgeelsvrv+pkqadEFtC+scFlv+hr
  gi|121638574|ref|YP_978798.1|  1 MPTDYDAPRRTeTDDVSEDSLEELKARRNEAASAVVDVDESESAESFELPGADLSGEELSVRVVPKQADEFTCSSCFLVQHR 82
                                   99*********56********************************************************************* PP

                        DUF4193 82 srlaeeedgqqiCrdCa 98
                                   srla+e++g +iC+dCa
  gi|121638574|ref|YP_978798.1| 83 SRLASEKNGVMICTDCA 99
                                   ****************7 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.3   0.0    0.0094        84      52      83 ..       7      38 ..       1      56 [. 0.81
   2 !   13.1   0.4   8.2e-06     0.073       9      40 ..      66      99 ..      57     100 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0094
                                   -EEETTTS---HHHHHHHHHTCHHHHHHHHTT CS
                         ArfGap 52 kvrsltldkwedeelellkalgNkkaneilea 83
                                   + r ++ d+ +++ le lka  N+ a ++   
  gi|121638574|ref|YP_978798.1|  7 APRRTETDDVSEDSLEELKARRNEAASAVVDV 38
                                   5688899*****************99988665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.2e-06
                                   CSCCCCB-TTT..-SBS--EEETTTTEEE-HHHH CS
                         ArfGap  9 kepenkvCaDC..gakeptWaslnlgvflCieCs 40
                                   k+ ++ +C  C   +++++ as + gv++C++C+
  gi|121638574|ref|YP_978798.1| 66 KQADEFTCSSCflVQHRSRLASEKNGVMICTDCA 99
                                   3445559****9999******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 672.68
//
Query:       gi|121638575|ref|YP_978799.1|  [L=216]
Description: hypothetical protein BCG_2713 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-14   53.6   0.0    5.4e-14   53.0   0.0    1.3  1  LytR_C    LytR cell envelope-related transcriptional attenuat


Domain annotation for each model (and alignments):
>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0     3e-18   5.4e-14       1      85 []      90     179 ..      90     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3e-18
                         LytR_C   1 evkVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee........ttivyreaaaaaakalaaalglgelqedsv 72 
                                    ++kV+VlN++g+ G+Aa++a aL++ Gf+  +   a+n++ +         +i++++a++a+a al    +++el +ds+
  gi|121638575|ref|YP_978799.1|  90 DTKVHVLNASGRGGQAADIAGALQDLGFAQPT---AANDPIYagtrldcqGQIRFGTAGQATAAALWLVAPCTELYHDSR 166
                                    589*************************9999...66664446779999******888889******************* PP

                         LytR_C  73 kdasvtvvlGkdf 85 
                                    +d+sv++ lG+df
  gi|121638575|ref|YP_978799.1| 167 ADDSVDLALGTDF 179
                                    ************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1606.07
//
Query:       gi|121638576|ref|YP_978800.1|  [L=290]
Description: extragenic suppressor protein suhB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-62  211.4   0.2    2.1e-62  211.1   0.2    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.1   0.2   1.2e-66   2.1e-62       5     268 ..      11     280 ..       7     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 211.1 bits;  conditional E-value: 1.2e-66
                                    HHHHHHHHHHHHHHHHHHHTT...TSEEEESTTT....CCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCC CS
                     Inositol_P   5 vtkaavelaakagevlreefs...enelvieeks....kegeedlvtaadeaveelilealaekfpshkilgeetlakge 77 
                                    + ++a +laa+a++ +r +     + + + + ++    k++++d+vt +d ++e+l++++la+ +p+++ilgee++++++
  gi|121638576|ref|YP_978800.1|  11 LRSVAENLAAEAAAFVRGRRAevfGISRAGDGDGavraKSSPTDPVTVVDTDTERLLRDRLAQLRPGDPILGEEGGGPAD 90 
                                    567888999999999998888555566666666699999***************************************** PP

                                    CT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETC....EEEEECTTS CS
                     Inositol_P  78 kseltedgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflng....eklplsrap 153
                                     + +++d++tw++DPiDGT+nFv gip +aVsig  v g  v+G++a++++ ++ysaa g Ga+l +    ++l++ + +
  gi|121638576|ref|YP_978800.1|  91 VTATPSDRVTWVLDPIDGTVNFVYGIPAYAVSIGAQVGGITVAGAVADVAARTVYSAATGLGAHLTDergrHVLRCTGVD 170
                                    9****************************************************************997888889999999 PP

                                    EGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTT CS
                     Inositol_P 154 piseallvtlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaG 233
                                    ++s all t f +s r + ++a+ll++v ++v++   r++gs+al+l++va+G++day+e+g ++ WD+AAG++i  eaG
  gi|121638576|ref|YP_978800.1| 171 ELSMALLGTGFGYSVRCREKQAELLAHVVPLVRDV--RRIGSAALDLCMVAAGRLDAYYEHG-VQVWDCAAGALIAAEAG 247
                                    *********************************99..*************************.***************** PP

                                    EEEEESSSCSSSTTSSEEEEESCHHHHHHHHHHHC CS
                     Inositol_P 234 Gvvtdakgegrlllargiiaanqkelaellaaave 268
                                    ++v+  + +  +  a+ +++a+++ +a+ l+aa++
  gi|121638576|ref|YP_978800.1| 248 ARVLLSTPR--AGGAGLVVVAAAPGIADELLAALQ 280
                                    ****99988..777877777775555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1932.06
//
Query:       gi|121638577|ref|YP_978801.1|  [L=265]
Description: polyphosphate glucokinase ppgK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-16   58.8   4.7    3.6e-13   49.7   2.3    2.6  2  ROK       ROK family


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   2.3     2e-17   3.6e-13       3     162 ..      22     176 ..      20     185 .. 0.83
   2 !    8.8   0.0   5.5e-05      0.98     210     289 ..     190     257 ..     176     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2e-17
                                    EEEE-SSEEEEEEEETTS-EEEEEEE..EEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGC CS
                            ROK   3 gidiGgtkialalvdeegeilarekv..etptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpn 80 
                                    gid+Gg  i+  +vd +  +l   ++   tp++ t+ ++ ++iae+v+      + ++ +g+  pG++  + g + +++n
  gi|121638577|ref|YP_978801.1|  22 GIDVGGSGIKGGIVDLDTGQLIGDRIklLTPQPATPLAVAKTIAEVVNGF----GWRGPLGVTYPGVV--THGVVRTAAN 95 
                                    9**************99887755555338999999999999999988887....45679*********..6666666666 PP

                                    ..GCCCCTTHHHHHHHHHT.S-EEEEEHHHHHHHHHHHHCTTTTTS.-EEEEEESSSEEEEEEETTEEE--TTS-TT-GG CS
                            ROK  81 ..itwenfdlvekleerln.vpvevenDvnaaalaEavfgaskdve.nviyvtvgtGvGaGviingklitGrnGvagelG 156
                                        w  ++  +++ ++l+   v + nD+ aa laE+  ga k+    v+++t gtG+G +vi ng li       +e+G
  gi|121638577|ref|YP_978801.1|  96 vdKSWIGTNARDTIGAELGgQQVTILNDADAAGLAETRYGAGKNNPgLVVLLTFGTGIGSAVIHNGTLIP-----NTEFG 170
                                    4467999999****99986378*******************99887267899****************95.....48899 PP

                                    GSBS-T CS
                            ROK 157 Hiqldp 162
                                    H+ +  
  gi|121638577|ref|YP_978801.1| 171 HLEVGG 176
                                    998874 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHH CS
                            ROK 210 vaeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllGaaa 289
                                    +    + + a+++ + ++ + n++ p+ ++ gGg+s              k++   +++++  +v+a l++ ag++Gaa+
  gi|121638577|ref|YP_978801.1| 190 KNDWTYPKWAKQVTRVLIAIENAIWPDLFIAGGGISRKA----------DKWVPLLENRTP--VVPAALQNTAGIVGAAM 257
                                    4555677889999999******************98644..........455555556666..68888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1761.94
//
Query:       gi|121638578|ref|YP_978802.1|  [L=528]
Description: RNA polymerase sigma factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-28   98.3   0.9      2e-28   98.3   0.9    3.7  4  Sigma70_r3    Sigma-70 region 3
    6.2e-23   80.4   0.4    2.2e-22   78.6   0.3    2.0  2  Sigma70_r2    Sigma-70 region 2
    4.6e-21   74.1   3.2    1.2e-18   66.4   0.4    2.9  2  Sigma70_r4    Sigma-70, region 4
    1.5e-16   60.1   0.4    5.3e-16   58.3   0.4    2.0  1  Sigma70_r1_2  Sigma-70 factor, region 1.2


Domain annotation for each model (and alignments):
>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.25   1.1e+03      56      73 ..     193     209 ..     186     213 .. 0.77
   2 ?   -1.2   0.0       0.5   2.2e+03      29      57 ..     220     248 ..     219     256 .. 0.81
   3 !   98.3   0.9   4.5e-32     2e-28       1      76 [.     374     449 ..     374     451 .. 0.96
   4 ?   -3.0   0.0       1.8   8.2e+03      23      40 ..     489     506 ..     488     512 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                                    SSTTXBSTTTXBXSSSXX CS
                     Sigma70_r3  56 eeedtelgdlleddeaes 73 
                                     e+d++ gd++ d+  es
  gi|121638578|ref|YP_978802.1| 193 TEKDKASGDFVWDE-DES 209
                                    68899999999999.444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.5
                                    HHTXXHHHHHHHHHHHXXXEETTXBSSSS CS
                     Sigma70_r3  29 eLglseekVrevleaarepvSldlpvgee 57 
                                    eL  s + Vr +l+   ++ +l+ +   e
  gi|121638578|ref|YP_978802.1| 220 ELTASADSVRAYLKQIGKVALLNAEEEVE 248
                                    67788999*****9999999998887665 PP

  == domain 3  score: 98.3 bits;  conditional E-value: 4.5e-32
                                    XHHHHHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXBSTTTXBXSSSXXHHH CS
                     Sigma70_r3   1 EklnkikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSldlpvgeeedtelgdlleddeaespee 76 
                                    E +nk+ r+qreL q+lgrePtpeE+A+e+++++ekV+e+ + arep+Sld+ +g+e+d++lgd++ed+ea+ +++
  gi|121638578|ref|YP_978802.1| 374 EVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVD 449
                                    789******************************************************************9987776 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.8
                                    HHHHHHHHTXXHHHHHHH CS
                     Sigma70_r3  23 peEiAeeLglseekVrev 40 
                                     +Ei +  g++ e++r++
  gi|121638578|ref|YP_978802.1| 489 LDEIGQVYGVTRERIRQI 506
                                    678999999999999987 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.9   8.4e+03      47      61 ..     226     240 ..     221     244 .. 0.69
   2 !   78.6   0.3   4.8e-26   2.2e-22       1      70 [.     295     364 ..     295     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHH CS
                     Sigma70_r2  47 vsfsawllriarnaa 61 
                                    +s++a+l  i + a+
  gi|121638578|ref|YP_978802.1| 226 DSVRAYLKQIGKVAL 240
                                    578888888766555 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 4.8e-26
                                    HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 
                                    l+e++l+lv++la+r++g+g  + Dl+Qe++l+l+rave+fd ++g++fs+++++++r+a+ +++ +++r
  gi|121638578|ref|YP_978802.1| 295 LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQAR 364
                                    789**************************************************************99988 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1   0.00073       3.3       5      45 ..     379     418 ..     375     421 .. 0.77
   2 !   66.4   0.4   2.6e-22   1.2e-18       1      50 []     463     516 ..     463     516 .. 0.98

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00073
                                    S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                     Sigma70_r4   5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAl 45 
                                    L   +re l+    e+ T eE++++++i+ e V  i+ +A+
  gi|121638578|ref|YP_978802.1| 379 LGRIQRELLQDLGREP-TPEELAKEMDITPEKVLEIQQYAR 418
                                    5555666666655555.99**************99999997 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 2.6e-22
                                    HHHHS-HHHHHHHHHHH....TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrf....geglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                                    +L++L+ere  v++lrf    g+++Tl EIg+++g++rer+rqie++++ kLR+
  gi|121638578|ref|YP_978802.1| 463 VLDTLSEREAGVVRLRFgltdGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRH 516
                                    69***************************************************7 PP

>> Sigma70_r1_2  Sigma-70 factor, region 1.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.4   1.2e-19   5.3e-16       1      34 []     226     259 ..     226     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.2e-19
                                    HHHHHHHHHHHHSX--THHHHHHHHHHHHCCHHH CS
                   Sigma70_r1_2   1 DpvrlYLrEIGriPLLtaeEEveLAkrieaGdea 34 
                                    D+vr+YL++IG++ LL+aeEEveLAkrieaG++a
  gi|121638578|ref|YP_978802.1| 226 DSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYA 259
                                    9******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 3814.09
//
Query:       gi|121638579|ref|YP_978803.1|  [L=142]
Description: hypothetical protein BCG_2717 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-27   93.5   0.1    1.1e-26   93.2   0.1    1.1  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.1   6.2e-31   1.1e-26       4     120 ..      13     120 ..      10     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 6.2e-31
                                    STTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHHHH CS
                  Ribonuc_L-PSP   4 apaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladiedfaevn 83 
                                    ++++a  Ys+av++g lv+v+G++++         +d+++qtr+al++++ +L +aga+l+dvV+++++++di++++ev 
  gi|121638579|ref|YP_978803.1|  13 EFESAVGYSRAVRIGPLVVVAGTTGSG--------DDIAAQTRDALRRIEIALGQAGATLADVVRTRIYVTDISRWREVG 84 
                                    678899*****************9985........8******************************************** PP

                                    HHHHHHSSSSTS--EEEEEE-SBSG.GG-SEEEEEEEE CS
                  Ribonuc_L-PSP  84 evyaeafdelkeaParsaveVaaLp.kgakvEIeaiav 120
                                    ev+a+af ++   P++s+veV+aL  +g++vEIea a+
  gi|121638579|ref|YP_978803.1|  85 EVHAQAFGKIR--PVTSMVEVTALIaPGLLVEIEADAY 120
                                    **********5..***********99*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1047.01
//
Query:       gi|121638580|ref|YP_978804.1|  [L=129]
Description: hypothetical protein BCG_2718c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-26   90.6   0.0    5.7e-26   90.3   0.0    1.1  1  DUF952    Protein of unknown function (DUF952)


Domain annotation for each model (and alignments):
>> DUF952  Protein of unknown function (DUF952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   3.2e-30   5.7e-26       4      89 ..      16     103 ..      13     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.2e-30
                                    HHHHHHHHHHSEE---HHHHHHTSEE-EEHHHHHHHHHHHSTT--SEEEEEEESGGGTTTEEEEEG....GGGSEEEEES CS
                         DUF952   4 lpeweaakaegeyagssldakdGFIHlStaeqvpetaarffagqedlvllkidasklaaavkweas....eggelfPHlY 79 
                                     +ew++a+++g +++ + d k+G+IHlSt eqv+  a+r+++g++dlvll id+++l+++v+we+     + ++lfPHlY
  gi|121638580|ref|YP_978804.1|  16 VQEWSHARERGGIYP-ESD-KTGYIHLSTLEQVHLPANRLYRGRADLVLLYIDPAALDSPVRWEPGvptdPRSMLFPHLY 93 
                                    689************.667.8*******************************************9999976679****** PP

                                    S-EEGGGEEE CS
                         DUF952  80 gplplkaVvs 89 
                                    gplp+ aV+ 
  gi|121638580|ref|YP_978804.1|  94 GPLPVRAVIG 103
                                    ********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 973.11
//
Query:       gi|121638581|ref|YP_978805.1|  [L=85]
Description: hypothetical protein BCG_2719c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 598.47
//
Query:       gi|121638582|ref|YP_978806.1|  [L=324]
Description: transmembrane alanine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-45  154.2  17.7    5.5e-45  154.0  17.7    1.0  1  Virul_fac_BrkB   Virulence factor BrkB
  ------ inclusion threshold ------
       0.82    9.4   2.2        0.9    9.3   0.2    1.8  2  Sh_2             Metapneumovirus Small hydrophobic protein


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0  17.7   6.1e-49   5.5e-45       2     257 ..      26     283 ..      25     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 6.1e-49
                 Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgl.lg.....lddelqeqlldllaevlpegaa.evvedilqrllnqaslg 74 
                                    +d ++  +a+ a+ + lSl Plll +l+ l++  +     + +++++ +l+ + +++ ++++ e++e+++ +++n+a+++
  gi|121638582|ref|YP_978806.1|  26 DDSIFSESAQAAFWSALSLPPLLLGMLGSLAYvAPlfgpdTLPAIEKSALSTAHSFFSPSVVnEIIEPTIGDITNNARGE 105
                                    5778899************************963367899999*************8887887***************** PP

                 Virul_fac_BrkB  75 llglavll..wsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglgle 152
                                    + +l++l+  w++s+++sa+ +a+ +++++++ r+ +r+r+ +l+l++++lv+l++++ ++v++++ +     +++  l 
  gi|121638582|ref|YP_978806.1| 106 VASLGFLIslWAGSSAISAFVDAVVEAHDQTPLRHPVRQRFFALFLYVVMLVFLVATAPVMVVGPRKVS---EHIPESL- 181
                                    ******************************************************************444...4556433. PP

                 Virul_fac_BrkB 153 lsell.llqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgali 231
                                        + ll+++ +++++l l++ ++llYrv+ +v  + +++++Ga+la +++l++++++ +yl++  + + +YG+l++ i
  gi|121638582|ref|YP_978806.1| 182 ----AnLLRYGYYPALILGLTVGVILLYRVALPVPLPTHRLVLGAVLAIAVFLIATLGLRVYLAWITRTGYTYGALATPI 257
                                    ....237************************************************************************* PP

                 Virul_fac_BrkB 232 illlWlylsalilLlGaelnaelqer 257
                                    ++ll+ ++ +++++lGaelna++qe+
  gi|121638582|ref|YP_978806.1| 258 AFLLFAFFGGFAIMLGAELNAAVQEE 283
                                    ***********************987 PP

>> Sh_2  Metapneumovirus Small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.15   1.3e+03      39      51 ..     153     165 ..     146     175 .. 0.82
   2 ?    9.3   0.2    0.0001       0.9      35      59 ..     219     244 ..     214     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.15
                           Sh_2  39 ilaliflvatiGl 51 
                                    +++l+flvat  +
  gi|121638582|ref|YP_978806.1| 153 VVMLVFLVATAPV 165
                                    789******9765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0001
                           Sh_2  35 vicailal.iflvatiGlsvklavtv 59 
                                    v+ a+la+ +fl+at+Gl v la+  
  gi|121638582|ref|YP_978806.1| 219 VLGAVLAIaVFLIATLGLRVYLAWIT 244
                                    7778887649************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1996.77
//
Query:       gi|121638583|ref|YP_978807.1|  [L=82]
Description: hypothetical protein BCG_2721c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-28   97.6   0.4      3e-28   97.3   0.4    1.1  1  DUF3039   Protein of unknown function (DUF3039)
  ------ inclusion threshold ------
      0.017   15.1   0.8       0.29   11.1   0.0    2.8  3  ADK_lid   Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.4   3.4e-32     3e-28       2      56 .]      24      79 ..      23      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3.4e-32
                        DUF3039  2 gdaerfaHYvkkdkiaesavtGtpVvALCGkvwvptrdpk.kfPvCpeCkeiyesl 56
                                   +d+++++HYvkkdkiaesav+G++VvALCG+v+++tr+pk ++PvCp+Ck+iy++l
  gi|121638583|ref|YP_978807.1| 24 SDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTRAPKpGSPVCPDCKRIYDTL 79
                                   69***************************************************986 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.15   1.3e+03      21      29 ..      16      24 ..      10      26 .. 0.84
   2 ?    0.7   0.0     0.058   5.2e+02       6      19 ..      51      63 ..      48      66 .. 0.70
   3 ?   11.1   0.0   3.2e-05      0.29       3      12 ..      68      77 ..      67      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                                   TTB-TTT-- CS
                        ADK_lid 21 eglCDkCGe 29
                                   e ++D +G+
  gi|121638583|ref|YP_978807.1| 16 ERVDDGTGS 24
                                   789999997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.058
                                   TT--EEETTTB--S CS
                        ADK_lid  6 kCGrsYhvvfnpPk 19
                                    CG+++  v++ Pk
  gi|121638583|ref|YP_978807.1| 51 LCGEVFP-VTRAPK 63
                                   5999998.444454 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 3.2e-05
                                   E-TTT--EEE CS
                        ADK_lid  3 vCpkCGrsYh 12
                                   vCp+C+r+Y 
  gi|121638583|ref|YP_978807.1| 68 VCPDCKRIYD 77
                                   8********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 692.87
//
Query:       gi|121638584|ref|YP_978808.1|  [L=148]
Description: hypothetical protein BCG_2722 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-27   93.7   3.4    7.9e-27   93.2   3.4    1.3  1  DUF3099   Protein of unknown function (DUF3099)


Domain annotation for each model (and alignments):
>> DUF3099  Protein of unknown function (DUF3099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   3.4   4.4e-31   7.9e-27       1      71 [.      33     104 ..      33     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 4.4e-31
                        DUF3099   1 lITdAarslsedlrrRqrrYlilmgiRvvclilavvlvsv.engwlalvllvlavvLPwvAVvlANdrperk 71 
                                    lI+ Aa+s++ ++r R+r+Yl+lm++Rv++lila++++ + +ng+++l++++++v+LPw+AV++ANdrp+r+
  gi|121638584|ref|YP_978808.1|  33 LISAAAPSYEVEHRTRVRKYLTLMAFRVPALILAAIAYGAwHNGLISLLIVAASVPLPWMAVLIANDRPPRR 104
                                    799*******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1144.25
//
Query:       gi|121638585|ref|YP_978809.1|  [L=323]
Description: RNA polymerase sigma factor SigB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-26   91.3   1.5    1.7e-25   88.9   0.9    2.4  3  Sigma70_r3    Sigma-70 region 3
      3e-22   78.2   0.2    7.9e-22   76.8   0.0    1.8  2  Sigma70_r2    Sigma-70 region 2
    1.1e-19   69.7   2.9    2.8e-19   68.3   0.8    2.6  3  Sigma70_r4    Sigma-70, region 4
    2.6e-12   46.5   0.0    7.9e-12   45.0   0.0    1.9  1  Sigma70_r1_2  Sigma-70 factor, region 1.2
      0.003   17.5   0.0          4    7.5   0.0    2.8  2  HTH_15        Helix-turn-helix domain of alkylmercury lyase


Domain annotation for each model (and alignments):
>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.9   4.9e-29   1.7e-25       1      77 [.     169     245 ..     169     246 .. 0.98
   2 ?    0.0   0.0      0.26   9.2e+02      21      47 ..     242     267 ..     240     284 .. 0.75
   3 ?   -0.3   0.0      0.32   1.2e+03      23      42 ..     284     303 ..     277     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 4.9e-29
                                    XHHHHHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXBSTTTXBXSSSXXHHHC CS
                     Sigma70_r3   1 EklnkikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSldlpvgeeedtelgdlleddeaespeea 77 
                                    E+ nk++r++re+ q+lgre+t+eE+A+e g++++k+ ++le +r+pvSld+pvg+ee+  lgd++ed ea+s+e+a
  gi|121638585|ref|YP_978809.1| 169 EQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENA 245
                                    799**********************************************************************9986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                                    XXHHHHHHHHTXXHHHHHHHHHHHXXX CS
                     Sigma70_r3  21 PtpeEiAeeLglseekVrevleaarep 47 
                                    + ++ iAe L  ++  V+ +l+  + +
  gi|121638585|ref|YP_978809.1| 242 AENAVIAELLHTDIRSVLATLDERE-H 267
                                    677889*****99999999987544.3 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.32
                                    HHHHHHHHTXXHHHHHHHHH CS
                     Sigma70_r3  23 peEiAeeLglseekVrevle 42 
                                     + i +  gls e+Vr++ +
  gi|121638585|ref|YP_978809.1| 284 LDQIGKLFGLSRERVRQIER 303
                                    56789999********9855 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   2.2e-25   7.9e-22       1      70 [.      90     159 ..      90     160 .. 0.97
   2 ?   -2.9   0.0       1.7   6.1e+03       8      27 ..     176     195 ..     173     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2.2e-25
                                    HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 
                                    l+e++l+lv++la+r++g+g    Dl+Qe++l+l+ra+e+fd ++g++fs+++++++r+a+ + + +++r
  gi|121638585|ref|YP_978809.1|  90 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSR 159
                                    789************************************************************9999988 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                    HHHHHHHHCT-THHHHHHHH CS
                     Sigma70_r2   8 lvkrlarrllgsgadaeDlv 27 
                                    ++kr +++ lg+ a+ e+l+
  gi|121638585|ref|YP_978809.1| 176 RIKREMHQHLGREATDEELA 195
                                    66777777777777777776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   5.2e+03      10      23 ..      96     112 ..      91     114 .. 0.63
   2 ?   -0.2   0.0       0.2   7.3e+02      18      34 ..     186     202 ..     178     210 .. 0.82
   3 !   68.3   0.8   7.9e-23   2.8e-19       1      50 []     258     311 ..     258     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                                    HHHHHHHH...TTT--H CS
                     Sigma70_r4  10 revlelrf...geglTl 23 
                                    r v++l     g+g++l
  gi|121638585|ref|YP_978809.1|  96 RLVVSLAKrytGRGMPL 112
                                    66776666547777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.2
                                    TTT--HHHHHHHHTS-H CS
                     Sigma70_r4  18 geglTleEIgerlgiSr 34 
                                    g++ T eE++++ gi+ 
  gi|121638585|ref|YP_978809.1| 186 GREATDEELAAESGIPI 202
                                    789999*******9985 PP

  == domain 3  score: 68.3 bits;  conditional E-value: 7.9e-23
                                    HHHHS-HHHHHHHHHHH....TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrf....geglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                                    +La+L+ere +v++lrf    g+++Tl +Ig+ +g+SrerVrqie++ + kLR+
  gi|121638585|ref|YP_978809.1| 258 VLATLDEREHQVIRLRFglddGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRH 311
                                    59***************************************************7 PP

>> Sigma70_r1_2  Sigma-70 factor, region 1.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   2.2e-15   7.9e-12       1      34 []      25      58 ..      25      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.2e-15
                                   HHHHHHHHHHHHSX--THHHHHHHHHHHHCCHHH CS
                   Sigma70_r1_2  1 DpvrlYLrEIGriPLLtaeEEveLAkrieaGdea 34
                                   D vr YL+ IG++ LL+a+ EveLAkrieaG++a
  gi|121638585|ref|YP_978809.1| 25 DLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYA 58
                                   89*****************************975 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0015       5.3      33      58 ..     186     211 ..     169     216 .. 0.87
   2 !    7.5   0.0    0.0011         4      30      55 ..     276     301 ..     254     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                         HTH_15  33 GepVtveeLAaatgrsveevrqaLaa 58 
                                    G+  t eeLAa+ g +++++++ L+ 
  gi|121638585|ref|YP_978809.1| 186 GREATDEELAAESGIPIDKINDLLEH 211
                                    777899****************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                         HTH_15  30 LakGepVtveeLAaatgrsveevrqa 55 
                                    L +G+p t++++ +  g s e+vrq+
  gi|121638585|ref|YP_978809.1| 276 LDDGQPRTLDQIGKLFGLSRERVRQI 301
                                    889*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2541.34
//
Query:       gi|121638586|ref|YP_978810.1|  [L=230]
Description: Iron-dependent repressor and activator ideR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-29  102.1   0.0    2.7e-29  101.0   0.0    1.6  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
      1e-21   76.9   0.1    3.7e-21   75.1   0.0    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    2.2e-09   37.4   2.3    2.3e-09   37.4   0.3    2.1  2  FeoA            FeoA domain
    1.8e-05   25.2   1.0    0.00029   21.2   0.3    2.6  3  HTH_27          Winged helix DNA-binding domain
    6.7e-05   22.7   0.5    0.00027   20.8   0.1    2.2  3  MarR_2          MarR family
     0.0002   20.8   0.1    0.00092   18.7   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0013   18.6   0.2      0.011   15.7   0.2    2.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.005   16.9   0.1      0.012   15.7   0.1    1.7  1  HemN_C          HemN C-terminal domain
     0.0052   16.7   0.0      0.014   15.3   0.0    1.7  2  MarR            MarR family
  ------ inclusion threshold ------
      0.039   13.9   0.2       0.14   12.2   0.2    2.0  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.046   13.8   0.1       0.12   12.4   0.1    1.8  1  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   1.7e-32   2.7e-29       1      69 [.      65     133 ..      65     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.7e-32
                                    -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                  Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                    TekGr lA  ++r+hrl+er+Lvdv+g++wee+h eA+r+Eh++se++++rl++ l++p+++P g+pip
  gi|121638586|ref|YP_978810.1|  65 TEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIP 133
                                    9*******************************************************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.3e-24   3.7e-21       1      60 []       3      62 ..       3      62 .. 0.98
   2 ?   -1.5   0.0       1.9   3.1e+03      22      34 ..      75      87 ..      73      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.3e-24
                                   X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                 Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                   +Lv++tE+YL+tIY+l+ee++ + ++++aerL++s+++Vs++++++e+dG++ ++++++l
  gi|121638586|ref|YP_978810.1|  3 ELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHL 62
                                   599*******************************************************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                   SB-HHHHHHHHTS CS
                 Fe_dep_repress 22 vvktkdlaerLnv 34
                                   v ++ +laerL v
  gi|121638586|ref|YP_978810.1| 75 VMRKHRLAERLLV 87
                                   678899****976 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.9   4.7e+03       3      28 ..      62      85 ..      60      89 .. 0.62
   2 !   37.4   0.3   1.4e-12   2.3e-09       1      73 [.     152     228 ..     152     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.9
                                   GGG--TT-EEEEEEE-TT.SSHHHHH CS
                           FeoA  3 LsdlkeGergeiarisdedpellrrL 28
                                   L+  ++G +  ia ++++  +l+ rL
  gi|121638586|ref|YP_978810.1| 62 LELTEKGRALAIAVMRKH--RLAERL 85
                                   566667777777777765..455554 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 1.4e-12
                                    EEGGG--TT..-EEEEEEE-T...T.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                           FeoA   1 vpLsdlkeG..ergeiarisd...edpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                    v+L++l+ G   +++++++ +    d +l +rL++ G+vp+ar++v    p+gg ++v  g ++v L+ e+A+a+ Ve
  gi|121638586|ref|YP_978810.1| 152 VRLTELPAGspVAVVVRQLTEhvqGDIDLITRLKDAGVVPNARVTVE-TTPGGGVTIVIPGHENVTLPHEMAHAVKVE 228
                                    57999999965566777888899999*********************.7999999999999999*************8 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   1.8e-07   0.00029       7      68 .]      10      68 ..       8      68 .. 0.90
   2 ?   -2.7   0.0       5.3   8.7e+03      43      43 ..     136     136 ..     108     158 .. 0.53
   3 ?    1.8   0.0      0.21   3.4e+02      37      68 .]     179     203 ..     135     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-07
                         HTH_27  7 lvLhlir..hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   ++L++i+  ++++   l a++++rl+ +  ++s  ++++++ GL+      +  ++++++lT+kG
  gi|121638586|ref|YP_978810.1| 10 MYLRTIYdlEEEGVTPLrARIAERLDQSGPTVSQTVSRMERDGLL------RVAGDRHLELTEKG 68
                                   679999998888888889***************************......556668*******9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                         HTH_27  43 t 43 
                                    +
  gi|121638586|ref|YP_978810.1| 136 V 136
                                    3 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.21
                         HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                      + +L  +G+v       +  +++v+ T+ G
  gi|121638586|ref|YP_978810.1| 179 DLITRLKDAGVV-------PNARVTVETTPGG 203
                                    344555555555.......2334777777766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.6e-07   0.00027      25      54 ..      28      57 ..      10      62 .. 0.85
   2 ?   -3.7   0.0         7   1.1e+04      26      34 ..      80      88 ..      75      88 .. 0.71
   3 ?   -1.9   0.0       1.9   3.1e+03      41      52 ..     180     196 ..     179     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                   HHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 25 gelarrlglsksavsrilkrLvaaGLverr 54
                                   + +a+rl+ s ++vs+++ r+++ GL++  
  gi|121638586|ref|YP_978810.1| 28 ARIAERLDQSGPTVSQTVSRMERDGLLRVA 57
                                   67************************9754 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7
                                   HHHHHHTSS CS
                         MarR_2 26 elarrlgls 34
                                    la+rl ++
  gi|121638586|ref|YP_978810.1| 80 RLAERLLVD 88
                                   578888775 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                                    HHHHHHHTTSE.....E CS
                         MarR_2  41 ilkrLvaaGLv.....e 52 
                                    ++ rL +aG v     +
  gi|121638586|ref|YP_978810.1| 180 LITRLKDAGVVpnarvT 196
                                    57899999988665541 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.7e-07   0.00092      22      48 .]      29      55 ..      27      55 .. 0.94
   2 ?   -2.0   0.0       1.7   2.8e+03      38      47 ..     181     190 ..     180     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.7e-07
                         HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                    +Aerl+ S +tv++ + r+e++Gl++
  gi|121638586|ref|YP_978810.1| 29 RIAERLDQSGPTVSQTVSRMERDGLLR 55
                                   69**********************975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                         HTH_24  38 lkrLeeeGlI 47 
                                    + rL+++G++
  gi|121638586|ref|YP_978810.1| 181 ITRLKDAGVV 190
                                    679*****97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   6.9e-06     0.011      24      59 ..      27      64 ..      11      69 .. 0.81
   2 ?   -1.0   0.0       1.1   1.8e+03      42      57 ..     181     195 ..     179     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EEEEE CS
                      HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglis.rg.rriri 59
                                   ++ +A++l  +  tvs++ s+++r+gl++  g r++++
  gi|121638586|ref|YP_978810.1| 27 RARIAERLDQSGPTVSQTVSRMERDGLLRvAGdRHLEL 64
                                   788**************************645343665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                    HHHHHHTTSEEETEEE CS
                      HTH_Crp_2  42 lseLkreglisrgrri 57 
                                    +++Lk++g++ + r +
  gi|121638586|ref|YP_978810.1| 181 ITRLKDAGVVPNAR-V 195
                                    799*****997544.5 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   7.2e-06     0.012      25      65 ..      29      69 ..      27      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.2e-06
                         HemN_C 25 afeqrfgldleellaaaleklqeqGLLeldg.grlrltprGr 65
                                   ++++r  ++  +++ +++ +++++GLL  +g ++l lt++Gr
  gi|121638586|ref|YP_978810.1| 29 RIAERLDQS-GPTVSQTVSRMERDGLLRVAGdRHLELTEKGR 69
                                   678888888.889999**************999********9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.7e-06     0.014       8      48 ..      11      55 ..       7      57 .. 0.90
   2 ?   -3.7   0.0       7.2   1.2e+04      45      52 ..     179     186 ..     177     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.7e-06
                                   HHHHHHHSTTEEHH....HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  8 iLrilyeqgplsvs....eLakklgvskstvtrvldrLekkGlie 48
                                    Lr++y+ ++  v+     +a++l  s +tv+ ++ r+e++Gl++
  gi|121638586|ref|YP_978810.1| 11 YLRTIYDLEEEGVTplraRIAERLDQSGPTVSQTVSRMERDGLLR 55
                                   688888888888888889*************************97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.2
                                    TSEEEEEE CS
                           MarR  45 GlieRsks 52 
                                    +li+R k+
  gi|121638586|ref|YP_978810.1| 179 DLITRLKD 186
                                    57888776 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   8.4e-05      0.14      20      60 .]      31      69 ..      27      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.4e-05
                                   HHHHTS-HHHHHHHHHHHHHHHTS-SEEESS.SEEEE-HHHH CS
                          HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeRtg.rglrLTeaGe 60
                                   Ae+L  s p+vs+ ++r+E+     L+   g r+l+LTe G+
  gi|121638586|ref|YP_978810.1| 31 AERLDQSGPTVSQTVSRMERDG---LLRVAGdRHLELTEKGR 69
                                   9******************964...44433315688888886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.6e-05      0.12      29      59 ..      29      59 ..      18      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-05
                                   HHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvre 59
                                    +aerld s  t+s+ +  +e+ gL++v + 
  gi|121638586|ref|YP_978810.1| 29 RIAERLDQSGPTVSQTVSRMERDGLLRVAGD 59
                                   59*************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1506.90
//
Query:       gi|121638587|ref|YP_978811.1|  [L=352]
Description: hypothetical protein BCG_2725c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-85  287.6  34.4    2.4e-85  287.4  34.4    1.0  1  DUF4192   Domain of unknown function (DUF4192)


Domain annotation for each model (and alignments):
>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.4  34.4   1.3e-89   2.4e-85       1     319 []      13     321 ..      13     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 287.4 bits;  conditional E-value: 1.3e-89
                        DUF4192   1 PgeLlaalPallGFhPedSvVlvaldggrgrlgpvlRvDlpraeagleavardlaellaregadavvavvvddr...gqd 77 
                                    P++L+aalPa+lGF+Pe+S+Vlv l  g  +lg v+R+Dl ++   l++ +++lael+a++++ a++av+vd++   +++
  gi|121638587|ref|YP_978811.1|  13 PATLIAALPAILGFVPEKSLVLVSLAAG--ELGSVMRADLCDE---LADRVGHLAELVAAANPAAAIAVIVDANgaqCPR 87 
                                    99************************99..***********99...6789*********************999866332 PP

                        DUF4192  78 ...rvrplvdalrealaaagvpvaaalvvseiaaggrwwsylcccpeeGtvpdpaasplaaaavlaGrvvegsReelear 154
                                       ++r+l++al++al+++++ + aa+vv+++aaggrw++++ +c+++G+++dp+aspla aavl+Gr+++++R++l+a+
  gi|121638587|ref|YP_978811.1|  88 cneEYRQLCAALAAALSQRDIVLWAAHVVDRVAAGGRWHCVD-GCGCSGVIDDPSASPLAMAAVLDGRQLYPRRSDLQAV 166
                                    788***************************************.************************************* PP

                        DUF4192 155 lapvegaaaraaqrraaeraaaaleralarprdaerrsdpaevrraaleavraalarvaagaglsdaeeaarlavaLtdv 234
                                    +a  + ++       + +++a al  ++a+ r+ ++r+d+    r+++e ++aa arva+g++lsd  e+arl++aL d 
  gi|121638587|ref|YP_978811.1| 167 IAV-DDPV-------RSAELAVALGHQAAD-REIAHRADSVGCSRQDVENALAAAARVADGQSLSDT-ELARLGCALGDA 236
                                    *95.4443.......333444445544443.23344467899*************************.************ PP

                        DUF4192 235 rvRDaalalalgeeaaaaerLwlalarrlpgplrAaalaLlAvvawarGdgalAgvaLeaAleadPghslakLLlqalna 314
                                    rvRD+++ala+ge+a aae+Lw+ lar lp+p+r +al+LlA++a+arGdg+lAgv+L+aAl ++Pgh++a +L++al++
  gi|121638587|ref|YP_978811.1| 237 RVRDMLYALAVGENAGAAESLWALLARVLPEPWRVEALVLLAFSAYARGDGPLAGVSLQAALCCEPGHRMAGMLDTALQS 316
                                    ******************************************************************************** PP

                        DUF4192 315 GlpPe 319
                                    Gl+Pe
  gi|121638587|ref|YP_978811.1| 317 GLRPE 321
                                    ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.19s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2732.37
//
Query:       gi|121638588|ref|YP_978812.1|  [L=468]
Description: soluble pyridine nucleotide transhydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-56  191.7   3.2      2e-56  191.4   3.2    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.1e-27   93.7   0.1    2.1e-25   89.1   0.0    2.6  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    6.2e-22   77.9   8.8    1.1e-18   67.6   0.4    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      1e-11   44.7   3.8    5.1e-08   32.5   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-11   43.9   5.7    6.8e-11   42.2   0.7    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    1.1e-08   34.6   4.3      6e-05   22.3   2.3    3.0  3  GIDA            Glucose inhibited division protein A
    2.5e-07   30.2   1.8    0.00069   19.0   0.1    2.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    5.3e-07   29.8   2.5     0.0039   17.4   0.3    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.4e-06   27.3   7.4     0.0034   16.2   1.6    3.6  4  HI0933_like     HI0933-like protein
    2.4e-06   27.4  10.1      0.058   13.0   0.1    3.4  3  DAO             FAD dependent oxidoreductase
    3.7e-05   23.0  12.5    0.00014   21.1   3.4    3.3  4  FAD_binding_2   FAD binding domain
    0.00043   19.6   6.2       0.21   10.8   0.5    3.2  4  FAD_binding_3   FAD binding domain
    0.00061   19.1   5.3       0.03   13.6   1.2    2.6  2  Thi4            Thi4 family
    0.00065   19.6   5.4     0.0012   18.8   0.1    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0026   18.3   0.2      0.038   14.5   0.1    2.4  2  XdhC_C          XdhC Rossmann domain
      0.003   16.8   0.1      0.016   14.4   0.0    2.1  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0042   16.5   0.0     0.0094   15.3   0.0    1.5  1  ThiF            ThiF family
  ------ inclusion threshold ------
      0.012   15.0   0.3      0.046   13.1   0.0    2.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.018   15.3   0.8       0.11   12.8   0.0    2.4  2  TrkA_N          TrkA-N domain
       0.02   14.5   4.6      0.031   13.8   0.3    2.8  4  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.053   14.0   0.6       0.39   11.2   0.1    2.3  2  NAD_binding_7   Putative NAD(P)-binding
       0.23   10.5   5.8        3.8    6.5   0.8    3.0  3  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   3.2   2.5e-59     2e-56       1     294 []       4     325 ..       4     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 2.5e-59
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................... 57 
                                    +d+vviG+Gp+G +aa+  a+ g  v++ve    l+g c+n g ++sk+l+++      +                    
  gi|121638588|ref|YP_978812.1|   4 YDIVVIGSGPGGQKAAIASAKLGKSVAIVErgrmLGGVCVNTGTIPSKTLREAVLYLTGMNqrelygasyrvkdritpad 83 
                                    69***************************999********************9999998889999*************** PP

                                    ......HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC......TCEEEEEESEEEE---EEE-BCTCTTC.TTBEE CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ......evvkklnqgielllgeevvkidpgkkkvklekkke......gdeekiaydklvlAtGssprdlgipGvaenvgk 125
                                           v+ k    +++ l ++ v+++ g++++ + ++         ++++++ d++++AtG +p ++   Gv    ++
  gi|121638588|ref|YP_978812.1|  84 llartqHVIGKEVDVVRNQLMRNRVDLIVGHGRFIDPHTILvedqarREKTTVTGDYIIIATGTRPARP--SGV---EFD 158
                                    ****98444444455777777788888888888888776657788888999******************..888...444 PP

                                    CCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 126 lvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgts 205
                                      r lds+  l lk lp ++vvvG+G+iG+E+A+++a lg +vt+ve rd++l  +d+e+ +al+ +l++  v++++g++
  gi|121638588|ref|YP_978812.1| 159 EERVLDSDGILDLKSLPSSMVVVGAGVIGIEYASMFAALGTKVTVVEKRDNMLDFCDPEVVEALKFHLRDLAVTFRFGEE 238
                                    5689**************************************************************************** PP

                                    EEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 206 vkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggp 284
                                    v+++d  +    ++l +g++i+a++v++++G++ +t+ l+  ++gle++ rg+i vd++ +t+v++iya+GDv+   g p
  gi|121638588|ref|YP_978812.1| 239 VTAVDVGSAGTVTTLASGKQIPAETVMYSAGRQGQTDHLDlHNAGLEVQGRGRIFVDDRFQTKVDHIYAVGDVI---GFP 315
                                    **999888755599************************************************************...*** PP

                                    --HHHHHHHH CS
                                    xxxxxxxxxx RF
                    Pyr_redox_2 285 elaqaAvqqG 294
                                    +la ++++qG
  gi|121638588|ref|YP_978812.1| 316 ALAATSMEQG 325
                                    *****99998 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.36     3e+02      57      81 ..     175     199 ..     126     218 .. 0.83
   2 !   89.1   0.0   2.6e-28   2.1e-25       2     109 ..     345     452 ..     344     453 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                                    TTTTBEEEEEEECTTHHHHHHHHHH CS
                  Pyr_redox_dim  57 aktgkvlGahivGpgageliqelav 81 
                                     ++  v+Ga ++G + ++++++l +
  gi|121638588|ref|YP_978812.1| 175 PSSMVVVGAGVIGIEYASMFAALGT 199
                                    56788*************9998765 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 2.6e-28
                                    EEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                  Pyr_redox_dim   2 ptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                    p  +++ pev++vG te e+++  i+++vg +++++++r ++ +++ g++Kl++  ++ k+lG+hi+G +a+e+++  ++
  gi|121638588|ref|YP_978812.1| 345 PIGIYSIPEVSYVGATEVELTKSSIPYEVGVARYRELARGQIAGDSYGMLKLLVSTEDLKLLGVHIFGTSATEMVHIGQA 424
                                    6789**************************************************************************** PP

                                    HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                  Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                    ++ +g +ve l d ++ +Pt+sea+k+a
  gi|121638588|ref|YP_978812.1| 425 VMGCGGSVEYLVDAVFNYPTFSEAYKNA 452
                                    *************************987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   3.1e-05     0.025       2      35 ..       6      39 ..       5      47 .. 0.93
   2 !   67.6   0.4   1.3e-21   1.1e-18       1      74 [.     177     251 ..     177     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +vv+G+G  g  +A a a+lgk+V +ver+ +l 
  gi|121638588|ref|YP_978812.1|  6 IVVIGSGPGGQKAAIASAKLGKSVAIVERGRMLG 39
                                   8****************************98775 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 1.3e-21
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ve 74 
                                    ++vvvG+G+ig+E+A+++a+lg kVtvve +d++l  +D+e+ ++l+ +l+++ ++++++++v++++  + g v+
  gi|121638588|ref|YP_978812.1| 177 SMVVVGAGVIGIEYASMFAALGTKVTVVEKRDNMLDFCDPEVVEALKFHLRDLAVTFRFGEEVTAVDVGSAGtVT 251
                                    58*****************************************************************88888665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   2.3   0.00016      0.13       1      32 [.       7      37 ..       7      41 .. 0.93
   2 !   32.5   0.0   6.2e-11   5.1e-08     119     305 .]     132     309 ..     128     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                   ++iG GP G +aai+  k+g  ++ i+E+g++
  gi|121638588|ref|YP_978812.1|  7 VVIGSGPGGQKAAIASAKLGK-SVAIVERGRM 37
                                   79******************9.8******975 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 6.2e-11
                    Pyr_redox_3 119 sketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                    +k t++ +++iiAtG     +  ++++ e+ v  +  + ++ k     +vV+G++  ++++A  +++ g +Vtvv ++++
  gi|121638588|ref|YP_978812.1| 132 EKTTVTGDYIIIATGT-RPARPSGVEFDEERVLDSDGILDL-KSLPSSMVVVGAGVIGIEYASMFAALGTKVTVVEKRDN 209
                                    6789999********9.555556899999777777788888.55578999***************************986 PP

                    Pyr_redox_3 199 iekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsf..lkk 276
                                    + +          p + + l+  ++  ++++ f +ev++++  +     + ++gk++ + + v++  G + +++   l++
  gi|121638588|ref|YP_978812.1| 210 MLDF-------CDPEVVEALKFHLRDLAVTFRFGEEVTAVDVGSAGTVTTLASGKQIPA-ETVMYSAGRQGQTDHldLHN 281
                                    6655.......58999999999999888***************999999999*999987.66688899887776622556 PP

                    Pyr_redox_3 277 slfeldedgrpvlteeteetnvpglflaG 305
                                    +++e +  gr+ +++   +t+v+ ++ +G
  gi|121638588|ref|YP_978812.1| 282 AGLEVQGRGRIFVDD-RFQTKVDHIYAVG 309
                                    999998888888875.6889******998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.7   8.3e-14   6.8e-11       1      69 [.       5      74 ..       5     147 .. 0.61
   2 ?    4.2   0.4     0.028        23       3      32 ..     179     208 ..     177     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 8.3e-14
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiareflerlrq 69
                                   D+vV+G+gp+G  AAia+a+ G++v++ve+ ++lGG   + +  +  + + +   +++   re++ +  +
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIASAKLGKSVAIVERGRMLGGVCVNTGTIPSKTLREAVlYLTGMNQRELYGASYR 74
                                   9**************************************9998887776655544444445555555533 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                   FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                    vVvG+g+ G+  A   a  G kv +ve+r+
  gi|121638588|ref|YP_978812.1| 179 VVVGAGVIGIEYASMFAALGTKVTVVEKRD 208
                                    9**************************986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   2.3   7.4e-08     6e-05       1     150 [.       5     147 ..       5     161 .. 0.78
   2 !   10.4   0.0   0.00031      0.25       2      42 ..     178     216 ..     177     228 .. 0.85
   3 ?   -1.1   0.0      0.95   7.7e+02     349     384 ..     297     332 ..     293     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.4e-08
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEESTT CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilNrs 80 
                                    d++ViG G  G  AA+a+a+lG +v+++ ++  +++  +C ++ g i + +l + +  l g+  +    a+   r+   +
  gi|121638588|ref|YP_978812.1|   5 DIVVIGSGPGGQKAAIASAKLGKSVAIV-ERGRMLGG-VCVNT-GTIPSKTLREAVLYLTGMNQRELYGASY--RVK-DR 78 
                                    79*************************9.55555554.48775.5555556777777776665554443333..221.23 PP

                                    S-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA  81 kGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                      pa    r+q    +    v+++l + + +++i +    +++++  v+    ++++t++ + ++iatGt
  gi|121638588|ref|YP_978812.1|  79 ITPADLLARTQHVIGKEVDVVRNQLMR-NRVDLIVGHGRFIDPHTILVEDQARREKTTVTGDYIIIATGT 147
                                    349999999999999999999999998.9999*****9999998888888999999999999*******9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00031
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSS CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnp 42 
                                    ++V+G+G  G+e A   a lG kv+ + +k d+++   C p
  gi|121638588|ref|YP_978812.1| 178 MVVVGAGVIGIEYASMFAALGTKVTVV-EKRDNMLDF-CDP 216
                                    69***********************99.777776665.555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.95
                                    TSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHH CS
                           GIDA 349 tLetkkvkgLflAGqinGteGYeEaaa..qGllAGina 384
                                    +++tk v+++++ G++ G     +a++  qG lA+  a
  gi|121638588|ref|YP_978812.1| 297 RFQTK-VDHIYAVGDVIGFPAL-AATSmeQGRLAAYHA 332
                                    67888.9***********9743.333345888888766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00043      0.35      30      61 ..       5      36 ..       1     105 [. 0.67
   2 !   19.0   0.1   8.4e-07   0.00069      28      66 ..     175     213 ..     164     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                    ++viG G  G++A+ ++++lg +V +++   
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIASAKLGKSVAIVERGR 36
                                   689***********************998754 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 8.4e-07
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66 
                                    p+ ++v+G+Gv G++ +++ ++lg kVtv+++r + l  
  gi|121638588|ref|YP_978812.1| 175 PSSMVVVGAGVIGIEYASMFAALGTKVTVVEKRDNMLDF 213
                                    7889****************************9988765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   4.8e-06    0.0039       1      35 [.       8      42 ..       8      73 .. 0.87
   2 !   11.8   0.1   0.00026      0.21       1      30 [.     180     209 ..     180     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                   ++G+G +G  aA + ak g++v ++e+++ lGG +
  gi|121638588|ref|YP_978812.1|  8 VIGSGPGGQKAAIASAKLGKSVAIVERGRMLGGVC 42
                                   8*******************************977 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00026
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    +vGaG+ G  +A+  a  g +v+++ekrd 
  gi|121638588|ref|YP_978812.1| 180 VVGAGVIGIEYASMFAALGTKVTVVEKRDN 209
                                    8**************************985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   4.1e-06    0.0034       1      36 [.       4      39 ..       4      47 .. 0.91
   2 ?   -2.4   0.0       1.8   1.5e+03     149     165 ..     132     148 ..     122     158 .. 0.83
   3 !    6.9   0.3    0.0027       2.2       2      35 ..     177     210 ..     176     212 .. 0.91
   4 !    5.3   0.0     0.008       6.5     110     163 ..     217     269 ..     213     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +d++viG G+ G  aAi+ ak gk+V+++e+++ lg
  gi|121638588|ref|YP_978812.1|  4 YDIVVIGSGPGGQKAAIASAKLGKSVAIVERGRMLG 39
                                   589****************************99887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                    TTEEEEESEEEE----S CS
                    HI0933_like 149 seeeleadklvlAtGGl 165
                                    ++++++ d++++AtG  
  gi|121638588|ref|YP_978812.1| 132 EKTTVTGDYIIIATGTR 148
                                    678999********975 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0027
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                    +++v+G+G  G+  A   a+ g +V+++ek +++
  gi|121638588|ref|YP_978812.1| 177 SMVVVGAGVIGIEYASMFAALGTKVTVVEKRDNM 210
                                    579**************************98765 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.008
                                    HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE--- CS
                    HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtG 163
                                    ++v+al+ +l++  v++r  +ev++v+  + g  +v+t  s++++ a++++ + G
  gi|121638588|ref|YP_978812.1| 217 EVVEALKFHLRDLAVTFRFGEEVTAVDVGSAG--TVTTlASGKQIPAETVMYSAG 269
                                    79************************887777..444446999999999988777 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   2.3    0.0016       1.3       1      35 [.       5      40 ..       5      77 .. 0.87
   2 !   13.0   0.1   7.1e-05     0.058       3      30 ..     179     208 ..     177     210 .. 0.93
   3 !    9.7   0.0    0.0007      0.57     145     232 ..     215     300 ..     212     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                   d+v+iG+G  G  +A + a+ g  V+++e+g+ +g g
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIASAKLGksVAIVERGRMLG-G 40
                                   9******************9999********9988.5 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.1e-05
                                    EEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO   3 viiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                    v++G+G+iG+  A   a+ g  Vt++ek+d
  gi|121638588|ref|YP_978812.1| 179 VVVGAGVIGIEYASMFAALGtkVTVVEKRD 208
                                    9***************99999*******95 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0007
                                    HHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEEEEEEEEEE--GGGHH..HHHTT.CTTTSEEEE CS
                            DAO 145 pakltaalaraaealGveilegtevtgleeed.gkvwgverttp.gendaadavVnaaGawsd..llgll.keldlpisp 219
                                    + +++ al   +++l+v++++g+evt+++  + g v+++    + g +  a++v  +aG + +   l+l+   l    ++
  gi|121638588|ref|YP_978812.1| 215 DPEVVEALKFHLRDLAVTFRFGEEVTAVDVGSaGTVTTL----AsGKQIPAETVMYSAGRQGQtdHLDLHnAGL--E-VQ 287
                                    56689999999*****************66334555555....3376656799******664332333333333..4.55 PP

                                    EEEEEEEEEECCT CS
                            DAO 220 vrgqvlvlkplse 232
                                     rg ++v ++ + 
  gi|121638588|ref|YP_978812.1| 288 GRGRIFVDDRFQT 300
                                    5776666655444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.4   1.7e-07   0.00014       1      36 [.       5      40 ..       5      46 .. 0.92
   2 ?   -2.0   0.0       1.7   1.4e+03     166     204 ..     109     150 ..      75     159 .. 0.75
   3 !    6.3   0.1    0.0054       4.4       2      33 ..     178     209 ..     177     213 .. 0.93
   4 ?   -0.6   0.0      0.68   5.5e+02     374     402 ..     282     312 ..     249     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   D++ViGsG +G  AA++ a+ G++va+ve +   gg
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIASAKLGKSVAIVERGRMLGG 40
                                   99***************************9987776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                    EEEECTT...EEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 166 eLivedg...rvtGavvenpesgrevrirakavvlatgGfgr 204
                                    +Liv  g   + +++ ve+++  ++++++ + +++atg  ++
  gi|121638588|ref|YP_978812.1| 109 DLIVGHGrfiDPHTILVEDQARREKTTVTGDYIIIATGTRPA 150
                                    566655555556788888778888888888899999998885 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0054
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                     +V+G+G+ G   A   a  G kv+vvek ++
  gi|121638588|ref|YP_978812.1| 178 MVVVGAGVIGIEYASMFAALGTKVTVVEKRDN 209
                                    59**************************9875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.68
                                    -EEEBETTSBE..STTEEESSBTEEE-STCE CS
                  FAD_binding_2 374 gGvetdengrv..ldadgqpipGLYAaGeva 402
                                    +G+e+  +gr   +d+ ++ ++  YA+G v+
  gi|121638588|ref|YP_978812.1| 282 AGLEVQGRGRIfvDDRFQTKVDHIYAVGDVI 312
                                    6888888888877888899*********998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.5   0.00026      0.21       1      33 [.       3      35 ..       3      39 .. 0.93
   2 ?   -0.5   0.0      0.68   5.6e+02     142     166 ..     125     149 ..     119     170 .. 0.79
   3 !    9.8   0.2   0.00051      0.42       5      35 ..     179     209 ..     176     220 .. 0.92
   4 ?   -2.3   0.0       2.4     2e+03     105     138 ..     216     249 ..     208     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                   EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   e+d++++G+Gp G  +a   ++ G +v +ve+ 
  gi|121638588|ref|YP_978812.1|  3 EYDIVVIGSGPGGQKAAIASAKLGKSVAIVERG 35
                                   5799***************************95 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                    EEECCTTEEEEEEEEEEEE--GTT- CS
                  FAD_binding_3 142 vrdketgeeetvrakYlvGaDGgrS 166
                                    v d++  e++tv+ +Y++ a G r 
  gi|121638588|ref|YP_978812.1| 125 VEDQARREKTTVTGDYIIIATGTRP 149
                                    4577888999*********999885 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00051
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                    ++VGaG  G+  a++ +  G +v++vekr++
  gi|121638588|ref|YP_978812.1| 179 VVVGAGVIGIEYASMFAALGTKVTVVEKRDN 209
                                    79**************************986 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.4
                                    HHHHHHHHHHHHHHTEEETCSEEEECCEECCCCC CS
                  FAD_binding_3 105 teleriLvehaeerglqvrfktevesleqdeegv 138
                                    +e+  +L  h++  ++++rf++ev+++     g 
  gi|121638588|ref|YP_978812.1| 216 PEVVEALKFHLRDLAVTFRFGEEVTAVDVGSAGT 249
                                    677788899999999********99987666554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.2   3.7e-05      0.03      17      66 ..       3      51 ..       1      90 [. 0.84
   2 !    6.6   0.2     0.005         4      18      50 ..     176     207 ..     167     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSE CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsa 66
                                   e D+v++G+G+ G  aa   ak  +  vai+er   +GG     G + s+
  gi|121638588|ref|YP_978812.1|  3 EYDIVVIGSGPGGQKAAIASAKL-GKSVAIVERGRMLGGVCVNTGTIPSK 51
                                   78***************999999.99********9999988888776665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.005
                                    EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                           Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailers 50 
                                    s +v+vGaG  G+  a ++a   + kv+++e++
  gi|121638588|ref|YP_978812.1| 176 SSMVVVGAGVIGIEYASMFAAL-GTKVTVVEKR 207
                                    679*****************99.*******986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.4      0.15   1.2e+02       2      30 ..       6      34 ..       5      47 .. 0.93
   2 !   18.8   0.1   1.4e-06    0.0012       3      44 ..     179     220 ..     177     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                   + viG+G  G++ a + a+ g +V +v++
  gi|121638588|ref|YP_978812.1|  6 IVVIGSGPGGQKAAIASAKLGKSVAIVER 34
                                   78***********************9986 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.4e-06
                                    EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                     v+GaG++G + a++fa+ g +V++v+ +++ l+ +  ++ +
  gi|121638588|ref|YP_978812.1| 179 VVVGAGVIGIEYASMFAALGTKVTVVEKRDNMLDFCDPEVVE 220
                                    69**************************99999877665555 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.56   4.5e+02       2      31 ..       7      36 ..       6     107 .. 0.83
   2 !   14.5   0.1   4.6e-05     0.038       1      34 [.     178     211 ..     178     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.56
                                   EEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                         XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpre 31
                                   v++G g+ +q+ a   a+lg +v +v+  +
  gi|121638588|ref|YP_978812.1|  7 VVIGSGPGGQKAAIASAKLGKSVAIVERGR 36
                                   899*******************99998755 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.6e-05
                                    EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG CS
                         XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa 34 
                                    +v++Gag ++ + a++ aalg +vtvv++r+++ 
  gi|121638588|ref|YP_978812.1| 178 MVVVGAGVIGIEYASMFAALGTKVTVVEKRDNML 211
                                    69****************************9765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.85   6.9e+02       3      22 ..       4      23 ..       2      34 .. 0.59
   2 !   14.4   0.0     2e-05     0.016     138     208 ..     126     192 ..     109     220 .. 0.80
   3 ?   -4.0   0.0       7.5   6.1e+03     111     128 ..     231     248 ..     226     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.85
                    K_oxygenase  3 lDligiGiGpsnLsLaille 22
                                   +D++ iG Gp     ai+++
  gi|121638588|ref|YP_978812.1|  4 YDIVVIGSGPGGQKAAIASA 23
                                   66666666665555555444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
                    K_oxygenase 138 kd.aegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeife 208
                                    +d a+ e+++++   +++++Gt+p+ P+ +e ++ +erv+ s+ +l  k     + +++VvG+G  + e + 
  gi|121638588|ref|YP_978812.1| 126 EDqARREKTTVTGDYIIIATGTRPARPSGVE-FD-EERVLDSDGILDLK---SLPSSMVVVGAGVIGIEYAS 192
                                    34377788999999****************9.55.49*********998...67899*******88877554 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 7.5
                    K_oxygenase 111 eqvrfgeeveevepdeee 128
                                     + rfgeev++v++ ++ 
  gi|121638588|ref|YP_978812.1| 231 VTFRFGEEVTAVDVGSAG 248
                                    567999999999887654 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05    0.0094       8      54 ..     163     220 ..     156     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHT..SEEEEE--SHHHHHHHHHHHHHTTT.........EEEEEESSB-- CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                           ThiF   8 lgedgqekLrd..skvllvGaGglGsellknLalsGvg.........kltlvDnDkie 54 
                                    l++dg   L++  s++++vGaG +G e + ++a++G +          l++ D +++e
  gi|121638588|ref|YP_978812.1| 163 LDSDGILDLKSlpSSMVVVGAGVIGIEYASMFAALGTKvtvvekrdnMLDFCDPEVVE 220
                                    556677778888899**********************999999999999999999998 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       2.3   1.9e+03      38      67 ..       5      34 ..       1      37 [. 0.83
   2 ?   13.1   0.0   5.6e-05     0.046      38      70 ..     177     209 ..     163     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydr 67
                                    + +iG G  Gq++a   +++g  v +++r
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIASAKLGKSVAIVER 34
                                   67899********99999999999888766 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-05
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                     + ++G+G IG + a +++a+g kv++++++ +
  gi|121638588|ref|YP_978812.1| 177 SMVVVGAGVIGIEYASMFAALGTKVTVVEKRDN 209
                                    6889***********************998865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.4   1.1e+03       1      29 [.       6      34 ..       6      37 .. 0.85
   2 ?   12.8   0.0   0.00013      0.11       2      49 ..     179     226 ..     178     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29
                                   i++iG G  G++ a    + g+ +v ++++
  gi|121638588|ref|YP_978812.1|  6 IVVIGSGPGGQKAAIASAKlGK-SVAIVER 34
                                   79***********999999666.5988885 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                                    EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-T CS
                         TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgda 49 
                                    +++G+G +G + a  + + g  +v+v++k+++ ++    e +e+++ + 
  gi|121638588|ref|YP_978812.1| 179 VVVGAGVIGIEYASMFAAlGT-KVTVVEKRDNMLDFCDPEVVEALKFHL 226
                                    8*****************777.6*******9999988888888777665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.33   2.7e+02       3      30 ..       6      33 ..       4      38 .. 0.92
   2 ?   -3.2   0.0       6.6   5.4e+03     116     140 ..      41      65 ..      36      75 .. 0.75
   3 ?   13.8   0.3   3.8e-05     0.031       3      37 ..     178     212 ..     176     235 .. 0.83
   4 ?   -3.0   0.0       5.6   4.6e+03      21      43 ..     234     257 ..     228     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.33
                                   EEEE--STTHHHHHHHHHHCTSEEEEE- CS
                 UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvD 30
                                   i+viG+G  G   a++ a++g+ v +v 
  gi|121638588|ref|YP_978812.1|  6 IVVIGSGPGGQKAAIASAKLGKSVAIVE 33
                                   99**********************9985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.6
                                    EEEE-S---TTHHHHCHHHHHHHHC CS
                 UDPG_MGDP_dh_N 116 vvvvkSTvpvgtaeelvkkileeas 140
                                    v v+  T+p +t +e+v  +  +++
  gi|121638588|ref|YP_978812.1|  41 VCVNTGTIPSKTLREAVLYLTGMNQ 65 
                                    6788899999999988876665555 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 3.8e-05
                                    EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHH CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvd 37 
                                    ++v+G+G +G+  a ++a++g +v++v + ++  d
  gi|121638588|ref|YP_978812.1| 178 MVVVGAGVIGIEYASMFAALGTKVTVVEKRDNMLD 212
                                    579************************98776655 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.6
                                    HCTSEEEEE-S.-HHHHHHHCTTS CS
                 UDPG_MGDP_dh_N  21 eighevigvDi.deekvdklnsgk 43 
                                    + g ev+ vD+ ++ +v +l sgk
  gi|121638588|ref|YP_978812.1| 234 RFGEEVTAVDVgSAGTVTTLASGK 257
                                    568999999993445788887775 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.1   8.7e+02       7      38 ..       3      34 ..       1      80 [. 0.81
   2 ?   11.2   0.1   0.00048      0.39       9      41 ..     177     211 ..     170     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                  NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvap 38
                                   +  ++v+G G+ +++ +   ++ g+ v +v  
  gi|121638588|ref|YP_978812.1|  3 EYDIVVIGSGPGGQKAAIASAKLGKSVAIVER 34
                                   56799******999999999999999988865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00048
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev..k 41 
                                    +++vvG+G ++ + ++ +++ g kvtvv ++    
  gi|121638588|ref|YP_978812.1| 177 SMVVVGAGVIGIEYASMFAALGTKVTVVEKRDnmL 211
                                    689*************************9984332 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8    0.0047       3.8       1      34 [.       5      36 ..       5      40 .. 0.92
   2 ?    4.0   0.1     0.027        22       2      36 ..     178     210 ..     177     214 .. 0.91
   3 ?    0.9   0.0      0.22   1.8e+02     112     161 ..     239     287 ..     221     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                   D+vviG+Gp g + A  +  ak g +v ++e + 
  gi|121638588|ref|YP_978812.1|  5 DIVVIGSGPGGQKAAIAS--AKLGKSVAIVERGR 36
                                   9**************999..**********9875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.027
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                    +vv+GaG  g+  A     a+ g kv+++e  +++
  gi|121638588|ref|YP_978812.1| 178 MVVVGAGVIGIEYASMF--AALGTKVTVVEKRDNM 210
                                    69***************..**********987765 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                  Lycopene_cycl 112 veeeea..geslvvleggrkirarlvvdarglaslkkarrlglQtfyGveve 161
                                    v+++++  + ++ +l+ g++i+a +v+ + g   ++++ +++  +  G+ev+
  gi|121638588|ref|YP_978812.1| 239 VTAVDVgsAGTVTTLASGKQIPAETVMYSAG---RQGQTDHLDLHNAGLEVQ 287
                                    3444432235677899***************...555555555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2988.45
//
Query:       gi|121638589|ref|YP_978813.1|  [L=324]
Description: hypothetical protein BCG_2727 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-47  159.8   0.1    1.1e-46  159.5   0.1    1.1  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   0.1   6.4e-51   1.1e-46       2     212 ..      44     260 ..      43     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 6.4e-51
                                    EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEE..EEE.TTT.SEEEEEEEE- CS
                           PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprl..yak.dsgsrdllvlqgre 76 
                                    ++Gf ++G++  la+ +L + l+ e v+++  d+ll+++++rp ++++ +  ++ + p+l  ya  ds ++++l+l g e
  gi|121638589|ref|YP_978813.1|  44 LEGFSDAGHAIRLAAAHLKAALDTELVASFAIDELLDYRSRRPLMTFKTDhfTHSDDPELslYALrDSIGTPFLLLAGLE 123
                                    89**********************************************************987777888*********** PP

                                    HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH..CT-CEEEEHHHHHHHHHH CS
                           PAC2  77 pilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele..eseyggivgitglLlsaa 154
                                    p+l++e+f++a+  +ae+lgv++++ Lg ++    + vphtrp  +t++++++el+++++   se +++++++ lL++++
  gi|121638589|ref|YP_978813.1| 124 PDLKWERFITAVRLLAERLGVRQTIGLGTVP----MAVPHTRPITMTAHSNNRELISDFQpwISEIQVPGSASNLLEYRM 199
                                    *******************************....*********************999657779*************** PP

                                    HHTT-EEEEEEEEEECCC...--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                           PAC2 155 kergipavgllaevphyl...pdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                    +++g+++vg++++vphyl   ++P+aa+alle ++k   l++++  L e a+e++++++e+
  gi|121638589|ref|YP_978813.1| 200 AQHGHEVVGFTVHVPHYLtqtDYPAAAQALLEQVAKTGSLQLPLAALAEAAAEVQAKIDEQ 260
                                    ******************9988************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2266.63
//
Query:       gi|121638590|ref|YP_978814.1|  [L=341]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-28   99.8   0.3    4.8e-23   82.1   0.2    2.1  2  Abhydrolase_1    alpha/beta hydrolase fold
    6.2e-26   92.4   5.4    8.9e-26   91.9   5.4    1.2  1  Abhydrolase_6    Alpha/beta hydrolase family
    5.9e-17   61.7   0.4      1e-16   61.0   0.4    1.3  1  Hydrolase_4      Serine aminopeptidase, S33
    1.1e-05   25.2   0.0       0.23   11.0   0.0    3.1  2  DLH              Dienelactone hydrolase family
    0.00037   20.3   0.0      0.064   13.0   0.0    2.3  2  Abhydrolase_5    Alpha/beta hydrolase family
    0.00055   19.8   2.2        8.4    6.1   0.1    3.2  3  Abhydrolase_2    Phospholipase/Carboxylesterase
     0.0013   18.9   0.0       0.39   10.8   0.0    2.3  2  Abhydrolase_4    TAP-like protein
     0.0019   18.1   0.0     0.0032   17.3   0.0    1.3  1  Lipase_3         Lipase (class 3)
     0.0038   16.0   0.0     0.0059   15.3   0.0    1.2  1  Ndr              Ndr family
     0.0078   16.1   0.1      0.023   14.6   0.0    1.8  2  Ser_hydrolase    Serine hydrolase
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.051   13.2   0.0    1.9  2  Esterase         Putative esterase
      0.012   14.5   0.0      0.021   13.7   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme
      0.014   15.1   0.2      0.049   13.3   0.1    1.8  2  PGAP1            PGAP1-like protein
      0.023   14.2   0.0      0.038   13.5   0.0    1.4  1  DUF900           Alpha/beta hydrolase of unknown function (DU
      0.044   12.8   0.0      0.072   12.1   0.0    1.2  1  DUF1057          Alpha/beta hydrolase of unknown function (DU
      0.047   13.8   0.0       0.07   13.2   0.0    1.2  1  Thioesterase     Thioesterase domain
      0.062   12.8   0.1        4.7    6.6   0.0    3.2  4  Peptidase_S9     Prolyl oligopeptidase family
      0.081   11.9   0.0       0.13   11.2   0.0    1.2  1  Chlorophyllase   Chlorophyllase
       0.13   11.5   0.0       0.26   10.6   0.0    1.4  1  DUF915           Alpha/beta hydrolase of unknown function (DU
       0.21   10.8   0.0        0.3   10.3   0.0    1.2  1  Hyaluronidase_1  Hyaluronidase protein (HylP)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.2   5.3e-26   4.8e-23       1     111 [.      38     145 ..      38     160 .. 0.92
   2 !   16.0   0.0   7.8e-06     0.007     206     257 .]     223     282 ..     181     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 5.3e-26
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p+++++hG++++s  w +  +   La+ +f+vi++Dl+G+g+S+++ a    dy+ a++a+ ++ +l  l+++++t+vGh
  gi|121638590|ref|YP_978814.1|  38 PAILLIHGIGDNSTTWNG--VHAKLAQ-RFTVIAPDLLGHGQSDKPRA----DYSVAAYANGMRDLLSVLDIERVTIVGH 110
                                    79****************..******9.*******************5....8*************************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESE....CSSCC CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllga....idpaa 111
                                    S+GG +a+++a ++p+ V++l+l++a     d ++
  gi|121638590|ref|YP_978814.1| 111 SLGGGVAMQFAYQFPQLVDRLILVSAggvtKDVNI 145
                                    *************************9776545554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.8e-06
                                    C.........THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 206 e.........lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                    +         l++++ p+ +i+gt+D + p ++     ++ p+++l++++++gH+ f ++p
  gi|121638590|ref|YP_978814.1| 223 QmvtmldrcyLTEAI-PVQIIWGTKDVVLPVRHAHMAHAAMPGSQLEIFEGSGHFPFHDDP 282
                                    244444445555555.***************999999999*****************9876 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   5.4   9.9e-29   8.9e-26       1     219 [.      40     287 ..      40     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 9.9e-29
                                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT....TTSEEEEEETCHHHH CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa..gggpvvlvGHSlGGal 78 
                                    +ll+HG g +++ W    ++a+la++++v+apDl GhG sd p  d++  a++a+  ++l +  +  +v +vGHSlGG +
  gi|121638590|ref|YP_978814.1|  40 ILLIHGIGDNSTTWN--GVHAKLAQRFTVIAPDLLGHGQSDKPRADYSV-AAYANGMRDLLSvlDIERVTIVGHSLGGGV 116
                                    89************9..999999***************88888888877.8886655555555579************** PP

                                    HHHHHHCC.......EE.EEES-.............----TTTS----TTHHHHHHTT-CCCCH.....CCH......S- CS
                  Abhydrolase_6  79 alaaapla.....lvvg.vlldppp...........talpagllaaalelllallallrllawl.....sre......pl 130
                                    a++    a     lv + +l+++ +                      l++   ++allrl+  l     + +      + 
  gi|121638590|ref|YP_978814.1| 117 AMQ---FAyqfpqLVDRlILVSAGGvtkdvnivfrlA---------SLPMGSEAMALLRLPLVLpavqiA-GrivgkaIG 183
                                    ***...7777788555569999944332222222221.........222222222222222222121121.123333322 PP

                                    HSCCCCHHH.CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC.............EEECTT-CHHHHCHHCCCH.... CS
                  Abhydrolase_6 131 prlfladed.adaawrarlarlaallaglgllpaaawadlpvpl.............lvlggeDplvprllerlla.... 192
                                    + ++ +d++   ++  +   + a  + g+ l+++ +w++  v++             +++g++D ++p  +++++     
  gi|121638590|ref|YP_978814.1| 184 TTSLGHDLPnVLRILDDLPEPTASAAFGRTLRAVVDWRGQMVTMldrcylteaipvqIIWGTKDVVLP--VRHAHMahaa 261
                                    22444444411222222222222222233344566666666666555554444444335468888777..4444442235 PP

                                    STTEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 193 qagarlpvvlpgaGHlphleepdevae 219
                                    ++g +l ++++g+GH+p+ ++p+++++
  gi|121638590|ref|YP_978814.1| 262 MPGSQL-EIFEGSGHFPFHDDPARFID 287
                                    588888.***************99976 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.4   1.1e-19     1e-16       6     237 ..      39     280 ..      36     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.1e-19
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrg..hvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                    +++l+HG+++ s   + + ++La++ f v+a D  GhG+s+  r+   v+ +   ++Dl ++++        ++++++Gh
  gi|121638590|ref|YP_978814.1|  39 AILLIHGIGDNSTTWNGVHAKLAQR-FTVIAPDLLGHGQSDKPRAdySVAAYANGMRDLLSVLDI-------ERVTIVGH 110
                                    699*******************976.***************666622566666666777666644.......469***** PP

                    Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikakl.......kappllkl.......llkllgkllpklqv.....snnlk 144
                                    S+GG +a++++ + p+ v++lil+++  ++ +++       +      l       +l  l  +lp +q+      + + 
  gi|121638590|ref|YP_978814.1| 111 SLGGGVAMQFAYQFPQLVDRLILVSAG-GVTKDVnivfrlaS------LpmgseamALLRLPLVLPAVQIagrivGKAIG 183
                                    ************************999.56666645555441......22222222334445555555558888877777 PP

                    Hydrolase_4 145 adslsrdpevvaayeadplvhgkitvrlllelldamkrleeraakit.......lPllllhGeaDkvvdpeasrelyerl 217
                                    ++sl +d  +v ++  d l   + ++ ++++l  ++++  + ++ ++       +P++++ G++D v + + ++ +++++
  gi|121638590|ref|YP_978814.1| 184 TTSLGHDLPNVLRIL-DDLPEPTASAAFGRTLRAVVDWRGQMVTMLDrcylteaIPVQIIWGTKDVVLPVRHAHMAHAAM 262
                                    777777766655443.44556666777777666666666666666666667789***************99999999998 PP

                    Hydrolase_4 218 gskdktlklypglyHellnE 237
                                    +    +l++++g  H  +++
  gi|121638590|ref|YP_978814.1| 263 P--GSQLEIFEGSGHFPFHD 280
                                    8..79**********99987 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00025      0.23      13     121 ..      37     126 ..      26     134 .. 0.69
   2 !    8.1   0.0    0.0019       1.7     117     194 ..     209     282 ..     205     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                            DLH  13 kpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksv 92 
                                     p+++ i+ i  +  + + + ++la+  + ++aPdl+  ++   +d++ a   +    +++  ++ ++dl   +  l   
  gi|121638590|ref|YP_978814.1|  37 GPAILLIHGIGDNSTTWNGVHAKLAQR-FTVIAPDLLGHGQ---SDKPRADYSV----AAY--ANGMRDL---LSVL--- 100
                                    688888888888888888888888876.8888898887777...3333332222....222..3445555...2222... PP

                            DLH  93 pevstkkvgvvGfCmGGalalllaaevpe 121
                                       + ++v +vG  +GG +a+++a + p+
  gi|121638590|ref|YP_978814.1| 101 ---DIERVTIVGHSLGGGVAMQFAYQFPQ 126
                                    ...456899**************999954 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                            DLH 117 aevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsr 194
                                    a + ++ a+v + G+++          + p++++ g++D + p  +++  + a+    +  +l++++g gH  + d++
  gi|121638590|ref|YP_978814.1| 209 AFGRTLRAVVDWRGQMVTMLDRCYLTEAIPVQIIWGTKDVVLPVRHAHMAHAAM----PGSQLEIFEGSGHFPFHDDP 282
                                    44567889999999666665556666778****************988888777....88999********5444444 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   7.1e-05     0.064      55      89 ..     101     136 ..      88     160 .. 0.84
   2 ?    4.9   0.0     0.022        20      99     143 ..     235     278 ..     229     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                  Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaee.ekiegvvflas 89 
                                    ++e+  + GhslGG va +fa +  + ++ ++++++
  gi|121638590|ref|YP_978814.1| 101 DIERVTIVGHSLGGGVAMQFAYQFpQLVDRLILVSA 136
                                    689999***************997468888887765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                  Abhydrolase_5  99 lskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnhagf 143
                                    ++++v  i+gt+D vl+v++++ a+  +p  +++   eG  h  f
  gi|121638590|ref|YP_978814.1| 235 EAIPVQIIWGTKDVVLPVRHAHMAHAAMPG-SQLEIFEGSGHFPF 278
                                    6789999****************9999996.56777788877655 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0094       8.4      15      35 ..      38      58 ..      34      79 .. 0.82
   2 ?    5.7   0.1     0.013        11     102     137 ..     100     135 ..      87     141 .. 0.85
   3 !    6.1   0.0    0.0096       8.6     153     198 ..     233     274 ..     223     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0094
                                   EEEEEE--TT--SHHHHHHHH CS
                  Abhydrolase_2 15 avviflHGlGdsghawaeaak 35
                                   ++++++HG+Gd+   w  + +
  gi|121638590|ref|YP_978814.1| 38 PAILLIHGIGDNSTTWNGVHA 58
                                   589**********99977665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                    --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES CS
                  Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafs 137
                                    ++ +r+ i+G S G+ +a++ a++ p+ + + + +s
  gi|121638590|ref|YP_978814.1| 100 LDIERVTIVGHSLGGGVAMQFAYQFPQLVDRLILVS 135
                                    6889*********************99988877665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0096
                                    GGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT-- CS
                  Abhydrolase_2 153 vtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyegla 198
                                    +t ++p+  i+g++D v+p++++ +a+ ++  ++     +++eg++
  gi|121638590|ref|YP_978814.1| 233 LTEAIPVQIIWGTKDVVLPVRHAHMAHAAMPGSQL----EIFEGSG 274
                                    56789******************999987655544....4444444 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016        14      34      77 ..      37      78 ..      20      91 .. 0.72
   2 !   10.8   0.0   0.00044      0.39      30      93 ..     232     295 ..     206     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                  Abhydrolase_4 34 aapvLllqnerDpaTPyeg.akklakalggavlvtvegeGHgala 77
                                    + +Ll+ + +D+ T  +g ++kla++++   ++  +  GHg++ 
  gi|121638590|ref|YP_978814.1| 37 GPAILLIHGIGDNSTTWNGvHAKLAQRFT---VIAPDLLGHGQSD 78
                                   389***********998873578888888...5555555888764 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00044
                  Abhydrolase_4  30 takgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                      ++a+pv ++ ++ D + P + a  ++ a++g++l + eg+GH  + +  +   + v+++++t
  gi|121638590|ref|YP_978814.1| 232 YLTEAIPVQIIWGTKDVVLPVRHAHMAHAAMPGSQLEIFEGSGHFPFHDDPARFIDIVERFMDT 295
                                    455679999999********************************87764444444566666655 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.6e-06    0.0032      57      86 ..      95     124 ..      70     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                                    HHHHHTT-EEEEEEEETHHHHHHHHHHHHH CS
                       Lipase_3  57 rllekypeysivvtGHSLGgalAlLaaldl 86 
                                    +ll+     +++++GHSLGg++A+ +a+++
  gi|121638590|ref|YP_978814.1|  95 DLLSVLDIERVTIVGHSLGGGVAMQFAYQF 124
                                    45555555689***************9986 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.6e-06    0.0059      52     137 ..      60     141 ..      30     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-06
                                    HHTTSEEEEEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES CS
                            Ndr  52 ilekfvilhvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLin 131
                                    ++++f ++  d  G+ +  ++ ++     s+   a+ +  +l  ++++ v  +G   G  + ++fa ++p++v  l+L++
  gi|121638590|ref|YP_978814.1|  60 LAQRFTVIAPDLLGHGQSDKPRAD----YSVAAYANGMRDLLSVLDIERVTIVGHSLGGGVAMQFAYQFPQLVDRLILVS 135
                                    555555555555555544443332....377788888999999999*********************************9 PP

                                    ---S-- CS
                            Ndr 132 itskaa 137
                                    + + ++
  gi|121638590|ref|YP_978814.1| 136 AGGVTK 141
                                    987766 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.023      55      93 ..     103     140 ..      40     174 .. 0.76
   2 ?   -1.5   0.0       2.1   1.9e+03     115     154 ..     237     277 ..     231     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                    TTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGG CS
                  Ser_hydrolase  55 ekvvlvAHSlgclavlhaaelqlakkvagalLVapadve 93 
                                    e+v++v HSlg  +++++a  q ++ v++ +LV+   v+
  gi|121638590|ref|YP_978814.1| 103 ERVTIVGHSLGGGVAMQFA-YQFPQLVDRLILVSAGGVT 140
                                    569****************.*************987765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                    CHCEEEEETTBTTC-HHHHH.HHHHHCT-EEEEETT-TTSS CS
                  Ser_hydrolase 115 fpslvvaSenDpyvsfeeae.elaeawgaelvdlgeaGHin 154
                                    +p +++  + D ++++ +a+ + a+  g++l   + +GH+ 
  gi|121638590|ref|YP_978814.1| 237 IPVQIIWGTKDVVLPVRHAHmAHAAMPGSQLEIFEGSGHFP 277
                                    67788888889999988886245677799999999999985 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.68   6.1e+02      20      76 ..      33      85 ..      16      96 .. 0.66
   2 ?   13.2   0.0   5.7e-05     0.051     117     147 ..     105     135 ..      97     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.68
                                   GTTTEEEEEEE--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTT CS
                       Esterase 20 pgrkypvvylldGltgwdqnfrakelleslaregeiaeviivvvprggessfysdwd 76
                                    +++ p+++l +G     +n +++ ++++  ++ ++ +++++ +  g  ++  +d+ 
  gi|121638590|ref|YP_978814.1| 33 IAGSGPAILLIHG---IGDNSTTWNGVHAKLAQ-RFTVIAPDLLGHGQSDKPRADYS 85
                                   5677899999999...55666666666544554.68888888888887775555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.7e-05
                                    EEEEEETHHHHHHHHHHHCSTTTCCEEEEES CS
                       Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvssfS 147
                                     +++G+S+GG +A+  a + p++  + +  S
  gi|121638590|ref|YP_978814.1| 105 VTIVGHSLGGGVAMQFAYQFPQLVDRLILVS 135
                                    68********************998888777 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.021      15     110 ..      35     123 ..      32     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                Chlorophyllase2  15 geYpvllflhGylllnslYsqlLkhiashgfivvapqlykvaeada.keiksaakvlnWlakgLesvlpeevepdlskla 93 
                                    g+ p +l++hG+  +++ ++ + +++a  +f v+ap l    ++d  +   s+a+     a+g++  l    + d+++++
  gi|121638590|ref|YP_978814.1|  35 GSGPAILLIHGIGDNSTTWNGVHAKLAQ-RFTVIAPDLLGHGQSDKpRADYSVAAY----ANGMRDLLS---VLDIERVT 106
                                    667999*******************996.8*******9997666553333344444....455554443...5699**** PP

                Chlorophyllase2  94 lsgHSrGgktafalalg 110
                                    ++gHS Gg +a++ a +
  gi|121638590|ref|YP_978814.1| 107 IVGHSLGGGVAMQFAYQ 123
                                    ************99987 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   1.8e+03       3      33 ..      36      66 ..      35      94 .. 0.77
   2 ?   13.3   0.1   5.5e-05     0.049      90     126 ..     102     135 ..      90     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                          PGAP1  3 sGipVlFvpGnagsykqvrslAseaaeayqe 33
                                   sG  +l+++G + + + +  + ++ a+ ++ 
  gi|121638590|ref|YP_978814.1| 36 SGPAILLIHGIGDNSTTWNGVHAKLAQRFTV 66
                                   67889*****999999998887777776655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.5e-05
                          PGAP1  90 ptsviliGHSmGGivaraaltlknyikqsvntiltla 126
                                    +++v ++GHS+GG va  + +  +  +q v+ ++ ++
  gi|121638590|ref|YP_978814.1| 102 IERVTIVGHSLGGGVA--MQFAYQ-FPQLVDRLILVS 135
                                    689*************..444444.477777777665 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.2e-05     0.038      67     111 ..      76     120 ..      23     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                         DUF900  67 nyDresaeasrdalekllrylatkksakkihllaHSmGtwlvlea 111
                                    ++D+  a +s +a ++ +r l    + ++++++ HS G  ++++ 
  gi|121638590|ref|YP_978814.1|  76 QSDKPRADYSVAAYANGMRDLLSVLDIERVTIVGHSLGGGVAMQF 120
                                    78*************************************999975 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     8e-05     0.072      91     153 ..      91     152 ..      74     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                        DUF1057  91 syskalleelelkgklillghsRGcenaLqlavtlea.h.GlvlinptGlrvhkgirplsrleti 153
                                    + +  ll  l++ +++ ++ghs G+  a+q a +++  +  l+l+ + G++  k ++++ rl ++
  gi|121638590|ref|YP_978814.1|  91 NGMRDLLSVLDI-ERVTIVGHSLGGGVAMQFAYQFPQlVdRLILVSAGGVT--KDVNIVFRLASL 152
                                    333445555555.79********************6414145566555554..455555576665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-05      0.07       5      86 ..      42     123 ..      38     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                    EE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST.SHHHCTTCHHHHHHHH..HHHHHHH-SSSSEEEEEETHHHHHHH CS
                   Thioesterase   5 lfppagGsasvfrslasklsdpvvevlavqlpgre.rdepplesieelaaey..aealrqiqpegPyalfGhSlGgllAf 81 
                                    l +++g +++  +  ++kl ++   v+a  l g++ + ++p +   ++aa+   +  l+++ +   ++++GhSlGg +A+
  gi|121638590|ref|YP_978814.1|  42 LIHGIGDNSTTWNGVHAKLAQR-FTVIAPDLLGHGqS-DKP-RADYSVAAYAngMRDLLSVLDIERVTIVGHSLGGGVAM 118
                                    5566666777777777777776.67777777777632.222.22233333331123355666667899************ PP

                                    HHHHH CS
                   Thioesterase  82 evArq 86 
                                    ++A q
  gi|121638590|ref|YP_978814.1| 119 QFAYQ 123
                                    **987 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.2   1.8e+02     128     158 ..      21      52 ..      14      64 .. 0.77
   2 ?    6.6   0.0    0.0052       4.7      60      88 ..      99     127 ..      74     139 .. 0.82
   3 ?   -0.1   0.0       0.6   5.4e+02     145     186 ..     238     275 ..     218     295 .. 0.77
   4 ?   -3.4   0.0         6   5.4e+03     149     162 ..     319     332 ..     317     338 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                                    HHHHHHH-CGGG--.---EEEEEEETT-SSS- CS
                   Peptidase_S9 128 ykelspyspldnvk.aypplLlihGlaDdrvp 158
                                    +++++ y+ + +++   p++LlihG  D+ ++
  gi|121638590|ref|YP_978814.1|  21 FRTVHGYRRAFRIAgSGPAILLIHGIGDNSTT 52 
                                    556666666666668899**********9875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0052
                                    S--GGGEEEEEETHHHHHHHHHHHH-GGG CS
                   Peptidase_S9  60 yvdserlaitGgSyGGyltgaalnqrpdl 88 
                                    + d er+ i G+S GG +++  + q p+l
  gi|121638590|ref|YP_978814.1|  99 VLDIERVTIVGHSLGGGVAMQFAYQFPQL 127
                                    7899************9998888877775 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.6
                                    EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                   Peptidase_S9 145 plLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH 186
                                    p+ +i G++D   p+ +a +  aa+      ++l if ++gH
  gi|121638590|ref|YP_978814.1| 238 PVQIIWGTKDVVLPVRHAHMAHAAMPG----SQLEIFEGSGH 275
                                    666889999999999999988888754....67778888888 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 6
                                    EEETT-SSS-THHH CS
                   Peptidase_S9 149 ihGlaDdrvppaea 162
                                    ++G aD+rv + +a
  gi|121638590|ref|YP_978814.1| 319 VTGSADTRVAVLNA 332
                                    68889999887665 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.13      43     142 ..      34     125 ..      30     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                 Chlorophyllase  43 aGtypvvlflhGtllsnkfyskllnhiashGfivvaPqlykllpPsaqdeidsaaevieWlseglkavlptsveanlskl 122
                                    aG  p +l++hG+  + +++  +   +a   f v+aP l    + ++ d      +v+ ++ +g++  l      +++++
  gi|121638590|ref|YP_978814.1|  34 AGSGPAILLIHGIGDNSTTWNGVHAKLAQ-RFTVIAPDLL---GHGQSDKPRADYSVAAYA-NGMRDLLS---VLDIERV 105
                                    688899*******9999999999999986.6******986...556666666666666654.45666664...35899** PP

                 Chlorophyllase 123 alvGhsrGGktafalalgys 142
                                    ++vGhs GG  a+  a ++ 
  gi|121638590|ref|YP_978814.1| 106 TIVGHSLGGGVAMQFAYQFP 125
                                    ***********999988876 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.26      91     122 ..      91     122 ..      77     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                         DUF915  91 kvlseLkkkYnikkfnavGhSmGglaltsYle 122
                                    + + +L +   i+++ +vGhS Gg  +++++ 
  gi|121638590|ref|YP_978814.1|  91 NGMRDLLSVLDIERVTIVGHSLGGGVAMQFAY 122
                                    5589999999**************99999975 PP

>> Hyaluronidase_1  Hyaluronidase protein (HylP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00034       0.3     114     175 ..     132     195 ..     115     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                                    SXXXXXSSS-SS-------SS--SS-SS------TTS-SS----..--SSS-SS------SSSS CS
                Hyaluronidase_1 114 lfvdykgttnavnivmrqpttpnfssalnitsanengsamqlrg..vekalgtlkithenpsvd 175
                                     +v   g t+ vniv+r  + p  s a+ +        a+q+ g  v ka+gt  + h+ p v 
  gi|121638590|ref|YP_978814.1| 132 ILVSAGGVTKDVNIVFRLASLPMGSEAMALLRLPLVLPAVQIAGriVGKAIGTTSLGHDLPNVL 195
                                    4677889***********************************775589***********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2145.01
//
Query:       gi|121638591|ref|YP_978815.1|  [L=228]
Description: hypothetical protein BCG_2729 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-23   81.8   0.0    2.4e-14   53.5   0.0    2.0  2  PhzC-PhzF  Phenazine biosynthesis-like protein


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.3e-18   2.4e-14       3     106 ..      10     108 ..       8     134 .. 0.83
   2 !   26.8   0.0   1.8e-10   3.2e-06     179     238 ..     138     197 ..     113     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.3e-18
                                    ET-SSTTS.SEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHHHHHH CS
                      PhzC-PhzF   3 aFtespfk.GNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasahalaek 81 
                                    +Ft+s ++ GNp++V++  ++++ +  q++Aa+ ++seT F+  ps  +  +   + TP+ E++++GH+t+++   l e+
  gi|121638591|ref|YP_978815.1|  10 VFTDSDGNfGNPLGVINA-SKVEHRDRQQLAAQSGYSETIFVDLPSPGSTTAHATIHTPRTEIPFAGHPTVGASWWLRER 88 
                                    899988766******975.567777789**************999988999999*************************9 PP

                                    CT-S-SCEEEEEETTEEEEE.EEEE CS
                      PhzC-PhzF  82 glvasaetveletkaGilpvkslke 106
                                    g         l+ +aGi+ v  +++
  gi|121638591|ref|YP_978815.1|  89 GTP----INTLQVPAGIVQVS-YHG 108
                                    976....55677788888883.444 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.8e-10
                                    HHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHHHHHHHHHCC-SSS CS
                      PhzC-PhzF 179 eikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsgaLaaylseklnlee 238
                                    + +++p+++++     ++ s+ ++++RmFa  lG+ ED +tG+A+  +  yls+ l +++
  gi|121638591|ref|YP_978815.1| 138 DPADFPDDIAHYLWTWTDRSAGSLRARMFAANLGVTEDEATGAAAIRITDYLSRDLTITQ 197
                                    5566777777777888899999*******************************9998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1589.81
//
Query:       gi|121638592|ref|YP_978816.1|  [L=164]
Description: hypothetical protein BCG_2730c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-43  147.6   0.0    2.8e-43  147.4   0.0    1.0  1  DUF1794   Domain of unknown function (DUF1794)


Domain annotation for each model (and alignments):
>> DUF1794  Domain of unknown function (DUF1794)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   1.6e-47   2.8e-43       2     149 .]       9     162 ..       8     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.6e-47
                                    CGGGGGGBEEEEEEEEEEETTCEEEEEEEEEEEEESSSSEEEEEEEEEETTT..EEEEEEEEEE.CTSCTEEEEEEEETT CS
                        DUF1794   2 llpLawLvGtWrGeGeggyptieefafgqeiefshdggpylaYesrtwrlde..plhrEsGywrledgtdevelllahps 79 
                                    l++L++L+G+W G+G+g+ypti++f++ +e++f+h g+p+l+Y+++t+ + +  plh+E+Gy+r     + vel+lahps
  gi|121638592|ref|YP_978816.1|   9 LQALSPLLGSWAGRGAGKYPTIRPFEYLEEVVFAHVGKPFLTYTQQTRAVADgkPLHSETGYLR-VCRPGCVELVLAHPS 87 
                                    899**********************************************99556**********.47899********** PP

                                    TEEEEEEEEEETCCCEEEEE.....CEEEEE.CTSSSEEEEEEEEEEECTCEEEEEEEEETTCECEEEEEEEEEE CS
                        DUF1794  80 GvvelyeGevkngrksleLa.....sdaiartstakevtaakrlyglvdgdLeyveemaafgqelqshlsarLkR 149
                                    G++e+++G+++ ++  +eL+     +++i   +takevta+ r y++  ++L+y  +m+a+gq+lq+hl a L+R
  gi|121638592|ref|YP_978816.1|  88 GITEIEVGTYSVTGDVIELElstraDGSIGLAPTAKEVTALDRSYRIDGDELSYSLQMRAVGQPLQDHLAAVLHR 162
                                    ***********8887888887666669********************8888**********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1178.01
//
Query:       gi|121638593|ref|YP_978817.1|  [L=154]
Description: transcriptional regulator NrdR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-14   52.6   0.0    7.1e-14   52.2   0.0    1.2  1  ATP-cone       ATP cone domain
  ------ inclusion threshold ------
      0.031   13.8   3.6       0.72    9.4   0.1    2.5  3  TF_Zn_Ribbon   TFIIB zinc-binding
      0.064   13.2   0.8          2    8.4   0.1    2.3  2  Cys_rich_CPXG  Cysteine-rich CPXCG
       0.11   12.0   1.0        5.3    6.6   0.1    2.4  2  zf-ribbon_3    zinc-ribbon domain
       0.68   10.9   5.4          1   10.4   0.1    3.1  3  zf-C2H2_4      C2H2-type zinc finger
          3    7.9   6.4        9.9    6.2   6.5    1.8  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        4.4    7.4   6.0         34    4.5   6.0    2.3  1  Ogr_Delta      Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.8e-17   7.1e-14       2      83 ..      47     131 ..      46     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.8e-17
                                    EEE-TTS-EEE--HHHHHHHHHHHHHH...-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHHH CS
                       ATP-cone   2 kViKRdGtvepfdvekIkraiekAceg...seeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaayi 78 
                                     V+KR G +epf++ek+++ + +Ac+g   +++ ++ +a++ve+ vr  +  +i++ +++  +   l+e +++a++++++
  gi|121638593|ref|YP_978817.1|  47 AVVKRSGVTEPFSREKVISGVRRACQGrqvDDDALNLLAQQVEDSVRAAGSPEIPSHDVGLAILGPLRELDEVAYLRFAS 126
                                    59***************************99999********************************************** PP

                                    HHHHH CS
                       ATP-cone  79 lyrnl 83 
                                    +yr +
  gi|121638593|ref|YP_978817.1| 127 VYRSF 131
                                    ***87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0068        17       2      18 ..       2      19 ..       1      22 [. 0.81
   2 ?    9.4   0.1   0.00028      0.72       2      14 ..      30      42 ..      29      45 .. 0.78
   3 ?   -3.5   0.0         3   7.7e+03      25      32 ..      71      79 ..      70      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0068
                                   EETTTTCEE.CHEETSTT CS
                   TF_Zn_Ribbon  2 kCPnCgstn.lveDperg 18
                                    CP C +++  v D  ++
  gi|121638593|ref|YP_978817.1|  2 HCPFCRHPDsRVIDSRET 19
                                   6******99899997655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00028
                                   EETTTTCEECHEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                    CP+Cg ++++++
  gi|121638593|ref|YP_978817.1| 30 SCPECGRRFTTVE 42
                                   5*******96554 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3
                                   S.SBEEEEC CS
                   TF_Zn_Ribbon 25 C.GlVledn 32
                                   C G  ++d+
  gi|121638593|ref|YP_978817.1| 71 CqGRQVDDD 79
                                   777777775 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00078         2       2      20 ..       2      20 ..       1      24 [. 0.85
   2 ?    3.2   0.1     0.033        84       2      12 ..      30      40 ..      29      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00078
                  Cys_rich_CPXG  2 qCPyCgeeievlvDlsagd 20
                                   +CP+C ++ + ++D  + d
  gi|121638593|ref|YP_978817.1|  2 HCPFCRHPDSRVIDSRETD 20
                                   7************987765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.033
                  Cys_rich_CPXG  2 qCPyCgeeiev 12
                                   +CP Cg ++++
  gi|121638593|ref|YP_978817.1| 30 SCPECGRRFTT 40
                                   6*****99887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.016        40       4      14 ..       2      11 ..       1      14 [. 0.65
   2 ?    6.6   0.1    0.0021       5.3       4       9 ..      30      35 ..      27      40 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                    zf-ribbon_3  4 rCPnCGaplss 14
                                   +CP C +p +s
  gi|121638593|ref|YP_978817.1|  2 HCPFCRHP-DS 11
                                   67777666.55 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                    zf-ribbon_3  4 rCPnCG 9 
                                   +CP+CG
  gi|121638593|ref|YP_978817.1| 30 SCPECG 35
                                   677777 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5      0.35     9e+02       3       6 ..       3       6 ..       2      12 .. 0.76
   2 ?   10.4   0.1   0.00039         1       2      14 ..      30      42 ..      29      47 .. 0.86
   3 ?   -0.8   0.1       1.5   3.9e+03      14      19 ..     142     147 ..     128     151 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                      zf-C2H2_4 3 CpiC 6
                                  Cp+C
  gi|121638593|ref|YP_978817.1| 3 CPFC 6
                                  9999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00039
                      zf-C2H2_4  2 kCpiCgksFsskk 14
                                    Cp Cg++F++ +
  gi|121638593|ref|YP_978817.1| 30 SCPECGRRFTTVE 42
                                   5********9976 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                      zf-C2H2_4  14 kaLlrH 19 
                                    +aL+ H
  gi|121638593|ref|YP_978817.1| 142 EALRAH 147
                                    335666 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.5    0.0039       9.9      20      45 ..       2      36 ..       1      37 [. 0.87
   2 ?    5.3   1.3    0.0077        20      18      27 ..      28      37 ..      21      45 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0039
                  Zn_Tnp_IS1595 20 vCPhCgsrkayrikt.........rglfqCkeCrk 45
                                   +CP+C +  ++ i +         r++  C eC++
  gi|121638593|ref|YP_978817.1|  2 HCPFCRHPDSRVIDSretdegqaiRRRRSCPECGR 36
                                   6*****997777766679***************98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
                  Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                   ++ CP Cg r
  gi|121638593|ref|YP_978817.1| 28 RRSCPECGRR 37
                                   4669999954 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.0     0.013        34       1      43 [.       2      44 ..       2      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                      Ogr_Delta  1 rCPhCgap.aaartsrnlsk.dvreryyqCsnfeCgatfvaaeei 43
                                   +CP C++p +++  sr++++ +  +r  +C    Cg +f++ e++
  gi|121638593|ref|YP_978817.1|  2 HCPFCRHPdSRVIDSRETDEgQAIRRRRSCPE--CGRRFTTVETA 44
                                   8****998688999999988345559999977..99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1104.78
//
Query:       gi|121638594|ref|YP_978818.1|  [L=165]
Description: hypothetical protein BCG_2732c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-07   30.3   0.0    4.9e-07   29.7   0.0    1.3  1  LysM      LysM domain


Domain annotation for each model (and alignments):
>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.7e-11   4.9e-07       2      44 .]     116     163 ..     115     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.7e-11
                                    EE-TT--HHHHHHHC.......TCHHHHHHHHCTCSSCGG--TTEEEEEE CS
                           LysM   2 tVkkGDTLwsIAkry.......gitveklleaNnlsspdkifpGqkLkiP 44 
                                    +V +G++L ++A r+       ++  ++++e+N+l++p  + +Gq+L+ P
  gi|121638594|ref|YP_978818.1| 116 RVETGESLHDVAVRVapnaptrQVA-DRIRELNGLQTPA-LAVGQTLIAP 163
                                    79***********************.*************.*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1234.79
//
Query:       gi|121638595|ref|YP_978819.1|  [L=217]
Description: LexA repressor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-30  103.1   0.1    7.7e-30  102.5   0.1    1.3  1  LexA_DNA_bind    LexA DNA binding domain
    1.3e-15   57.1   0.0    1.9e-15   56.5   0.0    1.3  1  Peptidase_S24    Peptidase S24-like
    0.00067   19.4   0.1     0.0015   18.3   0.1    1.6  1  HTH_IclR         IclR helix-turn-helix domain
    0.00073   20.0   0.0     0.0012   19.3   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
      0.002   18.0   0.7     0.0037   17.1   0.3    1.6  2  MarR_2           MarR family
     0.0076   16.2   0.0      0.013   15.4   0.0    1.4  1  MarR             MarR family
  ------ inclusion threshold ------
      0.019   15.0   0.1        0.1   12.7   0.0    2.1  2  HTH_20           Helix-turn-helix domain
      0.026   14.6   0.0      0.046   13.7   0.0    1.3  1  Pollen_allerg_1  Pollen allergen
       0.04   13.9   0.1      0.068   13.2   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.041   13.4   0.1       0.09   12.4   0.1    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.097   12.7   0.0       0.15   12.1   0.0    1.3  1  HTH_6            Helix-turn-helix domain, rpiR family
       0.14   11.7   0.0       0.27   10.8   0.0    1.4  1  Sigma70_r4       Sigma-70, region 4
        0.2   12.1   0.0       0.36   11.3   0.0    1.4  1  FaeA             FaeA-like protein
       0.22    9.2   0.0       0.29    8.8   0.0    1.0  1  CobN-Mg_chel     CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.1     6e-33   7.7e-30       2      65 .]       6      69 ..       5      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 6e-33
                                   X---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-CCG CS
                  LexA_DNA_bind  2 kkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgkpRa 65
                                   ++LTerQr++ld+i+as++++gypPsirei++a+gl+S+s+v+++L++LerKGy++rdp++pRa
  gi|121638595|ref|YP_978819.1|  6 SALTERQRTILDVIRASVTSRGYPPSIREIGDAVGLTSTSSVAHQLRTLERKGYLRRDPNRPRA 69
                                   78*************************************************************8 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   1.5e-18   1.9e-15       2      69 ..     137     203 ..     136     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.5e-18
                                    XXSSTT.CCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SSTTSTEEEECT CS
                  Peptidase_S24   2 vpGdSM.eptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnneypplying 69 
                                    v GdSM e+ + dGd ++V++++ +++Gdiv++ ++ge  a++K +++ +g+++l+++n+  +p+  n+
  gi|121638595|ref|YP_978819.1| 137 VIGDSMvEAAICDGDWVVVRQQNVADNGDIVAAMIDGE--ATVKTFKRAGGQVWLMPHNPAFDPIPGND 203
                                    88************************************..*******************9999998876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.1e-06    0.0015      19      52 .]      30      64 ..      10      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                                   -BHHHHHHHHTS-.HHHHHHHHHHHHHTTSEE... CS
                       HTH_IclR 19 ltlselArrtglp.kStvhRlLqtLvelGyveqdg 52
                                    +++e+ ++ gl+  S+v + L+tL++ Gy+++d+
  gi|121638595|ref|YP_978819.1| 30 PSIREIGDAVGLTsTSSVAHQLRTLERKGYLRRDP 64
                                   6899*******962699****************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.6e-07    0.0012       1      53 [.       8      65 ..       8      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.6e-07
                         HTH_27  1 ltrqqalvLhlir....hrrrrkkladlcgrlnvedshis.yslkkLtekGLvertgd 53
                                   lt+ q+ +L +ir     r+ + +++++ +++ +++++ +   l+ L++kG++ r + 
  gi|121638595|ref|YP_978819.1|  8 LTERQRTILDVIRasvtSRGYPPSIREIGDAVGLTSTSSVaHQLRTLERKGYLRRDPN 65
                                   7999************99*******************9999************55443 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.9e-06    0.0037       2      56 ..       7      65 ..       6      68 .. 0.89
   2 ?   -3.6   0.0       8.4   1.1e+04       8      19 ..      98     109 ..      93     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                                   T--HHHHHHHHHHHCTTTS...EEEHHHHHHHHTSSH.HHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  2 gltpaqarvLaaLgrrpgr...dltvgelarrlglsk.savsrilkrLvaaGLverrpg 56
                                   +lt  q+ +L +++++      + +++e+ ++ gl+  s+v   l+ L+++G+++r p+
  gi|121638595|ref|YP_978819.1|  7 ALTERQRTILDVIRASVTSrgyPPSIREIGDAVGLTStSSVAHQLRTLERKGYLRRDPN 65
                                   688888888888888887788877*******************************9887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.4
                                    HHHHHHHHCTTT CS
                         MarR_2   8 arvLaaLgrrpg 19 
                                    a vL+ ++++++
  gi|121638595|ref|YP_978819.1|  98 APVLGRIAAGGP 109
                                    678888888876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.9e-06     0.013      17      52 ..      29      65 ..       8      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.9e-06
                                   TEEHHHHHHHHTS.-HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR 17 plsvseLakklgv.skstvtrvldrLekkGlieRsks 52
                                   p+s+ e+++++g+ s+s+v  +l++Le+kG+++R ++
  gi|121638595|ref|YP_978819.1| 29 PPSIREIGDAVGLtSTSSVAHQLRTLERKGYLRRDPN 65
                                   567888888888725799****************876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.9e-05       0.1      12      58 ..      12      64 ..       6      67 .. 0.84
   2 ?   -0.8   0.0       1.3   1.6e+03       5      29 ..      90     114 ..      85     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHH.....STCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHCTTEEEEC CS
                         HTH_20 12 RrrilraL.....araegltaselaerldlsknt.lsyHLrvLeeagLvevvr 58
                                   +r il+ +     +r+ + +  e+ ++++l+ ++ + ++Lr+Le+ g++++  
  gi|121638595|ref|YP_978819.1| 12 QRTILDVIrasvtSRGYPPSIREIGDAVGLTSTSsVAHQLRTLERKGYLRRDP 64
                                   6777777777788888899999*******888888*************99865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                    HHHS-HHHHHHHHHHSTCTTB-HHH CS
                         HTH_20   5 eALahPvRrrilraLaraegltase 29 
                                    +AL +P+ + +l  +a +++  a+e
  gi|121638595|ref|YP_978819.1|  90 DALPEPTFAPVLGRIAAGGPILAEE 114
                                    6888899999999998888888877 PP

>> Pollen_allerg_1  Pollen allergen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.046      12      56 ..     152     194 ..     144     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                Pollen_allerg_1  12 ylavlvenvggagdisaVevkqggsseWtpmsrnwGavWqlnssp 56 
                                    +++v  +nv+  gdi+a  + ++   + ++ +r+ G+vW ++ +p
  gi|121638595|ref|YP_978819.1| 152 WVVVRQQNVADNGDIVAAMIDGE--ATVKTFKRAGGQVWLMPHNP 194
                                    899999***************55..479***********999865 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.3e-05     0.068      20      54 ..      28      63 ..       7      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                   EEHHHHHHHHHTT.SSHHHHHHHHHHHHHTTSEEET CS
                      HTH_Crp_2 20 lpltqeelAsmlG.ltretvsrilseLkreglisrg 54
                                    p + +e+++ +G ++ ++v   l+ L+r+g+++r 
  gi|121638595|ref|YP_978819.1| 28 YPPSIREIGDAVGlTSTSSVAHQLRTLERKGYLRRD 63
                                   578889*******9999****************963 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     7e-05      0.09      19      48 .]      31      61 ..       8      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                         HTH_24 19 sqreLAerlgl.SpstvnrrlkrLeeeGlIk 48
                                   s+re+ +++gl S s v  +l+ Le++G+++
  gi|121638595|ref|YP_978819.1| 31 SIREIGDAVGLtSTSSVAHQLRTLERKGYLR 61
                                   899*******955789*************86 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.15      10      63 ..       4      59 ..       1      61 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   H-----HHHHHHHHHHHH-S-.--TT--HHHHHHHTT-.-HHHHHHHH---S-SSH CS
                          HTH_6 10 kkekltksekkiaeyilaspd.kaielsikalAkaaav.SeativrfakkLGfkGF 63
                                   + + lt+  ++i+++i+as+    + +si+++  a +  S +++    ++L  kG+
  gi|121638595|ref|YP_978819.1|  4 ADSALTERQRTILDVIRASVTsRGYPPSIREIGDAVGLtSTSSVAHQLRTLERKGY 59
                                   6789**************986156889*********95499**********99999 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.27       4      33 ..       7      42 ..       6      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                   HS-HHHHHHHHHHH......TTT--HHHHHHHHTS- CS
                     Sigma70_r4  4 sLpererevlelrf......geglTleEIgerlgiS 33
                                    L+er+r++l   +      g + +  EIg+  g++
  gi|121638595|ref|YP_978819.1|  7 ALTERQRTILDVIRasvtsrGYPPSIREIGDAVGLT 42
                                   7*******************7777********9997 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.36      15      51 ..      29      66 ..      14      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                   ---HHHHHHHHTS.-HHHHHHHHHHHHHHSSEEEE--S CS
                           FaeA 15 pckTreiAdalgl.saYQaRyYLeqLekegkikrspvr 51
                                   p   rei da+gl s   + + L +Le++g ++r p r
  gi|121638595|ref|YP_978819.1| 29 PPSIREIGDAVGLtSTSSVAHQLRTLERKGYLRRDPNR 66
                                   66679*******93457899**************9977 PP

>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00022      0.29     260     294 ..      27      61 ..      19      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00022
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 260 nyppgegrlgnavgLdvpaSlvnlLkalkeeGYdv 294
                                     ypp+  ++g avgL + +S+++ L++l+++GY  
  gi|121638595|ref|YP_978819.1|  27 GYPPSIREIGDAVGLTSTSSVAHQLRTLERKGYLR 61 
                                    699******************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1561.54
//
Query:       gi|121638596|ref|YP_978820.1|  [L=699]
Description: transmembrane alanine and glycine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-50  168.8  24.3      1e-09   38.7   0.1    7.7  7  LGFP      LGFP repeat
  ------ inclusion threshold ------
       0.12   12.6   0.5       0.24   11.6   0.5    1.4  1  DUF4381   Domain of unknown function (DUF4381)
       0.22   11.5   0.0         19    5.3   0.0    2.4  2  DUF723    Protein of unknown function (DUF723)


Domain annotation for each model (and alignments):
>> LGFP  LGFP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.88   5.2e+03      40      52 ..      44      56 ..      36      57 .. 0.84
   2 !   27.7   0.0   4.8e-10   2.9e-06       4      51 ..      62     107 ..      59     109 .. 0.88
   3 !   38.2   0.1   2.5e-13   1.5e-09       1      53 []     112     168 ..     112     168 .. 0.89
   4 !   18.1   2.7     5e-07     0.003       1      50 [.     170     235 ..     170     238 .. 0.68
   5 !   38.7   0.1   1.7e-13     1e-09       6      51 ..     245     289 ..     240     291 .. 0.88
   6 !   36.3   0.1   9.9e-13   5.9e-09       1      53 []     294     350 ..     294     350 .. 0.91
   7 !   19.9   0.1   1.3e-07   0.00079       1      32 [.     352     381 ..     352     387 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.88
                           LGFP 40 aIrdkWaalGwer 52
                                   a++++W+++G+ +
  gi|121638596|ref|YP_978820.1| 44 AMMAAWEKAGGDT 56
                                   7899*****9865 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 4.8e-10
                           LGFP   4 PttdetatpdggGryqhFegGsiyWspatGahavkgaIrdkWaalGwe 51 
                                      +d +  p g+G   +F gG+++ +patGa   +g+++dk+++lG++
  gi|121638596|ref|YP_978820.1|  62 RKGDVY--PIGDGFALDFAGGKMFFTPATGAKYLYGPLLDKYESLGGA 107
                                    556664..4999**********************************97 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 2.5e-13
                           LGFP   1 LGyPttdeta.tpdggGryqhFegG...siyWspatGahavkgaIrdkWaalGwerG 53 
                                    LG+Pt +e++  + ++ r+++F+ +   +i+W+p++Ga++v+ga+ ++W +lG   G
  gi|121638596|ref|YP_978820.1| 112 LGFPTINEVPgLAGPDSRVSTFSAAdnpVIFWTPEHGAFVVRGALNAAWDKLGSSGG 168
                                    9********96667889*****775555*************************8765 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 5e-07
                           LGFP   1 LGyPttdetatpdggGryqhFegGsiyWspatG.........ahavkg.........aIrdkWaalGw 50 
                                    LG+P++det   dg    q+F+gG + W+ at          a + kg         aI  +W+a+G+
  gi|121638596|ref|YP_978820.1| 170 LGAPVGDETY--DGEVTAQKFSGGEVSWNRATKefttvpavlAEQLKGlqvaidpsaAINMAWRAAGG 235
                                    9*******55..*****************999756555555544444444444444455555555555 PP

  == domain 5  score: 38.7 bits;  conditional E-value: 1.7e-13
                           LGFP   6 tdetatpdggGryqhFegGsiyWspatGahavkgaIrdkWaalGwe 51 
                                    + +++   g+G  q+F gG+++ spatGa+av g+I++k+++lG++
  gi|121638596|ref|YP_978820.1| 245 GGQYP-ISGDGIAQDFVGGKVFFSPATGANAVEGEILAKYESLGGP 289
                                    55655.6899**********************************86 PP

  == domain 6  score: 36.3 bits;  conditional E-value: 9.9e-13
                           LGFP   1 LGyPttdetatpdggG.ryqhFegG...siyWspatGahavkgaIrdkWaalGwerG 53 
                                    LG+P+++et++  g   r  +F+ +   +i+W p++Ga++v+ga+ ++W +l +++G
  gi|121638596|ref|YP_978820.1| 294 LGFPIANETDGGFGPSsRIVRFSAAdkpVIFWAPDHGAFVVRGAMVAAWDKLRGPNG 350
                                    9*******997766667*****886666**************************998 PP

  == domain 7  score: 19.9 bits;  conditional E-value: 1.3e-07
                           LGFP   1 LGyPttdetatpdggGryqhFegGsiyWspat 32 
                                    LG+P++d+t   dg+ + q+F+gG i W+ a 
  gi|121638596|ref|YP_978820.1| 352 LGAPVGDQTV--DGDVVSQKFTGGMISWNRAK 381
                                    9*******66..****************8765 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5     4e-05      0.24      18      51 ..     419     454 ..     407     475 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                        DUF4381  18 apGwwlllaalll...llllvlalwllrrrkrnrreA 51 
                                    ++ ww l aa+l    +++++l+++ lrrr+r  ++A
  gi|121638596|ref|YP_978820.1| 419 TWHWWWLGAAALGvllVVMVALVVFGLRRRRRG-YDA 454
                                    455555544444434555555555555555553.222 PP

>> DUF723  Protein of unknown function (DUF723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.012        72      17      48 ..     126     158 ..     124     168 .. 0.77
   2 ?    5.3   0.0    0.0032        19      17      42 ..     308     333 ..     299     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                         DUF723  17 phlklveFegvakPvvinCPlHGnvty.styka 48 
                                    p+ ++  F+   +Pv    P HG  ++ + ++a
  gi|121638596|ref|YP_978820.1| 126 PDSRVSTFSAADNPVIFWTPEHGAFVVrGALNA 158
                                    7788999****************8543155555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0032
                         DUF723  17 phlklveFegvakPvvinCPlHGnvt 42 
                                    p  ++v F+   kPv    P HG  +
  gi|121638596|ref|YP_978820.1| 308 PSSRIVRFSAADKPVIFWAPDHGAFV 333
                                    45789******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4672.21
//
Query:       gi|121638597|ref|YP_978821.1|  [L=82]
Description: hypothetical protein BCG_2735 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 646.34
//
Query:       gi|121638598|ref|YP_978822.1|  [L=397]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-43  148.5   9.5    1.6e-43  148.5   9.5    2.2  3  TerC      Integral membrane protein TerC family
  ------ inclusion threshold ------
       0.77   10.0   3.0       0.69   10.1   0.3    2.1  2  DUF4381   Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4       0.2   1.8e+03     134     178 ..       7      51 ..       3      63 .. 0.64
   2 !  148.5   9.5   1.8e-47   1.6e-43       1     180 [.      69     276 ..      69     277 .. 0.91
   3 ?   -3.3   0.0      0.71   6.3e+03      67      72 ..     308     313 ..     297     335 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.2
                           TerC 134 vitavilsilvlrflakllakllerfptlkylalalllligvklv 178
                                    v+t  i+ i +l+++  +l+   + +ptl+ +++    ++g+ ++
  gi|121638598|ref|YP_978822.1|   7 VWTLTIVLIAGLMLVDYVLHVRKTHVPTLRQAVIQSATFVGIAIL 51 
                                    556666666666666666666666666666666666666666554 PP

  == domain 2  score: 148.5 bits;  conditional E-value: 1.8e-47
                           TerC   1 ltlvlleivLsiDNlvviallvkk..lpeeqqkkalllGilgAlvlRillillavallelfdlilligglfLlytavkel 78 
                                    ++++l + +Ls+DNl+v+++++++  +p+  q+k+ll+Gi++Alv+R  +i++++al+e f+  ++++gl+Ll++a ++ 
  gi|121638598|ref|YP_978822.1|  69 FACYLTDEALSVDNLFVFLVIISSfgVPRLAQQKVLLFGIAFALVTRTGFIFVGAALIENFNSAFYLFGLVLLVMAGNLA 148
                                    57899******************99******************************************************* PP

                           TerC  79 lekr........le.nklvkeekkkkkktkst.................llavviqielaDlvfslDSvlaavaitsdlf 132
                                    +           l+ + + + +++  ++++++                 ll+v+i++  +D++f++DS++a +++t++++
  gi|121638598|ref|YP_978822.1| 149 RPTGlesrdaetLKrSVIIRLADRFLRTSQDYngdrlftvsnnkrmmtpLLLVMIAVGGTDILFAFDSIPALFGLTQNVY 228
                                    99886666655533345555555555555555************************************************ PP

                           TerC 133 ivitavilsilvlrflakllakllerfptlkylalalllligvklvle 180
                                    +v++a ++s+l+lr+l++l+  ll+r+ +l+y+++++l++igvkl+le
  gi|121638598|ref|YP_978822.1| 229 LVFAATAFSLLGLRQLYFLIDGLLDRLVYLSYGLAVILGFIGVKLMLE 276
                                    *********************************************997 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.71
                           TerC  67 glfLly 72 
                                     ++L+ 
  gi|121638598|ref|YP_978822.1| 308 IVLLIT 313
                                    222222 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.21   1.8e+03      22      44 ..       8      29 ..       4      44 .. 0.44
   2 ?   10.1   0.3   7.7e-05      0.69      24      70 ..     305     356 ..     291     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
                        DUF4381 22 wlllaalllllllvlalwllrrr 44
                                   w+l ++l++ +l+++ ++l+ r+
  gi|121638598|ref|YP_978822.1|  8 WTLTIVLIA-GLMLVDYVLHVRK 29
                                   555523333.3333333322222 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.7e-05
                        DUF4381  24 llaalllllllvlalwllrrrkrn.....rreAlreLaalr.adeadakella 70 
                                    ++ +++ll+  ++ +w  r r +n     rr A + L+    +++a++++++ 
  gi|121638598|ref|YP_978822.1| 305 VI-IIVLLITTAASFWSARGRAQNamaraRRYATAYLDLHYeTESAERDKIFT 356
                                    33.67889999********6666668999999****99888655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2763.10
//
Query:       gi|121638599|ref|YP_978823.1|  [L=386]
Description: acyl-CoA dehydrogenase fadE20 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-46  158.7   2.5    1.6e-46  158.2   2.5    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.1e-31  108.4   0.1    1.2e-30  106.4   0.0    2.0  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      2e-24   85.6   0.0    3.4e-24   84.9   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    2.7e-08   34.2   0.3    3.8e-08   33.7   0.3    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
     0.0017   18.9   0.0      0.014   16.0   0.0    2.1  2  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   2.5   4.4e-50   1.6e-46       1     149 [.     236     384 ..     236     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 4.4e-50
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g Gf + m++l +eR+++a++a++ ++++le++l+ya++rkafg+ ++++q  r+ lae+a+e++++r +v + +++  a
  gi|121638599|ref|YP_978823.1| 236 GMGFIYLMQNLPQERISIAIMAAAGMESVLEQTLQYAKERKAFGRSIGSFQNSRFLLAELATEATVVRIMVDEFIKLHLA 315
                                    57****************************************************************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    gk +  +a+maK++a+e  +++ d+++ql+Gg+Gy++eypv+r+y d+rv +i++Gt+ei+++ii+r+l
  gi|121638599|ref|YP_978823.1| 316 GKLTAEQAAMAKWYATEKQVYLNDRCLQLHGGYGYMREYPVARAYLDSRVQTIYGGTTEIMKEIIGRGL 384
                                    ******************************************************************986 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.0   3.4e-34   1.2e-30       2     113 .]      14     125 ..      13     125 .. 0.97
   2 ?   -1.7   0.0       1.3   4.6e+03      38      62 ..     214     240 ..     200     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 3.4e-34
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--.S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGag.ldyleaaivaeelaradaglal 80 
                                    +e+e +r++ r+f+++++ap+++ew++++ ++r +w +++++G+lg++vpeeygG g +d+ ++ +++ee  ++ ++ ++
  gi|121638599|ref|YP_978823.1|  14 PEHELFRESYRAFLDRHVAPYHDEWEKTKIVDRGVWLEAGKQGFLGMAVPEEYGGGGnADFRYNTVITEETCAGRYS-GI 92 
                                    89***********************99999************************999799************99998.79 PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasge 113
                                    ++g+h+++vap +l+ +teeqkrr+ p +++ge
  gi|121638599|ref|YP_978823.1|  93 GFGLHNDIVAPYLLALATEEQKRRWFPNFCTGE 125
                                    9******************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                    HHHHHTTCTSTTS-.GGGTS-.-S-HH CS
                  Acyl-CoA_dh_N  38 kklaelGllgitvp.eeygGa.gldyl 62 
                                    +  ael ++ ++vp e   G+ g++++
  gi|121638599|ref|YP_978823.1| 214 QDTAELSFTDVAVPaENLLGQeGMGFI 240
                                    566788888888884334455234322 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   9.6e-28   3.4e-24       1      97 []     129     224 ..     129     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 9.6e-28
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    a+a+TEp++Gsd+++++t+a+++ g++yvlnG+K++itn+  ++l++v+a+ ++p+ +a+g+sl++v+r++ g++ +r  
  gi|121638599|ref|YP_978823.1| 129 AIAMTEPGTGSDLQGITTRAVKH-GDHYVLNGSKTFITNGINSDLVIVVAQ-TDPEkGAQGFSLLVVERGMAGFERGRQL 206
                                    78****************77444.447************************.455558******************9999 PP

                                    -BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfedv 97 
                                    +k+Gl+  +t+el f+dv
  gi|121638599|ref|YP_978823.1| 207 DKIGLDAQDTAELSFTDV 224
                                    ***************997 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.3   1.1e-11   3.8e-08      12     131 ..     262     371 ..     251     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.1e-11
                                    HHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  12 raalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalav 91 
                                    +++l++++++a+er+   +g+++  +++  + lae+a++    r ++ + ++       agk        +a++a+ +a+
  gi|121638599|ref|YP_978823.1| 262 ESVLEQTLQYAKERKA--FGRSIGSFQNSRFLLAELATEATVVRIMVDEFIKL----HLAGKLT----AEQAAMAKWYAT 331
                                    899*************..***********************************....5556553....67799******* PP

                                    HHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                  Acyl-CoA_dh_2  92 elaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                    e  +   d++ +++Gg+++  e+p+ R++ D ++ +++ +
  gi|121638599|ref|YP_978823.1| 332 EKQVYLNDRCLQLHGGYGYMREYPVARAYLDSRVQTIYGG 371
                                    *********************************9998866 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.8e-06     0.014      89     118 ..      91     120 ..      80     126 .. 0.90
   2 ?    0.0   0.1      0.33   1.2e+03      48     113 ..     262     324 ..     259     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                    --TTHHHHHTHHHHHHHHS-HHHHHHHHHH CS
                  Acyl-CoA_ox_N  89 slplglhfsMFlptlkgqgteeQqakWlpr 118
                                    +  +glh  ++ p l+ ++teeQ+++W p 
  gi|121638599|ref|YP_978823.1|  91 GIGFGLHNDIVAPYLLALATEEQKRRWFPN 120
                                    56799**********************997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHHHHHHHTTSBTTCHHHHHHHH..HHHHTHSS--TTHHHHHTHHH.HHHHHS-HHHHH CS
                  Acyl-CoA_ox_N  48 eealrkatrllkklrelqierkeseeeallagplgtglldeslplglhfsMFlp.tlkgqgteeQqa 113
                                    e+ l+++++++k  + ++++  +     + ++ l++ l  e + +++++  F++  l g  t+eQ a
  gi|121638599|ref|YP_978823.1| 262 ESVLEQTLQYAKERKAFGRSIGSF----QNSRFLLAELATEATVVRIMVDEFIKlHLAGKLTAEQAA 324
                                    556677777777777777754444....444556699999999999999999997799999999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2812.35
//
Query:       gi|121638600|ref|YP_978824.1|  [L=495]
Description: GTP-binding protein hflX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-33  113.1   0.0    1.5e-32  112.1   0.0    1.5  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    7.7e-30  103.3  10.0    1.5e-29  102.4   7.1    2.5  2  GTP-bdg_M     GTP-binding GTPase Middle Region
      3e-21   75.6   0.0    5.8e-21   74.7   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    6.7e-06   26.3   0.0    1.3e-05   25.4   0.0    1.5  1  Dynamin_N     Dynamin family
    6.6e-05   22.5   0.0     0.0002   20.9   0.0    1.8  2  FeoB_N        Ferrous iron transport protein B
    0.00084   19.0   0.2     0.0014   18.2   0.2    1.3  1  DAO           FAD dependent oxidoreductase
     0.0013   18.8   0.0     0.0024   17.9   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0031   17.4   0.0       0.21   11.5   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.017   14.5   0.0        1.5    8.2   0.0    2.3  2  Arf           ADP-ribosylation factor family
      0.018   15.4   1.4      0.059   13.8   0.1    2.5  3  AAA_16        AAA ATPase domain
      0.024   14.3   3.5       0.61    9.7   0.1    3.3  4  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.048   14.2   0.0        0.1   13.1   0.0    1.4  1  AAA_23        AAA domain
      0.056   12.9   0.0      0.094   12.1   0.0    1.3  1  SRPRB         Signal recognition particle receptor beta subun
      0.074   12.6   0.3         15    5.1   0.0    2.6  2  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.11   13.1   0.4       0.31   11.6   0.2    1.8  1  ABC_tran      ABC transporter
       0.24   10.4   0.0       0.36    9.8   0.0    1.2  1  IIGP          Interferon-inducible GTPase (IIGP)


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   1.3e-35   1.5e-32       2      89 .]      90     177 ..      89     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1.3e-35
                      GTP-bdg_N   2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRt 81 
                                    +sl+El++La+tag +v++ ++q+r+kpdp+tyiG+Gk+ e++e++ ++ ad+vi+d eLsp+q   Lek+++vkViDRt
  gi|121638600|ref|YP_978824.1|  90 ASLAELAALAETAGSQVLEGLIQRRDKPDPSTYIGSGKAAELREVIVATGADTVICDGELSPAQLTALEKAVQVKVIDRT 169
                                    69****************************************************************************** PP

                      GTP-bdg_N  82 qLILdIFA 89 
                                    +LILdIFA
  gi|121638600|ref|YP_978824.1| 170 ALILDIFA 177
                                    *******8 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.7   7.9e+02      47      72 ..      40      65 ..      27      73 .. 0.79
   2 !  102.4   7.1   1.3e-32   1.5e-29       1      79 []     179     265 ..     179     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                                   XHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M 47 leldrrlireriaklkkeLekvkkkr 72
                                   l l+ r   +r+a l +eL++v++ +
  gi|121638600|ref|YP_978824.1| 40 LALEDRSALRRVAGLSTELADVSEVE 65
                                   5567788999**********998765 PP

  == domain 2  score: 102.4 bits;  conditional E-value: 1.3e-32
                                    H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..........XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGg........igtrGpGetkleldrrlireriaklkkeLekvkkkr 72 
                                    +A+++e+k+QV lAq++y+lprL+g+g+++srq+Gg        +g+rGpGetk+e+drr+irer+akl+++++++k+ r
  gi|121638600|ref|YP_978824.1| 179 HATSREGKAQVSLAQMEYMLPRLRGWGESMSRQAGGragdsgggVGLRGPGETKIETDRRRIRERMAKLRRDIRAMKQVR 258
                                    9********************************7744444443378********************************** PP

                                    H.....T CS
                      GTP-bdg_M  73 elqrkkR 79 
                                    ++qr++R
  gi|121638600|ref|YP_978824.1| 259 DTQRSRR 265
                                    *****99 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   5.2e-24   5.8e-21       2     114 .]     273     395 ..     272     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 5.2e-24
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHC....T CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflalee....a 76 
                                    +aivG++N+GKS+L+naltg+ + v+d  ++T++++++r ++++ ++++l+Dt+G++   +   +l +af++  e    a
  gi|121638600|ref|YP_978824.1| 273 IAIVGYTNAGKSSLLNALTGAGVLVQDALFATLEPTTRRAEFGDgRPVVLTDTVGFVR--HLPTQLVEAFRSTLEevvhA 350
                                    8****************************************8877**********776..66667777777744445449 PP

                                    SEEEEEEETT....TTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
                       MMR_HSR1  77 dlillvvdas....eeklkpldeeleellee...akkplilvlnk 114
                                    dl+++vvd s     ++++++++ + e++ +   +  p +lv+nk
  gi|121638600|ref|YP_978824.1| 351 DLLVHVVDGSdghpLAQIDAVRQVISEVIADhdgDPPPELLVVNK 395
                                    ********7765553345555555555544354455557778887 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.1e-08   1.3e-05       1      37 [.     273     309 ..     273     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.1e-08
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EE CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrple 37 
                                    ia+vG +++GKSS+lnaL+g+ +l+ ++   T  p++
  gi|121638600|ref|YP_978824.1| 273 IAIVGYTNAGKSSLLNALTGAGVLVQDALFATLEPTT 309
                                    89***********************999988888875 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.8e-07    0.0002       2      88 ..     272     359 ..     271     368 .. 0.85
   2 ?   -2.7   0.0       3.4   3.8e+03     128     153 ..     405     429 ..     387     431 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHHCTSSS CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardflleeepd 80 
                                    ++a+vG  n+Gk++l+naltga   v      t e ++ + ++ + + v ++D  G     ++   e    ++    ++d
  gi|121638600|ref|YP_978824.1| 272 SIAIVGYTNAGKSSLLNALTGAGVLVQDALFATLEPTTRRAEFGDgRPVVLTDTVGFVRHLPTQLVEAFRSTLEEVVHAD 351
                                    589************************9999999999999998776999999*999988777777776655555566788 PP

                                    EEEEEEEG CS
                         FeoB_N  81 vvvnvvda 88 
                                    ++v+vvd 
  gi|121638600|ref|YP_978824.1| 352 LLVHVVDG 359
                                    88888886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                    HHHHHHHTS-EEEEBTTTTBTHHHHH CS
                         FeoB_N 128 kkLsekLgvpvvktsakkkegieell 153
                                    +kL++ L    v +sa++++gi++l+
  gi|121638600|ref|YP_978824.1| 405 AKLRHGLPG-AVFVSARTGDGIDALR 429
                                    444444433.3567888888888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.3e-06    0.0014      99     299 ..      42     247 ..      16     296 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTS.EEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEET CS
                            DAO  99 ldkllallleagldaelldaeevrelepalpgll.galfypdtgqvdpakltaalaraaealGveilegtevtgleeedg 177
                                    l+++ al++ agl +el d +ev+ ++  l++++  ++++ +   +d ++ +a la+ ae++G ++leg  +++ +++d 
  gi|121638600|ref|YP_978824.1|  42 LEDRSALRRVAGLSTELADVSEVEYRQLRLERVVlVGVWTEG-SAADNRASLAELAALAETAGSQVLEG-LIQRRDKPDP 119
                                    445555555567777776666666555224444437888888.666***********************.8888777763 PP

                                    CEEEEEEECTEEE..EEEEEEEE--GGGHHHH.HTT..CTTTSEEEEEEEEEEEE.EECCTHSTGSGCSEEEEE...EEE CS
                            DAO 178 kvwgverttpgen..daadavVnaaGawsdll.gll..keldlpispvrgqvlvl.kplseklvspaailpvpe...tdd 248
                                      + +     g+    + + v++a+Ga + +  g l   +l       ++  + + +++ + l+  a++++ +e    + 
  gi|121638600|ref|YP_978824.1| 120 S-TYI-----GSGkaAELREVIVATGADTVICdGELspAQL--T-ALEKAVQVKViDRTALILDIFAQHATSREgkaQVS 190
                                    3.444.....2221123567******998655544433333..2.22222222221222222222222222222557778 PP

                                    TTTTEEEEEE..........TTSEEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGGG CS
                            DAO 249 dgrgvyvtpr..........kdgrvlvGgtad.eesgdddpevdeedidellealrklfPql 299
                                     + + y++pr                +Gg a    +g +   + e +i+  ++++r+++ +l
  gi|121638600|ref|YP_978824.1| 191 LAQMEYMLPRlrgwgesmsrQ-----AGGRAGdSGGGVGLRGPGETKIETDRRRIRERMAKL 247
                                    888888888844333332220.....222221211222225555555555555555555554 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.1e-06    0.0024      57     100 ..     388     432 ..     366     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                   MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelar.epnsvviSaekelnldeLkeki 100
                                    p l+v+NK+D +s+  l +l++  p +v++Sa+++ ++d+L  ++
  gi|121638600|ref|YP_978824.1| 388 PELLVVNKVDVASDLMLAKLRHgLPGAVFVSARTGDGIDALRRRM 432
                                    7899*****************9569****************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00019      0.21     100     125 ..     271     296 ..     231     331 .. 0.69
   2 ?    3.5   0.0     0.052        58      50      99 ..     390     434 ..     367     438 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                    SEEEEECSTTSSHHHHHHHHCTT--- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelel 125
                                      +++vG + +GKS+L+nal++   l
  gi|121638600|ref|YP_978824.1| 271 PSIAIVGYTNAGKSSLLNALTGAGVL 296
                                    56889***************997544 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.052
                                    EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                    ++v+nK+D++++   l +l++ l       ++vsa+t++g+++l++++++
  gi|121638600|ref|YP_978824.1| 390 LLVVNKVDVASDLM-LAKLRHGLPG----AVFVSARTGDGIDALRRRMAE 434
                                    799********999.5555555544....58999**********998876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.028        32      16      36 ..     272     292 ..     254     316 .. 0.81
   2 ?    8.2   0.0    0.0013       1.5      82     140 ..     350     411 ..     338     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.028
                                    EEEEEESTTSSHHHHHHHHHH CS
                            Arf  16 rilllGLDnaGKtTilkklkl 36 
                                     i ++G  naGK+ +l+ l+ 
  gi|121638600|ref|YP_978824.1| 272 SIAIVGYTNAGKSSLLNALTG 292
                                    5789*************9975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                    ESEEEEEEETT-CT...THHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHT CS
                            Arf  82 tdavifvvDsadre...RleeakeeLkalleeeelkevallvlaNKqDlpealseeelrell 140
                                     d +++vvD +d +    ++  ++ +++++++++    + l++ NK D++++l  ++lr+ l
  gi|121638600|ref|YP_978824.1| 350 ADLLVHVVDGSDGHplaQIDAVRQVISEVIADHDGDPPPELLVVNKVDVASDLMLAKLRHGL 411
                                    6889*******98644488999*****************************99999888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.6   1.8e+03      72      88 ..      98     113 ..      46     181 .. 0.59
   2 ?   -1.0   0.0       1.7     2e+03      34      93 ..     124     183 ..     120     250 .. 0.60
   3 ?   13.8   0.1   5.3e-05     0.059      10     148 ..     255     400 ..     247     447 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                         AAA_16  72 laqalareellrqllde 88 
                                    la+++  +++l+ l ++
  gi|121638600|ref|YP_978824.1|  98 LAETA-GSQVLEGLIQR 113
                                    44444.22333333333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                         AAA_16  34 GvGKsslvrellralekdggif....lrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                    G+GK + +re+  a  +d +i+      ++ + le+    ++ +++++r  l+ ++ ++++++ 
  gi|121638600|ref|YP_978824.1| 124 GSGKAAELREVIVATGADTVICdgelSPAQLTALEK----AVQVKVIDRTALILDIFAQHATSR 183
                                    788888888777444444344442222222222222....334556666666666666655433 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5.3e-05
                         AAA_16  10 eqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggif...lrgkcdqlesaipy.....salaqalaree 80 
                                    +q++++ ++ r+++  +++ ++G+   GKssl+++l     ++g+++   l ++ +  ++ +++     ++l+++    +
  gi|121638600|ref|YP_978824.1| 255 KQVRDTQRSRRRHSDvPSIAIVGYTNAGKSSLLNALT----GAGVLVqdaLFATLEPTTRRAEFgdgrpVVLTDTV---G 327
                                    6777777744444445*****************8888....44444433333333333444455554322344444...7 PP

                         AAA_16  81 llrqlldeaesaeleawrekleeala.........avpelagaea....srllellkrllallsrderplvlvlDdlqwa 147
                                    ++r l ++    ++ea+r +lee++           ++      +     ++++++++ +a    d +p +lv+  ++ a
  gi|121638600|ref|YP_978824.1| 328 FVRHLPTQ----LVEAFRSTLEEVVHadllvhvvdGSDGH----PlaqiDAVRQVISEVIADHDGDPPPELLVVNKVDVA 399
                                    77777777....6666666666666655556544422222....123347777777777755555455566666666655 PP

                         AAA_16 148 d 148
                                     
  gi|121638600|ref|YP_978824.1| 400 S 400
                                    5 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.85   9.5e+02       7      21 ..     121     135 ..     120     153 .. 0.79
   2 ?   -2.3   0.0       2.5   2.8e+03      95     142 ..     150     192 ..     140     195 .. 0.52
   3 ?    3.3   0.1     0.047        53       3      21 ..     273     291 ..     271     300 .. 0.87
   4 ?    9.7   0.1   0.00054      0.61      84     160 ..     319     405 ..     291     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.85
                                    ESTTCCHHHHHHHHH CS
                           cobW   7 GflGsGKTtLlnhll 21 
                                     ++GsGK + l++++
  gi|121638600|ref|YP_978824.1| 121 TYIGSGKAAELREVI 135
                                    589*****9999998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                    THHHHHTTSHHHHHCCCECEEEEEEETTTH....CCHCCHHHHHHHHHHTS CS
                           cobW  95 ePapvafteeelksdltldavvavvDaknl...eaeeekieekaedqlaaa 142
                                    +Pa+++        +l+  + v v+D ++l     +++ ++++++ q+  a
  gi|121638600|ref|YP_978824.1| 150 SPAQLT--------ALEKAVQVKVIDRTALildIFAQHATSREGKAQVSLA 192
                                    455552........2333334444444444444245566666666666666 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.047
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    + ++G+  +GK++Lln+l+
  gi|121638600|ref|YP_978824.1| 273 IAIVGYTNAGKSSLLNALT 291
                                    789*************986 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00054
                                    SEEEEEECTTTT..HHHHHTT..SHHHHHCCCECEEEEEEETTTH...CCHCCHHHHHHHHHHTSS......EEEEE-HH CS
                           cobW  84 dviliEttGlae..Papvaft..eeelksdltldavvavvDaknl..eaeeekieekaedqlaaad......llvlnKtD 151
                                     v+l  t+G +   P++++ +   ++l++ + +d +v vvD++     a+ +  ++ + + +a  d      llv+nK+D
  gi|121638600|ref|YP_978824.1| 319 PVVLTDTVGFVRhlPTQLV-EafRSTLEEVVHADLLVHVVDGSDGhpLAQIDAVRQVISEVIADHDgdpppeLLVVNKVD 397
                                    4788899996651255553.246999****************8878855666666666666665544444449******* PP

                                    HHCHC..HH CS
                           cobW 152 lldeealle 160
                                    ++++  l +
  gi|121638600|ref|YP_978824.1| 398 VASDLML-A 405
                                    *998844.4 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-05       0.1      21      42 ..     272     293 ..     268     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                         AAA_23  21 ltlItGpNGaGKTTildAikla 42 
                                      +I+G + aGK+++l+A++ a
  gi|121638600|ref|YP_978824.1| 272 SIAIVGYTNAGKSSLLNALTGA 293
                                    578****************965 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.4e-05     0.094       3      86 ..     270     360 ..     268     408 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                                    --EEEEE-STTSSHHHHHHHHHHS..S---B---SS-EEETTG...GGTT-SEEEETT-GC.CSHHHHHHHHHHGG.... CS
                          SRPRB   3 kpavllvGlsdsGKTslftrLttd..svkktvtSqessaalkvksekgskltliDfPGhek.lrqklleklkakss.... 75 
                                     p++ +vG +++GK sl++ Lt     v+++  +  + ++ + +  +g  + l D  G ++ l ++l+e ++   +    
  gi|121638600|ref|YP_978824.1| 270 VPSIAIVGYTNAGKSSLLNALTGAgvLVQDALFATLEPTTRRAEFGDGRPVVLTDTVGFVRhLPTQLVEAFRSTLEevvh 349
                                    68999*****************88777788888885566777778999**********9865899999986543222212 PP

                                    EEEEEEEEETT CS
                          SRPRB  76 lkglvfvvDSt 86 
                                    +  lv+vvD +
  gi|121638600|ref|YP_978824.1| 350 ADLLVHVVDGS 360
                                    45588888865 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        15       3      24 ..     270     291 ..     268     304 .. 0.87
   2 ?    4.6   0.1     0.018        20      92     136 ..     348     401 ..     338     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                    EEEEEEEESTTSSHHHHHHHHH CS
                       GTP_EFTU   3 irnigiighvDhGKtTLtdrLl 24 
                                    +  i+i+g +++GK++L+ +L+
  gi|121638600|ref|YP_978824.1| 270 VPSIAIVGYTNAGKSSLLNALT 291
                                    5689***************997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                                    HT-SEEEEEEETTTB........STHHHHHHHHHHHHTTTEEEEEEESCGST.H CS
                       GTP_EFTU  92 rvlDgavlvvdaveG........vepqteevlrlalkegvpiivfiNKmDrl.k 136
                                      +D+ v vvd ++G        v +   ev+        p  +++NK+D + +
  gi|121638600|ref|YP_978824.1| 348 VHADLLVHVVDGSDGhplaqidaVRQVISEVIADHDGDPPPELLVVNKVDVAsD 401
                                    568999*********7666666566666666666666666699*******8742 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00027      0.31      14      33 ..     273     292 ..     267     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                    EEEEESTTSSHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  14 vaivGenGaGKStLlkllag 33 
                                    +aivG + aGKS+Ll++l+g
  gi|121638600|ref|YP_978824.1| 273 IAIVGYTNAGKSSLLNALTG 292
                                    79****************98 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00032      0.36      32      64 ..     267     299 ..     235     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                                    HT--EEEEEEESTTSSHHHHHHHHTT--TTSTT CS
                           IIGP  32 esaklkiavtGdsGnGkssFinaLRliGheeed 64 
                                    +s + +ia++G + +Gkss +naL + G   +d
  gi|121638600|ref|YP_978824.1| 267 HSDVPSIAIVGYTNAGKSSLLNALTGAGVLVQD 299
                                    344568******************999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3128.48
//
Query:       gi|121638601|ref|YP_978825.1|  [L=289]
Description: diaminopimelate epimerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-63  212.9   5.0    1.8e-42  144.4   0.3    2.1  2  DAP_epimerase  Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4   0.3   9.9e-47   1.8e-42       1     120 [.       3     141 ..       3     142 .. 0.96
   2 !   70.8   0.6   6.2e-24   1.1e-19       2     118 ..     158     272 ..     157     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 9.9e-47
                                    EEEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEE................EEETTEEEEEEEETTTE CS
                  DAP_epimerase   1 fakshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvk................psgeediklryfnrdgs 64 
                                    fak+hG++nd+v+++dv+aelvl+a++vaalcdr++g+gadgvl+v+                 ++ +d  ++y+n+dgs
  gi|121638601|ref|YP_978825.1|   3 FAKGHGTQNDFVLLPDVDAELVLTAARVAALCDRRKGLGADGVLRVTtagaaqavgvldslpeGVRVTDWYMDYRNADGS 82 
                                    89*********************************************99999999999888876777888888******* PP

                                    EESTTHCCHHHHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS...EEEEEE--EE CS
                  DAP_epimerase  65 eaemCGnGvrvfaaylreggletkkevtvetlgGeleievkddgek...vkvdmGkasl 120
                                    +a+mCGnGvrvfa+ylr++gle ++e++v++l+G++++++++++++   v+vdmGka++
  gi|121638601|ref|YP_978825.1|  83 AAQMCGNGVRVFAHYLRASGLEVRDEFVVGSLAGPRPVTCHHVEAAyadVSVDMGKANR 141
                                    *********************************************9***********97 PP

  == domain 2  score: 70.8 bits;  conditional E-value: 6.2e-24
                                    EEECSSEEEEEEECCTTCSSHHH.HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCC.HHHHHHH CS
                  DAP_epimerase   2 akshGnpndvvvvddveaelvle.aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnG.vrvfaay 79 
                                    a+++Gnp++++v  ++  + +   +  ++   d  ++p++++v++ ++  +  + +r+++r+ +e+++CG+G v++++a+
  gi|121638601|ref|YP_978825.1| 158 AVDVGNPHLACVDSQLTVDGLAAlDVGAPVSFDGAQFPDGVNVEVLTAPVDGAVWMRVHERGVGETRSCGTGtVAAAVAA 237
                                    799************99999988999****************************************************** PP

                                    HHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE-- CS
                  DAP_epimerase  80 lreggletkkevtvetlgGeleievkddgekvkvdmGka 118
                                    l++ g   + ++tv+++gGe++++v+d ++   +  G+ 
  gi|121638601|ref|YP_978825.1| 238 LAAVGSP-TGTLTVHVPGGEVVVTVTDATS---FLRGPS 272
                                    ****977.9*****************9974...666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2420.94
//
Query:       gi|121638602|ref|YP_978826.1|  [L=314]
Description: tRNA delta(2)-isopentenylpyrophosphate transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-70  235.5   0.0    7.5e-70  235.3   0.0    1.0  1  IPPT            IPP transferase
    0.00025   21.2   0.8     0.0067   16.6   0.7    2.6  1  AAA_33          AAA domain
     0.0038   16.6   0.0     0.0057   16.1   0.0    1.3  1  IPT             Isopentenyl transferase
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.029   14.4   0.0    1.5  1  AAA_5           AAA domain (dynein-related subfamily)
      0.022   14.5   1.6      0.049   13.4   0.4    2.2  2  Cytidylate_kin  Cytidylate kinase
      0.084   13.3   0.0       0.13   12.7   0.0    1.4  1  AAA             ATPase family associated with various cellula
        0.1   13.2   0.0       0.74   10.4   0.0    2.2  1  AAA_18          AAA domain
       0.14   12.4   0.0        0.3   11.4   0.0    1.5  1  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> IPPT  IPP transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.3   0.0   3.3e-73   7.5e-70       1     227 [.      40     286 ..      40     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 3.3e-73
                                    TTBTT-HTTTT---HHHHTTS-EESSS-B-TTS---HHHHHHHHHHHHHHHHHTT-EEEEEES-HHHHHHHHCTG-S--B CS
                           IPPT   1 qvYrgmdIgTakptaeeragvphhlidildpdeeysvadFqkdalkaieeilargkipilvGGTglYikallegldelpe 80 
                                    q+YrgmdIgTak   +er+g+phh +d+ld++e+ +va++q++a + ie i arg +p++vGG++lY+++ll+++ ++p+
  gi|121638602|ref|YP_978826.1|  40 QLYRGMDIGTAKLPVSERRGIPHHQLDVLDVTETATVARYQRAAAADIEAIAARGAVPVVVGGSMLYVQSLLDDW-SFPA 118
                                    89*************************************************************************.7*** PP

                                    --HHHHHHHHHHHHHSHHHHHHHHHHHC-HHHHTTS-TT-HHHHHHHHHHHHHHSS-HH...........ECEEEEEECS CS
                           IPPT  81 adeelraeleeeaeeeglealheelkevdpeaaakihpndrqRiiRalevyeetgkpls...........ellviglesd 149
                                    +d+++ra++e++++e g ++lh+el++ dp+aaa i p+d +R++Ralev+e+tg+p++           +++++gl+ +
  gi|121638602|ref|YP_978826.1| 119 TDPSVRARWERRLAEVGVDRLHAELARRDPAAAAAILPTDARRTVRALEVVELTGQPFAasaprigaprwDTVIVGLDCQ 198
                                    ************8899*******************************************9999999999878*****88* PP

                                    HHHHHHHHHHHHHHHHHTTHHHHHHHHHH.......CCCCSTTSHHHHHHHT...TSS-HHHHHHHHHHHHHHHHHHHHH CS
                           IPPT 150 reelyeridkRvdemleaGlleEveklla.......kalqaigykelleyle...gelsleeaieklkaatrqyaKrQlt 219
                                    + +l+er+++R+d m+++Gl+eEv++ll+       +a +a+gy ++++ l+   g   + +a+e++   tr+y++rQ++
  gi|121638602|ref|YP_978826.1| 199 TTILDERLARRTDLMFDQGLVEEVRTLLRnglregvTASRALGYAQVIAALDagaGADMMRAAREQTYLGTRRYVRRQRS 278
                                    ****************************8777777667*************94322334889****************** PP

                                    HHHTTCCE CS
                           IPPT 220 Wfrkkkei 227
                                    Wfr+++++
  gi|121638602|ref|YP_978826.1| 279 WFRRDHRV 286
                                    ***99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7     3e-06    0.0067       4      76 ..       6      92 ..       4     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                         AAA_33  4 lvGlpGsGKstlaerllkklg....avllssdt.........................lrrrlfgtdqqsktdytrvldrly 56
                                   ++G+ G+GKs+la  ++++lg    +++++ d+                                          +vld + 
  gi|121638602|ref|YP_978826.1|  6 IIGPTGAGKSQLALDVAARLGarvsVEIVNADAmqlyrgmdigtaklpvserrgiphhQ---------------LDVLDVTE 72
                                   79********************999999***9977655555555554444444444430...............34444444 PP

                         AAA_33 57 qilnelarkalsagrnvild 76
                                     + ++ ++a++a + +i+ 
  gi|121638602|ref|YP_978826.1| 73 TATVARYQRAAAADIEAIAA 92
                                   44444444444444444433 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.5e-06    0.0057       5     107 ..       5     111 ..       1     134 [. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                            IPT   5 lifGatttGKtaeaiklaketga....pvivlDRvqcyselavgsGrpleeelegtrRiylddrslseGvidaeeanerL 80 
                                    +i G+t+ GK++ a  +a + ga     ++ +D +q y  + +g+ +   +e +g+    ld   ++e   + +++++  
  gi|121638602|ref|YP_978826.1|   5 AIIGPTGAGKSQLALDVAARLGArvsvEIVNADAMQLYRGMDIGTAKLPVSERRGIPHHQLDVLDVTETA-TVARYQRAA 83 
                                    79***********999998876522116799*************99988889888888888888887765.444667777 PP

                            IPT  81 ikevesykdeegl.ilEGGSiSLlkrma 107
                                     + +e+  +++++ ++ GGS+  ++ + 
  gi|121638602|ref|YP_978826.1|  84 AADIEAIAARGAVpVVVGGSMLYVQSLL 111
                                    7777777776665577777776666555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.029       2      34 ..       4      36 ..       3      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltr 34
                                   + ++Gp+G gKs+la  +aa+l+++v +   ++
  gi|121638602|ref|YP_978826.1|  4 LAIIGPTGAGKSQLALDVAARLGARVSVEIVNA 36
                                   5689******************66555544444 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   2.2e-05     0.049       2      26 ..       5      29 ..       4     137 .. 0.72
   2 ?   -0.2   0.2      0.31   6.9e+02     139     172 ..     122     148 ..     118     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                   EEE-STTSSHHHHHHHHHHHHT-EE CS
                 Cytidylate_kin  2 aiDGPagsGKssvaralaeklglky 26
                                   ai GP+g+GKs +a  +a +lg+++
  gi|121638602|ref|YP_978826.1|  5 AIIGPTGAGKSQLALDVAARLGARV 29
                                   899*************999999864 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                    -HHHHHHHHHHHHHHTT----HHHHHHHHHHHHH CS
                 Cytidylate_kin 139 sveeRakRRlkqlkakgtsvsleellaeikeRDk 172
                                    sv++R +RRl++       v +++l ae+++RD 
  gi|121638602|ref|YP_978826.1| 122 SVRARWERRLAE-------VGVDRLHAELARRDP 148
                                    777788888887.......667899999999985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.8e-05      0.13       3      35 ..       6      42 ..       4      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                                   EESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakelg....vefleisgsell 35
                                   ++Gp G GK+ la  va  lg    ve+++ ++++l 
  gi|121638602|ref|YP_978826.1|  6 IIGPTGAGKSQLALDVAARLGarvsVEIVNADAMQLY 42
                                   79*****************983333555555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.74       2      25 ..       5      31 ..       4     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                         AAA_18  2 lltGtpGvGKttlakeLskrlgf...g 25
                                   ++ G+ G+GK++la  ++ rlg    +
  gi|121638602|ref|YP_978826.1|  5 AIIGPTGAGKSQLALDVAARLGArvsV 31
                                   589**************9999544441 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.3       8      31 ..       4      27 ..       2      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                         AAA_22  8 lvvtGesGtGKTtllrrlleqlde 31
                                   l+++G++G+GK+ l+  ++ +l +
  gi|121638602|ref|YP_978826.1|  4 LAIIGPTGAGKSQLALDVAARLGA 27
                                   79*************999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2053.05
//
Query:       gi|121638603|ref|YP_978827.1|  [L=231]
Description: hypothetical protein BCG_2741c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1830.30
//
Query:       gi|121638604|ref|YP_978828.1|  [L=301]
Description: integral membrane alanine and valine and leucine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.7  27.2     0.0085   16.3   4.3    4.3  4  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.029   14.4   0.2      0.029   14.4   0.2    2.0  2  PA        PA domain


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0011        10       3      39 ..       7      43 ..       5      48 .. 0.87
   2 !   16.3   4.3   9.5e-07    0.0085      70     136 ..      55     121 ..      44     122 .. 0.93
   3 !    5.1   3.2    0.0027        24       2      56 ..     164     220 ..     163     236 .. 0.84
   4 !    5.6   3.2    0.0019        17      97     136 ..     233     272 ..     222     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                           EamA  3 gillallaalfwaiyfvlskillrkvspltltfvrfl 39
                                   + +lal aal+ +i++v+ ++  r+v   +++++ +l
  gi|121638604|ref|YP_978828.1|  7 ATILALGAALLAGIGYVTLQRSARQVTAEEYVGHLTL 43
                                   579********************99999988887666 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.5e-07
                           EamA  70 lgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    lg l+ v+ f l+ +al+ +s+  +  +++++ +f+l++ + l + + t ++++ +vl   +v++i+
  gi|121638604|ref|YP_978828.1|  55 LGSLAAVASFTLQAIALTMGSVVLVQSLQATALLFALLIDARLTHHRCTPREWMWAVLLAGAVAVIV 121
                                    7888999********************************************************9997 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0027
                           EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrf..liagillliiallkegkl 56 
                                    +++lla++++ + a+ +vl+k +++++   ++t +r+  l a il+l+i l+ +++ 
  gi|121638604|ref|YP_978828.1| 164 SAVLLAVASSATLAVFTVLTKGVVTELGEGFATLIRTpeLYAWILVLPIGLMLQQSS 220
                                    6899***************************99999944599999999988887766 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0019
                           EamA  97 itslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    it   Pv++ +l++ +l e l    ++ ++l+ + v++++
  gi|121638604|ref|YP_978828.1| 233 ITVARPVIASVLGITVLDEVLHTGRVALVALVAVVVVVVV 272
                                    56678***************************99999986 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.2e-06     0.029      25      72 ..      72     135 ..      55     160 .. 0.70
   2 ?   -2.0   0.6      0.43   3.9e+03      41      41 ..     275     275 ..     252     300 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-06
                             PA  25 k.GkivLvqr......tf...............aeKarnAqaaGAagviivndgelgaatgasgnegepd 72 
                                    + G++vLvq+       f               +e ++++  aGA++vi+ +        +a+g+ + p 
  gi|121638604|ref|YP_978828.1|  72 TmGSVVLVQSlqatalLFallidarlthhrctpREWMWAVLLAGAVAVIVMSGN------PAAGTTRAPF 135
                                    449999998666555433888888899999999******************522......2222333332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.43
                             PA  41 n 41 
                                    +
  gi|121638604|ref|YP_978828.1| 275 V 275
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2047.32
//
Query:       gi|121638605|ref|YP_978829.1|  [L=158]
Description: hypothetical protein BCG_2743 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1097.83
//
Query:       gi|121638606|ref|YP_978830.1|  [L=450]
Description: hypothetical protein BCG_2744 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-44  147.8  33.7    4.1e-19   68.7   2.5    4.7  4  DUF349       Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   5.9   2.1e-15   3.7e-11       2      75 .]     140     213 ..     139     213 .. 0.93
   2 !   68.7   2.5   2.3e-23   4.1e-19       1      74 [.     217     289 ..     217     290 .. 0.97
   3 !   63.6   9.7   8.8e-22   1.6e-17       1      75 []     294     366 ..     294     366 .. 0.95
   4 ?   -9.6  15.7         1   1.8e+04      10      55 ..     398     441 ..     370     447 .. 0.69

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.1e-15
                         DUF349   2 LwkrFraacdafferrkahfeeqdaereenlekKealieeaealaksttdwksatkrlkelqeeWkeiGpVprk 75 
                                    L +r+ +++d+++   +a ++ +++ r++  ++Keal +eae+la+++t+wk a +rl+++ +eWk+i  V+rk
  gi|121638606|ref|YP_978830.1| 140 LADRLTSIRDRAEVIAAADRSRREEHRAAQTARKEALAAEAEELAANATQWKVAGDRLRAILDEWKTISGVDRK 213
                                    6778888888888888999999************************999***********************97 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 2.3e-23
                         DUF349   1 aLwkrFraacdafferrkahfeeqdaereenlekKealieeaealaksttdwksatkrlkelqeeWkeiGpVpr 74 
                                    aLwkr+++a+d+f++rr  hf+e+d+er    + Ke l+e+ae+l +s tdw ++++++++l + Wk++G++ +
  gi|121638606|ref|YP_978830.1| 217 ALWKRYSTARDTFNRRRGSHFAELDRERSGVRQSKERLCERAEELSES-TDWTATSAEFRKLLADWKAAGRASK 289
                                    69*******************************************999.5********************9876 PP

  == domain 3  score: 63.6 bits;  conditional E-value: 8.8e-22
                         DUF349   1 aLwkrFraacdafferrkahfeeqdaereenlekKealieeaealaksttdwksatkrlkelqeeWkeiGpVprk 75 
                                    aLw+rF+aa+d ff +r+a+ +e++ae  +n ++Keal++eae l+++  + ++a+++l+++ e+W +iG+V r+
  gi|121638606|ref|YP_978830.1| 294 ALWRRFKAAQDSFFTARNAATAEKEAELRANADAKEALLAEAERLDTT--NHEAARAALRSIAEKWDAIGKVSRE 366
                                    69*******************************************554..569*******************986 PP

  == domain 4  score: -9.6 bits;  conditional E-value: 1
                         DUF349  10 cdafferrkahfeeqdaereenlekKealieeaealaksttdwksa 55 
                                    + + f++r+++fe q ++ +++   Kea  +ea+a a++  +w +a
  gi|121638606|ref|YP_978830.1| 398 RAEQFRARAEQFEHQAEKAAAAGRTKEA--DEAKANAEQWRQWAEA 441
                                    4445666777777776666666666665..5666655554466444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1465  (0.0817112); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2867.31
//
Query:       gi|121638607|ref|YP_978831.1|  [L=204]
Description: hypothetical protein BCG_2745c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.8    7.9   3.9         16    5.4   4.1    2.1  2  UPF0139   Uncharacterised protein family (UPF0139)


Domain annotation for each model (and alignments):
>> UPF0139  Uncharacterised protein family (UPF0139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.02   3.6e+02      43      58 ..      74      89 ..      70      92 .. 0.80
   2 ?    5.4   4.1    0.0009        16      33      59 ..      87     113 ..      80     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.02
                        UPF0139 43 lmlklkwcaWvalvcs 58
                                   + l  ++ aW+alv+ 
  gi|121638607|ref|YP_978831.1| 74 VALPSRVFAWLALVFG 89
                                   66778999*****986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0009
                        UPF0139  33 llgmifsllglmlklkwcaWvalvcsl 59 
                                    ++g+ fs+l+l+ +   +aWval  s+
  gi|121638607|ref|YP_978831.1|  87 VFGVGFSMLALLTRRWALAWVALAGSA 113
                                    678889****************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1497.01
//
Query:       gi|121638608|ref|YP_978832.1|  [L=512]
Description: (dimethylallyl)adenosine tRNA methylthiotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-30  107.1   0.0      2e-30  106.4   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    9.1e-29   99.4   0.0    1.8e-28   98.5   0.0    1.5  1  UPF0004      Uncharacterized protein family UPF0004
     0.0035   17.4   0.0      0.013   15.5   0.0    2.0  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.035   14.1   0.1      0.086   12.8   0.1    1.7  1  TRAM         TRAM domain
      0.053   13.7   0.1       0.15   12.2   0.1    1.9  1  TRAM_2       TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.0   5.6e-34     2e-30       1     166 [.     172     349 ..     172     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 5.6e-34
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.............TTHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.............pdfvell 67 
                                    v+++ gCn+ C+fC++p+    +gr+ ++s+ +il+ev++l +++gv ev+l+g+++++y               f+ell
  gi|121638608|ref|YP_978832.1| 172 VSISVGCNNSCTFCIVPS---LRGREVDRSPADILAEVRSL-VNDGVLEVTLLGQNVNAYgvsfadpalprnrGAFAELL 247
                                    57899************8...9*******************.9***************************9998899999 PP

                                    HHHHHTCCCTEEEEEEECSSCHG.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  68 erlaklavpgiritvetngtlpd.eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                    +++  ++    r++++++++    ++++e++++ +  +  ++++l++++d+ +l+ m+r +  e++l  +e+ r+a i+ 
  gi|121638608|ref|YP_978832.1| 248 RACGDID-GLERVRFTSPHPAEFtDDVIEAMAQTRnvCPALHMPLQSGSDR-ILRAMRRSYRAERYLGIIERVRAA-IPH 324
                                    9999996.9999*****9999559***************************.************************.*** PP

                                    ...EEEEEEEBTTTSHHHHHHHHHH CS
                                    ...xxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 145 ...vvdrivglpGendeeleellel 166
                                       ++d ivg+pGe++e++ ++l+ 
  gi|121638608|ref|YP_978832.1| 325 aaiTTDLIVGFPGETEEDFAATLDV 349
                                    *********************9985 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   4.9e-32   1.8e-28       2      98 .]      27     125 ..      26     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 4.9e-32
                                    EEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS..T.--EEEEEEHHH CS
                        UPF0004   2 vaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk..kpekkvvvlGCma 79 
                                    +++ t+GCqmN++dse+la+lL+++gy++++d +eAdvv++nTCavre+a+++++ +l++l+  k  +p+++++v GC+a
  gi|121638608|ref|YP_978832.1|  27 YQVRTYGCQMNVHDSERLAGLLEAAGYRRATDGSEADVVVFNTCAVRENADNRLYGNLSHLAPRKraNPDMQIAVGGCLA 106
                                    5789*********************************************************9999777************ PP

                                    HS-HHHHHHH-TTS-EEE- CS
                        UPF0004  80 qrekeellkeepevdlvlg 98 
                                    q++++ +l+++p vd+v+g
  gi|121638608|ref|YP_978832.1| 107 QKDRDAVLRRAPWVDVVFG 125
                                    *****************98 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.7e-06     0.013      46     112 ..      56     126 ..      22     130 .. 0.70
   2 ?   -2.4   0.0       1.3   4.7e+03      26      39 ..     212     225 ..     194     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-06
                    B12-binding  46 airaekpdvvglSalltsqleav...kelvel..lkrirprvkvvvGGahpsldpeetleaklgiddvvvge 112
                                    a    ++dvv++ +    + ++     +l +l  +kr++p++ ++vGG  ++ d + +l+ ++  +dvv+g+
  gi|121638608|ref|YP_978832.1|  56 ATDGSEADVVVFNTCAVRENADNrlyGNLSHLapRKRANPDMQIAVGGCLAQKDRDAVLRRAPW-VDVVFGT 126
                                    44455788888854322222222123566666999************************98566.9999996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                    B12-binding  26 dagfeVqllganve 39 
                                    d   eV+llg nv+
  gi|121638608|ref|YP_978832.1| 212 DGVLEVTLLGQNVN 225
                                    22236666666654 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.4e-05     0.086       2      61 ..     404     469 ..     403     469 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                                    XXXXXEEEEEE.EEE-.TTSEEEEEET.....TEEEEETT-....-T..TEEEEEEEEEE-SSEEEEEE CS
                           TRAM   2 syvGstqeVlv.eglsksegegiGrtdn....gkvvfvpgd....lpgIGdfVeVkItkvkrqyLrGel 61 
                                    + vG+ +eVlv +g++ ++++ ++r+ +    g+ v +  +     p  Gd+ + k+t++ ++ L +++
  gi|121638608|ref|YP_978832.1| 404 ALVGQAVEVLVaTGEG-RKDTVTARMSGrardGRLVHFTAGqprvRP--GDVITTKVTEAAPHHLIADA 469
                                    689********77899.9999*****999999999988888788888..*************9999875 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.3e-05      0.15       1      62 [.     406     468 ..     406     469 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                                    BTSEEEEEEEE..EETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEEEE CS
                         TRAM_2   1 iGktvevlvdg..eeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLiGe 62 
                                    +G+ vevlv      ++ +++R    A +    v++t+++ ++ +Gd+++ k+t+a  + Li+ 
  gi|121638608|ref|YP_978832.1| 406 VGQAVEVLVATgeGRKDTVTARMSGRARDG-RLVHFTAGQPRVRPGDVITTKVTEAAPHHLIAD 468
                                    89*******998756668899999999753.46888887776559****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3302.61
//
Query:       gi|121638609|ref|YP_978833.1|  [L=284]
Description: hypothetical protein BCG_2747 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-97  323.4   0.0      1e-96  323.2   0.0    1.0  1  DUF5131   Protein of unknown function (DUF5131)


Domain annotation for each model (and alignments):
>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.2   0.0  5.8e-101     1e-96       2     247 .]       5     243 ..       4     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 323.2 bits;  conditional E-value: 5.8e-101
                        DUF5131   2 tkIewtdatwnpvtGCtkvspgCdnCyaerlakrlkaakaekyglklt...gkkaervrlseekleeplrwkkprrvfvn 78 
                                    + Iewt atwnpvtGC++vspgCd+Cya++lakrlka+++ ky+++     +     v++++++l+ep+rw++pr+vfvn
  gi|121638609|ref|YP_978833.1|   5 SAIEWTGATWNPVTGCDRVSPGCDHCYAMTLAKRLKAMGSDKYQTDGDprtSGPGFGVTIHPRSLDEPFRWRSPRTVFVN 84 
                                    89****************************************96664411134445799********************* PP

                        DUF5131  79 slsDlfhekvpdefidrvfaviaatpqhtflvlTKrpermrellkeaaeearvpenvwlGvsvenqkeaderiekLlavp 158
                                    s++Dlfh++v   fi++vf+v++atpqht+++lTKr+ r+r+l+++     ++p+nvw+Gvsven ++  +rie+L++vp
  gi|121638609|ref|YP_978833.1|  85 SMADLFHARVALWFIREVFEVMRATPQHTYQILTKRSLRLRRLAHK----LEWPSNVWMGVSVENVDA-FRRIEDLRQVP 159
                                    *******************************************999....67*************998.6********** PP

                        DUF5131 159 aavrflSvEPlLgpv...dlsgidwvivGGEsGpkarpmhpdWarslrdqcaaagvpFffkqwgewapaelarvgkkaag 235
                                    aavrflS+EPlLgp+   +l  idwvi+GGEsGp+ rp++p+W+r++rd+c+aa+vpFffkqwg         ++ ka g
  gi|121638609|ref|YP_978833.1| 160 AAVRFLSCEPLLGPLdgiNLGSIDWVIAGGESGPNFRPIDPQWVRHIRDTCTAADVPFFFKQWGG--------RTPKAFG 231
                                    **************9888899*******************************************9........6789*** PP

                        DUF5131 236 rlldgrtwdelP 247
                                    r+ldgr wde+P
  gi|121638609|ref|YP_978833.1| 232 RELDGRCWDEMP 243
                                    ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1908.61
//
Query:       gi|121638610|ref|YP_978834.1|  [L=330]
Description: hypothetical protein BCG_2748c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2547.90
//
Query:       gi|121638611|ref|YP_978835.1|  [L=174]
Description: recombination regulator RecX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-25   88.5   1.5    1.8e-23   83.3   0.2    1.8  2  RecX      RecX family


Domain annotation for each model (and alignments):
>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   2.4e-05      0.43      70     117 ..      12      54 ..       8      54 .. 0.90
   2 !   83.3   0.2     1e-27   1.8e-23       1     116 [.      39     161 ..      39     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                                    -HHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHTT--HHHHHHHHH CS
                           RecX  70 deeeqarelaekklkklkkeedekekqklvrfLarrGFssevirevlk 117
                                    ++eeqar+l+ + l++       + ++ l+ +La+rG++ ++ ++vl+
  gi|121638611|ref|YP_978835.1|  12 EREEQARALCLRLLTAR-----SRTRAELAGQLAKRGYPEDIGNRVLD 54 
                                    67899*********998.....799****************9999986 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1e-27
                                    SGGGT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH----HHHHHHHHHTTT--HHHHHHHHTTS-HHHH...HHH CS
                           RecX   1 LakkgfpeevieavierlkeeglldDerfAesfvrsrlrsrgyGprrikqeLkqkGiseelieqaleeldeeeq...are 77 
                                    Lak+g+pe++ ++v++rl++ gl+dD++fAe++v+sr ++  +++r++++eL+ kG+++++i ++l  +d  ++   a++
  gi|121638611|ref|YP_978835.1|  39 LAKRGYPEDIGNRVLDRLAAVGLVDDTDFAEQWVQSRRANAAKSKRALAAELHAKGVDDDVITTVLGGIDAGAErgrAEK 118
                                    799****************************************************************8887777788999 PP

                                    HHHHHHHHT....TTS-HHHHHHHHHHHHHHTT--HHHHHHHH CS
                           RecX  78 laekklkkl....kkeedekekqklvrfLarrGFssevirevl 116
                                    l++ +l++     + +++ +  ++lv++LarrG+ +  + ev+
  gi|121638611|ref|YP_978835.1| 119 LVRARLRREvlidDGTDEARVSRRLVAMLARRGYGQTLACEVV 161
                                    999999999777666777999***************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1376.32
//
Query:       gi|121638612|ref|YP_978836.1|  [L=790]
Description: DNA recombination protein RecA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-136  453.6   1.7   6.4e-131  435.6   1.9    2.3  2  RecA             recA bacterial DNA recombination protein
    5.5e-17   61.9   0.0    4.8e-13   49.2   0.0    2.6  2  LAGLIDADG_3      LAGLIDADG-like domain
      5e-12   45.9   0.0    8.5e-12   45.2   0.0    1.3  1  Intein_splicing  Intein splicing domain
      7e-09   35.3   0.0    1.5e-08   34.2   0.0    1.4  1  Rad51            Rad51
    1.7e-07   30.9   0.7      2e-05   24.0   0.2    3.2  2  ATPase           KaiC
     0.0013   18.4   0.0     0.0024   17.6   0.0    1.4  1  AAA_24           AAA domain
     0.0018   18.2   0.0     0.0038   17.2   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0066   16.1   0.7        0.1   12.1   0.0    2.6  2  AAA_25           AAA domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.028   14.0   0.0    1.5  1  CobU             Cobinamide kinase / cobinamide phosphate gua
      0.027   14.9   0.0      0.064   13.7   0.0    1.6  1  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.6   1.9  3.5e-134  6.4e-131       1     245 [.       9     252 ..       9     259 .. 0.99
   2 !   15.5   0.0   4.9e-06    0.0088     220     263 .]     667     710 ..     656     710 .. 0.75

  Alignments for each domain:
  == domain 1  score: 435.6 bits;  conditional E-value: 3.5e-134
                                    HHHHHHHHHHHHHH-TTSS--TTS--.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT CS
                           RecA   1 kaleaalkqiekkfGkgsimklgdekeklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkk 80 
                                    kale a++qiek++Gkgs+m+lgde+ ++ +++i++Gs+ald+alGiGGlp+Gr+ieiyGpessGktt+alha+a+aq +
  gi|121638612|ref|YP_978836.1|   9 KALELAVAQIEKSYGKGSVMRLGDEA-RQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA 87 
                                    79***********************9.79*************************************************** PP

                                    T--EEEEESS----HHHHHHTT--GGG-EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------H CS
                           RecA  81 ggvaafidaehaldpkyakklGvdidellvsqpdtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvgl 160
                                    ggvaafidaehaldp+yakklGvd+d+llvsqpdtGeqaleiad+l+rsga+d++v+dsvaalvp+ae+eGemgds+vgl
  gi|121638612|ref|YP_978836.1|  88 GGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGL 167
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES---------EEEEEEEE CS
                           RecA 161 qarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeikekeevignktkvkv 240
                                    qarlmsqalrk+tga+++s t++ifinq+r+kiGvmfg+petttGG+alkfyasvr+dvrr+e++k++ +++gn+t+vkv
  gi|121638612|ref|YP_978836.1| 168 QARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMFGSPETTTGGKALKFYASVRMDVRRVETLKDGTNAVGNRTRVKV 247
                                    ******************************************************************************** PP

                                    EEESS CS
                           RecA 241 vknkv 245
                                    vknk 
  gi|121638612|ref|YP_978836.1| 248 VKNKC 252
                                    ***96 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.9e-06
                                    EEES---------EEEEEEEEEEESSS----EEEEEEETTTEE- CS
                           RecA 220 rrieeikekeevignktkvkvvknkvappfkeaeldilygeGis 263
                                    rr+ +   + e++ + +   vv    +ppfk+ae+dilyg+Gis
  gi|121638612|ref|YP_978836.1| 667 RRARTFDLEVEELHTLVAEGVVVHNCSPPFKQAEFDILYGKGIS 710
                                    55555555555566666667888899****************97 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0005       0.9       5      51 ..     364     409 ..     361     421 .. 0.92
   2 !   49.2   0.0   2.7e-16   4.8e-13       3      82 ..     462     554 ..     460     555 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0005
                                    HHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HS CS
                    LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIes 51 
                                    a L G+  +DG   + ++k++ i++ +  + l++dv r+ ++lG  +
  gi|121638612|ref|YP_978836.1| 364 ARLLGYLIGDGRDGWVGGKTP-INFINVQRALIDDVTRIAATLGCAA 409
                                    7899********999999999.*********************9765 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.7e-16
                                    HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC.............ECCC CS
                    LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy.............rlli 69 
                                    + ++L Glf++DG+vs ++++  ++ +t++s++l+ ++  lLlr+G+ st++   ++++r++               ++i
  gi|121638612|ref|YP_978836.1| 462 VGNLLFGLFESDGWVSREQTGALRVGYTTTSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIvngrriqskrqvfEVRI 541
                                    56789**************98777******************************8888888878999999***999**** PP

                                    HCHCTTCGGGTTT CS
                    LAGLIDADG_3  70 isgenlkrFleki 82 
                                    ++++n+ +F+e +
  gi|121638612|ref|YP_978836.1| 542 SGMDNVTAFAESV 554
                                    **********976 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   4.7e-15   8.5e-12      10     134 .]     268     691 ..     263     691 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.7e-15
                                    EEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-E CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing  10 vkieelvekegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdl 89 
                                     +ie++v+ +   +++   +d  l++  v   +  +++ ++ ++++ g  + aTp+Hk+l+    g+  + a eL++gd 
  gi|121638612|ref|YP_978836.1| 268 HRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAIVWATPDHKVLTE--YGW--RAAGELRKGDR 343
                                    488999997777777788899999*************************************9..9**..*********** PP

                                    EEEE............................................................................ CS
                                    xxxx............................................................................ RF
                Intein_splicing  90 iavp............................................................................ 93 
                                    +a p                                                                            
  gi|121638612|ref|YP_978836.1| 344 VAQPrrfdgfgdsapipadharllgyligdgrdgwvggktpinfinvqraliddvtriaatlgcaahpqgrislaiahrp 423
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|121638612|ref|YP_978836.1| 424 gerngvadlcqqagiygklawektipnwffepdiaadivgnllfglfesdgwvsreqtgalrvgytttseqlahqihwll 503
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|121638612|ref|YP_978836.1| 504 lrfgvgstvrdydptqkrpsivngrriqskrqvfevrisgmdnvtafaesvpmwgprgaaliqaipeatqgrrrgsqaty 583
                                    ******************************************************************************** PP

                                    ....................................................................HSCEEEEEEEEE CS
                                    ....................................................................xxxxxxxxxxxx RF
                Intein_splicing  94 ....................................................................dadvvwdkvksi 105
                                                                                                         +++ +  ++++
  gi|121638612|ref|YP_978836.1| 584 laaemtdavlnyldergvtaqeaaamigvasgdprggmkqvlgasrlrrdrvqaladalddkflhdmlAEELRYSVIREV 663
                                    *******************************************************************9999********* PP

                                    EEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Intein_splicing 106 evedeeeyVYdltvednhNFvangiivHN 134
                                      +   +  +dl+ve+ h  va+g++vHN
  gi|121638612|ref|YP_978836.1| 664 LPTRRAR-TFDLEVEELHTLVAEGVVVHN 691
                                    ***9999.9*******************9 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.5e-12   1.5e-08      12     240 ..      34     255 ..      22     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.5e-12
                                    HHHSS-EE--S-HHHHHHHT.SSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHH CS
                          Rad51  12 krsellqlttGskklDelLg.GGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlve 90 
                                     r+ +  + tGs +lD  Lg GG++ g + ei+G   sGkt ++      +q       + g a++id+e ++ p+    
  gi|121638612|ref|YP_978836.1|  34 ARQPISVIPTGSIALDVALGiGGLPRGRVIEIYGPESSGKTTVALHAVANAQA------AGGVAAFIDAEHALDPD---- 103
                                    6788889**********9955********************887666555554......45689***********7.... PP

                                    HHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGG.CH-------...THHHHHHHHHHH CS
                          Rad51  91 iaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtaly.Rtdfsgrge...lakRqqklgkll 166
                                     a++ ++d++++l   +       +  e+ l+ a +l+ +  + ++++Dsv+al  R++ +g      +    + +++ l
  gi|121638612|ref|YP_978836.1| 104 YAKKLGVDTDSLLVSQP-------DTGEQALEIADMLIRSGALDIVVIDSVAALVpRAELEGEMGdshVGLQARLMSQAL 176
                                    69999*****9996654.......677788888889999999***********8669**887543011444444455666 PP

                                    HHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-ST.........TEEEEEEES-SS CS
                          Rad51 167 rtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkg.........eeRivkvvdsPn 237
                                    r+++   ++ + + +  nq  ++++    +f + p+   gG+ l   +++R+ +r+ +          ++  vkvv+  +
  gi|121638612|ref|YP_978836.1| 177 RKMTGALNNSGTTAIFINQLRDKIGV---MF-GSPETTTGGKALKFYASVRMDVRRVETlkdgtnavgNRTRVKVVKNKC 252
                                    666555566667777789**999988...55.6778889*************9998655444555664333356666666 PP

                                    S-S CS
                          Rad51 238 lpe 240
                                    l+e
  gi|121638612|ref|YP_978836.1| 253 LAE 255
                                    665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   1.1e-08     2e-05       1     167 [.      41     207 ..      41     250 .. 0.70
   2 ?   -1.1   0.0      0.54   9.6e+02     115     131 ..     385     401 ..     382     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.1e-08
                         ATPase   1 vktgIeglDeil.kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                    ++tg   lD  l  gG+p+grv+ i+G   +GKt++al+ + +  +  g    f+  e         ak+lG+d++ l  
  gi|121638612|ref|YP_978836.1|  41 IPTGSIALDVALgIGGLPRGRVIEIYGPESSGKTTVALHAVANA-QAAGGVAAFIDAEHALD--PDYAKKLGVDTDSLLV 117
                                    58888889*99989************************966665.66699999998776544..467899****999987 PP

                         ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTai 159
                                    ++  +  +a e a+  ++ ++  d+  +i+++a  + + + +  + Ds  gl    ++ ++ + lr+++  l++ g+Tai
  gi|121638612|ref|YP_978836.1| 118 SQPDTGEQALEIADMLIR-SGALDI-VVIDSVAALVPRAELEGEMGDSHVGL----QARLMSQALRKMTGALNNSGTTAI 191
                                    744444444444333222.222232.34566667777777777777777777....777788889999999999999999 PP

                         ATPase 160 lvsekss........s 167
                                    ++++ ++         
  gi|121638612|ref|YP_978836.1| 192 FINQLRDkigvmfgsP 207
                                    9999887666666533 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                         ATPase 115 ikeikakrvviDsitgl 131
                                    i+ i+++r +iD +t +
  gi|121638612|ref|YP_978836.1| 385 INFINVQRALIDDVTRI 401
                                    8899***********98 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0024       3      78 ..      61     151 ..      59     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                         AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie............swedfldevvelaael 63 
                                    + i iyGp+ +GKTt+a+++       g  ++fid e+   +ld+d  +++             + e+ l+ ++ l +  
  gi|121638612|ref|YP_978836.1|  61 RVIEIYGPESSGKTTVALHAvanaqaaGGVAAFIDAEH---ALDPDYAKKLGvdtdsllvsqpdTGEQALEIADMLIRSG 137
                                    5788**********************************...556666665555678888866666666666666667777 PP

                         AAA_24  64 adyktlviDtidele 78 
                                    a ++++viD++  l+
  gi|121638612|ref|YP_978836.1| 138 A-LDIVVIDSVAALV 151
                                    6.9999999998775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0038      21      67 ..      61     107 ..      57     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesisklde 67 
                                    +++ iYGpe+sGKt++  +++ n +  +    +++a +  + +++++
  gi|121638612|ref|YP_978836.1|  61 RVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKK 107
                                    5778********************99998888888766665555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   5.8e-05       0.1      28      55 ..      56      82 ..      51      98 .. 0.86
   2 ?    1.2   0.1      0.14   2.4e+02     134     158 ..     130     154 ..      93     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                         AAA_25 28 gllpagelallaGapgtGKttlaldlal 55
                                   g lp+g ++ ++G++ +GKtt+al+ ++
  gi|121638612|ref|YP_978836.1| 56 G-LPRGRVIEIYGPESSGKTTVALHAVA 82
                                   4.5*********************9876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                         AAA_25 134 eaaieevegvrlvviDplsralggd 158
                                    ++ + +   ++ vviD+++++++  
  gi|121638612|ref|YP_978836.1| 130 ADMLIRSGALDIVVIDSVAALVPRA 154
                                    3333333669*********998774 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.028       3     122 ..      65     193 ..      63     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                           CobU   3 vtGgarSGKSefAekla...eeskekvvYiATaealDeemaeRiarHrerR.paeWetveepldlaealkeeekkevvLv 78 
                                    + G+  SGK ++A + +   +++++   +i + +alD ++a+++    ++   ++ +t e+ l++a++l ++ + ++v++
  gi|121638612|ref|YP_978836.1|  65 IYGPESSGKTTVALHAVanaQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLlVSQPDTGEQALEIADMLIRSGALDIVVI 144
                                    78*************9955444556779*****************99999878999*************999889***** PP

                           CobU  79 Dcltlwltnllleeeaek.....veekleeeveellealkelkatvvlV 122
                                    D+++ ++ ++ le e  +     + + +++++++++ al+++ +t +++
  gi|121638612|ref|YP_978836.1| 145 DSVAALVPRAELEGEMGDshvglQARLMSQALRKMTGALNNSGTTAIFI 193
                                    *******988776554446888666678888888999998888888886 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.064       3      98 ..      65     184 ..      63     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                    EESSTTSSHHHHH.HHHHHHH..THEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTSTSEE CS
                            AAA   3 lyGppGtGKTlla.kavakel..gvefleisgsellsk..................yvgesekkirelfkeakekakpsi 61 
                                    +yGp   GKT++a +ava+    g     i++   l+                     ge++ +i++++  +++ a   i
  gi|121638612|ref|YP_978836.1|  65 IYGPESSGKTTVAlHAVANAQaaGGVAAFIDAEHALDPdyakklgvdtdsllvsqpDTGEQALEIADML--IRSGA-LDI 141
                                    79*********9945676663332223333333333223444455555555554456677777777777..67777.89* PP

                                    EEEETGGGHHHHH......TTCCCHHHHHHHHHHHHHHHHTTT CS
                            AAA  62 lfiDEidalaksr......sgseseeeervvnqLlteldgvkk 98 
                                    ++iD + al+++        +s+ + + r+++q l+++ g  +
  gi|121638612|ref|YP_978836.1| 142 VVIDSVAALVPRAelegemGDSHVGLQARLMSQALRKMTGALN 184
                                    ************9995544333444555666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.57
# Mc/sec: 4149.56
//
Query:       gi|121638613|ref|YP_978837.1|  [L=57]
Description: hypothetical protein BCG_2751 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-11   42.5   7.2      6e-11   42.0   7.2    1.3  1  FhuF_C    FhuF 2Fe-2S C-terminal domain


Domain annotation for each model (and alignments):
>> FhuF_C  FhuF 2Fe-2S C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   7.2   3.4e-15     6e-11       1      21 []      37      57 .]      37      57 .] 0.99

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.4e-15
                         FhuF_C  1 RrsCCLyYrlpggeyCgsCPL 21
                                   RrsCCL+Yr+p g++Cg+CPL
  gi|121638613|ref|YP_978837.1| 37 RRSCCLFYRVPAGGKCGDCPL 57
                                   9*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 320.96
//
Query:       gi|121638614|ref|YP_978838.1|  [L=68]
Description: hypothetical protein BCG_2752c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-28   98.3   0.1    2.6e-28   98.2   0.1    1.0  1  DUF3046   Protein of unknown function (DUF3046)


Domain annotation for each model (and alignments):
>> DUF3046  Protein of unknown function (DUF3046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.1   1.5e-32   2.6e-28       1      61 [.       5      65 ..       5      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.5e-32
                        DUF3046  1 MRlteFwelveeeFGsayarslardhvlselggrTaeeAleaGvdprdVWralcdafdvPe 61
                                   +RlteF+e+v+ +FG+ay++s++ dhvl++++gr+a++A+e+Gv+prdVWralc++fdvP+
  gi|121638614|ref|YP_978838.1|  5 VRLTEFHERVALHFGAAYGSSVLLDHVLTGFDGRSAAQAIEDGVEPRDVWRALCADFDVPH 65
                                   59**********************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 465.09
//
Query:       gi|121638615|ref|YP_978839.1|  [L=388]
Description: alanine rich transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-08   32.4   0.0    1.3e-07   31.7   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    1.7e-07   30.4   0.0    3.9e-06   25.9   0.0    2.0  2  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
  ------ inclusion threshold ------
        0.2   11.2   0.0       0.39   10.2   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.2e-11   1.3e-07      67     159 ..     285     369 ..     281     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.2e-11
                                    HHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS-- CS
                Glyco_tran_28_C  67 aeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaaekl 146
                                    ae++ +adLvI+ +G+g++a +l +g+p+++vp       +q + a  ++++g a +++  ++  + L++a+ e+++ + 
  gi|121638615|ref|YP_978839.1| 285 AELLTRADLVICGGGHGMVAKTLLAGVPMVVVPGGG----DQWEIANRVVRQGSAVLIRPLTA--DALVAAVNEVLSSPR 358
                                    688999****************************99....*****************998777..**********99998 PP

                                    -S---SSCH..CH CS
                Glyco_tran_28_C 147 rlaekskasaask 159
                                      ++  +a+  ++
  gi|121638615|ref|YP_978839.1| 359 FREAARRAA--AS 369
                                    744444442..33 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.3   0.0    0.0098        59     114     144 ..      84     114 ..      61     119 .. 0.85
   2 !   25.9   0.0   6.6e-10   3.9e-06     345     415 ..     295     363 ..     284     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0098
                          UDPGT 114 lqeskfdvvladpvlpcgellAellkiptvy 144
                                    l + + + v++d ++ cg + Aell ip v 
  gi|121638615|ref|YP_978839.1|  84 LRALEPELVVSDVITACGGMAAELLGIPWVE 114
                                    5555667899******************885 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 6.6e-10
                          UDPGT 345 vtHaGangvyEaisnGvPmvglPlFgdqrdNikrmeakgaavtlnvkemtsedllnAlkevindksykeni 415
                                    +  +G   v  ++  GvPmv++P  gdq + ++r++ +g+av   ++ +t++ l  A++ev+  + ++e +
  gi|121638615|ref|YP_978839.1| 295 ICGGGHGMVAKTLLAGVPMVVVPGGGDQWEIANRVVRQGSAVL--IRPLTADALVAAVNEVLSSPRFREAA 363
                                    334455557899***************************9986..6789****************999976 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   6.5e-05      0.39     114     169 ..     308     367 ..     282     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.5e-05
                                    HTT--EEEETTTTHCHHCHTTT....SEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHH CS
                Glycos_transf_1 114 aaglpviasnaggpaevvkdge....tGllvkpnnaealaeairklledeelrerlgena 169
                                     ag+p +++  gg    +++ +    + +l+ p  a+al++a++++l+++  re+ +++a
  gi|121638615|ref|YP_978839.1| 308 LAGVPMVVVPGGGDQWEIANRVvrqgSAVLIRPLTADALVAAVNEVLSSPRFREAARRAA 367
                                    589*******99988888888889999999***9****************9998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2627.06
//
Query:       gi|121638616|ref|YP_978840.1|  [L=149]
Description: epoxide hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-52  176.9   0.8    1.9e-52  176.6   0.8    1.0  1  LEH       Limonene-1,2-epoxide hydrolase catalytic domain
    3.4e-15   56.5   1.1    4.9e-15   56.0   1.1    1.2  1  SnoaL_2   SnoaL-like domain
    0.00014   21.7   0.5     0.0012   18.6   0.5    1.9  1  SnoaL     SnoaL-like polyketide cyclase
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.24   11.5   0.0    1.3  1  WI12      Wound-induced protein WI12


Domain annotation for each model (and alignments):
>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.8   4.1e-56   1.9e-52       2     124 ..      16     134 ..      15     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 4.1e-56
                                    HHHHHHHHHHHHHHHT-HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT.TTT-EEEEEEEEEEEETTEEEEEEEE CS
                            LEH   2 epirvVeaFlaalqeddydaavrrlatdlevyeneglstihGraeaiallerlsadilavevkilriaadgsaVltERlD 81 
                                    e+ir+VeaFl+alq++d+d+++++l++dl vyen+g+s+i+G +++++ll+r+ ++++++evki+ri+adg+aVltER+D
  gi|121638616|ref|YP_978840.1|  16 EAIRAVEAFLNALQNEDFDTVDAALGDDL-VYENVGFSRIRGGRRTATLLRRM-QGRVGFEVKIHRIGADGAAVLTERTD 93 
                                    79***************************.***********************.************************** PP

                                    EEEE..TTEEEEEEEEEEEEEETTEEEEEEEE--HHHHHHHHH CS
                            LEH  82 rliladGplivqltvmGvfeVedgrivlWRdYfDvndllkata 124
                                    +li+  Gpl+vq++v+GvfeV+dgri+lWRdYfDv+d++k ++
  gi|121638616|ref|YP_978840.1|  94 ALII--GPLRVQFWVCGVFEVDDGRITLWRDYFDVYDMFKGLL 134
                                    ****..*********************************9876 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   1.1   1.1e-18   4.9e-15       1     102 []      21     120 ..      21     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.1e-18
                                    HHHHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEET CS
                        SnoaL_2   1 vraflaalnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipa 79 
                                    v+afl+al++ d+d+++a + +d v+e++ + ++rG  + +  +r+++    +++++ih++ adg  v++e t       
  gi|121638616|ref|YP_978840.1|  21 VEAFLNALQNEDFDTVDAALGDDLVYENVgFSRIRGGRRTATLLRRMQG-RVGFEVKIHRIGADGAAVLTERTDAL--II 97 
                                    89***************************9999**************86.89******************865553..57 PP

                                    TSSEEEEEEEEEEEEETTEEEEE CS
                        SnoaL_2  80 tgrgvtvrgvdvfrvrdGkiveh 102
                                     + +v++++++vf+v+dG+i+ +
  gi|121638616|ref|YP_978840.1|  98 GPLRVQFWVCGVFEVDDGRITLW 120
                                    7889****************976 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   2.8e-07    0.0012       3     124 ..      20     131 ..      17     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.8e-07
                                    HHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEES CS
                          SnoaL   3 vlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGtht 82 
                                    +++++ +++++ d+d++d ++ +d v++n +  + rG    +  +++++  +  ++v+++++ a+g  v ++ t ++   
  gi|121638616|ref|YP_978840.1|  20 AVEAFLNALQNEDFDTVDAALGDDLVYENVGFSRIRGGRRTATLLRRMQGRV-GFEVKIHRIGADGAAVLTERT-DALII 97 
                                    667777888999*************************************999.79***********99999988.55555 PP

                                    SEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHH CS
                          SnoaL  83 geflGipptGkkvkfeeitllrvedGkIveewdviDllgllr 124
                                    g++        +v+f  + +++v dG+I  ++d++D +++++
  gi|121638616|ref|YP_978840.1|  98 GPL--------RVQFWVCGVFEVDDGRITLWRDYFDVYDMFK 131
                                    555........**************************99876 PP

>> WI12  Wound-induced protein WI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.24      10      60 ..      69     125 ..      62     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                           WI12  10 geasfefkprsvdafgstviaeGtdet.....rklyWvh.aWtvkdGvitqvreyfn 60 
                                    g+++fe k + + a g +v++e td+      r   Wv  ++ v dG+it  r+yf+
  gi|121638616|ref|YP_978840.1|  69 GRVGFEVKIHRIGADGAAVLTERTDALiigplRVQFWVCgVFEVDDGRITLWRDYFD 125
                                    67889999999999999*****99984222224557985489*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1178.18
//
Query:       gi|121638618|ref|YP_978842.1|  [L=424]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-27   93.9  17.0    8.9e-27   93.3  17.0    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3  17.0     5e-31   8.9e-27      17      93 .]       2      78 ..       1      78 [. 0.99

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 5e-31
                                   HHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--XX CS
                             PE 17 dlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaagsYaaaEaa 93
                                   dla+igs++saa+aaa+apt a+laa+aDeVS+a+Aalf+ h+q+yqals qa+afh+qfvqal+a+a sYa+aEaa
  gi|121638618|ref|YP_978842.1|  2 DLASIGSTVSAASAAASAPTVAILAAGADEVSIAVAALFGMHGQAYQALSVQASAFHQQFVQALTAGAYSYASAEAA 78
                                   89*************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2967.93
//
Query:       gi|121638619|ref|YP_978843.1|  [L=82]
Description: hypothetical protein BCG_2757c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-13   49.3   0.2    6.7e-13   48.8   0.2    1.4  1  DUF3046      Protein of unknown function (DUF3046)
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.023   15.0   0.0    1.3  1  Gallidermin  Gallidermin


Domain annotation for each model (and alignments):
>> DUF3046  Protein of unknown function (DUF3046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.2   7.5e-17   6.7e-13      21      61 ..      33      73 ..      22      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 7.5e-17
                        DUF3046 21 slardhvlselggrTaeeAleaGvdprdVWralcdafdvPe 61
                                   +   dhvl+++ggr a  A+e+Gv+pr  W+alc +fdvP+
  gi|121638619|ref|YP_978843.1| 33 WCWLDHVLTGFGGRNAICAIEDGVEPRVAWWALCTDFDVPR 73
                                   6677************************************8 PP

>> Gallidermin  Gallidermin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.6e-06     0.023      18      38 ..      47      67 ..      44      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                                   XXXXXXXXXXXXXXXXXXXXX CS
                    Gallidermin 18 nakesndsgaepRiaSkflCt 38
                                   na+ + ++g epR+a + lCt
  gi|121638619|ref|YP_978843.1| 47 NAICAIEDGVEPRVAWWALCT 67
                                   8999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 623.11
//
Query:       gi|121638620|ref|YP_978844.1|  [L=195]
Description: hypothetical protein BCG_2758c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.3   0.2       0.17   11.7   0.2    1.2  1  YycC      YycC-like protein
       0.22    9.3   0.0       0.28    9.0   0.0    1.0  1  Ycf1      Ycf1
       0.81   10.3   8.2        1.7    9.3   7.7    1.7  2  PEHE      PEHE domain


Domain annotation for each model (and alignments):
>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   2.8e-05      0.17      13      48 ..       1      36 [.       1      39 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                           YycC 13 kLskkLnvPLEhlMHmPkHILlqKlaelekeeeeen 48
                                   +L ++L+v + h  H+P   L+q++ e+ +++e+++
  gi|121638620|ref|YP_978844.1|  1 MLVDELGVKIVHAQHVPAPYLVQRMREIHERDENRQ 36
                                   68899***********************99988765 PP

>> Ycf1  Ycf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   4.6e-05      0.28     219     264 ..      15      60 ..       8      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 4.6e-05
                           Ycf1 219 ripspiltkklketseteereeseeetdveiekasetkgtkqeqer 264
                                     +p+p l ++++e+ e +e  +++ ++dv+  + +  +g +q++++
  gi|121638620|ref|YP_978844.1|  15 HVPAPYLVQRMREIHERDENRQRHAQVDVQRRRDQPERGQHQHRRN 60 
                                    79*******************9999999977777666666664432 PP

>> PEHE  PEHE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.7   0.00028       1.7      36     114 ..      29     113 ..      24     131 .. 0.86
   2 ?   -0.7   0.3      0.35   2.1e+03      43      77 ..     118     131 ..     108     155 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                           PEHE  36 HaklE.ekerkRwdlqrnreqqrreslrqRkeskk.....grntpqpgsenpltkqppspddsesihvldevpvvasplp 109
                                    H++ E +++ +  d+qr r q +r+++++R+++++     gr+   +  + p++    +p  +    vl+ v   a ++ 
  gi|121638620|ref|YP_978844.1|  29 HERDEnRQRHAQVDVQRRRDQPERGQHQHRRNRDAdhhpdGRTLAGQIVAHPVSHRVRQPRPVAIADVLPRVGPRADCVV 108
                                    9999999999********************98888999999999999999999999999999998888888888887777 PP

                           PEHE 110 plspe 114
                                    + s +
  gi|121638620|ref|YP_978844.1| 109 AHSLQ 113
                                    66655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.35
                           PEHE  43 erkRwdlqrnreqqrreslrqRkeskkgrntpqpg 77 
                                    +r+R+                      g+++ q++
  gi|121638620|ref|YP_978844.1| 118 RRERRR---------------------GQTAHQRL 131
                                    222222.....................33333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1307.02
//
Query:       gi|121638621|ref|YP_978845.1|  [L=270]
Description: membrane alanine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.7   0.2       0.16   11.7   0.2    2.2  3  DUF2937   Protein of unknown function (DUF2937)


Domain annotation for each model (and alignments):
>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     9e-06      0.16     100     155 ..      27      82 ..      13      88 .. 0.85
   2 ?   -1.6   0.1      0.11   1.9e+03     110     110 ..     191     191 ..     157     230 .. 0.49
   3 ?   -2.0   0.1      0.14   2.6e+03      25      47 ..     241     263 ..     240     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-06
                        DUF2937 100 sllerlvvllraadaeileetlenfspavpltpeglafglvgalllallvelllal 155
                                    +l+++ + ++ +++a +l++  ++ ++++ +t+  l++glv+all+a+ +   l++
  gi|121638621|ref|YP_978845.1|  27 DLVAQKISVAIDPRARLLRRRRRALRWGLVFTAGCLLWGLVTALLAAWGWFTSLLV 82 
                                    578888999999***********************************998765554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.11
                        DUF2937 110 r 110
                                    +
  gi|121638621|ref|YP_978845.1| 191 S 191
                                    2 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.14
                        DUF2937  25 dqYqqrLeghldelkrqlagfqa 47 
                                    + Y+  L+g+ d l    ++f++
  gi|121638621|ref|YP_978845.1| 241 QRYREELAGATDRLVAWAQAFDE 263
                                    789999***99999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2010.64
//
Query:       gi|121638622|ref|YP_978846.1|  [L=270]
Description: hypothetical protein BCG_2760c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-63  213.2  32.6    3.9e-63  213.0  32.6    1.0  1  PspA_IM30        PspA/IM30 family
  ------ inclusion threshold ------
       0.93   10.1   6.4       0.26   11.8   2.7    2.0  2  EF-G-binding_N   Elongation factor G-binding protein, N-termi
        5.8    7.1  10.9         12    6.0   1.6    2.4  2  Fib_alpha        Fibrinogen alpha/beta chain family
        7.2    6.9  12.1       0.88    9.9   3.4    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
        7.4    6.5  15.6        9.3    6.1  15.6    1.1  1  TFIIA            Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0  32.6   1.1e-66   3.9e-63       1     218 [.       3     241 ..       3     243 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 1.1e-66
                      PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtk 80 
                                    ++f++++++l+a +s+++d+++DP+++++qai+++q+++++++q++aqvi++q+qle++l++q ++++kl++++++ALt 
  gi|121638622|ref|YP_978846.1|   3 NPFVKAWKYLMALFSSKIDEHADPKVQIQQAIEEAQRTHQALTQQAAQVIGNQRQLEMRLNRQLADIEKLQVNVRQALTL 82 
                                    68****************************************************************************** PP

                      PspA_IM30  81 g..............eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaak 146
                                    +              ++++A++++a+++++e+++e+l+t+++q+ sa++q++k++e++++++++++a++++l++++++ak
  gi|121638622|ref|YP_978846.1|  83 AdqataagdaakateYNNAAEAFAAQLVTAEQSVEDLKTLHDQALSAAAQAKKAVERNAMVLQQKIAERTKLLSQLEQAK 162
                                    ******************************************************************************** PP

                      PspA_IM30 147 aqeavqkslgkls...tesatdslerieeKieerearadaaaelae.saqdldakleaagiqkev.s..eqvlarlkae 218
                                    +qe+v++sl+++s   ++++t+sl+++++Kie+r+a+a+++aelae s+q+++ ++e+agiq+++ s  eq++a++++e
  gi|121638622|ref|YP_978846.1| 163 MQEQVSASLRSMSelaAPGNTPSLDEVRDKIERRYANAIGSAELAEsSVQGRMLEVEQAGIQMAGhSrlEQIRASMRGE 241
                                    **********************************************88888**************99*********986 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.96   3.5e+03      50      55 ..      39      44 ..      14      80 .. 0.64
   2 ?   11.8   2.7   7.3e-05      0.26      14      79 ..     106     178 ..      94     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.96
                 EF-G-binding_N 50 eeqkel 55
                                     +++l
  gi|121638622|ref|YP_978846.1| 39 RTHQAL 44
                                   222222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.3e-05
                 EF-G-binding_N  14 veqllnayrsvnDkkvveavkalaaekIlel.......fpelseeqkelLeqiddiktkekaeklLeeLkeyV 79 
                                    ++ql+ a +sv D k+++    +aa++ +++       ++++  e+++lL+q+++ k +e++   L+++ e+ 
  gi|121638622|ref|YP_978846.1| 106 AAQLVTAEQSVEDLKTLHDQALSAAAQAKKAvernamvLQQKIAERTKLLSQLEQAKMQEQVSASLRSMSELA 178
                                    579**************98777777777776666788888888899****************99999998875 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.3    0.0038        14      59     112 ..      28      77 ..       6      82 .. 0.52
   2 ?    6.0   1.6    0.0034        12      55     110 ..     113     161 ..      93     199 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0038
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHH CS
                      Fib_alpha  59 keikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvle 112
                                    ++i++ ++e+q++++    ++++ ++ +  ++ +l+ ++++q   i++Lq +++
  gi|121638622|ref|YP_978846.1|  28 VQIQQAIEEAQRTHQ---ALTQQAAQVIG-NQRQLEMRLNRQLADIEKLQVNVR 77 
                                    344444444444444...34455554444.555555555555555555555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                      Fib_alpha  55 eelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                    e+ v+++k+ + ++        ++  + +k +e++ + l+++i +  + + +L + 
  gi|121638622|ref|YP_978846.1| 113 EQSVEDLKTLHDQA-------LSAAAQAKKAVERNAMVLQQKIAERTKLLSQLEQA 161
                                    22222222222222.......44444555555555555555555555444444322 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.4   0.00025      0.88      23      79 ..      29      78 ..      23     100 .. 0.60
   2 ?    1.2   1.6      0.13   4.6e+02      33      52 ..     153     177 ..      99     196 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                         DUF948 23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79
                                   ++++ ++ea++t + l++q+ +++ + ++l    n+ l+d+++       l  +v++
  gi|121638622|ref|YP_978846.1| 29 QIQQAIEEAQRTHQALTQQAAQVIGNQRQLEMRLNRQLADIEK-------LQVNVRQ 78
                                   4555555666666666666666666666655555555555555.......4444443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                         DUF948  33 atieele.....kqvdpilkevedl 52 
                                    + + +le     +qv + l+ + +l
  gi|121638622|ref|YP_978846.1| 153 KLLSQLEqakmqEQVSASLRSMSEL 177
                                    2222222222224555555555555 PP

>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  15.6    0.0026       9.3      49     192 ..      21     178 ..       9     262 .. 0.42

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0026
                          TFIIA  49 dpkpeeaqspqfvlqlpqslkqalqasaaaa...............sqapastsqslpslvipagksvqslta....... 106
                                    d + +++ + q++ +++q+++qal ++aa++                      + ++ ++ +          +       
  gi|121638622|ref|YP_978846.1|  21 DEHADPKVQIQQAIEEAQRTHQALTQQAAQVignqrqlemrlnrqlA------DIEKLQVNVR---------Qaltladq 85 
                                    55666666666666666667777666666554443333322111110......1111111111.........11222221 PP

                          TFIIA 107 ...nssaataatfslpakleppvqipa.gvtlqtasg..........qlykvnvqasgaqqiaaqplqqvvqqsqgsaaq 172
                                            + a+     ++e++    a   +l ta++          q+++   qa++a ++ a  lqq++ ++++  +q
  gi|121638622|ref|YP_978846.1|  86 ataA----GDAAK----ATEYNNAAEAfAAQLVTAEQsvedlktlhdQALSAAAQAKKAVERNAMVLQQKIAERTKLLSQ 157
                                    1111....11111....111111111111222222221112222322333333355555555555555555543333333 PP

                          TFIIA 173 ssvaalqaq.sqqaqalaepq 192
                                     + a++q+q s ++++++e  
  gi|121638622|ref|YP_978846.1| 158 LEQAKMQEQvSASLRSMSELA 178
                                    333333333322222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2164  (0.120698); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 1920.03
//
Query:       gi|121638623|ref|YP_978847.1|  [L=112]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-12   45.2   0.6    8.7e-12   45.2   0.6    1.9  2  HTH_31    Helix-turn-helix domain
    5.1e-10   39.2   0.5    7.9e-10   38.7   0.1    1.5  2  HTH_3     Helix-turn-helix
    5.3e-06   26.4   0.0    6.9e-06   26.0   0.0    1.2  1  HTH_19    Helix-turn-helix domain
    5.6e-06   26.1   0.1    1.1e-05   25.1   0.1    1.7  1  HTH_25    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.6   1.9e-15   8.7e-12       3      59 ..      10      65 ..       9      71 .. 0.95
   2 ?   -0.3   0.2       0.3   1.4e+03      16      24 ..      77      85 ..      72     100 .. 0.56

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.9e-15
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59
                                   G+ Lr +R  +G +++ev + ++vs  +ls +E+Gr  +ps + l a+++al+l+ +
  gi|121638623|ref|YP_978847.1| 10 GDVLRGARMSQGRTLREVSDSARVSLGYLSEIERGRK-EPSSELLSAICTALQLPLS 65
                                   99***********************************.8**************9965 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.3
                         HTH_31 16 sqeevAerl 24
                                   +qe +A+++
  gi|121638623|ref|YP_978847.1| 77 RQERLARAT 85
                                   344444443 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   1.8e-13   7.9e-10       2      53 ..      14      65 ..      13      67 .. 0.94
   2 ?   -2.9   0.0       1.7   7.6e+03      34      41 ..      74      81 ..      72      84 .. 0.49

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.8e-13
                                   HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                          HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                   + +R  +g +++e+++ + vs  ++s iE+G+ +Ps e l +++ aL+++l+
  gi|121638623|ref|YP_978847.1| 14 RGARMSQGRTLREVSDSARVSLGYLSEIERGRKEPSSELLSAICTALQLPLS 65
                                   66899*******************************************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                   SCSBHHHH CS
                          HTH_3 34 rnPsletl 41
                                   r+ ++e+l
  gi|121638623|ref|YP_978847.1| 74 RMARQERL 81
                                   55555554 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.5e-09   6.9e-06       2      57 ..      11      65 ..      10      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.5e-09
                         HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidle 57
                                   + L+ aR   g t++e+++ +++s +++s+iE g+k +ps+ell +i+ al ++l 
  gi|121638623|ref|YP_978847.1| 11 DVLRGARMSQGRTLREVSDSARVSLGYLSEIERGRK-EPSSELLSAICTALQLPLS 65
                                   567778888889***********************9.***********99988876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.5e-09   1.1e-05       2      34 ..      13      45 ..      12      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.5e-09
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                         HTH_25  2 LraaRearglsleevaketkIrkdylealEedd 34
                                   Lr aR+++g +l+ev++  +++  yl ++E+++
  gi|121638623|ref|YP_978847.1| 13 LRGARMSQGRTLREVSDSARVSLGYLSEIERGR 45
                                   9*****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 738.39
//
Query:       gi|121638624|ref|YP_978848.1|  [L=209]
Description: pgp synthase pgsA3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.6   1.8    1.2e-13   51.6   1.8    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   1.8   6.5e-18   1.2e-13       1      66 []      28      98 ..      28      98 .. 0.86
   2 ?    0.1   2.9     0.083   1.5e+03      26      40 ..     160     185 ..     100     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 6.5e-18
                                   S-HHHHHHHHHHHHHHHHHGGGS-H.........HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  1 nlPnaiTllrlllsvlailllltyyp.......lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   nl+n++Tllrl+++ + +l l  +y+        v+a +++  a++tD +DG lAR +++ +++G++ D++aD
  gi|121638624|ref|YP_978848.1| 28 NLANILTLLRLVMVPVFLLAL--FYGgghhsaaRVVAWAIFATACITDRFDGLLARNYGMATEFGAFVDPIAD 98
                                   689*********966555433..3334799999888888999******************888*********9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.083
                                    ..................HHHHHHHHHHHHH CS
                CDP-OH_P_transf  26 p................lvlailllliaslt 40 
                                                     +     ++ +a+l+
  gi|121638624|ref|YP_978848.1| 160 IglfvlplsgplhvaavV-----VMAAAILL 185
                                    033333333444233321.....22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1578.64
//
Query:       gi|121638625|ref|YP_978849.1|  [L=174]
Description: N-acetylglutamate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   40.1   0.0    5.2e-10   39.6   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-09   38.5   0.0    2.1e-09   37.6   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.8e-05   24.7   0.0    2.5e-05   24.2   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0079   16.3   0.0      0.014   15.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.053   13.6   0.0    1.9  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.065   13.2   0.0        0.1   12.6   0.0    1.3  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.7e-13   5.2e-10      33     117 .]      47     127 ..      21     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.7e-13
                                    C.EEEEEEET...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHH CS
                 Acetyltransf_1  33 e.gllvaeed...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaa 108
                                      +++vae+    g+++G+  l+  +    + ++i+ +aV+p+  g+G+G a ++ l++ ar+ +++++++ ++e     
  gi|121638625|ref|YP_978849.1|  47 VqEFWVAEHPdlyGKVVGCGALHVLWS---DLGEIRTVAVDPAMTGHGIGHAIVDRLLQVARDLQLQRVFVLTFE----- 118
                                    3478888888899**************...9***********************************998552433..... PP

                                    HHHHHHTTE CS
                 Acetyltransf_1 109 irlYeklGF 117
                                     +++ ++GF
  gi|121638625|ref|YP_978849.1| 119 TEFFARHGF 127
                                    567777887 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   7.1e-13   2.1e-09       4      76 .]      49     129 ..      46     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 7.1e-13
                                    EEEEEEET...TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHH.H...TTSEEEEE.EEEE.THHHHHHHHHH CS
                 Acetyltransf_7   4 evfVaedd...gkivGfialslld...aeitrlaVdpeyrgkGiGraLle.a...aekgiile.qlel.naekaikfYek 71 
                                    e++Vae+    gk+vG+ al++l+   +ei  +aVdp+  g+GiG+a+++ +   a + ++l+ +  l       +f+++
  gi|121638625|ref|YP_978849.1|  49 EFWVAEHPdlyGKVVGCGALHVLWsdlGEIRTVAVDPAMTGHGIGHAIVDrLlqvA-RDLQLQrVFVLtF---ETEFFAR 124
                                    79***999***********9999999888888*****************9533321.3333332222222...367**** PP

                                    TTEEE CS
                 Acetyltransf_7  72 lGFee 76 
                                    +GF+e
  gi|121638625|ref|YP_978849.1| 125 HGFTE 129
                                    ***85 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   8.2e-09   2.5e-05      32     110 ..      49     132 ..      23     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.2e-09
                Acetyltransf_10  32 lllvaeeg...gkivGvielrdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYekl 104
                                     ++vae     gk+vG+++l   +    +i  ++Vdp+  g Gig+a+++++++ a++ +++    v   +   +f+ ++
  gi|121638625|ref|YP_978849.1|  49 EFWVAEHPdlyGKVVGCGALHVLWsdlgEIRTVAVDPAMTGHGIGHAIVDRLLQVARDLQLQ---RVFVLTFETEFFARH 125
                                    5666666545578898885544333445****************************888877...555567889****** PP

                Acetyltransf_10 105 GFkav.g 110
                                    GF+++ g
  gi|121638625|ref|YP_978849.1| 126 GFTEIeG 132
                                    **99844 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.8e-06     0.014      27      75 ..      78     126 ..      72     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.8e-06
                Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylekhp 75 
                                    +  + V++++ G+Gi+ ++v++ l+ ar+ +l+ v + ++  +++ +h 
  gi|121638625|ref|YP_978849.1|  78 IRTVAVDPAMTGHGIGHAIVDRLLQVARDLQLQRVFVLTFETEFFARHG 126
                                    56678**************************999999999999999885 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.39   1.2e+03       2      18 ..      12      28 ..      11      65 .. 0.86
   2 ?   13.6   0.0   1.8e-05     0.053      76     127 ..      78     129 ..      73     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.39
                                   EEEE-GGGHHHHHHHHH CS
                 Acetyltransf_9  2 irelteedldevlellk 18
                                   +r+++++d++++++l++
  gi|121638625|ref|YP_978849.1| 12 VRRARTSDVPAIKQLVD 28
                                   68999999999999876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.8e-05
                                    EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-EE CS
                 Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGyei 127
                                    +  Vav+p  +g+g+ +++++r+l+ +r+ + + ++   ++ +++ r G+  
  gi|121638625|ref|YP_978849.1|  78 IRTVAVDPAMTGHGIGHAIVDRLLQVARDLQLQRVFVLTFETEFFARHGFTE 129
                                    778***************************99999999***********975 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05       0.1      17      79 ..      71     134 ..      60     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                    EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EE CS
                           FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfek 79 
                                    l +d ge+  + v+p + + G g  +v  l +  +  + + v++++ +++  +++ ++ + ++ 
  gi|121638625|ref|YP_978849.1|  71 LWSDLGEIRTVAVDPAMTGHGIGHAIVDRLLQVARDlQLQRVFVLTFETEFFARHGFTEIEGTP 134
                                    56789*************************9999998889999999999999999888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1441.18
//
Query:       gi|121638626|ref|YP_978850.1|  [L=883]
Description: cell division transmembrane protein ftsK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-67  225.9   0.4    4.2e-65  219.5   0.4    2.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
    1.3e-27   95.9   0.0    2.3e-27   95.1   0.0    1.4  1  FtsK_alpha     FtsK alpha domain
    4.4e-24   84.1   0.1    1.5e-23   82.4   0.1    2.0  1  FtsK_gamma     Ftsk gamma domain
    6.9e-06   25.9   9.7    2.3e-05   24.2   7.5    2.4  2  FtsK_4TM       4TM region of DNA translocase FtsK/SpoIIIE
    2.4e-05   24.6   0.0    4.3e-05   23.7   0.0    1.3  1  DUF87          Helicase HerA, central domain
    0.00092   18.2   0.0      0.034   13.1   0.0    2.1  2  AAA_10         AAA-like domain
     0.0032   16.6   0.0     0.0056   15.8   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
      0.007   15.2   0.0      0.011   14.6   0.0    1.2  1  Adeno_IVa2     Adenovirus IVa2 protein
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.042   14.2   0.0    1.8  1  AAA_16         AAA ATPase domain
      0.016   14.1   0.0      0.043   12.7   0.0    1.6  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.027   13.6   0.0      0.045   12.9   0.0    1.2  1  DUF815         Protein of unknown function (DUF815)
      0.041   13.6   0.1      0.095   12.5   0.1    1.5  1  AAA_29         P-loop containing region of AAA domain
      0.066   13.0   0.2       0.19   11.5   0.2    1.8  1  MaAIMP_sms     Putative methionine and alanine importer, smal
       0.15   11.3   0.0       0.24   10.6   0.0    1.2  1  Septin         Septin
       0.19   11.2   0.0       0.33   10.4   0.0    1.3  1  AAA_7          P-loop containing dynein motor region
        3.3    7.5   5.8        7.5    6.3   5.8    1.6  1  Bax1-I         Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.5   0.4   3.8e-68   4.2e-65       1     243 []     501     702 ..     501     702 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 3.8e-68
                                    BHHHHHTSHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TT CS
                   FtsK_SpoIIIE   1 rLlevleskkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDyk 80 
                                    rL +vl+ +++r+++++l + lgk+i g+ + ++l+km+ hllvaG+tgsGKS ++n++++Sl+t++tPeeV++iliD+k
  gi|121638626|ref|YP_978850.1| 501 RLADVLTARETRRDHHPLVIGLGKDIEGDFISANLAKMP-HLLVAGSTGSGKSSFVNSMLVSLLTRATPEEVRMILIDPK 579
                                    58999**********************************.**************************************** PP

                                    SSSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-....... CS
                   FtsK_SpoIIIE  81 gvelsalediphllsvavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddla 160
                                    +vel+ +e+iphl++ +++t+p++a++al++Lv+eme+ry+ +++++vr+i+++++++ + +  +               
  gi|121638626|ref|YP_978850.1| 580 MVELTPYEGIPHLIT-PIITQPKKAAAALAWLVDEMEQRYQDMQASRVRHIDDFNDKVRSGAITA--------------- 643
                                    ***************.*************************************999998855553............... PP

                                    ...............-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES- CS
                   FtsK_SpoIIIE 161 aeneritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqr 240
                                                         + ++re+++ p++v+ivde+++L+++ap+d    vedaivR+++k+raag+Hl+latqr
  gi|121638626|ref|YP_978850.1| 644 --------------------PLGSQREYRPYPYVVAIVDELADLMMTAPRD----VEDAIVRITQKARAAGIHLVLATQR 699
                                    ....................34689**************************....************************* PP

                                    --T CS
                   FtsK_SpoIIIE 241 lsv 243
                                    +sv
  gi|121638626|ref|YP_978850.1| 700 PSV 702
                                    *96 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0     2e-30   2.3e-27       1     101 []     396     494 ..     396     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2e-30
                     FtsK_alpha   1 LPsldlLeeeekekkkedeeelekkaklieetleefgieakvveisvGPvvtqyevepapgvkvskiaaleddlalaLaa 80 
                                    LPsldlL + +    k+++++ ++ a  i e+l +f+++a v+++++GP+vt+yeve+ pgvkv+ki+al++++a a+a+
  gi|121638626|ref|YP_978850.1| 396 LPSLDLLISGDPP--KKRSAANTHMAGAIGEVLTQFKVDAAVTGCTRGPTVTRYEVELGPGVKVEKITALQRNIAYAVAT 473
                                    8********9999..7788888899******************************************************* PP

                     FtsK_alpha  81 ksirieapipGksvvGievPn 101
                                    +s+r+ apipGks+vGievPn
  gi|121638626|ref|YP_978850.1| 474 ESVRMLAPIPGKSAVGIEVPN 494
                                    ********************9 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.1   1.3e-26   1.5e-23       5      62 ..     808     865 ..     804     866 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 1.3e-26
                     FtsK_gamma   5 elfeeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegskpReVli 62 
                                    ++f +avelvv+++  StS+lQR+lr+G+++A+rl+d +e +GiVgp+egsk+ReVl+
  gi|121638626|ref|YP_978850.1| 808 DVFLQAVELVVSSQFGSTSMLQRKLRVGFAKAGRLMDLMETRGIVGPSEGSKAREVLV 865
                                    6899*****************************************************8 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   7.5     2e-08   2.3e-05      50     166 ..     173     291 ..     172     296 .. 0.91
   2 ?    0.4   0.0      0.41   4.6e+02     106     134 ..     402     430 ..     376     437 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                       FtsK_4TM  50 vGAwladlllslfGlsawllvvlllawglrllrrk.slerrllrllgalllllasaalfalrlasled.elpggaGGvlG 127
                                    +GAw+ +ll  ++G ++++l+++++a+++ l+r + ++++r + +lga l+ l++ +l +l   s e+ e + +a+G++G
  gi|121638626|ref|YP_978850.1| 173 LGAWVDALLRTFIGSAVVMLPLVAAAVAVVLMRTSpNPDSRPRLILGASLIGLSFLGLCHLWAGSPEApESRLRAAGFIG 252
                                    7********************************9725567888899************999888886658899******* PP

                       FtsK_4TM 128 rllaaalstllgftGatllllvllliglslvlgfswlel 166
                                      +++ ls+ l +  a+ ll + +l+gl+l+ g+++ e+
  gi|121638626|ref|YP_978850.1| 253 FAIGGPLSDGLTAWIAAPLLFIGALFGLLLLAGITIREV 291
                                    *********************************998876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                       FtsK_4TM 106 lfalrlasledelpggaGGvlGrllaaal 134
                                    l +   ++  ++ + +++G++G++l ++ 
  gi|121638626|ref|YP_978850.1| 402 LISGDPPKKRSAANTHMAGAIGEVLTQFK 430
                                    5555556666778899*********9985 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.8e-08   4.3e-05      24      60 ..     539     578 ..     526     580 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.8e-08
                          DUF87  24 rHlAilgsTGsGKSntvavLleelle...kkgatililDp 60 
                                     Hl++ gsTGsGKS +v ++l +ll       ++++++Dp
  gi|121638626|ref|YP_978850.1| 539 PHLLVAGSTGSGKSSFVNSMLVSLLTratPEEVRMILIDP 578
                                    7************************88876678******8 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   3.1e-05     0.034      21      61 ..     538     582 ..     530     605 .. 0.80
   2 ?    2.8   0.0      0.04        45     259     313 ..     673     731 ..     656     738 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                         AAA_10  21 asasliiGdlGnGKSvlakllvlyisllg....gkaliiDpkker 61 
                                     ++ l+ G++G GKS +++ + + ++ +      ++++iDpk  +
  gi|121638626|ref|YP_978850.1| 538 MPHLLVAGSTGSGKSSFVNSMLVSLLTRAtpeeVRMILIDPKMVE 582
                                    6899***********9999988777766667779*******9765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.04
                         AAA_10 259 kkllkelvRiG...Rsynaavylvtqsad.DvlkeelknniglklaFretdkeeikkvL 313
                                    + +++ +vRi    R+    ++l+tq ++ Dv    +k+n++ +laF      + + +L
  gi|121638626|ref|YP_978850.1| 673 RDVEDAIVRITqkaRAAGIHLVLATQRPSvDVVTGLIKTNVPSRLAFATSSLTDSRVIL 731
                                    5566666776532266666789****9765*****************977766666655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     5e-06    0.0056     120     162 ..     529     575 ..     473     588 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                          T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallkeinks....derivt 162
                                    +++++ +++   +lv+G TgsGK+ +++++l  + ++    + r+++
  gi|121638626|ref|YP_978850.1| 529 DFISANLAKMPHLLVAGSTGSGKSSFVNSMLVSLLTRatpeEVRMIL 575
                                    688888889999***************99987766553443445554 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.5e-06     0.011      75     134 ..     527     587 ..     506     590 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.5e-06
                     Adeno_IVa2  75 dGelsslnyglqPviGviyGPtGsGksqllrnlissklisPiPetv..ifitPekdmipPee 134
                                    +G+  s n+ + P + ++ G tGsGks ++ +++ s l   +Pe v  i+i P+   ++P e
  gi|121638626|ref|YP_978850.1| 527 EGDFISANLAKMPHL-LVAGSTGSGKSSFVNSMLVSLLTRATPEEVrmILIDPKMVELTPYE 587
                                    688999999999998.679*************************984466777766667765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.7e-05     0.042      25      97 ..     539     609 ..     529     694 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                         AAA_16  25 elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleaw 97 
                                    + +l+ G  G+GKss v++ l +l ++      ++i++  k ++l   +py  +  ++      + + ++ +++a++ aw
  gi|121638626|ref|YP_978850.1| 539 PHLLVAGSTGSGKSSFVNSMLVSLLTRatpeevRMILIDPKMVEL---TPYEGIPHLI------TPIITQpKKAAAALAW 609
                                    689**************9999988888899887788899999999...9994444444......4444431222333333 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.043      16      52 ..     539     579 ..     533     621 .. 0.84
   2 ?   -3.0   0.0       2.3   2.6e+03     260     281 ..     678     699 ..     657     701 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairarg....draivlDlt 52 
                                     h+l++G+tGsGK+  ++++l ++  r+     r+i +D++
  gi|121638626|ref|YP_978850.1| 539 PHLLVAGSTGSGKSSFVNSMLVSLLTRAtpeeVRMILIDPK 579
                                    599***********999998888888776666899999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                  TrwB_AAD_bind 260 elksllaegRkfGgavvlglqs 281
                                    ++ ++ +++R  G+ +vl+ q 
  gi|121638626|ref|YP_978850.1| 678 AIVRITQKARAAGIHLVLATQR 699
                                    4667789999999999999986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     4e-05     0.045      54      93 ..     539     582 ..     528     619 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg....Lrlievekedlk 93 
                                     ++L+ G+ G+GKSs v ++l ++ ++     +r+i ++ + ++
  gi|121638626|ref|YP_978850.1| 539 PHLLVAGSTGSGKSSFVNSMLVSLLTRAtpeeVRMILIDPKMVE 582
                                    589***************98877666555666999999877654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.5e-05     0.095      24      47 ..     540     563 ..     528     569 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                         AAA_29  24 atlltGpsGsGKSTllDAiqalLv 47 
                                      l++G +GsGKS+++ ++ + L+
  gi|121638626|ref|YP_978850.1| 540 HLLVAGSTGSGKSSFVNSMLVSLL 563
                                    5799************99877555 PP

>> MaAIMP_sms  Putative methionine and alanine importer, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00017      0.19       4      41 ..     265     302 ..     263     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                     MaAIMP_sms   4 aAiimmvLFiviiWGGLvlaliaLrrePDeksGilGts 41 
                                    a i   +LFi  ++G L la i++r  PD    ++Gt 
  gi|121638626|ref|YP_978850.1| 265 AWIAAPLLFIGALFGLLLLAGITIREVPDAMRAMFGTR 302
                                    5566679*****************************95 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00022      0.24       7      33 ..     541     567 ..     538     584 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                    EEEEEBTTSSCCCCCCTTSSSS----- CS
                         Septin   7 lmvvGesglGkttlintlfetdlieee 33 
                                    l+v+G+ g Gk++++n+++ + l++++
  gi|121638626|ref|YP_978850.1| 541 LLVAGSTGSGKSSFVNSMLVSLLTRAT 567
                                    89*****************99988874 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.33      29      58 ..     534     563 ..     528     574 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                          AAA_7  29 llknkkpvllvGptGtGKtviikdllkkld 58 
                                     l++  ++l+ G+tG+GK++ ++++l +l 
  gi|121638626|ref|YP_978850.1| 534 NLAKMPHLLVAGSTGSGKSSFVNSMLVSLL 563
                                    56677799****************887765 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.8    0.0067       7.5      11     110 ..     153     281 ..     149     301 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0067
                         Bax1-I  11 lalglllt.alvaavvlsspa..........qlflslhivlflv..vilaplalvflslsaarlkkkssalalallllft 77 
                                    + lgl++  a+ ++      +           ++l++    f++  v+++pl++  ++++++r+  ++ +   + l+l +
  gi|121638626|ref|YP_978850.1| 153 VLLGLAVVvAASSW------FdaarplgawvDALLRT----FIGsaVVMLPLVAAAVAVVLMRTSPNPDS--RPRLILGA 220
                                    33444433233333......13344455554333333....33333555577777555566566555555..9******* PP

                         Bax1-I  78 lleGlslspillvyt............................gaiilqaflltaaifggl 110
                                     l+Gls+  ++++ +                             a+i+  +l  +a+fg l
  gi|121638626|ref|YP_978850.1| 221 SLIGLSFLGLCHLWAgspeapesrlraagfigfaiggplsdglTAWIAAPLLFIGALFGLL 281
                                    ************9997777744444444444444444444443333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 5790.83
//
Query:       gi|121638627|ref|YP_978851.1|  [L=104]
Description: hypothetical protein BCG_2765 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-16   58.3   0.1    7.4e-16   58.0   0.1    1.1  1  ABM            Antibiotic biosynthesis monooxygenase
  ------ inclusion threshold ------
       0.28   11.0   0.6        5.8    6.8   0.2    2.5  3  TTc_toxin_rep  Tripartite Tc toxins repeat


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   8.3e-20   7.4e-16       1      73 [.       2      70 ..       2      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 8.3e-20
                                   CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHH CS
                            ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfk 73
                                   +v+v+a++++kp++ + ++d +++av ++ ++epGc  y+l++     ++++++e+W++++al+ah  +p++ 
  gi|121638627|ref|YP_978851.1|  2 PVVVVATLTAKPESVDTVRDILTRAVDDV-HREPGCQLYALHE---TGETFIFVEQWADAEALKAHSGAPAVA 70
                                   699**************************.9***********7...5556******************99876 PP

>> TTc_toxin_rep  Tripartite Tc toxins repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2   0.00065       5.8      18      31 ..       5      18 ..       4      21 .. 0.91
   2 ?   -2.5   0.0      0.52   4.6e+03      28      39 ..      26      37 ..      24      39 .. 0.72
   3 ?    1.7   0.0     0.025   2.3e+02      29      38 ..      69      78 ..      64      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00065
                  TTc_toxin_rep 18 VlssltedpeeVDa 31
                                   V  +lt++pe VD+
  gi|121638627|ref|YP_978851.1|  5 VVATLTAKPESVDT 18
                                   789**********8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.52
                  TTc_toxin_rep 28 eVDalFdagGqQ 39
                                    VD++  + G+Q
  gi|121638627|ref|YP_978851.1| 26 AVDDVHREPGCQ 37
                                   588877777777 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.025
                  TTc_toxin_rep 29 VDalFdagGq 38
                                   V ++F+a+G+
  gi|121638627|ref|YP_978851.1| 69 VATMFTAAGE 78
                                   7799*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 854.73
//
Query:       gi|121638628|ref|YP_978852.1|  [L=272]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-48  164.9   4.6    9.3e-48  162.8   4.6    1.8  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.8e-44  151.5   1.7    1.1e-43  149.0   1.7    1.9  1  adh_short     short chain dehydrogenase
    3.3e-08   33.6   1.4    5.5e-08   32.9   1.4    1.3  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8   4.6   1.6e-51   9.3e-48       1     233 [.      15     268 ..      15     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 1.6e-51
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHH......HHHHHHHHHTT......SE.E.EE--TTSHHHHHHHHHHHHHH CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeak......krveelaeelg......ae.v.lecDVtdeeqvealveevvek 66 
                                    Gaa+g+Gra A +la+ Ga+++++d+ e+ +      +++++la+ ++         v  + DV+d++++  + ++  ++
  gi|121638628|ref|YP_978852.1|  15 GAARGLGRAHAVRLAADGANIIAVDICEQIAsvpyplSTADDLAATVElvedagGGiVaRQGDVRDRASLSVALQAGLDE 94 
                                    9************************97764211222233444444333321110333479******************** PP

                                    HSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTT.... CS
                   adh_short_C2  67 fgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnyn.... 139
                                    fg+lDi+v nagia        ++ ++++++++dvnl+++f++++ a+p l+++g  gsiv +ss ++ +++ + +    
  gi|121638628|ref|YP_978852.1|  95 FGRLDIVVANAGIAMM------QAGDDGWRDVIDVNLTGVFHTVQVAIPtLIEQGtgGSIVLISSAAGLVGIGSSDpgsl 168
                                    **************99......7789***********************88887799************99876665666 PP

                                    HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHST..TSS.....-B-HHHHHHHHH CS
                   adh_short_C2 140 aygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearap..lgr.....lgtpeevaeaal 212
                                     y+aaK+++++l+r+ A++l+p++iRvN+v+p  ++T++ ++   f++ l  ++  ap  lg+     l++p+++a+a++
  gi|121638628|ref|YP_978852.1| 169 GYAAAKHGVVGLMRAYANHLAPQNIRVNSVHPCGVDTPMINNEF-FQQWLTTADMDAPhnLGNalpveLVQPTDIANAVA 247
                                    9**************************************55432.5554444433333225542222378********** PP

                                    HHCSGGGTT--SEEEEESTTG CS
                   adh_short_C2 213 fLasdeasyitGqtlvvDgGl 233
                                    +Las+ea+y+tG tl vD+G+
  gi|121638628|ref|YP_978852.1| 248 WLASEEARYVTGVTLPVDAGF 268
                                    ********************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   1.7   1.8e-47   1.1e-43       1     190 [.       9     211 ..       9     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 1.8e-47
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEES............CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHH CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdr............seekleevakelkeegakalaiqvDvtdreevealv 68 
                                    kv+++tGa++G+Gra a +la++Ga++++vd+            ++++l+++++ ++++g  ++a q+Dv+dr++++ ++
  gi|121638628|ref|YP_978852.1|   9 KVAFITGAARGLGRAHAVRLAADGANIIAVDIceqiasvpyplsTADDLAATVELVEDAGGGIVARQGDVRDRASLSVAL 88 
                                    89***************************99632233333333256788899999999999******************* PP

                                    HHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-.... CS
                      adh_short  69 ekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpv.... 143
                                    ++  +++g+ld++v+NAGi    ++ +  ++ w++vi+vNltgvf++++ ++p+++ ++ +G+Iv +sS ag+v+     
  gi|121638628|ref|YP_978852.1|  89 QAGLDEFGRLDIVVANAGI----AMMQAGDDGWRDVIDVNLTGVFHTVQVAIPTLIeQGTGGSIVLISSAAGLVGIgssd 164
                                    *******************....566677888***********************978899***********99874444 PP

                                    TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 144 agvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                    +g   Y+A+K++v+gl+r+ a+ lap++irvn+v+P +vdT+m +++
  gi|121638628|ref|YP_978852.1| 165 PGSLGYAAAKHGVVGLMRAYANHLAPQNIRVNSVHPCGVDTPMINNE 211
                                    77889**************************************8775 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   1.4   9.3e-12   5.5e-08       4     161 ..      12     182 ..      10     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 9.3e-12
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..........--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHH CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsa........aadedskaliaelealgaevevvaaDvsdkdavealleei 75 
                                    +itG++ gLG++ a  la++ga+ +++   ++        ++ +d +a+++ +e+ g  + +++ Dv d+++++ +l++ 
  gi|121638628|ref|YP_978852.1|  12 FITGAARGLGRAHAVRLAADGANIIAVDICEQiasvpyplSTADDLAATVELVEDAGGGIVARQGDVRDRASLSVALQAG 91 
                                    79********************999886666578999998778888889999**************************** PP

                                    HHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHH.....HHHHTTTS--SEEEEEEEHHHHH--....TT- CS
                             KR  76 kaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawn.....LhelledesldffvlfSSiagllgs....agq 146
                                     +e++++  v+  Ag+++     +  ++ ++ v+   ++G+ +     + +l+e+ +   +vl+SS+agl+g     +g 
  gi|121638628|ref|YP_978852.1|  92 LDEFGRLDIVVANAGIAMM----QAGDDGWRDVIDVNLTGVFHtvqvaIPTLIEQGTGGSIVLISSAAGLVGIgssdPGS 167
                                    ****************865....567777888888888887551111155566679999***********9853333788 PP

                                    HHHHHHHHHHHHHHH CS
                             KR 147 anYaaaNaflDalae 161
                                      Yaaa + + +l++
  gi|121638628|ref|YP_978852.1| 168 LGYAAAKHGVVGLMR 182
                                    999999875544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1840.55
//
Query:       gi|121638629|ref|YP_978853.1|  [L=296]
Description: hypothetical protein BCG_2767 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-41  142.0   0.0    2.7e-41  141.6   0.0    1.1  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   1.5e-45   2.7e-41       2     186 ..      11     193 ..      10     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.5e-45
                                    HHHHHHHHHHHHHH.HHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHG.CHCCCCT--HHHHHHHHHHHHHHHHHHHHH CS
                            LCM   2 lgvaaaralesrra.adglidDplaeslvsaaglellerkadkelekek.eeekkekkapelnrgiavRtrffddllkaa 79 
                                    +g ++  a+e++++  ++l+dD+la  ++ +  ++l+   a++    ++    ++e++ ++l++ +a+R+rf+ d l++a
  gi|121638629|ref|YP_978853.1|  11 FGPMVLAAVEQNEPpGRRLVDDDLADLFLPRPLRWLA--GATRSAVLRRlLISASEWSGRGLWANLACRKRFIGDKLDEA 88 
                                    56678899*****99*****************88874..444444444445678899*********************** PP

                                    HHCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT- CS
                            LCM  80 lsaagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfd 159
                                    l    i+ vViLGAGlDtrayRl    ++ vfEvD p ++++K++t+++  +e + ++r+v++D+++dd+ +aLa++g++
  gi|121638629|ref|YP_978853.1|  89 L--GDIDAVVILGAGLDTRAYRLTRRVRMPVFEVDLPVNIARKAKTVRRVLGELPLSVRLVALDFEHDDLLTALAEHGYR 166
                                    *..56*************************************************************************** PP

                                    TTSEEEEEEESSGGGS-HHHHHHHHHH CS
                            LCM 160 pekptawvaeGvlvYLtpeasdallea 186
                                    +e + ++v+eGv+ YLt+ a++++le 
  gi|121638629|ref|YP_978853.1| 167 TEYRVFFVCEGVTQYLTERAVRRTLEG 193
                                    ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2299.40
//
Query:       gi|121638630|ref|YP_978854.1|  [L=558]
Description: hypothetical protein BCG_2768c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-13   49.0   0.1    1.3e-12   47.7   0.1    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.6e-11   42.5   0.0    1.5e-09   37.7   0.0    2.5  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.2e-10   41.8   5.2    4.3e-10   39.9   5.2    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.7e-10   41.1   0.0    5.4e-10   40.2   0.0    1.5  1  RNase_J_C      Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   2.9e-16   1.3e-12       8     145 ..      56     173 ..      39     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.9e-16
                                    -TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEE CS
                  Lactamase_B_2   8 gpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnv 87 
                                    g dl  + +r        d+l++i+a++lth+H DH+  +++l +lrp ++p++++k +la +++++      +     +
  gi|121638630|ref|YP_978854.1|  56 GVDLILPDMRH-----VEDRLDDIEALVLTHGHEDHIGAIPFLLKLRP-DIPVVGSKFTLALVAEKCREYRITPV----F 125
                                    44444442222.....578899***********************999.5****************999999998....9 PP

                                    EEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S- CS
                  Lactamase_B_2  88 heldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgy 145
                                    +e+  g+s++ g   +e++ ++++h+++         +l+ ++ +g  +++++gD ++
  gi|121638630|ref|YP_978854.1| 126 VEVREGQSTRHG--VFECEYFAVNHSTPD--------ALAIAVYTGAGTILHTGDIKF 173
                                    99999******9..689***********9........9999999***********984 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.052   2.3e+02      34      47 ..      77      90 ..      68     103 .. 0.83
   2 !   37.7   0.0   3.3e-13   1.5e-09       9      52 ..     368     411 ..     361     431 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.052
                          RMMBL 34 vilvHGeeeatsal 47
                                   ++l HG+e+++ a 
  gi|121638630|ref|YP_978854.1| 77 LVLTHGHEDHIGAI 90
                                   899******99875 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 3.3e-13
                          RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeatsalarllk 52 
                                    + +++SgHa+  ell l ++++prnv++vHG +++++a a+l++
  gi|121638630|ref|YP_978854.1| 368 ARVHVSGHAYAGELLFLYNGVRPRNVMPVHGTWRMLRANAKLAA 411
                                    4588*********************************9999985 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   5.2   9.7e-14   4.3e-10       5     162 ..      28     182 ..      24     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 9.7e-14
                                    SSEEEEEEETTCEEEES--SCHHHHHHHH......HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal......elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                    + n+++ e+ g++++iD+G+  +  ++        +++ ++  ++d++a++lTH+H DHiG+ + l + ++  +++ ++ 
  gi|121638630|ref|YP_978854.1|  28 GRNMTVFEHLGRLLIIDCGVLFPGHDEPGvdlilpDMRHVEDRLDDIEALVLTHGHEDHIGAIPFLLKLRPDIPVVGSKF 107
                                    679****************9999999888999999******************************************999 PP

                                    HHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                    Lactamase_B  79 apalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                    + al  e    ++          ++  ++v e   +  + +  ++ ++ + ++ ++ + v+ g g++l tGD  +    +
  gi|121638630|ref|YP_978854.1| 108 TLALVAEKCREYR---------ITPVFVEVREGQSTRHGVFECEYFAVNHSTPDALAIAVYTGAGTILHTGDIKFDQLPP 178
                                    9998888885543.........33444555555555555555567888999**********************9988888 PP

                                    CCCC CS
                    Lactamase_B 159 ridl 162
                                    ++++
  gi|121638630|ref|YP_978854.1| 179 DGRP 182
                                    7777 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.2e-13   5.4e-10       2      73 .]     490     558 .]     489     558 .] 0.98

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.2e-13
                      RNase_J_C   2 PeivsRGfvyvkeseeLieeakkvvretieealeekesdwnelkrkirealkkflykktkrrPmIlPviveV 73 
                                    P + sRGf    e+ + +e a  +v++ +e+    + +d   + + +r++++k++ ++++r+PmI+P ++eV
  gi|121638630|ref|YP_978854.1| 490 PHLHSRGFS---EDPKALEPAVRKVEAELESLVAANVTDPIRIAQGVRRTVGKWVGETYRRQPMIVPTVIEV 558
                                    999*****6...9**********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4150.89
//
Query:       gi|121638631|ref|YP_978855.1|  [L=300]
Description: dihydrodipicolinate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-77  258.4   0.0    5.8e-77  258.2   0.0    1.0  1  DHDPS         Dihydrodipicolinate synthetase family
    0.00088   19.0   0.5       0.38   10.3   0.1    2.4  2  Peripla_BP_6  Periplasmic binding protein
  ------ inclusion threshold ------
       0.14   11.2   2.5      0.077   12.0   0.3    1.6  2  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.2   0.0   9.7e-81   5.8e-77       3     288 ..      13     295 ..      11     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 258.2 bits;  conditional E-value: 9.7e-81
                                    SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                          DHDPS   3 sgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                    + ++ta+vtpf  dg ld + +++l+++l+++g dglvv GttGEs+t    ek++l++ + ea+++r  viag+G   t
  gi|121638631|ref|YP_978855.1|  13 GTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDT 92 
                                    5689**************************************************************************** PP

                                    HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE CS
                          DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKe 162
                                    + +i+lak  ++ Ga+g+l+vtPYY kp q+gl+ hf a++ at+lp++lY++p+r+ + ++p+t+ +La  +nivgvK+
  gi|121638631|ref|YP_978855.1|  93 AHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKD 172
                                    ******************************************************************************** PP

                                    -SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          DHDPS 163 avgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllpliki 242
                                    a  dl+   +i++     l+ ysGdd+l l+ l +Ga+G isv++++a+ ++r+l+ a   Gd+a+a+++n  + pl ++
  gi|121638631|ref|YP_978855.1| 173 AKADLHSGAQIMAD--TGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNA 250
                                    *****887777766..89************************************************************** PP

                                    CCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                          DHDPS 243 lfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                    +   + v l k++l+l G++v++  r P + ++ e+ ++l+a+++a
  gi|121638631|ref|YP_978855.1| 251 MSRLGGVTLSKAGLRLQGIDVGD-PRLPQVAATPEQIDALAADMRA 295
                                    ***********************.*********9999999888765 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0   0.00076       4.6      42      80 ..      19      56 ..       5      67 .. 0.78
   2 !   10.3   0.1   6.4e-05      0.38     206     271 ..      70     135 ..      60     145 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00076
                                   EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSHH CS
                   Peripla_BP_6 42 kielverDdaydpdraaeaarrlvdqdgvdalvgplssa 80
                                    ++  + D   d+++aa+ a++lvd +g+d+lv   +++
  gi|121638631|ref|YP_978855.1| 19 MVTPFSGDGSLDTATAARLANHLVD-QGCDGLVVSGTTG 56
                                   56777889999**************.9999888765554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.4e-05
                                    HHHHHHHTT-SSSCEEEECCC-CHHHHHHHHH...HHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTT CS
                   Peripla_BP_6 206 llkaaaeaGldakrillvswsgseedlkalgg...eaaegvlavtpyfpdldnpavrafvaayeaaygg 271
                                    l   ++++G +a+ i+++++  ++++++ +++   e+a g+l+vtpy+   + p +r ++a+++a +++
  gi|121638631|ref|YP_978855.1|  70 LRAVLEAVGDRARVIAGAGTYDTAHSIRLAKAcaaEGAHGLLVVTPYY---SKPPQRGLQAHFTAVADA 135
                                    334457889999888888777666666555551115555666666666...566677777777666555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   1.3e-05     0.077     230     285 ..      38      94 ..      32     127 .. 0.78
   2 ?   -2.2   0.1      0.26   1.6e+03     265     296 ..     174     209 ..     154     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                    HHHHHHTTESEEEE--GGGTSSTT---.HHHCHHHHHHHH..SS-EEEESS--SHHH CS
                         FMN_dh 230 akraveaGvdgivvSNHGGRqldgapa.tidvLpeiveavggrievlvDgGirrGsD 285
                                    a+ +v+ G+dg+vvS   G +  ++    i+ L ++ eavg+r+ v++  G    ++
  gi|121638631|ref|YP_978855.1|  38 ANHLVDQGCDGLVVSGTTGESPTTTDGeKIELLRAVLEAVGDRARVIAGAGTYDTAH 94 
                                    7889***************9877776427******************9998766555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.26
                                    HHHH..SS-EEEESS--..SHHHHHHH..HHTT-SE CS
                         FMN_dh 265 veavggrievlvDgGir..rGsDvlkA..lalGAda 296
                                     + + + +++++D G    +G D+l    la+GA++
  gi|121638631|ref|YP_978855.1| 174 KADLHSGAQIMADTGLAyySGDDALNLpwLAMGATG 209
                                    334445789999999853378888874448888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2008.72
//
Query:       gi|121638632|ref|YP_978856.1|  [L=250]
Description: FAD-dependent thymidylate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-56  190.8   0.4    2.5e-56  190.5   0.4    1.0  1  Thy1      Thymidylate synthase complementing protein
  ------ inclusion threshold ------
      0.068   13.1   2.2      0.099   12.6   2.2    1.2  1  CHASE3    CHASE3 domain


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.4   2.8e-60   2.5e-56       8     187 ..      32     224 ..      26     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 2.8e-60
                                    HHHHHHHHHHHHHTTCSSHHHH..SGCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTT CS
                           Thy1   8 peklvaaaarvcygsseeaeele.eeekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRY 86 
                                      +lv++a r cy+s++   +   ++++++++++++++ gh s+lehas++f+i+g+Sr+++++l+rHR++s+sq SqRY
  gi|121638632|ref|YP_978856.1|  32 GPALVEFAGRACYQSWS---KPNpKTATNAGYLRHIIDVGHFSVLEHASVSFYITGISRSCTHELIRHRHFSYSQLSQRY 108
                                    5689*********9982...2223358999************************************************** PP

                                    SGCCCTCBS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHT...............TCHHHHHGGGSBTTBEEEEEEEEE CS
                           Thy1  87 vesskeafvippeieqkeeleelyeeamekaleaykellea...............gvarEdaryvLPlatktklvvtmN 151
                                    v +++ ++v+pp +e++ +l+ + +ea ++a ++y ell++               ++ar++ar vLP+at+t++vvt+N
  gi|121638632|ref|YP_978856.1| 109 VPEKDSRVVVPPGMEDDADLRHILTEAADAARATYSELLAKleakfadqpnailrrKQARQAARAVLPNATETRIVVTGN 188
                                    *****55********88899999************99999888888888998998899********************** PP

                                    HHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
                           Thy1 152 lrsLlhflelracsrAqwEirelaeemleelkkvaP 187
                                    +r+++hf+++ra+++A+ Eir+la e+l++l++vaP
  gi|121638632|ref|YP_978856.1| 189 YRAWRHFIAMRASEHADVEIRRLAIECLRQLAAVAP 224
                                    ***********************************9 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.2   1.1e-05     0.099      45     122 ..     137     213 ..     132     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                         CHASE3  45 eqaraeiqealeelreltadnpeqqerldrlealieqkl.aeleetialrreggleaalalvrsdegkelmdeiralia 122
                                    ++ara+++e l++l++  ad+p+   r +++++++++ l +  e  i +  +   +a++  ++ + + ++  eir+l+ 
  gi|121638632|ref|YP_978856.1| 137 DAARATYSELLAKLEAKFADQPNAILRRKQARQAARAVLpNATETRIVVTGN--YRAWRHFIAMRASEHADVEIRRLAI 213
                                    789************************************8888887877765..8888888888888777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1989.80
//
Query:       gi|121638633|ref|YP_978857.1|  [L=91]
Description: type I restriction/modification system specificity determinant hsdS' [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 713.02
//
Query:       gi|121638634|ref|YP_978858.1|  [L=540]
Description: type I restriction/modification system DNA methylase hsdM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-126  421.2   0.0   3.2e-126  420.8   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
    5.3e-26   91.9   0.0    9.9e-26   91.0   0.0    1.5  1  HsdM_N           HsdM N-terminal domain
    0.00026   20.6   0.0    0.00054   19.6   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.056   12.9   0.0    1.8  2  AviRa            RRNA methyltransferase AviRa
       0.12   12.0   1.0        1.5    8.5   1.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
       0.15   12.6   0.0       0.34   11.4   0.0    1.6  1  Eco57I           Eco57I restriction-modification methylase
        0.2   11.2   0.0       0.32   10.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.8   0.0  1.3e-129  3.2e-126       2     312 .]     177     503 ..     176     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.8 bits;  conditional E-value: 1.3e-129
                       N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiy 81 
                                    ++dl+G+vYEy+l++fa++egk+gGeffTP +v+k+ive+lep+sg+ vyDp+cGsgg++vq+ek+++e+dg+ k++siy
  gi|121638634|ref|YP_978858.1| 177 ARDLMGEVYEYFLGNFARAEGKRGGEFFTPPSVVKVIVEVLEPSSGR-VYDPCCGSGGMFVQTEKFIYEHDGDPKDVSIY 255
                                    79********************************************8.******************************** PP

                       N6_Mtase  82 GqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfreavapksna 161
                                    Gqe+ e+t+r+akmNl++hgi++k +++r++dt++++++  d ++d+v+aNppfn+k+w  +++e+d+r+r +v+p++na
  gi|121638634|ref|YP_978858.1| 256 GQESIEETWRMAKMNLAIHGIDNKGLGARWSDTFARDQHP-DVQMDYVMANPPFNIKDW--ARNEEDPRWRFGVPPANNA 332
                                    ****************************************.******************..8899*************** PP

                       N6_Mtase 162 dlafllhiieslkpkGraavvlangvLfr.ggkegkIrkalvekdlveavialpeklFyntsiptcilvlkkekae.... 236
                                    ++a+++hi+++l+p+Gra+vv+ang++++ ++ eg+Ir ++ve+dlv++++alp++lF++t+ip+c+++++k+ka+    
  gi|121638634|ref|YP_978858.1| 333 NYAWIQHILYKLAPGGRAGVVMANGSMSSnSNGEGDIRAQIVEADLVSCMVALPTQLFRSTGIPVCLWFFAKDKAAgkqg 412
                                    ****************************999*******************************************999*** PP

                       N6_Mtase 237 ...rkgkvlfidaseefkkkdrkknklteediekildtykek............skevdkfskvveleeiaendynlnvg 301
                                       r+g+vlfida+e  +  dr++++lt+e+i +i dt++++            +++v++f+k+++l ei+++dy+l++g
  gi|121638634|ref|YP_978858.1| 413 sidRCGQVLFIDARELGDLVDRAERALTNEEIVRIGDTFHAWrgsksaavkgimYEDVPGFCKSATLAEIKATDYALTPG 492
                                    ******************************************************************************** PP

                       N6_Mtase 302 ryveteeeeed 312
                                    ryv+t ++e+d
  gi|121638634|ref|YP_978858.1| 493 RYVGTPAVEDD 503
                                    *****999875 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   3.9e-29   9.9e-26       1     137 []      18     164 ..      18     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 3.9e-29
                                    HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC.................--..--------...... CS
                         HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee.....yken.....aleeleeklksk..eafy 68 
                                    l+++lwkaad+LRg++ as+yk++ilgL+FlK+++d ++er+e++ +e        +     +l +  e++  +    f+
  gi|121638634|ref|YP_978858.1|  18 LKDTLWKAADKLRGSLSASQYKDVILGLVFLKYVSDAYDERREAIRAElaaegM--EesqieDLIDDPEQY--QgyGVFV 93 
                                    7899*****************************************999655331..233332222233344..25699** PP

                                    S-CCCSHHHHHHS.........--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHHH CS
                         HsdM_N  69 ipeelrWkelakk.........kdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviekf 137
                                    +p  +rWk la++         + ++++g+ +++a++a+ ++n++l g++  + ++++     +++++++L ++i+ f
  gi|121638634|ref|YP_978858.1|  94 VPVSARWKFLAENtkgkpavggEPAKNIGQLIDEAMDAVMKANPTLGGTLP-R-LYNK-----DNIDQRRLGELIDLF 164
                                    *************99*99999977778***********************5.5.4444.....5799********987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00054      21     109 ..     211     310 ..     209     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                    HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..........EEEEE-STT CS
                            MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..........vevvasdvl 90 
                                    k+++e l+   sg+v D +cG G + ++  k+  e++ +  dv+ +  es +e+++  k++          + +++sd +
  gi|121638634|ref|YP_978858.1| 211 KVIVEVLEP-SSGRVYDPCCGSGGMFVQTEKFIYEHDGDPKDVSIYGQESIEETWRMAKMNlaihgidnkgLGARWSDTF 289
                                    577888888.8899*****************9999888888888877777777666666655555555888889999987 PP

                                    T..TSTTS-EEEEEE---STT CS
                            MTS  91 e..eveekkfdlivsNPPfha 109
                                    +  + ++ ++d+++ NPPf  
  gi|121638634|ref|YP_978858.1| 290 ArdQHPDVQMDYVMANPPFNI 310
                                    62156699***********75 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05     0.056      55     101 ..     222     273 ..     209     294 .. 0.67
   2 ?   -2.8   0.0       1.4   3.6e+03      72      87 ..     472     487 ..     469     488 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                          AviRa  55 ltlyDpCCGgayLl.tvlgllhgk....kikkvlasDvdeevlelakkNLsL 101
                                     ++yDpCCG++ +   +  +++++    k  ++++ +  ee+ ++ak NL++
  gi|121638634|ref|YP_978858.1| 222 GRVYDPCCGSGGMFvQTEKFIYEHdgdpKDVSIYGQESIEETWRMAKMNLAI 273
                                    479******9876514456776551111234678888888888888888876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                          AviRa  72 gllhgkkikkvlasDv 87 
                                    g++++++++++ a+D 
  gi|121638634|ref|YP_978858.1| 472 GFCKSATLAEIKATDY 487
                                    9*************95 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0   0.00057       1.5      31     131 ..     223     308 ..     212     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00057
                                    -EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH.HH--EEEEES-HHHHHHHHHHHHHTT-GGG...EE CS
                        UPF0020  31 pllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear.aelklygsDldrrvvqgareNaekagvgdl...ie 106
                                    + +DP CGsG++ +      ++ +               e++   +++++yg +++++  + a+ N+   g++++     
  gi|121638634|ref|YP_978858.1| 223 RVYDPCCGSGGMFVQ----TEKFI--------------YEHDGDpKDVSIYGQESIEETWRMAKMNLAIHGIDNKglgAR 284
                                    678999999998873....33333..............133333478889999999999999999999999988733356 PP

                                    EEE--GGG--STTS---EEEE---- CS
                        UPF0020 107 fsqadaakLrlkegevdvivtnpPY 131
                                    +s+  a++ + ++ ++d + +npP+
  gi|121638634|ref|YP_978858.1| 285 WSDTFARDQH-PDVQMDYVMANPPF 308
                                    6666677777.88899999999998 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.34       2     104 ..     298     406 ..     297     408 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                         Eco57I   2 kfdviiGNPPYqeseakkelkaleek..........akdiyqkFvekalkle.dkylaliiparfl.asgkglkefrekl 69 
                                    ++d ++ NPP+  ++    ++ +ee           +++ y   ++  +kl+  ++ ++++ +  + ++ +g  ++r+++
  gi|121638634|ref|YP_978858.1| 298 QMDYVMANPPFNIKD----WARNEEDprwrfgvppaNNANYAWIQHILYKLApGGRAGVVMANGSMsSNSNGEGDIRAQI 373
                                    79*********9888....5544444567799***99999************5567889999999989999999*****9 PP

                         Eco57I  70 lkdkklkklvefedskevFkdveikggilvflkdk 104
                                    ++   ++ +v ++ +   F ++ i  ++ +f kdk
  gi|121638634|ref|YP_978858.1| 374 VEADLVSCMVALPTQ--LFRSTGIPVCLWFFAKDK 406
                                    999888888887765..6***************98 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.32       4      82 ..     224     309 ..     221     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                Methyltransf_15   4 ilDlfsGaGGnviqfalv.........fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdl 74 
                                    + D+++G+GG  +q  +            ++++ e+ +e+  +a+ N  + g+++k     + + +++a+ +   +++d 
  gi|121638634|ref|YP_978858.1| 224 VYDPCCGSGGMFVQTEKFiyehdgdpkDVSIYGQESIEETWRMAKMNLAIHGIDNK--GLGARWSDTFARDQHPDVQMDY 301
                                    77********999888776666766554489**********************998..456789999999999******* PP

                Methyltransf_15  75 vflSpPwG 82 
                                    v++ pP  
  gi|121638634|ref|YP_978858.1| 302 VMANPPFN 309
                                    ******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.57
# Mc/sec: 2860.41
//
Query:       gi|121638635|ref|YP_978859.1|  [L=138]
Description: hypothetical protein BCG_2773c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   48.3   0.1    1.4e-12   48.1   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1     8e-17   1.4e-12       1     121 [.       5     123 ..       5     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8e-17
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    ++lD s+ ++++ + +++ +++ l+e+ + l+ + ++  E+   +++      +++++++   +++al+++++ + ++ +
  gi|121638635|ref|YP_978859.1|   5 YLLDKSAAYRAHLPAVRH-RLEPLMER-GLLARCGITDLEFGVSARS------REDHRTLGTYRRDALEYVNTPDTVWVR 76 
                                    68999*******999999.68888988.******************9......*************************** PP

                                    HHHHHHHHH.......SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  81 aaeialkyg.......llpnDaliaAtAkehgikliatfDedfrrvak 121
                                    a+ei + +        +++ D++iaA+A++hgi++  ++D df+r+a+
  gi|121638635|ref|YP_978859.1|  77 AWEIQEALTdkgfhrsVKIPDLIIAAVAEHHGIPVM-HYDQDFERIAA 123
                                    ************************************.********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.58
# Mc/sec: 721.87
//
Query:       gi|121638636|ref|YP_978860.1|  [L=88]
Description: hypothetical protein BCG_2774c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-09   37.0   1.5    2.3e-09   37.0   1.5    1.4  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
       0.08   12.8   0.2      0.086   12.7   0.2    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   1.5   2.5e-13   2.3e-09       2      42 ..      16      56 ..      15      60 .. 0.92
   2 ?   -3.7   0.0       1.4   1.2e+04       9      12 ..      72      75 ..      71      80 .. 0.53

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.5e-13
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-------H CS
                 VapB_antitoxin  2 rtnIeiDDeLlaeAirltglktKrEaVnlALreLiqrrkre 42
                                   rt I+iDD+Lla+A +  g +tK+ +V+ ALr+ ++  +++
  gi|121638636|ref|YP_978860.1| 16 RTMIDIDDDLLARAAKELGTTTKKDTVHAALRAALRASAAR 56
                                   899*****************************988877766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                                   XXXX CS
                 VapB_antitoxin  9 DeLl 12
                                   ++L+
  gi|121638636|ref|YP_978860.1| 72 EALV 75
                                   4444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.6e-06     0.086      10      64 ..       1      55 [.       1      79 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
                                   CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCH CS
                        3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaal 64
                                   m +g a v++s g++ +++di+++ l++a++++ ++++k   + +l ++ +++a+
  gi|121638636|ref|YP_978860.1|  1 MHRGYALVVCSPGVTRTMIDIDDDLLARAAKELGTTTKKDTVHAALRAALRASAA 55
                                   67899****************************9988887666666643333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.36s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 507.74
//
Query:       gi|121638637|ref|YP_978861.1|  [L=131]
Description: hypothetical protein BCG_2775c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-15   57.8   0.0    1.7e-15   57.6   0.0    1.0  1  PIN           PIN domain
  ------ inclusion threshold ------
       0.18   12.1   0.0        0.3   11.3   0.0    1.4  1  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   1.9e-19   1.7e-15       1     120 [.       1     125 [.       1     126 [. 0.97

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.9e-19
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    +++DTs+++a+++ge +a  ++++le+  +  +sa  + El+++  r  ++r +  +lv++ll+  ++++  +da++a+ 
  gi|121638637|ref|YP_978861.1|   1 MIVDTSAIVAIVSGESGAQVLKEALERSPNSRMSAPNYVELCAIMQR--RDRPEISRLVDRLLDDYGIQVEAVDADQARV 78 
                                    68*********************************************..******************************* PP

                                    HHHHHHHHH........SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  81 aaeialkyg........llpnDaliaAtAkehgikliatfDedfrrva 120
                                    aa+ ++ yg        l++ D + +A+A+ +g +l+  + +df +++
  gi|121638637|ref|YP_978861.1|  79 AAQAYRDYGrgsghparLNLGDTYSYALAQVTGEPLL-FRGDDFTHTD 125
                                    *************************************.9999998775 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.4e-05       0.3      15      45 ..      57      87 ..      52      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH CS
                   Glutaredoxin 15 akrlLkelgvkfeeidvdkdeeireelkels 45
                                   + rlL+++g+++e +d d+   + ++ +++ 
  gi|121638637|ref|YP_978861.1| 57 VDRLLDDYGIQVEAVDADQARVAAQAYRDYG 87
                                   679*****************99999998884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 723.26
//
Query:       gi|121638638|ref|YP_978862.1|  [L=89]
Description: hypothetical protein BCG_2776c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-20   72.9   8.4    3.3e-20   72.6   8.4    1.1  1  PSK_trans_fac  Rv0623-like transcription factor
     0.0015   18.4   0.1     0.0015   18.4   0.1    2.5  2  RHH_1          Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.16   11.7   0.8       0.18   11.5   0.8    1.0  1  Orbi_NS3       Orbivirus NS3
        0.7    8.3   6.6       0.74    8.3   6.6    1.0  1  FUSC           Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   8.4   7.4e-24   3.3e-20       1      82 []       1      88 [.       1      88 [. 0.83

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 7.4e-24
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX--HHHHHHHHHHHHHT...S--SS-SSTTSTTTX CS
                  PSK_trans_fac  1 MaLnIkdpeverlareLarltgeskteAvrrAleerlerlrre...raepllerllallrraaa...kaekedrspdeklly 76
                                   M+LnIk++++++l+reLa++tg+++t+Av++A+++rl++l+re   rae++++   + lr+ +    +++k+  +++e +ly
  gi|121638638|ref|YP_978862.1|  1 MSLNIKSQRTVALVRELAARTGTNQTAAVEDAVARRLSELDREdraRAEARRAAAEQTLRDLDKllsDDDKRLIRRHEVDLY 82
                                   *****************************************99777444444444444444444666899999********* PP

                                   XXXXXX CS
                  PSK_trans_fac 77 Deeglp 82
                                   D++glp
  gi|121638638|ref|YP_978862.1| 83 DDSGLP 88
                                   ****98 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.3e-07    0.0015      10      37 ..      10      37 ..       7      39 .. 0.93
   2 ?   -1.5   2.0      0.61   2.7e+03      22      35 ..      44      57 ..      35      61 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-07
                                   HHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1 10 llerLdelarrrgrSrSelIReAlreyl 37
                                   ++++++ela+r+g ++ +++++A++++l
  gi|121638638|ref|YP_978862.1| 10 TVALVRELAARTGTNQTAAVEDAVARRL 37
                                   799*********************9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.61
                                   TSSHHHHHHHHHHH CS
                          RHH_1 22 grSrSelIReAlre 35
                                   +r r e+ R+A+++
  gi|121638638|ref|YP_978862.1| 44 DRARAEARRAAAEQ 57
                                   45556665666665 PP

>> Orbi_NS3  Orbivirus NS3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8     4e-05      0.18      24      82 ..      14      72 ..       4      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                       Orbi_NS3 24 dkamsnttgatqtqkaekaafasyaeafrddvrlrqikrhvneqilpklksdlselkkk 82
                                    + ++  tg+ qt   e a     +e  r+d    + +r   eq l  l   ls+  k+
  gi|121638638|ref|YP_978862.1| 14 VRELAARTGTNQTAAVEDAVARRLSELDREDRARAEARRAAAEQTLRDLDKLLSDDDKR 72
                                   4678889************************99999***********999999987665 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.6   0.00017      0.74     569     625 ..      10      67 ..       3      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00017
                           FUSC 569 avlrLrraleralaaearaaldavlaala.frapaaarsarrlrapaaalraldaala 625
                                     v  +r++++r+ +++++a  dav ++l+  +++++ar+++r++a++++lr+ld+ l 
  gi|121638638|ref|YP_978862.1|  10 TVALVRELAARTGTNQTAAVEDAVARRLSeLDREDRARAEARRAAAEQTLRDLDKLLS 67 
                                    4555666666666677777777777777776688888888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 496.83
//
Query:       gi|121638639|ref|YP_978863.1|  [L=364]
Description: type I restriction/modification system specificity determinant hsdS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-07   32.2   0.0    1.4e-07   31.9   0.0    1.1  1  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   7.8e-12   1.4e-07       2     165 ..       5     160 ..       4     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.8e-12
                                    TT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HHHCCTEE-HHHHCCTT---B-TT-EEEE-S.SSTT-EEEESS CS
                    Methylase_S   2 edwevvkLgdvfeikkgktpkkk..elkengkypyiragilnnkvvkdglgykkkyilpkgdilissr.atiGkvayrdk 78 
                                    e++e+v+Lgd  ++ +g t      + + +g yp+++a+        + +gy+ + +  +  i+++    ++G+  y d 
  gi|121638639|ref|YP_978863.1|   5 EKVEKVRLGDHLDFSNGHTSGHTspASEPGGRYPVYGAN--------GVIGYSAQHNARGPLIVVGRVgSYCGSLRYCDS 76 
                                    6899**********888887666699999**********........9*****************976799********* PP

                                    -BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHHHH CS
                    Methylase_S  79 kyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldntiel 158
                                    ++++ +++   + k k +++++ y+ ll +   l+++  gs+qp l++  l+++ ++    +   +I +iL ++d++i+ 
  gi|121638639|ref|YP_978863.1|  77 DVWVTDNALACRAK-KPEETRYWYYALLGF--GLNRYRAGSGQPLLSQGVLRNVSVSAVAAPDRPRIGEILGAFDDKIAA 153
                                    *************9.555656666666655..8999999*************************************9998 PP

                                    HHHHHHH CS
                    Methylase_S 159 ekkikne 165
                                    + + +++
  gi|121638639|ref|YP_978863.1| 154 NDRVIEA 160
                                    8877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1939.71
//
Query:       gi|121638640|ref|YP_978864.1|  [L=90]
Description: hypothetical protein BCG_2778c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 509.77
//
Query:       gi|121638641|ref|YP_978865.1|  [L=43]
Description: hypothetical protein BCG_2779c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 258.39
//
Query:       gi|121638642|ref|YP_978866.1|  [L=159]
Description: dihydrofolate reductase dfrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-44  151.8   0.0    1.3e-44  151.8   0.0    1.0  1  DHFR_1    Dihydrofolate reductase


Domain annotation for each model (and alignments):
>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   0.0   7.2e-49   1.3e-44       1     159 [.       1     156 [.       1     158 [. 0.88

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 7.2e-49
                                    EEEEEEEEETT-EEEBTTB-SS--HHHHHHHHHHHTTCEEEEEHHHHHCC-...S--TTCEEEEE-S-TT---TTEEEES CS
                         DHFR_1   1 kislivAvaengvIGkdnklpwhlpeDlkrFkklTtgkpvimGrkTfeslg..krpLpnrkniVltrnedlkvegvevvs 78 
                                    ++ li+A+a+ gvIG+ +++pw+lpeD ++F+++T+g++++mGr+T++sl+   rpLp+r+n+Vl+r++d+ ++g+evv 
  gi|121638642|ref|YP_978866.1|   1 MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPakVRPLPGRRNVVLSRQADFMASGAEVVG 80 
                                    6789**********************************************98889************************* PP

                                    SHHHHCCCCTTS.SEEEEEE-HHHHHHCGGG-SEEEEEEES...S----SEE-----CCCEEEEEEEEE--CTTC-S-EE CS
                         DHFR_1  79 sleealalakeekeevfviGGaeiYkqalpladklylTeid...aefegdtffpeideeewelvereehekdeknkyayt 155
                                    sleeal    +   e +viGG+++Y+ alp+a++ ++Te+d    + +gd+ +p +d e+w+ +  e +   ++++++y+
  gi|121638642|ref|YP_978866.1|  81 SLEEAL----TS-PETWVIGGGQVYALALPYATRCEVTEVDiglPREAGDALAPVLD-ETWRGETGEWRF--SRSGLRYR 152
                                    ******....33.589*************************7664458********6.589877776665..44555555 PP

                                    EEEE CS
                         DHFR_1 156 fvty 159
                                       y
  gi|121638642|ref|YP_978866.1| 153 LYSY 156
                                    5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 841.39
//
Query:       gi|121638643|ref|YP_978867.1|  [L=263]
Description: thymidylate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-119  398.4   0.0   1.4e-119  398.2   0.0    1.0  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.2   0.0  7.6e-124  1.4e-119       2     268 .]       3     263 .]       2     263 .] 0.98

  Alignments for each domain:
  == domain 1  score: 398.2 bits;  conditional E-value: 7.6e-124
                                    HHHHHHHHHHHH-EEEE-TTSSEEEEEEEEEEEEEGGGCB----SSST--HHHHHHHHHHHHTT--BTHHHHTTT--TTH CS
                Thymidylat_synt   2 qYldlvrkileeGeekedRtgtgtisvfgaqlrfdlsegefPllTtkkvflksvieEllWflsgetnvkeLqekgvkiWd 81 
                                     Y dl+r +le+G+ k+dRtgtgt+s+fg+q+r+dls g fPllTtkkv++ksv+ EllWfl+g++n+ +L+e+gv+iWd
  gi|121638643|ref|YP_978867.1|   3 PYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAG-FPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWD 81 
                                    59************************************9.**************************************** PP

                                    HHHHHTTB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETE CS
                Thymidylat_synt  82 ewadeegdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegk 161
                                    ewa+++g+lgp+YG+qwr+++a++g++idq++  +d l+++pdsRriivsawn+ e+++maLppCh++fqfyv   ++g+
  gi|121638643|ref|YP_978867.1|  82 EWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYV---ADGR 158
                                    *********************************************************99**************...5668 PP

                                    EEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHHHTS---S--EEEE--SSTH CS
                Thymidylat_synt 162 LslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeqlereprelpklelnkekkv 241
                                    Ls+qlyqRSaD+flGvpFNiasyalLthm+a + gl++ge+i+t gd+HiY+nhveqv+ ql+repr++pkl l+ +++ 
  gi|121638643|ref|YP_978867.1| 159 LSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLA-DRD- 236
                                    **************************************************************************8.444. PP

                                    SGGG--GGGEEEES----SXXXXXXX. CS
                Thymidylat_synt 242 siedfeledfelenYkphpkikakvav 268
                                    si+++++ed++++nY+php+ika+vav
  gi|121638643|ref|YP_978867.1| 237 SIFEYTYEDIVVKNYDPHPAIKAPVAV 263
                                    8************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1440.81
//
Query:       gi|121638644|ref|YP_978868.1|  [L=245]
Description: alanine rich hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-65  218.4   0.0    9.2e-65  218.2   0.0    1.0  1  DLH            Dienelactone hydrolase family
    1.7e-06   28.1   0.1    0.00022   21.2   0.0    2.3  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    0.00063   19.5   0.1     0.0014   18.3   0.1    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
     0.0012   18.4   0.0       0.49    9.8   0.0    2.3  2  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.016   14.7   1.4       0.14   11.6   1.1    2.0  1  Esterase_phd   Esterase PHB depolymerase
      0.036   12.7   0.0      0.053   12.2   0.0    1.1  1  AXE1           Acetyl xylan esterase (AXE1)
      0.042   14.0   0.0        8.1    6.5   0.0    2.2  2  Thioesterase   Thioesterase domain


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   0.0   3.6e-68   9.2e-65       3     215 ..      17     242 ..      15     244 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 3.6e-68
                            DLH   3 aylatpkna.kkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa........ldpndeaeaaraldelvskv 73 
                                    + l+tp+ + ++p+vv+++++ Gv+d++++++++la  GYv+l+Pd+Y+r++        ++++d++e+ar+++++++ +
  gi|121638644|ref|YP_978868.1|  17 VRLFTPDGPgRWPGVVMFPDAGGVRDTFDRMAAKLAGFGYVVLLPDVYYREGdwapfdmkTAFGDPQERARIMFMIGTLT 96 
                                    5789********************************************************999***************** PP

                            DLH  74 aeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG.....lspekeleeaakikapi 147
                                      ++v++d++a ++yl+s+pev  +++gv+G+C+GG++++++a +  ++v+aa+af++     +sp++++  a++i+a++
  gi|121638644|ref|YP_978868.1|  97 -PDRVTRDADALLNYLASRPEVIGDRFGVCGYCIGGRMSVVVAGRLpDRVAAAAAFHPgglvaNSPDSPHLLADRISATV 175
                                    .*********************************************99******************************** PP

                            DLH 148 lalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervlelfkq 215
                                    ++  +e+D++++ad++ekl++a++aa+v++++++Yp a+H+Fa ++++sy+++a+e++w++++e+f++
  gi|121638644|ref|YP_978868.1| 176 YIGGAENDPSFTADHAEKLDKAFSAAGVPHRIECYP-AAHGFAVPDNPSYDAAADERHWAAMTETFGA 242
                                    ************************************.*****************************87 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   8.6e-08   0.00022      10      61 ..     108     160 ..     105     167 .. 0.92
   2 ?    3.4   0.0     0.024        61     183     209 ..     216     242 ..     198     245 .] 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.6e-08
                                    HHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS.SEEEEEEES--SB--SS CS
                         BAAT_C  10 inyllrhpkvkkdkigllGiSkGgelalllasflk.kisavvlingsavvveg 61 
                                    +nyl ++p+v +d+ g++G + Gg + +++a +l+  + a+ +  ++  v + 
  gi|121638644|ref|YP_978868.1| 108 LNYLASRPEVIGDRFGVCGYCIGGRMSVVVAGRLPdRVAAAAAFHPGGLVANS 160
                                    79*********************************99***9999999888766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.024
                                    EE--B-HHHHHHHHHHHHHHHHHHHHH CS
                         BAAT_C 183 vlyGGetkahakAqedsWkkilkFlkk 209
                                     +++++++++a+A+e  W+++ + +  
  gi|121638644|ref|YP_978868.1| 216 FAVPDNPSYDAAADERHWAAMTETFGA 242
                                    7899***************99876655 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   5.4e-07    0.0014      73     164 ..     120     221 ..      97     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.4e-07
                                    SSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.....CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCC CS
                  Abhydrolase_1  73 dkltlvGhSmGGmialayaaeyperVkalvllga.....idpaaslieaqrqqaksfpdffdgyaadcarnpagpllade 147
                                    d++ + G++ GG+++  +a + p+rV+a ++  +     ++p + +  a+r +a  + + ++++    a  ++ +  a++
  gi|121638644|ref|YP_978868.1| 120 DRFGVCGYCIGGRMSVVVAGRLPDRVAAAAAFHPgglvaNSPDSPHLLADRISATVYIGGAENDPSFTADHAEKLDKAFS 199
                                    677799*********************************9**************************99999999999999 PP

                                    SCHHHHHHHHHHHHHH.....H CS
                  Abhydrolase_1 148 laaleqrhrlvdalkf.....p 164
                                    +a ++ r ++  a ++     +
  gi|121638644|ref|YP_978868.1| 200 AAGVPHRIECYPAAHGfavpdN 221
                                    9999999998776666666663 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00019      0.49      43      94 ..      99     150 ..      88     160 .. 0.89
   2 !    6.3   0.0    0.0023       5.8     151     206 ..     180     235 ..     157     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                    HHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEE CS
                   Peptidase_S9  43 nefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaava 94 
                                    +  +D  a + +la++  v  +r ++ G   GG ++ +++++ pd+ +aa+a
  gi|121638644|ref|YP_978868.1|  99 RVTRDADALLNYLASRPEVIGDRFGVCGYCIGGRMSVVVAGRLPDRVAAAAA 150
                                    55678889999**********************************9998887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0023
                                    ETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHH.HHHHHHHHHHH CS
                   Peptidase_S9 151 GlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakv.eelarllaFlk 206
                                    +++D   +  +a+kl +a   +g+++++  +p   Hg++ p++   +  a++ ++++
  gi|121638644|ref|YP_978868.1| 180 AENDPSFTADHAEKLDKAFSAAGVPHRIECYPA-AHGFAVPDNPSyDAAADERHWAA 235
                                    7899****************************6.6********99999999999975 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   5.5e-05      0.14       4     131 ..      18     155 ..      15     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                   Esterase_phd   4 rlylppGarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwn...wykdtdraGr..... 75 
                                    rl+ p G  r   p vvm+       + f    rm +    +G+vvl p+   r      ++    + d +++ r     
  gi|121638644|ref|YP_978868.1|  18 RLFTPDGPGR--WPGVVMFPDAGGVRDTF---DRMAAKLAGFGYVVLLPDVYYREGDWAPFDmktAFGDPQERARimfmi 92 
                                    6666666666..66666666666666666...366666666666666666666654333322111344545544422222 PP

                   Esterase_phd  76 G..eaavvv....alvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaav.alhsGl 131
                                    G   ++ v+    al + l++   v   r  v G   G+ ++ ++a   pd+ aa  a h G 
  gi|121638644|ref|YP_978868.1|  93 GtlTPDRVTrdadALLNYLASRPEVIGDRFGVCGYCIGGRMSVVVAGRLPDRVAAAaAFHPGG 155
                                    111344444111145556677778888999*********************998651678764 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05     0.053     153     206 ..      99     153 ..      91     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHH.H-SS-SEEEEES- CS
                           AXE1 153 rvflDavrlveivaslpevDeeRvavlGasqGGalalavaa.lekrikavvadyP 206
                                    rv  Da  l++ +as pev  +R +v+G   GG ++++va+ l +r++a++a  P
  gi|121638644|ref|YP_978868.1|  99 RVTRDADALLNYLASRPEVIGDRFGVCGYCIGGRMSVVVAGrLPDRVAAAAAFHP 153
                                    56679999****************************9998758888888887665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0032       8.1       3      28 ..      31      57 ..      29      70 .. 0.85
   2 ?    5.4   0.0    0.0069        18      43      90 ..      99     144 ..      87     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0032
                                   EEEE--TTCCSGGGHHHHHHCTTC.EE CS
                   Thioesterase  3 LflfppagGsasvfrslasklsdp.vv 28
                                   +++fp+agG    f ++a+kl +  +v
  gi|121638644|ref|YP_978868.1| 31 VVMFPDAGGVRDTFDRMAAKLAGFgYV 57
                                   79*******************986444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0069
                                    HCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHC CS
                   Thioesterase  43 pplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesq 90 
                                    +  +++++l +++a   + i ++  + + G++ Gg +   vA +L ++
  gi|121638644|ref|YP_978868.1|  99 RVTRDADALLNYLASRPEVIGDR--FGVCGYCIGGRMSVVVAGRLPDR 144
                                    56677778888888877777777..99*****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.60
# Mc/sec: 1233.14
//
Query:       gi|121638645|ref|YP_978869.1|  [L=260]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-60  204.6   3.5    1.8e-60  204.4   3.5    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    4.9e-50  169.7   0.3    5.8e-50  169.5   0.3    1.1  1  adh_short       short chain dehydrogenase
    1.5e-07   31.5   0.9    2.2e-07   31.0   0.9    1.2  1  KR              KR domain
     0.0013   18.7   0.7     0.0029   17.6   0.7    1.6  1  ADH_zinc_N      Zinc-binding dehydrogenase
     0.0054   16.6   1.9     0.0057   16.6   0.8    1.7  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.016   14.6   0.2      0.036   13.4   0.2    1.6  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.017   15.0   0.3      0.025   14.5   0.3    1.2  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.028   13.8   0.2       0.07   12.4   0.0    1.8  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.077   12.4   0.4       0.12   11.8   0.1    1.5  2  Epimerase       NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.4   3.5     9e-64   1.8e-60       1     233 [.      15     244 ..      15     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 9e-64
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga +gIG aiA++la++Ga+vvlt +++ea   ++e+a+++g ++  + + + de++ +++v+ + e+fg++Dil+nnag
  gi|121638645|ref|YP_978869.1|  15 GASRGIGLAIAQQLAAAGAHVVLTARRQEA---ADEAAAQVGDRAlgVGAHAVDEDAARRCVDLTLERFGSVDILINNAG 91 
                                    999**********************99999...899999999886599******************************** PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                      p+  gp+le + + f++++dvnl + ++ +  ++   m e+ g++vn++s+g+    p   +y+a+Kaal+++t++lA
  gi|121638645|ref|YP_978869.1|  92 TNPA-YGPLLEQDHARFAKIFDVNLWAPLMWTSLVVTaWMGEHgGAVVNTASIGGMHQSPAMGMYNATKAALIHVTKQLA 170
                                    ***9.*******************************99665544************************************ PP

                                    HHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                   adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                     el p +iRvNa++pg+++T++a+++   ++ ++ l+a + lgr+g+p ++a+a++fL+sd+as+itG+t+++DgGl
  gi|121638645|ref|YP_978869.1| 171 LELSP-RIRVNAICPGVVRTRLAEALW--KDHEDPLAATIALGRIGEPADIASAVAFLVSDAASWITGETMIIDGGL 244
                                    *****.9*******************9..7888*******************************************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   0.3   2.9e-53   5.8e-50       2     193 ..      10     198 ..       9     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 2.9e-53
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    ++++tGas+GIG+aia++la++Ga+vv+++r++e++ e+a+++++   +al + +   d++++++ v+   +++g++d+L
  gi|121638645|ref|YP_978869.1|  10 TAIITGASRGIGLAIAQQLAAAGAHVVLTARRQEAADEAAAQVGD---RALGVGAHAVDEDAARRCVDLTLERFGSVDIL 86 
                                    79****************************************997...6******************************* PP

                                    EE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    +nNAG     gp  e + +++ ++++vNl ++++ t +v++a++ +++G++vn++S+ g  +++ + +Y A+Kaa+++ t
  gi|121638645|ref|YP_978869.1|  87 INNAGTnPAYGPLLEQDHARFAKIFDVNLWAPLMWTSLVVTAWMGEHGGAVVNTASIGGMHQSPAMGMYNATKAALIHVT 166
                                    ******88899********************************************************************* PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmakelrek 193
                                    ++la el+p+ irvna++PG+v+T +a++l ++
  gi|121638645|ref|YP_978869.1| 167 KQLALELSPR-IRVNAICPGVVRTRLAEALWKD 198
                                    *********8.***************9988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.9   1.1e-10   2.2e-07       3     156 ..      11     162 ..       9     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                     +itG+  g+Gl++a++la+ ga h+vl++R+   +e++++  a++ ++   v + a+D   +da +++++   ++++++
  gi|121638645|ref|YP_978869.1|  11 AIITGASRGIGLAIAQQLAAAGA-HVVLTARR---QEAADEAAAQVGDRALGVGAHAVD---EDAARRCVDLTLERFGSV 83 
                                    69*******************98.8999***9...344444567777777777777776...9999************** PP

                                    -EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  83 kGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNafl 156
                                       i+ Ag+    ++l e++ +++++++   + +      l+      e+   +v ++Si+g+  s+  + Y a+ a l
  gi|121638645|ref|YP_978869.1|  84 DILINNAGTNPaYGPLLEQDHARFAKIFDVNLWAPLMWTSLVVTawmgEHGGAVVNTASIGGMHQSPAMGMYNATKAAL 162
                                    ********975389***********999877776544444333333338999999999**9999999999999987755 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   1.5e-06    0.0029       1      71 [.      19      95 ..      19     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.T.....T.ESEEEETTTCHHHHHHHHHT..TTSSEEEEEESSCSHHH CS
                     ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.l.....G.adevinykeadlverikelt..ggegvdvvfecvGsgat 71
                                   g+Gla  q ++a+Ga+v+ +++ +e ++ a+        G   +++++   d   r+ +lt  + + vd+ ++ +G++ +
  gi|121638645|ref|YP_978869.1| 19 GIGLAIAQQLAAAGAHVVLTARRQEAADEAAAqVgdralGvGAHAVDE---DAARRCVDLTleRFGSVDILINNAGTNPA 95
                                   8******************99999999777663633333222334444...77777777777633489999999997766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   2.9e-06    0.0057       1      39 [.      15      52 ..      15     104 .. 0.85
   2 ?   -3.7   0.0       4.6   9.1e+03      36      58 ..     200     222 ..     189     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTT CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaee 39
                                   GA+ ++G +++++l+a+g  +v++ +R++e ++e +a+ 
  gi|121638645|ref|YP_978869.1| 15 GASRGIGLAIAQQLAAAG-AHVVLTARRQEAADEAAAQV 52
                                   9****************5.9***********99866543 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.6
                                    HCTTTCEEEE--TT-CCHHHHHH CS
                 NAD_binding_10  36 eaeeglevvegdvtdvedlaeal 58 
                                    e+  ++++  g + +++d+a+a+
  gi|121638645|ref|YP_978869.1| 200 EDPLAATIALGRIGEPADIASAV 222
                                    45556777888888888888887 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.8e-05     0.036      31      76 ..       3      49 ..       1      65 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                   BS-GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                   2-Hacid_dh_C 31 gkelsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeee 76
                                   + +l+g+t  i G+ r IG a+a+ l+a g++v+ + r++++ +e++
  gi|121638645|ref|YP_978869.1|  3 SLDLTGRTAIITGASRgIGLAIAQQLAAAGAHVVLTARRQEAADEAA 49
                                   56899*********988*********************988776333 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.3e-05     0.025      10      46 ..      20      56 ..      11      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                   CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHH CS
                        3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksl 46
                                   +G  ia+++a+ag +Vvl+ +++ea+++a++++ ++ 
  gi|121638645|ref|YP_978869.1| 20 IGLAIAQQLAAAGAHVVLTARRQEAADEAAAQVGDRA 56
                                   799***************************9998754 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.5e-05      0.07      31      75 ..       3      47 ..       1      63 [. 0.88
   2 ?   -2.5   0.0       1.4   2.8e+03      95     108 ..     230     243 ..     212     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                   T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHH CS
                  THF_DHG_CYH_C 31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlae 75
                                   + +l+g+++++ G+s+ +g ++a+ L++++a V ++ ++ +  +e
  gi|121638645|ref|YP_978869.1|  3 SLDLTGRTAIITGASRGIGLAIAQQLAAAGAHVVLTARRQEAADE 47
                                   5799*****************************999888766655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                    GGGS-TT-EEEE-- CS
                  THF_DHG_CYH_C  95 aemvkegavviDvG 108
                                    a+++  ++++iD G
  gi|121638645|ref|YP_978869.1| 230 ASWITGETMIIDGG 243
                                    67888888998876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.1e-05      0.12       2      41 ..      12      51 ..      11      97 .. 0.73
   2 ?   -3.3   0.0       2.5   4.9e+03     139     155 ..     152     168 ..     136     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCH CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarle 41
                                   ++tGa+  iG a++++l+++g +v+  +r+++a  +a+ +
  gi|121638645|ref|YP_978869.1| 12 IITGASRGIGLAIAQQLAAAGAHVVLTARRQEAADEAAAQ 51
                                   89*******************9988888886666555443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                    SSHHHHHHHHHHHHHHH CS
                      Epimerase 139 nspYaaaKlageklvea 155
                                       Y a+K+a  +++++
  gi|121638645|ref|YP_978869.1| 152 MGMYNATKAALIHVTKQ 168
                                    45678888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1674.76
//
Query:       gi|121638646|ref|YP_978870.1|  [L=117]
Description: hypothetical protein BCG_2784c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 827.00
//
Query:       gi|121638647|ref|YP_978871.1|  [L=394]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-59  199.5  32.2    3.4e-59  199.5  32.2    3.2  4  PPE       PPE family
    2.9e-19   69.8  17.2    2.9e-19   69.8  17.2    5.8  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
      0.039   13.7   1.1      0.083   12.7   1.1    1.5  1  RecC_C    RecC C-terminal domain


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.5  32.2   5.7e-63   3.4e-59       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -1.2   1.2      0.32   1.9e+03      82     101 ..     176     195 ..     169     225 .. 0.63
   3 ?   -5.1   5.8         3   1.8e+04      83     103 ..     282     302 ..     252     344 .. 0.62
   4 ?   -1.5   0.3      0.39   2.3e+03      32      63 ..     327     358 ..     303     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 5.7e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+ns+++yaG+g++pl+aA a+W+gLa el+++a+++esv+ +l++e+W Gp+s++m+ aa+pylaWL+ +a++a+
  gi|121638647|ref|YP_978871.1|   5 ALPPEINSTRMYAGAGAAPLMAAGATWNGLAVELSTTASSVESVIMQLTTEQWLGPASMSMVVAAQPYLAWLTYTAESAA 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aAaqa a aaa+eaA+a++vppae+aanra laalvatn++GqntpaI+atea+y emwaqda am++Y+a+saaa
  gi|121638647|ref|YP_978871.1|  85 HAAAQAMASAAAFEAAFAMTVPPAEVAANRALLAALVATNVLGQNTPAIMATEAHYGEMWAQDALAMYGYAASSAAA 161
                                    *************************************************************************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHHHHHS- CS
                            PPE  82 aAaqaeaaaaaYeaAlaamv 101
                                    +A  a  aaa+  aA a++v
  gi|121638647|ref|YP_978871.1| 176 MAGLAGQAAAVSHAAAASTV 195
                                    34444444444444444444 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 3
                                    HHHHHHHHHHHHHHHHHS--H CS
                            PPE  83 AaqaeaaaaaYeaAlaamvpp 103
                                    Aa  ++ aaa  a la +v+p
  gi|121638647|ref|YP_978871.1| 282 AAADAVPAAAAAAGLAHTVTP 302
                                    222223333333334444443 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHH CS
                            PPE  32 aelasaaaelesvlaelaaeaWqGpssaamaa 63 
                                    a +++aa +++s +++l+++ W  p  a  +a
  gi|121638647|ref|YP_978871.1| 327 AGWSTAAPAMTSGTTALEGSGWAVPEEAGPVA 358
                                    56788899999999999999998776555554 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -33.0  42.7         3   1.8e+04      34      62 ..      86     115 ..       5     232 .. 0.77
   2 ?    1.3   4.8      0.11   6.5e+02      28      54 ..     277     303 ..     259     310 .. 0.44
   3 !   69.8  17.2   4.8e-23   2.9e-19       1      79 [.     311     390 ..     311     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: -33.0 bits;  conditional E-value: 3
                       PE_PPE_C  34 sgttaaaaaaaagaalg.gmPlaaagagga 62 
                                     +++a+a+aaa++aa++  +P a ++a++a
  gi|121638647|ref|YP_978871.1|  86 AAAQAMASAAAFEAAFAmTVPPAEVAANRA 115
                                    222222333333322223455555555544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                       PE_PPE_C  28 aaaaalsgttaaaaaaaagaalggmPl 54 
                                    +a  ++ + +++aaaaaag a   +P+
  gi|121638647|ref|YP_978871.1| 277 PATVTAAADAVPAAAAAAGLAHTVTPV 303
                                    222222222222222222222224444 PP

  == domain 3  score: 69.8 bits;  conditional E-value: 4.8e-23
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    +A+lG+A++vG+LSVP+ W++aapa+++  +al ++ +a++++a++ aa++gm++ + +a+ga+++a+prygf+p vmp+
  gi|121638647|ref|YP_978871.1| 311 TASLGEASSVGGLSVPAGWSTAAPAMTSGTTALeGSGWAVPEEAGPVAAMPGMAGISGAAKGAGAYAGPRYGFKPIVMPK 390
                                    59***************************9999644555677788889999****9999999999**************8 PP

>> RecC_C  RecC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   1.4e-05     0.083     109     192 ..      32     140 ..      11     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                         RecC_C 109 eslevdldlggtgLtgtldglrergllrwrpsklkakdllraWlehLalca...........................lp 161
                                      l+v+l+ +  +++  + +l+++++l   p++++     + +l++L ++a                            +
  gi|121638647|ref|YP_978871.1|  32 NGLAVELSTTASSVESVIMQLTTEQWLG--PASMSMVVAAQPYLAWLTYTAesaahaaaqamasaaafeaafamtvppAE 109
                                    5577888888888888899999775554..********************9************************96655 PP

                         RecC_C 162 aeeArelLaellalyrqGlrqpLpffpktal 192
                                    +++ r+lLa+l+a   +G+++p  +++++ +
  gi|121638647|ref|YP_978871.1| 110 VAANRALLAALVATNVLGQNTPAIMATEAHY 140
                                    567799*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2113.85
//
Query:       gi|121638648|ref|YP_978872.1|  [L=275]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-29  100.7  14.1    4.1e-29  100.7  14.1    2.5  4  PE             PE family
    1.5e-18   67.5  15.7    1.5e-18   67.5  15.7    4.2  3  PE_PPE_C       Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7  14.1   4.6e-33   4.1e-29       1      93 []       1      94 [.       1      94 [. 0.97
   2 ?   -3.8   0.0       1.9   1.7e+04      13      23 ..      98     108 ..      97     112 .. 0.67
   3 ?   -3.4   1.8       1.4   1.3e+04      34      34 ..     158     158 ..     133     185 .. 0.50
   4 ?   -2.9   1.4      0.99   8.9e+03      26      42 ..     169     185 ..     152     195 .. 0.56

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 4.6e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaap.ttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqala 81
                                   Msf++++Pe+laaaa++l++igsa+ a+naaaaap tt+v++aaaDe+S+ +A+lf+a+++ yq++sa+aaa+ + fv++l 
  gi|121638648|ref|YP_978872.1|  1 MSFLTTQPEELAAAAGKLETIGSAMVAQNAAAAAPtTTGVIPAAADEISVLQASLFTAYGTLYQQVSAEAAAVYDLFVKTLG 82
                                   9***************************99988874789******************************************* PP

                                   HHHHHHHS--XX CS
                             PE 82 aaagsYaaaEaa 93
                                    +ag+Yaa+Eaa
  gi|121638648|ref|YP_978872.1| 83 VSAGTYAATEAA 94
                                   **********97 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHH CS
                             PE  13 aaaadlagigs 23 
                                    aaa+ l gi+s
  gi|121638648|ref|YP_978872.1|  98 AAASPLSGIAS 108
                                    67777777776 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.4
                                    H CS
                             PE  34 a 34 
                                    a
  gi|121638648|ref|YP_978872.1| 158 A 158
                                    2 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.99
                                    HHHHHHHHHHHH----S CS
                             PE  26 saanaaaaapttavlaa 42 
                                    s+  aa aa+  a +aa
  gi|121638648|ref|YP_978872.1| 169 SELGAAEAAVGEAPIAA 185
                                    33334444443333333 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -9.7  16.5         2   1.8e+04       2      33 ..      13      44 ..       5     119 .. 0.59
   2 ?   -2.2   7.6       0.9   8.1e+03      19      68 ..     135     182 ..     131     191 .. 0.55
   3 !   67.5  15.7   1.7e-22   1.5e-18       1      80 []     193     273 ..     193     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: -9.7 bits;  conditional E-value: 2
                       PE_PPE_C  2 AglGqAatvGaLSVPpsWaaaapaasaaaaal 33
                                   A++G+  t+G+  V ++ aaaap+++ + +a+
  gi|121638648|ref|YP_978872.1| 13 AAAGKLETIGSAMVAQNAAAAAPTTTGVIPAA 44
                                   55555555555555555555555555544444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.9
                       PE_PPE_C  19 WaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaap 68 
                                    Wa+aa+ +  ++ a +g  +aa++aa +++l g+ l  +ga+ aa+g+ap
  gi|121638648|ref|YP_978872.1| 135 WASAASDL--LGLASGGLLPAAEEAALEEGLEGAGLSELGAAEAAVGEAP 182
                                    54433332..2223344455555555555566777777777766555544 PP

  == domain 3  score: 67.5 bits;  conditional E-value: 1.7e-22
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    +Agl +A+++GaLSVPpsWa++a  +s++++    g+t+aa  +aag++++gmP+ a++++++ag++apryg +p vmp+
  gi|121638648|ref|YP_978872.1| 193 AAGLSRASSIGALSVPPSWAGQANLVSSTSTLQgAGWTTAAPHGAAGTVIPGMPGLASATRSSAGFGAPRYGAKPIVMPK 272
                                    69**************************9999989999999999***********************************9 PP

                       PE_PPE_C  80 p 80 
                                    p
  gi|121638648|ref|YP_978872.1| 273 P 273
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1877.46
//
Query:       gi|121638649|ref|YP_978873.1|  [L=382]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-55  186.5  29.5    3.4e-55  186.5  29.5    2.2  3  PPE       PPE family
    1.3e-16   61.3  12.9    1.3e-16   61.3  12.9    5.5  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5  29.5   3.7e-59   3.4e-55       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -2.8   0.6      0.69   6.1e+03      25      35 ..     184     194 ..     174     224 .. 0.48
   3 ?   -5.7   3.8         2   1.8e+04      33      33 ..     297     297 ..     274     337 .. 0.44

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 3.7e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPEvnsa++y G+g++ llaAaaaW+g+a e+++aa+++ sv++ l++e W Gp+s +maaa++pyl WL+ +a++++
  gi|121638649|ref|YP_978873.1|   5 ALPPEVNSARMYGGAGAADLLAAAAAWNGIAVEVSTAASSVGSVITRLSTEHWMGPASLSMAAAVQPYLVWLTCTAESSA 84 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aAaqa a aaa+e+A+a +vppae++anra la l+atn++Gqn +aIaatea y emwaqda+am++Y+aasa a
  gi|121638649|ref|YP_978873.1|  85 LAAAQAMASAAAFETAFALTVPPAEVVANRALLAELTATNILGQNVSAIAATEARYGEMWAQDASAMYGYAAASAVA 161
                                    **************************************************************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.69
                                    HHHHHHHHHHH CS
                            PPE  25 aaWdgLaaela 35 
                                    aa  +  a+ +
  gi|121638649|ref|YP_978873.1| 184 AAVGQAGASAS 194
                                    22222222222 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 2
                                    H CS
                            PPE  33 e 33 
                                    +
  gi|121638649|ref|YP_978873.1| 297 T 297
                                    3 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -12.9  19.5         2   1.8e+04      28      57 ..      80     110 ..       5     143 .. 0.64
   2 ?   -3.2   9.0       1.8   1.6e+04      25      67 ..     156     195 ..     142     232 .. 0.49
   3 ?   -1.7   7.6      0.62   5.6e+03      42      65 ..     266     288 ..     250     299 .. 0.54
   4 !   61.3  12.9   1.4e-20   1.3e-16       2      79 ..     301     378 ..     300     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: -12.9 bits;  conditional E-value: 2
                       PE_PPE_C  28 aaaaalsgttaaaaaaaagaalg.gmPlaaa 57 
                                    a ++al +++a+a+aaa+++a++  +P a +
  gi|121638649|ref|YP_978873.1|  80 AESSALAAAQAMASAAAFETAFAlTVPPAEV 110
                                    2233334444444444444444454555444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                       PE_PPE_C  25 aasaaaaal.sgttaaaaaaaagaalggmPlaaagaggaaggaa 67 
                                    aasa+aa l + t ++  ++ ag a +++++++aga+++    a
  gi|121638649|ref|YP_978873.1| 156 AASAVAARLnPLTRPSHITNPAGLAHQAAAVGQAGASAS----A 195
                                    333333333322222222222222222233322222222....2 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.62
                       PE_PPE_C  42 aaaagaalggmPlaaagaggaagg 65 
                                    a a+g+++g++P+++a+a+ a ++
  gi|121638649|ref|YP_978873.1| 266 ADAMGTVGGAAPGGGAAAAVA-HA 288
                                    445555555666666665555.22 PP

  == domain 4  score: 61.3 bits;  conditional E-value: 1.4e-20
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    A lG+A+ vG+LSVP+sW++aapa++a aa  +  +a++++ ++ a+++ +P++ ++a++ ++ ++pryg++p vmp+
  gi|121638649|ref|YP_978873.1| 301 ADLGNASVVGRLSVPASWSTAAPATAAGAALDGTGWAVPEEDGPIAVMPPAPGMVVAANSVGADSGPRYGVKPIVMPK 378
                                    99****************************999999999*******************999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2785.57
//
Query:       gi|121638650|ref|YP_978874.1|  [L=150]
Description: hypothetical protein BCG_2788c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-05   24.4   0.0    3.2e-05   23.7   0.0    1.3  1  FMN_red   NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-09   3.2e-05      70     151 ..      49     127 ..      35     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-09
                                    HHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEE CS
                        FMN_red  70 iaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraava 149
                                    + +ad+ +++tP   g +sg+lK+a+D++ + +  +  rg+ +++     g+ g+++ae++   + + lg++  ++ +v+
  gi|121638650|ref|YP_978874.1|  49 MLEADGYLLGTPANLGYISGALKHAFDVCYY-PCLDTTRGRSFGAY--IHGNEGTEGAERAVDAITTGLGWVQAAETVVV 125
                                    889**************************63.44555666665555..44669999999999999989999999987777 PP

                                    ET CS
                        FMN_red 150 vg 151
                                    +g
  gi|121638650|ref|YP_978874.1| 126 MG 127
                                    65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 977.21
//
Query:       gi|121638651|ref|YP_978875.1|  [L=157]
Description: hypothetical protein BCG_2789c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   21.9   2.0    0.00013   21.9   2.0    2.2  2  TPR_2     Tetratricopeptide repeat
     0.0009   19.3   0.4     0.0025   17.9   0.1    2.0  2  TPR_8     Tetratricopeptide repeat
      0.005   16.7   0.8     0.0063   16.4   0.8    1.2  1  DUF3611   Protein of unknown function (DUF3611)
     0.0078   16.7   2.5     0.0078   16.7   2.5    2.1  3  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.083   13.6   1.9      0.083   13.6   1.9    2.9  2  TPR_6     Tetratricopeptide repeat
       0.11   12.3   0.3       0.27   11.1   0.3    1.6  1  TPR_1     Tetratricopeptide repeat
       0.15   10.9   0.0       0.14   11.0   0.0    1.0  1  LMBR1     LMBR1-like membrane protein
       0.17   12.0   1.5       0.26   11.4   0.4    1.9  2  TPR_7     Tetratricopeptide repeat
          5    7.9   9.5        7.5    7.4   9.5    1.2  1  DUF4282   Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.8   7.7e+03       8      14 ..      66      72 ..      64      75 .. 0.48
   2 !   21.9   2.0   6.3e-08   0.00013       3      31 ..     121     149 ..     119     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                          TPR_2  8 Glayykl 14
                                   G ay +l
  gi|121638651|ref|YP_978875.1| 66 GFAYQRL 72
                                   4444443 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 6.3e-08
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                     +y+l++ay ++gd  +A+ea++ Al+l+
  gi|121638651|ref|YP_978875.1| 121 RWYRLARAYDYAGDRRRAREAMKTALQLE 149
                                    5**************************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         9   1.8e+04       3       9 ..      68      74 ..      65      75 .. 0.63
   2 !   17.9   0.1   1.2e-06    0.0025       3      31 ..     121     149 ..     120     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9
                                   HHHHHHH CS
                          TPR_8  3 ayynlgs 9 
                                   ay++l++
  gi|121638651|ref|YP_978875.1| 68 AYQRLAR 74
                                   4666665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                     +y+l+++y+  gd   A e+++ al+l+
  gi|121638651|ref|YP_978875.1| 121 RWYRLARAYDYAGDRRRAREAMKTALQLE 149
                                    6*************************986 PP

>> DUF3611  Protein of unknown function (DUF3611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.8   3.1e-06    0.0063      20      83 ..       7      78 ..       1      93 [. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-06
                        DUF3611 20 WlQlvLgv.....vsalillfallgrslaeetnaglgfgl...flavlglvvllfsifwafrytrlarrLra 83
                                   ++Ql++++     v+ l++l  +++  + + + a++g+gl   +l v+gl ++++++   f y rlar +++
  gi|121638651|ref|YP_978875.1|  7 YVQLIIAFmcvamVAYLVMLGRVAVAMIGSGRAAAAGLGLallILPVIGLWAMIATLRAGFAYQRLARLIAE 78
                                   5666665511000555555555555444334444445554447999**********************9944 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.3   8.6e+03      32      44 ..      30      42 ..      24      48 .. 0.64
   2 ?   -1.9   0.1       2.5     5e+03      46      58 ..      70      82 ..      68      88 .. 0.46
   3 !   16.7   2.5   3.9e-06    0.0078       4      55 ..      97     149 ..      95     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                         TPR_19 32 AeallalgqldeA 44
                                   A a++ +g+ ++A
  gi|121638651|ref|YP_978875.1| 30 AVAMIGSGRAAAA 42
                                   5566666665555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                         TPR_19 46 alLdalpeedpdd 58
                                   + L++l +ed  d
  gi|121638651|ref|YP_978875.1| 70 QRLARLIAEDGLD 82
                                   4455555555544 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 3.9e-06
                         TPR_19   4 egdyaeAlalleqa.lqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                    + d a+Al +  +  l++d+++++ +++LA+a+  +g+   A+++++++++ +
  gi|121638651|ref|YP_978875.1|  97 QRDAADALFAAVRTeLEDDADDWRRWYRLARAYDYAGDRRRAREAMKTALQLE 149
                                    789999988888877********************************998765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.8      0.79   1.6e+03       9      13 ..      68      72 ..      61     111 .. 0.46
   2 ?   13.6   1.9   4.2e-05     0.083       4      28 ..     123     147 ..     122     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.79
                                   HHHHH CS
                          TPR_6  9 syrkl 13
                                   +y++l
  gi|121638651|ref|YP_978875.1| 68 AYQRL 72
                                   55443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                    y+la++y  +gd ++A+ea++  ++
  gi|121638651|ref|YP_978875.1| 123 YRLARAYDYAGDRRRAREAMKTALQ 147
                                    9********99*********98775 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00013      0.27       4      30 ..     122     148 ..     119     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                    +y+l+ ay + g+   A e+ + AL+l
  gi|121638651|ref|YP_978875.1| 122 WYRLARAYDYAGDRRRAREAMKTALQL 148
                                    ************************998 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     7e-05      0.14     124     193 ..       3      95 ..       1     149 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                          LMBR1 124 yenaiiyllllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvelPrslwr........... 192
                                    +++++++l++++++++++ y++++   + ++    + +   ++a  +Gl llil   +Gl ++ + + r           
  gi|121638651|ref|YP_978875.1|   3 RRTLYVQLIIAFMCVAMVAYLVML-GRVAVA----MIGSGRAAAAGLGLALLILP-VIGLWAM-IATLRagfayqrlarl 75 
                                    67899*******************.999998....88888888888888777654.3799999.6666756666666666 PP

                          LMBR1 193 ...................e 193
                                                       +
  gi|121638651|ref|YP_978875.1|  76 iaedgldidasalprrasgR 95 
                                    66555555555555544444 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.6   1.3e+04       2       7 ..      69      74 ..      68      79 .. 0.58
   2 ?   11.4   0.4   0.00013      0.26       2      29 ..     122     149 ..     122     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.6
                          TPR_7  2 LlnLar 7 
                                   + +Lar
  gi|121638651|ref|YP_978875.1| 69 YQRLAR 74
                                   445554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00013
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                    +++Lar+y   Gd+++A e  + +L+l+
  gi|121638651|ref|YP_978875.1| 122 WYRLARAYDYAGDRRRAREAMKTALQLE 149
                                    579****************999977765 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.5    0.0038       7.5      15      70 ..      12      67 ..       3      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                        DUF4282 15 vlYilgivlialvllslivgafaalseslsagggllllllaviafllmilllRivl 70
                                   ++++ +++++ lv+l+ +  a++ + ++  ag gl ll+l vi+  +mi+ lR+++
  gi|121638651|ref|YP_978875.1| 12 IAFMCVAMVAYLVMLGRVAVAMIGSGRAAAAGLGLALLILPVIGLWAMIATLRAGF 67
                                   344444444444444555555555589999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1201.67
//
Query:       gi|121638652|ref|YP_978876.1|  [L=245]
Description: dihydrodipicolinate reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-31  106.8   0.0      1e-30  106.2   0.0    1.3  1  DapB_C          Dihydrodipicolinate reductase, C-terminus
      6e-24   84.5   1.1    2.1e-22   79.6   1.1    2.2  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.036   14.5   0.3       0.38   11.2   0.0    2.3  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   1.8e-34     1e-30       1     114 [.     108     235 ..     108     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.8e-34
                                    HHHHHHHHHHHHCCCSTTT-E.EEEEEEESTT--SSS-HHHHHHHHHHH...................-S-E..TTCCCE CS
                         DapB_C   1 Gvnlllklveeaakllkeayd.veiiEkHhnkKaDaPSGTAlalaeaiaegke...............arkk..keigih 62 
                                    G++l ++++++aa++    +d +e+iE Hh +KaDaPSGTA+++a+ iae ++               ar++  ++i +h
  gi|121638652|ref|YP_978876.1| 108 GAVLSMHFAKQAARF----FDsAEVIELHHPHKADAPSGTAARTAKLIAEARKglppnpdatstslpgARGAdvDGIPVH 183
                                    8899***********....777***************************55556677777777889997777668***** PP

                                    EEETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSS.E CS
                         DapB_C  63 svRgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkg.l 114
                                    +vR+ g+v+++evlf+ ege+++i+h++l+r++F++G+lla++ +  +++g +
  gi|121638652|ref|YP_978876.1| 184 AVRLAGLVAHQEVLFGTEGEILTIRHDSLDRTSFVPGVLLAVRRI-AERPGlT 235
                                    ********************************************9.4545534 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   1.1   3.5e-26   2.1e-22       1     124 []       1     105 [.       1     105 [. 0.92

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 3.5e-26
                                    EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S-HH CS
                         DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTtpe 78 
                                    ++v+v+Ga+G++G ++v+av +a+dl+l+a +d+ +                          ++l++  ++v+iDFT+p+
  gi|121638652|ref|YP_978876.1|   1 MRVGVLGAKGKVGATMVRAVAAADDLTLSAELDAGD------------------------PLSLLTDgnTEVVIDFTHPD 56 
                                    89********************************64........................4455555589********** PP

                                    HHHHHHHHHHHTT-EEEE--SS--HHHHHHHHH.HTTT..SEEEE-S-- CS
                         DapB_N  79 avlenlklalekgvklViGTTGlseeelaelee.lakk..igvviapNf 124
                                    +v+ nl++++++g+++V+GTTG+++e+ +++e+ l +k  ++v+iapNf
  gi|121638652|ref|YP_978876.1|  57 VVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESwLVAKpnTSVLIAPNF 105
                                    *********************************8555569********8 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.3e-05      0.38       1      27 [.       2      28 ..       2      59 .. 0.82
   2 ?    0.7   0.0      0.12     7e+02       3      17 ..      72      86 ..      71     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                                   EEEEETTTSHHHHHHHHHHHCTSSEEE CS
                 Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevel 27
                                   +v+++Ga G vG+ ++r ++   +++l
  gi|121638652|ref|YP_978876.1|  2 RVGVLGAKGKVGATMVRAVAAADDLTL 28
                                   79***************9988666554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                   EEETTTSHHHHHHHH CS
                 Semialdhyde_dh  3 aivGatGyvGqellr 17
                                   a+vG tG + +++ +
  gi|121638652|ref|YP_978876.1| 72 AVVGTTGFTAERFQQ 86
                                   799999999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1893.02
//
Query:       gi|121638653|ref|YP_978877.1|  [L=134]
Description: hypothetical protein BCG_2791c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1003.13
//
Query:       gi|121638654|ref|YP_978878.1|  [L=153]
Description: hypothetical protein BCG_2792 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   45.0   0.0    1.3e-11   44.7   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      2e-10   40.9   0.0    2.9e-10   40.4   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.5e-10   38.7   0.0    1.1e-09   38.3   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00019   21.3   0.0    0.00032   20.6   0.0    1.3  1  FR47             FR47-like protein
  ------ inclusion threshold ------
       0.07   12.9   0.0      0.091   12.5   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
       0.12   12.3   0.0       0.26   11.3   0.0    1.6  2  Acetyltransf_13  ESCO1/2 acetyl-transferase
       0.16   11.7   0.0       0.21   11.3   0.0    1.2  1  Acetyltransf_16  GNAT acetyltransferase, Mec-17


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   5.1e-15   1.3e-11      32     117 .]      40     122 ..      13     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 5.1e-15
                                    TC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHH CS
                 Acetyltransf_1  32 ae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaair 110
                                     + + ++ae +g++iG+ ++ ++   +++++ i+ l+V+++ +++G+G +Ll+ +++   +   + i l++ e n +a++
  gi|121638654|ref|YP_978878.1|  40 GGwSMWIAESGGQPIGMTMFGPDIA-HPDRIQIDALYVAENSQRHGIGGRLLNRALHSHPSA--DMI-LWCAEKNSKARG 115
                                    3347888***************999.9******************************77777..445.557899****** PP

                                    HHHHTTE CS
                 Acetyltransf_1 111 lYeklGF 117
                                    +Yek  F
  gi|121638654|ref|YP_978878.1| 116 FYEKKDF 122
                                    ***9766 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.1e-13   2.9e-10       4      75 ..      43     123 ..      40     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.1e-13
                                    EEEEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEEEEEEEE..THHHHHHHHHH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae....kgiileqlel..naekaikfYek 71 
                                    ++++ae +g+++G+  + ++       +i  l+V+++ +++GiG +Ll+ a +      +il+      +++ka++fYek
  gi|121638654|ref|YP_978878.1|  43 SMWIAESGGQPIGMTMFGPDIahpdrIQIDALYVAENSQRHGIGGRLLNrALHshpsADMILW---CaeKNSKARGFYEK 119
                                    69************99999988875555555*****************954223343223333...32222399****** PP

                                    TTEE CS
                 Acetyltransf_7  72 lGFe 75 
                                      F+
  gi|121638654|ref|YP_978878.1| 120 KDFH 123
                                    9996 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   4.4e-13   1.1e-09      20     117 ..      31     133 ..      25     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 4.4e-13
                Acetyltransf_10  20 ealrerieegealllvaeeggkivGvi......elrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvna 93 
                                    e++ + ++ g   +++ae gg+++G+       +  d+ +i  l+V+++ ++ Gig +Ll+++++    ++    l + +
  gi|121638654|ref|YP_978878.1|  31 ESYPQSLKRGGWSMWIAESGGQPIGMTmfgpdiAHPDRIQIDALYVAENSQRHGIGGRLLNRALHSHPSAD-M-ILWCAE 108
                                    5666777888999*************9555533335555*************************9963333.2.455555 PP

                Acetyltransf_10  94 sp.yavpfYeklGFkavgeeqeenG 117
                                    ++ +a++fYek  F+  g+ ++++ 
  gi|121638654|ref|YP_978878.1| 109 KNsKARGFYEKKDFHIDGRTFTWKP 133
                                    555**************99998775 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00032      17      78 ..      64     123 ..      58     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                    EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-E CS
                           FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfe 78 
                                     ++d  ++ al+v ++ +r G g+rl +   +++      +++l+ +++N++++ +yek  f 
  gi|121638654|ref|YP_978878.1|  64 AHPDRIQIDALYVAENSQRHGIGGRLLN---RALHShPSADMILWCAEKNSKARGFYEKKDFH 123
                                    566777899***************9954...55555478899****************98776 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.6e-05     0.091      62     101 ..      69     108 ..      64     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                           PanZ  62 aelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaee 101
                                     +++ l V e   r G+g +Ll++a++++P+        e
  gi|121638654|ref|YP_978878.1|  69 IQIDALYVAENSQRHGIGGRLLNRALHSHPSADMILWCAE 108
                                    578999***********************98765443333 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.8   9.8e+03       8      16 ..      25      33 ..      21      33 .. 0.71
   2 ?   11.3   0.0    0.0001      0.26       7      33 ..      71      97 ..      65     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.8
                Acetyltransf_13  8 sriWvsssh 16
                                    ++Wv +s+
  gi|121638654|ref|YP_978878.1| 25 PKLWVEESY 33
                                   689999875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                Acetyltransf_13  7 isriWvssshRrkgiAtkLldaarenf 33
                                   i +++v+++++r+gi  +Ll+ a +++
  gi|121638654|ref|YP_978878.1| 71 IDALYVAENSQRHGIGGRLLNRALHSH 97
                                   899******************998765 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.3e-05      0.21     109     133 ..      74      98 ..      65     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                                    EEE-GGGTTSSHHHHHHHHHHHHHT CS
                Acetyltransf_16 109 FyvheseqrkGlGkklfeamlkeek 133
                                     yv e++qr+G+G +l++  l+++ 
  gi|121638654|ref|YP_978878.1|  74 LYVAENSQRHGIGGRLLNRALHSHP 98 
                                    6****************99998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1085.90
//
Query:       gi|121638655|ref|YP_978879.1|  [L=309]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-09   36.3   0.1      7e-09   35.5   0.1    1.4  1  Fer2           2Fe-2S iron-sulfur cluster binding domain
    9.8e-06   26.2   0.1    4.5e-05   24.1   0.1    2.0  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    3.4e-05   24.1   0.0    5.2e-05   23.5   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    0.00022   21.3   0.0       0.35   11.0   0.0    2.2  2  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   1.6e-12     7e-09       6      77 ..     236     300 ..     231     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.6e-12
                                    EEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2   6 kevevevadgettlldaaeenggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77 
                                    +++ + v+++++  ld++ +  +  + ysC++g CgtC+v+vl+g+v +  + +eg++      +l C++++
  gi|121638655|ref|YP_978879.1| 236 SRRVLRVPANRS-ALDVMLDW-DPTTAYSCQQGFCGTCKVRVLAGQVDRRGRIIEGDN-----EMLVCVSRA 300
                                    677788999999.99999976.89999********************66679999999.....57***9986 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     1e-08   4.5e-05       1     108 [.     112     202 ..     112     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqda 80 
                                    ++ gG G++P++ ++ra+ ++         +y+ r +e + +   l+e+ + +pgr++v+a       +++g+   v++ 
  gi|121638655|ref|YP_978879.1| 112 FVIGGIGVTPILPMIRAAEQR---GIDWRAIYAGRGREYMPF---LDEVVAVAPGRVTVWAD------DEHGRFASVDEL 179
                                    578**************9996...7899*********97765...55556669**9888876......333344556655 PP

                                    HHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  81 lleellslkkeethvyvCGppgMikavr 108
                                    l         ++t vyvCGppgM +avr
  gi|121638655|ref|YP_978879.1| 180 L-AG----AGPTTAVYVCGPPGMLEAVR 202
                                    5.33....4679*************996 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.2e-08   5.2e-05       2      97 ..       7     101 ..       6     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                                    EEEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--.TT-HHHHHH. CS
                  FAD_binding_6   2 lkltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvy.pgGkmsqaL. 79 
                                    +++t++e v +d+  ++++ p         +G h+ ++l+  +    R+Y+++  +  +    + ++++  gG  s  + 
  gi|121638655|ref|YP_978879.1|   7 AVVTKRELVAPDVVALTLADPGGGLLPAWSPGGHIDVQLPSGR---RRQYSLCGVPGRRTDYRIAIRRIaDGGGGSIEMh 83 
                                    6799*****************9999999************444...6*******************99967888899996 PP

                                    HCS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  80 delkigdtleikGPlGkf 97 
                                    +   +gdt e++GP   f
  gi|121638655|ref|YP_978879.1|  84 EAFDVGDTCEFEGPRNAF 101
                                    67************9887 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   7.8e-05      0.35       3      22 ..     109     128 ..     107     132 .. 0.89
   2 !    8.3   0.0   0.00052       2.3     134     152 ..     184     202 ..     174     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                                    xxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6   3 nvllvagGiGitpfisilkd 22 
                                     vl+v gGiG+tp++++++ 
  gi|121638655|ref|YP_978879.1| 109 DVLFVIGGIGVTPILPMIRA 128
                                    599**************985 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00052
                                    xxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6 134 nssvgvfvCGppklvkevk 152
                                    + +++v+vCGpp++++ v+
  gi|121638655|ref|YP_978879.1| 184 GPTTAVYVCGPPGMLEAVR 202
                                    67899**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2174.65
//
Query:       gi|121638656|ref|YP_978880.1|  [L=356]
Description: hypothetical protein BCG_2794c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-78  261.7   0.0    8.5e-78  261.5   0.0    1.1  1  Metal_hydrol  Predicted metal-dependent hydrolase
     0.0078   15.5   0.2      0.011   15.0   0.2    1.2  1  AurF          P-aminobenzoate N-oxygenase AurF


Domain annotation for each model (and alignments):
>> Metal_hydrol  Predicted metal-dependent hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   9.5e-82   8.5e-78       2     247 ..      79     336 ..      78     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 9.5e-82
                   Metal_hydrol   2 vRrvkfdfeeevprhWipgdpvathfinalsllfpegErffirsvreardqikdpeLkeevkgFigQEamHareHeafne 81 
                                    +R+v+fd++ ++p h++p++p+ath++n+l++l+p+gE+ff+r++++ ++ ikd++L+ +v+gFigQEamH+++H+ +++
  gi|121638656|ref|YP_978880.1|  79 PRDVEFDWT-NLPFHYVPNEPMATHVLNVLHMLLPAGEEFFVRVFKKTLPLIKDDQLRLDVQGFIGQEAMHSQAHSGVVD 157
                                    8*******9.9********************************************************************* PP

                   Metal_hydrol  82 aleaqgldveklekrvrkl.kk.llerkl...skklk.......laltaalEhftAvlaelvlkneelleaa.dpemrdL 148
                                    +++aqg+dv+++++++r+l +k l  +     s++ +       ++++aa+Eh+tAv++e++l++++l++ + dp m+d+
  gi|121638656|ref|YP_978880.1| 158 HFDAQGVDVTAFTNQIRWLfEKlL-GE-SprrSPRRQyswlleqVSFIAAIEHYTAVMGEWILNSPQLDAVGaDPVMLDM 235
                                    *********998777777655531.22.1122222224444455**************************999******* PP

                   Metal_hydrol 149 lrWHaaEEvEHksvafDvyqavg.syllRvlamllvtvllllllllrgtlallkqdkkllklrelerllklllgakrgll 227
                                    lrWH+aEEvEHk+vafD+++++  +y+++v+a l+vt+++ll l++rg++++++ d+ l    +  r + ++ +a+rgl+
  gi|121638656|ref|YP_978880.1| 236 LRWHGAEEVEHKAVAFDTMKHLRaGYWRQVRAQLTVTPVMLL-LWIRGVRFMYSVDPYLPP-GTKPRWRDYFKAARRGLV 313
                                    ***************************************998.88888**********876.333444466667677554 PP

                   Metal_hydrol 228 r...gllpellkylrpgFhPsde 247
                                        +ll+ + +y++pgFhPs+ 
  gi|121638656|ref|YP_978880.1| 314 PglpRLLRVVGHYYKPGFHPSQL 336
                                    412256666666********985 PP

>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.3e-06     0.011     127     233 ..     173     280 ..     131     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-06
                                    HH...--S---HHHHHHHHHHHH--SHHH.HHHHHHHHHHHHHHHHHHHHHHHHT-SSS-HHHHHHHHHHHHHHHHHHHH CS
                           AurF 127 ig...advpgmyrvrrllrelakllktia.rglvffaavlvgEeiidalqrelmrdeelqPlvrrvmriHvaEEarHisf 202
                                    i+   +++ g  ++r  +r+  +ll++++  + +   ++++gE i+++ q + + ++   P++  + r H aEE+ H  +
  gi|121638656|ref|YP_978880.1| 173 IRwlfEKLLGESPRRSPRRQYSWLLEQVSfIAAIEHYTAVMGEWILNSPQLDAVGAD---PVMLDMLRWHGAEEVEHKAV 249
                                    3355444555555555556666666666546788899999***********999998...******************** PP

                                    HHHHHHHHHHHS-HHHHHHHHHHHHHHHHHH CS
                           AurF 203 areelrrrvprlsraerallrlllalalraf 233
                                    a + +++  ++  r+ ra l +  +++l ++
  gi|121638656|ref|YP_978880.1| 250 AFDTMKHLRAGYWRQVRAQLTVTPVMLLLWI 280
                                    *****99999998888887777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2650.94
//
Query:       gi|121638657|ref|YP_978881.1|  [L=156]
Description: hypothetical protein BCG_2795c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-19   70.3   3.0    2.4e-19   70.0   3.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   3.0   1.4e-23   2.4e-19       3     143 .]       8     154 ..       7     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.4e-23
                                    EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSS...TTTEEEEECCCS.SEEEEEEEEEETTTTEEEEE CS
                Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpa...rgvegtvrvggr.gtvreelvevdpegrllsyr 78 
                                    +vtv+v+i+a p+ V+ l++d++++++  +ev+ ++l++ g+++   ++ +g+   ggr +t++++++++dp gr+++++
  gi|121638657|ref|YP_978881.1|   8 SVTVTVEIDANPDLVYGLITDLPTLASLAEEVVAMQLRK-GDDVrkgAVFVGRNENGGRrWTTTCTVTDADP-GRVFAFD 85 
                                    69************************************9.77766874556999999999************.******* PP

                                    EE..SSS-TSEEEEEEEEECCETEEEE.EEEEEEEE--TT--HHHH.HHHHHHHH.......HHHHHHHHHHHHH CS
                Polyketide_cyc2  79 iv.kpvpvanyvatwtvtpdgggtrvt.wtgefdagplggpfekpa.aakavkgd.......leagLerLkarle 143
                                    ++ +  p++  ++ + + ++++g+rvt  t++ ++     +f+++a +a +vk +       ++++L+rLk r+e
  gi|121638657|ref|YP_978881.1|  86 VRsGIIPIS--RWQYGIVATEHGCRVTeSTWDRRP----SWFRAVArMATGVKDRasvntehIRRTLQRLKDRAE 154
                                    *76677777..************998864555576....66665555667777778888889*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1196.80
//
Query:       gi|121638658|ref|YP_978882.1|  [L=179]
Description: lrp/asnC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   56.6   0.0      2e-15   56.1   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.8e-15   55.4   0.2    6.2e-15   54.7   0.2    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.5e-14   53.7   0.1    2.7e-14   52.9   0.1    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.1e-05   23.9   0.1    6.3e-05   22.9   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    0.00072   19.3   0.0     0.0013   18.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.002   18.0   0.0     0.0045   16.9   0.0    1.6  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   6.6e-19     2e-15       1      48 []      32      79 ..      32      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.6e-19
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   lde dr+IL+lL  ++r++++ LA+ +g+ pst++ r++rL++ G+I+
  gi|121638658|ref|YP_978882.1| 32 LDEVDRRILSLLHGDARMPNNALADTVGIAPSTCHGRVRRLVDLGVIR 79
                                   79*********************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.2   2.1e-18   6.2e-15       1      41 [.      32      72 ..      32      73 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.1e-18
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                   LDe+Dr+IL++L  daR+++ +LA+ vG+++st++ RvrrL
  gi|121638658|ref|YP_978882.1| 32 LDEVDRRILSLLHGDARMPNNALADTVGIAPSTCHGRVRRL 72
                                   8***************************************9 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   8.9e-18   2.7e-14       2      74 ..      99     171 ..      98     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 8.9e-18
                                    EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                     v+l+++++  +++f++++++  +V+ +y ++G +d++l+v++rd+e+l+ f++e l++  +va t+ts+++e
  gi|121638658|ref|YP_978882.1|  99 SVNLQSSARGKIRSFIQQIRRKRQVMDVYFLAGADDFILHVAARDTEDLRSFVVENLNADADVAGTQTSLIFE 171
                                    56666555778***********************************************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   2.1e-08   6.3e-05       9      55 ..      33      79 ..      29      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.1e-08
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   ++v rril++L++++ +  ++la++++++++t++ ++r L++ g ++
  gi|121638658|ref|YP_978882.1| 33 DEVDRRILSLLHGDARMPNNALADTVGIAPSTCHGRVRRLVDLGVIR 79
                                   7899***************************************9997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.4e-07    0.0013       8      49 ..      39      79 ..      38      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.4e-07
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   iL +l   ++ + +  lA+  g+++St h+ ++ Lv lG ++
  gi|121638658|ref|YP_978882.1| 39 ILSLLHGDAR-MPNNALADTVGIAPSTCHGRVRRLVDLGVIR 79
                                   6666666666.9***************************886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-06    0.0045       8      52 ..      37      79 ..      31      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   +r+L  L+   +  +  ++la++ g+ +s+ + +++rLv+ G ++
  gi|121638658|ref|YP_978882.1| 37 RRILSLLHGDAR--MPNNALADTVGIAPSTCHGRVRRLVDLGVIR 79
                                   566777766665..8999************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1279.98
//
Query:       gi|121638659|ref|YP_978883.1|  [L=132]
Description: L-alanine dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-29  102.6   0.0    2.5e-29  102.3   0.0    1.1  1  AlaDh_PNT_N  Alanine dehydrogenase/PNT, N-terminal domain
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.17   11.6   0.0    1.2  1  DUF3225      Protein of unknown function (DUF3225)


Domain annotation for each model (and alignments):
>> AlaDh_PNT_N  Alanine dehydrogenase/PNT, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0   2.7e-33   2.5e-29       1      86 [.       4      89 ..       4     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 2.7e-33
                                   EE---SSTT----SS-HHHHHHHHHTT-EEEEETTTTGGGTC-HHHHHHTTEEEESCHHHHCTTSSEEEESS--.CHCGGGS CS
                    AlaDh_PNT_N  1 gvpkEikagErRvaltPatvkkLvkaGhevlVesgaGegagfsdeeYeeaGaeivesaeevlaeadlilkVkepseeelell 82
                                   g+p E+k++E Rva+tPa+v++L+++Ghevl+++gaGeg++++d+++++aGa++v +a++v+a+adl+lkVkep ++e+ +l
  gi|121638659|ref|YP_978883.1|  4 GIPTETKNNEFRVAITPAGVAELTRRGHEVLIQAGAGEGSAITDADFKAAGAQLVGTADQVWADADLLLKVKEPIAAEYGRL 85
                                   89******************************************************************************** PP

                                   -TTC CS
                    AlaDh_PNT_N 83 kegq 86
                                   ++g+
  gi|121638659|ref|YP_978883.1| 86 RHGR 89
                                   9986 PP

>> DUF3225  Protein of unknown function (DUF3225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.9e-05      0.17      58     108 ..      13      67 ..       7      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                                    HHHHHS--TT...---EEEEEEEEE.ETTTEEEEEEEEE-SS-SS-EEEEEEEEE CS
                        DUF3225  58 afRaarpsvg...laRellrtvvtt.fGeDvavasvefrregseriGRqsqtWvr 108
                                    +fR a +++g   l+R+  ++ +++  Ge  a+++ +f+ +g++ +G   q+W+ 
  gi|121638659|ref|YP_978883.1|  13 EFRVAITPAGvaeLTRRGHEVLIQAgAGEGSAITDADFKAAGAQLVGTADQVWAD 67 
                                    7888877754222678888888864389*************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 877.70
//
Query:       gi|121638660|ref|YP_978884.1|  [L=239]
Description: L-alanine dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-81  271.4   0.3    4.6e-81  271.2   0.3    1.0  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.2e-07   31.3   0.1    1.9e-07   30.6   0.1    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.1e-06   27.8   0.0    3.4e-06   27.1   0.0    1.3  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    9.5e-06   25.9   0.2    1.4e-05   25.3   0.2    1.2  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    2.5e-05   23.5   0.3    3.3e-05   23.1   0.3    1.1  1  GIDA            Glucose inhibited division protein A
    0.00016   22.2   0.1     0.0003   21.3   0.1    1.4  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00022   20.5   0.4    0.00028   20.2   0.4    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00073   19.8   0.3     0.0011   19.2   0.3    1.3  1  TrkA_N          TrkA-N domain
     0.0014   17.4   0.4     0.0019   17.0   0.4    1.1  1  HI0933_like     HI0933-like protein
     0.0026   17.7   1.0     0.0074   16.2   1.0    1.8  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0049   17.3   0.2     0.0073   16.7   0.2    1.3  1  NAD_binding_7   Putative NAD(P)-binding
     0.0097   15.2   1.6       0.18   11.1   0.1    2.2  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
  ------ inclusion threshold ------
      0.012   14.7   2.5      0.018   14.1   2.5    1.2  1  FAD_binding_2   FAD binding domain
      0.014   15.0   0.1      0.024   14.2   0.1    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.018   14.4   3.6      0.025   13.9   3.6    1.1  1  FAD_oxidored    FAD dependent oxidoreductase
      0.027   14.0   0.3      0.049   13.2   0.3    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.072   12.3   0.3       0.11   11.7   0.3    1.2  1  Thi4            Thi4 family
       0.12   12.4   0.5       0.18   11.8   0.5    1.2  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
       0.15   11.3   0.0       0.23   10.7   0.0    1.2  1  NAS             Nicotianamine synthase protein


Domain annotation for each model (and alignments):
>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.2   0.3   4.9e-84   4.6e-81       1     213 [.       9     220 ..       9     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 4.9e-84
                                    HHHHHHHHCSCGCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHC CS
                    AlaDh_PNT_C   1 AvleaakalekffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlk 79 
                                    A++++a++l +++gg+g+l+Ggvpgvepa v+viG+G+aG +A+++a+g+ga+VtvlD+++++l+ql++ + ++ +++++
  gi|121638660|ref|YP_978884.1|   9 AAQVGAYHLMRTQGGRGVLMGGVPGVEPADVVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAeFCGR-IHTRY 87 
                                    789******************************************************************9****.***** PP

                                    HHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETTGGGT-SBTT--TBBTTSEEEEETTEEEEEBS CS
                    AlaDh_PNT_C  80 sqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvAidqGGnvetsrltthgepvveekgvvhygva 159
                                    s++ +l+ avk+ad+vig+vl+pG+kaPkLv+++ v++Mkpg+V+vD+AidqGG++e sr+tt ++p++ +++ ++y+va
  gi|121638660|ref|YP_978884.1|  88 SSAYELEGAVKRADLVIGAVLVPGAKAPKLVSNSLVAHMKPGAVLVDIAIDQGGCFEGSRPTTYDHPTFAVHDTLFYCVA 167
                                    ******************************************************************************** PP

                                    TGGGGSHHHHHHHHHHHHHHHHHHHCHHHTCCHHHCTSHHHHCCEEEETTEESS CS
                    AlaDh_PNT_C 160 nlpgavprtasalltnntlpyleelladkglkkalkedealrkglvvkkGkvtn 213
                                    n+p++vp+t++++ltn+t+py++el ad+g+++a+++++al+kgl +++G++++
  gi|121638660|ref|YP_978884.1| 168 NMPASVPKTSTYALTNATMPYVLEL-ADHGWRAACRSNPALAKGLSTHEGALLS 220
                                    *************************.************************9875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1     2e-10   1.9e-07      36     127 ..      36     136 ..      14     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2e-10
                                    TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH........CHHHHTCEECSHHHHHHH-SEEEE-S-.-STTTT CS
                   2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkee........eeeelgvelvsleellaesDivslhlp.ltpetr 106
                                       v +iG+G  G ++a++++++g+ v++ d + +k +        + ++   +  +le +++++D v+ ++    ++  
  gi|121638660|ref|YP_978884.1|  36 PADVVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRqldaefcgRIHTRYSSAYELEGAVKRADLVIGAVLvPGAKAP 115
                                    56799**************************99886554545556444444446779*********99876552467889 PP

                                    TSBSHHHHHCSTTTEEEEESS CS
                   2-Hacid_dh_C 107 hlinaeelakmkkgailiNta 127
                                    +l++++  a+mk+ga+l+ +a
  gi|121638660|ref|YP_978884.1| 116 KLVSNSLVAHMKPGAVLVDIA 136
                                    9*****************987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.6e-09   3.4e-06      11     113 ..      35     137 ..      30     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.6e-09
                                    TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-S CS
                   Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisataseepi 89 
                                    + + v++iGaG  +  +a+     g++ v+v+  ++++ ++l  e+ +  ++++ +  el+ ++++ad+vi a+  + + 
  gi|121638660|ref|YP_978884.1|  35 EPADVVVIGAGTAGYNAARIANGMGAT-VTVLDINIDKLRQLDAEFcGRIHTRYSSAYELEGAVKRADLVIGAVLVPGAK 113
                                    5688**************999999998.**************99986888999********************9665554 PP

                                    B-HHHHHCCHHH.S..EEEEE--S CS
                   Shikimate_DH  90 lekeeveealkkrkkplllvDiav 113
                                      k   ++++++ k   +lvDia+
  gi|121638660|ref|YP_978884.1| 114 APKLVSNSLVAHMKPGAVLVDIAI 137
                                    444444444444444689***995 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   1.5e-08   1.4e-05       2      89 ..      39     135 ..      38     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......EEE-SSHHHHHHHCSEEE..E-SSSHHHHHHH CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......akaaesieelvasldvvi..tmvkagkavdev 72 
                                    + +iG G+ G n a+     g +v+v + + +k+++l ae         + a+++e +v+++d+vi  ++v+  ka + v
  gi|121638660|ref|YP_978884.1|  39 VVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAEFcgrihtrYSSAYELEGAVKRADLVIgaVLVPGAKAPKLV 118
                                    679**********************************99967788888999999999*****999854567777777777 PP

                                    HHSHCCC--TT-EEEE- CS
                  NAD_binding_2  73 iegllealkkgdilidg 89 
                                     ++l++++k+g++l+d 
  gi|121638660|ref|YP_978884.1| 119 SNSLVAHMKPGAVLVDI 135
                                    777************96 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   3.5e-08   3.3e-05       1      38 [.      38      75 ..      38      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.5e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                                   dv+ViG+G AG+ AA  a  +Ga v+ +  ++d++ +l
  gi|121638660|ref|YP_978884.1| 38 DVVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQL 75
                                   7***************************9999998765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   3.2e-07    0.0003       2      49 ..      39      86 ..      38      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-07
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqek 49
                                   vvv+G+G+ g  +A +++ +g+ Vtv++ +   lr+lD+e+  +++++
  gi|121638660|ref|YP_978884.1| 39 VVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAEFCGRIHTR 86
                                   8*****************************99999****987776655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4     3e-07   0.00028       2      30 ..      38      66 ..      37     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve 30
                                   dvvviG+G AG++aa+ ++  ga vt+++
  gi|121638660|ref|YP_978884.1| 38 DVVVIGAGTAGYNAARIANGMGATVTVLD 66
                                   8******************9******996 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.2e-06    0.0011       1      67 [.      39     104 ..      39     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEE CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadavi 67 
                                    +++iG+G+ G++ a+  +  g   v+v d + +++++l +e++  ++  +++   Le a +++ad+vi
  gi|121638660|ref|YP_978884.1|  39 VVVIGAGTAGYNAARIANGmGA-TVTVLDINIDKLRQLDAEFCGRIHTRYSSAYELEGA-VKRADLVI 104
                                    79*****************666.6******************99999999888887776.77777777 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4     2e-06    0.0019       2      34 ..      38      70 ..      37      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                   dv+viG+G AG  aA  a+  g+ V++l+ +  
  gi|121638660|ref|YP_978884.1| 38 DVVVIGAGTAGYNAARIANGMGATVTVLDINID 70
                                   8***************************98755 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.0   7.9e-06    0.0074       2      42 ..      39      79 ..      38     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                   v viGaGt G   a ++   g +V+++di+ ++l++  ++ 
  gi|121638660|ref|YP_978884.1| 39 VVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAEF 79
                                   89****************************99998876655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   7.7e-06    0.0073       8      69 ..      37     107 ..      33     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.7e-06
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvk...laeeelekdlegadlviaat 69 
                                      v+v+G+G+ +++ +r     ga+vtv++ ++ +  +      ++++    +  ele+ +++adlvi a+
  gi|121638660|ref|YP_978884.1|  37 ADVVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQldaefcGRIHtrySSAYELEGAVKRADLVIGAV 107
                                    689***************************99743333445555334311123445689999999999875 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.045        43      78     112 ..      35      72 ..      30      92 .. 0.57
   2 !   11.1   0.1   0.00019      0.18      69     111 ..      89     139 ..      82     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.045
                                    CCSSEEEE-SS-TT-B-GGGS...-TT-EEEE---EEC CS
                  THF_DHG_CYH_C  78 readivvvavGkpelikaemv...kegavviDvGinrv 112
                                    + ad+vv+++G ++   a          +v+D+ i+++
  gi|121638660|ref|YP_978884.1|  35 EPADVVVIGAGTAGYNAARIAngmGATVTVLDINIDKL 72 
                                    45677777777666543332210022235566666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                    TSCCHHHHHCCSSEEEE-S.....S-TT-B-GGGS...-TT-EEEE---EE CS
                  THF_DHG_CYH_C  69 ktkdlaeitreadivvvav.....Gkpelikaemv...kegavviDvGinr 111
                                    ++ +l+  +++ad+v+ av       p+l++++ v   k+gav++D+ i++
  gi|121638660|ref|YP_978884.1|  89 SAYELEGAVKRADLVIGAVlvpgaKAPKLVSNSLVahmKPGAVLVDIAIDQ 139
                                    45689999******999984442235789*999877779********9987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.5   1.9e-05     0.018       1      29 [.      38      66 ..      38      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavve 29
                                   Dv+ViG+G AG+ AA  a+  G++v+v++
  gi|121638660|ref|YP_978884.1| 38 DVVVIGAGTAGYNAARIANGMGATVTVLD 66
                                   9***************9999*****9986 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.5e-05     0.024       6      92 ..      38     133 ..      34     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                    -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-.......HHHHHHHHTT-EEEEHHHHHHT-SEEE..E-S-HHHHHHH CS
                           IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregs.......ksvkkAkeegfevltvaeavkkadvvm..iliPDelqkev 76 
                                     ++viG G+ G + a+     g  v+v   + +       + + + + +  + ++++ avk+ad+v+  +l+P     ++
  gi|121638660|ref|YP_978884.1|  38 DVVVIGAGTAGYNAARIANGMGATVTVLDINIDklrqldaEFCGRIHTRYSSAYELEGAVKRADLVIgaVLVPGAKAPKL 117
                                    699*************9999999888743332212222223455566667789999*********96559********** PP

                                    HHHHTGGG--TT-EEE CS
                           IlvN  77 yeeeiepnlkegkala 92 
                                    +++++  ++k g++l+
  gi|121638660|ref|YP_978884.1| 118 VSNSLVAHMKPGAVLV 133
                                    ************9985 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.6   2.6e-05     0.025       1      28 [.      38      65 ..      38      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLv 28
                                   DvvV+G+g+aG+ AA  A  +Ga+v ++
  gi|121638660|ref|YP_978884.1| 38 DVVVIGAGTAGYNAARIANGMGATVTVL 65
                                   9************************987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   5.2e-05     0.049       3      42 ..      39      78 ..      37     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                   EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                 UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42
                                   ++viG+G  G   a + + +g +v+++Di+  k ++l ++
  gi|121638660|ref|YP_978884.1| 39 VVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAE 78
                                   89*******************************9999876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00012      0.11      18      48 ..      37      66 ..      32      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                   +Dvv++GaG++G  aa++     +  v++l+
  gi|121638660|ref|YP_978884.1| 37 ADVVVIGAGTAGYNAARIANGM-GATVTVLD 66
                                   7***************975544.77777665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   0.00019      0.18      25     109 ..      38     135 ..      24     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                    EEEEE--SHHHHHHHHHHHHCT-EEEEE-..S-HHHHHHHHCTT.....-.EE--HHHCTTT-SEEEE-S...SSS..SS CS
                  AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivte..vdPicalqaameG.....f.evvtleevvkkadivvttt...Gnk..di 91 
                                     +vv+G G  G  +a+  +g+Ga v+v +  +d +  l a   G     + +  +le +vk+ad+v+ +    G+k   +
  gi|121638660|ref|YP_978884.1|  38 DVVVIGAGTAGYNAARIANGMGATVTVLDinIDKLRQLDAEFCGrihtrYsSAYELEGAVKRADLVIGAVlvpGAKapKL 117
                                    589***********************975227999999999887443333235679999999999887642335542367 PP

                                    B-HHHHCCS-TTEEEEE- CS
                  AdoHcyase_NAD  92 itlehlkkmkddaivcni 109
                                    +++  +++mk  a++ +i
  gi|121638660|ref|YP_978884.1| 118 VSNSLVAHMKPGAVLVDI 135
                                    888888888888887766 PP

>> NAS  Nicotianamine synthase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.23     167     227 ..      74     133 ..      61     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                            NAS 167 sadedlssrmsfhtadvldvteelkaydvvflAAlvGmakeeKakviehlakkmakGavlv 227
                                    + d+++  r+  + + + +++ ++k  d+v+ A lv +ak++K  v + l+ +m++Gavlv
  gi|121638660|ref|YP_978884.1|  74 QLDAEFCGRIHTRYSSAYELEGAVKRADLVIGAVLVPGAKAPKL-VSNSLVAHMKPGAVLV 133
                                    55666677777778888999999**************9999996.899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1601.92
//
Query:       gi|121638661|ref|YP_978885.1|  [L=344]
Description: alanine rich oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     9e-120  400.0   1.1   1.1e-119  399.7   1.1    1.0  1  NMO           Nitronate monooxygenase
    0.00051   19.4   0.3    0.00069   18.9   0.3    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
    0.00065   18.8   0.3       0.18   10.7   0.2    2.3  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00081   18.9   0.1     0.0014   18.1   0.1    1.3  1  His_biosynth  Histidine biosynthesis protein
     0.0019   17.4   1.1      0.017   14.2   1.6    2.0  2  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.013   14.9   0.7      0.025   13.9   0.7    1.6  1  ThiG          Thiazole biosynthesis protein ThiG
      0.022   14.1   0.2      0.039   13.3   0.2    1.4  1  TMP-TENI      Thiamine monophosphate synthase
      0.057   12.8   0.0       0.12   11.8   0.0    1.5  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
        0.4    9.7   5.6       0.73    8.8   5.6    1.4  1  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.7   1.1  5.5e-123  1.1e-119       7     331 .]       8     340 ..       4     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 399.7 bits;  conditional E-value: 5.5e-123
                            NMO   7 llkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdkPfgvnlflpkkdaadra..ekyk 84 
                                    ++   p+v +p++gg+s+++LaaavsnaGgLG++a+gyl+aDrla++i++++a+t+ P+g+nlf+p++++ad+a  e+y+
  gi|121638661|ref|YP_978885.1|   8 IA--VPIVGAPMAGGPSTPALAAAVSNAGGLGFVAGGYLSADRLADDIAAARAATTGPIGANLFVPQPSVADWAqlEYYA 85 
                                    44..69************************************************************************** PP

                            NMO  85 keleeaalelnieegvr.......fyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvearGa 157
                                    +elee+a+++++e+g++       ++rk+evv+d+++evvsf+fg+p+++vv+rl+++g+++++t++sv+ea +++a+Ga
  gi|121638661|ref|YP_978885.1|  86 DELEEVAEYYHTEVGQPvygddddWVRKLEVVADVRPEVVSFTFGAPPPDVVQRLSALGLLVSITVTSVYEAGVAIAAGA 165
                                    ******************************************************************************** PP

                            NMO 158 DalivqGpeaGGhqG....tpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesda 233
                                    D+l+vqGp+aGGh+G    ++e+g+++l++L++++ +a+d+P++AaGG+ ++++vaa+L++GA ++q+gt++Ll++e+++
  gi|121638661|ref|YP_978885.1| 166 DSLVVQGPAAGGHRGtfapDMEPGTESLHQLLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLADEAGT 245
                                    ***************9999999999******************************************************* PP

                            NMO 234 kdahkkklleaklddteltsavsGrpaRalatelleeleeakiatlalpeahelakkiraalveagnteegllwagqgid 313
                                    ++ah+++l+++++d+t++t+a+sGr+aR+la+++++ l+  ++a+l++pe+h+++k+iraa+v+a+++++++lwag+++ 
  gi|121638661|ref|YP_978885.1| 246 NAAHRAALKNPEFDATLVTRAFSGRYARGLANNFTRLLD--HVAPLGYPEVHQMTKPIRAAAVQADDPHGTNLWAGSAH- 322
                                    ***************************************..**************************************. PP

                            NMO 314 rldkiisvkeLiesLvee 331
                                    r++++ +++++i+sL+++
  gi|121638661|ref|YP_978885.1| 323 RKTRPGPAADIIASLTPD 340
                                    ***************975 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   3.5e-07   0.00069     230     280 ..     189     241 ..     135     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.5e-07
                                    HHHHHHHHHHHTT..T.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG CS
                         DHO_dh 230 alkvirelykrlk..keipiIgvGGiesgeDalekieaGAslvqvytalvfeg 280
                                    +++ +++l +r+   +++p+++ GG+ ++eD+   ++ GA + qv+tal  ++
  gi|121638661|ref|YP_978885.1| 189 GTESLHQLLDRIGsaHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLAD 241
                                    56777777777652258*******************************98765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0027       5.3      33      82 ..       8      59 ..       5     179 .. 0.67
   2 !   10.7   0.2   9.2e-05      0.18     203     249 ..     201     247 ..     187     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                                   ESSSEEE-SSTTT.-SHHHHHHHHHTTSEEEE-SS.S-HHHHHHHHHHHHTS CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          IMPDH 33 lniPlvsaamdtv.tesemAialareGgigvihkn.lsieeqaeevkkvkrs 82
                                   + +P+v a+m    +   +A a++++Gg+g++    ls+++ a+ +++ + +
  gi|121638661|ref|YP_978885.1|  8 IAVPIVGAPMAGGpSTPALAAAVSNAGGLGFVAGGyLSADRLADDIAAARAA 59
                                   789*******86526779*************986426677777777666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.2e-05
                                    HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgev 249
                                     + ++vp++a GG+ + +d++  l  Ga a  +G  l   +E+ ++ 
  gi|121638661|ref|YP_978885.1| 201 GSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLADEAGTNA 247
                                    56899********************************9999998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   7.3e-07    0.0014     181     224 ..     195     238 ..     187     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.3e-07
                                    HHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHH CS
                   His_biosynth 181 eltkelaeavkipviasGGvgsledlkelksegvdavivgsaly 224
                                    +l++++ +a ++p++a+GG g+ ed++++ + g+ a+ vg+al+
  gi|121638661|ref|YP_978885.1| 195 QLLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALL 238
                                    5788999999*******************************996 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.19   3.8e+02     150     172 ..      40      62 ..      33      93 .. 0.82
   2 !   14.2   1.6   8.8e-06     0.017     255     309 ..     186     240 ..     145     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                                    S--EE-GGG--HHHHHHHTS-TT CS
                   Glu_synthase 150 eGgqlpgeKvseeiakiRkikpg 172
                                     Gg+l ++++  +ia+ R  + g
  gi|121638661|ref|YP_978885.1|  40 AGGYLSADRLADDIAAARAATTG 62 
                                    59****************99876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.8e-06
                                    HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHH CS
                   Glu_synthase 255 lelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalia 309
                                    +e +    +q l + g  + v l a+Ggl t++dv+  l  GA a ++gta l+a
  gi|121638661|ref|YP_978885.1| 186 MEPGTESLHQLLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLA 240
                                    55677789*******************************************9987 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   1.3e-05     0.025     166     213 ..     196     243 ..     141     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                           ThiG 166 alkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                     l  i +  +vP++   G+g+++d+a+++  Ga a  + ta+  a++ 
  gi|121638661|ref|YP_978885.1| 196 LLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLADEA 243
                                    456667777********************************9888775 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     2e-05     0.039      86     173 ..     134     229 ..     115     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                       TMP-TENI  86 vaearellgpdliiGlSvhsleeaeeaealgadYigv.GpifpTdtKkda..eplgleglkelaeale....iPvvaiGG 158
                                    ++ +++l + +l++ ++v s  ea  a a+gad ++v Gp    +  + a     g e l +l +++     +P+va GG
  gi|121638661|ref|YP_978885.1| 134 PDVVQRLSALGLLVSITVTSVYEAGVAIAAGADSLVVqGPAAGGHRGTFApdMEPGTESLHQLLDRIGsahdVPLVAAGG 213
                                    566777888899********************7665448887766666554455688999999988888888******** PP

                       TMP-TENI 159 i.tlenvaevleagad 173
                                    + t+e+va+vl+ ga 
  gi|121638661|ref|YP_978885.1| 214 LgTAEDVAAVLRRGAI 229
                                    945789*****99985 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.1e-05      0.12     128     167 ..     194     233 ..     184     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                                    HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                   G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                    ++++++i ++ ++p++a+G + t edv ++l+ Gaia  +
  gi|121638661|ref|YP_978885.1| 194 HQLLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQV 233
                                    6788999999**************************9765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.6   0.00037      0.73     224     318 ..     151     252 ..     144     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                                    E-SHHHHHHHHHTTESEEEE--..GGGTSSTT--...-HHHCHHHHHHHH....SS-EEEESS--SHHHHHHHHHTT-SE CS
                         FMN_dh 224 vltaedakraveaGvdgivvSN..HGGRqldgap...atidvLpeiveavgg..rievlvDgGirrGsDvlkAlalGAda 296
                                    v ++ +a  a++aG+d +vv     GG+   +ap   +  + L ++ +++g+  ++++++ gG  + +Dv+  l  GA a
  gi|121638661|ref|YP_978885.1| 151 VTSVYEAGVAIAAGADSLVVQGpaAGGHRGTFAPdmePGTESLHQLLDRIGSahDVPLVAAGGLGTAEDVAAVLRRGAIA 230
                                    678889999***********74437888777766333689999999999996558************************* PP

                                    EEESHHHHHHHHHHHHHHHHHH CS
                         FMN_dh 297 vllGRpflyglaagGeeGverv 318
                                      +G ++l +  ag ++  + +
  gi|121638661|ref|YP_978885.1| 231 AQVGTALLLADEAGTNAAHRAA 252
                                    *******999777655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2437.99
//
Query:       gi|121638662|ref|YP_978886.1|  [L=438]
Description: zinc protease pepR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-38  131.2   0.0    8.5e-38  130.2   0.0    1.5  1  Peptidase_M16_C  Peptidase M16 inactive domain
    1.2e-35  122.7   0.0    3.7e-35  121.1   0.0    1.9  2  Peptidase_M16    Insulinase (Peptidase family M16)
  ------ inclusion threshold ------
      0.031   14.5   0.1      0.054   13.7   0.1    1.3  1  NUMOD3           NUMOD3 motif (2 copies)


Domain annotation for each model (and alignments):
>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.0   1.4e-41   8.5e-38       3     180 ..     180     354 ..     179     357 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 1.4e-41
                                    -HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEESSSSSEEEE CS
                Peptidase_M16_C   3 tredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkkldeeqahls 82 
                                    tr +l++f+ + Y+pe+mv+a++G+vdh+ lv+l++++fg+   +  +p  p+++++    +  p+  l  +d eq+h+s
  gi|121638662|ref|YP_978886.1| 180 TRAQLQSFHLRRYTPERMVVAAAGNVDHDGLVALVREHFGSRLVRGRRPVAPRKGTGR--VNGSPRLTLVSRDAEQTHVS 257
                                    899****************************************999565566655555..89999999999999****** PP

                                    EEEEEECTCTHTTHHHHHHHHHHHHSSTTSHHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECTTHHHHHHHHHHH CS
                Peptidase_M16_C  83 lafegpskendeddlalavlntlLgggmesrLytnlrekeglaysvsafndsyrdsglfgisatadpenveevvevilke 162
                                    l+ ++p++   e+  al+vl t Lggg +srL++++re +glaysv++ +d + dsg ++++a + pe++++v  v+ ++
  gi|121638662|ref|YP_978886.1| 258 LGIRTPGR-GWEHRWALSVLHTALGGGLSSRLFQEVRETRGLAYSVYSALDLFADSGALSVYAACLPERFADVMRVTADV 336
                                    ********.*********************************************************************** PP

                                    HHHHHHHTS-HHHHHHHH CS
                Peptidase_M16_C 163 lrklkkeglteeelerak 180
                                    l+ ++++g+te+e   ak
  gi|121638662|ref|YP_978886.1| 337 LESVARDGITEAECGIAK 354
                                    ************976665 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   6.2e-39   3.7e-35       1     147 [.      25     171 ..      25     173 .. 0.98
   2 ?   -3.3   0.1       1.3   7.7e+03     110     134 ..     389     413 ..     384     420 .. 0.67

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 6.2e-39
                                    EEEEEE-TSSSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEEEE CS
                  Peptidase_M16   1 rvalesdppaktsavglvvdaGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyvevl 80 
                                    rv++e  p  ++++vg++v++GSr+e   ++G+AH+leh++fk+T ++++  +a+ +++ Gg+lnA+t +e+t+Yy++vl
  gi|121638662|ref|YP_978886.1|  25 RVVTEFLPAVHSASVGVWVGVGSRDEGATVAGAAHFLEHLLFKSTPTRSAVDIAQAMDAVGGELNAFTAKEHTCYYAHVL 104
                                    6889999999********************************************************************** PP

                                    GGGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHTTTSGGGSHSS- CS
                  Peptidase_M16  81 skdlekaldvladvfkaplleesevererkvvekeveavdaepekvveenlhaaayrekalgrsllg 147
                                     +dl+ a+d+ adv+ + +   ++ve er+vv++e+++ d+ pe+++ ++  aa + ++++gr+++g
  gi|121638662|ref|YP_978886.1| 105 GSDLPLAVDLVADVVLNGRCAADDVEVERDVVLEEIAMRDDDPEDALADMFLAALFGDHPVGRPVIG 171
                                    ***************************************************************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHCCHHHHHHHHHHHHH CS
                  Peptidase_M16 110 kvvekeveavdaepekvveenlhaa 134
                                    + +++++e+v  e  ++v ++l + 
  gi|121638662|ref|YP_978886.1| 389 EHTLRQIEQVTVEEVNAVARHLLSR 413
                                    5567777777777777777777665 PP

>> NUMOD3  NUMOD3 motif (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     9e-06     0.054      11      36 ..     371     395 ..     366     395 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-06
                         NUMOD3  11 KmsealkGennpfyGKkhSeE.Tkrki 36 
                                    +ms    G+++ +yGK++S E T+r+i
  gi|121638662|ref|YP_978886.1| 371 RMSRL--GRSELNYGKHRSIEhTLRQI 395
                                    79999..**************9*9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3273.02
//
Query:       gi|121638663|ref|YP_978887.1|  [L=752]
Description: polynucleotide phosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-36  125.3   0.0    8.9e-18   65.1   0.0    2.5  2  RNase_PH    3' exoribonuclease family, domain 1
    7.6e-22   77.6   1.1    2.1e-21   76.2   1.1    1.8  1  PNPase      Polyribonucleotide nucleotidyltransferase, RNA bi
    3.2e-14   53.0   0.7    7.9e-14   51.8   0.7    1.7  1  S1          S1 RNA binding domain
    5.5e-11   42.1   0.9    1.4e-10   40.9   0.9    1.7  1  KH_1        KH domain
    2.7e-07   30.5   2.5     0.0062   16.5   0.2    3.2  2  RNase_PH_C  3' exoribonuclease family, domain 2
     0.0053   16.6   0.0      0.016   15.0   0.0    1.8  1  KH_2        KH domain
  ------ inclusion threshold ------
      0.082   13.0   0.7       0.36   11.0   0.7    2.1  1  KH_5        NusA-like KH domain
       0.11   12.4   0.4        0.4   10.6   0.0    2.1  2  KH_4        KH domain


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0     7e-19   1.6e-15       3     132 .]      25     156 ..      23     156 .. 0.87
   2 !   65.1   0.0     4e-21   8.9e-18       2     132 .]     355     487 ..     354     487 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 7e-19
                                    EEEEEEES.SSSTTSEEEEEEECC.EEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C........S...HH CS
                       RNase_PH   3 Rslsietg.vlsqanGSaylelGd.tkvlasvtgpieerpseer.ddaegaldveveyapfasger.....rregrpsde 74 
                                    R +++etg ++ qa G ++  l+d + +l + t+++ +   +e+ d+++  l+v+ve  ++a+g++     rregrps  
  gi|121638663|ref|YP_978887.1|  25 RTIRFETGrLALQAAGAVVAYLDDdNMLLSATTASKNP---KEHfDFFP--LTVDVEERMYAAGRIpgsffRREGRPSTD 99 
                                    99******9**************977777777888876...5555****..***************************** PP

                                    HHHHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHH.HCHHHHHHHHHCTCEE CS
                       RNase_PH  75 eielsrlleralrpsillekkpkstididitvlssdggslld.alinaaslALadagip 132
                                    +i+++rl++r lrps++   +  ++i+i++t+ls d g l+d ++inaas+  +  g+p
  gi|121638663|ref|YP_978887.1| 100 AILTCRLIDRPLRPSFVDGLR--NEIQIVVTILSLDPGDLYDvLAINAASASTQLGGLP 156
                                    *******************99..79999999999988666651668****987766665 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 4e-21
                                    EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CC....EEEECCCCECCCCEC-C...S...HHHHH CS
                       RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddae....galdveveyapfasgerrregrpsdeeie 77 
                                    +R+ls+e  v+++a+GSa++e G+t++l + t++  + ++++ d+ +    ++ + +++++pf++ge+ r g p+++ei 
  gi|121638663|ref|YP_978887.1| 355 IRALSAEVAVVPRAHGSALFERGETQILGVTTLDMIKMAQQI-DSLGpetsKRYMHHYNFPPFSTGETGRVGSPKRREIG 433
                                    79*********************************9966666.6555677789***************88899******* PP

                                    HHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                       RNase_PH  78 lsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       l eral p+++  ++  + i+ + + l s+g s+ + +++a++lAL++ag+p
  gi|121638663|ref|YP_978887.1| 434 HGALAERALVPVLPSVEEFPYAIRQVSEALGSNG-STSMGSVCASTLALLNAGVP 487
                                    **************966666**************.******************98 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   1.1   9.3e-25   2.1e-21       2      82 ..     274     350 ..     273     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 9.3e-25
                                    HHHHHHTTTHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHHHHHHHHHHTS-TTTS CS
                         PNPase   2 leekvaelaeerisealtiteKqeRyaaldeikekvveafaaeleeedeedekeikeifkalekkvvRsrildegvRiDG 81 
                                    ++ +v ++a+++++ alti +K eR++++deik++vv+++a ++    e +eke++++++al+kk+vR+ril++++RiDG
  gi|121638663|ref|YP_978887.1| 274 VYYSVSSVATDELAAALTIGGKAERDQRIDEIKTQVVQRLADTY----EGREKEVGAALRALTKKLVRQRILTDHFRIDG 349
                                    678999***********************************666....889***************************** PP

                                    - CS
                         PNPase  82 R 82 
                                    R
  gi|121638663|ref|YP_978887.1| 350 R 350
                                    * PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.7   3.5e-17   7.9e-14       2      72 ..     663     732 ..     662     734 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3.5e-17
                                    STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
                             S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriil 72 
                                    p +ge++ G+V++ t++GafV l+ g +g+v++s l   +r+ + ++v+ vGd+++v++ ++dk  + i+l
  gi|121638663|ref|YP_978887.1| 663 PTVGERFLGTVVKTTDFGAFVSLLPGRDGLVHISKLGKGKRIAKVEDVVNVGDKLRVEIADIDKRGK-ISL 732
                                    789**********************************99*************************988.887 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.9   6.1e-14   1.4e-10       2      65 ..     598     655 ..     597     656 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 6.1e-14
                                    EEEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
                           KH_1   2 lrilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                                    ++i+vP +++g +IG++G++I+ I eetga+I ++       d+ +v +   +  + ++A+++i+
  gi|121638663|ref|YP_978887.1| 598 TTIKVPVDKIGEVIGPKGKVINAITEETGAQISIE-------DDGTVFVGAtDGPSAQAAIDKIN 655
                                    799******************************76.......35699994444446888888876 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   5.3e-05      0.12       1      50 [.     159     209 ..     159     237 .. 0.73
   2 !   16.5   0.2   2.8e-06    0.0062       1      67 []     490     572 ..     490     572 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                                    S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTS...EEEEEEEECSS CS
                     RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtk...evvtlmkeggs 50 
                                    +p+++v+v+++d++ v  pt ++  ++ ++ +++vag+    +v  +m e ++
  gi|121638663|ref|YP_978887.1| 159 GPIGGVRVALIDGTWVGFPTVDQ--IERAVFDMVVAGRIvegDVAIMMVEAEA 209
                                    599********************..**********987677766666666554 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.8e-06
                                    S--EEEEEEEETTE................EEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSC..EEHHHHHHHHH CS
                     RNase_PH_C   1 apviavtvgkvddq................fvlDptkeEedlsegdltlavagtkevvtlmkeggsq..ldeetlleaie 62 
                                    apv+++++g+v d+                 + D    E++   gd+++ vagtk+ vt ++++ +   ++ + l  a+e
  gi|121638663|ref|YP_978887.1| 490 APVAGIAMGLVSDDiqvegavdgvverrfvTLTDILGAEDA--FGDMDFKVAGTKDFVTALQLDTKLdgIPSQVLAGALE 567
                                    58888888888854445555555556676677788888844..56********************9999*********** PP

                                    HHHHH CS
                     RNase_PH_C  63 lAkkg 67 
                                     Ak++
  gi|121638663|ref|YP_978887.1| 568 QAKDA 572
                                    **985 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.2e-06     0.016      27      66 ..     598     637 ..     585     642 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                                    EEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCE CS
                           KH_2  27 viiviresqpgivIGkgGsnikkigkelrkdieklegkkV 66 
                                    ++i + + + g vIG +G+ i++i++e + +i +  ++ V
  gi|121638663|ref|YP_978887.1| 598 TTIKVPVDKIGEVIGPKGKVINAITEETGAQISIEDDGTV 637
                                    788889999***********************76555555 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00016      0.36      16      43 ..     604     630 ..     597     634 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                           KH_5  16 vdpvGaivgkkGsrikavsseLkgekid 43 
                                    vd +G+++g kG+ i+a+ +e  g +i 
  gi|121638663|ref|YP_978887.1| 604 VDKIGEVIGPKGKVINAITEET-GAQIS 630
                                    9******************997.77776 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018       0.4      30      54 ..     597     621 ..     576     622 .. 0.87
   2 ?   -2.2   0.2       1.7   3.9e+03       9      35 ..     708     734 ..     706     740 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                           KH_4  30 eielnvegedlGrvIGkrGrtldAl 54 
                                    + +++v  +++G vIG +G++++A+
  gi|121638663|ref|YP_978887.1| 597 VTTIKVPVDKIGEVIGPKGKVINAI 621
                                    567889999***************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                           KH_4   9 kalvddpeevevteeeeeeeveielnv 35 
                                    + +v+  ++++v++ + +++ +i l +
  gi|121638663|ref|YP_978887.1| 708 EDVVNVGDKLRVEIADIDKRGKISLIL 734
                                    567777889999999666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (752 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 4378.79
//
Query:       gi|121638664|ref|YP_978888.1|  [L=171]
Description: hypothetical protein BCG_2802c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   14.3   0.1      0.016   13.9   0.1    1.1  1  P22_CoatProtein  P22 coat protein - gene protein 5
      0.048   13.0   0.1      0.073   12.4   0.1    1.3  1  GSK-3_bind       Glycogen synthase kinase-3 binding
       0.13   12.4   1.3         17    5.5   0.0    2.7  2  PCSK9_C2         Proprotein convertase subtilisin-like/kexin 


Domain annotation for each model (and alignments):
>> P22_CoatProtein  P22 coat protein - gene protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.6e-06     0.016     255     299 ..      21      64 ..      10      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                                    S--TS..--TT-EEEEEEEEEETTTTT-EE.EEEEEEEEEE..ESS CS
                P22_CoatProtein 255 sattgatlkaGDvlsiagvkainqvtKqal.sqlatFtvvadaata 299
                                    sat+ a lk GD +++ag+    q tK++  s + +F vva  +++
  gi|121638664|ref|YP_978888.1|  21 SATNVAELKVGDCVKLAGTPDRPQATKAECgSPASNFKVVA--VVQ 64 
                                    688888************************555678****7..443 PP

>> GSK-3_bind  Glycogen synthase kinase-3 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05     0.073      38      89 ..      23      72 ..      12      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                     GSK-3_bind 38 gevdrlvaqiGetlqldaaqdsPaspcaapGaplraprvlaavradkarspa 89
                                   ++v +   ++G+ ++l  + d+P ++ a  G+p +  +v+a v+ d+a+ pa
  gi|121638664|ref|YP_978888.1| 23 TNVAE--LKVGDCVKLAGTPDRPQATKAECGSPASNFKVVAVVQEDHAECPA 72
                                   44444..489**************************************9998 PP

>> PCSK9_C2  Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0035        21      24      38 ..      15      29 ..      13      54 .. 0.83
   2 ?    5.5   0.0    0.0029        17      12      34 ..      86     108 ..      76     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                       PCSK9_C2 24 VLTGCssHsevedls 38
                                   V TGCss  +v +l+
  gi|121638664|ref|YP_978888.1| 15 VATGCSSATNVAELK 29
                                   77*****99999886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0029
                       PCSK9_C2  12 tetrarCseedhVLTGCssHsev 34 
                                    ++t+  C   d V+ GC+s  ++
  gi|121638664|ref|YP_978888.1|  86 GSTNTICLDIDWVIGGCMSVDPT 108
                                    567788************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 917.15
//
Query:       gi|121638665|ref|YP_978889.1|  [L=89]
Description: 30S ribosomal protein S15 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-36  122.7   2.5      6e-36  122.5   2.5    1.0  1  Ribosomal_S15  Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.5   2.5   3.3e-40     6e-36       1      81 []       8      88 ..       8      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 3.3e-40
                                   HHHHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCTST CS
                  Ribosomal_S15  1 kkelikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdverYkklieklglr 81
                                   kke++++++ he+DtGspe qiallt+rI +ltehlk +k+D+hsrrgLl+lv++Rr+l+kY+ + dverY++lie+lglr
  gi|121638665|ref|YP_978889.1|  8 KKEILRSYGLHETDTGSPEAQIALLTKRIADLTEHLKVHKHDHHSRRGLLLLVGRRRRLIKYISQIDVERYRSLIERLGLR 88
                                   899****************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 501.70
//
Query:       gi|121638666|ref|YP_978890.1|  [L=331]
Description: bifunctional riboflavin kinase/FMN adenylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-51  173.3   0.2    5.6e-51  172.6   0.2    1.3  1  FAD_syn          FAD synthetase
    2.3e-34  118.0   0.0    7.8e-34  116.3   0.0    1.8  2  Flavokinase      Riboflavin kinase
     0.0027   17.9   0.0     0.0066   16.7   0.0    1.7  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.04   13.4   0.2          8    5.9   0.2    2.2  2  ATP-sulfurylase  ATP-sulfurylase


Domain annotation for each model (and alignments):
>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   0.2   1.2e-54   5.6e-51       4     151 ..      20     167 ..      17     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 1.2e-54
                        FAD_syn   4 edegavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlvv 83 
                                    ++ ++v+t+G FDGvH+GH +l+++av+a +++g+p+v++tF+phP+ev+ + ++pa+Lttl++++el+++lg++++lv+
  gi|121638666|ref|YP_978890.1|  20 DWGRCVLTIGVFDGVHRGHAELIAHAVKAGRARGVPAVLMTFDPHPMEVVYPGSHPAQLTTLTRRAELVQDLGIEVFLVM 99 
                                    6779**************************************************************************** PP

                        FAD_syn  84 dFtkefaelsaeeFiekllveklkvkavvvGfdfrfGkkregdvellkelgaklgfevevvpkvelee 151
                                    +Ft++f++l++++Fi++llve+l+v +vvvG++f+fGkk +g+v++l+++g+++gf ve+++ v++++
  gi|121638666|ref|YP_978890.1| 100 PFTTDFMKLTPDRFIHELLVEHLHVVEVVVGENFTFGKKAAGNVDTLRRAGERFGFAVESMSLVSEHH 167
                                    *************************************************************9997765 PP

>> Flavokinase  Riboflavin kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.59   2.7e+03      13      65 ..      44      98 ..      33     124 .. 0.58
   2 !  116.3   0.0   1.7e-37   7.8e-34       1     111 []     195     328 ..     195     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.59
                                   S-SSCHTTTT--EEEEE-S-B-GTSEEEEEEEE.EEEEEEEETTTSSE..EEEEET CS
                    Flavokinase 13 kGkkrGrelgfpTaNlelekllpkkGVYavrvk.gvaniGvrptfknk..vEvhil 65
                                   +  k Gr  g+p + +++ +  p + VY +     ++++  r  + ++  +Ev+++
  gi|121638666|ref|YP_978890.1| 44 HAVKAGRARGVPAVLMTF-DPHPMEVVYPGSHPaQLTTLTRRAELVQDlgIEVFLV 98
                                   555666666666666655.2335556665555433334444433333345566554 PP

  == domain 2  score: 116.3 bits;  conditional E-value: 1.7e-37
                                    HTS-EEEEEEEES-SSCHTTTT--EEEEE-..S-B-GTSEEEEEEEE..................EEEEEEEETTTSSE. CS
                    Flavokinase   1 LgrpyslsgkVvkGkkrGrelgfpTaNlel..ekllpkkGVYavrvk..................gvaniGvrptfknk. 59 
                                    Lgrp++++g Vv+G++rG elgfpTaN+++   +++p++GVYa++++                  +++++G++ptf+++ 
  gi|121638666|ref|YP_978890.1| 195 LGRPHRVEGVVVRGEGRGAELGFPTANVAPpmYSAIPADGVYAAWFTvlghgpvtgtvvpgeryqAAVSVGTNPTFSGRt 274
                                    89***************************8877888****************************************9966 PP

                                    ..EEEEETT--S--TTSEEEEEEEEEEEE----SSHHHHHHHHHHHHHHHHHHH CS
                    Flavokinase  60 ..vEvhildfsedlygkelrvellkflRpekkFdsleaLkaqikkDvekarell 111
                                      vE+++ld+++dlyg+++ +++++++R +kkF+s+ +L+a++ +D e+ar+ll
  gi|121638666|ref|YP_978890.1| 275 rtVEAFVLDTTADLYGQHVALDFVGRIRGQKKFESVRQLVAAMGADTERARDLL 328
                                    78************************************************9875 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0066       1     141 [.      26     180 ..      26     181 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                    EEEE--TT--HHHHHHHHHHHHHSSES..EEEEEESSTHCSST.-.....SCSSTHHHHHHHHHHH.TTCTTEEEEEEES CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleed..livgvpsdeppkkk.k.....kplasaeeRlemlela.kevdevisvdpwe 71 
                                    l+ G+FD +H GH++l+  a k +       v+++ d+ p            l+++  R e ++ + +ev  v+++  + 
  gi|121638666|ref|YP_978890.1|  26 LTIGVFDGVHRGHAELIAHAVKAGRARgvPAVLMTFDPHPMEVvYpgshpAQLTTLTRRAELVQDLgIEVFLVMPFTTD- 104
                                    578***********************99977777777766543212244566677777777777775444444433333. PP

                                    EHH......HHHHHTTTTEEEEEEEHHHHHHHHCHH.......HHHHHHHHHHHEEEEEEHTTCEEE.EEEECCTTTCSH CS
                CTP_transf_like  72 ltr......evlkklkpdklylvigadvledfsewk.......eleeilgnvklvvvsrpekqanvl.lkaekrtngiSs 137
                                             +++++l ++    v+   v e+f + k        l++  ++++++v+s +     ++   ++++t   Ss
  gi|121638666|ref|YP_978890.1| 105 --FmkltpdRFIHELLVE-HLHVVEVVVGENFTFGKkaagnvdTLRRAGERFGFAVESMS-----LVsEHHSNETVTFSS 176
                                    ..2333667666666665.23333333333444444345555566666666666666666.....111223334444577 PP

                                    HHHH CS
                CTP_transf_like 138 tkir 141
                                    t+ir
  gi|121638666|ref|YP_978890.1| 177 TYIR 180
                                    7777 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0018         8      29      49 ..      32      53 ..      19      65 .. 0.75
   2 ?    5.1   0.0     0.003        14     164     196 ..     140     189 ..     111     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                                   S---HHHHHHHHHHHHH.TSEE CS
                ATP-sulfurylase 29 nplHraHeellkralee.eadg 49
                                   + +Hr+H+el+ +a+++ +a g
  gi|121638666|ref|YP_978890.1| 32 DGVHRGHAELIAHAVKAgRARG 53
                                   569*************876654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.003
                                    T...............EEEECCCC..GCCGGEEE--HHHHHCCHHTT--- CS
                ATP-sulfurylase 164 g...............evasektc..hkkeevesisgtelrkllregeei 196
                                                     v+s+++   h+++e++++s+t++r+ + +g  +
  gi|121638666|ref|YP_978890.1| 140 AgnvdtlrragerfgfAVESMSLVseHHSNETVTFSSTYIRSCVDAGDMV 189
                                    5555555555555555455555556799****************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1791.77
//
Query:       gi|121638667|ref|YP_978891.1|  [L=587]
Description: hypothetical protein BCG_2805 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-09   35.5   0.0    1.6e-08   34.7   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    8.5e-08   32.3   0.1      2e-07   31.1   0.1    1.6  1  AAA_31       AAA domain
      2e-07   31.4   1.9      0.031   14.8   0.0    4.2  4  TPR_19       Tetratricopeptide repeat
    0.00041   19.9   0.5    0.00076   19.0   0.5    1.3  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00072   20.0   0.5        2.4    9.0   0.0    3.8  3  TPR_6        Tetratricopeptide repeat
     0.0033   18.1   8.4        6.3    7.9   0.0    4.7  4  TPR_14       Tetratricopeptide repeat
     0.0036   16.9   0.0     0.0073   15.9   0.0    1.5  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.3         13    6.2   0.0    3.8  4  TPR_2        Tetratricopeptide repeat
      0.014   14.6   0.1      0.021   14.0   0.1    1.2  1  ArsA_ATPase  Anion-transporting ATPase
      0.016   14.7   0.1      0.041   13.4   0.1    1.7  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.023   14.0   0.5      0.039   13.2   0.5    1.4  1  MipZ         ATPase MipZ
      0.079   13.6  11.5       0.36   11.5   1.2    3.1  3  TPR_16       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0     1e-11   1.6e-08       1      55 [.     322     483 ..     322     545 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1e-11
                                    EEEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlaileglendiep......................... 54 
                                    +a++s kGGvGKTt+++  + a ar rg rV +vD+D +   l+  +  ++  ++                         
  gi|121638667|ref|YP_978891.1| 322 LAFVSAKGGVGKTTMTVLVGNAVARlRGDRVMAVDVDADLGDLSARFSERGGPQTniehfvssqhtkryadvrvhtvmnk 401
                                    5899*********************99************99998866666555556666887777777777777777777 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121638667|ref|YP_978891.1| 402 drlemlgaqndprstykfgpedygaamqilethcnvilldcgtpvngplfsnilndvtglvvvasedvrgvegalvtldw 481
                                    77777777777777777777777777777777777777777777777777777776666666666655544444444444 PP

                                    .C CS
                                    .x RF
                           CbiA  55 .d 55 
                                     +
  gi|121638667|ref|YP_978891.1| 482 lG 483
                                    43 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   1.3e-10     2e-07       4      77 ..     322     398 ..     319     480 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                         AAA_31   4 IaianqKGGvGKTTtsvnlaaala.klgkkvLlvDlDpQan.attglgiekneiektlyevl..ieeknikeaiiktk 77 
                                    +a++  KGGvGKTT +v ++ a+a  +g +v+ vD+D+    ++ +++ e+   ++++ + +   ++k+++++ ++t 
  gi|121638667|ref|YP_978891.1| 322 LAFVSAKGGVGKTTMTVLVGNAVArLRGDRVMAVDVDADLGdLSARFS-ERGGPQTNIEHFVssQHTKRYADVRVHTV 398
                                    799*********************789**********97540444333.45555666666653224455555555444 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0023       3.4       2      31 ..      18      47 ..      17      50 .. 0.90
   2 ?    4.4   0.1     0.037        56      27      50 ..     102     125 ..      98     143 .. 0.80
   3 !   14.8   0.0   2.1e-05     0.031       5      50 ..     190     236 ..     186     243 .. 0.94
   4 ?   -1.0   0.0       1.8   2.7e+03       5      15 ..     422     432 ..     419     433 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                         TPR_19  2 laegdyaeAlalleqalqedpknaearllL 31
                                   +++gd+a+A a++ ++  e+p++++ +l+L
  gi|121638667|ref|YP_978891.1| 18 YQSGDLANARAAFGRLTVENPDMSDGWLGL 47
                                   689************9999*********98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.037
                         TPR_19  27 arllLAeallalgqldeAealLda 50 
                                    + l++A al+ + + deA a+Ld+
  gi|121638667|ref|YP_978891.1| 102 IGLAYASALIIADRHDEAAATLDD 125
                                    66889*****************96 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.1e-05
                         TPR_19   5 gdyaeAlalleqalqedpk.naearllLAeallalgqldeAealLda 50 
                                    g+++ Al+l eq+ + +p   a++ l  A +l +lg+ d+A+ +L+a
  gi|121638667|ref|YP_978891.1| 190 GQFQFALELAEQVSTTNPRvTADVTLTRAWCLRELGDDDAARVALSA 236
                                    89999***************************************987 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.8
                         TPR_19   5 gdyaeAlalle 15 
                                    +dy +A+++le
  gi|121638667|ref|YP_978891.1| 422 EDYGAAMQILE 432
                                    69*******98 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   5.1e-07   0.00076       4      41 ..     320     358 ..     319     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.1e-07
                           ParA   4 kviavlSgKGGVGKStvavnlAlaLa.kkglkvgllDaD 41 
                                    +++a +S+KGGVGK+t++v +  a+a  +g +v  +D+D
  gi|121638667|ref|YP_978891.1| 320 HKLAFVSAKGGVGKTTMTVLVGNAVArLRGDRVMAVDVD 358
                                    67899******************9994589999999998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0016       2.4       4      32 ..      11      39 ..       8      39 .. 0.85
   2 ?   -0.9   0.1       2.2   3.3e+03       6      24 ..     102     124 ..     101     125 .. 0.81
   3 !    6.6   0.0    0.0089        13       6      23 ..     217     234 ..     212     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                                   HHHH.HHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6  4 ykla.lsyrklgdtdkAlealerlikeYPd 32
                                   + +a +sy+++ d ++A++a+ rl  e Pd
  gi|121638667|ref|YP_978891.1| 11 FDAAvKSYQSG-DLANARAAFGRLTVENPD 39
                                   55555789989.*************99998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                    HHHHHHHH....HHHHHHHHHHH CS
                          TPR_6   6 lalsyrkl....gdtdkAleale 24 
                                    ++l+y ++    +++d+A ++l+
  gi|121638667|ref|YP_978891.1| 102 IGLAYASAliiaDRHDEAAATLD 124
                                    68899985589899999999986 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0089
                                    HHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAleal 23 
                                    +a+++r+lgd d+A+ al
  gi|121638667|ref|YP_978891.1| 217 RAWCLRELGDDDAARVAL 234
                                    79*****99******988 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0042       6.3      13      42 ..      19      48 ..       9      50 .. 0.90
   2 !    6.8   0.1    0.0094        14       5      26 ..     104     125 ..     100     144 .. 0.88
   3 ?    2.4   0.2      0.24   3.6e+02       2      33 ..     176     208 ..     175     217 .. 0.79
   4 ?    2.9   0.2      0.17   2.6e+02       3      25 ..     213     235 ..     211     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0042
                         TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                                   ++Gd++ A+a++ r+   +Pd  + wl l 
  gi|121638667|ref|YP_978891.1| 19 QSGDLANARAAFGRLTVENPDMSDGWLGLL 48
                                   79*********************9998875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0094
                         TPR_14   5 lalaeallalGdpdeAiallrr 26 
                                    la+a+al  ++++deA+a l++
  gi|121638667|ref|YP_978891.1| 104 LAYASALIIADRHDEAAATLDD 125
                                    79****************9987 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.24
                         TPR_14   2 eallalaeal.lalGdpdeAiallrralalaPd 33 
                                    +a +ala+   + lG+++ A++l++++  ++P 
  gi|121638667|ref|YP_978891.1| 176 DAVAALASTAaASLGQFQFALELAEQVSTTNPR 208
                                    67889998651679****999999999999986 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.17
                         TPR_14   3 allalaeallalGdpdeAiallr 25 
                                    ++l +a+ l++lGd d+A+ +l 
  gi|121638667|ref|YP_978891.1| 213 VTLTRAWCLRELGDDDAARVALS 235
                                    67889999**********98886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0073      29     122 ..     316     412 ..     296     462 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                         AAA_25  29 llpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal........... 97 
                                    l   ++la + + +g+GKtt+++ ++ ava+ +   g       +V+ v+ + +  +l  R+++ g  +           
  gi|121638667|ref|YP_978891.1| 316 LADVHKLAFVSAKGGVGKTTMTVLVGNAVARLR---G------DRVMAVDVDADLGDLSARFSERGGPQtniehfvssqh 386
                                    56668999**********************633...4......4899999999999999999999955556788899988 PP

                         AAA_25  98 .rddarllvldlagveslpLfakdrg 122
                                     ++ a+++v++++++++l ++ ++++
  gi|121638667|ref|YP_978891.1| 387 tKRYADVRVHTVMNKDRLEMLGAQND 412
                                    87788888888888855555444433 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0085        13       5      33 ..      11      39 ..       7      40 .. 0.85
   2 ?   -2.8   0.1       6.4   9.6e+03       8      22 ..     107     121 ..     105     123 .. 0.78
   3 ?    1.4   0.0      0.29   4.3e+02      10      30 ..     185     205 ..     181     208 .. 0.81
   4 ?    3.1   0.0     0.084   1.3e+02       6      23 ..     216     233 ..     211     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0085
                          TPR_2  5 ynlGlayyklgdyeeAleafekAleldPn 33
                                   +  +   y++gd++ A++af +    +P+
  gi|121638667|ref|YP_978891.1| 11 FDAAVKSYQSGDLANARAAFGRLTVENPD 39
                                   55677789*************99998886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.4
                          TPR_2   8 GlayyklgdyeeAle 22 
                                    + a++ +++++eA++
  gi|121638667|ref|YP_978891.1| 107 ASALIIADRHDEAAA 121
                                    667888899999975 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.29
                          TPR_2  10 ayyklgdyeeAleafekAlel 30 
                                    a++ lg+++ Ale+ e++   
  gi|121638667|ref|YP_978891.1| 185 AAASLGQFQFALELAEQVSTT 205
                                    67889*********9997555 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.084
                          TPR_2   6 nlGlayyklgdyeeAlea 23 
                                     +++++++lgd + A+ a
  gi|121638667|ref|YP_978891.1| 216 TRAWCLRELGDDDAARVA 233
                                    69************9866 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.021       2      38 ..     321     358 ..     320     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                    EEEEEEESTTSSHHHHHHHHHHHHHHT.TS-EEEEE-S CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsek.gkkvllistD 38 
                                    k+ +v+ KGGVGKtt+   ++  +++  g +v+ + +D
  gi|121638667|ref|YP_978891.1| 321 KLAFVSAKGGVGKTTMTVLVGNAVARLrGDRVMAVDVD 358
                                    788**************999999998624566666555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.8e-05     0.041       4      50 ..     322     370 ..     319     471 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                       CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhel.gesvlviDlspd.nlLrlhFnv 50 
                                    la+   +GGvG+t++++  + a+ +l g++v+++D+ +d   L   F++
  gi|121638667|ref|YP_978891.1| 322 LAFVSAKGGVGKTTMTVLVGNAVARLrGDRVMAVDVDADlGDLSARFSE 370
                                    6667789****************987489******98873345555654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.6e-05     0.039       4      58 ..     323     378 ..     320     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                    EE--SSTTSSHHHHHHHHHHHHHT.TT--EEEEE--TTT-HHHHHHHHHHHHHHHH CS
                           MipZ   4 vlgnekGGsGksttavhvavaLlk.kGarvaaidldlrqrtlarylenraataerk 58 
                                     +   kGG Gk+t++v v  a+++ +G rv a+d+d+    l+  +  r   +++ 
  gi|121638667|ref|YP_978891.1| 323 AFVSAKGGVGKTTMTVLVGNAVARlRGDRVMAVDVDADLGDLSARFSERGGPQTNI 378
                                    56778*************99999757**********97766665556665555555 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0022       3.3       8      47 ..      18      54 ..      12      75 .. 0.82
   2 ?   -1.9   0.3       3.9   5.8e+03      39      57 ..     105     123 ..      99     125 .. 0.72
   3 ?   11.5   1.2   0.00024      0.36       5      56 ..     184     234 ..     177     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                         TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq 47
                                   +++gd + A+aa+ +++  +   Pd  + +l+l  +  ++
  gi|121638667|ref|YP_978891.1| 18 YQSGDLANARAAFGRLTVEN---PDMSDGWLGLLACGDHH 54
                                   799*****************...**999999998887765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                         TPR_16  39 llgdaalrqgrlaeAaaly 57 
                                    +++ a+  + r++eAaa +
  gi|121638667|ref|YP_978891.1| 105 AYASALIIADRHDEAAATL 123
                                    5666777778889998655 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00024
                         TPR_16   5 raalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAa.al 56 
                                    +aa+ +g+++ A++++e++   +   P+ +a+  l +++++ ++g+ ++A+ al
  gi|121638667|ref|YP_978891.1| 184 TAAASLGQFQFALELAEQVSTTN---PRvTADVTLTRAWCLRELGDDDAARvAL 234
                                    689999*****************...555*********************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3595.59
//
Query:       gi|121638668|ref|YP_978892.1|  [L=228]
Description: transcriptional repressor sirR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-31  106.5   0.0    1.6e-30  105.0   0.0    1.7  2  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    2.2e-23   82.2   0.1    3.5e-23   81.5   0.1    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    2.4e-21   75.8   0.0    7.3e-21   74.2   0.0    1.8  2  FeoA             FeoA domain
    7.5e-07   29.6   0.0    1.5e-06   28.6   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
    2.6e-05   24.1   0.1    8.3e-05   22.5   0.0    1.8  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    5.2e-05   23.0   0.1    0.00011   21.9   0.1    1.7  1  MarR_2           MarR family
    7.6e-05   22.7   0.1    0.00028   20.9   0.0    2.1  2  HTH_20           Helix-turn-helix domain
    7.9e-05   22.1   0.0    0.00013   21.5   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00012   22.0   0.0    0.00027   20.8   0.0    1.6  1  MarR             MarR family
    0.00019   21.0   0.0    0.00042   19.9   0.0    1.6  1  GntR             Bacterial regulatory proteins, gntR family
    0.00035   20.3   0.0    0.00074   19.2   0.0    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00048   19.9   0.0     0.0011   18.8   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0012   18.6   0.1     0.0027   17.5   0.1    1.6  1  HTH_10           HTH DNA binding domain
     0.0014   18.5   0.1     0.0024   17.7   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0019   18.3   0.0     0.0034   17.4   0.0    1.4  1  HemN_C           HemN C-terminal domain
      0.002   17.9   0.4        1.6    8.5   0.0    3.3  2  MerR             MerR family regulatory protein
      0.002   18.0   0.0     0.0044   16.9   0.0    1.6  1  HTH_36           Helix-turn-helix domain
      0.002   17.9   0.2      0.013   15.3   0.0    2.3  2  HTH_IclR         IclR helix-turn-helix domain
     0.0022   18.3   0.0     0.0038   17.5   0.0    1.4  1  Rrf2             Transcriptional regulator
     0.0046   17.3   0.2     0.0073   16.7   0.2    1.4  1  Penicillinase_R  Penicillinase repressor
     0.0063   16.4   0.1      0.013   15.5   0.1    1.4  1  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.035   13.9   0.1    1.7  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.017   15.3   0.0      0.035   14.3   0.0    1.5  1  Ribosomal_S25    S25 ribosomal protein
      0.023   14.8   0.0       0.04   14.0   0.0    1.3  1  DUF2250          Uncharacterized protein conserved in archaea
      0.066   13.0   0.5        1.1    9.1   0.1    2.4  2  HTH_23           Homeodomain-like domain
       0.12   12.0   0.1       0.19   11.4   0.1    1.2  1  DUF4423          Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.8   3.3e+03      20      36 ..      35      51 ..      30      57 .. 0.76
   2 !  105.0   0.0   2.3e-33   1.6e-30       1      69 [.      72     140 ..      72     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                                   HHHHHHCT--CCCHHHH CS
                  Fe_dep_repr_C 20 rfLvdvlgvdweeahee 36
                                   ++L++ +gv+++ a e 
  gi|121638668|ref|YP_978892.1| 35 KMLAERIGVSASTASES 51
                                   68889999999888776 PP

  == domain 2  score: 105.0 bits;  conditional E-value: 2.3e-33
                                    -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                  Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                    T++Gr++A+ +vrrhrlle+fLv+ lg+ w+e+h+eAe lEha+s++l+ r+d+ lgfp+++Phg pip
  gi|121638668|ref|YP_978892.1|  72 TDSGRRAALAMVRRHRLLETFLVNELGYRWDEVHDEAEVLEHAVSDRLMARIDAKLGFPQRDPHGAPIP 140
                                    9*******************************************************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.1   5.1e-26   3.5e-23       1      60 []       9      69 ..       9      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.1e-26
                                   X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                 Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                   dL+++++dYL++I+t++e ++++v+tk+laer++vs+s++se+++kL+++G+v++eky+++
  gi|121638668|ref|YP_978892.1|  9 DLSAVAQDYLKVIWTAQEwSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHEKYGAV 69
                                   6999******************************************************986 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         6   4.1e+03      22      34 ..      49      61 ..      38      64 .. 0.76
   2 !   74.2   0.0   1.1e-23   7.3e-21       1      72 [.     152     226 ..     152     228 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6
                                   SSHHHHHHHHT-- CS
                           FeoA 22 pellrrLremGlv 34
                                    e  r+L+e Glv
  gi|121638668|ref|YP_978892.1| 49 SESIRKLAEQGLV 61
                                   6677999999986 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 1.1e-23
                                    EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEE...TTEEEEE-HHHHTTEEE CS
                           FeoA   1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrv...gdtrvaLgreeAqaIlV 72 
                                    ++L  + +G++g++arisd+dp++lr+++++G+ +++r++v+ar+ f+g+++v++   ++ +v+Lg+++AqaI+V
  gi|121638668|ref|YP_978892.1| 152 RQLWACRDGDTGTVARISDADPQMLRYFASIGISLDSRLRVLARREFAGMISVAIdsaDGATVDLGSPAAQAIWV 226
                                    57899**************************************************7766779************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   2.2e-09   1.5e-06      15      68 .]      28      75 ..      17      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.2e-09
                         HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                    +++++ ++l++r  v++s++s+s++kL e+GLv         ++  v+lTd+G
  gi|121638668|ref|YP_978892.1| 28 SQDKVSTKMLAERIGVSASTASESIRKLAEQGLV------DHEKYGAVTLTDSG 75
                                   5688999***************************......5567789****998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.2e-07   8.3e-05      21      61 ..      31      73 ..      18      76 .. 0.86
   2 ?   -2.5   0.0       7.5   5.2e+03      22      33 ..     193     204 ..     181     208 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES- CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrr.irild 61
                                   +++ + lA+++G++ +t s  +++L ++gl++  +++ ++++d
  gi|121638668|ref|YP_978892.1| 31 KVSTKMLAERIGVSASTASESIRKLAEQGLVDhEKYGaVTLTD 73
                                   578899**************************54455699988 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.5
                                    HHHHHHHHHTTS CS
                      HTH_Crp_2  22 ltqeelAsmlGl 33 
                                    l ++e A m+ +
  gi|121638668|ref|YP_978892.1| 193 LARREFAGMISV 204
                                    556667777665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.7e-07   0.00011      22      54 ..      32      64 ..       6      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                                   EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   ++ + la+r g+s s++s  +++L ++GLv  +
  gi|121638668|ref|YP_978892.1| 32 VSTKMLAERIGVSASTASESIRKLAEQGLVDHE 64
                                   77889*************************765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     4e-07   0.00028      19      58 ..      21      65 ..      10      68 .. 0.86
   2 ?   -2.4   0.0       7.5   5.1e+03      41      50 ..     186     195 ..     185     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4e-07
                                   H.....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 19 L.....araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                   +     ++ + ++ + laer+++s +t+s  +r+L+e gLv+ ++
  gi|121638668|ref|YP_978892.1| 21 IwtaqeWSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHEK 65
                                   1556668889999****************************9886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.5
                                    HHHHHHHHHH CS
                         HTH_20  41 lsyHLrvLee 50 
                                    l+ +LrvL++
  gi|121638668|ref|YP_978892.1| 186 LDSRLRVLAR 195
                                    5667888876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.9e-07   0.00013      18      47 ..      32      61 ..      18      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-07
                         HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                    s + LAer+g+S st ++ +++L e+Gl+
  gi|121638668|ref|YP_978892.1| 32 VSTKMLAERIGVSASTASESIRKLAEQGLV 61
                                   566679**********************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.9e-07   0.00027      13      48 ..      27      62 ..      15      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.9e-07
                                   HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                   ++q+  s + La+++gvs st+++ +++L ++Gl++
  gi|121638668|ref|YP_978892.1| 27 WSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVD 62
                                   4566677889************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.1e-07   0.00042      22      56 ..      30      63 ..      12      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.1e-07
                                   SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                   dk  s + La+++gVs++t  e++r+L+++glv  
  gi|121638668|ref|YP_978892.1| 30 DKV-STKMLAERIGVSASTASESIRKLAEQGLVDH 63
                                   778.8899************************965 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.1e-06   0.00074      10      52 ..      27      70 ..      26      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                       HTH_DeoR 10 kqqgklsveelvellgvSeaTiRRDLneLeeqglltR.thGGav 52
                                   ++q+k+s++ l+e+ gvS  T+   +++L+eqgl+    +G ++
  gi|121638668|ref|YP_978892.1| 27 WSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHeKYGAVT 70
                                   789*******************************7551444444 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06    0.0011      22      56 ..      31      65 ..      27      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                   CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   + +++ +ae++gv+ s++ e++r+L + GlV+ ek
  gi|121638668|ref|YP_978892.1| 31 KVSTKMLAERIGVSASTASESIRKLAEQGLVDHEK 65
                                   5677889************************9987 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.9e-06    0.0027      23      47 ..      31      55 ..      29      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                         HTH_10 23 rvtlkeLAkelGIskstlsehLrka 47
                                   +v++k LA+++G+s+st+se +rk 
  gi|121638668|ref|YP_978892.1| 31 KVSTKMLAERIGVSASTASESIRKL 55
                                   58999******************94 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.5e-06    0.0024      21      46 ..      37      62 ..      28      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                                   HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 21 laeelglsqstvShHLkkLreaGLVe 46
                                   lae +g+s st S+  +kL e+GLV+
  gi|121638668|ref|YP_978892.1| 37 LAERIGVSASTASESIRKLAEQGLVD 62
                                   89***********************6 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.9e-06    0.0034      19      65 ..      30      76 ..      28      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                         HemN_C 19 eGldlaafeqrfgldleellaaaleklqeqGLLeldg.grlrltprGr 65
                                   ++++ + +++r+g++ + + ++ ++kl eqGL+ +++ g + lt+ Gr
  gi|121638668|ref|YP_978892.1| 30 DKVSTKMLAERIGVSASTASES-IRKLAEQGLVDHEKyGAVTLTDSGR 76
                                   78999**********8888777.*************999******998 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2      0.02        14       2      25 ..      34      61 ..      33      77 .. 0.77
   2 !    8.5   0.0    0.0024       1.6       2      23 ..     162     183 ..     161     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                                   HHHHHHHHTTTHHH....HHHHHHTTSS CS
                           MerR  2 IgevAeltGvsprt....LRyYEreGLi 25
                                   ++ +Ae+ Gvs++t    +R + ++GL+
  gi|121638668|ref|YP_978892.1| 34 TKMLAERIGVSASTasesIRKLAEQGLV 61
                                   6889*********966666777777766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                                    HHHHHHHHTTTHHHHHHHHHTT CS
                           MerR   2 IgevAeltGvsprtLRyYEreG 23 
                                    +g vA++++  p++LRy  ++G
  gi|121638668|ref|YP_978892.1| 162 TGTVARISDADPQMLRYFASIG 183
                                    699**************88888 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.4e-06    0.0044      27      55 .]      33      61 ..      20      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                         HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                   s + la+r g+s +T+s  i++L++ G++
  gi|121638668|ref|YP_978892.1| 33 STKMLAERIGVSASTASESIRKLAEQGLV 61
                                   8899***********************85 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.013      20      49 ..      33      62 ..      26      65 .. 0.90
   2 ?   -0.6   0.1       1.7   1.2e+03      36      42 ..      86      92 ..      67      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                   BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                   + + lA+r+g++ St++  ++ L e+G+v 
  gi|121638668|ref|YP_978892.1| 33 STKMLAERIGVSASTASESIRKLAEQGLVD 62
                                   5678************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                   HHHHHHH CS
                       HTH_IclR 36 hRlLqtL 42
                                   hRlL t+
  gi|121638668|ref|YP_978892.1| 86 HRLLETF 92
                                   9999997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.5e-06    0.0038      17      68 ..      23      72 ..      13      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.5e-06
                                   HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEES CS
                           Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLa 68
                                    a+e ++ +vs++ +aer ++s+s ++  ++kL+++glv  ++   G ++L+
  gi|121638668|ref|YP_978892.1| 23 TAQEWSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHEK--YGAVTLT 72
                                   566667778******************************8764..4445555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.1e-05    0.0073       8      58 ..      17      68 ..      10      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHS-EEHHHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEETT CS
                Penicillinase_R  8 vmeilwekgeatvkevvee.leeekelaysTVktllrrLvkKgllsrekegr 58
                                    ++++w+++e + ++v ++ l+e+  ++ sT    +r+L ++gl+++ek g 
  gi|121638668|ref|YP_978892.1| 17 YLKVIWTAQEWSQDKVSTKmLAERIGVSASTASESIRKLAEQGLVDHEKYGA 68
                                   589*************99978888*************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.8e-05     0.013      13      43 ..      29      59 ..      26      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                         HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   ++++s + LAe+++vS +t    I++L e+g
  gi|121638668|ref|YP_978892.1| 29 QDKVSTKMLAERIGVSASTASESIRKLAEQG 59
                                   4559***********************9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     5e-05     0.035      19      41 ..      33      55 ..      30      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                  HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrL 41
                                   s + LAer+G+S+st+ + +r+L
  gi|121638668|ref|YP_978892.1| 33 STKMLAERIGVSASTASESIRKL 55
                                   7788*****************99 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.1e-05     0.035      57      87 ..      32      62 ..      15      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
                  Ribosomal_S25 57 itpsvvserlkingslArraLreleekglik 87
                                   +++ +++er+ +++s A + +r+l+e+gl+ 
  gi|121638668|ref|YP_978892.1| 32 VSTKMLAERIGVSASTASESIRKLAEQGLVD 62
                                   67899***********************996 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-05      0.04       8      76 ..      15      86 ..      10      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                        DUF2250  8 elalkvlkhlkkanvdY..aksiakeleipleevrellkkLeelGLlervegktikrteaklKkk.sevhkh 76
                                   +++lkv+  +++   d    k++a+++ ++ + ++e ++kL e GL+++ +  ++  t+  ++ + + v++h
  gi|121638668|ref|YP_978892.1| 15 QDYLKVIWTAQEWSQDKvsTKMLAERIGVSASTASESIRKLAEQGLVDHEKYGAVTLTDSGRRAAlAMVRRH 86
                                   567888888888888853379**************************9999877777776666551334444 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0016       1.1      16      46 ..      26      60 ..      18      63 .. 0.76
   2 ?    1.5   0.0      0.41   2.9e+02       4      35 ..      82     116 ..      79     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                         HTH_23 16 e....GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   e    + s++  A++ gvs +T +  +++ +e Gl
  gi|121638668|ref|YP_978892.1| 26 EwsqdKVSTKMLAERIGVSASTASESIRKLAEQGL 60
                                   3444689999**************66666678887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.41
                         HTH_23   4 ereRlrillllae...GlsvreIAreLgvsrrTvy 35 
                                    +++R r l  +++   G+++ e+ +e  v ++ v+
  gi|121638668|ref|YP_978892.1|  82 MVRRHRLLETFLVnelGYRWDEVHDEAEVLEHAVS 116
                                    7899999999997889******9999888777777 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00028      0.19      33      80 ..      28      73 ..      10      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                        DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqte 80
                                    + k +++ la+r++  +sa+ ++++++ L + gl++ ++ g +  t+
  gi|121638668|ref|YP_978892.1| 28 SQDKVSTKMLAERIG--VSASTASESIRKLAEQGLVDHEKYGAVTLTD 73
                                   556678899******..********************99998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1603.53
//
Query:       gi|121638669|ref|YP_978893.1|  [L=410]
Description: acyl-CoA dehydrogenase fadE21 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-43  147.3   4.3    5.8e-43  146.7   4.3    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.6e-22   78.0   0.0    9.2e-22   77.1   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.3e-14   54.7   0.3    2.4e-14   53.7   0.3    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    6.7e-10   39.6   0.7    5.1e-09   36.8   0.3    2.5  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   4.3   1.3e-46   5.8e-43       1     149 [.     253     402 ..     253     403 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 1.3e-46
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G + a  ++++eRl+va+++lg+++++ + +++ya++r+  g+ ++++ql++ kla+m++    ++++v++a+e+l+a
  gi|121638669|ref|YP_978893.1| 253 GDGRDSARANFAVERLGVALMSLGIINECHRLCVDYAKTRTLWGRNIGQFQLIQLKLAKMEVARINVQNMVFQAIERLKA 332
                                    689999************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    gk+   aeas++Kl+ se+a++va +a+ql+Gg+Gy++ey+ve+l+rda++l i++G++e+q   ia++l
  gi|121638669|ref|YP_978893.1| 333 GKQLtLAEASAIKLYSSEAATDVAMEAVQLFGGNGYMAEYRVEQLARDAKSLMIYAGSNEVQVTHIAKGL 402
                                    **9989*************************************************************987 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   2.1e-25   9.2e-22       1      97 []     140     241 ..     140     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.1e-25
                                    EEE---SS-SS-.GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE....TS---...----EEEEEEE..GGG CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsd.vasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar....tekpd...rarglslflvprdapg 72 
                                    a a+TEp++Gsd   ++kt  ++rdg++y+lnG+K++itn+++a++++v+a+    +  p+   r+r + +f++++++pg
  gi|121638669|ref|YP_978893.1| 140 AWAITEPDSGSDaFGGMKT-HVTRDGEDYILNGHKTFITNGPYADVLVVYAKladgE--PAsdwRNRPVLVFVLDAGMPG 216
                                    569*********4466676.89******************************98533..335799*************** PP

                                    EEE-----BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  73 vsvrrieeklGlrglptgelvfedv 97 
                                    ++ ++  +k+G+++ ptgel+f++v
  gi|121638669|ref|YP_978893.1| 217 LTQGKPFKKMGMMSSPTGELFFDNV 241
                                    ***********************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.3   5.4e-18   2.4e-14       1     133 [.     268     391 ..     268     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 5.4e-18
                                    .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    lg+a + lG+   +    v++a++r+    g+++ +++ +ql+la+++ +    + ++ +a++r     +agk++   + 
  gi|121638669|ref|YP_978893.1| 268 LGVALMSLGIINECHRLCVDYAKTRTL--WGRNIGQFQLIQLKLAKMEVARINVQNMVFQAIER----LKAGKQL---TL 338
                                    57999**********************..***********************************....99****8...99 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    aea++ +++ +e a++++ ++++++Gg+++ +e++++ l RDa+ + ++a+ n
  gi|121638669|ref|YP_978893.1| 339 AEASAIKLYSSEAATDVAMEAVQLFGGNGYMAEYRVEQLARDAKSLMIYAGSN 391
                                    **********************************************9999876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.3   1.1e-12   5.1e-09       2     111 ..       6     134 ..       5     136 .. 0.76
   2 ?   -3.0   0.0       2.6   1.2e+04      58      86 ..     255     283 ..     252     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.1e-12
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHH.HHTTCTSTTS-...GGGTS--S...............-HH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkkl.aelGllgitvp...eeygGagl...............dyl 62 
                                    ++  ++rd+vr+f+++e++ph +  ++ +  p+ + +kl  + Gl  +      +   G  +               ++ 
  gi|121638669|ref|YP_978893.1|   6 DTDLMVRDAVRQFIDKEIRPHQDALETGELSPYPIARKLfSQFGLDVLLAEsvnQMLDGERAkrekrdssgsfgladQAS 85 
                                    66789***************999998666556667666645666633333333355555443555566666666664588 PP

                                    HHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHT CS
                  Acyl-CoA_dh_N  63 eaaivaeelaradaglalllgvhsslvapailrfGteeqkrryLpklas 111
                                      a+++ ela +++gl ++++v+ +l+a +i+  Gt +q++r++p l++
  gi|121638669|ref|YP_978893.1|  86 MVAVLVSELAGVSIGLLSTVAVSLGLGAATIMSRGTLAQQERWVPTLVT 134
                                    99999**********999***************************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                    -S-HHHHHHHHHHHHHH-HHHHHHHHHHH CS
                  Acyl-CoA_dh_N  58 gldyleaaivaeelaradaglalllgvhs 86 
                                    g d   a  ++e l+ a ++l+++  +h 
  gi|121638669|ref|YP_978893.1| 255 GRDSARANFAVERLGVALMSLGIINECHR 283
                                    55666666788888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2993.50
//
Query:       gi|121638670|ref|YP_978894.1|  [L=401]
Description: lipid-transfer protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-22   80.1   0.0    2.5e-21   76.2   0.0    2.5  2  Thiolase_N       Thiolase, N-terminal domain
    3.9e-10   39.5   0.0    1.3e-09   37.8   0.0    1.9  1  Thiolase_C       Thiolase, C-terminal domain
    3.3e-06   26.9   0.9    6.6e-05   22.6   0.9    2.4  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
      0.002   17.9   0.2       0.21   11.4   0.1    2.6  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
      0.011   14.4   0.0       0.02   13.6   0.0    1.3  1  SpoVAD           Stage V sporulation protein AD (SpoVAD)
       0.06   13.1   0.0        0.1   12.4   0.0    1.3  1  DSBA             DSBA-like thioredoxin domain
       0.11   12.6   0.1        4.3    7.4   0.0    2.8  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   9.6e-25   2.5e-21       1     260 []      10     234 ..      10     234 .. 0.88
   2 ?    0.9   0.0     0.094   2.4e+02       3      45 ..     248     292 ..     246     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 9.6e-25
                                    EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEEE CS
                     Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqniarqaalkagipeevpav 79 
                                    v++++  +t++ k  g  +   + ++++e ++++l +ag+d+ ev++ +vG v  +  +gq     a  ++g+   +p v
  gi|121638670|ref|YP_978894.1|  10 VYVIGVGMTKFEK-PGRREGWDYPDMARESGTKALRDAGIDYREVEQGYVGYVYGEsTSGQ----RALYELGM-TGIPIV 83 
                                    799**********.9**************************************98755555....67889999.999*** PP

                                    EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                     Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlta 159
                                     vn+ cs g +a++l+aq+i+ g ad+v+a G E+m        +d r++    + ka      d     +   + G ++
  gi|121638670|ref|YP_978894.1|  84 NVNNNCSTGSTALYLGAQAIRGGLADCVLALGFEKMQPGALGGGADDRESPLGRHVKAL--AEIDEFGFPVAPWMFGAAG 161
                                    ************************************98888887666544333333333..323334445577899**** PP

                                    HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS- CS
                     Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtv 239
                                    ++  kky+ + e+ ++   k+h+++++++ a+ F+de               + d+ + s++  ++L kl          
  gi|121638670|ref|YP_978894.1| 162 REHMKKYGTTAEHFAKIGYKNHKHSVNNPYAQ-FQDEY--------------TLDDILASKMISDPLTKL---------- 216
                                    ********************************.***98..............89****************.......... PP

                                    BTTSB--BEEEEEEEEEEEHH CS
                     Thiolase_N 240 tAgnasqisDGaaavllmses 260
                                       ++s+ sDG+aav+l+se+
  gi|121638670|ref|YP_978894.1| 217 ---QCSPTSDGSAAVVLASED 234
                                    ...9**************996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.094
                                    EEEEEE.E--EE.TTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGC CS
                     Thiolase_N   3 ivsaar.tpigk.fggslkdlsaeeLlaealkallekagvdpeev 45 
                                    iv+ a+ t + + f gs +++   ++  +a++++ ++ g+ p++ 
  gi|121638670|ref|YP_978894.1| 248 IVGQAMtTDFAStFDGSARNIIGYDMTVQAAQRVYQQSGLGPKDF 292
                                    6665551689999***********************999999876 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0     5e-13   1.3e-09      25     106 ..     275     374 ..     260     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5e-13
                                    HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHH CS
                     Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasG 86 
                                    + a+++v ++ gl  +d  ++E+++ F+a  L   +al+l                      vN  GG i+ GHPlGa+G
  gi|121638670|ref|YP_978894.1| 275 VQAAQRVYQQSGLGPKDFGVIELHDCFSANELLLYEALGLCGpgeapeliddnqttyggrWVVNPSGGLISKGHPLGATG 354
                                    6799************************************9999**************9999****************** PP

                                    HHHHHHHHHHHHHCTTSEEE CS
                     Thiolase_C  87 aRivvtllselkkeggklgv 106
                                      +++ l+ +l+   +   v
  gi|121638670|ref|YP_978894.1| 355 LAQCAELTWQLRGTAEARQV 374
                                    *****999999865544444 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.9   2.6e-08   6.6e-05     131     207 ..      42     120 ..      12     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.6e-08
                                    HHHHHTT.GGGSCTTHHHHHSTTHHHH.HHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                  ketoacyl-synt 131 aldedgs.evkaspkavgavlanviag.risyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                    al+++g  ++++    vg+v    ++g r  y+lg++G p v v   Cs++ +a+ +  q++r g ad++la G e  ++
  gi|121638670|ref|YP_978894.1|  42 ALRDAGIdYREVEQGYVGYVYGESTSGqRALYELGMTGiPIVNVNNNCSTGSTALYLGAQAIRGGLADCVLALGFEK-MQ 120
                                    444444444444444455544444444166678*****6677899*****************************994.44 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   8.3e-05      0.21       3      37 ..      85     119 ..      83     122 .. 0.93
   2 ?    3.8   0.0     0.021        53      41      65 ..     210     234 ..     203     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEG CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetl 37 
                                    +n++Cs+  +al + +++i+ g a +vL  g e++
  gi|121638670|ref|YP_978894.1|  85 VNNNCSTGSTALYLGAQAIRGGLADCVLALGFEKM 119
                                    89**************************9998886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                                    S-TTTHHHHTTB-EEEEEEEEEEES CS
                    ACP_syn_III  41 lDwkdrstavlfGDGAgAvvlease 65 
                                     D+  + ++   +DG +Avvl  ++
  gi|121638670|ref|YP_978894.1| 210 SDPLTKLQCSPTSDGSAAVVLASED 234
                                    5666778888899********9873 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-06      0.02      54     130 ..      34     113 ..      23     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-06
                                    HHHHHHHHHHHHTT--GGG-SEEEEEESSGGGHHHHHHHHHH...---EEEB--GGGHHHHHHHHHHHHHHTTS-SEEEE CS
                         SpoVAD  54 lleeavkkalkkanlkkedidfllaGDLlnqlisssfaarel...kiPflglygaCstsaeslalaallvdggfakrvla 130
                                    + +e+ +kal+ a+++  +++    G +    +s + a  el   +iP + +   Cst + +l l+a ++ gg+a+ vla
  gi|121638670|ref|YP_978894.1|  34 MARESGTKALRDAGIDYREVEQGYVGYVYGESTSGQRALYELgmtGIPIVNVNNNCSTGSTALYLGAQAIRGGLADCVLA 113
                                    67778888999999999999998999999988888777766522279******************************998 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05       0.1     128     187 ..      41      98 ..      31     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                                    HHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHH CS
                           DSBA 128 evaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldt 187
                                    +++++aG+d  e+++ + +  ++e  + + +a ++lg+tG+P+v v++    +G++ l  
  gi|121638670|ref|YP_978894.1|  41 KALRDAGIDYREVEQGYVGYVYGESTSGQ-RALYELGMTGIPIVNVNNN-CSTGSTALYL 98 
                                    7899******************9998876.67799************98.8888876655 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   3.1e+03      29      45 ..      38      54 ..      31      59 .. 0.82
   2 ?    7.4   0.0    0.0017       4.3      24      51 ..     272     299 ..     246     303 .. 0.72
   3 ?    1.5   0.0      0.11   2.9e+02      88     107 ..     347     366 ..     345     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                   HHHHHHHHHT--GGGEE CS
                Ketoacyl-synt_C 29 aiekalaeagvdpedvd 45
                                     +kal++ag+d ++v+
  gi|121638670|ref|YP_978894.1| 38 SGTKALRDAGIDYREVE 54
                                   5689*******999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                                    HHHHHHHHHHHHHHT--GGGEEEEE-SS CS
                Ketoacyl-synt_C  24 eaqaraiekalaeagvdpedvdyveahg 51 
                                    +   +a +++++++g+ p+d +++e h+
  gi|121638670|ref|YP_978894.1| 272 DMTVQAAQRVYQQSGLGPKDFGVIELHD 299
                                    4456799********************7 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.11
                                    -B-GGGHHHHHHHHHHHHHH CS
                Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalk 107
                                    GH ++A G+a+++ +  +l+
  gi|121638670|ref|YP_978894.1| 347 GHPLGATGLAQCAELTWQLR 366
                                    9**********999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2575.85
//
Query:       gi|121638671|ref|YP_978895.1|  [L=459]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-29  101.4   0.4    3.5e-29  101.4   0.4    1.7  2  OrfB_IS605      Probable transposase
      7e-15   54.7   0.4    1.5e-14   53.7   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.7e-11   41.3   0.1    1.7e-10   40.2   0.1    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.5   8.9e+03      71      87 ..     168     184 ..     164     187 .. 0.60
   2 !  101.4   0.4   5.9e-33   3.5e-29       4     117 ..     205     320 ..     200     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                     OrfB_IS605  71 kkasrklarlhrkrsrr 87 
                                    ++ +r++ rl +k + r
  gi|121638671|ref|YP_978895.1| 168 HENTRRVERLIAKGRSR 184
                                    45566777776665544 PP

  == domain 2  score: 101.4 bits;  conditional E-value: 5.9e-33
                     OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtw..flykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                    v+ +++++++++++++g+D+G+++Latv+t dg+    ++++r+l++++ +l+   +  ++++k+s++y++++++++rlh
  gi|121638671|ref|YP_978895.1| 205 VQRPQQPKVTDPGSRVGVDVGVRRLATVATADGAVleRVPNPRPLDAALNELRHVCRARSRCTKGSRRYRERTTEISRLH 284
                                    44455699***************************99******************************************* PP

                     OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                    r++++ r+h+lh l+thl+kt+ +++ve L+ ++m 
  gi|121638671|ref|YP_978895.1| 285 RRVNDVRTHHLHCLTTHLAKTHGRIVVEGLDAAGML 320
                                    **********************************98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.4   2.5e-18   1.5e-14       6      68 ..     345     407 ..     341     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.5e-18
                 OrfB_Zn_ribbon   6 eqleykakeyGikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                    + l+yk  +yG +++++++++ +SktC++Cg++++     + ++C++C ++++rD  AaiN+++
  gi|121638671|ref|YP_978895.1| 345 RHLSYKTGWYGSQLVVADRWFpSSKTCHVCGHVQEI-GWAEHWQCDSCSASHQRDDCAAINLAR 407
                                    679*********************************.9999*********************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   2.9e-14   1.7e-10       1      39 [.      11      48 ..      11      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.9e-14
                 HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerk 39
                                   M  +a+++ l PT eQ+++lar+fG+ R +YN+  a  k
  gi|121638671|ref|YP_978895.1| 11 M-VQAFRFTLDPTAEQARALARHFGARRKAYNWTVATLK 48
                                   6.68*****************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3044.81
//
Query:       gi|121638672|ref|YP_978896.1|  [L=193]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-17   63.2   3.4    3.5e-17   62.9   3.4    1.1  1  Resolvase  Resolvase, N terminal domain
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.071   13.3   0.0    1.6  1  HTH_17     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   3.4   3.9e-21   3.5e-17       2     143 ..      53     189 ..      52     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 3.9e-21
                                    EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                      Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                    ++YaRvS+++q+ +l+rQ+++++a+a+ +++ ++k++++   S+ + +R+++ +ll++ +    + +vve+ dR+ R  +
  gi|121638672|ref|YP_978896.1|  53 AVYARVSSADQKPDLDRQVARVTAWATTEQIAVDKVVTEV-GSALNGHRRKFLALLRDPSV---KRIVVEHRDRFCRFGS 128
                                    79***************************999999*****.*****99*999999998888...899************* PP

                                    S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHH.HHHHHHCT-TTHHHHHHHH CS
                      Resolvase  82 dlltlleelrekgvslvsldegidtstpm.grlllqilaalaef.erelirertkeglaaakak 143
                                    ++++    l+++g +lv++d+  + +++  + ++  + +++a++  ++  ++r k++laaa+++
  gi|121638672|ref|YP_978896.1| 129 EYVEA--ALAAQGRELVVVDS-AEVDDDLvRDMTEILTSMCARLyGKRAAQNRAKRALAAAAEE 189
                                    ****9..99999999999997.555566645555555566677635666778888899988876 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     8e-06     0.071      12      37 ..      11      38 ..       7      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-06
                         HTH_17 12 gvsrstvyrlirrgelpaa...kiGrrwr 37
                                   gv r t+yr+ ++g l ++   k Gr ++
  gi|121638672|ref|YP_978896.1| 11 GVARVTAYRWFHAGLL-PVparKAGRLIL 38
                                   99************99.554755666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1344.10
//
Query:       gi|121638673|ref|YP_978897.1|  [L=298]
Description: tRNA pseudouridine synthase B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-52  176.2   0.0    6.6e-52  175.8   0.0    1.2  1  TruB_N         TruB family pseudouridylate synthase (N termin
    1.9e-22   78.8   3.3    6.5e-22   77.1   3.3    2.0  1  TruB_C         tRNA Pseudouridine synthase II, C terminal
    7.4e-13   48.4   1.3    1.7e-12   47.3   1.3    1.6  1  TruB_C_2       tRNA pseudouridylate synthase B C-terminal dom
  ------ inclusion threshold ------
      0.026   14.6   0.2      0.046   13.8   0.2    1.4  1  DKCLD          DKCLD (NUC011) domain
       0.34    9.1   1.3       0.43    8.8   1.3    1.1  1  Peptidase_A21  Peptidase family A21


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.0   1.8e-55   6.6e-52       1     149 []      27     179 ..      27     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.8e-55
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHH CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleev 80 
                                    +r++ +++vGh+GtLDp+atGvLv+++++aTk+l  l+ a+K+Y atirlg++t+teDaeg++l++  +++lt e+++++
  gi|121638673|ref|YP_978897.1|  27 RRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAA 106
                                    89****************************************************************88************ PP

                                    HHHC-EEE---------------------------------EEEEEEEEEEEEEE....EEEEEEEESTTTTH CS
                         TruB_N  81 lkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep....evelevecskGtYi 149
                                    +++++Gei+qvp+ +SA+kv G+r+y+lar+g +v++++r+++i+++ell+ +++    ++++e++cs+GtYi
  gi|121638673|ref|YP_978897.1| 107 MERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRdqliDIDVEIDCSSGTYI 179
                                    ****************************************************98889999************9 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   3.3   1.8e-25   6.5e-22       1      56 []     236     291 ..     236     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.8e-25
                                    SEEEE--HHHHHHHHTT---B-----S-EEEE-TTS-EEEEEEEETTEEEEEEESS CS
                         TruB_C   1 FprrdvteaeArdlrhGrrLeaagikgvvAaiaPdGrliALleerggrarsvvVfr 56 
                                    F+rrd+t+aeA++ ++Gr L+a+gi+gv+Aa+++dGr+iALl+++g r+rsv+V+r
  gi|121638673|ref|YP_978897.1| 236 FARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLR 291
                                    99****************************************************97 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   1.3   4.6e-16   1.7e-12       1      42 [.     180     221 ..     180     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.6e-16
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHH CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLeda 42 
                                    R L++D+G aLg+g+hv++LRRtrvg f+ +++ +l+dL++ 
  gi|121638673|ref|YP_978897.1| 180 RALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAER 221
                                    99*************************************984 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.3e-05     0.046      42      58 .]       7      23 ..       5      23 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                   EEEEEEE-SSS-HHHHH CS
                          DKCLD 42 GvinLDKPsnPsSHEVV 58
                                   G++ +DKP++ +SH+VV
  gi|121638673|ref|YP_978897.1|  7 GIVVIDKPAGMTSHDVV 23
                                   99**************9 PP

>> Peptidase_A21  Peptidase family A21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.3   0.00012      0.43     598     647 ..      85     136 ..      64     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHCHH..TTTTCC-SC-SSTTSS-SC-HHCHHHHHHHCCHCCHHH CS
                  Peptidase_A21 598 atasvikgvaea..avgavqsaleklegavksvrgkvaaRlvGsikaRraRr 647
                                    a   v+++v  +   ++a+++a+e+l g ++ v+ +v+a +vG+ +a r  r
  gi|121638673|ref|YP_978897.1|  85 AEGQVLQSVPAKhlTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLAR 136
                                    45567777754322689**************************988755333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2241.37
//
Query:       gi|121638674|ref|YP_978898.1|  [L=227]
Description: hypothetical protein BCG_2812c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-25   88.1   0.0    7.3e-25   86.9   0.0    1.6  1  4PPT_N    4'-phosphopantetheinyl transferase N-terminal domai
    5.2e-10   39.5   0.0    8.9e-10   38.7   0.0    1.3  1  ACPS      4'-phosphopantetheinyl transferase superfamily


Domain annotation for each model (and alignments):
>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   8.1e-29   7.3e-25       1      67 [.      36     102 ..      36     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 8.1e-29
                         4PPT_N   1 eeeelirkavakRkaeFlaGRicAraalarlgleavpllsgerraPlwpaglvgSIsHtdglaaAav 67 
                                    ee+ li+++vakR++eF++ R+cAr al +lg +++p+l+g++++P wp+g+vgS++H++g+  A+v
  gi|121638674|ref|YP_978898.1|  36 EEAPLIARSVAKRRNEFITVRHCARIALDQLGVPPAPILKGDKGEPCWPDGVVGSLTHCAGYRGAVV 102
                                    68889************************************************************99 PP

>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   9.9e-14   8.9e-10       1      83 [.     110     184 ..     110     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 9.9e-14
                                    EEEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTTS-SSSS--GGG-EEEE- CS
                           ACPS   1 gvGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKalgpglrklldfksievled 80 
                                    +vGiD e    ++      ++++l+ i  ++Er+   ++  +a  ++   l++aKEA +Ka++p  +++l+f++++++ +
  gi|121638674|ref|YP_978898.1| 110 SVGIDAE---PHD----VLPNGVLDAISLPAERADMPRTMPAAL-HWDRILFCAKEATYKAWFPLTKRWLGFEDAHITFE 181
                                    69*****...555....48899**************99777776.7****************************887776 PP

                                    TTS CS
                           ACPS  81 stg 83 
                                     ++
  gi|121638674|ref|YP_978898.1| 182 TDS 184
                                    554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1723.29
//
Query:       gi|121638675|ref|YP_978899.1|  [L=324]
Description: hypothetical protein BCG_2813c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-13   52.0   0.0    2.7e-13   50.9   0.0    1.6  1  Metallophos    Calcineurin-like phosphoesterase
    0.00018   21.7   0.0      0.027   14.6   0.0    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0     3e-17   2.7e-13       2     204 .]      16     250 ..      15     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3e-17
                                    EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.H CS
                    Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee.e 80 
                                    +++ i+DlH   + g+ + ++ l+   +++   d++++aGD+ +r+d   + l+ll++ ++   +v++++GNHe ++  +
  gi|121638675|ref|YP_978899.1|  16 TLWAISDLH-TGHLGNKPVAESLY---PSS-PDDWLIVAGDVAERTDEIRWSLDLLRRRFA---KVIWVPGNHE-LWTtN 86 
                                    6799*****.88888888888888...333.88*************999988888999999...9*********.55545 PP

                                    HHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE........................THHHHHH CS
                    Metallophos  81 llnkygylgif.sepwrsdaevfnnlplaslgsgs.lkvlllhGgspel........................lvsldkl 134
                                      + + +       + +++    + + ++     + + v++  Gg++ +                        + +  ++
  gi|121638675|ref|YP_978899.1|  87 RDPMQIFGRARyDYLVNMC----DEMGVVT--PEHpFPVWTERGGPATIvpmfllydysflpeganskaegvaIAKERNV 160
                                    5555554443334444444....3333333..112355555555522223333333333444445555566775555555 PP

                                    HHHHHSCHHHHCC...HHHHHH........HHHHTTCSEEEEEESSESS.........CSSSCSCCHHHHHHHHHHTTES CS
                    Metallophos 135 gslnleleapepg...dewlkd........lekrekadwvivlgHsply.........rgsgylfgdealedllkkygvd 194
                                       + +l +pep    d w ++        le+ +  +++++++H pl             + + g   ++d+  +y++ 
  gi|121638675|ref|YP_978899.1| 161 VATDEFLLSPEPYptrDAWCHErvaatrarLEQLDWMQPTVLVNHFPLLrqpcdalfyPEFSLWCGTTKTADWHTRYNAV 240
                                    5555555555555676777777777777777777777779**********999999999999999999999********* PP

                                    EEEEESSSSE CS
                    Metallophos 195 lvisGHtHvy 204
                                      ++GH H +
  gi|121638675|ref|YP_978899.1| 241 CSVYGHLHIP 250
                                    ********85 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.1e-06     0.027       4      63 ..      18      86 ..      16     117 .. 0.66
   2 !    5.2   0.0    0.0025        22     118     157 ..     238     279 ..     181     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                  Metallophos_2  4 aiiSDlHsnldaleavlealkevgv.daiihaGDl.eeeepe..vleellela.pvlaVrGNnD....e 63
                                    +iSDlH      + v+e l   ++ d +i+aGD+ e ++    +l+ l++++ +v+ V+GN++    +
  gi|121638675|ref|YP_978899.1| 18 WAISDLHTGHLGNKPVAESLYPSSPdDWLIVAGDVaERTDEIrwSLDLLRRRFaKVIWVPGNHElwttN 86
                                   589****6666666666666665552689999**94222221345555555559**********44330 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0025
                  Metallophos_2 118 gsdvvvcGHtHvpevekeggvlv..vnPGsvgeprdgdpety 157
                                    ++ + v+GH H+p+ +  +gv++  v  G ++e r ++p ++
  gi|121638675|ref|YP_978899.1| 238 NAVCSVYGHLHIPRTTWYDGVRFeeVSVGYPREWRRRKPYSW 279
                                    444789********9999999774456676666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2339.19
//
Query:       gi|121638676|ref|YP_978900.1|  [L=187]
Description: lipoprotein lppV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-55  187.6   0.0    1.5e-55  187.3   0.0    1.1  1  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.0   8.4e-60   1.5e-55       5     152 ..      31     176 ..      28     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 8.4e-60
                                    HHHH.HHHHHHHHHHHGGG--HHHHHHHHHHHHHHHHHHHHHHSTT--EEE---HHHH-EESSS-TTTEEE-B---EEES CS
                           LppA   5 ealtskeevaeaedelrqkPslEeaeeqleallariadaisalvpgltWktdedrsrngCedpyeetdgrrvalesvvsa 84 
                                    e++ s+e+vae+e+ lr+kP lE+a++q++a+++++a+ai+alvpgltW+td+d++ +gC+++ye+t+++ +++ ++v++
  gi|121638676|ref|YP_978900.1|  31 EGPLSPEKVAELENPLRAKPPLEDAKDQYRAAVTQLANAITALVPGLTWRTDMDTW-TGCGGEYEWTRAKAAYF-MIVFS 108
                                    67899***************************************************.*****************.***** PP

                                    S---HHHHHHHHHHHHHHHHTTT--EEE-S-BSSS-EEEEEEET.TEEEEEEESSSEEEEEE---EE- CS
                           LppA  85 gpipddqWpqaleiVrelAakygatevevfkDepgdhdvrftgpeGgeiklgtakaavltittgCrLp 152
                                    gpipdd+W qa++iV++ ++++gat+++v+k++p+dhdv+f+g++G+e+k++t+kaavlt++++Cr++
  gi|121638676|ref|YP_978900.1| 109 GPIPDDKWLQAVQIVKDGVEQFGATGFGVMKNKPADHDVYFAGHGGVEFKFSTQKAAVLTAQSDCRIS 176
                                    ******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1261.64
//
Query:       gi|121638677|ref|YP_978901.1|  [L=562]
Description: hypothetical protein BCG_2815c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-77  258.3   3.7    2.9e-77  258.3   3.7    2.5  2  Abhydrolase_8  Alpha/beta hydrolase
      2e-06   27.9   0.1    0.00085   19.3   0.0    2.4  2  Cutinase       Cutinase
    4.8e-05   23.1   0.1    8.5e-05   22.3   0.1    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00051   19.4   0.0    0.00095   18.5   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0013   19.1   1.7     0.0013   19.1   1.7    2.1  2  Nnf1           Nnf1
     0.0055   16.3   0.0       0.01   15.3   0.0    1.4  1  DUF900         Alpha/beta hydrolase of unknown function (DUF9
     0.0057   16.5   0.0      0.012   15.5   0.0    1.5  1  Lipase_3       Lipase (class 3)
     0.0058   16.8   2.0     0.0064   16.6   0.1    1.9  2  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.024   14.2   0.1    1.3  1  DUF2974        Protein of unknown function (DUF2974)
      0.021   15.2   3.7       0.13   12.7   3.0    2.5  3  ZapB           Cell division protein ZapB
       0.34   11.2   2.2        7.1    6.9   0.1    2.5  2  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
       0.39   10.5   3.7       0.61    9.9   0.2    2.6  3  DivIC          Septum formation initiator
       0.43    9.9  10.6        2.5    7.4  10.4    2.1  1  DUF4407        Domain of unknown function (DUF4407)
        2.9    7.9   5.1          7    6.7   1.1    2.5  2  DUF2205        Short coiled-coil protein


Domain annotation for each model (and alignments):
>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2      0.39     5e+02      23     103 ..     115     211 ..      99     219 .. 0.59
   2 !  258.3   3.7   2.3e-80   2.9e-77       1     178 []     277     466 ..     277     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                  Abhydrolase_8  23 VtvpGvdttlrrtlatmvaearglraeaaaae..eaagkpesvAviAWlgYeaP...............agaskevatdd 85 
                                    V +pG+ +t  +  +t  +++ +l+ae+ a+    +a   e   ++  ++ +aP                +++   a+++
  gi|121638677|ref|YP_978901.1| 115 VPIPGLRSTEAQWARTLAKQT-ELQAELDAIMaeANAVDEELASAVNMADGDAPipadsgppvgpegltPTQLASDANEE 193
                                    778999988766555544443.4444443333002233333444566677777766666666666655544555555556 PP

                  Abhydrolase_8  86 rAaagAaeLnallrdlra 103
                                    r ++  a+L+a l+ l+a
  gi|121638677|ref|YP_978901.1| 194 RLREERARLQAHLERLQA 211
                                    666666666666666666 PP

  == domain 2  score: 258.3 bits;  conditional E-value: 2.3e-80
                  Abhydrolase_8   1 DpagkvlaavavGdldrAerVsVtvpGvdttlrrtlatmvaearglraeaaaaeeaagkpesvAviAWlgYeaP...... 74 
                                    Dp+++vlaavavG++d+A++VsVtvpGv++t+r++l++mv+ear+lr+e++++ +aagkp+svA+iAW+gY++P      
  gi|121638677|ref|YP_978901.1| 277 DPNQQVLAAVAVGNPDTAANVSVTVPGVGSTTRGALPGMVTEARDLRSEVIRQLNAAGKPASVATIAWMGYHPPpnpldt 356
                                    9******************************************************************************* PP

                  Abhydrolase_8  75 ..agaskevatddrAaagAaeLnallrdlratsvpgqhlallgHSYGSlvaslAldd....aaseVsdvvlyGSPGleae 148
                                      ag++++++td++A+agAa+L+++l+++ra++ p++hl++lgHSYGSl+aslAl+d    +a++V+dvv+yGSPGle++
  gi|121638677|ref|YP_978901.1| 357 gsAGDLWQTMTDGQAHAGAADLSRYLQQVRANN-PSGHLTVLGHSYGSLTASLALQDldaqSAHPVNDVVFYGSPGLELY 435
                                    **9*****************************9.***********************99999****************** PP

                  Abhydrolase_8 149 saakLgledarvfvmrgadDlienv.pelaa 178
                                    s+a+Lgl++++++vm++++Dli+n+ ++la+
  gi|121638677|ref|YP_978901.1| 436 SPAQLGLDHGHAYVMQAPHDLITNLvAPLAP 466
                                    ************************9899875 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0083        11     101     133 ..     265     302 ..     255     328 .. 0.77
   2 !   19.3   0.0   6.6e-07   0.00085      53     122 ..     366     430 ..     358     457 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0083
                                    .........S-HHHHHHEEEEEEES-TTCCCCTTS-TT CS
                       Cutinase 101 a.....tatlpaavadkvaavvlfGdpsnvaglpevsk 133
                                          + ++p++ +++v a+v  G+p+++a+++   +
  gi|121638677|ref|YP_978901.1| 265 PetyltQLQIPEDPNQQVLAAVAVGNPDTAANVSVTVP 302
                                    344444555999*****************999985555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.6e-07
                                    STTSS-HHHHHHHHHHHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.....S-HHHHHHEEEEEEES-T CS
                       Cutinase  53 lyegseeagakeaaalvqslaskCPdtkivlgGYSqGaqvidnaieggatatlpaavadkvaavvlfGdp 122
                                    + +g+++aga+++++ +q++ ++ P  ++ ++G S G+  +  a+++     l+a++a  v  vv++G p
  gi|121638677|ref|YP_978901.1| 366 MTDGQAHAGAADLSRYLQQVRANNPSGHLTVLGHSYGSLTASLALQD-----LDAQSAHPVNDVVFYGSP 430
                                    5678899****************************************.....****************99 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   6.7e-08   8.5e-05      54     106 ..     362     429 ..     298     452 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.7e-08
                                    H...........SHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHH....GGGEEEEEEESE CS
                  Abhydrolase_1  54 y...........gtasvaddldrildalgddkltlvGhSmGGmialayaaey....perVkalvllga 106
                                                g a++ ++l+++++  + ++lt++GhS+G+++a+ ++++      ++V+ +v+ g+
  gi|121638677|ref|YP_978901.1| 362 LwqtmtdgqahaGAADLSRYLQQVRANNPSGHLTVLGHSYGSLTASLALQDLdaqsAHPVNDVVFYGS 429
                                    0444444444448899*********************************9998888888888888887 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.4e-07   0.00095      60      97 ..     376     413 ..     370     441 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.4e-07
                    Hydrolase_4  60 dDlaafvekvkeehpelplfllGhSmGGliallyllry 97 
                                    +Dl+ ++++v++++p   l++lGhS G+l+a l+l++ 
  gi|121638677|ref|YP_978901.1| 376 ADLSRYLQQVRANNPSGHLTVLGHSYGSLTASLALQDL 413
                                    7********************************99653 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.7     1e-06    0.0013      17     102 ..     136     217 ..     120     223 .. 0.76
   2 ?   -3.3   0.1         9   1.1e+04      33      41 ..     249     257 ..     236     281 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                                    HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHCCHH-T................TTSSTTTHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  17 siraefeeIleerdvvekLneLDdlieeAkerreegeeeasrpe......vpphtLpPeeliaahlapakkeeqeeLear 90 
                                    + +ae+++I+ e + v++  eL   ++ A   ++         +      v p+ L+P++l++    + ++ee+++L+a+
  gi|121638677|ref|YP_978901.1| 136 ELQAELDAIMAEANAVDE--ELASAVNMADGDAPI--------PadsgppVGPEGLTPTQLASDANEERLREERARLQAH 205
                                    456666666666666663..666666666655543........0344444999*************************** PP

                                    HHHHHHHHHHHH CS
                           Nnf1  91 lqeleaenaela 102
                                    l++l+ae ++l 
  gi|121638677|ref|YP_978901.1| 206 LERLQAEYDQLS 217
                                    *******99986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9
                                    HHHHHHHHH CS
                           Nnf1  33 ekLneLDdl 41 
                                     +L eLD++
  gi|121638677|ref|YP_978901.1| 249 GRLGELDAV 257
                                    344444433 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.2e-06      0.01      73     122 ..     371     420 ..     358     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                         DUF900  73 aeasrdalekllrylatkksakkihllaHSmGtwlvlealrqlaieadep 122
                                    a+a +++l + l++++ +++  ++++l HS G+  +  al+ l ++  +p
  gi|121638677|ref|YP_978901.1| 371 AHAGAADLSRYLQQVRANNPSGHLTVLGHSYGSLTASLALQDLDAQSAHP 420
                                    6677899*************************************999864 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.2e-06     0.012      50     107 ..     377     432 ..     339     463 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.2e-06
                                    HHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHHHHTT-SS---EEEEEES---- CS
                       Lipase_3  50 qvlkelkrllekypeysivvtGHSLGgalAlLaaldlvengenekkkvtvvtfGqPrv 107
                                    ++ + l+++ +++p+  ++v GHS G+ +A+La  dl ++  +      vv +G+P  
  gi|121638677|ref|YP_978901.1| 377 DLSRYLQQVRANNPSGHLTVLGHSYGSLTASLALQDLDAQSAH--PVNDVVFYGSPGL 432
                                    56778899999999***********************999966..5667777888865 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         2   2.6e+03     134     174 ..      83     131 ..      27     164 .. 0.51
   2 !   16.6   0.1     5e-06    0.0064      53     103 ..     379     430 ..     364     441 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                    CCTTTHCCHHHHHHHHHHHHHHHHHTCCS........-TTSCSEHHCEE CS
                   Thioesterase 134 peelledeellsellpalradyraleqys........lrpeaaqklrat 174
                                    ++   + ++ l+ l +a++a+++++            lr+++aq++r+ 
  gi|121638677|ref|YP_978901.1|  83 ADGIVKVQSELAALRHAAAAAELTIDALInrvvpipgLRSTEAQWARTL 131
                                    4444444444444444444444444444445555444455555533332 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5e-06
                                    HHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHC.T-SEEEEEEESCC CS
                   Thioesterase  53 aeyaealrqiqpegPyalfGhSlGgllAfevArqLesq.Glavkslflidss 103
                                    ++y++++r+ +p g +++ GhS+G+l A  + + L +q +++v+ +++ +s+
  gi|121638677|ref|YP_978901.1| 379 SRYLQQVRANNPSGHLTVLGHSYGSLTASLALQDLDAQsAHPVNDVVFYGSP 430
                                    789*************************999999****99******999987 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.8e-05     0.024      72     125 ..     379     433 ..     365     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                        DUF2974  72 lkYlnkilees.egkiylgGhSkGGnlAvyaamnaeddlqeriskiysfDgpGfs 125
                                    ++Yl+++ ++  +g++++ GhS G   A +a+ +++ +  + ++ ++   +pG++
  gi|121638677|ref|YP_978901.1| 379 SRYLQQVRANNpSGHLTVLGHSYGSLTASLALQDLDAQSAHPVNDVVFYGSPGLE 433
                                    58****976551678**************************************96 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.4     3e+03      16      37 ..      82     103 ..      78     114 .. 0.60
   2 ?   12.7   3.0   0.00011      0.13      10      65 ..     124     209 ..     120     215 .. 0.93
   3 ?    6.1   1.6     0.012        15      21      62 ..     193     251 ..     189     254 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                           ZapB  16 aidtitlLqmeieeLkeeneel 37 
                                    a d i + q e+++L++  ++ 
  gi|121638677|ref|YP_978901.1|  82 AADGIVKVQSELAALRHAAAAA 103
                                    5666666677777666655443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                           ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenrele..............................eeneqlkeereawq 59 
                                    E+++  ++ + t+Lq e+++ ++e ++  ee +                                 +  e+l+eer+ +q
  gi|121638677|ref|YP_978901.1| 124 EAQWARTLAKQTELQAELDAIMAEANAVDEELASAVnmadgdapipadsgppvgpegltptqlasdANEERLREERARLQ 203
                                    8899999**********************98887778****************************99999********** PP

                           ZapB  60 erlkkL 65 
                                    ++l+ L
  gi|121638677|ref|YP_978901.1| 204 AHLERL 209
                                    ***988 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.012
                           ZapB  21 tlLqmeieeLkeeneelkeenrele.................eeneqlkeereawqerl 62 
                                    ++L++e ++L++  e l+ e ++l+                   + +l +e +a + rl
  gi|121638677|ref|YP_978901.1| 193 ERLREERARLQAHLERLQAEYDQLSvraardyhngildgdavGRLAALTDELSAARGRL 251
                                    45777777777777777777777766555555666666655555555556666666665 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4     0.084   1.1e+02      37      60 ..     133     156 ..      81     162 .. 0.73
   2 ?    6.9   0.1    0.0055       7.1      34      95 ..     195     256 ..     190     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.084
                                    HHHHHHHHHHHHHHHHHHHHHHCC CS
                   Seryl_tRNA_N  37 krrelqveleelqaerNelskeIg 60 
                                    k+ elq+el+++ ae N++ +e +
  gi|121638677|ref|YP_978901.1| 133 KQTELQAELDAIMAEANAVDEELA 156
                                    344444444444444444444443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0055
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkelea 95 
                                    l e+r +lq++le lqae  +ls   ++   ++    + + + ++l +el+a+  +l el+a
  gi|121638677|ref|YP_978901.1| 195 LREERARLQAHLERLQAEYDQLSVRAARDYHNGILDGDAVGRLAALTDELSAARGRLGELDA 256
                                    789********************999999999977778888999999999999888887765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.1   5.2e+03      27      50 ..      87     110 ..      84     114 .. 0.61
   2 ?    0.5   0.1       0.4   5.2e+02      24      45 ..     132     153 ..     116     161 .. 0.53
   3 ?    9.9   0.2   0.00047      0.61      21      47 ..     194     220 ..     190     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC  27 aalqaelaklkaeneeLeaevkdL 50 
                                    ++ q ela+l+   ++ e  ++ L
  gi|121638677|ref|YP_978901.1|  87 VKVQSELAALRHAAAAAELTIDAL 110
                                    556666666666666655555544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  24 qeiaalqaelaklkaeneeLea 45 
                                    ++ ++lqael+++ ae ++ ++
  gi|121638677|ref|YP_978901.1| 132 AKQTELQAELDAIMAEANAVDE 153
                                    3334444444444444444444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00047
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  21 qlkqeiaalqaelaklkaeneeLeaev 47 
                                    +l++e+a+lqa+l++l+ae ++L  + 
  gi|121638677|ref|YP_978901.1| 194 RLREERARLQAHLERLQAEYDQLSVRA 220
                                    689999************999997665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.4     0.002       2.5     130     264 ..     108     271 ..      12     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.002
                        DUF4407 130 a..............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..................gtgttg 177
                                    +               +a+ a+  a++++lqae+da  a+++a  +e+++ ++ +                   +   + 
  gi|121638677|ref|YP_978901.1| 108 DalinrvvpipglrsTEAQWARTLAKQTELQAELDAIMAEANAVDEELASAVNMADgdapipadsgppvgpeglT---PT 184
                                    134444455555444555666666666677777777666666666666666555555556666665555543221...22 PP

                        DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarlealdrltked 257
                                         ++ ++ +++ +++qa l+ l+a+ d+ + +aa++     l+ ++  + aa +++ +a++G l +l+a d+  ++ 
  gi|121638677|ref|YP_978901.1| 185 QLASDANEERLREERARLQAHLERLQAEYDQLSVRAARDYHNGILDGDAVGRLAALTDELSAARGRLGELDAVDEALSRA 264
                                    23333444447777777777777777777777777777777777777777777777777777777777777777777666 PP

                        DUF4407 258 atallar 264
                                    +  +l++
  gi|121638677|ref|YP_978901.1| 265 PETYLTQ 271
                                    6666665 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.14   1.8e+02      21      45 ..     131     154 ..     120     157 .. 0.80
   2 ?    6.7   1.1    0.0055         7       8      38 ..     189     219 ..     183     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                        DUF2205  21 LqqqakeLqssLqaLaervdeVkee 45 
                                    L +q  eLq+ L+a+++  ++V ee
  gi|121638677|ref|YP_978901.1| 131 LAKQ-TELQAELDAIMAEANAVDEE 154
                                    4444.68**************9998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0055
                        DUF2205   8 edveklerearerLqqqakeLqssLqaLaer 38 
                                    +  e+  re+r+rLq++ + Lq+  ++L+ r
  gi|121638677|ref|YP_978901.1| 189 DANEERLREERARLQAHLERLQAEYDQLSVR 219
                                    45567779**************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3387.91
//
Query:       gi|121638678|ref|YP_978902.1|  [L=108]
Description: hypothetical protein BCG_2816c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   18.2   7.9      0.003   17.8   7.9    1.3  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.098   11.7   0.1       0.13   11.3   0.1    1.2  1  Cas_Csy1  CRISPR-associated protein (Cas_Csy1)


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   7.9   3.3e-07     0.003       2      85 ..       2      85 ..       1      95 [. 0.95

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-07
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83
                                   ++++pe+   +aa++ +q e l   + + +  ++a q gW+Ga+a a +a ++ w  a + l +   +++  l++aa + + 
  gi|121638678|ref|YP_978902.1|  2 FQISPEQWMHSAAQVTTQGEGLAVGHLSSDYRMQAAQFGWQGASAMALNAKMDDWLDASRALLTRIGDHAFGLQEAAIQHAA 83
                                   699**********************************************************************999988777 PP

                                   HH CS
                         WXG100 84 aD 85
                                   a+
  gi|121638678|ref|YP_978902.1| 84 AE 85
                                   76 PP

>> Cas_Csy1  CRISPR-associated protein (Cas_Csy1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.4e-05      0.13     298     330 ..      33      75 ..      23      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
                       Cas_Csy1 298 elrkla.eaGWskdeeckLkraqklWLdpeRae...........e 330
                                    +++  a + GW+ ++ ++L+++   WLd+ Ra            +
  gi|121638678|ref|YP_978902.1|  33 RMQ--AaQFGWQGASAMALNAKMDDWLDASRALltrigdhafglQ 75 
                                    344..4499**********************98888844444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 757.49
//
Query:       gi|121638679|ref|YP_978903.1|  [L=209]
Description: hypothetical protein BCG_2817 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.7   0.1    2.2e-08   34.3   0.1    1.1  1  DUF3558   Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.2e-12   2.2e-08      13     145 ..      51     176 ..      42     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-12
                        DUF3558  13 tapaasssassssttsssaapavpldtsgvlfdpCglltddqlaelggdkekeeaastgangpgCsWqaadsagygvsvs 92 
                                     a +  s+a+++stt +s+  a+   t++++fdpC +++ d+++ lg++      + ++++g  C+++a +  +++v+  
  gi|121638679|ref|YP_978903.1|  51 DAVQLRSTAAPMSTTMKSPIVAT---TDPSPFDPCRDIPFDVIQRLGLA----YTPPEAEEGLRCHFDAGN-YQMAVEPI 122
                                    44444566777777777666666...***********************....9999************87.66666655 PP

                        DUF3558  93 fswyegspirrerateerl.....ditieGrpaviar..dpgd.....easCevavgvadgqvvv 145
                                      w++         ++++l     ++ti+G++a+++   +p+       +sC v++ ++ g v++
  gi|121638679|ref|YP_978903.1| 123 -IWRT---------YAQTLppdaiETTIAGHRAAQYWvrKPTYhnsfwYSSCMVTFKTSYG-VIQ 176
                                    .4555.........3334467788***********99654444545555559999999998.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1368.73
//
Query:       gi|121638680|ref|YP_978904.1|  [L=549]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-67  226.2   0.2    7.4e-67  225.8   0.2    1.2  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    6.2e-27   95.0   0.0    1.3e-26   94.0   0.0    1.5  1  PepX_C         X-Pro dipeptidyl-peptidase C-terminal non-cata
    0.00059   19.4   0.1       0.38   10.2   0.0    2.3  2  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.19   11.6   0.0    1.6  2  Abhydrolase_3  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.8   0.2   1.7e-70   7.4e-67       1     269 []      49     310 ..      49     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.8 bits;  conditional E-value: 1.7e-70
                                    TS-EEEEEEEEE..TTSSSEEEEEEEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TTTT CS
                  Peptidase_S15   1 DGvrLavdiyrPetkskeklPvlltrtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGtggSeGeftvgds 80 
                                    DGv+L +d+y P  ++++++ +ll r PYg++   +s +             ++arGY+vV+q+vrGt+gS G+f++ + 
  gi|121638680|ref|YP_978904.1|  49 DGVQLVADHYAP--ATSQPVGTLLVRGPYGRRF-PFSLVFAR---------IYAARGYHVVLQSVRGTFGSGGVFEP-MV 115
                                    9***********..****************775.44444422.........29************************.** PP

                                    THHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCSECTTEEBCCHHHHHHHH CS
                  Peptidase_S15  81 deaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyyregGlvrapgglswedl 160
                                    +ea+dgad+++Wl++qpw +G+ g++G+ YlG+tq++++++++p+l+a+v++++ +d+   +++ +G ++++++l w+dl
  gi|121638680|ref|YP_978904.1| 116 NEAADGADTVAWLREQPWFTGRFGTIGLPYLGFTQWALLHDPPPELAAAVITVGPHDFRA-SVWGTGSFTVNDFLGWSDL 194
                                    ************************************************************.******************* PP

                                    HCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHH......THHHHCCCC--SSSHHHHTT-HHHHHCT--S-EEEE CS
                  Peptidase_S15 161 dllaealtsrradegdalkaaaryeaasdellaeldrq......tpveselletgdydafWkdrnlsedadkvkapvllv 234
                                     +++e+  + ra  ++ ++ ++ +++a+  +l+e +r+      +++es++ +t++ d+fW++ ++  ++d+v++pvllv
  gi|121638680|ref|YP_978904.1| 195 VSHQEDPGRIRAGIRQLTAPRRVARTAATLPLGESARTllgtgaPWFESWVEHTDRDDPFWDRLRFPAALDRVQVPVLLV 274
                                    ******************************************************************************** PP

                                    EECCSSTTCCHHHHHHHHHCCTT-..EEEEECECTTC CS
                  Peptidase_S15 235 gGwnDwnvkngaiklyealkapgv..klilgpwtHvy 269
                                    gGw+D ++++++++ y++l+++gv   l++gpwtH++
  gi|121638680|ref|YP_978904.1| 275 GGWQD-IFLRQTLQQYRHLRDRGVhvALTVGPWTHTQ 310
                                    *****.*****************************96 PP

>> PepX_C  X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0   2.8e-30   1.3e-26       6     220 ..     339     542 ..     336     544 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 2.8e-30
                         PepX_C   6 tppvrlqvldggsgstwrtedawpspntkattlylsqrgagstgdgtlsaaspls.deaaaseedlydptnp........ 76 
                                      pvr++v ++g    wr  ++wp+++t+   +yl+       ++g+l   +p+s +++a++ + ++dpt+         
  gi|121638680|ref|YP_978904.1| 339 PSPVRVFVTGQG----WRHLPDWPPATTER-AWYLQ-------PGGRLGESAPASgTPPATFRYHPADPTPTtggpllss 406
                                    579******888....*********99976.*****.......7766666666661567778888888877799999999 PP

                         PepX_C  77 ....ldqdqreeradslafttaplaedtelvGapkakLrvssdapdadlsvtLvdvdpdGeatlitkGwlrlsnRasdee 152
                                         d +    rad+l+ft apl++d+ + G+p ++L  ssd p  d++v++++vd++G++++++ G+ rl+       
  gi|121638680|ref|YP_978904.1| 407 nggyRDDSRLATRADVLCFTGAPLTHDLCVHGNPVVELVHSSDNPYVDVFVRVSEVDAKGRSRNVSDGYRRLG------- 479
                                    99988888899*************************************************************6....... PP

                         PepX_C 153 peplePGevydleieLqptayrfpkGhrlrlsvsssdfpmilpnpetdtltldlakl.kakntvhtgae 220
                                          + +  +++eL+++a+rf + +r+r+ +++s fp + +n++t ++ l++ +l +a+++vh+g +
  gi|121638680|ref|YP_978904.1| 480 ------DAPELVRVELDAIAHRFRADSRIRVLIAGSWFPRYARNLGTPEPILTGRQLkPATHAVHFGRS 542
                                    ......99999**************************************99999999999999999865 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   8.5e-05      0.38       8     120 ..      87     193 ..      80     203 .. 0.88
   2 !    6.9   0.0   0.00084       3.8     113     209 ..     238     331 ..     220     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.5e-05
                                    HHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GG CS
                   Peptidase_S9   8 qlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpd 87 
                                     + a+rGy vv   +rG+ g G  f+         ne++D  + + +l ++ +  + r +  G  y G++  a+l + p 
  gi|121638680|ref|YP_978904.1|  87 RIYAARGYHVVLQSVRGTFGSGGVFEP------MVNEAADGADTVAWLREQPWF-TGRFGTIGLPYLGFTQWALLHDPPP 159
                                    46689**************99999887......6789999999*********76.589************999999**** PP

                                    G-SEEEEESE---CCCHHCSTTSTHH.HCCCC-- CS
                   Peptidase_S9  88 lFkaavaevpvvdvlrydsdtdllte.eymewgn 120
                                      +aav+ v+ +d +++   t  +t   + +w +
  gi|121638680|ref|YP_978904.1| 160 ELAAAVITVGPHDFRASVWGTGSFTVnDFLGWSD 193
                                    ****************999987788877777765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00084
                                    H.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSS CS
                   Peptidase_S9 113 e.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkp 191
                                    + +++ w ++++  + ++++     +   ++++p+Ll+ G++D  + + ++l+ ++ L+++g++v l + p   H  ++ 
  gi|121638680|ref|YP_978904.1| 238 ApWFESWVEHTDRDDPFWDRLRFPAALD-RVQVPVLLVGGWQD--IFLRQTLQQYRHLRDRGVHVALTVGPW-TH-TQML 312
                                    4477778877777787877777666555.69***********9..566****************99988775.45.3334 PP

                                    HHHH.HHHHHHHHHHHHHC CS
                   Peptidase_S9 192 rakv.eelarllaFlkeal 209
                                    ++      ++ l++l+ +l
  gi|121638680|ref|YP_978904.1| 313 TKGLaTGARESLDWLDAHL 331
                                    4444466666677776666 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       2.7   1.2e+04      50      64 ..     119     133 ..     117     137 .. 0.84
   2 ?   11.6   0.0   4.2e-05      0.19     141     200 ..     241     302 ..     220     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHTHH CS
                  Abhydrolase_3  50 edalaalrwlaeqaw 64 
                                     d+ + + wl+eq w
  gi|121638680|ref|YP_978904.1| 119 ADGADTVAWLREQPW 133
                                    5899999****9987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.2e-05
                                    HHHHSSGGGGGSTTTSGGGCS.-SST.---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEE CS
                  Abhydrolase_3 141 wrlylpeadrddplaspllae.dlsg.lpptlvvvaefDplrdegeayaerlraagveveli 200
                                    ++ ++++ drddp    l+ +  l++   p+l+v +++D++ +++ + +++lr+ gv+v l 
  gi|121638680|ref|YP_978904.1| 241 FESWVEHTDRDDPFWDRLRFPaALDRvQVPVLLVGGWQDIFLRQTLQQYRHLRDRGVHVALT 302
                                    57788899*****9998877435666256*****************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4121.65
//
Query:       gi|121638681|ref|YP_978905.1|  [L=118]
Description: hypothetical protein BCG_2819c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-28   98.5   0.1    3.2e-28   98.4   0.1    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.1   1.8e-32   3.2e-28       1     110 [.       3     113 ..       3     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.8e-32
                                    -TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCH.S.....EEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEE CS
                     PemK_toxin   1 krGeIvlvdldpsrgseqgkrRpvvVvsndafnek.n.....tvivvpltskdkdkkklpfhveleseildlngldkdsw 74 
                                    +rGeI+ vdldp rgse + +Rp+vVvsnd+ n++       +++vvp+ts++  +k +pf+v l+++   ++gl+ d++
  gi|121638681|ref|YP_978905.1|   3 RRGEIWQVDLDPARGSEANNQRPAVVVSNDRANATaTrlgrgVITVVPVTSNI--AKVYPFQVLLSAT---TTGLQVDCK 77 
                                    69****************************999875367899***********..7789******975...7788899** PP

                                    EECCCEEEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                     PemK_toxin  75 vkldqirtvdkarlrkkigklsredlaevqralakl 110
                                    ++++qir+++++rl ++ig++s+++la++++al+++
  gi|121638681|ref|YP_978905.1|  78 AQAEQIRSIATERLLRPIGRVSAAELAQLDEALKLH 113
                                    *********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 929.52
//
Query:       gi|121638682|ref|YP_978906.1|  [L=347]
Description: hypothetical protein BCG_2820c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-25   87.9   0.4    3.9e-25   87.9   0.4    3.3  4  DUF2293   Uncharacterized conserved protein (DUF2293)


Domain annotation for each model (and alignments):
>> DUF2293  Uncharacterized conserved protein (DUF2293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.12   2.1e+03      26      38 ..       7      19 ..       1      27 [. 0.52
   2 ?   -2.6   0.1      0.39     7e+03      44      68 ..     195     201 ..     176     210 .. 0.51
   3 ?   -1.7   0.9       0.2   3.6e+03      63      75 ..     235     247 ..     226     252 .. 0.74
   4 !   87.9   0.4   2.2e-29   3.9e-25       1      85 []     257     343 ..     257     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.12
                        DUF2293 26 sgrvgrtekiple 38
                                   ++rv+r+++++l+
  gi|121638682|ref|YP_978906.1|  7 EQRVARAAQAALA 19
                                   3444444444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.39
                        DUF2293  44 AvlAhiRHthTdYDeLlkegveree 68 
                                                        v++  
  gi|121638682|ref|YP_978906.1| 195 V------------------VVRWSR 201
                                    2..................233444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.2
                        DUF2293  63 gvereeARravee 75 
                                    ++er+eARra e+
  gi|121638682|ref|YP_978906.1| 235 RRERDEARRANED 247
                                    47899***98776 PP

  == domain 4  score: 87.9 bits;  conditional E-value: 2.2e-29
                        DUF2293   1 alrdlfpriPetdaeaiiehafkkgsgrvgrteki.plerr.vqlAvlAhiRHthTdYDeLlkegvereeARraveekvl 78 
                                    a+r+lfp++P+ +aeai++ha ++gsgr+gr+++  +l+ + v+lAv A +RH +T +DeLl++gv+re+AR++v e+v+
  gi|121638682|ref|YP_978906.1| 257 AIRTLFPNCPAGRAEAIARHAATRGSGRIGRSAAGrALDPEaVRLAVAASVRHIDTSFDELLMSGVDRETARHRVGEHVE 336
                                    699*****************************9997777666************************************** PP

                        DUF2293  79 dvlvkWr 85 
                                    +vl++Wr
  gi|121638682|ref|YP_978906.1| 337 EVLRDWR 343
                                    ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2472.70
//
Query:       gi|121638683|ref|YP_978907.1|  [L=155]
Description: hypothetical protein BCG_2821 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-25   86.4   3.5    1.5e-24   85.7   3.5    1.3  1  DUF1778   Protein of unknown function (DUF1778)
    1.6e-05   25.2   0.0    2.5e-05   24.6   0.0    1.4  1  ParD      Antitoxin ParD
     0.0028   17.4   0.0     0.0056   16.5   0.0    1.5  1  HicB      HicB family


Domain annotation for each model (and alignments):
>> DUF1778  Protein of unknown function (DUF1778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   3.5   2.5e-28   1.5e-24       1      77 [.      72     148 ..      72     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 2.5e-28
                        DUF1778   1 RLelRispeakeliqrAAalsgktltdFvleaaleaAekviedherieLseedfqafvaaLdeppkpnprLlkaarr 77 
                                    RL++R+spe+++++++AAal+g++l+ Fvl+aa+++A++ +++++rieLse++f++fvaaLdep ++ p+L ++arr
  gi|121638683|ref|YP_978907.1|  72 RLNFRLSPEQEQALRHAAALTGQSLSGFVLSAAVDHAHDLLARANRIELSEAAFRRFVAALDEPDEAAPELVRLARR 148
                                    9**************************************************************************76 PP

>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.2e-09   2.5e-05       3      42 ..      72     111 ..      70     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.2e-09
                           ParD   3 rLsIditpeqhqrlkAvAAlqGksikeYvLerlleepkea 42 
                                    rL+  ++peq q+l+ +AAl G+s+  +vL+   +++++ 
  gi|121638683|ref|YP_978907.1|  72 RLNFRLSPEQEQALRHAAALTGQSLSGFVLSAAVDHAHDL 111
                                    89999**************************999877665 PP

>> HicB  HicB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.4e-07    0.0056      18      48 ..      71     101 ..      64     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.4e-07
                           HicB  18 GkFnlRvspeLHarlalaAaeqgvSLNqfve 48 
                                    G++n+R+spe +++l  aAa  g SL  fv 
  gi|121638683|ref|YP_978907.1|  71 GRLNFRLSPEQEQALRHAAALTGQSLSGFVL 101
                                    99************************88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1046.66
//
Query:       gi|121638684|ref|YP_978908.1|  [L=209]
Description: hypothetical protein BCG_2822c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1510.91
//
Query:       gi|121638685|ref|YP_978909.1|  [L=134]
Description: hypothetical protein BCG_2823 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1031.98
//
Query:       gi|121638686|ref|YP_978910.1|  [L=63]
Description: hypothetical protein BCG_2824 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 539.33
//
Query:       gi|121638687|ref|YP_978911.1|  [L=384]
Description: hypothetical protein BCG_2825 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   44.4   0.0    2.5e-11   43.8   0.0    1.3  1  rve       Integrase core domain
  ------ inclusion threshold ------
       0.19   12.5   0.5        2.5    8.9   0.1    2.4  2  Mub_B2    Mub B2-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.8e-15   2.5e-11       4     117 ..     140     252 ..     137     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.8e-15
                            rve   4 pgelwqvDvt.vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngseytska 82 
                                      +++++D++ ++  +  g++a+ l+++d  ++++    ++++ +a+ +l+ +++  +rf    + ++ sD g e+++++
  gi|121638687|ref|YP_978911.1| 140 VPGVIEADTVaHCGPSLIGEFARTLTMTDLVTGWTENASIRNN-AAKWILEGIKECQQRFPFP-MTVFDSDCGGEFINHD 217
                                    56789999999777677777***********************.5555555555555555554.89************** PP

                            rve  83 frefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                    ++ +l+  +i ++++rp++ +d++ vE+ + ++ +
  gi|121638687|ref|YP_978911.1| 218 VAGWLQARDIAQTRSRPYQKNDQAHVESKNNHVVR 252
                                    ******************************99866 PP

>> Mub_B2  Mub B2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00028       2.5      24      40 ..     159     176 ..     158     185 .. 0.79
   2 ?    1.0   0.0     0.082   7.3e+02      19      42 ..     292     317 ..     283     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                                    EEEEEEEE.ETTT--EE. CS
                         Mub_B2  24 tftrtatv.DkVTgWtat 40 
                                    +f rt t+ D+VTgWt++
  gi|121638687|ref|YP_978911.1| 159 EFARTLTMtDLVTGWTEN 176
                                    699997766*******93 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.082
                                    EEEEEEEEEEEEEET.TT--EE...E CS
                         Mub_B2  19 vtqtvtftrtatvDk.VTgWta.tgs 42 
                                    +t tv+  r+ ++Dk  T W+  ++s
  gi|121638687|ref|YP_978911.1| 292 YTSTVNGRRKRIYDKpATPWQRlQAS 317
                                    789999999999*9955669986444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2670.07
//
Query:       gi|121638688|ref|YP_978912.1|  [L=85]
Description: hypothetical protein BCG_2826 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.026   14.4   0.0    1.4  1  Tautomerase  Tautomerase enzyme


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-06     0.026       8      32 ..      34      58 ..      30      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                                   STCS-HHHHHHHHHHHHHHHHHHHT CS
                    Tautomerase  8 vegrsaeqKaeLaervTealvealg 32
                                   +e++++eq +++++ +++al++++g
  gi|121638688|ref|YP_978912.1| 34 TEKPTNEQSDAVIDVLSDALMKTFG 58
                                   6889*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 576.75
//
Query:       gi|121638689|ref|YP_978913.1|  [L=103]
Description: hypothetical protein BCG_2827 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 764.79
//
Query:       gi|121638690|ref|YP_978914.1|  [L=202]
Description: hypothetical protein BCG_2829 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.044   13.6   0.9      0.091   12.6   0.9    1.6  1  HTH_23        Homeodomain-like domain
       0.05   13.1   1.7       0.23   11.0   0.1    2.2  2  TF_Zn_Ribbon  TFIIB zinc-binding
      0.072   12.9   0.1       0.76    9.6   0.0    2.5  3  zf-HYPF       HypF finger
       0.26   11.4   4.1        8.7    6.5   0.2    2.5  2  DUF2752       Protein of unknown function (DUF2752)


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9     2e-05     0.091      11      48 ..      82     122 ..      72     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                         HTH_23  11 llllae....GlsvreIAreLgvsrrTvyrwlkryreeGleg 48 
                                    + +la     +   r+IA+   ++  Tv+ wl+r+ +e +e+
  gi|121638690|ref|YP_978914.1|  82 VSALAAkatsRVGFRRIATDVARPAETVRGWLRRF-AERVEA 122
                                    555554455678889********************.677776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.2e-05      0.23      12      29 ..      12      29 ..       7      30 .. 0.80
   2 ?    0.9   0.3     0.074   3.3e+02      21      27 ..      55      61 ..      54      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.2e-05
                                   HEETSTTCEEESSSSBEE CS
                   TF_Zn_Ribbon 12 veDpergelvCtdCGlVl 29
                                   ++  + gel C++CG Vl
  gi|121638690|ref|YP_978914.1| 12 ERRLAAGELSCPSCGGVL 29
                                   556689********9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.074
                                   EESSSSB CS
                   TF_Zn_Ribbon 21 vCtdCGl 27
                                   +Ct CG+
  gi|121638690|ref|YP_978914.1| 55 RCTGCGV 61
                                   5888885 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00017      0.76      11      28 ..       9      26 ..       7      30 .. 0.88
   2 ?   -1.1   0.3      0.38   1.7e+03      24      28 ..      56      60 ..      55      65 .. 0.86
   3 ?   -1.5   0.0       0.5   2.3e+03      15      24 ..     164     173 ..     162     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                                   -TTSTTTT-TT---TTTS CS
                        zf-HYPF 11 dpldRRfhaqfisCtnCG 28
                                   d+  RR  a   sC++CG
  gi|121638690|ref|YP_978914.1|  9 DQVERRLAAGELSCPSCG 26
                                   5667*************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.38
                                   -TTTS CS
                        zf-HYPF 24 CtnCG 28
                                   Ct CG
  gi|121638690|ref|YP_978914.1| 56 CTGCG 60
                                   9***9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.5
                                    TTTT-TT--- CS
                        zf-HYPF  15 RRfhaqfisC 24 
                                    RRf  +++s 
  gi|121638690|ref|YP_978914.1| 164 RRFSLPTVSL 173
                                    9**9999885 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5    0.0033        15       8      16 ..      19      27 ..      15      32 .. 0.83
   2 ?    6.5   0.2     0.002       8.7      11      20 ..      56      65 ..      53      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0033
                        DUF2752  8 GipCPGCGl 16
                                    ++CP CG+
  gi|121638690|ref|YP_978914.1| 19 ELSCPSCGG 27
                                   689*****8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.002
                        DUF2752 11 CPGCGltRav 20
                                   C GCG+t+ +
  gi|121638690|ref|YP_978914.1| 56 CTGCGVTHVL 65
                                   *******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1490.27
//
Query:       gi|121638691|ref|YP_978915.1|  [L=469]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-27   95.1   0.0    5.1e-27   94.4   0.0    1.4  1  rve            Integrase core domain
    9.9e-11   41.4   0.1    3.3e-10   39.8   0.0    1.9  2  Mu-transpos_C  Mu transposase, C-terminal
    3.2e-10   40.0   0.5    1.6e-09   37.7   0.5    2.3  1  HTH_28         Helix-turn-helix domain
    1.4e-07   32.0   3.0    1.4e-07   32.0   3.0    2.4  3  HTH_32         Homeodomain-like domain
    3.6e-06   26.6   0.0    1.1e-05   25.1   0.0    1.9  2  rve_3          Integrase core domain
    3.9e-05   23.3   0.4    3.9e-05   23.3   0.4    2.5  2  HTH_23         Homeodomain-like domain
    4.2e-05   23.5   0.6    0.00014   21.8   0.1    2.2  2  HTH_29         Winged helix-turn helix
  ------ inclusion threshold ------
        0.1   12.5   0.5         21    5.0   0.1    2.8  2  DUF4817        Helix-turn-helix domain (DUF4817)
       0.13   12.5   0.0       0.35   11.1   0.0    1.7  2  DDE_Tnp_IS240  DDE domain
       0.14   12.4   0.6       0.38   11.0   0.6    1.8  1  HTH_17         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   2.8e-30   5.1e-27       2     118 ..     159     272 ..     158     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.8e-30
                            rve   2 trpgelwqvDvt.vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngseyts 80 
                                    ++p+ lw++Dv   +r +d + k yl++++dd+srl+ ++ + + +d+  ++a+l+ a+a++g   p +v+ Dngs y++
  gi|121638691|ref|YP_978915.1| 159 EHPNALWTGDVLhGIR-IDLR-KTYLFAFLDDHSRLVPGYRWGHAEDTVRLAAALRPALASRGV--PNAVYVDNGSPYVD 234
                                    79**********6666.4444.7*****************************************..9************* PP

                            rve  81 kafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                      + + +a+lg+r+ ++ pgrpq +Gk+Erf+rt++++
  gi|121638691|ref|YP_978915.1| 235 AWLLRACAKLGVRLVHSTPGRPQGRGKIERFFRTVREQ 272
                                    ***********************************987 PP

>> Mu-transpos_C  Mu transposase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   7.2e+03      17      38 ..     281     304 ..     267     308 .. 0.56
   2 !   39.8   0.0   1.9e-13   3.3e-10       4      52 ..     341     388 ..     339     392 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                    S--EEEEEE-..SHHHHSS-SEEE CS
                  Mu-transpos_C  17 irlngnrYws..peLaglvgkkVv 38 
                                      + g++Y++  +eL +l  + V+
  gi|121638691|ref|YP_978915.1| 281 PDVVGRHYVAdlAELNRLFTAWVE 304
                                    445678888855566666655555 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 1.9e-13
                                    SEEBEEEE--TTT.S--EEEEEE-SHHHHSS-SEEEEEE-GGGTTEEEEE CS
                  Mu-transpos_C   4 llpretrtvqrdG.irlngnrYwspeLaglvgkkVvvryDPrdlsrvyVy 52 
                                    +l++e r+v+++  ++l+gnrY+ +   +lvg+kV++ +DP dl+r+ V+
  gi|121638691|ref|YP_978915.1| 341 FLWEEHRRVTKTAtVSLHGNRYEIDP--ALVGRKVELVFDPFDLTRIEVR 388
                                    99**********99**********99..669*****************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.5     9e-13   1.6e-09       1      49 [.      38      86 ..      38      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9e-13
                         HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWikryeegGiagLvprrr 49
                                   qR +++++la+ +  +   r++ isr+t+ rWi+ +++gG+++Lvp +r
  gi|121638691|ref|YP_978915.1| 38 QRGKMVRELASREHTDPFGRRVRISRQTIDRWIRGWRAGGFDALVPNPR 86
                                   7899******************************************998 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   3.0   7.7e-11   1.4e-07       1      71 [.      65     134 ..      65     135 .. 0.90
   2 ?   -3.0   0.1       6.6   1.2e+04      30      39 ..     230     239 ..     196     258 .. 0.52
   3 ?   -2.2   0.1       3.8   6.8e+03      23      34 ..     253     270 ..     232     308 .. 0.51

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.7e-11
                         HTH_32   1 TvsrwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaere.gvkvShstvyr 71 
                                    T+ rw++ ++++G+++L + pr+  ++++++ev +  +al+re+p+ ++  +++ l + + g  + ++t +r
  gi|121638691|ref|YP_978915.1|  65 TIDRWIRGWRAGGFDALVPNPRQ-CTPRTPAEVLELAVALRRENPQRTAAAIRRIL-RTQlGWAPDERTLQR 134
                                    89******************999.6668*************999************.666477788888877 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                         HTH_32  30 sdevrariia 39 
                                    s+ v a++++
  gi|121638691|ref|YP_978915.1| 230 SPYVDAWLLR 239
                                    3444444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.8
                         HTH_32  23 rgrpr......klsdevr 34 
                                    +grp+      ++   vr
  gi|121638691|ref|YP_978915.1| 253 PGRPQgrgkieRFFRTVR 270
                                    444432221333333333 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         4   7.2e+03      36      51 ..      56      71 ..      39      72 .. 0.64
   2 !   25.1   0.0   6.2e-09   1.1e-05       2      52 ..     245     305 ..     244     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                          rve_3 36 frslaearekleawre 51
                                    r+++  r+ +++w++
  gi|121638691|ref|YP_978915.1| 56 GRRVRISRQTIDRWIR 71
                                   5566778899999986 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 6.2e-09
                          rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneel..........frslaearekleawred 52 
                                    g++l ++ pg+Pq  g++E+f++t+r+++l e              +lae++++ +aw+e 
  gi|121638691|ref|YP_978915.1| 245 GVRLVHSTPGRPQGRGKIERFFRTVREQFLVEITgepdvvgrhyVADLAELNRLFTAWVET 305
                                    899***************************9988888999999978999999999999975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       3.4   6.1e+03       6      20 ..      13      26 ..      10      32 .. 0.66
   2 !   23.3   0.4   2.2e-08   3.9e-05       3      49 ..      35      81 ..      33      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                         HTH_23  6 eRlrillllaeGlsv 20
                                   eR+r++ l++  + +
  gi|121638691|ref|YP_978915.1| 13 ERARAIGLFR-YQLI 26
                                   8999998877.4455 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.2e-08
                         HTH_23  3 sereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                   s ++R ++++ la +  +    r+  +sr+T++rw++ +r++G+++l
  gi|121638691|ref|YP_978915.1| 35 STKQRGKMVRELASREHTDPFGRRVRISRQTIDRWIRGWRAGGFDAL 81
                                   5678888999999999999999**********************998 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   7.9e-08   0.00014      20      54 ..      57      91 ..      57      98 .. 0.88
   2 ?   -3.5   0.0       6.4   1.1e+04      30      46 ..     196     212 ..     196     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.9e-08
                         HTH_29 20 kllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                   +++++sr+t++rw++ +++gG +al +++r+  pr
  gi|121638691|ref|YP_978915.1| 57 RRVRISRQTIDRWIRGWRAGGFDALVPNPRQCTPR 91
                                   6799************************9976555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.4
                         HTH_29  30 yrwlkrfeegGlaalld 46 
                                    yrw ++ ++ +laa+l+
  gi|121638691|ref|YP_978915.1| 196 YRWGHAEDTVRLAAALR 212
                                    67777777777777654 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.014        26      30      49 ..      55      74 ..      36      77 .. 0.79
   2 ?    5.0   0.1     0.012        21      19      53 ..     112     144 ..     108     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                        DUF4817 30 FpnrsvPsrstirrlvkkfe 49
                                   F++r   sr+ti+r+++  +
  gi|121638691|ref|YP_978915.1| 55 FGRRVRISRQTIDRWIRGWR 74
                                   77555559********9655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                        DUF4817  19 vtatqrafrrrFpnrsvPsrstirrlvkkfeetGs 53 
                                    ++a +r +r++ +   +P+++t +r++ ++  tG 
  gi|121638691|ref|YP_978915.1| 112 AAAIRRILRTQLG--WAPDERTLQRNFHRLGLTGA 144
                                    68899********..9**********999888885 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.2   1.1e+04      30      54 ..      96     121 ..      94     125 .. 0.69
   2 ?   11.1   0.0   0.00019      0.35      11      74 ..     173     236 ..     172     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.2
                  DDE_Tnp_IS240  30 ildflvskrRdt.kaakaflrkalkk 54 
                                    +l+ +v  rR+  + ++a++r++l+ 
  gi|121638691|ref|YP_978915.1|  96 VLELAVALRRENpQRTAAAIRRILRT 121
                                    77888888886525577788888775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                  DDE_Tnp_IS240  11 vkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasal 74 
                                    ++i  +++Yl++ +D ++r + ++   +  dt   +a+lr al +  + p+++ +D  s y  a 
  gi|121638691|ref|YP_978915.1| 173 IRIDLRKTYLFAFLDDHSRlVPGYRWGHAEDTVRLAAALRPALASR-GVPNAVYVDNGSPYVDAW 236
                                    788889*************8889**********************9.9*********999*9884 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   0.00021      0.38      28      49 ..      53      72 ..      39      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                         HTH_17 28 paakiGrrwriprsdleewlek 49
                                    +   Grr+ri+r  +++w+++
  gi|121638691|ref|YP_978915.1| 53 DP--FGRRVRISRQTIDRWIRG 72
                                   34..4999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3231.13
//
Query:       gi|121638692|ref|YP_978916.1|  [L=270]
Description: hypothetical protein BCG_2831 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-18   64.8   0.0    1.6e-17   64.1   0.0    1.3  1  AAA_22    AAA domain
    8.3e-06   25.6   0.3    1.5e-05   24.8   0.3    1.3  1  AAA_30    AAA domain
    4.1e-05   23.0   0.0    5.4e-05   22.6   0.0    1.1  1  DUF2075   Uncharacterized conserved protein (DUF2075)
    0.00034   21.0   2.3     0.0058   17.0   1.1    2.4  2  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
       0.02   14.9   0.0        3.3    7.7   0.0    2.2  2  ResIII    Type III restriction enzyme, res subunit
      0.021   13.9   0.0      0.039   13.0   0.0    1.4  1  T2SSE     Type II/IV secretion system protein
      0.037   14.0   0.0      0.064   13.3   0.0    1.3  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
       0.16   11.6   0.0       0.29   10.7   0.0    1.4  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.17   11.4   0.0       0.26   10.8   0.0    1.2  1  AAA_7     P-loop containing dynein motor region
       0.27   11.1   0.0        1.3    8.9   0.0    1.8  2  ATPase_2  ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   8.7e-21   1.6e-17       4     137 .]      44     173 ..      42     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 8.7e-21
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseelleal 82 
                                    +++i+v+tGe+G+GKT+ +r  l +ld        r++   ++lp +t + + + ++++  lg +  +       l  + 
  gi|121638692|ref|YP_978916.1|  44 DRRIGVITGEVGAGKTVAVRAALASLD--------RSRHTVIYLPDPTvGVQGIHHRIVASLGGQPLT---HHATLAPQA 112
                                    589***********************8........77777888888888**************99999...555555555 PP

                         AAA_22  83 eqalrarav....ielliiDEaqhlrseealeeLrsllnl...srkgvqliLvGtpelrkll 137
                                    ++al a ++    +++++++Ea+ l   ++le Lr l n    s+++++ +L+G+p lr+++
  gi|121638692|ref|YP_978916.1| 113 ADALAAEQAergrTPVVVVEEAHLL-GYDQLEALRLLTNHdldSSSPFACLLIGQPTLRRRM 173
                                    55555555556666***********.9*********9999999****************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.3   8.2e-09   1.5e-05      17     108 ..      44     145 ..      33     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.2e-09
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa....eelgieastiakllkrlk......grarl 86 
                                    ++r+ v+tG  G+GKt a++a+ + ++++ ++vi l       + +     ++lg +  t +  l  ++      ++a+ 
  gi|121638692|ref|YP_978916.1|  44 DRRIGVITGEVGAGKTVAVRAALASLDRSRHTVIYLPDPTVGVQGIHhrivASLGGQPLTHHATLAPQAadalaaEQAER 123
                                    56799************************99***9999999888888444458999999999999888899998866777 PP

                         AAA_30  87 epgtllivDEagmvdtkqlaal 108
                                     +  +++v Ea +++ +ql+al
  gi|121638692|ref|YP_978916.1| 124 GRTPVVVVEEAHLLGYDQLEAL 145
                                    8889*************99987 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     3e-08   5.4e-05       2     101 ..      46     138 ..      45     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-08
                        DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkae 81 
                                    ++ ++tG+ G+GKtv   ++la l  d++++t++yl      v+ + +++  +  ++  ++ ++   +   +l      +
  gi|121638692|ref|YP_978916.1|  46 RIGVITGEVGAGKTVAVRAALASL--DRSRHTVIYLPDPTVGVQGIHHRIVASLGGQPLTHHATLAPQAADALA-----A 118
                                    6779********************..9***************************44444444444444444444.....7 PP

                        DUF2075  82 ekkeepkedvvivDEAhrll 101
                                    e++e+ +  vv+v EAh+l 
  gi|121638692|ref|YP_978916.1| 119 EQAERGRTPVVVVEEAHLLG 138
                                    889**************985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   3.3e-06    0.0058      25     160 ..      46     150 ..      40     164 .. 0.66
   2 ?   -3.1   0.0       5.1   9.1e+03     120     120 ..     238     238 ..     203     261 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                    ++ +++Ge G GK+  vr++l +l +++  +++               +q +  +++++ l+ +     l ++++     
  gi|121638692|ref|YP_978916.1|  46 RIGVITGEVGAGKTVAVRAALASLDRSRHTVIYLPDPTV--------GVQGI-HHRIVASLGGQ----PLTHHAT----- 107
                                    6779***********************766666666666........56888.54888888877....3333333..... PP

                         AAA_16 105 laavpelagaeasrllellkrll.allsrderplvlvlDdlqwadeaslqllaaLlr 160
                                    la              ++  +l+ ++++r +r+ v+v+++++ +  ++l++l++L  
  gi|121638692|ref|YP_978916.1| 108 LA-------------PQAADALAaEQAER-GRTPVVVVEEAHLLGYDQLEALRLLTN 150
                                    12.............22223333345555.555777777777777777777776654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                         AAA_16 120 l 120
                                    +
  gi|121638692|ref|YP_978916.1| 238 N 238
                                    2 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0019       3.3       9      53 ..      32      74 ..      25      87 .. 0.79
   2 ?    5.0   0.0     0.012        22     124     149 ..     117     141 ..     101     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                   HHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                         ResIII  9 eeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgk 53
                                    ea+ ++   +   +++ g+i  + G+GKT+   ++ ++l ++++
  gi|121638692|ref|YP_978916.1| 32 NEAVARIGWCI--ADRRIGVITGEVGAGKTVAVRAALASLDRSRH 74
                                   56667776666..5889999************9999999998877 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                                    ...HHHTTT-SEEEEETGGGTTS.TT CS
                         ResIII 124 eseellrdrfdviiiDEaHrlgakks 149
                                    + e+++r+r +v+++ EaH lg++ +
  gi|121638692|ref|YP_978916.1| 117 AAEQAERGRTPVVVVEEAHLLGYD-Q 141
                                    678999*************99994.3 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.039     125     166 ..      41      82 ..      18     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                          T2SSE 125 avrerglilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                     ++ r + +++G  g GKt+ + a+l+ ++ s + ++ + Dp
  gi|121638692|ref|YP_978916.1|  41 CIADRRIGVITGEVGAGKTVAVRAALASLDRSRHTVIYLPDP 82 
                                    567888999***********************9999999888 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.064       5      45 ..      33      71 ..      26      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  5 eetealgkklakalgdvilLeGdLGaGKTtlvrglakalgv 45
                                   e++ ++g  +a+  +++ +++G++GaGKT+ vr+ +++l+ 
  gi|121638692|ref|YP_978916.1| 33 EAVARIGWCIAD--RRIGVITGEVGAGKTVAVRAALASLDR 71
                                   555566666666..677899**************9998865 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.29       4      32 ..      49      77 ..      46      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                   EEEESTTCCHHHHHHHHHCT--SS-EEEE CS
                           cobW  4 vltGflGsGKTtLlnhllenraglklavi 32
                                   v+tG +G+GKT  +++ l+  +  +  vi
  gi|121638692|ref|YP_978916.1| 49 VITGEVGAGKTVAVRAALASLDRSRHTVI 77
                                   8*****************88888888877 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.26      33      65 ..      45      77 ..      36      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                          AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsl 65
                                   ++  +++G++G GKtv ++  l +ld+++++++
  gi|121638692|ref|YP_978916.1| 45 RRIGVITGEVGAGKTVAVRAALASLDRSRHTVI 77
                                   5556799*******************8888776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0007       1.3      20      54 ..      45      79 ..      38      83 .. 0.91
   2 ?   -0.6   0.0      0.57     1e+03      99     131 ..     106     138 ..      89     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0007
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                   ++i +i+G  g GKt  ++ ++  l+ +   viy+
  gi|121638692|ref|YP_978916.1| 45 RRIGVITGEVGAGKTVAVRAALASLDRSRHTVIYL 79
                                   6799*********************999999*997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                       ATPase_2  99 sklvfkaielllekikkkgkkiiiiiDelqkli 131
                                     +l+ +a ++l ++  ++g+ +++++ e+  l+
  gi|121638692|ref|YP_978916.1| 106 ATLAPQAADALAAEQAERGRTPVVVVEEAHLLG 138
                                    567778888888999999999****99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1888.67
//
Query:       gi|121638693|ref|YP_978917.1|  [L=278]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-28   96.7   0.0    2.3e-27   95.5   0.0    1.6  2  rve       Integrase core domain
    6.9e-16   58.1   0.2    1.6e-15   56.9   0.2    1.6  1  HTH_21    HTH-like domain
    1.1e-13   50.7   0.0    2.5e-13   49.6   0.0    1.6  1  rve_3     Integrase core domain
     0.0064   16.6   0.0      0.011   15.9   0.0    1.4  1  rve_2     Integrase core domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   5.9e+03      69     100 ..      32      63 ..      22      68 .. 0.72
   2 !   95.5   0.0   5.2e-31   2.3e-27       2     118 ..     103     222 ..     102     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                            rve  69 rvlsDngseytskafrefladlgirvsftrpg 100
                                    rv+  n   y ++++  +l++ gi+v ++ + 
  gi|121638693|ref|YP_978917.1|  32 RVHAANYGVYGARKVWLTLNREGIEVARCTVE 63 
                                    56666666777788888888888888888765 PP

  == domain 2  score: 95.5 bits;  conditional E-value: 5.2e-31
                            rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve.....pervlsDngs 76 
                                    ++p++lw +D+t+v+  ++ g+ay+++v+d++ r+il++ + + m++s+vl+++e+a++ +++++       ++++D+gs
  gi|121638693|ref|YP_978917.1| 103 PAPNRLWVADLTYVS--TWAGFAYVAFVTDAYARRILGWRVASTMATSMVLDAIEQAIWTRQQEGvldlkDVIHHTDRGS 180
                                    68*************..77888*****************************************99****999******** PP

                            rve  77 eytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                    +yts +f e la+ gi++s+ ++g+++dn+++E +++++k+e
  gi|121638693|ref|YP_978917.1| 181 QYTSIRFSERLAEAGIQPSVGAVGSSYDNALAETINGLYKTE 222
                                    ***************************************997 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.2   3.6e-19   1.6e-15       5      59 ..      25      78 ..      20      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 3.6e-19
                         HTH_21  5 allalireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59
                                   +l+++i +++++++g+YG+r++w  L+re g+ v +++V+RlM +lGL g +r k
  gi|121638693|ref|YP_978917.1| 25 ELKEHISRVHAANYGVYGARKVWLTLNRE-GIEVARCTVERLMTKLGLSGTTRGK 78
                                   58999************************.89******************99987 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   5.5e-17   2.5e-13       2      67 .]     195     261 ..     194     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.5e-17
                          rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneel.frslaearekleawredYNteRPHssLgykTP 67 
                                    gi++s++a+g+ ++N+l+E +ng +++el++    +rs+++++ ++++w++++N++R  + +g ++P
  gi|121638693|ref|YP_978917.1| 195 GIQPSVGAVGSSYDNALAETINGLYKTELIKPGKpWRSIEDVELATARWVDWFNHRRLYQYCGDVPP 261
                                    89*****************************887899**********************99999998 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-06     0.011       2      40 ..     214     253 ..     213     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-06
                          rve_2   2 sfFgsLKtElvyge.tfktleeleaaiedYIewYNnkRlk 40 
                                     + g++KtEl+    ++ ++e +e+a    ++w+N+ Rl 
  gi|121638693|ref|YP_978917.1| 214 TINGLYKTELIKPGkPWRSIEDVELATARWVDWFNHRRLY 253
                                    56699******8554***********************83 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2018.12
//
Query:       gi|121638694|ref|YP_978918.1|  [L=108]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-09   36.8   2.3    1.5e-08   34.8   2.3    1.9  1  HTH_Tnp_1  Transposase
     0.0049   17.0   0.5      0.014   15.6   0.0    2.0  3  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.072   13.5   0.0      0.088   13.2   0.0    1.3  1  DUF1323    Putative transcription regulator (DUF1323)
      0.094   12.8   0.1       0.22   11.7   0.0    1.8  2  MerR_1     MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   2.3   3.4e-12   1.5e-08       5      75 .]       7      83 ..       4      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3.4e-12
                      HTH_Tnp_1  5 rrwsdefKariVresle.......pgksvsevArrhgvs.pnqLykWrrqyregeeaspaefeltaleeenrelkrela 75
                                   rr+++e ++r+Vr + e       + + +sevAr +gv  +++ +kW+rq++ + +a+p +   t++++e+++l+r +a
  gi|121638694|ref|YP_978918.1|  7 RRYPPELRERAVRMVAEirgqhdsEWAAISEVARLLGVGcAETVRKWVRQAQVDAGARPGT--TTEESAELKRLRRDNA 83
                                   9************996532222224578**********6489*******************..8888888888887654 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.5   1.1e+04      33      40 ..       4      11 ..       3      12 .. 0.75
   2 !   15.6   0.0   3.1e-06     0.014       4      24 ..      35      56 ..      35      66 .. 0.90
   3 ?   -2.3   0.0       1.2   5.3e+03       3      10 ..      68      75 ..      68      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                         HTH_17 33 Grrwripr 40
                                   G ++r+p 
  gi|121638694|ref|YP_978918.1|  4 GSSRRYPP 11
                                   77899986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.1e-06
                         HTH_17  4 veEaAelLgv.srstvyrlirr 24
                                   ++E+A+lLgv +  tv++++r+
  gi|121638694|ref|YP_978918.1| 35 ISEVARLLGVgCAETVRKWVRQ 56
                                   68********9*********98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                         HTH_17  3 tveEaAel 10
                                   t+eE Ael
  gi|121638694|ref|YP_978918.1| 68 TTEESAEL 75
                                   78888877 PP

>> DUF1323  Putative transcription regulator (DUF1323)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.088       4      34 ..      36      67 ..      33     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                        DUF1323  4 eelaellGy.arqtinrWvRkegWkteplpGv 34
                                    e+a+llG+  + t+ +WvR+ +    ++pG 
  gi|121638694|ref|YP_978918.1| 36 SEVARLLGVgCAETVRKWVRQAQVDAGARPGT 67
                                   699*****94589**********999999997 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.4e+03      33      44 ..       4      15 ..       2      22 .. 0.65
   2 ?   11.7   0.0   4.8e-05      0.22       3      28 ..      35      61 ..      34      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                   TS-EEEEHHHHH CS
                         MerR_1 33 ggrryYtdedie 44
                                   g  r+Y +e  e
  gi|121638694|ref|YP_978918.1|  4 GSSRRYPPELRE 15
                                   445888877554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.8e-05
                                   HHHHHHHHTS.-HHHHHHHHHHTT-S- CS
                         MerR_1  3 igevakilgv.tthtlrywekegllkp 28
                                   i+eva++lgv  + t+r w ++  +  
  gi|121638694|ref|YP_978918.1| 35 ISEVARLLGVgCAETVRKWVRQAQVDA 61
                                   9*******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 886.33
//
Query:       gi|121638695|ref|YP_978919.1|  [L=113]
Description: hypothetical protein BCG_2834c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-17   63.3   0.1    2.3e-17   62.9   0.1    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   1.3e-21   2.3e-17       1      69 [.      26      91 ..      26      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.3e-21
                                   EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEE CS
                    CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriyklt 69
                                   m+vlv+YDi +d++rr+ +akil  + ++rvQ+S Fe  l++ ql+kl +r++++  +  d+iriyk++
  gi|121638695|ref|YP_978919.1| 26 MFVLVIYDI-SDNRRRASLAKILAGF-GYRVQESAFEAMLTKGQLAKLVARIDRFAIDC-DNIRIYKIR 91
                                   9********.****************.***************************99977.9******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 823.27
//
Query:       gi|121638696|ref|YP_978920.1|  [L=338]
Description: hypothetical protein BCG_2835c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-73  246.8   0.0    2.6e-73  246.6   0.0    1.0  1  Cas_Cas1         CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.098   11.8   0.0       0.26   10.4   0.0    1.6  2  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.0   2.9e-77   2.6e-73       1     281 [.       4     283 ..       4     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 2.9e-77
                                    EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSST CS
                       Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlepeesgn 80 
                                    lyv+++ ++++  ++r++v++e+    ++p+e++++i +fg+ +++t+++  +++++ ++ +++ +g+y+gr++ +  + 
  gi|121638696|ref|YP_978920.1|   4 LYVSDSVSRISFADGRVIVWSEELGESQYPIETLDGITLFGRPTMTTPFIVEMLKRERDIQLFTTDGHYQGRISTPDVSY 83 
                                    79*******************99999****************************************************** PP

                                    HHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHH CS
                       Cas_Cas1  81 velrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaak 160
                                    +  +r+Q+++ dd++++l+l k+iv+ k+ nq++++r +++ +   +++e i+++++ l+ +++  sl eL g+EG+aak
  gi|121638696|ref|YP_978920.1|  84 APRLRQQVHRTDDPAFCLSLSKRIVSRKILNQQALIRAHTSGQ---DVAESIRTMKHSLAWVDRSGSLAELNGFEGNAAK 160
                                    ************************************8877777...9********************************* PP

                                    HHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHH CS
                       Cas_Cas1 161 aYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpl 240
                                    aYf a+++l+++ef f+gRs+rpp D +N++ s+gY+lly++++ aie+  L+ yiGfLH+d++g+ +La DLmE++R++
  gi|121638696|ref|YP_978920.1| 161 AYFTALGHLVPQEFAFQGRSTRPPLDAFNSMVSLGYSLLYKNIIGAIERHSLNAYIGFLHQDSRGHATLASDLMEVWRAP 240
                                    ******************************************************************************** PP

                                    HCHHHHHHHHHTTSS-GGGEEEETT..EEEE-HHHHHHHHHHH CS
                       Cas_Cas1 241 lvDrlvlslinkrqlkekdFekeen..gvlLteegrkkfleaf 281
                                    ++D +vl+li  + ++++ F+k+++  +v+ t+e+ + +++af
  gi|121638696|ref|YP_978920.1| 241 IIDDTVLRLIADGVVDTRAFSKNSDtgAVFATREATRSIARAF 283
                                    ************************9999*******99999987 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   2.9e-05      0.26     211     265 ..      41      98 ..      30     116 .. 0.83
   2 ?   -2.3   0.0      0.22     2e+03      31      48 ..     277     294 ..     266     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.9e-05
                Lip_A_acyltrans 211 pfFgepaatttspaklalktk.aavipvaiirkkdgskytvsvhPaldlsste..Dve 265
                                     +Fg+p++tt+ +  ++++ + +++ ++   ++++ s + vs+ P l+ +     D +
  gi|121638696|ref|YP_978920.1|  41 TLFGRPTMTTPFIVEMLKRERdIQLFTTDGHYQGRISTPDVSYAPRLRQQVHRtdDPA 98 
                                    69****************9999************************998765332544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.22
                Lip_A_acyltrans  31 esvlrkilkglgrlaakf 48 
                                    +s++r ++++++r a ++
  gi|121638696|ref|YP_978920.1| 277 RSIARAFGNRIARTATYI 294
                                    555566666666655533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2461.73
//
Query:       gi|121638697|ref|YP_978921.1|  [L=336]
Description: hypothetical protein BCG_2837c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-93  311.8   0.0      6e-93  311.6   0.0    1.0  1  Cas_Csm6  CRISPR-associated protein (Cas_Csm6)


Domain annotation for each model (and alignments):
>> Cas_Csm6  CRISPR-associated protein (Cas_Csm6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.6   0.0   3.4e-97     6e-93       1     288 [.      62     335 ..      62     336 .] 0.97

  Alignments for each domain:
  == domain 1  score: 311.6 bits;  conditional E-value: 3.4e-97
                       Cas_Csm6   1 teveIiereeidnvhefDvFyevFrkilkeiedeneddtiLlNvsSGTPaMksalvllavlgekrlkpvQVsTPekksne 80 
                                    t+v+I++ +++++vh+fD+F++vFr++l+e+++e++d+tiLlN+sSGTPaM++alv+++v+g++r+++vQVsTP++++++
  gi|121638697|ref|YP_978921.1|  62 TDVRIVT-YTNPSVHRFDLFVPVFRNHLVELSAEFPDRTILLNTSSGTPAMQAALVAINVFGIPRTTAVQVSTPARALSK 140
                                    79*****.9*********************************************************************** PP

                       Cas_Csm6  81 ..ekegskdyDveteweldedneegaenRckeveiaslrellkreqikklieaYdYeaAleiaaslkseenekvlkLlel 158
                                      ++e++++yD+e +w++++dn++ga+nRc+e+++a+l +ll+r+++k+li +YdY+aA++iaa+  s+ +++v++L++ 
  gi|121638697|ref|YP_978921.1| 141 pgDRESPDAYDLELMWDANDDNQPGAPNRCFEATSAALGALLERANLKQLIVSYDYSAAVTIAAD--SRLPDQVSNLIRG 218
                                    99***************************************************************..************* PP

                       Cas_Csm6 159 akarknldlsevnklarktaldllPvkesekkklfeYllalklklkreeladfvrritplvvelleailkekckidikdy 238
                                    a++r++l++  ++k++++ta++++P     ++k++eY++al+l++kre++a+f+r++tp+++ +l+a+++++++      
  gi|121638697|ref|YP_978921.1| 219 AMHRSRLEHLVAPKFFKDTAFTYDP-----ANKVAEYISALALLAKREQWAEFARSATPAITIVLRAAVAKHLP------ 287
                                    *************************.....********************************************...... PP

                       Cas_Csm6 239 Catkkknedkyekrdkkkl.kdpellealekefkeefkdkdvysihlkali 288
                                       + +  d + ++d++kl ++pe+++al++++k++++++++y+++++al+
  gi|121638697|ref|YP_978921.1| 288 ---EDRYLDDMGRVDRRKLeREPEIRCALKHPPKSPNAEWYLYTKDWLALL 335
                                    ...233345569******999**************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2634.72
//
Query:       gi|121638698|ref|YP_978922.1|  [L=375]
Description: hypothetical protein BCG_2838c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-10   40.4   0.0    6.7e-10   39.4   0.0    1.6  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.8e-14   6.7e-10       1     152 [.      11     263 ..      11     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.8e-14
                                    EEEESS-EE----................................................................... CS
                          RAMPs   1 kletltPlhiGdg................................................................... 13 
                                    +l +l P++iG+g                                                                   
  gi|121638698|ref|YP_978922.1|  11 TLRCLGPVFIGSGekrtskeyhvegdrvyfpdmellyadipahkrksfeafvmntdgaqataplkewvepnavkldpakh 90 
                                    6899**************************************************************************** PP

                                    .......................................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.. CS
                          RAMPs  14 .........................kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkek 68 
                                                             k+   +e+  +++d+ g+Py+PGS++kG+lRs +++ l+ ++     +    + +
  gi|121638698|ref|YP_978922.1|  91 rgyevkigsieprrasrgrggrmtrKKLTLNEIHAFIKDPLGRPYVPGSTVKGMLRSIYLQSLVHKRTAQPVRVPGHQTR 170
                                    ************************************************************77774444333333333333 PP

                                    ........HHHHHH--S............SS--SEEEEE...................................EEEEEE CS
                          RAMPs  69 qrvkkgd.leeaiFGne.........eeskiagrvffeDarpvkipgqileeskqikstpsp............klsgse 126
                                    +++++g+ +e++ + +            ++ + ++++ D+  + +  +                           ++ + 
  gi|121638698|ref|YP_978922.1| 171 EHRQYGErFERKELRKSgrpntrpqdAVNDLFQAIRVTDSPALRTSDL-------------LicqkmdmnvhgkPDGLPL 237
                                    333333343333332222223334444444444555555432222222.............1222233333333556666 PP

                                    EEEEEEEEEEE--SSS-EEEEEE... CS
                          RAMPs 127 lrelldhsterrtrvaidrktktngk 152
                                    +re+l ++t +++rv +d + + +g+
  gi|121638698|ref|YP_978922.1| 238 FRECLAPGTSISHRVVVDTSPTARGG 263
                                    66666666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2956.02
//
Query:       gi|121638699|ref|YP_978923.1|  [L=302]
Description: hypothetical protein BCG_2839c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-26   92.3   0.0    2.2e-26   91.5   0.0    1.3  1  Csm4_C    CRISPR Csm4 C-terminal domain
  ------ inclusion threshold ------
      0.067   13.2   0.0      0.082   12.9   0.0    1.1  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> Csm4_C  CRISPR Csm4 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   2.5e-30   2.2e-26       4      90 ..     210     296 ..     208     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.5e-30
                         Csm4_C   4 kkymlLSlllpkeeeledlleeaaYelikrsGfvssessae.qlkkkdvymfaeGSvfkkkleGkvvdvspegfehpvyr 82 
                                       m+L+++lp+++ele +l +a+Y+l+krsGfv+s+++a+  l+k+d+y fa+GSvf++ ++G ++dvs  g+ hpvy 
  gi|121638699|ref|YP_978923.1| 210 ASLMTLTTSLPTDDELEAALAGATYRLVKRSGFVASSTYADmPLRKRDIYKFAAGSVFSRPFQGGILDVSLGGN-HPVYS 288
                                    568**************************************9****************************8888.***** PP

                         Csm4_C  83 ygkalflp 90 
                                    y+ +lfl 
  gi|121638699|ref|YP_978923.1| 289 YARPLFLA 296
                                    ******96 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-06     0.082     135     212 ..     126     192 ..      69     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                                    EEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                          RAMPs 135 terrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                      ++++ ai++ +k +++     +++ + + e    +g++ l   s++elg+l  lL+ +      lGg ++ GfG++
  gi|121638699|ref|YP_978923.1| 126 HAVSAKAAIHNGKKDADP-----YRVGYFRFE--LDAGLWLLATGSESELGLLTRLLKGI----SALGGERTSGFGAF 192
                                    556677788888888888.....999999999..999***********************....************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2401.49
//
Query:       gi|121638700|ref|YP_978924.1|  [L=236]
Description: hypothetical protein BCG_2840c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-14   52.1   0.1    1.3e-13   51.5   0.1    1.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1     7e-18   1.3e-13       1     213 []      13     208 ..      13     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 7e-18
                                    EEEESS-EE----.................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HH CS
                          RAMPs   1 kletltPlhiGdg...kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdle 77 
                                    +l++lt l iG+g    + +  + + +++   +lP IPG+SlkG +R++l + +g   + +++ y++++e+        +
  gi|121638700|ref|YP_978924.1|  13 TLTVLTGLQIGAGdgfSAIGAVDKPVVRDPLSRLPMIPGTSLKGKVRTLLSRQYG---ADTETFYRKPNEDHA-----HI 84 
                                    689999999999988888888899999***********************98888...778888888888877.....9* PP

                                    HHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-E CS
                          RAMPs  78 eaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkggl 157
                                    +++FG++ e+   gr+ f+D+++                      ++   ++  +  te+++++ai+r t +++      
  gi|121638700|ref|YP_978924.1|  85 RRLFGDT-EEYMTGRLVFRDTKL--------------------TNKDDLEARGAKTLTEVKFENAINRVTAKANL----- 138
                                    *******.*************99....................66778889999***************999888..... PP

                                    EEEEEEESS..............................HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                          RAMPs 158 ftleaipae................rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                     + e + ++                + + +      +   e+ +a+   L+ll      lGg  ++G+G+v+
  gi|121638700|ref|YP_978924.1| 139 RQMERVIPGsefafslvyevsfgtpGEEQKASLPSSDEIIEDFNAIARGLKLL--ELDYLGGSGTRGYGQVK 208
                                    77555555557666666666666664444444444455555566666666666..777889999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1780.43
//
Query:       gi|121638701|ref|YP_978925.1|  [L=124]
Description: hypothetical protein BCG_2841c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-20   72.3   0.1    6.6e-20   72.1   0.1    1.0  1  Csm2_III-A  Csm2 Type III-A


Domain annotation for each model (and alignments):
>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.1   3.7e-24   6.6e-20       6     113 ..       7     120 ..       4     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3.7e-24
                                    HHHHHHHHHH..HHHH..TTS-STTTHHHHHHHHHHHHHHHHTHHHH.HHHTHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                     Csm2_III-A   6 elvekaeeig..kelkk.kklktsqiRkfydevkrieekikkkkeee.seeilrklkllkpklaYaagreeavkelsev. 80 
                                    ++v++ae i    + k+  +l+t+q+R +++ ++++  + +++ + +  +++++k+++l+++++Y++gre avk+++   
  gi|121638701|ref|YP_978925.1|   7 DYVKQAEVIRglPKKKNgFELTTTQLRVLLSLTAQLFDEAQQSANPTlPRQLKEKVQYLRVRFVYQSGREDAVKTFVRNa 86 
                                    78899998873333333345*******************98888888999***************************988 PP

                                    .HHHHHHH--SH.HHHHHHHHHHHHHHHHHHCT- CS
                     Csm2_III-A  81 .lkkaidkvkkskekfkrfvdffEAivAYhkyyg 113
                                     l +a++ + +s++ + rf++++EA+ AY+ky  
  gi|121638701|ref|YP_978925.1|  87 kLLEALEGIGDSRDGLLRFCRYMEALAAYKKYLD 120
                                    8******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 910.17
//
Query:       gi|121638702|ref|YP_978926.1|  [L=812]
Description: hypothetical protein BCG_2842c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-36  121.9   0.0    1.1e-34  118.1   0.0    2.6  3  Csm1_B    Csm1 subunit domain B
    0.00055   20.1   0.1     0.0015   18.7   0.1    1.7  1  HD        HD domain
      0.007   16.7   0.0      0.022   15.1   0.0    1.8  1  mCpol     minimal CRISPR polymerase domain
  ------ inclusion threshold ------
      0.045   13.5   0.2      0.081   12.6   0.2    1.3  1  DUF2616   Protein of unknown function (DUF2616)
       0.11   12.8   0.1        0.4   11.0   0.0    1.9  2  Vps39_1   Vacuolar sorting protein 39 domain 1


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   3.1e-38   1.1e-34       1      94 []     283     376 ..     283     376 .. 0.99
   2 ?    0.3   0.0      0.18   6.3e+02      36      54 ..     621     639 ..     617     670 .. 0.63
   3 ?   -3.5   0.0       2.7   9.6e+03      60      76 ..     774     790 ..     760     801 .. 0.73

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 3.1e-38
                                    --SS--HHHHHHHHHHHHHHHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS- CS
                         Csm1_B   1 IsskgAlksLrgRSfylellleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkL 80 
                                    I+s+gA+k+Lr+RSfyle+l+e+++dell +++lsranl Y+gGGh+ylLlpnte++++++e++e+e n+wll++f+++L
  gi|121638702|ref|YP_978926.1| 283 IHSSGAAKMLRARSFYLEMLTEHLIDELLARVGLSRANLNYSGGGHAYLLLPNTESARKSVEQFEREANDWLLENFATRL 362
                                    89****************************************************************************** PP

                                    EEEEEEEEE-TTTT CS
                         Csm1_B  81 ylalayvelsaedl 94 
                                    ++a+++v+l+a+dl
  gi|121638702|ref|YP_978926.1| 363 FIATGSVPLAANDL 376
                                    ************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                    CCCEEEEETTEEEEEEE-- CS
                         Csm1_B  36 ranllYagGGhfylLlpnt 54 
                                    +a ++Y+gG  ++++ +  
  gi|121638702|ref|YP_978926.1| 621 EATIIYSGGDDVFVVGAWD 639
                                    68899*9999888765544 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHCCCCT CS
                         Csm1_B  60 kleeiekelnewllkef 76 
                                     ++++ ++l +w+ +  
  gi|121638702|ref|YP_978926.1| 774 PFQQFANRLHQWFQDPT 790
                                    57889999999997654 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   4.2e-07    0.0015      28     121 ..       8     108 ..       2     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.2e-07
                                    HHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH................HHHHHHHHHTTCCH CS
                             HD  28 lllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld................ledvaklirehhes 91 
                                    + +++LlHDiGk++++         + +   H+ +g+   ++v +r+  +                   ++++i++hh s
  gi|121638702|ref|YP_978926.1|   8 AIIGCLLHDIGKPVQRA-----ALGYPG--RHSAIGRAFMKKVWLRDSRNpsqftdevdeadigvsDRRILDAISYHHSS 80 
                                    6799**********775.....333444..699999999999988886669999999999999999999*********** PP

                                    HHHHHHHH.HHHCCTSCHHHHHHHHHHHHHH CS
                             HD  92 wegkkrpr.glaerqlslearivklaDrlaa 121
                                      ++     + +  + +  a i+ +aD++aa
  gi|121638702|ref|YP_978926.1|  81 ALRT---AaENGRLAADAPAYIAYIADNIAA 108
                                    *976...345555677778888888888876 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.2e-06     0.022      48      91 ..     621     668 ..     616     678 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                          mCpol  48 gasvifaaGDsilaksslee..dllvelsrvyqkit..gltvSiGvGk 91 
                                    +a++i+++GD++ +    +   +  +el++ +++ t  +ltvS+G+G 
  gi|121638702|ref|YP_978926.1| 621 EATIIYSGGDDVFVVGAWDDviEFGIELRERFHEFTqgKLTVSAGIGM 668
                                    689*************9988878889999999999999*********6 PP

>> DUF2616  Protein of unknown function (DUF2616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.2e-05     0.081       8      94 ..     392     477 ..     389     478 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                        DUF2616   8 lkySklyrsakdsekkkkvykkWlkeiekikaaleskkveeseaedkCefClev...veeedklfCkkClfPllcsesvd 84 
                                    l+yS lyr+++++ + kk+ +  ++    + ++l+s++   ++   +C+ C++v   v+ +d+  C+ C      s++++
  gi|121638702|ref|YP_978926.1| 392 LRYSGLYRELSEQLSAKKLARYSAD----QLRELNSRDHDGQKGDRECSVCHTVnrtVSADDEPKCSLCQALTAASSQIQ 467
                                    79********988877776554433....344445555555555667*****9977677888999****887778999** PP

                        DUF2616  85 eelatyallS 94 
                                    +e + ++l+S
  gi|121638702|ref|YP_978926.1| 468 SESRRFLLIS 477
                                    ********98 PP

>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011       0.4      15      78 ..     371     434 ..     360     451 .. 0.85
   2 ?   -2.1   0.0       1.3   4.5e+03      39      67 ..     718     748 ..     711     764 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                        Vps39_1  15 klvgpLlrleNaCdlkdveeiLkkekkykeLidlYygkklheeALeLlkeladedeedeedssl 78 
                                      + +L+r +N+++ + +++ L  +  y+eL +    kkl + + + l+el ++d++ ++++ +
  gi|121638702|ref|YP_978926.1| 371 LAANDLMRRPNESASQASNRALRYSGLYRELSEQLSAKKLARYSADQLRELNSRDHDGQKGDRE 434
                                    45789************************************************87777766654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                        Vps39_1  39 ekkykeLidlYygkklheeAL..eLlkelad 67 
                                    e+ky+++ d++ g+++  +A   +Ll+ la+
  gi|121638702|ref|YP_978926.1| 718 EEKYRHIADYFSGNEERGMAFiyKLLELLAE 748
                                    6788899999999888777753356655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 4547.83
//
Query:       gi|121638703|ref|YP_978927.1|  [L=314]
Description: hypothetical protein BCG_2843c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-17   63.5   0.2    3.9e-17   62.7   0.2    1.5  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
  ------ inclusion threshold ------
       0.31   10.2   0.7        5.9    6.1   0.0    2.8  3  MRF_C1       Myelin gene regulatory factor -C-terminal domain


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.2   4.3e-21   3.9e-17       1      86 []     184     299 ..     184     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 4.3e-21
                                    EEEEEEE-EE..TEEESS--HHHHHHHHHHHHHHHTSS.................EECHHHHHH................ CS
                    CRISPR_Cas6   1 lrfltPtrfk..krkgllpsprlvfssllrrwnalaglkgk..............ptveeeleg................ 48 
                                    ++fltPt+fk  + ++++p+prlvf+sl++++ a+   ++                       +                
  gi|121638703|ref|YP_978927.1| 184 VEFLTPTAFKqsGEYVFWPDPRLVFQSLAQKYGAIVDGEEPdpgliaefgqsvrlS-------Afrvasapfavgaarvp 256
                                    69*********999*********************999844666655555443330.......03334444555555666 PP

                                    EEEEEEEE--.....HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                    CRISPR_Cas6  49 GfvGevkysg.....eleelekllrfaeylgvGkktafGlGkv 86 
                                    Gf+G+++++        + +  ll+f+e++g G k+++G+G++
  gi|121638703|ref|YP_978927.1| 257 GFTGSATFTVrgvdtFASYIAALLWFGEFSGCGIKASMGMGAI 299
                                    ********33434456666666*******************85 PP

>> MRF_C1  Myelin gene regulatory factor -C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.028   2.5e+02      17      27 ..      55      65 ..      53      66 .. 0.86
   2 ?   -2.3   0.0      0.28   2.5e+03       8      15 ..      85      92 ..      85      98 .. 0.80
   3 ?    6.1   0.0   0.00066       5.9      18      33 ..     110     125 ..     109     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.028
                         MRF_C1 17 keLcklTgnLE 27
                                    +L++lT  LE
  gi|121638703|ref|YP_978927.1| 55 EHLSRLTLTLE 65
                                   69*****9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.28
                         MRF_C1  8 iFmEnVgA 15
                                   ++mE++ A
  gi|121638703|ref|YP_978927.1| 85 VLMESIPA 92
                                   79***977 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.00066
                         MRF_C1  18 eLcklTgnLEtrIeel 33 
                                    +L++ T++LE +I+ l
  gi|121638703|ref|YP_978927.1| 110 ALARSTTSLEWKISTL 125
                                    69***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1769.02
//
Query:       gi|121638704|ref|YP_978928.1|  [L=215]
Description: hypothetical protein BCG_2844c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-59  200.9   0.1    1.6e-59  200.7   0.1    1.0  1  DUF1802   Domain of unknown function (DUF1802)
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.082   13.1   0.0    1.3  1  Cas9_C    Cas9 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.7   0.1   1.8e-63   1.6e-59       1     173 [.      38     208 ..      38     209 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 1.8e-63
                        DUF1802   1 ALkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpekveikawA 80 
                                    ALkew++av+aL +Grq+vllrKggi e+r  Fev+++eflL+Ptv+h++ae+++pe+++ll p+a++st+e v ++a A
  gi|121638704|ref|YP_978928.1|  38 ALKEWSAAVHALLDGRQTVLLRKGGIGEKR--FEVAAHEFLLFPTVAHSHAERVRPEHRDLLGPAAADSTDECVLLRAAA 115
                                    9*****************************..************************************************ PP

                        DUF1802  81 eveeavevsdeealealsklhiwteeave.drlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpeseaeea 159
                                    +v++a++v+++e l+a+++lhiwt+e+v+ drl+++pk++l vl++ +++l+epv+l+++pey+gc swv+lp + ++ a
  gi|121638704|ref|YP_978928.1| 116 KVVAALPVNRPEGLDAIEDLHIWTAESVRaDRLDFRPKHKLAVLVVCAIPLAEPVRLARRPEYGGCTSWVQLPLT-PQLA 194
                                    *************************************************************************99.**** PP

                        DUF1802 160 kPVlsdeefeerka 173
                                    +PV+++++++e++a
  gi|121638704|ref|YP_978928.1| 195 EPVHDEAALAEVAA 208
                                    *********99876 PP

>> Cas9_C  Cas9 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.1e-06     0.082      68     102 ..      39      73 ..      23      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-06
                         Cas9_C  68 kkgwrvavnkvlssgkvtvirrnalgepRlksqag 102
                                     k+w++av ++l   + +++r+ ++ge R++ +a+
  gi|121638704|ref|YP_978928.1|  39 LKEWSAAVHALLDGRQTVLLRKGGIGEKRFEVAAH 73 
                                    467**************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1197.94
//
Query:       gi|121638705|ref|YP_978929.1|  [L=294]
Description: hypothetical protein BCG_2845c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-24   85.3   0.5    7.6e-24   85.0   0.5    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.5   4.2e-28   7.6e-24       3     231 ..      36     272 ..      34     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 4.2e-28
                         AbiEii   3 LfalslsaladklvFkGGTaLslayg.lipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigege 81 
                                    L++   ++ +++lvFkGGT+L+++   +  RfS D+D+s   ++++e   ++ e+++ +    +e g++ ++        
  gi|121638705|ref|YP_978929.1|  36 LSQ-TVQFGDNRLVFKGGTSLRKCRLgNVGRFSTDLDFS---APDDEVVLEVCELIDGARVGGFEFGVQSTRG------- 104
                                    556.678899************77655************...99***************99999999986533....... PP

                         AbiEii  82 dyeglrlrypaefggyarqkikieigfreavppaerreippyleel..ggpafevpvysleellaeKllalldrgrdrsr 159
                                    d+++++lr+  +  g +r+   +e++ r+  +p e   + ++      g++ +++pv+  +e +aeKl        + + 
  gi|121638705|ref|YP_978929.1| 105 DGRHWQLRVRHTELGEPRIVASVEFARRPLALPSELLAFIQLPIHKayGFGLPTLPVVAEAEACAEKLARYR----RVAL 180
                                    777777777776688888888*******999***********9999************************77....9999 PP

                         AbiEii 160 aRDlyDlalLleaeldaeala.....eallaylasrgr..............pgelrlaplellreaeadealradwkaf 220
                                    aRDlyDl + +++ +d + ++     ++  +++++r+               +++++ ++++ l+ ++a++a++a+ +++
  gi|121638705|ref|YP_978929.1| 181 ARDLYDLNHFASRTIDEPLVRrlwvlKVWGDVVDDRRGtrplrvedvlaarsEHDFQPDSIGVLTRPVAMAAWEARVRKR 260
                                    ************888888855332555665555555558999*******************************9999999 PP

                         AbiEii 221 lamllggepd.p 231
                                     a l + + d +
  gi|121638705|ref|YP_978929.1| 261 FAFLTDLDADeQ 272
                                    998887777743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1694.87
//
Query:       gi|121638706|ref|YP_978930.1|  [L=295]
Description: hypothetical protein BCG_2846c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-49  165.3   0.1    1.7e-48  164.6   0.1    1.3  1  AbiEi_1   AbiEi antitoxin C-terminal domain
    7.3e-19   67.6   0.9    1.9e-18   66.3   0.2    2.0  2  AbiEi_4   Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.1   1.9e-52   1.7e-48       2     143 .]      85     237 ..      82     237 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 1.9e-52
                        AbiEi_1   2 LPleaflpslmkhlardyyag....llsAawlhGaahrqp.qriqvlvpkpakkipkglarvefvvrinvaalptkdva. 75 
                                    LPl+++l       ard++ag    ++sAaw++G+++rqp +ri++++p pak++p+gla++++vvri+++a++t+++a 
  gi|121638706|ref|YP_978930.1|  85 LPLRSWL-------ARDQNAGfmlaGASAAWHLGYLDRQPdGRIPIWLP-PAKRLPDGLASYVSVVRIPWNAADTALLAp 156
                                    6666666.......89*******999***********************.****************************** PP

                        AbiEi_1  76 .............aeaggvpvssPeatavdlatrpsavggldnvlevLdelaeevkpeeLeellsgrpasvlqRlgyLLe 142
                                                 a+a+g+p+++Pea++v++atrp+++g++++++++Ld+l++++++e+Le+llsgrp+s++qR++yLL+
  gi|121638706|ref|YP_978930.1| 157 rpallvrrrldlvAWATGLPALGPEALLVQIATRPASFGPWADLVPHLDDLVADCSDERLERLLSGRPTSAWQRASYLLD 236
                                    *******************************************************************************8 PP

                        AbiEi_1 143 e 143
                                    +
  gi|121638706|ref|YP_978930.1| 237 S 237
                                    5 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.2   2.2e-22   1.9e-18       1      49 []       9      73 ..       9      73 .. 0.99
   2 ?   -1.7   0.0      0.39   3.5e+03      22      36 ..     221     238 ..     208     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.2e-22
                        AbiEi_4  1 erlpelasrqv.Glfttrel............ea.aGisp.salrrLvrkGwLvrlr.rGvYali 49
                                   +r+p++asr+v Gl+++r++            ea +G++p sa+r+L+r+GwLv+l+ +G++a+i
  gi|121638706|ref|YP_978930.1|  9 RRIPTWASRVVsGLARDRPVvvtkedltqrltEAgCGRDPdSAIRELRRIGWLVQLPvKGTWAFI 73
                                   79*************************************************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.39
                        AbiEi_4  22 aGispsa...lrrLvrkG 36 
                                    +G+++sa    ++L+++G
  gi|121638706|ref|YP_978930.1| 221 SGRPTSAwqrASYLLDSG 238
                                    678888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1635.44
//
Query:       gi|121638707|ref|YP_978931.1|  [L=181]
Description: hypothetical protein BCG_2847c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-60  203.9   0.1    1.9e-60  203.7   0.1    1.0  1  DUF1802   Domain of unknown function (DUF1802)
  ------ inclusion threshold ------
      0.073   13.3   0.0       0.13   12.4   0.0    1.3  1  Cas9_C    Cas9 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7   0.1   2.1e-64   1.9e-60       1     173 [.       4     174 ..       4     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 2.1e-64
                        DUF1802   1 ALkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpekveikawA 80 
                                    ALkew++av+aL +Grq+vllrKggi e+r  Fev+++eflL+Ptv+h++ae+++pe+++ll p+a++st+e v ++a A
  gi|121638707|ref|YP_978931.1|   4 ALKEWSAAVHALLDGRQTVLLRKGGIGEKR--FEVAAHEFLLFPTVAHSHAERVRPEHRDLLGPAAADSTDECVLLRAAA 81 
                                    9*****************************..************************************************ PP

                        DUF1802  81 eveeavevsdeealealsklhiwteeave.drlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpeseaeea 159
                                    +v++a++v+++e l+a+++lhiwt+e+v+ drl+++pk++l vl++ +++l+epv+l++tpey+gc swv+lp + ++ a
  gi|121638707|ref|YP_978931.1|  82 KVVAALPVNRPEGLDAIEDLHIWTAESVRaDRLDFRPKHRLAVLVVSAIPLAEPVRLARTPEYGGCTSWVQLPVT-PTLA 160
                                    **************************************************************************9.9*** PP

                        DUF1802 160 kPVlsdeefeerka 173
                                    +PV+++++++e++a
  gi|121638707|ref|YP_978931.1| 161 APVHDEAALAEVAA 174
                                    *********99876 PP

>> Cas9_C  Cas9 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.5e-05      0.13      69     102 ..       6      39 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                         Cas9_C  69 kgwrvavnkvlssgkvtvirrnalgepRlksqag 102
                                    k+w++av ++l   + +++r+ ++ge R++ +a+
  gi|121638707|ref|YP_978931.1|   6 KEWSAAVHALLDGRQTVLLRKGGIGEKRFEVAAH 39 
                                    67**************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1011.37
//
Query:       gi|121638708|ref|YP_978932.1|  [L=89]
Description: hypothetical protein BCG_2848c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-34  116.0   1.5    8.2e-34  115.8   1.5    1.0  1  DUF2277   Uncharacterized conserved protein (DUF2277)


Domain annotation for each model (and alignments):
>> DUF2277  Uncharacterized conserved protein (DUF2277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   1.5   4.6e-38   8.2e-34       1      78 []       1      84 [.       1      84 [. 0.98

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 4.6e-38
                        DUF2277  1 MCrnIktLrnlePpateeeiraAAlqyVRKvsGvrkpsaaneeaferAveeiaaaterLLdeLetra......ppkrreeva 76
                                   MCrnI++Lr+l+Ppat  ei+aAA+qyVRKvsG+++psaa++eafe+Av+e++a+t+rLLd+L+ r+      pp+rr+ va
  gi|121638708|ref|YP_978932.1|  1 MCRNITELRGLQPPATPVEIAAAARQYVRKVSGITHPSAATAEAFEAAVAEVTATTTRLLDALPPRRqppktvPPLRRPDVA 82
                                   *****************************************************************999999999****9999 PP

                        DUF2277 77 ar 78
                                   ar
  gi|121638708|ref|YP_978932.1| 83 AR 84
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.57
# Mc/sec: 466.63
//
Query:       gi|121638709|ref|YP_978933.1|  [L=130]
Description: hypothetical protein BCG_2849c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-16   60.5   0.1    2.5e-16   60.3   0.1    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.023   14.9   0.0    1.5  1  PIN_10    PIN like domain
      0.041   14.0   0.0       0.06   13.4   0.0    1.2  1  Mut7-C    Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   4.3e-20   2.5e-16       1     117 [.       4     119 ..       4     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.3e-20
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeia 78 
                                    ++lD++v +++  +++  ++aa +++e+++el++ a+++ El++ ++   +++++a+ ++ +l++ ++ ++ + i+ ++a
  gi|121638709|ref|YP_978933.1|   4 VLLDSHVAYWWSaEPQRLSMAASQAIEHADELAVAAISWFELAWLAEQ--ERIQLAIPVLSWLQQlAEHVRTVGITPSVA 81 
                                    689*******99************************************..***************9999*********** PP

                                    HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                            PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfr 117
                                    ++a ++ +    +p+D li+AtA+ehg +l+ t+D+++r
  gi|121638709|ref|YP_978933.1|  82 ATAVALPSSFPGDPADRLIYATAIEHGWRLV-TKDRRLR 119
                                    *******************************.*****97 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.8e-06     0.023      28      67 ..      84     123 ..      62     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
                         PIN_10  28 vvhlrdkfaagtkDeeWiaalaeggwvvltkDrrirkrpa 67 
                                    +v l+  f+ + +D   +a++ e+gw ++tkDrr+r+ ++
  gi|121638709|ref|YP_978933.1|  84 AVALPSSFPGDPADRLIYATAIEHGWRLVTKDRRLRSHRH 123
                                    5556666666777776666666*************99876 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05      0.06       9      56 ..      64     122 ..      60     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                         Mut7-C   9 lgklakyLRllGydalyasdv...........edeellalaakekrillTrdreLlkra 56 
                                    l++la+++R +G+   +a ++           +d+ + a+a +++  l+T+dr+L +++
  gi|121638709|ref|YP_978933.1|  64 LQQLAEHVRTVGITPSVAATAvalpssfpgdpADRLIYATAIEHGWRLVTKDRRLRSHR 122
                                    899**********99988866789999999999*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 712.72
//
Query:       gi|121638710|ref|YP_978934.1|  [L=71]
Description: hypothetical protein BCG_2850c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-09   37.3   0.0    2.1e-09   37.0   0.0    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.2e-13   2.1e-09       5      50 ..       2      46 ..       1      62 [. 0.87

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.2e-13
                                   EHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH CS
                PhdYeFM_antitox  5 siseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqe 50
                                   +++e ka++ +lldev++gee + It++G+ va+lv++   ++l+ 
  gi|121638710|ref|YP_978934.1|  2 TATEVKAKILSLLDEVAQGEE-IEITKHGRTVARLVAATGPHALKG 46
                                   68*******************.**************9987777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 398.93
//
Query:       gi|121638711|ref|YP_978935.1|  [L=249]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-51  174.4   0.0    4.3e-51  173.6   0.0    1.3  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.9e-28   99.9   0.3      3e-27   96.0   0.3    2.0  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.19   11.3   0.0    1.3  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.6   0.0   7.2e-55   4.3e-51       3     226 ..      11     225 ..       9     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 7.2e-55
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                     + v  ++lnrP+  Nalsa+l++ + +al+++e d  + +v+LtG d +F+aG+dlke+a++      +    +   w 
  gi|121638711|ref|YP_978935.1|  11 DERVRTLTLNRPQSRNALSAALRDRFFAALADAEADDDIDVVILTGADPVFCAGLDLKELAGQ------TALPDISPRWP 84 
                                    5678899******************************************************95......45566677776 PP

                                    HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                          ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                    +   + kpvi a+nGaa+ GGlelal cDi ia+++a+f+ + +++Gl+p  g++ +l++kvG  +A+++ l+g+ +sa 
  gi|121638711|ref|YP_978935.1|  85 A---MTKPVIGAINGAAVTGGLELALYCDILIASEHARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAT 161
                                    6...579************************************************************************* PP

                                    HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfes 226
                                    +al++Glv +vv+++qll +a+ +a+ ++ + ++a+r+l +++++  e++ a++l +ea   ++
  gi|121638711|ref|YP_978935.1| 162 DALRAGLVTEVVAHDQLLPTARRVAASIVGNNQNAVRALLASYHRIDESQTAAGLWLEACAAKQ 225
                                    ********************************************99999999888887766555 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.3   5.1e-31     3e-27       1     210 [.      14     212 ..      14     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 5.1e-31
                                    .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHH CS
                          ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYkln 80 
                                    v+++tLnrp++ NaLs ++ +++ +al + e+dd++++v+l+ga    fCAG D+++l+ +    +            + 
  gi|121638711|ref|YP_978935.1|  14 VRTLTLNRPQSRNALSAALRDRFFAALADAEADDDIDVVILTGAD-PVFCAGLDLKELAGQTALPD------------IS 80 
                                    5899***************************************76.9***********99888855............55 PP

                                    HHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-H CS
                          ECH_2  81 yliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkg 159
                                     +   ++kpv+  ++G ++ gG+ l++ + + +++e+++fA    ++Gl P  G s  L++  g  l++ + lTG+ l++
  gi|121638711|ref|YP_978935.1|  81 PRWPAMTKPVIGAINGAAVTGGLELALYCDILIASEHARFADTHARVGLLPTWGLSVRLPQKVGiGLARRMSLTGDYLSA 160
                                    78899*******************************************************976669************** PP

                                    HHHHHTTS--EE--GGGHHHHHHHHHTT.........--------......- CS
                          ECH_2 160 adalaaglathyvpseklealeeaLaelessd.eeaveevleelaeeaeeee 210
                                    +dal agl t +v +++l   ++++a+    + ++av+++l+++++  e+++
  gi|121638711|ref|YP_978935.1| 161 TDALRAGLVTEVVAHDQLLPTARRVAASIVGNnQNAVRALLASYHRIDESQT 212
                                    *****************98888888776554458999999999986655533 PP

>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.2e-05      0.19      60      99 ..      23      61 ..      14      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHHHT-TTS----HHHHTTEEEEEEEE---EE-- CS
                        AMMECR1 60 vaenAlaaAfeDpRFspvtaeElpeleveVsvLtepepiv 99
                                    ++nAl+aA++D+ F  ++ +E ++ +++V +Lt  +p++
  gi|121638711|ref|YP_978935.1| 23 QSRNALSAALRDRFFAALADAEADD-DIDVVILTGADPVF 61
                                   5789******************998.89999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1518.19
//
Query:       gi|121638712|ref|YP_978936.1|  [L=360]
Description: sn-glycerol-3-phosphate transport ATP-binding protein ABC transporter ugpC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-29  103.3   0.0    2.2e-29  102.7   0.0    1.3  1  ABC_tran         ABC transporter
    1.1e-07   32.3   1.7    1.3e-05   25.7   0.7    2.7  2  CysA_C_terminal  CysA C-terminal regulatory domain
      7e-07   30.0   0.1    2.6e-06   28.2   0.1    2.0  1  OB_MalK          MalK OB fold domain
    6.7e-05   22.8   0.0      0.012   15.4   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00017   21.6   0.0    0.00026   21.0   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.001   19.0   0.0     0.0019   18.1   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
     0.0017   18.6   0.0      0.003   17.9   0.0    1.5  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.023   15.1   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.024   14.2   0.2       0.12   11.9   0.0    2.2  3  AAA_25           AAA domain
      0.028   14.1   0.0      0.062   13.1   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.045   14.2   0.0      0.082   13.3   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.047   13.1   0.0        9.2    5.6   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.062   13.0   0.0       0.11   12.2   0.0    1.5  1  AAA_30           AAA domain
      0.087   13.0   0.8        0.3   11.2   0.5    2.1  1  AAA_33           AAA domain
      0.092   12.7   0.2       0.28   11.2   0.1    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.5   1.1       0.75   10.0   0.3    2.6  2  TOBE_2           TOBE domain
       0.16   12.0   0.0       0.33   11.1   0.0    1.5  1  TcpA             Toxin-coregulated pilus subunit TcpA


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.0   2.1e-32   2.2e-29       2     136 ..      22     163 ..      21     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 2.1e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    +n++l++  ge +++vG++G+GKSt l++lagl+  ++G+i + + d+++  l+   + +++++q+  l p++tv+ n  
  gi|121638712|ref|YP_978936.1|  22 DNLDLDIADGEFLVLVGPSGCGKSTTLRVLAGLEPIESGRISIGDVDVTH--LPPRARDVAMVFQNYALYPNMTVAANmg 99 
                                    89***********************************************9..99************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               + ++++ ++++ l+l++l d++     ++LSgGq+qrva+ ra++++p+++++DEp 
  gi|121638712|ref|YP_978936.1| 100 falrnagmsraDTRRRVLEVADMLELTDLLDRKP----AKLSGGQRQRVAMGRAIVRRPRVFCMDEPL 163
                                    *******998777777999999999999888887....*****************************7 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.039        41       7      29 ..      57      78 ..      56      83 .. 0.77
   2 !   25.7   0.7   1.2e-08   1.3e-05       1      42 [.     242     280 ..     242     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.039
                CysA_C_terminal  7 vedGklriGglalp.vPelagadg 29
                                   +e G++ iG++++  +P  + a++
  gi|121638712|ref|YP_978936.1| 57 IESGRISIGDVDVThLP--PRARD 78
                                   789*********99888..54444 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.2e-08
                CysA_C_terminal   1 NlFhGrvedGklriGglalpvPelagadgqevvayVRPhDle 42 
                                    Nl+++ v  G +r  +la+pvP +++a  ++v ++VRP+  +
  gi|121638712|ref|YP_978936.1| 242 NLIDAAVAHGVVRAPDLAIPVP-DPAA--ERVLVGVRPESWD 280
                                    9*********************.7777..7********9766 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   2.4e-09   2.6e-06       1      51 [.     237     277 ..     237     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.4e-09
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPE 51 
                                    G PaMN+++a v   g +v + ++++p+p+ +         ++v++G+RPE
  gi|121638712|ref|YP_978936.1| 237 GAPAMNLIDAAVA-HG-VVRAPDLAIPVPDPA--------AERVLVGVRPE 277
                                    99***********.66.8************98........9********** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.012       1      23 [.      33      55 ..      33      91 .. 0.77
   2 ?    5.4   0.0     0.013        14     227     275 ..     126     171 ..     100     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   + vl+Gp g+GKS+ L+ l +l 
  gi|121638712|ref|YP_978936.1| 33 FLVLVGPSGCGKSTTLRVLAGLE 55
                                   579****************9993 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                         AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkll 275
                                    +d  ++ +++lS G+++  a+  a+ r++   ++++ DEp ++L+ kl 
  gi|121638712|ref|YP_978936.1| 126 TDLLDRKPAKLSGGQRQRVAMGRAIVRRP---RVFCMDEPLSNLDAKLR 171
                                    55566678889999999999999999999...*************9876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.4e-07   0.00026      43      67 ..      29      53 ..      20      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                          Rad17 43 rkkriLLisGPsGCgkstvvkvLsk 67
                                   +  + L++ GPsGCgkst+++vL+ 
  gi|121638712|ref|YP_978936.1| 29 ADGEFLVLVGPSGCGKSTTLRVLAG 53
                                   5556899****************85 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0019      90     131 ..      21      63 ..       4      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                    +++l   ++d ++ vlvG+SG GKSt + +l++ + ++ g +s
  gi|121638712|ref|YP_978936.1|  21 VDNLDLDIADgEFLVLVGPSGCGKSTTLRVLAGLEPIESGRIS 63 
                                    5667777777799*******************98888888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.8e-06     0.003       5      33 ..      31      59 ..      28     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeea 33
                                     +lv++G+sG+GK+t+lr l+   ++e+
  gi|121638712|ref|YP_978936.1| 31 GEFLVLVGPSGCGKSTTLRVLAGLEPIES 59
                                   5799***************9998877653 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.2e-05     0.023      23      45 ..      30      52 ..      22      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                   ++e ++l+G+sG+GKs+ +r l+
  gi|121638712|ref|YP_978936.1| 30 DGEFLVLVGPSGCGKSTTLRVLA 52
                                   34789**************9876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.12      26      53 ..      24      51 ..       5      54 .. 0.78
   2 ?   -1.8   0.0       1.8   1.9e+03      81      98 ..     107     131 ..      91     160 .. 0.64
   3 ?   -2.8   0.0       3.8     4e+03     171     189 ..     177     195 ..     165     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                         AAA_25 26 vkgllpagelallaGapgtGKttlaldl 53
                                   ++  ++ ge+ +l+G++g+GK+t +  l
  gi|121638712|ref|YP_978936.1| 24 LDLDIADGEFLVLVGPSGCGKSTTLRVL 51
                                   5555789****************87655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                         AAA_25  81 dsedelrrRlravgeal.......r 98 
                                    +s++++rrR+ +v   l       r
  gi|121638712|ref|YP_978936.1| 107 MSRADTRRRVLEVADMLeltdlldR 131
                                    5566667777666655544433322 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.8
                         AAA_25 171 aleriarrtgaavllvhHv 189
                                    ++  ++rr+g +++ v H 
  gi|121638712|ref|YP_978936.1| 177 QISGLQRRLGTTTVYVTHD 195
                                    5667889999999999995 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.8e-05     0.062      13      39 ..      22      48 ..      19      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                   d+ +++i   ++ +l+GpsG GKST l
  gi|121638712|ref|YP_978936.1| 22 DNLDLDIADGEFLVLVGPSGCGKSTTL 48
                                   55667777445999***********76 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.8e-05     0.082       2      51 ..      35      84 ..      34      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfk 51
                                   +l+Gp G+GK+++ + +a    +e  +is  ++   ++  ++++++++f+
  gi|121638712|ref|YP_978936.1| 35 VLVGPSGCGKSTTLRVLAGLEPIESGRISIGDVDVTHLPPRARDVAMVFQ 84
                                   79***************998777777777777776666677777777776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0094       9.9      24      40 ..      31      47 ..      23      53 .. 0.84
   2 ?    5.6   0.0    0.0087       9.2     120     202 ..     119     197 ..      70     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0094
                                   SSEEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnl 40
                                    +f ++vGp G+GKs  
  gi|121638712|ref|YP_978936.1| 31 GEFLVLVGPSGCGKSTT 47
                                   57899**********76 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0087
                                    HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 120 kkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                     +++ el    + ++  LSgG+++ va+    Ai   ++  ++++De  ++LD+k +    + +   + +     + +++
  gi|121638712|ref|YP_978936.1| 119 VADMLELTDLLDRKPAKLSGGQRQRVAMG--RAIV--RRPRVFCMDEPLSNLDAKLRVSTRSQISGLQRRLGTTTVYVTH 194
                                    33333333333345669******977765..3443..4444667999999999988777766666555554444444444 PP

                                    HHC CS
                                    xxx RF
                          SMC_N 200 eml 202
                                    +++
  gi|121638712|ref|YP_978936.1| 195 DQV 197
                                    444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.11      19      45 ..      32      58 ..      26     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                    + vl+Gp G GK+t+l++l+ +   +
  gi|121638712|ref|YP_978936.1| 32 EFLVLVGPSGCGKSTTLRVLAGLEPIE 58
                                   3789***************98776555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00029       0.3       2      21 ..      34      53 ..      33     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                         AAA_33  2 vllvGlpGsGKstlaerllk 21
                                   ++lvG++G+GKst ++ l+ 
  gi|121638712|ref|YP_978936.1| 34 LVLVGPSGCGKSTTLRVLAG 53
                                   589***********998874 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00027      0.28       2      20 ..      34      52 ..      33      58 .. 0.90
   2 ?   -2.6   0.0       4.7     5e+03      45      75 ..     200     229 ..     181     238 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                   EEEE--SSSSHHHHHHHGG CS
                          AAA_5  2 vlLvGppGtgKselaerla 20
                                   ++LvGp+G+gKs+  + la
  gi|121638712|ref|YP_978936.1| 34 LVLVGPSGCGKSTTLRVLA 52
                                   68************99987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                                    B--.........--------G-SEEEEESGG CS
                          AAA_5  45 reikngttslvdsplvraaregeilvlDEve 75 
                                    + + ++ ++l+d++l  ++ +++ l++D v+
  gi|121638712|ref|YP_978936.1| 200 MTMGDRVAVLKDGVLQ-QVDTPRALYDDPVN 229
                                    3334555666666666.66677777777666 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.4   1.4e+03      51      66 ..     192     208 ..     175     210 .. 0.73
   2 ?   10.0   0.3   0.00071      0.75       1      76 []     272     351 ..     272     351 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                         TOBE_2  51 nadr.dsalapGdtVel 66 
                                    ++++  +a++ Gd+V++
  gi|121638712|ref|YP_978936.1| 192 VTHDqVEAMTMGDRVAV 208
                                    34442479999999987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00071
                         TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpn....adrdsalapGdtVelswdpddavvl 76 
                                    +++RPE   +a+ g+ ++l+ +Ve ve lG ++ ++ +  +++ +  r p     +dr++a+++G+ +++  + + ++++
  gi|121638712|ref|YP_978936.1| 272 VGVRPESWDVASIGTPGSLTVHVELVEELGFESFVYATPVDQRGWSSRAPRivfrTDRRTAVRVGESLAIVPHSQEVRLF 351
                                    79********6333356**************9999976666555555333211102223588888888888777777665 PP

>> TcpA  Toxin-coregulated pilus subunit TcpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.33      31      69 ..      94     132 ..      62     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                    TEEEEEEEEEEEEE-HHHHHHHHHHHGGG-SEEEEEES- CS
                           TcpA  31 kaankafaikvsdlskdqckslvssvadlfsfievkera 69 
                                     aan +fa++ +++s++  +  v +vad++ + ++ +r 
  gi|121638712|ref|YP_978936.1|  94 VAANMGFALRNAGMSRADTRRRVLEVADMLELTDLLDRK 132
                                    69***************************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2538.95
//
Query:       gi|121638713|ref|YP_978937.1|  [L=210]
Description: sn-glycerol-3-phosphate-binding lipoprotein ugpB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-19   70.4   0.4    3.2e-19   70.0   0.4    1.1  1  SBP_bac_1     Bacterial extracellular solute-binding protein
    1.2e-17   64.6   0.1    1.7e-17   64.2   0.1    1.2  1  SBP_bac_8     Bacterial extracellular solute-binding protein
    7.1e-05   22.5   5.0    0.00014   21.6   5.0    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
     0.0021   17.5   0.1     0.0026   17.2   0.1    1.1  1  SBP_bac_6     Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.017   14.5   0.9      0.038   13.4   0.9    1.6  1  UCR_Fe-S_N    Ubiquitinol-cytochrome C reductase Fe-S subunit
       0.14   12.2   0.3        0.3   11.1   0.3    1.6  1  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.4   1.1e-22   3.2e-19       8     166 ..      51     203 ..      43     210 .] 0.85

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.1e-22
                                    HHHHHHHHHHHHHHHTTEEEEEEEE..CHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECT CS
                      SBP_bac_1   8 aalqalvakafekehpgikVeiesv..gsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapg 85 
                                    aa ++l+  +f+ + p   V++++   +++++aqk+ +a+ ++d p Dv+  d++w+ ++a  g+l+ ld++++   +++
  gi|121638713|ref|YP_978937.1|  51 AAERELI-GRFQDRFPTLSVKLIDAgkDYDEVAQKFNAALIGTDVP-DVVLLDDRWWFHFALIGVLTALDDLFGQVGVDT 128
                                    3455566.8999999******999999*****************88.*****************************9999 PP

                                    TCCTEEEEHHHHTHHHHCE.EE...ES.EEEE.EEEEEEEETTTHHCTTGGG..SHBHHHHHHHHHHHHHHCTCTHCCHC CS
                      SBP_bac_1  86 vkdaadklsssvlpkilds.kv...ly.vPly.aargliYNkdlfekagldp..pwtWdelveaakklkekgkkpiggar 157
                                    ++         ++++ l++ ++   +y vP+  ++ +++YNk  + +agl+     +W+e+ e++ +l    +++     
  gi|121638713|ref|YP_978937.1| 129 TD---------YVDSLLADyEFngrHYaVPYArSTPLFYYNKAAWQQAGLPDrgLQSWSEFDEWGPELQRVVGAG----- 194
                                    65.........77777776677789*******77*****************9*999**************88888..... PP

                                    CEEHHHHHH CS
                      SBP_bac_1 158 ggsasgtay 166
                                    ++++++ ++
  gi|121638713|ref|YP_978937.1| 195 RSAHGWANA 203
                                    444443333 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.1   5.7e-21   1.7e-17      12     138 ..      67     202 ..      55     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 5.7e-21
                                    EEEEEEE-..-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG......GSTTHHH-HHHHHTT--TS. CS
                      SBP_bac_8  12 vkvnvvta..asndleqklkaalaagtapdidvvwanedalatlaeeglladls......dldnlddltdalaavgydgk 83 
                                      v+++ a  ++++++qk++aal   ++pd+ v++ ++ ++  +   g+l +l+       +d+ d++++ la+++++g 
  gi|121638713|ref|YP_978937.1|  67 LSVKLIDAgkDYDEVAQKFNAALIGTDVPDV-VLLDDRWWFHFAL-IGVLTALDdlfgqvGVDTTDYVDSLLADYEFNGR 144
                                    56777777779*************99****7.6888889988555.699999988889777799999999********** PP

                                    ----EEEEEEE-EEEEEHHHHHHS.....---BHHHHHHHHHHHHHH-SEGG---GGGG CS
                      SBP_bac_8  84 lygvPyasetpyvliynkdlleka....edpktwdellaaakklkgkfglpdpasgwlq 138
                                    +y+vPya +tp +++ynk+++++a    +  ++w+e+ ++ ++l+  +g  ++a gw+ 
  gi|121638713|ref|YP_978937.1| 145 HYAVPYARSTP-LFYYNKAAWQQAglpdRGLQSWSEFDEWGPELQRVVGAGRSAHGWAN 202
                                    **********9.***********999999***************999999999999975 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   5.0   4.5e-08   0.00014       2      25 ..       4      25 ..       3      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.5e-08
                     TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                   l+RR+FL   +AaaAA++++gca+
  gi|121638713|ref|YP_978937.1|  4 LNRRQFLA--LAAAAAGVTAGCAG 25
                                   79******..************97 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   8.5e-07    0.0026       2      90 ..      93     192 ..      92     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.5e-07
                      SBP_bac_6   2 plpdlilsfdkdflekfieeglfqpld..........panlpnvnkdfaeeglkdp.dgkyypygvgplvlavnkdrlkg 70 
                                    ++pd++l +d+++  +f+  g++++ld          +++++++      +++  + +++ +py+ ++ ++++nk ++ +
  gi|121638713|ref|YP_978937.1|  93 DVPDVVL-LDDRWWFHFALIGVLTALDdlfgqvgvdtTDYVDSLL-----ADYEFNgRHYAVPYARSTPLFYYNKAAWQQ 166
                                    68*****.***********************99955555555555.....999999777777****************** PP

                      SBP_bac_6  71 rpvP....ksWaDL..ldPeykgkva 90 
                                      +P    +sW+++  + Pe++  v+
  gi|121638713|ref|YP_978937.1| 167 AGLPdrglQSWSEFdeWGPELQRVVG 192
                                    ****99999***99555677766555 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   1.3e-05     0.038      10      30 ..       5      24 ..       2      26 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                     UCR_Fe-S_N 10 tRRDFLyiATgavgaVGaaaa 30
                                   +RR FL +A++a+g+  a++a
  gi|121638713|ref|YP_978937.1|  5 NRRQFLALAAAAAGV-TAGCA 24
                                   7*******9988775.55544 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3    0.0001       0.3       4      25 ..       3      22 ..       2      28 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                   CytB6-F_Fe-S  4 PDmsrRqllNlllvGaialtaa 25
                                   P ++rRq+l l+  +a+++ta+
  gi|121638713|ref|YP_978937.1|  3 P-LNRRQFLALAA-AAAGVTAG 22
                                   6.9*****98764.44455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1681.49
//
Query:       gi|121638714|ref|YP_978938.1|  [L=275]
Description: sn-glycerol-3-phosphate transport integral membrane protein ABC transporter ugpE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-14   54.2  16.2    1.5e-14   54.2  16.2    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.07   1.2e+03      37      37 ..      25      25 ..       5      83 .. 0.56
   2 !   54.2  16.2   8.3e-19   1.5e-14       3     181 ..      86     266 ..      84     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.07
                   BPD_transp_1 37 i 37
                                   +
  gi|121638714|ref|YP_978938.1| 25 P 25
                                   1 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 8.3e-19
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                    +lG+l+a   ++ +++++ ++  +ii+ l++P  + +i  +   +++s lg  ++ + i+l l  +++ ++++r+ + sl
  gi|121638714|ref|YP_978938.1|  86 TLGVLSAfglVFVRFPGRTAVFLVIIAALMVPNQITVISNY---ALISHLGLRNTFAGIILPLAGVAFGTFLMRNHFLSL 162
                                    79********999**********************777755...456********************************* PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgydyseis 154
                                    p + +eaar++Ga+ wq++ +vvlP++ p++++  ++++++ +++++++ ++  +       +g+++l+  +      + 
  gi|121638714|ref|YP_978938.1| 163 PAEIIEAARMDGARWWQLLLRVVLPMSRPTMVAVGVITVVNEWNEYLWPFLMSDDESvaplpIGLTFLQQAE------GV 236
                                    ************************************************977776655433333333333222......22 PP

                   BPD_transp_1 155 ...nggvlalviavlllnlvadilqrlldp 181
                                         +++++++a+l+++lv+ +lqr   +
  gi|121638714|ref|YP_978938.1| 237 tnwGPVMAVTLLAMLPILLVFIALQRQMIK 266
                                    355679999999**********99997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1589.60
//
Query:       gi|121638715|ref|YP_978939.1|  [L=303]
Description: sn-glycerol-3-phosphate transport integral membrane protein ABC transporter ugpA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-22   77.7  10.0    1.4e-21   77.1  10.0    1.4  1  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
      0.017   15.3   1.5      0.029   14.5   0.1    2.0  2  Phage_holin_3_5  Bacteriophage holin Hol, superfamily III


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1  10.0   1.5e-25   1.4e-21       2     184 ..      95     302 ..      63     303 .] 0.94

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.5e-25
                   BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviill 60 
                                    ++lG+ +a  l r  ++++l+r  +++++ +   ++++  ++vf                    + +++ ++ ++v i++
  gi|121638715|ref|YP_978939.1|  95 MVLGLALAmlLDRPLRGRNLVRSTVFAPFVISGAAVGLAAQFVFdphfgliqdllrrigvgvpDFYQDARWALFMVTITY 174
                                    5788999988899999***********************************************99*************** PP

                   BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.... 136
                                    ++ +++y+++i+ aal+ + +dl eaa+++Gasrw +fr+v+lP++ p+++ + i +++++l  + ++  ++ +++    
  gi|121638715|ref|YP_978939.1| 175 VWKNLGYTFVIYLAALQGVRRDLLEAAEIDGASRWAVFRRVLLPQLRPTTFFLSITVLINSLQVFDVINVMTRGGPegtg 254
                                    ***********************************************************************988777766 PP

                   BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                     +t++ +++ +   ++ +  g+ +++i++l+l++v++  +r+ d+  r
  gi|121638715|ref|YP_978939.1| 255 TTTMVYQVYVETFRNFRAGYGATVATIMFLVLLAVTYYQVRVMDRGQR 302
                                    77777777777777777799******************9999999866 PP

>> Phage_holin_3_5  Bacteriophage holin Hol, superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.45   4.1e+03      53      62 ..      94     103 ..      77     133 .. 0.64
   2 ?   14.5   0.1   3.3e-06     0.029      15      50 ..     183     219 ..     173     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.45
                Phage_holin_3_5  53 svvcglavil 62 
                                    s+v gla  +
  gi|121638715|ref|YP_978939.1|  94 SMVLGLALAM 103
                                    2334444444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.3e-06
                Phage_holin_3_5  15 llillallggvsgemwr.adkaglsgwallrrlllrs 50 
                                     +i+la+l gv  ++   a+  g s wa++rr+ll  
  gi|121638715|ref|YP_978939.1| 183 FVIYLAALQGVRRDLLEaAEIDGASRWAVFRRVLLPQ 219
                                    79**********9998625789***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1673.05
//
Query:       gi|121638716|ref|YP_978940.1|  [L=439]
Description: DNA-damage-inducible protein F dinF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-43  147.0  32.9    6.5e-27   94.2   8.3    2.2  2  MatE      MatE


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   8.3   3.6e-31   6.5e-27       1     160 [.      19     178 ..      19     179 .. 0.97
   2 !   58.9  16.6   2.6e-20   4.6e-16       3     157 ..     239     393 ..     238     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 3.6e-31
                           MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                    P++   ++e l+ l+d+ +vgrlg+ +lA+++i++ +l l+++ +++ls ++t+++++++Ga+n+ +a +  +q+++l+l
  gi|121638716|ref|YP_978940.1|  19 PALGVLAAEPLYLLFDIAVVGRLGAISLAGLAIGSLVLGLVGSQATFLSYGTTARAARRYGAGNRVAAVTEGVQATWLAL 98 
                                    78888999************************************************************************ PP

                           MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                    +l+++++++v + + +++s + + + ++++a  +lri+ilg+pa++++l+ +g+lrg+ +t +pl  +++++   ++l++
  gi|121638716|ref|YP_978940.1|  99 GLGALVVVVVEATATPLVSAIASGDGITAAALPWLRIAILGTPAILVSLAGNGWLRGVHDTVRPLRYVVAGFGSSALLCP 178
                                    ***********************************************************************998888876 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 2.6e-20
                           MatE   3 alenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllll 82 
                                    ++  l++++++     +++r+g+ alAa++++l+++ ll ++l +l++a+++lvg alGa++   ak ++ + + ++ll 
  gi|121638716|ref|YP_978940.1| 239 IVRTLAFQVCYVSAAAVAARFGAAALAAHQVVLQLWGLLALVLDSLAIAAQSLVGAALGAGDAGHAKAVAWRVTAFSLLA 318
                                    6677888999999999**************************************************************** PP

                           MatE  83 sliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnip 157
                                    + i+a+++ l s  +  lft+d  vl+++  +  ++++ +p+ ++ ++ +g+l gag++ ++  ++++s+l++++
  gi|121638716|ref|YP_978940.1| 319 AGILAAALGLGSSVLPGLFTDDRSVLAAIGVLWWFMVVQLPFAGIVFAVDGVLLGAGDAAFMRTATVASALVGFL 393
                                    *********************************************************************988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2490.21
//
Query:       gi|121638717|ref|YP_978941.1|  [L=336]
Description: hypothetical protein BCG_2857c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-14   53.1   0.1    7.1e-14   52.4   0.1    1.4  1  DHHA1     DHHA1 domain
    4.7e-14   52.4   0.0    1.1e-13   51.3   0.0    1.6  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   7.9e-18   7.1e-14       3     138 .]     201     335 ..     199     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7.9e-18
                                    HHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC.....TCEEEEEECHCCHHH...HHHHHHHHHHHTHGBT.TCEE CS
                          DHHA1   3 slneerkelekeleelkealaklkaeellekaeevk.....gvkvlvaevgeewda...galgiaadklksklkk.pviv 73 
                                    +++ +++ + + l++ + +    + + +l +a+ v+        v+v+ ++ ew a     +++++d +++  ++ ++++
  gi|121638717|ref|YP_978941.1| 201 EIGVDNATVSRTLMDSHPFTWLPLLSRVLGSAQLVSeavggRGLVYVVVDNREWVAarsEEVESIVDIVRT--TQqAEVA 278
                                    56667777777777888888888888888888888888887444444444466655223677777******..888**** PP

                                    EEEEEECT.EEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                          DHHA1  74 fvakeegd.kvkvsarskkdgvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                    +v+ke ++ +++vs+r+k   v+++++a+       +gGGGH+lAaG ++  +++++a++ l++a+
  gi|121638717|ref|YP_978941.1| 279 AVFKEVEPhRWSVSMRAK--TVNLAAVASG------FGGGGHRLAAGYTTT-GSIDDAVASLRAAL 335
                                    ******************..9*********......**************5.99*******99875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   1.2e-17   1.1e-13       2     100 ..      36     177 ..      35     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.2e-17
                                    EEEE-ECSSSHHHHHHHHHHHH.............................................CECS--TCGGCG. CS
                                    xxxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxxxxx. RF
                            DHH   2 ilivghknpDtDsigSaialan.............................................llvDhneksqav. 35 
                                    + +v+h +pD+D ig+ +ala                                              ++vD  + ++   
  gi|121638717|ref|YP_978941.1|  36 VGVVCHVHPDADTIGAGLALALvldgcgkrvevsfaapatlpeslrslpgchllvrpevmrrdvdlvVTVDIPSVDRLGa 115
                                    7799************9999996666666666666666666666666666666666666666666555999888877651 PP

                                    CCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  36 egeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllg 100
                                     g++ +++ ++++iDHH++++ f t     f+++++ st ++vae+l+++++ i++++a ++++g
  gi|121638717|ref|YP_978941.1| 116 LGDLTDSGRELLVIDHHASNDLFGTA---NFIDPSADSTTTMVAEILDAWGKPIDPRVAHCIYAG 177
                                    567****************9767777...7*********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1848.78
//
Query:       gi|121638718|ref|YP_978942.1|  [L=183]
Description: ribosome-binding factor A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-22   77.6   0.0    1.1e-21   77.3   0.0    1.1  1  RBFA      Ribosome-binding factor A


Domain annotation for each model (and alignments):
>> RBFA  Ribosome-binding factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   6.1e-26   1.1e-21       1     105 []       6     113 ..       6     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 6.1e-26
                                    TCHHHHHHHHHHHHHHHHHCT-HCCTGHHCEEEEEEESTTSSEEEEEEEESS-...HH.HHHHHHHHHHHTHHHHHHHHH CS
                           RBFA   1 RqervaeliqrelseilqeelkdprlgklvtiteVkvsrDlskakVyvsvlgs...ee.ekeevlkaLkkaagflrrela 76 
                                    R++r+a++i   ++++++ e+kdp l   vtit+ kv++Dl+ a+Vy++v+g    +e + + +++aL++a+g lr++++
  gi|121638718|ref|YP_978942.1|   6 RARRLAKRIAAIVASAIEYEIKDPGL-AGVTITDAKVTADLHDATVYYTVMGRtlhDEpNCAGAAAALERAKGVLRTKVG 84 
                                    789***********************.59***********************866533667777999************* PP

                                    HHC-SSSG-EEEEESSSTTTT--XXXXX. CS
                           RBFA  77 krlklrktPeLkFvlDesleqakeiekll 105
                                      + +r+tP+L+F lD+  ++ +++++ll
  gi|121638718|ref|YP_978942.1|  85 AGTGVRFTPTLTFTLDTISDSVHRMDELL 113
                                    **************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1034.39
//
Query:       gi|121638719|ref|YP_978943.1|  [L=900]
Description: translation initiation factor IF-2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-33  115.5   5.0      4e-32  111.3   2.4    3.0  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.4e-33  112.8   0.9      2e-32  111.4   0.9    1.8  1  IF-2         Translation-initiation factor 2
    1.5e-23   82.3   0.0    1.3e-14   53.7   0.0    2.4  2  IF2_N        Translation initiation factor IF-2, N-terminal r
      4e-08   33.3   0.1      1e-07   32.0   0.1    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
    3.3e-07   30.6   4.3     0.0026   18.1   0.1    3.2  3  GTP_EFTU_D2  Elongation factor Tu domain 2
      4e-07   29.8   0.0    7.4e-07   28.9   0.0    1.4  1  Ras          Ras family
     0.0005   20.3   0.0    0.00081   19.6   0.0    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.003   17.0   0.0       0.01   15.2   0.0    1.8  1  SRPRB        Signal recognition particle receptor beta subuni


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   2.4   1.8e-35     4e-32       6     190 ..     401     561 ..     397     565 .. 0.89
   2 ?    0.3   0.0      0.19   4.3e+02      67     125 ..     695     755 ..     654     759 .. 0.70

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.8e-35
                                    EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..TTCSSEEEEEEEESSSGGG CS
                       GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..ketkkylinliDtPGHvdF 83 
                                    ++++ghvDhGKt L+d++ +++                    e ++ giT ++ a ++    +++++li++iDtPGH+ F
  gi|121638719|ref|YP_978943.1| 401 VTVMGHVDHGKTRLLDTIRKAN------------------VREAEAGGITQHIGAYQVAvdLDGSQRLITFIDTPGHEAF 462
                                    789**************99332..................33445789******999997449***************** PP

                                    HHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                       GTP_EFTU  84 skevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygek 163
                                    +    rg++++D+a+lvv+a++Gv+pqt e +++a++ +vpi+v++NK+D+ +a+  +i  ++ +        l   ++ 
  gi|121638719|ref|YP_978943.1| 463 TAMRARGAKATDIAILVVAADDGVMPQTVEAINHAQAADVPIVVAVNKIDKEGADPAKIRGQLTEYG------LVPEEFG 536
                                    ***************************************************************9444......6666777 PP

                                    TTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                       GTP_EFTU 164 gekevpvvfgSalkgegvktllealve 190
                                    g  ++ +v +Sa++g ++++l ea+  
  gi|121638719|ref|YP_978943.1| 537 G--DTMFVDISAKQGTNIEALEEAVLL 561
                                    6..599*************99999865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                                    CSSEEEEEE...EESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEE CS
                       GTP_EFTU  67 tkkylinli...DtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpi 125
                                    +++ ++nli   D  G v+  +e   g++v D +vl v +++Gv   te++++la++ +  i
  gi|121638719|ref|YP_978943.1| 695 KETSQLNLIlkgDNAGTVEALEEALMGIQVDDEVVLRV-IDRGVGGITETNVNLASASDAVI 755
                                    45556666666688899999999999998888777655.6789*********9999877655 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.9   8.9e-36     2e-32       3     105 .]     689     791 ..     687     791 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 8.9e-36
                                    CHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT..SSTEEEECEEEESSB-HHHHHHHHHSTEEEEEESSSCTHHHH CS
                           IF-2   3 elfeeikeegkelnviikaDvqGsleAlkeaLekles.eevkvkvihsgvGaitesDvelasasnaiiigFnvkvskkak 81 
                                    +l +++k e+++ln+i+k+D  G++eAl+eaL  ++  +ev ++vi+ gvG ite++v+lasas+a+iigFnv+++ ka+
  gi|121638719|ref|YP_978943.1| 689 DLDSALK-ETSQLNLILKGDNAGTVEALEEALMGIQVdDEVVLRVIDRGVGGITETNVNLASASDAVIIGFNVRAEGKAT 767
                                    5666677.789************************98******************************************* PP

                                    HCCCCCTSEEEEESSHHHHHHHHH CS
                           IF-2  82 klaekegvkirlynvIYkliddvk 105
                                    +la++egv+ir+y+vIY++id+++
  gi|121638719|ref|YP_978943.1| 768 ELASREGVEIRYYSVIYQAIDEIE 791
                                    *********************996 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0     6e-18   1.3e-14       3      52 ..       5      53 ..       3      55 .. 0.95
   2 !   26.3   0.0   2.1e-09   4.7e-06       5      53 ..     316     362 ..     314     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 6e-18
                          IF2_N  3 kirVyeLAkeLgvkskevikkLfkelGievkshsssLDeetaeliaeefg 52
                                   k rV+eLAkeLgv+skev+++L +e+G  vks+ss++++ +a  ++e fg
  gi|121638719|ref|YP_978943.1|  5 KARVHELAKELGVTSKEVLARL-SEQGEFVKSASSTVEAPVARRLRESFG 53
                                   89********************.77************************9 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.1e-09
                          IF2_N   5 rVyeLAkeLgvkskevikkLfkelGievkshsssLDeetaeliaeefgi 53 
                                    + +++A+++   ++ +++ Lf+ lG + +++++s+ +et+el+  e+++
  gi|121638719|ref|YP_978943.1| 316 SLSDFADKIDANPAALVQALFN-LGEM-VTATQSVGDETLELLGSEMNY 362
                                    679*******************.****.***************999985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   4.6e-11     1e-07       2     114 .]     401     510 ..     400     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.6e-11
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE..ETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk..lkg..keielvDtpGliegaseekglgkaflaleead 77 
                                    v ++G+   GK+ L+ ++ +++++ ++  g T++i  ++v+  l+g  + i+++DtpG  e         +a    + +d
  gi|121638719|ref|YP_978943.1| 401 VTVMGHVDHGKTRLLDTIRKANVREAEAGGITQHIGAYQVAvdLDGsqRLITFIDTPG-HE----AFTAMRARG-AKATD 474
                                    789********************************999988553333367********.44....333333333.33479 PP

                                    EEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +++lvv a  +++ p+  e  +  + a+ p+++++nk
  gi|121638719|ref|YP_978943.1| 475 IAILVVAAD-DGVMPQTVEAINHAQAADVPIVVAVNK 510
                                    999999877.77999988888888889*******998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.6     1e+04      20      52 ..     402     430 ..     401     432 .. 0.69
   2 !   12.8   0.2   5.2e-05      0.12       1      48 [.     591     631 ..     591     660 .. 0.78
   3 !   18.1   0.1   1.2e-06    0.0026       1      72 [.     822     888 ..     822     891 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.6
                                    EEEC.TCTTSEEEEEEEEEEEEETEEESEEETTS CS
                    GTP_EFTU_D2  20 rilg.ndtskkeivtrissletfhededeavaga 52 
                                     ++g +d  +k   tr   + +  ++++ea+ag+
  gi|121638719|ref|YP_978943.1| 402 TVMGhVD-HGK---TRLLDTIRK-ANVREAEAGG 430
                                    6777444.466...777777777.8889988885 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.2e-05
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea 48 
                                    G va++ v +Gtl++Gd v+    d       +r++++  +h++  e+
  gi|121638719|ref|YP_978943.1| 591 GPVATVLVQRGTLRVGDSVVA--GDA--Y---GRVRRMVDEHGEDVEV 631
                                    679*****************9..442..2...8999999888855554 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.2e-06
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.ivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                    G +a++ v sG+++++ + r+l+ n +     +   i sl +++ d++e+++g  +G+ ++  ++++    Gd+
  gi|121638719|ref|YP_978943.1| 822 GLIAGCLVTSGVMRRNAKARLLRdNIV---VaENLSIASLRREKDDVTEVRDGFECGLTLGYADIKE----GDV 888
                                    568999***************887776...3579**************************9766665....554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.3e-10   7.4e-07       3     152 ..     402     555 ..     400     564 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.3e-10
                                    EEEESTTSSHHHHHHHHHHSSCSSSCTT..TSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   3 vlvGdsavGKtslllrfvkdkFkeeyes..TigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                     ++G    GKt ll    k + +e      T ++  y+  +++dg++  ++  DT G e f+++r    + ++ ++lv +
  gi|121638719|ref|YP_978943.1| 402 TVMGHVDHGKTRLLDTIRKANVREAEAGgiTQHIGAYQVAVDLDGSQRLITFIDTPGHEAFTAMRARGAKATDIAILVVA 481
                                    58999999*****9998888888777651166677899999999**********************************88 PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG..G-SS-HHHHH..HHHHHHT..SEEEEEBTTTTCTHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDlee..kravsteege..elakelg..lkfletSAktnenveea 152
                                     ++      + + ve i++    +vpiv+  nK+D e     +++ +  e   + +e+g  ++f+++SAk+ +n+e +
  gi|121638719|ref|YP_978943.1| 482 ADDGV----MPQTVEAINHAQAADVPIVVAVNKIDKEGadPAKIRGQLTEygLVPEEFGgdTMFVDISAKQGTNIEAL 555
                                    87754....457788899988899***********998553344433322113557777689*************865 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.6e-07   0.00081       2     120 .]     401     513 ..     400     513 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.6e-07
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                    v ++G    GKt ll+ + + +++e e   i   +   +v     v+ d   ++  + + Dt G+e f +++    ++ +
  gi|121638719|ref|YP_978943.1| 401 VTVMGHVDHGKTRLLDTIRKANVREAEAGGITQHIGAYQV-A---VDLD--GSQRLITFIDTPGHEAFTAMRARGAKATD 474
                                    56789999***************99988777776666665.2...2333..345578999******************** PP

                                    EEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TTT CS
                            Roc  82 lailvydsrssenlkeWlkelkkv.agkspvilvgnkiDl 120
                                    +ailv+ ++ +  + + ++ +++  a + p+++ +nkiD+
  gi|121638719|ref|YP_978943.1| 475 IAILVVAAD-DGVMPQTVEAINHAqAADVPIVVAVNKIDK 513
                                    *****9764.4445666777765516677999999***95 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06      0.01       4     137 ..     399     525 ..     396     530 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                    -EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG......GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq..essaalkv...ksekgskltliDfPGheklrqklleklkaksslkg 78 
                                    p v ++G  d GKT l+  + + +v+++ +    +   a++v    +  +  +t+iD PGhe +         + + +  
  gi|121638719|ref|YP_978943.1| 399 PVVTVMGHVDHGKTRLLDTIRKANVREAEAGGitQHIGAYQVavdLDGSQRLITFIDTPGHEAFTAMRARG-AKATDIAI 477
                                    678899*****************99888776433444455554322445566899********98766666.44555778 PP

                                    EEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHH CS
                          SRPRB  79 lvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaL 137
                                    lv   D  + p+ v+           i+  +   v+i++A nK +   a ++ +i+ +L
  gi|121638719|ref|YP_978943.1| 478 LVVAADDGVMPQTVEA----------INHAQAADVPIVVAVNKIDKEGADPA-KIRGQL 525
                                    8888888888887654..........34445567788888888887776544.566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (900 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5901.86
//
Query:       gi|121638720|ref|YP_978944.1|  [L=99]
Description: hypothetical protein BCG_2860c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-20   71.7   0.1    3.7e-20   71.6   0.1    1.0  1  DUF448    Protein of unknown function (DUF448)


Domain annotation for each model (and alignments):
>> DUF448  Protein of unknown function (DUF448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.1     2e-24   3.7e-20       1      74 [.       2      82 ..       2      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2e-24
                         DUF448  1 RkCivcrekkpkkeLiRvvrtpe....gevvlDltgklpGRGaYvcpseeclekaikkkaleralk.akvp..eevyeele 74
                                   R+C++cr++    eL+Rvv+         v++D    lpGRGa+++p ++c ++ai+++a++ral+ a  p  + v e+le
  gi|121638720|ref|YP_978944.1|  2 RTCVGCRKRGLAVELLRVVAVSTgngnYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRRAFARALRiAGSPdtSAVVEYLE 82
                                   9*******************987554324*************************************666668888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 699.88
//
Query:       gi|121638721|ref|YP_978945.1|  [L=347]
Description: transcription elongation factor NusA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-26   90.2   0.2    1.9e-25   88.7   0.1    1.9  2  KH_5      NusA-like KH domain
    3.3e-17   62.9   0.1      2e-08   34.6   0.0    2.4  2  NusA_N    NusA N-terminal domain
     0.0001   22.1   1.1       0.02   14.7   0.0    3.3  3  KH_2      KH domain
    0.00015   21.6   0.1       0.15   11.9   0.0    2.7  3  KH_1      KH domain
  ------ inclusion threshold ------
      0.084   13.2   0.0        1.4    9.3   0.0    2.6  2  DUF5334   Family of unknown function (DUF5334)


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.1   5.3e-29   1.9e-25       1      68 [.     214     281 ..     214     282 .. 0.98
   2 ?   -3.1   0.0       2.4   8.6e+03      23      44 ..     303     323 ..     300     323 .. 0.68

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 5.3e-29
                           KH_5   1 aGertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68 
                                    aG+r+k+aV+s+   +++ Ga++g +G+r+++v+seL+gekid++++++D+a+f+analsPa+v sV 
  gi|121638721|ref|YP_978945.1| 214 AGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANALSPAKVVSVS 281
                                    69****************************************************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                           KH_5  23 vgkkGsrikavsseLkgekidv 44 
                                    +gk+G++ + +   L g +id+
  gi|121638721|ref|YP_978945.1| 303 IGKEGQNAR-LAARLTGWRIDI 323
                                    888998876.555666777765 PP

>> NusA_N  NusA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   5.7e-12     2e-08       4      59 ..       6      61 ..       5      64 .. 0.95
   2 !   26.7   0.0   1.6e-09   5.8e-06      85     120 ..      64     100 ..      59     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.7e-12
                                   CCCCCCCCCS---HHHHHHHHHHHHHHHHHCCT-SSS-EEEEE-TTT--EEEEEEE CS
                         NusA_N  4 ealeelakekgiskevviealeeaLakaykknygedenveveidretgeikvyskk 59
                                    al +++ ++gis ++++e++++aL++ay+   g+++++++eidr+tg ++v+++ 
  gi|121638721|ref|YP_978945.1|  6 AALHAIEVDRGISVNELLETIKSALLTAYRHTQGHQTDARIEIDRKTGVVRVIARE 61
                                   6899****************************999999**************9876 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.6e-09
                                    -TTBEEEE.E----SSCCHCHHHHHHHHHHHHHHHCC CS
                         NusA_N  85 kvGdtvee.evtpkdfgriaaqtakqvivqkireaer 120
                                    + G+ ++e + tp+ fgriaa+ta+qv++q+ r+ae 
  gi|121638721|ref|YP_978945.1|  64 EAGNLISEwDDTPEGFGRIAATTARQVMLQRFRDAEN 100
                                    679999998668***********************97 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.072   2.6e+02      14      34 ..      42      62 ..      30      65 .. 0.83
   2 ?    2.7   0.1     0.032   1.1e+02      35      54 ..     231     250 ..     189     260 .. 0.69
   3 !   14.7   0.0   5.7e-06      0.02       6      48 ..     268     311 ..     265     325 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.072
                                   TEEEEEEECCSCEEEEEEEES CS
                           KH_2 14 gvskveIertanrviivires 34
                                   + +++eI+r++  v+++ re 
  gi|121638721|ref|YP_978945.1| 42 TDARIEIDRKTGVVRVIARET 62
                                   5789*****999999999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
                                    CHHHHHTGGGHHHHHHHHHH CS
                           KH_2  35 qpgivIGkgGsnikkigkel 54 
                                     +g  IG  G++++++ +el
  gi|121638721|ref|YP_978945.1| 231 AKGACIGPMGQRVRNVMSEL 250
                                    58889999999999887665 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 5.7e-06
                                    HHHHTECET.EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHH CS
                           KH_2   6 laveikkag.vskveIertanrviiviresqpgivIGkgGsnik 48 
                                    +a+ ++ a  vs  +I++ta+++++v+ + q  ++IGk+G+n +
  gi|121638721|ref|YP_978945.1| 268 VANALSPAKvVSVSVIDQTARAARVVVPDFQLSLAIGKEGQNAR 311
                                    555565555567778999***********************976 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   6.5e+03      30      50 ..      43      57 ..      41      69 .. 0.54
   2 !   11.9   0.0   4.1e-05      0.15      12      45 ..     233     275 ..     229     293 .. 0.75
   3 !    6.9   0.0    0.0015       5.4       3      41 ..     291     328 ..     289     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                                   T-EEEEESSTT...T.-EEEE CS
                           KH_1 30 gakIkvpksedegsderevti 50
                                    a+I ++ ++       +v++
  gi|121638721|ref|YP_978945.1| 43 DARIEID-RK-----TGVVRV 57
                                   5666654.32.....233433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.1e-05
                                    HHHHTGGGHHHHHHHHHH.T-EEEEES.STT..........T. CS
                           KH_1  12 griIGkgGsnIkeIreet.gakIkvpk.sedeg.......sde 45 
                                    g+ IG+ G+++++ ++e  g kI++++ ++d+        s+ 
  gi|121638721|ref|YP_978945.1| 233 GACIGPMGQRVRNVMSELsGEKIDIIDyDDDPArfvanalSPA 275
                                    788************9866*******87766546666665554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0015
                                    EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT. CS
                           KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksede 41 
                                    r+ vP  + ++ IGk G+n +   + tg +I++ + +++
  gi|121638721|ref|YP_978945.1| 291 RVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG-DAP 328
                                    788999999999*************99*****873.333 PP

>> DUF5334  Family of unknown function (DUF5334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25   8.9e+02      29      49 ..     155     175 ..     141     189 .. 0.85
   2 ?    9.3   0.0   0.00039       1.4      22      67 ..     251     294 ..     244     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                        DUF5334  29 ydydtdetetvlveevtrnar 49 
                                      y++++   + v  vtr ar
  gi|121638721|ref|YP_978945.1| 155 ESYEHGNRLRCYVVGVTRGAR 175
                                    57999999**********998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00039
                        DUF5334  22 kGdtvdvydydtdetetvlveevtrnarTvElvVrdsdtgetrtlv 67 
                                    +G+++d+ dyd+d      v +    a+ v + V d+ + ++r++v
  gi|121638721|ref|YP_978945.1| 251 SGEKIDIIDYDDDPAR--FVANALSPAKVVSVSVIDQTARAARVVV 294
                                    7***********9875..5667777888888888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2441.99
//
Query:       gi|121638722|ref|YP_978946.1|  [L=183]
Description: hypothetical protein BCG_2862c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-12   46.8   0.0    7.2e-12   45.5   0.0    1.6  2  DUF150    RimP N-terminal domain
    2.1e-10   40.6   0.2    3.2e-10   40.0   0.2    1.3  1  DUF150_C  RimP C-terminal SH3 domain
  ------ inclusion threshold ------
       0.25   11.2   0.0       0.37   10.7   0.0    1.2  1  ISP3_C    ISP3 C-terminal


Domain annotation for each model (and alignments):
>> DUF150  RimP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   1.2e-15   7.2e-12       9      73 .]      22      89 ..      15      89 .. 0.95
   2 ?   -2.6   0.0       1.3   7.9e+03      26      41 ..     127     142 ..     121     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.2e-15
                         DUF150  9 lglelvdvelskegrgrvlriyidkdggvtlddcekvSraisalLdv...edpieeeYtLEVsSPGld 73
                                    g+e+ dv +  ++r  ++ +++d d+ ++ld ++++Sr  salLd     + i + Y LEVsSPG++
  gi|121638722|ref|YP_978946.1| 22 AGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSRRASALLDGldgANKIRGRYLLEVSSPGVE 89
                                   69********************************************98889999************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                         DUF150  26 vlriyidkdggvtldd 41 
                                    ++ ++i +d g  +++
  gi|121638722|ref|YP_978946.1| 127 TVALVIREDRGWAVRE 142
                                    5555555555555544 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   5.4e-14   3.2e-10       1      70 []      92     157 ..      92     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.4e-14
                       DUF150_C   1 LktaedFarflGelVkvklklpvegrkkftGkivevdeetitlevdgkkrkkettipladidkArlvpef 70 
                                    L+ +++F+r+ G++V+++l+    ++ ++tG++ e  + t+ l +++  + +  +ipla+i+kA++++ef
  gi|121638722|ref|YP_978946.1|  92 LTSEKHFRRARGRKVELVLS----DGSRLTGRVGEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEF 157
                                    7899****************....**********************998888888**************8 PP

>> ISP3_C  ISP3 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.3e-05      0.37       9      57 ..     100     151 ..      94     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.3e-05
                                    HHH-EEEEEE-TTS-EEEEEE.EEETTTTEEEEEETT..EEEEEETTTEEEE CS
                         ISP3_C   9 lkngldvevllqdgtrleckl.kldlsekvlelsldk..kvrvIplsdvkav 57 
                                     + g +ve++l+dg+rl  ++ ++   +  l ++ d    vr+Ipl+++ + 
  gi|121638722|ref|YP_978946.1| 100 RARGRKVELVLSDGSRLTGRVgEMRAGTVALVIREDRgwAVREIPLAEIVKA 151
                                    567999*************9945666777777777754469*****998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1342.72
//
Query:       gi|121638723|ref|YP_978947.1|  [L=181]
Description: transmembrane alanine rich protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0001   22.0   2.0     0.0001   22.0   2.0    3.9  4  TAT_signal     TAT (twin-arginine translocation) pathway sign
  ------ inclusion threshold ------
      0.012   15.0   5.3      0.021   14.3   5.3    1.4  1  SfLAP          Sap, sulfolipid-1-addressing protein
       0.28   10.7   5.4       0.45   10.1   5.4    1.2  1  SseC           Secretion system effector C (SseC) like family


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.0   1.7e-08    0.0001       2      24 ..      16      38 ..      15      40 .. 0.94
   2 ?    3.6   4.8     0.011        66      10      21 ..      61      72 ..      61      75 .. 0.56
   3 ?   -1.0   1.1       0.3   1.8e+03      14      21 ..      78      85 ..      77      87 .. 0.54
   4 ?   -2.8   1.7       1.2     7e+03      15      22 ..     157     164 ..     156     169 .. 0.42

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-08
                     TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                   +SRR  L g+AA+aA++++ +c+
  gi|121638723|ref|YP_978947.1| 16 ISRRGVLAGGAALAALGVVSACG 38
                                   8*********************8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.011
                     TAT_signal 10 gsAAaaAAaalg 21
                                   g++AaaAA+a g
  gi|121638723|ref|YP_978947.1| 61 GALAAAAATAIG 72
                                   455566665554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.3
                     TAT_signal 14 aaAAaalg 21
                                   aaA+++++
  gi|121638723|ref|YP_978947.1| 78 AAALTVVA 85
                                   55555554 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.2
                     TAT_signal  15 aAAaalgg 22 
                                    + +a  ++
  gi|121638723|ref|YP_978947.1| 157 GLLASIAA 164
                                    44444332 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   5.3   3.5e-06     0.021      73     147 ..      22      95 ..       2     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-06
                          SfLAP  73 ivlGvlllllaaveavrrpkassrselprllsrleslleggalwvAlvlgllsakplllylaalaaigasgasvg 147
                                    ++ G++l +l++v a    +a ++ +++ l s l++++  gal++A+++++++++ +   l+++a+  +s+a + 
  gi|121638723|ref|YP_978947.1|  22 LAGGAALAALGVVSACGE-SAPKAPAVEELRSPLDQARHDGALAAAAATAIGIPPQVAAALTVVATQRTSHARAL 95 
                                    667888999********9.999*******************************7776666666666666666544 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.4   7.6e-05      0.45      90     177 ..      22     113 ..      19     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.6e-05
                           SseC  90 vAgglmdaalgiadevvaaattkslideemqpimdvvdkaqlageivgavvaavavvaavvavgsaakgaaaavksg... 166
                                    +Agg+++aalg++++  ++a  + +++e   p+  +     la ++++a+ +  +v+aa ++v++  ++ a+a+++    
  gi|121638723|ref|YP_978947.1|  22 LAGGAALAALGVVSACGESAPKAPAVEELRSPLDQARHDGALAAAAATAIGIPPQVAAALTVVATQRTSHARALATEiar 101
                                    69****************************76666667777888888888888889999988888888888877655545 PP

                           SseC 167 .aaklaeavaea 177
                                     a+kl +a++e+
  gi|121638723|ref|YP_978947.1| 102 aAGKLVSATSET 113
                                    455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1298.27
//
Query:       gi|121638724|ref|YP_978948.1|  [L=162]
Description: hypothetical protein BCG_2864 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-44  152.2   5.6    1.4e-44  152.0   5.6    1.0  1  DUF4439     Domain of unknown function (DUF4439)
  ------ inclusion threshold ------
       0.07   13.5   0.1      0.077   13.3   0.1    1.1  1  NSP2_assoc  Non-essential region of nsp2 of arterivirus polyp


Domain annotation for each model (and alignments):
>> DUF4439  Domain of unknown function (DUF4439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   5.6   1.5e-48   1.4e-44       1     130 [.      25     161 ..      25     162 .] 0.99

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 1.5e-48
                        DUF4439   1 alqaalaaEhaavYgYgvvsarldgarraaarealaaHrarrdalaallsargatppaaeaaYelpfevtdaasaarlaa 80 
                                    al++ala Eha++YgYg+vsa +++  +  +++al++Hr+rrd+++++lsarg+t+p a+a+Y+lp++v++aa+aarla+
  gi|121638724|ref|YP_978948.1|  25 ALCDALAVEHATIYGYGIVSALSPPGVNFLVADALKQHRHRRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAV 104
                                    899***************************************************************************** PP

                        DUF4439  81 elEedlaaayaalv.aaddadlRstaadaLteaavraarWraelg......afPGlp 130
                                    ++E+d a+a++a+v +a++ad+R +a +aLte+av+a+rW++ lg      afPG +
  gi|121638724|ref|YP_978948.1| 105 RMENDGATAWRAVVeHAETADDRVFASTALTESAVMATRWNRVLGawpitaAFPGGD 161
                                    *******************************************************87 PP

>> NSP2_assoc  Non-essential region of nsp2 of arterivirus polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.6e-06     0.077      82     172 ..      65     156 ..      21     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-06
                     NSP2_assoc  82 sredePLDLsrpapaatttlvreqtpdnpgsdagalpvtvrefvptglilr.hvehcGtesgdsssPLdlsdaqtldqPL 160
                                     r+d  + Ls    +a  + ++ q+p + +s a+a   +vr       + r  veh  t  +   +   l ++ ++    
  gi|121638724|ref|YP_978948.1|  65 RRDDVIVMLSARGVTAPIAAAGYQLPMQVSSAADAARLAVRMENDGATAWRaVVEHAETADDRVFASTALTESAVMATRW 144
                                    45566677899999999999********************98777666655168*****999999999999999999*** PP

                     NSP2_assoc 161 nLsLaaWPvkat 172
                                    n  L aWP+ a+
  gi|121638724|ref|YP_978948.1| 145 NRVLGAWPITAA 156
                                    ********9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1178.73
//
Query:       gi|121638725|ref|YP_978949.1|  [L=582]
Description: prolyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-38  132.3   0.0    2.4e-38  131.9   0.0    1.1  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    7.1e-21   74.6   0.0    1.4e-20   73.6   0.0    1.5  1  tRNA_edit       Aminoacyl-tRNA editing domain
    7.3e-13   48.5   0.0    1.9e-12   47.1   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.054   13.6   0.0       0.11   12.6   0.0    1.4  1  DUF1198         Protein of unknown function (DUF1198)


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.0   5.2e-42   2.4e-38       1     179 []      96     471 ..      96     471 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 5.2e-42
                                    EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBC.TTTB-SEEEEEEEEEEES.GGGHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxx RF
                   tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsr.GLlRvreFhqkdgyvfha.easld 77 
                                    ++l+dr +++y L+Pt+ee f+  ++ e   s k+ Pl lyqiqtkyRdE++  r G+lR reF +kd y+f   +a l+
  gi|121638725|ref|YP_978949.1|  96 FRLKDRRGNDYLLGPTHEELFTLTVKGE-YSSyKDFPLTLYQIQTKYRDEAR-PRaGILRAREFVMKDSYSFDIdAAGLK 173
                                    89**************************.777688*****************.666******************8899** PP

                                    HHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                   tRNA-synt_2b  78 dslrdlikaisriferlglefraiielmsaksadykdkkefeavses................................. 124
                                      +r   +a++rif rl +  ++i+   s + + ++ ++ef a s+s                                 
  gi|121638725|ref|YP_978949.1| 174 AAYRAHREAYQRIFDRLQVR-YVIVSAVS-GAMGGSASEEFLAESPSgedafvrclesgytanveavvtarpdtlpidgl 251
                                    *****************988.55555544.4577********************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                   tRNA-synt_2b 125 ................................................................................ 124
                                                                                                                    
  gi|121638725|ref|YP_978949.1| 252 peavvhdtgdtptiaslvawaneadlgrtvtaadtlknvlikvrqpggdtellaigvpgdrevddkrlgaalepadyall 331
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                   tRNA-synt_2b 125 ................................................................................ 124
                                                                                                                    
  gi|121638725|ref|YP_978949.1| 332 ddddfakhpflvkgyigpkalrennvrylvdprivdgtswitgadqpgrhvvglvagrdftadgtieaaevregdpspdg 411
                                    ******************************************************************************** PP

                                    .....TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHHHHH CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 125 .....ltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsaileqn 179
                                         + +gieig+i++lg ++ +++ a+vl e+++  +  m+ ++igv+Rl++++ eq+
  gi|121638725|ref|YP_978949.1| 412 agplvMARGIEIGHIFQLGSKYTDAFTADVLGEDGKPVRLTMGSYGIGVSRLVAVVAEQH 471
                                    *********************************************************996 PP

>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   3.1e-24   1.4e-20       3     123 .]     261     391 ..     259     391 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.1e-24
                      tRNA_edit   3 gtktieelaaalg.......vdpsaiaKtlvlkd....kkgelvlvllpgdreldlkklakllgakklrlaseeelrell 71 
                                    +t+ti+ l+a ++       v +++++K++++k+    +++el+++ +pgdre+d k+l ++l  ++ +l ++++++++ 
  gi|121638725|ref|YP_978949.1| 261 DTPTIASLVAWANeadlgrtVTAADTLKNVLIKVrqpgGDTELLAIGVPGDREVDDKRLGAALEPADYALLDDDDFAKHP 340
                                    5667777777777777778899***************99999************************************** PP

                      tRNA_edit  72 gvepGgvgPlglkaagvpvllDeslkeyptvvvgagengatlelspedlrkl 123
                                     +++G++gP +l +++v++l+D+++++ + +++ga+++g+++   ++ +r++
  gi|121638725|ref|YP_978949.1| 341 FLVKGYIGPKALRENNVRYLVDPRIVDGTSWITGADQPGRHVVGLVA-GRDF 391
                                    *******************************************9999.8876 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   4.3e-16   1.9e-12       5      81 ..     491     565 ..     487     577 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.3e-16
                                    EESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                 HGTP_anticodon   5 iplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                    +  n+ + ++   a  la++L + g++v ldd++ s+g k+++a+llg p++vvvG   + +g+v++rdr ++++++
  gi|121638725|ref|YP_978949.1| 491 VIANK-DAQARAGATALAADLDRLGVEVLLDDRQASPGVKFKDAELLGMPWIVVVGRGWA-DGVVELRDRFSGQTRE 565
                                    34444.4468899*******************************************9998.*********9997754 PP

>> DUF1198  Protein of unknown function (DUF1198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05      0.11      23      66 ..     178     221 ..     169     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHHHHHHT--THHHHHHHHTS-HHHHHHHHHHHHHS-H CS
                        DUF1198  23 dtrraikrlserLkiepvyveslldemGktageefvrylsrgne 66 
                                      r a +r+ +rL+++ v v ++   mG +a+eef+    +g++
  gi|121638725|ref|YP_978949.1| 178 AHREAYQRIFDRLQVRYVIVSAVSGAMGGSASEEFLAESPSGED 221
                                    5799*******************************987666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3625.94
//
Query:       gi|121638726|ref|YP_978950.1|  [L=530]
Description: integral membrane efflux protein efpA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-43  148.2  47.6    2.8e-43  148.2  47.6    1.7  2  MFS_1          Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.043   13.6   1.0      0.071   12.9   0.2    1.9  2  Iron_permease  Low affinity iron permease


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.2  47.6   3.2e-47   2.8e-43       4     351 ..      61     449 ..      58     451 .. 0.87
   2 ?   -1.5   0.1       0.1     9e+02     155     315 ..     493     507 ..     478     523 .. 0.46

  Alignments for each domain:
  == domain 1  score: 148.2 bits;  conditional E-value: 3.2e-47
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                    +++l++++++++++alp  ++++l +s +  ++++t+y l+++ ++l++Grl+d +Gr+r++++g++lf ++++l+++a 
  gi|121638726|ref|YP_978950.1|  61 MQLLATMDSTVAIVALP-KIQNELSLSDAGRSWVITAYVLTFGGLMLLGGRLGDTIGRKRTFIVGVALFTISSVLCAVAW 139
                                    57899************.******************************************************66666443 PP

                          MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                       +l+++r+ qG+g++++ p+g+al+a  fpk + r+ a+++++a++++G+++g ++gg+l+  ++Wr++f+++ +++l
  gi|121638726|ref|YP_978950.1| 140 DEATLVIARLSQGVGSAIASPTGLALVATTFPKgPARNAATAVFAAMTAIGSVMGLVVGGALT-EVSWRWAFLVNVPIGL 218
                                    3336***********************************************************.899************* PP

                          MFS_1 163 lafvlfllllpeepperkrkspkeee...........................................kgtgpaplvpa 199
                                    +++ l+   l+e+++er +   +                                              ++t++ p+vp 
  gi|121638726|ref|YP_978950.1| 219 VMIYLARTALRETNKERMKLDATGAIlatlactaavfafsigpekgwmsgitigsglvalaaavafvivERTAENPVVP- 297
                                    **99*9*******9999999999999*****************************************************. PP

                          MFS_1 200 wkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlll 279
                                    + +++ ++ l   + a+ll++ ++++l++ + ly+q+ lg+s +l ag+ +  + +++ i+  ++++l+ r+++  r l 
  gi|121638726|ref|YP_978950.1| 298 FHLFRDRNRLV-TFSAILLAGGVMFSLTVCIGLYVQDILGYS-ALRAGVGFIPFVIAMGIGLGVSSQLVSRFSP--RVLT 373
                                    99999999885.9999999999********************.5666633333333333446699999999888..4444 PP

                          MFS_1 280 allllllaalglallavt...ssavllllvlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggal 351
                                    ++++ ll+ ++l+   +      ++  l++ +++G  g g+++++l+  a   ++ ++ g +s+++ +++slgg l
  gi|121638726|ref|YP_978950.1| 374 IGGGYLLFGAMLYGSFFMhrgVPYFPNLVMPIVVGGiGIGMAVVPLTLSAIAGVGFDQIGPVSAIALMLQSLGGPL 449
                                    44444444444444444444566666666777777779999988888888888888*****************976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.1
                          MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplyl 234
                                    ++++++ +++++                                                                    
  gi|121638726|ref|YP_978950.1| 493 WVAGAAIIVGGM-------------------------------------------------------------------- 504
                                    222222222222.................................................................... PP

                          MFS_1 235 qevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfgl 314
                                                                                                                  +l
  gi|121638726|ref|YP_978950.1| 505 ------------------------------------------------------------------------------AL 506
                                    ..............................................................................11 PP

                          MFS_1 315 g 315
                                    +
  gi|121638726|ref|YP_978950.1| 507 F 507
                                    1 PP

>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.4   1.3e+04      12      25 ..     115     128 ..     112     136 .. 0.76
   2 ?   12.9   0.2   7.9e-06     0.071      12      76 ..     179     239 ..     170     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.4
                  Iron_permease  12 agseiafvlallvi 25 
                                     g++ +f++++++ 
  gi|121638726|ref|YP_978950.1| 115 IGRKRTFIVGVALF 128
                                    68999999998764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.9e-06
                  Iron_permease  12 agseiafvlallvivvwavsgplfkysdtwQLviNtgttiitFlmvfliqnsqnrdskaiqlkLd 76 
                                    a   +a ++a+  +++++v+g+l + s  w  ++N++  ++   m++l   +  r++++ ++kLd
  gi|121638726|ref|YP_978950.1| 179 ATAVFAAMTAIGSVMGLVVGGALTEVSWRWAFLVNVPIGLV---MIYLAR-TALRETNKERMKLD 239
                                    455667889999*************************6665...888754.55677777799998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 3464.76
//
Query:       gi|121638727|ref|YP_978951.1|  [L=405]
Description: multifunctional enzyme siroheme synthase cysG: uroporphyrin-III c-methyltransferase + precorrin-2 oxidase + ferrochelatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-46  157.0   5.9    1.2e-45  156.1   5.9    1.5  1  TP_methylase   Tetrapyrrole (Corrin/Porphyrin) Methylases
    3.4e-22   78.8   0.4    1.4e-21   76.9   0.4    2.1  2  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.035   13.5   0.0       0.23   10.8   0.0    2.2  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   5.9     2e-49   1.2e-45       2     211 ..     162     372 ..     161     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 2e-49
                   TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                    + lVG GpGdpel+Tvr++r+l++advv++d+   +e+l +l++     + + +k    ++ a+++i++ l+e++r+g  
  gi|121638727|ref|YP_978951.1| 162 VALVGGGPGDPELITVRGRRLLAQADVVVADRLAPPELLAELPPHV--EVIDAAKIPYGRAMAQDAINAVLIERARSGNF 239
                                    689*****************************66888888888763..333333333366667***************** PP

                   TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeerelea 156
                                    Vv+l++GDP+v+ +g e+v a++   agi+v v+PGv+s+ a++a +g+p+t++  ++ ++     l + ++e+   ++a
  gi|121638727|ref|YP_978951.1| 240 VVRLKGGDPFVFARGYEEVLACAH--AGIPVTVVPGVTSAIAVPAMAGVPVTHRAMTHEFVvvsghLAPGHPESLVNWDA 317
                                    *******************66666..****************************99999999****777799******** PP

                   TP_methylase 157 llangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtlee 211
                                    l+a ++t+vll+a+++++  +++L++  + +dt pv vv++++t+ +++ r+tl++
  gi|121638727|ref|YP_978951.1| 318 LAALTGTIVLLMAVERIELFVDVLLKGgRTADT-PVLVVQHGTTAAQQTLRATLAD 372
                                    ***************************777755.*******************986 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.4   2.3e-25   1.4e-21       3     104 .]      10     114 ..       8     114 .. 0.94
   2 ?   -3.0   0.0       1.6   9.8e+03       8      24 ..     350     366 ..     347     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.3e-25
                  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..elvklaeeel.ekdlegadlviaatddrelneria 79 
                                    l+l gkkv+vvGgG+vA+r++  l+++ga+v+v+ap v++++e  ++++l+ +++ ++dl+ga  +iaatdd+ +n +++
  gi|121638727|ref|YP_978951.1|  10 LRLAGKKVVVVGGGTVAQRRLPLLIASGADVHVIAPSVTPAVEamDQITLSVRDYrDGDLDGAWYAIAATDDARVNVAVV 89 
                                    6799**********************************8888877899999888846*********************** PP

                  NAD_binding_7  80 eaakarrilvnvadkpelcdfifpa 104
                                    ++a++rri++ +ad + +++ ++pa
  gi|121638727|ref|YP_978951.1|  90 AEAERRRIFCVRADIAVEGTAVTPA 114
                                    ******************9999997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                  NAD_binding_7   8 kkvlvvGgGevAarkvr 24 
                                      vlvv  G+ Aa+   
  gi|121638727|ref|YP_978951.1| 350 TPVLVVQHGTTAAQQTL 366
                                    67899999998887655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.9e-05      0.23      29      73 ..       7      51 ..       2      64 .. 0.83
   2 ?   -1.1   0.0      0.18   1.1e+03     135     155 ..     139     159 ..     133     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.9e-05
                                   GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C 29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                   l g +l+gk+v ++G G ++q+   +l a g++v ++ +s ++  
  gi|121638727|ref|YP_978951.1|  7 LVGLRLAGKKVVVVGGGTVAQRRLPLLIASGADVHVIAPSVTPAV 51
                                   67889*********************9999999999999887665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.18
                                    HHHHHHHHTTSCCEEEES--S CS
                   2-Hacid_dh_C 135 eaLleaLksgkiagaalDvfe 155
                                     a+ eaL++g i +   Dv++
  gi|121638727|ref|YP_978951.1| 139 SAIREALQQGVITAQSSDVLS 159
                                    68999*********9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3085.09
//
Query:       gi|121638728|ref|YP_978952.1|  [L=457]
Description: cobyrinic acid a,c-diamide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-24   87.3   0.0    1.5e-24   86.7   0.0    1.2  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    1.3e-19   70.5   0.0    2.1e-19   69.8   0.0    1.3  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
    2.1e-13   50.5   0.6    5.7e-09   36.1   0.0    2.5  2  AAA_26     AAA domain
     0.0018   18.1   0.0     0.0037   17.1   0.0    1.6  1  DJ-1_PfpI  DJ-1/PfpI family
     0.0089   15.9   0.0      0.021   14.6   0.0    1.6  2  SNO        SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.037   13.9   0.0    1.6  1  MobB       Molybdopterin guanine dinucleotide synthesis prote


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   4.9e-28   1.5e-24       2     190 ..     256     435 ..     255     440 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 4.9e-28
                       GATase_3   2 iavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvl 79 
                                    +a++  +a+ + +    ++L+a++++ v+f p   e+l+e  d+v+lpGg+++ + ++l+++ +++++i+e+a+ag+pv 
  gi|121638728|ref|YP_978952.1| 256 VAIAAGRAFTFGYaeHAEMLRAAGAEVVEFDP-LSETLPEGTDAVVLPGGFPEQFTAELSANDTVRRQINELAAAGAPVH 334
                                    8888899998877799****************.9999******************************************* PP

                       GATase_3  80 giCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel.....aaegeevkGyEiHsGrtilkek 154
                                    ++C+Gl +L +e+            ++++g++  + +f+++  +g   + + +      + ge+v G+E+H+  ++ +++
  gi|121638728|ref|YP_978952.1| 335 AECAGLLYLVSELDG----------HPMCGVVAGSARFTQHLKLGYRDAVA-VvdsalYSVGERVVGHEFHRTAVTFADS 403
                                    ************874..........69999999999999953333333332.2467877789****************** PP

                       GATase_3 155 akpllkvkvggnng.ekdGavkksedgnvlGtYlHgl 190
                                     +p+  + +g+  +  +dGav++     v ++YlH +
  gi|121638728|ref|YP_978952.1| 404 YQPAWVY-QGQDVDdVRDGAVHS----GVHASYLHTH 435
                                    ***9999.3333336******77....9*******98 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   7.1e-23   2.1e-19       1     122 [.       6     191 ..       6     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 7.1e-23
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    +a+a+  +G+GKTt+a++L+ al ++g+ V++++++p+     +       ++                           
  gi|121638728|ref|YP_978952.1|   6 VAVAAPASGSGKTTIATGLIGALRQAGHTVAPFKVGPDFIDPGY-------HALaagrpgrnldpvlvgerligplyahg 78 
                                    699***********************************444443.......22255555556699*************** PP

                                    ...............................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEE CS
                                    ...............................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                           CbiA  55 ...............................................dlkrllellealgkkkall...lkiagvvlnrv 84 
                                                                                   d+   + +++al ++++ +    +iagv+lnrv
  gi|121638728|ref|YP_978952.1|  79 vagadiaviegvlglfdgrigpaggapaagstahvaallgapvilvvDARGQSHSVAALLHGFSTFdtaTRIAGVILNRV 158
                                    ******************************************************************************** PP

                                    SS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  85 dgeneetllkealeelkqrygvpvlgviprdeavaeap 122
                                    ++ ++e+ l++a+++     gv vlg ipr+ ++ e+p
  gi|121638728|ref|YP_978952.1| 159 GSARHEQVLRQACDQA----GVAVLGAIPRTAEL-ELP 191
                                    *******999999997....***********998.665 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   3.4e-05       0.1       3      36 ..       6      39 ..       4      41 .. 0.88
   2 !   36.1   0.0   1.9e-12   5.7e-09     118     197 ..     108     191 ..      80     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                         AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                   + v++   g+GKT++++gL+ al++ g  v+ fK
  gi|121638728|ref|YP_978952.1|  6 VAVAAPASGSGKTTIATGLIGALRQAGHTVAPFK 39
                                   679999*****************99998887666 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.9e-12
                         AAA_26 118 llnadiaknlgapvilVarg..glgtinqllltiealrqknvrvlGvilNkvrnp...envetlekksgipvlGvvPylp 192
                                     ++a +a+ lgapvilV+ +  +++++++ll   +++ +   r++GvilN+v ++   + +++++ + g+ vlG++P ++
  gi|121638728|ref|YP_978952.1| 108 GSTAHVAALLGAPVILVVDArgQSHSVAALLHGFSTFDT-ATRIAGVILNRVGSArheQVLRQACDQAGVAVLGAIPRTA 186
                                    67899************9883255679999999999988.79*********9877443599999999************9 PP

                         AAA_26 193 dleap 197
                                    +le p
  gi|121638728|ref|YP_978952.1| 187 ELELP 191
                                    99865 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-06    0.0037      52     118 ..     286     352 ..     248     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                                    EEGGGCTCCG-SEEEE--BHHH..HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE CS
                      DJ-1_PfpI  52 aslddvkaaeyDalvlpGGrag..perlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrv 118
                                      l++  ++  Da+vlpGG       +l++n+ v+  + e a +g +v a Cag + L+++  l+g+ +
  gi|121638728|ref|YP_978952.1| 286 DPLSETLPEGTDAVVLPGGFPEqfTAELSANDTVRRQINELAAAGAPVHAECAGLLYLVSE--LDGHPM 352
                                    45677778889********8741145677777888888888899**********8777764..555555 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   5.1e+03     126     150 ..     146     170 ..     130     181 .. 0.72
   2 !   14.6   0.0   7.1e-06     0.021       8      87 ..     268     349 ..     263     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                    EEEESS--EEEEE-.TTTCEEEEEC CS
                            SNO 126 tavfiraPvieeilddeavkvlyel 150
                                    ta+ i   +++++++  +++vl++ 
  gi|121638728|ref|YP_978952.1| 146 TATRIAGVILNRVGSARHEQVLRQA 170
                                    6677777778899999999999875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.1e-06
                                    HHHHHHHHHHTTSEEEEE-S.GGGG.CC-SEEEE-SS-HHHHH.HHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCE CS
                            SNO   8 veehveaikkclaenktvkr.kedl.aevdaliiPGGestams.kliertglyedllefvknsekvvlGtCaGlillske 84 
                                    + eh e +++++ae        e l ++ da+++PGG    ++  l  +  +  ++ e ++ +  +v+  CaGl++l  e
  gi|121638728|ref|YP_978952.1| 268 YAEHAEMLRAAGAEVVEFDPlSETLpEGTDAVVLPGGFPEQFTaELSANDTVRRQINELAAAG-APVHAECAGLLYLVSE 346
                                    57999999999999977765256665789********66555414444555577788887777.9************999 PP

                                    ETT CS
                            SNO  85 len 87 
                                    l++
  gi|121638728|ref|YP_978952.1| 347 LDG 349
                                    876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.037       7      34 ..      12      39 ..       5      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                           MobB  7 ksgsGKTtLleklipelkarglrvgtiK 34
                                    sgsGKTt+ + li +l++ g +v+  K
  gi|121638728|ref|YP_978952.1| 12 ASGSGKTTIATGLIGALRQAGHTVAPFK 39
                                   69**********************9777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3143.33
//
Query:       gi|121638729|ref|YP_978953.1|  [L=207]
Description: cob(I)yrinic acid a,c-diamide adenosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-56  190.4   0.0    3.3e-56  190.2   0.0    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
  ------ inclusion threshold ------
       0.17   10.9   0.2       0.23   10.5   0.2    1.1  1  MtrH            Tetrahydromethanopterin S-methyltransferase M


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.0   3.7e-60   3.3e-56       4     172 .]      24     207 .]      21     207 .] 0.92

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 3.7e-60
                 CobA_CobO_BtuR   4 lihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKg.ekesgElaalkkl...........eielerlgkegfv.... 67 
                                    ++ v+tG+GKGK+tAA+G+alRa++agl ++v+qF+K+ ++++gE+aa+++l            +e++++g +g+     
  gi|121638729|ref|YP_978953.1|  24 ILAVHTGEGKGKSTAAFGMALRAWNAGLDIAVFQFVKSaKWKVGEEAAFRQLgrlhdqhgiggAVEWHKMG-AGWSwtrt 102
                                    789***********************************66*****************9998766*******.88886665 PP

                 CobA_CobO_BtuR  68 kmeeeekeedaaaakealekakealaseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaA 147
                                    + ++ ++ + aaaa+++ ++++ +la++++d+++lDE++y+lk+g+ld++ev+++l+++p ++++v+TGr+ap++l++aA
  gi|121638729|ref|YP_978953.1| 103 SRKAGTDVDRAAAAADGCAEIALRLATQRHDFYLLDEFTYPLKWGWLDVDEVVDVLRARPGHQHVVITGRDAPQRLVAAA 182
                                    444555566677888999999999999***************************************************** PP

                 CobA_CobO_BtuR 148 DlvtemkkvkHpydkgikarkGiey 172
                                    Dlvtem+kvkHp+d+g k +kGie+
  gi|121638729|ref|YP_978953.1| 183 DLVTEMTKVKHPMDAGRKGQKGIEW 207
                                    ************************8 PP

>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   2.6e-05      0.23     166     260 ..      33     128 ..      24     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.6e-05
                           MtrH 166 egegtaekgllelaeeaGiekplid.vavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkekekaa 244
                                    +g++ta  g+   a +aG+++ +   v       g  aa +    +  ++G+      h + + W w r  +k  ++  +
  gi|121638729|ref|YP_978953.1|  33 KGKSTAAFGMALRAWNAGLDIAVFQfVKSAKWKVGEEAAFRQLGRLHDQHGIGGAVEWHKMGAGWSWTRTSRKAGTDVDR 112
                                    5778888899999999999998766234456677889**************9999999***************9999888 PP

                           MtrH 245 eyevadvganlvqvil 260
                                       +ad  a +   ++
  gi|121638729|ref|YP_978953.1| 113 AAAAADGCAEIALRLA 128
                                    8888887776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1765.10
//
Query:       gi|121638730|ref|YP_978954.1|  [L=629]
Description: magnesium chelatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-17   61.7   8.2    4.4e-17   61.7   8.2    2.5  2  AAA_lid_2        AAA lid domain
    2.9e-13   50.0   0.0    4.9e-13   49.3   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    5.3e-13   49.5   0.1      1e-12   48.6   0.1    1.5  1  VWA_2            von Willebrand factor type A domain
    6.9e-09   36.2   0.0    1.1e-08   35.5   0.0    1.2  1  VWA              von Willebrand factor type A domain
    7.5e-09   35.3   0.6    5.3e-08   32.5   0.0    2.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.7e-07   29.1   0.0    1.1e-06   27.9   0.0    1.6  1  MCM              MCM P-loop domain
     0.0019   17.9   0.1     0.0043   16.8   0.1    1.5  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.038   13.9   0.0    1.6  1  VWA_3            von Willebrand factor type A domain
      0.033   14.0   0.0      0.096   12.6   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
      0.033   14.6   0.0       0.19   12.1   0.0    2.2  2  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.7   8.5e+03      51      57 ..     209     216 ..     205     223 .. 0.65
   2 !   61.7   8.2   2.5e-20   4.4e-17       2      71 ..     231     300 ..     230     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.7
                      AAA_lid_2  51 LaHRlr.r 57 
                                    LaHR+   
  gi|121638730|ref|YP_978954.1| 209 LAHRIAaA 216
                                    67887632 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 2.5e-20
                      AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeive 71 
                                    +++a+l++++ v+g Radl+++r+A A+Aa++g  +V ++D+++aa+l+L+HR rr+p++++  ++++++
  gi|121638730|ref|YP_978954.1| 231 RRIAALCAAFDVDGMRADLVVARTAAAHAAWRGVRTVEEQDIQAAAELALPHRRRRDPFDDHGIDRDQLD 300
                                    6899********************************************************9966666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   2.7e-16   4.9e-13       3     138 .]      32     166 ..      30     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.7e-16
                                    EEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.............--------G-SEEEEES CS
                          AAA_5   3 lLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDE 73 
                                    l+ G++Gt+Ks+ ++ laa+l      +e+  v l+ + te+ ++g+++++    +g+ +++++ l ra  +g +l++DE
  gi|121638730|ref|YP_978954.1|  32 LIRGEKGTAKSTAVRGLAALLsvatgSTETGLVELPLGATEDRVVGSLDLQrvmrDGEHAFSPGLLARA--HGGVLYVDE 109
                                    788*********************88889999******************99*9999999999999866..8******** PP

                                    GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                          AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                    v+ ++++ +++Ll      r+++e  g   ++++      f +i+t+np +    el p+l++Rf
  gi|121638730|ref|YP_978954.1| 110 VNLLHDHLVDILLDAAAMGRVHVERDGISHSHEAR-----FVLIGTMNPEE---GELRPQLLDRF 166
                                    **********************8888888877775.....*********99...77889999999 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   5.8e-16     1e-12       1     106 [.     452     558 ..     452     559 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.8e-16
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsd.gpevlipltkdkakilnalrnleakgggtn 77 
                                    ++fv+D SgSm+++d    r++a+  a+ +ll +   ++d+v+++tf+  ++++l+++t++     ++l +  + gg+t 
  gi|121638730|ref|YP_978954.1| 452 VIFVVDASGSMAARD----RMAAVSGATLSLLRDAyqRRDKVAVITFRQhEATLLLSPTSSAHIAGRRLARFST-GGKTP 526
                                    79************8....**************54446***********889********99999999999997.7**** PP

                          VWA_2  78 laaaLqlarkalkkrr...kgekrvivlitDg 106
                                    la++L  ar+++ +++   + ++  +v++tDg
  gi|121638730|ref|YP_978954.1| 527 LAEGLLAARALIIREKvrdRARRPLVVVLTDG 558
                                    **********996666678999*********9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   6.3e-12   1.1e-08       2     127 ..     452     573 ..     452     591 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.3e-12
                                    EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGSSC CS
                            VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgggtt 79 
                                    ++fv+D+Sgsm  ++++  v  +  +l+++ +  +++++v++++f  + ++   s ++  s + + + l ++  s+gg+t
  gi|121638730|ref|YP_978954.1| 452 VIFVVDASGSMaARDRMAAVSGATLSLLRDAY--QRRDKVAVITFRQHeATLLLSPTS--SAHIAGRRLARF--STGGKT 525
                                    79*********7778888**************..***********9875777777777..446777777775..888888 PP

                                    -HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHH CS
                            VWA  80 ntgkalkyaleklfkssagaRenakkviilltdGksndg.dpkeaanea 127
                                     ++++l +a+  +++++ + R+  + ++++ltdG+ + g dp+  +++a
  gi|121638730|ref|YP_978954.1| 526 PLAEGLLAARALIIREKVRDRA-RRPLVVVLTDGRATAGpDPLGRSRTA 573
                                    8***********9999999887.88899********9977888777666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.33   5.9e+02       3      50 ..       7      56 ..       6      65 .. 0.75
   2 !   32.5   0.0     3e-11   5.3e-08      93     158 ..      88     153 ..      82     161 .. 0.94
   3 ?   -2.3   0.0       1.3   2.4e+03     187     202 ..     160     175 ..     155     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.33
                   Mg_chelatase  3 kdvkGqeeakraleiaaaGg..HnlllvGppGsGKtmlakrlpsllppls 50
                                   + ++G+++ + al ++a        l+ G  G+ K+   + l++ll+  +
  gi|121638730|ref|YP_978954.1|  7 SAIVGHDRLRLALLLCAVRPeiGGALIRGEKGTAKSTAVRGLAALLSVAT 56
                                   5677788888888777764311346999***************9998655 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 3e-11
                   Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    g +   pG +++ah GvL++DE+  ++ + +++L +    g+v+++r   + ++ arf l+ +mNp
  gi|121638730|ref|YP_978954.1|  88 GEHAFSPGLLARAHGGVLYVDEVNLLHDHLVDILLDAAAMGRVHVERDGISHSHEARFVLIGTMNP 153
                                    666889***********************************************************9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                   Mg_chelatase 187 gplldRidlqvevkkl 202
                                      lldR+ l+v+v+++
  gi|121638730|ref|YP_978954.1| 160 PQLLDRFGLTVDVQAS 175
                                    579*********9875 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   6.1e-10   1.1e-06      61     178 ..      32     158 ..       7     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.1e-10
                                    EEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSE.........EEEESSSSSEEEEETHHHHTTTSEEEEESGG CS
                            MCM  61 llvgdpgtaKsqlLkyveklapravytsgkgssaagLtaa.........vvrdeetgefvleaGalvladkGvcciDefd 131
                                    l+ g+ gtaKs+ ++ +++l++ a+  + +g  +  L a+          +r  + ge ++  G l  a++Gv+++De++
  gi|121638730|ref|YP_978954.1|  32 LIRGEKGTAKSTAVRGLAALLSVATGSTETGLVELPLGATedrvvgsldLQRVMRDGEHAFSPGLLARAHGGVLYVDEVN 111
                                    667888888888888777777777766666666666655411211111134556678899******************** PP

                                    GSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                            MCM 132 kmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                      +++  + l++a     +++ + Gi  + +ar  ++  +np++g+ 
  gi|121638730|ref|YP_978954.1| 112 LLHDHLVDILLDAAAMGRVHVERDGISHSHEARFVLIGTMNPEEGEL 158
                                    *******************************************9975 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.4e-06    0.0043      25     142 ..      31     152 ..      23     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                                    EEEECSTTSSHHHHHHHHHH....HSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEE CS
                Sigma54_activat  25 vlitGesGtGKellaraihe....askrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLD 100
                                     li+Ge+Gt K++  r + +    a+  +e+ +v++  +a++++++ s     ++    G ++   Gl+ +a+gG+l++D
  gi|121638730|ref|YP_978954.1|  31 ALIRGEKGTAKSTAVRGLAAllsvATGSTETGLVELPLGATEDRVVGS--LDLQRVMRDGEHAFSPGLLARAHGGVLYVD 108
                                    589999999999987777665444666778889999999999999998..4567777788888899************** PP

                                    TGGGS-HHHHHHHHHH..HHHSEEESBTSSSEEE--EEEEEEES CS
                Sigma54_activat 101 eigelplelQekLlrv..lqegevervGsskeikvdvriiaatn 142
                                    e++ l  +l   Ll +  + + +ver G s+++++ + +i + n
  gi|121638730|ref|YP_978954.1| 109 EVNLLHDHLVDILLDAaaMGRVHVERDGISHSHEARFVLIGTMN 152
                                    *************9762255566788898888888888887666 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-05     0.038       3     110 ..     452     562 ..     450     575 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                          VWA_3   3 vvivvDvsssmsaen...klvkdaLsvalrqLptndkiavllfgtkprplf.pgsravsaaelqealqkikelelslgas 78 
                                    v++vvD+s sm a     +   ++Ls++  + + +dk+av+ f+     l      +++ a ++ a++++   ++   a+
  gi|121638730|ref|YP_978954.1| 452 VIFVVDASGSMAARDrmaAVSGATLSLLRDAYQRRDKVAVITFRQHEATLLlSPTSSAHIAGRRLARFSTGGKTP--LAE 529
                                    89*********99988844444667777777**************655555366667777889999999988777..678 PP

                          VWA_3  79 nlegaLkealrqp.akpgevrsvilltDgssaq 110
                                     l++a + ++r + + ++++  v++ltDg +++
  gi|121638730|ref|YP_978954.1| 530 GLLAARALIIREKvRDRARRPLVVVLTDGRATA 562
                                    8888888888877778899999*******9854 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.096       3     116 ..      32     157 ..      30     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                          AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsd.....ilGtevfeeke..kefefkkGpv...fanllladein 72 
                                    l++g  G+ak ++v+ la  l++           lP       ++G+  +++     e  f++G +      +l +de+n
  gi|121638730|ref|YP_978954.1|  32 LIRGEKGTAKSTAVRGLAALLSVATGSTETGLVELPLGatedrVVGSLDLQRVMrdGEHAFSPGLLaraHGGVLYVDEVN 111
                                    78888999999999999999988877766665556644011125554433332233677788887622145699****** PP

                          AAA_3  73 rappktqsallea..meerqvtvegethklpepflvlatqnPieqe 116
                                        +    ll+a  m   +v  +g +h+ +  f+++ t nP e e
  gi|121638730|ref|YP_978954.1| 112 LLHDHLVDILLDAaaMGRVHVERDGISHSHEARFVLIGTMNPEEGE 157
                                    ***********9622666667778899***************8754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.19       2     129 ..      32     171 ..      31     174 .. 0.67
   2 ?   -1.2   0.0       1.4   2.5e+03      45     106 ..     438     492 ..     435     502 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                    EEESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.............TS.E CS
                            AAA   2 llyGppGtGKTllakavakelgve.......fleisgsellskyvgesekkirelfkeakeka.............kp.s 60 
                                    l+ G +Gt K+++++ +a  l+v        ++e+ +    + +vg    +++ ++      +             ++  
  gi|121638730|ref|YP_978954.1|  32 LIRGEKGTAKSTAVRGLAALLSVAtgstetgLVELPLGATEDRVVGS--LDLQRVM------RdgehafspgllarAHgG 103
                                    6789****************975533333446666666665443332..2333333......22223345666777455* PP

                                    EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEESS.GGGSTHHHHSTTSSEEEE CS
                            AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..........eskvivigatnr.pdkldpallrgRfdrkie 129
                                    +l +DE+  l+ +            v+ Ll +    + +          e+++++ig+ n  + +l p+ll +Rf   + 
  gi|121638730|ref|YP_978954.1| 104 VLYVDEVNLLHDHL-----------VDILLDAAAMGRVHverdgishshEARFVLIGTMNPeEGELRPQLL-DRFGLTVD 171
                                    **********9888...........555555444444444455555558899********9899*******.**987765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                            AAA  45 kirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivi 106
                                    ++r  ++e +e +  +i+++D   ++a ++  +   ++  +++ L  + ++ +    kv vi
  gi|121638730|ref|YP_978954.1| 438 DVRRAIRESREGN-LVIFVVDASGSMAARD--RMAAVSGATLSLLRDAYQRRD----KVAVI 492
                                    6777788878877.6777777777776666..444444444444444433333....35555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4245.85
//
Query:       gi|121638731|ref|YP_978955.1|  [L=156]
Description: hypothetical protein BCG_2871c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-13   48.7   0.0    7.6e-13   48.5   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.8e-06   26.2   0.0    1.2e-05   25.7   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.093   12.5   0.0       0.17   11.6   0.0    1.4  1  PH_17            PH domain


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   1.3e-16   7.6e-13      28     124 ..      47     146 ..      13     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.3e-16
                Acetyltransf_10  28 egealllvaeeggkivGvielrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpf 100
                                    ++  ++++ + +g++  +++l++++       +i++l+ ++++rgqG +++Ll a+++e+ +        ++a+ y  ++
  gi|121638731|ref|YP_978955.1|  47 AETRHFWLETPDGEVTCTLRLMEEHaggekvfRIGRLCTKRDARGQGHSNRLLCAALAEVGDY----PCRIDAQAYLTAM 122
                                    67778888888889999998855555899999***************************9666....789********** PP

                Acetyltransf_10 101 YeklGFkavgeeqeenGirfvpMe 124
                                    Y ++GF++ g+e+ ++Gi +vpM 
  gi|121638731|ref|YP_978955.1| 123 YAQHGFVRDGDEFLDDGIPHVPML 146
                                    ***********************6 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     2e-09   1.2e-05       4      76 .]      51     130 ..      25     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2e-09
                                    EEEEEEETTEEEEEEEEEEES..........TCTEEEEE-GGGTTSSHHHHHHHHTT..SE...EEEE.EEEETHHHHHH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld..........aeitrlaVdpeyrgkGiGraLleaae..kg...iile.qlelnaekaik 67 
                                    +++ +e  +++v    ++l+           + i+rl+++ ++rg+G   +Ll aa    g   +++  q++l      +
  gi|121638731|ref|YP_978955.1|  51 HFW-LETPDGEV---TCTLRLmeehaggekvFRIGRLCTKRDARGQGHSNRLLCAALaeVGdypCRIDaQAYL-----TA 121
                                    445.33222222...222222334466655677888*****************76223434445888899999.....44 PP

                                    HHHHTTEEE CS
                 Acetyltransf_7  68 fYeklGFee 76 
                                    +Y+++GF++
  gi|121638731|ref|YP_978955.1| 122 MYAQHGFVR 130
                                    *******85 PP

>> PH_17  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.17      24      46 ..      47      69 ..      41      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                          PH_17 24 penrllEihSpDgrealiLRckd 46
                                   +e r + + +pDg  +++LR  +
  gi|121638731|ref|YP_978955.1| 47 AETRHFWLETPDGEVTCTLRLME 69
                                   58999***************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1146.83
//
Query:       gi|121638732|ref|YP_978956.1|  [L=493]
Description: malate:quinone oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-208  693.6   0.0   1.3e-208  693.4   0.0    1.0  1  Mqo            Malate:quinone oxidoreductase (Mqo)
    8.5e-12   45.3   0.0    1.3e-11   44.7   0.0    1.3  1  DAO            FAD dependent oxidoreductase
      0.008   15.5   0.0        0.1   11.8   0.0    2.1  2  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.4   0.0  2.3e-212  1.3e-208       2     489 .]       6     490 ..       5     490 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.4 bits;  conditional E-value: 2.3e-212
                            Mqo   2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGHsalcElnYtpekedgsidiskAvkine 81 
                                    ++dvvliGaGimsatlgvll++lep++si+++erld+va+ess +wnnaGtGHsalcE+nYtpe +dgsidi+kAv++ne
  gi|121638732|ref|YP_978956.1|   6 RTDVVLIGAGIMSATLGVLLRRLEPNWSITLIERLDAVAAESSGPWNNAGTGHSALCEMNYTPEMPDGSIDITKAVRVNE 85 
                                    68****************************************************************************** PP

                            Mqo  82 qfevsrqfwaylvekgllkdpkefinkvpHlsfvageenveflkkRyealkksplfegmeysedkeelkewlPlvmegRd 161
                                    qf+v+rqfway+ e+g+l+d ++f+n+vpH+sfv+g++ ve+l++R +al+ +plf+g e+ e+++e++++lP+++++R 
  gi|121638732|ref|YP_978956.1|  86 QFQVTRQFWAYAAENGILTDVRSFLNPVPHVSFVHGSRGVEYLRRRQKALAGNPLFAGTEFIESPDEFARRLPFMAAKRA 165
                                    ******************************************************************************** PP

                            Mqo 162 akekvaatrieeGtdvnfgaltrqllkalekkkgvelklkhevkdlkreedgkWkvkvkdlktgekkkvkakfvfiGaGG 241
                                     +e+va+++++ Gtdv+fgal++ql+ ++ + +g++  ++hev++l+r++dg+W+v++ +++tgek+k+++kfvf+GaGG
  gi|121638732|ref|YP_978956.1| 166 FSEPVALNWAADGTDVDFGALAKQLIGYCVQ-NGTTALFGHEVRNLSRQSDGSWTVTMCNRRTGEKRKLNTKFVFVGAGG 244
                                    *****************************66.99999******************************************* PP

                            Mqo 242 galklLqksgipeakgyggfPvsGqflvcknpevveqheakvYgkaavgaPPmsvpHlDtRvidgkksllfGPfagfstk 321
                                     +l++Lqksgi+e+kg++gfP++G+fl++ np+++++h+akvYg  a gaPP+   HlD R+++gk++l+fGP+ag+s+k
  gi|121638732|ref|YP_978956.1| 245 DTLPVLQKSGIKEVKGFAGFPIGGRFLRAGNPALTASHRAKVYGFPAPGAPPLGALHLDLRFVNGKSWLVFGPYAGWSPK 324
                                    ******************************************************************************** PP

                            Mqo 322 flkegslldllksvklsnllpllavglknldLvkYlieqvlkskedrlealreflpeakkedWelvvaGqRvqvikkdee 401
                                    flk+g++ dl++s++++nll++l vgl++  L +Yli+q++ s+ +r++alref+p+a ++dWel+ aGqRvqvi++de+
  gi|121638732|ref|YP_978956.1| 325 FLKHGQISDLPRSIRPDNLLSVLGVGLTERRLLNYLISQLRLSEPERVSALREFAPSAIDSDWELTIAGQRVQVIRRDER 404
                                    ******************************************************************************** PP

                            Mqo 402 kggvlefGtevvasadgslaalLGasPGAstavsimlevlekcfkeklkseewkeklkelipsygkkleedaelleevrk 481
                                    +ggvlefGt+v+ +adgs+a+lLG sPGAstav+iml+vl+kcf+++++  +w ++lke++ps+g +l+++++l++ev++
  gi|121638732|ref|YP_978956.1| 405 NGGVLEFGTTVIGDADGSIAGLLGGSPGASTAVAIMLDVLQKCFANRYQ--SWLPTLKEMVPSLGVQLSNEPALFDEVWS 482
                                    ************************************************6..9**************************** PP

                            Mqo 482 etakvLkl 489
                                    +++k+Lkl
  gi|121638732|ref|YP_978956.1| 483 WSTKALKL 490
                                    ******97 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.2e-15   1.3e-11       1     205 [.       8     247 ..       8     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.2e-15
                                    EEEEECTSHHHHHHHHHHHHT..T...EEEEESSSSTTSSGG..GSSEEEEESSS...STHHSTH..........HHHHH CS
                            DAO   1 dvviiGGGiiGlstAyeLarr..g...VtllekgdiagsgaS..grnsgllhsgl...rylpeas..........elarl 60 
                                    dvv iG+Gi+ ++    L rr  +   +tl+e+ d ++ ++S  ++n+g  hs+l    y+pe            ++ + 
  gi|121638732|ref|YP_978956.1|   8 DVVLIGAGIMSATLGVLL-RRlePnwsITLIERLDAVAAESSgpWNNAGTGHSALcemNYTPEMPdgsiditkavRVNEQ 86 
                                    89****************.55554899*******9999666633699999999998884455433788999988766667 PP

                                    HHHHHHHHHHHHHHHSSTTSEEE....EEEEEEESSHHHHHHHHHHHHHH..HHTTTTEEEEEH.HHHHHHSTT..ST.. CS
                            DAO  61 slealeelreleeelgididyrr....tGllslaadeeelealdkllall..leagldaellda.eevrelepa..lp.. 129
                                     + ++++++  + e+gi +d+r       ++s  ++++  e+l++++++l  +++ + +e++++ +e +++ p    +  
  gi|121638732|ref|YP_978956.1|  87 FQVTRQFWAYAA-ENGILTDVRSflnpVPHVSFVHGSRGVEYLRRRQKALagNPLFAGTEFIESpDEFARRLPFmaAKra 165
                                    777789995555.56997776644444555555579999****99999986544444779988889*******9752266 PP

                                    ...TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEEEEEEE..EEE--G CS
                            DAO 130 ...gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve...rttpgendaada..vVnaaG 201
                                       ++ +  +  d+  vd  +l++ l   + ++G + l+g+ev++l++++++ w+v    r t ge+++ ++  v + aG
  gi|121638732|ref|YP_978956.1| 166 fsePV-ALNWAADGTDVDFGALAKQLIGYCVQNGTTALFGHEVRNLSRQSDGSWTVTmcnRRT-GEKRKLNTkfVFVGAG 243
                                    76433.33467888899*****************************9988888*****96444.7665444456999999 PP

                                    GGHH CS
                            DAO 202 awsd 205
                                      + 
  gi|121638732|ref|YP_978956.1| 244 GDTL 247
                                    8873 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.026   1.6e+02       1      35 [.       6      42 ..       6      56 .. 0.75
   2 !   11.8   0.0   1.7e-05       0.1     109     180 ..     188     262 ..     163     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.026
                                   EEEEEEE--SHHHHHHHHHHHHTTHH....EEEEESSSS CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvr....vvlvekrst 35
                                   +tdV+ +GaG   ++l+ lL++   +     +l+e+ + 
  gi|121638732|ref|YP_978956.1|  6 RTDVVLIGAGIMSATLGVLLRRL--EpnwsITLIERLDA 42
                                   59******************987..22344666766655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHTEEETCSEEEECCEECCCCC.CCEEEECCTTEEEEEEEEEE.EE--GTT-HHHHHHTGG.EEEEE CS
                  FAD_binding_3 109 riLvehaeerglqvrfktevesleqdeegv.taevrdketgeeetvrakYl.vGaDGgrStvrktlgie.fegee 180
                                    + L+   ++ g++  f++ev++l ++ +g  t ++ +++tge+++++ k++ vGa G   +v ++ gi+ ++g+ 
  gi|121638732|ref|YP_978956.1| 188 KQLIGYCVQNGTTALFGHEVRNLSRQSDGSwTVTMCNRRTGEKRKLNTKFVfVGAGGDTLPVLQKSGIKeVKGFA 262
                                    66667778899**********998777765267777**************989**************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3381.87
//
Query:       gi|121638733|ref|YP_978957.1|  [L=597]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-32  111.7  19.5    2.6e-32  111.0  19.5    1.4  1  PE              PE family
  ------ inclusion threshold ------
        0.4   11.2  10.6       0.72   10.4  10.6    1.4  1  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0  19.5   2.9e-36   2.6e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 2.9e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   M +vv++P++++aaa++la+igsa+s+an aaa pt +v+aaaaDeVS++iAalf+aha++yq+ls+qaaafh +fvqal++
  gi|121638733|ref|YP_978957.1|  1 MLYVVASPDLMTAAATNLAEIGSAISTANGAAALPTVEVVAAAADEVSTQIAALFGAHARSYQTLSTQAAAFHSRFVQALTT 82
                                   889******************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   aa+sYa+ Eaa
  gi|121638733|ref|YP_978957.1| 83 AAASYASVEAA 93
                                   *********97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  10.6     8e-05      0.72       8      99 ..       7      99 ..       3     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8e-05
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYe 88
                                    pd + ++a+ + e+ + i++a+ aa +++++ v+     ++ + ++ + a  ++ ++  ++ aa ++ + + L++AAa Y 
  gi|121638733|ref|YP_978957.1|  7 SPDLMTAAATNLAEIGSAISTANGAAaLPTVEVVAAAADEVSTQIAALFGAHARSYQTLSTQAAAFHSRFVQALTTAAASYA 88
                                   689999*****************99989****************************************************** PP

                  T7SS_ESX_EspC 89 atDeeaagald 99
                                    ++ ++a+ l+
  gi|121638733|ref|YP_978957.1| 89 SVEAANASPLQ 99
                                   ******99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 4115.90
//
Query:       gi|121638734|ref|YP_978958.1|  [L=346]
Description: hypothetical protein BCG_2874 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-17   63.2   0.1    2.6e-17   62.9   0.1    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
    6.3e-12   46.6   6.5    8.6e-12   46.1   6.5    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    3.8e-09   36.6   0.1    9.4e-09   35.3   0.1    1.6  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00073   19.5   0.0     0.0011   18.9   0.0    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
     0.0029   17.2   0.1       0.01   15.4   0.0    1.7  2  DUF900         Alpha/beta hydrolase of unknown function (DUF9
     0.0048   16.8   0.0     0.0072   16.2   0.0    1.3  1  Lipase_3       Lipase (class 3)
  ------ inclusion threshold ------
      0.052   12.7   0.0      0.073   12.2   0.0    1.1  1  PAE            Pectinacetylesterase
       0.22   11.2   0.0       0.31   10.7   0.0    1.2  1  PGAP1          PGAP1-like protein
       0.23   10.9   0.0       0.35   10.3   0.0    1.2  1  DUF676         Putative serine esterase (DUF676)


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   1.3e-20   2.6e-17       4     140 ..      51     201 ..      48     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.3e-20
                    Hydrolase_4   4 kavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelplfl 80 
                                    +++v+ vHG++++     ela+++a++Gfa+yalD r  Grs         ++++ +y + l+  ++ + e+++ +++ +
  gi|121638734|ref|YP_978958.1|  51 HHTVLAVHGYTDYF-FHTELADHFANRGFAFYALDLRKCGRSRapgQTPHFITDLARYDTELEHSLSIINEQNRSAKVLV 129
                                    689*********97.4568***********************99954555799*************************** PP

                    Hydrolase_4  81 lGhSmGGliallyl..lrypd.......kvaglilsaPalkikaklk.appllklllkllgkllpklqv....s 140
                                    +GhS GGli+ l+l  l  ++        v+gl+l +P+l+++ +     pl  ++   ++++ pk+      +
  gi|121638734|ref|YP_978958.1| 130 YGHSAGGLIVSLWLdrL--RQrgeitraGVTGLVLNSPFLDLQGPAIlRLPLTSAFFAAMARMRPKWVArppkE 201
                                    **************653..443467777899***********97764344455557777777777777644332 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   6.5   4.3e-15   8.6e-12       1     216 [.      54     317 ..      54     321 .. 0.61

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.3e-15
                                    EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT...........TTSEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrsdpppldledladlaalldelaa.........gggpvvlv 70 
                                    vl +HG     +  ++++La  +a + ++ +a+Dl+ +Grs  p  +   + dla++ +el +         +  +v + 
  gi|121638734|ref|YP_978958.1|  54 VLAVHGYT--DYF-FHTELADHFANRgFAFYALDLRKCGRSRAPGQTPHFITDLARYDTELEHslsiineqnRSAKVLVY 130
                                    6889**44..333.3789988888888777*********88776666666666655555555555579999999999*** PP

                                    EETCHHHHHHHHHHCC...........EEEEES-..----TTTS----TTHHHHHH....TT-CCCCHCCH....S-HSC CS
                  Abhydrolase_6  71 GHSlGGalalaaapla.........lvvgvlldppptalpagllaaalelllalla....llrllawlsre....plprl 133
                                    GHS GG++++++++ +          v g++l++    + ++ ++a+l+l+l+       +++++ w++r      ++++
  gi|121638734|ref|YP_978958.1| 131 GHSAGGLIVSLWLDRLrqrgeitraGVTGLVLNS---PFLDLQGPAILRLPLTSAFfaamARMRPKWVARPpkegGYGCT 207
                                    ***********77777999999766445566666...2233333333333332222112244447888654455667778 PP

                                    CCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC..........EEEC.......TT-C.............HH CS
                  Abhydrolase_6 134 fladedadaawrarlarlaallaglgllpaaawadlpvpl..........lvlg.......geDp.............lv 183
                                    +++d d + +++  + ++  +   +g+    a ++  ++l          l+l+       ++Dp             ++
  gi|121638734|ref|YP_978958.1| 208 LHRDYDGEFDYNLQWKPVGGFPVTFGWIH--ASRRGHARLhrgidvgvpnLILCsdhtvreKADPatlhrgdavldvtHI 285
                                    88888877777777777765555555443..1111111112244445676777544455554455666666667665555 PP

                                    HHCHHCCCHSTTEEETCE...SSS-HHH..HSHHH CS
                  Abhydrolase_6 184 prllerllaqagarlpvvlpgaGHlphl..eepde 216
                                     r++ +++  ++ +  + +++a H ++l   +p++
  gi|121638734|ref|YP_978958.1| 286 TRWAGCIGN-RSTV--IAVADAKHDVFLslPQPRQ 317
                                    566666664.4444..6699****88873356655 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   4.7e-12   9.4e-09       3      94 ..      54     146 ..      52     178 .. 0.88
   2 ?   -2.0   0.0       1.1   2.2e+03     222     254 ..     277     310 ..     254     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.7e-12
                                    EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB......CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                  Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin.....ddygtasvaddldrildalgddkltl 77 
                                    ++ +hG+++   +++   la+++a +gf +++lDlr +g+S+++  +++      +y t  ++ +l  i ++    k+ +
  gi|121638734|ref|YP_978958.1|  54 VLAVHGYTD---YFFHTELADHFANRGFAFYALDLRKCGRSRAPGQTPHfitdlARYDTE-LEHSLSIINEQNRSAKVLV 129
                                    566666666...556667*****************************9999999999996.999999************* PP

                                    EEETHHHHHHHHHHHHH CS
                  Abhydrolase_1  78 vGhSmGGmialayaaey 94 
                                     GhS GG+i++ ++ + 
  gi|121638734|ref|YP_978958.1| 130 YGHSAGGLIVSLWLDRL 146
                                    *************9886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                    CSSSCHHHHHHHHHCHTS.EEEEEEETCSSSHHH CS
                  Abhydrolase_1 222 Dplvppkaledlaqllpk.krlvvisdagHlafl 254
                                    D + +  ++ ++a+ + + +++++++da H++fl
  gi|121638734|ref|YP_978958.1| 277 DAVLDVTHITRWAGCIGNrSTVIAVADAKHDVFL 310
                                    6666666777777777777899999999999997 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.4e-07    0.0011      68     112 ..     122     169 ..      79     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.4e-07
                                    ETTCEEEEEEETHHHHHHHHHHHHHHHTT---...EEEEEEESE-SST CS
                  Abhydrolase_3  68 adpsrivlaGdSaGGnlaaavalrardegepk...vagqvliyPvtdl 112
                                       +++ + G SaGG ++   + r+r++ge++   v+g+vl +P +dl
  gi|121638734|ref|YP_978958.1| 122 NRSAKVLVYGHSAGGLIVSLWLDRLRQRGEITragVTGLVLNSPFLDL 169
                                    46789***********************9888899*********9987 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.76   1.5e+03      18      32 ..      50      64 ..      43      68 .. 0.81
   2 !   15.4   0.0   5.1e-06      0.01      78     140 ..     109     169 ..     104     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.76
                         DUF900 18 akeilvfvhGynnsF 32
                                   a++ ++ vhGy   F
  gi|121638734|ref|YP_978958.1| 50 AHHTVLAVHGYTDYF 64
                                   5678999****9877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.1e-06
                         DUF900  78 dalekllrylatkksakkihllaHSmGtwlvlealrqlaieadepaveakikeviLaAPDidv 140
                                    ++le+ l++++++++  k+ +  HS G  +v   l  l+++ +   + a ++ ++L++P +d+
  gi|121638734|ref|YP_978958.1| 109 TELEHSLSIINEQNRSAKVLVYGHSAGGLIVSLWLDRLRQRGE--ITRAGVTGLVLNSPFLDL 169
                                    689*************************************997..578899999999997775 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.6e-06    0.0072      47      97 ..     107     157 ..      62     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.6e-06
                                    HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHHHHTT-SS---E CS
                       Lipase_3  47 lreqvlkelkrllekypeysivvtGHSLGgalAlLaaldlvengenekkkv 97 
                                      ++++++l+ + e+++++++ v GHS Gg + +L    l+++ge ++  v
  gi|121638734|ref|YP_978958.1| 107 YDTELEHSLSIINEQNRSAKVLVYGHSAGGLIVSLWLDRLRQRGEITRAGV 157
                                    556788999999***********************9999999998765555 PP

>> PAE  Pectinacetylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05     0.073     145     190 ..     122     168 ..     115     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                            PAE 145 kkakkvlLsGcSAGglaailhcdklrellp.keakvkclsdaGfFld 190
                                    +++ kvl+ G SAGgl + l++d+lr++ + ++a v +l+    Fld
  gi|121638734|ref|YP_978958.1| 122 NRSAKVLVYGHSAGGLIVSLWLDRLRQRGEiTRAGVTGLVLNSPFLD 168
                                    56789*********************987744445766666666665 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.31      32     106 ..      64     140 ..      48     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                          PGAP1  32 qelrkllknqnkkeldfftvdfne....elsaldGrtlldqaeylndaIkyIlslysssekeptsviliGHSmGGivar 106
                                    + + +l+++ +++ + f++ d+ +    +   +  + + d a+y +  +++ ls+  +++++  +v++ GHS GG++  
  gi|121638734|ref|YP_978958.1|  64 FFHTELADHFANRGFAFYALDLRKcgrsRAPGQTPHFITDLARY-DTELEHSLSII-NEQNRSAKVLVYGHSAGGLIVS 140
                                    55555555555566777777765421112233334456677777.44455558888.7888999***********9864 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.35      69     127 ..     116     167 ..     109     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                         DUF676  69 evvkkkkdknkkiSfvghSlGgliaraaiaklkekemtlkeaikglepvtfitlasPhL 127
                                    +++++++ + +k+ + ghS Ggli++  + +l+++ +  +        vt + l+sP+L
  gi|121638734|ref|YP_978958.1| 116 SIINEQNRS-AKVLVYGHSAGGLIVSLWLDRLRQRGEITR------AGVTGLVLNSPFL 167
                                    566666666.8*******************9997766444......3455566667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2424.99
//
Query:       gi|121638735|ref|YP_978959.1|  [L=459]
Description: mycothione reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-45  153.1   0.4    1.3e-44  152.6   0.4    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.6e-28   99.1   0.2    4.1e-28   97.8   0.0    1.8  2  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    2.7e-14   53.5   0.0    5.9e-14   52.4   0.0    1.6  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    6.9e-09   35.4   0.0    9.9e-09   34.9   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    9.7e-07   28.2   0.4      3e-06   26.6   0.0    1.9  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    0.00028   20.9   0.5       0.29   11.1   0.1    2.9  3  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.032   12.9   0.0        5.6    5.5   0.0    2.2  2  HI0933_like    HI0933-like protein
      0.049   13.5   0.0      0.086   12.7   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.097   12.1   0.1        1.4    8.3   0.0    2.5  3  PP_kinase_C    Polyphosphate kinase C-terminal domain 2


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.6   0.4   6.6e-48   1.3e-44       1     278 [.       4     307 ..       4     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 6.6e-48
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH...................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias...................... 57 
                                    +d+++iG G +   + ++ a + a +   +  +gtcln+gc+++k ++ +ae a++++                      
  gi|121638735|ref|YP_978959.1|   4 YDIAIIGTGSGNSILDERYASKRAAICEQGtFGGTCLNVGCIPTKMFVYAAEVAKTIRgasrygidahidrvrwddvvsr 83 
                                    699********999999999988888777799*************************9********************** PP

                                    ............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEE CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgk 125
                                                e  ++   +i+++ +++ ++  ++ +++ l   +++ +e+++++++v+A Gs+p ++  p+       
  gi|121638735|ref|YP_978959.1|  84 vfgridpialsgEDYRRCAPNIDVYRTHTRFGPVQADGRYLL---RTDAGEEFTAEQVVIAAGSRPVIP--PAI---LAS 155
                                    ************88899999*******999999999999999...457799******************..555...334 PP

                                    CCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 126 lvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgts 205
                                    +v++ +s+  ++ ++lp++iv+vG+G+i+ E+A +++ lg++vtlv +++ llr +d+ + ++ ++     + e++++ +
  gi|121638735|ref|YP_978959.1| 156 GVDYHTSDTVMRIAELPEHIVIVGSGFIAAEFAHVFSALGVRVTLVIRGSCLLRHCDDTICERFTRIAST-KWELRTHRN 234
                                    5799*****************************************************9999999988887.588888899 PP

                                    EEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 206 vkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDva 278
                                    v++ +++g+ + + l+dg +i+adl++va+G+  + +ll+ e++g+ + e+g++ vde++rt+  g++a+GDv 
  gi|121638735|ref|YP_978959.1| 235 VVDGQQRGSGVALRLDDGCTINADLLLVATGRVSNADLLDaEQAGVDV-EDGRVIVDEYQRTSARGVFALGDVS 307
                                    999999999999************************************.************************9 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.6   1.1e+04      46      81 ..     161     196 ..     152     200 .. 0.72
   2 !   97.8   0.0     2e-31   4.1e-28       1     109 [.     345     454 ..     345     455 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.6
                                    HTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                  Pyr_redox_dim  46 etkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                     +++++++    +   ++G  +++ + + ++++l v
  gi|121638735|ref|YP_978959.1| 161 TSDTVMRIAELPEHIVIVGSGFIAAEFAHVFSALGV 196
                                    566777776667777888888888888877777765 PP

  == domain 2  score: 97.8 bits;  conditional E-value: 2e-31
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqela 80 
                                    +p++vftdp++a+vGlte++A a+g++i+v+  ++ ++++ +a+++t+g+vKl++++ +g++lGahi+G++a++liq l 
  gi|121638735|ref|YP_978959.1| 345 VPAAVFTDPQIAAVGLTENQAVAKGLDISVKIQDYGDVAYGWAMEDTSGIVKLITERGSGRLLGAHIMGYQASSLIQPLI 424
                                    79****************************************************************************** PP

                                    HHHHTTSBHH.HHHTSBSSSSSTGGGGHCH CS
                  Pyr_redox_dim  81 vaikagltve.dladtihihPtlsealkea 109
                                    +a+++glt++ ++  +  ihP l e++++a
  gi|121638735|ref|YP_978959.1| 425 QAMSFGLTAAeMARGQYWIHPALPEVVENA 454
                                    **********77999*********998775 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   2.9e-17   5.9e-14       1      77 [.     174     246 ..     174     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.9e-17
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                    ++v+vG+G+i+ E+A ++++lg +Vt+v r++ llr +D+++ +++++  + +  e++++++v+  ++ ++gv    
  gi|121638735|ref|YP_978959.1| 174 HIVIVGSGFIAAEFAHVFSALGVRVTLVIRGSCLLRHCDDTICERFTRIASTK-WELRTHRNVVDGQQRGSGV---A 246
                                    79*********************************************999988.*********9999998883...3 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     5e-12   9.9e-09     111     305 .]     120     304 ..     112     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5e-12
                    Pyr_redox_3 111 degfevetske.tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya..gqkvvViGgknSavDaAlelvrkg 187
                                    d+ + ++t+ + +++A++v+iA+G   +P  +    ++   + y++ + ++ +a   +++v++G +  a++ A  + + g
  gi|121638735|ref|YP_978959.1| 120 DGRYLLRTDAGeEFTAEQVVIAAGS--RPVIPPAILAS--GVDYHTSDTVMRIAelPEHIVIVGSGFIAAEFAHVFSALG 195
                                    6778899999769***********9..99988877776..6777777777777745699********************* PP

                    Pyr_redox_3 188 aeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGy 267
                                     +Vt+v+rgs + ++          +i +r+ ++ + +k ++ ++ +v + +++ + + ++ +dg ++++ d  ++atG 
  gi|121638735|ref|YP_978959.1| 196 VRVTLVIRGSCLLRH-------CDDTICERFTRIAS-TKWELRTHRNVVDGQQRGSGVALRLDDGCTINA-DLLLVATGR 266
                                    *********976665.......678899***99877.5589999999*****************987664.777889*** PP

                    Pyr_redox_3 268 kpdlsflkkslfeld.edgrpvlteeteetnvpglflaG 305
                                     +++++l++++   d edgr+ ++ e + t   g+f  G
  gi|121638735|ref|YP_978959.1| 267 VSNADLLDAEQAGVDvEDGRVIVD-EYQRTSARGVFALG 304
                                    ********9555555277777776.57788899999877 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.5     3e+03       2      14 ..       3      15 ..       2      18 .. 0.78
   2 !   26.6   0.0   1.5e-09     3e-06     141     227 ..     127     206 ..     115     232 .. 0.80
   3 ?   -1.8   0.0      0.66   1.3e+03     293     339 ..     225     265 ..     209     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                    K_oxygenase  2 ilDligiGiGpsn 14
                                   ++D+++iG G  n
  gi|121638735|ref|YP_978959.1|  3 TYDIAIIGTGSGN 15
                                   7899999998765 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.5e-09
                    K_oxygenase 141 egeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelk 220
                                    ++  ee++a+++v++ G++p iP+++ +       +H+s++  r+   + +++i++vGsG  aae ++   +    v ++
  gi|121638735|ref|YP_978959.1| 127 TDAGEEFTAEQVVIAAGSRPVIPPAILAS---GVDYHTSDTVMRI--AELPEHIVIVGSGFIAAEFAHV-FSALG-VRVT 199
                                    466899*******************9964...4679***999999..68899*************6654.43333.5777 PP

                    K_oxygenase 221 lvtrsea 227
                                    lv+r++ 
  gi|121638735|ref|YP_978959.1| 200 LVIRGSC 206
                                    7777665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.66
                    K_oxygenase 293 erlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                    ++ +l+++r+v + +++g+ +v l l++       t+++d +++ATG
  gi|121638735|ref|YP_978959.1| 225 TKWELRTHRNVVDGQQRGS-GVALRLDD-----GCTINADLLLVATG 265
                                    5678899999999999986.89999888.....77899999999999 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0029       5.8     128     155 ..     118     144 ..      97     145 .. 0.71
   2 ?   -2.9   0.0         3     6e+03     125     153 ..     166     194 ..     157     196 .. 0.52
   3 !   11.1   0.1   0.00015      0.29     106     155 ..     218     266 ..     209     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                  NAD_binding_9 128 eeradgqavlladgaslaadaVvLAlGh 155
                                    + +++++ ++++ g++++a++Vv+A G 
  gi|121638735|ref|YP_978959.1| 118 Q-ADGRYLLRTDAGEEFTAEQVVIAAGS 144
                                    3.334568999999***********995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                  NAD_binding_9 125 vdleeradgqavlladgaslaadaVvLAl 153
                                     +++e +++  ++ ++    ++ +V+ Al
  gi|121638735|ref|YP_978959.1| 166 MRIAELPEHIVIVGSGFIAAEFAHVFSAL 194
                                    55555555554444444455555555555 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00015
                  NAD_binding_9 106 ellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    ++++ ++ + +++ hr +vvd ++r++g+a++l+dg ++ ad + +A+G 
  gi|121638735|ref|YP_978959.1| 218 RFTRIASTKWELRTHR-NVVDGQQRGSGVALRLDDGCTINADLLLVATGR 266
                                    5555666677777765.7999***************************95 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0037       7.3     134     165 ..     116     145 ..     101     164 .. 0.83
   2 ?    5.5   0.0    0.0028       5.6     117     169 ..     220     271 ..     165     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0037
                                    EEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 134 svekeedgkfrvktkseeeleadklvlAtGGl 165
                                     v  ++dg++ ++t+ +ee++a+++v+A G+ 
  gi|121638735|ref|YP_978959.1| 116 PV--QADGRYLLRTDAGEEFTAEQVVIAAGSR 145
                                    44..678899******************9976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0028
                                    HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                    HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                    +++ +++ +lr++++v + +++ +g + ++++++ +++ad l++AtG  S + 
  gi|121638735|ref|YP_978959.1| 220 TRIASTKWELRTHRNVVDGQQRGSG-VALRLDDGCTINADLLLVATGRVSNAD 271
                                    5788889999999999999887777.999**9***************998765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.086       2      51 ..     175     224 ..     174     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                    + ++G+G + a+ a+vf + g++V+lv + +  l+++ ++i +++ + ++
  gi|121638735|ref|YP_978959.1| 175 IVIVGSGFIAAEFAHVFSALGVRVTLVIRGSCLLRHCDDTICERFTRIAS 224
                                    789************************99999999999999888877765 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00073       1.4      51      69 ..     192     210 ..     183     224 .. 0.84
   2 ?   -2.7   0.0       1.7   3.4e+03      46      58 ..     271     283 ..     270     289 .. 0.87
   3 ?    0.3   0.0      0.21   4.2e+02      41      77 ..     417     453 ..     402     455 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00073
                    PP_kinase_C  51 sqaGVkiklivrgicclrp 69 
                                    s  GV+++l++rg c lr 
  gi|121638735|ref|YP_978959.1| 192 SALGVRVTLVIRGSCLLRH 210
                                    789************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                    PP_kinase_C  46 kLyeAsqaGVkik 58 
                                     L +A qaGV+++
  gi|121638735|ref|YP_978959.1| 271 DLLDAEQAGVDVE 283
                                    5899******996 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.21
                    PP_kinase_C  41 keiidkLyeAsqaGVkiklivrgicclrpgvkglsen 77 
                                    +++i+ L++A + G +   + rg + + p  +++ en
  gi|121638735|ref|YP_978959.1| 417 SSLIQPLIQAMSFGLTAAEMARGQYWIHPALPEVVEN 453
                                    689**************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2957.10
//
Query:       gi|121638736|ref|YP_978960.1|  [L=372]
Description: nickel-transport integral membrane protein nicT [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-99  330.5  12.4    8.2e-99  330.5  12.4    1.6  2  NicO      High-affinity nickel-transport protein
  ------ inclusion threshold ------
      0.086   13.0   0.1      0.086   13.0   0.1    5.4  7  MHYT      Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.18   1.6e+03     253     279 ..      19      45 ..       8      49 .. 0.58
   2 !  330.5  12.4  9.1e-103   8.2e-99       2     282 ..      64     353 ..      63     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.18
                           NicO 253 lwaaiisleleivGavlvllfallllg 279
                                     ++a+++ +l ++ av+v+l  + +l 
  gi|121638736|ref|YP_978960.1|  19 ALTAAEWWRLGLMFAVIVALHLVGWLT 45 
                                    444555555555556666666666665 PP

  == domain 2  score: 330.5 bits;  conditional E-value: 9.1e-103
                           NicO   2 lvliglsflyGvrHAvdagHgkai...irklmqagktalkrGillslgsslvvvlvavllvvaavlvlr.....ltslse 73 
                                    ++++++++++G+rHA+da+H++ai   +rklm++g+++l++G+++slg+s+vv+++av+lv++++++       +++l++
  gi|121638736|ref|YP_978960.1|  64 IGVGLTAYTLGLRHAFDADHIAAIdntTRKLMSDGHRPLAVGFFFSLGHSTVVFGLAVMLVTGLKAIVGpvendSSTLHH 143
                                    57899**********************************************************9998766666899**** PP

                           NicO  74 tgaaigtei.asFllvilllnllllrklrklfrklerlgrapaaeleaalakrgllsrilgklfrlitkswhmypvgflf 152
                                    ++++igt+i ++Fl++i++ln+++l+ ++++f++l+r g++++aele++l++rgll r+lg++++  tkswhmypvgflf
  gi|121638736|ref|YP_978960.1| 144 YTGLIGTSIsGAFLYLIGILNVIVLVGIVRVFAHLRR-GDYDEAELEQQLDNRGLLIRFLGRFTKSLTKSWHMYPVGFLF 222
                                    *************************************.****************************************** PP

                           NicO 153 glGfdtateiallaidpsealkgdsfdsilalpalfavGlrlcdgadivlmfaalnwaflg.grklvyamsitgtsitva 231
                                    glGfdtateiall++  ++a++g ++++il+lp+lfa+G++l+d++d+ +m++a++waf++ +rk++y++++tg+s++va
  gi|121638736|ref|YP_978960.1| 223 GLGFDTATEIALLVLAGTSAAAGLPWYAILCLPVLFAAGMCLLDTIDGSFMNFAYGWAFSSpVRKIYYNITVTGLSVAVA 302
                                    ******************************************************************************** PP

                           NicO 232 lliglivtlklvakkfalsgslwaaiisleleivGavlvllfallllgasl 282
                                    llig++++l+l+a++++++g +w++++ l+l++vG+v+v++fal++ +a+l
  gi|121638736|ref|YP_978960.1| 303 LLIGSVELLGLIANQLGWQGPFWDWLGGLDLNTVGFVVVAMFALTWAIALL 353
                                    ************************************************987 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.5      0.18   1.6e+03      29      47 ..      31      50 ..      13      59 .. 0.55
   2 ?   -1.5   1.1      0.32   2.9e+03      10      22 ..      41      54 ..      29      86 .. 0.48
   3 ?   -0.3   0.2      0.14   1.2e+03      27      47 ..     105     125 ..      97     131 .. 0.78
   4 ?    2.9   1.1     0.014   1.2e+02       8      39 ..     143     174 ..     141     179 .. 0.84
   5 ?   -2.4   0.5      0.61   5.5e+03      22      43 ..     225     246 ..     218     254 .. 0.64
   6 ?   13.0   0.1   9.6e-06     0.086      14      43 ..     280     310 ..     275     322 .. 0.81
   7 ?    0.9   0.2     0.058   5.2e+02      32      46 ..     339     353 ..     327     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                           MHYT 29 alSlliaivas.vlAlalav 47
                                   + ++++a+ ++ +l ++l+v
  gi|121638736|ref|YP_978960.1| 31 MFAVIVALHLVgWLTVTLLV 50
                                   33344444444455555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                           MHYT 10 tGMaAftlpg.pig 22
                                   +G + +tl + p +
  gi|121638736|ref|YP_978960.1| 41 VGWLTVTLLVePAR 54
                                   33333333222333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.14
                           MHYT  27 ltalSlliaivasvlAlalav 47 
                                    +++ Sl+ ++v+ +lA++l++
  gi|121638736|ref|YP_978960.1| 105 GFFFSLGHSTVVFGLAVMLVT 125
                                    567788888899999999886 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.014
                           MHYT   8 HYtGMaAftlpgpigydpaltalSlliaivas 39 
                                    HYtG  +++++g+  y +++  + +l+ iv +
  gi|121638736|ref|YP_978960.1| 143 HYTGLIGTSISGAFLYLIGILNVIVLVGIVRV 174
                                    ***********999999998888888877755 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.61
                           MHYT  22 gydpaltalSlliaivasvlAl 43 
                                    g+d+a+ ++ l++a ++++++l
  gi|121638736|ref|YP_978960.1| 225 GFDTATEIALLVLAGTSAAAGL 246
                                    5555555555666666666655 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 9.6e-06
                           MHYT  14 Aftlpg.pigydpaltalSlliaivasvlAl 43 
                                    Af+ p+  i+y+++ t+lS+++a+++  + l
  gi|121638736|ref|YP_978960.1| 280 AFSSPVrKIYYNITVTGLSVAVALLIGSVEL 310
                                    9999999*************99998875555 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.058
                           MHYT  32 lliaivasvlAlala 46 
                                    +++a+ a + A+al+
  gi|121638736|ref|YP_978960.1| 339 VVVAMFALTWAIALL 353
                                    567777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2569.87
//
Query:       gi|121638737|ref|YP_978961.1|  [L=110]
Description: hypothetical protein BCG_2877 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-07   29.2   0.0    7.4e-07   28.9   0.0    1.1  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.19   11.0   0.0       0.25   10.6   0.0    1.2  1  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   8.2e-11   7.4e-07       5      70 ..      30      94 ..      26     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 8.2e-11
                                   EEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTE..CCHCTT-HH CS
                           cobW  5 ltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellretgveivelenGci..Cctlredll 70
                                   l +++GsGKTt+l + l e++++  + vi++++  +++Da+  r t+v++++ + G +  C+    d+ 
  gi|121638737|ref|YP_978961.1| 30 LMSSPGSGKTTVLGAALdEHADQFAIGVIEGDIT-TDLDAANGRGTQVSLLNNQHGFCaeCHL---DAP 94
                                   7899*************8888999**********.******9999998888888884423333...444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.8e-05      0.25      23      46 ..      32      55 ..      20      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.8e-05
                     Zeta_toxin 23 GqpGAGKselaellkdelerqgnv 46
                                    +pG+GK++++ ++ de++ q  +
  gi|121638737|ref|YP_978961.1| 32 SSPGSGKTTVLGAALDEHADQFAI 55
                                   58***************9755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 593.62
//
Query:       gi|121638738|ref|YP_978962.1|  [L=71]
Description: hypothetical protein BCG_2878 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   21.9   0.0    0.00011   21.8   0.0    1.0  1  cobW      CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.3e-09   0.00011     126     176 ..       6      57 ..       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.3e-09
                                    CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC...HHHHHHHHHHHHTTS-EE CS
                           cobW 126 aeeekieekaedqlaaadllvlnKtDlldee.allekleerlrqlnpeakvl 176
                                    +e+++++  ++  +   d+++l K+Dl++   a++++  + +r++n++a++l
  gi|121638738|ref|YP_978962.1|   6 TEGKDKPLMYPATFRSRDVVLLDKIDLVPFLdADVDAYIAHVREVNAAATIL 57 
                                    799****************************9***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 474.51
//
Query:       gi|121638739|ref|YP_978963.1|  [L=258]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-65  220.9   0.6      2e-65  220.7   0.6    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    6.8e-47  159.5   0.1    8.2e-47  159.2   0.1    1.1  1  adh_short     short chain dehydrogenase
     0.0013   18.7   3.2     0.0074   16.2   3.2    2.0  1  KR            KR domain
  ------ inclusion threshold ------
      0.081   12.4   0.6       0.11   12.0   0.1    1.5  2  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.7   0.6   4.4e-69     2e-65       4     234 .]      20     251 ..      14     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 4.4e-69
                                    TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGC CS
                   adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapkl 83 
                                    sgIG a+ +++ +eGa++v+ d++ ea     ++a+el+  ++++DV de++v+ l++ ++e++g++Di++nnagi+p+ 
  gi|121638739|ref|YP_978963.1|  20 SGIGLAAGRRMRAEGATIVVGDVDVEA---GGAAADELSGLFVPTDVCDEDAVNGLFDGAAETYGRIDIAFNNAGISPPE 96 
                                    8*************************9...78889999999**************************************8 PP

                                    SS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH..HCTSCCEEEEEEEGGGTSBSTTTT.HHHHHHHHHHHHHHHHHHHHG CS
                   adh_short_C2  84 kgpfletsreefdraldvnlyslfllakaalp..lmkeggsivnlssvgaervvpnyn.aygaaKaalealtrylAvelg 160
                                    ++ +++t+ + ++r++dvnl+s++l+++aal+  +++ +gsivn++s+ a ++ +  +  y+a+K+++ a++r l v+++
  gi|121638739|ref|YP_978963.1|  97 DNLIENTELAAWQRVQDVNLKSVYLCCRAALRhmVLAGKGSIVNTASFVAVMGSATSQiSYTASKGGVLAMSRELGVQFA 176
                                    888999**************************6333455**************999888********************* PP

                                    GGTEEEEEEEE--BHCTGGGGS.TTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                   adh_short_C2 161 pkgiRvNavspgpikTlaasgi.kgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                    ++giRvNa +pgp++T++ +++ ++++e  ++   + plgr+++p+e+a+a++fLasd+as+it +t+ vDgG++
  gi|121638739|ref|YP_978963.1| 177 RQGIRVNALCPGPVNTPLLQELfAKNPERAARRMVHVPLGRFAEPDEIAAAVAFLASDDASFITASTFLVDGGIS 251
                                    ******************77752668899999999**************************************85 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.2   0.1   1.8e-50   8.2e-47       2     193 ..      12     201 ..      11     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 1.8e-50
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    v+++tG++sGIG+a  +++ +eGa++vv d   e+  ++a+el       l++++Dv d+++v+ l++ a++ +g++d+ 
  gi|121638739|ref|YP_978963.1|  12 VAVITGGGSGIGLAAGRRMRAEGATIVVGDVDVEAGGAAADELSG-----LFVPTDVCDEDAVNGLFDGAAETYGRIDIA 86 
                                    89*****************************************96.....7***************************** PP

                                    EE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-T.TBHHHHHHHHHHHH CS
                      adh_short  82 vnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpva.gvaaYsAsKaavag 158
                                     nNAGi   +++ +++++ ++w+rv +vNl++v+l++ra+l++m+ + +G+Ivn++S ++ +++a ++++Y+AsK++v +
  gi|121638739|ref|YP_978963.1|  87 FNNAGIspPEDNLIENTELAAWQRVQDVNLKSVYLCCRAALRHMVLAGKGSIVNTASFVAVMGSAtSQISYTASKGGVLA 166
                                    ******877778889999999***************************************9998725889********** PP

                                    HHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                      adh_short 159 ltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                    ++r+l  ++a++girvna++PG+v+T++ +el +k
  gi|121638739|ref|YP_978963.1| 167 MSRELGVQFARQGIRVNALCPGPVNTPLLQELFAK 201
                                    *****************************998776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.2   1.7e-06    0.0074       4     152 ..      14     160 ..      12     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    +itGG  g+Gl+  r + ++ga+   +++      e+  a  +el+       +v+ Dv d+dav+ l++ + ++ ++i 
  gi|121638739|ref|YP_978963.1|  14 VITGGGSGIGLAAGRRMRAEGATI--VVGDV--DVEAGGAAADELSG-----LFVPTDVCDEDAVNGLFDGAAETYGRID 84 
                                    8********************974..45555..23334445666666.....58899*********************** PP

                                    EEEE-----..----TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--T.T-HHHHHH CS
                             KR  84 GvihaAgvl..rdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsa.gqanYaaa 152
                                      ++ Ag++  +d+l+e+++ +++++v    +k +    ++  +         +v ++S  +++gsa  q +Y+a 
  gi|121638739|ref|YP_978963.1|  85 IAFNNAGISppEDNLIENTELAAWQRVQDVNLKSVYLCCRAALRhmvlAGKGSIVNTASFVAVMGSAtSQISYTAS 160
                                    ********8446***************9999998766554444323333445678888888888876258888875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.4e-05      0.11       2      87 ..      14     105 ..      13     153 .. 0.83
   2 ?   -3.4   0.0       1.2   5.2e+03      64      87 ..     220     244 ..     217     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHH....HH.T-SEEEE--S-- CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfk....ee.qpdavihlAavg 75 
                                    ++tG+   iG a  +++ ++g ++++ d + +a+  a++e    +v  d++d++a++ lf+    ++ ++d+ ++ A+++
  gi|121638739|ref|YP_978963.1|  14 VITGGGSGIGLAAGRRMRAEGATIVVGDVDVEAGGAAADELSgLFVPTDVCDEDAVNGLFDgaaeTYgRIDIAFNNAGIS 93 
                                    79*********************99999998888877766669**************99983322235688888888888 PP

                                    -HHHHHHSHHHH CS
                      Epimerase  76 gvaassedpadf 87 
                                     ++++ ++++++
  gi|121638739|ref|YP_978963.1|  94 PPEDNLIENTEL 105
                                    888887777665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.2
                                    T-SEEEE--S.---HHHHHHSHHHH CS
                      Epimerase  64 qpdavihlAa.vggvaassedpadf 87 
                                    +pd++  + a  ++ +as+++++ f
  gi|121638739|ref|YP_978963.1| 220 EPDEIAAAVAfLASDDASFITASTF 244
                                    6899999988899999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1729.59
//
Query:       gi|121638740|ref|YP_978964.1|  [L=455]
Description: aldehyde dehydrogenase aldC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.1e-155  516.5   0.1   5.8e-155  516.3   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.3   0.1  3.2e-159  5.8e-155       9     462 .]       4     447 ..       1     447 [. 0.98

  Alignments for each domain:
  == domain 1  score: 516.3 bits;  conditional E-value: 3.2e-159
                                    EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                         Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                     + inPat+ev+a+v + +a+ vd+av++A++a+++wa+l +++Ra+ Lr++a++++++ +ela+le+++ G p+ +a+ 
  gi|121638740|ref|YP_978964.1|   4 TQLINPATEEVLASVDHTDANAVDDAVQRARAAQRRWARLAPAQRAAGLRAFAAAVQAHLDELAALEVANSGHPIVSAEW 83 
                                    6789**************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHH CS
                         Aldedh  89 eveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpls 168
                                    e   + dvl +ya+  e+l+g+ +p++ g   ++++eP+Gvvg+ItPWNfP+++a+w++apalaaGN+v++KPae tpl+
  gi|121638740|ref|YP_978964.1|  84 EAGHVRDVLAFYAASPERLSGRQIPVA-GGVDVTFNEPMGVVGVITPWNFPMVIASWAIAPALAAGNAVLVKPAELTPLT 162
                                    **************************5.99************************************************** PP

                                    HHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTS CS
                         Aldedh 169 alllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivleda 248
                                    +++l el+ eagl++++l+v++g+g  vge +v+hp+++k+ ftGstevg+++++ aa+++krvtlElGGk+++iv+ d+
  gi|121638740|ref|YP_978964.1| 163 TMRLGELAVEAGLDEDLLQVLPGKGTVVGERFVTHPDIRKIVFTGSTEVGKRVMAGAAAQVKRVTLELGGKSANIVFHDC 242
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHH CS
                         Aldedh 249 DldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeak 328
                                    Dl++a++ + +g+f naGQ C+a sr+lvq+s+yd+f+e l  a+ ++ vgdp  ++t++GPl+s+a+++kv +yv +  
  gi|121638740|ref|YP_978964.1| 243 DLERAATTAPAGVFDNAGQDCCARSRILVQRSVYDRFMELLEPAVHSIVVGDPGSRATEMGPLVSRAHRDKVAGYVPDDA 322
                                    ***************************************************************************98765 PP

                                    HTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHH CS
                         Aldedh 329 eegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdler 408
                                         +   g   +a   +g+++ Ptvl+  ++ +r +++EiFGPV++v++f+de++ai++aNdt yGL+++++t+dl+r
  gi|121638740|ref|YP_978964.1| 323 ----PVAFRG---TAPAGRGFWFPPTVLT-PKRGDRTVTDEIFGPVVVVLTFDDEADAISLANDTAYGLSGSIWTDDLSR 394
                                    ....577777...56789***********.8************************************************* PP

                                    HHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 409 aervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                    a+rva+++e Gn+ +N+++ ++ ++ pfgG+kqSg+Gre g+++  ++te+k+v
  gi|121638740|ref|YP_978964.1| 395 ALRVARAVESGNLSVNSHSSVRFNT-PFGGFKQSGVGRELGPDAPLQFTETKNV 447
                                    *************************.**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3386.91
//
Query:       gi|121638741|ref|YP_978965.1|  [L=308]
Description: amidotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-70  234.7   0.0    1.1e-69  234.5   0.0    1.0  1  Peptidase_C26  Peptidase C26
    6.9e-13   48.8   0.0    1.1e-12   48.1   0.0    1.2  1  GATase         Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   0.0   1.3e-73   1.1e-69       1     216 []      66     279 ..      66     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 1.3e-73
                  Peptidase_C26   1 pvigitaneeslkkeavqdaeesylaasyveavekagglpvllpiee.deedvkaildkldgllltGgqdvePslygeep 79 
                                    pv+g+ta++e + ++ v+d+ + yl+a+y+e +++agg++vllp++  d+e+v  +ld+l++l++tGg+d++P+ yg+ep
  gi|121638741|ref|YP_978965.1|  66 PVVGLTAYLE-QVRTGVWDIPAGYLPADYFEGITMAGGVAVLLPPQPvDPESVGCVLDSLHALVITGGYDLDPAAYGQEP 144
                                    9*******97.58999******************************99******************************** PP

                  Peptidase_C26  80 sekeeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsll 159
                                    ++++++ +p+Rda+e+aL+r al+rg+P+lgiCrG+q+lnvalGGtl+q++ ++ g++ hr+ + ++++  v++ +g+ l
  gi|121638741|ref|YP_978965.1| 145 HPATDHPRPGRDAWEFALLRGALQRGMPVLGICRGTQVLNVALGGTLHQHLPDILGHSGHRAGNGVFTRLPVHTASGTRL 224
                                    ******************************************************************************** PP

                  Peptidase_C26 160 aellgseeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                    ael+g e+++v ++Hhqai++++e+l v+Av+ DgviEa+e++  ++fvl+vQwHPE
  gi|121638741|ref|YP_978965.1| 225 AELIG-ESADVPCYHHQAIDQVGEGLVVSAVDVDGVIEALELPG-DTFVLAVQWHPE 279
                                    *****.**************************************.66*********9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   1.2e-16   1.1e-12      62     176 ..     161     283 ..     152     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.2e-16
                                    HHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE........EEECEEEEEEEEEEEETTT......CGGTTTTSEEEEEEE CS
                         GATase  62 eaikearenkiPiLGICLGmQllaiefgrkvv........kekekehhggtmrlgddet......allyglknevierhr 127
                                    ++++ a+++++P+LGIC G Q+l  ++g++++        +    +h+ g+  ++  +       +l++  +++ ++  +
  gi|121638741|ref|YP_978965.1| 161 ALLRGALQRGMPVLGICRGTQVLNVALGGTLHqhlpdilgH---SGHRAGNGVFTRLPVhtasgtRLAELIGESADVPCY 237
                                    567889999********************988777665442...344444443333333556888888888899****** PP

                                    EEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTS CS
                         GATase 128 Hryevnpkelepaglevtakseddeelmeiiekkn.p.fvgvQFHPEstst 176
                                    H  ++++   + +gl+v+a++ d+  ++e+ e++    + +vQ+HPE+++ 
  gi|121638741|ref|YP_978965.1| 238 HHQAIDQ---VGEGLVVSAVDVDG--VIEALELPGdTfVLAVQWHPEKSLD 283
                                    *******...***********887..5666666665889********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2466.87
//
Query:       gi|121638742|ref|YP_978966.1|  [L=457]
Description: glutamine synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.2e-101  337.8   0.0   7.9e-101  337.5   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
     0.0015   18.3   0.2      0.016   14.9   0.2    2.3  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.5   0.0  8.8e-105  7.9e-101       2     342 ..     122     450 ..     121     452 .. 0.96

  Alignments for each domain:
  == domain 1  score: 337.5 bits;  conditional E-value: 8.8e-105
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                    ++PRs+l+r+l+rl+++Gl + v++ElEF++fd+  +++ + s ++  ++    +++ +  + + + +++e+l+r+i   
  gi|121638742|ref|YP_978966.1| 122 VSPRSILRRQLDRLKARGLVADVATELEFIVFDQPYRQA-WASGYRGLTP----ASDYNIDYAILASSRMEPLLRDIRLG 196
                                    58*******************************998866.7777776665....46778889999999************ PP

                                    HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT CS
                     Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg 161
                                    ++ +g+++ea++ E++ gQ+Ei++++++al ++Dn++++K+ +ke+A++hg++ tFm+K+ e ++G+++H+h+Sl  +dg
  gi|121638742|ref|YP_978966.1| 197 MAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTFMAKYDE-REGNSCHIHVSLRGTDG 275
                                    ***********************************************************987.99*************** PP

                                    EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEE CS
                     Gln-synt_C 162 knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvEl 241
                                    +++fad+++++++s+++r+f++G+l++++++t+++apt+nSYkR+ + + aP+alawg +NR+++lR++  ++++ rvE+
  gi|121638742|ref|YP_978966.1| 276 SAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVG-HGQNIRVEC 354
                                    *********************************************************************9.999****** PP

                                    ECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHH CS
                     Gln-synt_C 242 RlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasleeAlealeedellkevlgeeviea 321
                                    R+p++++N YLa+Aal+a+gl Gie++l+++ep+ +++y+ ++ e     +lP +l +A   +e+++l++e++ge+v+++
  gi|121638742|ref|YP_978966.1| 355 RVPGGDVNQYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVE-----RLPVTLADAAVLFEDSALVREAFGEDVVAH 429
                                    *****************************************9955.....7***************************** PP

                                    HHHHHHHCHHHHHCT--HHHH CS
                     Gln-synt_C 322 ylalkraEleeleeevsdwel 342
                                    yl+  r El++++++v+dwe+
  gi|121638742|ref|YP_978966.1| 430 YLNNARVELAAFNAAVTDWER 450
                                    *******************96 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.8e-06     0.016      51      82 ..      85     114 ..      22     115 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                                    -EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE- CS
                     Gln-synt_N  51 SDmlLkPdlstavidPfreekktarvicdvyd 82 
                                     Dm++ Pdlst+ ++P+ +   ta+vi+d ++
  gi|121638742|ref|YP_978966.1|  85 GDMVMTPDLSTLRLIPWLPG--TALVIADLVW 114
                                    6*****************84..6****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3293.31
//
Query:       gi|121638743|ref|YP_978967.1|  [L=285]
Description: methionine aminopeptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-50  171.9   0.3    1.6e-50  171.7   0.3    1.0  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.3   8.9e-55   1.6e-50       1     209 []      48     276 ..      48     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 8.9e-55
                                    HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTT.....TCEESSSSEEEEGGGGGSTTTBCSSSB--TTE CS
                  Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhg.....arglafppivasgenaavlhytpndrvlkegd 75 
                                    e++r a+ria+ al+++ +a+ pgvt++el+++++++ l ++g      ++ +fp++++++ n+ ++h++p+++v+ +gd
  gi|121638743|ref|YP_978967.1|  48 EKMRVAGRIAAGALAEAGKAVAPGVTTDELDRIAHEY-LVDNGaypstLGYKGFPKSCCTSLNEVICHGIPDSTVITDGD 126
                                    68*********************************99.8899999999999***************************** PP

                                    EEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                  Peptidase_M24  76 lvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                    +v+id++a + g ++D+  T+  G+  +e+r l++ ++ea+ +ai+ vkpG+ ls i+++++ ++ + g+  +++ ++GH
  gi|121638743|ref|YP_978967.1| 127 IVNIDVTAYIGGVHGDTNATFPAGDVADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGY-NVVRDFTGH 205
                                    ***********************99999******************************************.999****** PP

                                    EESSSSSEEEEEESS..STTCSSB--TTBEEEEEE.........EEEEETTT.......E.EEEEBEEEEEES CS
                  Peptidase_M24 156 gvGlevhdegpsvsr..esndgrkleeGmvftiEp.........giyfapge.......g.gvriedtvlvte 209
                                    g+G  +h +   v +  ++  ++ +++Gm+ftiEp         +i+  +g+       + ++++e+t+lvt+
  gi|121638743|ref|YP_978967.1| 206 GIGTTFHNG-LVVLHydQPAVETIMQPGMTFTIEPminlgaldyEIW-DDGWtvvtkdrKwTAQFEHTLLVTD 276
                                    *******88.77655444558999***********554444444333.3355666666655**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1986.70
//
Query:       gi|121638744|ref|YP_978968.1|  [L=194]
Description: hypothetical protein BCG_2884c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-15   56.0   0.1      6e-15   55.1   0.1    1.5  1  DUF1707   Domain of unknown function (DUF1707)
     0.0019   18.1   0.0     0.0035   17.2   0.0    1.7  1  DUF2154   Cell wall-active antibiotics response 4TMS YvqF


Domain annotation for each model (and alignments):
>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   6.7e-19     6e-15       1      53 []      11      63 ..      11      63 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 6.7e-19
                        DUF1707  1 lRasdadReravelLrealaeGrLtldEfdeRleaalaArtrgeLaalvaDLP 53
                                   lR+sdad + ++++L++a+a G +++dEf++R++++  Artr+eL+ lv DLP
  gi|121638744|ref|YP_978968.1| 11 LRVSDADPNGTMRRLHNAVALGLINIDEFEQRSSRVSFARTRSELDGLVGDLP 63
                                   7***************************************************9 PP

>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.8e-07    0.0035      18      73 ..      98     154 ..      69     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-07
                        DUF2154  18 nissiiGdttiDLtkavlpegetvivirkliGdvkilVPedvevsve.asvifGdvk 73 
                                     + + +G++++DL ka  ++   vi +  ++G++++ +P++ + s++ ++v +G+++
  gi|121638744|ref|YP_978968.1|  98 ALVRRLGSIELDLVKARFAGPVVVIELDMMFGSLEVRLPNGASASIDdVEVYVGSAS 154
                                    566779***************************************972588888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 1057.40
//
Query:       gi|121638745|ref|YP_978969.1|  [L=126]
Description: hypothetical protein BCG_2885 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-19   68.2   0.0    1.1e-18   67.9   0.0    1.0  1  PIN       PIN domain
     0.0042   17.8   0.0     0.0046   17.7   0.0    1.2  1  PIN_3     PIN domain
  ------ inclusion threshold ------
      0.031   14.8   0.0      0.037   14.5   0.0    1.1  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   1.8e-22   1.1e-18       1     116 [.       2     120 ..       2     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.8e-22
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBC CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpid 74 
                                    i++DT+v+ +++ r+++ ++ ar+ le+     ++lvtsa +++Ell+ +       +++ +l  +l l ++ ++i+p+ 
  gi|121638745|ref|YP_978969.1|   2 IFVDTNVFMYAVgRDHPLRMPAREFLEHSlehqDRLVTSAEAMQELLNAYVP----VGRNSTLDSALTLvRALTEIWPVE 77 
                                    79**************************************************....999999999999999********* PP

                                    HHHHHHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                            PIN  75 aeiaeeaaeialkyg.llpnDaliaAtAkehgikliatfDedf 116
                                    a+++++a+ ++ ++  l++ D+l++A+++++g + i tfD  +
  gi|121638745|ref|YP_978969.1|  78 AADVAHARTLHHRHPgLGARDLLHLACCQRRGVTRIKTFDHTL 120
                                    ****************************************876 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.7e-07    0.0046       2      71 ..       2      73 ..       1     119 [. 0.65

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.7e-07
                          PIN_3  2 vvlDtnvlldallfdsp...aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakv 71
                                   +++Dtnv++ a+ +d p    ar  l+   +++ +lv+s++++ El  +++ ++ ++    +a  +  +l+++
  gi|121638745|ref|YP_978969.1|  2 IFVDTNVFMYAVGRDHPlrmPAREFLEHSLEHQDRLVTSAEAMQELL-NAYVPVGRNSTLDSALTLVRALTEI 73
                                   689*************9777777777777999**************9.5545544454444444444444433 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.2e-06     0.037       1      50 [.       2      52 ..       2      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-06
                         PIN_12  1 ifiDTnifldeffrlsee..ealkklleliesgkiklivpdivldEflknre 50
                                   if+DTn+f+      ++      +++le+  +++++l++++  ++E+l+ + 
  gi|121638745|ref|YP_978969.1|  2 IFVDTNVFMY-AVGRDHPlrMPAREFLEHSLEHQDRLVTSAEAMQELLNAYV 52
                                   9********5.44444445756677778888889*************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 702.37
//
Query:       gi|121638746|ref|YP_978970.1|  [L=603]
Description: penicillin-binding lipoprotein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-35  123.3   0.0    1.9e-35  122.6   0.0    1.3  1  Transpeptidase  Penicillin binding protein transpeptidase dom
    5.2e-25   88.0   0.0    7.4e-25   87.5   0.0    1.2  1  MecA_N          NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   2.1e-39   1.9e-35       2     289 ..     326     581 ..     325     595 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 2.1e-39
                                    EEEEEETTT-BEEEEEEESE-TTTHHCCTCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS. CS
                 Transpeptidase   2 aavvldaktgevlamaskpsydpnakvgkneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqs 81 
                                    ++vv+ ++tge+la+a++   d ++ v          +++ y+PGStfK++ta aa+e+ + +p++ l ++g    g ++
  gi|121638746|ref|YP_978970.1| 326 MIVVIKPSTGEILAIAQNAGADADGPVA---------TTGLYPPGSTFKMITAGAAVERDLATPETLLGCPGEIDIGHRT 396
                                    79*****************999999988.........***********************************98888888 PP

                                    ECTCCCC-SSSSEEEHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--.B--SSH.HHHHHHHHT CS
                 Transpeptidase  82 ikdweqdnkgsegitlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaG.vptrkw.legatisfg 159
                                    i ++   +   + + +++a+++S+nt f++l+ +l++  l ++++++g+G + ++d   +++G vp++    e+    fg
  gi|121638746|ref|YP_978970.1| 397 IPNYGGFD--LGVVPMSRAFASSCNTTFAELSSRLPPRGLTQAARRYGIGLDYQVDGITTVTGsVPPTVDlAERTEDGFG 474
                                    *******8..6677*************************************************77777444555544589 PP

                                    TT.SBB-HHHHHHHHHHHHTTTEEE--BSEEEEEECTTEEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTTGCG.TC CS
                 Transpeptidase 160 iG.ltvtplqlaqayaaiangGklvkPhlvkaivdpdgvrkvkpkelnklpisketaekvkeglkgvvsrgsgtata.av 237
                                    +G + ++p+ +a ++a++a  Gk+  P+l+          + +  e   +pis++ ++ ++ +++ vv++g    ta ++
  gi|121638746|ref|YP_978970.1| 475 QGkVLASPFGMALVAATVAA-GKTPVPQLIA--------GRPTAVEGDATPISQKMIDALRPMMRLVVTNG----TAkEI 541
                                    99******************.*********4........3456677889**********************....44467 PP

                                    TTS.--EEEEEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEEEECTCS CS
                 Transpeptidase 238 egy.kvagKTGTAevagkkgngkkegakiswfvgyapadnpkyavavlieqpk 289
                                    +g  +v gKTG Ae+ g +         +swf+gy  +    +a+a li  ++
  gi|121638746|ref|YP_978970.1| 542 AGCgEVFGKTGEAEFPGGS---------HSWFAGYRGD----LAFASLIVGGG 581
                                    7888***********9822.........36*****987....99999988888 PP

>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   8.3e-29   7.4e-25       2     117 .]      32     139 ..      31     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 8.3e-29
                                    HHHHHHHHHHHHHTT-HHHHHCTB--BSSBSS-HHHHHHHHHHHCCCTT-EEEEEEEEEEEEEETTEEEEEEEEEEEETT CS
                         MecA_N   2 aeeaaetFldawakgdykkaasllseqskkeisekeavekyqaiydglqvkklkieakkvkkdkentaeipykvsmntpa 81 
                                    + +aae+F++a+a gd+++aa+l+++++       ea e+++a+++glq+  l++ +  ++k+ e+t +++y++s+++p+
  gi|121638746|ref|YP_978970.1|  32 PGPAAEKFFAALAIGDTASAAQLSDNPN-------EAREALNAAWAGLQAAHLDA-QVLSAKYAEDTGTVAYRFSWHLPK 103
                                    6789************************.......********************.888999****************** PP

                                    EEEEEEEEEEEEEEETTEEEE---GGGTSTT--TT- CS
                         MecA_N  82 gkiktldskltltkeeeewkidWepslifPqleend 117
                                    ++i+t+d +l+++++e++w ++W++s ++P+l+e++
  gi|121638746|ref|YP_978970.1| 104 DRIWTYDGQLKMARDEGRWHVRWTTSGLHPKLGEHQ 139
                                    *********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3962.04
//
Query:       gi|121638747|ref|YP_978971.1|  [L=93]
Description: hypothetical protein BCG_2887 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-21   74.0   0.0    7.2e-21   73.8   0.0    1.1  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
  ------ inclusion threshold ------
       0.09   11.4   0.0       0.09   11.4   0.0    1.0  1  T7SS_ESX1_EccB   Type VII secretion system ESX-1, transport T


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0     8e-25   7.2e-21       1      73 [.       1      72 [.       1      74 [. 0.97

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 8e-25
                                   CEEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHHHHHHH CS
                PhdYeFM_antitox  1 mkivsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslplnaerlaesgaeve 73
                                   m+i +is  k +l+e++d+v +++++++It++G+p+aVlv ++e+e+lqe t+++l +p+ +e++ae++a++ 
  gi|121638747|ref|YP_978971.1|  1 MRILPISTIKGKLNEFVDAVSSTQDQITITKNGAPAAVLVGADEWESLQE-TLYWLAQPGIRESIAEADADIA 72
                                   9*************************************************.****************999876 PP

>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     1e-05      0.09     380     433 ..      18      69 ..       2      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1e-05
                                    TSSEE......EEESSBE..EEEEEECSTT..CEEEEEEEETTSEEEEE-SHHH CS
                 T7SS_ESX1_EccB 380 sadgsgatvdavylppgtgalvqatgaepaseargslfyvsdtGvRYgipdeet 433
                                    +a   ++t d+++++++ +     +ga++ ++ +++l++++  G+R +i+++++
  gi|121638747|ref|YP_978971.1|  18 DA--VSSTQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAEADA 69 
                                    33..456889*******999999************************9999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 653.40
//
Query:       gi|121638748|ref|YP_978972.1|  [L=87]
Description: hypothetical protein BCG_2888 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-13   50.3   0.7    3.4e-13   50.0   0.7    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    0.00094   19.2   0.0     0.0012   18.8   0.0    1.2  1  YoeB_toxin       YoeB-like toxin of bacterial type II toxin-a
      0.005   16.8   0.0      0.007   16.3   0.0    1.2  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.029   14.4   0.0    1.1  1  Toxin_YhaV       Toxin with endonuclease activity, of toxin-a


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.7   7.6e-17   3.4e-13       1      90 []       5      85 ..       5      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 7.6e-17
                                   EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEE CS
                     ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilr 82
                                   vr+t +A++dl k+           + + + +e a+ +l + p++  ++ + +l g++++r+g yr++Yridde+++vvilr
  gi|121638748|ref|YP_978972.1|  5 VRFTTTARRDLHKLP---------PRILAAVVEFAFGDLSREPLRVGKPLRRELAGTFSARRGTYRLLYRIDDEHTTVVILR 77
                                   89************9.........56799999********77777766444445599************************* PP

                                   EEEHHHHC CS
                     ParE_toxin 83 vlhrsedy 90
                                   v hr+++y
  gi|121638748|ref|YP_978972.1| 78 VDHRADIY 85
                                   ****9876 PP

>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-07    0.0012      29      77 ..      33      77 ..      19      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
                                   HHHHSTTSSTT--EE-SGGGTTEEEEESSSSEEEEEEEESSEEEEEESS CS
                     YoeB_toxin 29 eikRdpfeGiGkPepLkedlsglwsRRideehRlvYlveddeltilsar 77
                                   +++R+p++ +GkP  L+ +l+g++s R   + Rl+Y+++d++ t++  r
  gi|121638748|ref|YP_978972.1| 33 DLSREPLR-VGKP--LRRELAGTFSAR-RGTYRLLYRIDDEHTTVVILR 77
                                   67788886.7886..9*********99.5689**********9999877 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-06     0.007       4      84 ..       8      86 ..       5      87 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                ParE-like_toxin  4 trrfkkalkklkek.lkadldkavkeiiedPe.lGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGtheNfY 83
                                   t+++++ l kl  + l+a ++ a  ++ ++P  +G++    L+g     f+ +  +++l Y++d++++++v+l v  +   Y
  gi|121638748|ref|YP_978972.1|  8 TTTARRDLHKLPPRiLAAVVEFAFGDLSREPLrVGKPLRRELAGT----FSARRGTYRLLYRIDDEHTTVVILRVDHRADIY 85
                                   778999999999998888899999999999953799999999885....67899************************9999 PP

                ParE-like_toxin 84 r 84
                                   r
  gi|121638748|ref|YP_978972.1| 86 R 86
                                   8 PP

>> Toxin_YhaV  Toxin with endonuclease activity, of toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.4e-06     0.029      36      99 ..      21      79 ..       8      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.4e-06
                     Toxin_YhaV 36 kllaaiaklilekipadPtaseyrlgktLgekykhwkrakllqryRLFFRydseskiivlaWvn 99
                                   ++laa+ + ++ +++++P     r gk+L+ +    + a+ +  yRL +R+d e+ ++v++ v+
  gi|121638748|ref|YP_978972.1| 21 RILAAVVEFAFGDLSREPL----RVGKPLRRELAGTFSARRG-TYRLLYRIDDEHTTVVILRVD 79
                                   5667777777777766665....7899999999999999877.8***************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 619.39
//
Query:       gi|121638749|ref|YP_978973.1|  [L=284]
Description: hypothetical protein BCG_2889c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-39  135.0   0.1    2.1e-39  133.9   0.1    1.6  1  DUF4081          Domain of unknown function (DUF4081)
    6.2e-09   35.7   0.3    1.7e-08   34.3   0.0    1.8  2  FR47             FR47-like protein
    3.3e-06   27.3   0.2      5e-06   26.7   0.2    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00013   22.3   0.1    0.00028   21.2   0.1    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00019   21.4   0.0    0.00032   20.6   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> DUF4081  Domain of unknown function (DUF4081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.1   5.9e-43   2.1e-39       1     105 []      54     156 ..      54     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 5.9e-43
                        DUF4081   1 gelwgveddgelealcfaGanlvPvaadaealrafAdralrrgrrcsSivGpaeavlaLwerLeeawgparevRaeQpll 80 
                                    gelw++  +g+ e+lcfaGanl+P+++ + +l+afAd a++++rrcsS+vG+a+ vl++w+rLe+ wgpar+vR++Qpl+
  gi|121638749|ref|YP_978973.1|  54 GELWTR--RGAHESLCFAGANLIPLRGGPIDLNAFADVAMSTPRRCSSLVGRADLVLPMWQRLEPVWGPARDVRDNQPLM 131
                                    799999..************************************************************************ PP

                        DUF4081  81 aidgapavapdprVrrvreeeldrl 105
                                    a++++p++a+d+ Vr+vr+eeld++
  gi|121638749|ref|YP_978973.1| 132 ALATHPSCAIDTGVRQVRPEELDSY 156
                                    ***********************87 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   4.1e+03       9      44 ..     150     187 ..     143     192 .. 0.58
   2 !   34.3   0.0   4.6e-12   1.7e-08      19      80 ..     214     275 ..     207     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                    T--EEEEEEE-TTSSEEEEEE-GGG..-SSSHHHHHHH CS
                           FR47   9 lgelaawilrkdggelgalqvlpeh..rrrGlgsrlvk 44 
                                    ++el   +++  + ++g + v+p     +rG+ +r++ 
  gi|121638749|ref|YP_978973.1| 150 PEELDSYLVAAVDMFIGEVGVDPRLgdGGRGYRRRVAG 187
                                    55555555555566677777777652236777777765 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 4.6e-12
                                    -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                    + +g++ ++ v+pe r+ Glg+  ++ la+ i+  g +++l+v+  Nt +++ y ++Gf++i
  gi|121638749|ref|YP_978973.1| 214 PAVGQIQGVWVHPEWRGIGLGTAGTATLAAVIVGSGRIASLYVNSFNTVARAAYARVGFKEI 275
                                    4569*******************************************************998 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   1.4e-09     5e-06      55     117 .]     199     272 ..     151     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                                    T............TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  55 d............ekggvayieslaVspeyrgkGlGsaLlealeerareegikki.vlaveedndaairlYeklGF 117
                                    +            +++ v+ i +++V+pe+rg GlG+a   +l+      g  +i  l+v + n+ a++ Y ++GF
  gi|121638749|ref|YP_978973.1| 199 EhgqvifkaevgsQSPAVGQIQGVWVHPEWRGIGLGTAGTATLAAVIVGSG--RIaSLYVNSFNTVARAAYARVGF 272
                                    355566666667778899*************************99877774..4669999999********99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   7.8e-08   0.00028      24      76 .]     209     274 ..     154     274 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.8e-08
                                    S.......TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEE.EEEETHH..HHHHHHHHTTEEE CS
                 Acetyltransf_7  24 d.......aeitrlaVdpeyrgkGiGraLlea...ae..kgiile.qlelnae..kaikfYeklGFee 76 
                                            ++i +++V+pe+rg G+G+a  +    ++  +g + +  l++n+    a++ Y++ GF+e
  gi|121638749|ref|YP_978973.1| 209 VgsqspavGQIQGVWVHPEWRGIGLGTAGTATlaaVIvgSG-R-IaSLYVNSFntVARAAYARVGFKE 274
                                    1223335567888************9987763222335666.2.223455221248899*******96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     9e-08   0.00032      36     110 ..     197     276 ..     183     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9e-08
                Acetyltransf_10  36 aeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkav 109
                                     +e g+++  +e+ +++    +i+ + V+pe+rg G+g+a   ++ + +    +++ +l vn+ +  a++ Y ++GFk++
  gi|121638749|ref|YP_978973.1| 197 RFEHGQVIFKAEVgSQSPavgQIQGVWVHPEWRGIGLGTAGTATLAAVIVGS-GRIaSLYVNSFNtVARAAYARVGFKEI 275
                                    555555555556633333666999******************9999997444.4446********99***********99 PP

                Acetyltransf_10 110 g 110
                                    g
  gi|121638749|ref|YP_978973.1| 276 G 276
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2097.84
//
Query:       gi|121638750|ref|YP_978974.1|  [L=387]
Description: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-131  439.2   0.1   1.1e-131  439.1   0.1    1.0  1  GcpE      GcpE protein
  ------ inclusion threshold ------
      0.068   12.7   0.4       0.47   10.0   0.3    2.0  2  MR_MLE_C  Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.1   0.1  1.3e-135  1.1e-131       1     348 [.      21     361 ..      21     364 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.1 bits;  conditional E-value: 1.3e-135
                                    .--EEETTEEESTTS--EEEEE--S-TT-HHHHHHHHHHHHHCT-SEEEEEE-SHHHHHHHHHHHHHHHHTT-SS-EEEE CS
                           GcpE   1 trevkvgkvkiGgeapiavqsMtntdtadveatvkqikrlaeaGaelvRvtvqdeeeaealkeikeklkkkglkvplvaD 80 
                                    tr+ +vg+v +G+++p++vqsM++t+t+dv++t++qi++l++aG+++vRv+++++e+a+al+ei +++     ++p+vaD
  gi|121638750|ref|YP_978974.1|  21 TRQLMVGNVGVGSDHPVSVQSMCTTKTHDVNSTLQQIAELTAAGCDIVRVACPRQEDADALAEIARHS-----QIPVVAD 95 
                                    7999****************************************************************.....******* PP

                                    E-SSCHHHHHHHHCC-SEEEE-TTTSSSTTHHHHHHHHHHHHHHHHT-EEEEEEEGGG--HHHHHHHCC.THHHHHHHHH CS
                           GcpE  81 ihfnpklaleaaeagvdkvRiNPGnigdgkkkeekvkelveaakekgtaiRiGvNhGSLskrllskygd.tpealvesal 159
                                    ihf+p++  +a++ag+++vR+NPGni++    + +v e+ +aa + g++iRiGvN+GSL+kr+++kyg+ tpealvesal
  gi|121638750|ref|YP_978974.1|  96 IHFQPRYIFAAIDAGCAAVRVNPGNIKE---FDGRVGEVAKAAGAAGIPIRIGVNAGSLDKRFMEKYGKaTPEALVESAL 172
                                    ***************************9...799***********************************99********* PP

                                    HHHHHHHHTT--GEEEEEE-SSHHHHHHHHHHHHHH--S-EEE--TT-ECHHHHHHHHHHHHHHHHHTT--SEE---ECS CS
                           GcpE 160 efleilekldfkdiviSlKasnvvvmveayrllaeeldyplHlGvTEAGegedgriksavgigaLLaegiGdTiRvSLte 239
                                     +++++e+++f di+iS+K+ ++vvmv+ay+lla+++dyplHlGvTEAG   +g+iksav++gaLL++giGdTiRvSL++
  gi|121638750|ref|YP_978974.1| 173 WEASLFEEHGFGDIKISVKHNDPVVMVAAYELLAARCDYPLHLGVTEAGPAFQGTIKSAVAFGALLSRGIGDTIRVSLSA 252
                                    ******************************************************************************** PP

                                    -CCHHHHHHHHHHHHTTS--SS-EEEE----TTS-CHHHHHHHHHHHHCCCHHCG-EEEEESSTCCHHHHCCCSSEEEEE CS
                           GcpE 240 dpeeEvkvakeiLqalrlrksktelisCPsCgRtlfdlqelveeveealehlkkglkiavmGCiVNGpgEaadAdlGivg 319
                                     p+eEvkv++++L++l+lr ++ e++sCPsCgR ++d+ +l++ev++ l+ l+ +l++avmGC+VNGpgEa++AdlG+++
  gi|121638750|ref|YP_978974.1| 253 PPVEEVKVGNQVLESLNLRPRSLEIVSCPSCGRAQVDVYTLANEVTAGLDGLDVPLRVAVMGCVVNGPGEAREADLGVAS 332
                                    ******************************************************************************** PP

                                    BTTCEEEEETTEEEECEESSCHHHHHHHH CS
                           GcpE 320 gkgkvslykkkevvkkvpeeeavdellel 348
                                    g+gk ++++++ev+k+vpe+++v++l+e+
  gi|121638750|ref|YP_978974.1| 333 GNGKGQIFVRGEVIKTVPEAQIVETLIEE 361
                                    **************************986 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   5.2e-05      0.47      80     154 ..      71     144 ..      45     154 .. 0.77
   2 ?   -0.1   0.0     0.062   5.6e+02       9      41 ..     177     209 ..     166     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.2e-05
                                    SSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHH.HHHHHHHHHHTT-EEEE CS
                       MR_MLE_C  80 Pvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGite.arkvaalaeafgvpvap 154
                                     +p+++d ++lae++ r+ +ip++a+ + + r+ f+++  + ++ +v+++++++  +++ + +va+ a a+g+p+ +
  gi|121638750|ref|YP_978974.1|  71 ACPRQEDADALAEIA-RHsQIPVVADIHFQPRYIFAAI--DAGCAAVRVNPGNIKEFDGrVGEVAKAAGAAGIPIRI 144
                                    5888899********.6669***************998..5557888888888888875255778888888877655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.062
                                    HHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHH CS
                       MR_MLE_C   9 lvaeqgfravKlkvggddvaedvervravreav 41 
                                    l +e+gf  +K+ v ++d+   v+  +++ +++
  gi|121638750|ref|YP_978974.1| 177 LFEEHGFGDIKISVKHNDPVVMVAAYELLAARC 209
                                    46899*********9999988888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3291.40
//
Query:       gi|121638751|ref|YP_978975.1|  [L=404]
Description: hypothetical protein BCG_2891c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-52  177.2   0.0    4.7e-52  176.8   0.0    1.1  1  Peptidase_M50   Peptidase family M50
    7.9e-10   38.4   0.1    1.6e-09   37.5   0.1    1.5  1  PDZ_6           PDZ domain
    6.9e-05   23.1   0.0    0.00013   22.2   0.0    1.4  1  PDZ_2           PDZ domain
    0.00015   22.1   0.0    0.00027   21.2   0.0    1.5  1  PDZ             PDZ domain
  ------ inclusion threshold ------
      0.041   13.8   0.0      0.071   13.0   0.0    1.3  1  Dehydratase_MU  Dehydratase medium subunit
      0.063   12.8   0.0      0.082   12.4   0.0    1.2  1  Acyl_transf_1   Acyl transferase domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.0   1.6e-55   4.7e-52       2     245 ..      10     371 ..       9     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 1.6e-55
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                  Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka.fl 80 
                                    f+l+++i+v++HE+GH++vA+++g+kv+++ +gfGp+l+s+++geteY ++++pLGG++++ag+ p eel ++e+++ + 
  gi|121638751|ref|YP_978975.1|  10 FALAILISVALHECGHMWVARRTGMKVRRYFVGFGPTLWSTRRGETEYGVKAVPLGGFCDIAGMTPVEELDPDERDRaMY 89 
                                    899******************************************************************988877766** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX.................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                  Peptidase_M50  81 kkspwqrllivlAGplanfilailvfvv.................................................... 108
                                    k+  w+r+++++AGp +n+ + ++++ +                                                    
  gi|121638751|ref|YP_978975.1|  90 KQATWKRVAVLFAGPGMNLAICLVLIYAialvwglpnlhpptravigetgcvaqevsqgkleqctgpgpaalagirsgdv 169
                                    *********************99999999*********************************************999999 PP

                                    ....................................................-EEECE...CTTTSCEE-SEEEC-..XX CS
                                    ....................................................xxxxxx...xxxxxxxxxxxxxxx..xx RF
                  Peptidase_M50 109 ....................................................pkkske...seeekrgviGvspkp..vk 131
                                                                                             +    +  + g iGv ++   ++
  gi|121638751|ref|YP_978975.1| 170 vvkvgdtpvssfdemaaavrkshgsvpivverdgtaivtyvdiestqrwipnG----QggeLQPATVGAIGVGAARvgPV 245
                                    99999999999999999999999999999999999999999877777766430....13456677788888877767766 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXX..........XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                  Peptidase_M50 132 kegllealkegvektlkvvvltvk..........algklitg.klslktlggpisiaqlaseaaeagls.sflqllalis 199
                                    ++g+++a+   +  t +++v + k          al++ i g + +++t   +++   + ++++++gl+ +f+++la ++
  gi|121638751|ref|YP_978975.1| 246 RYGVFSAMPATFAFTGDLTVEVGKalaalptkvgALVRAIGGgQRDPQTPISVVGASIIGGDTVDHGLWvAFWFFLAQLN 325
                                    777777777777777776666666555566666688888888899999999999999999*******998********** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 200 vnLgilNLlPipvLDGghllfalleairrkplserkeevanlvgla 245
                                    ++L+ +NLlP+ ++DGgh++ a++e+ir+   s+r + +a  v ++
  gi|121638751|ref|YP_978975.1| 326 LILATINLLPLLPFDGGHIAVAVFERIRNMVRSARGKVAAAPVNYL 371
                                    ****************************999999998888777665 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   5.2e-13   1.6e-09       8      56 .]     148     201 ..     141     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 5.2e-13
                          PDZ_6   8 g........sPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvvrr 56 
                                    g        +PA+ AG+r GD++++v+++pv   s ++ aa++r + + sv +vv+r
  gi|121638751|ref|YP_978975.1| 148 GkleqctgpGPAALAGIRSGDVVVKVGDTPV--SSFDEMAAAVR-KSHGSVPIVVER 201
                                    5555555569*********************..***********.888888888876 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.5e-08   0.00013      25      59 ..     157     191 ..     139     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.5e-08
                                    SGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS CS
                          PDZ_2  25 gPaakaglkagDvilkvdgkkvksledlislllkk 59 
                                    gPaa ag+++gDv++kv++++v+s +++  +++k 
  gi|121638751|ref|YP_978975.1| 157 GPAALAGIRSGDVVVKVGDTPVSSFDEMAAAVRKS 191
                                    8*********************9999998888743 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   9.1e-08   0.00027      35      81 ..     156     199 ..     139     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.1e-08
                                    TTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEEE CS
                            PDZ  35 pggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLti 81 
                                    pg+aa a+ ++ GD++++v++++v+++  +e ++a+++s+g+v++++
  gi|121638751|ref|YP_978975.1| 156 PGPAALAG-IRSGDVVVKVGDTPVSSF--DEMAAAVRKSHGSVPIVV 199
                                    55666666.******************..777778888888888877 PP

>> Dehydratase_MU  Dehydratase medium subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.071      21     102 ..     161     242 ..     158     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                 Dehydratase_MU  21 laGiEEegvpyevvveetsdvaelAhqAaklSrlgvGigiqskgtvvihqkklpeesplellsq.pladketlRalGanA 99 
                                    laGi   +v ++v ++  s+ +e+A  A ++S+ +v i ++++gt+++++ +++  +  +   q  + +++t+ a+G  A
  gi|121638751|ref|YP_978975.1| 161 LAGIRSGDVVVKVGDTPVSSFDEMAA-AVRKSHGSVPIVVERDGTAIVTYVDIESTQRWIPNGQgGELQPATVGAIGVGA 239
                                    78999999999999999999999995.7889*************************9999999999************** PP

                 Dehydratase_MU 100 Arl 102
                                    Ar+
  gi|121638751|ref|YP_978975.1| 240 ARV 242
                                    *95 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05     0.082      67     146 ..     141     221 ..      82     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHHHHTT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS..HHHHHHH..T CS
                  Acyl_transf_1  67 aavqialaellkskGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel.aeeeeklrcqd 145
                                    +a ++++  l ++ G+ paa++G   G +   v ++ +ss++ + a+v+ s    ++ +++d  a+   + +e  +r+++
  gi|121638751|ref|YP_978975.1| 141 VAQEVSQGKLEQCTGPGPAALAGIRSGDVVVKVGDTPVSSFDEMAAAVRKSHGSVPIVVERDGTAIVTyVDIESTQRWIP 220
                                    56678888888**************************************************988776669********99 PP

                                    T CS
                  Acyl_transf_1 146 d 146
                                    +
  gi|121638751|ref|YP_978975.1| 221 N 221
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3129.03
//
Query:       gi|121638752|ref|YP_978976.1|  [L=413]
Description: 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-37  129.4   1.6    2.8e-37  128.3   1.6    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
    5.8e-35  119.3   0.0    1.4e-34  118.1   0.0    1.7  1  DXP_redisom_C    1-deoxy-D-xylulose 5-phosphate reductoisomer
    6.3e-35  119.9   0.0    1.2e-34  119.0   0.0    1.5  1  DXPR_C           DXP reductoisomerase C-terminal domain
  ------ inclusion threshold ------
      0.013   15.8   0.4      0.048   13.9   0.4    2.0  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.032   14.7   0.2       0.15   12.5   0.2    2.1  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.072   13.1   0.1       0.13   12.3   0.1    1.3  1  CoA_binding_3    CoA-binding domain


Domain annotation for each model (and alignments):
>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   1.6   9.2e-41   2.8e-37       1     129 []      15     135 ..      15     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 9.2e-41
                                    EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESH CS
                DXP_reductoisom   1 vviLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvellaeqakefkpklvavadeeaaeelkealkekelktevlvGe 79 
                                    vv+LGsTGSIGtq+L+vi++npd+fevv+laa g ++++l++q +++ ++ +avade+aa+++ +           ++G+
  gi|121638752|ref|YP_978976.1|  15 VVVLGSTGSIGTQALQVIADNPDRFEVVGLAAgGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIP---------YHGS 85 
                                    79******************************999****************************9999.........78** PP

                                    HHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHHHH CS
                DXP_reductoisom  80 ealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLVvaG 129
                                    +a+++l+e++eadvv++a+vGa GL+ptlaa+k+g+r+aLANKEsLV++G
  gi|121638752|ref|YP_978976.1|  86 DAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGG 135
                                    ************************************************98 PP

>> DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   4.7e-38   1.4e-34       1      84 []     147     230 ..     147     230 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 4.7e-38
                                    EEE-SHHHHHHHHHSGCCCCTTEEEEEEEE--GTTTTS-HHHHCT-SHHHHHS-SS----HHHHHHHHHSHHHHHHHHHH CS
                  DXP_redisom_C   1 ilpvDsEhsaifqllkeekkkevekiiltasGGpfrklkleeleevtveealkhPnWsmGkkitvdsatlmNkglEviea 80 
                                    i+pvDsEhsa++q+l+  + +ev+k++ltasGGpfr +++++le+vt+e+a +hP+WsmG+  t++sa+l+NkglEvie+
  gi|121638752|ref|YP_978976.1| 147 IVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGAHPTWSMGPMNTLNSASLVNKGLEVIET 226
                                    79****************************************************************************** PP

                                    HHHC CS
                  DXP_redisom_C  81 kllf 84 
                                    +llf
  gi|121638752|ref|YP_978976.1| 227 HLLF 230
                                    ***9 PP

>> DXPR_C  DXP reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0     4e-38   1.2e-34       2     114 ..     263     380 ..     262     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 4e-38
                                    -SS-THHHHHHHHHTTS-...------HHHHEEEEEB---TTTTCHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHTTSS CS
                         DXPR_C   2 gtpDMrlpIayaLayper...gverldlaklgsltFekpdlerFpclklayealkaggtapavlnAAnEvaveaFlegki 78 
                                    ++pDM+lpI+ aL +p+r    ++++d+ +++s++Fe++d++ Fp+++la++a+ agg ++av+nAAnE+a +aFl+g+i
  gi|121638752|ref|YP_978976.1| 263 SPPDMKLPISLALGWPRRvsgAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRI 342
                                    78****************7644999******************************************************* PP

                                    -TTHHHHHHHHHHH..TTT....SSHHHHHHHHHHHHH CS
                         DXPR_C  79 sFldIaeiieevle..seekseaksledileldaeare 114
                                    +F  I+ ii++vl+  +++  e+ +++d+l+++++are
  gi|121638752|ref|YP_978976.1| 343 GFPAIVGIIADVLHaaDQWAVEPATVDDVLDAQRWARE 380
                                    **************98778999***************8 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.6e-05     0.048       1      95 [.      15     122 ..      15     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                    EEEE--.SHHHHHHHHHHHCTCCT-G..EEEEEESSHHHHHHHHCHH...........TTTCEEEEE--TTTHHHHHHHH CS
                Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvda..eitvadrskeklealaaka...........lgvrfeaialdaenyeavLaal 66 
                                    v+++G+ Gs+G  +++++a++ d ++   ++  + +++ l +  a++           + +r+  i    ++ +  L++ 
  gi|121638752|ref|YP_978976.1|  15 VVVLGStGSIGTQALQVIADNPDRFEvvGLAAGGAHLDTLLRQRAQTgvtniavadehAAQRVGDIPYHGSDAATRLVEQ 94 
                                    89********************9886555556666666666666555999999999999999999999999999877774 PP

                                    HTTSSEEEE-SSGGGHHHHHHHHHHHT-E CS
                Sacchrp_dh_NADP  67 lkegdlvvnlsppissldvlkaCietgvh 95 
                                     +e+d+v+n+++  ++l    a+++tg++
  gi|121638752|ref|YP_978976.1|  95 -TEADVVLNALVGALGLRPTLAALKTGAR 122
                                    .667********99999999999999986 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.9e-05      0.15       1      36 [.      14      50 ..      14     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                                   EEEEETTTSHHHHHHHHHHHCTSS.EEEEEEEESTTT CS
                 Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpe.velvvllsssrs 36
                                   +v ++G tG +G++ l++++++p+ +e+v l++   +
  gi|121638752|ref|YP_978976.1| 14 RVVVLGSTGSIGTQALQVIADNPDrFEVVGLAAGGAH 50
                                   699******************8865888888775554 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.2e-05      0.13      70     149 ..      29     104 ..      14     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                  CoA_binding_3  70 lrrlrrngrnerrvvavgggeelakqiranpelgfrvvgvfddrddarseevagvpvlgnladlveyvretrvdevylaL 149
                                    l+ ++ n  +  +v++++gg++l   +r+++++g   ++v d+++++r+     +p+ g+ +++ ++v++t+ d v+ aL
  gi|121638752|ref|YP_978976.1|  29 LQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVG---DIPYHGS-DAATRLVEQTEADVVLNAL 104
                                    555566666677899*******************************9999...6999997.7888999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3122.59
//
Query:       gi|121638753|ref|YP_978977.1|  [L=85]
Description: hypothetical protein BCG_2893 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-07   31.2   1.2    2.1e-07   30.6   0.7    1.5  2  RHH_1           Ribbon-helix-helix protein, copG family
     0.0011   19.1   0.1     0.0016   18.5   0.1    1.3  1  ParD_like       ParD-like antitoxin of type II bacterial toxi
     0.0078   16.1   0.4     0.0078   16.1   0.4    1.8  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
      0.023   14.9   1.1        1.6    9.0   1.1    2.0  1  TetR_C_6        BetI-type transcriptional repressor, C-termin
      0.025   15.0   0.0      0.036   14.4   0.0    1.3  1  ParD            Antitoxin ParD
      0.039   13.8   0.0      0.054   13.4   0.0    1.3  1  RHH_4           Ribbon-helix-helix domain
       0.11   11.8   0.0       0.14   11.5   0.0    1.2  1  SeqA_N          SeqA protein N-terminal domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.7   8.3e-11   2.1e-07       1      37 [.       2      38 ..       2      39 .. 0.96
   2 ?   -2.4   0.0       2.2   5.5e+03      17      26 ..      71      80 ..      69      81 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 8.3e-11
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   r++ir+d+el++++ ++a+r+gr++ +++++A+r+ l
  gi|121638753|ref|YP_978977.1|  2 RTTIRIDDELYREVKAKAARSGRTVAAVLEDAVRRGL 38
                                   89********************************866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                   HHHHHTSSHH CS
                          RHH_1 17 larrrgrSrS 26
                                   la++++  +S
  gi|121638753|ref|YP_978977.1| 71 LAEAMNDGVS 80
                                   7777776655 PP

>> ParD_like  ParD-like antitoxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   6.1e-07    0.0016       3      27 ..       4      28 ..       2      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.1e-07
                      ParD_like  3 ivkiddeLhdsarresaaqsRSina 27
                                    ++iddeL+ ++++++a++ R+++a
  gi|121638753|ref|YP_978977.1|  4 TIRIDDELYREVKAKAARSGRTVAA 28
                                   69*********************98 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   3.1e-06    0.0078       1      15 [.       1      15 [.       1      38 [. 0.85
   2 ?   -3.2   0.1       3.2   8.3e+03      11      16 ..      70      75 ..      69      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                                   XXXXXXXXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLlaeA 15
                                   Mrt+I iDDeL +e+
  gi|121638753|ref|YP_978977.1|  1 MRTTIRIDDELYREV 15
                                   9**********9997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                                   XXXXXX CS
                 VapB_antitoxin 11 LlaeAi 16
                                    laeA+
  gi|121638753|ref|YP_978977.1| 70 ALAEAM 75
                                   578887 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.1   0.00062       1.6      60      91 ..      50      84 ..       5      85 .] 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00062
                                   HHHH...TTSCTTSTHHHHHHHHHHHHHHHHHHHH CS
                       TetR_C_6 60 elae...gglradadaeaaAerlaAlidGLwlraa 91
                                   ++++   gglr+++d+   A+   A+ dG ++ a+
  gi|121638753|ref|YP_978977.1| 50 RVQPsgkGGLRPGVDLSSNAALAEAMNDGVSVDAV 84
                                   45555568999999999999999999999998775 PP

>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.036       1      36 [.       1      34 [.       1      50 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                           ParD  1 MsrLsIditpeqhqrlkAvAAlqGksikeYvLerll 36
                                   M r +I i +e + ++kA AA +G+++   vLe   
  gi|121638753|ref|YP_978977.1|  1 M-RTTIRIDDELYREVKAKAARSGRTVAA-VLEDAV 34
                                   6.99**********************975.666554 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.054      12      47 ..       2      36 ..       1      51 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaeidadr 47
                                   rT+ir+ ++ +++ ++ A+r g tv+a++++   +r
  gi|121638753|ref|YP_978977.1|  2 RTTIRIDDELYREVKAKAARSGRTVAAVLEDA-VRR 36
                                   9**************************99987.555 PP

>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.3e-05      0.14       3      22 ..       4      23 ..       1      38 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                         SeqA_N  3 tIevDeeLYrYIasntqaiG 22
                                   tI +D+eLYr + ++  + G
  gi|121638753|ref|YP_978977.1|  4 TIRIDDELYREVKAKAARSG 23
                                   799******97777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 634.06
//
Query:       gi|121638754|ref|YP_978978.1|  [L=147]
Description: hypothetical protein BCG_2894 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-13   49.2   0.0    7.9e-13   49.0   0.0    1.0  1  PIN       PIN domain
     0.0077   16.0   0.1      0.016   15.0   0.1    1.5  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   8.8e-17   7.9e-13       2     120 ..       3     133 ..       2     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 8.8e-17
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkil 71 
                                    ++D +vl++++  +  +++ +r lle+l    e l +++ vla +++v+++      +++ + a + v++ll ++a   l
  gi|121638754|ref|YP_978978.1|   3 CVDVNVLVYAHrADLREHADYRGLLERLanddEPLGLPDSVLAGFIRVVTNrrvftEPTSPQDAWQAVDTLLAAPAAMRL 82 
                                    8***********7777788888888888888************************************************* PP

                                    EBCHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  72 pidaeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                      +++++   +++a+  +    +++Da++aA A+e++++ + ++D+ f+r  
  gi|121638754|ref|YP_978978.1|  83 RPGERHWMAFRQLASDVDangNDIADAHLAAYALENNATWL-SADRGFARFR 133
                                    *****************************************.******9976 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.8e-06     0.016      30      69 ..     101     140 ..      91     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                        DUF5615  30 lglegasDeeileyAkeedriivTkDkDFgellllggppp 69 
                                    ++ + + D +  +yA e++++ +++D+ F +  +l+ ++p
  gi|121638754|ref|YP_978978.1| 101 ANGNDIADAHLAAYALENNATWLSADRGFARFRRLRWRHP 140
                                    333459***********************99977766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1239.69
//
Query:       gi|121638755|ref|YP_978979.1|  [L=220]
Description: cell surface lipoprotein mpb83 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-26   92.8   0.0    2.3e-26   92.5   0.0    1.1  1  Fasciclin  Fasciclin domain


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.3e-30   2.3e-26       2     128 .]      95     217 ..      94     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.3e-30
                                    GGHHHHHHHH.....TTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHH CS
                      Fasciclin   2 dlstfvslle.....kaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkas 76 
                                    +lst+ s+l+     + +l+++L ++ g++TvFaPtn+Af+klp+++ ++l++d k l++iL+yHv++++ s s++  + 
  gi|121638755|ref|YP_978979.1|  95 MLSTLTSALSgklnpDVNLVDTL-NG-GEYTVFAPTNAAFDKLPAATIDQLKTDAKLLSSILTYHVIAGQASPSRIDGT- 171
                                    577888888777777889*****.66.7************************************************976. PP

                                    EEEECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                      Fasciclin  77 etlatllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                      ++t l+ga+l+v     +++++vn+ a +v+  ++++n  +++id+vL+p
  gi|121638755|ref|YP_978979.1| 172 --HQT-LQGADLTVIGA--RDDLMVNN-AGLVCGGVHTANATVYMIDTVLMP 217
                                    ..999.***********..9*******.**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1560.17
//
Query:       gi|121638756|ref|YP_978980.1|  [L=695]
Description: integral membrane C-type cytochrome biogenesis protein dipZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-33  116.2   0.0    2.9e-33  115.4   0.0    1.4  1  Thioredoxin_10  Thioredoxin like C-terminal domain
    6.6e-21   75.2  10.4    9.1e-21   74.7  10.4    1.2  1  DsbD            Cytochrome C biogenesis protein transmembrane
    1.7e-12   47.4   0.0    3.8e-12   46.2   0.0    1.5  2  AhpC-TSA        AhpC/TSA family
    1.1e-08   34.9   0.0    2.1e-08   34.0   0.0    1.3  1  Redoxin         Redoxin
    2.1e-05   24.7   0.0    5.2e-05   23.5   0.0    1.6  2  Thioredoxin_8   Thioredoxin-like
     0.0015   18.5   3.6      0.017   15.0   1.5    2.6  2  MerE            MerE protein
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.046   13.3   0.0    1.5  1  GSHPx           Glutathione peroxidase
      0.055   13.5   0.0      0.055   13.5   0.0    2.1  3  Thioredoxin     Thioredoxin
       0.97    9.2  10.2      0.088   12.6   5.7    1.5  2  Bax1-I          Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> Thioredoxin_10  Thioredoxin like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   1.4e-36   2.9e-33       1     142 []     568     695 .]     568     695 .] 0.99

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 1.4e-36
                 Thioredoxin_10   1 tpEtYLGyaraenfaspeklkedkaatytlpeklalnefaLsGkWtveeesitaasegarirlrfkArdvhlVlgeggpg 80 
                                    tpEtY+G+ +  n+++ ++++e++ a +++p +la+n+faL+G+W ++++ +t++ ++a+i+l+++A+dv++V+g  g+g
  gi|121638756|ref|YP_978980.1| 568 TPETYFGVGKVVNYGGGGAYDEGS-AVFDYPPSLAANSFALRGRWALDYQGATSDGNDAAIKLNYHAKDVYIVVG--GTG 644
                                    8**********************9.**************************************************..*** PP

                 Thioredoxin_10  81 tvkvtldgkagadagkdvdadgtitvsg.prlyqlvrqeevgegtleiefldpGveaYaFTFG 142
                                    t++v +dgk+            t+ +sg p+++q+v  ++ +++tle++ +++G+++++FT+G
  gi|121638756|ref|YP_978980.1| 645 TLTVVRDGKP-----------ATLPISGpPTTHQVVAGDRLASETLEVR-PSKGLQVFSFTYG 695
                                    **********...........9***************************.999*********9 PP

>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7  10.4   4.6e-24   9.1e-21       2     211 ..     122     338 ..     121     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 4.6e-24
                           DsbD   2 flaGllsflsPCilpliPa.ylsyisgvsvedvktekkkv.....kvllkal...lFvlGlslvfvslglsaaflgqllk 72 
                                    fl+Gl++ +sPCilp++P+ ++s   +v   +v + ++ v     ++l  +l     + Gl+l f  + l  ++l ++l+
  gi|121638756|ref|YP_978980.1| 122 FLGGLITGISPCILPVLPViFFSGAQSVDAAQVAKPEGAVavrrkRALSATLrpyRVIGGLVLSFGMVTLLGSALLSVLH 201
                                    9*****************82456555566666655545554577666666653314566899999999999999999999 PP

                           DsbD  73 dvkevirrva..glivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaas 150
                                      +++ir +a  +l++i  Gl f     +e l  +     i +k+ +++ + + lGl+ ++   PC+gP+la+++++ a+
  gi|121638756|ref|YP_978980.1| 202 LPQDAIRWAAlvALVAIGAGLIFPR---FEQLLEKPF-SRIPQKQIVTRSNGFGLGLALGVLYVPCAGPILAAIVVAGAT 277
                                    9999998765115555556666654...444443333.357788888899************************998888 PP

                           DsbD 151 keslakgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvll 211
                                        + +++l   ++lG a+p+l+++l  +++ +++  +++ ++ ++ia+g + +ll v l
  gi|121638756|ref|YP_978980.1| 278 ATIGLGTVVLTATFALGAALPLLFFALAGQRIAERVGAFRRRQREIRIATGSVTILLAVAL 338
                                    8755555566678***************************************999998866 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       7.8   1.5e+04      55      73 ..      90     108 ..      87     113 .. 0.77
   2 !   46.2   0.0   1.9e-15   3.8e-12      12     123 ..     412     522 ..     399     523 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7.8
                                    CCCTTEEEEEEESSSCHHH CS
                       AhpC-TSA  55 fkergvevigvsvdspesh 73 
                                     +er +++++v +d+  + 
  gi|121638756|ref|YP_978980.1|  90 SRERSCQLVAVPADPRPKR 108
                                    578999****999987655 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 1.9e-15
                                    STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH......HHHHHHHH-H.SSE CS
                       AhpC-TSA  12 nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe......shkkfiekeslnfp 85 
                                    +   ++++l+ ++gk+v++ f++  +c  C++ +p     y+++k+ g+ vigv + + +      +++k ++  ++ +p
  gi|121638756|ref|YP_978980.1| 412 TPGNKPIDLKSLRGKVVLIDFWAY-SCINCQRAIPHVVGWYQAYKDSGLAVIGVHTPEYAfekvpgNVAKGAANLGISYP 490
                                    344578******************.*****************************995555699999************** PP

                                    EEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  86 llsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                    +++D++ ++ ++y          ++a ++id+ g++r+
  gi|121638756|ref|YP_978980.1| 491 IALDNNYATWTNYRNR------YWPAEYLIDATGTVRH 522
                                    ****************......**************98 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0     1e-11   2.1e-08       7     134 ..     401     527 ..     398     539 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1e-11
                                    ---E.....CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...... CS
                        Redoxin   7 Pdft.....lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...... 75 
                                    Pd++     l +   ++++++l++++gk+v++ f++   c  C++ +p +   ++ +k++g  v++v + + af      
  gi|121638756|ref|YP_978980.1| 401 PDLKgitgwLNT--PGNKPIDLKSLRGKVVLIDFWAY-SCINCQRAIPHVVGWYQAYKDSGLAVIGVHTPEYAFekvpgn 477
                                    555555555544..6889*******************.**********999999999*******************9888 PP

                                    HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESS CS
                        Redoxin  76 vkefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevep 134
                                    v + ++++g+++p+++D + a   ++  r           p+  +id+ g v++++ ++
  gi|121638756|ref|YP_978980.1| 478 VAKGAANLGISYPIALDNNYATWTNYRNR---------YWPAEYLIDATGTVRHIKFGE 527
                                    8888888********************88.........8899999*******9998776 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.5   1.3e+04      28      45 ..      87     104 ..      81     110 .. 0.70
   2 !   23.5   0.0   2.6e-08   5.2e-05       1      95 []     425     520 ..     425     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.5
                                    HHHHHTTSEEEEEEE-SS CS
                  Thioredoxin_8  28 eklkkkkkveivyvsldk 45 
                                    ++ + ++ +++v+v+ d 
  gi|121638756|ref|YP_978980.1|  87 QQRSRERSCQLVAVPADP 104
                                    44444788999**99995 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.6e-08
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS....-TTSEE.EE-TT-HHHHTT CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkkn....kkpwlsvpfddkkrnklkk 76 
                                    gkvvl+ f+a+ c +c++ +p++   y+ +k + ++ ++ v+  +   +fek+  +      +  +s+p   +++++ + 
  gi|121638756|ref|YP_978980.1| 425 GKVVLIDFWAYSCINCQRAIPHVVGWYQAYK-DSGLAVIGVHTPEY--AFEKVPGNVakgaANLGISYPIALDNNYATWT 501
                                    79****************************9.69999999998765..5655555554333556899999999999**** PP

                                    -S--TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  77 kynvkaiPtlvvldkngev 95 
                                    +y+   +P  +++d  g+v
  gi|121638756|ref|YP_978980.1| 502 NYRNRYWPAEYLIDATGTV 520
                                    *********9999988876 PP

>> MerE  MerE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.081   1.6e+02      14      39 ..     118     142 ..     107     151 .. 0.75
   2 !   15.0   1.5   8.5e-06     0.017      15      59 ..     247     293 ..     235     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.081
                           MerE  14 pltGylwGalavltcPchlpilaivl 39 
                                    +l G+l G ++ +  Pc lp+l +++
  gi|121638756|ref|YP_978980.1| 118 ALVGFLGGLITGI-SPCILPVLPVIF 142
                                    5678887776665.5*******8875 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.5e-06
                           MerE  15 ltGylwG.alavltcPchlpila.ivlaGttaGaflgeywviaalal 59 
                                     +G+  G al vl  Pc  pila iv+aG+ta   lg     a++al
  gi|121638756|ref|YP_978980.1| 247 SNGFGLGlALGVLYVPCAGPILAaIVVAGATATIGLGTVVLTATFAL 293
                                    4677555479************63789*****998887766666666 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.046      12      59 ..     416     464 ..     409     473 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                                    SEEEGGGGTTSEEEEEEEESSSTTHH.HHHHHHHHHHHHGGGTEEEEEE CS
                          GSHPx  12 ekvkleklrgkvvlivnvaskCglte.qykeleelqkrykdkglvilgf 59 
                                    ++++l++lrgkvvli   a  C   +    ++   ++ ykd+gl ++g 
  gi|121638756|ref|YP_978980.1| 416 KPIDLKSLRGKVVLIDFWAYSCINCQrAIPHVVGWYQAYKDSGLAVIGV 464
                                    789*******************9999899*****************996 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   2.1         9   1.8e+04      29      33 ..      65      69 ..      64      70 .. 0.90
   2 ?   -4.1   0.0       8.3   1.7e+04      73      92 ..     297     316 ..     296     321 .. 0.80
   3 ?   13.5   0.0   2.8e-05     0.055      19      52 ..     426     460 ..     419     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 9
                                   TSHHH CS
                    Thioredoxin 29 wCghC 33
                                   wCg C
  gi|121638756|ref|YP_978980.1| 65 WCGRC 69
                                   ***** PP

  == domain 2  score: -4.1 bits;  conditional E-value: 8.3
                                    SSEEEEEETTEEEEEEESS- CS
                    Thioredoxin  73 iPtlklfkngkevkkyegar 92 
                                    +P l ++ +g+++++ +ga 
  gi|121638756|ref|YP_978980.1| 297 LPLLFFALAGQRIAERVGAF 316
                                    69999999999999999884 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.8e-05
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSE CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd.kvk 52 
                                    k vl++F+A  C  C++  P++    +++kd  + 
  gi|121638756|ref|YP_978980.1| 426 KVVLIDFWAYSCINCQRAIPHVVGWYQAYKDsGLA 460
                                    789********************999999985444 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.1   8.3e+03     148     171 ..     128     152 ..     114     162 .. 0.48
   2 ?   12.6   5.7   4.4e-05     0.088      11     174 ..     184     346 ..     176     372 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.1
                         Bax1-I 148 salelai.sylgvllfsglilyDtq 171
                                    + ++  i  +l v++fsg   +D  
  gi|121638756|ref|YP_978980.1| 128 TGISPCIlPVLPVIFFSGAQSVDAA 152
                                    2222233235566666666666654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.4e-05
                         Bax1-I  11 lalgllltalvaavvlsspa.qlflslhivlflvvilaplalv.flslsaarlkkkssalalallllftlleGlslspil 88 
                                    l++g+ +t l++a+++ +   q  ++    + lv+i a+l++  f  l+ +   + +++  +++     +  Gl l+++ 
  gi|121638756|ref|YP_978980.1| 184 LSFGM-VTLLGSALLSVLHLpQDAIRWAALVALVAIGAGLIFPrFEQLLEKPFSRIPQK--QIVTRSNGFGLGLALGVLY 260
                                    33344.33333333322222455556666667777777777777777776666676666..8888888888888888887 PP

                         Bax1-I  89 lvytgaiilqaflltaaifgglslyalttkrdlsglggflfagligliiaslvnlFlp.ssalelaisylgvllfsglil 167
                                    +  +g i++  +++ a + +gl +++lt+   l    ++lf +l g  ia  v  F +  + + +a    +++l ++ ++
  gi|121638756|ref|YP_978980.1| 261 VPCAGPILAAIVVAGATATIGLGTVVLTATFALGAALPLLFFALAGQRIAERVGAFRRrQREIRIAT-GSVTILLAVALV 339
                                    77779999999999999**************************************966544444444.445666677777 PP

                         Bax1-I 168 yDtqkii 174
                                    +D    +
  gi|121638756|ref|YP_978980.1| 340 FDLPAAL 346
                                    7764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 4308.07
//
Query:       gi|121638757|ref|YP_978981.1|  [L=193]
Description: hypothetical protein BCG_2897 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-27   94.5   0.3    7.1e-27   94.2   0.3    1.1  1  Fasciclin  Fasciclin domain


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.3     4e-31   7.1e-27       2     128 .]      69     191 ..      68     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 4e-31
                                    GGHHHHHHHH.....TTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHH CS
                      Fasciclin   2 dlstfvslle.....kaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkas 76 
                                    +l+t+ ++l+     + +l+++L ++ g++TvFaPtn+Af+klp+++ ++l+++++ l++iL+yHvv+++ s ++++ + 
  gi|121638757|ref|YP_978981.1|  69 ELTTLTAALSgqlnpQVNLVDTL-NS-GQYTVFAPTNAAFSKLPASTIDELKTNSSLLTSILTYHVVAGQTSPANVVGT- 145
                                    6788888888777778899****.66.7***********************************************9976. PP

                                    EEEECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                      Fasciclin  77 etlatllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       +t l+ga+++v+ +  +++++v + a vv+  ++++n  +++id+vL+p
  gi|121638757|ref|YP_978981.1| 146 --RQT-LQGASVTVTGQ--GNSLKVGN-ADVVCGGVSTANATVYMIDSVLMP 191
                                    ..899.***********..99******.**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 1110.34
//
Query:       gi|121638758|ref|YP_978982.1|  [L=104]
Description: hypothetical protein BCG_2898 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-27   94.1   0.7    4.2e-27   93.8   0.7    1.1  1  DUF2631   Protein of unknown function (DUF2631)


Domain annotation for each model (and alignments):
>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.7   2.3e-31   4.2e-27       1      66 []      18      85 ..      18      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.3e-31
                        DUF2631  1 astelekkkg..teVdtadvPSaaWGWsgespkttriaGlisvlallamliGnhqGhvedifLigfAa 66
                                   aste+e+  g  +eVdta+vPSaaWG s++ ++t++i+Gl++  +llaml+Gnh Ghved+fLi+fAa
  gi|121638758|ref|YP_978982.1| 18 ASTEVEHFAGsqHEVDTAEVPSAAWGRSRIDHRTWHIVGLCIFGFLLAMLRGNHVGHVEDWFLITFAA 85
                                   79********9999****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 773.32
//
Query:       gi|121638759|ref|YP_978983.1|  [L=287]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-11   43.3  15.2    5.7e-11   42.7  15.2    1.2  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
       0.62    9.7   0.1       0.62    9.7   0.1    2.9  5  DUF3098   Protein of unknown function (DUF3098)
        5.5    6.2   8.2        3.9    6.7   0.4    2.6  2  PorA      Porin PorA


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7  15.2   9.5e-15   5.7e-11       1     211 [.       9     220 ..       9     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.5e-15
                           DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvkte.kkkv.kvllkallFvlGlslvfvslglsaaflgqllkdvkevi 78 
                                    af aGl++ l PC ++++Payl  +   + +  +t+  + v ++   ++  +lG+ +vf  +g+ +  + + ++ +  + 
  gi|121638759|ref|YP_978983.1|   9 AFAAGLVAALNPCGFAMLPAYLLLVVHGQDSAGRTGpLSAVgRAAAATVGMALGFLTVFGIFGALTISAATAVQRYLPYA 88 
                                    699*******************99988887877887445568999999**************998888888888999999 PP

                           DsbD  79 rrvaglivillGlhfl.gvfkievleklklllkikkkaelsvlgalllGltFalgwsPC.igPvlasvlalaaskeslak 156
                                    ++++gl  i lG  +l g   +++l+  +l + +    ++     +  G+++a+ +  C igP la v  +    +s+  
  gi|121638759|ref|YP_978983.1|  89 TVLIGLALIALGGWLLlG-RGLTALTPRSLGVRWA--PTVRLGSMYGYGISYAVASLSCtIGPFLA-VTGAGLRGGSVVG 164
                                    999999999887555504.3466676666665555..55544667899******998885689886.5555556677888 PP

                           DsbD 157 gallllvyvlGlaipfllvglllellk.kklkslkkyskaveiaggvllvllGvll 211
                                    ++ + l+yv Gl++++ ++++ +  +    +  l++   +v+ ++g llv++G+++
  gi|121638759|ref|YP_978983.1| 165 SVAIYLAYVAGLTLVVGVLAVAAATASsALADRLRRILPFVNRISGALLVVVGLYV 220
                                    888999*******99866666655554045679********************985 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.4       1.7     1e+04      14      25 ..      56      67 ..      53      69 .. 0.60
   2 ?    9.7   0.1    0.0001      0.62       7      30 ..      87     110 ..      85     116 .. 0.90
   3 ?   -2.5   0.1      0.65   3.9e+03      46      58 ..     145     157 ..     142     163 .. 0.79
   4 ?   -3.9   0.3       1.8   1.1e+04      16      20 ..     177     181 ..     168     187 .. 0.48
   5 ?   -3.3   0.2       1.2     7e+03      14      21 ..     211     218 ..     207     225 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
                        DUF3098 14 laviilGfiLms 25
                                    + ++lGf+   
  gi|121638759|ref|YP_978983.1| 56 TVGMALGFLTVF 67
                                   455677777554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0001
                        DUF3098   7 yillliglaviilGfiLmsGggsd 30 
                                    y  +ligla+i+lG +L+ G g +
  gi|121638759|ref|YP_978983.1|  87 YATVLIGLALIALGGWLLLGRGLT 110
                                    7789****************9976 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.65
                        DUF3098  46 rlAPivvliGfvi 58 
                                    +++P+++++G ++
  gi|121638759|ref|YP_978983.1| 145 TIGPFLAVTGAGL 157
                                    6899999999765 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 1.8
                        DUF3098  16 viilG 20 
                                     +++G
  gi|121638759|ref|YP_978983.1| 177 TLVVG 181
                                    22222 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 1.2
                        DUF3098  14 laviilGf 21 
                                    ++++++G+
  gi|121638759|ref|YP_978983.1| 211 ALLVVVGL 218
                                    44455553 PP

>> PorA  Porin PorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.2    0.0068        41     277     300 .]      79     102 ..      73     102 .. 0.89
   2 ?    6.7   0.4   0.00065       3.9     266     299 ..     185     218 ..     181     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0068
                           PorA 277 kllgrtlpivllvlGlvllvaglv 300
                                     +++r+lp++++++Gl l+++g +
  gi|121638759|ref|YP_978983.1|  79 TAVQRYLPYATVLIGLALIALGGW 102
                                    6899*****************976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00065
                           PorA 266 veqakegrdklkllgrtlpivllvlGlvllvagl 299
                                    v+ a+  +   ++l+r+lp+v  + G++l+v+gl
  gi|121638759|ref|YP_978983.1| 185 VAAATASSALADRLRRILPFVNRISGALLVVVGL 218
                                    4555566668999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2162.43
//
Query:       gi|121638760|ref|YP_978984.1|  [L=173]
Description: hypothetical protein BCG_2900c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-15   56.1   0.0    4.5e-15   55.7   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    9.7e-11   41.6   0.0    1.3e-10   41.2   0.0    1.2  1  Redoxin        Redoxin
    5.3e-06   26.8   0.0    3.9e-05   24.1   0.0    2.2  2  Thioredoxin_2  Thioredoxin-like domain
    9.5e-06   25.5   0.0    0.00018   21.4   0.0    2.1  2  Thioredoxin    Thioredoxin
     0.0003   21.1   0.0    0.00047   20.4   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.074   12.8   0.0    1.8  2  Thioredoxin_9  Thioredoxin
       0.12   12.0   0.8        3.2    7.5   0.0    2.5  2  Pentapeptide   Pentapeptide repeats (8 copies)
       0.13   12.2   0.6       0.28   11.2   0.6    1.5  1  PetL           Cytochrome B6-F complex subunit VI (PetL)
       0.16   11.2   0.1       0.68    9.2   0.0    1.9  2  DUF929         Domain of unknown function (DUF929)


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.2e-18   4.5e-15       7     110 ..      43     144 ..      37     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.2e-18
                                    --EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES.SSCHHHHHHHHH-H.SSE CS
                       AhpC-TSA   7 dfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv.dspeshkkfiekeslnfp 85 
                                    +f++++  g +++ + ++gkp+vl f++  wcp+C++e+p+l++++ +     v+ +g+ +  ++ ++++f+ k++lnf+
  gi|121638760|ref|YP_978984.1|  43 QFTATTLSGAPFDGASLQGKPAVLWFWTP-WCPFCNAEAPSLSQVAAANP--AVTFVGIATrADVGAMQSFVSKYNLNFT 119
                                    79***************************.***************98887..89999999966677************** PP

                                    EEE-TTSHHHHHTT-EETTTTECSC CS
                       AhpC-TSA  86 llsDeegkvakaygvlkeekglalr 110
                                     l D +g +  +y+v+++++ + +r
  gi|121638760|ref|YP_978984.1| 120 NLNDADGVIWARYNVPWQPAFVFYR 144
                                    ****************877333333 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   6.4e-14   1.3e-10       9     106 ..      44     137 ..      33     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6.4e-14
                                    -ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHHTT-TS CS
                        Redoxin   9 ftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgkeglkf 87 
                                    ft   ++  g +++ ++++gk++v+ f++  +cP C+ae+p l ++a+   + +v++v++ +  d   +++f++k++l+f
  gi|121638760|ref|YP_978984.1|  44 FT--ATTLSGAPFDGASLQGKPAVLWFWTP-WCPFCNAEAPSLSQVAAA--NPAVTFVGIATRADVGaMQSFVSKYNLNF 118
                                    44..4568999*******************.***************777..899*******9999999************ PP

                                    EEEE-TTSHHHHHTT-TTE CS
                        Redoxin  88 pvlsDgsaaftkalGlrle 106
                                    + l D+++ + + ++++++
  gi|121638760|ref|YP_978984.1| 119 TNLNDADGVIWARYNVPWQ 137
                                    ***************9965 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.62   1.2e+03      71      90 ..      22      41 ..       7      53 .. 0.73
   2 !   24.1   0.0     2e-08   3.9e-05       3     105 ..      59     164 ..      57     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.62
                  Thioredoxin_2 71 elarkygvrgtPtivfldgk 90
                                   +++ ++g+  tP  v  d++
  gi|121638760|ref|YP_978984.1| 22 AVVLMFGLANTPRAVAADER 41
                                   56678999999999999998 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2e-08
                  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkel....ddvtvrvllfplkpsfepkavaiwcakekkkafkd............i 66 
                                     +gkp +++f++p+Cp+C +    l+++    ++vt+  ++                 +++  a++              
  gi|121638760|ref|YP_978984.1|  59 LQGKPAVLWFWTPWCPFCNAEAPSLSQVaaanPAVTFVGIATR---------------ADV-GAMQSfvskynlnftnlN 122
                                    589****************977788888443344444433333...............333.233333333333333333 PP

                  Thioredoxin_2  67 eenvelarkygvrgtPtivfldgk...eivarlpGyvpaeel 105
                                    ++  +   +y+v + P++vf+ ++   + v++ + +++++el
  gi|121638760|ref|YP_978984.1| 123 DADGVIWARYNVPWQPAFVFYRADgtsTFVNNPTAAMSQDEL 164
                                    455666677999999999998887767777777777777776 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     9e-08   0.00018       7      56 ..      51      98 ..      45     118 .. 0.72
   2 ?    2.8   0.0     0.059   1.2e+02      53      85 ..     118     149 ..     104     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9e-08
                                   HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEE CS
                    Thioredoxin  7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakv 56
                                    + F+ +  +  k+ ++ F+ pwC+ C a aP l ++a +    v+++ +
  gi|121638760|ref|YP_978984.1| 51 GAPFDGASLQ-GKPAVLWFWTPWCPFCNAEAPSLSQVAAANP-AVTFVGI 98
                                   5566666666.7999***********************9998.7777655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.059
                                    EEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                    Thioredoxin  53 lakvdvdenedlakkyevegiPtlklfkngkev 85 
                                    + +++ d+   + ++y+v   P++++++++ ++
  gi|121638760|ref|YP_978984.1| 118 FTNLN-DADGVIWARYNVPWQPAFVFYRADGTS 149
                                    55554.4444677899***********987633 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.4e-07   0.00047       1      93 [.      61     147 ..      61     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S-- CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynv 80 
                                    gk  +L f++ wcp c a  p+l+++         v +v +    +  +++++++k + ++++   +d     ++ +ynv
  gi|121638760|ref|YP_978984.1|  61 GKPAVLWFWTPWCPFCNAEAPSLSQVAAANP---AVTFVGIATRADVGAMQSFVSKYNLNFTN--LND-ADGVIWARYNV 134
                                    57889********************999985...9**********************555554..443.46788999999 PP

                                    TT-SEEEEE-TT- CS
                  Thioredoxin_8  81 kaiPtlvvldkng 93 
                                       P +v  + +g
  gi|121638760|ref|YP_978984.1| 135 PWQPAFVFYRADG 147
                                    8888888766665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.074      37      84 ..      57     104 ..      30     116 .. 0.80
   2 ?   -0.6   0.0      0.52     1e+03      98     120 ..     137     159 ..     131     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                    HT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHH CS
                  Thioredoxin_9  37 ksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenl 84 
                                    +s++ k  +l + ++wC+ + +  P l ++a +np +++  ++  ++ 
  gi|121638760|ref|YP_978984.1|  57 ASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADV 104
                                    5677888899999**********************9987666655555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                                    SSEEEEE-TT--EEEEEESS-HH CS
                  Thioredoxin_9  98 iPtliildeegeelgvwgerPae 120
                                    +P+++++ ++g+   v  + +a 
  gi|121638760|ref|YP_978984.1| 137 QPAFVFYRADGTSTFVNNPTAAM 159
                                    699******99988555555554 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0016       3.2      23      40 .]      44      61 ..      40      61 .. 0.77
   2 ?    2.4   0.3     0.061   1.2e+02      27      37 ..     115     125 ..     112     125 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                   ECT-B-TT-EECCEEECT CS
                   Pentapeptide 23 LtgAnlsgAdLsganLsg 40
                                   +t ++lsgA + ga L+g
  gi|121638760|ref|YP_978984.1| 44 FTATTLSGAPFDGASLQG 61
                                   788888888888888876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.061
                                    B-TT-EECCEE CS
                   Pentapeptide  27 nlsgAdLsgan 37 
                                    nl++++L++a+
  gi|121638760|ref|YP_978984.1| 115 NLNFTNLNDAD 125
                                    44444444443 PP

>> PetL  Cytochrome B6-F complex subunit VI (PetL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00014      0.28      12      25 ..      16      29 ..      16      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHH CS
                           PetL 12 ggalaiAlgLffGL 25
                                   ++a aiA++L+fGL
  gi|121638760|ref|YP_978984.1| 16 IVAVAIAVVLMFGL 29
                                   5899*********9 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00034      0.68      11      78 ..      17      81 ..      10      90 .. 0.53
   2 ?   -0.1   0.0      0.23   4.6e+02     100     135 ..      84     119 ..      80     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                         DUF929 11 liivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdl...asngkvevyfvswegCPvgaaesW 78
                                   ++++++vv+++     n   +++    a e l+ + + +s+ ++   + +gk++v++    +CP++ ae+ 
  gi|121638760|ref|YP_978984.1| 17 VAVAIAVVLMFGLA--NTPRAVA----ADERLQFTATTLSGAPFdgaSLQGKPAVLWFWTPWCPFCNAEAP 81
                                   22222222222222..3332222....22222222333444443111246****************99875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                         DUF929 100 sdeypniPgLiFknftpnskvefysiYiyneylnas 135
                                    s++ +  P+ +F +  +   v     +++ ++ln +
  gi|121638760|ref|YP_978984.1|  84 SQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFT 119
                                    677888999999999998888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1276.03
//
Query:       gi|121638761|ref|YP_978985.1|  [L=364]
Description: ribosomal RNA large subunit methyltransferase N [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-21   77.6   0.0    2.2e-21   77.0   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
     0.0042   17.2   0.0     0.0083   16.3   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.094   13.0   0.0       0.17   12.2   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   3.6e-25   2.2e-21       2     162 ..     121     290 ..     120     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 3.6e-25
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHH......HTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelka......ekg.vkevilgggepllypdfvellerlakla 74 
                                    + + gC ++C+fCa+++    +g  r+ls+ eile+v++++a       ++  ++v++g+gepl+++  v ++ +++  +
  gi|121638761|ref|YP_978985.1| 121 SSQAGCGMACPFCATGQ----GGLTRNLSTAEILEQVRAGAAalrddfGDRlSNVVFMGMGEPLANYARVLAAVQRITAR 196
                                    7899************6....9***************999735999884456**************************99 PP

                                    ......CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 ......vpgiritvetngtlpdeeklerllelg.vdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrv 145
                                           + + +tv+t g+ p    ++ l++++   +++l+l+a+dd   ++l ++n ++ ++e l+a ++++++ ++rv
  gi|121638761|ref|YP_978985.1| 197 ppsgfgISARAVTVSTVGLAP---AIRNLADARlGVTLALSLHAPDDGlrDTLVPVNNRWRISEALDAARYYANVTGRRV 273
                                    *********************...**************************999****99********************* PP

                                    EEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                    Radical_SAM 146 vdrivglpGendeelee 162
                                    ++ + +++ +nd+ +++
  gi|121638761|ref|YP_978985.1| 274 SIEYALIRDVNDQPWRA 290
                                    ************98775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0083       6      78 ..     124     197 ..     121     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                        Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilk...dlkksei.kiqglvltG.GePLhyenkkellklvkrlkeey 78 
                                    +gC ++C++C + +       + +t e+leq+ +    l ++   + +++v++G GePL  +n   +l  v+r+  + 
  gi|121638761|ref|YP_978985.1| 124 AGCGMACPFCATGQ--GGLTRNLSTAEILEQVRAgaaALRDDFGdRLSNVVFMGmGEPL--ANYARVLAAVQRITARP 197
                                    89********9655..333444455555544444332333332212367**********..99********9998876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.17      12      84 ..     123     198 ..     113     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                        Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk......esiegltllG.GEPllpenaeallelvkevkeekp 84 
                                     +gC ++C++C   +     + +  t e+le++ + ++       ++ + ++++G GEPl+  n+  +l  v+++ ++ p
  gi|121638761|ref|YP_978985.1| 123 QAGCGMACPFCATGQGG--LTRNLSTAEILEQVRAGAAAlrddfgDRLSNVVFMGmGEPLA--NYARVLAAVQRITARPP 198
                                    68*********966643..3333333333333333222211123367799999999*****..****9999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:02.64
# Mc/sec: 418.30
//
Query:       gi|121638762|ref|YP_978986.1|  [L=306]
Description: integral membrane phosphatidate cytidylyltransferase cdsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-60  204.8  17.9    2.4e-60  204.6  17.9    1.0  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6  17.9   1.3e-64   2.4e-60       3     265 ..      37     304 ..      35     305 .. 0.97

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 1.3e-64
                                    HHHHHHHHHHHHHHTTTSH.HHHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHH...HHHHHHHHHHTTTSSSHHHHHHH CS
                   CTP_transf_1   3 RvitalvlilivliilllgglvflllvavvvilalkElirlvrlkkrekrllllllslvlllllllflylesliallklv 82 
                                     ++++l ++l+++++l++ + v++++vav++++a++E++r  r++    +++ ll+   ++++l++ + +  + a ++ +
  gi|121638762|ref|YP_978986.1|  37 AIVVGLSIGLVLIAVLVFVPRVWVAIVAVATLVATHEVVRRLREAGYLIPVIPLLIGGQAAVWLTWPFGAVGALAGFGGM 116
                                    57889999999999****************************************************************** PP

                                    HHHHHHHHHHH---...........HHHHHHHHHHHHHHHHHTHHHH.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1  83 lllvlvllllvlkvl........kskskklervilallallyvvlllqslllienikeglllvllllalvvaaDigaYff 154
                                    ++++++++l++++ +         s  ++l++v+++++++++v+l+ ++ +++ ++++g  +v++++++v+a+D+g+Y +
  gi|121638762|ref|YP_978986.1| 117 VVVCMIWRLFMQDSVtrpttggaPSPGNYLSDVSATVFLAVWVPLFCSFGAMLVYPENGSGWVFCMMIAVIASDVGGYAV 196
                                    ************9999******99999***************************************************** PP

                                    HHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SS CS
                   CTP_transf_1 155 GklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgiKD 234
                                    G lfGk+ ++p+iSPkK++eGf g+lv+ +++++++a++l     ++++ ++ll++l++l++ +GDLveS +KR++giKD
  gi|121638762|ref|YP_978986.1| 197 GVLFGKHPMVPTISPKKSWEGFAGSLVCGITATIITATFLVG---KTPWIGALLGVLFVLTTALGDLVESQVKRDLGIKD 273
                                    *****************************************9...79********************************* PP

                                    S-S-SSSSS-HHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1 235 sGkliPGhGGilDRlDsllfaapvvylllel 265
                                    +G+l+PGhGG++DRlD++l +a+ ++++l+l
  gi|121638762|ref|YP_978986.1| 274 MGRLLPGHGGLMDRLDGILPSAVAAWIVLTL 304
                                    **************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1915.77
//
Query:       gi|121638763|ref|YP_978987.1|  [L=185]
Description: ribosome recycling factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-59  197.9   0.7    1.2e-58  197.6   0.7    1.1  1  RRF          Ribosome recycling factor
     0.0021   18.6   3.5     0.0021   18.6   3.5    2.0  2  DUF883       Bacterial protein of unknown function (DUF883)
  ------ inclusion threshold ------
       0.12   12.7   2.1       0.21   11.9   2.1    1.4  1  Phage_TAC_4  Phage tail assembly chaperone


Domain annotation for each model (and alignments):
>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.6   0.7   2.1e-62   1.2e-58       2     162 .]      21     183 ..      20     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.6 bits;  conditional E-value: 2.1e-62
                                    HHHHHHSS-SSSSCGGGTTSEEEETTEEEEGGGTEEEEESSTTEEEEEESSCCHHHHHHHHHHHSCC-SEEEEESSEEEE CS
                            RRF   2 kkelsklrtgranpslldnikVeyygkktpLnqlAqvsvkeartllitpfdkslvkaiekaIlksdlglnpqqdgevlrv 81 
                                    +++ls++rtgranp+++ +i+++yyg+ t ++qlA+++v+ear+++i+p++ + + aie+aI++sdlg+np++dg  +rv
  gi|121638763|ref|YP_978987.1|  21 RDDLSTIRTGRANPGMFSRITIDYYGAATLITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRV 100
                                    579***************************************************************************** PP

                                    E--SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            RRF  82 pipplTeErrkelvkeakkaaekakvairniRrdankklkklekk..iseDdvkkaekeiqkltdkyikeidellkakek 159
                                     +p+lTeErr+elvk+ak+++e+akv++rniRr+a+++l++++k+    eD+v +aek+++k t++y+ +idel+k+ke 
  gi|121638763|ref|YP_978987.1| 101 AVPQLTEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEgeAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEG 180
                                    ********************************************559********************************9 PP

                                    HHT CS
                            RRF 160 ell 162
                                    ell
  gi|121638763|ref|YP_978987.1| 181 ELL 183
                                    996 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.2   1.2e+03      13      33 ..       8      28 ..       2      33 .. 0.52
   2 !   18.6   3.5   3.4e-07    0.0021      14      71 ..     113     170 ..     102     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.2
                         DUF883 13 dleellkeaadeageeaeelR 33
                                   d+ee +++a + a+++++++R
  gi|121638763|ref|YP_978987.1|  8 DAEEKMEKAVAVARDDLSTIR 28
                                   444444444444555544444 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.4e-07
                         DUF883  14 leellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVre 71 
                                    l + +k++++ea+ +++++R++++e+l+r r++ ++ e++v +  k+  +++ +yV +
  gi|121638763|ref|YP_978987.1| 113 LVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQ 170
                                    444456778899999*****************************************75 PP

>> Phage_TAC_4  Phage tail assembly chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   3.6e-05      0.21      23      82 ..     119     176 ..     111     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                    Phage_TAC_4  23 ldgekakveftfkamdrkelaeleeereqseakeeekaaaeedleasidkglaldaelik 82 
                                    + ge+ak  + ++ + rk+++el   r++ ea e+e  +ae+dl + +++ + +  el+k
  gi|121638763|ref|YP_978987.1| 119 HKGEEAK--VSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVK 176
                                    4555555..5689*******************************9999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1408.17
//
Query:       gi|121638764|ref|YP_978988.1|  [L=261]
Description: uridylate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-28  100.1   0.2    1.7e-28   99.9   0.2    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.2   9.3e-33   1.7e-28       2     241 .]      32     239 ..      31     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 9.3e-33
                                    EEEEEE-TTCCCCTCC....HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHH CS
                      AA_kinase   2 rvVvKlGGssltdkee....aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeageva 77 
                                    rv +KlGG +++ ++     +++  +a+qia+ ++ g +++vV+Ggg+f +g   ++ g++++++               
  gi|121638764|ref|YP_978988.1|  32 RVLLKLGGEMFGGGQVgldpDVVAQVARQIADVVRGGVQIAVVIGGGNFFRGAQLQQLGMERTRS--------------- 96 
                                    899*********88889***********************************9999899999998............... PP

                                    HHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEE CS
                      AA_kinase  78 trdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgr 157
                                      d++++lg+ +++  l+  l++ g+  +  +a++ g+      + e +      + le+g v++++ + g      l  
  gi|121638764|ref|YP_978988.1|  97 --DYMGMLGTVMNSLALQDFLEKEGIVTRVQTAITMGQ------VAEPYLPLRAVRHLEKGRVVIFGAGMG------LPY 162
                                    ..9***********************************......99999988889999***9999988663......349 PP

                                    E-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EE CS
                      AA_kinase 158 gssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipv 237
                                    +s+Dt+aa  A ++gAd ++ ++ VdGV+  dp+++p a+ll+ +s++e+++        G +v +  a+ +++ +g+p+
  gi|121638764|ref|YP_978988.1| 163 FSTDTTAAQRALEIGADVVLMAKAVDGVFAEDPRVNPEAELLTAVSHREVLD-------RGLRVADATAFSLCMDNGMPI 235
                                    9***************************************************.......********************* PP

                                    EEEE CS
                      AA_kinase 238 vItn 241
                                     ++n
  gi|121638764|ref|YP_978988.1| 236 LVFN 239
                                    **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1585.89
//
Query:       gi|121638765|ref|YP_978989.1|  [L=252]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-24   85.8   0.1    3.2e-24   84.8   0.1    1.5  1  Trans_reg_C  Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
       0.16   11.6   0.0       0.27   10.8   0.0    1.3  1  GerE         Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.1   3.6e-28   3.2e-24       3      76 ..     161     232 ..     159     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 3.6e-28
                                    EEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEE CS
                    Trans_reg_C   3 eveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYr 76 
                                    ++ lt +efkl+ +L++++gr ++r++L++evwg++ ++  rtvdvh++rLR kL++ e ++++I tvrgvGY+
  gi|121638765|ref|YP_978989.1| 161 DLGLTLTEFKLMNFLVQHAGRAFTRTRLMREVWGYECHGRIRTVDVHVRRLRAKLGA-E-HESMIDTVRGVGYM 232
                                    6789*****************************************************.5.455**********8 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     3e-05      0.27      31      49 ..     201     219 ..     194     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHHHHHT-SS CS
                           GerE  31 ekTVkvhksnimkKLnvks 49 
                                     +TV vh++++  KL++++
  gi|121638765|ref|YP_978989.1| 201 IRTVDVHVRRLRAKLGAEH 219
                                    69**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1807.27
//
Query:       gi|121638766|ref|YP_978990.1|  [L=439]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-27   95.5   0.9    5.4e-27   94.4   0.9    1.6  1  OrfB_IS605      Probable transposase
    6.5e-14   51.6   0.1    1.7e-13   50.3   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.4e-08   34.1   1.6      2e-08   33.6   0.1    2.1  2  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
       0.26   11.2   2.3       0.27   11.2   0.6    2.0  2  ChW             Clostridial hydrophobic W


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.9   1.2e-30   5.4e-27       4     117 ..     206     321 ..     201     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.2e-30
                     OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtw..flykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                    v+ +++ +++ + +++g+D+G+++Latv++ +gt    ++++r+l+++++ l++  +  ++++k+s++y +++++l+rlh
  gi|121638766|ref|YP_978990.1| 206 VQRPQQRRVALPDSRVGVDVGVRRLATVADAEGTVleQVPNPRPLDAALRGLRRVSRARSRCTKGSRRYCERTTELSRLH 285
                                    4445559999*************************99******************************************* PP

                     OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                    r++++ r+h+lh l+t+l+kt+ +++ve L+ ++m 
  gi|121638766|ref|YP_978990.1| 286 RRVNDVRTHHLHVLTTRLAKTHGRIVVEGLDAAGML 321
                                    **********************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1   3.7e-17   1.7e-13       6      68 ..     346     408 ..     343     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.7e-17
                 OrfB_Zn_ribbon   6 eqleykakeyGikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                    + l+yk  +yG +++++++++ +SktC+ C ++++    ++ ++C+ C  +++rD nAaiN+++
  gi|121638766|ref|YP_978990.1| 346 RHLSYKTGWYGSSLVVADRWFpSSKTCHACRHVQDI-GWDEIWQCDGCSITHQRDDNAAINLAR 408
                                    679*********************************.9999*********************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   4.4e-12     2e-08       4      35 ..      14      45 ..      12      59 .. 0.86
   2 ?   -3.3   0.1       1.5   6.7e+03      22      30 ..     370     378 ..     369     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 4.4e-12
                 HTH_OrfB_IS605  4 kaykyrlyPTpeQeeklartfGcvRfVYNkaL 35
                                   +a+++ l+PT++Q++ lar+fG+ R ++N+  
  gi|121638766|ref|YP_978990.1| 14 QAFRFTLNPTQTQAASLARHFGARRKAFNWTV 45
                                   69****************************65 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                 HTH_OrfB_IS605  22 rtfGcvRfV 30 
                                    +t+ ++R+V
  gi|121638766|ref|YP_978990.1| 370 KTCHACRHV 378
                                    8999***98 PP

>> ChW  Clostridial hydrophobic W
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.9   1.3e+04       9      16 ..      54      61 ..      53      62 .. 0.77
   2 ?   11.2   0.6   5.9e-05      0.27       1      14 [.     377     391 ..     377     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                            ChW  9 nwvkdGei 16
                                    w++dG  
  gi|121638766|ref|YP_978990.1| 54 AWRADGTE 61
                                   5999*975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.9e-05
                            ChW   1 HVQniGWqn.wvkdG 14 
                                    HVQ+iGW   w +dG
  gi|121638766|ref|YP_978990.1| 377 HVQDIGWDEiWQCDG 391
                                    *******65688998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2819.53
//
Query:       gi|121638767|ref|YP_978991.1|  [L=295]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-13   50.7   0.2    2.8e-13   50.2   0.2    1.2  1  Resolvase  Resolvase, N terminal domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.2   1.6e-17   2.8e-13       2     145 ..     153     291 ..     152     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-17
                                    EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                      Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                    ++ aR S+++q+ +l+rQ+  ++a+a+++++ + k++++   S+   +R+ +  ll + +    + +v+++ dRL+R  +
  gi|121638767|ref|YP_978991.1| 153 AVCARLSSADQKVDLDRQVVGVTAWATAEQIPVGKVVTEV-GSALYGRRRTFLTLLGDPTV---RRIVMKRRDRLGRFGF 228
                                    5789*************************999999*****.****************9988...689************* PP

                                    S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHH.HHHHHHCT-TTHHHHHHHHHH CS
                      Resolvase  82 dlltlleelrekgvslvsldegidtstpm.grlllqilaalaef.erelirertkeglaaakakGk 145
                                    ++++    l++ g +lv++d+  d +++  g ++  + +++a++  ++   +r ++++aaa+++G 
  gi|121638767|ref|YP_978991.1| 229 ECVQA--VLAADGRELVVVDS-ADVDDDVvGDITEILTSICARLyGKRAAGNRAARAVAAAARAGG 291
                                    ****9..78999999999997.88888888*************95567788999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2218.34
//
Query:       gi|121638768|ref|YP_978992.1|  [L=139]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   53.3   0.0    3.5e-14   52.5   0.0    1.5  1  MarR             MarR family
    5.6e-09   35.8   1.1    9.1e-09   35.1   0.1    1.8  2  MarR_2           MarR family
    1.6e-05   24.4   0.0    3.3e-05   23.4   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    1.6e-05   24.8   2.1    2.6e-05   24.2   0.1    2.2  2  HTH_20           Helix-turn-helix domain
    0.00048   20.1   0.1     0.0011   18.8   0.0    1.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0018   18.1   0.0     0.0035   17.2   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.021   15.1   0.0    1.5  1  Rrf2             Transcriptional regulator
      0.012   15.6   0.0      0.019   14.9   0.0    1.3  1  HTH_11           HTH domain
      0.022   14.6   0.0      0.037   13.9   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
      0.036   14.3   0.0      0.097   12.9   0.0    1.7  1  HTH_34           Winged helix DNA-binding domain
      0.064   13.5   0.3       0.17   12.1   0.0    1.8  2  SelB-wing_2      Elongation factor SelB, winged helix
      0.084   12.7   0.0       0.14   12.0   0.0    1.4  1  HxlR             HxlR-like helix-turn-helix
       0.09   12.5   0.0         10    6.0   0.1    2.4  2  OxoDH_E1alpha_N  2-oxoisovalerate dehydrogenase E1 alpha subu
       0.21   11.9   0.0       0.38   11.0   0.0    1.3  1  A_thal_3526      Plant protein 1589 of unknown function (A_th


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   2.7e-17   3.5e-14       1      58 [.      33      90 ..      33      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.7e-17
                                   --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                           MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                   ltl++fv+Lr+l+++++ls +eLa++ +v++ ++ +vl++Le++G + R  s +  R+
  gi|121638768|ref|YP_978992.1| 33 LTLPEFVCLRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVARPASVSSGRS 90
                                   8*****************************************************9997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   7.1e-12   9.1e-09       1      55 [.      31      83 ..      31      90 .. 0.92
   2 ?   -1.4   0.1       1.8   2.3e+03       6      12 ..     113     119 ..      93     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 7.1e-12
                                   TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   lglt+ ++  L  L  +pg  l+ +elar+  ++++a++ +l++L++aG v r +
  gi|121638768|ref|YP_978992.1| 31 LGLTLPEFVCLRMLSQSPG--LSSAELARHASVTPQAMNTVLRKLEDAGAVARPA 83
                                   69*****************..****************************998755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                    HHHHHHH CS
                         MarR_2   6 aqarvLa 12 
                                    a+arvLa
  gi|121638768|ref|YP_978992.1| 113 ADARVLA 119
                                    3444444 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.6e-08   3.3e-05       9      45 ..      41      77 ..      41      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.6e-08
                         HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                   L+ L + p++s +eLA++  ++p++ n+ l++Le++G
  gi|121638768|ref|YP_978992.1| 41 LRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAG 77
                                   7899********************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     2e-08   2.6e-05      16      56 ..      41      81 ..      40      84 .. 0.96
   2 ?   -0.6   0.2       1.1   1.5e+03       9      21 ..     111     123 ..     100     137 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                                   HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   lr+L++  gl+ +ela+  +++++ ++  Lr+Le+ag+v +
  gi|121638768|ref|YP_978992.1| 41 LRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVAR 81
                                   7999**********************************975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                    -HHHHHHHHHHST CS
                         HTH_20   9 hPvRrrilraLar 21 
                                        +r+l+ L+ 
  gi|121638768|ref|YP_978992.1| 111 RAADARVLARLTA 123
                                    4444555555533 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     9e-07    0.0011      22      53 ..      50      81 ..      38      87 .. 0.90
   2 ?   -2.9   0.0       5.4   6.9e+03       6      12 ..     117     123 ..     115     136 .. 0.45

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9e-07
                                   HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                      HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisr 53
                                   l+ +elA++  +t++ ++ +l++L+++g + r
  gi|121638768|ref|YP_978992.1| 50 LSSAELARHASVTPQAMNTVLRKLEDAGAVAR 81
                                   7899************************9975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                                    HHHHHHC CS
                      HTH_Crp_2   6 fLlrlae 12 
                                    +L rl++
  gi|121638768|ref|YP_978992.1| 117 VLARLTA 123
                                    4444422 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0035       1      54 [.      28      81 ..      28      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                           TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                   L+ lGL+  E+ +   L ++  ++  e+a+++ v  +  + vLr+Led+G V r
  gi|121638768|ref|YP_978992.1| 28 LSPLGLTLPEFVCLRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVAR 81
                                   56799***********************************************87 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.7e-05     0.021      19      56 ..      43      80 ..      37      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                   HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                   + +++  +ss+e+a++ ++ p+ +  +l+kL+ ag v 
  gi|121638768|ref|YP_978992.1| 43 MLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVA 80
                                   34444449***************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.019       6      44 ..      41      78 ..      37      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                         HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   l++L ++ g +s++eLA++ +v+ ++    +++Le++g+
  gi|121638768|ref|YP_978992.1| 41 LRMLSQSPG-LSSAELARHASVTPQAMNTVLRKLEDAGA 78
                                   678855555.**************************994 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.9e-05     0.037       8      45 ..      41      79 ..      40      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                                   HHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  8 LklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                   L++L++++ l++ ela++  +++ +    L+kL++aG V
  gi|121638768|ref|YP_978992.1| 41 LRMLSQSPgLSSAELARHASVTPQAMNTVLRKLEDAGAV 79
                                   799*********************************966 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.097       4      72 ..      39     106 ..      37     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                         HTH_34   4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkky 72 
                                      l +L++    + +el    ++t  ++ + l+kLe+ag + +  +++++ +    ++T  Gr+ +k+ 
  gi|121638768|ref|YP_978992.1|  39 VCLRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVARPASVSSG-RSLPATLTARGRALAKRA 106
                                    5678899999999999********************************99.88999*******988875 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.17      15      50 ..      48      81 ..      45      85 .. 0.94
   2 ?   -1.6   0.1       2.6   3.3e+03      26      26 ..     118     118 ..      98     136 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                   --EEHHHHHHHCSSSS-HCCHHHHHHHHHHTTSEEE CS
                    SelB-wing_2 15 pGmskeeLrsrlaprlpaklfqallealvargilav 50
                                   pG+s +eL + +   + + +++ +l +l+++g++a+
  gi|121638768|ref|YP_978992.1| 48 PGLSSAELARHA--SVTPQAMNTVLRKLEDAGAVAR 81
                                   9***********..6******************996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                                    C CS
                    SelB-wing_2  26 l 26 
                                    l
  gi|121638768|ref|YP_978992.1| 118 L 118
                                    1 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.14      23      76 ..      54     106 ..      38     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                    HHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                           HxlR  23 elkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                    el+r+  +++ + + + Lr+Le  g + r +  + +     +lt++Gr+l++  
  gi|121638768|ref|YP_978992.1|  54 ELARHA-SVTPQAMNTVLRKLEDAGAVARPASVSSGRSLPATLTARGRALAKRA 106
                                    666666.788899999*********************************98755 PP

>> OxoDH_E1alpha_N  2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.032        41      27      39 ..      15      27 ..      12      29 .. 0.86
   2 ?    6.0   0.1     0.008        10      24      35 ..      72      83 ..      71      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                OxoDH_E1alpha_N 27 eAGavrRPdvdva 39
                                   + Gav RP+v++a
  gi|121638768|ref|YP_978992.1| 15 RVGAVLRPEVSAA 27
                                   78********986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.008
                OxoDH_E1alpha_N 24 eipeAGavrRPd 35
                                   ++++AGav+RP+
  gi|121638768|ref|YP_978992.1| 72 KLEDAGAVARPA 83
                                   5789*******7 PP

>> A_thal_3526  Plant protein 1589 of unknown function (A_thal_3526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.38      21      42 ..      54      75 ..      52      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                    A_thal_3526 21 aLeeqanIepeftslVWkkLek 42
                                    L+++a+++p+  ++V++kLe 
  gi|121638768|ref|YP_978992.1| 54 ELARHASVTPQAMNTVLRKLED 75
                                   699*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1126.84
//
Query:       gi|121638769|ref|YP_978993.1|  [L=473]
Description: amidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.2e-112  374.4   0.0   9.3e-112  374.2   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.2   0.0  5.2e-116  9.3e-112       1     451 []      33     451 ..      33     451 .. 0.97

  Alignments for each domain:
  == domain 1  score: 374.2 bits;  conditional E-value: 5.2e-116
                                    HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS CS
                        Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaek 80 
                                    ++vea ++r+eavn++lnal++++++ a+ +Aa  + ++a      ++ GvP+++KDn+dv+g+p+++G++a+e y a  
  gi|121638769|ref|YP_978993.1|  33 DVVEAAIARAEAVNPALNALAYAAFDVARDAAAMGTGQEA------FFSGVPTFIKDNVDVAGQPSMHGTDAWEPYAAVA 106
                                    69************************************98......********************************** PP

                                    --HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHH CS
                        Amidase  81 DatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPA 160
                                    D+++++++  +G v lgkT+++ef++++ +e++ +gp+rNPw++++t+G+SS+Gs+A+vAag+vp+a+++D+GGSiRiPA
  gi|121638769|ref|YP_978993.1| 107 DSEITRVVLGTGLVSLGKTQLSEFGFSAVAEHPRLGPVRNPWNTDYTAGASSSGSGALVAAGVVPIAHANDGGGSIRIPA 186
                                    ******************************************************************************** PP

                                    HHCTSEEEE--TTSC--TTB-.-SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-E CS
                        Amidase 161 sfcglvGlKPtygrvSragvv.alessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglr 239
                                    +++glvGlKP++gr++ ++ + +l+ ++  +G+l+r+v+d+a+++r++ + +++  ++++   +++d+++++k++   lr
  gi|121638769|ref|YP_978993.1| 187 ACNGLVGLKPSRGRLPLEPEYrRLPVGIVANGVLTRTVRDTAAFYREAERLWRN--HQLP---PVGDVTSPVKQR---LR 258
                                    *********************99**************************88866..7777...469******999...** PP

                                    EEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE.-CCGGGHHH.HHHHHHHHHHHHHTTT-SSSSS---SS-SCC CS
                        Amidase 240 iGvvkedgvasldpevqravekalkaLeeaGhevveve.lpsleeals.lyylilvaeassnlarylgvryerlsetkvl 317
                                    i+vv+     +++pev+++++k++  Lee+Gh+v++v+ +p+++++++ +++++ +++ +++ +                
  gi|121638769|ref|YP_978993.1| 259 IAVVTRSVLREASPEVRQLTLKLAGLLEELGHRVEHVDhPPAPASFVDdFVLYWGFLALAQVRS---------------G 323
                                    *************************************989999999999999999999998855...............8 PP

                                    CCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHC CS
                        Amidase 318 sellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktid 397
                                    ++++ ++ + + ++e++  + +++ ++ ++     +  a ++ r+lrr+ +++f ++Dvll+Pt++ ++p+ g+  +t d
  gi|121638769|ref|YP_978993.1| 324 RRTFGRTFDPTRLDELTLGLARHTGRNLHR-----LPLAIMRLRMLRRRSVRFFGTYDVLLTPTVAEATPQVGYLAPT-D 397
                                    9***************************99.....8***************************************987.8 PP

                                    SHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                        Amidase 398 sytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                    ++tvl +l  ++ ++ ++n++g pa+s+p+++s+dg+PvG+++ +++++e+ lL
  gi|121638769|ref|YP_978993.1| 398 YQTVLDRLSSWVVFTPVQNVTGVPAISLPLAQSADGMPVGMMLSADTGREALLL 451
                                    **************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.35
# Mc/sec: 4020.22
//
Query:       gi|121638770|ref|YP_978994.1|  [L=271]
Description: elongation factor Ts [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-63  212.1   0.2    8.4e-63  211.7   0.2    1.1  1  EF_TS           Elongation factor TS
  ------ inclusion threshold ------
       0.23   10.2   0.0       0.32    9.8   0.0    1.1  1  Glyco_hydro_71  Glycosyl hydrolase family 71


Domain annotation for each model (and alignments):
>> EF_TS  Elongation factor TS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   0.2   9.4e-67   8.4e-63       1     208 []      67     270 ..      67     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 9.4e-67
                          EF_TS   1 avivevnsETDFVAknekFqelvkkvaeaaleekakdleellalkledetveealkekiakigEkielrrfakleaekev 80 
                                    ++++e+n+ETDFVAkn++Fq+l+++v++aa+++k++d+++l+ ++++d+tve+a++e+ akigEk+elrr+a +++   +
  gi|121638770|ref|YP_978994.1|  67 GALIELNCETDFVAKNAEFQTLADQVVAAAAAAKPADVDALKGASIGDKTVEQAIAELSAKIGEKLELRRVAIFDG---T 143
                                    689************************************************************************9...8 PP

                          EF_TS  81 vasYiHgn.....grigvlvalegksdealkelakqiAmhiaAmnPqylsedevdaevlekekeilkeqakeegkpekii 155
                                    v++Y+H++       +gvlv+++g+++    ++a+ +A++iaA + +yls+d+v+++++++e++i++e+a++egkpe+ +
  gi|121638770|ref|YP_978994.1| 144 VEAYLHRRsadlpPAVGVLVEYRGDDA----AAAHAVALQIAALRARYLSRDDVPEDIVASERRIAEETARAEGKPEQAL 219
                                    8*******999999**********988....8************************************************ PP

                          EF_TS 156 ekiveGrlekflkevcLleQeyvkddkktVeqvlkeaskelkvvkfvrfevGe 208
                                     kiveGrl+ f+k+ +LleQ+ v d+kktV+++l+ a+    v++fvrfevG+
  gi|121638770|ref|YP_978994.1| 220 PKIVEGRLNGFFKDAVLLEQASVSDNKKTVKALLDVAGV--MVTRFVRFEVGQ 270
                                    ************************************999..**********95 PP

>> Glyco_hydro_71  Glycosyl hydrolase family 71
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   3.5e-05      0.32     280     357 ..      55     130 ..      43     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.5e-05
                 Glyco_hydro_71 280 aitedklvlwyRphpkkakcssgdttgnpanaelleDkvfvvallkspatvtvsvggkesetfsvkaGvnklsvpfng 357
                                      t + lv+       + +c ++d ++++a++++l D+v+++a +++pa+v    g +  ++ +v++ + +ls+++ +
  gi|121638770|ref|YP_978994.1|  55 RATAEGLVAAKDGALIELNC-ETDFVAKNAEFQTLADQVVAAAAAAKPADVDALKGASIGDK-TVEQAIAELSAKIGE 130
                                    5666777777777778899*.7799**************************99988777744.778888888887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2179.07
//
Query:       gi|121638771|ref|YP_978995.1|  [L=287]
Description: 30S ribosomal protein S2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-96  322.3   0.0    1.2e-96  322.1   0.0    1.0  1  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
      0.025   14.9   0.0       0.87    9.9   0.0    2.4  2  PucR          Purine catabolism regulatory protein-like famil


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.1   0.0  1.3e-100   1.2e-96       1     215 []       9     224 ..       9     224 .. 1.00

  Alignments for each domain:
  == domain 1  score: 322.1 bits;  conditional E-value: 1.3e-100
                   Ribosomal_S2   1 LLeagvhfGhqtrrwnpkmkpyIygerngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakran 80 
                                    LL++g+hfGhqtrrwnpkmk++I++ rngi+iidl++tl+ +++ay++vke++a+gg++lfvgtkkqa+e v+++a+r++
  gi|121638771|ref|YP_978995.1|   9 LLDSGTHFGHQTRRWNPKMKRFIFTDRNGIYIIDLQQTLTFIDKAYEFVKETVAHGGSVLFVGTKKQAQESVAAEATRVG 88 
                                    89****************************************************************************** PP

                   Ribosomal_S2  81 gyyvnerWlgGtLTNfktikksikklkeleeleedgeld.ltkkealklkkekekleknlggikkmkklPdlvvvldpkk 159
                                    ++yvn+rWlgG+LTNf+t++k++++lkele++e++g ++  tkke l l++ek+kle++lggi++m+k+P++++v+d++k
  gi|121638771|ref|YP_978995.1|  89 MPYVNQRWLGGMLTNFSTVHKRLQRLKELEAMEQTGGFEgRTKKEILGLTREKNKLERSLGGIRDMAKVPSAIWVVDTNK 168
                                    **************************************99**************************************** PP

                   Ribosomal_S2 160 ekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaieeg 215
                                    e+iav Ea+klgipviai+Dtn+dpd+vdypIp+Ndd+irs  l+++v+a+a++eg
  gi|121638771|ref|YP_978995.1| 169 EHIAVGEARKLGIPVIAILDTNCDPDEVDYPIPGNDDAIRSAALLTRVIASAVAEG 224
                                    *****************************************************998 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.7e-05      0.87      57     102 ..      51      96 ..      33     113 .. 0.85
   2 ?    2.5   0.0     0.018   1.6e+02      63     100 ..     151     186 ..     134     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.7e-05
                           PucR  57 ealaelvrelaeagvaaLviklgreipeelieaadelglPlielpe 102
                                    ++  e+v+e +++g + L+++++++ +e++ + a + g+P +  ++
  gi|121638771|ref|YP_978995.1|  51 DKAYEFVKETVAHGGSVLFVGTKKQAQESVAAEATRVGMPYVNQRW 96 
                                    56789*****************99****************887666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.018
                           PucR  63 vrelaeagvaaLviklgreipeelieaadelglPliel 100
                                    +r++a+   a  v+ ++   +  ++  a++lg+P+i++
  gi|121638771|ref|YP_978995.1| 151 IRDMAKVPSAIWVVDTN--KEHIAVGEARKLGIPVIAI 186
                                    78888888888888884..46678999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2137.49
//
Query:       gi|121638772|ref|YP_978996.1|  [L=249]
Description: hypothetical protein BCG_2912 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-12   45.5   0.0    1.1e-11   44.8   0.0    1.4  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   6.1e-16   1.1e-11       2      88 ..      65     151 ..      64     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.1e-16
                                    EESSEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEEEEB..STSSCS CS
                  Peptidase_M23   2 fhkGidiaapkgtpVlAaadGtVvfagkkegyGnvviidhgdgystlyahlskisvkegqkVkaGqvIGtvg..stgrst 79 
                                     h+G+d+a  +g+pV+Aa + tVvfag   +   vv + h +g+ t y  + + +v++gq V+a +vIG       g+++
  gi|121638772|ref|YP_978996.1|  65 GHRGVDLAGRPGQPVYAAGSATVVFAGLL-AGRPVVSLAHPGGLRTSYEPVVA-QVRVGQPVSAPTVIGALAagHPGCQA 142
                                    69**************************7.7799****************988.8**************87632677899 PP

                                    SSEEEEEEE CS
                  Peptidase_M23  80 gphLhfeir 88 
                                    + +Lh+  +
  gi|121638772|ref|YP_978996.1| 143 AACLHWGAM 151
                                    *****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1892.08
//
Query:       gi|121638773|ref|YP_978997.1|  [L=408]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-63  213.8  28.7    1.3e-63  213.8  28.7    2.0  2  PPE       PPE family
    2.5e-17   63.6   7.4    2.5e-17   63.6   7.4    5.6  5  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.8  28.7   1.5e-67   1.3e-63       1     157 [.       5     161 ..       5     162 .. 0.98
   2 ?   -2.4   0.4       0.5   4.5e+03      94     117 ..     185     208 ..     168     217 .. 0.54

  Alignments for each domain:
  == domain 1  score: 213.8 bits;  conditional E-value: 1.5e-67
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns ++yaGpgsgp++aAaaaWd+Laael  aa  ++  ++el+++ W Gp++a+m+aa++py+aWLsa+a qae
  gi|121638773|ref|YP_978997.1|   5 VLPPEINSGRMYAGPGSGPMMAAAAAWDSLAAELGLAAGGYRLAISELTGAYWAGPAAASMVAAVTPYVAWLSATAGQAE 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +a++qa+aaaaaYe A+a++vpp++++anra l+alvatnffGqntpaIaatea+y+emwaqdaaam+aY+ ++a a
  gi|121638773|ref|YP_978997.1|  85 QAGMQARAAAAAYELAFAMTVPPPVVVANRALLVALVATNFFGQNTPAIAATEAQYAEMWAQDAAAMYAYAGSAAIA 161
                                    ***********************************************************************999866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.5
                                    HHHHHHS--HHHHHHHHHHHHHHH CS
                            PPE  94 eaAlaamvppaeiaanraelaalv 117
                                     +   +++p+a+ aa  + l++l 
  gi|121638773|ref|YP_978997.1| 185 ATVSSTVPPLATTAAVPQLLQQLS 208
                                    233444555555555555555555 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.0      0.24   2.1e+03      34      54 ..      20      42 ..       7      52 .. 0.62
   2 ?   -2.9  11.3       1.5   1.4e+04      19      62 ..      57      98 ..      53     116 .. 0.57
   3 ?   -6.9  12.9         2   1.8e+04      19      58 ..     144     185 ..     127     209 .. 0.45
   4 ?    0.7   1.4      0.11     1e+03      44      70 ..     258     291 ..     252     308 .. 0.68
   5 !   63.6   7.4   2.7e-21   2.5e-17       1      80 []     325     404 ..     325     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                       PE_PPE_C 34 sgttaaaaaaaagaalg..gmPl 54
                                   ++ +++aaaaa++++++  g+++
  gi|121638773|ref|YP_978997.1| 20 GSGPMMAAAAAWDSLAAelGLAA 42
                                   44455666666666665444444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                       PE_PPE_C 19 WaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagagga 62
                                   Wa++a+a + aa +   ++ +a+a++a++a  gm ++aa+a+ +
  gi|121638773|ref|YP_978997.1| 57 WAGPAAASMVAAVTPYVAWLSATAGQAEQA--GMQARAAAAAYE 98
                                   877776555555554444444555555555..555555554443 PP

  == domain 3  score: -6.9 bits;  conditional E-value: 2
                       PE_PPE_C  19 Waaaapaasaaaaal.sgttaaaaaaaagaalg.gmPlaaag 58 
                                    Wa+ a+a+ a a ++  +t+ ++ +aa+ +  + +++++aa+
  gi|121638773|ref|YP_978997.1| 144 WAQDAAAMYAYAGSAaIATELTPFTAAPVTTSPaALAGQAAA 185
                                    444444444422222122222222222222221122222222 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.11
                       PE_PPE_C  44 aagaalggmPlaaagagga.......aggaapry 70 
                                     a++a++g+P++a  +g++       + +a+pr 
  gi|121638773|ref|YP_978997.1| 258 LAQQAIPGTPGGAGDSGSSvldswgpTIFAGPRA 291
                                    5667777888877777666666666655555554 PP

  == domain 5  score: 63.6 bits;  conditional E-value: 2.7e-21
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalg.gmPlaaagaggaaggaaprygfrptvmpr 79 
                                    sA+lG++++ G+LSVPp Waa a  a++aa  l+g  ++a  ++a++al  g P+a+ag++++ gg +++ygfr  vm+r
  gi|121638773|ref|YP_978997.1| 325 SAALGKGSSAGSLSVPPDWAARARWANPAAWRLPGDDVTALRGTAENALLrGFPMASAGQSTG-GGFVHKYGFRLAVMQR 403
                                    8*********************************************99989************.**************** PP

                       PE_PPE_C  80 p 80 
                                    p
  gi|121638773|ref|YP_978997.1| 404 P 404
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2912.73
//
Query:       gi|121638774|ref|YP_978998.1|  [L=325]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-37  129.9  18.9    6.8e-37  127.6  14.6    2.8  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.0   0.1    0.0064   1.2e+02      58      75 ..       2      19 ..       1      24 [. 0.85
   2 !  127.6  14.6   3.8e-41   6.8e-37      24     248 ..      27     264 ..      19     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.0064
                 Bac_luciferase 58 llaalaaaTerirlgtav 75
                                   + a  a +T+r+r+g a+
  gi|121638774|ref|YP_978998.1|  2 TVASTAHHTRRLRFGLAA 19
                                   67899**********987 PP

  == domain 2  score: 127.6 bits;  conditional E-value: 3.8e-41
                 Bac_luciferase  24 ylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfgl 103
                                    +++++a+a+E++Gfd + +++h+ ++    ++f+ ++a+a+aT+r+  gt v++   rhP+ +A++aa +  l++GRf+l
  gi|121638774|ref|YP_978998.1|  27 QMRAFAQAVEAAGFDVLAFPDHLVPS---VSPFAGATAAAMATQRLHTGTLVLNNDFRHPVDTAREAAGVATLAEGRFEL 103
                                    7899*******************986...9************************************************** PP

                 Bac_luciferase 104 glgtggpaveerrfGv...dhderyarlrEfvevlrrlwrgeevdfeGeffsv.kgalllprpgqgpiPvyvaaaspagl 179
                                    glg+g++ +e+++ G+   + ++r+arl E  +++r+l+  e+vdf+G++++v ++a +l  p++ ++P++v++ + + l
  gi|121638774|ref|YP_978998.1| 104 GLGAGHRRSEYDAAGItfdSGATRVARLIESAHLIRALLDAEPVDFDGQHYRVhAEAGSLVAPPKVRVPLLVGGNGTEVL 183
                                    ****************8888889****************99999**********66666666655559************ PP

                 Bac_luciferase 180 elaarhadglllag..eppeeaaelierlra.gaae........agrdpa..dirvgisltvivadteeeAraearalia 246
                                    +l +r+ad++ lag    +++ + ++ +++a g a         ag + +  ++  +i++ v+ +d +++A + a a + 
  gi|121638774|ref|YP_978998.1| 184 RLGGRIADIVGLAGisHNRDATQVRFTHFDAdGLADriavvrhaAGDRFEaiELNALIQAVVCTNDRNAAAAELA-ATLG 262
                                    ***************988889999999998853333577776666666664455556666666666666666665.4442 PP

                 Bac_luciferase 247 gl 248
                                    g+
  gi|121638774|ref|YP_978998.1| 263 GI 264
                                    32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2091.40
//
Query:       gi|121638775|ref|YP_978999.1|  [L=298]
Description: site-specific tyrosine recombinase XerC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-49  166.0   0.0    9.2e-49  165.5   0.0    1.2  1  Phage_integrase  Phage integrase family
      1e-21   77.0   2.7    1.7e-21   76.3   1.0    2.2  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
       0.09   13.3   0.0       0.19   12.2   0.0    1.5  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
       0.22   11.9   0.0        3.4    8.0   0.0    2.0  1  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.0   2.1e-52   9.2e-49       2     170 ..     109     283 ..     108     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.1e-52
                                    HHHHHHHHHHHHCCGC......HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHH CS
                Phage_integrase   2 vltedeverllaalee......slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplsee 75 
                                    vl++d++ r +aa+e+      +l++rd+l++elly+tG+R+sEl++L+v+d+d+ ++ ++v    gKg+k+r+vp+++ 
  gi|121638775|ref|YP_978999.1| 109 VLRQDQALRAMAAAESgaeqgdPLALRDRLIVELLYATGIRVSELCGLDVDDIDTGHRLVRV---LGKGNKQRTVPFGQP 185
                                    799***********************************************************...*************** PP

                                    HHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHH CS
                Phage_integrase  76 alellkellska...leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvq 152
                                    a+ +l+ +l +    l++ae+ ++l++ +rg++l  +++r+a++++v + +  +++ pH lRhs+at+Lle g+dlrvvq
  gi|121638775|ref|YP_978999.1| 186 AADALHAWLVDGrraLVTAESGHALLLGARGRRLDVRQARTAVHQTVAAVDGAPDMGPHGLRHSAATHLLEGGADLRVVQ 265
                                    *********999999***************************************************************** PP

                                    HHHT-SSCCHHHHHHCCC CS
                Phage_integrase 153 kllGHssisttqiYthva 170
                                    +llGHss++ttq Ythva
  gi|121638775|ref|YP_978999.1| 266 ELLGHSSLATTQLYTHVA 283
                                    ****************97 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   1.0   3.9e-25   1.7e-21       1      84 []       5      87 ..       5      87 .. 0.99
   2 ?   -3.1   0.0       2.2   9.9e+03      72      80 ..     186     194 ..     155     209 .. 0.57
   3 ?   -1.5   0.0      0.71   3.2e+03      25      57 ..     260     291 ..     258     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.9e-25
                                   HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHH CS
                Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvr 82
                                   l++f eyL +++g+s +T+raY+ dLr+++ fla+ +++sl++lt + +r++la+++ +g ++t+larr+sa+++F +++vr
  gi|121638775|ref|YP_978999.1|  5 LDEFDEYLALQCGRSVHTRRAYLGDLRSLFAFLAD-RGSSLDALTLSVLRSWLAATAGAGAARTTLARRTSAVKAFTAWAVR 85
                                   799********************************.********************************************** PP

                                   TT CS
                Phage_int_SAM_1 83 eg 84
                                   +g
  gi|121638775|ref|YP_978999.1| 86 RG 87
                                   97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                                    HHHHHHHHH CS
                Phage_int_SAM_1  72 alrsFfqfl 80 
                                    a  +++++l
  gi|121638775|ref|YP_978999.1| 186 AADALHAWL 194
                                    333333333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHH.TS--TTT--HHHHHHHHHS-- CS
                Phage_int_SAM_1  25 dLrrflkflaergkesleqlttedvraflaele 57 
                                    dLr +++ l +    + +ql t+  +a l++ +
  gi|121638775|ref|YP_978999.1| 260 DLRVVQELLGH-SSLATTQLYTHVAVARLRAVH 291
                                    78888888888.777777777777666666555 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.3e-05      0.19       1      82 [.       4      87 ..       4      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                Phage_int_SAM_4  1 Llerfrealrl.aglserTiksYlsaikrflrflkkk..apeeltkedieaYlnyLanerklsastqknalnalsffykkvl 79
                                   +l++f+e+l l  g s  T+++Yl  ++ + +fl  +  + + lt   +++ l+  a    ++ +t  +  +a ++f  +++
  gi|121638775|ref|YP_978999.1|  4 ILDEFDEYLALqCGRSVHTRRAYLGDLRSLFAFLADRgsSLDALTLSVLRSWLAATA-GAGAARTTLARRTSAVKAFTAWAV 84
                                   589999***88789********************74455999999999999999999.777899999999**********99 PP

                Phage_int_SAM_4 80 ere 82
                                   +r 
  gi|121638775|ref|YP_978999.1| 85 RRG 87
                                   886 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00077       3.4      19      93 ..      20      93 ..       8      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00077
                                   HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHH..HHTS---HHHHHHHHHHHHHHHHHHHHTTS--S-H CS
                Phage_int_SAM_5 19 kgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYL..kkkkglsentiskyfkklkavlnkAikegilkknp 93
                                     t r y   l++l  Fl +   +++ ++ + l   + +L  + + g +++t ++  +  ka+   A+++g+l  +p
  gi|121638775|ref|YP_978999.1| 20 VHTRRAYLGDLRSLFAFLADRGSSLDALTLSVL---RSWLaaTAGAGAARTTLARRTSAVKAFTAWAVRRGLLAGDP 93
                                   566677777777788888555566666665555...5688766888***************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2113.17
//
Query:       gi|121638776|ref|YP_979000.1|  [L=283]
Description: mycobactin utilization protein viuB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-35  121.8   0.5    3.3e-35  121.2   0.5    1.3  1  SIP            Siderophore-interacting protein
    3.3e-35  120.9   1.1    1.4e-34  118.9   0.0    2.3  3  FAD_binding_9  Siderophore-interacting FAD-binding domain


Domain annotation for each model (and alignments):
>> SIP  Siderophore-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.5   3.7e-39   3.3e-35       1     119 []     134     262 ..     134     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 3.7e-39
                            SIP   1 adwvllagDeTAlPAiaaiLeelpadaqvravievpdaadelelsapaaveltwlvrega........aaagelLaealr 72 
                                    adw+llagDe+A+PAiaa Le+lp+da +ra+iev+ ++de+ l+ap+ave++w++r+g+        a +++ L+ea++
  gi|121638776|ref|YP_979000.1| 134 ADWHLLAGDESAIPAIAAALEALPPDAIGRAFIEVAGPDDEIGLTAPDAVEVNWVYRGGRadlvpedrAGDHAPLIEAVT 213
                                    79****************************************************************99999********* PP

                            SIP  73 elelpagelyvwvagEaavv.kalRrhlvkergldrk.qvaamgYWrrg 119
                                    ++++ +g+++v+++gEa++v ++lR ++++erg+d k + +++gYWrrg
  gi|121638776|ref|YP_979000.1| 214 TTAWLPGQVHVFIHGEAQAVmHNLRPYVRNERGVDAKwASSISGYWRRG 262
                                    *****************987699************996789******97 PP

>> FAD_binding_9  Siderophore-interacting FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   1.6e-38   1.4e-34       1     120 [.      10     127 ..      10     128 .. 0.96
   2 ?   -0.2   0.0      0.13   1.1e+03     104     119 ..     167     182 ..     159     184 .. 0.82
   3 ?   -2.4   0.0      0.57   5.1e+03      94     104 ..     243     253 ..     221     256 .. 0.63

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.6e-38
                  FAD_binding_9   1 qvvrverlspslrrvtltgeelagfk.sdgtDqhikLllpepgqtepelppelteeglqeweelpederpvmRtYtvral 79 
                                    +vv++++l+p+++rv+l+g+++++f  sd+tD++ikL++++++ +  +lp++lt ++   +++lp+++rp++Rt+tvr++
  gi|121638776|ref|YP_979000.1|  10 EVVATRHLAPHMVRVVLGGSGFDTFVpSDFTDSYIKLVFVDDDVDVGRLPRPLTLDS---FADLPTAKRPPVRTMTVRHV 86 
                                    5999********************98799*************************999...5679**************** PP

                  FAD_binding_9  80 daeaeeldidfvlHgdegpaarwAaqAqpGdelaivgPgga 120
                                    da+a+e+++d+vlHg++g+a++wAa Aq G+ + ++gPgga
  gi|121638776|ref|YP_979000.1|  87 DAAAREIAVDIVLHGEHGVAGPWAAGAQRGQPIYLMGPGGA 127
                                    ***************************************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                  FAD_binding_9 104 aqAqpGdelaivgPgg 119
                                    + A p+de+++++P++
  gi|121638776|ref|YP_979000.1| 167 EVAGPDDEIGLTAPDA 182
                                    66899*********86 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.57
                  FAD_binding_9  94 gdegpaarwAa 104
                                    +++g+ a+wA+
  gi|121638776|ref|YP_979000.1| 243 NERGVDAKWAS 253
                                    34488888987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2281.28
//
Query:       gi|121638777|ref|YP_979001.1|  [L=389]
Description: hypothetical protein BCG_2917c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-70  235.6   0.5    4.9e-70  235.0   0.5    1.3  1  DNA_processg_A  DNA recombination-mediator protein A
    1.4e-06   28.4   2.7    5.8e-06   26.3   2.7    2.1  1  DprA_WH         DprA winged helix domain
     0.0033   17.0   6.3      0.034   13.7   6.3    2.3  1  LDcluster4      SLOG cluster4 family
     0.0047   16.8   0.0      0.012   15.5   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.093   12.5   0.0       0.22   11.3   0.0    1.6  1  cpYpsA          Circularly permutated YpsA SLOG family
       0.23   11.4   1.0       0.38   10.7   0.2    1.7  2  DUF1979         Domain of unknown function (DUF1979)
        2.8    8.0  11.1        1.6    8.7   2.4    3.5  3  YAcAr           YspA, cpYpsA-related SLOG family


Domain annotation for each model (and alignments):
>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.0   0.5   1.9e-73   4.9e-70       4     209 ..      70     287 ..      67     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.0 bits;  conditional E-value: 1.9e-73
                 DNA_processg_A   4 kagiklltledkeYPeklkei...........kdpPlvLfvkG..nlellekravaiVGtRkaseygkevakklakelae 70 
                                    ++g +l+t++d+e+P +  ++            ++PlvL++ G  +l+ +  ra+a+VGtR+a++yg++va++la+ lae
  gi|121638777|ref|YP_979001.1|  70 RRGGRLITPDDDEWPVLAFAAfsgagararpcGHSPLVLWALGpaRLDEVAPRAAAVVGTRAATAYGEHVAADLAAGLAE 149
                                    56789***********999987888888877779*********77777888***************************** PP

                 DNA_processg_A  71 agitivSGlAlGiDaaahraaleaggktvavlgtgldkiyPkenrklleeiaeegglllseyppgtkpkkenFpeRnrii 150
                                    +++++vSG+A+GiD aahraal+++g tvavl++g+d+ yP+ +++ll++ia ++g+l++eyppg +p++++F++Rnr++
  gi|121638777|ref|YP_979001.1| 150 RDVAVVSGGAYGIDGAAHRAALDSEGITVAVLAGGFDIPYPAGHSALLHRIA-QHGVLFTEYPPGVRPARHRFLTRNRLV 228
                                    ***************************************************9.66************************* PP

                 DNA_processg_A 151 aglseavlvveaaekSGalitaelAlelgrevfavpgditskesagtnklikegaklvt 209
                                    a++++a +vvea+ +SGa +ta +A++lgr v avpg++ts++sag+++l+++ga+lvt
  gi|121638777|ref|YP_979001.1| 229 AAVARAAVVVEAGLRSGAANTAAWARALGRVVAAVPGPVTSSASAGCHTLLRHGAELVT 287
                                    ********************************************************997 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   2.7   2.3e-09   5.8e-06       3      60 ..     309     367 ..     306     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.3e-09
                        DprA_WH   3 appaepplddlerrvLaaL.gpePvhvDqLvrrtglpaaevsaaLleLELaGlverlpG 60 
                                    + +a+  l++ er+v +aL g  + ++D+++  +gl +a+v+  L  LE aGl e + G
  gi|121638777|ref|YP_979001.1| 309 PGAALDVLSEAERQVYEALpGRGAATIDEIAVGSGLLPAQVLGPLAILEVAGLAECRDG 367
                                    45777889***********999********************************99887 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   6.3   1.3e-05     0.034       5      65 ..     125     183 ..     122     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                     LDcluster4   5 gVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpa 65 
                                    +V+G  +  a+   ++ a +l+  +A++++ +++Gg  G+  aa ++a + +G+tv +l +
  gi|121638777|ref|YP_979001.1| 125 AVVGTRA--ATAYGEHVAADLAAGLAERDVAVVSGGAYGIDGAAHRAALDSEGITVAVLAG 183
                                    6888777..55555789***************************************99876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.7e-06     0.012       6      62 ..     316     372 ..     315     375 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                                    HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                           TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                    Lse E +vY aL  +g at+deia  +g+  ++v   L  Le +Gl e ++gr ++ 
  gi|121638777|ref|YP_979001.1| 316 LSEAERQVYEALPGRGAATIDEIAVGSGLLPAQVLGPLAILEVAGLAECRDGRWRIL 372
                                    89*********************************************9999886655 PP

>> cpYpsA  Circularly permutated YpsA SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.6e-05      0.22       1      97 [.     154     264 ..     154     283 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                                    EE----TTHHHHHHHHHHHTT.....--EE-E...E-GG......G--TTSS--TTS.--EE-SS--HHHHHHHHHHTSS CS
                         cpYpsA   1 ivsGGQtGvDraaLdaAlaag.....ievgGw...vPkg......rlaedGsiperY.plretessdyaeRtekNvrdsd 65 
                                    +vsGG  G+D aa +aAl+ +     +  gG+    P+g      r+a  G++ ++Y p     +++  +R +     + 
  gi|121638777|ref|YP_979001.1| 154 VVSGGAYGIDGAAHRAALDSEgitvaVLAGGFdipYPAGhsallhRIAQHGVLFTEYpPGVRPARHRFLTRNRLVAAVAR 233
                                    79****************99999999555665433355522222267777777777854444555666777777777777 PP

                                    EEEEEESSS--HHHHHHHHHHHHTT--EEEEE CS
                         cpYpsA  66 gtliltlgklsgGteltvelarelkkpllvvd 97 
                                    + ++ ++  l+ G++ t++ ar l + + +v 
  gi|121638777|ref|YP_979001.1| 234 AAVV-VEAGLRSGAANTAAWARALGRVVAAVP 264
                                    7666.456688999999999999999887775 PP

>> DUF1979  Domain of unknown function (DUF1979)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00015      0.38      15      40 ..      38      63 ..      33      65 .. 0.93
   2 ?   -3.8   0.0       4.8   1.2e+04      34      42 ..     161     169 ..     158     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                        DUF1979 15 nvrfGqdGvDLsefkmtsrGieraae 40
                                    vr Gq G +L++     rGi+raa+
  gi|121638777|ref|YP_979001.1| 38 RVRRGQVGNELAQHTGARRGIDRAAD 63
                                   59**********************96 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.8
                        DUF1979  34 Gieraaers 42 
                                    Gi+ aa r+
  gi|121638777|ref|YP_979001.1| 161 GIDGAAHRA 169
                                    999999985 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.054   1.4e+02      36      48 ..      51      64 ..      37      65 .. 0.84
   2 ?    8.7   2.4   0.00064       1.6       8      57 ..     132     178 ..     124     182 .. 0.80
   3 ?   -0.1   0.2      0.36   9.1e+02      33      54 ..     236     257 ..     217     280 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.054
                          YAcAr 36 hGga.kGaDrlAar 48
                                   h+ga +G+Dr A++
  gi|121638777|ref|YP_979001.1| 51 HTGArRGIDRAADD 64
                                   88999*****9986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00064
                          YAcAr   8 grdfadleliwatLdklhaeapidmvlvhGgakGaDrlAarWA.aergvel 57 
                                      +++++  + a L + +ae    +++v+Gga G+D  A r A +++g+++
  gi|121638777|ref|YP_979001.1| 132 ATAYGEH--VAADLAAGLAERD--VAVVSGGAYGIDGAAHRAAlDSEGITV 178
                                    4567777..9999999999995..9****************9966777766 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.36
                          YAcAr  33 vlvhGga.kGaDrlAarWAaerg 54 
                                    v+v+ g  +Ga    a+WA++ g
  gi|121638777|ref|YP_979001.1| 236 VVVEAGLrSGAAN-TAAWARALG 257
                                    3444444344444.334555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2962.63
//
Query:       gi|121638778|ref|YP_979002.1|  [L=503]
Description: hypothetical protein BCG_2918c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-84  282.1   0.0    2.8e-84  281.6   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.7e-38  131.1   0.0    2.8e-38  130.5   0.0    1.3  1  ChlI             Subunit ChlI of Mg-chelatase
    2.8e-23   82.4   0.2    5.8e-23   81.3   0.2    1.6  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
      4e-10   39.6   0.0    6.7e-10   38.8   0.0    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    4.5e-09   36.4   0.0    0.00089   19.3   0.1    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-07   31.6   0.0     0.0011   18.7   0.0    2.6  3  Sigma54_activat  Sigma-54 interaction domain
    1.1e-05   24.7   0.0     0.0011   18.1   0.0    2.2  2  MCM              MCM P-loop domain
    1.2e-05   25.2   0.0     0.0084   15.9   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.6e-05   24.5   0.0     0.0011   19.3   0.0    2.3  2  AAA_22           AAA domain
    4.3e-05   24.0   0.0    0.00023   21.6   0.0    2.2  1  AAA              ATPase family associated with various cellul
     0.0006   19.6   0.0     0.0011   18.8   0.0    1.4  1  AAA_30           AAA domain
     0.0011   19.4   0.2     0.0039   17.6   0.2    2.2  1  AAA_16           AAA ATPase domain
     0.0082   16.7   0.0      0.015   15.8   0.0    1.5  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.059   13.3   0.0    1.7  1  NACHT            NACHT domain
      0.026   14.1   0.0      0.041   13.4   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.049   13.5   0.0      0.088   12.7   0.0    1.4  1  NTPase_1         NTPase
       0.11   12.2   0.0       0.17   11.6   0.0    1.2  1  AAA_24           AAA domain
       0.11   12.7   0.0       0.36   11.0   0.0    1.9  1  AAA_33           AAA domain
       0.21   11.7   0.0        2.4    8.3   0.0    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.6   0.0     3e-87   2.8e-84       1     204 [.     190     393 ..     190     396 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.6 bits;  conditional E-value: 3e-87
                   Mg_chelatase   1 dlkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfr 79 
                                    dl+dv+Gq++a+ a+e+aaaG H+l+l+GppG GKtmla+rlp+llp+ls +e+lev++i+svag  + ++ l++r+pf+
  gi|121638778|ref|YP_979002.1| 190 DLADVVGQSQARFAVEVAAAGAHHLMLTGPPGVGKTMLAQRLPGLLPSLSGSESLEVTAIHSVAGlLSGDTPLITRPPFV 269
                                    89***************************************************************8889999******** PP

                   Mg_chelatase  80 aphhsaskaalvGggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    aphhs+s aalvGggs  ++pG++s+ah+GvLfLDE++e++ ++le+LR+Pledge++++r +  + +parfqlv+a+Np
  gi|121638778|ref|YP_979002.1| 270 APHHSSSVAALVGGGSgMARPGAVSRAHRGVLFLDECAEISLSALEALRTPLEDGEIRLARRDGVACYPARFQLVLAANP 349
                                    ****************99************************************************************** PP

                   Mg_chelatase 159 cpcgklkdkekectcsekeierYlsklsgplldRidlqvevkklea 204
                                    cpc+ ++   ++c c++++++rYl klsgplldR+dl+v++++l+a
  gi|121638778|ref|YP_979002.1| 350 CPCAPAD--PQDCICAAATKRRYLGKLSGPLLDRVDLRVQMHRLRA 393
                                    ***9876..789*****************************99875 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.0   2.9e-41   2.8e-38       1     121 []      21     143 ..      21     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 2.9e-41
                           ChlI   1 vevdvskglpkftivGlpdtavkeskervrsalknsgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieae. 79 
                                    +e+d+++glp++++vGlpd+a +es++rvr+a++n+g ++p  ++t+ L+Pa l+k Gs +D+++A ++l+a+++++ e 
  gi|121638778|ref|YP_979002.1|  21 IEADITSGLPGVHLVGLPDAALQESRDRVRAAVTNCGNSWPMARLTLALSPATLPKMGSVYDIALAAAVLSAQQKKPWEr 100
                                    89************************************************************************999987 PP

                           ChlI  80 .eetlflGeLsldGslrpvkgvlpialaakkegikkvivpken 121
                                     e+tl+lGeLsldG++rpv+gvlp++laak++g   v+vp++n
  gi|121638778|ref|YP_979002.1| 101 lENTLLLGELSLDGRVRPVRGVLPAVLAAKRDGWPAVVVPADN 143
                                    89**************************************998 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   6.2e-26   5.8e-23       1      93 []     401     497 ..     401     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 6.2e-26
                 Mg_chelatase_C   1 gesSaevrerVaaAreiqkeRfake....naelsgeelrevceldeeaeelleeaierlglsaRaydrilkvArTiADLe 76 
                                    ges+++vr+rVa Are++++R++ +    nae+sg  lr+ ++++++a+  l++a++r+ ls R++dr+l+vA+++ADL+
  gi|121638778|ref|YP_979002.1| 401 GESTSQVRQRVALAREAAAQRWRPHgfrtNAEVSGPLLRRKFRPSSAAMLPLRTALDRGLLSIRGVDRTLRVAWSLADLA 480
                                    699*******************6658999*************************************************** PP

                 Mg_chelatase_C  77 gseeieeehlaeAlqyR 93 
                                    g+++++ +++a Al++R
  gi|121638778|ref|YP_979002.1| 481 GRTSPGIDEVAAALSFR 497
                                    ***************99 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   7.1e-13   6.7e-10      28     175 ..       4     146 ..       1     156 [. 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.1e-13
                                    SEEEEEEEETTEEEEEEEEEEEESS-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GG CS
                          Lon_C  28 GvvtGlawtevGGdlltieavllpgkgklkltGklgdvmkesaqaalsyvrsraeelgidkevfekkdihihvPeGavPk 107
                                    G +  +a   + G+++ iea +++g   ++l G     ++es       vr+ ++++g +   +  +++ + +   ++Pk
  gi|121638778|ref|YP_979002.1|   4 GRAFSVAVRGLDGEIVEIEADITSGLPGVHLVGLPDAALQESRD----RVRAAVTNCGNS---WPMARLTLALSPATLPK 76 
                                    667778888899*********************99999999876....577777777766...5566889999999**** PP

                                    GGGGGHHHHHHHHHHHHTS--B-T..TBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGG CS
                          Lon_C 108 dGPsaGvtlatalvslltgkkvrk..dvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekd 175
                                     G    ++la+a++s+ ++k+ ++  +  + Ge++L Grv p+ G+   +laakr g   v++P +n  +
  gi|121638778|ref|YP_979002.1|  77 MGSVYDIALAAAVLSAQQKKPWERleNTLLLGELSLDGRVRPVRGVLPAVLAAKRDGWPAVVVPADNLPE 146
                                    *******************998743378899***********************************9765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   9.4e-07   0.00089       1      24 [.     213     241 ..     213     252 .. 0.78
   2 !   14.6   0.0   2.7e-05     0.025      66     124 ..     298     351 ..     275     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-07
                                    EEEEE--SSSSHHHHHHHGGGGB.....S CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.....n 24 
                                    +++L GppG+gK++la+rl  +l      
  gi|121638778|ref|YP_979002.1| 213 HLMLTGPPGVGKTMLAQRLPGLLpslsgS 241
                                    79*****************9998666643 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.7e-05
                                    -SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                          AAA_5  66 geilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                      +l+lDE  +++ ++l++L ++le+ +++l+ ++++   ++      f+++ +anp +
  gi|121638778|ref|YP_979002.1| 298 RGVLFLDECAEISLSALEALRTPLEDGEIRLARRDGVACYPAR-----FQLVLAANPCP 351
                                    469***************************9999999866664.....********987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       9.9   9.4e+03     118     151 ..      70     103 ..      64     109 .. 0.74
   2 !   10.0   0.0   0.00057      0.53      14      42 ..     203     231 ..     194     245 .. 0.84
   3 !   18.7   0.0   1.2e-06    0.0011      81     123 ..     285     327 ..     281     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.9
                                    HHSEEESBTSSSEEE--EEEEEEESS-HHHHHHT CS
                Sigma54_activat 118 qegevervGsskeikvdvriiaatnedleeavee 151
                                       ++ ++Gs   i +   +++a ++++ e +e+
  gi|121638778|ref|YP_979002.1|  70 SPATLPKMGSVYDIALAAAVLSAQQKKPWERLEN 103
                                    5566778888888888888888888888777766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00057
                                    HHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellarai 42 
                                     ++ +a+   ++++tG  G+GK++la+ +
  gi|121638778|ref|YP_979002.1| 203 AVEVAAAGAHHLMLTGPPGVGKTMLAQRL 231
                                    45667777899***************976 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.2e-06
                                    TSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE CS
                Sigma54_activat  81 AekekkGlfekadgGtlfLDeigelplelQekLlrvlqegeve 123
                                    +  ++ G++++a+ G+lfLDe +e++l++ e L + l++ge++
  gi|121638778|ref|YP_979002.1| 285 SGMARPGAVSRAHRGVLFLDECAEISLSALEALRTPLEDGEIR 327
                                    556789********************************99986 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.018        17      41      80 ..     195     234 ..     175     251 .. 0.81
   2 !   18.1   0.0   1.2e-06    0.0011     112     174 ..     288     350 ..     278     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                    H---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHH CS
                            MCM  41 fggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekl 80 
                                    +g ++ +   ++   g  +++l g pg++K+ l +++  l
  gi|121638778|ref|YP_979002.1| 195 VGQSQARFAVEVAAAGAHHLMLTGPPGVGKTMLAQRLPGL 234
                                    555566666677889999*************998877655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.2e-06
                                    EEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                            MCM 112 leaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                       Ga+  a++Gv+ +De  +++ +  +al   +E+ +i +a+   va+ +ar  ++ Aanp 
  gi|121638778|ref|YP_979002.1| 288 ARPGAVSRAHRGVLFLDECAEISLSALEALRTPLEDGEIRLARRDGVACYPARFQLVLAANPC 350
                                    578***************************************98889**************96 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     9e-06    0.0084       6      51 ..     191     229 ..     187     237 .. 0.76
   2 ?    5.8   0.0     0.011        10      84     130 ..     297     343 ..     292     388 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                         RuvB_N   6 leeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlak 51 
                                    l++ +gq++ +  ++++ +          h++l+GpPG+Gkt la+
  gi|121638778|ref|YP_979002.1| 191 LADVVGQSQARFAVEVAAAG-------AHHLMLTGPPGVGKTMLAQ 229
                                    67778887766555554333.......469**************97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                         RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGpsarsikldl 130
                                    ++ vlf+de   +s ++ e l + +ed ++ +   +G ++   +++l
  gi|121638778|ref|YP_979002.1| 297 HRGVLFLDECAEISLSALEALRTPLEDGEIRLARRDGVACYPARFQL 343
                                    5789*************************999999988877766665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06    0.0011       4      30 ..     210     236 ..     207     276 .. 0.86
   2 ?    2.7   0.0      0.15   1.4e+02      87     117 ..     294     322 ..     286     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqld 30 
                                    +a +l++tG++G+GKT+l++rl   l+
  gi|121638778|ref|YP_979002.1| 210 GAHHLMLTGPPGVGKTMLAQRLPGLLP 236
                                    57899****************976665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                         AAA_22  87 raravielliiDEaqhlrseealeeLrslln 117
                                    +++++ ++l +DE   + s  ale Lr+ l+
  gi|121638778|ref|YP_979002.1| 294 SRAHR-GVLFLDECAEI-SLSALEALRTPLE 322
                                    44445.9**********.******9998666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.5e-07   0.00023       1     130 [.     214     388 ..     214     390 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-07
                                    EEEESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSSS.........................STTHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel....gvefleisgsellsk.........................yvgesekkirelfk 51 
                                    ++l+GppG+GKT+la+ +   l    g+e le+ +   +                           +vg ++        
  gi|121638778|ref|YP_979002.1| 214 LMLTGPPGVGKTMLAQRLPGLLpslsGSESLEVTAIHSVAGllsgdtplitrppfvaphhsssvaaLVGGGSGM------ 287
                                    589**************999975555455444444444422555677888888876665333222233333333...... PP

                                    HHHHTS...TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS............................ CS
                            AAA  52 eakeka...kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkk............................ 99 
                                     a+  a   ++  +lf+DE  ++  s            +++L t l++ + +                            
  gi|121638778|ref|YP_979002.1| 288 -ARPGAvsrAHrGVLFLDECAEISLSA-----------LEALRTPLEDGEIRlarrdgvacyparfqlvlaanpcpcapa 355
                                    .333335553339**********9999...........999999999999999999999999999999999999999999 PP

                                    .SSTEEEEEEESS..GGGSTHHHHSTTSSEEEET CS
                            AAA 100 .eskvivigatnr..pdkldpallrgRfdrkiei 130
                                      +++i+ +at+r    kl+ +ll +R+d ++++
  gi|121638778|ref|YP_979002.1| 356 dPQDCICAAATKRryLGKLSGPLL-DRVDLRVQM 388
                                    966799999999999999999999.999988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0011       4     115 ..     197     324 ..     194     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                         AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgi..........east 72 
                                    ++Qa+ + ++++ g+   +ltGp+G GKt++ + l  ++ +  g + + ++  + +A  L+ ++ +          ++s+
  gi|121638778|ref|YP_979002.1| 197 QSQARFAVEVAAAGAHHLMLTGPPGVGKTMLAQRLPGLLPSLsGSESLEVTAIHSVAGLLSGDTPLitrppfvaphHSSS 276
                                    689999*******************************9999989888888888889999998777555555566668999 PP

                         AAA_30  73 iakllkrlk.....grarlepgtllivDEagmvdtkqlaallkaaeka 115
                                    +a l+         g+++ +++ +l  DE + ++ + l+al + +e+ 
  gi|121638778|ref|YP_979002.1| 277 VAALVGGGSgmarpGAVSRAHRGVLFLDECAEISLSALEALRTPLEDG 324
                                    999986666999986677777899999999999999999998877774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   4.1e-06    0.0039      13      45 ..     201     232 ..     196     421 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-06
                         AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrell 45 
                                    + a+e +++g  + ++l+G++GvGK+ l+++l+
  gi|121638778|ref|YP_979002.1| 201 RFAVEVAAAGA-HHLMLTGPPGVGKTMLAQRLP 232
                                    66777677776.899**************9998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.015       2      43 ..     215     261 ..     214     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                         AAA_18   2 lltGtpGvGKttlakeLskrl.gf....gvnlrdvakenglllevdp 43 
                                    +ltG+pGvGKt la++L  +l  +    + +++ +++  gll +++p
  gi|121638778|ref|YP_979002.1| 215 MLTGPPGVGKTMLAQRLPGLLpSLsgseSLEVTAIHSVAGLLSGDTP 261
                                    69***************555533355566677777777777766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-05     0.059       3      20 ..     214     231 ..     212     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                                    EEEEC-TTTCHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                    ++l+G++G+GKT+L+q+l
  gi|121638778|ref|YP_979002.1| 214 LMLTGPPGVGKTMLAQRL 231
                                    689*************98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.041      22      53 ..     200     231 ..     192     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                          AAA_7  22 ysyllelllknkkpvllvGptGtGKtviikdl 53 
                                     ++ +e   +  ++++l+Gp G+GKt+++++l
  gi|121638778|ref|YP_979002.1| 200 ARFAVEVAAAGAHHLMLTGPPGVGKTMLAQRL 231
                                    567888889999****************9986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.3e-05     0.088       1      23 [.     213     235 ..     213     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-05
                                    EEEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   1 kvfiTGppGvGKtTlvkkvlell 23 
                                    ++++TGppGvGKt l +++  ll
  gi|121638778|ref|YP_979002.1| 213 HLMLTGPPGVGKTMLAQRLPGLL 235
                                    789************99986655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.17       5      24 ..     214     232 ..     211     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                         AAA_24   5 iliyGpsgiGKTtlakelgp 24 
                                    ++++Gp+g+GKT+la +l p
  gi|121638778|ref|YP_979002.1| 214 LMLTGPPGVGKTMLAQRL-P 232
                                    799*************99.4 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00038      0.36       3      20 ..     215     232 ..     214     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                         AAA_33   3 llvGlpGsGKstlaerll 20 
                                    +l G+pG+GK+ la+rl 
  gi|121638778|ref|YP_979002.1| 215 MLTGPPGVGKTMLAQRLP 232
                                    899************985 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0025       2.4       6      77 ..     214     306 ..     211     318 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                                    EEEE--TTSSHHHHHHHHHHHTT-.......................-EEEEEGGG---...........----THHHHH CS
                          AAA_2   6 illlgptgvGktelakalaellfv...................kkekkliradaselle...........eeevehlvsr 55 
                                    ++l+gp gvGkt+la+ l  ll                     +                          +   +++v+ 
  gi|121638778|ref|YP_979002.1| 214 LMLTGPPGVGKTMLAQRLPGLLPSlsgseslevtaihsvagllS--------------GdtplitrppfvAPHHSSSVAA 279
                                    67899999999999999988887666555555555544444432..............0222222244442233444444 PP

                                    HHH.....HTTT-HHHHTTSEEEEETG CS
                          AAA_2  56 lig.....appgyvgaeegGivllDEi 77 
                                    l+g     a+pg v+++ +G+++lDE 
  gi|121638778|ref|YP_979002.1| 280 LVGggsgmARPGAVSRAHRGVLFLDEC 306
                                    433222236788888888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3105.90
//
Query:       gi|121638779|ref|YP_979003.1|  [L=128]
Description: hypothetical protein BCG_2919c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-28   98.5   0.2    2.3e-28   98.2   0.2    1.1  1  UPF0102   Uncharacterised protein family UPF0102
     0.0056   16.6   0.0     0.0068   16.3   0.0    1.1  1  SfsA      Sugar fermentation stimulation protein RE domain
  ------ inclusion threshold ------
      0.022   15.2   0.0      0.033   14.6   0.0    1.4  1  DUF234    Archaea bacterial proteins of unknown function
       0.13   12.3   0.0       0.18   11.8   0.0    1.1  1  Mrr_cat   Restriction endonuclease
       0.15   11.4   0.0       0.16   11.3   0.0    1.1  1  NucS      Endonuclease NucS


Domain annotation for each model (and alignments):
>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.2   6.5e-32   2.3e-28       1      79 []      16     108 ..      16     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 6.5e-32
                                    HHHHHHHHHHHTT-EEEEEEEEETTEEEEEEE....TTEEEEEEEEE-......-------HHHHHHHHHHHHHHH.... CS
                        UPF0102   1 gEelaaeyLekkgyeilernwrcragEiDiia....tevlvfvEVKtRssekfgspaeavtprKqrrlrraaeayl.... 72 
                                    gE+la++yL++ g++il+rnwrcr+gE+D+ia    t+++vfvEVKtR+ + +g  a+avt+rK rrlrr+a ++l    
  gi|121638779|ref|YP_979003.1|  16 GEALAVDYLTSMGLRILNRNWRCRYGELDVIAcdaaTRTVVFVEVKTRTGDGYGGLAHAVTERKVRRLRRLAGLWLadqe 95 
                                    7***********************************999***************************************** PP

                                    ......EEEEEEE CS
                        UPF0102  73 ......rfDvvav 79 
                                          r+Dv+ v
  gi|121638779|ref|YP_979003.1|  96 erwaavRIDVIGV 108
                                    ***********87 PP

>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-06    0.0068      18      83 ..      26      90 ..      10     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                                   ......EEES-EETTEE-SEEEE-S..SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHH CS
                           SfsA 18 lagyeeikrevkygnsriDfllekee.eekcyvEVKsvtleeggialfPdapteRgqkhleeLaelv 83
                                    +g++ + r+ ++    +D+   + + ++ ++vEVK+ t    g++    a+teR ++ l+ La l 
  gi|121638779|ref|YP_979003.1| 26 SMGLRILNRNWRCRYGELDVIACDAAtRTVVFVEVKTRTGD--GYGGLAHAVTERKVRRLRRLAGLW 90
                                   3567778888888888899874443359999*****99988..699999**************9875 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.3e-06     0.033      61      91 ..      33      64 ..      16      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                         DUF234 61 GrwWk.keeeiDivaldeeekkalfgEvKwkn 91
                                    r W+ +  e+D++a d ++++++f+EvK ++
  gi|121638779|ref|YP_979003.1| 33 NRNWRcRYGELDVIACDAATRTVVFVEVKTRT 64
                                   566763677********************876 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.18      10      72 ..      17      86 ..      13      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T........S-B-HHHHHHHHHH CS
                        Mrr_cat 10 eklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk........nkvgvkeVqeliga 72
                                   e+l+ ++l ++G + ++++ r + g  D+ia  ++  +  ++v++K ++        ++v +++V++l+  
  gi|121638779|ref|YP_979003.1| 17 EALAVDYLTSMGLRILNRNWRCRYGELDVIACDAA-TRTVVFVEVKTRTgdgygglaHAVTERKVRRLRRL 86
                                   789999********889999999*******97654.6689********55677777789999999999875 PP

>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.5e-05      0.16     120     161 ..      24      66 ..       8      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                           NucS 120 LieeGfkpvareyavaiGivdiLgkdeegk.lvivelkrrkae 161
                                    L   G + ++r++    G +d+++ d   + +v ve+k r ++
  gi|121638779|ref|YP_979003.1|  24 LTSMGLRILNRNWRCRYGELDVIACDAATRtVVFVEVKTRTGD 66 
                                    667899****************9999877615679*****886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 828.72
//
Query:       gi|121638780|ref|YP_979004.1|  [L=276]
Description: formate dehydrogenase accessory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-81  273.2   0.1    2.3e-81  273.0   0.1    1.0  1  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.0   0.1   1.3e-85   2.3e-81       1     236 [.      26     275 ..      26     276 .] 0.93

  Alignments for each domain:
  == domain 1  score: 273.0 bits;  conditional E-value: 1.3e-85
                                    E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEE.............EE-S....... CS
                      FdhD-NarQ   1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeas.............vavatra.kae 66 
                                    ++Eepl+i+vng++++++m+tp+++ el+ Gfll+eg+++++ed+  ++++ ++ +             va+a+++ ++ 
  gi|121638780|ref|YP_979004.1|  26 AVEEPLEIRVNGTPVTVTMRTPGSDFELVQGFLLAEGVVAHREDVLTVSYCGRRVEgnatgastynvldVALAPGVkPPD 105
                                    58*************************************************776667777888888888*******5555 PP

                                    ...---------------.---...--H------..-----EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEE CS
                      FdhD-NarQ  67 dkeerrtakrvvtsgCglcgkesleelletlelp..esdlklsaeallrlmdalrekqelfketggvHaaalfdadgell 144
                                     +  +rt+  ++ts+Cg+cgk+sl+++ + ++++  +++++++a++l +++d+lr++q++f++tgg+Haaalf  dg +l
  gi|121638780|ref|YP_979004.1| 106 VD-VTRTF--YTTSSCGVCGKASLQAVSQVSRFApgGDPATVAADTLKAMPDQLRRAQKVFARTGGLHAAALFGVDGAML 182
                                    45.68999..**************88866666656799****************************************** PP

                                    EEEEESSHHHHHHHHHHHHHT..TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEE CS
                      FdhD-NarQ 145 avreDvGRHnAlDkviGaall.egldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvr 223
                                    avreD+GRHnA+DkviG+a+  +++ l +++l+vsgR+s+e+ qKa++agipvl++vsap+slav lA+++g+tlv+f+r
  gi|121638780|ref|YP_979004.1| 183 AVREDIGRHNAVDKVIGWAFErDRIPLGASVLLVSGRASFELTQKALMAGIPVLAAVSAPSSLAVSLADASGITLVAFLR 262
                                    *******************9748889****************************************************** PP

                                    TTEEEEEE-GGGE CS
                      FdhD-NarQ 224 gkrfnvYtgaeRi 236
                                    g+++nvYt a+Ri
  gi|121638780|ref|YP_979004.1| 263 GDSMNVYTRADRI 275
                                    ************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1870.94
//
Query:       gi|121638781|ref|YP_979005.1|  [L=779]
Description: formate dehydrogenase H fdhF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-26   93.2   0.0    2.2e-26   92.8   0.0    1.2  1  Molybdopterin    Molybdopterin oxidoreductase
    1.5e-08   34.6   0.3      6e-08   32.7   0.0    2.2  3  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   2.5e-30   2.2e-26       1     292 [.     132     432 ..     132     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 2.5e-30
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    Rl +Pmv   + g++ ++++sWd A++lia++l+       pdr + f++++ +s+e+ + ++ l++ +g +nl   ++ 
  gi|121638781|ref|YP_979005.1| 132 RLAHPMVL--RPGDDHYRPISWDAAYQLIAEQLNG---LDSPDRAV-FYTSGRTSNEAAFCYQLLVRSFGTNNLPDCSNM 205
                                    99****97..699**********************...55565655.88899999****************999888888 PP

                                    GGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-H....... CS
                  Molybdopterin  81 adlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryae....... 153
                                    ++ + ++a     +ds      s +++d+e++dli++ G N+ +++p + + + k a+ ++ak+i++ p  ++       
  gi|121638781|ref|YP_979005.1| 206 CHESSGAA----LTDSIGIGKGSVTIGDVEHADLIVIAGQNPGTNHPRMLSVLGK-AKANGAKIIAVNPLPEAglirfkd 280
                                    88888877....6666777778999***********************9555555.55556********99889999999 PP

                                    ..........CGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCC......TCHHHHHHEECHHHCCCCCCCEECCSHHHHH CS
                  Molybdopterin 154 ..........llkfadewlaikpgtdaalalamghvilqelkv......dkeflrkytygkeetdmpllvtleeetgkkk 217
                                                  ade + i+ g d al++++g  +l+          d +f+++++ g++ ++  +l++  + +   +
  gi|121638781|ref|YP_979005.1| 281 pqkvngvvghGIPIADEFVQIRLGGDMALFAGLGRLLLEAEERvpgsvvDRSFVDNHCAGFDGYRRRTLQVGLDTVMDAT 360
                                    ********995678**********************9998765566666**********************999999999 PP

                                    HCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHH CS
                  Molybdopterin 218 evvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekv 292
                                    ++  ++ +++a+ + + +    i + +gl+++++  a++  v n++ll g++g+pg+g+  ++G  +++g   ++
  gi|121638781|ref|YP_979005.1| 361 GIELAQLQRVAAMLMASQR-TVICWAMGLTQHAHAVATIGEVTNVLLLRGMIGKPGAGVCPVRGHSNVQG--DRT 432
                                    9999999999998888777.8******************************************9666666..333 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.99   8.9e+03      11      45 ..       7      39 ..       5      45 .. 0.80
   2 ?   -2.7   0.0      0.64   5.7e+03      67      96 ..     468     497 ..     453     507 .. 0.68
   3 !   32.7   0.0   6.6e-12     6e-08       1      57 [.     660     717 ..     660     771 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.99
                                   BSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT-- CS
                Molydop_binding 11 qlhsqtrtrpvlrlakpepevveinpedAaalGik 45
                                   +++ ++++r+vl++++++   v + p++ +a G++
  gi|121638781|ref|YP_979005.1|  7 RWQRSAASRDVLADYDEQ--AVTVAPRKREAAGVR 39
                                   677888888888888866..699999998888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.64
                                    SSB-TTEEEEESSHCC.....S-GHCTS-- CS
                Molydop_binding  67 ervrpGvvfmpfgwweagekggnaNaltdd 96 
                                     ++r G v + +g + ++ ++++  a+t +
  gi|121638781|ref|YP_979005.1| 468 RAMRDGRVSVFMGMGGNFASATPDTAVTEA 497
                                    458999999999998866666666666655 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 6.6e-12
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTE CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrG 57 
                                    l+L t rs+dq++++++  ++++++ +++  vv inp+d ++ G++ Gd+V + s++ 
  gi|121638781|ref|YP_979005.1| 660 LVLQTLRSHDQYNTTIYGLDDRYRGVKGGrRVVFINPADIETFGLTAGDRVDLVSEWT 717
                                    7899*************************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5211.14
//
Query:       gi|121638782|ref|YP_979006.1|  [L=101]
Description: hypothetical protein BCG_2922c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-52  174.8   4.2      5e-52  174.6   4.2    1.0  1  DUF2469   Protein of unknown function (DUF2469)


Domain annotation for each model (and alignments):
>> DUF2469  Protein of unknown function (DUF2469)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   4.2   2.8e-56     5e-52       1     100 []       1     100 [.       1     100 [. 0.99

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 2.8e-56
                        DUF2469   1 msaedlekyetevelalyreyrdvvslfkyvveterrfylanevdlkvrseegevyfevkledawvwdvyrsarfvkkvr 80 
                                    msaedlekyete+el+lyrey+d+v++f+yvveterrfylan+v++ +r+++gevyfe++l+dawvwd+yr+arfvk+vr
  gi|121638782|ref|YP_979006.1|   1 MSAEDLEKYETEMELSLYREYKDIVGQFSYVVETERRFYLANSVEMVPRNTDGEVYFELRLADAWVWDMYRPARFVKQVR 80 
                                    9******************************************************************************* PP

                        DUF2469  81 vltfkdvnveelekeelelp 100
                                    v+tfkdvn+ee+ek el+lp
  gi|121638782|ref|YP_979006.1|  81 VVTFKDVNIEEVEKPELRLP 100
                                    *****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 769.24
//
Query:       gi|121638783|ref|YP_979007.1|  [L=264]
Description: ribonuclease HII [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-47  162.5   0.0    1.2e-47  162.3   0.0    1.1  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3   0.0   6.9e-52   1.2e-47       1     198 []      36     215 ..      36     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 6.9e-52
                                    EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-HHHH CS
                      RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinlnei 80 
                                    +G+DE+GrG+++Gplvvaa+++ + r++  + ++++DSKkLs+q+re+L++li+     r++va+++++ +++e++++++
  gi|121638783|ref|YP_979007.1|  36 AGVDEVGRGACAGPLVVAACVLGPGRIA--SLAALDDSKKLSEQAREKLFPLIC-----RYAVAYHVVFIPSAEVDRRGV 108
                                    6**************************5..78899*******************.....********************* PP

                                    HHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHH.HHHHHHHHH CS
                      RNase_HII  81 kaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverd.eelellkrk 159
                                    ++a+++ ++++++ l+v++ ++l dg++ p  l+++   +i+        +d++++++aaAS++Akv+rd +++ l +++
  gi|121638783|ref|YP_979007.1| 109 HVANIEGMRRAVAGLAVRPGYVLSDGFRVPG-LPMPSLPVIG--------GDAAAACIAAASVLAKVSRDrVMVALDADH 179
                                    *******************************.**********........****************************** PP

                                    CS.H.--TTSSTTSHHHHHHHHHHHHHS--TTB-TTSHHH CS
                      RNase_HII 160 pg.tldkgsGyasdektrallkkgatsklpdivrlsfktv 198
                                    pg ++++++Gy++ +++ral++ g+++    ++r+sf +v
  gi|121638783|ref|YP_979007.1| 180 PGyGFAEHKGYSTPAHSRALARLGPCP----QHRYSFINV 215
                                    ***************************....******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1933.31
//
Query:       gi|121638784|ref|YP_979008.1|  [L=294]
Description: signal peptidase I lepB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-13   49.3   0.0    3.9e-08   33.1   0.0    2.5  2  Peptidase_S24  Peptidase S24-like
    7.9e-06   25.7   0.0    2.2e-05   24.3   0.0    1.9  1  Peptidase_S26  Signal peptidase, peptidase S26


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   4.3e-12   3.9e-08       2      39 ..      92     138 ..      91     154 .. 0.87
   2 !   13.5   0.0   5.7e-06     0.051      33      59 ..     164     189 ..     160     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.3e-12
                                    XXSSTTCCTXX.....TTXEEEEECTS....---TTSEEEEEETTCE CS
                  Peptidase_S24   2 vpGdSMeptll.....dGdlilVdkfs....epkrGdivvfrlpgee 39 
                                    +p++SMeptl+      Gd+i+Vdk s    +p++Gd++vfr p+ +
  gi|121638784|ref|YP_979008.1|  92 IPSESMEPTLHgcstcVGDRIMVDKLSyrfgSPQPGDVIVFRGPPSW 138
                                    8********97555558*******9999999************9987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.7e-06
                                    EEETTCE-EEEEEEEEETTEEEEE.SS CS
                  Peptidase_S24  33 frlpgeeeayiKrviglpgdrvllasn 59 
                                    f  p+e+ +++Krvi  +g++v+++s+
  gi|121638784|ref|YP_979008.1| 164 FVPPDEN-DLVKRVIAVGGQTVQCRSD 189
                                    6667777.***************9987 PP

>> Peptidase_S26  Signal peptidase, peptidase S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.4e-09   2.2e-05      44     123 ..     163     251 ..     119     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.4e-09
                  Peptidase_S26  44 gylprgv.pllKrVlalagqev.cvadgavtidgvavsea......lerDrkgrplpslq.gcrvlaegelfllskevad 114
                                    g++p++   l+KrV+a+ gq+v c++d+++t++g ++ e+      + +D +  p    + g  ++++g +++++++  +
  gi|121638784|ref|YP_979008.1| 163 GFVPPDEnDLVKRVIAVGGQTVqCRSDTGLTVNGRPLKEPyldpatMMADPSIYPCLGSEfGPVTVPPGRVWVMGDNRTH 242
                                    455444348*************778999******6655541111113445444444333336789*************** PP

                  Peptidase_S26 115 SfDsRYfGp 123
                                    S DsR   p
  gi|121638784|ref|YP_979008.1| 243 SADSRAHCP 251
                                    *****7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2056.83
//
Query:       gi|121638785|ref|YP_979009.1|  [L=113]
Description: 50S ribosomal protein L19 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-50  169.1   1.1    2.7e-50  169.0   1.1    1.0  1  Ribosomal_L19  Ribosomal protein L19


Domain annotation for each model (and alignments):
>> Ribosomal_L19  Ribosomal protein L19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   1.1   1.5e-54   2.7e-50       5     111 .]       6     112 ..       2     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 1.5e-54
                  Ribosomal_L19   5 eiekeqlkkdlpefkvGdtvkVkvkikegkkeRiqafeGvviarkgkgisetftvRkisegvgvervfplhspkiekiev 84 
                                     ++k +l++d+p+f++Gdt++V+vk++eg keR+q+f+Gvvi+r+g gi+etftvRk s+gvgver+fp+hsp+i++iev
  gi|121638785|ref|YP_979009.1|   6 FVDKPSLRDDIPAFNPGDTINVHVKVIEGAKERLQVFKGVVIRRQGGGIRETFTVRKESYGVGVERTFPVHSPNIDHIEV 85 
                                    5788899************************************************************************* PP

                  Ribosomal_L19  85 vrrgkvrrakLyYLrelkgkaarikek 111
                                    v+rg+vrrakLyYLrel+gk+a+ikek
  gi|121638785|ref|YP_979009.1|  86 VTRGDVRRAKLYYLRELRGKKAKIKEK 112
                                    *************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 800.91
//
Query:       gi|121638786|ref|YP_979010.1|  [L=314]
Description: alanine rich lipoprotein lppW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2386.94
//
Query:       gi|121638787|ref|YP_979011.1|  [L=230]
Description: tRNA (guanine-N(1)-)-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-70  235.1   0.0      6e-70  234.9   0.0    1.0  1  tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.029   14.3   0.0    1.6  1  Rrp40_N      Exosome complex exonuclease Rrp40 N-terminal dom


Domain annotation for each model (and alignments):
>> tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.9   0.0   6.7e-74     6e-70       2     195 .]      22     224 ..      21     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 6.7e-74
                                    GGSHHHHHHHHHHHHHHHHHHHHCSSCEEEEEEETSSHHHHHHHHHHHCCGHHCGG-TTEEEESSCGGHHHHCCCHHHCG CS
                    tRNA_m1G_MT   2 kkasekelvslevqllrdytanrrntvddelygggagmvlkaepelealesvntekwkvilltptGkkftqelaeeLsek 81 
                                    +ka+e++lv+l+v++lr++t++ +++vdd +yggg+gmv+ka  ++eal++++  ++ +i++tp G  ftq++a++++++
  gi|121638787|ref|YP_979011.1|  22 GKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTE 101
                                    69**************************************************99************************** PP

                                    GGEEEEETTTSSBECCGGTTSSE.....EEEEESSSSTTCSTTHHHHHHHHHHHHTTTC..EEB-S-CCC......CHCT CS
                    tRNA_m1G_MT  82 eklvylcgdyegvdervdddkvd.....eysIGdfVlkggekgalvlidavkrllaGvl.ntaslpedsfs...nrllek 152
                                    ++lv+ cg+yeg+d+rv++d+++     e+sIGd+Vl gge++a+v+++av rllaGvl n+as+++ds+s   ++lle+
  gi|121638787|ref|YP_979011.1| 102 SHLVFACGRYEGIDQRVVQDAARrmrveEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLgNPASHQDDSHStglDGLLEG 181
                                    *********************999***********************************************999999*** PP

                                    S..CTTSEHHTEHHHHHHHHHCCCTTTHHHHHHHHHHHSCSXS CS
                    tRNA_m1G_MT 153 pnytrpltlrglkVpeiLlsgnhakienWrlkealertvprRk 195
                                    p+ytrp ++rgl+Vpe+Llsg+ha+i++Wr++ +l+rt  rR+
  gi|121638787|ref|YP_979011.1| 182 PSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRP 224
                                    ******************************************7 PP

>> Rrp40_N  Exosome complex exonuclease Rrp40 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.3e-06     0.029      11      44 ..      56     102 ..      56     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-06
                        Rrp40_N  11 GPGL.rhtP..........plst..liatraGiLhtkpkkqalwiEs 44 
                                    GPG   ++P          +++t  +++t aG+L t+ + q++  Es
  gi|121638787|ref|YP_979011.1|  56 GPGMvMKAPvwgealdeicSSETllIVPTPAGVLFTQATAQRWTTES 102
                                    9999899999998777776546699*****************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1692.15
//
Query:       gi|121638788|ref|YP_979012.1|  [L=176]
Description: 16S rRNA-processing protein RimM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   73.7   0.3    1.6e-20   73.1   0.3    1.3  1  RimM             RimM N-terminal domain
      5e-12   45.7   0.1    6.8e-11   42.1   0.2    2.2  2  PRC              PRC-barrel domain
     0.0088   16.2   0.0        3.4    7.9   0.0    2.3  2  Ribosomal_L35Ae  Ribosomal protein L35Ae
  ------ inclusion threshold ------
          1    9.7   5.2         31    4.9   3.6    3.0  2  FLgD_tudor       FlgD Tudor-like domain


Domain annotation for each model (and alignments):
>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.3   3.6e-24   1.6e-20       1      83 [.       4      92 ..       4      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 3.6e-24
                                   EEEEEEEEETTTTEEEEEE-SSSGGGGGGSSSEEEE.......ETTEEEEE-EEEEEEETTEEEEEETT--SHHHHHTTTT- CS
                           RimM  1 evGkIvgahGlkGevkVkpftdfpealfkygrvlle......akkgetreltvesvrvhkkgvivklegvddrdaAealkga 76
                                   +vG++v++hG+ Gev V+  td+p+++f++g+ l +        +g   ++ +esvr h+++++v+l+gv drdaA al+g+
  gi|121638788|ref|YP_979012.1|  4 VVGRVVKSHGVTGEVVVEIRTDDPADRFAPGTRLRAkgpfdgGAEGSAVSYVIESVRQHGGRLLVRLAGVADRDAADALRGS 85
                                   59**********************************9**99955566677******************************** PP

                                   EEEEETT CS
                           RimM 77 elfvprs 83
                                      ++++
  gi|121638788|ref|YP_979012.1| 86 LFVIDAD 92
                                   9999887 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.088     4e+02      45      73 ..      40      69 ..      34      72 .. 0.82
   2 !   42.1   0.2   1.5e-14   6.8e-11       2      78 ..     101     172 ..     100     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.088
                                   TTT.....-EEEEEGG..CEECCCTEEEET CS
                            PRC 45 ggflgigekevliPfd.lavkigkdriivd 73
                                   +g +++g +  ++ ++ + v+ +++r++v+
  gi|121638788|ref|YP_979012.1| 40 KGPFDGGAEGSAVSYViESVRQHGGRLLVR 69
                                   455567899999999999****99999985 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 1.5e-14
                                    EECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.....CEECCCTEEEETTS-G CS
                            PRC   2 defrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfd....lavkigkdriivdapke 77 
                                    d ++ ++l+G+ V t +Ge +G+V++v +++++g+++a++ +         +evl+Pf+      v+++++++ +d+p +
  gi|121638788|ref|YP_979012.1| 101 DTYYDHQLVGLMVQTATGEGVGVVTEV-VHTAAGELLAVKRDS--------DEVLVPFVraivTSVSLDDGIVEIDPPHG 171
                                    789************************.9999**********8........9*************************998 PP

                                    G CS
                            PRC  78 l 78 
                                    l
  gi|121638788|ref|YP_979012.1| 172 L 172
                                    7 PP

>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00077       3.4      59      86 ..       2      29 ..       1      37 [. 0.83
   2 !    6.0   0.0    0.0029        13       5      40 ..      49      84 ..      47      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00077
                                   -EEEEEEEEECTTTTEEEEEETT--SSS CS
                Ribosomal_L35Ae 59 rviwGkvtrahGnsgvvrakFkknLppk 86
                                   + + G+v+++hG +g v ++ +++ p+ 
  gi|121638788|ref|YP_979012.1|  2 ELVVGRVVKSHGVTGEVVVEIRTDDPAD 29
                                   5689*************99888877766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                                   EEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT CS
                Ribosomal_L35Ae  5 avflgykrgkrnqrentaLlkiegvkskeeaefylG 40
                                   +  ++y     +q+  + L+++ gv +++ a+   G
  gi|121638788|ref|YP_979012.1| 49 GSAVSYVIESVRQHGGRLLVRLAGVADRDAADALRG 84
                                   77899999999******************9988776 PP

>> FLgD_tudor  FlgD Tudor-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.084   3.8e+02      27      48 ..      52      72 ..      14      81 .. 0.87
   2 ?    4.9   3.6     0.007        31      18      42 ..     141     164 ..     107     167 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.084
                                   EEEEEEEEEE.ETTEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                     FLgD_tudor 27 vygtVdsVslstggglmLnLgl 48
                                   v+  ++sV+   gg l+++L++
  gi|121638788|ref|YP_979012.1| 52 VSYVIESVRQ-HGGRLLVRLAG 72
                                   7789999999.99999999884 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.007
                                    TEEEEE-EEEEEEEEEEEE.ETTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     FLgD_tudor  18 GtsvaattlvygtVdsVslstgggl 42 
                                    ++ + + + v++ V+sVsl ++g +
  gi|121638788|ref|YP_979012.1| 141 DSDEVLVPFVRAIVTSVSL-DDGIV 164
                                    5566677899*********.99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1305.00
//
Query:       gi|121638789|ref|YP_979013.1|  [L=80]
Description: hypothetical protein BCG_2929c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-20   71.4   0.2    4.8e-20   71.2   0.2    1.1  1  KH_4      KH domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.022   14.6   0.0    1.5  1  KH_1      KH domain
       0.11   12.4   0.3       0.15   11.9   0.3    1.5  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.2     8e-24   4.8e-20       2      62 ..       7      67 ..       6      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 8e-24
                           KH_4  2 elvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaaa 62
                                   ++ve++++++vd+p++v+v++ ++++++++e++v+++dlG+vIG+ Grt++Al++lv ++ 
  gi|121638789|ref|YP_979013.1|  7 DAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALRTLVAGIG 67
                                   689******************************************************9876 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-06     0.022       1      26 [.      35      60 ..      35      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                                   EEEEEEGGGHHHHHHTGGGHHHHHHH CS
                           KH_1  1 tlrilvPsslvgriIGkgGsnIkeIr 26
                                   t++++v+ +  g++IG+gG++   +r
  gi|121638789|ref|YP_979013.1| 35 TVEVHVHPDDLGKVIGRGGRTATALR 60
                                   6899****************976666 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.5e-05      0.15      24      54 ..      32      63 ..       8      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                   S.CEEEEEEEESCHHHHHTGGGHHHHHHHHHH CS
                           KH_2 24 a.nrviiviresqpgivIGkgGsnikkigkel 54
                                   + + v++ ++    g vIG+gG++  ++++ +
  gi|121638789|ref|YP_979013.1| 32 RgRTVEVHVHPDDLGKVIGRGGRTATALRTLV 63
                                   33789999***************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 641.55
//
Query:       gi|121638790|ref|YP_979014.1|  [L=162]
Description: 30S ribosomal protein S16 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-22   78.0   0.2    6.5e-22   77.4   0.2    1.3  1  Ribosomal_S16  Ribosomal protein S16
  ------ inclusion threshold ------
        1.9    9.0   7.4        2.6    8.5   5.4    2.2  2  DUF5476        Family of unknown function (DUF5476)


Domain annotation for each model (and alignments):
>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.2   7.3e-26   6.5e-22       1      62 []       9      67 ..       9      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7.3e-26
                                   EESCTTCEEEEEEEEETTSSTTSSESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTTEEEE CS
                  Ribosomal_S16  1 RfGrknrPfYrivvadsrkprdgrpiEklGtYdPlakkkekkevelneerikyWlgvGAqpt 62
                                   R G+ ++P Yr+ vad+r++rdgr iE++G Y+P +   e++ +e+n er++yWl+vGAqpt
  gi|121638790|ref|YP_979014.1|  9 RLGKIRNPQYRVAVADARTRRDGRAIEVIGRYHPKE---EPSLIEINSERAQYWLSVGAQPT 67
                                   89********************************44...4557******************9 PP

>> DUF5476  Family of unknown function (DUF5476)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.23   2.1e+03       6      14 ..      94     102 ..      92     120 .. 0.77
   2 ?    8.5   5.4   0.00029       2.6       4      40 ..     123     157 ..     122     162 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                        DUF5476   6 KvkvPKvdt 14 
                                    Kv +PK++ 
  gi|121638790|ref|YP_979014.1|  94 KVAAPKPSK 102
                                    777788765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00029
                        DUF5476   4 spKvkvPKvdtaqvkapePaPLteepkgvefGgdddd 40 
                                    +pK k P  ++a  ka+ePaP  e+p     Gg++ +
  gi|121638790|ref|YP_979014.1| 123 KPKKKSPAKKAA--KAAEPAPQPEQPDTPALGGEQAE 157
                                    699999999888..9******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1205.78
//
Query:       gi|121638791|ref|YP_979015.1|  [L=147]
Description: hypothetical protein BCG_2931c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-30  104.6   0.0    4.3e-30  104.4   0.0    1.0  1  SnoaL_4       SnoaL-like domain
      0.007   17.0   0.0     0.0088   16.7   0.0    1.2  1  SnoaL_2       SnoaL-like domain
     0.0075   16.1   0.1     0.0094   15.8   0.1    1.2  1  Scytalone_dh  Scytalone dehydratase


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   7.2e-34   4.3e-30       2     126 ..      14     137 ..      13     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 7.2e-34
                                    HHHHHHHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESH.HHHHHHHHSHHHHHH-EEEEE---EEEEE CS
                        SnoaL_4   2 rledreaIrdlvarygyylDtkdweeladlFtedavvdytgvgegvlegr.dairaalrealdgfaltqHllsnplield 80 
                                    +++dr +I++l+  y+ ++D++++++l+ +Ft+da++dy+++  g + gr  +i+++l++ l++f++++H+l+n  +++d
  gi|121638791|ref|YP_979015.1|  14 EISDRLEIQQLLVDYSSAIDQRRFDDLDRVFTPDAYIDYRAL--GGIDGRyPKIKQWLSQVLGNFPVYAHMLGNFSVRVD 91 
                                    689*************************************98..8899977***************************** PP

                                    TTEEEEEEEEEEEEEETTEEEEEE..EEEEEEEEEEETTEEEEEEE CS
                        SnoaL_4  81 gdtAtgrayllatlvrdgdggrqvlaggryedelvredggWrisrr 126
                                    gdtA+ r  ++  +v +gd+ + +++g +y+d++vr+ +gWri rr
  gi|121638791|ref|YP_979015.1|  92 GDTASSRVICFNPMVFAGDRQQVLFCGLWYDDDFVRTPDGWRIIRR 137
                                    ******************9998888******************998 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0088       3      89 ..      27     117 ..      25     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                    HHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHH.HHHHHHHHHHHHEEEEEEEEEEE..EEETTEEEEEEEEEEEEE CS
                        SnoaL_2   3 aflaalnagdldalaalfapdvvwedp.ggelrGre.airaffralfaafpdlrfeihdv..vadgdrvavewtvtgtip 78 
                                    ++  a++++++d+l+++f+pd+      +g ++Gr   i++++ +++ +fp + + + ++   +dgd++  ++ +   + 
  gi|121638791|ref|YP_979015.1|  27 DYSSAIDQRRFDDLDRVFTPDAYIDYRaLGGIDGRYpKIKQWLSQVLGNFPVYAHMLGNFsvRVDGDTASSRVICFNPMV 106
                                    57789*****************9988879999999879999*************99999998999999999887765566 PP

                                    TTSSEEEEEEE CS
                        SnoaL_2  79 atgrgvtvrgv 89 
                                      g++ +v ++
  gi|121638791|ref|YP_979015.1| 107 FAGDRQQVLFC 117
                                    66666666555 PP

>> Scytalone_dh  Scytalone dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.6e-06    0.0094       3      45 ..      14      56 ..      12      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                   -HHHHHHHHHHHHHHHHHHHHT-HHHHHTTEEEEEEEEEHHHH CS
                   Scytalone_dh  3 tfedylglkkvlfewadsydskdwdrlrkviaptlridyrsll 45
                                   +++d l +++ l +++ + d + +d l +v +p+  idyr l+
  gi|121638791|ref|YP_979015.1| 14 EISDRLEIQQLLVDYSSAIDQRRFDDLDRVFTPDAYIDYRALG 56
                                   57899***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1231.13
//
Query:       gi|121638792|ref|YP_979016.1|  [L=291]
Description: D-alanyl-D-alanine carboxypeptidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-35  120.9   0.0    8.3e-35  120.4   0.0    1.1  1  Peptidase_S11    D-alanyl-D-alanine carboxypeptidase
    7.3e-12   45.3   0.2      1e-11   44.9   0.2    1.2  1  Beta-lactamase2  Beta-lactamase enzyme family
    0.00016   20.5   0.1    0.00016   20.5   0.1    2.0  3  Peptidase_S13    D-Ala-D-Ala carboxypeptidase 3 (S13) family
  ------ inclusion threshold ------
      0.014   14.6   0.0       0.86    8.7   0.0    2.2  2  Transpeptidase   Penicillin binding protein transpeptidase do


Domain annotation for each model (and alignments):
>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   1.9e-38   8.3e-35      13     237 ..      42     257 ..      34     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.9e-38
                                    SSEEEEEETTTTEEEEEESTTS-BE-GGGHHHHHHHHHHHHHHTTSS-TTSEEE--GGGHGCCSGTTSSTTS-TTT-EEE CS
                  Peptidase_S11  13 aksailvdantGkvLyeknadevveiASltKlmTaylvlealkkgklkeddkvtisedayalgnnkevsniflkkgskvs 92 
                                    a+++i+ d+++G+vL+ ++++   ++AS  K++ a++ l++l    l+ +   +++++ ++ +       + +k+g+ ++
  gi|121638792|ref|YP_979016.1|  42 AQTWIVADLDSGQVLAGRDQNVAHPPASTIKVLLALVALDEL---DLNSTVVADVADTQAECN------CVGVKPGRSYT 112
                                    99*******************************999999999...777777777777777666......78899****** PP

                                    HHHHHHHHHCC--HHHHHHHHHHHHSSHHHHHHHHHHHHHHTT-TT-B-SSSSSTSHTTC..BB-HHHHHHHHHHHHHHH CS
                  Peptidase_S11  93 vkdLlegllvssgNdAavalAekiaGsekaFvkmMnkkakelGlkntkfvnptGLdnenq..vssArdlailakallkdl 170
                                     ++Ll gll+ sgNdAa  lA++++ +++  v +Mn+ka  lG + t+ ++p GLd ++    s+A dl ++ +a++ + 
  gi|121638792|ref|YP_979016.1| 113 ARQLLDGLLLVSGNDAANTLAHMLG-GQDVTVAKMNAKAATLGATSTHATTPSGLDGPGGsgASTAHDLVVIFRAAMAN- 190
                                    *********************9875.57888***************************98889***********99976. PP

                                    HHHHHGGGESEEEET.TECTEEEESSTGGGGTTTSEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEE CS
                  Peptidase_S11 171 peelkitkeksltfn.gikklnyknknkllyrktlnvdglktGytkkAgeclvatavenqmrlisVvl 237
                                    p   +it e+s++f   + +   +n+++ll+r+     g ktGyt++A +++v+ a +++ rl+   +
  gi|121638792|ref|YP_979016.1| 191 PVFAQITAEPSAMFPsDNGEQLIVNQDELLQRYP-GAIGGKTGYTNAARKTFVGAAARGGRRLVIAMM 257
                                    667789999999997347777889999***9999.88899**********************988776 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.2   2.2e-15     1e-11       1     201 [.      50     255 ..      50     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.2e-15
                                    TTTTSEE.EESTTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGHHHHTSSSTSGGGSTTSEEEHHHHHHHHHHTT CS
                Beta-lactamase2   1 ldtgeel.gvnadeefpaaStiKvpillalleavlegklslderltltaedivggsgilqklpgktlslrdlltlmiavS 79 
                                    ld+g++l g +++  +p aStiKv+++      v+ ++l+l+ ++    +d + +      +pg++++ r+ll   + vS
  gi|121638792|ref|YP_979016.1|  50 LDSGQVLaGRDQNVAHPPASTIKVLLA-----LVALDELDLNSTVVADVADTQAECNCVGVKPGRSYTARQLLDGLLLVS 124
                                    68899887999****************.....466679**********************9******************* PP

                                    -HHHHHHHHHHHT.HH....HHHHHHHHCTHTTSB--SHTTCCHHHTTSSTTEE-HHHHHHHHHHHHHTTSSHHHHHHHH CS
                Beta-lactamase2  80 DNtAtnlLidrlg.le....avnawlkelglretrlrrklpdleaadkdkrntttardlarllealargellspeellei 154
                                     N A+n L   lg ++     +na +++lg ++t+  ++  +l++  ++  + +ta+dl+ +++a + + + ++    ++
  gi|121638792|ref|YP_979016.1| 125 GNDAANTLAHMLGgQDvtvaKMNAKAATLGATSTHATTP-SGLDG--PGGSGASTAHDLVVIFRAAMANPVFAQI---TA 198
                                    ************734322226799999999999998866.34443..7789************998888777773...22 PP

                                    ....HH.T-STTTTTTTTTT.....TTSEEEEEEEEETTEEEE.EEEEEETTEEEEEE CS
                Beta-lactamase2 155 ....ls.nqqfrdrlaaglp.....egvrvahKtGeldgvrhd.vGivyadgrpyvva 201
                                        +  +    +++  + +         +  KtG  +++r   vG    +gr+ v+a
  gi|121638792|ref|YP_979016.1| 199 epsaMFpSDNGEQLIVNQ-DellqrYPGAIGGKTGYTNAARKTfVGAAARGGRRLVIA 255
                                    233444233333333322.223333345788888887777777455555588888876 PP

>> Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.7      0.66     3e+03      48      56 ..       3      11 ..       2      13 .. 0.88
   2 !   20.5   0.1   3.6e-08   0.00016      21      69 ..      45      93 ..      36     104 .. 0.88
   3 ?   -1.6   0.1      0.18   8.1e+02     275     388 ..     114     143 ..      88     158 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.66
                                   HHHHHHHHH CS
                  Peptidase_S13 48 KllTAaaAl 56
                                   Kl+TA+aAl
  gi|121638792|ref|YP_979016.1|  3 KLMTATAAL 11
                                   9*******9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.6e-08
                                   EEEEETTTTEEEEEESTTSEB--GGGHHHHHHHHHHHHT-TT-EEEEEE CS
                  Peptidase_S13 21 vvvqdaetgkelydhqgdtpllPAStqKllTAaaAlltLganfrftTev 69
                                    +v d+++g++l+ ++++++  PASt K+l A+ Al +L+ n      v
  gi|121638792|ref|YP_979016.1| 45 WIVADLDSGQVLAGRDQNVAHPPASTIKVLLALVALDELDLNSTVVADV 93
                                   579*************************************997665555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHT-HHHHHHHHHHHHHHHCS-BSHHHHHHHHHHHHHHTT--CTTSB-S-SSS-STT-BBEHHHHHHHHHHH CS
                  Peptidase_S13 275 sellkkmmkkSdNliAesllrevakeikrpgsfeagldavrerLskagidtanlvLeDgSGLSrknlvtaktlaqlLeai 354
                                     +ll  ++  S N  A++l  +++ +                                                      
  gi|121638792|ref|YP_979016.1| 114 RQLLDGLLLVSGNDAANTLAHMLGGQD----------------------------------------------------- 140
                                    455555566666666666666665443..................................................... PP

                                    HCTCCHHHHHHCS-BTTTSGGGTTSSTHCTTTTT CS
                  Peptidase_S13 355 adqpalqalldsLPvAGesGtlenrfkltstpav 388
                                                                     v
  gi|121638792|ref|YP_979016.1| 141 -------------------------------VTV 143
                                    ...............................333 PP

>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00019      0.86      43      61 ..      65      83 ..      42     133 .. 0.88
   2 ?    3.9   0.0    0.0058        26     244     289 ..     229     262 ..     216     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00019
                                   BB-GGGGHHHHHHHHHHTT CS
                 Transpeptidase 43 yePGStfKvvtaaaaleag 61
                                    +P+St+Kv++a+ al++ 
  gi|121638792|ref|YP_979016.1| 65 HPPASTIKVLLALVALDEL 83
                                   58**************985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0058
                                    EEEEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEEEECTCS CS
                 Transpeptidase 244 gKTGTAevagkkgngkkegakiswfvgyapadnpkyavavlieqpk 289
                                    gKTG +            +a  ++fvg a   ++++++a+++   k
  gi|121638792|ref|YP_979016.1| 229 GKTGYT------------NAARKTFVGAAARGGRRLVIAMMYGLVK 262
                                    333333............344679******9*********986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2118.95
//
Query:       gi|121638793|ref|YP_979017.1|  [L=195]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-09   35.8   0.5    1.2e-08   34.6   0.5    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.011   15.9   0.9      0.011   15.9   0.9    2.6  3  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
      0.016   15.4   4.3      0.036   14.3   0.1    2.4  3  TetR_C_6   BetI-type transcriptional repressor, C-terminal


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.5     2e-12   1.2e-08       1      46 [.      16      61 ..      16      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2e-12
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   +l a    ++e Gy++++ + I krAGvs gal+r+F ++ + ++a
  gi|121638793|ref|YP_979017.1| 16 LLQASIDTIIEVGYARASAAVITKRAGVSVGALFRHFETMGDFMAA 61
                                   68999999*****************************998887665 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4      0.14   8.5e+02      23      28 ..      11      16 ..       1      79 [. 0.62
   2 ?   -1.6   0.0      0.53   3.2e+03      33      49 ..      60      76 ..      52      90 .. 0.59
   3 ?   15.9   0.9   1.9e-06     0.011      21     104 ..     101     190 ..      83     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
                                   HHHHHH CS
                      TetR_C_31 23 rtlAry 28
                                   +t+Ar+
  gi|121638793|ref|YP_979017.1| 11 ETVARL 16
                                   333332 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.53
                                   HHCCSCHHHHHHHHHHH CS
                      TetR_C_31 33 eaarrPeLraalarlrr 49
                                   +a+  + Lr+ l     
  gi|121638793|ref|YP_979017.1| 60 AATAYEVLRRQLETFTK 76
                                   44444444444444333 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.9e-06
                                    HHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHH.CS.S-HHHHHHHHHHHH....HHHHHHHHHSGTS-H. CS
                      TetR_C_31  21 rertlAryelfleaarrPeLraalarlrralrealaallaal.Gl.pdpeeaarllvaal....dGllldrLagpaadp. 93 
                                     +  + +yel+++a+ ++ L + l+    ++ + + ++ +al G+   pee+  ++va++    dG+ + r ++p  +p 
  gi|121638793|ref|YP_979017.1| 101 GSTNAVLYELMVAARTDEKLKETLQNVLGQYSAKIHDAARALpGAeSFPEETFPVIVALMtnvfDGAAIVRGVLP--QPe 178
                                    4556789*********************99999777777766333445677777776666222366666655665..332 PP

                                    .HHHHHHHHHHH CS
                      TetR_C_31  94 .raevrellral 104
                                     ++    +l+al
  gi|121638793|ref|YP_979017.1| 179 lEEQRIPMLTAL 190
                                    355555555555 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.1     0.043   2.6e+02      41     112 ..       4      73 ..       1      76 [. 0.52
   2 ?    0.4   0.1      0.12   7.4e+02      44      63 ..      61      80 ..      43      96 .. 0.60
   3 ?   14.3   0.1     6e-06     0.036      21     103 ..     102     185 ..      90     195 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.043
                                    HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHH CS
                       TetR_C_6  41 elqrenyarlrsnlrallaelaegglradadaeaaAerlaAlidGLwlraalapeeldaeraralvrrhlda 112
                                     +q++ ++++ ++l+a++  + e    a+a a+ ++ r a +  G   r+    +++ a++a++++rr l++
  gi|121638793|ref|YP_979017.1|   4 TQQQRREETVARLLQASIDTIIE-VGYARASAAVITKR-AGVSVGALFRHFETMGDFMAATAYEVLRRQLET 73 
                                    45566666666777777777766.33333333333333.233334444443333677777777777777765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHH CS
                       TetR_C_6 44 renyarlrsnlrallaelae 63
                                   +++y+ lr++l    +++ae
  gi|121638793|ref|YP_979017.1| 61 ATAYEVLRRQLETFTKQVAE 80
                                   23355555555555555554 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHHHHH.HHHHHHTCTTCHH CS
                       TetR_C_6  21 aelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaAerlaAlidGL.wlraalapeelda 99 
                                     + av  +++++a++d+ l+e ++    ++ + + ++ ++l  ++ ++++    + + ++ + dG   +r++l  +el++
  gi|121638793|ref|YP_979017.1| 102 STNAVLYELMVAARTDEKLKETLQNVLGQYSAKIHDAARALPGAESFPEETFPVIVALMTNVFDGAaIVRGVLPQPELEE 181
                                    5678999********************************9999999999999999999********66788888899988 PP

                                    HHHH CS
                       TetR_C_6 100 erar 103
                                    +r+ 
  gi|121638793|ref|YP_979017.1| 182 QRIP 185
                                    8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1416.15
//
Query:       gi|121638794|ref|YP_979018.1|  [L=611]
Description: D-amino acid aminohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-18   66.0   1.7    1.2e-12   48.1   0.3    2.2  2  Amidohydro_3  Amidohydrolase family
    1.6e-07   31.0   0.0     0.0028   17.0   0.0    2.4  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.27   11.3   0.2       0.46   10.5   0.2    1.3  1  RHINO         RAD9, RAD1, HUS1-interacting nuclear orphan pro


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3     2e-16   1.2e-12       1     142 [.      60     215 ..      60     238 .. 0.79
   2 !   17.3   0.1   4.3e-07    0.0025     407     473 .]     494     575 ..     419     575 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2e-16
                   Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt.................pkgrwivg 63 
                                    ev+Da G+ v+PGF+D+HtH     +++ +l +p+ r +  +gv+t++ +++  +                         
  gi|121638794|ref|YP_979018.1|  60 EVVDAAGKWVVPGFIDVHTH-----YDAEVLLDPGLRESVRHGVTTVLLGNCSLStvyansedaadlfsrveA------- 127
                                    79******************.....99999******************************9955555555552....... PP

                   Amidohydro_3  64 eGw..........deaqfaeerfpyalaeldevledapvllaaldtHaavrnsaa.ldlagiteatpdp....aggeilr 128
                                      +          d   +++++   +  ++d+      ++++ l +H+++r  ++ ld+a +++ +p +    +++++l 
  gi|121638794|ref|YP_979018.1| 128 --VprefvlgalrDNQTWSTPA-E-YIEAIDAL--PLGPNVSSLLGHSDLRTAVLgLDRATDDTVRPTEaelaKMAKLLD 201
                                    ..45444444442555555555.3.99999999..8889999*********776525665555444444679******** PP

                   Amidohydro_3 129 dangegatgllreg 142
                                    +a ++g +g++  +
  gi|121638794|ref|YP_979018.1| 202 EALEAGMLGMSGMD 215
                                    *********98644 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.3e-07
                   Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear...................vrltvv 467
                                     ls+e a+  +T + A+ +g     GtL+ G +AD++v+d  p ++d++ + + +                   v++t v
  gi|121638794|ref|YP_979018.1| 494 FLSIERAVYRLTGELAEWFGIGA--GTLRQGDRADFAVID--PTHLDESVDGYHEeavpyygglrrmvnrndatVVATGV 569
                                    589********************..**************7..66666665544445678888888888888888999999 PP

                   Amidohydro_3 468 dGrvvy 473
                                    +G vv+
  gi|121638794|ref|YP_979018.1| 570 GGTVVF 575
                                    998886 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-07    0.0028       1      53 [.      68     110 ..      68     221 .. 0.73
   2 !   11.7   0.0   1.9e-05      0.12     275     341 ..     490     571 ..     439     574 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-07
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEE CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttva 53 
                                    +v+PG+ID+H+H+   +l         ++p  ++e +++g++t l + +    
  gi|121638794|ref|YP_979018.1|  68 WVVPGFIDVHTHYDAEVL---------LDPG-LRESVRHGVTTVLLGNCSLST 110
                                    59***********65544.........5555.666666666666666665444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.9e-05
                                    TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT.................CGGGTTTCTSEEEEE CS
                   Amidohydro_1 275 deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.di.................laafvglkkdgnvkk 336
                                     ++  ls+++a++  T   A+ +g+   +G++  G +AD++v+d+ ++                 l  +v+ ++  +v+ 
  gi|121638794|ref|YP_979018.1| 490 AGQPFLSIERAVYRLTGELAEWFGI--GAGTLRQGDRADFAVIDPtHLdesvdgyheeavpyyggLRRMVNRND-ATVVA 566
                                    4455589999999999999******..8***************9984444566677777777777555555544.44444 PP

                                    EEETT CS
                   Amidohydro_1 337 vivkG 341
                                    + v+G
  gi|121638794|ref|YP_979018.1| 567 TGVGG 571
                                    54555 PP

>> RHINO  RAD9, RAD1, HUS1-interacting nuclear orphan protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   7.7e-05      0.46     224     243 ..     237     256 ..     235     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.7e-05
                          RHINO 224 TWRrRkhllkyLrerGkLsk 243
                                    TWR R++l+  Lr rG++ +
  gi|121638794|ref|YP_979018.1| 237 TWRERRKLISVLRHRGRILQ 256
                                    ****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 4016.33
//
Query:       gi|121638795|ref|YP_979019.1|  [L=585]
Description: transmembrane serine/threonine-protein kinase I pknI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-21   75.5   0.0    3.1e-20   72.6   0.0    1.9  1  Pkinase         Protein kinase domain
    5.2e-12   45.6   0.0    7.1e-12   45.2   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
     0.0018   17.1   0.0     0.0027   16.6   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
     0.0041   17.1  11.8       0.12   12.3   0.1    3.6  4  APH             Phosphotransferase enzyme family
     0.0041   16.5   0.0      0.008   15.5   0.0    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.36   11.0   0.0    1.7  1  Acyl-CoA_dh_C   Acetyl-CoA dehydrogenase C-terminal like
       0.19   12.0   0.2       0.19   12.0   0.2    3.1  3  CD24            CD24 protein
       0.21   12.1   1.3       0.84   10.3   1.3    2.1  1  LPAM_1          Prokaryotic membrane lipoprotein lipid attach


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   1.4e-23   3.1e-20       1     200 [.      12     205 ..      12     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.4e-23
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    y++++ lG  ++G+Vy + +       A+K+++   a +++  ++++rE ++ ++l hp+i+++ +  e + +l++ ++y
  gi|121638795|ref|YP_979019.1|  12 YTVVRMLGCSAMGEVYLVQHPGFPGWQALKVLSPAMAADDEFrRRFQRETEVAARLFHPHILEVHDRGEFDGQLWIAMDY 91 
                                    6788999*************************998877766669************************************ PP

                                    -TTEBHHHHHHHHSS..--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE....EEE-SGTTSEESSSSCS CS
                        Pkinase  80 veggeladllerkgs..lseeeakkiakqilegleylHskgiiHrDlKpeNiLidekge....lKitDFGlakelesssk 153
                                    v+g + ++++ ++    l+  e+  i++ ++ +l+y H++g++HrD+ p+N+ + ++      + ++DFG+a++      
  gi|121638795|ref|YP_979019.1|  92 VDGIDATQHMADRFPavLPVGEVLAIVTAVAGALDYAHQRGLLHRDVNPANVVLTSQSAgdqrILLADFGIASQ------ 165
                                    *****9999995443349999*********************************965445677********975...... PP

                                    BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTS CS
                        Pkinase 154 ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsge 200
                                           + Y APE+  + +++  +D ++l+++ + l++g pp   +
  gi|121638795|ref|YP_979019.1| 166 -------PSYPAPELSAGADVDGRADQYALALTAIHLFAGAPPVDRS 205
                                    .......56999******************************99844 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   3.2e-15   7.1e-12       5     152 ..      16     165 ..      12     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.2e-15
                                    EEEEEESSEEEEEEEEETTTTSSEEEEEEEEEST..TSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE- CS
                    Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtlke..eateeekeelleeakimkklkhpnivkllgvctkeepllivtey 82 
                                    + lG  a G+V+  +  g    +    a+K+l+    a++e ++++ +e+++  +l hp+i++++     +++l+i ++y
  gi|121638795|ref|YP_979019.1|  16 RMLGCSAMGEVYLVQHPGFPGWQ----ALKVLSPamAADDEFRRRFQRETEVAARLFHPHILEVHDRGEFDGQLWIAMDY 91 
                                    66777777888777777444444....5566644114555559**************************9********** PP

                                    -TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE....TTEEEE-STTTHEE CS
                    Pkinase_Tyr  83 vkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse....nkvvkisDfGLard 152
                                    v+g d  +++ ++  + l + ++l +++ vA +++y +++ l+Hrd+   Nv+l++    ++ + ++DfG+a++
  gi|121638795|ref|YP_979019.1|  92 VDGIDATQHMADRFPAVLPVGEVLAIVTAVAGALDYAHQRGLLHRDVNPANVVLTSqsagDQRILLADFGIASQ 165
                                    ******************************************************997888889********987 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0027     314     363 ..     119     167 ..     111     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                 Pkinase_fungal 314 DaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakels 363
                                     a++g     ++ g+LHrD+   N+++t s++ g+++ lL+D+ +a++ s
  gi|121638795|ref|YP_979019.1| 119 TAVAGALDYAHQRGLLHRDVNPANVVLT-SQSAGDQRILLADFGIASQPS 167
                                    4555555556699***************.88999*********9998866 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.4   0.00017      0.37      13     105 ..      26     118 ..      15     129 .. 0.76
   2 !   12.3   0.1   5.2e-05      0.12     155     187 ..     120     155 ..     101     164 .. 0.66
   3 ?   -1.1   2.9      0.67   1.5e+03      84     116 ..     206     239 ..     156     345 .. 0.44
   4 ?   -0.2   0.2      0.35   7.9e+02      84     122 ..     306     346 ..     294     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                    EEEEEETT..--EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-..B--B-CTTBS-EEETTEEEEEEE----EE-SSHH CS
                            APH  13 tylvttpa..gryvlrrnppa..raaeeirrevallrlLakagv..pvPevlagdtddeeigllfalieyvpgrsllrkl 86 
                                    +ylv++p+  g  +l++ +pa    +e+ rr++++  + a++ +  ++ ev++    +e+ g l+ ++ yv+g ++++  
  gi|121638795|ref|YP_979019.1|  26 VYLVQHPGfpGWQALKVLSPAmaADDEFRRRFQRETEV-AARLFhpHILEVHD---RGEFDGQLWIAMDYVDGIDATQ-- 99 
                                    78888888866667999999995555555666666666.55558778888888...9********************9.. PP

                                    HHHHHHHHHHHHHHHHCCH CS
                            APH  87 saaqlpellealgeflaal 105
                                    ++a++  ++  +ge+la +
  gi|121638795|ref|YP_979019.1| 100 HMADRFPAVLPVGEVLAIV 118
                                    7777766666666666655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                                    HHHHH--SSS-EEEE-SS-SGGGEEEC.....TTEE CS
                            APH 155 alaallpgelptvllHgDlhpgNllvd...pddgrv 187
                                    a+a  l+ + +++llH+D +p N++++   ++d+r+
  gi|121638795|ref|YP_979019.1| 120 AVAGALDYAHQRGLLHRDVNPANVVLTsqsAGDQRI 155
                                    33333333678****************887777776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.67
                                    S..HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB- CS
                            APH  84 r..klsaaqlpellealgeflaalhqvdpaalpla 116
                                    +  +l+++ l ++  +l+++ + l+++  a++p +
  gi|121638795|ref|YP_979019.1| 206 HtgPLQPPKLSAFRPDLARLDGVLSRA-LATAPAD 239
                                    233344444444444444444444444.2222222 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.35
                                    S.HHHHHHHHHHHHHHHHHHC.CHHCH.-STTTB-SHHCHT CS
                            APH  84 r.klsaaqlpellealgefla.alhqvdpaalpladflaqd 122
                                    + +++++ ++ +l+ ++ +la +l ++++a+  +a++++++
  gi|121638795|ref|YP_979019.1| 306 PaAPTPQRRGSMLQSAAGVLArRLDNFSTATKAPASPTRRR 346
                                    24556788899999999988867888888888888888664 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-06     0.008     122     166 ..     116     160 ..      86     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                            Kdo 122 allkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                    a++ av+ +    h++g+ H+d+++ n+ l  + +++++i l D+
  gi|121638795|ref|YP_979019.1| 116 AIVTAVAGALDYAHQRGLLHRDVNPANVVLTSQSAGDQRILLADF 160
                                    78899999999***********************9*********9 PP

>> Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.36      14      74 ..     318     377 ..     296     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                  Acyl-CoA_dh_C  14 lkelaaaleaalealqeateallakaakgdpeealaaavpyLelfGdvvigwlllrqalaA 74 
                                    l++ a  l++ l+++ +at+a ++  +   p+++l +av  L l+G  ++g +  r  +  
  gi|121638795|ref|YP_979019.1| 318 LQSAAGVLARRLDNFSTATKAPASPTRR-RPRRILVGAVAVLLLAGLFAVGIVIGRKTNTT 377
                                    7889999*****************8887.9*********************9998877655 PP

>> CD24  CD24 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.3e-05      0.19      18      43 ..     300     326 ..     296     329 .. 0.89
   2 ?   -7.6   6.4         8   1.8e+04      13      27 ..     384     398 ..     374     404 .. 0.52
   3 ?   -6.1   4.0         8   1.8e+04      16      26 ..     567     577 ..     559     583 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-05
                           CD24  18 sa.aPnPanAtTkaaggaLqStASLlv 43 
                                    sa aP Pa  t +  g+ LqS+A+ l+
  gi|121638795|ref|YP_979019.1| 300 SArAPAPAAPTPQRRGSMLQSAAGVLA 326
                                    5669*******************9885 PP

  == domain 2  score: -7.6 bits;  conditional E-value: 8
                           CD24  13 sSqntsaaPnPanAt 27 
                                    +  + sa+P+ +++t
  gi|121638795|ref|YP_979019.1| 384 PPTSGSAVPSAPTTT 398
                                    444556666655544 PP

  == domain 3  score: -6.1 bits;  conditional E-value: 8
                           CD24  16 ntsaaPnPanA 26 
                                    +ts+a+  + +
  gi|121638795|ref|YP_979019.1| 567 TTSTATLTPPT 577
                                    45554433333 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00037      0.84       2      16 ..     348     362 ..     348     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                         LPAM_1   2 KKillalgalllLsG 16 
                                    ++il+ ++a+llL+G
  gi|121638795|ref|YP_979019.1| 348 RRILVGAVAVLLLAG 362
                                    8*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3741.40
//
Query:       gi|121638796|ref|YP_979020.1|  [L=370]
Description: hypothetical protein BCG_2936c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-14   51.6   0.0    1.3e-13   51.0   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
    7.8e-05   22.3   7.7     0.0007   19.2   1.5    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.4e-17   1.3e-13       2     299 ..      55     330 ..      54     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.4e-17
                                    EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.HHHHHHHHHHT.SSSEEEE CS
                   Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.giealleaaee.lplglri 79 
                                    +lPGl+DaH H+   l+++    ++ +++ +a++ +e+ + ++l   +++  d++  +++  ++++++a ++ +   +  
  gi|121638796|ref|YP_979020.1|  55 ILPGLVDAHCHVG--LGKH---GNVELDEAIAQAETERDVGALLLRDCGSPTDTRGLDDHeDLPRIIRAGRHlA--RPKR 127
                                    89**********6..4433...46669***************************99988898888888888842..3333 PP

                                    EEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHH CS
                   Amidohydro_1  80 lggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkge 158
                                    +++++ ++  ++ + + a++e+ ++g + ++k   ++ ++ ++++  ap  sd+ lk+a++ a+++++ v++H+ ++++ 
  gi|121638796|ref|YP_979020.1| 128 YIAGFAVELeDESQLPAAVAEQARRG-DGWVKLV-GDWIDRQIGDL-APLWSDDVLKAAIDTAHAQGARVTAHVFSEDAL 204
                                    33333333338888888899999999.6777744.45555444443.5666789********************776666 PP

                                    HHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEE........HHHHHHHHSEHHHH CS
                   Amidohydro_1 159 vedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagva........hcpfsnsilrsgre 230
                                        ++a+++ iehgt l +       d+i l+l+hg+ l pt ++l  e+    g+a          +   +  + g  
  gi|121638796|ref|YP_979020.1| 205 P-GLINAGIDCIEHGTGLTD-------DTIALMLEHGTALVPTLINL--EN--FPGIAdaagryptYAAHMRDLYARGYG 272
                                    5.79999999**********.......****************6666..55..333443355555422233344899999 PP

                                    HHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT- CS
                   Amidohydro_1 231 alrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalgl 299
                                    +++ a ++Gv v  gtD   +g++++    +r+a +++       ++ g+++ eal +a++++ + lg+
  gi|121638796|ref|YP_979020.1| 273 RVAAAREAGVPVYAGTD---AGSTIEH---GRIADEVAA-----LQRIGMTAHEALGAACWDARRWLGR 330
                                    99999999*********...7777733...444443333.....2399**************9999997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.6   0.00049       4.4       7      21 ..      52      66 ..      51      84 .. 0.85
   2 !   19.2   1.5   7.8e-08    0.0007     212     386 ..     136     298 ..      76     317 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00049
                   Amidohydro_3  7 GrlvlPGFvDsHtHl 21
                                   G+  lPG+vD+H H+
  gi|121638796|ref|YP_979020.1| 52 GGWILPGLVDAHCHV 66
                                   8889**********5 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.8e-08
                   Amidohydro_3 212 ldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavd. 290
                                    l++ ++l++ +   +++  +g vkl +d  +  r +    p        +d++l++ ++ a+++g +v  h++ ++a+  
  gi|121638796|ref|YP_979020.1| 136 LEDESQLPAAVA-EQARRGDGWVKLVGD--WIDRQIGDLAP------LWSDDVLKAAIDTAHAQGARVTAHVFSEDALPg 206
                                    333333333333.567778899999999..66666666665......557888**************************7 PP

                   Amidohydro_3 291 dvldafeaaaekngnqdrr...rlehaegv..tesqiervaalqvaagvqpvfnf.edelldsrlgperargstpvkell 364
                                     + ++++   +  g++d      leh++++  t  ++e +  +  aag  p +++  +        +  arg+ +v++ +
  gi|121638796|ref|YP_979020.1| 207 LINAGIDCIEHGTGLTDDTialMLEHGTALvpTLINLENFPGIADAAGRYPTYAAhMR--------DLYARGYGRVAAAR 278
                                    666777777888888888888999****999955555566666666666655555211........3458999******* PP

                   Amidohydro_3 365 nagvkvalgsDapvgpfdpwpr 386
                                    +agv+v +g+D   g++ ++ r
  gi|121638796|ref|YP_979020.1| 279 EAGVPVYAGTD--AGSTIEHGR 298
                                    ***********..555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2624.64
//
Query:       gi|121638797|ref|YP_979021.1|  [L=525]
Description: signal recognition particle protein ffh [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-68  230.9   0.0    1.5e-68  230.3   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
    3.8e-30  104.4   0.9    7.5e-30  103.5   0.3    1.9  1  SRP_SPB          Signal peptide binding domain
    4.9e-21   74.7   0.2    1.2e-20   73.5   0.2    1.7  1  SRP54_N          SRP54-type protein, helical bundle domain
    4.2e-05   23.6   0.0    0.00014   22.0   0.0    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00018   21.2   0.1    0.00044   19.9   0.1    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00091   19.6   1.6     0.0023   18.3   0.2    2.4  3  AAA_16           AAA ATPase domain
    0.00098   19.3   0.0     0.0021   18.2   0.0    1.7  1  AAA_33           AAA domain
     0.0015   17.8   0.1     0.0028   17.0   0.1    1.4  1  Zeta_toxin       Zeta toxin
     0.0027   17.3   6.7      0.074   12.6   2.7    3.2  2  AAA_25           AAA domain
     0.0029   17.5   0.0     0.0067   16.3   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0031   16.5   0.3     0.0031   16.5   0.3    2.1  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0039   17.7   0.0     0.0093   16.5   0.0    1.6  1  AAA_18           AAA domain
     0.0068   16.2   0.0      0.025   14.3   0.0    1.9  1  AAA_24           AAA domain
      0.007   16.3   0.0      0.074   13.0   0.1    2.2  2  AAA_31           AAA domain
  ------ inclusion threshold ------
       0.01   15.6   0.2      0.031   14.0   0.2    1.8  1  AAA_30           AAA domain
      0.012   15.1   0.1        1.7    8.0   0.0    2.3  2  SRPRB            Signal recognition particle receptor beta su
      0.021   14.7   0.6       0.32   10.9   0.1    2.4  2  NTPase_1         NTPase
      0.024   13.8   0.9       0.52    9.4   0.0    2.7  4  ArsA_ATPase      Anion-transporting ATPase
      0.033   14.3   0.5       0.32   11.1   0.2    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
      0.037   14.3   0.0      0.092   13.0   0.0    1.6  1  AAA_22           AAA domain
      0.044   13.8   0.1      0.089   12.8   0.1    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.059   13.3   1.6      0.087   12.7   0.5    1.8  2  NACHT            NACHT domain
      0.076   12.7   0.1       0.13   11.9   0.1    1.4  1  Thymidylate_kin  Thymidylate kinase
      0.084   12.9   0.0        1.7    8.7   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
       0.11   12.4   0.1       0.21   11.5   0.1    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.14   11.9   0.0       0.96    9.2   0.0    2.1  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
        4.3    7.2  13.9         13    5.7  13.9    1.8  1  Collagen         Collagen triple helix repeat (20 copies)


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.0   2.3e-71   1.5e-68       1     196 []     100     302 ..     100     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 2.3e-71
                                    SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.......SSTTS...CHHH CS
                          SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.......kkeea...dpaa 70 
                                    p+v++l+GlqG+GKTt ++KLaa+l+ +g+++llva+D  R+aAv+QL++++e++gvpv++       +   +   dp+a
  gi|121638797|ref|YP_979021.1| 100 PTVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAVNQLQVVGERAGVPVFAphpgaspE---SgpgDPVA 176
                                    689*********************************************************987775432...23469*** PP

                                    HHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEEST CS
                          SRP54  71 vakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltkl 150
                                    va++++ +a+++++dvv+vDTaGrl +d+elm++ ++i+++++pdevl+vlda++gq+av++a aF e vg+tgv ltkl
  gi|121638797|ref|YP_979021.1| 177 VAAAGLAEARAKHFDVVIVDTAGRLGIDEELMAQAAAIRDAINPDEVLFVLDAMIGQDAVTTAAAFGEGVGFTGVALTKL 256
                                    ******************************************************************************** PP

                                    TSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 151 DgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                    Dgda+gGaals+++ +++Pi f ++Gek+ed+++f+p+r++sr+lg
  gi|121638797|ref|YP_979021.1| 257 DGDARGGAALSVREVTGVPILFASTGEKLEDFDVFHPDRMASRILG 302
                                    ********************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.3   1.1e-32   7.5e-30       2      99 .]     334     431 ..     333     431 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.1e-32
                                    SCTHHHHHHHHHHHCCCCCCHHHHCCC......H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHTTS CS
                        SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae.akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiArGsGt 80 
                                    +tl+d+leq+  ++kmGp+ +ll+m+Pg  ++  +  e ++k+l+r++aii+ MT++Er++p+ ++++sR+ RiA+GsG+
  gi|121638797|ref|YP_979021.1| 334 LTLEDFLEQMLAVRKMGPIGNLLGMLPGAAQMkDALAEVDDKQLDRVQAIIRGMTPQERADPK-IINASRRLRIANGSGV 412
                                    79**************************8888533346679**********************.999************* PP

                                    -HHHHHHHHHHHHHHHHHT CS
                        SRP_SPB  81 svqevnellkqfeqmkkmm 99 
                                    +v+evn+l+++f + +kmm
  gi|121638797|ref|YP_979021.1| 413 TVSEVNQLVERFFEARKMM 431
                                    ******************9 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.2   1.8e-23   1.2e-20       1      75 []       5      82 ..       5      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.8e-23
                                   HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                        SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                   L+++l++al++l+gk++++++d++++ +e++ aLleaDV+++vv+ +i ++k++a g  +    l+p+qqv+kiv++eL
  gi|121638797|ref|YP_979021.1|  5 LSDRLTAALQGLRGKGRLTDADIDATTREIRLALLEADVSLPVVRAFIHRIKERARG-AEvssaLNPAQQVVKIVNEEL 82
                                   799**************************************************9999.66699999************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     2e-07   0.00014       9      55 ..     110     305 ..     102     384 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    G+GKTtla +La+ l  +g+  llv +D q++++    +++++  +                                  
  gi|121638797|ref|YP_979021.1| 110 GSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAVNQLQVVGE--Ragvpvfaphpgaspesgpgdpvavaaaglaeara 187
                                    9*******************************97633333333..24588888899999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121638797|ref|YP_979021.1| 188 khfdvvivdtagrlgideelmaqaaairdainpdevlfvldamigqdavttaaafgegvgftgvaltkldgdarggaals 267
                                    99999999999999888888888888888888888888888777665555555555555555555555555555555555 PP

                                    .....................................C CS
                                    .....................................x RF
                           CbiA  55 .....................................d 55 
                                                                         d
  gi|121638797|ref|YP_979021.1| 268 vrevtgvpilfastgekledfdvfhpdrmasrilgmgD 305
                                    55555555555555555555555555555555555551 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   6.6e-07   0.00044       2     141 ..     102     248 ..     101     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.6e-07
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHH. CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefge.vsiDaellret..gveivelenGciCctlredllkelea. 75 
                                    v++l+G  GsGKTtL  +l    + +g    ++  +++   ++++  +  +  gv+++  + G  + +   d +++++a 
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAarLRGQGHTPLLVACDLQRpAAVNQLQVVGEraGVPVFAPHPGASPESGPGDPVAVAAAg 181
                                    7899***************9875667777888889999867787766644435899************666655554441 PP

                                    HHHHH.TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHT CS
                           cobW  76 leere.erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaa 141
                                    l+e + +++dv+++ t G l    +++ ++  ++++++ d v++v+Da  + ++  +++  +++++ +
  gi|121638797|ref|YP_979021.1| 182 LAEARaKHFDVVIVDTAGrLGIDEELMAQAAAIRDAINPDEVLFVLDA-MIGQDAVTTAAAFGEGVGF 248
                                    55544699**********99999999999*******************.4446666666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.4   4.2e+03      40      91 ..      47      92 ..      46     101 .. 0.67
   2 !   18.3   0.2   3.5e-06    0.0023      23      63 ..      98     139 ..      89     230 .. 0.76
   3 ?   -1.2   0.0       3.5   2.3e+03      83      86 ..     366     369 ..     296     428 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.4
                         AAA_16 40 lvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91
                                   +vr++ ++++++    +rg  +++ +  p ++++++  +eel+  l+ e+++
  gi|121638797|ref|YP_979021.1| 47 VVRAFIHRIKER----ARGAEVSS-ALNPAQQVVKIV-NEELISILGGETRE 92
                                   577788888888....66666666.223446688888.77999888888544 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.5e-06
                         AAA_16  23 rp.elvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                    +p  +v+l G +G+GK++l+ +l+ +l+++ g++ l   cd  
  gi|121638797|ref|YP_979021.1|  98 TPpTVVMLAGLQGSGKTTLAGKLAARLRGQ-GHTpLLVACDLQ 139
                                    44489************************9.777788888877 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.5
                         AAA_16  83 rqll 86 
                                    ++ l
  gi|121638797|ref|YP_979021.1| 366 KDAL 369
                                    2222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-06    0.0021       1      24 [.     102     125 ..     102     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg 24 
                                    +v+l Gl+GsGK+tla +l+++l 
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAARLR 125
                                    89*****************99887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.2e-06    0.0028      13      43 ..      97     128 ..      88     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                     Zeta_toxin  13 qerPklillgGqpGAGKselaellkdele.rq 43 
                                    +  P++++l+G +G+GK++la +l+++l+ ++
  gi|121638797|ref|YP_979021.1|  97 KTPPTVVMLAGLQGSGKTTLAGKLAARLRgQG 128
                                    4679**********************998444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.039        26      85     138 ..       4      60 ..       2      65 .. 0.85
   2 !   12.6   2.7   0.00011     0.074      34     154 ..     101     201 ..      98     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.039
                         AAA_25  85 elrrRlravgealrddarllvldlagv.eslpLfakdrggtl..ltadvdaleaaie 138
                                     l  Rl a+++ lr ++rl+  d++    +++L+ ++++ +l  + a+++++ ++++
  gi|121638797|ref|YP_979021.1|   4 SLSDRLTAALQGLRGKGRLTDADIDATtREIRLALLEADVSLpvVRAFIHRIKERAR 60 
                                    5789********************9999******99999999766777777776665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                         AAA_25  34 elallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagve 112
                                    ++++laG +g+GKttla  la+ +  +G+           + l+v+++ ++    + l+ vge +   +   +   +g  
  gi|121638797|ref|YP_979021.1| 101 TVVMLAGLQGSGKTTLAGKLAARLRgQGH-----------TPLLVACDLQRPAAVNQLQVVGERA---GVPVFAPHPGA- 165
                                    589*******************9986655...........4477888888877778888777776...44444443332. PP

                         AAA_25 113 slpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsra 154
                                         ++++g    ++ + +a  a++++ +  ++v++D+  r+
  gi|121638797|ref|YP_979021.1| 166 -----SPESGPGDpVAVA-AAGLAEARA-KHFDVVIVDTAGRL 201
                                    .....3444444423333.334445566.45888888887775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05    0.0067       2      36 ..     100     134 ..      99     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylL 36 
                                    ++vv+l+Gl gsGK+t+a +l+ +L+ +g++  l+
  gi|121638797|ref|YP_979021.1| 100 PTVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLV 134
                                    5799**********************999876655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   4.7e-06    0.0031      30     131 ..     101     199 ..      91     216 .. 0.80
   2 ?   -0.6   0.3      0.76   5.1e+02      14      46 ..     416     449 ..     406     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                                    EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-------..-----------HCCCTSTTEEEEEE-----HHHHH CS
                           MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspft..GGsilGDklRleelavdegvfiRslpsrGalGGla 107
                                    +vv l G+ G+Gk tl  +l+++lr +G+   ++a D   p +     ++G++  +  +a ++g+    +p +G    +a
  gi|121638797|ref|YP_979021.1| 101 TVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAvnQLQVVGERAGVPVFAPHPGA----SPESGPGDPVA 176
                                    68899********************************8877551156789*************97....56666666666 PP

                                    HHHHHHHHHHHHTT-SEEEEEEES CS
                           MeaB 108 aktrevvllleaaGfDvvlietvG 131
                                     ++   ++   a  fDvv+++t G
  gi|121638797|ref|YP_979021.1| 177 VAAAG-LAEARAKHFDVVIVDTAG 199
                                    65554.45567999********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                                    HHHHHHHHHGG.G-S-SEEEEEEE-TTSSHHHHH CS
                           MeaB  14 eakellerlla.kaGraqvvGltGvPGaGkstlv 46 
                                    e ++l+er ++ +   + ++G  G+PG G+  ++
  gi|121638797|ref|YP_979021.1| 416 EVNQLVERFFEaRKMMSSMLGGMGIPGIGRKSAT 449
                                    5667777776514456789999*******76555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-05    0.0093       1      22 [.     103     124 ..     103     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                    ++l+G +G+GKttla  L+ rl
  gi|121638797|ref|YP_979021.1| 103 VMLAGLQGSGKTTLAGKLAARL 124
                                    79****************9997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.8e-05     0.025       4     138 ..     102     259 ..     100     273 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                         AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdieswedfldevvel................ 59 
                                     +++ G +g+GKTtla +l       g +pl++ ++    ++++  +++   +                           
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLaarlrgqGHTPLLVACDLqRPAAVNQLQVV---GE---------Ragvpvfaphpgaspes 169
                                    6899**********************99999998887223333333322...11.........12223334445566777 PP

                         AAA_24  60 ..............aaeladyktlviDtideleelclaevirqnekaeskedkgdgkG.ygelaeefrrllkklqelrkn 124
                                                  +a  ++++++++Dt++ l   +++e++ q+ + ++   ++     +++ a   ++++++  ++++ 
  gi|121638797|ref|YP_979021.1| 170 gpgdpvavaaaglaEARAKHFDVVIVDTAGRL--GIDEELMAQAAAIRDA--INPDEVlFVLDAMIGQDAVTTAAAFGEG 245
                                    77777777778888999999************..9999999998886665..3333333555555555555555555555 PP

                         AAA_24 125 vifiahektrkded 138
                                    v f++ + t+ d+d
  gi|121638797|ref|YP_979021.1| 246 VGFTGVALTKLDGD 259
                                    55555555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00011     0.074      12      46 ..     110     144 ..     101     154 .. 0.89
   2 ?    0.4   0.0      0.81   5.4e+02     115     131 ..     187     203 ..     178     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt 46 
                                    G GKTT + +laa l  +g+  Llv +D Q  a++
  gi|121638797|ref|YP_979021.1| 110 GSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAV 144
                                    99****************************98776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.81
                         AAA_31 115 kdeYDyiiiDcpPsLgl 131
                                     +++D++i+D+   Lg+
  gi|121638797|ref|YP_979021.1| 187 AKHFDVVIVDTAGRLGI 203
                                    578********999986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.7e-05     0.031      14     104 ..      96     205 ..      92     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgk...aAkvLa...eelgieastiakllkrlk...... 81 
                                    ++++  v++l G  G+GKtt+ ++l++ ++ +g++ +++A   +   a ++L+   e +g++    +   +         
  gi|121638797|ref|YP_979021.1|  96 AKTPPTVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACDLQrpaAVNQLQvvgERAGVPVFAPHPGASPESgpgdpv 175
                                    56667899************************988888886544111333344555455553333333333333555555 PP

                         AAA_30  82 .......grarlepgtllivDEagmvdtkq 104
                                           ++ar ++ +++ivD ag +++++
  gi|121638797|ref|YP_979021.1| 176 avaaaglAEARAKHFDVVIVDTAGRLGIDE 205
                                    555555533556666999999999986553 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0026       1.7       5      25 ..     102     122 ..      98     139 .. 0.86
   2 ?    4.5   0.0     0.031        21      46      98 ..     187     242 ..     175     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0026
                                    EEEEE-STTSSHHHHHHHHHH CS
                          SRPRB   5 avllvGlsdsGKTslftrLtt 25 
                                     v+l+Gl+ sGKT+l  +L  
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAA 122
                                    589************999976 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
                                    .GGTT-SEEEETT-GCCSHHHHHHHHHHGG.E..EEEEEEEETTS-HHHHHHHHHH CS
                          SRPRB  46 ekgskltliDfPGheklrqklleklkakss.l..kglvfvvDStidpkevkevAEl 98 
                                     k++ + ++D  G   +  +l+ +  a +  +    ++fv+D+ i +  v++ A +
  gi|121638797|ref|YP_979021.1| 187 AKHFDVVIVDTAGRLGIDEELMAQAAAIRDaInpDEVLFVLDAMIGQDAVTTAAAF 242
                                    578899999****99999999988666555232268**************999976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00049      0.32       2      27 ..     103     128 ..     102     132 .. 0.91
   2 ?    1.5   0.1      0.38   2.5e+02      89     130 ..     182     225 ..     175     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                                    EEEE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg 27 
                                    v++ G +G+GKtTl  k++  l+ +g
  gi|121638797|ref|YP_979021.1| 103 VMLAGLQGSGKTTLAGKLAARLRGQG 128
                                    789*******************9887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.38
                                    HHHHH.HHH-EEEE---STTGGG-HHHHH..HHHHHHTTTSEEEE CS
                       NTPase_1  89 lrkal.seadviviDEiGkmElkskkfke..aveevLksekpvla 130
                                    l +a  ++ dv+++D  G++    + +++  a+++++++++ vl+
  gi|121638797|ref|YP_979021.1| 182 LAEARaKHFDVVIVDTAGRLGIDEELMAQaaAIRDAINPDE-VLF 225
                                    555555899**********9877776655226888888776.444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00079      0.52       3      38 ..     102     137 ..     100     143 .. 0.93
   2 ?    1.7   0.0      0.17   1.1e+02     120     133 ..     185     198 ..     173     200 .. 0.86
   3 ?   -2.6   0.0       3.6   2.4e+03     148     205 ..     336     391 ..     334     406 .. 0.60
   4 ?   -3.7   0.0       7.6   5.1e+03     147     169 ..     416     438 ..     413     449 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                    v++++G  G GKtt++  +a++l  +g+  ll++ D
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACD 137
                                    7999*****************************988 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                                    HHCSSSSEEEEESB CS
                    ArsA_ATPase 120 vkeeeydvvvlDta 133
                                     +++++dvv++Dta
  gi|121638797|ref|YP_979021.1| 185 ARAKHFDVVIVDTA 198
                                    56899********9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.6
                                    HHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHH.HHHHHHHHHHHHHHTSTT CS
                    ArsA_ATPase 148 leklleklvklkeklsplakqlvkllglggvsieealeel.eetkeeikkveeiltdpe 205
                                    le +le+++ +++ ++p+ + l ++l+  + ++++al+e+ ++++++++++   +t +e
  gi|121638797|ref|YP_979021.1| 336 LEDFLEQMLAVRK-MGPIGNLL-GMLPG-AAQMKDALAEVdDKQLDRVQAIIRGMTPQE 391
                                    5667777766665.77777776.55544.444444555551455677777766666555 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 7.6
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                    ArsA_ATPase 147 vleklleklvklkeklsplakql 169
                                     +++l+e++++ ++++s+++  +
  gi|121638797|ref|YP_979021.1| 416 EVNQLVERFFEARKMMSSMLGGM 438
                                    56788888888888888876554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       8.2   5.5e+03      70      86 ..      35      51 ..      17      80 .. 0.61
   2 ?   11.1   0.2   0.00048      0.32       2      86 ..     103     230 ..     102     245 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.2
                                   HHHHHCTSEEEEEEETT CS
                       MMR_HSR1 70 flaleeadlillvvdas 86
                                    lal ead+ l vv+a 
  gi|121638797|ref|YP_979021.1| 35 RLALLEADVSLPVVRAF 51
                                   34455667766666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00048
                                    EEEEESTTSSHHHHHHHHHTSTEEESSST.TSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkp.gtTrdinegrvklkgke................................. 47 
                                    v+++G   +GK+tL  +l  +    +++p  +  d ++     ++ +                                 
  gi|121638797|ref|YP_979021.1| 103 VMLAGLQGSGKTTLAGKLAARLRGQGHTPlLVACDLQRPAAV-NQLQvvgeragvpvfaphpgaspesgpgdpvavaaag 181
                                    788999999999999999876444444442333333222221.1111333345666777777777788888888888888 PP

                                    ..........EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                       MMR_HSR1  48 ..........ielvDtpGliegaseekglgkaflaleeadlillvvdas 86 
                                              +++vDt+G +  ++e    + a+++ ++ d +l+v+da 
  gi|121638797|ref|YP_979021.1| 182 laearakhfdVVIVDTAGRLGIDEELMAQAAAIRDAINPDEVLFVLDAM 230
                                    8888888888********765222222555555556667********65 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.092       6     115 ..     101     214 ..      97     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka.........erlss 75 
                                    +++++ G  G+GKTtl+ +l+ +l       + + p +v ++l+ +    +l + + +  g++  a          +++ 
  gi|121638797|ref|YP_979021.1| 101 TVVMLAGLQGSGKTTLAGKLAARLRG-----QgHTPLLVACDLQRPAAVNQL-QVVGERAGVPVFAphpgaspesGPGDP 174
                                    578999*****************943.....246888888888888855555.888888888888888888877766677 PP

                         AAA_22  76 eellealeqalraravielliiDEaqhlr.seealeeLrsl 115
                                     ++ +a    +ra++   ++i+D a +l   ee++ +   +
  gi|121638797|ref|YP_979021.1| 175 VAVAAAGLAEARAKHF-DVVIVDTAGRLGiDEELMAQAAAI 214
                                    7777666666666666.899999888885434444444333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.089       2      24 ..     103     128 ..     102     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                    EEEE--SSSSHHHHHHHGGGGB...S CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal...n 24 
                                    v+L G +G+gK++la +laa+l   +
  gi|121638797|ref|YP_979021.1| 103 VMLAGLQGSGKTTLAGKLAARLrgqG 128
                                    89********************6433 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00013     0.087       2      26 ..     102     126 ..     101     135 .. 0.87
   2 ?   -2.4   0.0         6     4e+03      79      89 ..     219     229 ..     206     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                    CEEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawae 26 
                                    +v+l G +GsGKTtL+ kla  ++ 
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAARLRG 126
                                    7899***************998865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                                    SCCCEEEEEE- CS
                          NACHT  79 lperlLlilDg 89 
                                    +p+ +L++lD+
  gi|121638797|ref|YP_979021.1| 219 NPDEVLFVLDA 229
                                    6899******8 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0002      0.13       3      26 ..     107     130 ..     105     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                    ESTTSSHHHHHHHHHHHHHHTTE. CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik 26 
                                    Gl G+GKtt a +l++rl+ +g+ 
  gi|121638797|ref|YP_979021.1| 107 GLQGSGKTTLAGKLAARLRGQGHT 130
                                    99*******************975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0025       1.7      26      54 ..     102     130 ..      63     143 .. 0.79
   2 ?    1.2   0.0       0.5   3.3e+02     127     157 ..     184     218 ..     179     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                    EEEEEESTTSTHHHHHHHHHHHH-S.... CS
                         ResIII  26 rglikmaTGtGKTlvaaklierllkkgke 54 
                                     ++++   G+GKT +a kl++rl+ +g+ 
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAARLRGQGHT 130
                                    55688889****************99883 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                                    HHHTTT-SEEEEETGGGTTS.T....TTHHHHHT- CS
                         ResIII 127 ellrdrfdviiiDEaHrlgakk....swreilekf 157
                                    e++ ++fdv+i+D a rlg ++    +  +i +++
  gi|121638797|ref|YP_979021.1| 184 EARAKHFDVVIVDTAGRLGIDEelmaQAAAIRDAI 218
                                    677899********999998744433444455555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00032      0.21       1      28 [.     102     129 ..     102     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                           MobB   1 vlgivgksgsGKTtLleklipelkargl 28 
                                    v+ ++g +gsGKTtL  kl + l+ +g 
  gi|121638797|ref|YP_979021.1| 102 VVMLAGLQGSGKTTLAGKLAARLRGQGH 129
                                    68899******************99986 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0014      0.96       2      33 ..     108     139 ..     107     144 .. 0.91
   2 ?   -0.1   0.0         1   6.8e+02      99     137 ..     186     226 ..     175     242 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                         CLP1_P   2 pkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33 
                                     + sGK+Tla  L+ ++  +g++p++v +D+ 
  gi|121638797|ref|YP_979021.1| 108 LQGSGKTTLAGKLAARLRGQGHTPLLVACDLQ 139
                                    578***************************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                         CLP1_P  99 kkakasgliIntpGwv..kglgaellleliealepdvvvvl 137
                                    ++ + +++i++t G    +++ +    ++ +a++pd v+++
  gi|121638797|ref|YP_979021.1| 186 RAKHFDVVIVDTAGRLgiDEELMAQAAAIRDAINPDEVLFV 226
                                    45556789999999752145556666778899999888775 PP

>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  13.9     0.019        13      17      52 ..     452     492 ..     436     495 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                                    XX-----XXXXEEEE-TTSS---.....------------- CS
                       Collagen  17 krGepGeaGekGekGpaGekGpp.....GaaGkpGapGekG 52 
                                    ++G++G++G+k +kG +G++ p+     G +G pG +G +G
  gi|121638797|ref|YP_979021.1| 452 SKGAKGKSGKKSKKGTRGPTPPKvkspfGVPGMPGLAGLPG 492
                                    34555555555555555544332110113333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3129.32
//
Query:       gi|121638798|ref|YP_979022.1|  [L=626]
Description: hypothetical protein BCG_2938 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-13   49.8   0.0    7.4e-13   48.9   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
    1.1e-08   35.0   0.0    2.1e-08   34.1   0.0    1.4  1  SWI2_SNF2   SWI2/SNF2 ATPase
    8.3e-05   22.4   0.0    0.00025   20.9   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
    0.00035   20.9   0.0    0.00078   19.8   0.0    1.6  1  Helicase_C  Helicase conserved C-terminal domain
     0.0031   17.3   0.1     0.0089   15.8   0.1    1.8  1  AAA_30      AAA domain
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.029   14.7   0.1    1.5  1  AAA_19      AAA domain
      0.043   12.5   0.0      0.069   11.9   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
      0.062   12.6   0.0       0.11   11.8   0.0    1.3  1  DnaB_C      DnaB-like helicase C terminal domain
       0.12   12.8   0.0       0.37   11.2   0.0    1.8  1  AAA         ATPase family associated with various cellular ac
        0.2   11.1   0.0       0.34   10.3   0.0    1.2  1  PhoH        PhoH-like protein
       0.32   10.5   5.2        0.4   10.2   0.1    3.0  3  AAA_25      AAA domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   4.5e-16   7.4e-13       7     170 ..      68     217 ..      62     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.5e-16
                                    HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GE CS
                         ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeig 86 
                                    +Q +a+ + l     ++ + +l +++ G+GKT  a++++++ll+ +  e++ ++vp+++l  q+ ++ +    +      
  gi|121638798|ref|YP_979022.1|  68 WQRRALVQYL---G-TQPRDFLAVATPGSGKTSFALRIAAELLRYHTVEQVTVVVPTEHLKVQWAHAAAAHGLSL---DP 140
                                    5555555544...4.7899999*******************************************9988888776...34 PP

                                    EEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHH.HHHT-.--SEEEE CS
                         ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswre.ilekf.keavllg 164
                                    k+ +++ +++      + + +++t+ ++ ++       +    + r+ ++++DE H+ g++k+w   i e+f ++  +l+
  gi|121638798|ref|YP_979022.1| 141 KFANSNPQTS-----PEYHGVMVTYAQVASHP----TLHRVRTEARKTLVVFDEIHHGGDAKTWGDaIREAFgDATRRLA 211
                                    5555544444.....56777777777777777....477778888888****************9967888878899*** PP

                                    EESS-S CS
                         ResIII 165 lTATpe 170
                                    lT+Tp 
  gi|121638798|ref|YP_979022.1| 212 LTGTPF 217
                                    *****7 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-11   2.1e-08      26     201 ..      89     270 ..      78     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                      SWI2_SNF2  26 tqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakagee.kpkqaesrkeLkellekesekiifttiqK 104
                                    t GSGK+   + +a++ll+   +  +v vv+  + L+ Q ++ +a+ g + +pk a+s+     + + e +++++t  q 
  gi|121638798|ref|YP_979022.1|  89 TPGSGKTSFALRIAAELLR-YHTVEQVTVVVPTEHLKVQWAHAAAAHGLSlDPKFANSNP----QTSPEYHGVMVTYAQV 163
                                    88*********99999999.667777777888899******9999886551454555554....4445678999999998 PP

                      SWI2_SNF2 105 feeeekeklevlsereniivlvDEaHRs.qygelakklrkalpnaa.figFTGTPilkkd.........kktkevFg.ey 172
                                     ++   + ++v +e ++ +v++DE H     ++  + +r+a+ +a+ ++++TGTP  ++d          +   v   + 
  gi|121638798|ref|YP_979022.1| 164 ASHP--TLHRVRTEARKTLVVFDEIHHGgDAKTWGDAIREAFGDATrRLALTGTPFRSDDspipfvsyqPDADGVLRsQA 241
                                    8754..34788999999*******99863678999*******998736**********9966666544323333333467 PP

                      SWI2_SNF2 173 idkYtikeaveDgavvpilYesrlaklel 201
                                     ++Y  +ea +Dg+v p+++ +   +++ 
  gi|121638798|ref|YP_979022.1| 242 DHTYGYAEALADGVVRPVVFLAYSGQARW 270
                                    78***************887665555544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00025       4     144 ..      69     201 ..      67     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                                    HHHHHHHHH..TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 Qaeaiplil..gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    Q++a+ + l  + +d+l+ a  GsGKT  +l  + + +   +  t  ++ +v+Pt+ L  q ++ +   +  +d +    
  gi|121638798|ref|YP_979022.1|  69 QRRALVQYLgtQPRDFLAVATPGSGKTSFALRIAAELL---RYHTVEQVTVVVPTEHLKVQWAHAAAAHGLSLDPKFA-- 143
                                    66666666644568*************99888888777...589999****************999888887664443.. PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCT.TEEEEEEETHHHHHHT.TTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnls.qvrflVlDEadrlldq.gfsdfinr 144
                                     ++ +++        +++ v+ t  +++++ + ++++++ + +++V+DE++   d    +d i++
  gi|121638798|ref|YP_979022.1| 144 NSNPQTS-------PEYHGVMVTYAQVASHPTLHRVRTEaRKTLVVFDEIHHGGDAkTWGDAIRE 201
                                    2222222.......234444555555555443233333304467999999988777556666655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.8e-07   0.00078      57     110 ..     366     419 ..     334     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.8e-07
                                    HHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  57 eileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    + +++f +g+s+ L+a +++++G+d+p++++ +      ++  + q+iGR  R 
  gi|121638798|ref|YP_979022.1| 366 ARITEFAQGTSRWLVAVRMVSEGVDVPRLSVGVYATNASTPLFFAQAIGRFVRS 419
                                    56899*********************************************9995 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.4e-06    0.0089       3     100 ..      66     189 ..      64     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                         AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKt.talkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrl 80 
                                    +  Q++a+ + l+++ r  ++++ +G+GKt +al+ ++e+++ +  ++v ++ pt+    + a+++ +++ +++    + 
  gi|121638798|ref|YP_979022.1|  66 RGWQRRALVQYLGTQPRDFLAVATPGSGKTsFALRIAAELLRYHtVEQVTVVVPTEHLKVQWAHAAAAHGLSLDPKFANS 145
                                    56699999999999999************84689999*****99679999999999998888876666555555333333 PP

                         AAA_30  81 k.......................grarlepg.tllivDEagmv 100
                                    +                       +r+r e++ tl++ DE+   
  gi|121638798|ref|YP_979022.1| 146 NpqtspeyhgvmvtyaqvashptlHRVRTEARkTLVVFDEIHHG 189
                                    33666666667777777777788866777777799999998655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.8e-05     0.029      10      54 ..      81     123 ..      69     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA 54 
                                     + +l +a pG+GKT     i a+l++ ++v  e++++v +t++ 
  gi|121638798|ref|YP_979022.1|  81 PRDFLAVATPGSGKTSFALRIAAELLRYHTV--EQVTVVVPTEHL 123
                                    4557789**********************88..9*******9874 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.2e-05     0.069     116     216 ..     106     217 ..      94     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                                    HHH-TTS-EEE--SSHHHH.............-----------------EEEE-HHHHHHHT......TTS-S-S-SEEE CS
                                    xxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 116 erhvsssalrvlvyggqkk.............mkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvv 182
                                     r+    +++v+v +++ k              ++k  +  p++  +y+ v++tY  ++++    +   v ++ +   vv
  gi|121638798|ref|YP_979022.1| 106 LRYHTVEQVTVVVPTEHLKvqwahaaaahglsLDPKFANSNPQTSPEYHGVMVTYAQVASHP---TLHRVRTEARKTLVV 182
                                    5555555666666666655666777777777767777788999999*************666...566666788899*** PP

                                    ES-GGGT--TT...SHHHHHHHH---S-EEEE-S--S CS
                                    xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 183 lDEghtlknst...skaaeavskLstsnrwiltGTPi 216
                                     DE h  +  +     ++ea    ++ +r+ ltGTP 
  gi|121638798|ref|YP_979022.1| 183 FDEIHHGGDAKtwgDAIREAFG--DATRRLALTGTPF 217
                                    ******9999623356666666..7***********7 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.7e-05      0.11      15      53 ..      78     117 ..      74     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                                    SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE..EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                         DnaB_C  15 GlqkgdliiiAarpsmGktalalniaenaavkeklp..vav 53 
                                    G q+ d++ +A  p+ Gkt++al ia++    ++++   +v
  gi|121638798|ref|YP_979022.1|  78 GTQPRDFLAVA-TPGSGKTSFALRIAAELLRYHTVEqvTVV 117
                                    78888888886.6*************998864443332333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.37       4      69 ..      87     188 ..      84     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                    ESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSSS................................STTHHHHHHH CS
                            AAA   4 yGppGtGKTllakavakel....gvefleisgsellsk................................yvgesekkir 47 
                                    + +pG GKT++a  +a el     ve +++ +++   k                                +v  ++   +
  gi|121638798|ref|YP_979022.1|  87 VATPGSGKTSFALRIAAELlryhTVEQVTVVVPTEHLKvqwahaaaahglsldpkfansnpqtspeyhgvMVTYAQVASH 166
                                    678***************85544233222222222222444555555666666668888888888877553333333334 PP

                                    HHHHHHHHTSTSEEEEEETGGG CS
                            AAA  48 elfkeakekakpsilfiDEida 69 
                                     ++ +++++a+++ +++DEi+ 
  gi|121638798|ref|YP_979022.1| 167 PTLHRVRTEARKTLVVFDEIHH 188
                                    4555566666568899999986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00021      0.34      23      58 ..      85     120 ..      68     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                    EEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S CS
                           PhoH  23 faiGpaGtGKtylavalavealkkkkvkriiltrpa 58 
                                     a++  G+GKt +a+ +a+e+l+ ++v+++ ++ p+
  gi|121638798|ref|YP_979022.1|  85 LAVATPGSGKTSFALRIAAELLRYHTVEQVTVVVPT 120
                                    578889**********************99988776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00024       0.4      37      74 ..      85     125 ..      69     133 .. 0.74
   2 ?    0.9   0.1      0.18     3e+02      88     146 ..     315     357 ..     284     384 .. 0.60
   3 ?   -1.8   0.1       1.2   1.9e+03     166     188 ..     559     581 ..     522     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                         AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg...pvapeqgkV 74 
                                    l ++ pg+GKt +al +a+++++ + +      v++e+ kV
  gi|121638798|ref|YP_979022.1|  85 LAVATPGSGKTSFALRIAAELLRYHTVEQvtvVVPTEHLKV 125
                                    5689*****************96553322322333355555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                         AAA_25  88 rRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlv 146
                                    rRlr+++++++d ++  + +               + ++++++++l  ++++ e++ +v
  gi|121638798|ref|YP_979022.1| 315 RRLRQLRAHVPDAGGMIIAS---------------DRTTARAYARLLTTMTA-EEPTVV 357
                                    44444444443333332222...............22345677778888887.667666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                         AAA_25 166 galvealeriarrtgaavllvhH 188
                                    +++  +l++++r+++  v + hH
  gi|121638798|ref|YP_979022.1| 559 ASVHGQLRDLRRELHTLVSIAHH 581
                                    55566777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3356.81
//
Query:       gi|121638799|ref|YP_979023.1|  [L=808]
Description: PII uridylyl-transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-13   48.5   0.2    3.2e-12   46.7   0.2    2.0  1  HD             HD domain
    1.7e-10   41.2   0.1    1.1e-08   35.3   0.1    2.4  1  GlnD_UR_UTase  GlnD PII-uridylyltransferase
    0.00022   20.9   0.6       0.51   10.1   0.1    3.1  2  ACT            ACT domain
     0.0057   16.1   0.0      0.011   15.1   0.0    1.4  1  GlnE           Glutamate-ammonia ligase adenylyltransferase
  ------ inclusion threshold ------
      0.048   13.7   2.4      0.096   12.7   0.2    2.6  3  ACT_6          ACT domain
       0.12   13.0   0.2         38    5.0   0.0    3.0  3  ACT_4          ACT domain
       0.13   11.7   0.0       0.31   10.5   0.0    1.6  1  HDOD           HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2   1.2e-15   3.2e-12       2     109 ..     431     536 ..     430     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-15
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH...H CS
                             HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld...l 78 
                                    + H +e+a  a+ la +++    ++ll l+aLlHDiGkg+  d              H++ gae++  v+ rlgl+   +
  gi|121638799|ref|YP_979023.1| 431 DRHVVETAVHAAPLATRVA---RPDLLALGALLHDIGKGRGTD--------------HSVLGAELVIPVCTRLGLSppdV 493
                                    68****************8...******************998..............*********************** PP

                                    HHHHHHHHTTCCHHHHHHHH.........H...HHHCCTSCHH CS
                             HD  79 edvaklirehheswegkkrp.........r...glaerqlsle 109
                                    ++++kl+r+h+    +++r+             +l++ ++ le
  gi|121638799|ref|YP_979023.1| 494 WTLSKLVRHHLLLPITATRRdlndpktieAvseALGGDPQLLE 536
                                    ***************9999977766555414454444444444 PP

>> GlnD_UR_UTase  GlnD PII-uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   4.4e-12   1.1e-08      11     142 ..     177     288 ..     165     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.4e-12
                  GlnD_UR_UTase  11 karrgrsdtllepniKlGpGGlRdiefivqvlqlirGgrdpelrerstlealeelvergllteee..akelreayrflrr 88 
                                     +r gr  + +ep++KlG+GGlRd++++                    + al++l++r  + + +  a  l  ayr l +
  gi|121638799|ref|YP_979023.1| 177 WRRCGRIAQRAEPDLKLGRGGLRDVQLL----D---------------ALALAQLIDRHGIGHTDlpAGSLDGAYRTLLD 237
                                    45555555489*************9765....3...............3346667777777666533789********** PP

                  GlnD_UR_UTase  89 lehrLqlladrqthrLpfdeeeqrrlaealgyredkaafmkelfqhaerVrrlf 142
                                    ++  L+ +++r  ++L+++     ++ +alg+ +d+ ++ ++l  + ++++ + 
  gi|121638799|ref|YP_979023.1| 238 VRTELHRVSGRGRDHLLAQ--FADEISAALGF-GDRFDLARTLSSAGRTIGYHA 288
                                    *******************..***********.999999999999888887765 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0002      0.51       5      47 ..     613     655 ..     611     671 .. 0.78
   2 !    7.6   0.0    0.0012       3.1       2      60 ..     730     787 ..     729     789 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                    EEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEE CS
                            ACT   5 vgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvv 47 
                                    + +pD+ Gl ++ +++la + + ++s+++  +     ++++v 
  gi|121638799|ref|YP_979023.1| 613 IVAPDERGLVSKAAAVLALNSLRVHSASVNVHQGVAITEFVVS 655
                                    6799****************************88544444443 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                                    EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                            ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                    +l+v++ Dr GlLa ++gal  +g  i+ + + + + + a  vf+v v+ e d+ +++e
  gi|121638799|ref|YP_979023.1| 730 ILEVRAMDRAGLLALLAGALEGAGAGIVWAKVNTFGST-AADVFCVTVPAELDARAAVE 787
                                    699******************99988877777777776.67777777777777666666 PP

>> GlnE  Glutamate-ammonia ligase adenylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.4e-06     0.011     124     157 ..      54      87 ..      31     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-06
                                    TCC-SEEEEE-HHHHTT---TT--EEEEEEE--- CS
                           GlnE 124 gepqqllvlGmGklGgaELnysSDiDliflyded 157
                                    +++++++++G G lG +EL   SD+D+++l+d +
  gi|121638799|ref|YP_979023.1|  54 ADASGFAIVGVGGLGRRELLPYSDLDVLLLHDGK 87 
                                    45669*************************9976 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.5e+03      11      30 ..     337     356 ..     336     365 .. 0.84
   2 ?   -2.2   0.0       1.7   4.3e+03       9      38 ..     615     644 ..     613     648 .. 0.82
   3 ?   12.7   0.2   3.7e-05     0.096       3      64 ..     729     792 ..     728     800 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                          ACT_6  11 drpGltasLtsvlaefgvni 30 
                                    + pGl+ +++++ a+ g +i
  gi|121638799|ref|YP_979023.1| 337 HDPGLVLRVAAASADTGLPI 356
                                    579***********999887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                          ACT_6   9 GpdrpGltasLtsvlaefgvnilDieqavi 38 
                                     pd  Gl+++ ++vla +  ++    + v+
  gi|121638799|ref|YP_979023.1| 615 APDERGLVSKAAAVLALNSLRVHSASVNVH 644
                                    58999**********999999887777776 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 3.7e-05
                          ACT_6   3 llitvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlf 64 
                                    l++ v  +dr+Gl+a L+++l   g+ i+  ++ +++++ + +  v++p++  a a++e+ Ll+
  gi|121638799|ref|YP_979023.1| 729 LILEVRAMDRAGLLALLAGALEGAGAGIVWAKVNTFGSTAADVFCVTVPAEldARAAVEQHLLE 792
                                    67778889*****************************************666699999999987 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   5.3e+03      10      23 ..     396     409 ..     392     411 .. 0.84
   2 ?    4.2   0.1     0.025        64      10      53 ..     612     653 ..     608     655 .. 0.84
   3 ?    5.0   0.0     0.015        38       9      39 ..     731     761 ..     728     772 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                          ACT_4  10 eveaedrkglLadi 23 
                                    ++ea dr+gl++++
  gi|121638799|ref|YP_979023.1| 396 TIEALDRTGLWGRL 409
                                    699*******9876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                          ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkkdglaeikit 53 
                                     ++a d++gl+++ ++v++ +  +++s ++  +  +g+a  ++ 
  gi|121638799|ref|YP_979023.1| 612 VIVAPDERGLVSKAAAVLALNSLRVHSASVNVH--QGVAITEFV 653
                                    6899*****************999999999994..567776665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.015
                          ACT_4   9 leveaedrkglLaditqviseekanivsvna 39 
                                    lev a dr glLa ++ +++ ++a iv  ++
  gi|121638799|ref|YP_979023.1| 731 LEVRAMDRAGLLALLAGALEGAGAGIVWAKV 761
                                    89******************99999986665 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.31      96     132 ..     431     465 ..     419     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHH CS
                           HDOD  96 wehslavAlvarelaeelgledpeeaflaGLLhdiGk 132
                                     +h +++A+ a  la+++  +d   + l++LLhdiGk
  gi|121638799|ref|YP_979023.1| 431 DRHVVETAVHAAPLATRVARPD--LLALGALLHDIGK 465
                                    5899***********9998855..************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.61
# Mc/sec: 4009.88
//
Query:       gi|121638800|ref|YP_979024.1|  [L=112]
Description: nitrogen regulatory protein P-II glnB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-41  140.1   2.6    3.5e-41  139.9   2.6    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   2.6   1.9e-45   3.5e-41       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.9e-45
                                    EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-S CS
                           P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaakt 80 
                                    i+ai++p++l++vk+ Le+agv g+tv+e++G+G+qkghte+yrgaey+v+++pkv++e+vv+d+ v+kvv+ i++aa+t
  gi|121638800|ref|YP_979024.1|   4 ITAIVKPFTLDDVKTSLEDAGVLGMTVSEIQGYGRQKGHTEVYRGAEYSVDFVPKVRIEVVVDDSIVDKVVDSIVRAART 83 
                                    89****************************************************************************** PP

                                    SSTTSEEEEEEEESEEEETTTT CS
                           P-II  81 geiGDGkiFvlpveevirirtg 102
                                    g+iGDGk++v+pv++++r+rtg
  gi|121638800|ref|YP_979024.1|  84 GKIGDGKVWVSPVDTIVRVRTG 105
                                    *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 634.67
//
Query:       gi|121638801|ref|YP_979025.1|  [L=477]
Description: ammonium-transport integral membrane protein amt [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-138  460.9  37.8   3.4e-138  460.7  37.8    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.7  37.8  1.9e-142  3.4e-138       1     399 []      16     441 ..      16     441 .. 0.97

  Alignments for each domain:
  == domain 1  score: 460.7 bits;  conditional E-value: 1.9e-142
                                    HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-..........T CS
                Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign..........l 70 
                                    a++l+s+alv++m++g+a++++g+vrsk+vln++++++++++vv++l+ l+Gys+afg++  v++++gn          +
  gi|121638801|ref|YP_979025.1|  16 AWMLVSSALVLLMTPGLAFFYGGMVRSKSVLNMIMMSISAMGVVTVLWALYGYSIAFGDD--VGNIAGNpsqywglkglI 93 
                                    7**********************************************************9..*****************6 PP

                                    TTTSCCGCCTTCCHHH............HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.S CS
                Ammonium_transp  71 glsaagvqdetlldgl............fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeg 138
                                    g++a++++ +t+++++            f++fql+fa+++++++sgava+r+kf a+llf+ l++t+vy+pvahwv++ +
  gi|121638801|ref|YP_979025.1|  94 GVNAVAADPSTQTAAVniplagtlpatvFVAFQLMFAIITVALISGAVADRLKFGAWLLFAGLWATFVYFPVAHWVFAFD 173
                                    6666666666666666667777777777***************************************************9 PP

                                    SHHHHTT--........-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGG CS
                Ammonium_transp 139 gwlaklgvl.......iDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGs 211
                                    g++a++g +       iDfAg+t+VH+++gva+L++a+vlgkr+g+    ++ +++hnlpf++lG++lLwfgW+gFNaGs
  gi|121638801|ref|YP_979025.1| 174 GFAAEHGGWianklhaIDFAGGTAVHINAGVAALMLAIVLGKRRGWP---ATLFRPHNLPFVMLGAALLWFGWYGFNAGS 250
                                    9999999999999999******************************9...9***************************** PP

                                    GSSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHH CS
                Ammonium_transp 212 altankrararaavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlg 291
                                    a+tan++a a ++vtT++A+aa++l++ll++r+++gk ++lg+a+Gi+AGlVAiT++c+ v+++gAl++G+ Agvl+ l+
  gi|121638801|ref|YP_979025.1| 251 ATTANGVAGA-TFVTTTIATAAAMLGWLLTERVRDGKATTLGAASGIVAGLVAITPSCSSVNVLGALAVGVSAGVLCALA 329
                                    **********.********************************************************************* PP

                                    HHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC....SSHSSTTGGGT-C.HHHHHHHHHHHHHHHHHHHHHH CS
                Ammonium_transp 292 vkklkeklkidDsldvvavHgvgGiwGllavgifaaekvv....askisggllsgeg.kqlvvqligilvilayafvvtl 366
                                    v  lk kl++dDsldvv+vH+vgG++G+l+vg++aa++++    ++++s+gl++g+g +ql +q++g++ +l+y+ ++tl
  gi|121638801|ref|YP_979025.1| 330 VG-LKFKLGFDDSLDVVGVHLVGGLVGTLLVGLLAAPEAPaingVAGVSKGLFYGGGfAQLERQALGACSVLVYSGIITL 408
                                    *8.***********************************99****9***********99********************** PP

                                    HHHHHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
                Ammonium_transp 367 illlllklllgLrvseeeeevglDvaehgetay 399
                                    il+l+lk+++gLr+++e+e++g+D+aeh+e++y
  gi|121638801|ref|YP_979025.1| 409 ILALILKFTIGLRLDAEQESTGIDEAEHAESGY 441
                                    ******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2610.55
//
Query:       gi|121638802|ref|YP_979026.1|  [L=422]
Description: cell division protein ftsY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-73  244.6   0.7      8e-73  244.3   0.7    1.1  1  SRP54            SRP54-type protein, GTPase domain
    6.1e-07   29.4   2.5    1.1e-06   28.5   2.5    1.3  1  AAA_30           AAA domain
    1.6e-06   28.3   0.0    3.5e-06   27.2   0.0    1.5  1  SRP54_N          SRP54-type protein, helical bundle domain
    2.1e-06   28.2   1.9    2.6e-06   27.9   0.7    1.8  2  AAA_16           AAA ATPase domain
    5.4e-05   23.3   0.0    0.00017   21.7   0.0    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00088   18.3   5.6      0.012   14.6   5.6    2.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0025   18.2   0.3     0.0043   17.4   0.3    1.4  1  AAA_19           AAA domain
     0.0034   17.7   0.0     0.0075   16.5   0.0    1.5  1  AAA_22           AAA domain
     0.0035   17.1   0.0     0.0051   16.5   0.0    1.2  1  AAA_24           AAA domain
     0.0038   17.1   1.2      0.063   13.2   0.1    2.2  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0052   16.1   0.1     0.0086   15.4   0.1    1.2  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.025   14.7   0.1    1.8  1  AAA_33           AAA domain
      0.014   15.5   1.0      0.039   14.0   0.5    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
      0.027   14.9   0.2      0.083   13.3   0.2    1.8  1  AAA              ATPase family associated with various cellul
      0.028   14.4   0.2      0.081   12.9   0.2    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.052   13.8   0.0      0.092   13.0   0.0    1.4  1  AAA_28           AAA domain
      0.058   13.1   1.7        4.4    7.0   0.2    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.063   13.2   1.3       0.95    9.4   0.7    2.2  2  NTPase_1         NTPase
      0.091   12.7   0.0       0.14   12.1   0.0    1.2  1  Rad17            Rad17 P-loop domain
       0.11   12.2   0.1       0.25   11.1   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
       0.14   12.1   0.1       0.24   11.3   0.1    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.14   11.4   0.1       0.24   10.7   0.1    1.3  1  VirC1            VirC1 protein
       0.15   11.7   0.1       0.26   10.9   0.1    1.3  1  Thymidylate_kin  Thymidylate kinase
       0.16   12.4   0.1       0.37   11.2   0.1    1.6  1  AAA_17           AAA domain
       0.16   12.1   0.0        0.5   10.5   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.26   10.8   0.0        1.8    8.1   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
       0.83    9.2   4.8          8    6.0   4.8    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
        1.1    8.8   6.1        2.4    7.6   2.6    2.6  2  SKG6             Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.3   0.7   1.2e-75     8e-73       1     196 []     223     422 .]     223     422 .] 0.99

  Alignments for each domain:
  == domain 1  score: 244.3 bits;  conditional E-value: 1.2e-75
                                    SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHH CS
                          SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekak 80 
                                    p+v+l+vG++G+GKTtt++KLa++l ++g++v+l aaDtfRaaA++QL+t+a ++g+ v++  e+adpa+va++av+k  
  gi|121638802|ref|YP_979026.1| 223 PSVLLVVGVNGTGKTTTVGKLARVLVADGRRVVLGAADTFRAAAADQLQTWAARVGAAVVRGPEGADPASVAFDAVDKGI 302
                                    6799**************************************************************************** PP

                                    HTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH....SSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSST CS
                          SRP54  81 eekidvvlvDTaGrlqndkelmeelkkikkvv....kpdevllvldattgqeavkqakaFkeavgitgviltklDgdakg 156
                                    + ++dvvl+DTaGrl+++  lm+el+k+k+vv    + devllvldat+gq+ ++qa+ F+e+v+i+g++ltklDg+akg
  gi|121638802|ref|YP_979026.1| 303 AAGADVVLIDTAGRLHTKVGLMDELDKVKRVVtrraSVDEVLLVLDATIGQNGLAQARVFAEVVDISGAVLTKLDGTAKG 382
                                    ********************************999999****************************************** PP

                                    THHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 157 GaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                    G+++ +++el++P+k++g+Ge  +dl++f+p ++v++llg
  gi|121638802|ref|YP_979026.1| 383 GIVFRVQQELGVPVKLVGLGEGPDDLAPFEPAAFVDALLG 422
                                    *************************************985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   2.5   1.7e-09   1.1e-06      19     103 ..     224     320 ..     212     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-09
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkv..Laeelgieastiakllkrlk.............g 82 
                                     v +++G+ GtGKtt++++l++++ a+g+rv+ g+A t +aA++  L++     a+++   + r               +
  gi|121638802|ref|YP_979026.1| 224 SVLLVVGVNGTGKTTTVGKLARVLVADGRRVVlGAADTFRAAAAdqLQT----WAARVGAAVVRGPegadpasvafdavD 299
                                    4889***********************9887747888766655311553....333333333222235566788888843 PP

                         AAA_30  83 rarlepg.tllivDEagmvdtk 103
                                     + +++g +++++D ag + tk
  gi|121638802|ref|YP_979026.1| 300 -KGIAAGaDVVLIDTAGRLHTK 320
                                    .678888899999999998775 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   5.4e-09   3.5e-06       2      75 .]     138     202 ..     137     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.4e-09
                                    HHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                        SRP54_N   2 gkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75 
                                    g++l +++    g++ +de+ +++    +e++Ll aD+g  ++ +++++++  ++ + ++++  + + +++d L
  gi|121638802|ref|YP_979026.1| 138 GRGLLGLI----GGGDLDEDSWQD----VEDTLLVADLGPAATASVVSQLRS-RLASGNVRTEADARAVLRDVL 202
                                    56666666....4799********....**********************99.666599*99999999999965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.6     3e+03      80      88 ..     140     148 ..      68     208 .. 0.62
   2 !   27.9   0.7   4.1e-09   2.6e-06      20     142 ..     219     348 ..     195     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.6
                         AAA_16  80 ellrqllde 88 
                                    +ll  ++  
  gi|121638802|ref|YP_979026.1| 140 GLLGLIGGG 148
                                    333333333 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 4.1e-09
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa..ipysalaqalareellrqlldeaesaeleaw 97 
                                    ++g p+++l++G  G+GK++ v +l+r l +dg  ++ g +d +++a    ++++a    +  +   ++++++s +++a 
  gi|121638802|ref|YP_979026.1| 219 HAGHPSVLLVVGVNGTGKTTTVGKLARVLVADGRRVVLGAADTFRAAaaDQLQTWAARVGAAVVRGPEGADPASVAFDAV 298
                                    57889***************************************333112234477777665555555555555555555 PP

                         AAA_16  98 rekleealaavpelagaea.......srllellkrll.allsrderplvlvlD 142
                                    ++ + + +  v  ++ a++        + l+++kr + +++s  ++ ++lvlD
  gi|121638802|ref|YP_979026.1| 299 DKGIAAGAD-VVLIDTAGRlhtkvglMDELDKVKRVVtRRASV-DE-VLLVLD 348
                                    554444443.333333333556666788888888888777776.55.788888 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.6e-07   0.00017       9      87 ..     233     379 ..     225     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.6e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    G+GKTt++ +Lar l  +g+rV+l  aD+ + ++a       d+ +                                  
  gi|121638802|ref|YP_979026.1| 233 GTGKTTTVGKLARVLVADGRRVVLGAADTFRAAAA-------DQLQtwaarvgaavvrgpegadpasvafdavdkgiaag 305
                                    9***************************9988887.......22223555578888888888888888888888888888 PP

                                    .................................................CCHCCCHHHHHHCHCHHHH..........EE CS
                                    .................................................xxxxxxxxxxxxxxxxxxx........xxxx RF
                           CbiA  55 .................................................dlkrllellealgkkkall........lkia 77 
                                                                                     +l                +        ++i 
  gi|121638802|ref|YP_979026.1| 306 advvlidtagrlhtkvglmdeldkvkrvvtrrasvdevllvldatigqnGL----------------AqarvfaevVDIS 369
                                    888888888888888888888888888888777555555544433322222................1233333445778 PP

                                    EEEEEEESS. CS
                                    xxxxxxxxxx RF
                           CbiA  78 gvvlnrvdge 87 
                                    g vl++ dg 
  gi|121638802|ref|YP_979026.1| 370 GAVLTKLDGT 379
                                    8888888876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   5.6   1.9e-05     0.012      21      67 ..     215     261 ..     204     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                    HHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB  21 rllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                    r+l++aG+  v+ + Gv G+Gk t+v +l+  l++ G+rv + a D 
  gi|121638802|ref|YP_979026.1| 215 RALPHAGHPSVLLVVGVNGTGKTTTVGKLARVLVADGRRVVLGAADT 261
                                    5689************************************9888774 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   6.7e-06    0.0043       9      69 ..     222     303 ..     214     366 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.7e-06
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae.................. 68 
                                    + +vllv++  GtGKT+++ +  ++lv+ g++    +l +  +f   Aa++l++  a +ga+                  
  gi|121638802|ref|YP_979026.1| 222 HPSVLLVVGVNGTGKTTTVGKLARVLVADGRR---VVLGAadTFRAAAADQLQTWAARVGAAvvrgpegadpasvafdav 298
                                    67899**********************99954...455550155555667777766555555566666666655555555 PP

                         AAA_19  69 ....a 69 
                                        a
  gi|121638802|ref|YP_979026.1| 299 dkgiA 303
                                    55540 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0075       4     111 ..     222     329 ..     219     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelkaerlsseel 78 
                                    + ++l+v+G  GtGKTt++ +l++ l+++      +++vv     ++ +++   +++ + ++  a+ ++ ++  +  +  
  gi|121638802|ref|YP_979026.1| 222 HPSVLLVVGVNGTGKTTTVGKLARVLVAD------GRRVVlgaadTFRAAAADQLQTWAARVGAAVVRGPEG-ADPASVA 294
                                    67899*********************987......8888889888888888889999999999999999888.6666666 PP

                         AAA_22  79 lealeqalraravielliiDEaqhlr.s...eealee 111
                                    ++a+ + + a a+  +++iD a +l  +   ++ l +
  gi|121638802|ref|YP_979026.1| 295 FDAVDKGIAAGAD--VVLIDTAGRLHtKvglMDELDK 329
                                    6999999999999..9999999998542444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     8e-06    0.0051       4      78 ..     225     318 ..     222     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8e-06
                         AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtek....Glksldadkfpdieswedfldevvel................aael 63 
                                     +l++G +g+GKTt++ +l  ++l+ d  +     ++   a+  +++++w++ + ++v                  +   
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKL-ARVLVADGRRvvlgAADTFRAAAADQLQTWAARVGAAVVRgpegadpasvafdavdKGIA 303
                                    5799***************.888888655431101223344555555588888888888899999999999999999999 PP

                         AAA_24  64 adyktlviDtidele 78 
                                    a+ +++ iDt++ l 
  gi|121638802|ref|YP_979026.1| 304 AGADVVLIDTAGRLH 318
                                    999999999998875 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   9.9e-05     0.063       1      30 [.     225     254 ..     225     269 .. 0.94
   2 ?    2.6   0.1      0.19   1.2e+02      54      95 ..     303     344 ..     297     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-05
                           MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                    vl +vg +g+GKTt + kl ++l a g rv
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLARVLVADGRRV 254
                                    6889***********************998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                           MobB  54 kAGAkevlvaskerlalikeleeaelsleellarlsevDlvl 95 
                                    +AGA+ vl+ +  rl     l ++  +++++++r ++vD vl
  gi|121638802|ref|YP_979026.1| 303 AAGADVVLIDTAGRLHTKVGLMDELDKVKRVVTRRASVDEVL 344
                                    69*********9999887777554677999999999999887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.3e-05    0.0086      10      57 ..     217     265 ..     208     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                     Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdelerqgnvvrl.dpDdlRel 57 
                                     p   +P ++l++G  G GK+++  +l++ l ++g+ v+l  +D++R+ 
  gi|121638802|ref|YP_979026.1| 217 LPHAGHPSVLLVVGVNGTGKTTTVGKLARVLVADGRRVVLgAADTFRAA 265
                                    567799************************9966665555268999975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.9e-05     0.025       1      38 [.     225     267 ..     225     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-05
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg....avll.ssdtlrrrlf 38 
                                    ++l+vG++G+GK+t + +l++ l      v+l + dt+r + +
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLARVLVadgrRVVLgAADTFRAAAA 267
                                    789***************9988877767444414455444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   6.1e-05     0.039       4      93 ..     228     359 ..     225     377 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-05
                                    EEESTTSSHHHHHHHHHT...............S.TEEESSSTTSSSSEEEEEEEETTEE.................... CS
                       MMR_HSR1   4 ivGrpNvGKStLinaltg...............e.kaivsdkpgtTrdinegrvklkgke.................... 47 
                                    +vG   +GK+t + +l +               + +a ++d+ +t    + + v  +g+e                    
  gi|121638802|ref|YP_979026.1| 228 VVGVNGTGKTTTVGKLARvlvadgrrvvlgaadTfRAAAADQLQTWAARVGAAVV-RGPEgadpasvafdavdkgiaaga 306
                                    7788888888888888754444444444444321344444444444444444333.221133344444444444444444 PP

                                    .EEEEECGGCSS...HHHHHH.HHHHHHHHHHCTSEEEEEEETT..TTCSHHH CS
                       MMR_HSR1  48 .ielvDtpGlie...gaseek.glgkaflaleeadlillvvdas..eeklkpl 93 
                                     ++l+Dt+G ++   g  +e  ++++ + +  ++d +llv+da+  +++l++ 
  gi|121638802|ref|YP_979026.1| 307 dVVLIDTAGRLHtkvGLMDELdKVKRVVTRRASVDEVLLVLDATigQNGLAQA 359
                                    4********7653332333333455555555558********88775555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00013     0.083       1      38 [.     226     282 ..     226     354 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                    EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS.........S CS
                            AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk.........y 38 
                                    +l++G  GtGKT+++  +a+ l           ++ ++  +++ l+          +
  gi|121638802|ref|YP_979026.1| 226 LLVVGVNGTGKTTTVGKLARVLvadgrrvvlgAADTFRAAAADQLQTwaarvgaavV 282
                                    699*****************9855533222222334444444444444444444431 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00013     0.081       2      37 ..     226     262 ..     225     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtt 37 
                                    +l+vG  GtgK++ + +la++l  +   +v++ +dt 
  gi|121638802|ref|YP_979026.1| 226 LLVVGVNGTGKTTTVGKLARVLvADGRRVVLGAADTF 262
                                    689*******************977777777777775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.092       4      41 ..     228     272 ..     225     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                         AAA_28   4 itGgestGKTtlleaLa....argypvv...pEaareileeklak 41 
                                    ++G  +tGKTt++ +La    a+g +vv   ++++r    ++l++
  gi|121638802|ref|YP_979026.1| 228 VVGVNGTGKTTTVGKLArvlvADGRRVVlgaADTFRAAAADQLQT 272
                                    78999************5555559999966666666666666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.019        12      43      79 ..     219     255 ..     181     269 .. 0.85
   2 ?    7.0   0.2    0.0069       4.4      42     127 ..     272     359 ..     258     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                      IstB_IS21  43 fiekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                    +  +   ++++G  G+GK+     l++  v++g +v+
  gi|121638802|ref|YP_979026.1| 219 HAGHPSVLLVVGVNGTGKTTTVGKLARVLVADGRRVV 255
                                    5556667899***********************9997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                      IstB_IS21  42 sfiekkenivllGpsGvGKshlaialgveavraglsvlfv.rvedLveelkrarrdgklaralkrllkv.d.llilDdlg 118
                                     + ++  + v+ Gp G+  + +a     ++++ag  v+ + ++ +L +++ + ++ +k++r ++r + v + ll+lD   
  gi|121638802|ref|YP_979026.1| 272 TWAARVGAAVVRGPEGADPASVAFDAVDKGIAAGADVVLIdTAGRLHTKVGLMDELDKVKRVVTRRASVdEvLLVLDA-T 350
                                    5888889999*************************9988725679*******************99999543566664.3 PP

                      IstB_IS21 119 llpldqaea 127
                                    + +   a+a
  gi|121638802|ref|YP_979026.1| 351 IGQNGLAQA 359
                                    333333444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.7    0.0015      0.95       3      30 ..     227     254 ..     225     258 .. 0.90
   2 ?    1.9   0.0      0.29   1.9e+02      82     114 ..     291     324 ..     263     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                                    EEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkv 30 
                                    ++ G  G+GKtT v k++++l  +g +v
  gi|121638802|ref|YP_979026.1| 227 LVVGVNGTGKTTTVGKLARVLVADGRRV 254
                                    68899****************9999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                                    HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHH CS
                       NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkf 114
                                     ++a +a++k +  +adv++iD  G++  k+  +
  gi|121638802|ref|YP_979026.1| 291 ASVAFDAVDKGIaAGADVVLIDTAGRLHTKVGLM 324
                                    467777888777789**********998877554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.14      39      73 ..     216     251 ..     196     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                          Rad17  39 vLesrkkr.iLLisGPsGCgkstvvkvLskelgikl 73 
                                     L+++ +  +LL+ G  G gk+t+v  L++ l+ + 
  gi|121638802|ref|YP_979026.1| 216 ALPHAGHPsVLLVVGVNGTGKTTTVGKLARVLVADG 251
                                    5777777569********************999765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00038      0.25      24      51 ..     225     252 ..     213     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                         AAA_29  24 atlltGpsGsGKSTllDAiqalLvpakk 51 
                                    + l++G +G+GK+T +  ++ +Lv++ +
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLARVLVADGR 252
                                    6899*******************99874 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00038      0.24       2      48 ..     223     269 ..     222     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkd 48 
                                    + v+++ G+ g+GK+t   +l++ Lv++g++v+l   d+ R     +
  gi|121638802|ref|YP_979026.1| 223 PSVLLVVGVNGTGKTTTVGKLARVLVADGRRVVLGAADTFRAAAADQ 269
                                    578999**************************999999999876655 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00037      0.24      12      44 ..     233     265 ..     226     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                          VirC1  12 GaGkttalmglcsalasdgkrvalfeadenrPl 44 
                                    G+Gktt++  l   l++dg+rv l  ad  r  
  gi|121638802|ref|YP_979026.1| 233 GTGKTTTVGKLARVLVADGRRVVLGAADTFRAA 265
                                    99***********************99987754 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00041      0.26       3      29 ..     230     256 ..     228     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                                    ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                                    G++G+GKtt + +l++ l + g++vvl
  gi|121638802|ref|YP_979026.1| 230 GVNGTGKTTTVGKLARVLVADGRRVVL 256
                                    9*********************99775 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00057      0.37       1     108 [.     229     346 ..     229     352 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00057
                                    EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT..T.SHSSHHHHCTSHHHHHH.HHH.HHHHHHHHHHHHS CS
                         AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg..g.lakardemrklpleekk.elq.keaaekiaeeakk 71 
                                    +G+ G GK+t + kl++ +       +l a d +r+ a+++    +a+   ++ ++p+  +   +  + + + ia  a+ 
  gi|121638802|ref|YP_979026.1| 229 VGVNGTGKTTTVGKLARVLvadgRRVVLGAADTFRAAAADQlqTwAARVGAAVVRGPEGADPaSVAfDAVDKGIA--AGA 306
                                    79*************9988777688899*******9987774211122333333444333220233134444444..478 PP

                                    SEEEEEE-SEEEETTEEEESSH...HHHHHHH..SEEEEE CS
                         AAA_17  72 kgvlvdghprikeqagfldglp...kevleelkpdaiill 108
                                    + vl+d+  r+ ++ g++d+l+   + v + +++d ++l+
  gi|121638802|ref|YP_979026.1| 307 DVVLIDTAGRLHTKVGLMDELDkvkRVVTRRASVDEVLLV 346
                                    8999999999999977655555111555677777777664 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00077       0.5       5      96 ..     225     344 ..     222     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                                    -EEEE--TTSSHHHHHHHHHHHTT-...........-EEEEEGGG---..----THHHHHHHHHTTT-HHHH..TTS... CS
                          AAA_2   5 silllgptgvGktelakalaellfv.......kkekkliradaselle..eeevehlvsrligappgyvgae..egG... 70 
                                     +l++g +g+Gkt +  +la++l +       +  +++  a a +l++  +   + +v   +ga p+ v+++  ++G   
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLARVLVAdgrrvvlGAADTFRAAAADQLQTwaARVGAAVVRGPEGADPASVAFDavDKGiaa 304
                                    57899******************867777777777777777777777764444456666677777777776522455999 PP

                                    ................EEEEETGGG-------------HHHH CS
                          AAA_2  71 ................ivllDEidKihpkessgadvSregVq 96 
                                                    + l+DE+dK+++    ++  S ++V+
  gi|121638802|ref|YP_979026.1| 305 gadvvlidtagrlhtkVGLMDELDKVKR--VVTRRASVDEVL 344
                                    9**99999999****999*******999..777777777775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2     8e+02     138     161 ..     150     173 ..     146     185 .. 0.77
   2 ?    8.1   0.0    0.0028       1.8      35      56 ..     225     246 ..     214     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                          AAA_7 138 rkklefkeikdvqlvaamgppggg 161
                                    +++ ++++++d+ lva  gp +  
  gi|121638802|ref|YP_979026.1| 150 LDEDSWQDVEDTLLVADLGPAATA 173
                                    55669***********99998766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0028
                          AAA_7  35 pvllvGptGtGKtviikdllkk 56 
                                     +l+vG  GtGKt+++ +l + 
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLARV 246
                                    4799***********9988765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.8     0.012         8       2     153 ..     225     379 ..     224     393 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefge.vsiDaellret..gveivelenGciCctlredllkeleal 76 
                                    v++++G  G+GKTt + +l     ++g+++ +   +     + D+    ++  g+ +v   +G  + +++ d++   ++ 
  gi|121638802|ref|YP_979026.1| 225 VLLVVGVNGTGKTTTVGKLArvLVADGRRVVLGAADTFRaAAADQLQTWAArvGAAVVRGPEGADPASVAFDAV---DKG 301
                                    67889999999999999988655566666666566655424555544433323555777777777766444443...333 PP

                                    HHHHTT-SEEEEEECTTTTHHHHHTT.....SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                           cobW  77 eereerldviliEttGlaePapvaft.....eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                     +     dv+li t G ++ +  ++      ++ +++++ +d v+ v+Da  + +++  +++ + + +  +   vl+K D
  gi|121638802|ref|YP_979026.1| 302 IAAG--ADVVLIDTAGRLHTKVGLMDeldkvKRVVTRRASVDEVLLVLDA-TIGQNGLAQARVFAEVVDISGA-VLTKLD 377
                                    3344..79********888877744457788889999*************.5568888888888888888775.567777 PP

                                    HH CS
                           cobW 152 ll 153
                                      
  gi|121638802|ref|YP_979026.1| 378 GT 379
                                    65 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.6    0.0038       2.4      21      38 .]      15      32 ..       9      32 .. 0.91
   2 ?    1.5   0.1      0.31     2e+02       7      17 ..     272     282 ..     268     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                           SKG6 21 aViiivLlailifvrRRk 38
                                    V+i++L  +l+++rRR+
  gi|121638802|ref|YP_979026.1| 15 LVVIAALTLGLVLYRRRR 32
                                   69**************96 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.31
                           SKG6   7 sntvaIavaVa 17 
                                    ++++ +++aV+
  gi|121638802|ref|YP_979026.1| 272 TWAARVGAAVV 282
                                    899*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.82u 0.40s 00:00:01.22 Elapsed: 00:00:00.59
# Mc/sec: 2151.30
//
Query:       gi|121638803|ref|YP_979027.1|  [L=1205]
Description: chromosome partition protein smc [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-74  248.7   0.0    4.9e-74  248.5   0.0    1.1  1  SMC_N      RecF/RecN/SMC N terminal domain
    3.9e-21   75.5   0.0    1.4e-20   73.8   0.0    2.0  1  SMC_hinge  SMC proteins Flexible Hinge Domain
    3.2e-18   66.6   0.1    4.6e-09   36.5   0.0    2.4  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    3.5e-16   60.3   0.0    3.5e-16   60.3   0.0    3.1  3  AAA_23     AAA domain
    1.2e-11   45.0   0.0    1.2e-08   35.1   0.0    2.2  2  AAA_15     AAA ATPase domain
    5.8e-06   26.0   0.0    1.1e-05   25.0   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
    0.00046   20.7   0.1      0.066   13.7   0.0    3.6  3  ABC_tran   ABC transporter
     0.0087   16.4   2.3        5.4    7.5   0.0    5.5  6  FlaC_arch  Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
       0.22   11.8   5.9          4    7.7   0.0    3.9  4  AAA_22     AAA domain
       0.25   11.6   6.4        1.1    9.5   0.0    4.7  4  XhlA       Haemolysin XhlA


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.5   0.0   2.8e-77   4.9e-74       1     219 [.       2    1185 ..       2    1186 .. 1.00

  Alignments for each domain:
  == domain 1  score: 248.5 bits;  conditional E-value: 2.8e-77
                                     EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkka 77  
                                     +lk+l++++Fks+a   ++l+f++++ta+vGpNGSGKsn++dA+ +v+Ge+ ak+lr  k++d+i++ ++++a + +a
  gi|121638803|ref|YP_979027.1|    2 YLKSLTLKGFKSFA-APTTLRFEPGITAVVGPNGSGKSNVVDALAWVMGEQGAKTLRGGKMEDVIFAgTSSRAPLGRA 78  
                                     699**********8.****************************************************9999******* PP

                                     EEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                          SMC_N   78 eveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.................... 135 
                                     ev++ +dn+d++l+ie +evsi+rr++r+g sey+ing++++  +v+ell+++gi +e                    
  gi|121638803|ref|YP_979027.1|   79 EVTVSIDNSDNALPIEYTEVSITRRMFRDGASEYEINGSSCRLMDVQELLSDSGIGREmhvivgqgkleeilqsrped 156 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  157 rrafieeaagvlkhrkrkekalrkldtmaanlarltdlttelrrqlkplgrqaeaaqraaaiqadlrdarlrlaaddl 234 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  235 vsrraereavfqaeaamrrehdeaaarlavaseelaahesavaelstraesiqhtwfglsalaervdatvriaserah 312 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  313 hldiepvavsdtdprkpeeleaeaqqvavaeqqllaeldaararldaaraeradrerraaeadrahlaavreeadrre 390 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  391 glarlagqvetmrarvesidesvarlseriedaamraqqtraefetvqgrigeldqgevgldehhertvaalrlader 468 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  469 vaelqsaeraaerqvaslraridalavglqrkdgaawlahnrsgaglfgsiaqlvkvrsgyeaalaaalgpaadalav 546 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  547 dgltaagsavsalkqadggravlvlsdwpapqapqsasgemlpsgaqwaldlvesppqlvgamiamlsgvavvndlte 624 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  625 amglveirpelravtvdgdlvgagwvsggsdrklstlevtseidkarselaaaealaaqlnaalagalteqsagqdaa 702 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  703 eqalaalnesdtaisamyeqlgrlgqearaaeeewnrllqqrteqeavrtqtlddviqletqlrkaqetqrvqvaqpi 780 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  781 drqaisaaadrargvevearlavrtaeeranavrgradslrraaaaerearvraqqaraarlhaaavaaavadcgrll 858 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  859 agrlhravdgasqlrdasaaqrqqrlaamaavrdevntlsarvgeltdslhrdelanaqaalrieqleqmvleqfgma 936 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1|  937 padliteygphvalpptelemaefeqarergeqviapapmpfdrvtqerrakraeralaelgrvnplaleefaaleer 1014
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|121638803|ref|YP_979027.1| 1015 ynflstqledvkaarkdllgvvadvdarilqvfndafvdverefrgvftalfpggegrlrltepddmlttgievearp 1092
                                     ****************************************************************************** PP

                                     .........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                     .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  136 .........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204 
                                              lLSgGek+L+a+a+l+Ai +++p+p+y++De++aaLD+ n +++ +l+++ ++++Q+i+i++++ ++e 
  gi|121638803|ref|YP_979027.1| 1093 pgkkitrlsLLSGGEKALTAVAMLVAIFRARPSPFYIMDEVEAALDDVNLRRLLSLFEQLREQSQIIIITHQKPTMEV 1170
                                     ****************************************************************************** PP

                                     -SCEEEEEEEETTEE CS
                                     xxxxxxxxxxxxxxx RF
                          SMC_N  205 adklvgvtkvengvs 219 
                                     ad+l+gvt++++g++
  gi|121638803|ref|YP_979027.1| 1171 ADALYGVTMQNDGIT 1185
                                     *********999875 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   7.7e-24   1.4e-20       3     116 ..     514     628 ..     512     629 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 7.7e-24
                      SMC_hinge   3 gvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns.gav 81 
                                    g++G +a+l++v++gye+A++aalg++++al v+   +a ++++ lk++++gra ++  d   ++ ++++  +  + ga+
  gi|121638803|ref|YP_979027.1| 514 GLFGSIAQLVKVRSGYEAALAAALGPAADALAVDGLTAAGSAVSALKQADGGRAVLVLSDWPAPQAPQSASGEMLPsGAQ 593
                                    89***********************************************************9999999999888889*** PP

                      SMC_hinge  82 plidlvevddelrkalryllgdtlvvdsldeAeel 116
                                    +++dlve +++l  a+  +l+++ vv++l eA  l
  gi|121638803|ref|YP_979027.1| 594 WALDLVESPPQLVGAMIAMLSGVAVVNDLTEAMGL 628
                                    *******************************9765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.3e-09   2.4e-06       1      65 [.      26      84 ..      26      98 .. 0.82
   2 !   36.5   0.0   2.5e-12   4.6e-09     219     299 ..    1056    1166 ..     977    1170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieef 65
                                   +++++GpNgsGKSn+ dal ++     ++e++  +l+gg+++++i     +++p +++e +++  
  gi|121638803|ref|YP_979027.1| 26 ITAVVGPNGSGKSNVVDALAWV-----MGEQGAKTLRGGKMEDVIFAGTSSRAPLGRAEVTVS-I 84
                                   79*****************988.....778888888888888888888888888888777776.4 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.5e-12
                         AAA_21  219 r.............................gvvflengdgqelparelSdGtkrl.l.alltallralkkgsllliDE 265 
                                     r                               v   +++ + + ++ lS G k l + a+l+a++ra+++ ++++ DE
  gi|121638803|ref|YP_979027.1| 1056 RefrgvftalfpggegrlrltepddmlttgIEVEARPPGKKITRLSLLSGGEKALtAvAMLVAIFRARPS-PFYIMDE 1132
                                     1555555555555555555555555666556666677888999999*********758************.******* PP

                         AAA_21  266 pEngLHPkllrrllellkelsrngaQviltTHS.p 299 
                                     +E+ L+   lrrll l+++l++  +Q+i+ TH+ p
  gi|121638803|ref|YP_979027.1| 1133 VEAALDDVNLRRLLSLFEQLRE-QSQIIIITHQkP 1166
                                     ********************99.*********855 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0     2e-19   3.5e-16       1     196 [.       5     199 ..       5     227 .. 0.65
   2 ?   -4.1   2.0        10   1.8e+04     183     183 ..     390     390 ..     320     484 .. 0.57
   3 ?   -2.5   4.0       3.3     6e+03     149     184 ..     710     757 ..     654     780 .. 0.45

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2e-19
                         AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay..vel 77 
                                    +L++++f+sf   +++ F++g+t+++GpNG+GK+ ++dA+ ++++++  + ++ +g+++e+  ++ +s++   +   v++
  gi|121638803|ref|YP_979027.1|   5 SLTLKGFKSFaAPTTLRFEPGITAVVGPNGSGKSNVVDALAWVMGEQ--GAKTLRGGKMEDVIFAGTSSRAPLGRaeVTV 82 
                                    69********77799*******************************7..5555558888888888666644444422666 PP

                         AAA_23  78 tfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerlee 157
                                    ++ n d+     ie++   +   + +   ++ e+ + + +   ++ell+ + i  ++ ++ gq++ ee++++++++r + 
  gi|121638803|ref|YP_979027.1|  83 SIDNSDNAL--PIEYTEVSITRRMFRDGASEYEINGSSCRLMDVQELLSDSGIGREMHVIVGQGKLEEILQSRPEDRRAF 160
                                    677777754..555544444444434444444444445555677788888888888889999999988888888886666 PP

                         AAA_23 158 lekeleeledekkllekleqekekekeleeleeeleeil 196
                                    +e++   l+ +k++ ++l ++    ++l  l +  +e+ 
  gi|121638803|ref|YP_979027.1| 161 IEEAAGVLKHRKRKEKALRKLDTMAANLARLTDLTTELR 199
                                    666654444444444444333333332222222222222 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 10
                         AAA_23 183 k 183
                                    +
  gi|121638803|ref|YP_979027.1| 390 E 390
                                    1 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.3
                         AAA_23 149 kdkkerleelekeleeledekkllekl.....eqekekek.......e 184
                                    ++   ++ ++ ++l  l +e++  e++     +q+ e+e+        
  gi|121638803|ref|YP_979027.1| 710 NESDTAISAMYEQLGRLGQEARAAEEEwnrllQQRTEQEAvrtqtldD 757
                                    222223333333333333333333333333221111111122222221 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   6.8e-12   1.2e-08       1      49 [.       1      50 [.       1      99 [. 0.88
   2 !    7.7   0.0    0.0014       2.5     287     364 ..    1085    1163 ..     999    1165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.8e-12
                         AAA_15  1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnn 49
                                   M++k++++k F+s+   +++ +++ +t ++G+N+sGKS++++al +   +
  gi|121638803|ref|YP_979027.1|  1 MYLKSLTLKGFKSFAApTTLRFEPGITAVVGPNGSGKSNVVDALAWVMGE 50
                                   ********************************************998765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                         AAA_15  287 k........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnk 356 
                                               +  + l+  + G + l  +++l + ++ +     ++ +++++E Ea L   + + l  l+  l +++ 
  gi|121638803|ref|YP_979027.1| 1085 GievearppGKKITRLSLLSGGEKALTAVAMLVAIFRAR-----PSPFYIMDEVEAALDDVNLRRLLSLFEQLREQS- 1156
                                     055555566777888888899999999999999999999.....99*******************************. PP

                         AAA_15  357 tQviitTH 364 
                                      Q+ii TH
  gi|121638803|ref|YP_979027.1| 1157 -QIIIITH 1163
                                     .******* PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.3e-09   1.1e-05       6      46 ..       8      48 ..       3      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.3e-09
                         AAA_29  6 lvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   l    +f   +t+++++ g+t ++Gp+GsGKS ++DA++ ++
  gi|121638803|ref|YP_979027.1|  8 LKGFKSFAApTTLRFEP-GITAVVGPNGSGKSNVVDALAWVM 48
                                   55566788889999995.58******************9998 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.7e-05     0.066      13      41 ..      26      53 ..      17     141 .. 0.83
   2 ?   -2.4   0.1       3.4   6.1e+03      53      80 ..     331     384 ..     313     448 .. 0.53
   3 ?    2.4   0.0      0.11     2e+02     106     134 ..    1100    1132 ..    1058    1135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGe 41
                                   ++a+vG+nG+GKS ++ +la  +  ++G 
  gi|121638803|ref|YP_979027.1| 26 ITAVVGPNGSGKSNVVDALAWVMG-EQGA 53
                                   789**************9987654.4554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                                    -HHHCCHCEEEE-SS--S-TTSBHHHH............................H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx............................x RF
                       ABC_tran  53 eleslrkeigvlpqepqlfpeltvren............................e 80 
                                    ele   ++++v +q+  l  el +++                             e
  gi|121638803|ref|YP_979027.1| 331 ELEAEAQQVAVAEQQ--LLAELDAARArldaaraeradrerraaeadrahlaavrE 384
                                    455555555555555..223332222224444555444443333333333333331 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                                     SGGS-HHHHHHHHHHHHHH....HTSSEEEEES CS
                                     xxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                       ABC_tran  106 pssLSgGqkqrvalarall....kkpkllllDE 134 
                                      s LSgG+k   a+a++++    + ++++++DE
  gi|121638803|ref|YP_979027.1| 1100 LSLLSGGEKALTAVAMLVAifraRPSPFYIMDE 1132
                                     389*******99988876422224556777776 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.1   3.7e+03       6      37 ..     273     304 ..     265     305 .. 0.71
   2 !    7.5   0.0     0.003       5.4       9      39 ..     392     422 ..     389     446 .. 0.90
   3 ?   -4.0   0.0        10   1.8e+04       5      18 ..     663     676 ..     657     684 .. 0.55
   4 ?   -0.2   0.0      0.76   1.4e+03      16      37 ..     887     908 ..     882     913 .. 0.81
   5 ?    1.9   0.0      0.17     3e+02       5      40 ..    1011    1046 ..    1008    1048 .. 0.87
   6 ?   -0.6   0.1         1   1.8e+03      29      47 ..    1132    1152 ..    1128    1156 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                      FlaC_arch   6 EnklsklsteletvkkeneelsksveelkenV 37 
                                    E+ + +lst+ e+++ +   ls   e+++ +V
  gi|121638803|ref|YP_979027.1| 273 ESAVAELSTRAESIQHTWFGLSALAERVDATV 304
                                    66777788888888877777777777777666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                      FlaC_arch   9 lsklsteletvkkeneelsksveelkenVkd 39 
                                    l +l  ++et+++  e++ +sv +l e+++d
  gi|121638803|ref|YP_979027.1| 392 LARLAGQVETMRARVESIDESVARLSERIED 422
                                    6778889999999999999999999999976 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 10
                      FlaC_arch   5 lEnklsklstelet 18 
                                    + ++++k  +el+ 
  gi|121638803|ref|YP_979027.1| 663 VTSEIDKARSELAA 676
                                    33455555555554 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.76
                      FlaC_arch  16 letvkkeneelsksveelkenV 37 
                                    ++ v++e + ls  v el ++ 
  gi|121638803|ref|YP_979027.1| 887 MAAVRDEVNTLSARVGELTDSL 908
                                    7788999999999998888765 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.17
                      FlaC_arch    5 lEnklsklsteletvkkeneelsksveelkenVkdl 40  
                                     lE++ + lst+le vk+  ++l   v +++ ++ ++
  gi|121638803|ref|YP_979027.1| 1011 LEERYNFLSTQLEDVKAARKDLLGVVADVDARILQV 1046
                                     8999999**********9999999999999888766 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1
                      FlaC_arch   29 sveelkenV..kdllsLYEvV 47  
                                     +ve   ++V  ++llsL+E+ 
  gi|121638803|ref|YP_979027.1| 1132 EVEAALDDVnlRRLLSLFEQL 1152
                                     444444444459999999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0023         4       4      25 ..      23      44 ..      20      57 .. 0.89
   2 ?   -3.6   0.1       7.1   1.3e+04      46      64 ..     187     202 ..     155     230 .. 0.49
   3 ?   -2.4   0.3       2.9   5.1e+03      44      89 ..     706     752 ..     676     771 .. 0.50
   4 ?    4.5   0.0     0.022        39      80     124 ..    1114    1157 ..    1087    1165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0023
                         AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                   + gi++v+G+ G+GK+ ++  l
  gi|121638803|ref|YP_979027.1| 23 EPGITAVVGPNGSGKSNVVDAL 44
                                   5799************988766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.1
                         AAA_22  46 tlpsstsskdllrellral 64 
                                    +l+ +t   dl +el r+l
  gi|121638803|ref|YP_979027.1| 187 NLARLT---DLTTELRRQL 202
                                    222222...2222222222 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.9
                         AAA_22  44 fvtlpsst.sskdllrellralglelkaerlsseell.ealeqalrar 89 
                                    +  l++s    + ++++l r  ++ + a++ +  +ll ++ eq + ++
  gi|121638803|ref|YP_979027.1| 706 LAALNESDtAISAMYEQLGRLGQE-ARAAEEEWNRLLqQRTEQEAVRT 752
                                    333333331233333333333333.33334444444444444444444 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.022
                         AAA_22   80 ealeqalraravielliiDEaqh.lrseealeeLrsllnl..srkgvq 124 
                                     ++l   +rar   ++ i DE++  l  + +l+ L sl++   +  + q
  gi|121638803|ref|YP_979027.1| 1114 AMLVAIFRARPS-PFYIMDEVEAaL-DDVNLRRLLSLFEQlrE--QSQ 1157
                                     455556677777.9*********99.89999999999886432..333 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.53   9.4e+02      25      49 ..     172     196 ..     164     201 .. 0.86
   2 ?    9.5   0.0   0.00061       1.1       3      45 ..     403     445 ..     401     447 .. 0.94
   3 ?    0.5   0.0       0.4   7.1e+02      17      44 ..     466     493 ..     454     496 .. 0.88
   4 ?   -3.1   0.2       5.4   9.6e+03       4      38 ..     892     926 ..     890     928 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.53
                           XhlA  25 ekaaeaeekiknleedlkklesnqk 49 
                                    +++++a+ k++ +  +l++l++ ++
  gi|121638803|ref|YP_979027.1| 172 KRKEKALRKLDTMAANLARLTDLTT 196
                                    67899***************99876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00061
                           XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                    + r+e i++ +  l+er+++  ++a  ++++ + ++ ++ +l 
  gi|121638803|ref|YP_979027.1| 403 RARVESIDESVARLSERIEDAAMRAQQTRAEFETVQGRIGELD 445
                                    689************************************9997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.4
                           XhlA  17 eervdkleekaaeaeekiknleedlkkl 44 
                                    +erv +l+  ++ ae ++ +l  +++ l
  gi|121638803|ref|YP_979027.1| 466 DERVAELQSAERAAERQVASLRARIDAL 493
                                    459*********************9987 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.4
                           XhlA   4 erlerietkldnleervdkleekaaeaeekiknle 38 
                                    ++++++ +++ +l + + + e+ +a a  +i++le
  gi|121638803|ref|YP_979027.1| 892 DEVNTLSARVGELTDSLHRDELANAQAALRIEQLE 926
                                    56667777777777766666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1655  (0.0923086); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.37u 0.39s 00:00:01.76 Elapsed: 00:00:00.61
# Mc/sec: 5971.45
//
Query:       gi|121638804|ref|YP_979028.1|  [L=93]
Description: acylphosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-23   83.5   0.0    1.1e-23   83.4   0.0    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   6.3e-28   1.1e-23       2      84 ..       9      91 ..       8      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 6.3e-28
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++v+G+VQgvgFR+++r +A elgl+Gy+ N++dg+V +va+g++++ +k+l+ l+ + ++ rv +v +++++++e+ ++F
  gi|121638804|ref|YP_979028.1|  9 TAWVHGWVQGVGFRWWTRCRALELGLTGYAANHADGRVLVVAQGPRAACQKLLQLLQGDTTPGRVAKVVADWSQSTEQITGF 90
                                   578***************************************************************************9999 PP

                Acylphosphatase 84 e 84
                                   +
  gi|121638804|ref|YP_979028.1| 91 S 91
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 595.06
//
Query:       gi|121638805|ref|YP_979029.1|  [L=137]
Description: hypothetical protein BCG_2945c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-09   37.4   0.0    3.4e-09   37.1   0.0    1.1  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   1.9e-13   3.4e-09       5      99 ..      34     130 ..      29     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.9e-13
                                    SB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEE..EEECCECT.CEEEEEEEEEEE-SS-H..HHHHHHHHHH CS
                           OsmC   5 gpsPeelllaalasCfaitlravakkkgikledlevevea..erdpegak.giteirlkvevkipgadseeklkklleka 81 
                                     ++P+ell  ala+C +++    ++++  +  ++ v+v++  +rd+e+     ++++l+++   ++++ +e+l  ++++a
  gi|121638805|ref|YP_979029.1|  34 VFTPGELLKIALAACSGMASDQPLARRLGDDYQAVVKVSGaaDRDQERYPlIEETMELDLSGL-TEDE-KERLLVVINRA 111
                                    589******************999999554445555555422777764335335566666663.3333.37888888999 PP

                                    .HHHSHHHHHHCT-SSSEE CS
                           OsmC  82 .ekrCpvsntlkngvkvel 99 
                                     e  C+v +tlk+g++v+l
  gi|121638805|ref|YP_979029.1| 112 vELACTVGRTLKSGTTVNL 130
                                    89**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 933.57
//
Query:       gi|121638806|ref|YP_979030.1|  [L=289]
Description: formamidopyrimidine-DNA glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-35  120.2   0.3    1.5e-34  119.1   0.1    1.7  2  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina
    7.1e-29   99.7   0.0    1.2e-28   98.9   0.0    1.3  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
    3.6e-10   39.5   6.4    3.6e-10   39.5   6.4    2.3  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
  ------ inclusion threshold ------
      0.022   14.9   1.3      0.048   13.8   1.3    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.03   13.1   0.0      0.043   12.6   0.0    1.2  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
      0.043   13.5   0.2      0.059   13.0   0.2    1.2  1  TackOD1         Thaumarchaeal output domain 1
       0.29   11.1   3.0        0.8    9.7   1.5    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.1   5.9e-38   1.5e-34       1     116 []       1     124 [.       1     124 [. 0.93
   2 ?   -1.9   0.0         2   5.1e+03      51      51 ..     179     179 ..     154     224 .. 0.57

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 5.9e-38
                                    X--HHHHHHHHHHHHHHHTT-EEEEEEE-SSHHHTS...THHHHHTT-.SEEEEEEEEETTEEEEEE.........EEEE CS
                 Fapy_DNA_glyco   1 MPElpEVetvrrglrrhllgkkiakvevlkdktlrg...spaafakalkgrkiasvgrrGKyllleldg.......gevl 70 
                                    MPElpEVe+vrrgl+ h++g++i++v+v++++++r+    pa+++++l+g++i+  +rrGKyl+l+l++       +++l
  gi|121638806|ref|YP_979030.1|   1 MPELPEVEVVRRGLQAHVTGRTITEVRVHHPRAVRRhdaGPADLTARLRGARINGTDRRGKYLWLTLNTagvhrptDTAL 80 
                                    **************************************99***************************768888888**** PP

                                    EEE-TTTEEESS........TTEEEEEEEGGGEEEEEEETT---EE CS
                 Fapy_DNA_glyco  71 vvhlgmtGrllikeaeeeppkhtkvrlelddgtelaFvDpRrfGrv 116
                                    vvhlgm+G++l+   +     h ++   lddgt l+F D+R+fG +
  gi|121638806|ref|YP_979030.1|  81 VVHLGMSGQMLL-G-AVPCAAHVRISALLDDGTVLSFADQRTFGGW 124
                                    ***********9.3.3333369**********************76 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                    E CS
                 Fapy_DNA_glyco  51 a 51 
                                    +
  gi|121638806|ref|YP_979030.1| 179 V 179
                                    2 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   4.6e-32   1.2e-28       1      88 [.     144     231 ..     144     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 4.6e-32
                                    ---BTTSTTS-HHHHHHHHHT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHH CS
                           H2TH   1 LgpeplseaftvdalaerlkkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqeikevlke 80 
                                    L+++pl+ +f++da+++ l++k++++k++LLDq++v+G+GNiyadE+L+rak++++++a++l++++l ++++++++v++e
  gi|121638806|ref|YP_979030.1| 144 LARDPLDPRFDCDAVVKVLRRKHSELKRQLLDQRVVSGIGNIYADEALWRAKVNGAHVAATLRCRRLGAVLHAAADVMRE 223
                                    899***************************************************************************** PP

                                    HHHTTTTG CS
                           H2TH  81 aielgksg 88 
                                    a++ g+++
  gi|121638806|ref|YP_979030.1| 224 ALAKGGTS 231
                                    **966554 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.1   2.8e+03       8      19 ..      20      29 ..      20      32 .. 0.80
   2 ?   -4.0   0.7       5.6   1.4e+04       6       9 ..     206     209 ..     205     209 .. 0.65
   3 !   39.5   6.4   1.4e-13   3.6e-10       1      30 []     257     286 ..     257     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                                   --BBEEEECTTE CS
                   zf-FPG_IleRS  8 wryiervgqagr 19
                                   +r+i++v++  +
  gi|121638806|ref|YP_979030.1| 20 GRTITEVRV--H 29
                                   799****98..3 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.6
                                    TT-- CS
                   zf-FPG_IleRS   6 RCwr 9  
                                    RC+r
  gi|121638806|ref|YP_979030.1| 206 RCRR 209
                                    7775 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 1.4e-13
                                    TSB-TTT--BBEEEECTTEEEEE-TTTT.. CS
                   zf-FPG_IleRS   1 GepCpRCwryiervgqagrstyfCprCqkv 30 
                                    Ge C+RC+ +i+r+++++rs+++CprCq++
  gi|121638806|ref|YP_979030.1| 257 GENCRRCGAVIRRERFMNRSSFYCPRCQPR 286
                                    677*************************96 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   1.9e-05     0.048      15      40 .]     257     284 ..     257     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                  Auto_anti-p27  15 aetCpvCgvPLmrdr..kggkvyCvaCd 40 
                                    +e+C +Cg+++ r+r  ++   yC++C+
  gi|121638806|ref|YP_979030.1| 257 GENCRRCGAVIRRERfmNRSSFYCPRCQ 284
                                    689**************99********6 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.043     174     241 ..     154     223 ..     140     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                    H.HHHHHHHHHS.XXXHHHHH..HHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTX CS
                           FbpA 174 eleefkellskkekdlvkaLv..kafqGlspllaeelleragldketsakelseedlerlyealqellee 241
                                    +++++ ++l++k  +l+++L+  + ++G+++ +a e+l+ra+++ +  a++l  + l ++ +a  ++++e
  gi|121638806|ref|YP_979030.1| 154 DCDAVVKVLRRKHSELKRQLLdqRVVSGIGNIYADEALWRAKVNGAHVAATLRCRRLGAVLHAAADVMRE 223
                                    33567778888899******833569********************999999999999998888887765 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.3e-05     0.059     105     131 ..     259     285 ..     248     289 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                        TackOD1 105 hhftCgnvgpeeeflkegkleCpkCkt 131
                                    ++ +Cg+v   e+f+++++  Cp+C+ 
  gi|121638806|ref|YP_979030.1| 259 NCRRCGAVIRRERFMNRSSFYCPRCQP 285
                                    799**********************85 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.37   9.6e+02      44      58 ..     202     216 ..     193     221 .. 0.80
   2 ?    9.7   1.5   0.00031       0.8      29      53 ..     258     284 ..     251     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.37
                 OrfB_Zn_ribbon  44 grtfkCpnCgfeadr 58 
                                      t++C++ g+++++
  gi|121638806|ref|YP_979030.1| 202 AATLRCRRLGAVLHA 216
                                    6789******99887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00031
                 OrfB_Zn_ribbon  29 ktCseCgsknke..alsgrtfkCpnCg 53 
                                     +C +Cg++ ++    ++  f+Cp+C+
  gi|121638806|ref|YP_979030.1| 258 ENCRRCGAVIRRerFMNRSSFYCPRCQ 284
                                    68*********99889999*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2102.16
//
Query:       gi|121638807|ref|YP_979031.1|  [L=240]
Description: ribonuclease III [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-36  123.3   0.0    9.9e-36  122.7   0.0    1.2  1  Ribonucleas_3_3  Ribonuclease-III-like
    1.9e-20   73.4   0.0    6.4e-20   71.7   0.0    1.9  2  Ribonuclease_3   Ribonuclease III domain
    9.1e-16   58.3   0.0    1.4e-15   57.7   0.0    1.3  1  dsrm             Double-stranded RNA binding motif
     0.0024   18.1   0.0     0.0072   16.6   0.0    1.8  1  DND1_DSRM        double strand RNA binding domain from DEAD E


Domain annotation for each model (and alignments):
>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   2.2e-39   9.9e-36       2     122 ..      18     144 ..      17     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 2.2e-39
                Ribonucleas_3_3   2 eelleqaltHkSfangrk..ghNerLefLGdavLklsvseyllek.aekdegeltklraslvseeslaeiAkelg...Lg 75 
                                    +ell+ altH+S+a+++   ++NerLefLGdavL l+++++l+++ ++++eg+l+klras+v++++la++A++l    Lg
  gi|121638807|ref|YP_979031.1|  18 DELLSLALTHRSYAYENGglPTNERLEFLGDAVLGLTITDALFHRhPDRSEGDLAKLRASVVNTQALADVARRLCaegLG 97 
                                    69***********777764489*******************98773677***********************985555** PP

                Ribonucleas_3_3  76 kvlrlrkgeeetegsgrekvladaleAliGAiyldkgaevaqefvee 122
                                     +++l++ge++t+g +++++lad +e+l+GAiyl++g+e+a+e++++
  gi|121638807|ref|YP_979031.1|  98 VHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILR 144
                                    *********************************************86 PP

>> Ribonuclease_3  Ribonuclease III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   1.4e-23   6.4e-20       1     105 []      41     134 ..      41     134 .. 0.91
   2 ?   -1.8   0.0       1.1     5e+03      50      77 ..     174     185 ..     167     227 .. 0.44

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.4e-23
                                    HHHHHHHHHHHHHHHHHHHHHHCTTSSHHHHHHHHHHHTSHHHHHHHHHCTTCHCCHCHH..............HHCCST CS
                 Ribonuclease_3   1 erLeflGDavlklaittylfetypdahegrlsklrsklvsnenlarlakklglpkflrasefdpprnwlppgyklsddek 80 
                                    erLeflGDavl l it++lf+++pd++eg+l klr+++v+ ++la +a++l  + + ++               l+++e+
  gi|121638807|ref|YP_979031.1|  41 ERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVH-----------V--LLGRGEA 107
                                    8************************************************9955555552...........1..19***** PP

                                    TCHCTSHH..HHHHHHHHHHHHHHHCT CS
                 Ribonuclease_3  81 edddadkv..ladvvEAliGaiyldsg 105
                                    ++ +adk+  lad +E+l+Gaiyl+ g
  gi|121638807|ref|YP_979031.1| 108 NTGGADKSsiLADGMESLLGAIYLQHG 134
                                    *999999888**************976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                    CTTCHCCHCHH..............HHC CS
                 Ribonuclease_3  50 klglpkflrasefdpprnwlppgyklsd 77 
                                     lg p++l++s                +
  gi|121638807|ref|YP_979031.1| 174 GLGAPSYLVTS----------------T 185
                                    55666666632................1 PP

>> dsrm  Double-stranded RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   3.1e-19   1.4e-15       1      67 []     162     227 ..     162     227 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.1e-19
                                    HHHHHHHHHHHTTSEEEEEEEEEESSTSSSEEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH CS
                           dsrm   1 pKskLqeycqkkgkppnyeyvseegpphslpkFvvtvkvngklygsGvgsnKKeAeqsAAedalekL 67 
                                    +K+ Lqe+   +g + + + v ++gp+h  ++F++ v+v + +ygsGvg++KKeAeq+AA++a++ L
  gi|121638807|ref|YP_979031.1| 162 WKTSLQELTAARGLGAPSYLVTSTGPDHD-KEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAAWKAL 227
                                    6999************************9.*********************************9876 PP

>> DND1_DSRM  double strand RNA binding domain from DEAD END PROTEIN 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06    0.0072       6      77 ..     165     228 ..     161     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                      DND1_DSRM   6 lLeelCeknkwgsPvYelhseagpdgkllflYkVvipgietslkgvvvifmpdklastkeeAkelaAeqvLe 77 
                                     L+el + + +g P Y + s +gpd+ + f+  Vv+   e + +g    +  ++ ++  e+   +aA ++Le
  gi|121638807|ref|YP_979031.1| 165 SLQELTAARGLGAPSYLVTS-TGPDHDKEFTAVVVVMDSEYG-SG----V--GRSKKEAEQKAAAAAWKALE 228
                                    69**************9987.7*********99999888876.33....2..23333333333344445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1698.48
//
Query:       gi|121638808|ref|YP_979032.1|  [L=207]
Description: hypothetical protein BCG_2948c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-28   98.2   0.2    4.2e-28   97.9   0.2    1.1  1  YceD      Large ribosomal RNA subunit accumulation protein Yc


Domain annotation for each model (and alignments):
>> YceD  Large ribosomal RNA subunit accumulation protein YceD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.2   2.3e-32   4.2e-28       1     118 [.      84     193 ..      84     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 2.3e-32
                           YceD   1 ldgrvsatvtleCdrClepvelpldveftelfveeeeeaedeedeedeedeeeilaeedeiDlselireelllalPlkpl 80 
                                    ++g+v a+ + eC+rCl pv+ +++v +telf++ +++ +++  e   ede+  +++ ++iDl++ i +++ l+lP+ p+
  gi|121638808|ref|YP_979032.1|  84 VTGTVAAPTVGECARCLSPVRGRVQVALTELFAYPDSATDETT-E---EDEVGRVVD-ETIDLEQPIIDAVGLELPFSPV 158
                                    6899*****************************9999976664.3...555555555.59******************** PP

                           YceD  81 ckpdckgeklcsqcganlneeecdceeekedprfaaLk 118
                                    c+pdc g  lc+qcg  l  e+ ++ +e++dpr+a+L 
  gi|121638808|ref|YP_979032.1| 159 CRPDCPG--LCPQCGVPLASEP-GHRHEQIDPRWAKLV 193
                                    *******..************9.99***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1519.35
//
Query:       gi|121638809|ref|YP_979033.1|  [L=245]
Description: hypothetical protein BCG_2949c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-07   30.2  24.4    0.00041   20.7  12.0    3.8  3  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
      3e-06   27.3  20.2    0.00021   21.4   3.9    3.8  4  DivIVA        DivIVA protein
    0.00051   20.1  26.4     0.0042   17.2   5.9    3.7  3  ATP-synt_B    ATP synthase B/B' CF(0)
    0.00076   19.4  13.4      0.079   12.8   4.8    3.0  3  HrpE          HrpE/YscL/FliH and V-type ATPase subunit E
     0.0011   19.5  16.4      0.056   14.0  10.0    3.3  3  V-ATPase_G    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
        1.8    9.6   6.2        9.3    7.3   6.1    2.5  1  Rotamase      PPIC-type PPIASE domain
        1.8    8.2   8.4        4.9    6.8   1.5    2.2  2  YkyA          Putative cell-wall binding lipoprotein
          2    9.2   7.1          2    9.2   0.5    3.1  2  FIVAR         FIVAR domain
        2.1    7.7  21.8         35    3.7  15.7    3.3  3  DUF3552       Domain of unknown function (DUF3552)
        2.1    9.0  21.7       0.25   12.0   7.1    3.4  4  DUF883        Bacterial protein of unknown function (DUF883)
        2.5    7.4  15.3        1.2    8.5   1.4    2.7  3  vATP-synt_E   ATP synthase (E/31 kDa) subunit
        9.1    6.1  14.3        3.9    7.3   8.2    2.8  3  SCAB_CC       Coiled-coil regions of plant-specific actin-bin


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  12.0   2.7e-07   0.00041      20      78 ..      73     131 ..      53     134 .. 0.91
   2 !    6.9   1.8    0.0054       8.1      23      50 ..     131     158 ..     126     176 .. 0.80
   3 !    9.3   1.4   0.00098       1.5      21      59 ..     179     217 ..     157     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2  20 rlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaea 78 
                                     +  A  eae  +++A+ eA+ril++A+a+a ++ +e +q+ +++va  reea + a+a
  gi|121638809|ref|YP_979033.1|  73 MVSSATTEAESILNHARTEADRILSDAKAQADRMVSEARQHSERMVADAREEAIRIATA 131
                                    566899**********************************************9887776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2  23 aArkeaereveaAeaeAarilreAeaka 50 
                                    aA++e e++v++A+ae +r++++ + + 
  gi|121638809|ref|YP_979033.1| 131 AAKREYEASVSRAQAECDRLIENGNISY 158
                                    799****************999876554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00098
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2  21 lEaArkeaereveaAeaeAarilreAeakakalqaeyeq 59 
                                    + aA  e+ r v+ A+aeA+r+  e +  + +  ae+e+
  gi|121638809|ref|YP_979033.1| 179 VAAANAESTRLVDTAHAEADRLRGECDIYVDNKLAEFEE 217
                                    225556666666666677666666666666555555555 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   3.9   1.4e-07   0.00021      55     116 ..      49     110 ..      36     112 .. 0.82
   2 !   12.5   5.4   7.6e-05      0.11      76     117 ..      92     133 ..      92     144 .. 0.89
   3 !    5.9   4.4    0.0088        13      69     121 ..     118     168 ..     113     179 .. 0.77
   4 !    6.2   0.6    0.0068        10      88     117 ..     176     205 ..     162     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                                    XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  55 lkeykeleetLkktlvv.aqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeei 116
                                    l++ +++ ++ +++++  a+  a+ + ++a++eae i++ A+ +a++i+++a+ +a+++ +e 
  gi|121638809|ref|YP_979033.1|  49 LDDAQDVLDA-RDSMLQdAKTHADSMVSSATTEAESILNHARTEADRILSDAKAQADRMVSEA 110
                                    5666666666.5555542778899********************************9998875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.6e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  76 aeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeie 117
                                    a+++ + ak++a+ +++eA++ +e++v++a+eea +ia+  +
  gi|121638809|ref|YP_979033.1|  92 ADRILSDAKAQADRMVSEARQHSERMVADAREEAIRIATAAK 133
                                    5677789*****************************998755 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0088
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  69 lvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkr 121
                                    +  a e a ++ ++ak+e e  ++ A+++ ++++e+ + + +k+ +e   +k+
  gi|121638809|ref|YP_979033.1| 118 VADAREEAIRIATAAKREYEASVSRAQAECDRLIENGNISYEKAVQE--GIKE 168
                                    556788889999999******************99888888777664..3333 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0068
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  88 eliikeAekkaekiveeaeeeakkiaeeie 117
                                    + ++++A+++++++v++a+ ea++++ e +
  gi|121638809|ref|YP_979033.1| 176 NEVVAAANAESTRLVDTAHAEADRLRGECD 205
                                    3468899999999******99999999887 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   5.9   2.8e-06    0.0042      46     110 ..      49     113 ..      36     118 .. 0.83
   2 ?    2.7  13.1     0.084   1.3e+02      42     103 ..     121     183 ..     115     201 .. 0.78
   3 ?    3.5   1.6     0.047        70      55      84 ..     174     203 ..     167     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                     ATP-synt_B  46 rkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdr 110
                                     ++a+ +l+++   l++A+  A+ ++ +A+ eae + + +++ea + +   k++A   ++ +++ 
  gi|121638809|ref|YP_979033.1|  49 LDDAQDVLDARDSMLQDAKTHADSMVSSATTEAESILNHARTEADRILSDAKAQADRMVSEARQH 113
                                    57889999999999999999999999999999999999999999999999999998888888875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.084
                     ATP-synt_B  42 Aeerrke.aaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaae 103
                                    A+e +   a a++ e+e+    A+ae +++i+n++ + ek+ +e ++e ++ + + +  Aaa+
  gi|121638809|ref|YP_979033.1| 121 AREEAIRiATAAKREYEASVSRAQAECDRLIENGNISYEKAVQEGIKEQQRLVSQNEVVAAAN 183
                                    444443315678899*****************************9999999887777666654 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.047
                     ATP-synt_B  55 eaeqqlkeAraeAaeiiknAkkeaeklkee 84 
                                    ++ +  + A ae+ ++++ A +ea +l+ e
  gi|121638809|ref|YP_979033.1| 174 SQNEVVAAANAESTRLVDTAHAEADRLRGE 203
                                    445556667777777777777777776665 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.3    0.0095        14      33      65 ..      60      92 ..      48      93 .. 0.68
   2 !   12.8   4.8   5.3e-05     0.079      25      66 ..      83     126 ..      80     154 .. 0.81
   3 !    8.4   0.2    0.0012       1.8      32      90 ..     175     236 ..     158     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0095
                           HrpE 33 rellaeArlqAeqllaqarekaeellevaveqA 65
                                   + +l++A+  A++++  a   ae +l+ a  +A
  gi|121638809|ref|YP_979033.1| 60 DSMLQDAKTHADSMVSSATTEAESILNHARTEA 92
                                   346777888888888888888877777776655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.3e-05
                           HrpE  25 qlaeslr..arellaeArlqAeqllaqarekaeellevaveqAe 66 
                                    ++ ++ r  a+ +l +A+ qA+ ++ +ar++ e++++ a e+A+
  gi|121638809|ref|YP_979033.1|  83 SILNHARteADRILSDAKAQADRMVSEARQHSERMVADAREEAI 126
                                    5555555227889*******************999999999986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0012
                           HrpE  32 arellaeArlqAeqllaqarekaeel...levaveqAeaqFWeqAnalLrglqqeRealeeq 90 
                                     +e++a A    + l++ a+  a++l   ++  v++ +a+F e  n  Lr + + R++l+  
  gi|121638809|ref|YP_979033.1| 175 QNEVVAAANAESTRLVDTAHAEADRLrgeCDIYVDNKLAEFEEFLNGTLRSVGRGRHQLRTA 236
                                    4789****************9999875558999*********************99999765 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.6    0.0096        14      10      41 ..      64      95 ..      58     102 .. 0.65
   2 !   14.0  10.0   3.7e-05     0.056      11      89 ..      98     176 ..      94     178 .. 0.94
   3 ?    3.1   0.0     0.089   1.3e+02      17      69 ..     176     231 ..     174     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0096
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     V-ATPase_G 10 LqAEkeAaeivkeArkrkakrlkqAkeeAekE 41
                                    +A  +A+ +v++A ++ +  l  A++eA + 
  gi|121638809|ref|YP_979033.1| 64 QDAKTHADSMVSSATTEAESILNHARTEADRI 95
                                   45667777777777777777777777777654 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.7e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHH CS
                     V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkkn 89 
                                    +A  +A+++v+eAr++ ++++ +A+eeA +   + +++ e+   + +ae+    e+ + + ek ++e ike ++ v++n
  gi|121638809|ref|YP_979033.1|  98 DAKAQADRMVSEARQHSERMVADAREEAIRIATAAKREYEASVSRAQAECDRLIENGNISYEKAVQEGIKEQQRLVSQN 176
                                    78899**********************************************99********************999887 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.089
                                    HHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHSHHHHHHH CS
                     V-ATPase_G  17 aeivkeArkrkakrlkqAkeeAek...Eieeyrakkekefkekeaeklgseeelek 69 
                                    +e+v++A  + ++ +  A++eA +   E + y  +k +ef+e+ + +l s +   +
  gi|121638809|ref|YP_979033.1| 176 NEVVAAANAESTRLVDTAHAEADRlrgECDIYVDNKLAEFEEFLNGTLRSVGRGRH 231
                                    57899999999999999*****7655599***********9999888776655555 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.1    0.0062       9.3      13      56 ..      83     126 ..      45     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0062
                                    --HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEE CS
                       Rotamase  13 keraeakakaeeileqlksgedtFeelArkySddknsakngGdl 56 
                                       + a+++a++il+++k+++d++ + Ar++S+     +++ ++
  gi|121638809|ref|YP_979033.1|  83 SILNHARTEADRILSDAKAQADRMVSEARQHSERMVADAREEAI 126
                                    445789**************************655555555554 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7    0.0075        11      45     112 ..      38     108 ..      32     119 .. 0.56
   2 ?    6.8   1.5    0.0033       4.9       9      73 ..     129     193 ..     121     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0075
                           YkyA  45 gmdefdkikklsdealenveeReellekekesieeake.efekikeeieei..edeelkkeaeelieamee 112
                                      d +d+i  + d+a++ +++R ++l+  k+  ++    + +++++++++   e + + ++a++ ++ m +
  gi|121638809|ref|YP_979033.1|  38 IDDIKDAIPGELDDAQDVLDARDSMLQDAKTHADSMVSsATTEAESILNHArtEADRILSDAKAQADRMVS 108
                                    444488999999*************9998765544322022333333333333333333333333333333 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0033
                           YkyA   9 aleeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReelleke 73 
                                    a     e+E ++  +q +  +l ++ +  ye+ ++ g++e+++++++ + + +   e + l+++ 
  gi|121638809|ref|YP_979033.1| 129 ATAAKREYEASVSRAQAECDRLIENGNISYEKAVQEGIKEQQRLVSQNEVVAAANAESTRLVDTA 193
                                    555667899*******************************9999999988888777777777665 PP

>> FIVAR  FIVAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5    0.0014         2      12      51 ..      65     101 ..      41     110 .. 0.76
   2 ?    1.8   1.2      0.28   4.2e+02      22      50 ..     126     155 ..     118     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                    HHHHHCSCCCCCC-CCHHHHHHHHHHHHHHHC...TSTTT CS
                          FIVAR  12 atntktssnysnydqdkkdaynnalsaAnailnktnnpna 51 
                                      +t+++s  s ++++  + +n a ++A  il   ++ +a
  gi|121638809|ref|YP_979033.1|  65 DAKTHADSMVSSATTEAESILNHARTEADRIL---SDAKA 101
                                    34556678888888888888888888888888...66555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                                    CCC-CCHHHHHHHHHHHHHHHC....TSTT CS
                          FIVAR  22 snydqdkkdaynnalsaAnailnkt.nnpn 50 
                                    + + ++ k +y++++s A+a  ++  +n n
  gi|121638809|ref|YP_979033.1| 126 IRIATAAKREYEASVSRAQAECDRLiENGN 155
                                    567777889999999999653333334444 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  15.7     0.023        35      22      81 ..      67     126 ..      58     172 .. 0.60
   2 ?   -1.8   5.9       1.2   1.8e+03      24      24 ..     174     174 ..     126     204 .. 0.46
   3 ?    2.8   0.5     0.044        66      26      54 ..     176     204 ..     169     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.023
                        DUF3552  22 kkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrnelq 81 
                                    k  a++ +++A++eA++i+++A+ eA+ +   a  +a   + ++r+  e+ + + r+e  
  gi|121638809|ref|YP_979033.1|  67 KTHADSMVSSATTEAESILNHARTEADRILSDAKAQADRMVSEARQHSERMVADAREEAI 126
                                    444555555666666666666655555555555555555555555555555555555543 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                        DUF3552  24 i 24 
                                    +
  gi|121638809|ref|YP_979033.1| 174 S 174
                                    1 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.044
                        DUF3552  26 ekkiaeAeeeAkkiieeAkkeAeakkkea 54 
                                    ++ +a A++e +++++ A+ eA+ ++ e 
  gi|121638809|ref|YP_979033.1| 176 NEVVAAANAESTRLVDTAHAEADRLRGEC 204
                                    556789999*************9998775 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   7.1   0.00017      0.25       5      67 ..      50     112 ..      47     118 .. 0.90
   2 ?   10.7   8.9   0.00042      0.63       6      66 ..      84     144 ..      80     147 .. 0.90
   3 ?    2.0   6.4      0.22   3.2e+02      10      60 ..     110     164 ..     107     190 .. 0.63
   4 ?    0.7   0.7      0.53   7.9e+02      34      46 ..     191     203 ..     157     244 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                         DUF883   5 aeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                    ++ +++l+  +++l++a+ +a++ ++++  ++e+ l++ar ++++   +++++a++++ +a++
  gi|121638809|ref|YP_979033.1|  50 DDAQDVLDARDSMLQDAKTHADSMVSSATTEAESILNHARTEADRILSDAKAQADRMVSEARQ 112
                                    6889999999999***************************99999999999999999988865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00042
                         DUF883   6 eleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                     l++++++++ +l++a+++a++ ++e+R+  e ++++are++ + + a++++ ++ + +a+
  gi|121638809|ref|YP_979033.1|  84 ILNHARTEADRILSDAKAQADRMVSEARQHSERMVADAREEAIRIATAAKREYEASVSRAQ 144
                                    468899999****************************************999999988876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.22
                         DUF883  10 lladleellkeaadeageeaeelRerleerlerarerlrdaeea....vaerake 60 
                                    +++  e ++ +a +ea + a +++++ e++++ra+++++++ e+    +++ ++e
  gi|121638809|ref|YP_979033.1| 110 ARQHSERMVADAREEAIRIATAAKREYEASVSRAQAECDRLIENgnisYEKAVQE 164
                                    4556677777777777777777777777777777777777766633334444444 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.53
                         DUF883  34 erleerlerarer 46 
                                    + ++++++r+r +
  gi|121638809|ref|YP_979033.1| 191 DTAHAEADRLRGE 203
                                    3333333333333 PP

>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.2   2.9e+02      64      89 ..      53      78 ..      47      82 .. 0.78
   2 ?    8.5   1.4   0.00078       1.2       3      52 ..      63     112 ..      61     119 .. 0.72
   3 ?    4.4   5.5     0.014        21       5      49 ..     120     164 ..     116     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    vATP-synt_E 64 lkvLkareevleevfeeaekkLaeve 89
                                   + vL ar+ +l++++ +a   ++  +
  gi|121638809|ref|YP_979033.1| 53 QDVLDARDSMLQDAKTHADSMVSSAT 78
                                   67999999999999998887776655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00078
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                    vATP-synt_E   3 rqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkk 52 
                                     q+A+  A+   ++a+ e+e++++++  e+   +  a++++ + ++ +++
  gi|121638809|ref|YP_979033.1|  63 LQDAKTHADSMVSSATTEAESILNHARTEADRILSDAKAQADRMVSEARQ 112
                                    57888888888888888888888888888887777777777777666555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.014
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                    vATP-synt_E   5 eAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqael 49 
                                    +A+e+A +I + a+ e+e  ++++++e    ie+   + eK ++ 
  gi|121638809|ref|YP_979033.1| 120 DAREEAIRIATAAKREYEASVSRAQAECDRLIENGNISYEKAVQE 164
                                    8************************99999998865555555542 PP

>> SCAB_CC  Coiled-coil regions of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4     0.077   1.1e+02      68      99 ..      64      95 ..      48     102 .. 0.55
   2 ?    7.3   8.2    0.0026       3.9      49     125 ..      81     154 ..      72     162 .. 0.81
   3 ?    0.4   0.2      0.33   4.9e+02      73      94 ..     168     189 ..     157     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.077
                        SCAB_CC 68 kqasedakklveeersfaraeiesaraavqrv 99
                                   + a   a  +v  + + a+  +++ar+ + r+
  gi|121638809|ref|YP_979033.1| 64 QDAKTHADSMVSSATTEAESILNHARTEADRI 95
                                   44444445555555555555555555444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                        SCAB_CC  49 regellqekaevkklasflkqasedakklveeersfaraeiesaraavqrveealeeeeksskaskkqdveelkeev 125
                                     e+ l + ++e  ++   l  a  +a ++v e+r  ++  + +ar  + r+ +a + e + s +  + + ++l e+ 
  gi|121638809|ref|YP_979033.1|  81 AESILNHARTEADRI---LSDAKAQADRMVSEARQHSERMVADAREEAIRIATAAKREYEASVSRAQAECDRLIENG 154
                                    566666666776665...67788999**************************9999888777766666999998875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.33
                        SCAB_CC  73 dakklveeersfaraeiesara 94 
                                    + ++lv ++ ++a a+ es r 
  gi|121638809|ref|YP_979033.1| 168 EQQRLVSQNEVVAAANAESTRL 189
                                    5677888888888887777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 1756.10
//
Query:       gi|121638810|ref|YP_979034.1|  [L=261]
Description: thioesterase tesA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-61  207.7   0.0    2.9e-61  207.5   0.0    1.0  1  Thioesterase     Thioesterase domain
    1.4e-08   35.6   0.5    1.9e-08   35.2   0.5    1.1  1  Abhydrolase_6    Alpha/beta hydrolase family
      9e-08   32.1   0.1    5.7e-05   22.9   0.1    2.1  2  Abhydrolase_1    alpha/beta hydrolase fold
    1.1e-05   24.8   0.0     0.0001   21.7   0.0    2.0  2  Hydrolase_4      Serine aminopeptidase, S33
     0.0035   17.2   0.0     0.0087   15.9   0.0    1.8  2  Abhydrolase_3    alpha/beta hydrolase fold
     0.0036   16.9   0.0        1.5    8.3   0.0    2.2  2  DLH              Dienelactone hydrolase family
     0.0056   16.4   0.0     0.0091   15.7   0.0    1.3  1  Esterase         Putative esterase
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.022   14.5   0.0    1.3  1  PGAP1            PGAP1-like protein
      0.023   14.5   0.0      0.039   13.8   0.0    1.4  1  Abhydrolase_2    Phospholipase/Carboxylesterase
       0.12   11.4   0.0       0.17   10.9   0.0    1.2  1  Chlorophyllase   Chlorophyllase
       0.14   11.1   0.0       0.31   10.0   0.0    1.6  2  DUF1057          Alpha/beta hydrolase of unknown function (DU
       0.19   10.6   0.0       0.27   10.1   0.0    1.2  1  Chlorophyllase2  Chlorophyllase enzyme


Domain annotation for each model (and alignments):
>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.5   0.0     2e-64   2.9e-61       2     230 ..      30     253 ..      29     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 2e-64
                                    EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSS.SEEEEEETHHHH CS
                   Thioesterase   2 pLflfppagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpeg.PyalfGhSlGgl 78 
                                    +L++fp+agG a+ +  +++++s++ v+ +avq+pg++  ++ pplesi +la+e++++++++   + P+a+fGhS+Gg+
  gi|121638810|ref|YP_979034.1|  30 TLYIFPHAGGTAKDYVAFSREFSAD-VKRIAVQYPGQHdrSGLPPLESIPTLADEIFAMMKPSARIDdPVAFFGHSMGGM 108
                                    799*********************8.*************99************************999************ PP

                                    HHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHHTHHHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHHHH CS
                   Thioesterase  79 lAfevArqLesqGlavkslflidssapseteaqeasrraedeefveeltdlggtepeelledeellsellpalradyral 158
                                    lAfevA +++s G+ v ++f++++sap +  ++++ +  +d+e+++++t+++g+ ++++ +d+e++   lp+lra+  a+
  gi|121638810|ref|YP_979034.1| 109 LAFEVALRYQSAGHRVLAFFVSACSAPGH-IRYKQLQDLSDREMLDLFTRMTGM-NPDFFTDDEFFVGALPTLRAVR-AI 185
                                    ***************************99.***********************9.*******************987.** PP

                                    TCCS-TTSCSEHHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCCHHHSHHHHHHHHHHHHH CS
                   Thioesterase 159 eqyslrpeaaqklratlfngsddklkdldtlelaerweqktsgevsvhvlegdhfylledrleavleiiekk 230
                                      ys++pe + +++++ f g++d++++ d  +++  w+++t++e+s++v++gdhfyl+ d+l+++++ ie+k
  gi|121638810|ref|YP_979034.1| 186 AGYSCPPETKLSCPIYAFIGDKDWIATQD--DMDP-WRDRTTEEFSIRVFPGDHFYLN-DNLPELVSDIEDK 253
                                    *****************************..8899.**********************.7*********997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.5   1.3e-11   1.9e-08      17     211 ..      45     240 ..      30     250 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.3e-11
                                    HHHHHHHCCTCEEEEE--TTS.TS-GGCS--HHHCHHHHHHHCCTT.........TTSEEEEEETCHHHHHHHHHHCC.. CS
                  Abhydrolase_6  17 apLaallaagvhvlapDlpGh.Grsdpppldledladlaalldelaa.......gggpvvlvGHSlGGalalaaapla.. 86 
                                    + + + ++a+v  +a+++pG+   +     +l++l+ +  l+de+ a        ++pv  +GHS+GG+la +   +a  
  gi|121638810|ref|YP_979034.1|  45 VAFSREFSADVKRIAVQYPGQhD-R----SGLPPLESIPTLADEIFAmmkpsarIDDPVAFFGHSMGGMLAFE---VAlr 116
                                    35666668888889*******42.2....444446666666666666666777688889**********9999...6644 PP

                                    ........EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCH CS
                  Abhydrolase_6  87 ......lvvgvlldppptalpagllaaalelllallallrllawlsreplprlfladedadaawrarlarlaallaglgl 160
                                          +v + ++++       + ++ + ++l+ l ++++l+ + ++  ++++f+    +d+ ++ +l +l+a +a  g+
  gi|121638810|ref|YP_979034.1| 117 yqsaghRVLAFFVSA-----CSAPGHIRYKQLQDLSDREMLDLFTRMTGMNPDFFT---DDEFFVGALPTLRAVRAIAGY 188
                                    444444222333333.....222255666666666666666555543356667777...455555555555555553332 PP

                                    T.TCCHHTT-TTGC........EEECTT-CHHHHCHHCCCHSTTEEETCE...SSS-HHH CS
                  Abhydrolase_6 161 l.paaawadlpvpl........lvlggeDplvprllerllaqagarlpvvlpgaGHlphl 211
                                      p  + + l +p+        ++ +++D++ p  ++++ + + + +  v+p ++H+++ 
  gi|121638810|ref|YP_979034.1| 189 ScP--PETKLSCPIyafigdkdWI-ATQDDMDP--WRDRTT-EEFSI-RVFP-GDHFYLN 240
                                    214..3344444443323333233.69999999..889998.66666.5555.9997665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.8e-08   5.7e-05      72     114 ..      95     138 ..      76     164 .. 0.80
   2 !    7.1   0.0    0.0025       3.7     208     251 ..     194     237 ..     167     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.8e-08
                                    TSSEEEEEETHHHHHHHHHHHHH...GGGEEEEEEESECSSCCHHH CS
                  Abhydrolase_1  72 ddkltlvGhSmGGmialayaaey...perVkalvllgaidpaasli 114
                                    dd+++  GhSmGGm+a+++a++y    +rV a+   +   +a+ +i
  gi|121638810|ref|YP_979034.1|  95 DDPVAFFGHSMGGMLAFEVALRYqsaGHRVLAFFVSAC--SAPGHI 138
                                    78899******************999999999876655..344444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                                    HHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                  Abhydrolase_1 208 knvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                    ++ ++p++ ++g++D++++ + ++ +++ + +++ ++++++ H+
  gi|121638810|ref|YP_979034.1| 194 TKLSCPIYAFIGDKDWIATQDDMDPWRDRTTEEFSIRVFPGDHF 237
                                    56789************************9999********998 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   6.7e-08    0.0001      67     115 ..      86     136 ..      67     176 .. 0.71
   2 ?    1.0   0.0      0.14   2.1e+02     187     209 ..     193     215 ..     176     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.7e-08
                    Hydrolase_4  67 ekvk.eehpelplfllGhSmGGliallyllrypdkva.glilsaPalkika 115
                                     ++k +   + p+  +GhSmGG++a++++lry++  +  l ++ +a++ + 
  gi|121638810|ref|YP_979034.1|  86 AMMKpSARIDDPVAFFGHSMGGMLAFEVALRYQSAGHrVLAFFVSACSAPG 136
                                    55554455667*********************9944435555555554444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                    Hydrolase_4 187 aakitlPllllhGeaDkvvdpea 209
                                     +k++ P+  ++G++D++  +++
  gi|121638810|ref|YP_979034.1| 193 ETKLSCPIYAFIGDKDWIATQDD 215
                                    67899*************98765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.8e-06    0.0087      70     108 ..      95     133 ..      53     214 .. 0.76
   2 ?   -1.2   0.0      0.99   1.5e+03      26      63 ..     177     214 ..     159     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                                    TCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE CS
                  Abhydrolase_3  70 psrivlaGdSaGGnlaaavalrardegepkvagqvliyP 108
                                     + ++++G S GG la  valr +++g+  +a+ v  + 
  gi|121638810|ref|YP_979034.1|  95 DDPVAFFGHSMGGMLAFEVALRYQSAGHRVLAFFVSACS 133
                                    4689*********************98666666555444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.99
                                    HHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTH CS
                  Abhydrolase_3  26 kelgavvvsvdYrlAPehpfPaavedalaalrwlaeqa 63 
                                      l+av     Y   Pe+++  ++   +    w+a+q+
  gi|121638810|ref|YP_979034.1| 177 PTLRAVRAIAGYSCPPETKLSCPIYAFIGDKDWIATQD 214
                                    55666667778999999998888887777777777774 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0038       5.6      91     127 ..      89     126 ..      72     142 .. 0.74
   2 !    8.3   0.0     0.001       1.5     141     195 ..     194     244 ..     189     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0038
                            DLH  91 svpevstkkvgvvGfCmGGalalllaaev.pevdaava 127
                                    + +   ++ v+  G  mGG la+++a +   +  +++a
  gi|121638810|ref|YP_979034.1|  89 KPSARIDDPVAFFGHSMGGMLAFEVALRYqSAGHRVLA 126
                                    4455677899****************887333344445 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                            DLH 141 akikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                    +k+++pi+a++g++D + ++d+++  +  +     ++ + v+p  +H ++nd+ +
  gi|121638810|ref|YP_979034.1| 194 TKLSCPIYAFIGDKDWIATQDDMDPWRDRT---TEEFSIRVFP-GDHFYLNDNLP 244
                                    6899*****************988887777...6788999999.57877777655 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06    0.0091      49     145 ..      21     126 ..      16     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                                    CCHCCT.EEEEEECCCSS-TTTTTSBTTSB..B.TTEEETTCCCCCCHC........HHHHTHHHHHHHHHCSEECCCEE CS
                       Esterase  49 laregeiaeviivvvprggessfysdwdlg..arfyenategpgaeaye........tfltqeLlplldanfrtapdgra 118
                                    +++ +++a+  +++ ++gg++++y  +     a  ++ a ++pg+++            l++e++ + + + r+++   a
  gi|121638810|ref|YP_979034.1|  21 SGDAKQAAPTLYIFPHAGGTAKDYVAFSREfsADVKRIAVQYPGQHDRSglpplesiPTLADEIFAMMKPSARIDDP-VA 99 
                                    66777788888888888888877665555555555555555555555444335546667889999999999999999.** PP

                                    EEEETHHHHHHHHHHHCSTTTCCEEEE CS
                       Esterase 119 vaGqSmGGlgALilalkhpdrFgsvss 145
                                     +G+SmGG+ A  +al++     +v++
  gi|121638810|ref|YP_979034.1| 100 FFGHSMGGMLAFEVALRYQSAGHRVLA 126
                                    ****************99766555555 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.022      77     119 ..      82     124 ..      73     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                          PGAP1  77 kyIlslysssekeptsviliGHSmGGivaraaltlknyikqsv 119
                                     +I  +++ s +    v   GHSmGG++a  ++   + + + v
  gi|121638810|ref|YP_979034.1|  82 DEIFAMMKPSARIDDPVAFFGHSMGGMLAFEVALRYQSAGHRV 124
                                    5788999999999999*************66555444444444 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.039      86     136 ..      76     127 ..      10     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                    HHHHHHHHHHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEE CS
                  Abhydrolase_2  86 saekleelidaelkkg.ipssriiigGFSqGaalalylaltlpkklggivaf 136
                                    s+++l + i a +k + +  + ++++G S+G++la + al ++    +++af
  gi|121638810|ref|YP_979034.1|  76 SIPTLADEIFAMMKPSaRIDDPVAFFGHSMGGMLAFEVALRYQSAGHRVLAF 127
                                    55555555555555555556779*********************99999987 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.17     122     143 ..      98     119 ..      82     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                 Chlorophyllase 122 lalvGhsrGGktafalalgyss 143
                                    +a  Ghs GG  af +al+y s
  gi|121638810|ref|YP_979034.1|  98 VAFFGHSMGGMLAFEVALRYQS 119
                                    8999****************74 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00021      0.31      37     130 ..      30     122 ..      12     161 .. 0.80
   2 ?   -2.1   0.0         1   1.5e+03     270     295 ..     229     254 ..     212     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                        DUF1057  37 tvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskalleelelkgklillghsRGce 116
                                    t   ++ + G+ +D+     ++  ++++ i+v yPG +  +g +  + + +  ++    +  ++ +++ ++++ghs G+ 
  gi|121638810|ref|YP_979034.1|  30 TLYIFPHAGGTAKDYVAFSREFS-ADVKRIAVQYPGQHDRSGLPPLESIPTLADEIFAMMKPSARIDDPVAFFGHSMGGM 108
                                    66667777888888877777775.578889************9999999888888777777799**************** PP

                        DUF1057 117 naLqlavtleahGl 130
                                     a  +a  ++  G 
  gi|121638810|ref|YP_979034.1| 109 LAFEVALRYQSAGH 122
                                    **999999877774 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                        DUF1057 270 svfvakdghfqnkkraelvaevvksi 295
                                       +  d  ++n + +elv ++ ++ 
  gi|121638810|ref|YP_979034.1| 229 IRVFPGDHFYLNDNLPELVSDIEDKT 254
                                    44455677789999999999987765 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00018      0.27      92     116 ..      98     122 ..      80     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                Chlorophyllase2  92 lalsgHSrGgktafalalgkaktsl 116
                                    +a  gHS Gg  af++al ++++  
  gi|121638810|ref|YP_979034.1|  98 VAFFGHSMGGMLAFEVALRYQSAGH 122
                                    8999**************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1945.49
//
Query:       gi|121638811|ref|YP_979035.1|  [L=103]
Description: hypothetical protein BCG_2951 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 770.12
//
Query:       gi|121638812|ref|YP_979036.1|  [L=583]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-77  259.4   0.0    5.5e-77  259.1   0.0    1.1  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.048   14.0   0.0      0.089   13.1   0.0    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.1   0.0   6.2e-81   5.5e-77       1     422 [.      12     469 ..      12     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 259.1 bits;  conditional E-value: 6.2e-81
                                    HHHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-E CS
                    AMP-binding   1 leeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGav 73 
                                    l+e+a+++pd +a+++       +g   +lT++++++r++ +A  L+  G+ +gdrVa+l+p+++e+v+a+l++l+aG +
  gi|121638812|ref|YP_979036.1|  12 LQERADQQPDSTAYTYidygsdpKGFADSLTWSQVYSRACIIAEELKLCGL-PGDRVAVLAPQGLEYVLAFLGALQAGFI 90 
                                    5899**********9999****98899********************7798.7*************************** PP

                                    EEEEET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-T CS
                    AMP-binding  74 vvplnp...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekp 150
                                    +vpl++   +   ++++ +l+ds++ +++  + s  +  + + aa+ + + + +v++ d l+        ++ +      
  gi|121638812|ref|YP_979036.1|  91 AVPLSTpqyGIHDDRVSAVLQDSKPVAIL--TTSSVVGDVTKYAASHDGQPAPVVVEVDLLDLD------SPRQ------ 156
                                    *****99889999****************..444444445555555555555666664443322......2222...... PP

                                    SCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTT....T-EEEESS-TTSCHHHHHHHHHHHH CS
                    AMP-binding 151 eeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklke....ddvvlsilplahifglilelllall 226
                                    +++ + +    ay++YTSG+T +P GV++sh n++anv++ +++ +f+  +    + +v+s+lpl+h++glil+++++l+
  gi|121638812|ref|YP_979036.1| 157 MPAFSRQHTGAAYLQYTSGSTRTPAGVIVSHTNVIANVTQ-SMYGYFGD-PakipTGTVVSWLPLYHDMGLILGICAPLV 234
                                    22335677899**************************999.57767542.3356699*********************** PP

                                    TT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                    AMP-binding 227 sGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffr 304
                                    +  + vl+++ ++ ++p+++++l+++ +  + a+++ ++e  ++  ++   +++  dl  +  +++g e++  +++r+f 
  gi|121638812|ref|YP_979036.1| 235 ARRRAVLMSPMSFlRRPARWMQLLATSGRCFSAAPNFAFELAVRrTSDQ--DMAGLDLRDVVGIVSGSERIHVATVRRFI 312
                                    *************666*********666666666666677667744333..456668888777789************** PP

                                    HHHTC......EEEEEEEEGGGSSECEE..................CHCTTTCTSTTS-BEE-......TTEEEEEE-TT CS
                    AMP-binding 305 alfge......evlegYGlTEttgvvtv..................lpleedkkklgsvGkpl......pgvevkivDee 354
                                    ++f +      ++  +YGl+E+t  v+                   + + +++ + gsvG+ l          v+iv++e
  gi|121638812|ref|YP_979036.1| 313 ERFAPynlsptAIRPSYGLAEATLYVAApeagaapktvrfdyeqltAGQARPCGTDGSVGTELisygspDPSSVRIVNPE 392
                                    **********99**************7778888899999999999944455555567777555555553477******** PP

                                    TSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.........TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 355 tgepvpdgeeGellvrgpgvmkgYlkkpeataeafds.........egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                    t+ + p+g++Ge++v+g +v++gY++kp++ta++fd+         +++ wlrTGDlg++  dG+l+i+gR+kdl+++
  gi|121638812|ref|YP_979036.1| 393 TMVENPPGVVGEIWVHGDHVTMGYWQKPKQTAQVFDAklvdpapaaPEGpWLRTGDLGVIS-DGELFIMGRIKDLLIV 469
                                    ***********************************978999999974466**********9.9************987 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.089       1      91 [.     471     564 ..     471     566 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--.EEEEE- CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsv.kvelve 78 
                                    G n +P  ie+ ++ei +  +    v ++  e+ +  ++  ++  ++ + + +l+++++++++++ ++ +++v ++ lv+
  gi|121638812|ref|YP_979036.1| 471 GRNHYPDDIEATIQEITGGRAAAIAVPDDITEQLVAIIEFKRRGsTAEEVMLKLRSVKREVTSAISKSHSLRVaDLVLVS 550
                                    7799************998876544444444444444555555533344567899****************9649***** PP

                                    TT-S----.----- CS
                AMP-binding_C_2  79 pgtlprse.gKakr 91 
                                    pg++p ++ gK +r
  gi|121638812|ref|YP_979036.1| 551 PGSIPITTsGKIRR 564
                                    *****965169887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3739.59
//
Query:       gi|121638813|ref|YP_979037.1|  [L=1876]
Description: phenolpthiocerol synthesis type-I polyketide synthase ppsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.6e-119  397.1   0.1   1.2e-118  396.2   0.1    1.4  1  Acyl_transf_1    Acyl transferase domain
      9e-94  313.8   0.1    2.3e-93  312.4   0.1    1.8  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.8e-61  207.2   0.0    3.2e-61  206.4   0.0    1.5  1  KR               KR domain
    9.2e-46  154.7   0.1    2.6e-45  153.3   0.1    1.9  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.9e-30  105.0   0.1    8.7e-16   58.0   0.0    2.8  2  PP-binding       Phosphopantetheine attachment site
    1.2e-16   60.9   2.8    2.1e-16   60.1   2.8    1.4  1  PS-DH            Polyketide synthase dehydratase
    1.8e-16   60.6   0.0    4.6e-16   59.3   0.0    1.7  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.9e-05   24.2   1.0    0.00012   21.5   0.2    2.8  3  Thiolase_N       Thiolase, N-terminal domain
    0.00042   19.8   0.2     0.0092   15.5   0.2    2.7  1  adh_short        short chain dehydrogenase
     0.0035   16.9   0.0       0.17   11.4   0.0    2.7  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.2   0.1    7e-122  1.2e-118       1     316 [.     632     949 ..     632     951 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.2 bits;  conditional E-value: 7e-122
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfv+sG+GsQwaGMG++Ll++++afaa++a+++++f +q+gfs++dvl+n +  +l +i+++q++L+ +q+al+el++s+
  gi|121638813|ref|YP_979037.1| 632 VFVYSGRGSQWAGMGRQLLADEPAFAAAVAELEPVFVEQAGFSLHDVLANGE--ELVGIEQIQLGLIGMQLALTELWCSY 709
                                    8***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS..HHHHHHH...TT.EEEEEEECCCC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel.aeeeeklr.cqddvvgavansprrv 158
                                    Gv+p++v+GHS+GE+Aaavvagal+++e+l+++++rsrlm++l+g+g+ma +el a+++e+l+ ++++v+++++nspr++
  gi|121638813|ref|YP_979037.1| 710 GVQPDLVIGHSMGEVAAAVVAGALTPAEGLRVTATRSRLMAPLSGQGGMALLELdAPTTEALIaDFPQVTLGIYNSPRQT 789
                                    ******************************************************9999999999**************** PP

                                    ECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHH CS
                  Acyl_transf_1 159 visgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywv 238
                                    vi+g++e+++el++rv++++++a+++n++va+h+p++da+++a++s+lad++pr+p++  is+t++d +++++++ae+w+
  gi|121638813|ref|YP_979037.1| 790 VIAGPTEQIDELITRVRARDRFASRVNIEVAPHNPAMDALQPAMRSELADLTPRTPTIGIISTTYADLHTQPVFDAEHWA 869
                                    ******************************************************************************** PP

                                    HHHHCHCCHCCHHTTS...SSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHC CS
                  Acyl_transf_1 239 anlrspvrfaeavlsa...aetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahlt 315
                                    +n+r+pv f++a++sa   a+ ++++f+eis+H+ll++a+++tl+sa++++++t +G+l+rd++d +vtf+++l+kah++
  gi|121638813|ref|YP_979037.1| 870 TNMRNPVHFQQAIASAgsgADGAYHTFIEISAHPLLTQAIIDTLHSAQPGARYTSLGTLQRDTDD-VVTFRTNLNKAHTI 948
                                    ******************9**********************************************.************99 PP

                                    T CS
                  Acyl_transf_1 316 g 316
                                    +
  gi|121638813|ref|YP_979037.1| 949 H 949
                                    8 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.4   0.1   1.3e-96   2.3e-93       2     253 .]     102     351 ..     101     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 1.3e-96
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgisp 79 
                                    ep+a+vGmg+rfPgg + +e++w+ L+e r++is++p +rw++ +  +p+  aa   +t++g fl+ +d+fd+eff+isp
  gi|121638813|ref|YP_979037.1| 102 EPIAVVGMGCRFPGGIScPEALWDFLCERRSSISQVPPQRWQPFEGGPPEVAAALARTTRWGSFLPdIDAFDAEFFEISP 181
                                    89********************************************99999999999*********************** PP

                                    HHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  80 reaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagris 159
                                    +ea++mdpqqrllle+aweale+ag++p +l+ s++gvf+G++ ++y+a+a+ d  +  v++++   g  + ++ia+r+s
  gi|121638813|ref|YP_979037.1| 182 SEADKMDPQQRLLLEVAWEALEHAGIPPGTLRRSATGVFAGACLSEYGAMASADLSQ--VDGWS-NSGG-AMSIIANRLS 257
                                    ***********************************************9988888777..89999.7777.89******** PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlG 239
                                    y+l+lrGpsv+vdtACsSslva+h+a+qslr++++ +a+a Gv+lll+p  ++gf++ g+lsp+g+c+afd+ adGfv+G
  gi|121638813|ref|YP_979037.1| 258 YFLDLRGPSVAVDTACSSSLVAIHLACQSLRTQDCHLAIAAGVNLLLSPAVFRGFDQVGALSPTGQCRAFDATADGFVRG 337
                                    ******************************************************************************** PP

                                    -EEEEEEEEECHHH CS
                  ketoacyl-synt 240 EGvGavvLkrleda 253
                                    EG+G+vvLkrl+da
  gi|121638813|ref|YP_979037.1| 338 EGAGVVVLKRLTDA 351
                                    ***********997 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0   1.8e-64   3.2e-61       1     179 [.    1491    1683 ..    1491    1684 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 1.8e-64
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS...............--HHHHHHHHHHHHTT-EEEE----TT-H CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsa.............aadedskaliaelealgaevevvaaDvsdk 65  
                                     ++ylitGGlG+LGl +a+wla++ga++lvl++R++             ++ ++  + i++le +g++ve+vaaDv  +
  gi|121638813|ref|YP_979037.1| 1491 AAYLITGGLGALGLLMADWLADRGAHRLVLTGRTPlpprrdwqldtldTELRRRIDAIRALEMRGVTVEAVAADVGCR 1568
                                     68********************************99888888888777555566679********************* PP

                                     HHHHHHHHHHHHHS.S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH- CS
                             KR   66 davealleeikaee.ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllg 142 
                                     ++v+all++ ++++ +pi+G+ihaAg+++d+l+++mt ++++qv++pK+ G+++Lh ++++ s+dff+l++S+ag++g
  gi|121638813|ref|YP_979037.1| 1569 EDVQALLAARDRDGaAPIRGIIHAAGITNDQLVTSMTGDAVRQVMWPKIGGSQVLHDAFPPGSVDFFYLTASAAGIFG 1646
                                     **************9*************************************************************** PP

                                     -TT-HHHHHHHHHHHHHHHHHHHHHHTEEEEEE--BT CS
                             KR  143 sagqanYaaaNaflDalaeyrrsqglpavsinwglwa 179 
                                      +gq++YaaaN++lDala+ rr+qg++++s++w +w+
  gi|121638813|ref|YP_979037.1| 1647 IPGQGSYAAANSYLDALARARRQQGCHTMSLDWVAWR 1683
                                     ************************************8 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.1   1.4e-48   2.6e-45       1     118 []     359     477 ..     359     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 1.4e-48
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG.SCTSE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar.kqpla 79 
                                    +avi gsav++dg++n+l+apn++aq +++++a+ +ag++p++vdyveahgtgt lgDpiE++al +v+g+++  ++pl 
  gi|121638813|ref|YP_979037.1| 359 LAVICGSAVTQDGRSNGLMAPNPAAQMAVLRAAYTNAGMQPSEVDYVEAHGTGTLLGDPIEARALGTVLGRGRPeDSPLL 438
                                    69**********************************************************************9999**** PP

                                    EE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT-S CS
                Ketoacyl-synt_C  80 vgSvKsniGHleaAaGvaelikvvlalkhgvipptlnle 118
                                    +gSvK+n+GH+eaAaG+a++ik+vla++hg+ipp++++e
  gi|121638813|ref|YP_979037.1| 439 IGSVKTNLGHTEAAAGIAGFIKTVLAVQHGQIPPNQHFE 477
                                    *************************************95 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   9.8e-15   1.8e-11       2      67 .]      14      79 ..      13      79 .. 0.97
   2 !   58.0   0.0   4.8e-19   8.7e-16       2      67 .]    1767    1832 ..    1766    1832 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 9.8e-15
                     PP-binding  2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                   +l++ + + +g+ ++e+dpd +l dlG+ S +av l ++l+e +g ++++ d++ehpt+++laayl
  gi|121638813|ref|YP_979037.1| 14 WLIDYLVTNIGCTPDEVDPDLSLADLGVSSRDAVVLSGELSELLGRTVSPIDFWEHPTINALAAYL 79
                                   788999999*******************************************************97 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 4.8e-19
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                      lr+++a  l+vp++e+d d ++ +lGl+Sl+a+++ ++ e+  g+e++ ++lf+hpt+++la yl
  gi|121638813|ref|YP_979037.1| 1767 GLRRIIAAELRVPEKELDTDRPFAELGLNSLMAMAIRREAEQFVGIELSATMLFNHPTVKSLASYL 1832
                                     599************************************************************996 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   2.8   1.1e-19   2.1e-16       9     291 ..    1003    1261 ..     992    1264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-19
                                     --.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B--SS-EEEE CS
                          PS-DH    9 rsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlpedepvevq 86  
                                      sas+ ++++++rl ++  p+   Hr +   v+P+ + l  +l+Aa++l       +l +v+++++++ +  +p+ +q
  gi|121638813|ref|YP_979037.1| 1003 VSASPPSHLWQARLAPDAKPYQGGHRFHQVEVVPASVVLHTILSAATELG----YSALSEVRFEQPIFAD--RPRLIQ 1074
                                     4558999******************************************9....789**********555..9***** PP

                                     EEEEE-TTS-E....EEEEEEE-SS-TT....EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HHHHHHHH CS
                          PS-DH   87 lslepeedgadrawvefeifSregggee...wtehatGtvrlaegaaaaavdlealqarcaepaslrsvssaefYerl 161 
                                     +++  +         +++++S  ++g+    wt+h+t++++  +++ a ++  + + + ++++++ r++ + ++ e l
  gi|121638813|ref|YP_979037.1| 1075 VVADNR---------AISLASSPAAGTPsdrWTRHVTAQLSSSPSDSASSLNEHHRANGQPPERAHRDLIP-DLAELL 1142
                                     ***999.........5677777776666688**********888877545555555444444444444444.699999 PP

                                     HHHSEEE-GGG--EEEEEEE.TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEEEEEEE CS
                          PS-DH  162 aargleyGpsFqglralwrg.dgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylPvaier 238 
                                     a rg++ G  F +  a w++  +     + lpe+l +g+      P llDaa++l   al   + ++ ++y+P +ie+
  gi|121638813|ref|YP_979037.1| 1143 AMRGID-GLPFSWTVASWTQhSSNLTVAIDLPEALPEGST----GP-LLDAAVHLA--AL--SDVADSRLYVPASIEQ 1210
                                     999**9.999***999999845567788999999997764....44.79*****66..34..46899*********** PP

                                     EEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE- CS
                          PS-DH  239 lrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrv 291 
                                     +++       g +  v+  ++++++++i++d+t+ ++   + ++++ lr r++
  gi|121638813|ref|YP_979037.1| 1211 ISLGD--VVTGPRSSVTLNRTAHDDDGITVDVTVAAHGEVPSLSMRSLRYRAL 1261
                                     ***97..3344556788888****************99999********9987 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   2.6e-19   4.6e-16       2     102 ..     480     584 ..     479     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.6e-19
                 KAsynt_C_assoc   2 npeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeeskeeslprLlvlsgrteeaveal 77 
                                    np+ip ++++r+kVv+++t+wp +     +gv+sfGfGG+n+Hv++++ ++ ++++ +  ++  + lv++g+t + v+a+
  gi|121638813|ref|YP_979037.1| 480 NPHIP-FTDLRMKVVDTQTEWPATGhprrAGVSSFGFGGTNAHVVIEQGQEVRPAPGQGLSPAVSTLVVAGKTMQRVSAT 558
                                    9****.***************99888999**********************99999999899999999************ PP

                 KAsynt_C_assoc  78 lekleeh.lldaellsllneilseei 102
                                    +  l+++ +   ++++l++ +++ + 
  gi|121638813|ref|YP_979037.1| 559 AGMLADWmEGPGADVALADVAHTLNH 584
                                    ******95444677777777776655 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   6.8e-08   0.00012      57     113 ..     247     301 ..     185     307 .. 0.87
   2 ?   -3.3   0.0       2.5   4.5e+03       2      48 ..     361     405 ..     360     407 .. 0.80
   3 ?   -2.4   0.0       1.4   2.5e+03      42      78 ..    1205    1242 ..    1187    1255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.8e-08
                                    TSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEE CS
                     Thiolase_N  57 gegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvE 113
                                    g+ ++ia+ ++  +++    p+v+v+ +csS+l a++la+qs++++++  ++a Gv 
  gi|121638813|ref|YP_979037.1| 247 GAMSIIANRLSYFLDL--RGPSVAVDTACSSSLVAIHLACQSLRTQDCHLAIAAGVN 301
                                    5556677777777777..7899*********************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                    EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEE CS
                     Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdev 48 
                                    vi ++a t+ g+++g ++  +a ++  ++l+a+ ++ag++p+evd+v
  gi|121638813|ref|YP_979037.1| 361 VICGSAVTQDGRSNGLMAPNPAAQM--AVLRAAYTNAGMQPSEVDYV 405
                                    6777888888888888888888876..58899999999999999987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                                     GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEE CS
                     Thiolase_N   42 peevdevivGnvlqa.gegqniarqaalkagipeevpa 78  
                                     p++++++ +G v+++  +  +++r a+ + gi  +v++
  gi|121638813|ref|YP_979037.1| 1205 PASIEQISLGDVVTGpRSSVTLNRTAHDDDGITVDVTV 1242
                                     7889***********77777799999999999777665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   5.1e-06    0.0092       4     163 ..    1494    1667 ..    1491    1674 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-06
                                     EEESTTSHHHHHHHHHHHHTT-EEEE.EESCH.............HHHHHHHHHHHHT...TSEEEEEE-TTTSHHHH CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvv.vdrse.............ekleevakelkee...gakalaiqvDvtdreev 64  
                                     l+tG+ + +G+ +a+ la +Ga+ +v ++r++              +l++ ++ ++++   g ++ a+++Dv  re+v
  gi|121638813|ref|YP_979037.1| 1494 LITGGLGALGLLMADWLADRGAHRLVlTGRTPlpprrdwqldtldTELRRRIDAIRALemrGVTVEAVAADVGCREDV 1571
                                     8999999999999999999999988867766422222211111113444555555555666889************** PP

                                     HHHHHHHHHHH.SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTS CS
                      adh_short   65 ealvekavkkl.gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkv 141 
                                     +al+++   +   ++  +++ AGit+++ + +++ +++++v+   + g   l  a+ p     s      ++S ag  
  gi|121638813|ref|YP_979037.1| 1572 QALLAARDRDGaAPIRGIIHAAGITNDQLVTSMTGDAVRQVMWPKIGGSQVLHDAFPPG----SVDFFYLTASAAGIF 1645
                                     **99887655449****************************988877776666665554....455556788888888 PP

                                     B-TTBHHHHHHHHHHHHHHHHH CS
                      adh_short  142 pvagvaaYsAsKaavagltrsl 163 
                                     + +g+ +Y+A+   +++l+r+ 
  gi|121638813|ref|YP_979037.1| 1646 GIPGQGSYAAANSYLDALARAR 1667
                                     8888888888877777777765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   9.5e-05      0.17      42     153 ..    1557    1665 ..    1535    1667 .. 0.75
   2 ?    2.2   0.0     0.063   1.1e+02      32      66 ..    1823    1857 ..    1798    1864 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                                     TSEEEE--TTSHHHHHHHHHHHHHHH.SSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCT CS
                   adh_short_C2   42 gaevlecDVtdeeqvealveevvekf.gklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmk 118 
                                       e++++DV  +e+v+al ++  ++    + +++++agi+++  + +++++ + +++++  ++ +   l  a+ p   
  gi|121638813|ref|YP_979037.1| 1557 TVEAVAADVGCREDVQALLAARDRDGaAPIRGIIHAAGITND--QLVTSMTGDAVRQVMWPKIGGSQVLHDAFPP--- 1629
                                     2346***************9998887799*************..99************98888776555555444... PP

                                     SC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  119 eg..gsivnlssvgaervvpnynaygaaKaalealtr 153 
                                      g       ++s ++  ++p++  y+aa   l al+r
  gi|121638813|ref|YP_979037.1| 1630 -GsvDFFYLTASAAGIFGIPGQGSYAAANSYLDALAR 1665
                                     .322345556777788888888888888888888877 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.063
                                     HHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHH CS
                   adh_short_C2   32 krveelaeelgaevlecDVtdeeqvealveevvek 66  
                                      +v++la+ l ++v + DV++++q+ al + + + 
  gi|121638813|ref|YP_979037.1| 1823 PTVKSLASYLAKRVAPHDVSQDNQISALSSSAGSV 1857
                                     4799999999999**************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.99u 0.30s 00:00:01.29 Elapsed: 00:00:00.50
# Mc/sec: 11264.62
//
Query:       gi|121638814|ref|YP_979038.1|  [L=1538]
Description: phenolpthiocerol synthesis type-I polyketide synthase ppsB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.9e-110  367.1   0.1   1.8e-109  366.1   0.1    1.5  1  Acyl_transf_1    Acyl transferase domain
      1e-97  326.7   0.2    2.1e-97  325.7   0.2    1.6  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.2e-47  162.2   1.2    1.9e-46  158.2   0.0    2.4  2  KR               KR domain
      2e-41  140.7   2.9    3.3e-41  140.0   0.9    2.4  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    5.2e-13   48.9   0.0    1.2e-12   47.7   0.0    1.5  1  adh_short        short chain dehydrogenase
    1.3e-12   47.8   0.0    3.3e-12   46.6   0.0    1.7  1  PP-binding       Phosphopantetheine attachment site
    2.9e-12   47.0   0.0    6.8e-12   45.8   0.0    1.6  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    6.9e-06   25.6   0.1    6.6e-05   22.4   0.1    2.6  3  Thiolase_N       Thiolase, N-terminal domain
    0.00017   21.2   0.0     0.0004   20.0   0.0    1.5  1  NmrA             NmrA-like family
    0.00019   21.0   0.0    0.00033   20.2   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00025   21.0   2.0    0.00047   20.1   0.0    2.5  2  NAD_binding_10   NAD(P)H-binding
     0.0044   16.2   0.0      0.007   15.5   0.0    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.016   15.0   0.7        3.9    7.1   0.0    2.8  2  SAT              Starter unit:ACP transacylase in aflatoxin b
      0.046   14.3   0.1       0.17   12.5   0.1    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.077   13.3   0.3       0.22   11.8   0.0    2.0  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.092   12.1   0.0       0.14   11.5   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.1   0.1  1.6e-112  1.8e-109       1     316 [.     561     882 ..     561     884 .. 0.97

  Alignments for each domain:
  == domain 1  score: 366.1 bits;  conditional E-value: 1.6e-112
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfv+sG+GsQwaGMG++Ll++++afaa++a+++++f +q+gfs+ dv++     +l +i+++q++L+ +q+ l+el++s+
  gi|121638814|ref|YP_979038.1| 561 VFVYSGRGSQWAGMGRQLLADEPAFAAAVAELEPVFVEQAGFSLRDVIATGK--ELVGIEQIQLGLIGMQLTLTELWRSY 638
                                    8***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS..HHHHHHH...TT.EEEEEEECCCC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel.aeeeeklr.cqddvvgavansprrv 158
                                    Gv+p++v+GHS+GE+Aaavvagal+++e+l+++++r rlm++l+g+g+ma ++l a+ +e+l+ + ++v+++++nspr++
  gi|121638814|ref|YP_979038.1| 639 GVQPDLVIGHSMGEVAAAVVAGALTPAEGLRVTATRARLMAPLSGQGGMALLGLdAAATEALIaDYPQVTVGIYNSPRQT 718
                                    ******************************************************9666666666**************** PP

                                    ECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHH CS
                  Acyl_transf_1 159 visgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywv 238
                                    vi+g++e+++el++rv++++++a+++n++va+h+p++da+++a++s+lad++pr+p++  is+t++d ++++ ++ae+w+
  gi|121638814|ref|YP_979038.1| 719 VIAGPTEQIDELIARVRAQNRFASRVNIEVAPHNPAMDALQPAMRSELADLTPRTPTIGIISTTYADLHTQPIFDAEHWA 798
                                    ******************************************************************************** PP

                                    HHHHCHCCHCCHHTTS...SSECC-CCEECSSSSCCHCCCCCCCHH....GGG-TCCCCCCTEETTSS-HHHCHHHHHHH CS
                  Acyl_transf_1 239 anlrspvrfaeavlsa...aetiplvfveispHslllaalektlks....aedvksatlvGklkrdltdflvtflyllak 311
                                    +n+r+pvrf++a++sa   a+  +++f+eis+H+ll++a+ +tl++     + ++++  +G+l+rd +d  vtf+++l +
  gi|121638814|ref|YP_979038.1| 799 TNMRNPVRFQQAIASAgsgADGTYHTFIEISAHPLLTQAIADTLEDahrpTKSAAKYLSIGTLQRDADD-TVTFRTNLYT 877
                                    ******************99**************************988888899999***********.*******999 PP

                                    HHHCT CS
                  Acyl_transf_1 312 ahltg 316
                                    a++++
  gi|121638814|ref|YP_979038.1| 878 ADIAH 882
                                    99887 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.7   0.2  1.8e-100   2.1e-97       2     253 .]      34     283 ..      33     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 325.7 bits;  conditional E-value: 1.8e-100
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgisp 79 
                                    epva+vG+g+rfPg +d +e+fw+ L++gr+ais++padrwda+++y+p++ ++g+++tk+ggf++ v+ fd+effgi+p
  gi|121638814|ref|YP_979038.1|  34 EPVAVVGIGCRFPGDVDgPESFWDFLVAGRNAISTVPADRWDAEAFYHPDPLTPGRMTTKWGGFVPdVAGFDAEFFGITP 113
                                    8***************99************************************************************** PP

                                    HHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  80 reaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagris 159
                                    rea+amdpqqr+lle+aweale+ag++p++l g+r++v++Gv  ++y+ + a +++  +v+a++  +g+ +++++ gris
  gi|121638814|ref|YP_979038.1| 114 REAAAMDPQQRMLLEVAWEALEHAGIPPDSLGGTRTAVMMGVYFNEYQSMLAASPQ--NVDAYS-GTGN-AHSITVGRIS 189
                                    *********************************************99765555544..69****.****.********** PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlG 239
                                    y lglrGp+v+vdtACsSslvavh+a+qslr +e d+alaGGv+ +l pe+ ++ sa+gllsp+grc afd++adGfv+G
  gi|121638814|ref|YP_979038.1| 190 YLLGLRGPAVAVDTACSSSLVAVHLACQSLRLRETDLALAGGVSITLRPETQIAISAWGLLSPQGRCAAFDAAADGFVRG 269
                                    ******************************************************************************** PP

                                    -EEEEEEEEECHHH CS
                  ketoacyl-synt 240 EGvGavvLkrleda 253
                                    EG+G+vvLkrl+da
  gi|121638814|ref|YP_979038.1| 270 EGAGVVVLKRLTDA 283
                                    ***********997 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.15   1.6e+02      23      85 ..     469     536 ..     467     553 .. 0.68
   2 !  158.2   0.0   1.7e-49   1.9e-46       2     179 ..    1153    1327 ..    1152    1328 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                                    HHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE..----TT-HHHHHHHHHHHHHHS..S---EE CS
                             KR  23 kgarhlvllsRsaaadedskaliaeleal.gaevev..vaaDvsdkdavealleeikaee..ppikGv 85 
                                     g ++lv+++++a+  ++ ++ +a + +  gaev v  va  v ++ a +a++ ++ a++  ++i+G 
  gi|121638814|ref|YP_979038.1| 469 TGVSTLVVTGKTAQRMAATAQVLADWMEGpGAEVAVadVAHTVNHHRARQATFGTVVARDraQAIAGL 536
                                    68999*******98777777777666553388776611344666677777777776665555677776 PP

  == domain 2  score: 158.2 bits;  conditional E-value: 1.7e-49
                                     EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                             KR    2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79  
                                     + l++G++G++G +l+r+la+ ga+++v ++R+  + +  ++l++ l+a+g++  +vaaD +d++a+++l++++ +e 
  gi|121638814|ref|YP_979038.1| 1153 SQLVIGATGNIGPHLIRQLARMGAKTIVAMARK--PGAL-DELTQCLAATGTDLIAVAADATDPAAMQTLFDRFGTEL 1227
                                     789******************************..3444.4599********************************** PP

                                     S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHHH CS
                             KR   80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaflD 157 
                                     pp++G++ aA + r +ll+emt++d++++++pK++++  Lh+l+ ++++ +fvlfSS++gllgs+  a+Y+a++aflD
  gi|121638814|ref|YP_979038.1| 1228 PPLEGIYLAAFAGRPALLSEMTDDDVTTMFRPKLDALALLHRLSLKSPVRHFVLFSSVSGLLGSRWLAHYTATSAFLD 1305
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHTEEEEEE--BT CS
                             KR  158 alaeyrrsqglpavsinwglwa 179 
                                     ++a  rr++glpa++++wglw+
  gi|121638814|ref|YP_979038.1| 1306 SFAGARRTMGLPATVVDWGLWK 1327
                                     *********************7 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.4   2.7e+03      15      43 ..     115     143 ..     109     145 .. 0.85
   2 !  140.0   0.9   2.9e-44   3.3e-41       1     117 [.     291     405 ..     291     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                                    TSSSTSTTHHHHHHHHHHHHHHHT--GGG CS
                Ketoacyl-synt_C  15 hnsltapngeaqaraiekalaeagvdped 43 
                                    ++ +++p+++ + ++  +al+ ag+ p++
  gi|121638814|ref|YP_979038.1| 115 EAAAMDPQQRMLLEVAWEALEHAGIPPDS 143
                                    56678999999999***********9986 PP

  == domain 2  score: 140.0 bits;  conditional E-value: 2.9e-44
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +av++gsavn+dg++n++tapn +aq ++i++al++ +v+p++v+yveahgtgt lgDpiE+eal++++g+++  + +a+
  gi|121638814|ref|YP_979038.1| 291 LAVVRGSAVNQDGRSNGVTAPNTAAQCDVIADALRSGDVAPDSVNYVEAHGTGTVLGDPIEFEALAATYGHGG--DACAL 368
                                    69*********************************************************************99..67*** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    g+vK+niGHleaAaG+a++ik+ la+++ +ipp+l++
  gi|121638814|ref|YP_979038.1| 369 GAVKTNIGHLEAAAGIAGFIKATLAVQRATIPPNLHF 405
                                    ************************************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   1.1e-15   1.2e-12       4     160 ..    1155    1308 ..    1153    1317 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-15
                                     EEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80  
                                     lv+Ga++ IG  + ++la++Gak++v ++r++ +l e+ + l ++g++++a+++D td +++++l+++   +l +l+ 
  gi|121638814|ref|YP_979038.1| 1155 LVIGATGNIGPHLIRQLARMGAKTIVaMARKPGALDELTQCLAATGTDLIAVAADATDPAAMQTLFDRFGTELPPLEG 1232
                                     89***********************99*************************************************** PP

                                     EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHH CS
                      adh_short   81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavag 158 
                                     ++  A   +++  se++++++  ++   l ++ ll r+ l+        + v  sSv g+ ++ ++a Y+A+ a++++
  gi|121638814|ref|YP_979038.1| 1233 IYLAAFAGRPALLSEMTDDDVTTMFRPKLDALALLHRLSLKS----PVRHFVLFSSVSGLLGSRWLAHYTATSAFLDS 1306
                                     **9999999***************************999888....66789*************************99 PP

                                     HH CS
                      adh_short  159 lt 160 
                                     ++
  gi|121638814|ref|YP_979038.1| 1307 FA 1308
                                     97 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0     3e-15   3.3e-12       5      67 .]    1431    1494 ..    1427    1494 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3e-15
                     PP-binding    5 elvaevlgv.pleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +l+a+v+g+ p+e++dp++ +f lG+DSl++v+l++al+e +g  +p s++f++pt+ +l++yl
  gi|121638814|ref|YP_979038.1| 1431 ALAATVMGMpPTEPLDPSAGFFQLGMDSLMSVTLQRALSESLGEFLPASVVFDYPTVYSLTDYL 1494
                                     7899*****666669**********************************************997 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   6.1e-15   6.8e-12       2     102 ..     409     513 ..     409     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.1e-15
                 KAsynt_C_assoc   2 npeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeeskeeslprLlvlsgrteeaveal 77 
                                    np i+  +++r+ V+t++ pwp       ++v+sfG GG+n+Hvi+++ ++  + +e  e+   + lv+ g+t++ + a+
  gi|121638814|ref|YP_979038.1| 409 NPAID-AASTRFFVPTQNSPWPTAEgprrAAVSSFGLGGTNAHVIIEQGSELAPVSEGGEDTGVSTLVVTGKTAQRMAAT 487
                                    89999.899*************9989999**********************99999999999****************** PP

                 KAsynt_C_assoc  78 lekleehlld.aellsllneilseei 102
                                    ++ l+++ +   +++++++ +++ + 
  gi|121638814|ref|YP_979038.1| 488 AQVLADWMEGpGAEVAVADVAHTVNH 513
                                    ******95541566666666665443 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.3   2.5e+03      25      47 ..     124     146 ..     118     174 .. 0.70
   2 !   22.4   0.1   5.9e-08   6.6e-05      75     112 ..     195     232 ..     177     251 .. 0.90
   3 ?   -1.6   0.0       1.3   1.4e+03      18      73 ..     825     881 ..     811     886 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHHHTS-GGGCCE CS
                     Thiolase_N  25 eLlaealkallekagvdpeevde 47 
                                     +l e+++++le+ag++p+++  
  gi|121638814|ref|YP_979038.1| 124 RMLLEVAWEALEHAGIPPDSLGG 146
                                    56678888899999999887754 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.9e-08
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                      pav+v+ +csS+l av+la+qs++  e d ++agGv
  gi|121638814|ref|YP_979038.1| 195 RGPAVAVDTACSSSLVAVHLACQSLRLRETDLALAGGV 232
                                    5699*********************************8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
                                    TTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS- CS
                     Thiolase_N  18 lkdlsaeeLlaealkallekag.vdpeevdevivGnvlqagegqniarqaalkagip 73 
                                    + ++sa+ Ll++a+ + le+a   ++++ +++ +G+    +++    r     a+i+
  gi|121638814|ref|YP_979038.1| 825 FIEISAHPLLTQAIADTLEDAHrPTKSAAKYLSIGTLQRDADDTVTFRTNLYTADIA 881
                                    567899***************966677889999999888888888888877777775 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.6e-07    0.0004       2      63 ..    1155    1221 ..    1155    1224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.6e-07
                                     EESSTTSHHHHHHHHHHHHHT-EE.EEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHT CS
                           NmrA    2 lviGaTGrqGksvvrallkaghkv.ralvRdt..kselakslkeaGvelv..kgdlddkeslvealk 63  
                                     lviGaTG++G +++r l++ g k+  a+ R++    el + l++ G  l+  ++d+ d + ++++++
  gi|121638814|ref|YP_979038.1| 1155 LVIGATGNIGPHLIRQLARMGAKTiVAMARKPgaLDELTQCLAATGTDLIavAADATDPAAMQTLFD 1221
                                     7******************99986268889999999*************98789999***9999986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00033       2     115 ..    1155    1284 ..    1154    1290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                     EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHHT... CS
                      Epimerase    2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl...........elveldltdrsalerlfkeeq... 64  
                                     lV+GatG iG +l+++l++ g + +++++r++     ++l++l             v +d td++a++ lf++++   
  gi|121638814|ref|YP_979038.1| 1155 LVIGATGNIGPHLIRQLARMGAKtIVAMARKP-----GALDELtqclaatgtdlIAVAADATDPAAMQTLFDRFGtel 1227
                                     8********************77588888883.....3333333457899**9999*********9999998765111 PP

                                     .-SEEEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH....TCTEEEEEEE CS
                      Epimerase   65 .pdavihlAa.vggvaassedpadfieknlqgtlnlleaarka....gvkrllflsS 115 
                                      p + i lAa  g +a  se   d + + ++  l+ l  +++      v+ ++ +sS
  gi|121638814|ref|YP_979038.1| 1228 pPLEGIYLAAfAGRPALLSEMTDDDVTTMFRPKLDALALLHRLslksPVRHFVLFSS 1284
                                     144556666657777777777777777777777777777664422225557777777 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   2.2e+03      49      87 ..     996    1043 ..     991    1048 .. 0.66
   2 !   20.1   0.0   4.2e-07   0.00047       1      58 [.    1158    1220 ..    1158    1287 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                     T-CCHHHHHHTT-SEEEES---TCC....HHHH.......HHHHHHHHHH CS
                 NAD_binding_10   49 tdvedlaealkgadaVvsalggggk....deeg.......aknivdaake 87  
                                     +d+++l +al+g+d V+ a    g+    +  +       ++++++a+ +
  gi|121638814|ref|YP_979038.1|  996 SDPAALLDALRGVDNVLYAPPVPGElldiE--SayqvfhaTRRLAAAMVA 1043
                                     68999**********999874444434321..133445556666666655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.2e-07
                                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CT..TTCEEEE--TT-CCHHHHHH CS
                 NAD_binding_10    1 GAtGkvGrllvkellargghevtalvRnpeklaele...ae..eglevvegdvtdvedlaeal 58  
                                     GAtG++G +l+++l++ g  +++a++R+p  l+el    a+    l +v +d+td+++++  +
  gi|121638814|ref|YP_979038.1| 1158 GATGNIGPHLIRQLARMGAKTIVAMARKPGALDELTqclAAtgTDLIAVAADATDPAAMQTLF 1220
                                     9*****************999*********999987444331134446789999999988766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.2e-06     0.007       2      78 ..    1155    1225 ..    1154    1237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.2e-06
                                     EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                Polysacc_synt_2    2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78  
                                     lv Ga+G iG +l+rq++++ +k+i+ + r+  +l+e+++ l ++ +      ++++v +d +d + +++++++++ 
  gi|121638814|ref|YP_979038.1| 1155 LVIGATGNIGPHLIRQLARMGAKTIVAMARKPGALDELTQCLAATGT------DLIAVAADATDPAAMQTLFDRFGT 1225
                                     799*************************************9954333......346788999999999999988765 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.012        13     104     128 ..     642     666 ..     620     682 .. 0.77
   2 ?    7.1   0.0    0.0035       3.9     180     237 ..     700     748 ..     667     751 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                            SAT 104 stylvGlCtGllaAaavacskslse 128
                                    +  ++G++ G +aAa+va + + +e
  gi|121638814|ref|YP_979038.1| 642 PDLVIGHSMGEVAAAVVAGALTPAE 666
                                    4589*************99877666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0035
                            SAT 180 alaefneekglppasrvyisavssss.vtisGpPstleallksskakkkkkksklpiya 237
                                    ++             +v +++++s++ ++i+Gp + +++l+++ +a+++    ++ i+ 
  gi|121638814|ref|YP_979038.1| 700 LI---------ADYPQVTVGIYNSPRqTVIAGPTEQIDELIARVRAQNRFAS-RVNIEV 748
                                    33.........34468899*****999*****************99999876.777765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015      0.17       5      50 ..    1157    1198 ..    1155    1216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                     E.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                  F420_oxidored    5 i.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50  
                                     i ++Gn+g  l+++l++ g    + +va  r+p  ++el + l   +
  gi|121638814|ref|YP_979038.1| 1157 IgATGNIGPHLIRQLARMG---AKTIVAMARKPGALDELTQCLA--A 1198
                                     6579***************...5556699********9998776..3 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.9   1.1e+04     106     130 .]    1025    1049 ..    1023    1049 .. 0.91
   2 ?   11.8   0.0    0.0002      0.22       2      66 ..    1155    1219 ..    1154    1224 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.9
                                     CSCHCCSHHHHHTHHHHHHCTSEEE CS
                Sacchrp_dh_NADP  106 rtnyalreavlklkekakeagvtav 130 
                                     +++y++ +a+++l+++  ++ +ta+
  gi|121638814|ref|YP_979038.1| 1025 ESAYQVFHATRRLAAAMVASSATAI 1049
                                     7899************999999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                                     EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHH CS
                Sacchrp_dh_NADP    2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaal 66  
                                     l+iGa G++G  +++ lar +    +i+ + r+   l++l + +  +g++++a+a da +++a ++ l
  gi|121638814|ref|YP_979038.1| 1155 LVIGAtGNIGPHLIRQLARMGAK--TIVAMARKPGALDELTQCLaaTGTDLIAVAADATDPAA-MQTL 1219
                                     79*******************98..9*******9999999876678**************999.6665 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.14       1      73 [.    1155    1222 ..    1155    1234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                     EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHH CS
                  GDP_Man_Dehyd    1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllae 73  
                                     L+ G +G iG +l+++L + g + ++ + r+     g +++l++     + ++l  + +D tD ++++ l+++
  gi|121638814|ref|YP_979038.1| 1155 LVIGATGNIGPHLIRQLARMGAKTIVAMARKP----GALDELTQCLA-ATGTDLIAVAADATDPAAMQTLFDR 1222
                                     899*******************9987666554....45555554433.456799***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.92u 0.31s 00:00:01.23 Elapsed: 00:00:00.47
# Mc/sec: 9841.37
//
Query:       gi|121638815|ref|YP_979039.1|  [L=2188]
Description: phenolpthiocerol synthesis type-I polyketide synthase ppsC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.2e-103  345.2   0.0   7.5e-103  344.4   0.0    1.4  1  Acyl_transf_1    Acyl transferase domain
    7.1e-95  317.4   0.0    1.4e-94  316.4   0.0    1.5  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    2.4e-62  210.0   0.5    6.2e-62  208.7   0.5    1.7  1  KR               KR domain
    1.2e-51  175.7   6.1    3.5e-51  174.2   6.1    1.8  1  PS-DH            Polyketide synthase dehydratase
    7.5e-43  145.3   1.0    4.8e-42  142.7   0.4    2.8  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.7e-23   84.2   0.4    9.7e-23   81.7   0.2    2.6  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    7.9e-21   74.4   0.4    4.5e-20   72.0   0.2    2.4  2  ADH_zinc_N       Zinc-binding dehydrogenase
    3.8e-12   46.1   0.1    1.3e-11   44.3   0.1    1.9  1  adh_short        short chain dehydrogenase
    2.1e-11   43.8   0.5    5.5e-11   42.5   0.5    1.6  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.8e-11   43.6   0.1    8.2e-11   42.1   0.1    1.9  1  PP-binding       Phosphopantetheine attachment site
    3.1e-08   34.0   0.0    7.6e-08   32.8   0.0    1.6  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    4.6e-06   26.5   0.7    1.2e-05   25.1   0.7    1.7  1  ADH_N            Alcohol dehydrogenase GroES-like domain
      3e-05   23.5   0.1    0.00013   21.5   0.1    2.0  2  Thiolase_N       Thiolase, N-terminal domain
     0.0095   15.7   1.0       0.26   11.0   0.7    2.9  2  SAT              Starter unit:ACP transacylase in aflatoxin b
  ------ inclusion threshold ------
       0.14   12.1   0.1       0.48   10.3   0.0    1.8  2  Sigma70_ECF      ECF sigma factor


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.4   0.0  6.3e-106  7.5e-103       1     317 [.     572     890 ..     572     891 .. 0.98

  Alignments for each domain:
  == domain 1  score: 344.4 bits;  conditional E-value: 6.3e-106
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfv+sG+GsQwaGMG++Ll++++afaa+ia++++ f +q gfs+ dv++     +l +i+++q++L+ +q+al++l++s+
  gi|121638815|ref|YP_979039.1| 572 VFVYSGRGSQWAGMGRQLLADEPAFAAAIAELEPEFVAQGGFSLRDVIAGGK--ELVGIEQIQLGLIGMQLALTALWRSY 649
                                    8***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS..HHHHHHH...TT.EEEEEEECCCC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel.aeeeeklr.cqddvvgavansprrv 158
                                    Gv+p+av+GHS+GE+Aaavvagal+++ +l+++++rsrlm++l+g+g ma +el ae +e+l+ + ++v++++++spr++
  gi|121638815|ref|YP_979039.1| 650 GVTPDAVIGHSMGEVAAAVVAGALTPAQGLRVTAVRSRLMAPLSGQGTMALLELdAEATEALIaDYPEVSLGIYASPRQT 729
                                    ******************************************************9777777777**************** PP

                                    ECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHH....HHHCHHH CS
                  Acyl_transf_1 159 visgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldes....serelsa 234
                                    visg++  ++el+ +v++++ +a ++n++va+h+p++da+++a++s+lad++p++p+++ is+t++d      s + ++a
  gi|121638815|ref|YP_979039.1| 730 VISGPPLLIDELIDKVRQQNGFATRVNIEVAPHNPAMDALQPAMRSELADLTPQPPTIPIISTTYADLGislgSGPRFDA 809
                                    ********************9*********************************************9999999******* PP

                                    HHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHH CS
                  Acyl_transf_1 235 eywvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahl 314
                                    e+w++n+r+pvrf++a+++a    +++f+eis+H+ll++ + +tl+   dv ++  +G+l+rd +d   +f ++l++ h+
  gi|121638815|ref|YP_979039.1| 810 EHWATNMRNPVRFHQAIAHA-GADHHTFIEISAHPLLTHSISDTLRASYDVDNYLSIGTLQRDAHD-TLEFHTNLNTTHT 887
                                    ********************.7789*****************************************.************* PP

                                    CT- CS
                  Acyl_transf_1 315 tgs 317
                                    t++
  gi|121638815|ref|YP_979039.1| 888 THP 890
                                    985 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.4   0.0   1.2e-97   1.4e-94       2     253 .]      35     288 ..      34     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 316.4 bits;  conditional E-value: 1.2e-97
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S...TTEGGTTSTHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld...vddfdpeffgi 77 
                                    ep+a++Gmg+rfPgg++ +e+fw+lL++gr++i ++pa+rwdad++y ++ +++g+i +  ggfl+    d+fd+eff+i
  gi|121638815|ref|YP_979039.1|  35 EPIAVIGMGCRFPGGVNnPEQFWDLLCAGRSGIVRVPAQRWDADAYYCDDHTVPGTICSTEGGFLTswqPDEFDAEFFSI 114
                                    89*************999***********************************************999899********* PP

                                    HHHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTT..GGGSCTTHHHHHSTTHHH CS
                  ketoacyl-synt  78 spreaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgs..evkaspkavgavlanvia 155
                                    sprea+amdpqqrll+e+awealedag+++++++g+++ vf+Gv+a dy    +l  + +  + +a+  ++g+ +an++a
  gi|121638815|ref|YP_979039.1| 115 SPREAAAMDPQQRLLIEVAWEALEDAGVPQHTIRGTQTSVFVGVTAYDYML--TLAGRLRpvDLDAYI-PTGN-SANFAA 190
                                    ***********************************************9944..444333344788888.****.****** PP

                                    HHHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-S CS
                  ketoacyl-synt 156 grisyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadG 235
                                    gr++y lg+rGp+v++dtACsSslvavh+a+qslr +e+d+al+GG++lll+p+  +++s++g+lsp+grck+fd++adG
  gi|121638815|ref|YP_979039.1| 191 GRLAYILGARGPAVVIDTACSSSLVAVHLACQSLRGRESDMALVGGTNLLLSPGPSIACSRWGMLSPEGRCKTFDASADG 270
                                    ******************************************************************************** PP

                                    B-BB-EEEEEEEEECHHH CS
                  ketoacyl-synt 236 fvlGEGvGavvLkrleda 253
                                    +v+GEG+++vvLkrl+da
  gi|121638815|ref|YP_979039.1| 271 YVRGEGAAVVVLKRLDDA 288
                                    ***************997 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.5   5.1e-65   6.2e-62       1     180 []    1802    1980 ..    1802    1980 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 5.1e-65
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     g yli+GG+GgLG ++arwlae+ga  +vl +Rs a++++ +a iael+a+g ++ev+  D++++d  e+l++++++ 
  gi|121638815|ref|YP_979039.1| 1802 GGYLIVGGMGGLGFVVARWLAEQGAGLIVLNGRS-APSDEVAAAIAELNASGSRIEVITGDITEPDTAERLVRAVEDA 1878
                                     67********************************.67888888*********************************** PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     + +++Gv+h+A+vl+d+ + +mt+++ ++v+apKv+G+w Lh +++ +++d++++fSS+a+llg++gq++YaaaN+++
  gi|121638815|ref|YP_979039.1| 1879 GFRLAGVVHSAMVLADEIVLNMTDSAARRVFAPKVTGSWRLHVATAARDVDWWLTFSSAAALLGTPGQGAYAAANSWV 1956
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BTT CS
                             KR  157 Dalaeyrrsqglpavsinwglwae 180 
                                     D+l+++rrs glpav inwg+wa+
  gi|121638815|ref|YP_979039.1| 1957 DGLVAHRRSAGLPAVGINWGPWAD 1980
                                     **********************86 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   6.1   2.9e-54   3.5e-51       1     293 [.     928    1219 ..     928    1223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 2.9e-54
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---...-EEEEEEEE----. CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltges..kavelrdvsilkalv 76  
                                     hpllG  v+ +++  +v++++l+++ l wL+DH++d+ vvlPga+y e+al+Aa++++  +  +++ + ++ ++++l 
  gi|121638815|ref|YP_979039.1|  928 HPLLGVGVTDPTNGTRVWESELDPDLL-WLADHVIDDLVVLPGAAYAEIALAAATDTFAVEqdQPWMISELDLRQMLH 1004
                                     9**********************9988.******************************555558*************9 PP

                                     B--SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE....E-H CS
                          PS-DH   77 lpedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrsvss 154 
                                     + ++  + ++++l+ + +++     ++ei++r+g+++ wt+hat+tv+ ae  a  ++d e  +++ ++     ++++
  gi|121638815|ref|YP_979039.1| 1005 VTPG--TVLVTTLTGD-EQRC----QVEIRTRSGSSG-WTTHATATVARAEPLA--PLDHEGQRREVTTADLEDQLDP 1072
                                     9964..5555556555.5555....9**********8.**********887766..7777777677777777789*** PP

                                     HHHHHHHHHHSEEE-GGG--EEEEEEE.TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG........... CS
                          PS-DH  155 aefYerlaargleyGpsFqglralwrg.dgealaelrlpeelaggesayvlhPallDaalQllaaal........... 220 
                                     +++Y+rl+ +g ++Gp+Fqg+  l ++ +g a+a++rlp+++++g+++++lhP+++D alQ+l+a+            
  gi|121638815|ref|YP_979039.1| 1073 DDLYQRLRGAGQQHGPAFQGIVGLAVTqAGVARAQVRLPASARTGSREFMLHPVMMDIALQTLGATRtatdlaggqda 1150
                                     **********************999997999******************************9988889******9998 PP

                                     ----------EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--X CS
                          PS-DH  221 saeaekadaaylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrver 293 
                                      +  +++ a+++Pv++  ++vy+     ++ ++++  l+++g +++v++++l+d++G++++ ++++++  +++
  gi|121638815|ref|YP_979039.1| 1151 RQGPSSNSALVVPVRFAGVHVYG---DITRGVRAVGSLAAAG-DRLVGEVVLTDANGQPLLVVDEVEMAVLGS 1219
                                     55678999**************8...4456699999998887.59*********************9987765 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6   4.3e+03      16      44 ..     119     147 ..     114     149 .. 0.85
   2 !  142.7   0.4     4e-45   4.8e-42       1     117 [.     296     412 ..     296     413 .. 0.98
   3 ?   -2.9   0.0       5.7   6.8e+03      41      66 ..    1466    1493 ..    1448    1498 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                                    SSSTSTTHHHHHHHHHHHHHHHT--GGGE CS
                Ketoacyl-synt_C  16 nsltapngeaqaraiekalaeagvdpedv 44 
                                    + +++p+++ + ++  +al++agv  +++
  gi|121638815|ref|YP_979039.1| 119 AAAMDPQQRLLIEVAWEALEDAGVPQHTI 147
                                    56788889999999**********99888 PP

  == domain 2  score: 142.7 bits;  conditional E-value: 4e-45
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +av++gsavn+dga+ ++t png aq+++++kal +++++++d+dyveahgtgtplgDpiEl +l+kvf+++a +++l +
  gi|121638815|ref|YP_979039.1| 296 LAVVRGSAVNQDGASSGVTVPNGPAQQALLAKALTSSKLTAADIDYVEAHGTGTPLGDPIELDSLSKVFSDRAGSDQLVI 375
                                    69*********************************************************************999999*** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    gSvK+n+GHleaAaGva+l+k+vla+++g+ip +ln+
  gi|121638815|ref|YP_979039.1| 376 GSVKTNLGHLEAAAGVAGLMKAVLAVHNGYIPRHLNF 412
                                    ************************************8 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.7
                                     GGGEEEEE-SS-..SSHHHHHHHHHHHH CS
                Ketoacyl-synt_C   41 pedvdyveahgt..gtplgDpiElealk 66  
                                     p + d ++ h    g p+gD++E++ ++
  gi|121638815|ref|YP_979039.1| 1466 PGRLDALNVHEVkrGRPQGDQVEVRVVA 1493
                                     67777777776333999******99876 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2   8.1e-26   9.7e-23       1     133 []    1639    1778 ..    1639    1778 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 8.1e-26
                                     TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--....S-EEE-CHHHCTTT CS
                   ADH_zinc_N_2    1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp...lsaallkpakkrkg 70  
                                     lG++ v d+r+ df+    + t+g gvDvvl++++gea+ ++ +++l++gGr++++g +++   +s +l+++ak ++ 
  gi|121638815|ref|YP_979039.1| 1639 LGVEYVGDSRSVDFAdeilELTDGYGVDVVLNSLAGEAI-QRGVQILAPGGRFIELGkKDVyadASLGLAALAKSASF 1715
                                     7999999******************************99.9999***888*******666676666666666666666 PP

                                     -EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   71 rsvkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                       v++ + +++++ + +++l+++++ +++Gkl++ +   f+l++aa+A+r+++sg+++GKiV+
  gi|121638815|ref|YP_979039.1| 1716 SVVDLDLNLKLQPARYRQLLQHILQHVADGKLEVLPVTAFSLHDAADAFRLMASGKHTGKIVI 1778
                                     6666666665666699999******************9************************7 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.1   2.5e+03      47      84 ..     190     227 ..     174     243 .. 0.74
   2 !   72.0   0.2   3.8e-23   4.5e-20       1      96 [.    1607    1703 ..    1607    1739 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                    HHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEE CS
                     ADH_zinc_N  47 verikeltggegvdvvfecvGsgatleaalkllkpgGr 84 
                                      r++ + g +g+ vv++++ s + +   l++   +Gr
  gi|121638815|ref|YP_979039.1| 190 AGRLAYILGARGPAVVIDTACSSSLVAVHLACQSLRGR 227
                                    56777788899********9998888888887766665 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 3.8e-23
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalk 77  
                                     gvG+aav +Ak++Ga+++++++s+ k+e++ +lG+++v ++ +  d+ ++i elt+g gvdvv++ ++ g+++++ ++
  gi|121638815|ref|YP_979039.1| 1607 GVGMAAVSIAKMIGARIYTTAGSDAKREMLSRLGVEYVGDS-RSvDFADEILELTDGYGVDVVLNSLA-GEAIQRGVQ 1682
                                     9****************************************.666***********************.********* PP

                                     CEEEEEEEEECSC..TSSEEE CS
                     ADH_zinc_N   78 llkpgGrlvvvGg..gkgeee 96  
                                     +l+pgGr+   G   ++ + +
  gi|121638815|ref|YP_979039.1| 1683 ILAPGGRFIELGKkdVYADAS 1703
                                     *********999755554444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   1.1e-14   1.3e-11       4     161 ..    1805    1961 ..    1804    1969 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.1e-14
                                     EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT...TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee...gakalaiqvDvtdreevealvekavkklgkl 78  
                                     l++G+++G+G  +a+ la++Ga ++v++ ++++  eva+ + e+   g+++ +i++D+t+ + +e+lv+++++   +l
  gi|121638815|ref|YP_979039.1| 1805 LIVGGMGGLGFVVARWLAEQGAGLIVLNGRSAPSDEVAAAIAELnasGSRIEVITGDITEPDTAERLVRAVEDAGFRL 1882
                                     89************************77666665555555544444499***************************** PP

                                     SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                      adh_short   79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156 
                                       +v+ A +  ++ + ++++++ +rv++  +tg   l  a +            + sS a++ + +g+ aY+A+   v
  gi|121638815|ref|YP_979039.1| 1883 AGVVHSAMVLADEIVLNMTDSAARRVFAPKVTGSWRLHVATAAR----DVDWWLTFSSAAALLGTPGQGAYAAANSWV 1956
                                     **********************************9998775554....5667899******************99888 PP

                                     HHHHH CS
                      adh_short  157 agltr 161 
                                     +gl+ 
  gi|121638815|ref|YP_979039.1| 1957 DGLVA 1961
                                     88875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.5   4.6e-14   5.5e-11       4     152 ..    1811    1960 ..    1808    1963 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 4.6e-14
                                     TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE...E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2    4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae...v..lecDVtdeeqvealveevvekfgklDilvnn 76  
                                      g+G+ +A+ lae+Ga +++ + + +  ++v+++ +el+a+   +  +  D+t++++ e+lv++v++   +l ++v++
  gi|121638815|ref|YP_979039.1| 1811 GGLGFVVARWLAEQGAGLIVLNGRSAPSDEVAAAIAELNASgsrIevITGDITEPDTAERLVRAVEDAGFRLAGVVHS 1888
                                     599**************999998888877777777777744334355******************************* PP

                                     ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                   adh_short_C2   77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealt 152 
                                     a +  +  + +l+++++  +r+++ ++++ ++l  +++ ++++    ++ ss +a  ++p++ ay+aa   + +l+
  gi|121638815|ref|YP_979039.1| 1889 AMVLAD--EIVLNMTDSAARRVFAPKVTGSWRL--HVATAARDVDWWLTFSSAAALLGTPGQGAYAAANSWVDGLV 1960
                                     ***999..************************9..56667788899**********************98888876 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   6.8e-14   8.2e-11       3      66 ..    2078    2140 ..    2074    2141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 6.8e-14
                     PP-binding    3 lrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaay 66  
                                     + + ++ vl+ + ++id + +l  lGlDSl+ +el ++le+ +g+++p++ ++++pt+++la +
  gi|121638815|ref|YP_979039.1| 2078 IADEIRAVLR-SGDPIDHHRPLETLGLDSLMGLELRNRLEASLGITLPVALVWAYPTISDLATA 2140
                                     5666777777.8889999*******************************************986 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.4e-11   7.6e-08      11      98 ..     424     520 ..     419     531 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.4e-11
                 KAsynt_C_assoc  11 grlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeesk....eeslprLlvlsgrteeaveallekle 82 
                                     rl++  + ++wp +     +gv+sfG++G+n+Hv++++++ + ++  ++      +  + lv+ g+t+  v a+++ l+
  gi|121638815|ref|YP_979039.1| 424 SRLRIAADGIDWPTTGrprrAGVSSFGVSGTNAHVVIEQAPDPMAAAGTEpqrgPVPAVSTLVVFGKTAPRVAATASVLA 503
                                    689999999***98877999*********************777666666444434455566777999999999999999 PP

                 KAsynt_C_assoc  83 ehlldaells.llneil 98 
                                    ++l+ +     l++ ++
  gi|121638815|ref|YP_979039.1| 504 DWLDGPGAAVpLADVAH 520
                                    99766544431444444 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.7     1e-08   1.2e-05       2      61 ..    1485    1544 ..    1484    1551 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                                     TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                          ADH_N    2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvv 61  
                                     ++v ++v aag++ sD+  + g       +  ++G E vG v ++g+ev++++vG+rV++
  gi|121638815|ref|YP_979039.1| 1485 DQVEVRVVAAGLNFSDVLKAMGVYPGLDGAAPVIGGECVGYVTAIGDEVDGVEVGQRVIA 1544
                                     79***************98888766666666799************************86 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.5   5.4e+03      24      46 ..     126     148 ..     123     154 .. 0.85
   2 !   21.5   0.1   1.1e-07   0.00013      75     113 ..     200     238 ..     181     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.5
                                    HHHHHHHHHHHHHHHTS-GGGCC CS
                     Thiolase_N  24 eeLlaealkallekagvdpeevd 46 
                                    + Ll e+++++le+agv+++++ 
  gi|121638815|ref|YP_979039.1| 126 QRLLIEVAWEALEDAGVPQHTIR 148
                                    578999***********998875 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-07
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEE CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvE 113
                                      pav ++ +csS+l av+la+qs++  e+d++++gG+ 
  gi|121638815|ref|YP_979039.1| 200 RGPAVVIDTACSSSLVAVHLACQSLRGRESDMALVGGTN 238
                                    6799*********************************85 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.7   0.00022      0.26     130     237 ..     664     759 ..     638     762 .. 0.82
   2 ?   -1.1   0.0       1.1   1.3e+03     177     217 ..    1270    1311 ..    1265    1330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                            SAT 130 vplaveavrvafrlGlevarvaarleegsssssesWslavtglseeelekalaefneekglppasrvyisavssss.vti 208
                                    v++av a  ++   Gl+v++v++rl    +  s++ ++a  +l+ e+ e+++a++ e         v  ++++s++ ++i
  gi|121638815|ref|YP_979039.1| 664 VAAAVVAGALTPAQGLRVTAVRSRLM---APLSGQGTMALLELDAEATEALIADYPE---------VSLGIYASPRqTVI 731
                                    46778888888888999999999999...4445678888888999999999998865.........45588888888*** PP

                            SAT 209 sGpPstleallksskakkkkkksklpiya 237
                                    sGpP  +++l+++ + ++   + ++ i+ 
  gi|121638815|ref|YP_979039.1| 732 SGPPLLIDELIDKVRQQNGFAT-RVNIEV 759
                                    *************999988765.777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                            SAT  177 lekalaefneekglppa.srvyisavssssvtisGpPstlea 217 
                                     l++ ++++   ++ ++a  r+ is +s +++++  pP++ ++
  gi|121638815|ref|YP_979039.1| 1270 LRDRITDLELASAADEAtLRAAISRTSWDGIVVVCPPRANDE 1311
                                     55556666655665644489*****************98744 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.8   4.5e+03      14      34 ..    1254    1274 ..    1253    1290 .. 0.76
   2 ?   10.3   0.0    0.0004      0.48      86     117 ..    2040    2069 ..    2018    2120 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.8
                    Sigma70_ECF   14 GdaeaaeqllelvydeLrrla 34  
                                     Gd +a + ll+++++ Lr+  
  gi|121638815|ref|YP_979039.1| 1254 GDPAAGDPLLPALQSSLRDRI 1274
                                     9****************9643 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                    Sigma70_ECF   86 ilidhaRrrkrqkRGGdvvraeldeeedsvds 117 
                                     +l d a r+  q+RGG+ +ra+ld  ++   +
  gi|121638815|ref|YP_979039.1| 2040 KLHDSAARKSGQRRGGGAIRAQLDALDAA--E 2069
                                     8999*******************987755..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 1.03u 0.32s 00:00:01.35 Elapsed: 00:00:00.47
# Mc/sec: 13923.23
//
Query:       gi|121638816|ref|YP_979040.1|  [L=1827]
Description: phenolpthiocerol synthesis type-I polyketide synthase ppsD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-96  321.8   0.1      7e-96  320.7   0.1    1.6  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    9.8e-96  321.0   1.3      2e-95  320.0   1.3    1.5  1  Acyl_transf_1    Acyl transferase domain
    9.4e-62  208.9   2.6      2e-61  207.9   1.8    2.0  2  PS-DH            Polyketide synthase dehydratase
    2.6e-56  190.4   1.0    6.8e-56  189.0   0.2    2.2  2  KR               KR domain
    4.3e-42  142.9   0.3    1.7e-41  140.9   0.2    2.2  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.6e-11   44.6   0.0    3.4e-11   43.6   0.0    1.5  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    7.1e-11   42.1   0.2    5.4e-10   39.2   0.0    2.3  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    3.7e-10   39.6   0.0      1e-09   38.1   0.0    1.7  1  adh_short        short chain dehydrogenase
    2.2e-08   34.3   0.0    6.8e-08   32.8   0.0    2.0  1  PP-binding       Phosphopantetheine attachment site
    1.8e-06   27.5   0.1    1.5e-05   24.5   0.1    2.4  1  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.7   0.1   3.9e-99     7e-96       2     253 .]      36     285 ..      35     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 320.7 bits;  conditional E-value: 3.9e-99
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgisp 79 
                                    epva+vG+g+rfPg+++ +e+fw+lL +g d i+++p drwdad++ydp++ a g+++tk+ggf+  vd+fd+ ffgi+p
  gi|121638816|ref|YP_979040.1|  36 EPVAVVGIGCRFPGNVTgPESFWQLLADGVDTIEQVPPDRWDADAFYDPDPSASGRMTTKWGGFVSdVDAFDADFFGITP 115
                                    79**************99************************************************************** PP

                                    HHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  80 reaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagris 159
                                    rea amdpq+r+lle+aweale+ag++p++l+g+r+gv++G+++ dy   +  +++  + +a+   +g+  ++ + gri+
  gi|121638816|ref|YP_979040.1| 116 REAVAMDPQHRILLEVAWEALEHAGIPPDSLSGTRTGVMMGLSSWDYTI-VNIERRA-DIDAYL-STGT-PHCAAVGRIA 191
                                    ***********************************************54.4444344.589999.9998.99******** PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlG 239
                                    y lglrGp+v+vdtACsSslva+h+a+qslr +e dvalaGGv+l+l+p + +++s++ +lsp+grc++fd++adGfv+G
  gi|121638816|ref|YP_979040.1| 192 YLLGLRGPAVAVDTACSSSLVAIHLACQSLRLRETDVALAGGVQLTLSPFTAIALSKWSALSPTGRCNSFDANADGFVRG 271
                                    ******************************************************************************** PP

                                    -EEEEEEEEECHHH CS
                  ketoacyl-synt 240 EGvGavvLkrleda 253
                                    EG+G+vvLkrl+da
  gi|121638816|ref|YP_979040.1| 272 EGCGVVVLKRLADA 285
                                    ***********997 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.0   1.3   1.1e-98     2e-95       1     315 [.     566     873 ..     566     880 .. 0.94

  Alignments for each domain:
  == domain 1  score: 320.0 bits;  conditional E-value: 1.1e-98
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vfv+sGqGsQwa MG +Ll++++afa+++a++d+ f +q gfs+ + l++ +  ++ +i+ +qp+L+ +q+al+el++s+
  gi|121638816|ref|YP_979040.1| 566 VFVYSGQGSQWASMGQQLLANEPAFAKAVAELDPIFVDQVGFSLQQTLIDGD--EVVGIDRIQPVLVGMQLALTELWRSY 643
                                    8***************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS..HHHHHHH...TT.EEEEEEECCCC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel.aeeeeklr.cqddvvgavansprrv 158
                                    Gv p+av+GHS+GE++aavvagal++e +l+++ +rsrlm++l+g+g+ma +el a   e+l+   ++v++av++spr++
  gi|121638816|ref|YP_979040.1| 644 GVIPDAVIGHSMGEVSAAVVAGALTPEQGLRVITTRSRLMARLSGQGAMALLELdADAAEALIaGYPQVTLAVHASPRQT 723
                                    ******************************************************9555555555**************** PP

                                    ECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHH CS
                  Acyl_transf_1 159 visgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywv 238
                                    vi+g++e+++ +++ v+ +++ a++++v+va+h p +d+i ++l+salad++p++p ++ is+t+  es +++ +a+yw 
  gi|121638816|ref|YP_979040.1| 724 VIAGPPEQVDTVIAAVATQNRLARRVEVDVASHHPIIDPILPELRSALADLTPQPPSIPIISTTY--ESAQPVADADYWS 801
                                    *************************************************************9987..6789********* PP

                                    HHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHC CS
                  Acyl_transf_1 239 anlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahlt 315
                                    anlr+pvrf++av++a  + +++f+eispH++l++al +tl+   +  s t++ ++ r+l++    f ++la ++++
  gi|121638816|ref|YP_979040.1| 802 ANLRNPVRFHQAVTAA-GVDHNTFIEISPHPVLTHALTDTLD---PDGSHTVMSTMNRELDQ-TLYFHAQLAAVGVA 873
                                    **************99.999**********************...5567899999*****99.66666666655554 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   1.8   1.1e-64     2e-61       1     295 [.     910    1196 ..     910    1198 .. 0.92
   2 ?   -3.9   0.0       3.4   6.1e+03     106     130 ..    1534    1560 ..    1531    1565 .. 0.76

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1.1e-64
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---......-EEEEEEEE-- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltges.....kavelrdvsilk 73  
                                     hpllG++++ + +  +v+++++ ++ +pwL+DH+v+g++++P+ag+ e+al+Aa ++ g++       ++++++++++
  gi|121638816|ref|YP_979040.1|  910 HPLLGAHIEMPRNGDHVWQTDVGTEVCPWLADHKVFGQPIMPAAGFAEIALAAASEALGTAadavaPNIVINQFEVEQ 987 
                                     9************************************************************99998889999****** PP

                                     --.B--SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE.... CS
                          PS-DH   74 alvlpedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrs 151 
                                     +l l+  +++ ++++l + +d++     ++ei+Sr++gge   +hat++v+  +++       +  +++++ pa+++ 
  gi|121638816|ref|YP_979040.1|  988 MLPLD--GHTPLTTQLIRGGDSQI----RVEIYSRTRGGE-FCRHATAKVEQSPRE------CAHAHPEAQGPATGTT 1052
                                     **999..56666666777877777....***********9.8*********55443......4666677888889999 PP

                                     E-HHHHHHHHHHHSEEE-GGG--EEEEEEE.TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG..------ CS
                          PS-DH  152 vssaefYerlaargleyGpsFqglralwrg.dgealaelrlpeelaggesayvlhPallDaalQllaaal..saeaek 226 
                                     vs+a+fY  l+++g ++Gp+F +l+++ r  dg+a+ e+++p+e+ ++   y+lhP++lDaalQ+++aa+  ++ a +
  gi|121638816|ref|YP_979040.1| 1053 VSPADFYALLRQTGQHHGPAFAALSRIVRLaDGSAETEISIPDEAPRHP-GYRLHPVVLDAALQSVGAAIpdGEIAGS 1129
                                     *****************************9899**********999775.5*************9999999988899* PP

                                     ----EEEEEEEEEEE-S...-BTS--EEEEEE.----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XXX CS
                          PS-DH  227 adaaylPvaierlrvyrpssaageelwvharl.eeegarsivadltlvdedGrvvaeieglrlrrverea 295 
                                     a+a ylPv++e++rvyr     g++++++a+l + +g+++  ++++l++++G + ae++g+ lrrver+a
  gi|121638816|ref|YP_979040.1| 1130 AEASYLPVSFETIRVYR---DIGRHVRCRAHLtNLDGGTGKMGRIVLINDAGHIAAEVDGIYLRRVERRA 1196
                                     ****************8...56889*******888889999***************************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.4
                                     EEE-SS-TT...EEEEEEEEEE----- CS
                          PS-DH  106 fSregggee..wtehatGtvrlaegaa 130 
                                     fS ++++ e  w+  atG +r++e++a
  gi|121638816|ref|YP_979040.1| 1534 FSMSRDNLErvWAPKATGALRMHEATA 1560
                                     56666666667**********998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   3.6e+03      38      85 ..    1249    1296 ..    1241    1326 .. 0.71
   2 !  189.0   0.2   3.8e-59   6.8e-56       1     180 []    1439    1616 ..    1439    1616 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                     -HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS..S---EE CS
                             KR   38 dedskaliaelealgaevevvaaDvsdkdavealleeikaee..ppikGv 85  
                                     ++ ++++++++++   +v+   aD+ d++av a+++e   +   pp+  v
  gi|121638816|ref|YP_979040.1| 1249 KSMADDFVQQWRSPMRRVH--TADIHDESAVLAAFAETAGDPehPPVGVV 1296
                                     4555566666666666555..57999999999999888776654555444 PP

  == domain 2  score: 189.0 bits;  conditional E-value: 3.8e-59
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     ++y++tGGlGgLGl++arwl+++ga ++vl +Rs  +++++ + +ael+   ae+ vv+ Dv+++   e+l+e+++++
  gi|121638816|ref|YP_979040.1| 1439 ASYVVTGGLGGLGLVVARWLVDRGAGRVVLGGRS-DPTDEQCNVLAELQT-RAEIVVVRGDVASPGVAEKLIETARQS 1514
                                     68********************************.667777779999987.79************************* PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     +++++Gv+haA v++d+l+ +m+ ++le+v apK +Ga  +he+++d++ld+++ fSS+a+llgs+gqa+Ya+a+a+l
  gi|121638816|ref|YP_979040.1| 1515 GGQLRGVVHAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATADCELDWWLGFSSAASLLGSPGQAAYACASAWL 1592
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BTT CS
                             KR  157 Dalaeyrrsqglpavsinwglwae 180 
                                     Dal+ +rr++glpa +inwg+w+e
  gi|121638816|ref|YP_979040.1| 1593 DALVGWRRASGLPAAVINWGPWSE 1616
                                     **********************86 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.2   7.5e+03      17      43 ..     119     145 ..     115     147 .. 0.82
   2 !  140.9   0.2   9.6e-45   1.7e-41       1     117 [.     293     411 ..     293     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                    SSTSTTHHHHHHHHHHHHHHHT--GGG CS
                Ketoacyl-synt_C  17 sltapngeaqaraiekalaeagvdped 43 
                                     +++p+++ + ++  +al+ ag+ p++
  gi|121638816|ref|YP_979040.1| 119 VAMDPQHRILLEVAWEALEHAGIPPDS 145
                                    567888888899999********9986 PP

  == domain 2  score: 140.9 bits;  conditional E-value: 9.6e-45
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG..SCTS CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar..kqpl 78 
                                    +av++gsa+nsdg++n++tapn+ aq+++i++al+ a+v+p++v+yve hgtgt lgDpiE+e+l++++g ++   ++p+
  gi|121638816|ref|YP_979040.1| 293 LAVVRGSATNSDGRSNGMTAPNALAQRDVITSALKLADVTPDSVNYVETHGTGTVLGDPIEFESLAATYGLGKGqgESPC 372
                                    69*******************************************************************988878999** PP

                                    EEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  79 avgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    a+gSvK+niGHleaAaGva++ik+vla+++g ip +l++
  gi|121638816|ref|YP_979040.1| 373 ALGSVKTNIGHLEAAAGVAGFIKAVLAVQRGHIPRNLHF 411
                                    **************************************8 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.9e-14   3.4e-11       2     104 ..     415     520 ..     415     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.9e-14
                 KAsynt_C_assoc   2 npeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeeskeeslprLlvlsgrteeaveal 77 
                                    np i+  + +rl V+te  pwp  +    ++v+sfG +G+n+Hv++++++ +  + +    +  + l++sg+t++ v + 
  gi|121638816|ref|YP_979040.1| 415 NPAID-ASATRLFVPTESAPWPAAAgprrAAVSSFGLSGTNAHVVVEQAPDTAVAAAGG-MPYVSALNVSGKTAARVASA 492
                                    89999.899**************99999************************9999999.899999************** PP

                 KAsynt_C_assoc  78 lekleehlldaells.llneilseeisr 104
                                    ++ l+++   +   + l++ +++ ++ r
  gi|121638816|ref|YP_979040.1| 493 AAVLADWMSGPGAAApLADVAHTLNRHR 520
                                    *******777666662344444444444 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.44   7.9e+02      31      66 ..    1249    1287 ..    1227    1327 .. 0.61
   2 !   39.2   0.0     3e-13   5.4e-10       4     152 ..    1448    1596 ..    1445    1598 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.44
                                     HHHHHHHHHHTTSE...EEE--TTSHHHHHHHHHHHHHH CS
                   adh_short_C2   31 kkrveelaeelgae...vlecDVtdeeqvealveevvek 66  
                                     k+ +++++++  +    v  +D+ de++v a+++e++ +
  gi|121638816|ref|YP_979040.1| 1249 KSMADDFVQQWRSPmrrVHTADIHDESAVLAAFAETAGD 1287
                                     333444444444442235999999999999999988765 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 3e-13
                                     TSHHHHHHHHHHHTT-.EEEEEESSGGHHHHHHHHHHHTT.SE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2    4 sgIGraiAkalaeeGa.evvltdlneeakkrveelaeelg.ae.v.lecDVtdeeqvealveevvekfgklDilvnna 77  
                                      g+G  +A+ l ++Ga +vvl  +++  +++++ lae    ae v ++ DV+++   e+l+e+++++ g+l ++v++a
  gi|121638816|ref|YP_979040.1| 1448 GGLGLVVARWLVDRGAgRVVLGGRSDPTDEQCNVLAELQTrAEiVvVRGDVASPGVAEKLIETARQSGGQLRGVVHAA 1525
                                     599************9569999999999888888877544244536******************************** PP

                                     ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                   adh_short_C2   78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealt 152 
                                     ++ ++  + + ++sr++++r+ + ++++++++ +a + +  ++   +  ss ++  + p+++ay+ a a l al+
  gi|121638816|ref|YP_979040.1| 1526 AVIED--SLVFSMSRDNLERVWAPKATGALRMHEATADCELDW--WLGFSSAASLLGSPGQAAYACASAWLDALV 1596
                                     *****..****************************99987665..788999999999999999999988888775 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   5.8e-13     1e-09       4     152 ..    1442    1588 ..    1440    1598 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.8e-13
                                     EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79  
                                     +vtG+ +G+G+ +a+ l+ +Ga  vv++ ++++  e ++ l e+  +a+++++++Dv++   +e+l+e+a++  g+l 
  gi|121638816|ref|YP_979040.1| 1442 VVTGGLGGLGLVVARWLVDRGAGRVVLGGRSDPTDEQCNVLAELqtRAEIVVVRGDVASPGVAEKLIETARQSGGQLR 1519
                                     8*********************999988877888777777776656789***************************** PP

                                     EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short   80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152 
                                      +v+ A++ +++ + ++s ++ erv +   tg++ + +a ++  l+         sS a++ +++g+aaY+++
  gi|121638816|ref|YP_979040.1| 1520 GVVHAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATADCELDWW----LGFSSAASLLGSPGQAAYACA 1588
                                     **************************************9999844444....457888888888888888877 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   3.8e-11   6.8e-08       3      65 ..    1712    1779 ..    1710    1781 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.8e-11
                     PP-binding    3 lrelvaevlgvplee.....idpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaa 65  
                                      ++ +a v+g  +++     + +d +l +lGlDSl+av++ +  ++ fgve p++ +++  +l +l+a
  gi|121638816|ref|YP_979040.1| 1712 MCARIAAVMGYTDQStvepaVPLDKPLTELGLDSLMAVRIRNGARADFGVEPPVALILQGASLHDLTA 1779
                                     56667777777443333333579****************************************99976 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   8.6e-09   1.5e-05      72     112 ..     196     234 ..     116     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.6e-09
                                    S-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  72 ipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                    +    pav+v+ +csS+l a++la+qs++  e dv++agGv
  gi|121638816|ref|YP_979040.1| 196 L--RGPAVAVDTACSSSLVAIHLACQSLRLRETDVALAGGV 234
                                    4..6699*********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.95u 0.30s 00:00:01.25 Elapsed: 00:00:00.47
# Mc/sec: 11591.96
//
Query:       gi|121638817|ref|YP_979041.1|  [L=1488]
Description: phenolpthiocerol synthesis type-I polyketide synthase ppsE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-74  248.7   0.1    4.9e-73  245.8   0.0    2.3  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    4.6e-47  161.1   0.0    7.6e-47  160.4   0.0    1.4  1  Acyl_transf_1    Acyl transferase domain
    2.9e-43  146.6   1.0    3.3e-42  143.2   1.0    2.6  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.5e-26   93.1   0.0    2.6e-26   92.3   0.0    1.3  1  Condensation     Condensation domain
    1.4e-16   60.9   0.0    2.8e-16   60.0   0.0    1.5  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.7e-13   50.7   0.1    7.1e-13   48.7   0.0    2.3  2  PP-binding       Phosphopantetheine attachment site
    0.00014   21.4   0.1    0.00025   20.5   0.1    1.3  1  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.8   0.0   1.9e-76   4.9e-73       2     252 ..       6     261 ..       5     262 .. 0.94
   2 ?   -0.3   0.0      0.26   6.7e+02      45     127 ..     567     647 ..     560     682 .. 0.73

  Alignments for each domain:
  == domain 1  score: 245.8 bits;  conditional E-value: 1.9e-76
                                    --EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispr 80 
                                    + +a+vGm++rfPg++dv++fw++L++g+++i +l +++ +  ++  +++++a+ ++++++ +ld +d+fd+ ffg++p 
  gi|121638817|ref|YP_979041.1|   6 NAIAVVGMAGRFPGAKDVSAFWSNLRRGKESIVTLSEQELRDAGV--SDKTLADPAYVRRAPLLDgIDEFDAGFFGFPPL 83 
                                    68**********************************999999999..6******************************** PP

                                    HHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH..HHHHHHHHHTT......GGGSCTTHHHHHSTT CS
                  ketoacyl-synt  81 eaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdy..aalaaldedgs......evkaspkavgavlan 152
                                     a+ +dpq+rl+l++aw+aledag +p++ dg ++gv+  ++ + y  ++l ++++++       + ++++ ++++ ++ 
  gi|121638817|ref|YP_979041.1|  84 AAQVLDPQHRLFLQCAWHALEDAGADPARFDG-SIGVYGTSSPSGYllHNLLSHRDPNAvlaeglNFDQFSLFLQN-DKD 161
                                    ***************************99887.89*********99996666666666567777677788899999.*** PP

                                    HHHHHHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTT CS
                  ketoacyl-synt 153 viagrisyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpk 232
                                    ++a+ris+a++lrGps++v+tACsSslvavh+a+ sl sge+d+alaGG++l++ ++  ++ s   ++s+ g+c++fd +
  gi|121638817|ref|YP_979041.1| 162 FLATRISHAFNLRGPSIAVQTACSSSLVAVHLACLSLLSGECDMALAGGSSLCIPHRVGYFTSPGSMVSAVGHCRPFDVR 241
                                    ******************************************************************************** PP

                                    B-SB-BB-EEEEEEEEECHH CS
                  ketoacyl-synt 233 adGfvlGEGvGavvLkrled 252
                                    adG+v+G GvG+vvLk+l+ 
  gi|121638817|ref|YP_979041.1| 242 ADGTVFGSGVGLVVLKPLAA 261
                                    ****************9976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                                    TSBTSSTTEEE-BSS.EEE..S..TTEGGTTSTHHHHHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEES CS
                  ketoacyl-synt  45 klydpparaagkiktklggfld..vddfdpeffgispreaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvg 122
                                    +lyd ++ +a++ +t  +gf d    d+ +e+f  ++ ++e++d++q  l ++ + al  a+l +  + g r+g +iG +
  gi|121638817|ref|YP_979041.1| 567 GLYDTEPVFAQHFDTCAAGFRDetGIDLHAEVFDGTATDLERIDRSQPALFTVEY-AL--AKLVD--TFGVRAGAYIGYS 641
                                    5667777778888888888888655577789999999999999999987766544.44..34444..5788889999999 PP

                                    STHH.H CS
                  ketoacyl-synt 123 agdy.a 127
                                     g+y a
  gi|121638817|ref|YP_979041.1| 642 TGEYiA 647
                                    888841 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.0     3e-50   7.6e-47       1     275 [.     551     825 ..     551     868 .. 0.91

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 3e-50
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    vf+f+GqG+Q  GM+  L++t+++fa+  + ++  f++++g+ ++  + +     l++i+ +qpaL+ v+ ala l  ++
  gi|121638817|ref|YP_979041.1| 551 VFLFPGQGAQHVGMAKGLYDTEPVFAQHFDTCAAGFRDETGIDLHAEVFDGTATDLERIDRSQPALFTVEYALAKLVDTF 630
                                    7********************************************99999999*************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECCCCEC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavansprrvvi 160
                                    Gvr +a +G S GE+ aa  ag   +  a++ v lr rlm + ++pg+m av+l + +  +  +++v ++++n+p++ v+
  gi|121638817|ref|YP_979041.1| 631 GVRAGAYIGYSTGEYIAATLAGVFDLQTAIKTVSLRARLMHE-SPPGAMVAVALGPDDVTQYLPPEVELSAVNDPGNCVV 709
                                    ***************************************987.79*********999*********************** PP

                                    CEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHH.HHHCHHHHHHHH CS
                  Acyl_transf_1 161 sgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldes.serelsaeywva 239
                                    +g+++++r+l +r+ ++g+ ++++++  a+h  ++d++  + ++ l    +r+p+ +  s ++ + + ++++++ + w +
  gi|121638817|ref|YP_979041.1| 710 AGPKDQIRALRQRLTEAGIPVRRVRATHAFHTSAMDPMLGQFQEFLSRQQLRPPRTPLLSNLTGSWMsDQQVVDPASWTR 789
                                    ************************************************************999998879999******** PP

                                    HHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCC CS
                  Acyl_transf_1 240 nlrspvrfaeavlsaaetiplvfveispHslllaal 275
                                     ++sp+rfa+ +  +++   ++ ve+ p   l+   
  gi|121638817|ref|YP_979041.1| 790 QISSPIRFADELDVVLAAPSRILVEVGPGGSLTGSA 825
                                    ************99999999*****99876666544 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         5   1.3e+04      28      45 ..      97     114 ..      88     126 .. 0.75
   2 !  143.2   1.0   1.3e-45   3.3e-42       1     117 [.     270     389 ..     270     390 .. 0.98
   3 ?   -0.2   0.0      0.38   9.8e+02      21      52 ..     710     741 ..     696     747 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                                    HHHHHHHHHHT--GGGEE CS
                Ketoacyl-synt_C  28 raiekalaeagvdpedvd 45 
                                    ++  +al++ag dp++ d
  gi|121638817|ref|YP_979041.1|  97 QCAWHALEDAGADPARFD 114
                                    788899*******98875 PP

  == domain 2  score: 143.2 bits;  conditional E-value: 1.3e-45
                                    SEEEEEEEEEE--.STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG..SCT CS
                Ketoacyl-synt_C   1 yavikgsavnsdg.ahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar..kqp 77 
                                    +avi+gsa+n+dg a++++ apn++aqa++i++a+a +g+d ++v+yve+hgtgtplgDpiE+++l+++f+ +++  ++p
  gi|121638817|ref|YP_979041.1| 270 HAVIRGSAINNDGsAKMGYAAPNPAAQADVIAEAHAVSGIDSSTVSYVECHGTGTPLGDPIEIQGLRAAFEVSQTsrSAP 349
                                    69********************************************************************999888999* PP

                                    SEEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  78 lavgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    + +gSvKsniGHle AaG+a+lik++l+lk++++p+tl++
  gi|121638817|ref|YP_979041.1| 350 CVLGSVKSNIGHLEVAAGIAGLIKTILCLKNKALPATLHY 389
                                    ***************************************8 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.38
                                    TTHHHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                Ketoacyl-synt_C  21 pngeaqaraiekalaeagvdpedvdyveahgt 52 
                                      ++ q ra+++ l eag+  ++v+  +a  t
  gi|121638817|ref|YP_979041.1| 710 AGPKDQIRALRQRLTEAGIPVRRVRATHAFHT 741
                                    478999**************999987655444 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0     1e-29   2.6e-26      15     341 ..    1027    1359 ..    1024    1457 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1e-29
                                     HHHHHHSSSSSTTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT----.-EEEE-T... CS
                   Condensation   15 wflekleeessaynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileereve.levleisd.. 89  
                                     +fl    +++  + ++++l+l++++ l  ++ +l++++++hdaLR+ ++ + +g   Q+i   +e++ l    + d  
  gi|121638817|ref|YP_979041.1| 1027 YFLDRGLRDTGRCRVPLILRLDPKIGLPDIRAVLTAVVNHHDALRLHLVGN-DGIWEQHIAAPAEFTgLSNRSVPDgv 1103
                                     777777788888999*********************************855.*********66666524444444422 PP

                                     .TSSSHHHH.HHHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT-- CS
                   Condensation   90 leeseeeea.ieefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekgee 166 
                                     +++s ee+a +  ++  +l e+    ++pL  +++       ++l l++H  ++D  S +il+ d+ +++ q + gee
  gi|121638817|ref|YP_979041.1| 1104 AAGSPEERAaVLGILA-ELLEDQTDPNAPLAAVHIAAAHGGPHYLCLAIHAMVTDDSSRQILATDIVTAFGQRLAGEE 1180
                                     4556666665333333.45555566789************************************************** PP

                                     -----S--.HHHHHHHHHHHHCSHHHHHHHHHHH.HHHH......S.---BSS---SS---S-EEEEEEEE-S-HHHH CS
                   Condensation  167 lplpqktp.YkdyaeweqqyleskdlekeeaYWs.eqlegelpvlq.Lpkdkarpakrsfkadrlsikldeeteeklr 241 
                                     + l +++  ++++  + +  ++  +  ++++YW  +  + +l  ++ Lp+ ++  + r  +  +ls +l+ e +++l 
  gi|121638817|ref|YP_979041.1| 1181 ITLEPVSTgWREWSLRCAALATHPAALDTRSYWIeNSTKATLWLADaLPNAHTAHPPRADELTKLSSTLSVEQTSELD 1258
                                     *********************************83455666666678***98888877777789999*********** PP

                                     HHHHSTSS-HHHHHHHHHHHHHHHHHT-SEEEEEEEEESSTT..CSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHH CS
                   Condensation  242 klakeqgvtlndvllaalgllLskytgqddivvgteisgRes..eikdiermvGlFvntlPlridvkeaktfselikr 317 
                                     +  +    +++++llaalg ++ +  g+  ++v +e+ gR    +++d+ r+vG+F+  +P+ +  + +      + +
  gi|121638817|ref|YP_979041.1| 1259 DGRRRFRRSIQTILLAALGRTIAQTVGEGVVAVELEGEGRSVlrPDVDLRRTVGWFTTYYPVPLACATGLGALAQLDA 1336
                                     *****************************************999**************************999***** PP

                                     HHHHHHHHHCCTTS-HHHHHHCSS CS
                   Condensation  318 vkedllkaephqgypleeLvkdle 341 
                                     v ++l+++ ph g++++ L++  +
  gi|121638817|ref|YP_979041.1| 1337 VHNTLKSV-PHYGIGYGLLRYVYA 1359
                                     ********.**********98655 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.1e-19   2.8e-16       1     106 [.     392     501 ..     392     507 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.1e-19
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi...vgvNsfGfGGsnvHviLksnkkekrkeesk.eeslprLlvlsgrteeavea 76 
                                    Pnpe++ l++  + V ++  pw+ +    +gv+sfG+GG+n+Hv+L++++ e ++ +++ e+  p++++ls++t++a+ +
  gi|121638817|ref|YP_979041.1| 392 PNPELR-LDQSPFVVQSKYGPWECDGvrrAGVSSFGVGGTNAHVVLEEAPAEASEVSAHaEPAGPQVILLSAQTAAALGE 470
                                    9*****.***************8776679*********************998888887799****************** PP

                 KAsynt_C_assoc  77 llekleehlldaellsllneilseeisr.lp 106
                                      ++l++ l++++  +l + +++ +++r ++
  gi|121638817|ref|YP_979041.1| 471 SRTALAAALETQDGPRLSDVAYTLARRRkHN 501
                                    ********88888888888888777766565 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   2.8e-16   7.1e-13       2      67 .]     938    1000 ..     937    1000 .. 0.94
   2 ?   -4.0   0.0         7   1.8e+04       3      23 ..    1114    1131 ..    1113    1133 .. 0.65

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.8e-16
                     PP-binding    2 klrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +l++++++ lgv+   +d ++++fdlG+DSl+a+++++a   e g++i++ dl+e+ptla+l+a++
  gi|121638817|ref|YP_979041.1|  938 TLQRIWSQCLGVSS--VDRNANFFDLGGDSLMAISIAMAAANE-GLTITPQDLYEYPTLASLTAAV 1000
                                     5899********85..569************************.******************9875 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7
                     PP-binding    3 lrelvaevlgvpleeidpdtd 23  
                                     ++ ++ae+l+    +  p+++
  gi|121638817|ref|YP_979041.1| 1114 VLGILAELLEDQ-TD--PNAP 1131
                                     788999999944.33..4555 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1     1e-07   0.00025      76     111 ..     175     210 ..     159     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1e-07
                                    SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEE CS
                     Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagG 111
                                     p+++v+ +csS+l av+la+ s+ +ge+d+++agG
  gi|121638817|ref|YP_979041.1| 175 GPSIAVQTACSSSLVAVHLACLSLLSGECDMALAGG 210
                                    57899******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.91u 0.30s 00:00:01.21 Elapsed: 00:00:00.51
# Mc/sec: 8766.93
//
Query:       gi|121638818|ref|YP_979042.1|  [L=331]
Description: daunorubicin-DIM-transport ATP-binding protein ABC transporter drrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-27   97.3   0.0    1.6e-27   96.7   0.0    1.3  1  ABC_tran  ABC transporter
    7.9e-09   35.7   0.1     0.0014   18.5   0.0    2.6  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00014   21.5   0.1    0.00034   20.3   0.1    1.6  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.019   15.7   0.0      0.056   14.2   0.0    1.8  2  DUF4162   Domain of unknown function (DUF4162)
      0.021   15.3   0.0      0.036   14.6   0.0    1.3  1  AAA_23    AAA domain
      0.051   13.2   0.0      0.086   12.5   0.0    1.4  1  SRP54     SRP54-type protein, GTPase domain
      0.066   13.5   0.2       0.67   10.2   0.0    2.4  2  AAA_28    AAA domain
      0.068   13.7   0.0       0.23   12.0   0.0    2.0  2  AAA_18    AAA domain
      0.077   13.4   0.1       0.12   12.7   0.1    1.7  1  AAA_16    AAA ATPase domain
       0.09   12.1   0.1        9.5    5.5   0.0    2.2  2  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   8.9e-31   1.6e-27       1     136 [.      25     168 ..      25     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 8.9e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vs+k+++ge+++++G+nGaGK+t++ +l+ l++p++G+  + g d+ + e   +r++i v  q+  +++ l+ ++n 
  gi|121638818|ref|YP_979042.1|  25 LDDVSFKVRRGEVIGLLGPNGAGKTTMVDILSTLTRPDAGSAIIAGYDVVS-EPAGVRRSIMVTGQQVAVDDALSGEQNl 103
                                    79************************************************9.7888999***************99999* PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                +++++++++l++++l++  +++v     ++SgG+++r+ +a+ l+ +p++ +lDEpt
  gi|121638818|ref|YP_979042.1| 104 vlfgrlwglsksAARKRAAELLEQFSLVHAGKRRV----GTYSGGMRRRIDIACGLVVQPQVAFLDEPT 168
                                    **********9888888******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.7e-05     0.031       2      24 ..      38      60 ..      37      78 .. 0.84
   2 !   18.5   0.0   7.9e-07    0.0014     231     297 ..     135     198 ..      88     203 .. 0.81
   3 ?   -1.8   0.0       1.2   2.2e+03     148     204 ..     250     302 ..     243     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    +l GpNg+GK++  d+l+ l r
  gi|121638818|ref|YP_979042.1| 38 IGLLGPNGAGKTTMVDILSTLTR 60
                                   689***************99865 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 7.9e-07
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    ++ +   S G++r + ++  l  ++    + ++DEp +gL+P+    +++l+ + ++ g+  +ltT+
  gi|121638818|ref|YP_979042.1| 135 KRRVGTYSGGMRRRIDIACGLVVQP---QVAFLDEPTTGLDPRSRQAIWDLVASFKKLGIATLLTTQ 198
                                    5555566777777777777777777...899************************999999999997 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                         AAA_21 148 tsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlge 204
                                    ++ + sll++++     ++++ +  + +++ ++ +r+l +  r++++++iel d+  
  gi|121638818|ref|YP_979042.1| 250 VAALGSLLPEHHR----AMLTPDSDRITMPAPDGIRMLVEAARRIDEARIELADIAL 302
                                    5555566666666....8888888899999999999999999999999999988754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.9e-07   0.00034      13      49 ..      26      62 ..      23      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-07
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   d+ ++++++ +++ l Gp+G+GK+T++D +++l  p+
  gi|121638818|ref|YP_979042.1| 26 DDVSFKVRRGEVIGLLGPNGAGKTTMVDILSTLTRPD 62
                                   56678888666999****************9998776 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         6   1.1e+04       4      16 ..      11      23 ..      10      36 .. 0.74
   2 ?   14.2   0.0   3.1e-05     0.056       1      80 [.     222     314 ..     222     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6
                                   HHHHTTS-SSEEE CS
                        DUF4162  4 eeiKrsygknrie 16
                                   + +++ ygk++i+
  gi|121638818|ref|YP_979042.1| 11 NGVRKTYGKGKIV 23
                                   5689999888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.1e-05
                                    E-HHHHHTTS-SSEEEEE.-------..........--.-EEE.E-TTS-EEEEE--.-----------.----EEEEEE CS
                        DUF4162   1 GtleeiKrsygknrieve.adaeellee........pg.veev.eeeggelelkled.eeaanellkal.tsgveirsFe 67 
                                    Gt +e+K++ g +  e+   d ++l ++        p+  + + + + +++++  +d      e  +++ ++++e+  ++
  gi|121638818|ref|YP_979042.1| 222 GTANELKHRAGDTFCEIVpRDLKDLDAIvaalgsllPEhHRAMlTPDSDRITMPAPDgIRMLVEAARRIdEARIELADIA 301
                                    88899999999999998884444444444445556655233335666688999999988899999999*77********* PP

                                    EE---HHHHHHHH CS
                        DUF4162  68 eeePsLndIFiek 80 
                                    +++PsL+d+F+  
  gi|121638818|ref|YP_979042.1| 302 LRRPSLDDVFLAM 314
                                    **********975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     2e-05     0.036      21      40 ..      37      56 ..      17      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                         AAA_23 21 ltlItGpNGaGKTTildAik 40
                                   +  + GpNGaGKTT +d + 
  gi|121638818|ref|YP_979042.1| 37 VIGLLGPNGAGKTTMVDILS 56
                                   67789**********99875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.8e-05     0.086       3      40 ..      37      74 ..      35     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                   vi l+G++GaGKTt +  L+ l + ++ +++++  D+ 
  gi|121638818|ref|YP_979042.1| 37 VIGLLGPNGAGKTTMVDILSTLTRPDAGSAIIAGYDVV 74
                                   7889****************999999999999999875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00037      0.67       3      31 ..      39      78 ..      37     101 .. 0.81
   2 ?    0.6   0.0      0.32   5.8e+02      57      83 ..     193     218 ..     175     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                         AAA_28  3 vitGgestGKTtlleaLa..ar.........gypvvpEaa 31
                                    ++G+ ++GKTt++  L+   r         gy vv E+a
  gi|121638818|ref|YP_979042.1| 39 GLLGPNGAGKTTMVDILStlTRpdagsaiiaGYDVVSEPA 78
                                   589**************96612455566788899998876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                         AAA_28  57 ervleeqleeeaaaaankvlfcDrgll 83 
                                      +l  q+ eea+a +++++++D g++
  gi|121638818|ref|YP_979042.1| 193 T-LLTTQYLEEADALSDRIILIDHGII 218
                                    4.4667778888889999999998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.9     7e+03      53      82 ..       2      28 ..       1      29 [. 0.78
   2 ?   12.0   0.0   0.00013      0.23       1      25 [.      38      60 ..      38     129 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.9
                         AAA_18 53 dedkldklldaleenssaleegknlvidgh 82
                                   + d ++++++++++    +++gk + +d++
  gi|121638818|ref|YP_979042.1|  2 RNDDMAVVVNGVRKT---YGKGKIVALDDV 28
                                   667888999999997...579999999875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfg 25
                                   I+l G+ G+GKtt+ + Ls ++   
  gi|121638818|ref|YP_979042.1| 38 IGLLGPNGAGKTTMVDILSTLT--R 60
                                   89****************9885..3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.8e-05      0.12      18      62 ..      31      74 ..      16     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdg.gif.lrgkcdq 62
                                   +vr+g  e++ l G+ G GK+++v+ l   l++ + g + ++g  + 
  gi|121638818|ref|YP_979042.1| 31 KVRRG--EVIGLLGPNGAGKTTMVDILS-TLTRPDaGSAiIAGYDVV 74
                                   56666..7899*************8888.566653233324444433 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.012        21       8      36 ..      25      52 ..      19      54 .. 0.81
   2 ?    5.5   0.0    0.0053       9.5     140     172 ..     175     207 ..     167     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                         ATPase  8 lDeilkgGipegrvvlitGepGtGKtifa 36
                                   lD++    + +g+v+ + G  G+GKt+++
  gi|121638818|ref|YP_979042.1| 25 LDDVS-FKVRRGEVIGLLGPNGAGKTTMV 52
                                   66664.457899***************96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0053
                         ATPase 140 aReilrqlvrvlkklgvTailvsekssseeaag 172
                                     R+ +  lv  +kklg+ ++l+++  ++++a +
  gi|121638818|ref|YP_979042.1| 175 SRQAIWDLVASFKKLGIATLLTTQYLEEADALS 207
                                    69999*******************877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2303.73
//
Query:       gi|121638819|ref|YP_979043.1|  [L=289]
Description: daunorubicin-DIM-transport integral membrane protein ABC transporter drrB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-07   30.1  13.3    2.5e-07   30.1  13.3    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    0.00017   21.1  16.8    0.00017   21.1  16.8    2.1  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
        3.1    8.1  10.0       0.69   10.2   6.1    2.0  2  DUF3021          Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.6     0.048   2.9e+02       5      23 ..      50      68 ..      48      75 .. 0.83
   2 !   30.1  13.3   4.2e-11   2.5e-07     155     340 ..      82     278 ..      67     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.048
                ABC2_membrane_3  5 iitlllPiilvlllglifs 23
                                   ++t+  Pii+++++++ f 
  gi|121638819|ref|YP_979043.1| 50 LTTVGAPIIFMVGFYIPFA 68
                                   389999******9999875 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 4.2e-11
                ABC2_membrane_3 155 elsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafglg 232
                                     +sn  +++ +l+ + ++++ a+   +  +++   ++  +  ++++ pl+ +l+++   +  +++ l++ l+  +++g  
  gi|121638819|ref|YP_979043.1|  82 VASNLGQYITPLVTLQAVSFAAIGSGFRAATDSLLGVNRRFQSMPMAPLTPLLARVWVAVDRCFTGLVISLVcgYVIG-- 159
                                    457778888888888888888888888888888888888888999999998888875555455555555444333566.. PP

                ABC2_membrane_3 233 ipfg.nlglll...llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffa 308
                                    + f  + ++++   ll++  g ++++ + l++++++n++++  l+++ il+++++++gl+pl+ +p++++ + +  P+++
  gi|121638819|ref|YP_979043.1| 160 FRFHrGALYIVgfcLLVIAIGAVLSFAADLVGTVTRNPDAMLPLLSLPILIFGLLSIGLMPLKLFPHWIHPFVRNQPISQ 239
                                    6666666665533466666666666666688999********************************************** PP

                ABC2_membrane_3 309 pglgllrli.......tgdplweil.lsliilalfavvyl 340
                                    +  +l  l+       ++   w+++ + l++l++f+v++ 
  gi|121638819|ref|YP_979043.1| 240 FVAALRALAgdttktaSQ-VSWPVMaPTLTWLFAFVVILA 278
                                    *****9999999887433.4778777*********99985 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  16.8   2.8e-08   0.00017      14     207 ..      38     246 ..      22     248 .. 0.80
   2 ?   -2.1   0.8      0.37   2.2e+03     132     145 ..     267     280 ..     254     286 .. 0.47

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-08
                  ABC2_membrane  14 rwrdpslgllwrliqplllalvfgtvfgn.........lg.nsedglnr......pgllffsvlflafsaltsvapvfer 77 
                                    r+  psl+    +++++   ++f++ f+          +g  s++++++      p +   +v f a  + ++  + +++
  gi|121638819|ref|YP_979043.1|  38 RFAAPSLL-NGEVLTTVGAPIIFMVGFYIpfaipwnqfVGgASSGVASNlgqyitPLVTLQAVSFAA--IGSGFRAATDS 114
                                    44445444.5667777777777777777555545444433333333344688877888888888888..77888889999 PP

                  ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf....flflllllltalaasslgllisa 153
                                      gv  r  ++p+  + + +la+v+v + + +   +i l++ y++ g++  r+    + f+ll+++++ ++s+ + l+++
  gi|121638819|ref|YP_979043.1| 115 LLGVNRRFQSMPM-APLTPLLARVWVAVDRCFTGLVISLVCGYVI-GFRFHRGalyiVGFCLLVIAIGAVLSFAADLVGT 192
                                    9************.**************99999999999999998.****955545677788888888888999999*** PP

                  ABC2_membrane 154 lapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                    ++++ + +  l sl +l++ lls  ++p++  p+w+  + +  P++ +v alr+
  gi|121638819|ref|YP_979043.1| 193 VTRNPDAMLPLLSLPILIFGLLSIGLMPLKLFPHWIHPFVRNQPISQFVAALRA 246
                                    ********************************99*****************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.37
                  ABC2_membrane 132 lflllllltalaas 145
                                    l +l++++++la+s
  gi|121638819|ref|YP_979043.1| 267 LTWLFAFVVILALS 280
                                    33333333333333 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.77   4.6e+03     108     108 ..      67      67 ..      28     110 .. 0.64
   2 ?   10.2   6.1   0.00012      0.69       8      96 ..     144     234 ..     139     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.77
                        DUF3021 108 y 108
                                    +
  gi|121638819|ref|YP_979043.1|  67 F 67 
                                    1 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                        DUF3021   8 iliGiligliislvislfsgettllestavlkqvllsaliGvlfalaslifese..rlsllkqtlihflvvlllvlllal 85 
                                     ++G++i+l+++ vi + ++ + l+ +   l ++ + a++++ + l + +  +    l+ll+  ++ f+++++++++l l
  gi|121638819|ref|YP_979043.1| 144 CFTGLVISLVCGYVIGFRFHRGALYIVGFCLLVIAIGAVLSFAADLVGTVTRNPdaMLPLLSLPILIFGLLSIGLMPLKL 223
                                    689********99****9**999998888888888889************88883356666666699************* PP

                        DUF3021  86 llgWfplsvig 96 
                                    + +W++  v +
  gi|121638819|ref|YP_979043.1| 224 FPHWIHPFVRN 234
                                    *****985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1926.70
//
Query:       gi|121638820|ref|YP_979044.1|  [L=276]
Description: daunorubicin-DIM-transport integral membrane protein ABC transporter drrC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-13   49.1  20.8    6.5e-13   48.6  20.8    1.2  1  ABC2_membrane    ABC-2 type transporter
    2.5e-07   30.1  18.0    2.5e-07   30.1  18.0    1.9  2  ABC2_membrane_3  ABC-2 family transporter protein
    0.00097   18.5  19.5    0.00097   18.5  19.5    1.7  2  ABC2_membrane_2  ABC-2 family transporter protein
     0.0022   18.0  11.4     0.0022   18.0  11.4    1.6  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6  20.8   1.5e-16   6.5e-13       7     207 ..      34     237 ..      28     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.5e-16
                  ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgnlg...nsedgl.nr.pgllffsvlflafsaltsvapvferergv 81 
                                    ++r + ++ rd  ++++  ++ p+l+++v+  v gnl    + ++gl ++ p +  +++++ +  ++ ++ +++er  g+
  gi|121638820|ref|YP_979044.1|  34 TNRLLTRWARDY-ITVIGAIVLPILFMVVLNIVLGNLAyvvTHDSGLySIvPLIALGAAITGS--TFVAIDLMRERSFGL 110
                                    555555666666.777********************888886666664666777777777777..7777779******** PP

                  ABC2_membrane  82 lerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfeda 161
                                    l+r++v p+ ++++ +++++l++++++l+ +l++l + ++l g++    +l++ l+++++ ++++++++  + ++ + +a
  gi|121638820|ref|YP_979044.1| 111 LARLWVLPV-HRASGLISRILANAIRTLVTTLVMLGTGVVL-GFRFR-QGLIPSLMWISVPVILGIAIAAMVTTVALYTA 187
                                    *********.*******************999999999998.****6.66667777777666666666666666666666 PP

                  ABC2_membrane 162 sqla....slvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                    ++++     lv  + +++s  ++p++s p+w+q +    P++ya+ a+r+
  gi|121638820|ref|YP_979044.1| 188 QTVVvegvELVQAIAIFFSTGLVPLNSYPGWIQPFVAHQPVSYAIAAMRG 237
                                    666433338999************************************96 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.2      0.12   5.3e+02       3      24 ..      47      68 ..      45      76 .. 0.77
   2 !   30.1  18.0   5.6e-11   2.5e-07     160     340 ..      79     263 ..      70     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                ABC2_membrane_3  3 fliitlllPiilvlllglifsn 24
                                   ++i  ++lPi+++++l+++++n
  gi|121638820|ref|YP_979044.1| 47 TVIGAIVLPILFMVVLNIVLGN 68
                                   5667789999999988887664 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 5.6e-11
                ABC2_membrane_3 160 asflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafglgipfg. 236
                                     + +v+li++ +++ +++f+a  + +E++ +++ +++v +v +++ ++s+il+ ++  l+++l++l+  +++g  + f  
  gi|121638820|ref|YP_979044.1|  79 LYSIVPLIALGAAITGSTFVAIDLMRERSFGLLARLWVLPVHRASGLISRILANAIRTLVTTLVMLGtgVVLG--FRFRq 156
                                    578999************************************************************9777***..99998 PP

                ABC2_membrane_3 237 nlglllllfllfglayialgyllssl..fknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgll 314
                                    +l+  l ++ +  ++ ia++++++++   + ++ +   + +v  ++++f++gl+pl++ p++++ +    P ++ + ++ 
  gi|121638820|ref|YP_979044.1| 157 GLIPSLMWISVPVILGIAIAAMVTTValYTAQTVVVEGVELVQAIAIFFSTGLVPLNSYPGWIQPFVAHQPVSYAIAAMR 236
                                    888888777777777777777776663233333344449999999*********************************** PP

                ABC2_membrane_3 315 rlitgd.plweillsliilalfavvyl 340
                                      ++g   l++++  l++ a+++vv+ 
  gi|121638820|ref|YP_979044.1| 237 GFAMGGpVLSPMIGMLVWTAGICVVCA 263
                                    ******677777788888888888775 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4     0.098   4.4e+02     257     281 ..      42      72 ..      18      79 .. 0.63
   2 !   18.5  19.5   2.2e-07   0.00097      81     280 ..      82     270 ..      74     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.098
                ABC2_membrane_2 257 a......lgstatnllilllllavllvlgyv 281
                                    a      +g+ +  +l++++l +vl  l+yv
  gi|121638820|ref|YP_979044.1|  42 ArdyitvIGAIVLPILFMVVLNIVLGNLAYV 72 
                                    1555555566666666666666666666665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.2e-07
                ABC2_membrane_2  81 mavlipviaalfgadaia....gEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgiv 155
                                    +  li++ aa++g++ +a    +E+  g l++l  +Pv R++ l++ ++++++  l+ ++v+l+ +v   l++    g  
  gi|121638820|ref|YP_979044.1|  82 IVPLIALGAAITGSTFVAidlmRERSFGLLARLWVLPVHRASGLISRILANAIRTLVtTLVMLGTGV--VLGFRFRQGLI 159
                                    45566666999999998766669*******************************9999999999884..55888889999 PP

                ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsl 235
                                    ++l+++ + v++ ++++++v+ +al ++  +v+    +++  a+++f+ + ++  ++  g+++++  +            
  gi|121638820|ref|YP_979044.1| 160 PSLMWISVPVILGIAIAAMVTTVALYTAQTVVVE--GVELVQAIAIFFSTGLVPLNSYPGWIQPFVAH------------ 225
                                    **************99999977899888888888..999***********999999999999999944............ PP

                ABC2_membrane_2 236 lsptsayntllneilagsdlna..lgstatnllilllllavllvlgy 280
                                     +p s+  ++ + + +g+++ +  +g+ + +++i ++++av+l++gy
  gi|121638820|ref|YP_979044.1| 226 -QPVSYAIAAMRGFAMGGPVLSpmIGMLVWTAGI-CVVCAVPLAIGY 270
                                    .679999999999999997555433333333333.445666666666 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  11.4   4.8e-07    0.0022      16     161 ..      45     187 ..      40     208 .. 0.73
   2 ?   -3.0   0.3       1.3     6e+03     134     144 ..     248     258 ..     228     268 .. 0.48

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.8e-07
                ABC2_membrane_4  16 wllvlaallvpllallyfnll.gk.tgldpaefyslsvfgftlllllplilgi.iasylifrEeqndtlknLltiPvsrt 92 
                                    +++v++a+++p+l +++ n + g+  ++ ++   ++s   + l+ l  +i+g  + ++ + rE++ + l  L+++Pv+r+
  gi|121638820|ref|YP_979044.1|  45 YITVIGAIVLPILFMVVLNIVlGNlAYVVTHDSGLYS--IVPLIALGAAITGStFVAIDLMRERSFGLLARLWVLPVHRA 122
                                    7999*******99888887652442223333333333..34477899999999788999********************* PP

                ABC2_membrane_4  93 klllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi.ialvll 161
                                    + l++ +++ ++     +lvt+l+++ +++++gf +f  +l+ +l+++++ ++l++++a ++  +al ++
  gi|121638820|ref|YP_979044.1| 123 SGLISRILANAIR----TLVTTLVMLGTGVVLGF-RFRQGLIPSLMWISVPVILGIAIAAMVTtVALYTA 187
                                    *******998776....55666666667777775.58889999999999988888877766542444443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                ABC2_membrane_4 134 vlellkkclel 144
                                    ++ +l+++  +
  gi|121638820|ref|YP_979044.1| 248 MIGMLVWTAGI 258
                                    22233322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1817.34
//
Query:       gi|121638821|ref|YP_979045.1|  [L=422]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-26   91.8   0.0    8.2e-26   90.5   0.0    1.7  1  PapA_C          Phthiocerol/phthiodiolone dimycocerosyl trans
    6.8e-07   28.3   0.0    8.3e-07   28.0   0.0    1.2  1  Condensation    Condensation domain
  ------ inclusion threshold ------
      0.075   12.8   0.0       0.12   12.1   0.0    1.3  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer


Domain annotation for each model (and alignments):
>> PapA_C  Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   1.4e-29   8.2e-26       1     121 [.     300     407 ..     300     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.4e-29
                                    HHHHHHHHHHHHHHHHHCTHHHHC--BGGGGGG-S-SSS--.EEEE-S---TT----TTEEEEEEE.........EEEEE CS
                         PapA_C   1 lveLarrvsaqlradLadGvvqqsllhpaeqlaaakpglPp.vvitNlGvipalrlPegLevedfrsviaselgaaapap 79 
                                    +v+La ++ a+lradLa+Gv+qqs lh+   +++++pglPp v++t+   +p +r+P+gLe+ed++         +++++
  gi|121638821|ref|YP_979045.1| 300 IVDLASDIVATLRADLANGVIQQSGLHFGTAFEGTPPGLPPlVFCTDATSFPTMRTPPGLEIEDIK---------GQFYC 370
                                    69***************************************************************9.........***** PP

                                    BSS---EEEEEEEETTEEEEEEECS.....-SSCHHHHHHHH CS
                         PapA_C  80 aasrevviylvstfngrLsIellhssgtfsdaaaarlldaie 121
                                    + s ++++y++  ++g+L Ie++++      a++ ++l+ai+
  gi|121638821|ref|YP_979045.1| 371 SISVPLDLYSCAVYAGQLIIEHHGH-----IAEPGKSLEAIR 407
                                    ************************9.....788888888876 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.4e-10   8.3e-07      25     162 ..      20     147 ..       8     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.4e-10
                                    STTEEEEEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSSSHHHHHHHHHH CS
                   Condensation  25 saynmqavlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdleeseeeeaieefaq 104
                                    +  +++++++l+g +d+++l++a+++l+e h++L   +++  +g   +v ++  +  + v++ + +++ +     +    
  gi|121638821|ref|YP_979045.1|  20 YEVFTSMTIQLRGVIDVDALSDAFDALLETHPVLASHLEQSSDGGWNLVADDLLHSGICVIDGTAATNGSP----SG--- 92 
                                    5567789999****************************9999****************9999995554443....22... PP

                                    HHHTC--SCCCS.-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHH CS
                   Condensation 105 kdlqepfdLekg.pLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqle 162
                                       + +++L+++ +L++ +l+   e ++ l+l +HH ++DG    +l+ +l++ Y+ + 
  gi|121638821|ref|YP_979045.1|  93 ---NAELRLDQSvSLLHLQLIL-REGGAELTLYLHHCMADGHHGAVLVDELFSRYTDAV 147
                                    ...34689999989******99.9*******************************8654 PP

>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.12     133     197 ..     120     187 ..     111     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                 WES_acyltransf 133 lkvHHAliDGvgglkllarlldldpddpprpep.pqvpprdr..srtqlrasgalvglvaglgkvlgs 197
                                    l +HH+++DG  g+ l+ +l ++  d+ +   p p +p++++   ++ l+ +g++++ ++g+ + +++
  gi|121638821|ref|YP_979045.1| 120 LYLHHCMADGHHGAVLVDELFSRYTDAVTTGDPgPITPQPTPlsMEAVLAQRGIRKQGLSGAERFMSV 187
                                    668***************99999877655433312223333343444444445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2953.42
//
Query:       gi|121638822|ref|YP_979046.1|  [L=2111]
Description: multifunctional mycocerosic acid synthase membrane-associated mas [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.6e-114  382.7   6.2   2.9e-114  381.9   6.2    1.4  1  Acyl_transf_1    Acyl transferase domain
      2e-93  312.6   0.1      2e-93  312.6   0.1    2.1  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    9.7e-57  191.8   0.3      2e-55  187.5   0.0    2.7  2  KR               KR domain
    2.1e-53  181.5   4.6    4.4e-53  180.4   4.6    1.6  1  PS-DH            Polyketide synthase dehydratase
    3.9e-41  139.8   0.4      1e-40  138.4   0.4    1.8  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    2.4e-22   79.3   0.7    7.4e-21   74.5   0.1    3.0  3  ADH_zinc_N       Zinc-binding dehydrogenase
    7.7e-21   75.5   0.1    1.5e-19   71.4   0.0    2.9  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    7.8e-16   58.5   0.0    1.7e-15   57.4   0.0    1.6  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    2.5e-10   40.6   0.2    1.3e-09   38.3   0.0    2.4  3  PP-binding       Phosphopantetheine attachment site
    1.5e-08   34.3   0.0    1.9e-07   30.8   0.0    2.5  2  adh_short        short chain dehydrogenase
    5.8e-06   25.9   1.3    9.1e-06   25.2   0.5    1.7  2  Thiolase_N       Thiolase, N-terminal domain
    2.3e-05   24.2   0.2    8.9e-05   22.3   0.1    2.2  2  ADH_N            Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
       0.14   11.5   0.1       0.31   10.3   0.1    1.6  1  ThiF             ThiF family


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.9   6.2  2.1e-117  2.9e-114       1     317 [.     534     850 ..     534     852 .. 0.99

  Alignments for each domain:
  == domain 1  score: 381.9 bits;  conditional E-value: 2.1e-117
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHH.HH CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaell.ks 79 
                                    v+vfsGqGsQwa+MG++Ll+++++faa+ia++++++++++gfsv++++++++  ++++i++vqpa++avq+ala+++ ++
  gi|121638822|ref|YP_979046.1| 534 VWVFSGQGSQWAAMGTQLLASEPVFAATIAKLEPVIAAESGFSVTEAITAQQ--TVTGIDKVQPAVFAVQVALAATMeQT 611
                                    7***************************************************..************************** PP

                                    TT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.....HHHHHHH..TT.EEEEEEEC CS
                  Acyl_transf_1  80 kGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel....aeeeeklrcqddvvgavansp 155
                                    +Gvrp+avvGHS+GE+Aaavvagals+e+a++++++rs+lm+++ag+g+m +vel    +++e+++r +ddvv++v++sp
  gi|121638822|ref|YP_979046.1| 612 YGVRPGAVVGHSMGESAAAVVAGALSLEDAARVICRRSKLMTRIAGAGAMGSVELpakqVNSELMARGIDDVVVSVVASP 691
                                    ********************************************************99999******************* PP

                                    CCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHH CS
                  Acyl_transf_1 156 rrvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsae 235
                                    +++vi+g+++++r+l++r+++++v+a++++v+va+hspqvd+i d+la+aladiap++pkv+++s+t +d++++++++++
  gi|121638822|ref|YP_979046.1| 692 QSTVIGGTSDTVRDLIARWEQRDVMAREVAVDVASHSPQVDPILDDLAAALADIAPMTPKVPYYSATLFDPREQPVCDGA 771
                                    ******************************************************************************** PP

                                    HHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHC CS
                  Acyl_transf_1 236 ywvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahlt 315
                                    ywv+nlr++v+fa+av++a+e++++vf+e+spH+ll++a+e+t +s  d+++a+l+G ++r++    + ++ ll+++h++
  gi|121638822|ref|YP_979046.1| 772 YWVDNLRNTVQFAAAVQAAMEDGYRVFAELSPHPLLTHAVEQTGRS-LDMSVAALAG-MRREQPL-PHGLRGLLTELHRA 848
                                    *********************************************7.**********.*******.*************9 PP

                                    T- CS
                  Acyl_transf_1 316 gs 317
                                    g+
  gi|121638822|ref|YP_979046.1| 849 GA 850
                                    97 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.6   0.1   1.4e-96     2e-93       3     253 .]       7     255 ..       5     255 .. 0.96
   2 ?   -4.0   0.3       6.4   8.9e+03     220     246 ..     605     632 ..     596     636 .. 0.72

  Alignments for each domain:
  == domain 1  score: 312.6 bits;  conditional E-value: 1.4e-96
                                    -EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispr 80 
                                    pva++Gmg+r+Pgg + ++++we+Ll+g d ++e+p drwdad++ydp++ ++g++ +++ggfld v+ fd+effgis+r
  gi|121638822|ref|YP_979046.1|   7 PVAVIGMGCRLPGGINsPDKLWESLLRGDDLVTEIPPDRWDADDYYDPEPGVPGRSVSRWGGFLDdVAGFDAEFFGISER 86 
                                    8*************999*************************************************************** PP

                                    HHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHH CS
                  ketoacyl-synt  81 eaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagrisy 160
                                    ea+++dpqqrllle++wea+e+agl+p++l gs+++vf+G++++dy  l++ + +g    asp++v+ ++++v++gri++
  gi|121638822|ref|YP_979046.1|  87 EATSIDPQQRLLLETSWEAIEHAGLDPASLAGSSTAVFTGLTHEDY--LVLTTTAG--GLASPYVVTGLNNSVASGRIAH 162
                                    ********************************************99..55555556..46677666667*********** PP

                                    HHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB- CS
                  ketoacyl-synt 161 alglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlGE 240
                                    +lgl+Gp++t dtACsS+l+avh+a++sl++gead+alaGG  +ll+p a+++ sa+g+ls++grc++fd++adGfv++E
  gi|121638822|ref|YP_979046.1| 163 TLGLHGPAMTFDTACSSGLMAVHLACRSLHDGEADLALAGGCAVLLEPHACVAASAQGMLSSTGRCHSFDADADGFVRSE 242
                                    ******************************************************************************** PP

                                    EEEEEEEEECHHH CS
                  ketoacyl-synt 241 GvGavvLkrleda 253
                                    G+++v+Lkrl da
  gi|121638822|ref|YP_979046.1| 243 GCAMVLLKRLPDA 255
                                    **********887 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.4
                                    B-TTSGGGTTBTTB.-SB-BB-EEEEEE CS
                  ketoacyl-synt 220 lspdgrckafdpka.dGfvlGEGvGavv 246
                                     ++++++   +p+a  G  +GE ++avv
  gi|121638822|ref|YP_979046.1| 605 AATMEQTYGVRPGAvVGHSMGESAAAVV 632
                                    4444777777888888999999988887 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.22     3e+02      16      75 ..     671     738 ..     658     747 .. 0.69
   2 !  187.5   0.0   1.4e-58     2e-55       1     179 [.    1765    1942 ..    1765    1943 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                                    HHHHHHHHHS-EEEEE-SS.........--HHHHHHHHHHHHTT-EEEE----TT-HH.HHHHHHHHH CS
                             KR  16 larwlaekgarhlvllsRsa.......aadedskaliaelealgaevevvaaDvsdkd.avealleei 75 
                                    +   l+++g   +v+    +        ++++ ++lia++e++++  + va+Dv++++ +v  +l+++
  gi|121638822|ref|YP_979046.1| 671 VNSELMARGIDDVVVSVVASpqstvigGTSDTVRDLIARWEQRDVMAREVAVDVASHSpQVDPILDDL 738
                                    55666666655554432222344677677888999*******************98652566666555 PP

  == domain 2  score: 187.5 bits;  conditional E-value: 1.4e-58
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     g+y+itGGlGgLGl +a  la+ g  ++vl++Rs +++++++++i+ l+a ga++ v    ++++d   +l+++++a+
  gi|121638822|ref|YP_979046.1| 1765 GSYIITGGLGGLGLFFASKLAAAGCGRIVLTARS-QPNPKARQTIEGLRAAGADIVVECGNIAEPDTADRLVSAATAT 1841
                                     89********************************.99***************************************** PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     + p++Gv+h+A v++d++l++ t+e +++  +pKv G+wnLh+++  ++ld+f lfSS a+llgs+gq++YaaaN+++
  gi|121638822|ref|YP_979046.1| 1842 GLPLRGVLHSAAVVEDATLTNITDELIDRDWSPKVFGSWNLHRATLGQPLDWFCLFSSGAALLGSPGQGAYAAANSWV 1919
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BT CS
                             KR  157 Dalaeyrrsqglpavsinwglwa 179 
                                     D +a++rr+qglp+ +i+wg+w 
  gi|121638822|ref|YP_979046.1| 1920 DVFAHWRRAQGLPVSAIAWGAWG 1942
                                     **********************7 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   4.6   3.2e-56   4.4e-53       1     291 [.     896    1175 ..     896    1182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 3.2e-56
                                     BTTB.-EE--..-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B CS
                          PS-DH    1 hpllGsrvrsa.sdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvl 77  
                                     hpllGs+vr + +++++v++ ++ ++ l wL DH+v++ + lPga+y emal+Aa++++ge+   e+rd++++++l l
  gi|121638822|ref|YP_979046.1|  896 HPLLGSHVRLTeEPERHVWQGDVGTSVLSWLSDHQVHNVAALPGAAYCEMALAAAAEVFGEA--AEVRDITFEQMLLL 971 
                                     9**********99**********************************************887..9************* PP

                                     --SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-----.--B--HHHHHHHS-SEE....E-H CS
                          PS-DH   78 pedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaa.aaavdlealqarcaepaslrsvss 154 
                                     +e++p++ + s+ +   g     v f++ + ++g++  t+hat+ +r+ae++  ++  d++al      +a++ +v++
  gi|121638822|ref|YP_979046.1|  972 DEQTPIDAVASIDAP--GV----VNFTVETNRDGET--TRHATAALRAAEDDCpPPGYDITAL-----LQAHPHAVNG 1036
                                     *******99999999..34....59*********97..*********8876557888899999.....4444555999 PP

                                     HHHHHHHHHHSEEE-GGG--EEEEEEE...TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG--------- CS
                          PS-DH  155 aefYerlaargleyGpsFqglralwrg...dgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekada 229 
                                     ++  e++a+rg+++G +F gl+++++    +  +lae++lp++++ +++ay++hPallDa++Q+++a + ++ ++++ 
  gi|121638822|ref|YP_979046.1| 1037 TAMRESFAERGVTLGAAFGGLTTAHTAeagAATVLAEVALPASIRFQQGAYRIHPALLDACFQSVGAGV-QAGTATGG 1113
                                     999*******************999987556699*****************************998888.6789**** PP

                                     -EEEEEEEEEEE-S...-BTS--EEEEEE...----SS-EEEEEEEE-SS-BEEEEEESEEEEE- CS
                          PS-DH  230 aylPvaierlrvyrpssaageelwvharl...eeegarsivadltlvdedGrvvaeieglrlrrv 291 
                                     + lP+++ +lr y+   + ++  ++++rl    ++g r+ +adl+++de G+v++ ++glr+   
  gi|121638822|ref|YP_979046.1| 1114 LLLPLGVRSLRAYG---PTRNARYCYTRLtkaFNDGTRGGEADLDVLDEHGTVLLAVRGLRMGTG 1175
                                     *************9...566889******877667888***********************9655 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.4   7.5e-44     1e-40       2     117 ..     264     376 ..     263     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 7.5e-44
                                    EEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEEE CS
                Ketoacyl-synt_C   2 avikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplavg 81 
                                    av++g+a+n+dg++++lt p+ +aq +++++ala agv+pe+v++veahgtgtp+gDpiE+++l++v+g+++   p+a+g
  gi|121638822|ref|YP_979046.1| 264 AVVRGTATNQDGRTETLTMPSEDAQVAVYRAALAAAGVQPETVGVVEAHGTGTPIGDPIEYRSLARVYGAGT---PCALG 340
                                    9*********************************************************************98...9**** PP

                                    -THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  82 SvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    S Ksn+GH+ a aG+++lik++l+l+hgv+pp l++
  gi|121638822|ref|YP_979046.1| 341 SAKSNMGHSTASAGTVGLIKAILSLRHGVVPPLLHF 376
                                    ***********************************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   5.1e+03      42      90 ..     778     825 ..     770     838 .. 0.74
   2 !   74.5   0.1   5.4e-24   7.4e-21       1     102 [.    1570    1676 ..    1570    1703 .. 0.85
   3 ?    1.5   0.1      0.19   2.7e+02       1      40 [.    1775    1821 ..    1775    1844 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                                    TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC CS
                     ADH_zinc_N  42 kea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg 90 
                                    +++ ++ ++++++  ++g+ v  e +  +  l+ a++ + +   + v ++
  gi|121638822|ref|YP_979046.1| 778 RNTvQFAAAVQAAM-EDGYRVFAELSP-HPLLTHAVEQTGRSLDMSVAAL 825
                                    56778999999999.679999999999.8888888888888777777776 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 5.4e-24
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalk 77  
                                     gvG+aa+ +A+a Gae++a+++++ k+++++++G+++v+++ +  ++ e+i++ t+g gvd+v++ +  ga+ +a l+
  gi|121638822|ref|YP_979046.1| 1570 GVGQAAISIARAKGAEIFATAGNPAKRAMLRDMGVEHVYDS-RSvEFAEQIRRDTDGYGVDIVLNSLT-GAAQRAGLE 1645
                                     9****************************************.655***********************.********* PP

                                     CEEEEEEEEECSC..TSSEEE...EEHHH.H CS
                     ADH_zinc_N   78 llkpgGrlvvvGg..gkgeee...fdlrn.l 102 
                                     ll+ gGr+v +G   ++g++    f++r+ l
  gi|121638822|ref|YP_979046.1| 1646 LLAFGGRFVEIGKadVYGNTRlglFPFRRgL 1676
                                     ************9999998885555555543 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.19
                                     HHHHHHHHHHHHTT-.EEEEEESSHHHH......HHHHHTTESEEEE CS
                     ADH_zinc_N    1 gvGlaavqlAkalGa.eviavdsseekl......elakklGadevin 40  
                                     g+Gl+    ++a+G+ +++ +++s+ +       e ++  Gad v+ 
  gi|121638822|ref|YP_979046.1| 1775 GLGLFFASKLAAAGCgRIVLTARSQPNPkarqtiEGLRAAGADIVVE 1821
                                     67888888888888888888777665321122224444446666665 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1   1.5e+03      76     101 ..     450     475 ..     418     497 .. 0.73
   2 !   71.4   0.0   1.1e-22   1.5e-19       2     133 .]    1603    1741 ..    1602    1741 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                                    --GGG...-..-HHHHHHHHHHHHHHH CS
                   ADH_zinc_N_2  76 eflfsmkas.aqadileelaalieeGk 101
                                     +l   ++s a +++ ++la+++ee++
  gi|121638822|ref|YP_979046.1| 450 FMLS-STSSdALRQTARQLATWVEEHQ 475
                                    2333.23336677779********986 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 1.1e-22
                                     T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--..S-EEE-CHHHCTTT-EE CS
                   ADH_zinc_N_2    2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp.lsaallkpakkrkgrsv 73  
                                     G+++v+d+r+ +f+    ++t+g gvD+vl+++ g+a  +a l++l+ gGr+v+ig +++   ++l+  ++ r+g ++
  gi|121638822|ref|YP_979046.1| 1603 GVEHVYDSRSVEFAeqirRDTDGYGVDIVLNSLTGAAQ-RAGLELLAFGGRFVEIGkADVyGNTRLGLFPF-RRGLTF 1678
                                     99*******999999***99****************99.*******888*******776655555555555.999*** PP

                                     EE--GGG...-....-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   74 kyeflfsmkas...aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                     +y  l  m+ +   + +++l+++++l ++G l+ +   ++pl+eaa+A+r++ ++ ++GK+Vl
  gi|121638822|ref|YP_979046.1| 1679 YYLDLALMSVTqpdRVRELLATVFKLTADGVLTAPQCTHYPLAEAADAIRAMSNAEHTGKLVL 1741
                                     **99997666688977777**************999999***********************8 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   1.3e-18   1.7e-15      12     108 ..     389     497 ..     384     501 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.3e-18
                 KAsynt_C_assoc  12 rlkVvteptpwpggi......vgvNsfGfGGsnvHviLksnkkekrkeesk...eeslprLlvlsgrteeaveallekle 82 
                                     l V++  tpwp+g       v+v+sfG++G+nvH+i+++++ e +++es+    e  prL++ls+ +++a+++++ +l+
  gi|121638822|ref|YP_979046.1| 389 GLFVPQAVTPWPNGNdhtpkrVAVSSFGMSGTNVHAIVEEAPAEASAPESSpgdAEVGPRLFMLSSTSSDALRQTARQLA 468
                                    67899*********99**************************9988888888888999********************** PP

                 KAsynt_C_assoc  83 ehlldaells.llneilseeisr..lpyR 108
                                    ++ ++++++    + +++ ++ r   p+R
  gi|121638822|ref|YP_979046.1| 469 TWVEEHQDCVaASDLAYTLARGRahRPVR 497
                                    **776666551433333333333325555 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.5   1.2e+04      34      48 ..     601     615 ..     600     616 .. 0.87
   2 ?   -3.5   0.0       9.9   1.4e+04       1      16 [.    1692    1707 ..    1692    1711 .. 0.83
   3 !   38.3   0.0   9.2e-13   1.3e-09       3      67 .]    2031    2096 ..    2029    2096 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                     PP-binding  34 avellaaleeefgve 48 
                                    +v+l+a +e+++gv+
  gi|121638822|ref|YP_979046.1| 601 QVALAATMEQTYGVR 615
                                    5899*********95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.9
                     PP-binding    1 eklrelvaevlgvple 16  
                                     +++rel+a+v+++ ++
  gi|121638822|ref|YP_979046.1| 1692 DRVRELLATVFKLTAD 1707
                                     689********99765 PP

  == domain 3  score: 38.3 bits;  conditional E-value: 9.2e-13
                     PP-binding    3 lrelvaevlgvplee.idpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     lr+l+ e+  v l + id+d ++ ++GlDSl ++e+   +e e g+++++ ++ +++t ++la+yl
  gi|121638822|ref|YP_979046.1| 2031 LRRLLVEQASVILRRtIDADRSFIEYGLDSLGMLEMRTHVETETGIRLTPKVIATNNTARALAQYL 2096
                                     667777777764333389***********************************99*********97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.32   4.3e+02       3      38 ..    1562    1597 ..    1560    1615 .. 0.88
   2 !   30.8   0.0   1.4e-10   1.9e-07       4     160 ..    1768    1923 ..    1766    1939 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                                     EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH CS
                      adh_short    3 vlvtGassGIGraiakelakeGakvvvvdrseekle 38  
                                     vl+  a++G+G+a      ++Ga++++++ +++k +
  gi|121638822|ref|YP_979046.1| 1562 VLIHSATGGVGQAAISIARAKGAEIFATAGNPAKRA 1597
                                     89999**********************999988764 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.4e-10
                                     EEESTTSHHHHHHHHHHHHTT-EEEE.EESCHH..HHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvv.vdrsee..kleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78  
                                     ++tG+ +G+G+ +a +la++G+  +v ++rs+   k++++++ l+++ga++++  +++++ + +++lv++a +   +l
  gi|121638822|ref|YP_979046.1| 1768 IITGGLGGLGLFFASKLAAAGCGRIVlTARSQPnpKARQTIEGLRAAGADIVVECGNIAEPDTADRLVSAATATGLPL 1845
                                     8********************98777577775422577888888888******************************* PP

                                     SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                      adh_short   79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156 
                                       + + A++ ++++  ++++e ++r  +  ++g  +l ra l +            sS a++ +++g+ aY+A+   v
  gi|121638822|ref|YP_979046.1| 1846 RGVLHSAAVVEDATLTNITDELIDRDWSPKVFGSWNLHRATLGQ----PLDWFCLFSSGAALLGSPGQGAYAAANSWV 1919
                                     *********88888888888888888888888888888877766....556788999999999999999999987766 PP

                                     HHHH CS
                      adh_short  157 aglt 160 
                                     + ++
  gi|121638822|ref|YP_979046.1| 1920 DVFA 1923
                                     6665 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.5   6.6e-09   9.1e-06      62     112 ..     156     204 ..     143     226 .. 0.85
   2 ?   -4.3   0.0       6.5     9e+03      23      46 ..     284     307 ..     269     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.6e-09
                                    HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEE CS
                     Thiolase_N  62 iarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGv 112
                                     +  +a+ +g+  + pa+t + +csSgl+av+la++s+  gead ++agG+
  gi|121638822|ref|YP_979046.1| 156 ASGRIAHTLGL--HGPAMTFDTACSSGLMAVHLACRSLHDGEADLALAGGC 204
                                    55567788888..89***********************************8 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 6.5
                                    HHHHHHHHHHHHHHHHTS-GGGCC CS
                     Thiolase_N  23 aeeLlaealkallekagvdpeevd 46 
                                    +e+ + ++ +a+l+ agv+pe+v 
  gi|121638822|ref|YP_979046.1| 284 SEDAQVAVYRAALAAAGVQPETVG 307
                                    566677888999999999999986 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.3     1e+04      38      58 ..     304     321 ..     303     354 .. 0.75
   2 !   22.3   0.1   6.5e-08   8.9e-05       1      67 [.    1446    1512 ..    1446    1524 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.3
                                    EEEEEEEEESTT-CS--TT-E CS
                          ADH_N  38 EivGeveevgpevkklkvGdr 58 
                                    E+vG+ve++g ++    +Gd 
  gi|121638822|ref|YP_979046.1| 304 ETVGVVEAHGTGT---PIGDP 321
                                    8999999999654...56665 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.5e-08
                                     TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE- CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplisc 67  
                                     pg++ + v++++i+  D+ i+ g+  +    +  lG ++vG+v +vg++v++ +vGdrV       c
  gi|121638822|ref|YP_979046.1| 1446 PGQIEVAVSMSSINFADVLIAFGRFPIIDDREPQLGMDFVGVVTAVGEGVTGHQVGDRVGGFSEGGC 1512
                                     57999*****************997777777779*************************98666666 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00023      0.31      22      48 ..    1769    1795 ..    1748    1797 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                                     EEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   22 llvGaGglGsellknLalsGvgkltlv 48  
                                        G+GglG +++  La++G+g++ l+
  gi|121638822|ref|YP_979046.1| 1769 ITGGLGGLGLFFASKLAAAGCGRIVLT 1795
                                     4559********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.08u 0.32s 00:00:01.40 Elapsed: 00:00:00.49
# Mc/sec: 12918.71
//
Query:       gi|121638823|ref|YP_979047.1|  [L=580]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-70  237.1   0.0    3.3e-70  236.8   0.0    1.1  1  AMP-binding   AMP-binding enzyme
  ------ inclusion threshold ------
      0.036   14.3   0.0       0.11   12.7   0.0    1.8  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.0   3.7e-74   3.3e-70       5     422 ..      14     467 ..      10     468 .. 0.84

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 3.7e-74
                                    HHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                    AMP-binding   5 aaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                    a+ +p ++a+++       +g   tlT+++l++r+ ++A+ L + G   gdrV+i +p+++e+vva+l++l+aG ++vpl
  gi|121638823|ref|YP_979047.1|  14 ARLQPHDPAFTFmdyeqdwDGVAITLTWSQLYRRTLNVARELSRCG-STGDRVVISAPQGLEYVVAFLGALQAGRIAVPL 92 
                                    667888899988888999989999*******************867.569****************************** PP

                                    ET...TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCC CS
                    AMP-binding  78 np...tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeee 154
                                    +    + t e+   +l+ds + +++  + s +++ + ++ a+++  +   +++ d l+     ++ +    k        
  gi|121638823|ref|YP_979047.1|  93 SVpqgGVTDERSDSVLSDSSPVAIL--TTSSAVDDVVQHVARRPGESPPSIIEVDLLDLD-APNGYT---FK-------- 158
                                    *99999*******************..667777777777777777777777775554433.222222...22........ PP

                                    S-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHCSCCTT.T-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                    AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk...letrfklke.ddvvlsilplahifglilelllallsGat 230
                                    e +  ++ay++YTSG+T +P GV++sh+n+  n  +l    + +++++ + ++ ++s+lp++h++gl++++++++l G  
  gi|121638823|ref|YP_979047.1| 159 EDEYPSTAYLQYTSGSTRTPAGVVMSHQNVRVNFEQLMsgyFADTDGIPPpNSALVSWLPFYHDMGLVIGICAPILGGYP 238
                                    2233479***********************7777776445555555543379**************************** PP

                                    EEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                    AMP-binding 231 vvllpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                     vl ++ ++l+ p+++++l++    + + ++P ++  l++ ++ + +++ +dl+ + ++l+g e+++++++++f ++f +
  gi|121638823|ref|YP_979047.1| 239 AVLTSPVSFLQrPARWMHLMA-SDFHAFSAAPNFAFELAARRTTDDDMAGRDLGNILTILSGSERVQAATIKRFADRFAR 317
                                    *********666********9.*************9998855454567888****88889******************** PP

                                    ......EEEEEEEEGGGSSECEE................CHCTTTCTSTTS-B...............EE-T.TEEEEEE CS
                    AMP-binding 310 ......evlegYGlTEttgvvtv................lpleedkkklgsvG...............kplp.gvevkiv 351
                                           +  +YGl+E+t+ v++                l          s+G                 lp    v+iv
  gi|121638823|ref|YP_979047.1| 318 fnlqerVIRPSYGLAEATVYVATskpgqppetvdfdtesL----------SAGhakpcagggatslisYMLPrSPIVRIV 387
                                    ****98899************8889999876655554431..........3334434444667666666667799***** PP

                                    -TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.........TCC.EEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 352 DeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds.........egr.wlrTGDlgrldedGyleivgRkkdlik 421
                                    D +t  ++pdg++Ge++v+g +v+ gY++kp++ +++f           +++ wlrTGD g+++ dG ++i+gR+kdl++
  gi|121638823|ref|YP_979047.1| 388 DSDTCIECPDGTVGEIWVHGDNVANGYWQKPDESERTFGGkivtpspgtPEGpWLRTGDSGFVT-DGKMFIIGRIKDLLI 466
                                    **************************************956888999874566**********9.9***********998 PP

                                    E CS
                    AMP-binding 422 l 422
                                    +
  gi|121638823|ref|YP_979047.1| 467 V 467
                                    6 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.9   8.1e+03      52      77 ..      43      67 ..       4      70 .. 0.62
   2 ?   12.7   0.0   1.3e-05      0.11       4      70 ..     454     529 ..     451     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.9
                                   T.CCSCHCTHHHHHHHHCCHSSEEEE CS
                   Mur_ligase_C 52 elgertrtfhdefgrlasaladslvv 77
                                    l+ rt +   e+ r+ s   d++v+
  gi|121638823|ref|YP_979047.1| 43 QLYRRTLNVARELSRCGST-GDRVVI 67
                                   5677777777777777765.666555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.3e-05
                                    SSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSS..........SSEEEEEEEESTT.CCSCHCTHHHHHHHHCC CS
                   Mur_ligase_C   4 RlevvgeadgvtvidDyahnpdslsaalkalreiap..........dkrlilvfgpggelgertrtfhdefgrlasa 70 
                                     + ++g+ ++++++   +h pd ++a+++ +               +++l+++   ++ +g+ +++ ++++g++  +
  gi|121638823|ref|YP_979047.1| 454 KMFIIGRIKDLLIVYGRNHSPDDIEATIQEITRGRCaaisvpgdrsTEKLVAIIE-LKKRGDSDQDAMARLGAIKRE 529
                                    57889999999988889**************555447888888888888888888.788888888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3769.17
//
Query:       gi|121638824|ref|YP_979048.1|  [L=920]
Description: transmembrane transport protein mmpL7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-75  252.3  52.9    1.4e-63  214.8  19.7    3.0  2  MMPL           MMPL family
  ------ inclusion threshold ------
      0.023   14.7   0.3          4    7.5   0.0    2.8  2  DUF1664        Protein of unknown function (DUF1664)
      0.091   13.1   0.2        3.3    8.1   0.0    2.9  3  BLOC1_2        Biogenesis of lysosome-related organelles comp
       0.12   12.3   0.5        9.9    6.1   0.0    2.3  2  Serine_rich    Serine rich protein interaction domain
       0.12   12.6   0.2       0.12   12.6   0.2    3.8  4  DUF948         Bacterial protein of unknown function (DUF948)
       0.17   12.3   0.1         64    4.1   0.0    3.1  3  FlaC_arch      Flagella accessory protein C (FlaC)
       0.27   10.8   0.0       0.27   10.8   0.0    2.5  3  Fzo_mitofusin  fzo-like conserved region


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8  19.7   5.6e-67   1.4e-63       2     319 ..      75     379 ..      74     391 .. 0.97
   2 !   41.0  25.2   4.4e-14   1.1e-10      14     290 ..     609     908 ..     501     915 .. 0.76

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 5.6e-67
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    l+p+da+++ a++r+++afp+ ++s++i+++v+ eg+++l++ +++ ++d+ v +l++dt+hvg+v d++sdp +a + +
  gi|121638824|ref|YP_979048.1|  75 LLPQDAKTAAATSRIAQAFPG-TGSNAIAYLVV-EGGSTLEP-QDQPYYDAAVGALRADTRHVGSVLDWWSDPVTAPLGT 151
                                    79*******************.99999999999.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    S+Dg++a+a+v+l+g++g+t+a+es++a+r+++++++p egl+++++ pa+t+++ ++++++++++i++v++v+++++Ll
  gi|121638824|ref|YP_979048.1| 152 SPDGRSATAMVWLRGEAGTTQAAESLDAVRSVLRQLPPSEGLRASIVVPAITNDMPMQITAWQSATIVTVAAVIAVLLLL 231
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                     +  S+ aa+++llt+ +sl++a++l+++++ +++ + s f+++l+ vl+i++ t+ ++l       +++ g+d+ ++++
  gi|121638824|ref|YP_979048.1| 232 RARLSVRAAAIVLLTADLSLAVAWPLAAVVRGHDWGTDSVFSWTLAAVLTIGTITAATML-------AARLGSDAGHSAA 304
                                    ************************************************************.......999********** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.lakprrkrkkrwW 319
                                     +++++ ++ +  G++vai +  L++ar p+l++vG+a +lGv+v+++++lT+lPAl++l+G ++ l++p   ++++ W
  gi|121638824|ref|YP_979048.1| 305 PTYRDSLPAFALPGACVAIFTGPLLLARTPALHGVGTA-GLGVFVALAASLTVLPALIALAGASRqLPAP---TTGAGW 379
                                    ************************************99.*************************888888...666777 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 4.4e-14
                           MMPL  14 drleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf...................... 70 
                                    dr++a + +  +  +++  +v ++++  +   + +++v +l + +++  ++++++s++                      
  gi|121638824|ref|YP_979048.1| 609 DRISAISTQtMSALSSAPRMVAQMRSALA---QVRSFVPKLETTIQDAMPQIAQASAMlknlsadfadtgeggfhlsrkd 685
                                    33333333332333333333332222222...233444444444444444444444446666667777777777766666 PP

                           MMPL  71 lsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveear...pleglkvevtGpaatladlrdasdrd 144
                                    l+dp    v++ + S+Dg+a+r+ ++ +g + + +a++++++++ a+ +a     l + +v v+G a ++a +rda  +d
  gi|121638824|ref|YP_979048.1| 686 LADPSyrhVRESMFSSDGTATRLFLYSDG-QLDLAAAARAQQLEIAAGKAMkygSLVDSQVTVGGAAQIAAAVRDALIHD 764
                                    55777889********************8.6777778999999999999999999************************* PP

                           MMPL 145 lklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLv 223
                                    + l+ v+ l v++  L+ + r  v  + + + v+ s+laalg+ ++++++ll  el+  v+  ++++l + G+ Y   Lv
  gi|121638824|ref|YP_979048.1| 765 AVLLAVILLTVVA--LASMWRGAVHGAAVGVGVLASYLAALGVsIALWQHLLDRELNALVPLVSFAVLASCGVPY---LV 839
                                    9998887777765..67778888887777788*******************************************...78 PP

                           MMPL 224 sRyreelaagedreeaviravastgkvvtaaGl..tvaiamlgLvvarlpvlaqvGvaialGvlvdvli 290
                                    + ++  + a e + +    av + g v   a+l  ++ + ++  +  +++vl+q+G+++ lG+ v + +
  gi|121638824|ref|YP_979048.1| 840 AGIKAGRIADEATGARSKGAVSGRGAVAPLAALggVFGAGLVLVSGGSFSVLSQIGTVVVLGLGVLITV 908
                                    88888888888886666778888888876665544999999999999*********9876665554444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.019        48      55     112 ..     510     567 ..     479     576 .. 0.49
   2 ?    7.5   0.0    0.0016         4      69     118 ..     602     651 ..     590     655 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                    +s+++  +++s  +d++d++++ + + +++ ++ ++ +    ++++++ ++++e  e+
  gi|121638824|ref|YP_979048.1| 510 KSMKSIIEQMSGAVDQLDSTVNVTLAGARQAQQYLDPMLAAARNLKNKTTELSEYLET 567
                                    3333333444444455555554444444444444444444444444444444444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                        DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                    +++ +  d  ++is+++ + ++++ + ++++++ + +v++ v +le++++
  gi|121638824|ref|YP_979048.1| 602 NELSTGADRISAISTQTMSALSSAPRMVAQMRSALAQVRSFVPKLETTIQ 651
                                    56777789999************************************997 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0013       3.3      47      88 ..     489     530 ..     482     534 .. 0.88
   2 ?    0.3   0.0      0.34   8.8e+02      46      68 ..     547     569 ..     537     572 .. 0.72
   3 ?   -0.0   0.0      0.43   1.1e+03      36      62 ..     629     652 ..     606     669 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                        BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                     + +++l ++  ++ p ++ i+ ++  ++++  av++LD+ +
  gi|121638824|ref|YP_979048.1| 489 GRLADQLGQQAGSFVPAVTAIKSMKSIIEQMSGAVDQLDSTV 530
                                    566789999999***************************975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.34
                        BLOC1_2  46 lekkleklnekyeelqpylqqid 68 
                                    + + + +l++k  el++yl+ i 
  gi|121638824|ref|YP_979048.1| 547 MLAAARNLKNKTTELSEYLETIH 569
                                    45566788888888888888875 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.43
                        BLOC1_2  36 ykklkdvaaslekkleklnekyeelqp 62 
                                    ++++++++a++++++ kl+    ++q 
  gi|121638824|ref|YP_979048.1| 629 VAQMRSALAQVRSFVPKLET---TIQD 652
                                    44555555555555555555...4444 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0039       9.9      85     146 ..     505     565 ..     486     572 .. 0.88
   2 ?    4.2   0.1     0.016        40       7      60 ..     601     654 ..     597     669 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0039
                    Serine_rich  85 qlqkledsdqilqetsqeLdsceWslealasdkkqekpddlDrlvmvartvpdDvkqlasfi 146
                                     + +++  ++i++++s + d+ + ++++     +q  +  lD +++ ar++++ + +l  ++
  gi|121638824|ref|YP_979048.1| 505 AVTAIKSMKSIIEQMSGAVDQLDSTVNVTLAGARQA-QQYLDPMLAAARNLKNKTTELSEYL 565
                                    577899999******************999999887.99************99998887765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                    Serine_rich   7 letlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefl 60 
                                    +++l+   +++++  ++ +s +ss  R  +++++ l+++r+ v +l+t++++ +
  gi|121638824|ref|YP_979048.1| 601 MNELSTGADRISAISTQTMSALSSAPRMVAQMRSALAQVRSFVPKLETTIQDAM 654
                                    667777777888888999999****************************99865 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.3   5.0         7   1.8e+04       3      24 ..     216     237 ..     215     244 .. 0.76
   2 ?   12.6   0.2   4.8e-05      0.12      33      88 ..     507     562 ..     498     563 .. 0.92
   3 ?    3.2   0.0     0.041   1.1e+02      41      78 ..     610     647 ..     582     675 .. 0.59
   4 ?   -3.6   0.0       5.4   1.4e+04       8      31 ..     825     851 ..     825     853 .. 0.66

  Alignments for each domain:
  == domain 1  score: -6.3 bits;  conditional E-value: 7
                         DUF948   3 glIaAiAFvvLviflivvllkl 24 
                                    + I+ +A v+ v++l ++ l++
  gi|121638824|ref|YP_979048.1| 216 ATIVTVAAVIAVLLLLRARLSV 237
                                    6788899999998888776665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.8e-05
                         DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                    ++i+++++ +++++  v++l ++vn++l++ ++  + +dp+ +a+++l ++  el+
  gi|121638824|ref|YP_979048.1| 507 TAIKSMKSIIEQMSGAVDQLDSTVNVTLAGARQAQQYLDPMLAAARNLKNKTTELS 562
                                    5789999999**************************************99988876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.041
                         DUF948  41 qvdpilkevedllakvnelledvneklekvdplteava 78 
                                    ++ +i++++  +l+ + ++++++++ l++v +++ +++
  gi|121638824|ref|YP_979048.1| 610 RISAISTQTMSALSSAPRMVAQMRSALAQVRSFVPKLE 647
                                    45555555555555555555555555555555443333 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 5.4
                         DUF948   8 iAFvvLviflivvllkl...kktldea 31 
                                    ++F+vL+ + ++ l+     ++++dea
  gi|121638824|ref|YP_979048.1| 825 VSFAVLASCGVPYLVAGikaGRIADEA 851
                                    589999999998886422226666665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.05   1.3e+02      14      38 ..     507     531 ..     504     535 .. 0.90
   2 ?    0.6   0.0      0.29   7.5e+02      18      52 ..     553     602 ..     544     603 .. 0.77
   3 ?    4.1   0.0     0.025        64       8      40 ..     618     653 ..     613     655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.05
                      FlaC_arch  14 teletvkkeneelsksveelkenVk 38 
                                    t ++++k+ +e++s  v++l+ +V+
  gi|121638824|ref|YP_979048.1| 507 TAIKSMKSIIEQMSGAVDQLDSTVN 531
                                    57999*****************995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                      FlaC_arch  18 tvkkeneelsksveelkenV...............kdllsLYEvVsnqvN 52 
                                    ++k++  els+ +e++   +               +++++ Y++V  ++N
  gi|121638824|ref|YP_979048.1| 553 NLKNKTTELSEYLETIHTWIvgftncpddvlctamRKVIEPYDIVVTGMN 602
                                    56777777788787777777777777777777777999999999988877 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.025
                      FlaC_arch   8 klsklst...eletvkkeneelsksveelkenVkdl 40 
                                     +s ls+   +++ +++ + ++++ v +l+ +++d 
  gi|121638824|ref|YP_979048.1| 618 TMSALSSaprMVAQMRSALAQVRSFVPKLETTIQDA 653
                                    57778888889**********************985 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.27      96     155 ..     509     568 ..     498     572 .. 0.93
   2 ?   -1.0   0.0      0.45   1.2e+03      94     132 ..     627     665 ..     607     672 .. 0.44
   3 ?   -4.8   1.1       6.6   1.7e+04      22      42 ..     766     786 ..     760     796 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                  Fzo_mitofusin  96 qqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                     + ++s +++++ +vd+ +++++  ++  ++  + l+ +   a+ l+nk+++l++ Le+ 
  gi|121638824|ref|YP_979048.1| 509 IKSMKSIIEQMSGAVDQLDSTVNVTLAGARQAQQYLDPMLAAARNLKNKTTELSEYLETI 568
                                    6889**************************************************999976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                  Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekle 132
                                     +  ++ s++a++++ v + e+++++ + ++ +  ++l+
  gi|121638824|ref|YP_979048.1| 627 RMVAQMRSALAQVRSFVPKLETTIQDAMPQIAQASAMLK 665
                                    233344444555555555544444444444444444333 PP

  == domain 3  score: -4.8 bits;  conditional E-value: 6.6
                  Fzo_mitofusin  22 slgvlvvggvvlravgWrvia 42 
                                     l  +++ +vv  a  Wr  +
  gi|121638824|ref|YP_979048.1| 766 VLLAVILLTVVALASMWRGAV 786
                                    566788999999999999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (920 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 5699.77
//
Query:       gi|121638825|ref|YP_979049.1|  [L=413]
Description: transposase for insertion sequence element IS1533 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-16   61.2   0.0      2e-16   60.3   0.0    1.4  1  rve            Integrase core domain
    5.2e-06   26.0   0.0    1.5e-05   24.6   0.0    1.8  1  Sigma70_r4_2   Sigma-70, region 4
    0.00024   20.8   0.1    0.00067   19.4   0.0    1.7  2  HTH_38         Helix-turn-helix domain
    0.00048   19.6   0.0     0.0009   18.7   0.0    1.4  1  GerE           Bacterial regulatory proteins, luxR family
    0.00077   19.2   0.0     0.0021   17.8   0.0    1.8  1  HTH_23         Homeodomain-like domain
     0.0012   18.9   0.0     0.0025   17.8   0.0    1.6  1  HTH_7          Helix-turn-helix domain of resolvase
     0.0047   16.7   0.0        5.1    7.0   0.0    2.8  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0055   16.5   0.0      0.011   15.5   0.0    1.4  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
       0.02   14.9   0.1        0.1   12.6   0.0    2.1  2  HTH_29         Winged helix-turn helix
      0.031   14.2   0.3       0.53   10.2   0.0    3.0  4  MarR_2         MarR family
      0.034   13.7   0.1        2.4    7.8   0.1    2.4  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.046   12.7   0.0      0.064   12.2   0.0    1.1  1  TnsD           Tn7-like transposition protein D
      0.082   12.4   0.0       0.21   11.2   0.0    1.7  1  Sigma70_r4     Sigma-70, region 4
       0.14   12.0   0.1        3.4    7.5   0.0    2.4  2  HTH_IclR       IclR helix-turn-helix domain
       0.23   12.1   0.0       0.41   11.3   0.0    1.3  1  RPA_C          Replication protein A C terminal


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   1.7e-19     2e-16       5     118 ..     116     244 ..     113     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.7e-19
                            rve   5 gelwqvDvt..vvripdggg......kayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngs 76 
                                    ge+ q+D++   +++p g g      ++ +l++v+++sr++la+ l+++  a++++a ++r ++ +g v p+++++D   
  gi|121638825|ref|YP_979049.1| 116 GEIAQCDFWfpPIELPVGFGqtrtakQLPVLTMVCAYSRWLLAMLLPSR-CAEDLFAGWWRLIEALGAV-PRVLVWDGEG 193
                                    8999*****99999999999*****************************.*******************.*******776 PP

                            rve  77 eytsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                    ++  +          ++++f   l  +v  +rp++p+ +G++Er+h +l++ 
  gi|121638825|ref|YP_979049.1| 194 AIG-RwrggrselttECQAFRGTLAAKVLICRPADPEAKGLIERAHDYLERS 244
                                    555.88*******************************************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.3e-08   1.5e-05      21      47 ..      13      39 ..      10      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                   HHHTS---HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrl 47
                                   l++ egl++k IA++lgis +tVks+l
  gi|121638825|ref|YP_979049.1| 13 LHRAEGLPIKMIARVLGISKNTVKSAL 39
                                   89***********************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.6e-07   0.00067       5      37 ..       2      35 ..       1      39 [. 0.93
   2 ?   -3.4   0.0         7   8.4e+03      25      32 ..      77      84 ..      71      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.6e-07
                         HTH_38  5 LsleeReeIerll.aeGlslreIArrLgrspsTI 37
                                   L+ e+  eI rl+ aeGl ++ IAr Lg s++T+
  gi|121638825|ref|YP_979049.1|  2 LTVEDWAEIRRLHrAEGLPIKMIARVLGISKNTV 35
                                   899999******658******************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7
                         HTH_38 25 eIArrLgr 32
                                    IA r+g 
  gi|121638825|ref|YP_979049.1| 77 VIAERIGW 84
                                   69999995 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.5e-07    0.0009      15      39 ..      16      40 ..      14      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-07
                                   CTTS-HHHHHHHHTS-HHHHHHHHH CS
                           GerE 15 aeGksnkeIAeelniSekTVkvhks 39
                                   aeG+  k+IA+ l+iS++TVk+ ++
  gi|121638825|ref|YP_979049.1| 16 AEGLPIKMIARVLGISKNTVKSALE 40
                                   89*******************9765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0021      12      36 ..      12      37 ..       1      44 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                         HTH_23 12 lllae.GlsvreIAreLgvsrrTvyr 36
                                   +l++  Gl+++ IAr Lg+s++Tv  
  gi|121638825|ref|YP_979049.1| 12 RLHRAeGLPIKMIARVLGISKNTVKS 37
                                   566655******************75 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.1e-06    0.0025       9      39 ..       5      36 ..       2      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                                   HHHGGGGSSTT.TT--STTTSSSS---SSSS- CS
                          HTH_7  9 ndinrvvkLle.eGisiskIAkevnisRsTvY 39
                                   +d++++++L++ eG +i+ IA+ ++is+ Tv+
  gi|121638825|ref|YP_979049.1|  5 EDWAEIRRLHRaEGLPIKMIARVLGISKNTVK 36
                                   69*******96378****************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0057       6.8      12      35 ..      13      36 ..      10      40 .. 0.81
   2 !    7.0   0.0    0.0043       5.1      10      31 ..      65      86 ..      57      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0057
                  HTH_AsnC-type 12 LqedaRisyaeLAervGlSestvl 35
                                   L +   ++ + +A+ +G+S +tv 
  gi|121638825|ref|YP_979049.1| 13 LHRAEGLPIKMIARVLGISKNTVK 36
                                   56666679999***********97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0043
                  HTH_AsnC-type 10 eaLqedaRisyaeLAervGlSe 31
                                   e+Lq+ + ++ + +Aer+G+ +
  gi|121638825|ref|YP_979049.1| 65 ELLQAYPTMPATVIAERIGWER 86
                                   79*****************865 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.1e-06     0.011       7      55 ..     222     270 ..     217     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-06
                          rve_3   7 yiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNt 55 
                                    + +p +P   gl+E+ +  l + +l  + f s a+ +++l aw++  Nt
  gi|121638825|ref|YP_979049.1| 222 ICRPADPEAKGLIERAHDYLERSFLPGRVFASPADFNAQLGAWLALVNT 270
                                    569****************************************987776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.7e-05       0.1       7      34 ..      14      40 ..      13      44 .. 0.88
   2 ?   -1.4   0.0       2.1   2.5e+03      42      54 ..     192     204 ..     189     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-05
                         HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlk 34
                                   + aeG++ +++iA++lg+s+ tv  +l+
  gi|121638825|ref|YP_979049.1| 14 HRAEGLP-IKMIARVLGISKNTVKSALE 40
                                   679***9.**************988776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                         HTH_29  42 aalldrrrsgrpr 54 
                                    ++++ r+r+gr+ 
  gi|121638825|ref|YP_979049.1| 192 EGAIGRWRGGRSE 204
                                    4577799999975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00044      0.53       7      42 ..       6      39 ..       2      42 .. 0.82
   2 ?   -2.2   0.0       3.4     4e+03      15      36 ..      68      87 ..      65      87 .. 0.78
   3 ?   -1.8   0.0       2.5     3e+03       7      19 ..     173     185 ..     171     190 .. 0.85
   4 ?   -1.9   0.0       2.6   3.1e+03      46      54 ..     229     237 ..     229     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHH CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsril 42
                                   ++  +  L+r++g  l ++ +ar lg+sk +v  +l
  gi|121638825|ref|YP_979049.1|  6 DWAEIRRLHRAEG--LPIKMIARVLGISKNTVKSAL 39
                                   5555667999***..***************998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                   HCTTTSEEEHHHHHHHHTSSHH CS
                         MarR_2 15 grrpgrdltvgelarrlglsks 36
                                    + p   + ++ +a+r g ++s
  gi|121638825|ref|YP_979049.1| 68 QAYPT--MPATVIAERIGWERS 87
                                   55666..89999****998775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.5
                                    HHHHHHHHHCTTT CS
                         MarR_2   7 qarvLaaLgrrpg 19 
                                    ++r++ aLg+ p+
  gi|121638825|ref|YP_979049.1| 173 WWRLIEALGAVPR 185
                                    9*******99886 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.6
                                    HHTTSEEEE CS
                         MarR_2  46 vaaGLverr 54 
                                    +a+GL+er 
  gi|121638825|ref|YP_979049.1| 229 EAKGLIERA 237
                                    699****95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.002       2.4      12      38 ..      13      39 ..      10      41 .. 0.83
   2 ?    3.4   0.0     0.046        55      10      29 ..      65      84 ..      57      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                         HTH_24 12 LqknprisqreLAerlglSpstvnrrl 38
                                   L +  +++++ +A+ lg+S++tv+  l
  gi|121638825|ref|YP_979049.1| 13 LHRAEGLPIKMIARVLGISKNTVKSAL 39
                                   56677889999************9876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.046
                         HTH_24 10 elLqknprisqreLAerlgl 29
                                   elLq+ p ++ + +Aer+g 
  gi|121638825|ref|YP_979049.1| 65 ELLQAYPTMPATVIAERIGW 84
                                   799***************95 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.4e-05     0.064     190     231 ..       9      50 ..       6     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                           TnsD 190 rlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkk 231
                                    ++++L+  egl +k iA+ lg++ +tV++ ++++++ k+++ 
  gi|121638825|ref|YP_979049.1|   9 EIRRLHRAEGLPIKMIARVLGISKNTVKSALESNQQPKYERA 50 
                                    67899999**************************97775543 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.21      17      39 ..      15      37 ..       9      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                   HTTT--HHHHHHHHTS-HHHHHH CS
                     Sigma70_r4 17 fgeglTleEIgerlgiSrerVrq 39
                                   + egl+ + I+++lgiS+ +V++
  gi|121638825|ref|YP_979049.1| 15 RAEGLPIKMIARVLGISKNTVKS 37
                                   4799*****************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0029       3.4      15      37 ..      15      37 ..      12      41 .. 0.84
   2 ?    1.6   0.0      0.21   2.5e+02      16      33 ..      71      87 ..      61      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                                   TBSS-BHHHHHHHHTS-HHHHHH CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhR 37
                                   ++++l ++ +Ar +g++k tv  
  gi|121638825|ref|YP_979049.1| 15 RAEGLPIKMIARVLGISKNTVKS 37
                                   56789***************965 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                   BSS-BHHHHHHHHTS-HH CS
                       HTH_IclR 16 pqeltlselArrtglpkS 33
                                   p  +  + +A+r+g+ +S
  gi|121638825|ref|YP_979049.1| 71 P-TMPATVIAERIGWERS 87
                                   4.4999*********998 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.41      62      90 ..      13      41 ..       9      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                   SXSTTTEEHHHHHHHSTSXHHHHHHHHHH CS
                          RPA_C 62 peseeGvhvdeiaqklrlsvndvkqavde 90
                                    ++ eG+ ++ ia+ l++s+n+vk+a+++
  gi|121638825|ref|YP_979049.1| 13 LHRAEGLPIKMIARVLGISKNTVKSALES 41
                                   6789**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2707.52
//
Query:       gi|121638826|ref|YP_979050.1|  [L=176]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-09   36.6   0.0    5.6e-09   36.0   0.0    1.2  1  IstB_IS21  IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   3.1e-13   5.6e-09       7      56 ..      69     118 ..      66     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.1e-13
                      IstB_IS21   7 rlrlaklpaqktledidfraarsldkrkvkeLatlsfiekkenivllGps 56 
                                    r+r+a++pa+k le++df++ar+l++ ++++L tl+fi++++n+v+lGp+
  gi|121638826|ref|YP_979050.1|  69 RIRAARFPARKSLEEFDFEHARGLKRDTIAHLGTLDFITARDNVVFLGPA 118
                                    799*********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1341.39
//
Query:       gi|121638827|ref|YP_979051.1|  [L=233]
Description: lipoprotein lppX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-59  199.6   1.6    4.9e-59  199.4   1.6    1.0  1  LppX_LprAFG  LppX_LprAFG lipoprotein
     0.0028   17.7   0.1      0.014   15.4   0.0    1.9  2  DUF3108      Protein of unknown function (DUF3108)


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   1.6   5.5e-63   4.9e-59       2     192 .]      48     232 ..      47     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 5.5e-63
                                    HHHH..HHHHHHHHHT-SEEEEEEEEEC--TTS.TEEEEEEEEETTTT.EEEEEEEEEETTCEEEEEEEEETTEEEEEEC CS
                    LppX_LprAFG   2 aakl..laesakatkslksvhlaltvngkvdgl.pvesvegdltnqpagaakgnakvtlagqavdvkfvvvdgklyaklp 78 
                                    +a l  +++s +atk+l+svh+a++++gkvd+l +++s+++d++++p  aakg +++   ++++ v+f+v+++++++kl+
  gi|121638827|ref|YP_979051.1|  48 PALLaeIRQSLDATKGLTSVHVAVRTTGKVDSLlGITSADVDVRANPL-AAKGVCTY---NDEQGVPFRVQGDNISVKLF 123
                                    66665689****************************************.********...******************** PP

                                    TTEEEEEEEHGHCHHHHCGG-TTTSHHHHCCTEEEEEEEEEEEETTEEEEEEEEEE-HHHHHHH-CCG-SSS.EEEEEEE CS
                    LppX_LprAFG  79 petwsdlgpaekiydpavlLdpdkGlanvLagvtdakaegreeidGtatvkitGtvdadvvsaivpslkedgtvpitlWi 158
                                     ++ws+lg+  + ++++++Ldp++G++++L+gvt+++a+g+e+idG++t+kitGt++a++v++++p++k++  +p+t+Wi
  gi|121638827|ref|YP_979051.1| 124 -DDWSNLGSI-SELSTSRVLDPAAGVTQLLSGVTNLQAQGTEVIDGISTTKITGTIPASSVKMLDPGAKSA--RPATVWI 199
                                    .9********.99**********************************************************..******* PP

                                    ESSTT--EEEEEEEECTCEEEEEEEESTT---TT CS
                    LppX_LprAFG 159 aedgelrlvrvvvdkesgesveltlskwgkpvtv 192
                                    a+dg+++lvr+++d++sg+ ++lt skw++pv+v
  gi|121638827|ref|YP_979051.1| 200 AQDGSHHLVRASIDLGSGS-IQLTQSKWNEPVNV 232
                                    *******************.************98 PP

>> DUF3108  Protein of unknown function (DUF3108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.11   9.8e+02      39      64 ..      57      83 ..      51      97 .. 0.76
   2 !   15.4   0.0   1.5e-06     0.014     171     223 ..     175     222 ..     155     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.11
                        DUF3108 39 sve.tdpvyrisltarttglldlffkv 64
                                   s++ t+   ++ +++rttg +d +  +
  gi|121638827|ref|YP_979051.1| 57 SLDaTKGLTSVHVAVRTTGKVDSLLGI 83
                                   555456677899999999999988665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.5e-06
                        DUF3108 171 gkyetlkvrpvvreagvfkekrdievWladdanriPvrieadlkvGsvtaeLt 223
                                    g++ +  v++  + a   k+ r  +vW+a d+ +  vr + dl  Gs  ++Lt
  gi|121638827|ref|YP_979051.1| 175 GTIPASSVKMLDPGA---KSARPATVWIAQDGSHHLVRASIDL--GSGSIQLT 222
                                    333333333333333...99**********************9..77766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1746.73
//
Query:       gi|121638828|ref|YP_979052.1|  [L=2112]
Description: polyketide synthase pks1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-92  308.8   1.1      3e-92  308.8   1.1    2.2  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.5e-59  201.0   3.2    1.5e-59  201.0   3.2    3.6  4  KR               KR domain
    9.3e-59  199.5   2.4    1.6e-58  198.7   2.4    1.4  1  Acyl_transf_1    Acyl transferase domain
    5.3e-58  196.6   4.0    5.3e-58  196.6   4.0    2.0  2  PS-DH            Polyketide synthase dehydratase
    8.7e-46  154.8   2.8    3.2e-45  153.0   2.8    2.1  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    2.6e-16   60.9   1.5    1.4e-15   58.5   0.0    3.1  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    8.8e-16   58.1   0.1    1.4e-13   51.0   0.1    3.7  3  ADH_zinc_N       Zinc-binding dehydrogenase
    5.6e-15   55.8   0.0    1.3e-14   54.6   0.0    1.7  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
      9e-15   54.6   0.8      9e-15   54.6   0.8    3.4  4  adh_short        short chain dehydrogenase
    9.5e-15   54.7   0.0    2.4e-14   53.4   0.0    1.7  1  PP-binding       Phosphopantetheine attachment site
      1e-10   41.6   0.7      1e-10   41.6   0.7    2.5  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      7e-07   29.1   0.1    2.1e-06   27.6   0.1    1.8  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    1.9e-06   27.4   0.9    5.9e-06   25.8   0.2    2.1  2  Thiolase_N       Thiolase, N-terminal domain
    2.2e-06   27.1   1.0    5.3e-06   25.9   1.0    1.7  1  Docking          Erythronolide synthase docking
    3.7e-05   23.3   0.3    7.7e-05   22.3   0.3    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.023   13.8   0.1      0.059   12.5   0.0    1.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.06   12.7   0.0        0.1   12.0   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.081   12.9   4.7          1    9.4   0.4    3.2  2  YAcAr            YspA, cpYpsA-related SLOG family


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.8   1.1     3e-95     3e-92       2     253 .]      47     294 ..      46     294 .. 0.97
   2 ?   -1.9   0.1         2     2e+03      95     153 ..     330     389 ..     328     406 .. 0.63

  Alignments for each domain:
  == domain 1  score: 308.8 bits;  conditional E-value: 3e-95
                                    --EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTS.SCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHH CS
                  ketoacyl-synt   2 epvaivGmgarfPggnd.veefwelLlegrdaiselpadr.wdadklydpparaagkiktklggfld.vddfdpeffgis 78 
                                    epva+vG+g+rfPgg+d ++ +w+++ +grd +se+p+dr wd+++lydp+++a+gk++t++g+fld +  fd+ ffgi 
  gi|121638828|ref|YP_979052.1|  47 EPVAVVGIGCRFPGGVDgPDGLWDVVSAGRDVVSEFPTDRgWDVEGLYDPDPDAEGKTYTRWGAFLDdATGFDAGFFGIA 126
                                    89****************************************************************************** PP

                                    HHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHH CS
                  ketoacyl-synt  79 preaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagri 158
                                    p+e+ amdpqqrl+le++weale+ag++p +l+gs++gv++G+ a++y++    +++g+  +++   +g+ + +v++gr+
  gi|121638828|ref|YP_979052.1| 127 PSEVLAMDPQQRLMLEVSWEALEHAGIDPLSLRGSATGVYTGIFAASYGN----RDTGG-LQGYG-LTGT-SISVASGRV 199
                                    **********************************************9976....44454.88899.9999.********* PP

                                    HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-B CS
                  ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvl 238
                                    sy lgl+Gp+v+vdtACsSslva+h a++slrsge+d+alaGGv+++  p+ ++gfs+++ l++dgrckaf+++adG+ +
  gi|121638828|ref|YP_979052.1| 200 SYVLGLQGPAVSVDTACSSSLVAIHWAMSSLRSGECDLALAGGVTVMGLPSIFVGFSRQRGLAADGRCKAFAAAADGTGW 279
                                    ******************************************************************************** PP

                                    B-EEEEEEEEECHHH CS
                  ketoacyl-synt 239 GEGvGavvLkrleda 253
                                    GEG+G+vvL+rl+da
  gi|121638828|ref|YP_979052.1| 280 GEGAGVVVLERLSDA 294
                                    *************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                    HHHHHHHHHTS-HHTCTTGG...EEEEEEESSTHHHHHHHHHHHTT.GGGSCTTHHHHHSTTH CS
                  ketoacyl-synt  95 aawealedagltpeeldgsr...vgvfiGvgagdyaalaaldedgs.evkaspkavgavlanv 153
                                    + + al++agl+++++d  +   ++ ++G  ++ +   a+l+ +g+ +    p +vg++ +n+
  gi|121638828|ref|YP_979052.1| 330 VIQAALANAGLSAADVDVVEahgTATTLGDPIEAQ---ALLSTYGQgRPAEQPLWVGSIKSNM 389
                                    56789*******99985444434777777777755...3444444434555556777644444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4       1.2   1.2e+03     149     172 ..     743     766 ..     738     771 .. 0.82
   2 ?   -0.5   0.2      0.99   9.8e+02       4      36 ..    1537    1574 ..    1535    1678 .. 0.56
   3 !  201.0   3.2   1.5e-62   1.5e-59       1     179 [.    1724    1903 ..    1724    1904 .. 0.98
   4 ?   -3.5   0.0       8.3   8.2e+03     103     133 ..    1984    2014 ..    1980    2028 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHTEEE CS
                             KR 149 YaaaNaflDalaeyrrsqglpavs 172
                                     aaaNa+ D +a++ r+ ++ avs
  gi|121638828|ref|YP_979052.1| 743 QAAANAIADRFAAQGRRVHQLAVS 766
                                    58**********998887777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.99
                                     EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS....... CS
                             KR    4 litGGlGgLGlelarwlaekgarhlvllsRsa.....a 36  
                                     li  G+Gg+G++ ++   + g +  v  sR +     a
  gi|121638828|ref|YP_979052.1| 1537 LIHAGTGGVGMAAVQLARQWGVEVFVTASRGKwdtlrA 1574
                                     66667777777666655556666666666654333330 PP

  == domain 3  score: 201.0 bits;  conditional E-value: 1.5e-62
                                     SEEEEETTTSHHHHHHHHHHH.HHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwla.ekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77  
                                     gt++itG++G++G +lar+l+ + g rhlvl sR++   e +++l a l++ ga+ +vva+Dv+d++av+ l++++++
  gi|121638828|ref|YP_979052.1| 1724 GTVVITGATGAVGGVLARHLVgAYGVRHLVLASRRGDRAEGAAELAADLTEAGAKGQVVACDVADRAAVAGLFAQLSR 1801
                                     899******************5579***********999999************************************ PP

                                     HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR   78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNaf 155 
                                     e pp++GvihaAgvl+d+ ++++t +++++vl++Kv++awnLh++++d +l +fvl+SSia+++gs+gq+nY+aaNaf
  gi|121638828|ref|YP_979052.1| 1802 EYPPVRGVIHAAGVLDDAVITSLTPDRIDTVLRAKVDAAWNLHQATSDLDLSMFVLCSSIAATVGSPGQGNYSAANAF 1879
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHHTEEEEEE--BT CS
                             KR  156 lDalaeyrrsqglpavsinwglwa 179 
                                     lD+la++r++ gl+++s++wglw+
  gi|121638828|ref|YP_979052.1| 1880 LDGLAAHRQAAGLAGISLAWGLWE 1903
                                     ***********************8 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.3
                                     HHHHHHHTTTTHHHHHHHHHTTTS--SEEEE CS
                             KR  103 edleqvlapKvkGawnLhelledesldffvl 133 
                                     +d   ++++K + a+ Lh l +de+l+++v 
  gi|121638828|ref|YP_979052.1| 1984 DDTGDATSSKSALAQRLHGLAADEQLELLVG 2014
                                     5666778899999999*********999984 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.7   2.4   1.6e-61   1.6e-58       3     317 ..     582     891 ..     580     893 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 1.6e-61
                                    EE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHTT- CS
                  Acyl_transf_1   3 vfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellkskGv 82 
                                    vf+GqG+Q  GMG+eL+ + ++fa++ ++ +  +  +  + + dv+  ++  lld+++f+qpaL+av++a +++l+  Gv
  gi|121638828|ref|YP_979052.1| 582 VFPGQGAQRIGMGRELYGELPVFAQAFDAVADELDRHLRLPLRDVIWGADADLLDSTEFAQPALFAVEVASFAVLRDWGV 661
                                    9******************************************************************************* PP

                                    TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.HHHHHHH..TT.EEEEEEECCCCECCE CS
                  Acyl_transf_1  83 rpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavelaeeeeklrcqddvvgavansprrvvisg 162
                                     p+ v+GHS+GElAaa++ag l++++a+  vv r+rlm+ l   g+m av+ +e e +    + v  a+ n p++vvisg
  gi|121638828|ref|YP_979052.1| 662 LPDFVMGHSVGELAAAHAAGVLTLADAAMLVVARGRLMQALPAGGAMVAVAASEDEVEPLLGEGVGIAAINAPESVVISG 741
                                    ****************************************************99999999******************** PP

                                    EHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHHHHHH CS
                  Acyl_transf_1 163 sqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywvanlr 242
                                     q+a +++  r +++g+++++ +v+ a+hsp ++++ ++ a   a +  r+p++   s ++ + + +   sa+ywv+ +r
  gi|121638828|ref|YP_979052.1| 742 AQAAANAIADRFAAQGRRVHQLAVSHAFHSPLMEPMLEEFARVAARVQAREPQLGLVSNVTGELAGPDFGSAQYWVDHVR 821
                                    ******************************************************************************** PP

                                    CHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT- CS
                  Acyl_transf_1 243 spvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltgs 317
                                     pvrfa+  +++   +   f+e  p s l+  +e+ l      ++a +v  l +d  + l  +l +++++++tg+
  gi|121638828|ref|YP_979052.1| 822 RPVRFADSARHLQTLGATHFIEAGPGSGLTGSIEQSLAP----AEAMVVSMLGKDRPE-LASALGAAGQVFTTGV 891
                                    ************9*************************4....556666666677777.7778888888888887 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.6   4.0   5.4e-61   5.3e-58       1     297 [.     941    1215 ..     941    1216 .. 0.93
   2 ?   -2.9   0.3       3.1   3.1e+03     183     246 ..    1922    1981 ..    1915    2019 .. 0.73

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 5.4e-61
                                     BTTB.-EE--.-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B- CS
                          PS-DH    1 hpllGsrvrsasdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvlp 78  
                                     h llG+ v+ ++++evv   rl+la++pwL+DH+v+g v++Pgag++e+++ A+ ++     +  ++++++ ++lv+ 
  gi|121638828|ref|YP_979052.1|  941 HALLGAVVERPDSDEVVLTGRLSLADQPWLADHVVNGVVLFPGAGFVELVIRAGDEVG----CALIEELVLAAPLVMH 1014
                                     99*******************************************************9....999************* PP

                                     -SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-------B--HHHHHHHS-SEE....E-HHH CS
                          PS-DH   79 edepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaaaaavdlealqarcaepaslrsvssae 156 
                                     ++ +v+vq+++ ++ d++     +++++Sr++++++w ++a+G + +a++++  ++dl+ ++++ ae     sv+ ++
  gi|121638828|ref|YP_979052.1| 1015 PGVGVQVQVVVGAA-DESG--HRAVSVYSRGDQSQGWLLNAEGMLGVAAAET--PMDLSVWPPEGAE-----SVDISD 1082
                                     **************.5555..359**********99**********998877..8999999555555.....588999 PP

                                     HHHHHHHHSEEE-GGG--EEEEEEETTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG----------EEEE CS
                          PS-DH  157 fYerlaargleyGpsFqglralwrgdgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekadaaylPv 234 
                                      Y +la+rg+ yGp+Fqgl a+wr+ +e +ae+ +p e+    +++ +hPa+lDa+l++l++a+ ++++++++++lP+
  gi|121638828|ref|YP_979052.1| 1083 GYAQLAERGYAYGPAFQGLVAIWRRGSELFAEVVAPGEAGVAVDRMGMHPAVLDAVLHALGLAV-EKTQASTETRLPF 1159
                                     ************************************999999999*******************.789********** PP

                                     EEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEEE--XXXXX CS
                          PS-DH  235 aierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlrrvereals 297 
                                      +  ++++      g+  +v+ar +++ga+  +++++++d++G +v++++ l +r++++e+l+
  gi|121638828|ref|YP_979052.1| 1160 CWRGVSLHA-----GGAGRVRARFASAGAD--AISVDVCDATGLPVLTVRSLVTRPITAEQLR 1215
                                     *******95.....6779999999999976..6678899*******************99876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                     TEEEEEE---GGGSSTTTT-SB.-HHHHHHHHHHG..GG----------EEEEEEEEEEE-S... CS
                          PS-DH  183 gealaelrlpeelaggesayvl.hPallDaalQllaaalsaeaekadaaylPvaierlrvyrpss 246 
                                     ++ la ++ +e+++  ++a+++ hP  + ++l        a + +a+a++lP  ++ l+ +++++
  gi|121638828|ref|YP_979052.1| 1922 RSGLAPMSPAEAVELFDAALAIdHPLAVATLLDRA-----ALDARAQAGALPALFSGLARRPRRR 1981
                                     46677777778888888888888999988888854.....3468999999999999999987333 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   2.8   3.2e-48   3.2e-45       1     117 [.     302     419 ..     302     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 3.2e-48
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG.SCTSE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar.kqpla 79 
                                    +av++gsavn+dga+n+ltapng aq+r+i++ala+ag++++dvd+veahgt+t+lgDpiE++al +++g+++  +qpl+
  gi|121638828|ref|YP_979052.1| 302 LAVVRGSAVNQDGASNGLTAPNGLAQQRVIQAALANAGLSAADVDVVEAHGTATTLGDPIEAQALLSTYGQGRPaEQPLW 381
                                    69**********************************************************************99****** PP

                                    EE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  80 vgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    vgS+Ksn+GH++aAaGva++ik+v+a++hgv+p+tl++
  gi|121638828|ref|YP_979052.1| 382 VGSIKSNMGHTQAAAGVAGVIKMVQAMRHGVMPATLHV 419
                                    *************************************8 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.9   8.8e+03      96     119 ..    1422    1446 ..    1369    1447 .. 0.87
   2 !   58.5   0.0   1.4e-18   1.4e-15       4     133 .]    1580    1711 ..    1577    1711 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.9
                                     HHHHHH----EEEE.EEGGGHHHHH CS
                   ADH_zinc_N_2   96 lieeGklrpvvdrv.fpleeaaeAh 119 
                                      +++G++r+ v  v   + +++ A+
  gi|121638828|ref|YP_979052.1| 1422 PLQAGQVRVAVAAVgVNFRDVVAAL 1446
                                     5789999999999999999998885 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 1.4e-18
                                     SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHE.EEEEEEEE----.S-EEE-CHHHCTTT-EEEE- CS
                   ADH_zinc_N_2    4 devidyrtedfe....aatggegvDvvldtvggealleaslkvl.pggGrlvsiggpplsaallkpakkrkgrsvkye 76  
                                     d++ d+rt +fe    a+t+g+gvDvvld+++ge +++asl++l +g Gr++++g++    +++++   ++ ++v+y 
  gi|121638828|ref|YP_979052.1| 1580 DHIGDSRTCEFEekflAVTEGRGVDVVLDSLAGE-FVDASLRLLvRG-GRFLEMGKT--DIRDAQE-IAANYPGVQYR 1652
                                     7777999999999999****************99.66*******777.*******73..3333333.33667777776 PP

                                     -GGG...-....-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   77 flfsmkas...aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                      +  +++    + +++l+e+ +l++  +l+  +  +++   a+ A+r + ++r++GK+Vl
  gi|121638828|ref|YP_979052.1| 1653 AFD-LSEAgpaRMQEMLAEVRELFDTRELHRLPVTTWDVRCAPAAFRFMSQARHIGKVVL 1711
                                     665.555568867777*************999999************************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.9   2.9e+03      28      54 ..     831     858 ..     821     899 .. 0.52
   2 !   51.0   0.1   1.4e-16   1.4e-13       1      90 [.    1544    1633 ..    1544    1666 .. 0.88
   3 ?    2.1   0.0      0.18   1.8e+02       2      76 ..    2013    2081 ..    2013    2089 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.9
                                    HHHHHTTESEEEETTTC.HHHHHHHHHT CS
                     ADH_zinc_N  28 elakklGadevinykea.dlverikelt 54 
                                    + ++ lGa+++i +     l   i++  
  gi|121638828|ref|YP_979052.1| 831 RHLQTLGATHFIEAGPGsGLTGSIEQSL 858
                                    5677778888877733333444443333 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 1.4e-16
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT.ESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklG.adevinykea.dlverikeltggegvdvvfecvGsgatleaal 76  
                                     gvG+aavqlA+ +G+ev++++s   k + ++ +G  d  i  +++ +++e+  + t+g+gvdvv++ ++ g+ ++a+l
  gi|121638828|ref|YP_979052.1| 1544 GVGMAAVQLARQWGVEVFVTASRG-KWDTLRAMGfDDDHIGDSRTcEFEEKFLAVTEGRGVDVVLDSLA-GEFVDASL 1619
                                     9******************99888.69*******655666666999***********************.******** PP

                                     HCEEEEEEEEECSC CS
                     ADH_zinc_N   77 kllkpgGrlvvvGg 90  
                                     +ll +gGr+  +G 
  gi|121638828|ref|YP_979052.1| 1620 RLLVRGGRFLEMGK 1633
                                     *********99996 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.18
                                     HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N    2 vGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltg.gegvdvvfecvGsgatleaal 76  
                                     vGl  +q+A+ lG ++ a d++++      +lG d +      +l  r+k +tg + ++ v+f+++  ++++ +++
  gi|121638828|ref|YP_979052.1| 2013 VGLVCLQAAAVLG-RPSAEDVDPD--TEFGDLGFDSLTAV---ELRNRLKTATGlTLPPTVIFDHPT-PTAVAEYV 2081
                                     6777777777777.4555555555..44777888888888...79999999999999**********.99988776 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.3e-17   1.3e-14       1     112 []     422     545 ..     422     545 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.3e-17
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeesk........eeslprLlvlsg 68 
                                    P+p+++ +++g + V te+ +w+ +     ++v+sfG++G+n+H+iL++++ + ++e++          +++   +v+s+
  gi|121638828|ref|YP_979052.1| 422 PSPRVD-WTSGAVSVLTEAREWSVDGrprrAAVSSFGISGTNAHLILEEAPVPAPAEAPVeasestggPRPSMVPWVISA 500
                                    99****.***************87766889*********************555544444445566444445555689** PP

                 KAsynt_C_assoc  69 rteeaveallekleehlldaellsllneilseeisr.lpyRGyav 112
                                    r++ea++a++ +l +h + ++ l+ ++   s + ++ +++R+ +v
  gi|121638828|ref|YP_979052.1| 501 RSAEALTAQAGRLMAHVQANPGLDPIDVGCSLASRSvFEHRAVVV 545
                                    ****************************99999888899*99886 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.1   3.1e+03       4      32 ..     737     765 ..     736     780 .. 0.81
   2 ?   -0.1   0.1      0.53   5.3e+02     135     168 ..    1274    1307 ..    1264    1315 .. 0.83
   3 ?   -0.3   0.1      0.61     6e+02       3      33 ..    1536    1566 ..    1534    1573 .. 0.88
   4 !   54.6   0.8     9e-18     9e-15       2     161 ..    1725    1885 ..    1724    1892 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                                    EEESTTSHHHHHHHHHHHHTT-EEEEEES CS
                      adh_short   4 lvtGassGIGraiakelakeGakvvvvdr 32 
                                    +v+ +++    aia+++a++G +v  ++ 
  gi|121638828|ref|YP_979052.1| 737 VVISGAQAAANAIADRFAAQGRRVHQLAV 765
                                    45666678899**********99976655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                                     EEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHG CS
                      adh_short  135 sSvagkvpvagvaaYsAsKaavagltrslakela 168 
                                      S  g+ ++ ++++Y+A+  a++ l + l  + a
  gi|121638828|ref|YP_979052.1| 1274 ESAGGQASSVVGSVYAATHTALEVLQSWLGADRA 1307
                                     5889999**************9999887776655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.61
                                     EEEESTTSHHHHHHHHHHHHTT-EEEEEESC CS
                      adh_short    3 vlvtGassGIGraiakelakeGakvvvvdrs 33  
                                     vl+  +++G+G a ++   + G++v+v++++
  gi|121638828|ref|YP_979052.1| 1536 VLIHAGTGGVGMAAVQLARQWGVEVFVTASR 1566
                                     8999**********************97654 PP

  == domain 4  score: 54.6 bits;  conditional E-value: 9e-18
                                     EEEEESTTSHHHHHHHHHHH.HTT-EEEE.EESC...HHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                      adh_short    2 vvlvtGassGIGraiakela.keGakvvv.vdrs...eekleevakelkeegakalaiqvDvtdreevealvekavkk 74  
                                     +v++tGa++ +G  +a++l+ + G++++v ++r+   +e ++e+a+ l e+gak  ++++Dv+dr++v  l+++   +
  gi|121638828|ref|YP_979052.1| 1725 TVVITGATGAVGGVLARHLVgAYGVRHLVlASRRgdrAEGAAELAADLTEAGAKGQVVACDVADRAAVAGLFAQLSRE 1802
                                     69****************98468***9994444411123345556666666999************************ PP

                                     HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                      adh_short   75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152 
                                     + ++  +++ AG+  ++ + +l+ ++++ v+   + ++ +l +a  +          v  sS+a+ v+++g+  YsA+
  gi|121638828|ref|YP_979052.1| 1803 YPPVRGVIHAAGVLDDAVITSLTPDRIDTVLRAKVDAAWNLHQATSDL----DLSMFVLCSSIAATVGSPGQGNYSAA 1876
                                     ********************************************9999....57899********************* PP

                                     HHHHHHHHH CS
                      adh_short  153 Kaavagltr 161 
                                      a+++gl+ 
  gi|121638828|ref|YP_979052.1| 1877 NAFLDGLAA 1885
                                     ****99975 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.4e-17   2.4e-14       7      67 .]    2020    2081 ..    2015    2081 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.4e-17
                     PP-binding    7 vaevlgv.pleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +a vlg+ ++e++dpdt + dlG+DSl+avel ++l+ + g+++p++++f+hpt+ ++a+y+
  gi|121638828|ref|YP_979052.1| 2020 AAAVLGRpSAEDVDPDTEFGDLGFDSLTAVELRNRLKTATGLTLPPTVIFDHPTPTAVAEYV 2081
                                     58899*9667779***********************************************97 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.71   7.1e+02       7      42 ..     746     782 ..     741     794 .. 0.72
   2 !   41.6   0.7     1e-13     1e-10      21     152 ..    1752    1884 ..    1730    1894 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT CS
                   adh_short_C2   7 GraiAkalaeeGaevvltdlneea.kkrveelaeelg 42 
                                    + aiA ++a++G +v    ++ +     +e++ ee+ 
  gi|121638828|ref|YP_979052.1| 746 ANAIADRFAAQGRRVHQLAVSHAFhSPLMEPMLEEFA 782
                                    7899999999999998888887775566666666555 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 1e-13
                                     EEEEESSGGHHHHHHHHHHHTT...SE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HH CS
                   adh_short_C2   21 vvltdlneeakkrveelaeelg...ae..vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsre 93  
                                     +vl+ ++ ++++ ++ela++l    a+  v++cDV+d+++v+ l++++ +++  + +++++ag+ ++  + +++++ +
  gi|121638828|ref|YP_979052.1| 1752 LVLASRRGDRAEGAAELAADLTeagAKgqVVACDVADRAAVAGLFAQLSREYPPVRGVIHAAGVLDD--AVITSLTPD 1827
                                     566666666666677777666522233457*************************************..99******* PP

                                     HHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                   adh_short_C2   94 efdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealt 152 
                                      +d++l  ++ ++++l +a   l  + +  v +ss++a+++ p++  y+aa a l +l+
  gi|121638828|ref|YP_979052.1| 1828 RIDTVLRAKVDAAWNLHQATSDL--DLSMFVLCSSIAATVGSPGQGNYSAANAFLDGLA 1884
                                     *******************9997..44789***********************999875 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   2.1e-09   2.1e-06       2      60 ..    1426    1481 ..    1425    1487 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.1e-09
                                     TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                          ADH_N    2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60  
                                     g+v++ v+a+g++  D+  + g   + +++p  lG E +G+v e+gpev++l+vGd V+
  gi|121638828|ref|YP_979052.1| 1426 GQVRVAVAAVGVNFRDVVAALG-MYPGQAPP--LGAEGAGVVLETGPEVTDLAVGDAVM 1481
                                     79*******************9.57777777..9***********************98 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   5.9e-09   5.9e-06      75     117 ..     206     248 ..     193     265 .. 0.89
   2 ?   -2.8   0.0       3.3   3.3e+03      28      48 ..     328     348 ..     308     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.9e-09
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTT CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsn 117
                                    + pav v+ +csS+l a++ a+ s+++ge+d ++agGv  m+ 
  gi|121638828|ref|YP_979052.1| 206 QGPAVSVDTACSSSLVAIHWAMSSLRSGECDLALAGGVTVMGL 248
                                    6799**********************************99975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHTS-GGGCCEE CS
                     Thiolase_N  28 aealkallekagvdpeevdev 48 
                                    +++++a+l++ag+++++vd v
  gi|121638828|ref|YP_979052.1| 328 QRVIQAALANAGLSAADVDVV 348
                                    6799************99977 PP

>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.0   5.4e-09   5.3e-06       4      26 .]      18      40 ..      16      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.4e-09
                        Docking  4 eKLRdYLKRvTaDLrqtRrRLrE 26
                                   eKL +YLK+v  +L +tR RLrE
  gi|121638828|ref|YP_979052.1| 18 EKLFHYLKKVAVELDETRARLRE 40
                                   8*********************9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   7.7e-08   7.7e-05       1     121 [.    1726    1867 ..    1726    1879 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.7e-08
                                     EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHHT-S CS
                      Epimerase    1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl...........elveldltdrsalerlfkeeqpd 66  
                                     +++tGatG +G  l+++l  +  ++ ++l++++ ++++++ e l           ++v +d+ dr+a++ lf++   +
  gi|121638828|ref|YP_979052.1| 1726 VVITGATGAVGGVLARHLVGAYgVRHLVLASRRGDRAEGAAE-LaadlteagakgQVVACDVADRAAVAGLFAQLSRE 1802
                                     68*****************99876644444443333322222.23578***********************9986544 PP

                                     E.....EEE--S.---HHH...HHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTS CS
                      Epimerase   67 a.....vihlAa.vggvaa...ssedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGk 121 
                                     +     vih+A+   +      + ++   ++++ +  ++nl +a ++ ++  ++ +sS +++ G 
  gi|121638828|ref|YP_979052.1| 1803 YppvrgVIHAAGvLDDAVItslTPDRIDTVLRAKVDAAWNLHQATSDLDLSMFVLCSSiAATVGS 1867
                                     444444*****9543333311133455677899************************96666664 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   2.6e+03     112     139 ..    1337    1364 ..    1333    1366 .. 0.82
   2 ?   12.5   0.0     6e-05     0.059       1     127 [.    1726    1859 ..    1726    1865 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                                     HHHHHHTT-SEEEEEEEGGGSS--SHHH CS
                Polysacc_synt_2  112 ieaaieagvkkvvliStDKAvnPtnvmG 139 
                                     ++ a++ +  ++vli tD Av+   + G
  gi|121638828|ref|YP_979052.1| 1337 ARSAQAENPGRIVLIDTDAAVDASVLAG 1364
                                     56778888889**********9877766 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6e-05
                                     EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                Polysacc_synt_2    1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77  
                                     v++tGa+G++G  l r+++    +++++l +r   +    ++ l ++l++   k +  +v +dv+d++ ++ ++ +l+
  gi|121638828|ref|YP_979052.1| 1726 VVITGATGAVGGVLARHLVGAyGVRHLVLASRRGDRAEGAAE-LAADLTEAGAKGQ--VVACDVADRAAVAGLFAQLS 1800
                                     79***************9987799999999998877665554.5566666666555..7899*********9999886 PP

                                     -SE.....EEE------HHHH....HHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                Polysacc_synt_2   78 vdv.....vfhaAAlKhVPlv....eenpleaiktNvlgtenvieaaieagvkkvvliS 127 
                                      ++     v+haA +    ++       +  +++  v ++ n+ +a+ + + + +vl S
  gi|121638828|ref|YP_979052.1| 1801 REYppvrgVIHAAGVLDDAVItsltPDRIDTVLRAKVDAAWNLHQATSDLDLSMFVLCS 1859
                                     54433344999998654333300003344455566777777777777777777777766 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001       0.1       2      74 ..    1728    1799 ..    1727    1813 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                     EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                  GDP_Man_Dehyd    2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74  
                                     iTG +G +G  la++L+  +   h +       +++  ++la d  +e+  + +++ +D+ D++++  l+a+ 
  gi|121638828|ref|YP_979052.1| 1728 ITGATGAVGGVLARHLVGAYGVRHLVLASRRGDRAEGAAELAADL-TEAGAKGQVVACDVADRAAVAGLFAQL 1799
                                     9****************9966666666666666788888888876.467889****************99985 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4     0.001         1      27      60 ..     732     765 ..     729     770 .. 0.85
   2 ?    3.4   0.4     0.074        74      28      58 ..    1532    1561 ..    1520    1566 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                          YAcAr  27 eapidmvlvhGgakGaDrlAarWAae.rgvelvrf 60 
                                    +ap + v+++G++  a+++A+r+Aa+ r v+++++
  gi|121638828|ref|YP_979052.1| 732 NAP-ESVVISGAQAAANAIADRFAAQgRRVHQLAV 765
                                    678.89******************75388888765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.074
                          YAcAr   28 apidmvlvhGgakGaDrlAarWAaergvelv 58  
                                     a+ + vl+h g+ G+   A + A++ gve+ 
  gi|121638828|ref|YP_979052.1| 1532 AG-ESVLIHAGTGGVGMAAVQLARQWGVEVF 1561
                                     44.79***********************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 1.10u 0.30s 00:00:01.40 Elapsed: 00:00:00.46
# Mc/sec: 13761.40
//
Query:       gi|121638829|ref|YP_979053.1|  [L=705]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-63  214.8   0.0    2.2e-63  214.3   0.0    1.3  1  AMP-binding    AMP-binding enzyme
    2.3e-11   44.5   0.2      9e-11   42.6   0.1    2.1  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.1e-07   31.2   0.0    4.5e-07   30.1   0.0    1.6  1  PP-binding     Phosphopantetheine attachment site
  ------ inclusion threshold ------
      0.024   14.1   0.2      0.048   13.2   0.2    1.4  1  DUF4400        Domain of unknown function (DUF4400)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.0     5e-67   2.2e-63       6     419 ..      17     390 ..      10     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 5e-67
                                    HHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHH CS
                    AMP-binding   6 aktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaee 85 
                                    a + d++a+ +      +T ++ ++ + rl+ +Lr++G+ +gdrV+++lp sp++v +lla+l  G+++   np+l +++
  gi|121638829|ref|YP_979053.1|  17 AGWYDRPAF-Y--AADVVTHGQIHDGAARLGEVLRNRGLSSGDRVLLCLPDSPDLVQLLLACLARGVMAFLANPELHRDD 93 
                                    456699***.6..6788******************99******************************************* PP

                                    HHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEE CS
                    AMP-binding  86 layiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayii 165
                                     a + +++e+ +++  ++++l    ++  +    ++ v   +a+e      + e++   ++a  p   e+   d lay  
  gi|121638829|ref|YP_979053.1|  94 HALAARNTEPALVV--TSDAL----RDRFQ----PSRV--AEAAE-----LMSEAA---RVA--PGGYEPMGGDALAYAT 151
                                    **************..76555....22222....2221..11111.....112222...222..222346899******* PP

                                    EE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHH CS
                    AMP-binding 166 YTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkll 245
                                    YTSGTTG PK+++++h+  +++v ++ +++  +l+++d+ l+ + +++++gl  +++++l+ G++ v+ +   +  p++ 
  gi|121638829|ref|YP_979053.1| 152 YTSGTTGPPKAAIHRHADPLTFVDAM-CRKALRLTPEDTGLCSARMYFAYGLGNSVWFPLATGGSAVINSAPVT--PEAA 228
                                    *************************8.88889999*********************************665554..4555 PP

                                    HHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSEC CS
                    AMP-binding 246 lelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvv 324
                                    + l ++++++v++gvP ++ ++++s +++      ++ slr v+++ge+l+  l++++ + fg+ ++l+g G TE +  +
  gi|121638829|ref|YP_979053.1| 229 AILSARFGPSVLYGVPNFFARVIDSCSPD------SFRSLRCVVSAGEALELGLAERLMEFFGGiPILDGIGSTEVGQTF 302
                                    568999******************98898......999****************************************99 PP

                                    EECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEE CS
                    AMP-binding 325 tvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrl 404
                                    +  ++ +++ +lg+ G++lp  e+++v ++ g   ++g+eG l+vrgp ++kgY+++p+      + e +wl T D + +
  gi|121638829|ref|YP_979053.1| 303 V-SNRVDEW-RLGTLGRVLPPYEIRVVAPD-GTTAGPGVEGDLWVRGPAIAKGYWNRPDSPVA--N-E-GWLDTRDRVCI 375
                                    8.7756665.679****************9.9999**********************987644..3.4.6********** PP

                                    ETTSEEEEEEECCCE CS
                    AMP-binding 405 dedGyleivgRkkdl 419
                                    d dG + +  R++d+
  gi|121638829|ref|YP_979053.1| 376 DSDGWVTYRCRADDT 390
                                    *************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1     2e-14     9e-11       1      76 []     402     480 ..     402     480 .. 0.90
   2 ?   -2.0   0.0       1.7   7.5e+03      27      56 ..     650     674 ..     642     701 .. 0.62

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2e-14
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE  +++ +aVaeaaVv+v++ +  ++l af v  +g +     + ++L + +  +l +++vp+++ +vd+lp+t +GK
  gi|121638829|ref|YP_979053.1| 402 EVERLIIEDEAVAEAAVVAVRESTGASTLQAFLVATSGaT-IdgsVMRDLHRGLLNRLSAFKVPHRFAVVDRLPRTPNGK 480
                                    89*********************888********976742.234588999999999***********************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                    ---EEEEEE------HHHHHHHHHHHHT-T CS
                  AMP-binding_C  27 ealvafVvlkdgsealeeeLkahvrkelgp 56 
                                    e lva++    g++   + + +++r+ lg+
  gi|121638829|ref|YP_979053.1| 650 EELVAVIAD--GEK---QRVADRLRALLGT 674
                                    556666554..542...3444444443333 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0     1e-10   4.5e-07       1      67 []     548     615 ..     548     615 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1e-10
                     PP-binding   1 eklrelvaevlgvpleeidpdtd..lfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67 
                                    +++++ +a+ lg p ++ ++d+d  +++lG+DS ++v+l  +l +  g+++p ++ +++ +++ la+yl
  gi|121638829|ref|YP_979053.1| 548 DAVCAEAAKMLGEP-DPWSVDQDlaFSELGFDSQMTVTLCKRLAAVTGLRLPETVGWDYGSISGLAQYL 615
                                    579999******65.454778886689****************************************97 PP

>> DUF4400  Domain of unknown function (DUF4400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.1e-05     0.048     107     152 ..     416     461 ..     410     470 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                        DUF4400 107 vltflvRlavlllwlplflllalvalvDGlvrRdlRrfgagressf 152
                                    + +++vR ++  ++l +fl++   a +DG v+Rdl+r    r s+f
  gi|121638829|ref|YP_979053.1| 416 AAVVAVRESTGASTLQAFLVATSGATIDGSVMRDLHRGLLNRLSAF 461
                                    67899********************************999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 3977.99
//
Query:       gi|121638830|ref|YP_979054.1|  [L=199]
Description: hypothetical protein BCG_2970c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   48.0   0.0    1.6e-12   47.6   0.0    1.1  1  DUF98     p-hydroxybenzoic acid synthase
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.65   10.2   0.1    1.9  2  Plk4_PB1  Polo-like Kinase 4 Polo Box 1


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.8e-16   1.6e-12       3     141 ..      24     173 ..      22     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.8e-16
                                    --S-HHHHHHHHHSS-EEEEEEEEEEEE--H..HHHHHHTS-TT-EEEEEEEEEEE..TTEEEEEEEEEEEGGGS-HH.. CS
                          DUF98   3 gDGsvTrhlelltqekveveliemeaeesee..eeapkeveelkkpllrRqVwlra..ngqklayAeSwwneeeleky.. 76 
                                    + G  Tr l+++   +v v+++++++++ +   +e ++  +   + +l+R + l++  +++ ++ AeS + +++l +   
  gi|121638830|ref|YP_979054.1|  24 ANGTLTRVLNIVADDEVIVQIVKQRIHDVSPklSEFEQLGQVGVGRVLQRYIILKGrnSEHLFVAAESLIAIDRLPAAii 103
                                    679*********************9999877444555555555899*********98666677899*******9976511 PP

                                    ..HHHSSS-HHHHHHHTT--BEEEEEEEEEEE--.HHHHH.HT.SS-EEEEEEEEEEETTEEEEEEEEEE CS
                          DUF98  77 ..lkekdqpiwksLtkerlelfReirglalgead.eLeea.fg.ekgpfwsRhYrlfhkgkpltvirEvF 141
                                      l + + p+++ ++ +++e+f+e  ++ +g+   +L+ + ++ ++ + ++R Yr+++ g+p++v++E F
  gi|121638830|ref|YP_979054.1| 104 trLTQTNDPLGEVMAASHIETFKEEAKVWVGDLPgWLALHgYQnSRKRAVARRYRVISGGQPIMVVTEHF 173
                                    225669*************************99888874324447889********************99 PP

>> Plk4_PB1  Polo-like Kinase 4 Polo Box 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   7.3e-05      0.65      15      51 ..      26      64 ..      14      87 .. 0.78
   2 ?   -0.4   0.0      0.14   1.3e+03      38      75 ..     148     184 ..     142     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.3e-05
                       Plk4_PB1 15 ktkkavvsilesgeVclellkkk..ngeekvvevlriSs 51
                                    t + v++i++++eV+++++k++  + + k++e  ++ +
  gi|121638830|ref|YP_979054.1| 26 GTLTRVLNIVADDEVIVQIVKQRihDVSPKLSEFEQLGQ 64
                                   567789****************96555566666666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                       Plk4_PB1  38 ngeekvvevlriSsdGqeiiiyqpesgkevplndrpse 75 
                                    ++++ v+  +r+ s Gq i+++  +  + v  +d p+e
  gi|121638830|ref|YP_979054.1| 148 SRKRAVARRYRVISGGQPIMVVTEHFLRSV-FRDAPHE 184
                                    567788888999999999999988877775.5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.59
# Mc/sec: 1021.63
//
Query:       gi|121638831|ref|YP_979055.1|  [L=619]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-76  257.0   0.0      3e-76  256.7   0.0    1.1  1  AMP-binding      AMP-binding enzyme
     0.0015   18.8   0.2     0.0029   17.9   0.2    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.041   14.1   0.0       0.12   12.6   0.0    1.8  1  Mur_ligase_C     Mur ligase family, glutamate ligase domain
      0.049   14.1   0.0       0.11   13.0   0.0    1.5  1  DUF4012          Protein of unknown function (DUF4012)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.7   0.0   6.7e-80     3e-76       2     422 ..      48     505 ..      47     506 .. 0.85

  Alignments for each domain:
  == domain 1  score: 256.7 bits;  conditional E-value: 6.7e-80
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                    +++a ++p++ a+ +        g  +t+T+ ++++r+  +A  L    + +gdrVail+p+++e+++a++++l+aG+++
  gi|121638831|ref|YP_979055.1|  48 QKAASQYPNRAAYKFidydtdpAGFTETVTWWQVHRRAMIVAEELWI-YASSGDRVAILAPQGLEYIIAFMGVLQAGLIA 126
                                    7899*********889999*998889*******************97.79****************************** PP

                                    EEEET...TS-HHHHHHHHHHHTESEEE......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCS CS
                    AMP-binding  75 vplnp...tltaeelayiledseakvli......atvdsel.leklleaaakleavklvivldadellkeeelkeeeese 144
                                    vpl     +   e+++ +l+ds +++++      +  + +  ++++++a++  ++  +v+ +da +l+ ++ l       
  gi|121638831|ref|YP_979055.1| 127 VPLPVpqfGIHDERISSALRDSAPSIILttssviD--EVTTyAPHACAAQG--QSAPIVVAVDALDLSSSRAL------- 195
                                    ***988889999****************5432211..11222333333332..33334444443332222111....... PP

                                    CTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHH CS
                    AMP-binding 145 ekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglilell 222
                                           ++ + +  ++ay++YTSG+T  P GV+lsh+n+++n+ +l ++++  ++ k  ++ +s+lp++h++gl+l+++
  gi|121638831|ref|YP_979055.1| 196 -------DPTRFERPSTAYLQYTSGSTRAPAGVVLSHKNVITNCVQL-MSDYigDSEKVPSTPVSWLPFYHDMGLMLGII 267
                                    .......2234566789*****************************8.676753333336777***************** PP

                                    HHHHTT-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHH CS
                    AMP-binding 223 lallsGatvvllpkdaald.pklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspell 300
                                    l++++  t vl+++ a+l+ p+++++l++k+++++  +++  +e  ++  ++ +  ++  dl+++r++++g+e+++ ++l
  gi|121638831|ref|YP_979055.1| 268 LPMINQDTAVLMSPMAFLQrPARWMQLLAKHRAQISSAPNFGFELAVRrTSDDD--MAGLDLGHVRTIVTGAERVNVATL 345
                                    *****************666************************9999554444..6777******************** PP

                                    HHHHHHHTC......EEEEEEEEGGGSSECEE.........................CHCTTTCTSTTS-BEE-TTEEEE CS
                    AMP-binding 301 rffralfge......evlegYGlTEttgvvtv.........................lpleedkkklgsvGkplpgvevk 349
                                    r+f ++f +      ++  +YGl+E+t+ v++                          +   + ++l s+G p +   v+
  gi|121638831|ref|YP_979055.1| 346 RRFTERFAPfnlsetAIRPSYGLAEATVYVATagpgrapksvcfdyqqlsvgqakrtEN-GSEGANLVSYGAP-RASTVR 423
                                    ********9*****99**************7779999999999******9999999544.4555666789999.6779** PP

                                    EE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE..........TCC.EEEEEEEEEEETTSEEEEEEECCC CS
                    AMP-binding 350 ivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds..........egr.wlrTGDlgrldedGyleivgRkkd 418
                                    ivD+et  + p g++Ge++v+g +v  gY+++p++t+ +f +          e + wlrTGDlg++  +G+l+i+gR+k+
  gi|121638831|ref|YP_979055.1| 424 IVDPETRMENPAGTVGEIWVQGDNVGLGYWRNPQQTEATFRArlvtpspgtsE-GpWLRTGDLGVIF-EGELFITGRIKE 501
                                    ****************************************9789999998743.66*********98.7*********** PP

                                    EEEE CS
                    AMP-binding 419 likl 422
                                    l+++
  gi|121638831|ref|YP_979055.1| 502 LLVV 505
                                    9976 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   6.4e-07    0.0029       1      91 [.     507     600 ..     507     602 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.4e-07
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----H..HHHHHHHHHHHHHHHHHHSS--.EEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdel..kelealekkiakklksklgvsv.kvel 76 
                                    G n +P  ie+ ++ei +      i v  +++ ++l   +E+ + g +de   ++l+++++++a+++ ++  ++v +v +
  gi|121638831|ref|YP_979055.1| 507 GANHYPEDIEATIQEITGGR-VVAIAVP-DDRTEKLVTIIELMKrGRTDEEekNRLRTVKREVASAISRSHRLRVaDVVM 584
                                    889************98754.4455555.556777777788877566665422668999**************9659*** PP

                                    E-TT-S----.----- CS
                AMP-binding_C_2  77 vepgtlprse.gKakr 91 
                                    v+pg++p ++ gK +r
  gi|121638831|ref|YP_979055.1| 585 VAPGSIPVTTsGKVRR 600
                                    *******975269887 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05      0.12       8      61 ..     496     540 ..     492     553 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                                    EEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTH CS
                   Mur_ligase_C   8 vgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfh 61 
                                    +g+ + ++v+d  +h p+ ++a+++ +    + +r+++++ p ++   rt++ +
  gi|121638831|ref|YP_979055.1| 496 TGRIKELLVVDGANHYPEDIEATIQEI----TGGRVVAIAVP-DD---RTEK-L 540
                                    556566555555***************....99********7.66...4443.3 PP

>> DUF4012  Protein of unknown function (DUF4012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05      0.11      49     123 ..      48     121 ..      30     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                        DUF4012  49 vkktpvlp.ltpeeaalygerlglylrdanltpdfpraaelakelweaqtggkvDgviavdpvalsalleatGpvt 123
                                     k+ + +p   + +   y++ ++ + + +++++   ra+ +a+elw +++  + D v ++ p+ l+++++ +G ++
  gi|121638831|ref|YP_979055.1|  48 QKAASQYPnRAAYKFIDYDTDPAGFTETVTWWQVHRRAMIVAEELWIYAS--SGDRVAILAPQGLEYIIAFMGVLQ 121
                                    44455555333444455667888899************************..67*****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.55
# Mc/sec: 3405.28
//
Query:       gi|121638832|ref|YP_979056.1|  [L=381]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-47  162.2   5.3    2.5e-47  161.8   5.3    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   5.3   1.4e-51   2.5e-47      36     312 ..      34     346 ..      21     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 1.4e-51
                 Bac_luciferase  36 Gfdavwvaehhggpgga.....................ldaftllaala.aaTerirlgtavtplytrhPavlAqqaatL 93 
                                    G d+ wv++h++    +                      +++t+l+ la +  +r+rlg++vt + +r+Pav+Aq+aatL
  gi|121638832|ref|YP_979056.1|  34 GADSYWVGDHLNALVPRsiatseylgiaakfvpkidanYEPWTMLGNLAfGLPSRLRLGVCVTDAGRRNPAVTAQAAATL 113
                                    77778888887754333677778888888888888888********9986889*************************** PP

                 Bac_luciferase  94 dhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrg.eev.dfeGeffsvkgalllprpgqgpiP.vy 170
                                    + l++GR++lg+g g+++   + +Gv++ +++ar++E++  +r+lw++ +e  + e  +f +++al   +p  g  P ++
  gi|121638832|ref|YP_979056.1| 114 HLLTRGRAILGIGVGEREGN-EPYGVEWTKPVARFEEALATIRALWNSnGELiSRESPYFPLHNALFDLPPYRGKWPeIW 192
                                    ********************.*************************5555555*********6666555565666999** PP

                 Bac_luciferase 171 vaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagld 249
                                    vaa++p++l+ ++r+ad++++    +p ++ +++e +r++a+ agrdp +i+ ++ + +i +++++++++ ++  + +++
  gi|121638832|ref|YP_979056.1| 193 VAAHGPRMLRATGRYADAWIPIVvVRPSDYSRALEAVRSAASDAGRDPMSITPAAVRGIITGRNRDDVEEALESVVVKMT 272
                                    **************************************************************999999999977777776 PP

                 Bac_luciferase 250 ...........fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagv 312
                                               +  +   ga++ + ++ i+++ d++   + a+ vp++l+++ +  Gtp++v++++a++++ g+
  gi|121638832|ref|YP_979056.1| 273 algvpgeawarHGVEHPMGADFSGVQDIIPQTMDKQTVLSYAAKVPAALMKEVVFSGTPDEVIDQVAEWRDHGL 346
                                    77778998874333333466677777899*****************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:01.18
# Mc/sec: 973.41
//
Query:       gi|121638833|ref|YP_979057.1|  [L=270]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-24   84.3   0.0    1.3e-23   83.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.5e-20   72.5   0.0      6e-20   71.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.3e-15   56.2   0.0    4.1e-15   55.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.8e-13   50.0   0.0    6.6e-13   49.2   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    9.2e-10   38.2   0.0    1.3e-09   37.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-07   31.5   0.0    1.9e-07   31.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.3e-05   22.3   0.0    4.9e-05   22.1   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    0.00028   20.5   0.0    0.00044   19.9   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00068   19.6   0.0      0.001   19.0   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.068   12.7   0.0       0.15   11.6   0.0    1.5  1  MTS              Methyltransferase small domain
       0.17   10.9   0.0       0.23   10.5   0.0    1.3  1  Pox_MCEL         mRNA capping enzyme
       0.18   11.5   0.0       0.28   10.9   0.0    1.4  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   8.7e-27   1.3e-23       1      94 [.      85     178 ..      85     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 8.7e-27
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                    L+v cG G  a +l+++   a+++g+Dl+++ +kl+k++ + +g  ++fv++dae+lpf d+sfD+v+  e+ h  +  +
  gi|121638833|ref|YP_979057.1|  85 LEVSCGHGGGASYLTRTLhpASYTGLDLNQAGIKLCKKRHRLPG--LDFVRGDAENLPFDDESFDVVLNVEASHCYPHFR 162
                                    899************88899************************..9********************************* PP

                                    HHHHHHHHHEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGll 94 
                                    ++l+e++RvL+pgG++
  gi|121638833|ref|YP_979057.1| 163 RFLAEVVRVLRPGGYF 178
                                    **************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0     4e-23     6e-20       1      97 []      84     176 ..      84     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 4e-23
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vL++ cG+G  + +l + l+ a++tg+D++++ ++ +++r++   + ++fv+gdae+lpf+d+sfD+v+ + a h+++  
  gi|121638833|ref|YP_979057.1|  84 VLEVSCGHGGGASYLTRTLHPASYTGLDLNQAGIKLCKKRHR--LPGLDFVRGDAENLPFDDESFDVVLNVEASHCYP-- 159
                                    9******************88********************5..458***********************98866665.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    + +++l+e+ rvL+pgG
  gi|121638833|ref|YP_979057.1| 160 HFRRFLAEVVRVLRPGG 176
                                    799*************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   2.7e-18   4.1e-15       4     127 ..      81     206 ..      78     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.7e-18
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    g++vl++ CG G  +  l  +    a ++G+D ++  i+l++++ +   l  + F +gd+e+l+  + de+fD++l  e+
  gi|121638833|ref|YP_979057.1|  81 GKQVLEVSCGHGGGASYLT-RTLHPASYTGLDLNQAGIKLCKKRHR---LPGLDFVRGDAENLP--FDDESFDVVLNVEA 154
                                    789***************9.55566******************866...55556**********..************** PP

                Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr.......llaelp.akveeesk 127
                                     ++ ++   +l e+ rvl+pgg++  +d r       ++a+l+   +++ s+
  gi|121638833|ref|YP_979057.1| 155 SHCYPHFRRFLAEVVRVLRPGGYFPYADLRpnneiaaWEADLAaTPLRQLSQ 206
                                    *************************999997777666555555533333333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   4.4e-16   6.6e-13       1      99 []      85     178 ..      85     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 4.4e-16
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le+ cG G  +++l + l++++ytg+D++++ i +  +k ++  +++  +v+ +a++l  +d+  sfD+v+  ++ h+ +
  gi|121638833|ref|YP_979057.1|  85 LEVSCGHGGGASYLTRTLHPASYTGLDLNQAGI-KLCKKRHRLPGLD--FVRGDAENLPFDDE--SFDVVLNVEASHCYP 159
                                    8********************************.5555555555555..66666666666665..*************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    + r++l+++ ++L+pgG++
  gi|121638833|ref|YP_979057.1| 160 HFRRFLAEVVRVLRPGGYF 178
                                    *****************85 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   8.9e-13   1.3e-09      44     149 ..      77     178 ..      68     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.9e-13
                                    -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEE CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvs 123
                                     ++ g++vl+v++G g  a  l+++++     ++lD+n+  +k  +k+ +  g   ++f+ ++ae+Lpf+d+sfDvv   
  gi|121638833|ref|YP_979057.1|  77 VDLGGKQVLEVSCGHGGGASYLTRTLHPA-SYTGLDLNQAGIKLCKKRHRLPG---LDFVRGDAENLPFDDESFDVVLNV 152
                                    567899******************99886.5789*************999877...79******************9988 PP

                                    S-GGG-S-HHHHHHHHHHHEEEEEEE CS
                Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrl 149
                                          +   + L e+ rvl+pGG +
  gi|121638833|ref|YP_979057.1| 153 EASHCYPHFRRFLAEVVRVLRPGGYF 178
                                    89999*******************86 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.3e-10   1.9e-07      14     119 ..      71     182 ..      56     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                Methyltransf_23  14 erllpk.lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                    +r+++  +  g+ vL++ cG+G  +++l +  +  s+tg Dl+ + +++ +     +   ++  d+++ ++++++fd++ 
  gi|121638833|ref|YP_979057.1|  71 HRTATQvDLGGKQVLEVSCGHGGGASYLTRTLHpaSYTGLDLNQAGIKLCKkrhRLPGLDFVRGDAENLPFDDESFDVVL 150
                                    5555333666889***************6654444********999999888786666677777777888899******* PP

                Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllse 119
                                    + e  +  p++ + l+ + + l+pgGy+   +
  gi|121638833|ref|YP_979057.1| 151 NVEASHCYPHFRRFLAEVVRVLRPGGYFPYAD 182
                                    ***************************96666 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.3e-08   4.9e-05     116     219 ..      79     182 ..      43     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.3e-08
                Methyltransf_29 116 gkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRg.vpailavlg.tkrlpyPsrsfdli...hCsrC 190
                                       ++vl+v Cg    ga  l r +   s +  D  +a +++   R  +p +  v g ++ lp+  +sfd++     s C
  gi|121638833|ref|YP_979057.1|  79 LGGKQVLEVSCGHGG-GASYLTRTLHPASYTGLDLNQAGIKLCKKRHrLPGLDFVRGdAENLPFDDESFDVVlnvEASHC 157
                                    44579*******986.7888899********************999548998888873578*********9633368899 PP

                Methyltransf_29 191 ridwteedgilllevdRvlRpgGyfvlsa 219
                                      ++ +    +l ev RvlRpgGyf ++ 
  gi|121638833|ref|YP_979057.1| 158 YPHFRR----FLAEVVRVLRPGGYFPYAD 182
                                    888875....8**************8875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     3e-07   0.00044      14     101 ..      81     171 ..      71     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3e-07
                           MetW  14 gsrvldlGcGdGellellkeekq.vdgrGleldeegvaecvak....Glsviqgdldkdlenfedksfdyvvlsqtlqat 88 
                                    g +vl++ cG+G   ++l  + +  +  Gl+l+++g++ c ++    Gl  ++gd+++    f+d+sfd+v+   +    
  gi|121638833|ref|YP_979057.1|  81 GKQVLEVSCGHGGGASYLTRTLHpASYTGLDLNQAGIKLCKKRhrlpGLDFVRGDAEN--LPFDDESFDVVLNVEASHCY 158
                                    578*********9999998876614557************99888889*******986..479*******9988888888 PP

                           MetW  89 rnpkevldellri 101
                                     + ++ l e++r+
  gi|121638833|ref|YP_979057.1| 159 PHFRRFLAEVVRV 171
                                    8888999998888 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.7e-07     0.001     109     160 ..     132     184 ..     125     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.7e-07
                                    EES-TTS-S--TT-EEEEEEE.S---SS-HHHHHHHHHHHEEEEEEEEEEEEG CS
                 Methyltransf_8 109 vacdlakvPledesvdvavfc.lslmgtnladflkeanrvlkvGGllkvaevk 160
                                    v  d  ++P +des dv++    s     ++ fl e+ rvl++GG++  a+++
  gi|121638833|ref|YP_979057.1| 132 VRGDAENLPFDDESFDVVLNVeASHCYPHFRRFLAEVVRVLRPGGYFPYADLR 184
                                    567999***********99763688899******************9988876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.8e-05      0.15      32     133 ..      81     176 ..      73     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STTT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfhag 110
                                     ++vl + cG G  +  l +    a+ t +d + + ++++k+  +  +l  ++v  d+ +  +++++fd+++       +
  gi|121638833|ref|YP_979057.1|  81 GKQVLEVSCGHGGGASYLTRTLHPASYTGLDLNQAGIKLCKKRHRLPGL--DFVRGDAENlPFDDESFDVVLN-----VE 153
                                    468**************************************99998887..5666666552456789998874.....23 PP

                                    CHCHHHHHHHHHHHHHHHEEEEE CS
                            MTS 111 katelavaeeliaeAkeaLkegG 133
                                        +   ++++ae  ++L++gG
  gi|121638833|ref|YP_979057.1| 154 ASHCYPHFRRFLAEVVRVLRPGG 176
                                    33335556666666666666666 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.23      51     107 ..      67     124 ..      64     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                       Pox_MCEL  51 iseyasktkldesnklkvLdldcgkGgDLeKy.ekgeIsklvatDiaeesieeckeRY 107
                                    i++y + +++ +    +vL+++cg Gg      +  + +++ + D +++ i+ ck+R 
  gi|121638833|ref|YP_979057.1|  67 INLYHRTATQVDLGGKQVLEVSCGHGGGASYLtRTLHPASYTGLDLNQAGIKLCKKRH 124
                                    8899999999999999**********9877651456789******************8 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.28      20      60 ..      75     115 ..      56     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                         DUF938  20 sylakttervLEiasGtGqHAvffApalpnlkwqpsdqdee 60 
                                     +++  +++vLE++ G G  A ++  +l ++ +   d ++ 
  gi|121638833|ref|YP_979057.1|  75 TQVDLGGKQVLEVSCGHGGGASYLTRTLHPASYTGLDLNQA 115
                                    467777889***********************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1468.99
//
Query:       gi|121638834|ref|YP_979058.1|  [L=418]
Description: hypothetical protein BCG_2974 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-09   38.3   0.0    2.2e-09   37.6   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.066   13.1   0.0    1.6  2  NAD_binding_10   NAD(P)H-binding
       0.11   12.4   0.3        0.5   10.3   0.1    1.9  2  KR               KR domain


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   3.7e-13   2.2e-09       1     128 [.      10     135 ..      10     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.7e-13
                                    EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE-...-TTTHHHHHHHHHTTSSEEEE- CS
                Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial...daenyeavLaallkegdlvvnl 76 
                                    +++ Ga G+ G+ +ae la +++  a+i++a+rs e+l+ +   +lg+++    l   da+++   L+a+ + +++v+  
  gi|121638834|ref|YP_979058.1|  10 IVLYGAtGFSGKLTAEHLAHSGST-ARIALAGRSSERLRGVRM-MLGPNAADWPLilaDASQPLT-LEAMAARAQVVLTT 86 
                                    7999******************98.6***********988865.567777766551115555555.9************* PP

                                    SSGG..GHHHHHHHHHHHT-EEEE.SS-BCGCCSCHCCSHHHHHTHHHHHHCTSE CS
                Sacchrp_dh_NADP  77 sppi..ssldvlkaCietgvhyvd.tsiskeertnyalreavlklkekakeagvt 128
                                    ++p+  ++l++++aC+++g++y d t       ++ + r+ +  ++++a++ g+ 
  gi|121638834|ref|YP_979058.1|  87 VGPYtrYGLPLVAACAKAGTDYADlT-G-----ELMFCRNSIDLYHKQAADTGAR 135
                                    ****9*******************63.4.....3677888888888888877765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.066       1      88 [.      14     104 ..      14     124 .. 0.81
   2 ?   -3.7   0.0       1.5   9.2e+03     110     136 ..     349     375 ..     343     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                    TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCH CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaele.....aeeglevvegdvtdvedlaealkgadaVvsalggggkd 74 
                                    GAtG  G+l +++l+++g   ++ +  R++e+l  ++     +++   ++ +d++++ +l++  + a++V++++g+  + 
  gi|121638834|ref|YP_979058.1|  14 GATGFSGKLTAEHLAHSGsTARIALAGRSSERLRGVRmmlgpNAADWPLILADASQPLTLEAMAARAQVVLTTVGPYTR- 92 
                                    9*****************777777778******9766554445567779************************997543. PP

                                    HHHHHHHHHHHHHC CS
                 NAD_binding_10  75 eegaknivdaakea 88 
                                          +v+a+ +a
  gi|121638834|ref|YP_979058.1|  93 --YGLPLVAACAKA 104
                                    ..344455555554 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                                    HHHHHHCCHHHHHHHHHHHHHHHHSSS CS
                 NAD_binding_10 110 gewnkellkaylaakraaeellrasgl 136
                                    g  ++ ++++ ++a +  + ll +sgl
  gi|121638834|ref|YP_979058.1| 349 GARYRATFAHNVDAYKSTAVLLAQSGL 375
                                    556677888889999999999999987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.3e-05       0.5       4      37 ..      11      45 ..      10      87 .. 0.73
   2 ?   -0.7   0.0       0.2   1.2e+03      76      99 ..     380     404 ..     358     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.3e-05
                                   EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..- CS
                             KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaa 37
                                   ++ G++G  G+ +a++la++g  ++++l +Rs++ 
  gi|121638834|ref|YP_979058.1| 11 VLYGATGFSGKLTAEHLAHSGsTARIALAGRSSER 45
                                   578******************999********533 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                    HHHS.S---EEEE---------TTT CS
                             KR  76 kaee.ppikGvihaAgvlrdkllee 99 
                                    +++  ++++Gv+  A ++ d+ll++
  gi|121638834|ref|YP_979058.1| 380 DRDRlAELRGVLTPAAAMGDALLAR 404
                                    4444589************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2592.24
//
Query:       gi|121638835|ref|YP_979059.1|  [L=241]
Description: hypothetical protein BCG_2975c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-11   43.7   0.0    5.6e-11   43.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.9e-09   38.0   0.0    3.2e-09   37.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.9e-09   36.3   0.0    1.1e-08   35.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    9.1e-08   32.1   0.0      1e-07   31.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    3.6e-06   26.1   0.0    4.6e-06   25.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0073   16.1   0.0      0.022   14.6   0.0    1.7  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.052   12.6   0.0      0.067   12.2   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.18   11.3   0.0       0.24   10.9   0.0    1.1  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.21   11.3   0.0       0.46   10.2   0.0    1.6  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   2.8e-14   5.6e-11       1      86 [.      43     124 ..      43     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.8e-14
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssgalhhlsd 79 
                                    vL++G+G G++t+ +++r+  +kv+++++  e l+ +r+r+  +++nv++ + d+  dlp e++++D+v++ g+l hls+
  gi|121638835|ref|YP_979059.1|  43 VLEVGAGIGDHTQFFLDRG--CKVLCTEPRGENLDVIRQRFG-SNPNVTVDHLDLdGDLPAEAHQYDVVYCYGVLYHLSR 119
                                    9*****************5..********************6.569*********777*************888999886 PP

                                    HHHHHHH CS
                Methyltransf_25  80 edlekal 86 
                                    +   +al
  gi|121638835|ref|YP_979059.1| 120 PA--EAL 124
                                    64..333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.6e-12   3.2e-09       1      82 [.      44     125 ..      44     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.6e-12
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC.CTSS-TT-EEEEEEES-CCC-CCHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadae.klpfednsfDlvvssevlhhvedpek 79 
                                    L+vG+G G +++ + +rg++v+++++  e l++ +++   +++ v++ + d+  +lp e +++D+v+++ vl h+ +p++
  gi|121638835|ref|YP_979059.1|  44 LEVGAGIGDHTQFFLDRGCKVLCTEPRGENLDVIRQRFGSNPN-VTVDHLDLDgDLPAEAHQYDVVYCYGVLYHLSRPAE 122
                                    89**************************************996.88888888867************************9 PP

                                    HHH CS
                Methyltransf_11  80 alk 82 
                                    al+
  gi|121638835|ref|YP_979059.1| 123 ALA 125
                                    997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   5.5e-12   1.1e-08       1      87 [.      44     125 ..      44     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.5e-12
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le+G+G G+ ++ +l++  +++++++++  + ++  ++++ ++ n  +++++l+ +  +   + +++D+v++ +vl hl 
  gi|121638835|ref|YP_979059.1|  44 LEVGAGIGDHTQFFLDR--GCKVLCTEPRGENLDVIRQRFGSNPNVTVDHLDLDGDLPA---EAHQYDVVYCYGVLYHLS 118
                                    8****************..**************99999999999766555555544433...338**************9 PP

                Methyltransf_12  81 direvld 87 
                                     ++e+l+
  gi|121638835|ref|YP_979059.1| 119 RPAEALA 125
                                    9998886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   5.3e-11     1e-07      15     107 ..      32     129 ..      18     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.3e-11
                Methyltransf_23  15 rllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                     +l+ +  +++vL++G+G G  ++ + ++g++v   +++ e+ + ++     ++   +++     + + ++ ++d++++ 
  gi|121638835|ref|YP_979059.1|  32 ATLGLDLGNKSVLEVGAGIGDHTQFFLDRGCKVLCTEPRGENLDVIRqrfgsNPNVTVDHLDLDGDLPAEAHQYDVVYCY 111
                                    3444466689******************************99999987666644444444444456777888******** PP

                Methyltransf_23  90 evlehvpdppellrqiat 107
                                     vl+h+  p+e+l+ + +
  gi|121638835|ref|YP_979059.1| 112 GVLYHLSRPAEALAWMCD 129
                                    *************99876 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.3e-09   4.6e-06     113     232 ..      37     153 ..      22     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                                    --TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GG.GS-T.---EEEEEEES CS
                 Methyltransf_9 113 dlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgie.qlpe.leafdtvfsmG 190
                                    dl ++++l+vG g G h    + +g k v+  +P       ++ +r+  g++ ++++  l ++ +lp+  + +d+v+  G
  gi|121638835|ref|YP_979059.1|  37 DLGNKSVLEVGAGIGDHTQFFLDRGCK-VLCTEPRGEN---LDVIRQRFGSNPNVTVDHLDLDgDLPAeAHQYDVVYCYG 112
                                    789***************999999986.7889999875...5889999999988887778886479987999******** PP

                                    -GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-.BSS-TT-EE-- CS
                 Methyltransf_9 191 vlyhrrsPldhllqlkdqlvkgGelvletlv.ieGdenavlvP 232
                                    vlyh + P + l  + d  v    l+let v   G+ +  lv 
  gi|121638835|ref|YP_979059.1| 113 VLYHLSRPAEALAWMCDRAVD--LLLLETCVsYSGEDEPFLVS 153
                                    *************99998765..68999987246777666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.022       4      98 ..      40     128 ..      37     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsn 81 
                                    +++vl++G+G G+ t  + ++   +++v   +   e + + r++    g++ nv++ + d    l+   e  ++D++ + 
  gi|121638835|ref|YP_979059.1|  40 NKSVLEVGAGIGDHTQFFLDR---GCKVLCTEPRGENLDVIRQR---FGSNpNVTVDHLDLDGdLP--AEAHQYDVVYCY 111
                                    788999999999999999977...57799999999999998886...77778**********99**..67799******* PP

                Methyltransf_31  82 evlnaladpdkileeie 98 
                                    +vl++l+ p+++l  ++
  gi|121638835|ref|YP_979059.1| 112 GVLYHLSRPAEALAWMC 128
                                    **********9998665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05     0.067      31      84 ..      40      93 ..      13     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                   TSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                         RrnaAD 31 kltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqD 84
                                   ++ vle+g+G G  T+ +++r  +v   E + + + + ++++ ++++++v h D
  gi|121638835|ref|YP_979059.1| 40 NKSVLEVGAGIGDHTQFFLDRGCKVLCTEPRGENLDVIRQRFGSNPNVTVDHLD 93
                                   678**********************************************97776 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.24      56     136 ..      40     118 ..      25     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                Methyltransf_PK  56 vkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglq.eftPeegrYdliWiqWcvgh 134
                                    +k +l++GaGiG  t+ +L +   kv   ep  + l+ ++++++++  +v+ v  + l+ +   e+++Yd++++  ++ h
  gi|121638835|ref|YP_979059.1|  40 NKSVLEVGAGIGDHTQFFLDR-GCKVLCTEPRGENLDVIRQRFGSNP-NVT-VDHLDLDgDLPAEAHQYDVVYCYGVLYH 116
                                    6789**********9987766.568999****************944.433.4445666155556899*******99999 PP

                Methyltransf_PK 135 Lt 136
                                    L+
  gi|121638835|ref|YP_979059.1| 117 LS 118
                                    96 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.46      26      45 ..      40      59 ..      24     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                         DUF938 26 tervLEiasGtGqHAvffAp 45
                                   ++ vLE+++G G+H  ff  
  gi|121638835|ref|YP_979059.1| 40 NKSVLEVGAGIGDHTQFFLD 59
                                   3459*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1592.75
//
Query:       gi|121638836|ref|YP_979060.1|  [L=321]
Description: hypothetical protein BCG_2976c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-15   57.7   0.0    1.9e-15   57.3   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain
  ------ inclusion threshold ------
       0.02   13.8   0.0      0.027   13.3   0.0    1.1  1  Peptidase_M35    Deuterolysin metalloprotease (M35) family
        0.1   13.3   0.0       0.18   12.5   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
       0.14   11.9   0.0        0.2   11.4   0.0    1.2  1  Met_10           Met-10+ like-protein
       0.14   12.0   0.1       0.41   10.5   0.0    1.8  1  T2SSM_b          Type II secretion system (T2SS), protein M s


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   5.2e-19   1.9e-15       1     172 [.     133     290 ..     133     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 5.2e-19
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg.gkyfpfavgdtn 79 
                                    dvGan+g     ++      + ++ v+a+EP p    +  +l+an   +a +  ++ + ++  ++++  +   f v  ++
  gi|121638836|ref|YP_979060.1| 133 DVGANVG-----IHSL--AWARLAPVVALEPAPG---THSRLEAN---VAANGLQDRIRTLRTAAGDaVGEVDFFVAADS 199
                                    9******.....5554..346799**********...********...99999999999998888777666666666666 PP

                Methyltransf_21  80 gfstssvlg.gedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefetel 158
                                     fs+    g ++ ++ ++vp++tld +  e  +  + llkiDvEG E  v+ Ga ++l+r +p l+ vE+ + ++  +++
  gi|121638836|ref|YP_979060.1| 200 AFSSLNDTGrIRIRERTRVPCTTLDALAAEL-PLPVGLLKIDVEGLERAVIAGAAELLRRDRPVLL-VEIYGGAA-SNPD 276
                                    6666654447999**************9999.899******************************9.***98763.3467 PP

                Methyltransf_21 159 fdeirqflrecgyr 172
                                    +++ ++ +r +gy+
  gi|121638836|ref|YP_979060.1| 277 PERTIADIRAYGYE 290
                                    77777778888886 PP

>> Peptidase_M35  Deuterolysin metalloprotease (M35) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-06     0.027      92     174 ..     171     258 ..     159     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-06
                                    XXXXXXXXXX.XXXXXXX.XXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Peptidase_M35  92 eGlteealtt.laaGetl.edefdiast...sdlseGGavtirsdGfvpivtdgkvtGyipyksneleievdaakaaavt 166
                                    +Gl +   t   aaG+++ e +f +a+    s l + G + ir    vp +t ++++  +p     l+i+v++ + a ++
  gi|121638836|ref|YP_979060.1| 171 NGLQDRIRTLrTAAGDAVgEVDFFVAADsafSSLNDTGRIRIRERTRVPCTTLDALAAELPLPVGLLKIDVEGLERAVIA 250
                                    5555443332135677663678889876112567889******************************************9 PP

                                    XXXXXXXX CS
                  Peptidase_M35 167 kalklldr 174
                                     a +ll r
  gi|121638836|ref|YP_979060.1| 251 GAAELLRR 258
                                    99988876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05      0.18       1      70 [.     131     196 ..     131     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs 70 
                                    +Ld+G+  G ++la+a+    a v++++++++   + +++++++gl  +++ ++  a d     g++D+ v+
  gi|121638836|ref|YP_979060.1| 131 ILDVGANVGIHSLAWARL---APVVALEPAPGTHSRLEANVAANGLqdRIRTLRTAAGDA---VGEVDFFVA 196
                                    8***************98...79******************9999877666665554433...244555555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.6e-05       0.2      98     158 ..     125     182 ..     112     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                                    --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES CS
                         Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpile 158
                                      ++  ++dv A +G ++++ a+      v+a +  P +   l+ n++ N ++++++++ +
  gi|121638836|ref|YP_979060.1| 125 LYPDRCILDVGANVGIHSLAWAR---LAPVVALEPAPGTHSRLEANVAANGLQDRIRTLRT 182
                                    5677889***************8...56799************************998765 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.41      11      69 ..     165     228 ..     160     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                        T2SSM_b  11 taslagaalqqrvralvsaaggsltssqvlpageegk.....vrriavrvslegeleaLqklLa 69 
                                    +a++a++ lq+r+r+l +aag  + ++ +  a   +       +ri++r +++++ + L +l a
  gi|121638836|ref|YP_979060.1| 165 EANVAANGLQDRIRTLRTAAGDAVGEVDFFVAADSAFsslndTGRIRIRERTRVPCTTLDALAA 228
                                    689******************9999988877665544567778888888888888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2383.66
//
Query:       gi|121638837|ref|YP_979061.1|  [L=243]
Description: hypothetical protein BCG_2977 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-16   60.3   0.0    2.9e-16   60.0   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.6e-20   2.9e-16       1     171 [.      45     214 ..      45     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.6e-20
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranll........tlavgndvglyelivegksg..gky 70 
                                    dvGan g  ++ a l+  +++ +g+++++EP+      f  l+   +        + a+g+++g+++  ++g++g  ++ 
  gi|121638837|ref|YP_979061.1|  45 DVGANSG--QYAAGLR--RAAYKGRIVSFEPLSG---PFTILESKAStdplwdcrQHALGDSDGTVTINIAGNAGqsSSV 117
                                    9******..7777775..689**********999...666665444467799999******************9999999 PP

                Methyltransf_21  71 fpfavgdtngfstssvlggedaryievpvvtldsfleei.kksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvh 149
                                    +p+  + +n f  + ++     +++e +  +lds+  e+ + + + +lk+Dv+G+E +vL G++ +++ + + +  +E +
  gi|121638837|ref|YP_979061.1| 118 LPMLKSHQNAFPPANYV-----GTQEASIHRLDSVAPEFlGMNGVAFLKVDVQGFEKQVLAGGKSTIDDHCVGMQ-LELS 191
                                    99999999999999755.....9********************************************99888886.9*** PP

                Methyltransf_21 150 kfk.efetelfdeirqflrecgy 171
                                    + + +++++l  e +++  ++g+
  gi|121638837|ref|YP_979061.1| 192 FLPlYEGGMLIPEALDLVYSLGF 214
                                    *******9999999998888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1724.88
//
Query:       gi|121638838|ref|YP_979062.1|  [L=275]
Description: glycosyl transferase family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-24   85.3   0.0    1.3e-23   83.6   0.0    1.8  2  Glycos_transf_2  Glycosyl transferase family 2
    3.5e-14   53.2   0.0    4.2e-14   53.0   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.7e-06   26.6   0.0    7.3e-06   25.6   0.0    1.5  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.019   15.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      0.026   15.0   0.1       0.13   12.8   0.0    2.1  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   3.7e-27   1.3e-23       1     122 [.      26     148 ..      26     202 .. 0.88
   2 ?   -1.0   0.0      0.38   1.4e+03       2      17 ..     213     228 ..     212     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 3.7e-27
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    s++ipt N ++ l+++l+s+++q +  dfe+++vD gStDet +i+  +a + +   +i+r+  +G   a+n+g++ atg
  gi|121638838|ref|YP_979062.1|  26 SIIIPTLNVAAVLPACLDSIARQ-TCGDFELVLVDGGSTDETLDIANIFAPNLGERLIIHRDTDQGVYDAMNRGVDLATG 104
                                    8**********************.***************************999999999999***************** PP

                                    SEEEEEESSEEE-TT.HHHHHHHHHHH..TTCEEEEEEEEEECC CS
                Glycos_transf_2  81 dyilflDaDdepdpd.wleklvealekd.gadvvlgqrprifge 122
                                     ++lfl aDd   +  +l ++++++ ++ + d+v+g +  ++ +
  gi|121638838|ref|YP_979062.1| 105 TWLLFLGADDSLYEAdTLARVAAFIGEHePSDLVYGDVIMRSTN 148
                                    *********9987776*********9984556666666655554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                                    EEEEESS-TTTHHHHH CS
                Glycos_transf_2   2 vviptyNeektlletl 17 
                                    vv+ +yNe   l +t+
  gi|121638838|ref|YP_979062.1| 213 VVVASYNEFGGLSNTI 228
                                    89******88777776 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.2e-17   4.2e-14       2     128 ..      23     146 ..      22     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                    +++++++pt+n ++vl ++l+s+++q+ +++e+v+v+ +s++etl+ a  +a +l+  r+  ++++ + g  +  +a+n+
  gi|121638838|ref|YP_979062.1|  23 PMFSIIIPTLNVAAVLPACLDSIARQTCGDFELVLVDGGSTDETLDIANIFAPNLGE-RLI-IHRDTDQG--V-YDAMNR 97 
                                    579*********************************************999999988.765.56666555..4.599*** PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvv.ePdtlkrllqff.ltpkvgavgtpvflln 128
                                    +++ ++++++l++ +D+ + e dtl+r+++f+ +++  + v+++v ++ 
  gi|121638838|ref|YP_979062.1|  98 GVDLATGTWLLFLGADDSLyEADTLARVAAFIgEHEPSDLVYGDVIMRS 146
                                    **************999999*************999*****99987764 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     2e-09   7.3e-06      27     106 ..      50     129 ..      26     149 .. 0.80
   2 ?   -2.4   0.0      0.71   2.5e+03     175     199 ..     178     200 ..     167     239 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2e-09
                Glyco_tranf_2_2  27 deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc.fissDkfekilkl 105
                                      ++el++vd+gS++++l  + +i + nl   l    d+  +   a NrG++ a +  +lFl aD+ ++  D +++++ +
  gi|121638838|ref|YP_979062.1|  50 CGDFELVLVDGGSTDETL-DIANIFAPNLGERLIIHRDTDQGVYDAMNRGVDLATGTWLLFLGADDsLYEADTLARVAAF 128
                                    4589************77.68999999988755555588888889******************98747899999999876 PP

                Glyco_tranf_2_2 106 i 106
                                    i
  gi|121638838|ref|YP_979062.1| 129 I 129
                                    6 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.71
                Glyco_tranf_2_2 175 flevGGyDErfrGhgaEDfdlllRl 199
                                    f  +G y+ r+      D+d+ +R 
  gi|121638838|ref|YP_979062.1| 178 FGTIGPYNLRY--RVLADWDFNIRC 200
                                    55555555555..334445544443 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   5.2e-06     0.019      55     127 ..      74     151 ..      31     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                                    HTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHT......SSEEEEESSSEE CS
                   NTP_transf_3  55 larlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasg......advvvptyeger 127
                                    ++ lg r++  +d ++g   ++  +++ a   +++l+l +D  l+++++++r++a + +++      +dv++ +++ ++
  gi|121638838|ref|YP_979062.1|  74 APNLGERLIIHRDTDQGVYDAMNRGVDLA-TGTWLLFLGADDSLYEADTLARVAAFIGEHEpsdlvyGDVIMRSTNFRW 151
                                    34568889999999************987.9************************998777544555555555555555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05      0.13       2      89 ..      33     121 ..      32     129 .. 0.68
   2 ?   -0.9   0.0      0.68   2.5e+03      64      88 ..     141     165 ..     131     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                Glyco_tranf_2_4   2 neadiLpeflahhlalgf.d.rilvydndstDgtrailkel.pevk...llhvdksyederrqvellkalla..ryaead 73 
                                    n a++Lp++l+ + +  + d +++++d +stD+t +i     p++    ++h d++         +++a+++  + a ++
  gi|121638838|ref|YP_979062.1|  33 NVAAVLPACLDSIARQTCgDfELVLVDGGSTDETLDIANIFaPNLGerlIIHRDTDQG-------VYDAMNRgvDLATGT 105
                                    56889999999987776633469***********999977447755453444444332.......444444411235889 PP

                Glyco_tranf_2_4  74 wvlvvDaDEflvvpds 89 
                                    w+l++ aD  l   d 
  gi|121638838|ref|YP_979062.1| 106 WLLFLGADDSLYEADT 121
                                    ********99887774 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.68
                Glyco_tranf_2_4  64 allaryaeadwvlvvDaDEflvvpd 88 
                                     ++ r  + +w  ++D D +l+ ++
  gi|121638838|ref|YP_979062.1| 141 DVIMRSTNFRWGGAFDLDRLLFKRN 165
                                    5666778899999*****9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1981.52
//
Query:       gi|121638839|ref|YP_979063.1|  [L=366]
Description: glycosyl transferase family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2390.14
//
Query:       gi|121638840|ref|YP_979064.1|  [L=245]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-72  242.5   0.0    3.9e-72  242.3   0.0    1.0  1  CmcI             Cephalosporin hydroxylase
      2e-05   25.5   0.0      4e-05   24.6   0.0    1.5  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.0   4.4e-76   3.9e-72       3     205 ..      50     244 ..      48     245 .] 0.98

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 4.4e-76
                           CmcI   3 ylykfswlgvpiiklpqDlvayQeliwelkPdliietGiahGGsalfsasllallkskrkvlaididireknrqaieahp 82 
                                    +++k++++g++++k+++D+++yQe+++el+P+l+ie+G+++GGsa+++a++++++++ +kvl++d ++++ +++a+++  
  gi|121638840|ref|YP_979064.1|  50 VWTKTTYMGINCWKSVSDMWNYQEILSELQPSLVIEFGTRYGGSAVYFANIMRQIGQPFKVLTVDNSHKALDPRARRE-- 127
                                    799**********************************************************************99998.. PP

                           CmcI  83 lasrieliegssvdpeiveqvkslake.kekvlvilDsdHthehvlaeLeayaplvsaGsYivveDtviedlpesafsdr 161
                                      +++ ++e+ss+dp+i+eq+++l++e + k+++ilDsdH+++hvlae+++++pl+saG+Y+vveD++i+++p+     +
  gi|121638840|ref|YP_979064.1| 128 --PDVLFVESSSTDPAIAEQIQRLKNEyPGKIFAILDSDHSMNHVLAEMKLLRPLLSAGDYLVVEDSNINGHPVL----P 201
                                    ..*************************99**********************************************....9 PP

                           CmcI 162 pwgkgnnPkeAveeflkeepe.feidkeieekllitvapdgfLkr 205
                                    ++g+g  P+eA+e++ +e+p+ +++d+e+e+k+++t+ap+gfL r
  gi|121638840|ref|YP_979064.1| 202 GFGPG--PYEAIEAYEDEFPNdYKHDAERENKFGWTSAPNGFLIR 244
                                    ****9..*************99*********************98 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.5e-09     4e-05       1     105 [.      84     191 ..      84     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.5e-09
                Methyltransf_24   1 vEiGvysGvstlwllralrrnga.grlvavdhdpgaeeaaalareaglddrvrlikads.....eealasla...agsiD 71 
                                    +E G+ +G s+++++  +r+ g+  ++++vd+ +  ++ +  ar+   +  v ++++ s      e++++l+        
  gi|121638840|ref|YP_979064.1|  84 IEFGTRYGGSAVYFANIMRQIGQpFKVLTVDNSH--KALDPRARR---EPDVLFVESSStdpaiAEQIQRLKneyP---G 155
                                    69******************99999*******99..455555555...5555555555544444555555553322...2 PP

                Methyltransf_24  72 ..llfiDgghaaeavledleallprlapggvvlfdD 105
                                      ++++D +h+ ++vl+++++l+p+l+ g ++++ D
  gi|121638840|ref|YP_979064.1| 156 kiFAILDSDHSMNHVLAEMKLLRPLLSAGDYLVVED 191
                                    559999***********************9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1659.35
//
Query:       gi|121638841|ref|YP_979065.1|  [L=82]
Description: hypothetical protein BCG_2981c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 566.17
//
Query:       gi|121638842|ref|YP_979066.1|  [L=129]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-07   31.1   0.2    4.7e-07   29.7   0.2    1.6  1  DDE_Tnp_1    Transposase DDE domain
    5.7e-05   23.3   0.0    7.7e-05   22.9   0.0    1.2  1  DDE_Tnp_1_6  Transposase DDE domain
      0.003   17.9   0.6     0.0045   17.3   0.6    1.3  1  DDE_Tnp_1_2  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.2   7.8e-11   4.7e-07      56     203 ..       3     110 ..       1     121 [. 0.69

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.8e-11
                      DDE_Tnp_1  56 pgnvhdskglkqlldelrpr...kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnk 132
                                     gn hd ++l + ++++  r    + +v+aD+GY+ +++ d+l++ gv  + ++                   rk    +
  gi|121638842|ref|YP_979066.1|   3 HGNPHDAPQLAPAVERITTRagrPPGTVTADRGYGEKRVEDDLHDLGVRTVAIP-------------------RKGRPSQ 63 
                                    59***************999****************************999888...................2222222 PP

                      DDE_Tnp_1 133 iltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrvea 203
                                    +++ +++r  +                         +  + R + E  +++lkr +g++r +  g +++++
  gi|121638842|ref|YP_979066.1|  64 ARRAEEQRPSF------------------------RRTVKWRTGSEGRISTLKRNYGWNRSCIDGTEGTRI 110
                                    22222222222........................345555666666666666666666666666666655 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.3e-08   7.7e-05      59     124 ..      60     124 ..      47     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                    DDE_Tnp_1_6  59 elaekarerikseegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    +  ++ r++ + + +++  k R  + Eg ++++krn+g +r  + G++ +++++   +l++Nl k+
  gi|121638842|ref|YP_979066.1|  60 RPSQARRAEEQRPSFRRTVKWRT-GSEGRISTLKRNYGWNRSCIDGTEGTRIWTRHGILTHNLIKI 124
                                    45566666666777777777775.***************************************996 PP

>> DDE_Tnp_1_2  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.6   7.5e-07    0.0045       1      66 [.      30      98 ..      30     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.5e-07
                    DDE_Tnp_1_2  1 vlaDrgYrsralrealkergI.rasipplgrpakn..kaapkkqarederarnvvErsfgwlkrrrsla 66
                                   v aDrgY  +++ + l  +g+ +++ip +grp++    ++++ + r+  + r   E++++ lkr ++ +
  gi|121638842|ref|YP_979066.1| 30 VTADRGYGEKRVEDDLHDLGVrTVAIPRKGRPSQArrAEEQRPSFRRTVKWRTGSEGRISTLKRNYGWN 98
                                   789******************677899999999987434444444555666777799999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 920.77
//
Query:       gi|121638843|ref|YP_979067.1|  [L=449]
Description: glycosyl transferase family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   32.9   0.0    4.1e-08   32.5   0.0    1.1  1  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
    2.7e-06   27.4   0.1    4.1e-06   26.9   0.1    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
     0.0026   17.0   0.0        1.9    7.7   0.0    2.2  2  Glyco_trans_1_3  Glycosyl transferase family 1


Domain annotation for each model (and alignments):
>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   6.8e-12   4.1e-08     294     419 ..     293     417 ..     259     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.8e-12
                          UDPGT 294 anaiAsaLakipqkvlWrfdg.kkPstLakntllvkWlPqndlLgHPktkAFvtHaGangvyEaisnGvPmvglPlFgdq 372
                                    ++ + +aLa++p +v+    g    +t+  n+ + ++lP  +     +    v  +G+ +   a++ GvP++g+    dq
  gi|121638843|ref|YP_979067.1| 293 LQLVLNALAELPVTVIAATAGrSDLKTVPANAFVADYLPGEAAAA--RSAVVVCNGGSLTTQQALVAGVPVIGVAGNLDQ 370
                                    5678899**********9999445689999*********999765..4556899************************** PP

                          UDPGT 373 rdNikrmeakgaavtlnvkemtsedllnAlkevindksykenimrLs 419
                                    + N++ +e  ga+v l ++ + s+ ++ A+ +vi    y++ + rL+
  gi|121638843|ref|YP_979067.1| 371 HLNMEAVERAGAGVLLRTERLKSQRVAGAVMQVISRSEYRQAAARLA 417
                                    *****************************************999997 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   6.8e-10   4.1e-06       5     152 ..     283     414 ..     279     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.8e-10
                                    EE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHH CS
                Glyco_tran_28_C   5 tGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRAGagt 84 
                                    t G+ g + L +lvl +l++l  +     v+ +t  r++ ++ +  + +       ++ +  ++a +++ +v++ +G  t
  gi|121638843|ref|YP_979067.1| 283 TLGTSGGRNLLQLVLNALAELPVT-----VIAATAGRSDLKTVPANAFV------ADYLP-GEAAAARSAVVVCNGGSLT 350
                                    679999999999999999999987.....78887777666666644444......699**.888888999********** PP

                                    HHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS---S---S CS
                Glyco_tran_28_C  85 iaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaaeklrlaeks 152
                                      ++l++g+p I v        +q  N +++e+aga+ +l+ ++l+ ++++ a+ ++ + ++  ++ +
  gi|121638843|ref|YP_979067.1| 351 TQQALVAGVPVIGVAGNL----DQHLNMEAVERAGAGVLLRTERLKSQRVAGAVMQVISRSEYRQAAA 414
                                    **************9999....********************************99999998755544 PP

>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00031       1.9      74     125 ..     113     164 ..      43     191 .. 0.69
   2 !    7.3   0.1   0.00041       2.4     254     315 ..     339     398 ..     293     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00031
                Glyco_trans_1_3  74 lqvaaklaknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqq 125
                                       ++ l+k v+a    +++ +pdlvv D        a+  ++P i++ n  
  gi|121638843|ref|YP_979067.1| 113 FYAMRTLRKYVEADLRVLDEIAPDLVVGDLRISLSVSARLAGIPYIAIANAY 164
                                    356889999999999999*************999999***********9975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00041
                Glyco_trans_1_3 254 araviagagftLmtealyLkkPlLavPvarqFeqvlnalyLerlgyGaavdakdldkedvkd 315
                                    +  v++++g      al  + P+  + va+  +q ln   +er g G+ + ++ l++++v+ 
  gi|121638843|ref|YP_979067.1| 339 SAVVVCNGGSLTTQQALVAGVPV--IGVAGNLDQHLNMEAVERAGAGVLLRTERLKSQRVAG 398
                                    23466777765566788888886..6789**********************99999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.19s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3689.72
//
Query:       gi|121638844|ref|YP_979068.1|  [L=406]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-85  287.3  22.7    1.1e-85  287.3  22.7    1.7  2  ArsP_1    Predicted permease


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.3  22.7   6.3e-90   1.1e-85       2     293 ..      18     329 ..      17     330 .. 0.98
   2 ?   -1.0   0.4     0.043   7.7e+02       8      30 ..     347     369 ..     342     383 .. 0.66

  Alignments for each domain:
  == domain 1  score: 287.3 bits;  conditional E-value: 6.3e-90
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1   2 laealtlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkG 80 
                                    +++al+l+as+++e+l+aL+lgf++s+++q++v++++i++lLg +r+r  +l++a+ lG+++++Cs++av+lar+l++kG
  gi|121638844|ref|YP_979068.1|  18 IGHALALTASMTWEILWALILGFALSAVVQAVVRRSTIVTLLGdDRPR--TLVIATGLGAASSSCSYAAVALARSLFRKG 95 
                                    5799********************************************..9999************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                         ArsP_1  81 aplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek...... 154
                                    a+++aa+aF +++++++++++i++++l+gwq+++a++v++ i+++v+++++ +lf  ++l +aare+ae+gl+       
  gi|121638844|ref|YP_979068.1|  96 ANFTAAMAFEIGSTNLVVELGIILALLMGWQFTAAEFVGGPIMILVLAVLF-RLFVGARLIDAAREQAERGLAGsmegha 174
                                    **************************************************9.********************99****** PP

                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx...xxx RF
                         ArsP_1 155 ...............ltlkpklealkafaknevkewlelgkyLiiGvaiagviqaflpesvllsll..ggnsvs...ssl 214
                                                   l++ p +++   +a+  v+ewl+++++Li+G++iag+i+a++pes+++s++  +++++s     +
  gi|121638844|ref|YP_979068.1| 175 amdmsikregsfwrrLLSPPGFTS---IAHVFVMEWLAILRDLILGLLIAGAIAAWVPESFWQSFFlaNHPAWSavwGPI 251
                                    *************98889999998...*************************************9988999**988889* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1 215 lamligvvlyvcslgevpfiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglvin 293
                                    +++++++v++vcs+g+vp++a+l++ g+++G+++Af ++++ll lp+l+i++k++++++++vllg++++s+v+ag++i+
  gi|121638844|ref|YP_979068.1| 252 IGPIVAIVSFVCSIGNVPLAAVLWNGGISFGGVIAF-IFADLLILPILNIYRKYYGARMMLVLLGTFYASMVVAGYLIE 329
                                    ************************************.***************************************997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.043
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1   8 lfasilleallaLvlgflisgai 30 
                                    ++a i ++  ++L ++fl+++a 
  gi|121638844|ref|YP_979068.1| 347 MTAEISWNYTTWLNVIFLVIAAA 369
                                    56667777777777777666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2745.66
//
Query:       gi|121638845|ref|YP_979069.1|  [L=310]
Description: formyltetrahydrofolate deformylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-37  126.5   0.0    1.2e-36  126.1   0.0    1.1  1  Formyl_trans_N  Formyl transferase
      1e-10   41.2   0.0    3.8e-10   39.3   0.0    2.1  1  ACT             ACT domain
     0.0071   16.3   0.0      0.038   14.0   0.0    2.1  2  ACT_6           ACT domain
  ------ inclusion threshold ------
      0.031   14.9   0.0      0.072   13.7   0.0    1.6  1  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.0   2.7e-40   1.2e-36       1     181 []     116     292 ..     116     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 2.7e-40
                                    -EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT- CS
                 Formyl_trans_N   1 kkivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelka 80 
                                    k++++++s + ++l +ll + + g+le +vv+v+ n++++a     + ++ p+  + + + ++ ++  e+ + +l + ++
  gi|121638845|ref|YP_979069.1| 116 KRVAIMASTEDHCLLDLLWRNRRGELEMSVVMVIANHPDLA--AHVRPFGVPFIHIPATRDTRTEA--EQRQLQLLSGNV 191
                                    69**************************************9..78888999998888776555533..3344568889** PP

                                    SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT- CS
                 Formyl_trans_N  81 dlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaed 160
                                    dl+vla ym++l++ +++a+  +++niH+S+LP+f Gaa++qra e+G+k  G+t h+v+e lD+G+i+ q+ v+++++ 
  gi|121638845|ref|YP_979069.1| 192 DLVVLARYMQILSPGFLEAIGCPLINIHHSFLPAFTGAAPYQRARERGVKLIGATAHYVTEVLDEGPIIEQDVVRVDHTH 271
                                    ******************************************************************************** PP

                                    -HHHHHHHHHHHHHHHHHHHH CS
                 Formyl_trans_N 161 tkeeleqrvadaehkalveal 181
                                    t+++l +  ad+e  +l +a+
  gi|121638845|ref|YP_979069.1| 272 TVDDLVRVGADVERAVLSRAV 292
                                    ****************99986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   8.5e-14   3.8e-10       3      62 ..      33      91 ..      31      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 8.5e-14
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHH CS
                            ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevleal 62
                                   l+++++DrPG++a+v++ la++g Ni+s+ q+s+ ++ +g +    +    +l +++++l
  gi|121638845|ref|YP_979069.1| 33 LLLRCHDRPGIIAAVSTFLARAGANIISLDQHSTAPE-GGTFLQRAIFHLPGLTAAVDEL 91
                                   7889******************************887.5555555555555555555555 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.5e-06     0.038      10      35 ..      38      63 ..      35      68 .. 0.93
   2 ?   -1.2   0.0      0.47   2.1e+03      13      32 ..      82     101 ..      80     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-06
                          ACT_6 10 pdrpGltasLtsvlaefgvnilDieq 35
                                   +drpG++a+++  la+ g+ni+ + q
  gi|121638845|ref|YP_979069.1| 38 HDRPGIIAAVSTFLARAGANIISLDQ 63
                                   8*********************9888 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
                          ACT_6  13 pGltasLtsvlaefgvnilD 32 
                                    pGlta++ ++  +fg +++D
  gi|121638845|ref|YP_979069.1|  82 PGLTAAVDELQRDFGSTVAD 101
                                    99***999999999999988 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.072       8      44 ..      32      68 ..      30      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                          ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkk 44
                                   rl + ++dr+g++a +++ ++ ++ani s+  +++  
  gi|121638845|ref|YP_979069.1| 32 RLLLRCHDRPGIIAAVSTFLARAGANIISLDQHSTAP 68
                                   6778899***********************9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2089.30
//
Query:       gi|121638846|ref|YP_979070.1|  [L=161]
Description: phosphopantetheine adenylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-19   68.9   0.0    5.7e-19   68.7   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
    1.2e-06   28.3   0.0    1.4e-06   28.1   0.0    1.2  1  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
  ------ inclusion threshold ------
      0.024   13.8   0.0      0.039   13.2   0.0    1.3  1  Pantoate_ligase  Pantoate-beta-alanine ligase
        0.1   12.0   0.0       0.15   11.6   0.0    1.3  1  ATP-sulfurylase  ATP-sulfurylase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   1.3e-22   5.7e-19       2     141 ..       6     131 ..       5     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.3e-22
                                    EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHHHHHT CS
                CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrevlkkl 80 
                                    ++G+FDp++lGH +++e+a+++++e ++v++  ++ +     ++++++eR++m+++  ++ +++ +     l+ +++++ 
  gi|121638846|ref|YP_979070.1|   6 CPGSFDPVTLGHVDIFERAAAQFDE-VVVAILVNPAKT----GMFDLDERIAMVKEStTHLPNLRVQVGHGLVVDFVRSC 80 
                                    78***********************.999888877766....9**************999999999999*********** PP

                                    TTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                CTP_transf_like  81 kpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                    +    ++v g ++ +df  ++el++   n+++++v       ++++++++r++++Ss+  +
  gi|121638846|ref|YP_979070.1|  81 GMT--AIVKGLRTGTDF--EYELQMAQMNKHIAGV------DTFFVATAPRYSFVSSSLAK 131
                                    ***..************..****************......3579************9876 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.2e-10   1.4e-06       9      70 ..      11      74 ..       8     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.2e-10
                 Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvke..dkslfsyeerlklvkkGikdlknvtlhegsdYli 70
                                   +P tlGh  + e+aa++ d v + ++ +   + +f  +er+++vk+ +++l n+ ++ g   ++
  gi|121638846|ref|YP_979070.1| 11 DPVTLGHVDIFERAAAQFDEVVVAILVNpaKTGMFDLDERIAMVKESTTHLPNLRVQVGHGLVV 74
                                   69*****************999887765114568********************9998876665 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.7e-06     0.039      35      60 ..      16      41 ..      14      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-06
                                   HHHHHHHHHHHHSSEEEEEEEEEGGG CS
                Pantoate_ligase 35 GHlsLvkaakeendvvvvSiFvNplq 60
                                   GH+++ ++a+++ d vvv+i vNp++
  gi|121638846|ref|YP_979070.1| 16 GHVDIFERAAAQFDEVVVAILVNPAK 41
                                   9***********************97 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.2e-05      0.15      30      88 ..      12      68 ..       9     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                                   ---HHHHHHHHHHHHHTSEEEEEEEB-SB-STTSTTHHHHHHHHHHHHHHHS-GGGEEE CS
                ATP-sulfurylase 30 plHraHeellkraleeeadglllhplvgptkpgdvpaevrvrayealieeylpkdrvvl 88
                                   p+  +H  +++ra+  + d +++  lv p k+g ++ + r++ +++ + + lp+ rv +
  gi|121638846|ref|YP_979070.1| 12 PVTLGHVDIFERAAA-QFDEVVVAILVNPAKTGMFDLDERIAMVKESTTH-LPNLRVQV 68
                                   67779**********.6999**************************9999.99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1079.79
//
Query:       gi|121638847|ref|YP_979071.1|  [L=188]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-47  161.1   0.0    2.5e-47  160.9   0.0    1.0  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.7e-06   26.2   0.0      6e-06   25.9   0.0    1.1  1  MTS              Methyltransferase small domain
    0.00054   19.3   0.0    0.00073   18.8   0.0    1.1  1  RsmJ             Ribosomal RNA large subunit methyltransferas
     0.0045   16.4   0.1     0.0062   16.0   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0077   16.9   0.1      0.011   16.4   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.02   14.6   0.0        5.7    6.6   0.0    2.1  2  N6_N4_Mtase      DNA methylase
       0.13   13.3   0.0        0.2   12.7   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
       0.14   11.9   0.0       0.17   11.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.9   0.0   1.1e-50   2.5e-47       1     180 [.       2     180 ..       2     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 1.1e-50
                                    EEXXSCCCTTXEEEXTTXXXXXSSSHHHHHHHHHHHCCC..HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHH CS
                  Cons_hypoth95   1 lriigGkakgrkLkvlegkstRPttdrvrealFnilaae..iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavk 78 
                                    +riigG a+gr+++v++ ++tRPttdrvre+lFni+ a+  ++g  vLDl+aGsGalglEAlSRga+++++ve+d++ ++
  gi|121638847|ref|YP_979071.1|   2 TRIIGGVAGGRRIAVPP-RGTRPTTDRVRESLFNIVTARrdLTGLAVLDLYAGSGALGLEALSRGAASVLFVESDQRSAA 80 
                                    59***************.6*****************99999*************************************** PP

                                    HHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH..HHHHHHHHHTT-EEEEEEEEEEEECCSS CS
                  Cons_hypoth95  79 ilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakell.ieevlelleekkllkenalvvvetekeke 157
                                    ++ +n+e+l+l++  a+l++ a+ a+    ++++++d+v  DPPy+ + + + ++l++l ++++ +e+++ vve+ ++ +
  gi|121638847|ref|YP_979071.1|  81 VIARNIEALGLSG--ATLRRGAVAAVVAA-GTTSPVDLVLADPPYNVDSAdVDAILAALGTNGWTREGTVAVVERATTCA 157
                                    **********998..99999999999887.778899**********998889**************************** PP

                                    S--.-TTEEEEEEEEETTEEEEE CS
                  Cons_hypoth95 158 lpespenlelvkekkygettlal 180
                                    ++++pe+++ + ++ yg+t l l
  gi|121638847|ref|YP_979071.1| 158 PLTWPEGWRRWPQRVYGDTRLEL 180
                                    *******************9876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.7e-09     6e-06      33     120 ..      45     135 ..      26     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.7e-09
                                    SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-S...TTTTSTTS-EEEEEE---ST CS
                            MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasd...vleeveekkfdlivsNPPfh 108
                                      vlDl +G G+lg++++++    +v +v+ d r+ ++  +n+ea +l+ ++++      v+++ +   +dl++  PP+ 
  gi|121638847|ref|YP_979071.1|  45 LAVLDLYAGSGALGLEALSRGAA-SVLFVESDQRSAAVIARNIEALGLSgATLRRGAvaaVVAAGTTSPVDLVLADPPYN 123
                                    469**************997766.8************************64433333000333334589*********** PP

                                    TTCHCHHHHHHH CS
                            MTS 109 agkatelavaee 120
                                     ++a  +a+  +
  gi|121638847|ref|YP_979071.1| 124 VDSADVDAILAA 135
                                    999977766655 PP

>> RsmJ  Ribosomal RNA large subunit methyltransferase D, RlmJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.2e-07   0.00073      41     150 ..      27     138 ..      22     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.2e-07
                                    T--GGGHHHHHHHHHTTTTSS--EEE-HHHHHH.HHS-TT-EEEEE---TTHHHHHHHHTTT-TTEEEESS-HHHHHHHS CS
                           RsmJ  41 dlpaeleryldvvrklnkgeklryYpGspllar.rllReqDrlvlteLhpkdaalLkaelakdkrvrvkkadGfaalkak 119
                                    ++ ++l + + + r+l     l++Y+Gs  l   +l R + +++++e  +  aa++ ++++      ++   G  a+   
  gi|121638847|ref|YP_979071.1|  27 RVRESLFNIVTARRDLTGLAVLDLYAGSGALGLeALSRGAASVLFVESDQRSAAVIARNIEALGLSGATLRRGAVAAVVA 106
                                    5566666667777777777789*******997515679************************999999999999999999 PP

                                    -S-TTS-EEEEE----SSCC.HHHHHHHHHHH CS
                           RsmJ 120 lppkekRglvliDPPyeakd.eydrvvaalre 150
                                    ++ ++   lvl DPPy+ +  + d+++aal  
  gi|121638847|ref|YP_979071.1| 107 AGTTSPVDLVLADPPYNVDSaDVDAILAALGT 138
                                    999999***********9888*******9954 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.8e-06    0.0062     143     210 ..      20      92 ..      19     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                           PrmA 143 GtHpTTklclealeklvkege.....evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkve 210
                                    Gt pTT    e+l ++v +++      vlD+ +GSG L + a+  ga++v+ v  D+ +  v ++N+e  +++
  gi|121638847|ref|YP_979071.1|  20 GTRPTTDRVRESLFNIVTARRdltglAVLDLYAGSGALGLEALSRGAASVLFVESDQRSAAVIARNIEALGLS 92 
                                    788899888888888766655455569*********************************9999999876554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   5.1e-06     0.011       1      86 [.      47     133 ..      47     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS..STTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf..edgsfDlvvssgalhhl 77 
                                    vLdl +G+G l l+++ r g+a+v+ v+ +++  + +++++e+ gl  +++++g + ++      + +Dlv++      +
  gi|121638847|ref|YP_979071.1|  47 VLDLYAGSGALGLEALSR-GAASVLFVESDQRSAAVIARNIEALGLsGATLRRGAVAAVVAagTTSPVDLVLA-DPPYNV 124
                                    9*****************.69**********************999999999999988653236779999998.443345 PP

                                    SHHHHHHHH CS
                Methyltransf_25  78 sdedlekal 86 
                                    + +d++++l
  gi|121638847|ref|YP_979071.1| 125 DSADVDAIL 133
                                    666666665 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0026       5.7     194     219 ..      46      72 ..      34      84 .. 0.83
   2 ?    6.3   0.0     0.003       6.8       1      15 [.     113     127 ..     113     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0026
                                    EEEETT-TTTHHHHHHHHTT-EEEE.E CS
                    N6_N4_Mtase 194 ivlDpFaGSGtTavaakelgrkfiG.i 219
                                     vlD +aGSG  + +a++ g  ++  +
  gi|121638847|ref|YP_979071.1|  46 AVLDLYAGSGALGLEALSRGAASVLfV 72 
                                    59**************99988877644 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.003
                                    EEEEEE--SSSSSCS CS
                    N6_N4_Mtase   1 vdlivtdpPYntgkd 15 
                                    vdl+++dpPYn+ + 
  gi|121638847|ref|YP_979071.1| 113 VDLVLADPPYNVDSA 127
                                    89*********9887 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.8e-05       0.2      15     100 ..      59     141 ..      50     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                Methyltransf_24  15 lralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiDgghaaeavledlea 90 
                                    l+al r +a +++ v+ d+   + aa++++    +gl+  ++l+++   +++a   ++++Dl++ D  + ++   +d++a
  gi|121638847|ref|YP_979071.1|  59 LEALSRGAA-SVLFVESDQ---RSAAVIARnieaLGLSG-ATLRRGAVAAVVAAGTTSPVDLVLAD--PPYNVDSADVDA 131
                                    567888887.999******...65566655465466665.9*********9998888*********..569999999999 PP

                Methyltransf_24  91 llprlapggv 100
                                    +l  l  +g+
  gi|121638847|ref|YP_979071.1| 132 ILAALGTNGW 141
                                    9999988886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.4e-05      0.17       4      94 ..      44     133 ..      41     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.4e-05
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsne 82 
                                    gl vlDl +G+G+l++e+ ++    a v  ++ ++++  +   n + lgl+ +++++g + +   +  + +++Dl+l++ 
  gi|121638847|ref|YP_979071.1|  44 GLAVLDLYAGSGALGLEALSR--GAASVLFVESDQRSAAVIARNIEALGLSGATLRRGAVAAVVAAgTT-SPVDLVLADP 120
                                    789****************55..578899999999999999999******************6656555.89***99997 PP

                Methyltransf_31  83 vl.naladpdkil 94 
                                    +   + ad d+il
  gi|121638847|ref|YP_979071.1| 121 PYnVDSADVDAIL 133
                                    6654555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1421.94
//
Query:       gi|121638848|ref|YP_979072.1|  [L=1127]
Description: pyruvate carboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-67  224.7   0.1    1.3e-66  224.1   0.1    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.5e-54  184.0   0.0    6.2e-54  182.8   0.0    1.7  2  PYC_OADA         Conserved carboxylase domain
    2.4e-39  134.3   0.1    5.3e-39  133.2   0.1    1.6  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.4e-35  121.6   0.0      3e-35  120.6   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    3.1e-26   92.5   0.0    7.1e-26   91.3   0.0    1.7  1  HMGL-like        HMGL-like
    2.2e-14   53.1   1.2      5e-14   51.9   1.2    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    3.1e-08   33.3   1.1     0.0021   17.9   0.3    2.6  2  Biotin_lipoyl_2  Biotin-lipoyl like
    1.4e-06   28.0   0.0    3.1e-06   26.9   0.0    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00011   22.0   1.2    0.00027   20.9   1.2    1.6  1  RnfC_N           RnfC Barrel sandwich hybrid domain
    0.00084   18.9   0.0     0.0014   18.2   0.0    1.3  1  ATP-grasp        ATP-grasp domain
     0.0041   17.0   0.3       0.01   15.7   0.3    1.6  1  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.049   13.7   0.0      0.087   12.9   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   0.1     9e-70   1.3e-66       2     210 ..     117     323 ..     116     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 9e-70
                                    HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                    CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                    k++a +a+++++ pv  ssa    +++e l++a+ + +P  +ka +g+GG+Gmr + + + l e++++a++ea++afg++
  gi|121638848|ref|YP_979072.1| 117 KSRAIAAAREAGLPVLMSSAP-SASVDELLSVAAGMPFPLFVKAVAGGGGRGMRRVGDIAALPEAIEAASREAESAFGDP 195
                                    77889999********99987.99******************************************************** PP

                                    -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                    CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtve 161
                                    +v++e+ + +p++iEv++l+D+ g+vi++ er++s+q+r+qkvie AP++ L++e r ++  +av+ +r++g++ agtve
  gi|121638848|ref|YP_979072.1| 196 TVYLEQAVINPRHIEVQILADNLGDVIHLYERDCSVQRRHQKVIELAPAPHLDAELRYKMCVDAVAFARHIGYSCAGTVE 275
                                    ******************************************************************************** PP

                                    EEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                    CPSase_L_D2 162 flldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    flld+ ++ey++iE+N+R++ve++++e++T +dlv+ +++ia+ge+Le+
  gi|121638848|ref|YP_979072.1| 276 FLLDE-RGEYVFIEMNPRVQVEHTVTEEITDVDLVASQLRIAAGETLEQ 323
                                    ****7.*****************************************97 PP

>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   4.9e+03       3      13 ..     733     743 ..     732     746 .. 0.83
   2 !  182.8   0.0   4.2e-57   6.2e-54       1     196 [.     820    1009 ..     820    1011 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                    CCT--CCHHHH CS
                       PYC_OADA   3 kheiPGGqltn 13 
                                    +h  PGGql +
  gi|121638848|ref|YP_979072.1| 733 THDTPGGQLAS 743
                                    6999****987 PP

  == domain 2  score: 182.8 bits;  conditional E-value: 4.2e-57
                                     HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TTS CS
                       PYC_OADA    1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegryk 78  
                                     Vy+heiPGGql+nl++qa ++gl+d+fee+ ++ya +++ lG +vkVTP+SkvvgdlA+ +v  +++++++  ++   
  gi|121638848|ref|YP_979072.1|  820 VYHHEIPGGQLSNLRQQAIALGLGDRFEEIEEAYAGADRVLGRLVKVTPTSKVVGDLALALVGAGVSADEFASDPARF 897 
                                     9***************************************************************************** PP

                                     S--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTSSSHHHHHHHHHSHHHHHH CS
                       PYC_OADA   79 dipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleekakteedvlsyalypkvaek 156 
                                      ip+sv ++l+GelG ppgg+pe+l++++l g+ +   rp+++l++ d    + +l++   +++ +l  +l+p  +++
  gi|121638848|ref|YP_979072.1|  898 GIPESVLGFLRGELGDPPGGWPEPLRTAALAGRGA--ARPTAQLAADD----EIALSSVGAKRQATLNRLLFPSPTKE 969 
                                     ******************************99888..9********77....66777777899*************** PP

                                     HHHHHHHHHHHH..CTTTS......-SEEEEEETTEEEE. CS
                       PYC_OADA  157 flkfreeygdvsvlptkvffeglkvgeeveveveggkyli 196 
                                     f ++re+ygd+s+l+ ++ff+gl++gee++v++e+g  l+
  gi|121638848|ref|YP_979072.1|  970 FNEHREAYGDTSQLSANQFFYGLRQGEEHRVKLERGVELL 1009
                                     ***********************************98875 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.1   3.5e-42   5.3e-39       1     110 []       1     111 [.       1     111 [. 0.98

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 3.5e-42
                                    ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEE.SSTTCCGGG-HHHHHHHHHHTT-SEEE CS
                  Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelg.pasasesYlniekivkaakesgadavh 79 
                                    +++kvl+anrGeiA+r +ra+ elg+ tvavy  ed+ns+h  +ade++++g  +++ ++Yl++++iv++a+++gada++
  gi|121638848|ref|YP_979072.1|   1 MFSKVLVANRGEIAIRAFRAAYELGVGTVAVYPYEDRNSQHRLKADESYQIGdIGHPVHAYLSVDEIVATARRAGADAIY 80 
                                    689*************************************************668999********************** PP

                                    --SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                  Biotin_carb_N  80 pGyGflsEnaefaeaveeagivfiGPsaeal 110
                                    pGyGflsEn+++a+a+++agi f+GPsae+l
  gi|121638848|ref|YP_979072.1|  81 PGYGFLSENPDLAAACAAAGISFVGPSAEVL 111
                                    ****************************986 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0     2e-38     3e-35       1     108 []     339     446 ..     339     446 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 2e-38
                                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGv 80 
                                    ++Ri++Edp+++f+p++G++++l++ +g+gvR+d + + g+e+spy+Ds+l Kl ++g++  +a++r+rra+ae+ri+Gv
  gi|121638848|ref|YP_979072.1| 339 QCRITTEDPANGFRPDTGRISALRTAGGAGVRLDGSTNLGAEISPYFDSMLVKLTCRGRDLPTAVSRARRAIAEFRIRGV 418
                                    79****************************************************************************** PP

                                    -BSHHHHHHHHH-HHHHHT---TTTCCC CS
                  Biotin_carb_C  81 ktnieflrailedeefakgeldtkflee 108
                                    +tni+fl+a+l+d++f++g+++t+f++e
  gi|121638848|ref|YP_979072.1| 419 STNIPFLQAVLDDPDFRAGRVTTSFIDE 446
                                    **************************85 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   4.8e-29   7.1e-26       2     260 ..     524     795 ..     523     798 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 4.8e-29
                                    -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHH..T-SEE--........TSGGGT.THHHHHHHS---TT-B..... CS
                      HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdea..gvdeiEv........gfpaaseddfevvraiakavkka..... 65 
                                    v ++dtt RD++q+l +++++++   ++a  L++    + ++E+          +++ ed++e++ ++ +a+++      
  gi|121638848|ref|YP_979072.1| 524 VGVTDTTFRDAHQSLlATRVRTSGLSRVAPYLARTmpQLLSVECwggatydvALRFLKEDPWERLATLRAAMPNIclqml 603
                                    5679**********99*****************98335667777****************************99955555 PP

                                    ......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTT.. CS
                      HMGL-like  66 ...r.ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsled.. 139
                                       r  +++  + e +  a+v+ ++ +g +++++f+a ++         ++  +++ ++e   a+ + ++ ++  l+d  
  gi|121638848|ref|YP_979072.1| 604 lrgRnTVGYTPYPEIVTSAFVQEATATGIDIFRIFDALNN-------IESMRPAIDAVRETGSAIAEVAMCYTGDLTDpg 676
                                    5442577777777788999*********************.......234444455555555555555555555555511 PP

                                    TBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--E CS
                      HMGL-like 140 asrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadr 219
                                    ++  +l++ ++++e++++aGa  ++i+D+ G+l P +a++l+sal++r +  +++++H+H++ G  +a  +aA +aGad 
  gi|121638848|ref|YP_979072.1| 677 EQLYTLDYYLKLAEQIVDAGAHVLAIKDMAGLLRPPAAQRLVSALRSRFD--LPVHLHTHDTPGGQLASYVAAWHAGADA 754
                                    455799********************************************..**************************** PP

                                    EEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHH CS
                      HMGL-like 220 vdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsi 260
                                    vdg+ + l +++  +al  +vaa++++++dtgl l+ ++++
  gi|121638848|ref|YP_979072.1| 755 VDGAAAPLAGTTSQPALSSIVAAAAHTEYDTGLSLSAVCAL 795
                                    ***********************************998876 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   1.2   3.3e-17     5e-14      15      72 ..    1068    1125 ..    1059    1126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.3e-17
                                     .ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                  Biotin_lipoyl   15 gvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72  
                                     gvv+v v vG+ V agq++a++eamKme +i+ap+aG+v+ + v++ ++ve gdll++
  gi|121638848|ref|YP_979072.1| 1068 GVVTVGVCVGERVGAGQTIATIEAMKMEAPITAPVAGTVERVAVSDTAQVEGGDLLVV 1125
                                     378899**************************************************96 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.8e-05     0.042       5      35 ..    1062    1091 ..    1061    1096 .. 0.87
   2 !   17.9   0.3   1.4e-06    0.0021       4      32 ..    1097    1125 ..    1094    1127 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                Biotin_lipoyl_2    5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDs 35  
                                     Iaap++G V+++ V+ G rV aG+++a+++ 
  gi|121638848|ref|YP_979072.1| 1062 IAAPFAG-VVTVGVCVGERVGAGQTIATIEA 1091
                                     8999999.567******************86 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.4e-06
                Biotin_lipoyl_2    4 sIaapvsGrVaqlnVkdGqrVkaGdvLae 32  
                                     +I+apv+G+V++++V d  +V+ Gd+L++
  gi|121638848|ref|YP_979072.1| 1097 PITAPVAGTVERVAVSDTAQVEGGDLLVV 1125
                                     79*************************86 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.1e-09   3.1e-06      27     174 ..     143     291 ..     129     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.1e-09
                                    HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevs 99 
                                     l +v + + +p+fVK++  G   G+ +v   + l eaie+a +       d +v  E+a+ + r iev +l ++   v 
  gi|121638848|ref|YP_979072.1| 143 ELLSVAAGMPFPLFVKAVAGGGGRGMRRVGDIAALPEAIEAASREaesafgDPTVYLEQAViNPRHIEVQILADNLGDVI 222
                                    5567788899******************************99875444445889*****999***********8888988 PP

                                    EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    ++ e+  +  + + ++k     ++l    +l++e + k+   a+   + ++ +  + v f+l+e ge v+ E+N+
  gi|121638848|ref|YP_979072.1| 223 HLYERDCS--VQRRHQKV----IELAPAPHLDAELRYKMCVDAVAFARHIGYSCAGTVEFLLDERGEYVFIEMNP 291
                                    88887665..44556666....566666677777777777777777788888888899***************96 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.2   1.8e-07   0.00027      45      92 ..    1073    1121 ..    1059    1127 .] 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                         RnfC_N   45 lvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgsgve 92  
                                      v vg++V  Gq ia+ e+  + ap+ a+v+GtV +++   +a+ +g +
  gi|121638848|ref|YP_979072.1| 1073 GVCVGERVGAGQTIATIEAmKMEAPITAPVAGTVERVAVSDTAQVEGGD 1121
                                     46789************99778*************99988877766644 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.5e-07    0.0014      15     160 ..     139     293 ..     124     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.5e-07
                                    CCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEET CS
                      ATP-grasp  15 eskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsa 86 
                                    +s +el ++a+ + +p+ vK ++ g  G+G   v + + l++a+ea+        ++ +v++E+ v   + + v +  + 
  gi|121638848|ref|YP_979072.1| 139 ASVDELLSVAAGMPFPLFVK-AVAGGGGRGMRRVGDIAALPEAIEAAsreaesafGDPTVYLEQAVINPRHIEVQILADN 217
                                    567799999999********.788889******************9999999999999********99999999999999 PP

                                    TC-.EEE--EEEEEEETTEEEEEEECEE-SCHHHH.HHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS- CS
                      ATP-grasp  87 eGe.tafypvvetvqedgilrlsvapaevsekaqk.kaeeiakkiveeLggvGvfavElFvledgellvnElapRp 160
                                     G  ++ y+    vq++   ++ +apa++ +++++ k    a   ++++g+    +vE+ + e ge ++ E+ pR+
  gi|121638848|ref|YP_979072.1| 218 LGDvIHLYERDCSVQRRHQKVIELAPAPHLDAELRyKMCVDAVAFARHIGYSCAGTVEFLLDERGEYVFIEMNPRV 293
                                    9985789999999**99999999999988776544145555668899*******************9999*****8 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   6.9e-06      0.01      41      74 ..    1076    1109 ..    1062    1117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.9e-06
                                     TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                          GCV_H   41 vgtkvkkgeslaavEsvKaasevyapvsGevvev 74  
                                     vg++v +g+++a++E+ K+ +++ apv G+v  v
  gi|121638848|ref|YP_979072.1| 1076 VGERVGAGQTIATIEAMKMEAPITAPVAGTVERV 1109
                                     799***************************9866 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.8e-05     0.087      33     159 ..     154     294 ..     115     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
                                    SEEEEESS-------B--SS--TTE....................EEEE---SEEEEEEEEE.SSS.EEEEEEEEEEEET CS
                    ATP-grasp_3  33 klvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkplSvsllsdgek.vlvlavnrqliek 98 
                                    +l vK + G+gg ++r v +  ++ +aie  +             l q+ i+ +++ v++l+d+   v  l   +  +++
  gi|121638848|ref|YP_979072.1| 154 PLFVKAVAGGGGRGMRRVGDIAALPEAIEAASreaesafgdptvyLEQAVINPRHIEVQILADNLGdVIHLYERDCSVQR 233
                                    678999************999999999998878999**************************985504444444455555 PP

                                    ....TEEEEEEES----HHHHHHHHHHHHHTTST..T--EEEEEEEEESS..SEEEEEEESS-- CS
                    ATP-grasp_3  99 aekefvyaGnvtpietelkeevvelaeevvekle..glaGyvGvDlvlkd.eepyviEvNPRlt 159
                                    ++++++   +++p+++ ++e  ++++ ++v+  +  g      v+++l + +e ++iE NPR++
  gi|121638848|ref|YP_979072.1| 234 RHQKVI---ELAPAPHLDAELRYKMCVDAVAFARhiGYSCAGTVEFLLDErGEYVFIEMNPRVQ 294
                                    444443...66777766666666666666554422255555569******777788******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 7882.52
//
Query:       gi|121638849|ref|YP_979073.1|  [L=210]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-32  111.7  13.3    2.5e-32  111.7  13.3    1.7  2  VKOR      Vitamin K epoxide reductase family
  ------ inclusion threshold ------
       0.43    9.7  14.1       0.11   11.7   9.2    2.3  2  FTR1      Iron permease FTR1 family


Domain annotation for each model (and alignments):
>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7  13.3   2.8e-36   2.5e-32       1     123 [.      24     156 ..      24     157 .. 0.97
   2 ?   -1.5   0.5      0.31   2.7e+03      60      72 ..     187     199 ..     174     209 .. 0.53

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 2.8e-36
                                    HHHHHHHHHHHHHHHHHHHHHH....HT---SS-SSSS...HHHHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-.... CS
                           VKOR   1 llllvlalvGllvsiyltleklglk.tsssaalCdiss.vsCdkvlnSpyasilgvplsllGllayalvlllalapl... 75 
                                    +++l+ +++Gl++s+ lt+ek+++  ++ ++++C++++ vsC +v+++p+as+lg+p++llG++ +++v+++++++    
  gi|121638849|ref|YP_979073.1|  24 WWVLIGGVIGLFASMTLTVEKVRILlDPIYVPSCNVNPiVSCGSVMTTPQASLLGFPNPLLGIAGFTVVVVTGVLAVakv 103
                                    689999*****************99**********************************************999988999 PP

                                    .....HHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHHHH CS
                           VKOR  76 .....lwlllllgslagvvfslyLiylslfvigalCpyClvsavlsllllvla 123
                                         +w++l++g+l+gv+f+++Li++sl++igalCpyC+v+++++++llv++
  gi|121638849|ref|YP_979073.1| 104 plprwYWIGLAVGILVGVAFVHWLIFQSLYRIGALCPYCMVVWAVIATLLVVV 156
                                    **************************************************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHH CS
                           VKOR  60 Gllayalvlllal 72 
                                    + l++++v+ll +
  gi|121638849|ref|YP_979073.1| 187 ATLWFTTVFLLIM 199
                                    3333333333333 PP

>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1     0.079   7.1e+02     172     192 ..      22      42 ..       3      49 .. 0.59
   2 ?   11.7   9.2   1.2e-05      0.11     150     196 ..      90     133 ..      90     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.079
                           FTR1 172 vvlGaliavvlglliyrglvk 192
                                    +   +li+ v+gl++ + l++
  gi|121638849|ref|YP_979073.1|  22 SAWWVLIGGVIGLFASMTLTV 42 
                                    444444555555554444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.2e-05
                           FTR1 150 avLfvaaivaytvkrvsalilgvvlGaliavvlglliyrglvklslq 196
                                    +v++v++++a ++    +l+++ ++G+++++++g++++ +l+  sl 
  gi|121638849|ref|YP_979073.1|  90 TVVVVTGVLAVAK---VPLPRWYWIGLAVGILVGVAFVHWLIFQSLY 133
                                    79***********...9***********************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1541.25
//
Query:       gi|121638850|ref|YP_979074.1|  [L=255]
Description: membrane or hypothetical protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-17   63.9   0.0    2.7e-17   63.4   0.0    1.1  1  Thioredoxin_4  Thioredoxin
    1.4e-05   25.0   1.2     0.0013   18.5   0.0    2.2  2  DSBA           DSBA-like thioredoxin domain
     0.0043   17.3   0.2       0.75   10.1   0.0    2.4  2  Multi_ubiq     Multiubiquitin


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   4.5e-21   2.7e-17       9     163 ..      73     235 ..      68     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.5e-21
                                    S-TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-......---STTTHHHHHHHTT--TTHHHHHHH CS
                  Thioredoxin_4   9 GnpdApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdf....pldkekeslkaamaarcageespeaflai 84 
                                    G ++ + +v  yed+ Cp C  fe+  ++++++ +d G v   + ++       ++++s +aa aa c+++es eaf  +
  gi|121638850|ref|YP_979074.1|  73 GTSNPKAVVSFYEDFLCPACGIFERGFGPTVSKLVDIGAVAADYTMVaildSASNQHYSSRAAAAAYCVADESIEAFRRF 152
                                    77888999******************************99999999964432224449********************** PP

                                    HHHHHTHHHHTTS-HHHHH.............HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEETTEEE-TT-- CS
                  Thioredoxin_4  85 kallysqqeewaeslkelaae........aldkdekfeacleeekldalveaeskeakkagiestPtfiingekveepqt 156
                                    +a+l+s++ ++ae  k++  +        ++    k+ +c++++k+   +e+ +  a + ++ +tPt+ +ng+ +e+ +t
  gi|121638850|ref|YP_979074.1| 153 HAALFSKDIQPAELGKDFPDNarlielarEAGVVGKVPDCINSGKY---IEKVDGLAAAVNVHATPTVRVNGTEYEW-ST 228
                                    ***********999566544444454444666689999*******9...8888**********************95.55 PP

                                    HHHHHHH CS
                  Thioredoxin_4 157 yeelkal 163
                                    +++l a 
  gi|121638850|ref|YP_979074.1| 229 PAALVAK 235
                                    5555554 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.2    0.0022        13       2      20 ..      81      99 ..      80     109 .. 0.85
   2 !   18.5   0.0   2.2e-07    0.0013      64     177 ..     108     224 ..     102     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0022
                                   EEEEEBTTBHHHHHHHHHH CS
                           DSBA  2 vdeffDvlCPyCylgkerl 20
                                   v ++ D+lCP C ++++ +
  gi|121638850|ref|YP_979074.1| 81 VSFYEDFLCPACGIFERGF 99
                                   89**********9999865 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.2e-07
                                    HHHHHHHHHT....GGSSHHH.HHHHHHHHHHHHHHHHGHHHHHHHHHHHHHTS.......SS-TSSHHHHHHHHHHTTS CS
                           DSBA  64 dlkrlaeaegiplrfpkdklk.nstraarlllaagaeglaekvvrelfealwse.......gqaitddqellevaekaGl 135
                                    d+  +a+ +     ++    +  s+raa++++ ++ e    +++r+++ al+s+       g+++ d++ l e+a++aG+
  gi|121638850|ref|YP_979074.1| 108 DIGAVAADYTMVAILDSASNQhYSSRAAAAAYCVADESI--EAFRRFHAALFSKdiqpaelGKDFPDNARLIELAREAGV 185
                                    555666666666666666555578888888888888875..9**********992222222345556777********** PP

                                    .HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEETTC.E CS
                           DSBA 136 daeeldealeseavkeavrentaaaqslgvtGvPtvvvdgk.r 177
                                     + ++   ++s++++e+v+    +a++++v  +Ptv v+g  +
  gi|121638850|ref|YP_979074.1| 186 -VGKVPDCINSGKYIEKVD---GLAAAVNVHATPTVRVNGTeY 224
                                    .99************9997...599999**********99644 PP

>> Multi_ubiq  Multiubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0056        34      36      57 ..      40      64 ..      28      73 .. 0.89
   2 !   10.1   0.0   0.00013      0.75       2      27 ..     216     241 ..     216     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0056
                     Multi_ubiq 36 vleivty...gedgeirdgesVdLk 57
                                   v++ivt+   ++dg+ ++g+ V+++
  gi|121638850|ref|YP_979074.1| 40 VFYIVTSrddKKDGVAGPGDAVRVT 64
                                   8999999999*************98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                     Multi_ubiq   2 kiivNgrpfewpdpvitGreivalAg 27 
                                    +++vNg+++ew  p    ++i+++ g
  gi|121638850|ref|YP_979074.1| 216 TVRVNGTEYEWSTPAALVAKIKEIVG 241
                                    589****************9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1594.39
//
Query:       gi|121638851|ref|YP_979075.1|  [L=376]
Description: lipase/esterase lipN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-72  242.9   0.1    4.3e-72  242.4   0.1    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold
    0.00032   19.7   0.0    0.00061   18.8   0.0    1.4  1  COesterase     Carboxylesterase family
  ------ inclusion threshold ------
      0.036   13.5   0.0       0.19   11.2   0.0    2.0  2  Peptidase_S9   Prolyl oligopeptidase family
      0.051   12.4   0.0      0.097   11.5   0.0    1.3  1  Say1_Mug180    Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.4   0.1   9.5e-76   4.3e-72       1     210 [.     137     349 ..     137     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 9.5e-76
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHH.HHTETTCEEEEEEET CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqaw.elgadpsrivlaGdS 79 
                                    lv++HGGG++lg+ldthdalcr  +++++++v+s+dYrlAPehp+Paaveda+aa+ w++e+a+ e+ga p r++++GdS
  gi|121638851|ref|YP_979075.1| 137 LVFYHGGGWTLGDLDTHDALCRLTCRDADIQVLSIDYRLAPEHPAPAAVEDAYAAFVWAHEHASdEFGALPGRVAVGGDS 216
                                    69*************************************************************99*************** PP

                                    HHHHHHHHHHHHHHHTT---....EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS..GGGGGST CS
                  Abhydrolase_3  80 aGGnlaaavalrardegepk....vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp..eadrddp 153
                                    aGGnl+a+v++ ard+ + +    ++ q+l+yP td+ + ++ s+     + +g llt++++d+f ++yl   + d +dp
  gi|121638851|ref|YP_979075.1| 217 AGGNLSAVVCQLARDKARYEggptPVLQWLLYPRTDF-TAQTRSM---GLFGNGFLLTKRDIDWFHTQYLRdsDVDPADP 292
                                    ***************954445666***********99.7767888...6789******************53688888** PP

                                    TTSGGGCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 154 laspllaedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                    ++spllae+lsgl+p+l++va+fDplrdege ya++lraag++v+l+    ++Hgf+
  gi|121638851|ref|YP_979075.1| 293 RLSPLLAESLSGLAPALIAVAGFDPLRDEGESYAKALRAAGTAVDLRYLGSLTHGFL 349
                                    ********************************************************7 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-07   0.00061     102     198 ..     131     221 ..     112     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                                    TSSEEEEEEE--STTTS-BGCGS-T..HHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHHHHHHHHGG. CS
                     COesterase 102 kkklPVlVwihGggfqtgsaseydg..saLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlALrWVkenIa. 178
                                      + P lV+ hGgg + g+  ++d+  +  ++  ++ v +i YRl +         e p  +++ D  +A+ W +e+ + 
  gi|121638851|ref|YP_979075.1| 131 GGATPLLVFYHGGGWTLGDLDTHDAlcRLTCRDADIQVLSIDYRLAP---------EHPAPAAVEDAYAAFVWAHEHASd 201
                                    4567***************998665114555666***********86.........789999***************964 PP

                                    GGTEEEEEEEEEEETHHHHH CS
                     COesterase 179 sFGGdpervtlfGesAGaas 198
                                    +FG  p rv + G+sAG+ +
  gi|121638851|ref|YP_979075.1| 202 EFGALPGRVAVGGDSAGGNL 221
                                    7****************975 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.3e-05      0.19      48     117 ..     192     259 ..     184     277 .. 0.81
   2 ?   -0.8   0.0       0.2   8.9e+02     161     188 ..     321     348 ..     307     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTSTHHHCCC CS
                   Peptidase_S9  48 fiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdllteeyme 117
                                    f+ a e++ +e+ + + r+a+ G S+GG l++++   + d+ ++     pv+ +l y  ++  +t+++  
  gi|121638851|ref|YP_979075.1| 192 FVWAHEHASDEFGALPGRVAVGGDSAGGNLSAVVCQLARDKARYEGGPTPVLQWLLYPRTD--FTAQTRS 259
                                    777888999999999*****************99997777766666778999999888876..6665554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                                    HHHHHHHHHH--S-SEEEEEETTS-SST CS
                   Peptidase_S9 161 ealklvaaLqkkgknvlllifpdegHgv 188
                                    e++ +++aL+ +g+ v+l++     Hg+
  gi|121638851|ref|YP_979075.1| 321 EGESYAKALRAAGTAVDLRYLGSLTHGF 348
                                    788999************9999988886 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05     0.097     122     208 ..     134     221 ..     124     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                    Say1_Mug180 122 DpvllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvkskgf..knvvv 199
                                     p+l+++HGGg+ l+   +    L  l     d+ +l  DY +   ++            +  ++      g     v v
  gi|121638851|ref|YP_979075.1| 134 TPLLVFYHGGGWTLGDLDTH-DALCRLTCRDADIQVLSIDYRLAPEHPAPAAVEDAYAAFVWAHEHASDEFGAlpGRVAV 212
                                    59************866554.566666666679999999***99977777666666666677777777777763358999 PP

                    Say1_Mug180 200 lGdSaGGnl 208
                                     GdSaGGnl
  gi|121638851|ref|YP_979075.1| 213 GGDSAGGNL 221
                                    9******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2027.38
//
Query:       gi|121638852|ref|YP_979076.1|  [L=56]
Description: hypothetical protein BCG_2992 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.019   14.2   0.0       0.02   14.1   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family
        0.2   11.5   0.0       0.21   11.5   0.0    1.2  1  Herpes_gI     Alphaherpesvirus glycoprotein I


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.2e-06      0.02     247     281 ..       2      34 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-06
                                    HHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG--- CS
                   Aldo_ket_red 247 alryalsqpavgivipgasnieqlednldalelkl 281
                                     +r+ +  + ++ivip++ n+ ++  n+da++++ 
  gi|121638852|ref|YP_979076.1|   2 LIRWHI--QLGNIVIPKSVNPMRIASNFDAFDFPR 34 
                                    599***..9**********************9864 PP

>> Herpes_gI  Alphaherpesvirus glycoprotein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.3e-05      0.21     114     134 ..      34      54 ..      19      56 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                      Herpes_gI 114 rlatePellrirkptvddaGv 134
                                    r  teP+l+rirkp++++aG+
  gi|121638852|ref|YP_979076.1|  34 RSMTEPGLVRIRKPSISQAGE 54 
                                    45799***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                      104  (0.00580066); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 390.50
//
Query:       gi|121638853|ref|YP_979077.1|  [L=282]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-44  151.3   0.0      3e-42  144.8   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.0   1.7e-46     3e-42      14     291 ..      30     265 ..      23     268 .. 0.94

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.7e-46
                                    TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHHH CS
                   Aldo_ket_red  14 eiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksglskenireslees 93 
                                    e s++e  +++ +ale G++++DtA +Y    +e  +G+a+++s++ ree++++tK+    a++++g++  + +e++++s
  gi|121638853|ref|YP_979077.1|  30 ELSDDETERAVSAALEIGCRLIDTAYAY---GNEAAVGRAIAASGVAREELFVTTKL----ATPDQGFT--RSQEACRAS 100
                                    6789************************...9*************************....55555555..569****** PP

                                    HHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHT CS
                   Aldo_ket_red  94 lkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkvkivavqveynllreleee 173
                                    l rLg+dyvDl+l+H+p p + ++ ++++ + + + eG +r+iGvSnf++e++e++     v+++++q+e ++l  l++ 
  gi|121638853|ref|YP_979077.1| 101 LDRLGLDYVDLYLIHWPAPPVGKYVDAWGGMIQSRGEGHARSIGVSNFTAEHIENLIDLTFVTPAVNQIELHPL--LNQD 178
                                    ********************************************************9999**************..**** PP

                                    THHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTT CS
                   Aldo_ket_red 174 gllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgvslaqlalryals 253
                                    +l+++ ++++v +  y+pl+ G l                               ++++ ++a e+ +++aq+ lr+ l 
  gi|121638853|ref|YP_979077.1| 179 ELRKANAQHTVVTQSYCPLALGRLL-----------------------------DNPTVTSIASEYVKTPAQVLLRWNL- 228
                                    ********************99998.............................57899********************. PP

                                    STT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                   Aldo_ket_red 254 qpavgivipgasnieqlednldalelklseeevaelde 291
                                     + ++ v++ + ++e++  n+d+++++l +e +++l  
  gi|121638853|ref|YP_979077.1| 229 -QLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGG 265
                                    .9*******************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2028.55
//
Query:       gi|121638854|ref|YP_979078.1|  [L=237]
Description: hypothetical protein BCG_2994c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-12   46.6   0.0    3.4e-12   46.4   0.0    1.1  1  DUF1524   Protein of unknown function (DUF1524)
    1.1e-06   28.4   0.0    1.8e-06   27.7   0.0    1.4  1  HNH_4     HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   3.8e-16   3.4e-12       2     125 ..      90     216 ..      89     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.8e-16
                        DUF1524   2 prdeefrrallnaklysssrkklryilakelesalreedeeege..akklt......iEHilPqslaekwegagqedeek 73 
                                    +rd+ ++r+l ++++ s +r +  ++ +++l+ +++++++   +  a   +      i+Hi+P s+a++  ga  + + +
  gi|121638854|ref|YP_979078.1|  90 TRDDILDRDLVDKTYVSIKR-CPNAVATGTLR-DPYTNTTVAFQrgA---SvgqsvqIDHIVPLSYAWDM-GAYRWPNSE 163
                                    799************99998.999********.89977555555222...2466888*************.********* PP

                        DUF1524  74 reelvndlgNLtlltkslN...sslsnkpfleKrdlykksslrlnrklaekdewd 125
                                    r +++nd++NL++++++ N    +   + ++++++++   + +  + +a+   + 
  gi|121638854|ref|YP_979078.1| 164 RMRFANDPANLLAVQGQANqdkGDSPPAQWMPPNKAF--ACQYAMQFIAVLRGYS 216
                                    *******************654444467789999998..7888777777666655 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   2.1e-10   1.8e-06       1      54 [.     121     190 ..     121     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-10
                                    -SSSSSB--GGGGGG....SEEEESSTTTT---...............BSGGGEEEES-GGGGTSSSSSS CS
                          HNH_4   1 clYsgekIsiedlsd.tkeydiDHilPrsrskd...............DsvsNkVLvlrdaNqeKsnrtP 54 
                                    ++Y+++++ +++  +  ++++iDHi+P s+ +d               +   N+  v+ +aNq+K+++ P
  gi|121638854|ref|YP_979078.1| 121 DPYTNTTVAFQRGASvGQSVQIDHIVPLSYAWDmgayrwpnsermrfaNDPANLLAVQGQANQDKGDSPP 190
                                    79*******99998889*************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1702.03
//
Query:       gi|121638855|ref|YP_979079.1|  [L=737]
Description: ATP-dependent DNA helicase RecG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-22   80.1   0.0    1.5e-18   67.2   0.0    2.4  2  Helicase_C       Helicase conserved C-terminal domain
    5.2e-18   65.4   0.1    1.5e-17   63.9   0.1    1.7  2  DEAD             DEAD/DEAH box helicase
    4.2e-10   39.9   0.0    8.1e-10   39.0   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
    1.1e-06   28.3   0.0    4.6e-06   26.3   0.0    1.8  2  RecG_wedge       RecG wedge domain
    0.00013   21.8   2.1    0.00028   20.7   1.4    2.0  2  AAA_30           AAA domain
     0.0076   15.0   0.1      0.016   13.9   0.0    1.5  2  SNF2_N           SNF2 family N-terminal domain
     0.0084   16.1   0.0      0.016   15.2   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.16   11.2   0.0       0.26   10.5   0.0    1.2  1  ERCC3_RAD25_C    ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00024      0.55      39      90 ..     374     426 ..     322     444 .. 0.83
   2 !   67.2   0.0   6.6e-22   1.5e-18       9     110 ..     508     628 ..     500     629 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                    TTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG.GTSSSTSTTESEEEE CS
                     Helicase_C  39 kgikvavlhgelpqnereeileqfnkgesdvLiatdv.aerGidipkvnlVin 90 
                                    ++ +va l+g++++ +++++ ++  +g++ ++i t + +++ +d+ ++ +V+ 
  gi|121638855|ref|YP_979079.1| 374 NATRVALLTGSMTAGQKKQVRAEIASGQVGIVIGTHAlLQEAVDFHNLGMVVV 426
                                    4689**************************99999863799****99998874 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 6.6e-22
                                    HHHHTTTTSEEEEEESSHHHHHH.............HHHH...HHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSS CS
                     Helicase_C   9 llkleeeggkilifvntidrlek.............vkll...lekk....gikvavlhgelpqnereeileqfnkgesd 68 
                                    ++++ + g+++++++++id+ ++               l+   +  +    +++ a +hg+l+++++++++++f++ge+d
  gi|121638855|ref|YP_979079.1| 508 IIEEAAAGRQAYVVAPRIDESDDtdvqggvrpsataEGLFsrlR--SaelaELRLALMHGRLSADDKDAAMAAFRAGEVD 585
                                    55667899999999999997766555556555555423334332..134669**************************** PP

                                    EEEESGGGTSSSTSTTESEEEESSSS.SSHHHHHHHHTTSSST CS
                     Helicase_C  69 vLiatdvaerGidipkvnlVinfdlp.rnvtsyiqriGRtgRa 110
                                    vL++t+v+e G+d+p+++++  +d++ +++++++q +GR+gR+
  gi|121638855|ref|YP_979079.1| 586 VLVCTTVIEVGVDVPNATVMLVMDADrFGISQLHQLRGRIGRG 628
                                    **************************778*************7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.9   1.1e+04     114     129 ..     124     139 ..     105     143 .. 0.74
   2 !   63.9   0.1   6.7e-21   1.5e-17       4     173 ..     292     464 ..     289     466 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.9
                                    CTSSHCTTEEEEEEET CS
                                    xxxxxxxxxxxxxxxx RF
                           DEAD 114 tgklnlsqvrflVlDE 129
                                    +g ++l +  fl+lD 
  gi|121638855|ref|YP_979079.1| 124 KGAMQLTHPAFLILDS 139
                                    6778899999999995 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 6.7e-21
                                    HHHHHHHHHTT......CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                    xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                           DEAD   4 Qaeaiplilgg......gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                    Q+e+++ + +g       + l+++e+GsGKT ++++++lq v     + g ++ +++Pt+ La q+l+ ++ ++ ++   
  gi|121638855|ref|YP_979079.1| 292 QREVLDVLSDGlaanrpLNRLLQGEVGSGKTIVAVLAMLQMV-----DAGYQCALLAPTEVLAAQHLRSIRDVLGPLAmg 366
                                    6666666664444443346789********************.....99**************************65555 PP

                                    .........SEEEEEETTSSHHHHHHHH....HTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHH CS
                                    .........xxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 .........lrvlliiggvaardqlskl....dng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdf 141
                                              rv l++g+ +a  q++++     +g v iv+gt+  l++ ++     ++++ ++V+DE +r+  + ++d+
  gi|121638855|ref|YP_979079.1| 367 gqlggaenaTRVALLTGSMTA-GQKKQVraeiASGqVGIVIGTHALLQEAVD-----FHNLGMVVVDEQHRFGVE-QRDQ 439
                                    777788887788777774444.33333312224447********99999775.....*****************9.8888 PP

                                    HHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                           DEAD 142 inrilnqlpqitcdgklqrqvivlSATlp.kdv 173
                                    +++ + +   it       +++v++AT+  ++v
  gi|121638855|ref|YP_979079.1| 440 LRAKAPAG--ITP------HLLVMTATPIpRTV 464
                                    88844333..332......39999999986665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.6e-13   8.1e-10       2     169 ..     286     459 ..     285     461 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.6e-13
                                    -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                    +el   Q e+++ l + l ++r  + l++ + G+GKT+va+ ++ ++  +g+  ++ +l+p++ l  q l+ ++++l + 
  gi|121638855|ref|YP_979079.1| 286 FELTAGQREVLDVLSDGLAANRPLNRLLQGEVGSGKTIVAVLAMLQMVDAGY--QCALLAPTEVLAAQHLRSIRDVLGPL 363
                                    688999*************9******************************99..9******************9999998 PP

                                    ..................GEEEESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTT CS
                         ResIII  82 yke...............igkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlg 145
                                    ++                +g  + g+kk+   e++s +  i++ t   l+++           + ++  ++++DE Hr+g
  gi|121638855|ref|YP_979079.1| 364 AMGgqlggaenatrvallTGSMTAGQKKQVrAEIASGQVGIVIGTHALLQEAV----------DFHNLGMVVVDEQHRFG 433
                                    75455444444444444333334444443345555566666666655555555..........555555*********** PP

                                    S.TTTHHHHHT---...SEEEEEESS- CS
                         ResIII 146 akkswreilekfke...avllglTATp 169
                                      ++  ++  k ++     ll +TATp
  gi|121638855|ref|YP_979079.1| 434 V-EQRDQLRAKAPAgitPHLLVMTATP 459
                                    *.6555554444445559999*****9 PP

>> RecG_wedge  RecG wedge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.1e-09   4.6e-06      16     128 ..      21     135 ..       9     144 .. 0.83
   2 ?   -1.3   0.0      0.68   1.5e+03     131     160 ..     166     195 ..     160     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.1e-09
                     RecG_wedge  16 LkklgietiedllyyfPrdyedrrkivpiseik..edekvtvkgklv...nvekkkissltiisavlsdgisqvlLkWfn 90 
                                     +++g++t++dll ++Pr y +    v i + +  ++e++t++  ++   ++  kk+ + + +   +  g ++v  ++fn
  gi|121638855|ref|YP_979079.1|  21 DEQFGMRTVDDLLRHYPRSYVEGAARVGIGDARpeAGEHITIVDVITdtySFPMKKKPNRKCLRITVGGGRNKVTATFFN 100
                                    3689****************9999999998887224688998887752227899************************** PP

                     RecG_wedge  91 qeyikkklktlkekevlvtGlvkkgefGaleiknPeie 128
                                     +yi + l   k+ +v+++G v     Ga++++ P + 
  gi|121638855|ref|YP_979079.1| 101 ADYIMRDLT--KHTKVMLSGEV-GYYKGAMQLTHPAFL 135
                                    *********..99*******99.445599999999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.68
                     RecG_wedge 131 tgeqereilPvysLtegisqkelrkivken 160
                                     +e er  +P+y+ ++ ++   + k v++ 
  gi|121638855|ref|YP_979079.1| 166 VEEFERRFFPIYPASTKVQSWDIFKCVRQV 195
                                    56778999*******999998888888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2   4.9e+03      56      82 ..      14      45 ..      13      64 .. 0.59
   2 !   20.7   1.4   1.2e-07   0.00028      13     114 ..     303     446 ..     287     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                         AAA_30 56 gkaAkvLaeelgieastiakllkrlk.......g 82
                                   ++aA++L e++g+  +t++ ll+ +        +
  gi|121638855|ref|YP_979079.1| 14 ATAADALDEQFGM--RTVDDLLRHYPrsyvegaA 45
                                   5688888888775..5677777554455555540 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.2e-07
                         AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.La............eelgi..eastiakll 77 
                                    l++++ +  +l+G  G+GKt +   +   + +ag++ ++lApt+  A++ L+             +lg   +a ++a l+
  gi|121638855|ref|YP_979079.1| 303 LAANRPLNRLLQGEVGSGKTIVAVLAMLQMVDAGYQCALLAPTEVLAAQhLRsirdvlgplamgGQLGGaeNATRVALLT 382
                                    4556667789**********9988888888889***********966665995554444444432444355777777777 PP

                         AAA_30  78 krlk...........................grarlepgtllivDEagmvdtkqlaallkaaek 114
                                     +++                           +++++++  +++vDE    + +q ++l ++a +
  gi|121638855|ref|YP_979079.1| 383 GSMTagqkkqvraeiasgqvgivigthallqEAVDFHNLGMVVVDEQHRFGVEQRDQLRAKAPA 446
                                    7777888999999999999999999999*9977889999***************9999988876 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4     3e+03      59      77 ..     312     330 ..     310     353 .. 0.76
   2 !   13.9   0.0   7.2e-06     0.016     124     220 ..     376     464 ..     371     490 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                    EE---TTS--HHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  59 iLaDemGLGKTvqvlalil 77 
                                    +L  e G GKT+ ++  +l
  gi|121638855|ref|YP_979079.1| 312 LLQGEVGSGKTIVAVLAML 330
                                    577799*****97665544 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.2e-06
                                    EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         SNF2_N 124 lrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavsk 202
                                    +rv   +g+ +  +k+++ a+    + ++vi t   l+         +++   +  +vv+DE h+++ +   +++  +  
  gi|121638855|ref|YP_979079.1| 376 TRVALLTGSMTAGQKKQVRAEIASGQVGIVIGTHALLQ---------EAVDFHNLGMVVVDEQHRFGVEqRDQLRAKAPA 446
                                    55666666555555555555556667789999988888.........3456677889***********954566666666 PP

                                    ---S-EEEE-S--SSS-H CS
                                    xxxxxxxxxxxxxxxxxx RF
                         SNF2_N 203 LstsnrwiltGTPiqnsl 220
                                      t + +++t+TPi++ +
  gi|121638855|ref|YP_979079.1| 447 GITPHLLVMTATPIPRTV 464
                                    779************976 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.2e-06     0.016      12      72 ..      76     133 ..      60     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.2e-06
                                    EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                tRNA_anti-codon  12 drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                    ++ ++k + i++  g  ++++++f+  a++++ +l++ + v  +G+v+ ++g  ++l+++ 
  gi|121638855|ref|YP_979079.1|  76 KKPNRKCLRITVGGGRNKVTATFFN--ADYIMRDLTKHTKVMLSGEVGYYKGA-MQLTHPA 133
                                    577889999****************..**************************.***9986 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.26      79     151 ..     557     628 ..     546     634 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                  ERCC3_RAD25_C  79 klkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLra 151
                                    +l+ ++++G+ s  ++ + + +f++  +v++++   v +  +D+P+a+v++ ++++     q  q  Gri r 
  gi|121638855|ref|YP_979079.1| 557 ELRLALMHGRLSADDKDAAMAAFRAG-EVDVLVCTTVIEVGVDVPNATVMLVMDADRFGISQLHQLRGRIGRG 628
                                    5788899****************987.899***********************99988889999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 5262.93
//
Query:       gi|121638856|ref|YP_979080.1|  [L=553]
Description: hypothetical protein BCG_2996c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-74  251.2   0.0      2e-74  250.5   0.0    1.3  1  Dak1_2         Dihydroxyacetone kinase family
    4.5e-26   91.8  13.6    1.1e-25   90.5  13.6    1.7  1  Dak2           DAK2 domain
  ------ inclusion threshold ------
        3.1    8.2   9.4       0.17   12.3   0.6    3.1  3  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.5   0.0   3.3e-78     2e-74       2     313 .]     245     553 .]     244     553 .] 0.96

  Alignments for each domain:
  == domain 1  score: 250.5 bits;  conditional E-value: 3.3e-78
                         Dak1_2   2 fgYCtefllklekaeefdeeklreeLeelGDSlvvvgdde.lvkVHvHtndPgavleaalkyGelskikienMreqheel 80 
                                    +++++++ll+  +a  +++++lr++L+elG+S+ +++     ++VHvHt+d+ga++ea+l++G++s+i i+ +   +   
  gi|121638856|ref|YP_979080.1| 245 PQFEVMYLLAVCDA--AAADQLRDRLKELGESVAIAAAPPdSYSVHVHTDDAGAAVEAGLAVGRVSRIVISALGSGT--- 319
                                    68********9999..9*******************66544**********************************99... PP

                         Dak1_2  81 lkktdseadepkeekeeavvavaageglaelfkslgvdevieggqt.....mnPstedllkaiekvnakevivLpnnkni 155
                                         s  ++  +++ +av+av++g+g+aelf ++g ++v++ g+      ++ s ++l++a+ +++a++v+vLpn + +
  gi|121638856|ref|YP_979080.1| 320 -----SGLPAGGWTRGRAVLAVVDGDGAAELFAGEG-ACVLRPGPDavtpaADISAHQLVRAVVDTGAAHVMVLPNGYVA 393
                                    .....56679**************************.99**9999986666667777*********************** PP

                         Dak1_2 156 ilaaeqaaelaedk..nvvviptktivqGlaallvfdpersleenveamaeaakavktgevtyAvrdtkidggeikkgdl 233
                                    ++++ + +++a  +  +vv +pt ++vqGlaal+v+d++r++ ++ ++ma+aa+a ++g+v++A++++ +++g++k+gd 
  gi|121638856|ref|YP_979080.1| 394 AEELVAGCTAAIGWgvDVVPVPTGSMVQGLAALAVHDAARQAVDDGYSMARAAGASRHGSVRIATQKALTWAGTCKPGDG 473
                                    ************99967*************************************************************** PP

                         Dak1_2 234 lgiadgkivvvgkdleeaakkllkklldedselvtilygedvseeeaealaekleekypdvevevyeGgqplyvylisvE 313
                                    lgia++++++v++d+ +aa  l++ ll+++++lvt+l+g++v+e+ a  l++++++++p++e+  y++g+ ++ +li+vE
  gi|121638856|ref|YP_979080.1| 474 LGIAGDEVLIVADDVAAAAIGLVDLLLASGGDLVTVLIGAGVTEDVAVVLERHVHDHHPGTELVSYRTGHRGDALLIGVE 553
                                    *******************************************************************************8 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5  13.6   1.9e-29   1.1e-25       1     173 [.      38     214 ..      38     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.9e-29
                                    TTS-S-HHHHHHHHHHHHHHHHHC-.....--SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC........... CS
                           Dak2   1 pvGDGDtGtnmargaeavlkaleel.....eeaslaevlkalakallsgagGtsGvlysqflralakalkekee...... 69 
                                    pv+D+DtG nm  +++a++ +++ +     + +++a+v++ala ++l+ga+G+sGv++sq+lr++a+  +++++      
  gi|121638856|ref|YP_979080.1|  38 PVADSDTGVNMLFTMRAAVVEADLHansqaDAEDVARVAAALAAGALNGARGNSGVILSQILRGIAEVTATAAAasgavl 117
                                    699**************9987765555778999************************************99666689999 PP

                                    ..TT---HHHHHHHHH.HHHHHHH---TTSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSG CS
                           Dak2  70 ..ldaedlaaalkaal.eaiqavgkarpgdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgr 146
                                      +da++l+aal +++   + ++ +   + +T++ vlr+a+ a++++   e l+ a+++a +aa  ++e+T+e+l +l  
  gi|121638856|ref|YP_979080.1| 118 raVDANALGAALWRGVeLVVASM-GGVEVPGTIVSVLRAAAGAVDQCAH-EGLAGAVTAAGDAAVIALEKTPEQLDVLAD 195
                                    99**************5555566.667789****************877.89**************************** PP

                                    GGGGGGGGTTS--HHHHHHHHHHHHHH CS
                           Dak2 147 AsylgerslgvvDpGAvglalileala 173
                                    A        g vD+G++gl+++l+al+
  gi|121638856|ref|YP_979080.1| 196 A--------GAVDAGGRGLLVLLDALR 214
                                    *........***************986 PP

>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       0.4   2.4e+03      21      61 ..     132     168 ..     127     205 .. 0.56
   2 ?   12.3   0.6   2.8e-05      0.17      13     102 ..     333     418 ..     328     424 .. 0.82
   3 ?   -0.5   0.2      0.26   1.6e+03      46      81 ..     425     456 ..     420     467 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.4
                  Ribosomal_S11  21 GaevlvksaGglgvkasrkssPyaaqlaaekaaekvldkGi 61 
                                    G e++v+s Gg+ v +   s   aa  a +++a++    G+
  gi|121638856|ref|YP_979080.1| 132 GVELVVASMGGVEVPGTIVSVLRAAAGAVDQCAHE----GL 168
                                    55566666666666555544444444444443333....33 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.8e-05
                  Ribosomal_S11  13 iititdlkGaevlvksaGglgvkasrkssPyaaqlaaekaaekvldkGikavevkvkgpGpGreaalralaraGlkigri 92 
                                    ++ + d  Ga+ l +  G+++++   ++   aa   a++ +++v+d+G   ++v+v   G  +   l   a +   ig  
  gi|121638856|ref|YP_979080.1| 333 VLAVVDGDGAAELFAGEGACVLRPGPDAVTPAADISAHQLVRAVVDTGA--AHVMVLPNGYVAAEELV--AGCTAAIGWG 408
                                    78899********************9888889***************95..68888877766655554..4555567777 PP

                  Ribosomal_S11  93 edvtPiPhdg 102
                                     dv P+P+ +
  gi|121638856|ref|YP_979080.1| 409 VDVVPVPTGS 418
                                    8999999866 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                  Ribosomal_S11  46 qlaaekaaekvldkGikavevkvkgpGpGreaalra 81 
                                     la ++aa++++d G +      +++G+ r+ ++r 
  gi|121638856|ref|YP_979080.1| 425 ALAVHDAARQAVDDGYSM----ARAAGASRHGSVRI 456
                                    566778888888888764....56666666666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3901.32
//
Query:       gi|121638857|ref|YP_979081.1|  [L=227]
Description: uracil-DNA glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-18   65.0   0.0    1.1e-17   64.4   0.0    1.3  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   6.4e-22   1.1e-17       3     151 ..      55     213 ..      53     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 6.4e-22
                                    C-CTT-SEEEEESSTCHH.HHHHSSSS.-STT--HH.HHHHHCCCCCCCHHG................CTEEEEESSS.. CS
                            UDG   3 egppdakvvivGeaPgae.edatglpFsgragnllr.kllneaglkrdlese................qgvyitnvvkcr 64 
                                    ++  +++v+ivG++P+++ ++a gl Fs+++  +++ + l  a++  +++++                +gv+++n v+  
  gi|121638857|ref|YP_979081.1|  55 FPFDNVRVLIVGQDPYPTpGHAVGLSFSVAPDVRPWpRSL--ANIFDEYTADlgyplpsngdltpwaqRGVLLLNRVL-- 130
                                    66789**************************988885555..445555555566669999******************.. PP

                                    ..SEC.GCTTCCCCTCCHH.HHHHHHHHHH....SSEEEEESHHHHHH..HHHHSCESCCCSCT..SEEEEES-SSTTTT CS
                            UDG  65 ppgnr.dtptsaeikacap.lleeeiellk....prlivllGktaakallgeklgklrgklleak.irvlplphPsplnr 137
                                      + r ++p s+    +++  +e  i++l     p +++l+G++a             +  l a    ++ +phPspl++
  gi|121638857|ref|YP_979081.1| 131 --TVRpSNPASHR-GKGWEaVTECAIRALAaraaPLVAILWGRDASTL----------KPMLAAGnCVAIESPHPSPLSA 197
                                    ..65556899999.89********************************..........788888768899********** PP

                                    T..TTTSHHHHHHHHH CS
                            UDG 138 n..ffksnpelkaeaw 151
                                    +  ff+s+p+++a+++
  gi|121638857|ref|YP_979081.1| 198 SrgFFGSRPFSRANEL 213
                                    ***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1486.89
//
Query:       gi|121638858|ref|YP_979082.1|  [L=333]
Description: thiamine monophosphate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-16   61.0   2.0    1.3e-16   61.0   2.0    1.9  2  AIRS         AIR synthase related protein, N-terminal domain
    8.7e-06   25.9   0.4    1.6e-05   25.1   0.4    1.5  1  AIRS_C       AIR synthase related protein, C-terminal domain
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.064   13.3   0.1    1.6  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   2.0   2.2e-20   1.3e-16       1      92 [.      43     152 ..      43     154 .. 0.95
   2 ?   -1.6   0.1      0.76   4.6e+03      39      71 ..     217     242 ..     209     267 .. 0.49

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.2e-20
                                    SSSEE........EEEEEEEE.EECCTCCCC.........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHH CS
                           AIRS   1 dDaav........vvttdshnrpvlvepvhf.........iGakavavnlsDlaamGArPlalllslalp......wlee 57 
                                    dDaa+        vv+td     +lv++ hf         +G+ka+a+n+ D+ amGAr +a+++ +  p      ++++
  gi|121638858|ref|YP_979082.1|  43 DDAALvsagdgrtVVSTD-----MLVQDSHFrldwstpqdVGRKAIAQNAADIEAMGARATAFVVGFGAPaetpaaQASA 117
                                    8999555666666*****.....********************************************************* PP

                                    HHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEE CS
                           AIRS  58 vvrglaeaaeelgvplvgGdtsfsneptisvtavG 92 
                                    +v+g+ e a ++g+ +vgGd+ +  + ++svta+G
  gi|121638858|ref|YP_979082.1| 118 LVDGMWEEAGRIGAGIVGGDLVSCRQWVVSVTAIG 152
                                    ************************99********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.76
                                    TTEEEE.EEEEEEEECHHHHHHHHHHHHHHHTT- CS
                           AIRS  39 mGArPl.alllslalpwleevvrglaeaaeelgv 71 
                                    +GA+ +            ++++++l++ ae+ gv
  gi|121638858|ref|YP_979082.1| 217 VGAQAMiD--------VSDGLLADLRHIAEASGV 242
                                    33333332........333344444444444444 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.4   2.7e-09   1.6e-05       1      95 [.     166     250 ..     166     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.7e-09
                                    STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHH CS
                         AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaema 80 
                                    k+G vl ++g+lG  +ag++l   ++e+ ++      l    l+p   y   a+aa+  ++ a+ Dv++ GLl +l  +a
  gi|121638858|ref|YP_979082.1| 166 KAGSVLAVVGELGRSAAGYALWCNGIEDFAE------LRRRHLVPQPPYGHGAAAAA-VGAQAMIDVSD-GLLADLRHIA 237
                                    68****************8886666665554......67777777777777777777.8**********.8********* PP

                                    HTTTEEEEEECGTHH CS
                         AIRS_C  81 pasgvgaeidldkvp 95 
                                    +as  g++idl++  
  gi|121638858|ref|YP_979082.1| 238 EAS--GVRIDLSAAA 250
                                    ***..5566655222 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.064     118     163 ..      28      83 ..      14     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                    CTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........... CS
                    Lactamase_B 118 ggrralyvtggpghghghgvveygggkvlftGDallagetgridl..........t 163
                                      +r++++t+  g+g + + v++g+g+++++ D+l + ++ r+d+           
  gi|121638858|ref|YP_979082.1|  28 VRGRRQPATVLLGPGDDAALVSAGDGRTVVSTDMLVQDSHFRLDWstpqdvgrkaI 83 
                                    6789999*************************************954444333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2349.18
//
Query:       gi|121638859|ref|YP_979083.1|  [L=459]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-27   96.1   1.4    3.2e-27   95.1   1.4    1.5  1  OrfB_IS605      Probable transposase
    5.7e-14   51.8   0.4    1.3e-13   50.6   0.4    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      2e-09   36.8   1.0    4.1e-09   35.8   0.1    2.1  2  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   1.4   5.4e-31   3.2e-27       4     117 ..     205     320 ..     200     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 5.4e-31
                     OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtw..flykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                    v+ +++++++ +++++g+D+G+++Latv+t dgt+   + ++r+l +++++l+   +  ++++k+s++y++++++++rlh
  gi|121638859|ref|YP_979083.1| 205 VQRPQQPKVVHPGSRVGVDVGVRRLATVATADGTAieQVENPRPLGAALRELRHVCRARSRCTKGSRRYRERTTQISRLH 284
                                    444556999**************************999****************************************** PP

                     OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                    r++++ r+h+lh l+t+l++t+ +++ve L+  +m 
  gi|121638859|ref|YP_979083.1| 285 RRVNDVRTHHLHVLTTRLAQTHGRIVVEGLDATEML 320
                                    *******************************99997 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.4   2.2e-17   1.3e-13       6      68 ..     345     407 ..     341     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.2e-17
                 OrfB_Zn_ribbon   6 eqleykakeyGikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                    + l+yk  +yG  ++++++++ +SktC+ C ++++    +++++C++C ++++rD  AaiN+++
  gi|121638859|ref|YP_979083.1| 345 RHLSYKTVWYGSALVVADRWFpSSKTCHACRHVQDI-GWDEQWQCDRCSVVHQRDDCAAINLAR 407
                                    679*********************************.99***********************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   6.8e-13   4.1e-09       4      39 ..      13      48 ..      11      57 .. 0.90
   2 ?   -4.0   0.1       1.8   1.1e+04      24      33 ..     104     113 ..     103     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.8e-13
                 HTH_OrfB_IS605  4 kaykyrlyPTpeQeeklartfGcvRfVYNkaLaerk 39
                                   +a+++ l PT+ Q+ +lar+fG+ R +YN+  a  k
  gi|121638859|ref|YP_979083.1| 13 QAFRFTLDPTEDQAKALARHFGARRKAYNWTVATLK 48
                                   69****************************998766 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.8
                 HTH_OrfB_IS605  24 fGcvRfVYNk 33 
                                    +G+v   +N+
  gi|121638859|ref|YP_979083.1| 104 AGAVEAYWNW 113
                                    6888889**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3184.09
//
Query:       gi|121638860|ref|YP_979084.1|  [L=194]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-18   65.2   2.1      9e-18   64.8   2.1    1.1  1  Resolvase  Resolvase, N terminal domain
  ------ inclusion threshold ------
      0.028   14.5   0.1       0.18   11.9   0.0    1.9  2  Imm21      Immunity protein 21
      0.041   14.1   0.1      0.087   13.0   0.1    1.5  1  HTH_17     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   2.1   1.5e-21     9e-18       2     142 ..      53     188 ..      52     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.5e-21
                                    EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                      Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                    ++YaRvS+++q+ +l+rQ+++++a+a+++++ ++k++++   S+ +++R+++ +ll++ +      +vve+ dR+ R  +
  gi|121638860|ref|YP_979084.1|  53 AVYARVSSADQKADLDRQVARVTAWAAAQQMPVDKVVTEV-GSAFNEHRRKFLSLLRDPSV---HRIVVEHRDRFCRLGS 128
                                    79***************************999********.*****99********99998...589************* PP

                                    S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHH.HHHHHHCT-TTHHHHHHH CS
                      Resolvase  82 dlltlleelrekgvslvsldegidtstpm.grlllqilaalaef.erelirertkeglaaaka 142
                                    ++++    ++++g +lv++d+  +  ++  + ++  + +++a++  ++   +rtk++laaa+ 
  gi|121638860|ref|YP_979084.1| 129 KYVQA--AFAAQGRELVVVDS-AEVGDDLvRDMTEILTSMCARLyGKRAAENRTKRALAAAAG 188
                                    ****9..77778888888885.44444443444444444445552677777899999999875 PP

>> Imm21  Immunity protein 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.18      48     107 ..      23      85 ..      22     107 .. 0.75
   2 ?    0.5   0.0     0.093   5.6e+02     110     130 ..     136     157 ..     109     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                          Imm21  48 vGlvkv..gdeealVlgdePasttyl.pehralvrwiaadseaellaaveaaladaaeweeev 107
                                    +Gl+ v       l+l dePa  + + + +++ +r   ad++a+l  +v++++a aa  +  v
  gi|121638860|ref|YP_979084.1|  23 AGLLSVmaRRVGRLILVDEPAGDAGMrSPTAVYARVSSADQKADLDRQVARVTAWAAAQQMPV 85 
                                    6888884444456********988761567889****************99998544443333 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.093
                          Imm21 110 evd.gpvvlfDsaepgseleda 130
                                      + +++v++Dsae g +l + 
  gi|121638860|ref|YP_979084.1| 136 AAQgRELVVVDSAEVGDDLVRD 157
                                    4444688899999998776643 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.087      12      39 ..      11      40 ..       5      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                         HTH_17 12 gvsrstvyrlirrgelpaa..kiGrrwrip 39
                                   gv r t+yr+ r+g l ++  ++Gr ++++
  gi|121638860|ref|YP_979084.1| 11 GVARGTAYRWFRAGLLSVMarRVGRLILVD 40
                                   999*************66695599978776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1387.86
//
Query:       gi|121638861|ref|YP_979085.1|  [L=181]
Description: hypothetical protein BCG_3001 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-54  183.5   6.3    2.7e-54  183.2   6.3    1.0  1  DUF3515   Protein of unknown function (DUF3515)


Domain annotation for each model (and alignments):
>> DUF3515  Protein of unknown function (DUF3515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   6.3   1.5e-58   2.7e-54       2     158 ..      18     174 ..      15     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 1.5e-58
                        DUF3515   2 vlavalvvavlvvaallsdkaeaepvalasvpApkadsaeCaallaalPdelgdlrraeladpapagtaaWgepe.geev 80 
                                    +la a++ ++lvvaa ++  + ++pv +++vpAp+a+ + C+allaalP++lg++rra++a+p++ag++aW++ + +++v
  gi|121638861|ref|YP_979085.1|  18 ALAAAVIGVILVVAANRQ--PPERPVVIPAVPAPQATGPGCKALLAALPQRLGEYRRAPVAEPTTAGATAWRTGPnSTPV 95 
                                    567778888888888755..899*************************************************9998**** PP

                        DUF3515  81 vlrCGvdrPaefteaselqevdgvqWlevsdaeagsd.astwyavdrevyValtvpagagstplqelsdaiaetlpakp 158
                                    +lrCG+drPaef+++s++q+vd+vqW++v  +++++  +stwy+vdr+vyValt+p+g+g+t++qelsd+i++t+pa p
  gi|121638861|ref|YP_979085.1|  96 ILRCGLDRPAEFVVGSAIQVVDRVQWFQVAAQNPDEPgRSTWYTVDRPVYVALTLPSGSGPTAIQELSDVIDHTIPAVP 174
                                    ********************************9988789*************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1387.71
//
Query:       gi|121638862|ref|YP_979086.1|  [L=373]
Description: D-alanyl-alanine synthetase A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-73  246.7   0.0    1.9e-73  246.4   0.0    1.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.2e-30  106.0   0.0      2e-30  105.3   0.0    1.4  1  Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
    3.2e-08   33.3   0.0    2.3e-06   27.3   0.0    2.1  1  ATP-grasp        ATP-grasp domain
    3.6e-08   33.6   0.0     0.0044   17.1   0.0    2.1  2  ATP-grasp_3      ATP-grasp domain
    0.00044   19.9   0.0     0.0036   16.9   0.0    2.3  1  ATP-grasp_4      ATP-grasp domain
    0.00052   19.6   0.0     0.0086   15.6   0.0    2.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00083   19.0   0.0     0.0097   15.5   0.0    2.0  2  RimK             RimK-like ATP-grasp domain
     0.0027   17.0   0.0       0.21   10.8   0.0    2.1  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.4   0.0   8.3e-77   1.9e-73       1     204 []     158     363 ..     158     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.4 bits;  conditional E-value: 8.3e-77
                                    HHHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE- CS
                Dala_Dala_lig_C   1 llkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEea 80 
                                    ll+a Glpv +y+vl++ +++ ++     +++e+lg+pvfVKpar GSS+Gvs+v+s+++l +a+++a ++d kv+vE+a
  gi|121638862|ref|YP_979086.1| 158 LLAADGLPVGAYAVLRPPRSTLHR-----QECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAA 232
                                    68899*******************.....999************************************************ PP

                                    -ESEEEEEEEEE..TSSCEEEEEEEEE-SS......SSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT-- CS
                Dala_Dala_lig_C  81 iegreievavlg..neklevsevgeivvkk......gfydyeakysddkaqlevpaklekeveekiqelalkaykaldlr 152
                                    i+gre+e++vl+  +++le+s++gei+v++      +fyd+++ky dd+a+l+vpak++++v+e+i++la++a++a+d+r
  gi|121638862|ref|YP_979086.1| 233 ISGRELECGVLEmpDGTLEASTLGEIRVAGvrgredSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCR 312
                                    ************9999************99999999******************************************** PP

                                    SEEEEEEEEETTTEEEEEEEESS---STTSHHHHHHHCTT--HHHHHHHHHH CS
                Dala_Dala_lig_C 153 GlaRvDfflteegeivlnEvNtlPGfTeiSlfpklakasGlefkkLvdqlie 204
                                    GlaRvDfflt ++ +v+nE+Nt+PGfT+iS++p++++asG+++++L++++ie
  gi|121638862|ref|YP_979086.1| 313 GLARVDFFLT-DDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIE 363
                                    *********9.77799**********************************96 PP

>> Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   8.9e-34     2e-30       1     102 [.      12     140 ..      12     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 8.9e-34
                                    EEEEEEE-SSTTHHHHHHHHHHHHHHCHCCTEEEEEEEE-TTS-E........HHHHHHHHTTHHH.............. CS
                Dala_Dala_lig_N   1 kiavlfGGkStEhevSlvsaksvlkaldkekyeviligitkegkw........kkkaekleskekk.............. 58 
                                    ++av+fGG+S+Eh +S+vsa s+l++ld+++++vi +git  g+w              l+ ++++              
  gi|121638862|ref|YP_979086.1|  12 RVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWvltdanpdA-----LTITNRElpqvksgsgtelal 86 
                                    69*******************************************998555440.....444444455666777888999 PP

                                    ..........TCCCCHCCCTCE--SEEEEE-TTTTTTSSHHHHHHHHTT--BSS CS
                Dala_Dala_lig_N  59 ..........klkkeeekekkaeldvvfpvlhGkngEDGtlqgllellgipyvG 102
                                               +      e+ +++dvvfpvlhG++gEDGt+qgllel+g+pyvG
  gi|121638862|ref|YP_979086.1|  87 padprrggqlVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVG 140
                                    999999999888899999***********************************9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     1e-09   2.3e-06       4     157 ..     162     332 ..     159     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1e-09
                                    TT--B-EEEEECCHH..HHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC..GTTCEEEEE---...... CS
                      ATP-grasp   4 lglpvprflaveske..eleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal..keekvivEefvp...... 73 
                                     glpv  +++++       ++ +e+lglpv vK +r+g++  G s v s ++l+ a++ +  ++ kvivE  ++      
  gi|121638862|ref|YP_979086.1| 162 DGLPVGAYAVLRPPRstLHRQECERLGLPVFVKPARGGSS-IGVSRVSSWDQLPAAVARArrHDPKVIVEAAISgrelec 240
                                    5788888888876653356899***********6666665.8***************99988778888888886211111 PP

                                    .......-SEEEEEEE.EE..ETTC-.EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEE CS
                      ATP-grasp  74 .......fekElsvlv.vr..saeGe.tafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavE 142
                                            + E s l+ +r   ++G+  +fy+   ++  d+   +  +pa+v+++ ++ ++++a ++ ++++  G+  v 
  gi|121638862|ref|YP_979086.1| 241 gvlempdGTLEASTLGeIRvaGVRGReDSFYDFATKYL-DD-AAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVD 318
                                    11110002345555433233366666234555554444.33.34556799****************************** PP

                                    EEEETTCTEEEEEEE CS
                      ATP-grasp 143 lFvledgellvnEla 157
                                    +F+++dg  ++nE+ 
  gi|121638862|ref|YP_979086.1| 319 FFLTDDG-PVINEIN 332
                                    ****777.5689985 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.3e-05     0.029       3      75 ..     151     238 ..     150     250 .. 0.84
   2 !   17.1   0.0     2e-06    0.0044     113     156 ..     291     333 ..     285     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                    SHHHHHHHHTTT.S---.............-EESS--SSSEEEEESS-------B--SS--TTE.............EEE CS
                    ATP-grasp_3   3 dKlktykkLkeagvkvP.........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......lvq 67 
                                    dK +t k L + g++v          ++l+ +e+e+   ++ vKp++G+ + +v+ v  ++++ aa++         +v 
  gi|121638862|ref|YP_979086.1| 151 DKEFTKKLLAADGLPVGayavlrpprSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARrhdpkvIVE 230
                                    56666666666666665666666679999***********************************9999888999999999 PP

                                    E---SEEE CS
                    ATP-grasp_3  68 efieGkpl 75 
                                    + i+G++l
  gi|121638862|ref|YP_979086.1| 231 AAISGREL 238
                                    99**9987 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2e-06
                                    ---HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEES CS
                    ATP-grasp_3 113 etelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNP 156
                                    + + +e +++la ++ +++ +++G++ vD+ l+d++p++ E+N 
  gi|121638862|ref|YP_979086.1| 291 DDQVAEAIRQLAIRAFAAI-DCRGLARVDFFLTDDGPVINEINT 333
                                    45558999***********.***********************5 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.6e-06    0.0036       2      67 ..     188     239 ..     187     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                    ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfa 67 
                                     lPv +KP+ g +S+GV+++++ +++ aava+ +++              + +++vE  i G E  
  gi|121638862|ref|YP_979086.1| 188 GLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRH--------------DPKVIVEAAISGRELE 239
                                    58****************************998865..............2234566666666655 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.9e-06    0.0086      32     177 ..     182     332 ..     151     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
                                    HHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEE..ETTS-EEE CS
                    CPSase_L_D2  32 aiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlr..Dakgnvit 109
                                    +  +++g Pv +k+a g+   G   +++ ++l ++v++a+++       ++v ve  ++g +e+E+ vl   D +  + t
  gi|121638862|ref|YP_979086.1| 182 QECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHD------PKVIVEAAISG-RELECGVLEmpDGTLEAST 254
                                    567899***********************************99......8*******998.9******873355555666 PP

                                    EEEEEECCEC............TCCCCEEEE.S-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEE CS
                    CPSase_L_D2 110 vcerenslql............rtqkvievA.PsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEv 176
                                    ++e+     +              ++  e   P+  ++d+  +a+r+ a+++  +++ +g + v+f l    +  ++ E+
  gi|121638862|ref|YP_979086.1| 255 LGEIRVAGVRgredsfydfatkYLDDAAELDvPA-KVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTD--DGPVINEI 331
                                    6665544444312222222222222333332233.46888888899999999999999999999988874..44455566 PP

                                    E CS
                    CPSase_L_D2 177 N 177
                                    N
  gi|121638862|ref|YP_979086.1| 332 N 332
                                    6 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   2.6e+02       3      57 ..     151     205 ..     149     224 .. 0.86
   2 !   15.5   0.0   4.3e-06    0.0097     126     177 ..     293     345 ..     284     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                                    -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEE CS
                           RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvv 57 
                                    dK  + klLa ++++v   a+ r +  + +  e  +l+ Pv vK   g   i+v 
  gi|121638862|ref|YP_979086.1| 151 DKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVS 205
                                    77778899***************99999999999899*******99998888875 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.3e-06
                                    ---HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--SHHHHHHHT CS
                           RimK 126 qlseeekelAikaakamelv.vaGvDllrakrgllvlEvnsspglekiektlg 177
                                    q+ e  ++lAi+a  a++   +a vD + +++g+++ E+n+ pg + i+++ +
  gi|121638862|ref|YP_979086.1| 293 QVAEAIRQLAIRAFAAIDCRgLARVDFFLTDDGPVINEINTMPGFTTISMYPR 345
                                    6778899******99999863789************************99865 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.011        24      21      78 ..     151     206 ..     145     222 .. 0.85
   2 !   10.8   0.0   9.3e-05      0.21     227     273 ..     297     342 ..     293     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                    ATPgrasp_ST  21 dKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilv 78 
                                    dK  +k+l+ ++gl+v + ++v++  ++  + +++ +   + v++Kpa+g +  G++ 
  gi|121638862|ref|YP_979086.1| 151 DKEFTKKLLAADGLPVGA-YAVLRPPRSTLHRQECERLGLP-VFVKPARGGSSIGVSR 206
                                    999***************.9999999888887887776656.*******988888765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.3e-05
                    ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpglaivqi 273
                                    ++ +la +a + + + g+  +D+ l++++ p++ E+N++pg + + +
  gi|121638862|ref|YP_979086.1| 297 AIRQLAIRAFAAIDCRGLARVDFFLTDDG-PVINEINTMPGFTTISM 342
                                    5678999999999****************.***********987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2334.72
//
Query:       gi|121638863|ref|YP_979087.1|  [L=334]
Description: NAD(P)H-dependent glycerol-3-phosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-51  173.2   0.1    6.3e-51  172.5   0.1    1.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    3.5e-49  166.8   1.3    6.6e-49  165.9   1.3    1.5  1  NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogen
    1.5e-10   40.9   0.0    3.5e-10   39.7   0.0    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
      2e-07   31.5   0.0    1.5e-06   28.7   0.0    2.4  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.9e-05   24.9   0.0    5.4e-05   23.4   0.0    1.8  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0012   18.7   0.3     0.0024   17.8   0.3    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0026   17.1   0.0      0.014   14.8   0.0    2.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0046   17.5   0.1      0.011   16.2   0.1    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.025   15.1   0.1      0.066   13.7   0.1    2.0  1  XdhC_C          XdhC Rossmann domain
      0.041   13.5   0.0        0.2   11.2   0.0    2.0  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.051   13.8   0.0       0.15   12.3   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.061   12.6   1.4       0.08   12.2   0.2    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.1   4.2e-54   6.3e-51       2     154 ..       8     162 ..       7     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 4.2e-54
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa 81 
                                    +av+GaG+wGtalAkvla++g ev+lw+r++e++++in+++ n +yLpg  lp +++at+d +eal ga++++l vP q+
  gi|121638863|ref|YP_979087.1|   8 VAVMGAGAWGTALAKVLADAGGEVTLWARRAEVADQINTTRYNPDYLPGALLPPSIHATADAEEALGGASTVLLGVPAQT 87 
                                    9******************************************************************************* PP

                                    HHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--..EEEEESS--HHHHHTT--EEEEEEES-H CS
                 NAD_Gly3P_dh_N  82 lrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeek..vavlsGpslAeEvakgkptavviaskdk 154
                                    +r  l+++++ll++ a+lvsl+KGie gtl+++s+vi ++++ e+  vav+sGp+lA+E+a+ +p+a+v+a++d+
  gi|121638863|ref|YP_979087.1|  88 MRANLERWAPLLPEGATLVSLAKGIELGTLMRMSQVIISVTGAEPaqVAVISGPNLASEIAECQPAATVVACSDS 162
                                    *******************************************9999*************************986 PP

>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   1.3   4.4e-52   6.6e-49       1     141 [.     184     323 ..     184     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 4.4e-52
                                    -HHHHHHHHHHHHHHHHHHHHHHHTTH-HHHHHHHHHHHHHHHHHHHHHHTSSGGGGGSTTTHHHHHHHHHSCT.HHHHH CS
                 NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglglgdntkaalitrglaEmarlakalgakpetflglaglgDlivtctsgksRNrrf 80 
                                    Dv+G+e++ga+KN+iA+a+G++ g+glg+nt aa+itrglaE++rl++alga+  t++glag+gDl++tcts  sRNr+f
  gi|121638863|ref|YP_979087.1| 184 DVVGTEIGGACKNIIALACGMAVGIGLGENTAAAIITRGLAEIIRLGTALGANGATLAGLAGVGDLVATCTSPRSRNRSF 263
                                    9******************************************************************************* PP

                                    HHHHHCT--HHHHHHHHCC--HHHHHHHHHHHHHHHTT.G.HHHHHHHHHHHS---HHHHH CS
                 NAD_Gly3P_dh_C  81 GeelgkgesleeiekelnqvleGvetakevyellkkkgvemplleavykilyegkspeeli 141
                                    Ge+lg+ge+l+++ k  + v+eGv ++++v +l+++++vempl++av++++++g+s++e+i
  gi|121638863|ref|YP_979087.1| 264 GERLGRGETLQSAGKACH-VVEGVTSCESVLALASSYDVEMPLTDAVHRVCHKGLSVDEAI 323
                                    ************999776.***************************************997 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.3e-13   3.5e-10       1     107 [.       8     114 ..       8     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.3e-13
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGG CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKay 79 
                                    +a++GaGa G+ la  La ag +vtl++r++  +++++++ ++ +       l+p+ +++a++++ l+ ++ v++ v+a+
  gi|121638863|ref|YP_979087.1|   8 VAVMGAGAWGTALAKVLADAGGEVTLWARRAeVADQINTTRYNPDYLP-GALLPPSIHATADAEEALGGASTVLLGVPAQ 86 
                                    69*****************************77777999999888887.4555666555555799*************** PP

                                    GHHHHHHHHGGGECTCEEEEEESSSSCH CS
                           ApbA  80 qteealeeikplldpntvvlllqNGlgh 107
                                     + ++le+ +pll + ++ ++l  G++ 
  gi|121638863|ref|YP_979087.1|  87 TMRANLERWAPLLPEGATLVSLAKGIEL 114
                                    **********************999654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     1e-09   1.5e-06       2      96 ..       8     110 ..       7     111 .. 0.92
   2 ?   -1.2   0.0       2.1   3.1e+03      13      47 ..     142     173 ..     131     196 .. 0.66
   3 ?   -2.4   0.0         5   7.4e+03      18      49 ..     273     302 ..     262     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1e-09
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.............-EEECECHHHHHHH-SEEEE- CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.............vkvtavdneeaaeeadvvvla 68 
                                    +++ GaG  g ala+ l+ ag    e+++   r  e a+++  + +             + +ta d+eea+  a  v+l 
  gi|121638863|ref|YP_979087.1|   8 VAVMGAGAWGTALAKVLADAG---GEVTLW-ARRAEVADQINTTRYnpdylpgallppsIHATA-DAEEALGGASTVLLG 82 
                                    89*******************...****77.9999999999855545***********999999.*************** PP

                                    S-HHHHHHHHHHCGHHHHTTSEEEEESS CS
                  F420_oxidored  69 vkpedveevlselakdalkgklvisvla 96 
                                    v+ + + + l+ +a+ + +g +++s + 
  gi|121638863|ref|YP_979087.1|  83 VPAQTMRANLERWAPLLPEGATLVSLAK 110
                                    *************9999*******9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                    HHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                  F420_oxidored  13 alasgllaagaqpheivvansrnpekaeelaeelg 47 
                                     las ++++  ++  +v a+s +  +a +l+++l+
  gi|121638863|ref|YP_979087.1| 142 NLASEIAECQ-PAATVV-ACS-DSGRAVALQRALN 173
                                    5666666675.445555.744.4455666666665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5
                                    HHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                  F420_oxidored  18 llaagaqpheivvansrnpekaeelaeelgvk 49 
                                    l++ag ++ ++v +   + e++ +la+++ v+
  gi|121638863|ref|YP_979087.1| 273 LQSAG-KACHVVEG-VTSCESVLALASSYDVE 302
                                    55666.66677766.88888888888888754 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.6e-08   5.4e-05       2      88 ..       8     107 ..       7     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.6e-08
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..............EEE-SSHHHHHHHCSEEEE-SSSHH CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..............akaaesieelvasldvvitmvkagk 67 
                                    ++++G G  G+ +a+ l++ag +v+++ r++e ++++ +++              ++a++++ee++ ++ +v++ v+a +
  gi|121638863|ref|YP_979087.1|   8 VAVMGAGAWGTALAKVLADAGGEVTLWARRAEVADQINTTRynpdylpgallppsIHATADAEEALGGASTVLLGVPA-Q 86 
                                    89************************************99999**********************************9.6 PP

                                    HHHHHHHSHCCC--TT-EEEE CS
                  NAD_binding_2  68 avdeviegllealkkgdilid 88 
                                     +++ +e+ ++ l +g++l+ 
  gi|121638863|ref|YP_979087.1|  87 TMRANLERWAPLLPEGATLVS 107
                                    789999999999999998886 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.6e-06    0.0024       1      37 [.       7      43 ..       7      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealek 37
                                   +vav+GaG  G+ +a+v+a ag eV+l  +++e +++
  gi|121638863|ref|YP_979087.1|  7 TVAVMGAGAWGTALAKVLADAGGEVTLWARRAEVADQ 43
                                   69**************************999988776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.3e-06     0.014      37      77 ..       6      46 ..       4      58 .. 0.85
   2 ?   -0.8   0.0      0.55   8.3e+02      84     144 ..     113     175 ..      85     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.3e-06
                                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                   2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                   +tv+++G+G+ G+a+ak+l+  g +v+ + r+ +  ++ ++
  gi|121638863|ref|YP_979087.1|  6 STVAVMGAGAWGTALAKVLADAGGEVTLWARRAEVADQINT 46
                                   79*****************************9886664444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.55
                                    SHHHHHHH-SEEEE-S--STTTTTSBS....HHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTT CS
                   2-Hacid_dh_C  84 sleellaesDivslhlpltpetrhlin....aeelakmkkgailiNtaRGglvdeeaLleaLksg 144
                                    +l +l++ s++++ ++ ++p+   +i+    a+e+a++++ a ++ ++  g     aL +aL+sg
  gi|121638863|ref|YP_979087.1| 113 ELGTLMRMSQVIISVTGAEPAQVAVISgpnlASEIAECQPAATVVACSDSGR--AVALQRALNSG 175
                                    6677777777777777777777777763333556677788887777776553..34666666666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.5e-06     0.011       2      37 ..       8      43 ..       7      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.5e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrl 37
                                   v+v+G+G  g  lA++la+ g +Vt+  r+ ++  +
  gi|121638863|ref|YP_979087.1|  8 VAVMGAGAWGTALAKVLADAGGEVTLWARRAEVADQ 43
                                   89***************************9998744 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.4e-05     0.066       1      35 [.       8      50 ..       8     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG........- CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa........t 35
                                   ++++Gag  + ala+++a +g +vt+   r+e+a        +
  gi|121638863|ref|YP_979087.1|  8 VAVMGAGAWGTALAKVLADAGGEVTLWARRAEVAdqinttryN 50
                                   579****************************988555444442 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014       0.2       6      37 ..       7      38 ..       4      52 .. 0.87
   2 ?   -1.3   0.0      0.92   1.4e+03      52      96 ..      67     111 ..      62     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT CS
                           IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglreg 37
                                   ++av+G G+ G a a+ l d+g +v++  r+ 
  gi|121638863|ref|YP_979087.1|  7 TVAVMGAGAWGTALAKVLADAGGEVTLWARRA 38
                                   8************************9877665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.92
                                    EEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEE.ESSS CS
                           IlvN  52 ltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkala.fahG 96 
                                    ++++ea   a  v++ +P +++++ + e+ +p l eg++l+  a+G
  gi|121638863|ref|YP_979087.1|  67 ADAEEALGGASTVLLGVPAQTMRANL-ERWAPLLPEGATLVsLAKG 111
                                    56789999999999999999998888.7788999998876415555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.8e-05      0.15       1      40 [.      10      49 ..      10      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40
                                   + GaG+ G ++A  La+ag +v+l+ +r  +  ++ + ++
  gi|121638863|ref|YP_979087.1| 10 VMGAGAWGTALAKVLADAGGEVTLWARRAEVADQINTTRY 49
                                   56***********************999998877777776 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   5.4e-05      0.08     144     178 ..       7      41 ..       3      50 .. 0.82
   2 ?   -2.6   0.1       1.7   2.6e+03     147     178 ..     282     313 ..     232     323 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll 178
                                     ++v G+G+ G+ lA +la++g evtl  +r ++ 
  gi|121638863|ref|YP_979087.1|   7 TVAVMGAGAWGTALAKVLADAGGEVTLWARRAEVA 41 
                                    57899999999999999999999999988888775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                    EES-SHHHHHHHHH.HHHHT-EEEEEESSSSSS CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 147 vvGgGyiGvElAaa.laklgkevtlveardrll 178
                                    vv  G++++E   a ++++ +e +l +a  r++
  gi|121638863|ref|YP_979087.1| 282 VV-EGVTSCESVLAlASSYDVEMPLTDAVHRVC 313
                                    33.266666666662344566676666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2139.37
//
Query:       gi|121638864|ref|YP_979088.1|  [L=214]
Description: hypothetical protein BCG_3004 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-13   48.3   0.0    9.2e-13   47.9   0.0    1.1  1  CofC          Guanylyl transferase CofC like
    3.4e-09   37.2   3.6    4.6e-09   36.8   3.6    1.2  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0058   16.4   0.2       0.01   15.6   0.2    1.5  1  DUF2064       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.5e-16   9.2e-13       3     146 ..      12     166 ..      10     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.5e-16
                           CofC   3 viiPvsainsaktrlseilseeerkellkamlldvidalkrld....vlvvsedeevleyaldelgvevvkek..ekd.. 74 
                                    +ii v++ + aktrl++++s + r+++++aml+d   a++++     + v++ de     a   lg++v+ +   e d  
  gi|121638864|ref|YP_979088.1|  12 LIIAVKRLAAAKTRLAPVFSAQTRENVVLAMLVDTLTAAAGVGslrsITVITPDEAAAAAAA-GLGADVLADPtpEDDpd 90 
                                    69*************************************99643346889999998887777.99****98754333344 PP

                           CofC  75 .lntaveka..feeieekeviiipsdiPlikkedvkdllelekr.advviaPargGGtnllllrksalevkyedfs 146
                                     lnta+  a   ++   ++++++  d+P ++ +++ + +  +++     +a   g Gt +l     al+ +++  s
  gi|121638864|ref|YP_979088.1|  91 pLNTAITAAerVVAEGASNIVVLQGDLPALQTQELAEAISAARHhRRSFVADRLGTGTAVLCAFGTALHPRFGPDS 166
                                    5*****999766777889999************9999888766415678899999999999877777777766555 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   3.6   7.8e-13   4.6e-09      26     138 ..      42     159 ..      18     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 7.8e-13
                                    HHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTS..S-SHHHHHHHHHHH..H.SSSCEEEEETT-TT-- CS
                   NTP_transf_3  26 llervldalraag.vdevvvvggdeevlaalarlgvrvvededp..gkgplaslaaalra..aadadavlvlacDmPllt 100
                                    +l  +l a++ +g ++ ++v+++de+ +aa+a+lg++v++d+ p  +  pl +  +a+++  a++a+ ++vl +D+P l+
  gi|121638864|ref|YP_979088.1|  42 MLVDTLTAAAGVGsLRSITVITPDEAAAAAAAGLGADVLADPTPedDPDPLNTAITAAERvvAEGASNIVVLQGDLPALQ 121
                                    4444555555554468*************************99954589***999999998888**************** PP

                                    HHHHHHHHHCHHHHTSSEEEEESSSEEEECC.EEEGGGH CS
                   NTP_transf_3 101 pelverllaaaaasgadvvvptyegerghpl.lfrarll 138
                                    ++ +++ + aa+ ++ + +v+ + g+    l +f ++l 
  gi|121638864|ref|YP_979088.1| 122 TQELAEAISAAR-HHRRSFVADRLGTGTAVLcAFGTALH 159
                                    *********987.66667777777777666634455554 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.7e-06      0.01      45      90 ..      92     136 ..      43     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                    HHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHHTTT-S CS
                        DUF2064  45 lgeRlarafdrafeageepvlliGsDcpqltaalleqAfeaLeead 90 
                                    l + + + ++r++++g ++++++  D+p l+ + l++A++a +++ 
  gi|121638864|ref|YP_979088.1|  92 LNTAITA-AERVVAEGASNIVVLQGDLPALQTQELAEAISAARHHR 136
                                    3333333.3444689999***********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1572.07
//
Query:       gi|121638865|ref|YP_979089.1|  [L=742]
Description: polyphosphate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-75  250.6   0.0    3.7e-74  247.8   0.0    2.1  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
      1e-72  244.0   0.2    1.7e-72  243.3   0.2    1.3  1  PP_kinase      Polyphosphate kinase middle domain
    7.8e-54  181.7   0.0    6.2e-53  178.8   0.0    2.2  2  PP_kinase_C    Polyphosphate kinase C-terminal domain 2
    1.7e-36  124.8   0.0    4.2e-36  123.5   0.0    1.7  1  PP_kinase_N    Polyphosphate kinase N-terminal domain
    6.3e-13   48.8   0.0    1.5e-06   28.1   0.0    2.5  2  PLDc_2         PLD-like domain


Domain annotation for each model (and alignments):
>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.8   0.0     1e-77   3.7e-74       1     166 [.     386     552 ..     386     553 .. 0.98
   2 ?    0.1   0.1      0.14     5e+02      49      70 ..     602     623 ..     596     625 .. 0.90

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 1e-77
                                    SHHHHHHHS-EEEECTTB-S.CHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS--H CS
                  PP_kinase_C_1   1 sifeairkkdillhhPyesf.esvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArfdee 79 
                                    sif+++r+ d+l+hhPy+sf +sv++++e+Aa+dp+vlaik+tlYr++ ds+iv+aLi+Aae+gkqv++lvE+kArfde+
  gi|121638865|ref|YP_979089.1| 386 SIFATLREGDVLVHHPYDSFsTSVQRFIEQAAADPNVLAIKQTLYRTSGDSPIVRALIDAAEAGKQVVALVEIKARFDEQ 465
                                    689*****************8889******************************************************** PP

                                    HHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S---EEEEEESS-SS---SS-EEEEEEEE--HHHHHHHHHHHH CS
                  PP_kinase_C_1  80 nNiewakkleeagvkvvygvvglkvhaklllvvrreeeklrryvhlgtGnynektaklYtDlslltadeelgedveklfn 159
                                    +Ni+wa++le+agv+v+yg+vglk+h+k++lvvrre+ ++rry+h+gtGnyn+kta+lY+D++llta +++g+d+++lfn
  gi|121638865|ref|YP_979089.1| 466 ANIAWARALEQAGVHVAYGLVGLKTHCKTALVVRREGPTIRRYCHVGTGNYNSKTARLYEDVGLLTAAPDIGADLTDLFN 545
                                    ******************************************************************************** PP

                                    HHTT--- CS
                  PP_kinase_C_1 160 vltgksk 166
                                     ltg+s+
  gi|121638865|ref|YP_979089.1| 546 SLTGYSR 552
                                    ****987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                    --HHHHHHHHHHHTT-EEEEEE CS
                  PP_kinase_C_1  49 dskivkaLieAaengkqvtvlv 70 
                                    d ++++aL +A ++g ++ v+v
  gi|121638865|ref|YP_979089.1| 602 DEQVIDALYRASRAGVRIEVVV 623
                                    5689**************9998 PP

>> PP_kinase  Polyphosphate kinase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.3   0.2   4.7e-76   1.7e-72       2     202 .]     168     376 ..     167     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.3 bits;  conditional E-value: 4.7e-76
                                    HHHHHHHHHHHTTGGG---EE--TTTS-----TT-EEEEEEEESST-SS-..EEEEEE--TTS-SEEEE-.......... CS
                      PP_kinase   2 qkefleeyFeeevfpvLtplavdpshpfpflsnkslnlavelrkkekeekekefalvkvPsvlpRfielp.......... 71 
                                    +++ l++yF+e+vfpvLtplavdp+hpfpf+s++slnlav++r++e++++  +fa+vkvP++++Rf+el           
  gi|121638865|ref|YP_979089.1| 168 ERDRLSTYFNEQVFPVLTPLAVDPAHPFPFVSGLSLNLAVTVRQPEDGTQ--HFARVKVPDNVDRFVELAareaseeaag 245
                                    7899****************************************965555..9*********************999965 PP

                                    T.TSS-.EEEEHHHHHHCCHHHH-TTSEEEEEEEEEEE-SSS----.---.-------------------EEEEETT--H CS
                      PP_kinase  72 peeegkerfilledvIeanldelFpgyevleaylfrvtRnadleidedeaedlleeiekeLkkRrrgevvRLeveaempe 151
                                     e +   rf+++e++I+a+l+ lFpg+e++e+++fr+tRnad+e++ed  edll+++e+eL +Rr+g++vRLe++++m e
  gi|121638865|ref|YP_979089.1| 246 TEGRTALRFLPMEELIAAFLPVLFPGMEIVEHHAFRITRNADFEVEEDRDEDLLQALERELARRRFGSPVRLEIADDMTE 325
                                    3344444************************************************************************* PP

                                    HHHCCHTTTT---TTT.EEEE-S--GGGGGCS...--TTTSSS----B--H CS
                      PP_kinase 152 ellkfLlkeleldeedvyeidgpldltdlmklvgkdrpeLkyppftpqtpp 202
                                    ++l++Ll+el++++ dv+e++g+ldl+ l++++  drp+Lk+++f p t+p
  gi|121638865|ref|YP_979089.1| 326 SMLELLLRELDVHPGDVIEVPGLLDLSSLWQIYAVDRPTLKDRTFVPATHP 376
                                    *********************************99************9996 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16   5.6e+02      40      61 ..     435     456 ..     404     464 .. 0.83
   2 !  178.8   0.0   1.7e-56   6.2e-53       1     167 [.     559     727 ..     559     732 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                    PP_kinase_C  40 dkeiidkLyeAsqaGVkikliv 61 
                                    d+ i+++L++A++aG ++  +v
  gi|121638865|ref|YP_979089.1| 435 DSPIVRALIDAAEAGKQVVALV 456
                                    7889***********9987666 PP

  == domain 2  score: 178.8 bits;  conditional E-value: 1.7e-56
                    PP_kinase_C   1 Llvaplnlrekllelidreieaakag....kkakiilklNsledkeiidkLyeAsqaGVkiklivrgicclrpgvkglse 76 
                                    Llvap+ +r+ +++ ++re++a++a+     k++i lk+N+l+d+++id+Ly+As+aGV+i+++vrgic+lrpg +g+se
  gi|121638865|ref|YP_979089.1| 559 LLVAPHGIRAGIIDRVEREVAAHRAEgahnGKGRIRLKMNALVDEQVIDALYRASRAGVRIEVVVRGICALRPGAQGISE 638
                                    89******************9998642222589*********************************************** PP

                    PP_kinase_C  77 nikvisivdrfLEhaRiyifenggeeevyisSaDlmtRnldrRvevlvpvedeklkkelkeilelqlkDnvkareldedg 156
                                    ni v+si++rfLEh+Ri +f+    +e +i+SaD+m+RnldrRvev+++v++++l ++l+e++e  l+  ++ +el +dg
  gi|121638865|ref|YP_979089.1| 639 NIIVRSILGRFLEHSRILHFRA--IDEFWIGSADMMHRNLDRRVEVMAQVKNPRLTAQLDELFESALDPCTRCWELGPDG 716
                                    ********************87..678***************************************************** PP

                    PP_kinase_C 157 eykkvkekeek 167
                                    +++   +++++
  gi|121638865|ref|YP_979089.1| 717 QWTASPQEGHS 727
                                    **998876655 PP

>> PP_kinase_N  Polyphosphate kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   1.2e-39   4.2e-36       1     107 []      53     159 ..      53     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.2e-39
                                    XXXHHHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHCCHHHHH.HTT-..-----------HHHHHHHHH CS
                    PP_kinase_N   1 ylnRelSwLkFneRVLeeAedervplleRlkFlaIfssNlDEFfmvRvaslkrqleakvekksedgltpeeqlkaiseev 80 
                                    ylnRelSwL+Fn+RVL+ A+d+++plleR kFlaIf+sNlDEF+mvRva+lkr+ e +++ +s+dgltp+eql +i e++
  gi|121638865|ref|YP_979089.1|  53 YLNRELSWLDFNARVLALAADKSMPLLERAKFLAIFASNLDEFYMVRVAGLKRRDEMGLSVRSADGLTPREQLGRIGEQT 132
                                    89***************************************************9999999******************** PP

                                    HHHHHHHHHHHHHTHHHHHHHTTEEE. CS
                    PP_kinase_N  81 eelveeqekileeellpeLaeegikll 107
                                    ++l +++ +++ +++lp+L eegi+++
  gi|121638865|ref|YP_979089.1| 133 QQLASRHARVFLDSVLPALGEEGIYIV 159
                                    ************************985 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.8e-07    0.0021      22     132 ..     435     547 ..     424     548 .. 0.83
   2 !   28.1   0.0   4.2e-10   1.5e-06       9     131 ..     590     701 ..     585     703 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.8e-07
                         PLDc_2  22 dreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidgk.......tv 94 
                                    d+ i++al++aa+ g++v  l+     +a++ ++a+ ++ ++l  +agv v          H K++l+ ++       ++
  gi|121638865|ref|YP_979089.1| 435 DSPIVRALIDAAEAGKQVVALVEI---KARFDEQANIAWARAL-EQAGVHVAYGLV-GLKTHCKTALVVRRegptirrYC 509
                                    6789*******************9...6777666666666666.******987553.2568*******7444566666** PP

                         PLDc_2  95 ivGSsNltkrgldlnlElnvviedkelakeleeeFerl 132
                                     vG+ N++ +  +l  ++++ +  +++ + l++ F++l
  gi|121638865|ref|YP_979089.1| 510 HVGTGNYNSKTARLYEDVGLLTAAPDIGADLTDLFNSL 547
                                    *******************************9999875 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 4.2e-10
                         PLDc_2   9 kksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlyl 88 
                                    k +i++ +  + +d++++dal++a++ gv+++++++       +  ++ ++ ++e ++   +  r+   l+   H+ ++ 
  gi|121638865|ref|YP_979089.1| 590 KGRIRLKMNAL-VDEQVIDALYRASRAGVRIEVVVRG-----ICALRPGAQGISENIIVRSILGRF---LE---HSRILH 657
                                    66899999999.************************9.....454455555555554544444333...34...999999 PP

                         PLDc_2  89 id.gktvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                    ++  +   +GS+ + +r+ld++ E++  +++++l+++l+e Fe+
  gi|121638865|ref|YP_979089.1| 658 FRaIDEFWIGSADMMHRNLDRRVEVMAQVKNPRLTAQLDELFES 701
                                    96467899**********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5171.87
//
Query:       gi|121638866|ref|YP_979090.1|  [L=317]
Description: hydrolase mutT1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-16   59.7   0.0    5.9e-16   58.7   0.0    1.5  1  NUDIX       NUDIX domain
    9.7e-13   48.2   0.1    3.6e-12   46.4   0.1    1.8  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   6.6e-20   5.9e-16      16     131 .]      35     146 ..      17     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 6.6e-20
                                    E..EEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEC CS
                          NUDIX  16 e..vLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfleeve 93 
                                       + +++r   + ++W+lP+Gkv+pgEt+   A+RE+ EEtG +a+l + l     ++p+d p++  + + y+ +++  
  gi|121638866|ref|YP_979090.1|  35 PveIAVIHRP--RYDDWSLPKGKVDPGETAPVGAVREILEETGHRANLGRRLLT--VTYPTDSPFRGVKKVHYWAARSTG 110
                                    2557778888..7888************777************88877755543..456777777778999999999999 PP

                                    SGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHHH CS
                          NUDIX  94 gelepndenevsevrwvpleellkeklaaesrkllpwl 131
                                    ge +p+   ev+e+ w+p+ +++ + ++a++rk+l ++
  gi|121638866|ref|YP_979090.1| 111 GEFTPG--SEVDELIWLPVPDAMNKLDYAQDRKVLCRF 146
                                    999998..**************9999999999998775 PP

>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1     4e-16   3.6e-12       2      82 ..     157     236 ..     156     242 .. 0.91
   2 ?    0.1   0.0     0.062   5.6e+02     117     185 ..     234     300 ..     233     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4e-16
                                    EEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                     His_Phos_1   2 yLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEid 81 
                                    ++vRHG     +++  +  +  pL+++Gr+qAeal   l + + + +y+ +  R++qT+e++a++l+++++ ++ L E +
  gi|121638866|ref|YP_979090.1| 157 LVVRHGTAGS-KAHFSGDDSKRPLDKRGRAQAEALVPQLLAFGATDVYAADRVRCHQTMEPLAAELNVTIHNEPTLTEES 235
                                    78****6666.55578889999*******************************************************976 PP

                                    - CS
                     His_Phos_1  82 f 82 
                                    +
  gi|121638866|ref|YP_979090.1| 236 Y 236
                                    6 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.062
                                    -BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE-SS- CS
                     His_Phos_1 117 EsledvaaRvaaaleelaarhegetvlvVsHggvirallarllglpleelrrleldnaslsvlefdegg 185
                                    Es++   +R ++ + +++++ ++   ++++ g vi  l++++ + +  ++++ +    s  vl++ +g+
  gi|121638866|ref|YP_979090.1| 234 ESYANNPKRGRHRVLQIVEQVGT--PVICTQGKVIPDLITWWCERDGVHPDKSRNRKGSTWVLSLSAGR 300
                                    77888888888889999999986..79***************999999998888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2094.51
//
Query:       gi|121638867|ref|YP_979091.1|  [L=205]
Description: DNA-binding protein HU hupB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-26   92.6   0.2    1.3e-26   92.6   0.2    2.8  2  Bac_DNA_binding  Bacterial DNA-binding protein
     0.0026   17.8   1.3     0.0034   17.5   0.0    1.8  2  HU-HIG           HU domain fused to wHTH, Ig, or Glycine-rich
      0.005   16.7   0.0     0.0091   15.9   0.0    1.4  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.031   14.4   0.1    1.5  1  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
      0.045   13.9   0.0      0.082   13.1   0.0    1.4  1  HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1


Domain annotation for each model (and alignments):
>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.2   3.6e-30   1.3e-26       1      89 [.       1      89 [.       1      90 [. 0.98
   2 ?   -1.6   6.1      0.87   3.1e+03      55      88 ..     127     162 ..     113     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 3.6e-30
                                   EEHHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEEEEEE- CS
                Bac_DNA_binding  1 mtkkeLieeiaektgltkkdakrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvvkFkps 82
                                   m+k+eLi+ + +k g  +++a+++ve+++dti  a++kg++v+++gFG f+ ++r+ar +rnp+Tge+vk++++ v+ F+p+
  gi|121638867|ref|YP_979091.1|  1 MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPG 82
                                   9********************************************************************************* PP

                                   HHHHHHH CS
                Bac_DNA_binding 83 kelkeav 89
                                    ++k  v
  gi|121638867|ref|YP_979091.1| 83 AQFKAVV 89
                                   ***9876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.87
                                    E--BS-B-TTT--B--B--EEEEEEE..E-HHHHHH CS
                Bac_DNA_binding  55 rkartgrnpkTgekvkiparkvvkFk..pskelkea 88 
                                     k+   + p ++ + k pa+k vk +  p+k++ +a
  gi|121638867|ref|YP_979091.1| 127 AKKAATKAPAKKAATKAPAKKAVKATksPAKKVTKA 162
                                    333345667777777778888877642255555555 PP

>> HU-HIG  HU domain fused to wHTH, Ig, or Glycine-rich motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.4e-07    0.0034      36     121 ..       5      92 ..       1      95 [. 0.85
   2 ?   -1.7   0.4      0.83     3e+03     109     109 ..     154     154 ..     114     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.4e-07
                         HU-HIG  36 eLceeiskrstlsrgdvkavldaledelkeaLadGerVeLgelGyFslslks.kgvedekevransikkkki.nfrpgkk 113
                                    eL++  ++  +  r +  a+++ + d++++a  +G +V + ++G F    ++ + + ++ + ++ ++k  ++  frpg++
  gi|121638867|ref|YP_979091.1|   5 ELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAaRVARNPRTGETVKVKPTSVpAFRPGAQ 84 
                                    6666677777777888899*********************************455555888999********77****** PP

                         HU-HIG 114 lkkelkka 121
                                    +k  +++a
  gi|121638867|ref|YP_979091.1|  85 FKAVVSGA 92 
                                    **998876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.83
                         HU-HIG 109 r 109
                                    +
  gi|121638867|ref|YP_979091.1| 154 S 154
                                    1 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-06    0.0091       3      49 ..       6      52 ..       6      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-06
                HU-CCDC81_bac_2  3 LansiaeaegisyeeAlqkiekeveelkqeLeeegrveleniGeLsl 49
                                   L++ + ++ g + ++A+ ++e+ v+++ ++ +++ +v++ + G++ +
  gi|121638867|ref|YP_979091.1|  6 LIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQ 52
                                   778899999***********************************976 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.8e-06     0.031      12      61 ..      12      59 ..       8      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.8e-06
                HU-CCDC81_euk_2 12 aaaglsrdvVescvqetfqalgdllrngknvelefkgiGvLsirnrkvkm 61
                                   +++g +r+++ ++v++++ ++ +++++g +v+++  g+Gv+  r+r++++
  gi|121638867|ref|YP_979091.1| 12 QKLGSDRRQATAAVENVVDTIVRAVHKGDSVTIT--GFGVFEQRRRAARV 59
                                   678889*************************987..79***999999876 PP

>> HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.3e-05     0.082      20      87 ..      17      86 ..      10      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                HU-CCDC81_euk_1 20 tteqllliWdalgeyieeqlekgkgvhipnfGtFtfeapdldlkadknell..rdkklrrPvFvvdekfk 87
                                   +++q +++ +++ + i + + kg +v+i +fG F   ++   ++ +  + +  + k    P F +  +fk
  gi|121638867|ref|YP_979091.1| 17 DRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGEtvKVKPTSVPAFRPGAQFK 86
                                   6789999999************************988655555544333320022222256666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2304  (0.128507); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 1370.05
//
Query:       gi|121638868|ref|YP_979092.1|  [L=198]
Description: isopropylmalate isomerase small subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-24   84.4   0.0    4.6e-23   82.0   0.0    1.9  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   2.6e-27   4.6e-23       1     129 [.       1     116 [.       1     118 [. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.6e-27
                                    CCCCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE- CS
                    Aconitase_C   1 mekllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvvia 80 
                                    me + + +G+ +++ +snvdtd++ip  f++ ++++g++  l+ ++r           ++++v++  +++    +++v++
  gi|121638868|ref|YP_979092.1|   1 MEAFHTHSGIGVPLRRSNVDTDQIIPAVFLKRVTRTGFEDGLFAGWRS----------DPAFVLNLSPFD--RGSVLVAG 68 
                                    78899***************************************9984..........4679********..77777766 PP

                                    -SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                    Aconitase_C  81 gknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                      +fG+GSSRehA +al ++G+++vi+  F++If+ n+ k glL  e++
  gi|121638868|ref|YP_979092.1|  69 -PDFGTGSSREHAVWALMDYGFRVVISSRFGDIFRGNAGKAGLLAAEVA 116
                                    .*******************************************87766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1482.69
//
Query:       gi|121638869|ref|YP_979093.1|  [L=473]
Description: isopropylmalate isomerase large subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     5e-157  523.6   0.0   5.6e-157  523.4   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)
     0.0014   17.5   0.0      0.002   16.9   0.0    1.1  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.4   0.0  6.3e-161  5.6e-157       1     461 []      13     464 ..      13     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 523.4 bits;  conditional E-value: 6.3e-161
                      Aconitase   1 ekiwdahlveeeg.....iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealekn 75 
                                    ekiwd+h+v + g     + y+ d +l+++vt++qa+ +l+ a+++vrr++ tlat dh+vp+      +      +++ 
  gi|121638869|ref|YP_979093.1|  13 EKIWDDHIVVSGGgcapdLIYI-DLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATEDHNVPTV-----D------IDQP 80 
                                    79*****996633354447788.****************************************9.....3......3667 PP

                      Aconitase  76 ledefernkeryefLksaakafgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaea 152
                                    ++d+++r  +++e+L++++++fgir+  +g   qGIvH+v+++ gl++pg+t+v++DSHT+++g++G+la+G+G++e+e+
  gi|121638869|ref|YP_979093.1|  81 IADPVSR--TQVETLRRNCAEFGIRLHSMGdieQGIVHVVGPQLGLTQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEH 158
                                    89*****..*********************9************************************************* PP

                      Aconitase 153 vllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttg 232
                                    vl++q+l l+  k++ v+++G+l++gv+akD++la+i+k+++ g++g+v+E+ G+++esLs+e+r+Ti+NM++E+GA++g
  gi|121638869|ref|YP_979093.1| 159 VLATQTLPLRPFKTMAVNVDGRLPDGVSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAG 238
                                    ******************************************************************************** PP

                      Aconitase 233 lfpvdektleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlstlepsvagpkrPqdavplselvk.k. 309
                                    ++++de+t+++L+  gr++a+ +++++d+a  ++ +l++d +a++d+++ ld+++l+p v+++++P + vpl   v+ + 
  gi|121638869|ref|YP_979093.1| 239 MVAPDETTYAFLR--GRPHAP-TGAQWDTALVYWqRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPLAAAVPdPq 315
                                    *************..******.7***********88****************************************9753 PP

                      Aconitase 310 efkeelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvk 388
                                     +++++e++aaekal+y +l++gt +++++vd++++gSCTN+++ed+r +a++l+     g+kv++gv+++++PGS +v+
  gi|121638869|ref|YP_979093.1| 316 LMTDDAERQAAEKALAYmDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAEVLR-----GRKVADGVRMLIVPGSMRVR 390
                                    69999************9*************************************.....******************** PP

                      Aconitase 389 ayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                                    a++eaeGl ei+++aG+++++agCs+C+g n+d+l++ge+++ +sNRNFegRqg+++r++L+SP++++a+A+ G
  gi|121638869|ref|YP_979093.1| 391 AQAEAEGLGEIFTDAGAQWRQAGCSMCLGmNPDQLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRG 464
                                    ***********************************************************************988 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-07     0.002     285     366 ..     340     426 ..     311     447 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-07
                         DUF521 285 kakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvtt.srevkeeaerlglveklekaGvkvlsdtCmvv.. 360
                                    + +e  vd+v++G c    +e+lr +ae+l+g+k++++v+++++  s  v+++ae++gl e+  +aG++  +  C ++  
  gi|121638869|ref|YP_979093.1| 340 AMREIAVDAVFVGsCTNGRIEDLRVVAEVLRGRKVADGVRMLIVPgSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMClg 419
                                    4567789999999678889******************999887751677*******************987766644433 PP

                         DUF521 361 .splikk 366
                                     +p   +
  gi|121638869|ref|YP_979093.1| 420 mNPDQLA 426
                                    3555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3414.76
//
Query:       gi|121638870|ref|YP_979094.1|  [L=233]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-16   58.1   0.2    7.2e-14   51.7   0.2    2.3  1  IclR      Bacterial transcriptional regulator
    5.2e-10   39.0   0.9    1.6e-09   37.4   0.5    2.1  2  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.0   0.4      0.078   12.9   0.1    2.2  2  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.2   1.2e-17   7.2e-14       7     126 ..     124     229 ..     119     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.2e-17
                                    TSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEE CS
                           IclR   7 saiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAapi 86 
                                    + +G rlp+ a + +K+lLa+ d++ + a+l +        + +       ++La+v ++G+a +  E e gv++++ap+
  gi|121638870|ref|YP_979094.1| 124 VPVGARLPMTAGSGAKVLLAHTDAATQAAVLPK--------AVFS-----ARALAEVCRRGWAQSVAEREPGVASVSAPV 190
                                    569*******************99999999999........3333.....467899************************ PP

                                    E-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHH CS
                           IclR  87 fdasgevvaAvsvsgptarlteeelkeellalvreaArki 126
                                    +d +g v+aA+svsgp+ r+ ++   +  +a +  aA+++
  gi|121638870|ref|YP_979094.1| 191 RDGRGVVIAAISVSGPIDRMGRRPGVR-WAADLLSAADAL 229
                                    ********************9999998.666666666665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.5   2.7e-13   1.6e-09       2      48 ..      10      54 ..       9      57 .. 0.95
   2 ?   -2.6   0.0      0.86   5.1e+03       7      18 ..      85      96 ..      84     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.7e-13
                                   HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                   ld+a+ +L a+ae p +  l+el++rt+lp++t++Rl + L+ ++++
  gi|121638870|ref|YP_979094.1| 10 LDKAVGVLHAVAESPCG--LAELCDRTDLPRATAYRLAAALEVHRLL 54
                                   8*************997..**************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.86
                                   HHHCT-CTTBSS CS
                       HTH_IclR  7 aiLdalaeapqe 18
                                   a+L +l+ a++e
  gi|121638870|ref|YP_979094.1| 85 AVLPQLRDATGE 96
                                   799999999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.3e-05     0.078       9      55 ..      15      58 ..       9      63 .. 0.90
   2 ?   -2.1   0.0      0.61   3.7e+03       8      18 ..     161     171 ..     158     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                    vL+a++ +p   +  +el++r++l+++++ r+ + L+ + L+ r  
  gi|121638870|ref|YP_979094.1| 15 GVLHAVAESP---CGLAELCDRTDLPRATAYRLAAALEVHRLLGRGQ 58
                                   69*******9...9************************999987765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.61
                                    HHHHHHHHCTT CS
                         MarR_2   8 arvLaaLgrrp 18 
                                    ar+La++ rr+
  gi|121638870|ref|YP_979094.1| 161 ARALAEVCRRG 171
                                    45666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1745.03
//
Query:       gi|121638871|ref|YP_979095.1|  [L=286]
Description: hypothetical protein BCG_3011c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2340.55
//
Query:       gi|121638872|ref|YP_979096.1|  [L=163]
Description: hypothetical protein BCG_3012 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-21   75.4   0.0    4.7e-21   74.8   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    1.6e-09   37.9   0.1    1.9e-09   37.6   0.1    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    1.4e-05   24.7   0.0      2e-05   24.2   0.0    1.2  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   7.9e-25   4.7e-21       3      88 .]      14     100 ..      11     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 7.9e-25
                                    HHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEEEEEEE CS
                 Putative_PNPOx   3 eelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde...lgrgvrieG 79 
                                    +e+++f+++s++++lAT+++dG+P++++++++  dg+  i++ t a+s+k+ nl+++prv++l+ d +   + rgv++eG
  gi|121638872|ref|YP_979096.1|  14 AEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVIDGE--IWLETKAKSQKAVNLRRDPRVSFLLEDGDtydTLRGVSFEG 91 
                                    599**********************************..**************************9999*********** PP

                                    EEEEESCHH CS
                 Putative_PNPOx  80 taelvsdge 88 
                                      e+v+++e
  gi|121638872|ref|YP_979096.1|  92 VTEIVEEPE 100
                                    ******986 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   3.2e-13   1.9e-09       2     133 ..      13     138 ..      12     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.2e-13
                                    HHHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEE CS
                   Pyridox_ox_2   2 reeilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslny 79 
                                    ++ei ++++++++g+la+   dg+p+++ + y+v ++++++ +  +s++a  lr  p v++ +++ d +++         
  gi|121638872|ref|YP_979096.1|  13 EAEIADFVNSSRTGTLATIGpDGQPHLTAMWYAVIDGEIWLETKAKSQKAVNLRRDPrVSFLLEDGDTYDT--------L 84 
                                    789*****************8999*******************9999999999956669999999777333........4 PP

                                    EEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEE CS
                   Pyridox_ox_2  80 rSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlk 133
                                    r V   G  e v+++e  +++  +++e+++  + ++++p+ ++ +++   +r+ 
  gi|121638872|ref|YP_979096.1|  85 RGVSFEGVTEIVEEPEALHRVGVSVWERYTGPYTDECKPMVDQMMNKRVGVRIV 138
                                    67999************************8888999999999999997777765 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.3e-09     2e-05       4      94 ..      14     105 ..      12     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.3e-09
                  Pyrid_ox_like   4 kklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkky.....vsv 78 
                                    +++++ v++ +t+ L+t+  dg+ +   M  + +  dg++w  tk +s+k+ ++r+d++v++++ d   ++y     vs+
  gi|121638872|ref|YP_979096.1|  14 AEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVI--DGEIWLETKAKSQKAVNLRRDPRVSFLLEDG--DTYdtlrgVSF 89 
                                    578999*************9*******9998876..79**************************984..44533444788 PP

                  Pyrid_ox_like  79 sGtaevvedrakieel 94 
                                    +G+ e+ve+++ ++  
  gi|121638872|ref|YP_979096.1|  90 EGVTEIVEEPEALHRV 105
                                    8899999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1274.25
//
Query:       gi|121638873|ref|YP_979097.1|  [L=490]
Description: glutamyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-75  254.0   0.0      2e-75  253.6   0.0    1.1  1  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.6   0.0   1.1e-79     2e-75       2     311 ..       7     323 ..       6     326 .. 0.94

  Alignments for each domain:
  == domain 1  score: 253.6 bits;  conditional E-value: 1.1e-79
                                    -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---S........SEEEE CS
                   tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwd........ekpty 73 
                                    Vr+Rf P+PtG +H+G  ++al+n+++A++++G+f+ RieDTd++r  ee   + l++l wlg++wd        ++p++
  gi|121638873|ref|YP_979097.1|   7 VRVRFCPSPTGTPHVGLVRTALFNWAYARHTGGTFVFRIEDTDAQRDSEESYLALLDALRWLGLDWDegpevggpYGPYR 86 
                                    9******************************************************************************* PP

                                    GGGGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTT CS
                   tRNA-synt_1c  74 qsdrfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidee 153
                                    qs+r ++++++  +L++ G AY ++ t+ee+e+   +   +g + +  yd+  ++l++ +     aeg++ vvRl+++  
  gi|121638873|ref|YP_979097.1|  87 QSQRAEIYRDVLARLLAAGEAYHAFSTPEEVEARHVA---AGRNPKLGYDNFDRHLTDAQRAAYLAEGRQPVVRLRMPDD 163
                                    *******************************986655...343468899999999999999999**************99 PP

                                    SSGGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHT...T-..S.- CS
                   tRNA-synt_1c 154 ssvefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwlleal...gl..evp 228
                                       +++Dlvrg + ++  ++ d+ ++++ + P Y + ++ dDal++ithvlr+e+ l +tp++++l +al   g+  ++p
  gi|121638873|ref|YP_979097.1| 164 DL-AWNDLVRGPVTFAAGSVPDFALTRASGDPLYTLVNPCDDALMKITHVLRGEDLLPSTPRQLALHQALiriGVaeRIP 242
                                    55.*****************************************************************974433322569 PP

                                    EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHH CS
                   tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafd 308
                                    +f+h++ +l++  kklSKR+ +      + ++ ++ +e lln+l++lGw+++++++lf  +e+  +fd+  + +s++ fd
  gi|121638873|ref|YP_979097.1| 243 KFAHLPTVLGEGTKKLSKRDPQSN--LFAHRDRGFIPEGLLNYLALLGWSIADDHDLFGLDEMVAAFDVADVNSSPARFD 320
                                    ********************9988..77889************************************************* PP

                                    HHH CS
                   tRNA-synt_1c 309 rkk 311
                                    +kk
  gi|121638873|ref|YP_979097.1| 321 QKK 323
                                    998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3527.20
//
Query:       gi|121638874|ref|YP_979098.1|  [L=239]
Description: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-68  230.2   0.0    2.5e-68  230.0   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
    3.5e-10   40.6   1.2    9.5e-10   39.2   0.2    2.2  2  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.0   0.0   2.8e-72   2.5e-68       1     218 []      36     234 ..      36     234 .. 0.97

  Alignments for each domain:
  == domain 1  score: 230.0 bits;  conditional E-value: 2.8e-72
                                    .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHH CS
                  FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsvee 80 
                                    k+vc+g+nya+h++e+g     pp       pv+flk++++++gp++pir+Pa +  +++E+ELa+vig+++++v ++++
  gi|121638874|ref|YP_979098.1|  36 KVVCVGKNYADHIAEMGGR---PPA-----DPVIFLKPNTAIIGPNTPIRLPANASPVHFEGELAIVIGRACKDV-PAAQ 106
                                    689*************844...555.....578******************************************.9*** PP

                                    HHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSH CS
                  FAA_hydrolase  81 AedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifsp 160
                                    A d i+Gyt++nDvsaRd q+++    +w+++k+ dtf+p+Gpwivt  +  dp+dlelr+ vng+++q+++t+ mi+++
  gi|121638874|ref|YP_979098.1| 107 AVDNILGYTIGNDVSARDQQQSDG---QWTRAKGHDTFCPVGPWIVTDLAPFDPADLELRTVVNGDVKQHARTSLMIHDI 183
                                    ************************...***************************************************** PP

                                    HHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                  FAA_hydrolase 161 aeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                      +++++sa++tL pGdliltGTp+gvg        ++dgD+v+++ieg+G+l+n+V+
  gi|121638874|ref|YP_979098.1| 184 GAIVEWISAIMTLLPGDLILTGTPAGVG-------PIEDGDTVSITIEGIGTLTNPVV 234
                                    **************************98.......5*******************995 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.2   1.1e-13   9.5e-10      21      50 .]       2      31 ..       1      31 [. 0.96
   2 ?   -1.3   0.1      0.46   4.2e+03      25      40 ..     203     219 ..     199     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.1e-13
                                   EEEEESS-TTSS-EEEEEEEEGGGSEEE-S CS
                        DUF2437 21 tvvvlagdpfgavqpTGervpLadVrLLAP 50
                                   t +++a++pfg++++TG+++pLadVrLLAP
  gi|121638874|ref|YP_979098.1|  2 TAREIAEHPFGTPTFTGRSWPLADVRLLAP 31
                                   6799*************************9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.46
                                    ESS-TTS.S-EEEEEEE CS
                        DUF2437  25 lagdpfg.avqpTGerv 40 
                                    l+g+p g ++ + G +v
  gi|121638874|ref|YP_979098.1| 203 LTGTPAGvGPIEDGDTV 219
                                    78888855888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1954.10
//
Query:       gi|121638875|ref|YP_979099.1|  [L=445]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-43  149.5  37.7    4.2e-43  147.6  30.5    2.1  3  MFS_1       Major Facilitator Superfamily
    0.00061   18.8   9.0        0.2   10.5   7.0    2.4  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
      0.012   14.9  26.1      0.085   12.1  26.1    2.2  1  MFS_4       Uncharacterised MFS-type transporter YbfB
        0.2   10.5  17.7      0.051   12.4  10.2    2.2  2  Sugar_tr    Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.031   1.4e+02      60      84 ..       9      31 ..       8      39 .. 0.75
   2 !  147.6  30.5   9.4e-47   4.2e-43       5     353 .]      22     356 ..      18     356 .. 0.90
   3 !   14.3   0.7   3.2e-06     0.014     109     173 ..     327     395 ..     325     443 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.031
                          MFS_1 60 Grrr.vlllglllfalglllllfass 84
                                   G+r+ +++++l ++a++ +l++  ++
  gi|121638875|ref|YP_979099.1|  9 GARWaIMIVSLGVTASS-FLFI--NG 31
                                   999*9*********999.5544..44 PP

  == domain 2  score: 147.6 bits;  conditional E-value: 9.4e-47
                          MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.s 83 
                                    ++ s+l ++ +++++p  l ++ g   s +gll+++ ++g +v+++ +G+l d +G r v+ +g +l+a+++++++ + +
  gi|121638875|ref|YP_979099.1|  22 TASSFLFINGVAFLIP-RLENARGTPLSHAGLLASMPSWGLVVTMFAWGYLLDHVGERMVMAVGSALTAAAAYAAA-SvH 99 
                                    5677888888999999.99999**99*********************************************55555.348 PP

                          MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                    sl ++ v+ +l G++ag+ ++ag+ l++ wfp+++rg+a+g+ +++  lG++ g+l+ + la+  g +a  ++ a+v+ l
  gi|121638875|ref|YP_979099.1| 100 SLLWIGVFLFLGGMAAGGCNSAGGRLVSGWFPPQQRGLAMGIRQTAQPLGIASGALVIPELAER-GVHAGLMFPAVVCTL 178
                                    888999********************************************************55.8************** PP

                          MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgl 243
                                    a+v  +l ++++p+++++k++++e           + +  + +  lw + +a++l ++  + ++t++ ++l  ++g+s +
  gi|121638875|ref|YP_979099.1| 179 AAVASVLGIVDPPRKSRTKASEQE-----------LASPYRGSSILWRIHAASALLMMPQTVTVTFMLVWLINHHGWS-V 246
                                    ***766666666666666666666...........456688899999999999999999999****************.* PP

                          MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfv.fpsl 321
                                     +ag+l+ +++l+ga +++ +gr+sd++g+  r+    l++++aa+ l+lla+ ++    + vl++i +   ++  +++ 
  gi|121638875|ref|YP_979099.1| 247 AQAGVLVTISQLLGALGRVAVGRWSDHVGS--RMRPVRLIAAAAAATLFLLAAVDNEGSRYDVLLMIAIsVIAVLdNGLE 324
                                    ***************************999..88888888888888888888888999999999999995555559**** PP

                          MFS_1 322 lalasdlappeeagtasglfntagslggalgp 353
                                    +++++++a+p  +g+a+g+ nt++ l++a gp
  gi|121638875|ref|YP_979099.1| 325 ATAITEYAGPYWSGRALGIQNTTQRLMAAAGP 356
                                    *****************************998 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 3.2e-06
                          MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll....p 173
                                    +i++++ +   gra+g+ +++  l a+ gp+l g l++ + ++ ++ +++++ l a+ l+ + l    +
  gi|121638875|ref|YP_979099.1| 327 AITEYAGPYWSGRALGIQNTTQRLMAAAGPPLFGSLITTAAYPTAWALCGVFPLAAVPLVPVRLlppgL 395
                                    67888888889********************9999999999*************996655444433330 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   7.0   4.4e-05       0.2     258     369 ..      46     156 ..      13     157 .. 0.90
   2 !    7.5   0.0   0.00037       1.7      26      83 ..     239     296 ..     227     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                     MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaavey 337
                                    + + +G l  +   + +++ f   +ll+ +G + ++ ++  ++++     a+++++ ++ ++ +L g++ g + +a+ + 
  gi|121638875|ref|YP_979099.1|  46 PLSHAGLLASMPSWGLVVTMFAWGYLLDHVGERMVMAVGSALTAAAAYAAASVHSLLWIGVFLFLGGMAAGGCNSAGGRL 125
                                    55667777888888889999999***********************999******************************* PP

                     MFS_1_like 338 vskiapksleatgqgllsglyfglGralGsli 369
                                    vs  +p++ ++  +g+ +++   lG a+G+l+
  gi|121638875|ref|YP_979099.1| 126 VSGWFPPQQRGLAMGIRQTA-QPLGIASGALV 156
                                    ****************9988.68999999875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00037
                     MFS_1_like  26 lkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsll 83 
                                    +++ g ++++ g++++i  l+  l++  +g  +D++g r+  v+l + ++a++++ l 
  gi|121638875|ref|YP_979099.1| 239 INHHGWSVAQAGVLVTISQLLGALGRVAVGRWSDHVGSRMRPVRLIAAAAAATLFLLA 296
                                    468999*********************************9977776666666555333 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  26.1   1.9e-05     0.085      14     252 ..      34     270 ..      15     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                          MFS_4  14 piLPallaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGv 93 
                                     ++P l ++ +  ls+aglla++   G  v  ++  + l +  eR+++ +g  +t++++ a a ++s++++ +  fl G+
  gi|121638875|ref|YP_979099.1|  34 FLIPRLENARGTPLSHAGLLASMPSWGLVVTMFAWGYLLDHVGERMVMAVGSALTAAAAYAAASVHSLLWIGVFLFLGGM 113
                                    5899**************************************************************************** PP

                          MFS_4  94 asAvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsassl.Wlalavlsavllllvalllpra 172
                                    a++    +g+ lv     +++r+  +++      lGia ++l+++ l + g++a  +   ++  l+av+ +l ++  pr+
  gi|121638875|ref|YP_979099.1| 114 AAGGCNSAGGRLVSGWFPPQQRGLAMGIRQTAQPLGIASGALVIPELAERGVHAGLMfPAVVCTLAAVASVLGIVDPPRK 193
                                    *****************************************************999955778999*****9999999988 PP

                          MFS_4 173 alreasaaaeaakaeqkslpllalllaYglaGfGYiitatFlvaiardg.aggalleallWllvGlaaivgvlvwlrvak 251
                                    ++++as++  a  + + s  l+++ +a  l  +   +t tF+     ++ + + +++    +lv ++ ++g+l    v +
  gi|121638875|ref|YP_979099.1| 194 SRTKASEQELA-SPYRGSSILWRIHAASALLMMPQTVTVTFMLVWLINHhGWSVAQA---GVLVTISQLLGALGRVAVGR 269
                                    88888777666.7888899999*******************9776655313333333...34455555555544443333 PP

                          MFS_4 252 r 252
                                     
  gi|121638875|ref|YP_979099.1| 270 W 270
                                    2 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  10.2   1.1e-05     0.051      45     188 ..      47     187 ..      15     192 .. 0.86
   2 ?    2.4   0.8     0.012        55      44     100 ..     245     303 ..     192     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                    ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                       Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                     +  gl++s+ + G +++ +  g+l d +G + +++++++l+ ++a   a  +   s+  + v  +l G+++G+++    
  gi|121638875|ref|YP_979099.1|  47 LSHAGLLASMPSWGLVVTMFAWGYLLDHVGERMVMAVGSALTAAAAYAAASVH---SLLWIGVFLFLGGMAAGGCNSAGG 123
                                    45789*************************************99999888888...778888889*************** PP

                                    HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                       Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                     ++s   p++ Rg  +++ q+a  +Gi  +a +   l++ + + g  ++  ++ + a++ ++++
  gi|121638875|ref|YP_979099.1| 124 RLVSGWFPPQQRGLAMGIRQTAQPLGIASGALVIPELAERGVHAGLMFPAVVCTLAAVASVLGI 187
                                    *******************************999999777777888888888888887766665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                                    ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..S CS
                       Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..n 100
                                    s  + g++v i ++ +++G + +g ++d +G +   +  ++ + ++++   aa ++  +
  gi|121638875|ref|YP_979099.1| 245 SVAQAGVLVTISQLLGALGRVAVGRWSDHVGSRMRPVRLIAAAAAATLFLLAAVDNegS 303
                                    66688999999999999999999999999998876666555555555555555444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2987.58
//
Query:       gi|121638876|ref|YP_979100.1|  [L=336]
Description: 3-isopropylmalate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-85  288.0   0.0    1.2e-85  287.7   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
       0.16   11.0   0.0       0.21   10.7   0.0    1.1  1  IFRD      Interferon-related developmental regulator (IFRD)


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.7   0.0   1.3e-89   1.2e-85       1     333 [.       2     330 ..       2     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 287.7 bits;  conditional E-value: 1.3e-89
                                    EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.SSSS CS
                         Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.ekev 79 
                                    k+a++ gdgiGpev+++a+kvl+a++  +   ++  ++d+G+  +++tge lp+  ++ +++ d++llga+g p  +++v
  gi|121638876|ref|YP_979100.1|   2 KLAIIAGDGIGPEVTAEAVKVLDAVV--P--GVQKTSYDLGARRFHATGEVLPDSVVAELRNHDAILLGAIGDPSvPSGV 77 
                                    5789**********************..4..58899***************************************55555 PP

                                    SHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEH CS
                         Iso_dh  80 rpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyse 159
                                         Ll+Lr eld   nlrp++++   +v+spl      ++d+v+vRe t+g Y g+  +++   +++eva ++ + ++
  gi|121638876|ref|YP_979100.1|  78 LERGLLLRLRFELDHHINLRPARLY--PGVASPLSG--NPGIDFVVVREGTEGPYTGNGGAIRVG-TPNEVATEVSVNTA 152
                                    54446799*****************..799999997..4679****************9999986.7************* PP

                                    HHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE- CS
                         Iso_dh 160 eeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtk 238
                                     +++r++  afe A++r +k++tlv+K nvl+ +  lw ++v+ev e  ypd+e+  q vD+a+ +++++p +fdVivt+
  gi|121638876|ref|YP_979100.1| 153 FGVRRVVADAFERARRR-RKHLTLVHKTNVLTLAGgLWLRTVDEVGE-CYPDVEVAYQHVDAATIHMITDPGRFDVIVTD 230
                                    *****************.****************99***********.******************************** PP

                                    HHHHHHHHHHHHHHTTSGCC-EEEEEET..SS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHH CS
                         Iso_dh 239 NlfGDilSDeaaalvGslGllpSaslge..kkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiek 316
                                    NlfGDi+ D+aaa+ G++Gl++S ++ +   +  +fE+vHGsapdiag+++a p+a+i+S+al+L + lg+++aA+++++
  gi|121638876|ref|YP_979100.1| 231 NLFGDIITDLAAAVCGGIGLAASGNIDAtrANPSMFEPVHGSAPDIAGQGIADPTAAIMSVALLLSH-LGEHDAAARVDR 309
                                    ***************************988889**********************************.************ PP

                                    HHHHHHHH....TSCCHHHCT CS
                         Iso_dh 317 Avekvlea....givTkDlag 333
                                    Ave+ l+     +  T D+++
  gi|121638876|ref|YP_979100.1| 310 AVEAHLATrgseRLATSDVGE 330
                                    ******987666778888875 PP

>> IFRD  Interferon-related developmental regulator (IFRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.3e-05      0.21     193     242 ..     284     334 ..     252     336 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
                           IFRD 193 vtaalsawglLltllpssklnkkleedl.eealealvelLdssdvevriAA 242
                                     taa+ +++lLl++l ++++++ +++ +   ++ + +e L  sdv  riAA
  gi|121638876|ref|YP_979100.1| 284 PTAAIMSVALLLSHLGEHDAAARVDRAVeAHLATRGSERLATSDVGERIAA 334
                                    69************************998558999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2422.35
//
Query:       gi|121638877|ref|YP_979101.1|  [L=528]
Description: D-3-phosphoglycerate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-61  207.3   0.0      2e-61  206.4   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    8.9e-38  129.0   0.5    1.5e-37  128.3   0.5    1.4  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
      8e-09   35.1   0.2    2.6e-08   33.5   0.2    2.0  1  ACT             ACT domain
    2.7e-06   27.6   0.1    1.5e-05   25.2   0.0    2.1  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0035   17.4   0.0     0.0082   16.2   0.0    1.6  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0071   15.9   0.0      0.016   14.8   0.0    1.6  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.029   14.2   0.0    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.078   13.4   0.0       0.49   10.9   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
       0.08   13.5   0.0       0.26   11.9   0.0    1.8  1  ACT_4           ACT domain
       0.11   13.3   0.0       0.65   10.8   0.0    2.3  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
       0.14   12.6   0.0       0.38   11.2   0.0    1.8  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
       0.17   12.5   0.1       0.17   12.5   0.1    2.4  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0   1.3e-64     2e-61       1     178 []     107     281 ..     107     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 1.3e-64
                                    HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                                    lallla++r++++ad+++re++w ++++++g+e+ gktvG++GlGrIGq va+r++afg+ v+ayd++ ++ + +++lg+
  gi|121638877|ref|YP_979101.1| 107 LALLLAASRQIPAADASLREHTW-KRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPAR-AAQLGI 184
                                    589********************.9*********************************************988.99**** PP

                                    EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSG CS
                   2-Hacid_dh_C  81 elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplp 160
                                    el sl++lla++D++s+hlp tpet +li++e+lak k+g+i++N+aRGglvde+aL++a+  g++++a+lDvf++ep +
  gi|121638877|ref|YP_979101.1| 185 ELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCT 264
                                    ******************************************************************************** PP

                                    TCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 161 edspllelpnviltPHia 178
                                     dspl+el +v++tPH++
  gi|121638877|ref|YP_979101.1| 265 -DSPLFELAQVVVTPHLG 281
                                    .77*************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.5     1e-40   1.5e-37       1     134 []       6     313 ..       6     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 1e-40
                                    EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaa 80 
                                    vli ++l +++++ l + +vev+  d +++++ll+++++adal+vrs t v+aevl+a+pkLk++aragvG DnvD+daa
  gi|121638877|ref|YP_979101.1|   6 VLIADKLAPSTVAALGD-QVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAA 84 
                                    7999*************.55888888****************************************************** PP

                                    HHTT-EEEE-TTTTHHHHHHHH.......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
                     2-Hacid_dh  81 kerGilVtnvpgystesvAElt.......................................................... 102
                                    ++rG+lV+n+p+++ +s+AE++                                                          
  gi|121638877|ref|YP_979101.1|  85 TARGVLVVNAPTSNIHSAAEHAlalllaasrqipaadaslrehtwkrssfsgteifgktvgvvglgrigqlvaqriaafg 164
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|121638877|ref|YP_979101.1| 165 ayvvaydpyvsparaaqlgiellslddllaradfisvhlpktpetaglidkealaktkpgviivnaargglvdeaalada 244
                                    ******************************************************************************** PP

                                    .....................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 .....................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                         a+T eaq ++++ +ae+++ +l+ge +++avn
  gi|121638877|ref|YP_979101.1| 245 itgghvraagldvfatepctdsplfelaqvvvtphlgASTAEAQDRAGTDVAESVRLALAGEFVPDAVN 313
                                    *****************************************************************9998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   1.7e-11   2.6e-08       3      64 ..     456     515 ..     454     518 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.7e-11
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                    l+++  DrPG+L++++++l+ +g+Ni  ++ +++ +  ++ +++ +  d++++++v  a+ +
  gi|121638877|ref|YP_979101.1| 456 LIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAE--GPGATILLRLDQDVPDDVRTAIAA 515
                                    789999******************************..8*****************999987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         1   1.5e+03     103     133 ..      83     112 ..      76     120 .. 0.75
   2 !   25.2   0.0   9.9e-09   1.5e-05       1      90 [.     143     231 ..     143     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                                    HHHHTT-EEEEEEEESHHHHHHHT-EEEEEE CS
                  NAD_binding_2 103 elkekglkfldaPVSGGeegAekGtLsimvG 133
                                    +++++g+ +++aP S     Ae++  +++++
  gi|121638877|ref|YP_979101.1|  83 AATARGVLVVNAPTSNIHSAAEHAL-ALLLA 112
                                    5788999999999998887777765.55555 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9.9e-09
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llea 79 
                                    ++g++GlG +G+  a+++++ g  v++y+   + + ++++ g+  + s+ +l+a++d++ + +++++++  +i++  l++
  gi|121638877|ref|YP_979101.1| 143 TVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPA-RAAQLGI-ELLSLDDLLARADFISVHLPKTPETAGLIDKeALAK 220
                                    58***************************775544.3444566.566899************************999999 PP

                                    --TT-EEEE-S CS
                  NAD_binding_2  80 lkkgdilidgs 90 
                                     k+g i+++ +
  gi|121638877|ref|YP_979101.1| 221 TKPGVIIVNAA 231
                                    *******9876 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.5e-06    0.0082      21     109 ..     139     230 ..     128     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.5e-06
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HHHHHHHCTT-EE--HHHCTTT-SEEEE....-SSSSSSB-HH CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdP.icalqaameGfevvtleevvkkadivvt....ttGnkdiitle 95 
                                    + Gk++ v+G G +G+  a+ + ++Ga v+    dP ++  +aa  G e+  l++++++ad++      t  +  +i +e
  gi|121638877|ref|YP_979101.1| 139 IFGKTVGVVGLGRIGQLVAQRIAAFGAYVVA--YDPyVSPARAAQLGIELLSLDDLLARADFISVhlpkTPETAGLIDKE 216
                                    67*************************8765..6773455788889**************97643122245667899999 PP

                                    HHCCS-TTEEEEE- CS
                  AdoHcyase_NAD  96 hlkkmkddaivcni 109
                                     l+k k  +i+ n 
  gi|121638877|ref|YP_979101.1| 217 ALAKTKPGVIIVNA 230
                                    99999999998885 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.016       3      72 ..     140     207 ..     138     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                    HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH CS
                           IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel 72 
                                     gk++ v+G G  G+  a+ +   g  vv + ++   s ++A + g+e l+++++ ++ad++ + +P + 
  gi|121638877|ref|YP_979101.1| 140 FGKTVGVVGLGRIGQLVAQRIAAFGAYVV-A-YDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTP 207
                                    58********************9998875.3.44455899**************************9764 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.029       1      39 [.     143     181 ..     143     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekal 39 
                                    +v+v+G G +G+ +a+ +a+ g  Vv +d   + +++a+
  gi|121638877|ref|YP_979101.1| 143 TVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQ 181
                                    69***************************9665555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.49       6      51 ..     140     185 ..     137     240 .. 0.74
   2 ?   -1.8   0.0         3   4.4e+03      36      78 ..     431     470 ..     414     491 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                  NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkla 51 
                                     gk+v vvG G++++  +++++++ga+v+ ++p v+++   ++ ++
  gi|121638877|ref|YP_979101.1| 140 FGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIE 185
                                    589***************************9998755544333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                  NAD_binding_7  36 vapevkeeleelvklaeeelekdlegadlviaatddrelneri 78 
                                    + p+    ++++v+++ ++++   +g+ l+i  +d++    +i
  gi|121638877|ref|YP_979101.1| 431 YGPQ---LSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKI 470
                                    3333...677888888888888888888888888777655555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.26       9      53 ..     456     500 ..     451     506 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                          ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikit 53 
                                    l +   dr+g+L++i +++  +++ni++ +++++ +   a+i ++
  gi|121638877|ref|YP_979101.1| 456 LIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLR 500
                                    668889**************************9876666666665 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00044      0.65       2      74 ..     143     207 ..     142     227 .. 0.77
   2 ?   -2.1   0.0       4.5   6.7e+03       6      42 ..     314     350 ..     310     382 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                    EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGG CS
                   GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngt 74 
                                     v+++G+G+ig+  ++ + +       v ++dp  + a+  a+++g+e   +l++lla  ++d+++v  p + 
  gi|121638877|ref|YP_979101.1| 143 TVGVVGLGRIGQLVAQRIAAF---GAYVVAYDPYVSPAR--AAQLGIE-LLSLDDLLA--RADFISVHLPKTP 207
                                    59************9555555...677779*****9999..569***9.567999999..99*******9943 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.5
                                    ETTSHHHHHHHHHHHHTTTTE.EEEEEECSSHHHHHHH CS
                   GFO_IDH_MocA   6 iGaGkigskhlrplnesqrle.evvalldpdaeraeav 42 
                                    +G+G + ++ + p+ +  r++  ++++l+ + + +  v
  gi|121638877|ref|YP_979101.1| 314 VGGGVVNEEVA-PWLDLVRKLgVLAGVLSDELPVSLSV 350
                                    67766666666.88888888777788887776666555 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.38      22      72 ..     156     201 ..     154     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                    HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE CS
                 UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivi 72 
                                    +++++++ ga v++yDP+v+++++++     g+e++ sl++ l+ ad i +
  gi|121638877|ref|YP_979101.1| 156 VAQRIAAFGAYVVAYDPYVSPARAAQ----LGIELL-SLDDLLARADFISV 201
                                    57889999*************99987....588888.68999999988765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.8   5.7e+03      57      78 ..      82     103 ..      33     127 .. 0.65
   2 ?   12.5   0.1   0.00011      0.17       2      86 ..     144     218 ..     143     233 .. 0.72
   3 ?   -2.7   0.1       6.4   9.5e+03      67      94 ..     389     414 ..     357     416 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.8
                                    HHHHH-SEEEE-S-HHHHHHHH CS
                  F420_oxidored  57 eaaeeadvvvlavkpedveevl 78 
                                    +aa+   v+v+  +++++++++
  gi|121638877|ref|YP_979101.1|  82 DAATARGVLVVNAPTSNIHSAA 103
                                    4444444555555554444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                    +g++G G++g+ +a++++a g     +v a ++  + a   a++lg+++ +    +++++ad  +++v+  +++e++  +
  gi|121638877|ref|YP_979101.1| 144 VGVVGLGRIGQLVAQRIAAFG---AYVV-AYDPYVSPA--RAAQLGIELLS--LDDLLARAD--FISVHLPKTPETAGLI 213
                                    8********************...8887.755555544..44566655555..889999899..5688999999988888 PP

                                    GHHHH CS
                  F420_oxidored  82 akdal 86 
                                     k+al
  gi|121638877|ref|YP_979101.1| 214 DKEAL 218
                                    44433 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.4
                                    E-S-HHHHHHHHHHCGHHHHTTSEEEEE CS
                  F420_oxidored  67 lavkpedveevlselakdalkgklvisv 94 
                                    la    +++e++++   ++ +++ v++v
  gi|121638877|ref|YP_979101.1| 389 LAAERGVTAEICKAS--ESPNHRSVVDV 414
                                    444444445555544..66667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3499.13
//
Query:       gi|121638878|ref|YP_979102.1|  [L=480]
Description: alanine rich dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-08   33.4   3.3    1.9e-07   31.2   0.1    3.2  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      2e-06   27.2   0.2    3.4e-06   26.5   0.2    1.3  1  Thi4           Thi4 family
    4.3e-06   26.3   1.4    6.7e-06   25.7   1.4    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    4.1e-05   23.3   1.2    9.3e-05   22.2   0.4    2.0  2  DAO            FAD dependent oxidoreductase
    0.00025   20.4   1.0    0.00042   19.7   1.0    1.3  1  FAD_binding_3  FAD binding domain
    0.00068   18.8   3.4    0.00068   18.8   3.4    2.1  3  FAD_binding_2  FAD binding domain
     0.0063   15.3   1.2      0.011   14.5   1.2    1.3  1  HI0933_like    HI0933-like protein
     0.0096   15.2   0.3      0.018   14.3   0.3    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.021   14.7   0.3      0.036   14.0   0.3    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.032   13.5   0.2      0.047   12.9   0.2    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.054   12.8   1.2       0.47    9.7   0.1    2.3  2  Amino_oxidase  Flavin containing amine oxidoreductase
      0.089   11.8   0.2       0.14   11.2   0.2    1.2  1  Lycopene_cycl  Lycopene cyclase protein
       0.22   12.1   0.3       0.46   11.1   0.3    1.5  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.41    9.7   2.1       0.56    9.2   2.1    1.1  1  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.5e-10   1.9e-07       1      48 [.       5      55 ..       5      66 .. 0.91
   2 ?    0.2   0.0       0.7     9e+02       9      31 ..     232     254 ..     229     278 .. 0.76
   3 ?   -0.4   0.2       1.1   1.4e+03       5      18 ..     451     464 ..     446     469 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.5e-10
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE...TTCEECTS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev...pgvrvdyg 48
                                   +vG+G  Gl++A  +a+ag++v+++e++  +GG a+s+ +   p+v +d+ 
  gi|121638878|ref|YP_979102.1|  5 VVGSGPNGLATAVICARAGLNVQVVEAQATFGGGARSAADfefPEVLHDVC 55
                                   8************************************97766688888875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.7
                                    HHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8   9 lvaAylLakagfdvlllekrdrl 31 
                                    l+a  ++++ +++v+++++++  
  gi|121638878|ref|YP_979102.1| 232 LAAGVEITEPQRSVVVFDTAPTA 254
                                    56667778888999999998865 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                                    SHHHHHHHHHHHCC CS
                  NAD_binding_8   5 GlsGlvaAylLaka 18 
                                    G+ G +aA++L + 
  gi|121638878|ref|YP_979102.1| 451 GMCGWYAARTLLRT 464
                                    88899999888665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   2.6e-09   3.4e-06      18      58 ..       1      40 [.       1      51 [. 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.6e-09
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                   +Dv +vG+G+ GL++a + a++ +l+v ++e++ ++GGGa 
  gi|121638878|ref|YP_979102.1|  1 MDVTVVGSGPNGLATAVICARA-GLNVQVVEAQATFGGGAR 40
                                   7*******************99.****************85 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.4   5.2e-09   6.7e-06       1      40 [.       2      41 ..       2      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.2e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                   Dv VvG+gp G+a A+ +araG +v +ve +   GG + s
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVVEAQATFGGGARS 41
                                   9**********************************98765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.4   7.3e-08   9.3e-05       1      39 [.       2      42 ..       2      64 .. 0.95
   2 ?   -1.8   0.0       1.4   1.8e+03     147     172 ..     216     241 ..     151     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.3e-08
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgr 39
                                   dv ++G+G  Gl+tA   ar+g  V ++e++  +g ga ++
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGlnVQVVEAQATFGGGARSA 42
                                   89*********************************998776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHTT-EEEESECEEEE CS
                            DAO 147 kltaalaraaealGveilegtevtgl 172
                                    + + al ++++a+G+++  g e+t+ 
  gi|121638878|ref|YP_979102.1| 216 AIADALIADLRAHGGRLAAGVEITEP 241
                                    56678888888889999888888764 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.0   3.3e-07   0.00042       3      36 ..       2      35 ..       1      43 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.3e-07
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                   dV +VG+Gp Gl +a + ++aG +v +ve ++t 
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVVEAQATF 35
                                   8****************************99986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.4   5.3e-07   0.00068       1      38 [.       2      39 ..       2      44 .. 0.91
   2 ?   -3.0   0.0       2.3   2.9e+03     122     155 ..     172     229 ..     141     240 .. 0.60
   3 ?   -1.0   0.2      0.57   7.3e+02      71     123 ..     261     333 ..     227     391 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                   Dv V+GsG  GLa A+ +a+aGl+v vve    fgg +
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVVEAQATFGGGA 39
                                   999*****************************999954 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                                    T..........................EEEE-.STT-......HHHHHHHHHHHHHHTCT CS
                  FAD_binding_2 122 t..........................artlhdaadarretlvtghallarlvesarkag 155
                                    +                          a  +h+++++  ++++  +a++ +l++ +r++g
  gi|121638878|ref|YP_979102.1| 172 RalftgvaahaisplpslvsagaglmlATLAHSVGWP--IPVGGTQAIADALIADLRAHG 229
                                    4444444444444444444444444444455556666..667777777777777777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.57
                                    HHTTT-S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SST....................E CS
                  FAD_binding_2  71 kaldeladqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsat....................a 123
                                      l+++++++l ++  +a+ ++vd+  +  +p+s  +  + +  +lGg++ +                    a
  gi|121638878|ref|YP_979102.1| 261 DKLPHRYAKALRRYRFRAGIAKVDFVLSDEIPWSDPRLRRAATLHLGGTRDQmaraeadvaagrhadwpmvlA 333
                                    3445555666666667788888888888888888844445555555555555444444444444444455541 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.2   8.2e-06     0.011       2      36 ..       2      36 ..       1      40 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   dv v+G G+ Gl +A+ +a++g +V ++e++ ++g
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVVEAQATFG 36
                                   89****************************99887 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   1.4e-05     0.018       2      35 ..       2      35 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                   dv v+G+Gp Gla+a   a+ag++v +ve++ t+
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVVEAQATF 35
                                   8999999999999999999999999999766665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.8e-05     0.036       2      34 ..       3      35 ..       2      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v+v+G+G  G   a ++a+agl+V++v+ ++ +
  gi|121638878|ref|YP_979102.1|  3 VTVVGSGPNGLATAVICARAGLNVQVVEAQATF 35
                                   9**************************998765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.7e-05     0.047       2      30 ..       5      32 ..       4      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                   ++G GP Gla+a+ + +agl ++ ++E +
  gi|121638878|ref|YP_979102.1|  5 VVGSGPNGLATAVICARAGL-NVQVVEAQ 32
                                   8*******************.799***87 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00037      0.47       3      32 ..      12      41 ..      11      48 .. 0.92
   2 ?    1.2   0.1      0.14   1.8e+02     396     439 ..     411     451 ..     400     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHTTEEEEEEESSSSSBTTS-E CS
                  Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvGGRirt 32
                                   GLa+A   ++aG++V+v+Ea+  +GG +r+
  gi|121638878|ref|YP_979102.1| 12 GLATAVICARAGLNVQVVEAQATFGGGARS 41
                                   9*************************7776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                    SSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHH CS
                  Amino_oxidase 396 gsysyvsvgpghedydplakpegdprlffAGehtsreypgt.veg 439
                                    g+ s++++ +g++ + ++ ++ ++p ++++ ++t    pg+ v+g
  gi|121638878|ref|YP_979102.1| 411 GANSTWRAIAGPTPRLNPWRT-PIPKVYLCSAATP---PGAgVHG 451
                                    6667789999999999*****.************9...9999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00011      0.14       1      35 [.       2      34 ..       2      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                   Dv v+G+Gp gl+ A     a++gl+v ++ea + 
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVIC--ARAGLNVQVVEAQAT 34
                                   9***********999988..**********99765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00036      0.46       2      35 ..       3      36 ..       2      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   v+vvG+G  gl  A + a+ g +V+vve++ ++ 
  gi|121638878|ref|YP_979102.1|  3 VTVVGSGPNGLATAVICARAGLNVQVVEAQATFG 36
                                   89**************************998876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.1   0.00044      0.56       1      28 [.       2      29 ..       2      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00044
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   dv+V+G G  G++ A+ +ar+G++v  +
  gi|121638878|ref|YP_979102.1|  2 DVTVVGSGPNGLATAVICARAGLNVQVV 29
                                   79***********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3703.44
//
Query:       gi|121638879|ref|YP_979103.1|  [L=153]
Description: hypothetical protein BCG_3019 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1067.44
//
Query:       gi|121638880|ref|YP_979104.1|  [L=67]
Description: hypothetical protein BCG_3020c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-05   23.1   0.1     0.0023   17.9   0.0    2.1  2  HisKA     His Kinase A (phospho-acceptor) domain
    0.00029   21.1   0.2    0.00038   20.8   0.2    1.3  1  HAMP      HAMP domain
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.068   13.2   0.0    1.3  1  G-gamma   GGL domain


Domain annotation for each model (and alignments):
>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.011        63      34      60 ..      15      41 ..       2      46 .. 0.79
   2 !   17.9   0.0   3.9e-07    0.0023       3      19 ..      51      67 .]      49      67 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.011
                                   HSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                          HisKA 34 teelkeyletiesearrldhlvedlLd 60
                                   ++  +  l  +++e+r l    +dlL+
  gi|121638880|ref|YP_979104.1| 15 DPHARLPLPLARDEIRYLGTTFNDLLQ 41
                                   4566667888999***********965 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHHHHHHHHHH CS
                          HisKA  3 grflagvaHELrtPLsa 19
                                   ++f+++  HELrtPL++
  gi|121638880|ref|YP_979104.1| 51 RQFVSDAGHELRTPLAS 67
                                   89*************86 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   6.3e-08   0.00038      20      53 .]      11      45 ..       1      45 [. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.3e-08
                                   HTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHHH CS
                           HAMP 20 iaaGdldtrlpv.sgrDEiGeLarafNaMldrLre 53
                                   i+a d ++rlp    rDEi+ L+ +fN++l+rL++
  gi|121638880|ref|YP_979104.1| 11 ISATDPHARLPLpLARDEIRYLGTTFNDLLQRLQD 45
                                   44446677899988*******************96 PP

>> G-gamma  GGL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.068      11      32 ..      39      61 ..      34      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                        G-gamma 11 i.eqLkkeLkrerikvSkAceel 32
                                   + ++L++ L+rer+ vS A  el
  gi|121638880|ref|YP_979104.1| 39 LlQRLQDALERERQFVSDAGHEL 61
                                   559****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 507.32
//
Query:       gi|121638881|ref|YP_979105.1|  [L=321]
Description: lipoprotein lppY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-84  280.0   0.0    2.2e-41  140.6   0.0    2.1  2  DUF1529   Domain of Unknown Function (DUF1259)
  ------ inclusion threshold ------
      0.059   13.4   0.0       0.12   12.5   0.0    1.5  1  DUF3701   Phage integrase protein


Domain annotation for each model (and alignments):
>> DUF1529  Domain of Unknown Function (DUF1259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   1.9e-44   1.7e-40       2     120 ..      53     173 ..      52     174 .. 0.98
   2 !  140.6   0.0   2.4e-45   2.2e-41       2     120 ..     196     314 ..     195     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.9e-44
                        DUF1529   2 aidkilgrkgtlkgg..vykvtipRndlkvtidgvelkpalglttwaaFqslgggkalvmGdlvlledEvnpvikalren 79 
                                    +++++lgr+g+l ++   y++++pRndl++t+ gv +kp l+l+ +aaF++++++++l+mGdlv++e+E+ +v++al+++
  gi|121638881|ref|YP_979105.1|  53 PVADALGRSGKLGDNntAYRINLPRNDLHITSYGVDIKPGLSLGGYAAFARYDNNETLLMGDLVITEEELPKVTDALQAH 132
                                    6899********99889*************************************************************** PP

                        DUF1529  80 gievtalHnhlleeqPrlfylHieavgdavklArklraald 120
                                    gi++talH+hll+++P ++++Hi+++gda++lA++l+aald
  gi|121638881|ref|YP_979105.1| 133 GIAQTALHKHLLQQDPPVWWTHIHGMGDAARLAQGLKAALD 173
                                    ****************************************9 PP

  == domain 2  score: 140.6 bits;  conditional E-value: 2.4e-45
                        DUF1529   2 aidkilgrkgtlkggvykvtipRndlkvtidgvelkp.alglttwaaFqslgggkalvmGdlvlledEvnpvikalreng 80 
                                     +d++lgrkgt++gg +k++ipR+d+ + +dg+ l++ +l+ltt ++Fq++g+g+a+++Gd++l++ Ev++vi+a+r+++
  gi|121638881|ref|YP_979105.1| 196 GVDQALGRKGTQDGGLLKYSIPRKDT-IIEDGHVLPAvSLNLTTVINFQPVGRGRAAINGDFILIAPEVQEVIRAMRAGN 274
                                    589***********************.999999999857***************************************** PP

                        DUF1529  81 ievtalHnhlleeqPrlfylHieavgdavklArklraald 120
                                    i++++lHnh l+e+Prlfy+H++av+dav+lAr+lr a+d
  gi|121638881|ref|YP_979105.1| 275 ITIVELHNHGLTEEPRLFYMHYWAVDDAVTLARALRPAMD 314
                                    **************************************98 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05      0.12      22      71 ..     123     170 ..     122     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                        DUF3701  22 prvarrLaaagvktLaeLiarinrrgkrWwravprlGaakArrieafLaa 71 
                                    p+v+++L+a+g++  a   ++ ++    Ww+++ ++G   A r+++ L+a
  gi|121638881|ref|YP_979105.1| 123 PKVTDALQAHGIAQTALHKHLLQQDPPVWWTHIHGMGD--AARLAQGLKA 170
                                    6899*********9999999999*************96..5566655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2623.29
//
Query:       gi|121638882|ref|YP_979106.1|  [L=219]
Description: hypothetical protein BCG_3022 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-31  109.3   0.8    2.5e-31  108.9   0.8    1.1  1  UPF0014      Uncharacterised protein family (UPF0014)
    7.9e-14   52.3   0.0    9.8e-14   52.0   0.0    1.2  1  ABC_tran     ABC transporter
    3.7e-05   24.2   0.2      5e-05   23.7   0.2    1.5  1  AAA_16       AAA ATPase domain
     0.0056   16.4   0.1      0.011   15.5   0.0    1.5  2  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.03   14.6   0.0    1.7  1  AAA_22       AAA domain
      0.016   15.0   0.0      0.028   14.2   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.017   15.1   0.0      0.036   14.0   0.0    1.5  1  NACHT        NACHT domain
      0.033   13.8   0.1      0.056   13.0   0.1    1.3  1  AAA_25       AAA domain
      0.063   13.8   0.0        0.1   13.2   0.0    1.3  1  AAA_18       AAA domain
       0.07   12.9   0.0      0.098   12.4   0.0    1.1  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.079   12.9   0.0       0.12   12.2   0.0    1.2  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.8   1.5e-34   2.5e-31     151     242 .]     112     203 ..     107     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 1.5e-34
                        UPF0014 151 eeiealLalGatpkeAvkeivreairaaliPtinsmatvGlVsLPGmmtGqiLaGaspleAvkyqilimfmilastalst 230
                                    +e+ a+L+lG++++eA+ +  r+a+r+aliP+i+s+++vGl+sLPG+m+G+iLaG++pl+A++yqi++m+++la+ta+++
  gi|121638882|ref|YP_979106.1| 112 TELLARLCLGQSAREAFLPHQRSALRTALIPAIDSTKVVGLISLPGAMSGLILAGVDPLTAIRYQIVVMYLLLAATAVAA 191
                                    67889*************************************************************************** PP

                        UPF0014 231 vlvvlllyrrlf 242
                                    +++  l+ r lf
  gi|121638882|ref|YP_979106.1| 192 LTCARLAERALF 203
                                    ******999887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0     6e-17   9.8e-14       1      80 [.      21     106 ..      21     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 6e-17
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vs ++ +g++ a+ G +G+GK+tLl+ll +l +pt+G+++ldg +l++ +  +lr+++g + q p +  +  + e  
  gi|121638882|ref|YP_979106.1|  21 LRQVSAHFPAGRCSAVRGASGSGKTTLLRLLNRLIDPTSGKVWLDGVPLTDLDVLVLRRRVGLVAQAPVVLTDAVLNEVr 100
                                    6899***************************************************************8888777444435 PP

                                    .....H CS
                                    .....x RF
                       ABC_tran  80 .....e 80 
                                          
  gi|121638882|ref|YP_979106.1| 101 vgrpdL 106
                                    555552 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   3.1e-08     5e-05      14      52 ..      19      59 ..      10     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.1e-08
                         AAA_16 14 salervrsgrp..elvllsGesGvGKsslvrellralekdg 52
                                   ++l++v+++ p  ++  ++G+sG+GK++l+r l r +  + 
  gi|121638882|ref|YP_979106.1| 19 TVLRQVSAHFPagRCSAVRGASGSGKTTLLRLLNRLIDPTS 59
                                   6789999999999********************98877772 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.7e-06     0.011      19      50 ..      32      63 ..      21     101 .. 0.81
   2 ?   -2.5   0.0       2.2   3.6e+03      20      59 ..     149     191 ..     130     206 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                   r++++ G+ G+GKtt+l+ l+++++   g+v 
  gi|121638882|ref|YP_979106.1| 32 RCSAVRGASGSGKTTLLRLLNRLIDPTSGKVW 63
                                   5899****************999988866665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                         AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrvi...glAptgkaA 59 
                                    v+ l   +G+    +l+++  + + + +   +   +lA t+ aA
  gi|121638882|ref|YP_979106.1| 149 VVGLISLPGAMSGLILAGVDPLTAIRyQIV-VmylLLAATAVAA 191
                                    444555555555555555544443331211.1122455555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05      0.03       6      30 ..      32      56 ..      30     155 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                   ++ +v G sG+GKTtllr l +  d
  gi|121638882|ref|YP_979106.1| 32 RCSAVRGASGSGKTTLLRLLNRLID 56
                                   678899************9998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.028      17      46 ..      26      55 ..       8      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalL 46
                                   +++  +g    + G+sGsGK+Tll  ++ l+
  gi|121638882|ref|YP_979106.1| 26 AHFP-AGrCSAVRGASGSGKTTLLRLLNRLI 55
                                   5554.5558899***********96555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.2e-05     0.036       2      21 ..      33      52 ..      32      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                    ++++G++GsGKTtLl+ l 
  gi|121638882|ref|YP_979106.1| 33 CSAVRGASGSGKTTLLRLLN 52
                                   679*************9765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.5e-05     0.056      28      76 ..      26      76 ..      11      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                         AAA_25 28 gllpagelallaGapgtGKttla..ldlalavatGkpwlgpvapeqgkVly 76
                                    + pag  +++ Ga+g+GKttl+  l+  ++ ++Gk wl+ v+ +   Vl+
  gi|121638882|ref|YP_979106.1| 26 AHFPAGRCSAVRGASGSGKTTLLrlLNRLIDPTSGKVWLDGVPLTDLDVLV 76
                                   578*******************72255566666888888844447777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.1e-05       0.1       3      22 ..      36      55 ..      35      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                         AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                   + G++G+GKttl + L+++ 
  gi|121638882|ref|YP_979106.1| 36 VRGASGSGKTTLLRLLNRLI 55
                                   679*************9984 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05     0.098       6      24 ..      38      56 ..      34      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                         AAA_21  6 GpNgsGKSnLLdaldllar 24
                                   G+ gsGK++LL++l  l +
  gi|121638882|ref|YP_979106.1| 38 GASGSGKTTLLRLLNRLID 56
                                   999***********99854 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.6e-05      0.12      87     121 ..      18      53 ..       6      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                     + l+++++++   ++s++ G SG GK+tL+  l+ 
  gi|121638882|ref|YP_979106.1|  18 ATVLRQVSAHFPAgRCSAVRGASGSGKTTLLRLLNR 53 
                                    455667777776559***************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1604.00
//
Query:       gi|121638883|ref|YP_979107.1|  [L=333]
Description: ketol-acid reductoisomerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-69  231.9   0.1      4e-69  231.4   0.1    1.2  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    3.1e-60  202.6   0.1      4e-60  202.3   0.1    1.1  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    1.6e-06   27.6   0.0    2.7e-06   26.9   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.9e-05   24.9   0.0    6.4e-05   23.2   0.0    1.8  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0002   21.9   0.0    0.00055   20.5   0.0    1.8  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.066   13.3   0.0       0.13   12.3   0.0    1.4  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.4   0.1   1.3e-72     4e-69       2     165 .]      12     175 ..      11     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 1.3e-72
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81 
                                    ++g+k+ viGyGsqGha++l lrdsg++v vgl++gs+s  k +e+g++v t ae++k+advvm+l+PD++q+e++  +i
  gi|121638883|ref|YP_979107.1|  12 IQGRKVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSRPKVEEQGLDVDTPAEVAKWADVVMVLAPDTAQAEIFAGDI 91 
                                    89****************************************************************************** PP

                                    GGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTH CS
                           IlvN  82 epnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGa 161
                                    epnlk g+al f+hG+n+hfglikpp+dv v++vAPkgpGhlvr+++ +gkGvp+l+aveqd  g++ +lal+yak+iG+
  gi|121638883|ref|YP_979107.1|  92 EPNLKPGDALFFGHGLNVHFGLIKPPADVAVAMVAPKGPGHLVRRQFVDGKGVPCLVAVEQDPRGDGLALALSYAKAIGG 171
                                    ******************************************************************************** PP

                                    HHH- CS
                           IlvN 162 traG 165
                                    traG
  gi|121638883|ref|YP_979107.1| 172 TRAG 175
                                    ***9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3   0.1   1.3e-63     4e-60       1     144 []     181     324 ..     181     324 .. 1.00

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 1.3e-63
                                    HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHH CS
                           IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltag 80 
                                    Fk+EtetDlfgEq+vLcGg+ elv+agFe++veaGy+ elAyfe+lhelklivdl+yegG+a+m++s+Sdtae+g++ +g
  gi|121638883|ref|YP_979107.1| 181 FKDETETDLFGEQTVLCGGTEELVKAGFEVMVEAGYPAELAYFEVLHELKLIVDLMYEGGLARMYYSVSDTAEFGGYLSG 260
                                    9******************************************************************************* PP

                                    HHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                           IlvC  81 prviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                    prvi++ +ke+m++il+eiq+G+f+ +++++ + g+++l++lr+++aeh+ie vgkklr+lm+w
  gi|121638883|ref|YP_979107.1| 261 PRVIDAGTKERMRDILREIQDGSFVHKLVADVEGGNKQLEELRRQNAEHPIEVVGKKLRDLMSW 324
                                    **************************************************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     9e-10   2.7e-06      34     105 ..      12      84 ..       3      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9e-10
                                    GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--STTT CS
                   2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpltpet 105
                                    ++g++vG+iG+G+ G+a    l+  g++v +  ++ ++++ ++ee+g+++++  e+ +++D+v++ +p t++ 
  gi|121638883|ref|YP_979107.1|  12 IQGRKVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSRpKVEEQGLDVDTPAEVAKWADVVMVLAPDTAQA 84 
                                    89*********************999999887777776667999************************99876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.2e-08   6.4e-05       1      86 [.      16     101 ..      16     109 .. 0.96
   2 ?   -1.8   0.0         1     3e+03     129     146 ..     194     211 ..     186     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.2e-08
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                    k+g+iG G  G+   l l ++g +v v   + ++ +  v+e+   +++++e+++ +dvv+++ +++++ + +  ++ ++l
  gi|121638883|ref|YP_979107.1|  16 KVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSRPKVEEQGLDVDTPAEVAKWADVVMVLAPDTAQAEIFAGDIEPNL 95 
                                    69***************************************999**************************99999***** PP

                                    -TT-EE CS
                  NAD_binding_2  81 kkgdil 86 
                                    k+gd l
  gi|121638883|ref|YP_979107.1|  96 KPGDAL 101
                                    ***976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                    EEEEEE-HHHHHHHHHHH CS
                  NAD_binding_2 129 simvGGseeafervkpvl 146
                                    ++++GG+ee +++  +v+
  gi|121638883|ref|YP_979107.1| 194 TVLCGGTEELVKAGFEVM 211
                                    666666666665544444 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.8e-07   0.00055       1      71 [.      16      80 ..      16      99 .. 0.78
   2 ?   -3.6   0.0       5.7   1.7e+04      74      93 ..     272     291 ..     269     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71
                                   k+g+iG+G++g+a  + l  +g    +++v+ ++   ++ +  ee g +v +   +e+a+ advv +  + 
  gi|121638883|ref|YP_979107.1| 16 KVGVIGYGSQGHAHSLSLRDSG---VQVRVGLKQGSRSRPK-VEEQGLDVDT--PAEVAKWADVVMVLAPD 80
                                   79********************...****996666555555.5565778888..9*********9876654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.7
                                    HHHHHHHCGHHHHTTSEEEE CS
                  F420_oxidored  74 veevlselakdalkgklvis 93 
                                    + ++l+e+++ ++ +klv +
  gi|121638883|ref|YP_979107.1| 272 MRDILREIQDGSFVHKLVAD 291
                                    67889999888888888866 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05      0.13      19      83 ..      10      75 ..       5      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                   S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHH.HHHHCTT-EE--HHHCTTT-SEEE CS
                  AdoHcyase_NAD 19 vllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPica.lqaameGfevvtleevvkkadivv 83
                                    ++ G+++ v+GyG  G   + sl+  G +v v       +  +   +G++v t  ev+k ad+v+
  gi|121638883|ref|YP_979107.1| 10 SIIQGRKVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSrPKVEEQGLDVDTPAEVAKWADVVM 75
                                   4799***************************99755544330344555777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2505.84
//
Query:       gi|121638884|ref|YP_979108.1|  [L=168]
Description: acetolactate synthase 3 regulatory subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-27   94.6   0.7    1.5e-26   92.4   0.1    2.0  2  ALS_ss_C        Small subunit of acetolactate synthase
    5.9e-19   67.7   0.2    1.9e-18   66.0   0.0    1.9  2  ACT_5           ACT domain
    8.7e-19   67.0   0.4    2.3e-18   65.6   0.1    1.9  2  ACT             ACT domain
    1.7e-05   25.3   1.0    4.6e-05   23.9   0.2    2.0  3  ACT_4           ACT domain
     0.0036   17.3   0.5      0.057   13.4   0.1    2.7  3  ACT_6           ACT domain
     0.0056   17.0   0.2      0.047   14.1   0.2    2.1  2  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0068   16.7   0.1     0.0086   16.4   0.1    1.2  1  THOC7           Tho complex subunit 7
  ------ inclusion threshold ------
      0.036   13.4   0.1      0.066   12.6   0.1    1.5  1  PPR_long        Pentacotripeptide-repeat region of PRORP


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.31     7e+02      25      55 ..      47      77 ..      39      82 .. 0.66
   2 !   92.4   0.1   6.7e-30   1.5e-26       1      74 []      87     160 ..      87     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                                   TT-EEEEEETTEEEEEEEE-HHHHHHHHHHS CS
                       ALS_ss_C 25 frakivdvspdsliieltgteekidaliell 55
                                    r+ iv  ++d+ + ++t++ +k+ ++i+ +
  gi|121638884|ref|YP_979108.1| 47 SRMIIVVSAEDTPLEQITKQLNKLINVIKIV 77
                                   5555666666777777777777777666655 PP

  == domain 2  score: 92.4 bits;  conditional E-value: 6.7e-30
                                    EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                       ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                    RElaLiKV+a++ +rs+++e ++ fra+++dvsp+sl++e+tg+++k++al+++l+pfgi e++++G v l+RG
  gi|121638884|ref|YP_979108.1|  87 RELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRG 160
                                    9************************************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   8.5e-22   1.9e-18       1      62 []      14      76 ..      14      76 .. 0.98
   2 ?   -1.5   0.0         1   2.3e+03      22      34 ..     122     134 ..     116     143 .. 0.53

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 8.5e-22
                          ACT_5  1 dapgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                   d+pgvL Rv  +++rrgF+++sl + +te ++++r+ ++V++ + ++e++++Ql+KLi+V+k+
  gi|121638884|ref|YP_979108.1| 14 DKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMIIVVSAeDTPLEQITKQLNKLINVIKI 76
                                   68**********************************************************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                          ACT_5  22 slnmsttedggtv 34 
                                    sl++++t++ g++
  gi|121638884|ref|YP_979108.1| 122 SLTVEATGNRGKL 134
                                    5555554444433 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.1     1e-21   2.3e-18       1      66 [.       6      71 ..       6      72 .. 0.98
   2 ?   -0.6   0.0      0.54   1.2e+03      26      59 ..      71     105 ..      71     109 .. 0.57

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1e-21
                                   EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                   ++l+v+v+D+PG+Larv++++++rg+Ni+s+ ++ +e+k  +++++v+ +++ +le++ ++l+kl+
  gi|121638884|ref|YP_979108.1|  6 HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMIIVVSAEDTPLEQITKQLNKLI 71
                                   789*************************************************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
                                    SEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHHHH CS
                            ACT  26 iNidsieqrssedk.vagivfvvivvdeedleevl 59 
                                    iN+++i    +e +   +++ + + +d+ + ++v+
  gi|121638884|ref|YP_979108.1|  71 INVIKIVEQDDEHSvSRELALIKVQADAGSRSQVI 105
                                    78888887777776544444444445555555555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   2.1e-08   4.6e-05       8      78 ..       7      76 ..       5      77 .. 0.92
   2 ?   -2.1   0.0       2.7   6.1e+03      21      38 ..     102     119 ..      92     130 .. 0.69
   3 ?   -1.8   0.0       2.3     5e+03       9      28 ..     123     142 ..     120     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                          ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                                   +l+v +ed++g+La++++++s  + ni+s+ + +++ +   ++ i v+ +d+  L+++ ++L+++ +Vi++
  gi|121638884|ref|YP_979108.1|  7 TLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMIIVVSAEDT-PLEQITKQLNKLINVIKI 76
                                   799*******************************877889999999999997.599999999999999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                          ACT_4  21 aditqviseekanivsvn 38 
                                    ++++++++  +an+ +v+
  gi|121638884|ref|YP_979108.1| 102 SQVIEAVNLFRANVIDVS 119
                                    567777777777777765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.3
                          ACT_4   9 leveaedrkglLaditqvis 28 
                                    l+vea+ ++g L  +++v++
  gi|121638884|ref|YP_979108.1| 123 LTVEATGNRGKLEALLRVLE 142
                                    78889989998888888876 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   2.6e-05     0.057       7      65 ..      10      70 ..       7      74 .. 0.87
   2 ?    0.2   0.0      0.34   7.6e+02      14      33 ..      99     118 ..      89     120 .. 0.80
   3 ?   -0.5   0.0      0.56   1.3e+03      14      35 ..     132     154 ..     121     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                          ACT_6  7 vtGpdrpGltasLtsvlaefgvni..lDieqavihgrlsLgllvsgpedalarlekaLlfl 65
                                   v+ +d+pG++a+++++ ++ g ni  l ++     +r   +++vs+++  l+++ k+L +l
  gi|121638884|ref|YP_979108.1| 10 VLVEDKPGVLARVAALFSRRGFNIesLAVGATECKDRSRMIIVVSAEDTPLEQITKQLNKL 70
                                   6668**************99999833557889999****************9999999875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.34
                          ACT_6  14 GltasLtsvlaefgvnilDi 33 
                                    G  +++ +++  f++n++D+
  gi|121638884|ref|YP_979108.1|  99 GSRSQVIEAVNLFRANVIDV 118
                                    55578888899999999997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.56
                          ACT_6  14 GltasLtsvlaefgvn.ilDieq 35 
                                    G + +L++vl  fg++ i+ +++
  gi|121638884|ref|YP_979108.1| 132 GKLEALLRVLEPFGIReIAQSGM 154
                                    66778888888888753555555 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   2.1e-05     0.047      30      74 ..      31      75 ..      17     103 .. 0.74
   2 ?    0.7   0.0      0.31     7e+02      43      74 ..     117     149 ..     102     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                   EEEEEEEXXSST.TSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSC CS
                 Saccharop_dh_N 30 fevlefevGkkk.kdtSyaelevsaedeevLeeileeltelgaelv 74
                                   f+++++ vG+++ kd S   + vsaed + Le+i ++l++l + ++
  gi|121638884|ref|YP_979108.1| 31 FNIESLAVGATEcKDRSRMIIVVSAED-TPLEQITKQLNKLINVIK 75
                                   9********976478899988899888.789*****9999844333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                                    SXEEEEEEEEES.SHHHHHHHHHHHHHHHHHSC CS
                 Saccharop_dh_N  43 dtSyaelevsae.deevLeeileeltelgaelv 74 
                                    d S  +l+v+a+ ++ +Le++l+ l+ +g + +
  gi|121638884|ref|YP_979108.1| 117 DVSPESLTVEATgNRGKLEALLRVLEPFGIREI 149
                                    667778999887245689999999999988776 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.8e-06    0.0086       5      54 ..      46      94 ..      44     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                          THOC7  5 ksRLlnv...eerplkrltkrllklltsla.esteeeleqlkedllldfaafel 54
                                   +sR+++v   e+ pl ++tk+l+kl++++        ++ ++ ++  ++a  + 
  gi|121638884|ref|YP_979108.1| 46 RSRMIIVvsaEDTPLEQITKQLNKLINVIKiV-----EQDDEHSVSRELALIKV 94
                                   79999999********************7442.....33333333333333333 PP

>> PPR_long  Pentacotripeptide-repeat region of PRORP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.9e-05     0.066     164     200 ..      89     125 ..      60     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHTSSB-HHHHHH CS
                       PPR_long 164 aaLLkvsakagredkvYelLhklreavrqvsestaev 200
                                     aL+kv a+ag+  +v e ++ +r +v +vs+++++v
  gi|121638884|ref|YP_979108.1|  89 LALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125
                                    59*******************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1249.87
//
Query:       gi|121638885|ref|YP_979109.1|  [L=618]
Description: acetolactate synthase 1 catalytic subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-56  189.6   0.2    8.2e-56  188.3   0.2    1.7  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    8.3e-53  177.8   0.3    1.6e-52  176.9   0.3    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    1.7e-48  164.3   0.0    1.7e-48  164.3   0.0    2.0  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
     0.0068   16.2   0.0      0.011   15.5   0.0    1.2  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.2   1.8e-59   8.2e-56       2     168 ..      39     204 ..      38     206 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.8e-59
                                    EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                   TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                    t+a+a++r L++lgv+++fg+pG+ +lp++d l +++++r+vl+rhEqga++aA+gya +tg++gv+++tsgpGatn++t
  gi|121638885|ref|YP_979109.1|  39 TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVT 118
                                    99****************************************************************************** PP

                                    HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEH CS
                   TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpk 161
                                     la+A+ d+iP+++++g++++ l+g++++q e d++++  p+tk+++ v+s +++p++l++A+ +a+sgrpg+v++++pk
  gi|121638885|ref|YP_979109.1| 119 PLADAQMDSIPVVAITGQVGRGLIGTDAFQ-EADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPK 197
                                    ******************************.************************************************* PP

                                    HHCC-EE CS
                   TPP_enzyme_N 162 dvlleev 168
                                    dvl+ ++
  gi|121638885|ref|YP_979109.1| 198 DVLQGQC 204
                                    **99876 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.9   0.3   3.5e-56   1.6e-52       1     137 []     228     363 ..     228     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 3.5e-56
                                    HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SE CS
                   TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDl 80 
                                    +++aa+l++aa++pv++vGggv+r +a+e+lrelae +giPvvttlm++g++p++h ++lgm g+hg+ aa +al+++Dl
  gi|121638885|ref|YP_979109.1| 228 VREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDL 307
                                    679***************************************************************************** PP

                                    EEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                   TPP_enzyme_M  81 vlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                    ++alG+rfdd r+tg+ + fapeak+ih didpaeigkn+++d++ivgdvk+++++L
  gi|121638885|ref|YP_979109.1| 308 LIALGTRFDD-RVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITEL 363
                                    **********.9*****************************************9987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.9       1.1   5.1e+03      25      54 ..     101     135 ..      88     144 .. 0.71
   2 !  164.3   0.0   3.8e-52   1.7e-48       1     152 [.     426     578 ..     426     579 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                    TTTS-TTTHHHHHHHHHH....HST.TSEEEEEEE CS
                   TPP_enzyme_C  25 gglgtmGyglpaAiGakl....akp.drevvaivG 54 
                                     + ++m  + p+A+ +      a+  + +vvai+G
  gi|121638885|ref|YP_979109.1| 101 RVGVCMATSGPGATNLVTpladAQMdSIPVVAITG 135
                                    46678888888888877776443432469999998 PP

  == domain 2  score: 164.3 bits;  conditional E-value: 3.8e-52
                                    ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEE CS
                   TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvl 80 
                                    ++G++++waa+++++++prs+l+sgglgtmG+++paA+Gak+a p+ ev+ai GDG+f+m+ qelat++ +++p++v ++
  gi|121638885|ref|YP_979109.1| 426 GVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALI 505
                                    69****************************************************************************** PP

                                    E-SBCCCHHHHHHHHTCCTTTTSBB...BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH.CSSSEEEEE CS
                   TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagk..dlkpvdfaklaealGakgarvekadveeleealkeal.ekkgpalie 152
                                    nN+ +gm++++q+ f+++r+s+++      + +df+klaealG+ g+r+e++  e++ +++ +a+  ++ p++i+
  gi|121638885|ref|YP_979109.1| 506 NNGNLGMVRQWQSLFYAERYSQTDLAthSHRIPDFVKLAEALGCVGLRCERE--EDVVDVINQARaINDCPVVID 578
                                    **********************99878767888*******************..**********98788899998 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-06     0.011      24      78 ..     227     281 ..     214     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                                    -SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G. CS
                          CO_dh  24 alkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkd 78 
                                    +++++ak+i  a++P+l vG+ v + e  e+     +   ++vv t +     +d
  gi|121638885|ref|YP_979109.1| 227 QVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPD 281
                                    5689****************************************99765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4097.73
//
Query:       gi|121638886|ref|YP_979110.1|  [L=112]
Description: low molecular weight protein antigen 6 cfp6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   69.3   4.8    2.8e-19   69.0   4.8    1.2  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   4.8   1.6e-23   2.8e-19       1      72 [.      39     109 ..      39     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.6e-23
                          bPH_6   1 RprvrvdpdGvevrnlfrtrrlpWsaiagvrfpegrrlarldlrdgelvplpavqlgddpelvadalrrlrd 72 
                                    R r+ +d+ Gv+vr l+++r ++W++i g+rf +g++ ar+ l+dg++++lpav+++++p l++++ +r+++
  gi|121638886|ref|YP_979110.1|  39 RLRTLADERGVTVRTLVGSRAVRWDDIDGLRFHRGSW-ARATLKDGTELRLPAVTFATLPHLTEASSGRVPN 109
                                    899*********************************7.*******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 920.06
//
Query:       gi|121638887|ref|YP_979111.1|  [L=279]
Description: hypothetical protein BCG_3027c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-19   70.1   8.9    1.8e-19   70.1   8.9    1.8  3  DoxX      DoxX
    9.6e-05   22.3   0.8    0.00026   20.9   0.8    1.7  1  DoxD      TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   8.9   2.1e-23   1.8e-19       1      77 [.     114     194 ..     114     200 .. 0.96
   2 ?   -4.1   0.4         2   1.8e+04      74      80 ..     224     230 ..     221     234 .. 0.47
   3 ?   -3.5   0.3       1.8   1.6e+04      52      55 ..     261     264 ..     249     272 .. 0.48

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.1e-23
                           DoxX   1 lllllRlllgvlfiahGlqkltg....fglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtl 76 
                                    +ll+lR+ lg+++iahGlqkl+g     gl+g+++sl ++g +++e+lay+ a +E+v+g+ll+lGl+t+laA++ +++l
  gi|121638887|ref|YP_979111.1| 114 GLLILRVGLGAVLIAHGLQKLFGwwdgQGLAGFQNSLSDIGYQHAEILAYVSAGGEIVAGVLLVLGLFTPLAAAGALAFL 193
                                    69**********************99999999********************************************9998 PP

                           DoxX  77 l 77 
                                    +
  gi|121638887|ref|YP_979111.1| 194 I 194
                                    7 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2
                           DoxX  74 vtllvat 80 
                                    v+++va+
  gi|121638887|ref|YP_979111.1| 224 VVMAVAV 230
                                    3444443 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.8
                           DoxX  52 Elvg 55 
                                     +++
  gi|121638887|ref|YP_979111.1| 261 GIAA 264
                                    2222 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.8   2.9e-08   0.00026      75     142 ..     169     242 ..     151     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.9e-08
                           DoxD  75 EiivGlllliGlltRlsslvafalalgials..........ayWlgstcedEyqiglllvaaelvliltgsgklslDy 142
                                    Ei++G+ll++Gl+t l++ +a+a  +  +l+          ay+l      Eyqi l+++a++  +il+g g+++lD+
  gi|121638887|ref|YP_979111.1| 169 EIVAGVLLVLGLFTPLAAAGALAFLINGLLAgisaqhsrpvAYFLQD--GHEYQITLVVMAVA--VILSGPGRYGLDA 242
                                    9******************9988765444432222222333456655..68*****9999865..6889*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1857.28
//
Query:       gi|121638888|ref|YP_979112.1|  [L=373]
Description: lipoprotein lppZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-16   58.1   0.0    3.7e-15   56.1   0.0    1.8  2  GSDH           Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.93    9.7   0.0    2.6  2  NHL            NHL repeat
       0.34   10.9   1.9       0.51   10.4   1.9    1.2  1  Mito_fiss_reg  Mitochondrial fission regulator


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   6.1e-19   3.7e-15      12     202 ..      86     252 ..      76     274 .. 0.79
   2 ?   -0.4   0.0     0.096   5.7e+02     270     323 ..     285     340 ..     260     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.1e-19
                                    TS-EEEEET.TTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE- CS
                           GSDH  12 dgrlLvter.sGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararls 90 
                                     +++Lv+er +G ++ ++   + ++++++v  v  +g+gGl+d++l+p+++++rl+Y + ++       ++++v+r+   
  gi|121638888|ref|YP_979112.1|  86 SKTALVAERiTGAVEEIS--ISAEPKVKTVIPVDPAGDGGLMDIVLSPTYSQDRLMYAYISTP------TDNRVVRVAD- 156
                                    3789*****99****999..444589***********************************66......3344555544. PP

                                    SS..-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TT CS
                           GSDH  91 edeaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrlnkdGsvpadnpfvgkag 170
                                    +d       ++i++ +pk  ++a + + l+f++  tL+v +Gd+++++ a d++s +Gk+lr+++  ++ +  p +    
  gi|121638888|ref|YP_979112.1| 157 GD-----IPKDILTGIPK--GAAGNTGALIFTSPTTLVVMTGDAGDPALAADPQSLAGKVLRIEQPTTIDQTPPTT---- 225
                                    22.....2577*******..66677788999999******************************999997777764.... PP

                                    S-TTEEEE--SCE---EE-TTT--EEEEEE-- CS
                           GSDH 171 akpeiwsyGhRnpqGlaldpdtgeLwesEhGp 202
                                    a + i s       Gl +dp  g L+  +  p
  gi|121638888|ref|YP_979112.1| 226 ALSGIGS-----GGGLCIDPVDGSLYVADRTP 252
                                    3433333.....33666666666666666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                                    TTEEEEEETTTTEEEEEEE.EEEEEEEEEEEEE.ESS-.-EEEEEE-TTS-EEEEE CS
                           GSDH 270 kgdllvggLksqsllrlel.degekvveeerll.eelgeriRdVeqgpdGalyvlt 323
                                    +g +lv  ++++  + ++l  ++++v+ e  ++ +++++   +++  pdG+++ +t
  gi|121638888|ref|YP_979112.1| 285 DGTVLVNLINTKLTVAVRLaPSTGAVTGEPDVVrKDTHAHAWALRMSPDGNVWGAT 340
                                    55555555555555666662223445555555556666677777777777777665 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00016      0.93       6      20 ..     235     250 ..     234     253 .. 0.92
   2 ?   -1.0   0.0      0.38   2.2e+03       4      16 ..     325     337 ..     323     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                                    EEEEE.TTTEEEEEEC CS
                            NHL   6 Gvavd.snGdiyVaDs 20 
                                    G+++d  +G +yVaD+
  gi|121638888|ref|YP_979112.1| 235 GLCIDpVDGSLYVADR 250
                                    9**************5 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                                    EEEEEEETTTEEE CS
                            NHL   4 PhGvavdsnGdiy 16 
                                    ++ ++++++G+++
  gi|121638888|ref|YP_979112.1| 325 AWALRMSPDGNVW 337
                                    6889999****98 PP

>> Mito_fiss_reg  Mitochondrial fission regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   8.5e-05      0.51     162     193 ..      31      64 ..       6      89 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.5e-05
                  Mito_fiss_reg 162 epksssaspslep.ssslp.pppppppppippes 193
                                    ++++  ++p+l+p +ss+p pppp pp p p+e+
  gi|121638888|ref|YP_979112.1|  31 QSQPFTTEPELRPqPSSTPpPPPPLPPVPFPKEC 64 
                                    3333444444433233333133333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2842.01
//
Query:       gi|121638889|ref|YP_979113.1|  [L=204]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-24   84.2   0.1    1.2e-23   83.9   0.1    1.1  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.1   6.7e-28   1.2e-23       1     147 [.      22     162 ..      22     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6.7e-28
                                    HTTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                  Flavin_Reduct   1 mrrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                    m+ + +pv+vvtt +++++p+g+ +s+ t+ s +Pp +++ l ++  t+++  +++++++++ls+ q  la+ f++++  
  gi|121638889|ref|YP_979113.1|  22 MGMLDHPVFVVTT-QADGHPAGCLVSFATQTSVQPPSFMVGLPRSTGTSEVASRSEHLAVHVLSQRQHVLAELFGSQTE- 99 
                                    667789*******.99************************************************************877. PP

                                    CCCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECC CS
                  Flavin_Reduct  81 rtddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlyw 147
                                    ++++k  fa ++w+ +p g p+l++a a++  ++ ++ ++gd   +++e v+v+ ++  + e Lly 
  gi|121638889|ref|YP_979113.1| 100 EEVNK--FARCSWRAGPCGMPILDDAAAWFIGRTASRSDVGDYVAYLLEPVSVWAPEC-S-EDLLYL 162
                                    88998..**************************************************9.4.358885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1613.40
//
Query:       gi|121638890|ref|YP_979114.1|  [L=207]
Description: hypothetical protein BCG_3030 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1446.58
//
Query:       gi|121638891|ref|YP_979115.1|  [L=509]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.4e-104  349.4   0.0   1.8e-104  349.0   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    3.2e-36  124.4   0.1    4.5e-36  124.0   0.1    1.2  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
       0.15   12.4   0.0       0.24   11.8   0.0    1.3  1  SLX9       Ribosome biogenesis protein SLX9


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.0   0.0    3e-108  1.8e-104       2     273 .]      28     321 ..      27     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 349.0 bits;  conditional E-value: 3e-108
                                    EEEEEEEEEB--SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N   2 viGlEiHaqlktksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfyp 81 
                                    v GlE+H++l+t++K+F++++t+ +g epn++v++v+l+lPG+lPvln++ave+ai+++lalncei + ++f+RKnyfyp
  gi|121638891|ref|YP_979115.1|  28 VLGLEVHVELSTATKMFCGCTTT-FGGEPNTQVCPVCLGLPGSLPVLNRAAVESAIRIGLALNCEIVPWCRFARKNYFYP 106
                                    78*******************65.******************************************************** PP

                                    TCTTSEEEEESSS.SEEEEEEEE......TEEEEEEEEEEEE---EEEE........EETTEEEEETTSTT-EEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N  82 dlpkgyQitqkeeplakeGslel......ekkvrierihlEeDaaksvh........eekeeslvdlnRaGvpLiEivte 147
                                    d+pk+yQi+q++ep+a +G+l++      + +v+ier+h+EeD++k +h        + ++ sl+d+nRaGvpLiEivt+
  gi|121638891|ref|YP_979115.1| 107 DMPKNYQISQYDEPIAINGYLDApledgtTWRVEIERAHMEEDTGKLTHigsetgriHGATGSLIDYNRAGVPLIEIVTK 186
                                    **********************99999988899********************999856669****************** PP

                                    S....TB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS..--EEEEEE-SHHHHHHHHHHHH CS
                                    x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 148 p....dlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeee.gtrvEiKnlnslksiekaieyei 222
                                    p      r p+ ar++v++lr+llral+vsd +m++Gs+RcD+NvS++  ++g++e gtr+E Kn+nslks+e a++ye+
  gi|121638891|ref|YP_979115.1| 187 PivgaGARAPQIARSYVTALRDLLRALDVSDVRMDQGSMRCDANVSLK--PAGTTEfGTRTETKNVNSLKSVEVAVRYEM 264
                                    *555556999**************************************..6688888*********************** PP

                                    HHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                                    xxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 223 erqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                                    +rq ++l       qeTr+f+e+ g t++ R+ke+aedYryfpepdl p++ s+el+e
  gi|121638891|ref|YP_979115.1| 265 QRQGAILasggritQETRHFHEA-GYTSAGRTKETAEDYRYFPEPDLEPVAPSRELVE 321
                                    **********************9.**************************99999875 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.1   7.6e-40   4.5e-36       3     146 ..     361     504 ..     359     506 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 7.6e-40
                                    HHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHH CS
                      GatB_Yqey   3 feevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiiee 82 
                                    + ++v++ga+++ a +w+ n l+++ n+ g+ ++el +tp+q+a +++l++egk+s++ a++v+e +l+++++pe++++ 
  gi|121638891|ref|YP_979115.1| 361 VAATVEHGASSEAARAWWGNFLAQKANEAGIGLDELAITPAQVAAVVALVDEGKLSNSLARQVVEGVLAGEGEPEQVMTA 440
                                    678999************************************************************************** PP

                                    CTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHH CS
                      GatB_Yqey  83 kgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellke 146
                                    +gL  ++d++  +++v+e++a+np++++++++gk  a +++vG vMk+t+G+ad+++v+el+ e
  gi|121638891|ref|YP_979115.1| 441 RGLALVRDDSLTQAAVDEALAANPDVADKIRGGKVAAAGAIVGAVMKATRGQADAARVRELVLE 504
                                    ********9****************************************************987 PP

>> SLX9  Ribosome biogenesis protein SLX9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.24      42     113 ..     200     279 ..     191     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                           SLX9  42 kklvtdlesLadaLpdleeeege.kkekkekeqaqqgkvkkae.......kslkskpgalkrkkklekkEmerfkkvLa. 112
                                     + vt l++L  aL+  +    + ++++++  ++ + k            +++ ++ ++lk  +  ++ Em+r +++La 
  gi|121638891|ref|YP_979115.1| 200 RSYVTALRDLLRALDVSD---VRmDQGSMRCDANVSLKP---AgttefgtRTETKNVNSLKSVEVAVRYEMQRQGAILAs 273
                                    567899999999999333...222233333322222222...2334566569**************************95 PP

                           SLX9 113 .....h 113
                                         +
  gi|121638891|ref|YP_979115.1| 274 ggritQ 279
                                    555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3612.27
//
Query:       gi|121638892|ref|YP_979116.1|  [L=343]
Description: 6-phosphofructokinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.1e-103  345.0   0.1   3.5e-103  344.8   0.1    1.0  1  PFK         Phosphofructokinase
    5.9e-05   22.4   0.1    9.3e-05   21.8   0.1    1.3  1  NAD_kinase  ATP-NAD kinase
  ------ inclusion threshold ------
      0.032   13.8   0.0      0.063   12.9   0.0    1.5  1  AIRC        AIR carboxylase


Domain annotation for each model (and alignments):
>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.8   0.1  5.9e-107  3.5e-103       1     283 [.       2     298 ..       2     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 344.8 bits;  conditional E-value: 5.9e-107
                                    EEEEEEESS--TTHHHHHHHHHHHHHHTT.-EEEEETTHHHHHHTT-EEEE-SGG.GTT-TT--S-TT-----GGGGSHH CS
                            PFK   1 riailtsGGdapGmNaairavvrtaikkg.levygireGfeGlieeeiekltled.vsgilsegGtiLgsaRskefkere 78 
                                    ri++lt GGd+pG+Na+iravvrt+ +++  +v+g+++Gf+Gl+e++  +l+ +d  + +l++gGt+Lg+aR ++ k r 
  gi|121638892|ref|YP_979116.1|   2 RIGVLTGGGDCPGLNAVIRAVVRTCHARYgSSVVGFQNGFRGLLENRRVQLHNDDrNDRLLAKGGTMLGTARVHPDKLRA 81 
                                    7************************9888799**************7777877652888******************99* PP

                                    HHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT---TT-S--EEHHHHHHHHHHHHHHHH CS
                            PFK  79 grkkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTidNDipgtdytiGfdTAlntiveaidklk 158
                                    g+ +++++l+++gid L+ iGG+g+l++a+ lsee  +    +++vg+PkTidNDi +td+t+G dTAl++++eaid+l+
  gi|121638892|ref|YP_979116.1|  82 GLPQIMQTLDDNGIDVLIPIGGEGTLTAASWLSEE--N----VPVVGVPKTIDNDIDCTDVTFGHDTALTVATEAIDRLH 155
                                    *********************************88..7....9************************************* PP

                                    HHHHHHT-EEEEEES-TT-THHHHHHHHHHT-SEEE-TTS---HHHHHHHHHHHHT.T-S-EEEEEESSS..S-...... CS
                            PFK 159 stakshkrvfvvEvmGrncGwlAlmaglaggadvilipEepfdieeliekikklrkkgkkksiivvaEgakdkeg..... 233
                                    sta+sh+rv++vEvmGr++Gw+Al agla+ga++ lipE+pfdiee+++ +k + ++g ++ i+vvaEgak   g     
  gi|121638892|ref|YP_979116.1| 156 STAESHERVMLVEVMGRHAGWIALNAGLASGAHMTLIPEQPFDIEEVCRLVKGRFQRGDSHFICVVAEGAKPAPGtimlr 235
                                    ***********************************************************************655567888 PP

                                    ...............HHHHHHHHHHHHSS-EEEEE-GGGGG-S---HHHHHHHHHHHHHHHHH CS
                            PFK 234 .............iiaeelakeieektgievrvtvlGhlqrGgspsafDrilatrlGikavel 283
                                                 ++a +la e+e++ +++vrvtvlGh+qrGg+p+a+Dr+latr+G++a+++
  gi|121638892|ref|YP_979116.1| 236 eggldefgherftGVAAQLAVEVEKRINKDVRVTVLGHIQRGGTPTAYDRVLATRFGVNAADA 298
                                    889**********************9**********************************875 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.6e-08   9.3e-05      72     109 ..      88     124 ..      47     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-08
                                    -TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEE CS
                     NAD_kinase  72 eafadagvdliivvGGDGTaldvarllqkaeiPvlgvn 109
                                    +++ d+g+d++i +GG GT +++++l ++ ++Pv+gv+
  gi|121638892|ref|YP_979116.1|  88 QTLDDNGIDVLIPIGGEGTLTAASWLSEE-NVPVVGVP 124
                                    67789********************9996.*******9 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.063      43      87 ..      83     127 ..      73     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                    HHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE-- CS
                           AIRC  43 lleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvks 87 
                                    l +++++ +++g++v+I + G     +    s  ++PV+gvP + 
  gi|121638892|ref|YP_979116.1|  83 LPQIMQTLDDNGIDVLIPIGGEGTLTAASWLSEENVPVVGVPKTI 127
                                    567999*************99999999999************775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2406.45
//
Query:       gi|121638893|ref|YP_979117.1|  [L=494]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.2e-160  534.0   0.4   3.6e-160  533.8   0.4    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.8   0.4    2e-164  3.6e-160       1     450 [.      25     476 ..      25     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 533.8 bits;  conditional E-value: 2e-164
                                    HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT.......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-S CS
                        Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkra.rgkekgpLhGvPisvKDnidvkgvpttaGskalenypae 79 
                                    e+++a+l++iea++e+++a+++v+ +eala+Aa++dk+ a  +   + L+GvP+++KD +++ ++ptt+Gsk+le+++++
  gi|121638893|ref|YP_979117.1|  25 EITRACLDQIEATDETYHAFLHVAADEALAAAAAVDKQVAaGEPLPSALAGVPLALKDVFTTSDMPTTCGSKILEGWRSP 104
                                    79**************************************66666789******************************** PP

                                    S--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHH CS
                        Amidase  80 kDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiP 159
                                    +Dat+++rL++aG+ ilgkTnmdefamgsstens++gptrNPw+++r+pGGS GGsAAa+Aa ++plaiG+DtGGSiR+P
  gi|121638893|ref|YP_979117.1| 105 YDATLTARLRAAGIPILGKTNMDEFAMGSSTENSAYGPTRNPWNLDRVPGGSGGGSAAALAAFQAPLAIGSDTGGSIRQP 184
                                    ******************************************************************************** PP

                                    HHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----..HHHHHHHHCTT---TT CS
                        Amidase 160 AsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvip..eesedlaeelkkslkg 237
                                    A+++ +vG+KPtyg vSr+g+va++ssld+ Gp+ar+v d+all +vi+g+dp+dsts +    + +++ ++++  +l+g
  gi|121638893|ref|YP_979117.1| 185 AALTATVGVKPTYGTVSRYGLVACASSLDQGGPCARTVLDTALLHQVIAGHDPRDSTSVDAEvpDVVGAARAGAVGDLRG 264
                                    ***********************************************************9877899999*********** PP

                                    -EEEEEGGGC.SS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS...---SS CS
                        Amidase 238 lriGvvkedg.vasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry...erlse 313
                                    +r+Gvv++++  + ++p v +++e+a+++L+++G+ev ev++p++++al++yylil++e ssnlar++++ry     +++
  gi|121638893|ref|YP_979117.1| 265 VRVGVVRQLHgGEGYQPGVLASFEAAVEQLTALGAEVSEVDCPHFDHALAAYYLILPSEVSSNLARFDAMRYglrVGDDG 344
                                    *********999*************************************************************9999*** PP

                                    -SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCC CS
                        Amidase 314 tkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekd 393
                                    t++ +e+++ +ra+++g+evkrri+ g+yalsa+++++yy++aqkvr+l+ r++++a++++Dvl+sPt+pt+a+rlgek 
  gi|121638893|ref|YP_979117.1| 345 TRSAEEVMAMTRAAGFGPEVKRRIMIGTYALSAGYYDAYYNQAQKVRTLIARDLDAAYRSVDVLVSPTTPTTAFRLGEKV 424
                                    *******************************************************************************7 PP

                                    HHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCC.T.TECEEEEEEESTT-HHHH CS
                        Amidase 394 ktidsytvlynlldftavvvpvnlaglpalsvpagks.edglPvGvqvigkafqeetl 450
                                       d+++++y+++ +t    p nlag+  +svp+g s +dglPvG+q++++a+++ +l
  gi|121638893|ref|YP_979117.1| 425 ---DDPLAMYLFDLCT---LPLNLAGHCGMSVPSGLSpDDGLPVGLQIMAPALADDRL 476
                                    ...89***********...******************999**************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3524.80
//
Query:       gi|121638894|ref|YP_979118.1|  [L=99]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-16   60.5   0.1    1.9e-16   60.1   0.1    1.2  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1     1e-20   1.9e-16       1      62 []      20      91 ..      20      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1e-20
                                   --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S-.-....HHHHHTT-SSEETTEEEE CS
                    Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp.....vlReDe.v....reelLknApetedgyfvV 62
                                   l+e El+++a++l++il +v q+q+vd+tgv  + +p     v+R+De v    ++++L +Ap+  dg f V
  gi|121638894|ref|YP_979118.1| 20 LTETELDSFAGQLDAILTHVSQIQAVDVTGVQATDNPlkdvnVTRPDEtVpcltQRQVLDQAPDAVDGRFAV 91
                                   79*********************************************85489*9999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 722.05
//
Query:       gi|121638895|ref|YP_979119.1|  [L=218]
Description: hypothetical protein BCG_3035 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00038   20.2   0.0    0.00066   19.4   0.0    1.4  1  ACT       ACT domain
  ------ inclusion threshold ------
      0.056   14.0   0.0       0.12   13.0   0.0    1.5  2  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.4e-08   0.00066       1      64 [.       4      67 ..       4      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.4e-08
                                   EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64
                                   + lr++++DrPG L+ ++ al+  g  i s+ + + + ++a    vv+++  + +++++ a ++
  gi|121638895|ref|YP_979119.1|  4 YLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDTLITAAEA 67
                                   679*********************************9987777777777776666666666555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05      0.12       9      58 ..       6      54 ..       3      73 .. 0.82
   2 ?   -3.5   0.0       1.9   1.7e+04       6      20 ..     102     116 ..      99     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                          ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkd 58
                                   l++e  dr+g L++++ ++ + +a+i s+ +++r  +g+a  ++ ve+  
  gi|121638895|ref|YP_979119.1|  6 LRIELADRPGSLGSLAVALGSVGADILSLDVVERG-NGYAIDDLVVELPP 54
                                   799******************************86.99999888888765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                          ACT_4   6 tvrleveaedrkglL 20 
                                    t+rl+v ++  +++L
  gi|121638895|ref|YP_979119.1| 102 TARLQVLVNEAPRVL 116
                                    678888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1532.20
//
Query:       gi|121638896|ref|YP_979120.1|  [L=691]
Description: NAD-dependent DNA ligase LigA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.6e-126  419.7   0.0   8.4e-126  419.4   0.0    1.1  1  DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
    1.2e-31  108.5   1.0    2.3e-31  107.5   1.0    1.5  1  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
    1.1e-22   79.8   0.1    2.4e-22   78.8   0.1    1.6  1  HHH_2            Helix-hairpin-helix motif
    1.2e-13   51.2   0.0    1.9e-13   50.5   0.0    1.3  1  BRCT             BRCA1 C Terminus (BRCT) domain
    1.8e-08   34.9   0.1    4.9e-08   33.5   0.1    1.7  1  HHH_5            Helix-hairpin-helix domain
      4e-08   33.1   0.0    1.1e-07   31.7   0.0    1.7  1  PTCB-BRCT        twin BRCT domain
    9.1e-08   32.0   5.2    9.1e-08   32.0   5.2    1.9  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      6e-06   25.9   0.1      2e-05   24.2   0.1    2.0  1  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.027   14.6   0.5      0.055   13.6   0.5    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.33   11.3   2.1        3.6    7.9   0.1    2.5  2  Bactofilin       Polymer-forming cytoskeletal


Domain annotation for each model (and alignments):
>> DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.4   0.0  4.7e-129  8.4e-126       3     318 .]      13     328 ..      11     328 .. 0.97

  Alignments for each domain:
  == domain 1  score: 419.4 bits;  conditional E-value: 4.7e-129
                                    HHHHHHHHHHHHHHHHHHHHCTT-SSC-HCHHHHHHHHHHHHHHHSGGG--TTSCCG-SS.SS--CTS-EEE-SS----- CS
                DNA_ligase_aden   3 akkeleelrellrkydyeYyvldePlvsDaeyDrllkelkelEekfPelitpdSPtqrvg.aeleaefkkveHeapllSL 81 
                                    + +++++l+e++r+++++Yyv+d+P++sDae+D+ll++l++lEe++Pel tpdSPtq vg a ++++f+ v H +++lSL
  gi|121638896|ref|YP_979120.1|  13 VLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGgAGFATDFEPVDHLERMLSL 92 
                                    56799*******************************************************99****************** PP

                                    EEE-SHHHHHHHHHHHHHHSSS--S-EEEEEEEESSEEEEEEEETTEEEEEEE-TTSSEEEB-HHHHCT-TTS-SB-SSS CS
                DNA_ligase_aden  82 dnafdedelkaflerieealgnkekvayvvelKiDGlavsllYengvlvraatRGdGttGedvtaNvktiksiPlklkvd 161
                                    dnaf +del+a+  ri++++g++++  y++elKiDG+a+sl+Y++g l+ra tRGdG+tGedvt N++ti+++P++l+  
  gi|121638896|ref|YP_979120.1|  93 DNAFTADELAAWAGRIHAEVGDAAH--YLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPG 170
                                    ***********************97..**************************************************976 PP

                                    S...--SEEEEEEEEE--HHHHHHHHHHHHHCT----SSHHHHHHHHHT-SSHHHHHTS--EEEEEEEEEEESS---.SB CS
                DNA_ligase_aden 162 n...lpeelevRGEvylrkedFeklNeerleegeklfaNpRNaAaGslRqldpkitakrkLkliayglglvekeelevkt 238
                                    +   +pe levRGEv++r +dF++lN++++eeg+ +faNpRN+AaGslRq+dp++ta+r+L++i++glg+ve+++  ++t
  gi|121638896|ref|YP_979120.1| 171 DdypVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFR--PAT 248
                                    668899*******************************************************************55..56* PP

                                    HHHHHHHHHHCT--B-TT-EEECSHHHHHHHHHHHHHHGGGSSS-EEEEEEEESBHHHHHHH-EETSCESSEEEEE---C CS
                DNA_ligase_aden 239 qsealkvlkklglkvseelklvksieevleyieelekkRdeleyeiDGvVvkvdelalqeeLGftakaPrwAiAyKfpae 318
                                     ++a+ +l+ +gl+vse+++l+ ++ +v e i+++ ++R+e+++eiDGvVvkvde+alq++LG t++aPrwAiAyK+p+e
  gi|121638896|ref|YP_979120.1| 249 LHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPE 328
                                    ******************************************************************************86 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   1.0   1.3e-34   2.3e-31       1      78 [.     331     408 ..     331     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.3e-34
                                    G--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB   1 etkledievqVGRtGaltpvAeLepvelaGttVsratLhnedeierkdirigdtVvvekaGdvIPevvgvvlekreee 78 
                                    +tkl di+v+VGRtG++tp+A ++pv++aG+tV +atLhn++ei+rk++ igdtVv++kaGdvIPev+g v+e r+++
  gi|121638896|ref|YP_979120.1| 331 QTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGS 408
                                    69*************************************************************************986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.1   1.3e-25   2.4e-22       1      64 []     527     590 ..     527     590 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.3e-25
                          HHH_2   1 rllfaLGIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFeneknreli 64 
                                    r+l+aL+IrhVG ++A++La++F+slda+++as+++L++v+++G++iA++++e+F+ +++re++
  gi|121638896|ref|YP_979120.1| 527 RVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIV 590
                                    799**********************************************************997 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.1e-16   1.9e-13       5      78 ..     611     682 ..     607     683 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.1e-16
                                    TTTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHH CS
                           BRCT   5 lfhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldc 78 
                                     + g+++v+tg+l++f rd+++e i   GGk  ++vskkt+++v+g++   ++ky +a +l++pi++e+ +  +
  gi|121638896|ref|YP_979120.1| 611 TLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDS--PGSKYDKAVELGVPILDEDGFRRL 682
                                    5889********************************************..99****************988765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   2.7e-11   4.9e-08       5      51 ..     532     577 ..     529     580 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.7e-11
                                    HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHH CS
                          HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeri 51 
                                    ls+  +Gp  A+al+   ++s++++aaa++++La++ G+G+  A  +
  gi|121638896|ref|YP_979120.1| 532 LSIRHVGPTAARALATE-FGSLDAIAAASTDQLAAVEGVGPTIAAAV 577
                                    7999*************.***********************999765 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0     6e-11   1.1e-07       4      58 ..     618     673 ..     615     676 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6e-11
                                    EEEC.B-TTCHHHHHHHHHHTT-EEESSEETT-SEEEECSS-CHHHHHHHHCT-EE CS
                      PTCB-BRCT   4 cvtg.ysgddrkslqklieamGaeyskdltksvTHLicksgeGekyekAkkwgipv 58 
                                     vtg ++g +r+++++ i+a G++  + ++k++ ++++ ++ G+ky+kA++ g+p+
  gi|121638896|ref|YP_979120.1| 618 VVTGsLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPI 673
                                    5554245667999******************************************8 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.2   7.5e+03       8      17 ..     385     394 ..     383     394 .. 0.80
   2 !   32.0   5.2   5.1e-11   9.1e-08       1      26 [.     417     444 ..     417     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                 DNA_ligase_ZBD   8 avvReegeai 17 
                                     v+R+ g++i
  gi|121638896|ref|YP_979120.1| 385 VVIRKAGDVI 394
                                    477****997 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 5.1e-11
                 DNA_ligase_ZBD   1 hCPvCGsavv.ReegeaiyRCtn.lsCp 26 
                                    +CP+CGs++   +eg+a++RC+n   Cp
  gi|121638896|ref|YP_979120.1| 417 TCPECGSPLApEKEGDADIRCPNaRGCP 444
                                    7*********99***************9 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.1e-08     2e-05       1      29 [.     551     579 ..     551     580 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                    sl+++ +as ++L+a++GVGp  A a+ +
  gi|121638896|ref|YP_979120.1| 551 SLDAIAAASTDQLAAVEGVGPTIAAAVTE 579
                                    7899**********************976 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   3.1e-05     0.055      16      38 ..     416     439 ..     413     439 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                  Auto_anti-p27  16 etCpvCgvPLmrdr.kggkvyCva 38 
                                    +tCp+Cg+PL  ++ ++ ++ C++
  gi|121638896|ref|YP_979120.1| 416 TTCPECGSPLAPEKeGDADIRCPN 439
                                    79************989999**95 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.002       3.6      34      80 ..     338     384 ..     333     390 .. 0.92
   2 ?    2.1   0.2      0.13   2.4e+02      20      60 ..     618     660 ..     612     670 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                     Bactofilin  34 klvvgeggkvegnikaeevvvaGtvkGnveaeekvelkktakveGdi 80 
                                    ++ vg++g+++     + v+vaG+  G+ + ++  e+k ++++ Gd 
  gi|121638896|ref|YP_979120.1| 338 RVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDT 384
                                    6899***************************************9986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                     Bactofilin  20 ridGkveGdi.eakgklvvgeggkvegnika.eevvvaGtvkG 60 
                                    ++ G+++G   + +++ +v++ggk  g+++  ++ vvaG   G
  gi|121638896|ref|YP_979120.1| 618 VVTGSLTGFSrDDAKEAIVARGGKAAGSVSKkTNYVVAGDSPG 660
                                    5566666655545678999999999999998566889998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4768.37
//
Query:       gi|121638897|ref|YP_979121.1|  [L=337]
Description: hypothetical protein BCG_3037c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-89  299.1   0.1    4.6e-89  298.9   0.1    1.0  1  Meth_synt_2    Cobalamin-independent synthase, Catalytic doma
  ------ inclusion threshold ------
      0.041   13.6   0.6       0.19   11.5   0.1    2.4  2  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9   0.1   5.1e-93   4.6e-89       1     323 [.       4     328 ..       4     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 5.1e-93
                                    S-BB-.-SB---SS----------------.-HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE.E CS
                    Meth_synt_2   1 lpTtt.iGSfPqtaevrearaevkkgelse.eeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf.a 77 
                                    ++T+t iGS+P+ta++++a+++v++ ++++ + +e ++r++++++++r+++l vDv+++++p Rg++++++++a++++ a
  gi|121638897|ref|YP_979121.1|   4 FATATgIGSWPGTAAREAAQVVVGELAGALaYLTELPARGVGADMLGRAGGLLVDVAIDTVP-RGYRIAARPGAVTRRaA 82 
                                    789999***********************989*****************************9.***************99 PP

                                    --SS--EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHH CS
                    Meth_synt_2  78 ftkngwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalr 157
                                    ++ +++++++++++++++      +r+++++vk++a+++++++++ ++l++G+++i+++++vr   d+a+++a++++a+r
  gi|121638897|ref|YP_979121.1|  83 SLLDEDMDALEEAWETAG------LRGCGRAVKVQAPGPVTLVAG-LELANGHRAITDPGAVR---DLAASLAEGVAAHR 152
                                    ******************......9********************.*****************...9************* PP

                                    HHHH.HHHHTT-SEEEEE-T...TSSTT--SSG..GGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCH...HH CS
                    Meth_synt_2 158 devk.dLeaaGikviQiDep...alreGlplkk..adwaayldwaveafrldtiaaaddtqvhtHlCyselndil...sa 228
                                    ++++ +L+++  +v+Q+Dep   a+++G+++++   +++a+ld++v++++ldt++aa+d++v++H+C+++l+++l   s+
  gi|121638897|ref|YP_979121.1| 153 AALArRLDTP--VVVQFDEPslpAALGGRLTGVtaLSPVAPLDETVAEALLDTCIAAVDADVALHSCSPDLPWDLlqrSR 230
                                    ***99*****..*******999999******998899******************************************* PP

                                    HHTT--SEEEESBSSS-SSGGGGTTTT---SEEEEBSS-TTSS.S--THHHHHHHHHCHHCT......S-STSB-BB-SS CS
                    Meth_synt_2 229 iaaldvDvitieasrsdeellealeevkygrgvglGvydihsp.rvpsmeeiaalikkaldv......apkerlwvnPdC 301
                                    i+a++vD++t++a++ d  +++a++e  +gr+v+lG++++++p r+psmee+aa++++++d+      a+++rl+v+P+C
  gi|121638897|ref|YP_979121.1| 231 ISAVSVDASTLQAADLD--AVAAFVE--SGRTVVLGLVPVTAPeRAPSMEEVAAAAVAVTDRlgvprsALRDRLGVSPAC 306
                                    *****************..*******..***************************************999********** PP

                                    -STTS-HHHHHHHHHHHHHHHH CS
                    Meth_synt_2 302 GLktrkreearaalknmvdaAk 323
                                    GL+++++++ar+a+++++d+A+
  gi|121638897|ref|YP_979121.1| 307 GLANATGQWARTAVGLARDVAE 328
                                    ********************97 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.1e-05      0.19      32      56 ..     146     170 ..     141     214 .. 0.89
   2 ?   -1.3   0.0       0.2   1.8e+03      11      26 ..     265     282 ..     259     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                                    -TTHHHHHHHHHHTT--EEE--SSH CS
                  PEP-utilizers  32 GGmtSHaAivArelgiPaVvgvgea 56 
                                     G   H A +Ar l+ P+Vv+ +e 
  gi|121638897|ref|YP_979121.1| 146 EGVAAHRAALARRLDTPVVVQFDEP 170
                                    68899***************98875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.2
                                    S---HHHHTTS-..GEEE CS
                  PEP-utilizers  11 eetspsdiagld..kaaG 26 
                                    + t p+  + ++  +aa+
  gi|121638897|ref|YP_979121.1| 265 PVTAPERAPSMEevAAAA 282
                                    668999999999643333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2703.11
//
Query:       gi|121638898|ref|YP_979122.1|  [L=209]
Description: lipoprotein lpqA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-13   48.4   0.5    4.6e-12   46.2   0.5    1.9  1  PknH_C    PknH-like extracellular domain


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.5   2.6e-16   4.6e-12       7     175 ..      43     194 ..      41     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.6e-16
                                    GGGS--HHHHHHHHT-S.......--EE-S-B-S-B-S--EES..SGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT CS
                         PknH_C   7 dslLltpaelaailGtp......eaasatesdttppdtaasvd..ppeClgvasageesvYggsgvtavagqtlrdsadd 78 
                                      +Ll+++ ++ai+G+       +++ +t + +     +  ++  p eC+ ++  +e++v+g+  ++a++++t++d++d+
  gi|121638898|ref|YP_979122.1|  43 ATILLDQSRMQAITGSGddltiiPTMDTTYPVDV----DDFAQpiPRECRFIY--AETAVFGSE-IEAFHKTTFQDRPDG 115
                                    579***********99887666544443333222....2222235999****9..99999*966.*************** PP

                                    -SEEEEEEEEE-SSHHHHHHHHHHHHHHHHTTTT-EEEEEETTEEEEEEE---B--TT-EEEEEE.ESSTT--EEEEEEE CS
                         PknH_C  79 gaslvsqavvafptadaAqaffaalaaqwrrCagvttttdsggatetwtvgdvsdddgvltatvtvtsggdgarcqrala 158
                                    +   +s+a++a+++a +A+++f++la  ++ Ca      +++g+ +  +++   ++            ++ +  c r ++
  gi|121638898|ref|YP_979122.1| 116 SL--ISEAAAAYRDAGTARRAFDTLAVTVHDCAA-----SPAGWLFVSRWTAGGNS-----------LHIRAGDCGRDYR 177
                                    *9..******************************.....79999999999999988...........356778******* PP

                                    EETTEEEEEEEEE.SS- CS
                         PknH_C 159 vranvvvdvevcgfedg 175
                                    v +  +++v++cgf+ +
  gi|121638898|ref|YP_979122.1| 178 VLSAALLEVTFCGFPES 194
                                    *************9553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1351.67
//
Query:       gi|121638899|ref|YP_979123.1|  [L=120]
Description: ESAT-6 like protein 8 esxQ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00016   21.8   0.4     0.0002   21.6   0.4    1.1  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   1.1e-08    0.0002       3      78 ..       5      80 ..       3      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-08
                                   CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  3 kvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78
                                   ++++ ++++   ++++  ++ +++ +++++e  a + + +G+ + + q+++++w+qa++ l++a+   ++al+q++
  gi|121638899|ref|YP_979123.1|  5 MYSYPAMTANVGDMAGYTGTTQSLGADIASERTAPSRACQGDLGMSHQDWQAQWNQAMEALARAYRRCRRALRQIG 80
                                   689999*******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 973.53
//
Query:       gi|121638900|ref|YP_979124.1|  [L=437]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-58  195.8  22.3    4.7e-58  195.8  22.3    2.0  2  PPE       PPE family
  ------ inclusion threshold ------
      0.089   13.0   1.8       0.17   12.2   1.8    1.5  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8  22.3   5.2e-62   4.7e-58       1     157 [.      11     167 ..      11     168 .. 0.99
   2 ?   -2.6   0.5      0.58   5.2e+03      60      90 ..     307     337 ..     301     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 5.2e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall+aGpg+g+l aAaa W++L+ae+a++a+el++v+a++ a+ WqGps++ ++aa++py+aWL +a+a+++
  gi|121638900|ref|YP_979124.1|  11 ASPPEVHSALLSAGPGPGSLQAAAAGWSALSAEYAAVAQELSAVVAAVGAGVWQGPSAELFVAAYVPYVAWLVQASADSA 90 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA ++eaaaa Y  Ala+m++++e+aan+ ++a+lvatnffG+nt++Ia +ea+y +mw+q+a++m+aYea++ aa
  gi|121638900|ref|YP_979124.1|  91 AAAGEHEAAAAGYVCALAEMPTLPELAANHLTHAVLVATNFFGINTIPIALNEADYVRMWVQAATVMSAYEAVVGAA 167
                                    ************************************************************************99876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.58
                                    HHHHHTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  60 amaaaaapylaWLsaaaaqaeeaAaqaeaaa 90 
                                    a+aaa++p +a L+  a  a+  A  a+a a
  gi|121638900|ref|YP_979124.1| 307 ALAAAVVPGVAGLAGVAGLAALPAVGAAAGA 337
                                    6788889999989888888888877776655 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   1.9e-05      0.17       7      53 ..      28      75 ..      26     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHH CS
                         WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaef 53
                                     l++aaa  ++ ++e  ++ q+l a v+a+ ++ W+G +a+ f a++
  gi|121638900|ref|YP_979124.1| 28 GSLQAAAAGWSALSAEYAAVAQELSAVVAAVgAGVWQGPSAELFVAAY 75
                                   6799***************************999*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3226.09
//
Query:       gi|121638902|ref|YP_979126.1|  [L=96]
Description: ESAT-6 like protein 9 esxR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-17   62.3   4.1    4.2e-17   62.1   4.1    1.1  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.17   12.0   0.0    1.2  1  Xpo1      Exportin 1-like protein


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   4.1   4.7e-21   4.2e-17       1      85 [.       3      87 ..       3      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4.7e-21
                                   CHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  1 qikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82
                                   qi++++ ++ ++a ++++ a++l+++ +++++e++ l+s+W+G+++ ++q+++++w+qa+++lv+a++++s ++++++ a+ 
  gi|121638902|ref|YP_979126.1|  3 QIMYNYPAMMAHAGDMAGYAGTLQSLGADIASEQAVLSSAWQGDTGITYQGWQTQWNQALEDLVRAYQSMSGTHESNTMAML 84
                                   79****************************************************************************9998 PP

                                   HHH CS
                         WXG100 83 daD 85
                                     D
  gi|121638902|ref|YP_979126.1| 85 ARD 87
                                   776 PP

>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.17      15      49 ..      49      84 ..      47      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                                   HHHHHTTTTSTTHHHHHHHHHCT..HHHHHHHHHHH CS
                           Xpo1 15 lflqeypnnWpsffddllsllss.spsglelllriL 49
                                   + +q ++ +W+++++dl+++ +s s ++  +++ +L
  gi|121638902|ref|YP_979126.1| 49 ITYQGWQTQWNQALEDLVRAYQSmSGTHESNTMAML 84
                                   67999**************99996666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 706.56
//
Query:       gi|121638903|ref|YP_979127.1|  [L=97]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-07   30.2   5.5    4.6e-07   30.0   5.5    1.1  1  WXG100         Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.014   15.9  11.9      0.016   15.7  11.9    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
      0.076   13.2   1.2      0.093   13.0   1.2    1.1  1  EIIA-man       PTS system fructose IIA component


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   5.5   7.7e-11   4.6e-07       8      85 ..      10      87 ..       4      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.7e-11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  8 elrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85
                                   +l ++ ++f+++a+ ++  + + +++  + q+  +G++a afq++ +++ +aa+k++++L+  + +l +aa ++  aD
  gi|121638903|ref|YP_979127.1| 10 QLIASHTAFAAKAGLMRHTIGQAEQQAMSAQAFHQGESAAAFQGAHARFVAAAAKVNTLLDIAQANLGEAAGTYVAAD 87
                                   77888999********************************************************************99 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7  11.9   2.7e-06     0.016      10      96 ..       6      92 ..       1      95 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                  T7SS_ESX_EspC 10 dhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYeatD 91
                                   +h+ +l a h++ aa++   + +  +a ++ ++       ++++a++ a+a   aa++++++ ++   ++L +AA++Y a+D
  gi|121638903|ref|YP_979127.1|  6 AHIPQLIASHTAFAAKAGLMRHTIGQAEQQAMSAQAFHQGESAAAFQGAHARFVAAAAKVNTLLDIAQANLGEAAGTYVAAD 87
                                   788999999***************6666667777789999****************************************** PP

                  T7SS_ESX_EspC 92 eeaag 96
                                    +aa+
  gi|121638903|ref|YP_979127.1| 88 AAAAS 92
                                   **997 PP

>> EIIA-man  PTS system fructose IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   1.6e-05     0.093       3      76 ..      11      81 ..      10      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                   EEEESBCHHHHHHHHHHCCHSSS-SCEEEEEC-TTS-CCCHHHHHHHHHCTS--TTEEEEEESSCCCHHHHHHH CS
                       EIIA-man  3 vivsHgelAeglaelleelagedqekviavggtpdesigtlaekikeaieevdsedevlvLvDlggatpfneaa 76
                                   +i+sH ++A+ +  + + + + +q++  a+++ ++es+  ++ + ++ +++   +++v +L D+  a +  +a 
  gi|121638903|ref|YP_979127.1| 11 LIASHTAFAAKAGLMRHTIGQAEQQAMSAQAFHQGESAAAFQGAHARFVAA---AAKVNTLLDIAQANLGEAAG 81
                                   69*******9988777777666999*************9999999998844...57999999999888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 659.53
//
Query:       gi|121638904|ref|YP_979128.1|  [L=435]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-58  195.8  22.3    4.6e-58  195.8  22.3    2.1  3  PPE       PPE family
  ------ inclusion threshold ------
       0.21   11.8   4.1       0.16   12.2   1.8    2.0  2  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8  22.3   5.2e-62   4.6e-58       1     157 [.       8     164 ..       8     165 .. 0.99
   2 ?   -1.8   0.1      0.32   2.9e+03      29      44 ..     201     216 ..     181     233 .. 0.61
   3 ?   -3.6   0.6       1.2     1e+04      60      88 ..     305     333 ..     298     340 .. 0.65

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 5.2e-62
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    a+pPEv+sall+aGpg+g+l aAaa W++L+ae+a++a+el++v+a++ a+ WqGps++ ++aa++py+aWL +a+a+++
  gi|121638904|ref|YP_979128.1|   8 ASPPEVHSALLSAGPGPGSLQAAAAGWSALSAEYAAVAQELSAVVAAVGAGVWQGPSAELFVAAYVPYVAWLVQASADSA 87 
                                    68****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +aA ++eaaaa Y  Ala+m++++e+aan+ ++a+lvatnffG+nt++Ia +ea+y +mw+q+a++m+aYea++ aa
  gi|121638904|ref|YP_979128.1|  88 AAAGEHEAAAAGYVCALAEMPTLPELAANHLTHAVLVATNFFGINTIPIALNEADYVRMWVQAATVMSAYEAVVGAA 164
                                    ************************************************************************99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHHH CS
                            PPE  29 gLaaelasaaaelesv 44 
                                    +La+ l++aa+++++v
  gi|121638904|ref|YP_979128.1| 201 ELAKFLEMAAQAFTEV 216
                                    4555555555555444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.2
                                    HHHHHTHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  60 amaaaaapylaWLsaaaaqaeeaAaqaea 88 
                                    a+aaa++p +a ++  a  a+  A  a+a
  gi|121638904|ref|YP_979128.1| 305 ALAAAVVPGVAGVTGLAGLAAVPAVGAAA 333
                                    56777777777777777777666665555 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   1.8e-05      0.16       7      53 ..      25      72 ..      23     101 .. 0.91
   2 ?   -1.3   0.0       0.3   2.7e+03      70      84 ..     202     216 ..     199     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHH CS
                         WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaef 53
                                     l++aaa  ++ ++e  ++ q+l a v+a+ ++ W+G +a+ f a++
  gi|121638904|ref|YP_979128.1| 25 GSLQAAAAGWSALSAEYAAVAQELSAVVAAVgAGVWQGPSAELFVAAY 72
                                   6799***************************999*********99987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHHHHHH CS
                         WXG100  70 isealkqaanafeda 84 
                                    +++ l++aa+af+++
  gi|121638904|ref|YP_979128.1| 202 LAKFLEMAAQAFTEV 216
                                    566666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3105.29
//
Query:       gi|121638905|ref|YP_979129.1|  [L=104]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-20   70.7  11.9    1.2e-19   70.4  11.9    1.1  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4  11.9   6.6e-24   1.2e-19       4      92 ..       3      91 ..       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.6e-24
                                   XXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  4 vvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaag 85
                                   ++v+Pe laaa+a +++++++l+aa+a aa+++tav+a+aaD VS + A  fsa ++e+ a++ ++++++ + + a+ +++ 
  gi|121638905|ref|YP_979129.1|  3 LRVVPEGLAAASAAVEALTARLAAAHAGAAPAITAVVAPAADPVSLQSAVGFSALGSEHAAIAGEGVEELGRSGVAVGESGI 84
                                   89******************************************************************************** PP

                                   HHHS--X CS
                             PE 86 sYaaaEa 92
                                    Yaa +a
  gi|121638905|ref|YP_979129.1| 85 GYAAGDA 91
                                   *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.32
# Mc/sec: 967.86
//
Query:       gi|121638906|ref|YP_979130.1|  [L=415]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-154  514.6   0.0   1.6e-154  514.4   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      2e-05   24.9   0.0    5.2e-05   23.6   0.0    1.7  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.4   0.0  1.7e-158  1.6e-154       1     380 [.       1     379 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 514.4 bits;  conditional E-value: 1.7e-158
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l+++e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121638906|ref|YP_979130.1|   1 MTSSH-LIDTEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.89999********************************************************************* PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121638906|ref|YP_979130.1|  80 PKLRQGSYFPdWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **********9***************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121638906|ref|YP_979130.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    v+ai+a++p+aa+QrCr+H+++nl+a++pk ++ +v++ l+siy+++dae+++++++++l++l++k+p+vae+ld+a++d
  gi|121638906|ref|YP_979130.1| 239 VAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTD 318
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    +laf+afp+qi+r+i+s+N++ErLN+e+rRrt+vvgiFP+++si+rlvgavlae+hdew+e
  gi|121638906|ref|YP_979130.1| 319 LLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIE 379
                                    ***********************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.8e-09   5.2e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.8e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121638906|ref|YP_979130.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3061.56
//
Query:       gi|121638907|ref|YP_979131.1|  [L=367]
Description: tRNA-specific 2-thiouridylase MnmA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-118  395.4   0.0   2.1e-118  395.2   0.0    1.0  1  tRNA_Me_trans  tRNA methyl transferase
    8.4e-05   22.2   0.0    0.00012   21.8   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0019   17.9   0.0     0.0026   17.5   0.0    1.2  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.015   14.4   0.0      0.029   13.5   0.0    1.5  1  NAD_synthase   NAD synthase
      0.029   14.5   0.0      0.068   13.3   0.0    1.5  1  Smoa_sbd       Styrene monooxygenase A putative substrate bin
       0.11   12.0   0.5       0.31   10.5   0.3    1.8  2  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.2   0.0  6.9e-122  2.1e-118       1     356 []       1     353 [.       1     353 [. 0.97

  Alignments for each domain:
  == domain 1  score: 395.2 bits;  conditional E-value: 6.9e-122
                  tRNA_Me_trans   1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg...keccaeedlkdaervaeklgiplevvdfekeykek 77 
                                    +kv++a+SgGVDSsvaaa++ ++g+ev+gv+++l++  ++ +   ++cc++ed++da+rva++lgip++v+df++++ke+
  gi|121638907|ref|YP_979131.1|   1 MKVLAAMSGGVDSSVAAARMVDAGHEVVGVHMALSTAPGTLRtgsRGCCSKEDAADARRVADVLGIPFYVWDFAEKFKED 80 
                                    69***********************************777766779********************************** PP

                  tRNA_Me_trans  78 vfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYarvsleeeknevellrakdkkkDQsyfLsqls 157
                                    v+++f+++y++G+TPnP+v+CN++iKf+al  +a++ lg+d++atGHYar+s        +l+ra+d++kDQsy+L+ l+
  gi|121638907|ref|YP_979131.1|  81 VINDFVSSYARGETPNPCVRCNQQIKFAALSARAVA-LGFDTVATGHYARLSGG------RLRRAVDRDKDQSYVLAVLT 153
                                    ***********************************9.***************98......8******************* PP

                  tRNA_Me_trans 158 kealekllfPlgeltKeevrkiAkeaglavaekkdSqgiCfigkrkfkdflkkyleekeGkiieietgevlGeheGllsy 237
                                     ++l++++fP+g++ K+++r+ A+++glava+k+dS++iCfi++ ++k fl ++++ ++G +++++ g vl++h+G++ +
  gi|121638907|ref|YP_979131.1| 154 AQQLRHAAFPIGDTPKRQIRAEAARRGLAVANKPDSHDICFIPSGNTKAFLGERIGVRRGVVVDAD-GVVLASHDGVHGF 232
                                    ******************************************************************.************* PP

                  tRNA_Me_trans 238 TiGqrkGlkiag...aeeplyVvekdakkntvlvgkgedeealaskklrvkelnwlaeelkekealelevkvrhkqelvk 314
                                    TiGqr+Gl+iag   +++p+yV+ +da+++tv+vg+    ++l++++l+ + + ++a +++++  +++ v+vr + e+v+
  gi|121638907|ref|YP_979131.1| 233 TIGQRRGLGIAGpgpNGRPRYVTAIDADTATVHVGD---VTDLDVQTLTGRAPVFTAGAAPSG-PVDCVVQVRAHGETVS 308
                                    ************999*********************...9*****************999887.8*************** PP

                  tRNA_Me_trans 315 akvelkedetvevkldekvravtpGQaavlYkgd....evLGggii 356
                                    a++el+ d ++ v+l+++ r+v++GQ++vlY+ d    evLG+++i
  gi|121638907|ref|YP_979131.1| 309 AVAELIGD-ALFVQLHAPLRGVARGQTLVLYRPDpagdEVLGSATI 353
                                    ********.9*********************8666666******98 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     4e-08   0.00012       5      37 ..       2      34 ..       1      84 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-08
                           ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlkn 37
                                   kvla +SgG+DS Vaa +++  G +vv vh+  
  gi|121638907|ref|YP_979131.1|  2 KVLAAMSGGVDSSVAAARMVDAGHEVVGVHMAL 34
                                   79****************************963 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.8e-07    0.0026      20      92 ..       3      86 ..       1     110 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-07
                   Asn_synthase 20 vGalLSGGlDSSliaalaarqsk.............splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldal 88
                                   v a +SGG+DSS+ aa +    +               l+t s g    + ++a+ a++va+ lg++ +   + e+  +d++
  gi|121638907|ref|YP_979131.1|  3 VLAAMSGGVDSSVAAARMVDAGHevvgvhmalstapGTLRTGSRGC--CSKEDAADARRVADVLGIPFYVWDFAEKFKEDVI 82
                                   66789*************999889***********999********..9*****************9777777766666666 PP

                   Asn_synthase 89 pdvi 92
                                    d +
  gi|121638907|ref|YP_979131.1| 83 NDFV 86
                                   6655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.8e-06     0.029      20      84 ..       2      76 ..       1     122 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                                   EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE-.....-SSST.......THHHHHHHHHHHHHHTSEEEE---HHH CS
                   NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalll.....Pssvs.......seedvedalalaenlgievktidikpi 84
                                   +v+  +SGGvDSs++aa  v+a   ++v+++ +     P++         s+ed+ da+ +a+ lgi + + d ++ 
  gi|121638907|ref|YP_979131.1|  2 KVLAAMSGGVDSSVAAARMVDAG--HEVVGVHMalstaPGTLRtgsrgccSKEDAADARRVADVLGIPFYVWDFAEK 76
                                   677889**********9999886..5666766622222221111222222789999999999999999888887665 PP

>> Smoa_sbd  Styrene monooxygenase A putative substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.068      49      98 ..     265     314 ..     248     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                       Smoa_sbd  49 gvGelfeipaltlsGpceillleavpggpldawkdvktpeehlerllell 98 
                                     vG++  + + tl+G++ ++   a p gp+d++ +v++  e +  + el+
  gi|121638907|ref|YP_979131.1| 265 HVGDVTDLDVQTLTGRAPVFTAGAAPSGPVDCVVQVRAHGETVSAVAELI 314
                                    79***********************************9999888887776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3    0.0001      0.31       2      31 ..       3      32 ..       2      37 .. 0.90
   2 ?   -2.3   0.0      0.85   2.5e+03     177     197 ..      82     102 ..      70     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                   EEEE--SSHHHHHHHHHHHHH-SEEEEEEE CS
                           QueC  2 avvllSGGlDSttvlalakkegkevealtf 31
                                   ++  +SGG+DS++++a + ++g+ev  +++
  gi|121638907|ref|YP_979131.1|  3 VLAAMSGGVDSSVAAARMVDAGHEVVGVHM 32
                                   67889********************99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.85
                                    HHH-B-STTS.-BTTTTSSSH CS
                           QueC 177 leetlsCYegeeegkaCgeCd 197
                                    ++  +s Y+ +e+ ++C +C+
  gi|121638907|ref|YP_979131.1|  82 INDFVSSYARGETPNPCVRCN 102
                                    566789999999999**9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2607.14
//
Query:       gi|121638908|ref|YP_979132.1|  [L=393]
Description: cysteine desulfurase iscS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-62  211.3   0.0    2.5e-62  211.0   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    5.2e-07   29.2   0.2    8.2e-07   28.6   0.2    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.09   11.4   0.0       0.14   10.8   0.0    1.2  1  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.0   0.0   4.3e-66   2.5e-62       2     370 ..       3     369 ..       2     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 4.3e-66
                                    EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                    Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                    yld aAtt+  +++++a++   ++  +n+ +s+h+ g  a + +eeare +a+ ++a+  +e+ift G+te+ nl+++++
  gi|121638908|ref|YP_979132.1|   3 YLDHAATTPMHPAAIEAMAAV-QRTIGNA-SSLHTSGRSARRRIEEARELIADKLGARP-SEVIFTAGGTESDNLAVKGI 79 
                                    9******************99.999****.9***************************7.******************98 PP

                                    CCC....-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--..TTEEEEEEESBETTTTEB CS
                    Aminotran_5  82 ars....lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln..ektklvaithvsnvtGti 155
                                      +      ++++iv+te+ehha l   + l + +ga+v+++p  ++g++   +l+++l+  ++++lv++++++n+ Gti
  gi|121638908|ref|YP_979132.1|  80 YWArrdaEPHRRRIVTTEVEHHAVLDSVNWLVEHEGAHVTWLPTAADGSVSATALREALQshDDVALVSVMWANNEVGTI 159
                                    7666675556789**********************************************6559***************** PP

                                    --HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEE CS
                    Aminotran_5 156 qpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevs 235
                                     p++e+  +a + g+ ++ Da qavg+ p+d+ + g+  +++ ghK+ gP+G+G+l  r+   +   pl+ gg+      
  gi|121638908|ref|YP_979132.1| 160 LPIAEMSVVAMEFGVPMHSDAIQAVGQLPLDFGASGLSAMSVAGHKFGGPPGVGALLLRR--DVTCVPLMHGGG------ 231
                                    ************************************************************..677889999999...... PP

                                    TTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH.HCTSTTEEEES.-B-CTCBSEEEE CS
                    Aminotran_5 236 leettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyller.lkslpgvrlygpdkaerrasivsf 314
                                     +e+        +++GTp va+++g+++a+++    gle+  ++ + l+++l+e+ l+++++v l+g+d+  r a+   f
  gi|121638908|ref|YP_979132.1| 232 -QERD-------IRSGTPDVASAVGMATAAQIA-VDGLEENSARLRLLRDRLVEGvLAEIDDVCLNGADDPMRLAGNAHF 302
                                    .7877.......99*****************99.6778888888888888777652788********************* PP

                                    EETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHH CS
                    Aminotran_5 315 nfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdr 370
                                    +f+g++ + + +lLd +gI+ ++G++c+    qp+++++a+        g++R+Sl++ + e++vd+
  gi|121638908|ref|YP_979132.1| 303 TFRGCEGDALLMLLDANGIECSTGSACTagvaQPSHVLIAMGvdaasarGSLRLSLGHTSVEADVDA 369
                                    ***************************99999*********99**********************96 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   1.4e-10   8.2e-07      39     168 ..      49     180 ..       9     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.4e-10
                                    HHHHHHTT-S..EEEEES-HHHHHHHHH......HHH--TTEEEEEETT..-HHHHSSTTHHHHCC--EEEEE-EBTTTB CS
                Beta_elim_lyase  39 davaelfgke..aalfvpqGtaAnsill......killqrgeevivtep..ahihfdetgaiaelagvklrdlknkeaGk 108
                                    + +a+ +g+    ++f++ Gt ++++++      +  ++++   ivt +   h   d    ++e +g++++ l+++++G 
  gi|121638908|ref|YP_979132.1|  49 ELIADKLGARpsEVIFTAGGTESDNLAVkgiywaRRDAEPHRRRIVTTEveHHAVLDSVNWLVEHEGAHVTWLPTAADGS 128
                                    445555555443789*************65555433344444445554477999************************** PP

                                    E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                    +++ +l++a++ +    ++++l+s+  +nn   G++++++e+   + +a + g+p+h D+
  gi|121638908|ref|YP_979132.1| 129 VSATALREALQSH----DDVALVSVMWANNE-VGTILPIAEM---SVVAMEFGVPMHSDA 180
                                    ************4....55***********6.8999998776...567899******998 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.3e-05      0.14      45     130 ..      13     101 ..       8     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.3e-05
                                    -HHHHHHHHHHHTT-.....S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT CS
                    Aminotran_3  45 hPkvvkavkeqaakl.....shvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKlarkyarekkatek 119
                                    hP+ ++a+++++ ++      h+s g  +   ++++ e +++ ++   ++v++ + G+e+   A+K +  +ar   ++++
  gi|121638908|ref|YP_979132.1|  13 HPAAIEAMAAVQRTIgnassLHTS-GRSARRRIEEARELIADKLGARPSEVIFTAGGTESDNLAVKGIY-WARRDAEPHR 90 
                                    777777776665443111115777.888899999999999******9*******************876.588888**** PP

                                    -EEEEETTT-- CS
                    Aminotran_3 120 tkiiafkgafH 130
                                     +i++ +   H
  gi|121638908|ref|YP_979132.1|  91 RRIVTTEVEHH 101
                                    ****9887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 2047.24
//
Query:       gi|121638909|ref|YP_979133.1|  [L=304]
Description: hypothetical protein BCG_3049c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-21   73.8   0.0    1.3e-20   73.4   0.0    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   7.5e-25   1.3e-20       1     133 [.      81     222 ..      81     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 7.5e-25
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraag 80 
                                    +++v+g   +++ +++++v+ H s+lDv+++  +l       +  ++a +++++ + +g ++r l++i+i+R s +r  g
  gi|121638909|ref|YP_979133.1|  81 RITVSG-SPVRNLRGVLVVSGHVSWLDVFCIGSVL-------PGSFVARADMFTGRTIGIVARILKIIPIERASLRRLPG 152
                                    588999.999999********************99.......89************************************ PP

                Acyltransferase  81 sleniselleegklvviFPEGtrsre...................gellpfkkGlvrlaakakkgvpivPva 133
                                    ++++i+++l++g+ vv FPEGt+++                    +++  f+  ++++a++a  g p+ P+ 
  gi|121638909|ref|YP_979133.1| 153 VVDTIARRLRAGQTVVAFPEGTTWCGrpgddagrpaaragagcshRGCGAFYPAMFQAAIDA--GRPVQPLR 222
                                    ******************************************999999**************..******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1950.02
//
Query:       gi|121638910|ref|YP_979134.1|  [L=246]
Description: hypothetical protein BCG_3050c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-28   98.6   0.0    4.4e-28   98.0   0.0    1.3  1  Acetyltransf_5  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.14   11.7   0.0        0.4   10.2   0.0    1.7  1  Autoind_synth   Autoinducer synthase


Domain annotation for each model (and alignments):
>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   4.9e-32   4.4e-28       1     101 []       8     110 ..       8     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 4.9e-32
                 Acetyltransf_5   1 LRyevFreemgaegea.aapeldiDefDavcdhllvideae.evVGtyRllrpdeaerlegfysesefdlsklaalrrrl 78 
                                    LRy+vF    g+  +a a +++d D+fD++cdhllv+d+++ e+VG+yR+l p+ a +++g+y+++efd+ ++++lr++l
  gi|121638910|ref|YP_979134.1|   8 LRYDVFSTTPGFALPAaADTRRDGDRFDEYCDHLLVRDDDTgELVGCYRMLAPAGAIAAGGLYTATEFDVCAFDPLRPSL 87 
                                    8***************56666****************999988************************************* PP

                 Acetyltransf_5  79 lElgRscvhpeyRnkralellwa 101
                                    +E+gR++v++ +Rn+ +++l+wa
  gi|121638910|ref|YP_979134.1|  88 VEMGRAVVREGHRNGGVVLLMWA 110
                                    *********************95 PP

>> Autoind_synth  Autoinducer synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   4.4e-05       0.4      14      76 ..       6      70 ..       1     134 [. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.4e-05
                  Autoind_synth 14 frLRkevFkdRLeWdvqiidGmer..DqyDnlkttyllgvkdegrvigsvRlletkgPnmltdtF 76
                                    rLR +vF+   +++    +   r  D++D+     l+  +d g+++g+ R+l   g     + +
  gi|121638910|ref|YP_979134.1|  6 QRLRYDVFSTTPGFALPAAADTRRdgDRFDEYCDHLLVRDDDTGELVGCYRMLAPAGAIAAGGLY 70
                                   5788888888888887777666552279**99999999999************877765444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1681.32
//
Query:       gi|121638911|ref|YP_979135.1|  [L=318]
Description: electron transfer flavoprotein (alpha-subunit) fixB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-35  121.6   1.9    2.6e-35  120.3   1.9    1.8  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    9.7e-29  100.5  14.7    2.2e-28   99.4  14.7    1.6  1  ETF        Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   1.9     3e-39   2.6e-35       2      84 .]     194     276 ..     193     276 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 3e-39
                                    -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHGGG CS
                      ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhlaGm 81 
                                    +L+ea +vv+gGrG++s+en++++e+la+ lgaavgasRa+vd+g++p + qvGqtGktv+P+lyia+GisGaiqh aGm
  gi|121638911|ref|YP_979135.1| 194 ELTEATIVVAGGRGVGSAENFSVVEALADSLGAAVGASRAAVDSGYYPGQFQVGQTGKTVSPQLYIALGISGAIQHRAGM 273
                                    79****************************************************************************** PP

                                    TT- CS
                      ETF_alpha  82 kes 84 
                                    ++s
  gi|121638911|ref|YP_979135.1| 274 QTS 276
                                    987 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4  14.7   2.4e-32   2.2e-28       1     179 [.       4     173 ..       4     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.4e-32
                                    EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHH CS
                            ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeataka 80 
                                    vlvl+eh+ +g l++v++e+++aAr+l     ge +avvvG p ++  l + l+a Ga+k+++++++  + y+  + +++
  gi|121638911|ref|YP_979135.1|   4 VLVLVEHA-EGALKKVSAELITAARAL-----GEPAAVVVGVPGTAAPLVDGLKAAGAAKIYVAESDLVDKYLITPAVDV 77 
                                    79*****7.******************.....99********999999******************************** PP

                                    HHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTS CS
                            ETF  81 laalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpga 160
                                    la l+++  p  vl++ata gk++a+rlAa+ g +l+ dv+++ +  g  + +++i+gg+ + e + +  + v+tvr+ga
  gi|121638911|ref|YP_979135.1|  78 LAGLAESSAPAGVLIAATADGKEIAGRLAARIGSGLLVDVVDVREG-G--VGVHSIFGGAFTVEAQANGDTPVITVRAGA 154
                                    *********************************************8.8..99**************************** PP

                                    S----S-TT---EEEE--H CS
                            ETF 161 fepaaimaakkkeveevev 179
                                    +e++++ +a+++  +ev++
  gi|121638911|ref|YP_979135.1| 155 VEAEPAAGAGEQVSVEVPA 173
                                    ***5544444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2263.98
//
Query:       gi|121638912|ref|YP_979136.1|  [L=266]
Description: electron transfer flavoprotein (beta-subunit) fixA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-41  140.4   3.0    7.3e-41  140.0   3.0    1.1  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   3.0   4.1e-45   7.3e-41       2     181 ..      25     214 ..      24     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 4.1e-45
                                    EEEE-EC.CCCE-HHHHHHHHHHHHHHHH...HT..--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCH CS
                            ETF   2 lvlaehgvdgklnpvdlealeaArrlkek...ag..gevtavvvGppeaeealrealaamGadkvilvddpalagydaea 76 
                                    ++l+++++d++l+++ + a+e+A++++ek   +g  g+vt++++Gp++a ea+r+al+ mGadk+++++d+ + g+d  +
  gi|121638912|ref|YP_979136.1|  25 FTLDREAADAVLDEINERAVEEALQIREKeaaDGieGSVTVLTAGPERATEAIRKALS-MGADKAVHLKDDGMHGSDVIQ 103
                                    68899999*********************999444599********************.********************* PP

                                    HHHHHHHHHHHC.--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSE CS
                            ETF  77 takalaalikke.dpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpa 152
                                    t  ala ++  + + +lv+ag++++ g  + v++ +A++Lg+p++t+  ++ +eggk+t +R+++   g+  ++ea+lpa
  gi|121638912|ref|YP_979136.1| 104 TGWALARALGTIeGTELVIAGNESTdGvgGAVPAIIAEYLGLPQLTHLRKVSIEGGKITGERETDE--GV-FTLEATLPA 180
                                    ***********989***********99***************************************..99.99******* PP

                                    EEEE-TTSS--.....--S-TT---EEEE--HHH CS
                            ETF 153 vltvrpgafep.....aaimaakkkeveevevad 181
                                    v++v+++++ep     ++imaakkkev+++++a+
  gi|121638912|ref|YP_979136.1| 181 VISVNEKINEPrfpsfKGIMAAKKKEVTVLTLAE 214
                                    ******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2224.20
//
Query:       gi|121638913|ref|YP_979137.1|  [L=274]
Description: hypothetical protein BCG_3053 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-21   76.2   0.1    4.1e-21   75.4   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    3.6e-18   66.1   0.2    8.5e-18   64.9   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
    4.6e-13   49.2   0.0    6.2e-13   48.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.5e-12   47.6   0.0    2.7e-12   46.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    5.4e-08   33.5   0.0    9.3e-08   32.7   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.7e-05   24.8   0.0    2.9e-05   24.0   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
    0.00047   19.6   0.0     0.0016   17.9   0.0    1.8  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0089   15.2   0.0      0.013   14.7   0.0    1.1  1  Pox_MCEL         mRNA capping enzyme
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.015   15.0   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      0.025   14.2   0.1      0.054   13.1   0.0    1.5  2  MetW             Methionine biosynthesis protein MetW
      0.029   14.4   0.0      0.042   13.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.045   13.3   0.0      0.084   12.4   0.0    1.4  1  MTS              Methyltransferase small domain
       0.14   11.5   0.0        0.2   11.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.25   10.4   0.0       0.34    9.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1   3.2e-24   4.1e-21       1      96 []      66     157 ..      66     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.2e-24
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    L++GcG G+ a  +a  +++v++vD+++++++ +++++++    ve+++a++ +lp++d+s+D+vv ++v++h+ d++++
  gi|121638913|ref|YP_979137.1|  66 LEAGCGEGYGADLIACVARQVIAVDYDETAVAHVRSRYPR----VEVMQANLAELPLPDASVDVVVNFQVIEHLWDQARF 141
                                    799************888*************999988887....567********************************* PP

                                    HHHHHHHEEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                    ++e+aRvL+  Gll++
  gi|121638913|ref|YP_979137.1| 142 VRECARVLRGSGLLMV 157
                                    ************9985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.1   6.6e-21   8.5e-18       1      97 []      65     153 ..      65     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 6.6e-21
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vL++GcG+G  +  +a    + +v++vD++e++++++r+r+    ++ve++q+++ +lp++d+s+D+vv +++++hl+  
  gi|121638913|ref|YP_979137.1|  65 VLEAGCGEGYGADLIACV--ARQVIAVDYDETAVAHVRSRY----PRVEVMQANLAELPLPDASVDVVVNFQVIEHLW-- 136
                                    8********999999955..59*******************....9************************877*****.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    d++++++e+arvL+  G
  gi|121638913|ref|YP_979137.1| 137 DQARFVRECARVLRGSG 153
                                    6679*********9776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   4.8e-16   6.2e-13       6     113 ..      64     161 ..      61     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 4.8e-16
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                     vl++GCG+G+ +  +a   +   +v+ +D++e+a+ + r++     + +ve+ q++  el+  l d+++D+++ ++v+ 
  gi|121638913|ref|YP_979137.1|  64 DVLEAGCGEGYGADLIA---CVARQVIAVDYDETAVAHVRSR-----YPRVEVMQANLAELP--LPDASVDVVVNFQVIE 133
                                    69***************...55678****************8.....99*************..9*************** PP

                Methyltransf_31  86 aladpdkileeiervlkpggilliedpr 113
                                    +l d++ + +e  rvl+  g l++++p+
  gi|121638913|ref|YP_979137.1| 134 HLWDQARFVRECARVLRGSGLLMVSTPN 161
                                    **************************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   2.1e-15   2.7e-12      13     163 ..      53     198 ..      42     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.1e-15
                Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqf.deqeaaepqgkfdlIvlrev 91 
                                    ++rl+p + +   vL+ GcG+G+ +++++    +v++vD ++ av+ +++++  + ++  +  e + p+++ d++v+++v
  gi|121638913|ref|YP_979137.1|  53 YQRLAP-RCTARDVLEAGCGEGYGADLIACVARQVIAVDYDETAVAHVRSRYPRVEVMQaNLAELPLPDASVDVVVNFQV 131
                                    688888.788899*************9977777**************98444444443302335555999********** PP

                Methyltransf_23  92 lehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlevv 163
                                    +eh+ d ++ +r  a+ l+  G+l++s+p++   +  +    + ++p   h +  +a++l  ll +aG+ +v
  gi|121638913|ref|YP_979137.1| 132 IEHLWDQARFVRECARVLRGSGLLMVSTPNRITFSPGR---DTPINPF--HTRELNADELTSLLIDAGFVDV 198
                                    *******************99********997666665...3335555..7788888888888888888777 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   7.3e-11   9.3e-08       1      98 [.      66     154 ..      66     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.3e-11
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le GcG G  ++ ++      ++++vD+++ a+++ + +  + e  ++n  el   d       +s+D+vv ++v++hl 
  gi|121638913|ref|YP_979137.1|  66 LEAGCGEGYGADLIACV--ARQVIAVDYDETAVAHVRSRYPRVEVMQANLAELPLPD-------ASVDVVVNFQVIEHLW 136
                                    89********9999988..999***********888888777775444444444444.......3*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    d ++++++++++L+  G 
  gi|121638913|ref|YP_979137.1| 137 DQARFVRECARVLRGSGL 154
                                    *************98876 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   2.9e-05      63     157 ..      52     158 ..      40     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                                    HHHHHCTS-TTS-EEEES-TT-HHHHH--.S-..EEEEES..S-SST........TEEES-TTS-S--TT-EEEEEEES- CS
                 Methyltransf_8  63 iirklkkkkdnlvvadlGcGeakiaeavr.ekekvrsfdl..vavne........rvvacdlakvPledesvdvavfcls 131
                                    + ++l  +     v + GcGe   a  +    ++v+++d   +av +        +v+  +la++Pl d svdv+v    
  gi|121638913|ref|YP_979137.1|  52 VYQRLAPRCTARDVLEAGCGEGYGADLIAcVARQVIAVDYdeTAVAHvrsryprvEVMQANLAELPLPDASVDVVVNFQV 131
                                    55666777777788899999977663332134456665542133322112222225778899************996554 PP

                                    -.-SS-HHHHHHHHHHHEEEEEEEEEE CS
                 Methyltransf_8 132 l.mgtnladflkeanrvlkvGGllkva 157
                                    +    + a f++e  rvl+  Gll+v+
  gi|121638913|ref|YP_979137.1| 132 IeHLWDQARFVRECARVLRGSGLLMVS 158
                                    414568899***************986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.2e-06    0.0016      50     156 ..      64     162 ..      36     171 .. 0.71
   2 ?   -1.2   0.0       0.8     1e+03     201     217 ..     183     199 ..     179     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                                    EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG- CS
                Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnv 129
                                    +vl+  +G g   ++l   v +  +v+ +D++e+ +   + +     + ++e +qan  eLp  d s Dvv     +  +
  gi|121638913|ref|YP_979137.1|  64 DVLEAGCGEGY-GADLIACVAR--QVIAVDYDETAVAHVRSR-----YPRVEVMQANLAELPLPDASVDVVVNFQVIEHL 135
                                    55555555553.3344443332..466666666655544443.....569*******************98666678999 PP

                                    S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                Ubie_methyltran 130 tDklkaLkeayrvlkpGGrlvvlefsk 156
                                     D+ + ++e  rvl+  G l+v    +
  gi|121638913|ref|YP_979137.1| 136 WDQARFVRECARVLRGSGLLMVSTPNR 162
                                    ******************999865555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.8
                                    HHHHHHHHHHTTEEEEE CS
                Ubie_methyltran 201 qetlkeliedaGfksve 217
                                    +++l +l+ daGf  v 
  gi|121638913|ref|YP_979137.1| 183 ADELTSLLIDAGFVDVA 199
                                    68999********9986 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.9e-06     0.013      63     113 ..      60     109 ..      50     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.9e-06
                       Pox_MCEL  63 snklkvLdldcgk..GgDLeKyekgeIsklvatDiaeesieeckeRYnklrse 113
                                      ++ vL+ +cg+  G+DL+ + +    + +a+D +e+++++ + RY + + +
  gi|121638913|ref|YP_979137.1|  60 CTARDVLEAGCGEgyGADLIACVA---RQVIAVDYDETAVAHVRSRYPRVEVM 109
                                    56799******97336****9976...578*****************655444 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.1e-05     0.015      22     143 ..      40     156 ..      36     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                           NodS  22 danefeqerlaqilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqf 101
                                    d  ++  +r++ + +      ++ d+le Gc  G  ++ +a +++++  vd  e a+a+ r r  +   +  +++++ ++
  gi|121638913|ref|YP_979137.1|  40 DIENYWFRRHQVVYQRLAPRCTARDVLEAGCGEGYGADLIACVARQVIAVDYDETAVAHVRSRYPR---VEVMQANLAEL 116
                                    555666667766666556667889*************************************99766...77778888887 PP

                           NodS 102 s.tdekfdlivvaevlyyiedvaelraavrnlvsllapdgqlv 143
                                       d+  d++v  +v+ ++ d a++   vr+  ++l+ +g l+
  gi|121638913|ref|YP_979137.1| 117 PlPDASVDVVVNFQVIEHLWDQARF---VRECARVLRGSGLLM 156
                                    6257889999999999888888775...666666666666655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.2e-05     0.054      16     111 ..      64     161 ..      47     165 .. 0.73
   2 ?   -2.6   0.0       2.7   3.5e+03     142     167 ..     241     266 ..     239     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                           MetW  16 rvldlGcGdGellellke.ekqvdgrGleldeegvaecvakG..lsviqgdldkdlenfedksfdyvvlsqtlqatrnpk 92 
                                     vl+ GcG+G   +l++   +qv +  ++ de++va++ ++   ++v+q +l       +d s d+vv  q +  + + +
  gi|121638913|ref|YP_979137.1|  64 DVLEAGCGEGYGADLIACvARQVIA--VDYDETAVAHVRSRYprVEVMQANLA--ELPLPDASVDVVVNFQVIEHLWDQA 139
                                    5999******988888641466655..77888888888877522666666664..35679******************** PP

                           MetW  93 evldellrigrr...aivsfPn 111
                                    + ++e  r+ r     +vs Pn
  gi|121638913|ref|YP_979137.1| 140 RFVRECARVLRGsglLMVSTPN 161
                                    ****999886541114666666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                           MetW 142 nihlltikdfvelceelnlkvedrva 167
                                    ++  +t +df+ ++   +  ++d++ 
  gi|121638913|ref|YP_979137.1| 241 DVAAVTTADFEMVAAGHDRDIDDSLD 266
                                    56778999999999999988888765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.042      21      82 ..      57     113 ..      48     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                Methyltransf_32  21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrl 82 
                                    a +++a +v+++G+G+gY +  +a        +v+++d  e  v++ + r  +++  ++++l
  gi|121638913|ref|YP_979137.1|  57 APRCTARDVLEAGCGEGYGADLIAC----VARQVIAVDYDETAVAHVRSRYPRVE-VMQANL 113
                                    55678899****************9....6889****************999998.444544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05     0.084      25     137 ..      54     157 ..      49     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                    HHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEE CS
                            MTS  25 etlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdliv 102
                                    + l  + ++++vl  GcG G+ +  +a      +v +vd d  A++  +  +     +vev++ ++ e  ++++++d++v
  gi|121638913|ref|YP_979137.1|  54 QRLAPRcTARDVLEAGCGEGYGADLIACVAR--QVIAVDYDETAVAHVRSRYP----RVEVMQANLAElPLPDASVDVVV 127
                                    55666667899*********96655555544..499*********99887654....46778888877345688889887 PP

                                    E---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                            MTS 103 sNPPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                        f+  ++  l    ++++e +++L+ +G L++
  gi|121638913|ref|YP_979137.1| 128 N---FQVIEH--LWDQARFVRECARVLRGSGLLMV 157
                                    5...444444..23356788888888887776655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016       0.2     163     243 ..      63     136 ..      53     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNILaevlie 241
                                    + vl  G+G G  a       a++v+avD+De Av   ++   + +v + +l   ++  l++ +++dv+v     +v+ +
  gi|121638913|ref|YP_979137.1|  63 RDVLEAGCGEGYGADL-IACVARQVIAVDYDETAVAHVRSRYPRVEVMQaNL---AELPLPD-ASVDVVVNF---QVIEH 134
                                    6799999999976633.3345899***********99999888877777344...3445556.889999864...33333 PP

                           PrmA 242 la 243
                                    l 
  gi|121638913|ref|YP_979137.1| 135 LW 136
                                    33 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00027      0.34      32      91 ..      63     119 ..      50     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                    SEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHH CS
                         RrnaAD  32 ltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetp 91 
                                      vle g G+G     +a  a+qv ++  de  +++++     +++++v++++  +  +p
  gi|121638913|ref|YP_979137.1|  63 RDVLEAGCGEGYGADLIACVARQVIAVDYDETAVAHVRS---RYPRVEVMQANLAELPLP 119
                                    579************99*********************9...699******998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2078.85
//
Query:       gi|121638914|ref|YP_979138.1|  [L=526]
Description: hypothetical protein BCG_3054 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-19   70.1   0.1    3.6e-19   69.0   0.1    1.6  1  DUF1957         Domain of unknown function (DUF1957)
    9.5e-16   57.9   0.0    4.2e-15   55.8   0.0    2.1  1  Glyco_hydro_57  Glycosyl hydrolase family 57
  ------ inclusion threshold ------
        0.2   11.7   0.0       0.49   10.5   0.0    1.5  2  EcoEI_R_C       EcoEI R protein C-terminal


Domain annotation for each model (and alignments):
>> DUF1957  Domain of unknown function (DUF1957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1     6e-23   3.6e-19      23      99 ..     444     522 ..     423     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 6e-23
                                    HHHHHHHHHHHHHHHHBTHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHS---HH..HHHHHHHHS---S--... CS
                        DUF1957  23 kervlnqaaRElLLaqssdWafiittgtaveYAekrikehlerftelyealesgeidee..lleeleekdniFpeidyr 99 
                                    +++v++q++RE+LL+ ssdW+f++++++a++YA+ r++ h+++ +e++ al++g+ d++  l+e  +++d +F  +d+r
  gi|121638914|ref|YP_979138.1| 444 RDHVADQILRETLLTVSSDWPFMVSKDSAADYARYRAHLHAHATREIAGALAAGRRDTArrLAEGWNRADGLFGALDAR 522
                                    679************************************************99997766557777888*********98 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   7.1e-19   4.2e-15       1     203 [.      13     244 ..      13     392 .. 0.71

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7.1e-19
                                    EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-H...HHHHH...... CS
                 Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylnge...kksyl...... 71 
                                    ++v+h+H+p+  ++g ++ +++w+ +  a  Y++l+  l  + + +    ++  ++++++ +l ++   + ++       
  gi|121638914|ref|YP_979138.1|  13 TLVLHTHLPWLAHHGRWPVGEEWLYQSWAAAYLPLLQVLAALADENRHRLITLGMTPVVNAQLDDPyclNGVHHwlanwq 92 
                                    589****************************************9999999999*************99999999555555 PP

                                    ....HHHHHHHHHHHHHHHH---HH.........HHHHHHHHHHHHHHHHH....HHHHT.TT-HHHHHHHHHHCTSEEE CS
                 Glyco_hydro_57  72 ....pateellelieeglerctelk.........ldlavlfnlaisgplle....qiqkwlnkevlelfrelqesgqvEl 134
                                        +a ++ + +          ++          + + +f +  + +  +    ++ +w      +l+r l++ g vEl
  gi|121638914|ref|YP_979138.1|  93 lraeEAASVRYAR----------QSksadypsctPEALRAFGIRECADAARaldnFATRW-RHGGSPLLRGLIDAGTVEL 161
                                    5555444444444..........44333333332444556666666666668999999**.******************* PP

                                    EEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C............ CS
                 Glyco_hydro_57 135 ltspyyHpllpllpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftde............ 202
                                    l+ p +Hp+ pll      e  ++++    +  +  +P+g+w+pE+a+ p ++  +a +G + +++d+            
  gi|121638914|ref|YP_979138.1| 162 LGGPLAHPFQPLLAP-RLREFALREGLADAQLRLAHRPKGIWAPECAYAPGMEVDYATAGVSHFMVDGpslhgdtalgrp 240
                                    *************87.4444455555555566677********************************9766555444444 PP

                                    ...- CS
                 Glyco_hydro_57 203 ...l 203
                                       +
  gi|121638914|ref|YP_979138.1| 241 vgkT 244
                                    4432 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.3e-05      0.49      53     121 ..     306     366 ..     285     372 .. 0.80
   2 ?   -3.3   0.0       1.5   8.8e+03      67      95 ..     422     450 ..     408     456 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.3e-05
                      EcoEI_R_C  53 alweayellekkvspq.ltdlidlirkiagldeeletrserverafkrwikekkfteeqrewLelildhi 121
                                    +  +a+        +  ++d++d++r  + +++e   r+  v +af+ +++ + + e +  wL+++l  +
  gi|121638914|ref|YP_979138.1| 306 RADRAV--------DVhVADFVDVVRNRLLSESERIGRPAHVIAAFDTELFGHWWYEGP-TWLQRVLRAL 366
                                    333333........33589*********************************9888776.5999988766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                      EcoEI_R_C  67 pq.ltdlidlirkiagldeeletrserver 95 
                                    +  lt +   ++++a ld  +++r++ +++
  gi|121638914|ref|YP_979138.1| 422 DTaLTTIDKALAQTASLD-GPLPRDHVADQ 450
                                    345778888888888886.57788777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3748.85
//
Query:       gi|121638915|ref|YP_979139.1|  [L=414]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-43  147.1   0.0    5.1e-43  146.6   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.5e-31  109.0   6.1    3.6e-30  105.2   1.2    2.5  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-27   97.1   0.0    2.3e-27   96.1   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
      1e-26   94.2   0.9    5.5e-26   91.8   0.9    2.1  1  Glyco_transf_5   Starch synthase catalytic domain
    1.2e-26   94.0   5.0    1.2e-26   94.0   5.0    2.4  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      6e-13   49.0   0.0    1.4e-12   47.8   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00059   18.5   0.0     0.0077   14.8   0.0    2.0  2  Glycogen_syn     Glycogen synthase
     0.0008   19.5   0.1     0.0019   18.2   0.1    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   2.3e-46   5.1e-43      12     172 .]     213     372 ..     206     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 2.3e-46
                                    TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                    ++++  +l+vgrle+eKgv+ +i a+++l+++ +p + l+iaG+g++++ l ++a ++ +   ++f+g++++++l +ll+
  gi|121638915|ref|YP_979139.1| 213 RTGPAELLYVGRLEYEKGVHDAIAALPRLRRT-HPGTTLTIAGEGTQQDWLIDQARKHRVLRATRFVGHLDHTELLALLH 291
                                    678899***********************997.*********************************************** PP

                                    CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                    +ad++vlps++E+fG+v+lEA aag+p ++sn+gg+ e v +g+tG+ ++p +++ la+a+r++l+d+  ++r  ++ar+
  gi|121638915|ref|YP_979139.1| 292 RADAAVLPSHYEPFGLVALEAAAAGTPLVTSNIGGLGEAVINGQTGVSCAPRDVAGLAAAVRSVLDDPAAAQRRARAARQ 371
                                    ********************************************************************999999999998 PP

                                    H CS
                Glycos_transf_1 172 r 172
                                    r
  gi|121638915|ref|YP_979139.1| 372 R 372
                                    6 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   1.2   1.6e-33   3.6e-30       1     170 []      15     204 ..      15     204 .. 0.75
   2 !    5.9   0.3    0.0053        12      49     102 ..     271     322 ..     231     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.6e-33
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvv..tpgddgpleeev...................elvvrvprvplpllkrllrsla 59 
                                    +GG +rhv++L+ aLa++Gh+V+v+  +p++ +  +                        ++ +     + l+    +++
  gi|121638915|ref|YP_979139.1|  15 IGGLGRHVHHLSTALAAAGHDVVVLsrCPSGTD--PSTHpssdevtegvrviaaaqdpHEFTFGNDMMAWTLAMGHAMIR 92 
                                    7************************66443333..333333656677756654442222222222222233333444444 PP

                 Glyco_transf_4  60 flrrlrrllkre......kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrr 133
                                    + +rl++           +pDvvHah++  +  a +al++ +++p+V t+H +++ r+ ++ ++ lsr ++a+e +l+r 
  gi|121638915|ref|YP_979139.1|  93 AGLRLKK----LgtdrswRPDVVHAHDWLVAHPA-IALAQFYDVPMVSTIHATEAGRHSGWVSGALSRQVHAVESWLVRE 167
                                    4555555....2444477*********9998666.555556**************999********************** PP

                 Glyco_transf_4 134 adrviavSeatadelrerygvppekitVipnGvDler 170
                                    +d +i++S ++ de+ e++g   + itVi nG+D +r
  gi|121638915|ref|YP_979139.1| 168 SDSLITCSASMNDEITELFGPGLAEITVIRNGIDAAR 204
                                    ********************66699*********876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0053
                 Glyco_transf_4  49 pllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVlt 102
                                    +l++ +      +  l +ll+r +  v+ +h+++++++al a++   g plV++
  gi|121638915|ref|YP_979139.1| 271 VLRATRFVGHLDHTELLALLHRADAAVLPSHYEPFGLVALEAAA--AGTPLVTS 322
                                    4444444555567789999*************999999988888..7*****86 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0     1e-30   2.3e-27       3     134 .]     218     358 ..     216     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1e-30
                                    EEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEE CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadvf 76 
                                     +l+vGrl e +kgv+  + a+p+lr+ +   +l+i+G+g++++ l ++a+  ++    +f+G++  ++l +ll++ad +
  gi|121638915|ref|YP_979139.1| 218 ELLYVGRL-EYEKGVHDAIAALPRLRRTHpgTTLTIAGEGTQQDWLIDQARkhRVLRATRFVGHLdhTELLALLHRADAA 296
                                    689*****.666**************77458*********9556887777646555789******8777*********** PP

                                    EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    v+Ps  e fgl++lEa+aag+p V++++gg+ e+v  g++g+ ++p+d++ la+a+  +l+d
  gi|121638915|ref|YP_979139.1| 297 VLPShyEPFGLVALEAAAAGTPLVTSNIGGLGEAVinGQTGVSCAPRDVAGLAAAVRSVLDD 358
                                    ******************************988888**********************9987 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.9   2.4e-29   5.5e-26       1     240 [.       2     192 ..       2     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.4e-29
                 Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry.gaikeekkeleevaelskaaedevevevekvkvakl 79 
                                    +il+v++E++p +  GGL+++v++L+ aLa++ghdv v++    g+ ++++ +  ev                       
  gi|121638915|ref|YP_979139.1|   2 RILMVSWEYPP-VVIGGLGRHVHHLSTALAAAGHDVVVLSRCPsGTDPSTHPSSDEV----------------------- 57 
                                    7**********.9*************************9977744444433222222....................... PP

                 Glyco_transf_5  80 kkdgvdvyf.ldnpeffdreglYgdkgedyednaerfalfsraalellekl.......gwkpdvihahDWhtalvpallk 151
                                      +gv+v+   ++p+ f     +g+      d      ++++a++++  +l       +w+pdv+hahDW  a+ ++ l+
  gi|121638915|ref|YP_979139.1|  58 -TEGVRVIAaAQDPHEF----TFGN------DMMAWTLAMGHAMIRAGLRLkklgtdrSWRPDVVHAHDWLVAHPAIALA 126
                                    .25*****977777755....4543......444444489********999999**9999******************** PP

                 Glyco_transf_5 152 elykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflk.agivyadavttVSptyakEil 230
                                    ++y       ++++v tiH ++  ++ ++   a                 +++v+ ++ + ++++d ++t+S ++ +Ei+
  gi|121638915|ref|YP_979139.1| 127 QFY-------DVPMVSTIHATEAGRHSGWVSGA----------------LSRQVHAVEsWLVRESDSLITCSASMNDEIT 183
                                    **9.......5***********99888842221................2368888888********************* PP

                 Glyco_transf_5 231 tpefgggleg 240
                                    + + g gl +
  gi|121638915|ref|YP_979139.1| 184 ELF-GPGLAE 192
                                    976.778876 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   5.0   5.4e-30   1.2e-26       1     160 []      16     199 ..      16     199 .. 0.73
   2 ?    5.3   8.4     0.011        24      41     146 ..     267     393 ..     208     405 .. 0.60

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 5.4e-30
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt.......papapgapeleedgvrvhrlpvprrp.....spladlaalral..... 63 
                                    gG gr+v++l+ aLaa+Gh+V+vl        p+ +p+++ ++ +gvrv+     +++     +   ++a++ a+     
  gi|121638915|ref|YP_979139.1|  16 GGLGRHVHHLSTALAAAGHDVVVLSrcpsgtdPSTHPSSD-EVTEGVRVIAAAQDPHEftfgnD---MMAWTLAMghami 91 
                                    8************************555444333333344.67779999876655554332221...2333322222222 PP

                Glyco_trans_4_4  64 ...rrll...rqrrerpdvvhahspt.aglaarlarrrrgiplvvtlhglllrrgsgavrrly....ralerrllrrada 132
                                        rl      r++rpdvvhah+++ a +a++la+   ++p v t+h+++  r+sg+v  ++    +a+e++l+r  d 
  gi|121638915|ref|YP_979139.1|  92 ragLRLKklgTDRSWRPDVVHAHDWLvAHPAIALAQ-FYDVPMVSTIHATEAGRHSGWVSGALsrqvHAVESWLVRESDS 170
                                    2113322335669***********986888888888.99*********9997777777666665444888********** PP

                Glyco_trans_4_4 133 vlvvseaeaeelra.lgvpadrvvvvpng 160
                                    +++ s+++ +e+++ +g   + ++v++ng
  gi|121638915|ref|YP_979139.1| 171 LITCSASMNDEITElFGPGLAEITVIRNG 199
                                    **************8998899*******8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                Glyco_trans_4_4  41 rvhrlpvprrpspladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlh................ 104
                                    r hr  v r+ + ++ l++ + l +ll  +r    v+ +h+ + gl+a+ a+ ++g+plv +                  
  gi|121638915|ref|YP_979139.1| 267 RKHR--VLRATRFVGHLDH-TELLALL--HRADAAVLPSHYEPFGLVALEAA-AAGTPLVTSNIgglgeavingqtgvsc 340
                                    3333..2333333444444.4556666..899999******99*********.********9965555555555555444 PP

                Glyco_trans_4_4 105 ............glllrrgsgavrrlyralerrllrradavlvvseaeaeelra 146
                                                   l+++++ ++r +ra+ +rl + +d  +v ++    +l+a
  gi|121638915|ref|YP_979139.1| 341 aprdvaglaaavRSVLDDPAA-AQRRARAARQRLTSDFDWPTVATATAQVYLAA 393
                                    444444332211111223333.33333455566666666666666666666665 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   6.1e-16   1.4e-12       3      87 ..     297     383 ..     290     388 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.1e-16
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                    + ps++e + l+ +Eaaa+G++++t+ + gl+e + +g++++  +  d++ la+++r +l++p+ ++++a+aar+r  ++
  gi|121638915|ref|YP_979139.1| 297 VLPSHYEPFGLVALEAAAAGTPLVTSNIGGLGEAVINGQTGVSCAprDVAGLAAAVRSVLDDPAAAQRRARAARQRLTSD 376
                                    569999*********************************9999999********************************** PP

                Glyco_trans_1_2  81 htydhra 87 
                                    +++   a
  gi|121638915|ref|YP_979139.1| 377 FDWPTVA 383
                                    *998776 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.038        84     144     181 ..     109     145 ..      72     154 .. 0.76
   2 !   14.8   0.0   3.4e-06    0.0077     470     505 ..     294     329 ..     269     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.038
                                    EEEEEETGGGHH.HHHHHHHTT-SEEEEEEESS-HHHHH CS
                   Glycogen_syn 144 vvahfhewlaGv.gliltrkrkldvatvftthatllGry 181
                                     v h h+wl    ++ l+  +  dv  v t hat  Gr+
  gi|121638915|ref|YP_979139.1| 109 DVVHAHDWLVAHpAIALA--QFYDVPMVSTIHATEAGRH 145
                                    46799***9654155555..45677788999***99998 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-06
                                    SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHH CS
                   Glycogen_syn 470 hlGvfpsyyepwGytpaectvmGipsvttnlsGfGc 505
                                       v+ps+yep+G    e +  G p vt+n+ G+G 
  gi|121638915|ref|YP_979139.1| 294 DAAVLPSHYEPFGLVALEAAAAGTPLVTSNIGGLGE 329
                                    4579*****************************994 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   8.5e-07    0.0019      12     109 ..      21     140 ..      14     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.5e-07
                Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitp.kkg.....a.kdeleaegihvhrlkvd............rkgpleylka...fklkkl 69 
                                    h+ +l  +La++g++V+v+++   g     + + +++ eg++v+    d            +  +++ +++   ++lkkl
  gi|121638915|ref|YP_979139.1|  21 HVHHLSTALAAAGHDVVVLSRcPSGtdpstHpSSDEVTEGVRVIAAAQDpheftfgndmmaWTLAMGHAMIragLRLKKL 100
                                    89999**************8632221122235778899******9965555555555555433344444325557***** PP

                Glyco_trans_4_2  70 ikkik..PDvvhahyakpygllgslaarlsgvipvvlsvwGl 109
                                     ++++  PDvvhah  + ++  + ++a +   +p+v +++ +
  gi|121638915|ref|YP_979139.1| 101 GTDRSwrPDVVHAHD-WLVAHPAIALAQFYD-VPMVSTIHAT 140
                                    9887444********.556777888889997.9***999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2603.67
//
Query:       gi|121638916|ref|YP_979140.1|  [L=129]
Description: hypothetical protein BCG_3056 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 942.28
//
Query:       gi|121638917|ref|YP_979141.1|  [L=182]
Description: hypothetical protein BCG_3057 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-36  124.9   5.0    2.8e-22   78.8   0.4    2.1  2  DUF4333   Domain of unknown function (DUF4333)
  ------ inclusion threshold ------
       0.13   12.6   0.1       0.29   11.6   0.1    1.5  1  Rtt106    Histone chaperone Rttp106-like


Domain annotation for each model (and alignments):
>> DUF4333  Domain of unknown function (DUF4333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.4   3.1e-26   2.8e-22       4      78 .]      23      97 ..      20      97 .. 0.97
   2 !   48.5   0.4   8.8e-17   7.9e-13      15      77 ..     106     167 ..      99     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 3.1e-26
                        DUF4333  4 vgcslp.gflgskvldkaaveagvaqvLtesygakkvsdVtCpsglkvevGatftCtltvdGetltVtvtvtdddG 78
                                   ++cs++ g  +s++++ka+v++++++++t++ g+ k+++VtCps+l++evGa+ +C+++++++t++V+vtvt++dG
  gi|121638917|ref|YP_979141.1| 23 TACSFSiGTSHSHSVSKAEVARQITAKMTDAAGN-KPESVTCPSDLPAEVGAELNCEMKIKDRTFNVNVTVTSVDG 97
                                   799999999************************9.****************************************9 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 8.8e-17
                        DUF4333  15 kvldkaaveagvaqvLtesygakkvsdVtCpsglkvevGatftCtltvdGetltVtvtvtddd 77 
                                    +++dk++v++ ++++L + +ga ++++VtCp++lk+ +Ga+ +C lt++ +t+++ v vt++d
  gi|121638917|ref|YP_979141.1| 106 ETVDKNQVANIISDKLFQRVGA-RPDSVTCPDNLKGVEGAKLRCRLTDGSKTYGISVIVTSVD 167
                                    79********************.**************************************98 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.2e-05      0.29      46      77 ..      80     114 ..      71     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                         Rtt106  46 svtsrtfdlvvelkk...eeveFsmidqeelegid 77 
                                    +++ rtf+++v++++    +v+F+m++  + ++++
  gi|121638917|ref|YP_979141.1|  80 KIKDRTFNVNVTVTSvdgSDVKFDMVETVDKNQVA 114
                                    6899*********66777*******9987776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 1123.89
//
Query:       gi|121638918|ref|YP_979142.1|  [L=300]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-09   37.4   9.1    2.1e-07   30.4   1.3    3.9  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
     0.0002   21.0   0.3     0.0002   21.0   0.3    3.2  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0007       6.3       3      30 ..     124     156 ..     122     157 .. 0.65
   2 !    7.5   0.7    0.0004       3.6       2      28 ..     146     175 ..     146     178 .. 0.93
   3 ?   -1.1   0.0      0.21   1.9e+03      21      33 ..     182     194 ..     180     197 .. 0.44
   4 !   30.4   1.3   2.3e-11   2.1e-07       2      36 .]     219     253 ..     218     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0007
                                    EEETTEEE-T.....TEEEETTEEE-TTEEEET CS
                        Hexapep   3 vIGsnvlIgp.....faviggnVkIGdnvkIga 30 
                                    ++G++v I++        ig  V+IGd  +I a
  gi|121638918|ref|YP_979142.1| 124 FLGKGVEIHAtpelaQLEIGRWVHIGDKNTIRA 156
                                    677777777766666666667777777666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0004
                                    EEEETTEEE-T...TEEEETTEEE-TTEEE CS
                        Hexapep   2 tvIGsnvlIgp...faviggnVkIGdnvkI 28 
                                    ++IG++++I++      +g+ V++G++ +I
  gi|121638918|ref|YP_979142.1| 146 VHIGDKNTIRAhegSLRFGDKVVLGRDNVI 175
                                    68************99***********999 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.21
                                    EE-TTEEEETTEE CS
                        Hexapep  21 kIGdnvkIgagvv 33 
                                    +IGd v  + +++
  gi|121638918|ref|YP_979142.1| 182 EIGDSVLMADWCY 194
                                    4555444444433 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 2.3e-11
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    ++IG +++Ig  + ++ +++IG+++++g+++v++g
  gi|121638918|ref|YP_979142.1| 219 VRIGPDTWIGVKVSVLRGTTIGRGCVLGSHAVVRG 253
                                    78*******************************86 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.76   6.8e+03      10      17 ..       6      15 ..       6      19 .. 0.67
   2 ?   -1.7   0.0      0.27   2.5e+03      18      23 ..     146     151 ..     141     156 .. 0.63
   3 ?    0.0   0.2     0.082   7.3e+02       6      22 ..     165     185 ..     161     188 .. 0.58
   4 !   21.0   0.3   2.3e-08    0.0002       1      28 [.     218     247 ..     218     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.76
                                   E-TT-EE..S CS
                      Hexapep_2 10 iGanagi..G 17
                                   +G+++g+  G
  gi|121638918|ref|YP_979142.1|  6 LGSSSGVvwG 15
                                   6999996466 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.27
                                    EEE-TT CS
                      Hexapep_2  18 vslGdn 23 
                                    v++Gd+
  gi|121638918|ref|YP_979142.1| 146 VHIGDK 151
                                    677775 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.082
                                    TT-EE-TT-EE....SEEE-T CS
                      Hexapep_2   6 dnCliGanagi....GvslGd 22 
                                    d +++G + +i     +++Gd
  gi|121638918|ref|YP_979142.1| 165 DKVVLGRDNVIntylDIEIGD 185
                                    555555544433344888888 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 2.3e-08
                                    .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                      Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                    pv+IG ++ iG+   +  G+++G++cv+g+
  gi|121638918|ref|YP_979142.1| 218 PVRIGPDTWIGVKVSVlrGTTIGRGCVLGS 247
                                    8************66559**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 2241.92
//
Query:       gi|121638919|ref|YP_979143.1|  [L=360]
Description: hypothetical protein BCG_3059 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   44.5   7.8    9.8e-07   28.6   2.2    2.5  2  PQQ_2     PQQ-like domain
    2.1e-08   34.4  23.1      0.014   15.9   0.6    6.6  7  PQQ_3     PQQ-like domain
    6.8e-05   22.6   1.2    0.00083   19.2   0.0    3.2  4  PQQ       PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.3   5.4e-10   3.2e-06      11     150 ..      32     236 ..      28     238 .. 0.87
   2 !   28.6   2.2   1.6e-10   9.8e-07      17     161 ..     189     340 ..     148     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.4e-10
                          PQQ_2  11 atGaelWrvdlarplgggvsravlsg.gtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqli 89 
                                    ++G++ W v+l    ggg+++++ +g + l+v+   g ++++ + t   +W++ + g   ++ ++  gr++v +  gql+
  gi|121638919|ref|YP_979143.1|  32 NNGRQRWCVRL--VQGGGFAGPLFDGfDNLYVG-QPGAIISF-PPTQWTRWRQPVIGMPSTPRFLGHGRLLVSTHLGQLL 107
                                    68999999999..56888888887775788886.88999988.7999********8887777799*************** PP

                          PQQ_2  90 aldaedGkr....................................................................... 98 
                                     +d++ G +                                                                       
  gi|121638919|ref|YP_979143.1| 108 VFDTRRGMVvgspvdlvdgidptdatrgladcaparpgcpvaaapafssvngtvvvsvwqpgepaaklvglkyhaeqlvr 187
                                    *********************************************************99999999999999999999999 PP

                          PQQ_2  99 lWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel 150
                                     W+  ++   +a ++ s+  + +g tv+v + + +l al+++dGk  W+++l
  gi|121638919|ref|YP_979143.1| 188 EWT-SDAV--SAGVLASPVLSADGSTVYVNGRDHRLWALNAADGKAKWSAPL 236
                                    999.3333..3555555555555**************************998 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.6e-10
                          PQQ_2  17 Wrvdl.arplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva..sdgqliald. 92 
                                    W++d    +  + +   + +g+t++v ++  rl al+aa+Gk +W++ l   ++++p ++   ++v    +d +l+a+  
  gi|121638919|ref|YP_979143.1| 189 WTSDAvSAGVLASPV-LSADGSTVYVNGRDHRLWALNAADGKAKWSAPLGFLAQTPPALTPHGLIVSGggPDTALAAFRd 267
                                    555442223333333.34499****************************8888999977777777776677779999874 PP

                          PQQ_2  93 .aedGkrlWstqqrse.epae.lrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtselsr 161
                                      +  + +W++++ ++ ++a+ +++    +v ++    g++++ l ++dp++G  + +++l +a+ + + +s 
  gi|121638919|ref|YP_979143.1| 268 aGDHAEGAWRRDDVTAlSTASlAGTGVGYTVISGPNHDGTPGLSLLVFDPANGHTVNSYPLpGATGYPVGVSV 340
                                    3444566***8888876777754555555555777777788********************666554444443 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00066         4       1      31 [.      34      65 ..      34      70 .. 0.83
   2 ?    3.8   0.0     0.015        90       4      39 ..      77     112 ..      76     113 .. 0.80
   3 ?    0.5   0.1      0.15   9.1e+02      10      29 ..     144     166 ..     141     172 .. 0.79
   4 !   15.9   0.6   2.3e-06     0.014       9      40 .]     194     227 ..     186     227 .. 0.80
   5 !    5.7   0.1    0.0038        23       1      36 [.     228     265 ..     228     268 .. 0.83
   6 ?   -2.7   0.1       1.6   9.8e+03       8      16 ..     293     301 ..     276     307 .. 0.49
   7 !   11.8   1.2   4.4e-05      0.26       6      37 ..     325     359 ..     325     360 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00066
                          PQQ_3  1 GevlWsvql.pgpvnsspavdg.glvyvgtgdG 31
                                   G+++W v+l  g + ++p++dg + +yvg + G
  gi|121638919|ref|YP_979143.1| 34 GRQRWCVRLvQGGGFAGPLFDGfDNLYVGQP-G 65
                                   99*****997456779************966.5 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.015
                          PQQ_3   4 lWsvqlpg.pvnssp.avdgglvyvgtgdGtlyAlDae 39 
                                    +W++++ g p  s+p  ++ g++ v+t+ G l  +D++
  gi|121638919|ref|YP_979143.1|  77 RWRQPVIGmP--STPrFLGHGRLLVSTHLGQLLVFDTR 112
                                    8999997757..77944467999999999****99975 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                          PQQ_3  10 pg.pvnsspavd..gglvyvgtg 29 
                                    pg pv ++pa++  +g+v+v+ +
  gi|121638919|ref|YP_979143.1| 144 PGcPVAAAPAFSsvNGTVVVSVW 166
                                    66688889988655899999876 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 2.3e-06
                          PQQ_3   9 lpgpvnssp..avdgglvyvgtgdGtlyAlDaet 40 
                                    + + v +sp   +dg +vyv + d++l Al+a++
  gi|121638919|ref|YP_979143.1| 194 VSAGVLASPvlSADGSTVYVNGRDHRLWALNAAD 227
                                    3557888896666899***************986 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0038
                          PQQ_3   1 GevlWsvqlpgpvnsspavd.gglvyvgtg.dGtlyAl 36 
                                    G+ +Ws +l+  ++++pa+   gl++ g+g d  l A+
  gi|121638919|ref|YP_979143.1| 228 GKAKWSAPLGFLAQTPPALTpHGLIVSGGGpDTALAAF 265
                                    8899*******999999776369988888888888887 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 1.6
                          PQQ_3   8 qlpgpvnss 16 
                                    ++++ v s+
  gi|121638919|ref|YP_979143.1| 293 GVGYTVISG 301
                                    233333333 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 4.4e-05
                          PQQ_3   6 svqlpgpvnssp...avdgglvyvgtgdGtlyAlD 37 
                                    s++lpg++++++   +  +++v+++t+dG +y++ 
  gi|121638919|ref|YP_979143.1| 325 SYPLPGATGYPVgvsVGNDRRVVTATSDGQVYSFA 359
                                    578999777777654445899***********996 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.8   1.7e+04      18      24 ..      32      38 ..      31      43 .. 0.80
   2 !   19.2   0.0   1.4e-07   0.00083       2      33 ..     210     241 ..     210     246 .. 0.86
   3 ?   -3.2   0.0       1.7     1e+04      28      37 ..     319     328 ..     317     329 .. 0.79
   4 ?    0.2   0.0      0.14   8.2e+02       3      13 ..     346     356 ..     343     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.8
                                   TTCCEEE CS
                            PQQ 18 dTGkvlW 24
                                   ++G+ +W
  gi|121638919|ref|YP_979143.1| 32 NNGRQRW 38
                                   6899999 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.4e-07
                                    EEEEEETTSEEEEEETTTCCEEEEEESSSCGS CS
                            PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvl 33 
                                    +vy+  +d +l+Al+a++Gk +W+ ++g   +
  gi|121638919|ref|YP_979143.1| 210 TVYVNGRDHRLWALNAADGKAKWSAPLGFLAQ 241
                                    699999999****************9986655 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                                    SSSCGSSESE CS
                            PQQ  28 tggpvlslpi 37 
                                    +g+ v+s+p+
  gi|121638919|ref|YP_979143.1| 319 NGHTVNSYPL 328
                                    6888999886 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.14
                                    EEEEETTSEEE CS
                            PQQ   3 vylgsadGyly 13 
                                    v+ ++ dG++y
  gi|121638919|ref|YP_979143.1| 346 VVTATSDGQVY 356
                                    5555******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 2811.21
//
Query:       gi|121638920|ref|YP_979144.1|  [L=227]
Description: hypothetical protein BCG_3060c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-13   49.5   0.0    1.5e-12   48.4   0.0    1.6  1  DUF3298   Protein of unknown function (DUF3298)


Domain annotation for each model (and alignments):
>> DUF3298  Protein of unknown function (DUF3298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   8.4e-17   1.5e-12       2      83 .]     145     220 ..     144     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 8.4e-17
                                    HCBSSCT.HHHHHHHHHHHHHHHHTCH-TTS-HCCCCTTTTTSS-TTTSSEEEETTEEEEEE-TTSSS-GGG-SEEEEEE CS
                        DUF3298   2 dLfkegsaylqrlakiikeqikkenekqqedeyaglperrdkedilgyqnfyltddglviyfppYeiaPyaaGapefeip 81 
                                     Lf +g+ +l+ + +i+++++ ++         a+lp   +  d++ yqnf++tdd+l++yf ++e+ P   Ga ++ +p
  gi|121638920|ref|YP_979144.1| 145 TLFVPGTTPLDSIYPIVQRELARQT----GFGAAILPS--TGLDPAHYQNFAITDDSLIFYFAQGELLPSFVGACQAQVP 218
                                    59***********************....666677776..89************************************** PP

                                    HC CS
                        DUF3298  82 ys 83 
                                    +s
  gi|121638920|ref|YP_979144.1| 219 RS 220
                                    86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 1711.11
//
Query:       gi|121638921|ref|YP_979145.1|  [L=358]
Description: hypothetical protein BCG_3061c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-20   72.2   0.1    4.8e-20   71.3   0.1    1.5  1  Thump_like       THUMP domain-like
  ------ inclusion threshold ------
      0.012   16.3   0.1      0.024   15.3   0.1    1.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.1   5.3e-24   4.8e-20       2      78 .]     281     356 ..     280     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 5.3e-24
                     Thump_like   2 rafevlevlpfskkklkkllrergigkanikkRgfpldpeeLrkklklkdggraatLvlTrvgegkagkavallcer 78 
                                    r+fevle+l f++++l++ l ++++g+a+i++Rg+++dp++Lr++l+l+ g+r+  +v+Tr+g g+    +a++c++
  gi|121638921|ref|YP_979145.1| 281 RGFEVLEQLAFDERRLRQVLSALDCGAAEILVRGVAIDPDALRRRLRLR-GSRPLAVVITRIGAGSLSHVTAYVCRP 356
                                    9***********************************************9.999**********************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   2.7e-06     0.024       1      57 [.      66     120 ..      66     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed 57 
                                    v d+ c  G+ ++al +     + +g Di++  l+ ar+++++ g+++++ ++d+ +
  gi|121638921|ref|YP_979145.1|  66 VHDATCSIGTELAALRELA--VRAVGSDIDPVRLAMARHNLAALGMEADLCRADVLH 120
                                    56899**********9995..***********************99*9999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2299.29
//
Query:       gi|121638922|ref|YP_979146.1|  [L=327]
Description: hypothetical protein BCG_3062c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-23   83.2   0.2      7e-23   81.1   0.1    2.1  2  Methyltransf_11  Methyltransferase domain
    3.3e-20   72.6   0.5    1.3e-19   70.7   0.1    2.2  3  Methyltransf_25  Methyltransferase domain
    9.5e-17   61.2   0.0    4.2e-16   59.1   0.0    1.9  2  Methyltransf_31  Methyltransferase domain
    3.4e-14   53.4   0.2    4.5e-13   49.8   0.0    2.2  2  Methyltransf_12  Methyltransferase domain
    5.9e-12   45.4   0.0      9e-12   44.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.7e-12   45.4   0.0      3e-11   43.5   0.0    2.0  2  Methyltransf_23  Methyltransferase domain
      3e-06   27.0   0.0    4.7e-06   26.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00079   19.1   0.0     0.0013   18.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
     0.0082   16.0   0.0      0.013   15.3   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.012   15.2   0.0       0.02   14.4   0.0    1.3  1  MTS              Methyltransferase small domain
      0.012   14.2   0.0      0.016   13.8   0.0    1.2  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.081   12.3   0.0       0.13   11.6   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.3   3.5e+03      55      74 ..      57      76 ..      17      81 .. 0.71
   2 !   81.1   0.1   4.7e-26     7e-23       1      96 []      82     179 ..      82     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                                   TSS-TT-EEEEEEES-CCC- CS
                Methyltransf_11 55 lpfednsfDlvvssevlhhv 74
                                   + ++ + fD++v  ev+  +
  gi|121638922|ref|YP_979146.1| 57 VDYARGRFDAIVPDEVIAQL 76
                                   46778889999888777665 PP

  == domain 2  score: 81.1 bits;  conditional E-value: 4.7e-26
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                    L++GcGtG ++  l ++g  +r   +Dls+ m+k+a ++++  gl ++ +vadae +p+ d+ fDlvv + vlhh++d+e
  gi|121638922|ref|YP_979146.1|  82 LELGCGTGFFLLNLIQAGvaRRGSVTDLSPGMVKVATRNGQALGLDIDGRVADAEGIPYDDDAFDLVVGHAVLHHIPDVE 161
                                    89*************9999999999*******************99999******************************* PP

                                    HHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                      l+e++RvLkpgG++v+
  gi|121638922|ref|YP_979146.1| 162 LSLREVVRVLKPGGRFVF 179
                                    ****************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.4   6.6e+03      54      65 ..      53      64 ..      17      73 .. 0.53
   2 !   70.7   0.1   8.5e-23   1.3e-19       2      97 .]      82     175 ..      81     175 .. 0.94
   3 ?   -2.2   0.0       4.8   7.1e+03      73      89 ..     234     251 ..     221     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.4
                                   BCCGBSSSTTTE CS
                Methyltransf_25 54 daedlpfedgsf 65
                                   d + ++++ g+f
  gi|121638922|ref|YP_979146.1| 53 DQRCVDYARGRF 64
                                   222333444444 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 8.5e-23
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    L+lGcGtG ++l+l +++ + +   +D+s++m++ a ++ ++ gl+++ +++dae +p++d+ fDlvv   +lhh++  d
  gi|121638922|ref|YP_979146.1|  82 LELGCGTGFFLLNLIQAGVARRGSVTDLSPGMVKVATRNGQALGLDIDGRVADAEGIPYDDDAFDLVVGHAVLHHIP--D 159
                                    9****************548999**********************************************656***98..7 PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +e  l+e+ rvLkpgG
  gi|121638922|ref|YP_979146.1| 160 VELSLREVVRVLKPGG 175
                                    7788***********9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.8
                                    T.GGGSSHHHHHHHHHHH CS
                Methyltransf_25  73 a.lhhlsdedlekalkei 89 
                                    + lh ++++dl+++ +++
  gi|121638922|ref|YP_979146.1| 234 VdLHTFTPQDLQRIAHNA 251
                                    347888888888887776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.63   9.5e+02      70      87 ..      59      76 ..      17      80 .. 0.72
   2 !   59.1   0.0   2.8e-19   4.2e-16       6     109 ..      80     179 ..      77     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.63
                Methyltransf_31 70 ledekfDlilsnevlnal 87
                                   +++ +fD i+ +ev++ l
  gi|121638922|ref|YP_979146.1| 59 YARGRFDAIVPDEVIAQL 76
                                   556899999999998655 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 2.8e-19
                Methyltransf_31   6 rvlDlGCGtGeltfelae.elgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                    r l+lGCGtG+++++l +  +  ++ v   D s+ ++++A+ n q lgld +  +++d+e ++  + d+ fDl++ ++vl
  gi|121638922|ref|YP_979146.1|  80 RALELGCGTGFFLLNLIQaGVARRGSV--TDLSPGMVKVATRNGQALGLD-IDGRVADAEGIP--YDDDAFDLVVGHAVL 154
                                    579**************6533345554..5*******************8.************..*************** PP

                Methyltransf_31  85 naladpdkileeiervlkpggilli 109
                                    ++++d +  l+e+ rvlkpgg+++ 
  gi|121638922|ref|YP_979146.1| 155 HHIPDVELSLREVVRVLKPGGRFVF 179
                                    ***********************96 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.4   5.9e+02      34      76 ..      25      73 ..       9      80 .. 0.64
   2 !   49.8   0.0     3e-16   4.5e-13       1      99 []      82     177 ..      82     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.4
                Methyltransf_12 34 edakeklakrennnnnnvelealdlldldgg......ssfDlvvasnvl 76
                                   +++  kla+   ++++  +++++ +++ d++      + fD++v  +v+
  gi|121638922|ref|YP_979146.1| 25 ARHDSKLAQVLYHDWEAENYDEKWSISYDQRcvdyarGRFDAIVPDEVI 73
                                   3455556666666666666665555555555999999999999866665 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 3e-16
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    Le+GcGtG +l  l ++    +  ++D+sp ++ + +++  +  +++ +    +a+ +  +d+  +fDlvv + vlhh++
  gi|121638922|ref|YP_979146.1|  82 LELGCGTGFFLLNLIQAGVARRGSVTDLSPGMV-KVATRNGQALGLDIDGRVADAEGIPYDDD--AFDLVVGHAVLHHIP 158
                                    8****************9888888*********.77777777776666655555555555554..9************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d++ +l+++ ++LkpgGr+
  gi|121638922|ref|YP_979146.1| 159 DVELSLREVVRVLKPGGRF 177
                                    *****************96 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0     6e-15     9e-12      44     150 ..      74     178 ..      63     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6e-15
                                    -S--TTEEEEES-TT-HHHHHHHHH.HHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsds.vgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                    a+++  ++l++ +Gtg + ++l ++ v ++g   v D+++ m+kv+ +  +  g  +i+  +a+ae +p++dd+fD+v  
  gi|121638922|ref|YP_979146.1|  74 AQLPYDRALELGCGTGFFLLNLIQAgVARRG--SVTDLSPGMVKVATRNGQALG-LDIDGRVADAEGIPYDDDAFDLVVG 150
                                    56666789**********9999875255556..568**********98877777.59********************988 PP

                                    ES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       l  ++D + +L+e+ rvlkpGGr+v
  gi|121638922|ref|YP_979146.1| 151 HAVLHHIPDVELSLREVVRVLKPGGRFV 178
                                    8889**********************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   1.5e+03      70      92 ..      51      73 ..       7      79 .. 0.58
   2 !   43.5   0.0     2e-14     3e-11      25     119 ..      80     181 ..      59     258 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                Methyltransf_23 70 qfdeqeaaepqgkfdlIvlrevl 92
                                   ++d+ + ++  g+fd Iv  ev+
  gi|121638922|ref|YP_979146.1| 51 SYDQRCVDYARGRFDAIVPDEVI 73
                                   34445666677788888876666 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 2e-14
                Methyltransf_23  25 rvLdiGcGtGillevlrengf..svtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                                    r L++GcGtG +l  l + g+     + Dlsp +v+ a          ++      +d++ ++++++ fdl+v   vl+h
  gi|121638922|ref|YP_979146.1|  80 RALELGCGTGFFLLNLIQAGVarRGSVTDLSPGMVKVATrngqalglDIDGR---VADAEGIPYDDDAFDLVVGHAVLHH 156
                                    88********98888877776689************9988887754433333...344558999999************* PP

                Methyltransf_23  95 vpdppellrqiatllkpgGylllse 119
                                    +pd++  lr + + lkpgG++++  
  gi|121638922|ref|YP_979146.1| 157 IPDVELSLREVVRVLKPGGRFVFAG 181
                                    ********************99864 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   3.1e-09   4.7e-06      24     145 ..      57     180 ..      29     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.1e-09
                           NodS  24 nefeqerlaqil.rlslaqgsiadalevGcaaGalterl..apyckrltvvdvveeaiararervke.sshiswivsdvq 99 
                                     ++ + r+ +i+    +aq     ale+Gc +G +  +l  a +++r +v d+ +  ++ a +  +    +i   v+d +
  gi|121638922|ref|YP_979146.1|  57 VDYARGRFDAIVpDEVIAQLPYDRALELGCGTGFFLLNLiqAGVARRGSVTDLSPGMVKVATRNGQAlGLDIDGRVADAE 136
                                    568888888887345678999999***********99985567899*******998887665544431569********* PP

                           NodS 100 qfst.dekfdlivvaevlyyiedvaelraavrnlvsllapdgqlvfG 145
                                     +   d+ fdl+v   vl++i dv+    ++r++v++l+p+g++vf 
  gi|121638922|ref|YP_979146.1| 137 GIPYdDDAFDLVVGHAVLHHIPDVE---LSLREVVRVLKPGGRFVFA 180
                                    99862578***********999976...589***************6 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.5e-07    0.0013      13     102 ..      77     171 ..      64     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.5e-07
                           MetW  13 pgsrvldlGcGdGe.llellkeekqvdgrG..leldeegvaecvak....Glsviqgdldkdlenfedksfdyvvlsqtl 85 
                                    p  r l+lGcG G  ll+l++   +v  rG   +l+   v+ ++      Gl +    +d +   ++d++fd+vv    l
  gi|121638922|ref|YP_979146.1|  77 PYDRALELGCGTGFfLLNLIQA--GVARRGsvTDLSPGMVKVATRNgqalGLDIDGRVADAEGIPYDDDAFDLVVGHAVL 154
                                    45789********735677765..67666621455555555555442222677777778888889*************** PP

                           MetW  86 qatrnpkevldellrig 102
                                      + + +  l+e++r+ 
  gi|121638922|ref|YP_979146.1| 155 HHIPDVELSLREVVRVL 171
                                    **************995 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.8e-06     0.013      74     157 ..     104     180 ..      94     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.8e-06
                                    S-EEEES-TT-HHHHH--S-..EEEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEE CS
                 Methyltransf_8  74 lvvadlGcGeakiaeavrekekvrsfdlvavnervvacdlakvPledesvdvavfclslm.gtnladflkeanrvlkvGG 152
                                     +v dl  G +k+a++ ++      +d+   +    + d   +P +d++ d++v    l    +++  l+e+ rvlk+GG
  gi|121638922|ref|YP_979146.1| 104 GSVTDLSPGMVKVATRNGQA---LGLDI---DG--RVADAEGIPYDDDAFDLVVGHAVLHhIPDVELSLREVVRVLKPGG 175
                                    57888888888888444443...45554...33..457999************97766652679**************** PP

                                    EEEEE CS
                 Methyltransf_8 153 llkva 157
                                     +  a
  gi|121638922|ref|YP_979146.1| 176 RFVFA 180
                                    98776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05      0.02      32     109 ..      78     156 ..      66     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfha 109
                                     +++l lGcG+G+  ++l ++    +  ++d +   +++a++n +a +l+++ +  d+     +++ fdl+v    +h+
  gi|121638922|ref|YP_979146.1|  78 YDRALELGCGTGFFLLNLIQAGVARRGSVTDLSPGMVKVATRNGQALGLDIDGRVADAEGiPYDDDAFDLVVGHAVLHH 156
                                    46799*********************************************76666665441345689999986544444 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.016     169     223 ..     132     185 ..      67     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                Methyltransf_29 169 vlgtkrlpyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsappvy 223
                                    v  ++ +py   +fdl+      +++  +  + l ev Rvl+pgG fv++++p +
  gi|121638922|ref|YP_979146.1| 132 VADAEGIPYDDDAFDLVVGH-AVLHHIPDVELSLREVVRVLKPGGRFVFAGEPTT 185
                                    34467799********9765.456666677789******************9976 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.7e-05      0.13     163     260 ..      79     181 ..      70     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.7e-05
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakk.vvavDiDevAvkvakeNaelNkveaklevalseell.keekadvivaNILaevl. 239
                                    ++ l +G+G+G   +   + g ++    +D+ +  vkva +N +  +++   +va +e ++ ++  +d++v   + + + 
  gi|121638922|ref|YP_979146.1|  79 DRALELGCGTGFFLLNLIQAGVARrGSVTDLSPGMVKVATRNGQALGLDIDGRVADAEGIPyDDDAFDLVVGHAVLHHIp 158
                                    67899******999999999966515678*****************99998889877888754789*****998888883 PP

                           PrmA 240 .iel.aedikklvkeggllilSG 260
                                     +el + ++ +++k+gg++++ G
  gi|121638922|ref|YP_979146.1| 159 dVELsLREVVRVLKPGGRFVFAG 181
                                    33443578999*********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2136.36
//
Query:       gi|121638923|ref|YP_979147.1|  [L=254]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-46  156.2   0.1    1.1e-45  155.9   0.1    1.0  1  ECH_1          Enoyl-CoA hydratase/isomerase
    9.3e-20   71.4   0.1      1e-19   71.2   0.1    1.0  1  ECH_2          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.076   13.0   0.3        1.3    9.0   0.0    2.3  2  Peptidase_S49  Peptidase family S49
       0.12   11.9   0.0       0.19   11.3   0.0    1.2  1  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.1   2.6e-49   1.1e-45       3     229 ..      15     240 ..      13     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 2.6e-49
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                     ag+a + l rP + Na++ ++  E+++a ++l     v av+L Gg ++F+aG d+ e+   + +++++     ++  +
  gi|121638923|ref|YP_979147.1|  15 DAGLAMLLLSRP-PTNAMTRQVYREVVAAANELGRRDDVAAVILYGGHEIFSAGDDMPELRTLSAQEADTAARIRQQAVD 93 
                                    6899999*****.********************88889************************98777777777789999* PP

                                    HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                          ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                    ++  +pkp++aa+ G+a+g+Gl lala+D ++ +dn +fg++e++ Glip   g  +l+r+ G s+A+e++  g+ + a+
  gi|121638923|ref|YP_979147.1|  94 AVAAIPKPTVAAITGYALGAGLTLALAADWRVSGDNVKFGATEILAGLIPSGDGMARLTRAAGPSRAKELVFSGRFFDAE 173
                                    ******************************************************************************** PP

                                    HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                          ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfs 229
                                    eal  Gl+d +v+ +++ + a ++a++ ++ +p al+++k+ +   +e a ae ++ae++ + ++f+
  gi|121638923|ref|YP_979147.1| 174 EALALGLIDDMVAPDDVYDAAAAWARRFLDGPPHALAAAKAGISDVYELAPAERIAAERRRYVEVFA 240
                                    **********************************************************999888776 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.1   2.3e-23     1e-19       3     186 ..      20     199 ..      18     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.3e-23
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                    ++ L rp   Na++ ++ r++ +a +e  + d+v++v+l g g++ f+AG D+ +l++   +++++     r   +   +
  gi|121638923|ref|YP_979147.1|  20 MLLLSRPP-TNAMTRQVYREVVAAANELGRRDDVAAVILYG-GHEIFSAGDDMPELRTLSAQEADT---AARIRQQAVDA 94 
                                    56677775.5*******************************.88*************999997655...56777788999 PP

                                    HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHH CS
                          ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgad 161
                                    +a +pkp+va + G+++G G+ l++ +  rv  ++ +f   E+  Gl+P   g+  L+r+ g + ++ l  +G+ +++++
  gi|121638923|ref|YP_979147.1|  95 VAAIPKPTVAAITGYALGAGLTLALAADWRVSGDNVKFGATEILAGLIPSGDGMARLTRAAGpSRAKELVFSGRFFDAEE 174
                                    ************************************************************98789*************** PP

                                    HHHTTS--EE--GGGHHHHHHHHHT CS
                          ECH_2 162 alaaglathyvpseklealeeaLae 186
                                    ala+gl + +v  +++ + ++a a+
  gi|121638923|ref|YP_979147.1| 175 ALALGLIDDMVAPDDVYDAAAAWAR 199
                                    ***********99998887776665 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.054   2.4e+02       6      33 ..      99     126 ..      94     137 .. 0.88
   2 ?    9.0   0.0   0.00029       1.3     118     148 ..     165     195 ..     153     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.054
                                    T--EEEEEEEEEETHHHHHHTTSSEEEE CS
                  Peptidase_S49   6 kkPvvasaenvaaSggYylasaadkiva 33 
                                     kP va + ++a  +g  la aad  v+
  gi|121638923|ref|YP_979147.1|  99 PKPTVAAITGYALGAGLTLALAADWRVS 126
                                    69*********************98775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00029
                                    HCCHEEEHHHHHHTTSSSEETSHHHHHHHHH CS
                  Peptidase_S49 118 AegrvltgqqAlklgLvdelgtvddavaele 148
                                     +gr + +++Al+lgL+d +   dd+++ ++
  gi|121638923|ref|YP_979147.1| 165 FSGRFFDAEEALALGLIDDMVAPDDVYDAAA 195
                                    5789**********************99887 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.2e-05      0.19      63     119 ..      70     123 ..      50     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                            DLH  63 araldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                    +  l+ l +++  +   +++++av+++++ p  ++   +++G+ +G+ l+l+laa  
  gi|121638923|ref|YP_979147.1|  70 MPELRTLSAQE-ADTAARIRQQAVDAVAAIP--KPTVAAITGYALGAGLTLALAADW 123
                                    33444555666.6677778889*********..888999***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1572.34
//
Query:       gi|121638924|ref|YP_979148.1|  [L=288]
Description: hypothetical protein BCG_3064c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   26.3   0.4     0.0011   19.1   0.4    3.0  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   5.9e-08    0.0011       3      58 ..      15     115 ..      13     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.9e-08
                                    EEEEEEE.EEETTSE......EEEEEES.SSSTTT..EESSEEECBT...............................TS CS
                          NUDIX   3 rravgvv.llnekge......vLlvrrs.kkpfpg..WelPgGkvep...............................gE 41 
                                    r+a+ v+ +++++        v+l+rr+   +f++    +PgG+v++                                E
  gi|121638924|ref|YP_979148.1|  15 RPAATVMlVRDPDAGsasglaVFLMRRHaAMDFAAgvMVFPGGGVDDrdrdadlgrlgawagpppqwwaqrfgiepdlAE 94 
                                    677777768888844689999*******95555555778***************************************** PP

                                    HHHHHHHHHHHHHHSE....E CS
                          NUDIX  42 tpeeAArREleEEtGl....e 58 
                                    ++  AA+RE++EE G+    +
  gi|121638924|ref|YP_979148.1|  95 ALVCAAARETFEESGVlfagP 115
                                    999************733332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1942.22
//
Query:       gi|121638925|ref|YP_979149.1|  [L=287]
Description: ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-23   83.0   0.0    3.5e-23   82.6   0.0    1.2  1  ABC_tran   ABC transporter
    1.4e-09   38.2   0.6     0.0008   19.3   0.1    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0014   19.0   0.7     0.0047   17.3   0.7    1.8  1  AAA_16     AAA ATPase domain
     0.0071   16.9   0.0      0.012   16.2   0.0    1.3  1  AAA_23     AAA domain
     0.0098   15.4   0.0       0.21   11.0   0.1    2.1  2  SMC_N      RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.023   15.0   0.1       0.26   11.6   0.1    2.1  1  AAA_22     AAA domain
      0.024   14.4   0.0       0.72    9.6   0.0    2.2  2  IstB_IS21  IstB-like ATP binding protein
      0.038   11.5   0.0      0.052   11.1   0.0    1.0  1  DUF3584    Protein of unknown function (DUF3584)
      0.055   13.2   0.0      0.092   12.4   0.0    1.2  1  AAA_15     AAA ATPase domain
      0.058   13.0   0.0       0.12   12.0   0.0    1.4  1  cobW       CobW/HypB/UreG, nucleotide-binding domain
      0.062   13.0   0.2      0.095   12.4   0.2    1.5  1  AAA_30     AAA domain
      0.069   13.6   0.0        0.2   12.1   0.0    1.8  2  AAA        ATPase family associated with various cellular act
      0.071   12.9   0.0       0.12   12.1   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   2.6e-26   3.5e-23       4     136 ..      40     188 ..      37     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.6e-26
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.. RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren.. 79 
                                    +++ ++ +e+++ivG+nGaGK++Ll++ a  ++p +G   + g+ l + + ++lr+++g  +    +++  + +vr+   
  gi|121638925|ref|YP_979149.1|  40 LDWAVELDERWVIVGPNGAGKTSLLRIAAAAEHPSSGVAFVLGERLGRVDVSELRARVGLSSSAlaERVPGDERVRDLvv 119
                                    6789999*****************************************************999985556666668888** PP

                                    ................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     +  ++ ++l++lg ++l++++      +LS+G+++rv +aral+++p+llllDEp 
  gi|121638925|ref|YP_979149.1| 120 sagyavlgrwreryeaVDYHRAIDMLESLGAEHLANRTY----GTLSEGERKRVLIARALMTDPELLLLDEPA 188
                                    *******999887665555569999********999999....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.8e-07    0.0008       3      19 ..      51      67 ..      50      96 .. 0.87
   2 !   17.5   0.0     2e-06    0.0028     220     298 ..     144     221 ..      92     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.8e-07
                         AAA_21  3 vliGpNgsGKSnLLdal 19
                                   v++GpNg+GK++LL++ 
  gi|121638925|ref|YP_979149.1| 51 VIVGPNGAGKTSLLRIA 67
                                   8**************97 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2e-06
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQvilt 295
                                     +  l  ++  ++++  lS+G ++   l++  l +++   lll+DEp +gL+     +l++rl++l  +  +    ++l+
  gi|121638925|ref|YP_979149.1| 144 MLESLGAEHLANRTYGTLSEGERKR-VLIARALMTDP--ELLLLDEPAAGLDLggreELVARLADLAADPDA--PALVLV 218
                                    55666778889999***********.56666666665..9*************8888888888888877766..999999 PP

                         AAA_21 296 THS 298
                                    TH 
  gi|121638925|ref|YP_979149.1| 219 THH 221
                                    996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   3.4e-06    0.0047      28     127 ..      51     207 ..      44     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                         AAA_16  28 llsGesGvGKsslvrellralekd.ggiflrgkcdql......esaipy......salaqalareellrqlldeaesael 94 
                                    +++G+ G GK+sl+r ++ a   + g+ f+ g+          +           sala+    +e +r+l   a  a l
  gi|121638925|ref|YP_979149.1|  51 VIVGPNGAGKTSLLRIAAAAEHPSsGVAFVLGERLGRvdvselR----ArvglssSALAERVPGDERVRDLVVSAGYAVL 126
                                    699***********888854444456666443333332322221....123445477999999999***999999999** PP

                         AAA_16  95 eawrekleeala.................................................avpelagaeasrllellkr 125
                                    ++wre+ e+ +                                                  +++ l+  +++ l + l++
  gi|121638925|ref|YP_979149.1| 127 GRWRERYEA-VDyhraidmleslgaehlanrtygtlsegerkrvliaralmtdpelllldePAAGLDLGGREELVARLAD 205
                                    ***996544.3357766666666666666666666666666666665555555555555444444444444444444444 PP

                         AAA_16 126 ll 127
                                    l+
  gi|121638925|ref|YP_979149.1| 206 LA 207
                                    44 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.4e-06     0.012      23      37 ..      51      65 ..      46      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.4e-06
                         AAA_23 23 lItGpNGaGKTTild 37
                                   +I+GpNGaGKT++l+
  gi|121638925|ref|YP_979149.1| 51 VIVGPNGAGKTSLLR 65
                                   8************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00015      0.21      28      41 ..      51      64 ..      43      96 .. 0.80
   2 ?    2.7   0.0     0.054        74     136     185 ..     160     205 ..      74     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                   EEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnll 41
                                   +ivGpNG+GK++ll
  gi|121638925|ref|YP_979149.1| 51 VIVGPNGAGKTSLL 64
                                   8***********97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.054
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                    +LS Ge++ v +    A   +    l llDe +a LD   +++++ +l  
  gi|121638925|ref|YP_979149.1| 160 TLSEGERKRVLI----ARALMTDPELLLLDEPAAGLDLGGREELVARLAD 205
                                    788888874433....3333344458899********9988888777764 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00019      0.26       9      71 ..      51     146 ..      49     225 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka................ 70 
                                    v++G+ G+GKT llr  +   +        +++v+fv    ++  + ++l+ ++       +++                
  gi|121638925|ref|YP_979149.1|  51 VIVGPNGAGKTSLLRIAAAAEHP-------SSGVAFVLGERLGrvDVSELRARVGLSSSALAERvpgdervrdlvvsagy 123
                                    79************998888753.......45555555555553333333333332222222224444444555555555 PP

                         AAA_22  71 ......................e 71 
                                                          e
  gi|121638925|ref|YP_979149.1| 124 avlgrwreryeavdyhraidmlE 146
                                    55555555555555555555554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00052      0.72      40      71 ..      39      70 ..      19      96 .. 0.68
   2 ?    2.5   0.0     0.075     1e+02      77     113 ..     135     171 ..     126     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00052
                      IstB_IS21 40 tlsf.iekkenivllGpsGvGKshlaialgvea 71
                                    l++ +e  e  v++Gp G+GK+ l   ++ +a
  gi|121638925|ref|YP_979149.1| 39 PLDWaVELDERWVIVGPNGAGKTSLL-RIAAAA 70
                                   477856778999**********9873.233333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.075
                      IstB_IS21  77 svlfvrvedLveelkrarrdgklaralkrllkvdlli 113
                                    +v + r+ d++e+l +++  ++   +l++  + ++li
  gi|121638925|ref|YP_979149.1| 135 AVDYHRAIDMLESLGAEHLANRTYGTLSEGERKRVLI 171
                                    799**************************99999999 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.7e-05     0.052      14      36 ..      44      66 ..      42      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                        DUF3584 14 ldldghtnieGtNaaGKTtLlrL 36
                                   ++ld++  i+G N+aGKT+Llr+
  gi|121638925|ref|YP_979149.1| 44 VELDERWVIVGPNGAGKTSLLRI 66
                                   6799999**************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.7e-05     0.092      19      41 ..      44      65 ..      40      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                         AAA_15 19 idlseeltvliGkNnsGKSsile 41
                                   ++l+e   v++G+N++GK+s+l+
  gi|121638925|ref|YP_979149.1| 44 VELDE-RWVIVGPNGAGKTSLLR 65
                                   78999.99*************97 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.5e-05      0.12       4      37 ..      51      85 ..      49     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.5e-05
                                   EEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-S CS
                           cobW  4 vltGflGsGKTtLlnhll.enraglklavivNefg 37
                                   v++G+ G+GKT+Ll+    +++ +  +a +++e  
  gi|121638925|ref|YP_979149.1| 51 VIVGPNGAGKTSLLRIAAaAEHPSSGVAFVLGERL 85
                                   89************988866667777888887754 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.9e-05     0.095      22      50 ..      51      80 ..      43     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                         AAA_30 22 vltGpAGtGKttalkalreaweaa.ggrvi 50
                                   v++Gp G+GKt +l+ +++a + + g   +
  gi|121638925|ref|YP_979149.1| 51 VIVGPNGAGKTSLLRIAAAAEHPSsGVAFV 80
                                   89*************998877666464433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015       0.2       3      46 ..      52     104 ..      50     119 .. 0.78
   2 ?   -1.5   0.0       2.2   3.1e+03      59      67 ..     179     187 ..     144     258 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                    EESSTTSSHHHHHHHHHHH..........HTHEEEEEETTTCSSSSTTHHHHHH CS
                            AAA   3 lyGppGtGKTllakavake..........lgvefleisgsellskyvgesekki 46 
                                    ++Gp G GKT+l +  a            lg ++ ++++sel+   vg s++ +
  gi|121638925|ref|YP_979149.1|  52 IVGPNGAGKTSLLRIAAAAehpssgvafvLGERLGRVDVSELR-ARVGLSSSAL 104
                                    79************99988677766666557888888888888.5566666555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                    SEEEEEETG CS
                            AAA  59 psilfiDEi 67 
                                    p  l++DE 
  gi|121638925|ref|YP_979149.1| 179 PELLLLDEP 187
                                    455555553 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     9e-05      0.12      16      39 ..      41      64 ..      31      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++ ++l++  +++Gp+G+GK++ll
  gi|121638925|ref|YP_979149.1| 41 DWAVELDERWVIVGPNGAGKTSLL 64
                                   56777778899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1887.69
//
Query:       gi|121638926|ref|YP_979150.1|  [L=409]
Description: phosphoserine phosphatase serB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-29  102.1   0.1    8.9e-29  101.2   0.1    1.5  1  HAD              haloacid dehalogenase-like hydrolase
    5.9e-21   74.2   0.6    7.3e-19   67.5   1.0    3.1  3  ACT_6            ACT domain
    3.9e-20   73.1   0.3    5.6e-20   72.5   0.3    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    4.5e-12   46.2   0.0    1.7e-11   44.3   0.0    1.9  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    8.5e-11   41.4   1.1    7.4e-05   22.4   0.2    2.7  2  ACT              ACT domain
    1.2e-05   25.0   0.0    0.00024   20.7   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    2.4e-05   24.5   0.0    0.00028   21.0   0.0    2.5  1  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0016   18.2   0.0      0.008   16.0   0.1    2.1  2  ACT_7            ACT domain
     0.0033   16.8   0.0       0.11   11.8   0.0    2.1  2  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.23   11.5   0.0    1.4  1  Toxin_ToxA       Proteinaceous host-selective toxin ToxA
       0.17   11.3   0.0       0.25   10.8   0.0    1.1  1  DUF705           Protein of unknown function (DUF705)
       0.23   11.3   0.0       0.45   10.3   0.0    1.6  1  Acid_PPase       Acid Phosphatase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.1   5.9e-32   8.9e-29       1     187 [.     182     349 ..     182     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 5.9e-32
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvaev 80 
                                    ++fD+D TL++g+ +e+l+ + +++g+  + ++++ + +l+++         +  +   a+lagl++ +++++++ ++  
  gi|121638926|ref|YP_979150.1| 182 IVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFA---------ESLQRRVATLAGLPATVIDDVAEQLE-- 250
                                    79**********9999888877777666555555555555554.........444556********777777777773.. PP

                            HAD  81 irpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaalr 159
                                        l+ pga++ ++  r+ G+r+ vvSgg+r+++epl++el  d v ++ele +d  ltg+  + g++v + gk++alr
  gi|121638926|ref|YP_979150.1| 251 ----LM-PGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDFVASNELEIVDgILTGR--VVGPIVDRPGKAKALR 323
                                    ....66.************************************9999999************..**************** PP

                            HAD 160 ewlaaegegidleevvayGDspsDlpll 187
                                    +  +a  +g + e +va+GD+ +D+ +l
  gi|121638926|ref|YP_979150.1| 324 D--FASQYGVPMEQTVAVGDGANDIDML 349
                                    *..***********************98 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   1.0   4.9e-22   7.3e-19       3      73 ..       7      79 ..       6      82 .. 0.90
   2 ?    2.2   0.0      0.12   1.7e+02      44      75 ..     138     169 ..     136     170 .. 0.91
   3 ?   -1.8   0.0       2.1   3.2e+03      11      29 ..     314     332 ..     308     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 4.9e-22
                          ACT_6  3 llitvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlflakelgltv 73
                                   +litvtG+d+pG+t++L++vla++gv +l +eq+vi+grl+Lg+lvs+p d  + ++l+ ++  + +  gl+v
  gi|121638926|ref|YP_979150.1|  7 VLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDvaDGTALRDDVASAIHGVGLDV 79
                                   79***********************************************444477779999988888888887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                          ACT_6  44 LgllvsgpedalarlekaLlflakelgltvef 75 
                                    L l+vs+p   +++l+ aL ++a+e  ++v +
  gi|121638926|ref|YP_979150.1| 138 LELRVSVPPGCVGPLQIALTKVAAEEHVDVAV 169
                                    6789*********************9999865 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                          ACT_6  11 drpGltasLtsvlaefgvn 29 
                                    drpG  ++L +  +++gv+
  gi|121638926|ref|YP_979150.1| 314 DRPGKAKALRDFASQYGVP 332
                                    9999999999999999986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.3   3.8e-23   5.6e-20       2     210 .]     180     353 ..     179     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.8e-23
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                    +++vfD+d TL++ge     vi+ +                     aa  + +g+++ +++     a+++g+ ++ ++l 
  gi|121638926|ref|YP_979150.1| 180 RLIVFDVDSTLVQGE-----VIEML---------------------AARAGAQGQVAAITE-----AAMRGELDFAESL- 227
                                    68*************.....*****.....................999999*********.....*************. PP

                                    CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                      Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..... 156
                                                q++  t a l   a  +  +a++l+++p+a+ ++++L++ g++ ++++g++++  e +a++l      
  gi|121638926|ref|YP_979150.1| 228 ------------QRRVATLAGL--PATVIDDVAEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMldfva 293
                                    ............7777777777..7777777888899************************************7745443 PP

                                    ...GGGESEEEEHHCES.....STTT......SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    ...xxxxxxxxxxxxxx.....xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 ...ddyfdaviasdiet.....vakp......spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        +++d        +     v +p      + ++++  + +++++ e++++VGDg+nD+ +l aAg
  gi|121638926|ref|YP_979150.1| 294 sneLEIVD--------GiltgrVVGPivdrpgKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAG 353
                                    33222223........23435555556644466666666666778*********************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.99   1.5e+03       1      11 [.     182     192 ..     182     195 .. 0.88
   2 !   44.3   0.0   1.2e-14   1.7e-11     188     245 ..     318     374 ..     315     384 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.99
                                    EEEEIIIIIS- CS
                    Hydrolase_3   1 ialDlDGTLln 11 
                                    i++D+D TL++
  gi|121638926|ref|YP_979150.1| 182 IVFDVDSTLVQ 192
                                    89*******86 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.2e-14
                                    HHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                    Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                    K++al+++a+++++++e+++a+GDg NDi ML aaglg+A  na++ + ++Ad    +
  gi|121638926|ref|YP_979150.1| 318 KAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAGLGIAF-NAKPALREVADASLSH 374
                                    9***************************************7.9*********987666 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   4.9e-08   7.4e-05       3      49 ..       9      52 ..       7      69 .. 0.80
   2 !   17.1   0.0   2.3e-06    0.0035       2      63 ..      97     160 ..      96     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.9e-08
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEE CS
                            ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvviv 49
                                   + v   D+PG+ +++f +la++g+ + ++eq   + +   ++  v+v
  gi|121638926|ref|YP_979150.1|  9 ITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGR---LTLGVLV 52
                                   778999*************************999984...4443333 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.3e-06
                                    EEEE.EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHHHHHHHH CS
                            ACT   2 vlrv.gvpDrPGlLarvfgaladrgiNidsieqrssedk.vagivfvvivvdeedleevlealk 63 
                                    +++v g p   G++++v++ +a +g+Nid+i   s+ +  + ++ ++v  ++  +l+ +l ++ 
  gi|121638926|ref|YP_979150.1|  97 TIFVlGRPITAGAFSAVAREVAALGVNIDFIRGISDYPVtGLELRVSVPPGCVGPLQIALTKVA 160
                                    56664666899*********************99999887777777777777777777776665 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.082   1.2e+02       2      18 ..     179     195 ..     178     216 .. 0.81
   2 !   20.7   0.0   1.6e-07   0.00024     163     211 ..     315     362 ..     299     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.082
                                    SEEEEE-TBTTTB.S-H CS
                           S6PP   2 klllvsdLDntlvdgdn 18 
                                    k+l+v d+D+tlv+g+ 
  gi|121638926|ref|YP_979150.1| 179 KRLIVFDVDSTLVQGEV 195
                                    689**********7764 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.6e-07
                                    T-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--H CS
                           S6PP 163 raskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqe 211
                                    r +k++Alr +a+++++++eq++ +Gd  nD+++l +  lg+   na++
  gi|121638926|ref|YP_979150.1| 315 RPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAGLGIAF-NAKP 362
                                    679********************************999999864.5555 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.9e-07   0.00028       1     173 [.     182     354 ..     182     360 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                          HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkp 80 
                                    i+FD+D Tl+  e + + a++  + + ++  ++e  +r  + +    +l++         +++ l  ++ +   + ++++
  gi|121638926|ref|YP_979150.1| 182 IVFDVDSTLVQGEVIEMLAARAGA-QGQVAAITEAAMRGELDFAE--SLQRRV------ATLAGLPATVIDDVAE-QLEL 251
                                    677777777776655554444444.33344555554444333333..222222......2455555666666666.8999 PP

                          HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgie.......syFdvivtsedvekk..KP.dpeviekaleklkl 150
                                    ++g++ ++ +L++ g+++g+v+ + r+ +e   ++l ++       ++ d i+t+  v+     P +++ ++ +  ++++
  gi|121638926|ref|YP_979150.1| 252 MPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDfvasnelEIVDGILTGRVVGPIvdRPgKAKALRDFASQYGV 331
                                    ************************999888776666554333333388999999999987666663478888999999** PP

                          HAD_2 151 kkeeviyvGDsptDieaakkagi 173
                                      e+++ vGD  +Di    +ag+
  gi|121638926|ref|YP_979150.1| 332 PMEQTVAVGDGANDIDMLGAAGL 354
                                    ***********988876655554 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.3e-06     0.008       8      40 ..       4      36 ..       3      38 .. 0.81
   2 ?   -3.6   0.0       6.6   9.9e+03      26      34 ..     278     286 ..     269     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.3e-06
                                   EEEE-S-.---SS--HHHHHHHHHHTTT---EE CS
                          ACT_7  8 klsvvgsglpfdvtGivaklaspLaeagIsifq 40
                                   k+sv  +   +d++G++++l+++La++g++++ 
  gi|121638926|ref|YP_979150.1|  4 KVSVLITVTGMDQPGVTSALFEVLAQHGVELLN 36
                                   66666664444*******************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.6
                                    HHHHHHHTT CS
                          ACT_7  26 klaspLaea 34 
                                    ++++pLa++
  gi|121638926|ref|YP_979150.1| 278 RIIEPLARE 286
                                    799999986 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   7.6e-05      0.11       2      99 ..     181     276 ..     180     292 .. 0.80
   2 ?    2.8   0.0     0.045        67     162     182 ..     326     346 ..     318     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkg..lwnelmdrvlkelheqgvseadikkvlrsiplspglvel 79 
                                    l+vfD D t+++ +  +++   ++a+ + + + e   +g   + e ++r +++l   g   + i +v +++ l pg    
  gi|121638926|ref|YP_979150.1| 181 LIVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGelDFAESLQRRVATLA--GLPATVIDDVAEQLELMPGARTT 258
                                    89************************99999988765441247888888888876..45666788889999999999999 PP

                Put_Phosphatase  80 ikslakkkleldliiiSDaN 99 
                                    i++l+  +l++ + ++S   
  gi|121638926|ref|YP_979150.1| 259 IRTLR--RLGFRCGVVSGGF 276
                                    99994..5788888888665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.045
                Put_Phosphatase 162 qaregveyerliYvGDganDl 182
                                    +++ gv +e+ + vGDganD+
  gi|121638926|ref|YP_979150.1| 326 ASQYGVPMEQTVAVGDGANDI 346
                                    46789999************7 PP

>> Toxin_ToxA  Proteinaceous host-selective toxin ToxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.23      44      96 ..     157     208 ..     138     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                     Toxin_ToxA  44 vrvglsrvvdnslrvditntgranrlivtewdssltrgdvyellgdyalitgr 96 
                                     +v  +  vd +++ d+  + r++rliv + ds+l +g+v e+l   a  +g+
  gi|121638926|ref|YP_979150.1| 157 TKVAAEEHVDVAVE-DYGLAWRTKRLIVFDVDSTLVQGEVIEMLAARAGAQGQ 208
                                    44444444444443.56667799*********************999988886 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.25     121     149 ..     166     194 ..     154     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                         DUF705 121 ssiikelslylkikhvvvfDlDstLitde 149
                                      +++  +l ++ k ++vfD+DstL+  e
  gi|121638926|ref|YP_979150.1| 166 DVAVEDYGLAWRTKRLIVFDVDSTLVQGE 194
                                    44468899*****************9765 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0003      0.45       4      68 ..     180     273 ..     177     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                                    SEEEE-STTTSSSS-TTTS........................S-S-EEE-TTS......-EEETT--EE---TTHHHHH CS
                     Acid_PPase   4 klivFDLDyTLWpfevdtl........................vsaplkkeskks.....evvDrrgeelklypdveeil 54 
                                    +livFD+D TL + ev  +                          + l+++  ++     +v+D   e+l+l+p +++ +
  gi|121638926|ref|YP_979150.1| 180 RLIVFDVDSTLVQGEVIEMlaaragaqgqvaaiteaamrgeldFAESLQRRVATLaglpaTVIDDVAEQLELMPGARTTI 259
                                    89**********999877779999999999998777777666644444444444478888999**************999 PP

                                    HHHHHTT--EEEEE CS
                     Acid_PPase  55 eelkskevklavaS 68 
                                    ++l++ + +  v S
  gi|121638926|ref|YP_979150.1| 260 RTLRRLGFRCGVVS 273
                                    99998666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2847.30
//
Query:       gi|121638927|ref|YP_979151.1|  [L=573]
Description: cytochrome C oxidase polypeptide I ctaD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-151  504.8  66.0   2.3e-151  504.5  66.0    1.0  1  COX1             Cytochrome C and Quinol oxidase polypeptide 
  ------ inclusion threshold ------
       0.32   11.0   6.7        2.9    7.9   0.4    2.9  3  p53-inducible11  Tumour protein p53-inducible protein 11


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.5  66.0  2.5e-155  2.3e-151       2     432 .]      40     483 ..      39     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 504.5 bits;  conditional E-value: 2.5e-155
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-H CS
                           COX1   2 igllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafp 76 
                                    ig++y+++ + ++++ggll+ll+r++la+p     ++e++nql+t+Hg++m+++ atp+++gf+n+++pl++ga+d+afp
  gi|121638927|ref|YP_979151.1|  40 IGIMYCVACISFFFIGGLLALLMRTELAAPglqflSNEQFNQLFTMHGTIMLLFYATPIVFGFANLVLPLQIGAPDVAFP 119
                                    89**************************997777777******************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHH...CSS-STTTTTTTC.........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COX1  77 rlnalsfwlvvlgvvllllsll...gaattgwteYapls........evdlwllglllvvvssllgainfivtilkrrap 145
                                    rlna+sfwl+v+g+++ +++++   gaa+ gwt+Y+pl+        ++dlw++gl++++++++lga+n+i+t++ +rap
  gi|121638927|ref|YP_979151.1| 120 RLNAFSFWLFVFGATIGAAGFItpgGAADFGWTAYTPLTdaihspgaGGDLWIMGLIVAGLGTILGAVNMITTVVCMRAP 199
                                    ********9999999988899889888***************************************************** PP

                                    TT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                           COX1 146 gmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdplldqhlfWffgHpeVyililpalgivy 222
                                    gmt++++p+f+w++++t+ilil+a+p l++al  l +dr+lg +++++  g  ll+qhlfWffgHpeVyi+ lp++giv+
  gi|121638927|ref|YP_979151.1| 200 GMTMFRMPIFTWNIMVTSILILIAFPLLTAALFGLAADRHLGaHIYDAanGGVLLWQHLFWFFGHPEVYIIALPFFGIVS 279
                                    **********************************************9989****************************** PP

                                    HHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCCTTS-CHCHH CS
                           COX1 223 yilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatlwrgsirfkt 302
                                    +i+p+f+++p+f+y+ +v+a+++i+ ls+ vwaHH+f tg   +l  ++s++++liavP+g+k+fnw++t+w+g+++f+t
  gi|121638927|ref|YP_979151.1| 280 EIFPVFSRKPIFGYTTLVYATLSIAALSVAVWAHHMFATGA--VLLPFFSFMTYLIAVPTGIKFFNWIGTMWKGQLTFET 357
                                    ***************************************98..9************************************ PP

                                    HHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHHHHHHHH CS
                           COX1 303 pmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserlaklhfwl 382
                                    pmlf++gf+v+f++gGltGvlla+p+++++v ++y+vvaHfH+vl+g++vf++fa+iy+++pk+tgr+l+erl+klhfwl
  gi|121638927|ref|YP_979151.1| 358 PMLFSVGFMVTFLLGGLTGVLLASPPLDFHVTDSYFVVAHFHYVLFGTIVFATFAGIYFWFPKMTGRLLDERLGKLHFWL 437
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                           COX1 383 lfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                    +fiG++ +fl +h+lG  gmprr+ady +     + +q lnv++tig+++
  gi|121638927|ref|YP_979151.1| 438 TFIGFHTTFLVQHWLGDEGMPRRYADYLP----TDGFQGLNVVSTIGAFI 483
                                    ***************************65....68*************96 PP

>> p53-inducible11  Tumour protein p53-inducible protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4   0.00032       2.9      90     133 ..     189     232 ..     182     243 .. 0.89
   2 ?    5.4   0.4    0.0019        17     131     178 ..     296     347 ..     288     350 .. 0.82
   3 ?   -2.4   0.0      0.46   4.1e+03      56      77 ..     400     421 ..     396     432 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00032
                p53-inducible11  90 tkisilalrlyGgallalalilWnalttaekviirwtLllealy 133
                                    + ++++++r  G +++ + + +Wn + t+  ++i + Ll+ al+
  gi|121638927|ref|YP_979151.1| 189 MITTVVCMRAPGMTMFRMPIFTWNIMVTSILILIAFPLLTAALF 232
                                    4566789********************************99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0019
                p53-inducible11 131 alylaiqvlvtavtlveseslstaavl....lllsrllalvislyfYallgr 178
                                     +y ++ + +++v+++ +++++t+avl    + ++ l+a+ + + f++ +g 
  gi|121638927|ref|YP_979151.1| 296 LVYATLSIAALSVAVWAHHMFATGAVLlpffSFMTYLIAVPTGIKFFNWIGT 347
                                    68999********************983333467788888888999988875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.46
                p53-inducible11  56 WqllsavvftalallalvfPdt 77 
                                    + l+ ++vf+++a + + fP+ 
  gi|121638927|ref|YP_979151.1| 400 YVLFGTIVFATFAGIYFWFPKM 421
                                    5789999******999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3704.44
//
Query:       gi|121638928|ref|YP_979152.1|  [L=359]
Description: FeIII-dicitrate-binding periplasmic lipoprotein fecB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-17   63.2   0.1    3.8e-17   62.6   0.1    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   2.1e-21   3.8e-17       1     236 [.      92     332 ..      92     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.1e-21
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee...aivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                    i++ls ++ + l alG+  ++v+ +  +s ++    l     + + vg+++ +d+ ++aa++PDl+++s+gl  t + + 
  gi|121638928|ref|YP_979152.1|  92 IVVLSGDQLDALCALGLQSRIVAAALPNSSSSQPSYLGTtvhDLPGVGTRSAPDLRAIAAAHPDLILGSQGL--TPQLYP 169
                                    8************************9999999888777799999****************************..****** PP

                                    HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TT CS
                   Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsn 157
                                    +l++++ptv+       +++++++r +g ++ + ++ ++l++ + +   ++++++d     + +v  +a+     v g n
  gi|121638928|ref|YP_979152.1| 170 QLAAIAPTVFTAAPG--ADWENNLRGVGAATARIAAVDALITGFAEHATQVGTKHDATHFQASIVQLTANT--MRVYGAN 245
                                    **********99998..9****************************************6666666666666..669999* PP

                                    STTTHHHHTS--EES.TTT--........STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHT CS
                   Peripla_BP_2 158 syigdlldalgieni.aaesk........kseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkn 228
                                    ++   +l+a+g++    + +         + +++      ++a+d+d+++ s+  ++ + ++++ ++ ++ + +l A + 
  gi|121638928|ref|YP_979152.1| 246 NFPASVLSAVGVDRPpSQRFTdkayieigTTAADLAKSPDFSAADADIVYLSCA-SEAAAERAAVILDSDPWRKLSANRD 324
                                    *************994555447777777656666666666777***********.************************* PP

                                    T-EEEE-H CS
                   Peripla_BP_2 229 grVyalds 236
                                    +rV+ +++
  gi|121638928|ref|YP_979152.1| 325 NRVFVVND 332
                                    ****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2795.94
//
Query:       gi|121638929|ref|YP_979153.1|  [L=346]
Description: NADP-dependent alcohol dehydrogenase adhC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-29  100.6   2.4      8e-29   99.7   2.4    1.4  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    2.3e-16   60.0   0.1    4.7e-16   59.0   0.0    1.5  2  ADH_zinc_N     Zinc-binding dehydrogenase
     0.0005   21.1   0.0     0.0008   20.5   0.0    1.3  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
      0.006   15.9   0.0      0.011   15.0   0.0    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.038   13.3   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.14   12.6   0.0       0.26   11.7   0.0    1.3  1  NAD_binding_7  Putative NAD(P)-binding
       0.18   11.7   0.0       0.31   10.9   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   2.4   3.1e-32     8e-29       1     108 [.      28     143 ..      28     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 3.1e-32
                                    TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT-GG CS
                          ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkegeen 79 
                                    p++v i++k agiC+sD+h++k  ++ + ++p+++GHEi+G+v +vg+ev+k++ GdrV v +++  c eC++C++g e+
  gi|121638929|ref|YP_979153.1|  28 PHDVAIDIKFAGICHSDIHTVKA-EWGQPNYPVVPGHEIAGVVTAVGSEVTKYRQGDRVGVGCFVDsCRECNSCTRGIEQ 106
                                    689*******************9.8************************************999888************* PP

                                    G-TTBEETTTS........S-SSSBSEEEECGGGEEE CS
                          ADH_N  80 lCeeakllgvs........ldGgfaeyvvvpekklvk 108
                                    +C+ ++ ++++        ++Gg++e +vv+e+++++
  gi|121638929|ref|YP_979153.1| 107 YCKPGANFTYNsigkdgqpTQGGYSEAIVVDENYVLR 143
                                    **88888888888899999*************99976 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   6.4e+03      20      67 ..      72     120 ..      66     124 .. 0.52
   2 !   59.0   0.0   1.8e-19   4.7e-16       1     129 [.     185     307 ..     185     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                                    EESSHHHHHHHHHTTESEEEET.TTC.HHHHHHHHHTTTSSEEEEEESSC CS
                     ADH_zinc_N  20 vdsseeklelakklGadeviny.kea.dlverikeltggegvdvvfecvG 67 
                                    v s   k ++  + G+  ++++ +e+ +    i++ ++  g+++ ++ +G
  gi|121638929|ref|YP_979153.1|  72 VGSEVTKYRQGDRVGVGCFVDScRECnSCTRGIEQYCK-PGANFTYNSIG 120
                                    44444455666666666666665444445555555553.35555555555 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1.8e-19
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                    g+G+++v+l +a+Ga v++ + s +k e   +lGa+ ++ +      +  ++l g  g+d+++++v ++  l ++l+ll+
  gi|121638929|ref|YP_979153.1| 185 GLGHMGVKLGAAMGADVTVLSQSLKKMEDGLRLGAKSYYAT---ADPDTFRKLRG--GFDLILNTVSANLDLGQYLNLLD 259
                                    89***************************************...45889999994..9********************** PP

                                    EEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  81 pgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                     +G+lv  G+++++  ++++ l+l ++s+ Gs+ g+   e +e+l+++a
  gi|121638929|ref|YP_979153.1| 260 VDGTLVELGIPEHPMAVPAFALALMRRSLAGSNIGG-IAETQEMLNFCA 307
                                    ************************************.999999999876 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.1e-07    0.0008       1     107 [.     217     316 ..     217     336 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-07
                                    TT-SEEEETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GG CS
                   ADH_zinc_N_2   1 lGAdevidyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflf 79 
                                    lGA+  +     + f +++ ++g+D++l+tv  +  l + l++l+  G+lv++g p  + a+++ a+   +rs+  + + 
  gi|121638929|ref|YP_979153.1| 217 LGAKSYYATAdPDTF-RKL-RGGFDLILNTVSANLDLGQYLNLLDVDGTLVELGIPEHPMAVPAFALALMRRSLAGSNIG 294
                                    577776744535566.577.678*********66666*******888*****9965544444444444444555555554 PP

                                    G...-.-HHHHHHHHHHHHHHH----EE CS
                   ADH_zinc_N_2  80 smkasaqadileelaalieeGklrpvvd 107
                                        +  a+  +e++++++e+ ++p ++
  gi|121638929|ref|YP_979153.1| 295 ----G-IAE-TQEMLNFCAEHGVTPEIE 316
                                    ....3.555.778888888888887775 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.3e-06     0.011      28      99 ..     175     245 ..     170     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtv 99 
                                    + +v +iG G  G   ++  +++ga+Vtvl  + +++e    lgak     +++ +++++     d++  tv
  gi|121638929|ref|YP_979153.1| 175 NTRVAIIGLGGLGHMGVKLGAAMGADVTVLSQSLKKMEDGLRLGAK-SYYATADPDTFRKLRGGFDLILNTV 245
                                    579************************************999***9.7888999999999999999998887 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.038      35      73 ..     174     212 ..     166     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                    TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                    ++ +v+iiGlG +G+   k+ +a+g++v++ ++s kk e
  gi|121638929|ref|YP_979153.1| 174 ANTRVAIIGLGGLGHMGVKLGAAMGADVTVLSQSLKKME 212
                                    5789****************************9988766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.26       7      55 ..     175     223 ..     173     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkl.aeeel 55 
                                    + +v ++G G ++   v+  ++ ga+vtv+++ +k+  +  ++l a++++
  gi|121638929|ref|YP_979153.1| 175 NTRVAIIGLGGLGHMGVKLGAAMGADVTVLSQSLKKMED-GLRLgAKSYY 223
                                    679******************************655544.3443133332 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.31       2      52 ..     178     228 ..     177     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek 52 
                                    va+iG G +G+   ++ a+ g +V+++  s +++e++l+  +ks+   +  
  gi|121638929|ref|YP_979153.1| 178 VAIIGLGGLGHMGVKLGAAMGADVTVLSQSLKKMEDGLRLGAKSYYATADP 228
                                    9*****************************999999988777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2153.10
//
Query:       gi|121638930|ref|YP_979154.1|  [L=124]
Description: hypothetical protein BCG_3070c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-29  100.5   0.0    7.7e-29  100.3   0.0    1.0  1  DUF3349          Protein of unknown function (DUF3349)
  ------ inclusion threshold ------
      0.056   13.3   0.1        2.4    8.1   0.1    2.1  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   8.6e-33   7.7e-29       2      94 ..      10     105 ..       9     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 8.6e-33
                                    HHHHHHHHHHHH-TT-B-HHHHHHHHHHHCTT.--HHHHHHHHHHHHHH--...SSS.BSHHHCHHHHHHHCTS---HHH CS
                        DUF3349   2 llasileWLragYPegvPeqdyvpLlalLrrr.Lsdeevkevaeelvaeaa..eadeavdeedieelitkvteeepseed 78 
                                    +++s+l+WL+ gYPegvP  d+v+Ll+lLr++ L++e++ ev+++++++++   ad+ +d+++i+e+i++vt++++ +e+
  gi|121638930|ref|YP_979154.1|  10 FFRSVLRWLQVGYPEGVPGPDRVALLSLLRSTpLTEEQIGEVVRHFTENGSpaVADRVIDRDEIAEFISEVTHHDAGPEN 89 
                                    789****************************99*****************66699************************* PP

                                    HHHHHHHHHTTT-GCC CS
                        DUF3349  79 varVaarLaaggwpla 94 
                                    ++rVa  Laa+gwpla
  gi|121638930|ref|YP_979154.1|  90 IQRVAGILAAAGWPLA 105
                                    **************97 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00027       2.4       7      29 ..      37      59 ..      33     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00027
                                   HHTT.---HHHHHHHHHHHHTTS CS
                Glycos_trans_3N  7 lrdgeeLtaeeirfaihgilkge 29
                                   l++   Lt+e+i +++++++++ 
  gi|121638930|ref|YP_979154.1| 37 LLRSTPLTEEQIGEVVRHFTENG 59
                                   66777899999999999988843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 798.13
//
Query:       gi|121638931|ref|YP_979155.1|  [L=94]
Description: hypothetical protein BCG_3071c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 647.11
//
Query:       gi|121638932|ref|YP_979156.1|  [L=324]
Description: ribonucleotide-diphosphate reductase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-90  303.6   0.0    1.6e-90  303.4   0.0    1.0  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.4   0.0   8.8e-95   1.6e-90       2     279 .]      14     285 ..      13     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 8.8e-95
                                    T-TTS-SSHHHHHHHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSSHHH CS
                 Ribonuc_red_sm   2 fvlfpikypeiwelykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevqipea 81 
                                    +++++++++++ e++++l+ nfW+pe+v++s+D+ +w  +L+  ek+++++v+++l++ldti++++++ +l++++ +p++
  gi|121638932|ref|YP_979156.1|  14 INWNRLQDEKDAEVWDRLTGNFWLPEKVPVSNDIPSWG-TLTAGEKQLTMRVFTGLTMLDTIQGTVGAVSLIPDALTPHE 92 
                                    89***********************************9.5**************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSCHHHHHHHHHHHHHHHCCC CS
                 Ribonuc_red_sm  82 rafygfqaamEniHaesYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskkdeekfaerlvafallegilf 161
                                    +a+++++a+mE++Ha+sYs +++tl+ +++e+d++f++ een +lq+kae++ ++y+ ++     ++r+va++lle++lf
  gi|121638932|ref|YP_979156.1|  93 EAVLTNIAFMESVHAKSYSQIFSTLC-STAEIDDAFRWSEENRNLQRKAEIVLQYYRGDE----PLKRKVASTLLESFLF 167
                                    **************************.*****************************9655....356************* PP

                                    HHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                 Ribonuc_red_sm 162 ysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkeen.elenkeleeeveelikeavelEkefitdalp 240
                                    ysgF++++++++r +l+++a++i+li+rDe++H++++g++f++ ++   + +++el+++++el+ e++++E e+++d+++
  gi|121638932|ref|YP_979156.1| 168 YSGFYLPMYWSSRAKLTNTADMIRLIIRDEAVHGYYIGYKFQRGLALVdDVTRAELKDYTYELLFELYDNEVEYTQDLYD 247
                                    ********************************************99999******************************7 PP

                                    T.BTTCHHHHHHHHHHHHHHHHHHCTT---SS-TT..---C CS
                 Ribonuc_red_sm 241 vellglnkedvkqYieyvadrllmnlgyeklYnve..eenP 279
                                       +gl+ edvk++++y+a+++lmnlgye+l++ +  ++nP
  gi|121638932|ref|YP_979156.1| 248 E--VGLT-EDVKKFLRYNANKALMNLGYEALFPRDetDVNP 285
                                    7..7999.9************************98778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2325.22
//
Query:       gi|121638933|ref|YP_979157.1|  [L=524]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-17   62.0   0.0      9e-15   54.7   0.0    2.9  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.2e-16   60.3   0.0    2.4e-15   56.0   0.0    2.2  2  FMO-like       Flavin-binding monooxygenase-like
      3e-13   49.8   1.6    7.3e-13   48.6   0.0    2.5  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.6e-10   38.1   0.0    4.2e-06   26.1   0.0    3.0  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    8.9e-06   25.1   0.0    0.00018   20.8   0.0    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.5e-05   22.5   0.3    0.00063   19.4   0.0    2.4  3  DAO            FAD dependent oxidoreductase
    0.00047   19.3   0.0    0.00081   18.6   0.0    1.4  1  FAD_binding_2  FAD binding domain
     0.0025   17.1   0.1     0.0045   16.3   0.1    1.4  1  FAD_binding_3  FAD binding domain
     0.0025   17.8   0.1      0.059   13.4   0.0    2.5  3  NAD_binding_9  FAD-NAD(P)-binding
     0.0044   17.5   0.7      0.021   15.4   0.1    2.1  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.048   12.9   0.0    1.6  2  Amino_oxidase  Flavin containing amine oxidoreductase
      0.044   13.0   0.3        0.1   11.8   0.1    1.7  2  Thi4           Thi4 family
       0.14   10.9   0.5       0.22   10.2   0.5    1.3  1  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   6.5e-18     9e-15       1     204 [.      26     227 ..      26     242 .. 0.81
   2 ?    2.7   0.0     0.046        63     234     270 ..     327     362 ..     281     377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.5e-18
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeekls 79 
                                    +IiG G  Gl++ai+l+k g+ d++ilEk+  +g ++++        +         ip     s + +p+   k+    
  gi|121638933|ref|YP_979157.1|  26 VIIGTGFSGLGMAIALQKQGV-DFVILEKAdDVGGTWRDNTYPGCACD---------IPS-HLYSFSFEPKADWKHLFSY 94 
                                    7********************.8*******999999986444443333.........322.2333334455556666778 PP

                    Pyr_redox_3  80 rkealeYlrevaksfelp..iklfeeVesvkkedeg..fevetske.tyeAkkviiAtGefdkPnklnipGeek...lvk 151
                                     +e+l Yl+ v++++ l+  i+ ++ V +   +d++   +v t  + +y A+++i  +G  ++P +++i G ++    + 
  gi|121638933|ref|YP_979157.1|  95 WDEILGYLKGVTDKYGLRryIEFNSLVDRGYWDDDEcrWHVFTADGrEYVAQFLISGAGALHIPSFPEIAGRDEfagPAF 174
                                    89***************777999999988776555434667666655*************************98544578 PP

                    Pyr_redox_3 152 hyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekees 204
                                    h+++ ++  +++g++v+++G + Sa+ +  e+v + ae +++ r+ ++   ++
  gi|121638933|ref|YP_979157.1| 175 HSAQWDHSIDLTGKRVAIVGTGASAIQIVPEIVGQVAELQLYQRTPPWVVPRT 227
                                    999999999************************************99866544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.046
                    Pyr_redox_3 234 evkeikekeeeykvktedgkkvevkddvvlatGykpd 270
                                    ++++i+++   ++   +  + +++ d +v+atG++ +
  gi|121638933|ref|YP_979157.1| 327 RIDRITHD-GIVTADGTGREVFREADVIVYATGFHVT 362
                                    67777764.5555555555666777778888***976 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   1.7e-18   2.4e-15       3     225 ..      24     229 ..      22     250 .. 0.87
   2 ?    1.8   0.0     0.046        64     299     332 ..     325     361 ..     275     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.7e-18
                       FMO-like   3 kvaviGaGvsGlasikccleegleptcfersddiGGlwrfkenveeGrasiyksvvsnsskemscfsdfplpedypnflh 82 
                                    +  +iG+G sGl    +  ++g++ + +e++dd+GG wr  +n+  G a        +    +  fs  p  +    f  
  gi|121638933|ref|YP_979157.1|  24 RAVIIGTGFSGLGMAIALQKQGVDFVILEKADDVGGTWR--DNTYPGCA-------CDIPSHLYSFSFEPKADWKHLFSY 94 
                                    6679********99999999******************8..55555555.......566667788887787777778888 PP

                       FMO-like  83 nsklleylklfakefdllkyiqfkttvcsvkkrpdfstsGqwevvtekegkkesavfdavmvctGhhvnphlplesfpGi 162
                                     +++l ylk  +++++l +yi+f++ v       d     +w+v t  +g++ +a f  ++  +G +  p +p     G 
  gi|121638933|ref|YP_979157.1|  95 WDEILGYLKGVTDKYGLRRYIEFNSLVDRGYWDDD---ECRWHVFTA-DGREYVAQF--LISGAGALHIPSFPE--IAGR 166
                                    99**********************99876655555...569***995.899888877..677888888888885..6699 PP

                       FMO-like 163 ekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvlsrvsd 225
                                    ++f G  fhs ++ +   ++gkrv ++G G s+ +i  e+  + +++ l  r+  wv+ r  +
  gi|121638933|ref|YP_979157.1| 167 DEFAGPAFHSAQWDHSIDLTGKRVAIVGTGASAIQIVPEIVGQVAELQLYQRTPPWVVPRTNE 229
                                    ***********************************************************9876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.046
                       FMO-like 299 kssvkeltetsaifedgt...veedidvvifatGytf 332
                                      ++ ++t   ++  dgt   v+ + dv+++atG+  
  gi|121638933|ref|YP_979157.1| 325 TDRIDRITHDGIVTADGTgreVFREADVIVYATGFHV 361
                                    56788899999999999833345589********964 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   5.3e-16   7.3e-13       1      67 [.      27      94 ..      27      95 .. 0.94
   2 ?   -2.1   0.4       3.3   4.6e+03       1       8 [.     192     199 ..     192     202 .. 0.89
   3 ?   -3.0   0.0       6.5   8.9e+03      42      54 ..     479     495 ..     467     502 .. 0.55

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.3e-16
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---E.EETTHHHHCHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahif.hgsgyypnvrrllre 67
                                   I+G+G+sGl +A +L+k+g+d ++lek+d++GG ++++++pg+++d + h + +++++   +++l+ +
  gi|121638933|ref|YP_979157.1| 27 IIGTGFSGLGMAIALQKQGVDFVILEKADDVGGTWRDNTYPGCACDIPSHLYsFSFEPKADWKHLFSY 94
                                   9**************************************************98888888888888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                                    EE--SHHH CS
                  NAD_binding_8   1 IvGaGlsG 8  
                                    IvG+G+s+
  gi|121638933|ref|YP_979157.1| 192 IVGTGASA 199
                                    9*****97 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.5
                                    T....CEECTS---EEE CS
                  NAD_binding_8  42 g....vrvdygahifhg 54 
                                    g     ++ y ++++ +
  gi|121638933|ref|YP_979157.1| 479 GkntvLWCGYTWQYWLT 495
                                    12345666677777766 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0025       3.5       6      39 ..      26      57 ..      23      74 .. 0.87
   2 !   26.1   0.0   3.1e-09   4.2e-06     110     219 ..     112     215 ..      95     227 .. 0.83
   3 ?    1.4   0.0      0.11   1.5e+02     323     341 ..     342     360 ..     323     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                    K_oxygenase  6 igiGiGpsnLsLailleevkkelkalflerqpef 39
                                   ++iG G s L++ai+l+++   ++ + le+ +++
  gi|121638933|ref|YP_979157.1| 26 VIIGTGFSGLGMAIALQKQG--VDFVILEKADDV 57
                                   89****************99..999999998764 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.1e-09
                    K_oxygenase 110 eeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvG..tepkiPevleklegkervvHsseylerkee 187
                                       ++f++ v++  +d++e   +++v +     + +e+ a+ l+ g G    p+ Pe++ + e     +Hs++  +++  
  gi|121638933|ref|YP_979157.1| 112 RRYIEFNSLVDRGYWDDDE--CRWHVFT----ADGREYVAQFLISGAGalHIPSFPEIAGRDEFAGPAFHSAQWDHSI-- 183
                                    5567788888888888765..4567776....34689***********8779*********9999*************.. PP

                    K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkvel 219
                                    +l++kr+a+vG G Sa +i+ +++ + ++ +l
  gi|121638933|ref|YP_979157.1| 184 DLTGKRVAIVGTGASAIQIVPEIVGQVAELQL 215
                                    89********************9999885544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                    K_oxygenase 323 sgeeetlevdavvlATGYr 341
                                    +g+e   e+d++v+ATG++
  gi|121638933|ref|YP_979157.1| 342 TGREVFREADVIVYATGFH 360
                                    66777889*********97 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.3e-07   0.00018       2     156 ..      24     201 ..      23     241 .. 0.79
   2 ?    1.8   0.1     0.081   1.1e+02     208     250 ..     330     370 ..     315     389 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeiasevvkklnqgielllg 72 
                                    + v+iG G+ Gl +a+ l+++g++ +++e         +++t ++  c +++ l +++ +++   +++ ++  +i  +l+
  gi|121638933|ref|YP_979157.1|  24 RAVIIGTGFSGLGMAIALQKQGVDFVILEkaddvggtwRDNTYPGCACDIPSHLYSFSFEPKADWKHLFSYWDEILGYLK 103
                                    679*************************8888888999999999999999999999998887666888888888777777 PP

                                    CTCEEEEESC.EEEEETEEEC...............TCEEEEEESEEEE---E..EE-BCTCTTC.TTBEECCSECHHHH CS
                                    xxxxxxxxxx.xxxxxxxxxx...............xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  73 eevvkidpgk.kkvklekkke...............gdeekiaydklvlAtGs..sprdlgipGvaenvgklvrtldsae 134
                                      v++  +g  + ++ + +++                d++++ ++ l+   G+   p  + i G  e +g    +++sa+
  gi|121638933|ref|YP_979157.1| 104 -GVTDK-YGLrRYIEFNSLVDrgywdddecrwhvftADGREYVAQFLISGAGAlhIPSFPEIAGRDEFAG---PAFHSAQ 178
                                    .34444.33325556655666777777777888888999*************965566669999977775...5577777 PP

                                    HHCC.SS-TSEEEEES-SHHHHH CS
                                    xxxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 135 alkl.kllpkrivvvGgGyiGvE 156
                                      ++ +l+ kr+++vG G+ ++ 
  gi|121638933|ref|YP_979157.1| 179 WDHSiDLTGKRVAIVGTGASAIQ 201
                                    5554055559********99876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.081
                                    EEEETTEEEEEEETTSCE..EEESEEEE-S-EEES-HHCSHCCT- CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 208 eidgngeklevvledgee..idadlvvvavGvrpstelleeklgl 250
                                    +i+ +g    + +++g+e   +ad +v+a+G+   ++     +++
  gi|121638933|ref|YP_979157.1| 330 RITHDGI--VTADGTGREvfREADVIVYATGFHVTDSY--TYVQI 370
                                    4444443..34555666677788888888888877654..33444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.6e-07   0.00063       2      41 ..      25      65 ..      24     112 .. 0.85
   2 ?   -0.6   0.0      0.57   7.9e+02     180     205 ..     337     362 ..     313     396 .. 0.68
   3 ?   -1.4   0.0         1   1.4e+03      37      68 ..     463     493 ..     419     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.6e-07
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns 41
                                    viiG G  Gl+ A +L+++g   ++lek+d++g g+   n+
  gi|121638933|ref|YP_979157.1| 25 AVIIGTGFSGLGMAIALQKQGvdFVILEKADDVG-GTWRDNT 65
                                   69****************99**************.9977776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                                    EEEEEECTEEE..EEEEEEEE--GGGHH CS
                            DAO 180 wgverttpgen..daadavVnaaGawsd 205
                                    ++  + t g++  ++ad +V a+G +++
  gi|121638933|ref|YP_979157.1| 337 VTA-DGT-GREvfREADVIVYATGFHVT 362
                                    222.222.3222347799******8865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1
                                    GGSSEEEEESSSSTHHSTHHHHHHHHHHHHHH CS
                            DAO  37 Sgrnsgllhsglrylpeaselarlslealeel 68 
                                    S  nsg ++s++   +++   + ++ ++++++
  gi|121638933|ref|YP_979157.1| 463 SVWNSGGCRSWY-LDEHGKNTVLWCGYTWQYW 493
                                    677888888854.3555556778888888888 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.9e-07   0.00081       2      37 ..      25      60 ..      24     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.9e-07
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                   +++iG+G++GL  A++++++G + +++ek++ +gg+
  gi|121638933|ref|YP_979157.1| 25 AVIIGTGFSGLGMAIALQKQGVDFVILEKADDVGGT 60
                                   69*****************************99995 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.3e-06    0.0045       2      35 ..      23      56 ..      22      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   t  +I+G+G +Gl  a  L+++Gv+ v++ek ++
  gi|121638933|ref|YP_979157.1| 23 TRAVIIGTGFSGLGMAIALQKQGVDFVILEKADD 56
                                   7789**************************9865 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   4.3e-05     0.059       1      72 [.      26      94 ..      26     116 .. 0.81
   2 ?    1.5   0.0      0.19   2.6e+02       1      20 [.     191     210 ..     191     231 .. 0.79
   3 ?   -3.5   0.0       6.8   9.3e+03     135     154 ..     337     358 ..     323     359 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftddp...ptfaeW 72
                                   +i+G G++Gl ++ +L ++      ++  + +++    g+ wr++  +     +p++  s+  + +   +++  +
  gi|121638933|ref|YP_979157.1| 26 VIIGTGFSGLGMAIALQKQ-----GVDFVILEKADDV-GGTWRDNTYPGCACDIPSHLYSFSFEPKadwKHLFSY 94
                                   7***************988.....6********9998.9*****9998888888888777554433556555555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    aivG G++++ ++ +++ + 
  gi|121638933|ref|YP_979157.1| 191 AIVGTGASAIQIVPEIVGQV 210
                                    8**********999988775 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.8
                  NAD_binding_9 135 avlladgasl..aadaVvLAlG 154
                                         +g+++  +ad +v A+G
  gi|121638933|ref|YP_979157.1| 337 VTADGTGREVfrEADVIVYATG 358
                                    3333344443368999999998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.5e-05     0.021       1      35 [.      24      58 ..      24      65 .. 0.91
   2 ?   -0.2   0.1       1.1   1.6e+03       1      13 [.     189     201 ..     189     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   ++v++G G++gl +A al++ g +  ++e +d + 
  gi|121638933|ref|YP_979157.1| 24 RAVIIGTGFSGLGMAIALQKQGVDFVILEKADDVG 58
                                   68***************************999876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                    EEEEECSSHHHHH CS
                      Pyr_redox   1 kvvvvGgGyiglE 13 
                                    +v++vG G +++ 
  gi|121638933|ref|YP_979157.1| 189 RVAIVGTGASAIQ 201
                                    799******9986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.5e-05     0.048       1      35 [.      32      63 ..      32      97 .. 0.87
   2 ?   -2.6   0.2       1.9   2.6e+03     234     264 ..     328     361 ..     324     364 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEE CS
                  Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrs 35
                                   ++GL  A  L+ +G+d+++lE  d vGG   t+r+
  gi|121638933|ref|YP_979157.1| 32 FSGLGMAIALQKQGVDFVILEKADDVGG---TWRD 63
                                   69**************************...4444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                    EEE.ETTCEEEEETTSTEE..EESEEEE-S-HHH CS
                  Amino_oxidase 234 ikr.egdgvtvtledgevv..eaDaVvvTvplgv 264
                                    i+r   dg+ +   +g++v  eaD +v ++ + v
  gi|121638933|ref|YP_979157.1| 328 IDRiTHDGIVTADGTGREVfrEADVIVYATGFHV 361
                                    55553455444445555556********998876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.6e-05       0.1      20      58 ..      25      61 ..      20      65 .. 0.88
   2 ?   -2.9   0.0       2.4   3.3e+03      12      30 ..     182     200 ..     174     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                    vi+G+G sGL  a  l k+ ++  +ile+   +GG +w
  gi|121638933|ref|YP_979157.1| 25 AVIIGTGFSGLGMAIALQKQ-GVDFVILEKADDVGG-TW 61
                                   69******************.********9888765.55 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                                    HHHHTEEEEEEE--SHHHH CS
                           Thi4  12 llkyaesDvvivGaGssGL 30 
                                     +++    v+ivG+G+s +
  gi|121638933|ref|YP_979157.1| 182 SIDLTGKRVAIVGTGASAI 200
                                    5666777899999999976 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00016      0.22       2      36 ..      24      58 ..      23      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   + ++iG G +Gl  Ai+++k+g + ++leka+ +g
  gi|121638933|ref|YP_979157.1| 24 RAVIIGTGFSGLGMAIALQKQGVDFVILEKADDVG 58
                                   579***************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3545.16
//
Query:       gi|121638934|ref|YP_979158.1|  [L=246]
Description: AsnC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-12   46.9   0.0    3.8e-12   45.8   0.0    1.6  1  TetR_N          Bacterial regulatory proteins, tetR family
    3.4e-05   24.6   4.6    4.5e-05   24.1   1.4    2.2  2  TetR_C_15       Tetracyclin repressor-like, C-terminal domain
    3.7e-05   24.0   0.4    6.8e-05   23.1   0.4    1.5  1  TetR_C_24       Tetracyclin repressor-like, C-terminal domain
     0.0081   15.9   0.0       0.02   14.7   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   14.6   0.2      0.055   12.8   0.0    1.8  2  LysR_substrate  LysR substrate binding domain
      0.018   14.6   0.0      0.031   13.9   0.0    1.3  1  Ribosomal_S3Ae  Ribosomal S3Ae family
       0.12   12.3   0.0       0.27   11.1   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.5e-15   3.8e-12       1      47 []      35      80 ..      35      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.5e-15
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   I+daA + + + G + ++vr+IA++AG++k+ +Yr+F++K +Llea+
  gi|121638934|ref|YP_979158.1| 35 IVDAAFRAIDRLGPE-LSVRQIAEEAGTAKPKIYRHFTDKSDLLEAI 80
                                   89*************.*****************************97 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.25   6.5e+02      31      67 ..      18      55 ..       6      57 .. 0.82
   2 !   24.1   1.4   1.8e-08   4.5e-05       3     105 ..     104     215 ..     102     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.25
                      TetR_C_15 31 apslgel.elvealeqriaealaalLarrrpelppedl 67
                                    +++++  e+ + ++++i++a+ + ++r  pel+++++
  gi|121638934|ref|YP_979158.1| 18 DARSERWrEHRKKVRNEIVDAAFRAIDRLGPELSVRQI 55
                                   45778887888999999999999999999999987765 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.8e-08
                      TetR_C_15   3 eealdalvdallaahrenpalrrvlleeapslgel.elveale..qriaealaalLa..rrrpelppedlelaafvavea 77 
                                    +e++++ v++++ +  ++p ++rv+ + + s +++ + v+ l+  ++i+ a+a++++   r  el  + lelaaf a+ +
  gi|121638934|ref|YP_979158.1| 104 REVIRRSVEEYVNLVDQHPNVLRVFIQGR-SAKQSeATVRTLNegREITLAMAEMFNneLREMELNRAALELAAFAAFGS 182
                                    799************************99.55555466666652279999******6225778889999*********** PP

                      TetR_C_15  78 veallhlaleedp.....adrealiaelkrlll 105
                                    + + +++ l  +p     + re+++a+l++ ++
  gi|121638934|ref|YP_979158.1| 183 AASATEWWLGPEPdsprrMPREQFVAHLTTIMM 215
                                    ***********9988888889999999988876 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   2.7e-08   6.8e-05       2      91 ..     101     190 ..     100     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.7e-08
                                    SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHH CS
                      TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalail 81 
                                    +s++e +r+ v+++v+++ ++++  +v+++ + a + e+  +  +  re++  ++++ +   ++ e++++  +laa+a +
  gi|121638934|ref|YP_979158.1| 101 DSAREVIRRSVEEYVNLVDQHPNVLRVFIQGRSAKQSEATVRTLNEGREITLAMAEMFNNELREMELNRAALELAAFAAF 180
                                    6899**************************************************************************** PP

                                    HHHHCHHHC- CS
                      TetR_C_24  82 gmlnwvyrWy 91 
                                    g   + ++W+
  gi|121638934|ref|YP_979158.1| 181 GSAASATEWW 190
                                    *********7 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.7e-06      0.02      10      38 ..      41      69 ..      38      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                                   CT-CTTBSS-BHHHHHHHHTS-HHHHHHH CS
                       HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRl 38
                                   +a+ + ++el+++++A+++g +k++ +R+
  gi|121638934|ref|YP_979158.1| 41 RAIDRLGPELSVRQIAEEAGTAKPKIYRH 69
                                   79999**********************96 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.055      32      78 ..      12      58 ..      10      60 .. 0.96
   2 ?   -0.9   0.0      0.34   8.8e+02     135     173 ..     133     171 ..      91     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                   STTEEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTTEEEEEEEEE CS
                 LysR_substrate 32 yPevelelvegdseelldllaegelDlairagppedsglearpLaee 78
                                    P+v+++ +++ + e+ +++++  +D+a+ra +   ++l +r++aee
  gi|121638934|ref|YP_979158.1| 12 KPGVKVDARSERWREHRKKVRNEIVDAAFRAIDRLGPELSVRQIAEE 58
                                   69******************************************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                                    EESSHHHHHHHHHTTS-BEEEEGGGHHCCCHTTTEEEEE CS
                 LysR_substrate 135 evnsleallalvaaGlGiallprsavrdeladgrlvalp 173
                                    ++ + ea ++    G  i+l+ + + ++el++ +l  + 
  gi|121638934|ref|YP_979158.1| 133 SAKQSEATVRTLNEGREITLAMAEMFNNELREMELNRAA 171
                                    455666666666666666666666666666666665444 PP

>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.031      86     169 ..      92     174 ..      84     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                    EEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-ST.T.B---HHHHHHHHHHHHHHHHHHHHHS-HH CS
                 Ribosomal_S3Ae  86 nFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkr.n.sYakssqkkaIrkkmveilteeaseldlk 163
                                     F  ++l++D  r ++r+    +e  v+   +   +lrvf+ +   k+ + +  + ++ ++I   m e++++e++e++l+
  gi|121638934|ref|YP_979158.1|  92 IFPSLDLATDSAREVIRRS---VEEYVNLVDQHPNVLRVFIQGRSAKQsEaTVRTLNEGREITLAMAEMFNNELREMELN 168
                                    7999*************95...899***********************76677778999********************9 PP

                                    HHHHHH CS
                 Ribosomal_S3Ae 164 elvkkl 169
                                    +   +l
  gi|121638934|ref|YP_979158.1| 169 RAALEL 174
                                    887666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.27      15      36 ..      49      70 ..      30      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                   SEEHHHHHHHHTS-HHHHHHHH CS
                          HTH_5 15 elcvcelaeelglsqstvShHL 36
                                   el+v ++aee g  ++++ +H+
  gi|121638934|ref|YP_979158.1| 49 ELSVRQIAEEAGTAKPKIYRHF 70
                                   59*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 2143.60
//
Query:       gi|121638935|ref|YP_979159.1|  [L=693]
Description: ribonucleotide-diphosphate reductase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.7e-145  484.1   0.2   2.4e-143  478.5   0.2    2.1  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    5.4e-28   96.9   9.4    7.3e-28   96.4   7.6    2.2  2  RNR_N            Ribonucleotide reductase N-terminal
    6.4e-12   45.3   0.1    4.6e-11   42.6   0.0    2.5  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
       0.13   12.9   0.0       0.22   12.1   0.0    1.4  1  Fib_succ_major   Fibrobacter succinogenes major domain (Fib_s
       0.17   12.2   0.2        0.4   11.0   0.2    1.5  1  T4bSS_IcmS       Type IVb secretion, IcmS, effector-recruitme


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.5   0.2  6.6e-147  2.4e-143       1     523 [.     155     672 ..     155     673 .. 0.96

  Alignments for each domain:
  == domain 1  score: 478.5 bits;  conditional E-value: 6.6e-147
                                    EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAa 80 
                                    +sCf+l+ved++esI +++++a +lsk+ggGv+l l+++R+ g+++k++e+++sG++++mkl+++ +++++q G+R+GA 
  gi|121638935|ref|YP_979159.1| 155 VSCFLLRVEDNMESIGRSINSALQLSKRGGGVALLLTNIREHGAPIKNIENQSSGVIPIMKLLEDAFSYANQLGARQGAG 234
                                    69****************************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                Ribonuc_red_lgC  81 mvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygee.....feeey 155
                                    +vyl+++HpDi  f+d+K +++++e+ r+++l+++v++pd  +e +k+++d++LfsP+   ++e++yg       ++e+y
  gi|121638935|ref|YP_979159.1| 235 AVYLHAHHPDIYRFLDTK-RENADEKIRIKTLSLGVVIPDITFELAKRNDDMYLFSPY---DVERVYGVPfadisVTEKY 310
                                    ******************.88999**********************************...788899966556779**** PP

                                    ............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                Ribonuc_red_lgC 156 eeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyes......... 226
                                     e++++a+i+k+++ka+e f+++ae ++e+g+P+++f Dt+Nr+n++     gkI+ +NlC+Ei++++++s         
  gi|121638935|ref|YP_979159.1| 311 YEMVDDARIRKTKIKAREFFQTLAELQFESGYPYIMFEDTVNRANPI----DGKITHSNLCSEILQVSTPSlfnedlsya 386
                                    ***********************************************....59*************************** PP

                                    .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 227 ....vavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidv.nkyplpeiekntkktRriGlGvmglada 301
                                        +++CnL+s+n+ak +          d  +++++i++++raL++v d  +   +p+ie++++++++iGlG m+l+ +
  gi|121638935|ref|YP_979159.1| 387 kvgkDISCNLGSLNIAKTM----------DSPDFAQTIEVAIRALTAVSDQtHIKSVPSIEQGNNDSHAIGLGQMNLHGY 456
                                    *******************..........8889*****************967779************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX......X............ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx......xxxx......... RF
                Ribonuc_red_lgC 302 laklgipydseealkfarkitelltyyaykaSvelAkerg.pfplfekskyskgilpvdef......eeke......... 365
                                    la+ +i y+s+e+++f++ ++ ++ y+a++aS+++A erg  f++fe+sky++g+  +d++      +  +         
  gi|121638935|ref|YP_979159.1| 457 LARERIFYGSDEGIDFTNIYFYTVLYHALRASNRIAIERGtHFKGFERSKYASGE-FFDKYtdqiweP--Ktqkvrqlfa 533
                                    ****************************************99************6.999996665541..0567889999 PP

                                    ...........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 366 ........kedweeLreeikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtv.geflevnpvfeeeLkkl 436
                                            + dw++L+e+++ +G++n+++ a++PTgsiS+i++ +s+i+Pi+++v+++++ + g++++  p++       
  gi|121638935|ref|YP_979159.1| 534 dagiriptQDDWRRLKESVQAHGIYNQNLQAVPPTGSISYINHSTSSIHPIVSKVEIRKEGKiGRVYYPAPYM------- 606
                                    99999999****************************************************8889988886665....... PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 437 glwseellkkilesvqgleeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwkl 516
                                                          ++  ++++ a++i  e++i+++aa+++++dq+ S+t++++++at++dv+++ ++Aw++
  gi|121638935|ref|YP_979159.1| 607 ---------------------TNDNLEYYEDAYEIGYEKIIDTYAAATQHVDQGLSLTLFFKDTATTRDVNKAQIYAWRK 665
                                    .....................6899******************************************************* PP

                                    XXXXXXX CS
                                    xxxxxxx RF
                Ribonuc_red_lgC 517 GlKgvty 523
                                    G+K+++y
  gi|121638935|ref|YP_979159.1| 666 GIKTLYY 672
                                    ******9 PP

>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   7.6     2e-31   7.3e-28       7      82 .]       1      76 [.       1      76 [. 0.99
   2 ?   -1.6   0.0      0.81   2.9e+03      54      68 ..     505     519 ..     488     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2e-31
                          RNR_N  7 elnlkdedgkiqlekDkeAleaYlkehvnpntvkfesleekldyLvendYyeeevlekYskefieelyklayskkF 82
                                   +lnl+d+dgkiq++kD+eA+++Y+ +hvn+ntv+f++ +ekldyL++++Yye+evl++Ys++f+++l ++ay+kkF
  gi|121638935|ref|YP_979159.1|  1 MLNLYDADGKIQFDKDREAAHQYFLQHVNQNTVFFHNQDEKLDYLIRENYYEREVLDQYSRNFVKTLLDRAYAKKF 76
                                   79*************************************************************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                          RNR_N  54 ndYyeeevlekYske 68 
                                     +Y   e+++kY+++
  gi|121638935|ref|YP_979159.1| 505 SKYASGEFFDKYTDQ 519
                                    578888999999876 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.3e-14   4.6e-11       2      82 ..      78     150 ..      77     151 .. 0.96
   2 ?   -1.2   0.0      0.57   2.1e+03      48      69 ..     318     339 ..     262     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.3e-14
                Ribonuc_red_lgN   2 kltynalkvledrYllkdeng.eivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGt 80 
                                    ++t++++ +++ +Y lk+ +g +++E+ +++  +vAl+la          +d++lae + d +   +f+pa+Pt++n+G+
  gi|121638935|ref|YP_979159.1|  78 FPTFLGAFKYYTSYTLKTFDGkRYLERFEDRVVMVALTLAA---------GDTALAELLVDEIIDGRFQPATPTFLNSGK 148
                                    6899*****************89*****************9.........*****************************9 PP

                Ribonuc_red_lgN  81 el 82 
                                    ++
  gi|121638935|ref|YP_979159.1| 149 KQ 150
                                    87 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.57
                Ribonuc_red_lgN  48 kleedkdlaeefydlmssqkfl 69 
                                    +  + k +a+ef++ +++++f 
  gi|121638935|ref|YP_979159.1| 318 RIRKTKIKAREFFQTLAELQFE 339
                                    4556666788999999998885 PP

>> Fib_succ_major  Fibrobacter succinogenes major domain (Fib_succ_major)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05      0.22      57      96 ..     489     564 ..     423     662 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                 Fib_succ_major  57 d......................................argl.cPeGWhiPtdedwqaLeaylgkseaeadagskLks 96 
                                    +                                       r+l ++ G +iPt++dw +L++ ++ +  ++   + L++
  gi|121638935|ref|YP_979159.1| 489 NriaiergthfkgferskyasgeffdkytdqiwepktqkVRQLfADAGIRIPTQDDWRRLKESVQAHGIYN---QNLQA 564
                                    355555555555555555555555556655667776555455579*****************999877633...33333 PP

>> T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00011       0.4      16      66 ..     611     658 ..     605     662 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                     T4bSS_IcmS  16 ddfdddasaisaeeveedtglleqliraadqlaSlaLffglkatvekaeva 66 
                                     ++++da  i +e +    +   + ++  dq  Sl+Lff++ at+++ + a
  gi|121638935|ref|YP_979159.1| 611 LEYYEDAYEIGYEKI---IDTYAAATQHVDQGLSLTLFFKDTATTRDVNKA 658
                                    479999999999994...455678899999****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4861.13
//
Query:       gi|121638936|ref|YP_979160.1|  [L=150]
Description: ribonucleotide reductase stimulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-46  155.8   0.0    5.7e-46  155.6   0.0    1.1  1  Flavodoxin_NdrI  NrdI Flavodoxin like


Domain annotation for each model (and alignments):
>> Flavodoxin_NdrI  NrdI Flavodoxin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.6   0.0   3.2e-50   5.7e-46       1     119 [.       9     130 ..       9     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 3.2e-50
                                    EEE--TT-HHHHHHHHH-S-EEEE-SSTT--.---SS-EEEEEE--TTSSSSTS......S-HHHHHHHTSHHHHHCEEE CS
                Flavodoxin_NdrI   1 vvysSlsgntkrFvekleleaqripleekeeelevdepyvlivptygegeekka......vpkqvieflnkeknrkllrG 74 
                                    v++sS+s+nt+rFv+kl+++a+ripl+    ++evdepyvli+ptyg+g+ + +      vpkqvi fln+ +nr++lrG
  gi|121638936|ref|YP_979160.1|   9 VYFSSVSENTHRFVQKLGIPATRIPLHG---RIEVDEPYVLILPTYGGGRANPGldaggyVPKQVIAFLNNDHNRAQLRG 85 
                                    89***********************987...699***************98555667799******************** PP

                                    EEEEE-GGGGGGTTHHHHHHHHHHT--EEEEEETT--HHHHHHHH CS
                Flavodoxin_NdrI  75 viasGnrnfgeqyalaakkiakkfkvPllykfelrGtkeDvervr 119
                                    via+Gn+nfg+++++a++++++k++vP+ly+fel+Gt++Dv++vr
  gi|121638936|ref|YP_979160.1|  86 VIAAGNTNFGAEFCYAGDVVSRKCSVPYLYRFELMGTEDDVAAVR 130
                                    ******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1142.07
//
Query:       gi|121638937|ref|YP_979161.1|  [L=79]
Description: glutaredoxin electron transport component of nrdEF (glutaredoxin-like protein) nrdH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-15   56.3   0.0    3.1e-15   56.1   0.0    1.1  1  Glutaredoxin  Glutaredoxin
     0.0087   16.4   0.0      0.009   16.4   0.0    1.2  1  DUF836        Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.05   13.8   0.0    1.1  1  SH3BGR        SH3-binding, glutamic acid-rich protein


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   5.3e-19   3.1e-15       1      60 []       3      61 ..       3      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 5.3e-19
                                   EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                   Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                   v+++tkp C++C+++ ++L+++g++++ +d++ d+e+r+++++l g+ + P+v+ +++h+
  gi|121638937|ref|YP_979161.1|  3 VTVYTKPACVQCSATSKALDKQGIAYQKVDISLDSEARDYVMAL-GYLQAPVVVAGNDHW 61
                                   89******************************************.************996 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06     0.009       1      41 [.       2      38 ..       2      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                   -EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CC CS
                         DUF836  1 kltLyskpgChlCeqakekLkelkleegleleviDIakdee 41
                                   ++t y+kp C  C   +++L     ++g+  +++DI  d e
  gi|121638937|ref|YP_979161.1|  2 TVTVYTKPACVQCSATSKALD----KQGIAYQKVDISLDSE 38
                                   689******************....5788899999995554 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.4e-06      0.05      21      49 ..      15      43 ..       3      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
                                   HHHHHHHHHTT--EEEEETTT-HHHHHHH CS
                         SH3BGR 21 qevlriLdakkiefdevDitkdeeerelm 49
                                   + + + Ld + i +++vDi+ d e r+++
  gi|121638937|ref|YP_979161.1| 15 SATSKALDKQGIAYQKVDISLDSEARDYV 43
                                   566788****************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 624.77
//
Query:       gi|121638938|ref|YP_979162.1|  [L=122]
Description: hypothetical protein BCG_3078c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 671.55
//
Query:       gi|121638939|ref|YP_979163.1|  [L=184]
Description: hypothetical protein BCG_3079c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-34  116.7   0.0    9.6e-34  116.4   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    5.5e-06   26.2   0.0    6.9e-06   25.9   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   1.1e-37   9.6e-34       2     152 ..       9     155 ..       8     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.1e-37
                                    EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEE.TTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEE CS
                        FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelid.ladlilpcalcdkdlesegqtsddvaellekiaaadaliivt 80 
                                    kil+++GSlr+ s++r++ae aa+ ++  g++v++++ l+d  lp  ++++d +++ + ++ v +l+e+  +a+a ++vt
  gi|121638939|ref|YP_979163.1|   9 KILALVGSLRAASFNRQIAELAAKVAPD-GVTVTMFEgLGD--LP--FYNEDIDTATEVPAPVSALREAASDAHAALVVT 83 
                                    9*************************88.9******87999..8*..*******99************************ PP

                                    EECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETS CS
                        FMN_red  81 PeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgk 152
                                    PeYngs+++++Kna+D+lsr+ g+ +l++Kp+a+++ + gr gg  a+ + r+ +++ g+ vv+++ ++v++
  gi|121638939|ref|YP_979163.1|  84 PEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGGSMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPF 155
                                    ***************************************************************998888765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   7.7e-10   6.9e-06       2     131 ..       9     118 ..       8     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.7e-10
                                    EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTTCHHHHHHHHHHHHCSSE CS
                   Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeekpadveseqiekllaada 80 
                                    kiL ++++ r   sf++++a+     ++k  p+ vtv+    +  lp+ ++ d+    ++ e pa v + + e+  +a+a
  gi|121638939|ref|YP_979163.1|   9 KILALVGSLRA-ASFNRQIAE----LAAKVAPDGVTVTMFEGLgDLPFYNE-DID---TATEVPAPVSALR-EAASDAHA 78 
                                    89999999999.488555555....44444444488888888877788876.665...6666589******.******** PP

                                    EEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEE CS
                   Flavodoxin_2  81 ivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvi 131
                                     ++++P ++ ++Pa+ K+ iD   ++   f        ++g+Lk+k++ vi
  gi|121638939|ref|YP_979163.1|  79 ALVVTPEYNGSIPAVIKNAIDWLSRP---F--------GDGALKDKPLAVI 118
                                    *********************97554...4........2567777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1025.79
//
Query:       gi|121638940|ref|YP_979164.1|  [L=204]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   53.5   0.4    2.5e-14   52.8   0.4    1.3  1  TetR_N         Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.036   13.5   0.2      0.059   12.8   0.2    1.2  1  Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
       0.12   12.2   0.1       0.21   11.4   0.1    1.4  1  LacI           Bacterial regulatory proteins, lacI family
       0.18   12.1   4.5       0.26   11.6   0.4    2.4  2  HTH_18         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.4   5.6e-18   2.5e-14       1      43 [.      32      74 ..      32      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 5.6e-18
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeL 43
                                   +l+aAr+l+a+ G da t++++A++AGv+kg+l+r+F+s+++L
  gi|121638940|ref|YP_979164.1| 32 LLEAARRLIARSGADAITMDDVAAAAGVGKGTLFRRFGSRAGL 74
                                   79**************************************999 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.3e-05     0.059     106     139 ..      34      67 ..      29      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                  Ribosomal_L18 106 etararilkaGGeiltlDqLalraPtGkntvLlr 139
                                    e+ar+ i ++G + +t+D++a  a  Gk t++ r
  gi|121638940|ref|YP_979164.1|  34 EAARRLIARSGADAITMDDVAAAAGVGKGTLFRR 67 
                                    78***************************98755 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.7e-05      0.21       1      15 [.      49      63 ..      49      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                                   -HHHHHHHCTS-HHH CS
                           LacI  1 tikDVArlAGVSkaT 15
                                   t++DVA +AGV k T
  gi|121638940|ref|YP_979164.1| 49 TMDDVAAAAGVGKGT 63
                                   8**********9987 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   5.7e-05      0.26      29      66 ..      29      68 ..      25      73 .. 0.80
   2 ?    1.7   0.4     0.071   3.2e+02      29      46 ..     113     130 ..     112     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHHHHHHSSS..---HHHHHHHTT-S-HHHHHHH CS
                         HTH_18 29 rrlRlerArrlLlent..glsvaeiAlalGFsdlsrFsra 66
                                   r+l le+Arrl++++   + +++++A+a+G +  + F+r+
  gi|121638940|ref|YP_979164.1| 29 RALLLEAARRLIARSGadAITMDDVAAAAGVGKGTLFRRF 68
                                   66778999998887432267**********9999988886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.071
                                    HHHHHHHHHHHHHSSS-- CS
                         HTH_18  29 rrlRlerArrlLlentgl 46 
                                     r+R+ +A+++Ll+++++
  gi|121638940|ref|YP_979164.1| 113 ERMRFVHAHHQLLSEANR 130
                                    58999*******975544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1117.01
//
Query:       gi|121638941|ref|YP_979165.1|  [L=346]
Description: DNA polymerase IV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-39  135.5   0.0      3e-39  134.4   0.0    1.5  2  IMS              impB/mucB/samB family
    2.5e-08   34.6   0.7    4.7e-08   33.8   0.7    1.4  1  IMS_C            impB/mucB/samB family C-terminal domain
    2.6e-05   24.3   0.0    6.7e-05   23.0   0.0    1.8  1  IMS_HHH          IMS family HHH motif
      0.004   17.6   0.0     0.0078   16.6   0.0    1.4  1  BAF              Barrier to autointegration factor
     0.0044   17.6   0.0     0.0096   16.5   0.0    1.6  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.015   14.9   1.0      0.079   12.6   0.0    2.5  3  HTH_Tnp_IS1      InsA C-terminal domain
      0.017   15.0   0.0      0.052   13.4   0.0    1.9  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.058   13.6   0.0       0.13   12.6   0.0    1.5  1  Cdd1             Pathogenicity locus
       0.12   11.5   0.2       0.33   10.0   0.2    1.7  2  Dus              Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.0   1.5e-42     3e-39       1     149 [.      12     159 ..      12     160 .. 0.95
   2 ?   -3.4   0.0       4.2   8.4e+03      67      89 ..     257     279 ..     250     297 .. 0.60

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 1.5e-42
                                    EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHH CS
                            IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrras 77 
                                    +D+d+F+asve++r+peL g Pv+v+++ +    r++v+++syeArayGv++gm+++ a + cp++ +++++ ++y+ as
  gi|121638941|ref|YP_979165.1|  12 VDLDQFLASVELLRHPELAGLPVIVGGNGDPtepRKVVTCASYEARAYGVRAGMPLRTAARRCPEATFLPSNPAAYNAAS 91 
                                    7**************************9888999********************************************** PP

                                    HHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                            IMS  78 kkileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                    ++++++l++ +   ve  + DEayl +     +      ++a+e+rk i +++gl++siGi++nk  AK+a+
  gi|121638941|ref|YP_979165.1|  92 EEVVALLRDLGY-PVEVWGWDEAYLAVAPGTPDDP---IEVAEEIRKVILSQTGLSCSIGISDNKQRAKIAT 159
                                    **********66.8***************655554...68******************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                                    EEE-HHHHHHHHHHHHHHHHH-S CS
                            IMS  67 kvdlekyrraskkileilkrfis 89 
                                    + dl+   ++ +++ e+++r  +
  gi|121638941|ref|YP_979165.1| 257 PRDLTCRSEMESAVTELAQRTLN 279
                                    55555555555555555555543 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.7   2.3e-11   4.7e-08       8     104 ..     247     343 ..     243     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.3e-11
                          IMS_C   8 pksissektfpepyd.esklkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreileaalkL 85 
                                    p+s s+  tfp++ + +s+ ++ + eLa++     ++  ++   + +++r++ f  +++ ++L  p+ d++ i++aa+  
  gi|121638941|ref|YP_979165.1| 247 PRSRSHAVTFPRDLTcRSEMESAVTELAQRTLNEVVASSRTVTRVAVTVRTATFYtRTKIRKLQAPSTDPDVITAAARHV 326
                                    78999******93333433555555666666666688888889999999999665599999******************* PP

                          IMS_C  86 lrrlidepglpirligvsa 104
                                    l+  ++   +p+rl+gv++
  gi|121638941|ref|YP_979165.1| 327 LDLFEL--DRPVRLLGVRL 343
                                    *66666..*********97 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.3e-08   6.7e-05       3      32 .]     174     203 ..     172     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.3e-08
                        IMS_HHH   3 dvkefLwplpitkipGiGgklgekLeklGi 32 
                                    + ++ ++++ +  ++G+G+k+ ++L+klGi
  gi|121638941|ref|YP_979165.1| 174 NWMAIMGDRTVEALWGVGPKTTKRLAKLGI 203
                                    6788999**********************9 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.9e-06    0.0078      14      45 ..     178     209 ..     173     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                            BAF  14 pmgdKevtalaGigevlgkkLeekGfdkAyvv 45 
                                     mgd++v+al G+g++  k+L++ G+++ y++
  gi|121638941|ref|YP_979165.1| 178 IMGDRTVEALWGVGPKTTKRLAKLGINTVYQL 209
                                    59**************************9997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.8e-06    0.0096       7      48 ..     187     226 ..     181     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                                    STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHH CS
                          HHH_5   7 vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktA 48 
                                    + G+Gpkt ++l++ Gi++v +la+ d   L +   +G++tA
  gi|121638941|ref|YP_979165.1| 187 LWGVGPKTTKRLAKLGINTVYQLAHTDSGLLMST--FGPRTA 226
                                    559************************9999998..888887 PP

>> HTH_Tnp_IS1  InsA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.1   2.1e+03       2      11 ..      53      62 ..      53      64 .. 0.86
   2 ?   -2.0   0.0       1.4   2.8e+03       3      18 ..     114     129 ..     113     130 .. 0.84
   3 ?   12.6   0.0     4e-05     0.079      18      38 ..     186     206 ..     182     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                    HTH_Tnp_IS1  2 tYeArkPGvk 11
                                   +YeAr  Gv+
  gi|121638941|ref|YP_979165.1| 53 SYEARAYGVR 62
                                   7****99986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                    HTH_Tnp_IS1   3 YeArkPGvkekIvemA 18 
                                    Y A  PG+ +  +e A
  gi|121638941|ref|YP_979165.1| 114 YLAVAPGTPDDPIEVA 129
                                    89999***99888877 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 4e-05
                    HTH_Tnp_IS1  18 AfNGaGvraTARtlkvGiNTv 38 
                                    A  G+G + T R  k GiNTv
  gi|121638941|ref|YP_979165.1| 186 ALWGVGPKTTKRLAKLGINTV 206
                                    677*****************9 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.052       7      30 ..     188     211 ..     183     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                DNA_pol_lambd_f   7 yGVGpktAkkwyakGirtledlra 30 
                                    +GVGpkt k++ + Gi t+ +l  
  gi|121638941|ref|YP_979165.1| 188 WGVGPKTTKRLAKLGINTVYQLAH 211
                                    9******************99876 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05      0.13       9      42 ..     185     218 ..     181     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                           Cdd1   9 qdiPniGkalaedlvelGirsveelkgedpeely 42 
                                    + + ++G+++ + l +lGi++v +l++ d   l+
  gi|121638941|ref|YP_979165.1| 185 EALWGVGPKTTKRLAKLGINTVYQLAHTDSGLLM 218
                                    66789*********************99876655 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   2.6e+03     182     205 ..      32      55 ..      30      74 .. 0.71
   2 ?   10.0   0.2   0.00016      0.33      17      77 ..     270     328 ..     258     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                    -SS-EEEESS--SHHHHHHHHHHH CS
                            Dus 182 vsipviaNGdIkdaedaqaileet 205
                                    +++ v +NGd ++++++  + ++ 
  gi|121638941|ref|YP_979165.1|  32 LPVIVGGNGDPTEPRKVVTCASYE 55 
                                    567888999999999998888764 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                                    HHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHH CS
                            Dus  17 vrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklvad 77 
                                    v+e+++   +  e+v++   v++ +v++r+ ++  + + + +Q  + dp+++++aA+ v d
  gi|121638941|ref|YP_979165.1| 270 VTELAQR--TLNEVVASSRTVTRVAVTVRTATFYTRTKIRKLQAPSTDPDVITAAARHVLD 328
                                    4555555..789*********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1968.71
//
Query:       gi|121638942|ref|YP_979166.1|  [L=287]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-49  166.0   0.0    8.3e-49  165.7   0.0    1.1  1  adh_short     short chain dehydrogenase
    2.3e-39  135.3   0.2    2.8e-39  135.0   0.2    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      2e-16   60.4   0.2      3e-16   59.8   0.2    1.2  1  KR            KR domain
     0.0003   20.4   0.1    0.00045   19.8   0.1    1.3  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.18   11.1   0.0       0.26   10.6   0.0    1.2  1  DUF1776       Fungal family of unknown function (DUF1776)


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.0   2.3e-52   8.3e-49       3     189 ..      15     203 ..      13     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 2.3e-52
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSE.EEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegak.alaiqvDvtdreevealvekavkklgkldvL 81 
                                     +vtGa+sGIGra+a +la++Ga+++++dr  + l++++   +++ga+   +  +Dv+d+++v a+ +++ +++ ++dv+
  gi|121638942|ref|YP_979166.1|  15 CFVTGAASGIGRATALRLAAQGAELYLTDRDRDGLAQTVCDARALGAQvPEHRVLDVSDYQDVAAFAADIHARHPSMDVV 94 
                                    68*******************************************555268999************************** PP

                                    EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                     n AG++  g++ +l+ ++w r++++Nl+g+++++++++p m+ ++++G+ vnvsS ag+v++++ aaYsAsK +++gl+
  gi|121638942|ref|YP_979166.1|  95 LNIAGVSAWGTVDQLTHDQWSRMVAINLMGPIHVIETLVPPMVaAGRGGHLVNVSSAAGLVGLPWHAAYSASKYGLRGLS 174
                                    *******************************************999********************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmake 189
                                    + l+ +la++gi v++v+PG+v+T+++++
  gi|121638942|ref|YP_979166.1| 175 EVLRFDLARHGIGVSVVVPGAVKTPLVNT 203
                                    *************************9876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.2   7.9e-43   2.8e-39       1     208 [.      19     234 ..      19     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 7.9e-43
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE...EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev...lecDVtdeeqvealveevvekfgklDilvnn 76 
                                    GaasgIGra+A +la++Gae+ ltd+++++ +++v ++ ++lga+v     +DV+d ++v+a+++++ +++ ++D+++n 
  gi|121638942|ref|YP_979166.1|  19 GAASGIGRATALRLAAQGAELYLTDRDRDGlAQTVCDA-RALGAQVpehRVLDVSDYQDVAAFAADIHARHPSMDVVLNI 97 
                                    9*****************************66666665.55999988889****************************** PP

                                    ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                   adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaaKaalealtr 153
                                    ag++    g + +++ +++ r++++nl + +++++ ++p ++++g  g +vn+ss ++ +++p ++ay+a+K +l +l+ 
  gi|121638942|ref|YP_979166.1|  98 AGVSAW--GTVDQLTHDQWSRMVAINLMGPIHVIETLVPpMVAAGrgGHLVNVSSAAGLVGLPWHAAYSASKYGLRGLSE 175
                                    ******..*******************************86666567********************************* PP

                                    HHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.....HHHHHHHHHHHSTTSS-B-HHHHH CS
                   adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikg.....fdelleelearaplgrlgtpeeva 208
                                     l  +l+++gi v +v pg++kT++++ ++       d   +++ +    g+++tpe+ a
  gi|121638942|ref|YP_979166.1| 176 VLRFDLARHGIGVSVVVPGAVKTPLVNTVEIagvdrDDPRVNRWVE-RFSGHAVTPEKAA 234
                                    ************************9765542112213333333333.2345556666655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.2   8.5e-20     3e-16       4     153 ..      16     167 ..      14     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 8.5e-20
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EE.EE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaev.evvaaDvsdkdavealleeikaeeppi 82 
                                    ++tG++ g+G+++a  la++ga +l l+ R+   ++  ++++   +alga+v e + +Dvsd ++v+a  ++i+a++p++
  gi|121638942|ref|YP_979166.1|  16 FVTGAASGIGRATALRLAAQGA-ELYLTDRD---RDGLAQTVCDARALGAQVpEHRVLDVSDYQDVAAFAADIHARHPSM 91 
                                    69*******************9.599****9...5566669999********556778********************** PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaaN 153
                                      v++ Agv++ ++++++t +++ +++a  + G  ++ e+l +      +  ++v +SS+agl+g + +a+Y+a  
  gi|121638942|ref|YP_979166.1|  92 DVVLNIAGVSAWGTVDQLTHDQWSRMVAINLMGPIHVIETLVPpmvaaGRGGHLVNVSSAAGLVGLPWHAAYSASK 167
                                    *********************************9888776655577778999*********************975 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.3e-07   0.00045       2     103 ..      16     133 ..      15     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH....H.T-SEEE CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke....e.qpdavi 69 
                                    +VtGa+  iG+a++ +l+++g e+   dr++++ ++   +         e   ld+ d ++++++ ++    +  +d+v+
  gi|121638942|ref|YP_979166.1|  16 FVTGAASGIGRATALRLAAQGAELYLTDRDRDGLAQTVCDARalgaqvpEHRVLDVSDYQDVAAFAADiharHpSMDVVL 95 
                                    7**************************9997776655554447999999888899999998888766522225568**** PP

                                    E--S---HHH....HHHSHHHHHHHHTHHHHHHHHHHH CS
                      Epimerase  70 hlAavggvaa....ssedpadfieknlqgtlnlleaar 103
                                    ++A+v+ +++    ++++ ++++ +nl+g  +++e + 
  gi|121638942|ref|YP_979166.1|  96 NIAGVSAWGTvdqlTHDQWSRMVAINLMGPIHVIETLV 133
                                    ****9998762222445555566678888888887765 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.3e-05      0.26     105     195 ..     103     191 ..      93     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.3e-05
                        DUF1776 105 tgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkre 184
                                     g +++++ ++w   +  +l+ pi +++ l+p + ++   +   +v   s    + lp ha  +     l+ l evL+ +
  gi|121638942|ref|YP_979166.1| 103 WGTVDQLTHDQWSRMVAINLMGPIHVIETLVPPMVAA--GRGGHLVNVSSAAGLVGLPWHAAYSASKYGLRGLSEVLRFD 180
                                    6899******************************984..45555666667888899************************ PP

                        DUF1776 185 lrphnidvtqi 195
                                    l++h+i v+ +
  gi|121638942|ref|YP_979166.1| 181 LARHGIGVSVV 191
                                    *****999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1895.00
//
Query:       gi|121638943|ref|YP_979167.1|  [L=216]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   46.9   0.6    3.9e-12   45.8   0.6    1.7  1  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.018   15.2   0.1      0.087   13.0   0.0    2.1  2  TetR_C_9  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.6   4.3e-16   3.9e-12       1      46 [.      26      71 ..      26      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.3e-16
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   Il aArel++e  +++++vr+I  rAGv+++ +Y yF+sK   l++
  gi|121638943|ref|YP_979167.1| 26 ILRAARELLEETPFAELSVRAISLRAGVARSGFYFYFDSKYSVLAQ 71
                                   9***************************************998876 PP

>> TetR_C_9  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.14   1.3e+03      46      63 ..      20      37 ..       6      86 .. 0.64
   2 ?   13.0   0.0   9.7e-06     0.087       3      82 ..      95     172 ..      93     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                                   HHHTHHHHHHHHHHHHHH CS
                       TetR_C_9 46 dfyllplaraaqrlieeG 63
                                   d + + + raa+ l+ee 
  gi|121638943|ref|YP_979167.1| 20 DRHRQAILRAARELLEET 37
                                   556666667776666653 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.7e-06
                                    -HHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHS-HHHHHHHHHHHTHHHHHHHHHHHHHHHHTTSB-S--HHHHHHHHH CS
                       TetR_C_9   3 speeklrrhlakvidtyydypylyrllaalvrdadeeeakdiadfyllplaraaqrlieeGvkaGvirpldpqlfyiavl 82 
                                    spe+ + r +  v   y +   + r   a  r  ++ e +di +   + l r + +++e+ vkaG+  p+  +l  +  +
  gi|121638943|ref|YP_979167.1|  95 SPEQFVNRMIGSVAAVYANNDPVLRACNA-AR-QSDMEIRDILERQFQVLLRETIGVFEAEVKAGTAHPISEDLPTLVRT 172
                                    78888889888888888776555554433.34.467899*******************************9888665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1488.23
//
Query:       gi|121638944|ref|YP_979168.1|  [L=492]
Description: cytochrome P450 136 cyp136 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-67  225.9   0.0      1e-66  225.6   0.0    1.0  1  p450           Cytochrome P450
     0.0021   17.0   0.0     0.0032   16.4   0.0    1.2  1  Me-amine-dh_H  Methylamine dehydrogenase heavy chain (MADH)


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.6   0.0   1.1e-70     1e-66       6     439 ..      62     466 ..      56     481 .. 0.89

  Alignments for each domain:
  == domain 1  score: 225.6 bits;  conditional E-value: 1.1e-70
                                    EHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTS CS
                           p450   6 plplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgk 85 
                                     lp++g+++++ r + +   l+ l k+ gp++       p v   gp+a++ ++ +++++ s++    ++    +pf ++
  gi|121638944|ref|YP_979168.1|  62 GLPILGHMIEMLR-GGPDY-LMFLYKTKGPVVFGDSAVLPGVAALGPDAAQVIYSNRNKDYSQQ---GWVPV-IGPFFHR 135
                                    68999**999995.55555.566666669****************************9777775...66664.569**** PP

                                    SSTTCGHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHT CS
                           p450  86 gvlfangekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdl 164
                                    g+++ + e+++ +Rr++  ++  +  l  + e ++++++++v+     ++++  + +++ +   +ld+ +++++g++ + 
  gi|121638944|ref|YP_979168.1| 136 GLMLLDFEEHMFHRRIMQEAFVRS-RLaGYLEQMDRVVSRVVADDWVVNDAR--FLVYPAMKALTLDIASMVFMGHEPG- 211
                                    ***********************9.888999999999999999988899999..**********************966. PP

                                    TTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHH CS
                           p450 165 ledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdflda 244
                                         + elv++v++ ++++ ++  + +   + +   p   +r l+ a++ l+++  + ++erre         +d+l +
  gi|121638944|ref|YP_979168.1| 212 ----TDHELVTKVNKAFTIT-TRAGNAVIRTS-V--PPFTWWRGLR-ARELLENYFTARVKERREAS------GNDLLTV 276
                                    ....33469*******9988.66766666666.3..2334566665.99999999999999999864......456**** PP

                                    HHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHH CS
                           p450 245 lllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyl 324
                                    l++++ + +g+  +sd+++++ ++ l++a++dT++st + + y+La +Pe q+++r E d++  +  +++++ l++l+ l
  gi|121638944|ref|YP_979168.1| 277 LCQTE-DDDGN-RFSDADIVNHMIFLMMAAHDTSTSTATTMAYQLAAHPEWQQRCRDESDRHGDG--PLDIESLEQLESL 352
                                    ****6.77776.9************************************************9766..7************ PP

                                    HHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--T CS
                           p450 325 davikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflP 404
                                    d v +E+ Rl ++v    +R++ +d+++ gy +pkGt+vi +++  hr pe++ +P +FdpeRF + ++++kr+ +af P
  gi|121638944|ref|YP_979168.1| 353 DLVMNESIRLVTPVQ-WAMRQTVRDTELLGYYLPKGTNVIAYPGMNHRLPEIWTDPLTFDPERFTEPRNEHKRHRYAFTP 431
                                    ***************.888**************************************************9********** PP

                                    TEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEEST CS
                           p450 405 FGaGpRnCiGerlArmelklflatlLqnFevelqp 439
                                    FG G++ CiG+ ++++e+k +l++lL+++++el +
  gi|121638944|ref|YP_979168.1| 432 FGGGVHKCIGMVFGQLEIKTILHRLLRRYRLELSR 466
                                    ********************************855 PP

>> Me-amine-dh_H  Methylamine dehydrogenase heavy chain (MADH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.6e-07    0.0032      56     131 ..     152     225 ..     131     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-07
                                    EEEETTEEEEEEEEEEE-TTT--EEEEEEETTS----BS--GGGEEE-TTSSEEEEEE-SSSSEEEEEETTTTEEE CS
                  Me-amine-dh_H  56 vysriargkrtdyvevldaqtlkvladielpeaprflvgvyprmtsltpdnktllfyqfspspavgvvdlegksfk 131
                                    + +   r +   y+e +d +  +v+ad  + +  rflv  yp m +lt d   ++f    p     +v   +k+f+
  gi|121638944|ref|YP_979168.1| 152 MQEAFVRSRLAGYLEQMDRVVSRVVADDWVVNDARFLV--YPAMKALTLDIASMVFMGHEPGTDHELVTKVNKAFT 225
                                    556677889999***************9999999***6..9********************999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3626.29
//
Query:       gi|121638945|ref|YP_979169.1|  [L=490]
Description: GntR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-30  105.9  18.9    6.4e-17   62.1   0.7    3.7  4  FCD       FCD domain
    1.4e-15   56.6   1.0    2.3e-07   30.4   0.1    2.6  2  GntR      Bacterial regulatory proteins, gntR family
    4.1e-07   30.2   0.0      0.012   15.9   0.0    2.5  2  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.15     9e+02       6      31 ..      45      70 ..      41      71 .. 0.85
   2 !   62.1   0.7   1.1e-20   6.4e-17       1     124 [.     103     226 ..     103     227 .. 0.93
   3 ?   -3.6   0.2       2.4   1.5e+04      11      28 ..     304     321 ..     299     324 .. 0.52
   4 !   54.8   1.6     2e-18   1.2e-14       1     124 [.     357     483 ..     357     484 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                            FCD  6 RalLEpeaarlaarratdadlaelee 31
                                   R  + ++++r+a+r +  +++a++++
  gi|121638945|ref|YP_979169.1| 45 RFCVSRSVLREAVRLVEHHQVARMRR 70
                                   666788999************99986 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 1.1e-20
                            FCD   1 dlyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlr 80 
                                    dl+ +R +LEp+aa laa+++++  +++l+++l+a e+  + g    +    ++F+r+lae ++npvl+ +++ l++ ++
  gi|121638945|ref|YP_979169.1| 103 DLLGARLVLEPLAASLAAEHIDEPGIERLRAVLRAEERW-RPG----LPPPPEQFYRVLAEQSKNPVLQLFIDILMRLTK 177
                                    67889****************************877776.445....55789**************************** PP

                            FCD  81 rlrrlals.....sperleeslaeHraildAirardadaAraamrrHle 124
                                    r+ + + +     + e + +++ eH +i++A+ a+d++ A+++ +rH+e
  gi|121638945|ref|YP_979169.1| 178 RYVQKSGTqsageAVEAAGQVHNEHSDIVAAVTAGDSAWAKTLSERHVE 226
                                    *999988899999999*******************************98 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                            FCD  11 peaarlaarratdadlae 28 
                                    ++++r+a+r    + +a 
  gi|121638945|ref|YP_979169.1| 304 RAVLREAVRLLEYHAIAH 321
                                    455555555555444444 PP

  == domain 4  score: 54.8 bits;  conditional E-value: 2e-18
                            FCD   1 dlyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlr 80 
                                    dl  +R ++E   ++ +++r+++ ++a++ + l + +   +++d+ ++a  +++FH  la+aagn +l+ +l  l + +r
  gi|121638945|ref|YP_979169.1| 357 DLRCVRDAIEIDNVAKVVKRRSEPEVASFLDTLGRPRLDNPTDDVRAAAVEEFRFHVGLARAAGNTMLDLFLLILVELFR 436
                                    57789****************************************************************99999999999 PP

                            FCD  81 rlrrlals...sperleeslaeHraildAirardadaAraamrrHle 124
                                    r ++++ +   +  +  ++ + H +il+Ai ++d   Ar  +rrHl+
  gi|121638945|ref|YP_979169.1| 437 RHLSSTEQalpTWSDVVAVGHAHVRILEAIGSGDDSLARCRTRRHLD 483
                                    9777777756577777777778***********************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   3.9e-11   2.3e-07       2      59 ..      14      71 ..      13      77 .. 0.91
   2 !   24.4   0.1   2.9e-09   1.7e-05       2      61 ..     268     327 ..     267     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.9e-11
                                   HHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR  2 yeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   ++++++r+++dI++  +  G+ L se++L+++f Vsr+++ReA r  e  +++  r+g
  gi|121638945|ref|YP_979169.1| 14 ASKIARRIEADIVRRGWPIGASLGSESALQQRFCVSRSVLREAVRLVEHHQVARMRRG 71
                                   5789***************************************998888887777665 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.9e-09
                                    HHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                           GntR   2 yeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61 
                                    +e +++ + +dI +  ++ G+   +e +L +++ Vsr ++ReA r Le   +++ r+g G
  gi|121638945|ref|YP_979169.1| 268 AEVLAATIGDDIAASGWQVGSVFGTETALLERYQVSRAVLREAVRLLEYHAIAHMRRGPG 327
                                    567889999******************************************999999866 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.5e-05      0.27      30      67 ..      41      78 ..      34      84 .. 0.90
   2 !   15.9   0.0     2e-06     0.012      30      79 ..     295     344 ..     289     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                           Rrf2 30 eiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                   ++ +r+ +s+s+l+  ++  +++ + + +rG++GG+ +
  gi|121638945|ref|YP_979169.1| 41 ALQQRFCVSRSVLREAVRLVEHHQVARMRRGPNGGLFI 78
                                   68899******************************866 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2e-06
                                    HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBHHHH CS
                           Rrf2  30 eiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlldv 79 
                                    ++ er+++s+ +l+  ++ L+ + + + +rG+gGG++ + p  + ++  +
  gi|121638945|ref|YP_979169.1| 295 ALLERYQVSRAVLREAVRLLEYHAIAHMRRGPGGGLVVTTPQPQASIDTI 344
                                    6889*********************************9999888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3612.95
//
Query:       gi|121638946|ref|YP_979170.1|  [L=721]
Description: acyl-CoA dehydrogenase fadE22 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-41  140.3  17.9    2.6e-22   79.7   7.6    2.4  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-27   96.8   8.2    1.5e-19   70.7   0.0    3.9  5  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    8.7e-17   61.1   0.0    2.8e-16   59.5   0.0    1.9  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.028   14.6   0.4      0.057   13.6   0.4    1.5  1  Patatin        Patatin-like phospholipase
       0.55   10.5   4.5        9.1    6.6   0.0    3.7  4  Nterm_IS4      Insertion element 4 transposase N-terminal


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   7.6   7.1e-26   2.6e-22       8     131 ..     204     328 ..     200     343 .. 0.95
   2 !   66.0   2.6   1.1e-21     4e-18       1     150 []     567     712 ..     567     712 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 7.1e-26
                                    TTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------.HH CS
                  Acyl-CoA_dh_1   8 metlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd.ra 86 
                                     ++l+  R ++aa a+g a+ +++ a++ya+ r++fg++++ +q+v++++a+m + +e+a ++v++aa+a+ +++++ r 
  gi|121638946|ref|YP_979170.1| 204 ESALARARTLLAAEAVGGAADCVDSAVAYAKVRQQFGRTIATFQAVKHHCANMLVAAESAIAAVWDAARAAAEDEEQfRL 283
                                    57899****************************************************************999999999** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHH CS
                  Acyl-CoA_dh_1  87 easmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvl 131
                                    +a++a ++a  +  + a+l +q++Gg G+++e+  + ++r+a+v+
  gi|121638946|ref|YP_979170.1| 284 AAAVAAALAFPAYARNAELNIQVHGGIGFTWEHDAHLHLRRALVT 328
                                    *****************************************9987 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 1.1e-21
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++G++va  tl +eR++++ ++   +++    ++++++rr +      ++     +++ + ae +a+rll++r a++  +
  gi|121638946|ref|YP_979170.1| 567 NSGWTVARATLGNERVSIG-GSGSYYEAMAAKLVQLVQRRSD------AFAGAPIRVGAFLAEDHALRLLNLRRAARSVE 639
                                    79****************7.99******************98......6788899************************* PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGH...HHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeyp...verlyrdarvlrigeGtseiqrniiarrll 150
                                    g+ +++e +++Kl+++e++ e a+ a+ l+G +  l ++p   + r ++ ar + i++Gtse+ rn+ia+r+l
  gi|121638946|ref|YP_979170.1| 640 GAGPGPEGNITKLKVAEHMIEGAAIAAALWGPEIALLDGPgrvIGRTVMGARGMAIAGGTSEVTRNQIAERIL 712
                                    ***********************************98888899****************************86 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   4.2e-23   1.5e-19       1     112 [.       6     116 ..       6     117 .. 0.90
   2 ?   -0.1   0.1       0.4   1.4e+03      51      90 ..     216     259 ..     211     268 .. 0.68
   3 ?   -1.9   0.1       1.5   5.2e+03      33      51 ..     276     294 ..     254     337 .. 0.55
   4 !   28.3   0.1   6.2e-10   2.2e-06      18     111 ..     367     455 ..     356     457 .. 0.76
   5 ?   -2.6   0.1       2.3   8.3e+03      61     100 ..     663     701 ..     653     707 .. 0.67

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 4.2e-23
                                    THHHHHHHHHHHHHHHHHTHHHHHHHH..HHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewd..eegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                    t+++++l   +r+f+  +    aa++   ++g     +w+ laelG+lg+++ e +gG+g +  e ++v+eel+ra a+ 
  gi|121638946|ref|YP_979170.1|   6 TDDHRELSGVARAFLTSQKVRWAARASldAAGDARPPFWQNLAELGWLGLHIDERHGGSGYGLSELVVVIEELGRAVAP- 84 
                                    799*************9998888888753444434458*************************************9888. PP

                                    HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasg 112
                                      +l v + +++ ++++ Gt++q++r Lp l++g
  gi|121638946|ref|YP_979170.1|  85 --GLFVPTVIASAVVAKEGTDDQRARLLPALIDG 116
                                    ..78899999999******************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                                    -GGGTS--..S-.HHHHHHHHHHHHHH-HHHHH.HHHHHHHTTH CS
                  Acyl-CoA_dh_N  51 peeygGag..ld.yleaaivaeelaradaglal.llgvhsslva 90 
                                     e++gGa   +d ++++a v ++++r+ a +++  + + ++lva
  gi|121638946|ref|YP_979170.1| 216 AEAVGGAAdcVDsAVAYAKVRQQFGRTIATFQAvKHHCANMLVA 259
                                    58889987553348888888888888777766656666666664 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHTTCTSTTS- CS
                  Acyl-CoA_dh_N  33 prelwkklaelGllgitvp 51 
                                    ++e + +la++  +++++p
  gi|121638946|ref|YP_979170.1| 276 EDEEQFRLAAAVAAALAFP 294
                                    2222223332233333333 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 6.2e-10
                                    HTHHHHHHHHHHTSGHHHH.HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHH CS
                  Acyl-CoA_dh_N  18 elaphaaewdeegefprel.wkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrf 96 
                                    +++  aae+ +    ++++ ++kl e G++  ++p  +g a  +++e++++ ee+++a++  ++ +++   + + +++++
  gi|121638946|ref|YP_979170.1| 367 RIRSDAAEIAA---LEKDAqRDKLIETGYVMPHWPRPWGRAA-GAVEQLVIEEEFSAAGIE-RPDYSITGWV-ILTLIQH 440
                                    33333444432...23343499****************7665.79************9987.6678885544.469**** PP

                                    S-HHHHHHHHHHHHT CS
                  Acyl-CoA_dh_N  97 GteeqkrryLpklas 111
                                    Gt+ q +r++ k ++
  gi|121638946|ref|YP_979170.1| 441 GTPWQIERFVEKALR 455
                                    ***********9987 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHHH-HHHHHHHHHHHHTTH.HHHHHHS-HH CS
                  Acyl-CoA_dh_N  61 yleaaivaeelaradaglalllgvhsslva.pailrfGtee 100
                                    +++aa++  e+a  d +++++  +   ++a  + ++ Gt e
  gi|121638946|ref|YP_979170.1| 663 AIAAALWGPEIALLDGPGRVIGRT--VMGArGMAIAGGTSE 701
                                    578899999999999998774333..233324556666666 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   6.9e+03      62      77 ..     158     173 ..     137     191 .. 0.63
   2 !   59.5   0.0   7.8e-20   2.8e-16       1      97 []     461     555 ..     461     555 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                                    EEEEEE..GGGEEE-- CS
                  Acyl-CoA_dh_M  62 slflvprdapgvsvrr 77 
                                     +++++r+++gvsv  
  gi|121638946|ref|YP_979170.1| 158 DVLVLERGRKGVSVDV 173
                                    3677778888888754 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 7.8e-20
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    +  ++Ep+aGsd+asvkt+a++ +g ++ +nG+K+w  +a+++   l  +rt+ ++ ++ g+++++++  apgv+vr+++
  gi|121638946|ref|YP_979170.1| 461 CQLFSEPDAGSDAASVKTRATRVEG-GWEINGQKVWTCGAQYCARGLATVRTDPDApKHAGITTVIIDMLAPGVEVRPLR 539
                                    67789*************6655555.9************************5555599*********************9 PP

                                    -BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfedv 97 
                                    + +G    ++ e++f+dv
  gi|121638946|ref|YP_979170.1| 540 QITGDS--EFNEVFFNDV 555
                                    866655..5779999986 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   1.6e-05     0.057     126     180 ..     227     298 ..     173     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                        Patatin 126 s.................lftanqavpaittataatastanranglytedddddvdladavraSsafPglfp 180
                                    +                 +f a + + a++ + a++a  a ++ ++++++d+++++la av+a++afP + +
  gi|121638946|ref|YP_979170.1| 227 DsavayakvrqqfgrtiaTFQAVKHHCANMLVAAESAIAAVWDAARAAAEDEEQFRLAAAVAAALAFPAYAR 298
                                    3555555566666666666777788999****************************************9875 PP

>> Nterm_IS4  Insertion element 4 transposase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0025       9.1      12      50 ..      89     127 ..      85     137 .. 0.76
   2 ?   -1.9   0.0       1.1     4e+03      75      90 ..     204     219 ..     202     222 .. 0.88
   3 ?    1.8   0.5     0.078   2.8e+02      13      77 ..     223     288 ..     221     292 .. 0.80
   4 ?    0.1   0.1      0.26   9.4e+02      42      84 ..     326     369 ..     323     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                      Nterm_IS4  12 ppelvdevlaetgtaevRkrkLPaevvvylvlalaLfrd 50 
                                    p+ + ++v+a+ gt ++R r+LPa +   l+ ++ L ++
  gi|121638946|ref|YP_979170.1|  89 PTVIASAVVAKEGTDDQRARLLPALIDGTLTAGVGLDSQ 127
                                    55556789***************9776666666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                      Nterm_IS4  75 ksaitqaRkrLGaepl 90 
                                    +sa+++aR+ L ae++
  gi|121638946|ref|YP_979170.1| 204 ESALARARTLLAAEAV 219
                                    699******9999986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.078
                      Nterm_IS4  13 pelvdevlaetgtaevRkrkLPaevvvylvlalaLfrde.syeevvrrLtagleeeaewelpaksa 77 
                                    ++ vd+++a ++++++  r++ + + v    a +L + e  ++ v++   a++e+e++++l a+ a
  gi|121638946|ref|YP_979170.1| 223 ADCVDSAVAYAKVRQQFGRTIATFQAVKHHCANMLVAAEsAIAAVWDAARAAAEDEEQFRLAAAVA 288
                                    5789*****************999888887776666655379999999999999998776665544 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.26
                      Nterm_IS4  42 vlalaLfrde.syeevvrrLtagleeeaewelpaksaitqaRkr 84 
                                    ++++ Lf ++ ++++v +r +ag +++ + +lpa++   +aR r
  gi|121638946|ref|YP_979170.1| 326 LVTVGLFGGDaPVRDVFERTAAGVTRAISLDLPAQAEELRARIR 369
                                    56777887776999999999999999999999999876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 5214.30
//
Query:       gi|121638947|ref|YP_979171.1|  [L=507]
Description: ATP-dependent DNA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-48  162.5   0.0    1.3e-47  162.1   0.0    1.1  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    2.5e-11   44.2   0.0    5.2e-09   36.7   0.0    2.9  3  DNA_ligase_A_N  DNA ligase N terminus
    4.2e-11   43.3   0.1    1.4e-10   41.7   0.0    2.0  2  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    0.00098   19.5   0.0     0.0015   18.9   0.0    1.3  1  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.0   2.8e-51   1.3e-47       1     204 []     186     380 ..     186     380 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 2.8e-51
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLA++++s+++al+++ ++++i+E K+DG+R+q+h+ +d+v++++R+l d+ta++pe+v+a+ ++      +++ DGE+
  gi|121638947|ref|YP_979171.1| 186 PMLAQTATSVHDALERH-GGTTIFEAKLDGARVQIHRANDQVRIYTRSLDDVTARLPEVVEATLALPVR---DLVADGEA 261
                                    9***************8.78888****************************************877776...59****** PP

                                    EEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEE CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaesle 160
                                    +a++++ ++++ fq++asr+ ++++v+ +  +++l++f+FDiL+ dg++l++ p  eR + L  ++ + ++rv   ++l 
  gi|121638947|ref|YP_979171.1| 262 IALCPD-NRPQRFQVTASRFGRSVDVAAARATQPLSVFFFDILHRDGTDLLEAPTTERLAALDALV-PARHRV---DRLI 336
                                    ***999.9**********************************************************.888888...899* PP

                                    ESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 161 vkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                    ++d  +++++l+ ++++g+EG+++K p ++Y +g+r+++wlKvK
  gi|121638947|ref|YP_979171.1| 337 TSDPTDAANFLDATLAAGHEGVMAKAPAARYLAGRRGAGWLKVK 380
                                    *******************************************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01        46      12      66 ..      13      65 ..       5      67 .. 0.74
   2 !   36.7   0.0   1.2e-12   5.2e-09     104     173 .]      70     140 ..      62     140 .. 0.91
   3 ?    3.5   0.0     0.018        80      60      96 ..     131     167 ..     129     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
                                   HCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH..SS-CCCS------HHHHHH CS
                 DNA_ligase_A_N 12 ieestkkrlekrailanffrkvesagpedlypalrL..llPdydgreygigesllak 66
                                   +++ t++rl k+a +a++++    a++++l+ ++    l +++ +r +g+g+ +l+ 
  gi|121638947|ref|YP_979171.1| 13 VAA-TSSRLTKVARIAALLHRA--APDTQLVTII-VswLSGELPQRHIGVGWAALRS 65
                                   455.899************332..2333333333.247999999*******999976 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 1.2e-12
                                    ------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                 DNA_ligase_A_N 104 akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriilkdlriglsektvldala 173
                                    a+++ lt+  v+++L k+ +  gkgs++++++++++l+++a++ E+ +l r++ ++lr g++ + + da a
  gi|121638947|ref|YP_979171.1|  70 APQPALTVTGVDATLSKIGTLsGKGSQAQRAALVAELFSAATEAEQTFLLRLLGGELRQGAKGGIMADAVA 140
                                    67889*************6558****************************************999999875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.018
                                    -HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHH CS
                 DNA_ligase_A_N  60 gesllakalaealglskkkikdalakvgDlgevaeev 96 
                                    ++ ++a a+a+a+gl+ ++++ a    gDl+ +a++ 
  gi|121638947|ref|YP_979171.1| 131 KGGIMADAVAQAAGLPAATVQRAAMLGGDLAAAAAAG 167
                                    5668999*********99999985557****998875 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   1.1e+04      17      41 ..      83     107 ..      77     118 .. 0.69
   2 !   41.7   0.0   3.1e-14   1.4e-10       1      99 []     399     492 ..     399     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                    EEEEEEEE-SS--HHHHHHHHHHHG CS
                 DNA_ligase_A_C  17 kleyvgkvgtGfsdaeleelrkklk 41 
                                    +l+ +g  +   s+a++++l ++l 
  gi|121638947|ref|YP_979171.1|  83 TLSKIGTLSGKGSQAQRAALVAELF 107
                                    5677777777788888888888884 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 3.1e-14
                                    GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEE CS
                 DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeit 78 
                                    r+g+++ + lg++d  +g +++vgk+  G++da+l++ ++++ e+   +      v       v ++Pe vveV+ + ++
  gi|121638947|ref|YP_979171.1| 399 RRGKLSNIHLGARDpaTGGFVMVGKTFKGMTDAMLDWQTTRFHEIAVGPTDG--YV-------VQLRPEQVVEVALDGVQ 469
                                    68999**********99*************************6555443322..22.......3489************* PP

                                    CTSSSTT..EECT-EEEEE-TTS CS
                 DNA_ligase_A_C  79 asgkyka..slRfPrfkrlReDk 99 
                                    +s +y+   +lRf+r++r+R Dk
  gi|121638947|ref|YP_979171.1| 470 RSSRYPGglALRFARVVRYRADK 492
                                    **********************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.3e-07    0.0015       4     161 .]     207     380 ..     204     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-07
                                    EEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH....ECCEEEEEEEES.......... CS
                     RNA_ligase   4 vvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla..neelilyGElig.......... 69 
                                    + + KlDG++++i+  ++ v++ +Rs +  +             a l + +++ la  +++l+  GE i           
  gi|121638947|ref|YP_979171.1| 207 IFEAKLDGARVQIHRANDqVRIYTRSLDDvT-------------ARLPEVVEATLAlpVRDLVADGEAIAlcpdnrpqrf 273
                                    6789***********9777*******88831.............222223333444677899999999997765443333 PP

                                    ...SS..TTSS...................EEEEEEEEEEECTTBECE--HHHHHHHHHCCT.B..EEEEE.SS...HHH CS
                     RNA_ligase  70 ..hsikygglpk..................efyvFdifdirdkeeqrylspdevealakglg.tvpvlyegkfl...aae 125
                                               +                    + Fdi++ +     + l+   +e la+ l+  vp  ++ ++l   +  
  gi|121638947|ref|YP_979171.1| 274 qvT--------AsrfgrsvdvaaaratqplSVFFFDILHRD---GTDLLEAPTTERLAA-LDaLVPARHRVDRLitsDPT 341
                                    320........034444455555666666699******544...666666666699998.55789999888888543333 PP

                                    HHCCC...HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                     RNA_ligase 126 ellel..llskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                    +++++          EG+  k + ++y    +   ++Kvk
  gi|121638947|ref|YP_979171.1| 342 DAANFldA-TLAAGHEGVMAKAPAARYLaGRRgAGWLKVK 380
                                    33333431.45669***********999877799999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3682.62
//
Query:       gi|121638948|ref|YP_979172.1|  [L=758]
Description: carbon starvation protein A cstA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   9.3e-156  518.4  20.9   9.3e-156  518.4  20.9    2.4  3  CstA        Carbon starvation protein CstA
    1.2e-31  109.5   3.0    1.2e-31  109.5   3.0    3.4  4  CstA_5TM    5TM C-terminal transporter carbon starvation CstA
  ------ inclusion threshold ------
        2.7    8.2   4.4        9.7    6.5   0.1    3.1  2  MLTD_N      MltD lipid attachment motif


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1      0.81   4.8e+03     136     157 ..      43      64 ..      38      66 .. 0.77
   2 !  518.4  20.9  1.6e-159  9.3e-156       1     372 [.      67     442 ..      67     445 .. 0.98
   3 ?   -0.4   0.2      0.07   4.2e+02     189     205 ..     687     703 ..     654     719 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.81
                           CstA 136 illililvlavlalvvvkalae 157
                                    i+++ + v+++la+ vv  + +
  gi|121638948|ref|YP_979172.1|  43 IFFVAVAVIGALAWTVVAFFRN 64 
                                    6778888999999999887765 PP

  == domain 2  score: 518.4 bits;  conditional E-value: 1.6e-159
                           CstA   1 mnavllvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAaqf 80 
                                    +nav++vv+a ++++i++rfY++ i+ kv++ +d++aTPae l+dg+dyvpt+++v+fghhFa+iagagPlvGpvlA q+
  gi|121638948|ref|YP_979172.1|  67 VNAVWIVVAAGCTYIIGFRFYARLIEMKVVRPRDDHATPAEILDDGTDYVPTDRRVVFGHHFAAIAGAGPLVGPVLATQM 146
                                    79****************************************************************************** PP

                           CstA  81 GylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkalaespa 160
                                    GylP+ +Wi+vGav+ag+v+D++vl++svrr+g+slg+++++elg +a+++al+ i +i+ +v+avlalvvv+ala+sp+
  gi|121638948|ref|YP_979172.1| 147 GYLPSSIWIVVGAVLAGCVQDYLVLWISVRRRGRSLGQMVRDELGATAGVAALVGIPVIITIVIAVLALVVVRALAKSPW 226
                                    ******************************************************************************** PP

                           CstA 161 avfsviltipialllGvllrklrkg.vleasvigvvllllavvvgsev.eea.laelltlsketlaivlivYvfvAsvlP 237
                                    +vfs+++tipia+++G++lr+lr+g v e+s+ig+ llllavv g +v +++  a++++ls +tl+++li Y+f+AsvlP
  gi|121638948|ref|YP_979172.1| 227 GVFSIAMTIPIAIFMGCYLRFLRPGrVSEVSLIGIGLLLLAVVSGDWVaHTSwGAAWFSLSPVTLCWLLISYGFAASVLP 306
                                    ************************************************76666789************************ PP

                           CstA 238 vwlllaPrdYlstflligtivllalgilvvapelklpavtef.vdgegpvfagslfPllfitiACGaiSGFHslvssgtt 316
                                    vwlllaPrdYlstf+++gti+lla+g++ ++p +++pav++f  +g+gpvfagslfP+lfitiACGa+SGFH+l+ sgtt
  gi|121638948|ref|YP_979172.1| 307 VWLLLAPRDYLSTFMKVGTIALLAIGVCAAHPIIEAPAVSKFaGSGNGPVFAGSLFPFLFITIACGALSGFHALICSGTT 386
                                    ******************************************999*********************************** PP

                           CstA 317 skllekesdarlvgygamllEslvailalvaaavlepaayfalnsaaavlgttvea 372
                                    +k+leke ++r++gy +m++Es+va++al++aa+l+++ yf+ln++   + +++++
  gi|121638948|ref|YP_979172.1| 387 PKMLEKEGQMRVIGYCGMMTESFVAVIALLTAAILDQHLYFTLNAPSLHTHDSAAT 442
                                    *********************************************98777655555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.07
                           CstA 189 asvigvvllllavvvgs 205
                                     s++ vv+++l vv+g 
  gi|121638948|ref|YP_979172.1| 687 LSIVFVVVVVLVVVAGV 703
                                    22222222222222222 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.5   8.8e+03      48      70 ..     150     172 ..     137     174 .. 0.65
   2 ?   -1.3   0.7      0.44   2.7e+03      80     105 ..     210     236 ..     182     245 .. 0.63
   3 !  109.5   3.0     2e-35   1.2e-31       2     116 .]     503     633 ..     502     633 .. 0.92
   4 ?   -3.3   0.1       1.9   1.1e+04      52      57 ..     691     696 ..     670     707 .. 0.49

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                       CstA_5TM  48 vatliavalavllllwggintlW 70 
                                    ++++ +v+ avl++ ++++ +lW
  gi|121638948|ref|YP_979172.1| 150 PSSIWIVVGAVLAGCVQDYLVLW 172
                                    44555555555555666899998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.44
                       CstA_5TM  80 LAalaLlvvtvwll.ktgrkalvtliP 105
                                    +A laL+vv ++ +  +g   +++ iP
  gi|121638948|ref|YP_979172.1| 210 IAVLALVVVRALAKsPWGVFSIAMTIP 236
                                    455555555555554444444444444 PP

  == domain 3  score: 109.5 bits;  conditional E-value: 2e-35
                       CstA_5TM   2 avaytfailfvalfalTtlDtatRlaRyilqellgelk..kkaltn.ky.vatliavalavllllwg............g 65 
                                    a++y+fai+f+alf+lTt+D++tR aR++++++lg++    ++l+n ++ ++++++++++v++  wg            g
  gi|121638948|ref|YP_979172.1| 503 AFWYHFAIMFEALFILTTVDAGTRAARFMISDALGNFGgvLRKLQNpSWrPGAWACSLVVVAA--WGsilllgvtdplgG 580
                                    79***********************************99955556647889999999998888..88888888999999* PP

                       CstA_5TM  66 intlWplFGaaNQlLAalaLlvvtvwllktgr..kalvtliPmvfmlvvtlta 116
                                    intl+plFG+aNQlLA++a +v+tv+++k+gr  +a++  iP+++ l+vtlta
  gi|121638948|ref|YP_979172.1| 581 INTLFPLFGIANQLLAGIAPTVITVVVIKKGRlkWAWIPGIPLLWDLAVTLTA 633
                                    ****************************999988999999**********997 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.9
                       CstA_5TM  52 iavala 57 
                                    ++v+++
  gi|121638948|ref|YP_979172.1| 691 FVVVVV 696
                                    111111 PP

>> MLTD_N  MltD lipid attachment motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.3     0.088   5.3e+02      22      32 ..     154     164 ..     153     165 .. 0.94
   2 ?    6.5   0.1    0.0016       9.7      12      22 ..     522     532 ..     520     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.088
                         MLTD_N  22 alaaaalLaGC 32 
                                    ++  +a LaGC
  gi|121638948|ref|YP_979172.1| 154 WIVVGAVLAGC 164
                                    8899******* PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                         MLTD_N  12 dALtRavqisa 22 
                                    dA+tRa+++++
  gi|121638948|ref|YP_979172.1| 522 DAGTRAARFMI 532
                                    8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 5433.45
//
Query:       gi|121638949|ref|YP_979173.1|  [L=141]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-10   40.1   8.0    6.8e-10   39.4   8.0    1.4  1  DoxX      DoxX
  ------ inclusion threshold ------
      0.012   15.5   2.3      0.049   13.5   2.3    1.8  1  DoxD      TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   8.0   7.6e-14   6.8e-10       2      84 ..      17      93 ..      16      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 7.6e-14
                           DoxX  2 llllRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvatltv 83
                                   l l Rl+ g+lf   G   l+g+    ++ s +++ +    +  ++a+++Elv+gll++ Gl+tR +A++    ++va +++
  gi|121638949|ref|YP_979173.1| 17 LSLFRLVYGLLFAGYGSMILFGW----PVTSAQPVEF--GSWPGWYAGVIELVAGLLIATGLFTRAVAFVASGEMAVAYFWM 92
                                   6689*****************87....8888888888..89***************************************** PP

                           DoxX 84 h 84
                                   h
  gi|121638949|ref|YP_979173.1| 93 H 93
                                   9 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.3   5.4e-06     0.049      72     142 ..      58     135 ..      55     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-06
                           DoxD  72 tlvEiivGlllliGlltRlsslvaf.alalgials....ayW.lgstcedEyqi.glllvaaelvliltgsgklslDy 142
                                    +++E ++Gll+  Gl+tR +++va   +a+ ++      a W +g     + +  ++l   + ++l++tg+g +s+D+
  gi|121638949|ref|YP_979173.1|  58 GVIELVAGLLIATGLFTRAVAFVASgEMAVAYFWMhqpyALWpIGGPPDGNGGTpAILFCFGFFLLVFTGGGIYSIDA 135
                                    689******************999735888887422222556334333333333245666666777778888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1073.11
//
Query:       gi|121638950|ref|YP_979174.1|  [L=107]
Description: multidrugs-transport integral membrane protein mmr [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-29  101.1  10.3    5.3e-29  100.7  10.3    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
     0.0014   18.8  13.6     0.0017   18.5  13.6    1.2  1  EamA            EamA-like transporter family
  ------ inclusion threshold ------
      0.058   13.0  11.3       0.11   12.1  11.3    1.4  1  EmrE            Putative multidrug resistance efflux transpor
      0.061   12.7   6.0      0.059   12.7   5.3    1.2  1  TPT             Triose-phosphate Transporter family
        2.4    6.9   5.7        2.4    6.9   5.7    1.1  1  CreD            Inner membrane protein CreD


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7  10.3   1.5e-32   5.3e-29       1      93 []       1      94 [.       1      94 [. 0.98

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.5e-32
                                   XX-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----HHHHHHHHHHHHHHHHHHHHH--- CS
                 Multi_Drug_Res  1 mnwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvAYavwsGiGtvlivlvgillfges 81
                                   m +++l++Ai++evv+++lLk++egft+l+p+++++vgygi+f+lL++++++ ++++vAYa+ws+iGt++ivlv++l++g++
  gi|121638950|ref|YP_979174.1|  1 MIYLYLLCAIFAEVVATSLLKSTEGFTRLWPTVGCLVGYGIAFALLALSISHgMQTDVAYALWSAIGTAAIVLVAVLFLGSP 82
                                   7899**********************************************999***************************** PP

                                   -----HHHHHHH CS
                 Multi_Drug_Res 82 lslkkliglali 93
                                   +s++k++g++li
  gi|121638950|ref|YP_979174.1| 83 ISVMKVVGVGLI 94
                                   **********98 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  13.6   4.7e-07    0.0017      37     136 ..       4     102 ..       1     103 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.7e-07
                           EamA  37 rfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnasli..tslePvftlilsvlllg 114
                                     +l+++i+  ++a    ++         l+  + +l+g  +af l+  +++++  + ++++  +++  + +++ +vl+lg
  gi|121638950|ref|YP_979174.1|   4 LYLLCAIFAEVVATSLLKST---EGFTRLWPTVGCLVGYGIAFALLALSISHGMQTDVAYAlwSAIGTAAIVLVAVLFLG 80 
                                    55666666633333333333...334569999**********************9988877669999************* PP

                           EamA 115 ekltlkqllgivlillGvllil 136
                                     ++++++++g++li++Gv+ ++
  gi|121638950|ref|YP_979174.1|  81 SPISVMKVVGVGLIVVGVVTLN 102
                                    ******************9876 PP

>> EmrE  Putative multidrug resistance efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  11.3     3e-05      0.11       9     105 ..       5     104 ..       1     107 [] 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                           EmrE   9 llvivllkkgelkellkelkkkplfwllwg.siGfglfYallcfaaayapgWlvA.atwq.itivagllllplfkrkkip 85 
                                     l++ ++ +   ++llk+    ++ w ++g  +G+g+ +all+++ +++    vA a w  i   a +l+++lf ++ i 
  gi|121638950|ref|YP_979174.1|   5 YLLCAIFAEVVATSLLKSTEGFTRLWPTVGcLVGYGIAFALLALSISHGMQTDVAyALWSaIGTAAIVLVAVLFLGSPIS 84 
                                    333333333367788888888999998887369************99987665553788624556778999999****** PP

                           EmrE  86 lkalllsllillGvvlvqle 105
                                    + +++   li++Gvv ++l 
  gi|121638950|ref|YP_979174.1|  85 VMKVVGVGLIVVGVVTLNLA 104
                                    ****************9986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.3   1.6e-05     0.059     244     287 ..      56      99 ..      40     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                            TPT 244 spvthsvantvKrvvvIvlsvlvfknpvsllnaiGtavaivGvf 287
                                    + v++++ +++  + ++ ++vl+++ p+s+++++G+ + +vGv+
  gi|121638950|ref|YP_979174.1|  56 TDVAYALWSAIGTAAIVLVAVLFLGSPISVMKVVGVGLIVVGVV 99 
                                    57999*************************************97 PP

>> CreD  Inner membrane protein CreD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.7   0.00066       2.4     321     382 ..      28      88 ..       2     103 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00066
                           CreD 321 rihpiqYlLvGlalvlFYlLllslsEhlgFelAYliaalavvllislYlssvlkskkrgllf 382
                                    r+ p   +LvG +++ F lL ls+s  ++ ++AY++ ++  ++ i l +  +l+s  + + +
  gi|121638950|ref|YP_979174.1|  28 RLWPTVGCLVGYGIA-FALLALSISHGMQTDVAYALWSAIGTAAIVLVAVLFLGSPISVMKV 88 
                                    555666689999975.99****************9766666666655555555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 841.04
//
Query:       gi|121638951|ref|YP_979175.1|  [L=202]
Description: DeoR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-10   39.8  10.7    4.1e-10   39.8  10.7    2.6  3  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
    1.3e-08   34.5   0.1    3.2e-08   33.2   0.1    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
    0.00021   21.7  12.4    0.00045   20.6   4.5    2.3  2  TetR_C_28  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
          1    9.6  14.3        0.1   12.8   6.2    3.0  3  TetR_C_6   BetI-type transcriptional repressor, C-terminal


Domain annotation for each model (and alignments):
>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.6      0.21   9.2e+02      47      65 ..      15      33 ..       7      44 .. 0.73
   2 ?   -0.5   0.1      0.31   1.4e+03       4      24 ..      67      89 ..      63      91 .. 0.69
   3 !   39.8  10.7   9.1e-14   4.1e-10       3     106 ..      87     183 ..      85     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHHHHHHCSS CS
                      TetR_C_31 47 lrralrealaallaalGlp 65
                                   +r+a++ea++++ a+ Gl 
  gi|121638951|ref|YP_979175.1| 15 RRQAIVEAAERVIARQGLG 33
                                   5788888899998888883 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
                                   CHHHHHHHHHCCCCCT..THHHH CS
                      TetR_C_31  4 eeladlladlldrala..drert 24
                                   +++a + adll+++ +  d +r 
  gi|121638951|ref|YP_979175.1| 67 AHAANASADLLAQWRSdlDKDRD 89
                                   67788888888888776655554 PP

  == domain 3  score: 39.8 bits;  conditional E-value: 9.1e-14
                                    CCHHHHHHHHHCCCCCTTHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHHHHHHHHH CS
                      TetR_C_31   3 reeladlladlldraladrertlAryelfleaarrPeLraalarlrralrealaallaalGlpdpeeaarllvaaldGll 82 
                                     ++la+ la+l   +lad +r+  + el+++aa+rPeL+++++ + ++l+++l+    ++G+    +aa +++ + dG+ 
  gi|121638951|ref|YP_979175.1|  87 DRDLAATLARLTTVYLADQDRYRTLNELYMAAAHRPELQRLARLWPDGLLALLEP---RIGR----RAANAVTVFFDGAT 159
                                    5799********99*************************************8887...8888....489999******** PP

                                    HHHHHSGTS-H..HHHHHHHHHHHT- CS
                      TetR_C_31  83 ldrLagpaadp..raevrellralld 106
                                    l++L+++  +p  ++e+++++++l++
  gi|121638951|ref|YP_979175.1| 160 LHALITG--TPlsTDELTDAIARLVA 183
                                    *******..56669999999999986 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   7.1e-12   3.2e-08       1      46 [.      19      64 ..      19      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7.1e-12
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   I++aA++++a++G  +++ r++A++A+v  g+  +yF + ++L ea
  gi|121638951|ref|YP_979175.1| 19 IVEAAERVIARQGLGGLSHRRVAAEANVPVGSTTYYFNDLDALREA 64
                                   89************************************99999888 PP

>> TetR_C_28  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   2.6    0.0066        29      18      49 ..      61      92 ..      49     103 .. 0.68
   2 !   20.6   4.5     1e-07   0.00045       9      93 ..      98     183 ..      90     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0066
                                   HHHHHHHHHGGGSHHHHHHHHHHHHHHS--TT CS
                      TetR_C_28 18 allaallaalaedpellepwrewyrrwlerle 49
                                    ++aal  a+ ++ +ll+ wr ++++ ++  +
  gi|121638951|ref|YP_979175.1| 61 LREAALAHAANASADLLAQWRSDLDKDRDLAA 92
                                   45688888888888888888888877765443 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1e-07
                                    HHHT..S-..-HHHHHHHHHGGGSHHHHHHHHHHHHHHS--TTGG-HHHHHHHHHHHHHHHHHHHHHHSSS---HHHHHH CS
                      TetR_C_28   9 ratf..deeerallaallaalaedpellepwrewyrrwlerleadgldpvlatlvrlAadGlwlaellglppldpeeraa 86 
                                     ++   d++  ++l  l +a+a+ pel+++ r w +  l+ le   +  ++a  v    dG+ l++l+ + pl+ +e+  
  gi|121638951|ref|YP_979175.1|  98 TTVYlaDQDRYRTLNELYMAAAHRPELQRLARLWPDGLLALLEPR-IGRRAANAVTVFFDGATLHALITGTPLSTDELTD 176
                                    34334456889999**************************99955.4467889999999********************* PP

                                    HHHHHHH CS
                      TetR_C_28  87 llerLle 93 
                                     ++rL +
  gi|121638951|ref|YP_979175.1| 177 AIARLVA 183
                                    ****986 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.2   5.5e+03      55      61 ..      20      26 ..       8      45 .. 0.50
   2 ?   -0.9   0.3      0.41   1.8e+03      55      68 ..      74      86 ..      57     103 .. 0.46
   3 ?   12.8   6.2   2.3e-05       0.1      19     111 ..     104     183 ..      83     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                   HHHHHHH CS
                       TetR_C_6 55 rallael 61
                                   +++ +++
  gi|121638951|ref|YP_979175.1| 20 VEAAERV 26
                                   2222222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                                   HHHHHHHHHTTSCT CS
                       TetR_C_6 55 rallaelaegglra 68
                                   ++lla+ ++  l +
  gi|121638951|ref|YP_979175.1| 74 ADLLAQWRS-DLDK 86
                                   233333333.3333 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHHHHHHHHHHHTCTTCH CS
                       TetR_C_6  19 rraelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaAerlaAlidGLwlraalapeeld 98 
                                    +++ +++  +++ +aa++pel++l r     + + l all+             ++aA +++ + dG +l+a++   +l+
  gi|121638951|ref|YP_979175.1| 104 DQDRYRTLNELYMAAAHRPELQRLAR----LWPDGLLALLEPRIG---------RRAANAVTVFFDGATLHALITGTPLS 170
                                    33445555556666666666666654....333333334443333.........79************************ PP

                                    HHHHHHHHHHHHH CS
                       TetR_C_6  99 aeraralvrrhld 111
                                     +++ ++++r ++
  gi|121638951|ref|YP_979175.1| 171 TDELTDAIARLVA 183
                                    *****99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1469.34
//
Query:       gi|121638952|ref|YP_979176.1|  [L=136]
Description: hypothetical protein BCG_3092 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-16   58.3   0.1      1e-15   57.9   0.1    1.2  1  DUF732    Protein of unknown function (DUF732)
  ------ inclusion threshold ------
       0.43   10.3   1.9       0.66    9.7   1.9    1.3  1  DUF2759   Protein of unknown function (DUF2759)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.1   1.1e-19     1e-15      10      94 ..      39     129 ..      29     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.1e-19
                         DUF732  10 lllaapAaAd.......saddaFlaalnqagiaygspdaaialGkavCkkldsGksaeavvaevkndnsglspeqaaqfv 82 
                                    +  +ap aA        + d+ Fl +l++ gi++ +pdaa+  Gk vC  l  G++ ++vv+++++++++l  + ++  v
  gi|121638952|ref|YP_979176.1|  39 TTRSAPTAAPpstlqspDLDSVFLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPAL-GDRTTAYV 117
                                    4556666664455666778889*******************************************987775.7899999* PP

                         DUF732  83 gaAvsayCPeql 94 
                                    + ++++yCP++ 
  gi|121638952|ref|YP_979176.1| 118 AVSIRTYCPKYD 129
                                    *********985 PP

>> DUF2759  Protein of unknown function (DUF2759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.9   7.4e-05      0.66      22      41 ..       1      20 [.       1      21 [. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.4e-05
                        DUF2759 22 llgvlFaglavavFGWFsvm 41
                                   +l+v+ ++ a ++ GWF+++
  gi|121638952|ref|YP_979176.1|  1 MLAVGVGIGAAILLGWFTLA 20
                                   79****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1005.57
//
Query:       gi|121638953|ref|YP_979177.1|  [L=547]
Description: phosphoglucomutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-38  130.2   0.1    7.8e-38  129.3   0.1    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      1e-27   96.6   0.0    1.8e-27   95.8   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-11   44.5   0.0    7.6e-11   42.6   0.0    2.0  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.4e-07   29.7   0.0    1.4e-06   28.3   0.0    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.1   1.7e-41   7.8e-38       2     134 ..      40     181 ..      39     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 1.7e-41
                                    GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEE...EB- CS
                      PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillg...llp 78 
                                    ++fgtsG+Rg++  g++++ ++++++qai+ey +a+++++++++GrDt+  s+ +  +++++laan+v +++ +   ++p
  gi|121638953|ref|YP_979177.1|  40 VAFGTSGHRGSALTGTFNELHILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSrdrYTP 119
                                    57******************************************************************9999999***** PP

                                    HHHHHHHHHHCC......ECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                      PGM_PMM_I  79 tPavsfairklk......adagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                    tPa+s+ai +++      +++gi++t+SHnpp + giK++++nGgp++++++++I+++++++
  gi|121638953|ref|YP_979177.1| 120 TPAISHAILTYNrgrteaLADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEI 181
                                    ******************9***************************************9987 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0     4e-31   1.8e-27       1     113 [.     323     442 ..     323     443 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 4e-31
                                    HHHHHHHHHHHHHHCH..CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                    PGM_PMM_III   1 dgdqllallakyllee..klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                    +++++la++++yl ++   ++ g +v ktv++s++++rv++  g++lve++vG+k++++ +    + +GgEeS++++fl+
  gi|121638953|ref|YP_979177.1| 323 NPNHYLAVAIEYLYTHrpSWPAGIAVGKTVVSSSIIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLR 402
                                    68***********99999999999*******************************************************9 PP

                                    T.....BSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                    PGM_PMM_III  79 e.....attkDGilaallvleilaetgkslselleellkk 113
                                    +     +t+kDGi++all++eila tg ++s+ +++l  +
  gi|121638953|ref|YP_979177.1| 403 RdgsvwTTDKDGIIMALLAAEILAVTGATPSQRYHALAGE 442
                                    99**99999***********************99887655 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   1.1e+04      29      60 ..      88     120 ..      84     125 .. 0.77
   2 !   42.6   0.0   1.7e-14   7.6e-11       3     102 ..     209     318 ..     207     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                    T-TTHHHHHHHHHHTT-.EEEES-----TT-TT CS
                     PGM_PMM_II  29 hGaggeilkellkelgv.dvvelnaepdpdfpt 60 
                                    hG ++  + ++l+ l + +vv + + +d   pt
  gi|121638953|ref|YP_979177.1|  88 HGLSEPAWVSALEVLAAnQVVAVVDSRDRYTPT 120
                                    888999999999999997777777777766665 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.7e-14
                                    HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TT......SS----T..T-TTTTH CS
                     PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfpt......kapnpee..kealkll 74 
                                    Y+++l + vd++ai+++g+++ +dpl+Ga+ ++++e+ ++ g+d++ +n   d+++        + +++++  ++a++ l
  gi|121638953|ref|YP_979177.1| 209 YVDDLPNVVDIAAIREAGVRIGADPLGGASVDYWGEIAHRHGLDLTVVNPLVDATWRFmtldtdGKIRMDCssPDAMAGL 288
                                    ******************************************************98877799998888888545577777 PP

                                    HHHG..GGGG-SEEEEE-TTS-BEEEEETT CS
                     PGM_PMM_II  75 ielv..kkegadlglafDgDaDRlgvvder 102
                                    i+++  ++e+++++  +D DaDR+g+v+++
  gi|121638953|ref|YP_979177.1| 289 IRTMfgNRERYQIATGNDADADRHGIVTPD 318
                                    77653355689****************875 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.2e-10   1.4e-06      24      71 ..     493     540 ..     453     543 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.2e-10
                                    HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHHHHHHHH CS
                     PGM_PMM_IV  24 sikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarlaeevae 71 
                                       +glk+++++++++  RpSGTe++ ++y+E+    ++l ++++  +e
  gi|121638953|ref|YP_979177.1| 493 AALGGLKVTTANAWFA-ARPSGTEDVYKIYAESFrGPQHLVEVQQTARE 540
                                    46789***********.*****************988888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 4099.43
//
Query:       gi|121638954|ref|YP_979178.1|  [L=132]
Description: camphor resistance protein CrcB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-26   92.3   5.0    2.1e-26   92.0   5.0    1.0  1  CRCB             CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
      0.099   12.7   8.9        1.8    8.6   1.9    2.1  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   5.0   2.4e-30   2.1e-26       2      93 ..      11     120 ..      10     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 2.4e-30
                                    HHHHHHHHHHHHHHHH.HHHHBE....BHHHHHHHHHHHHHHHHHHH..............HHTTTHHHHHS-SHHHHHH CS
                           CRCB   2 lvalggalGallRyllssllnkr....plgtlavNvlGsfllgllla..............llttGflGglTTfStfvle 63 
                                    +v++ggalGal+R +ls l+++     p+ t++vNv+G+fl+g++++              ll+tG++GglTTfSt+ +e
  gi|121638954|ref|YP_979178.1|  11 AVFAGGALGALARAALSALAIPDparwPWPTFTVNVVGAFLVGYFTTrllerlplssyrrpLLGTGLCGGLTTFSTMQVE 90 
                                    799*************999888899999****************999999998888888888****************** PP

                                    HHHHHHHT-HHHHHHHHHHHHHHHHHHHHH CS
                           CRCB  64 lvslleegellaallyvllsvvlgllavvl 93 
                                    ++s++e+g++  a++y ++s+ lgllav l
  gi|121638954|ref|YP_979178.1|  91 TISMIEHGHWGLAAAYSVVSITLGLLAVHL 120
                                    *************************99865 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.9    0.0002       1.8      42      79 ..       9      53 ..       8      66 .. 0.72
   2 ?    8.6   0.8    0.0002       1.8      48      92 ..      78     129 ..      71     132 .] 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0002
                Phage_holin_3_6 42 aagvlallalllllvalalala.a.....lwlaali.vaavllvl 79
                                   +a+v+a  al++l  a++ ala       +w  +++ v +++lv 
  gi|121638954|ref|YP_979178.1|  9 LAAVFAGGALGALARAALSALAiPdparwPWPTFTVnVVGAFLVG 53
                                   6999*********99996555422556668888888665555553 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0002
                Phage_holin_3_6  48 llalllllvalalala.a......lwlaalivaavllvlagvlalvglkklk 92 
                                    + +l++++ + +  ++ +      l++a+ +v + l +la+ la v +++++
  gi|121638954|ref|YP_979178.1|  78 CGGLTTFSTMQVETISmIehghwgLAAAYSVVSITLGLLAVHLATVLVRRVR 129
                                    344444444444333222333345589999999***********99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1041.76
//
Query:       gi|121638955|ref|YP_979179.1|  [L=126]
Description: camphor resistance protein CrcB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-24   86.4   7.1    1.5e-24   86.1   7.1    1.1  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
      0.023   14.8   4.3      0.023   14.8   4.3    2.9  2  DUF3180   Protein of unknown function (DUF3180)
      0.077   12.7  12.6      0.064   12.9   5.8    2.2  2  DUF4203   Domain of unknown function (DUF4203)
        1.1    9.5   6.8        1.3    9.2   0.6    2.3  2  DUF3493   Low psii accumulation1 / Rep27
        9.1    6.4  10.9        5.7    7.1   0.3    3.2  3  DUF4235   Protein of unknown function (DUF4235)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   7.1   4.2e-28   1.5e-24       3      94 ..      15     120 ..      13     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 4.2e-28
                                    HHHHHHHHHHHHHHH.HHHHBE.....BHHHHHHHHHHHHHHHHHHH.........HHTTTHHHHHS-SHHHHHHHHHHH CS
                           CRCB   3 valggalGallRyllssllnkr.....plgtlavNvlGsfllgllla.........llttGflGglTTfStfvlelvsll 68 
                                    v+l+g +G++lR+l+++ +++r     p+gtl+vN++G++llg+l++         l +tGf+G++TTfSt++le+ +l 
  gi|121638955|ref|YP_979179.1|  15 VMLIGGIGSVLRFLVDRSVARRlartfPYGTLTVNITGAALLGFLAGlalpkdaalLAGTGFVGAYTTFSTWMLETQRLG 94 
                                    899************9988888****999****************99887777776699********************* PP

                                    HHT-HHHHHHHHHHHHHHHHHHHHHH CS
                           CRCB  69 eegellaallyvllsvvlgllavvlg 94 
                                    e++++++al+++++svvlgl+a++lg
  gi|121638955|ref|YP_979179.1|  95 EDRQMVSALANIVVSVVLGLAAALLG 120
                                    **********************9987 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   6.6      0.22     8e+02      76      91 ..      48      63 ..       4      66 .. 0.47
   2 ?   14.8   4.3   6.4e-06     0.023      75     129 ..      68     121 ..      64     126 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.22
                        DUF3180 76 salvGAllaGvyaGll 91
                                   + ++GA+l+G+ aGl+
  gi|121638955|ref|YP_979179.1| 48 VNITGAALLGFLAGLA 63
                                   3345555555555554 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.4e-06
                        DUF3180  75 AsalvGAllaGvyaGllvyllragelpaaaedllaavvavlaavalvvaglwlEr 129
                                    A+ l+G+ ++G+y+ +  ++l++++l    +++++a+++++++v+l  a+ +l +
  gi|121638955|ref|YP_979179.1|  68 AALLAGTGFVGAYTTFSTWMLETQRLGE-DRQMVSALANIVVSVVLGLAAALLGQ 121
                                    8899*****************9999988.56677888888888888665554433 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.8   1.8e-05     0.064      73     147 ..       9      83 ..       2      86 .. 0.82
   2 ?    4.3   1.0    0.0077        28      48      75 ..      96     124 ..      81     126 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                        DUF4203  73 lfwelglfllgalgGlllallilsllegglitslpskaiflvivvlgllgavlslkl.qklllivatsvvGaaavv 147
                                    +  ++g++l+g   G +l +l+  +++++l +++p  ++ + i++ +llg+++ l l ++++l++ t++vGa++++
  gi|121638955|ref|YP_979179.1|   9 VAIWIGVMLIGG-IGSVLRFLVDRSVARRLARTFPYGTLTVNITGAALLGFLAGLALpKDAALLAGTGFVGAYTTF 83 
                                    455678888887.56666666666667999999999888899**************9999*************987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0077
                        DUF4203  48 p.sslvqgaslvaalvvGllgGllallfw 75 
                                    + + ++  a++v+++v+Gl+ +ll  +++
  gi|121638955|ref|YP_979179.1|  96 DrQMVSALANIVVSVVLGLAAALLGQWIA 124
                                    35778889999999999999999866555 PP

>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8     0.026        92      22      75 ..      11      60 ..       6      62 .. 0.59
   2 ?    9.2   0.6   0.00037       1.3      26      74 ..      71     119 ..      69     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.026
                        DUF3493 22 lYlafaaSaliGalifllrllaaragaesapeleea..lenlaiqvgavalfvfLl 75
                                   ++++++  ++iG    +lr+l  r   + a  l+ +  +  l +++++ al++fL+
  gi|121638955|ref|YP_979179.1| 11 IWIGVMLIGGIGS---VLRFLVDR---SVARRLARTfpYGTLTVNITGAALLGFLA 60
                                   5555555555554...44444444...22334444411568999999999999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00037
                        DUF3493  26 faaSaliGalifllrllaaragaesapeleealenlaiqvgavalfvfL 74 
                                    +a  +++Ga+++++  +  ++   ++ ++ +al n+ + v+  ++ ++L
  gi|121638955|ref|YP_979179.1|  71 LAGTGFVGAYTTFSTWMLETQRLGEDRQMVSALANIVVSVVLGLAAALL 119
                                    5778****************9*****************99877777766 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0016       5.7      52      74 ..      17      39 ..       4      41 .. 0.89
   2 ?    1.9   0.2     0.066   2.4e+02       4      27 ..      60      83 ..      53     104 .. 0.78
   3 ?    3.3   1.0     0.024        87       3      19 ..     107     123 ..     106     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0016
                        DUF4235 52 isGavlavvrvaadRgtargver 74
                                   + G +++v+r ++dR  ar  +r
  gi|121638955|ref|YP_979179.1| 17 LIGGIGSVLRFLVDRSVARRLAR 39
                                   56999**************9988 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.066
                        DUF4235  4 lglvlglvaGavagkafaavWkkv 27
                                   +gl+l+  a+++ag  f  +++ +
  gi|121638955|ref|YP_979179.1| 60 AGLALPKDAALLAGTGFVGAYTTF 83
                                   677777778888888887777655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.024
                        DUF4235   3 llglvlglvaGavagka 19 
                                    ++++vlgl+a+++++ +
  gi|121638955|ref|YP_979179.1| 107 VVSVVLGLAAALLGQWI 123
                                    5899*********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 891.38
//
Query:       gi|121638956|ref|YP_979180.1|  [L=369]
Description: hypothetical protein BCG_3096 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-61  202.8   0.0    1.1e-20   73.7   0.0    3.1  3  DUF190    Uncharacterized ACR, COG1993


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0     6e-21   1.1e-16       2      95 ..       7     103 ..       6     105 .. 0.95
   2 !   64.9   0.0   3.4e-22   6.1e-18       2      96 ..     127     220 ..     126     221 .. 0.98
   3 !   73.7   0.0   6.4e-25   1.1e-20       2      95 ..     248     343 ..     247     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6e-21
                                    EEEEEEETT-E...ETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHH CS
                         DUF190   2 lLrIyigesdr...legkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieafl 78 
                                    +L+ y+ge++r     g+ l +a+++l+ ++++a  ++lrG  +fg +++++ ++ l+lsed Pv++ +vd e+ki++++
  gi|121638956|ref|YP_979180.1|   7 KLTAYFGERQRavgGAGRFLADAMLDLFGSHNVATSVMLRGTTSFGPKHEFRCDQSLSLSEDPPVTVAAVDIESKIRSLV 86 
                                    689999999996555699************************************************************** PP

                                    HHHHT----SEEEEEEE CS
                         DUF190  79 pelkelvkeglvtlekv 95 
                                    + +++++++glvtle+ 
  gi|121638956|ref|YP_979180.1|  87 DDVTAMTDRGLVTLERA 103
                                    ***************87 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 3.4e-22
                                    EEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHHHHH CS
                         DUF190   2 lLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieaflpel 81 
                                    +L+Iy g++ r+ g p+y +i+el++++g+agatvl G+ G   ++r ++a+++  + ++P++i +v t+ +++    el
  gi|121638956|ref|YP_979180.1| 127 KLTIYAGRQVRVAGAPAYYTICELLHRHGFAGATVLLGVDGTA-HGRRRRARFFGRNVNVPLMIIAVGTPAQVAVAAMEL 205
                                    79***************************************98.999********************************* PP

                                    HT----SEEEEEEEE CS
                         DUF190  82 kelvkeglvtlekve 96 
                                    ++ + + l+t+e+v+
  gi|121638956|ref|YP_979180.1| 206 TAALPNPLLTIERVR 220
                                    *************96 PP

  == domain 3  score: 73.7 bits;  conditional E-value: 6.4e-25
                                    EEEEEEETT-EETTEEHHHHHHHHHHHT.T-S--EEEE-S---------------------EEEEEEEE-HHHHHHHHHH CS
                         DUF190   2 lLrIyigesdrlegkplyeaivelaree.glagatvlrGieGfgassrihtakllelsedlPvvieivdteekieaflpe 80 
                                    +L++++ e++++eg p+++a+v++++++  ++gat+lrGi+Gf  +++ h +kl++l + +Pv+  ivdt+++i++ ++ 
  gi|121638956|ref|YP_979180.1| 248 KLMVHTAEATHHEGLPIHRALVHRLMQSeTARGATALRGIWGFYGDHKPHGDKLFQLVRRVPVTTIIVDTPQAIARSFDI 327
                                    799*********************99987899************************************************ PP

                                    HHT----.SEEEEEEE CS
                         DUF190  81 lkelvke.glvtlekv 95 
                                    ++el++  glvt e v
  gi|121638956|ref|YP_979180.1| 328 VDELTNWhGLVTSEMV 343
                                    *****966******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2492.42
//
Query:       gi|121638957|ref|YP_979181.1|  [L=174]
Description: hypothetical protein BCG_3097c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-18   64.7   0.8    1.2e-17   64.3   0.8    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.8   6.8e-22   1.2e-17      15     111 ..      18     133 ..       6     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 6.8e-22
                 Bac_luciferase  15 lgaasaslrylvelaraaEelGfdavwvaehhggpgga....................ldaftllaalaaaTerirlgta 74 
                                     ga++ +++ + ++a+aa++ Gf ++wv+eh  + +                      ld++  l+ +aaa +r+ + t+
  gi|121638957|ref|YP_979181.1|  18 IGAGA-DPAVVDAVAVAADDCGFATLWVGEHVVMVDRPasrypysrdgviavpaqadwLDPMIALSFAAAASSRVDVATG 96 
                                    33444.8888999*******************9877778***************************************** PP

                 Bac_luciferase  75 vtplytrhPavlAqqaatLdhlsgGRfglglgtggpa 111
                                    v+ l+ ++P+++A++aa+Ld+lsg R+ lg+ + gp 
  gi|121638957|ref|YP_979181.1|  97 VLLLPEHNPVIVAKEAASLDRLSGRRLTLGVASDGPR 133
                                    *******************************996665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1205.78
//
Query:       gi|121638958|ref|YP_979182.1|  [L=118]
Description: hypothetical protein BCG_3098c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-25   89.6   0.4    2.5e-25   89.4   0.4    1.0  1  DUF488    Protein of unknown function, DUF488


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.4   1.4e-29   2.5e-25       2     122 .]       9     115 ..       8     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.4e-29
                         DUF488   2 lervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferYaae 79 
                                    + rvy+   ++dg rvlvD R wP     g++k++ +           w+k+++ps+elr+w++h+p r++ef +rY++e
  gi|121638958|ref|YP_979182.1|   9 VARVYEdIDPDDGQRVLVD-RIWPH----GIRKDDQRVGI--------WCKDVAPSKELREWYHHQPeRFDEFASRYQEE 75 
                                    689***9************.*****....***********........*******************99*********** PP

                         DUF488  80 leskeaakealeelkelakkg.vaLlcaekdperchrvvlaeyl 122
                                    l ++    +al+el++l  ++ v+ ++a +   r+h+ vla+ l
  gi|121638958|ref|YP_979182.1|  76 LHDS----AALAELRKLTGRSvVTPVTATRHVARSHAAVLAQLL 115
                                    **96....89*******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 877.71
//
Query:       gi|121638959|ref|YP_979183.1|  [L=424]
Description: hypothetical protein BCG_3099 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-13   49.8  29.4    5.3e-13   49.1  29.4    1.3  1  DUF222    Domain of unknown function (DUF222)
    0.00055   20.0   0.8      0.001   19.2   0.8    1.4  1  HNH       HNH endonuclease
  ------ inclusion threshold ------
      0.026   14.4   0.3      0.045   13.6   0.3    1.4  1  HNH_5     HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1  29.4   8.9e-17   5.3e-13       6     301 .]      25     323 ..      20     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 8.9e-17
                         DUF222   6 eeleaaarrlaavevllvael.....aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalraGd 80 
                                    e+l+ aa++ +a++++ v        ++ +++++  ++ +a+++a + r s+a++sr +  A+al  ++p + aal  G 
  gi|121638959|ref|YP_979183.1|  25 ERLKSAAAAGQARAAAAVDAArraaeGAAGVPAARRGRGLASEIALARRDSPARGSRHLGFAKALVYEMPHTLAALDCGA 104
                                    444444444444444433333333568888999999999***************************************** PP

                         DUF222  81 idlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvr.rdeeaarrreltltkded 159
                                    +++  ++ I+     l d  d +++d+++    +    +  a++ +++++++ rldp +v  r+++a+++r +t++++ d
  gi|121638959|ref|YP_979183.1| 105 LSEWRATLIVRESACL-DVADRRALDAELCGDPGDLEGMGDARVVAAARAIAYRLDPQAVVdRAANAENDRTVTIRPAPD 183
                                    **********999999.77777777877777778888899*******************9977888888*********** PP

                         DUF222 160 GmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvhvtaeel 239
                                     m++++  l+ +++  + a+L + a++ c        Rs+ q  aD L++ +        +++ a+vp+ + v++++++ 
  gi|121638959|ref|YP_979183.1| 184 TMTYLTALLPVAQGVSVYAALTRAADTRCDG------RSRGQVMADTLVERV--------TGRDAAVPTPIAVNLVMSDE 249
                                    *****************************88......************987........58899*************** PP

                         DUF222 240 taaagg...aaltgggglLpasdvrrLAkdAt........la.ifdepagrpld.lgrtkrtasaalrralraRD 301
                                    t  +++   a l g +g++pa+ +r + ++A         l+ + ++p++ +l  +   +r+ +++l+ +++ RD
  gi|121638959|ref|YP_979183.1| 250 TLLGAAntpAQLCG-YGPIPAAVARTMVASAVtdqrsratLRrLYAHPQAGALVsMESRARLFPRGLAAFIELRD 323
                                    *9999999777777.************999876666666666677777777776355556888888888888887 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.8   1.7e-07     0.001       3      44 ..     330     366 ..     324     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-07
                            HNH   3 yCgrkfhksealevdHiipisqggaddieNlqllCksCHnkk 44 
                                    yC+ +++     + dH +p+++gg+++  N    C++C+ +k
  gi|121638959|ref|YP_979183.1| 330 YCDAPIR-----HRDHAHPWADGGPTSAHNGLGTCERCNYAK 366
                                    7888865.....55*************************888 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   7.5e-06     0.045       4      44 ..     331     367 ..     324     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-06
                          HNH_5   4 Cgkeiaekel.seeHIiPeslGGkltisnlvtlCkkCNqkkg 44 
                                    C+ +     + +++H  P + GG ++ +n   +C++CN  k+
  gi|121638959|ref|YP_979183.1| 331 CDAP-----IrHRDHAHPWADGGPTSAHNGLGTCERCNYAKQ 367
                                    3333.....3369*************************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3217.57
//
Query:       gi|121638960|ref|YP_979184.1|  [L=307]
Description: hypothetical protein BCG_3100c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-29  100.9   0.1      1e-28  100.0   0.1    1.5  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
     0.0033   16.6   0.0       0.34   10.0   0.0    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.1   1.1e-32     1e-28       1     221 []      27     228 ..      27     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.1e-32
                                    EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG. CS
                      HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle. 79 
                                    r+ l ++ga+ +  e aa++ aD v++D+Edava ++K aAR ++     + +a         VR+n+  ++++++dl+ 
  gi|121638960|ref|YP_979184.1|  27 RSWLLVNGAHGDRFESAAHSRADIVVLDIEDAVAPKDKHAARDNAVRWFGDGNA-------DWVRINGFGTPWWADDLAm 99 
                                    678899************************************999888887777.......46****************9 PP

                                    HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHHHTT CS
                      HpcH_HpaI  80 vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsadlg 159
                                    ++d+ + +v++ +ve+ + ++e  + l +           ++++a +E+a+g++ ++eIaa++g   +++G  D+ +d g
  gi|121638960|ref|YP_979184.1| 100 LADSPVGGVMLAMVESVDHVTETAKRLPN-----------VPIVALVETARGLERINEIAAAKGTFRLAFGIGDFRRDTG 168
                                    99**************9999887776655...........56************************************** PP

                                    -TTSTTSHHHHHHHHHHHHTTHCEEE.EEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHHHH CS
                      HpcH_HpaI 160 tkrspegtevldareriltaaraagi.aaldtvasdiddaegflaegalfvalGfdgkllinp 221
                                      ++p    + +ar+r+ +aaraag+ +a+d+ +++ +   +++++ a   + G++gk +++p
  gi|121638960|ref|YP_979184.1| 169 FGEDP--ATLAYARSRFTIAARAAGLpSAIDGPTIGSNAL-KLIEATAVSAEFGMTGKICLSP 228
                                    *9965..5688**************9679******98766.67788889999*****999876 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0017        15      28      57 ..      44      73 ..      37      80 .. 0.84
   2 !   10.0   0.0   3.8e-05      0.34     252     335 .]     207     286 ..     188     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0017
                 C-C_Bond_Lyase 28 klegltslvlclEDavseeeveaAeenlke 57
                                   +++ +  +vl++EDav+ ++ +aA +n ++
  gi|121638960|ref|YP_979184.1| 44 AHSRADIVVLDIEDAVAPKDKHAARDNAVR 73
                                   56777889****************999876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.8e-05
                 C-C_Bond_Lyase 252 glirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldiles.ak.ggvfkseyankmnEvkphraWAekilkr 329
                                    +li+ +a   + G++GK ++ P q ++v++ l+ s++e   A++  ++ a+ gg ++    +      p  a A+kil+ 
  gi|121638960|ref|YP_979184.1| 207 KLIEATAVSAEFGMTGKICLSPDQCPVVNEGLSPSQDEIVWAKEFFAEfARdGGEIRNG--S----DLPRIARATKILDL 280
                                    577777788899*********************************99874425666555..3....34889999999999 PP

                 C-C_Bond_Lyase 330 akvyGv 335
                                    a++yG+
  gi|121638960|ref|YP_979184.1| 281 ARAYGI 286
                                    999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2095.48
//
Query:       gi|121638961|ref|YP_979185.1|  [L=158]
Description: hypothetical protein BCG_3101 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-23   83.4   0.5    2.1e-23   83.2   0.5    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
      8e-11   42.3   0.0    1.1e-10   41.8   0.0    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.5   2.4e-27   2.1e-23       4     143 .]      10     154 ..       8     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.4e-27
                                    EEEEEEESS-HHHHHHHHTTTTGGGGT-TTEE.EEECSE.STSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE. CS
                Polyketide_cyc2   4 vtvsvviaappekVwalvsdfenwprWhpeva.rveleg.gggpargvegtvrvggrgtvreelvevdpegrllsyriv. 80 
                                    +++s++iaa  +++w++++df+++++W ++v+ ++ l   ++g a g+ ++v+vg+ +t++e+++e+dp +++l+yri+ 
  gi|121638961|ref|YP_979185.1|  10 TRRSRTIAARQQTIWDVLADFGSLSSWVEGVDhSCVLNHgPDGGALGSTRRVQVGR-NTLVERVIEFDP-PTTLAYRIEg 87 
                                    5789****************************777777544444345558999999.9***********.********88 PP

                                    .SSS-TSEEEEEEEEECCE.T..EEEEEEEEEEE..E--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  81 kpvpvanyvatwtvtpdgg.g..trvtwtgefda..gplggpfekpaaakavkgdleagLerLkarle 143
                                     p ++++++ +wt+ p+++ g  t vt t ++++  +pl++++ + ++ +a++++  + L++L++rle
  gi|121638961|ref|YP_979185.1|  88 LPARLRKVTNRWTLRPADPvGavTVVTLTSTIEIggNPLARLA-ELVVGRAMAKRSNTMLAGLAQRLE 154
                                    9***************995346899999999997668887776.7889******************98 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.3e-14   1.1e-10       1     123 [.      16     139 ..      16     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.3e-14
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTT...EEECTTCCCCCEE CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppee...itfklvegdfksl 77 
                                    ++a  +++++++ad+ s++ ++ ++  ++vl+  ++g     +   +  + ++++rv +  p      + +      ++ 
  gi|121638961|ref|YP_979185.1|  16 IAARQQTIWDVLADFGSLSSWVEGVDHSCVLNHGPDGGALGSTRRVQVGRNTLVERVIEFDPPTtlaYRIEGLPARLRKV 95 
                                    68999******************************944443344444444444555544444445553333333478999 PP

                                    EEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  78 egkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervld 123
                                     ++Wt+++ +p   g  t+v+l+ +++ ++++l+ l++ v +r+  
  gi|121638961|ref|YP_979185.1|  96 TNRWTLRPADPV--GAVTVVTLTSTIEIGGNPLARLAELVVGRAMA 139
                                    ***********7..9************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1090.51
//
Query:       gi|121638962|ref|YP_979186.1|  [L=603]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-59  199.7   0.0    8.8e-59  199.4   0.0    1.1  1  Sulfatase  Sulfatase
    5.3e-05   23.4   3.6    8.3e-05   22.8   0.2    2.3  2  DUF4976    Domain of unknown function (DUF4976)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   0.0   9.8e-63   8.8e-59       1     309 []       5     389 ..       5     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 9.8e-63
                                    EEEEEEEESSE-TT..GSGGGTTTSCSSHHH.HHHH..HTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT CS
                      Sulfatase   1 pnvvliladdlgag..dlglyggktattpnl.drla..eeglrftnfysaaplcspsraalltgryphnsgvasntevgg 75 
                                    p+++++++d  +a   + ++     +  + l  r +  e+g+ ft++y+++ +c+psr++++tg+yp+ +gv+++ ++g+
  gi|121638962|ref|YP_979186.1|   5 PDIIIVMTDEERAVppYESAEVLAWR-QRSLtGRRWfdEHGISFTRHYTGSLACVPSRPTIFTGQYPDLHGVTQTDGIGK 83 
                                    78999*****9999994444444444.34453555579****************************************** PP

                                    ........HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC....CTTTSE.EEETSSSCHHTCCCCCCCCCEC CS
                      Sulfatase  76 ........gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk....nrgfdr.flgfptgsaalkdpekseynge 142
                                            + ++ +++tL++++++aGY+t++ gkwh ++ + +++++    + + ++ ++++++++++l+  + ++y  +
  gi|121638962|ref|YP_979186.1|  84 rfddsrlrWLRAGEVPTLGNWFRAAGYDTHYDGKWHISHADLEDPATgaplATNDNEgVVDSAAVRRYLDADPLGPYGFS 163
                                    ********************************************999****7777777*********************9 PP

                                    TCCC.............TTTTCSHHHHHHHHHHHHH....HCCC.TSSEEEEEEE-TTSS..............STCTCG CS
                      Sulfatase 143 vlrv.............ppeggysddrlldealefl....larn.dkpfflylatlapHa..............ppeapd 190
                                    +++              ++++ + d+++++ ++++      +++ ++pf+l+ ++ +pH               p + ++
  gi|121638962|ref|YP_979186.1| 164 GWVGpephgaglansgfRRDPLVADRVVAWLTERYArrraGDTAaMRPFLLVASFVNPHDivlfpawvwrsplkPSPLDP 243
                                    9999********777777777777777777777777*99955556**************************998779999 PP

                                    GHTCCGSTTTTCCCCCCH............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEE CS
                      Sulfatase 191 eyakkyatffddgseaar............................qlleaylnsveyvDdligrvlaaLeenglldntl 242
                                    +++ +  t ++d+s++++                            ++++ y++ +++vD  i+rv  a+ ++g +++++
  gi|121638962|ref|YP_979186.1| 244 PHVPAAPTADEDLSTKPAaqvayreayysgygltrmvsrnyarnaqRYRDLYYRLHAEVDGPIDRVRRAV-TEGGSEDAM 322
                                    999999999999999977788888999999999999999*******************************.********* PP

                                    EEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC..EEECSEEEGGGHHHHHHHHTTE CS
                      Sulfatase 243 vvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap..rvseelvshiDlfptildlagi 309
                                    +v tSDhg+ l  +++   ++k++n y++ trvP++++  geka+  r++++++sh+Dl+pt+l++ag+
  gi|121638962|ref|YP_979186.1| 323 LVRTSDHGDLL--GAHGGLHQKWFNLYDEATRVPFVIARIGEKATqpRTVSAPTSHVDLVPTLLSAAGV 389
                                    ***********..99****************************************************96 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4     0.069   6.2e+02      24      55 ..     267     296 ..     254     304 .. 0.74
   2 !   22.8   0.2   9.3e-09   8.3e-05      60      98 ..     529     567 ..     522     571 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.069
                        DUF4976  24 kalyYhyyeyPaehavkrhygvrteryklihf 55 
                                     ++yY  y    + +v+r y+ + +ry+ + +
  gi|121638962|ref|YP_979186.1| 267 REAYYSGYGL--TRMVSRNYARNAQRYRDLYY 296
                                    5667776666..99*************86655 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 9.3e-09
                        DUF4976  60 dewelyDlkkDpkelknlyddpeyeevvkelkkkleelr 98 
                                    d+welyDl +Dp e  n + dp+ +e+ ++l+  l+++r
  gi|121638962|ref|YP_979186.1| 529 DQWELYDLTADPIEAYNRWTDPQLHELRQHLRMLLKQQR 567
                                    89******************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 4107.42
//
Query:       gi|121638963|ref|YP_979187.1|  [L=133]
Description: hydroxylaminobenzene mutase hab [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.035   13.3   1.3      0.043   13.0   1.3    1.1  1  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion


Domain annotation for each model (and alignments):
>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.3   2.4e-06     0.043     158     250 ..       2     129 ..       1     133 [] 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-06
                  MIG-14_Wnt-bd 158 pklllvlllwlvllvlalyerleqlkdpfysiwss........al................ilkilaiilavlyflyLly 213
                                     kll+++ l l+l+ l +   ++ lk+p +   s+        +l                 ++++a+i+  +y+ +L  
  gi|121638963|ref|YP_979187.1|   2 QKLLFTIGLALFLIGLLTGLVIPALKNPRMALSSHlegvlngmFLvvlgllwphidlpeawQVIAVALIVYSAYANWLAT 81 
                                    6899999999999999999999********99999888766651156677788888999989999*************** PP

                  MIG-14_Wnt-bd 214 lifrsfseirskrvk.............egdiRfkflilltllvlavlvi 250
                                    l+  ++ + r+   +             eg + f +l+l  ++v+ v+++
  gi|121638963|ref|YP_979187.1|  82 LLAAAWGAGRKF--ApiatgdhkapaakEGFVSFLLLSLSVAIVIGVVIV 129
                                    ****99999993..337899988776655444555544444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1045.45
//
Query:       gi|121638964|ref|YP_979188.1|  [L=275]
Description: hypothetical protein BCG_3104c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-37  128.7   0.9    4.1e-37  128.3   0.9    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.9   2.3e-41   4.1e-37      27     210 ..      18     218 ..       9     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 2.3e-41
                 Bac_luciferase  27 elaraaEelGfdavwvaehhggpgga.................ldaftllaalaaaTerirlgtavtplytrhPavlAqq 89 
                                    el  a+E+ Gf+++++aeh ++p  +                 ld+f+ laa+aa T+ + lgt++  ++ r+P+v+A++
  gi|121638964|ref|YP_979188.1|  18 ELGAALEHRGFESLFLAEHTHIPVNTqspypgggpipekyyrtLDPFVALAAAAATTQSLVLGTGIALIPERDPIVTAKE 97 
                                    677899****************98889***************************************************** PP

                 Bac_luciferase  90 aatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgp.iP 168
                                    +a+Ld +s+GRf++g+g g+  +e +++Gvd + r +  +E ++++ ++w++e  +f+G ++  + ++ +p+p+ +p +P
  gi|121638964|ref|YP_979188.1|  98 VASLDLVSQGRFRFGVGVGWLREEVANHGVDPAVRGRVIDERLRAIIEIWTQEQAEFHGTYVDFDPIYCWPKPVTKPyPP 177
                                    **************************************************88888******************9999666 PP

                 Bac_luciferase 169 vyvaaaspaglelaarhadglllageppeeaaelierlraga 210
                                    +yv++ +pa+    ar   g++  + +p+ +   ++rlra+a
  gi|121638964|ref|YP_979188.1| 178 LYVGG-GPANFPRIARLNAGWIAISPSPQRLSGPLQRLRAMA 218
                                    88876.79*****************99999999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1920.49
//
Query:       gi|121638965|ref|YP_979189.1|  [L=1110]
Description: serine/threonine-protein kinase transcriptional regulatory protein pknK [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-42  144.7   0.0    5.6e-42  143.9   0.0    1.3  1  Pkinase      Protein kinase domain
    3.8e-32  111.6   0.0      6e-32  110.9   0.0    1.2  1  Pkinase_Tyr  Protein tyrosine kinase
    5.6e-12   46.4   0.7    5.6e-12   46.4   0.7    2.9  3  AAA_16       AAA ATPase domain
    2.1e-06   28.0   0.0    6.5e-06   26.5   0.0    1.8  1  AAA_22       AAA domain
      0.002   17.7   1.5       0.13   11.9   0.0    3.4  3  AAA_25       AAA domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.033   14.1   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
      0.036   13.1   0.0      0.066   12.2   0.0    1.4  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.085   12.8   0.1       0.32   10.9   0.0    2.1  2  DUF5375      Family of unknown function (DUF5375)
       0.12   12.5   0.1        2.2    8.5   0.0    2.6  2  AAA_33       AAA domain
       0.16   12.1   0.0          1    9.4   0.0    2.3  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   3.1e-45   5.6e-42       2     253 ..      27     272 ..      26     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 3.1e-45
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEE.EEESSEEEEEEE- CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyev.feekdelylvley 79 
                                     ++e++G+G+fG+Vy++v+ + ++ vAvK+++++ ++++ e ++lrE + + +l+ hp+iv++++v +    + ++v+ y
  gi|121638965|ref|YP_979189.1|  27 DNVEEIGRGGFGVVYRCVQPSLDRAVAVKVLSTDLDRDNLE-RFLREQRAMGRLSgHPHIVTVLQVgVLAGGRPFIVMPY 105
                                    6789********************************99885.9*********************99345588899***** PP

                                    -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS.BCTTT CS
                        Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk.ltsfv 158
                                      +++l++l++r+g l+ +e+ +i  +++ +le  H+ g +HrD+Kp NiL+ + ge ++tDFG+a+ +   ++ +  + 
  gi|121638965|ref|YP_979189.1| 106 HAKNSLETLIRRHGPLDWRETLSIGVKLAGALEAAHRVGTLHRDVKPGNILLTDYGEPQLTDFGIARIAGGFETaTGVIA 185
                                    *********************************************************************99888677899 PP

                                    SCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS..-HH CS
                        Pkinase 159 gtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeasei..see 236
                                    g++ + APEvl++ + ++++Dv+slG +l+++ltg+  ++ ++g+      + q+      l+ t++ +p  ++   + +
  gi|121638965|ref|YP_979189.1| 186 GSPAFTAPEVLEGASPTPASDVYSLGATLFCVLTGHAAYERRSGER----VIAQF------LRITSQPIPDLRKQglPAD 255
                                    ****************************************666655....44442......2222223333322222666 PP

                                    HHHHHHHHT-SSGCCST CS
                        Pkinase 237 akdllkkllkkdpkkRl 253
                                    +   +++ +++ p +R+
  gi|121638965|ref|YP_979189.1| 256 VAAAIERAMARHPADRP 272
                                    66666666666666665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   3.4e-35     6e-32       4     251 ..      29     273 ..      26     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.4e-35
                                    EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEE.SSSSEEEEEE CS
                    Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvct.keepllivte 81 
                                     +++G+G fG V+++       + +  VavK+l+ + ++++ e++l+e + m +l  hp+iv +l v +  +++ +iv+ 
  gi|121638965|ref|YP_979189.1|  29 VEEIGRGGFGVVYRCVQP----SLDRAVAVKVLSTDLDRDNLERFLREQRAMGRLsGHPHIVTVLQVGVlAGGRPFIVMP 104
                                    689************998....8899*****************************99*******99977688889***** PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEE CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvk 161
                                    y ++++L++ +r++   +l+ +++ls+ +++A ++e  ++   +Hrd+   N+Ll++    +++DfG+ar        ++
  gi|121638965|ref|YP_979189.1| 105 YHAKNSLETLIRRH--GPLDWRETLSIGVKLAGALEAAHRVGTLHRDVKPGNILLTDYGEPQLTDFGIARIA--GGFETA 180
                                    *************9..******************************************************88..666677 PP

                                    TTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BB....TTSBHHHHHH CS
                    Pkinase_Tyr 162 keeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekp....ekcpeelyel 237
                                    ++    +  ++apE+l+  + t +sDv+s G +l+ ++t g+  y++ + e+v++++ + +  + p    +  p++++  
  gi|121638965|ref|YP_979189.1| 181 TGVIAGSPAFTAPEVLEGASPTPASDVYSLGATLFCVLT-GHAAYERRSGERVIAQFLRITSQPIPdlrkQGLPADVAAA 259
                                    888889999******************************.************9999866666665511215689999*** PP

                                    HHHHT-SSGGGS-- CS
                    Pkinase_Tyr 238 mkkcweedpeeRpt 251
                                    +++ ++++p++Rp 
  gi|121638965|ref|YP_979189.1| 260 IERAMARHPADRPA 273
                                    ************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.7   3.1e-15   5.6e-12      10     164 ..     349     484 ..     345     491 .. 0.70
   2 ?   -1.3   0.2       1.4   2.6e+03      82     127 ..     771     812 ..     703     822 .. 0.54
   3 ?   -3.8   0.1       8.1   1.5e+04     107     126 ..    1035    1054 ..    1001    1078 .. 0.48

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.1e-15
                         AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqlld 87 
                                    ++L+++l+  + gr +l+l++ +sG GKs+l+ +++++l++dg+ +  l+ ++d++ +   +s         +ll+ + +
  gi|121638965|ref|YP_979189.1| 349 SRLTDILR--AGGRRRLILIHAPSGFGKSTLAAQWREELSRDGAAVawLTIDNDDNNEVWFLS---------HLLESIRR 417
                                    68888888..446669**************************977757889999992221112.........33333333 PP

                         AAA_16  88 eaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql.laaLlrlles 164
                                              r +l e+l+ v e +g+   + +++l++l++ ++++++ + +v+Dd +++ ++  q+ l +Ll+++ +
  gi|121638965|ref|YP_979189.1| 418 V---------RPTLAESLGHVLEEHGD--DAGRYVLTSLIDEIHENDDRIAVVIDDWHRVSDSRTQAaLGFLLDNGCH 484
                                    3.........33333333333333333..7889*******666666666*********8888777777*****99776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                         AAA_16  82 lrqlldeaesaeleawrekleealaavpelagaeasrllellkrll 127
                                     r++l ea+    +a+ ++  ++l+av+e+ ++  +r+ +ll++++
  gi|121638965|ref|YP_979189.1| 771 GRAELPEAT----QADLRAEADVLRAVAEVFADRVERVDDLLAEAM 812
                                    222222211....111111222233555555555577777666665 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 8.1
                         AAA_16  107 avpelagaeasrllellkrl 126 
                                     a++++++++a + + +l+++
  gi|121638965|ref|YP_979189.1| 1035 AGDSADRDQACQRAGALAAA 1054
                                     22222222222222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.6e-09   6.5e-06       4     126 ..     360     489 ..     356     492 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.6e-09
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdllrellralglelkaerlsse 76 
                                    ++++++++++sG GK+tl+++ +e+l ++ +a          + e v +    ++s + ++  l++ lg+ l++ +++  
  gi|121638965|ref|YP_979189.1| 360 RRRLILIHAPSGFGKSTLAAQWREELSRDGAAVAwltidndDNNE-VWFLSHLLESIRRVRPTLAESLGHVLEEHGDDAG 438
                                    6899**********************8765554478887533333.3333444447999999999999999999999999 PP

                         AAA_22  77 ell.ealeqalraravielliiDEaqhlr.s..eealeeLrsllnlsrkgvqli 126
                                    +++ + l + +++ +++ +++iD+ ++++ s  ++al +L   l+++ +++qli
  gi|121638965|ref|YP_979189.1| 439 RYVlTSLIDEIHENDDRIAVVIDDWHRVSdSrtQAALGFL---LDNGCHHLQLI 489
                                    99999999999999999***********662568888888...44466777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   6.5e+02      70     110 ..      50      90 ..      43      97 .. 0.85
   2 !   11.9   0.0     7e-05      0.13      32     118 ..     360     447 ..     332     476 .. 0.68
   3 ?    2.0   0.1     0.074   1.3e+02      84     139 ..     672     730 ..     667     737 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                         AAA_25  70 eqgkVlyvsaEdsedelrrRlravgealrddarllvldlag 110
                                    + ++V ++s++ ++d+l+r lr++++  r+ ++ +++++ +
  gi|121638965|ref|YP_979189.1|  50 RAVAVKVLSTDLDRDNLERFLREQRAMGRLSGHPHIVTVLQ 90 
                                    6789***************9999998888888888888755 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7e-05
                         AAA_25  32 agelallaGapgtGKttlaldlalava.tGkpwlg..pvapeqgkVlyvs..aEdsedelrrRlravgeal....rddar 102
                                    +  l+l+ +++g GK+tla ++  +++  G  +++  +    +  V+++s  +E  + ++r+ l++ + ++     dda+
  gi|121638965|ref|YP_979189.1| 360 RRRLILIHAPSGFGKSTLAAQWREELSrDGAAVAWltIDNDDNNEVWFLShlLESIR-RVRPTLAESLGHVleehGDDAG 438
                                    56799*****************99999755544445333348888888885456666.8888888888777788755555 PP

                         AAA_25 103 llvldlagveslpLfa 118
                                     +vl+        L++
  gi|121638965|ref|YP_979189.1| 439 RYVLTS-------LID 447
                                    555552.......222 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.074
                         AAA_25  84 delrrRlravgeal.....rddarllvldlagveslpLfakdrggtlltadvdaleaaiee 139
                                    +el+rR++a+++++     + d  l++ d a+   ++L+++d  +   ++++  l a +++
  gi|121638965|ref|YP_979189.1| 672 AELHRRASAWFAENgylheAVDHALAAGDPARA--VDLVEQDETNLPEQSKMTTLLAIVQK 730
                                    69*********9998888855555555555443..55555443333344455555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.033      17     132 ..     358     468 ..     349     481 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                       ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk 96 
                                     ++++ ++i  p g GK++L  +  e+l+  +  v +++  ++++++    + +  e+ ++++ +l       +l ++l+
  gi|121638965|ref|YP_979189.1| 358 GGRRRLILIHAPSGFGKSTLAAQWREELSRDGAAVAWLTIDNDDNNEVWFLS-HLLESIRRVRPTL-----AESLGHVLE 431
                                    4578899*********************999999998876666666665555.2223333333333.....444555677 PP

                       ATPase_2  97 eksklvfka.ielllekikkkgkkiiiiiDelqklid 132
                                    e+  ++ ++ +++l+++i ++  +i+++iD+  ++ d
  gi|121638965|ref|YP_979189.1| 432 EHGDDAGRYvLTSLIDEIHENDDRIAVVIDDWHRVSD 468
                                    7777776662799******************998874 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05     0.066      17      67 ..     349     399 ..     339     404 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                                    HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB  17 ellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                    + l+ +l   Gr + + +    G Gkstl  +  +el r G  va l +D 
  gi|121638965|ref|YP_979189.1| 349 SRLTDILRAGGRRRLILIHAPSGFGKSTLAAQWREELSRDGAAVAWLTIDN 399
                                    5578899999999999999999***************************95 PP

>> DUF5375  Family of unknown function (DUF5375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.32       3      73 ..     375     450 ..     373     458 .. 0.76
   2 ?   -3.2   0.1       4.3   7.7e+03       5      44 ..     731     770 ..     729     775 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                        DUF5375   3 rtlspalraalyrravacawltlceeqkryasl...tlarlera..ietelegfylrqhgrergreiacalledll 73 
                                     tl+ + r  l r   a awlt+ ++++    +    l+ + r     +e  g  l +hg++ gr +  +l++++ 
  gi|121638965|ref|YP_979189.1| 375 STLAAQWREELSRDGAAVAWLTIDNDDNNEVWFlshLLESIRRVrpTLAESLGHVLEEHGDDAGRYVLTSLIDEIH 450
                                    6788999999*************998876554400044444443114467789******************99876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                        DUF5375   5 lspalraalyrravacawltlceeqkryasltlarlerai 44 
                                    l+  +  + +r  +a aw  +  ++   a+ +l+r+e+a+
  gi|121638965|ref|YP_979189.1| 731 LPTSMVVSRARLQLAIAWANILLQRPAPATGALNRFETAL 770
                                    5556666677888999999988887778888888888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0012       2.2       1      44 [.     363     425 ..     363     522 .. 0.68
   2 ?    0.9   0.1      0.25   4.5e+02      44     106 ..     673     740 ..     626     750 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg.......avllssdt............lrrrlfgtdqqs 44 
                                    l+l++ ++G GKstla ++ ++l        + +++ d+             +rr+++t  +s
  gi|121638965|ref|YP_979189.1| 363 LILIHAPSGFGKSTLAAQWREELSrdgaavaWLTIDNDDnnevwflshlleSIRRVRPTLAES 425
                                    6788889************98888887876666666666777777777776444555544444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                         AAA_33  44 sktdytrvldrlyqilnelarkalsagrnvil......datnlsr.rerarflklarrlgvpvrivvvet 106
                                     + +++ +++  ++ l+e ++ al+ag ++ +      d tnl + +++  +l++++  + p ++vv ++
  gi|121638965|ref|YP_979189.1| 673 ELHRRASAWFAENGYLHEAVDHALAAGDPARAvdlveqDETNLPEqSKMTTLLAIVQ--KLPTSMVVSRA 740
                                    333455577889999999999999999887777889999999998799999999999..77777777665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00058         1       8      55 ..     370     462 ..     363     764 .. 0.77
   2 ?   -0.5   0.0      0.69   1.2e+03      33      73 ..    1022    1062 ..    1011    1079 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00058
                                    TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx................................ RF
                           CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep................................ 54 
                                    +G GK+tlaa     l+r+g  V+ +  D++ nn    l  l + i++                                
  gi|121638965|ref|YP_979189.1| 370 SGFGKSTLAAQWREELSRDGAAVAWLTIDNDDNNEVWfLSHLLESIRRvrptlaeslghvleehgddagryvltslidei 449
                                    9******************************9986546444444444444565556666666666655555555555555 PP

                                    ............C CS
                                    ............x RF
                           CbiA  55 ............d 55 
                                                d
  gi|121638965|ref|YP_979189.1| 450 henddriavvidD 462
                                    5555555555550 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.69
                                     EEEEESSCCCCHHTTEB-HHHHCCHCCCHHHHHHCHCHHHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   33 vDaDpqannlaileglendiepdlkrllellealgkkkall 73  
                                       +D ++    +  g++ d+++ ++r + l++a++++ ++l
  gi|121638965|ref|YP_979189.1| 1022 AELDEDSAVRLLSAGDSADRDQACQRAGALAAAIDGTRRPL 1062
                                     556777777667899*******************9997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 7669.70
//
Query:       gi|121638966|ref|YP_979190.1|  [L=412]
Description: hypothetical protein BCG_3106 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-05   22.1   0.0    0.00015   21.5   0.0    1.2  1  DUF2204   Nucleotidyl transferase of unknown function (DUF220
     0.0032   17.2   0.2       0.51   10.2   0.1    3.2  2  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.7e-08   0.00015       4      81 ..     253     330 ..     250     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-08
                        DUF2204   4 alaevlkvLeekgv..kfvviGgtvvelalgrkrlekDvDlFiteksqlleedfyreiaeeedwdvgstelgtvkliakv 81 
                                    a+  ++ +Le +gv  +  v+Gg+ + la++++ +++D+D     + ++le    re+a+e +w     +    +++ + 
  gi|121638966|ref|YP_979190.1| 253 AFTALAAKLERRGVvgQVHVVGGAAMLLAYNSRVTTRDIDALFSTDGPMLE--AIREVADEMGWPRTWLNNQASGYVSRT 330
                                    56678899****99555679********************77777777776..58*********5444333444555555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   5.7e-05      0.51      16      38 ..      50      72 ..      38      82 .. 0.86
   2 !    3.3   0.0    0.0086        77      20      36 ..     305     321 ..     302     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.7e-05
                         HTH_23 16 eGlsvreIAreLgvsrrTvyrwl 38
                                   + ++v+++Ar++gvs +  + +l
  gi|121638966|ref|YP_979190.1| 50 DLWTVERAARHWGVSASRARAIL 72
                                   48**************9998776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0086
                         HTH_23  20 vreIAreLgvsrrTvyr 36 
                                    +re+A+e+g++r ++ +
  gi|121638966|ref|YP_979190.1| 305 IREVADEMGWPRTWLNN 321
                                    69**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2671.28
//
Query:       gi|121638967|ref|YP_979191.1|  [L=340]
Description: virulence-regulating transcriptional regulator VirS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-37  128.2   3.3    6.5e-37  127.4   3.3    1.4  1  Arabinose_bd  Arabinose-binding domain of AraC transcription 
    1.8e-16   60.2   0.8    4.5e-16   58.9   0.4    2.0  2  HTH_18        Helix-turn-helix domain
    1.2e-06   28.4   0.0     0.0002   21.4   0.0    2.6  2  HTH_AraC      Bacterial regulatory helix-turn-helix proteins,
    1.1e-05   25.0   1.9       0.14   12.0   0.2    3.2  3  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.015   15.1   0.4        1.2    8.9   0.0    2.7  2  HTH_38        Helix-turn-helix domain
      0.016   15.0   0.1      0.066   13.0   0.1    2.1  2  HTH_30        PucR C-terminal helix-turn-helix domain
      0.029   14.4   3.3      0.087   12.9   1.1    2.7  3  HTH_20        Helix-turn-helix domain
      0.039   13.8   0.9       0.28   11.0   0.0    2.7  3  HTH_8         Bacterial regulatory protein, Fis family
       0.16   12.2   1.3        1.8    8.8   0.2    3.1  2  HTH_28        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Arabinose_bd  Arabinose-binding domain of AraC transcription regulator, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   3.3   3.3e-40   6.5e-37       1     186 [.      23     207 ..      23     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 3.3e-40
                   Arabinose_bd   1 GldpdallrragldpalladpdarvplaqyarlweaaaralgdpalGlrlgrrlrpgslgllgyaalssptlgeAlqrlv 80 
                                    G+dp ++lrr++++p   ++ da ++la + r++ea a++l++p++Glrl+r + +g lg+++++a++++tl  +l+++ 
  gi|121638967|ref|YP_979191.1|  23 GADPLPFLRRFDIPPGIEHQEDAFMSLAGFVRMLEASAAELDCPDFGLRLARWQGLGILGPVAVIARNAATLFGGLEAIG 102
                                    99****************************************************************************** PP

                   Arabinose_bd  81 rylrllsdalelrl.eegegdlarlrlevae..ilaalraflevlelllaallrllrwllgrrlpllrVefehpapadaa 157
                                    ryl ++s al+l++ ++++++ +r+ +ev+e  i+ +l+     +el +a+ +r++r l g++ +++  +f+h++ + +a
  gi|121638967|ref|YP_979191.1| 103 RYLYVHSPALTLTVsSTTARSNVRFGYEVTEpgIPYPLQG----YELSMANAARMIRLLGGPQARARVFSFRHAQLGTDA 178
                                    **************76889999******999655554566....*********************************779 PP

                   Arabinose_bd 158 eyrrlFgcpvrFgapanalvfdaadldlp 186
                                    +yr+++gc+vrFg+ + ++++d++++ +p
  gi|121638967|ref|YP_979191.1| 179 AYREALGCTVRFGRTWCGFEVDHRLAGRP 207
                                    9************************9999 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.76   1.5e+03      29      54 ..     235     259 ..     232     260 .. 0.75
   2 !   58.9   0.4   2.3e-19   4.5e-16       1      80 [.     256     333 ..     256     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHHHSSS---HHHHHHH CS
                         HTH_18  29 rrlRlerArrlLlentglsvaeiAla 54 
                                     ++ +  ArrlL  + + s  +iA +
  gi|121638967|ref|YP_979191.1| 235 SERVVGLARRLL-PTGQCSAEAIADQ 259
                                    677888999988.5577888888865 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 2.3e-19
                                    HHHHHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHHHH CS
                         HTH_18   1 laaalgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPseyrr 80 
                                    +a++l++++rtLqr++ +  gl  ++++ r R  +A r L++ +gl +++iA  lG+s++s+++r +r +fg+tP++yr+
  gi|121638967|ref|YP_979191.1| 256 IADQLDMHPRTLQRRLAA-EGLRCHDLIERERRAQAARYLAQ-PGLYLSQIAVLLGYSEQSALNRSCRCWFGMTPRQYRA 333
                                    699***************.*********************86.***********************************96 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.021        42      12      30 ..     254     272 ..     248     276 .. 0.86
   2 !   21.4   0.0     1e-07    0.0002      11      41 ..     301     332 ..     294     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                                    HHHHHHTTSSHHHHHHHHH CS
                       HTH_AraC  12 ediAdelgfSrsyFsrlFk 30 
                                    e iAd+l +++++++r++ 
  gi|121638967|ref|YP_979191.1| 254 EAIADQLDMHPRTLQRRLA 272
                                    679*************975 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1e-07
                                    HHHHHHHTTS.SHHHHHHHHHHHSSS-HHHHH CS
                       HTH_AraC  11 iediAdelgf.SrsyFsrlFkketGmtPsqyr 41 
                                    + +iA  lg+  +s + r ++ ++GmtP+qyr
  gi|121638967|ref|YP_979191.1| 301 LSQIAVLLGYsEQSALNRSCRCWFGMTPRQYR 332
                                    789*******99*******************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.9   3.8e+03      25      37 ..     182     194 ..     181     195 .. 0.86
   2 !   10.8   0.0   0.00016      0.32      20      40 ..     253     273 ..     252     278 .. 0.84
   3 !   12.0   0.2     7e-05      0.14       4      32 ..     284     313 ..     282     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                         HTH_23  25 reLgvsrrTvyrw 37 
                                    ++Lg++ r  + w
  gi|121638967|ref|YP_979191.1| 182 EALGCTVRFGRTW 194
                                    689****998888 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                         HTH_23  20 vreIAreLgvsrrTvyrwlkr 40 
                                     ++IA++L++++rT++r l +
  gi|121638967|ref|YP_979191.1| 253 AEAIADQLDMHPRTLQRRLAA 273
                                    589*************87765 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 7e-05
                         HTH_23   4 ereRlrillllae.GlsvreIAreLgvsrr 32 
                                     ++R+++++ la+ Gl  ++IA +Lg s++
  gi|121638967|ref|YP_979191.1| 284 RERRAQAARYLAQpGLYLSQIAVLLGYSEQ 313
                                    689*************************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00063       1.2      15      40 ..     244     270 ..     233     272 .. 0.82
   2 ?    3.6   0.1     0.029        58      12      35 ..     289     313 ..     282     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00063
                         HTH_38  15 rllaeG.lslreIArrLgrspsTIsRE 40 
                                    rll  G +s  +IA +L+ +p T +R 
  gi|121638967|ref|YP_979191.1| 244 RLLPTGqCSAEAIADQLDMHPRTLQRR 270
                                    5666787999*************9995 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.029
                         HTH_38  12 eIerll.aeGlslreIArrLgrsps 35 
                                    + +r l + Gl l++IA +Lg+s +
  gi|121638967|ref|YP_979191.1| 289 QAARYLaQPGLYLSQIAVLLGYSEQ 313
                                    55555525678899********976 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         3     6e+03      16      29 ..      99     112 ..      96     113 .. 0.73
   2 ?   13.0   0.1   3.3e-05     0.066      12      34 ..     250     272 ..     246     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                                    HHHHHHHTS-HHHH CS
                         HTH_30  16 satAkaLhvHrnTl 29 
                                    +a  + L+vH   l
  gi|121638967|ref|YP_979191.1|  99 EAIGRYLYVHSPAL 112
                                    5677889***8765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.3e-05
                                    TT-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_30  12 ggnisatAkaLhvHrnTlryRLr 34 
                                    +++++a A++L +H+ Tl+ RL 
  gi|121638967|ref|YP_979191.1| 250 QCSAEAIADQLDMHPRTLQRRLA 272
                                    5999*****************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.4   8.7e+03      15      26 ..      52      64 ..      50      71 .. 0.56
   2 ?   12.9   1.1   4.3e-05     0.087      18      59 ..     244     287 ..     228     289 .. 0.83
   3 ?   -0.0   0.0      0.47   9.4e+02      21      43 ..     295     317 ..     292     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                                   HHHHH.STCTTB- CS
                         HTH_20 15 ilraL.araeglt 26
                                   + r+L a+a++l 
  gi|121638967|ref|YP_979191.1| 52 FVRMLeASAAELD 64
                                   6667744444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.3e-05
                                    HHSTCTTB-HHHHHHHHTS-HHHHHHHH..HHHHHCTTEEEECT CS
                         HTH_20  18 aLaraegltaselaerldlskntlsyHL..rvLeeagLvevvre 59 
                                     L + +  +a+++a++ld+++ tl ++L  + L+ ++L+e++r 
  gi|121638967|ref|YP_979191.1| 244 RLLPTGQCSAEAIADQLDMHPRTLQRRLaaEGLRCHDLIERERR 287
                                    55577889********************7777988*****9995 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.47
                                    TCTTB-HHHHHHHHTS-HHHHHH CS
                         HTH_20  21 raegltaselaerldlskntlsy 43 
                                       gl +s++a +l+ s +++ +
  gi|121638967|ref|YP_979191.1| 295 AQPGLYLSQIAVLLGYSEQSALN 317
                                    567899*********99999765 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.28      25      40 ..     257     272 ..     254     273 .. 0.91
   2 ?   -0.5   0.2      0.56   1.1e+03      20      28 ..     286     294 ..     283     294 .. 0.88
   3 ?   -2.8   0.0         3   5.9e+03      22      31 ..     302     311 ..     301     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                    HHHHTS-HHHHHHHHH CS
                          HTH_8  25 ArlLGisRrtLyrKLk 40 
                                    A+ L++++rtL r+L+
  gi|121638967|ref|YP_979191.1| 257 ADQLDMHPRTLQRRLA 272
                                    99************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.56
                                    -HHHHHHHH CS
                          HTH_8  20 nkskAArlL 28 
                                    ++++AAr+L
  gi|121638967|ref|YP_979191.1| 286 RRAQAARYL 294
                                    699****98 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3
                                    HHHHHHHTS- CS
                          HTH_8  22 skAArlLGis 31 
                                    s+ A lLG s
  gi|121638967|ref|YP_979191.1| 302 SQIAVLLGYS 311
                                    78899***87 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00088       1.8      11      50 ..     244     287 ..     236     289 .. 0.79
   2 ?    2.3   0.2     0.093   1.9e+02       1      28 [.     286     314 ..     286     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00088
                         HTH_28  11 a....Gh.svreaArelgisrrtvyrWikryeegGiagLvprrrr 50 
                                    +    G  s+ ++A +l +++rt++r + + e   +++L  r rr
  gi|121638967|ref|YP_979191.1| 244 RllptGQcSAEAIADQLDMHPRTLQRRLAA-EGLRCHDLIERERR 287
                                    44444778999*****************66.88888999988887 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.093
                         HTH_28   1 qRleiikllaa.GhsvreaArelgisrrt 28 
                                    +R+++ ++la+ G   +++A +lg s+++
  gi|121638967|ref|YP_979191.1| 286 RRAQAARYLAQpGLYLSQIAVLLGYSEQS 314
                                    68999999998566889999999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2305.06
//
Query:       gi|121638968|ref|YP_979192.1|  [L=495]
Description: monooxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-15   54.4   0.0    5.5e-13   48.2   0.0    2.7  2  FMO-like       Flavin-binding monooxygenase-like
    6.4e-10   38.7   0.0    2.7e-07   30.1   0.0    2.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.3e-10   38.2   0.0    2.2e-06   27.1   0.0    2.8  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    3.5e-08   33.5   0.2      1e-06   28.8   0.0    3.3  4  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.1e-08   32.9   0.1    5.6e-07   29.1   0.1    2.4  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.7e-07   29.7   2.9     0.0001   22.1   0.1    3.6  4  DAO            FAD dependent oxidoreductase
    5.7e-05   22.5   0.0    0.00085   18.6   0.0    2.4  3  Thi4           Thi4 family
     0.0012   18.0   0.5        1.3    8.0   0.0    3.0  3  Lycopene_cycl  Lycopene cyclase protein
      0.004   17.2   1.4       0.43   10.6   0.0    3.6  4  NAD_binding_9  FAD-NAD(P)-binding
     0.0085   15.5   0.0      0.018   14.4   0.0    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.015   15.8   0.1          9    6.9   0.0    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.089   12.9   0.0        2.6    8.1   0.0    2.7  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
       0.17   11.1   1.8        5.6    6.1   0.1    2.3  2  FAD_binding_3  FAD binding domain
        0.2   10.4   0.0        0.3    9.8   0.0    1.2  1  MCRA           MCRA family


Domain annotation for each model (and alignments):
>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.06        77       4      41 ..       7      46 ..       5      55 .. 0.74
   2 !   48.2   0.0   4.3e-16   5.5e-13      88     331 ..      83     349 ..      74     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.06
                       FMO-like  4 vaviGaGvsGlasikccleeglept..cfersddiGGlwr 41
                                   v +iGaG+sG+ +      e  + t   +er + +GG w 
  gi|121638968|ref|YP_979192.1|  7 VLIIGAGLSGIGTACHVTAEFPDKTiaLLERRERLGGTWD 46
                                   789*******9876544555444431168********996 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 4.3e-16
                       FMO-like  88 eylklfakefdllkyiqfkttvcsvkkrpdfstsGqwevvteke..gkkesavfdavmvctGhhvnphlplesfpGiekf 165
                                    +y+   a ef++   i +  +v +      +s   +w v   +e  g +++   d ++ ctG++ +    l  fpG+++f
  gi|121638968|ref|YP_979192.1|  83 QYIADTATEFGIDEKIHYGLKVNT---AEWSSRQCRWTVAGVHEatGETRTYTCDYLISCTGYYNYDAGYLPDFPGVHRF 159
                                    677788888888888888766554...556788999***87776225666777899**********9999999******* PP

                       FMO-like 166 kGqyfhsrdykepevfkgkrvlviGlGnsggdiavels....rtaeqvllstrsGswvls............r......v 223
                                     G+++h +++ e   ++gk+v+viG G ++  +   ++     +a++v +  rs s+++s            r      v
  gi|121638968|ref|YP_979192.1| 160 GGRCVHPQHWPEDLDYSGKKVVVIGSGATAVTLVPAMAgsnpGSAAHVTMLQRSPSYIFSlpavdkisevlgRflpdrwV 239
                                    *****************************998754443111157999999999999875433222111111132222223 PP

                       FMO-like 224 sdsGypwdmllvtrfksllkn..ilptalsnwlvekklnkrfnhenyglkpkkralakepvlndelparilaGavkvks. 300
                                    ++ G   ++ +++++ +  ++   l ++l+ w v ++l + ++  n++ +      +   v n +l +++  Ga +v + 
  gi|121638968|ref|YP_979192.1| 240 YEFGRRRNIAIQRKLYQACRRwpKLMRRLLLWEVRRRLGRSVDMSNFTPNYLPWDERLCAVPNGDLFKTLASGAASVVTd 319
                                    3445556777777777776653358889999999*************988888777778899***********9987552 PP

                       FMO-like 301 svkeltetsaifedgtveedidvvifatGyt 331
                                    +++ +te+ ++ + g +e + d+++ atG  
  gi|121638968|ref|YP_979192.1| 320 QIETFTEKGILCKSG-REIEADIIVTATGLN 349
                                    788899999888777.56668********76 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.1e-10   2.7e-07       1     177 [.       5     216 ..       5     234 .. 0.64
   2 !    5.6   0.0    0.0063       8.1     206     240 ..     321     351 ..     300     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.1e-10
                                    CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                    xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                    +dv++iG+G  G+ +a ++ +      ++l+e +++ l+g+  l   + gv++d + ++                     
  gi|121638968|ref|YP_979192.1|   5 FDVLIIGAGLSGIGTACHVTAefPDKTIALLE-RRERLGGTWDL-FRYPGVRSDSDMFTfgykfrpwrdvkvladgassr 82 
                                    59***************999965588899995.33343332222.33444444444444556888888888888887777 PP

                                    ............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC..TCEEEEEESEEEE---EEE-BC....TCTTC CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                    Pyr_redox_2  58 ............evvkklnqgielllgeevvkidpgkkkvklekkke..gdeekiaydklvlAtGssprdl....gipGv 119
                                                +      ++i++ l+++  +    +++ ++    e  g+++++++d+l+ +tG  + d     + pGv
  gi|121638968|ref|YP_979192.1|  83 qyiadtatefgiD------EKIHYGLKVNTAEWSSRQCRWTVAGVHEatGETRTYTCDYLISCTGYYNYDAgylpDFPGV 156
                                    7777776554332......345555555544555444444443333355****************966666544588999 PP

                                    .TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHH..HHHT-..EEEEEESSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..xxxxxxxxxxx RF
                    Pyr_redox_2 120 aenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaal..aklgk..evtlveardrl 177
                                       +g+ v++ +  e l +    k++vv+G+G+++v l  a+  ++ g+  +vt++++ +  
  gi|121638968|ref|YP_979192.1| 157 HRFGGRCVHPQHWPEDLDYSG--KKVVVIGSGATAVTLVPAMagSNPGSaaHVTMLQRSPSY 216
                                    555555544444444443333..77***********98555411333434489999888765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                                    EEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 206 vkeidgngeklevvledgeeidadlvvvavGvrps 240
                                    +++++++g       ++g+ei+ad +v+a+G+ ++
  gi|121638968|ref|YP_979192.1| 321 IETFTEKG----ILCKSGREIEADIIVTATGLNIQ 351
                                    44444333....57888999999999999998765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0015       1.9       2      38 ..       4      40 ..       2      45 .. 0.55
   2 !   27.1   0.0   1.7e-09   2.2e-06     100     228 ..      83     216 ..      81     261 .. 0.82
   3 ?   -1.2   0.0       0.7   8.9e+02     324     339 ..     332     347 ..     312     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                    K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                   ++D+ +iG+G s ++ a+++     ++++  ler+++
  gi|121638968|ref|YP_979192.1|  4 HFDVLIIGAGLSGIGTACHVTAEFPDKTIALLERRER 40
                                   4555555555555555555544444555555555544 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.7e-09
                    K_oxygenase 100 dYlrWvasqle..eqvrfgeeveevepdeeeee.elltveskdaegeeeelearnlvlgvG....tepkiPevleklegk 172
                                    +Y++  a ++   e++++g +v++ e+++++ + ++  v+   a+ge++++++  l+  +G       ++P++    +  
  gi|121638968|ref|YP_979192.1|  83 QYIADTATEFGidEKIHYGLKVNTAEWSSRQCRwTVAGVHE--ATGETRTYTCDYLISCTGyynyDAGYLPDFPGVHRFG 160
                                    566666766643389**************986544444443..9*****************54444568**997766666 PP

                    K_oxygenase 173 ervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqk..kvelklvtrseal 228
                                     r+vH ++  e+   + ++k+++V+GsG +a  ++  ++ +++  +++++++ rs+++
  gi|121638968|ref|YP_979192.1| 161 GRCVHPQHWPEDL--DYSGKKVVVIGSGATAVTLVPAMAGSNPgsAAHVTMLQRSPSY 216
                                    9********9998..89**********************9965226999999999875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.7
                    K_oxygenase 324 geeetlevdavvlATG 339
                                    ++ +++e+d++v+ATG
  gi|121638968|ref|YP_979192.1| 332 KSGREIEADIIVTATG 347
                                    5668899********9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.1e-10     1e-06       1      51 [.       9      61 ..       9      73 .. 0.89
   2 ?   -0.3   0.0      0.99   1.3e+03       1      16 [.     182     197 ..     182     215 .. 0.64
   3 ?   -2.2   0.0       3.9     5e+03      20      32 ..     266     278 ..     256     288 .. 0.81
   4 ?   -1.9   0.0       3.3   4.2e+03       6      22 ..     401     420 ..     399     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.1e-10
                                   EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSSGGG-EECETTCEECTS--- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlGGraasyevpgvrvdygahi 51
                                   I+GaGlsG  +A++ + +  ++ + lle+r+rlGG +  +++pgvr d  + +
  gi|121638968|ref|YP_979192.1|  9 IIGAGLSGIGTACHVTAEfpDKTIALLERRERLGGTWDLFRYPGVRSDSDMFT 61
                                   9****************999**********************99887765555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.99
                                    EE--SHHHHHHHHHHH CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                                    ++G+G+++ ++  ++a
  gi|121638968|ref|YP_979192.1| 182 VIGSGATAVTLVPAMA 197
                                    89****9998765555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.9
                                    EEEEEE-SSSSSS CS
                  NAD_binding_8  20 fdvlllekrdrlG 32 
                                    ++ ll+e r+rlG
  gi|121638968|ref|YP_979192.1| 266 RRLLLWEVRRRLG 278
                                    5789999999998 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHC...CTEEE CS
                  NAD_binding_8   6 lsGlvaAylLak...agfdv 22 
                                    ++G+++++lL+    +g+ v
  gi|121638968|ref|YP_979192.1| 401 IAGAYLCRLLRHmadNGYTV 420
                                    78888888888532236655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   4.4e-10   5.6e-07       1     196 [.       8     213 ..       8     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.4e-10
                    Pyr_redox_3   1 iIiGaGPaGlaaaielk.kagledylilEkg.nignsiy..ryp...kemtfispsftsekleipdlnaiseetspafsl 73 
                                    +IiGaG  G+++a+++  ++  +++  lE+  ++g ++   ryp    +  +++  ++ +     d++++++++s     
  gi|121638968|ref|YP_979192.1|   8 LIIGAGLSGIGTACHVTaEFPDKTIALLERReRLGGTWDlfRYPgvrSDSDMFTFGYKFRP--WRDVKVLADGASS---- 81 
                                    69********999987526777899999*99899998752266633234456664433333..4566677777763.... PP

                    Pyr_redox_3  74 keeklsrkealeYlrevaksfelpiklfeeVesvkk..edegfevetsketyeAkkviiAtGef..dkPnklnipGeek. 148
                                     ++++ +++a e+      ++ l++++ e   +  +   ++  e + +++ty+++++i  tG++  d  +++++pG ++ 
  gi|121638968|ref|YP_979192.1|  82 -RQYI-ADTATEFGIDEKIHYGLKVNTAEWSSRQCRwtVAGVHEATGETRTYTCDYLISCTGYYnyDAGYLPDFPGVHRf 159
                                    .3443.45566666666666666666666544433333345566677888************9722557899****9976 PP

                    Pyr_redox_3 149 ..lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrk....gaeVtvvtrg 196
                                       ++h ++ +e  +y+g+kvvViG + +av     ++       a+Vt++ r+
  gi|121638968|ref|YP_979192.1| 160 ggRCVHPQHWPEDLDYSGKKVVVIGSGATAVTLVPAMAGSnpgsAAHVTMLQRS 213
                                    66799*99999888****************976554444322224667777665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   7.8e-08    0.0001       1      36 [.       6      44 ..       6      46 .. 0.91
   2 ?    3.2   0.3     0.042        54     152     204 ..      85     144 ..      70     198 .. 0.69
   3 ?   -1.8   0.1       1.4   1.8e+03       1      14 [.     179     192 ..     179     216 .. 0.69
   4 ?    2.2   0.0     0.086   1.1e+02     155     207 ..     308     353 ..     271     386 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.8e-08
                                   EEEEECTSHHHHHHHHHHHHT.T...EEEEESSSSTTSSG CS
                            DAO  1 dvviiGGGiiGlstAyeLarr.g...Vtllekgdiagsga 36
                                   dv+iiG+G  G++tA + +++ +   ++lle+++++g g+
  gi|121638968|ref|YP_979192.1|  6 DVLIIGAGLSGIGTACHVTAEfPdktIALLERRERLG-GT 44
                                   8*****************9877568********9999.76 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.042
                                    HHHHHHHTT-..EEEESECEEEEEEEE.TCEEEEE..EECT.EEE.E.EEEEEEE--GGGH CS
                            DAO 152 laraaealGv..eilegtevtgleeed.gkvwgve..rttp.gen.d.aadavVnaaGaws 204
                                    +a++a + G+  +i++g +v   e  +    w+v   + ++ ge+ + ++d+++ ++G + 
  gi|121638968|ref|YP_979192.1|  85 IADTATEFGIdeKIHYGLKVNTAEWSSrQCRWTVAgvH-EAtGETrTyTCDYLISCTGYYN 144
                                    66666666665567777777776553344558887853.4446663257799******984 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.4
                                    EEEEECTSHHHHHH CS
                            DAO   1 dvviiGGGiiGlst 14 
                                    +vv+iG+G + ++ 
  gi|121638968|ref|YP_979192.1| 179 KVVVIGSGATAVTL 192
                                    59******987765 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.086
                                    HHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH CS
                            DAO 155 aaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll 207
                                    +++++++ +++  +++ + e     +g+   ++g++ +ad +V a+G+  + l
  gi|121638968|ref|YP_979192.1| 308 TLASGAASVVTD-QIETFTE-----KGI-LCKSGREIEADIIVTATGLNIQML 353
                                    555555666666.6666633.....233.133365535688*******98854 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.6e-07   0.00085      18      58 ..       5      45 ..       2      94 .. 0.77
   2 ?    0.3   0.0      0.26   3.3e+02      13      38 ..     173     198 ..     164     215 .. 0.77
   3 ?   -1.9   0.0       1.3   1.6e+03     151     171 ..     331     351 ..     306     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.6e-07
                                   EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS--TTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailersvspGGGaw 58
                                    Dv+i+GaG sG+ +a  ++ + pd  +a+ler+  +GG +w
  gi|121638968|ref|YP_979192.1|  5 FDVLIIGAGLSGIGTACHVTAEfPDKTIALLERRERLGG-TW 45
                                   69***********9888888777***********99876.56 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                    HHHTEEEEEEE--SHHHHHHHHHHHH CS
                           Thi4  13 lkyaesDvvivGaGssGLtaayylak 38 
                                    l+y    vv++G+G++ +t    +a 
  gi|121638968|ref|YP_979192.1| 173 LDYSGKKVVVIGSGATAVTLVPAMAG 198
                                    6899999********99987766654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                    .-B-EEEEEEEEEE--GSSST CS
                           Thi4 151 cvDPlvirakvvvdatGhdge 171
                                    c     i+a ++v atG + +
  gi|121638968|ref|YP_979192.1| 331 CKSGREIEADIIVTATGLNIQ 351
                                    556667899999999997665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00098       1.3       1      35 [.       6      40 ..       6      53 .. 0.90
   2 ?    0.5   0.1      0.19   2.4e+02       2      38 ..     180     218 ..     179     222 .. 0.81
   3 !    5.7   0.0    0.0052       6.6     109     143 ..     313     350 ..     297     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00098
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                   Dv++iGaG+ g+  A ++t++ p+  + l+e  + 
  gi|121638968|ref|YP_979192.1|  6 DVLIIGAGLSGIGTACHVTAEFPDKTIALLERRER 40
                                   9********************99999999987665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpg..lkvvlieaspsllf 38 
                                    vvviG+G+  + l   ++ ++pg   +v++++ sps +f
  gi|121638968|ref|YP_979192.1| 180 VVVIGSGATAVTLVPAMAGSNPGsaAHVTMLQRSPSYIF 218
                                    8*********99988886666652278999999999887 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0052
                  Lycopene_cycl 109 vesveeeea...geslvvleggrkirarlvvdarglas 143
                                    ++sv+ ++    +e+ + ++ gr+i+a ++v a+gl  
  gi|121638968|ref|YP_979192.1| 313 AASVVTDQIetfTEKGILCKSGREIEADIIVTATGLNI 350
                                    4455444322348999*******************754 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00033      0.43       2      42 ..       9      45 ..       8      52 .. 0.90
   2 ?   -1.6   0.0       1.8   2.3e+03     130     154 ..     115     141 ..      81     142 .. 0.58
   3 ?    0.8   0.0      0.34   4.3e+02       1      35 [.     181     214 ..     181     221 .. 0.86
   4 ?    1.8   0.0      0.17   2.2e+02     134     154 ..     327     347 ..     306     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvw 42
                                   i+GaG +G+ ++ ++ a+     + +i l +++e   g+ w
  gi|121638968|ref|YP_979192.1|  9 IIGAGLSGIGTACHVTAE---FPDKTIALLERRERL-GGTW 45
                                   9*****************...68999******9887.7777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                  NAD_binding_9 130 radgqavlladg..aslaadaVvLAlG 154
                                    r + + v++a+g  +++++d+++ ++G
  gi|121638968|ref|YP_979192.1| 115 RWTVAGVHEATGetRTYTCDYLISCTG 141
                                    333444566655336789999999999 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.34
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpse 35 
                                    +++G G+++++++ +++ ++ ++s  ++t+  +s+
  gi|121638968|ref|YP_979192.1| 181 VVIGSGATAVTLVPAMAGSN-PGSAAHVTMLQRSP 214
                                    69***********9999995.88999999887766 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.17
                  NAD_binding_9 134 qavlladgaslaadaVvLAlG 154
                                      +l ++g++++ad +v A+G
  gi|121638968|ref|YP_979192.1| 327 KGILCKSGREIEADIIVTATG 347
                                    4577899*************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.4e-05     0.018       1      37 [.       6      44 ..       6      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                   FAD_oxidored  1 DvvVvGGgpaGvaAA..iaAaraGakvlLveergvlGGl 37
                                   Dv+++G+g++G+  A  ++A   +++ +L+e+r++lGG+
  gi|121638968|ref|YP_979192.1|  6 DVLIIGAGLSGIGTAchVTAEFPDKTIALLERRERLGGT 44
                                   9**********988855688999***************7 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.011        14       2      35 ..       7      42 ..       6      46 .. 0.79
   2 ?    6.9   0.0     0.007         9       1      33 [.     179     215 ..     179     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                                   EEEECSSHHHHHHHHHHHH.TT.SEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalae.lg.kkVtvversdkll 35
                                   v+++G+G++g+  A+  ++ +  k + ++er+++l 
  gi|121638968|ref|YP_979192.1|  7 VLIIGAGLSGIGTACHVTAeFPdKTIALLERRERLG 42
                                   89*************997645535558999998886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.007
                                    EEEEECSSHHHHHHHHHHHHTT....SEEEEEESSSS CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelg....kkVtvversdk 33 
                                    kvvv+G+G +++ l  a+a  +    ++Vt+++rs+ 
  gi|121638968|ref|YP_979192.1| 179 KVVVIGSGATAVTLVPAMAGSNpgsaAHVTMLQRSPS 215
                                    79***********999995554445589999999876 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.29   3.7e+02      14      34 ..       6      26 ..       2      40 .. 0.77
   2 ?    8.1   0.0    0.0021       2.6       9      45 ..     174     213 ..     169     221 .. 0.79
   3 ?   -2.0   0.0       2.6   3.3e+03      75      84 ..     338     347 ..     336     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.29
                                   EEEEES-SHHHHHHHHHHHCC CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlak 34
                                    vl+iGaG  +  +a h  a+
  gi|121638968|ref|YP_979192.1|  6 DVLIIGAGLSGIGTACHVTAE 26
                                   69******9999888888766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                                    ..TT-EEEEES-SHHHHHHHHHHHCC...T-CEEEEEESS CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlak...gvkkvvvaNRt 45 
                                    ++++kkv++iG G +a  ++ +++ +   ++ +v+ + R+
  gi|121638968|ref|YP_979192.1| 174 DYSGKKVVVIGSGATAVTLVPAMAGSnpgSAAHVTMLQRS 213
                                    5789******************998733345666666666 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                                    T-SEEEE-SS CS
                   Shikimate_DH  75 eadvvisata 84 
                                    ead++++at+
  gi|121638968|ref|YP_979192.1| 338 EADIIVTATG 347
                                    79*******8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.017        22       2      17 ..       5      20 ..       4      25 .. 0.88
   2 ?    6.1   0.1    0.0043       5.6     144     164 ..     122     142 ..      80     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                                   EEEEEE--SHHHHHHH CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmla 17
                                    dVlI+GaG++G+ +a
  gi|121638968|ref|YP_979192.1|  5 FDVLIIGAGLSGIGTA 20
                                   59**********9877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                                    ECCTTEEEEEEEEEEEE--GT CS
                  FAD_binding_3 144 dketgeeetvrakYlvGaDGg 164
                                     ++tge++t +++Yl+ + G+
  gi|121638968|ref|YP_979192.1| 122 HEATGETRTYTCDYLISCTGY 142
                                    7889**************996 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00023       0.3       4      47 ..       7      48 ..       4      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                                   EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS---------- CS
                           MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga 47
                                   + ++G+G++++ +A++    a++p + i +le+ + +gg++d  
  gi|121638968|ref|YP_979192.1|  7 VLIIGAGLSGIGTACHV--TAEFPDKTIALLERRERLGGTWDLF 48
                                   679*************8..699*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3476.54
//
Query:       gi|121638969|ref|YP_979193.1|  [L=308]
Description: acetyl-hydrolase/esterase lipR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-42  144.3   0.3    5.8e-42  143.9   0.3    1.1  1  Abhydrolase_3  alpha/beta hydrolase fold
    6.9e-11   41.6   0.0    9.3e-11   41.2   0.0    1.1  1  Say1_Mug180    Steryl acetyl hydrolase
    2.8e-05   24.3   0.3    3.9e-05   23.9   0.3    1.2  1  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.037   13.9   0.2      0.084   12.7   0.0    1.6  2  YjeF_N         YjeF-related protein N-terminus
      0.037   13.3   0.3        1.6    8.0   0.0    2.4  2  Hydrolase_4    Serine aminopeptidase, S33
       0.16   10.7   0.0       0.22   10.2   0.0    1.2  1  AXE1           Acetyl xylan esterase (AXE1)


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.3   1.9e-45   5.8e-42       1     210 [.      72     272 ..      72     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1.9e-45
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    l+y+HGG++ lgs++ ++ l+++la+++g++++ +dY +AP +++P a+e++ a++  l++     g+dp+  v+aGdSa
  gi|121638969|ref|YP_979193.1|  72 LIYLHGGAYALGSARGYRGLAAQLAAAAGMTALVPDYTRAPHAHYPVALEEMAAVYTRLLDD----GLDPKTTVIAGDSA 147
                                    69***********************************************************9....8************* PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                    GG l++a+a+++rd+g  ++a++ li+P+ dl + + e+++    + ++pl+ ++++ +++  y++ +d + p +sp+++
  gi|121638969|ref|YP_979193.1| 148 GGGLTLALAMALRDRGIQAPAALGLICPWADL-AVDIEATR---PALRDPLILPSMCTEWAPRYVGSSDPRLPGISPVYG 223
                                    ***************9999***********99.77667773...34445887788888889999999************* PP

                                    S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                     d+sglpp+++++a+ Dp+  ++ +   + +a +++ e++++ gm+H+f+
  gi|121638969|ref|YP_979193.1| 224 -DMSGLPPIVMQTAGDDPICVDADKIETACAASKTSIEHRRFAGMWHDFH 272
                                    .************************************************8 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   3.1e-14   9.3e-11     124     249 ..      71     191 ..      55     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.1e-14
                    Say1_Mug180 124 vllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylv.kskgfknvvvlGd 202
                                     l+ylHGG +al+  +    +L     +   m+ lv+DYt         +Yp  + e+ avy  l    +  k  v+ Gd
  gi|121638969|ref|YP_979193.1|  71 TLIYLHGGAYALGSAR-GYRGLAAQLAAAAGMTALVPDYTRAP----HAHYPVALEEMAAVYTRLLdDGLDPKTTVIAGD 145
                                    69***********876.5789999999999*********9876....789************9776145677999999** PP

                    Say1_Mug180 203 SaGGnlvLslllklsklnkvvlPkkaiaiSPWlnltildekekeylk 249
                                    SaGG l L l + l++      P    +i PW++l++  e  +  l+
  gi|121638969|ref|YP_979193.1| 146 SAGGGLTLALAMALRDR-GIQAPAALGLICPWADLAVDIEATRPALR 191
                                    ***************94.4579************9976666666665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   1.3e-08   3.9e-05       8     100 ..      80     173 ..      71     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.3e-08
                                    -TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHH CS
                   Thioesterase   8 pagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevAr 85 
                                    +a Gsa+ +r la++l +   + ++   p++    +   +  +ee+aa y+  l    + + ++++G S+Gg l+ ++A 
  gi|121638969|ref|YP_979193.1|  80 YALGSARGYRGLAAQLAAA--AGMTALVPDYTraPHAHYPVALEEMAAVYTRLLDDGLDPKTTVIAGDSAGGGLTLALAM 157
                                    478***************7..333333333333267777889************************************** PP

                                    HHHHCT.-SEEEEEEE CS
                   Thioesterase  86 qLesqG.lavkslfli 100
                                    +L+++G  a+++l+li
  gi|121638969|ref|YP_979193.1| 158 ALRDRGiQAPAALGLI 173
                                    *****72568888887 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.1   6.3e+03      39      77 ..      14      50 ..      13      70 .. 0.59
   2 ?   12.7   0.0   2.8e-05     0.084      11      58 ..     122     168 ..     117     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                         YjeF_N 39 GgdglaaArhLaqegakVtvllleeeekldedaeralel 77
                                   G++ l a r L  +g +V + +l+     ++   + +++
  gi|121638969|ref|YP_979193.1| 14 GARPLFASRRLGIAGRRVLLATLTA--GARAPKGTRFQR 50
                                   6677788888888888887755544..333334444444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.8e-05
                         YjeF_N  11 avaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv 58 
                                    ++a+v ++ll ++  ++k +v++G+   Gg  la+A  L+ +g+++ +
  gi|121638969|ref|YP_979193.1| 122 EMAAVYTRLL-DDGLDPKTTVIAGDSAGGGLTLALAMALRDRGIQAPA 168
                                    6778888888.79999****************************9755 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.016        48      77     117 ..     139     183 ..      66     204 .. 0.75
   2 ?    8.0   0.0   0.00053       1.6     193     235 ..     230     272 ..     222     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
                    Hydrolase_4  77 plfllGhSmGGliallyl..lrypd..kvaglilsaPalkikakl 117
                                      ++ G S GG ++l+++  lr +     a+l l++P+ +++ ++
  gi|121638969|ref|YP_979193.1| 139 TTVIAGDSAGGGLTLALAmaLRDRGiqAPAALGLICPWADLAVDI 183
                                    678899****99999888653333332344666777776666555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00053
                    Hydrolase_4 193 PllllhGeaDkvvdpeasrelyerlgskdktlklypglyHell 235
                                    P+ +  +++D+++  +++ e++ +++++  + + ++g++H+ +
  gi|121638969|ref|YP_979193.1| 230 PIVMQTAGDDPICVDADKIETACAASKTSIEHRRFAGMWHDFH 272
                                    889999**********************************987 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   7.2e-05      0.22     170     198 ..     134     163 ..     118     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                                    TEEEEEEEEEEETHHHHHHHHHH.HH-SS- CS
                           AXE1 170 evDeeRvavlGasqGGalalava.alekri 198
                                      D++ ++++G+s GG+l+la a al +r 
  gi|121638969|ref|YP_979193.1| 134 GLDPKTTVIAGDSAGGGLTLALAmALRDRG 163
                                    57999***************9874777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1948.82
//
Query:       gi|121638970|ref|YP_979194.1|  [L=276]
Description: short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-48  162.7   1.9    1.1e-47  162.0   1.9    1.2  1  adh_short       short chain dehydrogenase
    2.4e-35  122.2   3.4      3e-35  121.9   3.4    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.6e-13   51.0   0.9    2.8e-13   50.2   0.9    1.3  1  KR              KR domain
     0.0023   17.3   0.4     0.0064   15.8   0.4    1.9  1  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
     0.0037   17.2   2.4     0.0037   17.2   2.4    1.7  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   1.9   3.1e-51   1.1e-47       1     190 [.       7     198 ..       7     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 3.1e-51
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv+++tGa+sGIGra+a +l ++ ak+++ d   + l++++   +++ga++   ++Dv++re+v a  +++v+++g+++ 
  gi|121638970|ref|YP_979194.1|   7 KVAVITGAGSGIGRALALNLSEKRAKLALSDVDTDGLAKTVRLAQALGAQVKSDRLDVAEREAVLAHADAVVAHFGTVHQ 86 
                                    89****************************************************************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    ++nNAGi+ +g++ + + +++er+i+v + gv++ t+a+lp+ +++  G+Ivn+sS  g+ +v+g++aY A+K+av+g+t
  gi|121638970|ref|YP_979194.1|  87 VYNNAGIAYNGNVDKSEFKDIERIIDVDFWGVVNGTKAFLPHVIASGDGHIVNISSLFGLIAVPGQSAYNAAKFAVRGFT 166
                                    ******************************************************************************** PP

                                    HHHHHHH..GGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 161 rslakel..aptgirvnavaPGlvdTdmakel 190
                                    ++l++e+  a++ ++v++v+PG+++T++a+++
  gi|121638970|ref|YP_979194.1| 167 EALRQEMlvARHPVKVTCVHPGGIKTAVARNA 198
                                    ******7225666**************99876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   3.4   8.5e-39     3e-35       1     200 [.      13     216 ..      13     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 8.5e-39
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIGra+A  l e+ a+++l+d++ ++ +++ +la++lga+v   ++DV+++e+v a +++vv++fg+++ + nnag
  gi|121638970|ref|YP_979194.1|  13 GAGSGIGRALALNLSEKRAKLALSDVDTDGLAKTVRLAQALGAQVksDRLDVAEREAVLAHADAVVAHFGTVHQVYNNAG 92 
                                    889***************************999999********8889******************************** PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                    ia +  g++ + + ++++r++dv++ ++++ +ka+lp ++++g g ivn+ss+ + ++vp+++ay+aaK a+ ++t +l 
  gi|121638970|ref|YP_979194.1|  93 IAYN--GNVDKSEFKDIERIIDVDFWGVVNGTKAFLPhVIASGdGHIVNISSLFGLIAVPGQSAYNAAKFAVRGFTEALR 170
                                    ****..*******************************9777778***********************************9 PP

                                    HHH..GGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS CS
                   adh_short_C2 157 vel..gpkgiRvNavspgpikTlaasgikgfdelleelearaplgr 200
                                     e+  +++ ++v +v+pg ikT  a++++ +d   ++  a+   +r
  gi|121638970|ref|YP_979194.1| 171 QEMlvARHPVKVTCVHPGGIKTAVARNATVADGEDQQTFAEFFDRR 216
                                    9964478****************99888765554444444444444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.9   7.7e-17   2.8e-13       4     168 ..      10     174 ..       8     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 7.7e-17
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    +itG+  g+G++la  l ek a+ l+l s     ++  +++++  +alga+v+  ++Dv++++av a  +++ a++++++
  gi|121638970|ref|YP_979194.1|  10 VITGAGSGIGRALALNLSEKRAK-LAL-SDV--DTDGLAKTVRLAQALGAQVKSDRLDVAEREAVLAHADAVVAHFGTVH 85 
                                    8*****************99775.555.444..355556689999999******************************** PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDal 159
                                     v++ Ag++ ++ +++ + +d+e+++   + G+ n  +++ +    +   ++v +SS+ gl+  +gq++Y aa   + ++
  gi|121638970|ref|YP_979194.1|  86 QVYNNAGIAYNGNVDKSEFKDIERIIDVDFWGVVNGTKAFLPhviaSGDGHIVNISSLFGLIAVPGQSAYNAAKFAVRGF 165
                                    ********************************999999998866633345899********************9999999 PP

                                    HHHHHHHHH CS
                             KR 160 aeyrrsqgl 168
                                     e  r++ l
  gi|121638970|ref|YP_979194.1| 166 TEALRQEML 174
                                    998887765 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.8e-06    0.0064      34     125 ..       4     103 ..       1     127 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                    -TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-..B-GGGS..-TT-EEEE--- CS
                  THF_DHG_CYH_C  34 legkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpel..ikaemv..kegavviDvGi 109
                                     egk +v+ G+++ +g++lal L+ek a   + +  t+ la+++r a+ + + v + +l   ++e v  + +avv   G+
  gi|121638970|ref|YP_979194.1|   4 FEGKVAVITGAGSGIGRALALNLSEKRAKLALSDVDTDGLAKTVRLAQALGAQVKSDRLdvAEREAVlaHADAVVAHFGT 83 
                                    78*********************************************998776655443214444444455666666665 PP

                                    EEC....-TTEEE-SB-HHH CS
                  THF_DHG_CYH_C 110 nrv....ekgklvGDvdfee 125
                                     ++    ++    G+vd +e
  gi|121638970|ref|YP_979194.1|  84 VHQvynnAGIAYNGNVDKSE 103
                                    54445433333455555555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.4     1e-06    0.0037       1     161 [.      13     205 ..      13     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH...HHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla...eleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                    GA  ++Gr+l+  l +++  ++ +   +++ la   +l+++ g   v+ d +dv++ +++l++adaVv+ +g+ ++    
  gi|121638970|ref|YP_979194.1|  13 GAGSGIGRALALNLSEKR-AKLALSDVDTDGLAktvRLAQALG-AQVKSDRLDVAEREAVLAHADAVVAHFGTVHQvynn 90 
                                    677778888888888885.555554334443331113333233.4578999********************776665533 PP

                                    HHHH.............................HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHH CS
                 NAD_binding_10  74 deeg.............................aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaak 124
                                       g                             +k+ +  + ++g  ++v +s++     vpg+    + ++  + + + 
  gi|121638970|ref|YP_979194.1|  91 A--GiayngnvdksefkdieriidvdfwgvvngTKAFLPHVIASGDGHIVNISSLFGLIAVPGQSAYNAAKFAVRGFTEA 168
                                    0..245555556666788888899999999999*********************98888999998777778888999*** PP

                                    HHHHHHHHHSSSEEEEEEE-CEE-ST--SEEEEETTS CS
                 NAD_binding_10 125 raaeellrasgldwTivrpggLtdepttkyrvvekge 161
                                     ++e l+ +  ++ T v+pgg++   + +  v+++++
  gi|121638970|ref|YP_979194.1| 169 LRQEMLVARHPVKVTCVHPGGIKTAVARNATVADGED 205
                                    **********************998776666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1985.87
//
Query:       gi|121638971|ref|YP_979195.1|  [L=368]
Description: zinc-type alcohol dehydrogenase adhD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-29   99.8   3.4    1.6e-28   98.8   3.4    1.5  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.4e-22   80.1   2.1    2.6e-22   79.2   2.1    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    2.8e-06   28.4   0.2    4.7e-06   27.7   0.2    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    7.7e-05   22.3   4.6    0.00011   21.8   2.6    1.9  2  Glu_dehyd_C   Glucose dehydrogenase C-terminus


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   3.4   3.5e-32   1.6e-28       1     109 []      27     153 ..      27     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 3.5e-32
                                    TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG CS
                          ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenl 80 
                                    pgevl+k +aag+C+sDlh+ +g  +l+ ++p++ GHE +G++eevg +v+++k Gd+Vv++++ +cg+C++C +g++nl
  gi|121638971|ref|YP_979195.1|  27 PGEVLVKYTAAGLCHSDLHLTDG--DLPPRFPIVGGHEGSGVIEEVGAGVTRVKPGDHVVCSFIPNCGTCRYCCTGRQNL 104
                                    689*******************9..79***************************************************** PP

                                    -...................TTBEETTTS.S-SSSBSEEEECGGGEEEE CS
                          ADH_N  81 C...................eeakllgvs.ldGgfaeyvvvpekklvkl 109
                                    C                   ++++ +g+  + G+fae+ +v+++++vk+
  gi|121638971|ref|YP_979195.1| 105 CdmgatilegcmpdgsfrfhSQGTDFGAMcMLGTFAERATVSQHSVVKV 153
                                    ************99999987555555555699**************996 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   2.1   5.9e-26   2.6e-22       1     121 [.     195     320 ..     195     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 5.9e-26
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC..SHHHHHHHHH CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvG..sgatleaalk 77 
                                    g+G+ avq A a+G+  v++vd+ + k+e a k+Ga++++     +  +++ elt g+g+d+++  vG  + ++++aa++
  gi|121638971|ref|YP_979195.1| 195 GLGINAVQGATAAGCkYVVVVDPVAFKRETALKFGATHAFADAA-SAAAKVDELTWGQGADAALILVGtvDDEVVSAATA 273
                                    89*************99*************************44.9**********************9999******** PP

                                    CEEEEEEEEECSC..TSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHH CS
                     ADH_zinc_N  78 llkpgGrlvvvGg..gkgeee.fdlrnlllkeksilGsllgslreef 121
                                    ++ +gG++v+ G+  + + ++ ++  +l+l+ek+i+Gsl+gs++ ++
  gi|121638971|ref|YP_979195.1| 274 VIGKGGTVVITGLadPAKLTVhVSGTDLTLHEKTIKGSLFGSCNPQY 320
                                    ************997666666899*****************955444 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2     1e-09   4.7e-06       2     127 ..     229     361 ..     228     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                                    T-SEEE.ETTSTTHH..HHH-TT-EEEEEES-H..HHHH.HHHHHHE.EEEEEEEE--.--...S-EEE-CHHHCTTT-E CS
                   ADH_zinc_N_2   2 GAdevi.dyrtedfe..aatggegvDvvldtvg..gealleaslkvl.pggGrlvsig.gpp..lsaallkpakkrkgrs 72 
                                    GA++++ d  + +++  + t g+g D++l +vg   ++ ++a+ +v+ +g G++v  g ++p  l+  ++   +   +++
  gi|121638971|ref|YP_979195.1| 229 GATHAFaDAASAAAKvdELTWGQGADAALILVGtvDDEVVSAATAVIgKG-GTVVITGlADPakLTVHVSGTDLTLHEKT 307
                                    899999544444444789999**************888889999999555.99988886766675555666666566666 PP

                                    EEE--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS-- CS
                   ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesgra 127
                                    +k +++ s ++  q d + +l++l+++G+  l   v+ ++ le++++ +++l+ g+ 
  gi|121638971|ref|YP_979195.1| 308 IKGSLFGSCNP--QYD-IVRLLRLYDAGQlmLDELVTTTYNLEQVNQGYQDLRDGKN 361
                                    66666664333..567.9***********4445689999*************99986 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.14   6.2e+02     125     146 ..     162     183 ..     141     185 .. 0.79
   2 !   21.8   2.6   2.4e-08   0.00011      32     203 ..     186     357 ..     184     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                    Glu_dehyd_C 125 GvaaLlGvpedsevevdggelh 146
                                     v +  Gvp+++  +v++g+l 
  gi|121638971|ref|YP_979195.1| 162 AVLVGCGVPSGWGTAVNAGNLR 183
                                    4666679***********9986 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-08
                    Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv....dsretpvdeip.easeemdlvvE 106
                                    ++a++ G G lG+ a+   +a   g + v v++       + +   + Gat       s+ ++vde++  +  +  l++ 
  gi|121638971|ref|YP_979195.1| 186 DTAVIYGVGGLGINAVQGATA--AGCKYVVVVDPV---AFKRETALKFGATHAfadaASAAAKVDELTwGQGADAALILV 260
                                    6899*********99776664..788877777754...455555678999974322257788999996234566779999 PP

                    Glu_dehyd_C 107 aTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavd..tLaalpesllde 184
                                     T   +++ +a+  ++  G ++++G+  + ++ v ++   ++l l+ k + Gs   + +     v+  +L  + + +lde
  gi|121638971|ref|YP_979195.1| 261 GTVDDEVVSAATAVIGKGGTVVITGLADPAKLTVHVSG--TDLTLHEKTIKGSLFGSCNPQYDIVRllRLYDAGQLMLDE 338
                                    99999**********************99977777664..6778888888888766655444444411667777889*** PP

                    Glu_dehyd_C 185 lvtkvvdldeleeAfeddd 203
                                    lvt+ ++l+++++ ++d  
  gi|121638971|ref|YP_979195.1| 339 LVTTTYNLEQVNQGYQDLR 357
                                    ***************9633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2577.54
//
Query:       gi|121638972|ref|YP_979196.1|  [L=472]
Description: hypothetical protein BCG_3112 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-90  301.2   0.0    1.2e-89  300.6   0.0    1.3  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    9.2e-21   74.3   0.0    1.4e-20   73.8   0.0    1.3  1  DUF1298         Protein of unknown function (DUF1298)


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.6   0.0   1.3e-93   1.2e-89       1     264 []       4     268 ..       4     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 300.6 bits;  conditional E-value: 1.3e-93
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    L+++Dal+l+l+  ++++h+++++vl+p+++++g+ +++++r+++e+r++  p++r +++++plgl++p+Wved++fDld
  gi|121638972|ref|YP_979196.1|   4 LNGVDALMLYLDGGSAYNHTLKISVLDPSTDPDGW-SWPKARQMFEERAHLLPVFRLRYLPTPLGLHHPIWVEDPEFDLD 82 
                                    799********************************.8******************************************* PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                     HvRrv +paPG+++e+++lv++++++pLDr+rPlW+++v+EGl+ggr+A+++ +HHA+ DGvg+l++la +++++pd++
  gi|121638972|ref|YP_979196.1|  83 AHVRRVVCPAPGGMAEFCALVEQIYAHPLDRDRPLWQTWVVEGLDGGRVALVTLLHHAYSDGVGVLDMLAAFYNDTPDEA 162
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaal.earslvlpfaap..rtplntplsraR 237
                                    p+ +pp++pp+   +t++r+++al++l ++lgk++ +v++v+++++ ++e a+  +r+++ +f+++  + p+++ lsr+R
  gi|121638972|ref|YP_979196.1| 163 PVVAPPWEPPPL-PSTRQRLGWALRDLPSRLGKIAPTVRAVRDRVRIEREFAKdGDRRVPPTFDRSapPGPFQRGLSRSR 241
                                    *******99999.69**************************************999*******98766************ PP

                 WES_acyltransf 238 rfaaaslpLadvkavakalgvtiNDvv 264
                                    rf++ s+pLa+v++v+k+lgvtiNDv+
  gi|121638972|ref|YP_979196.1| 242 RFSCESFPLAEVREVSKTLGVTINDVF 268
                                    *************************95 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   1.5e-24   1.4e-20       2     144 ..     309     457 ..     308     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.5e-24
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaal...ikrl....lsnttlviS 74 
                                    GN  +v  + L  d+adPlerl++++ a ++ K+ ++++    + ++ ++llp+ + + l     r+     +  ++v+S
  gi|121638972|ref|YP_979196.1| 309 GNYSSVDYVWLRADIADPLERLHATHLAAEATKQHFAQTKDADVGAV-VELLPERLISGLaraNARTkgrfDTFKNVVVS 387
                                    8999999999*************************************.********99885542333666577779**** PP

                        DUF1298  75 NvpGPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    NvpGP+e+ yl   ++++++ +  +++g  ln+tv+Sy+++ ++ +++d  +v + ++l+  ++ + eel
  gi|121638972|ref|YP_979196.1| 388 NVPGPREPRYLGRWRVDQWFSTGQISHGATLNMTVWSYCDQFNLCVMADAVAVRNTWELVGGFRASHEEL 457
                                    ***************************************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3315.57
//
Query:       gi|121638973|ref|YP_979197.1|  [L=474]
Description: hypothetical protein BCG_3113 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-84  281.9   0.0    8.6e-84  281.4   0.0    1.2  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    6.2e-29  100.8   0.0    1.1e-28  100.0   0.0    1.4  1  DUF1298         Protein of unknown function (DUF1298)
  ------ inclusion threshold ------
       0.32    9.6   0.4         12    4.4   0.0    2.1  2  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.4   0.0   1.4e-87   8.6e-84       2     264 .]       5     273 ..       4     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.4 bits;  conditional E-value: 1.4e-87
                 WES_acyltransf   2 splDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDldy 81 
                                    +p+D++fl le+a++p+h++a++++e+p kg+++++ +rl++a++++++++p++++    ++lg++ ++W+++e +D++y
  gi|121638973|ref|YP_979197.1|   5 NPIDLSFLLLERANRPNHMAAYTIFEKP-KGQKSSFGPRLFDAYRHSQAAKPFNHK---LKWLGTDVAAWETVE-PDMGY 79 
                                    89**************************.***************************...9*************9.***** PP

                 WES_acyltransf  82 HvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddpp 161
                                    H+R++alpaPG++++++e+vs L++ +LDr++P+We+++i+G+e+griAillkvHHAliDG ggl+ ++++l+++pdd++
  gi|121638973|ref|YP_979197.1|  80 HIRHLALPAPGSMQQFHETVSFLNTGLLDRGHPMWECYIIDGIERGRIAILLKVHHALIDGEGGLRAMRNFLSDSPDDTT 159
                                    ******************************************************************************** PP

                 WES_acyltransf 162 rpeppqvpprdr..srtqlrasg......alvglvaglgkvlgsvagvvssagrlleaal..earslvlpfaaprtpln. 230
                                    ++ p++++++++  +rt +++s+      +l+g+++gl+k++++++gv+++a++l ++al  +ar+++lpf+a+rt++n 
  gi|121638973|ref|YP_979197.1| 160 LAGPWMSAQGADrpRRTPATVSRraqlqgQLQGMIKGLTKLPSGLFGVSADAADLGAQALslKARKASLPFTARRTLFNn 239
                                    ********999887667666666788888******************************999*****************9 PP

                 WES_acyltransf 231 tplsraRrfaaaslpLadvkavakalgvtiNDvv 264
                                    t+ s+aR++ +++lpLadvka+aka+g+++NDvv
  gi|121638973|ref|YP_979197.1| 240 TAKSAARAYGNVELPLADVKALAKATGTSVNDVV 273
                                    9********************************7 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   1.8e-32   1.1e-28       2     144 ..     313     457 ..     312     458 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.8e-32
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl..lsnttlviSNvpGP 79 
                                    GN++++ l+p++  +a P+erl+++++a++r+K + + + t++ ++++l ll++ ++a ++  l  l+++++viSN+ GP
  gi|121638973|ref|YP_979197.1| 313 GNRVSAELVPMGAPKASPVERLKEINAATTRAKDKGRGMQTTSRQAYALLLLGSLTVADALPLLgkLPSANVVISNMKGP 392
                                    9***********************************************************988888************** PP

                        DUF1298  80 qeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    +e+lylaGapl+a+ ++ ++ pg +ln+t+ S +  l i++ + +++v++p++l++ +++a++el
  gi|121638973|ref|YP_979197.1| 393 TEQLYLAGAPLVAFSGLPIVPPGAGLNVTFASINTALCIAIGAAPEAVHEPSRLAELMQRAFTEL 457
                                    ***************************************************************98 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1    0.0043        26     115     144 ..     109     140 ..      93     142 .. 0.84
   2 ?    4.4   0.0    0.0021        12     238     272 ..     256     290 ..     221     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0043
                                    CS.-SEEEEEEE.SSTTEEEEEEEEECCT--T CS
                   Condensation 115 kg.pLfraalfk.iaenrlllllsvHHiivDG 144
                                    +g p +  ++++ i+  r  +ll+vHH ++DG
  gi|121638973|ref|YP_979197.1| 109 RGhPMWECYIIDgIERGRIAILLKVHHALIDG 140
                                    55577777877537888999***********9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0021
                                    HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEE CS
                   Condensation 238 eklrklakeqgvtlndvllaalgllLskytgqddi 272
                                    + ++ lak++g+++ndv +++   +L+ y  + ++
  gi|121638973|ref|YP_979197.1| 256 ADVKALAKATGTSVNDVVMTVIDDALHHYLAEHQA 290
                                    567899*******************9999777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3566.81
//
Query:       gi|121638974|ref|YP_979198.1|  [L=503]
Description: chain-fatty-acid-CoA ligase fadD13 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-99  332.7   0.0      3e-99  332.5   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    7.5e-20   71.7   0.5    2.1e-19   70.3   0.5    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.5   0.0  3.3e-103     3e-99       2     422 ..       9     404 ..       8     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 332.5 bits;  conditional E-value: 3.3e-103
                                    HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                    AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                    +++a   p   a+v   ++ ++TY+++++ +nr A +L++lG+ kgdrVa+l+pns+e+  ++++++k+Gav+vp+n++l
  gi|121638974|ref|YP_979198.1|   9 RQRATVSPRLQAYVEPSTDVRMTYAQMNALANRCADVLTALGIAKGDRVALLMPNSVEFCCLFYGAAKLGAVAVPINTRL 88 
                                    6778888999999998889************************************************************* PP

                                    -HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSE CS
                    AMP-binding  82 taeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddl 161
                                     a+e+++il+ds++kv+i  + +  ++ +++++a+ + + +v+    +++l e +l +++    +   +e+++e+  dd 
  gi|121638974|ref|YP_979198.1|  89 AAPEVSFILSDSGSKVVI--YGAPSAPVIDAIRAQADPPGTVTDWIGADSLAE-RLRSAA----A---DEPAVECGGDDN 158
                                    ******************..333334444455544444444433332222222.233333....2...2245689***** PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                    ++i+YTSGTTG+PKGV+++h++++++++s++   + +++ +d++l  lp++h+++l + ++++ ++G t++ +p+++a++
  gi|121638974|ref|YP_979198.1| 159 LFIMYTSGTTGHPKGVVHTHESVHSAASSWA--STIDVRYRDRLLLPLPMFHVAAL-TTVIFSAMRGVTLISMPQFDATK 235
                                    **************************99953..44456679**************9.*****************999954 PP

                                    HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGS CS
                    AMP-binding 242 pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEtt 321
                                       ++ li +++v +  +vP++l+ + + ++++    + d +  r++++gg+p++++l++ + a+ +e v++gY lTE +
  gi|121638974|ref|YP_979198.1| 236 ---VWSLIVEERVCIGGAVPAILNFMRQVPEFA----ELDAPDFRYFITGGAPMPEALIKIYAAKNIE-VVQGYALTESC 307
                                    ...4699999****************9987777....459999**********************997.*********** PP

                                    SECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEE CS
                    AMP-binding 322 gvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDl 401
                                    g  t l  e+  +k+gs+G++   ++v++  ++  + ++++ eGe+++++  + k Y+++peat++afd + +w+rTGD+
  gi|121638974|ref|YP_979198.1| 308 GGGTLLLSEDALRKAGSAGRATMFTDVAVRGDD--GVIREHGEGEVVIKSDILLKEYWNRPEATRDAFD-N-GWFRTGDI 383
                                    ***9877788999*****************998..56778889*************************9.5.7******* PP

                                    EEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 402 grldedGyleivgRkkdlikl 422
                                    g++d++Gyl+i +R+kd+i++
  gi|121638974|ref|YP_979198.1| 384 GEIDDEGYLYIKDRLKDMIIS 404
                                    ****9**************96 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.5   2.3e-23   2.1e-19       1      76 []     413     487 ..     413     487 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.3e-23
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+Es+++ +p+V+e+aV+G pde++Ge+++a+Vv +++ e  e+++++++ ++l+ y+ pkkv+f +++p++ +GK
  gi|121638974|ref|YP_979198.1| 413 EIESVIIGVPGVSEVAVIGLPDEKWGEIAAAIVVADQN-EVSEQQIVEYCGTRLARYKLPKKVIFAEAIPRNPTGK 487
                                    8*********************************9533.3468********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3420.33
//
Query:       gi|121638975|ref|YP_979199.1|  [L=295]
Description: hypothetical protein BCG_3115 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-17   62.0   1.6    1.1e-16   61.4   1.6    1.2  1  Band_7          SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.043   13.4   4.6      0.066   12.8   4.6    1.3  1  Virul_fac_BrkB  Virulence factor BrkB
      0.061   13.4   3.8       0.11   12.6   3.8    1.4  1  DUF2165         Predicted small integral membrane protein (DU


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   1.6   1.8e-20   1.1e-16       2     176 ..      56     245 ..      55     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.8e-20
                         Band_7   2 iieegevgvvvrfGklsr.vlepGlhfilP.....fgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrv.pdd 74 
                                    i+++ +++++++fG++ +  l++G+h ++P       +  ++++ +v + ++ +++tv+  ++  +  dv++++++ +  
  gi|121638975|ref|YP_979199.1|  56 IVGTRQFAIMTTFGRPTGvSLNNGFHGKWPwqmthPMDGAVQIDKYVKEGNTDQRITVRLGNQSTALADVSIRWQLkQAA 135
                                    79999*************779*********776666666679999999999999************************** PP

                         Band_7  75 apklvaaveresan.ldnlirrvlesalrevisemtleellsn....reelaeelknelneqlrkyGvevldvritdidp 149
                                    ap+l++++ ++++n   nli+r l+ al+ev++ ++  +  +        la+++++ l++++ ++ v + dv++ +i++
  gi|121638975|ref|YP_979199.1| 136 APELFQQY-KTFDNvRVNLIERNLSVALNEVFAGFNPLDPRNLdvspLPSLAKRAADILRQDVGGQ-VDIFDVNVPTIQY 213
                                    ********.777772569*******************99997778878******************.9************ PP

                         Band_7 150 ppevaqalaakqaaeaea.....qaeiaraea 176
                                     +  ++ +++ ++++a++      +++a+a+a
  gi|121638975|ref|YP_979199.1| 214 DQSTEDKINQLNQQRAQTsialeAQRTAEAQA 245
                                    *******************9966556666655 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.6   1.1e-05     0.066     162     216 ..       6      61 ..       1      74 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                 Virul_fac_BrkB 162 lrwlvallllvlafallYrvlpn...vkvrlraalpGallaallwllvkilfslylsn 216
                                    +  +v+++++v+ +a+l++ lp+   ++ r + ++++a++aa++++++  +  +  ++
  gi|121638975|ref|YP_979199.1|   6 V--FVVICVIVAGVAALFWRLPSddtTRSRAKTVTIAAVAAAAVFFFLGCFTIVGTRQ 61 
                                    3..3689999************966449999**************9998776655555 PP

>> DUF2165  Predicted small integral membrane protein (DUF2165)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.8   1.8e-05      0.11      70     126 ..       3      62 ..       1      65 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                        DUF2165  70 lEalaalll..llGavallralkasaaafnrakalailgltlgvllwf.vgflvvGGewF 126
                                    ++++  +++  ++G++al+ +l +++++  rak++ i++++++ + +f ++f +vG   F
  gi|121638975|ref|YP_979199.1|   3 WQIVFVVICviVAGVAALFWRLPSDDTTRSRAKTVTIAAVAAAAVFFFlGCFTIVGTRQF 62 
                                    56555555511679*************************988776666156777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2286.90
//
Query:       gi|121638976|ref|YP_979200.1|  [L=563]
Description: hypothetical protein BCG_3116 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   67.8   0.8    3.9e-18   66.4   0.8    1.8  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.8   2.2e-22   3.9e-18       2     204 .]     182     420 ..     181     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.2e-22
                        Patatin   2 vlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalg.rdpaalvddlrnlllnkifdrdl.........l 71 
                                    vl+GGG  g++++g +++L  ++g+ +d++ G+S G+ii++l+a + + p ++++++  + +++++  +           
  gi|121638976|ref|YP_979200.1| 182 VLGGGGGAGFVYIGGMQRL-LAAGQVPDYMIGSSFGSIIGSLVARElPVPIDEYAEWAKTVSYRAILGPErrrsrhglaG 260
                                    89****************9.9*************************4445555555555555555555525544444442 PP

                        Patatin  72 irelaanlaarlsgllgkgglfdaealrellrkv..........ladktlkrlsarlgklpllks............lft 129
                                     + l  +++a++   +  g              +          +a++  + ++a +++   +++            +  
  gi|121638976|ref|YP_979200.1| 261 MFTLRFDQFAHTLLSRADGERMR----------MsdlaipfdvvVAGVRRQPYAALPSRFRHRERstltlrslpflpIGI 330
                                    22222222222222222222222..........02223333333444444444444444433333666666699999999 PP

                        Patatin 130 anqavpaittataatastanranglytedddddvdladavraSsafPglfppvsldge...............lyvDGGi 194
                                     +  +++++++ a+   +   +   +++  ++dv+++da+  Ssa+Pg+++  + d +                +vDGG 
  gi|121638976|ref|YP_979200.1| 331 GPWVAARMWQVAAFIDLRVVKPIVISADGATRDVNVVDAASFSSAIPGVLHHETSDPRmlpildelcadqdvaAMVDGGA 410
                                    999999999999999999999999999999********************8888888866655555555556677***** PP

                        Patatin 195 lsNvPilaal 204
                                    +sNvP+++a+
  gi|121638976|ref|YP_979200.1| 411 ASNVPVELAW 420
                                    *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 4011.22
//
Query:       gi|121638977|ref|YP_979201.1|  [L=306]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.7e-114  380.5  15.1   5.8e-114  380.2  15.1    1.1  1  DUF808    Protein of unknown function (DUF808)


Domain annotation for each model (and alignments):
>> DUF808  Protein of unknown function (DUF808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.2  15.1  3.3e-118  5.8e-114       2     303 ..       4     291 ..       3     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.2 bits;  conditional E-value: 3.3e-118
                         DUF808   2 gllaLlDdiaalaklaaaslDDvaaaakkaakkaagvvvDDlavtaqqvsgvkaeRElpvvwkiakgSllNKlvillPaa 81 
                                    gl+ LlD +a+la+laaas+DD++aaa++a++kaagvv+DD+avt+q+v+ ++aeRElp++++ia gS++NKl+++lP a
  gi|121638977|ref|YP_979201.1|   4 GLFGLLDHVAVLARLAAASIDDIGAAAGRATAKAAGVVIDDTAVTPQYVHRITAERELPIIKRIAIGSVRNKLLLILPGA 83 
                                    89****************************************************************************** PP

                         DUF808  82 lllsafapwlitplLmlGgayLcfEGaeKvlekllhkeeeeeeeeeeaeeadlaelEkekvkgairtDfiLSaEiivial 161
                                    llls+++pwl+tplLmlG++yLc+EGaeKv+  +       + +     +a  + +E+e v+gairtDfiLSaEi+vial
  gi|121638977|ref|YP_979201.1|  84 LLLSQLVPWLLTPLLMLGATYLCYEGAEKVCGVIG-----GRGH-----DAAPQVAERELVAGAIRTDFILSAEIMVIAL 153
                                    **********************************6.....1222.....23456789*********************** PP

                         DUF808 162 gevaeeslltqvlvlvvvavliTvgvYGlValivklDdvGlalakkkksklarklGrglvkamPkllkllsvvGtaAmll 241
                                    +eva+++++ +++vlv+va++iT++vYG+Va+iv++DdvGl+l++ ++s++ +++G glv++mPkll++ls vG+ Aml+
  gi|121638977|ref|YP_979201.1| 154 NEVADQPFVPRLIVLVIVALVITAAVYGVVAVIVQMDDVGLRLTQ-TASRFGQRIGGGLVAGMPKLLSALSAVGMGAMLW 232
                                    *********************************************.669******************************* PP

                         DUF808 242 VgggilvhgleelglealaelvhhlaeavaeaaaalgavlewlvetllsavvGlvvGavvva 303
                                    Vgg+i+++g ++lg++a+++lvhhl +++     ++g++l+wlv+t++ a +Glv+G+vvva
  gi|121638977|ref|YP_979201.1| 233 VGGHIVLVGSDHLGWHAPYRLVHHLDDHLVG---SAGGALTWLVSTAACAATGLVIGIVVVA 291
                                    **************************99976...689***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2131.70
//
Query:       gi|121638978|ref|YP_979202.1|  [L=334]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-39  133.7  12.7    1.1e-38  133.4  12.7    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.024   14.1   0.3      0.024   14.1   0.3    1.9  2  PEP_mutase      Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.4  12.7   1.2e-42   1.1e-38      23     313 ..      17     297 ..       9     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 1.2e-42
                 Bac_luciferase  23 rylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfg 102
                                    +++ ++a aa + Gf a+w++e ++      daf+l++ +  +T ++ l ++ + + +r P+ lA  + ++  l+g R++
  gi|121638978|ref|YP_979202.1|  17 HEATDVALAAADTGFAALWIGEMAT-----YDAFALATSIGLRTPNMTLKVGPLAVGVRGPVGLALGVSSVASLTGCRVD 91 
                                    578899*******************.....9************************************************* PP

                 Bac_luciferase 103 lglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglela 182
                                    l lg+++pa++++++G++++  +  +rE++e lr +++g +v+++G++++ +g++l+   +++   + ++a +p +++la
  gi|121638978|ref|YP_979202.1|  92 LALGASSPAIVAGWHGRPWAHHVPVMRETIECLRSIFTGARVEYSGRHVNSRGFRLRGAAPDT--RIALGAFGPGMIRLA 169
                                    **************************************************9999999999666..9************** PP

                 Bac_luciferase 183 arhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea..raliagldfyaldsegagr 260
                                    a+had ++l++++p  + ++ + ++++aa+agr  a++r+++ ++v+v++ +++  + a  +a +      a  + g  +
  gi|121638978|ref|YP_979202.1| 170 AQHADEVVLNLASPFRVGRVRAAIDSAAAAAGR--AAPRLTVWVPVAVNPGAAAHSQLAaqLAVY-----LAPPGYGEMF 242
                                    *********************************..589999999999998888777777433333.....3333333333 PP

                 Bac_luciferase 261 eaeaa..eiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                     a +     + + ++  +++ a avp el+++ ++ G+p+ va+rl+aya+ag+d
  gi|121638978|ref|YP_979202.1| 243 SALGFdgLVRSARSRATRRELAVAVPSELLDRVCALGSPDRVAARLRAYADAGAD 297
                                    33333223455666666667777789***************************98 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.21   1.9e+03      22      38 ..      23      39 ..      21      54 .. 0.76
   2 ?   14.1   0.3   2.7e-06     0.024     156     179 ..     282     305 ..     246     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
                     PEP_mutase 22 akiveeagfkalatsSl 38
                                   a +++++gf al+++ +
  gi|121638978|ref|YP_979202.1| 23 ALAAADTGFAALWIGEM 39
                                   56889999***999755 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.7e-06
                     PEP_mutase 156 eeaieRaraYaeAGAdgvfvpglq 179
                                    ++  +R+raYa+AGAd+v v+ ++
  gi|121638978|ref|YP_979202.1| 282 DRVAARLRAYADAGADCVAVVPAT 305
                                    66789*************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2183.69
//
Query:       gi|121638979|ref|YP_979203.1|  [L=376]
Description: hypothetical protein BCG_3119c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-35  120.4  12.8    6.1e-35  120.4  12.8    1.9  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.2e-08   34.5   4.6    4.7e-08   33.4   4.6    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.5e-06   26.6   0.3    2.1e-05   25.2   0.3    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
     0.0025   18.0   0.0     0.0045   17.1   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.073   12.7   0.2        1.2    8.7   0.0    2.4  3  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7      0.48   1.7e+03      59      98 ..      16      55 ..       3      86 .. 0.68
   2 !  120.4  12.8   1.7e-38   6.1e-35       1     133 [.     223     355 ..     223     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.48
                                   HHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2 59 eraaaraealaaagkevtvedraearraaalavelaiaav 98
                                   +r a++  a ++++++++ e++++ r a +l +++ ++++
  gi|121638979|ref|YP_979203.1| 16 ARWARARSAEIERDRRLPDELVTRLREAGLLRATMPREVA 55
                                   4444444566788888888888888888777777766664 PP

  == domain 2  score: 120.4 bits;  conditional E-value: 1.7e-38
                                    .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    l+i+a+alG+Araa++++vela+++++ +s+++la+++atq+a a+a+++l+AAral+++++++a+++++++++v+v++r
  gi|121638979|ref|YP_979203.1| 223 LSIGAAALGNARAAIDDLVELAGGKKGLGSTRTLAERSATQAAAATAESALGAARALFYEVIEAAWQVSHDAEAVPVTMR 302
                                    5799**************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    ++ r+aa++av++++++v++++++aGg+a+++++plqR++RDa +a+aH  +n
  gi|121638979|ref|YP_979203.1| 303 NRLRLAATHAVRTSADVVRSMYDLAGGTAIYDNAPLQRRFRDAFTATAHFQVN 355
                                    *************************************************9988 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   4.6   1.3e-11   4.7e-08      15     130 ..     222     347 ..     216     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.3e-11
                                    -----..-SHHHHHHHHHHHHHHHTSB-CC..-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------........ CS
                  Acyl-CoA_dh_1  15 Rlavaaaalglarraleealeyarrrkafg..kplidhqlvreklaemaaeleaarllvyraaealdagkpd........ 84 
                                     l+++aaalg ar+a++ ++e+a   k  g  ++l++  + +   a+ +  l aar+l y+++ea+ +  +d        
  gi|121638979|ref|YP_979203.1| 222 ALSIGAAALGNARAAIDDLVELAGGKKGLGstRTLAERSATQAAAATAESALGAARALFYEVIEAAWQVSHDaeavpvtm 301
                                    6899***********************999999***************************98886655555555699999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHH CS
                  Acyl-CoA_dh_1  85 raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarv 130
                                    r +  +a   a ++  +v++++ +l Gg ++ +  p++r +rda +
  gi|121638979|ref|YP_979203.1| 302 RNRLRLAATHAVRTSADVVRSMYDLAGGTAIYDNAPLQRRFRDAFT 347
                                    99999999***********************************965 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   5.8e-09   2.1e-05       5      85 ..       9      85 ..       5     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.8e-09
                                   HHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHH CS
                  Acyl-CoA_dh_N  5 ealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvh 85
                                   e l ++++++a+ +     ae++++++ p+el+ +l e+Gll  t+p e+   +l +  a+ +ae +ar+da+ +  +++ 
  gi|121638979|ref|YP_979203.1|  9 EILAEKIARWARARS----AEIERDRRLPDELVTRLREAGLLRATMPREVAAPELAPGRALRCAEAVARGDASAGWCVSIA 85
                                   455566666666654....567777799*****************************************999877755542 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0045      21      97 .]     121     192 ..     109     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                                    EEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  21 aerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieeklGlrglptgelvfedv 97 
                                    a+  +g++v++G+  ++++ ++a++++  +    +d ++  s++++  ++ +++v +++++lGlrg+ +++ v +dv
  gi|121638979|ref|YP_979203.1| 121 ARSVDGGVVVSGRWPFCSGINHADIMFAGCF--VDD-RQVPSVVAL--NKDELQVLDTWHTLGLRGTGSHDCVADDV 192
                                    6677789***********************9..445.455555555..57899****************99999987 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   4.1e+03     176     200 ..     125     149 ..     122     157 .. 0.77
   2 ?    8.7   0.0   0.00034       1.2     258     271 ..     187     200 ..     179     201 .. 0.91
   3 ?    1.1   0.0     0.072   2.6e+02      29      59 ..     310     340 ..     304     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                                    SSEEEEEEEEEEEE-.--SSEEEE- CS
                         HpaB_N 176 ddGivVrGakvlaTgaaladeilvl 200
                                    d G+vV+G   + +g   ad ++  
  gi|121638979|ref|YP_979203.1| 125 DGGVVVSGRWPFCSGINHADIMFAG 149
                                    679****988888888888877765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00034
                                    EEEEEEEEEGGGEE CS
                         HpaB_N 258 vvfDdVfVPwerVf 271
                                    +v DdVfVP +rVf
  gi|121638979|ref|YP_979203.1| 187 CVADDVFVPADRVF 200
                                    578**********9 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.072
                                    STTTHHHHHHHHHHHHHTTSTTTHHHHEEEE CS
                         HpaB_N  29 hpafrpavrsvarlYdlahdpeykdlltats 59 
                                     +a+r+++++v ++Ydla   +  d +  + 
  gi|121638979|ref|YP_979203.1| 310 THAVRTSADVVRSMYDLAGGTAIYDNAPLQR 340
                                    56899************99988888765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2615.83
//
Query:       gi|121638980|ref|YP_979204.1|  [L=158]
Description: transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-28   97.4   0.0    4.6e-28   96.9   0.0    1.2  1  HxlR           HxlR-like helix-turn-helix
    4.8e-05   23.1   0.0    9.8e-05   22.1   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
    0.00021   21.3   0.0     0.0005   20.1   0.0    1.6  1  HTH_20         Helix-turn-helix domain
    0.00061   19.5   0.0     0.0012   18.6   0.0    1.6  1  HTH_IclR       IclR helix-turn-helix domain
     0.0017   18.2   0.0     0.0029   17.4   0.0    1.4  1  MarR_2         MarR family
     0.0042   16.6   0.0     0.0072   15.9   0.0    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.8   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.04   13.9   0.1      0.091   12.7   0.1    1.6  1  HTH_1          Bacterial regulatory helix-turn-helix protein,
      0.088   12.6   0.0       0.16   11.7   0.0    1.4  1  HTH_psq        helix-turn-helix, Psq domain
       0.13   12.5   0.0       0.21   11.8   0.0    1.3  1  HTH_34         Winged helix DNA-binding domain
       0.15   12.1   0.0       0.23   11.5   0.0    1.3  1  PadR           Transcriptional regulator PadR-like family
       0.17   11.7   0.5       0.29   10.9   0.1    1.6  2  HTH_8          Bacterial regulatory protein, Fis family
       0.18   11.9   0.0       0.27   11.3   0.0    1.2  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
       0.26   11.0   0.1       0.26   11.0   0.1    1.5  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   3.6e-31   4.6e-28       1      89 [.      21     108 ..      21     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 3.6e-31
                                    HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                           HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80 
                                    l+g++W+llil+e ++g +Rf++l+r+l +i++ +L++rLr+L + gl++r++y++ P+++eY+lte+Gr+l +++  l+
  gi|121638980|ref|YP_979204.1|  21 LVGERWTLLILREAFFGVRRFGQLARNL-GIPRPTLSSRLRMLVEVGLFDRVPYSSDPERHEYRLTEAGRDLFAAIVVLM 99 
                                    69**************************.9************************************************** PP

                                    HHHHHHHHC CS
                           HxlR  81 kwgeeylee 89 
                                    +wg+eyl++
  gi|121638980|ref|YP_979204.1| 100 QWGDEYLPR 108
                                    ******986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.7e-08   9.8e-05       9      44 ..      29      67 ..      28      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.7e-08
                                   HHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_5  9 klLae...gelcvcelaeelglsqstvShHLkkLreaGL 44
                                    +L+e   g + +++la+ lg++++t+S  L++L e GL
  gi|121638980|ref|YP_979204.1| 29 LILREaffGVRRFGQLARNLGIPRPTLSSRLRMLVEVGL 67
                                   567777778999*************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.9e-07    0.0005      27      55 ..      41      69 ..      38      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 27 aselaerldlskntlsyHLrvLeeagLve 55
                                   +++la+ l++++ tls +Lr L+e+gL +
  gi|121638980|ref|YP_979204.1| 41 FGQLARNLGIPRPTLSSRLRMLVEVGLFD 69
                                   589***********************965 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.5e-07    0.0012      20      47 ..      40      67 ..      28      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.5e-07
                                   BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                       HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGy 47
                                   ++ +lAr++g+p++t +  L+ Lve G+
  gi|121638980|ref|YP_979204.1| 40 RFGQLARNLGIPRPTLSSRLRMLVEVGL 67
                                   689***********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-06    0.0029      23      56 ..      40      73 ..      18      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                   EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   + g+lar lg++++++s +l+ Lv+ GL  r+p 
  gi|121638980|ref|YP_979204.1| 40 RFGQLARNLGIPRPTLSSRLRMLVEVGLFDRVPY 73
                                   89*************************9887765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.6e-06    0.0072      22      45 ..      43      66 ..      41      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                         HTH_24 22 eLAerlglSpstvnrrlkrLeeeG 45
                                   +LA+ lg++++t++ rl+ L+e G
  gi|121638980|ref|YP_979204.1| 43 QLARNLGIPRPTLSSRLRMLVEVG 66
                                   8*******************9966 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.019      27      64 ..      43      84 ..      36      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                   HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE CS
                           TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr....pklYra 64
                                   ++a++lg+pr++  + Lr L++ Gl +r++ +    ++ Yr 
  gi|121638980|ref|YP_979204.1| 43 QLARNLGIPRPTLSSRLRMLVEVGLFDRVPYSsdpeRHEYRL 84
                                   799************************999666777667765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.1e-05     0.091      20      60 .]      45      89 ..      39      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                                   HHHHTS-HHHHHHHHHHHHHHHTS-SEEE.......SSSEEEE-HHHH CS
                          HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeR.......tgrglrLTeaGe 60
                                   A+ Lg+  p++s +++    +++v Lf+R         +  rLTeaG+
  gi|121638980|ref|YP_979204.1| 45 ARNLGIPRPTLSSRLR---MLVEVGLFDRvpyssdpERHEYRLTEAGR 89
                                   99**********8765...5699*****977765433345******97 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.16      21      38 ..      43      60 ..      41      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                        HTH_psq 21 kAArkYgiPrsTLwrrkr 38
                                   ++Ar  giPr+TL++r+r
  gi|121638980|ref|YP_979204.1| 43 QLARNLGIPRPTLSSRLR 60
                                   899999*********998 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.21      17      74 ..      41      97 ..      37     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                         HTH_34 17 fvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74
                                   f +l   l++    Ls+ l++L + g   +   +++  +r  +r+T++Gr+ f++ v 
  gi|121638980|ref|YP_979204.1| 41 FGQLARNLGIPRPTLSSRLRMLVEVGLFDRV-PYSSDPERHEYRLTEAGRDLFAAIVV 97
                                   6677777888888999999999999987755.5566669999***********98775 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.23      55      74 ..      74      93 ..      52      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                   TSSS-EEEEEESHCCCHHHH CS
                           PadR 55 gegpprkyYrlTdaGrrela 74
                                   +++p+r  YrlT+aGr+ +a
  gi|121638980|ref|YP_979204.1| 74 SSDPERHEYRLTEAGRDLFA 93
                                   468*************9765 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.29      23      40 ..      43      60 ..      40      62 .. 0.90
   2 ?   -3.1   0.0       5.5     7e+03      15      24 ..      78      87 ..      78      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                   HHHHHHTS-HHHHHHHHH CS
                          HTH_8 23 kAArlLGisRrtLyrKLk 40
                                   + Ar LGi R tL  +L+
  gi|121638980|ref|YP_979204.1| 43 QLARNLGIPRPTLSSRLR 60
                                   679***********9997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.5
                                   HHTTT-HHHH CS
                          HTH_8 15 ertgGnkskA 24
                                   er+++++++A
  gi|121638980|ref|YP_979204.1| 78 ERHEYRLTEA 87
                                   7888888888 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.27      10      40 ..      36      94 ..      33     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                   HT-SSCHHHHCCTT--HHHHH............................HHHHSSS--H CS
                  Phage_CI_repr 10 ygvkmqkeLAdlLgiakssvs............................twvrRdffPg 40
                                    gv    +LA  Lgi++ ++s                            t   Rd f +
  gi|121638980|ref|YP_979204.1| 36 FGVRRFGQLARNLGIPRPTLSsrlrmlvevglfdrvpyssdperheyrlTEAGRDLFAA 94
                                   5899999**************88888888888888888888888888888888887765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       8.1     1e+04      19      21 ..     121     123 ..     121     124 .. 0.57
   2 ?   11.0   0.1   0.00021      0.26       2      13 ..     131     142 ..     130     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.1
                  zinc_ribbon_2  19 CGt 21 
                                    CG+
  gi|121638980|ref|YP_979204.1| 121 CGE 123
                                    665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                  zinc_ribbon_2   2 CpnCGaelqdna 13 
                                    C++CG+e+  ++
  gi|121638980|ref|YP_979204.1| 131 CTHCGEEITARN 142
                                    *******97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1141.18
//
Query:       gi|121638981|ref|YP_979205.1|  [L=379]
Description: hypothetical protein BCG_3121 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00021   20.9   0.0    0.00059   19.4   0.0    1.7  1  Cellulase  Cellulase (glycosyl hydrolase family 5)


Domain annotation for each model (and alignments):
>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.3e-08   0.00059      83     211 ..     150     282 ..      81     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.3e-08
                                    ESSTTTCSSSSTTTTHHH...HHHHHHHHHHHHHHHHTTTTTTEEEESSSS--STTCTCCT.....CHHHTTHHHHHHHH CS
                      Cellulase  83 Hseegwltkadgnssedt...aeeffkklwtqiAerykkndevvifelmNEPhgnntgaew.....tseeadevkayaee 154
                                    H+ +gw ++ +g +  d+   a   ++ ++t +  ++ ++d v++++l+NEP    +   +      +++ + v+++  +
  gi|121638981|ref|YP_979205.1| 150 HN-SGW-VQSPGAERLDDrryASTLYN-YVTGVLGQFRNDDRVLGWDLWNEPDNPAR---VyrkveRKDKLERVAELLPQ 223
                                    55.467.23333333333121233344.69999*******************99333...33423455566666667779 PP

                                    HHHHHHHHTTSSEEEEECHHHHTBHHHHHCT...SGSSSSTTEEEEEEEET.TTHHHTGCG CS
                      Cellulase 155 aikaIRavgpnrliivegnswsgnldgavln...dPndsqdnliysvHfYg.psdfaqtef 211
                                    ++   R v+p + +  +   w+gn    +        + ++  ++++H+Y+ p +f+++ +
  gi|121638981|ref|YP_979205.1| 224 VFRWARTVDPVQPLTSGV--WQGNWGDPGRRstiSAIQLDNADVITFHSYAaPAEFEGRIA 282
                                    999999****98888777..77765554544332224468999*******99999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2829.24
//
Query:       gi|121638982|ref|YP_979206.1|  [L=437]
Description: hypothetical protein BCG_3122c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-30  105.4  18.5    1.5e-30  105.4  18.5    3.0  3  PE             PE family
    6.5e-21   75.2   1.4    6.5e-19   68.6   1.4    2.5  1  Abhydrolase_3  alpha/beta hydrolase fold
    2.4e-08   33.3   0.2    3.3e-08   32.8   0.2    1.1  1  Say1_Mug180    Steryl acetyl hydrolase
  ------ inclusion threshold ------
      0.025   13.9   0.1      0.051   12.8   0.1    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
      0.079   12.6   0.2       0.53    9.9   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
       0.75    9.3   2.1       0.96    9.0   0.3    1.8  2  DUF2974        Protein of unknown function (DUF2974)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4  18.5     5e-34   1.5e-30       2      92 ..       3      93 ..       2      94 .. 0.98
   2 ?    1.6   0.1      0.12   3.4e+02      18      44 ..     111     137 ..     100     145 .. 0.85
   3 ?   -0.3   0.2      0.45   1.4e+03      38      54 ..     282     298 ..     275     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 5e-34
                                   XXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  2 sfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaa 83
                                   s+vv+ Pe+++aaa+d+a+igs +++a++ +a++tt+vlaaa+DeVSaaiAalfsah+q+yqalsaq a fhe+fvqal++a
  gi|121638982|ref|YP_979206.1|  3 SYVVALPEVMSAAATDVASIGSVVATASQGVAGATTTVLAAAEDEVSAAIAALFSAHGQDYQALSAQLAVFHERFVQALTGA 84
                                   89******************************************************************************** PP

                                   HHHHHS--X CS
                             PE 84 agsYaaaEa 92
                                   a+ YaaaE 
  gi|121638982|ref|YP_979206.1| 85 AKGYAAAEL 93
                                   *******96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHH----SSS CS
                             PE  18 lagigsalsaanaaaaapttavlaaaa 44 
                                     a+i ++++ a +a aa  t+v + aa
  gi|121638982|ref|YP_979206.1| 111 FATIHQEIQRAPTALAAGFTQVPPFAA 137
                                    688999999999999999999999886 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.45
                                    ----SSSSHHHHHHHHH CS
                             PE  38 avlaaaaDeVSaaiAal 54 
                                    +v++a a  +S++iA++
  gi|121638982|ref|YP_979206.1| 282 TVVPAMAGLISTQIAQH 298
                                    58999999999999974 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   1.4   2.2e-22   6.5e-19       1     210 [.     235     416 ..     235     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.2e-22
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    +v +HGG+f+l  +  h+   +  a ++ga+v  + Y l  e      v  a+a    l +++  +++  s++ ++GdSa
  gi|121638982|ref|YP_979206.1| 235 VVAIHGGAFILPPSIFHWLNYSVTAYQTGATVQVPIYPLVQEGGTAGTVVPAMAG---LISTQI-AQHGVSNVSVVGDSA 310
                                    6899***********************************9998776666555554...444432.346799********* PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                    GGnla+a+a+ + ++g+p ++ +vl++P++d+  t   +i                     ++++++  ++dpl+spl++
  gi|121638982|ref|YP_979206.1| 311 GGNLALAAAQYMVSQGNPVPSSMVLLSPWLDV-GT--WQIS--------------------QAWAGNLAVNDPLVSPLYG 367
                                    ******************************77.44..4551....................2334444579********* PP

                                    S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                     +l+glppt+v+ +  Dpl +++  + +    +g + +++  + ++H+++
  gi|121638982|ref|YP_979206.1| 368 -SLNGLPPTYVYSGSLDPLAQQAVVLEHTAVVQGAPFSFVLAPWQIHDWI 416
                                    .**********************************************986 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   1.1e-11   3.3e-08     125     238 ..     235     343 ..     213     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-11
                    Say1_Mug180 125 llylHGGgfalklipvtlvfLsnlrklfp.dmailvsDYtvtaakdqskkYplqvleslavydylvkskgfknvvvlGdS 203
                                    ++ +HGG f+l+  p ++  L+    +++   ++ v+ Y++++    + +    v  +  +    +   g+ nv v+GdS
  gi|121638982|ref|YP_979206.1| 235 VVAIHGGAFILP--PSIFHWLNYSVTAYQtGATVQVPIYPLVQEGGTAGT---VVPAMAGLISTQIAQHGVSNVSVVGDS 309
                                    5779***99876..99******999999956678899*****95444444...444456666777779************ PP

                    Say1_Mug180 204 aGGnlvLslllklsklnkvvlPkkaiaiSPWlnlt 238
                                    aGGnl L    ++   +   +P   +++SPWl++ 
  gi|121638982|ref|YP_979206.1| 310 AGGNLALAAAQYMVSQGN-PVPSSMVLLSPWLDVG 343
                                    *********999777565.57***********986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.7e-05     0.051      64     115 ..     289     344 ..     281     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                    Hydrolase_4  64 afvekvkeehpelplfllGhSmGGliallyl...lrypdkva.glilsaPalkika 115
                                     ++++  ++h+ +++ ++G S GG +al+++     + + v   ++l +P+l++ +
  gi|121638982|ref|YP_979206.1| 289 GLISTQIAQHGVSNVSVVGDSAGGNLALAAAqymVSQGNPVPsSMVLLSPWLDVGT 344
                                    5677778999999************999888766344444555*********9984 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00018      0.53      67     121 ..     295     350 ..     281     362 .. 0.80
   2 ?   -0.7   0.0      0.29   8.7e+02     203     227 ..     368     388 ..     358     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
                                    HHHCTTSSEEEEEETHHHHHHHHHHHHH...GGGE.EEEEEESECSSCCHHHHHHHHHH CS
                  Abhydrolase_1  67 ldalgddkltlvGhSmGGmialayaaey...perV.kalvllgaidpaaslieaqrqqa 121
                                     +++g+ ++ +vG S GG +ala+a+      ++V +++vll++   + + + +q  qa
  gi|121638982|ref|YP_979206.1| 295 IAQHGVSNVSVVGDSAGGNLALAAAQYMvsqGNPVpSSMVLLSP---WLDVGTWQISQA 350
                                    6789********************99879995566257888888...666666666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                                    HHHCTHHHHSEEEEEEETTCSSSCH CS
                  Abhydrolase_1 203 rlrelknvlaptlvisgtsDplvpp 227
                                    +l++    l pt+v+sg+ Dpl+  
  gi|121638982|ref|YP_979206.1| 368 SLNG----LPPTYVYSGSLDPLAQQ 388
                                    4444....56***********9976 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.35     1e+03      91     126 ..      29      65 ..      19      93 .. 0.79
   2 ?    9.0   0.3   0.00032      0.96      77     104 ..     294     321 ..     288     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.35
                        DUF2974  91 hSkGGnlAvyaamn.aeddlqeriskiysfDgpGfsk 126
                                     S+G   A+  ++  aed++++ i++ +s  g+ ++ 
  gi|121638982|ref|YP_979206.1|  29 ASQGVAGATTTVLAaAEDEVSAAIAALFSAHGQDYQA 65 
                                    5777777766555548999999999999999998775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00032
                        DUF2974  77 kileesegkiylgGhSkGGnlAvyaamn 104
                                    +i+++   ++ ++G S GGnlA+ aa  
  gi|121638982|ref|YP_979206.1| 294 QIAQHGVSNVSVVGDSAGGNLALAAAQY 321
                                    788888889**************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2821.20
//
Query:       gi|121638983|ref|YP_979207.1|  [L=150]
Description: hypothetical protein BCG_3123c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 983.77
//
Query:       gi|121638984|ref|YP_979208.1|  [L=283]
Description: hypothetical protein BCG_3124c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-29  101.2   0.4    1.5e-28  100.3   0.4    1.5  1  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai
    3.4e-12   47.1   3.1    3.4e-12   47.1   3.1    2.1  2  MDMPI_C   MDMPI C-terminal domain
    1.2e-07   32.3   0.1    2.1e-07   31.5   0.1    1.4  1  DinB_2    DinB superfamily
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.25   11.7   0.0    1.3  1  DUF664    Protein of unknown function (DUF664)


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.4   3.3e-32   1.5e-28       3     141 .]      22     160 ..      20     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.3e-32
                        MDMPI_N   3 eewaalaalvagLtdeqwaapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaad.....aeavdl 77 
                                    + w+ l+al++gL + +w+a sp+pGW+v+ +v+H++++++ l++++a      ++++d+ a  ++++      +++v+ 
  gi|121638984|ref|YP_979208.1|  22 AVWHSLDALLDGLLETDWQATSPLPGWDVKAVVSHIIGTESFLLGIAAP-----EPDTDVSALAHVRNPigvmnECWVRH 96 
                                    78********************************************654.....34445455545555566666****** PP

                        MDMPI_N  78 aaslapeallaafraavtrlaaalaalppdaiadrlgipggprslgeflrtrlvEavvHglDla 141
                                      + ++  ll++fra + ++++ la+l +d++ +++++p gp s+g+f+r+r++++++H++D++
  gi|121638984|ref|YP_979208.1|  97 LGTESGVGLLERFRAVTSQRRKVLASLSDDEWNAPTTTPSGPDSYGRFMRIRIFDCWMHEQDIR 160
                                    **************************************************************96 PP

>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.91   4.1e+03      11      43 ..      17      44 ..      14      78 .. 0.63
   2 !   47.1   3.1   7.6e-16   3.4e-12       2      89 ..     179     272 ..     178     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.91
                        MDMPI_C 11 latvvarraaapdsrvvlelegprtvhlhatdg 43
                                   la ++a ++      +   l+g   ++++at +
  gi|121638984|ref|YP_979208.1| 17 LAGLFAVWH-----SLDALLDGLLETDWQATSP 44
                                   555555555.....4566677777777777653 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 7.6e-16
                        MDMPI_C   2 laadgvdellatvvarraaapd.srvvlelegprtvhlhatdggrarlalwadg..adatvrGtaadlllllwGRlspdd 78 
                                    l +d ++  +++vv++ a+apd srv lel+gp ++ ++++++grar+ ++  g  ++at+r++  ++++l+ GR   ++
  gi|121638984|ref|YP_979208.1| 179 LVLDEIAATMGFVVGKLAKAPDgSRVLLELTGPLSRSIRVSVDGRARVVDDFGGpaPTATIRLDGLQFTRLAGGRPMSPA 258
                                    5689*****************************************977666666999**********************9 PP

                        MDMPI_C  79 t...levdGdrall 89 
                                    +   +e++Gd++l+
  gi|121638984|ref|YP_979208.1| 259 RsqdVELGGDKELA 272
                                    9**********997 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   4.8e-11   2.1e-07       4     124 ..      22     155 ..      20     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.8e-11
                         DinB_2   4 rararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlr.geeaprpgldpltp...............ps 67 
                                    ++++ l all++l e ++++  + ++w +  ++ H++ +e +ll  +  ++ ++ ++l  +                  s
  gi|121638984|ref|YP_979208.1|  22 AVWHSLDALLDGLLETDWQATSPLPGWDVKAVVSHIIGTESFLLGIAApEPDTDVSALAHVRNpigvmnecwvrhlgtES 101
                                    68999***************************************999974333333333333344444555555556579 PP

                         DinB_2  68 aaealaylaevrarllallealtdadldrpltaphpglgkltlgdvllfvlqHeqhH 124
                                       +l+++++v  + + +l++l+d+++++p t+p    g+ ++g+ +++ +   ++H
  gi|121638984|ref|YP_979208.1| 102 GVGLLERFRAVTSQRRKVLASLSDDEWNAPTTTP---SGPDSYGRFMRIRIFDCWMH 155
                                    999******************************9...77777777777666666666 PP

>> DUF664  Protein of unknown function (DUF664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.25      11     119 ..      25     138 ..      15     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                                    HHHHHHHTT--GGGTT--BTTB-S-HHHHHHHHHHHHHHHHHHHTT-S---TTTSHH......TTTSSS--.-SS---HH CS
                         DUF664  11 etllakleGLsdeqarrravpsstsllgLvkHvaevErgwfrrvlggeeevpldrsa......adpdadfe.laedetla 83 
                                    ++l+a l+GL + +  ++++ +++ + ++v H+ + E   ++ ++ +++ ++    a         ++ +     +e+  
  gi|121638984|ref|YP_979208.1|  25 HSLDALLDGLLETDWQATSPLPGWDVKAVVSHIIGTESFLLGIAAPEPD-TDVSALAhvrnpiGVMNECWVrHLGTESGV 103
                                    78999********************************998877666654.333333346677633344443255667777 PP

                                    HHHHHHHHHHHHHHHHHTT--HHHHTSB-T-..... CS
                         DUF664  84 dllaeyrravaradavvaaeldldetvrvpkapwge 119
                                    +ll+++r++  + ++v+a  l+ de  +  ++p g+
  gi|121638984|ref|YP_979208.1| 104 GLLERFRAVTSQRRKVLA-SLSDDEWNAPTTTPSGP 138
                                    89***************9.44434333333366655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2040.12
//
Query:       gi|121638985|ref|YP_979209.1|  [L=160]
Description: SsrA-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-58  196.6   0.1      2e-58  196.4   0.1    1.0  1  SmpB      SmpB protein


Domain annotation for each model (and alignments):
>> SmpB  SmpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.1   1.1e-62     2e-58       1     142 [.      12     152 ..      12     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 1.1e-62
                                    EEE-CHHHTTSEEEEEEEEEB---HHHHHHHHH--EESSSEEEEEESSCEEEEESEE---S--SS----TT--EEBB--H CS
                           SmpB   1 iakNkkarhdYeieetyeaGivLkGtEvkslragkvnlkdsyvkikngelfllnvhiseyekgnifnhdpkrkrkLLlhk 80 
                                    +a+N+karh+Y+i e +eaG++L+GtEvkslr+g+++l+ds+++i++ge++l n+hi ey++g+++nh+p+r+rkLLlh+
  gi|121638985|ref|YP_979209.1|  12 VASNRKARHNYSIIEVFEAGVALQGTEVKSLREGQASLADSFATIDDGEVWLRNAHIPEYRHGSWTNHEPRRNRKLLLHR 91 
                                    589***************************************************************************** PP

                                    HHHHHHHHHHHHHT-EEEEEEEEE.ESSEEEEEEEEEEC--SS--XXXXXXXXXXXXXXXXX CS
                           SmpB  81 keikklagkveekgltlvplklyfkkkglvKveialakgkklydkretlkerdakreieral 142
                                    ++i++l gk++e +++lvpl+lyf  +g+vKve+ala+gk+  dkr+++++rda+re+ r+l
  gi|121638985|ref|YP_979209.1|  92 RQIDTLVGKIREGNFALVPLSLYF-AEGKVKVELALARGKQARDKRQDMARRDAQREVLREL 152
                                    ************************.78******************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1144.44
//
Query:       gi|121638986|ref|YP_979210.1|  [L=297]
Description: cell division protein ftsX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-15   57.7   0.1    2.3e-15   57.0   0.1    1.4  1  FtsX_ECD  FtsX extracellular domain
    4.4e-07   30.3   4.1    4.4e-07   30.3   4.1    2.7  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX_ECD  FtsX extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.1   2.6e-19   2.3e-15       2      96 .]      57     152 ..      56     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.6e-19
                       FtsX_ECD   2 evsvflkdd.......ateeqiealeeklealpgVksvtfvskeealeefkeqlgednsellegltedeNpLpdsfevkl 74 
                                    e +vfl +d       ++   ++al+ek+e +++Vk v+f ++++a+++  +++  ++++++     d+  +p+sf+vkl
  gi|121638986|ref|YP_979210.1|  57 ESQVFLTEDvsandssCDTTACKALREKIETRSDVKAVRFLNRQQAYDDAIRKFP-QFKDVAGK---DS--FPASFIVKL 130
                                    6689999999999999***************************************.69999998...77..********* PP

                       FtsX_ECD  75 kdpekleevaeelkklpgVeeV 96 
                                    ++pe+ +++ +++k++pgV +V
  gi|121638986|ref|YP_979210.1| 131 ENPEQHKDFDTAMKGQPGVLDV 152
                                    *******************887 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       0.1   9.1e+02      22      40 ..      19      38 ..      11      66 .. 0.66
   2 ?   -0.8   0.8      0.24   2.2e+03      27      47 ..     172     192 ..     160     196 .. 0.64
   3 !   30.3   4.1   4.9e-11   4.4e-07       1      93 [.     200     292 ..     200     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.1
                           FtsX 22 lteillitlvalviG.lglg 40
                                   ++ i++i   a+ +G +g g
  gi|121638986|ref|YP_979210.1| 19 TMTIAMILTTAISVGlFGGG 38
                                   55566666666666633333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                           FtsX  27 litlvalviGlglgllaaqll 47 
                                    + ++valv ++g+ ll+a+++
  gi|121638986|ref|YP_979210.1| 172 AAFAVALVQAIGAILLIANMV 192
                                    445666666666666666654 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 4.9e-11
                           FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllllla 80 
                                    + eigi+r +G++++ + l +l+e++l +  +  i+++ + ++  l+    l+++ + +l   +d+ ++l+i   llll 
  gi|121638986|ref|YP_979210.1| 200 RTEIGIMRLVGASRWYTQLPFLVEAMLAATMGVGIAVAGLMVVRALFLENALNQFYQANLIAKVDYADILFITPWLLLLG 279
                                    57**********************************888888888888888888888*********************** PP

                           FtsX  81 llagllsiskilk 93 
                                    ++++ l ++  l+
  gi|121638986|ref|YP_979210.1| 280 VAMSGLTAYLTLR 292
                                    **99888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2205.87
//
Query:       gi|121638987|ref|YP_979211.1|  [L=229]
Description: cell division ATP-binding protein ftsE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-33  115.7   0.0    3.4e-33  115.1   0.0    1.3  1  ABC_tran         ABC transporter
    5.9e-12   46.0   0.0    1.7e-06   28.1   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.5e-06   27.1   0.0    9.1e-06   26.2   0.0    1.5  1  AAA_16           AAA ATPase domain
      8e-06   26.1   0.1    3.7e-05   23.9   0.1    2.0  1  AAA_33           AAA domain
    2.8e-05   23.7   0.1    0.00078   18.9   0.1    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    4.9e-05   23.3   0.0    0.00011   22.1   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
    6.5e-05   22.6   0.0    0.00013   21.6   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    9.4e-05   22.3   0.0      0.018   14.8   0.0    2.1  2  AAA_15           AAA ATPase domain
    0.00018   21.8   0.0     0.0008   19.7   0.0    1.9  1  AAA_22           AAA domain
     0.0012   18.4   0.0      0.017   14.7   0.0    2.2  2  AAA_25           AAA domain
     0.0026   18.3   0.0      0.041   14.4   0.0    2.1  2  AAA_18           AAA domain
      0.003   17.9   0.0      0.013   15.9   0.0    2.0  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.034   14.2   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
      0.012   15.5   0.0      0.021   14.8   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.019   14.7   0.0      0.066   12.9   0.0    1.9  2  AAA_30           AAA domain
      0.044   14.3   0.0      0.055   14.0   0.0    1.3  1  AAA_23           AAA domain
      0.045   13.0   0.0          1    8.6   0.0    2.1  2  Zeta_toxin       Zeta toxin
      0.059   13.1   0.0       0.11   12.2   0.0    1.6  2  AAA_24           AAA domain
      0.063   13.7   0.1       0.41   11.1   0.0    2.1  2  AAA              ATPase family associated with various cellul
      0.068   12.6   0.0       0.17   11.3   0.0    1.6  2  PhoH             PhoH-like protein
      0.075   13.3   0.1        2.2    8.6   0.1    2.4  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.077   12.9   0.0       0.18   11.7   0.0    1.6  2  NACHT            NACHT domain
      0.079   13.1   0.0       0.18   11.9   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.087   13.1   0.0       0.21   11.8   0.0    1.7  2  AAA_28           AAA domain
        0.1   11.8   0.3       0.42    9.8   0.3    1.9  1  NB-ARC           NB-ARC domain
       0.13   12.3   0.0       0.31   11.1   0.0    1.6  2  DUF87            Helicase HerA, central domain
       0.14   12.2   0.0       0.22   11.5   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.17   10.9   0.0        1.2    8.1   0.0    1.9  2  DUF3987          Protein of unknown function (DUF3987)
       0.17   11.3   0.0        0.3   10.6   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.18   11.9   0.0       0.36   10.9   0.0    1.6  1  Sigma54_activ_2  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0   5.7e-36   3.4e-33       1     136 [.      19     166 ..      19     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 5.7e-36
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvr 77 
                                    l+++++k+ +ge v ++G++G+GKSt+++ll+  ++pt+G++++ + ++++   +  ++lr+ ig+++q+ +l +++tv+
  gi|121638987|ref|YP_979211.1|  19 LDDINVKIDKGEFVFLIGPSGSGKSTFMRLLLAAETPTSGDVRVSKFHVNKlrgRHVPKLRQVIGCVFQDFRLLQQKTVY 98 
                                    799***************************************9999999999999************************* PP

                                    HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +n             + ++ + ++l+++gl++++++       +LSgG++qrva+ara++++p +ll+DEpt
  gi|121638987|ref|YP_979211.1|  99 DNvafalevigkrtdAINRVVPEVLETVGLSGKANRLP----DELSGGEQQRVAIARAFVNRPLVLLADEPT 166
                                    **********9988888888************888887....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05     0.007       1      20 [.      31      50 ..      31      76 .. 0.80
   2 !   28.1   0.0   2.8e-09   1.7e-06     190     303 .]      92     202 ..      84     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                   + +liGp gsGKS+++++l 
  gi|121638987|ref|YP_979211.1| 31 FVFLIGPSGSGKSTFMRLLL 50
                                   679***************93 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.8e-09
                         AAA_21 190 rslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEng 269
                                     + k+v +++ + +e++ + +++++r   + + ++  ++  ++ ++elS G ++  a++ a+  ++    +ll DEp  +
  gi|121638987|ref|YP_979211.1|  92 LQQKTVYDNVAFALEVIGKRTDAINRVVPEVLETVGLSGKANRLPDELSGGEQQRVAIARAFVNRP---LVLLADEPTGN 168
                                    55667777788888888888888888877788899999999999*********9999999999988...89********* PP

                         AAA_21 270 LHPkllrrllellkelsrngaQviltTHSpllld 303
                                    L+P+  r +++ll++ +r+g+ v+++TH+ +++d
  gi|121638987|ref|YP_979211.1| 169 LDPETSRDIMDLLERINRTGTTVLMATHDHHIVD 202
                                    *************999999**********98876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.5e-08   9.1e-06      20     116 ..      25     174 ..      16     212 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.5e-08
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd...ggiflrgkcdql.esaipysa.laqalareellrqlldeaesael 94 
                                    + + +e v+l+G+sG+GKs+ +r ll  +e+    ++ + + +  +l ++ +p +  ++ +  + + +r l +++  +++
  gi|121638987|ref|YP_979211.1|  25 KIDKGEFVFLIGPSGSGKSTFMRLLLA-AETPtsgDVRVSKFHVNKLrGRHVPKLRqVIGCV-F-QDFRLLQQKTVYDNV 101
                                    5556699*******************5.5544476244444444444444444433366666.4.666666666444444 PP

                         AAA_16  95 eawrekleeala...................................................avpelagaea 116
                                    + + e + +++                                                    ++++l+++ +
  gi|121638987|ref|YP_979211.1| 102 AFALEVIGKRTDainrvvpevletvglsgkanrlpdelsggeqqrvaiarafvnrplvlladePTGNLDPETS 174
                                    4444444444444444444444444445544443333334444444444444455555555554444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   6.2e-08   3.7e-05       2     118 ..      32     207 ..      31     226 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.2e-08
                         AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt............................................. 32 
                                    v+l+G++GsGKst+ + ll++++     v++s+                                               
  gi|121638987|ref|YP_979211.1|  32 VFLIGPSGSGKSTFMRLLLAAETptsgDVRVSKFHvnklrgrhvpklrqvigcvfqdfrllqqktvydnvafalevigkr 111
                                    89****************99988899999999866555444444444444444444444444444444433333333333 PP

                         AAA_33  33 ..lrrrlfgtdqqskt...............dytrvldr....lyqilnelarkalsagrnvildat..nlsrrerarfl 89 
                                      +                            + +r+ d+      q++ ++ar    +   +++d +  nl++++ ++++
  gi|121638987|ref|YP_979211.1| 112 tdA------------InrvvpevletvglsgKANRLPDElsggEQQRV-AIARAFVNRPLVLLADEPtgNLDPETSRDIM 178
                                    333............033333333334344322333333111133333.3443333444444445545577777777777 PP

                         AAA_33  90 klarrlgvpvrivvvetdeetlkeRlakR 118
                                     l++r++   + v + t +  + +  ++R
  gi|121638987|ref|YP_979211.1| 179 DLLERINRTGTTVLMATHDHHIVDSMRQR 207
                                    77777777777777777776666666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06   0.00078      24     207 ..      29     206 ..       8     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTE.EEEEEEEEETTEESSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkk.aeveitfdnedkklkiekeevsisrr 102
                                     +f +++Gp GSGKs ++  +l      ++  +r +k++  ++k + ++  k    +  +f++    l++++   ++   
  gi|121638987|ref|YP_979211.1|  29 GEFVFLIGPSGSGKSTFMRLLLAAET-PTSGDVRVSKFH--VNKLRGRHVPKLrQVIGCVFQDFRL-LQQKTVYDNVAFA 104
                                    3699*************998833333.344577877765..4443333333330334445544332.2333333444455 PP

                                    EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEE.CTTTTTS-HHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyll.DeidaaLDeknvkkvae 181
                                    ++  g+ + +in+   +  e   l  +a+  +++LSgGe++ va+a       +  +pl+ll De   +LD +  + + +
  gi|121638987|ref|YP_979211.1| 105 LEVIGKRTDAINRVVPEVLETVGLSGKANRLPDELSGGEQQRVAIARA-----FVNRPLVLLaDEPTGNLDPETSRDIMD 179
                                    5555555678999999999999999999999**********9999966.....4566777665***************** PP

                                    HHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          SMC_N 182 llkekskn.aQfivislreemlekadk 207
                                    ll++ + + + +++ +++++++  +++
  gi|121638987|ref|YP_979211.1| 180 LLERINRTgTTVLMATHDHHIVDSMRQ 206
                                    **9765554999999999999999844 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.9e-07   0.00011      87     143 ..      16      78 ..       4      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-07
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT.....-----S--------------S CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe.....lelktgevseklgrGkhTTta 143
                                    + +l++++ ++++ ++++l+G+SG GKSt++  ll        ++++++   ++ rG+h  + 
  gi|121638987|ref|YP_979211.1|  16 RPALDDINVKIDKgEFVFLIGPSGSGKSTFMRLLLAAetptsGDVRVSKFHVNKLRGRHVPKL 78 
                                    467889999998889******************998723333477777888888899997655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.2e-07   0.00013      16      39 ..      23      46 ..      18      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-07
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                    ++id  ++++l+GpsGsGKST++
  gi|121638987|ref|YP_979211.1| 23 NVKIDKGEFVFLIGPSGSGKSTFM 46
                                   67899666**************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     3e-05     0.018      14      43 ..      19      49 ..      18      75 .. 0.86
   2 ?    5.6   0.0     0.018        11     323     369 .]     156     201 ..     145     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                   l+d+ +++++  + +liG+ +sGKS+++++l
  gi|121638987|ref|YP_979211.1| 19 LDDINVKIDKGeFVFLIGPSGSGKSTFMRLL 49
                                   567777777767****************998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                    ++ +ll +EP  +L p+  + +++ll ++ +++   v++ TH  hi+
  gi|121638987|ref|YP_979211.1| 156 RPLVLLADEPTGNLDPETSRDIMDLLERINRTGT-TVLMATHDHHIV 201
                                    6789999*********************999996.9*********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06    0.0008       5     104 ..      29     170 ..      25     203 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...............................erpevvfvtlpsst.. 51 
                                      +++++G+sG+GK+t +r ll   +  +  +                                                
  gi|121638987|ref|YP_979211.1|  29 GEFVFLIGPSGSGKSTFMRLLLAAET--P--TSgdvrvskfhvnklrgrhvpklrqvigcvfqdF------------Rll 92 
                                    67899****************99863..2..2244667777777777766643332222222220............244 PP

                         AAA_22  52 sskdllrellralglelka..........................erlsseellealeqalraravielliiDEaqh.lr 104
                                     +k+++ +++ al++ +k+                          e    e+ + a+++a+ +r  + +l+ DE    l+
  gi|121638987|ref|YP_979211.1|  93 QQKTVYDNVAFALEVIGKRtdainrvvpevletvglsgkanrlpdELSGGEQQRVAIARAFVNR--PLVLLADEPTGnLD 170
                                    4555555555555555555555555555555555555544433333333333333333333333..44777777555564 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.9e-05     0.017      30      58 ..      26      54 ..       5     122 .. 0.86
   2 ?    1.8   0.0      0.26   1.5e+02     165     188 ..     173     196 ..     160     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                         AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                   + +ge++ l+G++g+GK+t+   l +a +
  gi|121638987|ref|YP_979211.1| 26 IDKGEFVFLIGPSGSGKSTFMRLLLAAET 54
                                   789****************9877777655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                         AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                    + + +++ leri  rtg +vl+  H
  gi|121638987|ref|YP_979211.1| 173 TsRDIMDLLERI-NRTGTTVLMATH 196
                                    446677888999.89*******999 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.8e-05     0.041       1      22 [.      32      53 ..      32     102 .. 0.70
   2 ?    1.8   0.0      0.54   3.2e+02      58      84 ..     175     206 ..     150     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.8e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                   ++l G++G+GK+t+ + L   +
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAE 53
                                   799**************94432 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.54
                         AAA_18  58 dklldaleenss.....aleegknlvidghla 84 
                                      ++d+le++++      ++ +++ ++d+ ++
  gi|121638987|ref|YP_979211.1| 175 RDIMDLLERINRtgttvLMATHDHHIVDSMRQ 206
                                    56788999998755555555555555555543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-05     0.013       1      65 [.      32      96 ..      32     113 .. 0.80
   2 ?   -1.1   0.0       4.2   2.5e+03      60      90 ..     167     197 ..     144     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-05
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee 65
                                   ++l Gpsg GKSt+++ L +a + ++++ + +++ +++ +  ++ + ++   +v++Df   ++++
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAETPTSGDVRVSKFHVNKLRGRHVPKLRQVIGCVFQDFRLLQQKT 96
                                   6899*************999888888888888998888899999988888888888887666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.2
                   RNA_helicase  60 qvkdeenpsdlaelirlvsstpyplnmasle 90 
                                     + d e+  d+++l++ ++ t  ++ ma  +
  gi|121638987|ref|YP_979211.1| 167 GNLDPETSRDIMDLLERINRTGTTVLMATHD 197
                                    3334423448888888888888888888655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.6e-05     0.034       2      22 ..      32      52 ..      31      65 .. 0.91
   2 ?   -2.8   0.0       9.6   5.7e+03      19      32 ..     180     193 ..     174     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                                   EEEE--SSSSHHHHHHHGGGG CS
                          AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                   v+L+Gp+G+gKs++++ l+aa
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAA 52
                                   89**************99986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.6
                                    GGGGBS--EEEEE- CS
                          AAA_5  19 laaalnreveyvql 32 
                                    l++++nr+ ++v++
  gi|121638987|ref|YP_979211.1| 180 LLERINRTGTTVLM 193
                                    55555555555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.4e-05     0.021      16     107 ..      27     120 ..      17     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                       ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienl.edkdk...yviyyialreesiskldefieeeeekkklekalgiavpkael 91 
                                    +  + e++f+ Gp gsGK+++++ ++      +++    ++ +++lr++   kl++ i+   ++ +l +++    + a +
  gi|121638987|ref|YP_979211.1|  27 D--KGEFVFLIGPSGSGKSTFMRLLLAAEtPTSGDvrvSKFHVNKLRGRHVPKLRQVIGCVFQDFRLLQQKTVYDNVAFA 104
                                    4..47899***************998877333333555889999999999999999988444444444444222222223 PP

                       ATPase_2  92 eeilkeksklvfkaie 107
                                     e++ +++  +++ + 
  gi|121638987|ref|YP_979211.1| 105 LEVIGKRTDAINRVVP 120
                                    3444444444455444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.066      18      45 ..      29      56 ..       3      84 .. 0.86
   2 ?   -0.8   0.0       1.7     1e+03     102     122 ..     174     194 ..     112     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                     +++l Gp G+GK+t ++ l +a +  
  gi|121638987|ref|YP_979211.1| 29 GEFVFLIGPSGSGKSTFMRLLLAAETPT 56
                                   45899**************997776555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                         AAA_30 102 tkqlaallkaaekagakvilv 122
                                    ++++ +ll++++++g++v+++
  gi|121638987|ref|YP_979211.1| 174 SRDIMDLLERINRTGTTVLMA 194
                                    456666777777777666654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.2e-05     0.055      21      47 ..      31      57 ..      18     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.2e-05
                         AAA_23 21 ltlItGpNGaGKTTildAiklaLyget 47
                                   ++ ++Gp G+GK+T+++ +  a +  +
  gi|121638987|ref|YP_979211.1| 31 FVFLIGPSGSGKSTFMRLLLAAETPTS 57
                                   56789***********99988866544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0017         1      15      50 ..      28      63 ..      16      81 .. 0.82
   2 ?    2.2   0.0      0.15        91     106     157 ..     170     220 ..     169     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                     Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50
                                   +   ++l G +G+GKs+ ++ll ++ +++++ vr++
  gi|121638987|ref|YP_979211.1| 28 KGEFVFLIGPSGSGKSTFMRLLLAAETPTSGDVRVS 63
                                   556799**************9999888777777775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                     Zeta_toxin 106 spdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaegRlvpke 157
                                    +p++ +++++ l+  +++   v++a++  + + ++++R+ e    gRlv  e
  gi|121638987|ref|YP_979211.1| 170 DPETSRDIMDLLERINRTGTTVLMATHDHHIVDSMRQRVVEL-SLGRLVRDE 220
                                    58899999999999999999*******************999.336888766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.11       5      23 ..      32      52 ..      28     103 .. 0.80
   2 ?   -2.7   0.0         7   4.2e+03      46     118 ..     177     184 ..     150     208 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                         AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                   ++++Gpsg+GK+t+++ l   
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLlaA 52
                                   689************988552 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7
                         AAA_24  46 ieswedfldevvelaaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaeefrrllkkl 118
                                    i                                                                 ++ll+++
  gi|121638987|ref|YP_979211.1| 177 I-----------------------------------------------------------------MDLLERI 184
                                    2.................................................................2222222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00069      0.41       1      49 [.      32      81 ..      32     101 .. 0.64
   2 ?    0.1   0.0       1.7     1e+03      92     117 ..     180     203 ..     140     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00069
                                   EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirel 49
                                   v l+Gp G GK+++++ +         +v++ ++ + +l+    g    k+r++
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAEtptsgDVRVSKFHVNKLR----GRHVPKLRQV 81
                                   579*************987764132223555555555555....4444444443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                                    HHHHTTTSSSTEEEEEEESSGGGSTH CS
                            AAA  92 eldgvkkkeskvivigatnrpdkldp 117
                                     l++ ++    ++v++at++ + +d+
  gi|121638987|ref|YP_979211.1| 180 LLERINRT--GTTVLMATHDHHIVDS 203
                                    33333332..2467777766554444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.17      15      48 ..      25      59 ..      14      67 .. 0.82
   2 ?   -2.4   0.0       4.6   2.8e+03     138     158 ..     179     201 ..     148     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                   HHHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS CS
                           PhoH 15 alkkndivfaiGpaGtGK.tylavalavealkkkk 48
                                    ++k ++vf iGp+G+GK t++ + la+e  ++++
  gi|121638987|ref|YP_979211.1| 25 KIDKGEFVFLIGPSGSGKsTFMRLLLAAETPTSGD 59
                                   466889************77899999988766665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                                    HHHTTB-TT-EEEE..EE----- CS
                           PhoH 138 mfltRlGenskvvv..tGdvtqi 158
                                     +l R+ +  + v+  t+d + +
  gi|121638987|ref|YP_979211.1| 179 DLLERINRTGTTVLmaTHDHHIV 201
                                    34445554444443123343333 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0037       2.2      62      89 ..     155     182 ..     101     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                        SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                    +++ +++ DE  ++lD+e+++ +++lle
  gi|121638987|ref|YP_979211.1| 155 NRPLVLLADEPTGNLDPETSRDIMDLLE 182
                                    3466677799999999999999999997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.18       3      21 ..      32      50 ..      30      82 .. 0.86
   2 ?   -2.4   0.0       6.4   3.9e+03     109     132 ..     177     200 ..     156     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   v+l G++GsGK+t+++ l 
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLL 50
                                   89************98654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.4
                                    HHHHHCTTTTT--EEEEEEECCCH CS
                          NACHT 109 Lselirkkllpeasllltvrpral 132
                                    + +l+++   +++++l++++    
  gi|121638987|ref|YP_979211.1| 177 IMDLLERINRTGTTVLMATHDHHI 200
                                    335555555566666666655544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00031      0.18       2      24 ..      32      54 ..      31      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                                   EEEEESTTSSHHHHHHHHHTSTE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltgeka 24
                                   v ++G + +GKSt+++ l+ ++ 
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAET 54
                                   789***************98533 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.21       2      29 ..      32      59 ..      31     113 .. 0.84
   2 ?   -1.8   0.0       5.5   3.3e+03     109     132 ..     156     179 ..     137     208 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                         AAA_28  2 ivitGgestGKTtlleaLaargypvvpE 29
                                   + ++G++++GK+t ++ L a ++p+  +
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAETPTSGD 59
                                   789***************9999988654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.5
                         AAA_28 109 ydlvfllp.papeidddgeRredle 132
                                      lv+l + p++ +d+ + R+  ++
  gi|121638987|ref|YP_979211.1| 156 RPLVLLADePTGNLDPETSRDI-MD 179
                                    4445555523445555555553.22 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3    0.0007      0.42      21      43 ..      30      52 ..      18     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                                   EEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                    +v+l G  G+GK+t ++  l  
  gi|121638987|ref|YP_979211.1| 30 EFVFLIGPSGSGKSTFMRLLLAA 52
                                   499************99877665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00052      0.31      14      45 ..      24      51 ..      15      54 .. 0.77
   2 ?   -2.5   0.0       7.4   4.4e+03     164     171 ..     173     180 ..     112     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                          DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLle 45
                                   v++d  ++    +  +g +GsGKS+++++Ll+
  gi|121638987|ref|YP_979211.1| 24 VKIDKGEF----VFLIGPSGSGKSTFMRLLLA 51
                                   55555555....456899************96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                          DUF87 164 aiarlldk 171
                                    + + + d 
  gi|121638987|ref|YP_979211.1| 173 TSRDIMDL 180
                                    22222222 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00037      0.22      13      42 ..      25      52 ..       8      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                                   HHHHCHTEEEEEEESTTSSHHHHHHHHHHH CS
                           TsaE 13 klakalgdvilLeGdLGaGKTtlvrglaka 42
                                   k+ k  g++++L G+ G+GK+t++r l++a
  gi|121638987|ref|YP_979211.1| 25 KIDK--GEFVFLIGPSGSGKSTFMRLLLAA 52
                                   3333..788****************99876 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0019       1.2      38      58 ..      31      51 ..      22      61 .. 0.89
   2 ?    0.6   0.0      0.38   2.3e+02     184     263 ..     111     194 ..     106     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                        DUF3987 38 ytlvvapsGerKSpvdklvlr 58
                                   +++ ++psG++KS+ ++l+l+
  gi|121638987|ref|YP_979211.1| 31 FVFLIGPSGSGKSTFMRLLLA 51
                                   7999************99876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                        DUF3987 184 RigresreverprlslllmiQpsvlkelia....npesresGllaRflfalppstagwrdvdsppipdavleayearfre 259
                                    R++   r v++   +++l++  ++l + ++    ++ ++ + ++ R l+ l+++++g+ d +++++  ++le++++  ++
  gi|121638987|ref|YP_979211.1| 111 RTDAINRVVPEVLETVGLSGKANRLPDELSggeqQRVAIARAFVNRPLVLLADEPTGNLDPETSRDIMDLLERINRTGTT 190
                                    88888899999999999999999999999988888999999999999999999999999988866666665655554444 PP

                        DUF3987 260 llae 263
                                    +l  
  gi|121638987|ref|YP_979211.1| 191 VLMA 194
                                    4444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00051       0.3      30      58 ..      26      54 ..      22      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkkld 58
                                   ++++  v+l+Gp+G+GK++ ++ ll +  
  gi|121638987|ref|YP_979211.1| 26 IDKGEFVFLIGPSGSGKSTFMRLLLAAET 54
                                   5677889**************99766544 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00061      0.36      24      49 ..      32      57 ..      21      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                                   EEEEEETT--HHHHHHCC--TTS-EE CS
                Sigma54_activ_2 24 vfltGekGsgkelvArlLhknsgpwl 49
                                   vfl+G+ Gsgk+++ rlL   ++p +
  gi|121638987|ref|YP_979211.1| 32 VFLIGPSGSGKSTFMRLLLAAETPTS 57
                                   9*****************99999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 1653.89
//
Query:       gi|121638988|ref|YP_979212.1|  [L=145]
Description: hypothetical protein BCG_3128c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1060.87
//
Query:       gi|121638989|ref|YP_979213.1|  [L=308]
Description: hypothetical protein BCG_3129c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-42  144.0   0.0    5.7e-42  143.6   0.0    1.2  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.17   12.1   0.0        0.3   11.3   0.0    1.3  1  CENP-C_C    Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   6.3e-46   5.7e-42       3     204 ..      89     292 ..      87     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 6.3e-46
                                    HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS......SEEEEE CS
                     MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig......dieGtV 76 
                                    +  +li+vv+++ v+++l v+v+al+  +++lg+alg++++ l+++l+aG+++++ek++ +GDlve++      +++GtV
  gi|121638989|ref|YP_979213.1|  89 VSIVLIYVVVVYEVIDVLPVPVGALVGPAAVLGAALGFGAQRLVQDLLAGFFIIVEKQYGFGDLVELSmvgspeNAAGTV 168
                                    66799*************************************************************************** PP

                                    EEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.TS- CS
                     MS_channel  77 ediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.dke 155
                                    ed++lr+tk+r+ +g+++t+Pn ++v  + +Nls+  ++ r++v+i v++s+d  ++++vl++ +e++++++ + +   +
  gi|121638989|ref|YP_979213.1| 169 EDVTLRVTKLRSSEGEVFTVPNGNIV--KSVNLSK--DWARAVVDIPVPTSADLGRVNEVLHQECEHARHDSLLGElLLD 244
                                    **************************..99*****..****************************999999999887678 PP

                                    EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT- CS
                     MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegi 204
                                     + v++   ++  ++++r +++t +p+++++  ++++  ++++l+++gi
  gi|121638989|ref|YP_979213.1| 245 EPTVMGVERIEVDTVTLRLVART-LPGKQFEAGRQLRVLVIRALTRAGI 292
                                    88999******************.9**********************99 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.3e-05       0.3      42      77 ..     166     202 ..     164     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                                    SEEE.EEETTEEEEEETT-EEEE-TT-EEEEEE-SSS CS
                       CENP-C_C  42 Grve.vtvsktsfvigkgsvFqvPagneysieNklnk 77 
                                    G+ve vt+  t+ ++++g vF vP gn  +  N +++
  gi|121638989|ref|YP_979213.1| 166 GTVEdVTLRVTKLRSSEGEVFTVPNGNIVKSVNLSKD 202
                                    66644999*******************9999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2277.23
//
Query:       gi|121638990|ref|YP_979214.1|  [L=378]
Description: peptide chain release factor 2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-56  189.6   1.0    5.2e-56  189.6   1.0    1.7  2  PCRF          PCRF domain
    2.7e-36  124.0   0.3    9.3e-36  122.3   0.0    1.9  2  RF-1          RF-1 domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.012   15.9   0.0    3.6  4  ABC_tran_CTD  ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   1.0   8.7e-60   5.2e-56       2     193 .]      36     228 ..      35     228 .. 0.92
   2 ?   -1.4   0.0      0.31   1.8e+03      29      55 ..     284     310 ..     275     332 .. 0.51

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 8.7e-60
                                    HHHHTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.........-S-..-GGGTHHHH CS
                           PCRF   2 eeeleelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelle.....edeelaelaeeeleele 76 
                                    ++++e+le+++sdp++w+dq++a+++++el++ +  ++++eel+++l+dl  + el++     + ++  ++a++el++l+
  gi|121638990|ref|YP_979214.1|  36 RSRIEKLEHEASDPHLWDDQTRAQRVTSELSHTQGELRRVEELRRRLDDLPVLYELAAeeagaAAADAVAEADAELKSLR 115
                                    6899************************************************99999423333223344445668***** PP

                                    HHHHHH..HHHHHT-..SSSTTSEEEEEEEE-SSTHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEESSS.SEEEEEEEE CS
                           PCRF  77 keleeleeelkklLlpkdendeknaileiraGaGGdeaalfaedLlrmYtryaerkgwkvevldaseeeagGikevtlei 156
                                    +++e++  e+++lL+  +e+de++a+++ir+GaGG +aa++ae+L+rmY r+ae++++ vev+d+s++e  Gik++t+++
  gi|121638990|ref|YP_979214.1| 116 ADIEAT--EVRTLLS--GEYDEREALVTIRSGAGGVDAADWAEMLMRMYIRWAEQHKYPVEVFDTSYAEEAGIKSATFAV 191
                                    ******..*******..**************************************************6555********* PP

                                    ESTTHHHHHGGG-EEEEEEEE-TTSSS--EEEEEEEE CS
                           PCRF 157 egegaYgkLkfEsGvHRvqRvpetesqgrihTStatV 193
                                    + + aYg+L +E+G+HR++R++++++q r++TS+a V
  gi|121638990|ref|YP_979214.1| 192 HAPFAYGTLSVEQGTHRLVRISPFDNQSRRQTSFAEV 228
                                    ***********************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                                    HHHHHTHHHHHHHHHHHHHTTTHHH.. CS
                           PCRF  29 kelaeleeivealeeleealedleeak 55 
                                    +e ++l++ ++a++ l+++l + + ++
  gi|121638990|ref|YP_979214.1| 284 NEKSQLQNKIAAMRVLQAKLLERKRLE 310
                                    333333333333333333333333322 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.37   2.2e+03      65      89 ..      35      59 ..      32      86 .. 0.42
   2 !  122.3   0.0   1.6e-39   9.3e-36       4     116 .]     238     345 ..     235     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHCCCCCHTTTTT-. CS
                           RF-1 65 Lkaklkekeleeekeeekkrrvkke 89
                                   L++++++ e e ++ +   ++++++
  gi|121638990|ref|YP_979214.1| 35 LRSRIEKLEHEASDPHLWDDQTRAQ 59
                                   7778865444443333222222221 PP

  == domain 2  score: 122.3 bits;  conditional E-value: 1.6e-39
                                    C.CE--GGGEEEEEE---SSSSSSGCSSSCEEEEEETTTTEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCH CS
                           RF-1   4 e.ieidekdleidtfrssGaGGQnVNktesaVrlthlptgvivvecqeeRsqekNrekAlerLkaklkekeleeekeeek 82 
                                    + i+i+e d+++d++rssG+GGQ+VN+t+saVrlth+p+g ivv+cq+e+sq +N+  A+++L+akl e+++ ee++e +
  gi|121638990|ref|YP_979214.1| 238 DhIDIPEGDVRVDVYRSSGPGGQSVNTTDSAVRLTHIPSG-IVVTCQNEKSQLQNKIAAMRVLQAKLLERKRLEERAELD 316
                                    3499************************************.8*************************8865555555555 PP

                                    TTTTT-.S.-S---S--ECEEEECGCTTEEEETT CS
                           RF-1  83 krrvkkekkkigtgssekiRtynkkpqsrvkdhr 116
                                    + ++       ++g+  ++R+y+++p+++vkd+r
  gi|121638990|ref|YP_979214.1| 317 ALKADG---GSSWGN--QMRSYVLHPYQMVKDLR 345
                                    555444...457898..***************98 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0     2e-06     0.012      18      62 ..      33      77 ..      30      79 .. 0.92
   2 ?    2.5   1.1     0.029   1.8e+02      37      61 ..      98     122 ..      85     124 .. 0.71
   3 ?   -4.1   0.4         3   1.8e+04      57      66 ..     156     165 ..     154     165 .. 0.83
   4 ?   -0.4   0.8      0.23   1.4e+03       8      27 ..     284     303 ..     281     321 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                   ABC_tran_CTD 18 eaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62
                                   e L  +i++le e +dp l  d+++ ++++ el   + eL + +e
  gi|121638990|ref|YP_979214.1| 33 EGLRSRIEKLEHEASDPHLWDDQTRAQRVTSELSHTQGELRRVEE 77
                                   77899**********************************988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                   ABC_tran_CTD  37 ysdpeklaelsaeleeleaeLeely 61 
                                     +  +++ae+ ael+ l+a++e+ +
  gi|121638990|ref|YP_979214.1|  98 AAAADAVAEADAELKSLRADIEATE 122
                                    3445779999999999999999876 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3
                   ABC_tran_CTD  57 LeelyerWee 66 
                                    L ++y rW e
  gi|121638990|ref|YP_979214.1| 156 LMRMYIRWAE 165
                                    789999**87 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.23
                   ABC_tran_CTD   8 releeleaeIeaLEeeiael 27 
                                    +e  +l ++I+a+   +a+l
  gi|121638990|ref|YP_979214.1| 284 NEKSQLQNKIAAMRVLQAKL 303
                                    44445555555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2956.84
//
Query:       gi|121638991|ref|YP_979215.1|  [L=456]
Description: NADPH:adrenodoxin oxidoreductase fprA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-10   39.7   0.0    8.5e-09   35.0   0.0    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.031   14.3   0.0        2.3    8.2   0.0    2.3  2  JAB            JAB1/Mov34/MPN/PAD-1 ubiquitin protease
      0.041   14.2   0.5        0.1   12.9   0.1    1.8  2  NTP_transf_3   MobA-like NTP transferase domain
      0.077   13.0   0.2       0.27   11.2   0.0    2.2  2  NAD_binding_9  FAD-NAD(P)-binding
       0.13   12.3   0.0        1.4    9.0   0.0    2.4  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   2.4e-12   8.5e-09       3     161 ..       6     166 ..       4     237 .. 0.72
   2 ?    2.1   0.0     0.026        92     215     241 ..     301     328 ..     269     365 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.4e-12
                                    EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgk 82 
                                    ++++G+Gp ++ aa  l +a   +  +  + ++    +l++++ l  ++ a   + ++k++++++e+ ++ + +++ +g+
  gi|121638991|ref|YP_979215.1|   6 IAIVGSGPSAFFAAASLLKAADTTEDL--DMAVDMLEMLPTPWGLVRSGVAP-DHPKIKSISKQFEKTAEDPRFRF-FGN 81 
                                    789999999998888888855554444..33333444455443333333332.23567899999******99****.888 PP

                                    EEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.........TTBEECCSECHHHHHHCCSS-TSEEEEES-SHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  83 kkvklekkkegdeekiaydklvlAtGssprdl.gipGv........aenvgklvrtldsaealklkllpkrivvvGgGyi 153
                                      v+  + ++  e +  yd+++ A G+++ ++ +ipG+         + vg    +  + e+++ +l  +r+vv+G+G++
  gi|121638991|ref|YP_979215.1|  82 -VVVG-EHVQPGELSERYDAVIYAVGAQSDRMlNIPGEdlpgsiaaVDFVGW-YNAHPHFEQISPDLSGARAVVIGNGNV 158
                                    .5555.5566888999**********9777777*****99999985444444.4899999999999999*********** PP

                                    HHHHHHHH CS
                                    xxxxxxxx RF
                    Pyr_redox_2 154 GvElAaal 161
                                    ++++A  l
  gi|121638991|ref|YP_979215.1| 159 ALDVARIL 166
                                    *****996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.026
                                    EEE.EEETTSCEEEESEEEE-S-EEES- CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 215 kle.vvledgeeidadlvvvavGvrpst 241
                                    ++    +++ ee++a+lvv +vG+r  +
  gi|121638991|ref|YP_979215.1| 301 RVAaKDTGEREELPAQLVVRSVGYRGVP 328
                                    333233445555************9765 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00063       2.3      85      97 ..     126     138 ..      57     146 .. 0.87
   2 ?    3.7   0.0     0.016        57      83      97 ..     352     366 ..     334     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00063
                                    SEEEEEEEESSSS CS
                            JAB  85 ervvGWYhshpdi 97 
                                      +vGWY  hp++
  gi|121638991|ref|YP_979215.1| 126 VDFVGWYNAHPHF 138
                                    678*********8 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                    TTSEEEEEEEESSSS CS
                            JAB  83 grervvGWYhshpdi 97 
                                    ++e+vvGW++ +p+ 
  gi|121638991|ref|YP_979215.1| 352 PNEYVVGWIKRGPTG 366
                                    679*******99987 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.9e-05       0.1      23      71 ..     175     232 ..     172     252 .. 0.75
   2 ?   -2.1   0.0       1.2   4.4e+03     113     151 ..     401     439 ..     376     449 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                    CCCHHHHHHHHHCTT.-CEEEEECSHCHHHH........HHTTC.TS-EEE-TTSS-S CS
                   NTP_transf_3  23 gkpllervldalraagvdevvvvggdeevla........alarl.gvrvvededpgkg 71 
                                     + +++++l++lr+ g++evv+vg++ +++a        +la+l gv+vv d+ +  g
  gi|121638991|ref|YP_979215.1| 175 RTDIADHALESLRPRGIQEVVIVGRRGPLQAafttlelrELADLdGVDVVIDPAELDG 232
                                    566899********************87766333333333333347999999876665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                    HHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHH CS
                   NTP_transf_3 113 asgadvvvptyegerghpllfrarllsalaallgdqgar 151
                                    ++ ++v+ + ++ +++    +++++++a+++++g+ ++r
  gi|121638991|ref|YP_979215.1| 401 DHADQVADWLAARQPKLVTSAHWQVIDAFERAAGEPHGR 439
                                    445555566666666555566777777777777765554 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.4e-05      0.27       1      49 [.       7      57 ..       7     152 .. 0.74
   2 ?   -3.9   0.1       3.5   1.2e+04      64      78 ..     401     415 ..     397     431 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.4e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlara..kkkspleitlfdp.sepgagrvwrtdqsee 49
                                   aivG Gp++  +++ Ll+ a   ++ ++ +++ +   +p+ g v +   +++
  gi|121638991|ref|YP_979215.1|  7 AIVGSGPSAFFAAASLLKAAdtTEDLDMAVDMLEMlPTPW-GLVRSGVAPDH 57
                                   8*******************66566668888888844446.66655555555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.5
                  NAD_binding_9  64 ddpptfaeWlrerga 78 
                                    d+ ++ a+Wl++r+ 
  gi|121638991|ref|YP_979215.1| 401 DHADQVADWLAARQP 415
                                    444777788877763 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00039       1.4       4      33 ..     139     168 ..     137     177 .. 0.89
   2 ?    0.3   0.0      0.19   6.9e+02      24      45 ..     179     200 ..     172     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00039
                                    HHHHS..TT-EEEEES-SHHHHHHHHHHHC CS
                   Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLla 33 
                                    +++ ++l+++++++iG+G++a  va+ Ll+
  gi|121638991|ref|YP_979215.1| 139 EQISPDLSGARAVVIGNGNVALDVARILLT 168
                                    567889*******************99985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                                    HHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH  24 aelvakhLlakgvkkvvvaNRt 45 
                                    a  +++ L  +g+++vv+++R 
  gi|121638991|ref|YP_979215.1| 179 ADHALESLRPRGIQEVVIVGRR 200
                                    6678899999**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3269.58
//
Query:       gi|121638992|ref|YP_979216.1|  [L=527]
Description: alkyldihydroxyacetonephosphate synthase agpS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-48  165.6   0.1    2.1e-48  165.1   0.1    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.1e-32  112.7   0.0    2.5e-32  111.5   0.0    1.6  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.1   2.4e-52   2.1e-48       2     248 ..     270     522 ..     269     524 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.4e-52
                                    -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHH CS
                  FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeele 81 
                                    p+++++++v f++++aav+a+r+iaqag+ pa ++l+d  +  l ++t+          + ll++ fe+ d+  + + ++
  gi|121638992|ref|YP_979216.1| 270 PRWQVTVSVVFDDWAAAVAATRTIAQAGLYPANCRLLDPAEALLNAGTSVG--------GGLLVLAFESADHPIDPWLHR 341
                                    999************************************************........********************* PP

                                    H.HHHHTTT-EEEEE............E..TGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                  FAD-oxidase_C  82 a.lveaileatgaadv..lvaqdeaeae..alwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldky 156
                                    a +++a +++t++a+    +++d++e++  a w+     +py rdal ++gv++++++t+++++ + +l++++ ++++  
  gi|121638992|ref|YP_979216.1| 342 AvAITAEHGGTVTAQRsrGTTSDATEHNaaANWRSAFLRMPYQRDALVRRGVIAETFETACTWDGFDTLHAAVTDAARTA 421
                                    **************976799******996666666666777*************************************** PP

                                    H.......EEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHH....HHHHHHTT---------------------- CS
                  FAD-oxidase_C 157 g.......levvlfgHagdgnlhlyilfdladeaeeeraeklvdev....vdlavelgGsisgEHGvGldkkaylerekg 225
                                            +++++f+H+++ +  +y+ + +   + + ++ +++de+     +++++ gG+i+++H+vG+d++a++ r++ 
  gi|121638992|ref|YP_979216.1| 422 IwkvcgtgVVTCRFTHVYPDGPAPYYGIYAG--GRWGSLDAQWDEIkaavSEAISASGGTITHHHAVGRDHRAWYDRQRP 499
                                    9*********************999999887..99999999999999999999*************************** PP

                                    -THHHHHHHHHHHH-TT--BSTT CS
                  FAD-oxidase_C 226 eeglalmrriKaalDPkgiLNPg 248
                                    +   a++r+ K+alDP+giLNPg
  gi|121638992|ref|YP_979216.1| 500 DPFAAALRAAKSALDPAGILNPG 522
                                    **********************9 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   2.8e-36   2.5e-32       1     133 [.      94     229 ..      94     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 2.8e-36
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC...SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav...atggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                    p++++rp+se++v+++l +++++g+ v+++GgGss++g++     +  v++d++++  +leid+ ++ a+++aG+ ++ +
  gi|121638992|ref|YP_979216.1|  94 PDLIARPRSEQDVIDVLDWCAREGIAVIPYGGGSSVVGGVEprfDEPVVTVDVTAMSAVLEIDRVSRAARIQAGAFGPSI 173
                                    899**********************************99999888888******************************** PP

                                    HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTS CS
                  FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladG 133
                                    +++l+++ l+l++ p+s+  +t+GG++at++gG+ +++y +i d  ++l++v++ G
  gi|121638992|ref|YP_979216.1| 174 EHQLRPHDLTLRHFPQSFGFSTLGGWLATRSGGHFATLYTHIDDLTESLRIVTPVG 229
                                    *****************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3604.18
//
Query:       gi|121638993|ref|YP_979217.1|  [L=146]
Description: hypothetical protein BCG_3133 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1159.78
//
Query:       gi|121638994|ref|YP_979218.1|  [L=359]
Description: molybdenum cofactor biosynthesis protein A moaA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-34  118.3   0.0    3.1e-34  117.7   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    9.6e-29  100.9   0.0    1.5e-28  100.3   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
      1e-05   25.8   0.0    1.8e-05   25.0   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    3.3e-05   24.0   0.0    6.5e-05   23.0   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.0     7e-38   3.1e-34       2     125 ..     203     326 ..     202     329 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 7e-38
                                    EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE-.-SST-SSEEEEETTT--EEEEE-TTTS--GGG--EEEE CS
                    Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleak.ketkgpakrykikdgkgeiglIapvsepFCasCnRlRl 80 
                                    e+rfIE+m+vg +++w+ +kv++++++le++e+r+  +e   k+ ++pa+ry ++dg+ ++g+Ia+ +epFCa+C+R Rl
  gi|121638994|ref|YP_979218.1| 203 EVRFIEYMDVGGATHWAWEKVFTKANMLESLEKRYGRIEPLpKHDTAPANRYALPDGT-TFGIIASTTEPFCATCDRSRL 281
                                    89*********************************9877765999************9.7******************** PP

                                    -TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT---- CS
                    Mob_synth_C  81 tadGklktCLfaeeeidlrdllregaseeeLkelikealarkkek 125
                                    tadG + +CL+a ++i+lr+ lr+ga++++L e + + ++r++++
  gi|121638994|ref|YP_979218.1| 282 TADGLWLHCLYAISGINLREPLRAGATHDDLVETVTTGWRRRTDR 326
                                    ******************************************987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   3.3e-32   1.5e-28       3     166 ..      33     196 ..      31     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.3e-32
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpgir 79 
                                    v   CnlrC++C   e+  + +r+  lsv ei ++v+ +  + gv  v ++ggepl +pd+ e+++ l+++    +  + 
  gi|121638994|ref|YP_979218.1|  33 VIDQCNLRCRYCMPEEHYTWLPRQDLLSVKEISAIVDVF-LSVGVSKVRITGGEPLIRPDLPEIVRTLSAKVgedSGLRD 111
                                    5678***********************************.8******************************9******** PP

                                    EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                    ++++tng+l+  + ++ l+ +g+ r++++l+++ +e+++ +   +++ ++v++++++ ++ag+ ++++ +++++G n++e
  gi|121638994|ref|YP_979218.1| 112 LAITTNGVLL-ADRVDGLKAAGMKRITVSLDTLQPERFKAIS-QRNSHDKVIAGIKAVAAAGFTDTKIDTTVMRGANHDE 189
                                    **********.*************************999999.77*********************************** PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    l +l+e+
  gi|121638994|ref|YP_979218.1| 190 LADLIEF 196
                                    ****998 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     4e-09   1.8e-05      12      98 ..      34     123 ..      26     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4e-09
                        Fer4_12  12 vsgCnlsCkgCfnke..twsfksgkeftkelleeiiedlkkesiegltllGGEPllpena.eallelvkevkeekp.ekd 87 
                                    +  Cnl+C++C+ +e  tw ++ ++  + + +  i++ +    ++++ ++GGEPl +    e++  l  +v e       
  gi|121638994|ref|YP_979218.1|  34 IDQCNLRCRYCMPEEhyTWLPR-QDLLSVKEISAIVDVFLSVGVSKVRITGGEPLIRPDLpEIVRTLSAKVGEDSGlRDL 112
                                    568*********9883344444.44557788899*****9****************444434444555555555544556 PP

                        Fer4_12  88 iwlytgytlee 98 
                                     + ++g+ l +
  gi|121638994|ref|YP_979218.1| 113 AITTNGVLLAD 123
                                    66777776665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.5e-08   6.5e-05       6      94 ..      35     123 ..      31     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-08
                        Fer4_14   6 sgCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype... 80 
                                     +Cnl C+ C   ++ tw  +    +++ ++++i++ +    +  +++ +tGGePL+  + +   ++v+ l  ++ e   
  gi|121638994|ref|YP_979218.1|  35 DQCNLRCRYCMpeEHYTWLPRQDLLSVK-EISAIVDVFLSVGV--SKVRITGGEPLIRPDLP---EIVRTLSAKVGEdsg 108
                                    68*********44444455555555544.45588855555444..789********885555...555555555522234 PP

                        Fer4_14  81 .kkiwletngtleie 94 
                                      +  + tng+l  +
  gi|121638994|ref|YP_979218.1| 109 lRDLAITTNGVLLAD 123
                                    588999999987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2828.00
//
Query:       gi|121638995|ref|YP_979219.1|  [L=131]
Description: pterin-4-alpha-carbinolamine dehydratase moaB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-22   77.8   0.0    6.6e-22   77.5   0.0    1.1  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   3.7e-26   6.6e-22       3      90 ..      32     119 ..      30     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3.7e-26
                      Pterin_4a   3 lseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilv.synkvtvrltThdaggltenD 81 
                                    l ++ ++++l +lpgW+l  + +l+r f++ +f + i+f+nrva +a+  nHhpdi+v + ++v+v+ +T ++g lt+ D
  gi|121638995|ref|YP_979219.1|  32 LADAAVSEKLGALPGWQL-LDMRLSRAFQCTNFDQSIDFMNRVASIANDINHHPDIAVlDKRSVRVTAWTRKLGYLTDID 110
                                    7788999999889****7.6779*********************************6659******************** PP

                      Pterin_4a  82 fklAakide 90 
                                    f+lAa +++
  gi|121638995|ref|YP_979219.1| 111 FDLAASVEA 119
                                    *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 939.56
//
Query:       gi|121638996|ref|YP_979220.1|  [L=170]
Description: molybdenum cofactor biosynthesis protein MoaC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-53  180.3   2.8    2.1e-53  180.1   2.8    1.1  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   2.8   1.2e-57   2.1e-53       1     136 []      19     153 ..      19     153 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 1.2e-57
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvdvsek++t r+A+A+g v ++++tl++i++++++kGdv+a+ariagi aaK+t +liplcHpl l+ v+v++++  e 
  gi|121638996|ref|YP_979220.1|  19 MVDVSEKPVTLRVAKASGLVIMKPSTLRMISDGAAAKGDVMAAARIAGIAAAKRTGDLIPLCHPLGLDAVSVTITPC-EP 97 
                                    9*************************************************************************998.79 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT-EEEEEEEEEEESS CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdkemvieevrlveKsgG 136
                                    ++v+i at++t g+tGvemEALtavsvaalt+yDm+Kavd++m+i+++ l eKsgG
  gi|121638996|ref|YP_979220.1|  98 DRVKILATTTTLGRTGVEMEALTAVSVAALTIYDMCKAVDRAMEISQIVLQEKSGG 153
                                    *******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1369.15
//
Query:       gi|121638997|ref|YP_979221.1|  [L=83]
Description: molybdenum cofactor biosynthesis protein MoaD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-18   65.4   0.1      6e-18   65.3   0.1    1.0  1  ThiS       ThiS family
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.58   10.3   0.0    1.9  1  ThiS-like  ThiS-like ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.1   6.7e-22     6e-18       1      77 []       6      83 .]       6      83 .] 0.98

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 6.7e-22
                                   EEETTCCHHHHT...CEEEEESSTSBHHHHHHHHHHHTCHHG.TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS  1 vllfaelrelag...eeelelaegstvaelleaLgerypela.lerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   vl+f+ +re+     +ee+e+++g+ v+ l+++L+++yp+l  +++rv +avN+ i+p    +t+l dgDeva++p VaGG
  gi|121638997|ref|YP_979221.1|  6 VLYFGAVREACDetpREEVEVQNGTDVGNLVDQLQQKYPRLRdHCQRVQMAVNQFIAPL---STVLGDGDEVAFIPQVAGG 83
                                   89*******9999**********************************************...******************9 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.4e-05      0.58      34      55 ..      57      78 ..      21      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.4e-05
                      ThiS-like 34 lNGFpikeDteLkegDevflIk 55
                                   +N F++   t L +gDev +I+
  gi|121638997|ref|YP_979221.1| 57 VNQFIAPLSTVLGDGDEVAFIP 78
                                   6999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 580.92
//
Query:       gi|121638998|ref|YP_979222.1|  [L=222]
Description: phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-15   57.8   0.0    1.9e-15   57.4   0.0    1.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    9.3e-07   29.4   0.0    1.4e-06   28.9   0.0    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    1.8e-06   27.9   0.0    3.4e-06   27.0   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
    8.8e-06   26.2   0.1     0.0023   18.2   0.1    2.8  2  Hydrolase       haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   4.2e-19   1.9e-15       2     176 ..      10     184 ..       9     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.2e-19
                          HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee....kieellrkyneekkkke 77 
                                    + D  gTl d ++++++a+ ++l ++g++ ls+++l + +  +lr  ++++  ++   +       +++r+y++++ +  
  gi|121638998|ref|YP_979222.1|  10 VCDWNGTLCDDRTILLDAVGQTLVNEGFEPLSQQQLIQRFARPLRTFFENACGRDLLTSewerVQSTFRRIYRSREAE-- 87 
                                    55888********************************************99988777765675555566666666666.. PP

                          HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviy 157
                                    v++++++ ++L + ++      + +   ++++++++++ gi + F+ i + +   ++K  p ++++++ +  l++ +v+ 
  gi|121638998|ref|YP_979222.1|  88 VTLVEDAYDVLAQGNRSAAGQFLLSLAPHDELMHFVQKYGIAKWFNEIRGRTRPDQEK--PMMLAELIMQRSLNPTRVVH 165
                                    *********************************************************9..889***************** PP

                          HAD_2 158 vGDsptDieaakkagikvi 176
                                    +GDs  D  aa ++g  ++
  gi|121638998|ref|YP_979222.1| 166 IGDSLEDAAAASAVGAISV 184
                                    *************997655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     3e-10   1.4e-06       1     187 [.       9     176 ..       9     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3e-10
                            HAD   1 alfDfDgTLldgdsle..lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfva 78 
                                    +++D++gTL d+ ++   +  + l+ +g ++l +  + + ++  +r+++++      +  + ll +  e++   ++r+++
  gi|121638998|ref|YP_979222.1|   9 IVCDWNGTLCDDRTILldAVGQTLVNEGFEPLSQQQLIQRFARPLRTFFEN------ACGRDLLTSEWERVQSTFRRIYR 82 
                                    79**********998888888888888877777777777666666666666......44444566666777788888887 PP

                            HAD  79 evirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaal 158
                                    +  ++ +l ++a+++la+  +    + ++S ++   +  + +++g    +a        ++ e++++  p  +  k+  l
  gi|121638998|ref|YP_979222.1|  83 SREAEVTLVEDAYDVLAQGNRSAAGQFLLSLAPHDELMHFVQKYG----IAK-------WFNEIRGRTRPDQE--KPMML 149
                                    777888788********999999999*******************....***.......99998888888888..***** PP

                            HAD 159 rewlaaegegidleevvayGDspsDlpll 187
                                    +e + +++ ++++  vv +GDs  D +++
  gi|121638998|ref|YP_979222.1| 150 AELIMQRSLNPTR--VVHIGDSLEDAAAA 176
                                    **99999999887..**********9887 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   7.6e-10   3.4e-06       7      72 ..     146     210 ..     143     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.6e-10
                                    SHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEE CS
                 Hydrolase_like   7 pemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddl 72 
                                    p+m+ +  ++ +++p +v+ iGD+   D a+A ++G+ svLV+    +p d+   +    +va +l
  gi|121638998|ref|YP_979222.1| 146 PMMLAELIMQRSLNPTRVVHIGDS-LEDAAAASAVGAISVLVTGASRQPPDRVMLKQLQPFVASSL 210
                                    668888888889************.*****************877777766555554445555555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   5.2e-07    0.0023     119     210 .]      90     180 ..       8     180 .. 0.54
   2 ?   -1.3   0.0      0.49   2.2e+03     138     156 ..     184     203 ..     182     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.2e-07
                                    BHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 119 vkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVG 197
                                    + ++a +++a+ ++     +ll+   +   ++  +++G ++ f+ + +++       +p ++ ++i +   +p +v+++G
  gi|121638998|ref|YP_979222.1|  90 LVEDAYDVLAQGNRSAAGQFLLSLAPHDELMHFVQKYGiAKWFNEIRGRTR--PDQEKPMMLAELIMQRSLNPTRVVHIG 167
                                    555555555555544445577777777777777777774444422222222..34457788888888888********** PP

                                    SSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxx RF
                      Hydrolase 198 DgvnDaaalaaAg 210
                                    D++ Daaa+ a+g
  gi|121638998|ref|YP_979222.1| 168 DSLEDAAAASAVG 180
                                    *********9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.49
                                    EEEESSEHHHHH.HHHHHTT CS
                                    xxxxxxxxxxxx.xxxxxxx RF
                      Hydrolase 138 vlltgdnpetae.raanqlG 156
                                    vl+tg ++++++   ++ql 
  gi|121638998|ref|YP_979222.1| 184 VLVTGASRQPPDrVMLKQLQ 203
                                    899******99945555565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1746.06
//
Query:       gi|121638999|ref|YP_979223.1|  [L=176]
Description: hypothetical protein BCG_3139 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-15   55.4   0.0    5.7e-15   55.0   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.7e-07   30.4   0.0    3.3e-07   30.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.075   13.1   1.4        1.2    9.3   0.8    2.7  3  Bd3614-deam      Bd3614-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   9.6e-19   5.7e-15       5     100 ..      22     113 ..      18     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 9.6e-19
                                    HHHHHHHHHHHHHHHTTTSCSEEEEEEE.TTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE--BH CS
                dCMP_cyt_deam_1   5 ekllelalkaakeaqkcsnfkVGavivk.ngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtlePCs 83 
                                    e ++ela+++a++a      ++Ga++++ ++ + + g n  +++g++ +HAE+n +++a+++   +l +++l+ t ePC+
  gi|121638999|ref|YP_979223.1|  22 EAAMELAIDTARHA----TAPFGAALLDvTTLRAFSGGNTYFESGDRFAHAETNVLRAAMST-LPELSNHVLISTAEPCP 96 
                                    67888899888888....99****************************************99.556777*********** PP

                                    HHHHHHHHHT-SEEEEE CS
                dCMP_cyt_deam_1  84 mCakaiiqsgikkvvvg 100
                                    mCa a + sg++ +++g
  gi|121638999|ref|YP_979223.1|  97 MCAAASVLSGVRAIIFG 113
                                    **************997 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   5.5e-11   3.3e-07      10     108 ..      24     117 ..      17     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.5e-11
                    MafB19-deam  10 alaevekatkikedkiga..vivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCdmCag 87 
                                    a++++ + +     + ga  ++v   + +  g++  e   +  aHaE ++l+ A+  l +   ++ +l  t epC+mCa 
  gi|121638999|ref|YP_979223.1|  24 AMELAIDTARHATAPFGAalLDVTTLRAFSGGNTYFE-SGDRFAHAETNVLRAAMSTLPEL--SNHVLISTAEPCPMCAA 100
                                    5555555556666666666677777777877777555.67889********9997777665..999************** PP

                    MafB19-deam  88 aivqaglkklvygagnpksln 108
                                    a v +g++ +++g++    ++
  gi|121638999|ref|YP_979223.1| 101 ASVLSGVRAIIFGTS----IE 117
                                    *************98....44 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.068     4e+02      30      46 ..      61      77 ..      41      87 .. 0.79
   2 ?    9.3   0.8   0.00019       1.2      77      96 ..      85     104 ..      60     114 .. 0.79
   3 ?    0.5   0.0       0.1     6e+02      88     134 ..     128     166 ..     107     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.068
                    Bd3614-deam 30 aenkvLHAEvnLlapll 46
                                   ++ +  HAE n+l  + 
  gi|121638999|ref|YP_979223.1| 61 SGDRFAHAETNVLRAAM 77
                                   667889*****997665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                    Bd3614-deam  77 garllvtlqcCkmCAalvva 96 
                                    + +l++t ++C mCAa  v 
  gi|121638999|ref|YP_979223.1|  85 NHVLISTAEPCPMCAAASVL 104
                                    56899**********97665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.1
                    Bd3614-deam  88 kmCAalvvaaadapgrevllkvvYleedkGaLardteLrrrglesri 134
                                    ++ A+ vvaa+ +p+r      vY     G L+ +t L  r  e+r+
  gi|121638999|ref|YP_979223.1| 128 RISASDVVAASTRPTR----PSVY----SGFLSHKTDLLYRNSENRR 166
                                    5567777777777666....4455....4888888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1235.10
//
Query:       gi|121639000|ref|YP_979224.1|  [L=415]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-154  514.6   0.0   1.6e-154  514.4   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      2e-05   24.9   0.0    5.2e-05   23.6   0.0    1.7  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.4   0.0  1.7e-158  1.6e-154       1     380 [.       1     379 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 514.4 bits;  conditional E-value: 1.7e-158
                Transposase_mut   1 mtekelllelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelri 80 
                                    mt+++ l+++e+l a + a++++dll+ ll+t++++l+ ae+d+ +ga ++ers+ersnqRnG+r+r+++Tra+t++++i
  gi|121639000|ref|YP_979224.1|   1 MTSSH-LIDTEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAI 79 
                                    56666.89999********************************************************************* PP

                Transposase_mut  81 PrdRsGsFsp.allerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLee 159
                                    P++R+Gs++p +ll+r+kR+e+al++vv+++y+ Gvstr++e+lve+l++ +++Sks+vS ++keldeaveafr+R+L++
  gi|121639000|ref|YP_979224.1|  80 PKLRQGSYFPdWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGV-TKLSKSQVSIMAKELDEAVEAFRTRPLDA 158
                                    **********9***************************************.77*************************** PP

                Transposase_mut 160 keypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGL 239
                                     +y++l++Dal+lkvRe+grvv+ ++lia+gv+a+G+reiLg++v+++E+++ Wla++++L++rGl+gv+lv+sDah+GL
  gi|121639000|ref|YP_979224.1| 159 GPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGL 238
                                    ******************************************************************************** PP

                Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaed 319
                                    v+ai+a++p+aa+QrCr+H+++nl+a++pk ++ +v++ l+siy+++dae+++++++++l++l++k+p+vae+ld+a++d
  gi|121639000|ref|YP_979224.1| 239 VAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTD 318
                                    ******************************************************************************** PP

                Transposase_mut 320 vlaflafpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    +laf+afp+qi+r+i+s+N++ErLN+e+rRrt+vvgiFP+++si+rlvgavlae+hdew+e
  gi|121639000|ref|YP_979224.1| 319 LLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIE 379
                                    ***********************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.8e-09   5.2e-05      17      96 .]     184     261 ..     179     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.8e-09
                           MULE  17 lltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHiakn 96 
                                     l+++gv+++g   +l++ +++ e+ +++  ++++l ++    +    + +D +++l  a+ +++p a  + C  H a+n
  gi|121639000|ref|YP_979224.1| 184 TLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARG-L-SGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAAN 261
                                    5789******************************877743.3.579******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2859.88
//
Query:       gi|121639001|ref|YP_979225.1|  [L=389]
Description: molybdenum cofactor biosynthesis protein moeB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-65  221.4   0.0    1.7e-65  220.8   0.0    1.1  1  ThiF          ThiF family
    4.6e-18   65.7   0.0    1.6e-17   63.9   0.0    1.9  2  Rhodanese     Rhodanese-like domain
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.083   13.0   0.0    2.0  2  Shikimate_DH  Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.8   0.0   2.8e-69   1.7e-65       1     240 [.      22     255 ..      22     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 2.8e-69
                                    THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHH CS
                                    xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaa 78 
                                    ysr+l +  +g  gq++L+d++vl +GaGglGs++l +La++Gvg + ++D D+++ sNl+Rq++++++d+G+pK+e+aa
  gi|121639001|ref|YP_979225.1|  22 YSRHLIIpdIGVNGQQRLKDARVLCIGAGGLGSPALLYLAAAGVGTIGIIDGDHVDESNLQRQIIHGTSDVGRPKVESAA 101
                                    788877788999******************************************************************** PP

                                    HHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  79 ealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktg 158
                                    ea++einp+v v+ ++e +t +++  e++ ++Dl+vd++Dn+++r+l+n+a+v  g+p++ ++  +f+gq+ v+ pg+ +
  gi|121639001|ref|YP_979225.1| 102 EAVAEINPHVRVTQYREMLTHDNA-LEIFGDHDLIVDGTDNFTTRYLINDAAVLAGKPYVWGSIYRFNGQTSVFWPGRGP 180
                                    *********************884.5****************************************************** PP

                                    ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 159 cyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerak 238
                                    cy+Cl p   + p++  vp+c +  g   ++++++a +a+++++e+lkll g  +  + +l  + +l+ +++++++ +++
  gi|121639001|ref|YP_979225.1| 181 CYRCLHP---APPPPGLVPSC-AEGG---VLGAICATIASIQVTEVLKLLTGVGTPLVGRLLMYEALDATYHQIRIAKNP 253
                                    ******9...***********.9999...*********************777767777777999999999999998888 PP

                                    EE CS
                                    xx RF
                           ThiF 239 ks 240
                                    ++
  gi|121639001|ref|YP_979225.1| 254 DC 255
                                    76 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.79   4.7e+03      65      99 ..      40      73 ..      22      74 .. 0.78
   2 !   63.9   0.0   2.7e-21   1.6e-17       5     106 ..     291     380 ..     287     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.79
                      Rhodanese 65 nkktvvvycdgggraaaaaallkklGyknvsvldG 99
                                   ++ +v ++++gg ++ a+ +l+  +G+ ++ ++dG
  gi|121639001|ref|YP_979225.1| 40 KDARVLCIGAGGLGSPALLYLAA-AGVGTIGIIDG 73
                                   67889999999999888888777.88666887777 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 2.7e-21
                      Rhodanese   5 lkell.ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaa 83 
                                    l+  + ++++  l+DvR+p+e++  hIpg++ +           ++      + l++l    +k++v+yc++g r+a+a 
  gi|121639001|ref|YP_979225.1| 291 LRTKQqSDQNFLLVDVREPAEFDIAHIPGSILI-----------PKGEIGSAAGLAQL--PLDKEIVLYCKSGIRSAQAL 357
                                    555553666667*********************...........33333333333443..679***************** PP

                      Rhodanese  84 allkklGyknvsvldGGfkawke 106
                                    ++lk++G++nv++ldGG+ +w +
  gi|121639001|ref|YP_979225.1| 358 TTLKAAGLHNVKHLDGGIAEWTR 380
                                    *********************86 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.083       8      56 ..      37      85 ..      31     137 .. 0.74
   2 ?   -0.0   0.0      0.14   8.5e+02      86     116 ..     282     311 ..     266     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                   S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                   Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56
                                   ++lk+++vl iGaG +++ ++ +L+a+gv  + ++  ++   ++l +++
  gi|121639001|ref|YP_979225.1| 37 QRLKDARVLCIGAGGLGSPALLYLAAAGVGTIGIIDGDHVDESNLQRQI 85
                                   5799***************************999987777777776665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                                    SS-SB-HHHHHCCHHH.S..EEEEE--SS-S CS
                   Shikimate_DH  86 eepilekeeveealkkrkkplllvDiavPRd 116
                                    +e +++ +e++  + +++++ llvD+  P +
  gi|121639001|ref|YP_979225.1| 282 PELVISCDELRTKQ-QSDQNFLLVDVREPAE 311
                                    56788888887554.556999****999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2737.35
//
Query:       gi|121639002|ref|YP_979226.1|  [L=320]
Description: thiosulfate sulfurtransferase cysA3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.6e-34  116.1   0.2    2.1e-15   57.2   0.0    2.1  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
       0.18   10.5   0.1       0.28    9.9   0.1    1.2  1  p450       Cytochrome P450


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.2   2.4e-19   2.1e-15       1     106 [.       9     118 ..       9     119 .. 0.83
   2 !   57.2   0.0   2.3e-19   2.1e-15       3      95 ..     149     256 ..     147     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.4e-19
                      Rhodanese   1 sakelkellekgkvallDvR.ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdggg 77 
                                    sa++++ +l+++kv+++ v  +  +Y++ hI gA+ +  ++ l ++ k++  +++++ +ll++ gi n++tv++y+ +++
  gi|121639002|ref|YP_979226.1|   9 SADWAESNLHAPKVVFVEVDeDTSAYDRDHIAGAIKLdWRTDLQDPVKRDFVDAQQFSKLLSErGIANEDTVILYGGNNN 88 
                                    689*****************66666************43334445555555556666666666***************** PP

                      Rhodanese  78 r.aaaaaallkklGyknvsvldGGfkawke 106
                                      aa a++ +k +G+++v++ldGG k+w  
  gi|121639002|ref|YP_979226.1|  89 WfAAYAYWYFKLYGHEKVKLLDGGRKKWEL 118
                                    *9999999******766***********86 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 2.3e-19
                      Rhodanese   3 kelkellekgkvallDvRppeeY...............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnk 66 
                                    +e+ + ++ ++  l+DvR+p+e+               ++ ghIpgA+nv++ ++ +++ + +++ el + +++ g+dn 
  gi|121639002|ref|YP_979226.1| 149 DEVLAAINVKN--LIDVRSPDEFsgkilapahlpqeqsQRpGHIPGAINVPWSRAANEDGTFKSDEELAKLYADAGLDNS 226
                                    67888888888..**********9999999999999987779************************************** PP

                      Rhodanese  67 ktvvvycdgggraaaaaallkk.lGyknvs 95 
                                    k+ + yc+ g+r++ ++  l++ lG++nv 
  gi|121639002|ref|YP_979226.1| 227 KETIAYCRIGERSSHTWFVLRElLGHQNVN 256
                                    ************999999999779977785 PP

>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   3.1e-05      0.28     398     433 ..     252     287 ..     246     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.1e-05
                                    SCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHE CS
                           p450 398 ksfaflPFGaGpRnCiGerlArmelklflatlLqnF 433
                                    ++   ++FG Gp++C+     rm l  f+++l q+F
  gi|121639002|ref|YP_979226.1| 252 HQNVNIAFGYGPHACPASAYSRMCLTTFFTSLTQRF 287
                                    566789*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2473.86
//
Query:       gi|121639003|ref|YP_979227.1|  [L=156]
Description: hypothetical protein BCG_3143 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.19   11.6   0.0    1.2  1  DUF2313   Uncharacterised protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2313  Uncharacterised protein conserved in bacteria (DUF2313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.1e-05      0.19      63     144 ..      19      96 ..      13     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                        DUF2313  63 nssetleeRRaavlaklnekgglsiayikklaesllGeeeveItenqparvganrerYifqVqvpgasgagenLeawgaa 142
                                    +s e+le+RRa++   l+++g   + +i +   +  G++++  ++    + g    rY ++ +v+g+   g++L+  + +
  gi|121639003|ref|YP_979227.1|  19 DSLEDLEQRRARLYDQLAATGDFRRGSISENYRRC-GKPNCVCAQEG--HPGHG-PRYLWTRTVAGRGTKGRQLSVEEVD 94 
                                    56679***************************999.*9999999999..33333.6999999999777777776654444 PP

                        DUF2313 143 vl 144
                                    ++
  gi|121639003|ref|YP_979227.1|  95 KV 96 
                                    44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1099.96
//
Query:       gi|121639004|ref|YP_979228.1|  [L=164]
Description: hypothetical protein BCG_3144 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.16   11.6   0.0    1.1  1  DDE_Tnp_ISL3  Transposase
       0.13   12.3   0.5       0.23   11.5   0.5    1.3  1  VHL_C         VHL box domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.8e-05      0.16      60      93 ..      88     121 ..      86     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                   DDE_Tnp_ISL3  60 mDmsaayksavkealPnAkivvDrFHvvklanea 93 
                                     D+++++ +++ + lP+A+ +vD +H  +++++ 
  gi|121639004|ref|YP_979228.1|  88 WDGAPWIWNLATAILPEATPIVDLYHARQHVHDL 121
                                    699************************9999885 PP

>> VHL_C  VHL box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   2.5e-05      0.23       6      25 ..      46      65 ..      44      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                                   XXX-HHHHHHHHHHHHH-XX CS
                          VHL_C  6 PVysLkercLqvvRkLVrpe 25
                                   P   L+ r+L+vvR+L r+e
  gi|121639004|ref|YP_979228.1| 46 PAHRLRARALRVVRRLPRQE 65
                                   7778************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1057.89
//
Query:       gi|121639005|ref|YP_979229.1|  [L=289]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-46  156.3   0.2    9.8e-46  155.8   0.2    1.2  1  BTAD         Bacterial transcriptional activator domain
    3.5e-15   55.8   0.0    6.2e-15   55.0   0.0    1.4  1  Trans_reg_C  Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
      0.035   14.9   5.4        2.4    9.2   0.0    3.8  4  TPR_14       Tetratricopeptide repeat
      0.041   14.4   0.5        1.5    9.4   0.1    3.1  3  TPR_19       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   0.2   2.2e-49   9.8e-46       1     146 []     101     246 ..     101     246 .. 1.00

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 2.2e-49
                                    BHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                           BTAD   1 vDlarfealvaagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraee 80 
                                    +Dl+rf a++++g +a+a+g + ea++ l+ Al+ wrGp+l+dl+++++++++ ++l+ + l ++++laea +++Gra+ 
  gi|121639005|ref|YP_979229.1| 101 CDLDRFVAAKESGLRASAKGYFSEAIRYLDSALQNWRGPVLGDLRSFMFVQMFSRALTGDELLVHTKLAEAAIACGRADV 180
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHHHHHH CS
                           BTAD  81 alaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpelralheeil 146
                                    ++++le+lva+hP+rE l++qlm+ ++  + q++A+ +Y+rl+++LaeeLgvep+p++ral+++il
  gi|121639005|ref|YP_979229.1| 181 VIPKLERLVAMHPYRESLWKQLMLGYYVNEYQSAAIDAYHRLKSTLAEELGVEPAPTIRALYHKIL 246
                                    *****************************************************************8 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.4e-18   6.2e-15       7      77 .]      22      93 ..      15      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.4e-18
                                   SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTS.TSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C  7 tpkefklLelLlenpgrvvsreeLleevwgede.dvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77
                                   tpk++++L++Ll ++++vv  + L++++w++++ + + rtv+++i++LR+ L+d++ ++r I   +  GYrl
  gi|121639005|ref|YP_979229.1| 22 TPKQRAVLAMLLLSRNQVVAADALVQAIWEKSPpARARRTVHTYICNLRRTLSDAGVDSRNILVSEPPGYRL 93
                                   9********************************99***********************************97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.7   7.8e+03       5      28 ..      27      50 ..      23      61 .. 0.57
   2 ?    5.7   0.0    0.0073        33      13      30 ..     118     135 ..     108     144 .. 0.84
   3 ?    9.2   0.0   0.00053       2.4       6      41 ..     167     202 ..     163     205 .. 0.92
   4 ?   -0.8   0.0      0.87   3.9e+03      20      36 ..     238     255 ..     216     263 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                         TPR_14  5 lalaeallalGdpdeAiallrral 28
                                   + la +ll + +  +A al +++ 
  gi|121639005|ref|YP_979229.1| 27 AVLAMLLLSRNQVVAADALVQAIW 50
                                   556666666666666555555554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0073
                         TPR_14  13 alGdpdeAiallrralal 30 
                                    a G + eAi++l+ al+ 
  gi|121639005|ref|YP_979229.1| 118 AKGYFSEAIRYLDSALQN 135
                                    6799***********995 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00053
                         TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlll 41 
                                    +laea  a G+ d  i  l+r++a +P  + +w +l
  gi|121639005|ref|YP_979229.1| 167 KLAEAAIACGRADVVIPKLERLVAMHPYRESLWKQL 202
                                    79*******************************887 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.87
                         TPR_14  20 AiallrralalaP.ddae 36 
                                     +al++++l++ P dd++
  gi|121639005|ref|YP_979229.1| 238 IRALYHKILRQLPmDDLV 255
                                    578999999998866665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00033       1.5      29      62 ..      27      59 ..      23      62 .. 0.91
   2 ?   -0.2   0.0      0.32   1.5e+03       7      19 ..     122     134 ..     117     138 .. 0.70
   3 ?    0.4   0.0      0.22   9.7e+02      25      42 ..     162     179 ..     150     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00033
                         TPR_19 29 llLAeallalgqldeAealLdalpeedpddarya 62
                                   + LA +ll+ +q+ +A al++a++e+ p  ar++
  gi|121639005|ref|YP_979229.1| 27 AVLAMLLLSRNQVVAADALVQAIWEKSPP-ARAR 59
                                   679*************************9.8876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                         TPR_19   7 yaeAlalleqalq 19 
                                    + eA+++l +alq
  gi|121639005|ref|YP_979229.1| 122 FSEAIRYLDSALQ 134
                                    5677777777776 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.22
                         TPR_19  25 aearllLAeallalgqld 42 
                                    + +   LAea +a g+ d
  gi|121639005|ref|YP_979229.1| 162 LLVHTKLAEAAIACGRAD 179
                                    556667899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2062.17
//
Query:       gi|121639006|ref|YP_979230.1|  [L=104]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-14   53.4  20.5    2.1e-12   47.8  20.5    2.0  1  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8  20.5   1.2e-16   2.1e-12       1      79 [.       6     100 ..       6     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.2e-16
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaal...sgttaaaaaaaagaalggmPl....aaagagga........... 62 
                                    sAglGqA++vG++SVPp+W++++p  +a++a+       +++a ++aagaa+ggmP+    ++ +++ga           
  gi|121639006|ref|YP_979230.1|   6 SAGLGQAQLVGSMSVPPTWQGSIPISMASSAMSglgVPPNPVALTQAAGAAGGGMPMmlmpMSISGAGAgmpgglmdrdg 85 
                                    8***************************9999988855566677777777777777744442333333356777778644 PP

                       PE_PPE_C  63 aggaaprygfrptvmpr 79 
                                    ag++++  + r tv+pr
  gi|121639006|ref|YP_979230.1|  86 AGWHVT--QARLTVIPR 100
                                    466666..55******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 918.22
//
Query:       gi|121639007|ref|YP_979231.1|  [L=282]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-60  202.3  24.1    4.5e-60  202.3  24.1    2.1  2  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3  24.1   2.5e-64   4.5e-60       1     157 [.       7     163 ..       7     164 .. 0.99
   2 ?    0.3   1.8     0.038   6.8e+02      75     102 ..     177     204 ..     159     223 .. 0.55

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 2.5e-64
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+nsa+++aG+gsgpl+aAa+aW+gLa +l ++a+++esvla+l+++ W+Gp+s++maaaa py+ WLs+ a qa+
  gi|121639007|ref|YP_979231.1|   7 WLPPEINSARMFAGAGSGPLFAAASAWEGLAVDLWASASSFESVLAALTTGPWTGPASMSMAAAASPYVGWLSTVASQAQ 86 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aA qa+aaa+a+eaAlaa+v+p+ ++anr  la+l+a+n++GqntpaIaate +y emwaqd+aam +Y+a ++++
  gi|121639007|ref|YP_979231.1|  87 LAAIQARAAATAFEAALAATVHPTAVTANRVSLASLIAANVLGQNTPAIAATEFDYLEMWAQDVAAMVGYHAGAKSV 163
                                    ************************************************************************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.038
                                    HHHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                            PPE  75 aaaqaeeaAaqaeaaaaaYeaAlaamvp 102
                                     a  a+++++q++ +a+  +aA++ +v+
  gi|121639007|ref|YP_979231.1| 177 LAGLAAQVGTQVAGMATTASAAVTPVVE 204
                                    4555555555555555444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2362.72
//
Query:       gi|121639008|ref|YP_979232.1|  [L=104]
Description: hypothetical protein BCG_3148c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 882.51
//
Query:       gi|121639009|ref|YP_979233.1|  [L=344]
Description: hypothetical protein BCG_3149 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-08   33.7   1.1    0.00069   19.7   0.0    3.2  4  Nitroreductase  Nitroreductase family
    0.00028   20.5   0.0      0.085   12.4   0.0    2.2  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   7.3e-05      0.66      23      43 ..       5      25 ..       1      37 [. 0.79
   2 ?    0.6   0.0     0.056     5e+02     107     143 ..      46      82 ..      30      94 .. 0.82
   3 ?   -2.7   0.0       0.6   5.4e+03       1      12 [.     112     124 ..     112     126 .. 0.88
   4 !   19.7   0.0   7.7e-08   0.00069      77     169 ..     202     297 ..     133     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.3e-05
                                   HHHHHHTS--GGG---EEEEE CS
                 Nitroreductase 23 ileaarraPsagnlqpwrfvv 43
                                    +  a raPs +n+qpwr v+
  gi|121639009|ref|YP_979233.1|  5 AVLLACRAPSVHNSQPWRWVA 25
                                   5556789***********997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.056
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GG CS
                 Nitroreductase 107 aaerayryalldagaaaqnllLaAtalGlgscpiggf 143
                                    a + + r a++++ga++  l +a+ta+ + + ++ ++
  gi|121639009|ref|YP_979233.1|  46 ATDHSGRQAIISCGAVLDHLRIAMTAAHWQANITRFP 82 
                                    56788899**************999999888877655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.6
                                    HHH--B--.-B-S CS
                 Nitroreductase   1 irkRrSiR.kFdd 12 
                                    i++Rr+ R +Fd+
  gi|121639009|ref|YP_979233.1| 112 ILQRRTDRlPFDS 124
                                    789*****99985 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 7.7e-08
                                    G............HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG CS
                 Nitroreductase  77 e............elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd 144
                                                 +++++++++ ++   ++v+          + ++++r ++l +g ++ ++lL++t++G+++c ++++ 
  gi|121639009|ref|YP_979233.1| 202 RlrvdlgrdfpvrSYQNRRAELADDRSKVLVL----------STPSDTRADALRCGEVLSTILLECTMAGMATCTLTHLI 271
                                    14444555555556677888888888888888..........9***********************************99 PP

                                    GGHHHHHHHH.T-S...SEEEEEEEEE CS
                 Nitroreductase 145 eaaeevrkll.glp.deeeivvliavG 169
                                    e ++  r++  gl  +  e+++li+vG
  gi|121639009|ref|YP_979233.1| 272 ESSDS-RDIVrGLTrQRGEPQALIRVG 297
                                    88863.333325555458888888888 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   9.5e-06     0.085     161     214 ..       3      68 ..       1      69 [. 0.76
   2 !    6.3   0.0   0.00073       6.5      66     111 ..     227     273 ..     200     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-06
                                    HHHHHHHHTS--GGG----EEE.E-SSEE..................EEE-S-HHHHHHHHHHHHHH CS
                 TM1586_NiRdase 161 keileaarlAPsAlNqqpwrfelkdddeiki.............kasvlgklskiDlGIallHfela 214
                                    k+++ +a  APs  N+qpwr   ++ +  ++               ++ g+   i +G +l H+ +a
  gi|121639009|ref|YP_979233.1|   3 KNAVLLACRAPSVHNSQPWRWVAESGS-EHTtvhlfvnrhrtvpATDHSGRQAIISCGAVLDHLRIA 68 
                                    7899999**************966643.333345588888887544666888889999999998875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00073
                                    SSEEEE----SS.HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST CS
                 TM1586_NiRdase  66 vpnyialvgekk.edleekaGYygeqlvLkltalGlgtcWvggtykk 111
                                     +++++l  + + ++   ++G ++  ++L++t +G++tc +    ++
  gi|121639009|ref|YP_979233.1| 227 RSKVLVLSTPSDtRADALRCGEVLSTILLECTMAGMATCTLTHLIES 273
                                    5666777776663444568999*****************77655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2638.57
//
Query:       gi|121639010|ref|YP_979234.1|  [L=116]
Description: hypothetical protein BCG_3150c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 832.92
//
Query:       gi|121639011|ref|YP_979235.1|  [L=193]
Description: hypothetical protein BCG_3151c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   22.1   0.0    0.00019   21.6   0.0    1.2  1  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.1e-08   0.00019       9     102 ..      99     191 ..      92     193 .] 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-08
                            rve   9 qvDvt.vvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngseytskafrefl 87 
                                    ++D++ ++    +g++a+ l  +d++ +++++  ++++ + +++la l++ v    +  +  +  Dng+ + +k +  ++
  gi|121639011|ref|YP_979235.1|  99 EGDTVaHCGPTLKGEFAHTLNLTDVHIGWVFTRTVRNN-ARTHILAGLKASVTEIPHG-ITGLDFDNGTVFLNKPVISWA 176
                                    678888666566666***********************.8888899999999888887.9******************** PP

                            rve  88 adlgirvsftrpgrp 102
                                     d+gi  ++ rp++ 
  gi|121639011|ref|YP_979235.1| 177 GDNGIYFTRFRPYKK 191
                                    *************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1484.97
//
Query:       gi|121639012|ref|YP_979236.1|  [L=110]
Description: hypothetical protein BCG_3152 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-12   47.4   0.5    2.1e-12   47.2   0.5    1.1  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.5   1.2e-16   2.1e-12      34     140 ..       2      86 ..       1      87 [. 0.91

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.2e-16
                                    EETTEEEEEEETTSHCCHCCCT--ECEEEEEEEEEEE-SEGGEEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTG CS
                   Pyridox_ox_2  34 vdgdslyfhgakgsrlaaalrgapvcvvvtevdglvlarsfnslnyrSVvvrGraeevtdeeekaealellvekivpgrw 113
                                    v+g++++f++a+g++l+ a      c v++e+d++++a+      + SV+v+ ra+++t+++  +ea ++ +   +p  w
  gi|121639012|ref|YP_979236.1|   2 VQGRTVLFRTAEGAKLFSAVA---KCAVAFEADDHNVAEG-----W-SVIVKVRAQVLTTDAGVREAERAQL---LP--W 67 
                                    789******************...****************.....*.*********************9987...55..6 PP

                                    G.CSB---CCCCCTEEEEEEEEEEEEEE CS
                   Pyridox_ox_2 114 e.nlrpptrkelkatsvlrlkieevsgr 140
                                    + +l+          + +r+ ++e++gr
  gi|121639012|ref|YP_979236.1|  68 TaTLK---------RHCVRVIPWEITGR 86 
                                    61444.........79***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 820.23
//
Query:       gi|121639013|ref|YP_979237.1|  [L=463]
Description: hypothetical protein BCG_3153c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-79  266.5   0.3    5.4e-79  265.7   0.3    1.4  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    8.9e-29  100.3   0.0    1.4e-28   99.6   0.0    1.3  1  DUF1298         Protein of unknown function (DUF1298)
  ------ inclusion threshold ------
      0.015   13.9   0.0      0.021   13.4   0.0    1.1  1  AATase          Alcohol acetyltransferase


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.7   0.3     9e-83   5.4e-79       1     264 []       4     256 ..       4     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 265.7 bits;  conditional E-value: 9e-83
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    L++lDa fl++e++++  hv+ ++ + +  +g ++ ++++++++++qr++ ++r+ q+++ +p++l+ap+Wv+d+dfDl+
  gi|121639013|ref|YP_979237.1|   4 LTTLDAGFLKAEDVDR--HVSLAIGALAVIEGPAP-DQEAFLSSLAQRLRPCTRFGQRLRLRPFDLGAPKWVDDPDFDLG 80 
                                    7899************..77777777777777777.799***************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    +Hv+r+alp+PG+e++l+el+++L++++LDr+rPlWev+viEGl+++++Ail+k+HH+++DG+++++lla l d++++d+
  gi|121639013|ref|YP_979237.1|  81 RHVWRIALPRPGNEDQLFELIADLMARRLDRGRPLWEVWVIEGLADSKWAILTKLHHCMADGIAATHLLAGLSDESMSDS 160
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrfa 240
                                     +++++++++++  +++ r++g++v++ ++l++ ++++ag+v++a+ ++e+a   + +++p+a+    ln p+s+ Rr++
  gi|121639013|ref|YP_979237.1| 161 FASNIHTTMQSQ--SASVRRGGFRVNPSEALTASTAVMAGIVRAAKGASEIA---AGVLSPAAS---SLNGPISDLRRYS 232
                                    ************..9************************************5...566666555...9************ PP

                 WES_acyltransf 241 aaslpLadvkavakalgvtiNDvv 264
                                    aa++pLadv++v+++++vtiNDv+
  gi|121639013|ref|YP_979237.1| 233 AAKVPLADVEQVCRKFDVTINDVA 256
                                    **********************95 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   2.4e-32   1.4e-28       3     144 ..     299     443 ..     297     444 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 2.4e-32
                        DUF1298   3 NqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaal...ikrl.lsnttlviSNvpG 78 
                                    N+++++l +Lp+d ++Pl+rlr ++++++r+K   +  + + l+++ ++ lp +++a++   ++rl ++ + +v +NvpG
  gi|121639013|ref|YP_979237.1| 299 NRVSLMLPNLPVDQENPLQRLRIVHSRLTRAKAGGQRQFGNTLMAI-ANRLPFPMTAWAvglLMRLpQRGVVTVATNVPG 377
                                    9*********************************************.9999******9966644447999999******* PP

                        DUF1298  79 PqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    P+++l+++G+++ ++ypv+p++ +   ++++lSya++l +g+++d d+v d  +l++ +e+a+++l
  gi|121639013|ref|YP_979237.1| 378 PRRPLQIMGRRVLDLYPVSPIAMQLRTSVAMLSYADDLYFGILADYDVVADAGQLARGIEDAVARL 443
                                    *************************************************************99865 PP

>> AATase  Alcohol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.5e-06     0.021     120     183 ..      94     155 ..      92     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-06
                         AATase 120 deelnellselvipvgdpkkPlwrlivlpsaddkkkwkkfv.fitdHllfDGisgvnffkdllee 183
                                    +++l+el+ +l+    d  +Plw + v++   d  kw   +     H++ DGi++ +++  l++e
  gi|121639013|ref|YP_979237.1|  94 EDQLFELIADLMARRLDRGRPLWEVWVIEGLADS-KW--AIlTKLHHCMADGIAATHLLAGLSDE 155
                                    56788999999999999999*********98666.45..5558899************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3430.70
//
Query:       gi|121639014|ref|YP_979238.1|  [L=332]
Description: hypothetical protein BCG_3154 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-13   49.5   1.3    7.5e-05   22.8   0.0    3.5  4  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
       0.25   10.9   0.0        0.7    9.4   0.0    1.7  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.3e-07    0.0066      15      45 ..       6      37 ..       2      41 .. 0.87
   2 !    7.2   0.0   0.00055       4.9     100     141 ..      44      85 ..      38     101 .. 0.85
   3 ?   -2.9   0.0       0.7   6.3e+03       3      24 ..     118     140 ..     116     145 .. 0.75
   4 !   22.8   0.0   8.4e-09   7.5e-05     107     170 .]     236     301 ..     219     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.3e-07
                                   --HHHHHHHHHHHHTS--GGG---EEEEEE.. CS
                 Nitroreductase 15 vpkeelekileaarraPsagnlqpwrfvvv.q 45
                                   +++e+++++l  a raPs +n+qpwr  v+ +
  gi|121639014|ref|YP_979238.1|  6 PDAETVRTVLTLAVRAPSIHNTQPWRWRVCpT 37
                                   689***********************988855 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00055
                                    TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE- CS
                 Nitroreductase 100 ldkserkaaerayryalldagaaaqnllLaAtalGlgscpig 141
                                     ++++ ++ + + r+ +l++g a++  ++a+++lG+ + +  
  gi|121639014|ref|YP_979238.1|  44 RPDMQLRSTDPDGRELILSCGVALHHCVVALASLGWQAKVNR 85 
                                    56788899999************************9886655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.7
                                    H--B--.-B-S----HHHHHHHH CS
                 Nitroreductase   3 kRrSiR.kFddepvpkeelekil 24 
                                    +Rr+ R +++  pvp  +++ + 
  gi|121639014|ref|YP_979238.1| 118 RRRTDRrAYSCWPVPGGDIALMA 140
                                    69999879999999988877655 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 8.4e-09
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH....HHHHHHT-S..SEEEEEEEEE- CS
                 Nitroreductase 107 aaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae....evrkllglpdeeeivvliavGy 170
                                      e ++r a l ag aa  +lL+Ata+Gl++cpi+ + e a+    + ++++g      +++l++vG+
  gi|121639014|ref|YP_979238.1| 236 GTETDDRLARLRAGEAASIVLLTATAMGLACCPITEPLEIAKtrdaVRAEVFGAG--GYPQMLLRVGW 301
                                    5788899999****************************76643343445555555..89999999997 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   7.8e-05       0.7     158     184 ..       9      35 ..       2      73 .. 0.71
   2 ?   -2.1   0.0      0.26   2.3e+03      79     103 ..     243     267 ..     228     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.8e-05
                                    HHHHHHHHHHHTS--GGG----EEE.E CS
                 TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelk 184
                                    e ++++l +a  APs  N+qpwr ++ 
  gi|121639014|ref|YP_979238.1|   9 ETVRTVLTLAVRAPSIHNTQPWRWRVC 35 
                                    6788999***************98854 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                                    HHHHHHHHHHHHHHHHHHHTT-EEE CS
                 TM1586_NiRdase  79 dleekaGYygeqlvLkltalGlgtc 103
                                     ++ +aG     ++L +ta Gl+ c
  gi|121639014|ref|YP_979238.1| 243 LARLRAGEAASIVLLTATAMGLACC 267
                                    4555667677778899999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2261.90
//
Query:       gi|121639015|ref|YP_979239.1|  [L=578]
Description: two component sensor histidine kinase devS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-26   91.9  10.7      2e-15   57.3   0.2    2.8  3  GAF_2        GAF domain
    4.8e-22   79.0   5.3    6.4e-13   49.5   0.0    2.9  3  GAF          GAF domain
    4.9e-17   62.5   0.2    5.1e-07   30.1   0.1    2.8  2  GAF_3        GAF domain
    1.7e-12   47.7   1.3    1.7e-12   47.7   1.3    3.3  3  HisKA_3      Histidine kinase
    1.1e-09   38.8   0.1    1.5e-08   35.1   0.1    2.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.8e-06   27.3   0.1    1.1e-05   25.4   0.1    2.2  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.045   13.2   0.0    1.7  2  CodY         CodY GAF-like domain
      0.027   14.3   0.0      0.048   13.5   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.2   8.8e-19     2e-15       2     137 ..      62     200 ..      61     201 .. 0.85
   2 !   39.6   2.6   2.6e-13   5.9e-10       3     138 .]     231     370 ..     229     370 .. 0.70
   3 ?   -2.2   0.1       2.1   4.7e+03       3      37 ..     431     463 ..     429     514 .. 0.54

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 8.8e-19
                                    HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE..EEEES-TTSTT-S-B.---TTHHHHHHHHTS-EEES-GGG- CS
                          GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrla..awgeaeeefgaaldr.plgeglvgealrtgrpvilndleed 77 
                                    +dle +l++++  ++ l +a++g + ++d +++  ++  ++ + +ee   ++ + p+g g++g  +++ +p+ l+d+ ++
  gi|121639015|ref|YP_979239.1|  62 LDLEATLRAIVHSATSLvDARYGAMEVHDRQHR--VLhfVYEGIDEETVRRIGHlPKGLGVIGLLIEDPKPLRLDDVSAH 139
                                    699*************889********996666..4445555555555555544488*********************** PP

                                    S-HHHHHHHHHTT--EEEEEE-TTS---EEEEE.S........--HHHHHHHHHHHHHHHHHH CS
                          GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnl.yankppa..fdeedlelLeelaeqiaiai 137
                                    p+++g p  h+++r+fl+vP++ +++ +G l l   ++  +  f+++d  l+++la+ ++ia+
  gi|121639015|ref|YP_979239.1| 140 PASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLtDKTN--GqpFSDDDEVLVQALAAAAGIAV 200
                                    *********************99889*******43444..345******************98 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 2.6e-13
                                    HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEE...EEEES-TTS.TT-S-B---TT.H.HHHHHHHTS-EEES-GG CS
                          GAF_2   3 dleelldlvldelvelg.aalgyillvdddgglrla...awgeaeeef.gaaldrplgeg.l.vgealrtgrpvilndle 75 
                                    ++ ++++lv  e+++l+ a+++ ++++ d ++  +    +      e  g+a+ + +g+  + +g +lr+   v++n ++
  gi|121639015|ref|YP_979239.1| 231 EPATVFRLVAAEALKLTaADAALVAVPVD-ED--MPaadVGELLVIETvGSAVASTVGRTiPvAGAVLRE---VFVNGIP 304
                                    67899**********98466666666443.44..231222222222222444444669998855566666...9****88 PP

                                    G-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEE.S......--HHHHHHHHHHHHHHHHHHH CS
                          GAF_2  76 edpdkkglp..aghaglrsflavPlisegrvvGvlnl.yankppafdeedlelLeelaeqiaiaie 138
                                    +  d+  l+   + a+ ++ l +Pl+++g v Gv+++ +  +p+af++e+le++ ++a+q+a+a++
  gi|121639015|ref|YP_979239.1| 305 RRVDRVDLEglDELADAGPALLLPLRARGTVAGVVVVlSQGGPGAFTDEQLEMMAAFADQAALAWQ 370
                                    86666666634666666777*******999***999867888888******************975 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE CS
                          GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrla 37 
                                    dl+++ +++  ++ +l ga+ g+  l    ++++ a
  gi|121639015|ref|YP_979239.1| 431 DLQDVIQEIRTTIYDLhGASQGITRLR---QRIDAA 463
                                    677777777777777666555555552...223333 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   2.8e-16   6.4e-13       1     133 []      63     200 ..      63     200 .. 0.81
   2 !   30.8   0.5   1.7e-10   3.8e-07       3     132 ..     233     368 ..     231     369 .. 0.62
   3 ?   -0.9   0.1         1   2.3e+03       3      62 ..     422     495 ..     420     523 .. 0.45

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.8e-16
                                    SHHHHHHHHHHHHHHHHTESEEEE..EEEEETT.EEECEEEEECC......EEEETTSHHHHHHHHHSSSEEESTGGTST CS
                            GAF   1 dleelldtvveelrellgadrval..ylpdydG.lhydipqasrw......lfmkngrgicgqvlatgqplvipdstpdp 71 
                                    dle +l+ +v ++ +l++a+++a   +  +++  lh+ ++++ +          + g g++g  ++ ++pl+++d++++p
  gi|121639015|ref|YP_979239.1|  63 DLEATLRAIVHSATSLVDARYGAMevHD-RQHRvLHF-VYEGIDEetvrriGHLPKGLGVIGLLIEDPKPLRLDDVSAHP 140
                                    89*****************999994322.22223466.555444443334366677999****************99999 PP

                                    T...HHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHHH CS
                            GAF  72 r...faqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvaval 133
                                        f +        ++ +r++l+vP+++++e +G+l+l+++++  pf+++++ l+q+la+ +++a+
  gi|121639015|ref|YP_979239.1| 141 AsigFPP-------YHPPMRTFLGVPVRVRDESFGTLYLTDKTNgqPFSDDDEVLVQALAAAAGIAV 200
                                    9555555.......358899*********************77778******************996 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.7e-10
                                    HHHHHHHHHHHHHHHTESEEEEEE.......EEETTEEE...........CEEEEECCEEEETTSHHHH....HHHHHSS CS
                            GAF   3 eelldtvveelrellgadrvalyl.......pdydGlhy...........dipqasrwlfmkngrgicg....qvlatgq 60 
                                     ++++ v++e+ +l++ad +++         +      +           +   as+  ++ ++    g    +v+ +g 
  gi|121639015|ref|YP_979239.1| 233 ATVFRLVAAEALKLTAADAALVAVpvdedmpA------AdvgellvietvGSAVASTVGRTIPVA---GavlrEVFVNGI 303
                                    589999*************9998733333321......022222332222233333333333333...222234444444 PP

                                    SEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE...SSSCSHHHHHHHHHHHHHHHHHH CS
                            GAF  61 plvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn...psppftreelellqvladqvava 132
                                    p ++++++        + +d l+  g+  +l +Pl+++g + G++v+ +   p   ft+e+le++ ++adq+a+a
  gi|121639015|ref|YP_979239.1| 304 PRRVDRVDL-------EGLDELADAGP--ALLLPLRARGTVAGVVVVLSqggPG-AFTDEQLEMMAAFADQAALA 368
                                    444443221.......23344555677..6*******************75554.5*****************98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE...............CEEEEECCEEEET.TSHHHHHHHHHSSSE CS
                            GAF   3 eelldtvveelrellgadrvalylpdydGlhy...............dipqasrwlfmkn.grgicgqvlatgqpl 62 
                                    ++ l  vv++l+++ +  r ++y    +G  +                 + ++r + + + + ++++ +la +   
  gi|121639015|ref|YP_979239.1| 422 QQRLSDVVDDLQDVIQEIRTTIYD--LHGASQgitrlrqridaavaqFADSGLRTSVQFVgPLSVVDSALADQAEA 495
                                    566777777787777777777776..44411112222222222111112222222111112333444444433333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.3e-10   7.4e-07       1     129 []      63     202 ..      63     202 .. 0.75
   2 !   30.1   0.1   2.3e-10   5.1e-07      78     126 ..     319     368 ..     272     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.3e-10
                          GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalse..sldedsalarralssgevvsepsfaeedg 77 
                                    +l+ +l ++++ + +l++a +ga  ++++++ ++ +   +   ++ + +  +l+++  ++ ++++   ++   ++ + ++
  gi|121639015|ref|YP_979239.1|  63 DLEATLRAIVHSATSLVDARYGAM-EVHDRQHRVLHFVYEgIDEETVRRigHLPKGLGVIGLLIEDPKPLRLDDVSAHPA 141
                                    678889999999999999999998.6666666554443333566666668899999999999999888876655444333 PP

                          GAF_3  78 ........lpdraalavPLvagrqviGvlal.astkprafdaedlelleslArqiataier 129
                                             p+r  l vP++++++++G+l+l   t++++f+++d+ l+++lA+ +++a+++
  gi|121639015|ref|YP_979239.1| 142 sigfppyhPPMRTFLGVPVRVRDESFGTLYLtDKTNGQPFSDDDEVLVQALAAAAGIAVAN 202
                                    3444445446788888*****99********55667888*******************987 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.3e-10
                          GAF_3  78 lpdraalavPLvagrqviGvlalast.kprafdaedlelleslArqiata 126
                                     + ++al++PL+a+ +v Gv+++ s+ +p+af++e+le++ ++A+q+a+a
  gi|121639015|ref|YP_979239.1| 319 ADAGPALLLPLRARGTVAGVVVVLSQgGPGAFTDEQLEMMAAFADQAALA 368
                                    35699********55*******85552799******************97 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         2   4.5e+03      52      65 ..      14      27 ..      11      31 .. 0.75
   2 !   47.7   1.3   7.4e-16   1.7e-12       2      64 ..     387     447 ..     386     452 .. 0.92
   3 ?   -1.9   0.1       2.2     5e+03      32      53 ..     491     512 ..     482     519 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHTT CS
                        HisKA_3 52 alqevRrllhnLrp 65
                                   a++ +R++l++Lr 
  gi|121639015|ref|YP_979239.1| 14 AMRPLRHTLSQLRL 27
                                   67778999999994 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 7.4e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        HisKA_3   2 RariARELHDsvgqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRrllhnLr 64 
                                    R riAR+LHD v q+L+ai l l+ a    ++++++++++l ++ + +++ +qe+R ++ +L+
  gi|121639015|ref|YP_979239.1| 387 RDRIARDLHDHVIQRLFAIGLALQGAVP--HERNPEVQQRLSDVVDDLQDVIQEIRTTIYDLH 447
                                    9*************************85..55666*************************998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                                    TT-HHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  32 ekdpekaaeqlreieelareal 53 
                                    +++++ ++e++ ++ ++a+ + 
  gi|121639015|ref|YP_979239.1| 491 DQAEAVVREAVSNAVRHAKAST 512
                                    3333466666666666666655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   6.6e-12   1.5e-08       7      83 ..     494     548 ..     489     578 .] 0.73

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.6e-12
                                    HHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHH CS
                      HATPase_c   7 rqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkk 83 
                                    + +++++v+Nav++ +ka++++v++k+++ dl+i+v+DnG+G+p e                        Gl+  ++
  gi|121639015|ref|YP_979239.1| 494 EAVVREAVSNAVRH-AKASTLTVRVKVDD-DLCIEVTDNGRGLPDEFTG--------------------SGLTNLRQ 548
                                    569***********.99*********877.**************96544....................33333333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   4.9e-09   1.1e-05      24      82 ..     485     539 ..     427     556 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.9e-09
                    HATPase_c_2  24 lseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpet 82 
                                    ++++l+d+ + +v Ea++Nav+ha+ +    +v+v+  + ++ l++ev+D+G+g  d  t
  gi|121639015|ref|YP_979239.1| 485 VDSALADQAEAVVREAVSNAVRHAKASTL--TVRVK--V-DDDLCIEVTDNGRGlPDEFT 539
                                    7788999******************9655..33333..3.366***********887665 PP

>> CodY  CodY GAF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.045     113     158 ..     158     205 ..     151     218 .. 0.85
   2 ?   -3.5   0.0       2.8   6.2e+03      88     118 ..     419     449 ..     415     453 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                    EEEEETTEEEEEEEEE..ESSS--THHHHHHHHHHHHHHHHHHHHHHH CS
                           CodY 113 vPiegggeRLGtlila..rvdkefedddliLaeyaaTvvGleilreka 158
                                    vP+    e  Gtl l+  ++ ++f+ddd +L++  a   G+ + +++ 
  gi|121639015|ref|YP_979239.1| 158 VPVRVRDESFGTLYLTdkTNGQPFSDDDEVLVQALAAAAGIAVANARL 205
                                    8999***********83356789******************9998876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                    ESTTSTSSSSTGGGGGGGSSSEEEEEEEEET CS
                           CodY  88 leidseltvfpeeekekfkkglttivPiegg 118
                                     e+++ l+ ++ + ++ +++  tti  ++g+
  gi|121639015|ref|YP_979239.1| 419 PEVQQRLSDVVDDLQDVIQEIRTTIYDLHGA 449
                                    5666666666777777777777777766665 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05     0.048       4      50 ..     494     539 ..     491     567 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                    HATPase_c_3   4 ekAlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeel 50 
                                    e ++ e v N++  A+a + ++ v+ ++  +  i ++D+G G++ e  
  gi|121639015|ref|YP_979239.1| 494 EAVVREAVSNAVRhAKASTLTVRVKVDD--DLCIEVTDNGRGLPDEFT 539
                                    67899******98888888777777764..589*********998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.58
# Mc/sec: 3023.11
//
Query:       gi|121639016|ref|YP_979240.1|  [L=217]
Description: two component transcriptional regulatory protein DevR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-23   82.7   0.0    3.4e-23   81.9   0.0    1.4  1  Response_reg   Response regulator receiver domain
    6.3e-18   64.1   0.1    1.2e-17   63.2   0.1    1.5  1  GerE           Bacterial regulatory proteins, luxR family
    3.6e-05   23.3   0.1    7.9e-05   22.2   0.1    1.6  1  Sigma70_r4_2   Sigma-70, region 4
     0.0022   17.5   0.1     0.0037   16.8   0.1    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0087   15.6   0.1       0.02   14.4   0.1    1.6  1  Sigma70_r4     Sigma-70, region 4
     0.0091   15.7   0.0      0.021   14.6   0.0    1.6  1  HTH_38         Helix-turn-helix domain
     0.0093   15.7   0.3      0.028   14.2   0.0    2.0  2  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.029   14.7   0.0    1.2  1  Fas_alpha_ACP  Fatty acid synthase subunit alpha Acyl carrier
      0.026   15.0   0.0      0.045   14.2   0.0    1.4  1  HTH_40         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.7e-26   3.4e-23       1     111 [.       4     115 ..       4     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.7e-26
                                    EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEES CS
                   Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilta 79 
                                    v++vdD+++vr++l +ll  + ++ +v+ea + +ea++ + + ++d+ +lD+++p+ +G+el++ +  + p+l+++ilt+
  gi|121639016|ref|YP_979240.1|   4 VFLVDDHEVVRRGLVDLLGaDPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTS 83 
                                    89*****************999**9******************************************************* PP

                                    STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    ++++e + +a+ aga+++++K+++  eL  a+
  gi|121639016|ref|YP_979240.1|  84 YTSDEAMLDAILAGASGYVVKDIKGMELARAV 115
                                    ************************99999887 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.1   5.8e-21   1.2e-17       3      57 .]     150     204 ..     148     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.8e-21
                                    S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHHHH CS
                           GerE   3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrvelvrla 57 
                                    L+++Er+ L ll eG++nk+IA++++++ekTVk+++s+++ KL+ + r++++++a
  gi|121639016|ref|YP_979240.1| 150 LTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFA 204
                                    9***************************************************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1     4e-08   7.9e-05      11      54 .]     150     192 ..     147     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4e-08
                                    S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    L+ ++r+ + l   egl+ k+IA ++ + e+tVk+++sR ++kL
  gi|121639016|ref|YP_979240.1| 150 LTDQERTLLGL-LSEGLTNKQIADRMFLAEKTVKNYVSRLLAKL 192
                                    66666666666.349*************************9998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.9e-06    0.0037      14      43 ..     163     190 ..     150     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                         HTH_24  14 knprisqreLAerlglSpstvnrrlkrLee 43 
                                    +  +++++++A+r  l   tv+ ++ rL  
  gi|121639016|ref|YP_979240.1| 163 E--GLTNKQIADRMFLAEKTVKNYVSRLLA 190
                                    5..9************************75 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.8e-06      0.02       2      48 ..     147     192 ..     147     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-06
                                    HHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   2 LasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    L+ L+++er+ l l   eglT ++I++r+ + + +V+   +r l kL
  gi|121639016|ref|YP_979240.1| 147 LSGLTDQERTLLGLL-SEGLTNKQIADRMFLAEKTVKNYVSRLLAKL 192
                                    789999***999996.6899************************998 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     1e-05     0.021       4      43 ..     149     187 ..     148     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                         HTH_38   4 hLsleeReeIerllaeGlslreIArrLgrspsTIsRElkR 43 
                                     L+ +eR ++  ll+eGl++++IA r+  +  T+ + + R
  gi|121639016|ref|YP_979240.1| 149 GLTDQER-TLLGLLSEGLTNKQIADRMFLAEKTVKNYVSR 187
                                    599****.9999**************98888888776655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3     6e+03       6      15 ..     127     136 ..     125     143 .. 0.76
   2 !   14.2   0.0   1.4e-05     0.028      12      41 ..     159     188 ..     150     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                         HTH_23   6 eRlrilllla 15 
                                    +R+ ++l+++
  gi|121639016|ref|YP_979240.1| 127 NRAAAALMAK 136
                                    6888888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                         HTH_23  12 lllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                     ll eGl+ ++IA+++   + Tv ++++r 
  gi|121639016|ref|YP_979240.1| 159 GLLSEGLTNKQIADRMFLAEKTVKNYVSRL 188
                                    46778**********************996 PP

>> Fas_alpha_ACP  Fatty acid synthase subunit alpha Acyl carrier domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.4e-05     0.029      19     124 ..     102     202 ..      87     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                  Fas_alpha_ACP  19 lkkkldevplsksikdlvgGkStlqNEilgdLqaEfgslpekaedlpleelaealqesfsGklGkqssslisrlvsskmp 98 
                                    + k ++ ++l++++kd+ +G+S l+N   + L a +  + ek++  pl+ l+++     +  lG  s++l ++ ++ +m 
  gi|121639016|ref|YP_979240.1| 102 VVKDIKGMELARAVKDVGAGRSLLDNRAAAALMAKLRGAAEKQD--PLSGLTDQE----RTLLGLLSEGLTNKQIADRMF 175
                                    558899999********************************987..666666543....345677777777777777774 PP

                  Fas_alpha_ACP  99 .ggfnlaairkyLekrwglgpgrqdsv 124
                                     +  ++ +  ++L  + g+++  q +v
  gi|121639016|ref|YP_979240.1| 176 lAEKTVKNYVSRLLAKLGMERRTQAAV 202
                                    133334444444555555555555555 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.045       7      39 ..     159     191 ..     153     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                         HTH_40   7 elleeglsieeIAkerglkesTIegHLaeliee 39 
                                     ll egl+ ++IA++  l+e+T+ +++ +l+ +
  gi|121639016|ref|YP_979240.1| 159 GLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAK 191
                                    5899************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1218.17
//
Query:       gi|121639017|ref|YP_979241.1|  [L=268]
Description: hypothetical protein BCG_3157c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-22   78.7   8.1    3.3e-20   73.0   2.3    2.2  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
        3.1    8.1   4.5         18    5.6   0.0    3.1  4  zf-HC3    zinc-finger


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   2.3   3.7e-24   3.3e-20       3     141 .]       8     137 ..       6     137 .. 0.90
   2 !    9.2   0.3   0.00018       1.6      17      70 ..     160     213 ..     152     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.7e-24
                                    SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                            Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                    + ++V++Dgs ++++A+ wA+++a +r+ +l+l++vidp+  +a++++  +++  ++ + + +++        ea g  v
  gi|121639017|ref|YP_979241.1|   8 RAVVVGIDGSRAATHAALWAVDEAVNRDIPLRLVYVIDPSQLSAAGEGGGQSAARAALHDASRKV--------EATGQPV 79 
                                    779**********************************************************9998........4566666 PP

                                    EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    ++++e+  +++   ++ e+++a +++vGs g++++++   GSv+  ++ +a cpV v++
  gi|121639017|ref|YP_979241.1|  80 KIETEVLCGRPLTKLMQESRSAAMLCVGSVGLDHVRG-RRGSVAATLAGSALCPVAVIH 137
                                    666666666667777788899***************9.78****************986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                            Usp  17 kAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada 70 
                                     +l++A+e+a+ rg +l+++ v+ +++++ v ++ + a  + +   +   ++++
  gi|121639017|ref|YP_979241.1| 160 VVLRHAFEEARLRGVPLRAVAVHAAETPDDVEQGSRLAHVHLSRRLAHWTRLYP 213
                                    589*************************99999998888877777777766666 PP

>> zf-HC3  zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.002        18       6      48 ..      66     105 ..      60     109 .. 0.77
   2 ?    3.0   0.1     0.014   1.2e+02      19      45 ..     120     147 ..     111     152 .. 0.75
   3 ?   -3.4   0.0       1.3   1.2e+04      10      18 ..     163     171 ..     162     181 .. 0.73
   4 ?   -2.0   0.1      0.48   4.3e+03      24      32 ..     245     253 ..     226     263 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.002
                                    ETTEEEEEETTT---BTTB-EE-TTS-EE---GGGTTT-GGG- CS
                         zf-HC3   6 adgrRHavdternrpepGeaftaLCgvevtPreedldtlaglw 48 
                                    +d++R +  t +    +  ++++LCg  +t   ++  ++a l+
  gi|121639017|ref|YP_979241.1|  66 HDASRKVEATGQP---VKIETEVLCGRPLTKLMQESRSAAMLC 105
                                    5666666666666...778999********8888888888877 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                                    --BTTB-EE-TTS-EE-.--GGGTTT-G CS
                         zf-HC3  19 rpepGeaftaLCgvevt.Preedldtla 45 
                                     +++  a  aLC v v  P +++  t++
  gi|121639017|ref|YP_979241.1| 120 SVAATLAGSALCPVAVIhPSPAEPATTS 147
                                    466777889******9999998866665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.3
                                    EEEEETTT- CS
                         zf-HC3  10 RHavdtern 18 
                                    RHa +++r 
  gi|121639017|ref|YP_979241.1| 163 RHAFEEARL 171
                                    999998886 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.48
                                    B-EE-TTS- CS
                         zf-HC3  24 eaftaLCgv 32 
                                    + ++ LCg+
  gi|121639017|ref|YP_979241.1| 245 HSAHELCGA 253
                                    334445553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1481.40
//
Query:       gi|121639018|ref|YP_979242.1|  [L=381]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-61  205.5  28.7    4.8e-61  205.5  28.7    1.9  2  PPE       PPE family
      2e-15   57.5   8.8      2e-15   57.5   8.8    5.0  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
     0.0028   17.5   0.8     0.0044   16.9   0.8    1.2  1  CCDC24    Coiled-coil domain-containing protein 24 family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5  28.7     8e-65   4.8e-61       2     157 ..       6     161 ..       5     162 .. 0.99
   2 ?   -2.2   0.6      0.67     4e+03     102     123 ..     175     195 ..     171     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 8e-65
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPE+nsa++y+Gpg++++l Aaa Wd+Laaelasaa+++ sv+a l++  W Gp+s++m+a  apy++WL+++aaq ++
  gi|121639018|ref|YP_979242.1|   6 LPPEINSARMYSGPGPNSMLVAAASWDALAAELASAAENYGSVIARLTGMHWWGPASTSMLAMSAPYVEWLERTAAQTKQ 85 
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    +A+qa+aaaaa+e+A+a++vppa+++anrael+al+a+n++Gqnt+aIaa ea+y+emwaqdaaam++Y+++saaa
  gi|121639018|ref|YP_979242.1|  86 TATQARAAAAAFEQAHAMTVPPALVTANRAELKALIASNLLGQNTAAIAAIEAQYAEMWAQDAAAMYGYATTSAAA 161
                                    ************************************************************************9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.67
                                    -HHHHHHHHHHHHHHHHT-TTS CS
                            PPE 102 ppaeiaanraelaalvatnffG 123
                                    +pa +aa +a++ + +atn +G
  gi|121639018|ref|YP_979242.1| 175 NPAGLAAQNAAV-TQAATNSAG 195
                                    455555555555.345556555 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -26.7  33.7         3   1.8e+04      62      62 ..     115     115 ..      18     217 .. 0.67
   2 ?   -2.3   1.1       1.5     9e+03      37      62 ..     266     291 ..     255     297 .. 0.50
   3 !   57.5   8.8   3.3e-19     2e-15       2      80 .]     300     377 ..     299     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: -26.7 bits;  conditional E-value: 3
                       PE_PPE_C  62 a 62 
                                    a
  gi|121639018|ref|YP_979242.1| 115 A 115
                                    2 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                       PE_PPE_C  37 taaaaaaaagaalggmPlaaagagga 62 
                                     + +a+ a+ga +  ++l +a +g+a
  gi|121639018|ref|YP_979242.1| 266 SENPAELAPGAFGIDAALSSAEKGAA 291
                                    44444444444433444444444433 PP

  == domain 3  score: 57.5 bits;  conditional E-value: 3.3e-19
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmprp 80 
                                    A++G+A ++G +SVPpsWa+++++  +a + ++ t +  ++  a+++ +g+P+ +ag+ ++a+g+ pryg+r tvm+rp
  gi|121639018|ref|YP_979242.1| 300 ASAGRAGSIGPMSVPPSWATPSSTPVSALSGAGLT-TLDGTDVAEHGTPGLPGVPAGTDKRASGVIPRYGVRLTVMSRP 377
                                    9*****************77666666666665555.5578889999999*****************************8 PP

>> CCDC24  Coiled-coil domain-containing protein 24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   7.4e-07    0.0044      35     148 ..      89     206 ..      73     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-07
                         CCDC24  35 eesdqlaeskp....aslLadpPllRdlleqeirlLlqs.L..qeka..aaegrdeeqllaqrsrrvldYvldaaaersa 105
                                    + ++++    +    a+ +  pP+l    ++e++ L+ s L  q+ a  aa + + ++++aq+ +++  Y++   ++++a
  gi|121639018|ref|YP_979242.1|  89 QARAAA----AafeqAHAMTVPPALVTANRAELKALIASnLlgQNTAaiAAIEAQYAEMWAQDAAAMYGYAT---TSAAA 161
                                    222222....14556999999999999999999999975245533334456678899***************...88999 PP

                         CCDC24 106 reespssrPesassks..taasaasgsssasalssasaelealkd 148
                                    r+ +p s+P++   +    a++aa ++ + +++++ +++l++l++
  gi|121639018|ref|YP_979242.1| 162 RQLTPFSSPQQTTNPAglAAQNAAVTQAATNSAGNTPTALSQLSS 206
                                    999999999999998877333334444445555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2097.35
//
Query:       gi|121639019|ref|YP_979243.1|  [L=380]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-60  204.0  26.9    1.4e-60  204.0  26.9    1.5  2  PPE       PPE family
    3.3e-17   63.1  11.2    3.3e-17   63.1  11.2    4.9  3  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
        3.6    7.6   9.1        1.8    8.5   3.2    2.5  2  DUF5529   Family of unknown function (DUF5529)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0  26.9   2.4e-64   1.4e-60       2     158 .]       6     162 ..       5     162 .. 0.99
   2 ?   -3.4   0.2       1.5     9e+03      75      87 ..     182     194 ..     176     211 .. 0.41

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 2.4e-64
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    lpPEvnsa++y+Gpg+g+llaAa  Wd+Laaela++a+++ svl++laa  W+Gp++++ma  aapy+ WL ++a++ ++
  gi|121639019|ref|YP_979243.1|   6 LPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHWRGPAAESMAVTAAPYIGWLYTTAEKTQQ 85 
                                    8******************************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                    +A qa+aaa a+e+A+a++ pp+++aanr +l al+atnffGqnt+aIaatea+y+emwaqdaaam++Y++asaaaa
  gi|121639019|ref|YP_979243.1|  86 TAIQARAAALAFEQAYAMTLPPPVVAANRIQLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAA 162
                                    *************************************************************************9985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHH CS
                            PPE  75 aaaqaeeaAaqae 87 
                                    +aa +++a   ++
  gi|121639019|ref|YP_979243.1| 182 QAAAVSQATDPLS 194
                                    3333333332222 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -20.4  25.7         3   1.8e+04      41      68 ..     143     170 ..      15     194 .. 0.68
   2 ?    0.0   0.6      0.28   1.7e+03      53      61 ..     284     292 ..     255     298 .. 0.57
   3 !   63.1  11.2   5.6e-21   3.3e-17       2      80 .]     300     376 ..     299     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: -20.4 bits;  conditional E-value: 3
                       PE_PPE_C  41 aaaaagaalggmPlaaagaggaaggaap 68 
                                    + a+ +aa+ g ++a+a+a+  + ++ p
  gi|121639019|ref|YP_979243.1| 143 MWAQDAAAMYGYATASAAAALLTPFSPP 170
                                    1122222222555555555554444444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.28
                       PE_PPE_C  53 Plaaagagg 61 
                                     + +ag+++
  gi|121639019|ref|YP_979243.1| 284 SASGAGGAA 292
                                    333333332 PP

  == domain 3  score: 63.1 bits;  conditional E-value: 5.6e-21
                       PE_PPE_C   2 AglGqAatvGaLSVPpsWaaaapaasaaaaal.sgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmprp 80 
                                    A++G+A+++G+LSVPpsW  aap++++++a    g t+ +++  a+++++g+P+ +++ag+a +g+ pryg+r tvm++p
  gi|121639019|ref|YP_979243.1| 300 ASVGRANSIGQLSVPPSW--AAPSTRPVSALSpAGLTTLPGTDVAEHGMPGVPGVPVAAGRA-SGVLPRYGVRLTVMAHP 376
                                    9*****************..7777777777764566777999999****************9.***************97 PP

>> DUF5529  Family of unknown function (DUF5529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.038   2.3e+02     116     165 ..     174     223 ..     154     226 .. 0.74
   2 ?    8.5   3.2   0.00031       1.8      46      96 ..     285     338 ..     266     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.038
                        DUF5529 116 lapgpatprlasasrpeelceleirikelelltitgdgfdsqrykflkal 165
                                     +p+  t+++a+ s++ +   l i     +l ++t   f  + + fl a+
  gi|121639019|ref|YP_979243.1| 174 TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAI 223
                                    45777888988888776655566777777888888889999999998875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00031
                        DUF5529  46 gaaagaagaaglrslhss...tsaiaihhppglgslserpcpppwpsglasipy 96 
                                    ++ ag+a++ g + l s    +s      pp+ +++s rp     p+gl+++p 
  gi|121639019|ref|YP_979243.1| 285 ASGAGGAASVGNTVLASVgraNSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPG 338
                                    233555555565555554110444456789********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2186.01
//
Query:       gi|121639020|ref|YP_979244.1|  [L=260]
Description: monophosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-45  153.8   0.0    7.9e-45  153.5   0.0    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.0   4.4e-49   7.9e-45       9     261 ..       9     251 ..       3     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 4.4e-49
                                    HHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEE CS
                     Inositol_P   9 avelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltw 88 
                                    a +la +a e+ r +f+  +l i++k    +  +vt+ad+ave+ ++++l + +p++ +lgee +++         g+ w
  gi|121639020|ref|YP_979244.1|   9 ALALADRADELTRVRFGALDLRIDTKP---DLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFGGSTT-----FTGRQW 80 
                                    667889999999999997777777555...8889*******************************9999.....66699* PP

                                    EEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETC.....EEEEECTTSEGGGTEEEEE CS
                     Inositol_P  89 ivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflng.....eklplsrappiseallvtl 163
                                    ivDPiDGTknFvrg p +a +i+ll++g+p +Gv+ +P+l+++++aa+g+Gaf +      ++l++s+     e ++ ++
  gi|121639020|ref|YP_979244.1|  81 IVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAARGRGAFASVdgarpHRLSVSSVA---ELHS-AS 156
                                    ****************************************************987755733334443333...4444.33 PP

                                    ESSSSSSHHHHCHHHHHHHCCCCCH.EEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEEEESSSC CS
                     Inositol_P 164 favssrkdtseasllekvesavsae.gvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGGvvtdakge 242
                                    +++ss + + +  l e+  ++  +  +vr++g+  l++++vaeG +d+  e + +  WD AA  ++++eaGG++t ++g 
  gi|121639020|ref|YP_979244.1| 157 LSFSSLSGWARLGLRERFIGLTDTVwRVRAYGDF-LSYCLVAEGAVDIAAEPQ-VSVWDLAALDIVVREAGGRLTSLDGV 234
                                    5677777777744444444444444888999776.***************999.***********************998 PP

                                    SSSTTSSEEEEESCHHHHH CS
                     Inositol_P 243 grlllargiiaanqkelae 261
                                      + +++g ++a+++ l++
  gi|121639020|ref|YP_979244.1| 235 --AGPHGGSAVATNGLLHD 251
                                    ..55666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1923.91
//
Query:       gi|121639021|ref|YP_979245.1|  [L=362]
Description: pyruvate formate lyase activating protein pflA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-15   57.8   0.1    2.9e-15   57.0   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.018   15.3   0.2      0.048   13.9   0.0    1.8  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.1   3.3e-19   2.9e-15       4     162 ..      84     235 ..      83     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.3e-19
                                    ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                    t gCnl+C+fC+++  +++++          +++++ + +e g++ v ++  +p+  ++++ +++ +++    gi+ + +
  gi|121639021|ref|YP_979245.1|  84 TAGCNLACKFCQNWDISKSREIDVLANRAAPADIARTA-HELGCRSVAFTYNDPTIFWEYAADVADACHD--QGIKAVAV 160
                                    68************996666666666666666666666.7889***************************..7******* PP

                                    ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGendeelee 162
                                    t g++  +e  +++ + +vd  +++l+a++++ + ++++    +  vl++l +lr    ++   ++++++pG nd++ e 
  gi|121639021|ref|YP_979245.1| 161 TAGYMC-PEPRAEFYR-RVDAANVDLKAFTED-FYRKVCV-SHLRNVLDTLAYLRHQ-TNVwLEITTLLIPGRNDSDAEV 235
                                    *****9.666666666.37*************.6666645.999************9.77789*************9554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-06     0.048       8      94 ..      79     164 ..      74     189 .. 0.63
   2 ?   -2.7   0.0      0.71   6.4e+03      13      24 ..     298     309 ..     283     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-06
                        Fer4_12   8 lslf.vsgCnlsCkgCfnketwsfksgkef.tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                    ++ f ++gCnl+Ck+C n ++ + ++ +   ++++ + i + +++   + + ++  +P      e  +++++ +  +++ 
  gi|121639021|ref|YP_979245.1|  79 TLSFgTAGCNLACKFCQNWDISKSREIDVLaNRAAPADIARTAHELGCRSVAFTYNDPTI--FWEYAADVADACHDQGI- 155
                                    4455589********998777655544433135555555555555555666666666666..45555566666666666. PP

                        Fer4_12  86 kdiwlytgy 94 
                                    k + ++ gy
  gi|121639021|ref|YP_979245.1| 156 KAVAVTAGY 164
                                    455555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.71
                        Fer4_12  13 sgCnlsCkgCfn 24 
                                     g + sC+gC +
  gi|121639021|ref|YP_979245.1| 298 VGGSTSCPGCRA 309
                                    456778999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2557.18
//
Query:       gi|121639022|ref|YP_979246.1|  [L=468]
Description: acyl-CoA dehydrogenase fadE24 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-29  101.6   0.6    7.8e-29  100.8   0.6    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-21   76.7   0.1      8e-21   74.8   0.0    2.0  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    7.3e-14   52.2   0.1    1.9e-13   50.9   0.1    1.7  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    1.8e-12   47.3   0.0    3.4e-12   46.4   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.6   1.7e-32   7.8e-29       9     136 ..     337     464 ..     334     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.7e-32
                                    TTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHH CS
                  Acyl-CoA_dh_1   9 etlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraea 88 
                                    e+l+  Rl+ aa a+g+ +++l+ ++ y+++r+afg+p++  q+v++++a++a+el+++rl+++r a+++++g p   ea
  gi|121639022|ref|YP_979246.1| 337 EALALARLGWAALAVGTSHAVLDYVVPYVKQRQAFGEPIAHRQAVAFMCANIAIELDGLRLITWRGASRAEQGLPFAREA 416
                                    78999*************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS CS
                  Acyl-CoA_dh_1  89 smaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeG 136
                                    ++aK ++s+  +++  + +qllGg+Gy++e+pver+yrd r+  ++eG
  gi|121639022|ref|YP_979246.1| 417 ALAKRLGSDKGMQIGLDGVQLLGGHGYTKEHPVERWYRDLRAIGVAEG 464
                                    ******************************************999999 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.8e-24     8e-21       2     110 ..     111     220 ..     110     223 .. 0.91
   2 ?   -1.4   0.0      0.79   3.5e+03      61      80 ..     334     353 ..     304     371 .. 0.54

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.8e-24
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--..S-HHHHHHHHHHHHHH-HHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGag..ldyleaaivaeelaradagla 79 
                                    ++q+ + +tv efaee l+p a+++d+++++p +l  k+aelG+++i++pe++ G     + +++++vae la++d+gla
  gi|121639022|ref|YP_979246.1| 111 DDQKLIIETVDEFAEEVLRPAAHDADDAATYPSDLTAKAAELGITAINIPEDFDGIAehRSSVTNVLVAEALAYGDMGLA 190
                                    89************************999**************************875567******************9 PP

                                    HHHHHHHHTTHHHHHHHS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_N  80 lllgvhsslvapailrfGteeqkrryLpkla 110
                                    l + +  + va a+ ++G+++q++ yL+++a
  gi|121639022|ref|YP_979246.1| 191 LPILAPGG-VASALTHWGSADQQATYLKEFA 220
                                    96656555.5579**************9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                                    HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N  61 yleaaivaeelaradaglal 80 
                                      ++a+++  l+ a +++++
  gi|121639022|ref|YP_979246.1| 334 DYSEALALARLGWAALAVGT 353
                                    34444444444444444444 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   4.2e-17   1.9e-13       2     127 ..     345     460 ..     344     465 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 4.2e-17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                    g aa a+G  +a+l+ +v ++++r+   +ge++a ++a+ +  a++a +ld +r+++ r a+r    a++g ++     +
  gi|121639022|ref|YP_979246.1| 345 GWAALAVGTSHAVLDYVVPYVKQRQA--FGEPIAHRQAVAFMCANIAIELDGLRLITWRGASR----AEQGLPF----AR 414
                                    679***********************..***********************************....9*****9....99 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                    ea++a+ l ++   ++  + +++ Gg++++ke+p++R +RD++a++
  gi|121639022|ref|YP_979246.1| 415 EAALAKRLGSDKGMQIGLDGVQLLGGHGYTKEHPVERWYRDLRAIG 460
                                    9999999************************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   7.6e-16   3.4e-12       1      94 [.     228     314 ..     228     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 7.6e-16
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS-------EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpdrarglslflvprdapgvsvrrie 79 
                                    ++a+TEpq   d +++ktta+++   +y+l+G K  i  aa+a+l++v a+        ++  lf+v++ a+g++v+   
  gi|121639022|ref|YP_979246.1| 228 CVAITEPQPLFDPTRLKTTAVRTPS-GYRLDGVKSLIPAAADAELFIVGAQlG------GKPALFIVESAASGLTVKAD- 299
                                    99****************9966665.5************************33......44569************997. PP

                                    -BSS-TTS-EEEEEE CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvf 94 
                                    +++G+rg++ g++++
  gi|121639022|ref|YP_979246.1| 300 PSMGIRGAALGQVEL 314
                                    69*******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3190.83
//
Query:       gi|121639023|ref|YP_979247.1|  [L=401]
Description: acyl-CoA dehydrogenase fadE23 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-34  116.9   0.9    1.5e-33  116.1   0.9    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.2e-25   88.2   0.1    8.6e-25   86.8   0.0    1.8  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    5.2e-11   43.0   1.9    5.5e-11   42.9   0.4    1.9  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.9   2.5e-37   1.5e-33       1     150 []     241     393 ..     241     393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2.5e-37
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTS...B-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrr...kafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                    gkGf+ +met++++R+ vaa+a+g+ r+alee+++ +       ++ kp   + + + ++ +m+a++ea+ ll +raa++
  gi|121639023|ref|YP_979247.1| 241 GKGFAGVMETFDNTRPIVAAMAVGIGRAALEEIRSVLTGAgveISYDKPSHTQSAAAAEFLRMEADWEASYLLSLRAAWQ 320
                                    79******************************999865543338999********************************* PP

                                    -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                    +d++ p+++easm K++a ++a +v+ + ++l G+ Gy+e+  +e+++rd+++l i+eGt++iq +++arrll
  gi|121639023|ref|YP_979247.1| 321 ADNNIPNSKEASMSKAKAGRMASDVTCKTVELAGTTGYSEQSLLEKWARDSKILDIFEGTQQIQQLVVARRLL 393
                                    ***********************************************************************86 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.4   1.4e+04      57      68 ..      76      87 ..      67      98 .. 0.62
   2 !   86.8   0.0   1.4e-28   8.6e-25       1      96 [.     130     224 ..     130     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.4
                                   ----EEEEEEE. CS
                  Acyl-CoA_dh_M 57 rarglslflvpr 68
                                   +++g ++++v +
  gi|121639023|ref|YP_979247.1| 76 NHNGANMAAVVQ 87
                                   567777766543 PP

  == domain 2  score: 86.8 bits;  conditional E-value: 1.4e-28
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS---.----EEEEEEE..GGGEEE--- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpd.rarglslflvprdapgvsvrri 78 
                                    a+a+TEp+ Gsd a+v+t +a+ dg+eyv+nGeKi++t +  at+++v+a     ++ ++  ++ f+vpr +pgv+v+r+
  gi|121639023|ref|YP_979247.1| 130 AMAITEPEFGSDSAAVST-TATLDGDEYVINGEKIFVTAGSRATHIVVWATlD--KSlGRPAIKSFIVPREHPGVTVERL 206
                                    79****************.77788888************************43..334699******************* PP

                                    --BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  79 eeklGlrglptgelvfed 96 
                                    e+klG++g +t+ ++f++
  gi|121639023|ref|YP_979247.1| 207 EHKLGIKGSDTAVIRFDN 224
                                    ****************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2     7e+03      49      64 ..     112     127 ..     104     172 .. 0.58
   2 !   42.9   0.4   9.2e-15   5.5e-11       2     133 ..     257     381 ..     256     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  49 arldAAralleraaar 64 
                                     +  A  + ler  + 
  gi|121639023|ref|YP_979247.1| 112 ISAVATDEQLERLGKV 127
                                    4444444444444433 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 9.2e-15
                                    HHHHHHHHHHHHHHHHHHHHHH.HHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelar.ervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    ++aa+a+G+ raal+e+ ++ + + v+ s  ++   ++a+ ++  +++a+++A  +l +raa++    a++++++     
  gi|121639023|ref|YP_979247.1| 257 IVAAMAVGIGRAALEEIRSVLTgAGVEISYDKPSHTQSAAAAEFLRMEADWEASYLLSLRAAWQ----ADNNIPN----S 328
                                    589****************999566668999999******************************....9999998....9 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    +ea++++a a ++a +++ + +e+aG++++ ++s l+   RD +++ ++++++
  gi|121639023|ref|YP_979247.1| 329 KEASMSKAKAGRMASDVTCKTVELAGTTGYSEQSLLEKWARDSKILDIFEGTQ 381
                                    *********************************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2671.27
//
Query:       gi|121639024|ref|YP_979248.1|  [L=323]
Description: NADPH quinone oxidoreductase fadB4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-27   95.5   0.8    4.1e-27   94.7   0.2    1.8  2  ADH_zinc_N    Zinc-binding dehydrogenase
    5.2e-18   66.4   0.0    1.1e-17   65.3   0.0    1.6  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.2e-07   31.6   0.0    3.8e-07   30.0   0.0    1.8  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.017   15.3   1.5      0.031   14.4   1.5    1.4  1  DapB_N        Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   6.2e+03      54      76 ..      24      43 ..      16      45 .. 0.75
   2 !   94.7   0.2   9.1e-31   4.1e-27       1     127 [.     149     282 ..     149     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                   TTTSSEEEEEESSCSHHHHHHHH CS
                     ADH_zinc_N 54 tggegvdvvfecvGsgatleaal 76
                                   t    + vv+e+ ++g ++++al
  gi|121639024|ref|YP_979248.1| 24 T---SAGVVIEVHAAGVAFPDAL 43
                                   3...6789999999999999987 PP

  == domain 2  score: 94.7 bits;  conditional E-value: 9.1e-31
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    g+G+ ++ lA alGa +++av+s++ek+ela   Ga+ v+ + e  ++++++elt+g+gvd+v++ vG g+ ++++l++l
  gi|121639024|ref|YP_979248.1| 149 GIGTSTLRLAPALGAsRTVAVVSTQEKAELATVAGATDVVLA-E-GFKDAVQELTNGRGVDIVVDPVG-GDRFTDSLRSL 225
                                    8*****************************************.5.6**********************.*********** PP

                                    EEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSC........HHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgs........lreefkealdl 127
                                    + gGrl v+G+ +ge + +++++lll+++ ++G+ +g         l ++++++ +l
  gi|121639024|ref|YP_979248.1| 226 AAGGRLLVIGFTGGEIPtVKVNRLLLNNIDVVGVGWGAwslthpdaLAQQWSQLERL 282
                                    ***********5554445*******************97777666666666666655 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   2.4e-21   1.1e-17       2     133 .]     183     319 ..     182     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.4e-21
                                    T-SEEE.ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.......S-EEE-CHHHCTTT-EE CS
                   ADH_zinc_N_2   2 GAdevi.dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpp......lsaallkpakkrkgrsv 73 
                                    GA+ v+     ++++++ t+g+gvD+v+d vgg+ + ++sl+ l+ gGrl++ig +            + + ++    +v
  gi|121639024|ref|YP_979248.1| 183 GATDVVlAEGfKDAVQELTNGRGVDIVVDPVGGDRF-TDSLRSLAAGGRLLVIGFTGgeiptvK--VNRLLLNNIDVVGV 259
                                    78888855554566669*******************.****9**777***99995334665421..11111122223333 PP

                                    EE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                     +     ++++a a+   +l +l+ +Gkl p+   v+pl++aa A++ le++ a+GK+Vl
  gi|121639024|ref|YP_979248.1| 260 GWGAWSLTHPDALAQQWSQLERLLRSGKLPPPEPVVYPLDQAAAAIASLENRTAKGKVVL 319
                                    33333323344666669************9999988***********************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   8.4e-11   3.8e-07       4      62 ..      28      85 ..      25      96 .. 0.89
   2 ?    1.4   0.0     0.064   2.9e+02      83     108 ..      79     105 ..      72     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 8.4e-11
                                   EEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE- CS
                          ADH_N  4 vlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvve 62
                                   v+i+v+aag+   D  + +g+ +++ ++p++lG Ei+G+v ++ p+ ++++ GdrVv  
  gi|121639024|ref|YP_979248.1| 28 VVIEVHAAGVAFPDALLTRGRYQYRPEPPFVLGAEIAGVVRSA-PDNSQVRSGDRVVGL 85
                                   99*************************************9996.56689*******965 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.064
                                    TBEETTTS.S-SSSBSEEEECGGGEEE CS
                          ADH_N  83 eakllgvs.ldGgfaeyvvvpekklvk 108
                                      +++g++ l Gg+ae  v++ + ++k
  gi|121639024|ref|YP_979248.1|  79 GDRVVGLTmLTGGMAEVAVLSPERVFK 105
                                    567788888899***999998888776 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.5     7e-06     0.031       3     101 ..     141     239 ..     140     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7e-06
                                    EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH......-SEEEE-S- CS
                         DapB_N   3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek......advliDFTt 76 
                                    v+v+Ga+G +G++ ++++ +    + va+v+++e    + ++ +++g   ++v + + +++++++      +d+++D   
  gi|121639024|ref|YP_979248.1| 141 VLVHGAAGGIGTSTLRLAPALGASRTVAVVSTQE----KAELATVAG--ATDVVLAEGFKDAVQEltngrgVDIVVDPVG 214
                                    89*******************9*******99998....444444444..566666655555444444469999******* PP

                                    HHHHHHHHHHHHHTT-EEEE--SS- CS
                         DapB_N  77 peavlenlklalekgvklViGTTGl 101
                                     + + + l+ +++ g  lViG TG 
  gi|121639024|ref|YP_979248.1| 215 GDRFTDSLRSLAAGGRLLVIGFTGG 239
                                    *********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2395.34
//
Query:       gi|121639025|ref|YP_979249.1|  [L=142]
Description: hypothetical protein BCG_3165c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.046   12.3   0.0      0.058   12.0   0.0    1.1  1  EspG            EspG protein
       0.05   13.6   0.1      0.075   13.0   0.1    1.3  1  pPIWI_RE_REase  REase associating with pPIWI_RE


Domain annotation for each model (and alignments):
>> EspG  EspG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-06     0.058     117     173 ..      27      85 ..      21      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-06
                                    E---TTT-TGGGSS-EE--SC-EEEE-.-TT--SSS.HHHHHHHHHHHTTS-EEE--B- CS
                           EspG 117 lesneqnrLLksLPiqlhlpyikvhta.lveeelkd.aksmrellefasklstsiiPnd 173
                                    l+ +++n+L+ s+P ql lp i++  a +v ++ +d a+  r l +fa   +t+ + +d
  gi|121639025|ref|YP_979249.1|  27 LNFDDYNELVISVPLQLTLPAIETSPAeVVAIDPNDpADHERPLFDFAGATCTAFVWYD 85 
                                    67789******************99873467888773567789***********99887 PP

>> pPIWI_RE_REase  REase associating with pPIWI_RE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.3e-06     0.075      14      55 ..      74     115 ..      65     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-06
                 pPIWI_RE_REase  14 lglevelWpelDayDllvefpdgtvwavDvKdytspelLark 55 
                                    +g++++ +  +D+ Dl++ef+dg+++ v+  d+  +  L+ k
  gi|121639025|ref|YP_979249.1|  74 AGATCTAFVWYDTGDLHLEFSDGHQIDVHPDDRVTAWELYGK 115
                                    5889999******************99999998888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1090.66
//
Query:       gi|121639026|ref|YP_979250.1|  [L=133]
Description: response regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.015   15.4   0.0    1.2  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   8.4e-07     0.015      14      84 ..      27      99 ..      10     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-07
                                   HHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEEEEESSTSHH CS
                   Response_reg 14 lrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpviiltahseee 84
                                   l + l     ++ +  e+++g  +++++++  +dl +lD +     G+ ++k++++e  + +p+++lt++ +++
  gi|121639026|ref|YP_979250.1| 27 LGKRLHpdLPDL-TYVEVATGPMVIRQMDRGGIDLAILDGEATPTGGMGIAKQLKDELaSCPPILVLTGRPDDT 99
                                   444444433455.556899999********************************877747799*****987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1015.93
//
Query:       gi|121639027|ref|YP_979251.1|  [L=409]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-55  185.6  29.8    6.2e-55  185.6  29.8    1.8  2  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.6  29.8   3.5e-59   6.2e-55       1     157 [.       5     161 ..       5     162 .. 0.99
   2 ?   -2.3   0.2      0.24   4.3e+03      94     134 ..     264     303 ..     257     325 .. 0.61

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 3.5e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns +++ G+g +p+laAaaaWdgLa+el +aa++++sv+a+la++aWqGp++ amaaaaapy+ WL+aaaaq++
  gi|121639027|ref|YP_979251.1|   5 VLPPEINSLRMFIGAGTAPMLAAAAAWDGLAEELGTAAQSFASVTAGLAGQAWQGPAALAMAAAAAPYAGWLTAAAAQSA 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     aA qa+a+a+ +eaA aa+v pa +aanr ++++lv+tn+fGqn+p Iaa+e  yeemwa+d+aam++Y + ++a+
  gi|121639027|ref|YP_979251.1|  85 GAAGQARAVASIFEAAQAATVLPAAVAANRDAFVQLVMTNLFGQNAPLIAAAEGVYEEMWAADVAAMSGYYSGASAI 161
                                    **********************************************************************9999886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.24
                                    HHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHH CS
                            PPE  94 eaAlaamvppaeiaanraelaalvatnffGqntpaIaatea 134
                                    ++A+a +v+p  i a  a laal +    G n+++  ate 
  gi|121639027|ref|YP_979251.1| 264 TSAHAGVVSPGFIGAPLA-LAALGQMARGGTNSAPGTATES 303
                                    566666666666665433.4455566666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2922.11
//
Query:       gi|121639028|ref|YP_979252.1|  [L=128]
Description: NADH dehydrogenase subunit A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-34  116.0   1.9    1.3e-33  115.1   1.9    1.4  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
      0.057   14.2   8.2        1.4    9.7   4.6    2.1  2  DUF4282      Domain of unknown function (DUF4282)
       0.13   12.2   0.0       0.21   11.6   0.0    1.4  1  DUF2888      Protein of unknown function (DUF2888)
        2.2    8.7   7.9         23    5.4   0.1    2.1  2  DUF2628      Protein of unknown function (DUF2628)


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   1.9   2.9e-37   1.3e-33       2      99 .]      19     127 ..      18     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 2.9e-37
                                    HHHHHHHCHSS-----HHHHS-SSSS--SS---............--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..H CS
                    Oxidored_q4   2 llllllsallgpkkpnkeklspYEcGfepvgea...........rlrfsvkfylvallFliFDvevvflfpwavslkelg 70 
                                    ++ +++++l+gp++ n++k+++YEcG+ep ++             +rf++k+yl+a+lF++FD+e+vfl+pwavs+++lg
  gi|121639028|ref|YP_979252.1|  19 VVSVVIASLVGPSRFNRSKQAAYECGIEPASTGartsigpgaasGQRFPIKYYLTAMLFIVFDIEIVFLYPWAVSYDSLG 98 
                                    68899************************9854467888888889*********************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHH-S-XX CS
                    Oxidored_q4  71 lfgliemllFllillvglvYewkkgaLeW 99 
                                    +f+l+em++F+l+++v+++Y+w++g+L+W
  gi|121639028|ref|YP_979252.1|  99 TFALVEMAIFMLTVFVAYAYVWRRGGLTW 127
                                    ****************************9 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0034        15      16      39 ..       3      26 ..       2      57 .. 0.80
   2 ?    9.7   4.6   0.00032       1.4      14      67 ..      67     121 ..      60     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                        DUF4282 16 lYilgivlialvllslivgafaal 39
                                   +Yi ++vl+al++ +++v++++a+
  gi|121639028|ref|YP_979252.1|  3 VYIPILVLAALAAAFAVVSVVIAS 26
                                   799999999999999999998887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00032
                        DUF4282  14 kvlYilgivlialvllslivgafaal.seslsagggllllllaviafllmilllR 67 
                                    ++ Y+l ++l +++ + +++   +a+ ++sl+ ++++ + ++++++f++++ ++R
  gi|121639028|ref|YP_979252.1|  67 PIKYYLTAMLFIVFDIEIVFLYPWAVsYDSLGTFALVEMAIFMLTVFVAYAYVWR 121
                                    6678888888888888555555444448999999********************9 PP

>> DUF2888  Protein of unknown function (DUF2888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05      0.21      96     133 ..      39      76 ..      12      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                        DUF2888  96 whsecmyenletdggtvivpgeatgqrfgtatevptmf 133
                                       ec  e   t   t i pg a+gqrf     + +m+
  gi|121639028|ref|YP_979252.1|  39 AAYECGIEPASTGARTSIGPGAASGQRFPIKYYLTAML 76 
                                    346999**********************9887776664 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0052        23      41      63 ..       3      32 ..       2      51 .. 0.76
   2 ?    5.1   4.2    0.0066        30      40      91 ..      69     121 ..      66     122 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0052
                        DUF2628 41 lwlkalvllviavavsvvlavl.......g 63
                                    +++ lvl ++a a++vv++v+       +
  gi|121639028|ref|YP_979252.1|  3 VYIPILVLAALAAAFAVVSVVIaslvgpsR 32
                                   589999999999999999999865555553 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0066
                        DUF2628  40 klwlkalvllviavavsvvlavl.gfsdavrlllalliaillgleanslyylk 91 
                                    k++l a++++v  + ++     + ++++  +++l  +  ++l++ ++++y ++
  gi|121639028|ref|YP_979252.1|  69 KYYLTAMLFIVFDIEIVFLYPWAvSYDSLGTFALVEMAIFMLTVFVAYAYVWR 121
                                    89*********999988776655244444444333333334445588888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1011.98
//
Query:       gi|121639029|ref|YP_979253.1|  [L=184]
Description: NADH dehydrogenase subunit B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-25   86.9   0.1    1.3e-24   86.5   0.1    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   7.1e-29   1.3e-24       3     131 .]      37     146 ..      36     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 7.1e-29
                                    HHHHHHT-TTTTHHHHHHTEEEEEET.TT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                    Oxidored_q6   3 Gcsisllaleedlldllelielryhe.tlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                    +c i+++a+  + +d+      r+++ +++a+++         +ad+++v G v++k+++ l++++++++++k+v a+G 
  gi|121639029|ref|YP_979253.1|  37 CCAIEMMATAGPRFDI-----ARFGMeRFSATPR---------QADLMIVAGRVSQKMAPVLRQIYDQMAEPKWVLAMGV 102
                                    4999999999999999.....4444326677777.........9************************************ PP

                                    HHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                    Oxidored_q6  82 CAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetllal 131
                                    CA++GG++   nn++    v+++++vvpvdi++pGCPp+pe +l+++l+l
  gi|121639029|ref|YP_979253.1| 103 CASSGGMF---NNYAI---VQGVDHVVPVDIYLPGCPPRPEMLLHAILKL 146
                                    ********...54544...569***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1642.70
//
Query:       gi|121639030|ref|YP_979254.1|  [L=236]
Description: NADH dehydrogenase subunit C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-39  135.9   0.0    1.7e-39  135.2   0.0    1.4  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.021   14.3   1.9       0.03   13.8   1.9    1.1  1  DUF2336         Uncharacterised protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   0.0   1.9e-43   1.7e-39       2     120 ..      95     216 ..      94     218 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 1.9e-43
                                    E--HHHHHHHHHHHHH...TT--EEEEEEEEETT...SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHH CS
                 Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek...eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgad 78 
                                    +v+++ l++va+ l+de+el+f+++  +++v+++   +++++ vy l s+++n+r+r++v++++++p++pS+  ++p+ d
  gi|121639030|ref|YP_979254.1|  95 HVRRDLLPRVAQRLRDEPELRFELCLGVSGVHYPhetGRELHAVYPLQSITHNRRLRLEVSAPDSDPHIPSLFAIYPTND 174
                                    789999**************************999999************************999*************** PP

                                    HHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                 Complex1_30kDa  79 wyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                    w+ERE+yD+fGi f+ghp l+ri +p+d++ghP Rkd+pl g
  gi|121639030|ref|YP_979254.1| 175 WHERETYDFFGIIFDGHPALTRIEMPDDWQGHPQRKDYPLGG 216
                                    ***************************************976 PP

>> DUF2336  Uncharacterised protein conserved in bacteria (DUF2336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.9   3.4e-06      0.03      76     120 ..      74     118 ..      66     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-06
                        DUF2336  76 eragedealreaLlrRpdLpaavaerLlsrvsealrdrllarfal 120
                                    er + ++a+ + +++R++L ++v+++Ll rv+++lrd++  rf+l
  gi|121639030|ref|YP_979254.1|  74 ERVEFEDAVEKVVVYRDELTLHVRRDLLPRVAQRLRDEPELRFEL 118
                                    67888999*****************************99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1802.27
//
Query:       gi|121639031|ref|YP_979255.1|  [L=440]
Description: NADH dehydrogenase subunit D [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.7e-109  363.7   0.0     6e-109  363.3   0.0    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.3   0.0  3.4e-113    6e-109       2     271 .]     155     440 .]     154     440 .] 0.99

  Alignments for each domain:
  == domain 1  score: 363.3 bits;  conditional E-value: 3.4e-113
                                    TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHS CS
                 Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtk 81 
                                    lGa+t++++ fr Re +l l+e++tG R++++yir+GGva+Dlp+++ ++i+e+lk+l++ l+e+ +ll++n i+k+Rt+
  gi|121639031|ref|YP_979255.1| 155 LGAMTPMFVGFRAREIVLTLFEKITGLRMNSAYIRPGGVAQDLPPNAATEIAEALKQLRQPLREMGELLNENAIWKARTQ 234
                                    8******************************************************************************* PP

                                    SSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--. CS
                 Complex1_49kDa  82 gvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe 161
                                    gvg+l+ + +++lg+tGp+lR++G+++DlRk+epY++Y++++fdv++ +++D+y Ry++rv+Em++S+kI+eq+l+kl+ 
  gi|121639031|ref|YP_979255.1| 235 GVGYLDLTGCMALGITGPILRSTGLPHDLRKSEPYCGYQHYEFDVITDDSCDAYGRYMIRVKEMWESMKIVEQCLDKLRP 314
                                    ******************************************************************************** PP

                                    S-SB---TTTS---................GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSS CS
                 Complex1_49kDa 162 gpvlaedkkvalpk................keevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgss 225
                                    gp++++d+k a+p                  + + +smealihhfklvteg++vp+g+vy+avE+p+Gelgv++vsdg++
  gi|121639031|ref|YP_979255.1| 315 GPTMISDRKLAWPAdlqvgpdglgnspkhiAKIMGSSMEALIHHFKLVTEGIRVPAGQVYVAVESPRGELGVHMVSDGGT 394
                                    *************99**************999************************************************ PP

                                    S-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                 Complex1_49kDa 226 kpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                    +pyr+++r+psf+nlq+++++++g ++aD++a+++s+d+v+g vDR
  gi|121639031|ref|YP_979255.1| 395 RPYRVHYRDPSFTNLQSVAAMCEGGMVADLIAAVASIDPVMGGVDR 440
                                    *********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3308.12
//
Query:       gi|121639032|ref|YP_979256.1|  [L=252]
Description: NADH dehydrogenase subunit E [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-48  164.1   0.0    2.2e-48  163.8   0.0    1.1  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.29   11.3   0.0    1.3  1  DUF3653          Phage protein


Domain annotation for each model (and alignments):
>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0   2.4e-52   2.2e-48       2     144 ..      45     187 ..      44     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 2.4e-52
                                    HHHHTTS--GGGGHHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHTTSSSS-SS---SEEEEEE-SHHHHTTTH CS
                2Fe-2S_thioredx   2 keiiakypekrsaliplLklvQeeegwlpeealeevaellgvppaevyevatFYsmfnlkpvgkyviqvCtttpCalrgs 81 
                                    keii +yp++rsal+plL+lvQ e+ +l+++ l+ +a++lg++ aev +va+FY+m++++p+g+y + vCt+t Ca++g 
  gi|121639032|ref|YP_979256.1|  45 KEIIGRYPDRRSALLPLLHLVQGEDSYLTPAGLRFCADQLGLTGAEVSAVASFYTMYRRRPTGEYLVGVCTNTLCAVMGG 124
                                    89****************************************************************************** PP

                                    HHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEESSSSEEES-HHHHHHHHHHH CS
                2Fe-2S_thioredx  82 eeilealekklgikagettadgkftleeveClGaCanaPvvqindevyedltpekveeilekl 144
                                    ++i+++l+++lg+ ++ett+dg +tl+++eC +aC+ aPvv++n e+++++tpe+++e++++l
  gi|121639032|ref|YP_979256.1| 125 DAIFDRLKEHLGVGHDETTSDGVVTLQHIECNAACDYAPVVMVNWEFFDNQTPESARELVDSL 187
                                    ************************************************************987 PP

>> DUF3653  Phage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.3e-05      0.29      19      54 ..      71     107 ..      66     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                        DUF3653  19 LitPeGrrfspkeleslqwqidqarlwvklYrra.eg 54 
                                      tP+G+rf + +l  + +++     +  +Yrr+ +g
  gi|121639032|ref|YP_979256.1|  71 YLTPAGLRFCADQLGLTGAEVSAVASFYTMYRRRpTG 107
                                    57*******************************9633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1789.89
//
Query:       gi|121639033|ref|YP_979257.1|  [L=445]
Description: NADH dehydrogenase I subunit F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-45  154.1   0.0    3.5e-45  153.6   0.0    1.2  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
    9.9e-32  108.9   0.0    1.7e-31  108.1   0.0    1.4  1  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi
    4.6e-09   36.0   0.6      8e-09   35.2   0.0    1.7  2  SLBB          SLBB domain


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.0   5.8e-49   3.5e-45       1     151 [.      54     229 ..      54     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 5.8e-49
                   Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkk......kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvi 74 
                                    vk++g++GrGGagf t++K+++ ++ +       +yl+vNa+E+EPg++kD  lm  +ph ++eG++iaa+a++a+++++
  gi|121639033|ref|YP_979257.1|  54 VKDSGLRGRGGAGFATGTKWSFIPQGDTgaaakpHYLVVNADESEPGTCKDIPLMLATPHVLIEGVIIAAYAIRAHHAFV 133
                                    79*********************99777999999********************************************** PP

                   Complex1_51K  75 gvrdekpeaiealekalaeakaagl...........ldievvklagkYpaGeekaLiesltgr.evprgkpp..advgv. 139
                                    +vr+e   ++++l++a+aea+aag+           l++ v+++ag+Y++Gee+aL++sl+gr + pr +pp  a +g+ 
  gi|121639033|ref|YP_979257.1| 134 YVRGEVVPVLRRLHNAVAEAYAAGFlgrniggsgfdLELVVHAGAGAYICGEETALLDSLEGRrGQPRLRPPfpAVAGLy 213
                                    **********************************999**********************************987788889 PP

                   Complex1_51K 140 ....vvnNveTlaavy 151
                                        v+nNveT+a+v+
  gi|121639033|ref|YP_979257.1| 214 gcptVINNVETIASVP 229
                                    99************98 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   2.8e-35   1.7e-31       2      85 .]     340     423 ..     339     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 2.8e-35
                                    HHHHHHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHHHHH CS
                    NADH_4Fe-4S   2 varrllefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkFree 81 
                                    ++rr++efy++esCGkCtpCreGt +l ++ er+++g+g++ed+d+l +++++i g+s+Calgd+aa pv+s +++Fr+e
  gi|121639033|ref|YP_979257.1| 340 AVRRWTEFYKHESCGKCTPCREGTFWLDKIYERLETGRGSHEDIDKLLDISDSILGKSFCALGDGAASPVMSSIKHFRDE 419
                                    6899**************************************************************************** PP

                                    HHH. CS
                    NADH_4Fe-4S  82 feah 85 
                                    + ah
  gi|121639033|ref|YP_979257.1| 420 YLAH 423
                                    *998 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       1.2   7.1e+03       1       8 [.     132     139 ..     132     140 .. 0.86
   2 !   35.2   0.0   1.3e-12     8e-09       3      56 ..     254     300 ..     252     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                    EEEEESSB CS
                           SLBB   1 vVtVtGeV 8  
                                    +V+V GeV
  gi|121639033|ref|YP_979257.1| 132 FVYVRGEV 139
                                    59*****7 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 1.3e-12
                                    EEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.........-E.EEE-SSSSS- CS
                           SLBB   3 tVtGeVkrPgnyevpigttlsdlieqaGGltddadlksvnLarl.avipgGpmmg 56 
                                     ++G+V+rPg ye+p+g+tl++l++ aGG+   ++l      ++ +  pgG++++
  gi|121639033|ref|YP_979257.1| 254 SLSGHVTRPGQYEAPLGITLRELLDYAGGVRAGHRL------KFwT--PGGSSTP 300
                                    689***************************998883......4444..7887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3229.45
//
Query:       gi|121639034|ref|YP_979258.1|  [L=806]
Description: NADH dehydrogenase subunit G [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-20   71.4   0.3    1.8e-19   69.5   0.3    2.1  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    6.8e-16   58.2   0.0    2.3e-09   36.7   0.0    2.1  2  Molybdopterin    Molybdopterin oxidoreductase
    2.6e-15   55.7   0.6    5.7e-15   54.6   0.6    1.6  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    6.1e-10   39.1   0.0    1.9e-09   37.5   0.0    1.8  1  Molydop_binding  Molydopterin dinucleotide binding domain
    5.5e-07   29.4   0.3    5.5e-07   29.4   0.3    2.1  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
     0.0015   18.5   0.3     0.0015   18.5   0.3    2.0  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
       0.24   11.3   5.1        1.7    8.6   0.2    2.9  3  Fer4             4Fe-4S binding domain
          1   10.0   6.5        6.3    7.5   0.2    2.7  2  Fer4_7           4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.3   8.2e-23   1.8e-19       2      80 ..      15      90 ..      14      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 8.2e-23
                         Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepn.vracstpvedGlkvetq 80
                                   ++vtlt+DG e++vp+G+ v++A+   g+++pr c +      l+++g+Cr+ClVeveg+++ +++c+t ++d ++v+tq
  gi|121639034|ref|YP_979258.1| 15 EMVTLTIDGVEISVPKGTLVIRAAELMGIQIPRFCDH----PLLEPVGACRQCLVEVEGQRKpLASCTTVATDDMVVRTQ 90
                                   68***********************************....9****************988857***************9 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     1e-12   2.3e-09       2     152 ..     291     432 ..     291     442 .. 0.86
   2 !   19.4   0.0   1.8e-07   0.00041     349     413 ..     575     639 ..     492     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1e-12
                                    --S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                  Molybdopterin   2 lkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                    +++P++R +   +G +v+ sW  A+++ a+ l +     g +    +  g+ +  e  ++++k+++   g  ++ +d  a
  gi|121639034|ref|YP_979258.1| 291 ITTPLIRDGGDPKGALVPTSWSHAMAVAAQGLAA---ARGRTG---VLVGGRVTWEDAYAYAKFARITLG--TNDIDFRA 362
                                    589*****9999*****************99999...777744...5566667788999999********..78888888 PP

                                    GGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB- CS
                  Molybdopterin  82 dlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigprya 152
                                    +   a+ +  + +   +   +  + +dle + +++l+G  +  e pi+  r+rkaa++  + v  i p  +
  gi|121639034|ref|YP_979258.1| 363 RPHSAEEA-DFLAARIAGRHMAVSYADLESAPVVLLVGFEPEDESPIVFLRLRKAARRHRVPVYTIAPFAT 432
                                    88777665.44444566677778888********************************99******99876 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.8e-07
                                    HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESS CS
                  Molybdopterin 349 pevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqhlkqav 413
                                    +  d ad   v  al    +vv l+ r++   ++aD+++P a  + k + ++n egr   +++a 
  gi|121639034|ref|YP_979258.1| 575 EPADFADPDAVLAALDATGFVVSLELRHSAVTERADVVFPVAPTTQKAGAFVNWEGRYRTFEPAL 639
                                    555666777777799999***************************************99999886 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.6   2.5e-18   5.7e-15       2      40 .]     101     139 ..     100     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.5e-18
                NADH-G_4Fe-4S_3   2 ktilellLanHpldCltCdknGnCeLQdlayelgveesr 40 
                                     +++ellL+nHpldC+ Cdk+G+C LQ+ a+  g ++sr
  gi|121639034|ref|YP_979258.1| 101 HGVMELLLINHPLDCPMCDKGGECPLQNQAMSNGRTDSR 139
                                    579****************************99999876 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   8.5e-13   1.9e-09      27      82 ..     730     785 ..     721     799 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 8.5e-13
                                    SSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
                Molydop_binding  27 pep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82 
                                    +++ +vv+++p++Aa+ G +dG+ V+v+++rGs++++ +vt+ ++  vv++p +   
  gi|121639034|ref|YP_979258.1| 730 TARtPVVRLSPDTAAEIGAADGEAVTVSTSRGSITLPCSVTD-MPDRVVWLPLNSAG 785
                                    34445*************************************.********987755 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.3   2.5e-10   5.5e-07       2      77 ..      20      81 ..      19      87 .. 0.80
   2 ?   -3.1   0.2       3.7   8.2e+03      19      40 ..     103     124 ..      92     124 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.5e-10
                                   ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSS......SSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2  2 tidgkevevevadgettlldaaeenggidipysCgg......ggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                   tidg e++v+    +t++  aae   gi ip +C +      g+C+ Clvev+            g++    k  ++C+t++
  gi|121639034|ref|YP_979258.1| 20 TIDGVEISVPK---GTLVIRAAELM-GIQIPRFCDHpllepvGACRQCLVEVE------------GQR----KPLASCTTVA 81
                                   67777666665...777*****966.***************999******977............555....3457777765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                                    HHHHHHHTTTTTSTTSSSSSS.S CS
                           Fer2  19 lldaaeenggidipysCgggg.C 40 
                                    +++ +  n+ +d p  C  gg C
  gi|121639034|ref|YP_979258.1| 103 VMELLLINHPLDCP-MCDKGGeC 124
                                    66667666677777.77778878 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.5         3   6.7e+03       8      18 ..     115     127 ..     115     136 .. 0.72
   2 !   18.5   0.3   6.6e-07    0.0015       5      50 ..     237     282 ..     234     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                                    -SSB..TT--EEE CS
                 Molybdop_Fe4S4   8 CpyC..gvgCgle 18 
                                    Cp+C  g  C+l+
  gi|121639034|ref|YP_979258.1| 115 CPMCdkGGECPLQ 127
                                    9999555567765 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.6e-07
                                    EEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCH CS
                 Molybdop_Fe4S4   5 ktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtll 50 
                                    +++C+ C +gC  +   + gk+ +    +d +vne  +C KGr + 
  gi|121639034|ref|YP_979258.1| 237 PSVCEHCASGCAQRTDHRRGKVLRRLAGDDPEVNEEWNCDKGRWAF 282
                                    79*********************87777889***********9765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00078       1.7       3      15 ..     159     171 ..     157     173 .. 0.87
   2 ?    4.5   0.1     0.015        33      15      24 .]     211     220 ..     211     220 .. 0.88
   3 ?   -4.2   0.1         8   1.8e+04       6      11 ..     238     243 ..     237     245 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00078
                                    EETTTSSS-THHH CS
                           Fer4   3 ideekCigCGaCv 15 
                                     d e+Ci C +C 
  gi|121639034|ref|YP_979258.1| 159 LDRERCILCARCT 171
                                    699*********6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                    HHHSTTTEEE CS
                           Fer4  15 vevCPvgAIt 24 
                                    v++CPvgA+t
  gi|121639034|ref|YP_979258.1| 211 VQICPVGALT 220
                                    789*****86 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 8
                                    TTSSS- CS
                           Fer4   6 ekCigC 11 
                                    + C +C
  gi|121639034|ref|YP_979258.1| 238 SVCEHC 243
                                    567777 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.6      0.03        67      28      45 ..     146     171 ..     113     173 .. 0.54
   2 ?    7.5   0.2    0.0028       6.3       9      46 ..     211     249 ..     208     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.03
                         Fer4_7  28 t........ekveidpekClgCgaCv 45 
                                    t        ++v +d e+C+ C +C 
  gi|121639034|ref|YP_979258.1| 146 TfakpinisAQVLLDRERCILCARCT 171
                                    13334444466788999999999996 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                         Fer4_7   9 vaaCpvkaieldeeenekgtekveidpekClgCga.Cva 46 
                                    v+ Cpv+a++ + +   ++  +++ +p+ C +C + C++
  gi|121639034|ref|YP_979258.1| 211 VQICPVGALTGTAYRFRARPFDLVSSPSVCEHCASgCAQ 249
                                    578*******9977555555889999*******999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (806 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 5376.32
//
Query:       gi|121639035|ref|YP_979259.1|  [L=410]
Description: NADH dehydrogenase subunit H [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-122  409.0  20.3   1.1e-122  409.0  20.3    1.3  2  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.0  20.3  6.2e-127  1.1e-122       2     298 ..      15     334 ..      14     335 .. 0.98
   2 ?   -4.1   0.0      0.43   7.7e+03      11      18 ..     357     364 ..     342     375 .. 0.47

  Alignments for each domain:
  == domain 1  score: 409.0 bits;  conditional E-value: 6.2e-127
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHC CS
                         NADHdh   2 klllllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilall 81 
                                    k+++++v+l+l+v++++l+eRk+l+r+q R GPnrvGp G lq+laD++Kl lKe+i+p + d++++++ap++++i+a++
  gi|121639035|ref|YP_979259.1|  15 KAIAVFVFLMLTVLVAILAERKLLGRMQLRPGPNRVGPKGALQSLADGIKLALKESITPGGIDRFVYFVAPIISVIPAFT 94 
                                    57888999999999****************************************************************** PP

                                    TTTTS-SSS...........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         NADHdh  82 afaviPfge...........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllav 150
                                    afa+iPfg+           +++dl v++l+il ls++gvygi+l+Gwas+s+Y+llG++Rs+aq+isyEva+gls+ +v
  gi|121639035|ref|YP_979259.1|  95 AFAFIPFGPevsvfghrtplQITDLPVAVLFILGLSAIGVYGIVLGGWASGSTYPLLGGVRSTAQVISYEVAMGLSFATV 174
                                    ********66778889999************************************************************* PP

                                    HHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHH CS
                         NADHdh 151 vllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvl 230
                                    +l+ag++s+s+iv+aq+++w+++l l++f+i+li+++ etnraPFDlpeae ELvaGfhtEYs++kfa+f+laey+nm++
  gi|121639035|ref|YP_979259.1| 175 FLMAGTMSTSQIVAAQDGVWYAFLLLPSFVIYLISMVGETNRAPFDLPEAEGELVAGFHTEYSSLKFAMFMLAEYVNMTT 254
                                    *********************9999******************************************************* PP

                                    HHHHHHHHCT.SS-HCCS............HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                         NADHdh 231 vsalavllFlgGwllpfs............gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                    vsala++lF+gGw++p++            +l+wf++Kv+ +lf+++w+ratlpRlRydq+m lgwk l+p++l++++++
  gi|121639035|ref|YP_979259.1| 255 VSALAATLFFGGWHAPWPlnmwasantgwwPLIWFTAKVWGFLFIYFWLRATLPRLRYDQFMALGWKLLIPVSLVWVMVA 334
                                    *****************************************************************************986 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.43
                                    HHHHHHHH CS
                         NADHdh  11 llvvallt 18 
                                    ++v+a ++
  gi|121639035|ref|YP_979259.1| 357 IVVAAAMV 364
                                    11111333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2521.66
//
Query:       gi|121639036|ref|YP_979260.1|  [L=211]
Description: NADH dehydrogenase subunit I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   62.0  12.0    1.8e-09   37.0   1.1    2.2  2  Fer4      4Fe-4S binding domain
    1.4e-12   48.0   5.6      4e-12   46.5   6.0    1.6  1  Fer4_7    4Fe-4S dicluster domain
      2e-11   43.2  10.0    3.7e-06   26.7   1.5    2.3  2  Fer4_2    4Fe-4S binding domain
    2.7e-11   44.3   2.0    1.5e-05   25.8   0.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    5.8e-11   42.3  17.2    6.2e-08   32.6   9.4    2.0  2  Fer4_10   4Fe-4S dicluster domain
    7.9e-11   41.6  12.2    1.7e-05   24.6   1.6    2.2  2  Fer4_6    4Fe-4S binding domain
      2e-09   37.5  17.7    1.1e-07   31.8   8.8    2.0  2  Fer4_9    4Fe-4S dicluster domain
    4.3e-09   36.7   0.3     0.0013   19.1   0.0    2.3  2  Fer4_8    4Fe-4S dicluster domain
    9.4e-09   35.3  20.7      1e-06   28.8  11.0    2.1  2  Fer4_21   4Fe-4S dicluster domain
    1.7e-08   34.9   2.1     0.0051   17.3   0.2    2.2  2  Fer4_17   4Fe-4S dicluster domain
    9.1e-08   32.0   7.9     0.0016   18.8   1.2    2.2  2  Fer4_4    4Fe-4S binding domain
    3.3e-06   27.6  15.9     0.0012   19.7   3.9    2.3  2  Fer4_3    4Fe-4S binding domain
    7.6e-06   26.7   1.2      0.031   15.1   0.1    2.2  2  Fer4_22   4Fe-4S dicluster domain
      1e-05   26.0   7.6      0.021   15.3   1.5    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00023   21.3   1.8       0.21   11.8   0.3    2.2  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   15.5  11.7      0.059   14.1   0.3    2.9  3  Fer4_15   4Fe-4S single cluster domain
        1.6    9.3   9.1         18    6.1   3.4    2.5  2  AFP       Insect antifreeze protein repeat


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   3.9     3e-10   3.2e-07       6      24 .]      79      97 ..      77      97 .. 0.95
   2 !   37.0   1.1   1.7e-12   1.8e-09       1      24 []     119     142 ..     119     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3e-10
                                   TTSSS-THHHHHSTTTEEE CS
                           Fer4  6 ekCigCGaCvevCPvgAIt 24
                                   ekCigC +C+ +CP +AI+
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACPADAIY 97
                                   9*****************6 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.7e-12
                                    EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                    ++i++ +CigCG+C+e+CP+ A+t
  gi|121639036|ref|YP_979260.1| 119 YQINYLRCIGCGLCIEACPTRALT 142
                                    589*******************86 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   6.0   3.8e-15     4e-12       1      52 []      80     140 ..      80     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.8e-15
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.........ekveidpekClgCgaCvavCPtga 52 
                                    +CigC+ C+ aCp++ai+++ ++n ++          + ++i++ +C+gCg C+++CPt a
  gi|121639036|ref|YP_979260.1|  80 KCIGCELCAWACPADAIYVEGADNTEEErfspgerygRVYQINYLRCIGCGLCIEACPTRA 140
                                    7*****************99776665333455555557789*****************976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.7   2.1e-07   0.00023       7      22 .]      78      93 ..      74      93 .. 0.92
   2 !   26.7   1.5   3.5e-09   3.7e-06       2      22 .]     118     138 ..     117     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
                         Fer4_2  7 tdrCigCgaCvsaCPa 22
                                    ++CigC+ C +aCPa
  gi|121639036|ref|YP_979260.1| 78 LEKCIGCELCAWACPA 93
                                   58*************8 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.5e-09
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                    +++++  rCigCg C+ aCP+
  gi|121639036|ref|YP_979260.1| 118 VYQINYLRCIGCGLCIEACPT 138
                                    689*****************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   3.9e-06    0.0041       1      22 [.      80     101 ..      80     119 .. 0.80
   2 !   25.8   0.1   1.5e-08   1.5e-05       1      26 [.     125     150 ..     125     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                    +C++C+ Ca +CP++ai  + +
  gi|121639036|ref|YP_979260.1|  80 KCIGCELCAWACPADAIYVEGA 101
                                    5****************87733 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.5e-08
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                    rC++Cg C+e+CPt+a++++ ++e++
  gi|121639036|ref|YP_979260.1| 125 RCIGCGLCIEACPTRALTMTYDYELA 150
                                    6*****************99555553 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   9.4   5.8e-11   6.2e-08       7      56 .]      79     137 ..      76     137 .. 0.95
   2 !   21.5   0.9   1.8e-07   0.00019       4      23 ..     121     140 ..     118     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.8e-11
                        Fer4_10   7 dtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    ++Ci+C+ C  aCPad+         ++ + ++ + ++ + ++++ +C+gcg C+eaCP
  gi|121639036|ref|YP_979260.1|  79 EKCIGCELCAWACPADAiyvegadntEEERFSPGERYGRVYQINYLRCIGCGLCIEACP 137
                                    79*********************99988999999999999999***************9 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.8e-07
                        Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                    i+  +Ci+Cg C +aCP+ +
  gi|121639036|ref|YP_979260.1| 121 INYLRCIGCGLCIEACPTRA 140
                                    77889************965 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.4   1.1e-07   0.00011       7      24 .]      79      96 ..      78      96 .. 0.96
   2 !   24.6   1.6   1.6e-08   1.7e-05       4      24 .]     121     141 ..     120     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                         Fer4_6  7 dkCigCgdCvrvCPegai 24
                                   +kCigC+ C+ +CP++ai
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACPADAI 96
                                   79**************98 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-08
                         Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                    i++ +CigCg C+ +CP+ a+
  gi|121639036|ref|YP_979260.1| 121 INYLRCIGCGLCIEACPTRAL 141
                                    67779*************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.5   2.5e-06    0.0026      33      51 .]      70      96 ..      49      96 .. 0.72
   2 !   31.8   8.8   1.1e-10   1.1e-07       1      50 [.      80     140 ..      80     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                         Fer4_9 33 e........eaCigCgaCveaCpkgai 51
                                   +        e+CigC+ C+ aCp +ai
  gi|121639036|ref|YP_979260.1| 70 QlnrypdglEKCIGCELCAWACPADAI 96
                                   23334455599************9987 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.1e-10
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........eaCigCgaCveaCpkga 50 
                                    kC+gC  C  aCpa+++  + a ++ + r                +CigCg C+eaCp+ a
  gi|121639036|ref|YP_979260.1|  80 KCIGCELCAWACPADAIYVEGADNTEEERFSPGerygrvyqinyLRCIGCGLCIEACPTRA 140
                                    7****************8877777766554433799********99************986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.2e-05     0.013       2      63 ..      78      93 ..      43     120 .. 0.75
   2 !   19.1   0.0   1.2e-06    0.0013       4      34 ..     125     156 ..     122     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                   lekCi+C++C  aCp                                               
  gi|121639036|ref|YP_979260.1| 78 LEKCIGCELCAWACP----------------------------------------------A 93
                                   456666666666666..............................................3 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.2e-06
                         Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaae 34 
                                    +Ci+Cg+C +aCp+   t   +   a +++a+
  gi|121639036|ref|YP_979260.1| 125 RCIGCGLCIEACPTRALTMtYDYELADDNRAD 156
                                    8************7666554555555555554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.1   1.1e-06    0.0011      39      57 ..      79      96 ..      68      98 .. 0.84
   2 !   28.8  11.0   9.6e-10     1e-06       6      59 .]      79     143 ..      78     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                        Fer4_21 39 deCvGCnlCssvCPvedci 57
                                   ++C+GC+lC+  CP  d+i
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACPA-DAI 96
                                   89************5.887 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.6e-10
                        Fer4_21   6 dkCigCgkCliaCedtshqai...........eidaktvl..........kvvedeCvGCnlCssvCPvedciem 59 
                                    +kCigC++C+ aC+    +ai           +      +          ++   +C+GC lC++ CP+  +++m
  gi|121639036|ref|YP_979260.1|  79 EKCIGCELCAWACP---ADAIyvegadnteeeR------FspgerygrvyQINYLRCIGCGLCIEACPT-RALTM 143
                                    79************...6899554443333222......1444444544477788*************7.77776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     5e-06    0.0052      34      59 ..      68      94 ..      46      96 .. 0.68
   2 !   17.3   0.2   4.9e-06    0.0051       1      21 [.     125     145 ..     112     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5e-06
                        Fer4_17 34 leeaeke.ekaslCieCgeCerkCPqg 59
                                    ++ ++  +  ++Ci+C++C+ +CP++
  gi|121639036|ref|YP_979260.1| 68 RHQLNRYpDGLEKCIGCELCAWACPAD 94
                                   33333433699**************86 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.9e-06
                        Fer4_17   1 rCiqCgyClpeCpsyeaydne 21 
                                    rCi+Cg C+++Cp+ + + ++
  gi|121639036|ref|YP_979260.1| 125 RCIGCGLCIEACPTRALTMTY 145
                                    699999999999985554333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   5.7e-06     0.006       2      16 ..      79      93 ..      78     103 .. 0.91
   2 !   18.8   1.2   1.5e-06    0.0016       3      17 .]     125     139 ..     123     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-06
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   e+CigC  C  aCP 
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACPA 93
                                   89************5 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.5e-06
                         Fer4_4   3 rCigCgsCvaaCPqg 17 
                                    rCigCg C+ aCP++
  gi|121639036|ref|YP_979260.1| 125 RCIGCGLCIEACPTR 139
                                    8************75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   4.1   8.4e-05     0.089       1      15 []      81      95 ..      81      95 .. 0.95
   2 !   19.7   3.9   1.1e-06    0.0012       1      15 []     126     140 ..     126     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-05
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gC++C  +CP +A
  gi|121639036|ref|YP_979260.1| 81 CIGCELCAWACPADA 95
                                   ************887 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-06
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCg+C e+CP++A
  gi|121639036|ref|YP_979260.1| 126 CIGCGLCIEACPTRA 140
                                    ************998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00069      0.73      78      94 ..      77      93 ..      25      96 .. 0.76
   2 !   15.1   0.1   2.9e-05     0.031      76      94 ..     120     138 ..      99     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                        Fer4_22 78 gesgCvGCgRCieacpv 94
                                   g ++C+GC  C  acp+
  gi|121639036|ref|YP_979260.1| 77 GLEKCIGCELCAWACPA 93
                                   66789999999999997 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.9e-05
                        Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                    +++   C+GCg Cieacp+
  gi|121639036|ref|YP_979260.1| 120 QINYLRCIGCGLCIEACPT 138
                                    5678899999999999996 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.5     2e-05     0.021       4      18 ..      79      93 ..      76     105 .. 0.91
   2 !   14.1   0.5   4.9e-05     0.051       5      18 ..     125     138 ..     121     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                        Fer4_13  4 dtCiacgaCvelaPd 18
                                   ++Ci+c++C++++P 
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACPA 93
                                   79************5 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.9e-05
                        Fer4_13   5 tCiacgaCvelaPd 18 
                                    +Ci+cg+C e++P 
  gi|121639036|ref|YP_979260.1| 125 RCIGCGLCIEACPT 138
                                    7************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0015       1.6      53      74 ..      73      94 ..      47     102 .. 0.80
   2 !   11.8   0.3    0.0002      0.21      83      97 ..     124     138 ..     117     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                        Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                                   r  +g  +ci ce c   cP +
  gi|121639036|ref|YP_979260.1| 73 RYPDGLEKCIGCELCAWACPAD 94
                                   5567778999999999999975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                        Fer4_18  83 leciscllcidacdk 97 
                                    l ci c+lci+ac +
  gi|121639036|ref|YP_979260.1| 124 LRCIGCGLCIEACPT 138
                                    679999999999965 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   5.6      0.15   1.6e+02       6      19 ..      79      92 ..      77      93 .. 0.90
   2 ?    3.7   0.1       0.1   1.1e+02      57      66 .]      89      98 ..      88      98 .. 0.86
   3 ?   14.1   0.3   5.6e-05     0.059       6      21 ..     124     139 ..     120     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                        Fer4_15  6 daCigcglCvaeap 19
                                   ++Cigc+lC+ ++p
  gi|121639036|ref|YP_979260.1| 79 EKCIGCELCAWACP 92
                                   68********9998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                        Fer4_15 57 raCPvdAIrv 66
                                    aCP+dAI v
  gi|121639036|ref|YP_979260.1| 89 WACPADAIYV 98
                                   59******87 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.6e-05
                        Fer4_15   6 daCigcglCvaeapev 21 
                                     +CigcglC++++p++
  gi|121639036|ref|YP_979260.1| 124 LRCIGCGLCIEACPTR 139
                                    59***********986 PP

>> AFP  Insect antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3      0.02        21       2       8 ..      81      87 ..      81      90 .. 0.89
   2 ?    6.1   3.4     0.017        18       2      11 ..     126     135 ..     126     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                            AFP  2 CTgsknC 8 
                                   C+g+++C
  gi|121639036|ref|YP_979260.1| 81 CIGCELC 87
                                   ******* PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                            AFP   2 CTgsknCteA 11 
                                    C+g+++C eA
  gi|121639036|ref|YP_979260.1| 126 CIGCGLCIEA 135
                                    ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1456.47
//
Query:       gi|121639037|ref|YP_979261.1|  [L=262]
Description: NADH dehydrogenase subunit J [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-30  105.3  25.0      3e-30  104.9  25.0    1.2  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        1.3    8.9  13.1       0.45   10.4   9.2    1.9  2  DUF2723      Protein of unknown function (DUF2723)
        1.3    8.9   7.3        2.2    8.2   7.3    1.3  1  DUF5090      Domain of unknown function (DUF5090)
        2.3    7.4   5.5        3.3    6.8   5.5    1.2  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9  25.0   6.6e-34     3e-30       1     144 []      31     176 ..      31     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 6.6e-34
                                    HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHH CS
                    Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaal 80 
                                    ga++v+++ n vysa+fL+++++++a++++ ++a Fl+++q++vY+GA+++lflFv+ml+  ++ e+ +++ r++++aa+
  gi|121639037|ref|YP_979261.1|  31 GAVGVVLAVNAVYSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLMLIGVDSAESLKETLRGQRVAAV 110
                                    699*********************************************************9999**************** PP

                                    HHHHHHHHHHTT--........--..------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
                    Oxidored_q3  81 ligllllallllllles..sssav..daqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                                    l+g+++ +ll+ ++++   +   +   + ++ ++n+e ++ l+f++yl++fel+s lL++a +ga+vl
  gi|121639037|ref|YP_979261.1| 111 LTGVGFGVLLISTIGQVatR--GFagLTVANANGNVEGLAALIFSRYLWAFELTSALLITAAVGAMVL 176
                                    *************9998541..333445567789********************************97 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.2    0.0001      0.45      51     148 ..      15     121 ..       3     132 .. 0.85
   2 ?    0.1   0.1      0.15   6.6e+02      43      90 ..     159     180 ..     119     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                        DUF2723  51 saltilflfltitlllr.........skakkiailgaglvgalafafsdtfWfsaveaeVYalsslftalvlwlilkwee 121
                                    ++ +++f++l++  ll             +++++++++++ a+ +   d + +  v++ VY+ + +++ l + +++ +++
  gi|121639037|ref|YP_979261.1|  15 TGEAVMFWVLSALALLGavgvvlavnAVYSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLMLIGVDS 94 
                                    555667777777777767888887777888899999****************************9999999999999999 PP

                        DUF2723 122 eadekrsdrwlvliayligLslgvhll 148
                                    +++ k+  r   ++a+l+g+++gv l+
  gi|121639037|ref|YP_979261.1|  95 AESLKETLRGQRVAAVLTGVGFGVLLI 121
                                    99988899***************9776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                        DUF2723  43 vnllsalssaltilflfltitlllrskakkiailgaglvgalafafsd 90 
                                      l sa                          +l++++vga+++a  +
  gi|121639037|ref|YP_979261.1| 159 FELTSA--------------------------LLITAAVGAMVLAHRE 180
                                    333333..........................4444444444444444 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.3    0.0005       2.2      61     124 ..      28      91 ..      16      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                        DUF5090  61 kavllipiyllviaengnkldflksksriifltlikivlsilvdlvvyfselsslfkvflllki 124
                                      +  ++++l v a ++  +  + ++  ++f ++ +++   +v++vvy + ++ lf+++l+l +
  gi|121639037|ref|YP_979261.1|  28 ALLGAVGVVLAVNAVYSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLMLIG 91 
                                    445568888889899999888899999999999999************************9865 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.5   0.00073       3.3      83     129 ..      43      89 ..      10     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00073
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Herpes_LMP1  83 lcllllmitlllialwnlhgqalylgivlfifgcllvlglwiyllel 129
                                       ++l +t++++a++ +  +al+lg+v +++    v+ l++++l l
  gi|121639037|ref|YP_979261.1|  43 YSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLML 89 
                                    45678889999****************98887666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1404  (0.0783089); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1920.74
//
Query:       gi|121639038|ref|YP_979262.1|  [L=99]
Description: NADH dehydrogenase subunit K [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-24   84.7   9.3    3.4e-24   84.5   9.3    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        1.2    9.4   6.5        2.3    8.5   2.1    2.1  2  DUF1430      Protein of unknown function (DUF1430)


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   9.3   3.7e-28   3.4e-24       2     102 ..       6      93 ..       5      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.7e-28
                                    HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                    Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81 
                                    +l+l++llf+iG+ gvllrrn++ +++++el++navnl++v++++++             + + +q+++++ +v++a+e+
  gi|121639038|ref|YP_979262.1|   6 YLYLSVLLFTIGASGVLLRRNAIVMFMCVELMLNAVNLAFVTFARMH-------------GHLDAQMIAFFTMVVAACEV 72 
                                    6899******************************************9.............9******************* PP

                                    HHHHHHHHHHHHHSSS-BCCG CS
                    Oxidored_q2  82 avgLallvrlyreygtddvqe 102
                                    +vgLa++++++r++++ +v++
  gi|121639038|ref|YP_979262.1|  73 VVGLAIIMTIFRTRKSASVDD 93 
                                    ******************997 PP

>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.4    0.0045        41      42      80 ..       5      41 ..       2      52 .. 0.59
   2 ?    8.5   2.1   0.00026       2.3      49      91 ..      42      84 ..      31      99 .] 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0045
                        DUF1430 42 eyliiqlivllillvlifiltkekiillvvlvllliell 80
                                   +yl++++++++i++  ++   + + i+++++v l+++++
  gi|121639038|ref|YP_979262.1|  5 NYLYLSVLLFTIGASGVL--LRRNAIVMFMCVELMLNAV 41
                                   677777666666655555..4555566666666666555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00026
                        DUF1430 49 ivllillvlifiltkekiillvvlvlllielllillvqekiek 91
                                    + ++ ++ ++   + ++i+++++v++  e+++ l++ + i  
  gi|121639038|ref|YP_979262.1| 42 NLAFVTFARMHGHLDAQMIAFFTMVVAACEVVVGLAIIMTIFR 84
                                   33444444455555699*****************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 713.49
//
Query:       gi|121639039|ref|YP_979263.1|  [L=633]
Description: NADH dehydrogenase subunit L [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-82  275.9  14.1    3.6e-82  275.9  14.1    2.7  4  Proton_antipo_M  Proton-conducting membrane transporter
    4.1e-24   84.4   0.0    1.9e-23   82.3   0.0    2.3  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0008   19.0   0.3     0.0008   19.0   0.3    3.0  3  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
      0.004   16.8   0.0     0.0078   15.9   0.0    1.4  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.9  14.1   7.9e-86   3.6e-82       1     291 [.     140     427 ..     140     429 .. 0.97
   2 ?   -3.5   0.2         1   4.5e+03     103     126 ..     450     472 ..     436     496 .. 0.64
   3 ?   -3.0   0.0      0.73   3.3e+03      38      65 ..     508     535 ..     492     548 .. 0.66
   4 ?   -0.6   0.2      0.13   5.9e+02      73     104 ..     602     633 .]     585     633 .] 0.72

  Alignments for each domain:
  == domain 1  score: 275.9 bits;  conditional E-value: 7.9e-86
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    a++ +lly+g+E+v+l++ylLig+w++kp+++ A+ k+f+++++g+  L +g++l ++  gtl+   ++     +++   
  gi|121639039|ref|YP_979263.1| 140 ADNYVLLYVGWEGVGLASYLLIGFWYHKPSAATAAKKAFVMNRVGDAGLAVGMFLTFSTFGTLSYAGVFAG-VPAASRAV 218
                                    7899******************************************************************9.55667778 PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiisml 159
                                    l+++ ll+l+g+ +Ksaqvpl+ Wl da +e+Ptpvsal+ Aat+v+agv+l++r  +l+   +++++  ++i++++++l
  gi|121639039|ref|YP_979263.1| 219 LTAIGLLMLLGACAKSAQVPLQAWLGDA-MEGPTPVSALIhAATMVTAGVYLIVRSGPLYN-LAPTAQLAVVIVGAVTLL 296
                                    89999***********************.********************************.****************** PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLa 239
                                    +g++++ a+ diKr lA S+is++Gym++a+++ +  g++ ai+hllth++fka+lFl +g+vi+++++++d+r+yggL+
  gi|121639039|ref|YP_979263.1| 297 FGAIIGCAKDDIKRALAASTISQIGYMVLAAGL-GPAGYAFAIMHLLTHGFFKAGLFLGSGAVIHAMHEEQDMRRYGGLR 375
                                    *********************************.********************************************** PP

                Proton_antipo_M 240 kkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasv 291
                                     + P++++++ ++ l++ G+Pp+agF+sk++i+eaa+ ++ i   l+  a++
  gi|121639039|ref|YP_979263.1| 376 AALPVTFATFGLAYLAIIGVPPFAGFFSKDAIIEAALGAGGIRGSLLGGAAL 427
                                    *************************************999998888766555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1
                Proton_antipo_M 103 lWlpday.veaPtpvsallAatlvk 126
                                    +W+p a+  eaP++++  +  +l++
  gi|121639039|ref|YP_979263.1| 450 RWTPGAHpHEAPAVMTWPM--ILLA 472
                                    5777776445665554322..3333 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.73
                Proton_antipo_M  38 lflltllgsliLLlgilllynltgtlef 65 
                                    + + t l+  +  +gi++ y++ gt  +
  gi|121639039|ref|YP_979263.1| 508 TWVATTLALGVVAVGIAVAYRMYGTAPI 535
                                    4455666666666666666666666554 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.13
                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlW 104
                                     +++   +++ +l +l+ ++lv +a++ ++lW
  gi|121639039|ref|YP_979263.1| 602 RQMQTGFARNYALSMLVGAVLVAAALLVVQLW 633
                                    66777777888888888889999999999999 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   4.2e-27   1.9e-23       1      58 []      71     128 ..      71     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 4.2e-27
                Proton_antipo_N   1 lftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayls 58 
                                    +ftW+++ggl++++g+++D+ls++++l++++v++l+h+YS+gYMa+d+ ++RFf yl+
  gi|121639039|ref|YP_979263.1|  71 VFTWIPAGGLQVDFGLQIDQLSMCFVLLISGVGSLIHIYSVGYMAEDPDRRRFFGYLN 128
                                    69******************************************************97 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.82   3.7e+03      58      82 ..     277     301 ..     263     323 .. 0.64
   2 !   19.0   0.3   1.8e-07    0.0008       1      48 [.     436     483 ..     436     533 .. 0.80
   3 ?   -0.9   0.1      0.23     1e+03     143     176 ..     589     622 ..     586     627 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.82
                        NADH5_C  58 itlplllKllallvtilGlllglel 82 
                                     +l +++ l++++v  + ll+g ++
  gi|121639039|ref|YP_979263.1| 277 YNLAPTAQLAVVIVGAVTLLFGAII 301
                                    5555555555555555555555544 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-07
                        NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGslls 48 
                                    Y +R+++++++g+ r  +  + +e    ++ p+++La+gs+++G ll 
  gi|121639039|ref|YP_979263.1| 436 YMTRVMLMTFFGEKRWTPGAHPHEAPAVMTWPMILLAVGSVFSGGLLA 483
                                    889*****************************************8885 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.23
                        NADH5_C 143 glaklllklskliqnlqkglikiyLlsflltlll 176
                                    +la+l++++s+ + ++q+g  + y ls+l+  +l
  gi|121639039|ref|YP_979263.1| 589 ALATLVSQTSNRLRQMQTGFARNYALSMLVGAVL 622
                                    578889999***************9888776555 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.7e-06    0.0078      79     179 ..     441     532 ..     432     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                Proton_antipo_C  79 ititefenkktl..syPhEsdntmlfpllvLvlftlfvGliGipfnqegidldilskwLtpsinllhknsnesvdwyefl 156
                                    + +t f +k+ +    PhE++  m+ p+++L++ ++f G + +           l +wL+p++   +++++    w    
  gi|121639039|ref|YP_979263.1| 441 MLMTFFGEKRWTpgAHPHEAPAVMTWPMILLAVGSVFSGGLLAV-------GGTLRHWLQPVVGSHEEATHALPTW---- 509
                                    4556677766333589*********************9865332.......23699******99988888875555.... PP

                Proton_antipo_C 157 tnaifSvsialfGifiAsllYkp 179
                                    + +++ +++  +Gi +A+ +Y+ 
  gi|121639039|ref|YP_979263.1| 510 VATTLALGVVAVGIAVAYRMYGT 532
                                    568899***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4087.06
//
Query:       gi|121639040|ref|YP_979264.1|  [L=553]
Description: NADH dehydrogenase subunit M [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-65  221.8  22.3    2.3e-65  220.7  22.3    1.5  1  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
      0.029   14.4   3.3      0.096   12.8   0.6    3.4  3  CrgA             Cell division protein CrgA
      0.075   13.1   0.0      0.075   13.1   0.0    3.7  4  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.7  22.3   3.8e-69   2.3e-65       1     292 [.     160     459 ..     160     460 .. 0.93

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 3.8e-69
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg.....tlefeelskal... 72 
                                    a d+ll+y+++E++l+p+y+Lig +++ + +++A++k++l++l+g li+L +++ ly +t      t +f+e++  +   
  gi|121639040|ref|YP_979264.1| 160 ALDVLLFYVFFEAMLIPMYFLIGGFGQGAGRSRAAVKFLLYNLFGGLIMLAAVIGLYVVTAqydsgTFDFREIVAGVaag 239
                                    679******************************************************998767777*********99988 PP

                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla.vssneisqll 150
                                      g++   + +l+l +++++++K++++p+h+Wlpda ve +tp +a l  a++ k+g ++++r  l l+   s   + l+
  gi|121639040|ref|YP_979264.1| 240 RYGADPAVFKALFLGFMFAFAIKAPLWPFHRWLPDAAVE-STPATAVLmMAVMDKVGTFGMLRYCLQLFpDPSTYFRPLI 318
                                    8899999999**************************555.5666665559*************9988886889999**** PP

                Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektr 230
                                    ++laii++++g++va+ qtd+ rl+Ay sish G+++ +++v+t +g +++ +++l h+l++a++Fl+ag +i +r  +r
  gi|121639040|ref|YP_979264.1| 319 VTLAIIGVIYGAIVAIGQTDMMRLIAYTSISHFGFIIAGIFVMTTQGQSGSTLYMLNHGLSTAAVFLIAGFLI-ARRGSR 397
                                    *********************************************************************6665.555*** PP

                Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvl 292
                                    +i++ygg +k+ Pila +++v +++++ lP++a F+s+fl+L + ++ +++++++ v+a vl
  gi|121639040|ref|YP_979264.1| 398 SIADYGGVQKVAPILAGTFMVSAMATVSLPGLAPFISEFLVLLGTFSRYWLAAAFGVTALVL 459
                                    ***********************************************999988877777666 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         2   1.2e+04      38      46 ..     207     215 ..     188     222 .. 0.55
   2 ?   -2.3   0.0      0.81   4.8e+03      28      43 ..     242     257 ..     235     258 .. 0.82
   3 ?   12.8   0.6   1.6e-05     0.096      32      85 ..     312     363 ..     308     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                           CrgA  38 mlglmllGl 46 
                                    ++   ++Gl
  gi|121639040|ref|YP_979264.1| 207 IMLAAVIGL 215
                                    222333333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.81
                           CrgA  28 kpsprwyvpvmlglml 43 
                                      +p ++++++lg+m 
  gi|121639040|ref|YP_979264.1| 242 GADPAVFKALFLGFMF 257
                                    578999*******996 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 1.6e-05
                           CrgA  32 rwyvpvmlglmllGllwlvvyYlageeipfmaelgawNlliGfgliivG.llmtt 85 
                                    +++ p++++l ++G+++  ++ + +++   m+ l a+  +  fg+ii+G ++mtt
  gi|121639040|ref|YP_979264.1| 312 TYFRPLIVTLAIIGVIYGAIVAIGQTD---MMRLIAYTSISHFGFIIAGiFVMTT 363
                                    6789****************9999875...559****************445555 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.075      51      83 ..      73     105 ..      32     111 .. 0.87
   2 ?   -0.6   0.4      0.24   1.4e+03      28      46 ..     159     177 ..     142     217 .. 0.63
   3 ?   -2.2   0.4      0.73   4.4e+03      31      54 ..     352     375 ..     321     386 .. 0.48
   4 ?   -0.6   0.2      0.24   1.4e+03      11      46 ..     437     471 ..     429     504 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                  Oxidored_q5_N  51 snlsyllglDslSapLilLSlWllpLmilASqk 83 
                                       +y+lg+D + + L+lL++ l+pL ++A ++
  gi|121639040|ref|YP_979264.1|  73 FGAGYTLGVDGIAVVLVLLTTVLIPLLLVAGWN 105
                                    567899***********************9776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                  Oxidored_q5_N  28 tlvslllallsllllnlss 46 
                                    +++ +ll+ +++  +  ++
  gi|121639040|ref|YP_979264.1| 159 IALDVLLFYVFFEAMLIPM 177
                                    3333333333333222222 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.73
                  Oxidored_q5_N  31 slllallsllllnlsssfslsnls 54 
                                     +++a +++++ + +s ++l++l+
  gi|121639040|ref|YP_979264.1| 352 GFIIAGIFVMTTQGQSGSTLYMLN 375
                                    222222222233333334444444 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.24
                  Oxidored_q5_N  11 liplvllskkkllwststlvslllallsllllnlss 46 
                                    l++l  +s+  +l +++ +  l+l+++ +l+l++  
  gi|121639040|ref|YP_979264.1| 437 LVLLGTFSR-YWLAAAFGVTALVLSAVYMLWLYQRV 471
                                    444444433.36656666666666666666877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3606.14
//
Query:       gi|121639041|ref|YP_979265.1|  [L=531]
Description: NADH dehydrogenase subunit N [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-70  235.9  17.2    9.9e-70  235.0  17.2    1.4  1  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.0  17.2   5.5e-74   9.9e-70       1     290 [.     169     465 ..     169     468 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.0 bits;  conditional E-value: 5.5e-74
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkk.pksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsl 79 
                                    +ndLl+++++lE+ +lplyl+ gl++++   s eA++k+fll++++s ++L+g++lly++tgtl ++ +  al +  + +
  gi|121639041|ref|YP_979265.1| 169 SNDLLTMFVALEVLSLPLYLMCGLARNRrLLSQEAAMKYFLLGAFSSAFFLYGVALLYGATGTLTLPGIRDALAARTDDS 248
                                    79*********************9876516899*********************************************** PP

                Proton_antipo_M  80 elllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisqlllilaiis 157
                                    ++l++  ll vgll+K+++vp+h W+pd+y++aPtp++ ++Aa + k+++++ + +++ +a      +++ +l ++ai++
  gi|121639041|ref|YP_979265.1| 249 MALAGVALLAVGLLFKVGAVPFHSWIPDVYQGAPTPITGFMAA-ATKVAAFGALLRVVYVAlpPLHDQWRPVLWAIAILT 327
                                    *****************************************65.777777776555555544899*************** PP

                Proton_antipo_M 158 mllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyere....ktrdir 233
                                    m +g++ a++qt++Kr+lAySs++h+G++l ++++++  g++a +++l+++++++++ F+++g v  +      +  d+ 
  gi|121639041|ref|YP_979265.1| 328 MTVGTVTAVNQTNVKRMLAYSSVAHVGFILTGVIADNPAGLSATLFYLVAYSFSTMGAFAIVGLVRGADGsagsEDADLS 407
                                    *****************************************************************8875556667889** PP

                Proton_antipo_M 234 ayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvas 290
                                      +gL ++ Pi+ ++l ++ll+ aG+P+t+gF+skf+++ aa +++++ lv++ v++s
  gi|121639041|ref|YP_979265.1| 408 HWAGLGQRSPIVGVMLSMFLLAFAGIPLTSGFVSKFAVFRAAASAGAVPLVIVgVISS 465
                                    ************************************************9999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3494.65
//
Query:       gi|121639042|ref|YP_979266.1|  [L=589]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-61  203.6 329.9    9.7e-09   35.0  15.7   11.7 12  Pentapeptide_2  Pentapeptide repeats (8 copies)
    1.9e-53  180.8  32.4    2.7e-53  180.3  32.4    1.2  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3  20.9   2.4e-09   2.1e-05       8      40 .]     186     218 ..     184     218 .. 0.72
   2 !   31.0  31.6   1.8e-11   1.6e-07       1      40 []     209     248 ..     209     248 .. 0.98
   3 !   32.6  35.2   5.9e-12   5.3e-08       1      39 [.     249     287 ..     249     288 .. 0.99
   4 !   31.7  33.6   1.1e-11     1e-07       1      40 []     259     298 ..     259     298 .. 0.98
   5 !   20.7  39.0   3.1e-08   0.00028       1      39 [.     289     327 ..     289     337 .. 0.98
   6 !   29.8  33.5   4.6e-11   4.1e-07       3      40 .]     338     375 ..     336     375 .. 0.97
   7 !   32.8  28.4   5.1e-12   4.6e-08       2      40 .]     377     415 ..     376     415 .. 0.98
   8 !   13.4  31.9   5.8e-06     0.052       3      40 .]     418     455 ..     406     455 .. 0.82
   9 !   35.0  15.7   1.1e-12   9.7e-09       2      37 ..     447     482 ..     446     484 .. 0.96
  10 !   14.1  20.8   3.5e-06     0.031       3      38 ..     491     526 ..     490     526 .. 0.97
  11 !   19.3  16.0   8.3e-08   0.00075       5      39 ..     525     559 ..     525     559 .. 0.97
  12 !   21.9  10.3   1.4e-08   0.00012       3      36 ..     553     586 ..     551     587 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.4e-09
                 Pentapeptide_2   8 sGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G gN+G +NlG gNtG +NlGsgN+G+ n+Gs
  gi|121639042|ref|YP_979266.1| 186 IGLGNIGVGNLGGGNTGEYNLGSGNSGNANVGS 218
                                    577777777777777777777777777777774 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.8e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+GsgN+G++N+GsgN G +NlGsgN+G++n+Gs
  gi|121639042|ref|YP_979266.1| 209 GNSGNANVGSGNSGNANVGSGNDGATNLGSGNIGNTNLGS 248
                                    8*************************************96 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 5.9e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+GsgN Gf+NlG+gN+Gs+NlGsgNtGs+n+G
  gi|121639042|ref|YP_979266.1| 249 GNVGNVNLGSGNRGFGNLGNGNFGSGNLGSGNTGSTNFG 287
                                    8*************************************9 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 1.1e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN G++N+G+gN+G++NlGsgNtGs+N+G gN Gs+n+Gs
  gi|121639042|ref|YP_979266.1| 259 GNRGFGNLGNGNFGSGNLGSGNTGSTNFGGGNLGSFNLGS 298
                                    8*************************************96 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 3.1e-08
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN Gs+N+GsgN+G+ N+G+gN G++NlG gN G++n+G
  gi|121639042|ref|YP_979266.1| 289 GNLGSFNLGSGNIGSSNIGFGNNGDNNLGLGNNGNNNIG 327
                                    8*************************************9 PP

  == domain 6  score: 29.8 bits;  conditional E-value: 4.6e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G lNsG gN+Gf+N+G+ N+G+fN+G++N+G++n+G+
  gi|121639042|ref|YP_979266.1| 338 IGALNSGIGNLGFGNSGNNNIGFFNSGNNNVGFFNSGN 375
                                    8************************************6 PP

  == domain 7  score: 32.8 bits;  conditional E-value: 5.1e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G++N+G  NtGf+N G +NtG++N+G++N+G+gn+G+
  gi|121639042|ref|YP_979266.1| 377 NFGFGNAGDINTGFGNAGDTNTGFGNAGFFNMGIGNAGN 415
                                    9************************************96 PP

  == domain 8  score: 13.4 bits;  conditional E-value: 5.8e-06
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +G++N Gs+N+G +N G+ ++G++N+G+ N+G+ n+Gs
  gi|121639042|ref|YP_979266.1| 418 MGVGNGGSFNVGVGNAGNQSVGFGNAGTLNVGFANAGS 455
                                    58888888888888888888888888888888888885 PP

  == domain 9  score: 35.0 bits;  conditional E-value: 1.1e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgn 37 
                                    N+G++N+Gs NtGf+N+Gs NtG f +G+ NtG+g 
  gi|121639042|ref|YP_979266.1| 447 NVGFANAGSINTGFANSGSINTGGFDSGDRNTGFGS 482
                                    9*********************************97 PP

  == domain 10  score: 14.1 bits;  conditional E-value: 3.5e-06
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    +G++N+G   +GffN+G+++ G +N G++ +G++nt
  gi|121639042|ref|YP_979266.1| 491 SGFGNTGMNSSGFFNTGNVSAGYGNNGDVQSGINNT 526
                                    59********************************97 PP

  == domain 11  score: 19.3 bits;  conditional E-value: 8.3e-08
                 Pentapeptide_2   5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    ++NsG +N+Gf+N+G g +G +N+G   tG+ n+G
  gi|121639042|ref|YP_979266.1| 525 NTNSGGFNVGFYNSGAGTVGIANSGLQTTGIANSG 559
                                    58*******************************99 PP

  == domain 12  score: 21.9 bits;  conditional E-value: 1.4e-08
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36 
                                    tG++NsG+ NtG +N+G  + G fN Gs  +G++
  gi|121639042|ref|YP_979266.1| 553 TGIANSGTLNTGVANTGDHSSGGFNQGSDQSGFF 586
                                    8999999999999999999999999999999987 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3  32.4     3e-57   2.7e-53       1     158 []       5     161 ..       5     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 3e-57
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns ++++G+gs+p+laA  aWd+Laaela aa+++ sv+++la+++WqG++ aamaaaaapy+ WL+aaaa+a+
  gi|121639042|ref|YP_979266.1|   5 VLPPEINSLRMFTGAGSAPMLAASVAWDRLAAELAVAASSFGSVTSGLAGQSWQGAA-AAMAAAAAPYAGWLAAAAARAA 83 
                                    59*****************************************************75.689******************* PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     a  qa+a+a+a+eaA+aa+v+p ++aanr+++++lv +n+fGqn+paIaa+ea ye+mwa+d+aam +Y+  ++aaa
  gi|121639042|ref|YP_979266.1|  84 GASVQAKAVASAFEAARAATVHPMLVAANRNAFVQLVLSNLFGQNAPAIAAAEAMYEQMWAADVAAMVGYHGGASAAA 161
                                    *************************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4178.96
//
Query:       gi|121639043|ref|YP_979267.1|  [L=633]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-62  207.6 351.0    4.3e-09   36.1  22.9   12.1 13  Pentapeptide_2  Pentapeptide repeats (8 copies)
    1.1e-55  188.1  34.1    1.1e-55  188.1  34.1    1.5  2  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  20.8   2.5e-10   2.2e-06       6      39 ..     208     241 ..     207     242 .. 0.94
   2 !   29.3  34.7   6.4e-11   5.7e-07       1      40 []     233     272 ..     233     272 .. 0.98
   3 !   29.1  35.2   7.5e-11   6.7e-07       1      40 []     243     282 ..     243     282 .. 0.98
   4 ?   -6.0  58.9         2   1.8e+04       4      39 ..     287     323 ..     258     324 .. 0.75
   5 !   34.7  24.1   1.4e-12   1.2e-08       3      39 ..     297     333 ..     296     334 .. 0.97
   6 !   20.3  35.2   4.3e-08   0.00038       2      39 ..     321     358 ..     321     363 .. 0.98
   7 !   33.4  31.2   3.4e-12   3.1e-08       3      39 ..     364     400 ..     362     401 .. 0.96
   8 !   29.5  31.2   5.4e-11   4.9e-07       1      39 [.     402     440 ..     402     441 .. 0.98
   9 !   23.7  23.2   3.6e-09   3.3e-05       1      39 [.     437     475 ..     437     477 .. 0.86
  10 !   36.1  22.9   4.8e-13   4.3e-09       1      38 [.     478     515 ..     478     516 .. 0.97
  11 !    4.4  16.7    0.0039        35      14      38 ..     524     548 ..     520     550 .. 0.72
  12 !   31.4  19.8   1.4e-11   1.3e-07       3      39 ..     557     593 ..     556     594 .. 0.97
  13 !   18.0  11.7   2.2e-07     0.002       3      36 ..     597     630 ..     595     631 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.5e-10
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    lN+G gN+G++NlG gN+G  NlGsgN+Gs+n+G
  gi|121639043|ref|YP_979267.1| 208 LNTGLGNIGSWNLGGGNVGLLNLGSGNFGSLNLG 241
                                    79*****************************998 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 6.4e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+GslN+G gNtG++NlG gN G++NlGsgN+G++n+G+
  gi|121639043|ref|YP_979267.1| 233 GNFGSLNLGGGNTGNANLGGGNWGFANLGSGNIGNTNFGN 272
                                    8**************************************6 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 7.5e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gNtG++N+G gN+Gf+NlGsgN+G++N+G+gN G++n+Gs
  gi|121639043|ref|YP_979267.1| 243 GNTGNANLGGGNWGFANLGSGNIGNTNFGNGNQGNLNFGS 282
                                    8**************************************6 PP

  == domain 4  score: -6.0 bits;  conditional E-value: 2
                 Pentapeptide_2   4 GslNsGsgN.tGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    G++N+G gN +G++NlGsgN+Gs+NlGsgN+Gs+n+G
  gi|121639043|ref|YP_979267.1| 287 GNGNFGFGNaFGDGNLGSGNVGSTNLGSGNFGSFNVG 323
                                    7777777775577788888888888888888888887 PP

  == domain 5  score: 34.7 bits;  conditional E-value: 1.4e-12
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G++N+GsgN+G+ NlGsgN+GsfN+GsgN+G+ n+G
  gi|121639043|ref|YP_979267.1| 297 FGDGNLGSGNVGSTNLGSGNFGSFNVGSGNMGMSNIG 333
                                    79**********************************9 PP

  == domain 6  score: 20.3 bits;  conditional E-value: 4.3e-08
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+Gs+N+G  N+Gf+NlG+ N G++N G++N+G+g tG
  gi|121639043|ref|YP_979267.1| 321 NVGSGNMGMSNIGFGNLGNNNLGFGNNGNNNIGFGLTG 358
                                    9***********************************99 PP

  == domain 7  score: 33.4 bits;  conditional E-value: 3.4e-12
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G lNsG gN+Gf+N+G+ N+G+fN+G+gN+G++n+G
  gi|121639043|ref|YP_979267.1| 364 IGALNSGIGNMGFGNSGNNNIGFFNSGNGNVGFFNSG 400
                                    8***********************************9 PP

  == domain 8  score: 29.5 bits;  conditional E-value: 5.4e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gNtG++N+G +NtGf+N G  NtG++N G+ N+G+gn+G
  gi|121639043|ref|YP_979267.1| 402 GNTGFGNAGDVNTGFWNGGPFNTGFGNGGNTNFGFGNAG 440
                                    8*************************************9 PP

  == domain 9  score: 23.7 bits;  conditional E-value: 3.6e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN G+ N+G gN G +N+GsgN G +N+G++N+G + +G
  gi|121639043|ref|YP_979267.1| 437 GNAGFQNMGHGNAGGVNVGSGNAGLANTGDFNSGGVVSG 475
                                    799999999999999999999999999999999987766 PP

  == domain 10  score: 36.1 bits;  conditional E-value: 4.8e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    gNtGs+NsG+ NtGf+N G  NtG fN+G++NtG+g t
  gi|121639043|ref|YP_979267.1| 478 GNTGSFNSGNLNTGFGNAGDLNTGLFNSGDVNTGIGST 515
                                    8*********************************9975 PP

  == domain 11  score: 4.4 bits;  conditional E-value: 0.0039
                 Pentapeptide_2  14 GffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    Gf+N+G+   G++N+G+  +G+gn 
  gi|121639043|ref|YP_979267.1| 524 GFGNTGTSVSGFNNSGNLTSGFGNM 548
                                    7777777777777777777777775 PP

  == domain 12  score: 31.4 bits;  conditional E-value: 1.4e-11
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G+ N+G +N+GffN+G+ N G+fN+G +N G+ n+G
  gi|121639043|ref|YP_979267.1| 557 SGFQNIGDANVGFFNSGNSNEGFFNTGMFNNGIYNSG 593
                                    59**********************************9 PP

  == domain 13  score: 18.0 bits;  conditional E-value: 2.2e-07
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsg 36 
                                    tG++NsG++ +G +N+G  + G fN G++  G++
  gi|121639043|ref|YP_979267.1| 597 TGIANSGNASSGVANSGDNSSGAFNQGDNQAGFF 630
                                    8999999999999999999999999999999987 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1  34.1   1.2e-59   1.1e-55       1     158 []       5     162 ..       5     162 .. 0.99
   2 ?   -4.2   1.2       1.8   1.6e+04      16      96 ..     188     199 ..     179     208 .. 0.50

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 1.2e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns ++++G+gs+p+laA  aWdgLaaela aa+++ sv+++la+++WqG+++aamaaaaapy+ WL+aaaa+a+
  gi|121639043|ref|YP_979267.1|   5 VLPPEINSLRMFTGAGSAPMLAASVAWDGLAAELAVAASSFGSVTSGLAGQSWQGAAAAAMAAAAAPYAGWLAAAAARAA 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     a aqa+a+a+a+eaA+aa+v+p ++aanr+++++lv +n+fGqn+paIaa+ea ye+mwa+d+aam +Y+  ++aaa
  gi|121639043|ref|YP_979267.1|  85 GASAQAKAVASAFEAARAATVHPMLVAANRNAFVQLVLSNLFGQNAPAIAAAEAMYEQMWAADVAAMVGYHGGASAAA 162
                                    *************************************************************************99985 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.8
                                    -SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  16 gsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaeeaAaqaeaaaaaYea 95 
                                    g+++++aA aa                                                                     
  gi|121639043|ref|YP_979267.1| 188 GAASMFAAPAA--------------------------------------------------------------------- 198
                                    33344433332..................................................................... PP

                                    H CS
                            PPE  96 A 96 
                                    A
  gi|121639043|ref|YP_979267.1| 199 A 199
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.37s 00:00:01.17 Elapsed: 00:00:00.61
# Mc/sec: 3123.23
//
Query:       gi|121639044|ref|YP_979268.1|  [L=213]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-16   60.4   0.9      2e-16   59.5   0.9    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
    0.00038   20.6   0.0      0.022   14.9   0.0    2.5  3  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.045   13.6   0.0    1.7  1  HTH_5        Bacterial regulatory protein, arsR family
      0.043   13.9   0.3       0.12   12.4   0.1    2.0  2  TetR_C_27    Tetracyclin repressor-like, C-terminal domain
      0.086   13.4   0.0       0.17   12.4   0.0    1.4  1  DUF134       Protein of unknown function  DUF134
       0.17   11.9   0.1       0.29   11.2   0.1    1.4  1  Cro          Cro


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.9   6.8e-20     2e-16       1      47 []      15      61 ..      15      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 6.8e-20
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Il aA+el+a rGy++t++r+IA+++Gv ++a+Y++F+ K+++l+al
  gi|121639044|ref|YP_979268.1| 15 ILGAAAELIALRGYSSTSTRDIAAAVGVEQPAIYKHFSAKRDILAAL 61
                                   899*****************************************996 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.5e-06     0.022      15      60 ..      19      65 ..      16      71 .. 0.85
   2 ?   -0.7   0.0       0.5   1.5e+03       7      29 ..      97     119 ..      91     128 .. 0.74
   3 ?    2.6   0.0     0.046   1.4e+02      62      90 ..     118     150 ..     113     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.5e-06
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH.H-HHHHHHHHHHH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWk.kkkeFieyvnela 60
                                   aael++ + y  +++++ia+ vgv++  +yk    k++  + + +la
  gi|121639044|ref|YP_979268.1| 19 AAELIALRGYSSTSTRDIAAAVGVEQPAIYKHFsAKRDILAALVRLA 65
                                   89****************************98767777776666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.5
                                    HS-HHHHHHHHHHHHHHH--S-H CS
                    HTH_Tnp_1_2   7 eLtakQkkaaellvendyekltl 29 
                                     L+a    ++ +l+++d+++ ++
  gi|121639044|ref|YP_979268.1|  97 HLHASPYVLVSILITPDLHQESF 119
                                    56666666788999999999886 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.046
                                    HHHHTT..HHHHHHHHHHHHHSSS-..-HHHHH CS
                    HTH_Tnp_1_2  62 efleee..raevykaLlrkilkgrs..svkAie 90 
                                    +f++e   +ae  +aL+++i++g+   +v+A++
  gi|121639044|ref|YP_979268.1| 118 SFVAERelVAEMERALVGLIETGQGegDVRAMH 150
                                    555543225788899********98889***96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.045      10      37 ..      24      52 ..       9      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                   HHTT.SSEEHHHHHHHHTS-HHHHHHHHH CS
                          HTH_5 10 lLae.gelcvcelaeelglsqstvShHLk 37
                                   +L+  ++++  ++a+++g+ q+++  H++
  gi|121639044|ref|YP_979268.1| 24 ALRGySSTSTRDIAAAVGVEQPAIYKHFS 52
                                   466688999******************97 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3     7e+03      39      60 ..      45      66 ..      37      67 .. 0.68
   2 ?   12.4   0.1   4.1e-05      0.12      33      90 ..     114     171 ..      83     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_27 39 evvekhieeleeqlaeIireGv 60
                                    ++ kh    ++ la ++r +v
  gi|121639044|ref|YP_979268.1| 45 PAIYKHFSAKRDILAALVRLAV 66
                                   5566777777777888777665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-05
                                    HHHH-HHHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSGGGTSHHHH CS
                      TetR_C_27  33 lieeelevvekhieeleeqlaeIireGvaaGeFkaadpeaaaravfdatarfhhPala 90 
                                    l +e++ + ++ ++e+e  l  +i+ G+ +G+ +a +p +aar+v + +  +  P +a
  gi|121639044|ref|YP_979268.1| 114 LHQESFVAERELVAEMERALVGLIETGQGEGDVRAMHPLSAARLVQALFDALALPEFA 171
                                    5677777888999********************************9998888877766 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.8e-05      0.17      38      80 ..      18      60 ..       7      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-05
                         DUF134 38 deleairlvdyedlkqeeaaklmGiskatlwrlltearkkiak 80
                                   + +e i l+ y   +  + a+ +G+ ++++++  ++ r  +a+
  gi|121639044|ref|YP_979268.1| 18 AAAELIALRGYSSTSTRDIAAAVGVEQPAIYKHFSAKRDILAA 60
                                   5689999**************************9988877765 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   9.6e-05      0.29      18      40 ..      36      58 ..      21      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                                   HHHHHTS-HHHHHHHHHCT-EEE CS
                            Cro 18 tAkdlgvkqsaIsKAlkakRnIy 40
                                    A ++gv+q aI K   akR+I 
  gi|121639044|ref|YP_979268.1| 36 IAAAVGVEQPAIYKHFSAKRDIL 58
                                   6899*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1112.71
//
Query:       gi|121639045|ref|YP_979269.1|  [L=382]
Description: dioxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-21   76.3   0.3    2.9e-20   73.2   0.3    2.0  1  Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic 
    3.1e-18   65.5   0.0    5.5e-18   64.7   0.0    1.4  1  Rieske           Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.3   3.2e-24   2.9e-20       2     209 ..     187     371 ..     186     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 3.2e-24
                                    HHHHGGGHHHHHESS-HHHHHHHHHHCCCCCTTTHHHHHHCS-TTS---EEEEE-SSSS-EEEEEES-THHHHHHHHHHH CS
                Ring_hydroxyl_A   2 eellrvaaetldikaNWKlaaEnflEsYHvpvlHpellrallpeeletaeaaeyagfgphgsgsyvgqpgdlrlepaaav 81 
                                     e+ +v++++++++aNWK+aaEn  E+YHv  lH+++l ++ p+  +          +  +++          +      
  gi|121639045|ref|YP_979269.1| 187 GEMVQVESWSHEWRANWKVAAENGHENYHVLGLHRQTLEPFVPGGGD---------LDVRQYSR---------WA--LRL 246
                                    68999********************************9999999999.........22222222.........22..222 PP

                                    HHHHHSHHHHHHHGCHHHHCEEEEEEEETTTEEEE..TTTTEEEEEEESSTT-EEEEEEEEEETT..S-HHHHHHHHHHH CS
                Ring_hydroxyl_A  82 reldaeaaapelegledeqdrgalhftifPnlsillapdhvvifrviPtgpettevelealvppdataseelkeelaavv 161
                                    r + + + ++++  l++ q+      + fPn+ + +a + vv+f +iP++ ++++v   +l  p+  a++   ++ +++v
  gi|121639045|ref|YP_979269.1| 247 RVPFTVPVEAKSLQLNEVQKSNLVVLWTFPNSALAIAGERVVWFGFIPQSIDRVQVLGGVLTTPELAADAAATAQTSQFV 326
                                    33444477777778888888888899***************************************766666666666666 PP

                                    HHHCSTTHHHHHHHHHHHHHHTTSTTTSBSCCCSCSSHHHHHHHHHHH CS
                Ring_hydroxyl_A 162 drtfgvveeeDaelceevQqglrsrgyepgpvlsrqEeavrhFhewvr 209
                                     +   ++++eD+  +e+vQ g+ sr  e+g ++s++  ++ +F+++++
  gi|121639045|ref|YP_979269.1| 327 MA---MINDEDRLGLEAVQVGAGSRFAERGHLSSKEWPGMLAFYRNLA 371
                                    66...5*******************99****9999999******9986 PP

>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   6.1e-22   5.5e-18       1      84 [.      52     136 ..      52     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 6.1e-22
                                    CEEEEEEGGGC-.TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGG.SEEETT.EEE-TTT--EEETTSBEEE CS
                         Rieske   1 swvavakesdvp.egdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplse.gkidekgvleCpcHgwaydadGkvik 78 
                                    sw+ va+++++  +gd++tv+v gep++v+rd dg+++Als +C+Hr + + e g++  + +l+C++H w+y  dG++++
  gi|121639045|ref|YP_979269.1|  52 SWMLVAHVDQLAkTGDYVTVSVAGEPVMVVRDVDGQLHALSPICRHRLMLMVEpGAGRID-TLTCQYHLWRYGLDGRLRG 130
                                    69**********9**************************************998998545.9****************** PP

                                    -TTHHH CS
                         Rieske  79 gPaprp 84 
                                    +P++++
  gi|121639045|ref|YP_979269.1| 131 APHMAA 136
                                    **9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2389.03
//
Query:       gi|121639046|ref|YP_979270.1|  [L=196]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1034.69
//
Query:       gi|121639047|ref|YP_979271.1|  [L=423]
Description: hypothetical protein BCG_3187c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-17   62.5   1.6    9.8e-17   61.0   0.5    2.2  2  DUF58     Protein of unknown function DUF58
     0.0024   17.7   0.2       0.03   14.2   0.0    2.1  2  Ntox5     Bacterial toxin 5


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.27   2.4e+03      49      79 ..      87     110 ..      59     118 .. 0.69
   2 !   61.0   0.5   1.1e-20   9.8e-17       1      85 [.     188     270 ..     188     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.27
                          DUF58  49 lspemslgstgdekletavsaaaslarqlld 79 
                                    +++        d ++e  vsa+a +  ++l+
  gi|121639047|ref|YP_979271.1|  87 TESV-------DAAVELTVSALAGMQFEALE 110
                                    3332.......57788888888877777665 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 1.1e-20
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqllde 80 
                                    g+++a++R+YvpgD+lr ++W ++AR+g+l+v  + + ra++v++++d  ++    +t  e+ e+ v+ aa +++++l++
  gi|121639047|ref|YP_979271.1| 188 GVEYADIRPYVPGDQLRAVNWVVSARRGRLHVTRRLTDRAADVVVLIDMYRQPAGPAT--EATERVVRGAAQVVQTALRN 265
                                    6799**********************************************99876665..9******************* PP

                          DUF58  81 gdrvg 85 
                                    gdr g
  gi|121639047|ref|YP_979271.1| 266 GDRAG 270
                                    **987 PP

>> Ntox5  Bacterial toxin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.03   2.6e+02      37     134 ..      56     158 ..      48     159 .. 0.72
   2 !   14.2   0.0   3.4e-06      0.03      43     111 ..     260     329 ..     219     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.03
                          Ntox5  37 qrglkgrelledpdrq.ivqaGhilsdwyvkklsrdeflmledadlnwes..qftevsGavldksavl..ieGvvvdlkt 111
                                    qr++   ++  dpd q   +  h++   +v   s d  + l  + l  ++   ++ vs   +  sav+   + +++  + 
  gi|121639047|ref|YP_979271.1|  56 QRPVPVIQVHGDPDSQrCFENEHVRVTVWVTTESVDAAVELTVSALAGMQfeALESVSRRTTTVSAVAqrWGRYPIRARV 135
                                    67777777778899773567889999999999999999999988887663214566666566666664216778888888 PP

                          Ntox5 112 arlweavGklkaGtvaaapvvel 134
                                    a +     ++ aGtv aa  v  
  gi|121639047|ref|YP_979271.1| 136 AVVARGGLLMGAGTVDAAEIVVF 158
                                    88777766778999999988765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.4e-06
                          Ntox5  43 relledpdrq.ivqaGhilsdwyvkklsrdeflmledadlnwesqftevsGavldksavlieGvvvdlkt 111
                                    + +l + dr  iv +G  +  w    +++++f  + d+ l   ++f++++G++  ++av  + vv+ + t
  gi|121639047|ref|YP_979271.1| 260 QTALRNGDRAgIVALGGNRPRWLGADIGQRQFYRVLDTVLGAGEGFENTTGTLAPRAAVPAGAVVIAFST 329
                                    56788889855***********************99999**********************999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2618.78
//
Query:       gi|121639048|ref|YP_979272.1|  [L=320]
Description: methanol dehydrogenase transcriptional regulatory protein moxR3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-63  212.5   0.0    4.3e-63  211.0   0.0    1.8  2  AAA_3            ATPase family associated with various cellul
    4.7e-18   64.8   2.2    4.7e-18   64.8   2.2    2.0  2  AAA_lid_2        AAA lid domain
    2.2e-11   43.9   0.0    6.6e-11   42.4   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
    9.8e-06   25.4   0.0    3.9e-05   23.4   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
     0.0012   19.3   0.0      0.004   17.6   0.0    2.0  1  AAA              ATPase family associated with various cellul
     0.0014   18.4   0.0      0.007   16.1   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.011   15.1   0.1       0.44    9.9   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.038   13.1   0.0      0.051   12.7   0.0    1.3  1  MCM              MCM P-loop domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.0   0.0   1.9e-66   4.3e-63       1     130 [.      42     171 ..      42     172 .. 0.99
   2 ?   -2.9   0.0       2.5   5.5e+03      26      49 ..     284     307 ..     276     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 1.9e-66
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqs 80 
                                    hvl+e++PGl+ktl+++++a al+l+f+r+qftpdllP+d+lG++++++++ +fef++Gp+f+nllladeinr+ppktq+
  gi|121639048|ref|YP_979272.1|  42 HVLIEDLPGLGKTLIARSFAAALGLDFTRVQFTPDLLPADLLGSTIYDMQSGRFEFRAGPIFTNLLLADEINRTPPKTQA 121
                                    9******************************************************************************* PP

                          AAA_3  81 alleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                    alleam+e qv+++g+thkl  pf+vlat+nPie+eGtyplpeaqldrf 
  gi|121639048|ref|YP_979272.1| 122 ALLEAMAEGQVSIDGQTHKLAMPFIVLATDNPIEYEGTYPLPEAQLDRFA 171
                                    *************************************************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                          AAA_3  26 efkriqftpdllPsdilGtevfee 49 
                                      +ri + p++    i G++v++e
  gi|121639048|ref|YP_979272.1| 284 VAHRITLRPEMWVRKIAGADVVSE 307
                                    467999999999999999888765 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.2   2.8e+03       9      26 ..      19      36 ..      13      39 .. 0.80
   2 !   64.8   2.2   2.1e-21   4.7e-18       2      60 ..     236     293 ..     235     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                      AAA_lid_2  9 ielgvsgrRadlallraA 26
                                   ie  v+g R +l+l+ +A
  gi|121639048|ref|YP_979272.1| 19 IERVVVGKRSALTLILTA 36
                                   677799999999999888 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 2.1e-21
                      AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepe 60 
                                    atr+h+++++g+s+r a+l l++ +rA+A+l grdyV+peDvke+a  + aHR++ +pe
  gi|121639048|ref|YP_979272.1| 236 ATRHHPQVAVGASPR-AELDLVQLSRARALLLGRDYVIPEDVKELATAAVAHRITLRPE 293
                                    89*************.**************************************94444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   5.4e+03      69      77 ..      14      22 ..       4      26 .. 0.83
   2 !   42.4   0.0     3e-14   6.6e-11       7     138 .]      48     170 ..      42     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                   EEEESGGG- CS
                          AAA_5 69 lvlDEvera 77
                                   +vlDE+er+
  gi|121639048|ref|YP_979272.1| 14 AVLDEIERV 22
                                   799***985 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3e-14
                                    -SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--HHHHHH CS
                          AAA_5   7 ppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraesevlns 84 
                                     pG gK+ +a+++aaal+  ++ vq+t d+ ++dl+g++ ++  +g+ +++ +p+        +l+ DE++r +++++++
  gi|121639048|ref|YP_979272.1|  48 LPGLGKTLIARSFAAALGLDFTRVQFTPDLLPADLLGSTIYDmqSGRFEFRAGPIF-----TNLLLADEINRTPPKTQAA 122
                                    59************************************999888************.....6899*************** PP

                                    HHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  85 Llslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    Ll  + e +++  +g++   a +      f v+at np +  +  +l +a ++Rf
  gi|121639048|ref|YP_979272.1| 123 LLEAMAEGQVS-IDGQTHKLAMP------FIVLATDNPIEyEGTYPLPEAQLDRF 170
                                    ***********.56666665666......**********9777778888888887 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.8e-08   3.9e-05      13     144 ..      31     153 ..      24     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.8e-08
                                    HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHT CS
                Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfeka 92 
                                    + i +++  + +vli+   G GK+l+ar+  +a    +   v++    +p++ll s+++ +++G F      ++G +   
  gi|121639048|ref|YP_979272.1|  31 TLILTAVLARGHVLIEDLPGLGKTLIARSFAAALG-LDFTRVQFTPDLLPADLLGSTIYDMQSGRFE----FRAGPIF-- 103
                                    556677788899****************9877665.4444577777789**************9995....5778765.. PP

                                    TTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS- CS
                Sigma54_activat  93 dgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatned 144
                                        l+ Dei++ p+++Q+ Ll+++ eg+v+  G++++  + + i+ at++ 
  gi|121639048|ref|YP_979272.1| 104 -TNLLLADEINRTPPKTQAALLEAMAEGQVSIDGQTHKLAMPF-IVLATDNP 153
                                    .468999************************999999888776.55666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.8e-06     0.004       6     128 ..      48     174 ..      43     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                                    STTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHH CS
                            AAA   6 ppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseee 82 
                                     pG GKTl+a++ a  lg +f +++  ++ll  +++g +  +++    e ++    +  l+ DEi +  ++         
  gi|121639048|ref|YP_979272.1|  48 LPGLGKTLIARSFAAALGLDFTRVQFtPDLLpADLLGSTIYDMQSGRFEFRAGPiFTNLLLADEINRTPPKT-------- 119
                                    59*******************999852677767777777666655444445444544789999999998888........ PP

                                    HHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEE CS
                            AAA  83 ervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrki 128
                                       +++Ll+++ + + +          ++iv+++ n         l++a l +Rf +++
  gi|121639048|ref|YP_979272.1| 120 ---QAALLEAMAEGQVSidgqthklAMPFIVLATDNPieyegTYPLPEAQL-DRFAIRL 174
                                    ...888888888887777777777644466665555444333334555555.6666665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.1e-06     0.007      29     115 ..      40     134 ..      24     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                         RuvB_N  29 reealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaalltnleek...........dvlfideihrl 96 
                                    r     hvl+   PGlGkt +a+  a+ lg ++ ++  +P l  a  l + + +++++           ++l+ dei r 
  gi|121639048|ref|YP_979272.1|  40 R----GHVLIEDLPGLGKTLIARSFAAALGLDFtRVQFTPDLLPADLLGSTIYDMQSGrfefragpiftNLLLADEINRT 115
                                    3....5************************99735677899988877778888887642222222333367888999999 PP

                         RuvB_N  97 sraveevlysamedfrldi 115
                                     ++++  l  am + ++ i
  gi|121639048|ref|YP_979272.1| 116 PPKTQAALLEAMAEGQVSI 134
                                    9999999999998877765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0002      0.44       5      45 ..      23      63 ..      20      69 .. 0.90
   2 ?    2.9   0.0     0.028        63     109     158 ..     106     153 ..      98     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                   Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                   v+G+++a + +  a+  + ++l+   pG GKt++a+ +++ 
  gi|121639048|ref|YP_979272.1| 23 VVGKRSALTLILTAVLARGHVLIEDLPGLGKTLIARSFAAA 63
                                   8899999999999999999****************998765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.028
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    +L+ DE+     k+  +L e + +g+v+i  +++k+  p  f ++a+ Np
  gi|121639048|ref|YP_979272.1| 106 LLLADEINRTPPKTQAALLEAMAEGQVSIDGQTHKLAMP--FIVLATDNP 153
                                    6888**************************999999877..667777777 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.051      59     175 ..      42     155 ..      23     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                    EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTC CS
                            MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcciDefdkmke 135
                                    +vl+   pg++K+ + ++ +  a    +t  + +     a+L  +   d ++g f + aG + +    +++ De+++   
  gi|121639048|ref|YP_979272.1|  42 HVLIEDLPGLGKTLIARSFA-AALGLDFTRVQFTPDllpADLLGSTIYDMQSGRFEFRAGPIFTN---LLLADEINRTPP 117
                                    56666666666666666655.33344455554443222267777777788888888888877754...7899******** PP

                                    HHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                            MCM 136 edrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                    +++ al+Eam + ++si   G + +L     vla  np++
  gi|121639048|ref|YP_979272.1| 118 KTQAALLEAMAEGQVSID--GQTHKLAMPFIVLATDNPIE 155
                                    *****************7..55688888899999999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2245.71
//
Query:       gi|121639049|ref|YP_979273.1|  [L=160]
Description: hypothetical protein BCG_3189c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.21   11.9   0.0    1.4  1  DUF4124   Domain of unknown function (DUF4124)


Domain annotation for each model (and alignments):
>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.2e-05      0.21       9      40 ..     121     153 ..     113     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                        DUF4124   9 aaaaevYkWvDanGvvhysdqP.ppdgkqaeqv 40 
                                      + e++ Wv  n v+h +d+  +p++++ e++
  gi|121639049|ref|YP_979273.1| 121 LFGDELWEWVNPNNVTHTGDRQpGPGRAALEEI 153
                                    567899**************7625555555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1117.18
//
Query:       gi|121639050|ref|YP_979274.1|  [L=319]
Description: hypothetical protein BCG_3190c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-11   41.8   1.8    9.7e-11   41.8   1.8    2.2  2  DUF4129          Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.049   13.3   1.2      0.086   12.5   0.1    1.9  3  DUF1345          Protein of unknown function (DUF1345)
       0.08   12.5  15.2          1    8.8  14.3    2.1  2  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
       0.36   10.8   7.3         64    3.5   0.0    2.8  2  Colicin_V        Colicin V production protein


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       0.9     4e+03      35      44 ..     208     217 ..     188     228 .. 0.62
   2 !   41.8   1.8   2.2e-14   9.7e-11       1      69 []     237     307 ..     237     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.9
                        DUF4129  35 paaalaalae 44 
                                     +++la++ae
  gi|121639050|ref|YP_979274.1| 208 RSESLARAAE 217
                                    2234444444 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 2.2e-14
                        DUF4129   1 ayrallraLaer.gldrrpgeTprEyarrv.riapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                    +y a++r L +  g+ ++  +Tp+E+++r+ +++  + a++aal+ lf ear++++ + +e++++++++lr
  gi|121639050|ref|YP_979274.1| 237 CYVAMERELSHVpGVAPQDFDTPTEVLARAvEHRALHGASAAALVSLFAEARFSPHVMNEEHREVAMRLLR 307
                                    7*****************************99999999*****************************9987 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05     0.086      11     101 ..      16     122 ..      12     141 .. 0.74
   2 ?   -3.1   0.0       1.2   5.4e+03     134     144 ..     168     179 ..     155     194 .. 0.45
   3 ?   -3.3   0.0       1.4   6.4e+03       9      22 ..     275     288 ..     265     309 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                        DUF1345  11 laalvylvlvllvllra.daeelrkraeredesrvlilllvllaalaslvaivlll................asakaekp 73 
                                    ++++v+l+l+ ++l+ +  a++    a++  ++++l+++++ laa+ +l+a+++ +                a       
  gi|121639050|ref|YP_979274.1|  16 VVVIVLLMLAGAALRGHlPADDGAPLAAAGGSRAALMFIVAALAATLALIALAIITrlrhplpvapsagelsA------- 88 
                                    5666677777777766636888888888888899999999999999999999888866666666655554432....... PP

                        DUF1345  74 ae.......kllhlalavatvvlsWllvhtvfalh 101
                                              +++++l  +  +l+Wll+ ++ a  
  gi|121639050|ref|YP_979274.1|  89 -MlggaagrPNWRVLLLGLGTILAWLLIAILLARL 122
                                    .045555556889999999999******9998865 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                        DUF1345 134 ftigmtf.qtsD 144
                                     tig     ++ 
  gi|121639050|ref|YP_979274.1| 168 STIGLFLmVVAG 179
                                    222222101222 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.4
                        DUF1345   9 wdlaalvylvlvll 22 
                                      +aalv l++ ++
  gi|121639050|ref|YP_979274.1| 275 ASAAALVSLFAEAR 288
                                    33333333333322 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  14.3   0.00023         1     122     231 ..      17     122 ..      15     133 .. 0.72
   2 ?    2.1   0.0     0.025   1.1e+02     145     191 ..     164     210 ..     149     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00023
                LPG_synthase_TM 122 lalvllgllallllggllaegaa.......vllllalallllavlalllllllrrrlarlarvlkrlarllarfarklas 194
                                    +++vll+l++++l g+l+a ++a         ++l++++++la+++ l +l++  rl++ ++v ++   l+a++++    
  gi|121639050|ref|YP_979274.1|  17 VVIVLLMLAGAALRGHLPADDGAplaaaggSRAALMFIVAALAATLALIALAIITRLRHPLPVAPSAGELSAMLGGAAG- 95 
                                    789999999**99999999999999999886666666666666666777777778888888888888888877776554. PP

                LPG_synthase_TM 195 akrklvlasprrlllafllslliwllealtlylllra 231
                                          + ++r lll ++  l+     +l+++ll+r 
  gi|121639050|ref|YP_979274.1|  96 ------RPNWRVLLLGLGTILAW----LLIAILLARL 122
                                    ......45777776666655555....4555555544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                LPG_synthase_TM 145 vllllalallllavlalllllllrrrlarlarvlkrlarllarfark 191
                                    +l++ +++l+l +v + l  ++++r+ a  +    r+ + +++ +  
  gi|121639050|ref|YP_979274.1| 164 ILFASTIGLFLMVVAGSLITSRRQRKSAPARISGDRIEAPAPSARSE 210
                                    66777777777777777777777777777777788887765544433 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   8.9     0.032   1.4e+02      22     112 ..      15     104 ..      12     122 .. 0.83
   2 ?    3.5   0.0     0.014        64      95     119 ..     159     183 ..     151     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.032
                      Colicin_V  22 vrevlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgallsklvsktglglldrllGai 101
                                    v  v+ ll++++a++ + l +++ a+l a   +s+a+  +i  +l+ +l+l++++++ +l + l  ++ +g l  +lG++
  gi|121639050|ref|YP_979274.1|  15 VVVVIVLLMLAGAALRGHLPADDGAPLAAA-GGSRAALMFIVAALAATLALIALAIITRLRHPLPVAPSAGELSAMLGGA 93 
                                    566788888888888888888888888888.6899999999999***********************************9 PP

                      Colicin_V 102 fGllkglllvv 112
                                     G  +  +l+ 
  gi|121639050|ref|YP_979274.1|  94 AGRPNWRVLLL 104
                                    99766665555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                      Colicin_V  95 drllGaifGllkglllvvlllllla 119
                                    d +lG +f    gl+l+v++ +l++
  gi|121639050|ref|YP_979274.1| 159 DDVLGILFASTIGLFLMVVAGSLIT 183
                                    8899***********9999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2320.40
//
Query:       gi|121639051|ref|YP_979275.1|  [L=208]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.3e-19   67.8  12.0    1.8e-18   66.9  12.0    1.5  1  TetR_C_11    Tetracyclin repressor-like, C-terminal domain
    1.1e-15   57.1   0.3    2.2e-15   56.1   0.3    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.034   14.3   0.0      0.059   13.5   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas


Domain annotation for each model (and alignments):
>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9  12.0     3e-22   1.8e-18       4     111 ..      85     192 ..      82     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 3e-22
                      TetR_C_11   4 tGslrgDLrallralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvl 83 
                                     G++++D+r ++ a+++ +++p+ +a+l++l+a++++d+el +++ +  +++  aa+r +lr Av+rGe  +d+d+++++
  gi|121639051|ref|YP_979275.1|  85 AGDIAADIRMMIAATRDVFTTPVVRAALPGLVADMTADAELNARVLA-RFADLFAAVRMRLREAVDRGEAHPDVDPDRLI 163
                                    59*********************************************.8999**************************** PP

                      TetR_C_11  84 dlllgpllyrllltge.plddafaerlvd 111
                                    +l+ g+ ++r+ll ++  ldda++++ ++
  gi|121639051|ref|YP_979275.1| 164 ELIGGATMLRMLLYPDdMLDDAWVDQTTA 192
                                    **********999988689******9876 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.3   3.8e-19   2.2e-15       1      47 []      26      72 ..      26      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 3.8e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Il+a++el+ + Gy++++++++A+rAG++k+alYr+++sK+eL++++
  gi|121639051|ref|YP_979275.1| 26 ILSATAELLVQIGYSNLSLAAVAERAGTTKSALYRRWSSKAELVHEA 72
                                   9*******************************************986 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.8e-06     0.059      15      55 ..      30      71 ..      22      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHH.HHH-HHHHHH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlyk.WkkkkeFiey 55
                                    aellv+  y +l+l+ +ae  g  +s ly+ W +k e +++
  gi|121639051|ref|YP_979275.1| 30 TAELLVQIGYSNLSLAAVAERAGTTKSALYRrWSSKAELVHE 71
                                   59****************************559999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1487.11
//
Query:       gi|121639052|ref|YP_979276.1|  [L=378]
Description: hypothetical protein BCG_3192 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-21   75.8   5.9    6.7e-21   75.3   5.9    1.2  1  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   5.9   3.7e-25   6.7e-21      39     215 ..      97     288 ..      63     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3.7e-25
                                    HHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS...........HHHHHHHHHHH.HHHHHHHCCH CS
                            APH  39 revallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr...........klsaaqlpell.ealgeflaal 105
                                     ++++ rl+ ++   pvP+v +++t ++++g++f+l+ yv+g ++ +           ++ +a+++++l +a +++la l
  gi|121639052|ref|YP_979276.1|  97 HQFEVIRLVGELTDvPVPRVRWIETTGDVLGTPFFLMDYVEGVVPPDvmpytfgdnwfADAPAERQRQLqDATVAALATL 176
                                    556677777765556*******************************************5555555555516679****** PP

                                    HCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC....HHHHHHHHHHHHHHHH--S...SS-EEEE-SS-SGGGE CS
                            APH 106 hqvdpaalpladflaqdlellrqlesatarllaselld....lleeleeqvlaalaallpg...elptvllHgDlhpgNl 178
                                    h++ p+a   ++fl q ++ +  l++  ++ +    +      +  l e+  ++l  ++p    + ++vll gD + gN+
  gi|121639052|ref|YP_979276.1| 177 HSI-PNAQNTFSFLTQGRTSDTTLHRHFNWVRSWYDFAvegiGRSPLLERTFEWLQSHWPDdaaAREPVLLWGDARVGNV 255
                                    ***.777777777779999999999998777776666666664445555599**************************** PP

                                    EEC..TTEEEEE---TT-EEEECCHHHHCCHHHCSCH CS
                            APH 179 lvdpddgrvtGviDfedaglgpplyDlavllrswtse 215
                                    l +  d + ++v+D+e++ lgp+  D+a+++ +  ++
  gi|121639052|ref|YP_979276.1| 256 LYR--DFQPVAVLDWEMVALGPRELDVAWMIFA--HR 288
                                    ***..67777********************933..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2941.76
//
Query:       gi|121639053|ref|YP_979277.1|  [L=374]
Description: hypothetical protein BCG_3193 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2456.55
//
Query:       gi|121639054|ref|YP_979278.1|  [L=448]
Description: flavin-containing monoamine oxidase AofH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-72  245.2   1.0    1.8e-72  245.1   1.0    1.0  1  Amino_oxidase  Flavin containing amine oxidoreductase
    3.7e-15   55.9   1.6    9.8e-15   54.5   0.9    2.1  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      2e-12   47.4  12.0      6e-12   45.8  12.0    1.7  1  DAO            FAD dependent oxidoreductase
    7.5e-10   38.5   1.3    7.8e-07   28.6   0.8    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.8e-07   30.6   0.8    1.8e-07   30.6   0.8    1.5  2  FAD_binding_2  FAD binding domain
    6.1e-07   29.9   1.2    0.00021   21.8   1.3    2.3  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.6e-06   26.2   3.6    4.6e-06   26.2   3.6    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    1.9e-05   24.1   0.1       0.14   11.3   0.1    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.2e-05   23.8   0.5    3.5e-05   23.1   0.5    1.2  1  Thi4           Thi4 family
    3.3e-05   22.8   1.1    5.1e-05   22.1   0.2    1.6  2  HI0933_like    HI0933-like protein
    0.00011   21.6   0.8    0.00019   20.8   0.8    1.3  1  FAD_binding_3  FAD binding domain
    0.00042   19.5   0.5    0.00042   19.5   0.5    1.5  2  GIDA           Glucose inhibited division protein A
     0.0024   17.0   0.7     0.0059   15.7   0.1    1.8  2  Lycopene_cycl  Lycopene cyclase protein
     0.0066   16.4   3.7       0.13   12.3   0.4    2.4  2  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.017   14.4   0.4      0.017   14.4   0.4    1.6  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.18   12.4   0.6        4.4    8.0   0.1    2.4  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   1.0   1.6e-75   1.8e-72       1     451 [.      17     444 ..      17     445 .. 0.90

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 1.6e-75
                                    HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEEEEE CS
                  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpgapkrvls 80 
                                    +aGLaaAr+L+++G++V+v+E+rdrvGGR  t r  G+++++G++++ ++++++l+l+ elg+++ ++ +d    + + +
  gi|121639054|ref|YP_979278.1|  17 FAGLAAARELTRQGHEVLVFEGRDRVGGRSLTGRVAGVPADMGGSFIGPTQDAVLALATELGIPTTPTHRDGR--NVIQW 94 
                                    69***************************************************************99866655..55555 PP

                                    TTEECC.TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                  Amino_oxidase  81 kggref.pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdvevwdr 159
                                    +g  +  +g++++++  +++l++ g+l+   +++e   r    a ++ +++ ++ld+ sl e+l+ + + +++  +++  
  gi|121639054|ref|YP_979278.1|  95 RGSARSyRGTIPKLS--LTGLIDIGRLR---WQFERIARGVPVAAPWDARRARELDDVSLGEWLRLVRATSSSR-NLMAI 168
                                    444433599999997..78999977777...666666666666666*****************99999999999.88888 PP

                                    HHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETT CS
                  Amino_oxidase 160 liepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealaeelrgldirlntrVkeikregd 239
                                    + + +  ++   +s l+a+  +   a   l+ l++++  +++ ++p gG +q+++a a+ ++g +++ln+ V++i+r+g 
  gi|121639054|ref|YP_979278.1| 169 MTRVTWGCEPDDVSMLHAA--RYVRAAGGLDRLLDVKNGAQQDRVP-GGTQQIAQAAAA-QLGARVLLNAAVRRIDRHGA 244
                                    8888999999999999998..88**********************9.************.******************** PP

                                    CEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCSTSECECECCCEEET CS
                  Amino_oxidase 240 gvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvilefdrkfwednalgqgvlvselttt 319
                                    gvtvt  +g+  ea  V+v++p+++  ai+f+Pplp+e ++ +++ + g ++k++ ++ ++fw+ ++       ++ +++
  gi|121639054|ref|YP_979278.1| 245 GVTVTSDQGQA-EAGFVIVAIPPAHRVAIEFDPPLPPEYQQLAHHWPQGRLSKAYAAYSTPFWRASG-----YSGQALSD 318
                                    ****8766665.*****************************************************87.....78888888 PP

                                    TTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHHHTGTSSTCSEEEEEECCTETTT.SSSE CS
                  Amino_oxidase 320 lgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLrklfgeevpepkatlvtrWhtdpla.rgsy 398
                                     +  fi +d   +++ + + +l+ +v ++ ++ l   + ee+ + +lr +++lfg+e+ +p +++  rW+t+++a +g  
  gi|121639054|ref|YP_979278.1| 319 EAPVFITFD--VSPHADGPGILMGFVDARGFDSL---PIEERRRDALRCFASLFGDEALDPLDYVDYRWGTEEFApGGPT 393
                                    888888855..5555555557*****97777666...******************************************* PP

                                    EE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                  Amino_oxidase 399 syvsvgpghedydplakpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                    ++v++g +++ y ++ ++ +++ +++A   t+ e++g+++gA++SG raAa++
  gi|121639054|ref|YP_979278.1| 394 AAVPPG-SWTKYGHWLRE-PVGPIHWASTETADEWTGYFDGAVRSGQRAAAEV 444
                                    ******.6**********.********************************98 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.9   8.7e-18   9.8e-15       1      67 [.      12      76 ..      12      77 .. 0.92
   2 ?   -2.7   0.0       6.7   7.5e+03      30      50 ..     310     331 ..     306     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 8.7e-18
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                   +vGaG++Gl+aA++L+++g++vl++e rdr+GGr+ + +v gv++d g + + ++  +++v +l+ e
  gi|121639054|ref|YP_979278.1| 12 VVGAGFAGLAAARELTRQGHEVLVFEGRDRVGGRSLTGRVAGVPADMGGSFIGPT--QDAVLALATE 76
                                   8*************************************************99885..5777777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.7
                                    SSSGGG-EECETT.CEECTS-- CS
                  NAD_binding_8  30 rlGGraasyevpg.vrvdygah 50 
                                    + +G+a s e p  +++d+ +h
  gi|121639054|ref|YP_979278.1| 310 GYSGQALSDEAPVfITFDVSPH 331
                                    5678999988887788888887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8  12.0   5.4e-15     6e-12       1     306 [.       9     382 ..       9     407 .. 0.60

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 5.4e-15
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSS..STHHSTH.................... CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsgl..rylpeas.................... 55 
                                    dvv++G+G +Gl++A+eL+r+g  V+++e +d++g    +gr +g+ +        p +                     
  gi|121639054|ref|YP_979278.1|   9 DVVVVGAGFAGLAAARELTRQGheVLVFEGRDRVGGrSLTGRVAGVPADMGgsFIGPTQDavlalatelgipttpthrdg 88 
                                    9********************99********9999547788888888653343223322233444444444443333333 PP

                                    ...HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESS...........................HHHHHHHHHHHHH CS
                            DAO  56 ...elarlslealeelreleeelgididyrrtGllslaad...........................eeelealdkllal 105
                                        ++r s++++                         ++                           +   + +d++ a+
  gi|121639054|ref|YP_979278.1|  89 rnvIQWRGSARSY-------------------------RGtipklsltglidigrlrwqferiargvP-VAAPWDARRAR 142
                                    3321112222222.........................112222222222222222222222222221.12223343333 PP

                                    HHHTTTTE.EEEEHHHHHHHSTTST.......TTSEEEEETTE.EEEEHHHHHHH......................... CS
                            DAO 106 lleaglda.elldaeevrelepalp.......gllgalfypdt.gqvdpakltaa......................... 151
                                     l  ++   e+l+   vr+ ++  +       +++ ++ +pd+   +++a++++a                         
  gi|121639054|ref|YP_979278.1| 143 EL-DDVSLgEWLRL--VRATSSS-RnlmaimtRVTWGC-EPDDvSMLHAARYVRAaggldrlldvkngaqqdrvpggtqq 217
                                    32.23333356644..4444442.12444554666554.56662666********************************* PP

                                    HHHH.HHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHHHTTCTTTSEEEEEEEEEEEE CS
                            DAO 152 lara.aealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdllgllkeldlpispvrgqvlvl 227
                                    +a+a a++lG+++l+++ v++++++ g +++v  t++ g+   a+a  v++a  +  + +    e+d+p+ p   q  + 
  gi|121639054|ref|YP_979278.1| 218 IAQAaAAQLGARVLLNAAVRRIDRH-GAGVTV--TSDqGQ---AEAgfVIVAIPPAHRVA---IEFDPPLPPEYQQLAHH 288
                                    6666589***************886.444555..666576...57777*****8887655...45577755655555555 PP

                                    EECCTHSTGSGCSEEEEE.........EEETTTTEEEEEE....TTS.EEEEEESSEEETTCSSTSCSHHHHHHHHHHHH CS
                            DAO 228 kplseklvspaailpvpe.........tdddgrgvyvtpr....kdg.rvlvGgtadeesgdddpevdeedidellealr 293
                                     p +  l++++a + +p+            d+  v++t +    +dg ++l+G  +   +g+d+  + ee++++ l+  +
  gi|121639054|ref|YP_979278.1| 289 WP-QGRLSKAYAAYSTPFwrasgysgqALSDEAPVFITFDvsphADGpGILMGFVD--ARGFDS-LPIEERRRDALRCFA 364
                                    33.33466678999999977777777655555555555546666555347788887..999999.666677777778888 PP

                                    HHSGG..GCG...EEEEE CS
                            DAO 294 klfPq..lgd...vlrkw 306
                                     lf +  l++   v ++w
  gi|121639054|ref|YP_979278.1| 365 SLFGDeaLDPldyVDYRW 382
                                    888554433311233455 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.8     7e-10   7.8e-07       2      39 ..       9      45 ..       8      61 .. 0.85
   2 !    8.3   0.0    0.0011       1.2     184     235 ..     214     264 ..     187     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7e-10
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclngg 39
                                   dvvv+G+G+AGlaaa++l ++g++v+++ +++  ++g+
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVF-EGRDRVGGR 45
                                   8***************************.666666554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                                    HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                      ++++++a  + G +v l++ v +id++g  ++ v++d+ + +a  v+va+
  gi|121639054|ref|YP_979278.1| 214 GTQQIAQAAAAQLGARVLLNAAVRRIDRHGAGVT-VTSDQGQAEAGFVIVAI 264
                                    5678999999********************8665.77777778999999997 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.8   1.6e-10   1.8e-07       1      38 [.       9      46 ..       9      50 .. 0.95
   2 ?   -3.2   0.1         3   3.3e+03     234     234 ..     220     220 ..     179     260 .. 0.51

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.6e-10
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                   Dv+V+G+G+AGLaAA e++++G++v+v e  +++gg +
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVFEGRDRVGGRS 46
                                   9*****************************99999865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                    H CS
                  FAD_binding_2 234 l 234
                                    +
  gi|121639054|ref|YP_979278.1| 220 Q 220
                                    1 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.3   1.9e-07   0.00021       2      37 ..      10      46 ..       9      54 .. 0.90
   2 ?    5.7   0.0     0.019        21      43      78 ..     216     248 ..     209     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rl 37
                                   vvvvG+G+ gl +A +l++ g++V v+e +d++  r 
  gi|121639054|ref|YP_979278.1| 10 VVVVGAGFAGLAAARELTRQGHEVLVFEGRDRVGgRS 46
                                   8*******************************98655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                                    HHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox  43 skilqeklekngievllntkveeiegsedgvesvkl 78 
                                    ++i q    ++g +vlln+ v +i+ ++ gv   ++
  gi|121639054|ref|YP_979278.1| 216 QQIAQAAAAQLGARVLLNAAVRRIDRHGAGV---TV 248
                                    67778888999*****************994...44 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.6   4.1e-09   4.6e-06       1      43 [.       9      51 ..       9      77 .. 0.87
   2 ?    0.5   0.1      0.26     3e+02      86     129 ..     212     252 ..     187     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.1e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43
                                   DvvVvG+g aG+aAA    r+G +vl+ e r+++GG +  g v
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVFEGRDRVGGRSLTGRV 51
                                   9***********************************8755543 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.26
                   FAD_oxidored  86 pevakavleemlaeagvtvllntrlvevekegkriesvtveske 129
                                    p   ++++++  a+ g +vlln+ ++++++ g    +vtv s++
  gi|121639054|ref|YP_979278.1| 212 PGGTQQIAQAAAAQLGARVLLNAAVRRIDRHG---AGVTVTSDQ 252
                                    55667788888888888888888888888887...566665544 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00013      0.14       1      30 [.      11      39 ..      11      46 .. 0.89
   2 !   10.5   0.0   0.00023      0.26      90     132 ..     222     264 ..     212     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                   +++GaG aGlaaa el + g  ++l+ E  
  gi|121639054|ref|YP_979278.1| 11 VVVGAGFAGLAAARELTRQGH-EVLVFEGR 39
                                   79******************9.69999965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                    Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAt 132
                                     a++   ++ l+  V+++++++ g +v++++++ eA +vi+A+
  gi|121639054|ref|YP_979278.1| 222 AAAQLGARVLLNAAVRRIDRHGAGVTVTSDQGQAEAGFVIVAI 264
                                    55666678999******************************96 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.5   3.2e-08   3.5e-05      18      60 ..       8      49 ..       6      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.2e-08
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60
                                    Dvv+vGaG +GL+aa+ l+++ + +v+++e +  +GG +  G
  gi|121639054|ref|YP_979278.1|  8 VDVVVVGAGFAGLAAARELTRQ-GHEVLVFEGRDRVGGRSLTG 49
                                   6*********************.*********99999876555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   4.6e-08   5.1e-05       2      36 ..       9      43 ..       8      50 .. 0.93
   2 ?   -1.8   0.0      0.87   9.7e+02     117     161 ..     221     263 ..     217     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.6e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   dv+v+G+G AGl aA ++ ++g++Vl++e  +++g
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVFEGRDRVG 43
                                   8*****************************99998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.87
                                    HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
                    HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                                    +++ + g ++ l+ +v++++++  g ++v+  ++++ ea  +++A
  gi|121639054|ref|YP_979278.1| 221 AAAAQLGARVLLNAAVRRIDRHGAG-VTVTS-DQGQAEAGFVIVA 263
                                    5667889999999999999887777.77777.8889999999988 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.8   1.7e-07   0.00019       2      33 ..       8      39 ..       7      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   +dV++VGaG aGl +a++L+++G +v++ e r
  gi|121639054|ref|YP_979278.1|  8 VDVVVVGAGFAGLAAARELTRQGHEVLVFEGR 39
                                   89************************998865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   3.7e-07   0.00042       1      37 [.       9      44 ..       9      67 .. 0.82
   2 ?   -3.0   0.1       2.6   2.9e+03      16      29 ..     221     236 ..     219     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                   dv+V+G+G AG++AA ++ r G++vl + +  d+++ 
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVF-EGRDRVGG 44
                                   79***********************998.55555554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                    HHHHHTT--EEEE..E CS
                           GIDA  16 laaarlGakvlLi..t 29 
                                    +aaa+lGa+vlL   +
  gi|121639054|ref|YP_979278.1| 221 AAAAQLGARVLLNaaV 236
                                    7899******997443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.2e-06    0.0059       1      33 [.       9      39 ..       9      46 .. 0.84
   2 ?   -1.4   0.0      0.84   9.4e+02     101     144 ..     228     268 ..     216     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.2e-06
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                                   Dvvv+GaG Agl+ A +l   ++g +v++ e+ 
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAAREL--TRQGHEVLVFEGR 39
                                   9*****************..7777777777765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.84
                  Lycopene_cycl 101 gvklleakvesveeeeageslvvleggrkirarlvvdarglasl 144
                                    ++ ll+a v ++  + a   + v+++  + +a +v++a + ++ 
  gi|121639054|ref|YP_979278.1| 228 ARVLLNAAVRRIDRHGA--GVTVTSDQGQAEAGFVIVAIP-PAH 268
                                    45678899999987766..455566666789999999998.443 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.4   0.00011      0.13       1      39 [.      11      44 ..      11      50 .. 0.83
   2 ?    4.6   0.2     0.025        28     103     152 ..     218     263 ..     214     265 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                   ++vGaG++Gla++++L ++      +e+ +f+ +   g g
  gi|121639054|ref|YP_979278.1| 11 VVVGAGFAGLAAARELTRQ-----GHEVLVFEGRDRvG-G 44
                                   69****************9.....59999999865525.5 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.025
                  NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLA 152
                                    ++++++a+l ++    +++a v +++++++g++v ++d+ + +a  V++A
  gi|121639054|ref|YP_979278.1| 218 IAQAAAAQLGAR---VLLNAAVRRIDRHGAGVTV-TSDQGQAEAGFVIVA 263
                                    444555555443...25699999********987.777777888888887 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.5e-05     0.017      30      61 ..       9      40 ..       6      46 .. 0.91
   2 ?   -2.9   0.6         3   3.4e+03      21      56 ..     213     248 ..     208     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                    v+v+G+G aGl+A++  ++ g +V v++ r 
  gi|121639054|ref|YP_979278.1|  9 DVVVVGAGFAGLAAARELTRQGHEVLVFEGRD 40
                                   69*************************99776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                                    CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                    AlaDh_PNT_C  21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtv 56 
                                    Gg + +++a    +G+ v   +A++   + ga Vtv
  gi|121639054|ref|YP_979278.1| 213 GGTQQIAQAAAAQLGARVLLNAAVRRIDRHGAGVTV 248
                                    555556666666666666666666666666666665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0039       4.4       2      36 ..      10      41 ..       9      70 .. 0.87
   2 ?    2.4   0.0      0.21   2.3e+02      48      73 ..     244     268 ..     203     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSC CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnp 36
                                   + ++GaG  g a a+ l+++g   he++v   r+ 
  gi|121639054|ref|YP_979278.1| 10 VVVVGAGFAGLAAARELTRQG---HEVLVFEGRDR 41
                                   6789*****************...****9888776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                                    -EEECECHHHHHHH-SEEEE-S-HHH CS
                  F420_oxidored  48 vkvtavdneeaaeeadvvvlavkped 73 
                                    ++vt ++ +  a ea +v++a++p++
  gi|121639054|ref|YP_979278.1| 244 AGVTVTSDQGQA-EAGFVIVAIPPAH 268
                                    566664455555.599*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3206.44
//
Query:       gi|121639055|ref|YP_979279.1|  [L=299]
Description: non-heme haloperoxidase hpx [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-21   75.4   0.0      3e-19   69.7   0.0    2.1  1  Abhydrolase_1    alpha/beta hydrolase fold
    1.1e-20   73.9   0.7      1e-19   70.8   0.7    2.0  1  Hydrolase_4      Serine aminopeptidase, S33
    1.6e-17   64.8   7.5      2e-17   64.6   7.5    1.1  1  Abhydrolase_6    Alpha/beta hydrolase family
    2.5e-05   24.3   0.0    6.2e-05   23.1   0.0    1.7  1  Abhydrolase_4    TAP-like protein
     0.0059   16.5   0.0       0.65    9.8   0.0    2.4  2  Ser_hydrolase    Serine hydrolase
  ------ inclusion threshold ------
      0.012   14.6   0.0      0.045   12.7   0.0    1.9  2  Chlorophyllase2  Chlorophyllase enzyme
      0.028   14.2   0.0       0.19   11.5   0.0    2.0  2  Abhydrolase_5    Alpha/beta hydrolase family
      0.046   13.2   0.0        1.4    8.3   0.0    2.3  2  Peptidase_S9     Prolyl oligopeptidase family
       0.12   12.0   0.0       0.19   11.4   0.0    1.2  1  FSH1             Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   1.5e-22     3e-19       2     255 ..      23     272 ..      22     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.5e-22
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHC..TTSSEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildal..gddkltlvG 79 
                                    ++v+ hG+      wa    + +La  +++vi++D+rG+g+S  + +     y++ ++a+dld +lda+  + ++ ++ G
  gi|121639055|ref|YP_979279.1|  23 PIVLTHGFVCAIRAWAY--QIADLAG-DYRVIAFDHRGHGRSGVPRR---GAYSLNHLAADLDSVLDATlaPRERAVVAG 96 
                                    89***************..******9.********************...9************88666533566777*** PP

                                    ETHHHHHHHHHHHHH....GGGEEEEEEESE...........CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHH CS
                  Abhydrolase_1  80 hSmGGmialayaaey....perVkalvllga...........idpaaslieaqrqqaksfpdffdgyaadcarnpagpll 144
                                    hSmGG + +a+  +y      r +a++l+++           ++ + +l+     +  s+ ++f g+  ++a  ++ +++
  gi|121639055|ref|YP_979279.1|  97 HSMGGITIAAWSDRYrhkvRRRTDAVALINTttgdlvrkvklLSVPRELSPVRVLAGRSLVNTFGGFPLPGAARALSRHV 176
                                    ***************44444445589999997788777777777777777777777777777777777777777777777 PP

                                    HCCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSS CS
                  Abhydrolase_1 145 adelaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDpl 224
                                     + la              +d + ++ +  +  ++ +++ + + +    ++  ++  l+l++    ++ptlvi+g  D+l
  gi|121639055|ref|YP_979279.1| 177 ISTLAVA------------ADADPSATRLVYELFTQMSAAGRGGCAKMLVEEVGSAHLNLDG---LTVPTLVIGGVRDRL 241
                                    6666654............4445555555566666666666677777777777777778777...677************ PP

                                    SCHHHHHHHHHCHTSEEEEEEETCSSSHHHH CS
                  Abhydrolase_1 225 vppkaledlaqllpkkrlvvisdagHlafle 255
                                    +p+++++++a+  p++  +v+ ++gH++ le
  gi|121639055|ref|YP_979279.1| 242 TPISQSRRIARTAPNVVGLVELPGGHCSMLE 272
                                    ***************************9987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.7   5.1e-23     1e-19       7     221 ..      24     257 ..      18     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 5.1e-23
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    +vl HG+   +++ a  +++La  ++ v+a+DhrGhGrs+  r    s++++ +Dl++++++     p+++ ++ GhSmG
  gi|121639055|ref|YP_979279.1|  24 IVLTHGFVCAIRAWAYQIADLAG-DYRVIAFDHRGHGRSGVPRRGAYSLNHLAADLDSVLDATL--APRERAVVAGHSMG 100
                                    89*******************86.8***************66666***************9998..566667******** PP

                    Hydrolase_4  87 Gliallyllrypd....kvaglilsaPalkikakl.........k.appllklllkllgkllpklqv..........snn 142
                                    G++ +++ +ry++    + +++ l+++  +    +         + ++p+  l+ + l +++  +++            +
  gi|121639055|ref|YP_979279.1| 101 GITIAAWSDRYRHkvrrRTDAVALINTTTGDL--VrkvkllsvpReLSPVRVLAGRSLVNTFGGFPLpgaaralsrhVIS 178
                                    ********888884444556677777765433..1224566666446666666666666666666668888888766334 PP

                    Hydrolase_4 143 lkadslsrdpevva.ayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskd 221
                                    ++a     dp+  +  ye    ++ + + + +  l++ + +++ + + +t+P+l++ G +D++++ ++sr+++++++   
  gi|121639055|ref|YP_979279.1| 179 TLAVAADADPSATRlVYELFTQMSAAGRGGCAKMLVEEVGSAHLNLDGLTVPTLVIGGVRDRLTPISQSRRIARTAPN-V 257
                                    45555556666655357777778888899999999999999999999999************************9985.4 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   7.5     1e-20     2e-17       1     218 [.      24     278 ..      24     280 .. 0.53

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1e-20
                                    EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-...GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEETCH CS
                  Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhGrs...dpppldled.ladlaalldelaagggpvvlvGHSlG 75 
                                    ++l HG+ +  ++W +  ++a l a++++v+a+D +GhGrs    + +++l+  +adl+ +ld+  a + ++v+ GHS+G
  gi|121639055|ref|YP_979279.1|  24 IVLTHGFVCAIRAWaY--QIADL-AGDYRVIAFDHRGHGRSgvpRRGAYSLNHlAADLDSVLDATLAPRERAVVAGHSMG 100
                                    79****9988888855..55444.555799********9664335566888885577799999999889999******** PP

                                    HHHHHHHHHCC........EE...EEES-..........................----TTT...S----TTHHHHHHTT CS
                  Abhydrolase_6  76 Galalaaapla......lvvg...vlldp...................pp.....talpagl...laaalelllallall 119
                                    G+  +a+ +        +  +    l+++                   p+                   ++l+ a++al 
  gi|121639055|ref|YP_979279.1| 101 GITIAAWSDRYrhkvrrR--TdavALINTttgdlvrkvkllsvprelsPVrvlagR-----SlvnTFGGFPLPGAARALS 173
                                    **7777555557876541..245577777333333333332222222211221110.....0111111111111111111 PP

                                    -C..CCCHCCH....S-HSCCCCHHHCCCCHCHCCCGHH.HHCCHHC...HTTCCHHTT-TTGCEEE.CTT-CHHH.HCH CS
                  Abhydrolase_6 120 rl..lawlsre....plprlfladedadaawrarlarla.allaglg...llpaaawadlpvpllvl.ggeDplvp.rll 187
                                    r+   ++ +++    +++rl ++       ++++ a+++  ++++l      ++ ++ +l+vp+lv+ g +D+l p    
  gi|121639055|ref|YP_979279.1| 174 RHviSTLAVAAdadpSATRLVYE------LFTQMSAAGRgGCAKMLVeevGSAHLNLDGLTVPTLVIgGVRDRLTPiSQS 247
                                    11111111111112122222222......22222222221333333354444577*********9996699996662114 PP

                                    HCCCH..STTEEETCE...SSS-HHHHSHHHHH CS
                  Abhydrolase_6 188 erlla..qagarlpvvlpgaGHlphleepdeva 218
                                    +r+++   ++++l v+l  +GH+ +le+ +ev+
  gi|121639055|ref|YP_979279.1| 248 RRIARtaPNVVGL-VEL-PGGHCSMLERHQEVN 278
                                    4444442244444.555.599*****8889997 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.1e-08   6.2e-05       7      89 ..     201     283 ..     195     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.1e-08
                  Abhydrolase_4   7 alaesllsCagwpvspqrprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdka 86 
                                      a ++  Ca++ v+++ + + + +  ++p+L++++ rD  TP ++ +++a++ ++ v +++  +GH+++ + ++ v+++
  gi|121639055|ref|YP_979279.1| 201 MSAAGRGGCAKMLVEEVGSAHLNLDGLTVPTLVIGGVRDRLTPISQSRRIARTAPNVVGLVELPGGHCSMLERHQEVNSH 280
                                    5556666699999999999998888668******************************************9999989988 PP

                  Abhydrolase_4  87 vda 89 
                                    ++a
  gi|121639055|ref|YP_979279.1| 281 LRA 283
                                    876 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00032      0.65      50      83 ..      85     117 ..      71     151 .. 0.75
   2 ?    4.5   0.0     0.014        28     106     168 ..     220     283 ..     168     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                                    HHC-STTEEEEEETCHHHHHHHHHHHTTSSSEEE CS
                  Ser_hydrolase  50 veaaeekvvlvAHSlgclavlhaaelqlakkvag 83 
                                      a +e++v+  HS+g ++++++   + ++kv++
  gi|121639055|ref|YP_979279.1|  85 TLAPRERAVVAGHSMGGITIAAWS-DRYRHKVRR 117
                                    444566789999***********9.555555543 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                    TTS-SSHHCCHCEEEEETTBTTC-HHHHHHHHHHCT-EEEEET.T-TTSSGGGT-SS-HHHHHH CS
                  Ser_hydrolase 106 aplpreklpfpslvvaSenDpyvsfeeaeelaeawgaelvdlg.eaGHinadsgfgswpeglal 168
                                    a+l+ + l +p+lv+    D + ++++++++a++    +  ++   GH  + +++++ ++ l+ 
  gi|121639055|ref|YP_979279.1| 220 AHLNLDGLTVPTLVIGGVRDRLTPISQSRRIARTAPNVVGLVElPGGHCSMLERHQEVNSHLRA 283
                                    667778899***********************99876665554246888888888887766655 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.045       3     123 ..      10     124 ..       8     143 .. 0.69
   2 ?   -1.2   0.0      0.39   7.8e+02     199     213 ..     265     279 ..     251     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                Chlorophyllase2   3 PkpllvvaPteageYpvllflhGylllnslYsqlLkhiashgfivvapqlykvaeadakei.ksaakvlnWlakgLesvl 81 
                                    P+++ v+ P +   Yp++ ++hG+++    +   ++ +a   + v+a       ++  + + +  a  ln la++L+svl
  gi|121639055|ref|YP_979279.1|  10 PLHTQVFGPPH--GYPIV-LTHGFVCAIRAWAYQIADLAG-DYRVIAFDHRGH-GR--SGVpRRGAYSLNHLAADLDSVL 82 
                                    66666666653..58876.489999777777777777775.577777764443.23..334145567899********** PP

                Chlorophyllase2  82 peevepdlsklalsgHSrGgktafalalgkak.tslkfsalig 123
                                       + p  ++ +++gHS Gg t++a    +++ ++    a+  
  gi|121639055|ref|YP_979279.1|  83 DATLAPR-ERAVVAGHSMGGITIAAWSDRYRHkVRRRTDAVAL 124
                                    ****998.66779********9998776654414445555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                Chlorophyllase2 199 yGHldmldddtglvg 213
                                     GH+ ml+ ++ + +
  gi|121639055|ref|YP_979279.1| 265 GGHCSMLERHQEVNS 279
                                    59*****99964333 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-05      0.19      56      76 ..      89     109 ..      71     126 .. 0.79
   2 ?   -0.2   0.0      0.37   7.3e+02      98     139 ..     226     267 ..     220     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                  Abhydrolase_5  56 lekfvvgGhslGGvvasrfaa 76 
                                     e+ vv+Ghs+GG+ ++ ++ 
  gi|121639055|ref|YP_979279.1|  89 RERAVVAGHSMGGITIAAWSD 109
                                    4789**********9998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.37
                  Abhydrolase_5  98 elskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgn 139
                                     l++++l i g +D + ++++ ++ +++ p+   +v++ Gg 
  gi|121639055|ref|YP_979279.1| 226 GLTVPTLVIGGVRDRLTPISQSRRIARTAPNVVGLVELPGGH 267
                                    5678999**************999999999999998888875 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00071       1.4      41      80 ..      67     106 ..      37     114 .. 0.78
   2 ?    2.5   0.0     0.043        85     142     167 ..     227     252 ..     211     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00071
                                    GHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHH CS
                   Peptidase_S9  41 gqnefdDfiaaaealakegyvdserlaitGgSyGGyltga 80 
                                    g ++++ + a ++ + +  ++ +er ++ G+S GG +++a
  gi|121639055|ref|YP_979279.1|  67 GAYSLNHLAADLDSVLDATLAPRERAVVAGHSMGGITIAA 106
                                    55556666666777888889999*************9987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.043
                                    ---EEEEEEETT-SSS-THHHHHHHH CS
                   Peptidase_S9 142 aypplLlihGlaDdrvppaealklva 167
                                     ++p+L+i G  D  +p++++ ++++
  gi|121639055|ref|YP_979279.1| 227 LTVPTLVIGGVRDRLTPISQSRRIAR 252
                                    789******************99876 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.4e-05      0.19     156     200 ..     223     267 ..     202     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.4e-05
                           FSH1 156 eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggH 200
                                    + d +++ptL + G +D + + ++s+++a++  n   +++ pggH
  gi|121639055|ref|YP_979279.1| 223 NLDGLTVPTLVIGGVRDRLTPISQSRRIARTAPNVVGLVELPGGH 267
                                    556789****************************9********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1978.59
//
Query:       gi|121639056|ref|YP_979280.1|  [L=160]
Description: hypothetical protein BCG_3196c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.6   0.2      0.056   13.9   0.2    1.7  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.1e-06     0.056       4      44 ..       5      45 ..       3     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-06
                                   HHHHHH.HHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHH CS
                        DUF4440  4 leeale.eafvagdaealaallapdavlvgpsgtvldkeell 44
                                   l ++++ + +va++ae ++ +++pd++++ ++   ++ +++ 
  gi|121639056|ref|YP_979280.1|  5 LLREMFdRMVVAKNAELIEHYYDPDFLMYSDG-LSQSFAKFR 45
                                   45555515678***************999755.344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1058.90
//
Query:       gi|121639057|ref|YP_979281.1|  [L=200]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   62.5   3.0    3.7e-17   61.9   0.1    2.5  3  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1     2e-21   3.7e-17       1      46 [.      22      67 ..      22      68 .. 0.98
   2 ?    0.3   0.1     0.034   6.2e+02      19      29 ..     142     152 ..     140     154 .. 0.82
   3 ?   -3.1   0.1      0.39   6.9e+03       4      12 ..     186     194 ..     185     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2e-21
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                   Il+aA+elf  +G++at+v+ IA +A vsk++lY++FpsK +L+e+
  gi|121639057|ref|YP_979281.1| 22 ILKAAAELFYCEGINATGVELIANKASVSKRTLYQHFPSKSALVEE 67
                                   9*******************************************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.034
                                    HHHHHHHHTSS CS
                         TetR_N  19 vreIAkrAGvs 29 
                                    ++++A++AG +
  gi|121639057|ref|YP_979281.1| 142 LARLAREAGAA 152
                                    6899*****87 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.39
                                    HHHHHHHHH CS
                         TetR_N   4 aArelfaer 12 
                                    aA+e+++++
  gi|121639057|ref|YP_979281.1| 186 AAAEVLIDQ 194
                                    788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1347.77
//
Query:       gi|121639058|ref|YP_979282.1|  [L=235]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-31  108.7   0.1    3.1e-31  108.3   0.1    1.1  1  adh_short       short chain dehydrogenase
    7.6e-20   71.5   0.5    9.3e-20   71.2   0.5    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    4.8e-05   23.3   0.3    0.00011   22.2   0.3    1.5  1  NAD_binding_10  NAD(P)H-binding
     0.0026   17.7   0.6     0.0062   16.5   0.6    1.7  1  KR              KR domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.027   14.0   0.1    1.5  2  Epimerase       NAD dependent epimerase/dehydratase family
       0.13   11.6   0.0       0.18   11.1   0.0    1.1  1  LIP             Secretory lipase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.1   1.1e-34   3.1e-31       2     189 ..       8     182 ..       7     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.1e-34
                                    EEEEESTTSHHHHHHHHHHH.HTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   2 vvlvtGassGIGraiakela.keGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    ++lvtGa +G+Gr+++ +l+ ++ akv+++ r+  +l   a  +     +++++q+Dvtd+ +v ++ + a      + +
  gi|121639058|ref|YP_979282.1|   8 TALVTGANRGMGREYVAQLLgRKVAKVYAATRN--PL---AIDVS--DPRVIPLQLDVTDAVSVAEAADLA----TDVGI 76 
                                    89************8777761455555555555..55...33444..357**********99988887777....99*** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    L+nNAGi++ +++ + + ++ +  +e+Nl+g++ l+ a+++  ++++sG+IvnvsSv +   ++ + +Y+ sKaa+ + t
  gi|121639058|ref|YP_979282.1|  77 LINNAGISRASSVLDKDTSALRGELETNLFGPLALASAFADR-IAERSGAIVNVSSVLA--WLPLGMSYGVSKAAMWSAT 153
                                    ******************************************.78*************9..788899************* PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmake 189
                                    +s++ elap+g++v++v+ GlvdTdm + 
  gi|121639058|ref|YP_979282.1| 154 ESMRIELAPRGVQVVGVYVGLVDTDMGRF 182
                                    **************************865 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.5   3.1e-23   9.3e-20       1     184 [.      13     185 ..      13     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3.1e-23
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                    Ga +g+Gr+ + +l   G +v+ +++  ++     +la +++   v  l++DVtd  +v+++++ +++    + il+nna
  gi|121639058|ref|YP_979282.1|  13 GANRGMGREYVAQLL--GRKVAKVYAATRN-----PLAIDVSDPrVipLQLDVTDAVSVAEAADLATD----VGILINNA 81 
                                    788999988654443..4455555555554.....4444444333448**********9999988765....68****** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                    gi+++  +++l+ + + ++  l++nl + ++la a++  +++++g+ivn+ssv a   +p    yg++Kaa+ + t ++ 
  gi|121639058|ref|YP_979282.1|  82 GISRA--SSVLDKDTSALRGELETNLFGPLALASAFADrIAERSGAIVNVSSVLA--WLPLGMSYGVSKAAMWSATESMR 157
                                    *****..*******************************666677*********55..899999***************** PP

                                    HHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                   adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikg 184
                                     el+p+g++v  v  g+++T++ + ++ 
  gi|121639058|ref|YP_979282.1| 158 IELAPRGVQVVGVYVGLVDTDMGRFADA 185
                                    **********************886654 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   3.7e-08   0.00011       1      61 [.      13      71 ..      13      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.7e-08
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT- CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga 61
                                   GA+ + Gr+ v++ll r+  +v a +Rnp  ++ ++ ++++  +++dvtd+ ++aea + a
  gi|121639058|ref|YP_979282.1| 13 GANRGMGREYVAQLLGRKVAKVYAATRNPLAID-VS-DPRVIPLQLDVTDAVSVAEAADLA 71
                                   9*****************999***********9.75.7******************98744 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   2.1e-06    0.0062       2     139 ..       8     134 ..       7     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeepp 81 
                                    t l+tG+  g+G+e + +l+ +  +++   +R+ +          ++  ++ +v  +++Dv+d+ +v+++ + ++     
  gi|121639058|ref|YP_979282.1|   8 TALVTGANRGMGREYVAQLLGRKVAKVYAATRN-P---------LAIDVSDPRVIPLQLDVTDAVSVAEAADLAT----D 73 
                                    569******************************.3.........234456789***************9999886....6 PP

                                    --EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiag 139
                                    +   i+ Ag++r + + ++++++l+  l+  + G   L  +++d   e+   +v +SS+ +
  gi|121639058|ref|YP_979282.1|  74 VGILINNAGISRASSVLDKDTSALRGELETNLFGPLALASAFADriaERSGAIVNVSSVLA 134
                                    7789**************************************9977778888999999876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   8.9e-06     0.027       1      79 [.       9      86 ..       9     134 .. 0.73
   2 ?   -2.4   0.0       0.9   2.7e+03     142     157 ..     142     157 ..     138     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.9e-06
                                   EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.T-SEEEE--S---HHH CS
                      Epimerase  1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkee.qpdavihlAavggvaa 79
                                   +lVtGa+  +G+  v +ll ++  +v + +r++ a   +  + +   +ld+td+++++++ +   ++ + i+ A+++   a
  gi|121639058|ref|YP_979282.1|  9 ALVTGANRGMGREYVAQLLGRKvAKVYAATRNPLAIDVSDPR-VIPLQLDVTDAVSVAEAADLAtDVGILINNAGISR--A 86
                                   59********************555*******7777765544.4889************9996555555555555443..3 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.9
                                    HHHHHHHHHHHHHHHH CS
                      Epimerase 142 YaaaKlageklveaya 157
                                    Y+++K+a+ + +e+++
  gi|121639058|ref|YP_979282.1| 142 YGVSKAAMWSATESMR 157
                                    8888888877777765 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     6e-05      0.18      59     138 ..     121     203 ..     111     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6e-05
                            LIP  59 lksekvtgiksdakvalwGYSgG.slAsawAae..lqpeYAPe.lelvGaalGgfvanltavaeavdgtvfaGlialaln 134
                                     +s+++ +++s      +G S+G s A+ w a+  +  e AP  +++vG+++G + ++++ +a a   ++ a ++  +l 
  gi|121639058|ref|YP_979282.1| 121 ERSGAIVNVSSVLAWLPLGMSYGvSKAAMWSATesMRIELAPRgVQVVGVYVGLVDTDMGRFADAP-KSDPADVVRQVLD 199
                                    4566677777766667789**9977899998853377899**5499***************99874.5666888888888 PP

                            LIP 135 glan 138
                                    g+  
  gi|121639058|ref|YP_979282.1| 200 GIEA 203
                                    8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1821.51
//
Query:       gi|121639059|ref|YP_979283.1|  [L=495]
Description: amidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-130  436.1   0.3   1.8e-130  435.9   0.3    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.9   0.3    1e-134  1.8e-130       1     450 [.      32     476 ..      32     477 .. 0.97

  Alignments for each domain:
  == domain 1  score: 435.9 bits;  conditional E-value: 1e-134
                                    HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS CS
                        Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaek 80 
                                    elve +l+ri+++n +lna+vtv++++a++ A+++d++rarg+e gpLhG+Pi+vKD+++++g++tt+G + l++y++++
  gi|121639059|ref|YP_979283.1|  32 ELVELYLSRIDTYNASLNAIVTVDPDAARRVAKRSDAARARGDELGPLHGLPITVKDSYETAGMRTTCGRRDLADYVPTQ 111
                                    79****************************************************************************** PP

                                    --HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHH CS
                        Amidase  81 DatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPA 160
                                    Da+ v+rL++aGa+i+gkTnm++  + ++++n+vfg+t+NPwd  rt+GGS+GG AAa+Aagl+ +++G+++GGS RiPA
  gi|121639059|ref|YP_979283.1| 112 DAEAVARLRRAGAIIMGKTNMPTGNQDVQASNPVFGRTNNPWDAARTSGGSAGGGAAATAAGLTSFDYGSEIGGSTRIPA 191
                                    ******************************************************************************** PP

                                    HHCTSEEEE--TTSC--TTB-.........-SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCT CS
                        Amidase 161 sfcglvGlKPtygrvSragvv.........alessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeel 231
                                    ++cgl+G+K t+  v+  g +         + ++ ++++G+  r ++d++ +l++++g++++d   s+      +la+++
  gi|121639059|ref|YP_979283.1| 192 HYCGLYGHKSTWRSVPLVGHIpsapgnpgrWGQADMACAGVQVRGARDIIPALEATVGPMRADGGFSY------ALAPPR 265
                                    *********666555555555555555****************************************8......68**** PP

                                    T---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT.-EEEEEE-CCGGGHHH.HHHHHHHHHHHHHTTT-SSSSS- CS
                        Amidase 232 kkslkglriGvvkedgvasldpevqravekalkaLeeaG.hevvevelpsleeals.lyylilvaeassnlarylgvrye 309
                                    + +lk++r++v+ ed+++ +d++v+ra+++a++aL++aG h v++  +  +++a+s  +++ lv+ a+++++        
  gi|121639059|ref|YP_979283.1| 266 AGALKDFRVAVWAEDPHCPIDADVRRAMDDAVAALRAAGaHVVEQPATIPVDMAVShNIFQSLVFGAFAVDR-------- 337
                                    ***************************************9999*************************9977........ PP

                                    --SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCC.HHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--B CS
                        Amidase 310 rlsetkvlsellpksraellgeevkrrielgnyalsaeassky.ylkaqkvrrllrrefakafeelDvllsPtaptpapr 388
                                            s+l p+s a+l ++ v++ + + ++al a+ +s+  +l+a+++r+++r+++a++f+e+Dvll+P++ptpap 
  gi|121639059|ref|YP_979283.1| 338 --------STLSPASAAALGLRAVRHPRGEAANALGATLQSHRaWLFADAARHEMRDRWAGFFNEFDVLLLPVTPTPAPL 409
                                    ........89********************************99************************************ PP

                                    CCCCCHHH.....CSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                        Amidase 389 lgekdkti.....dsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                    +++kd+++     d + v++ ++d +++++++n+ag+pa+++p++++++glP+G+q +g+a+ ++t+
  gi|121639059|ref|YP_979283.1| 410 HHNKDHDRlgrtiDVDGVSRSYWDQLKWNALANIAGTPATTMPITTTATGLPIGIQAMGPAGGDRTT 476
                                    ******9999999***************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3260.83
//
Query:       gi|121639060|ref|YP_979284.1|  [L=105]
Description: epoxide hydrolase mesTb [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 580.46
//
Query:       gi|121639061|ref|YP_979285.1|  [L=208]
Description: epoxide hydrolase mesTa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-07   30.9   0.0    2.6e-07   30.6   0.0    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.1e-06   29.4   1.9    1.7e-06   28.8   1.9    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.9e-11   2.6e-07       5      94 ..      52     137 ..      51     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.9e-11
                                    EE-STTTCGGGGTTGHHHHHHHHT.TSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                  Abhydrolase_1   5 ilhGlpgssdvwaerglapaLakd.gfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                    +l+G+p++s+ wa+  +   L+ + +f  i lD  G+g S+++ +     y+t+  ad ++++  a g+ + ++v++++ 
  gi|121639061|ref|YP_979285.1|  52 FLPGWPDGSYGWAK--VEAFLSSRfHFPRIYLDYIGHGDSDKPRD---YPYSTFERADLVEALWHAEGIAQTVVVAFDYS 126
                                    79************..99899998*********************...789***************************** PP

                                    HHHHHHHHHHH CS
                  Abhydrolase_1  84 Gmialayaaey 94 
                                    + ++l+++a+ 
  gi|121639061|ref|YP_979285.1| 127 CIVSLELLARR 137
                                    *******9986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   1.9   1.9e-10   1.7e-06       3      96 ..      52     173 ..      52     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.9e-10
                                    EE--GC.....GCHHHHHHHHCCT..CEEEEE--TTSTS-GGCS--HHHCHHH..HHHHCCTT....TTSEEEEEETCHH CS
                  Abhydrolase_6   3 llHGagssassWlvapLaallaag..vhvlapDlpGhGrsdpppldledladl..aalldelaa..gggpvvlvGHSlGG 76 
                                    +l+G + ++++W+   + a+l+++  +  + +D+ GhG ++++p d++   ++  a+l+++l +  g  + v+v+ ++ +
  gi|121639061|ref|YP_979285.1|  52 FLPGWPDGSYGWA--KVEAFLSSRfhFPRIYLDYIGHG-DSDKPRDYPY-STFerADLVEALWHaeGIAQTVVVAFDYSC 127
                                    89**999999998..7777778886633345*******.7677766644.555555566666555578899********* PP

                                    HHHHHHHHCC....................EEEEES-.............. CS
                  Abhydrolase_6  77 alalaaapla..................lvvgvlldp.............p 96 
                                    +++l++++                    l      ++             +
  gi|121639061|ref|YP_979285.1| 128 IVSLELLARRidreragndqrtritaclL-----ANGgifadghthawytT 173
                                    *****444446899999998874333321.....33333333243333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1156.14
//
Query:       gi|121639062|ref|YP_979286.1|  [L=286]
Description: peroxidase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   85.6   0.2    3.9e-22   79.1   0.2    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    2.2e-17   63.1   0.0    3.3e-17   62.6   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    8.8e-16   59.2   0.6    1.1e-15   58.8   0.6    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
      4e-06   26.5   0.1     0.0028   17.3   0.0    2.2  2  DLH            Dienelactone hydrolase family
    6.7e-06   25.7   0.1    0.00077   19.0   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00092   18.9   0.1     0.0043   16.7   0.1    1.9  1  FSH1           Serine hydrolase (FSH1)
     0.0011   19.0   0.0     0.0019   18.2   0.0    1.4  1  Abhydrolase_4  TAP-like protein
     0.0017   18.3   0.0     0.0029   17.5   0.0    1.4  1  Palm_thioest   Palmitoyl protein thioesterase
     0.0018   17.4   0.0     0.0024   17.0   0.0    1.1  1  DUF2048        Abhydrolase domain containing 18
     0.0034   17.5   0.0     0.0094   16.1   0.0    1.6  2  Thioesterase   Thioesterase domain
     0.0053   16.5   0.1      0.056   13.1   0.0    2.6  3  PGAP1          PGAP1-like protein
     0.0068   16.0   0.1      0.035   13.7   0.1    2.0  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
       0.05   13.6   0.0        0.1   12.6   0.0    1.4  1  UPF0227        Uncharacterised protein family (UPF0227)
      0.075   12.9   0.0       0.48   10.3   0.0    2.1  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.2   3.1e-25   3.9e-22       2     256 ..      40     272 ..      39     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 3.1e-25
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEET CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhS 81 
                                    ++++lh l++ +d+w    +++++a  ++ v+++D rGvg S+       d+ +t  +add  +++ alg d++ l+G+S
  gi|121639062|ref|YP_979286.1|  40 PVIFLHHLGAVLDNWDP-RVVDGIAA-KHPVVTFDNRGVGASEGQTP---DTVTT--MADDAIAFVRALGFDQVDLLGFS 112
                                    89***********9777.7888**99.*******************9...66666..*********************** PP

                                    HHHHHHHHHHHHHGGGEEEEEEESE..CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHH CS
                  Abhydrolase_1  82 mGGmialayaaeyperVkalvllga..idpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvd 159
                                    +GG++a   a++ p+ V++++l g+           +  ++++s   ++    +++ r  + + +++++a  ++      
  gi|121639062|ref|YP_979286.1| 113 LGGFVAQVIAQQEPQLVRKIILAGTgpAGGVGIGKVTFGTIRESIKATLTFRDPKELRFFTRTDSGKSAARQFVK----- 187
                                    *************************75555556667888889999999988889999999988888888888888..... PP

                                    HHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS CS
                  Abhydrolase_1 160 alkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpk 239
                                        ++k+ r ++ +  + +   + +lk+i  w t   +  l +++       p+l+  g++D +vp +++ dla+ lp+
  gi|121639062|ref|YP_979286.1| 188 ----RLKE-RKDNRDKSITVRAFRSQLKAIHAWGTQKPSD-LTSIGH------PVLIANGDDDTMVPTSNSLDLADRLPD 255
                                    ....4444.4444455888888889999999998888877.557777......*************************** PP

                                    EEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 240 krlvvisdagHlafleg 256
                                    ++l++++dagH  ++++
  gi|121639062|ref|YP_979286.1| 256 ATLRIYPDAGHGGIFQH 272
                                    ***********999886 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   2.5e-20   3.3e-17      34     233 ..      68     267 ..      42     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.5e-20
                    Hydrolase_4  34 vyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalki 113
                                    v+++D+rG G seg++   + ++++ dD+ afv+++  +    ++ llG S+GG++a+ +++++p+ v+++il+++  + 
  gi|121639062|ref|YP_979286.1|  68 VVTFDNRGVGASEGQTP--DTVTTMADDAIAFVRALGFD----QVDLLGFSLGGFVAQVIAQQEPQLVRKIILAGTGPAG 141
                                    99***********9998..99************999944....5678**************************9988777 PP

                    Hydrolase_4 114 kakl.....k.appllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplv.hgkitvrlllelldamkrlee. 185
                                       +       +++  k++l++  +  ++l++  ++++ + s  +++v+++++ +    + itvr +++ l+a+ +  + 
  gi|121639062|ref|YP_979286.1| 142 GVGIgkvtfGtIRESIKATLTFRDP--KELRFFTRTDSGK-SAARQFVKRLKERKDNrDKSITVRAFRSQLKAIHAWGTq 218
                                    6554334442244444444444444..2344444444444.344566776666666669********9999998765440 PP

                    Hydrolase_4 186 raakit...lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                    + +++t    P+l+  G++D+ v+ ++s +l++rl+  d tl++yp + H 
  gi|121639062|ref|YP_979286.1| 219 KPSDLTsigHPVLIANGDDDTMVPTSNSLDLADRLP--DATLRIYPDAGHG 267
                                    444555666***************************..9**********96 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.6   8.8e-19   1.1e-15       1     219 [.      41     278 ..      41     279 .. 0.67

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 8.8e-19
                                    EEEE-..-GC.....G..C.HHHHHHHHCCTCEEEEE--TTSTS-.GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEET CS
                  Abhydrolase_6   1 vlllH..GagssassW..l.vapLaallaagvhvlapDlpGhGrs.dpppldled.ladlaalldelaagggpvvlvGHS 73 
                                    v++lH  Ga +  + W  + v+ +    aa + v+++D +G G s    p++++  ++d  a++++l+   ++v l+G S
  gi|121639062|ref|YP_979286.1|  41 VIFLHhlGAVL--DNWdpRvVDGI----AAKHPVVTFDNRGVGASeGQTPDTVTTmADDAIAFVRALG--FDQVDLLGFS 112
                                    57777677666..67732233344....555566********96624444555553455599*****5..********** PP

                                    CHHHHHHHHHHCC.......EEEEES-..----TTT.......S----TTHHHHHHTT-C..CCCHCCH....S-HSCCC CS
                  Abhydrolase_6  74 lGGalalaaapla.....lvvgvlldppptalpagl.......laaalelllallallrl..lawlsre....plprlfl 135
                                    lGG++a+     a     lv++++l++   ++pag        +  ++e ++a l+ + +  l++++r     +++r+f+
  gi|121639062|ref|YP_979286.1| 113 LGGFVAQV---IAqqepqLVRKIILAG---TGPAGGvgigkvtFGTIRESIKATLTFRDPkeLRFFTRTdsgkSAARQFV 186
                                    ****8888...3344465555599999...66666666677775555555554444333334455544345568888888 PP

                                    CHHH..C....CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEEC..TT-CHHHHCHHCCCH....STTEEETCE.. CS
                  Abhydrolase_6 136 aded..a....daawrarlarlaallaglgllpaaawadlpvpllvlg..geDplvprllerlla....qagarlpvvlp 203
                                    + +   +    + + +++++  ++   ++g+  +++++ +  p+l+ +  ++D +vp      l     +++a+l  ++p
  gi|121639062|ref|YP_979286.1| 187 KRLKerKdnrdKSITVRAFRSQLKAIHAWGTQKPSDLTSIGHPVLI-AngDDDTMVP--TSNSLDladrLPDATL-RIYP 262
                                    855543144559999999999999999999999***********88.5315555777..4444443346688888.**** PP

                                    .SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 204 gaGHlphleepdevae 219
                                    +aGH   +++ +++++
  gi|121639062|ref|YP_979286.1| 263 DAGHGGIFQHHAQFVD 278
                                    ****555548899886 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0021       2.7      75     127 ..      84     133 ..      74     156 .. 0.85
   2 !   17.3   0.0   2.2e-06    0.0028     135     190 ..     218     269 ..     175     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                            DLH  75 eekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaava 127
                                     + v+  +++a+a++++ +    ++v + Gf +GG +a ++a+++p++ + ++
  gi|121639062|ref|YP_979286.1|  84 PDTVTTMADDAIAFVRALG---FDQVDLLGFSLGGFVAQVIAQQEPQLVRKII 133
                                    5678888899999999999...679******************9998876665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.2e-06
                            DLH 135 keleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFa 190
                                    ++ ++ + i +p+l+  g+ D+++p ++  +l+  l    +d+ l +Yp+agH+  
  gi|121639062|ref|YP_979286.1| 218 QKPSDLTSIGHPVLIANGDDDTMVPTSNSLDLADRL----PDATLRIYPDAGHGGI 269
                                    444556789******************988888877....9************955 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.013        16      64      89 ..     104     129 ..      71     137 .. 0.81
   2 !   19.0   0.0     6e-07   0.00077     142     205 ..     226     284 ..     183     286 .] 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                                    GGEEEEEETHHHHHHHHHHHH-GGG- CS
                   Peptidase_S9  64 erlaitGgSyGGyltgaalnqrpdlF 89 
                                    +++ + G S GG+++ +++ q+p+l 
  gi|121639062|ref|YP_979286.1| 104 DQVDLLGFSLGGFVAQVIAQQEPQLV 129
                                    667789*****************985 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 6e-07
                                    ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHH CS
                   Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFl 205
                                    + +p+L+  G+ D+ vp +++l l+++L +    + l+i+pd+gHg+   +++++ + + l+Fl
  gi|121639062|ref|YP_979286.1| 226 IGHPVLIANGDDDTMVPTSNSLDLADRLPD----ATLRIYPDAGHGGIF-QHHAQFVDDALQFL 284
                                    789*************************87....89*********7763.44455555555555 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.4e-06    0.0043     106     194 ..     108     259 ..      85     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.4e-06
                           FSH1 106 iiGFSqGaalaallaslleellkea................................shpslkfailvsGfkleepk... 150
                                    ++GFS G+++a+++a++  +l ++                                 + ++l+f+    + k+  ++   
  gi|121639062|ref|YP_979286.1| 108 LLGFSLGGFVAQVIAQQEPQLVRKIilagtgpaggvgigkvtfgtiresikatltfrDPKELRFFTRTDSGKSAARQfvk 187
                                    79************999999988779999999999999999999999999999988844555666555444443333566 PP

                           FSH1 151 .............................yeeyyeedkiqtptLhvlGelDtvvdeerseaLaeafknsskvl 194
                                                                  ++  + ++i  p+L   G++Dt+v+ ++s +La+   + +++ 
  gi|121639062|ref|YP_979286.1| 188 rlkerkdnrdksitvrafrsqlkaihawgTQKPSDLTSIGHPVLIANGDDDTMVPTSNSLDLADRLPD-ATLR 259
                                    6666666666666666666666667665544445678889************************9988.4443 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0019      28      85 ..     222     279 ..     206     286 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                  Abhydrolase_4  28 estakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgala.agntCvdk 85 
                                    + t    +pvL+ ++  D ++P++    la++l++a+l ++ ++GHg++   + + vd+
  gi|121639062|ref|YP_979286.1| 222 DLTSI-GHPVLIANGDDDTMVPTSNSLDLADRLPDATLRIYPDAGHGGIFqHHAQFVDD 279
                                    33332.39****************************************99444444444 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0029       1     195 [.      40     244 ..      40     253 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                   Palm_thioest   1 PvviwhGldsaesn.mqklaelieklig.tyvknveigeseaedrkasffgnlndqveavckklelangfhaiGfSQGgl 78 
                                    Pv+++h l++  +n   ++++ i ++++ ++  n  +g+se  ++ +++++ ++d ++ v ++l   ++++++GfS Gg 
  gi|121639062|ref|YP_979286.1|  40 PVIFLHHLGAVLDNwDPRVVDGIAAKHPvVTFDNRGVGASE-GQTPDTVTTMADDAIAFV-RAL-GFDQVDLLGFSLGGF 116
                                    77778877555555555677777777754666666677775.456666666666666666.443.3489*********** PP

                   Palm_thioest  79 flRaliercddkknvrnlislggpqaGvfgl...........llckvaekllasgavysklvqkslvqaqywrdpeklee 147
                                    ++  ++++  ++  vr++i  g+  aG  g+           +   ++ +  ++  ++++    + +  q+++  ++ ++
  gi|121639062|ref|YP_979286.1| 117 VAQVIAQQE-PQL-VRKIILAGTGPAGGVGIgkvtfgtiresIKATLTFRDPKELRFFTRTDSGKSAARQFVKRLKERKD 194
                                    ***999997.555.9***99986666666743444455555422222223333333566666666667777777774477 PP

                   Palm_thioest 148 YlkknkFLpdiNnerdhaknetykk..nllkleklvlvgfsdDtvvvPke 195
                                     ++k+   + +  + ++      +k   l+++ + vl++  dD+++vP  
  gi|121639062|ref|YP_979286.1| 195 NRDKSITVRAFRSQLKAIHAWGTQKpsDLTSIGHPVLIANGDDDTMVPTS 244
                                    77777777777666655433222223488888888888888888888865 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.9e-06    0.0024     169     340 ..      97     275 ..      86     285 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                        DUF2048 169 wlereGyGplgltGlSmGGhmaslaasnwpkplvlvpclswstasav....fteGvlsksiawdvLekqledgnyrerls 244
                                    ++   G+ ++ l G S+GG+ a++ a + p+ +  + +     a  v     t G +++si+  +  ++ ++ ++  r  
  gi|121639062|ref|YP_979286.1|  97 FVRALGFDQVDLLGFSLGGFVAQVIAQQEPQLVRKIILAGTGPAGGVgigkVTFGTIRESIKATLTFRDPKELRFFTR-- 174
                                    55666999**********************988877655555554332222788999999998877777666666666.. PP

                        DUF2048 245 tasdaaaeekaakldeakerkaekealrfmrl..lmdelthlknfsvpkdtsli....ivvaAkdDayvpresvaslqei 318
                                    t s  +a+ +   ++  kerk ++++    r   + ++++h      p d  +i     +   +dD  vp+++  +l + 
  gi|121639062|ref|YP_979286.1| 175 TDSGKSAARQF--VKRLKERKDNRDKSITVRAfrSQLKAIHAWGTQKPSDLTSIghpvLIANGDDDTMVPTSNSLDLADR 252
                                    44444444444..444455555555555544400445555555555566666553321344568999************* PP

                        DUF2048 319 wpgsevr.yldgGHvsayllkkk 340
                                     p+++ r y d+GH   +  + +
  gi|121639062|ref|YP_979286.1| 253 LPDATLRiYPDAGHGGIFQHHAQ 275
                                    ******9458****765555544 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.3e-06    0.0094      40      86 ..      79     124 ..      63     136 .. 0.87
   2 ?   -1.9   0.0       2.2   2.8e+03     145     169 ..     183     208 ..     175     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-06
                                    SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHH CS
                   Thioesterase  40 rdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArq 86 
                                    ++ +++++ +++a+  ++ +r+   +  ++l G+SlGg++A+ +A+q
  gi|121639062|ref|YP_979286.1|  79 SEGQTPDTVTTMADDAIAFVRALGFD-QVDLLGFSLGGFVAQVIAQQ 124
                                    56678999***************999.9*****************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHHHTCCS.-TTSCSE CS
                   Thioesterase 145 sellpalradyraleqys.lrpeaaq 169
                                    ++++++l++++++  +    r+++ q
  gi|121639062|ref|YP_979286.1| 183 RQFVKRLKERKDNRDKSItVRAFRSQ 208
                                    55566666666666555555555555 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.93   1.2e+03       3      20 ..      37      54 ..      36      74 .. 0.77
   2 !   13.1   0.0   4.4e-05     0.056      59     126 ..      78     136 ..      68     143 .. 0.72
   3 ?   -1.2   0.0       1.1   1.4e+03      59      78 ..     264     283 ..     263     286 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.93
                          PGAP1  3 sGipVlFvpGnagsykqv 20
                                   +G+pV+F++ ++  ++++
  gi|121639062|ref|YP_979286.1| 37 AGVPVIFLHHLGAVLDNW 54
                                   59******9877766666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.4e-05
                          PGAP1  59 aldGrtlldqaeylndaIkyIlslysssekeptsviliGHSmGGivaraaltlknyikqsvntiltla 126
                                    a +G+t    + + +daI+ +  l         +v l+G S+GG+va++++  +   +q v++i+  +
  gi|121639062|ref|YP_979286.1|  78 ASEGQTPDTVTTMADDAIAFVRALG------FDQVDLLGFSLGGFVAQVIAQQE---PQLVRKIILAG 136
                                    5566666666666777777755554......789*************8776554...57777777655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                          PGAP1  59 aldGrtlldqaeylndaIky 78 
                                    a +G++ + +a++++da++ 
  gi|121639062|ref|YP_979286.1| 264 AGHGGIFQHHAQFVDDALQF 283
                                    679*************9875 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   2.7e-05     0.035      60     251 ..      68     251 ..      66     265 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                    EEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TC CS
                  Peptidase_S15  60 vVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdly 139
                                    vV  d rG g+SeG++  + ++ a+d+ + ++   +     ++V  +G+S +G+++ ++a+++++ ++ i+ + ++    
  gi|121639062|ref|YP_979286.1|  68 VVTFDNRGVGASEGQTPDTVTTMADDAIAFVR---A--LGFDQVDLLGFSLGGFVAQVIAQQEPQLVRKIILAGTGPAGG 142
                                    7999***********99977777777777765...3..3457899***************96666666555444333332 PP

                                    CC.CSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHH......THHHHCCCC--SSS CS
                  Peptidase_S15 140 dd.yyregGlvrapgglswedldllaealtsrradegdalkaaaryeaasdellaeldrq......tpveselletgdyd 212
                                     +    + G++r           + +++lt r+++e +  ++ +  ++a+++ +++l+++      +   +   ++ +  
  gi|121639062|ref|YP_979286.1| 143 VGiGKVTFGTIR----------ESIKATLTFRDPKELRFFTRTDSGKSAARQFVKRLKERkdnrdkSITVRAFRSQLKAI 212
                                    222333333333..........4444455555555555555544444444444444444433334334445555555666 PP

                                    HHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHH CS
                  Peptidase_S15 213 afWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklye 251
                                    ++W  +++s d++ ++ pvl+++G  D++v   ++++l +
  gi|121639062|ref|YP_979286.1| 213 HAWGTQKPS-DLTSIGHPVLIANGDDDTMVPtSNSLDLAD 251
                                    778888888.89************9998887677766655 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.8e-05       0.1      40      80 ..      85     125 ..      69     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                        UPF0227  40 edpqqalkeleklvaelgddnillvGssLGGyyatrlgerf 80 
                                         ++   ++ v +lg d++ l G sLGG++a+ ++++ 
  gi|121639062|ref|YP_979286.1|  85 DTVTTMADDAIAFVRALGFDQVDLLGFSLGGFVAQVIAQQE 125
                                    555566777888999999999*****************974 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038      0.48     108     161 ..     220     266 ..      92     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                                    B--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S CS
                         BAAT_C 108 lipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGH 161
                                      ++  +  p+l+++g dD ++p+++s  ++++rL  a  +      +Yp+aGH
  gi|121639062|ref|YP_979286.1| 220 PSDLTSIGHPVLIANGDDDTMVPTSNSL-DLADRLPDATLR------IYPDAGH 266
                                    4455667889****************99.888999888777......799**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.39s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1544.56
//
Query:       gi|121639063|ref|YP_979287.1|  [L=119]
Description: hypothetical protein BCG_3203 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-30  103.4   0.0    1.1e-29  103.2   0.0    1.0  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0     6e-34   1.1e-29      23     129 ..      11     117 ..       2     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 6e-34
                                    ---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEEEEEE--HHHHHHHH CS
                F420H2_quin_red  23 vpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldvtAreveddekarlw 102
                                    vp+llL+ + rk+gk    pl +  d ++++vvas +G+ ++p+wy+Nl  nP+ ++q+g ++++v A  ++ de+arlw
  gi|121639063|ref|YP_979287.1|  11 VPTLLLEHRSRKSGKNFVAPLLYITDRNNVIVVASALGQAENPQWYRNLPPNPDTHIQIGSDRRPVRAVVASSDERARLW 90 
                                    699***************************************************************************** PP

                                    HHHHHH-THHHHHHHHHSSTS-EEEEE CS
                F420H2_quin_red 103 klvvenspsYadyqsktdreipvvVle 129
                                     ++v++++++++ qs+t+r ipv++l 
  gi|121639063|ref|YP_979287.1|  91 PRPVDAYADFDSCQSWTERGIPVIILR 117
                                    ***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 832.50
//
Query:       gi|121639064|ref|YP_979288.1|  [L=97]
Description: hypothetical protein BCG_3204 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 631.97
//
Query:       gi|121639065|ref|YP_979289.1|  [L=429]
Description: hypothetical protein BCG_3205 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-26   91.7   0.0    5.1e-26   91.2   0.0    1.2  1  DUF4143          Domain of unknown function (DUF4143)
    7.6e-19   68.1   0.0    2.6e-18   66.3   0.0    1.8  2  AAA_14           AAA domain
     0.0013   19.1   0.1     0.0029   18.0   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0023   18.1   0.0     0.0068   16.6   0.0    1.9  2  AAA_33           AAA domain
      0.003   17.4   0.0      0.012   15.4   0.0    2.0  2  DUF746           Domain of Unknown Function (DUF746)
  ------ inclusion threshold ------
      0.037   13.9   0.0      0.066   13.1   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.048   12.5   0.0      0.092   11.6   0.0    1.4  1  AAA_35           AAA-like domain
      0.055   13.7   0.0        2.6    8.2   0.0    2.4  2  AAA_28           AAA domain
      0.081   12.6   0.0       0.14   11.8   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      0.093   12.7   0.0       0.26   11.3   0.0    1.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.4   0.0       0.89    9.6   0.0    2.4  2  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
       0.15   11.5   0.0        0.3   10.5   0.0    1.5  1  SRPRB            Signal recognition particle receptor beta su
       0.21   11.5   0.0       0.35   10.8   0.0    1.3  1  Rad17            Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   3.7e-29   5.1e-26       1     122 []     210     371 ..     210     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 3.7e-29
                                    xxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143   1 erDirklagvrdpeelrk.......................................glverlppwsespnskkrlrksp 41 
                                    +rD+r+l++++++++l++                                       +lv+rlp+w  s+n++ +++k+ 
  gi|121639065|ref|YP_979289.1| 210 QRDVRELKRIEQTDRLPRfmrylaaitaqelnvaeaarvigvdagtirsdlalfetvYLVHRLPAW--SRNLTAKIKKRS 287
                                    69********99999999************************************************..************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  42 KlyfvDtGLlvallgldkeelleds.enkGallEnlVaqeLlky..sekegaklyyyrdkngaEvDfvielkggkivpiE 118
                                    K+++vD+G +++l g ++++l +   e  G ++E++V++eL+k   +++ +++ly++rd++g+E+D+++++ + ++v++E
  gi|121639065|ref|YP_979289.1| 288 KIHVVDSGFAAWLRGQSADSLARPTaEGAGPIMETFVINELMKLraATELEVDLYHFRDRDGREIDCILQTPDSRVVGVE 367
                                    **************999998666558999**************9998888****************************** PP

                                    xxxx RF
                        DUF4143 119 vKss 122
                                    vK+s
  gi|121639065|ref|YP_979289.1| 368 VKAS 371
                                    **96 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.9e-21   2.6e-18       3     129 ..      27     144 ..      25     146 .. 0.91
   2 ?   -1.7   0.0       1.9   2.7e+03      73     104 ..     269     300 ..     269     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.9e-21
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpe.wek 81 
                                    ++++i G+R++GKTtll+ql  el         +++d er +++adp   + +i++  +       flDE+q + + +  
  gi|121639065|ref|YP_979289.1|  27 RVVLINGPRQAGKTTLLQQLHAELG---GWLRSLDVDVERASARADP---EGYIMSAPR-----PTFLDEVQCAGDpLIL 95 
                                    799******************9999...8999999999999999999...599999633.....38******9966599* PP

                         AAA_14  82 alkslvdeg.knldvivtGSnskllskeiatslagrvaeielyplsfaE 129
                                    a+k   d++ +  +++++GS   l    +++slagrva ++l+pls+aE
  gi|121639065|ref|YP_979289.1|  96 AIKTATDRDrRPRQFFLSGSTRFLTVPTLSESLAGRVAILDLWPLSVAE 144
                                    *******886778**********************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                         AAA_14  73 iqevpewekalkslvdegknldvivtGSnskl 104
                                    ++++p w++ l   ++++++++v+ +G ++ l
  gi|121639065|ref|YP_979289.1| 269 VHRLPAWSRNLTAKIKKRSKIHVVDSGFAAWL 300
                                    689999*****999999989999888766555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0029      15      52 ..      15      58 ..       8     171 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                         AAA_16 15 alervrsgrp..elvllsGesGvGKsslvrellralekd....g 52
                                   +le++r+  +  ++vl+ G++  GK++l+++l+ +l +     +
  gi|121639065|ref|YP_979289.1| 15 MLEQLREVAEytRVVLINGPRQAGKTTLLQQLHAELGGWlrslD 58
                                   4444444444449********************98887644441 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-06    0.0068       1      39 [.      28      68 ..      28     135 .. 0.76
   2 ?   -2.5   0.0       3.8   5.2e+03      53      59 ..     223     229 ..     176     260 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg.avl.lssdtlrrrlfg 39
                                   +vl+ G+  +GK+tl+++l+++lg + + l+ d++r   ++
  gi|121639065|ref|YP_979289.1| 28 VVLINGPRQAGKTTLLQQLHAELGgWLRsLDVDVERASARA 68
                                   7999********************84446999998886665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                         AAA_33  53 drlyqil 59 
                                    drl +++
  gi|121639065|ref|YP_979289.1| 223 DRLPRFM 229
                                    3333333 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.6   3.6e+03      18      33 ..     142     157 ..     139     159 .. 0.81
   2 !   15.4   0.0     9e-06     0.012       3      39 ..     226     266 ..     224     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                         DUF746  18 aadllgtdegiiakwv 33 
                                    +a++ g+ ++iia++ 
  gi|121639065|ref|YP_979289.1| 142 VAERSGVRPEIIAQLF 157
                                    6888899999999975 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 9e-06
                         DUF746   3 relIrlL....sqplslaeaadllgtdegiiakwvreFrew 39 
                                    + + r+L     q+l +aeaa+ +g+d g+i+  ++ F + 
  gi|121639065|ref|YP_979289.1| 226 PRFMRYLaaitAQELNVAEAARVIGVDAGTIRSDLALFETV 266
                                    566666633336*********************99999775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.8e-05     0.066       8      42 ..      16      48 ..      12      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                       ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiie 42
                                   l++l+e++e    ++++i Gp++ GKt+Ll+++  
  gi|121639065|ref|YP_979289.1| 16 LEQLREVAEY--TRVVLINGPRQAGKTTLLQQLHA 48
                                   7788888888..89*****************9865 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05     0.092      14      53 ..      11      48 ..       6      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                         AAA_35 14 ierppieekcyeeiekpGalirikapkkmGKtSLlarila 53
                                   ier+++e+  ++e+ +   ++ i++p++ GKt Ll+++ a
  gi|121639065|ref|YP_979289.1| 11 IERHMLEQ--LREVAEYTRVVLINGPRQAGKTTLLQQLHA 48
                                   56666665..478888899*****************9876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0019       2.6       2      23 ..      29      52 ..      27      63 .. 0.85
   2 ?    2.9   0.1     0.086   1.2e+02      24      83 ..     198     256 ..     189     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                         AAA_28  2 ivitGgestGKTtlleaLaar..g 23
                                   + i G+  +GKTtll++L+a+  g
  gi|121639065|ref|YP_979289.1| 29 VLINGPRQAGKTTLLQQLHAElgG 52
                                   56789999***********87544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.086
                         AAA_28  24 ypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcDrgll 83 
                                     +++ ++ r++++   ++ ++ ++++++l +f + + +  ++e+  a+a +v+ +D g++
  gi|121639065|ref|YP_979289.1| 198 SRWFSDYLRTVTQRDVRELKR-IEQTDRLPRFMRYLAAITAQELNVAEAARVIGVDAGTI 256
                                    579999******999998887.66668999999988888888888888888888887765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.14       9      45 ..      13      49 ..       6      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                Sigma54_activat  9 kelleqikkvaktdlsvlitGesGtGKellaraihea 45
                                   +++leq+++va+++  vli+G   +GK++l +++h++
  gi|121639065|ref|YP_979289.1| 13 RHMLEQLREVAEYTRVVLINGPRQAGKTTLLQQLHAE 49
                                   57899******************************85 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.26      12      44 ..      17      51 ..       4      57 .. 0.78
   2 ?   -2.9   0.0       4.6   6.4e+03      64      78 ..     334     348 ..     322     378 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                   HHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE 12 kklakal..gdvilLeGdLGaGKTtlvrglakalg 44
                                   ++l +++  ++v+l++G+  aGKTtl ++l ++lg
  gi|121639065|ref|YP_979289.1| 17 EQLREVAeyTRVVLINGPRQAGKTTLLQQLHAELG 51
                                   344443344678******************99886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                                    SSEEEEE-TT-SSTH CS
                           TsaE  64 eglyHfDlYRledee 78 
                                     + + +DlY ++d +
  gi|121639065|ref|YP_979289.1| 334 ATELEVDLYHFRDRD 348
                                    444557888776543 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00065      0.89       8      48 ..     223     260 ..     220     261 .. 0.87
   2 ?   -1.3   0.0       1.6   2.2e+03       7      19 ..     269     281 ..     268     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00065
                                    HHHHHHHHHHHHHHHTT--EE-HHHHHHHCTS-HHHHHHHH CS
                 Put_DNA-bind_N   8 kRLplYlryLeelkeegveriSSteLaealgvtaaqvRKDL 48 
                                     RLp+++ryL ++ +++ ++    e a+ +gv+a ++R DL
  gi|121639065|ref|YP_979289.1| 223 DRLPRFMRYLAAITAQELNV---AEAARVIGVDAGTIRSDL 260
                                    6**************98555...567999999999999998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHH CS
                 Put_DNA-bind_N   7 ikRLplYlryLee 19 
                                    + RLp   r L++
  gi|121639065|ref|YP_979289.1| 269 VHRLPAWSRNLTA 281
                                    68*****999986 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00022       0.3       3      25 ..      26      48 ..      24      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                   --EEEEE-STTSSHHHHHHHHHH CS
                          SRPRB  3 kpavllvGlsdsGKTslftrLtt 25
                                   ++ vl+ G+ ++GKT+l+++L  
  gi|121639065|ref|YP_979289.1| 26 TRVVLINGPRQAGKTTLLQQLHA 48
                                   6789****************976 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.35      32      72 ..      12      53 ..       2      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                          Rad17 32 kewlkadvLesrk.kriLLisGPsGCgkstvvkvLskelgik 72
                                   ++ +  +  e ++  r++Li GP   gk+t ++ L  elg  
  gi|121639065|ref|YP_979289.1| 12 ERHMLEQLREVAEyTRVVLINGPRQAGKTTLLQQLHAELGGW 53
                                   4555555555444146*******************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2848.62
//
Query:       gi|121639066|ref|YP_979290.1|  [L=144]
Description: hypothetical protein BCG_3206c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-12   47.1   0.5    3.6e-12   46.9   0.5    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.5     2e-16   3.6e-12       1     117 [.       4     127 ..       4     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2e-16
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHHHHHH.HHTSEEEEBCH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar....rkskrekaaelvellll.lsalkilpida 75 
                                    +++D+s++++ll  e ++  a +l+++ ++ ++s l++ E+++ la+      +++ ++a+ ++++++ ++a++ ++++a
  gi|121639066|ref|YP_979290.1|   4 VYFDASAFVKLLTTETGSSLASALWDGCDAALSSRLAYPEVRAALAAaarnHDLTESELADAERDWEDfWAATRPVELTA 83 
                                    699***********************************************9555555555555555555*********** PP

                                    HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-E..EE.ESSTHHH CS
                            PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgik..liatfDedfr 117
                                     +  +a+ +a+ + l+ +Da+++A A++ g++  ++a  D++++
  gi|121639066|ref|YP_979290.1|  84 TVEQHAGHLARAHALRGADAVHLASALAVGDPglVVAVWDRRLH 127
                                    ******************************99987778888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1073.82
//
Query:       gi|121639067|ref|YP_979291.1|  [L=150]
Description: hypothetical protein BCG_3207c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   48.7   0.0    7.9e-13   48.0   0.0    1.3  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   4.4e-17   7.9e-13       4      70 ..      67     132 ..      66     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.4e-17
                                    EEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHHHH CS
                PhdYeFM_antitox   4 vsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslplnaerlaesga 70 
                                    vs++e++a+ls++ld++++g+e v+It rG p a+l +l+ ++ l++lt+     +++a+r   +g+
  gi|121639067|ref|YP_979291.1|  67 VSVTELRAHLSDWLDRARAGGE-VVITERGIPIARLAALDSTDTLERLTAEGVIGKATAQRPVAAGR 132
                                    89********************.**************************999999999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1167.49
//
Query:       gi|121639068|ref|YP_979292.1|  [L=114]
Description: hypothetical protein BCG_3208 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-23   81.5   0.0    4.1e-23   81.3   0.0    1.0  1  Gp49      Phage derived protein Gp49-like (DUF891)
  ------ inclusion threshold ------
       0.12   12.4   0.0        0.2   11.7   0.0    1.4  1  DUF1870   Domain of unknown function (DUF1870)


Domain annotation for each model (and alignments):
>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   4.6e-27   4.1e-23       2      89 ..      12     103 ..      11     104 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 4.6e-27
                           Gp49   2 eldalpkkarakilaaldlleeggpdlgkplvkkle....dglwElrpksaggiiRvlyafdpgrkvilLhafqKkt..q 75 
                                    ++ al  +a a++  a+dlle +gp lg+p+v+k++    ++++Elrp  ag +iR+l+afdp+r++ilL +++K++  +
  gi|121639068|ref|YP_979292.1|  12 WFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNdstfHNMKELRP--AGTSIRILFAFDPARQAILLLGGDKAGnwK 89 
                                    999*********************************************..7888***********************888 PP

                           Gp49  76 ktpkkeielAekrl 89 
                                    ++++++i++A++r 
  gi|121639068|ref|YP_979292.1|  90 RWYDNNIPIADQRS 103
                                    ************95 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05       0.2       9      46 ..      64     101 ..      54     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                    HHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HH CS
                        DUF1870   9 lRkilaltveeaaeyigkavdsatWknWesgalpipde 46 
                                    +R ++a+++   a  +  + ++  Wk+W ++++pi+d+
  gi|121639068|ref|YP_979292.1|  64 IRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQ 101
                                    78889999999999999999999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 893.92
//
Query:       gi|121639069|ref|YP_979293.1|  [L=109]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-10   40.6   0.4    2.3e-10   40.3   0.4    1.2  1  HTH_37      Helix-turn-helix domain
    5.6e-09   35.9   0.0    8.6e-09   35.3   0.0    1.3  1  HTH_3       Helix-turn-helix
    9.4e-08   32.3   2.0    9.4e-08   32.3   2.0    2.1  2  HTH_31      Helix-turn-helix domain
    0.00079   19.4   0.0     0.0012   18.8   0.0    1.3  1  HTH_19      Helix-turn-helix domain
      0.005   17.2   0.0      0.012   16.0   0.0    1.6  2  HTH_26      Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.024   14.4   0.1       0.03   14.1   0.1    1.1  1  DUF1810     Protein of unknown function (DUF1810)
      0.024   14.1   0.0      0.044   13.3   0.0    1.6  1  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.4   9.1e-14   2.3e-10      17      79 ..      35      98 ..      16      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 9.1e-14
                                   HHHHHHHHHHHHHC.T--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTEEEEEEE CS
                         HTH_37 17 aqlalaiaeliekr.elsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGqkveivv 79
                                   a la ++ae+++++ + +q+++a+l+g++q++vs+l+ g+ls  +l +L  +++alG+++ iv 
  gi|121639069|ref|YP_979293.1| 35 AVLAHRLAEIRKALgHARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVA 98
                                   45667799999999346899*****************************************985 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.4e-12   8.6e-09       1      53 [.      41      95 ..      41      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.4e-12
                                   HHHHHHHTTHHH.HHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHHTSEHH CS
                          HTH_3  1 lkelRkqlglsq.eeLAeklGvsrstisriEnG.ernPsletlkklakaLgvsld 53
                                   l+e+Rk+lg  + +++A+++Gvs++ +s++E+G  ++  l tl+++  aLg +l+
  gi|121639069|ref|YP_979293.1| 41 LAEIRKALGHARqADVAALMGVSQARVSKLESGdLSHTELGTLQAYVAALGGHLR 95
                                   789***9999999**************************************8875 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.6      0.51   1.3e+03      19      22 ..      14      17 ..       2      30 .. 0.49
   2 !   32.3   2.0   3.7e-11   9.4e-08       2      55 ..      37      91 ..      36      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.51
                         HTH_31 19 evAe 22
                                   +vA+
  gi|121639069|ref|YP_979293.1| 14 AVAQ 17
                                   4443 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 3.7e-11
                         HTH_31  2 LGalLralReraG.LsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                   L+++L++ R++ G  +q++vA++ gvs++++s+lE+G      +++l a++ alg
  gi|121639069|ref|YP_979293.1| 37 LAHRLAEIRKALGhARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALG 91
                                   89***********99************************999999*999999998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.6e-07    0.0012       3      53 ..      40      91 ..      38     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                         HTH_19  3 rLkeaReelgl.tqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53
                                   rL e+R+ lg   q+++a   g+s+++ s++E+g    ++ ++l++++ alg
  gi|121639069|ref|YP_979293.1| 40 RLAEIRKALGHaRQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALG 91
                                   9**********9**********************433566778866666655 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.7   6.9e+03      10      28 ..       9      28 ..       7      30 .. 0.60
   2 !   16.0   0.0   4.8e-06     0.012       5      51 ..      44      91 ..      40      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.7
                         HTH_26 10 gitkseLar.gtgisaatls 28
                                   +i +  +a+ ++++++a ++
  gi|121639069|ref|YP_979293.1|  9 DIRADAVAQgRVDLQRAAVA 28
                                   55555665546667776665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.8e-06
                         HTH_26  5 lmadrgi.tkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                   + ++ g   ++++a   g+s+a +s+l +g  +   l+tL++  +aLg
  gi|121639069|ref|YP_979293.1| 44 IRKALGHaRQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALG 91
                                   555555557899******************************999986 PP

>> DUF1810  Protein of unknown function (DUF1810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.2e-05      0.03      53     101 ..      22      72 ..      11      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                    B-SHHHHHHHHHSTTHHHHHHHHHHHHHH--S--HHHHS-TTHH..HHHHH CS
                        DUF1810  53 iesleearaylahpvLgkrlreiteallaleeksaeeilGsida..lKlrs 101
                                    ++ ++ ar+ +++ vL +rl ei +al ++++ ++ +++G   a   Kl+s
  gi|121639069|ref|YP_979293.1|  22 LQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALMGVSQArvSKLES 72 
                                    6777889999******************************85541156665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05     0.044      23      42 ..      53      72 ..      35      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHTS-HHHHHHHHH CS
                     Sigma70_r4 23 leEIgerlgiSrerVrqiek 42
                                   ++++++ +g+S+ rV+ +e+
  gi|121639069|ref|YP_979293.1| 53 QADVAALMGVSQARVSKLES 72
                                   799**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 783.31
//
Query:       gi|121639070|ref|YP_979294.1|  [L=115]
Description: hypothetical protein BCG_3210 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-05   22.4   0.0    0.00022   21.2   0.0    1.7  1  DUF2384          Protein of unknown function (DUF2384)
     0.0016   18.4   0.1      0.003   17.6   0.1    1.5  1  Rv2175c_C        Rv2175c C-terminal domain of unknown functio
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.039   14.0   0.0    1.4  1  HTH_3            Helix-turn-helix
      0.031   14.1   0.0      0.064   13.1   0.0    1.5  2  P22_Cro          DNA-binding transcriptional regulator Cro
      0.082   12.9   0.0       0.14   12.1   0.0    1.4  1  Phage_terminase  Phage terminase small subunit


Domain annotation for each model (and alignments):
>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.1e-08   0.00022       9      33 ..      71      95 ..      57     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.1e-08
                        DUF2384  9 eeraarWLrrPnpaLggrtPldlld 33
                                   ++ + +WL+  n+ L+g++P+dll 
  gi|121639070|ref|YP_979294.1| 71 PRGVGQWLHAKNRLLDGQRPVDLLA 95
                                   777899*****************96 PP

>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   8.3e-07     0.003       4      53 ..      58     107 ..      55     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.3e-07
                      Rv2175c_C   4 LpGtltvLrDgGfddeeilrWLFteDesLpg.rPidALregrkrEVkRrAq 53 
                                    L+ ++ +L+D+  + + + +WL  ++  L g rP+d L+++r ++V+  A 
  gi|121639070|ref|YP_979294.1|  58 LRDLVLLLSDS-LTPRGVGQWLHAKNRLLDGqRPVDLLAKDRYEDVRSAAE 107
                                    55666666664.67778889**********99***************9996 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.039       4      36 ..      17      49 ..      14      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                   HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCS CS
                          HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGernP 36
                                   ++k  g +q ++A+++ vs ++++ +  G+ +P
  gi|121639070|ref|YP_979294.1| 17 ALKPFGVTQVDVAAVIQVSDRAVRGWRTGDIRP 49
                                   67899**********************997666 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.064       5      32 ..      17      47 ..      14      55 .. 0.80
   2 ?   -3.3   0.0       2.4   8.4e+03      22      29 ..      70      77 ..      69      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                   HHHHHS.SHHHHHHHHTS-HHHHHHH..HTC CS
                        P22_Cro  5 vikhFG.gvekvAkalgvtksAVsqW..gee 32
                                   ++k FG ++  vA+++ v++ AV+ W  g+ 
  gi|121639070|ref|YP_979294.1| 17 ALKPFGvTQVDVAAVIQVSDRAVRGWrtGDI 47
                                   67778867889***************75554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                   -HHHHHHH CS
                        P22_Cro 22 tksAVsqW 29
                                   t+  V qW
  gi|121639070|ref|YP_979294.1| 70 TPRGVGQW 77
                                   67789999 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05      0.14      27      46 ..      27      46 ..      22      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                Phage_terminase 27 dIAkvLdvsestvrkWKakD 46
                                   d+A v++vs++ vr+W+  D
  gi|121639070|ref|YP_979294.1| 27 DVAAVIQVSDRAVRGWRTGD 46
                                   99**************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 832.64
//
Query:       gi|121639071|ref|YP_979295.1|  [L=206]
Description: hypothetical protein BCG_3211 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.9   2.7    1.3e-15   57.7   2.3    1.3  1  RES       RES domain


Domain annotation for each model (and alignments):
>> RES  RES domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   2.3     7e-20   1.3e-15       8     150 ..      18     158 ..      10     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 7e-20
                            RES   8 sdylaaapfsg.....pgaaagggRfnsa.gigvlYaAssvatAlaEvlvhrgrfldataglplllprdlrlldlevpda 81 
                                     ++ +  p ++     + +a+g+gR++++ ++gv+Ya+ +++ A aE + h   f+d+   +       +r+ ++ v + 
  gi|121639071|ref|YP_979295.1|  18 TYW-HQGPTRHpvtscADPARGPGRYHRTgEPGVWYASNKEQGAWAELFRH---FVDDGVDP---FEVRRRVGRVAV-TL 89 
                                    455.445555555559999********999********************7...44333333...444445555554.56 PP

                            RES  82 rlvdl.d.rgaalerlp..k..wadpasdysatqaiadalraagidGilypSarddpggrnlvlfddahpdaarv 150
                                    +++dl d r  ++ +l+  +  + ++  dy++tqaia a+r+a++d++l p a + pg   l++f +a p +  +
  gi|121639071|ref|YP_979295.1|  90 QVLDLtDeR--TRSHLGvdEtdLLSD--DYTTTQAIA-AARDANFDAVLAPAA-ALPGCQTLAVFVHALPNIEPE 158
                                    667774433..333333212124455..9*******9.78999**********.77**77*****9888877444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1486.53
//
Query:       gi|121639072|ref|YP_979296.1|  [L=421]
Description: hypothetical protein BCG_3212c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2960.18
//
Query:       gi|121639073|ref|YP_979297.1|  [L=344]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-20   71.8   7.2    6.8e-17   61.0   2.9    2.6  2  HTH_38        Helix-turn-helix domain
    4.6e-10   39.0  10.5      1e-08   34.7   0.7    2.7  2  HTH_23        Homeodomain-like domain
    3.4e-09   36.9   0.0      6e-09   36.1   0.0    1.4  1  rve           Integrase core domain
    3.3e-07   30.8  17.7    8.4e-07   29.5   8.2    3.4  3  HTH_32        Homeodomain-like domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.077   12.7   0.0    2.3  2  Sigma70_r4_2  Sigma-70, region 4
      0.017   14.7   0.6      0.042   13.5   0.1    1.8  2  HTH_50        Helix-turn-helix domain
      0.038   13.5   1.5       0.12   11.9   0.1    2.5  3  HTH_24        Winged helix-turn-helix DNA-binding
      0.041   14.0   0.1       0.22   11.6   0.0    2.2  2  HTH_7         Helix-turn-helix domain of resolvase
      0.053   13.6   0.5       0.16   12.0   0.1    2.0  2  HTH_35        Winged helix-turn-helix DNA-binding
      0.055   13.0   0.0       0.16   11.6   0.0    1.8  2  GerE          Bacterial regulatory proteins, luxR family
       0.07   13.2   0.2        8.3    6.6   0.0    2.5  2  HTH_20        Helix-turn-helix domain
       0.07   12.9   0.3       0.21   11.4   0.1    1.9  2  HTH_IclR      IclR helix-turn-helix domain
       0.13   12.7   0.0       0.36   11.3   0.0    1.8  2  HTH_40        Helix-turn-helix domain
       0.18   12.0   0.2       0.18   12.0   0.2    3.6  3  HTH_28        Helix-turn-helix domain
       0.22   11.4   0.2       0.22   11.4   0.2    2.7  3  MarR_2        MarR family
          4    7.5  10.6       0.62   10.1   1.6    3.2  2  HTH_29        Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   2.9   6.1e-20   6.8e-17       2      44 .]       6      48 ..       5      48 .. 0.97
   2 !   12.4   0.1   9.2e-05       0.1      11      33 ..      84     106 ..      83     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 6.1e-20
                         HTH_38  2 ykhLsleeReeIerllaeGlslreIArrLgrspsTIsRElkRn 44
                                    ++Ls eeR  I++l+  Gls+r+IA +Lgr+psT+sREl+Rn
  gi|121639073|ref|YP_979297.1|  6 SRYLSEEERINIADLRRSGLSIRKIADQLGRAPSTVSRELRRN 48
                                   69****************************************9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.2e-05
                         HTH_38  11 eeIerllaeGlslreIArrLgrs 33 
                                    e I+ lla+ +s  +IAr+L r+
  gi|121639073|ref|YP_979297.1|  84 ELIAELLAQRWSPQQIARHLRRK 106
                                    579*****************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.7   9.3e-12     1e-08       2      41 ..       9      48 ..       8      56 .. 0.90
   2 !   11.1   0.1   0.00024      0.26      10      29 ..      86     105 ..      84     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 9.3e-12
                         HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwlkry 41
                                   +se+eR+ i+ l + Gls+r+IA++Lg+ ++Tv+r l+r 
  gi|121639073|ref|YP_979297.1|  9 LSEEERINIADLRRSGLSIRKIADQLGRAPSTVSRELRRN 48
                                   689***********************************95 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                         HTH_23  10 illllaeGlsvreIAreLgv 29 
                                    i+ lla+++s+++IAr+L +
  gi|121639073|ref|YP_979297.1|  86 IAELLAQRWSPQQIARHLRR 105
                                    88999************976 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   5.4e-12     6e-09       6     118 ..     186     291 ..     182     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.4e-12
                            rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngseytskafre 85 
                                    ++w++D+ v++  ++g  + + + v   +rli   +l+++++  + +a++e + +    + ++ +++D+g e++  ++ +
  gi|121639073|ref|YP_979297.1| 186 GHWEGDLIVGK--NQG--SAIGTLVERQTRLIRLLHLPTHDAYCLRIAITETMSDLPVTL-VRSITWDQGIEMA--RHID 258
                                    69*********..899..9********************************999999999.*************..9*** PP

                            rve  86 fladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                    + adlg  v f+  ++p++++  E+ +++l++ 
  gi|121639073|ref|YP_979297.1| 259 ITADLGAPVYFCDSRSPWQRASNENSNGLLRQY 291
                                    ******************************996 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0035       3.9      28      66 ..       8      43 ..       2      44 .. 0.78
   2 !   29.5   8.2   7.5e-10   8.4e-07       1      72 [.      40     123 ..      40     124 .. 0.70
   3 ?    0.0   0.3       1.2   1.4e+03      12      27 ..     151     164 ..     145     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                         HTH_32 28 klsdevrariiallreeprWsprqlaarlaeregvkvSh 66
                                    ls+e+r  i +l+ +   +s r++a++l  r + +vS+
  gi|121639073|ref|YP_979297.1|  8 YLSEEERINIADLR-RS-GLSIRKIADQL-GRAPSTVSR 43
                                   599***********.66.89*********.444455665 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.5e-10
                         HTH_32   1 TvsrwlkRyneeGlegLk...........drprrgrpr.klsdevrariiallreeprWsprqlaarlaeregvk....v 64 
                                    Tvsr+l+R   + ++g +           +r rr r+r   ++++++ i +ll  + rWsp+q+a++l+++++++    +
  gi|121639073|ref|YP_979297.1|  40 TVSRELRRNS-R-RDGQYrpfeahrwavqRRVRRHRRRiDKNPDLCELIAELL-AQ-RWSPQQIARHLRRKYPDDrsmwL 115
                                    99******43.3.33322222221122214455555555599***********.77.9**********99996666999* PP

                         HTH_32  65 Shstvyri 72 
                                     h+++y+ 
  gi|121639073|ref|YP_979297.1| 116 CHESIYQA 123
                                    ******86 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.2
                         HTH_32  12 eGlegLkdrprrgrpr 27 
                                    + +++L++ +rr  pr
  gi|121639073|ref|YP_979297.1| 151 HRRAHLRPGRRR--PR 164
                                    455566666444..43 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-05     0.077      25      49 ..      23      47 ..       9      48 .. 0.91
   2 ?   -0.7   0.0         1   1.1e+03      25      36 ..      92     103 ..      86     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                   S---HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                    gls++ IA +lg  ++tV + l+R
  gi|121639073|ref|YP_979297.1| 23 SGLSIRKIADQLGRAPSTVSRELRR 47
                                   69******************99998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                                    S---HHHHHHHH CS
                   Sigma70_r4_2  25 eglsykEIAell 36 
                                    + +s ++IA+ l
  gi|121639073|ref|YP_979297.1|  92 QRWSPQQIARHL 103
                                    567888999877 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.7e-05     0.042       7      46 ..       8      47 ..       6      48 .. 0.92
   2 ?   -2.9   0.0       4.9   5.5e+03      14      33 ..      84     103 ..      84     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                         HTH_50  7 yveefErelikkayekYpStRklAkrLGvShtaianklrk 46
                                   y++e Er  i+++ ++  S+Rk+A +LG   +++ + lr+
  gi|121639073|ref|YP_979297.1|  8 YLSEEERINIADLRRSGLSIRKIADQLGRAPSTVSRELRR 47
                                   678889999999999999*****************99997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                         HTH_50  14 elikkayekYpStRklAkrL 33 
                                    eli++++++  S   +A++L
  gi|121639073|ref|YP_979297.1|  84 ELIAELLAQRWSPQQIARHL 103
                                    58899999888888888887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   1.4e+03      10      23 ..       7      20 ..       6      23 .. 0.87
   2 ?   11.9   0.1   0.00011      0.12      16      36 ..      23      43 ..      20      47 .. 0.88
   3 ?   -2.6   0.0       3.7   4.1e+03      30      40 ..      95     105 ..      94     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                         HTH_24 10 elLqknprisqreL 23
                                   ++L ++ ri++++L
  gi|121639073|ref|YP_979297.1|  7 RYLSEEERINIADL 20
                                   58999*****9998 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                         HTH_24 16 prisqreLAerlglSpstvnr 36
                                   +++s+r +A++lg  pstv+r
  gi|121639073|ref|YP_979297.1| 23 SGLSIRKIADQLGRAPSTVSR 43
                                   699****************99 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.7
                         HTH_24  30 Spstvnrrlkr 40 
                                    Sp+ + r+l+r
  gi|121639073|ref|YP_979297.1|  95 SPQQIARHLRR 105
                                    77888888886 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.22      14      40 ..      17      43 ..       7      48 .. 0.84
   2 ?   -0.7   0.0       1.4   1.6e+03       5      29 ..      75     101 ..      72     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                   GGSSTTTT--STTTSSSS---SSSS-- CS
                          HTH_7 14 vvkLleeGisiskIAkevnisRsTvYR 40
                                   +  L+++G si+kIA++++ ++sTv R
  gi|121639073|ref|YP_979297.1| 17 IADLRRSGLSIRKIADQLGRAPSTVSR 43
                                   567999******************966 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                    SS-HH.H.HGGGGSSTTTT--STTTSS CS
                          HTH_7   5 klskn.d.inrvvkLleeGisiskIAk 29 
                                     ++kn d  + + +Ll++  s ++IA+
  gi|121639073|ref|YP_979297.1|  75 RIDKNpDlCELIAELLAQRWSPQQIAR 101
                                    556665447888999999999999998 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.16       8      41 ..      17      50 ..      11      54 .. 0.92
   2 ?   -2.1   0.1       3.8   4.2e+03       2      14 ..      94     106 ..      84     107 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                         HTH_35  8 iAaLrkrgttLaalsreaglssstlsnaltrpwp 41
                                   iA Lr+ g ++++++ ++g ++st+s+ l+r ++
  gi|121639073|ref|YP_979297.1| 17 IADLRRSGLSIRKIADQLGRAPSTVSRELRRNSR 50
                                   8***************************999865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                         HTH_35   2 WhpadIiAaLrkr 14 
                                    W p++I   Lr++
  gi|121639073|ref|YP_979297.1|  94 WSPQQIARHLRRK 106
                                    5666666666655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.16      16      39 ..      23      46 ..       9      51 .. 0.86
   2 ?   -2.6   0.0       3.6   4.1e+03      13      28 ..      89     104 ..      86     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                   TTS-HHHHHHHHTS-HHHHHHHHH CS
                           GerE 16 eGksnkeIAeelniSekTVkvhks 39
                                   +G+s  +IA++l+ ++ TV+  ++
  gi|121639073|ref|YP_979297.1| 23 SGLSIRKIADQLGRAPSTVSRELR 46
                                   79*****************97665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                                    HHCTTS-HHHHHHHHT CS
                           GerE  13 llaeGksnkeIAeeln 28 
                                    lla+  s ++IA+ l 
  gi|121639073|ref|YP_979297.1|  89 LLAQRWSPQQIARHLR 104
                                    5666667789999886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0074       8.3      19      46 ..      20      46 ..       9      47 .. 0.91
   2 ?    4.0   0.0     0.047        53      27      46 ..      83     104 ..      74     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0074
                                   HSTCTTB-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_20 19 LaraegltaselaerldlskntlsyHLr 46
                                   L r+ gl+   +a++l+ +++t+s+ Lr
  gi|121639073|ref|YP_979297.1| 20 L-RRSGLSIRKIADQLGRAPSTVSRELR 46
                                   5.7899*******************998 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.047
                                    HHHHHHHH..TS-HHHHHHHHH CS
                         HTH_20  27 aselaerl..dlskntlsyHLr 46 
                                    ++ +ae+l  ++s++++ +HLr
  gi|121639073|ref|YP_979297.1|  83 CELIAELLaqRWSPQQIARHLR 104
                                    66689999888*********98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00019      0.21      16      39 ..      22      45 ..      17      47 .. 0.87
   2 ?   -3.3   0.0       7.4   8.3e+03      17      28 ..      92     103 ..      90     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                   BSS-BHHHHHHHHTS-HHHHHHHH CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlL 39
                                   + +l+++ +A+++g ++Stv+R L
  gi|121639073|ref|YP_979297.1| 22 RSGLSIRKIADQLGRAPSTVSREL 45
                                   5679*****************955 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.4
                                    SS-BHHHHHHHH CS
                       HTH_IclR  17 qeltlselArrt 28 
                                    q+++ +++Ar++
  gi|121639073|ref|YP_979297.1|  92 QRWSPQQIARHL 103
                                    678889999985 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.36       8      34 ..      20      46 ..      16      99 .. 0.81
   2 ?   -2.1   0.0       4.9   5.5e+03       7      21 ..      88     102 ..      83     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                         HTH_40  8 lleeglsieeIAkerglkesTIegHLa 34
                                   l ++glsi +IA++ g ++sT+ + L 
  gi|121639073|ref|YP_979297.1| 20 LRRSGLSIRKIADQLGRAPSTVSRELR 46
                                   6799******************98665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                         HTH_40   7 elleeglsieeIAke 21 
                                    ell +  s+++IA+ 
  gi|121639073|ref|YP_979297.1|  88 ELLAQRWSPQQIARH 102
                                    677888888999876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00016      0.18       1      35 [.      13      47 ..      13      53 .. 0.93
   2 ?    2.2   0.0      0.18   2.1e+02       6      23 ..      86     104 ..      84     108 .. 0.76
   3 ?   -0.4   3.1       1.1   1.3e+03      37      52 .]     149     164 ..     149     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWikr 35
                                   +R+ i  l  +G s+r +A +lg  ++tv+r ++r
  gi|121639073|ref|YP_979297.1| 13 ERINIADLRRSGLSIRKIADQLGRAPSTVSRELRR 47
                                   68999999999**********************99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                         HTH_28   6 ikllaaGh.svreaArelg 23 
                                    i +l+a++ s  ++Ar+l 
  gi|121639073|ref|YP_979297.1|  86 IAELLAQRwSPQQIARHLR 104
                                    6677777779999999986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                         HTH_28  37 eegGiagLvprrrrpr 52 
                                    +++ +a L+p rrrpr
  gi|121639073|ref|YP_979297.1| 149 RTHRRAHLRPGRRRPR 164
                                    67889**********8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2    0.0002      0.22      14      44 ..      20      47 ..      13      52 .. 0.87
   2 ?   -1.8   0.6       2.7     3e+03      45      62 .]      58      75 ..      56      75 .. 0.77
   3 ?   -2.1   0.0       3.3   3.7e+03      23      31 ..      95     103 ..      83     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                   HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                         MarR_2 14 Lgrrpgrdltvgelarrlglsksavsrilkr 44
                                   L+r++   l+++ +a+ lg  +s+vsr l+r
  gi|121639073|ref|YP_979297.1| 20 LRRSG---LSIRKIADQLGRAPSTVSRELRR 47
                                   56665...9******************9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
                                   HHHTTSEEEEESSSSSSS CS
                         MarR_2 45 LvaaGLverrpgpeDkRa 62
                                   ++a+ + ++r+  +++R+
  gi|121639073|ref|YP_979297.1| 58 FEAHRWAVQRRVRRHRRR 75
                                   678888888888888885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
                                    EHHHHHHHH CS
                         MarR_2  23 tvgelarrl 31 
                                    +++++ar+l
  gi|121639073|ref|YP_979297.1|  95 SPQQIARHL 103
                                    566666665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.6   0.00055      0.62       1      35 [.      14      47 ..      14      78 .. 0.87
   2 ?    2.6   0.0      0.12   1.4e+02       6      26 ..      88     107 ..      85     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                         HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkr 35
                                   R+ +  l + G+s ++ iA +lg  ++tv r l+r
  gi|121639073|ref|YP_979297.1| 14 RINIADLRRSGLS-IRKIADQLGRAPSTVSRELRR 47
                                   5667778899**8.***************997766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                         HTH_29   6 lllaeGvstvsqiAkllglsr 26 
                                     lla+ +s ++qiA+ l+  +
  gi|121639073|ref|YP_979297.1|  88 ELLAQRWS-PQQIARHLRRKY 107
                                    68999997.*****9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2163.78
//
Query:       gi|121639074|ref|YP_979298.1|  [L=153]
Description: hypothetical protein BCG_3214 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.5   0.1    1.9e-12   47.3   0.1    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1     1e-16   1.9e-12      55     158 ..      30     134 ..      16     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1e-16
                 Bac_luciferase  55 aftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvev 134
                                    +++ ++++++a   ++l t++  ++ r P+v A +a+ L++ + G f lglgt+ ++++  r+G+ ++++  rlr ++ +
  gi|121639074|ref|YP_979298.1|  30 SISNATVASPAAPGLELSTGIALAFPRGPFVPAAAAWELQEATSGKFQLGLGTQVRKNVVHRYGMAFHRPGPRLR-YLLA 108
                                    66778999999999*************************************************************.7778 PP

                 Bac_luciferase 135 lrrlw...rgeevdfeGeffsvkgall 158
                                    +++++   +++++d++Gef ++ ++ +
  gi|121639074|ref|YP_979298.1| 109 VKACFavfQTGTPDHHGEFDNP-DFIT 134
                                    8888856577*********443.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1266.32
//
Query:       gi|121639075|ref|YP_979299.1|  [L=992]
Description: hypothetical protein BCG_3215c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   8.9e-267  887.2   0.0   1.1e-266  886.8   0.0    1.0  1  UPF0182       Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  886.8   0.0  6.2e-271  1.1e-266       2     755 ..      20     820 ..      19     823 .. 0.95

  Alignments for each domain:
  == domain 1  score: 886.8 bits;  conditional E-value: 6.2e-271
                        UPF0182   2 llllavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlell.......ek 74 
                                    +++++ ++vlll+   l++ y+++lwf elgy+svf+t l tr+++ +v+++++  +++  l+la+r++ +       ++
  gi|121639075|ref|YP_979299.1|  20 IMIALGVIVLLLAGPRLIDAYVDWLWFGELGYRSVFTTMLATRIVVCLVAGVVVGGIVFGGLALAYRTRPVfvpdadnDP 99 
                                    5667777888888*******************************************************444788888899 PP

                        UPF0182  75 lerlrealekklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvl 154
                                    ++r+r+++  +l+l+ ++i+++++ll+g+va+s w++++lfl++ +fgv+Dp+fg+D++FY+F+lPf++l+ls++l+ v+
  gi|121639075|ref|YP_979299.1| 100 VARYRAVVLARLRLVGIGIPAAIGLLAGIVAQSYWARIQLFLHGGDFGVRDPQFGRDLGFYAFELPFYRLMLSYMLVSVF 179
                                    ******************************************************************************** PP

                        UPF0182 155 laliavllvyllsgeslgirl..kfaelskaarrhlsvllallllllalsywLdryellyskrg..vvtGagYtdvnavl 230
                                    la++a+l++++++g   girl  ++  ls++ar++l  l+++l+ll+a++ywLdryell ++rg   +tGagYtd+navl
  gi|121639075|ref|YP_979299.1| 180 LAFVANLVAHYIFG---GIRLsgRTGALSRSARVQLVSLVGVLVLLKAVAYWLDRYELLSHTRGgkPFTGAGYTDINAVL 256
                                    **************...6667777889**********************************777456************* PP

                        UPF0182 231 paktilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTreAyg 310
                                    pak+il++ial++a++++ ai+l++l++p+i+l+ll+l+++++g+ +p +v++++VkPn+++kE++Yi+r+I+aTr+Ayg
  gi|121639075|ref|YP_979299.1| 257 PAKLILMAIALICAAAVFSAIALRDLRIPAIGLVLLLLSSLIVGAGWPLIVEQISVKPNAAQKESEYISRSITATRQAYG 336
                                    ******************************************************************************** PP

                        UPF0182 311 L..dkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkF.edldvdrY.tidgeerqvviaaR 386
                                    L  d v++++++ ++  tae+++++++t++nirLlDp++++++f+q qq +n+Y F ++l++drY + +g+ r++v+aaR
  gi|121639075|ref|YP_979299.1| 337 LtsDVVTYRNYSGDSPATAEQVAADRATTSNIRLLDPTIVSPAFTQFQQGKNFYYFpDQLSIDRYlDRNGNLRDYVVAAR 416
                                    *9999*******99999***************************************99*******6679*********** PP

                        UPF0182 387 EldysalpeeaktwvnkhlvYTHGyGvvaspvnkvt........eeGlpeflvkdip....see.eeslkieepriYfGe 453
                                    El+ ++l +++++w+n+h+vYTHG+G++asp+n+v+        ++G+peflv+ ++        ++  ++++priYfG+
  gi|121639075|ref|YP_979299.1| 417 ELNPDRLIDNQRDWINRHTVYTHGNGFIASPANTVRgiandpnqNGGYPEFLVNVVGangtV-VsDGPAPLDQPRIYFGP 495
                                    *****************************************99989**********987753.25999***********9 PP

                        UPF0182 454 l....tndyvivgt..kvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnike 527
                                    +    ++dy+ivg   + +E+dy+++ +++ +tY+G+gGv++g +l r +fa+k+ + ++l+s+ i s+skilf+R++ +
  gi|121639075|ref|YP_979299.1| 496 VisntSADYAIVGRngDDREYDYETNIDTKRYTYTGSGGVPLGGWLARSVFAAKFAERNFLFSNVIGSNSKILFNRDPAQ 575
                                    9988899******954455*****9999**************************************************** PP

                        UPF0182 528 RvekvaPfLtlDsdpYlvvadgrlyWivDaYTtsdrYPySep...eeats..............geeevnYiRNSVKvvv 590
                                    Rve+vaP+Lt+Ds +Y++++++rl+WivD+YTt d+YPySe    +   s              ++++v+YiRNSVK++v
  gi|121639075|ref|YP_979299.1| 576 RVEAVAPWLTTDSAVYPAIVNKRLVWIVDGYTTLDNYPYSELtslS---SatadsnevafnrlvPDKKVSYIRNSVKATV 652
                                    ****************************************995542...12345678999999989************** PP

                        UPF0182 591 DAydGtvklYvvdeeDPiikawskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpk 670
                                    DAydGtv+lY+ de+DP++kaw+++Fpg++kp+s++ +eL +hlrYPedlFkvq+ llakYHv+dp +F++++d+W+vp 
  gi|121639075|ref|YP_979299.1| 653 DAYDGTVTLYQQDEKDPVLKAWMQVFPGTVKPKSDIAPELAEHLRYPEDLFKVQRMLLAKYHVNDPVTFFSTSDFWDVPL 732
                                    ******************************************************************************** PP

                        UPF0182 671 e...eeeqpvePyYlilklp..geekeefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqieari 745
                                    +   + ++ ++PyY+++k    ++++++++l+s+++  +r+ l+a+++a+sd+ +yg+l+++++p   +v+Gp+ +++ i
  gi|121639075|ref|YP_979299.1| 733 DpnpTASSYQPPYYIVAKNIakDDNSASYQLISAMNRFKRDYLAAYISASSDPATYGNLTVLTIPG--QVNGPKLANNAI 810
                                    *66555555********9863367889**************************************6..79********** PP

                        UPF0182 746 nqdpeisqql 755
                                    ++dp +sq+l
  gi|121639075|ref|YP_979299.1| 811 TTDPAVSQDL 820
                                    ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (992 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 6202.14
//
Query:       gi|121639076|ref|YP_979300.1|  [L=340]
Description: hypothetical protein BCG_3216c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-11   42.2   0.0      2e-10   40.8   0.0    1.7  1  PDZ_2        PDZ domain
    8.5e-09   35.2   0.3    1.7e-08   34.3   0.3    1.4  1  Lon_C        Lon protease (S16) C-terminal proteolytic domain
    3.7e-06   26.7   0.2    9.6e-06   25.4   0.0    1.8  2  PDZ_6        PDZ domain
    0.00022   21.1   0.1    0.00069   19.5   0.0    1.8  2  Tricorn_PDZ  Tricorn protease PDZ domain
    0.00052   20.3   0.0     0.0017   18.7   0.0    1.9  1  PDZ          PDZ domain
  ------ inclusion threshold ------
      0.037   14.1   0.0      0.074   13.1   0.0    1.5  1  PDZ_1        PDZ-like domain


Domain annotation for each model (and alignments):
>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   6.8e-14     2e-10      14      74 ..     134     193 ..     115     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.8e-14
                                    .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTE CS
                          PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgk 74 
                                    + v+v+sV + gP+ ++ l+agD i +vdg++v +l+++  ll ++kpG++V++ + R+++
  gi|121639076|ref|YP_979300.1| 134 KAVTVASVMDPGPSVDK-LQAGDAIDAVDGTPVGNLDQFTALLKNTKPGQEVTIDFRRKNE 193
                                    5799*********9999.****************************************986 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.3   5.5e-12   1.7e-08     109     176 ..     236     305 ..     232     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.5e-12
                                    GGGGHHHHHHHHHHHHTS--B..-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGT CS
                          Lon_C 109 GPsaGvtlatalvslltgkkv..rkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdl 176
                                    GPsaG+ +  a+v  lt  +   ++ va tG i++ G+v  iGG+  k+ aa+ ag +  ++P +n  + 
  gi|121639076|ref|YP_979300.1| 236 GPSAGLMFSLAVVDKLTSGHLvgSTFVAGTGTIAVDGKVGQIGGITHKMAAARAAGATVFLVPAKNCYEA 305
                                    9*************9997554125669************************************9997654 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       3.2   9.5e+03      20      30 ..      39      49 ..      39      51 .. 0.82
   2 !   25.4   0.0   3.2e-09   9.6e-06      16      56 .]     151     190 ..     138     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                          PDZ_6 20 DiilsvNGqpv 30
                                   D++ +++G+ v
  gi|121639076|ref|YP_979300.1| 39 DTLGEIDGKQV 49
                                   77789999987 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3.2e-09
                          PDZ_6  16 lrvGDiilsvNGqpveglsladvaallr.gsagesvvlvvrr 56 
                                    l++GD i +v+G+pv  ++l+++ all+ +++g++v++ +rr
  gi|121639076|ref|YP_979300.1| 151 LQAGDAIDAVDGTPV--GNLDQFTALLKnTKPGQEVTIDFRR 190
                                    9**************..*********************9998 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   8.3e+03      46      59 ..      41      54 ..      39      64 .. 0.63
   2 !   19.5   0.0   2.3e-07   0.00069      40      80 ..     151     192 ..     137     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
                                   EEEETTEE-BTTB- CS
                    Tricorn_PDZ 46 ilavdgepvskekg 59
                                   + ++dg++v +  g
  gi|121639076|ref|YP_979300.1| 41 LGEIDGKQVVQIVG 54
                                   55677777755444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.3e-07
                                    -.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE-ST CS
                    Tricorn_PDZ  40 vreGdlilavdgepvskekgiaelLvgka.gkeveLtvkrkd 80 
                                    +++Gd+i avdg pv++ +++  lL +++ g+ev+++++rk+
  gi|121639076|ref|YP_979300.1| 151 LQAGDAIDAVDGTPVGNLDQFTALLKNTKpGQEVTIDFRRKN 192
                                    689***********************97648********986 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.7e-07    0.0017      27      79 ..     135     186 ..     117     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.7e-07
                                    SEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEE CS
                            PDZ  27 gifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtL 79 
                                     + v++v+  g+   + l++GD I +v+g++v n+ + +a +++++++++vt+
  gi|121639076|ref|YP_979300.1| 135 AVTVASVMDPGPSVDK-LQAGDAIDAVDGTPVGNLDQFTALLKNTKPGQEVTI 186
                                    6889999999998888.******************************999985 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.5e-05     0.074      32      75 ..     136     178 ..     124     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                          PDZ_1  32 gvyvseasgsfklsskekkgviitsinnqptpnLdefievvkki 75 
                                    ++++s    ++++++  + g  i+ ++++p+ nLd+f+ ++k+ 
  gi|121639076|ref|YP_979300.1| 136 VTVASVMDPGPSVDK-LQAGDAIDAVDGTPVGNLDQFTALLKNT 178
                                    555555566666655.899999*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2530.25
//
Query:       gi|121639077|ref|YP_979301.1|  [L=472]
Description: hypothetical protein BCG_3217 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.8e-112  374.0   4.5   8.6e-112  373.7   4.5    1.1  1  Zincin_2  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.7   4.5  4.8e-116  8.6e-112       1     332 []      85     433 ..      85     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 373.7 bits;  conditional E-value: 4.8e-116
                                    --HHHHHHHHHHHHTGGGS--S-HHHHHHHHHHHHHHHHHHHHHHHT---SS--EEEE--HHHHHHHHHHHHHHTTHHHH CS
                       Zincin_2   1 VdwdlaarvArrlaragevdrseaaaavaelreaarlAelwldevtglpaaagsevevvdraeWveatleswrrllepva 80 
                                    V++dla++vA + ++         aa+++++++a++lA++wld +t+lpa+a+ ++  ++  +Wv++tl++w+rl++p+a
  gi|121639077|ref|YP_979301.1|  85 VNYDLARQVASSSIGFI---APIPAATNSAIADAVHLADTWLDGATSLPAGAT-KAVGWSPTDWVDNTLATWKRLCDPMA 160
                                    89999999999999976...4567888999***********************.************************** PP

                                    HHHH-----...........----------HHHHHHHHHHHHHHHHTT--BTTSSH---.---EEEE-HHHHHHHHHHTT CS
                       Zincin_2  81 eklaealae...........elaallrqvggavfgaqvGqalgeLssevlgqtdvglplapegrllLvapnvaaverele 149
                                    +++++ +a+           +l ++++q+gg +fg q+Gqalg Ls+evl++td+glpl+p+g +++++  v++++++le
  gi|121639077|ref|YP_979301.1| 161 QQISTVWASslpeeaksmagPLLSIMSQMGGIAFGSQLGQALGRLSREVLTSTDIGLPLGPKGVAAILPGAVESFAAGLE 240
                                    ********9*********************************************************************** PP

                                    --HHHHHHHHHHHHHHHHHHHHTSTHHHHHHHHHHHHHHT---...--------......................---- CS
                       Zincin_2 150 vdpedvrlwvalrEaaharlFaavpWLrehllsaveeyargitidtsalleleealr.............qealegglle 216
                                     + +++++++a rEaah+rlF++vpWL+++ll+ave+ya g++id++    +ee +r             +++l++g++e
  gi|121639077|ref|YP_979301.1| 241 QPRSEILTFLATREAAHHRLFSHVPWLASQLLGAVEAYAMGMKIDMTG---IEELARdinptsladpaamEQLLSQGVFE 317
                                    ************************************************...6666666668888887777777788**** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHTT-------SSHHHHH CS
                       Zincin_2 217 lvqtpeqraaldrLeallaLlEGwvdvVmdavgpevlpsvaalrerfrrrratggpaerllrrllGlelklrqyreaaal 296
                                    ++ tp+q++al+rLe+llaL+EGwv++V++a+  e++p  aal e++rrrra+ggpae+++++l+Glel++r++rea al
  gi|121639077|ref|YP_979301.1| 318 PKATPAQTQALERLETLLALIEGWVQTVVTAALGERIPGEAALSETLRRRRASGGPAEQTFATLVGLELRPRKLREAGAL 397
                                    ******************************************************************************** PP

                                    HHHHHHHH-HHHHGGGGS-GGGS--HHHHH-HHHHH CS
                       Zincin_2 297 vravveavGmegrdavWehPdlLPtaeelddpaawv 332
                                    ++++++avGm++rdavW+hPdlLP +++lddpaa++
  gi|121639077|ref|YP_979301.1| 398 WERLTRAVGMDARDAVWQHPDLLPATDDLDDPAAFI 433
                                    ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.60
# Mc/sec: 2357.61
//
Query:       gi|121639078|ref|YP_979302.1|  [L=299]
Description: hypothetical protein BCG_3218 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1606.97
//
Query:       gi|121639079|ref|YP_979303.1|  [L=66]
Description: hypothetical protein BCG_3219c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 467.01
//
Query:       gi|121639080|ref|YP_979304.1|  [L=447]
Description: ABC transporter ATP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-34  117.3   0.0    8.5e-34  116.3   0.0    1.5  1  ABC1      ABC1 family
    6.4e-08   32.8   3.9    2.2e-07   31.1   1.3    2.7  3  APH       Phosphotransferase enzyme family
    0.00043   19.9   0.0     0.0027   17.3   0.0    2.2  2  RIO1      RIO1 family
  ------ inclusion threshold ------
      0.081   12.3   0.0       0.61    9.4   0.0    2.1  1  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   1.9e-37   8.5e-34       2     118 ..     118     232 ..     117     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 1.9e-37
                           ABC1   2 elgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelrldleelvd 81 
                                    +lg+k++e F++f+++P+A+ASi+qVh+A  ++g+eVavK+q+pg ++++++Dl+++++++ +lk+++++ +  ++ +vd
  gi|121639080|ref|YP_979304.1| 118 QLGTKWRERFSSFNDTPVASASIGQVHKAIWSDGREVAVKIQYPGADEALRADLKTMQRMVGVLKQLSPGAD--VQGVVD 195
                                    699*********************************************************************..****** PP

                           ABC1  82 efskslleEldferEAknaekfrenfaklkevkvPkv 118
                                    e+ ++  +Eld++ EA+n+  f++ +++ ++++vP+v
  gi|121639080|ref|YP_979304.1| 196 ELVERTEMELDYRLEAANQRAFAKAYHDHPRFQVPHV 232
                                    ***********************************99 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.18   8.1e+02     104     150 ..      76     121 ..      16     148 .. 0.68
   2 !    3.9   0.3      0.01        45      33     102 ..     207     273 ..     134     278 .. 0.82
   3 !   31.1   1.3   4.8e-11   2.2e-07     151     200 ..     256     312 ..     174     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                                    CHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.HHHHHHH CS
                            APH 104 alhqvdpaalpladflaqdlellrqlesatarllaselld.lleelee 150
                                    al+   ++a+ ++ f+++++e l +l + +++l+as+++  l  +l  
  gi|121639080|ref|YP_979304.1|  76 ALSV--MEAAIPDEFGEPYREALTKLQKDAPPLPASKVHRvLDGQLGT 121
                                    3333..466677778888888888888888888888887765555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.01
                                    -HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHHHHHHH CS
                            APH  33 aaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellealgefl 102
                                    +  e++++ a+ ++ ++++  +vP v+a       ++  ++++e+++g ++++   + + +q++ ++  l+e+ 
  gi|121639080|ref|YP_979304.1| 207 YRLEAANQRAFAKAYHDHPRfQVPHVVA------SAP-KVVIQEWIEGVPMAEiirHGTTEQRDLIGTLLAELT 273
                                    5667788888888888887799999999......333.578888888888888888888899999999888876 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 4.8e-11
                                    H.......HHHHHHHH--S..SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEE CS
                            APH 151 q.......vlaalaallpg..elptvllHgDlhpgNllvdpddgrvtGviDfedaglgp 200
                                            ++ +l+a+l    + + +l+HgD hpgN+++ pd gr+ G+iDf+ + ++p
  gi|121639080|ref|YP_979304.1| 256 HgtteqrdLIGTLLAELTFdaPRRLGLMHGDAHPGNFMLLPD-GRM-GIIDFGAVAPMP 312
                                    14444455455555555557779*****************66.999.******988776 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.21   9.3e+02      14     171 ..     155     174 ..     142     179 .. 0.59
   2 !   17.3   0.0   6.1e-07    0.0027      69     150 ..     226     306 ..     199     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                                    EEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTE CS
                           RIO1  14 aiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgv 93 
                                    a                                                                               
  gi|121639080|ref|YP_979304.1| 155 A------------------------------------------------------------------------------- 155
                                    4............................................................................... PP

                                    EGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHH CS
                           RIO1  94 aapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveni 171
                                                                                               v+++ p a e L+ D++ +
  gi|121639080|ref|YP_979304.1| 156 -----------------------------------------------------------VKIQYPGADEALRADLKTM 174
                                    ...........................................................5555666666666666555 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.1e-07
                                    T--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHH.HHHHTSTEEESS-STTSEEEETT.EEEE CS
                           RIO1  69 gvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemr.klykeaglvHaDLSeyNvlvded.kvvi 146
                                     ++vP++++    v++ e+i+  gv+++++     ++e+++l  ++l+e+   + ++ gl H+D    N ++  d ++ i
  gi|121639080|ref|YP_979304.1| 226 RFQVPHVVASAPKVVIQEWIE--GVPMAEIIRHG-TTEQRDLIGTLLAELTfDAPRRLGLMHGDAHPGNFMLLPDgRMGI 302
                                    389******************..******99998.66788888888886552577899***********98888879*** PP

                                    --GT CS
                           RIO1 147 IDvs 150
                                    ID++
  gi|121639080|ref|YP_979304.1| 303 IDFG 306
                                    **97 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00014      0.61      76     147 ..     241     310 ..     134     318 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                                    EEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHH..HHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                        Pkinase  76 vleyveggeladllerkgslseeeakkiakqilegley..lHskgiiHrDlKpeNiLidekgelKitDFGlake 147
                                    ++e++eg  +a+++++ g    +e ++++ ++l+ l +    + g++H D  p N+++  +g + i+DFG ++ 
  gi|121639080|ref|YP_979304.1| 241 IQEWIEGVPMAEIIRH-G---TTEQRDLIGTLLAELTFdaPRRLGLMHGDAHPGNFMLLPDGRMGIIDFGAVAP 310
                                    5555555555555542.2...2233344444444443310346789************************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3062.83
//
Query:       gi|121639081|ref|YP_979305.1|  [L=92]
Description: transcriptional regulatory protein whiB-like whiB7 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-14   52.6   0.1    6.9e-14   52.2   0.1    1.1  1  Whib      Transcription factor WhiB
     0.0018   17.9   3.9     0.0039   16.9   3.9    1.6  1  AT_hook   AT hook motif


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   7.7e-18   6.9e-14       7      55 ..      20      68 ..      18      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 7.7e-18
                           Whib  7 CrgedpelffpekgdreeeAkavCarCpVrreCleealeegeeyGvwGG 55
                                   C+  dp+l+f+ + +  e Ak++C +Cp+rr+Cl+ al++ e++GvwGG
  gi|121639081|ref|YP_979305.1| 20 CHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGG 68
                                   8999******9999**********************************9 PP

>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.9   4.3e-07    0.0039       1      12 [.      80      91 ..      80      92 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-07
                        AT_hook  1 kRkRGRPrKaat 12
                                   kR+RGRPrK+a+
  gi|121639081|ref|YP_979305.1| 80 KRPRGRPRKDAV 91
                                   8********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 684.72
//
Query:       gi|121639082|ref|YP_979306.1|  [L=700]
Description: DNA helicase II [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-48  164.2   0.0    2.1e-45  155.6   0.0    2.2  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    2.1e-39  135.2   0.1    4.3e-39  134.2   0.1    1.5  1  AAA_19           AAA domain
    1.8e-38  132.8   0.0    2.7e-19   69.8   0.0    2.1  2  UvrD_C           UvrD-like helicase C-terminal domain
    8.1e-22   77.0   0.0    1.7e-21   76.0   0.0    1.6  1  HRDC             HRDC domain
    1.9e-09   37.2   0.2    3.2e-08   33.3   0.2    2.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    0.00074   19.3   9.2      0.025   14.3   9.2    2.6  1  AAA_30           AAA domain
  ------ inclusion threshold ------
        0.1   12.4   0.7         15    5.2   0.0    3.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.6   0.0   8.2e-49   2.1e-45       2     314 ..      13     286 ..      12     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 8.2e-49
                                    SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HH CS
                  UvrD-helicase   2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdder 81 
                                    +++qrea+  ++gp+ v+A+AG+GKT+++++ri+ l++ +++ + ++l+vTFT++Aa E+++R++++   a+        
  gi|121639082|ref|YP_979306.1|  13 DDQQREAVLAPRGPVCVLAGAGTGKTRTITHRIASLVASGHVAAGQVLAVTFTQRAAGEMRSRLRALDAAAR-------- 84 
                                    789**************************************************************9755554........ PP

                                    HHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHH CS
                  UvrD-helicase  82 lrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikel 161
                                         + +  ++  T+H+ ++++l+    r+  d ++++ld++        +++++      + +l+ ++++++      
  gi|121639082|ref|YP_979306.1|  85 ---TGSGVGAVQALTFHAAAYRQLRYFWSRVIADTGWQLLDSKF-------AVVARAAS---RTRLHASTDDVR------ 145
                                    ...45689*********************************999.......45555554...555666667766...... PP

                                    HCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS....TSCSHHHHHHHHHHHHHHHHHHHHTC...EEHHH CS
                  UvrD-helicase 162 sksrnikkeelslskskaeelrelvskakekqlspkelkkaf....ekasdlqkkiaeflkeyqeqkkeena...lDfsd 234
                                                       +l+  ++ ak +++ p+e+  a     +       +ia+++ ey+  k + +    lDf+d
  gi|121639082|ref|YP_979306.1| 146 -------------------DLAGEIEWAKASLIGPEEYVTAVaaarRDPPLDAAQIAAVYSEYEALKARGDGvtlLDFDD 206
                                    ...................67788888888888888888877765333334456788888888887776543444***** PP

                                    HHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHHHHHHS CS
                  UvrD-helicase 235 llhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflkkkkdf 314
                                    ll+ + ++ e++  +ae+++ ry+   +DEyQD  + Q r+l+    +++ l++vGD +Q IY+F gA ++++l ++++f
  gi|121639082|ref|YP_979306.1| 207 LLLHTAAAIENDAAVAEEFQDRYRCFVVDEYQDVTPLQQRVLSAWLGDRDDLTVVGDANQTIYSFTGASPRFLLDFSRRF 286
                                    ****************************************************************************9998 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.1   1.7e-42   4.3e-39       1     145 [.      16     271 ..      16     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.7e-42
                         AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........a 69 
                                    qreav  +++++++v+aG+GtGKTr+++h++a lv+ g+v++ ++l+v+ft+rAa e+r rl+al+a+           a
  gi|121639082|ref|YP_979306.1|  16 QREAV-LAPRGPVCVLAGAGTGKTRTITHRIASLVASGHVAAGQVLAVTFTQRAAGEMRSRLRALDAAartgsgvgavqA 94 
                                    89***.***********************************************************999999999999999 PP

                         AAA_19  70 tTiHrlal........................................................................ 77 
                                     T+H+ a                                                                         
  gi|121639082|ref|YP_979306.1|  95 LTFHAAAYrqlryfwsrviadtgwqlldskfavvaraasrtrlhastddvrdlageiewakasligpeeyvtavaaarrd 174
                                    99999988************************************************************************ PP

                         AAA_19  78 ...........................ldfddlltealelle.eaeeekklqeee.llivDEfqdvdelqyrLlkallge 128
                                                               ldfddll ++++++e +a+  +++q+++ +++vDE+qdv++lq+r+l+a+lg+
  gi|121639082|ref|YP_979306.1| 175 ppldaaqiaavyseyealkargdgvtlLDFDDLLLHTAAAIEnDAAVAEEFQDRYrCFVVDEYQDVTPLQQRVLSAWLGD 254
                                    **************************************999986677888999999************************ PP

                         AAA_19 129 kkklllvGDpdQliyvf 145
                                    +++l++vGD++Q+iy+f
  gi|121639082|ref|YP_979306.1| 255 RDDLTVVGDANQTIYSF 271
                                    *99*************9 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   4.2e-20   1.1e-16       2     136 ..     293     429 ..     292     444 .. 0.91
   2 !   69.8   0.0   1.1e-22   2.7e-19     284     348 ..     492     561 ..     439     562 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 4.2e-20
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C   2 vLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikallekneklediavLv 79 
                                    +Le+ yRSt++++ +an++++ + +r a +k     ++e+g    ++e  +e  Ea  +aa i +l    +  +++a+L+
  gi|121639082|ref|YP_979306.1| 293 RLERDYRSTPQVVSLANRVIAAARGRVAGSKLRlsGQREPGPVPSFHEHSDEPAEAATVAASIARLIASGTPPSEVAILY 372
                                    799*****************999999666544467999****************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  80 RsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkril 136
                                    R n++++  ++aL + gi + v ++e fF+r+eik++l  l+ +  ++ ++al+ ++
  gi|121639082|ref|YP_979306.1| 373 RVNAQSEVYEEALTQAGIAYQVRGGEGFFNRQEIKQALLALQRVSERDTDAALSDVV 429
                                    *************************************99999888888888887665 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 1.1e-22
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 284 k.ekipiiTiHqAKGlEFdvVflagleegtfPsyrskk....ekrleEEkRlfYVaiTRAkkrLfisysk 348
                                      + +++ ++H+AKGlE+d Vfl+gl++gt+P + +      ++ +eEE+Rl+YV+iTRA+  L +s++ 
  gi|121639082|ref|YP_979306.1| 492 VvQGVTLASLHAAKGLEWDAVFLVGLADGTLPISHALAhgpnSEPVEEERRLLYVGITRARVHLALSWAL 561
                                    248899**************************7777779999889**********************985 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   6.6e-25   1.7e-21       2      68 .]     630     696 ..     629     696 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 6.6e-25
                                    HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHHHH CS
                           HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeileai 68 
                                    ++ll +L++wR ++A+e++vp+yvvf+d+tL++iAe lPt+ ++L +i+g+g rkle+yg ++l+++
  gi|121639082|ref|YP_979306.1| 630 EELLLQLKSWRLSTAKEQNVPAYVVFTDNTLIAIAELLPTDDAALIAIPGIGARKLEQYGSDVLQLV 696
                                    78999***********************************************************986 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   1.3e-11   3.2e-08       4      51 ..     498     557 ..     495     558 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.3e-11
                       UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaarmgel.............rrrlLYtavTRAreklil 51 
                                      + h a+G+e++aV+++     + + + +              rrlLY+++TRAr +l l
  gi|121639082|ref|YP_979306.1| 498 LASLHAAKGLEWDAVFLVGLADGTLPIS-HalahgpnsepveeERRLLYVGITRARVHLAL 557
                                    5678*************76554444433.2477888899*****************98865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   9.2   9.8e-06     0.025       2      82 ..      12     116 ..      11     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.8e-06
                         AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLa.............e 64 
                                    l+++Q++av  l+  g   +++ ++AGtGKt ++++  + + a+g    g+v++++ t++aA +++              
  gi|121639082|ref|YP_979306.1|  12 LDDQQREAV--LAPRG--PVCVLAGAGTGKTRTITHRIASLVASGhvaaGQVLAVTFTQRAAGEMRsrlraldaaartgS 87 
                                    677888888..44444..5788899*********998777777777999*****************44433333322111 PP

                         AAA_30  65 elg.ieastiakllkrlk..........g 82 
                                    ++g ++a t +   +r+            
  gi|121639082|ref|YP_979306.1|  88 GVGaVQALTFHAAAYRQLryfwsrviadT 116
                                    12122444444444433345554555552 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.083   2.1e+02       3      21 ..      29      47 ..      27      78 .. 0.82
   2 ?    1.8   0.0     0.064   1.6e+02      62     131 ..     228     295 ..     216     304 .. 0.74
   3 ?    5.2   0.0    0.0059        15     186     229 ..     499     554 ..     478     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.083
                Viral_helicase1  3 vhGvpGcGKStlirkllrt 21
                                   v + +G GK++ i + + +
  gi|121639082|ref|YP_979306.1| 29 VLAGAGTGKTRTITHRIAS 47
                                   7788*********999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.064
                Viral_helicase1  62 kgkililDEylllhaGyill.laalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrrttyllp 131
                                    +++  ++DEy+ +++ +  +  a l   + + ++GD +Q  ++ +      +++   +s+r++   + +l 
  gi|121639082|ref|YP_979306.1| 228 RYRCFVVDEYQDVTPLQQRVlSAWLGDRDDLTVVGDANQTIYSFT---GASPRFLLDFSRRFPDAAVVRLE 295
                                    5888999***9998866666334455556789999*999888864...46888999999998877666665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0059
                Viral_helicase1 186 ttvhevqGltfdkVtlvllketdlelis.............esrenllvAlTRhrks 229
                                       h + Gl++d V lv l + +l  is             e+r  l+v++TR+r  
  gi|121639082|ref|YP_979306.1| 499 ASLHAAKGLEWDAVFLVGLADGTLP-IShalahgpnsepveEERRLLYVGITRARVH 554
                                    5679999999999999999887655.44589999999999988***********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 4125.87
//
Query:       gi|121639083|ref|YP_979307.1|  [L=84]
Description: glutaredoxin protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-12   45.9   0.0    6.6e-12   45.5   0.0    1.2  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.015   15.7   0.1       0.17   12.3   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
      0.028   14.4   0.0      0.041   13.9   0.0    1.3  1  Thioredoxin    Thioredoxin
      0.039   14.3   0.0      0.047   14.1   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
      0.052   14.0   0.0      0.056   13.9   0.0    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.097   12.6   0.0       0.16   11.9   0.0    1.4  1  HCBP_related   Haemolysin-type calcium binding protein relate
       0.17   12.1   0.0       0.18   12.0   0.0    1.3  1  SH3BGR         SH3-binding, glutamic acid-rich protein


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   2.6e-15   6.6e-12       2      55 ..       7      61 ..       6      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.6e-15
                                   EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH.TSSSSSEEEE CS
                   Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels.gvrtvPqvfi 55
                                   +++t+++C+yC + k +L+ ++++++e+d++ + ++ e + +++ g rtvP+v +
  gi|121639083|ref|YP_979307.1|  7 TIYTTSWCGYCLRLKTALTANRIAYDEVDIEHNRAAAEFVGSVNgGNRTVPTVKF 61
                                   89**************************************9999*99*****965 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.7e-05      0.17       8      33 ..       5      34 ..       3      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                  Thioredoxin_2  8 vlvvftdpdCpyCkklkkelkel....ddv 33
                                    l+++t+++C+yC +lk+ l  +    d+v
  gi|121639083|ref|YP_979307.1|  5 ALTIYTTSWCGYCLRLKTALTANriayDEV 34
                                   57899************9888773333333 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.041      24      83 ..       8      66 ..       3      83 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                   EEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                    Thioredoxin 24 eFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83
                                    ++ +wCg C +l+  l++   ++  +v + +  + ++     + + + +Pt+k++  + 
  gi|121639083|ref|YP_979307.1|  8 IYTTSWCGYCLRLKTALTANRIAYD-EVDIEHNRAAAEFVGSVNGGNRTVPTVKFADGST 66
                                   57899*********99988877777.5554444444444444445567788888776655 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.047       2      57 ..       9      67 ..       8      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                   ES-TTSHHHHHHHHHHHHHT--EEEE---TTTTHHHHHHH-..TT--SSEEE.TTS-EE CS
                        GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgehdeellakn..plgkvPvLe.ddgeal 57
                                   y +  + y+ r + aL+  ++++ +v+++  +  +e+      ++++vP+ +  dg  l
  gi|121639083|ref|YP_979307.1|  9 YTTSWCGYCLRLKTALTANRIAYDEVDIEHNRAAAEFVGSVngGNRTVPTVKfADGSTL 67
                                   6667799*********************999999999544447******9965566555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.056       2      41 ..       6      41 ..       5      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                   EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CC CS
                         DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdee 41
                                   lt+y++  C+ C ++k++L +    + +  +++DI+ ++ 
  gi|121639083|ref|YP_979307.1|  6 LTIYTTSWCGYCLRLKTALTA----NRIAYDEVDIEHNRA 41
                                   89******************4....456667899987765 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05      0.16      22      39 ..      51      68 ..      42      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                   HCBP_related 22 sgsyrieqieFaDGtvWd 39
                                   +g+  + +++FaDG++++
  gi|121639083|ref|YP_979307.1| 51 GGNRTVPTVKFADGSTLT 68
                                   4666699*********98 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05      0.18      26      52 ..      23      49 ..       5      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                   HHHHTT--EEEEETTT-HHHHHHHHHC CS
                         SH3BGR 26 iLdakkiefdevDitkdeeerelmren 52
                                    L a++i +devDi ++ +  e++   
  gi|121639083|ref|YP_979307.1| 23 ALTANRIAYDEVDIEHNRAAAEFVGSV 49
                                   689***********9998888877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 618.10
//
Query:       gi|121639084|ref|YP_979308.1|  [L=313]
Description: NADH pyrophosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-19   68.4   0.5      1e-18   67.6   0.2    1.5  2  NUDIX          NUDIX domain
    2.8e-09   36.5   0.0    5.8e-09   35.5   0.0    1.6  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
    1.4e-06   28.9   0.2    3.3e-06   27.7   0.2    1.6  1  NUDIX-like     NADH pyrophosphatase-like rudimentary NUDIX do


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   6.4e+03      15      41 ..      58      86 ..      42      95 .. 0.60
   2 !   67.6   0.2   1.7e-22     1e-18       4     124 ..     172     284 ..     169     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                   SEEEEEEES...SSSTTTEESSEEECBTTS CS
                          NUDIX 15 gevLlvrrs...kkpfpgWelPgGkvepgE 41
                                   g+vLl       +kp+p+ ++  G+ve g 
  gi|121639084|ref|YP_979308.1| 58 GRVLLGAAIelaDKPPPE-AVFLGRVEGGR 86
                                   235555544666566666.66677777554 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 1.7e-22
                                    EEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygde 81 
                                    +av++++ ++ ++ +l+r++   +p+  ++l +G+ve+gE++e +++RE++EE+Gl+++++++lg         +p++ +
  gi|121639084|ref|YP_979308.1| 172 PAVICLVHDGADRAVLARQA--AWPErmFSLLAGFVEAGESFEVCVAREIREEIGLTVRDVRYLG--------SQPWPFP 241
                                    799***************99..66666568***********************************........5677777 PP

                                    EEEEEEEE..EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTH CS
                          NUDIX  82 heilyvfl..eevegelepndenevsevrwvpleellkeklaaes 124
                                    +++++ f   +++++e     ++e++e+ w++ +e+ +++laa++
  gi|121639084|ref|YP_979308.1| 242 RSLMVGFHalGDPDEEFSFS-DGEIAEAAWFTRDEV-RAALAAGD 284
                                    88888888656666666666.***************.65555554 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   9.7e-13   5.8e-09       1      32 []     136     167 ..     136     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 9.7e-13
                  zf-NADH-PPase   1 rthrFCgrCGaptepaeggwarvCpaCglehY 32 
                                    ++ rF + +Gapt+pa++gw+rv+p +g+e +
  gi|121639084|ref|YP_979308.1| 136 DNARFSALDGAPTKPARAGWSRVNPITGHEEF 167
                                    589***************************88 PP

>> NUDIX-like  NADH pyrophosphatase-like rudimentary NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   5.5e-10   3.3e-06       9     102 .]      50     134 ..      41     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.5e-10
                     NUDIX-like   9 rgrllveseeseeelllpadssaalvgkdseelvfLGldeggapvfAvdvsareeeikeaeeeggafvelRavmlalsae 88 
                                    r+r+lv+     +++ll a+ + a  +k+ +e+vfLG+ egg +v+Av+   ++       +  ++ v+lR+++  +++ 
  gi|121639084|ref|YP_979308.1|  50 RNRVLVAN----GRVLLGAAIELA--DKPPPEAVFLGRVEGGRHVWAVRAALQPI---ADPDIPAEAVDLRGLGRIMDDT 120
                                    67777777....666666665554..59*********************999998...5677999*************** PP

                     NUDIX-like  89 daalaaqAralldW 102
                                     ++l+  A all+W
  gi|121639084|ref|YP_979308.1| 121 SSQLVSSASALLNW 134
                                    ************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2144.20
//
Query:       gi|121639085|ref|YP_979309.1|  [L=355]
Description: transmembrane cation transporter [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-27   94.7   4.2    7.2e-27   94.0   4.2    1.4  1  TrkA_N       TrkA-N domain
    5.7e-14   51.8   3.5    1.3e-13   50.7   3.5    1.6  1  Ion_trans_2  Ion channel
  ------ inclusion threshold ------
      0.012   15.8   4.5       0.04   14.2   0.7    2.7  2  PK_C         Pyruvate kinase, alpha/beta domain
       0.11   12.0   3.1       0.18   11.3   3.1    1.2  1  NmrA         NmrA-like family
       0.11   12.6   0.1       0.27   11.4   0.1    1.6  1  BATS         Biotin and Thiamin Synthesis associated domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   4.2     2e-30   7.2e-27       2     115 ..     150     266 ..     149     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 2e-30
                                    EEES-SHHHHHHHHHHHHTT....EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLsegg....kdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                    ++iG+G+ G++ +  + +++    + +vv+d+d  ++e++++ gl +v+gdat+ +vL+ ag ++a+++i+at+ d++ +
  gi|121639085|ref|YP_979309.1| 150 VVIGYGTKGKTAVAAMVSDElvpgE-IVVVDTDSGVLERAAAAGLVTVHGDATKSDVLRLAGTQHASSIIVATSRDDTAV 228
                                    8*****************888**66.****************************************************** PP

                                    HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                         TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                    l++l+a+e+ pk+ki+a ++++e+++ll++ gad+v++
  gi|121639085|ref|YP_979309.1| 229 LVTLTAREIAPKAKIVASIREAENQHLLRQSGADTVVV 266
                                    ************************************96 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   3.5   3.5e-17   1.3e-13       4      78 ..      49     129 ..      46     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.5e-17
                                    HHTCHHHHHHHHT.........T---HHHHHHHHHHHHTTS----SSTT-----HHH.HHHHHHHHHHHHHHHHHHHHHH CS
                    Ion_trans_2   4 llvlifgaviysl.....eegwekwsfldalYfsfvtltTiGYGdivpetdagrlft.ivyillGlalfalflavlgkvl 77 
                                    +++l+ + ++y       +++  + +fld+lY++ vtl+T GYGdi+p++++ r+++ +v++ l +a+++l++ ++ +vl
  gi|121639085|ref|YP_979309.1|  49 VALLLTAGIVYVDrdgylDAQGDRLTFLDCLYYAAVTLSTTGYGDITPISEFARAINiFVITPLRIAFLILLVGTTLEVL 128
                                    4455555555555699984445678************************9999****888889**********9999888 PP

                                    H CS
                    Ion_trans_2  78 t 78 
                                    t
  gi|121639085|ref|YP_979309.1| 129 T 129
                                    6 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.054   1.9e+02      20      47 ..      84     131 ..      79     196 .. 0.59
   2 ?   14.2   0.7   1.1e-05      0.04       3      65 ..     201     266 ..     199     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.054
                                    EEE-SSSHH.HHHHHHT-TSSEEEEEES...................H CS
                           PK_C  20 vvltesGet.Arliskyrpkvpiiavtp...................n 47 
                                    v+l+++G+     is++ + ++i+++tp                    
  gi|121639085|ref|YP_979309.1|  84 VTLSTTGYGdITPISEFARAINIFVITPlriaflillvgttlevlteT 131
                                    566666664245677777778888887755555555544444443221 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHT-SEEEEE-SSSHHHHHH....HHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH. CS
                           PK_C   3 iakaaveaaeelgakaIvvltesGetArli....skyrpkvpiiavtpneltarqlalyrGvypvlv 65 
                                    + + + ++a +++a+ I+v+t+  +tA l+     ++ pk++i+a  ++ + ++ l  + G  +v v
  gi|121639085|ref|YP_979309.1| 201 TKSDVLRLAGTQHASSIIVATSRDDTAVLVtltaREIAPKAKIVASIREAENQHLLRQS-GADTVVV 266
                                    5566788999*****************9752222789999*****99977765555543.4444443 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.1     5e-05      0.18       5      98 ..     152     256 ..     149     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                    STTSHHHHHHHHHHHH.HT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT.-SEEEE---GG....... CS
                           NmrA   5 GaTGrqGksvvrallk.aghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkg.vdvvfsvtgfy....... 75 
                                     + G  Gk  v+a+++ +  +  ++v dt+s +++  ++aG ++v+gd+   ++l+ a  + +  ++++t+         
  gi|121639085|ref|YP_979309.1| 152 IGYGTKGKTAVAAMVSdELVPGEIVVVDTDSGVLERAAAAGLVTVHGDATKSDVLRLAGTQhASSIIVATS-Rddtavlv 230
                                    45688888877777773557889999999*********************999998886651444444454.44888888 PP

                                    ...S-HHHHHHHHHHHHHHHS-SEEE CS
                           NmrA  76 ...skeiedgkklvdAakeaGvkhfi 98 
                                         ei+   k+v+ + ea  +h++
  gi|121639085|ref|YP_979309.1| 231 tltAREIAPKAKIVASIREAENQHLL 256
                                    88899***************999976 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.4e-05      0.27      16      59 ..     230     271 ..     205     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.4e-05
                                    HHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT--EEE-C---T CS
                           BATS  16 iiaalRlllPkagillsgResaefrdqlllklGansisagskte 59 
                                    + +++R + Pka+i++s Re  +++++ll + Ga+ +++ s+t+
  gi|121639085|ref|YP_979309.1| 230 VTLTAREIAPKAKIVASIRE--AENQHLLRQSGADTVVVSSETA 271
                                    56789***************..77777999*********99643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2632.73
//
Query:       gi|121639086|ref|YP_979310.1|  [L=1101]
Description: ATP-dependent DNA helicase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-39  134.7   0.0      2e-38  132.7   0.0    1.8  1  UvrD-helicase   UvrD/REP helicase N-terminal domain
    1.1e-29  104.0   0.0      3e-17   63.1   0.0    2.1  2  UvrD_C          UvrD-like helicase C-terminal domain
    3.1e-21   76.2   0.0    5.6e-21   75.4   0.0    1.4  1  AAA_19          AAA domain
    2.4e-13   50.6   0.0    2.5e-12   47.2   0.0    2.6  2  PDDEXK_1        PD-(D/E)XK nuclease superfamily
    3.7e-08   33.1   4.6     0.0016   18.2   0.8    2.7  2  UvrD_C_2        UvrD-like helicase C-terminal domain
     0.0024   17.6   1.3     0.0024   17.6   1.3    2.4  2  AAA_30          AAA domain
     0.0096   14.2   0.0      0.014   13.6   0.0    1.1  1  Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.0   7.7e-42     2e-38       2     314 ..      25     336 ..      24     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 7.7e-42
                                    SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HH CS
                  UvrD-helicase   2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdder 81 
                                    ++eq + ia + gp++v+A+AG+GKT ++a+r++ l++++  ep ++l +TFT+kAa  l  R++++l            
  gi|121639086|ref|YP_979310.1|  25 TAEQAAVIAAPPGPLVVIAGAGAGKTETMAARVVWLVANGYAEPGQVLGLTFTRKAAGQLLRRVRSRLARLAGIG----- 99 
                                    5789999999********************************************************998876555..... PP

                                    HHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHH CS
                  UvrD-helicase  82 lrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikel 161
                                    l      +    +sT H+f+  +l+ +   + l+p+ r+l+e++       +l ++++    d  l +dk+ +   + + 
  gi|121639086|ref|YP_979310.1| 100 LGCGDPAACAPVVSTYHAFAGSLLRDYGLLLPLEPDTRLLSETE-----LWQLAFDVVS-GYDGVLCTDKSPAA--V-TS 170
                                    45578889999*********************************.....6677777775.34443444444433..2.33 PP

                                    HCCCCCH.....HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS....TSCSHHHHHHHHHHHHHHHHHHHHTCEEH CS
                  UvrD-helicase 162 sksrnik.....keelslskskaeelrelvskakekqlspkelkkaf....ekasdlqkkiaeflkeyqeqkkeenalDf 232
                                    ++ r +        +  + +    el+ lv  ++ +  +  +  ++      +++ ++ ++  +l  + e++ + + +Df
  gi|121639086|ref|YP_979310.1| 171 IVVRLWGqlgehLVDTRALRDTHVELERLVHALPAGRYQRDRGPSQWllrmLATQTQRAELVPLLDALGERMHAGKVMDF 250
                                    444555544455555566666666777777777776666665554448887788888889999***************** PP

                                    HHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT....EEEEE-GGG--GGGGTB-THHHH CS
                  UvrD-helicase 233 sdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasghee....lfmvGDpkQsIYgFRgAdielfl 308
                                    +  +  + +l    +++ ++lr+ry+++l DEyQDT ++Q  +l+ l+ g       l+ vGDp QsIYg+RgA  +++ 
  gi|121639086|ref|YP_979310.1| 251 AMQMASAARLAATSPQVGQDLRRRYRVVLLDEYQDTGHAQRVVLSSLFGGGVDdglaLTAVGDPIQSIYGWRGASATNLP 330
                                    *********9999*************************************9889************************99 PP

                                    HHHHHS CS
                  UvrD-helicase 309 kkkkdf 314
                                    +++ df
  gi|121639086|ref|YP_979310.1| 331 RFTTDF 336
                                    999887 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   2.8e-13   7.1e-10      43     151 ..     391     503 ..     348     513 .. 0.80
   2 !   63.1   0.0   1.2e-20     3e-17     281     346 ..     653     770 ..     605     772 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.8e-13
                                    xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  43 ivvleaeteeeEaekiaatikall....ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdila 118
                                    ++    ++ + E e+ia+ ++           k  + avLvR n+da  i+++L++ gip  vv+   +++ +e+ ++ a
  gi|121639086|ref|YP_979310.1| 391 VRCALLPDVQAEREWIADHLRMRYqraeADGVKPPTAAVLVRRNADAAAIADTLRARGIPAEVVGLAGLLSIPEVAEVVA 470
                                    66677789999******9998777566566677889******************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 119 ylkllankqdkialkrilkrlvlgigkatveri 151
                                    +l+l+a ++  +a  r+l ++  ++g + ++++
  gi|121639086|ref|YP_979310.1| 471 MLRLVADPTAGAAAMRVLTGPRWRLGARDLAAL 503
                                    ***********************9999999888 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 1.2e-20
                                    xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                         UvrD_C 281 skkk.ekipiiTiHqAKGlEFdvVflagleegtfP............................................. 314
                                    ++   ++++++T+H+AKGlE+ vV +a+l+ g fP                                             
  gi|121639086|ref|YP_979310.1| 653 LTVAcDRVQVLTVHAAKGLEWQVVAVAHLSRGVFPstvsrsswltdpaelppllrgdrasagahgipvldtsavadrkql 732
                                    333479*****************************999999999999999999999999999888888888888888666 PP

                                    ......xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 315 ......syrskk....ekrleEEkRlfYVaiTRAkkrLfisy 346
                                          +    +     +r++EE+Rl+YVa+TRA + L +s 
  gi|121639086|ref|YP_979310.1| 733 sdkiseH----RrlldRRRVDEERRLLYVAVTRAEDTLLVSG 770
                                    6544433....1566699*********************996 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   2.2e-24   5.6e-21       2     144 ..      28     320 ..      27     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.2e-24
                         AAA_19   2 reavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae............. 68 
                                    ++av a++ ++l+v+aG+G GKT+++ ++v +lv++g  +p ++l ++ft++Aa +l  r+++ +a+             
  gi|121639086|ref|YP_979310.1|  28 QAAVIAAPPGPLVVIAGAGAGKTETMAARVVWLVANGYAEPGQVLGLTFTRKAAGQLLRRVRSRLARlagiglgcgdpaa 107
                                    456669*****************************************************9988888799*********** PP

                         AAA_19  69 ....atTiHrlal................................................................... 77 
                                         +T+H++a                                                                    
  gi|121639086|ref|YP_979310.1| 108 capvVSTYHAFAGsllrdyglllplepdtrllsetelwqlafdvvsgydgvlctdkspaavtsivvrlwgqlgehlvdtr 187
                                    ***********99******************************************************************* PP

                         AAA_19  78 ............................................................ldfddlltealelle..eae 95 
                                                                                                +df  ++  a+ l    + +
  gi|121639086|ref|YP_979310.1| 188 alrdthvelerlvhalpagryqrdrgpsqwllrmlatqtqraelvplldalgermhagkvMDFAMQMASAARL-AatSPQ 266
                                    ***********************************************99999998888886666666555444.346556 PP

                         AAA_19  96 eekklqeee.llivDEfqdvdelqyrLlkallgek.kk...lllvGDpdQliyv 144
                                      ++l++++ +++ DE+qd+   q  +l+ l+g + ++   l++vGDp Q+iy 
  gi|121639086|ref|YP_979310.1| 267 VGQDLRRRYrVVLLDEYQDTGHAQRVVLSSLFGGGvDDglaLTAVGDPIQSIYG 320
                                    7899999999********************99877554777***********96 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   3.9e+03      52      79 ..     813     840 ..     806     855 .. 0.76
   2 !   47.2   0.0   9.9e-16   2.5e-12      18     195 ..     919    1069 ..     902    1081 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                       PDDEXK_1  52 kldkedleelleeaveelwpellleeei 79 
                                    ++ +++++ l+++a+e++wp+++l+ ++
  gi|121639086|ref|YP_979310.1| 813 APAGDERNPLCDNAIEAVWPADPLAARR 840
                                    5566699999***********9988754 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 9.9e-16
                       PDDEXK_1   18 flryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaeklke 95  
                                     + r   +l++ ++ +a +lG ++Ha++++fy   +    dl +l   a+++ + +              +   ++l++
  gi|121639086|ref|YP_979310.1|  919 RQRLMCRLPKRPDPHA-WLGDAFHAWVQQFYG--AELLFDLGDLP-GAADREVGD--------------PEELAALQR 978 
                                     5555567766666666.***************..22222444444.122211111..............444445544 PP

                       PDDEXK_1   96 vleklverlaeeleakrgfrpvalelefggekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlll 172 
                                     ++++       + ++ +   +v +e+ +g  +  ++GriD v  d++g ++++D+Ktg++p  + +    +  +Ql++
  gi|121639086|ref|YP_979310.1|  979 AFTAS-----SWAARTPAAVEVPFEMPIG--DTVVRGRIDAVFvDPDGGATVVDWKTGKPPHGPAA--MRQAAVQLAV 1047
                                     44444.....3334555568888888888..678*******9999999***********6644444..555566**** PP

                       PDDEXK_1  173 Yllalaegeelkeege.pagalyl 195 
                                     Y la a+   ++ +++ +  a+y+
  gi|121639086|ref|YP_979310.1| 1048 YRLAWAAL--RGCPTSsVRTAFYY 1069
                                     *****999..66666643333333 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   4.7e-06     0.012       4      21 ..     662     679 ..     660     687 .. 0.89
   2 !   18.2   0.8   6.1e-07    0.0016      29      51 ..     746     768 ..     740     769 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.7e-06
                       UvrD_C_2   4 altihkaQGsefpaVivf 21 
                                    +lt+h a+G+e+++V v+
  gi|121639086|ref|YP_979310.1| 662 VLTVHAAKGLEWQVVAVA 679
                                    89*************995 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.1e-07
                       UvrD_C_2  29 rmgelrrrlLYtavTRAreklil 51 
                                    r+ ++ rrlLY+avTRA + l +
  gi|121639086|ref|YP_979310.1| 746 RRVDEERRLLYVAVTRAEDTLLV 768
                                    455679***********998865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.3   9.3e-07    0.0024      20      65 ..      38      87 ..      25     106 .. 0.80
   2 ?   -0.4   0.2      0.31   7.8e+02      81     127 ..     255     316 ..     219     318 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.3e-07
                         AAA_30 20 vavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLaee 65
                                     v+ ++AG+GKt +++a +  + a+g    g+v+gl+ t kaA +L + 
  gi|121639086|ref|YP_979310.1| 38 PLVVIAGAGAGKTETMAARVVWLVANGyaepGQVLGLTFTRKAAGQLLRR 87
                                   4688999*********9987777777889999************998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.31
                         AAA_30  81 k............grarlepg.tllivDEa...gmvdtkqlaallkaaekagakvilvGDerQ 127
                                    +            g ++l+++ ++++ DE    g +    l +l+    ++g  +  vGD+ Q
  gi|121639086|ref|YP_979310.1| 255 AsaarlaatspqvG-QDLRRRyRVVLLDEYqdtGHAQRVVLSSLFGGGVDDGLALTAVGDPIQ 316
                                    22222333344643.567777799999996111444555577777777777899999999877 PP

>> Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.6e-06     0.014     663     729 ..     733     799 ..     726     818 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-06
                                    S-HHHHS--TT---HHHHHHHHHHHHHHHEEEEEEEEEESBETTTTEB--B-HHHHHHHHHHHTTEE CS
                 Exonuc_V_gamma 663 fDlmakeprkgDrsrrdddrylfLeallsAreaLyiSYvgrsirdnserpPSvlvselldylaqnfa 729
                                     D +++++r  Dr r d++r l+  a+  A++ L++S     +   ++r PS ++ el d ++++ a
  gi|121639086|ref|YP_979310.1| 733 SDKISEHRRLLDRRRVDEERRLLYVAVTRAEDTLLVSGHHWGPTGTKPRGPSEFLCELKDIIDRSAA 799
                                    588999*******************************9999*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.25s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 7617.06
//
Query:       gi|121639087|ref|YP_979311.1|  [L=1055]
Description: ATP-dependent DNA helicase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-41  141.3   0.0    8.5e-41  140.5   0.0    1.4  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    1.2e-35  123.5   0.0    1.7e-35  123.1   0.0    1.1  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
      2e-14   53.7   0.0    2.4e-13   50.2   0.0    2.0  1  UvrD_C           UvrD-like helicase C-terminal domain
    3.4e-14   53.4   0.0    9.8e-14   51.9   0.0    1.8  1  AAA_19           AAA domain
     0.0014   18.4   4.9      0.069   12.9   0.7    2.8  2  AAA_30           AAA domain
     0.0092   15.7   0.1          2    8.1   0.1    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.044   13.0   0.1       0.11   11.8   0.0    1.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.061   13.6   0.2         14    5.9   0.0    2.8  2  AAA_22           AAA domain
      0.075   12.9   1.4        2.4    8.1   0.3    3.0  2  UvrD_C_2         UvrD-like helicase C-terminal domain
       0.11   12.3   0.0        0.3   10.9   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
        4.1    6.9   9.7        0.9    9.1   0.3    3.8  4  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.5   0.0   5.2e-44   8.5e-41       1     255 []     805    1047 ..     805    1047 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 5.2e-44
                       PDDEXK_1    1 rlSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleee 78  
                                     +l++s+l+++++Cplr+ ++++ g  ++ el + ++G+++Ha+++e  +       + ++ll ++++++w  l++   
  gi|121639087|ref|YP_979311.1|  805 TLTPSTLQALNDCPLRWLAERHGGT-NTRELPS-AVGSVLHALFAEPGR-------SESQLL-AELDRVWGHLPFGA- 871 
                                     589*********************9.4566766.8*********86666.......999999.9********99999. PP

                       PDDEXK_1   79 ilessarlrylaeklkevleklverlaeeleakrg.frpvalelefg........g.ekvrLkGriDrvd.dkegelr 145 
                                             +++++ + ++ +++++++ ++++++r+ +++v++e++++        + +k+rL+Gr Dr++ d+ g+l+
  gi|121639087|ref|YP_979311.1|  872 --------QWYSANELARHRAMIQAFVQWRAQSRSeLTEVGVEVDIDgaledgsgQaRKIRLRGRADRLErDPAGRLV 941 
                                     ........*************************999*******98888999***9569*************99***** PP

                       PDDEXK_1  146 iiDyKtgsappkskelaelkeglQlllYllalaeg.eelkeege.pagalylrleepkvkdeevvkkmalteeeleal 221 
                                     i+D Ktg++p  sk+  + +++ Ql++Y+la+aeg  +++   + p+ga ++ + +      ++ k+ +lt++ ++++
  gi|121639087|ref|YP_979311.1|  942 IVDIKTGKTP-VSKD--DAQQHAQLAMYQLAVAEGlVRAG---DePGGARLVYVGKSGAAGVAERKQDPLTPAARDEW 1013
                                     ********66.7777..9*****************33333...3488888888877888889999999********** PP

                       PDDEXK_1  222 lqeleelaeeilagefparpskkCeyCpyksvCr 255 
                                     ++ +++la++ ++++f ar ++ C++Cp ++ C+
  gi|121639087|ref|YP_979311.1| 1014 RNLVRQLAAATAGPQFIARRNDGCTHCPLRPGCP 1047
                                     ************99*******************7 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0     1e-38   1.7e-35       7     309 ..      11     301 ..       5     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1e-38
                                    HHHHS.-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHH CS
                  UvrD-helicase   7 eaias.lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrla 85 
                                    +a+a+ l+gp+lv+ ++G+GK++ l+e  + +i ++ ++p+++l++T   ++    ++ +++al  ++ +          
  gi|121639087|ref|YP_979311.1|  11 AALAPgLRGPVLVLGGPGTGKSTLLVEAAVAHIGAG-TDPESVLLLTGSGRMGMRARSALTTALLRSRTNG-------PC 82 
                                    66777789****************************.************9999999999999888776544.......34 PP

                                    HHHCTTSEEEEHHHHHHHHHHHHHGGTT.SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCC CS
                  UvrD-helicase  86 lqnlseanisTlHsfcqkilkkeanrig.ldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikelsks 164
                                     + ++e  + T+Hs+++ +l+k a+r+g   p++ +++e+d   ++ +ell+ + e+ + ++++++++   +l+      
  gi|121639087|ref|YP_979311.1|  83 RAAIREPVVRTVHSYAYAVLRKAAQRAGdALPRLLTSAEQD---AIIRELLAGDAEDGPAATTTWPAHLRPALT------ 153
                                    689************************989999*9999999...8***********999998999998888775...... PP

                                    CCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS.TSCSHHHHHHHHHHHHHHHHHHHHTC............EE CS
                  UvrD-helicase 165 rnikkeelslskskaeelrelvskakekqlspkelkkaf.ekasdlqkkiaeflkeyqeqkkeena............lD 231
                                               +  a+elr+l+ ++ e+ l+p+el++   ++ ++++ ++ +f ++y++ +  + a            l 
  gi|121639087|ref|YP_979311.1| 154 ----------TAGFATELRNLLARCAERGLDPLELQQLGrRRGRPEWIAAGQFAQRYEQVMLLRGAvglaapqatapaLS 223
                                    ..........47899**********************888999************************************* PP

                                    HHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHH CS
                  UvrD-helicase 232 fsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflk 309
                                     ++l+ a+le++  ++el++a r r++++l+D++Q+++++ +r++++la+g+e  ++ GDp+Q+++gFRg++++ +l 
  gi|121639087|ref|YP_979311.1| 224 AAELVGAALEAFAVDPELLAAERARVRTLLVDDAQQLDPQAARLVRMLAAGTELALIAGDPNQAVFGFRGGEPTGLLA 301
                                    ****************************************************9999*****************98876 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.5e-16   2.4e-13       3     347 ..     317     694 ..     315     696 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.5e-16
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                         UvrD_C   3 LekNyRStksLlkaankflenilnrralekek.ktvekgekivvleaeteeeEaekiaatikall.ekneklediavLvR 80 
                                    L+  +R  + + +a+  ++++  +r++ + ++ +  e g +++v+ a +   Ea  ia+ +++   +     +++av+vR
  gi|121639087|ref|YP_979311.1| 317 LTVSHRCAPAVARAVTGIARRLPGRSVGRRIEgTGTEVG-SVTVRLAGSAHAEAAMIADALRRAHlIDGVPWSQMAVIVR 395
                                    777788888888899999988888866663331334444.69*******************999889999********** PP

                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  81 snkdadkiskaLkkegipfnvvd.eekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatveriseelkklg 159
                                    s  +a+ + +aL + g+p+     +  +   + ++ +l +l+ +a   d     ++l +++ g+++ +++++ + l    
  gi|121639087|ref|YP_979311.1| 396 SVPRAVRLPRALAAAGVPVAPPAvGGPLSAEPAVRALLTVLEATADGLDGDQALLLLTGPIGGVDPVSLRQLRRTL---- 471
                                    ********************9998999*********************************************3333.... PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 160 lsltDfikedtleygeeFieliraleeknl......elllkkiektaeerqalvsk.yadlfkelaeklaelkekseskr 232
                                           +    ++  +F  l+ ++  ++       + +l++++   +++ ++ ++       +     a +++   ++r
  gi|121639087|ref|YP_979311.1| 472 ------QRARPGQTSRKFGDLLVEVLGGDAppsgpgSRALRRVRAVLTAAARCHRSgSLGGQDPRHTLWAAWQRSGLQRR 545
                                    ......34567788899*9999999999999*****55566644333333333222022233333333334455555555 PP

                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 233 .............kkeeklenlreLysllkelekkeeeeeveeklneileiatLseseleeskkkekipiiTiHqAKGlE 299
                                                 + ++ le++  L+++++ +       + +  l e ++  +L    +e     e++ +++ H+A G E
  gi|121639087|ref|YP_979311.1| 546 wlaasehggaaavQATRDLETVTALFDITDHYVSRTSGASLRG-LVEHVTALQLPVVRPEPAAPTEQVMVLSAHAALGHE 624
                                    666655566666555569****************888888777.888888888999999888888*************** PP

                                    xxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C 300 FdvVflagleegtfP......................syrskkekrleEEkRlfYVaiTRAkkrLfisys 347
                                    +d V++agl++g  P                      +  s +   l+EE+Rl+  a+ RA++rL +++ 
  gi|121639087|ref|YP_979311.1| 625 WDLVVIAGLQDGLWPntvprggvlgtqrlldeldgvtKDASMRAPLLAEERRLLVTAMGRARRRLLVTAV 694
                                    ***************77777777777777776666664444447779********************975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0     6e-17   9.8e-14      10     146 .]      18     292 ..      11     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 6e-17
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...............atTiHr 74 
                                    ++++lv++GpGtGK+++l+++    + +g  +pe++ll++  gr  ++ r +l++++++                +T+H+
  gi|121639087|ref|YP_979311.1|  18 RGPVLVLGGPGTGKSTLLVEAAVAHIGAG-TDPESVLLLTGSGRMGMRARSALTTALLRsrtngpcraairepvVRTVHS 96 
                                    5799**********999887655555555.478**********99999999887666668999****************9 PP

                         AAA_19  75 lal............................................................................. 77 
                                     a                                                                              
  gi|121639087|ref|YP_979311.1|  97 YAYavlrkaaqragdalprlltsaeqdaiirellagdaedgpaatttwpahlrpalttagfatelrnllarcaergldpl 176
                                    99999*************************************************************************** PP

                         AAA_19  78 .............................................ldfddlltealelle.....eaeeekklqeeelli 107
                                                                                 l + +l+  ale++           +   +  +l+
  gi|121639087|ref|YP_979311.1| 177 elqqlgrrrgrpewiaagqfaqryeqvmllrgavglaapqatapaLSAAELVGAALEAFAvdpelL--AAERA-RVRTLL 253
                                    ***********************************9999999888444444433333333544331..22222.3359** PP

                         AAA_19 108 vDEfqdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                    vD +q++d+++ rL++ l+  ++  l+ GDp+Q+++ fr
  gi|121639087|ref|YP_979311.1| 254 VDDAQQLDPQAARLVRMLAAGTELALIAGDPNQAVFGFR 292
                                    *******************444545666******99986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.7   4.2e-05     0.069      21      66 ..      21      69 ..       8     140 .. 0.73
   2 !    6.3   0.2    0.0042       6.9      52     129 ..     212     288 ..     191     342 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaag...grviglAptgkaAkvLaeel 66
                                   +++ G++GtGK+t+l +++ a+  ag   ++v++l+ +g++  + + +l
  gi|121639087|ref|YP_979311.1| 21 VLVLGGPGTGKSTLLVEAAVAHIGAGtdpESVLLLTGSGRMGMRARSAL 69
                                   6899***********9998888888778899999999998876666443 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                         AAA_30  52 lAptgkaAkvLaeelgi.....eastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDer 126
                                    lA  ++ A +L+++ ++     ea  ++  l     +a+ ++ + l+vD a  +d  q+a+l++ +++     +++GD++
  gi|121639087|ref|YP_979311.1| 212 LAAPQATAPALSAA-ELvgaalEAFAVDPELL----AAERARVRTLLVDDAQQLD-PQAARLVRMLAAGTELALIAGDPN 285
                                    44444444444422.22000113333333332....22334558999******99.67899999999955666778**** PP

                         AAA_30 127 Qla 129
                                    Q  
  gi|121639087|ref|YP_979311.1| 286 QAV 288
                                    964 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0012         2       2      21 ..      22      41 ..      21      74 .. 0.83
   2 !    5.1   0.0      0.01        16      54     102 ..     241     289 ..     210     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                   +v G pG GKStl+++++  
  gi|121639087|ref|YP_979311.1| 22 LVLGGPGTGKSTLLVEAAVA 41
                                   799************99866 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                Viral_helicase1  54 lmalvkstkgkililDEylllhaGyill.laalskaklvilfGDplQipf 102
                                    l a+ +  + ++l++D++++l++    l  +  ++ +l+++ GDp+Q  f
  gi|121639087|ref|YP_979311.1| 241 LLAAER-ARVRTLLVDDAQQLDPQAARLvRMLAAGTELALIAGDPNQAVF 289
                                    445544.36899*********997777733445677889999*****876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05      0.11       4      55 ..      21      73 ..      18     109 .. 0.75
   2 ?   -2.8   0.0       1.7   2.8e+03     121     139 ..     245     263 ..     242     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                        DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeer.tavylsvNhplvlvlrealakke 55
                                   vlV G++GtGK+ +l+++++++     +  ++ +l+++++  +  r+al+   
  gi|121639087|ref|YP_979311.1| 21 VLVLGGPGTGKSTLLVEAAVAHIGAGTDPeSVLLLTGSGRMGMRARSALTTAL 73
                                   799**************999995554444044556677777777777776655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                        DUF2075 121 krakvvvalvDegQelntg 139
                                    +ra+v  +lvD++Q+l  +
  gi|121639087|ref|YP_979311.1| 245 ERARVRTLLVDDAQQLDPQ 263
                                    5788889999999998766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0088        14       6      24 ..      19      37 ..      16     113 .. 0.83
   2 ?    4.6   0.0     0.023        37      88     124 ..     246     278 ..     212     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0088
                         AAA_22  6 gilvvtGesGtGKTtllrr 24
                                   g ++v G +GtGK+tll +
  gi|121639087|ref|YP_979311.1| 19 GPVLVLGGPGTGKSTLLVE 37
                                   678999*********9865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.023
                         AAA_22  88 aravielliiDEaqhlrseealeeLrsllnlsrkgvq 124
                                    +++ ++ l++D+aq l  ++a + +r+l+    + ++
  gi|121639087|ref|YP_979311.1| 246 RAR-VRTLLVDDAQQL-DPQAARLVRMLAA--GTELA 278
                                    333.599*********.6777777777766..55554 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.087   1.4e+02       3      21 ..     613     631 ..     611     635 .. 0.87
   2 ?    8.1   0.3    0.0015       2.4      31      51 ..     671     691 ..     657     692 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.087
                       UvrD_C_2   3 yaltihkaQGsefpaVivf 21 
                                     +l+ h a G e++ V+++
  gi|121639087|ref|YP_979311.1| 613 MVLSAHAALGHEWDLVVIA 631
                                    68899************95 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                       UvrD_C_2  31 gelrrrlLYtavTRAreklil 51 
                                     ++ rrlL ta+ RAr++l +
  gi|121639087|ref|YP_979311.1| 671 LAEERRLLVTAMGRARRRLLV 691
                                    3458**************987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018       0.3       9      39 ..       5      35 ..       3      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                         AAA_29  9 WgtfdghtieidlkgatlltGpsGsGKSTll 39
                                   Wg   g  +   l+g +l+ G  G+GKSTll
  gi|121639087|ref|YP_979311.1|  5 WGVEAGAALAPGLRGPVLVLGGPGTGKSTLL 35
                                   77777777777889999************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00056       0.9      34      58 ..      19      43 ..      13      79 .. 0.84
   2 ?    0.2   0.1      0.28   4.6e+02       2      42 ..     244     284 ..     229     291 .. 0.82
   3 ?   -1.9   0.1       1.3   2.1e+03      84     134 ..     502     565 ..     499     575 .. 0.67
   4 ?    0.5   0.1      0.24   3.9e+02      88     165 ..     883     960 ..     860    1025 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00056
                         AAA_25 34 elallaGapgtGKttlaldlalava 58
                                   + +l+ G pgtGK+tl+++ a+a  
  gi|121639087|ref|YP_979311.1| 19 GPVLVLGGPGTGKSTLLVEAAVAHI 43
                                   56889999************99865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.28
                         AAA_25   2 aeplelsavsvadlaapppprrwlvkgllpagelallaGap 42 
                                    ae+++ +++ v+d ++  p+   lv+ l +  elal+aG+p
  gi|121639087|ref|YP_979311.1| 244 AERARVRTLLVDDAQQLDPQAARLVRMLAAGTELALIAGDP 284
                                    56777888888888888888888888888888888888887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                         AAA_25  84 delrrRlravgeal............rddarllvldlagv.eslpLfakdrggtlltadvdale 134
                                    ++  rR+rav++a+            +++ +l + +  +  +++ L+a+++gg+++ +++++le
  gi|121639087|ref|YP_979311.1| 502 SRALRRVRAVLTAAarchrsgslggqDPRHTLWAAWQRSGlQRRWLAASEHGGAAAVQATRDLE 565
                                    5667899999988878888888887655666666655555677777777777777555555555 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.24
                         AAA_25  88 rRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv 165
                                    r + +++ ++r+++r  ++ + gv  +++ + +d  g++++  ++  ++++e+ +  rlv++D  +  ++ +++++ + 
  gi|121639087|ref|YP_979311.1| 883 RAMIQAFVQWRAQSRSELTEV-GVeVDIDGALEDGSGQARKIRLRGRADRLERDPAGRLVIVDIKTGKTPVSKDDAQQH 960
                                    555555555555555555543.444555555555555555555666666666666666777766655555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1055 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.86u 0.27s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 6528.73
//
Query:       gi|121639088|ref|YP_979312.1|  [L=72]
Description: hypothetical protein BCG_3228 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      123  (0.00686039); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 539.50
//
Query:       gi|121639089|ref|YP_979313.1|  [L=224]
Description: lipase lipV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-17   63.7  15.3    4.2e-17   63.5  15.3    1.0  1  Abhydrolase_6    Alpha/beta hydrolase family
    5.5e-12   45.9   0.1    2.6e-11   43.6   0.2    1.9  2  Abhydrolase_1    alpha/beta hydrolase fold
    1.8e-10   40.5   0.0    2.7e-10   39.9   0.0    1.3  1  Hydrolase_4      Serine aminopeptidase, S33
    8.5e-07   29.3   0.1    1.1e-06   29.0   0.1    1.6  1  Thioesterase     Thioesterase domain
    7.2e-05   22.5   0.0    8.9e-05   22.2   0.0    1.2  1  Esterase         Putative esterase
    0.00018   21.4   0.2     0.0003   20.7   0.2    1.4  1  Ser_hydrolase    Serine hydrolase
    0.00066   19.6   0.3    0.00089   19.2   0.3    1.2  1  Abhydrolase_3    alpha/beta hydrolase fold
    0.00079   19.3   0.0     0.0013   18.6   0.0    1.3  1  Lipase_3         Lipase (class 3)
     0.0027   17.5   0.0     0.0039   17.0   0.0    1.2  1  PGAP1            PGAP1-like protein
  ------ inclusion threshold ------
      0.015   14.2   0.1      0.023   13.6   0.1    1.2  1  Chlorophyllase2  Chlorophyllase enzyme
      0.021   14.4   0.0      0.027   14.0   0.0    1.2  1  DLH              Dienelactone hydrolase family
      0.034   14.1   0.0      0.047   13.6   0.0    1.2  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
      0.056   13.2   0.0      0.071   12.9   0.0    1.2  1  Abhydrolase_5    Alpha/beta hydrolase family
       0.06   12.9   0.0      0.091   12.3   0.0    1.2  1  LIDHydrolase     Lipid-droplet associated hydrolase
       0.07   12.2   0.0       0.13   11.4   0.0    1.3  1  DUF2048          Abhydrolase domain containing 18
      0.078   11.5   0.0        0.1   11.1   0.0    1.1  1  PAF-AH_p_II      Platelet-activating factor acetylhydrolase, 
      0.079   12.9   0.0       0.11   12.4   0.0    1.2  1  UPF0227          Uncharacterised protein family (UPF0227)
      0.079   12.4   0.1       0.11   11.9   0.1    1.2  1  DUF3530          Protein of unknown function (DUF3530)
      0.086   12.3   2.4       0.12   11.8   2.4    1.2  1  Esterase_phd     Esterase PHB depolymerase
      0.095   12.2   0.0       0.12   11.9   0.0    1.1  1  DUF2974          Protein of unknown function (DUF2974)
       0.13   11.8   0.7        0.2   11.1   0.7    1.2  1  Acyl_transf_1    Acyl transferase domain
       0.19   11.2   0.0       0.29   10.6   0.0    1.3  1  DUF3089          Protein of unknown function (DUF3089)


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5  15.3   5.2e-20   4.2e-17      30     219 ..       7     215 ..       2     216 .. 0.58

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5.2e-20
                                    EEE--TTST.S-GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC....EE.EEES-..----TTT CS
                  Abhydrolase_6  30 lapDlpGhG.rsdpppldled.ladlaalldelaagggpvvlvGHSlGGalalaaapla..lvvg.vlldppptalpagl 104
                                     apDl GhG +++ +p + ++ + +laalld  +  +gpvv+vGHS+GGa+a+++a++   +v++ vlldp +    ++ 
  gi|121639089|ref|YP_979313.1|   7 AAPDLLGHGrSPWAAPWTIDAnVSALAALLDNQG--DGPVVVVGHSFGGAVAMHLAAARpdQVAAlVLLDPAV---ALDG 81 
                                    69******96669999999888899999999995..******************444446777779*****33...2222 PP

                                    .........S----TTHHHHHHTT-C.....CCCHCCHS-HSCCCCHHH....C....CCCHCHCCCGHHHHCCHHCHTT CS
                  Abhydrolase_6 105 .........laaalelllallallrl.....lawlsreplprlfladed....a....daawrarlarlaallaglgllp 162
                                             + a + +l+++ a   +      aw     +p+ + a++d    a    ++ wr  l ++  +++ l    
  gi|121639089|ref|YP_979313.1|  82 srvrevvdaMLASPDYLDPAEA---RaekatGAWAD--VDPPVLDAELDehlvAlpngRYGWRISLPAMVCYWSELARDI 156
                                    2434442222222222222222...12334457774..233344444443332133337777777777777777666222 PP

                                    CCHHTT-TTGCEEE........CTT-CHHHHCHHCCCH.STTEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 163 aaawadlpvpllvl........ggeDplvprllerlla.qagarlpvvlpgaGHlphleepdevae 219
                                       ++++ +++ ++        + +D+l+++l +rl+a  +         ++GH++ +++p+eva+
  gi|121639089|ref|YP_979313.1| 157 --VLPPVGTATTLVravraspaYVSDQLLAALDKRLGAdFELL-----DFDCGHMVPQAKPTEVAA 215
                                    ..33333333322232233222266776666666666533333.....338***99999*****98 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.2   3.2e-14   2.6e-11      33     107 ..       7      78 ..       5     188 .. 0.83
   2 ?    0.9   0.0      0.36   2.9e+02     214     252 ..     166     205 ..     122     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.2e-14
                                    EEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE..C CS
                  Abhydrolase_1  33 illDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga..i 107
                                     ++Dl+G+g+S+ a  +     ++++    l ++ld  gd+++++vGhS+GG++a+++aa  p+ V+alvll++   
  gi|121639089|ref|YP_979313.1|   7 AAPDLLGHGRSPWAAPW-----TIDANVSALAALLDNQGDGPVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPavA 78 
                                    589********766654.....666666677799***************************************9531 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.36
                                    EEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSH CS
                  Abhydrolase_1 214 tlvisgtsDplvpp.kaledlaqllpkkrlvvisdagHla 252
                                    tlv + +  p+    + l  l++ l   +++ ++d+gH++
  gi|121639089|ref|YP_979313.1| 166 TLVRAVRASPAYVSdQLLAALDKRLGADFELLDFDCGHMV 205
                                    4444444444444447778888888888999999999986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   3.3e-13   2.7e-10      34     156 ..       6     121 ..       2     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.3e-13
                    Hydrolase_4  34 vyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalk 112
                                    ++a D  GhGrs+  + +    +d  v  laa+     +++++ p++++GhS GG++a+++++ +pd+va+l+l  Pa++
  gi|121639089|ref|YP_979313.1|   6 IAAPDLLGHGRSPwAAPW---TIDANVSALAAL----LDNQGDGPVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPAVA 78 
                                    6789999*****533333...344445545444....4677789***********************************9 PP

                    Hydrolase_4 113 ikaklkappllklllkllgkllpklqvsnnlkadslsrdpevva 156
                                    ++ + ++++++ ++l     l p     ++   ++   dp v++
  gi|121639089|ref|YP_979313.1|  79 LDGS-RVREVVDAMLASPDYLDPAEARAEKATGAWADVDPPVLD 121
                                    9954.477777776665555555444455555555555555555 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   1.3e-09   1.1e-06      56      97 ..      32      70 ..      13     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.3e-09
                                   HHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEE CS
                   Thioesterase 56 aealrqiqpegPyalfGhSlGgllAfevArqLesqGlavksl 97
                                   ++al+  q +gP++++GhS+Gg++A+ +A++   +  +v++l
  gi|121639089|ref|YP_979313.1| 32 LAALLDNQGDGPVVVVGHSFGGAVAMHLAAA---RPDQVAAL 70
                                   5789999*********************985...44445555 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.1e-07   8.9e-05     111     154 ..      37      89 ..      14     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                                    SEECCC.EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC........H CS
                       Esterase 111 rtapdg.ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps........n 154
                                    + + dg  +v+G+S+GG +A++la+ +pd+ +    + p v +         +
  gi|121639089|ref|YP_979313.1|  37 DNQGDGpVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPAVALDgsrvrevvD 89 
                                    44555579**********************98777776666555555555552 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   3.7e-07    0.0003      42      92 ..      28      78 ..      15     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.7e-07
                                   HHHHHHHHHHC-.STTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SG CS
                  Ser_hydrolase 42 Wvaaleaaveaa.eekvvlvAHSlgclavlhaaelqlakkvagalLVapadv 92
                                    v+al+a ++++  ++vv+v HS+g ++++h+a ++++++va+ +L  pa  
  gi|121639089|ref|YP_979313.1| 28 NVSALAALLDNQgDGPVVVVGHSFGGAVAMHLA-AARPDQVAALVLLDPAVA 78
                                   5667777776552679*****************.9***********999865 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.1e-06   0.00089      46     116 ..      22      80 ..      18     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                                    THHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTT CS
                  Abhydrolase_3  46 PaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlerte 116
                                    P  ++  ++al  l+++          +v++G S GG  a+++a +  d    +va++vl+ P++ l   +
  gi|121639089|ref|YP_979313.1|  22 PWTIDANVSALAALLDN-----QGDGPVVVVGHSFGGAVAMHLAAARPD----QVAALVLLDPAVAL---D 80 
                                    66778888888888888.....36779*****************65555....59********6644...1 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0013      53      83 ..      30      60 ..      19      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHTT-EEEEEEEETHHHHHHHHHH CS
                       Lipase_3 53 kelkrllekypeysivvtGHSLGgalAlLaa 83
                                   + l  ll+++ +  +vv+GHS+Gga+A+ +a
  gi|121639089|ref|YP_979313.1| 30 SALAALLDNQGDGPVVVVGHSFGGAVAMHLA 60
                                   5788999999*****************8544 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0039      91     126 ..      42      74 ..      29      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                          PGAP1  91 tsviliGHSmGGivaraaltlknyikqsvntiltla 126
                                      v+++GHS+GG va   + l++ ++++v  ++ l+
  gi|121639089|ref|YP_979313.1|  42 GPVVVVGHSFGGAVA---MHLAAARPDQVAALVLLD 74 
                                    569************...777778899999998775 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.023      92     129 ..      44      78 ..      28      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                Chlorophyllase2  92 lalsgHSrGgktafalalgkaktslkfsaligvdPvag 129
                                    ++++gHS Gg +a++la  + +   +++al+ +dP  +
  gi|121639089|ref|YP_979313.1|  44 VVVVGHSFGGAVAMHLAAARPD---QVAALVLLDPAVA 78 
                                    6899**************9999...9*********654 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.027      91     126 ..      35      71 ..      19     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                            DLH  91 svpevstkkvgvvGfCmGGalalllaaev.pevdaav 126
                                       ++ ++ v+vvG  +GGa+a+ laa   ++v+a v
  gi|121639089|ref|YP_979313.1|  35 LLDNQGDGPVVVVGHSFGGAVAMHLAAARpDQVAALV 71 
                                    234567899****************999878888876 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.7e-05     0.047      24      59 ..      44      80 ..      34     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                                   EEEEEETHHHHHHHHHHHHSS.SEEEEEEES--SB-- CS
                         BAAT_C 24 igllGiSkGgelalllasflk.kisavvlingsavvv 59
                                   + ++G+S+Gg +a+ la+  + ++ a+vl+ ++++  
  gi|121639089|ref|YP_979313.1| 44 VVVVGHSFGGAVAMHLAAARPdQVAALVLLDPAVALD 80
                                   679**************99999*******99988765 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.7e-05     0.071      59      88 ..      44      74 ..      27     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                  Abhydrolase_5 59 fvvgGhslGGvvasrfaaee.ekiegvvfla 88
                                    vv Ghs+GG+va ++aa   +++ ++v+l 
  gi|121639089|ref|YP_979313.1| 44 VVVVGHSFGGAVAMHLAAARpDQVAALVLLD 74
                                   799************9986648999999985 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011     0.091      68     121 ..      28      77 ..      24      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                   LIDHydrolase  68 kedflkellekaksekdvklilvGHSvGaYialevlkrlsersikkvvlLfPti 121
                                     ++ l +ll+   ++ d  +++vGHS G  +a++++   +++ +  +vlL P +
  gi|121639089|ref|YP_979313.1|  28 NVSALAALLD---NQGDGPVVVVGHSFGGAVAMHLAAARPDQ-VAALVLLDPAV 77 
                                    5556666665...679999******************99997.*******9987 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.13     163     210 ..      29      76 ..      24      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                        DUF2048 163 slvllhwlereGyGplgltGlSmGGhmaslaasnwpkplvlvpclsws 210
                                    +++l+  l+++G Gp+ + G S+GG  a   a++ p  ++ + +l ++
  gi|121639089|ref|YP_979313.1|  29 VSALAALLDNQGDGPVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPA 76 
                                    56788899999*****************99999999999988887665 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013       0.1     223     246 ..      37      60 ..      20      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                    T-EEEEEEEEEEETHHHHHHHHHH CS
                    PAF-AH_p_II 223 dnldtskvaviGHsFGgAtviksl 246
                                    dn     v+v+GHsFGgA +++  
  gi|121639089|ref|YP_979313.1|  37 DNQGDGPVVVVGHSFGGAVAMHLA 60 
                                    444455599*********998533 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11      49      93 ..      32      79 ..      19      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                        UPF0227 49 leklvaelgddnillvGssLGGyyatrlge.rfglrq..vllnPalkp 93
                                   l +l+ + gd  +++vG s GG +a +l++ r ++++  vll Pa++ 
  gi|121639089|ref|YP_979313.1| 32 LAALLDNQGDGPVVVVGHSFGGAVAMHLAAaRPDQVAalVLLDPAVAL 79
                                   44555555655699**************862667777799*****986 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014      0.11     182     234 ..      27      78 ..      22      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                        DUF3530 182 arlqaaiaflnqrgaenivllghgtgAywaarylaekksakvdaLvlvdarep 234
                                    a+++a  a+l+++g   +v++gh  g + a+ + a  ++ +v aLvl+d+   
  gi|121639089|ref|YP_979313.1|  27 ANVSALAALLDNQGDGPVVVVGHSFGGAVAMHLAAA-RPDQVAALVLLDPAVA 78 
                                    6677778899999999***************99999.9***********9765 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4   0.00015      0.12      88     178 ..      35     123 ..      19     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                   Esterase_phd  88 lvdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhsGlalGeaadvisaldvmrrGlrqapaaavdalveagay 167
                                    l d+ +     v v G s G+a+a  la   pd+ aa+ l         + v   +d+m   +     a + a   +ga+
  gi|121639089|ref|YP_979313.1|  35 LLDNQG--DGPVVVVGHSFGGAVAMHLAAARPDQVAALVLLDPAVALDGSRVREVVDAMLASPDYLDPAEARAEKATGAW 112
                                    444443..3458899**********************8887655555667788889999988887666666777777788 PP

                   Esterase_phd 168 pglpalvvqGd 178
                                      +   v++ +
  gi|121639089|ref|YP_979313.1| 113 ADVDPPVLDAE 123
                                    77765555555 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.12      80     111 ..      38      69 ..      24      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        DUF2974  80 eesegkiylgGhSkGGnlAvyaamnaeddlqe 111
                                    ++ +g+++++GhS GG +A+  a+  +d++ +
  gi|121639089|ref|YP_979313.1|  38 NQGDGPVVVVGHSFGGAVAMHLAAARPDQVAA 69 
                                    355778*************9998888888763 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00025       0.2      72     103 ..      31      62 ..      27      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                    HHHHHHHHTT-TTSEEEE-TTHHHHHHHHCCS CS
                  Acyl_transf_1  72 alaellkskGvrpaavvGHSlGElAaavvaga 103
                                    ala+ll  +G  p +vvGHS G   a + a+a
  gi|121639089|ref|YP_979313.1|  31 ALAALLDNQGDGPVVVVGHSFGGAVAMHLAAA 62 
                                    899*******************9988887776 PP

>> DUF3089  Protein of unknown function (DUF3089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00036      0.29      81     117 ..      30      65 ..      26     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                        DUF3089  81 aAfeaylakenkgrPiiLaGhsQGallllrLlkeeia 117
                                    +A++a l+++ +g P++++Ghs G++++++L + + +
  gi|121639089|ref|YP_979313.1|  30 SALAALLDNQGDG-PVVVVGHSFGGAVAMHLAAARPD 65 
                                    5777888888888.***************99887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1691.63
//
Query:       gi|121639090|ref|YP_979314.1|  [L=101]
Description: DNA-methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-18   64.5   0.0    8.9e-18   64.2   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0     5e-22   8.9e-18       6      81 .]      12      82 ..       8      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 5e-22
                                   HHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTTS CS
                  DNA_binding_1  6 VwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEgv 81
                                   V +l+ +Ip G+v tYg+iA+l+g  +++r Vg++++    + ++P+HRV++a+g+  +    ++r+ +lL+aEgv
  gi|121639090|ref|YP_979314.1| 12 VRSLVAAIPLGRVSTYGDIAALAG-LSSPRIVGWIMRT--DSSDLPWHRVIRASGRPAQH--LATRQLELLRAEGV 82
                                   7889********************.9***********8..99*************87755..79**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 755.00
//
Query:       gi|121639091|ref|YP_979315.1|  [L=292]
Description: hypothetical protein BCG_3231c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.5   0.0       0.26   11.1   0.0    1.7  2  XylR_N    Activator of aromatic catabolism


Domain annotation for each model (and alignments):
>> XylR_N  Activator of aromatic catabolism
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.4e-05      0.26      39      79 ..      20      60 ..      16      80 .. 0.82
   2 ?   -2.6   0.0      0.26   4.6e+03      69      89 ..      98     118 ..      87     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.4e-05
                         XylR_N 39 eslgverarglltrlGyasGardaelakklrpdaseeeafl 79
                                    ++g+  a+ +l+  G++ G+r++e++ +++ d+ ++ + +
  gi|121639091|ref|YP_979315.1| 20 VAFGLAGAQPILLGAGWEGGWRCGEVVLSMVADNARAAWSA 60
                                   678999************************99987777655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.26
                         XylR_N  69 rpdaseeeaflaGpqlhaleG 89 
                                     p+  ++e+++a  +lh+ +G
  gi|121639091|ref|YP_979315.1|  98 APEPRHDEVVSAAVRLHEATG 118
                                    455677889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2535.10
//
Query:       gi|121639092|ref|YP_979316.1|  [L=392]
Description: molybdopterin biosynthesis-like protein MoeZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-58  195.8   0.0      1e-57  195.3   0.0    1.1  1  ThiF             ThiF family
    8.4e-15   55.2   0.0    2.2e-14   53.8   0.0    1.7  2  Rhodanese        Rhodanese-like domain
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.055   13.5   0.1    1.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.039   13.6   0.0      0.082   12.6   0.0    1.5  1  SelB-wing_3      Elongation factor SelB, winged helix
      0.076   12.9   0.0       0.16   11.9   0.0    1.5  1  TIP39            TIP39 peptide
      0.097   12.2   0.3       0.28   10.7   0.1    1.9  2  DAO              FAD dependent oxidoreductase
       0.13   12.5   0.6       0.95    9.7   0.6    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.18   11.3   0.3        0.3   10.6   0.3    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.0   4.5e-61     1e-57       1     238 [.      23     258 ..      23     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 4.5e-61
                                    THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHH CS
                                    xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaa 78 
                                    ysr+l +  lg dgq++L++++vl++GaGglG + l +La++Gvg + +vD+D+++ sNl+Rq++++ +d+G++Ka++a+
  gi|121639092|ref|YP_979316.1|  23 YSRHLIIpdLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDESNLQRQVIHGVADVGRSKAQSAR 102
                                    788977788999******************************************************************** PP

                                    HHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE...EE. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx. RF
                           ThiF  79 ealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi...ip. 154
                                    +++ +inp + v+ ++ r+ +++ + +l++++Dl++d++Dn+++r+lvn+a+v  g+p++ ++  +fegq+ v+   +p 
  gi|121639092|ref|YP_979316.1| 103 DSIVAINPLIRVRLHELRLAPSN-AVDLFKQYDLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFwedAPd 181
                                    *********************88.56************************************************854447 PP

                                    CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCG.GGCCEEEECCTTTTEEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                           ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkek.lenslltqvdllesrfenve 233
                                    g    y++l+p   e p++ +vp+c +  g   +++ ++a va+++ +e++kl+ g  + l ++ll  +d+le++++++ 
  gi|121639092|ref|YP_979316.1| 182 GLGVNYRDLYP---EPPPPGMVPSC-AEGG---VLGIICASVASVMGTEAIKLITGIGEtLLGRLL-VYDALEMSYRTIT 253
                                    88889****99...***********.9999...*********************554440555555.9*********999 PP

                                    CEEEE CS
                                    xxxxx RF
                           ThiF 234 lerak 238
                                    +++++
  gi|121639092|ref|YP_979316.1| 254 IRKDP 258
                                    98876 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.5   7.9e+03      64      90 ..      40      65 ..      21      73 .. 0.71
   2 !   53.8   0.0     1e-17   2.2e-14       1     106 [.     290     383 ..     290     384 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.5
                      Rhodanese 64 dnkktvvvycdgggraaaaaallkklG 90
                                    ++ +v v+++gg +a  + +l+  +G
  gi|121639092|ref|YP_979316.1| 40 LKNARVLVIGAGGLGAPTLLYLAA-AG 65
                                   468888999988888666655555.55 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 1e-17
                      Rhodanese   1 sakelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggra 79 
                                    ++ el++ l++g+   l+DvR+p+e++  hI gA  +           +++l +  e l++l   +++t v+yc++g r+
  gi|121639092|ref|YP_979316.1| 290 TPRELRDWLDSGRKLaLIDVRDPVEWDIVHIDGAQLI-----------PKSLINSGEGLAKL--PQDRTAVLYCKTGVRS 356
                                    6789999997777557*********************...........88888888888888..99************** PP

                      Rhodanese  80 aaaaallkklGyknvsvldGGfkawke 106
                                    a+a a++kk+G+ +  +l GG+ aw++
  gi|121639092|ref|YP_979316.1| 357 AEALAAVKKAGFSDAVHLQGGIVAWAK 383
                                    ************99***********86 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.5e-05     0.055       8      43 ..      38      73 ..      32      93 .. 0.86
   2 ?   -3.1   0.0       3.4   7.7e+03      84     128 ..     283     324 ..     280     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                   S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEE CS
                   Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaN 43
                                   ++lk+++vl+iGaG ++  ++ +L+a+gv  + ++ 
  gi|121639092|ref|YP_979316.1| 38 KRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVD 73
                                   4799*************************9999986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                    SSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCC CS
                   Shikimate_DH  84 aseepilekeeveealkkrkkplllvDiavPRdvepevaeledvr 128
                                    a++   ++ +e+++ l++  ++l l+D+  P  ve ++ ++++++
  gi|121639092|ref|YP_979316.1| 283 AAKGSTITPRELRDWLDS-GRKLALIDVRDP--VEWDIVHIDGAQ 324
                                    566666777777777744.477888998888..777676666665 PP

>> SelB-wing_3  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05     0.082       3      26 ..     283     306 ..     281     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                                    HHTTS-BBHHHHHHHHT--HHHHH CS
                    SelB-wing_3   3 lkeegeitaaefRdllgtSRKyai 26 
                                    +++  +it  e+Rd l+ +RK a+
  gi|121639092|ref|YP_979316.1| 283 AAKGSTITPRELRDWLDSGRKLAL 306
                                    455578***************996 PP

>> TIP39  TIP39 peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     7e-05      0.16      16      48 ..     275     306 ..     273     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                          TIP39  16 vlADDAAFREkakLLaalERrkWLnSYmqKLLv 48 
                                    v+ADDAA   k   ++  E r WL+S  +KL +
  gi|121639092|ref|YP_979316.1| 275 VVADDAAQAAKGSTITPRELRDWLDSG-RKLAL 306
                                    89***********************94.55555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00013      0.28       1      27 [.      44      73 ..      44     182 .. 0.93
   2 ?   -0.7   0.0      0.38   8.5e+02     115     182 ..     297     363 ..     238     380 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                   EEEEECTSHHHHHHHHHHHHTT...EEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg...Vtlle 27
                                   +v++iG+G  G+ t ++La++g   + +++
  gi|121639092|ref|YP_979316.1| 44 RVLVIGAGGLGAPTLLYLAAAGvgtIGIVD 73
                                   59******************9877877776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                                    EEEH.HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHH...HHHHHHHTT-EEEESECEEEEEEEETCEEEE CS
                            DAO 115 llda.eevrelepalpgllgalfypdtgqvdpakltaa...laraaealGveilegtevtgleeedgkvwgv 182
                                    +ld+ ++++ ++   +++   ++  d++q+ p  l+++   la+  +++ + ++ +t v++ e+    ++ v
  gi|121639092|ref|YP_979316.1| 297 WLDSgRKLALIDV-RDPVEWDIVHIDGAQLIPKSLINSgegLAKLPQDRTAVLYCKTGVRSAEA----LAAV 363
                                    5555333333332.23666777777778888888887777788888888888888888888754....4444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00042      0.95       1      80 [.      45     143 ..      45     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE--TT CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaialdae 57 
                                    vl+iGaG+ G +++ +la+ +    +i ++d++     +l  ++                         +r+  ++l  +
  gi|121639092|ref|YP_979316.1|  45 VLVIGAGGLGAPTLLYLAAAGVG--TIGIVDFDVVDESNLQRQVihgvadvgrskaqsardsivainPLIRVRLHELRLA 122
                                    89*****************9866..8888888766655555444555556666666666555555554444444444444 PP

                                    THHHHHHHHHTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP  58 nyeavLaallkegdlvvnlsppi 80 
                                       a  + l k++dl+++ + ++
  gi|121639092|ref|YP_979316.1| 123 PSNA--VDLFKQYDLILDGTDNF 143
                                    3333..44556666666666555 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00013       0.3       2      42 ..      44      85 ..      43     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                   EEEEE--STTHHHHHHHHHHCTSEEEE.E-S-HHHHHHHCTT CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevig.vDideekvdklnsg 42
                                   ++ viG+G +G++t + la++g+  ig vD d    ++l+++
  gi|121639092|ref|YP_979316.1| 44 RVLVIGAGGLGAPTLLYLAAAGVGTIGiVDFDVVDESNLQRQ 85
                                   899*******************76554278887666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2764.51
//
Query:       gi|121639093|ref|YP_979317.1|  [L=285]
Description: hypothetical protein BCG_3233c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.6e-104  347.4   0.0   3.1e-104  347.1   0.0    1.1  1  DUF3152        Protein of unknown function (DUF3152)
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.036   13.9   0.0    1.3  1  Peptidase_M10  Matrixin
      0.049   13.8   0.0      0.066   13.3   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> DUF3152  Protein of unknown function (DUF3152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.1   0.0  5.3e-108  3.1e-104       1     207 []      73     283 ..      73     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 347.1 bits;  conditional E-value: 5.3e-108
                        DUF3152   1 lppGgeftekgagtfrvvpgtakkvgkgkekkftyvvevengldtsaygGddafaelvdatlanpksWtkdpkfafervd 80 
                                    lp+Gg+fte+g++t+rvvpgt+++vg+g+ k+f+y+ve+engld+++ygGd+afa++vd+tl+npk+Wt++p+faf r+d
  gi|121639093|ref|YP_979317.1|  73 LPDGGPFTEAGDKTWRVVPGTTPQVGQGTVKVFRYTVEIENGLDPTMYGGDNAFAQMVDQTLTNPKGWTHNPQFAFVRID 152
                                    79****************************************************************************** PP

                        DUF3152  81 egkdPdlrislvskettreaCgndieletsCkkaa......edrvlinearWvrGavpfegdigsyrqylinhevGhaiG 154
                                    +gk P++rislvs++t+r  Cg++++letsC++++      ++rv+inearWvrGavpfegd+gsyrqy+inhevGhaiG
  gi|121639093|ref|YP_979317.1| 153 SGK-PNFRISLVSPTTVRGGCGYEFRLETSCYNPSfggmdrQSRVFINEARWVRGAVPFEGDVGSYRQYVINHEVGHAIG 231
                                    ***.******************************99999999************************************** PP

                        DUF3152 155 yaaheaCekdGelaPvmmqqtlsvsnnelakldpdevvpadgatCkvnpWpyP 207
                                    y +he+C+++G+laPvmmqqt+s+sn+++ak+dpd v++ dg+tC++npWpyP
  gi|121639093|ref|YP_979317.1| 232 YLRHEPCDQQGGLAPVMMQQTFSTSNDDAAKFDPDFVKA-DGKTCRFNPWPYP 283
                                    ***********************************9887.************9 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     6e-06     0.036     104     151 ..     213     261 ..      84     264 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-06
                                    SSSEEHHHHHHHHHHHHTT.BESXS.STTSTTSSSCTXTTTXSSXHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10 104 eqgvslflVaaHEiGHalG.LeHss.dkdalmyplykeekkvrlskdDvk 151
                                    + g   ++V  HE+GHa+G L+H   d++  ++p++ ++++++ s+dD +
  gi|121639093|ref|YP_979317.1| 213 DVGSYRQYVINHEVGHAIGyLRHEPcDQQGGLAPVM-MQQTFSTSNDDAA 261
                                    55667789***********99997535666788888.6789999999975 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.066     105     165 ..     168     249 ..     132     274 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                   Reprolysin_5 105 sggvGlAwl...gqlcnsgsagsvstrveks.............nsvvvstatevqvvaHElGHnfG.avHDcdsss... 164
                                      g G++++    ++c++ s+g+++ +  ++             +  v   ++  +v+ HE+GH++G  +H +++++   
  gi|121639093|ref|YP_979317.1| 168 VRG-GCGYEfrlETSCYNPSFGGMDRQSRVFinearwvrgavpfEGDVG--SYRQYVINHEVGHAIGyLRHEPCDQQggl 244
                                    444.555553334567888888888776666889888888776444444..77899***********789*999885555 PP

                   Reprolysin_5 165 ....e 165
                                         
  gi|121639093|ref|YP_979317.1| 245 apvmM 249
                                    55543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2089.60
//
Query:       gi|121639094|ref|YP_979318.1|  [L=228]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-17   63.1   0.0    3.7e-17   61.9   0.0    1.7  1  TetR_N       Bacterial regulatory proteins, tetR family
     0.0039   17.5   0.0      0.006   16.8   0.0    1.3  1  TetR_C_24    Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.019   15.1   0.0        0.2   11.8   0.0    2.2  2  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.026   15.3   0.1      0.064   14.0   0.1    1.7  1  TetR_C_33    Tetracyclin repressor-like, C-terminal domain
      0.031   14.2   0.0      0.067   13.1   0.0    1.7  1  TetR_C_14    MftR C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0     1e-20   3.7e-17       1      47 []      44      90 ..      44      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1e-20
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l +A  +f +rGy+a++++eIA+rAGvsk+ lY++F+sK eL++a+
  gi|121639094|ref|YP_979318.1| 44 LLVVASDVFVDRGYHAAGMDEIADRAGVSKPVLYQHFSSKLELYLAV 90
                                   6889****************************************997 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06     0.006       3     111 ..     111     217 ..     109     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                    SHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHH CS
                      TetR_C_24   3 spaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailg 82 
                                    + ++rL+ +v+a+ ++i ++ +  ++++++    +pe +   ++ r + e++++++ +   a+  +++++++++a  ++g
  gi|121639094|ref|YP_979318.1| 111 DNRQRLHVAVQAFFDFIEHDSQGYRLIFENDFVTEPEVA---AQVRVATESCIDAVFALISADSGLDPHRARMIAVGLVG 187
                                    6789**********************9988555555544...57788889999999999999999*************** PP

                                    HHHCHHH.C--TTSSS-HHHHHHHHHHHHH CS
                      TetR_C_24  83 mlnwvyr.WyrpdGplspeeiadqyadlll 111
                                    m  + +r W ++d p+s+ +  +  ++++ 
  gi|121639094|ref|YP_979318.1| 188 MSVDCARyWLDADKPISKSDAVEGTVQFAW 217
                                    *99988668888888888777777777665 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.5e-05       0.2      15      47 ..      48      80 ..      30     131 .. 0.75
   2 ?    1.0   0.0      0.12   4.4e+02      17      40 ..     135     156 ..     125     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWk 47
                                   a  + v++ y+   +deia+  gvs+  ly+  
  gi|121639094|ref|YP_979318.1| 48 ASDVFVDRGYHAAGMDEIADRAGVSKPVLYQHF 80
                                   4456789999********************975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                                    HHHHHHHH--S-HHHHHHHHTS-H CS
                    HTH_Tnp_1_2  17 ellvendyekltldeiaeevgvsr 40 
                                     l+ end+  +t  e+a++v v+ 
  gi|121639094|ref|YP_979318.1| 135 RLIFENDF--VTEPEVAAQVRVAT 156
                                    6889****..9********99975 PP

>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.8e-05     0.064       4      77 ..     119     187 ..     116     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHH-HHHHHHCCSS--TT-S-H...GHHCCCCHHHHHHHHHHHGGG---TH--CCHHHHHHHHHHHHHH CS
                      TetR_C_33   4 larayrrfAlahpaeYallfgspvpgyaap...delaaagarvlalllaalaalvaaglppadavaaaralwaalhG 77 
                                    + +a+ +f   + + Y+l+f++     ++p   ++++ a +  +++++a+++a   +gl+ +   ++ar++ + l G
  gi|121639094|ref|YP_979318.1| 119 AVQAFFDFIEHDSQGYRLIFENDFV--TEPevaAQVRVATESCIDAVFALISAD--SGLD-P---HRARMIAVGLVG 187
                                    679*****************44442..344222477777777777777777543..5663.3...455555555555 PP

>> TetR_C_14  MftR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.067      33      93 ..     143     201 ..     111     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                    HHSHHHHHHHHHHHHHHHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                      TetR_C_14  33 ltvPaLqAhstlryaawrevvAefvAeRtgtdaddlvprtvaaavlaaalaayeqwladed 93 
                                     t+P++ A+  ++++   ++v +++ + +g+d++  +  +v+  ++++++   ++wl++++
  gi|121639094|ref|YP_979318.1| 143 VTEPEVAAQVRVATESCIDAVFALISADSGLDPHRARMIAVG--LVGMSVDCARYWLDADK 201
                                    589****************************99876666665..55666666677888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1491.91
//
Query:       gi|121639095|ref|YP_979319.1|  [L=90]
Description: hypothetical protein BCG_3235c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  105.3   0.0    1.7e-30  105.1   0.0    1.1  1  DUF3107   Protein of unknown function (DUF3107)


Domain annotation for each model (and alignments):
>> DUF3107  Protein of unknown function (DUF3107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   9.4e-35   1.7e-30       1      73 []       1      73 [.       1      73 [. 0.99

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 9.4e-35
                        DUF3107  1 meikIGvqdsaRelvieseqsadeveaaveealagdegvltLeDekGrrvlvpaakiaYVeiGseekrrVGFg 73
                                   me+kIG++ds+Relv++s+q++ eve+ v++al++d+g+ltL+De+Grr+l+++a+iaYVeiG +++rrVGFg
  gi|121639095|ref|YP_979319.1|  1 MEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRVGFG 73
                                   9***********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 688.53
//
Query:       gi|121639096|ref|YP_979320.1|  [L=186]
Description: hypothetical protein BCG_3236 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-05   24.8   0.4    2.6e-05   24.2   0.4    1.3  1  Mycobact_memb  Mycobacterium membrane protein


Domain annotation for each model (and alignments):
>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.4   1.5e-09   2.6e-05      42     118 ..      91     169 ..      78     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-09
                                    XXXXXXXXXEEB-B----TT..-----B---TTS------S-SS--B--EE-SSS------B--SS-S------BBTTB CS
                  Mycobact_memb  42 edskpfnPkkvkyevfGpag..tvadisyldadaepqridgaalPWsltikttlaavvgnvvaqgnsdsigCriivdgv 118
                                     +  p+nP++v+y v G+ +   ++++ y da + p    +++lPW+  ++ +    +  vva +  + + C i+  g+
  gi|121639096|ref|YP_979320.1|  91 PPPAPLNPRTVVYRVTGTKQlfDLVNVVYTDARGFPVTDFNVSLPWTKMVVLNPGVQTESVVATSLYSRLNCSIVNTGA 169
                                    56789************98733468999****99999999*******9999988888899************9986664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1379.36
//
Query:       gi|121639097|ref|YP_979321.1|  [L=231]
Description: hypothetical protein BCG_3237c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-59  198.8   5.4    8.2e-59  198.4   5.4    1.1  1  MiaE_2      tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
    0.00049   19.8   0.1    0.00065   19.4   0.1    1.2  1  MiaE        tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
     0.0036   17.7   0.4      0.091   13.2   0.0    2.2  2  DUF3486     Protein of unknown function (DUF3486)
  ------ inclusion threshold ------
       0.07   13.3   0.2       0.35   11.1   0.0    1.8  2  Ferritin_2  Ferritin-like domain


Domain annotation for each model (and alignments):
>> MiaE_2  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   5.4   1.8e-62   8.2e-59       6     184 ..      24     202 ..      20     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 1.8e-62
                                    HHHHHHHHHHHHHHHHHHHHHHHHCC-SSSTTHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHGGGHHHHHHHHHTT- CS
                         MiaE_2   6 avvdllgalayGelsaferlaedarlaPtladraalaklaaaefrhyelledrlaeiGveaeeamePfvaavddfhkrta 85 
                                    +v +l++ layGe++af rl+++ar+aP l +r  +a++aaae++hyell++ l+ +Gv++  am  + +a++++h+ t+
  gi|121639097|ref|YP_979321.1|  24 GVNELFALLAYGEVAAFYRLTDEARMAPDLRGRISMASMAAAEMGHYELLRNALERRGVDVVSAMSKYTSALENYHRLTT 103
                                    6899**************************************************************************** PP

                                    -SSHHHHHHHHHHHHHHHHHHHHHHCCCS-HHHHHHHHHHS--HHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHH CS
                         MiaE_2  86 PadwleslvkayvgdsvaadfyrevaeyldadtrelvlavlddtghaevaeekvraaladdprladrlalwgrrllGeal 165
                                    P+ wle+lvk+yv+d++aad+y e+a+ l  +  ++v a l +tgh+++++ +vraa+ +  + ++rlalw+rrllGea+
  gi|121639097|ref|YP_979321.1| 104 PSTWLEALVKTYVADALAADLYLEIADGLPDEVADVVRAALSETGHSQFVVAEVRAAVTASGKQRSRLALWSRRLLGEAI 183
                                    ******************************************************************************** PP

                                    HHHHHHHHHT--HHHH-XX CS
                         MiaE_2 166 tqaqrvvaerdalaelivg 184
                                    tqaq v a++d l +l+v 
  gi|121639097|ref|YP_979321.1| 184 TQAQLVLADHDELVDLVVS 202
                                    ****************986 PP

>> MiaE  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.5e-07   0.00065     106     190 ..      59     142 ..      36     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-07
                           MiaE 106 lvrlikeelehfeqvlelleaRnielakisasrYakglkaavrthepqrllDkLivgayieaRsceRlakLapyldeela 185
                                    +  ++  e+ h+e+ ++ le+R +++++   s+Y+++l++  r   p + l+ L+ +   +a + + +  +a  l +e+a
  gi|121639097|ref|YP_979321.1|  59 MASMAAAEMGHYELLRNALERRGVDVVSA-MSKYTSALENYHRLTTPSTWLEALVKTYVADALAADLYLEIADGLPDEVA 137
                                    889999*******************9985.69**********************99999999999999999988888888 PP

                           MiaE 186 kfyvs 190
                                        +
  gi|121639097|ref|YP_979321.1| 138 DVVRA 142
                                    76555 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.033   1.5e+02      25      65 ..      65     100 ..      46     124 .. 0.63
   2 !   13.2   0.0     2e-05     0.091       8      53 ..     130     173 ..     126     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                        DUF3486  25 kgftqdeIyeelnallaerGeykiSkSalnryaqrleevae 65 
                                     ++     ye l+++l+ rG+  +  Sa+ +y + le++ +
  gi|121639097|ref|YP_979321.1|  65 AEMGH---YELLRNALERRGVDVV--SAMSKYTSALENYHR 100
                                    44445...7888888888884444..578888887777643 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
                        DUF3486   8 dlLPeevreeLdeaLrekgftqdeIyeelnallaerGeykiSkSal 53 
                                    d LP+ev + + +aL e+g++q  +++e++a++ + G  + S+ al
  gi|121639097|ref|YP_979321.1| 130 DGLPDEVADVVRAALSETGHSQ-FVVAEVRAAVTASG-KQRSRLAL 173
                                    78*******************8.**************.88888666 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.8e-05      0.35      19      93 ..      33     109 ..      26     120 .. 0.68
   2 ?    0.1   0.1      0.19   8.5e+02      12      59 ..     117     155 ..     108     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.8e-05
                     Ferritin_2  19 fYtaalegaslddkalldaev..revaeeiakheeaHveflkaale..Gaaav.akptfdfafdpfadeksflalaavlE 93 
                                    +Y ++++ ++l+d+a + ++   r  + ++a+ e +H+e+l++ale  G   v a+ +++    +++++  + + + +lE
  gi|121639097|ref|YP_979321.1|  33 AYGEVAAFYRLTDEARMAPDLrgRISMASMAAAEMGHYELLRNALErrGVDVVsAMSKYTS---ALENYHRLTTPSTWLE 109
                                    666666666666667777776234456899***************9988887756666666...5555555555555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                     Ferritin_2  12 lEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflka 59 
                                    +  l+a+ Y + ++g         ++ev +v++  a  e++H +f  a
  gi|121639097|ref|YP_979321.1| 117 ADALAADLYLEIADGL--------PDEVADVVRA-ALSETGHSQFVVA 155
                                    4566677777776644........4444443332.2234444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1634.93
//
Query:       gi|121639098|ref|YP_979322.1|  [L=527]
Description: ATP-dependent RNA helicase rhlE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-51  172.9   0.0    1.2e-49  168.5   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    4.6e-29  101.0   0.1    8.3e-29  100.2   0.1    1.4  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.037   14.0   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
      0.084   12.2   0.0       0.23   10.8   0.0    1.7  1  CMS1        U3-containing 90S pre-ribosomal complex subunit
       0.11   11.2   0.0        5.3    5.7   0.0    2.1  2  UTP25       Utp25, U3 small nucleolar RNA-associated SSU proc
       0.12   13.4   0.7        0.6   11.1   0.1    2.4  2  LytR_C      LytR cell envelope-related transcriptional attenu


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0   3.9e-53   1.2e-49       2     172 ..      35     216 ..      34     220 .. 0.95
   2 ?    2.3   0.0     0.042   1.3e+02      44     105 ..     267     328 ..     248     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 3.9e-53
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                    +iQ+ ++pl+l+g+dv+++a+TG+GKT af +p+lq++++       + +p+al+v+PtreL+ q+ ++l + +ky++  
  gi|121639098|ref|YP_979322.1|  35 AIQELTLPLALDGEDVIGQARTGMGKTFAFGVPLLQRITSGdgtrPLTGAPRALVVVPTRELCLQVTDDLATAGKYLTag 114
                                    79************************************988998889999*************************96668 PP

                                    ............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHH CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfin 143
                                                l+v++i+gg +++ q+++l++g+d+vvgtpgrl+dl+++g+l+l  +++lVlDEad++ld gf ++i+
  gi|121639098|ref|YP_979322.1| 115 pdtddaaavrrrLSVVSIYGGRPYEPQIEALRAGADVVVGTPGRLLDLCQQGHLQLGGLSVLVLDEADEMLDLGFLPDIE 194
                                    99999*****99******************************************************************** PP

                                    HHHHHSHHHCTTSTTTSEEEEEESSBSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 144 rilnqlpqitcdgklqrqvivlSATlpkd 172
                                    ril+q+       +++rq +++SAT+p+ 
  gi|121639098|ref|YP_979322.1| 195 RILRQI-------PADRQSMLFSATMPDP 216
                                    ******.......67899********965 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.042
                                    TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                           DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtp 105
                                     +++  ++i + t+  a++++++l++++  ++  v+  +g+ a+++ l++++ g +d++v+t 
  gi|121639098|ref|YP_979322.1| 267 ARDRGATMIFTRTKRTAQKVADELTERGFAVG-AVHGDLGQLAREKALKAFRTGgIDVLVATD 328
                                    55566788899999999*********999888.7888899***********8667*****995 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.1   2.8e-32   8.3e-29       2     111 .]     257     365 ..     256     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 2.8e-32
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                    k+e + + l + +++g ++if++t+++++k ++ l +++g+ v ++hg+l q  re++l++f+ g +dvL+atdva+rGi
  gi|121639098|ref|YP_979322.1| 257 KVELVSRVL-QARDRGATMIFTRTKRTAQKvADEL-TERGFAVGAVHGDLGQLAREKALKAFRTGGIDVLVATDVAARGI 334
                                    777778888.8999************999865555.4668**************************************** PP

                                    TSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                    di++v++Vin+++p++ + y++riGRtgRag
  gi|121639098|ref|YP_979322.1| 335 DIDDVTHVINYQCPEDEKMYVHRIGRTGRAG 365
                                    *****************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.037      30      76 ..      53     106 ..      33     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                    EESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGG CS
                         ResIII  30 kmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkk 76 
                                    ++ TG+GKT+   + l +r+++  + +      ++l++vp+++l+ q  ++++ 
  gi|121639098|ref|YP_979322.1|  53 QARTGMGKTFAFgVPLLQRITSGDGTRpltgapRALVVVPTRELCLQVTDDLAT 106
                                    778*********7778888877666669********************998744 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.7e-05      0.23     179     209 ..     150     180 ..     139     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
                           CMS1 179 giavGtpgRildLleeeslsvdeLkrivlDa 209
                                     + vGtpgR+ldL +++ l++  L  +vlD 
  gi|121639098|ref|YP_979322.1| 150 DVVVGTPGRLLDLCQQGHLQLGGLSVLVLDE 180
                                    5789*************************96 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0    0.0096        29      76      97 ..      85     106 ..      81     112 .. 0.89
   2 ?    5.7   0.0    0.0018       5.3     326     417 ..     266     355 ..     212     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0096
                          UTP25  76 pkvLillptreaalevvelllk 97 
                                    p+ L+++ptre +l+v + l +
  gi|121639098|ref|YP_979322.1|  85 PRALVVVPTRELCLQVTDDLAT 106
                                    899*************998865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0018
                          UTP25 326 ssskssgiliyipsyfdfvrvrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkvi 405
                                    ++ +++ ++i+  +     +v + l e+ +  +a++    +   ++a ++F +g   vl+ t+ +   r  +i +v +vi
  gi|121639098|ref|YP_979322.1| 266 QARDRGATMIFTRTKRTAQKVADELTERGFAVGAVHGDLGQLAREKALKAFRTGGIDVLVATDVAA--RGIDIDDVTHVI 343
                                    467788889998888888999999999999999999999999999999**************9885..99********** PP

                          UTP25 406 lYklPenpefys 417
                                     Y+ Pe  ++y 
  gi|121639098|ref|YP_979322.1| 344 NYQCPEDEKMYV 355
                                    ********9996 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5   4.6e+03      18      43 ..      99     128 ..      93     155 .. 0.48
   2 ?   11.1   0.1    0.0002       0.6      11      34 ..     278     301 ..     277     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                         LytR_C  18 rvadaLeerG.f.tvgevgnagnadee....t 43 
                                    +v+d L+++G + t+g +++ ++a       +
  gi|121639098|ref|YP_979322.1|  99 QVTDDLATAGkYlTAGPDTDDAAA--VrrrlS 128
                                    566666666644333332221111..123442 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                         LytR_C  11 gvsGlAarvadaLeerGftvgevg 34 
                                     ++  A++vad+L+erGf+vg+v 
  gi|121639098|ref|YP_979322.1| 278 RTKRTAQKVADELTERGFAVGAVH 301
                                    67788***************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3715.91
//
Query:       gi|121639099|ref|YP_979323.1|  [L=407]
Description: hypothetical protein BCG_3239 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   21.9  12.3    0.00021   21.0   2.5    2.6  2  PQQ_2     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.5   1.2e-08   0.00021      14      98 ..      61     142 ..      20     175 .. 0.84
   2 !    4.8   3.9     0.001        18      25     175 ..     254     401 ..     160     407 .] 0.60

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-08
                          PQQ_2  14 aelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdg...qlia 90 
                                    ++lW+        + v  +v+ ggt++++ +g+++ + d+atG+ lW+++ +  ++g   v    v v   d+   q+++
  gi|121639099|ref|YP_979323.1|  61 KQLWTAAS---PATRV--PVVVGGTVATG-DGRQVDGRDPATGESLWSYARDTDLCGVTWVYHYAVAVYRYDRgcgQVST 134
                                    67888855...67788..999*******7.****************************988888888888777789**** PP

                          PQQ_2  91 ldaedGkr 98 
                                    +d  +G+r
  gi|121639099|ref|YP_979323.1| 135 IDGSTGRR 142
                                    ******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.001
                          PQQ_2  25 lgggvsravlsggtlfva.....tgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva..sdgqlialdaedGk 97 
                                    +g+ v   v+s++  +v      +  +r+  +d +tG+ + +t l +p  ++  va     +v+   +++l+ +da + +
  gi|121639099|ref|YP_979323.1| 254 SGARV--LVVSQNNTAVYlparsGAQPRVDVID-ETGATVSSTLLAKPPSTS-AVASRTGNLVTwwTGDALLVFDAGNLT 329
                                    33333..55566666666666666777777787.888888888887775555.5555555666666888999******** PP

                          PQQ_2  98 rlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvva.egt 175
                                    + ++++  +  +a++++   +a   ++++v+   g++ ++dp +G      ++++p+ ts++  +  +sg+ v++ +g+
  gi|121639099|ref|YP_979323.1| 330 QRYTIAAGE-TTAPVGPGVMMA---GQLLVPV-TGGIGVYDPVSGANNRYIPVTRPPSTSAV--IPAVSGSRVIEqRGD 401
                                    ****55555.777755554444...5566666.699999*******9999999999999976..888888888884333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2798.99
//
Query:       gi|121639100|ref|YP_979324.1|  [L=266]
Description: soj/parA-related protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-54  185.0   0.0    2.8e-54  183.7   0.0    1.6  2  AAA_31       AAA domain
    9.6e-26   90.3   0.0      2e-25   89.3   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.1e-12   46.1   0.0    5.7e-12   45.6   0.0    1.2  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    7.5e-10   38.5   0.2    0.00053   19.3   0.1    2.3  2  MipZ         ATPase MipZ
    1.7e-09   37.3   0.0    4.6e-09   35.9   0.0    1.7  1  ArsA_ATPase  Anion-transporting ATPase
    1.4e-08   34.5   0.2    3.8e-08   33.1   0.2    1.8  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.9e-07   30.8   0.0    1.8e-06   27.6   0.0    2.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0013   18.6   0.0     0.0021   17.9   0.0    1.3  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0039   16.5   0.1     0.0074   15.6   0.1    1.4  1  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.027   14.1   0.1       0.12   12.0   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain
      0.039   12.9   0.1      0.067   12.2   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.054   13.3   0.0       0.15   11.9   0.0    1.6  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.0   1.9e-57   2.8e-54       1     176 [.       4     178 ..       4     179 .. 0.98
   2 ?   -1.9   0.0       1.8   2.7e+03     103     123 ..     190     210 ..     183     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 1.9e-57
                         AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkven 80 
                                    ++v+a+anqKGGv+KTTt+  l+aa+ ++g +vLlvDlDpQ+ +t++lg + +++  +++evl+ e++ + +++ t++e 
  gi|121639100|ref|YP_979324.1|   4 TRVLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVHEVLLGEVEPNAVLV-TTMEG 82 
                                    589**********************************************************************9.7789* PP

                         AAA_31  81 ldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleql 160
                                    ++l+p++idLa+ae  l+    +e++lk++l k++d++D++iiDcpPsLg+lt n+L+a+d+ i+p+q+e +a +G+ q+
  gi|121639100|ref|YP_979324.1|  83 MTLLPANIDLAGAEAMLLMRAGREYALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQCEMLAHRGVGQF 162
                                    ******************************************************************************** PP

                         AAA_31 161 lktieevkkklnpkle 176
                                    l+t+ +v++ +np+l+
  gi|121639100|ref|YP_979324.1| 163 LRTVADVQQITNPNLR 178
                                    *************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                         AAA_31 103 keeilkellekvkdeYDyiii 123
                                    ++++ +++l +v d+YD+ ++
  gi|121639100|ref|YP_979324.1| 190 RTTHTRDVLLDVADRYDLQVL 210
                                    44556899999******8665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   1.4e-28     2e-25       1     128 []       7     230 ..       7     230 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.4e-28
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    +a+a++kGGv KTt++a+L++a+ ++g+rVllvD+Dpq+ +++   g  +d+ p                          
  gi|121639100|ref|YP_979324.1|   7 LAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTF-SLGQDPDKLPvsvhevllgevepnavlvttmegmtl 85 
                                    69****************************************9.888888888899999********************* PP

                                    ........................................................................CCHCCCHH CS
                                    ........................................................................xxxxxxxx RF
                           CbiA  55 ........................................................................dlkrllel 62 
                                                                                                            ++ ++l++
  gi|121639100|ref|YP_979324.1|  86 lpanidlagaeamllmragreyalkralakfsdrfdvviidcppslgvltlngltaadeaivplqcemlahrGVGQFLRT 165
                                    ******************************************************************************** PP

                                    HHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                           CbiA  63 lealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlg.viprdeavaeapargepv 128
                                    ++++++ ++++l+++g +++ +d++  +t+ ++ l ++  ry ++vl+  ipr++++aea a+g +v
  gi|121639100|ref|YP_979324.1| 166 VADVQQITNPNLRLLGALPTLYDSR--TTHTRDVLLDVADRYDLQVLApPIPRTVRFAEASASGSSV 230
                                    *************************..9***********************************9875 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   3.8e-15   5.7e-12       3     153 ..       6     157 ..       4     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.8e-15
                       CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqr.egwaraeldgapwrqaaleyapgldl 81 
                                    vla+   +GGv +t+ +a+L+ a+ e g +vl++Dl p+  L+++  +d ++   +  + +l + + ++  +  ++g++l
  gi|121639100|ref|YP_979324.1|   6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLpVSVHEVLLGEVEPNAVLVTTMEGMTL 85 
                                    67888889***************************************99887615667788888999999999******* PP

                       CBP_BcsQ  82 lPfG.elnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchv 153
                                    lP    l+ +e++ l   a ++ al++al++++ +++ +++D+p     lt + l+ ad  +  ++ ++ +h 
  gi|121639100|ref|YP_979324.1|  86 LPANiDLAGAEAM-LLMRAGREYALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQCEMLAHR 157
                                    **75234444444.44567778899*************************************99999998885 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   3.6e-07   0.00053       2      39 ..       6      43 ..       5      49 .. 0.93
   2 !   17.1   0.0   1.7e-06    0.0026      84     131 ..     106     151 ..      72     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.6e-07
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                           MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                   v+ ++n+kGG  k+tt   +  a+++kG rv  +dld 
  gi|121639100|ref|YP_979324.1|  6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDP 43
                                   6789********************************95 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.7e-06
                                    HHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEES CS
                           MipZ  84 aevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlnd 131
                                    +   +l++++a+++ ++d+++id+P s   l+  + + ad  + Pl  
  gi|121639100|ref|YP_979324.1| 106 E--YALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQC 151
                                    3..4899**************************************975 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   3.1e-12   4.6e-09       8     141 ..      12     136 ..       4     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.1e-12
                                    ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH.HHHHHHHCCHHGGGSC CS
                    ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe.veleeakqevqkeeea 86 
                                     KGGV Ktt  a++++ + ekg++vll+ +DP   l  s+ q+  k p  v+e L   E++p+ v +  ++   ++   a
  gi|121639100|ref|YP_979324.1|  12 QKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVHEVLL-GEVEPNaVLVTTME--GMTLLPA 88 
                                    59**************************************************9886.69**9933333333..4444444 PP

                                    CHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGG CS
                    ArsA_ATPase  87 llgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrl 141
                                     + l + e +l + +       e +   +l k+  ++ +dvv++D +P    l l
  gi|121639100|ref|YP_979324.1|  89 NIDLAGAEAMLLMRAGR-----EYALKRALAKF--SDRFDVVIIDCPPSLGVLTL 136
                                    45555677777666666.....66555666666..568********997555544 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   2.5e-11   3.8e-08       4     243 ..       5     247 ..       3     250 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.5e-11
                           ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs....ekkliPvea.....kgik 74 
                                    +v+av+  KGGV K+t+ ++l +a+ +kg +v l+D+D  G    +l +  ++ p +       ++ P  +     +g++
  gi|121639100|ref|YP_979324.1|   5 RVLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVhevlLGEVEPNAVlvttmEGMT 84 
                                    799**************************************866665554443332221112112334333333358888 PP

                           ParA  75 vmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                    ++  ++ l   ++ +++r+   + a+k+ l++ + +  D++iiD+PP  g   lt+      ++a++    + +a   v 
  gi|121639100|ref|YP_979324.1|  85 LLPANIDLAGAEAMLLMRAG-REYALKRALAKFS-DRFDVVIIDCPPSLG--VLTLNGLTAADEAIVPLQCEMLAHRGVG 160
                                    88888888866666666665.5667777777655.78**********999..5777777777888887777777777665 PP

                           ParA 155 kaiem...fkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllg.eipldpeireasdegkplvlkep 230
                                    + ++    ++++  + l ++  + ++  ++++++     ++   ++a+++++++l+  ip + +++eas +g+++++ + 
  gi|121639100|ref|YP_979324.1| 161 QFLRTvadVQQITNPNLRLLGALPTLYDSRTTHT-----RDVLLDVADRYDLQVLApPIPRTVRFAEASASGSSVMAGR- 234
                                    4444300044444455555555555554444444.....4444677788888777734777777788888877665554. PP

                           ParA 231 eseaakaleeiae 243
                                    +++ a a++e+a+
  gi|121639100|ref|YP_979324.1| 235 KNKGAVAYRELAQ 247
                                    4555666666666 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.2e-09   1.8e-06       7     255 ..      12     260 ..       6     266 .] 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                      Fer4_NifH   7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvkcves 86 
                                     kGG+ k+tt++ l aa++e+g++vl+v  DP+   t + lg       l +  ++ +  +v+ + v+ + ++g++ + +
  gi|121639100|ref|YP_979324.1|  12 QKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLT-FSLGQDPD--KLPVSVHEVLLGEVEPNAVLVTTMEGMTLLPA 88 
                                    59******************************99888.66665544..5666667777799*************998766 PP

                      Fer4_NifH  87 GGPepGvGCaG.rgvitaielleelgaydd.lDfvlyDv...LGDvvCGGfalPiredkaqevyivtsgelmalyaanni 161
                                        +G+        ++   l   l  ++d +D+v+ D    LG     G+        a+e ++  ++e+ a     + 
  gi|121639100|ref|YP_979324.1|  89 NIDLAGAEAMLlMRAGREYALKRALAKFSDrFDVVIIDCppsLGVLTLNGL------TAADEAIVPLQCEMLAHRGVGQF 162
                                    6655555443212334456677788899988*******7444555555554......479999************99999 PP

                      Fer4_NifH 162 akgiekyaksgg..vrlgGl...iinsrkvddereliekfaeelgtkvle.vvPrdeivrkaelrkktvieyapeseqak 235
                                     +++   ++  +  +rl G    +++sr +++ r+++ + a++ +++vl+  +Pr+    +a++    v+   +++  a 
  gi|121639100|ref|YP_979324.1| 163 LRTVADVQQITNpnLRLLGAlptLYDSR-TTHTRDVLLDVADRYDLQVLApPIPRTVRFAEASASGSSVMAGRKNKG-AV 240
                                    9999988876654599988623357777.99999**************98358888888888888888877666655.99 PP

                      Fer4_NifH 236 eyrelarkilenkklviPkp 255
                                     yrela+++l++ k+ +P p
  gi|121639100|ref|YP_979324.1| 241 AYRELAQALLKHWKTGRPLP 260
                                    9*******999888877766 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0021       6      99 ..      15     128 ..      13     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                     ATP_bind_1   6 GsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirel.itledvmedlglgpngalvvale........... 73 
                                    G+ Ktt v +l   + ++gr+v +v LDP    l+++   d  +l +++ +v    +++pn  lv+ +e           
  gi|121639100|ref|YP_979324.1|  15 GVAKTTTVASLGAAMVEKGRRVLLVDLDPQGC-LTFSLGQDPDKLpVSVHEVLLG-EVEPNAVLVTTMEgmtllpanidl 92 
                                    888**************************654.6667766666644999999988.9*********************** PP

                     ATP_bind_1  74 ..........flresldwldeelekeed..dyllfDtP 99 
                                               +re    l+++l k +d  d +++D+P
  gi|121639100|ref|YP_979324.1|  93 agaeamllmrAGREYA--LKRALAKFSDrfDVVIIDCP 128
                                    *****99877333333..566666663336*******9 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.9e-06    0.0074       3      41 ..       6      44 ..       4      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                          VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                   +++++  kGG  ktt++ +l +a++ +g+rv l + d  
  gi|121639100|ref|YP_979324.1|  6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQ 44
                                   6788999**************************998865 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.8e-05      0.12      11      38 ..      15      42 ..       6      45 .. 0.93
   2 ?   -1.2   0.0       0.9   1.3e+03      73      90 ..     110     126 ..     102     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-05
                                   TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                   G+ KTtt+a L a + ++g++vllv +D
  gi|121639100|ref|YP_979324.1| 15 GVAKTTTVASLGAAMVEKGRRVLLVDLD 42
                                   899*********************9888 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.9
                                    HHHHHHHHHTTSSEEEEE CS
                          SRP54  73 keavekakeekidvvlvD 90 
                                    k+a+ k+ + ++dvv++D
  gi|121639100|ref|YP_979324.1| 110 KRALAKFSD-RFDVVIID 126
                                    556666665.78*****9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.5e-05     0.067      38      69 ..      14      45 ..       3      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                                   TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB 38 PGaGkstlvealglelrrrGkrvavlavDPss 69
                                    G+ k t+v  lg+ ++++G+rv ++ +DP  
  gi|121639100|ref|YP_979324.1| 14 GGVAKTTTVASLGAAMVEKGRRVLLVDLDPQG 45
                                   599***************************75 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.9e-05      0.15       5      32 ..      16      43 ..      13      49 .. 0.92
   2 ?   -2.2   0.0         2   2.9e+03     118     149 ..      82     113 ..      76     154 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                         CLP1_P  5 sGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                   + K+T ++ L   +++kgr++++vDlD+
  gi|121639100|ref|YP_979324.1| 16 VAKTTTVASLGAAMVEKGRRVLLVDLDP 43
                                   569************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                         CLP1_P 118 gaellleliealepdvvvvldqeellnelkrd 149
                                    g++ll + i++  ++++++++  ++++  +  
  gi|121639100|ref|YP_979324.1|  82 GMTLLPANIDLAGAEAMLLMRAGREYALKRAL 113
                                    66666666777777777777765554433322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1833.57
//
Query:       gi|121639101|ref|YP_979325.1|  [L=203]
Description: acid phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-44  152.6   0.2    1.1e-44  152.4   0.2    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.033   13.5   0.0      0.058   12.7   0.0    1.4  1  Reo_sigma1  Reovirus viral attachment protein sigma 1


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.2   1.3e-48   1.1e-44       1     191 [.       8     191 ..       8     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.3e-48
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EE..EE-SSHHHHHHHHHHHHCTT--EEE-GGGS CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidai..ysSplkRarqTaeliaealglpveldegLr 78 
                                    l+L+RHGet+w++ gr  g t v+Lt++Gr+qAe +++ l + ++d    ++Sp +R+ +Ta+l++ + +   e++  L 
  gi|121639101|ref|YP_979325.1|   8 LLLLRHGETAWSTLGRHTGGTEVELTDTGRTQAELAGQLLGELELDDPivICSPRRRTLDTAKLAGLTVN---EVTGLLA 84 
                                    68****************************************88887778************99886333...677779* PP

                                    ----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHH CS
                     His_Phos_1  79 EidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarl 158
                                    E+d+G +egltt +i+e+ p++l +++  pa      gEs+++v +R+++a+  ++++ ++++vl VsHg++ ra+++r+
  gi|121639101|ref|YP_979325.1|  85 EWDYGSYEGLTTPQIRESEPDWLVWTHGCPA------GESVAQVNDRADSAVALALEHMSSRDVLFVSHGHFSRAVITRW 158
                                    *****************************99......******************************************* PP

                                    HT--GGGGGGB---TT-EEEEEE-SS-EEEEEE CS
                     His_Phos_1 159 lglpleelrrleldnaslsvlefdeggwrlvrl 191
                                    ++lpl+e  r+++++as+ +  f++g  +l  l
  gi|121639101|ref|YP_979325.1| 159 VQLPLAEGSRFAMPTASIGICGFEHGVRQLAVL 191
                                    *************************99888766 PP

>> Reo_sigma1  Reovirus viral attachment protein sigma 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.5e-06     0.058     109     154 ..      50      95 ..      37     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
                                    EEETTEEEEEE--EEEE---SCEEEEEETTSTB-TT--GGGG-BTT CS
                     Reo_sigma1 109 lkvddylvlslsafdtssiladGklvlnfvtGlspglltGdtePss 154
                                    l +dd +v++ ++  t   ++   l++n vtGl++ +  G+ e  +
  gi|121639101|ref|YP_979325.1|  50 LELDDPIVICSPRRRTLDTAKLAGLTVNEVTGLLAEWDYGSYEGLT 95 
                                    578*************************************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1392.36
//
Query:       gi|121639102|ref|YP_979326.1|  [L=372]
Description: isochorismate synthase entC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-70  235.2   0.0    1.1e-69  234.9   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.9   0.0     6e-74   1.1e-69       3     258 .]      97     360 ..      95     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 6e-74
                                    CHHHHHHHHHHHHHH..TTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETT.......EEEEEEESSE CS
                Chorismate_bind   3 edYaeavekvkeeir..agdlykvvlsrrlkaeleaavdplalyralrarnpapysflleled.......sellgaSPEl 73 
                                    +dY +++ ++++ ++  +g l+kvvl+r+++++++a++d+  l+r+l  + p++y +l++l +         l+gaSPEl
  gi|121639102|ref|YP_979326.1|  97 ADYLTRIGRARDLLAafDGPLHKVVLARAVQLTADAPLDARVLLRRLVVADPTAYGYLVDLTSagnddtgAALVGASPEL 176
                                    57899999999988622577***************************************66556667777889******* PP

                                    EEEEETTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEE CS
                Chorismate_bind  74 llkveggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevl 153
                                    l+ ++g+ r+ ++p aG+++r ++p+ d+a++++l++++K+r+Eh+++vd +r  L+++  ++ +++p  ++++r+++v+
  gi|121639102|ref|YP_979326.1| 177 LVARSGN-RVMCKPFAGSAPRAADPKLDAANAAALASSAKNRHEHQLVVDTMRVALEPL--CEDLTIPAQPQLNRTAAVW 253
                                    *****77.***************************************************..7****************** PP

                                    EEEEEEEEEESTT.--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEE..E CS
                Chorismate_bind 154 hlvstiegelked.vslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavv..k 230
                                    hl++ i+g+l++  ++++dl  al+Pt+av+G+P k+a e+i+elE  +Rg+YaGavg++d  g++ ++v IR+a++  +
  gi|121639102|ref|YP_979326.1| 254 HLCTAITGRLRNIsTTAIDLALALHPTPAVGGVPTKAATELIAELEG-DRGFYAGAVGWCDGRGDGHWVVSIRCAQLsaD 332
                                    **********9877999*****************************7.*****************************744 PP

                                    TTEEEEEEEEEEETT--HHHHHHHHHHH CS
                Chorismate_bind 231 dkelrlgaGaGIvadSdpeaEyeEtlaK 258
                                    ++ + + aG+GIva+Sdp++E+eEt++K
  gi|121639102|ref|YP_979326.1| 333 RRAALAHAGGGIVAESDPDDELEETTTK 360
                                    4778899******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2394.60
//
Query:       gi|121639103|ref|YP_979327.1|  [L=110]
Description: acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.8   0.0    1.3e-10   41.5   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      6e-08   32.6   0.0    6.9e-08   32.4   0.0    1.2  1  FR47             FR47-like protein
    8.9e-06   25.7   0.0      1e-05   25.5   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.2e-05   24.3   0.0    4.2e-05   23.9   0.0    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0065   16.1   0.0     0.0065   16.1   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.018   15.0   0.0    1.3  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
      0.035   13.8   0.0      0.042   13.5   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.079   12.4   0.0      0.087   12.3   0.0    1.1  1  Acetyltransf_15  Putative acetyl-transferase
        0.1   12.7   0.0       0.11   12.5   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   6.6e-14   1.3e-10      37     116 ..       5      86 ..       2      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 6.6e-14
                                    EEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                 Acetyltransf_1  37 vaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                    vae +g +++++  + +         +y+e+l+V p +r++Gl++ Ll +l++++ ++ ++++ + v ++n  ai+lY +
  gi|121639103|ref|YP_979327.1|   5 VAEVNGGVAAMALWFLNFStwDGVAGIYVEDLFVWPRFRRRGLARGLLSTLARECVDNRYTRLAWSVLNWNSDAIALYDR 84 
                                    677778788888666666677677899***************************************************98 PP

                                    TT CS
                 Acetyltransf_1 115 lG 116
                                     G
  gi|121639103|ref|YP_979327.1|  85 IG 86 
                                    77 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   3.4e-11   6.9e-08      27      80 ..      36      90 ..       8      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.4e-11
                                   EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT.-HHHHHHHHHHT-EEE CS
                           FR47 27 lqvlpehrrrGlgsrlvkalakeiaergktvllvvvas.NtpsirlyeklGfeki 80
                                   l v p +rrrGl++ l + la+e + + +t l++ v + N+ +i+ly ++G++  
  gi|121639103|ref|YP_979327.1| 36 LFVWPRFRRRGLARGLLSTLARECVDNRYTRLAWSVLNwNSDAIALYDRIGGQPQ 90
                                   7789*****************************988766************9976 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     5e-09     1e-05      53     105 ..      32      86 ..       3      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5e-09
                Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklG 105
                                    +++ lfV p +r++G+++ Ll ++ +e+ ++++   + +v   +  a+++Y ++G
  gi|121639103|ref|YP_979327.1|  32 YVEDLFVWPRFRRRGLARGLLSTLARECVDNRYTRlAWSVLNWNsDAIALYDRIG 86 
                                    899************************999999888666655444********99 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.1e-08   4.2e-05       7      73 ..       5      86 ..       2      86 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                                   EEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH..TTSEEE.....EE.EEEETHH.HHHHHHH CS
                 Acetyltransf_7  7 VaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea..aekgii.....le.qlelnae.kaikfYe 70
                                   Vae +g++  + al+ l+          + + l+V p +r++G++r Ll    +   +          + ln +  ai++Y 
  gi|121639103|ref|YP_979327.1|  5 VAEVNGGVAAM-ALWFLNfstwdgvagIYVEDLFVWPRFRRRGLARGLLSTlaR--ECVdnrytRLaWSVLNWNsDAIALYD 83
                                   77777666532.22222245555443334444*****************95332..333222221222233333489****9 PP

                                   HTT CS
                 Acetyltransf_7 71 klG 73
                                   + G
  gi|121639103|ref|YP_979327.1| 84 RIG 86
                                   987 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.3e-06    0.0065     190     243 .]      40      96 ..       2      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                GNAT_acetyltran 190 edyrrkgLAtivaaalileclkrglyP.sWDaa..neaSvaLaekLGYefekeYkvy 243
                                    + +rr+gLA+ + + l +ec+++ ++   W     n  ++aL+ ++G + ++e+++y
  gi|121639103|ref|YP_979327.1|  40 PRFRRRGLARGLLSTLARECVDNRYTRlAWSVLnwNSDAIALYDRIGGQPQHEWTIY 96 
                                    889*******************998753799988889999999***********998 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   9.2e-06     0.018       7      35 ..      33      61 ..      28      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.2e-06
                Acetyltransf_13  7 isriWvssshRrkgiAtkLldaarenfiy 35
                                   ++ ++v + +Rr+g+A+ Ll +++++++ 
  gi|121639103|ref|YP_979327.1| 33 VEDLFVWPRFRRRGLARGLLSTLARECVD 61
                                   7889******************9998875 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.042      89     144 ..      40      94 ..      26      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                    HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEEE CS
                 Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekevd 144
                                    +++r++gl++ ll++l++ ++++ r +r        N  ai+l++++G +++ e++
  gi|121639103|ref|YP_979327.1|  40 PRFRRRGLARGLLSTLARECVDN-RYTRLAWSVLNWNSDAIALYDRIGGQPQHEWT 94 
                                    6899*****************88.9***************************9986 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.087      73     106 ..      31      65 ..      16      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                Acetyltransf_15  73 leiYtlyvsekyrgkGlakklLeeslkelk.knYk 106
                                    + + +l+v +++r++Gla+ lL    +e + ++Y 
  gi|121639103|ref|YP_979327.1|  31 IYVEDLFVWPRFRRRGLARGLLSTLARECVdNRYT 65 
                                    455589****************9988875426665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05      0.11      73     107 ..      30      64 ..      10      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                                    EEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                 Acetyltransf_9  73 aagvtgVavapehrgrgvlskLlaraleemreegq 107
                                      +v +  v+p  r+rg+++ Ll ++ +e+ ++++
  gi|121639103|ref|YP_979327.1|  30 GIYVEDLFVWPRFRRRGLARGLLSTLARECVDNRY 64 
                                    56899999******************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 614.92
//
Query:       gi|121639104|ref|YP_979328.1|  [L=143]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          7    6.1  14.1       0.27   10.7   6.3    2.5  2  SKG6      Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.9     0.075   1.3e+03      22      29 ..      25      32 ..      23      33 .. 0.76
   2 ?   10.7   6.3   1.5e-05      0.27      15      32 ..      99     116 ..      99     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.075
                           SKG6 22 ViiivLla 29
                                   V++++Ll+
  gi|121639104|ref|YP_979328.1| 25 VVAAALLV 32
                                   88888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 1.5e-05
                           SKG6  15 aVaVPVaViiivLlaili 32 
                                    a+++PV++i++ +l++l+
  gi|121639104|ref|YP_979328.1|  99 AIGIPVGIIALGVLVLLF 116
                                    89**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 950.45
//
Query:       gi|121639105|ref|YP_979329.1|  [L=321]
Description: hypothetical protein BCG_3245 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-24   85.2   0.8    4.5e-24   84.5   0.8    1.3  1  DAGK_cat    Diacylglycerol kinase catalytic domain
     0.0086   15.3   0.2      0.012   14.9   0.2    1.2  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.8     5e-28   4.5e-24       2     115 ..       3     119 ..       2     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 5e-28
                                    EEEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT.... CS
                       DAGK_cat   2 llvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglle.... 77 
                                    +++ivNp++   ++    + +++ le   ++l++ +t+++g+++el + a ++gvdl+vv GGDGtvs+v+ng+l+    
  gi|121639105|ref|YP_979329.1|   3 AVLIVNPTATA-TTPAGRDLLAHALE-SRLQLTVEHTNHRGHGTELGQAAVADGVDLVVVHGGDGTVSAVVNGMLGrpgt 80 
                                    799*****973.33333344455555.4556*********************************************8777 PP

                                    .HHCTTSEEEEEE-SS--HHHHHCT--SSHHHHHHCHHC CS
                       DAGK_cat  78 .elatkpplgiiPlGtgNdlaralgigkdieealesiik 115
                                       +  p+++++P+G++N laralgi+ d+ +a++++i+
  gi|121639105|ref|YP_979329.1|  81 tPVRPVPAVAVVPGGSANVLARALGISADPIAATNQLIQ 119
                                    667777****************************99975 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.3e-06     0.012      68      98 ..      44      74 ..      10     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
                                   ECCC-TTTTTSSSEEEEEE-HHHHHHHHHHH CS
                     NAD_kinase 68 rkaleafadagvdliivvGGDGTaldvarll 98
                                   ++  +a + +gvdl++v GGDGT+ +v+  +
  gi|121639105|ref|YP_979329.1| 44 TELGQAAVADGVDLVVVHGGDGTVSAVVNGM 74
                                   5556677889***************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2330.18
//
Query:       gi|121639106|ref|YP_979330.1|  [L=84]
Description: transcriptional regulatory protein whiB-like whiB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-27   93.5   0.5    1.1e-26   93.2   0.5    1.1  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.5     6e-31   1.1e-26       1      64 []       3      71 ..       3      71 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 6e-31
                           Whib  1 WreraaCrgedpelffpekg.....dreeeAkavCarCpVrreCleealeegeeyGvwGGltereRraL 64
                                   Wr++a Cr+edpelffp ++     +++++Ak vC+rCpV++eCl +al++g++ GvwGG++e+eRraL
  gi|121639106|ref|YP_979330.1|  3 WRHKAVCRDEDPELFFPVGNsgpalAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRAL 71
                                   ******************99***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 647.30
//
Query:       gi|121639107|ref|YP_979331.1|  [L=501]
Description: two component sensor kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-44  149.8   0.3    1.6e-43  148.1   0.0    2.0  2  H_kinase_N   Signal transduction histidine kinase
    5.4e-22   77.7   2.9    1.2e-21   76.6   2.9    1.6  1  HisKA_2      Histidine kinase
    2.2e-08   34.7   1.7    5.5e-08   33.4   1.4    1.9  2  HWE_HK       HWE histidine kinase
    3.4e-08   34.0   0.0    1.1e-07   32.3   0.0    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.2e-06   26.4   0.0    1.2e-05   25.2   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0006   20.1   0.5      0.005   17.1   0.1    2.6  2  PAS_4        PAS fold


Domain annotation for each model (and alignments):
>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   5.4e-47   1.6e-43       1     143 []       4     150 ..       4     150 .. 0.94
   2 ?   -1.8   0.1      0.89   2.7e+03     100     122 ..     295     317 ..     252     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 5.4e-47
                                    HHHHHHHH----HHHHHHHHHHHHHTHHHHHHHTSEEEEEEE-TTS-EEEEEEE--SSS--S--S--TT-EE-GGGSHHH CS
                     H_kinase_N   1 LsdllaehtdlseadiewLhalvgdwqllAdlsfaDllLwvptredeavvvaqarPttgptlyqeDvVGevveeeeeplv 80 
                                    L dllaeht l+++++++Lha+vg+wqllAdlsfaD+l+wv+++++ +v+vaq+rP+tgpt++++D+VG+vv+++  plv
  gi|121639107|ref|YP_979331.1|   4 LGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRNDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLV 83 
                                    789***************************************************************************** PP

                                    HHHHH----------------...---EEEEEE.EETEEEEEEEEE-.-GGGS----HHHHHHHHHH CS
                     H_kinase_N  81 draleegrivrekdpdwsggv...pvreeaiPVrrrgkviAVltret.nlssartpsrleltylesa 143
                                     ++++ g   re++  +++++      +e+ PVr  ++v+AVltr++ +l+++r+ ++le++y+ +a
  gi|121639107|ref|YP_979331.1|  84 AATFSGGVPGREGAVGQQNSCqhdGHSVEVSPVRFGDQVVAVLTRHQpELAARRRSGHLETAYRLCA 150
                                    **************9999999777777******5558*******7764899999*********9886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.89
                                    -----EEEEEE.EETEEEEEEEE CS
                     H_kinase_N 100 gvpvreeaiPVrrrgkviAVltr 122
                                    ++++re    V+++ +++A l r
  gi|121639107|ref|YP_979331.1| 295 DATIREIHHRVKNNLQTVAALLR 317
                                    33445555555555455555555 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   2.9     4e-25   1.2e-21       1      69 [.     300     367 ..     300     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 4e-25
                        HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLv 69 
                                    EihHRvkNnLq++++lL+lqar++++ e +eal es +Rv sial+h+ L+ s d e+v+++e++++++
  gi|121639107|ref|YP_979331.1| 300 EIHHRVKNNLQTVAALLRLQARRTSNAEGREALIESVRRVSSIALVHDALSMSVD-EQVNLDEVIDRIL 367
                                    9****************************************************99.*********9986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.9   8.7e+03      40      60 ..     197     217 ..     196     234 .. 0.80
   2 !   33.4   1.4   1.8e-11   5.5e-08       1      70 [.     300     371 ..     300     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHHCTTS-EEHHH CS
                         HWE_HK  40 ALsaahdllsreewagaeLae 60 
                                    ALsa h +  ++e +g++L +
  gi|121639107|ref|YP_979331.1| 197 ALSAYHRMGLTTELEGVNLID 217
                                    999999998889989988865 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.8e-11
                                    HHHHHHHHHHHHHHHHHHHHSSSXS-HHHHHHHHHH..HHHHHHHHHHHHHHCTTS-EEHHHHHHHHHHHHH CS
                         HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesleefaeklsg..RLqALsaahdllsreewagaeLaelleeelapye 70 
                                    E++HRvKN L +v ++ r  +r++++ e  ++ +++  R+ +++ +hd ls +  ++++L+e++++ l  ++
  gi|121639107|ref|YP_979331.1| 300 EIHHRVKNNLQTVAALLRLQARRTSNAEGREALIESvrRVSSIALVHDALSMSVDEQVNLDEVIDRILPIMN 371
                                    89********************9999888777776444**************************99886655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.8e-11   1.1e-07       4     110 ..     397     493 ..     394     495 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.8e-11
                                    HHHHHHHHHHHHHHHHH....HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHH CS
                      HATPase_c   4 krLrqiisnlvdNavkf....atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGls 79 
                                    + L  +i +lv+Na+++    a+ +g+++++ ++s  +l + v D+G G+p+         fs         +   lGl 
  gi|121639107|ref|YP_979331.1| 397 TALIMVITELVQNAIEHafdpAAAEGSVTIRAERSARWLDVVVHDDGLGLPQ--------GFSL-------EKSDSLGLQ 461
                                    568889***********77544466666666665669**************9........4444.......34455**** PP

                                    HHHHHHH.HTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  80 ivkklve.lmgGeiwvesepgrGttftftlpl 110
                                    iv+ lv+  ++G++ +++  +rGt++++++p 
  gi|121639107|ref|YP_979331.1| 462 IVRTLVSaELDGSLGMRDARERGTDVVLRVPV 493
                                    ****88879*******************9986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   4.2e-09   1.2e-05      24      81 ..     391     450 ..     383     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.2e-09
                    HATPase_c_2  24 lseelldeirlaveEactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe 81 
                                    l+++++  + ++++E++ Na+eha + a  eg+v++r+e+++++l v+v+D+G g  +  
  gi|121639107|ref|YP_979331.1| 391 LDSDRATALIMVITELVQNAIEHAFDPAAaEGSVTIRAERSARWLDVVVHDDGLGlPQGF 450
                                    566777788899**************9999***********************9855554 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.7e-06     0.005       5     110 .]     178     286 ..     175     286 .. 0.84
   2 ?    1.6   0.0      0.11   3.2e+02      52     105 ..     284     339 ..     283     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                          PAS_4   5 pdalavldpdgrvlyaNaa..aaelfgappeellGktlaellpee.....daarleralrrvlegeepiefleelllpge 77 
                                     d+++ ld dg+v ya+++  +a++      el G  l +   +       a++++++++ +l+g+    ++e +  + +
  gi|121639107|ref|YP_979331.1| 178 GDGFIRLDVDGVVSYASPNalSAYHRMGLTTELEGVNLIDATRPLisdpfEAHEVDEHVQDLLAGDGKGMRME-V--DAG 254
                                    689999*************7666677788899999999987777777779**************964433333.2..678 PP

                          PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                    + +++lr lPl    G+ +g+ +++rD+Te +r
  gi|121639107|ref|YP_979331.1| 255 GATVLLRTLPL-VVAGRNVGAAILIRDVTEVKR 286
                                    99*********.79****************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                          PAS_4  52 leralrrvlegeepiefleelll.pgeerhyelrl..lPlrdesGevigvlvisrDi 105
                                    + r +r++++ +++i++ ++++  + +++  +lrl  ++  +++G+  ++++ +r +
  gi|121639107|ref|YP_979331.1| 284 VKRRDRALISKDATIREIHHRVKnNLQTVAALLRLqaRRTSNAEGR-EALIESVRRV 339
                                    67899999*******9999999998888888888877888899999.7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3508.64
//
Query:       gi|121639108|ref|YP_979332.1|  [L=71]
Description: acetyl-CoA carboxylase biotin carboxyl carrier protein subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-17   62.0   6.9    3.9e-17   61.8   6.9    1.0  1  Biotin_lipoyl    Biotin-requiring enzyme
    5.5e-07   29.3   9.8    3.9e-05   23.4   1.0    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
    8.2e-05   23.3   4.1     0.0038   17.9   0.6    2.0  2  HlyD_3           HlyD family secretion protein
    0.00051   20.0   2.5     0.0039   17.1   0.6    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0011   18.2   2.2      0.038   13.2   0.2    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0045   17.2   2.5       0.79   10.0   0.3    2.4  3  Peptidase_M23    Peptidase family M23
  ------ inclusion threshold ------
       0.01   15.7   1.3      0.011   15.6   1.3    1.2  1  GCV_H            Glycine cleavage H-protein
      0.012   15.6   0.5       0.66    9.9   0.1    2.0  2  DUF2118          Uncharacterized protein conserved in archaea
      0.021   14.3   0.8      0.035   13.5   0.7    1.4  2  NQRA             Na(+)-translocating NADH-quinone reductase s
      0.029   14.0   1.6        3.6    7.3   0.1    2.2  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   6.9   2.2e-20   3.9e-17      12      73 .]      10      70 ..       3      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.2e-20
                                   EEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl 12 veegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                   v+ +v+ev v++Gd++ +g+v++ +e+mKme+++ a++aG+v+++ v++Gd +++gdl+a+i
  gi|121639108|ref|YP_979332.1| 10 VA-SVLEVVVNEGDQIDKGDVVVLLESMKMEIPVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   33.599******************************************************97 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.4   4.9e-05     0.088       6      37 ..       6      37 ..       4      47 .. 0.83
   2 !   23.4   1.0   2.1e-08   3.9e-05       4      33 ..      41      70 ..      34      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                Biotin_lipoyl_2  6 aapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                    a + + V ++ V +G+++ +Gdv + l+s +
  gi|121639108|ref|YP_979332.1|  6 RAEIVASVLEVVVNEGDQIDKGDVVVLLESMK 37
                                   566667899***************98888765 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.1e-08
                Biotin_lipoyl_2  4 sIaapvsGrVaqlnVkdGqrVkaGdvLael 33
                                   ++ a  +G+V++++V  G++++aGd++a++
  gi|121639108|ref|YP_979332.1| 41 PVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   5557779*********************98 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0045       8.1       2      28 ..       5      31 ..       4      39 .. 0.90
   2 !   17.9   0.6   2.1e-06    0.0038       2      30 ..      42      70 ..      41      71 .] 0.94

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdell 28
                                   +rA +   v e+ v+eg+ + +gd+++
  gi|121639108|ref|YP_979332.1|  5 VRAEIVASVLEVVVNEGDQIDKGDVVV 31
                                   89999999****************986 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.1e-06
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdellei 30
                                   + A  +G+v+++ v++g+v+qagd ++ i
  gi|121639108|ref|YP_979332.1| 42 VLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   67999*********************998 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   2.2e-06    0.0039      42      81 ..      14      54 ..       7      57 .. 0.88
   2 !    9.2   0.3   0.00066       1.2      35      59 ..      44      68 ..      43      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                         RnfC_N 42 akplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                    +++v++gd++ kG+++   e+  +  pv a  +GtV +++
  gi|121639108|ref|YP_979332.1| 14 LEVVVNEGDQIDKGDVVVLLESmKMEIPVLAEAAGTVSKVA 54
                                   589*************9988876679***********9986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00066
                         RnfC_N 35 sqhiGapakplvkvgdkVlkGqkia 59
                                   +  +G+  k+ v+vgd ++ G++ia
  gi|121639108|ref|YP_979332.1| 44 AEAAGTVSKVAVSVGDVIQAGDLIA 68
                                   5678999*****************8 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2    0.0023       4.1      22      55 ..       5      37 ..       2      39 .. 0.83
   2 !   13.2   0.2   2.1e-05     0.038     105     139 ..      36      70 ..      34      71 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 22 vsarveGwveklyvnatgdkVkkGqpLaelyspe 55
                                   v a++ + v ++ vn +gd++ kG+ ++ l+s +
  gi|121639108|ref|YP_979332.1|  5 VRAEIVASVLEVVVN-EGDQIDKGDVVVLLESMK 37
                                   677788888999999.999999999999999876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 105 vqktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    ++ +++v a+++G+V + +v  G+++q+gd ++ i
  gi|121639108|ref|YP_979332.1|  36 MKMEIPVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70 
                                    567899***********************988876 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0037       6.6      50      70 ..      11      31 ..       3      44 .. 0.79
   2 ?    2.7   0.0     0.081   1.4e+02      13      27 ..      39      53 ..      32      54 .. 0.80
   3 !   10.0   0.3   0.00044      0.79      50      71 ..      48      69 ..      43      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0037
                                   EEESEESS-TTEEE-TTCEEE CS
                  Peptidase_M23 50 ahlskisvkegqkVkaGqvIG 70
                                   a + ++ v+eg+++++G+v+ 
  gi|121639108|ref|YP_979332.1| 11 ASVLEVVVNEGDQIDKGDVVV 31
                                   55567789**********985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.081
                                   T-EEEESSSEEEEEE CS
                  Peptidase_M23 13 gtpVlAaadGtVvfa 27
                                   + pVlA a+GtV ++
  gi|121639108|ref|YP_979332.1| 39 EIPVLAEAAGTVSKV 53
                                   569*********865 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00044
                                   EEESEESS-TTEEE-TTCEEEE CS
                  Peptidase_M23 50 ahlskisvkegqkVkaGqvIGt 71
                                   + +sk++v++g+ ++aG+ I+ 
  gi|121639108|ref|YP_979332.1| 48 GTVSKVAVSVGDVIQAGDLIAV 69
                                   56899***************96 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.3   6.2e-06     0.011      38      78 ..      17      57 ..       2      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.2e-06
                                   ---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                          GCV_H 38 lpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78
                                   + ++g++++kg+ +  +Es K+  +v a+  G+v +v   +
  gi|121639108|ref|YP_979332.1| 17 VVNEGDQIDKGDVVVLLESMKMEIPVLAEAAGTVSKVAVSV 57
                                   4478******************************9987665 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00037      0.66      94     122 ..      15      43 ..       3      50 .. 0.82
   2 ?    5.6   0.1    0.0079        14      87     112 ..      45      70 ..      42      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                        DUF2118  94 tlivdvGdrveegdtlaavttrkgevryl 122
                                     ++v++Gd++ +gd++  + + k e+  l
  gi|121639108|ref|YP_979332.1|  15 EVVVNEGDQIDKGDVVVLLESMKMEIPVL 43 
                                    5789********************99766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0079
                        DUF2118  87 pvegvkvtlivdvGdrveegdtlaav 112
                                    +++g +  + v vGd ++ gd +a +
  gi|121639108|ref|YP_979332.1|  45 EAAGTVSKVAVSVGDVIQAGDLIAVI 70 
                                    68899999***************986 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7     2e-05     0.035      40      80 ..      13      54 ..       5      63 .. 0.82
   2 ?    0.2   0.0      0.23   4.2e+02      42      57 ..      52      67 ..      52      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           NQRA 40 kpklkvkegdkVkkGqvlf.edKknpgvlftspasGevvein 80
                                    ++++v+egd++ kG+v++  +  + ++ + + a+G+v+++ 
  gi|121639108|ref|YP_979332.1| 13 VLEVVVNEGDQIDKGDVVVlLESMKMEIPVLAEAAGTVSKVA 54
                                   5789************87515667789***********9985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                           NQRA 42 klkvkegdkVkkGqvl 57
                                   k++v++gd +++G+ +
  gi|121639108|ref|YP_979332.1| 52 KVAVSVGDVIQAGDLI 67
                                   5788999999999876 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0029       5.2      35      57 ..      15      37 ..      11      54 .. 0.75
   2 ?    7.3   0.1     0.002       3.6      37      53 ..      54      70 ..      42      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                                   EES--TT-EEBTTSEEEEEEESS CS
                         PYNP_C 35 elhkklGdkVkkGeplatiYank 57
                                   e+ +  Gd+++kG++++ + + k
  gi|121639108|ref|YP_979332.1| 15 EVVVNEGDQIDKGDVVVLLESMK 37
                                   567788*********99875555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                                   S--TT-EEBTTSEEEEE CS
                         PYNP_C 37 hkklGdkVkkGeplati 53
                                    + +Gd +++G+ +a+i
  gi|121639108|ref|YP_979332.1| 54 AVSVGDVIQAGDLIAVI 70
                                   5789***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 517.37
//
Query:       gi|121639109|ref|YP_979333.1|  [L=101]
Description: anti-sigma factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-10   39.0   4.2    6.7e-10   39.0   4.2    1.8  2  zf-HC2    Putative zinc-finger


Domain annotation for each model (and alignments):
>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   4.2   3.7e-14   6.7e-10       1      34 [.      23      56 ..      23      57 .. 0.97
   2 ?   -3.1   0.1      0.57     1e+04      19      24 ..      84      89 ..      80      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.7e-14
                                   HCCHHHHHHHHHCCT-SCCCHCCCHHHHCHTCHH CS
                         zf-HC2  1 CeevrelLsaYlDGeLspeerarveaHLaeCpdC 34
                                   C ev + ++  lDGe++pe+r+r+++HL++Cp C
  gi|121639109|ref|YP_979333.1| 23 CAEVIAEVWTLLDGECTPETRERLRRHLEACPGC 56
                                   99******************************** PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.57
                                   CCHCCC CS
                         zf-HC2 19 eerarv 24
                                   +er r+
  gi|121639109|ref|YP_979333.1| 84 RERLRL 89
                                   466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 776.18
//
Query:       gi|121639110|ref|YP_979334.1|  [L=183]
Description: hypothetical protein BCG_3250c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1370.33
//
Query:       gi|121639111|ref|YP_979335.1|  [L=216]
Description: RNA polymerase sigma factor RpoE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-18   64.1   0.1    1.5e-17   63.1   0.1    1.5  1  Sigma70_r2    Sigma-70 region 2
    1.1e-16   60.2   0.0    2.5e-16   59.1   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
    1.8e-10   40.2   0.0    4.4e-10   38.9   0.0    1.7  2  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   2.6e-21   1.5e-17       6      70 ..      37      99 ..      35     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.6e-21
                                   HHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2  6 lplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70
                                   l+++++ a r+++++adaeDl+Qe++++++ + ++f+++++  ++awl+ri +n+ i+ +Rk++r
  gi|121639111|ref|YP_979335.1| 37 LDQLYGGALRMTRNPADAEDLLQETMVKAYAGFRSFRHGTN--LKAWLYRILTNTYINSYRKKQR 99
                                   789**********************************5555..*******************998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   4.1e-20   2.5e-16       3      54 .]     140     191 ..     138     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.1e-20
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    ++ eal++Lpe+ r+++   ++eg++ykEIAe+++++ gtV srl+R+r++L
  gi|121639111|ref|YP_979335.1| 140 EIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQL 191
                                    799**********************************************997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.75   4.5e+03      41      48 ..     129     136 ..     126     140 .. 0.54
   2 !   38.9   0.0   7.3e-14   4.4e-10       1      49 [.     144     192 ..     144     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.75
                                    HHHHHHHH CS
                     Sigma70_r4  41 ekrAlrkL 48 
                                    e +Al+ L
  gi|121639111|ref|YP_979335.1| 129 EVEALEAL 136
                                    55555554 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 7.3e-14
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    aL+ Lpe+ r+ +++  +eg +++EI+e+++ + ++V ++++r++r+LR
  gi|121639111|ref|YP_979335.1| 144 ALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQLR 192
                                    8***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1586.56
//
Query:       gi|121639112|ref|YP_979336.1|  [L=282]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-28  100.1   0.0    1.5e-28   99.6   0.0    1.2  1  adh_short       short chain dehydrogenase
      7e-28   97.8   0.2    9.6e-28   97.3   0.2    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.2e-07   31.8   0.1    1.8e-07   31.3   0.1    1.2  1  KR              KR domain
  ------ inclusion threshold ------
      0.036   13.9   0.1      0.065   13.0   0.1    1.4  1  DFP             DNA / pantothenate metabolism flavoprotein
      0.099   12.5   0.9       0.26   11.2   1.0    1.7  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   4.2e-32   1.5e-28       1     189 [.       6     203 ..       6     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 4.2e-32
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHH.......HHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHH CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseeklee.......vakelkeegakalaiqvDvtdreevealvekavk 73 
                                    k++++ Gas+GIG+aiak+ a++Ga+++++++++e+  +       +akel+e+g +al+i +D++d ++v  +v++ v+
  gi|121639112|ref|YP_979336.1|   6 KTMFISGASRGIGLAIAKRAARDGANIALIAKTAEPHPKlpgtvftAAKELEEAGGQALPIVGDIRDPDAVASAVATTVE 85 
                                    7899****************************9997654222222289******************************** PP

                                    HHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHH CS
                      adh_short  74 klgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAs 152
                                    ++g++d+ vnNA+  + g++ e+  ++++ +  + + g++ +++a++p+m+ +++ +I + s  +  ++++   +aY  +
  gi|121639112|ref|YP_979336.1|  86 QFGGIDICVNNASAINLGSITEVPMKRFDLMNGIQVRGTYAVSQACIPHMKGRENPHILTLSPPILlEKKWLRPTAYMMA 165
                                    **************************************************************988758899999****** PP

                                    HHHHHHHHHHHHHHHGGGTEEEEEEEESSBS.SHHHHH CS
                      adh_short 153 KaavagltrslakelaptgirvnavaPGlvd.Tdmake 189
                                    K +++  +  +a+e++ +gi  n++ P  +  T+ +++
  gi|121639112|ref|YP_979336.1| 166 KYGMTLCALGIAEEMRADGIASNTLWPRTMVaTAAVQN 203
                                    *************************9965443877665 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.2   2.7e-31   9.6e-28       1     193 [.      12     215 ..      12     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 2.7e-31
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..H......HHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEE CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..k......krveelaeelgaev.lecDVtdeeqvealveevvekfgklD 71 
                                    Ga +gIG aiAk++a+ Ga+++l     e   k       +++el+e++g+++ +  D++d+++v+++v+++ve+fg++D
  gi|121639112|ref|YP_979336.1|  12 GASRGIGLAIAKRAARDGANIALIAKTAEPhpKlpgtvfTAAKELEEAGGQALpIVGDIRDPDAVASAVATTVEQFGGID 91 
                                    999*******************98877765332232222345566666666658************************** PP

                                    EEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEE.GGGTSBSTTTTHHHHHHHHH CS
                   adh_short_C2  72 ilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlss.vgaervvpnynaygaaKaal 148
                                    i+vnna   +   g+++e++ + fd +  +++++++++++a++p+mk +    i++ls  +  e+ +   +ay++aK ++
  gi|121639112|ref|YP_979336.1|  92 ICVNNASAINL--GSITEVPMKRFDLMNGIQVRGTYAVSQACIPHMKGRenPHILTLSPpILLEKKWLRPTAYMMAKYGM 169
                                    ***********..*******************************999766699****96257788899999********* PP

                                    HHHHHHHHHHHGGGTEEEEEEEE.--BHCTGGGGSTTHHHHHHHHH CS
                   adh_short_C2 149 ealtrylAvelgpkgiRvNavsp.gpikTlaasgikgfdelleele 193
                                      ++  +A e+ ++gi  N+  p  +++T a++++ g de +++++
  gi|121639112|ref|YP_979336.1| 170 TLCALGIAEEMRADGIASNTLWPrTMVATAAVQNLLGGDEAMARSR 215
                                    **********************956778888888887777665544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1     5e-11   1.8e-07       2     123 ..       7     131 ..       6     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5e-11
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH....HHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedsk....aliaelealgaevevvaaDvsdkdavealleeika 77 
                                    t +i G+  g+Gl++a+  a++ga +++l++++a+++++      +  +ele+ g +   +  D+ d+dav++++++  +
  gi|121639112|ref|YP_979336.1|   7 TMFISGASRGIGLAIAKRAARDGA-NIALIAKTAEPHPKLPgtvfTAAKELEEAGGQALPIVGDIRDPDAVASAVATTVE 85 
                                    5689******************98.69999999855554443333699******************************** PP

                                    HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHT CS
                             KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhell 123
                                    +++ i  +++ A +++ + ++e+ +++++ +    v+G+  + +++
  gi|121639112|ref|YP_979336.1|  86 QFGGIDICVNNASAINLGSITEVPMKRFDLMNGIQVRGTYAVSQAC 131
                                    ***************************************9999987 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.8e-05     0.065      22      79 ..       9      63 ..       7      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                   EEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHH CS
                            DFP 22 fisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveea 79
                                   fis  S G  G+a+A++aa+ Ga++ l++   + ++p ++  + ++ a+e++ea  +a
  gi|121639112|ref|YP_979336.1|  9 FISGASRG-IGLAIAKRAARDGANIALIAKTAE-PHP-KLPGTVFTAAKELEEAGGQA 63
                                   56666766.6******************99843.333.56666677788887776555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   7.1e-05      0.26       1      62 [.      12      91 ..      12     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH...........HHHCT.TTCEEEE--TT-CCHHHHHHT.......T-S CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekla...........eleae.eglevvegdvtdvedlaealk.......gad 62
                                   GA+ ++G +++k+++++g  ++ +++ ++e  +           ele++  ++  ++gd+ d++++a+a++       g+d
  gi|121639112|ref|YP_979336.1| 12 GASRGIGLAIAKRAARDG-ANIALIAKTAEPHPklpgtvftaakELEEAgGQALPIVGDIRDPDAVASAVAttveqfgGID 91
                                   9****************5.99999999988666344555555556664435666788999999999999875555554555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2013.80
//
Query:       gi|121639113|ref|YP_979337.1|  [L=62]
Description: hypothetical protein BCG_3253 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 454.30
//
Query:       gi|121639114|ref|YP_979338.1|  [L=72]
Description: hypothetical protein BCG_3254 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-06   28.4   0.0    1.7e-06   28.1   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   9.7e-11   1.7e-06      58     102 ..       3      46 ..       2      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.7e-11
                      tRNA_edit  58 klrlaseeelrellgvepGgvgPlglkaagvpvllDeslkeyptv 102
                                    k+++a+++  ++++g+++Gg++P+g   +++++++D s+++ ++v
  gi|121639114|ref|YP_979338.1|   3 KAAMAKPAAAEQATGYVVGGISPFGQ-RKRLRTVVDVSALSWDRV 46 
                                    689**********************9.8********999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 494.41
//
Query:       gi|121639115|ref|YP_979339.1|  [L=474]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-33  114.1   2.6    9.4e-33  114.1   2.6    1.5  2  APH              Phosphotransferase enzyme family
    2.7e-18   67.0   0.0    6.1e-18   65.8   0.0    1.6  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    8.7e-08   32.4   0.0    1.7e-07   31.5   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0097   15.6   0.0      0.048   13.3   0.0    2.1  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0097   15.8   0.0      0.016   15.1   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.059   13.3   0.0       0.13   12.3   0.0    1.5  1  FR47             FR47-like protein
      0.084   12.5   0.0       0.14   11.7   0.0    1.2  1  RIO1             RIO1 family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   6.8e+03      63     100 ..     158     194 ..     125     198 .. 0.66
   2 !  114.1   2.6   3.7e-36   9.4e-33       6     238 ..     210     432 ..     206     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                    -EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHH CS
                            APH  63 ddeeigllfalieyvpgrsllrklsaaqlpellealge 100
                                     +e+ g++f  +e+v  + ++  +  +++++l+++l +
  gi|121639115|ref|YP_979339.1| 158 ICEQDGTVFDRYERVLRAKMHA-DEVDIDEDLVRRLLR 194
                                    4455555666666666666666.556666666666655 PP

  == domain 2  score: 114.1 bits;  conditional E-value: 3.7e-36
                                    --.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                            APH   6 sggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr 84 
                                    s+g++n  y++++   ++++r+++ ++a e++r e+++l  +a++     P+++ ++  +e+ g+++ +  +v g+ ++ 
  gi|121639115|ref|YP_979339.1| 210 SAGTDNAMYRLGE---DLAVRIPRIGWAIESLRTEQQWLPRIAAHLGvASPVPVGLGSPAEGFGWPWSVCRWVAGENPSA 286
                                    789**********...9**********************8888665565555666669********************** PP

                                    HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.HHHHHHHHHHHHHHHH--SS CS
                            APH  85 klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselld.lleeleeqvlaalaallpge 163
                                         +  +++e+l++f+  l ++dp   p+a ++a+  e+++ + +a    la++ +  ++ ++++ +++  ++  p +
  gi|121639115|ref|YP_979339.1| 287 -AEFVEPNRAVEDLADFITTLRATDPMGGPPAKRGAPLGEQDAEVRAA----LAALDGIiDVHAATA-AWESALRVPPYA 360
                                    .778899****************************9988888888888....333333345677777.88888888888* PP

                                    S-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHHCS-HHHHCCC CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrswtseldpeflaallrayeqeaglarla 238
                                    +p+ + HgDl+  N+l    +gr+tGviDf+++g+g+p +Dl ++++ +  ++++ f+ a ++a   ++ ++r +
  gi|121639115|ref|YP_979339.1| 361 GPPMWFHGDLSRFNILTA--QGRLTGVIDFGLMGVGDPSVDLIIAWNLLSAPARAQFRVAVGAADD-DWMRGRGR 432
                                    ******************..**************************77**************9996.57666665 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   2.4e-21   6.1e-18       2     137 ..      15     152 ..      15     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.4e-21
                 Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmry.lpepltleeaeewlera...waeeseeegygwaivl.kdtgviGsvglrdlee 76 
                                    ++L pl+ +D++a +    d++++r+  + p t++  e++++++   w ++ + ++  + i++  +t ++G++ lr +++
  gi|121639115|ref|YP_979339.1|  15 VTLSPLCLDDVDAHL-AGGDERLVRWlSGMPSTRASVEAYIRHCreqWVTGGPLRS--FGIRTvAET-IVGTIDLR-FDG 89 
                                    589*******99976.489999999*6556************87888887666666..677654777.9****999.444 PP

                 Acetyltransf_3  77 edee...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    e  +   +++ y l ps++g+G+at av  +++ya +e+g+++ v+++++eN+aS+rv+ ++Gf
  gi|121639115|ref|YP_979339.1|  90 EGLAsgqVNVAYGLYPSWRGRGLATRAVDLVCQYA-AEHGATEAVIKVEPENSASARVALRAGF 152
                                    4444688****************************.6777***********************9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   6.5e-11   1.7e-07      34     117 .]      68     152 ..      34     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.5e-11
                                    EEEE.EEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHH CS
                 Acetyltransf_1  34 gllv.aeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaair 110
                                    + +      ++++G+i l+ + +   +g+v + ++l+  p++rg+Gl+++ ++ + ++a e+g+++ v+ ve+ n a+ r
  gi|121639115|ref|YP_979339.1|  68 RSFGiRTVAETIVGTIDLRFDGEglASGQVNVAYGLY--PSWRGRGLATRAVDLVCQYAAEHGATEAVIKVEPENSASAR 145
                                    33333444599**********9997666666666666..*************************8889************ PP

                                    HHHHTTE CS
                 Acetyltransf_1 111 lYeklGF 117
                                    +  + GF
  gi|121639115|ref|YP_979339.1| 146 VALRAGF 152
                                    **99999 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.9e-05     0.048      89     143 ..     105     158 ..      97     159 .. 0.87
   2 ?   -1.5   0.0      0.72   1.8e+03      11      41 ..     277     309 ..     274     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                    HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                 Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                    ++ rg+gl+t+ +  +++y+ ++ +++  v+  +++N ++ r+  +aGf++++++
  gi|121639115|ref|YP_979339.1| 105 PSWRGRGLATRAVDLVCQYAAEH-GATEAVIKVEPENSASARVALRAGFAFVRRI 158
                                    6789****************999.666666777789**************99875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.72
                                    HHC..TSCCCHHHH-----HHHHHHHHHHHC.S CS
                 Acetyltransf_8  11 rWm..nrprvaewweeagtleevrellakldad 41 
                                    rW+  ++p +ae+ e +  +e+++++ ++l+a+
  gi|121639115|ref|YP_979339.1| 277 RWVagENPSAAEFVEPNRAVEDLADFITTLRAT 309
                                    6773358999********999999999998865 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.2e-06     0.016      60     124 ..     104     170 ..      66     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                Acetyltransf_10  60 dpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqeenGirfvpMe 124
                                     p++rg+G++++ ++ v+++a ++g  +  ++v+  + +  ++  + GF  v + +e++G  f ++e
  gi|121639115|ref|YP_979339.1| 104 YPSWRGRGLATRAVDLVCQYAAEHGATEaVIKVEPENsASARVALRAGFAFVRRICEQDGTVFDRYE 170
                                    499******************99999999*****99988899******************9987666 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.9e-05      0.13      30      78 ..     104     153 ..      97     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                                    -GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-E CS
                           FR47  30 lpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfe 78 
                                     p+ r+rGl++r v  + +  ae g t +++ v ++N++s r+  + Gf 
  gi|121639115|ref|YP_979339.1| 104 YPSWRGRGLATRAVDLVCQYAAEHGATeAVIKVEPENSASARVALRAGFA 153
                                    5899*******************998725567999******998888886 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.5e-05      0.14     129     150 ..     367     389 ..     364     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                                    ESS-STTSEEEETT.EEEE--GT CS
                           RIO1 129 HaDLSeyNvlvded.kvviIDvs 150
                                    H+DLS +N+l  ++    +ID++
  gi|121639115|ref|YP_979339.1| 367 HGDLSRFNILTAQGrLTGVIDFG 389
                                    **************555699985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3138.92
//
Query:       gi|121639116|ref|YP_979340.1|  [L=252]
Description: hypothetical protein BCG_3256c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-65  218.9   0.0    6.4e-65  218.8   0.0    1.0  1  SRAP      SOS response associated peptidase (SRAP)


Domain annotation for each model (and alignments):
>> SRAP  SOS response associated peptidase (SRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   3.6e-69   6.4e-65       1     219 []       1     231 [.       1     231 [. 0.86

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 3.6e-69
                           SRAP   1 MCgRyaltlapeelaeeleaeeedke...lrpsynvaptqkvpvvvaeeeeeeeeeeerklqamkwGlvPswakd..... 72 
                                    MCgR+a+t++p++lae+++a +e +     + synvapt+++++vv++++e  ++e +r+++ m+wGl+Psw k      
  gi|121639116|ref|YP_979340.1|   1 MCGRFAVTTDPAQLAEKITAIDEATGcggGKTSYNVAPTDTIATVVSRHSE-PDDEPTRRVRLMRWGLIPSWIKAgpgga 79 
                                    *****************99643333355679**************987777.445669***************6522111 PP

                           SRAP  73 pkklglktiNaRsetlaekplfrsalkkkRcvvpadGFYEWk.......kkgkekqPyfikrkdgkllalAGLydvweee 145
                                    p+ +g  +iNaR++++a++p+frsa+++kRc+vp+dG+YEW+        + ++k+P+f++r+dg ll+ AGL++vw++ 
  gi|121639116|ref|YP_979340.1|  80 PDAKGPPLINARADKVATSPAFRSAVRSKRCLVPMDGWYEWRvdpdatpGRPNAKTPFFLHRHDGALLFTAGLWSVWKSY 159
                                    45668************************************54455543334689**********************987 PP

                           SRAP 146 geeeklytytiiTteankqlaelHdRmPviLeeeelraWLdprkedskelqellkpaeeeelevypVskeVnkv 219
                                     ++ +l ++t+iTt+a  +lae+HdRmP+ L ee++++WL+p+   + e   l +p + +++++++Vs+ Vn+v
  gi|121639116|ref|YP_979340.1| 160 RSAPPLLSCTVITTDAVGELAEIHDRMPLLLAEEDWDDWLNPDAPPDPE--LLARPPDVRDIALRQVSTLVNNV 231
                                    789***************************************4444444..456999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1783.40
//
Query:       gi|121639117|ref|YP_979341.1|  [L=450]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.1e-120  401.7   0.0   3.5e-120  401.5   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.5   0.0  1.9e-124  3.5e-120       2     415 ..       8     417 ..       7     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 401.5 bits;  conditional E-value: 1.9e-124
                                    ECSS--EEEEE--B-HHHHHHHHHHHGGGBSS....EEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..- CS
                  EPSP_synthase   2 ekgkrlegevkvpGsksisnralllAaLaege....stitnlLdseDvrsmlealreLgaeiikldeekevviveglggs 77 
                                    +++++++++v+vpGsks++nral+lAaLa+ +    sti++ L+s+D++ ml+al++Lg    ++d  +++++v+g   +
  gi|121639117|ref|YP_979341.1|   8 TAPTPVRATVTVPGSKSQTNRALVLAALAAAQgrgaSTISGALRSRDTELMLDALQTLG---LRVDGVGSELTVSG---R 81 
                                    57899************************9999999***********************...799999********...9 PP

                                    -EE-HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET...SS- CS
                  EPSP_synthase  78 feapeelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg...lkl 154
                                    +e++ ++ +d+g +gt+lr++++l+al s++v+++Gd+++r RPi++lldaLr+lG+ ++   g + +p++v+g   l +
  gi|121639117|ref|YP_979341.1|  82 IEPGPGARVDCGLAGTVLRFVPPLAALGSVPVTFDGDQQARGRPIAPLLDALRELGVAVD---G-TGLPFRVRGngsLAG 157
                                    999999******************************************************...4.789*****999**** PP

                                    BEEEEETSSTTHHHHHHHHHHHTTSBS.EEEEES..-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE CS
                  EPSP_synthase 155 kgveikaevsSqqvtsllllaallaeg.ttelee..lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyv 231
                                    ++v i+a+ sSq+v+ lll+aa +++g t+++++  l+s+p+i +t+ ml+++g++i++ +t+++++v++++ + + ++ 
  gi|121639117|ref|YP_979341.1| 158 GTVAIDASASSQFVSGLLLSAASFTDGlTVQHTGssLPSAPHIAMTAAMLRQAGVDIDD-STPNRWQVRPGPVAAR-RWD 235
                                    ***********************************************************.89999********999.*** PP

                                    --B-HHHHHHHHHHHHHTT-EEEEES--GGGGH.HH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTS CS
                  EPSP_synthase 232 vegDassAayflvaAaitggevtvenvginslq.Gdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdea 310
                                    +e+D+++A+ fl aA+++gg+v+++++++ s+q +d  ++ +il++++a + + +++  v+gp+g+++ dvd++ + +++
  gi|121639117|ref|YP_979341.1| 236 IEPDLTNAVAFLSAAVVSGGTVRITGWPRVSVQpAD--HILAILRQLNAVVIHADSSLEVRGPTGYDGFDVDLRAVGELT 313
                                    *********************************888..8888*************999999999**************** PP

                                    BHGGGHHHHHH..HHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHH CS
                  EPSP_synthase 311 ptlavlaafae..gttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamala 388
                                    p +a+laa+a+  + ++++gia+lr +etdrlaa+ te+++lG++++e++dgl  i+a+  l+++ +++y+DhR+ama a
  gi|121639117|ref|YP_979341.1| 314 PSVAALAALASpgSVSRLSGIAHLRGHETDRLAALSTEINRLGGTCRETPDGLV-ITATP-LRPGIWRAYADHRMAMAGA 391
                                    ***********9999*************************************98.78887.******************* PP

                                    HHHHHSBSEEEEETTHHHHHHSSSHHH CS
                  EPSP_synthase 389 laglvaegeveiddiectdksfpefee 415
                                    ++gl+++g ve+ddi++t+k+ pef +
  gi|121639117|ref|YP_979341.1| 392 IIGLRVAG-VEVDDIAATTKTLPEFPR 417
                                    ********.****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3189.17
//
Query:       gi|121639118|ref|YP_979342.1|  [L=330]
Description: hypothetical protein BCG_3258 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-41  139.5   0.0    1.3e-40  139.1   0.0    1.2  1  RsgA_GTPase   RsgA GTPase
    6.8e-06   26.1   0.0    1.3e-05   25.2   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    2.8e-05   24.6   0.1    5.2e-05   23.8   0.1    1.4  1  ABC_tran      ABC transporter
    0.00034   21.0   0.6     0.0011   19.3   0.2    2.1  2  AAA_16        AAA ATPase domain
     0.0047   16.6   0.0     0.0091   15.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0068   16.7   0.1      0.013   15.8   0.1    1.4  1  AAA_22        AAA domain
  ------ inclusion threshold ------
       0.01   15.4   0.1       0.95    9.0   0.1    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.027   14.6   0.3      0.074   13.2   0.1    1.8  2  AAA_33        AAA domain
      0.028   14.6   0.0      0.046   13.9   0.0    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.087   12.7   0.0       0.18   11.7   0.0    1.5  1  NACHT         NACHT domain
        0.1   12.2   0.0       0.89    9.1   0.0    2.1  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.0   0.0       0.19   11.3   0.0    1.3  1  Ras           Ras family
       0.16   11.3   0.2       0.37   10.1   0.1    1.6  2  AIG1          AIG1 family
       0.17   11.8   0.0       0.34   10.8   0.0    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.21   11.4   0.1       0.51   10.2   0.1    1.6  1  HNH_repeat    Homing endonuclease repeat
       0.24   11.8   0.0       0.41   11.1   0.0    1.3  1  RNA_helicase  RNA helicase
        0.3   10.3   0.0       0.43    9.8   0.0    1.2  1  Septin        Septin


Domain annotation for each model (and alignments):
>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   0.0   1.2e-43   1.3e-40       3     166 ..      97     267 ..      95     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 1.2e-43
                                    --S-EETTTT..........EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHH CS
                    RsgA_GTPase   3 eRknelvrpk..........vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeel 72 
                                    +R+++l+r++          vaN dqllivv+l++p  ++ l+dr+L++a + g++p+++l+K+Dl+  e     + +++
  gi|121639118|ref|YP_979342.1|  97 PRRTVLRRTAddtdptervvVANADQLLIVVALADPPPRTGLVDRALIAAYAGGLTPILCLTKTDLAPAEP----FDKQF 172
                                    8999**999999*******************************************************9999....89999 PP

                                    HHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETT. CS
                    RsgA_GTPase  73 ealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelae. 151
                                    ++l+++v++  ++  + l ++++ll++k++vl+G+SGvGKStL+n+l+pe++ ++gev e  grG+hT+t++  l+l + 
  gi|121639118|ref|YP_979342.1| 173 ADLELTVTAAGVD--DPLLAVADLLAGKITVLLGHSGVGKSTLVNRLVPEADRAVGEVTE-IGRGRHTSTRSVALPLGDt 249
                                    9999999988888..99*****************************************98.8***********9998777 PP

                                    ...TEEEESS-SSSS--G CS
                    RsgA_GTPase 152 ...gglliDtPGfreldl 166
                                       +g++iDtPG+r+++l
  gi|121639118|ref|YP_979342.1| 250 lsgSGWVIDTPGIRSFGL 267
                                    7779***********997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.2e-08   1.3e-05       3      58 ..     201     263 ..     199     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                                    EEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEE......ETTEEEEEEECGGCSS CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvk......lkgkeielvDtpGlie 58 
                                    +++G++ vGKStL+n+l+ e    v++    g  r++ ++ v+      l+g +  ++DtpG i 
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEaDRAVGEVTeiGRGRHTSTRSVAlplgdtLSG-SGWVIDTPG-IR 263
                                    689***************8753444444433777788888777665554334.679******.53 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1     5e-08   5.2e-05       8      43 ..     194     229 ..     191     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-08
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeil 43 
                                    l +g++++++G++G GKStL++ l  + + + Ge++
  gi|121639118|ref|YP_979342.1| 194 LLAGKITVLLGHSGVGKSTLVNRLVPEADRAVGEVT 229
                                    5689**************************999994 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.5   1.5e+03     134     150 ..      66      82 ..      55     152 .. 0.58
   2 !   19.3   0.2   1.1e-06    0.0011      22      52 ..     197     225 ..     186     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                         AAA_16 134 erplvlvlDdlqwadea 150
                                    +r+ ++v Dd++ + + 
  gi|121639118|ref|YP_979342.1|  66 GRTPIVVGDDVDVVGDL 82 
                                    55555555555533331 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekdg 52 
                                    g   +++l G+sGvGKs+lv++l  ++ ++ 
  gi|121639118|ref|YP_979342.1| 197 G--KITVLLGHSGVGKSTLVNRLVPEADRAV 225
                                    4..789**************99887777773 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.6e-06    0.0091      22      39 ..     196     214 ..     190     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-06
                         AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                    +g +t+l G+sG+GKSTl+
  gi|121639118|ref|YP_979342.1| 196 AGkITVLLGHSGVGKSTLV 214
                                    46699*************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.2e-05     0.013       6      30 ..     198     222 ..     195     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqld 30 
                                    +i+v+ G+sG+GK+tl++rl+ ++d
  gi|121639118|ref|YP_979342.1| 198 KITVLLGHSGVGKSTLVNRLVPEAD 222
                                    799*****************98875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.057        61      94     145 ..     120     174 ..     111     187 .. 0.67
   2 ?    9.0   0.1    0.0009      0.95       7      29 ..     201     223 ..     198     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.057
                                    -SEEEEEEETTTB..STHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHH CS
                       GTP_EFTU  94 lDgavlvvdaveG..vepqteevlrlalkegvpiivfiNKmDrl.kaelkeivee 145
                                    +D  ++vv+ ++    +    + l  a + g+ +i++++K D +  + ++++  +
  gi|121639118|ref|YP_979342.1| 120 ADQLLIVVALADPppRTGLVDRALIAAYAGGLTPILCLTKTDLApAEPFDKQFAD 174
                                    555566665554422333345667778888999**********964445555444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0009
                                    EEEESTTSSHHHHHHHHHHHTTS CS
                       GTP_EFTU   7 giighvDhGKtTLtdrLlyktga 29 
                                    +++gh   GK+TL+ rL+ ++ +
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEADR 223
                                    679**************966654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   3.4e+03      62      78 ..      89     105 ..      53     127 .. 0.65
   2 ?   13.2   0.1     7e-05     0.074       2      22 ..     200     220 ..     199     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                         AAA_33  62 larkalsagrnvildat 78 
                                    lar++++a r ++l+ t
  gi|121639118|ref|YP_979342.1|  89 LARIVRRAPRRTVLRRT 105
                                    44455555555555444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkk 22 
                                    ++l G++G+GKstl+ rl+ +
  gi|121639118|ref|YP_979342.1| 200 TVLLGHSGVGKSTLVNRLVPE 220
                                    5789*************9854 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.4e-05     0.046       3      21 ..     201     219 ..     198     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                    EEESSTTSSHHHHHHCHCT CS
                            Roc   3 vlvGdsgvGKtsllkrfve 21 
                                    vl+G sgvGK++l++r+v 
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVP 219
                                    89**************985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.18       3      24 ..     200     221 ..     198     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                     +l G +G+GK+tL+ +l+ ++
  gi|121639118|ref|YP_979342.1| 200 TVLLGHSGVGKSTLVNRLVPEA 221
                                    6899*************99765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.42   4.4e+02     144     161 ..     154     171 ..     137     182 .. 0.82
   2 ?    9.1   0.0   0.00085      0.89       2      23 ..     199     220 ..     198     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.42
                                    EEEEE-HHHHCHC...HHH CS
                           cobW 144 llvlnKtDlldee.allek 161
                                    +l l+KtDl+++e ++ ++
  gi|121639118|ref|YP_979342.1| 154 ILCLTKTDLAPAEpFD-KQ 171
                                    6789*******99766.54 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                                    EEEEEESTTCCHHHHHHHHHCT CS
                           cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                    +tvl G  G GK+tL+n+l+ +
  gi|121639118|ref|YP_979342.1| 199 ITVLLGHSGVGKSTLVNRLVPE 220
                                    799****************943 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.19       3      22 ..     201     220 ..     198     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                    EEEESTTSSHHHHHHHHHHS CS
                            Ras   3 vlvGdsavGKtslllrfvkd 22 
                                    vl+G s+vGK++l++r v +
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPE 220
                                    99*************98865 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.7   4.9e+03     141     159 ..      84     102 ..      82     116 .. 0.78
   2 ?   10.1   0.1   0.00035      0.37       4      62 ..     201     265 ..     198     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.7
                                    HH-HHHHHHHHHTTTSEEE CS
                           AIG1 141 sspeaLkevlkecgnRvvl 159
                                    + p++L ++++   +R+vl
  gi|121639118|ref|YP_979342.1|  84 GRPDTLARIVRRAPRRTVL 102
                                    5789999999999999887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                                    EEESSTTSSHHHHHHHHHTS--.SS--TTTS---SS-EEEEE.EETTEEEE....EEE--SCCCT CS
                           AIG1   4 vlvGktgnGkSaTgNsilgkka.Fesklsaqsvtkkcqkksr.twdgkkin....ViDTPglfdl 62 
                                    vl+G +g+GkS+ +N ++ +      ++++ +  ++ +++s   + g +++    ViDTPg+ + 
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEADrAVGEVTEIGRGRHTSTRSVaLPLGDTLSgsgwVIDTPGIRSF 265
                                    8***************9865441223333333333333333336677777555559999999664 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.34       3      33 ..     201     231 ..     199     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                           MobB   3 givgksgsGKTtLleklipelkarglrvgti 33 
                                     + g+sg GK tL+++l+pe  +   +v  i
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEADRAVGEVTEI 231
                                    578****************988776666655 PP

>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00049      0.51      10      19 ..      61      70 ..      61      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                     HNH_repeat 10 qAaELGRtPk 19
                                   +A ELGRtP 
  gi|121639118|ref|YP_979342.1| 61 RARELGRTPI 70
                                   799******6 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.41       2      24 ..     201     223 ..     200     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                    +l G+sg+GKStl+++L+ +  +
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEADR 223
                                    689*************9877655 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00041      0.43       8      31 ..     201     224 ..     197     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                                    EEEEBTTSSCCCCCCTTSSSS--- CS
                         Septin   8 mvvGesglGkttlintlfetdlie 31 
                                    ++ G+sg+Gk+tl+n l+ + +  
  gi|121639118|ref|YP_979342.1| 201 VLLGHSGVGKSTLVNRLVPEADRA 224
                                    457**************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2207.27
//
Query:       gi|121639119|ref|YP_979343.1|  [L=427]
Description: linoleoyl-CoA desaturase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-37  128.7   5.2    4.5e-37  128.3   5.2    1.1  1  FA_desaturase    Fatty acid desaturase
  ------ inclusion threshold ------
      0.069   13.2   0.7       0.15   12.1   0.7    1.5  1  Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   5.2     5e-41   4.5e-37       2     252 ..      69     339 ..      66     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 5e-41
                  FA_desaturase   2 swlalllalllglfllgitg.slaHeaaHgalfkkrklnrwlndllgal..lglplgisysawrisH.lrHHay..tngp 75 
                                    +w+  +  l+lg+   +i    ++H+++Hg        + w+nd   +     + +  s+++wr++H ++HH+y  + g 
  gi|121639119|ref|YP_979343.1|  69 AWWTGA--LTLGVA-KIIENmEIGHNVMHG-------QWDWMNDPEIHSstWEWDMSGSSKHWRYTHnFVHHKYtnILGM 138
                                    355555..9****9.888888********9.......9****8877666225555556****************9999** PP

                  FA_desaturase  76 deDpdlaplalsrfeglfry.llrlllgllvlg...wllalvlglwlrrlarrrapsksrrrk........wrllawlll 143
                                    d+D+ +++l+ +r +++ ry +++ ++ + ++    w +al+++++ ++++ r ++ + + r         +++   +++
  gi|121639119|ref|YP_979343.1| 139 DDDVGYGMLRVTRDQRWKRYnIFNVVWNTILAIgfeWGVALQHLEIGKIFKGRADREAAKTRLrefsakagRQVFKDYVA 218
                                    **********9*********955555555555555699999999866666666665555555577778888999999999 PP

                  FA_desaturase 144 llawlglwlalllllglalllwlvplllllfllalvlnyveHyg................gdwgerqvetsasirsaswl 207
                                    ++a++ l  ++ + + l   + +v+ ++ +++   v  ++ H+                 g+w++rq+ +sa+++ a++ 
  gi|121639119|ref|YP_979343.1| 219 FPALTSLSPGATYRSTLT--ANVVANVIRNVWSNAV-IFCGHFPdgaekftktdmigepkGQWYLRQMLGSANFN-AGPA 294
                                    999999999999999888..8899999999988888.9****99*******************************.**** PP

                  FA_desaturase 208 lnlltgnlnyHieHHlfPgvpwyrLpelhrrlrellpehglpyrs 252
                                    l++++gnl+++ieHHl+P++p +rL+e++ r+re++++++lpy++
  gi|121639119|ref|YP_979343.1| 295 LRFMSGNLCHQIEHHLYPDLPSNRLHEISVRVREVCDRYDLPYTT 339
                                    *******************************************86 PP

>> Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   1.7e-05      0.15      14      32 ..     233     251 ..     228     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                Chlorovi_GP_rpt  14 atiPgtqniDIiGNVvatg 32 
                                    +t+++++++++i+NV +++
  gi|121639119|ref|YP_979343.1| 233 STLTANVVANVIRNVWSNA 251
                                    689*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2735.11
//
Query:       gi|121639120|ref|YP_979344.1|  [L=380]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-10   40.1   0.5    4.5e-10   39.3   0.5    1.4  1  Fer2           2Fe-2S iron-sulfur cluster binding domain
    1.1e-09   38.5   0.0    1.9e-09   37.8   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    1.7e-08   35.1   0.0    3.2e-08   34.2   0.0    1.5  1  NAD_binding_1  Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.053   13.6   0.0        0.1   12.7   0.0    1.4  1  NAD_binding_6  Ferric reductase NAD binding domain
        0.3   11.2   1.6        1.3    9.2   0.1    2.4  3  MlrC_C         MlrC C-terminus


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.5   1.3e-13   4.5e-10       5      76 ..     307     371 ..     302     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.3e-13
                                    TEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGGSE CS
                           Fer2   5 gkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCqti 76 
                                    gk v +   d  t+l+da e + g+ +p++C++g C++C+v+++eg+v        +g++ + g ++ +C++ 
  gi|121639120|ref|YP_979344.1| 307 GKSVAA---DAATSLMDAGEGA-GVQLPFGCRMGICQSCVVDLVEGHVrD----LRTGQRHEPGTRVQTCVSA 371
                                    444444...44888******88.*************************52....3456666667778999876 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.3e-13   1.9e-09      28      97 ..      88     161 ..      70     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.3e-13
                                    ----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEE...EE--TT-HHHHHH.HCS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  28 lglpvGqhvflrlkikgeaviRsYtpissenekGelell...vkvypgGkmsqaL.delkigdtleikGPlGkf 97 
                                    +++ +Gq++ + l ++g   +RsY+++ss+ ++G   ++   vk +p+G +s +L   +k+g+ +++ +P+G+f
  gi|121639120|ref|YP_979344.1|  88 FDYQPGQYIGIGLLVDGCWRWRSYSLTSSPAASGSARMVtvtVKAMPEGFLSTHLvAGVKPGTIVRLAAPQGNF 161
                                    6899***************************999866543339999*********888**************99 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.9e-12   3.2e-08       1     104 [.     173     266 ..     173     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.9e-12
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT.EEEEEEEESSCTTTSSSEESSHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg.rlkvvavvsreeagweggkgrvqd 79 
                                    ++ +G+Gi+Pv+s+lr+++++ ++ t vv ++ ++t +d+++ +el +la+ +pg rl v ++      +    +gr++ 
  gi|121639120|ref|YP_979344.1| 173 FLTAGSGITPVMSMLRTLVRR-NQITDVVHLHSAPTAADVMFGAELAALAADHPGyRLSVRET------RA---QGRLDL 242
                                    6789****************9.888******************************66544444......22...455555 PP

                                    HHHHHHHHHSSTTEEEEEECSHHHH CS
                  NAD_binding_1  80 alleellslkkeethvyvCGppgMi 104
                                      + + ++ +  e ++  CGp+g  
  gi|121639120|ref|YP_979344.1| 243 TRIGQQVP-DWRERQTWACGPEGVL 266
                                    55555555.4666777777777665 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.9e-05       0.1       4      28 ..     171     195 ..     170     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6   4 vllvagGiGitpfisilkdllkksk 28 
                                    +l++++G+Gitp++s+l+ l+++ +
  gi|121639120|ref|YP_979344.1| 171 ILFLTAGSGITPVMSMLRTLVRRNQ 195
                                    6899****************99877 PP

>> MlrC_C  MlrC C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.26   9.4e+02      14      49 ..     181     216 ..     175     241 .. 0.78
   2 ?   -2.2   0.0       1.1   3.9e+03      41      60 ..     288     307 ..     283     311 .. 0.78
   3 ?    9.2   0.1   0.00035       1.3      39      95 ..     312     370 ..     306     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                                    ----HHHHHHHHH-TT--EEEEEE-HHHHHHHHHH- CS
                         MlrC_C  14 gdvtalLrellargekkvlvasivDpeavaaaaaag 49 
                                      v+ +Lr l++r++ + +v +   p a+++++ a+
  gi|121639120|ref|YP_979344.1| 181 TPVMSMLRTLVRRNQITDVVHLHSAPTAADVMFGAE 216
                                    557899999999999777777777788877777665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                    HHHHHHHH-TT-EEEEEES- CS
                         MlrC_C  41 avaaaaaagvGatveltlGg 60 
                                    av   a ag+G+tv+++  g
  gi|121639120|ref|YP_979344.1| 288 AVSKTAPAGAGGTVTFARSG 307
                                    77888889999999987555 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHH-TT-EEEEEES-SS-TTS.--E.EEEEEEEEEEEEEEE--SSTTTT.-E CS
                         MlrC_C  39 peavaaaaaagvGatveltlGgkvdalhgepv.eltgtVealsdgrytaegpmltg.qe 95 
                                    ++a+  +++ag+Ga v+l +G +++  ++  v  ++g+V+ l+ g++++ g + +   +
  gi|121639120|ref|YP_979344.1| 312 ADAATSLMDAGEGAGVQLPFGCRMGICQSCVVdLVEGHVRDLRTGQRHEPGTRVQTcVS 370
                                    67899999*******************999995589************97766555344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2816.45
//
Query:       gi|121639121|ref|YP_979345.1|  [L=169]
Description: hypothetical protein BCG_3261c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1295.25
//
Query:       gi|121639122|ref|YP_979346.1|  [L=295]
Description: transcriptional regulatory protein pvdS [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.3e-111  369.9   0.4     5e-111  369.7   0.4    1.0  1  PPK2      Polyphosphate kinase 2 (PPK2)
  ------ inclusion threshold ------
      0.072   13.0   0.1       0.13   12.1   0.1    1.4  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.7   0.4  5.6e-115    5e-111       2     228 ..      33     259 ..      32     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.7 bits;  conditional E-value: 5.6e-115
                                    --HHHHHHHHHHHHHHHHHHHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHHTS-TTHHH CS
                           PPK2   2 lskdeyeeelaklqielvklqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEksqwylqRy 81 
                                    +s++ y++el++lq+e+vklqe+++++g++lvvifegrD+AGKgGaikr+te+lnprvar++al+aPt++E++qwy+qRy
  gi|121639122|ref|YP_979346.1|  33 ISDAVYQAELFRLQTEFVKLQEWARHSGARLVVIFEGRDGAGKGGAIKRITEYLNPRVARIAALPAPTDRERGQWYYQRY 112
                                    78899*************************************************************************** PP

                                    HTT---TT-EEEEES-GGGGGTHHHHHTSS-HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEE--HHHHHHHHHHHHHSS- CS
                           PPK2  82 vehlPakgeivlFdRswYnragvervmgfctdkeaerflreipefErmlvesgillvKfwlsiskeeqleRfkeRredPl 161
                                    ++hlPakgeivlFdRswYnragve+vmgfct++e+  flr++p fE+ml+++gill K+w+s+s++eql+Rfk+Rr+dP+
  gi|121639122|ref|YP_979346.1| 113 IAHLPAKGEIVLFDRSWYNRAGVEKVMGFCTPQEYVLFLRQTPIFEQMLIDDGILLRKYWFSVSDAEQLRRFKARRNDPV 192
                                    ******************************************************************************** PP

                                    CCC---CCCCCHHHCHHHHHHHHHHHHHHH--SSS-EEEEE-SSHHHHHHHHHHHHHHHHHHHHHHT CS
                           PPK2 162 kqwKlsplDlksrekWddytkakeemlartdteeaPWivveaddKkrarlnvirtllkalkyeekek 228
                                    +qwKlsp+Dl+s+ +W+dy++ak+em+ +tdt+++PW+vve+d Kk+arln++++ll++++y+++ek
  gi|121639122|ref|YP_979346.1| 193 RQWKLSPMDLESVYRWEDYSRAKDEMMVHTDTPVSPWYVVESDIKKHARLNMMAHLLSTIDYADVEK 259
                                    **************************************************************99876 PP

>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.5e-05      0.13      35      79 ..     202     246 ..     197     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                    EEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-E CS
                          CutA1  35 ieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpe 79 
                                    +eSvYrW++    ++E+++   t  + +  +e+ +k++   ++++
  gi|121639122|ref|YP_979346.1| 202 LESVYRWEDYSRAKDEMMVHTDTPVSPWYVVESDIKKHARLNMMA 246
                                    79*******************************999988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2025.31
//
Query:       gi|121639123|ref|YP_979347.1|  [L=469]
Description: hypothetical protein BCG_3263c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-89  298.4   0.9    7.7e-89  297.9   0.9    1.2  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    2.5e-19   69.7   0.1      4e-19   69.0   0.1    1.3  1  DUF1298         Protein of unknown function (DUF1298)


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.9   0.9   8.6e-93   7.7e-89       1     264 []       5     271 ..       5     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 297.9 bits;  conditional E-value: 8.6e-93
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    Ls++Da+f++le+++tpm+vg l +l++p++g ++   ++l+e++eqr++++pr+rqkv+e++lgla+pvW++d+dfD++
  gi|121639123|ref|YP_979347.1|   5 LSASDASFYQLENTATPMYVGLLLILRRPRAGLSY---EALLETVEQRLPQIPRYRQKVQEVKLGLARPVWIDDRDFDIT 81 
                                    799**************************777777...9***************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yHvRr+alp+PG++++l+el++rLa++pLD+srPlWe++++EGle++riA+++k H+Ali+Gv++l++ + ++d+++++p
  gi|121639123|ref|YP_979347.1|  82 YHVRRSALPSPGSDEQLHELIARLAARPLDKSRPLWEMYLVEGLEKNRIALYTKSHQALINGVTALAIGHVIADRTRRPP 161
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdr..srtqlrasg.alvglvaglgkvlgsvagvvssagrlleaal....earslvlpfaaprtplntpl 233
                                    ++pe ++vp+rd+  +r+ lra g +lv++ a+l++v ++vag+v+++g+l+e+++    +ar++++++a p++pln+++
  gi|121639123|ref|YP_979347.1| 162 AFPEDIWVPERDPgtTRLLLRAVGdWLVRPGAQLQAVGSAVAGLVTNSGQLVETGRkvldIARTVARGTA-PSSPLNATV 240
                                    *************887777777668*******************************99977888877765.5******** PP

                 WES_acyltransf 234 sraRrfaaaslpLadvkavakalgvtiNDvv 264
                                    sr+Rrf++a+++L+d+++v++++++++ Dvv
  gi|121639123|ref|YP_979347.1| 241 SRNRRFTVARASLDDYRTVRARYDCDVHDVV 271
                                    *****************************97 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   4.5e-23     4e-19       5     144 ..     322     464 ..     320     465 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.5e-23
                        DUF1298   5 igvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl....lsnttlviSNvpGPq 80 
                                    ++  l++Lp++  + + rl+++ +a++      + v ++ ++ l + l+pa + a  ++      ++ ++l+i+N pG q
  gi|121639123|ref|YP_979347.1| 322 VTPFLVDLPVGEGNAVVRLSQIAHATESNPTAASLVDARTIVTL-SGLAPATLHAMGVRVAtsfsARLFNLLITNAPGTQ 400
                                    556799*************************************9.***9999988775444555799************* PP

                        DUF1298  81 eelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    +++y+aG +l + y v p+l++qal i+v+Sy+g l +g+ +d+d+++d++ l   l +al+el
  gi|121639123|ref|YP_979347.1| 401 SQMYIAGTKLLETYSVPPLLHNQALAISVTSYNGMLYFGINADRDAMSDVDLLPGLLSQALDEL 464
                                    *************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3150.71
//
Query:       gi|121639124|ref|YP_979348.1|  [L=213]
Description: hypothetical protein BCG_3264 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1548.08
//
Query:       gi|121639125|ref|YP_979349.1|  [L=385]
Description: integral membrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-40  137.2  40.0    7.5e-40  136.9  40.0    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9  40.0   4.2e-44   7.5e-40       2     372 ..      13     367 ..      11     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 4.2e-44
                                    HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHH CS
                 Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglg.liepseedlevlselglilllFlaGleldlrelrknlksil 80 
                                    vll++ ++++g++arr+ l++i+++++aGl lG+ g   +++ + e + + + +g++lll+++Gle++  e+ + l+  l
  gi|121639125|ref|YP_979349.1|  13 VLLAV-LAVLGAVARRFALSPIPVYLLAGLSLGNGGILgVAAAG-EFIATGAPIGVVLLLLALGLEFSATEFASSLRHHL 90 
                                    33444.4444446********************98765277777.*********************************** PP

                                    HHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCH CS
                 Na_H_Exchanger  81 llallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvlla 160
                                      a + +++++   G ++++  +lg++ ++ l ++++  +++ +v++++l++++r+ +r    +l+++vl+D ++  +l 
  gi|121639125|ref|YP_979349.1|  91 PSAGVDIVLNATP-GAVAGW--LLGLDGVAILGLAGVTYISSSGVIARLLEDLRRLGNRETPAVLSVLVLEDFAMAAYLP 167
                                    *************.999999..689******************************************************* PP

                                    HHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHH CS
                 Na_H_Exchanger 161 vllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilg 240
                                    ++  la    ++++ l ++++ ++ +a+++ ++ +   w  ++ + +t+ d+e+ +l vl + l++a++ae+l+ s+++g
  gi|121639125|ref|YP_979349.1| 168 LFAVLA----TDGSWLEAVVGMTVAIAALLGAFAASYRWGHHVGRLVTHPDSEQLLLRVLGITLIVAAVAESLHASAAVG 243
                                    *****9....4444444444444444444444444444444544454557****************************** PP

                                    HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSS CS
                 Na_H_Exchanger 241 aflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllgl 320
                                    afl+Gl+l+ +e++ +++  l ++r +lf+++fF+ +Gls+d+  l   +s l+++l++ ++  +++++++++++r+ g+
  gi|121639125|ref|YP_979349.1| 244 AFLVGLTLT-GETADRARMVLTPLR-DLFATIFFLGIGLSVDPGKL---VSMLPVALALAAVTAATKVATGMFAARREGV 318
                                    *********.444444556688***.9*******************...9999999999999999*************** PP

                                    XHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHH CS
                 Na_H_Exchanger 321 slrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqG 372
                                     +r +l +g++++ rg+++l+++ l+ a+ ++   + al++++v+++ +v +
  gi|121639125|ref|YP_979349.1| 319 ARRGQLRAGTALVARGEFSLIIIGLAGAS-IPG--VAALATAYVFVMAIVGP 367
                                    ****************************9.555..56666666666666333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2704.00
//
Query:       gi|121639126|ref|YP_979350.1|  [L=160]
Description: hypothetical protein BCG_3266c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.2   1.0    1.1e-15   57.2   1.0    1.9  2  TrkA_C    TrkA-C domain


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1     0.098   1.8e+03      50      60 ..      22      32 ..      20      54 .. 0.72
   2 !   57.2   1.0     6e-20   1.1e-15       4      66 ..      90     154 ..      88     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.098
                                   T-EEEEEEEHH CS
                         TrkA_C 50 GDvllvvgsps 60
                                   GD++ +v+ +s
  gi|121639126|ref|YP_979350.1| 22 GDRIGIVARRS 32
                                   67776666554 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 6e-20
                                    EEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                         TrkA_C   4 vtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                    + ++ags +v+++l++ + r+r g+ +vai+R+ ++l +p++++vL++GDvl+v+g+ +++a ++
  gi|121639126|ref|YP_979350.1|  90 IHIRAGSLFVDRPLGDTRARTRtGASIVAIVRDeDVLASPGPTDVLRAGDVLIVIGTEDGIAGVE 154
                                    789******************************9**************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1152.02
//
Query:       gi|121639127|ref|YP_979351.1|  [L=244]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-06   25.9  12.9      6e-06   25.9  12.9    1.5  2  NnrU      NnrU protein
      0.002   18.5   3.4      0.002   18.5   3.4    2.5  3  PEMT      Phospholipid methyltransferase
     0.0082   16.1   1.1     0.0082   16.1   1.1    1.7  2  Lamprin   Lamprin
  ------ inclusion threshold ------
      0.026   15.0   0.2      0.088   13.2   0.2    1.9  1  ICMT      Isoprenylcysteine carboxyl methyltransferase (ICMT)
        3.3    7.7  10.8        0.5   10.4   5.3    2.3  2  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.5       2.6   9.4e+03      37     200 ..       8      19 ..       3      27 .. 0.46
   2 !   25.9  12.9   1.7e-09     6e-06       4     146 ..      54     207 ..      51     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.6
                           NnrU  37 lyslvsllglvlliigfgaaryevllWeppawlrhlalllmlvafillaaallpgnplsvglkadlaetgivritrHPml 116
                                    +y ++s                                                                          
  gi|121639127|ref|YP_979351.1|   8 IYGAAS-------------------------------------------------------------------------- 13 
                                    344444.......................................................................... PP

                           NnrU 117 lgvaiWAlaHllanGdlasvllfgglllwalvgviaidrrkrrrlgeewealaartsvvpfaaileedllavvlgvvlwl 196
                                                                                                                  +l
  gi|121639127|ref|YP_979351.1|  14 ------------------------------------------------------------------------------YL 15 
                                    ..............................................................................44 PP

                           NnrU 197 vlll 200
                                    v+l+
  gi|121639127|ref|YP_979351.1|  16 VFLV 19 
                                    4333 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.7e-09
                           NnrU   4 lglllFlgaHsvraapalRarliarlGergykilyslvsllglvlliigfgaaryevllWepp.awlrhlalllmlvafi 82 
                                    ++l +F++ Hsv+a+++++++  + +     +  y l++ ++l ll + +++++++  +W++  ++ r + ++l +++  
  gi|121639127|ref|YP_979351.1|  54 VLLGVFAVQHSVMARQGFKRWWTRFVPPSIERSTYVLLASVALLLLYWQWRTMPAV--IWDVRqPAGRVALWALFWLGWA 131
                                    56779**********************9999************************9..9*9987999************* PP

                           NnrU  83 llaaallpgnplsvglka..............dlaetgivritrHPmllgvai..WAlaHllanGdlasvllfgglllwa 146
                                     ++ +++  n++ + + +                +++ ++r++rHP++lg+++  WA+    ++ +  ++l+ +g   + 
  gi|121639127|ref|YP_979351.1| 132 TVLTSTFMINHFELFGLRqvylawrgkpyteiGFQAHLLYRWVRHPIMLGFVVafWAT----PMMTAGHLLFAIGATGYI 207
                                    ***********987655559999*999888777788889***********86433985....333344444444444444 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.3   1.2e+04      10      17 ..      54      61 ..      46      76 .. 0.48
   2 ?   -2.8   0.1       2.3   8.3e+03      75      88 ..      89     102 ..      83     109 .. 0.52
   3 !   18.5   3.4   5.5e-07     0.002       9      99 ..     125     219 ..     119     226 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                           PEMT 10 ialglllv 17
                                   ++lg++ v
  gi|121639127|ref|YP_979351.1| 54 VLLGVFAV 61
                                   33333222 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                           PEMT  75 glllallvllvyli 88 
                                    +ll+++ +ll+y+ 
  gi|121639127|ref|YP_979351.1|  89 VLLASVALLLLYWQ 102
                                    34444444444443 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 5.5e-07
                           PEMT   9 lialglllvlssiealgefgtfygdfFlelmd.......klvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllall 81 
                                    l++lg ++vl+s+  ++ f+ f     +   +           + +Yr++++P  +g +++f+++ ++t   +  l+a+ 
  gi|121639127|ref|YP_979351.1| 125 LFWLGWATVLTSTFMINHFELFGLRQVYLAWRgkpyteiGFQAHLLYRWVRHPIMLGFVVAFWATPMMTAGHL--LFAIG 202
                                    5666666666666666666555433322222233444555666779**********************98776..66666 PP

                           PEMT  82 vllvylialkfvEephla 99 
                                    ++  +l+al+ +Ee+ l 
  gi|121639127|ref|YP_979351.1| 203 ATGYILVALQ-FEERDLL 219
                                    6666777778.5554443 PP

>> Lamprin  Lamprin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.1   2.3e-06    0.0082      90     135 ..       4      49 ..       1      53 [. 0.89
   2 ?   -3.0   0.1       1.9   6.7e+03      31      45 ..     192     206 ..     174     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                        Lamprin  90 ygglgyhaapyhhalgglgyplgigagvvaphvvkskvaaplapvv 135
                                    y ++ y aa+y   l  +gy +g    vv p  v+  +aap+   v
  gi|121639127|ref|YP_979351.1|   4 YLTIIYGAASYLVFLVAFGYAIGFVGDVVVPRTVDHAIAAPIGQAV 49 
                                    7778899**********************************97655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                        Lamprin  31 lstgflghpvgglgy 45 
                                    +++g+l   +g  gy
  gi|121639127|ref|YP_979351.1| 192 MTAGHLLFAIGATGY 206
                                    334444444444444 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.5e-05     0.088      38      71 ..     168     200 ..     161     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                           ICMT  38 sglykylrHPnYllfvilelatllLlcnakltal 71 
                                    + ly+++rHP  l+fv+ +  + ++++  +l+ +
  gi|121639127|ref|YP_979351.1| 168 HLLYRWVRHPIMLGFVV-AFWATPMMTAGHLLFA 200
                                    679***********555.5555555554422222 PP

>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.3   0.00014       0.5      60     142 ..      42     130 ..       4     141 .. 0.69
   2 ?   -1.6   0.2      0.68   2.4e+03      87      87 ..     197     197 ..     177     222 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                         SpoIIM  60 giptilvllinGfvlG..av.aalvaefgglllflllilPhgilelpaiiiagaaglrlgkal....rsrrkalkeakre 132
                                      p+  ++++n ++lG  av ++++a++g +  ++   +P  i   + +++a++a l l +++       ++ ++ a+r 
  gi|121639127|ref|YP_979351.1|  42 AAPIGQAVVVNLVLLGvfAVqHSVMARQG-FKRWWTRFVPPSIERSTYVLLASVALLLLYWQWrtmpAVIWDVRQPAGRV 120
                                    344444559999****9988566666665.*************9999999999999999999988874456666677777 PP

                         SpoIIM 133 llklllllvp 142
                                    +l+ l++l  
  gi|121639127|ref|YP_979351.1| 121 ALWALFWLGW 130
                                    7777777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.68
                         SpoIIM  87 l 87 
                                    l
  gi|121639127|ref|YP_979351.1| 197 L 197
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1552.05
//
Query:       gi|121639128|ref|YP_979352.1|  [L=1048]
Description: transmembrane transport protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-44  150.3  57.4    1.1e-35  123.3  41.5    3.2  2  MFS_1         Major Facilitator Superfamily
    4.5e-22   79.2   3.1    3.5e-20   73.1   3.1    2.5  1  Patatin       Patatin-like phospholipase
    6.3e-20   71.0   0.0    1.3e-19   70.1   0.0    1.5  1  cNMP_binding  Cyclic nucleotide-binding domain
    1.5e-07   30.3  10.9    1.5e-07   30.3  10.9    2.6  3  MFS_3         Transmembrane secretion effector
    0.00042   19.3  10.2    0.00042   19.3  10.2    3.2  3  Sugar_tr      Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3  41.5     3e-39   1.1e-35       3     270 ..      31     340 ..      29     340 .. 0.88
   2 !   37.1  18.9   4.8e-13   1.7e-09       3     177 ..     285     474 ..     283     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 3e-39
                          MFS_1   3 laaflsalarsilgpalplalaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                    ++afl++l+++i+++a+p  +++++  ++  +++++l +y +++a++++ +Grl+d +Grrr++l g+l+f ++ +l+++
  gi|121639128|ref|YP_979352.1|  31 FGAFLAFLDSTIVNIAFP-DIQRSFPsYDIGSLSWILNGYNIVFAAFMVAAGRLADLLGRRRTFLSGVLVFTIAsGLCAV 109
                                    89****************.9*99997799999******************************************666666 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                      +++   l+++rvlqG+ga++l+pa++al+++ f   +r+ aigl++a+++++a lgp++ggll++++gWr+v +++ +
  gi|121639128|ref|YP_979352.1| 110 --AGSVeQLVAFRVLQGIGAAILVPASLALVVEGFDAARRAHAIGLWGAAAAIAAGLGPPIGGLLVEWAGWRWVLLVNVP 187
                                    ..66666************************************************************************* PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeee...............................................kgtg 192
                                    ++++a++      +  +++ +  +  +++                                               ++  
  gi|121639128|ref|YP_979352.1| 188 LGIVAAIA--TKRMLVESRASGRRRMPDLrgalllavtlglvtlglvkgpdwgwlsvatvgsflasvltsvgfvhsSRSH 265
                                    *****997..44444444444444455555899*********************************************** PP

                          MFS_1 193 paplvpawkallkdpvlw..illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdr 270
                                    paplv+   all+++ +    ll+ ++ +  gf+ +  +  lyl+ v ++s ll ag+++a +a+v+a++a  +gr++ r
  gi|121639128|ref|YP_979352.1| 266 PAPLVE--PALLRSRSFVagNLLTLVAAA--GFYCYGLTHVLYLNYVWHYS-LLKAGFAIAPAAVVAAVVAAALGRVAGR 340
                                    ******..666666656434455555555..5555666666666*******.***************9999999998866 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 4.8e-13
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll. 80 
                                    l+++++a++++++g++  l+l+   ++s   +g++++  a++aav +  lGr++ r+G+r ++l+g+l++a + +++l  
  gi|121639128|ref|YP_979352.1| 285 LLTLVAAAGFYCYGLTHVLYLNYVWHYSLLKAGFAIAPAAVVAAVVAAALGRVAGRHGHRVIVLVGALVWAGSlVWYLQr 364
                                    578999***********99******************************************9999999999993444444 PP

                          MFS_1  81 fa..sslw.lllvlrvlqGlgagalfp.agaaliadwfpkeergraigllsagfslGailgpllggllasslg....... 149
                                    ++  + +  ++l + +lqG+g ga +p ++ a++a+++++   +   +++s++ +lGa+lg ++  +l+           
  gi|121639128|ref|YP_979352.1| 365 VGsePDFLrVWLPGQLLQGIGVGATLPvLSSAALAEVAKGGSYATSSAVVSTTRQLGAVLGVAVMVILIGKPEhgtaeea 444
                                    437899999*************665551678899999999*****************************55557787665 PP

                          MFS_1 150 ....Wravfyilaivsllafvlfllll...peepp 177
                                        W     ++a+++++a+ +++++l    ++p+
  gi|121639128|ref|YP_979352.1| 445 lrrgW-----AMAAICFIAVAVAAAVLgrtNRNPV 474
                                    54444.....6666666665544444423322333 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   3.1   9.8e-24   3.5e-20       1     200 [.     790     946 ..     790     949 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 9.8e-24
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanla 80 
                                    Lvl+GGG+rg+++lg+l +L ++ g  +d ++GtS GA+ia + a+g+d+a  ++  ++ +++ +  +d           
  gi|121639128|ref|YP_979352.1| 790 LVLGGGGARGFAHLGVLDEL-ERVGVTIDRFAGTSMGAVIAVFGACGMDAATADAYAYEYFIRHNPLSD----------- 857
                                    8*******************.*******************************99999999999999999........... PP

                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglyteddd 160
                                          +  +gl  +    +ll+++++d  +++l + ++++                             +  + +    
  gi|121639128|ref|YP_979352.1| 858 ----YAFPVRGLVRGRRTLTLLEAAFGDRLVEELPKEFRCV---------------------------SVDLLARRPVVH 906
                                    ....7888888899999999999999999999999999999...........................556666666677 PP

                        Patatin 161 ddvdladavraSsafPglfppvsldgelyvDGGilsNvPi 200
                                    + ++l+d++ +S+ +Pg++pp+ ++g+l vDGG+l+N+P+
  gi|121639128|ref|YP_979352.1| 907 RRGRLVDVIGCSLRLPGIYPPQVYNGRLHVDGGVLDNLPV 946
                                    79*************************************8 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   3.5e-23   1.3e-19       2      86 ..     534     613 ..     533     615 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.5e-23
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    ++++ag ++f++Gdp dsly++++G+v+v    +d    vl++lg+G+++Gel+ll ++pr+atv+Al d++l++l++++
  gi|121639128|ref|YP_979352.1| 534 VELEAGCYLFHEGDPSDSLYVIRTGRVQV---LQDS--IVLKELGRGEVLGELGLLIDAPRSATVRALRDTKLVRLTKAQ 608
                                    5799*************************...4555..7*****************98********************** PP

                                    HHHHH CS
                   cNMP_binding  82 flell 86 
                                    f+e+ 
  gi|121639128|ref|YP_979352.1| 609 FDEIA 613
                                    **986 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3  10.9   4.1e-11   1.5e-07      61     194 ..      76     202 ..      70     228 .. 0.87
   2 ?   -3.0   2.0      0.49   1.7e+03     257     288 ..     378     409 ..     306     470 .. 0.70
   3 ?   -3.2   0.1      0.56     2e+03     143     175 ..     809     840 ..     808     846 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4.1e-11
                          MFS_3  61 lsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaA 140
                                    + + aG laD + rR+ +l + l+  ++s l +v       s+  l+a+ +l giGaa+  Pa  A v e  ++     A
  gi|121639128|ref|YP_979352.1|  76 FMVAAGRLADLLGRRRTFLSGVLVFTIASGLCAVAG-----SVEQLVAFRVLQGIGAAILVPASLALVVEGFDAARRAHA 150
                                    56889******************9999998877654.....67789********************************** PP

                          MFS_3 141 vaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevr 194
                                    + L      ia   GP +gG+lv ++G  ++  vn+   l +++a++  +  v+
  gi|121639128|ref|YP_979352.1| 151 IGLWGAAAAIAAGLGPPIGGLLVEWAGWRWVLLVNVP--LGIVAAIATKRMLVE 202
                                    ********************************99984..556666655554444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.49
                          MFS_3 257 GillgalGvGAilgalllsrLRerlsserlvl 288
                                    G ll ++GvGA l  l+++ L e+ +     +
  gi|121639128|ref|YP_979352.1| 378 GQLLQGIGVGATLPVLSSAALAEVAKGGSYAT 409
                                    55666666666666666666655554444444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.56
                          MFS_3 143 LnsvginiaRsvGPAlgGvlvaavGaalafavn 175
                                    L+ vg+ i R +G  +g  ++a++Ga    a++
  gi|121639128|ref|YP_979352.1| 809 LERVGVTIDRFAGTSMG-AVIAVFGACGMDAAT 840
                                    6789999******9986.567999997655555 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3  10.2   1.2e-07   0.00042      49     147 ..      63     158 ..      26     196 .. 0.76
   2 ?    0.6   0.3     0.054   1.9e+02     284     360 ..     176     249 ..     168     266 .. 0.66
   3 ?    0.9   8.3     0.044   1.6e+02      59     167 ..     324     446 ..     274     470 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                                    HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                    ++i++ ++++ ++  + ag l+d +GR+ ++l ++++f i++ l+a+a    sve+l++ Rvl Gig+ +    +  ++ 
  gi|121639128|ref|YP_979352.1|  63 SWILNGYNIVFAAFMVAAGRLADLLGRRRTFLSGVLVFTIASGLCAVAG---SVEQLVAFRVLQGIGAAILVPASLALVV 139
                                    677777888877888899*******************************...***************9988777766666 PP

                                    TTS-SCCHHHHHHHHHHHH CS
                       Sugar_tr 129 EiApkklRgalvslyqlai 147
                                    E   ++ R   ++l+  a 
  gi|121639128|ref|YP_979352.1| 140 EGFDAARRAHAIGLWGAAA 158
                                    6655555555555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.054
                                    SS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHH CS
                       Sugar_tr 284 lglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfi 360
                                    +g    llv++ +g+v ++at   +  ++  GRR++  l +a  +++++ l  v+l lv++   ++ ++++ +  f+
  gi|121639128|ref|YP_979352.1| 176 AGWRWVLLVNVPLGIVAAIATKRMLVESRASGRRRMPDLRGALLLAVTLGL--VTLGLVKGP-DWGWLSVATVGSFL 249
                                    555566899999999999999999999999999988654444333333333..467777775.33444444444444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.044
                                    HHHHHHHHHHHHHHTTHHH..HHHHHHHHHHHHHHHHH-TTTT...SS-TGGGGGHHHHHHHHHHHH.HHHHHHHHTTS. CS
                       Sugar_tr  59 aiiGslfagllgdrfGRkk..slliaavlfvigavlqaaakgk...nsvevlivgRvlvGigvGlas.vlvPmyisEiA. 131
                                    a++ +++a  lg + GR    +++ +++l+ +g+++ ++   +     + v + g++l GigvG++  vl++  ++E+A 
  gi|121639128|ref|YP_979352.1| 324 AVVAAVVAAALGRVAGRHGhrVIVLVGALVWAGSLVWYLQRVGsepDFLRVWLPGQLLQGIGVGATLpVLSSAALAEVAk 403
                                    4455666666666666654114555778889999999999988565566677778*********9863789999*****5 PP

                                    ...-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-....T CS
                       Sugar_tr 132 ...pkklRgalvslyqlaitfGilvaaifglglnktsn....a 167
                                        ++    + +  ql+ ++G  v  i+  + ++ ++    +
  gi|121639128|ref|YP_979352.1| 404 ggsYATSSAVVSTTRQLGAVLGVAVMVILIGKPEHGTAeealR 446
                                    5522333344444556666666555444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1048 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.46
# Mc/sec: 6828.45
//
Query:       gi|121639129|ref|YP_979353.1|  [L=949]
Description: preprotein translocase subunit SecA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.2e-126  419.8   0.2   9.3e-126  419.0   0.2    1.4  1  SecA_DEAD     SecA DEAD-like domain
    3.8e-67  226.2   4.8    5.7e-67  225.6   4.0    1.7  2  SecA_SW       SecA Wing and Scaffold domain
    6.1e-36  123.5   0.4    2.6e-35  121.4   0.1    2.4  2  SecA_PP_bind  SecA preprotein cross-linking domain
     0.0089   15.8   0.0      0.021   14.6   0.0    1.6  1  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.12   12.6   0.4       0.34   11.1   0.4    1.8  1  Lge1          Transcriptional regulatory protein LGE1


Domain annotation for each model (and alignments):
>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.0   0.2  2.6e-129  9.3e-126       5     289 ..       6     382 ..       2     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 419.0 bits;  conditional E-value: 2.6e-129
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD   5 lgsknerelkklkkiveeineleeelkalsdeeLrakteelkerlaegea...ldellpeafalvreaakrvlgmrhydv 81 
                                    l+  + r +k+lkk+++ + +l++++++l+d+eLrakt+e+k+rla++++   ld+llpeafa+ reaa+rvl++r++dv
  gi|121639129|ref|YP_979353.1|   6 LRLGEGRMVKRLKKVADYVGTLSDDVEKLTDAELRAKTDEFKRRLADQKNpetLDDLLPEAFAVAREAAWRVLDQRPFDV 85 
                                    555677899************************************87653334*************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  82 QliGglvlhegkiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseer 161
                                    Q++G+ +lh g++aemkTGEGKtl+ +lpaylnal+g+gvh+vtvndYLakrd+ewmg+v++flGl+vgvi ++++++er
  gi|121639129|ref|YP_979353.1|  86 QVMGAAALHLGNVAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDER 165
                                    ******************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 162 reaYeaditYgtnnelgfdyLrDnlalskeelvqrglnfaivDEvDsvLiDeArtpLiisgpaeeeselyeeakklvkel 241
                                    r aY+aditYgtnne+gfdyLrDn+a+s ++lvqrg+++aivDEvDs+LiDeArtpLiisgpa+ +s+ y+e+++l+  +
  gi|121639129|ref|YP_979353.1| 166 RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPLM 245
                                    *****************************************************************************888 PP

                                    xxxxx........................................................................... RF
                      SecA_DEAD 242 eeeed........................................................................... 246
                                    e++ +                                                                           
  gi|121639129|ref|YP_979353.1| 246 EKDVHyevdlrkrtvgvhekgvefvedqlgidnlyeaansplvsylnnalkakelfsrdkdyivrdgevlivdeftgrvl 325
                                    888888888999999999999*********************************************************** PP

                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 247 ..............akegveieeesqtlatitlqnffrlYeklaGmtGTaeteaeef 289
                                                  ake+vei+ e+qtlatitlqn+frlY+klaGmtGTa+tea+e+
  gi|121639129|ref|YP_979353.1| 326 igrrynegmhqaieAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAEL 382
                                    *******************************************************98 PP

>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.9     7e+03     133     161 ..     130     158 ..      26     170 .. 0.64
   2 !  225.6   4.0   1.6e-70   5.7e-67       1     198 [.     613     833 ..     613     834 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCT CS
                        SecA_SW 133 rvvlLevlDkaWkehLdamdeLregiglr 161
                                     + +L   D++W+  +++   L+ g+ l 
  gi|121639129|ref|YP_979353.1| 130 VNDYLAKRDSEWMGRVHRFLGLQVGVILA 158
                                    34467777777877777777777776665 PP

  == domain 2  score: 225.6 bits;  conditional E-value: 1.6e-70
                                    -B-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHCHHHHHHHHHHHHHHHHHCHHHHS. CS
                        SecA_SW   1 piesklvsksienaQkkvEernfdiRknlleYDdVmnkQRkviYkqRrevLegesedlrerildliedvveeiveesvpe 80 
                                    pie+k+v+++i++aQ++vE++nf++Rkn+l+YD+Vmn+QRkviY++Rr++Lege  +l+++ ld+++dv++++v+  + e
  gi|121639129|ref|YP_979353.1| 613 PIEAKMVTRAIKSAQTQVEQQNFEVRKNVLKYDEVMNQQRKVIYAERRRILEGE--NLKDQALDMVRDVITAYVDGATGE 690
                                    8**************************************************776..9*****************999887 PP

                                    SS.CSHHHHHHHHHCCCSSSTSST...................HHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHH CS
                        SecA_SW  81 eekeewdleglleelkeefsvele...................elaeellekaekayekkeeei......ellrelervv 135
                                      +e+wdl++l+++lk+ ++v ++                   el e ll++ae+ay+++e+e+        +r+ler+v
  gi|121639129|ref|YP_979353.1| 691 GYAEDWDLDALWTALKTLYPVGITadsltrkdheferddltreELLEALLKDAERAYAAREAELeeiageGAMRQLERNV 770
                                    7668****************9999**************************************99999*9656******** PP

                                    HHHHHHHHHHHHHHHHHHHHHHCCCTTSSSS-CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCT CS
                        SecA_SW 136 lLevlDkaWkehLdamdeLregiglrgygqkdPlqeYkkegfelFeemlarikeevvkkllkv 198
                                    lL+v+D++W+ehL++md+L+egiglr+++q+dPl+eY++eg+++F +ml+ +kee v +l++v
  gi|121639129|ref|YP_979353.1| 771 LLNVIDRKWREHLYEMDYLKEGIGLRAMAQRDPLVEYQREGYDMFMAMLDGMKEESVGFLFNV 833
                                    *************************************************************97 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.8     1e+04      12      58 ..      13      57 ..      10      65 .. 0.76
   2 !  121.4   0.1   7.3e-39   2.6e-35       3     111 .]     232     339 ..     230     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.8
                                   HHCCCHTTCCECCCTTTSEEEESHHHHHHHHHCCT-SSSTTSCCHCC CS
                   SecA_PP_bind 12 lvkklkeeedyevdekkktveltekGvekvekllkvkeelydeenle 58
                                   +vk+lk+ +dy+    +   +lt++ ++  ++++  k++l d++n e
  gi|121639129|ref|YP_979353.1| 13 MVKRLKKVADYVGTLSDDVEKLTDAELRAKTDEF--KRRLADQKNPE 57
                                   6788888899988888888889998888888877..56787777755 PP

  == domain 2  score: 121.4 bits;  conditional E-value: 7.3e-39
                                    HHHHHHHHHHHCCCHTTCCECCCTTTSEEEESHHHHHHHHHCCT-SSSTTSCCHCCHHHHHHHHHHHHHCSTTTTTEEEC CS
                   SecA_PP_bind   3 eelyekanklvkklkeeedyevdekkktveltekGvekvekllkvkeelydeenlelvhhvnqaLkAhtlferdvdYivk 82 
                                    +++y+++++l++ ++++ +yevd +k+tv + ekGve ve++l++ ++ly+++n  lv ++n+aLkA++lf+rd+dYiv+
  gi|121639129|ref|YP_979353.1| 232 SNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGI-DNLYEAANSPLVSYLNNALKAKELFSRDKDYIVR 310
                                    689******************************************.********************************** PP

                                    TTCEEEBSTTTSSEBTS--SSTTHHHHHH CS
                   SecA_PP_bind  83 dgeviivDeftGRlmegrrysdGLhqaie 111
                                    dgev+ivDeftGR++ grry++G+hqaie
  gi|121639129|ref|YP_979353.1| 311 DGEVLIVDEFTGRVLIGRRYNEGMHQAIE 339
                                    ****************************8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     6e-06     0.021      18     134 ..      98     214 ..      85     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                                    EEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng 97 
                                    +++++TG GKTl  ++p++ +        g+ + iv+    La+   + + ++  +++l+v +i+    + d++++   +
  gi|121639129|ref|YP_979353.1|  98 VAEMKTGEGKTLTCVLPAYLN-----ALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILAT-MTPDERRVA-YN 170
                                    5789***************44.....46788899999999***************9*****988775.555788887.9* PP

                                    CSEEEEEH.............HHHHHHHHCTSSHCTTEEEEEEETHHHHH CS
                                    xxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  98 vdivvgtp.............grlddllstgklnlsqvrflVlDEadrll 134
                                    +di++gt                lddl++      +   + ++DE+d +l
  gi|121639129|ref|YP_979353.1| 171 ADITYGTNnefgfdylrdnmaHSLDDLVQ------RGHHYAIVDEVDSIL 214
                                    ********666664444444444444444......444888888888776 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   9.4e-05      0.34      17      60 ..     615     658 ..     601     670 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                           Lge1  17 kiesklkeiesldkqleelklkvlkleleldlleeqierdaLrv 60 
                                    + + +++ i+s++ q e+++++v k+ l +d   +q+++ ++ +
  gi|121639129|ref|YP_979353.1| 615 EAKMVTRAIKSAQTQVEQQNFEVRKNVLKYDEVMNQQRKVIYAE 658
                                    66778999******************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (949 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.43
# Mc/sec: 6685.73
//
Query:       gi|121639130|ref|YP_979354.1|  [L=214]
Description: hypothetical protein BCG_3270c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-26   90.2   0.1    1.1e-25   89.0   0.1    1.7  1  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 
      1e-18   67.9   0.3    2.1e-18   66.9   0.2    1.6  2  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.28   11.9   0.0    1.6  1  FecR             FecR protein


Domain annotation for each model (and alignments):
>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.1   1.9e-29   1.1e-25       2      57 .]     155     210 ..     154     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.9e-29
                                    XXX-EEEEE-S--S-B-HHHHHHHHHHHT-SEEEEEETTTTEEEEEEEETTSCEEE CS
                Ribosom_S30AE_C   2 eepeivrtkrfelkpmsveeAilqmellghdFfvFrnaetgevnVvYrrkdgnYGL 57 
                                    e+ +ivrtk++++kpmsv++A+ qmel+ghdFf+F++++t++++VvYrr+  +YGL
  gi|121639130|ref|YP_979354.1| 155 EPGRIVRTKEHPAKPMSVDDALYQMELVGHDFFLFYDKDTERPSVVYRRHAYDYGL 210
                                    5679***************************************************8 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.2   3.5e-22   2.1e-18       1      86 []      16     112 ..      16     112 .. 0.89
   2 ?   -2.8   0.0         2   1.2e+04      50      70 ..     156     175 ..     150     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 3.5e-22
                                    EEEEECTS---HHHHHHHHHHHCCGGGG....-EEEEEEE......EE...EEEEEEEEECTTEEEEEEEEESSHHHHHH CS
                Ribosomal_S30AE   1 ieitgrnievtdalkeyvekklekleky...fieadVtls......kk...kkvevtirlakgkviraeeesedlyaaid 68 
                                    i ++grn+e++d+++ yv +kl++le++   +  +dV+l+      ++   ++ve+t r + g+v+r+e+ ++++yaa++
  gi|121639130|ref|YP_979354.1|  16 IVFKGRNVEIPDHFRIYVSQKLARLERFdrtIYLFDVELDhernrrQRkscQRVEITARGR-GPVVRGEACADSFYAALE 94 
                                    6789**********************996554789999997777652268999*****755.****************** PP

                                    HHHHHHHHHHHHCHHTTX CS
                Ribosomal_S30AE  69 lavdklerqlrkykeklk 86 
                                    +av kle +lr+ k+++k
  gi|121639130|ref|YP_979354.1|  95 SAVVKLESRLRRGKDRRK 112
                                    ***************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                    TTEEEEEEEEESSHHHHHHHH CS
                Ribosomal_S30AE  50 kgkviraeeesedlyaaidla 70 
                                    +g+++r +e ++    ++d+a
  gi|121639130|ref|YP_979354.1| 156 PGRIVRTKE-HPAKPMSVDDA 175
                                    677777544.35444555555 PP

>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.28       8      82 ..     108     192 ..     100     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                           FecR   8 gsraeilleDgsvvrlnenssl..........ekaadsskrrrevsllkGevlfdvakdkkrpfevktpsatigvrgtef 77 
                                    + r+++ + D++ v+l+e++++          + a  ++++ + v+ + G++  + ++ +++p++v+ + ++++  g +f
  gi|121639130|ref|YP_979354.1| 108 KDRRKVHYGDKTPVSLAEATAVvpapengfntRPAEAHDHDGAVVEREPGRIVRTKEH-PAKPMSVDDALYQMELVGHDF 186
                                    56899*******************9999999877777777777899999998555555.5569**************999 PP

                           FecR  78 .rvrks 82 
                                       +++
  gi|121639130|ref|YP_979354.1| 187 fLFYDK 192
                                    533222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1584.98
//
Query:       gi|121639131|ref|YP_979355.1|  [L=213]
Description: hypothetical protein BCG_3271c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00018   21.1   0.2    0.00026   20.5   0.2    1.3  1  Pribosyltran   Phosphoribosyl transferase domain
    0.00047   19.6   0.0    0.00075   19.0   0.0    1.2  1  UPRTase        Uracil phosphoribosyltransferase
     0.0016   18.0   0.0     0.0025   17.3   0.0    1.3  1  PRTase_2       Phosphoribosyl transferase
  ------ inclusion threshold ------
        0.4   10.4   6.1       0.72    9.6   0.1    2.5  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
        1.2    9.5   4.7         11    6.5   0.6    2.5  2  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   7.2e-08   0.00026      88     122 ..     175     208 ..     144     213 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.2e-08
                                    SEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEE CS
                   Pribosyltran  88 kkVliVDDildtGgTllaalelLkekgpeevriav 122
                                    + V++VDDi++tG T ++ ++ L ++g+  v+++ 
  gi|121639131|ref|YP_979355.1| 175 NEVVLVDDIITTGATARESVRVLQAAGVR-VGAVL 208
                                    67*************************95.55544 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-07   0.00075     119     157 ..     172     210 ..     157     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-07
                        UPRTase 119 iaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                      +++v+l+D +i TG++a + +++L+ +gv++  +l +
  gi|121639131|ref|YP_979355.1| 172 RPRNEVVLVDDIITTGATARESVRVLQAAGVRVGAVLAV 210
                                    46789***************************9999876 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     7e-07    0.0025     121     150 ..     174     203 ..     155     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-07
                       PRTase_2 121 akelvLvDDEistGktalnliralqeklpr 150
                                    ++e+vLvDD i+tG ta + +r lq++  r
  gi|121639131|ref|YP_979355.1| 174 RNEVVLVDDIITTGATARESVRVLQAAGVR 203
                                    579********************9998766 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.1     0.031   1.1e+02       6      12 ..      10      16 ..      10      18 .. 0.92
   2 ?    9.6   0.1    0.0002      0.72       3      21 ..      18      36 ..      17      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.031
                  zf-NADH-PPase  6 CgrCGap 12
                                   Cg CGap
  gi|121639131|ref|YP_979355.1| 10 CGGCGAP 16
                                   ******9 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                  zf-NADH-PPase  3 hrFCgrCGaptepaeggwa 21
                                   +r+C+ C+a+  +a+g+ +
  gi|121639131|ref|YP_979355.1| 18 TRWCAACAAELSVAAGEPH 36
                                   79*************9965 PP

>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.015        55      74     105 ..     114     145 ..     109     150 .. 0.83
   2 ?    6.5   0.6     0.003        11      70      95 ..     185     210 ..     154     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.015
                  Ribosomal_S11  74 GreaalralaraGlkigriedvtPiPhdgirr 105
                                    G ++  r  + aG ++gr +dvt +P   +r+
  gi|121639131|ref|YP_979355.1| 114 GGDPVSRMARIAGATLGRHHDVTVVPALRMRA 145
                                    66777788899***************877775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
                  Ribosomal_S11  70 gpGpGreaalralaraGlkigriedv 95 
                                    ++G+ +  ++r l++aG+++g++  v
  gi|121639131|ref|YP_979355.1| 185 TTGATARESVRVLQAAGVRVGAVLAV 210
                                    48999999*************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1525.74
//
Query:       gi|121639132|ref|YP_979356.1|  [L=280]
Description: hypothetical protein BCG_3272c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-06   26.9   3.5    1.3e-05   25.5   3.5    1.7  1  DUF2993   Protein of unknown function (DUF2993)


Domain annotation for each model (and alignments):
>> DUF2993  Protein of unknown function (DUF2993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   3.5   7.4e-10   1.3e-05      26     211 ..      58     242 ..      27     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.4e-10
                        DUF2993  26 edpeVsiggfPfltqllaGeld..............svsvaargvvvdgpglriesveltledvrldlsdilgkvrlvpv 91 
                                    ++++V+ig ++++  l   eld              +v+vaarg++ d+  l+  s+ + l++v++ ++       lv +
  gi|121639132|ref|YP_979356.1|  58 KEVTVRIGDHDVV--LTVTELDsalepqglavgqlgEVRVAARGISWDQHHLH--SAVAVLRNVHIRPGV----PPLVIA 129
                                    5556666666644..555555555556666666666***********866666..*************85....778889 PP

                        DUF2993  92 grltatvtlteadlnralasp.....llitdlq.............dlsnggvkltgnnlpvvveaglrlaagdgqlrle 153
                                    ++++++  l+ + +   l  +     +                    + +gg+++     +v v +++     +++l l+
  gi|121639132|ref|YP_979356.1| 130 APVELSSALPTEIFDDVLRQAtpqlrG-----ElsesgaarlrwarRPDWGGLEV-----DVDVAGTT----SQTTLWLR 195
                                    999999999988888888866333330.....13333334555555444444444.....35555544....56689999 PP

                        DUF2993 154 ltdleaglglpesavdlpaelldalleglselldlpglpfglrltevrvtdgglrltg 211
                                    ++ + +g               +  ++ +  +++lp+lp glr+t+v+++++ l+l++
  gi|121639132|ref|YP_979356.1| 196 PRTVITGQRR-----------WTLPARTPAYRVPLPELPHGLRITDVSLAADCLQLSA 242
                                    9999988777...........77788899999********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2203.62
//
Query:       gi|121639133|ref|YP_979357.1|  [L=583]
Description: lipoprotein LpqB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-69  235.1  16.0    1.5e-69  234.5  16.0    1.3  1  Gmad1     Lipoprotein LpqB beta-propeller domain
    6.6e-13   49.3   0.0    1.9e-12   47.9   0.0    1.8  1  Germane   Sporulation and spore germination


Domain annotation for each model (and alignments):
>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5  16.0   1.7e-73   1.5e-69       1     252 []     323     582 ..     323     582 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 1.7e-73
                          Gmad1   1 GqLvsvsggrvepvpGplgegavdlrsaAvSrdgqqvaavt.....apdggrtLvvgsyggeasevleggsltrpSwdrd 75 
                                    G+Lv  +++rv+pvpG++g++  ++++aAvSr+g+qva+v      apd++++L+vg+ ggea + ++g+sl+rpSw++d
  gi|121639133|ref|YP_979357.1| 323 GSLVAMDAQRVTPVPGAFGRMP-EQTAAAVSRSGRQVASVVtlgrgAPDEAASLWVGDLGGEAVQSADGHSLLRPSWSLD 401
                                    89*******************9.*****************99************************************** PP

                          Gmad1  76 galWvvedgaevvravrddaegevavveVdasalra...gpvtelrvSrDGtRaAvivekdgggkvyvavVvrdadGqks 152
                                    +a+Wvv+d++ v ra +d+a+g++a+++Vd+ a+++   g +++l++SrDGtRaA+++    gg+v +a+V++++ Gq++
  gi|121639133|ref|YP_979357.1| 402 DAVWVVVDTNVVLRAIQDPASGQPARIPVDSTAVASrfpGAINDLQLSRDGTRAAMVI----GGQVILAGVEQTQAGQFA 477
                                    **********************************************************....****************** PP

                          Gmad1 153 ltapvalatglleeavsvsWrsedtLvVlrsseggpvqalVsldgsesealpsgnlaapvvavsaapetlyvtddrgvlq 232
                                    lt+p++l++gl++++vs+sWr++d++vV r+++ +pv++ V+ldg++s+a ps+ l+ p++a++a+p+t+yv+  +gvl 
  gi|121639133|ref|YP_979357.1| 478 LTYPRRLGFGLGSSVVSLSWRTGDDIVVTRTDAAHPVSY-VNLDGVNSDA-PSRGLQTPLTAIAANPSTVYVAGPQGVLM 555
                                    ***************************************.**********.9***************************9 PP

                          Gmad1 233 ....sssglnWrevpegtsa...PvlP 252
                                         +s+ +W  vp+++     PvlP
  gi|121639133|ref|YP_979357.1| 556 ysasVESRPGWADVPGLMVPgaaPVLP 582
                                    999889999*********999999998 PP

>> Germane  Sporulation and spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   2.1e-16   1.9e-12       1     103 []     168     290 ..     168     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.1e-16
                        Germane   1 tlYfldadg.t.vpv.rlvrek.seelakalleeLlagpt....eglrsalpegtkllsvtvkdd...........vatv 61 
                                    tlYf+d++g t vp+ r+v+++  ++la++l+++Llagp       +r++l +  +l++ +++ d            a+v
  gi|121639133|ref|YP_979357.1| 168 TLYFADPTGkTvVPDpRYVAVSdRDQLATELVSKLLAGPRpemaRTVRNLLAPPLRLRGPVTRADggksgigrgygGARV 247
                                    79*******76999998888888***************9999**99**************9999889************* PP

                        Germane  62 dlskefl...gssseelalasivntltelpeiekVqflvdGkple 103
                                    d  k  l   +  s +l++a+i++tl+ ++   ++ + +dG ple
  gi|121639133|ref|YP_979357.1| 248 DMEK--LsttDPHSRQLLAAQIIWTLARADIRGPYVINADGAPLE 290
                                    ****..557777777779999*********999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3653.39
//
Query:       gi|121639134|ref|YP_979358.1|  [L=567]
Description: two component sensory transduction histidine kinase mtrB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-20   72.4   0.0    9.6e-20   71.2   0.0    1.7  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-16   60.3   6.1    2.6e-16   59.4   1.1    2.8  2  HisKA        His Kinase A (phospho-acceptor) domain
      1e-11   45.0   0.4    3.3e-11   43.4   0.4    2.0  1  HAMP         HAMP domain
    9.5e-05   22.4   0.1    0.00037   20.5   0.1    2.0  2  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
       0.17   12.4   3.3          1    9.9   0.0    3.2  4  DUF1472      Protein of unknown function (DUF1472)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.1   1.5e+04       5      17 ..     372     384 ..     370     395 .. 0.82
   2 !   71.2   0.0   2.7e-23   9.6e-20       2     110 ..     409     517 ..     408     519 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHHHH CS
                      HATPase_c   5 rLrqiisnlvdNa 17 
                                     Lr  ++n+++N 
  gi|121639134|ref|YP_979358.1| 372 DLRTTVNNALGNV 384
                                    6899999999996 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 2.7e-23
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                    d +r+++i++nl+ Na+++ ++ + +++++ a+ed++ ++v+D G G+ + + k++f +f + d s+ r++ggtGlGl+i
  gi|121639134|ref|YP_979358.1| 409 DARRVERILRNLIANAIDH-AEHKPVRIRMAADEDTVAVTVRDYGVGLRPGEEKLVFSRFWRsDPSRVRRSGGTGLGLAI 487
                                    7899***************.99999******999********************************************** PP

                                    HHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlpl 110
                                    + + ++l++G+++   epg+G +f++tlpl
  gi|121639134|ref|YP_979358.1| 488 SVEDARLHQGRLEAWGEPGEGACFRLTLPL 517
                                    ***9999*********************98 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   1.1   7.2e-20   2.6e-16       2      67 .]     296     362 ..     295     362 .. 0.96
   2 ?    2.4   0.3     0.044   1.6e+02      12      58 ..     372     420 ..     370     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.2e-20
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                    ++rf+++v+HELrtPL++++++a+++ ++ ++l++ l++  e ++se +r + l++dlL++sr +ag
  gi|121639134|ref|YP_979358.1| 296 QRRFTSDVSHELRTPLTTVRMAADLIYDHsADLDPTLRRSTELMVSELDRFETLLNDLLEISRHDAG 362
                                    68************************777889********************************997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                                    HHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                          HisKA  12 ELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedl 58 
                                    +Lrt ++  lgn+  L +e  ++l  +l +   ++e  arr+++++ +l
  gi|121639134|ref|YP_979358.1| 372 DLRTTVNNALGNVGHLAEEagIELLVDLPAEQVIAEVDARRVERILRNL 420
                                    7999999999999999777788888888888899999999*99999998 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.4   9.3e-15   3.3e-11       1      52 [.     232     283 ..     232     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 9.3e-15
                                    HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    l++r+++ P+r  +r a+r a+G+l++r pv+g D +++La +fN+M+++L 
  gi|121639134|ref|YP_979358.1| 232 LVSRQVVVPVRSASRIAERFAEGHLSERMPVRGEDDMARLAVSFNDMAESLS 283
                                    689***********************************************97 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7     6e+03       9      38 ..     312     342 ..     307     343 .. 0.77
   2 !   20.5   0.1     1e-07   0.00037      24      82 ..     405     459 ..     388     490 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                    HATPase_c_2   9 rtvrevaeavlrr.aglseelldeirlaveE 38 
                                     tvr++a  +  + a+l++ l+   +l v+E
  gi|121639134|ref|YP_979358.1| 312 TTVRMAADLIYDHsADLDPTLRRSTELMVSE 342
                                    5677777777555599999999999999999 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1e-07
                    HATPase_c_2  24 lseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpet 82 
                                    ++e ++ +++  +  +++Na+ ha +    +pv++r+  de+++ v+v+D G g +p +
  gi|121639134|ref|YP_979358.1| 405 IAEVDARRVERILRNLIANAIDHAEH----KPVRIRMAADEDTVAVTVRDYGVGLRPGE 459
                                    56667778888888899999999998....9*********************9955543 PP

>> DUF1472  Protein of unknown function (DUF1472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       0.3   1.1e+03      38      76 ..      19      61 ..       5      80 .. 0.66
   2 ?   -0.4   0.0      0.46   1.7e+03      56      92 ..     291     325 ..     259     329 .. 0.77
   3 ?    9.9   0.0   0.00028         1      35      98 ..     413     477 ..     401     480 .. 0.88
   4 ?   -3.4   0.0         4   1.4e+04      68      80 ..     509     521 ..     507     525 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.3
                        DUF1472 38 vtrsllpvcrdfpvvh....plrfrgltlqlpsavcvrlrlpl 76
                                   +tr l  + r + v       lr+  ltl l  av + l + l
  gi|121639134|ref|YP_979358.1| 19 MTRGLSALSRAVAVAWrrslQLRVVALTLGLSLAVILALGFVL 61
                                   5666666666666653221146666777777777777776555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.46
                        DUF1472  56 rfrgltlqlpsavcvrlrlplrpvhprliarllwrhg 92 
                                     f  l  ++ s v   lr pl  v  r+ a l++ h 
  gi|121639134|ref|YP_979358.1| 291 EFGNLQRRFTSDVSHELRTPLTTV--RMAADLIYDHS 325
                                    466777888999999999999987..78888888886 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00028
                        DUF1472  35 aaavtrsllpvcrdfpvvhplrfrgltlqlpsavcvr.lrlplrpvhprliarllwrhgtarcrr 98 
                                       + r+l+  + d    +p+r+r  + +   av vr   + lrp   +l+   +wr   +r+rr
  gi|121639134|ref|YP_979358.1| 413 VERILRNLIANAIDHAEHKPVRIRMAADEDTVAVTVRdYGVGLRPGEEKLVFSRFWRSDPSRVRR 477
                                    55678999999999999*******************945799********************998 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 4
                        DUF1472  68 vcvrlrlplrpvh 80 
                                     c rl lpl   h
  gi|121639134|ref|YP_979358.1| 509 ACFRLTLPLVRGH 521
                                    6999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2990.34
//
Query:       gi|121639135|ref|YP_979359.1|  [L=228]
Description: two component sensory transduction transcriptional regulatory protein mtrA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-29  102.1   0.2    3.4e-29  101.3   0.2    1.5  1  Response_reg  Response regulator receiver domain
    2.4e-26   91.6   0.5    8.8e-26   89.8   0.1    2.0  2  Trans_reg_C   Transcriptional regulatory protein, C terminal
  ------ inclusion threshold ------
      0.095   13.1   0.0       0.27   11.6   0.0    1.7  2  FleQ          Flagellar regulatory protein FleQ
       0.11   12.5   0.0       0.27   11.3   0.0    1.7  1  B12-binding   B12 binding domain
       0.13   12.6   0.2       0.38   11.1   0.1    1.8  2  TAL_effector  TAL effector repeat


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.2   9.6e-33   3.4e-29       1     112 []       8     117 ..       8     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 9.6e-33
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    +l+vdDd  ++e l+ +l+ eg+ ++a+  dg++al  ++e ++dl+llD+++pgm+G+++++ +r+++  +p+++lta+
  gi|121639135|ref|YP_979359.1|   8 ILVVDDDASLAEMLTIVLRGEGF-DTAVIGDGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLRADS-GVPIVMLTAK 85 
                                    8**********************.*******************************************87.********** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkale 112
                                    ++  d+v +l+ gadd+++Kpf+p+eL+++++
  gi|121639135|ref|YP_979359.1|  86 TDTVDVVLGLESGADDYIMKPFKPKELVARVR 117
                                    ****************************9985 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.4   1.4e+03      49      64 ..     112     127 ..     110     134 .. 0.79
   2 !   89.8   0.1   2.4e-29   8.8e-26       1      76 [.     149     224 ..     149     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHTTTTSS CS
                    Trans_reg_C  49 hisrLRkkLeddekkp 64 
                                     ++r+R  L+ + ++p
  gi|121639135|ref|YP_979359.1| 112 LVARVRARLRRNDDEP 127
                                    5899*****9987666 PP

  == domain 2  score: 89.8 bits;  conditional E-value: 2.4e-29
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYr 76 
                                    ge+++ltp ef+lL +L+++p++v++r+ Lle+vwg+++  d+r v+vh++rLR k+e+d+++p ++ tvrgvGY+
  gi|121639135|ref|YP_979359.1| 149 GEQISLTPLEFDLLVALARKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEKDPENPTVVLTVRGVGYK 224
                                    689************************************************************************7 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.5e-05      0.27       1      81 [.       7      88 ..       7      97 .. 0.82
   2 ?   -2.3   0.0       1.6   5.7e+03      58      76 ..     199     217 ..     193     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                           FleQ  1 kiLvidddaerrrdletiLeFlgeeveavsseel.saaleesssealavilgsvssleealealaekdphlPvlllgesdea 81
                                   +iLv+ddda+ ++ l+++L+  g ++ ++++     +a +e + +++++ l        ++ +++++d  +P+++l+ +++ 
  gi|121639135|ref|YP_979359.1|  7 RILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQaLTAVRELRPDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLTAKTDT 88
                                   69******************99999999998766477777777777777776666678889999999999999999887765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                           FleQ  58 ealealaekdphlPvlllg 76 
                                    + l+a +ekdp+ P ++l+
  gi|121639135|ref|YP_979359.1| 199 QRLRAKVEKDPENPTVVLT 217
                                    6788889999999988876 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.7e-05      0.27      18      68 ..      19      65 ..      16      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                    B12-binding 18 avlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleav 68
                                    +l  +lr +gf+  ++g  +   + + a+r+++pd+v+l + +   ++++
  gi|121639135|ref|YP_979359.1| 19 EMLTIVLRGEGFDTAVIGDGT---QALTAVRELRPDLVLLDL-MLPGMNGI 65
                                   578899***********9888...78999***********99.77777665 PP

>> TAL_effector  TAL effector repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   8.9e+03      16      25 ..      24      33 ..      24      35 .. 0.79
   2 ?   11.1   0.1   0.00011      0.38       3      18 ..      38      53 ..      38      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                                   HHHHTT--HH CS
                   TAL_effector 16 aLrqrGfSra 25
                                   +Lr+ Gf +a
  gi|121639135|ref|YP_979359.1| 24 VLRGEGFDTA 33
                                   6999999877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHH CS
                   TAL_effector  3 GaQALeAVlahgpaLr 18
                                   G QAL AV +++p+L+
  gi|121639135|ref|YP_979359.1| 38 GTQALTAVRELRPDLV 53
                                   89************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1205.11
//
Query:       gi|121639136|ref|YP_979360.1|  [L=214]
Description: thymidylate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-22   79.1   0.0    4.1e-22   78.8   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
    2.1e-05   24.8   0.4    2.7e-05   24.5   0.4    1.2  1  AAA_28           AAA domain
     0.0004   19.5   0.4     0.0006   18.9   0.4    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0023   18.5   0.0     0.0057   17.2   0.0    1.6  1  AAA_18           AAA domain
  ------ inclusion threshold ------
       0.06   13.2   0.0      0.085   12.7   0.0    1.2  1  dNK              Deoxynucleoside kinase
      0.066   13.1   0.0       0.13   12.2   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.086   12.1   0.0       0.35   10.0   0.0    1.8  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.099   12.3   0.2       0.28   10.8   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain
        0.1   12.7   0.3       0.22   11.6   0.3    1.6  1  AAA_33           AAA domain
       0.12   12.1   4.7      0.025   14.3   1.5    1.6  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   2.3e-25   4.1e-22       1     165 [.       5     187 ..       5     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.3e-25
                                    EEESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHH..TCS---HHH..HHHHHHHHHHHTTHHHHHH CS
                Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelll..keeeleeqt..eallfaadriehleekikp 75 
                                    iEG+DGaGK t +e+l  +++++g++ + l ++  g +++  i +  l  ++ +l+++   +a lfa dr   ++  i+ 
  gi|121639136|ref|YP_979360.1|   5 IEGVDGAGKRTLVEKLSGAFRAAGRSvATLAFPRYGQSVAADIAAEALhgEHGDLASSVyaMATLFALDR-AGAVHTIQG 83 
                                    8*************************999****9998888777655444877777665566*********.77777**** PP

                                    HHHTT-EEEEES-HHHHHHHHHT.....TTTTTCHHHHHHGGGTTS..E-SEEEEEESSHHHHHTSCCTTSS.....TTT CS
                Thymidylate_kin  76 alkqgktvivdRylfSslaYqga.....kegvdldlvlslnedvll..kPdltflldvdpevalkRlakrde.....lde 143
                                         ++vi+dRy++S++aY++a     + g  +++v++++   l+  kPd+ +ll v+ e a +R + r++       +
  gi|121639136|ref|YP_979360.1|  84 LCRGYDVVILDRYVASNAAYSAArlhenAAGKAAAWVQRIEFARLGlpKPDWQVLLAVSAELAGERSRGRAQrdpgrARD 163
                                    ********************997432112234578999999888889*************************88884447 PP

                                    SHHHHHHHHHHHHHHHHHHHH..T CS
                Thymidylate_kin 144 eeeeqldflrkvrerylelak..e 165
                                    + e++ + ++++ ++y ela+   
  gi|121639136|ref|YP_979360.1| 164 NYERDAELQQRTGAVYAELAAqgW 187
                                    77888999999*******997433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4   1.5e-08   2.7e-05       2     156 ..       3     183 ..       2     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                         AAA_28   2 ivitGgestGKTtlleaLa....ar....gypvvpEaareileekl....akgedalpwv..edllafaervleeqleee 67 
                                    i+i G  ++GK tl+e+L+    a      +  +p+++  +  + +      ++++l+++  + +  fa  +  +    +
  gi|121639136|ref|YP_979360.1|   3 IAIEGVDGAGKRTLVEKLSgafrAAgrsvATLAFPRYGQSVAADIAaealHGEHGDLASSvyAMATLFALDRAGAVHTIQ 82 
                                    899****************8776333333222336666666555543322444444544434566677777666666666 PP

                         AAA_28  68 aaaaankvlfcDrglldtlaYaraygge....aeaeleaaarekry.....dlvfllppapei..dddgeR.redleere 135
                                      +++ +v+++Dr +  ++aY+ a+  e    ++a++++ +++ r      d  +ll++++e+  ++   R + d+ +++
  gi|121639136|ref|YP_979360.1|  83 GLCRGYDVVILDRYVASNAAYSAARLHEnaagKAAAWVQRIEFARLglpkpDWQVLLAVSAELagERSRGRaQRDPGRAR 162
                                    777*******************8876652222233355544433333344488788888887756555555345778888 PP

                         AAA_28 136 aiderlrealrelgipviivp 156
                                    + +er  e+ ++ g  ++++ 
  gi|121639136|ref|YP_979360.1| 163 DNYERDAELQQRTGAVYAELA 183
                                    888888888888888877775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   3.3e-07    0.0006      32      65 ..       3      36 ..       1      99 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-07
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE CS
                           MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlav 65
                                   + + Gv GaGk tlve+l   +r++G+ va la 
  gi|121639136|ref|YP_979360.1|  3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAF 36
                                   7799****************************96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0057       1     127 [.       3     167 ..       3     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........... 69 
                                    I++ G+ G+GK tl + Ls         r+va+   +++++  +     +++ e  + ++ d+    ++           
  gi|121639136|ref|YP_979360.1|   3 IAIEGVDGAGKRTLVEKLSGAF--RAAGRSVATLAFPRYGQSVA----ADIAAEALHGEHGDLASSVYAmatlfaldrag 76 
                                    89****************9987..99999999999999999999....77777777777777777777777788888899 PP

                         AAA_18  70 .......aleegknlvidghlaeleseaakdikk..........................vvLtaspeelleRlekRgye 116
                                             +  +++++d  +a +  ++a +++                           v L +s e   eR + R ++
  gi|121639136|ref|YP_979360.1|  77 avhtiqgLCRGYDVVILDRYVASNAAYSAARLHEnaagkaaawvqriefarlglpkpdwqVLLAVSAELAGERSRGRAQR 156
                                    999998877889999**********9999999999*******************************************99 PP

                         AAA_18 117 eakikeneeae 127
                                    ++ ++++++ +
  gi|121639136|ref|YP_979360.1| 157 DPGRARDNYER 167
                                    99988777665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05     0.085       1     146 [.       3     156 ..       3     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                                    EEEEESTTSSHHHHHHHHHCCST...CEEEE-HHHHCCSSSS.....HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHH CS
                            dNK   1 ivveGnIgaGKstlvklLskklg...vkvfeEpvdkwtnvqk.....nlLekfYkdpsrwsfalqtyvllsrlkqqleal 72 
                                    i++eG  gaGK tlv+ Ls ++      v++    ++ +  +     + L+  + d +   +a+ t + l r  +  ++ 
  gi|121639136|ref|YP_979360.1|   3 IAIEGVDGAGKRTLVEKLSGAFRaagRSVATLAFPRYGQSVAadiaaEALHGEHGDLASSVYAMATLFALDRAGAVHTIQ 82 
                                    89****************9776433266777777777555448999999**********99*********9999888877 PP

                                    ...SSS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTC CS
                            dNK  73 ...atkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgre 146
                                       +  +vv+l+R + s++  + +a  +++ + +   + + +  +++   l+kpd  + L +s e   er + R++ 
  gi|121639136|ref|YP_979360.1|  83 glcRGYDVVILDRYVASNA-AYSAARLHENAAGKA--AAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQR 156
                                    77788999*****999999.444444444444333..3344455555577888999999999999888887777655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.1e-05      0.13       2      33 ..       3      34 ..       2      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                           MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                   ++i g  g+GK tL+ekl  +++a g +v+t+
  gi|121639136|ref|YP_979360.1|  3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATL 34
                                   78999************************997 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   5.1e+02       3      20 ..       2      19 ..       1      38 [. 0.78
   2 ?   10.0   0.0    0.0002      0.35     274     307 ..      68     101 ..      52     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                        DUF2075  3 vvlVtGvaGtGKtvvlln 20
                                   ++ ++Gv G+GK  +  +
  gi|121639136|ref|YP_979360.1|  2 LIAIEGVDGAGKRTLVEK 19
                                   5789********666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                        DUF2075 274 ssdtleevgseytiQGleldyvgviiGpdlvyrk 307
                                      ++l+++g ++tiQGl   y +vi+++ +  ++
  gi|121639136|ref|YP_979360.1|  68 TLFALDRAGAVHTIQGLCRGYDVVILDRYVASNA 101
                                    5689***********************9887764 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.28       4      36 ..       3      35 ..       1      53 [. 0.89
   2 ?   -1.1   0.0       0.7   1.3e+03      41      73 ..      74     106 ..      58     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllva 36
                                   i++ G+ GaGK t + KL+  +++ g++v+  a
  gi|121639136|ref|YP_979360.1|  3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA 35
                                   7788**********************9998776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.7
                                    STTHHHHHHHHHHHTTEEEEESSTTSCHHHHHH CS
                          SRP54  41 RaaAveQLktlaeklgvpvikkkeeadpaavak 73 
                                    Ra+Av  ++ l + ++v +++++ ++++a  a+
  gi|121639136|ref|YP_979360.1|  74 RAGAVHTIQGLCRGYDVVILDRYVASNAAYSAA 106
                                    777777777777777777776665555444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00013      0.22       1     122 [.       2     157 ..       2     179 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                         AAA_33   1 lvllvGlpGsGKstlaerl......lkklg...........avllssdtlrrrlfgtdqq..sktdytrvldrlyqilne 61 
                                    l+ + G+ G+GK tl+e+l      +   g           ++ ++ d++ ++l g++ +  s  +    l+ l +  + 
  gi|121639136|ref|YP_979360.1|   2 LIAIEGVDGAGKRTLVEKLsgafraA---GrsvatlafpryGQSVAADIAAEALHGEHGDlaSSVYAMATLFALDRAGAV 78 
                                    67889**************7775440...355555557788888999999999999666532444555556666665444 PP

                         AAA_33  62 larkalsagrn.vil...datnls...rrer......arflklarrlgvp.......vrivvvetdeetlkeRlakRaan 121
                                       + l +g++ vil    a n+    +  r       +  ++++r++++       +  v + ++ e++ eR + Ra++
  gi|121639136|ref|YP_979360.1|  79 HTIQGLCRGYDvVILdryVASNAAysaA--RlhenaaGKAAAWVQRIEFArlglpkpDWQVLLAVSAELAGERSRGRAQR 156
                                    4446777888845554442333223330..13333333333344444443444446678899999999999999999986 PP

                         AAA_33 122 g 122
                                     
  gi|121639136|ref|YP_979360.1| 157 D 157
                                    4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   1.4e-05     0.025      21      82 ..       3      80 ..       1     121 [. 0.62
   2 ?   -3.2   0.1       3.3   5.9e+03     156     176 ..     160     180 ..     157     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAp....tgkaAkvLaeelgieastiakllkrlk............g 82
                                    +++G+ G+GK t++++l  a++aag++v+ lA     ++ aA+  ae+l  e   +a+ +++++             
  gi|121639136|ref|YP_979360.1|  3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFprygQSVAADIAAEALHGEHGDLASSVYAMAtlfaldragavhT 80
                                   5799*****************************723322333333334333333333333333323333445555552 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                         AAA_30 156 Rqkeseeraaalalregdaee 176
                                    R +++ er+a l+ r+g + +
  gi|121639136|ref|YP_979360.1| 160 RARDNYERDAELQQRTGAVYA 180
                                    677788888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1160.16
//
Query:       gi|121639137|ref|YP_979361.1|  [L=495]
Description: S-adenosyl-L-homocysteine hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.7e-149  494.8   0.0   8.7e-149  494.6   0.0    1.0  1  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.4e-78  262.6   3.1    1.9e-78  262.1   3.1    1.2  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.6e-10   39.5   0.3    6.7e-10   38.6   0.3    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.4e-08   32.1   0.5    1.3e-07   31.4   0.5    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    5.9e-05   23.3   1.1    0.00049   20.3   1.1    2.2  1  TrkA_N         TrkA-N domain
    0.00014   22.2   0.1    0.00035   21.0   0.1    1.6  1  NAD_binding_7  Putative NAD(P)-binding
    0.00055   20.0   0.2     0.0012   18.9   0.2    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.013   14.9   1.2       0.14   11.5   1.2    2.2  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
       0.02   15.4   0.5      0.041   14.4   0.1    1.7  2  XdhC_C         XdhC Rossmann domain
       0.03   14.9   0.6      0.069   13.7   0.6    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.075   12.3   2.0       0.17   11.1   2.0    1.6  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.12   12.5   0.1       0.32   11.1   0.1    1.7  1  RNase_PH_C     3' exoribonuclease family, domain 2
       0.16   12.3   0.4       0.37   11.2   0.4    1.6  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.6   0.0  6.3e-152  8.7e-149       1     299 []      20     494 ..      20     494 .. 0.98

  Alignments for each domain:
  == domain 1  score: 494.6 bits;  conditional E-value: 6.3e-152
                                    --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstq 80 
                                    d+k++d+sla+fGrke+++ae+empglm+lr+eyae +plkgari+Gslhmt+qtavLietL+alGaevrWasCnifstq
  gi|121639137|ref|YP_979361.1|  20 DFKIADLSLADFGRKELRIAEHEMPGLMSLRREYAEVQPLKGARISGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQ 99 
                                    79****************************************************************************** PP

                                    HHHHHHHC.........CTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHHHH.H...... CS
                                    xxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxx. RF
                      AdoHcyase  81 deaaaaia.........eagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvkee.e.svle. 148
                                    d+aaaa++          +gvpvfawkgetleeyww +eq+l+w++ +k +n+ilDdGGD+t+lv +g+++e +  v+  
  gi|121639137|ref|YP_979361.1| 100 DHAAAAVVvgphgtpdePKGVPVFAWKGETLEEYWWAAEQMLTWPDPDKPANMILDDGGDATMLVLRGMQYEkAgVVPPa 179
                                    ***************9556***************************999*********************8845555554 PP

                                    .S..SHHHHHHHHHHHHHHTT..THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH....... CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      AdoHcyase 149 keedeeeekvvlellkksleed.kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD....... 220
                                    +e+d +e+kv+l+ll++  e+d +k+t++++++kGv+eetttGv rLy++a++g+L +painvndsvtkskfD       
  gi|121639137|ref|YP_979361.1| 180 EEDDPAEWKVFLNLLRTRFETDkDKWTKIAESVKGVTEETTTGVLRLYQFAAAGDLAFPAINVNDSVTKSKFDnkygtrh 259
                                    777899************999989******************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                      AdoHcyase 221 ................................................................................ 220
                                                                                                                    
  gi|121639137|ref|YP_979361.1| 260 slidginrgtdaliggkkvlicgygdvgkgcaeamkgqgarvsvteidpinalqammegfdvvtveeaigdadivvtatg 339
                                    ******************************************************************************** PP

                                    ............................................................................S-HH CS
                                    ............................................................................xxxx RF
                      AdoHcyase 221 ............................................................................hpsf 224
                                                                                                                hpsf
  gi|121639137|ref|YP_979361.1| 340 nkdiimlehikamkdhailgnighfdneidmaglersgatrvnvkpqvdlwtfgdtgrsiivlsegrllnlgnatgHPSF 419
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXTTSXXSXTTXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 225 vmsasftnqvlaqielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigveveGPfkpdhYr 299
                                    vms+sf+nq++aqiel++k+++y+++vy+lpk+lDekvar+h+e+lg++lt+ltkeqaey+gv+veGP+kpdhYr
  gi|121639137|ref|YP_979361.1| 420 VMSNSFANQTIAQIELWTKNDEYDNEVYRLPKHLDEKVARIHVEALGGHLTKLTKEQAEYLGVDVEGPYKPDHYR 494
                                    **************************************************************************9 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.1   3.1   1.4e-81   1.9e-78       1     162 []     253     415 ..     253     415 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.1 bits;  conditional E-value: 1.4e-81
                                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-S CS
                  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkad 80 
                                    n+yg+r+sl+dgi+r+td l++Gk+++++GyGdvGkGca+++kg+Garv vte+dPi+alqa+meGf+vvt+ee++ +ad
  gi|121639137|ref|YP_979361.1| 253 NKYGTRHSLIDGINRGTDALIGGKKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPINALQAMMEGFDVVTVEEAIGDAD 332
                                    89****************************************************************************** PP

                                    EEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TT.S-EEEEEGGGSBCHHHT CS
                  AdoHcyase_NAD  81 ivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkd.gkkiillaeGrllnlgc 159
                                    ivvt+tGnkdii+leh+k+mkd+ai++niGhfd+eid+a+le++++++++vkpqvd +t+ d g++ii+l+eGrllnlg+
  gi|121639137|ref|YP_979361.1| 333 IVVTATGNKDIIMLEHIKAMKDHAILGNIGHFDNEIDMAGLERSGATRVNVKPQVDLWTFGDtGRSIIVLSEGRLLNLGN 412
                                    ************************************************************999***************** PP

                                    S-- CS
                  AdoHcyase_NAD 160 atg 162
                                    atg
  gi|121639137|ref|YP_979361.1| 413 ATG 415
                                    *97 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.3   4.8e-13   6.7e-10      34     127 ..     273     362 ..     251     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.8e-13
                                    GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
                   2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                                    + gk+v i G+G++G+  a+ +k+ g++v +++  + +  ++  +g+++v++ee++ ++Div+ ++     ++++i  e+
  gi|121639137|ref|YP_979361.1| 273 IGGKKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPINALQAMMEGFDVVTVEEAIGDADIVVTATG----NKDIIMLEH 348
                                    789*******************************99988899999*****************98875....999****** PP

                                    HHCSTTTEEEEESS CS
                   2-Hacid_dh_C 114 lakmkkgailiNta 127
                                    +++mk++ail N++
  gi|121639137|ref|YP_979361.1| 349 IKAMKDHAILGNIG 362
                                    **********9987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.5   9.2e-11   1.3e-07       2      68 ..     273     338 ..     272     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 9.2e-11
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmili 68 
                                    + gkk+ + GyG  G+  a+ ++ +g  v v+  +   ++ +A+ egf+v+tv+ea+ +ad+v++ +
  gi|121639137|ref|YP_979361.1| 273 IGGKKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPI-NALQAMMEGFDVVTVEEAIGDADIVVTAT 338
                                    679****************************988877.7889*********************9866 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.1   3.5e-07   0.00049       1     112 [.     278     380 ..     278     383 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                    ++i+G+G+vG+  ae ++ +g +v+v + d+ ++ ++  eg++vv  +           i +ad+v++atg+++  i+++
  gi|121639137|ref|YP_979361.1| 278 VLICGYGDVGKGCAEAMKGQGARVSVTEIDPINALQAMMEGFDVVTVE---------EAIGDADIVVTATGNKD--IIML 346
                                    68*****************6657********99999999999877543.........34888888888888754..4444 PP

                                    HHHHHHTSS..SEEEEEESSGGGHHHHHHHTTSE CS
                         TrkA_N  81 llakelnpk..kkiiaraqdpehaellkklgadv 112
                                    +++k + ++  +  i   +++ +   l++ ga++
  gi|121639137|ref|YP_979361.1| 347 EHIKAMKDHaiLGNIGHFDNEIDMAGLERSGATR 380
                                    4444444443355666666666666666666665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.5e-07   0.00035       7      74 ..     275     343 ..     272     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeelekdlegadlviaatddrel 74 
                                    gkkvl+ G G+v+   ++ +  +ga+v v   +  ++l+  ++ +   ++e+ + +ad+v++at ++++
  gi|121639137|ref|YP_979361.1| 275 GKKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPINALQAMMEgFDVVTVEEAIGDADIVVTATGNKDI 343
                                    89***************************9888545555555444566679*************99875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2     9e-07    0.0012      12      92 ..     275     347 ..     268     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9e-07
                                    T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB- CS
                   Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepile 91 
                                    +kkvl+ G G +++  a+++  +g++ v v+  +++  ++l   ++g      ++  ++e++ +ad+v++at+ +++i+ 
  gi|121639137|ref|YP_979361.1| 275 GKKVLICGYGDVGKGCAEAMKGQGAR-VSVT--EIDPINALQAMMEGF-----DVVTVEEAIGDADIVVTATGNKDIIML 346
                                    79***********************9.8887..577788888888666.....66788999************9998875 PP

                                    H CS
                   Shikimate_DH  92 k 92 
                                    +
  gi|121639137|ref|YP_979361.1| 347 E 347
                                    3 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2    0.0001      0.14      34     100 ..     273     351 ..     257     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                    -TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.............CCHHHHHCCSSEEEE-SS-TT-B-GGGS-T CS
                  THF_DHG_CYH_C  34 legkkvvvvGrsnivgkplallLleknatVtvchskt.............kdlaeitreadivvvavGkpelikaemvke 100
                                    + gkkv++ G ++ vgk  a  ++ ++a V+v++                  ++e +  adivv+a+G++++i  e++k 
  gi|121639137|ref|YP_979361.1| 273 IGGKKVLICGYGD-VGKGCAEAMKGQGARVSVTEIDPinalqammegfdvVTVEEAIGDADIVVTATGNKDIIMLEHIKA 351
                                    5577777777665.6777777777776655555544322222222222224577888999************99999963 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.3     1e+04      13      38 ..      77     101 ..      70     115 .. 0.63
   2 ?   14.4   0.1   2.9e-05     0.041       1      76 [.     278     362 ..     278     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.3
                                    HHHHHHHHTEEEEEEES-GGGG-GGG CS
                         XdhC_C  13 larlaaalgfrvtvvdpreefatker 38 
                                    l++ + alg +v ++  +  f t+++
  gi|121639137|ref|YP_979361.1|  77 LIETLTALGAEVRWASCNI-FSTQDH 101
                                    6667777777777776655.234444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.9e-05
                                    EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE........-EEEE--S-HHHHHHHHHHHSS.S--SE CS
                         XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade........tavvvlthdhklDaealeaalr.kkaay 71 
                                    ++i+G g+v++ +a+ ++  g rv+v + ++  a ++ +++ d         +a +v+t   + D  +le++ + k+ a 
  gi|121639137|ref|YP_979361.1| 278 VLICGYGDVGKGCAEAMKGQGARVSVTEIDPINALQAMMEGFDVvtveeaigDADIVVTATGNKDIIMLEHIKAmKDHAI 357
                                    68*************************9999667666666665578888999*******************998677889 PP

                                    EEESS CS
                         XdhC_C  72 igllG 76 
                                    +g +G
  gi|121639137|ref|YP_979361.1| 358 LGNIG 362
                                    99888 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6     5e-05     0.069       3      74 ..     279     343 ..     277     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                                    EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH CS
                  F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv 74 
                                     i G+G++g++ a+ +  +g     + v+   + + +++l++ ++ +   v+ eea+ +ad+vv a   +d+
  gi|121639137|ref|YP_979361.1| 279 LICGYGDVGKGCAEAMKGQG---ARVSVT---EIDPINALQAMME-GFDVVTVEEAIGDADIVVTATGNKDI 343
                                    456*****************...999966...6677777777766.666777************99876665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.0   0.00013      0.17      29     123 ..     276     357 ..     254     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS--- CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPk 108
                                     kvl+ G G +G   +++ kg ga+V v++++p  +  l+++ +  +     +  +++ea+ +ad+v+++   +G+k   
  gi|121639137|ref|YP_979361.1| 276 KKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPINA--LQAMMEG-F-----DVVTVEEAIGDADIVVTA---TGNK--D 342
                                    58***************************9998654..4444444.2.....33568999********99...6766..5 PP

                                    SC-HHHHHTS-TTEE CS
                    AlaDh_PNT_C 109 LvteemvksMkpgsV 123
                                    ++  e++k+Mk+ ++
  gi|121639137|ref|YP_979361.1| 343 IIMLEHIKAMKDHAI 357
                                    788889999998776 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00023      0.32      23      44 ..     325     346 ..     320     358 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                    HHHHSSEEEEEEEETTSEEEEE CS
                     RNase_PH_C  23 Eedlsegdltlavagtkevvtl 44 
                                    Ee+++++d+ ++ +g+k++++l
  gi|121639137|ref|YP_979361.1| 325 EEAIGDADIVVTATGNKDIIML 346
                                    99*****************765 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00027      0.37       2      90 ..     277     370 ..     276     381 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                    EEEEESTSHHHHHHHHHHH.HHTTCEEEEEE-TS-HHHHHH...HHHEETTTEC-SS-EEEETTEEEETTEEEEEE--SS CS
                        Gp_dh_N   2 kvainGfGRIGrlvlrall.eekelevvaindltdletlay...llkyDsvhgrfkgeveaeeealvvngkkikvlaekd 77 
                                    kv i G+G +G+  + a+  +  +++v +i  +  l+ ++    ++  + + g  +  v+a++++ ++  ++ik +++++
  gi|121639137|ref|YP_979361.1| 277 KVLICGYGDVGKGCAEAMKgQGARVSVTEIDPINALQAMMEgfdVVTVEEAIGDADIVVTATGNKDIIMLEHIKAMKDHA 356
                                    899***************96555888888877666666655111556666689999999999888888888999999888 PP

                                    .GGGS-CHHHTSSE CS
                        Gp_dh_N  78 .peelpwkelgvdl 90 
                                       ++ + + ++d+
  gi|121639137|ref|YP_979361.1| 357 iLGNIGHFDNEIDM 370
                                    56788888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2707.05
//
Query:       gi|121639138|ref|YP_979362.1|  [L=211]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-35  119.3   0.3    1.4e-34  118.3   0.3    1.5  1  TetR_C_35    Bacterial Tetracyclin repressor,  C-terminal dom
    1.5e-09   37.5   0.0    3.2e-09   36.4   0.0    1.6  1  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.016   15.0   0.2      0.041   13.7   0.1    1.8  1  HTH_23       Homeodomain-like domain
       0.02   14.7   0.1      0.074   12.9   0.1    1.9  2  LacI         Bacterial regulatory proteins, lacI family
      0.024   14.7   0.1      0.046   13.8   0.1    1.4  1  HTH_7        Helix-turn-helix domain of resolvase
      0.039   14.1   0.0      0.059   13.5   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.067   13.3   0.0       0.13   12.3   0.0    1.4  1  HTH_3        Helix-turn-helix


Domain annotation for each model (and alignments):
>> TetR_C_35  Bacterial Tetracyclin repressor,  C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.3   5.6e-38   1.4e-34       3     105 .]      98     200 ..      96     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 5.6e-38
                      TetR_C_35   3 raairaavrafleeaaadpLvravltgeakedLlpllTtdseplleaAsarlaevlaeswpqldeadaevladavvRlal 82 
                                    ++a+ +++r f++e+aadpLv ++ltg ak+dLl+l+Ttds+p++++Asarla +++++w++ +++da+vl +a+vRl l
  gi|121639138|ref|YP_979362.1|  98 YEAFLQGFRSFFAESAADPLVISLLTGVAKPDLLQLITTDSAPIITRASARLAPAFTDTWVATTDNDANVLSRAIVRLCL 177
                                    6899**************************************************************************** PP

                      TetR_C_35  83 ShvvlPpedpeetaadlaevlap 105
                                    S+v++Ppe+++++aadla++++p
  gi|121639138|ref|YP_979362.1| 178 SYVSMPPEADHDVAADLARLITP 200
                                    ********************987 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.3e-12   3.2e-09       2      45 ..      29      72 ..      28      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.3e-12
                                   HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   lda r l+  r ++a t++++A++AG+s+ ++Y  F+s+++L++
  gi|121639138|ref|YP_979362.1| 29 LDAMRDLLLTRDWSAITLSDVARAAGISRQTIYNEFGSRQGLAQ 72
                                   89999************************************975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.6e-05     0.041      16      36 ..      40      62 ..      19      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                         HTH_23 16 e..GlsvreIAreLgvsrrTvyr 36
                                   +   ++ +++Ar+ g+sr+T+y+
  gi|121639138|ref|YP_979362.1| 40 DwsAITLSDVARAAGISRQTIYN 62
                                   3556899***************8 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6     4e+03      30      41 ..      24      35 ..      20      35 .. 0.79
   2 ?   12.9   0.1   2.9e-05     0.074       1      15 [.      45      59 ..      45      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHT CS
                           LacI 30 trerVeaameel 41
                                   +r+ V+ am+ l
  gi|121639138|ref|YP_979362.1| 24 LRDSVLDAMRDL 35
                                   688999999875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.9e-05
                                   -HHHHHHHCTS-HHH CS
                           LacI  1 tikDVArlAGVSkaT 15
                                   t+ DVAr+AG S +T
  gi|121639138|ref|YP_979362.1| 45 TLSDVARAAGISRQT 59
                                   89***********99 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.8e-05     0.046      22      39 ..      44      61 ..      38      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                   --STTTSSSS---SSSS- CS
                          HTH_7 22 isiskIAkevnisRsTvY 39
                                   i+ s++A++ +isR+T+Y
  gi|121639138|ref|YP_979362.1| 44 ITLSDVARAAGISRQTIY 61
                                   57799************* PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.059      17      45 ..      34      62 ..      26      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHH--S-HHHHHHHHTS-HHHHHH CS
                    HTH_Tnp_1_2 17 ellvendyekltldeiaeevgvsrsTlyk 45
                                    ll ++d+   tl+++a+  g+sr+T+y+
  gi|121639138|ref|YP_979362.1| 34 DLLLTRDWSAITLSDVARAAGISRQTIYN 62
                                   5899************************6 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.13      10      27 ..      44      61 ..      35      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHHTSSHHHHH CS
                          HTH_3 10 lsqeeLAeklGvsrstis 27
                                   +++ ++A+++G+sr+ti+
  gi|121639138|ref|YP_979362.1| 44 ITLSDVARAAGISRQTIY 61
                                   899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1195.86
//
Query:       gi|121639139|ref|YP_979363.1|  [L=60]
Description: rubredoxin rubB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-22   78.7   3.4    2.7e-22   78.5   3.4    1.0  1  Rubredoxin      Rubredoxin
  ------ inclusion threshold ------
      0.012   15.3   6.2       0.29   10.9   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.027   14.4   0.2        3.6    7.6   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.033   13.5   2.3          1    8.7   0.6    2.3  2  zf-RanBP        Zn-finger in Ran binding protein and others
      0.043   13.9   3.7       0.24   11.6   3.7    1.9  1  Zn-ribbon_8     Zinc ribbon domain
      0.052   13.3   0.9        3.4    7.5   0.0    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.064   13.0   1.7        4.8    7.0   0.1    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.066   13.0   0.3        5.2    6.9   0.0    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.07   13.1   0.0      0.088   12.8   0.0    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.076   12.6   0.7        1.4    8.6   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.69   10.0   5.2        1.7    8.8   5.2    1.7  1  PHD_4           PHD-finger


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   3.4   1.6e-25   2.7e-22       2      47 .]       7      52 ..       6      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.6e-25
                                   EEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                     Rubredoxin  2 yeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                   ++C  Cg++Yd+a G+p++gia+gT+++d+PddW CPdCg+ k++F
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDF 52
                                   79******************************************99 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00018      0.29       1      12 [.       7      18 ..       7      21 .. 0.83
   2 ?    6.6   1.7     0.004       6.5      15      22 ..      40      47 ..      40      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                   Rubredoxin_2  1 YvCsqCGfesak 12
                                   ++C qCGfe+  
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGFEYDE 18
                                   8*******9966 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.004
                   Rubredoxin_2 15 GrCpsCgs 22
                                   + Cp+Cg+
  gi|121639139|ref|YP_979363.1| 40 WSCPDCGA 47
                                   99****96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0022       3.6      44      57 ..       4      17 ..       1      19 [. 0.87
   2 ?    5.4   0.0     0.011        17      46      54 ..      39      47 ..      28      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                 OrfB_Zn_ribbon 44 grtfkCpnCgfead 57
                                    ++f+C +Cgfe+d
  gi|121639139|ref|YP_979363.1|  4 YKLFRCIQCGFEYD 17
                                   579*********98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                 OrfB_Zn_ribbon 46 tfkCpnCgf 54
                                    + Cp+Cg+
  gi|121639139|ref|YP_979363.1| 39 DWSCPDCGA 47
                                   677777775 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.014        23      19      26 ..       7      14 ..       1      15 [. 0.74
   2 ?    8.7   0.6   0.00062         1       3      11 ..      38      46 ..      37      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                                   SB-TTT-- CS
                       zf-RanBP 19 tkCvaCqa 26
                                    +C++C++
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGF 14
                                   58****86 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00062
                                   SSEE-SSS- CS
                       zf-RanBP  3 gdWdCskCl 11
                                   +dW C+ C+
  gi|121639139|ref|YP_979363.1| 38 DDWSCPDCG 46
                                   79******8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.7   0.00015      0.24       6      34 ..       7      47 ..       4      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                    Zn-ribbon_8  6 YrCeeCghefe...........vlqsisdaplta.CPeCgs 34
                                   +rC +Cg e++           +  + +d p+   CP+Cg+
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGFEYDealgwpedgiaAGTRWDDIPDDWsCPDCGA 47
                                   89*****9999999999998763333446667777*****8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.019        31      24      31 ..       9      16 ..       6      17 .. 0.88
   2 ?    7.5   0.0    0.0021       3.4      21      29 ..      39      47 ..      37      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                  A2L_zn_ribbon 24 CieCgasf 31
                                   Ci Cg+++
  gi|121639139|ref|YP_979363.1|  9 CIQCGFEY 16
                                   *****986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                  A2L_zn_ribbon 21 ylvCieCga 29
                                   + +C++Cga
  gi|121639139|ref|YP_979363.1| 39 DWSCPDCGA 47
                                   668*****8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0085        14      16      22 ..       9      15 ..       2      18 .. 0.71
   2 ?    7.0   0.1     0.003       4.8       2       7 ..      42      47 ..      41      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0085
                  zinc_ribbon_2 16 CpyCGtp 22
                                   C +CG++
  gi|121639139|ref|YP_979363.1|  9 CIQCGFE 15
                                   7777764 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.003
                  zinc_ribbon_2  2 CpnCGa 7 
                                   Cp CGa
  gi|121639139|ref|YP_979363.1| 42 CPDCGA 47
                                   778876 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.02        32      44      52 ..       6      14 ..       2      15 .. 0.81
   2 ?    6.9   0.0    0.0032       5.2      34      52 ..      27      47 ..      24      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.02
                 zinc_ribbon_10 44 kyrCpkCga 52
                                    +rC +Cg+
  gi|121639139|ref|YP_979363.1|  6 LFRCIQCGF 14
                                   59*****96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0032
                 zinc_ribbon_10 34 lapkeeleev..kyrCpkCga 52
                                    a   +++++   + Cp Cga
  gi|121639139|ref|YP_979363.1| 27 IAAGTRWDDIpdDWSCPDCGA 47
                                   5566667777668******98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.4e-05     0.088      71      98 ..       7      51 ..       3      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                                   EEETTTS-EEECHHHHH...................S-TTTSSS-EE CS
                           HypA 71 vrCreCgkefeleekal...................rCpkCgsadve 98
                                   +rC +Cg e++++                       +Cp+Cg+a+ +
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGFEYDEAL--GwpedgiaagtrwddipddwSCPDCGAAKSD 51
                                   79*****9998664..133467899*****************99765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.049        80       3      15 ..       7      19 ..       5      24 .. 0.78
   2 ?    8.6   0.1   0.00083       1.4       1      17 [.      38      54 ..      38      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.049
                         zf_UBZ  3 ylCerCgkeipes 15
                                   + C +Cg e  e+
  gi|121639139|ref|YP_979363.1|  7 FRCIQCGFEYDEA 19
                                   88*****987765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00083
                         zf_UBZ  1 dtylCerCgkeipesel 17
                                   d + C++Cg+  ++ e+
  gi|121639139|ref|YP_979363.1| 38 DDWSCPDCGAAKSDFEM 54
                                   6799*****97766666 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.2     0.001       1.7      51      67 ..      29      45 ..       3      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                          PHD_4 51 egvvnedlpnsWeCpkC 67
                                    g+  +d+p +W Cp C
  gi|121639139|ref|YP_979363.1| 29 AGTRWDDIPDDWSCPDC 45
                                   567789*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 335.62
//
Query:       gi|121639140|ref|YP_979364.1|  [L=55]
Description: rubredoxin rubA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-21   75.1   7.9    3.4e-21   75.0   7.9    1.0  1  Rubredoxin      Rubredoxin
  ------ inclusion threshold ------
      0.075   13.5   5.2       0.45   11.0   0.3    2.1  2  zf-H2C2_2       Zinc-finger double domain
        1.3    9.0   7.7        4.6    7.2   1.2    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   7.9   5.7e-25   3.4e-21       2      47 .]       4      50 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 5.7e-25
                                   EEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-B.GGGE CS
                     Rubredoxin  2 yeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgve.keqF 47
                                   y+C vC+yvYd+a+Gd++eg+++gT ++++PddW+CPdC+v+ k +F
  gi|121639140|ref|YP_979364.1|  4 YRCPVCDYVYDEANGDAREGFPAGTGWDQIPDDWCCPDCAVReKVDF 50
                                   9****************************************978777 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   7.6e-05      0.45      15      24 ..       4      13 ..       2      15 .. 0.90
   2 ?    4.9   0.6    0.0065        39      15      21 ..      37      43 ..      32      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.6e-05
                      zf-H2C2_2 15 yeCplCdkaF 24
                                   y Cp+Cd+++
  gi|121639140|ref|YP_979364.1|  4 YRCPVCDYVY 13
                                   99******98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0065
                      zf-H2C2_2 15 yeCplCd 21
                                   ++Cp C+
  gi|121639140|ref|YP_979364.1| 37 WCCPDCA 43
                                   8*****7 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.2   0.00077       4.6       4      11 ..       3      10 ..       2      14 .. 0.76
   2 ?    5.9   0.7     0.002        12       4      11 ..      36      43 ..      34      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00077
                 Zn_ribbon_SprT  4 vYrCtgCg 11
                                   +YrC+ C+
  gi|121639140|ref|YP_979364.1|  3 AYRCPVCD 10
                                   58888887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.002
                 Zn_ribbon_SprT  4 vYrCtgCg 11
                                    ++C++C 
  gi|121639140|ref|YP_979364.1| 36 DWCCPDCA 43
                                   59*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 313.39
//
Query:       gi|121639141|ref|YP_979365.1|  [L=416]
Description: transmembrane alkane 1-monooxygenase alkB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-34  119.8   9.8    1.7e-34  119.8   9.8    2.6  3  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   5.3     0.051   9.2e+02     131     174 ..      21      72 ..      12     113 .. 0.76
   2 ?   -2.5   0.0       0.2   3.5e+03     143     160 ..     109     126 ..      87     134 .. 0.47
   3 !  119.8   9.8   9.6e-39   1.7e-34       2     250 ..     138     369 ..     137     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.051
                  FA_desaturase 131 rrrk.wrllawlllllawlglwlalllllglall.......lwlvplllllf 174
                                    +r k ++l+++ l+++++l++ l+l++    +++       lw+ p+ll + 
  gi|121639141|ref|YP_979365.1|  21 WRDKkRYLWLMGLIAPTALVVMLPLIWGMNQLGWhaaaqvpLWIGPILLYVL 72 
                                    4444566777777777777777777776666666677799999999877654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.2
                  FA_desaturase 143 lllawlglwlalllllgl 160
                                    + + +l ++l+++l+ + 
  gi|121639141|ref|YP_979365.1| 109 IPFQYLSVVLGAYLFTAA 126
                                    223333333333333222 PP

  == domain 3  score: 119.8 bits;  conditional E-value: 9.6e-39
                  FA_desaturase   2 swlallla.lllglfllgitgslaHeaaHgalfkkrklnrwlndllgallglplgisysawrisH.lrHHaytngpdeDp 79 
                                    sw++ l + l +g++ +g++++ aHe +H    kk +l rwl+++       +++++y +++i+H ++HH ++++p eDp
  gi|121639141|ref|YP_979365.1| 138 SWAGKLGVaLSVGVL-GGVGINTAHEMGH----KKDSLERWLSKIT------LAQTCYGHFYIEHnRGHHVRVSTP-EDP 205
                                    688888555888888.99977********....8999*******99......889*****************6666.*** PP

                  FA_desaturase  80 dlaplalsrfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllg 159
                                     +a    +++e+l+ +l+r + g l+ ++ l+ +   +lrrl++ ++ + ++ r+ +l awl+ ++ w gl+++++ +l 
  gi|121639141|ref|YP_979365.1| 206 ASA----RFGETLWEFLPRSVIGGLRSAVHLEAQ---RLRRLGVSPWNPMTYLRNDVLNAWLMSVVLWGGLIAVFGPAL- 277
                                    ***....*********************655555...***************************996666666666544. PP

                  FA_desaturase 160 lall.lwlvplllllfllalvlnyveHyg......gdwgerqvetsasirsaswllnlltgnlnyHieHHlfPgvpwyrL 232
                                         +++++++++++ll  v ny+eHyg      ++ ++ + ++ +s++s++ + nl++++l++H++HH+ P+ +++ L
  gi|121639141|ref|YP_979365.1| 278 ---IpFVIIQAVFGFSLLEAV-NYLEHYGllrqksANGRYERCAPVHSWNSDHIVTNLFLYHLQRHSDHHANPTRRYQTL 353
                                    ...449***************.********************************************************** PP

                  FA_desaturase 233 pelhrrlrellpehglpy 250
                                    + ++    + lp  ++++
  gi|121639141|ref|YP_979365.1| 354 RSMA--GAPNLPSGYASM 369
                                    *998..446666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2262.35
//
Query:       gi|121639142|ref|YP_979366.1|  [L=495]
Description: cationic amino acid transport integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-56  191.1  44.8    3.5e-56  190.9  44.8    1.1  1  AA_permease_2  Amino acid permease
    5.9e-40  137.3  39.1    7.3e-40  137.0  39.1    1.1  1  AA_permease    Amino acid permease
      3e-18   65.6   3.8      3e-18   65.6   3.8    4.3  5  AA_permease_C  C-terminus of AA_permease
  ------ inclusion threshold ------
      0.053   14.2   1.2      0.053   14.2   1.2    5.4  4  PrgI           PrgI family protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9  44.8   7.8e-60   3.5e-56       1     402 [.      28     453 ..      28     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 7.8e-60
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn.laas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkva 77 
                                    l++++++++ +++vig+gif ++ ++a   +gpa++++++ia+  +    +l+yaE++s+lp  g +y++++a+fg+++a
  gi|121639142|ref|YP_979366.1|  28 LTWWDLVVFGVSVVIGAGIFTVTaSTAGdiTGPAIWISFLIAAATC-ALAALCYAEFASTLPVAGSAYTFSYATFGEFLA 106
                                    78******************9977555579*********9999988.58999*****888******************** PP

                  AA_permease_2  78 flsawfnwfayvpvlasilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilgilkil 153
                                    ++ +w +++  + ++a+++    syl +++g +++g+      +  + a +i++lva+++++g+k s+++  +++ +k+ 
  gi|121639142|ref|YP_979366.1| 107 WVIGWNLVLELAMGAAVVAKGWSSYLGTVFG-FGNGTghlgSLQLDWGALVIVTLVATLIALGTKLSSRFSAVVTAIKV- 184
                                    **************************99997.44444556677999*********************************. PP

                  AA_permease_2 154 lpliiliilglitvdg.ggfssl.................stetdtffpn.gwpgvllgllivlwsfdGfesaanvseev 214
                                     ++++++++g +++++ ++++++                 s  t+   ++ gw gvl+g +iv+++f+Gf+ +a ++ee 
  gi|121639142|ref|YP_979366.1| 185 SVVVLVVVVGAFYIRAaNYSPFIpepevqhhgggldqsvfSLLTGAQGSHyGWYGVLAGASIVFFAFIGFDIVATMAEET 264
                                    566777777766665549999889988887766655554433332244448****************************8 PP

                  AA_permease_2 215 kk..kdvpkaifigllivlvlyllvniaflgvvpddei.anlsnlgsvaalffeavggkvvaiivvilialsllgainta 291
                                    k+  +dvp++i  +l++v++ly+ v++++ g vp  ++ +++++ + ++a  f+a g  ++++i+++++  +l   ++ +
  gi|121639142|ref|YP_979366.1| 265 KRpqRDVPRGILASLGVVTLLYVAVSVVLSGMVPYTQLrTVPGRGPANLATAFQANGVYWASGIISVGALAGLTTVVMVL 344
                                    86669********************************9555666676799999999999********************* PP

                  AA_permease_2 292 vigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigali 371
                                    ++g++rvl+a+ardg  Pr +ak+  +g+p+r+++l+a+++   + +f +      + l ++ ++g ++ ++l+++g+++
  gi|121639142|ref|YP_979366.1| 345 MLGQCRVLFAMARDGLVPRQLAKTGSRGTPVRVTVLVAVLVATTASVFPI------TKLEEMVNVGTLFAFILVSAGVVV 418
                                    ****************************************9777777766......78999******************* PP

                  AA_permease_2 372 lrkkrphlkr....pgkilvaiigalfllfllval 402
                                    lr++rp+l+r    p+ +l+ i +++ +l+l+ +l
  gi|121639142|ref|YP_979366.1| 419 LRRTRPDLQRgftaPWVPLLPIAAVCACLWLMLNL 453
                                    ********999999999999999999999887654 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0  39.1   1.6e-43   7.3e-40       2     427 ..      33     451 ..      32     473 .. 0.84

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 1.6e-43
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                    ++v+ +  viG+g+f+ ++++++ + + ++++++l+a +  +l++l+ +e+a+  p++g++yt++  + g+ l++viG+n
  gi|121639142|ref|YP_979366.1|  33 LVVFGVSVVIGAGIFTVTASTAGDITGPAIWISFLIAAATCALAALCYAEFASTLPVAGSAYTFSYATFGEFLAWVIGWN 112
                                    78999999****************9888**************************************************** PP

                    AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvt.............gavflvvlliinlvgvkvygeaefilalikii 148
                                    +++  ++++a+   + s++++ +      +  ++              ++v+++++ ++  +g k++ +++ +++ ik+ 
  gi|121639142|ref|YP_979366.1| 113 LVLELAMGAAVVAKGWSSYLGTV------F-GFGNgtghlgslqldwgALVIVTLVATLIALGTKLSSRFSAVVTAIKVS 185
                                    66666666666655555555555......3.22224455577999999999999999999******************** PP

                    AA_permease 149 aiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfa..keeegafknfisvfvivvfaftGielvaiiagEvk 226
                                     ++ +++vg++++  ++ +++     ++++g+ +++ +++  +  + + +  ++++++++iv+faf G+ +va++a+E+k
  gi|121639142|ref|YP_979366.1| 186 VVVLVVVVGAFYIRAANYSPFIPEPEVQHHGGGLDQSVFSLLTgaQGSHYGWYGVLAGASIVFFAFIGFDIVATMAEETK 265
                                    *********9999999999998555666777667776666655557788999**************************** PP

                    AA_permease 227 dPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssans 306
                                     P++++P++il  +  +t++Yv ++++++ +vp++ l  + +   a   + ++++  gv  ++ +i ++ l+ ++ +++ 
  gi|121639142|ref|YP_979366.1| 266 RPQRDVPRGILASLGVVTLLYVAVSVVLSGMVPYTQLRTVPGRGPA--NLATAFQANGVYWASGIISVGALAGLTTVVMV 343
                                    ************************************9999966644..6777888899999******************* PP

                    AA_permease 307 slysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliils 386
                                    ++    Rvl+++a+dgl P+ l+k + rg P+r  +l++++++     as+ ++     + l  ++ + +l+ ++l+++ 
  gi|121639142|ref|YP_979366.1| 344 LMLGQCRVLFAMARDGLVPRQLAKTGSRGTPVRVTVLVAVLVATT---ASVFPI-----TKLEEMVNVGTLFAFILVSAG 415
                                    *******************************99544444443333...344444.....667899999999999999999 PP

                    AA_permease 387 ylrfRkalkyqgrsieelgfkaallplgvilvlaaliiill 427
                                     +++R++         + gf+a+ +pl++i ++ a++ ++l
  gi|121639142|ref|YP_979366.1| 416 VVVLRRTRPDL-----QRGFTAPWVPLLPIAAVCACLWLML 451
                                    99999883333.....4488888888888887777765443 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3     0.029   1.3e+02      24      44 ..      28      48 ..      24      53 .. 0.89
   2 ?   -4.4   0.5         4   1.8e+04      30      40 ..     182     192 ..     179     198 .. 0.53
   3 ?   -5.0   1.3         4   1.8e+04      32      47 ..     240     255 ..     235     257 .. 0.54
   4 ?   -1.7   0.4      0.74   3.3e+03      21      43 ..     276     299 ..     275     302 .. 0.77
   5 !   65.6   3.8   6.6e-22     3e-18       1      51 []     430     480 ..     430     480 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.029
                  AA_permease_C 24 LdsltwirfgvwmliglliYf 44
                                   L+++ ++ fgv ++ig  i+ 
  gi|121639142|ref|YP_979366.1| 28 LTWWDLVVFGVSVVIGAGIFT 48
                                   8999************99986 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 4
                  AA_permease_C  30 irfgvwmligl 40 
                                    i ++v++l+ +
  gi|121639142|ref|YP_979366.1| 182 IKVSVVVLVVV 192
                                    55555555533 PP

  == domain 3  score: -5.0 bits;  conditional E-value: 4
                  AA_permease_C  32 fgvwmliglliYflYg 47 
                                    +++   i ++ +++++
  gi|121639142|ref|YP_979366.1| 240 VLAGASIVFFAFIGFD 255
                                    4455555555555555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.74
                  AA_permease_C  21 mlqLdsltwirfgvwmli.glliY 43 
                                    +++L++ t++ ++v +++ g++ Y
  gi|121639142|ref|YP_979366.1| 276 LASLGVVTLLYVAVSVVLsGMVPY 299
                                    678999999999888887677777 PP

  == domain 5  score: 65.6 bits;  conditional E-value: 6.6e-22
                  AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYgirhs 51 
                                    F +P+vP+lP++++++ ++Lml+L++ltwirfg+w+++g+ iY++Yg+rhs
  gi|121639142|ref|YP_979366.1| 430 FTAPWVPLLPIAAVCACLWLMLNLTALTWIRFGIWLVAGTAIYVGYGRRHS 480
                                    899***********************************************8 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.2   1.2e-05     0.053       5      64 ..      16      78 ..      14     117 .. 0.73
   2 ?   -0.3   4.4       0.4   1.8e+03      21      64 ..     149     197 ..     142     228 .. 0.57
   3 ?   -2.6   2.8       2.1   9.2e+03      27      27 ..     314     314 ..     273     368 .. 0.56
   4 ?   -6.0   7.5         4   1.8e+04      61      61 ..     446     446 ..     376     479 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                           PrgI  5 DiseyeekiffgLtlRQliflvlallvaiglylllrafl...eelasvlvillavPvaalgfy 64
                                   D++e ++++   Lt+  l+++++ +++++g++ ++ +     +  a+++ +l+a+  +al+  
  gi|121639142|ref|YP_979366.1| 16 DTDEPTTRLRKDLTWWDLVVFGVSVVIGAGIFTVTASTAgdiTGPAIWISFLIAAATCALAAL 78
                                   777778888999*************************99*999999*******9997777433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                           PrgI  21 Qliflvlallvaiglylllrafl.eelasvlvill.....avPvaalgfy 64 
                                    Ql + +l++++ ++++++l   l + +++v+ +++     ++ v++ +fy
  gi|121639142|ref|YP_979366.1| 149 QLDWGALVIVTLVATLIALGTKLsSRFSAVV-TAIkvsvvVLVVVVGAFY 197
                                    5555566666666666666666642333333.233112113333333555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                           PrgI  27 l 27 
                                    +
  gi|121639142|ref|YP_979366.1| 314 A 314
                                    0 PP

  == domain 4  score: -6.0 bits;  conditional E-value: 4
                           PrgI  61 l 61 
                                    +
  gi|121639142|ref|YP_979366.1| 446 C 446
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3033.50
//
Query:       gi|121639143|ref|YP_979367.1|  [L=462]
Description: hypothetical protein BCG_3283 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-05   22.6   0.0       0.25   10.9   0.0    2.3  2  DAO             FAD dependent oxidoreductase
     0.0014   17.6   0.0       0.27   10.1   0.0    2.8  3  Trp_halogenase  Tryptophan halogenase
     0.0088   15.3   0.0       0.14   11.3   0.0    2.1  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.033   14.4   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.02   14.0   0.1       0.37    9.8   0.0    2.6  3  FAD_binding_2   FAD binding domain
      0.055   13.4   0.0       0.15   12.0   0.0    1.7  2  Glft2_N         Galactofuranosyltransferase 2 N-terminal
      0.061   12.5   0.0       0.15   11.2   0.0    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.11   11.8   0.0        5.9    6.1   0.0    2.4  3  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00011      0.25       4      32 ..       2      32 ..       1      61 [. 0.82
   2 !    9.6   0.0   0.00027       0.6     152     299 ..     117     273 ..      49     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                   EECTSHHHHHHHHHHHHT.T.EEEEESSSST CS
                            DAO  4 iiGGGiiGlstAyeLarr.g.Vtllekgdia 32
                                   +iG+ i+Gl++A+ L+     Vt++e+++ +
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDFyStVTVFERDELP 32
                                   9**************654459*******544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                                    HHHH.HHHTT-EEEESECEEE..EEEEETCEEEEE.......EECT.EEEEEEEEEEE--GGGHH..HH.HTT..CTT.. CS
                            DAO 152 lara.aealGveilegtevtg..leeedgkvwgve.......rttp.gendaadavVnaaGawsd..ll.gll..kel.. 213
                                    l+r+ ++   v+i+++  vt+  +e+++ +v+gv        ++ + +e  aad vV aaG +++   +  +   ++   
  gi|121639143|ref|YP_979367.1| 117 LRRRvLQLSNVQIVRR-LVTEpqFERRQQRVVGVLldspgsgQDRErEEFIAADLVVDAAGRGTRlpVWlTQWgyRRPae 195
                                    5555234445777777.77774347777899999987777653332233247899******9988753333333322233 PP

                                    T.SEE.EEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHH CS
                            DAO 214 d.lpi.spvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellea 291
                                    d + i     ++ +++ p  +   +++ + +   ++d++ g+ ++ ++dg ++v +t    +g  d + ++  +de++  
  gi|121639143|ref|YP_979367.1| 196 DtVDIgISYASHQFRI-PDGL--IAEKVVVAGA-SHDQSLGLGMLCYEDG-TWVLTT----FGVAD-AKPPPTFDEMRAL 265
                                    2344445577777888.6544..2233344444.9999999999999999.666565....36666.5555679999999 PP

                                    HHHHSGGG CS
                            DAO 292 lrklfPql 299
                                    + kl+P+ 
  gi|121639143|ref|YP_979367.1| 266 ADKLLPAR 273
                                    99999983 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00012      0.27       4      55 ..       2      50 ..       1      58 [. 0.92
   2 !    3.9   0.0    0.0088        20     158     212 ..     128     180 ..     105     190 .. 0.67
   3 ?   -0.7   0.0      0.22   4.9e+02     316     369 ..     308     363 ..     296     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                   EE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHH CS
                 Trp_halogenase  4 ivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrl 55
                                   ++G+ +aG  aA +l+       +vt+ e +e++     +at+p+ r+l+ l
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDFY---STVTVFERDELPEAPANRATVPQDRHLHML 50
                                   89*****************...78*********************9998865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0088
                                    HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.........S-EEE-SEEEE-SGGG-I CS
                 Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrled.........greveadlfiDcsGfrgl 212
                                    ++ rr  ++   +r++ +vv v ld           +         ++ + adl++D+ G   +
  gi|121639143|ref|YP_979367.1| 128 QIVRRLVTEPQFERRQQRVVGVLLD-----------SpgsgqdrerEEFIAADLVVDAAGRGTR 180
                                    3444444444555555555555555...........4444444444999**********97655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.22
                                    TTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--..HHHHHHHHHHHHH CS
                 Trp_halogenase 316 knvvalGlasgfvePlestsihliqaalrrLlallpdksde..paaiaefnrevar 369
                                    +++v  G+a ++ +P +++++ ++   + +L + l ++  +    ++ae nr++a+
  gi|121639143|ref|YP_979367.1| 308 RGIVPFGDAVASFNPTFGQGMTMTSLQAGHLRRALKARNSAmkGDLAAELNRATAK 363
                                    678999*****************999999999999776655323477777777665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   6.4e-05      0.14       6      58 ..       2      55 ..       1      62 [. 0.86
   2 ?    2.0   0.0     0.044        99     288     305 ..     312     329 ..     134     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                                   EE--SHHHHHHHHHHHHTTHHEEEEESSSS.SCCSSS--EEEHHHHHHHHHTT- CS
                  FAD_binding_3  6 IVGaGpaGlmlallLseaGvrvvlvekrst.tvvlpradglnqrtmellrqlGl 58
                                   ++Ga+ aGl +a++Ls     v++ e+ +  +++  ra + ++r + +l  +G 
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDFYSTVTVFERDELpEAPANRATVPQDRHLHMLMARGA 55
                                   9****************9788999999885145666*************99996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.044
                                    E-GGGTEEE-STTSHHHH CS
                  FAD_binding_3 288 laGDAaHihpPtgGqGlN 305
                                      GDA+    Pt GqG+ 
  gi|121639143|ref|YP_979367.1| 312 PFGDAVASFNPTFGQGMT 329
                                    46**************95 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.033       1      29 [.       2      30 ..       2      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                   ++Ga ++Gl+aA+ L++    v+++e+ +
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDFYSTVTVFERDE 30
                                   8****************8889*****975 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.12   2.6e+02       4      29 ..       2      27 ..       1      31 [. 0.78
   2 ?    9.8   0.0   0.00017      0.37     122     205 ..      95     183 ..      48     201 .. 0.66
   3 ?   -0.7   0.0      0.26   5.7e+02     316     354 ..     329     366 ..     233     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                                   EE--SHHHHHHHHHHHHTTT-EEEEE CS
                  FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavve 29
                                   ViG+ +AGL+AA  +++   +v+v e
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDFYSTVTVFE 27
                                   9***********87777666666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                                    TEEEE-.STT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT......EEEEEEEEET...TTTCEEEEE CS
                  FAD_binding_2 122 tartlhdaadarr.etlvtghallarlvesarkagvdfqerteadeLivedg......rvtGavvenp...esgrevrir 191
                                    t   +h ++++++   + + ++l   l +++    +++ +   +++L++e +      rv+G+ +  p   ++ +++++ 
  gi|121639143|ref|YP_979367.1|  95 T---GH-TLRKEFtAYVPSRPHLEWQLRRRV----LQLSNVQIVRRLVTEPQferrqqRVVGVLLDSPgsgQDREREEFI 166
                                    3...34.444444444444455555555555....77788888888988866666777********99988666666788 PP

                                    ES.EEEE-----GG.... CS
                  FAD_binding_2 192 ak.avvlatgGfgr...a 205
                                    a   vv+a+g  g     
  gi|121639143|ref|YP_979367.1| 167 AAdLVVDAAG-RGTrlpV 183
                                    8835555555.5542553 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.26
                                    E-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTS CS
                  FAD_binding_2 316 dashgldaegleatleaineeaangldkdfgrgidpadr 354
                                    ++++ l+a +l++ l+a+n +++ +l ++ +r++ +++ 
  gi|121639143|ref|YP_979367.1| 329 TMTS-LQAGHLRRALKARNSAMKGDLAAELNRATAKTTY 366
                                    4445.9999999999999999999999888887766655 PP

>> Glft2_N  Galactofuranosyltransferase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.2   9.4e+03     104     121 ..     227     244 ..     215     248 .. 0.68
   2 ?   12.0   0.0   6.8e-05      0.15      51      68 ..     288     305 ..     260     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.2
                        Glft2_N 104 eaveleldLkpfedGGwl 121
                                    +   l l +  +edG w+
  gi|121639143|ref|YP_979367.1| 227 HDQSLGLGMLCYEDGTWV 244
                                    445667777889999997 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.8e-05
                        Glft2_N  51 yfnafpasyWrrwsqlds 68 
                                     f afpas Wrr+ +l++
  gi|121639143|ref|YP_979367.1| 288 AFHAFPASRWRRYDKLER 305
                                    499***********9986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.9e-05      0.15       4      58 ..       1     128 [.       1     227 [. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                                    EEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                    Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeias................. 57 
                                    +viG+ +AGl aa+ l+     vt++e          + t++ ++ l    ++g++e+ + +                  
  gi|121639143|ref|YP_979367.1|   1 MVIGASIAGLCAARVLSDFYSTVTVFErdelpeapaNRATVPQDRHLHMLMARGAQEFDSLFPgllhdmvaagvpmlenr 80 
                                    7*************************777644444444444444444444444444444433376666666666666666 PP

                                    ...............................................H CS
                                    ...............................................x RF
                    Pyr_redox_2  58 ...............................................e 58 
                                                                                   +
  gi|121639143|ref|YP_979367.1|  81 pdciylgaaghvlgtghtlrkeftayvpsrphlewqlrrrvlqlsnvQ 128
                                    666666666666666666666666666666655555555444444443 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.023        52      22      49 ..       2      28 ..       1      32 [. 0.83
   2 ?    6.1   0.0    0.0026       5.9     103     168 ..     117     177 ..     104     187 .. 0.83
   3 ?   -3.4   0.0         2   4.5e+03     155     172 ..     214     231 ..     202     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                                   EE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 22 ivGaGssGLtaayylakkpdlkvailer 49
                                   ++Ga  +GL aa++l+      v+++er
  gi|121639143|ref|YP_979367.1|  2 VIGASIAGLCAARVLSDF-YSTVTVFER 28
                                   89*************987.566777776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0026
                                    HHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GS CS
                           Thi4 103 llskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGh 168
                                    l  +vlql+nv+++  ++ e    r +++v Gv +++    ++          +i a +vvda+G 
  gi|121639143|ref|YP_979367.1| 117 LRRRVLQLSNVQIVRRLVTEPQFERRQQRVVGVLLDSPGSGQDR-----EREEFIAADLVVDAAGR 177
                                    6679**********************9*******9998777775.....34567788888888776 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2
                                    EEEEEEEEEE--GSSSTT CS
                           Thi4 155 lvirakvvvdatGhdgei 172
                                     +i  kvvv  + hd ++
  gi|121639143|ref|YP_979367.1| 214 GLIAEKVVVAGASHDQSL 231
                                    567788999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3127.35
//
Query:       gi|121639144|ref|YP_979368.1|  [L=408]
Description: mannose-6-phosphate isomerase manA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-59  201.3   0.0    4.4e-59  200.6   0.0    1.3  1  PMI_typeI     Phosphomannose isomerase type I
  ------ inclusion threshold ------
      0.017   15.0   0.1        3.4    7.6   0.1    2.6  2  AraC_binding  AraC-like ligand binding domain
      0.043   13.5   0.0        3.8    7.3   0.0    2.6  2  Cupin_2       Cupin domain


Domain annotation for each model (and alignments):
>> PMI_typeI  Phosphomannose isomerase type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.0   7.3e-63   4.4e-59       4     368 ..       4     367 ..       1     370 [. 0.85

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 7.3e-63
                                    EEEEEEE-TTBEECGGSHHHHHHHHH-TT..TTSCEEEEEEC--TTS-EECTTTC....CCCHCHHHHHHHTGHHHCCHH CS
                      PMI_typeI   4 LqcgvqnyaWGkiGsesalakllaasdPsieedkpyaElWmgtHpkgpskvlnkk....lkdvvlkellaelresvgkkf 79 
                                    L+ +++ yaWG   s++a+a++ +   P     +p aElW g+Hp  p+  +  +    l +   +++  +l+ +   +f
  gi|121639144|ref|YP_979368.1|   4 LRGALRTYAWG---SRTAIAEFTGRPVPA---AHPEAELWFGAHPGDPAWLQTPHgqtsLLEALVADPEGQLGSASRARF 77 
                                    5667899****...9**************...9****************9766554467888888888889999999*** PP

                                    TSS-SEEEEEEEESS---EEE---HHHHHH..........HHHH.TCCCHCCCTTTEEEEESS.EEEEEEE..HHHHHHH CS
                      PMI_typeI  80 geelpfLfKvLsvekvlSiqvHPdKklaei..........lhaadpknYpddNhkpElaiAltdFeglcgfrpleeivef 149
                                    g+ lpfL KvL + ++lS+q+HP  ++a            +     +nY d  hkpEl +Al +Fe+l+gfr        
  gi|121639144|ref|YP_979368.1|  78 GDVLPFLVKVLAADEPLSLQAHPSAEQAVEgylreermgiPVSSPVRNYRDTSHKPELLVALQPFEALAGFR-------- 149
                                    ************************9988889999999998888999*************************8........ PP

                                    CCCEHCCHCCCECCHHCCHHHHHHCCHTTSHHHHCCCCHHCCHCHCCCTTTHHCCCHCCCCCCC.CCCC-H...HHCCCC CS
                      PMI_typeI 150 lkkvselaeligeetaksleelvslieagdpealkkkkvlqklFssllnsekekikqklallve.riqssd...aevnkt 225
                                      +++ + el+   ++++l+  + l ++g+ +a      l++lF++ + + +  i   +  +++ +iq      +e+ ++
  gi|121639144|ref|YP_979368.1| 150 --EAARTTELLRALAVSDLDPFIDLLSEGS-DADG----LRALFTTWITAPQPDIDVLVPAVLDgAIQYVSsgaTEFGAE 222
                                    ..4567778888888888888888887333.3333....689***99999999998877666541555444222555555 PP

                                    -HHHHCCHCHHHSTTTTCHCH.TTEEEEEE.TT.EECCHCCHHCECCEEEEEEEEES-EEEEECCCECCEEECHCCHCH. CS
                      PMI_typeI 226 dlaelidrlneqyPddiGlfa.llLNlvkLnpGEAmflkandphaylsGdivecmaasdnvvRaGlTpKfidvkelveml 304
                                      a+ +  l e yP+d G+ a llLN + L pGEA+fl a + hay++G  ve+ma+sdnv+R GlTpK +dv+el+  l
  gi|121639144|ref|YP_979368.1| 223 --AKTVLELGERYPGDAGVLAaLLLNRISLAPGEAIFLPAGNLHAYVRGFGVEVMANSDNVLRGGLTPKHVDVPELLRVL 300
                                    ..47788899********************************************************************99 PP

                                    EEEEEECCCCEE--BSCEECEEEEEEECCCCECCEEECCC.....TTEEEEE-TTS-EEEEEEECEEEE CS
                      PMI_typeI 305 tYkykpsdelklqqteslldasvlydppieefavektklk.....kgeatilplesasiliaveGtati 368
                                     +  +p+ ++ l +    +   ++++ p +efa +   l+     +     ++ ++++il+++eG at+
  gi|121639144|ref|YP_979368.1| 301 DF--APTPKARLRPPIRREGLGLVFETPTDEFAATLLVLDgdhlgHEVDASSGHDGPQILLCTEGSATV 367
                                    99..88888888887777777899999******9999776554323334456679************98 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0054        32      42      63 ..     247     268 ..     245     274 .. 0.86
   2 ?    7.6   0.1   0.00057       3.4      19      56 ..     350     387 ..     334     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0054
                                    EEEE-TT-EEEE-TTS-EEEEE CS
                   AraC_binding  42 tydlgpGdlfLlppgepHdyes 63 
                                    +  l pG+ ++lp g +H y  
  gi|121639144|ref|YP_979368.1| 247 RISLAPGEAIFLPAGNLHAYVR 268
                                    56799**************976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00057
                                    ETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TT CS
                   AraC_binding  19 hvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppg 56 
                                      hd  +i ++teG+++++ + +   l+ G+  ++  +
  gi|121639144|ref|YP_979368.1| 350 SGHDGPQILLCTEGSATVHGKCGSLTLQRGTAAWVAAD 387
                                    679****************************9999765 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00064       3.8      38      58 ..     247     267 ..     240     274 .. 0.91
   2 ?    3.2   0.0     0.012        70      13      51 ..     349     386 ..     341     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00064
                                    EEEEETTEEEEE-TT-EEEEE CS
                        Cupin_2  38 eveleaGdsvyfpagtpHrfr 58 
                                    ++ l +G++++ pag  H+++
  gi|121639144|ref|YP_979368.1| 247 RISLAPGEAIFLPAGNLHAYV 267
                                    67899*************985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                                    EECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-T CS
                        Cupin_2  13 shrHpgedeffyVleGegeltvdgeeveleaGdsvyfpa 51 
                                    s  H+g  +++ + eG ++++      +l++G ++ + a
  gi|121639144|ref|YP_979368.1| 349 SSGHDGP-QILLCTEGSATVHGKCGSLTLQRGTAAWVAA 386
                                    5569999.************9776689999998887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2659.40
//
Query:       gi|121639145|ref|YP_979369.1|  [L=346]
Description: hypothetical protein BCG_3285c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2704.68
//
Query:       gi|121639146|ref|YP_979370.1|  [L=465]
Description: phosphomannomutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-31  107.7   0.0    6.9e-31  106.8   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.7e-26   91.6   0.1    1.1e-25   90.1   0.0    1.8  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.6e-23   82.1   0.1    1.6e-22   80.1   0.1    2.1  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
      7e-10   39.0   0.0    1.5e-09   37.9   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   1.5e-34   6.9e-31       4     123 ..      12     128 ..       9     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.5e-34
                                    BBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHH CS
                      PGM_PMM_I   4 fgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavs 83 
                                     +++++Rg vg +e++++lv+ lg+a+a+ ++ e ++++vv+G+D+R ss+ la+a+aag++ +G++v+++gl++t+ ++
  gi|121639146|ref|YP_979370.1|  12 IKAYDVRGLVG-EEIDESLVTDLGAAFARLMRTE-DARPVVIGHDMRDSSPSLADAFAAGVTGQGLDVVRVGLASTDQLY 89 
                                    6789*******.67******************96.********************************************* PP

                                    HHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHH CS
                      PGM_PMM_I  84 fairklkadagimitaSHnppeyngiKvylsnGgpispev 123
                                    fa   l++ +  m+taSHnp+ yngiK++ +   p+  ++
  gi|121639146|ref|YP_979370.1|  90 FASGLLDCPG-AMFTASHNPAAYNGIKMCRAAAKPVGADT 128
                                    ********98.9*****************99988887765 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   2.4e-29   1.1e-25       5     114 .]     268     373 ..     264     373 .. 0.91
   2 ?   -3.1   0.0         2     9e+03      28      45 ..     384     401 ..     381     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.4e-29
                                    HHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS-- CS
                    PGM_PMM_III   5 llallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkD 84 
                                    +++++a++l++  ++ ga+++++v ts+a+ + ++++g++ ++++vG++y++++m e+ga +GgE+S+h++f+d+   + 
  gi|121639146|ref|YP_979370.1| 268 TALVAARELNR--EI-GATIIHNVITSRAVPELVAERGGTPLRSRVGHSYIKALMAETGAIFGGEHSAHYYFRDFWGADS 344
                                    45666776755..45.556************************************************************* PP

                                    HHHHHHHHHHHHHHHTS-HHHHHHHHHHHH CS
                    PGM_PMM_III  85 Gilaallvleilaetgkslselleellkky 114
                                    G+laal+vl++l e+ ++lsel  + +++y
  gi|121639146|ref|YP_979370.1| 345 GMLAALHVLAALGEQSRPLSELT-ADYQRY 373
                                    **********************9.668877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                    TTS-THHHHHHHHTT-EE CS
                    PGM_PMM_III  28 vmtslalervakklgikl 45 
                                    v +s  +e v+k++g ++
  gi|121639146|ref|YP_979370.1| 384 VDSSACVEAVLKSFGNRI 401
                                    779999999999998765 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.1   9.5e+03      60      87 ..     103     130 ..      95     131 .. 0.76
   2 !   80.1   0.1   3.6e-26   1.6e-22       3     103 .]     160     259 ..     159     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                                    TSS----TT-TTTTHHHHGGGGG-SEEE CS
                     PGM_PMM_II  60 tkapnpeekealkllielvkkegadlgl 87 
                                    t + np ++  +k++ +++k  gad gl
  gi|121639146|ref|YP_979370.1| 103 TASHNPAAYNGIKMCRAAAKPVGADTGL 130
                                    4566788888999999999999999886 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 3.6e-26
                                    HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-.EEEES-----TT-TTSS----TT-TTTTHHHHGGGG CS
                     PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgv.dvvelnaepdpdfptkapnpeekealkllielvkke 81 
                                    Y   l++ vd+     ++l+v++d+++G +g++++ +l+ ++   + +l +e d++fp++ +np ++++l +l+++v+++
  gi|121639146|ref|YP_979370.1| 160 YGAFLRSLVDT--SGLRPLRVAVDAGNGMAGHTAPAVLGVIDSiTLLPLYFELDGSFPNHEANPLDPANLVDLQAYVRDT 237
                                    55667777774..455889*********************99956666******************************** PP

                                    G-SEEEEE-TTS-BEEEEETTE CS
                     PGM_PMM_II  82 gadlglafDgDaDRlgvvderG 103
                                    gad+glafDgDaDR++vvderG
  gi|121639146|ref|YP_979370.1| 238 GADIGLAFDGDADRCFVVDERG 259
                                    ********************98 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   3.4e-13   1.5e-09       1      73 [.     378     454 ..     378     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.4e-13
                                    CCCCCHCC-TT..EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                     PGM_PMM_IV   1 linvrveekakvvaalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                    +in+ v +  + v+a+ + +++     +  +g+ ++l+d +++++R S+Tepllr++vE++s   ++ ++ +v +++
  gi|121639146|ref|YP_979370.1| 378 EINFTVVDSSACVEAVLKSFGNRivsiDHLDGVTVDLGDDSWFNLRSSNTEPLLRLNVEGRSVGDVDAVVRQVSAEI 454
                                    89999999977788888888886777777788888888888888*****************9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3388.22
//
Query:       gi|121639147|ref|YP_979371.1|  [L=163]
Description: hypothetical protein BCG_3287c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-48  162.1   0.0    1.2e-47  161.5   0.0    1.2  1  DUF3499   Protein of unknown function (DUF3499)


Domain annotation for each model (and alignments):
>> DUF3499  Protein of unknown function (DUF3499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.0   6.8e-52   1.2e-47       2     124 .]      22     160 ..      21     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 6.8e-52
                        DUF3499   2 RrCsrpgCsrpAvatltyvYadstavlGPLataaephsyDLCeeHaerltaPrGWelvrleeelaeaepdeddlvALAda 81 
                                    RrC+rpgC ++Avatlt+vY+dstav+GPLata+ephs+DLC  Ha r+taPrGWelvr++ +l +++pdeddlvALAda
  gi|121639147|ref|YP_979371.1|  22 RRCCRPGCPHYAVATLTFVYSDSTAVIGPLATAREPHSWDLCVGHAGRITAPRGWELVRHAGPL-PSHPDEDDLVALADA 100
                                    9************************************************************999.9************** PP

                        DUF3499  82 vreaaeee.................reeeaepepaeeakreeeekate................srrrghLrvlrd 124
                                    vre++ ++                 +                 ++a++                +rrrghLrvl+d
  gi|121639147|ref|YP_979371.1| 101 VREGGPSAgrrhhpggngaplhgfdD----------------FPAAATgaptgggvlappepgaGRRRGHLRVLPD 160
                                    ****9887555555554444444431................122222445555566666666699********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1223.19
//
Query:       gi|121639148|ref|YP_979372.1|  [L=139]
Description: hypothetical protein BCG_3288 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.5   0.1    2.1e-06   27.8   0.1    1.5  1  Zincin_1  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   1.2e-10   2.1e-06      44      90 ..      86     132 ..      39     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.2e-10
                                    -GGG--EEEEEHHHHHHH--TT--HHHHHHHHHHHHHHHHHTT-HHH CS
                       Zincin_1  44 agslpdrivlyrrpllavaetreeleeevretllHEighhfGldded 90 
                                     +++  rivl+r+p++++a+++eel e+ +e+l+ +++ ++ +d   
  gi|121639148|ref|YP_979372.1|  86 GNATRARIVLFRKPIERRAKDTEELGELLHEILVAQVAIYLDVDPSV 132
                                    566779********************************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 967.66
//
Query:       gi|121639149|ref|YP_979373.1|  [L=89]
Description: transcriptional regulatory protein whiB-like whiB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-27   95.4   2.4    2.6e-27   95.2   2.4    1.1  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   2.4   1.5e-31   2.6e-27       1      64 []      21      84 ..      21      84 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.5e-31
                           Whib  1 WreraaCrgedpelffpekgdreeeAkavCarCpVrreCleealeegeeyGvwGGltereRraL 64
                                   W++ra C+++dpe+ffpekg +++eAk++C  C+Vr+eCle+al+++e++G+wGGl+ereRr+L
  gi|121639149|ref|YP_979373.1| 21 WQDRALCAQTDPEAFFPEKGGSTREAKKICMGCEVRHECLEYALAHDERFGIWGGLSERERRRL 84
                                   **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 698.56
//
Query:       gi|121639150|ref|YP_979374.1|  [L=331]
Description: LPPG:FO 2-phospho-L-lactate transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-63  214.0   0.0    3.1e-63  213.7   0.0    1.0  1  UPF0052         Uncharacterised protein family UPF0052
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.27   11.0   0.0    1.6  1  AIMP2_LysRS_bd  AIMP2 lysyl-tRNA synthetase binding domain


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.7   0.0   3.5e-67   3.1e-63       1     257 [.       3     294 ..       3     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.7 bits;  conditional E-value: 3.5e-67
                                    EEEEE-CHHHHHHHHHHCCSS...............CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S CS
                        UPF0052   1 vvvlgGGtGlskllrglkevt...............aeltavvtvaDdggssGelrrelgllaigDirnvlval...idd 62 
                                    v+vl+GG+G++++l g++++                ++l+avv+v+Dd +++G       l++++D+++++++l   +d 
  gi|121639150|ref|YP_979374.1|   3 VTVLAGGVGGARFLLGVQQLLglgqfaansahsdadHQLSAVVNVGDDAWIHG-------LRVCPDLDTCMYTLgggVDP 75 
                                    89******************9********************************.......****************9888 PP

                                    -C..........HHHHHCH-B-SS......SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS-- CS
                        UPF0052  63 er..........lleeLfqyRfkg......dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpv 125
                                    +r          +++eL++y ++       d+dla+h++++++L+a     g +l++++eal++++++++r+lPatdd++
  gi|121639150|ref|YP_979374.1|  76 QRgwgqrdetwhAMQELVRYGVQPdwfelgDRDLATHLVRTQMLQA-----GyPLSQITEALCDRWQPGARLLPATDDRC 150
                                    8899999999**********6665**********************.....99*************************** PP

                                    EEEEEETTS-E.....EE.STTTGGGG-S....-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSC CS
                        UPF0052 126 elsaeledGee.....it.geskiseark.lkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvp 197
                                    e++++++d        i+ +e+++   r+ +++p+++ +f+++e+++aa e+++a+++Ad+i+l+p+++++Si++iL+vp
  gi|121639150|ref|YP_979374.1| 151 ETHVVITDPVDesrkaIHfQEWWV---RYrAQVPTHSfAFVGAEKSSAATEAIAALADADIIMLAPSNPVVSIGAILAVP 227
                                    ******8876677777********...88899************************************************ PP

                                    CHHHHHHH-SSEEEEE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S........-SEEEEE-S- CS
                        UPF0052 198 giaealreskakkvlvsnimtqkGetdgfsvsdhvkaieravg.....kgvakay........vdavlvntse 257
                                    gi++alre++a++v+ s+i++      +++++++++++++ +g     ++v+++y        +d +lv++++
  gi|121639150|ref|YP_979374.1| 228 GIRAALREATAPIVGYSPIIG------EKPLRGMADTCLSVIGvdstaAAVGRHYgarcatgiLDCWLVHDGD 294
                                    ********************9......999999999999999998888666667788888888*****98873 PP

>> AIMP2_LysRS_bd  AIMP2 lysyl-tRNA synthetase binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     3e-05      0.27      16      28 ..      58      70 ..      54      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                 AIMP2_LysRS_bd 16 ikvdLPTCMYrlp 28
                                   +++dL TCMY l+
  gi|121639150|ref|YP_979374.1| 58 VCPDLDTCMYTLG 70
                                   789*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2629.83
//
Query:       gi|121639151|ref|YP_979375.1|  [L=448]
Description: F420-0--gamma-glutamyl ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-43  146.3   0.3    9.4e-40  136.5   0.3    2.1  1  F420_ligase     F420-0:Gamma-glutamyl ligase
      1e-26   94.0   0.0      2e-26   93.1   0.0    1.5  1  Nitroreductase  Nitroreductase family
    0.00021   20.9   0.0      0.008   15.8   0.0    2.2  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   0.3   1.6e-43   9.4e-40       3     244 .]      19     219 ..      17     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 1.6e-43
                                    .-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H.......... CS
                    F420_ligase   3 ktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsli 82 
                                     +p+ ++gddl + v+ +       l+dgD+vvvt+kvv+k+eg++v   +  p e+  ++++kl  i+           
  gi|121639151|ref|YP_979375.1|  19 GLPEFRPGDDLSAAVAAAAP----WLRDGDVVVVTSKVVSKCEGRLVPAPED-P-EQRDRLRRKL--IED---------- 80 
                                    5899************9999....79*********************99887.4.4556999999..444.......... PP

                                    ........HHHHHHHHTEEEEEE-S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHH CS
                    F420_ligase  83 LkalakatrkvevvlsepsdevgnqlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkert 162
                                            + v v+ ++       +li+e+       +lGl+ + ag+d snv ++ l+llP dpd+sa+ +++ l+er+
  gi|121639151|ref|YP_979375.1|  81 --------EAVRVLARKD-----RTLITEN-------RLGLVQAAAGVDGSNVGRSELALLPVDPDASAATLRAGLRERL 140
                                    ........4566665543.....368999*.......******************************************* PP

                                    S---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEE CS
                    F420_ligase 163 gkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvlv 242
                                    g++v+V+i  +D+ gr+w+ ++++ a+g +gl  lr++ g +d +g+el +t+ av+de++++adLv G+    tPv++v
  gi|121639151|ref|YP_979375.1| 141 GVTVAVVI--TDTMGRAWRNGQTDAAVGAAGLAVLRNYAGVRDPYGNELVVTEVAVADEIAAAADLVKGKL-TATPVAVV 217
                                    ********..************************************************************9.99****** PP

                                    ES CS
                    F420_ligase 243 rg 244
                                    rg
  gi|121639151|ref|YP_979375.1| 218 RG 219
                                    *8 PP

>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   3.3e-30     2e-26       4     170 .]     260     428 ..     258     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 3.3e-30
                                    --B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHH CS
                 Nitroreductase   4 RrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeelklka 83 
                                    RrS+R F+ +pvp + +e  ++ a +aP  ++++p+rfv +q+ ++r++l++ +++++++   ++ l  +    e+   +
  gi|121639151|ref|YP_979375.1| 260 RRSVRRFSTDPVPGDLVEAAVAEALTAPAPHHTRPTRFVWLQTPAIRARLLDRMKDKWRSDLTSDGLPADAI--ERRVAR 337
                                    9************************************************************99999998876..899*** PP

                                    HHHHHHSSEEEEE....---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S.. CS
                 Nitroreductase  84 qkalagapvlivi....vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpde 159
                                     + l++ap +++     +  +++ + ++ + +     + +gaa+q ll+a++ +Glgsc+ig +  aa+ vr+ l+lp +
  gi|121639151|ref|YP_979375.1| 338 GQILYDAPEVVIPmlvpDGAHSYPDAARTDAEHTMFTVAVGAAVQALLVALAVRGLGSCWIGSTIFAADLVRDELDLPVD 417
                                    ****************9888888888888888888999****************************************88 PP

                                    SEEEEEEEEE- CS
                 Nitroreductase 160 eeivvliavGy 170
                                    +e++++ia+Gy
  gi|121639151|ref|YP_979375.1| 418 WEPLGAIAIGY 428
                                    **********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.013        78       8      28 ..     259     279 ..     254     318 .. 0.77
   2 !   15.8   0.0   1.3e-06     0.008      78     135 ..     371     431 ..     351     445 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.013
                                    H--B---B--S---HHHHHHH CS
                 TM1586_NiRdase   8 kRhsvRkYkdealeeelleel 28 
                                     R+svR+++  +++ +l+e+ 
  gi|121639151|ref|YP_979375.1| 259 LRRSVRRFSTDPVPGDLVEAA 279
                                    599999999999999988764 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST..............T-S-EEEEE-BS- CS
                 TM1586_NiRdase  78 edleekaGYygeqlvLkltalGlgtcWvggtykk...kkakvelkkgeklvivIalGyakt 135
                                    + + + +G   + l+  l  +Glg+cW+g+t      ++ +++l+ + + + +Ia+Gya++
  gi|121639151|ref|YP_979375.1| 371 TMFTVAVGAAVQALLVALAVRGLGSCWIGSTIFAadlVRDELDLPVDWEPLGAIAIGYADE 431
                                    556678888999999***************9876667888899999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3391.08
//
Query:       gi|121639152|ref|YP_979376.1|  [L=553]
Description: DNA methylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-07   29.5   0.0     0.0006   19.2   0.0    2.1  2  N6_Mtase  N-6 DNA Methylase
  ------ inclusion threshold ------
      0.016   15.7   0.0      0.031   14.8   0.0    1.4  1  Eco57I    Eco57I restriction-modification methylase


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.7e-08    0.0006      15      71 ..      30      84 ..      26     102 .. 0.83
   2 !    8.3   0.0   0.00014       1.2     120     189 ..     115     189 ..      93     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-08
                       N6_Mtase 15 rkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee 71
                                   +k a+ + k  G ++TP +v +++++ +++   + ++ p cG g +l + +  ++++
  gi|121639152|ref|YP_979376.1| 30 GKTAASADKVRGGYYTPPAVARFLAHWVHQAGPK-ILEPSCGDGRILRELSA-ITDH 84
                                   56788899999*****************988885.*********99877665.4445 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00014
                       N6_Mtase 120 fekdkkfdvvvaNppfnq.kewkektlekderfrea..vapksnadla..fllhiieslkpkGraavvlangvLf 189
                                    +++  + d v+ Npp+    +w++++      +  +  + p++  +    f+      ++++Gr+++v++   L 
  gi|121639152|ref|YP_979376.1| 115 KTQLGSWDGVAGNPPYIRfGNWASEQRDPALELMRRvgLRPTKLTNAWvpFVVASTTLARDGGRVGLVVPAELLQ 189
                                    346778999*******76257855555444433333566666544422248888888889*********988775 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.5e-06     0.031       4      82 ..     122     213 ..     120     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                         Eco57I   4 dviiGNPPYqeseakkelkaleek...............akdiyqkFvekalkle..dkylaliiparflasgkglkefr 66 
                                    d + GNPPY++     +++++++                 ++ ++ Fv  +++l+   ++++l++pa  l +  + +++r
  gi|121639152|ref|YP_979376.1| 122 DGVAGNPPYIRFG---NWASEQRDpalelmrrvglrptkLTNAWVPFVVASTTLArdGGRVGLVVPAELL-QVTYAAQLR 197
                                    7799********9...7776666688999********998999***********987789**********.999****** PP

                         Eco57I  67 ekllkdkklkklvefe 82 
                                    e+ll+  +  +lv+fe
  gi|121639152|ref|YP_979376.1| 198 EFLLSRYREITLVTFE 213
                                    ***9987766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3822.15
//
Query:       gi|121639153|ref|YP_979377.1|  [L=359]
Description: mannose-1-phosphate guanyltransferase manC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-43  147.0   0.0    9.2e-43  146.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    4.8e-12   46.5   0.1      6e-12   46.2   0.1    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.2e-09   37.5  10.7     0.0011   18.6   0.6    4.0  3  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
      0.041   12.0   0.1      0.055   11.6   0.1    1.1  1  DUF4954          Domain of unknown function (DUF4954)
       0.22   11.3  13.1        3.1    7.6   1.5    3.9  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
        0.3   10.2   0.0          1    8.4   0.0    1.6  2  Queuosine_synth  Queuosine biosynthesis protein


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   3.1e-46   9.2e-43       2     244 ..       8     235 ..       7     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 3.1e-46
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    av+L+GG+GtRL+PLt + +k+++p +g  + + + lsr+a++gie  ++  t+++ + +e ++++gs +g+++++++e+
  gi|121639153|ref|YP_979377.1|   8 AVVLVGGKGTRLRPLTLSAPKPMLPTAGL-PFLTHLLSRIAAAGIEH-VILGTSYKPAVFEAEFGDGSALGLQIEYVTEE 85 
                                    89***************************.*****************.9999**************************** PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEE CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrver 161
                                     + gt + +a +a  l+++     ++v++gD+l + ++ ++++++++++a  +vt+ +v+v +++++G++ +dee+rv  
  gi|121639153|ref|YP_979377.1|  86 HPLGTGGGIANVAGKLRNDT----AMVFNGDVLSGADLAQLLDFHRSNRA--DVTLQLVRVGDPRAFGCVPTDEEDRVVA 159
                                    *****************988....7*************************..9*************************** PP

                                    EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
                NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                                    f EK + ++ ++ +++G Yvf+++v++ +     +  r+ +   +++p++l++g+ + +   ++ +yW+D Gt++++++ 
  gi|121639153|ref|YP_979377.1| 160 FLEKTEDPP-TDQINAGCYVFERNVIDRI-----PQGREVSVEREVFPALLADGDCKIYGYVDA-SYWRDMGTPEDFVRG 232
                                    *********.99*****************.....88999999*************998866666.5***********998 PP

                                    HHH CS
                NTP_transferase 242 nek 244
                                    +++
  gi|121639153|ref|YP_979377.1| 233 SAD 235
                                    876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1     2e-15     6e-12       1     120 [.       8     135 ..       8     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2e-15
                                    EEEEEESS-TTTT....T.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHH......HHTTCTS-EEE-TTS CS
                   NTP_transf_3   1 aviLAGGrSsRmg....g.dKallplggkpllervldalraagvdevvvvggd.eevla......alarlgvrvvededp 68 
                                    av+L GG+++R+     + +K++lp +g p+l ++l +++aag+++v++ + + ++v +       + +l++++v++e+ 
  gi|121639153|ref|YP_979377.1|   8 AVVLVGGKGTRLRpltlSaPKPMLPTAGLPFLTHLLSRIAAAGIEHVILGTSYkPAVFEaefgdgSALGLQIEYVTEEH- 86 
                                    79**********7554427********************************9954443334444444677899999985. PP

                                    S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEE CS
                   NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvv 120
                                      g+++++a  + ++ ++d ++v+ +D+  l+ + +++ll+ +++++adv+ 
  gi|121639153|ref|YP_979377.1|  87 PLGTGGGIANVAGKL-RNDTAMVFNGDV--LSGADLAQLLDFHRSNRADVTL 135
                                    69************9.9***********..899********99999999865 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   4.5e-07    0.0013       4      35 ..     255     286 ..     254     287 .. 0.91
   2 !    6.1   0.3    0.0033       9.8      19      35 ..     287     303 ..     285     304 .. 0.57
   3 !   18.6   0.6   3.6e-07    0.0011       2      33 ..     305     335 ..     304     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.5e-07
                                    EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    +++++ + p+a + g++++G+++ Ig+g+++ 
  gi|121639153|ref|YP_979377.1| 255 VHDGAAVSPGALLIGGTVVGRGAEIGPGTRLD 286
                                    68899999********************9875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0033
                                    TEEE-TTEEEETTEEEE CS
                        Hexapep  19 nVkIGdnvkIgagvvig 35 
                                    +++I d+v+++ag+vi 
  gi|121639153|ref|YP_979377.1| 287 GAVIFDGVRVEAGCVIE 303
                                    44555666666666664 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3.6e-07
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                    ++IG ++ Igp a i+++V IGd++ Iga + 
  gi|121639153|ref|YP_979377.1| 305 SIIGFGARIGPRALIRDGV-IGDGADIGARCE 335
                                    68*****************.*********886 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.8e-05     0.055     218     271 ..     277     330 ..     257     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                        DUF4954 218 veiGegViledfiissGskikdgavisrcfvGqavklkkqfsaedsllfaNcqg 271
                                     eiG g  l+ ++i  G +++ g vi+r+++G + +++ ++ + d ++++ +++
  gi|121639153|ref|YP_979377.1| 277 AEIGPGTRLDGAVIFDGVRVEAGCVIERSIIGFGARIGPRALIRDGVIGDGADI 330
                                    589**************************************9999999987764 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4     0.012        36      16      30 ..     268     283 ..     263     286 .. 0.83
   2 ?    5.9   2.1    0.0036        11       4      33 ..     273     303 ..     271     304 .. 0.71
   3 ?    7.6   1.5     0.001       3.1       3      28 ..     306     332 ..     305     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                    E.SEEE-TT-EE-TT- CS
                      Hexapep_2  16 i.GvslGdncvvgaGv 30 
                                    i G+ +G+++ +g+G 
  gi|121639153|ref|YP_979377.1| 268 IgGTVVGRGAEIGPGT 283
                                    668***********96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                                    E-TT-EE-TT-EE.SEEE-TT-EE-TT-EE- CS
                      Hexapep_2   4 IGdnCliGanagi.GvslGdncvvgaGvvit 33 
                                    +G    iG+     G  + d++ v+aG+vi 
  gi|121639153|ref|YP_979377.1| 273 VGRGAEIGPGTRLdGAVIFDGVRVEAGCVIE 303
                                    5555556666666778888999999999996 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.001
                                    EE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                      Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvga 28 
                                    iIG    iG++a i  Gv +Gd++ +ga
  gi|121639153|ref|YP_979377.1| 306 IIGFGARIGPRALIrdGV-IGDGADIGA 332
                                    7999999******99655.788888886 PP

>> Queuosine_synth  Queuosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00033         1     162     185 ..      31      54 ..      29      61 .. 0.90
   2 ?   -1.4   0.0      0.34     1e+03      43     142 ..      96     215 ..      90     223 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                                    ---GGGG--HHHHHHHHHHT-EEE CS
                Queuosine_synth 162 aPtAglhFteelleklkakgveva 185
                                     PtAgl+F ++ll++++a+g+e +
  gi|121639153|ref|YP_979377.1|  31 LPTAGLPFLTHLLSRIAAAGIEHV 54 
                                    5*******************9865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
                                    GGGGG--TT-EEEEEEEEE-S-EEEE...E--.---EEEEEEEE.................EEEEEES-TT--TT-EEEE CS
                Queuosine_synth  43 dlvdlLregdlLvlNdtkviparllg...ekektggkvevlllkel...............wealvkpakklkageklel 104
                                    +++  Lr++ ++v+N      a l      ++++ + v++ l++                 + a++++++ + + ++++ 
  gi|121639153|ref|YP_979377.1|  96 NVAGKLRNDTAMVFNGDVLSGADLAQlldFHRSNRADVTLQLVRVGdprafgcvptdeedrVVAFLEKTEDP-PTDQINA 174
                                    666778888888888766555555544433334455666666653255555555555555544444444333.3344444 PP

                                    ....EEEEEEEETT.S-EEEEEE....HHHHHH--------- CS
                Queuosine_synth 105 ....lkaevlekeeegerlvkfeeeleelleelGevplppyi 142
                                        ++ +v+++   ++r v++e+e+  +l + G++ +  y+
  gi|121639153|ref|YP_979377.1| 175 gcyvFERNVIDR-IPQGREVSVEREVFPALLADGDCKIYGYV 215
                                    556677777776.33566777777777777777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2584.84
//
Query:       gi|121639154|ref|YP_979378.1|  [L=297]
Description: dTDP-RHA:A-D-GlcNAc-diphosphoryl polyprenol, A-3-L-rhamnosyl transferase wbbL1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-13   49.6   0.0    1.2e-12   48.3   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.9e-13   48.8   0.0    1.2e-12   48.0   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    5.4e-06   26.4   0.4    8.2e-06   25.9   0.4    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0002   20.9   0.0     0.0003   20.3   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0012   18.3   0.0     0.0025   17.3   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0075   15.9   0.0      0.014   15.0   0.0    1.4  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.039   14.5   0.0    1.8  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   4.6e-16   1.2e-12      10     215 ..       5     233 ..       1     248 [. 0.79

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.6e-16
                Glyco_tranf_2_3  10 tfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealra...v 86 
                                    t+   + l++ l+sl+  ++ +v v + +++s+++t + a   ++++p+v  r++++  nlg +++++   +++ +    
  gi|121639154|ref|YP_979378.1|   5 TYSPGPHLERFLASLSLATERPVSVLLADNGSTDGTPQAA---VQRYPNV--RLLPTGANLGYGTAVN---RTIAQlgeM 76 
                                    6778889999999999767899*************99954...66****6..8999988899666655...555553334 PP

                Glyco_tranf_2_3  87 k........sdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.nrstl......................vs 134
                                    +        +d+v++ + D+ ++P+++++ll ++ + p++ga+g   + +  + ++                      ++
  gi|121639154|ref|YP_979378.1|  77 AgdagepwvDDWVIVANPDVQWGPGSIDALLDAAsRWPRAGALG--PLIRdPDGSVypsarqmpslirggmhavlgpfWP 154
                                    45666677788***********************5555666655..4443134444467778899999999999976533 PP

                Glyco_tranf_2_3 135 algalefaerhlrflaarralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevf 213
                                      +   +a r+ r     r +g l  +Gs++l+rr+ + + +g+d+  f   +D++lg rl +ag+ ++yvp a+v + +
  gi|121639154|ref|YP_979378.1| 155 -RNPWTTAYRQERLEPSERPVGWL--SGSCLLVRRSAFGQVGGFDErYFMYMEDVDLGDRLGKAGWLSVYVPSAEVLHHK 231
                                    .34446677888888888888887..6*******************999999************************9986 PP

                Glyco_tranf_2_3 214 ps 215
                                      
  gi|121639154|ref|YP_979378.1| 232 AH 233
                                    54 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   4.7e-16   1.2e-12       5     168 ..       4     191 ..       1     193 [. 0.87

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.7e-16
                                    EESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS... CS
                Glycos_transf_2   5 ptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd... 81 
                                    +ty   + l+++l+sl    +   + ++++D+gStD+t++ + +    +p+vr++    n G+++a+n+ +++       
  gi|121639154|ref|YP_979378.1|   4 VTYSPGPHLERFLASLSLA-TERPVSVLLADNGSTDGTPQAAVQR---YPNVRLLPTGANLGYGTAVNRTIAQLGEMagd 79 
                                    799999*************.******************9999988...79*********************996543444 PP

                                    ........EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..................EEE CS
                Glycos_transf_2  82 ........yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..................gen 135
                                            ++++ + D+++ p+ +  l++a+ + +++++lg   r ++++   + + ++                  + +
  gi|121639154|ref|YP_979378.1|  80 agepwvddWVIVANPDVQWGPGSIDALLDAASRWPRAGALGPLIRDPDGSVYPSAR-QMpslirggmhavlgpfwprNPW 158
                                    999******************************99999999988877776655544.555899*********99988888 PP

                                    ECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
                Glycos_transf_2 136 erlyfkerkrslkgnlsfeigsaallrrealee 168
                                    +  y++er     + +   +gs+ l+rr+a+ +
  gi|121639154|ref|YP_979378.1| 159 TTAYRQERLEPSERPVGWLSGSCLLVRRSAFGQ 191
                                    888888888888888888999999999999966 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.4   3.2e-09   8.2e-06      68     140 ..     172     268 ..     156     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.2e-09
                Glyco_trans_2_3  68 rvvpsv.GsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes.lvkeksplt................ 129
                                    r+v +  Gs+ ++rrsa+ +vgg+d + +   ED d+g rl ++G+  ++vp++ + + k  +t                
  gi|121639154|ref|YP_979378.1| 172 RPVGWLsGSCLLVRRSAFGQVGGFDERYFMYMEDVDLGDRLGKAGWLSVYVPSAeVLHHKAHSTgrdpashlaahhksty 251
                                    5667667******************999***********************99976677777765665555444444444 PP

                Glyco_trans_2_3 130 ......lraalrQrkRw 140
                                             ++r   Rw
  gi|121639154|ref|YP_979378.1| 252 ifladrHSGWWRAPLRW 268
                                    44444444444444444 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07    0.0003     164     215 ..     178     229 ..     176     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                Glyco_tranf_2_2 164 ssssilinrraflevGGyDErfrGhgaEDfdlllRlaka.ikslekmpvelly 215
                                    s+s +l++r af +vGG+DEr+     ED dl  Rl+ka   s+ ++++e+l+
  gi|121639154|ref|YP_979378.1| 178 SGSCLLVRRSAFGQVGGFDERY-FMYMEDVDLGDRLGKAgWLSVYVPSAEVLH 229
                                    57999****************9.6789**********9845688888888874 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.7e-07    0.0025      99     163 ..     175     238 ..     159     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.7e-07
                Glyco_transf_21  99 gfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspap.iaqtsvprrsslra 163
                                    g   G+++++rr+a+ ++GGf +      eD  lg +l +aG+  v +p + +++++++  s+ r+
  gi|121639154|ref|YP_979378.1| 175 GWLSGSCLLVRRSAFGQVGGFDERYFMYMEDVDLGDRLGKAGWLSVYVPSAeVLHHKAH--STGRD 238
                                    5678*******************999999**************9888887634454443..34455 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.6e-06     0.014      22      67 ..     180     224 ..     174     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                Glyco_transf_7C  22 GvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleierpek 67 
                                      l++r++ f +++Gf+++++ +  ED +l +Rl k+g     ++ 
  gi|121639154|ref|YP_979378.1| 180 SCLLVRRSAFGQVGGFDERYFMY-MEDVDLGDRLGKAGWLSVYVPS 224
                                    56789******************.9*********999976555444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.039       7      81 ..      12      95 ..       7      96 .. 0.68
   2 ?   -1.9   0.0         2   5.1e+03      62      79 ..     240     256 ..     213     261 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                Glyco_tranf_2_4  7 Lpeflahhlalgfdr...ilvydndstDgt.railkelpevkllhvdksy...ederrqvellkallary...aeadwvlvv 78
                                   L++fla +  +  +r   +l++dn+stDgt  a ++++p+v+ll++  +    +  +r ++ l +++ ++   + +dwv+v+
  gi|121639154|ref|YP_979378.1| 12 LERFLASLSLA-TERpvsVLLADNGSTDGTpQAAVQRYPNVRLLPTGANLgygTAVNRTIAQLGEMAGDAgepWVDDWVIVA 92
                                   67777766443.22233399**********55667999******99976633333445566677777766333468999998 PP

                Glyco_tranf_2_4 79 DaD 81
                                     D
  gi|121639154|ref|YP_979378.1| 93 NPD 95
                                   765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                Glyco_tranf_2_4  62 lkallaryaeadwvlvvD 79 
                                      +l+a++ ++++++ +D
  gi|121639154|ref|YP_979378.1| 240 ASHLAAHH-KSTYIFLAD 256
                                    33333332.445555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2132.68
//
Query:       gi|121639155|ref|YP_979379.1|  [L=304]
Description: dTDP-rhamnose modification protein rmlD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-109  365.9   0.4   1.3e-109  365.7   0.4    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    5.4e-24   85.0   0.3    8.1e-24   84.4   0.3    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.7e-12   47.4   0.3    1.1e-09   38.2   0.0    2.3  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.6e-12   45.9   0.0    2.5e-11   43.1   0.0    1.9  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      4e-12   45.9   0.3    8.1e-11   41.6   0.0    2.1  2  NAD_binding_4    Male sterility protein
    5.7e-08   32.2   2.5    5.4e-05   22.5   0.1    3.0  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00054   19.9   6.6      0.018   14.9   6.3    2.4  1  NAD_binding_10   NAD(P)H-binding
    0.00089   19.8   0.0        1.7    9.3   0.0    2.5  2  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
     0.0073   16.6   0.1      0.063   13.5   0.0    2.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0093   15.9   0.7      0.018   15.0   0.2    1.7  2  KR               KR domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.7   0.4  7.4e-113  1.3e-109       2     284 ..       7     288 ..       6     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 365.7 bits;  conditional E-value: 7.4e-113
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHH CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaea 81 
                                    ++++tGa+GqlGs+L++q+a+eg ++lalt++++d+td++a+++++++   dvv+n+AAyt+vD aEs+e+ ayavna++
  gi|121639155|ref|YP_979379.1|   7 RLVITGAGGQLGSHLTAQAAREGRDMLALTSSQWDITDPAAAERIIRH--GDVVINCAAYTDVDGAESNEAVAYAVNATG 84 
                                    799********************************************9..99**************************** PP

                                    HHHHHHHHHHCT-EEEEEEEGGGS-S-....TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEE.SSSS CS
                  RmlD_sub_bind  82 vealAeaaaavgalLihvStDyVFdGe....kkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvy.gekg 156
                                    +++lA+a+a+vga LihvStDyVFdG+    ++rpYe++det+P++vY+r+KlaGEqavlaa ++a++vRt+wvy g +g
  gi|121639155|ref|YP_979379.1|  85 PQHLARACARVGARLIHVSTDYVFDGDfggaEPRPYEPTDETAPQGVYARSKLAGEQAVLAAFPEAAVVRTAWVYtGGTG 164
                                    ***************************999999******************************************888** PP

                                    S-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTS CS
                  RmlD_sub_bind 157 knfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadse 236
                                    k+fv++m rla+ + +++vv+Dq+gsPT+++dlAe+ll+l+++ ++     +v+H+aneg++s++++Ara+++e+gad++
  gi|121639155|ref|YP_979379.1| 165 KDFVAVMRRLAAGHGRVDVVDDQTGSPTYVADLAEALLALADAGVR----GRVLHAANEGVVSRFGQARAVFEECGADPQ 240
                                    *********************************************9....9***************************** PP

                                    EEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHH CS
                  RmlD_sub_bind 237 evkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlke 284
                                    +v+p+s+a++p+pA+RP++S+L++++++ +++++lr+wr+al+++l++
  gi|121639155|ref|YP_979379.1| 241 RVRPVSSAQFPRPAPRPSYSALSSRQWALAGLTPLRHWRSALATALAA 288
                                    *******************************************99875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.3   4.5e-27   8.1e-24       2     232 ..       9     211 ..       8     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.5e-27
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                    ++tGa G++Gs+l+ + +++g ++++l++                + d+td++a er+++  + d+vi++Aa+ +v+   
  gi|121639155|ref|YP_979379.1|   9 VITGAGGQLGSHLTAQAAREGRDMLALTSS---------------QWDITDPAAAERIIR--HGDVVINCAAYTDVDGAE 71 
                                    79****************************...............***************..9*********99999999 PP

                                    HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS....SSBSTCSTTS----SSHHHHHHHHHHHHHHHHH CS
                      Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae....qpkeettltgplkpnspYaaaKlageklveaya 157
                                    ++ a  +  n+ g ++l+ a+ + g+ rl+++s++ v+  d       p e t    +++p+  Ya++Klage+ v a+ 
  gi|121639155|ref|YP_979379.1|  72 SNEAVAYAVNATGPQHLARACARVGA-RLIHVSTDYVFDGDFGgaepRPYEPTD---ETAPQGVYARSKLAGEQAVLAAF 147
                                    99999999******************.***********8666622112344444...669*****************987 PP

                                    HHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT- CS
                      Epimerase 158 aqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdag 232
                                     +      ++r   +y  +       + + a++r++++g+  v +++d t      yv D+aea+l+++++  +g
  gi|121639155|ref|YP_979379.1| 148 PEA----AVVRTAWVYTGG-----TGKDFVAVMRRLAAGHGRVDVVDDQTG--SPTYVADLAEALLALADAGVRG 211
                                    766....788888888888.....555566788999999989999995555..5589*********999984444 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0014       2.6       2      27 ..      10      35 ..       9      39 .. 0.87
   2 !   38.2   0.0     6e-13   1.1e-09      58     165 ..      39     144 ..      34     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                                   EETTTSHHHHHHHHHHHHCT-CCEEE CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgi 27
                                   iTG  G+ Gs+l+ +  ++g ++  +
  gi|121639155|ref|YP_979379.1| 10 ITGAGGQLGSHLTAQAAREGRDMLAL 35
                                   9**************99999988765 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 6e-13
                                    E--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG.... CS
                  GDP_Man_Dehyd  58 kgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvY.... 133
                                    + D+tD ++ er++++   d v+n AA   Vd   ++ +  + vn++G ++L  a+ ++g    +r++++St+ v+    
  gi|121639155|ref|YP_979379.1|  39 QWDITDPAAAERIIRHG--DVVINCAAYTDVDGAESNEAVAYAVNATGPQHLARACARVG----ARLIHVSTDYVFdgdf 112
                                    78*************99..9*************9999999*****************998....69********966444 PP

                                    -S-SSSSB-TTS-----SHHHHHHHHHHHHHH CS
                  GDP_Man_Dehyd 134 GkvqevpqtEttpfyPrsPYaaaKlyadwivv 165
                                    G ++  p++ t  + P+  Ya +Kl+ ++ v 
  gi|121639155|ref|YP_979379.1| 113 GGAEPRPYEPTDETAPQGVYARSKLAGEQAVL 144
                                    7888999*******************998875 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.14   2.6e+02       1      18 [.       9      26 ..       9      34 .. 0.83
   2 !   43.1   0.0   1.4e-14   2.5e-11      50     225 ..      38     201 ..      27     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                      3Beta_HSD  1 vvtGgaGFlGralvkeLv 18
                                   v+tG++G lG++l  +  
  gi|121639155|ref|YP_979379.1|  9 VITGAGGQLGSHLTAQAA 26
                                   79**********987755 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 1.4e-14
                      3Beta_HSD  50 iegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgee 128
                                     + D+td +  e+ ++  dvvi  a+++dv g + +e   + vn  G + +  ac + g r l+++S+ + v++     +
  gi|121639155|ref|YP_979379.1|  38 SQWDITDPAAAERIIRHGDVVINCAAYTDVDGaESNEAVAYAVNATGPQHLARACARVGAR-LIHVST-DYVFD----GD 111
                                    578*****************************555666679******************75.899987.66777....45 PP

                      3Beta_HSD 129 ilngdEeleyesl....hqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalf 204
                                    +  g E  +ye++    +q +y++sK   E++vl+a               +R a +y  g  + + ++ + +  g+  +
  gi|121639155|ref|YP_979379.1| 112 FG-GAEPRPYEPTdetaPQGVYARSKLAGEQAVLAAFP---------EAAVVRTAWVYTGGTGKDFVAVMRRLAAGHGRV 181
                                    55.7888888776666799*****************98.........346899999996666555555555556666788 PP

                      3Beta_HSD 205 kigdeevlsdrvYvgNvawah 225
                                     ++d+++  +++Yv  +a a 
  gi|121639155|ref|YP_979379.1| 182 DVVDDQT-GSPTYVADLAEAL 201
                                    8888876.8999999999885 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.039        70       1      21 [.      10      30 ..      10      37 .. 0.82
   2 !   41.6   0.0   4.5e-14   8.1e-11      78     208 ..      45     160 ..      35     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.039
                                   EE-TTSHHHHHHHHHHHHHS- CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                   +TGa G LG++L ++  r+ +
  gi|121639155|ref|YP_979379.1| 10 ITGAGGQLGSHLTAQAAREGR 30
                                   8***********988776655 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 4.5e-14
                                    HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H. CS
                  NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyee 154
                                    ++++++++++ dv+i++aA +++d+  ++   +++vN +G +++ + ++++ +   l+hvST yv + + g  e ++y  
  gi|121639155|ref|YP_979379.1|  45 PAAAERIIRHGDVVINCAAYTDVDGAESNeavAYAVNATGPQHLARACARVGAR--LIHVSTDYVFDGDFGGAEPRPY-- 120
                                    567789999**************9854444449****************99777..******8888888878766666.. PP

                                    .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                  NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                              e+++++  +  Y +sK ++E+ v +a+ +    +++vR   +++
  gi|121639155|ref|YP_979379.1| 121 ----------EPTDETAPQGVYARSKLAGEQAVLAAFPE----AAVVRTAWVYT 160
                                    ..........6899999999*****************55....78999888876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1   0.00077       1.4       2      30 ..       9      37 ..       8      40 .. 0.85
   2 !   22.5   0.1     3e-08   5.4e-05      62     129 ..      41     105 ..      30     110 .. 0.92
   3 ?    0.5   0.0      0.15   2.7e+02     225     249 ..     183     207 ..     167     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00077
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEEE CS
                Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiille 30
                                   ++tGagG +Gs+l+ q +++    + l +
  gi|121639155|ref|YP_979379.1|  9 VITGAGGQLGSHLTAQAAREGRDMLALTS 37
                                   79**************9998877777665 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3e-08
                                    -TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG CS
                Polysacc_synt_2  62 dvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD 129
                                    d++d +  e++++  + dvv+++AA+  V  +e+n + a   N +g +++++a+ + g  +++ +StD
  gi|121639155|ref|YP_979379.1|  41 DITDPAAAERIIR--HGDVVINCAAYTDVDGAESNEAVAYAVNATGPQHLARACARVGA-RLIHVSTD 105
                                    89999999*****..99***************************************996.799****9 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                                    EEEE--.-EEEHHHHHHHH...... CS
                Polysacc_synt_2 225 ifvldmGepvkivdlakalielsgl 249
                                    +   + G p+ ++dla+al++l++ 
  gi|121639155|ref|YP_979379.1| 183 VVDDQTGSPTYVADLAEALLALADA 207
                                    3334689************999865 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   6.3     1e-05     0.018       1     180 [.      12     204 ..      12     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-......--TCC. CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal......ggggk. 73 
                                    GA G+ G++l+++++++g  +                  +l+  + d+td+++ ++ +++ d+V+ ++      g++++ 
  gi|121639155|ref|YP_979379.1|  12 GAGGQLGSHLTAQAAREG-RDM----------------LALTSSQWDITDPAAAERIIRHGDVVINCAaytdvdGAESNe 74 
                                    566666666666666664.222................345667788999999999999999998888666655333334 PP

                                    ......HHHHHHHHHHHHHHCT--EEEEEEETTTTS.....GCGCHHHHHHHHCC.HHHHHHHHHHHHHHHHSSSEEEEE CS
                 NAD_binding_10  74 ......deegaknivdaakeagvkRfvlvsaigvgd.....evpgefgewnkell.kaylaakraaeellrasgldwTiv 141
                                          +++g +++++a+ + g  R++ vs+  v d       p++ +++++++  + y++ k a e+ + a   +  +v
  gi|121639155|ref|YP_979379.1|  75 avayavNATGPQHLARACARVGA-RLIHVSTDYVFDgdfggAEPRPYEPTDETAPqGVYARSKLAGEQAVLAAFPEAAVV 153
                                    45555555559999********9.9999999888663333345666666666666255568899**************** PP

                                    EE-CEE-ST--S.EEEE...........ETTSS----EEEHHHHHHHHHHH CS
                 NAD_binding_10 142 rpggLtdepttk.yrvv...........ekgepfkggsisradVAdvlvav 180
                                    r ++   + t+k +++v           +  ++ +g+ +  ad+A++l+a+
  gi|121639155|ref|YP_979379.1| 154 RTAWVYTGGTGKdFVAVmrrlaaghgrvDVVDDQTGSPTYVADLAEALLAL 204
                                    *****9998665144444544433221111122234555566666666655 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00095       1.7      24      68 ..      76     122 ..      61     150 .. 0.73
   2 !    8.1   0.0    0.0022         4       3      72 ..     193     263 ..     191     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00095
                                    EEE-TT-TTHHHHHHHHHHTT-EEEES---..--TT-TTSS----TT CS
                     PGM_PMM_II  24 vidplhGaggeilkellkelgvdvvelnae..pdpdfptkapnpeek 68 
                                    v+ + +++g + l +++ ++g++++ +  +   d+df++  p+p e+
  gi|121639155|ref|YP_979379.1|  76 VAYAVNATGPQHLARACARVGARLIHVSTDyvFDGDFGGAEPRPYEP 122
                                    778999****************77776655337******77777652 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0022
                                    HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHH..HHHHHHHTT-EEEES-----TT-TTSS----TT-TTT CS
                     PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggei..lkellkelgvdvvelnaepdpdfptkapnpeekealk 72 
                                    Y+ +l+e++   a ++ + +v++ + +G+ + +  +  +++e g+d++ ++   +++fp  ap+p   +al+
  gi|121639155|ref|YP_979379.1| 193 YVADLAEALLALADAGVRGRVLHAANEGVVSRFgqARAVFEECGADPQRVRPVSSAQFPRPAPRPSY-SALS 263
                                    777777777733334444569999999999988335689**************************99.6665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.5e-05     0.063      47      84 ..      33      75 ..      18     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                                   TCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG......GHHH CS
                Sacchrp_dh_NADP 47 vrfeaialdaenyeavLaallkegdlvvnlsppi......ssld 84
                                     +++ + d+ +++a  ++++++gd+v+n++ ++      s+++
  gi|121639155|ref|YP_979379.1| 33 LALTSSQWDITDPAA-AERIIRHGDVVINCAAYTdvdgaeSNEA 75
                                   56788999*******.***************9996665544444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2     1e-05     0.018       4      77 ..       9      82 ..       7      95 .. 0.71
   2 ?   -2.1   0.0       1.7   3.1e+03      45      89 ..     171     217 ..     156     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE--.--TT-HHHHHHHHHHHHH CS
                             KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevva.aDvsdkdavealleeika 77
                                   +itG+ G+LG +l+ + a++g+  l+l+s +     d +a  + +++ ++ ++++a  Dv  +++ ea+  +++a
  gi|121639155|ref|YP_979379.1|  9 VITGAGGQLGSHLTAQAAREGRDMLALTSSQW-DITDPAAAERIIRHGDVVINCAAyTDVDGAESNEAVAYAVNA 82
                                   7****************************994.333333344445555666666552466666666666555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                    HHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS.S---E.EEE-- CS
                             KR  45 iaelealgaevevvaaDvsdkdavealleeikaee.ppikG.vihaA 89 
                                    +++l+a   +v+vv+    +++ v+ l e++ a + + ++G v+haA
  gi|121639155|ref|YP_979379.1| 171 MRRLAAGHGRVDVVDDQTGSPTYVADLAEALLALAdAGVRGrVLHAA 217
                                    44444444455555555555555555555555555555555455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2303.02
//
Query:       gi|121639156|ref|YP_979380.1|  [L=498]
Description: hypothetical protein BCG_3296 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-44  151.7   0.0    3.3e-44  150.7   0.0    1.5  2  LytR_cpsA_psr  Cell envelope-related transcriptional attenuat
      8e-13   49.2   3.2      8e-13   49.2   3.2    2.4  2  LytR_C         LytR cell envelope-related transcriptional att
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.27   11.1   0.0    1.9  1  POTRA_2        POTRA domain, ShlB-type


Domain annotation for each model (and alignments):
>> LytR_cpsA_psr  Cell envelope-related transcriptional attenuator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.7   0.0   5.5e-48   3.3e-44       1     151 [.      95     264 ..      95     265 .. 0.88
   2 ?   -4.1   0.0       2.6   1.6e+04      79      95 ..     419     435 ..     415     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 5.5e-48
                                    --SEEEEEEEEGGGTEEEEEEE-TTBEE---........--...-----EES-TTTTT.............-HHHHHHHH CS
                  LytR_cpsA_psr   1 rsDtimlvtvnakkkkvklvSipRDtlveip........ggeskatgekkinsayalg.............gaellvktv 59 
                                    ++Dti+l++v+++ k+++++SipRD++v  p        g  + +t+e+k   + ++g             g+e+l+ktv
  gi|121639156|ref|YP_979380.1|  95 NTDTIILIRVPNNGKSATAISIPRDSYVAAPglgktkinG-VYGQTRETKRAGLVQAGaspteaaaagteaGREALIKTV 173
                                    79***************************99666665541.233334555555555556667777777899********* PP

                                    HHHHTS---EEEEE-HHHHHHHHHHHT---B--------------------B---HHHHHH-------------SHHHHH CS
                  LytR_cpsA_psr  60 ekllginidyYvevdfegfaklvdalgGvevdvkedvkdkeeselklkaGeqkldGeqalayvRfRkddeegDlgRikrQ 139
                                     +l+g+++d+Y+e+ + gfa ++dalgGv+v++ke+v++   s+++++aG+qkl+G qal++vR+R+d+++gDl+R+ rQ
  gi|121639156|ref|YP_979380.1| 174 ADLTGVTVDHYAEIGLLGFALIADALGGVDVCLKEPVYEP-LSGADFPAGRQKLNGPQALSFVRQRHDLPRGDLDRVVRQ 252
                                    *************************************986.9************************************** PP

                                    HHHHHHHHHTT- CS
                  LytR_cpsA_psr 140 qqvleallkklk 151
                                    q+v++al++++ 
  gi|121639156|ref|YP_979380.1| 253 QAVMAALAHRVI 264
                                    *******99875 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.6
                                    HHHHHHHT---B----- CS
                  LytR_cpsA_psr  79 aklvdalgGvevdvked 95 
                                    ++++ +lgG+ v ++ +
  gi|121639156|ref|YP_979380.1| 419 QQVAKELGGLPVVADAS 435
                                    68899999999988765 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.5     9e+03      63      83 ..      12      29 ..       3      30 .. 0.46
   2 !   49.2   3.2   1.3e-16     8e-13       3      85 .]     365     449 ..     363     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                         LytR_C 63 glgelqedsvkdas.......vtvvlGk 83
                                   + +                  v +vlG+
  gi|121639156|ref|YP_979380.1| 12 RTA----------RaistalaVAIVLGT 29
                                   222..........122223567777775 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 1.3e-16
                         LytR_C   3 kVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee.ttivyreaaaa.aakalaaalglgelqedsvkdas.vtv 79 
                                    + +V+N t+++GlAa+v++ L+++Gft+g+vgn + + ++ +++++ ++a++  a+++a++lg+  +++d++  ++ v+v
  gi|121639156|ref|YP_979380.1| 365 TANVVNDTDINGLAAAVSKVLSSKGFTTGSVGNNDGDHVPgSQVRA-AKADDlGAQQVAKELGGLPVVADASIAPGsVRV 443
                                    568***************************88655554458****8.5555569*********88888888888889*** PP

                         LytR_C  80 vlGkdf 85 
                                    vl +d+
  gi|121639156|ref|YP_979380.1| 444 VLANDY 449
                                    *****9 PP

>> POTRA_2  POTRA domain, ShlB-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05      0.27      17      58 ..     355     396 ..     346     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                                    CCHHHHHCCCSSSEEEHHHHHHHHHHHHHHHHHTT-TT-EEE CS
                        POTRA_2  17 eeleallqpylgkclgladlnqlakeltnayiekGYvtsrvl 58 
                                    +el+ + ++ +   ++ +d+n la+++++ + +kG+ t  v+
  gi|121639156|ref|YP_979380.1| 355 DELAYTPAKTTANVVNDTDINGLAAAVSKVLSSKGFTTGSVG 396
                                    566666666677778999********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3538.16
//
Query:       gi|121639157|ref|YP_979381.1|  [L=229]
Description: hypothetical protein BCG_3297 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-05   23.9   0.1    0.00069   18.3   0.1    2.1  2  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.9e-08   0.00069      17      75 ..      18      77 ..       5     129 .. 0.82
   2 !    3.7   0.0     0.001        19     185     255 ..     161     226 ..     152     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.9e-08
                                   CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                    AMP-binding 17 sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvv 75
                                   +ge   l+   l + + + ++ Lr +l +++ +rVaillp  ++  ++l++++ +Ga ++
  gi|121639157|ref|YP_979381.1| 18 TGERIELSAVTLANWAAKTGNLLRdELAAGPASRVAILLPAHWQTAAVLFGVWWIGAQAI 77
                                   66778899999999******************************************9764 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.001
                                    HHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-S CS
                    AMP-binding 185 vanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvt 255
                                    +  +a+      ++l++ d+vls+++ a   +l+ +ll++l++Ga++v + +    dp++l + i+++kvt
  gi|121639157|ref|YP_979381.1| 161 LRDCAAS--AAARGLTAADRVLSTASWAGPDELVDGLLAILAAGASLVQVANP---DPAMLQRRIATEKVT 226
                                    5555553..22356778999999999999999999999999999999988844...456677777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1709.04
//
Query:       gi|121639158|ref|YP_979382.1|  [L=93]
Description: hypothetical protein BCG_3298 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-42  142.2   6.8    4.3e-42  142.1   6.8    1.0  1  DUF1490        Protein of unknown function (DUF1490)
  ------ inclusion threshold ------
       0.76   10.4   7.7        1.2    9.8   7.5    1.5  1  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   6.8   4.8e-46   4.3e-42       1      87 [.       1      87 [.       1      88 [. 0.99

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 4.8e-46
                        DUF1490  1 mvvqgllakaattvvtGvvGvaayevlrkavakaplreaaVaatalglrgaRkaeeaaEsarLkvaDvvaeAreriGeeapp 82
                                   m++q++laka+ttv+tG++Gv+aye+l+ka+akaplr++aV+a+alglrg+RkaeeaaEsarLkvaDv+aeAreriGee+p+
  gi|121639158|ref|YP_979382.1|  1 MAIQVFLAKATTTVITGLAGVTAYEILKKAAAKAPLRQTAVSAAALGLRGTRKAEEAAESARLKVADVMAEARERIGEESPT 82
                                   99******************************************************************************** PP

                        DUF1490 83 pavad 87
                                   pa++d
  gi|121639158|ref|YP_979382.1| 83 PAISD 87
                                   **987 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.5   0.00013       1.2      19      68 ..       7      60 ..       2      80 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXX CS
                  Ribosomal_60s 19 eaarvkllvkalegkdieellangaakla....aaaaaaaaaaaaaaaaaaaee 68
                                   +a+++ ++++ l+g++  e+l+++aak+     a+ aaa    +  +a++aae 
  gi|121639158|ref|YP_979382.1|  7 LAKATTTVITGLAGVTAYEILKKAAAKAPlrqtAVSAAALGLRGTRKAEEAAES 60
                                   57889999*******************987643333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 631.56
//
Query:       gi|121639159|ref|YP_979383.1|  [L=718]
Description: metal cation-transporting P-type atpase C ctpC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-45  156.4   0.2    2.3e-45  155.5   0.2    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    3.1e-40  137.6   4.5    6.3e-40  136.6   4.5    1.5  1  E1-E2_ATPase  E1-E2 ATPase
    1.3e-05   25.7   0.1    4.1e-05   24.1   0.1    1.9  1  HAD           haloacid dehalogenase-like hydrolase
    0.00054   19.8   1.0       0.24   11.1   0.9    2.2  2  Hydrolase_3   haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.2   5.2e-49   2.3e-45       1     210 []     402     622 ..     402     622 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 5.2e-49
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHHHHETTTE... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.......alalaaaletgsehpigkalvaaakarsgal...tgfatfigrg... 67 
                                    ++++vfDk+GTLt g+p+v+ +++          la aa  e+ s+hp+++a+++  ++r++++   ++ +++ g g   
  gi|121639159|ref|YP_979383.1| 402 VDAIVFDKTGTLTVGRPVVTNIVAMHkdwepeqVLAYAASSEIHSRHPLAEAVIRSTEERRISIpphEECEVLVGLGmrt 481
                                    689************************77776666666666666****************66666679999999999*** PP

                                    .....HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE.EE CS
                                    .....xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                      Hydrolase  68 .....ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagi.ev 137
                                         +++ g+p +l+a+   ++++  + ++++ +q++t  ll  ++ +++++ + d+  v+peaa+++ +L+a+gi ++
  gi|121639159|ref|YP_979383.1| 482 wadgrTLLLGSPSLLRAEkvRVSKKASEWVDKLRRQAETPLLLavDGTLVGLISLRDE--VRPEAAQVLTKLRANGIrRI 559
                                    ********************999999999999999999999999999***********..*****************99* PP

                                    EEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 138 vlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    v+ltgd+pe a+ +a++lG           i++  a++ pe+k+aa+reLq ++  v mVGDg+nDa+alaaA+
  gi|121639159|ref|YP_979383.1| 560 VMLTGDHPEIAQVVADELG-----------IDEwRAEVMPEDKLAAVRELQDDGYVVGMVGDGINDAPALAAAD 622
                                    *******************...........7777*******************99******************8 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   4.5   1.4e-43   6.3e-40      14     181 .]     227     386 ..     209     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 1.4e-43
                                    S-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEEE-TTTST CS
                   E1-E2_ATPase  14 teeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVtatgedte 93 
                                    te +++++ +++GD v++ ++  +p+Dg++v+g+a v++sa+TGE+lpv++  g++v++G+vvv+g++++++ a+g++t+
  gi|121639159|ref|YP_979383.1| 227 TEIQVPIDTVQIGDEVVVHEHVAIPVDGEVVDGEAIVNQSAITGENLPVSVVVGTRVHAGSVVVRGRVVVRAHAVGNQTT 306
                                    7889**************************************************************************** PP

                                    TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHH CS
                   E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalal 173
                                    +g+i++ veea+ +++p+q   +++++ +vp++++++++++li+          + ra+++l++a+Pca +l +p+a+++
  gi|121639159|ref|YP_979383.1| 307 IGRIISRVEEAQLDRAPIQTVGENFSRRFVPTSFIVSAIALLIT--------GDVRRAMTMLLIACPCAVGLSTPTAISA 378
                                    *******************************************9........78999*********************** PP

                                    HHHHHHHT CS
                   E1-E2_ATPase 174 garrlakk 181
                                    ++++ a++
  gi|121639159|ref|YP_979383.1| 379 AIGNGARR 386
                                    ***99985 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   9.2e-09   4.1e-05      86     187 ..     540     618 ..     488     619 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.2e-09
                            HAD  86 ldpgalellaahraaGd.rvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                     +p+a ++l + ra+G+ r+v+++g + ++++ +++elg    +++       + +e       v  e+k+aa+re    
  gi|121639159|ref|YP_979383.1| 540 VRPEAAQVLTKLRANGIrRIVMLTGDHPEIAQVVADELG----IDE-------WRAE-------VMPEDKLAAVRE---- 597
                                    569************************************....***.......8888.......888899999999.... PP

                            HAD 165 egegidleevvayGDspsDlpll 187
                                        +d   v  +GD+++D p+l
  gi|121639159|ref|YP_979383.1| 598 --LQDDGYVVGMVGDGINDAPAL 618
                                    ..66777767777********98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0014       6.3       5      55 ..     526     580 ..     522     588 .. 0.86
   2 !   11.1   0.9   5.3e-05      0.24     208     236 ..     607     635 ..     593     649 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0014
                                    IIIIIS-...TTS---HHHHHHHHHHHHTTSE.EEEE-SS-HHHHHHHHHHCCCC CS
                    Hydrolase_3   5 lDGTLln...sdkkisektkeaikklkekgik.vviATGRslravlpvleelgld 55 
                                    +DGTL+       ++ +++++++ kl+++gi  +v  TG +++ ++ v++elg+d
  gi|121639159|ref|YP_979383.1| 526 VDGTLVGlisLRDEVRPEAAQVLTKLRANGIRrIVMLTGDHPEIAQVVADELGID 580
                                    8***9665547778*****************648999******9999999**998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.3e-05
                                    EEESSGGGHHHHHHSSEEEEETTS-HHHH CS
                    Hydrolase_3 208 afGDgeNDieMLeaaglgvAmgnaseevk 236
                                     +GDg ND + L aa++g+Amg a   v 
  gi|121639159|ref|YP_979383.1| 607 MVGDGINDAPALAAADIGIAMGLAGTDVA 635
                                    58********************8765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 5136.47
//
Query:       gi|121639160|ref|YP_979384.1|  [L=222]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-10   39.1   6.8    4.5e-09   36.3   6.8    1.9  1  Cation_efflux  Cation efflux family


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   6.8   2.5e-13   4.5e-09      74     189 ..     101     213 ..      36     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.5e-13
                  Cation_efflux  74 sgllllglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgv 153
                                    +++ ++++a +l+ e+i +l  +++r + + + +++++++l+++ +l ++++r+g++l+s a +++  ++   a+++++v
  gi|121639160|ref|YP_979384.1| 101 VAVSFWLTAPYLVAESIRHLA-GEHRAETSVIGIGLTAIALLLMPVLGWANHRVGERLGSGATAGEGTQNYLCAAQAAAV 179
                                    7899*****************.********************************************************** PP

                  Cation_efflux 154 lvsalvillfnlksgplaDpvaslligliilysalk 189
                                    l+++ ++ ++ + +  ++Dp+++l+i+ i +  + +
  gi|121639160|ref|YP_979384.1| 180 LLGLAITAVWSNGW--WIDPAIGLAIAGIAVWQGIR 213
                                    *********98887..***********999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1387.34
//
Query:       gi|121639161|ref|YP_979385.1|  [L=394]
Description: hypothetical protein BCG_3301 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     4e-121  404.6   1.1   4.4e-121  404.4   1.1    1.0  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.4   1.1  2.5e-125  4.4e-121       1     368 []      10     387 ..      10     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 404.4 bits;  conditional E-value: 2.5e-125
                   CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpsee..kgesayflavnrnKrsvalDlkseegrel 78 
                                    L+G+rVld++q++aGpla+++L dlGAeVIkvE+p +g++aR+++ +     + ++yfl +nr+K+sv++Dl++e++++ 
  gi|121639161|ref|YP_979385.1|  10 LDGFRVLDFTQNVAGPLAGQVLVDLGAEVIKVEAP-GGEAARQITSVLPgrPPLATYFLPNNRGKKSVTVDLTTEQAKQQ 88 
                                    89*********************************.********999989999*************************** PP

                   CoA_transf_3  79 lkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvk 158
                                    ++rL+++ADVv+e frpg++e+lglg+++lr++nP+Liya++++yG +Gp+ +rpg+Dlv+ a++G+++ + +p+g+P+ 
  gi|121639161|ref|YP_979385.1|  89 MLRLADTADVVLEAFRPGTMEKLGLGPDDLRSRNPNLIYARLTAYGGNGPHGSRPGIDLVVAAEAGMTTGMPTPEGKPQI 168
                                    ******************************************************************************** PP

                   CoA_transf_3 159 vgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlley..latgevpe..rqgnrdp......aa 228
                                    + ++l+D ++g+++a+a+laall+rer+G ++v++v++++ a+ l+a+ql+++   a+ ++p+  ++ ++++      a+
  gi|121639161|ref|YP_979385.1| 169 IPFQLVDNASGHVLAQAVLAALLHRERNGVADVVQVAMYDVAVGLQANQLMMHlnRAASDQPKpePAPKAKRrkgvgfAT 248
                                    *****************************************************8844444444333333333457888** PP

                   CoA_transf_3 229 apygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvp 308
                                    +p++++rt+d +++i+a+ +k+w++lc ++grp+l ed+rfa+++sr+ n ael+ael+ +la++ta+ew++ll+a+g++
  gi|121639161|ref|YP_979385.1| 249 QPSDAFRTADRYIVISAYVPKHWQKLCYLIGRPDLVEDQRFAEQRSRSINYAELTAELELALASKTATEWVQLLQANGLM 328
                                    ******************************************************************************** PP

                   CoA_transf_3 309 aapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklGedt 368
                                    a+  +t+++v+d p +a+++l  ev +++ ++++v ++p+r+++++a v+ ++P+ Ge++
  gi|121639161|ref|YP_979385.1| 329 ACLAHTWKQVVDTPLFAESDLTLEVGRGA-DTITVIRTPARYASFRAVVTDPPPTAGEHN 387
                                    ****************************9.99***************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2755.61
//
Query:       gi|121639162|ref|YP_979386.1|  [L=764]
Description: transmembrane carbonic anhydrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-85  285.9  28.2    3.8e-85  285.9  28.2    1.7  2  Sulfate_transp  Sulfate permease family
    9.1e-41  139.7   0.0    1.4e-40  139.1   0.0    1.3  1  Pro_CA          Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.9  28.2   4.3e-89   3.8e-85       1     380 []      31     398 ..      31     400 .. 0.93
   2 ?   -1.9   0.0      0.12   1.1e+03     231     267 ..     705     741 ..     701     744 .. 0.89

  Alignments for each domain:
  == domain 1  score: 285.9 bits;  conditional E-value: 4.3e-89
                 Sulfate_transp   1 lkgDliaGitvallaiPqalayallaglppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakvaeeepekg 80 
                                    l++D++a+++v+l+a+P++l++a+++g+p+i+g++++vv+++v+ ++G+s+ +++Gp a l+++v+e+i+++       g
  gi|121639162|ref|YP_979386.1|  31 LRHDVPASLVVFLVALPLSLGIAIASGAPIIAGVIAAVVGGIVAGAVGGSPVQVSGPAAGLTVVVAELIDEL-------G 103
                                    79**********************************************************************.......* PP

                 Sulfate_transp  81 ieiattltllaGviqvllGllRLgflveflseavlsGfiaGaaivillsqikvllglervskkeslvsvlsslftnlekv 160
                                    + +++++t+ aG++q+++Gl+R+++ +  ++  v+++++aG++i+i+l+qi+vllg +   +++s+++++++l++ + ++
  gi|121639162|ref|YP_979386.1| 104 WPMLCLMTIAAGALQIVFGLSRMARAALAIAPVVVHAMLAGIGITIALQQIHVLLGGT---SHSSAWRNIVALPDGILHH 180
                                    *********************************************************8...******************* PP

                 Sulfate_transp 161 nlakvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaifelkreagvkivgeipsglpelslp.....k 235
                                    +l++v++g++++++Ll++++l +      v+++p++lva+  at++++++  ++ + +   g++   +  ++l       
  gi|121639162|ref|YP_979386.1| 181 ELHEVIVGGTVIAILLMWSKLPA-----KVRIIPGPLVAIAGATVLALLP-VLQTERIDLQGNFFDAIGLPKLAemspgG 254
                                    ********************977.....66********************.44445555545553333333333556668 PP

                 Sulfate_transp 236 vdwsl.lsallpdalaialvglleaiavsksldk.kkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGa 313
                                    ++ws+ +sa+++ +l+ial++++e+++++ ++dk ++g ++d n+E+v++G +N++s+l+gglp+tg+++rs  n++aGa
  gi|121639162|ref|YP_979386.1| 255 QPWSHeISAIALGVLTIALIASVESLLSAVGVDKlHHGPRTDFNREMVGQGSANVVSGLLGGLPITGVIVRSSANVAAGA 334
                                    999999****************************9999****************************************** PP

                 Sulfate_transp 314 ktqlsglvsalvvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklskldflillat 380
                                    +t++s++++++++ll+  ++t+l+e iPka+La+++iv+g + Lv+l+++k +w+  + +f+i+++t
  gi|121639162|ref|YP_979386.1| 335 RTRMSTILHGVWILLFASLFTNLVELIPKAALAGLLIVIGAQ-LVKLAHIKLAWR--TGNFVIYAIT 398
                                    ******************************************.************..5667776665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.12
                 Sulfate_transp 231 lslpkvdwsllsallpdalaialvglleaiavsksld 267
                                    +++++++   + a++ +a+ + ++g++  i+++++++
  gi|121639162|ref|YP_979386.1| 705 VQVERLTRHPILATAVAAADLQVIGIFFDISTARVYE 741
                                    677788889999*********************9975 PP

>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   0.0   1.6e-44   1.4e-40       2     156 .]     580     739 ..     579     739 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 1.6e-44
                                    EEEEETTTTS-HHHHTTS-TTSEEEEEETTG---TT..-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHSHHCCST CS
                         Pro_CA   2 lvigCsDSRvppelitdagpGdlFvvrnvgnlvppa..dssvlaaleyAvevlkvkhivVlGHskCGavkaalkaeksee 79 
                                    l+++C+DSR+ p++it +gpGdl++vrn gnlvp++  d sv aal++Av++l+v+++vV+GHs+C a++a+l++ + ++
  gi|121639162|ref|YP_979386.1| 580 LFLTCADSRILPNVITASGPGDLYTVRNLGNLVPTDpdDRSVDAALDFAVNQLGVSSVVVCGHSSCAAMTALLED-DPAN 658
                                    79*******************************9889899******************************88876.5578 PP

                                    TSSHHHHHHHHHHHHHHHCHHHHHTTS....SHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHTTS-EEEEEEEETTTTE CS
                         Pro_CA  80 eagaidkwlekirealekveeelesek....ekearerlleeenVaeqlenLlekpvvreavekgklkvhGlvydletGe 155
                                    +++ + +wle+++++l   ++++ + +        ++++l+ +nVa q+e+L+++p++++av++ +l+v+G+++d++t++
  gi|121639162|ref|YP_979386.1| 659 TTTPMMRWLENAHDSLVVFRNHHPARRsaesAGYPEADQLSIVNVAVQVERLTRHPILATAVAAADLQVIGIFFDISTAR 738
                                    89*************9996665555554444566668999*************************************987 PP

                                    E CS
                         Pro_CA 156 v 156
                                    v
  gi|121639162|ref|YP_979386.1| 739 V 739
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 5112.68
//
Query:       gi|121639163|ref|YP_979387.1|  [L=389]
Description: acyl-CoA dehydrogenase fadE25 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-50  169.1   2.3    1.3e-49  168.3   2.3    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-30  104.9   0.1    7.4e-30  103.0   0.1    2.0  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.4e-29  101.4   0.2    8.9e-29  100.4   0.2    1.5  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    8.9e-27   94.0   2.6    8.9e-27   94.0   2.6    2.2  3  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
     0.0059   15.7   0.1      0.013   14.6   0.1    1.5  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   2.3   3.5e-53   1.3e-49       1     149 [.     238     387 ..     238     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 3.5e-53
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g Gf+ a+ tl+h+R++++a+a+g+a+ al+ a++y ++rk+fg+ +  +q+v+++la+ma ++eaarl+vy aa+++++
  gi|121639163|ref|YP_979387.1| 238 GTGFKTALATLDHTRPTIGAQAVGIAQGALDAAIAYTKDRKQFGESISTFQAVQFMLADMAMKVEAARLMVYSAAARAER 317
                                    67****************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    g+pd +  +++ K fas++a+ev+++a+ql+GgaGy+++ pver++rda++++i+eGt++iqr +++r+l
  gi|121639163|ref|YP_979387.1| 318 GEPDlGFISAASKCFASDVAMEVTTDAVQLFGGAGYTTDFPVERFMRDAKITQIYEGTNQIQRVVMSRAL 387
                                    ****7777888*****************************************************999987 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   4.6e+03      66      89 ..      53      76 ..      45      88 .. 0.66
   2 !  103.0   0.1   2.1e-33   7.4e-30       1      97 []     131     226 ..     131     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                   EE..GGGEEE-----BSS-TTS-E CS
                  Acyl-CoA_dh_M 66 vprdapgvsvrrieeklGlrglpt 89
                                   v  +++g+   +i+e++G +g+++
  gi|121639163|ref|YP_979387.1| 53 VALNSSGFNAVHIPEEYGGQGADS 76
                                   555666777777777777666653 PP

  == domain 2  score: 103.0 bits;  conditional E-value: 2.1e-33
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    ++al+E++aGsd+as++t  a+ dg++++lnG+K+witn++++t+++v+a  ++pd +a+g+s f+v +d++g++v+++e
  gi|121639163|ref|YP_979387.1| 131 SYALSEREAGSDAASMRT-RAKADGDHWILNGAKCWITNGGKSTWYTVMAV-TDPDrGANGISAFMVHKDDEGFTVGPKE 208
                                    589***************.66666666************************.556669********************** PP

                                    -BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfedv 97 
                                    +klG++g pt+el+fe++
  gi|121639163|ref|YP_979387.1| 209 RKLGIKGSPTTELYFENC 226
                                    ****************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.2   2.5e-32   8.9e-29       2     111 ..      17     125 ..      16     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 2.5e-32
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                    ee++++r ++r++ae+e+aphaae+de+++fp+e++ +l   G+ ++++peeygG+g+d ++++iv+ee+ar+da+ +l+
  gi|121639163|ref|YP_979387.1|  17 EEHDEMRSAIRALAEKEIAPHAAEVDEKARFPEEALVALNSSGFNAVHIPEEYGGQGADSVATCIVIEEVARVDASASLI 96 
                                    9***************************************************************************8888 PP

                                    HHHHHHTTHHHHHHHS-HHHHHHHHHHHHT CS
                  Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklas 111
                                    ++v + l++  ++  G+ee k++ Lp la+
  gi|121639163|ref|YP_979387.1|  97 PAV-NKLGTMGLILRGSEELKKQVLPALAA 125
                                    887.6688889****************996 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1   4.1e+03      53      77 ..      25      49 ..      17      65 .. 0.64
   2 ?   -2.4   0.2       1.4   5.2e+03      35      61 ..     125     151 ..     121     160 .. 0.65
   3 !   94.0   2.6   2.5e-30   8.9e-27       3     133 ..     255     376 ..     254     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHTT----H CS
                  Acyl-CoA_dh_2 53 AAralleraaaraealaaagkevtv 77
                                   A ral e+ +a + a +++++++++
  gi|121639163|ref|YP_979387.1| 25 AIRALAEKEIAPHAAEVDEKARFPE 49
                                   4566666666666666666666644 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                    ---HHHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  35 addpatqlalaeaaarldAArallera 61 
                                    a+  ++ +al e +a  dAA + ++++
  gi|121639163|ref|YP_979387.1| 125 AEGAMASYALSEREAGSDAASMRTRAK 151
                                    455566666666666666666655544 PP

  == domain 3  score: 94.0 bits;  conditional E-value: 2.5e-30
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    i+a+a+G+A++al+++++++++r++  +ge+++ ++a+q+ la++a++++AAr+++++aaar    a++g++   ++   
  gi|121639163|ref|YP_979387.1| 255 IGAQAVGIAQGALDAAIAYTKDRKQ--FGESISTFQAVQFMLADMAMKVEAARLMVYSAAAR----AERGEP---DLGFI 325
                                    89***********************..***********************************....999999...78899 PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    +++++ +a++ a +++ ++++++Gg +++++ p++R++RDa+++++++++n
  gi|121639163|ref|YP_979387.1| 326 SAASKCFASDVAMEVTTDAVQLFGGAGYTTDFPVERFMRDAKITQIYEGTN 376
                                    9999********************************************998 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.6e-06     0.013      42     119 ..     284     357 ..     282     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                                    GGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-EE--HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT---- CS
                           HpaB  42 iekfshvqeklgelialrellyalliaaeaeaekdpsGvylPdlllanaarvlvtrlypriveilqdiaGGglitlPs 119
                                    i+ f++vq +l+++++ +e+ + ++++a+a ae+ ++++ ++      a ++++ ++  +++  + ++ GG+  t+ +
  gi|121639163|ref|YP_979387.1| 284 ISTFQAVQFMLADMAMKVEAARLMVYSAAARAERGEPDLGFI----SAASKCFASDVAMEVTTDAVQLFGGAGYTTDF 357
                                    689********************************7666554....35779999999999999999999988776443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3143.79
//
Query:       gi|121639164|ref|YP_979388.1|  [L=174]
Description: phosphoribosylaminoimidazole carboxylase catalytic subunit purE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-65  217.4   1.6    6.9e-65  217.2   1.6    1.1  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.2   1.6   3.8e-69   6.9e-65       1     146 [.       9     154 ..       9     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 3.8e-69
                                    EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-E CS
                           AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPV 80 
                                    +Vg+imGSdsD++vm +aa++l+e++++ evrvvSahrtpe +++ya+ a+ergl+viIagAGgaahLpg+va+ t+lPV
  gi|121639164|ref|YP_979388.1|   9 RVGVIMGSDSDWPVMADAAAALAEFDIPAEVRVVSAHRTPEAMFSYARGAAERGLEVIIAGAGGAAHLPGMVAAATPLPV 88 
                                    59****************************************************************************** PP

                                    EEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHH CS
                           AIRC  81 igvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelk 146
                                    igvPv   +l+gldsllSivqmP+gvpvatv+ig+a+nA+llA+++l++++++l++++ +++++l+
  gi|121639164|ref|YP_979388.1|  89 IGVPVPLGRLDGLDSLLSIVQMPAGVPVATVSIGGARNAGLLAVRMLGAANPQLRARIVAFQDRLA 154
                                    ************************************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1242.04
//
Query:       gi|121639165|ref|YP_979389.1|  [L=429]
Description: phosphoribosylaminoimidazole carboxylase ATPase subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-57  192.5   0.0    5.6e-57  192.0   0.0    1.2  1  ATP-grasp        ATP-grasp domain
    1.6e-16   59.7   0.0    3.5e-16   58.6   0.0    1.6  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    3.9e-08   33.0   0.1    8.6e-08   31.9   0.0    1.6  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.7e-05   24.0   0.0      5e-05   23.2   0.0    1.4  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00014   21.6   0.0     0.0024   17.5   0.0    2.1  2  RimK             RimK-like ATP-grasp domain
      0.008   15.7   0.0       0.26   10.8   0.0    2.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
       0.02   14.4   0.1      0.045   13.3   0.1    1.5  1  ATP-grasp_2      ATP-grasp domain
       0.17   11.9   0.0        0.6   10.1   0.0    1.8  2  ATP-grasp_3      ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.0   2.5e-60   5.6e-57       2     171 .]     125     297 ..     124     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 2.5e-60
                                    HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC..GTTCEEEEE----SEEEE CS
                      ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal..keekvivEefvpfekEls 79 
                                    +++g++vpr++ +++ +e++ +a+++++p+vvKa r+gydG+G  + r+ +d++++++++  ++  v+vEe+v++++Els
  gi|121639165|ref|YP_979389.1| 125 AAAGVAVPRYAGIKDPDEIDVFAARVDAPIVVKAVRGGYDGRGVRMARDVADARDFAREClaDGVAVLVEERVDLRRELS 204
                                    5789******************************************************999999**************** PP

                                    EEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHH.HHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEES CS
                      ATP-grasp  80 vlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkka.eeiakkiveeLggvGvfavElFvledgellvnElap 158
                                    +lv+rs  G+ a++pvv+tvq+dg+++l++apa++  +++++a +++a ++++eLg+vGv+avElF+++dg+llvnEla+
  gi|121639165|ref|YP_979389.1| 205 ALVARSPFGQGAAWPVVQTVQRDGTCVLVIAPAPALPDDLATAaQRLALQLADELGVVGVLAVELFETTDGALLVNELAM 284
                                    *********************************9887776665055666******************************* PP

                                    S--GGGGGHHHHB CS
                      ATP-grasp 159 RpHnsGhvtldaa 171
                                    RpHnsGh+t+d+a
  gi|121639165|ref|YP_979389.1| 285 RPHNSGHWTIDGA 297
                                    **********986 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.6e-19   3.5e-16       1      55 [.     324     384 ..     324     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.6e-19
                         PurK_C   1 avMvNlLGedaeeklee.........llaipgahlHlYgKeearpgRKmGHitvvgdsaeelee 55 
                                    +vM N+LG ++   ++           + +p+a++HlYgK+  rpgRK+GHi+++g++ ++l e
  gi|121639165|ref|YP_979389.1| 324 TVMANVLGAAQP--PAMsvderlhhlFARMPDARVHLYGKA-ERPGRKVGHINFLGSDVAQLCE 384
                                    79*********5..43345667888999*************.*****************99876 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.2   7.1e+03     187     209 ..      20      44 ..      17      45 .. 0.63
   2 !   31.9   0.0   3.8e-11   8.6e-08       1     174 [.     116     280 ..     116     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.2
                                    HHHHHS--HHHH..HHHHHTT--GC CS
                    CPSase_L_D2 187 aekaTGldlvke..aakialgekLe 209
                                      ++ G +l+ +  +a ialg++L+
  gi|121639165|ref|YP_979389.1|  20 VAMVGGGQLARMthQAAIALGQNLR 44 
                                    5566666666432277888998886 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 3.8e-11
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCC.TTTTEEEESSHHHHHHHHHHHHHHHHHHHS CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafgl.GGkGmrvarneeelaelvkkalaeakaafg 79 
                                    Dk  +++ l++++v v + +    ++ +e   +a+++  P+++ka  g+  G+G r+ar+ ++ ++ +++ la       
  gi|121639165|ref|YP_979389.1| 116 DKLVMRQRLAAAGVAVPRYAGI--KDPDEIDVFAARVDAPIVVKAVRGGyDGRGVRMARDVADARDFARECLADG----- 188
                                    7777888999999987776655..9********************876538*********************999..... PP

                                    TS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEE CS
                    CPSase_L_D2  80 nkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagt 159
                                       vlve+ ++  +e+ + v r   g           +q+    v+++AP+++L d+   a ++ a++++ e+gvvg   
  gi|121639165|ref|YP_979389.1| 189 -VAVLVEERVDLRRELSALVARSPFGQGAAWPVV-QTVQRDGTCVLVIAPAPALPDDLATAAQRLALQLADELGVVGVLA 266
                                    .69*******************998877655444.45788888899*******************************999 PP

                                    EEEEEETTTTEEEEE CS
                    CPSase_L_D2 160 veflldpkskeyyvi 174
                                    ve   + +++   v 
  gi|121639165|ref|YP_979389.1| 267 VELF-ETTDGALLVN 280
                                    9964.3345555555 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.2e-08     5e-05       2      90 ..     116     198 ..     115     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.2e-08
                                    BHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEES.C-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                         GARS_A   2 sKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKad.glaagKgvivakseeealkavkeilekkkfGeag 80 
                                    +K  +++ l++ag+  ++y+ ++dp+e++ +  +++a++ VvKa+ g   g+gv +a+++++a + ++e l        g
  gi|121639165|ref|YP_979389.1| 116 DKLVMRQRLAAAGVAVPRYAGIKDPDEIDVFAARVDAPI-VVKAVrGGYDGRGVRMARDVADARDFARECLA------DG 188
                                    68889999*******************************.***9736678*********************7......35 PP

                                    SSEEEEE--- CS
                         GARS_A  81 ekvviEelle 90 
                                      v++Ee+++
  gi|121639165|ref|YP_979389.1| 189 VAVLVEERVD 198
                                    7788888876 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0024       1      68 [.     114     180 ..     114     203 .. 0.87
   2 ?    1.7   0.0     0.075   1.7e+02     128     163 ..     245     282 ..     238     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                    HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTT.T--EEEEE-SHHHHHHH CS
                           RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegs.qGikvvlakkeqklkqv 68 
                                    a+dKl   + La a++ vp+ a ++d+++++ +  ++   +P+vvK v g   G +v +a++  ++++ 
  gi|121639165|ref|YP_979389.1| 114 AQDKLVMRQRLAAAGVAVPRYAGIKDPDEIDVFAARV--DAPIVVKAVRGGyDGRGVRMARDVADARDF 180
                                    789*********************************9..6********97526*********9988875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.075
                                    -HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEE.EEEE CS
                           RimK 128 seeekelAikaakamelv.vaGvDllrakrgll.vlEv 163
                                        ++lA++ a+ +++v v+ v+l+++ +g l v E+
  gi|121639165|ref|YP_979389.1| 245 ATAAQRLALQLADELGVVgVLAVELFETTDGALlVNEL 282
                                    566789******9998765999****998886515565 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00012      0.26       6     172 ..     128     282 ..     124     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                    T--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSST.TTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--.ES CS
                Dala_Dala_lig_C   6 GlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGS.SvGvskveseeelkeaieeafkydekvlvEeai.eg 83 
                                    G++v+ y+ ++  +         +   +++  p++VK++r G    Gv  ++ +++ +++ +e +     vlvEe +   
  gi|121639165|ref|YP_979389.1| 128 GVAVPRYAGIKDPDEI-------DVFAARVDAPIVVKAVRGGYdGRGVRMARDVADARDFARECLADGVAVLVEERVdLR 200
                                    5555555555544433.......345788999*********96268*******************************556 PP

                                    EEEEEEEEE..TSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS-.---HHHHHHHHHHHHHHHHHTT--SEEEEEEE CS
                Dala_Dala_lig_C  84 reievavlg..neklevsevgeivvkkgfydyeakysddkaqlevpa.klekeveekiqelalkaykaldlrGlaRvDff 160
                                    re+   v     ++  + +v++ v+++g          + + +  pa +l+++ + + q lal+  + l++ G+  v +f
  gi|121639165|ref|YP_979389.1| 201 RELSALVARspFGQGAAWPVVQTVQRDG----------TCVLVIAPApALPDDLATAAQRLALQLADELGVVGVLAVELF 270
                                    7877666651122333333333332222..........334444454246777777777777777777777777777777 PP

                                    EETTTEEEEEEE CS
                Dala_Dala_lig_C 161 lteegeivlnEv 172
                                     t++g +++nE+
  gi|121639165|ref|YP_979389.1| 271 ETTDGALLVNEL 282
                                    777777777776 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     2e-05     0.045      11     106 ..     124     202 ..     117     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                    HHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-E CS
                    ATP-grasp_2  11 lakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGk 90 
                                    la  gv+vp+ +  ++++e++  a+++++   vvKa v  G  G   Gv++++++ +a+++a+e l   +          
  gi|121639165|ref|YP_979389.1| 124 LAAAGVAVPRYAGIKDPDEIDVFAARVDAPI-VVKA-VRGGYDG--RGVRMARDVADARDFARECLADGVA--------- 190
                                    7889**********************99887.***9.5655555..59*****************998776......... PP

                                    EE--EEEEE---ECEE CS
                    ATP-grasp_2  91 kvekvlveealdikkE 106
                                        vlvee++d+++E
  gi|121639165|ref|YP_979389.1| 191 ----VLVEERVDLRRE 202
                                    ....566666666666 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027       0.6       1      60 [.     114     181 ..     114     207 .. 0.80
   2 ?   -1.3   0.0       0.9     2e+03     120     142 ..     244     266 ..     234     286 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                                    HTSHHHHHHHHTTT.S---....-EESS--.......SSSEEEEESS-.------B--SS--TTE... CS
                    ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleee.......ekklvvKprdG.aggesvrvveekeeaeaai 60 
                                    a+dKl + ++L +agv vP ++  + ++e        + ++vvK ++G  +g +vr++++  +a  + 
  gi|121639165|ref|YP_979389.1| 114 AQDKLVMRQRLAAAGVAVPRYAGIKDPDEIdvfaarvDAPIVVKAVRGgYDGRGVRMARDVADARDFA 181
                                    68*****************777666666667777777999****9886269********997766544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.9
                                    HHHHHHHHHTTSTT--EEEEEEE CS
                    ATP-grasp_3 120 vvelaeevvekleglaGyvGvDl 142
                                    + ++a+++  +l + +G+vGv  
  gi|121639165|ref|YP_979389.1| 244 LATAAQRLALQLADELGVVGVLA 266
                                    45556666666665556666533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2778.05
//
Query:       gi|121639166|ref|YP_979390.1|  [L=272]
Description: hypothetical protein BCG_3306 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   79.3   5.9    2.6e-22   79.3   5.9    1.8  2  GtrA      GtrA-like protein
  ------ inclusion threshold ------
        1.4    9.1   0.0        1.4    9.1   0.0    3.4  4  DUF4229   Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.31   2.8e+03      63      82 ..      31      50 ..      15      58 .. 0.64
   2 !   79.3   5.9   2.9e-26   2.6e-22       1     117 []      76     206 ..      76     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.31
                           GtrA 63 qflkFvlvsllglllnllil 82
                                   q + ++++s+l+  +++l++
  gi|121639166|ref|YP_979390.1| 31 QTVTYHFASILCSSVHSLVV 50
                                   55555555555555555544 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 2.9e-26
                           GtrA   1 rFlivGvlgtlvdlallllllel.lglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglllnl 79 
                                    +F+ivG+ ++++d+a++++l  + l+ +++ A++ia iva++ +++lnr w F+dr  +++++++l F+++s++g+ll++
  gi|121639166|ref|YP_979390.1|  76 KFAIVGGTTFIIDTAIFYTLKLTvLEPKPVTAKVIAGIVAVIASYVLNREWSFRDRGGRERHHEALLFFAFSGVGVLLSM 155
                                    7*****************9984459******************************************************* PP

                           GtrA  80 lilwllveklgleall.............aklvgiivalvlnyvlsklfvF 117
                                    + lw+  ++l+l   +             a ++g ++ +++++++ +++vF
  gi|121639166|ref|YP_979390.1| 156 APLWFSSYILQLRVPTvsltmeniadfisAYIIGNLLQMAFRFWAFRRWVF 206
                                    ************66556777777888888*********************9 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       0.2   1.8e+03      28      43 ..      35      52 ..      11      53 .. 0.48
   2 ?    9.1   0.0   0.00015       1.4      11      53 ..      85     126 ..      83     131 .. 0.81
   3 ?   -1.2   0.4      0.26   2.3e+03      32      32 ..     159     159 ..     140     204 .. 0.60
   4 ?   -0.8   0.1      0.18   1.6e+03      48      59 ..     245     256 ..     244     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                        DUF4229 28 p..vpllvaallAlvval 43
                                        +l + + +lvv++
  gi|121639166|ref|YP_979390.1| 35 YhfASILCSSVHSLVVSF 52
                                   134445555555555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00015
                        DUF4229  11 fvvltavillvarliglpvpllvaallAlvvalplSmvllkkl 53 
                                    f++ ta+++ +  l +l+ + + a ++A +va + S+vl + +
  gi|121639166|ref|YP_979390.1|  85 FIIDTAIFYTLK-LTVLEPKPVTAKVIAGIVAVIASYVLNREW 126
                                    566677777777.7777778899***************97765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.26
                        DUF4229  32 l 32 
                                    +
  gi|121639166|ref|YP_979390.1| 159 W 159
                                    2 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.18
                        DUF4229  48 vllkklRdrata 59 
                                     ll+ +R+ra++
  gi|121639166|ref|YP_979390.1| 245 TLLRAWRNRANR 256
                                    589******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1911.81
//
Query:       gi|121639167|ref|YP_979391.1|  [L=172]
Description: hypothetical protein BCG_3307c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   69.5   0.3      3e-19   69.0   0.3    1.3  1  bPH_2     Bacterial PH domain
     0.0013   19.1   0.0     0.0086   16.4   0.0    2.0  2  bPH_3     Bacterial PH domain
  ------ inclusion threshold ------
      0.069   11.4   0.7      0.088   11.1   0.7    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.3   5.1e-23     3e-19       1      79 [.      82     156 ..      82     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.1e-23
                          bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeelael 79 
                                    + +t++++t+rrv++r+G+l+r+ +dipl+rI +v++++ +++r++++gt++ie+a+++     l++ ++p+ +e+ +l
  gi|121639167|ref|YP_979391.1|  82 WLTTHFVVTNRRVMFRHGVLTRSGIDIPLARINSVEFRDRIFERIFRTGTLIIESASQD----PLEFYNIPRLREVHAL 156
                                    78999******************************************************....7*********999765 PP

>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.17     1e+03      34      55 ..      35      56 ..      32      66 .. 0.77
   2 !   16.4   0.0   1.4e-06    0.0086      24      66 ..      86     126 ..      82     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.17
                          bPH_3 34 fldpkmfggkdfeeipYksIks 55
                                   ++    fg   +++ p+++I++
  gi|121639167|ref|YP_979391.1| 35 LTGLAAFGSGFVNSTPWQQIAK 56
                                   5555668888999*******86 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-06
                          bPH_3  24 livvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgak 66 
                                     +vvTn+R+ f +      +  ++ip+  I+sv++ ++++   
  gi|121639167|ref|YP_979391.1|  86 HFVVTNRRVMFRHGV--LTRSGIDIPLARINSVEFRDRIFERI 126
                                    589******998876..35889***************997654 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   1.5e-05     0.088       8      73 ..      16      96 ..       9     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.5e-05
                        DUF2070  8 ifrlPswkvsllliillalligllaflssk............lfgillfglpalvaflltl.pvlrilggr..ltykrslf 73
                                   + r P+w + ++ +++l+ll+gl+af s++            ++  ++ g+ +++ + ltl p+l++l ++  +t +r +f
  gi|121639167|ref|YP_979391.1| 16 LHRHPHWNRLIWPVVVLVLLTGLAAFGSGFvnstpwqqiaknVIHAVIWGIWLVIVGWLTLwPFLSWLTTHfvVTNRRVMF 96
                                   5679**********************************9999666666666655555555527999999989777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1264.74
//
Query:       gi|121639168|ref|YP_979392.1|  [L=266]
Description: bifunctional protein birA: biotin operon repressor + biotin--[acetyl-coa-carboxylase] synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-12   47.0   2.0    3.2e-12   46.1   2.0    1.5  1  BPL_C          Biotin protein ligase C terminal domain
    8.4e-05   22.5   0.0    0.00015   21.6   0.0    1.4  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
       0.14   12.6   2.5       0.24   11.9   0.2    2.4  2  DraK_HK_N      DraK Histidine Kinase N-terminal domain
       0.15   11.8   0.1       0.27   11.0   0.1    1.4  1  Cupin_2        Cupin domain


Domain annotation for each model (and alignments):
>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   2.0   7.2e-16   3.2e-12       1      47 [.     218     264 ..     218     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 7.2e-16
                                    STTSEEEEEE.TSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                          BPL_C   1 hsGqeVtled.edgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                    ++G +V++e+ +++ v+Gia++Idd+G+L+l+ ++  ++ +++Gd+++
  gi|121639168|ref|YP_979392.1| 218 TIGSRVRVELpGGQDVVGIARDIDDQGRLCLDVGGR-TVVVSAGDVVH 264
                                    69**********************************.*********98 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.5e-08   0.00015      26     116 ..      57     147 ..      34     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.5e-08
                                    EEEEEEESS-B....-B--B-TT.SEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTEEEETTTE CS
                  BPL_LplA_LipB  26 lvvvrrqtgGr....nvwhspkg.eltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipvfikwpnD 100
                                    + +++ qt+Gr    + w  + +  +++s+ +++ + ++q      + +   lavl+++    +    + + +  kwpnD
  gi|121639168|ref|YP_979392.1|  57 VLIAEHQTAGRgrhgRGWAATARaQIILSVGVRVVDVPVQ--AWGWLSLAAGLAVLDSV---APLIAVPPAETGLKWPND 131
                                    5688999999998888888877777777777776664444..45555666677777777...255588999999****** PP

                                    EEETTEEEEEEEEEEE CS
                  BPL_LplA_LipB 101 lyvngrKlaGiavtst 116
                                    +++ g KlaGi+ ++ 
  gi|121639168|ref|YP_979392.1| 132 VLARGGKLAGILAEVA 147
                                    ***********99876 PP

>> DraK_HK_N  DraK Histidine Kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.38   1.7e+03      27      73 ..      34      78 ..      30      90 .. 0.61
   2 ?   11.9   0.2   5.3e-05      0.24      11      57 ..     183     233 ..     178     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.38
                                   HHTS---HHHHTTT-SS-S.EEEEE-TT-.--B-S---.-SSEEEEEE CS
                      DraK_HK_N 27 aagepitaelLeeqvpgdr.yvvVripggtpieaGedpvegrvisata 73
                                   a+    +a+lL+++  g +   vV i ++   +aG +   gr   ata
  gi|121639168|ref|YP_979392.1| 34 AQTGSTNADLLARAASGADiDGVVLIAEH--QTAG-RGRHGRGWAATA 78
                                   56666778888887776665444555553..4566.333555555554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHHHHHHHHHTS---HHHHTTT-SS-S.....EEEEE-TT-.-- CS
                      DraK_HK_N  11 vesraqrlasivdsrlaagepitaelLeeqvpgdr.....yvvVripggtpi 57 
                                     +  a rl++ ++ r+ + +  +++l +++    +     +v+V++pgg+ +
  gi|121639168|ref|YP_979392.1| 183 RNRIASRLLRELEARIIQWRNANPQLAANYRAR-SltigsRVRVELPGGQDV 233
                                    56789******************9999885443.235566********6433 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.9e-05      0.27      27      48 ..     243     264 ..     243     266 .] 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                                    ESEEEEEECTEEEEEETTEEEE CS
                        Cupin_2  27 eGegeltvdgeeveleaGdsvy 48 
                                    +G++ l v+g++v+++aGd+v+
  gi|121639168|ref|YP_979392.1| 243 QGRLCLDVGGRTVVVSAGDVVH 264
                                    699*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1838.52
//
Query:       gi|121639169|ref|YP_979393.1|  [L=548]
Description: propionyl-CoA carboxylase beta chain 5 accD5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     2e-200  666.7   0.1   2.3e-200  666.5   0.1    1.0  1  Carboxyl_trans  Carboxyl transferase domain
  ------ inclusion threshold ------
      0.021   14.3   1.3      0.031   13.8   0.1    1.9  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)
       0.27    9.0   0.1       0.47    8.2   0.1    1.2  1  Myosin_tail_1   Myosin tail


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.5   0.1  3.8e-204  2.3e-200       1     493 [.      50     545 ..      50     546 .. 0.96

  Alignments for each domain:
  == domain 1  score: 666.5 bits;  conditional E-value: 3.8e-204
                                    SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGC CS
                 Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpakg 79 
                                    k+h++Gkltareri  lld++sF+el++l++hr+t++++ +k+  +dgvvtg+G+++Gr v++++qd tv+ggslg+++g
  gi|121639169|ref|YP_979393.1|  50 KVHAKGKLTARERIYALLDEDSFVELDALAKHRSTNFNLgEKRPLGDGVVTGYGTIDGRDVCIFSQDATVFGGSLGEVYG 129
                                    579*************************************99************************************** PP

                                    EEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEE CS
                 Carboxyl_trans  80 ekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvim 159
                                    ek++k+qe+aik+g pligind++Ga  riqegv+sl  +++if++n +asg+Ipqisl++g++aGg++Y+pal+d+vim
  gi|121639169|ref|YP_979393.1| 130 EKIVKVQELAIKTGRPLIGINDGAGA--RIQEGVVSLGLYSRIFRNNILASGVIPQISLIMGAAAGGHVYSPALTDFVIM 207
                                    **************************..**************************************************** PP

                                    ETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECS CS
                 Carboxyl_trans 160 veetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPiveta 239
                                    v++ts++f+tGpdvik+v+g eevt+eelgGa++hm+ksG+ah++a+ +++a++ +r+llsylP   +nn ++aP+ ++a
  gi|121639169|ref|YP_979393.1| 208 VDQTSQMFITGPDVIKTVTG-EEVTMEELGGAHTHMAKSGTAHYAASGEQDAFDYVRELLSYLP---PNNSTDAPRYQAA 283
                                    ********************.*******************************************...7777777776654 PP

                                    SGSSSH.............HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEET CS
                 Carboxyl_trans 240 depdrd...........lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaG 308
                                     +               l++++Pd++++pyD++evi+rl d+ eFlEi++gyA+++VvGf+r++G+pvG+vAn+++++aG
  gi|121639169|ref|YP_979393.1| 284 APTG-PieenltdedleLDTLIPDSPNQPYDMHEVITRLLDD-EFLEIQAGYAQNIVVGFGRIDGRPVGIVANQPTHFAG 361
                                    3322.22334445555577**********************8.9************************************ PP

                                    TEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTT CS
                 Carboxyl_trans 309 qvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmd 388
                                     +l+i++++Kaarf+r+cd++n+P+v+l+dv+Gfl+G++qey+gi+++Gakl++a+ ea+vPkitvi+rkayGGay+vm+
  gi|121639169|ref|YP_979393.1| 362 -CLDINASEKAARFVRTCDCFNIPIVMLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVPKITVITRKAYGGAYCVMG 440
                                    .******************************************************************************* PP

                                    GGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHH CS
                 Carboxyl_trans 389 skingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpset 468
                                    sk++g d+++awpta+iaV+g++gav++++r+++a+a+++++d ++ r + ++eye++l+npyvaa+rg++Davi+ps+t
  gi|121639169|ref|YP_979393.1| 441 SKDMGCDANLAWPTAQIAVMGASGAVGFVYRQQLAEAAANGEDIDKLRLRLQQEYEDTLVNPYVAAERGYVDAVIPPSHT 520
                                    ******************************************************************************** PP

                                    HHTTSSSEEEHGGGHHHHHHHHHHH CS
                 Carboxyl_trans 469 raklvialelewkkarklparkrrn 493
                                    r+++ +al+l+++k  +lp++k++n
  gi|121639169|ref|YP_979393.1| 521 RGYIGTALRLLERKIAQLPPKKHGN 545
                                    ***********************98 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.69   4.1e+03     107     120 ..     182     195 ..     136     208 .. 0.67
   2 ?   13.8   0.1   5.2e-06     0.031      64     146 ..     382     464 ..     328     478 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.69
                                    -EEEEEEEEEEHHH CS
                           MdcE 107 pvigllvGkavsGa 120
                                    p i+l++G a+ G 
  gi|121639169|ref|YP_979393.1| 182 PQISLIMGAAAGGH 195
                                    56777777776665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.2e-06
                                    --EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTTTT...-SEEEEEET-EEE CS
                           MdcE  64 krpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahglq...anrlialpgvqva 140
                                    + pi++lvDv++   g  +E  Gi    a l  a+  A +   p i+++  ka  Ga+  +g +    +  +a p +q+a
  gi|121639169|ref|YP_979393.1| 382 NIPIVMLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATV---PKITVITRKAYGGAYCVMGSKdmgCDANLAWPTAQIA 458
                                    579*********************************9986...99*************99885522267889999***** PP

                                    SS-HHH CS
                           MdcE 141 vmdkas 146
                                    vm+   
  gi|121639169|ref|YP_979393.1| 459 VMGASG 464
                                    **9765 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   7.9e-05      0.47     558     588 ..     471     501 ..     469     512 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 7.9e-05
                  Myosin_tail_1 558 tqrleekaaaydklektkkRlqqeldDllvd 588
                                    +q+l e aa+ + ++k + Rlqqe++D+lv+
  gi|121639169|ref|YP_979393.1| 471 RQQLAEAAANGEDIDKLRLRLQQEYEDTLVN 501
                                    6999************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3421.50
//
Query:       gi|121639170|ref|YP_979394.1|  [L=156]
Description: hypothetical protein BCG_3310 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   54.6   0.0      3e-14   53.4   0.0    1.6  1  ACC_epsilon  Acyl-CoA carboxylase epsilon subunit


Domain annotation for each model (and alignments):
>> ACC_epsilon  Acyl-CoA carboxylase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   1.7e-18     3e-14       1      55 [.      91     141 ..      91     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.7e-18
                    ACC_epsilon   1 pllrVvrGnPtdeELAALtaVLaaraaaaaaaaaepapagsaWarperrlrrplr 55 
                                    p+++++rG+Ptd+ELAAL+aVL + ++++++a++ep     +W+ p ++lr+p++
  gi|121639170|ref|YP_979394.1|  91 PHIEILRGQPTDQELAALIAVLGSISGSTPPAQPEP----TRWGLPVDQLRYPVF 141
                                    8********************************999....68***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1153.93
//
Query:       gi|121639171|ref|YP_979395.1|  [L=222]
Description: Maf-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-40  138.1   0.0    2.8e-40  137.9   0.0    1.0  1  Maf           Maf-like protein
    0.00025   21.1   3.8     0.0049   17.0   0.9    2.4  2  DprA_WH       DprA winged helix domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.043   13.6   0.0    1.3  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.0   4.8e-44   2.8e-40       1     165 [.       3     201 ..       3     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 4.8e-44
                                    EEEEE---HHHHHHHHCT-..EEEE------............HHHHHHHHHHHHHHHHH.............TCEEEEE CS
                            Maf   1 kliLASaSprRkelLeqlg..fevvpsdvde............aeelvlrlAeaKaeava.............alvigaD 53 
                                    +l+L+SaSp R ++L+++g  + v++s+vde            ++++v  lA aKa +va             ++v+++D
  gi|121639171|ref|YP_979395.1|   3 RLVLGSASPGRLKVLRDAGiePLVIASHVDEdvviaalgpdavPSDVVCVLAAAKAAQVAttltgtqrivaadCVVVACD 82 
                                    69***************998779********************8899**************9999977666666677777 PP

                                    EEEEEC...E---SSHHHHHHHHHHHTTSEEEEEEEEEEEE.....EEE..EEEEEEEEEE----HHHHHHHHHCTSGCC CS
                            Maf  54 tvvvli...lgKPkdeeealemLkklsgrthevvTgvavlk.....ekevksfvettevtfkelsdeeieaYvatgepld 125
                                    ++++++   lgKP++ +ea+e++++++gr  +++Tg+ v++     +  +  ++  t+v+f + s +++eaY+a+ge l 
  gi|121639171|ref|YP_979395.1|  83 SMLYIEgrlLGKPASIDEAREQWRSMAGRAGQLYTGHGVIRlqdnkTVYRSAETAITTVYFGTPSASDLEAYLASGESLR 162
                                    777763567*********************************9987434455677899********************** PP

                                    STTS--TTCGGGGGCEEEECS-HHHHHT--HHHHHHHHCC CS
                            Maf 126 kAGaygiqgllglalverieGsysnVvGLPlaellelLke 165
                                    +AG+++++gl g+++++ ++G++snV+GL+l  l++l+++
  gi|121639171|ref|YP_979395.1| 163 VAGGFTLDGL-GGWFIDGVQGNPSNVIGLSLPLLRSLVQR 201
                                    *********9.888********************999875 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.9   8.2e-07    0.0049      13      47 ..      32      66 ..      23      67 .. 0.94
   2 !    4.6   0.1     0.006        36      31      44 ..     198     211 ..     197     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-07
                        DprA_WH 13 lerrvLaaLgpePvhvDqLvrrtglpaaevsaaLl 47
                                   +e+ v aaLgp++v+ D ++  + + aa+v+++L+
  gi|121639171|ref|YP_979395.1| 32 DEDVVIAALGPDAVPSDVVCVLAAAKAAQVATTLT 66
                                   6889*****************************97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.006
                        DprA_WH  31 Lvrrtglpaaevsa 44 
                                    Lv+r+gl++a++ a
  gi|121639171|ref|YP_979395.1| 198 LVQRCGLSVAALWA 211
                                    89********9976 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-06     0.043     123     161 ..      57      95 ..      35      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                                    TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH--- CS
                   CTP_transf_1 123 slllienikeglllvllllalvvaaDigaYffGklfGkt 161
                                     ++ +++  +g   ++++ ++vva+D++ Y+ G+l+Gk 
  gi|121639171|ref|YP_979395.1|  57 KAAQVATTLTGTQRIVAADCVVVACDSMLYIEGRLLGKP 95 
                                    5566788889999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1724.50
//
Query:       gi|121639172|ref|YP_979396.1|  [L=297]
Description: thiosulfate sulfurtransferase sseA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.8e-34  116.1   0.0    8.5e-17   61.6   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   2.7e-18   4.8e-14       1     106 [.      22     131 ..      22     132 .. 0.84
   2 !   61.6   0.0   4.7e-21   8.5e-17       4     106 ..     164     279 ..     161     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.7e-18
                      Rhodanese   1 sakelkellekgkvallDvRppee.YekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdggg 77 
                                    +a++l +++++++ a++   +++  Y+ ghIpgAv +  ++ l++++ ++    e+++el+++ gi +++tvv+y+d+++
  gi|121639172|ref|YP_979396.1|  22 TADWLSAHMGAPGLAIVESDEDVLlYDVGHIPGAVKIdWHTDLNDPRVRDYINGEQFAELMDRkGIARDDTVVIYGDKSN 101
                                    689**********999999977778************655555566666666667777777779**************** PP

                      Rhodanese  78 r.aaaaaallkklGyknvsvldGGfkawke 106
                                      aa a + ++  G+ +v++l+GG + w +
  gi|121639172|ref|YP_979396.1| 102 WwAAYALWVFTLFGHADVRLLNGGRDLWLA 131
                                    *77777889999**888********99976 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 4.7e-21
                      Rhodanese   4 elkellekgkvallDvRppeeY................ekghIpgAvnvskdtlsrakkseapllelpeellelgidnkk 67 
                                    ++ ++l+++   l+DvR+peeY                 +ghIp Av++++ ++ +++ + ++  el   +    i++++
  gi|121639172|ref|YP_979396.1| 164 DVLAILGAQP--LIDVRSPEEYtgkrthmpdypeegalRAGHIPTAVHIPWGKAADESGRFRSREELERLYDF--INPDD 239
                                    6677777776..**********9999999999*99997779********666666655555555555444444..59*** PP

                      Rhodanese  68 tvvvycdgggraaaaaallkk.lGykn.vsvldGGfkawke 106
                                    + vvyc+ g+r++ ++  l+  lG k  v+++dG++++w +
  gi|121639172|ref|YP_979396.1| 240 QTVVYCRIGERSSHTWFVLTHlLG-KAdVRNYDGSWTEWGN 279
                                    ***********9999998886699.666***********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2334.29
//
Query:       gi|121639173|ref|YP_979397.1|  [L=143]
Description: hypothetical protein BCG_3313 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-29  102.0   0.0    2.1e-29  101.8   0.0    1.0  1  SufE      Fe-S metabolism associated domain
  ------ inclusion threshold ------
        0.1   13.2   0.0       0.16   12.5   0.0    1.4  1  DUF4473   Domain of unknown function (DUF4473)
       0.11   12.5   0.0       0.15   12.1   0.0    1.3  1  SsgA      Streptomyces sporulation and cell division protein,


Domain annotation for each model (and alignments):
>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   3.5e-33   2.1e-29       2     121 ..      16     137 ..      15     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 3.5e-33
                                    HHHHHSSSHHHHHHHHHHHHHTS----CCC.CCCCEEECTSSSEEEEEEEEETTS...EEEEEEESSHHHHHHHHHHHHH CS
                           SufE   2 eefsllddweeryrylielgkklpplpeel.kteenkvkGCqsqvwlaaeledgk...lkfeadsdarivkGllalllev 77 
                                    ++f+++ + ++++r+l+e++++lp+lp +l +++++ v++Cqs+++l+++ +d +   l+f+a+ +a++++G++++l ++
  gi|121639173|ref|YP_979397.1|  16 SDFAEV-QGQDKLRLLLEFANELPALPSHLaESAMEPVPECQSPLFLHVDASDPNrvrLHFSAPAEAPTTRGFASILAAG 94 
                                    578888.7899*****************661567899*************99955588********************** PP

                                    CTTEECCCCTCC-TCHHHHHTTSHHHHCHHHHHHHHHHHHHHHH CS
                           SufE  78 lsgktpeeilavdledfleelglsehlspsRsnGlaamlkrika 121
                                    l+++++++ilav+  df++elgl++ +sp R +G++aml+rik+
  gi|121639173|ref|YP_979397.1|  95 LDEQPAADILAVPE-DFYTELGLAALISPLRLRGMSAMLARIKR 137
                                    **************.***************************97 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05      0.16       9      35 ..      88     114 ..      83     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                        DUF4473   9 aeLvaaGlsekaadglvkiaekfksef 35 
                                    a  +aaGl+e+ a+ ++++ e+f++e 
  gi|121639173|ref|YP_979397.1|  88 ASILAAGLDEQPAADILAVPEDFYTEL 114
                                    6789********************997 PP

>> SsgA  Streptomyces sporulation and cell division protein, SsgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.5e-05      0.15       5      43 ..      61      98 ..      58     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                                   EEEETTSTTEEEEEEE-SS---EEEEEEHHHHHHHTTS- CS
                           SsgA  5 lrYdaadPfaVrlafptdgdeevewvfaRelLaeGlrap 43
                                   l+ da+dP  Vrl+f++++++++++ fa  +La+Gl+++
  gi|121639173|ref|YP_979397.1| 61 LHVDASDPNRVRLHFSAPAEAPTTRGFA-SILAAGLDEQ 98
                                   67799**********************9.7999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 994.53
//
Query:       gi|121639174|ref|YP_979398.1|  [L=600]
Description: bifunctional protein acetyl-/propionyl-coenzyme A carboxylase (alpha chain) accA3: biotin carboxylase + biotin carboxyl carrier protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-78  261.7   0.0    6.1e-78  261.1   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.3e-43  148.1   0.5      5e-43  146.1   0.1    2.2  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    2.3e-37  127.4   0.0    8.1e-37  125.6   0.0    2.0  2  Biotin_carb_C    Biotin carboxylase C-terminal domain
    8.2e-18   64.0   3.4    2.5e-17   62.5   3.4    1.9  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.4e-09   37.8   0.2    7.6e-09   35.4   0.0    2.0  2  ATP-grasp        ATP-grasp domain
    2.9e-08   33.4   1.5    0.00063   19.5   0.2    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
    1.1e-05   25.1   0.0    2.3e-05   24.0   0.0    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      0.001   19.8   1.8        1.5    9.6   0.1    3.1  2  HlyD_3           HlyD family secretion protein
      0.001   18.3   2.1       0.41    9.8   0.2    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0019   18.6   3.2     0.0055   17.2   3.2    1.8  1  DUF2190          Uncharacterized conserved protein (DUF2190)
  ------ inclusion threshold ------
      0.079   12.2   0.0       0.23   10.7   0.0    1.7  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.092   12.9   2.9       0.29   11.3   0.1    3.0  3  LAL_C2           L-amino acid ligase C-terminal domain 2
       0.14   12.3   5.6        0.1   12.8   1.5    2.7  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.1   0.0   4.4e-81   6.1e-78       1     210 [.     125     333 ..     125     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.1 bits;  conditional E-value: 4.4e-81
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    Dk++a+++++++++p+vp+++ pv+ ++e++a+a+e+g P+ ikaa g+GGkGm+var+ +e+ el+++a++ea+aafg+
  gi|121639174|ref|YP_979398.1| 125 DKVTARHIAARAQAPLVPGTPDPVKGADEVVAFAEEYGLPIAIKAAHGGGGKGMKVARTIDEIPELYESAVREATAAFGR 204
                                    9******************************************************************************* PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                     +++ve++l++p+++E++v++D++gnv++ ++r++slq+r qk++e+AP+++Ltd +r++++ +a ++++e ++ gagtv
  gi|121639174|ref|YP_979398.1| 205 GECYVERYLDKPRHVEAQVIADQHGNVVVAGTRDCSLQRRYQKLVEEAPAPFLTDFQRKEIHDSAKRICKEAHYHGAGTV 284
                                    ******************************************************************************** PP

                                    EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                    CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    e+l+ + ++ + ++EvNtRl+ve++++e++ G+dlv ++++ia+gekL+ 
  gi|121639174|ref|YP_979398.1| 285 EYLVGQ-DGLISFLEVNTRLQVEHPVTEETAGIDLVLQQFRIANGEKLDI 333
                                    *****8.*****************************************85 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   0.1   3.7e-46     5e-43       2     110 .]      12     120 ..      11     120 .. 0.98
   2 ?   -1.2   0.1       2.1   2.9e+03       8      30 ..     403     425 ..     394     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 3.7e-46
                                    --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE-- CS
                  Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpG 81 
                                    i+kvl+anrGeiAvr+ira+r+ g+ +vavy+e+da+s+hvr+adea+ lg+++++esYl+ +ki++aa +sga+a+hpG
  gi|121639174|ref|YP_979398.1|  12 ISKVLVANRGEIAVRVIRAARDAGLPSVAVYAEPDAESPHVRLADEAFALGGQTSAESYLDFAKILDAAAKSGANAIHPG 91 
                                    78****************************************************************************** PP

                                    SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                  Biotin_carb_N  82 yGflsEnaefaeaveeagivfiGPsaeal 110
                                    yGfl+Ena+fa+av +ag+++iGPs++++
  gi|121639174|ref|YP_979398.1|  92 YGFLAENADFAQAVIDAGLIWIGPSPQSI 120
                                    *************************9976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                    ---HHHHHHHHHHHHHTT-EEEE CS
                  Biotin_carb_N   8 anrGeiAvriiravrelgietva 30 
                                    a+r+e+  r  ra++e+g+e +a
  gi|121639174|ref|YP_979398.1| 403 ADRAEALARARRALNEFGVEGLA 425
                                    789999**********9887655 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   5.9e-40   8.1e-37       1     107 [.     345     455 ..     345     456 .. 0.97
   2 ?   -2.9   0.0       5.1   7.1e+03      14      31 ..     536     553 ..     532     561 .. 0.79

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 5.9e-40
                                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGv 80 
                                    e+Rin Ed+ +nflp++G vt++++p+gpgvRvdsgve+gs +  ++Ds+laKlivhg++r+ealar+rraL+e+ +eG+
  gi|121639174|ref|YP_979398.1| 345 EFRINGEDAGRNFLPAPGPVTKFHPPSGPGVRVDSGVETGSVIGGQFDSMLAKLIVHGADRAEALARARRALNEFGVEGL 424
                                    89****************************************************************************** PP

                                    -BSHHHHHHHHH-HHHHHT....---TTTCC CS
                  Biotin_carb_C  81 ktnieflrailedeefakg....eldtkfle 107
                                    +t i+f+ra+++d++f+      +++t+++e
  gi|121639174|ref|YP_979398.1| 425 ATVIPFHRAVVSDPAFIGDangfSVHTRWIE 455
                                    ****************9886666789***98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.1
                                    EE--CE-SEEE---STTE CS
                  Biotin_carb_C  14 lpssGkvtelelpegpgv 31 
                                    +p +G+v ++++ eg++v
  gi|121639174|ref|YP_979398.1| 536 APMQGTVVKFAVEEGQEV 553
                                    788999999999888776 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   3.4   1.8e-20   2.5e-17       3      73 .]     534     599 ..     532     599 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.8e-20
                                    EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                    +++Pm G++v+     + v++G++V ag+ ++++eamKme++++a+k+G+++ + v+ G+++++g++la+i
  gi|121639174|ref|YP_979398.1| 534 VTAPMQGTVVK-----FAVEEGQEVVAGDLVVVLEAMKMENPVTAHKDGTITGLAVEAGAAITQGTVLAEI 599
                                    89*********.....*****************************************************97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   5.5e-12   7.6e-09      15     159 ..     149     302 ..     146     305 .. 0.85
   2 ?   -0.7   0.0      0.64   8.8e+02     115     142 ..     401     428 ..     389     434 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.5e-12
                                    CCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEET CS
                      ATP-grasp  15 eskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsa 86 
                                    + ++e+ ++aee glp+ +K + +g  GkG +v r  ++++++ e +        ++++++vE + +  + + + v+ ++
  gi|121639174|ref|YP_979398.1| 149 KGADEVVAFAEEYGLPIAIK-AAHGGGGKGMKVARTIDEIPELYESAvreataafGRGECYVERYLDKPRHVEAQVIADQ 227
                                    667899999***********.889999***************99999999999999************************ PP

                                    TC-EEE--EEEE.EEETTEEEEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                      ATP-grasp  87 eGetafypvvet.vqedgilrlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                    +G++++  +    +q++    +  apa++ ++ + k++++ ak+i++e  + G  +vE  v +dg + + E+  R
  gi|121639174|ref|YP_979398.1| 228 HGNVVVAGTRDCsLQRRYQKLVEEAPAPFLTDfQRKEIHDSAKRICKEAHYHGAGTVEYLVGQDGLISFLEVNTR 302
                                    **8766655443134333333445777776666899**************************9999999999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.64
                                    SCHHHHHHHHHHHHHHHHHTSSEEEEEE CS
                      ATP-grasp 115 sekaqkkaeeiakkiveeLggvGvfavE 142
                                    + ++ ++a + a+++++e+g+ G+ +v 
  gi|121639174|ref|YP_979398.1| 401 HGADRAEALARARRALNEFGVEGLATVI 428
                                    5567888999999**********99985 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   4.6e-07   0.00063       5      37 ..     534     566 ..     532     571 .. 0.89
   2 !   12.4   0.1   7.8e-05      0.11       5      33 ..     571     599 ..     568     600 .] 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.6e-07
                Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37 
                                    ++ap  G+V++ +V++Gq+V aGd+ ++l+  +
  gi|121639174|ref|YP_979398.1| 534 VTAPMQGTVVKFAVEEGQEVVAGDLVVVLEAMK 566
                                    899**********************99998665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.8e-05
                Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                    ++a  +G+++ l+V+ G  + +G vLae+
  gi|121639174|ref|YP_979398.1| 571 VTAHKDGTITGLAVEAGAAITQGTVLAEI 599
                                    67778***********************9 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.6e-08   2.3e-05      30     174 ..     156     301 ..     144     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.6e-08
                                    HHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-S......CEEEEE--.ESEEEEEEEEETSSCEEEEEE CS
                Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyde......kvlvEeai.egreievavlgneklevsevg 102
                                    +  ee g+p+ +K+a+ G   G++ +++ +e+ e  e+a++  +      +  vE+++ + r +e  v+ +++ +v ++g
  gi|121639174|ref|YP_979398.1| 156 AFAEEYGLPIAIKAAHGGGGKGMKVARTIDEIPELYESAVREATaafgrgECYVERYLdKPRHVEAQVIADQHGNVVVAG 235
                                    567999************************98887777766654111112678*****999*********9999988888 PP

                                    EEE-SSSSS-HHHHHC.TT-EEESS--.--HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C 103 eivvkkgfydyeakysddkaqlevpak.lekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                     +  +      + +y+  k   e pa  l++ ++++i++ a+++ k  + +G + v +++ ++g i + EvNt
  gi|121639174|ref|YP_979398.1| 236 TRDCS-----LQRRYQ--KLVEEAPAPfLTDFQRKEIHDSAKRICKEAHYHGAGTVEYLVGQDGLISFLEVNT 301
                                    77665.....567774..44455566526778999*************************************9 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.2    0.0029         4       2      30 ..     534     562 ..     533     567 .. 0.91
   2 !    9.6   0.1    0.0011       1.5       2      30 ..     571     599 ..     570     600 .] 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0029
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                    ++Ap +G+vv+  veeg+ v agd ++ +
  gi|121639174|ref|YP_979398.1| 534 VTAPMQGTVVKFAVEEGQEVVAGDLVVVL 562
                                    89**********************99865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                    ++A  dG+++ l ve+g  +++g++l+ei
  gi|121639174|ref|YP_979398.1| 571 VTAHKDGTITGLAVEAGAAITQGTVLAEI 599
                                    78999***********************9 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0003      0.41     102     138 ..     525     561 ..     519     567 .. 0.82
   2 !    8.3   0.1   0.00086       1.2     108     139 ..     568     599 ..     563     600 .] 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 102 tgkvqktvtvkapisGvVteknvreGqyvqpgdtlft 138
                                    tg + +   v+ap++G+V++ +v eGq v +gd ++ 
  gi|121639174|ref|YP_979398.1| 525 TGAAASGDAVTAPMQGTVVKFAVEEGQEVVAGDLVVV 561
                                    5666666789*******************99997765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00086
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    + +v+a  +G++t ++v  G  +++g++l++i
  gi|121639174|ref|YP_979398.1| 568 ENPVTAHKDGTITGLAVEAGAAITQGTVLAEI 599
                                    56899***********************9998 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.2     4e-06    0.0055      34      99 ..     523     596 ..     490     599 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                        DUF2190  34 Aat.daaaGetvtvaveGvf....veaaaaiavGdkVywdasgkvltt.ttatgn..vaGvaleaaaaagd.tvl 99 
                                    A+t  aa+G+ vt  ++G++    ve ++++ +Gd V + ++ k   + +ta  +  + G a+ea aa ++ tvl
  gi|121639174|ref|YP_979398.1| 523 AHTgAAASGDAVTAPMQGTVvkfaVEEGQEVVAGDLVVVLEAMKM-ENpVTAHKDgtITGLAVEAGAAITQgTVL 596
                                    4565789***********888*****************9999996.5556666566566*******998887776 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.23      19     105 ..     123     207 ..     116     215 .. 0.82
   2 ?   -2.0   0.0       1.3   1.7e+03     232     284 ..     269     321 ..     263     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                    ATPgrasp_ST  19 vddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksalld 98 
                                    + dK+  +++a ra  ++    g+ +  + ++e+ af +e+   ++iK+a+g gGkG+ v+  +++   l +s+++    
  gi|121639174|ref|YP_979398.1| 123 LGDKVTARHIAARAQAPLVP--GTPDPVKGADEVVAFAEEYGLPIAIKAAHGGGGKGMKVARTIDEIPELYESAVREATA 200
                                    78999999998888888766..7888889999999999999555*****************9999988888888887777 PP

                    ATPgrasp_ST  99 elerhvs 105
                                     + r  +
  gi|121639174|ref|YP_979398.1| 201 AFGRGEC 207
                                    7776655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                    ATPgrasp_ST 232 aakaaeklpglgylGwDivldeekgplllElNarpglaivqiangegllprlk 284
                                    a+++ ++ +++g+  +   + +++ +  lE+N+r  ++ +   + +g+   l+
  gi|121639174|ref|YP_979398.1| 269 AKRICKEAHYHGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEETAGIDLVLQ 321
                                    66666667777777777777788878889999998888777777777766665 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.65   8.9e+02       6      38 ..      19      48 ..      14      56 .. 0.75
   2 ?   -3.0   0.0         6   8.3e+03      47      71 ..     226     250 ..     225     251 .. 0.79
   3 ?   11.3   0.1   0.00021      0.29      49      74 ..     395     420 ..     374     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.65
                         LAL_C2  6 prpGrlkaveGleearalpgvveveltvkpGde 38
                                   +  G++ av+ + +a++++g   v ++++p +e
  gi|121639174|ref|YP_979398.1| 19 N-RGEI-AVRVI-RAARDAGLPSVAVYAEPDAE 48
                                   4.5666.77777.667777*********99876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6
                         LAL_C2  47 drlGyviatgdtaeeaeaaaeeaaa 71 
                                    d +G v++ g     ++++ +++++
  gi|121639174|ref|YP_979398.1| 226 DQHGNVVVAGTRDCSLQRRYQKLVE 250
                                    6789999999988888888887765 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00021
                         LAL_C2  49 lGyviatgdtaeeaeaaaeeaaaeir 74 
                                    l+  i++g++++ea+a+a++a++e  
  gi|121639174|ref|YP_979398.1| 395 LAKLIVHGADRAEALARARRALNEFG 420
                                    6778******************9865 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.71   9.7e+02      13      30 ..     220     237 ..     213     250 .. 0.76
   2 ?   12.8   1.5   7.5e-05       0.1       9      72 ..     527     599 ..     519     600 .] 0.67

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.71
                                    T-EEEESSSEEEEEEEEE CS
                  Peptidase_M23  13 gtpVlAaadGtVvfagkk 30 
                                    +++V+A ++G Vv ag++
  gi|121639174|ref|YP_979398.1| 220 EAQVIADQHGNVVVAGTR 237
                                    6789********999984 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-05
                                    EETTT-EEEESSSEEEEEEEEET....TTEEEEEEEECTC.EEEEEEEESE.ES...S-TTEEE-TTCEEEEE CS
                  Peptidase_M23   9 aapkgtpVlAaadGtVvfagkke....gyGnvviidhgdg.ystlyahlsk.is...vkegqkVkaGqvIGtv 72 
                                    aa+ g+ V+A+++GtVv+   +e     +G +v++  + +    + ah +  i+   v++g  + +G+v++++
  gi|121639174|ref|YP_979398.1| 527 AAASGDAVTAPMQGTVVKFAVEEgqevVAGDLVVVLEAMKmENPVTAHKDGtITglaVEAGAAITQGTVLAEI 599
                                    567799**********5544422244445777776665552556777754432244499*********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4246.30
//
Query:       gi|121639175|ref|YP_979399.1|  [L=261]
Description: RNA polymerase sigma factor SigF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   63.1   2.1    3.6e-17   61.6   1.1    2.1  2  Sigma70_r4       Sigma-70, region 4
    6.9e-13   48.5   0.1    5.5e-11   42.4   0.0    2.2  2  Sigma70_r3       Sigma-70 region 3
    1.6e-12   47.0   0.0    2.7e-12   46.3   0.0    1.4  1  Sigma70_r2       Sigma-70 region 2
    2.5e-10   39.9   2.3    3.7e-10   39.3   0.7    2.1  2  Sigma70_r4_2     Sigma-70, region 4
    1.3e-05   25.0   1.5      0.059   13.3   0.2    2.7  2  MarR_2           MarR family
    0.00023   21.5   4.0      0.014   15.7   0.2    2.5  2  TetR_C_11        Tetracyclin repressor-like, C-terminal domai
    0.00025   20.8   0.6     0.0011   18.7   0.1    2.3  3  HTH_23           Homeodomain-like domain
    0.00025   20.9   1.2      0.004   17.1   0.2    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00029   20.3   0.3       0.01   15.4   0.0    2.9  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00038   20.3   0.1     0.0087   16.0   0.0    2.3  2  MarR             MarR family
    0.00067   19.7   0.4      0.023   14.8   0.1    2.7  2  HTH_3            Helix-turn-helix
     0.0015   18.3   0.5        2.4    8.1   0.0    3.1  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0033   17.2   3.6        0.6    9.9   0.3    2.7  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.5   0.2       0.26   11.2   0.0    2.4  2  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
      0.015   15.2   0.1      0.026   14.4   0.1    1.4  1  Sigma70_ECF      ECF sigma factor
      0.018   15.0   0.3       0.15   12.0   0.1    2.3  2  HTH_37           Helix-turn-helix domain
      0.039   14.1   0.0        1.2    9.4   0.0    2.6  2  HTH_28           Helix-turn-helix domain
      0.054   13.4   0.1        5.1    7.1   0.1    2.7  2  HTH_5            Bacterial regulatory protein, arsR family
      0.065   13.1   0.0       0.18   11.7   0.0    1.7  1  Phage_antitermQ  Phage antitermination protein Q
      0.073   13.1   1.6          6    7.0   0.2    3.0  2  HTH_20           Helix-turn-helix domain
       0.08   12.8   0.1       0.33   10.8   0.0    2.1  2  IF2_N            Translation initiation factor IF-2, N-termin
       0.13   12.1   1.2        2.5    8.0   0.1    2.8  3  HTH_10           HTH DNA binding domain
       0.14   12.4   0.0       0.36   11.1   0.0    1.7  1  KORA             TrfB plasmid transcriptional repressor
       0.15   12.4   0.2       0.15   12.4   0.2    2.7  2  HTH_31           Helix-turn-helix domain
       0.15   12.2   0.1        0.9    9.7   0.0    2.3  2  HTH_AraC         Bacterial regulatory helix-turn-helix protei


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2   8.6e+02      15      34 ..     136     155 ..     134     158 .. 0.74
   2 !   61.6   1.1     5e-20   3.6e-17       1      50 []     209     258 ..     209     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                    HHHTTT--HHHHHHHHTS-H CS
                     Sigma70_r4  15 lrfgeglTleEIgerlgiSr 34 
                                    +r g+  + +E++++lg+ r
  gi|121639175|ref|YP_979399.1| 136 QRLGRAPSASELAAELGMDR 155
                                    5666667889******9865 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 5e-20
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                                    +L+ Lperer+vl+lrf++ +T+ +I+er giS+++V++++++ l +LR+
  gi|121639175|ref|YP_979399.1| 209 LLEALPERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAKSLARLRD 258
                                    599*********************************************95 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   7.7e-14   5.5e-11       5      66 ..     126     186 ..     122     195 .. 0.89
   2 ?    4.0   0.0     0.077        55      22      43 ..     230     251 ..     228     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 7.7e-14
                                    HHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXBSTTTX CS
                     Sigma70_r3   5 kikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSldlpvgeeedtelgdll 66 
                                    ++  a+  L+q+lgr+P++ E+A+eLg++ ++V e l a  +++ l+++ g  +d++    +
  gi|121639175|ref|YP_979399.1| 126 RLGTATADLSQRLGRAPSASELAAELGMDRAEVIEGLLAGSSYHTLSIDSGGGSDDDARA-I 186
                                    5667999*********************************************99998776.4 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                                    XHHHHHHHHTXXHHHHHHHHHH CS
                     Sigma70_r3  22 tpeEiAeeLglseekVrevlea 43 
                                    t + iAe++g+s+  V ++l  
  gi|121639175|ref|YP_979399.1| 230 TQTQIAERVGISQMHVSRLLAK 251
                                    6788************999865 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   3.7e-15   2.7e-12       2      70 ..      44     112 ..      43     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.7e-15
                                    HHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2   2 verylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 
                                    v+r lpl  ++arr+ g+g+  +Dl+Q a ++l  a+ rfd  +g +f ++++ ++ +++ +++R++++
  gi|121639175|ref|YP_979399.1|  44 VQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDVKTGSDFVSFAVPTIMGEVRRHFRDNSW 112
                                    8999***************************************************************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.1   1.5e+03      30      41 ..     145     156 ..     141     158 .. 0.75
   2 !   39.3   0.7   5.2e-13   3.7e-10       3      54 .]     205     256 ..     203     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                                    HHHHHHHT--HH CS
                   Sigma70_r4_2  30 kEIAellgiseg 41 
                                     E A++lg+  +
  gi|121639175|ref|YP_979399.1| 145 SELAAELGMDRA 156
                                    688999999765 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 5.2e-13
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                     lr +l++Lper+r++++lr+++ +++ +IAe+ gis   V + l++ +++L
  gi|121639175|ref|YP_979399.1| 205 VLRPLLEALPERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAKSLARL 256
                                    57779******************************************99987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00079      0.57      18      38 ..     138     158 ..     120     158 .. 0.82
   2 !   13.3   0.2   8.3e-05     0.059      20      44 ..     219     251 ..     206     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                                    TTSEEEHHHHHHHHTSSHHHH CS
                         MarR_2  18 pgrdltvgelarrlglsksav 38 
                                     gr  +++ela++lg++++ v
  gi|121639175|ref|YP_979399.1| 138 LGRAPSASELAAELGMDRAEV 158
                                    44445************9865 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.3e-05
                                    S........EEEHHHHHHHHTSSHHHHHHHHHH CS
                         MarR_2  20 r........dltvgelarrlglsksavsrilkr 44 
                                              +t++++a+r g+s+  vsr+l++
  gi|121639175|ref|YP_979399.1| 219 TvlvlrffdSMTQTQIAERVGISQMHVSRLLAK 251
                                    24555444448********************97 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.9e-05     0.014      27      96 ..      19      87 ..       8      95 .. 0.86
   2 ?    6.9   0.1      0.01       7.3      53     112 ..     127     189 ..     102     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                      TetR_C_11 27 agallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgpllyrlll 96
                                     +++r l++  + +pe+ + + + ++++    ++++ rr   rGe r d+   + + l+ +++++ + +
  gi|121639175|ref|YP_979399.1| 19 VPEMFRELVGLPAGSPEFQRHRDK-IVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDVKT 87
                                   45899*************877766.*************************99999999998888887655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                      TetR_C_11  53 leprraalravlrrAvarGelrada..dvelvld.lllgpllyrllltgeplddafaerlvda 112
                                    l   +a l ++l rA    el+a++  d + v++ ll+g  ++ l ++ +  +d++a++++d+
  gi|121639175|ref|YP_979399.1| 127 LGTATADLSQRLGRAPSASELAAELgmDRAEVIEgLLAGSSYHTLSIDSGGGSDDDARAITDT 189
                                    5667889999************9753377778876999999999999999**********997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.1   6.5e+03      17      32 ..     128     143 ..     118     144 .. 0.67
   2 ?   -2.2   0.0       5.7   4.1e+03      20      31 ..     144     155 ..     143     158 .. 0.80
   3 !   18.7   0.1   1.5e-06    0.0011       4      40 ..     215     251 ..     212     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.1
                         HTH_23  17 GlsvreIAreLgvsrr 32 
                                    G  +++ +++Lg+ ++
  gi|121639175|ref|YP_979399.1| 128 GTATADLSQRLGRAPS 143
                                    5556778889998775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                         HTH_23  20 vreIAreLgvsr 31 
                                     +e A+eLg+ r
  gi|121639175|ref|YP_979399.1| 144 ASELAAELGMDR 155
                                    578999999866 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.5e-06
                         HTH_23   4 ereRlrillllaeGlsvreIAreLgvsrrTvyrwlkr 40 
                                    ereR   +l + + +++++IA++ g+s+++v+r l +
  gi|121639175|ref|YP_979399.1| 215 ERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAK 251
                                    77888877777778*******************9876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.24   1.7e+02      21      38 ..     141     158 ..     116     162 .. 0.74
   2 !   17.1   0.2   5.6e-06     0.004      21      44 ..     228     251 ..     205     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.24
                                    EHHHHHHHHHTTSSHHHH CS
                      HTH_Crp_2  21 pltqeelAsmlGltretv 38 
                                      +  elA+ lG+ r  v
  gi|121639175|ref|YP_979399.1| 141 APSASELAAELGMDRAEV 158
                                    567899*******99988 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.6e-06
                                    EHHHHHHHHHTTSSHHHHHHHHHH CS
                      HTH_Crp_2  21 pltqeelAsmlGltretvsrilse 44 
                                    ++tq+++A+++G+++ +vsr+l++
  gi|121639175|ref|YP_979399.1| 228 SMTQTQIAERVGISQMHVSRLLAK 251
                                    7********************986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.86   6.2e+02      21      32 ..     132     143 ..     128     145 .. 0.83
   2 ?    0.9   0.0      0.48   3.4e+02      19      31 ..     143     155 ..     139     159 .. 0.85
   3 !   15.4   0.0   1.4e-05      0.01      17      38 ..     228     249 ..     227     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.86
                         HTH_24  21 reLAerlglSps 32 
                                    ++L++rlg  ps
  gi|121639175|ref|YP_979399.1| 132 ADLSQRLGRAPS 143
                                    79******9887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.48
                         HTH_24  19 sqreLAerlglSp 31 
                                    s +eLA +lg+ +
  gi|121639175|ref|YP_979399.1| 143 SASELAAELGMDR 155
                                    568*******986 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.4e-05
                         HTH_24  17 risqreLAerlglSpstvnrrl 38 
                                    +++q+++Aer+g+S+  v+r l
  gi|121639175|ref|YP_979399.1| 228 SMTQTQIAERVGISQMHVSRLL 249
                                    59*************9999976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.35   2.5e+02      17      33 ..     141     157 ..     137     160 .. 0.86
   2 !   16.0   0.0   1.2e-05    0.0087      15      40 ..     226     251 ..     218     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.35
                                    TEEHHHHHHHHTS-HHH CS
                           MarR  17 plsvseLakklgvskst 33 
                                    ++s seLa  lg++++ 
  gi|121639175|ref|YP_979399.1| 141 APSASELAAELGMDRAE 157
                                    57899*********985 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.2e-05
                                    STTEEHHHHHHHHTS-HHHHHHHHHH CS
                           MarR  15 qgplsvseLakklgvskstvtrvldr 40 
                                     ++++++++a+++g+s+++v+r+l +
  gi|121639175|ref|YP_979399.1| 226 FDSMTQTQIAERVGISQMHVSRLLAK 251
                                    578*******************9975 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.33   2.4e+02      12      24 ..     144     156 ..     133     159 .. 0.86
   2 !   14.8   0.1   3.2e-05     0.023      10      30 ..     229     249 ..     228     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                                    HHHHHHHHTSSHH CS
                          HTH_3  12 qeeLAeklGvsrs 24 
                                      eLA++lG+ r+
  gi|121639175|ref|YP_979399.1| 144 ASELAAELGMDRA 156
                                    579******9997 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHTSSHHHHHHHH CS
                          HTH_3  10 lsqeeLAeklGvsrstisriE 30 
                                    ++q+++Ae++G+s+ ++sr+ 
  gi|121639175|ref|YP_979399.1| 229 MTQTQIAERVGISQMHVSRLL 249
                                    8******************85 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.3   1.7e+03      20      32 ..     131     143 ..     129     145 .. 0.78
   2 !    6.9   0.1     0.008       5.7      19      35 ..     143     159 ..     136     160 .. 0.86
   3 !    8.1   0.0    0.0034       2.4      18      36 ..     229     247 ..     227     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                  HTH_AsnC-type  20 yaeLAervGlSes 32 
                                     a+L++r+G ++s
  gi|121639175|ref|YP_979399.1| 131 TADLSQRLGRAPS 143
                                    6899999997776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.008
                  HTH_AsnC-type  19 syaeLAervGlSestvl 35 
                                    s +eLA+++G+++++v+
  gi|121639175|ref|YP_979399.1| 143 SASELAAELGMDRAEVI 159
                                    678************97 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0034
                  HTH_AsnC-type  18 isyaeLAervGlSestvlr 36 
                                    ++ +++AervG+S+  v r
  gi|121639175|ref|YP_979399.1| 229 MTQTQIAERVGISQMHVSR 247
                                    7899*********987765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2    0.0056         4      16      35 ..     139     158 ..     131     162 .. 0.85
   2 !    9.9   0.3   0.00084       0.6      16      40 ..     217     250 ..     209     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0056
                                    BSS-BHHHHHHHHTS-HHHH CS
                       HTH_IclR  16 pqeltlselArrtglpkStv 35 
                                    +++ + selA+++g+ ++ v
  gi|121639175|ref|YP_979399.1| 139 GRAPSASELAAELGMDRAEV 158
                                    556688***********987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00084
                                    BSS.........-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR  16 pqe.........ltlselArrtglpkStvhRlLq 40 
                                     +          +t +++A+r g++   v+RlL+
  gi|121639175|ref|YP_979399.1| 217 ERTvlvlrffdsMTQTQIAERVGISQMHVSRLLA 250
                                    4445555555557778****************96 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.35   2.5e+02      10      25 ..     143     158 ..     137     166 .. 0.87
   2 ?   11.2   0.0   0.00036      0.26      10      30 ..     230     250 ..     228     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.35
                 YdaS_antitoxin  10 gqkaLAealgvsqqaV 25 
                                    ++++LA +lg+ ++ V
  gi|121639175|ref|YP_979399.1| 143 SASELAAELGMDRAEV 158
                                    789*******998877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00036
                 YdaS_antitoxin  10 gqkaLAealgvsqqaVsqWlk 30 
                                    +q++ Ae++g+sq++Vs++l+
  gi|121639175|ref|YP_979399.1| 230 TQTQIAERVGISQMHVSRLLA 250
                                    6999**************996 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.6e-05     0.026     121     179 ..     197     256 ..     175     261 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                    Sigma70_ECF 121 delleLdealerlls.ldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawl 179
                                     + +e  e l  ll+ l+++ + ++ lr+++ ++ + iAe++g+s+  v r la   a+l
  gi|121639175|ref|YP_979399.1| 197 LDQIENREVLRPLLEaLPERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAKSLARL 256
                                    44555567777777768889999999*************************987554544 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.2   8.9e+02      33      48 ..     143     158 ..     120     163 .. 0.81
   2 ?   12.0   0.1   0.00021      0.15      32      59 ..     229     256 ..     227     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                                    -HHHHHHHHT--HHHH CS
                         HTH_37  33 sqseaaqllgiaqPkv 48 
                                    s se+a+ lg+++++v
  gi|121639175|ref|YP_979399.1| 143 SASELAAELGMDRAEV 158
                                    6788888888888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00021
                                    --HHHHHHHHT--HHHHHHHHTT--TT- CS
                         HTH_37  32 lsqseaaqllgiaqPkvsrllrgklsrf 59 
                                     +q+++a++ gi+q +vsrll   l r+
  gi|121639175|ref|YP_979399.1| 229 MTQTQIAERVGISQMHVSRLLAKSLARL 256
                                    79*******************8877765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.45   3.2e+02      13      26 ..     140     155 ..     133     163 .. 0.83
   2 ?    9.4   0.0    0.0016       1.2      11      34 ..     227     250 ..     217     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.45
                         HTH_28  13 h..svreaArelgisr 26 
                                    +  s++e+A+elg++r
  gi|121639175|ref|YP_979399.1| 140 RapSASELAAELGMDR 155
                                    4458999******998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                         HTH_28  11 aGhsvreaArelgisrrtvyrWik 34 
                                    + ++++++A+++gis+ +v+r++ 
  gi|121639175|ref|YP_979399.1| 227 DSMTQTQIAERVGISQMHVSRLLA 250
                                    5589***************99986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.079        57      17      32 ..     143     158 ..     134     162 .. 0.87
   2 ?    7.1   0.1    0.0071       5.1      14      37 ..     227     250 ..     209     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                                    EHHHHHHHHTS-HHHH CS
                          HTH_5  17 cvcelaeelglsqstv 32 
                                    +++ela+elg+ ++ v
  gi|121639175|ref|YP_979399.1| 143 SASELAAELGMDRAEV 158
                                    579********99876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                                    SSEEHHHHHHHHTS-HHHHHHHHH CS
                          HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                     +++ +++ae +g+sq  vS+ L+
  gi|121639175|ref|YP_979399.1| 227 DSMTQTQIAERVGISQMHVSRLLA 250
                                    579999**********99998665 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.18      64     101 ..     214     251 ..     200     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                Phage_antitermQ  64 rpeelellvdyYvfgvskraiarklkisekevrkklqk 101
                                     ++e ++lv +++  +++++ia++++is+++v++ l+k
  gi|121639175|ref|YP_979399.1| 214 PERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAK 251
                                    478999**************************998876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0083         6      15      41 ..     134     158 ..     120     159 .. 0.84
   2 ?    4.1   0.1     0.066        47      19      45 ..     226     249 ..     202     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0083
                                    HHHHHSTCTTB-HHHHHHHHTS-HHHH CS
                         HTH_20  15 ilraLaraegltaselaerldlskntl 41 
                                    + + L  +++ +asela++l+++++++
  gi|121639175|ref|YP_979399.1| 134 LSQRL--GRAPSASELAAELGMDRAEV 158
                                    45666..9999**********999875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.066
                                    HSTCTTB-HHHHHHHHTS-HHHHHHHH CS
                         HTH_20  19 LaraegltaselaerldlskntlsyHL 45 
                                    +   + +t +++aer+++s+  +s+ L
  gi|121639175|ref|YP_979399.1| 226 F---DSMTQTQIAERVGISQMHVSRLL 249
                                    5...78999**********99998866 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.33       7      24 ..     145     162 ..     143     173 .. 0.88
   2 ?   -2.3   0.0       5.7   4.1e+03      40      52 ..     179     191 ..     179     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                          IF2_N   7 yeLAkeLgvkskevikkL 24 
                                    +eLA eLg++ +evi+ L
  gi|121639175|ref|YP_979399.1| 145 SELAAELGMDRAEVIEGL 162
                                    7**************988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                          IF2_N  40 Deetaeliaeefg 52 
                                    ++++a +i + +g
  gi|121639175|ref|YP_979399.1| 179 SDDDARAITDTLG 191
                                    6899****99988 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.67   4.8e+02      26      47 ..     120     141 ..     116     144 .. 0.80
   2 ?    0.7   0.0      0.67   4.8e+02      23      37 ..     141     155 ..     139     162 .. 0.78
   3 ?    8.0   0.1    0.0035       2.5      25      51 ..     230     256 ..     228     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.67
                         HTH_10  26 lkeLAkelGIskstlsehLrka 47 
                                    lkeL  +lG + ++ls++L +a
  gi|121639175|ref|YP_979399.1| 120 LKELHLRLGTATADLSQRLGRA 141
                                    7788888999999999999888 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.67
                         HTH_10  23 rvtlkeLAkelGIsk 37 
                                      +++eLA elG  +
  gi|121639175|ref|YP_979399.1| 141 APSASELAAELGMDR 155
                                    55789******9755 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0035
                         HTH_10  25 tlkeLAkelGIskstlsehLrkaeskl 51 
                                    t  ++A++ GIs++ +s  L k+  +l
  gi|121639175|ref|YP_979399.1| 230 TQTQIAERVGISQMHVSRLLAKSLARL 256
                                    5679****************9987765 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.36       8      57 ..     205     254 ..     200     261 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                           KORA   8 eiikgleelaeqtveiargvLVegkkqadvatelgltkqavsqavkrvwa 57 
                                     +++ le l e+ + +      ++ +q+++a+++g+++  vs++  + +a
  gi|121639175|ref|YP_979399.1| 205 VLRPLLEALPERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAKSLA 254
                                    5678899999999999999999********************99888766 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4       2.8     2e+03      17      25 ..     144     152 ..     117     162 .. 0.59
   2 ?   12.4   0.2   0.00021      0.15      10      36 ..     216     250 ..     202     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.8
                         HTH_31  17 qeevAerlg 25 
                                      e+A+ lg
  gi|121639175|ref|YP_979399.1| 144 ASELAAELG 152
                                    334444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00021
                         HTH_31  10 Rera..........GLsqeevAerlgvsestlsrlEq 36 
                                    R  +           ++q++ Aer+g+s+ ++srl  
  gi|121639175|ref|YP_979399.1| 216 R--ErtvlvlrffdSMTQTQIAERVGISQMHVSRLLA 250
                                    3..344777777779*******************976 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.8   2.8e+03      13      22 ..     146     155 ..     145     156 .. 0.87
   2 ?    9.7   0.0    0.0013       0.9      12      29 ..     232     249 ..     225     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.8
                                    HHHHHTTSSH CS
                       HTH_AraC  13 diAdelgfSr 22 
                                    ++A+elg++r
  gi|121639175|ref|YP_979399.1| 146 ELAAELGMDR 155
                                    79******97 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                    HHHHHHTTSSHHHHHHHH CS
                       HTH_AraC  12 ediAdelgfSrsyFsrlF 29 
                                    ++iA+ +g+S+++ srl+
  gi|121639175|ref|YP_979399.1| 232 TQIAERVGISQMHVSRLL 249
                                    79**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1917.56
//
Query:       gi|121639176|ref|YP_979400.1|  [L=145]
Description: anti-sigma factor rsbW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-05   24.1   0.2    6.1e-05   23.0   0.2    1.7  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   3.4e-09   6.1e-05       2      52 ..      23      73 ..      22     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.4e-09
                    HATPase_c_2  2 sadpehvrtvrevaeavlrraglseelldeirlaveEactNavehayleap 52
                                   +a++e+++ +r  + a+    +l+ ++++++rlav+E+ct+ ++ a ++a+
  gi|121639176|ref|YP_979400.1| 23 AARLENLALLRTLVGAIGTFEDLDFDAVADLRLAVDEVCTRLIRSALPDAT 73
                                   7999*************888************************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 996.27
//
Query:       gi|121639177|ref|YP_979401.1|  [L=137]
Description: protein usfY [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   13.9   0.3      0.024   13.8   0.3    1.1  1  CitMHS    Citrate transporter
       0.11   13.0   4.8       0.22   12.0   4.8    1.6  1  DUF202    Domain of unknown function (DUF202)
       0.18   10.6   0.0       0.19   10.4   0.0    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     4e-06     0.024     208     259 ..      58     105 ..      10     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-06
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                         CitMHS 208 ykkveWsv.lllfaGvfllvgaleqtGilealadll.gaggplvalalvlglia 259
                                    ++ v+W+  ll++aGv+++vgal ++G +++  +++ g      ++a+v+ +++
  gi|121639177|ref|YP_979401.1|  58 IDVVHWPGyLLIVAGVVGGVGALAAFGTGHHAEGMTfG------VVAIVVTVVG 105
                                    4668887515567999999********99998777733......2233333333 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.8   3.7e-05      0.22      19      65 ..      71     116 ..      46     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                         DUF202  19 alialglallrffltgepsalgkilglilivlgiltllvglvrylrr 65 
                                    a ++ g++ l+ f tg+++  g+ +g+++iv++++ l++ ++ ++r 
  gi|121639177|ref|YP_979401.1|  71 AGVVGGVGALAAFGTGHHAE-GMTFGVVAIVVTVVGLAWLAFEHRRI 116
                                    56789999999999******.9*******************999986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.2e-05      0.19     388     444 ..      66     126 ..      37     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.2e-05
                        DUF2207 388 lgliilglilillallllvll....lvfllilllillliaiivlllfsrllgrrteeGael 444
                                     +li++g++++++al++++++     + ++++++++ +++++ l++ +r++++  + ++ +
  gi|121639177|ref|YP_979401.1|  66 YLLIVAGVVGGVGALAAFGTGhhaeGMTFGVVAIVVTVVGLAWLAFEHRRIRKIADRWYTE 126
                                    466777777777777777777889999*******************999999877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1012.30
//
Query:       gi|121639178|ref|YP_979402.1|  [L=125]
Description: hypothetical protein BCG_3318c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.92    9.4   6.2          6    6.8   6.2    2.1  1  DUF5337   Family of unknown function (DUF5337)
        3.7    7.9   7.7        0.7   10.2   3.4    1.9  2  DUF3040   Protein of unknown function (DUF3040)
        5.1    6.8   9.5       0.87    9.3   1.8    2.3  2  DUF2244   Integral membrane protein (DUF2244)


Domain annotation for each model (and alignments):
>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.2     0.001         6      17      68 ..      27      89 ..      14      92 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.001
                        DUF5337 17 alviavtmllwlgaq..wi.......geqlglsnRyalLfd..LaAlAaliwalvvtyqlwra 68
                                   a+v av+++ +l +   ++        ++ g ++R+ l +   L+  Aa  wa++ ty++wra
  gi|121639178|ref|YP_979402.1| 27 AVVAAVVGVGFLIMGalLVstcsgvdTAACGPPQRILLALGgpLILCAAGLWAFLRTYRVWRA 89
                                   44444444444333221331111111245677888776665458888999************8 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.4   0.00012       0.7      35      83 ..      14      77 ..       6      79 .. 0.75
   2 ?   -0.6   0.1      0.28   1.7e+03      46      63 ..      96     113 ..      79     123 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                        DUF3040 35 rarrrslrrlavlavllfvaGllllvlG.vaaaa..............vvlgvvGfvvmlagvv 83
                                   ++  ++++ ++  av+++v+G+ +l++G +++++              ++l++ G ++++a+++
  gi|121639178|ref|YP_979402.1| 14 GRDDSEVHSAIRFAVVAAVVGVGFLIMGaLLVSTcsgvdtaacgppqrILLALGGPLILCAAGL 77
                                   455566677789999999**********777776888888888888877777777777777665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                        DUF3040  46 vlavllfvaGllllvlGv 63 
                                    + ++  f++ l++l+l +
  gi|121639178|ref|YP_979402.1|  96 WHGAGWFLLTLMVLTLCI 113
                                    444445555555555443 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.8   0.00015      0.87      19      48 ..      26      55 ..      20      58 .. 0.91
   2 ?    2.3   0.3      0.02   1.2e+02       8      29 ..      95     116 ..      91     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                        DUF2244 19 lalvslvialafllaGawpvlpFaglevla 48
                                   +a+v +v++++fl++Ga +v    g++ +a
  gi|121639178|ref|YP_979402.1| 26 FAVVAAVVGVGFLIMGALLVSTCSGVDTAA 55
                                   689999********************9887 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.02
                        DUF2244   8 sprgflllllalalvslviala 29 
                                    +++g+ ++ll l+++ l i+++
  gi|121639178|ref|YP_979402.1|  95 GWHGAGWFLLTLMVLTLCIGVP 116
                                    6899999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 848.96
//
Query:       gi|121639179|ref|YP_979403.1|  [L=449]
Description: L-lysine aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-75  254.5   0.0    1.7e-75  254.2   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.2   0.0   9.6e-80   1.7e-75       8     405 ..      34     444 ..      28     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 9.6e-80
                                    -SCEEEEEEEBTEEEET.TS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHH.....HHHHHHHHHH CS
                    Aminotran_3   8 nlllvitkaeGvyltdv.dgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnep.....alklaekllk 81 
                                     ++l++t++ G+yl+d+  g+rylD+    a+ +lG + P++v+  +  a+ ++    +  +n+      +++++e  ++
  gi|121639179|ref|YP_979403.1|  34 DIVLDLTRSGGSYLVDAiTGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAAL-NKPSNSDvysvaMARFVETFAR 112
                                    567899*********8549************************97655555444333.5555444110114455566677 PP

                                    HCT-...SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-.......EEEEETTT---SSHHHHHHSS--TTTTTTCTTB CS
                    Aminotran_3  82 lapk.gldkvflansGseAvetAlKlarkyarekkatekt.......kiiafkgafHGrtlgalsvtgskkkyktlfgpf 153
                                    +++   l ++f+++ G+ Ave+AlK+a+ ++  +++ +         +++ ++gafHGr  ++ls+t+ k+ + + f++f
  gi|121639179|ref|YP_979403.1| 113 VLGDpALPHLFFVEGGALAVENALKAAFDWKSRHNQAH-GidpalgtQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKF 191
                                    77662355*********************987765222.24567777********************************* PP

                                    -TSEEEE-TTBGGGT.B-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE CS
                    Aminotran_3 154 lpevvrlkypdeevl.keneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivD 232
                                      + + ++y  +    +  +  ea +l++++a  ++   ++a ++ EpiqgegG+ +  pef+a++relc++ d+lli+D
  gi|121639179|ref|YP_979403.1| 192 DWPRIDAPYMRPGLDePAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFD 271
                                    88888888887654314445667777777788789********************************************* PP

                                    -TTTTTTTTSSSSGGGGCTS--SEEEE-.GGGGTT.SS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHH CS
                    Aminotran_3 233 EvqtGfGrTGklfAlehagvspDlmtla.KaltgG.lplsavlataevmqalapgshgsTfgGnplacavalavleiiee 310
                                    EvqtG G TG+ +A+++++v+pD+++++ K +  G +    v   a+ + a+ p+   sT+gGn   ++ a+ +le+ie 
  gi|121639179|ref|YP_979403.1| 272 EVQTGCGLTGTAWAYQQLDVAPDIVAFGkKTQVCGvMAGRRVDEVADNVFAV-PSRLNSTWGGNLTDMVRARRILEVIEA 350
                                    ****************************889999955555554433333333.5669*********************** PP

                                    TTHHHHHHHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT CS
                    Aminotran_3 311 ekllenaqelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppli 389
                                    e l e+a + g++l+++L el+++   v+ + Rg+Glm+a+ l+  a+++  e++ ++ +  v++l+aG +++r++ppl+
  gi|121639179|ref|YP_979403.1| 351 EGLFERAVQHGKYLRARLDELAADFpAVVLDPRGRGLMCAFSLPTTADRD--ELIRQLWQRAVIVLPAGADTVRFRPPLT 428
                                    **********************99889*********************77..9*************************** PP

                                    --HHHHHHHHHHHHHH CS
                    Aminotran_3 390 itdeeidelleilkka 405
                                    ++ +eid+++ ++  a
  gi|121639179|ref|YP_979403.1| 429 VSTAEIDAAIAAVRSA 444
                                    *********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3329.97
//
Query:       gi|121639180|ref|YP_979404.1|  [L=150]
Description: AsnC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-13   48.3   0.2    8.4e-13   47.7   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    5.8e-13   48.6   0.1    1.4e-12   47.4   0.1    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      9e-13   47.8   4.3    1.6e-12   47.0   4.3    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      1e-06   28.5   0.6      2e-06   27.6   0.6    1.5  1  MarR_2          MarR family
    0.00012   21.7   0.6    0.00024   20.9   0.6    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00015   21.6   0.0     0.0003   20.6   0.0    1.5  1  MarR            MarR family
    0.00038   20.4   0.8    0.00084   19.4   0.1    1.8  2  HTH_20          Helix-turn-helix domain
    0.00046   20.3   2.3    0.00057   20.0   0.5    2.0  2  HTH_28          Helix-turn-helix domain
    0.00054   19.9   1.1    0.00067   19.6   0.1    1.7  2  HTH_11          HTH domain
     0.0015   18.3   0.9     0.0023   17.8   0.2    1.6  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0028   17.2   0.6     0.0054   16.3   0.6    1.5  1  HTH_CodY        CodY helix-turn-helix domain
     0.0053   16.3   0.1     0.0082   15.7   0.1    1.3  1  HTH_47          winged helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.027   14.3   0.1    1.7  1  HTH_10          HTH DNA binding domain
      0.021   14.3   0.7      0.067   12.7   0.7    1.9  1  Sigma70_r4      Sigma-70, region 4
      0.026   14.5   0.1      0.054   13.5   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.026   14.2   0.0      0.065   12.9   0.0    1.6  1  HTH_41          Helix-turn-helix domain
      0.034   13.8   1.6      0.036   13.7   0.4    1.6  2  GntR            Bacterial regulatory proteins, gntR family
      0.066   13.0   0.3       0.24   11.2   0.1    1.9  2  LexA_DNA_bind   LexA DNA binding domain
      0.069   13.7   0.0       0.14   12.7   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
      0.079   13.1   0.0       0.24   11.6   0.0    1.9  3  MIase           Muconolactone delta-isomerase
       0.18   11.9   0.0       0.37   10.8   0.0    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.2   9.9e-16   8.4e-13       1      48 []       5      52 ..       5      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 9.9e-16
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ld++dr + ++L +++r + +eLA r glS+s+v  r++rLe+ G+++
  gi|121639180|ref|YP_979404.1|  5 LDDIDRILVRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   799***899*************************************95 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.7   5.7e+03      48      60 ..       6      18 ..       4      23 .. 0.73
   2 !   47.4   0.1   1.6e-15   1.4e-12      10      75 .]      78     141 ..      71     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.7
                                   HHHHHHHHHTTTT CS
                 AsnC_trans_reg 48 ealerflreklas 60
                                   ++++r+l+++la+
  gi|121639180|ref|YP_979404.1|  6 DDIDRILVRELAA 18
                                   6788888888875 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 1.6e-15
                                    TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                 AsnC_trans_reg  10 peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                    p q +++ ++l+ ++eV++cy+v+G+ +y+l v+v++ +ale++l++ +++  +v rt+++i+l+t
  gi|121639180|ref|YP_979404.1|  78 PSQPDDAPARLEHIEEVESCYSVAGEESYVLLVRVASARALEDLLQR-IRTTANV-RTRSTIILNT 141
                                    33599999*************************************99.*****99.8999999975 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   4.3   1.9e-15   1.6e-12       1      42 []       5      46 ..       5      46 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.9e-15
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   LD+iDr ++++L +d+R + +eLA r GlS s+v+ RvrrLe
  gi|121639180|ref|YP_979404.1|  5 LDDIDRILVRELAADGRVTLSELATRAGLSVSAVQSRVRRLE 46
                                   8****************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.6   2.3e-09     2e-06      11      52 ..      13      52 ..       4      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-09
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                     +L++ ++  +t +ela r gls sav+ +++rL+++G v+
  gi|121639180|ref|YP_979404.1| 13 VRELAADGR--VTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   566777776..****************************995 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.6   2.8e-07   0.00024      15      49 ..      18      52 ..      15      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-07
                                   TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   a++++tlselA r+gl+ S+v   ++ L+ +G v+
  gi|121639180|ref|YP_979404.1| 18 ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   67889***************************996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-07    0.0003       9      47 ..      13      51 ..      11      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                                   HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                   +r l+  g  ++seLa + g+s s+v   ++rLe +G +
  gi|121639180|ref|YP_979404.1| 13 VRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVV 51
                                   577888999****************************87 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   9.8e-07   0.00084      16      54 ..      13      51 ..       5      55 .. 0.93
   2 ?   -1.5   0.0       3.3   2.8e+03      24      37 ..     115     128 ..     108     137 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.8e-07
                                   HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                         HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                    r+La ++ +t+sela r +ls + +  ++r Le+ g v
  gi|121639180|ref|YP_979404.1| 13 VRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVV 51
                                   6899*******************************9988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                                    TB-HHHHHHHHTS- CS
                         HTH_20  24 gltaselaerldls 37 
                                    ++ +++l +r++++
  gi|121639180|ref|YP_979404.1| 115 ARALEDLLQRIRTT 128
                                    44444444444443 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   6.6e-07   0.00057       6      41 ..      13      50 ..      10      58 .. 0.86
   2 ?   -1.1   0.1       2.5   2.1e+03      25      38 ..     114     127 ..     109     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.6e-07
                         HTH_28  6 iklla.aGh.svreaArelgisrrtvyrWikryeegGi 41
                                   +++la +G+ + +e+A + g+s + v++ ++r+e+ G+
  gi|121639180|ref|YP_979404.1| 13 VRELAaDGRvTLSELATRAGLSVSAVQSRVRRLESRGV 50
                                   5565548999*************************996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                         HTH_28  25 srrtvyrWikryee 38 
                                    s r + ++++r ++
  gi|121639180|ref|YP_979404.1| 114 SARALEDLLQRIRT 127
                                    66788888888776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.8e-07   0.00067       6      44 ..      13      50 ..       9      59 .. 0.88
   2 ?   -2.4   0.1       5.6   4.8e+03      26      31 ..     130     136 ..     118     138 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.8e-07
                         HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   ++ L +a+g ++ +eLA + ++S ++v+ ++++Le+ gv
  gi|121639180|ref|YP_979404.1| 13 VREL-AADGRVTLSELATRAGLSVSAVQSRVRRLESRGV 50
                                   4557.99****************************9994 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                         HTH_11  26 nv.Srrt 31 
                                    nv +r+t
  gi|121639180|ref|YP_979404.1| 130 NVrTRST 136
                                    3335555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.6e-06    0.0023      17      53 ..      16      52 ..      12      63 .. 0.92
   2 ?   -2.4   0.0       5.3   4.6e+03      25      31 ..     115     121 ..     104     131 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                   L + g+ t +e+a ++g++ s v++ +r+Le++G+V+
  gi|121639180|ref|YP_979404.1| 16 LAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   6678999*****************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.3
                                    HCHHCCC CS
                           TrmB  25 adeiaee 31 
                                    a+ +   
  gi|121639180|ref|YP_979404.1| 115 ARALEDL 121
                                    3333333 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   6.3e-06    0.0054       2      37 ..      19      54 ..      18      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-06
                       HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiiesr 37
                                   +Gr+t s++a r G+  s +   +r+Les G++   
  gi|121639180|ref|YP_979404.1| 19 DGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQGY 54
                                   79******************************9865 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   9.6e-06    0.0082      43      77 ..      18      52 ..       2      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-06
                                   -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 43 aDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   aDG+ +L ++A r+gl++ +v++ +r+L+  g+++
  gi|121639180|ref|YP_979404.1| 18 ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   9******************************9985 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.2e-05     0.027      23      49 ..      21      47 ..      18      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                         HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                   rvtl+eLA + G+s s+++ ++r+ es
  gi|121639180|ref|YP_979404.1| 21 RVTLSELATRAGLSVSAVQSRVRRLES 47
                                   89**********************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   7.9e-05     0.067      18      43 ..      19      44 ..       3      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4 18 geglTleEIgerlgiSrerVrqiekr 43
                                   +   Tl+E++ r g+S ++V ++ +r
  gi|121639180|ref|YP_979404.1| 19 DGRVTLSELATRAGLSVSAVQSRVRR 44
                                   6678************7766655554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.3e-05     0.054      21      54 ..      21      55 ..       6      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                   ++t  elA + Gl+ + v    ++L+ +g+++  +
  gi|121639180|ref|YP_979404.1| 21 RVTLSELATRAGLSVSAVQSRVRRLESRGVVQgYS 55
                                   68999**************************9433 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-05     0.065       8      37 ..      23      52 ..      21      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                         HTH_41  8 tIeelakeleLSvGlvQkALklLeddkais 37
                                   t +ela   +LSv  vQ+ +  Le+ ++++
  gi|121639180|ref|YP_979404.1| 23 TLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   789*************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   4.2e-05     0.036      11      55 ..       9      52 ..       4      55 .. 0.95
   2 ?   -3.0   0.0       6.8   5.8e+03       6      14 ..     118     126 ..     114     129 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                   HHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           GntR 11 edIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                   ++Il  el++  +  + +eLa++ g s + v+   rrLe++g+v+
  gi|121639180|ref|YP_979404.1|  9 DRILVRELAADGRV-TLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   589999********.****************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                                    HHHHHHHHH CS
                           GntR   6 yerLredIl 14 
                                     e L ++I+
  gi|121639180|ref|YP_979404.1| 118 LEDLLQRIR 126
                                    455666665 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.24      27      57 ..      23      52 ..      10      57 .. 0.90
   2 ?   -0.8   0.0       1.6   1.3e+03      35      52 ..     110     127 ..     109     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                   -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                  LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                   +  e+a + gl+  sav+++ ++Le +G+++
  gi|121639180|ref|YP_979404.1| 23 TLSELATRAGLS-VSAVQSRVRRLESRGVVQ 52
                                   567999999997.9***************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                    HTS-.HHHHHHHHHHHHH CS
                  LexA_DNA_bind  35 lglkSpsaveehLkaLer 52 
                                    ++++S++a e  L++ ++
  gi|121639180|ref|YP_979404.1| 110 VRVASARALEDLLQRIRT 127
                                    577899999999999876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.14       6      49 ..      10      52 ..       5      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                         HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                   +++++ ++  ++r++l++l+ r  ++ s++ + +++L+ +G+v+
  gi|121639180|ref|YP_979404.1| 10 RILVRELA-ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   55666677.89*******************************94 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.2   5.3e+03      32      41 ..      14      23 ..       9      46 .. 0.69
   2 ?   -2.2   0.0       5.7   4.9e+03      28      41 ..      39      52 ..      18      58 .. 0.74
   3 ?   11.6   0.0   0.00028      0.24      40      72 ..      94     126 ..      83     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.2
                          MIase 32 qelqrqGklv 41
                                   +el+++G++ 
  gi|121639180|ref|YP_979404.1| 14 RELAADGRVT 23
                                   6777777653 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                          MIase 28 karaqelqrqGklv 41
                                   + r+++l+++G ++
  gi|121639180|ref|YP_979404.1| 39 QSRVRRLESRGVVQ 52
                                   56677777777765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                          MIase  40 lvrlwrvvgeyanisifdvedndeLhelLssLP 72 
                                    + + + v+ge + + +++v+++ +L++lL+ + 
  gi|121639180|ref|YP_979404.1|  94 VESCYSVAGEESYVLLVRVASARALEDLLQRIR 126
                                    5678999**********************9865 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.37      18      44 ..      19      45 ..      11      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                        HTH_Mga 18 eksltldelakeLglseltlqsdiseL 44
                                   +++ tl+ela++ gls +++qs+++ L
  gi|121639180|ref|YP_979404.1| 19 DGRVTLSELATRAGLSVSAVQSRVRRL 45
                                   57889*****************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1088.79
//
Query:       gi|121639181|ref|YP_979405.1|  [L=415]
Description: hypothetical protein BCG_3321 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.3e-103  345.3   0.0   3.8e-103  345.1   0.0    1.0  1  DUF1338     Domain of unknown function (DUF1338)
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.054   13.7   0.0    1.6  1  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


Domain annotation for each model (and alignments):
>> DUF1338  Domain of unknown function (DUF1338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.1   0.0  4.2e-107  3.8e-103       1     324 []      11     371 ..      11     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 345.1 bits;  conditional E-value: 4.2e-107
                        DUF1338   1 elaralldalsekYlarvpkvralvelvraanaaslssegek..tdelerllvedHgAiRtggvtnegidalarlfaslG 78 
                                    +l++++++ ls++Y a+vp++++lve+++++n++ l+++++    ++l+r+++e+HgAiR+g  ++++++a+a+lfa++G
  gi|121639181|ref|YP_979405.1|  11 QLRARFAAGLSAMYAAEVPAYGTLVEVCAQVNSDYLTRHRRAerLGSLQRVTAERHGAIRVG--NPAELAAVADLFAAFG 88 
                                    689*********************************999877889999**************..**************** PP

                        DUF1338  79 yvpvgeydlp..ekklpahwtaFrpp.eedlaknlpRvFiSeLrve..dlsdaaqraieayvlaareiftkrllellekl 153
                                    + pvg+ydl+  e+ +p+++taFrp+ +++la+n++RvF+S+L +e  +  da++r++ +++la+r++f+++ll+ ++ +
  gi|121639181|ref|YP_979405.1|  89 MLPVGYYDLRtaESPIPVVSTAFRPIdANELAHNPFRVFTSMLAIEdrRYFDADLRTRVQTFLARRQLFDPALLAQARAI 168
                                    **********88899************99****************98889****************************** PP

                        DUF1338 154 eedggltagdaeafvaealetfrwqkeapvakadyelLaaeseyaAwvl.vngyaiNHlTprvldidalqafleergikl 232
                                    ++dgg++a+da afva+a+++f+++ + pv+k++y++L+++s++aA+++ v +++iNHlTprvldid+l+++++ergi++
  gi|121639181|ref|YP_979405.1| 169 AADGGCDADDAPAFVAAAVAAFALS-REPVEKSWYDELSRVSAVAADIAgVGSTHINHLTPRVLDIDDLYRRMTERGITM 247
                                    *************************.5699************************************************** PP

                        DUF1338 233 kdeieGppt.vspdglLrQtSfkAleeevkfaegsgeev.gavparfgEieqRgvlltnkgrnlydellkea........ 302
                                     d+i+Gpp+   pd+lLrQtSf+Al+e++ f++++g+++ g +++rfgE+e+Rgv+lt++gr+ y++ +++a        
  gi|121639181|ref|YP_979405.1| 248 IDTIQGPPRtDGPDVLLRQTSFRALAEPRMFRDEDGTVTpGILRVRFGEVEARGVALTPRGRERYEAAMAAAdpaavwat 327
                                    ************************************9999**************************************** PP

                        DUF1338 303 ...................g...epilyedFlpgnAagIFestl 324
                                                       g    pi+yedFlp++AagIF+s+l
  gi|121639181|ref|YP_979405.1| 328 hfpstdaemaaqglayyrgGdpsAPIVYEDFLPASAAGIFRSNL 371
                                    ************99999972567*******************96 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.1e-06     0.054      73     123 ..     219     283 ..     175     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
                                    TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE..............EEEETTS CS
                     Glyoxalase  73 tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysf..............yfrDpdG 123
                                    +  h+++++  v d+++ ++r+ e+g+   ++++  + +++ ++              +frD+dG
  gi|121639181|ref|YP_979405.1| 219 GSTHINHLTPRVLDIDDLYRRMTERGITMIDTIQGPPRTDGPDVllrqtsfralaeprMFRDEDG 283
                                    347***********************999998887777777776677777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3117.53
//
Query:       gi|121639182|ref|YP_979406.1|  [L=494]
Description: piperideine-6-carboxilic acid dehydrogenase pcd [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.7e-134  446.5   0.3   1.1e-133  446.2   0.3    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.2   0.3  5.9e-138  1.1e-133       9     459 ..      22     474 ..      15     477 .. 0.96

  Alignments for each domain:
  == domain 1  score: 446.2 bits;  conditional E-value: 5.9e-138
                                    EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                         Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                    ++   P+tg+v+ +++  t+e++d+a+aaA+++f aw+++pa+ R+++++++ +ll++++++la+l t e+Gk +aear+
  gi|121639182|ref|YP_979406.1|  22 LPASTPITGDVLFSIAPTTPEQADHAIAAAAATFTAWRSTPAPVRGALVARLGELLTAHQQDLATLVTVEVGKITAEARG 101
                                    77889*************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHH CS
                         Aldedh  89 eveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpl 167
                                    ev+e+idv+++ ++l ++l+g++++s ++g++ l +++PlGvvg+It++NfP++++aw++a al++G tvv+KP+e tpl
  gi|121639182|ref|YP_979406.1| 102 EVQEMIDVCQFSVGLSRQLYGRTIASeRAGHRLLETWHPLGVVGVITAFNFPVAVWAWNTAVALVCGDTVVWKPSELTPL 181
                                    ***********************99977**************************************************** PP

                                    HHHHHHHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEE CS
                         Aldedh 168 salllaelfeea....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpli 243
                                    +al++  l+ +a    g P+ v  ++ g g+e g++lv++p+v+++s tGs+++g+++  + a+++ rv+lElGG+n++i
  gi|121639182|ref|YP_979406.1| 182 TALACQALLSRAaadvGAPAAVGGLLLG-GAERGAQLVDDPRVALLSATGSVRMGQQVGPRVARRFGRVLLELGGNNAAI 260
                                    **99988887777777************.*************************************************** PP

                                    E-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHH CS
                         Aldedh 244 vledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekveky 323
                                    v ++aDl+ av+ iv++a g+aGQ+C++ +rl+v++s++d++v+++v a+++l +gdp ++dt vGPli+ea+++ + + 
  gi|121639182|ref|YP_979406.1| 261 VAPSADLELAVRCIVFAAAGTAGQRCTSLRRLIVHRSVADDVVARVVGAYRQLAIGDPSAPDTLVGPLIHEAAYRDMVAA 340
                                    ******************************************************************************** PP

                                    HHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE- CS
                         Aldedh 324 veeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvft 403
                                    +e+a+ +g +++ G  r+e g    y+v+P v+  ++++ +i+ +E+F+P+l+v++++d++eai++ N+ + GL++++ft
  gi|121639182|ref|YP_979406.1| 341 LERARTDGGEVIGGD-RREVGSPGAYYVAPAVVR-MPSQTAIVATETFAPILYVLTYDDLDEAIALNNAVPQGLSSSIFT 418
                                    **********98877.545665666********9.8******************************************** PP

                                    SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEE CS
                         Aldedh 404 kdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytev 459
                                    +dl++ae++ ++ ++G  ++N  t ga+   +fgG kq+g Gre+g++++++y++ 
  gi|121639182|ref|YP_979406.1| 419 TDLREAEHFLDQSDCGIANVNIGTSGAEIGGAFGGEKQTGGGRESGSDAWKAYMRR 474
                                    ***********************88888889**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3297.82
//
Query:       gi|121639183|ref|YP_979407.1|  [L=269]
Description: hypothetical protein BCG_3323c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-26   91.4   0.0    6.1e-26   91.0   0.0    1.1  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   3.4e-30   6.1e-26       2     121 ..      54     214 ..      45     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 3.4e-30
                                    xxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143   2 rDirklagvrdpeelrk.......................................glverlppwsespnskkrlrkspK 42 
                                    rD +++++ +++++l++                                       +l++r+p+w  s+n++kr++++pK
  gi|121639183|ref|YP_979407.1|  54 RDAADVSNLQRIADLPRlirllaarsaselnlsslatdaeipvrtlppyldlletlYLIDRIPAW--STNLSKRVVDRPK 131
                                    5666666666667777788899*******************************************..************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  43 lyfvDtGLlvallgldkeelleds....enkGallEnlVaqeLlky...sekegaklyyyrdkngaEvDfvielkggkiv 115
                                    ++++D+GL++ l +++++     +    +  Ga++E++V++eL+++   s++  ++l++yrd++gaEvD+++e+++g i+
  gi|121639183|ref|YP_979407.1| 132 VLLLDSGLAARLVNVSPTGAG--PhanpNAAGAIIETFVIAELRRQlgwSQQ-APRLFHYRDRDGAEVDLILETADGLIA 208
                                    ****************99843..234669*******************5555.9************************** PP

                                    xxxxxx RF
                        DUF4143 116 piEvKs 121
                                    +iE+Ks
  gi|121639183|ref|YP_979407.1| 209 AIEIKS 214
                                    *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2151.60
//
Query:       gi|121639184|ref|YP_979408.1|  [L=221]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-15   56.3   0.2    3.8e-15   55.4   0.2    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
     0.0033   17.6   0.0     0.0047   17.1   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
  ------ inclusion threshold ------
      0.065   13.9   0.2       0.46   11.2   0.2    2.4  1  NUDIX-like   NADH pyrophosphatase-like rudimentary NUDIX doma


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2   6.3e-19   3.8e-15       1      47 []      17      63 ..      17      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6.3e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+ ++e+f++r yd++ ++eIA+rAGvs++++Y+yFp+K++ ++a+
  gi|121639184|ref|YP_979408.1| 17 LLALGAEVFGKRPYDEVRIDEIAERAGVSRALMYHYFPDKRAFFAAV 63
                                   68889***************************************997 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.8e-07    0.0047      11      66 ..      11      74 ..       1     103 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.8e-07
                                   HHHHHHHHH.HHHHH......--S-HHHHHHHHTS-HHHHHHHH.H-HHHHH.HHHHHHHHHHHT CS
                    HTH_Tnp_1_2 11 kQkkaaell.vendy......ekltldeiaeevgvsrsTlykWk.kkkeFie.yvnelaeeflee 66
                                   + ++ aell    +       +++ +deiae  gvsr+ +y++  +k++F +  v+  a+++ ++
  gi|121639184|ref|YP_979408.1| 11 QDRR-AELLaLGAEVfgkrpyDEVRIDEIAERAGVSRALMYHYFpDKRAFFAaVVKDEADRLYAA 74
                                   4444.4444233333344444*********************99899998761456666666554 PP

>> NUDIX-like  NADH pyrophosphatase-like rudimentary NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   7.8e-05      0.46      33      97 ..     102     220 ..       2     221 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-05
                     NUDIX-like  33 l.........vgkdseelvfLGldeggapvfAvdvsareee....................................... 64 
                                    +         vg ++  +v+LG d+++++ +   + +r +e                                       
  gi|121639184|ref|YP_979408.1| 102 QnpeaawaayVGLGRSDPVLLGIDDEAKNRQMEHIMSRIAEvvsgidrdntldpeverdlrviihgwlaftfelcrqrim 181
                                    15555666667888899999998888777777777777777777777778888888888888888888888888888899 PP

                     NUDIX-like  65 ......ikeaeeeggafvelRavmlalsaedaalaaqAr 97 
                                          +++a+++++a  ++ +++ +++ae a ++a+Ar
  gi|121639184|ref|YP_979408.1| 182 dpstdaERLADACAHALLDAISRLPQIPAELADAMATAR 220
                                    99999899******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1789.09
//
Query:       gi|121639185|ref|YP_979409.1|  [L=1513]
Description: ATP-dependent helicase lhr [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-70  236.2   0.8    8.1e-70  234.5   0.1    2.1  2  DEAD_assoc    DEAD/H associated
    3.9e-26   91.9   0.0    7.7e-26   90.9   0.0    1.5  1  DEAD          DEAD/DEAH box helicase
    1.9e-14   53.9   0.0    3.3e-12   46.7   0.0    3.0  3  Helicase_C    Helicase conserved C-terminal domain
    2.8e-05   24.2   0.0    6.3e-05   23.0   0.0    1.6  2  ResIII        Type III restriction enzyme, res subunit
     0.0005   20.4   0.1     0.0064   16.8   0.1    2.5  1  AAA_22        AAA domain
    0.00099   18.7   0.4     0.0048   16.5   0.3    2.3  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.017   14.6   0.0       0.03   13.8   0.0    1.3  1  PhoH          PhoH-like protein
       0.14   12.1   0.1       0.35   10.8   0.1    1.6  1  Phage_base_V  Type VI secretion system, phage-baseplate injec


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   0.1   3.6e-73   8.1e-70       1     191 []     659     851 ..     659     851 .. 0.94
   2 ?   -1.2   0.0      0.65   1.5e+03      27      63 ..     998    1034 ..     976    1057 .. 0.83

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 3.6e-73
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlp......... 71 
                                    +Ptd+tllvErfrdelgdwr+++hsp+G rv+ +lal++ +rl++r+gid + +a+D+gi++ l      p         
  gi|121639185|ref|YP_979409.1| 659 VPTDSTLLVERFRDELGDWRVILHSPYGLRVHGPLALAVGRRLRDRYGIDEKPTASDNGIMVRL------Pdtvsageds 732
                                    8*************************************************************66......3333344554 PP

                     DEAD_assoc  72 ....llldellellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpl 147
                                        +     l  +++de++ +++ ++++s+lf++rFre Aaralllprr+pg+r plwqqr+raa+Ll+var+ypdfp+
  gi|121639185|ref|YP_979409.1| 733 ppgaE-----LFVFDADEIDPIVTTEVAGSALFASRFRESAARALLLPRRHPGRRSPLWQQRQRAARLLEVARKYPDFPI 807
                                    44432.....56799***************************************************************** PP

                     DEAD_assoc 148 lleavrevledqlDlerlaellrriaageirvvevetprpSpfA 191
                                    +le+vre+l++++D++ l el++ria++++rv+e et++pSpfA
  gi|121639185|ref|YP_979409.1| 808 VLETVRECLQNVYDVPILVELMARIAQRRVRVAEAETAKPSPFA 851
                                    *******************************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.65
                     DEAD_assoc   27 fGrrvnealalllaarlsrrfgidvqvaanDdgivll 63  
                                     f   v ++l+ ll +  + +++++ ++aa+  g+ l 
  gi|121639185|ref|YP_979409.1|  998 FTEAVADPLGELLGRYARTHTPFTTAAAAARFGLGLR 1034
                                     6678999*******************99998888774 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   3.5e-29   7.7e-26       1     170 [.      28     212 ..      28     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3.5e-29
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                    t+ Qa+a+ +i +g++ lv a+TGsGKTla+++ +l++++ +    ++  ++++l+v+P+++La ++ +nl++ +  ++ 
  gi|121639185|ref|YP_979409.1|  28 TAAQASAWAAIADGDNTLVIAPTGSGKTLAAFLWALDSLAGSepmsERPAATRVLYVSPLKALAVDVERNLRTPLAGLTr 107
                                    689************************************8879999999999************************7555 PP

                                    ...........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ...........lrvlliiggvaardqlskldngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfin 143
                                               +rv +  g+++    ++ +++ +d++++tp+ l+ +l s  + +l  v+++++DE++ +   +++ ++ 
  gi|121639185|ref|YP_979409.1| 108 laerqglpapqIRVGVRSGDTPPALRRQLVSQPPDVLITTPESLFLMLtSAARQTLTGVQTVIIDEIHAIAATKRGAHLA 187
                                    667777777666666555555554444445455*************886666677************************* PP

                                    HHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 144 rilnqlpqitcdgklqrqvivlSATlp 170
                                      l++l++ +++ ++q   i lSAT+ 
  gi|121639185|ref|YP_979409.1| 188 LSLERLDDLSSRRRAQ--RIGLSATVR 212
                                    ******9999888855..*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.79   1.8e+03      37      90 ..     110     171 ..      81     180 .. 0.77
   2 ?    2.9   0.0     0.061   1.4e+02       6      54 ..     265     308 ..     260     319 .. 0.73
   3 !   46.7   0.0   1.5e-15   3.3e-12      44     108 ..     335     399 ..     325     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.79
                                    HHT.....TSTEEEESTTSTHHHHHHHHHHHH.....TTSSSEEEESGGGTSSSTSTTESEEEE CS
                     Helicase_C  37 ekk.....gikvavlhgelpqnereeileqfn.....kgesdvLiatdvaerGidipkvnlVin 90 
                                    e++     +i+v v  g++p   r++ ++q         es +L+ t++a +   +++v++Vi+
  gi|121639185|ref|YP_979409.1| 110 ERQglpapQIRVGVRSGDTPPALRRQLVSQPPdvlitTPESLFLMLTSAARQT--LTGVQTVII 171
                                    44446666899999999********9999998666655566688888888874..456777776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.061
                                    HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHH CS
                     Helicase_C   6 llellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqne 54 
                                    l++l+   e+++ +++f+n+++ +e  +l  + ++i++a++  el  + 
  gi|121639185|ref|YP_979409.1| 265 LVDLI---ESHNSTIVFANSRRLAE--RLTARLNEIHAARCGIELAPDT 308
                                    45555...8999**********997..5555556787777766666555 PP

  == domain 3  score: 46.7 bits;  conditional E-value: 1.5e-15
                                    EEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  44 avlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                     ++hg++++++r  + e+ ++g+ + ++at+ +e Gid+  v+lVi++++p +v+s  qriGR+g
  gi|121639185|ref|YP_979409.1| 335 RAHHGSISKEQRAVVEEDLKRGQLKAVVATSSLELGIDMGAVDLVIQVQAPPSVASGLQRIGRAG 399
                                    578*************************************************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.8e-08   6.3e-05      22     169 ..      39     211 ..       1     213 [. 0.71
   2 ?   -3.9   0.0       5.4   1.2e+04      55      74 ..     273     292 ..     267     309 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.8e-08
                                    .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHG.......GGGTGG....... CS
                         ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleef.......kkflseayke... 84 
                                     +  + l+ ++TG+GKTl a + + ++l+ +++ +      ++l + p k+l    ++++       +            
  gi|121639185|ref|YP_979409.1|  39 ADGDNTLVIAPTGSGKTLAAfLWALDSLAGSEPMSerpaatRVLYVSPLKALAVDVERNLrtplaglT-------RLaer 111
                                    566789999********98844455566666555599********************99955555442.......22233 PP

                                    ........GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...... CS
                         ResIII  85 ........igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...... 148
                                              ++ sgd+  a  ++  s+  ++l+tt +sl   +        ++  +  + +iiDE H ++a k      
  gi|121639185|ref|YP_979409.1| 112 qglpapqiRVGVRSGDTPPAlrRQLVSQPPDVLITTPESLFLML----TSAARQTLTGVQTVIIDEIHAIAATKrgahla 187
                                    334444445556777777778777789999**************....5555566666778999********86666666 PP

                                    .TTHHH..HHT---SEEEEEESS- CS
                         ResIII 149 .swrei..lekfkeavllglTATp 169
                                     s +++  l + ++a ++gl+AT 
  gi|121639185|ref|YP_979409.1| 188 lSLERLddLSSRRRAQRIGLSATV 211
                                    67777733333355*********7 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.4
                                    .-EEEEESSHHHHHHHHHHG CS
                         ResIII  55 ekflflvprkslleqtleef 74 
                                    + ++++++++ l e++  ++
  gi|121639185|ref|YP_979409.1| 273 NSTIVFANSRRLAERLTARL 292
                                    25666677777766666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.9e-06    0.0064       8     114 ..      44     198 ..      39     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..........................................erpevvfv 45 
                                    ++v++++G+GKT+ +   +    + ++                                              ++++++v
  gi|121639185|ref|YP_979409.1|  44 TLVIAPTGSGKTLAAFLWALDSLAGSE--PmserpaatrvlyvsplkalavdvernlrtplagltrlaerqgLPAPQIRV 121
                                    789999999999887655554443333..2447899999999999999999999999999999999999999999999** PP

                         AAA_22  46 tlpsstsskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhlr...s.......eealeeLrs 114
                                     + s+ ++  l+r+l+++  + l +   + e l+ +l+ a+r++ + ++ +iiDE++ +    +        e l +L+s
  gi|121639185|ref|YP_979409.1| 122 GVRSGDTPPALRRQLVSQPPDVLIT---TPESLFLMLTSAARQTLTgVQTVIIDEIHAIAatkRgahlalsLERLDDLSS 198
                                    *************************...****************999***********9876524445222333333333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.1e-06    0.0048      18      98 ..      27     116 ..      10     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                         AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlravgea 96 
                                    p + +   +  + + g+ +l+++++g+GKt +a  +al+ + G++   + +p   +Vlyvs   + + +++r lr  ++ 
  gi|121639185|ref|YP_979409.1|  27 PTAAQASAWAAI-ADGDNTLVIAPTGSGKTLAAFLWALDSLAGSEPMSE-RPAATRVLYVSPLKAlAVDVERNLRTPLAG 104
                                    555555555555.67999*********************9988754444.58999*****97766556777777776666 PP

                         AAA_25  97 l..........r 98 
                                    l          +
  gi|121639185|ref|YP_979409.1| 105 LtrlaerqglpA 116
                                    644444444440 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05      0.03       6      45 ..      28      67 ..      24      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHH CS
                           PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealk 45
                                   t++Q+++  a+ + d + +i+p+G+GKt+ a   a++ l 
  gi|121639185|ref|YP_979409.1| 28 TAAQASAWAAIADGDNTLVIAPTGSGKTLAAFLWALDSLA 67
                                   889********************************99876 PP

>> Phage_base_V  Type VI secretion system, phage-baseplate injector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00016      0.35      35      92 ..      17      77 ..      10      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                   XXXE..EEXXSXBSSSBXXXXXXTTXEEEEEEXXT.TTXXEEEEEEEXXSSSXXSXXBTS- CS
                   Phage_base_V 35 tdwl..rwlaarAGktrswrapsvGEqvvllspsG.elatavvlpglysdafpapsnsada 92
                                    dw    ++a  A ++  w a+  G++ ++++p G   + a +l +l s a ++p ++  a
  gi|121639185|ref|YP_979409.1| 17 RDWFtsTFAAPTAAQASAWAAIADGDNTLVIAPTGsGKTLAAFLWALDSLAGSEPMSERPA 77
                                   5565224778899**********************4456699*********9999765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.86u 0.28s 00:00:01.14 Elapsed: 00:00:00.45
# Mc/sec: 10006.43
//
Query:       gi|121639186|ref|YP_979410.1|  [L=255]
Description: endonuclease VIII nei [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.5   0.1    3.4e-11   43.8   0.1    1.5  1  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina
    1.3e-10   41.1   0.0      2e-10   40.5   0.0    1.3  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
    0.00059   19.7   3.4     0.0016   18.3   3.4    1.8  1  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.014   15.3   4.8      0.032   14.1   4.8    1.7  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   7.7e-15   3.4e-11       1     102 [.       1      94 [.       1     125 [. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 7.7e-15
                                    X--HHHHHHHHHHHHHHHTT-EEEEEEE-SSHHHTSTHHHHHT.T-.SEEEEEEEEETTEEEEEE..EEEEEEE-TTTEE CS
                 Fapy_DNA_glyco   1 MPElpEVetvrrglrrhllgkkiakvevlkdktlrgspaafak.alkgrkiasvgrrGKyllleldggevlvvhlgmtGr 79 
                                    MPE   V +++++lrrhl g++++++++      r   + fa+  l+g+++++v +rGK+l++++ g+ ++  hl+m G+
  gi|121639186|ref|YP_979410.1|   1 MPEGDTVWHTAATLRRHLAGRTLTRCDI------R--VPRFAAvDLTGEVVDEVISRGKHLFIRT-GTASIHSHLQMDGS 71 
                                    9***************************......2..34455549********************.99************ PP

                                    ESS........TTEEEEEEEGGG CS
                 Fapy_DNA_glyco  80 llikeaeeeppkhtkvrlelddg 102
                                    +++ + +    + +++ le +++
  gi|121639186|ref|YP_979410.1|  72 WRVGNRPVRVDHRARIILEANQQ 94 
                                    ***44444444566677776533 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   4.5e-14     2e-10       1      63 [.     123     186 ..     123     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.5e-14
                                    ---BTTSTTS-HHHHHHHH.HT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS- CS
                           H2TH   1 Lgpeplseaftvdalaerl.kkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlaksls 63 
                                    Lgp+ l+++ + + +a++l     r+i ++LLDq++ aG+GN+y +E+ f +++ P+ + + + 
  gi|121639186|ref|YP_979410.1| 123 LGPDLLADDWDPQRAAANLiVAPDRPIAEALLDQRVLAGIGNVYCNELCFVSGVLPTAPVSAVA 186
                                    899999999999887777615669********************************99877765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.4   3.6e-07    0.0016       3      29 ..     230     254 ..     230     255 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-07
                                    -TTT--B-EEE--TT-SS-EEEETTTT CS
                      Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                    C+ CGt +++ +   D+r R++CpaC+
  gi|121639186|ref|YP_979410.1| 230 CRRCGTLIAYDT--TDERVRYWCPACQ 254
                                    **********99..7***********7 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.8   7.1e-06     0.032       4      28 ..     230     254 ..     227     255 .] 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                                    -TTT--BBEEEECTTEEEEE-TTTT CS
                   zf-FPG_IleRS   4 CpRCwryiervgqagrstyfCprCq 28 
                                    C+RC++ i+    ++r  y+Cp Cq
  gi|121639186|ref|YP_979410.1| 230 CRRCGTLIAYDTTDERVRYWCPACQ 254
                                    ************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1689.80
//
Query:       gi|121639187|ref|YP_979411.1|  [L=304]
Description: esterase lipoprotein lpqC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-10   41.5   1.0    1.5e-10   41.0   1.0    1.3  1  Esterase_phd  Esterase PHB depolymerase
    9.6e-06   25.2   1.1    2.7e-05   23.8   0.2    2.1  3  Peptidase_S9  Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.0   1.7e-14   1.5e-10       2     137 ..      43     174 ..      42     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.7e-14
                   Esterase_phd   2 ayrlylppGarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavv 81 
                                    +yrl++pp  +     lv+ lhG   +     a t ++++ad   + v+yp+   ++ a++        dr+   +   +
  gi|121639187|ref|YP_979411.1|  43 SYRLHVPPAEPS---GLVISLHGGGGTGAGQEALTDFDAVADAADLLVVYPDGYDKSWADGRG--ASPADRRHLDDVGFL 117
                                    6**********9...89*******999999999*********************999999865..468899999****** PP

                   Esterase_phd  82 valvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhsG.lalGeaa 137
                                    val+  lv++  + +  v+ +G+s G+ +++ la    d faava  +G l +G + 
  gi|121639187|ref|YP_979411.1| 118 VALAAKLVHDFDIAPGHVFATGMSNGGFMSNRLACDRADIFAAVAPVAGtLGVGVTC 174
                                    ********************************************9666524566555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.3   2.7e+03      17      31 ..      57      71 ..      52      82 .. 0.76
   2 !   23.8   0.2     3e-09   2.7e-05      48      99 ..     117     168 ..      91     175 .. 0.88
   3 ?   -1.3   0.0      0.14   1.3e+03     144     162 ..     180     198 ..     172     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.3
                                   EEEE--TTSSTTHCH CS
                   Peptidase_S9 17 vvvanirGsggyGea 31
                                   v+  ++ G++g G++
  gi|121639187|ref|YP_979411.1| 57 VISLHGGGGTGAGQE 71
                                   677788888888886 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3e-09
                                    HHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE-- CS
                   Peptidase_S9  48 fiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvv 99 
                                    ++a a +l+  + + + ++++tG S+GG++++ ++ +r d+F+a++ +++ +
  gi|121639187|ref|YP_979411.1| 117 LVALAAKLVHDFDIAPGHVFATGMSNGGFMSNRLACDRADIFAAVAPVAGTL 168
                                    588999999999*********************************9999875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.14
                                    -EEEEEEETT-SSS-THHH CS
                   Peptidase_S9 144 pplLlihGlaDdrvppaea 162
                                    +++L  hG+aD  vp++ +
  gi|121639187|ref|YP_979411.1| 180 VSVLEAHGTADPLVPFNGG 198
                                    678889*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2244.65
//
Query:       gi|121639188|ref|YP_979412.1|  [L=970]
Description: arylsulfatase atsB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-101  340.2   0.0   1.5e-101  339.8   0.0    1.1  1  Sulfatase        Sulfatase
    1.5e-09   38.1   6.1    2.9e-09   37.1   6.1    1.5  1  DUF1269          Protein of unknown function (DUF1269)
     0.0039   16.8   0.2       0.35   10.4   0.0    2.4  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.093   12.7   0.0    2.0  2  DUF4994          Domain of unknown function
      0.034   13.9  12.2        1.2    8.9   3.0    2.9  2  Gly-zipper_OmpA  Glycine-zipper domain
      0.073   13.4   0.1       0.33   11.3   0.0    2.1  2  Aft1_HRA         Aft1 HRA domain
      0.083   12.6  16.2       0.34   10.7  16.2    2.1  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
       0.11   12.7   8.1       0.23   11.8   8.1    1.4  1  DUF456           Protein of unknown function (DUF456)
       0.14   12.5   7.1        0.3   11.4   7.1    1.6  1  Acyl-CoA_dh_2    Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   0.0  7.8e-105  1.5e-101       1     308 [.     212     634 ..     212     635 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 7.8e-105
                                    EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT..... CS
                      Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg..... 75 
                                    pnv+++l+dd+g+g+ +++gg ++ tp+l+rla++gl++++f+++a +csp+raalltgr++h++g++s++e++g     
  gi|121639188|ref|YP_979412.1| 212 PNVLIVLIDDAGFGGPDTFGGAIR-TPTLSRLAQNGLIYNRFHVTA-VCSPTRAALLTGRNHHRVGFGSVCEFPGpypgy 289
                                    9**********************9.9*******************8.********************************* PP

                                    .HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.......CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC. CS
                      Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.......nrgfdrflgfptgsaalkdpekseyngevlrv. 146
                                       +p+++a+Lp++l+++GY t+a+gkwhl++++ q+++        ++gfd+f+gfp+g+a ++dp  s++n  ++ + 
  gi|121639188|ref|YP_979412.1| 290 sAVRPRSCAALPRILRDNGYVTGAFGKWHLTPDNVQGAAGpfdnwplGWGFDHFWGFPSGAAGQYDPIISQDNSVIGIPe 369
                                    *************************************9889********************************999998* PP

                                    ....TTTTCSHHHHHHHHHHHHH...HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.......... CS
                      Sulfatase 147 ....ppeggysddrlldealefl...larn.dkpfflylatlapHappeapdeyakkyatffddgseaar.......... 208
                                        + +++y+ d+l+d+a+e+l   +a+n +kp++ly+at a+Hap+++++e+a+ky+++fddg++ +r          
  gi|121639188|ref|YP_979412.1| 370 gsgeDGRPYYFPDDLTDKAIEWLhtvRAQNaTKPWMLYYATGATHAPHHVFKEWADKYRGEFDDGWDVYRqktferqkrl 449
                                    **************************66666*************************************9999******** PP

                                    ...............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEE.ESSSSCCCG. CS
                      Sulfatase 209 ...............................qlleaylnsveyvDdligrvlaaLeenglldntlvvft.SDhgaslee. 255
                                                                   +++e+++++ e++D+++gr+l+a+e++g++dntlv+++ +D+gas+e+ 
  gi|121639188|ref|YP_979412.1| 450 giippdaelterpdlfpawdsmseaqkrlfaRQMEVFAGFSENADWNVGRLLDAIEDLGESDNTLVFYIwGDNGASMEGt 529
                                    ******************************************************************************** PP

                                    ..................................................HHTTSSSCTTCSSSHHHHBEEEEEEETTTS CS
                      Sulfatase 256 ..................................................sngplrggkganayeggtrvPllvwwpgek 285
                                                                                      sn+pl++gk+++++ ggtr+Pl+v+wp ++
  gi|121639188|ref|YP_979412.1| 530 ntgsfnemtflngldldaerqlelieqyggiaalgdeftaphfasawahaSNTPLQWGKQMASHLGGTRDPLVVAWPARI 609
                                    ******************************************************************************** PP

                                    HC..EEECSEEEGGGHHHHHHHHTT CS
                      Sulfatase 286 ap..rvseelvshiDlfptildlag 308
                                    +p  rv+++++++iD++pt+l+++g
  gi|121639188|ref|YP_979412.1| 610 RPdgRVRSQFTHCIDIAPTVLAAIG 634
                                    **********************998 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   6.1   1.4e-12   2.9e-09       1      79 [.      66     144 ..      66     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.4e-12
                        DUF1269   1 AlsGalwGllvGllflnP..llGaavGAaaGAlvgalsdvgidddflkelgeklkpgtsalfllvekatvdkvlealakl 78 
                                    A++Ga +Gl +Gl  ++P  l++aa+GAa+GAl+g+++++ i+ ++ +++g++l +g++ +++++e +   +  +ala+ 
  gi|121639188|ref|YP_979412.1|  66 AAWGAGVGLAIGL--FSPalLASAALGAATGALAGTFAHHRIKTGLADKIGQALAAGRAVVIAVTEAQGRLEAGQALASS 143
                                    89**********7..68865667*******************************************99988888888665 PP

                        DUF1269  79 g 79 
                                     
  gi|121639188|ref|YP_979412.1| 144 P 144
                                    5 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        31      19      58 ..     233     271 ..     214     278 .. 0.79
   2 !   10.4   0.0   0.00018      0.35     128     234 ..     414     524 ..     342     554 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                                    S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-H CS
                   Phosphodiest  19 e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyP 58 
                                      ++p l++La++g+ +   r ++ ++  p  a+l+TG++ 
  gi|121639188|ref|YP_979412.1| 233 AiRTPTLSRLAQNGLIYN--RFHVTAVCSPTRAALLTGRNH 271
                                    458***************..999***************985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                    TBHHSBTCT.CSTTS..CHHHHHHHHHHHHHHHCHTHSHHHHHCT...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHH CS
                   Phosphodiest 128 etppryleddfnakv..pledkvdkavlqtwldaafakvvlekel...ekpdlllvyleetDtvgHkfGpdspevedalr 202
                                    + p  ++ +++++k+  +++d  d   +q+ ++++++   ++      e+pdl+  + +   ++   f  + + ++   +
  gi|121639188|ref|YP_979412.1| 414 HAPHHVF-KEWADKYrgEFDDGWDV-YRQKTFERQKRLGIIPPDAeltERPDLFPAWDSMSEAQKRLFARQMEVFAGFSE 491
                                    2222222.44555555555555553.4445577777666666555889*************9999999545555888889 PP

                                    HHHHHHHHHHHHHHHTTGTTTEEEE.EEES--- CS
                   Phosphodiest 203 rvDkaigdLlealderglsaetnii.lvSDHGm 234
                                    ++D ++g+Ll+a+++ g s++t ++ + +D G+
  gi|121639188|ref|YP_979412.1| 492 NADWNVGRLLDAIEDLGESDNTLVFyIWGDNGA 524
                                    9***************88888876526666665 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   2.8e+03      15      35 ..      42      60 ..      31      68 .. 0.81
   2 ?   12.7   0.0   4.7e-05     0.093      69      97 ..     719     747 ..     700     748 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                        DUF4994 15 allGkdkkdReyvieqaankt 35
                                    l+Gkd+++ +++++ +  + 
  gi|121639188|ref|YP_979412.1| 42 VLIGKDAEGSPVLVDTG--NR 60
                                   689***********988..44 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.7e-05
                        DUF4994  69 qLydlkkdegekenvaekhpekvkelkel 97 
                                     Ly l +d ++ +n+a++hp+kv el++l
  gi|121639188|ref|YP_979412.1| 719 ELYYLPDDFSQAKNLAAEHPDKVAELTQL 747
                                    69************************986 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.9   0.00064       1.3      27      42 ..      64      79 ..      57      81 .. 0.88
   2 ?    8.9   3.0   0.00063       1.2       3      15 ..      86      98 ..      84     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00064
                Gly-zipper_OmpA 27 tGAaiGAasGavaGll 42
                                   +GAa GA++G+ +Gl+
  gi|121639188|ref|YP_979412.1| 64 RGAAWGAGVGLAIGLF 79
                                   6*************87 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00063
                Gly-zipper_OmpA  3 gAavGAalGAaaG 15
                                   +Aa GAa+GA+aG
  gi|121639188|ref|YP_979412.1| 86 SAALGAATGALAG 98
                                   6777777777777 PP

>> Aft1_HRA  Aft1 HRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.33       6      52 ..      67     114 ..      63     122 .. 0.83
   2 ?   -2.3   0.0         3     6e+03      61      76 ..     268     291 ..     252     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                       Aft1_HRA   6 pWlatqslrsgPLSPAmLagPqqasq.spteesfesesfrtGfTPgts 52 
                                    +W+a  +l  g  SPA+La+ + +++ ++ + +f ++ ++tG+  + +
  gi|121639188|ref|YP_979412.1|  67 AWGAGVGLAIGLFSPALLASAALGAAtGALAGTFAHHRIKTGLADKIG 114
                                    7*****************998866551556999*********987766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                       Aft1_HRA  61 g........gggssfPapSpntaa 76 
                                    g        g+  +fP p p+ +a
  gi|121639188|ref|YP_979412.1| 268 GrnhhrvgfGSVCEFPGPYPGYSA 291
                                    234445555778899999998766 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  16.2   0.00017      0.34       9      44 ..      64     102 ..      60     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                    XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                Gly-zipper_YMGG   9 iGAaaGAvvGaliG...sgggkGAaiGAaaGalaGgaiG 44 
                                     GAa GA+vG +iG    +    Aa GAa+GalaG+ ++
  gi|121639188|ref|YP_979412.1|  64 RGAAWGAGVGLAIGlfsPALLASAALGAATGALAGTFAH 102
                                    477888888888887432334589***********8765 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.1   0.00011      0.23      60     117 ..      63     127 ..      57     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                         DUF456  60 skrgligaivGaivGffllpp......lGlllgpflgaflgEllrar..kdlreAlkaalgalvGf 117
                                     + +++ga+vG+ +G+f  p       lG+  g+++g+f+  ++ ++  +++ +Al+a++++++++
  gi|121639188|ref|YP_979412.1|  63 RRGAAWGAGVGLAIGLFS-PAllasaaLGAATGALAGTFAHHRIKTGlaDKIGQALAAGRAVVIAV 127
                                    57789**********973.31233455888888888888888888775455999999999999876 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.1   0.00015       0.3       3      66 ..      84     149 ..      82     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHHHC..TTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervr..assgekladdpatqlalaeaaarldAAralleraaarae 66 
                                    +a +alGaA +ala + ++ r +++  ++ g++la   a+ +a++ea+ rl+A +al  + ++++ 
  gi|121639188|ref|YP_979412.1|  84 LASAALGAATGALAGTFAHHRIKTGlaDKIGQALAAGRAVVIAVTEAQGRLEAGQALASSPMKSVA 149
                                    799******************999999999**************************9887777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (970 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 6062.47
//
Query:       gi|121639189|ref|YP_979413.1|  [L=305]
Description: hypothetical protein BCG_3329c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-21   75.5   0.0    6.5e-21   75.1   0.0    1.1  1  PseudoU_synth_2  RNA pseudouridylate synthase
  ------ inclusion threshold ------
      0.071   13.0   0.1       0.13   12.2   0.1    1.3  1  DUF3659          Protein of unknown function (DUF3659)


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   7.2e-25   6.5e-21       1     160 []      93     237 ..      93     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 7.2e-25
                PseudoU_synth_2   1 dlvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkY 80 
                                    d+vvv+KP+ +++ p +      +++t     r+e    el++ hRLD+ t G+ll+++ +e     + +f++  vrK+Y
  gi|121639189|ref|YP_979413.1|  93 DIVVVDKPHFLATMPRG----RHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQTMFARGLVRKTY 168
                                    589**************....88999999999999************************************9999***** PP

                PseudoU_synth_2  81 lalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhlaa 160
                                    la  + ap     a+   +  +++k+ g  + + e +  +a+t ++ ++++         l++l++ tGr+hQ+Rvh+aa
  gi|121639189|ref|YP_979413.1| 169 LARAPVAP---GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVERIARD--------GLYRLTPTTGRTHQLRVHMAA 237
                                    ***86444...444444455556679999**********************........9******************96 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.5e-05      0.13      20      52 ..      27      63 ..      24      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                        DUF3659 20 nvvGrvve..G...dlkkLaGkkvdedGnivdedGnvi 52
                                    v+++++   G    +k LaG  vd+dG +vd+ G+v+
  gi|121639189|ref|YP_979413.1| 27 SVLAELTArfGvaaRAKVLAGEVVDDDGAVVDS-GTVL 63
                                   566666665644447899*************97.7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2019.40
//
Query:       gi|121639190|ref|YP_979414.1|  [L=221]
Description: phosphate-transport system transcriptional regulatory protein phoU 1 phoY1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-24   85.1   4.0    4.1e-14   52.8   1.0    2.1  2  PhoU           PhoU domain
  ------ inclusion threshold ------
      0.041   14.0   0.2      0.073   13.2   0.2    1.5  1  DUF4677        Domain of unknown function (DUF4677)
       0.12   12.0   0.0       0.22   11.2   0.0    1.4  1  Peptidase_S77  Prohead core protein serine protease
       0.13   12.1   0.0       0.42   10.4   0.0    1.9  2  KNTase_C       KNTase C-terminal domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   1.0   9.1e-18   4.1e-14       2      89 .]      17     104 ..      16     104 .. 0.97
   2 !   33.5   0.1   9.8e-12   4.4e-08       3      89 .]     123     204 ..     121     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 9.1e-18
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                     +m +++  ++++a +al e d  +a++vi++ ++i +++ ++e++++ +la + p++ +lre++s+++i+ d ER+g  
  gi|121639190|ref|YP_979414.1|  17 GEMCSLAGIAMKRATQALLEADIGAAEQVIRDHERIVAMRAQVEKEAFALLALQHPVSGELREIFSAVQIIADTERMGAL 96 
                                    58999*****************************************99999***************************** PP

                                    HHHHHHHH CS
                           PhoU  82 avniaerv 89 
                                    av+ia+++
  gi|121639190|ref|YP_979414.1|  97 AVHIAKIT 104
                                    *****986 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.8e-12
                                    HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                    +ma+++    d a ++l+++d   a ++ +rdd +d+l++ +   l+     + +++  +r  ++   + r  ER +Dha
  gi|121639190|ref|YP_979414.1| 123 DMAKVAIALGDSARQVLVNRDPQEAAQLHDRDDAMDDLHRHLLSVLI-----DREWRHGVRVGVETALLGRFFERFADHA 197
                                    79999999999****************************99966544.....3444445888899999************ PP

                                    HHHHHHH CS
                           PhoU  83 vniaerv 89 
                                    v++ +rv
  gi|121639190|ref|YP_979414.1| 198 VEVGRRV 204
                                    ***9985 PP

>> DUF4677  Domain of unknown function (DUF4677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.6e-05     0.073      55     109 ..      49     103 ..      29     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                        DUF4677  55 fedvramrgaldeqashiqvlsddvcanqraivsmcqimttaprqgllavvgnkg 109
                                     e + amr  ++++a  +  l   v  + r i s +qi++ + r g+lav  +k 
  gi|121639190|ref|YP_979414.1|  49 HERIVAMRAQVEKEAFALLALQHPVSGELREIFSAVQIIADTERMGALAVHIAKI 103
                                    67889********************************************987665 PP

>> Peptidase_S77  Prohead core protein serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.9e-05      0.22      46      93 ..     102     149 ..      93     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                                    -TTSEE--HHHHHHHHHHHHHHTTTTT--EEEBS--SSSS--GGGEEE CS
                  Peptidase_S77  46 nrnkrlypkkvlekavkdyineqvktkqalgelnhpsranvdpaeaai 93 
                                    +  +r yp++vl + v++   +  k   alg+       n dp eaa 
  gi|121639190|ref|YP_979414.1| 102 KITRREYPNQVLPEEVRNCFADMAKVAIALGDSARQVLVNRDPQEAAQ 149
                                    556899***************************************995 PP

>> KNTase_C  KNTase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.094   4.2e+02      15      59 ..      60     102 ..      49     106 .. 0.71
   2 ?   10.4   0.0   9.4e-05      0.42      28     102 ..      93     166 ..      74     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.094
                       KNTase_C  15 eeeefv.kaieealvgelyEfigKlrnvrkegdetalatlalqlAq 59 
                                    e+e f   a++  + gel E++  ++ +    d++ +  la+++A+
  gi|121639190|ref|YP_979414.1|  60 EKEAFAlLALQHPVSGELREIFSAVQII---ADTERMGALAVHIAK 102
                                    4555541467777788999999887777...777888888888886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.4e-05
                       KNTase_C  28 vgelyEfigKlrnvrkegdetalatlalq.lAqyaallvgLsnrklysssatvlkEaleLpdrpkgfdelvekvme 102
                                    +g l  +i+K+   r+e ++++l+ ++++ +A  a + ++L + ++ +   + ++Ea +L dr +++d+l +++++
  gi|121639190|ref|YP_979414.1|  93 MGALAVHIAKIT--RREYPNQVLPEEVRNcFADMAKVAIALGDSARQVLVNRDPQEAAQLHDRDDAMDDLHRHLLS 166
                                    666777888886..66999******99985899999********************************99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1592.80
//
Query:       gi|121639191|ref|YP_979415.1|  [L=585]
Description: glycerol-3-phosphate dehydrogenase glpD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-48  164.2   5.3    8.8e-48  163.7   5.3    1.2  1  DAO            FAD dependent oxidoreductase
    5.5e-28   97.4   0.0    1.2e-27   96.3   0.0    1.6  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
    6.1e-10   38.7   7.1      1e-05   24.9   1.2    2.2  2  FAD_binding_2  FAD binding domain
      2e-09   37.4   1.4    9.9e-07   28.4   0.3    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    7.4e-08   32.0   2.1    4.4e-07   29.5   2.1    2.1  1  FAD_binding_3  FAD binding domain
    5.5e-05   22.5   0.7     0.0001   21.7   0.0    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00066   18.9   0.5    0.00066   18.9   0.5    1.7  2  GIDA           Glucose inhibited division protein A
    0.00098   19.3   1.0     0.0038   17.4   1.0    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0019   18.1   0.1     0.0037   17.2   0.1    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0044   17.6   2.7     0.0073   16.8   0.6    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0066   15.2   0.9       0.01   14.5   0.9    1.2  1  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.035   13.4   0.1    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.021   14.1   0.4      0.021   14.1   0.4    1.8  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   5.3   6.4e-51   8.8e-48       1     317 [.      37     366 ..      37     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 6.4e-51
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    dvv+iGGG++G+++A+++a+rg  V+l+e++ +++sg+S+r+s+++h+glryl++  e+  l++eal e++    +l+++
  gi|121639191|ref|YP_979415.1|  37 DVVVIGGGVVGSGCALDAATRGlkVALVEAR-DLASGTSSRSSKMFHGGLRYLEQL-EF-GLVREALYERELSLTTLAPH 113
                                    9******************************.7777***************99975.55.**********999999**** PP

                                    TSEEEEEEEEEES..SHHHHHHHH...HHHHHH.HHTTTTE.EEEEHHHHHHHSTTST..TTSEEEEETTEEEEEHHHHH CS
                            DAO  79 idyrrtGllslaa..deeeleald...kllall.leaglda.elldaeevrelepalp..gllgalfypdtgqvdpaklt 149
                                    +  + + l +l+      e+++++    l+++l ++  ++a + ++++ +++l+p+l+   l g++ y+d  +vd+a+ t
  gi|121639191|ref|YP_979415.1| 114 LVKPLPFLFPLTKrwW--ERPYIAagiFLYDRLgGAKSVPAqRHFTRAGALRLSPGLKrsSLIGGIRYYD-TVVDDARHT 190
                                    ***********85332..344433111444444755667774679**99******94445888*******.899****** PP

                                    HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.E.EEEE..EEE--GGGHHHH.HTT.CTTTSEEEEEE CS
                            DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttp.gen.d.aada..vVnaaGawsdll.gll.keldlpispvr 221
                                      +ar+a+  G+ ++  t+v++l +e+++v gv  r+++ g++ + +     vVna+G+w+d++ +l  ++ + ++++ +
  gi|121639191|ref|YP_979415.1| 191 MTVARTAAHYGAVVRCSTQVVALLREGDRVIGVGvRDSEnGAVaEvR--GhvVVNATGVWTDEIqALSkQRGRFQVRASK 268
                                    **********************9788889999977555557763223..356**********984444544478****** PP

                                    EEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGG.. CS
                            DAO 222 gqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad.eesgdddpevdeedidellealrklfPq.. 298
                                    g ++v+ p+++  vs     ++   ++++ +++v+p+   + ++G+t++ +  +  +p+++ +did++l  +++++ +  
  gi|121639191|ref|YP_979415.1| 269 GVHVVV-PRDR-IVSD---VAMI-LRTEKSVMFVIPWG-SHWIIGTTDTdWNLDLAHPAATKADIDYILGTVNAVLATpl 341
                                    ******.8766.3333...2333.899999******96.66889***96655666669******************8874 PP

                                    .GCGEEEEEEEEEE.E....TTSSE CS
                            DAO 299 .lgdvlrkwaGlrp.l....pdglp 317
                                      +d+   +aGlrp l    +d+  
  gi|121639191|ref|YP_979415.1| 342 tHADIDGVYAGLRPlLagesDDTSK 366
                                    449999********52443223333 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   8.4e-31   1.2e-27       1     124 [.     413     536 ..     413     538 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 8.4e-31
                                    --TTS---TT--.........TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHHHH CS
                          DAO_C   1 crTkklpLvGaenw..sknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvYav 78 
                                    ++T+k+ L+Ga+++    n+a ++ +  gl++ +++hL++rYGs +++vl++a++  +p+l +++++++ y++ e +Ya+
  gi|121639191|ref|YP_979415.1| 413 SITEKVSLLGADGYfaLVNQAEHVGALQGLHPYRVRHLLDRYGSLISDVLAMAAS--DPSLLSPITEAPGYLKVEAAYAA 490
                                    58**********98777777777777779*********************65555..579******************** PP

                                    HHS---SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHHTT--HH CS
                          DAO_C  79 rhEmartlvDvlaRRtrlafldadaalealpevaelmaeelgWdea 124
                                     +E a++l+D+laRR+r++++  ++++++++evae++a  lgW++a
  gi|121639191|ref|YP_979415.1| 491 AAEGALHLEDILARRMRISIEYPHRGVDCAREVAEVVAPVLGWTAA 536
                                    *******************************************987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.2   7.2e-09     1e-05       1      42 [.      37      78 ..      37      89 .. 0.93
   2 !   17.1   0.5   1.7e-06    0.0023     136     209 ..     182     254 ..     137     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.2e-09
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-- CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq 42
                                   Dv+ViG+G+ G  +Al aa +Glkva+ve  +  +g++  s+
  gi|121639191|ref|YP_979415.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSS 78
                                   9*******************************9999988775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.7e-06
                                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..... CS
                  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallke 209
                                    t+v+  +   +++++a ++g  ++ +t++++L++e++rv G+ v+++e+g   ++r + vv atg +   +++ 
  gi|121639191|ref|YP_979415.1| 182 TVVDDARHTMTVARTAAHYGAVVRCSTQVVALLREGDRVIGVGVRDSENGAVAEVRGHVVVNATGVWTD-EIQA 254
                                    5555566667788889999**********************************************9985.3333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.3   7.2e-10   9.9e-07       1      63 [.      37      99 ..      37     110 .. 0.89
   2 !    7.9   0.0    0.0012       1.7      98     144 ..     198     246 ..     157     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.2e-10
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiaref 63
                                   DvvV+GGg+ G  +A+ Aa +G kv+Lve r+   G++++   +   g +  eq+  g++re 
  gi|121639191|ref|YP_979415.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSSKMFHGGLRYLEQLEFGLVREA 99
                                   9***********************************999998888888777778888888774 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                   FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                    a +g  v   t++v+  +eg+r+ +v v+++e g   ++r++v++ ATg
  gi|121639191|ref|YP_979415.1| 198 AHYGAVVRCSTQVVALLREGDRVIGVGVRDSEnGaVAEVRGHVVVNATG 246
                                    5568889999**********************999*************8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.1   3.2e-10   4.4e-07       2     228 ..      36     304 ..      35     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.2e-10
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHT..T-HHHHHHHSEECCCCEEEEEE CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrql..Gledrilaegapnelmgealyn 78 
                                     dV+++G+G +G   al  +++G +v lve r+ ++ ++ r++ +    ++ l+ql  Gl +++l e    +l++ a   
  gi|121639191|ref|YP_979415.1|  36 FDVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSsRSSKMFHGGLRYLEQLefGLVREALYER-ELSLTTLAP-- 112
                                    69**********************************9999*************986558877777666.222223332.. PP

                                    E..........................................CCCC....CEEEEEHH..CHHCST-CEE--HHHHHHH CS
                  FAD_binding_3  79 e..........................................lsdt....pkaradle..lesspervtvypqteleri 110
                                                                               + +       + +  +   + ++ r+++  +++    
  gi|121639191|ref|YP_979415.1| 113 HlvkplpflfpltkrwwerpyiaagiflydrlggaksvpaqrhFTRAgalrLSPGL--KrsSLIGGIRYYDTVVDDARHT 190
                                    13467**********************98888777777766552222554322222..2335667777777777777777 PP

                                    HHHH..HHHHTEEETCSEEEECCEECCCCCCCE.EEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEE CS
                  FAD_binding_3 111 Lveh..aeerglqvrfktevesleqdeegvtae.vrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagv 187
                                    +  +  a+  g+ vr +t+v++l+++++ v  + vrd+e+g+  +vr   +v a G+++   ++l  ++  ++ v    +
  gi|121639191|ref|YP_979415.1| 191 MTVArtAAHYGAVVRCSTQVVALLREGDRVIGVgVRDSENGAVAEVRGHVVVNATGVWTDEIQALSKQRGRFQ-V--RAS 267
                                    75541155566*****************99765489*****************************97755555.5..577 PP

                                    EEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEE CS
                  FAD_binding_3 188 ldvlfdadlsdiveplvlilsaesrgvmviPlentlerfyv 228
                                     +v++ ++ ++iv+++ +il++e++++ viP+ +    +++
  gi|121639191|ref|YP_979415.1| 268 KGVHVVVPRDRIVSDVAMILRTEKSVMFVIPWGS----HWI 304
                                    7788778888899*******************99....333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.4e-08    0.0001       1      33 [.      36      68 ..      34     108 .. 0.79
   2 ?   -2.6   0.1       1.9   2.6e+03     194     237 ..     198     247 ..     180     267 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.4e-08
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   +dvvviGgG+ G  +al++a+ g+kv+lve+++
  gi|121639191|ref|YP_979415.1| 36 FDVVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   589999999999999999999999999996443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                    HHTTEEEEESCEEEEEEETTE.....EEEEEETTSCE...EEESEEEE-S-E CS
                                    xxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx...xxxxxxxxxxxx RF
                    Pyr_redox_2 194 ekeGvevklgtsvkeidgnge.....klevvledgee...idadlvvvavGv 237
                                     + G  v++ t+v+++ ++g+        v ++++     +    vv a+Gv
  gi|121639191|ref|YP_979415.1| 198 AHYGAVVRCSTQVVALLREGDrvigvG--VRDSENGAvaeVRGHVVVNATGV 247
                                    444555555555555555555333221..22222221233555555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.5   4.8e-07   0.00066       1      29 [.      37      65 ..      37      81 .. 0.87
   2 ?   -2.2   0.1       1.2   1.6e+03     119     174 ..     211     268 ..     187     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.8e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                   dv+ViGgG  G+ +Al aa +G+kv+L+ 
  gi|121639191|ref|YP_979415.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVE 65
                                   79*************************93 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                    EEEEECTTEEEEEEETTS-.....EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B- CS
                           GIDA 119 eeliveekkvkgvvtedge.....tikakavviatGtflkgkihigekelsaGrlgeltse 174
                                      l+ e ++v gv  +d e     +++ ++vv atG + +    i   + ++Gr +  +s+
  gi|121639191|ref|YP_979415.1| 211 VALLREGDRVIGVGVRDSEngavaEVRGHVVVNATGVWTD---EIQALSKQRGRFQVRASK 268
                                    4454555666665444332111114555699999999433...334456667776666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0   2.7e-06    0.0038       1      39 [.      40      78 ..      40      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                   ++G+G+ G+ +A  +a +g++v l+e+rd  +G +++ +
  gi|121639191|ref|YP_979415.1| 40 VIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSS 78
                                   8*****************************999988654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.7e-06    0.0037       2      34 ..      38      70 ..      37     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v viG G++G+g a  +a +gl+V lv+ ++ a
  gi|121639191|ref|YP_979415.1| 38 VVVIGGGVVGSGCALDAATRGLKVALVEARDLA 70
                                   89*************************987654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   5.3e-06    0.0073       2      32 ..      38      68 ..      37      77 .. 0.95
   2 ?   -1.5   0.1       2.8   3.9e+03      23      41 ..     268     282 ..     262     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                   vvv+GgG++g  +A  +a  g kV +ve++d
  gi|121639191|ref|YP_979415.1| 38 VVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   8***************************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                    SEEEEEESSSSSSTTSSHH CS
                      Pyr_redox  23 kkVtvversdkllrllDee 41 
                                    k V+vv+ +d++      +
  gi|121639191|ref|YP_979415.1| 268 KGVHVVVPRDRIV----SD 282
                                    779*******998....44 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   7.6e-06      0.01       1      32 [.      36      67 ..      36      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +dv+viGgG  G  +A+ aa+rg +V+l+e+ 
  gi|121639191|ref|YP_979415.1| 36 FDVVVIGGGVVGSGCALDAATRGLKVALVEAR 67
                                   59***************************986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.6e-05     0.035      25      61 ..      32      68 ..      21     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                   CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 25 gvepakvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                   g+e+  v+viGgGv+G   +  a+  g kV +++ r 
  gi|121639191|ref|YP_979415.1| 32 GTEQFDVVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   677889**************99999999999888775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.5e-05     0.021      17      57 ..      35      74 ..      27      85 .. 0.81
   2 ?   -2.1   0.1       1.3   1.8e+03     157     169 ..     236     248 ..     182     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                   + Dvv++G+G  G  +a   a++ +lkva++e++    G +
  gi|121639191|ref|YP_979415.1| 35 QFDVVVIGGGVVGSGCALDAATR-GLKVALVEARDLASGTS 74
                                   56*********************.********874444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                    EEEEEEEE--GSS CS
                           Thi4 157 irakvvvdatGhd 169
                                    +r +vvv+atG  
  gi|121639191|ref|YP_979415.1| 236 VRGHVVVNATGVW 248
                                    5566777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3900.23
//
Query:       gi|121639192|ref|YP_979416.1|  [L=198]
Description: soj/parA-related protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-55  185.3   0.0      1e-54  185.1   0.0    1.0  1  AAA_31       AAA domain
    4.2e-20   72.1   0.0    9.4e-20   71.0   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-12   47.2   0.0    2.3e-12   46.9   0.0    1.1  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    3.5e-10   39.6   0.2    0.00034   20.0   0.1    2.1  2  MipZ         ATPase MipZ
    8.8e-10   38.2   0.0    2.4e-09   36.8   0.0    1.7  1  ArsA_ATPase  Anion-transporting ATPase
    7.1e-08   32.2   0.7    1.4e-07   31.3   0.7    1.5  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00013   21.5   0.0     0.0002   20.9   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00063   19.6   0.0    0.00098   19.0   0.0    1.2  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0026   17.1   0.1     0.0047   16.3   0.1    1.4  1  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.076   12.6   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain
      0.026   13.5   0.1      0.042   12.8   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.029   14.2   0.0      0.097   12.5   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.082   12.5   0.2       0.11   12.0   0.2    1.2  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   0.0   7.5e-58     1e-54       1     176 [.       4     178 ..       4     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 7.5e-58
                         AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkven 80 
                                    ++v+a+anqKGGv+KTTt+  l+aa+ ++g +vLlvDlDpQ+ +t++lg + +++  +++evl+ e++ + +++ t++e 
  gi|121639192|ref|YP_979416.1|   4 TRVLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVHEVLLGEVEPNAVLV-TTMEG 82 
                                    589**********************************************************************9.7789* PP

                         AAA_31  81 ldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleql 160
                                    ++l+p++idLa+ae  l+    +e++lk++l k++d++D++iiDcpPsLg+lt n+L+a+d+ i+p+q+e +a +G+ q+
  gi|121639192|ref|YP_979416.1|  83 MTLLPANIDLAGAEAMLLMRAGREYALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQCEMLAHRGVGQF 162
                                    ******************************************************************************** PP

                         AAA_31 161 lktieevkkklnpkle 176
                                    l+t+ +v++ +np+l+
  gi|121639192|ref|YP_979416.1| 163 LRTVADVQQITNPNLR 178
                                    *************997 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   6.8e-23   9.4e-20       1      91 [.       7     194 ..       7     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 6.8e-23
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    +a+a++kGGv KTt++a+L++a+ ++g+rVllvD+Dpq+ +++   g  +d+ p                          
  gi|121639192|ref|YP_979416.1|   7 LAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTF-SLGQDPDKLPvsvhevllgevepnavlvttmegmtl 85 
                                    69****************************************9.888888888899999********************* PP

                                    ........................................................................CCHCCCHH CS
                                    ........................................................................xxxxxxxx RF
                           CbiA  55 ........................................................................dlkrllel 62 
                                                                                                            ++ ++l++
  gi|121639192|ref|YP_979416.1|  86 lpanidlagaeamllmragreyalkralakfsdrfdvviidcppslgvltlngltaadeaivplqcemlahrGVGQFLRT 165
                                    ******************************************************************************** PP

                                    HHHHCHCHHHH..EEEEEEEEESS...-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  63 lealgkkkalllkiagvvlnrvdgeneet 91 
                                    ++++++ ++++l+++g +++ +d++ ++t
  gi|121639192|ref|YP_979416.1| 166 VADVQQITNPNLRLLGALPTLYDSRTTHT 194
                                    ************************96554 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   1.7e-15   2.3e-12       3     153 ..       6     157 ..       4     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.7e-15
                       CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqr.egwaraeldgapwrqaaleyapgldl 81 
                                    vla+   +GGv +t+ +a+L+ a+ e g +vl++Dl p+  L+++  +d ++   +  + +l + + ++  +  ++g++l
  gi|121639192|ref|YP_979416.1|   6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLpVSVHEVLLGEVEPNAVLVTTMEGMTL 85 
                                    67888889***************************************99887615667788888999999999******* PP

                       CBP_BcsQ  82 lPfG.elnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchv 153
                                    lP    l+ +e++ l   a ++ al++al++++ +++ +++D+p     lt + l+ ad  +  ++ ++ +h 
  gi|121639192|ref|YP_979416.1|  86 LPANiDLAGAEAM-LLMRAGREYALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQCEMLAHR 157
                                    **75234444444.44567778899*************************************99999998885 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.4e-07   0.00034       2      39 ..       6      43 ..       5      49 .. 0.93
   2 !   17.9   0.0     1e-06    0.0014      83     131 ..     105     151 ..      71     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                           MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                   v+ ++n+kGG  k+tt   +  a+++kG rv  +dld 
  gi|121639192|ref|YP_979416.1|  6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDP 43
                                   6789********************************95 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1e-06
                                    HHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEES CS
                           MipZ  83 eaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlnd 131
                                     +   +l++++a+++ ++d+++id+P s   l+  + + ad  + Pl  
  gi|121639192|ref|YP_979416.1| 105 RE--YALKRALAKFSDRFDVVIIDCPPSLGVLTLNGLTAADEAIVPLQC 151
                                    33..489***************************************975 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.7e-12   2.4e-09       8     138 ..      12     133 ..       4     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.7e-12
                                    ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH.HHHHHHHCCHHGGGSC CS
                    ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe.veleeakqevqkeeea 86 
                                     KGGV Ktt  a++++ + ekg++vll+ +DP   l  s+ q+  k p  v+e L   E++p+ v +  ++   ++   a
  gi|121639192|ref|YP_979416.1|  12 QKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVHEVLL-GEVEPNaVLVTTME--GMTLLPA 88 
                                    59**************************************************9886.69**9933333333..4444444 PP

                                    CHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHT CS
                    ArsA_ATPase  87 llgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGht 138
                                     + l + e +l + +       e +   +l k+  ++ +dvv++D +P    
  gi|121639192|ref|YP_979416.1|  89 NIDLAGAEAMLLMRAGR-----EYALKRALAKF--SDRFDVVIIDCPPSLGV 133
                                    45555677777666666.....66555666666..568********997544 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.7   9.9e-11   1.4e-07       4     139 ..       5     145 ..       3     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.9e-11
                           ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs....ekkliPvea.....kgik 74 
                                    +v+av+  KGGV K+t+ ++l +a+ +kg +v l+D+D  G    +l +  ++ p +       ++ P  +     +g++
  gi|121639192|ref|YP_979416.1|   5 RVLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLTFSLGQDPDKLPVSVhevlLGEVEPNAVlvttmEGMT 84 
                                    799**************************************866665554443332221112112334333333348888 PP

                           ParA  75 vmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplaga 139
                                    ++  ++ l   ++ +++r+   + a+k+ l++ + +  D++iiD+PP  g   lt+      ++a
  gi|121639192|ref|YP_979416.1|  85 LLPANIDLAGAEAMLLMRAG-REYALKRALAKFS-DRFDVVIIDCPPSLGV--LTLNGLTAADEA 145
                                    88888888866666666665.5667777777655.78**********9984..444444444455 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07    0.0002       7      43 ..      12      48 ..       6      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                      Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43
                                    kGG+ k+tt++ l aa++e+g++vl+v  DP+   t
  gi|121639192|ref|YP_979416.1| 12 QKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQGCLT 48
                                   59******************************86555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.1e-07   0.00098       6      99 ..      15     128 ..      13     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.1e-07
                     ATP_bind_1   6 GsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirel.itledvmedlglgpngalvvale........... 73 
                                    G+ Ktt v +l   + ++gr+v +v LDP    l+++   d  +l +++ +v    +++pn  lv+ +e           
  gi|121639192|ref|YP_979416.1|  15 GVAKTTTVASLGAAMVEKGRRVLLVDLDPQGC-LTFSLGQDPDKLpVSVHEVLLG-EVEPNAVLVTTMEgmtllpanidl 92 
                                    888**************************654.6667766666644999999988.9*********************** PP

                     ATP_bind_1  74 ..........flresldwldeelekeed..dyllfDtP 99 
                                               +re    l+++l k +d  d +++D+P
  gi|121639192|ref|YP_979416.1|  93 agaeamllmrAGREYA--LKRALAKFSDrfDVVIIDCP 128
                                    *****99877333333..666666663336*******9 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.4e-06    0.0047       3      41 ..       6      44 ..       4      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                          VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                   +++++  kGG  ktt++ +l +a++ +g+rv l + d  
  gi|121639192|ref|YP_979416.1|  6 VLAVANQKGGVAKTTTVASLGAAMVEKGRRVLLVDLDPQ 44
                                   6788999**************************998865 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.5e-05     0.076      11      38 ..      15      42 ..       6      45 .. 0.93
   2 ?   -0.6   0.0      0.63   8.7e+02      73      90 ..     110     126 ..     101     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                                   TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                   G+ KTtt+a L a + ++g++vllv +D
  gi|121639192|ref|YP_979416.1| 15 GVAKTTTVASLGAAMVEKGRRVLLVDLD 42
                                   899*********************9888 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.63
                                    HHHHHHHHHTTSSEEEEE CS
                          SRP54  73 keavekakeekidvvlvD 90 
                                    k+a+ k+ + ++dvv++D
  gi|121639192|ref|YP_979416.1| 110 KRALAKFSD-RFDVVIID 126
                                    556666665.78*****9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.1e-05     0.042      38      69 ..      14      45 ..       3      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                   TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB 38 PGaGkstlvealglelrrrGkrvavlavDPss 69
                                    G+ k t+v  lg+ ++++G+rv ++ +DP  
  gi|121639192|ref|YP_979416.1| 14 GGVAKTTTVASLGAAMVEKGRRVLLVDLDPQG 45
                                   599***************************76 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05     0.097       5      32 ..      16      43 ..      13      49 .. 0.92
   2 ?   -1.0   0.0      0.93   1.3e+03     118     149 ..      82     113 ..      73     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                         CLP1_P  5 sGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                   + K+T ++ L   +++kgr++++vDlD+
  gi|121639192|ref|YP_979416.1| 16 VAKTTTVASLGAAMVEKGRRVLLVDLDP 43
                                   569************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.93
                         CLP1_P 118 gaellleliealepdvvvvldqeellnelkrd 149
                                    g++ll + i++  ++++++++  ++++  +  
  gi|121639192|ref|YP_979416.1|  82 GMTLLPANIDLAGAEAMLLMRAGREYALKRAL 113
                                    66666666666666666666665444433222 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.1e-05      0.11      41     149 ..      13     126 ..       3     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                         AAA_25  41 apgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv....eslp 115
                                     +g+ Ktt + +l++a++ +G+ +l  v   +  +l  s+ ++ d l+  +++v+    ++  +lv++ +g+     +++
  gi|121639192|ref|YP_979416.1|  13 KGGVAKTTTVASLGAAMVeKGRRVLL-VDLDPQGCLTFSLGQDPDKLPVSVHEVLLGEVEPNAVLVTTMEGMtllpANID 91 
                                    589********************999.445999********************997766777777777555510112344 PP

                         AAA_25 116 Lfakdrggtlltadvdaleaaieeveg.vrlvviD 149
                                    L+ +++    +++   al +a+ +  +  ++v+iD
  gi|121639192|ref|YP_979416.1|  92 LAGAEAMLLMRAGREYALKRALAKFSDrFDVVIID 126
                                    44444444444555557777777777778888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1390.53
//
Query:       gi|121639193|ref|YP_979417.1|  [L=203]
Description: acid phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-44  152.6   0.2    1.1e-44  152.4   0.2    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.033   13.5   0.0      0.058   12.7   0.0    1.4  1  Reo_sigma1  Reovirus viral attachment protein sigma 1


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.2   1.3e-48   1.1e-44       1     191 [.       8     191 ..       8     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.3e-48
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EE..EE-SSHHHHHHHHHHHHCTT--EEE-GGGS CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidai..ysSplkRarqTaeliaealglpveldegLr 78 
                                    l+L+RHGet+w++ gr  g t v+Lt++Gr+qAe +++ l + ++d    ++Sp +R+ +Ta+l++ + +   e++  L 
  gi|121639193|ref|YP_979417.1|   8 LLLLRHGETAWSTLGRHTGGTEVELTDTGRTQAELAGQLLGELELDDPivICSPRRRTLDTAKLAGLTVN---EVTGLLA 84 
                                    68****************************************88887778************99886333...677779* PP

                                    ----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHH CS
                     His_Phos_1  79 EidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarl 158
                                    E+d+G +egltt +i+e+ p++l +++  pa      gEs+++v +R+++a+  ++++ ++++vl VsHg++ ra+++r+
  gi|121639193|ref|YP_979417.1|  85 EWDYGSYEGLTTPQIRESEPDWLVWTHGCPA------GESVAQVNDRADSAVALALEHMSSRDVLFVSHGHFSRAVITRW 158
                                    *****************************99......******************************************* PP

                                    HT--GGGGGGB---TT-EEEEEE-SS-EEEEEE CS
                     His_Phos_1 159 lglpleelrrleldnaslsvlefdeggwrlvrl 191
                                    ++lpl+e  r+++++as+ +  f++g  +l  l
  gi|121639193|ref|YP_979417.1| 159 VQLPLAEGSRFAMPTASIGICGFEHGVRQLAVL 191
                                    *************************99888766 PP

>> Reo_sigma1  Reovirus viral attachment protein sigma 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.5e-06     0.058     109     154 ..      50      95 ..      37     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
                                    EEETTEEEEEE--EEEE---SCEEEEEETTSTB-TT--GGGG-BTT CS
                     Reo_sigma1 109 lkvddylvlslsafdtssiladGklvlnfvtGlspglltGdtePss 154
                                    l +dd +v++ ++  t   ++   l++n vtGl++ +  G+ e  +
  gi|121639193|ref|YP_979417.1|  50 LELDDPIVICSPRRRTLDTAKLAGLTVNEVTGLLAEWDYGSYEGLT 95 
                                    578*************************************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1374.98
//
Query:       gi|121639194|ref|YP_979418.1|  [L=372]
Description: isochorismate synthase entC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-70  235.2   0.0    1.1e-69  234.9   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.9   0.0     6e-74   1.1e-69       3     258 .]      97     360 ..      95     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 6e-74
                                    CHHHHHHHHHHHHHH..TTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETT.......EEEEEEESSE CS
                Chorismate_bind   3 edYaeavekvkeeir..agdlykvvlsrrlkaeleaavdplalyralrarnpapysflleled.......sellgaSPEl 73 
                                    +dY +++ ++++ ++  +g l+kvvl+r+++++++a++d+  l+r+l  + p++y +l++l +         l+gaSPEl
  gi|121639194|ref|YP_979418.1|  97 ADYLTRIGRARDLLAafDGPLHKVVLARAVQLTADAPLDARVLLRRLVVADPTAYGYLVDLTSagnddtgAALVGASPEL 176
                                    57899999999988622577***************************************66556667777889******* PP

                                    EEEEETTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEE CS
                Chorismate_bind  74 llkveggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevl 153
                                    l+ ++g+ r+ ++p aG+++r ++p+ d+a++++l++++K+r+Eh+++vd +r  L+++  ++ +++p  ++++r+++v+
  gi|121639194|ref|YP_979418.1| 177 LVARSGN-RVMCKPFAGSAPRAADPKLDAANAAALASSAKNRHEHQLVVDTMRVALEPL--CEDLTIPAQPQLNRTAAVW 253
                                    *****77.***************************************************..7****************** PP

                                    EEEEEEEEEESTT.--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEE..E CS
                Chorismate_bind 154 hlvstiegelked.vslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavv..k 230
                                    hl++ i+g+l++  ++++dl  al+Pt+av+G+P k+a e+i+elE  +Rg+YaGavg++d  g++ ++v IR+a++  +
  gi|121639194|ref|YP_979418.1| 254 HLCTAITGRLRNIsTTAIDLALALHPTPAVGGVPTKAATELIAELEG-DRGFYAGAVGWCDGRGDGHWVVSIRCAQLsaD 332
                                    **********9877999*****************************7.*****************************744 PP

                                    TTEEEEEEEEEEETT--HHHHHHHHHHH CS
                Chorismate_bind 231 dkelrlgaGaGIvadSdpeaEyeEtlaK 258
                                    ++ + + aG+GIva+Sdp++E+eEt++K
  gi|121639194|ref|YP_979418.1| 333 RRAALAHAGGGIVAESDPDDELEETTTK 360
                                    4778899******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2974.10
//
Query:       gi|121639195|ref|YP_979419.1|  [L=110]
Description: acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.8   0.0    1.3e-10   41.5   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      6e-08   32.6   0.0    6.9e-08   32.4   0.0    1.2  1  FR47             FR47-like protein
    8.9e-06   25.7   0.0      1e-05   25.5   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.2e-05   24.3   0.0    4.2e-05   23.9   0.0    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0065   16.1   0.0     0.0065   16.1   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.018   15.0   0.0    1.3  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
      0.035   13.8   0.0      0.042   13.5   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.079   12.4   0.0      0.087   12.3   0.0    1.1  1  Acetyltransf_15  Putative acetyl-transferase
        0.1   12.7   0.0       0.11   12.5   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   6.6e-14   1.3e-10      37     116 ..       5      86 ..       2      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 6.6e-14
                                    EEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                 Acetyltransf_1  37 vaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                    vae +g +++++  + +         +y+e+l+V p +r++Gl++ Ll +l++++ ++ ++++ + v ++n  ai+lY +
  gi|121639195|ref|YP_979419.1|   5 VAEVNGGVAAMALWFLNFStwDGVAGIYVEDLFVWPRFRRRGLARGLLSTLARECVDNRYTRLAWSVLNWNSDAIALYDR 84 
                                    677778788888666666677677899***************************************************98 PP

                                    TT CS
                 Acetyltransf_1 115 lG 116
                                     G
  gi|121639195|ref|YP_979419.1|  85 IG 86 
                                    77 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   3.4e-11   6.9e-08      27      80 ..      36      90 ..       8      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.4e-11
                                   EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT.-HHHHHHHHHHT-EEE CS
                           FR47 27 lqvlpehrrrGlgsrlvkalakeiaergktvllvvvas.NtpsirlyeklGfeki 80
                                   l v p +rrrGl++ l + la+e + + +t l++ v + N+ +i+ly ++G++  
  gi|121639195|ref|YP_979419.1| 36 LFVWPRFRRRGLARGLLSTLARECVDNRYTRLAWSVLNwNSDAIALYDRIGGQPQ 90
                                   7789*****************************988766************9976 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     5e-09     1e-05      53     105 ..      32      86 ..       3      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5e-09
                Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklG 105
                                    +++ lfV p +r++G+++ Ll ++ +e+ ++++   + +v   +  a+++Y ++G
  gi|121639195|ref|YP_979419.1|  32 YVEDLFVWPRFRRRGLARGLLSTLARECVDNRYTRlAWSVLNWNsDAIALYDRIG 86 
                                    899************************999999888666655444********99 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.1e-08   4.2e-05       7      73 ..       5      86 ..       2      86 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                                   EEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH..TTSEEE.....EE.EEEETHH.HHHHHHH CS
                 Acetyltransf_7  7 VaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea..aekgii.....le.qlelnae.kaikfYe 70
                                   Vae +g++  + al+ l+          + + l+V p +r++G++r Ll    +   +          + ln +  ai++Y 
  gi|121639195|ref|YP_979419.1|  5 VAEVNGGVAAM-ALWFLNfstwdgvagIYVEDLFVWPRFRRRGLARGLLSTlaR--ECVdnrytRLaWSVLNWNsDAIALYD 83
                                   77777666532.22222245555443334444*****************95332..333222221222233333489****9 PP

                                   HTT CS
                 Acetyltransf_7 71 klG 73
                                   + G
  gi|121639195|ref|YP_979419.1| 84 RIG 86
                                   987 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.3e-06    0.0065     190     243 .]      40      96 ..       2      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                GNAT_acetyltran 190 edyrrkgLAtivaaalileclkrglyP.sWDaa..neaSvaLaekLGYefekeYkvy 243
                                    + +rr+gLA+ + + l +ec+++ ++   W     n  ++aL+ ++G + ++e+++y
  gi|121639195|ref|YP_979419.1|  40 PRFRRRGLARGLLSTLARECVDNRYTRlAWSVLnwNSDAIALYDRIGGQPQHEWTIY 96 
                                    889*******************998753799988889999999***********998 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   9.2e-06     0.018       7      35 ..      33      61 ..      28      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.2e-06
                Acetyltransf_13  7 isriWvssshRrkgiAtkLldaarenfiy 35
                                   ++ ++v + +Rr+g+A+ Ll +++++++ 
  gi|121639195|ref|YP_979419.1| 33 VEDLFVWPRFRRRGLARGLLSTLARECVD 61
                                   7889******************9998875 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.042      89     144 ..      40      94 ..      26      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                    HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEEE CS
                 Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekevd 144
                                    +++r++gl++ ll++l++ ++++ r +r        N  ai+l++++G +++ e++
  gi|121639195|ref|YP_979419.1|  40 PRFRRRGLARGLLSTLARECVDN-RYTRLAWSVLNWNSDAIALYDRIGGQPQHEWT 94 
                                    6899*****************88.9***************************9986 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.087      73     106 ..      31      65 ..      16      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                Acetyltransf_15  73 leiYtlyvsekyrgkGlakklLeeslkelk.knYk 106
                                    + + +l+v +++r++Gla+ lL    +e + ++Y 
  gi|121639195|ref|YP_979419.1|  31 IYVEDLFVWPRFRRRGLARGLLSTLARECVdNRYT 65 
                                    455589****************9988875426665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05      0.11      73     107 ..      30      64 ..      10      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                                    EEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                 Acetyltransf_9  73 aagvtgVavapehrgrgvlskLlaraleemreegq 107
                                      +v +  v+p  r+rg+++ Ll ++ +e+ ++++
  gi|121639195|ref|YP_979419.1|  30 GIYVEDLFVWPRFRRRGLARGLLSTLARECVDNRY 64 
                                    56899999******************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 910.37
//
Query:       gi|121639196|ref|YP_979420.1|  [L=143]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          7    6.1  14.1       0.27   10.7   6.3    2.5  2  SKG6      Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.9     0.075   1.3e+03      22      29 ..      25      32 ..      23      33 .. 0.76
   2 ?   10.7   6.3   1.5e-05      0.27      15      32 ..      99     116 ..      99     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.075
                           SKG6 22 ViiivLla 29
                                   V++++Ll+
  gi|121639196|ref|YP_979420.1| 25 VVAAALLV 32
                                   88888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 1.5e-05
                           SKG6  15 aVaVPVaViiivLlaili 32 
                                    a+++PV++i++ +l++l+
  gi|121639196|ref|YP_979420.1|  99 AIGIPVGIIALGVLVLLF 116
                                    89**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 792.20
//
Query:       gi|121639197|ref|YP_979421.1|  [L=321]
Description: hypothetical protein BCG_3338 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-24   85.2   0.8    4.5e-24   84.5   0.8    1.3  1  DAGK_cat    Diacylglycerol kinase catalytic domain
     0.0086   15.3   0.2      0.012   14.9   0.2    1.2  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.8     5e-28   4.5e-24       2     115 ..       3     119 ..       2     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 5e-28
                                    EEEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT.... CS
                       DAGK_cat   2 llvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglle.... 77 
                                    +++ivNp++   ++    + +++ le   ++l++ +t+++g+++el + a ++gvdl+vv GGDGtvs+v+ng+l+    
  gi|121639197|ref|YP_979421.1|   3 AVLIVNPTATA-TTPAGRDLLAHALE-SRLQLTVEHTNHRGHGTELGQAAVADGVDLVVVHGGDGTVSAVVNGMLGrpgt 80 
                                    799*****973.33333344455555.4556*********************************************8777 PP

                                    .HHCTTSEEEEEE-SS--HHHHHCT--SSHHHHHHCHHC CS
                       DAGK_cat  78 .elatkpplgiiPlGtgNdlaralgigkdieealesiik 115
                                       +  p+++++P+G++N laralgi+ d+ +a++++i+
  gi|121639197|ref|YP_979421.1|  81 tPVRPVPAVAVVPGGSANVLARALGISADPIAATNQLIQ 119
                                    667777****************************99975 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.3e-06     0.012      68      98 ..      44      74 ..      10     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
                                   ECCC-TTTTTSSSEEEEEE-HHHHHHHHHHH CS
                     NAD_kinase 68 rkaleafadagvdliivvGGDGTaldvarll 98
                                   ++  +a + +gvdl++v GGDGT+ +v+  +
  gi|121639197|ref|YP_979421.1| 44 TELGQAAVADGVDLVVVHGGDGTVSAVVNGM 74
                                   5556677889***************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1754.30
//
Query:       gi|121639198|ref|YP_979422.1|  [L=84]
Description: transcriptional regulatory protein whiB-like whiB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-27   93.5   0.5    1.1e-26   93.2   0.5    1.1  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.5     6e-31   1.1e-26       1      64 []       3      71 ..       3      71 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 6e-31
                           Whib  1 WreraaCrgedpelffpekg.....dreeeAkavCarCpVrreCleealeegeeyGvwGGltereRraL 64
                                   Wr++a Cr+edpelffp ++     +++++Ak vC+rCpV++eCl +al++g++ GvwGG++e+eRraL
  gi|121639198|ref|YP_979422.1|  3 WRHKAVCRDEDPELFFPVGNsgpalAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRAL 71
                                   ******************99***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 476.75
//
Query:       gi|121639199|ref|YP_979423.1|  [L=501]
Description: two component sensor kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-44  149.8   0.3    1.6e-43  148.1   0.0    2.0  2  H_kinase_N   Signal transduction histidine kinase
    5.4e-22   77.7   2.9    1.2e-21   76.6   2.9    1.6  1  HisKA_2      Histidine kinase
    2.2e-08   34.7   1.7    5.5e-08   33.4   1.4    1.9  2  HWE_HK       HWE histidine kinase
    3.4e-08   34.0   0.0    1.1e-07   32.3   0.0    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.2e-06   26.4   0.0    1.2e-05   25.2   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0006   20.1   0.5      0.005   17.1   0.1    2.6  2  PAS_4        PAS fold


Domain annotation for each model (and alignments):
>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   5.4e-47   1.6e-43       1     143 []       4     150 ..       4     150 .. 0.94
   2 ?   -1.8   0.1      0.89   2.7e+03     100     122 ..     295     317 ..     252     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 5.4e-47
                                    HHHHHHHH----HHHHHHHHHHHHHTHHHHHHHTSEEEEEEE-TTS-EEEEEEE--SSS--S--S--TT-EE-GGGSHHH CS
                     H_kinase_N   1 LsdllaehtdlseadiewLhalvgdwqllAdlsfaDllLwvptredeavvvaqarPttgptlyqeDvVGevveeeeeplv 80 
                                    L dllaeht l+++++++Lha+vg+wqllAdlsfaD+l+wv+++++ +v+vaq+rP+tgpt++++D+VG+vv+++  plv
  gi|121639199|ref|YP_979423.1|   4 LGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRNDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLV 83 
                                    789***************************************************************************** PP

                                    HHHHH----------------...---EEEEEE.EETEEEEEEEEE-.-GGGS----HHHHHHHHHH CS
                     H_kinase_N  81 draleegrivrekdpdwsggv...pvreeaiPVrrrgkviAVltret.nlssartpsrleltylesa 143
                                     ++++ g   re++  +++++      +e+ PVr  ++v+AVltr++ +l+++r+ ++le++y+ +a
  gi|121639199|ref|YP_979423.1|  84 AATFSGGVPGREGAVGQQNSCqhdGHSVEVSPVRFGDQVVAVLTRHQpELAARRRSGHLETAYRLCA 150
                                    **************9999999777777******5558*******7764899999*********9886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.89
                                    -----EEEEEE.EETEEEEEEEE CS
                     H_kinase_N 100 gvpvreeaiPVrrrgkviAVltr 122
                                    ++++re    V+++ +++A l r
  gi|121639199|ref|YP_979423.1| 295 DATIREIHHRVKNNLQTVAALLR 317
                                    33445555555555455555555 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   2.9     4e-25   1.2e-21       1      69 [.     300     367 ..     300     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 4e-25
                        HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLv 69 
                                    EihHRvkNnLq++++lL+lqar++++ e +eal es +Rv sial+h+ L+ s d e+v+++e++++++
  gi|121639199|ref|YP_979423.1| 300 EIHHRVKNNLQTVAALLRLQARRTSNAEGREALIESVRRVSSIALVHDALSMSVD-EQVNLDEVIDRIL 367
                                    9****************************************************99.*********9986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.9   8.7e+03      40      60 ..     197     217 ..     196     234 .. 0.80
   2 !   33.4   1.4   1.8e-11   5.5e-08       1      70 [.     300     371 ..     300     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHHCTTS-EEHHH CS
                         HWE_HK  40 ALsaahdllsreewagaeLae 60 
                                    ALsa h +  ++e +g++L +
  gi|121639199|ref|YP_979423.1| 197 ALSAYHRMGLTTELEGVNLID 217
                                    999999998889989988865 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.8e-11
                                    HHHHHHHHHHHHHHHHHHHHSSSXS-HHHHHHHHHH..HHHHHHHHHHHHHHCTTS-EEHHHHHHHHHHHHH CS
                         HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesleefaeklsg..RLqALsaahdllsreewagaeLaelleeelapye 70 
                                    E++HRvKN L +v ++ r  +r++++ e  ++ +++  R+ +++ +hd ls +  ++++L+e++++ l  ++
  gi|121639199|ref|YP_979423.1| 300 EIHHRVKNNLQTVAALLRLQARRTSNAEGREALIESvrRVSSIALVHDALSMSVDEQVNLDEVIDRILPIMN 371
                                    89********************9999888777776444**************************99886655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.8e-11   1.1e-07       4     110 ..     397     493 ..     394     495 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.8e-11
                                    HHHHHHHHHHHHHHHHH....HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHH CS
                      HATPase_c   4 krLrqiisnlvdNavkf....atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGls 79 
                                    + L  +i +lv+Na+++    a+ +g+++++ ++s  +l + v D+G G+p+         fs         +   lGl 
  gi|121639199|ref|YP_979423.1| 397 TALIMVITELVQNAIEHafdpAAAEGSVTIRAERSARWLDVVVHDDGLGLPQ--------GFSL-------EKSDSLGLQ 461
                                    568889***********77544466666666665669**************9........4444.......34455**** PP

                                    HHHHHHH.HTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  80 ivkklve.lmgGeiwvesepgrGttftftlpl 110
                                    iv+ lv+  ++G++ +++  +rGt++++++p 
  gi|121639199|ref|YP_979423.1| 462 IVRTLVSaELDGSLGMRDARERGTDVVLRVPV 493
                                    ****88879*******************9986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   4.2e-09   1.2e-05      24      81 ..     391     450 ..     383     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.2e-09
                    HATPase_c_2  24 lseelldeirlaveEactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe 81 
                                    l+++++  + ++++E++ Na+eha + a  eg+v++r+e+++++l v+v+D+G g  +  
  gi|121639199|ref|YP_979423.1| 391 LDSDRATALIMVITELVQNAIEHAFDPAAaEGSVTIRAERSARWLDVVVHDDGLGlPQGF 450
                                    566777788899**************9999***********************9855554 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.7e-06     0.005       5     110 .]     178     286 ..     175     286 .. 0.84
   2 ?    1.6   0.0      0.11   3.2e+02      52     105 ..     284     339 ..     283     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                          PAS_4   5 pdalavldpdgrvlyaNaa..aaelfgappeellGktlaellpee.....daarleralrrvlegeepiefleelllpge 77 
                                     d+++ ld dg+v ya+++  +a++      el G  l +   +       a++++++++ +l+g+    ++e +  + +
  gi|121639199|ref|YP_979423.1| 178 GDGFIRLDVDGVVSYASPNalSAYHRMGLTTELEGVNLIDATRPLisdpfEAHEVDEHVQDLLAGDGKGMRME-V--DAG 254
                                    689999*************7666677788899999999987777777779**************964433333.2..678 PP

                          PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                    + +++lr lPl    G+ +g+ +++rD+Te +r
  gi|121639199|ref|YP_979423.1| 255 GATVLLRTLPL-VVAGRNVGAAILIRDVTEVKR 286
                                    99*********.79****************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                          PAS_4  52 leralrrvlegeepiefleelll.pgeerhyelrl..lPlrdesGevigvlvisrDi 105
                                    + r +r++++ +++i++ ++++  + +++  +lrl  ++  +++G+  ++++ +r +
  gi|121639199|ref|YP_979423.1| 284 VKRRDRALISKDATIREIHHRVKnNLQTVAALLRLqaRRTSNAEGR-EALIESVRRV 339
                                    67899999*******9999999998888888888877888899999.7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2742.85
//
Query:       gi|121639200|ref|YP_979424.1|  [L=71]
Description: acetyl-CoA carboxylase biotin carboxyl carrier protein subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-17   62.0   6.9    3.9e-17   61.8   6.9    1.0  1  Biotin_lipoyl    Biotin-requiring enzyme
    5.5e-07   29.3   9.8    3.9e-05   23.4   1.0    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
    8.2e-05   23.3   4.1     0.0038   17.9   0.6    2.0  2  HlyD_3           HlyD family secretion protein
    0.00051   20.0   2.5     0.0039   17.1   0.6    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0011   18.2   2.2      0.038   13.2   0.2    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0045   17.2   2.5       0.79   10.0   0.3    2.4  3  Peptidase_M23    Peptidase family M23
  ------ inclusion threshold ------
       0.01   15.7   1.3      0.011   15.6   1.3    1.2  1  GCV_H            Glycine cleavage H-protein
      0.012   15.6   0.5       0.66    9.9   0.1    2.0  2  DUF2118          Uncharacterized protein conserved in archaea
      0.021   14.3   0.8      0.035   13.5   0.7    1.4  2  NQRA             Na(+)-translocating NADH-quinone reductase s
      0.029   14.0   1.6        3.6    7.3   0.1    2.2  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   6.9   2.2e-20   3.9e-17      12      73 .]      10      70 ..       3      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.2e-20
                                   EEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl 12 veegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                   v+ +v+ev v++Gd++ +g+v++ +e+mKme+++ a++aG+v+++ v++Gd +++gdl+a+i
  gi|121639200|ref|YP_979424.1| 10 VA-SVLEVVVNEGDQIDKGDVVVLLESMKMEIPVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   33.599******************************************************97 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.4   4.9e-05     0.088       6      37 ..       6      37 ..       4      47 .. 0.83
   2 !   23.4   1.0   2.1e-08   3.9e-05       4      33 ..      41      70 ..      34      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                Biotin_lipoyl_2  6 aapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                    a + + V ++ V +G+++ +Gdv + l+s +
  gi|121639200|ref|YP_979424.1|  6 RAEIVASVLEVVVNEGDQIDKGDVVVLLESMK 37
                                   566667899***************98888765 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.1e-08
                Biotin_lipoyl_2  4 sIaapvsGrVaqlnVkdGqrVkaGdvLael 33
                                   ++ a  +G+V++++V  G++++aGd++a++
  gi|121639200|ref|YP_979424.1| 41 PVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   5557779*********************98 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0045       8.1       2      28 ..       5      31 ..       4      39 .. 0.90
   2 !   17.9   0.6   2.1e-06    0.0038       2      30 ..      42      70 ..      41      71 .] 0.94

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdell 28
                                   +rA +   v e+ v+eg+ + +gd+++
  gi|121639200|ref|YP_979424.1|  5 VRAEIVASVLEVVVNEGDQIDKGDVVV 31
                                   89999999****************986 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.1e-06
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdellei 30
                                   + A  +G+v+++ v++g+v+qagd ++ i
  gi|121639200|ref|YP_979424.1| 42 VLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70
                                   67999*********************998 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   2.2e-06    0.0039      42      81 ..      14      54 ..       7      57 .. 0.88
   2 !    9.2   0.3   0.00066       1.2      35      59 ..      44      68 ..      43      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                         RnfC_N 42 akplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                    +++v++gd++ kG+++   e+  +  pv a  +GtV +++
  gi|121639200|ref|YP_979424.1| 14 LEVVVNEGDQIDKGDVVVLLESmKMEIPVLAEAAGTVSKVA 54
                                   589*************9988876679***********9986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00066
                         RnfC_N 35 sqhiGapakplvkvgdkVlkGqkia 59
                                   +  +G+  k+ v+vgd ++ G++ia
  gi|121639200|ref|YP_979424.1| 44 AEAAGTVSKVAVSVGDVIQAGDLIA 68
                                   5678999*****************8 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2    0.0023       4.1      22      55 ..       5      37 ..       2      39 .. 0.83
   2 !   13.2   0.2   2.1e-05     0.038     105     139 ..      36      70 ..      34      71 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 22 vsarveGwveklyvnatgdkVkkGqpLaelyspe 55
                                   v a++ + v ++ vn +gd++ kG+ ++ l+s +
  gi|121639200|ref|YP_979424.1|  5 VRAEIVASVLEVVVN-EGDQIDKGDVVVLLESMK 37
                                   677788888999999.999999999999999876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 105 vqktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    ++ +++v a+++G+V + +v  G+++q+gd ++ i
  gi|121639200|ref|YP_979424.1|  36 MKMEIPVLAEAAGTVSKVAVSVGDVIQAGDLIAVI 70 
                                    567899***********************988876 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0037       6.6      50      70 ..      11      31 ..       3      44 .. 0.79
   2 ?    2.7   0.0     0.081   1.4e+02      13      27 ..      39      53 ..      32      54 .. 0.80
   3 !   10.0   0.3   0.00044      0.79      50      71 ..      48      69 ..      43      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0037
                                   EEESEESS-TTEEE-TTCEEE CS
                  Peptidase_M23 50 ahlskisvkegqkVkaGqvIG 70
                                   a + ++ v+eg+++++G+v+ 
  gi|121639200|ref|YP_979424.1| 11 ASVLEVVVNEGDQIDKGDVVV 31
                                   55567789**********985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.081
                                   T-EEEESSSEEEEEE CS
                  Peptidase_M23 13 gtpVlAaadGtVvfa 27
                                   + pVlA a+GtV ++
  gi|121639200|ref|YP_979424.1| 39 EIPVLAEAAGTVSKV 53
                                   569*********865 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00044
                                   EEESEESS-TTEEE-TTCEEEE CS
                  Peptidase_M23 50 ahlskisvkegqkVkaGqvIGt 71
                                   + +sk++v++g+ ++aG+ I+ 
  gi|121639200|ref|YP_979424.1| 48 GTVSKVAVSVGDVIQAGDLIAV 69
                                   56899***************96 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.3   6.2e-06     0.011      38      78 ..      17      57 ..       2      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.2e-06
                                   ---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                          GCV_H 38 lpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78
                                   + ++g++++kg+ +  +Es K+  +v a+  G+v +v   +
  gi|121639200|ref|YP_979424.1| 17 VVNEGDQIDKGDVVVLLESMKMEIPVLAEAAGTVSKVAVSV 57
                                   4478******************************9987665 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00037      0.66      94     122 ..      15      43 ..       3      50 .. 0.82
   2 ?    5.6   0.1    0.0079        14      87     112 ..      45      70 ..      42      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                        DUF2118  94 tlivdvGdrveegdtlaavttrkgevryl 122
                                     ++v++Gd++ +gd++  + + k e+  l
  gi|121639200|ref|YP_979424.1|  15 EVVVNEGDQIDKGDVVVLLESMKMEIPVL 43 
                                    5789********************99766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0079
                        DUF2118  87 pvegvkvtlivdvGdrveegdtlaav 112
                                    +++g +  + v vGd ++ gd +a +
  gi|121639200|ref|YP_979424.1|  45 EAAGTVSKVAVSVGDVIQAGDLIAVI 70 
                                    68899999***************986 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7     2e-05     0.035      40      80 ..      13      54 ..       5      63 .. 0.82
   2 ?    0.2   0.0      0.23   4.2e+02      42      57 ..      52      67 ..      52      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           NQRA 40 kpklkvkegdkVkkGqvlf.edKknpgvlftspasGevvein 80
                                    ++++v+egd++ kG+v++  +  + ++ + + a+G+v+++ 
  gi|121639200|ref|YP_979424.1| 13 VLEVVVNEGDQIDKGDVVVlLESMKMEIPVLAEAAGTVSKVA 54
                                   5789************87515667789***********9985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                           NQRA 42 klkvkegdkVkkGqvl 57
                                   k++v++gd +++G+ +
  gi|121639200|ref|YP_979424.1| 52 KVAVSVGDVIQAGDLI 67
                                   5788999999999876 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0029       5.2      35      57 ..      15      37 ..      11      54 .. 0.75
   2 ?    7.3   0.1     0.002       3.6      37      53 ..      54      70 ..      42      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                                   EES--TT-EEBTTSEEEEEEESS CS
                         PYNP_C 35 elhkklGdkVkkGeplatiYank 57
                                   e+ +  Gd+++kG++++ + + k
  gi|121639200|ref|YP_979424.1| 15 EVVVNEGDQIDKGDVVVLLESMK 37
                                   567788*********99875555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                                   S--TT-EEBTTSEEEEE CS
                         PYNP_C 37 hkklGdkVkkGeplati 53
                                    + +Gd +++G+ +a+i
  gi|121639200|ref|YP_979424.1| 54 AVSVGDVIQAGDLIAVI 70
                                   5789***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 396.13
//
Query:       gi|121639201|ref|YP_979425.1|  [L=101]
Description: anti-sigma factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-10   39.0   4.2    6.7e-10   39.0   4.2    1.8  2  zf-HC2    Putative zinc-finger


Domain annotation for each model (and alignments):
>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   4.2   3.7e-14   6.7e-10       1      34 [.      23      56 ..      23      57 .. 0.97
   2 ?   -3.1   0.1      0.57     1e+04      19      24 ..      84      89 ..      80      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.7e-14
                                   HCCHHHHHHHHHCCT-SCCCHCCCHHHHCHTCHH CS
                         zf-HC2  1 CeevrelLsaYlDGeLspeerarveaHLaeCpdC 34
                                   C ev + ++  lDGe++pe+r+r+++HL++Cp C
  gi|121639201|ref|YP_979425.1| 23 CAEVIAEVWTLLDGECTPETRERLRRHLEACPGC 56
                                   99******************************** PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.57
                                   CCHCCC CS
                         zf-HC2 19 eerarv 24
                                   +er r+
  gi|121639201|ref|YP_979425.1| 84 RERLRL 89
                                   466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 568.10
//
Query:       gi|121639202|ref|YP_979426.1|  [L=183]
Description: hypothetical protein BCG_3343c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 971.42
//
Query:       gi|121639203|ref|YP_979427.1|  [L=216]
Description: RNA polymerase sigma factor RpoE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-18   64.1   0.1    1.5e-17   63.1   0.1    1.5  1  Sigma70_r2    Sigma-70 region 2
    1.1e-16   60.2   0.0    2.5e-16   59.1   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
    1.8e-10   40.2   0.0    4.4e-10   38.9   0.0    1.7  2  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   2.6e-21   1.5e-17       6      70 ..      37      99 ..      35     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.6e-21
                                   HHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2  6 lplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70
                                   l+++++ a r+++++adaeDl+Qe++++++ + ++f+++++  ++awl+ri +n+ i+ +Rk++r
  gi|121639203|ref|YP_979427.1| 37 LDQLYGGALRMTRNPADAEDLLQETMVKAYAGFRSFRHGTN--LKAWLYRILTNTYINSYRKKQR 99
                                   789**********************************5555..*******************998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   4.1e-20   2.5e-16       3      54 .]     140     191 ..     138     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.1e-20
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    ++ eal++Lpe+ r+++   ++eg++ykEIAe+++++ gtV srl+R+r++L
  gi|121639203|ref|YP_979427.1| 140 EIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQL 191
                                    799**********************************************997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.75   4.5e+03      41      48 ..     129     136 ..     126     140 .. 0.54
   2 !   38.9   0.0   7.3e-14   4.4e-10       1      49 [.     144     192 ..     144     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.75
                                    HHHHHHHH CS
                     Sigma70_r4  41 ekrAlrkL 48 
                                    e +Al+ L
  gi|121639203|ref|YP_979427.1| 129 EVEALEAL 136
                                    55555554 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 7.3e-14
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    aL+ Lpe+ r+ +++  +eg +++EI+e+++ + ++V ++++r++r+LR
  gi|121639203|ref|YP_979427.1| 144 ALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQLR 192
                                    8***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1210.39
//
Query:       gi|121639204|ref|YP_979428.1|  [L=282]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-28  100.1   0.0    1.5e-28   99.6   0.0    1.2  1  adh_short       short chain dehydrogenase
      7e-28   97.8   0.2    9.6e-28   97.3   0.2    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.2e-07   31.8   0.1    1.8e-07   31.3   0.1    1.2  1  KR              KR domain
  ------ inclusion threshold ------
      0.036   13.9   0.1      0.065   13.0   0.1    1.4  1  DFP             DNA / pantothenate metabolism flavoprotein
      0.099   12.5   0.9       0.26   11.2   1.0    1.7  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   4.2e-32   1.5e-28       1     189 [.       6     203 ..       6     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 4.2e-32
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHH.......HHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHH CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseeklee.......vakelkeegakalaiqvDvtdreevealvekavk 73 
                                    k++++ Gas+GIG+aiak+ a++Ga+++++++++e+  +       +akel+e+g +al+i +D++d ++v  +v++ v+
  gi|121639204|ref|YP_979428.1|   6 KTMFISGASRGIGLAIAKRAARDGANIALIAKTAEPHPKlpgtvftAAKELEEAGGQALPIVGDIRDPDAVASAVATTVE 85 
                                    7899****************************9997654222222289******************************** PP

                                    HHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHH CS
                      adh_short  74 klgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAs 152
                                    ++g++d+ vnNA+  + g++ e+  ++++ +  + + g++ +++a++p+m+ +++ +I + s  +  ++++   +aY  +
  gi|121639204|ref|YP_979428.1|  86 QFGGIDICVNNASAINLGSITEVPMKRFDLMNGIQVRGTYAVSQACIPHMKGRENPHILTLSPPILlEKKWLRPTAYMMA 165
                                    **************************************************************988758899999****** PP

                                    HHHHHHHHHHHHHHHGGGTEEEEEEEESSBS.SHHHHH CS
                      adh_short 153 KaavagltrslakelaptgirvnavaPGlvd.Tdmake 189
                                    K +++  +  +a+e++ +gi  n++ P  +  T+ +++
  gi|121639204|ref|YP_979428.1| 166 KYGMTLCALGIAEEMRADGIASNTLWPRTMVaTAAVQN 203
                                    *************************9965443877665 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.2   2.7e-31   9.6e-28       1     193 [.      12     215 ..      12     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 2.7e-31
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..H......HHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEE CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..k......krveelaeelgaev.lecDVtdeeqvealveevvekfgklD 71 
                                    Ga +gIG aiAk++a+ Ga+++l     e   k       +++el+e++g+++ +  D++d+++v+++v+++ve+fg++D
  gi|121639204|ref|YP_979428.1|  12 GASRGIGLAIAKRAARDGANIALIAKTAEPhpKlpgtvfTAAKELEEAGGQALpIVGDIRDPDAVASAVATTVEQFGGID 91 
                                    999*******************98877765332232222345566666666658************************** PP

                                    EEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEE.GGGTSBSTTTTHHHHHHHHH CS
                   adh_short_C2  72 ilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlss.vgaervvpnynaygaaKaal 148
                                    i+vnna   +   g+++e++ + fd +  +++++++++++a++p+mk +    i++ls  +  e+ +   +ay++aK ++
  gi|121639204|ref|YP_979428.1|  92 ICVNNASAINL--GSITEVPMKRFDLMNGIQVRGTYAVSQACIPHMKGRenPHILTLSPpILLEKKWLRPTAYMMAKYGM 169
                                    ***********..*******************************999766699****96257788899999********* PP

                                    HHHHHHHHHHHGGGTEEEEEEEE.--BHCTGGGGSTTHHHHHHHHH CS
                   adh_short_C2 149 ealtrylAvelgpkgiRvNavsp.gpikTlaasgikgfdelleele 193
                                      ++  +A e+ ++gi  N+  p  +++T a++++ g de +++++
  gi|121639204|ref|YP_979428.1| 170 TLCALGIAEEMRADGIASNTLWPrTMVATAAVQNLLGGDEAMARSR 215
                                    **********************956778888888887777665544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1     5e-11   1.8e-07       2     123 ..       7     131 ..       6     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5e-11
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH....HHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedsk....aliaelealgaevevvaaDvsdkdavealleeika 77 
                                    t +i G+  g+Gl++a+  a++ga +++l++++a+++++      +  +ele+ g +   +  D+ d+dav++++++  +
  gi|121639204|ref|YP_979428.1|   7 TMFISGASRGIGLAIAKRAARDGA-NIALIAKTAEPHPKLPgtvfTAAKELEEAGGQALPIVGDIRDPDAVASAVATTVE 85 
                                    5689******************98.69999999855554443333699******************************** PP

                                    HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHT CS
                             KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhell 123
                                    +++ i  +++ A +++ + ++e+ +++++ +    v+G+  + +++
  gi|121639204|ref|YP_979428.1|  86 QFGGIDICVNNASAINLGSITEVPMKRFDLMNGIQVRGTYAVSQAC 131
                                    ***************************************9999987 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.8e-05     0.065      22      79 ..       9      63 ..       7      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                   EEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHH CS
                            DFP 22 fisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveea 79
                                   fis  S G  G+a+A++aa+ Ga++ l++   + ++p ++  + ++ a+e++ea  +a
  gi|121639204|ref|YP_979428.1|  9 FISGASRG-IGLAIAKRAARDGANIALIAKTAE-PHP-KLPGTVFTAAKELEEAGGQA 63
                                   56666766.6******************99843.333.56666677788887776555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   7.1e-05      0.26       1      62 [.      12      91 ..      12     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH...........HHHCT.TTCEEEE--TT-CCHHHHHHT.......T-S CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekla...........eleae.eglevvegdvtdvedlaealk.......gad 62
                                   GA+ ++G +++k+++++g  ++ +++ ++e  +           ele++  ++  ++gd+ d++++a+a++       g+d
  gi|121639204|ref|YP_979428.1| 12 GASRGIGLAIAKRAARDG-ANIALIAKTAEPHPklpgtvftaakELEEAgGQALPIVGDIRDPDAVASAVAttveqfgGID 91
                                   9****************5.99999999988666344555555556664435666788999999999999875555554555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 1546.42
//
Query:       gi|121639205|ref|YP_979429.1|  [L=62]
Description: hypothetical protein BCG_3346 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 434.11
//
Query:       gi|121639206|ref|YP_979430.1|  [L=72]
Description: hypothetical protein BCG_3347 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-06   28.4   0.0    1.7e-06   28.1   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   9.7e-11   1.7e-06      58     102 ..       3      46 ..       2      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.7e-11
                      tRNA_edit  58 klrlaseeelrellgvepGgvgPlglkaagvpvllDeslkeyptv 102
                                    k+++a+++  ++++g+++Gg++P+g   +++++++D s+++ ++v
  gi|121639206|ref|YP_979430.1|   3 KAAMAKPAAAEQATGYVVGGISPFGQ-RKRLRTVVDVSALSWDRV 46 
                                    689**********************9.8********999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 520.71
//
Query:       gi|121639207|ref|YP_979431.1|  [L=474]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-33  114.1   2.6    9.4e-33  114.1   2.6    1.5  2  APH              Phosphotransferase enzyme family
    2.7e-18   67.0   0.0    6.1e-18   65.8   0.0    1.6  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    8.7e-08   32.4   0.0    1.7e-07   31.5   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0097   15.6   0.0      0.048   13.3   0.0    2.1  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0097   15.8   0.0      0.016   15.1   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.059   13.3   0.0       0.13   12.3   0.0    1.5  1  FR47             FR47-like protein
      0.084   12.5   0.0       0.14   11.7   0.0    1.2  1  RIO1             RIO1 family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   6.8e+03      63     100 ..     158     194 ..     125     198 .. 0.66
   2 !  114.1   2.6   3.7e-36   9.4e-33       6     238 ..     210     432 ..     206     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                    -EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHH CS
                            APH  63 ddeeigllfalieyvpgrsllrklsaaqlpellealge 100
                                     +e+ g++f  +e+v  + ++  +  +++++l+++l +
  gi|121639207|ref|YP_979431.1| 158 ICEQDGTVFDRYERVLRAKMHA-DEVDIDEDLVRRLLR 194
                                    4455555666666666666666.556666666666655 PP

  == domain 2  score: 114.1 bits;  conditional E-value: 3.7e-36
                                    --.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                            APH   6 sggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr 84 
                                    s+g++n  y++++   ++++r+++ ++a e++r e+++l  +a++     P+++ ++  +e+ g+++ +  +v g+ ++ 
  gi|121639207|ref|YP_979431.1| 210 SAGTDNAMYRLGE---DLAVRIPRIGWAIESLRTEQQWLPRIAAHLGvASPVPVGLGSPAEGFGWPWSVCRWVAGENPSA 286
                                    789**********...9**********************8888665565555666669********************** PP

                                    HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.HHHHHHHHHHHHHHHH--SS CS
                            APH  85 klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselld.lleeleeqvlaalaallpge 163
                                         +  +++e+l++f+  l ++dp   p+a ++a+  e+++ + +a    la++ +  ++ ++++ +++  ++  p +
  gi|121639207|ref|YP_979431.1| 287 -AEFVEPNRAVEDLADFITTLRATDPMGGPPAKRGAPLGEQDAEVRAA----LAALDGIiDVHAATA-AWESALRVPPYA 360
                                    .778899****************************9988888888888....333333345677777.88888888888* PP

                                    S-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHHCS-HHHHCCC CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrswtseldpeflaallrayeqeaglarla 238
                                    +p+ + HgDl+  N+l    +gr+tGviDf+++g+g+p +Dl ++++ +  ++++ f+ a ++a   ++ ++r +
  gi|121639207|ref|YP_979431.1| 361 GPPMWFHGDLSRFNILTA--QGRLTGVIDFGLMGVGDPSVDLIIAWNLLSAPARAQFRVAVGAADD-DWMRGRGR 432
                                    ******************..**************************77**************9996.57666665 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   2.4e-21   6.1e-18       2     137 ..      15     152 ..      15     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.4e-21
                 Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmry.lpepltleeaeewlera...waeeseeegygwaivl.kdtgviGsvglrdlee 76 
                                    ++L pl+ +D++a +    d++++r+  + p t++  e++++++   w ++ + ++  + i++  +t ++G++ lr +++
  gi|121639207|ref|YP_979431.1|  15 VTLSPLCLDDVDAHL-AGGDERLVRWlSGMPSTRASVEAYIRHCreqWVTGGPLRS--FGIRTvAET-IVGTIDLR-FDG 89 
                                    589*******99976.489999999*6556************87888887666666..677654777.9****999.444 PP

                 Acetyltransf_3  77 edee...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    e  +   +++ y l ps++g+G+at av  +++ya +e+g+++ v+++++eN+aS+rv+ ++Gf
  gi|121639207|ref|YP_979431.1|  90 EGLAsgqVNVAYGLYPSWRGRGLATRAVDLVCQYA-AEHGATEAVIKVEPENSASARVALRAGF 152
                                    4444688****************************.6777***********************9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   6.5e-11   1.7e-07      34     117 .]      68     152 ..      34     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.5e-11
                                    EEEE.EEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHH CS
                 Acetyltransf_1  34 gllv.aeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaair 110
                                    + +      ++++G+i l+ + +   +g+v + ++l+  p++rg+Gl+++ ++ + ++a e+g+++ v+ ve+ n a+ r
  gi|121639207|ref|YP_979431.1|  68 RSFGiRTVAETIVGTIDLRFDGEglASGQVNVAYGLY--PSWRGRGLATRAVDLVCQYAAEHGATEAVIKVEPENSASAR 145
                                    33333444599**********9997666666666666..*************************8889************ PP

                                    HHHHTTE CS
                 Acetyltransf_1 111 lYeklGF 117
                                    +  + GF
  gi|121639207|ref|YP_979431.1| 146 VALRAGF 152
                                    **99999 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.9e-05     0.048      89     143 ..     105     158 ..      97     159 .. 0.87
   2 ?   -1.5   0.0      0.72   1.8e+03      11      41 ..     277     309 ..     274     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                    HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                 Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                    ++ rg+gl+t+ +  +++y+ ++ +++  v+  +++N ++ r+  +aGf++++++
  gi|121639207|ref|YP_979431.1| 105 PSWRGRGLATRAVDLVCQYAAEH-GATEAVIKVEPENSASARVALRAGFAFVRRI 158
                                    6789****************999.666666777789**************99875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.72
                                    HHC..TSCCCHHHH-----HHHHHHHHHHHC.S CS
                 Acetyltransf_8  11 rWm..nrprvaewweeagtleevrellakldad 41 
                                    rW+  ++p +ae+ e +  +e+++++ ++l+a+
  gi|121639207|ref|YP_979431.1| 277 RWVagENPSAAEFVEPNRAVEDLADFITTLRAT 309
                                    6773358999********999999999998865 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.2e-06     0.016      60     124 ..     104     170 ..      66     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                Acetyltransf_10  60 dpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqeenGirfvpMe 124
                                     p++rg+G++++ ++ v+++a ++g  +  ++v+  + +  ++  + GF  v + +e++G  f ++e
  gi|121639207|ref|YP_979431.1| 104 YPSWRGRGLATRAVDLVCQYAAEHGATEaVIKVEPENsASARVALRAGFAFVRRICEQDGTVFDRYE 170
                                    499******************99999999*****99988899******************9987666 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.9e-05      0.13      30      78 ..     104     153 ..      97     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                                    -GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-E CS
                           FR47  30 lpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfe 78 
                                     p+ r+rGl++r v  + +  ae g t +++ v ++N++s r+  + Gf 
  gi|121639207|ref|YP_979431.1| 104 YPSWRGRGLATRAVDLVCQYAAEHGATeAVIKVEPENSASARVALRAGFA 153
                                    5899*******************998725567999******998888886 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.5e-05      0.14     129     150 ..     367     389 ..     364     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                                    ESS-STTSEEEETT.EEEE--GT CS
                           RIO1 129 HaDLSeyNvlvded.kvviIDvs 150
                                    H+DLS +N+l  ++    +ID++
  gi|121639207|ref|YP_979431.1| 367 HGDLSRFNILTAQGrLTGVIDFG 389
                                    **************555699985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3534.96
//
Query:       gi|121639208|ref|YP_979432.1|  [L=252]
Description: hypothetical protein BCG_3349c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-65  218.9   0.0    6.4e-65  218.8   0.0    1.0  1  SRAP      SOS response associated peptidase (SRAP)


Domain annotation for each model (and alignments):
>> SRAP  SOS response associated peptidase (SRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   3.6e-69   6.4e-65       1     219 []       1     231 [.       1     231 [. 0.86

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 3.6e-69
                           SRAP   1 MCgRyaltlapeelaeeleaeeedke...lrpsynvaptqkvpvvvaeeeeeeeeeeerklqamkwGlvPswakd..... 72 
                                    MCgR+a+t++p++lae+++a +e +     + synvapt+++++vv++++e  ++e +r+++ m+wGl+Psw k      
  gi|121639208|ref|YP_979432.1|   1 MCGRFAVTTDPAQLAEKITAIDEATGcggGKTSYNVAPTDTIATVVSRHSE-PDDEPTRRVRLMRWGLIPSWIKAgpgga 79 
                                    *****************99643333355679**************987777.445669***************6522111 PP

                           SRAP  73 pkklglktiNaRsetlaekplfrsalkkkRcvvpadGFYEWk.......kkgkekqPyfikrkdgkllalAGLydvweee 145
                                    p+ +g  +iNaR++++a++p+frsa+++kRc+vp+dG+YEW+        + ++k+P+f++r+dg ll+ AGL++vw++ 
  gi|121639208|ref|YP_979432.1|  80 PDAKGPPLINARADKVATSPAFRSAVRSKRCLVPMDGWYEWRvdpdatpGRPNAKTPFFLHRHDGALLFTAGLWSVWKSY 159
                                    45668************************************54455543334689**********************987 PP

                           SRAP 146 geeeklytytiiTteankqlaelHdRmPviLeeeelraWLdprkedskelqellkpaeeeelevypVskeVnkv 219
                                     ++ +l ++t+iTt+a  +lae+HdRmP+ L ee++++WL+p+   + e   l +p + +++++++Vs+ Vn+v
  gi|121639208|ref|YP_979432.1| 160 RSAPPLLSCTVITTDAVGELAEIHDRMPLLLAEEDWDDWLNPDAPPDPE--LLARPPDVRDIALRQVSTLVNNV 231
                                    789***************************************4444444..456999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1968.91
//
Query:       gi|121639209|ref|YP_979433.1|  [L=450]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.1e-120  401.7   0.0   3.5e-120  401.5   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.5   0.0  1.9e-124  3.5e-120       2     415 ..       8     417 ..       7     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 401.5 bits;  conditional E-value: 1.9e-124
                                    ECSS--EEEEE--B-HHHHHHHHHHHGGGBSS....EEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..- CS
                  EPSP_synthase   2 ekgkrlegevkvpGsksisnralllAaLaege....stitnlLdseDvrsmlealreLgaeiikldeekevviveglggs 77 
                                    +++++++++v+vpGsks++nral+lAaLa+ +    sti++ L+s+D++ ml+al++Lg    ++d  +++++v+g   +
  gi|121639209|ref|YP_979433.1|   8 TAPTPVRATVTVPGSKSQTNRALVLAALAAAQgrgaSTISGALRSRDTELMLDALQTLG---LRVDGVGSELTVSG---R 81 
                                    57899************************9999999***********************...799999********...9 PP

                                    -EE-HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET...SS- CS
                  EPSP_synthase  78 feapeelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg...lkl 154
                                    +e++ ++ +d+g +gt+lr++++l+al s++v+++Gd+++r RPi++lldaLr+lG+ ++   g + +p++v+g   l +
  gi|121639209|ref|YP_979433.1|  82 IEPGPGARVDCGLAGTVLRFVPPLAALGSVPVTFDGDQQARGRPIAPLLDALRELGVAVD---G-TGLPFRVRGngsLAG 157
                                    999999******************************************************...4.789*****999**** PP

                                    BEEEEETSSTTHHHHHHHHHHHTTSBS.EEEEES..-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE CS
                  EPSP_synthase 155 kgveikaevsSqqvtsllllaallaeg.ttelee..lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyv 231
                                    ++v i+a+ sSq+v+ lll+aa +++g t+++++  l+s+p+i +t+ ml+++g++i++ +t+++++v++++ + + ++ 
  gi|121639209|ref|YP_979433.1| 158 GTVAIDASASSQFVSGLLLSAASFTDGlTVQHTGssLPSAPHIAMTAAMLRQAGVDIDD-STPNRWQVRPGPVAAR-RWD 235
                                    ***********************************************************.89999********999.*** PP

                                    --B-HHHHHHHHHHHHHTT-EEEEES--GGGGH.HH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTS CS
                  EPSP_synthase 232 vegDassAayflvaAaitggevtvenvginslq.Gdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdea 310
                                    +e+D+++A+ fl aA+++gg+v+++++++ s+q +d  ++ +il++++a + + +++  v+gp+g+++ dvd++ + +++
  gi|121639209|ref|YP_979433.1| 236 IEPDLTNAVAFLSAAVVSGGTVRITGWPRVSVQpAD--HILAILRQLNAVVIHADSSLEVRGPTGYDGFDVDLRAVGELT 313
                                    *********************************888..8888*************999999999**************** PP

                                    BHGGGHHHHHH..HHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHH CS
                  EPSP_synthase 311 ptlavlaafae..gttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamala 388
                                    p +a+laa+a+  + ++++gia+lr +etdrlaa+ te+++lG++++e++dgl  i+a+  l+++ +++y+DhR+ama a
  gi|121639209|ref|YP_979433.1| 314 PSVAALAALASpgSVSRLSGIAHLRGHETDRLAALSTEINRLGGTCRETPDGLV-ITATP-LRPGIWRAYADHRMAMAGA 391
                                    ***********9999*************************************98.78887.******************* PP

                                    HHHHHSBSEEEEETTHHHHHHSSSHHH CS
                  EPSP_synthase 389 laglvaegeveiddiectdksfpefee 415
                                    ++gl+++g ve+ddi++t+k+ pef +
  gi|121639209|ref|YP_979433.1| 392 IIGLRVAG-VEVDDIAATTKTLPEFPR 417
                                    ********.****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3160.00
//
Query:       gi|121639210|ref|YP_979434.1|  [L=330]
Description: hypothetical protein BCG_3351 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-40  138.5   0.0    2.5e-40  138.1   0.0    1.2  1  RsgA_GTPase   RsgA GTPase
    6.9e-06   26.1   0.0    1.3e-05   25.2   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    2.8e-05   24.6   0.1    5.2e-05   23.8   0.1    1.4  1  ABC_tran      ABC transporter
    0.00045   20.6   1.0     0.0012   19.3   0.2    2.1  2  AAA_16        AAA ATPase domain
     0.0047   16.6   0.0     0.0091   15.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0069   16.7   0.1      0.013   15.8   0.1    1.4  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.017   14.7   0.1       0.95    9.0   0.1    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.027   14.6   0.3      0.074   13.2   0.1    1.8  2  AAA_33        AAA domain
      0.028   14.6   0.0      0.046   13.9   0.0    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.087   12.7   0.0       0.18   11.7   0.0    1.5  1  NACHT         NACHT domain
       0.12   11.9   0.0       0.19   11.3   0.0    1.3  1  Ras           Ras family
       0.16   11.3   0.2       0.37   10.1   0.1    1.6  2  AIG1          AIG1 family
       0.17   11.8   0.0       0.34   10.8   0.0    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.19   11.3   0.0       0.89    9.1   0.0    2.0  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.21   11.4   0.1       0.51   10.2   0.1    1.6  1  HNH_repeat    Homing endonuclease repeat
       0.24   11.8   0.0       0.41   11.1   0.0    1.3  1  RNA_helicase  RNA helicase
        0.3   10.3   0.0       0.43    9.8   0.0    1.2  1  Septin        Septin


Domain annotation for each model (and alignments):
>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   0.0   2.4e-43   2.5e-40       3     166 ..      97     267 ..      95     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 2.4e-43
                                    --S-EETTTT..........EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHH CS
                    RsgA_GTPase   3 eRknelvrpk..........vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeel 72 
                                    +R+++l+r++          vaN dqllivv+l++p  ++ l+dr+L++a + g++p+++l+K+Dl+  e     + +++
  gi|121639210|ref|YP_979434.1|  97 PRRTVLRRTAddtdptervvVANADQLLIVVALADPPPRTGLVDRALIAAYAGGLTPILCLTKTDLAPAEP----FGKQF 172
                                    8999**999999*******************************************************9999....99999 PP

                                    HHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETT. CS
                    RsgA_GTPase  73 ealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelae. 151
                                    ++l+++v++  ++  + l ++++ll++k++vl+G+SGvGKStL+n+l+pe++ ++gev e  grG+hT+t++  l+l + 
  gi|121639210|ref|YP_979434.1| 173 ADLELTVTAAGVD--DPLLAVADLLAGKITVLLGHSGVGKSTLVNRLVPEADRAVGEVTE-IGRGRHTSTRSVALPLGDt 249
                                    9999999998888..99*****************************************98.8***********9998777 PP

                                    ...TEEEESS-SSSS--G CS
                    RsgA_GTPase 152 ...gglliDtPGfreldl 166
                                       +g++iDtPG+r+++l
  gi|121639210|ref|YP_979434.1| 250 lsgSGWVIDTPGIRSFGL 267
                                    7779***********997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.2e-08   1.3e-05       3      58 ..     201     263 ..     199     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                                    EEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEE......ETTEEEEEEECGGCSS CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvk......lkgkeielvDtpGlie 58 
                                    +++G++ vGKStL+n+l+ e    v++    g  r++ ++ v+      l+g +  ++DtpG i 
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEaDRAVGEVTeiGRGRHTSTRSVAlplgdtLSG-SGWVIDTPG-IR 263
                                    689***************8753444444433777788888777665554334.679******.53 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1     5e-08   5.2e-05       8      43 ..     194     229 ..     191     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-08
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeil 43 
                                    l +g++++++G++G GKStL++ l  + + + Ge++
  gi|121639210|ref|YP_979434.1| 194 LLAGKITVLLGHSGVGKSTLVNRLVPEADRAVGEVT 229
                                    5689**************************999994 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.5   1.6e+03     132     150 ..      64      82 ..      55     146 .. 0.56
   2 !   19.3   0.2   1.1e-06    0.0012      22      52 ..     197     225 ..     187     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.5
                         AAA_16 132 rderplvlvlDdlqwadea 150
                                    + +r+ ++v Dd++ + + 
  gi|121639210|ref|YP_979434.1|  64 ELGRTPIVVGDDVDVVGDL 82 
                                    5555555555555533331 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekdg 52 
                                    g   +++l G+sGvGKs+lv++l  ++ ++ 
  gi|121639210|ref|YP_979434.1| 197 G--KITVLLGHSGVGKSTLVNRLVPEADRAV 225
                                    4..789**************99887777773 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.6e-06    0.0091      22      39 ..     196     214 ..     190     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-06
                         AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                    +g +t+l G+sG+GKSTl+
  gi|121639210|ref|YP_979434.1| 196 AGkITVLLGHSGVGKSTLV 214
                                    46699*************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.2e-05     0.013       6      30 ..     198     222 ..     195     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqld 30 
                                    +i+v+ G+sG+GK+tl++rl+ ++d
  gi|121639210|ref|YP_979434.1| 198 KITVLLGHSGVGKSTLVNRLVPEAD 222
                                    799*****************98875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.096     1e+02      94     138 ..     120     166 ..     111     186 .. 0.66
   2 ?    9.0   0.1    0.0009      0.95       7      29 ..     201     223 ..     198     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.096
                                    -SEEEEEEETTTB..STHHHHHHHHHHHHTTTEEEEEEESCGST.HHH CS
                       GTP_EFTU  94 lDgavlvvdaveG..vepqteevlrlalkegvpiivfiNKmDrl.kae 138
                                    +D  ++vv+ ++    +    + l  a + g+ +i++++K D +   e
  gi|121639210|ref|YP_979434.1| 120 ADQLLIVVALADPppRTGLVDRALIAAYAGGLTPILCLTKTDLApA-E 166
                                    555566665554422333345667778888999*********9962.2 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0009
                                    EEEESTTSSHHHHHHHHHHHTTS CS
                       GTP_EFTU   7 giighvDhGKtTLtdrLlyktga 29 
                                    +++gh   GK+TL+ rL+ ++ +
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEADR 223
                                    679**************966654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   3.4e+03      62      78 ..      89     105 ..      53     127 .. 0.65
   2 ?   13.2   0.1     7e-05     0.074       2      22 ..     200     220 ..     199     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                         AAA_33  62 larkalsagrnvildat 78 
                                    lar++++a r ++l+ t
  gi|121639210|ref|YP_979434.1|  89 LARIVRRAPRRTVLRRT 105
                                    44455555555555444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkk 22 
                                    ++l G++G+GKstl+ rl+ +
  gi|121639210|ref|YP_979434.1| 200 TVLLGHSGVGKSTLVNRLVPE 220
                                    5789*************9854 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.4e-05     0.046       3      21 ..     201     219 ..     198     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                    EEESSTTSSHHHHHHCHCT CS
                            Roc   3 vlvGdsgvGKtsllkrfve 21 
                                    vl+G sgvGK++l++r+v 
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVP 219
                                    89**************985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.18       3      24 ..     200     221 ..     198     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                     +l G +G+GK+tL+ +l+ ++
  gi|121639210|ref|YP_979434.1| 200 TVLLGHSGVGKSTLVNRLVPEA 221
                                    6899*************99765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.19       3      22 ..     201     220 ..     198     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                    EEEESTTSSHHHHHHHHHHS CS
                            Ras   3 vlvGdsavGKtslllrfvkd 22 
                                    vl+G s+vGK++l++r v +
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPE 220
                                    99*************98865 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.7   4.9e+03     141     159 ..      84     102 ..      82     116 .. 0.78
   2 ?   10.1   0.1   0.00035      0.37       4      62 ..     201     265 ..     198     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.7
                                    HH-HHHHHHHHHTTTSEEE CS
                           AIG1 141 sspeaLkevlkecgnRvvl 159
                                    + p++L ++++   +R+vl
  gi|121639210|ref|YP_979434.1|  84 GRPDTLARIVRRAPRRTVL 102
                                    5789999999999999887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                                    EEESSTTSSHHHHHHHHHTS--.SS--TTTS---SS-EEEEE.EETTEEEE....EEE--SCCCT CS
                           AIG1   4 vlvGktgnGkSaTgNsilgkka.Fesklsaqsvtkkcqkksr.twdgkkin....ViDTPglfdl 62 
                                    vl+G +g+GkS+ +N ++ +      ++++ +  ++ +++s   + g +++    ViDTPg+ + 
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEADrAVGEVTEIGRGRHTSTRSVaLPLGDTLSgsgwVIDTPGIRSF 265
                                    8***************9865441223333333333333333336677777555559999999664 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.34       3      33 ..     201     231 ..     199     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                           MobB   3 givgksgsGKTtLleklipelkarglrvgti 33 
                                     + g+sg GK tL+++l+pe  +   +v  i
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEADRAVGEVTEI 231
                                    578****************988776666655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   1.2e+03     144     156 ..     154     166 ..     144     180 .. 0.81
   2 ?    9.1   0.0   0.00085      0.89       2      23 ..     199     220 ..     198     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                    EEEEE-HHHHCHC CS
                           cobW 144 llvlnKtDlldee 156
                                    +l l+KtDl+++e
  gi|121639210|ref|YP_979434.1| 154 ILCLTKTDLAPAE 166
                                    6789******998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                                    EEEEEESTTCCHHHHHHHHHCT CS
                           cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                    +tvl G  G GK+tL+n+l+ +
  gi|121639210|ref|YP_979434.1| 199 ITVLLGHSGVGKSTLVNRLVPE 220
                                    799****************943 PP

>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00049      0.51      10      19 ..      61      70 ..      61      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                     HNH_repeat 10 qAaELGRtPk 19
                                   +A ELGRtP 
  gi|121639210|ref|YP_979434.1| 61 RARELGRTPI 70
                                   799******6 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.41       2      24 ..     201     223 ..     200     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                    +l G+sg+GKStl+++L+ +  +
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEADR 223
                                    689*************9877655 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00041      0.43       8      31 ..     201     224 ..     197     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                                    EEEEBTTSSCCCCCCTTSSSS--- CS
                         Septin   8 mvvGesglGkttlintlfetdlie 31 
                                    ++ G+sg+Gk+tl+n l+ + +  
  gi|121639210|ref|YP_979434.1| 201 VLLGHSGVGKSTLVNRLVPEADRA 224
                                    457**************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2265.29
//
Query:       gi|121639211|ref|YP_979435.1|  [L=427]
Description: linoleoyl-CoA desaturase desA3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-37  128.7   5.2    4.5e-37  128.3   5.2    1.1  1  FA_desaturase    Fatty acid desaturase
  ------ inclusion threshold ------
      0.069   13.2   0.7       0.15   12.1   0.7    1.5  1  Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   5.2     5e-41   4.5e-37       2     252 ..      69     339 ..      66     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 5e-41
                  FA_desaturase   2 swlalllalllglfllgitg.slaHeaaHgalfkkrklnrwlndllgal..lglplgisysawrisH.lrHHay..tngp 75 
                                    +w+  +  l+lg+   +i    ++H+++Hg        + w+nd   +     + +  s+++wr++H ++HH+y  + g 
  gi|121639211|ref|YP_979435.1|  69 AWWTGA--LTLGVA-KIIENmEIGHNVMHG-------QWDWMNDPEIHSstWEWDMSGSSKHWRYTHnFVHHKYtnILGM 138
                                    355555..9****9.888888********9.......9****8877666225555556****************9999** PP

                  FA_desaturase  76 deDpdlaplalsrfeglfry.llrlllgllvlg...wllalvlglwlrrlarrrapsksrrrk........wrllawlll 143
                                    d+D+ +++l+ +r +++ ry +++ ++ + ++    w +al+++++ ++++ r ++ + + r         +++   +++
  gi|121639211|ref|YP_979435.1| 139 DDDVGYGMLRVTRDQRWKRYnIFNVVWNTILAIgfeWGVALQHLEIGKIFKGRADREAAKTRLrefsakagRQVFKDYVA 218
                                    **********9*********955555555555555699999999866666666665555555577778888999999999 PP

                  FA_desaturase 144 llawlglwlalllllglalllwlvplllllfllalvlnyveHyg................gdwgerqvetsasirsaswl 207
                                    ++a++ l  ++ + + l   + +v+ ++ +++   v  ++ H+                 g+w++rq+ +sa+++ a++ 
  gi|121639211|ref|YP_979435.1| 219 FPALTSLSPGATYRSTLT--ANVVANVIRNVWSNAV-IFCGHFPdgaekftktdmigepkGQWYLRQMLGSANFN-AGPA 294
                                    999999999999999888..8899999999988888.9****99*******************************.**** PP

                  FA_desaturase 208 lnlltgnlnyHieHHlfPgvpwyrLpelhrrlrellpehglpyrs 252
                                    l++++gnl+++ieHHl+P++p +rL+e++ r+re++++++lpy++
  gi|121639211|ref|YP_979435.1| 295 LRFMSGNLCHQIEHHLYPDLPSNRLHEISVRVREVCDRYDLPYTT 339
                                    *******************************************86 PP

>> Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   1.7e-05      0.15      14      32 ..     233     251 ..     228     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                Chlorovi_GP_rpt  14 atiPgtqniDIiGNVvatg 32 
                                    +t+++++++++i+NV +++
  gi|121639211|ref|YP_979435.1| 233 STLTANVVANVIRNVWSNA 251
                                    689*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3077.49
//
Query:       gi|121639212|ref|YP_979436.1|  [L=380]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-10   40.1   0.5    4.5e-10   39.3   0.5    1.4  1  Fer2           2Fe-2S iron-sulfur cluster binding domain
    1.1e-09   38.5   0.0    1.9e-09   37.8   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    1.7e-08   35.1   0.0    3.2e-08   34.2   0.0    1.5  1  NAD_binding_1  Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.053   13.6   0.0        0.1   12.7   0.0    1.4  1  NAD_binding_6  Ferric reductase NAD binding domain
        0.3   11.2   1.6        1.3    9.2   0.1    2.4  3  MlrC_C         MlrC C-terminus


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.5   1.3e-13   4.5e-10       5      76 ..     307     371 ..     302     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.3e-13
                                    TEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGGSE CS
                           Fer2   5 gkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCqti 76 
                                    gk v +   d  t+l+da e + g+ +p++C++g C++C+v+++eg+v        +g++ + g ++ +C++ 
  gi|121639212|ref|YP_979436.1| 307 GKSVAA---DAATSLMDAGEGA-GVQLPFGCRMGICQSCVVDLVEGHVrD----LRTGQRHEPGTRVQTCVSA 371
                                    444444...44888******88.*************************52....3456666667778999876 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.3e-13   1.9e-09      28      97 ..      88     161 ..      70     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.3e-13
                                    ----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEE...EE--TT-HHHHHH.HCS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  28 lglpvGqhvflrlkikgeaviRsYtpissenekGelell...vkvypgGkmsqaL.delkigdtleikGPlGkf 97 
                                    +++ +Gq++ + l ++g   +RsY+++ss+ ++G   ++   vk +p+G +s +L   +k+g+ +++ +P+G+f
  gi|121639212|ref|YP_979436.1|  88 FDYQPGQYIGIGLLVDGCWRWRSYSLTSSPAASGSARMVtvtVKAMPEGFLSTHLvAGVKPGTIVRLAAPQGNF 161
                                    6899***************************999866543339999*********888**************99 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.9e-12   3.2e-08       1     104 [.     173     266 ..     173     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.9e-12
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT.EEEEEEEESSCTTTSSSEESSHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg.rlkvvavvsreeagweggkgrvqd 79 
                                    ++ +G+Gi+Pv+s+lr+++++ ++ t vv ++ ++t +d+++ +el +la+ +pg rl v ++      +    +gr++ 
  gi|121639212|ref|YP_979436.1| 173 FLTAGSGITPVMSMLRTLVRR-NQITDVVHLHSAPTAADVMFGAELAALAADHPGyRLSVRET------RA---QGRLDL 242
                                    6789****************9.888******************************66544444......22...455555 PP

                                    HHHHHHHHHSSTTEEEEEECSHHHH CS
                  NAD_binding_1  80 alleellslkkeethvyvCGppgMi 104
                                      + + ++ +  e ++  CGp+g  
  gi|121639212|ref|YP_979436.1| 243 TRIGQQVP-DWRERQTWACGPEGVL 266
                                    55555555.4666777777777665 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.9e-05       0.1       4      28 ..     171     195 ..     170     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6   4 vllvagGiGitpfisilkdllkksk 28 
                                    +l++++G+Gitp++s+l+ l+++ +
  gi|121639212|ref|YP_979436.1| 171 ILFLTAGSGITPVMSMLRTLVRRNQ 195
                                    6899****************99877 PP

>> MlrC_C  MlrC C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.26   9.4e+02      14      49 ..     181     216 ..     175     241 .. 0.78
   2 ?   -2.2   0.0       1.1   3.9e+03      41      60 ..     288     307 ..     283     311 .. 0.78
   3 ?    9.2   0.1   0.00035       1.3      39      95 ..     312     370 ..     306     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                                    ----HHHHHHHHH-TT--EEEEEE-HHHHHHHHHH- CS
                         MlrC_C  14 gdvtalLrellargekkvlvasivDpeavaaaaaag 49 
                                      v+ +Lr l++r++ + +v +   p a+++++ a+
  gi|121639212|ref|YP_979436.1| 181 TPVMSMLRTLVRRNQITDVVHLHSAPTAADVMFGAE 216
                                    557899999999999777777777788877777665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                    HHHHHHHH-TT-EEEEEES- CS
                         MlrC_C  41 avaaaaaagvGatveltlGg 60 
                                    av   a ag+G+tv+++  g
  gi|121639212|ref|YP_979436.1| 288 AVSKTAPAGAGGTVTFARSG 307
                                    77888889999999987555 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHH-TT-EEEEEES-SS-TTS.--E.EEEEEEEEEEEEEEE--SSTTTT.-E CS
                         MlrC_C  39 peavaaaaaagvGatveltlGgkvdalhgepv.eltgtVealsdgrytaegpmltg.qe 95 
                                    ++a+  +++ag+Ga v+l +G +++  ++  v  ++g+V+ l+ g++++ g + +   +
  gi|121639212|ref|YP_979436.1| 312 ADAATSLMDAGEGAGVQLPFGCRMGICQSCVVdLVEGHVRDLRTGQRHEPGTRVQTcVS 370
                                    67899999*******************999995589************97766555344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 2041.51
//
Query:       gi|121639213|ref|YP_979437.1|  [L=140]
Description: L-lysine-epsilon aminotransferase lat' [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0023   16.7   0.0     0.0028   16.4   0.0    1.1  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.6e-07    0.0028       8      50 ..      34      77 ..      28      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-07
                                   -SCEEEEEEEBTEEEET.TS-EEEESSHHHHTTTT-BT-HHHHH CS
                    Aminotran_3  8 nlllvitkaeGvyltdv.dgkrylDlvssiavvnlGhahPkvvk 50
                                    ++l++t++ G+yl+d+  g+rylD+    a+ +lG + P++v+
  gi|121639213|ref|YP_979437.1| 34 DIVLDLTRSGGSYLVDAiTGRRYLDMFTFVASSALGMNPPALVD 77
                                   567899*********8549**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 800.04
//
Query:       gi|121639214|ref|YP_979438.1|  [L=150]
Description: AsnC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-13   48.3   0.2    8.4e-13   47.7   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    5.8e-13   48.6   0.1    1.4e-12   47.4   0.1    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      9e-13   47.8   4.3    1.6e-12   47.0   4.3    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      1e-06   28.5   0.6      2e-06   27.6   0.6    1.5  1  MarR_2          MarR family
    0.00012   21.7   0.6    0.00024   20.9   0.6    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00015   21.6   0.0     0.0003   20.6   0.0    1.5  1  MarR            MarR family
    0.00038   20.4   0.8    0.00084   19.4   0.1    1.8  2  HTH_20          Helix-turn-helix domain
    0.00046   20.3   2.3    0.00057   20.0   0.5    2.0  2  HTH_28          Helix-turn-helix domain
    0.00054   19.9   1.1    0.00067   19.6   0.1    1.7  2  HTH_11          HTH domain
     0.0015   18.3   0.9     0.0023   17.8   0.2    1.6  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0028   17.2   0.6     0.0054   16.3   0.6    1.5  1  HTH_CodY        CodY helix-turn-helix domain
     0.0053   16.3   0.1     0.0082   15.7   0.1    1.3  1  HTH_47          winged helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.027   14.3   0.1    1.7  1  HTH_10          HTH DNA binding domain
      0.021   14.3   0.7      0.067   12.7   0.7    1.9  1  Sigma70_r4      Sigma-70, region 4
      0.026   14.5   0.1      0.054   13.5   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.026   14.2   0.0      0.065   12.9   0.0    1.6  1  HTH_41          Helix-turn-helix domain
      0.034   13.8   1.6      0.036   13.7   0.4    1.6  2  GntR            Bacterial regulatory proteins, gntR family
      0.066   13.0   0.3       0.24   11.2   0.1    1.9  2  LexA_DNA_bind   LexA DNA binding domain
      0.069   13.7   0.0       0.14   12.7   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
      0.079   13.1   0.0       0.24   11.6   0.0    1.9  3  MIase           Muconolactone delta-isomerase
       0.18   11.9   0.0       0.37   10.8   0.0    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.2   9.9e-16   8.4e-13       1      48 []       5      52 ..       5      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 9.9e-16
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ld++dr + ++L +++r + +eLA r glS+s+v  r++rLe+ G+++
  gi|121639214|ref|YP_979438.1|  5 LDDIDRILVRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   799***899*************************************95 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.7   5.7e+03      48      60 ..       6      18 ..       4      23 .. 0.73
   2 !   47.4   0.1   1.6e-15   1.4e-12      10      75 .]      78     141 ..      71     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.7
                                   HHHHHHHHHTTTT CS
                 AsnC_trans_reg 48 ealerflreklas 60
                                   ++++r+l+++la+
  gi|121639214|ref|YP_979438.1|  6 DDIDRILVRELAA 18
                                   6788888888875 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 1.6e-15
                                    TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                 AsnC_trans_reg  10 peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                    p q +++ ++l+ ++eV++cy+v+G+ +y+l v+v++ +ale++l++ +++  +v rt+++i+l+t
  gi|121639214|ref|YP_979438.1|  78 PSQPDDAPARLEHIEEVESCYSVAGEESYVLLVRVASARALEDLLQR-IRTTANV-RTRSTIILNT 141
                                    33599999*************************************99.*****99.8999999975 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   4.3   1.9e-15   1.6e-12       1      42 []       5      46 ..       5      46 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.9e-15
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   LD+iDr ++++L +d+R + +eLA r GlS s+v+ RvrrLe
  gi|121639214|ref|YP_979438.1|  5 LDDIDRILVRELAADGRVTLSELATRAGLSVSAVQSRVRRLE 46
                                   8****************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.6   2.3e-09     2e-06      11      52 ..      13      52 ..       4      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-09
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                     +L++ ++  +t +ela r gls sav+ +++rL+++G v+
  gi|121639214|ref|YP_979438.1| 13 VRELAADGR--VTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   566777776..****************************995 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.6   2.8e-07   0.00024      15      49 ..      18      52 ..      15      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-07
                                   TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   a++++tlselA r+gl+ S+v   ++ L+ +G v+
  gi|121639214|ref|YP_979438.1| 18 ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   67889***************************996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-07    0.0003       9      47 ..      13      51 ..      11      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                                   HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                   +r l+  g  ++seLa + g+s s+v   ++rLe +G +
  gi|121639214|ref|YP_979438.1| 13 VRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVV 51
                                   577888999****************************87 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   9.8e-07   0.00084      16      54 ..      13      51 ..       5      55 .. 0.93
   2 ?   -1.5   0.0       3.3   2.8e+03      24      37 ..     115     128 ..     108     137 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.8e-07
                                   HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                         HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                    r+La ++ +t+sela r +ls + +  ++r Le+ g v
  gi|121639214|ref|YP_979438.1| 13 VRELAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVV 51
                                   6899*******************************9988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                                    TB-HHHHHHHHTS- CS
                         HTH_20  24 gltaselaerldls 37 
                                    ++ +++l +r++++
  gi|121639214|ref|YP_979438.1| 115 ARALEDLLQRIRTT 128
                                    44444444444443 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   6.6e-07   0.00057       6      41 ..      13      50 ..      10      58 .. 0.86
   2 ?   -1.1   0.1       2.5   2.1e+03      25      38 ..     114     127 ..     109     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.6e-07
                         HTH_28  6 iklla.aGh.svreaArelgisrrtvyrWikryeegGi 41
                                   +++la +G+ + +e+A + g+s + v++ ++r+e+ G+
  gi|121639214|ref|YP_979438.1| 13 VRELAaDGRvTLSELATRAGLSVSAVQSRVRRLESRGV 50
                                   5565548999*************************996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                         HTH_28  25 srrtvyrWikryee 38 
                                    s r + ++++r ++
  gi|121639214|ref|YP_979438.1| 114 SARALEDLLQRIRT 127
                                    66788888888776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.8e-07   0.00067       6      44 ..      13      50 ..       9      59 .. 0.88
   2 ?   -2.4   0.1       5.6   4.8e+03      26      31 ..     130     136 ..     118     138 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.8e-07
                         HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   ++ L +a+g ++ +eLA + ++S ++v+ ++++Le+ gv
  gi|121639214|ref|YP_979438.1| 13 VREL-AADGRVTLSELATRAGLSVSAVQSRVRRLESRGV 50
                                   4557.99****************************9994 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                         HTH_11  26 nv.Srrt 31 
                                    nv +r+t
  gi|121639214|ref|YP_979438.1| 130 NVrTRST 136
                                    3335555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.6e-06    0.0023      17      53 ..      16      52 ..      12      63 .. 0.92
   2 ?   -2.4   0.0       5.3   4.6e+03      25      31 ..     115     121 ..     104     131 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                   L + g+ t +e+a ++g++ s v++ +r+Le++G+V+
  gi|121639214|ref|YP_979438.1| 16 LAADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   6678999*****************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.3
                                    HCHHCCC CS
                           TrmB  25 adeiaee 31 
                                    a+ +   
  gi|121639214|ref|YP_979438.1| 115 ARALEDL 121
                                    3333333 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   6.3e-06    0.0054       2      37 ..      19      54 ..      18      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-06
                       HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiiesr 37
                                   +Gr+t s++a r G+  s +   +r+Les G++   
  gi|121639214|ref|YP_979438.1| 19 DGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQGY 54
                                   79******************************9865 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   9.6e-06    0.0082      43      77 ..      18      52 ..       2      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-06
                                   -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 43 aDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   aDG+ +L ++A r+gl++ +v++ +r+L+  g+++
  gi|121639214|ref|YP_979438.1| 18 ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   9******************************9985 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.2e-05     0.027      23      49 ..      21      47 ..      18      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                         HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                   rvtl+eLA + G+s s+++ ++r+ es
  gi|121639214|ref|YP_979438.1| 21 RVTLSELATRAGLSVSAVQSRVRRLES 47
                                   89**********************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   7.9e-05     0.067      18      43 ..      19      44 ..       3      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4 18 geglTleEIgerlgiSrerVrqiekr 43
                                   +   Tl+E++ r g+S ++V ++ +r
  gi|121639214|ref|YP_979438.1| 19 DGRVTLSELATRAGLSVSAVQSRVRR 44
                                   6678************7766655554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.3e-05     0.054      21      54 ..      21      55 ..       6      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                   ++t  elA + Gl+ + v    ++L+ +g+++  +
  gi|121639214|ref|YP_979438.1| 21 RVTLSELATRAGLSVSAVQSRVRRLESRGVVQgYS 55
                                   68999**************************9433 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-05     0.065       8      37 ..      23      52 ..      21      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                         HTH_41  8 tIeelakeleLSvGlvQkALklLeddkais 37
                                   t +ela   +LSv  vQ+ +  Le+ ++++
  gi|121639214|ref|YP_979438.1| 23 TLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   789*************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   4.2e-05     0.036      11      55 ..       9      52 ..       4      55 .. 0.95
   2 ?   -3.0   0.0       6.8   5.8e+03       6      14 ..     118     126 ..     114     129 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                   HHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           GntR 11 edIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                   ++Il  el++  +  + +eLa++ g s + v+   rrLe++g+v+
  gi|121639214|ref|YP_979438.1|  9 DRILVRELAADGRV-TLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   589999********.****************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                                    HHHHHHHHH CS
                           GntR   6 yerLredIl 14 
                                     e L ++I+
  gi|121639214|ref|YP_979438.1| 118 LEDLLQRIR 126
                                    455666665 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.24      27      57 ..      23      52 ..      10      57 .. 0.90
   2 ?   -0.8   0.0       1.6   1.3e+03      35      52 ..     110     127 ..     109     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                   -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                  LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                   +  e+a + gl+  sav+++ ++Le +G+++
  gi|121639214|ref|YP_979438.1| 23 TLSELATRAGLS-VSAVQSRVRRLESRGVVQ 52
                                   567999999997.9***************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                    HTS-.HHHHHHHHHHHHH CS
                  LexA_DNA_bind  35 lglkSpsaveehLkaLer 52 
                                    ++++S++a e  L++ ++
  gi|121639214|ref|YP_979438.1| 110 VRVASARALEDLLQRIRT 127
                                    577899999999999876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.14       6      49 ..      10      52 ..       5      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                         HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                   +++++ ++  ++r++l++l+ r  ++ s++ + +++L+ +G+v+
  gi|121639214|ref|YP_979438.1| 10 RILVRELA-ADGRVTLSELATRAGLSVSAVQSRVRRLESRGVVQ 52
                                   55666677.89*******************************94 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.2   5.3e+03      32      41 ..      14      23 ..       9      46 .. 0.69
   2 ?   -2.2   0.0       5.7   4.9e+03      28      41 ..      39      52 ..      18      58 .. 0.74
   3 ?   11.6   0.0   0.00028      0.24      40      72 ..      94     126 ..      83     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.2
                          MIase 32 qelqrqGklv 41
                                   +el+++G++ 
  gi|121639214|ref|YP_979438.1| 14 RELAADGRVT 23
                                   6777777653 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                          MIase 28 karaqelqrqGklv 41
                                   + r+++l+++G ++
  gi|121639214|ref|YP_979438.1| 39 QSRVRRLESRGVVQ 52
                                   56677777777765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                          MIase  40 lvrlwrvvgeyanisifdvedndeLhelLssLP 72 
                                    + + + v+ge + + +++v+++ +L++lL+ + 
  gi|121639214|ref|YP_979438.1|  94 VESCYSVAGEESYVLLVRVASARALEDLLQRIR 126
                                    5678999**********************9865 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.37      18      44 ..      19      45 ..      11      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                        HTH_Mga 18 eksltldelakeLglseltlqsdiseL 44
                                   +++ tl+ela++ gls +++qs+++ L
  gi|121639214|ref|YP_979438.1| 19 DGRVTLSELATRAGLSVSAVQSRVRRL 45
                                   57889*****************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 834.09
//
Query:       gi|121639215|ref|YP_979439.1|  [L=415]
Description: hypothetical protein BCG_3357 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.3e-103  345.3   0.0   3.8e-103  345.1   0.0    1.0  1  DUF1338     Domain of unknown function (DUF1338)
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.054   13.7   0.0    1.6  1  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


Domain annotation for each model (and alignments):
>> DUF1338  Domain of unknown function (DUF1338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.1   0.0  4.2e-107  3.8e-103       1     324 []      11     371 ..      11     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 345.1 bits;  conditional E-value: 4.2e-107
                        DUF1338   1 elaralldalsekYlarvpkvralvelvraanaaslssegek..tdelerllvedHgAiRtggvtnegidalarlfaslG 78 
                                    +l++++++ ls++Y a+vp++++lve+++++n++ l+++++    ++l+r+++e+HgAiR+g  ++++++a+a+lfa++G
  gi|121639215|ref|YP_979439.1|  11 QLRARFAAGLSAMYAAEVPAYGTLVEVCAQVNSDYLTRHRRAerLGSLQRVTAERHGAIRVG--NPAELAAVADLFAAFG 88 
                                    689*********************************999877889999**************..**************** PP

                        DUF1338  79 yvpvgeydlp..ekklpahwtaFrpp.eedlaknlpRvFiSeLrve..dlsdaaqraieayvlaareiftkrllellekl 153
                                    + pvg+ydl+  e+ +p+++taFrp+ +++la+n++RvF+S+L +e  +  da++r++ +++la+r++f+++ll+ ++ +
  gi|121639215|ref|YP_979439.1|  89 MLPVGYYDLRtaESPIPVVSTAFRPIdANELAHNPFRVFTSMLAIEdrRYFDADLRTRVQTFLARRQLFDPALLAQARAI 168
                                    **********88899************99****************98889****************************** PP

                        DUF1338 154 eedggltagdaeafvaealetfrwqkeapvakadyelLaaeseyaAwvl.vngyaiNHlTprvldidalqafleergikl 232
                                    ++dgg++a+da afva+a+++f+++ + pv+k++y++L+++s++aA+++ v +++iNHlTprvldid+l+++++ergi++
  gi|121639215|ref|YP_979439.1| 169 AADGGCDADDAPAFVAAAVAAFALS-REPVEKSWYDELSRVSAVAADIAgVGSTHINHLTPRVLDIDDLYRRMTERGITM 247
                                    *************************.5699************************************************** PP

                        DUF1338 233 kdeieGppt.vspdglLrQtSfkAleeevkfaegsgeev.gavparfgEieqRgvlltnkgrnlydellkea........ 302
                                     d+i+Gpp+   pd+lLrQtSf+Al+e++ f++++g+++ g +++rfgE+e+Rgv+lt++gr+ y++ +++a        
  gi|121639215|ref|YP_979439.1| 248 IDTIQGPPRtDGPDVLLRQTSFRALAEPRMFRDEDGTVTpGILRVRFGEVEARGVALTPRGRERYEAAMAAAdpaavwat 327
                                    ************************************9999**************************************** PP

                        DUF1338 303 ...................g...epilyedFlpgnAagIFestl 324
                                                       g    pi+yedFlp++AagIF+s+l
  gi|121639215|ref|YP_979439.1| 328 hfpstdaemaaqglayyrgGdpsAPIVYEDFLPASAAGIFRSNL 371
                                    ************99999972567*******************96 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.1e-06     0.054      73     123 ..     219     283 ..     175     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
                                    TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE..............EEEETTS CS
                     Glyoxalase  73 tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysf..............yfrDpdG 123
                                    +  h+++++  v d+++ ++r+ e+g+   ++++  + +++ ++              +frD+dG
  gi|121639215|ref|YP_979439.1| 219 GSTHINHLTPRVLDIDDLYRRMTERGITMIDTIQGPPRTDGPDVllrqtsfralaeprMFRDEDG 283
                                    347***********************999998887777777776677777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 2120.11
//
Query:       gi|121639216|ref|YP_979440.1|  [L=494]
Description: piperideine-6-carboxilic acid dehydrogenase pcd [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.7e-134  446.5   0.3   1.1e-133  446.2   0.3    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.2   0.3  5.9e-138  1.1e-133       9     459 ..      22     474 ..      15     477 .. 0.96

  Alignments for each domain:
  == domain 1  score: 446.2 bits;  conditional E-value: 5.9e-138
                                    EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                         Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                    ++   P+tg+v+ +++  t+e++d+a+aaA+++f aw+++pa+ R+++++++ +ll++++++la+l t e+Gk +aear+
  gi|121639216|ref|YP_979440.1|  22 LPASTPITGDVLFSIAPTTPEQADHAIAAAAATFTAWRSTPAPVRGALVARLGELLTAHQQDLATLVTVEVGKITAEARG 101
                                    77889*************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHH CS
                         Aldedh  89 eveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpl 167
                                    ev+e+idv+++ ++l ++l+g++++s ++g++ l +++PlGvvg+It++NfP++++aw++a al++G tvv+KP+e tpl
  gi|121639216|ref|YP_979440.1| 102 EVQEMIDVCQFSVGLSRQLYGRTIASeRAGHRLLETWHPLGVVGVITAFNFPVAVWAWNTAVALVCGDTVVWKPSELTPL 181
                                    ***********************99977**************************************************** PP

                                    HHHHHHHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEE CS
                         Aldedh 168 salllaelfeea....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpli 243
                                    +al++  l+ +a    g P+ v  ++ g g+e g++lv++p+v+++s tGs+++g+++  + a+++ rv+lElGG+n++i
  gi|121639216|ref|YP_979440.1| 182 TALACQALLSRAaadvGAPAAVGGLLLG-GAERGAQLVDDPRVALLSATGSVRMGQQVGPRVARRFGRVLLELGGNNAAI 260
                                    **99988887777777************.*************************************************** PP

                                    E-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHH CS
                         Aldedh 244 vledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekveky 323
                                    v ++aDl+ av+ iv++a g+aGQ+C++ +rl+v++s++d++v+++v a+++l +gdp ++dt vGPli+ea+++ + + 
  gi|121639216|ref|YP_979440.1| 261 VAPSADLELAVRCIVFAAAGTAGQRCTSLRRLIVHRSVADDVVARVVGAYRQLAIGDPSAPDTLVGPLIHEAAYRDMVAA 340
                                    ******************************************************************************** PP

                                    HHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE- CS
                         Aldedh 324 veeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvft 403
                                    +e+a+ +g +++ G  r+e g    y+v+P v+  ++++ +i+ +E+F+P+l+v++++d++eai++ N+ + GL++++ft
  gi|121639216|ref|YP_979440.1| 341 LERARTDGGEVIGGD-RREVGSPGAYYVAPAVVR-MPSQTAIVATETFAPILYVLTYDDLDEAIALNNAVPQGLSSSIFT 418
                                    **********98877.545665666********9.8******************************************** PP

                                    SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEE CS
                         Aldedh 404 kdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytev 459
                                    +dl++ae++ ++ ++G  ++N  t ga+   +fgG kq+g Gre+g++++++y++ 
  gi|121639216|ref|YP_979440.1| 419 TDLREAEHFLDQSDCGIANVNIGTSGAEIGGAFGGEKQTGGGRESGSDAWKAYMRR 474
                                    ***********************88888889**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2706.60
//
Query:       gi|121639217|ref|YP_979441.1|  [L=269]
Description: hypothetical protein BCG_3359c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-26   91.4   0.0    6.1e-26   91.0   0.0    1.1  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   3.4e-30   6.1e-26       2     121 ..      54     214 ..      45     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 3.4e-30
                                    xxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143   2 rDirklagvrdpeelrk.......................................glverlppwsespnskkrlrkspK 42 
                                    rD +++++ +++++l++                                       +l++r+p+w  s+n++kr++++pK
  gi|121639217|ref|YP_979441.1|  54 RDAADVSNLQRIADLPRlirllaarsaselnlsslatdaeipvrtlppyldlletlYLIDRIPAW--STNLSKRVVDRPK 131
                                    5666666666667777788899*******************************************..************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  43 lyfvDtGLlvallgldkeelleds....enkGallEnlVaqeLlky...sekegaklyyyrdkngaEvDfvielkggkiv 115
                                    ++++D+GL++ l +++++     +    +  Ga++E++V++eL+++   s++  ++l++yrd++gaEvD+++e+++g i+
  gi|121639217|ref|YP_979441.1| 132 VLLLDSGLAARLVNVSPTGAG--PhanpNAAGAIIETFVIAELRRQlgwSQQ-APRLFHYRDRDGAEVDLILETADGLIA 208
                                    ****************99843..234669*******************5555.9************************** PP

                                    xxxxxx RF
                        DUF4143 116 piEvKs 121
                                    +iE+Ks
  gi|121639217|ref|YP_979441.1| 209 AIEIKS 214
                                    *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1496.54
//
Query:       gi|121639218|ref|YP_979442.1|  [L=221]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-15   56.3   0.2    3.8e-15   55.4   0.2    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
     0.0033   17.6   0.0     0.0047   17.1   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
  ------ inclusion threshold ------
      0.065   13.9   0.2       0.46   11.2   0.2    2.4  1  NUDIX-like   NADH pyrophosphatase-like rudimentary NUDIX doma


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2   6.3e-19   3.8e-15       1      47 []      17      63 ..      17      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6.3e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+ ++e+f++r yd++ ++eIA+rAGvs++++Y+yFp+K++ ++a+
  gi|121639218|ref|YP_979442.1| 17 LLALGAEVFGKRPYDEVRIDEIAERAGVSRALMYHYFPDKRAFFAAV 63
                                   68889***************************************997 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.8e-07    0.0047      11      66 ..      11      74 ..       1     103 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.8e-07
                                   HHHHHHHHH.HHHHH......--S-HHHHHHHHTS-HHHHHHHH.H-HHHHH.HHHHHHHHHHHT CS
                    HTH_Tnp_1_2 11 kQkkaaell.vendy......ekltldeiaeevgvsrsTlykWk.kkkeFie.yvnelaeeflee 66
                                   + ++ aell    +       +++ +deiae  gvsr+ +y++  +k++F +  v+  a+++ ++
  gi|121639218|ref|YP_979442.1| 11 QDRR-AELLaLGAEVfgkrpyDEVRIDEIAERAGVSRALMYHYFpDKRAFFAaVVKDEADRLYAA 74
                                   4444.4444233333344444*********************99899998761456666666554 PP

>> NUDIX-like  NADH pyrophosphatase-like rudimentary NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   7.8e-05      0.46      33      97 ..     102     220 ..       2     221 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-05
                     NUDIX-like  33 l.........vgkdseelvfLGldeggapvfAvdvsareee....................................... 64 
                                    +         vg ++  +v+LG d+++++ +   + +r +e                                       
  gi|121639218|ref|YP_979442.1| 102 QnpeaawaayVGLGRSDPVLLGIDDEAKNRQMEHIMSRIAEvvsgidrdntldpeverdlrviihgwlaftfelcrqrim 181
                                    15555666667888899999998888777777777777777777777778888888888888888888888888888899 PP

                     NUDIX-like  65 ......ikeaeeeggafvelRavmlalsaedaalaaqAr 97 
                                          +++a+++++a  ++ +++ +++ae a ++a+Ar
  gi|121639218|ref|YP_979442.1| 182 dpstdaERLADACAHALLDAISRLPQIPAELADAMATAR 220
                                    99999899******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1205.22
//
Query:       gi|121639219|ref|YP_979443.1|  [L=1513]
Description: atp-dependent helicase lhr [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-70  236.2   0.8    8.1e-70  234.5   0.1    2.1  2  DEAD_assoc    DEAD/H associated
    3.9e-26   91.9   0.0    7.7e-26   90.9   0.0    1.5  1  DEAD          DEAD/DEAH box helicase
    1.9e-14   53.9   0.0    3.3e-12   46.7   0.0    3.0  3  Helicase_C    Helicase conserved C-terminal domain
    2.8e-05   24.2   0.0    6.3e-05   23.0   0.0    1.6  2  ResIII        Type III restriction enzyme, res subunit
     0.0005   20.4   0.1     0.0064   16.8   0.1    2.5  1  AAA_22        AAA domain
    0.00099   18.7   0.4     0.0048   16.5   0.3    2.3  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.017   14.6   0.0       0.03   13.8   0.0    1.3  1  PhoH          PhoH-like protein
       0.14   12.1   0.1       0.35   10.8   0.1    1.6  1  Phage_base_V  Type VI secretion system, phage-baseplate injec


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   0.1   3.6e-73   8.1e-70       1     191 []     659     851 ..     659     851 .. 0.94
   2 ?   -1.2   0.0      0.65   1.5e+03      27      63 ..     998    1034 ..     976    1057 .. 0.83

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 3.6e-73
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlp......... 71 
                                    +Ptd+tllvErfrdelgdwr+++hsp+G rv+ +lal++ +rl++r+gid + +a+D+gi++ l      p         
  gi|121639219|ref|YP_979443.1| 659 VPTDSTLLVERFRDELGDWRVILHSPYGLRVHGPLALAVGRRLRDRYGIDEKPTASDNGIMVRL------Pdtvsageds 732
                                    8*************************************************************66......3333344554 PP

                     DEAD_assoc  72 ....llldellellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpl 147
                                        +     l  +++de++ +++ ++++s+lf++rFre Aaralllprr+pg+r plwqqr+raa+Ll+var+ypdfp+
  gi|121639219|ref|YP_979443.1| 733 ppgaE-----LFVFDADEIDPIVTTEVAGSALFASRFRESAARALLLPRRHPGRRSPLWQQRQRAARLLEVARKYPDFPI 807
                                    44432.....56799***************************************************************** PP

                     DEAD_assoc 148 lleavrevledqlDlerlaellrriaageirvvevetprpSpfA 191
                                    +le+vre+l++++D++ l el++ria++++rv+e et++pSpfA
  gi|121639219|ref|YP_979443.1| 808 VLETVRECLQNVYDVPILVELMARIAQRRVRVAEAETAKPSPFA 851
                                    *******************************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.65
                     DEAD_assoc   27 fGrrvnealalllaarlsrrfgidvqvaanDdgivll 63  
                                     f   v ++l+ ll +  + +++++ ++aa+  g+ l 
  gi|121639219|ref|YP_979443.1|  998 FTEAVADPLGELLGRYARTHTPFTTAAAAARFGLGLR 1034
                                     6678999*******************99998888774 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   3.5e-29   7.7e-26       1     170 [.      28     212 ..      28     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3.5e-29
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                    t+ Qa+a+ +i +g++ lv a+TGsGKTla+++ +l++++ +    ++  ++++l+v+P+++La ++ +nl++ +  ++ 
  gi|121639219|ref|YP_979443.1|  28 TAAQASAWAAIADGDNTLVIAPTGSGKTLAAFLWALDSLAGSepmsERPAATRVLYVSPLKALAVDVERNLRTPLAGLTr 107
                                    689************************************8879999999999************************7555 PP

                                    ...........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ...........lrvlliiggvaardqlskldngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfin 143
                                               +rv +  g+++    ++ +++ +d++++tp+ l+ +l s  + +l  v+++++DE++ +   +++ ++ 
  gi|121639219|ref|YP_979443.1| 108 laerqglpapqIRVGVRSGDTPPALRRQLVSQPPDVLITTPESLFLMLtSAARQTLTGVQTVIIDEIHAIAATKRGAHLA 187
                                    667777777666666555555554444445455*************886666677************************* PP

                                    HHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 144 rilnqlpqitcdgklqrqvivlSATlp 170
                                      l++l++ +++ ++q   i lSAT+ 
  gi|121639219|ref|YP_979443.1| 188 LSLERLDDLSSRRRAQ--RIGLSATVR 212
                                    ******9999888855..*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.79   1.8e+03      37      90 ..     110     171 ..      81     180 .. 0.77
   2 ?    2.9   0.0     0.061   1.4e+02       6      54 ..     265     308 ..     260     319 .. 0.73
   3 !   46.7   0.0   1.5e-15   3.3e-12      44     108 ..     335     399 ..     325     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.79
                                    HHT.....TSTEEEESTTSTHHHHHHHHHHHH.....TTSSSEEEESGGGTSSSTSTTESEEEE CS
                     Helicase_C  37 ekk.....gikvavlhgelpqnereeileqfn.....kgesdvLiatdvaerGidipkvnlVin 90 
                                    e++     +i+v v  g++p   r++ ++q         es +L+ t++a +   +++v++Vi+
  gi|121639219|ref|YP_979443.1| 110 ERQglpapQIRVGVRSGDTPPALRRQLVSQPPdvlitTPESLFLMLTSAARQT--LTGVQTVII 171
                                    44446666899999999********9999998666655566688888888874..456777776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.061
                                    HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHH CS
                     Helicase_C   6 llellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqne 54 
                                    l++l+   e+++ +++f+n+++ +e  +l  + ++i++a++  el  + 
  gi|121639219|ref|YP_979443.1| 265 LVDLI---ESHNSTIVFANSRRLAE--RLTARLNEIHAARCGIELAPDT 308
                                    45555...8999**********997..5555556787777766666555 PP

  == domain 3  score: 46.7 bits;  conditional E-value: 1.5e-15
                                    EEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  44 avlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                     ++hg++++++r  + e+ ++g+ + ++at+ +e Gid+  v+lVi++++p +v+s  qriGR+g
  gi|121639219|ref|YP_979443.1| 335 RAHHGSISKEQRAVVEEDLKRGQLKAVVATSSLELGIDMGAVDLVIQVQAPPSVASGLQRIGRAG 399
                                    578*************************************************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.8e-08   6.3e-05      22     169 ..      39     211 ..       1     213 [. 0.71
   2 ?   -3.9   0.0       5.4   1.2e+04      55      74 ..     273     292 ..     267     309 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.8e-08
                                    .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHG.......GGGTGG....... CS
                         ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleef.......kkflseayke... 84 
                                     +  + l+ ++TG+GKTl a + + ++l+ +++ +      ++l + p k+l    ++++       +            
  gi|121639219|ref|YP_979443.1|  39 ADGDNTLVIAPTGSGKTLAAfLWALDSLAGSEPMSerpaatRVLYVSPLKALAVDVERNLrtplaglT-------RLaer 111
                                    566789999********98844455566666555599********************99955555442.......22233 PP

                                    ........GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...... CS
                         ResIII  85 ........igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...... 148
                                              ++ sgd+  a  ++  s+  ++l+tt +sl   +        ++  +  + +iiDE H ++a k      
  gi|121639219|ref|YP_979443.1| 112 qglpapqiRVGVRSGDTPPAlrRQLVSQPPDVLITTPESLFLML----TSAARQTLTGVQTVIIDEIHAIAATKrgahla 187
                                    334444445556777777778777789999**************....5555566666778999********86666666 PP

                                    .TTHHH..HHT---SEEEEEESS- CS
                         ResIII 149 .swrei..lekfkeavllglTATp 169
                                     s +++  l + ++a ++gl+AT 
  gi|121639219|ref|YP_979443.1| 188 lSLERLddLSSRRRAQRIGLSATV 211
                                    67777733333355*********7 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.4
                                    .-EEEEESSHHHHHHHHHHG CS
                         ResIII  55 ekflflvprkslleqtleef 74 
                                    + ++++++++ l e++  ++
  gi|121639219|ref|YP_979443.1| 273 NSTIVFANSRRLAERLTARL 292
                                    25666677777766666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.9e-06    0.0064       8     114 ..      44     198 ..      39     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..........................................erpevvfv 45 
                                    ++v++++G+GKT+ +   +    + ++                                              ++++++v
  gi|121639219|ref|YP_979443.1|  44 TLVIAPTGSGKTLAAFLWALDSLAGSE--PmserpaatrvlyvsplkalavdvernlrtplagltrlaerqgLPAPQIRV 121
                                    789999999999887655554443333..2447899999999999999999999999999999999999999999999** PP

                         AAA_22  46 tlpsstsskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhlr...s.......eealeeLrs 114
                                     + s+ ++  l+r+l+++  + l +   + e l+ +l+ a+r++ + ++ +iiDE++ +    +        e l +L+s
  gi|121639219|ref|YP_979443.1| 122 GVRSGDTPPALRRQLVSQPPDVLIT---TPESLFLMLTSAARQTLTgVQTVIIDEIHAIAatkRgahlalsLERLDDLSS 198
                                    *************************...****************999***********9876524445222333333333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.1e-06    0.0048      18      98 ..      27     116 ..      10     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                         AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlravgea 96 
                                    p + +   +  + + g+ +l+++++g+GKt +a  +al+ + G++   + +p   +Vlyvs   + + +++r lr  ++ 
  gi|121639219|ref|YP_979443.1|  27 PTAAQASAWAAI-ADGDNTLVIAPTGSGKTLAAFLWALDSLAGSEPMSE-RPAATRVLYVSPLKAlAVDVERNLRTPLAG 104
                                    555555555555.67999*********************9988754444.58999*****97766556777777776666 PP

                         AAA_25  97 l..........r 98 
                                    l          +
  gi|121639219|ref|YP_979443.1| 105 LtrlaerqglpA 116
                                    644444444440 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05      0.03       6      45 ..      28      67 ..      24      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHH CS
                           PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealk 45
                                   t++Q+++  a+ + d + +i+p+G+GKt+ a   a++ l 
  gi|121639219|ref|YP_979443.1| 28 TAAQASAWAAIADGDNTLVIAPTGSGKTLAAFLWALDSLA 67
                                   889********************************99876 PP

>> Phage_base_V  Type VI secretion system, phage-baseplate injector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00016      0.35      35      92 ..      17      77 ..      10      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                   XXXE..EEXXSXBSSSBXXXXXXTTXEEEEEEXXT.TTXXEEEEEEEXXSSSXXSXXBTS- CS
                   Phage_base_V 35 tdwl..rwlaarAGktrswrapsvGEqvvllspsG.elatavvlpglysdafpapsnsada 92
                                    dw    ++a  A ++  w a+  G++ ++++p G   + a +l +l s a ++p ++  a
  gi|121639219|ref|YP_979443.1| 17 RDWFtsTFAAPTAAQASAWAAIADGDNTLVIAPTGsGKTLAAFLWALDSLAGSEPMSERPA 77
                                   5565224778899**********************4456699*********9999765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.99u 0.33s 00:00:01.32 Elapsed: 00:00:00.56
# Mc/sec: 8153.14
//
Query:       gi|121639220|ref|YP_979444.1|  [L=255]
Description: endonuclease VIII nei [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.5   0.1    3.4e-11   43.8   0.1    1.5  1  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina
    1.3e-10   41.1   0.0      2e-10   40.5   0.0    1.3  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
    0.00059   19.7   3.4     0.0016   18.3   3.4    1.8  1  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.014   15.3   4.8      0.032   14.1   4.8    1.7  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   7.7e-15   3.4e-11       1     102 [.       1      94 [.       1     125 [. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 7.7e-15
                                    X--HHHHHHHHHHHHHHHTT-EEEEEEE-SSHHHTSTHHHHHT.T-.SEEEEEEEEETTEEEEEE..EEEEEEE-TTTEE CS
                 Fapy_DNA_glyco   1 MPElpEVetvrrglrrhllgkkiakvevlkdktlrgspaafak.alkgrkiasvgrrGKyllleldggevlvvhlgmtGr 79 
                                    MPE   V +++++lrrhl g++++++++      r   + fa+  l+g+++++v +rGK+l++++ g+ ++  hl+m G+
  gi|121639220|ref|YP_979444.1|   1 MPEGDTVWHTAATLRRHLAGRTLTRCDI------R--VPRFAAvDLTGEVVDEVISRGKHLFIRT-GTASIHSHLQMDGS 71 
                                    9***************************......2..34455549********************.99************ PP

                                    ESS........TTEEEEEEEGGG CS
                 Fapy_DNA_glyco  80 llikeaeeeppkhtkvrlelddg 102
                                    +++ + +    + +++ le +++
  gi|121639220|ref|YP_979444.1|  72 WRVGNRPVRVDHRARIILEANQQ 94 
                                    ***44444444566677776533 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   4.5e-14     2e-10       1      63 [.     123     186 ..     123     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.5e-14
                                    ---BTTSTTS-HHHHHHHH.HT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS- CS
                           H2TH   1 Lgpeplseaftvdalaerl.kkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlaksls 63 
                                    Lgp+ l+++ + + +a++l     r+i ++LLDq++ aG+GN+y +E+ f +++ P+ + + + 
  gi|121639220|ref|YP_979444.1| 123 LGPDLLADDWDPQRAAANLiVAPDRPIAEALLDQRVLAGIGNVYCNELCFVSGVLPTAPVSAVA 186
                                    899999999999887777615669********************************99877765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.4   3.6e-07    0.0016       3      29 ..     230     254 ..     230     255 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-07
                                    -TTT--B-EEE--TT-SS-EEEETTTT CS
                      Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                    C+ CGt +++ +   D+r R++CpaC+
  gi|121639220|ref|YP_979444.1| 230 CRRCGTLIAYDT--TDERVRYWCPACQ 254
                                    **********99..7***********7 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.8   7.1e-06     0.032       4      28 ..     230     254 ..     227     255 .] 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                                    -TTT--BBEEEECTTEEEEE-TTTT CS
                   zf-FPG_IleRS   4 CpRCwryiervgqagrstyfCprCq 28 
                                    C+RC++ i+    ++r  y+Cp Cq
  gi|121639220|ref|YP_979444.1| 230 CRRCGTLIAYDTTDERVRYWCPACQ 254
                                    ************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1454.12
//
Query:       gi|121639221|ref|YP_979445.1|  [L=304]
Description: esterase lipoprotein lpqC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-10   41.5   1.0    1.5e-10   41.0   1.0    1.3  1  Esterase_phd  Esterase PHB depolymerase
    9.6e-06   25.2   1.1    2.7e-05   23.8   0.2    2.1  3  Peptidase_S9  Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.0   1.7e-14   1.5e-10       2     137 ..      43     174 ..      42     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.7e-14
                   Esterase_phd   2 ayrlylppGarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavv 81 
                                    +yrl++pp  +     lv+ lhG   +     a t ++++ad   + v+yp+   ++ a++        dr+   +   +
  gi|121639221|ref|YP_979445.1|  43 SYRLHVPPAEPS---GLVISLHGGGGTGAGQEALTDFDAVADAADLLVVYPDGYDKSWADGRG--ASPADRRHLDDVGFL 117
                                    6**********9...89*******999999999*********************999999865..468899999****** PP

                   Esterase_phd  82 valvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhsG.lalGeaa 137
                                    val+  lv++  + +  v+ +G+s G+ +++ la    d faava  +G l +G + 
  gi|121639221|ref|YP_979445.1| 118 VALAAKLVHDFDIAPGHVFATGMSNGGFMSNRLACDRADIFAAVAPVAGtLGVGVTC 174
                                    ********************************************9666524566555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.3   2.7e+03      17      31 ..      57      71 ..      52      82 .. 0.76
   2 !   23.8   0.2     3e-09   2.7e-05      48      99 ..     117     168 ..      91     175 .. 0.88
   3 ?   -1.3   0.0      0.14   1.3e+03     144     162 ..     180     198 ..     172     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.3
                                   EEEE--TTSSTTHCH CS
                   Peptidase_S9 17 vvvanirGsggyGea 31
                                   v+  ++ G++g G++
  gi|121639221|ref|YP_979445.1| 57 VISLHGGGGTGAGQE 71
                                   677788888888886 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3e-09
                                    HHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE-- CS
                   Peptidase_S9  48 fiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvv 99 
                                    ++a a +l+  + + + ++++tG S+GG++++ ++ +r d+F+a++ +++ +
  gi|121639221|ref|YP_979445.1| 117 LVALAAKLVHDFDIAPGHVFATGMSNGGFMSNRLACDRADIFAAVAPVAGTL 168
                                    588999999999*********************************9999875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.14
                                    -EEEEEEETT-SSS-THHH CS
                   Peptidase_S9 144 pplLlihGlaDdrvppaea 162
                                    +++L  hG+aD  vp++ +
  gi|121639221|ref|YP_979445.1| 180 VSVLEAHGTADPLVPFNGG 198
                                    678889*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1671.78
//
Query:       gi|121639222|ref|YP_979446.1|  [L=970]
Description: arylsulfatase atsB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-101  340.2   0.0   1.5e-101  339.8   0.0    1.1  1  Sulfatase        Sulfatase
    1.5e-09   38.1   6.1    2.9e-09   37.1   6.1    1.5  1  DUF1269          Protein of unknown function (DUF1269)
     0.0039   16.8   0.2       0.35   10.4   0.0    2.4  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.093   12.7   0.0    2.0  2  DUF4994          Domain of unknown function
      0.034   13.9  12.2        1.2    8.9   3.0    2.9  2  Gly-zipper_OmpA  Glycine-zipper domain
      0.073   13.4   0.1       0.33   11.3   0.0    2.1  2  Aft1_HRA         Aft1 HRA domain
      0.083   12.6  16.2       0.34   10.7  16.2    2.1  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
       0.11   12.7   8.1       0.23   11.8   8.1    1.4  1  DUF456           Protein of unknown function (DUF456)
       0.14   12.5   7.1        0.3   11.4   7.1    1.6  1  Acyl-CoA_dh_2    Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   0.0  7.8e-105  1.5e-101       1     308 [.     212     634 ..     212     635 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 7.8e-105
                                    EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT..... CS
                      Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg..... 75 
                                    pnv+++l+dd+g+g+ +++gg ++ tp+l+rla++gl++++f+++a +csp+raalltgr++h++g++s++e++g     
  gi|121639222|ref|YP_979446.1| 212 PNVLIVLIDDAGFGGPDTFGGAIR-TPTLSRLAQNGLIYNRFHVTA-VCSPTRAALLTGRNHHRVGFGSVCEFPGpypgy 289
                                    9**********************9.9*******************8.********************************* PP

                                    .HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.......CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC. CS
                      Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.......nrgfdrflgfptgsaalkdpekseyngevlrv. 146
                                       +p+++a+Lp++l+++GY t+a+gkwhl++++ q+++        ++gfd+f+gfp+g+a ++dp  s++n  ++ + 
  gi|121639222|ref|YP_979446.1| 290 sAVRPRSCAALPRILRDNGYVTGAFGKWHLTPDNVQGAAGpfdnwplGWGFDHFWGFPSGAAGQYDPIISQDNSVIGIPe 369
                                    *************************************9889********************************999998* PP

                                    ....TTTTCSHHHHHHHHHHHHH...HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.......... CS
                      Sulfatase 147 ....ppeggysddrlldealefl...larn.dkpfflylatlapHappeapdeyakkyatffddgseaar.......... 208
                                        + +++y+ d+l+d+a+e+l   +a+n +kp++ly+at a+Hap+++++e+a+ky+++fddg++ +r          
  gi|121639222|ref|YP_979446.1| 370 gsgeDGRPYYFPDDLTDKAIEWLhtvRAQNaTKPWMLYYATGATHAPHHVFKEWADKYRGEFDDGWDVYRqktferqkrl 449
                                    **************************66666*************************************9999******** PP

                                    ...............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEE.ESSSSCCCG. CS
                      Sulfatase 209 ...............................qlleaylnsveyvDdligrvlaaLeenglldntlvvft.SDhgaslee. 255
                                                                   +++e+++++ e++D+++gr+l+a+e++g++dntlv+++ +D+gas+e+ 
  gi|121639222|ref|YP_979446.1| 450 giippdaelterpdlfpawdsmseaqkrlfaRQMEVFAGFSENADWNVGRLLDAIEDLGESDNTLVFYIwGDNGASMEGt 529
                                    ******************************************************************************** PP

                                    ..................................................HHTTSSSCTTCSSSHHHHBEEEEEEETTTS CS
                      Sulfatase 256 ..................................................sngplrggkganayeggtrvPllvwwpgek 285
                                                                                      sn+pl++gk+++++ ggtr+Pl+v+wp ++
  gi|121639222|ref|YP_979446.1| 530 ntgsfnemtflngldldaerqlelieqyggiaalgdeftaphfasawahaSNTPLQWGKQMASHLGGTRDPLVVAWPARI 609
                                    ******************************************************************************** PP

                                    HC..EEECSEEEGGGHHHHHHHHTT CS
                      Sulfatase 286 ap..rvseelvshiDlfptildlag 308
                                    +p  rv+++++++iD++pt+l+++g
  gi|121639222|ref|YP_979446.1| 610 RPdgRVRSQFTHCIDIAPTVLAAIG 634
                                    **********************998 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   6.1   1.4e-12   2.9e-09       1      79 [.      66     144 ..      66     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.4e-12
                        DUF1269   1 AlsGalwGllvGllflnP..llGaavGAaaGAlvgalsdvgidddflkelgeklkpgtsalfllvekatvdkvlealakl 78 
                                    A++Ga +Gl +Gl  ++P  l++aa+GAa+GAl+g+++++ i+ ++ +++g++l +g++ +++++e +   +  +ala+ 
  gi|121639222|ref|YP_979446.1|  66 AAWGAGVGLAIGL--FSPalLASAALGAATGALAGTFAHHRIKTGLADKIGQALAAGRAVVIAVTEAQGRLEAGQALASS 143
                                    89**********7..68865667*******************************************99988888888665 PP

                        DUF1269  79 g 79 
                                     
  gi|121639222|ref|YP_979446.1| 144 P 144
                                    5 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        31      19      58 ..     233     271 ..     214     278 .. 0.79
   2 !   10.4   0.0   0.00018      0.35     128     234 ..     414     524 ..     342     554 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                                    S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-H CS
                   Phosphodiest  19 e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyP 58 
                                      ++p l++La++g+ +   r ++ ++  p  a+l+TG++ 
  gi|121639222|ref|YP_979446.1| 233 AiRTPTLSRLAQNGLIYN--RFHVTAVCSPTRAALLTGRNH 271
                                    458***************..999***************985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                    TBHHSBTCT.CSTTS..CHHHHHHHHHHHHHHHCHTHSHHHHHCT...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHH CS
                   Phosphodiest 128 etppryleddfnakv..pledkvdkavlqtwldaafakvvlekel...ekpdlllvyleetDtvgHkfGpdspevedalr 202
                                    + p  ++ +++++k+  +++d  d   +q+ ++++++   ++      e+pdl+  + +   ++   f  + + ++   +
  gi|121639222|ref|YP_979446.1| 414 HAPHHVF-KEWADKYrgEFDDGWDV-YRQKTFERQKRLGIIPPDAeltERPDLFPAWDSMSEAQKRLFARQMEVFAGFSE 491
                                    2222222.44555555555555553.4445577777666666555889*************9999999545555888889 PP

                                    HHHHHHHHHHHHHHHTTGTTTEEEE.EEES--- CS
                   Phosphodiest 203 rvDkaigdLlealderglsaetnii.lvSDHGm 234
                                    ++D ++g+Ll+a+++ g s++t ++ + +D G+
  gi|121639222|ref|YP_979446.1| 492 NADWNVGRLLDAIEDLGESDNTLVFyIWGDNGA 524
                                    9***************88888876526666665 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   2.8e+03      15      35 ..      42      60 ..      31      68 .. 0.81
   2 ?   12.7   0.0   4.7e-05     0.093      69      97 ..     719     747 ..     700     748 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                        DUF4994 15 allGkdkkdReyvieqaankt 35
                                    l+Gkd+++ +++++ +  + 
  gi|121639222|ref|YP_979446.1| 42 VLIGKDAEGSPVLVDTG--NR 60
                                   689***********988..44 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.7e-05
                        DUF4994  69 qLydlkkdegekenvaekhpekvkelkel 97 
                                     Ly l +d ++ +n+a++hp+kv el++l
  gi|121639222|ref|YP_979446.1| 719 ELYYLPDDFSQAKNLAAEHPDKVAELTQL 747
                                    69************************986 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.9   0.00064       1.3      27      42 ..      64      79 ..      57      81 .. 0.88
   2 ?    8.9   3.0   0.00063       1.2       3      15 ..      86      98 ..      84     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00064
                Gly-zipper_OmpA 27 tGAaiGAasGavaGll 42
                                   +GAa GA++G+ +Gl+
  gi|121639222|ref|YP_979446.1| 64 RGAAWGAGVGLAIGLF 79
                                   6*************87 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00063
                Gly-zipper_OmpA  3 gAavGAalGAaaG 15
                                   +Aa GAa+GA+aG
  gi|121639222|ref|YP_979446.1| 86 SAALGAATGALAG 98
                                   6777777777777 PP

>> Aft1_HRA  Aft1 HRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.33       6      52 ..      67     114 ..      63     122 .. 0.83
   2 ?   -2.3   0.0         3     6e+03      61      76 ..     268     291 ..     252     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                       Aft1_HRA   6 pWlatqslrsgPLSPAmLagPqqasq.spteesfesesfrtGfTPgts 52 
                                    +W+a  +l  g  SPA+La+ + +++ ++ + +f ++ ++tG+  + +
  gi|121639222|ref|YP_979446.1|  67 AWGAGVGLAIGLFSPALLASAALGAAtGALAGTFAHHRIKTGLADKIG 114
                                    7*****************998866551556999*********987766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                       Aft1_HRA  61 g........gggssfPapSpntaa 76 
                                    g        g+  +fP p p+ +a
  gi|121639222|ref|YP_979446.1| 268 GrnhhrvgfGSVCEFPGPYPGYSA 291
                                    234445555778899999998766 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  16.2   0.00017      0.34       9      44 ..      64     102 ..      60     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                    XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                Gly-zipper_YMGG   9 iGAaaGAvvGaliG...sgggkGAaiGAaaGalaGgaiG 44 
                                     GAa GA+vG +iG    +    Aa GAa+GalaG+ ++
  gi|121639222|ref|YP_979446.1|  64 RGAAWGAGVGLAIGlfsPALLASAALGAATGALAGTFAH 102
                                    477888888888887432334589***********8765 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.1   0.00011      0.23      60     117 ..      63     127 ..      57     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                         DUF456  60 skrgligaivGaivGffllpp......lGlllgpflgaflgEllrar..kdlreAlkaalgalvGf 117
                                     + +++ga+vG+ +G+f  p       lG+  g+++g+f+  ++ ++  +++ +Al+a++++++++
  gi|121639222|ref|YP_979446.1|  63 RRGAAWGAGVGLAIGLFS-PAllasaaLGAATGALAGTFAHHRIKTGlaDKIGQALAAGRAVVIAV 127
                                    57789**********973.31233455888888888888888888775455999999999999876 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.1   0.00015       0.3       3      66 ..      84     149 ..      82     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHHHC..TTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervr..assgekladdpatqlalaeaaarldAAralleraaarae 66 
                                    +a +alGaA +ala + ++ r +++  ++ g++la   a+ +a++ea+ rl+A +al  + ++++ 
  gi|121639222|ref|YP_979446.1|  84 LASAALGAATGALAGTFAHHRIKTGlaDKIGQALAAGRAVVIAVTEAQGRLEAGQALASSPMKSVA 149
                                    799******************999999999**************************9887777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (970 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.56
# Mc/sec: 5259.71
//
Query:       gi|121639223|ref|YP_979447.1|  [L=305]
Description: hypothetical protein BCG_3365c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-21   75.5   0.0    6.5e-21   75.1   0.0    1.1  1  PseudoU_synth_2  RNA pseudouridylate synthase
  ------ inclusion threshold ------
      0.071   13.0   0.1       0.13   12.2   0.1    1.3  1  DUF3659          Protein of unknown function (DUF3659)


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   7.2e-25   6.5e-21       1     160 []      93     237 ..      93     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 7.2e-25
                PseudoU_synth_2   1 dlvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkY 80 
                                    d+vvv+KP+ +++ p +      +++t     r+e    el++ hRLD+ t G+ll+++ +e     + +f++  vrK+Y
  gi|121639223|ref|YP_979447.1|  93 DIVVVDKPHFLATMPRG----RHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQTMFARGLVRKTY 168
                                    589**************....88999999999999************************************9999***** PP

                PseudoU_synth_2  81 lalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhlaa 160
                                    la  + ap     a+   +  +++k+ g  + + e +  +a+t ++ ++++         l++l++ tGr+hQ+Rvh+aa
  gi|121639223|ref|YP_979447.1| 169 LARAPVAP---GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVERIARD--------GLYRLTPTTGRTHQLRVHMAA 237
                                    ***86444...444444455556679999**********************........9******************96 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.5e-05      0.13      20      52 ..      27      63 ..      24      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                        DUF3659 20 nvvGrvve..G...dlkkLaGkkvdedGnivdedGnvi 52
                                    v+++++   G    +k LaG  vd+dG +vd+ G+v+
  gi|121639223|ref|YP_979447.1| 27 SVLAELTArfGvaaRAKVLAGEVVDDDGAVVDS-GTVL 63
                                   566666665644447899*************97.7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1690.41
//
Query:       gi|121639224|ref|YP_979448.1|  [L=221]
Description: phosphate-transport system transcriptional regulatory protein phoU 1 phoY1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-24   85.1   4.0    4.1e-14   52.8   1.0    2.1  2  PhoU           PhoU domain
  ------ inclusion threshold ------
      0.041   14.0   0.2      0.073   13.2   0.2    1.5  1  DUF4677        Domain of unknown function (DUF4677)
       0.12   12.0   0.0       0.22   11.2   0.0    1.4  1  Peptidase_S77  Prohead core protein serine protease
       0.13   12.1   0.0       0.42   10.4   0.0    1.9  2  KNTase_C       KNTase C-terminal domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   1.0   9.1e-18   4.1e-14       2      89 .]      17     104 ..      16     104 .. 0.97
   2 !   33.5   0.1   9.8e-12   4.4e-08       3      89 .]     123     204 ..     121     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 9.1e-18
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                     +m +++  ++++a +al e d  +a++vi++ ++i +++ ++e++++ +la + p++ +lre++s+++i+ d ER+g  
  gi|121639224|ref|YP_979448.1|  17 GEMCSLAGIAMKRATQALLEADIGAAEQVIRDHERIVAMRAQVEKEAFALLALQHPVSGELREIFSAVQIIADTERMGAL 96 
                                    58999*****************************************99999***************************** PP

                                    HHHHHHHH CS
                           PhoU  82 avniaerv 89 
                                    av+ia+++
  gi|121639224|ref|YP_979448.1|  97 AVHIAKIT 104
                                    *****986 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.8e-12
                                    HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                    +ma+++    d a ++l+++d   a ++ +rdd +d+l++ +   l+     + +++  +r  ++   + r  ER +Dha
  gi|121639224|ref|YP_979448.1| 123 DMAKVAIALGDSARQVLVNRDPQEAAQLHDRDDAMDDLHRHLLSVLI-----DREWRHGVRVGVETALLGRFFERFADHA 197
                                    79999999999****************************99966544.....3444445888899999************ PP

                                    HHHHHHH CS
                           PhoU  83 vniaerv 89 
                                    v++ +rv
  gi|121639224|ref|YP_979448.1| 198 VEVGRRV 204
                                    ***9985 PP

>> DUF4677  Domain of unknown function (DUF4677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.6e-05     0.073      55     109 ..      49     103 ..      29     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                        DUF4677  55 fedvramrgaldeqashiqvlsddvcanqraivsmcqimttaprqgllavvgnkg 109
                                     e + amr  ++++a  +  l   v  + r i s +qi++ + r g+lav  +k 
  gi|121639224|ref|YP_979448.1|  49 HERIVAMRAQVEKEAFALLALQHPVSGELREIFSAVQIIADTERMGALAVHIAKI 103
                                    67889********************************************987665 PP

>> Peptidase_S77  Prohead core protein serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.9e-05      0.22      46      93 ..     102     149 ..      93     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                                    -TTSEE--HHHHHHHHHHHHHHTTTTT--EEEBS--SSSS--GGGEEE CS
                  Peptidase_S77  46 nrnkrlypkkvlekavkdyineqvktkqalgelnhpsranvdpaeaai 93 
                                    +  +r yp++vl + v++   +  k   alg+       n dp eaa 
  gi|121639224|ref|YP_979448.1| 102 KITRREYPNQVLPEEVRNCFADMAKVAIALGDSARQVLVNRDPQEAAQ 149
                                    556899***************************************995 PP

>> KNTase_C  KNTase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.094   4.2e+02      15      59 ..      60     102 ..      49     106 .. 0.71
   2 ?   10.4   0.0   9.4e-05      0.42      28     102 ..      93     166 ..      74     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.094
                       KNTase_C  15 eeeefv.kaieealvgelyEfigKlrnvrkegdetalatlalqlAq 59 
                                    e+e f   a++  + gel E++  ++ +    d++ +  la+++A+
  gi|121639224|ref|YP_979448.1|  60 EKEAFAlLALQHPVSGELREIFSAVQII---ADTERMGALAVHIAK 102
                                    4555541467777788999999887777...777888888888886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.4e-05
                       KNTase_C  28 vgelyEfigKlrnvrkegdetalatlalq.lAqyaallvgLsnrklysssatvlkEaleLpdrpkgfdelvekvme 102
                                    +g l  +i+K+   r+e ++++l+ ++++ +A  a + ++L + ++ +   + ++Ea +L dr +++d+l +++++
  gi|121639224|ref|YP_979448.1|  93 MGALAVHIAKIT--RREYPNQVLPEEVRNcFADMAKVAIALGDSARQVLVNRDPQEAAQLHDRDDAMDDLHRHLLS 166
                                    666777888886..66999******99985899999********************************99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1205.04
//
Query:       gi|121639225|ref|YP_979449.1|  [L=585]
Description: glycerol-3-phosphate dehydrogenase glpD2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-48  164.2   5.3    8.8e-48  163.7   5.3    1.2  1  DAO            FAD dependent oxidoreductase
    5.5e-28   97.4   0.0    1.2e-27   96.3   0.0    1.6  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
    6.1e-10   38.7   7.1      1e-05   24.9   1.2    2.2  2  FAD_binding_2  FAD binding domain
      2e-09   37.4   1.4    9.9e-07   28.4   0.3    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    7.4e-08   32.0   2.1    4.4e-07   29.5   2.1    2.1  1  FAD_binding_3  FAD binding domain
    5.5e-05   22.5   0.7     0.0001   21.7   0.0    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00066   18.9   0.5    0.00066   18.9   0.5    1.7  2  GIDA           Glucose inhibited division protein A
    0.00098   19.3   1.0     0.0038   17.4   1.0    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0019   18.1   0.1     0.0037   17.2   0.1    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0044   17.6   2.7     0.0073   16.8   0.6    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0066   15.2   0.9       0.01   14.5   0.9    1.2  1  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.035   13.4   0.1    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.021   14.1   0.4      0.021   14.1   0.4    1.8  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   5.3   6.4e-51   8.8e-48       1     317 [.      37     366 ..      37     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 6.4e-51
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    dvv+iGGG++G+++A+++a+rg  V+l+e++ +++sg+S+r+s+++h+glryl++  e+  l++eal e++    +l+++
  gi|121639225|ref|YP_979449.1|  37 DVVVIGGGVVGSGCALDAATRGlkVALVEAR-DLASGTSSRSSKMFHGGLRYLEQL-EF-GLVREALYERELSLTTLAPH 113
                                    9******************************.7777***************99975.55.**********999999**** PP

                                    TSEEEEEEEEEES..SHHHHHHHH...HHHHHH.HHTTTTE.EEEEHHHHHHHSTTST..TTSEEEEETTEEEEEHHHHH CS
                            DAO  79 idyrrtGllslaa..deeeleald...kllall.leaglda.elldaeevrelepalp..gllgalfypdtgqvdpaklt 149
                                    +  + + l +l+      e+++++    l+++l ++  ++a + ++++ +++l+p+l+   l g++ y+d  +vd+a+ t
  gi|121639225|ref|YP_979449.1| 114 LVKPLPFLFPLTKrwW--ERPYIAagiFLYDRLgGAKSVPAqRHFTRAGALRLSPGLKrsSLIGGIRYYD-TVVDDARHT 190
                                    ***********85332..344433111444444755667774679**99******94445888*******.899****** PP

                                    HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.E.EEEE..EEE--GGGHHHH.HTT.CTTTSEEEEEE CS
                            DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttp.gen.d.aada..vVnaaGawsdll.gll.keldlpispvr 221
                                      +ar+a+  G+ ++  t+v++l +e+++v gv  r+++ g++ + +     vVna+G+w+d++ +l  ++ + ++++ +
  gi|121639225|ref|YP_979449.1| 191 MTVARTAAHYGAVVRCSTQVVALLREGDRVIGVGvRDSEnGAVaEvR--GhvVVNATGVWTDEIqALSkQRGRFQVRASK 268
                                    **********************9788889999977555557763223..356**********984444544478****** PP

                                    EEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGG.. CS
                            DAO 222 gqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad.eesgdddpevdeedidellealrklfPq.. 298
                                    g ++v+ p+++  vs     ++   ++++ +++v+p+   + ++G+t++ +  +  +p+++ +did++l  +++++ +  
  gi|121639225|ref|YP_979449.1| 269 GVHVVV-PRDR-IVSD---VAMI-LRTEKSVMFVIPWG-SHWIIGTTDTdWNLDLAHPAATKADIDYILGTVNAVLATpl 341
                                    ******.8766.3333...2333.899999******96.66889***96655666669******************8874 PP

                                    .GCGEEEEEEEEEE.E....TTSSE CS
                            DAO 299 .lgdvlrkwaGlrp.l....pdglp 317
                                      +d+   +aGlrp l    +d+  
  gi|121639225|ref|YP_979449.1| 342 tHADIDGVYAGLRPlLagesDDTSK 366
                                    449999********52443223333 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   8.4e-31   1.2e-27       1     124 [.     413     536 ..     413     538 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 8.4e-31
                                    --TTS---TT--.........TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHHHH CS
                          DAO_C   1 crTkklpLvGaenw..sknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvYav 78 
                                    ++T+k+ L+Ga+++    n+a ++ +  gl++ +++hL++rYGs +++vl++a++  +p+l +++++++ y++ e +Ya+
  gi|121639225|ref|YP_979449.1| 413 SITEKVSLLGADGYfaLVNQAEHVGALQGLHPYRVRHLLDRYGSLISDVLAMAAS--DPSLLSPITEAPGYLKVEAAYAA 490
                                    58**********98777777777777779*********************65555..579******************** PP

                                    HHS---SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHHTT--HH CS
                          DAO_C  79 rhEmartlvDvlaRRtrlafldadaalealpevaelmaeelgWdea 124
                                     +E a++l+D+laRR+r++++  ++++++++evae++a  lgW++a
  gi|121639225|ref|YP_979449.1| 491 AAEGALHLEDILARRMRISIEYPHRGVDCAREVAEVVAPVLGWTAA 536
                                    *******************************************987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.2   7.2e-09     1e-05       1      42 [.      37      78 ..      37      89 .. 0.93
   2 !   17.1   0.5   1.7e-06    0.0023     136     209 ..     182     254 ..     137     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.2e-09
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-- CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq 42
                                   Dv+ViG+G+ G  +Al aa +Glkva+ve  +  +g++  s+
  gi|121639225|ref|YP_979449.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSS 78
                                   9*******************************9999988775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.7e-06
                                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..... CS
                  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallke 209
                                    t+v+  +   +++++a ++g  ++ +t++++L++e++rv G+ v+++e+g   ++r + vv atg +   +++ 
  gi|121639225|ref|YP_979449.1| 182 TVVDDARHTMTVARTAAHYGAVVRCSTQVVALLREGDRVIGVGVRDSENGAVAEVRGHVVVNATGVWTD-EIQA 254
                                    5555566667788889999**********************************************9985.3333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.3   7.2e-10   9.9e-07       1      63 [.      37      99 ..      37     110 .. 0.89
   2 !    7.9   0.0    0.0012       1.7      98     144 ..     198     246 ..     157     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.2e-10
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiaref 63
                                   DvvV+GGg+ G  +A+ Aa +G kv+Lve r+   G++++   +   g +  eq+  g++re 
  gi|121639225|ref|YP_979449.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSSKMFHGGLRYLEQLEFGLVREA 99
                                   9***********************************999998888888777778888888774 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                   FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                    a +g  v   t++v+  +eg+r+ +v v+++e g   ++r++v++ ATg
  gi|121639225|ref|YP_979449.1| 198 AHYGAVVRCSTQVVALLREGDRVIGVGVRDSEnGaVAEVRGHVVVNATG 246
                                    5568889999**********************999*************8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.1   3.2e-10   4.4e-07       2     228 ..      36     304 ..      35     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.2e-10
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHT..T-HHHHHHHSEECCCCEEEEEE CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrql..Gledrilaegapnelmgealyn 78 
                                     dV+++G+G +G   al  +++G +v lve r+ ++ ++ r++ +    ++ l+ql  Gl +++l e    +l++ a   
  gi|121639225|ref|YP_979449.1|  36 FDVVVIGGGVVGSGCALDAATRGLKVALVEARDLASGTSsRSSKMFHGGLRYLEQLefGLVREALYER-ELSLTTLAP-- 112
                                    69**********************************9999*************986558877777666.222223332.. PP

                                    E..........................................CCCC....CEEEEEHH..CHHCST-CEE--HHHHHHH CS
                  FAD_binding_3  79 e..........................................lsdt....pkaradle..lesspervtvypqteleri 110
                                                                               + +       + +  +   + ++ r+++  +++    
  gi|121639225|ref|YP_979449.1| 113 HlvkplpflfpltkrwwerpyiaagiflydrlggaksvpaqrhFTRAgalrLSPGL--KrsSLIGGIRYYDTVVDDARHT 190
                                    13467**********************98888777777766552222554322222..2335667777777777777777 PP

                                    HHHH..HHHHTEEETCSEEEECCEECCCCCCCE.EEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEE CS
                  FAD_binding_3 111 Lveh..aeerglqvrfktevesleqdeegvtae.vrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagv 187
                                    +  +  a+  g+ vr +t+v++l+++++ v  + vrd+e+g+  +vr   +v a G+++   ++l  ++  ++ v    +
  gi|121639225|ref|YP_979449.1| 191 MTVArtAAHYGAVVRCSTQVVALLREGDRVIGVgVRDSENGAVAEVRGHVVVNATGVWTDEIQALSKQRGRFQ-V--RAS 267
                                    75541155566*****************99765489*****************************97755555.5..577 PP

                                    EEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEE CS
                  FAD_binding_3 188 ldvlfdadlsdiveplvlilsaesrgvmviPlentlerfyv 228
                                     +v++ ++ ++iv+++ +il++e++++ viP+ +    +++
  gi|121639225|ref|YP_979449.1| 268 KGVHVVVPRDRIVSDVAMILRTEKSVMFVIPWGS----HWI 304
                                    7788778888899*******************99....333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.4e-08    0.0001       1      33 [.      36      68 ..      34     108 .. 0.79
   2 ?   -2.6   0.1       1.9   2.6e+03     194     237 ..     198     247 ..     180     267 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.4e-08
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   +dvvviGgG+ G  +al++a+ g+kv+lve+++
  gi|121639225|ref|YP_979449.1| 36 FDVVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   589999999999999999999999999996443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                    HHTTEEEEESCEEEEEEETTE.....EEEEEETTSCE...EEESEEEE-S-E CS
                                    xxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx...xxxxxxxxxxxx RF
                    Pyr_redox_2 194 ekeGvevklgtsvkeidgnge.....klevvledgee...idadlvvvavGv 237
                                     + G  v++ t+v+++ ++g+        v ++++     +    vv a+Gv
  gi|121639225|ref|YP_979449.1| 198 AHYGAVVRCSTQVVALLREGDrvigvG--VRDSENGAvaeVRGHVVVNATGV 247
                                    444555555555555555555333221..22222221233555555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.5   4.8e-07   0.00066       1      29 [.      37      65 ..      37      81 .. 0.87
   2 ?   -2.2   0.1       1.2   1.6e+03     119     174 ..     211     268 ..     187     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.8e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                   dv+ViGgG  G+ +Al aa +G+kv+L+ 
  gi|121639225|ref|YP_979449.1| 37 DVVVIGGGVVGSGCALDAATRGLKVALVE 65
                                   79*************************93 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                    EEEEECTTEEEEEEETTS-.....EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B- CS
                           GIDA 119 eeliveekkvkgvvtedge.....tikakavviatGtflkgkihigekelsaGrlgeltse 174
                                      l+ e ++v gv  +d e     +++ ++vv atG + +    i   + ++Gr +  +s+
  gi|121639225|ref|YP_979449.1| 211 VALLREGDRVIGVGVRDSEngavaEVRGHVVVNATGVWTD---EIQALSKQRGRFQVRASK 268
                                    4454555666665444332111114555699999999433...334456667776666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0   2.7e-06    0.0038       1      39 [.      40      78 ..      40      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                   ++G+G+ G+ +A  +a +g++v l+e+rd  +G +++ +
  gi|121639225|ref|YP_979449.1| 40 VIGGGVVGSGCALDAATRGLKVALVEARDLASGTSSRSS 78
                                   8*****************************999988654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.7e-06    0.0037       2      34 ..      38      70 ..      37     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v viG G++G+g a  +a +gl+V lv+ ++ a
  gi|121639225|ref|YP_979449.1| 38 VVVIGGGVVGSGCALDAATRGLKVALVEARDLA 70
                                   89*************************987654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   5.3e-06    0.0073       2      32 ..      38      68 ..      37      77 .. 0.95
   2 ?   -1.5   0.1       2.8   3.9e+03      23      41 ..     268     282 ..     262     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                   vvv+GgG++g  +A  +a  g kV +ve++d
  gi|121639225|ref|YP_979449.1| 38 VVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   8***************************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                    SEEEEEESSSSSSTTSSHH CS
                      Pyr_redox  23 kkVtvversdkllrllDee 41 
                                    k V+vv+ +d++      +
  gi|121639225|ref|YP_979449.1| 268 KGVHVVVPRDRIV----SD 282
                                    779*******998....44 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   7.6e-06      0.01       1      32 [.      36      67 ..      36      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +dv+viGgG  G  +A+ aa+rg +V+l+e+ 
  gi|121639225|ref|YP_979449.1| 36 FDVVVIGGGVVGSGCALDAATRGLKVALVEAR 67
                                   59***************************986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.6e-05     0.035      25      61 ..      32      68 ..      21     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                   CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 25 gvepakvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                   g+e+  v+viGgGv+G   +  a+  g kV +++ r 
  gi|121639225|ref|YP_979449.1| 32 GTEQFDVVVIGGGVVGSGCALDAATRGLKVALVEARD 68
                                   677889**************99999999999888775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.5e-05     0.021      17      57 ..      35      74 ..      27      85 .. 0.81
   2 ?   -2.1   0.1       1.3   1.8e+03     157     169 ..     236     248 ..     182     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                   + Dvv++G+G  G  +a   a++ +lkva++e++    G +
  gi|121639225|ref|YP_979449.1| 35 QFDVVVIGGGVVGSGCALDAATR-GLKVALVEARDLASGTS 74
                                   56*********************.********874444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                    EEEEEEEE--GSS CS
                           Thi4 157 irakvvvdatGhd 169
                                    +r +vvv+atG  
  gi|121639225|ref|YP_979449.1| 236 VRGHVVVNATGVW 248
                                    5566777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3702.00
//
Query:       gi|121639226|ref|YP_979450.1|  [L=471]
Description: flavoprotein disulfide reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-48  163.8   1.6    7.5e-48  163.3   1.6    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-24   86.6   0.4    3.8e-24   85.1   0.4    1.9  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.9e-18   66.2   2.7    5.2e-15   55.8   0.2    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.8e-05   24.1   0.3     0.0034   16.7   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.2e-05   23.8   0.1    6.7e-05   22.2   0.0    1.7  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    8.4e-05   21.8   5.6    0.00014   21.1   0.2    2.9  3  GIDA            Glucose inhibited division protein A
    0.00011   21.2   0.1     0.0002   20.3   0.1    1.4  1  Trp_halogenase  Tryptophan halogenase
    0.00041   19.2   1.1       0.28    9.9   0.8    2.4  2  HI0933_like     HI0933-like protein
     0.0034   16.8   1.1       0.19   11.0   0.4    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   15.0   3.6       0.54    9.5   0.4    2.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.024   14.0   0.5      0.041   13.2   0.1    1.5  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.093   11.8   6.0       0.15   11.0   0.0    2.7  4  Lycopene_cycl   Lycopene cyclase protein
       0.13   12.7   1.3        7.5    7.1   0.1    3.2  3  NAD_binding_7   Putative NAD(P)-binding
       0.25   11.3   8.9        4.1    7.4   0.1    3.4  4  NAD_binding_9   FAD-NAD(P)-binding
        0.3   11.4   1.9         17    5.7   0.2    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   1.6   6.2e-51   7.5e-48       2     294 .]       4     332 ..       3     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 6.2e-51
                                    SEEEE--SHHHHHHHHHHHH...HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                    xxxxxxxxxxxxxxxxxxxx...xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                    ++v++GgGpAG++aal +a+     a+vt+++    +g+ ++++c++sk++ ++ + + +++                  
  gi|121639226|ref|YP_979450.1|   4 RIVILGGGPAGYEAALVAATshpETAQVTVIDcdgIGGAAVLDDCVPSKTFIASTGLRTELRraphlgfhidfddakisl 83 
                                    89******************8666999****8888**************99988888877778***************** PP

                                    ................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC............TCEEEEEESEEEE---E CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ................evvkklnqgielllgeevvkidpgkkkvklekkke............gdeekiaydklvlAtGs 109
                                                    +        i+  l + +v+++ g++++ +++  +            g++ + ++d +++AtG+
  gi|121639226|ref|YP_979450.1|  84 pqiharvktlaaaqsaD--------ITAQLLSMGVQVIAGRGELIDSTP-GlarhrikataadGSTSEHEADVVLVATGA 154
                                    99999998766655551........443333345555555555555222.13555555555569999************* PP

                                    EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 110 sprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaal 189
                                    spr+l  p +++++    r+l+  + + l+ lp++++vvG+G++G E+  a+++lg+ vt+v   d++l+  d +++  l
  gi|121639226|ref|YP_979450.1| 155 SPRIL--PSAQPDG---ERILTWRQLYDLDALPDHLIVVGSGVTGAEFVDAYTELGVPVTVVASQDHVLPYEDADAALVL 229
                                    ****9..5553333...489************************************************************ PP

                                    HHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 190 eealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnv 268
                                    ee + ++Gv++  ++++  +++ g  + v+ +dg++++ +  ++ +G  p+t++l+ e++g++l +++++ vd+ +rt+ 
  gi|121639226|ref|YP_979450.1| 230 EESFAERGVRLFKNARAASVTRTGAGVLVTMTDGRTVEGSHALMTIGSVPNTSGLGlERVGIQLGRGNYLTVDRVSRTSA 309
                                    ************************9999**************************************************** PP

                                    TTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 269 pgiyaiGDvaggkggpelaqaAvqqG 294
                                    +giya+GD++   g + la +A +qG
  gi|121639226|ref|YP_979450.1| 310 TGIYAAGDCT---GLLPLASVAAMQG 332
                                    **********...**********998 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.4   3.2e-27   3.8e-24       1     109 [.     352     460 ..     352     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 3.2e-27
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqela 80 
                                    ++++vft+pe+a+vG+ +  + a  ++ +++ +p++ n+ra+++++++gfvK+ ++++tg v+G  +v+p a+eli  +a
  gi|121639226|ref|YP_979450.1| 352 VAATVFTRPEIAAVGVPQSVIDAGSVAARTIMLPLRTNARAKMSEMRHGFVKIFCRRSTGVVIGGVVVAPIASELILPIA 431
                                    5789**************************************************************************** PP

                                    HHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                  Pyr_redox_dim  81 vaikagltvedladtihihPtlsealkea 109
                                    va+++++tv++la+t++++P+ls +++ea
  gi|121639226|ref|YP_979450.1| 432 VAVQNRITVNELAQTLAVYPSLSGSITEA 460
                                    ************************99998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00087         1       1      29 [.       4      35 ..       4      47 .. 0.84
   2 !   55.8   0.2   4.4e-18   5.2e-15       1      79 [.     184     261 ..     184     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                                   EEEEECSSHHHHHHHHHHHHTT...SEEEEEE CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelg...kkVtvve 29
                                   ++v++GgG  g E+A ++a      ++Vtv++
  gi|121639226|ref|YP_979450.1|  4 RIVILGGGPAGYEAALVAATSHpetAQVTVID 35
                                   79**************9955443448999986 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 4.4e-18
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                    +++vvG+G++g E+  a++elg  Vtvv  +d++l+++D++a+ +l+e++ ++g+++  n+++++++ ++ gv  v+++
  gi|121639226|ref|YP_979450.1| 184 HLIVVGSGVTGAEFVDAYTELGVPVTVVASQDHVLPYEDADAALVLEESFAERGVRLFKNARAASVTRTGAGVL-VTMT 261
                                    789*****************************************************************999943.6655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.3    0.0085        10       1      28 [.       6      35 ..       6      57 .. 0.78
   2 !   16.7   0.0   2.8e-06    0.0034     120     305 .]     140     316 ..     130     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0085
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl..edylilE 28
                                   +I G+GPaG +aa+ +  +     ++++++
  gi|121639226|ref|YP_979450.1|  6 VILGGGPAGYEAALVAATSHPetAQVTVID 35
                                   79***********98876543114556665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.8e-06
                    Pyr_redox_3 120 ketyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                    +++ eA+ v++AtG    P+ l    ++       ++  ++ +   ++++V+G + ++++      + g  Vtvv ++++
  gi|121639226|ref|YP_979450.1| 140 TSEHEADVVLVATGA--SPRILPSAQPDGeRILTWRQLYDL-DALPDHLIVVGSGVTGAEFVDAYTELGVPVTVVASQDH 216
                                    567789999999999..999987776664133344455555.445789*****************************997 PP

                    Pyr_redox_3 199 iekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsf..lkk 276
                                    +   e        +d    lee  +e+ +++ +na++ +++++   + v+++dg++ve ++  ++ +G  p++s   l++
  gi|121639226|ref|YP_979450.1| 217 VLPYE-------DADAALVLEESFAERGVRLFKNARAASVTRTGAGVLVTMTDGRTVEGSHA-LMTIGSVPNTSGlgLER 288
                                    77764.......34444556666666569***************************998666.7779*****99833455 PP

                    Pyr_redox_3 277 slfeldedgrpvlteeteetnvpglflaG 305
                                     +++l + ++ +++     t   g++ aG
  gi|121639226|ref|YP_979450.1| 289 VGIQLGRGNYLTVD-RVSRTSATGIYAAG 316
                                    88888666666665.55667789999988 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.99   1.2e+03     193     221 ..       4      33 ..       2      35 .. 0.79
   2 !   22.2   0.0   5.6e-08   6.7e-05     133     248 ..     129     236 ..     119     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.99
                    K_oxygenase 193 riaVvGsGqSaaeifedllrrqkk.velkl 221
                                    ri++ G+G  + e +  ++++ ++ +++++
  gi|121639226|ref|YP_979450.1|   4 RIVILGGGPAGYEAALVAATSHPEtAQVTV 33 
                                    89*********9999888887654377765 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 5.6e-08
                    K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllr 212
                                     +++ + a+g+++e+ea  +++++G +p i + +++    er++   ++  +   ++ +++++VvGsG ++ae ++  ++
  gi|121639226|ref|YP_979450.1| 129 HRIKATAADGSTSEHEADVVLVATGASPRILPSAQPDG--ERILTWRQLY-DL--DALPDHLIVVGSGVTGAEFVDAYTE 203
                                    57888889*******************99988888754..6777665544.44..57899*************7765554 PP

                    K_oxygenase 213 rqkkvelklvtrsealeplddspfvneifsPeyvdy 248
                                        v +++v++++++ p +d++ ++ +++ ++ ++
  gi|121639226|ref|YP_979450.1| 204 L-G-VPVTVVASQDHVLPYEDADAAL-VLEESFAER 236
                                    4.3.68*************9998754.334444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.2e-07   0.00014       2     150 ..       5     154 ..       4     172 .. 0.75
   2 ?    1.8   0.2     0.083     1e+02       2      30 ..     185     213 ..     184     258 .. 0.87
   3 ?   -0.3   0.1      0.38   4.5e+02     354     380 ..     308     335 ..     297     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                    EEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--S....SSSEEE-TTHHHHHHHHHHHT-SHHHH.HHHHEEEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLi.thkldtiaels....CnpsiggiakgllvrEidalggliika.adkagiqfr 75 
                                    ++++GgG AG+eAAl aa +  +++ + + + d i+  +    C ps   ia+  l +E+++   l  ++  d a+i   
  gi|121639226|ref|YP_979450.1|   5 IVILGGGPAGYEAALVAATSHPETAQVtVIDCDGIGGAAvlddCVPSKTFIASTGLRTELRRAPHLGFHIdFDDAKI--S 82 
                                    899*****************99998886678888877644556*****************99764333321345555..3 PP

                                    EESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECT....TEEEE.EEETTS-EEEECEEEE--TT CS
                           GIDA  76 ilNrskGpavralraqvdrelyskevteklenepnleiieeeveelivee....kkvkg.vvtedgetikakavviatGt 150
                                     l     p+++a  +++   + s+++t++l +   +++i ++ e ++ +     +++k+     + ++ +a++v +atG+
  gi|121639226|ref|YP_979450.1|  83 -L-----PQIHAR-VKTLAAAQSADITAQLLS-MGVQVIAGRGELIDSTPglarHRIKAtAADGSTSEHEADVVLVATGA 154
                                    .3.....888886.777788888899999988.89999999999997766888666666233444556667799999998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                    +iV+G G  G e   a  +lG++v+ ++ 
  gi|121639226|ref|YP_979450.1| 185 LIVVGSGVTGAEFVDAYTELGVPVTVVAS 213
                                    69**********************99943 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.38
                                    SSBTEEE-CGGGTB-SHHHHHH.HHHHH CS
                           GIDA 354 kvkgLflAGqinGteGYeEaaa.qGllA 380
                                    + +g+++AG+ +G       aa qG +A
  gi|121639226|ref|YP_979450.1| 308 SATGIYAAGDCTGLLPLASVAAmQGRIA 335
                                    5789*********964443333577777 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.7e-07    0.0002       1      48 [.       4      51 ..       4      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--TH CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatips 48
                                   +ivi+GGG+aG+ aA + a+ + ++++vt+++ + ig   v +  +ps
  gi|121639226|ref|YP_979450.1|  4 RIVILGGGPAGYEAALVAATSHPETAQVTVIDCDGIGGAAVLDDCVPS 51
                                   69********************99************988887666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.8   0.00023      0.28       2      30 ..       4      35 ..       3      43 .. 0.81
   2 !    7.1   0.0    0.0016         2      81     170 ..     196     281 ..     192     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                                   SEEEE--SHHHHHHHHHH...HHTT--EEEE- CS
                    HI0933_like  2 dviviGgGaAGlmaAisa...akrgkrVllle 30
                                   +++++GgG+AG  aA+ a   + + ++V++++
  gi|121639226|ref|YP_979450.1|  4 RIVILGGGPAGYEAALVAatsHPETAQVTVID 35
                                   699***********999944345678999998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0016
                                    HHHHHHHHTT--EEE.-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                    HI0933_like  81 dlialveelgvelke.edsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklv 159
                                    ++++ ++elgv++++  +++ + p +d a d   +l++   e+gv+l  + + +sv+++  g + v++++++++e ++ +
  gi|121639226|ref|YP_979450.1| 196 EFVDAYTELGVPVTVvASQDHVLPYED-A-DAALVLEESFAERGVRLFKNARAASVTRTGAG-VLVTMTDGRTVEGSHAL 272
                                    677778888888765156778999884.3.3344799*******************999999.666666*********** PP

                                    E----SS-GGG CS
                    HI0933_like 160 lAtGGlSiPkl 170
                                    +++G+  +P++
  gi|121639226|ref|YP_979450.1| 273 MTIGS--VPNT 281
                                    **995..4443 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.4   0.00016      0.19       2      26 ..       5      29 ..       4      68 .. 0.81
   2 ?    4.3   0.0     0.017        21      80     125 ..     215     260 ..     183     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvl 26
                                   +v+ GGgpaG+ AA+ Aa +  +++
  gi|121639226|ref|YP_979450.1|  5 IVILGGGPAGYEAALVAATSHPETA 29
                                   89****************9876554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                   FAD_oxidored  80 kwn..tfepevakavleemlaeagvtvllntrlvevekegkriesvtv 125
                                    + +  ++e   a+ vlee  ae gv+++ n+r+ +v+++g     vt+
  gi|121639226|ref|YP_979450.1| 215 D-HvlPYEDADAALVLEESFAERGVRLFKNARAASVTRTG-AGVLVTM 260
                                    2.134899999***************************98.3333333 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4   0.00045      0.54      30      59 ..       4      36 ..       2      55 .. 0.84
   2 ?    5.4   0.2    0.0079       9.5      30      64 ..     184     218 ..     179     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00045
                                   EEEEESTSHHHHHHHHHHHHT...T-EEEEEES CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakgl...gakVtvlDv 59
                                   +++++GgG aG +A+ +a+      a+Vtv+D 
  gi|121639226|ref|YP_979450.1|  4 RIVILGGGPAGYEAALVAATShpeTAQVTVIDC 36
                                   89************9887764222699999986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0079
                                    EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                    + +v+G Gv G + + + ++lg  Vtv+  + ++l
  gi|121639226|ref|YP_979450.1| 184 HLIVVGSGVTGAEFVDAYTELGVPVTVVASQDHVL 218
                                    689***********************998777665 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.4   2.9e+03     241     262 ..     131     154 ..     127     156 .. 0.82
   2 ?   13.2   0.1   3.4e-05     0.041     212     261 ..     229     276 ..     211     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                    EEEEETTSTEE..EESEEEE-S-H CS
                  Amino_oxidase 241 vtvtledgevv..eaDaVvvTvpl 262
                                    ++ t  dg++   eaD V+v++  
  gi|121639226|ref|YP_979450.1| 131 IKATAADGSTSehEADVVLVATGA 154
                                    6777889999999*******9876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                  Amino_oxidase 212 lpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                    l e++ae  rg+++  n+r  +++r g gv vt++dg++ve+ + ++T+ 
  gi|121639226|ref|YP_979450.1| 229 LEESFAE--RGVRLFKNARAASVTRTGAGVLVTMTDGRTVEGSHALMTIG 276
                                    5567777..**************************************985 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6     0.042        50       2      31 ..       5      35 ..       4      46 .. 0.77
   2 ?   -3.5   0.0       3.3   3.9e+03      97     140 ..     105     153 ..      71     161 .. 0.59
   3 ?   -2.1   0.0       1.3   1.5e+03       2      37 ..     185     217 ..     184     223 .. 0.80
   4 ?   11.0   0.0   0.00013      0.15      91     164 ..     227     303 ..     218     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.042
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpg.lkvvlie 31
                                   +v+ G+GpAg   A   + ++p+  +v++i+
  gi|121639226|ref|YP_979450.1|  5 IVILGGGPAGYEAALVAATSHPEtAQVTVID 35
                                   79********998887766665414566665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                  Lycopene_cycl  97 lvengvklleakvesveeeea.geslv..vleggr..kirarlvvdarg 140
                                    l + gv+   ++ e +   +  ++ ++  + ++g   + +a +v++a+g
  gi|121639226|ref|YP_979450.1| 105 LLSMGVQVIAGRGELIDSTPGlARHRIkaTAADGStsEHEADVVLVATG 153
                                    4444555555555555555544332221133444445566777777777 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.3
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                    ++v+G+G  g          + g+ v+++ as++ +
  gi|121639226|ref|YP_979450.1| 185 LIVVGSGVTGAEFVDAY--TELGVPVTVV-ASQDHV 217
                                    79********9999988..8889999988.665544 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00013
                  Lycopene_cycl  91 eellerlvengvk.lleakvesveeeeageslvvleggrkirarlvvdarglaslk...karrlglQtfyGvevevdn 164
                                     +l+e+++e gv+ + +a+++sv+   a  +lv++ +gr+++++ ++   g   ++   +  r+g+Q  +G  + vd+
  gi|121639226|ref|YP_979450.1| 227 LVLEESFAERGVRlFKNARAASVTRTGA-GVLVTMTDGRTVEGSHALMTIGSVPNTsglGLERVGIQLGRGNYLTVDR 303
                                    56889999888873679*******9998.9************999888777332224558899999999998888875 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1   1.2e+02       9      39 ..       4      37 ..       2     156 .. 0.82
   2 ?    7.1   0.1    0.0062       7.5       9      41 ..     184     220 ..     178     272 .. 0.70
   3 ?   -2.9   0.0       7.9   9.4e+03      12      32 ..     371     391 ..     370     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleag...akvtvvape 39
                                   ++++ GgG+ +++ +   + +    a+vtv++ +
  gi|121639226|ref|YP_979450.1|  4 RIVILGGGPAGYEAALVAATSHpetAQVTVIDCD 37
                                   7899999999999887766543344999998765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0062
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev....k 41 
                                    + +vvG G  +a+ v    e g  vtvva +      
  gi|121639226|ref|YP_979450.1| 184 HLIVVGSGVTGAEFVDAYTELGVPVTVVASQDhvlpY 220
                                    789**************************99544432 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.9
                  NAD_binding_7  12 vvGgGevAarkvrklleagak 32 
                                    v+ +G+vAar +   l+++a+
  gi|121639226|ref|YP_979450.1| 371 VIDAGSVAARTIMLPLRTNAR 391
                                    677899**9998877777665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0051       6.1       1      41 [.       6      43 ..       6      56 .. 0.85
   2 ?    1.3   0.2      0.26   3.1e+02     112     155 ..     107     154 ..      94     155 .. 0.63
   3 ?   -3.4   0.1         7   8.4e+03       2      13 ..     187     198 ..     186     203 .. 0.82
   4 ?    7.4   0.1    0.0034       4.1     119     154 ..     241     276 ..     223     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrv 41
                                   +i G+Gp+G  ++   + ++  ++  ++t++d +++g g +
  gi|121639226|ref|YP_979450.1|  6 VILGGGPAGYEAALVAATSH--PETAQVTVIDCDGIG-GAA 43
                                   699*******9998888876..9***********998.544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                  NAD_binding_9 112 pegvtvevhraevvdleeradgq..avlladg..aslaadaVvLAlGh 155
                                    + gv+v   r+e +d ++  ++   + + adg  ++++ad V +A+G 
  gi|121639226|ref|YP_979450.1| 107 SMGVQVIAGRGELIDSTPGLARHriKATAADGstSEHEADVVLVATGA 154
                                    5566666666677777765554312555567732458*********95 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7
                  NAD_binding_9   2 ivGaGprGlavl 13 
                                    +vG G++G+ ++
  gi|121639226|ref|YP_979450.1| 187 VVGSGVTGAEFV 198
                                    8******98665 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0034
                  NAD_binding_9 119 vhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    + +a++ +++++++g+ v+ +dg++++  +  +++G
  gi|121639226|ref|YP_979450.1| 241 FKNARAASVTRTGAGVLVTMTDGRTVEGSHALMTIG 276
                                    4588******************************99 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.014        17       1      34 [.       7      42 ..       7      62 .. 0.83
   2 ?    4.4   0.1     0.038        46       1      30 [.     187     216 ..     187     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                   EE--SHHHHHHHHHHHCC...TEEEEEE-SSSSSSGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekrdrlGGr 34
                                   I+G+G +G  aA  +a      ++v++++  d++GG 
  gi|121639226|ref|YP_979450.1|  7 ILGGGPAGYEAALVAATShpeTAQVTVIDC-DGIGGA 42
                                   89******9999888774355889****96.577776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    +vG+G++G+ +  ++++ g+ v+++ ++d+
  gi|121639226|ref|YP_979450.1| 187 VVGSGVTGAEFVDAYTELGVPVTVVASQDH 216
                                    8********************999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3522.21
//
Query:       gi|121639227|ref|YP_979451.1|  [L=159]
Description: hypothetical protein BCG_3369 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-26   92.1   0.0    2.7e-26   91.8   0.0    1.1  1  AIG2_2    AIG2-like family
    5.3e-09   36.7   0.0    6.8e-09   36.4   0.0    1.1  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like


Domain annotation for each model (and alignments):
>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0     3e-30   2.7e-26       1      83 []      59     145 ..      59     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 3e-30
                         AIG2_2   1 eVfGvlweidlenlkdLDkqEgvedgiyrpievrVst....atgeevlaraYvlsnqpetkPsetYlkvlvkGAeesglP 76 
                                    +Vf+vl++++++++k+LD++Eg+e+gi+++i++rV++    +t++ vla++Yvl++++ + Ps++Yl v++++Ae +g+P
  gi|121639227|ref|YP_979451.1|  59 KVFVVLYDMTPADEKNLDRWEGSEFGIHQKIRCRVERissdTTTDPVLAWLYVLDAWEGGLPSARYLGVMADAAEIAGAP 138
                                    69*********************************55543477788********************************** PP

                         AIG2_2  77 edYvkrL 83 
                                    +dYv++L
  gi|121639227|ref|YP_979451.1| 139 SDYVHDL 145
                                    *****98 PP

>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   7.6e-13   6.8e-09       3     104 ..       6     113 ..       4     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.6e-13
                                    ESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.......ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TT CS
                          GGACT   3 vYGtLkrgepnhqrlllgarflesgpatlkgyrlyd......lggkypalvpgdgekVkGelyevddeelarLDelEpee 76 
                                    +YG+ +  +p+ + l ++++ +  g+ +l+g+rl        ++g    +v+++++kV  +ly++++++ ++LD++E++e
  gi|121639227|ref|YP_979451.1|   6 AYGSNM--HPEQM-LERAPHSPMAGTGWLPGWRLTFggedigWEGALATVVEDPDSKVFVVLYDMTPADEKNLDRWEGSE 82 
                                    7*****..78877.3334699999***********754445555566778899999*********************666 PP

                                    TTSEEEEEEEEEC....TTS-EEEEEEEEET CS
                          GGACT  77 pseYereevkvev...ledgeqveawvYvya 104
                                     +  ++ +++ve    +++ ++v aw+Yv +
  gi|121639227|ref|YP_979451.1|  83 FGIHQKIRCRVERissDTTTDPVLAWLYVLD 113
                                    777777777774358777888889****994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1230.11
//
Query:       gi|121639228|ref|YP_979452.1|  [L=389]
Description: N-acyl-L-amino acid amidohydrolase amiA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-26   93.2   0.1    2.2e-26   92.9   0.1    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
      0.003   17.5   0.0     0.0065   16.4   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.1   2.4e-30   2.2e-26       1     206 [.      75     384 ..      75     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.4e-30
                                    EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHH. CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                  Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGa. 78 
                                    +l++++D++p +e t +   p+++t + ++ +++G+d +++++l+a+ al+++ +     +  ++l+fq++EE + gGa 
  gi|121639228|ref|YP_979452.1|  75 ALRADMDALPmAERTGA---PYASTMP-NVAHACGHDAHTAILLGAALALASVPEL----PVGVRLIFQAAEELMPGGAi 146
                                    69********7777755...*****88.************************9999....99***********8889996 PP

                                    HHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE........................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                  Peptidase_M20  79 kallegleerekvdavfelhieepgileagklaigvv........................................... 115
                                     a+++g++   +v  +f+lh+  p + + gk+a++ +                                           
  gi|121639228|ref|YP_979452.1| 147 DAIAAGAL--AGVSRIFALHCD-PRLEV-GKVAVRQGpitsaadsieitlyspgghtsrphltadlvyglgtlvtglpgv 222
                                    77777888..599*******77.55555.99777777999**************************************** PP

                                    .................................................................EEEEEEEEEESHEEE CS
                                    .................................................................xxxxxxxxxxxxxxx RF
                  Peptidase_M20 116 .................................................................kvevelleggapvtl 130
                                                                                                     + +++ +++g p+++
  gi|121639228|ref|YP_979452.1| 223 lsrridprnstvlvwgavnagmaanaipqtgvlsgtvrtasrqtwvdleelvrqaisalllplaiEHTLQ-YRRGVPPVV 301
                                    *************************************************************885444444.49999999* PP

                                    CCHHHHHHHHHHHHHHH.TSCEEEEEESSSBHTHHHH.TTTEEEEE.EE.SS.G...GCTTSTTTEEEHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxx.xx.xx.x...xxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 131 ndsplvkalaeaaeelf.gekvelivsgpggtdarff.agiptvmi.fg.pg.s...glaHspnEyvdledlekgikvla 202
                                    n++  +++la a+e++  g+  ++  sg gg+d++++ +++p +m  +g  + +    + H+p  ++d+++l+ g++v++
  gi|121639228|ref|YP_979452.1| 302 NEEISTRILAHAIEAIGpGVLADTRQSG-GGEDFSWYlEEVPGAMArLGvWSgDglqLDLHQPTFDIDERALAIGLRVMV 380
                                    95555********9986676688889**.********9999977666776553457788999999999************ PP

                                    HHHH CS
                                    xxxx RF
                  Peptidase_M20 203 rlle 206
                                    +++e
  gi|121639228|ref|YP_979452.1| 381 NIIE 384
                                    *997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.2e-07    0.0065       9     104 ..     188     281 ..     184     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.2e-07
                                    EEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHH CS
                      M20_dimer   9 gkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRllpge 88 
                                     +it    +gH + p+  a+ ++ l  l++ l+   ++     +   t l ++ +++G a+n+ip++  ++ ++R+   +
  gi|121639228|ref|YP_979452.1| 188 IEITLYSPGGHTSRPHLTADLVYGLGTLVTGLPGVLSRRI--DPRNSTVLVWGAVNAGMAANAIPQTGVLSGTVRTASRQ 265
                                    5677777888888888888888888888888888888866..55556778899*************************** PP

                                    HHHHHHHHHHHHHTSC CS
                      M20_dimer  89 dpeevleeieeileke 104
                                    ++ +++e ++++++++
  gi|121639228|ref|YP_979452.1| 266 TWVDLEELVRQAISAL 281
                                    ***********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 2277.90
//
Query:       gi|121639229|ref|YP_979453.1|  [L=394]
Description: amidase amiB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-10   39.7   0.0      8e-10   38.8   0.0    1.5  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.4e-08   34.6   0.0    3.7e-08   33.3   0.0    1.7  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   8.9e-14     8e-10      28     184 ..      89     344 ..      79     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 8.9e-14
                                    TEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHH.HHHTTTCESEEEEEEEESSSBTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  28 GklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakalle.gleerekvdavfelhieepgile 106
                                    G  +++G++   ++ ++ + al++++d+      t+ ll +p+EE+g gG + +l+ g +  ++v  ++ +h + p+   
  gi|121639229|ref|YP_979453.1|  89 GIGHACGHNIIAASAVGTALALAEVADDL---GLTVALLGTPAEESG-GGKALMLQaGTF--DDVAVAVMVHPG-PTDIA 161
                                    667*************************7...349**********87.888999995443..344444445533.44444 PP

                                    HSTETEEEE....................................................................... CS
                                    xxxxxxxxx....................................................................... RF
                  Peptidase_M20 107 agklaigvv....................................................................... 115
                                     g  +  ++                                                                       
  gi|121639229|ref|YP_979453.1| 162 -GARSLALSevtvryrgkeshaavaphlgvnaadavtvaqvaigvlrqqlapgqmvhgivtdggqavnvipgqarlqyam 240
                                    .5544444466778888888888888888888888889999999999********************************* PP

                                    ............................EEEEEEEEEESHEEEC...CHHHHHHHHHHHHHHHTSCEEEEEES....SSB CS
                                    ............................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
                  Peptidase_M20 116 ............................kvevelleggapvtln...dsplvkalaeaaeelfgekvelivsg....pgg 160
                                                                ++e++   ++ap+ ++   d+ l+++++e +++l g+++ l++       g+
  gi|121639229|ref|YP_979453.1| 241 ravesdslrelqtrmfacfaagalaagcEYEID---EAAPAYAElkpDPWLADVCREEMQRL-GREPLLPALEaelpLGS 316
                                    *************************85445555...555555555689999**********9.988555533336789** PP

                                    HTHHHHTTT.EEE.EEEESS.G.GCTTS CS
                                    xxxxxxxxx.xxx.xxxxxx.x.xxxxx RF
                  Peptidase_M20 161 tdarffagi.ptv.mifgpg.s.glaHs 184
                                    td++ + ++ p +  ++g + + +++H+
  gi|121639229|ref|YP_979453.1| 317 TDMGNVTQVlPGIhPVIGLDaGaATVHQ 344
                                    ******7777855444563312366665 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   4.1e-12   3.7e-08       8     100 ..     170     258 ..     162     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.1e-12
                                    EEEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEEC.CE-CCCCEESSEEEEEEEEEHH CS
                      M20_dimer   8 ggkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgi.egGsaknvipdeaeakidiRll 85 
                                    +++++ +gk  H++ ap+ g+NA  +   +  ++  ++++      l++ ++  +++ +gG+a nvip++a++++ +R +
  gi|121639229|ref|YP_979453.1| 170 EVTVRYRGKESHAAvAPHLGVNAADAVTVAQVAIGVLRQQ------LAPGQMVHGIVtDGGQAVNVIPGQARLQYAMRAV 243
                                    5677799***************888666666666666333......4445555555517777****************** PP

                                    HHHHHHHHHHHHHHH CS
                      M20_dimer  86 pgedpeevleeieei 100
                                      +++ e+++++ + 
  gi|121639229|ref|YP_979453.1| 244 ESDSLRELQTRMFAC 258
                                    ******999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2694.47
//
Query:       gi|121639230|ref|YP_979454.1|  [L=268]
Description: purine nucleoside phosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-41  141.1   3.2    3.8e-41  140.9   3.2    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   3.2   2.1e-45   3.8e-41       1     234 []      29     266 ..      29     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2.1e-45
                                    CEEEEESSH..HHHHHHHHH....EEEEEEEEEE.....TTEEEEEEEETTEEEEEEE--.....SSHHHHHHHHHHHHH CS
                      PNP_UDP_1   1 kiaiivgsp..gevellaes....pleetpfgre....grgfkfvtGtlkgkpvvivstG.....iGkpnaavvaeirll 65 
                                    ++a+++gs+  + v++l +     p +e+p + +    g+ +++    ++ ++v +v+ G     +G++   vv ++r+ 
  gi|121639230|ref|YP_979454.1|  29 DVAVVLGSGwlPAVAALGSPttvlPQAELPGFVPptaaGHAGELLSVPIGAHRV-LVLAGrihayEGHDLRYVVHPVRAA 107
                                    589999999888888888889999999***999989999999999999955555.555566******************* PP

                                    HHC--SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE CS
                      PNP_UDP_1  66 kefgvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr 145
                                     + g+  ++ +++aGgl++dl+vG  v+++d++n++ rspl g       f+d +da ++p+lr+l+++    +++++ +
  gi|121639230|ref|YP_979454.1| 108 RAAGAQIMVLTNAAGGLRADLQVGQPVLISDHLNLTARSPLVG-----GEFVDLTDA-YSPRLRELARQ----SDPQLAE 177
                                    *****************************************99.....99*******.***********....99***** PP

                                    EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHH CS
                      PNP_UDP_1 146 GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaakna 225
                                    Gv+a   g+++et+ae+r+l++lgad+v+M+t+++ ++Ar +g+ ++++++v++laag+++++ +h+ev ++++++a+++
  gi|121639230|ref|YP_979454.1| 178 GVYAGLPGPHYETPAEIRMLQTLGADLVGMSTVHETIAARAAGAEVLGVSLVTNLAAGITGEPLSHAEVLAAGAASATRM 257
                                    ******************************************************************************** PP

                                    HHHHHHHHH CS
                      PNP_UDP_1 226 aalllalla 234
                                     all  ++a
  gi|121639230|ref|YP_979454.1| 258 GALLADVIA 266
                                    ****99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1721.39
//
Query:       gi|121639231|ref|YP_979455.1|  [L=534]
Description: phosphomannomutase pmmB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-40  136.4   0.0      9e-40  135.6   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.1e-20   72.7   0.1    1.1e-19   70.9   0.1    2.0  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-17   64.2   0.0    2.5e-17   63.1   0.0    1.6  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    6.5e-06   26.2   0.0    2.1e-05   24.6   0.0    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.0     2e-43     9e-40       3     133 ..      36     170 ..      34     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 2e-43
                                    GBBTTCEEEECCHCT..BSCCHHHHHHHHHHHHCHHC.STS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEE.EB- CS
                      PGM_PMM_I   3 kfgtsGlRgkvgege..ltpelveklgqaiaeylkae.akkkkvvvGrDtRvssrelaealaaglaanGvevillg.llp 78 
                                    +fgt+GlRg    g+  ++ ++v+++++a+a++l+ +  ++++v+vGrD+R+ s+ +a+a+a++laa+G++v+ll  ++p
  gi|121639231|ref|YP_979455.1|  36 AFGTAGLRGHLRGGPdaMNLAVVLRATWAVARVLTDRgLAGSPVIVGRDARHGSPAFAAAAAEVLAAAGFSVLLLPdPAP 115
                                    7***********9999*********************99***************************************** PP

                                    HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                      PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                    tP+v+fa+r+ +a+agi itaSHnp+++ng+Kvy   G ++  +++++Iea++++
  gi|121639231|ref|YP_979455.1| 116 TPVVAFAVRHTGAAAGIQITASHNPATDNGYKVYVDGGLQLLAPTDRQIEAAMAT 170
                                    ***************************************************9986 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   2.5e-23   1.1e-19      17      98 ..     207     291 ..     191     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 2.5e-23
                                    HHHT-EEEEE-TT-TTHHHHHHHHHHTT-...EEEES-----TT-TT.SS----TT-TTTTHHHHGGGGG-SEEEEE-TT CS
                     PGM_PMM_II  17 kksglkvvidplhGaggeilkellkelgv...dvvelnaepdpdfpt.kapnpeekealkllielvkkegadlglafDgD 92 
                                    ++ +++v+++plhG+gg ++ e l+++g+   ++v  +++p+pdfpt + pnpee+ a ++l  l+ + +ad+++a+D+D
  gi|121639231|ref|YP_979455.1| 207 AG-SVRVALTPLHGVGGAMAVETLRRAGFtevHTVATQFAPNPDFPTvTLPNPEEPGATDALLTLATDVDADVAIALDPD 285
                                    34.499************************999999******************************************** PP

                                    S-BEEE CS
                     PGM_PMM_II  93 aDRlgv 98 
                                    aDR++v
  gi|121639231|ref|YP_979455.1| 286 ADRCAV 291
                                    ****98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   5.5e-21   2.5e-17       2     111 ..     304     424 ..     303     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.5e-21
                                    HHHHHHHHHHHHHCH....CSTTTC.EEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHT.T..ECEEEETT.C CS
                    PGM_PMM_III   2 gdqllallakyllee....klkpga.gvvktvmtslalervakklgiklvetkvGdkyvleemkee.g..avlGgEeS.g 72 
                                    gd+++ ll +y+l++      +p++ +v++tv++s++l  +a+++ + +vet +G+k+++++ +++    +v+++Ee  g
  gi|121639231|ref|YP_979455.1| 304 GDETGWLLGDYILSQtddrASPPETrVVASTVVSSRMLAAIAAHHAAVHVETLTGFKWLARA-DANlPgtLVYAYEEAiG 382
                                    9***********999998767777779********************************999.44432469*******99 PP

                                    EEEETTTBSS--HHHHHHHHHHHHH...HHTS-HHHHHHHHH CS
                    PGM_PMM_III  73 hiifldeattkDGilaallvleila...etgkslselleell 111
                                    h + ++ +++kDGi aa+lv+ ++a    +g+s+ + l+el 
  gi|121639231|ref|YP_979455.1| 383 HCVDPTAVRDKDGISAAVLVCDLVAalkGQGRSVTDALDELA 424
                                    99999********************77666799999998765 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.8e-09   2.1e-05      38      55 ..     486     503 ..     448     508 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.8e-09
                                    EE.EEEETTCCEEEEEEE CS
                     PGM_PMM_IV  38 rlavRpSGTepllrvyvE 55 
                                    r+avRpSGTep+l++y+E
  gi|121639231|ref|YP_979455.1| 486 RVAVRPSGTEPKLKCYLE 503
                                    555**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3996.57
//
Query:       gi|121639232|ref|YP_979456.1|  [L=207]
Description: uracil phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-62  209.5   0.0    4.1e-62  209.3   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    1.4e-09   37.6   0.1    2.1e-09   37.1   0.1    1.2  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.0   4.5e-66   4.1e-62       1     206 [.       5     205 ..       5     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 4.5e-66
                        UPRTase   1 vsshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGeg 80 
                                    v++hpl++a lt+lRd++t+++ fr++++++++ll++ea+++  p+e+v+++tpl+++   +l+++   +lVp+lRaG+g
  gi|121639232|ref|YP_979456.1|   5 VVDHPLAAARLTTLRDERTDNAGFRAALRELTLLLIYEATRD-APCEPVPIRTPLAETVGSRLTKP--PLLVPVLRAGLG 81 
                                    679***************************************.***************99988775..99********** PP

                        UPRTase  81 meealrellpearvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                    m+++++++lpea vg +g+ r+e+t++pv y+  LP+++++  v++lDp++aTGgs+ + + lL++rg+   +I+vl+v+
  gi|121639232|ref|YP_979456.1|  82 MVDEAHAALPEAHVGFVGVARDEQTHQPVPYLDSLPDDLTDVPVMVLDPMVATGGSMTHTLGLLISRGA--ADITVLCVV 159
                                    ******************************************************************887..69******* PP

                        UPRTase 161 aseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                    a++eg+++l+++ p+v+++taa+De+l+e +yivpGlGD+GDR Fg
  gi|121639232|ref|YP_979456.1| 160 AAPEGIAALQKAAPNVRLFTAAIDEGLNEVAYIVPGLGDAGDRQFG 205
                                    *********************************************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   2.3e-13   2.1e-09      25     131 ..      64     166 ..      54     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.3e-13
                                    E--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHH CS
                   Pribosyltran  25 eyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTl 103
                                    +   kp+++v+++r G+ ++++ + +L e+ + +v + + ++  +++         +l+ d+ +  V + D +++tGg++
  gi|121639232|ref|YP_979456.1|  64 SRLTKPPLLVPVLRAGLGMVDEAHAALpEAHVGFVGVARDEQTHQPVPYLD-----SLPDDLTDVPVMVLDPMVATGGSM 138
                                    55579**********************755566666655555444444322.....39********************** PP

                                    HHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                   Pribosyltran 104 laalelLkekgpeevriavlvdkpatee 131
                                    +++l lL ++g++ + + ++v+ p++  
  gi|121639232|ref|YP_979456.1| 139 THTLGLLISRGAADITVLCVVAAPEGIA 166
                                    *********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1594.49
//
Query:       gi|121639233|ref|YP_979457.1|  [L=299]
Description: acid phosphatase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-47  161.1   1.3    1.1e-42  146.6   0.1    2.9  2  Phosphoesterase  Phosphoesterase family
  ------ inclusion threshold ------
      0.062   12.7   0.0       0.17   11.3   0.0    1.6  2  Sulfatase        Sulfatase


Domain annotation for each model (and alignments):
>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1     8e-06     0.072       2      22 ..      51      71 ..      50      72 .. 0.91
   2 !  146.6   0.1   1.2e-46   1.1e-42     105     356 .]      70     282 ..      69     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-06
                Phosphoesterase  2 khvViivqENrsfdhlfGtlk 22
                                    hvVi+v+ENrs + ++G+ +
  gi|121639233|ref|YP_979457.1| 51 AHVVIVVEENRSQAAIIGNKS 71
                                   7*****************976 PP

  == domain 2  score: 146.6 bits;  conditional E-value: 1.2e-46
                Phosphoesterase 105 edipvlwelaqeftlcDryFssvlggtepNrlflisgtsdpsGteggpsladpkktvlkgftqktigerLsekgvswaiY 184
                                    + +p++++la + +++ + F + ++++epN+l+l++g++     +g ++    ++++++g + +++g++L ++g++++ +
  gi|121639233|ref|YP_979457.1|  70 KSAPFINSLAANGAMMAQAF-AETHPSEPNYLALFAGNT-----FGLTK----NTCPVNGGALPNLGSELLSAGYTFMGF 139
                                    5689****************.99****************.....***99....89************************* PP

                Phosphoesterase 185 qealdnlakskvapfnyyvrklkklearrkalkqlglaakqlekfkkdvkngkLPqvsfikpngandeHpgadvaagdkl 264
                                     e+l ++++s+v+++ +y+rk+ ++ ++++  ++l++   ++++f k  ++  LP+vsf++pn++nd+H+g ++a+gd +
  gi|121639233|ref|YP_979457.1| 140 AEDL-PAVGSTVCSAGKYARKHVPWVNFSNVPATLSV---PFSAFPKPQNYPGLPTVSFVIPNADNDMHDG-SIAQGDAW 214
                                    ****.***************************99999...59*****************************.******** PP

                Phosphoesterase 265 ikevlealtsspqwaktllivtyDEngGfyDhVappvapvsdpdglkGdpyglgvrvPllviSpyakkgtvdhelfdhtS 344
                                    ++++l+a++++ +++++ll+vt+DE++G                       + ++++P++++++++++gt+++++ +h++
  gi|121639233|ref|YP_979457.1| 215 LNRHLSAYANWAKTNNSLLVVTWDEDDG-----------------------SSRNQIPTVFYGAHVRPGTYNETI-SHYN 270
                                    ****************************.......................589*********************.**** PP

                Phosphoesterase 345 vlrfiekrfglp 356
                                    vl+++e+++glp
  gi|121639233|ref|YP_979457.1| 271 VLSTLEQIYGLP 282
                                    **********97 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.17       4      94 ..      53     134 ..      51     141 .. 0.83
   2 ?   -2.2   0.0      0.24   2.1e+03     274     303 ..     247     275 ..     242     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                                    EEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTTS- CS
                      Sulfatase   4 vliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggglpqtea 83 
                                    v+i+++  ++ +  + g+k a  p++ +la++g +  ++++    + ps+++ l  +  +++g + nt    +  +   +
  gi|121639233|ref|YP_979457.1|  53 VVIVVEENRS-QAAIIGNKSA--PFINSLAANGAMMAQAFAE---THPSEPNYLALFAGNTFGLTKNTC---PVNGGALP 123
                                    6777777755.6789999885..*****************66...9*****************999986...66777778 PP

                                    HHHHHHHHTT- CS
                      Sulfatase  84 tLpellkeaGY 94 
                                    +L+  l +aGY
  gi|121639233|ref|YP_979457.1| 124 NLGSELLSAGY 134
                                    88888888887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.24
                                    BEEEEEEETTTSHCEEECSEEEGGGHHHHH CS
                      Sulfatase 274 rvPllvwwpgekaprvseelvshiDlfpti 303
                                    ++P++ ++ +  +  +++e +sh +++ t+
  gi|121639233|ref|YP_979457.1| 247 QIPTVFYGAHVRPG-TYNETISHYNVLSTL 275
                                    56777777776666.999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2078.28
//
Query:       gi|121639234|ref|YP_979458.1|  [L=420]
Description: hypothetical protein BCG_3376 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.027   13.9   0.1       0.33   10.4   0.0    2.2  2  AP_endonuc_2     Xylose isomerase-like TIM barrel
       0.14   12.8   0.1       0.35   11.5   0.1    1.6  1  Methyltransf_11  Methyltransferase domain
       0.32   11.0   2.6       0.43   10.6   1.3    1.8  2  Exotox-A_target  Exotoxin A, targeting


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.033     2e+02      59     114 ..      92     165 ..      69     180 .. 0.68
   2 ?   10.4   0.0   5.5e-05      0.33      83     136 ..     247     380 ..     197     414 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.033
                                    C...HTTCS.HHHHHHHHHHHHHHHHHH..............TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHH CS
                   AP_endonuc_2  59 d...erear.reesvdalkraielaaaL..............GapllvlhpGtagagpkgseeeawerlaesln 114
                                        +++++  +esv+al   + + +a+              G p+l + +G+  +  ++  + +w+ +ae++ 
  gi|121639234|ref|YP_979458.1|  92 VveeLLAEKpTAESVAALAASLAIVSAIgsvcelaavskffnGNPILGTVSGGLEHFTGKAGNKRWNSIAEVIG 165
                                    25544445568888888888888888888888888888999999999999999666666666666666666554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.5e-05
                                    TBSEEEEEBCC..................................................................... CS
                   AP_endonuc_2  83 GapllvlhpGt..................................................................... 93 
                                    G++ +++++Gt                                                                     
  gi|121639234|ref|YP_979458.1| 247 GIDPIQIMTGTatfytlrcylddrpiflgrngrisvfgseralaryladehdhdlsdlstyddirtaatdgslavavtdd 326
                                    55555666555666666666666666666666666666666666666666666666666666666666666666666666 PP

                                    ...........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTT CS
                   AP_endonuc_2  94 ...........agagpkgseeeawerlaeslneladyaekegvklalEtlagsg 136
                                               + +gp+  ++e++++++e l++++dy e+  v  alEt+ + g
  gi|121639234|ref|YP_979458.1| 327 nvyvlsglvddFADGPDAVDREQLDLAVELLRDIGDYSEDSAVDKALETTRPLG 380
                                    666666677777788889999****************************98766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.9e-05      0.35      22      74 ..      43     100 ..      30     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                                    EEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCT.SS-TT-EEEEEEES-CCC- CS
                Methyltransf_11  22 vgvDlskemlklakekaseegl....kvefvvadaekl.pfednsfDlvvssevlhhv 74 
                                    +g++    +++ +++ ++++ +    + ++  a a++l p edn+fDlvv+ e l   
  gi|121639234|ref|YP_979458.1|  43 YGFESVSDLVAFVRTDTENDLVdhpaWQDLTGAHAHNLnPAEDNQFDLVVVEELLAEK 100
                                    6666666666666666666655666666778899999*9************9988655 PP

>> Exotox-A_target  Exotoxin A, targeting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   7.8e+03      56      72 ..      87     104 ..      86     121 .. 0.63
   2 ?   10.6   1.3   7.2e-05      0.43      53     124 ..     167     234 ..     158     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                                    GHHH.HHHHHHHS.TTTT CS
                Exotox-A_target  56 rvdq.vvddllasrpvsG 72 
                                    ++d  vv++lla +p++ 
  gi|121639234|ref|YP_979458.1|  87 QFDLvVVEELLAEKPTAE 104
                                    555415677888888754 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.2e-05
                                    -GGGHHHHHHHHHHS.TTTT.......HHHHHHHHHSHHHHHHHHHHHHHHHHHHHCC-TT--HHHHTT--E CS
                Exotox-A_target  53 sfdrvdqvvddllasrpvsGaqdpealadlGeavretpeqarealaeaearleayvangaGadeddaaradv 124
                                    s+d v   +d+++++ p       e   ++ e + e+pe a e  ae ea  ++  a ++ ++e+da    v
  gi|121639234|ref|YP_979458.1| 167 SWDDVLAAIDEIIST-PEVD---AELSEKVAEELAEEPEGAEEVAAEVEATQDTQEAAESDDEEADAPGDSV 234
                                    899999999999988.7655...566677788999*******************999999999999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3056.53
//
Query:       gi|121639235|ref|YP_979459.1|  [L=308]
Description: hypothetical protein BCG_3377c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-10   41.0   0.2    1.6e-09   37.8   0.2    1.9  1  Abhydrolase_1  alpha/beta hydrolase fold
    9.6e-10   39.4  14.8    1.2e-09   39.2  14.8    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0019   17.5   0.1      0.027   13.7   0.1    2.0  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   2.6e-13   1.6e-09       7     253 ..      45     288 ..      42     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.6e-13
                                    -STTTCGGGGTTGHHHHHHHHT.TSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHH CS
                  Abhydrolase_1   7 hGlpgssdvwaerglapaLakd.gfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGm 85 
                                    hG p s   + +  +a++ a++ gf++i++D +G+g+S++       +++++   +d+ ++ da+ ++++ +vGhS  G 
  gi|121639235|ref|YP_979459.1|  45 HGTPSSRL-EGA--FADGAARRtGFRLIAIDRPGYGRSTFQAG---RNFRDW--PADVCALADAFELEEFGVVGHSGAGP 116
                                    55555443.333..677888889********************...678885..************************** PP

                                    HHHHHHHHHGGGEEEEEEESE............CSSCCHHHHHHHHHHHHHHCHHCHHHH...HHHHHHHHHHHHCCSCH CS
                  Abhydrolase_1  86 ialayaaeyperVkalvllga............idpaaslieaqrqqaksfpdffdgyaa...dcarnpagplladelaa 150
                                      +a  a  p    +l+++ga            + + ++ +++  + a s p+ f   +a   +ca+ + g++++  +aa
  gi|121639235|ref|YP_979459.1| 117 HLFACGAVIPR--TRLAFVGAlgpwgplatpdiMRSLNAADRCYARLARSGPRLFGALFAplgWCAKYTPGLFSTLLAAA 194
                                    *********77..6666666644466666666555555555555566655555555554322256666666666666666 PP

                                    HHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHH CS
                  Abhydrolase_1 151 leqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkal 230
                                    ++  ++        +++ rf ++ ++++    ++++    + + ++++++  +   l +v +pt ++ g+ D  vp  ++
  gi|121639235|ref|YP_979459.1| 195 VPAADKH------LLSDERFGRHLRAIQLEAFRQGSRGAAYESFLQFRPWGFD---LAEVAVPTHIWLGDRDSFVPRAMG 265
                                    6666553......6666677776666666666666666666666666666666...556999****************** PP

                                    HHHHHCHTSEEEEEEETCSSSHH CS
                  Abhydrolase_1 231 edlaqllpkkrlvvisdagHlaf 253
                                    e+l++++p++ l+   + gH+ +
  gi|121639235|ref|YP_979459.1| 266 EYLQRAIPHVDLHWAHGKGHFNI 288
                                    *********99999999999876 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2  14.8   1.9e-13   1.2e-09       5     218 ..      45     295 ..      19     297 .. 0.55

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.9e-13
                                    --GC.....GCHHHH....HHHHCCT..CEEEEE--TTSTS-GGCS....--HHHCHHHHHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   5 HGagssassWlvapL....aallaag..vhvlapDlpGhGrsdppp....ldledladlaalldelaagggpvvlvGHSl 74 
                                    HG++        ++L    a  +a++  ++ +a+D+pG+Grs+  +     d+   ad+ al+d++     ++ +vGHS 
  gi|121639235|ref|YP_979459.1|  45 HGTP-------SSRLegafADGAARRtgFRLIAIDRPGYGRSTFQAgrnfRDW--PADVCALADAFE--LEEFGVVGHSG 113
                                    4433.......33442222333333366899*********7744444333555..699999999997..9999******5 PP

                                    HHH.HHHHHHHCC....EE.EEES-..----TTT.........S----TTHHHHHHTT-C........CCCHCCH..... CS
                  Abhydrolase_6  75 GGa.lalaaapla..lvvg.vlldppptalpagl.........laaalelllallallrl........lawlsre..... 128
                                     G  l +    +a  ++ +  ++ +    +p+g          l+aa + +++l ++ ++        l+w +++     
  gi|121639235|ref|YP_979459.1| 114 AGPhLFAC---GAviPRTRlAFVGA---LGPWGPlatpdimrsLNAADRCYARLARSGPRlfgalfapLGWCAKYtpglf 187
                                    55425555...55334344677777...3333333333333443333333333333222222212222344433233322 PP

                                    .........S-HSCCCCHHHCCCCHCHCCCGHH...................HHCCHHCHTTCC.HHTT-TTGCEEE.CT CS
                  Abhydrolase_6 129 .........plprlfladedadaawrarlarla...................allaglgllpaa.awadlpvpllvl.gg 178
                                             ++++++l+de                                 a+ ++l ++p+  ++a + vp++++ g+
  gi|121639235|ref|YP_979459.1| 188 stllaaavpAADKHLLSDER------------FgrhlraiqleafrqgsrgaAYESFLQFRPWGfDLAEVAVPTHIWlGD 255
                                    22233333212223333333............022222222443333333333333333222222888888888885468 PP

                                    T-CHHHHCHHCCCH..STTEEETCE...SSS-HHHHSHHHHH CS
                  Abhydrolase_6 179 eDplvprllerlla..qagarlpvvlpgaGHlphleepdeva 218
                                    +D  vpr + ++l+  +++++l +   g GH+  + + d++ 
  gi|121639235|ref|YP_979459.1| 256 RDSFVPRAMGEYLQraIPHVDL-HWAHGKGHFNIE-DWDAIL 295
                                    888***********9*******.********9888.987765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   4.5e-06     0.027      29     232 ..      63     285 ..      59     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                    Hydrolase_4  29 aqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsa 108
                                    + Gf  +a+D  G+Grs  + g  ++f d+ +D+ a+ ++++     +++ ++GhS  G   ++ ++  p+  ++l +++
  gi|121639235|ref|YP_979459.1|  63 RTGFRLIAIDRPGYGRSTFQAG--RNFRDWPADVCALADAFE----LEEFGVVGHSGAGPHLFACGAVIPR--TRLAFVG 134
                                    5799*************88888..9*********99988887....4457789***999999999999999..8888888 PP

                    Hydrolase_4 109 Palkikaklkappllklllkllgkllpklqv..............................snnlkadslsrdpevvaay 158
                                    ++  + +   +p +++  l+ + +++ +l                                  +   + l +d+++ + +
  gi|121639235|ref|YP_979459.1| 135 ALGPWGPL-ATPDIMRS-LNAADRCYARLARsgprlfgalfaplgwcakytpglfstllaaAVPAADKHLLSDERFGRHL 212
                                    87555544.35555554.44444444444444555777888899999999999999999996666777788888888888 PP

                    Hydrolase_4 159 eadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                    +a +l   ++ + + ++e +        + a++ +P+ +  G++D  v+++  + l ++++  ++ l++ +g  H
  gi|121639235|ref|YP_979459.1| 213 RAIQLEaFRQGSRGAAYESFLQFRPWGFDLAEVAVPTHIWLGDRDSFVPRAMGEYLQRAIP--HVDLHWAHGKGH 285
                                    9888887788888888888888888888888899***************999999999999..688888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2311.19
//
Query:       gi|121639236|ref|YP_979460.1|  [L=103]
Description: hypothetical protein BCG_3378c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 734.22
//
Query:       gi|121639237|ref|YP_979461.1|  [L=365]
Description: adenosine deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     2e-110  369.2   0.0   2.3e-110  369.0   0.0    1.0  1  A_deaminase  Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.0   0.0  1.3e-114  2.3e-110       2     328 .]      13     351 ..      12     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.0 bits;  conditional E-value: 1.3e-114
                                    S-EEEEEEECCCSS-HHHHHHHHHHHCHT..SS-SCCCCCCCCHCHCCHHHHCCHCCCHHCCCHHHTCCCCCCHHHHHHC CS
                    A_deaminase   2 lpKvdlHvHldgclnpktllrlakkkgikeldekvveedeklltlqekfesLkeflydlsvdvlvlhwlievvrllavek 81 
                                    +pK+ lH+Hldg+l+p+t+l++a + g+++l++++v+++++++++q+++ sL+++l+++s++v+v++ ++e+++++a+e+
  gi|121639237|ref|YP_979461.1|  13 APKALLHDHLDGGLRPATVLDIAGQVGYDDLPATDVDALASWFRTQSHSGSLERYLEPFSHTVAVMQ-TPEALYRVAFEC 91 
                                    69*****************************************************************.************ PP

                                    CCCCHCTTCCCCCCCCSHHHHHHH-GCSTCCHHHHCCCCCCCCCCHCCT-EEEEEECCETT....TCCGHCCCHHHHHHC CS
                    A_deaminase  82 akdlakdfvkylevifsPlfeatagpqlpelevvlkvvdgfdsvedeskvkerlilvksrk....peewseeinelasyy 157
                                    a+dla+d+v+y+ev+f+P++++++g  l++++vv++v++gf+++e+++++++++i+v++ +    ++++s+ei+ela+++
  gi|121639237|ref|YP_979461.1|  92 AQDLAADSVVYAEVRFAPELHISCG--LSFDDVVDTVLTGFAAGEKACAADGQPITVRCLVtamrHAAMSREIAELAIRF 169
                                    *************************..*********************************999***************** PP

                                    CCCCCCCCCCCC-TTSTTGGGHHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHC CS
                    A_deaminase 158 rdytvvnldllndekiepaslflklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllala 237
                                    rd++vv++d++++e+++p++++l+++++++++++++t+HaGEa+gl++++eA+++++a+r+gHGvr+++d++++++  ++
  gi|121639237|ref|YP_979461.1| 170 RDKGVVGFDIAGAEAGHPPTRHLDAFEYMRDHNARFTIHAGEAFGLPSIHEAIAFCGADRLGHGVRIVDDIDVDADGGFQ 249
                                    ******************************************************************************** PP

                                    ...........T-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHHHHH CS
                    A_deaminase 238 ...........qiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseedlae 306
                                               +iple+cP+SNv++ga++++ae+P++ +++++++v++ntD++l+++t+++ e+++++++f+++++dla+
  gi|121639237|ref|YP_979461.1| 250 lgrlaailrdkRIPLELCPSSNVQTGAVASIAEHPFDLLARARFRVTVNTDNRLMSDTSMSLEMHRLVEAFGYGWSDLAR 329
                                    ******************************************************************************** PP

                                    HHHHHHHCSSS-HHHHHHHCHC CS
                    A_deaminase 307 larNsvkqsflsadekkklldk 328
                                    +++N++k++f+++d++ +++d+
  gi|121639237|ref|YP_979461.1| 330 FTVNAMKSAFIPFDQRLAIIDE 351
                                    *******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2533.87
//
Query:       gi|121639238|ref|YP_979462.1|  [L=427]
Description: thymidine phosphorylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-32  113.7   1.5    1.6e-32  113.1   1.5    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.2e-20   70.9   0.0    2.5e-19   68.7   0.0    2.1  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    3.1e-17   62.2   0.0    6.9e-17   61.0   0.0    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   1.5   2.7e-36   1.6e-32       4     234 ..      83     291 ..      81     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 2.7e-36
                                    BEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTS.T--ST--HHHHHHHHHHHSEEEEEHH CS
                Glycos_transf_3   4 lvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLeal.gvnleltpeeveklleevgvgflfap 82 
                                    +vD+++TGG+g+++   ++ + +vvAa+G  v++ ++r++++++G++D+Le++ g+  +l++++v++ l +vg + +fa 
  gi|121639238|ref|YP_979462.1|  83 TVDKHSTGGVGDKI---TLPLVPVVAACGGAVPQASGRGLGHTGGTLDKLESItGFTANLSNQRVREQLCDVGAA-IFAA 158
                                    79***********9...********************************************************88.5888 PP

                                    SSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHH CS
                Glycos_transf_3  83 eyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllaktt 162
                                     ++++++  +++ r+++  Tv +l  PLi++        +++sk+lae++ +++ +++v++++++ +    ++++la+t+
  gi|121639238|ref|YP_979462.1| 159 GQLAPADAKLYALRDITG-TVESL--PLIAS--------SIMSKKLAEGAGALVLDVKVGSGAFMRS--PVQARELAHTM 225
                                    89999*************.*****..*****........****************************..999******** PP

                                    HHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSS CS
                Glycos_transf_3 163 vaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkad 234
                                    v   + +g  t + l++++ +l+r  ++ale+    e++e+l +   g+ +   ++l+l +ag++l lag + 
  gi|121639238|ref|YP_979462.1| 226 VELGAaHGVPTRALLTEMNCPLGRTVGNALEV---AEALEVLAGG--GPPDV--VELTLRLAGEMLELAGIHG 291
                                    ***99999************************...8888888776..66665..8***********9998664 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.5e+03       5      19 ..     216     230 ..     214     234 .. 0.90
   2 !   68.7   0.0   4.2e-23   2.5e-19       3      74 ..     340     411 ..     338     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                    E-HHHHHHHHHHTTT CS
                         PYNP_C   5 idareiGlaaveLGA 19 
                                    ++are++  +veLGA
  gi|121639238|ref|YP_979462.1| 216 VQARELAHTMVELGA 230
                                    6899**********9 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 4.2e-23
                                    EEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHHEEE CS
                         PYNP_C   3 seidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkkaiki 74 
                                     +ida+++Glaa++LGAGR++++ ++++++G+++h+++G+ V  Gepl+t+Y+n +e++ +a ++l   ++i
  gi|121639238|ref|YP_979462.1| 340 GDIDAMAVGLAAWRLGAGRSRPGARVQHGAGVRIHRRPGEPVVVGEPLFTLYTNAPERFGAARAELAGGWSI 411
                                    689***********************************************************9999888776 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   1.2e-20   6.9e-17       3      63 .]      11      71 ..       9      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.2e-20
                                   HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                   +i+ +rdg+ L+++ i ++++++++g+v d q++A+LmA+  +G++  Eia ++ Am++sg
  gi|121639238|ref|YP_979462.1| 11 VIRTKRDGGRLSDAAIDWVVKAYTDGRVADEQMSALLMAIVWRGMDRGEIARWTAAMLASG 71
                                   799*******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2835.28
//
Query:       gi|121639239|ref|YP_979463.1|  [L=133]
Description: cytidine deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-10   41.4   0.4    1.3e-10   41.1   0.4    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    8.2e-09   35.8   1.4    4.1e-07   30.3   0.2    2.1  2  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.4   1.4e-14   1.3e-10      11      96 ..      13     103 ..       7     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.4e-14
                                    HHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE......EE--BH CS
                dCMP_cyt_deam_1  11 alkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv......tlePCs 83 
                                    a +aa  a+ ++s+f VGa+ + ++ +++tg+n e+ ++  t++AE   +++  ++gg +l    l++       l PC+
  gi|121639239|ref|YP_979463.1|  13 ATQAAAGAYvPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRL--LALACvdghgsVLMPCG 90 
                                    6788888999**********99999*********************999999988864455..455556999999***** PP

                                    HHHHHHHHHT-SE CS
                dCMP_cyt_deam_1  84 mCakaiiqsgikk 96 
                                    +C++++ + g ++
  gi|121639239|ref|YP_979463.1|  91 RCRQVLLEHGGSE 103
                                    ******9987655 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   4.5e-11   4.1e-07      46     102 ..       8      63 ..       3      79 .. 0.84
   2 !    4.9   0.1    0.0032        29       1      17 [.     115     131 ..     115     133 .] 0.86

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4.5e-11
                                    HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHH CS
                dCMP_cyt_deam_2  46 elkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlva 102
                                    +l+ +A +aa  +y+pys+   G a  ++dg+v++G  +E++ +  +L + ++A+v 
  gi|121639239|ref|YP_979463.1|   8 MLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCA-ECAVVC 63 
                                    57889*********************9******************99976.444443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0032
                                    HHHHSTT--SGGGGTS- CS
                dCMP_cyt_deam_2   1 LsslLPhsFgPkdLlsk 17 
                                    L +lLP++Fg +dL  +
  gi|121639239|ref|YP_979463.1| 115 LGDLLPDAFGLDDLPRE 131
                                    6799**********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 918.66
//
Query:       gi|121639240|ref|YP_979464.1|  [L=112]
Description: succinate dehydrogenase (cytochrome B-556 subunit) SDHC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-20   71.0   8.1    1.1e-19   70.7   8.1    1.1  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
  ------ inclusion threshold ------
       0.64   10.1   5.4       0.29   11.2   1.2    1.9  2  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   8.1   1.2e-23   1.1e-19      20     120 ..       1      96 [.       1      97 [. 0.89

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.2e-23
                        Sdh_cyt  20 awlsilhritGvallvglllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwDlglgle 99 
                                    +w +++hri+G+ +++ +l+++v   +a +++sp+++++v a ++ pi  +++ +l++a+l+H+lnGiR++l+D+   ++
  gi|121639240|ref|YP_979464.1|   1 MWSWVCHRISGATIFF-FLFVHVL-DAAMLRVSPQTYNAVLATYKTPIVGLMEYGLVAAVLFHALNGIRVILIDF---WS 75 
                                    8***************.5555544.3366788******************************************6...48 PP

                        Sdh_cyt 100 lesarksalavlalavalvlv 120
                                    +  ++++  ++++++v+l l+
  gi|121639240|ref|YP_979464.1|  76 EGPRYQRLMLWIIGSVFLLLM 96 
                                    89*************999875 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2   3.2e-05      0.29      31      83 ..      11      63 ..       3      69 .. 0.83
   2 ?    1.1   0.2     0.045     4e+02      13      45 ..      72     105 ..      66     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                 Fumarate_red_C 31 avlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLaaallhav 83
                                     ++ +f +v +l  ++L  ++++y+a l++ + P+v l++  ++aa+l+ha 
  gi|121639240|ref|YP_979464.1| 11 GATIFFFLFVHVLDAAMLRVSPQTYNAVLATYKTPIVGLMEYGLVAAVLFHAL 63
                                   4455566666667778888999*****************************96 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.045
                 Fumarate_red_C  13 tWWkknpfYrfYmlrEatavlvalfa.lvlllgl 45 
                                    + W++ p Y+  ml    +v+++l + + +++g+
  gi|121639240|ref|YP_979464.1|  72 DFWSEGPRYQRLMLWIIGSVFLLLMVpAGVVVGI 105
                                    5789999999999988888887766524455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 852.95
//
Query:       gi|121639241|ref|YP_979465.1|  [L=144]
Description: succinate dehydrogenase (hydrophobic membrane anchor subunit) sdhD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-16   60.5   2.8    2.1e-16   60.0   2.8    1.2  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   2.8   1.2e-20   2.1e-16       5     120 ..      18     126 ..      14     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.2e-20
                        Sdh_cyt   5 rplsphlqlyrlplgawlsilhritGvallv.glllllvwlllalslsspesfarvvallaspiklilllllllallyHl 83 
                                    +p sp+++ + ++ + ++++++r++Gv+l++ ++ +l+++l+ ++ ++   +f+ v++ +asp++    llll+++  H+
  gi|121639241|ref|YP_979465.1|  18 NPRSPRRRAGMPNFEKFAWLFMRFSGVVLVFlAIGHLFIMLMWDN-GVYRLDFNFVAQRWASPFWQTWDLLLLWLAQLHG 96 
                                    699***********************************9988888.89999***********8888777888888888** PP

                        Sdh_cyt  84 lnGiRhllwDlglglelesarksalavlalavalvlv 120
                                     nG+R ++ D+       s++ +  ++l  +++l+++
  gi|121639241|ref|YP_979465.1|  97 GNGLRTIIDDY-------SRKDTTRFWLNSLLVLSML 126
                                    **********8.......2333344444444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1029.47
//
Query:       gi|121639242|ref|YP_979466.1|  [L=590]
Description: succinate dehydrogenase flavoprotein subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-110  369.9   3.7   2.5e-110  369.4   3.7    1.2  1  FAD_binding_2   FAD binding domain
    1.1e-43  148.3   0.2    1.9e-43  147.5   0.2    1.4  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.9e-05   24.0   1.8       0.05   12.8   0.2    3.3  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.5e-05   22.3   0.7      0.085   12.1   0.1    2.9  3  Thi4            Thi4 family
    0.00082   19.1   1.4     0.0042   16.7   1.4    2.1  1  DAO             FAD dependent oxidoreductase
      0.003   16.3   1.7       0.12   11.1   0.7    2.8  3  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.088   12.1   0.2       0.14   11.4   0.2    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
      0.092   12.0   0.6        0.2   10.9   0.6    1.5  1  FAD_binding_3   FAD binding domain
        4.3    6.3   6.9        2.3    7.2   2.2    2.3  2  GIDA            Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.4   3.7  1.3e-113  2.5e-110       1     417 []       8     401 ..       8     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 369.4 bits;  conditional E-value: 1.3e-113
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HH CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqp 80 
                                    Dv+++G+G+AG++AA+ea     ++av++k  +++++t ++qGg++a+l  +     ++d++e+h +dt+k++d+ladq+
  gi|121639242|ref|YP_979466.1|   8 DVVIVGAGGAGMRAAVEA-GPRVRTAVLTKLYPTRSHTGAAQGGMCAAL-ANV----EDDNWEWHTFDTVKGGDYLADQD 81 
                                    9***************87.55568*************************.333....46********************* PP

                                    HHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SST......EEEE-.STT-......HHHHHHHHHHHHHHTC CS
                  FAD_binding_2  81 lveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsat......artlhdaadarretlvtghallarlvesarka 154
                                    +ve+++++a +av  Le++g+pf+rt++g++d+r++Gg++++      +r ++ aad+      tgh +l +l++++ k+
  gi|121639242|ref|YP_979466.1|  82 AVEIMCKEAIDAVLDLEKMGMPFNRTPEGRIDQRRFGGHTRDhgkapvRRACY-AADR------TGHMILQTLYQNCVKH 154
                                    *****************************************************.****......**************** PP

                                    TEEEEESEEEEEEEECTT....EEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHH CS
                  FAD_binding_2 155 gvdfqerteadeLivedg....rvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdgl 230
                                    +v+f+++ +a++L  ++      +tG+++ ++++g ++ ++akavv+atgG gr           ++ t+na++ tGdg+
  gi|121639242|ref|YP_979466.1| 155 DVEFFNEFYALDLALTQTpsgpVATGVIAYELATGDIHVFHAKAVVIATGGSGR----------MYKTTSNAHTLTGDGI 224
                                    **************98667789********************************..........**************** PP

                                    HHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH.HH CS
                  FAD_binding_2 231 alalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsraileke 303
                                    ++++r+g++l+d  me+ qfhPt+l     g giLi+ea+rgeGg l++ +G+rFm        +la+rd+v+r+++  e
  gi|121639242|ref|YP_979466.1| 225 GIVFRKGLPLED--MEFHQFHPTGLA----GLGILISEAVRGEGGRLLNGEGERFMeryaptiVDLAPRDIVARSMV-LE 297
                                    ************..************....9**********************************************.88 PP

                                    HHTTTS....CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBE CS
                  FAD_binding_2 304 iaeggs....eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetd 379
                                    + eg++    +++vy+d++h l++e lea+l++i e a++ l+      +dp ++ +p       v+p++hy mgG++t+
  gi|121639242|ref|YP_979466.1| 298 VLEGRGagplKDYVYIDVRH-LGEEVLEAKLPDITEFARTYLG------VDPVTELVP-------VYPTCHYLMGGIPTT 363
                                    8888888*************.**********************......*********.......*************** PP

                                    TTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                  FAD_binding_2 380 engrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                     +g+vl+++ +++pGLYAaGe+a+++vhganrlg nsl
  gi|121639242|ref|YP_979466.1| 364 VTGQVLRDNTSVVPGLYAAGECACVSVHGANRLGTNSL 401
                                    ************************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.2   9.7e-47   1.9e-43       2     128 .]     456     590 .]     455     590 .] 0.96

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 9.7e-47
                                    HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTB CS
                 Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaH 81 
                                     +L++ m+++++vfRtee+Lk+al+++++l+er+++++v+dk+k++N++l+ea+el  llelAe+++++Al+RkESrG+H
  gi|121639242|ref|YP_979466.1| 456 GALQQSMDNNAAVFRTEETLKQALTDIHALKERYSRITVHDKGKRFNTDLLEAIELGFLLELAEVTVVGALNRKESRGGH 535
                                    579***************************************************************************** PP

                                    EBTTS-SEETTT-SEEEEE...........TT-SS-EEEEEE--GGG--S---SS CS
                 Succ_DH_flav_C  82 aredfperdDenwlkhtlasld........aakeeveleyepveletlkpkeRsY 128
                                    ared+p+rdD n+++ht+a+ +        + +++v+l+++pv  +  +pkeR+Y
  gi|121639242|ref|YP_979466.1| 536 AREDYPNRDDVNYMRHTMAYKEigadkegpELRSDVRLDFKPVVQTRYEPKERKY 590
                                    *******************888999888887777899999**************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   2.5e-05      0.05       1      21 [.       7      27 ..       7      66 .. 0.85
   2 ?    2.5   0.0     0.036        71      93     114 ..     189     210 ..     149     227 .. 0.80
   3 !    6.3   0.0    0.0024       4.8     249     279 ..     359     391 ..     336     421 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                   CSEEEE--SHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq 21
                                   +dvv++G+G AG++aa +++ 
  gi|121639242|ref|YP_979466.1|  7 YDVVIVGAGGAGMRAAVEAGP 27
                                   69**************99875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.036
                                    TCEEEEEESEEEE---EEE-BC CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  93 gdeekiaydklvlAtGssprdl 114
                                    gd + + ++++v+AtG+s r  
  gi|121639242|ref|YP_979466.1| 189 GDIHVFHAKAVVIATGGSGRMY 210
                                    555667899*******987765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0024
                                    T-EEEETTEEE--TTSBESSTTEEE-GGGC....T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                    Pyr_redox_2 249 glelderggivvdeflrtnvpgiyaiGDva....g 279
                                    g++++ +g+++ d ++   vpg+ya+G +a    +
  gi|121639242|ref|YP_979466.1| 359 GIPTTVTGQVLRDNTS--VVPGLYAAGECAcvsvH 391
                                    6777777777777766..49**********55552 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   4.3e-05     0.085      18      64 ..       7      53 ..       2      97 .. 0.75
   2 ?   -1.2   0.0      0.49   9.8e+02     153     176 ..     190     213 ..     143     229 .. 0.76
   3 !    7.0   0.0    0.0015         3     203     233 ..     367     398 ..     362     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS..S--TTTTTTSTTB CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersv..spGGGawlGGqlf 64
                                    DvvivGaG +G+ aa   + +  +++a+l +        Ga  GG+  
  gi|121639242|ref|YP_979466.1|  7 YDVVIVGAGGAGMRAAVEAGPR--VRTAVLTKLYptRSHTGAAQGGMCA 53
                                   6***************887755..9999997654112345667777765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.49
                                    B-EEEEEEEEEE--GSSSTTTTHH CS
                           Thi4 153 DPlvirakvvvdatGhdgeivavv 176
                                    D  v +ak+vv atG  g + +++
  gi|121639242|ref|YP_979466.1| 190 DIHVFHAKAVVIATGGSGRMYKTT 213
                                    556788888999999888887765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0015
                                    HHHHHECEEETTEEE-T.HHHHHHHT-EB--S CS
                           Thi4 203 aivkktrevvpnlyvaG.mevaevdganRmGp 233
                                    +++++   vvp+ly+aG  +   v+ganR+G+
  gi|121639242|ref|YP_979466.1| 367 QVLRDNTSVVPGLYAAGeCACVSVHGANRLGT 398
                                    68899999*********457789*******96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.4   2.1e-06    0.0042       1     203 [.       8     206 ..       8     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                                    EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHH...HHHHHHHS CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg.VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeel...releeelg 76 
                                    dvvi+G+G +G+ +A e+  r  +++l k   + +  +g+++g   ++l++ ++      +  ++++     + l+++ +
  gi|121639242|ref|YP_979466.1|   8 DVVIVGAGGAGMRAAVEAGPRVrTAVLTKL-YPTRSHTGAAQGGMCAALANVEDD----NWEWHTFDTVkggDYLADQDA 82 
                                    9*****************54427******9.777666666665555558778876....666666666655466666556 PP

                                    STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTT.TEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHH CS
                            DAO  77 ididyrrtGllslaadeeelealdkllallleagl.daelldaeevrelepalpgllgalfypdtgqvdpakltaalara 155
                                    ++i  ++    +l      le++   + + ++ g  d + + ++ +r+     ++++ a++  d  +   +  ++ l++ 
  gi|121639242|ref|YP_979466.1|  83 VEIMCKEAIDAVLD-----LEKMGMPFNR-TPEGRiDQRRFGGH-TRDHGK--APVRRACYAAD-RT--GHMILQTLYQN 150
                                    55555554444442.....3333222222.33332266667776.665554..47888888666.33..55899999999 PP

                                    HHHTT-EEEESECEEEEEEEE....TCEEEEE...EECTEEE..EEEEEEEE--GGG CS
                            DAO 156 aealGveilegtevtgleeed....gkvwgve...rttpgen..daadavVnaaGaw 203
                                    + ++ ve++++  + +l  ++      ++gv     +t g +  ++a+avV+a+G  
  gi|121639242|ref|YP_979466.1| 151 CVKHDVEFFNEFYALDLALTQtpsgPVATGVIayeLAT-GDIhvFHAKAVVIATGGS 206
                                    99999999999888887443334443444444664333.444234679999999965 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.7   5.9e-05      0.12       1      26 [.       7      32 ..       7      52 .. 0.85
   2 ?    2.5   0.0     0.024        47     105     165 ..     137     206 ..     122     219 .. 0.67
   3 ?   -1.1   0.0       0.3     6e+02     372     384 ..     373     385 ..     355     393 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.9e-05
                                   -SEEEE--SHHHHHHHHHHHHTT--E CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrV 26
                                   +dv+++G+G AG+ aA++a+ r +  
  gi|121639242|ref|YP_979466.1|  7 YDVVIVGAGGAGMRAAVEAGPRVRTA 32
                                   59****************97665544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.024
                                    T.-CHHHHHHHHHHHHHHT-EEE-S--EEEE.........ECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 105 sdkaedivdallkelkeagvklrletevksv.........ekeedgkfrvktkseeeleadklvlAtGGl 165
                                    +++ + i+++l +++ + +v++  e    ++          ++   +++++t + + ++a+++v+AtGG 
  gi|121639242|ref|YP_979466.1| 137 DRTGHMILQTLYQNCVKHDVEFFNEFYALDLaltqtpsgpVATGVIAYELATGDIHVFHAKAVVIATGGS 206
                                    55566677777777777777776666665554433333322222234556666788999*********96 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.3
                                    BTTSTTEEE-GGG CS
                    HI0933_like 372 skkvpgLffaGEv 384
                                    +  vpgL+ aGE+
  gi|121639242|ref|YP_979466.1| 373 TSVVPGLYAAGEC 385
                                    4579********7 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   7.2e-05      0.14       1      30 [.       8      39 ..       8     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve..e 30
                                   Dvv+vG+g aG+ AA+ A  + ++ +L++  +
  gi|121639242|ref|YP_979466.1|  8 DVVIVGAGGAGMRAAVEAGPRVRTAVLTKlyP 39
                                   9*****************99999999987442 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6    0.0001       0.2       2      38 ..       7      42 ..       6      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38
                                   +dV+IVGaG aG+ +a +   + vr+ +++k   t  
  gi|121639242|ref|YP_979466.1|  7 YDVVIVGAGGAGMRAAVEAGPR-VRTAVLTKLYPTRS 42
                                   79***************99999.99999999765544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.2    0.0012       2.3       1      20 [.       8      27 ..       8      56 .. 0.75
   2 ?    0.9   0.2     0.097   1.9e+02     133     156 ..     188     209 ..     169     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                                   CEEEE-SSHHHHHHHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaaar 20
                                   dv+++G+G AG+ AA++a  
  gi|121639242|ref|YP_979466.1|  8 DVVIVGAGGAGMRAAVEAGP 27
                                   79**************9853 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.097
                                    ETTS-EEEECEEEE--TT-BT-EE CS
                           GIDA 133 tedgetikakavviatGtflkgki 156
                                    t d ++++akavviatG   +g++
  gi|121639242|ref|YP_979466.1| 188 TGDIHVFHAKAVVIATGG--SGRM 209
                                    55667899*********8..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4047.60
//
Query:       gi|121639243|ref|YP_979467.1|  [L=263]
Description: succinate dehydrogenase iron-sulfur subunit [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-30  103.7   0.0    1.4e-29  102.3   0.0    1.7  2  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    3.5e-11   43.4   2.8    6.5e-11   42.5   2.8    1.5  1  Fer4_8    4Fe-4S dicluster domain
    3.5e-10   39.8   4.0    5.8e-10   39.1   4.0    1.3  1  Fer4_10   4Fe-4S dicluster domain
    8.2e-06   26.3   2.4    1.6e-05   25.4   2.4    1.5  1  Fer4_17   4Fe-4S dicluster domain
     0.0016   18.6   6.4     0.0016   18.6   6.4    2.1  3  Fer4_9    4Fe-4S dicluster domain
     0.0027   17.9   1.0       0.63   10.3   0.1    2.3  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.9  11.9       0.11   13.2  10.7    2.5  2  Fer4_7    4Fe-4S dicluster domain
      0.041   14.6   4.1       0.74   10.6   0.5    2.6  2  Fer4_15   4Fe-4S single cluster domain
      0.058   13.2   9.5       0.13   12.1   5.0    2.5  2  Fer4      4Fe-4S binding domain
       0.18   12.4  10.5       0.62   10.7   4.2    2.6  2  Fer4_4    4Fe-4S binding domain
       0.83    9.4   9.5        1.6    8.5   0.3    2.5  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        2.9    9.0  14.4        7.3    7.8   0.2    2.7  2  Fer4_3    4Fe-4S binding domain
        2.9    8.2  17.1       0.56   10.4   7.6    2.8  2  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0     1e-32   1.4e-29       1     108 [.      25     139 ..      25     140 .. 0.92
   2 ?   -1.9   0.0       2.3   3.2e+03      29      56 ..     217     246 ..     206     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1e-32
                         Fer2_3   1 tlkvkRfdprrdrg...kqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatik 77 
                                    t+k+ Rf+p+++++   +  +q+++v+  ++d +l++L +ik  +d tl+fr+sC +g+CGs+a++inG ++laC+  ++
  gi|121639243|ref|YP_979467.1|  25 TVKIARFNPDEPDAfaaTGGWQSFRVPCLPSDRLLNLLIYIKGYLDGTLTFRRSCAHGVCGSDAMRINGVNRLACKVLMR 104
                                    689******99876544778************************************************************ PP

                         Fer2_3  78 dlakqks....eieleplpkfpvirDLvvDideml 108
                                    dl  +k+    ++++ep++++pv +DLvvD+++++
  gi|121639243|ref|YP_979467.1| 105 DLLPKKKgkslTVTVEPIRGLPVEKDLVVDMEPFF 139
                                    *97666555567********************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                         Fer2_3  29 dtvldaLlkik..eevdptlafrasCregi 56 
                                     + ld+L+++   ++  +t+++  sC  gi
  gi|121639243|ref|YP_979467.1| 217 AERLDILNEVDgvWRCRTTFNCTESCPRGI 246
                                    556788888862234477777778887765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   2.8   4.7e-14   6.5e-11       3      65 .]     174     246 ..     172     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 4.7e-14
                         Fer4_8   3 ekCieCgaCqsaCpvlrr...........tk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                     kCi C +C+++Cpv+ +            + ++++d+r+eaa+  ++ + l+e +++w+C t+ +Cte Cp gi
  gi|121639243|ref|YP_979467.1| 174 TKCILCACCTTSCPVFWHegsyfgpaaivNAhRFIFDSRDEAAA--ERLDILNEVDGVWRCRTTFNCTESCPRGI 246
                                    79***********94444444444444444449999****9777..6777778899****************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   4.0   4.2e-13   5.8e-10       4      56 .]     171     243 ..     168     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.2e-13
                        Fer4_10   4 idddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     d+ +Ci C+ C+++CP+ +                    ++++a +e+ ++  + ++v++C + ++C+e+CP
  gi|121639243|ref|YP_979467.1| 171 DDTTKCILCACCTTSCPVFWhegsyfgpaaivnahrfifdSRDEAAAERLDILNEVDGVWRCRTTFNCTESCP 243
                                    57889*************99********************99******************************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.4   1.1e-08   1.6e-05       1      60 [.     175     246 ..     175     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.1e-08
                        Fer4_17   1 rCiqCgyClpeCpsyeaydne..pkkllraakl..........glleeaeke.......ekaslCieCgeCerkCPqgl 60 
                                    +Ci C++C+ +Cp ++  +++  p+ +++a ++          +       +       + + +C +  +C+++CP g+
  gi|121639243|ref|YP_979467.1| 175 KCILCACCTTSCPVFWHEGSYfgPAAIVNAHRFifdsrdeaaaE-------RldilnevDGVWRCRTTFNCTESCPRGI 246
                                    6****************887555999999888888644443322.......14455445899**************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2         6   8.2e+03      11      17 ..      83      89 ..      77      99 .. 0.48
   2 !    7.9   5.3    0.0024       3.3      28      47 ..     168     187 ..     155     191 .. 0.69
   3 !   18.6   6.4   1.2e-06    0.0016       1      49 [.     175     245 ..     175     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
                         Fer4_9 11 aCpagvv 17
                                   +C ++++
  gi|121639243|ref|YP_979467.1| 83 VCGSDAM 89
                                   2444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0024
                         Fer4_9  28 lraaseeaCigCgaCveaCp 47 
                                     r ++ ++Ci C  C+  Cp
  gi|121639243|ref|YP_979467.1| 168 ARYDDTTKCILCACCTTSCP 187
                                    23333378999999999999 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.2e-06
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                    kC+ C  C+++Cp   ++++ ++  a ++a +                       ++C +   C+e Cp+g
  gi|121639243|ref|YP_979467.1| 175 KCILCACCTTSCPVFWHEGSYFGPAAIVNAHRFifdsrdeaaaerldilnevdgvWRCRTTFNCTESCPRG 245
                                    7***********88888888888888877776678888888888**************************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00045      0.63      46      73 ..     161     188 ..     132     191 .. 0.81
   2 !    6.1   0.1     0.009        12      53      82 ..     224     253 ..     204     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                        Fer4_18  46 alkekeerkekgagdcidcescvkvcPt 73 
                                     ++ +++ + +++++ci c  c + cP+
  gi|121639243|ref|YP_979467.1| 161 IQSPTDRARYDDTTKCILCACCTTSCPV 188
                                    4555677788999**************7 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.009
                        Fer4_18  53 rkekgagdcidcescvkvcPtgidirkGlq 82 
                                    ++ +g+  c +   c + cP gi++ k +q
  gi|121639243|ref|YP_979467.1| 224 NEVDGVWRCRTTFNCTESCPRGIEVTKAIQ 253
                                    45567778999999***********99988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.9    0.0014       1.9      27      50 ..     164     188 ..      77     190 .. 0.80
   2 ?   13.2  10.7   7.7e-05      0.11       1      52 []     175     246 ..     175     246 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                         Fer4_7  27 gtekveid.pekClgCgaCvavCPt 50 
                                    +t+++++d  +kC+ C  C + CP+
  gi|121639243|ref|YP_979467.1| 164 PTDRARYDdTTKCILCACCTTSCPV 188
                                    556777763789************7 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.7e-05
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek...............gtekv....eid.pekClgCgaCvavCPtga 52 
                                    +Ci C  C+  Cpv + e  ++  ++                 e++    e+d  ++C ++ +C + CP g+
  gi|121639243|ref|YP_979467.1| 175 KCILCACCTTSCPVFWHEGSYFGPAAivnahrfifdsrdeaAAERLdilnEVDgVWRCRTTFNCTESCPRGI 246
                                    7***********999999775322222222222222222223333344444444689************986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00054      0.74       4      52 ..     172     217 ..     170     220 .. 0.66
   2 ?    4.8   0.2     0.035        49       6      24 ..     230     248 ..     225     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                        Fer4_15   4 DrdaCigcglCvaeapevfelded.glasvllddgeiaegevpddeeeaa 52 
                                    D ++Ci c+ C + +p +  + ++ g a ++       +  +++ +e+aa
  gi|121639243|ref|YP_979467.1| 172 DTTKCILCACCTTSCPVFWHEGSYfGPAAIVN----AHRFIFDSRDEAAA 217
                                    789*************6555555446665552....22345555555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                        Fer4_15   6 daCigcglCvaeapevfel 24 
                                    ++C   ++C + +p+ +e 
  gi|121639243|ref|YP_979467.1| 230 WRCRTTFNCTESCPRGIEV 248
                                    79***********998875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.0   9.8e-05      0.13       3      20 ..     171     188 ..     169     189 .. 0.92
   2 ?    2.9   0.1      0.08   1.1e+02      13      21 ..     237     245 ..     237     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                                    EETTTSSS-THHHHHSTT CS
                           Fer4   3 ideekCigCGaCvevCPv 20 
                                     d+ kCi C  C   CPv
  gi|121639243|ref|YP_979467.1| 171 DDTTKCILCACCTTSCPV 188
                                    5999*************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.08
                                    HHHHHSTTT CS
                           Fer4  13 aCvevCPvg 21 
                                    +C e CP g
  gi|121639243|ref|YP_979467.1| 237 NCTESCPRG 245
                                    5******87 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.2   0.00045      0.62       3      15 ..     175     187 ..     173     197 .. 0.91
   2 ?    4.6   0.4     0.041        57       6      16 ..     231     244 ..     230     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                    +Ci C +C+ +CP
  gi|121639243|ref|YP_979467.1| 175 KCILCACCTTSCP 187
                                    8************ PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.041
                         Fer4_4   6 gCgs...CvaaCPq 16 
                                    +C+    C+ +CP 
  gi|121639243|ref|YP_979467.1| 231 RCRTtfnCTESCPR 244
                                    6887777******6 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.6     0.033        46      14      39 ..     166     189 ..     157     200 .. 0.81
   2 ?    8.5   0.3    0.0012       1.6      22      51 ..     227     257 ..     208     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.033
                                    HHHHHHHHTT----TT-HHHHCSTT- CS
                        Fer4_20  14 eeealeeAsRClqCkkapcvkgCPve 39 
                                    +++  ++ ++C+ C  a c+++CPv 
  gi|121639243|ref|YP_979467.1| 166 DRARYDDTTKCILC--ACCTTSCPVF 189
                                    556678999*****..99******95 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                                    TT----T.T-HHHHCSTT---HHHHHHHHHT CS
                        Fer4_20  22 sRClqCk.kapcvkgCPveidipefikkiae 51 
                                    +   +C+ + +c+++CP  i++ + i+++++
  gi|121639243|ref|YP_979467.1| 227 DGVWRCRtTFNCTESCPRGIEVTKAIQEVKR 257
                                    55566872457****************9986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   9.2      0.13   1.8e+02       1      13 [.     176     188 ..     176     189 .. 0.96
   2 ?    7.8   0.2    0.0053       7.3       4      14 ..     232     245 ..     230     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                         Fer4_3   1 CtgCgaCvevCPv 13 
                                    C+ C  C  +CPv
  gi|121639243|ref|YP_979467.1| 176 CILCACCTTSCPV 188
                                    ************7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0053
                         Fer4_3   4 Cg...aCvevCPvg 14 
                                    C+    C e+CP g
  gi|121639243|ref|YP_979467.1| 232 CRttfNCTESCPRG 245
                                    554447******98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.6   0.00041      0.56       4      21 ..     170     187 ..     167     188 .. 0.88
   2 ?    2.3   2.0      0.16   2.2e+02      12      21 ..     231     243 ..     231     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                         Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                    + dt +Ci C  C+++CP
  gi|121639243|ref|YP_979467.1| 170 YDDTTKCILCACCTTSCP 187
                                    56899************* PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                         Fer4_2  12 gCg...aCvsaCP 21 
                                    +C+    C+ +CP
  gi|121639243|ref|YP_979467.1| 231 RCRttfNCTESCP 243
                                    5877779*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1772.50
//
Query:       gi|121639244|ref|YP_979468.1|  [L=142]
Description: hypothetical protein BCG_3386c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-10   39.8   0.1    7.4e-10   39.4   0.1    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.068   13.1   0.0    1.3  1  DUF4411   Domain of unknown function (DUF4411)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   8.2e-14   7.4e-10       2     117 ..       4     127 ..       3     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 8.2e-14
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel..eelvtsalvlaEllyvlar....rkskrekaaelvelllllsalkilpid 74 
                                    +lD +vl+all r+++++e+ar+++ ++    ++++a++   +++v++      + +  +a++l+++    + +++++ +
  gi|121639244|ref|YP_979468.1|   4 LLDVNVLLALLdRDHVDHERARAWITGQieRGWASCAITQNGFVRVISQprypSPISVAHAIDLLARATHTRYHEFWSCT 83 
                                    79***************************9999*****************989888888888888888888888888844 PP

                                    HHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                            PIN  75 aeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfr 117
                                     +i++  ++++++ +    + + Da+++A+A +h+ + + tfD  ++
  gi|121639244|ref|YP_979468.1|  84 VSILD--SKVIDRSRlhspKQVTDAYLLALAVAHDGRFV-TFDQSIA 127
                                    44443..34444444456799***************999.***9875 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-06     0.068      99     126 ..      98     125 ..      65     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                        DUF4411  99 keflsvaDpfliAaAlaknatvVTkEvk 126
                                    ++ ++v D++l+A+A a++  +VT +++
  gi|121639244|ref|YP_979468.1|  98 HSPKQVTDAYLLALAVAHDGRFVTFDQS 125
                                    444599******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 941.72
//
Query:       gi|121639245|ref|YP_979469.1|  [L=80]
Description: hypothetical protein BCG_3387c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0009   19.1   1.3     0.0009   19.1   1.3    1.7  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.024   14.9   0.6      0.032   14.5   0.6    1.2  1  DUF4129   Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.3     1e-07    0.0009       1      38 [.       2      39 ..       2      40 .. 0.96
   2 ?   -2.2   0.2      0.52   4.7e+03      13      20 ..      70      77 ..      69      78 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-07
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                   r+++++d+++l ++ e+arr++r+ +e++ +++r++l+
  gi|121639245|ref|YP_979469.1|  2 RTTLSIDDDVLLAVKERARREKRTAGEILSDLARQALT 39
                                   89******************************999985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.52
                                   HHHHHHHH CS
                          RHH_1 13 rLdelarr 20
                                   ++d+l+++
  gi|121639245|ref|YP_979469.1| 70 LIDRLRDE 77
                                   68888765 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   3.6e-06     0.032       9      66 ..      13      76 ..      11      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-06
                        DUF4129  9 LaergldrrpgeTprEyarrv......riapspaaalaalaelfeearYGgrpasaeeyrrlve 66
                                   La + + rr+ +T++E++  +       + p+paa+ +++   fe +   g+++s +  +rl++
  gi|121639245|ref|YP_979469.1| 13 LAVKERARREKRTAGEILSDLarqaltNQNPQPAASQEDAFHGFEPLPHRGGAVSNALIDRLRD 76
                                   5556789***********66665557888888******9******9999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 568.78
//
Query:       gi|121639246|ref|YP_979470.1|  [L=204]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-08   32.8   0.1    1.4e-07   32.1   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0011   19.6   0.0     0.0019   18.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.078   12.5   0.0      0.099   12.2   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.11   12.1   0.0       0.13   11.9   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   3.1e-11   1.4e-07       1      97 []      51     140 ..      51     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.1e-11
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                    vL+l+ G+  ++lala+++   +vt++D+s+ +l +  ++a ++g+  ++++vq+d+  ++  + +f lv+s+    +++
  gi|121639246|ref|YP_979470.1|  51 VLELASGRSGTALALAAHG--RQVTAIDVSDVALLQLDSEAVRRGVadRLNLVQADLGCWEPGETRFALVLSR----LFW 124
                                    8*****************5..***************************************************5....456 PP

                                    HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                    d   +++++++++++ pgG
  gi|121639246|ref|YP_979470.1| 125 D---AAIFHRACEAVMPGG 140
                                    3...468888888888887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.2e-07    0.0019       1      72 [.      52     125 ..      52     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlh 72 
                                    L++++G+   a ala +g++v+++D+s+ +l +  ++a+++g+  ++++v+ad+      +  f lv+s+ +++
  gi|121639246|ref|YP_979470.1|  52 LELASGRSGTALALAAHGRQVTAIDVSDVALLQLDSEAVRRGVadRLNLVQADLGCWEPGETRFALVLSRLFWD 125
                                    7899***************************99999999999999999*****998877888999999887655 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05     0.099       4      58 ..      51     105 ..      49     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdv 58 
                                    +l l sG  G + ++a ++++v ai+++   l +    a   gv+d++ lv++d+
  gi|121639246|ref|YP_979470.1|  51 VLELASGRSGTALALAAHGRQVTAIDVSDVALLQLDSEAVRRGVADRLNLVQADL 105
                                    68999**********************************************9996 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.13      47      87 ..      57      97 ..      17     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                                   TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGG CS
                           TPMT 47 GkaldlvwlAeqgrevvGvelselAvekffeeanlepkvke 87
                                   G++  + +lA++gr+v ++++s+ A+ +  +ea  +  +++
  gi|121639246|ref|YP_979470.1| 57 GRSGTALALAAHGRQVTAIDVSDVALLQLDSEAVRRGVADR 97
                                   7888899*******************998877766554544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1526.87
//
Query:       gi|121639247|ref|YP_979471.1|  [L=221]
Description: moaD-moaE fusion protein moaX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-37  126.9   0.2    8.8e-37  125.8   0.1    1.5  2  MoaE       MoaE protein
    1.8e-18   66.9   0.1    1.1e-17   64.5   0.0    2.2  3  ThiS       ThiS family
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.19   11.9   0.1    1.3  1  Attacin_N  Attacin, N-terminal region


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         1     6e+03      24      35 ..       6      17 ..       5      30 .. 0.60
   2 !  125.8   0.1   1.5e-40   8.8e-37       1     112 [.      89     200 ..      89     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                                   EEEEEE------ CS
                           MoaE 24 vlFvGtvRdsfd 35
                                   vl+ G vR+  +
  gi|121639247|ref|YP_979471.1|  6 VLYFGAVREACK 17
                                   678888885433 PP

  == domain 2  score: 125.8 bits;  conditional E-value: 1.5e-40
                                    EESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEE CS
                           MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGel 80 
                                    lt+epl+v+e+ ++++ p+ G+ v+FvGtvR++++g++vt+L yeay+ m+ +tl +i+ee++++++  rvav+Hr+Gel
  gi|121639247|ref|YP_979471.1|  89 LTDEPLSVDEVLNAISGPSQGGAVIFVGTVRNNNNGHEVTKLYYEAYPAMVHRTLMDIIEECERQADGVRVAVAHRTGEL 168
                                    689***************************************************************************** PP

                                    ETTSEEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                           MoaE  81 evgeasvvvavssahRkeafeaceylidelKk 112
                                    ++g+a+vv+++s++hR++af+a++ +i++lK+
  gi|121639247|ref|YP_979471.1| 169 RIGDAAVVIGASAPHRAAAFDAARMCIERLKQ 200
                                    *******************************7 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.8e-21   1.1e-17       1      77 []       6      82 ..       6      82 .. 0.99
   2 ?   -2.7   0.0       1.7   9.9e+03      20      33 ..      92     105 ..      89     122 .. 0.72
   3 ?   -1.1   0.0      0.53   3.1e+03      23      48 ..     142     161 ..     137     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.8e-21
                                   EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG.TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela.lerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   vl+f+ +re+ +   e++ l++g+tv+ l+++L+ +yp la  ++rv++avN++i+p    +t+l dgD+va++p VaGG
  gi|121639247|ref|YP_979471.1|  6 VLYFGAVREACKvaHEKISLESGTTVDGLVDQLQIDYPPLAdFRKRVRMAVNESIAPA---STILDDGDTVAFIPQVAGG 82
                                   89****************************************99**************...******************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                    STSBHHHHHHHHHH CS
                           ThiS  20 egstvaelleaLge 33 
                                    e+ +v+e+l+a++ 
  gi|121639247|ref|YP_979471.1|  92 EPLSVDEVLNAISG 105
                                    56778888887754 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.53
                                    BHHHHHHHHHHHTCHHGTTTTEEEEE CS
                           ThiS  23 tvaelleaLgerypelalerrvavav 48 
                                    t+ +++e+ + +       ++v+vav
  gi|121639247|ref|YP_979471.1| 142 TLMDIIEECERQA------DGVRVAV 161
                                    7888888888888......8888887 PP

>> Attacin_N  Attacin, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.2e-05      0.19      10      56 ..      80     125 ..      75     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                      Attacin_N  10 tGgAdarlklt....lgtpdhnvlaqvFAagntqagpvtsGgtlayNnnGh 56 
                                    +Gg+d+ + lt      ++  n+++     g++q+g v   gt   NnnGh
  gi|121639247|ref|YP_979471.1|  80 AGGSDVYCRLTdeplSVDEVLNAIS-----GPSQGGAVIFVGTVRNNNNGH 125
                                    79*********9996667778***9.....********************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1737.20
//
Query:       gi|121639248|ref|YP_979472.1|  [L=177]
Description: molybdenum cofactor biosynthesis protein MoaC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-53  181.0   6.0    1.2e-53  180.8   6.0    1.0  1  MoaC      MoaC family
  ------ inclusion threshold ------
       0.07   13.8   0.6       0.11   13.1   0.2    1.5  2  DUF4402   Domain of unknown function (DUF4402)


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   6.0   1.3e-57   1.2e-53       1     136 []      19     153 ..      19     153 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.3e-57
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvdvs+k++t r+A+A+g v ++++tl++i +++++kGdv+a+ariagimaaK+t eliplcHpl ++ v+v+le++  +
  gi|121639248|ref|YP_979472.1|  19 MVDVSAKAVTLRRARASGAVLMKPSTLDMICHGTAAKGDVIATARIAGIMAAKRTGELIPLCHPLGIEAVTVTLEPQ-GA 97 
                                    9*************************************************************************998.79 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT-EEEEEEEEEEESS CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdkemvieevrlveKsgG 136
                                    ++++i atv+t ++tGvemEALtav+v+altvyDm+Kavd++m+i+++rl eKsgG
  gi|121639248|ref|YP_979472.1|  98 DRLSIAATVTTVARTGVEMEALTAVTVTALTVYDMCKAVDRAMTITDIRLDEKSGG 153
                                    *******************************************************9 PP

>> DUF4402  Domain of unknown function (DUF4402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         1   9.1e+03      73      73 ..      32      32 ..       9      62 .. 0.55
   2 ?   13.1   0.2   1.3e-05      0.11      21      94 ..      88     157 ..      83     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                        DUF4402 73 g 73
                                    
  gi|121639248|ref|YP_979472.1| 32 A 32
                                   1 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                        DUF4402  21 gtVtiapdGsrsatgsvsltsgttsaArftvsgeggssvtitlpasvtllgsggstmtvdnfttsltagggtgs 94 
                                     tVt++p+G+   + ++++    t+ Ar  v+ e+ + vt+t+ + + + +  ++ mt+++++ ++++gg++g 
  gi|121639248|ref|YP_979472.1|  88 VTVTLEPQGADRLSIAATV----TTVARTGVEMEALTAVTVTALTVYDMCKAVDRAMTITDIRLDEKSGGRSGH 157
                                    69999*****988888888....99*******************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1262.98
//
Query:       gi|121639249|ref|YP_979473.1|  [L=124]
Description: pterin-4-alpha-carbinolamine dehydratase moaB3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-21   75.3   0.0    3.8e-21   75.0   0.0    1.1  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   2.1e-25   3.8e-21       2      89 ..      24     111 ..      23     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.1e-25
                      Pterin_4a   2 klseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilv.synkvtvrltThdagglten 80 
                                    +l++ e++++l++lpgW+l  + +l+ +f f +f + ++fv ++aa+a++ nHhpdi+v + ++v+++++T +++ lt+ 
  gi|121639249|ref|YP_979473.1|  24 ALTDRELSERLTALPGWEL-VDGKLRHTFGFGSFDQSMKFVAKIAAIADKFNHHPDICVhNKRSVRLTCWTRQMHCLTRV 102
                                    699********999****8.6669*********************************7758899**************** PP

                      Pterin_4a  81 DfklAakid 89 
                                    Df+lA+++ 
  gi|121639249|ref|YP_979473.1| 103 DFDLAEAFS 111
                                    *****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 879.40
//
Query:       gi|121639250|ref|YP_979474.1|  [L=354]
Description: molybdenum cofactor biosynthesis protein A moaA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-32  110.8   0.0    6.5e-32  110.1   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    4.3e-28   98.8   0.0    6.2e-28   98.3   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    6.1e-06   26.4   0.0    1.4e-05   25.2   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    6.1e-06   26.5   0.0    1.1e-05   25.7   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   1.5e-35   6.5e-32       2     125 ..     198     321 ..     197     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.5e-35
                                    EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE-.-SST-SSEEEEETTT--EEEEE-TTTS--GGG--EEEE CS
                    Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleak.ketkgpakrykikdgkgeiglIapvsepFCasCnRlRl 80 
                                    e+rfIE+m+vg +++w+++kv++++++l ++ +++  ++a  k+ ++pa+ry+++dg+ ++g+Ia+ +epFCa+C+R Rl
  gi|121639250|ref|YP_979474.1| 198 EVRFIEYMDVGGATQWSMDKVFTKAQMLSTLGKKYGPIAALpKYDSAPANRYRLPDGT-TFGIIASTTEPFCATCDRSRL 276
                                    89******************************9998877765888*************.7******************** PP

                                    -TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT---- CS
                    Mob_synth_C  81 tadGklktCLfaeeeidlrdllregaseeeLkelikealarkkek 125
                                    tadG + +CL+a ++i+lr+ +r+gas +++ +++++ ++++ ++
  gi|121639250|ref|YP_979474.1| 277 TADGIWLHCLYALSGINLRESVRAGASANDVVQILQRGWRDRANR 321
                                    ****************************************99876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   1.4e-31   6.2e-28       3     166 ..      28     191 ..      26     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.4e-31
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpgir 79 
                                    v   CnlrC++C      ++ +r+  lsv+ei  +v+++    gv+ + l+ggepl ++d++ ++e ++++    +    
  gi|121639250|ref|YP_979474.1|  28 VIDQCNLRCRYCMPEAEYAWLPRADLLSVDEISLIVDAF-IAVGVDKIRLTGGEPLIRSDLAAIIEVISAKVgdgSGLQD 106
                                    5678***********99**********************.8*****************************99******** PP

                                    EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                    ++++tng+l+  +++++l+ +g+ r++++l+++ +++++ +   ++t  +v+e++e+ ++ag+ +++   v+++G+nd+e
  gi|121639250|ref|YP_979474.1| 107 LAITTNGVLL-ADQARKLKSAGMRRITISLDTLRPDRFKAIS-QRGTHYKVIEGIEAVAAAGFTDTKLDSVVIRGFNDDE 184
                                    **********.**************************99999.779********************************** PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    l +l+e+
  gi|121639250|ref|YP_979474.1| 185 LSDLIEF 191
                                    ****998 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     3e-09   1.4e-05       6      96 ..      30     120 ..      26     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3e-09
                        Fer4_14   6 sgCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype.kk 82 
                                     +Cnl C+ C    + +w  ++   +++e ++ i+  +    +  +++ ltGGePL+  +  +++++++  +  +    +
  gi|121639250|ref|YP_979474.1|  30 DQCNLRCRYCMpeAEYAWLPRADLLSVDE-ISLIV--DAFIAVGVDKIRLTGGEPLIRSDLAAIIEVISAKVGDGSGlQD 106
                                    68*********544445555666555554.44777..5555666699***********9999999999999999866689 PP

                        Fer4_14  83 iwletngtleiele 96 
                                      + tng+l  +  
  gi|121639250|ref|YP_979474.1| 107 LAITTNGVLLADQA 120
                                    999****9986655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.5e-09   1.1e-05      12     102 ..      29     122 ..      21     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.5e-09
                        Fer4_12  12 vsgCnlsCkgCfnke.twsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp..ekdi 88 
                                    +  Cnl+C++C+ ++      + +  + + +  i++ +    ++++ l+GGEPl ++   a++e++      ++  +   
  gi|121639250|ref|YP_979474.1|  29 IDQCNLRCRYCMPEAeYAWLPRADLLSVDEISLIVDAFIAVGVDKIRLTGGEPLIRSDLAAIIEVISAKVGDGSglQDLA 108
                                    568*********765233344556667788899**********************9999999999876555554457788 PP

                        Fer4_12  89 wlytgytleelskk 102
                                    + ++g+ l +  +k
  gi|121639250|ref|YP_979474.1| 109 ITTNGVLLADQARK 122
                                    88888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2416.78
//
Query:       gi|121639251|ref|YP_979475.1|  [L=116]
Description: hypothetical protein BCG_3393 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 785.35
//
Query:       gi|121639252|ref|YP_979476.1|  [L=128]
Description: hypothetical protein BCG_3394 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 860.31
//
Query:       gi|121639253|ref|YP_979477.1|  [L=381]
Description: transcriptional regulatory protein embR2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-44  151.5   3.7    3.2e-44  150.9   3.7    1.3  1  BTAD          Bacterial transcriptional activator domain
    2.4e-17   63.0   0.1    4.1e-17   62.3   0.1    1.4  1  FHA           FHA domain
    2.1e-14   53.6   0.0    4.3e-14   52.6   0.0    1.4  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
    3.4e-12   46.3   0.0    7.8e-12   45.1   0.0    1.6  1  Trans_reg_C   Transcriptional regulatory protein, C terminal
     0.0088   16.8  10.7      0.038   14.8   0.4    4.3  5  TPR_14        Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.42   11.2   4.1        2.9    8.5   0.2    3.2  3  TPR_19        Tetratricopeptide repeat
          1   10.2   9.6         51    4.9   0.0    5.0  5  TPR_4         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9   3.7   1.2e-47   3.2e-44       2     146 .]     106     250 ..     105     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.2e-47
                                    HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                           BTAD   2 DlarfealvaagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeea 81 
                                    D+arf  + +ag +a+aag +e+a ++l+aAla+wrGp+l+dl+++++++  +  l e+++ a++alaeae+++Gra+ +
  gi|121639253|ref|YP_979477.1| 106 DVARFISQRSAGLRAAAAGSFEQASDHLSAALAEWRGPVLDDLREFSFVTRLANSLVEDKIIAHTALAEAEIACGRADSV 185
                                    9******************************************************************************* PP

                                    HHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHHHHHH CS
                           BTAD  82 laelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpelralheeil 146
                                    ++ele+l+ ehP++E+l+rql++A++ s+rq++AL +Y+rl+ +Lae+Lgv+pgp++r l+e++l
  gi|121639253|ref|YP_979477.1| 186 ISELEELILEHPYHEALWRQLIAAYYVSERQSDALDAYRRLKTSLAEDLGVDPGPKVRTLYEQVL 250
                                    **************************************************************997 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.1   1.6e-20   4.1e-17       2      69 .]     303     366 ..     302     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.6e-20
                                    EEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   2 tiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                    +iGRs+++d+vl+d ++S +Ha+i+++++  ++ ++Dl+S nG++v g+ri +  ++ L++gd i++G
  gi|121639253|ref|YP_979477.1| 303 RIGRSKSNDMVLPDGKVSPYHAVIVNTGE--SFMITDLRSVNGVYVRGRRIAT--TATLNDGDHIRIG 366
                                    79***************************..*********************9..***********98 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.7e-17   4.3e-14       8      89 ..     291     373 ..     289     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.7e-17
                                    TT-EEEETTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-S.ECC--TTSEEEETTEEE CS
                   Yop-YscD_cpl   8 kGaeveLeegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerve.elelrpgdvlelGttel 86 
                                    +G++ +L +  ++iG+++++D+vL D +vs+ h+++  + es +++dl+s ng++v g+r++ +++l++gd++ +G  el
  gi|121639253|ref|YP_979477.1| 291 AGHRSPLGRLPLRIGRSKSNDMVLPDGKVSPYHAVIVNTGESFMITDLRSVNGVYVRGRRIAtTATLNDGDHIRIGDHEL 370
                                    799999*******************************************************96666***********999 PP

                                    EEE CS
                   Yop-YscD_cpl  87 alv 89 
                                    +++
  gi|121639253|ref|YP_979477.1| 371 TFE 373
                                    885 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0     3e-15   7.8e-12       7      77 .]      27      98 ..      22      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3e-15
                                   SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTS.TSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C  7 tpkefklLelLlenpgrvvsreeLleevwgede.dvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77
                                   tpk++++L++L+ +++r+v  + L+++ w++d  +++  tv +++s+LR+ ++ ++++++ I      GYrl
  gi|121639253|ref|YP_979477.1| 27 TPKQRAVLATLIIHRNRPVGIDSLIDAAWEQDRpEGSRATVYTYVSNLRRLVSTTGADSHSILASAPPGYRL 98
                                   9******************************999************************************97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.9   9.9e+03       7      22 ..      50      65 ..      48      72 .. 0.79
   2 ?    5.0   0.4      0.02        52      11      31 ..     120     140 ..     112     151 .. 0.82
   3 !   14.8   0.4   1.5e-05     0.038       3      42 ..     168     207 ..     167     209 .. 0.93
   4 ?    5.5   0.7     0.014        37       2      27 ..     201     226 ..     200     235 .. 0.89
   5 ?   -0.4   0.0       1.2     3e+03      23      40 ..     245     262 ..     240     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                         TPR_14  7 laeallalGdpdeAia 22
                                   l +a +++++p++++a
  gi|121639253|ref|YP_979477.1| 50 LIDAAWEQDRPEGSRA 65
                                   6778999999998876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                         TPR_14  11 llalGdpdeAiallrralala 31 
                                     +a+G +++A ++l +ala +
  gi|121639253|ref|YP_979477.1| 120 AAAAGSFEQASDHLSAALAEW 140
                                    5789**************964 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.5e-05
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    a+ alaea+ a G+ d  i  l++++  +P ++++w++l 
  gi|121639253|ref|YP_979477.1| 168 AHTALAEAEIACGRADSVISELEELILEHPYHEALWRQLI 207
                                    5679*********************************996 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.014
                         TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                    +++++l +a++ +++  +A++++rr+
  gi|121639253|ref|YP_979477.1| 201 ALWRQLIAAYYVSERQSDALDAYRRL 226
                                    689*********************97 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.2
                         TPR_14  23 llrralalaPddaeawll 40 
                                    l++++l+++  d ++  +
  gi|121639253|ref|YP_979477.1| 245 LYEQVLRQQALDTRVVVQ 262
                                    556666655544444333 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.084   2.2e+02       2      20 ..     121     139 ..     120     149 .. 0.82
   2 ?    8.5   0.2    0.0011       2.9      29      67 ..     170     209 ..     158     210 .. 0.92
   3 ?   -2.6   0.0       3.2   8.1e+03       5      21 ..     217     233 ..     214     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.084
                         TPR_19   2 laegdyaeAlalleqalqe 20 
                                     a+g +++A ++l++al+e
  gi|121639253|ref|YP_979477.1| 121 AAAGSFEQASDHLSAALAE 139
                                    5789999999999999887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                         TPR_19  29 llLAeallalgqldeAealLdalpeedpdd.aryasLlAk 67 
                                     +LAea +a g+ d  +  L++l +e p + a +++L+A+
  gi|121639253|ref|YP_979477.1| 170 TALAEAEIACGRADSVISELEELILEHPYHeALWRQLIAA 209
                                    579**************************87999999995 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                         TPR_19   5 gdyaeAlalleqalqed 21 
                                     d  +A ++l+  l+ed
  gi|121639253|ref|YP_979477.1| 217 SDALDAYRRLKTSLAED 233
                                    56667888888877764 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         7   1.8e+04       4      17 ..      31      44 ..      31      45 .. 0.77
   2 ?    2.1   0.0      0.16   4.2e+02       8      23 ..      51      66 ..      49      67 .. 0.85
   3 ?    1.4   0.5      0.27   6.8e+02       8      24 ..     117     133 ..     112     135 .. 0.82
   4 ?    4.9   0.0      0.02        51       3      18 ..     168     183 ..     167     190 .. 0.93
   5 ?    3.5   0.2     0.057   1.5e+02       6      23 ..     257     274 ..     252     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7
                          TPR_4  4 llaLArallalGdl 17
                                   +++LA +  ++ ++
  gi|121639253|ref|YP_979477.1| 31 RAVLATLIIHRNRP 44
                                   57899988888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                          TPR_4  8 ArallalGdldeAral 23
                                     a++++ +++  ra+
  gi|121639253|ref|YP_979477.1| 51 IDAAWEQDRPEGSRAT 66
                                   579********99986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.27
                          TPR_4   8 ArallalGdldeArall 24 
                                    +  ++a+G +++A ++l
  gi|121639253|ref|YP_979477.1| 117 GLRAAAAGSFEQASDHL 133
                                    66789********8887 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.02
                          TPR_4   3 allaLArallalGdld 18 
                                    a+ aLA+a  a G++d
  gi|121639253|ref|YP_979477.1| 168 AHTALAEAEIACGRAD 183
                                    899***********98 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.057
                          TPR_4   6 aLArallalGdldeAral 23 
                                     +  +++a+Gd  +A+++
  gi|121639253|ref|YP_979477.1| 257 TRVVVQAAAGDIIRALEH 274
                                    56789**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2488.85
//
Query:       gi|121639254|ref|YP_979478.1|  [L=214]
Description: hypothetical protein BCG_3396c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00024   19.9   0.0      0.036   12.8   0.0    2.0  2  Condensation  Condensation domain


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0   0.00041       7.3      32      63 ..      92     123 ..      88     129 .. 0.88
   2 !   12.8   0.0     2e-06     0.036     100     160 ..     150     207 ..     143     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00041
                                    EEEEES---HHHHHHHHHHHHHH-SSCCEEEE CS
                   Condensation  32 vlklegeldlerlekalqelierhdaLRtvfl 63 
                                    vl +++++d+ r++ a++++++ h+aL tvf+
  gi|121639254|ref|YP_979478.1|  92 VLIANSRVDQGRIRAAVEAVFDAHPALGTVFE 123
                                    6778999************************5 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-06
                                    HHHHHHHHTC--SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHH CS
                   Condensation 100 eefaqkdlqepfdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqq 160
                                     e++ +  + +fd+++g Lf ++l+  + +rl+l++s   ++vD  S++++++dl + Y++
  gi|121639254|ref|YP_979478.1| 150 AEVIAR-HSASFDMYTGRLFAVSLLPGSPDRLVLTASR--LCVDDASWQTVVEDLVRQYDE 207
                                    555554.7899***************999999999996..*****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1818.35
//
Query:       gi|121639255|ref|YP_979479.1|  [L=570]
Description: transposase fusion protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-24   86.7   0.4    4.1e-24   85.2   0.4    1.9  1  DEDD_Tnp_IS110  Transposase
    1.2e-20   73.6   0.3    3.7e-20   72.0   0.3    1.9  1  Transposase_20  Transposase IS116/IS110/IS902 family
    0.00025   21.0   0.0     0.0013   18.7   0.0    2.3  1  CMD             Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.4   6.8e-28   4.1e-24       1     152 [.       4     155 ..       4     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 6.8e-28
                 DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeegleallek.laakagevlvvveatghygallvaflleagitvvvvnpl 79 
                                    vG D +k++h+++++d+ g++l +++v+ + +g ++ + +  ++   e  +++e   + +a l   ll+ag++vv v+ +
  gi|121639255|ref|YP_979479.1|   4 VGTDAHKYSHTFVATDEVGRQLGEKTVKATTAGHATAIMWaREQFGLELIWGIEDCRNMSARLERDLLAAGQQVVRVPTK 83 
                                    8*********************************99999934455569******************************** PP

                 DEDD_Tnp_IS110  80 avkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlralLdq 152
                                     + ++rk+ +++ K+D++DA   A++++ r++  pl+ +de+ +eL+ lt +r+ lv++rt+++nrlr l ++
  gi|121639255|ref|YP_979479.1|  84 LMAQTRKSARSRGKSDPIDALAVARAVL-RETDLPLATHDETSRELKLLTDRRDVLVAQRTSAINRLRWLVHE 155
                                    ****************************.99999*********************************987765 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.3   6.1e-24   3.7e-20       3      87 .]     222     307 ..     220     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 6.1e-24
                 Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan.pe 81 
                                    +L +ipG+ ++taa ++ e+  ++rfks++++a+ a +ap++  SG+++++ r+s++Gnr+l++aL+++Al+ ir++ ++
  gi|121639255|ref|YP_979479.1| 222 ALLEIPGCAELTAAKIVGEAAGVTRFKSEAAFACHAAVAPIPVWSGNTAGQMRLSRSGNRQLNAALHRIALTQIRMTdSR 301
                                    6899**********************************************************************8877** PP

                 Transposase_20  82 lrayye 87 
                                     +ayy+
  gi|121639255|ref|YP_979479.1| 302 GQAYYQ 307
                                    ****97 PP

>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-07    0.0013      12      84 ..     423     496 ..     419     497 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-07
                                    HHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHHH CS
                            CMD  12 ealla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaae 84 
                                    eall+    +L+p  reL+ + ++++ gc +Cvd+ ++  + +G++ +++ ++   a +  +++ +raA a+ae
  gi|121639255|ref|YP_979479.1| 423 EALLQrASRKLPPSVRELAVFWTARSIGCSWCVDFGAMLQRLDGLDVDRLTDIDNYATSSKFSDDERAAIAYAE 496
                                    6667766789***************************9999999999999999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3544.75
//
Query:       gi|121639256|ref|YP_979480.1|  [L=312]
Description: RNA polymerase sigma factor SigJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-13   49.4   0.7    9.7e-13   47.7   0.7    1.8  1  Sigma70_r2    Sigma-70 region 2
    4.9e-11   42.1   0.1    7.4e-11   41.6   0.1    1.3  1  Sigma70_r4_2  Sigma-70, region 4
    2.9e-07   31.1   1.7    5.5e-07   30.2   0.0    2.3  2  SnoaL_2       SnoaL-like domain
    1.5e-05   24.4   0.0    3.1e-05   23.4   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4
     0.0039   17.6   0.0      0.012   16.0   0.0    1.9  1  DUF4440       Domain of unknown function (DUF4440)
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.34   11.2   0.0    1.7  1  SnoaL_3       SnoaL-like domain


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.7   3.2e-16   9.7e-13       2      69 ..       6      68 ..       6      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.2e-16
                                   HHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2  2 verylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69
                                   +e++++ ++++a+rl+g  adaeD+vQea+lr w   ++ d +   +++awl++++ ++ +d lR+++
  gi|121639256|ref|YP_979480.1|  6 FEALRQHLMSVAYRLTGTVADAEDIVQEAWLR-W---DSQD-TVIADPRAWLTTVVSRLGLDKLRSAA 68
                                   588999**************************.6...5666.66669******************976 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   2.5e-14   7.4e-11       5      53 ..     107     155 ..     103     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.5e-14
                                    HHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                   Sigma70_r4_2   5 realaeLperqreifllryleglsykEIAellgisegtVksrlsRArkk 53 
                                    +  l++L ++qr +f+l++ +  + +E+Ae+lg+se++ ++  sRArk+
  gi|121639256|ref|YP_979480.1| 107 MVVLERLRPDQRVAFVLHDGFAVPFAEVAEVLGTSEAAARQLASRARKA 155
                                    6689*******************************************97 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.81   2.4e+03      86      86 ..      53      53 ..       3     130 .. 0.61
   2 !   30.2   0.0   1.8e-10   5.5e-07       1     101 [.     175     281 ..     175     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.81
                                   E CS
                        SnoaL_2 86 v 86
                                    
  gi|121639256|ref|YP_979480.1| 53 T 53
                                   2 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.8e-10
                                    HHHHHHHHHTTCHHHHHHTEEEEEEEEET.TSE.......EESHHHHHHHHHHHHHHEEEEEEEEEEE.EEETTEEEEEE CS
                        SnoaL_2   1 vraflaalnagdldalaalfapdvvwedp.gge.......lrGreairaffralfaafpdlrfeihdv.vadgdrvavew 71 
                                    v +++aa++agdld++++l++pdv++++   g+       +rG + + +f+ +l ++++   f   ++ +++g+  a   
  gi|121639256|ref|YP_979480.1| 175 VGRLMAAMAAGDLDTVVSLLHPDVTFTGDsNGKaptavraVRGSDKVVRFILGLVQRYGPGLFGANQLaLVNGELGAYTA 254
                                    6799***********************6654445677889***********************999999999**998887 PP

                                    EEEEEEETTSSEEEEEEEEEEEEETTEEEE CS
                        SnoaL_2  72 tvtgtipatgrgvtvrgvdvfrvrdGkive 101
                                     + g    +g +   + ++ ++vrdGk+++
  gi|121639256|ref|YP_979480.1| 255 GLPG---VDGYRAMAPRITAITVRDGKVCA 281
                                    7754...6666666699999*******975 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     1e-08   3.1e-05       1      47 [.     109     155 ..     109     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1e-08
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrk 47 
                                    +L++L +++r  ++l  g   +++E++e+lg S+ ++rq+ +rA++ 
  gi|121639256|ref|YP_979480.1| 109 VLERLRPDQRVAFVLHDGFAVPFAEVAEVLGTSEAAARQLASRARKA 155
                                    599*****************************************986 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.1e-06     0.012       3      35 ..     173     205 ..     172     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                                    HHHHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS CS
                        DUF4440   3 aleealeeafvagdaealaallapdavlvgpsg 35 
                                    +++ +l++a++agd++++ +ll+pd++++g+s 
  gi|121639256|ref|YP_979480.1| 173 EVVGRLMAAMAAGDLDTVVSLLHPDVTFTGDSN 205
                                    567799***********************9983 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.34       3      46 ..     173     213 ..     172     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        SnoaL_3   3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevr 46 
                                    +++ ++ +a+a+gd+d++++l+++d++f g +++ ++   ++vr
  gi|121639256|ref|YP_979480.1| 173 EVVGRLMAAMAAGDLDTVVSLLHPDVTFTG-DSNGKA--PTAVR 213
                                    67788999********************99.666554..45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2248.08
//
Query:       gi|121639257|ref|YP_979481.1|  [L=438]
Description: hypothetical protein BCG_3399 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-93  312.8   0.0    3.5e-93  312.5   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.031   13.6   0.0      0.044   13.0   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.5   0.0   3.9e-97   3.5e-93      11     403 ..      13     425 ..       4     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 312.5 bits;  conditional E-value: 3.9e-97
                                    EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEE CS
                    Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkv 90 
                                     vi +++Gv + d  gk ylD++s+  vv++G+   ++++a++ qa +l +  +  +++ pa++lae l++ ap++l++v
  gi|121639257|ref|YP_979481.1|  13 PVIVRGDGVTIFDDRGKSYLDALSGLFVVQVGYGRAELAEAAARQAGTLGYFPLWGYATPPAIELAERLARYAPGDLNRV 92 
                                    5899**************************************************************************** PP

                                    EEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB- CS
                    Aminotran_3  91 flansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlke 170
                                    f+   G+eAvetA K+a++y + ++++ k+k+i+ + a+HG t+gal++tg  +  k+ f+p++p+  r++    ++++ 
  gi|121639257|ref|YP_979481.1|  93 FFTSGGTEAVETAWKVAKQYFKLTGKPGKHKVISRSIAYHGTTQGALAITGL-PLFKAPFEPLTPGGFRVPNTNFYRAPL 171
                                    ****************************************************.**********88888887666555555 PP

                                    HH....HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSG CS
                    Aminotran_3 171 ne....eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfA 246
                                    +       + a+ +++ea+e +  d+vaAv +Ep+q +gG ++a+p++++++re+c+++dvll+ DEv + fGr G +fA
  gi|121639257|ref|YP_979481.1| 172 HTdlkeFGRWAADRIAEAIEFEGPDTVAAVFLEPVQNAGGCIPAPPGYFERVREICDRYDVLLVSDEVICAFGRIGSMFA 251
                                    5522115556777888888899********************************************************** PP

                                    GGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS....B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                    Aminotran_3 247 lehagvspDlmtlaKaltgG.lplsavlataevmqalapgs....hgsTfgGnplacavalavleiieeekllenaqelg 321
                                    +e +g  pD++t aK+lt+G  pl a++a + + + +++g+    hg TfgG p+ +av la l+i+e+e l +++++ +
  gi|121639257|ref|YP_979481.1| 252 CEDLGYVPDMITCAKGLTSGySPLGAMIASDRLFEPFNDGEtmfaHGYTFGGHPVSAAVGLANLDIFEREGLSDHVKRNS 331
                                    ********************99********************************************************** PP

                                    HHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-EE..ETTTEEEE---T CS
                    Aminotran_3 322 aalkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlils..aGdnvirllppl 388
                                     al++ Le+l + +  ++++Rg G +++iel++++ +k+            ++ +++ e+G+++++   Gd v++++ppl
  gi|121639257|ref|YP_979481.1| 332 PALRATLEKLYDLP-IVGDIRGEGYFFGIELVKDQATKQtftdderarllGQVSAALFEAGLYCRTddRGDPVVQVAPPL 410
                                    ************99.*********************999**********9899***********9733688********* PP

                                    T--HHHHHHHHHHHH CS
                    Aminotran_3 389 iitdeeidelleilk 403
                                    i  + e d + +il 
  gi|121639257|ref|YP_979481.1| 411 ISGQPEFDTIETILR 425
                                    988888877766665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     5e-06     0.044     106     167 ..     154     237 ..      72     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-06
                                    T........................TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT CS
                Beta_elim_lyase 106 a........................GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkyg 161
                                                             G   ++++++ai+ +g   + ++++ l+   n+ g  + ++ + ++v++i+++y+
  gi|121639257|ref|YP_979481.1| 154 LtpggfrvpntnfyraplhtdlkefGRWAADRIAEAIEFEGP--DTVAAVFLEPVQNAGGCIPAPPGYFERVREICDRYD 231
                                    455555555556666666666666699************999..*************988899***************** PP

                                    -EEEEE CS
                Beta_elim_lyase 162 iplhlD 167
                                    + l+ D
  gi|121639257|ref|YP_979481.1| 232 VLLVSD 237
                                    *99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3233.42
//
Query:       gi|121639258|ref|YP_979482.1|  [L=405]
Description: penicillin-binding protein dacB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-36  123.9   0.0    9.3e-36  123.5   0.0    1.1  1  Peptidase_S11    D-alanyl-D-alanine carboxypeptidase
    1.3e-09   38.0   0.0    1.6e-09   37.7   0.0    1.2  1  Beta-lactamase2  Beta-lactamase enzyme family
  ------ inclusion threshold ------
      0.055   12.2   0.1        0.1   11.3   0.1    1.3  1  Peptidase_S13    D-Ala-D-Ala carboxypeptidase 3 (S13) family


Domain annotation for each model (and alignments):
>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   1.5e-39   9.3e-36       7     238 ..      88     310 ..      83     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.5e-39
                                    --.--SSSEEEEEETTTTEEEEEESTTS-BE-GGGHHHHHHHHHHHHHHTTSS-TTSEEE--GGGHGCCSGTTSSTTS-T CS
                  Peptidase_S11   7 epleiaaksailvdantGkvLyeknadevveiASltKlmTaylvlealkkgklkeddkvtisedayalgnnkevsniflk 86 
                                    +p +++a+++++ d+++G v+++++++ + ++AS+ K++ a+    ++  + l++++ v+  +d +a +      ++ ++
  gi|121639258|ref|YP_979482.1|  88 APGDVSAEAWLVADLDSGAVIAARDPHGRHRPASVIKVLVAM---ASI--NTLTLNKSVAGTADDAAVE----GTKVGVN 158
                                    5669*********************************87555...566..3335555555444433333....3588899 PP

                                    TT-EEEHHHHHHHHHCC--HHHHHHHHHHHHSSHHHHHHHHHHHHHHTT-TT-B-SSSSSTSHTTCBB-HHHHHHHHHHH CS
                  Peptidase_S11  87 kgskvsvkdLlegllvssgNdAavalAekiaGsekaFvkmMnkkakelGlkntkfvnptGLdnenqvssArdlailakal 166
                                     g  ++v++Ll+gll++sgNdAa alA +++G  +a  ++ n  a +lG ++t++ +p GLd ++   sA+d+ +  +++
  gi|121639258|ref|YP_979482.1| 159 TGGTYTVNQLLHGLLMHSGNDAAYALARQLGG-MPAALEKINLLAAKLGGRDTRVATPSGLDGPGMSTSAYDIGLFYRYA 237
                                    999**************************977.56779**************************************9999 PP

                                    HHH.HHHHHHGGGESEEEETT.ECTEEEESSTGGGGTTTSEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEE CS
                  Peptidase_S11 167 lkd.lpeelkitkeksltfng.ikklnyknknkllyrktlnvdglktGytkkAgeclvatavenqmrlisVvln 238
                                     ++ +   +  t+   +  +g +  ++++n n+lly++     g ktGyt+ Ag+++v+ a +++ rl++V l 
  gi|121639258|ref|YP_979482.1| 238 WQNpVFADIVATRTFDFPGHGdHPGYELENDNQLLYNYP-GALGGKTGYTDDAGQTFVGAANRDGRRLMTVLLH 310
                                    9986666665555555555546889************99.999****************************986 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.7e-13   1.6e-09       1     139 [.     102     236 ..     102     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.7e-13
                                    TTTTSEE.EESTTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGHHHHT.SSSTSGGGSTTSEEEHHHHHHHHHHT CS
                Beta-lactamase2   1 ldtgeel.gvnadeefpaaStiKvpillalleavlegklslderltltaediv.ggsgilqklpgktlslrdlltlmiav 78 
                                    ld+g+++ + +++ ++  aS+iKv+++     ++  ++l l++ +  ta+d + +g+     ++g+t+++ +ll+  + +
  gi|121639258|ref|YP_979482.1| 102 LDSGAVIaARDPHGRHRPASVIKVLVA-----MASINTLTLNKSVAGTADDAAvEGTK-VGVNTGGTYTVNQLLHGLLMH 175
                                    688998867799***************.....45556***********9997616665.67899**************** PP

                                    T-HHHHHHHHHHH.....THHHHHHHHHHCTHTTSB--SHTTCCHHHTTSSTTEE-HHHHHHHHHH CS
                Beta-lactamase2  79 SDNtAtnlLidrl.....gleavnawlkelglretrlrrklpdleaadkdkrntttardlarllea 139
                                    S N A+++L + l      le +n ++++lg r+tr++++  +l    +++  +t+a d + + + 
  gi|121639258|ref|YP_979482.1| 176 SGNDAAYALARQLggmpaALEKINLLAAKLGGRDTRVATPS-GL----DGPGMSTSAYDIGLFYRY 236
                                    *************5554335789**************9763.22....345666666666655555 PP

>> Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.7e-05       0.1      20      66 ..      96     142 ..      87     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                    EEEEEETTTTEEEEEESTTSEB--GGGHHHHHHHHHHHHT-TT-EEE CS
                  Peptidase_S13  20 gvvvqdaetgkelydhqgdtpllPAStqKllTAaaAlltLganfrft 66 
                                    + +v d+++g++++ ++   + +PAS  K+l A+a ++tL  n + +
  gi|121639258|ref|YP_979482.1|  96 AWLVADLDSGAVIAARDPHGRHRPASVIKVLVAMASINTLTLNKSVA 142
                                    5679***********************************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2840.21
//
Query:       gi|121639259|ref|YP_979483.1|  [L=497]
Description: sugar-transport integral membrane protein sugI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-85  287.4  23.0    2.2e-85  287.2  23.0    1.0  1  Sugar_tr  Sugar (and other) transporter
    1.1e-34  120.0  64.9    3.7e-33  114.9  38.7    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.14   11.9   0.9       0.76    9.6   0.1    2.6  2  TraD      Conjugal transfer protein TraD
        8.2    4.6   8.0        3.4    5.9   3.1    2.2  2  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.2  23.0   4.8e-89   2.2e-85       3     452 .]      56     480 ..      54     480 .. 0.93

  Alignments for each domain:
  == domain 1  score: 287.2 bits;  conditional E-value: 4.8e-89
                                    HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                       Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                    l+aa  g+l+gYd+  i+++l +l+   +f l+++++  e       l++  +++G+i+G+l +g+l++ +GRkks + +
  gi|121639259|ref|YP_979483.1|  56 LTAASVGVLYGYDLSAIAGALLSLS--EEFELTTREQ--E-------LLTTTAVLGQIAGALGGGILANAIGRKKSVVLI 124
                                    789999**************99999..8888888885..3.......789999*************************** PP

                                    HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgln 162
                                    ++ + + a+l a++    sv +l+v+R+l+G+ +Gl  v+vP+y++E Ap+++Rg lv+ yqla+  Gi+v++ +g+ l+
  gi|121639259|ref|YP_979483.1| 125 VAGYAVFALLGATSV---SVPMLVVARLLLGVTIGLSVVVVPVYVAESAPAAVRGSLVTAYQLATLSGIVVGYLVGYLLA 201
                                    ***************...*************************************************************9 PP

                                    TSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....H CS
                       Sugar_tr 163 ktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekasw 242
                                     +++   wr ++gl+++pa lll ll+ +P++ r+++ kg+  +a+  l++++ e+d d ela+++++ ++        +
  gi|121639259|ref|YP_979483.1| 202 GSHG---WRAMFGLAAAPATLLLPLLWRMPDTARWYLLKGRIADARSALRRIQPEADIDAELADMAAAVDER----GGGI 274
                                    9999...**************************************************************999....4569 PP

                                    TTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHH CS
                       Sugar_tr 243 kellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtl 319
                                    +e++++  +++++l +++l ++ q tGinai+yysp++f  +g+      l+  ++v v   +a+++++flvdr+GRR++
  gi|121639259|ref|YP_979483.1| 275 GEMVRR-PYLRATLFVIALGFLVQITGINAIIYYSPRLFAAMGFAGYfamLALPAMVQVAGLAAVCASLFLVDRLGRRPI 353
                                    999999.78**************************************876666677777777888888************ PP

                                    HHHHHHHHHHHHHHHH..HHHHTTSS...CHHHH.HHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH CS
                       Sugar_tr 320 lllGaagmaicfvilgivalllvakskaasivai.vfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwla 398
                                    ll G+a+m+ + ++l   + + ++++ + + v+  ++++lfi+ f++g+g+++wv+++E fp+++Rs ++++  ++  +a
  gi|121639259|ref|YP_979483.1| 354 LLSGIATMITADAVLI--TVFANDSDGGTGLVLGfAGVLLFIIGFNFGFGSLVWVYAAESFPSRLRSMGSSLMLTSTLTA 431
                                    ***************4..666666655666666526799***************************************** PP

                                    HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGGT CS
                       Sugar_tr 399 nflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieelf 452
                                    n +++ +  +++  +gg++vf+vf+ +av+      f  petkgr+leei   +
  gi|121639259|ref|YP_979483.1| 432 NAIVAAFSLTMLRVLGGAGVFAVFGTFAVV-----AFVAPETKGRKLEEIRHFW 480
                                    *************************99876.....5789**********98765 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9  38.7   8.3e-37   3.7e-33       3     341 ..      60     424 ..      58     425 .. 0.82
   2 !   19.2  18.3   1.1e-07   0.00048      54     166 ..     343     464 ..     343     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 8.3e-37
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                     +++l++++ s+++ al   l+e++ ++  e+ ll+t+  lg+++++l +G l++ +Gr++ ++l ++++a+++ll++ +
  gi|121639259|ref|YP_979483.1|  60 SVGVLYGYDLSAIAGALL-SLSEEFELTTREQELLTTTAVLGQIAGALGGGILANAIGRKKSVVLIVAGYAVFALLGA-T 137
                                    567899999999999999.9*****************************************************66666.3 PP

                          MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                      s+++l+v+r+l G++ g+++ ++ +++a+ +p   rg+ +  +++++  G+++g+l+g lla s gWra+f ++a+ +
  gi|121639259|ref|YP_979483.1| 138 sVSVPMLVVARLLLGVTIGLSVVVVPVYVAESAPAAVRGSLVTAYQLATLSGIVVGYLVGYLLAGSHGWRAMFGLAAAPA 217
                                    37788*************************************************************************** PP

                          MFS_1 162 llafvlfllll............peepperkrkspkeee............kgtgpaplvp..........awkallkdp 207
                                     l+  l ll+             +                           + +  a+l++          ++++++++p
  gi|121639259|ref|YP_979483.1| 218 TLL--LPLLWRmpdtarwyllkgR--------------IadarsalrriqpEADIDAELADmaaavderggGIGEMVRRP 281
                                    ***..5335554333333333330..............233445444444422233333336666668999999999999 PP

                          MFS_1 208 vl...w.illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalll 283
                                    +l   + ++ +++l+  +g++++ +++p  l   +g++g++ +++l+a+++++g+++   + +l+drlgrr++ll +++ 
  gi|121639259|ref|YP_979483.1| 282 YLratLfVIALGFLVQITGINAIIYYSPR-LFAAMGFAGYFAMLALPAMVQVAGLAAVCASLFLVDRLGRRPILLSGIAT 360
                                    8854425777788888889999*******.5*******99999999********99876777777*****9999999999 PP

                          MFS_1 284 lllaalglallavt.....ssavllll......vlvliGfglgfvfpsllalasdlappeeagtasglf 341
                                    +++a + l+ + +      +    +l+      +l++iGf +gf  ++++++a++++p + + + s+l+
  gi|121639259|ref|YP_979483.1| 361 MITADAVLITVFANdsdggT----GLVlgfagvLLFIIGFNFGF-GSLVWVYAAESFPSRLRSMGSSLM 424
                                    99987777777777654321....3334567888888***9997.8*************9999888875 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-07
                          MFS_1  54 rlsdrfGrrrvlllglllfalg.lllll.fa.ss......lw.lllvlrvlqGlgagalfpagaaliadwfpkeergrai 123
                                    +l+dr+Grr++ll g+++++ + ++l++ fa  s      +  +  vl ++ G+   ++ +++ +++a+ fp + r+++ 
  gi|121639259|ref|YP_979483.1| 343 FLVDRLGRRPILLSGIATMITAdAVLITvFAnDSdggtglVLgFAGVLLFIIGFNF-GFGSLVWVYAAESFPSRLRSMGS 421
                                    589********************999998966223444553334455555677765.566677799************** PP

                          MFS_1 124 gllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                    +l+ +++  + ++ ++++  ++  lg  +vf +++ ++++afv
  gi|121639259|ref|YP_979483.1| 422 SLMLTSTLTANAIVAAFSLTMLRVLGGAGVFAVFGTFAVVAFV 464
                                    *****************************************88 PP

>> TraD  Conjugal transfer protein TraD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00017      0.76      22      50 ..      61      91 ..      49      96 .. 0.82
   2 ?   -1.2   0.1       0.4   1.8e+03      11      24 ..     289     302 ..     288     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                           TraD 22 G..lddldralLlGaLlelaellredeeeaa 50
                                      l  +d  +++GaLl+l+e+ + +++e++
  gi|121639259|ref|YP_979483.1| 61 VgvLYGYDLSAIAGALLSLSEEFELTTREQE 91
                                   3477889999**************9999997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.4
                           TraD  11 lielGgLVvkAGld 24 
                                    +i lG LV+ +G++
  gi|121639259|ref|YP_979483.1| 289 VIALGFLVQITGIN 302
                                    699********975 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3     0.024   1.1e+02     322     378 ..      80     134 ..      78     141 .. 0.69
   2 ?    5.9   3.1   0.00075       3.4     132     192 ..     141     201 ..     135     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.024
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 322 EtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklaklvlvvsllsll 378
                                     ++F+l++ e +llt +++++g ++G l gG+l + +    k+++ +v+  ++++ll
  gi|121639259|ref|YP_979483.1|  80 SEEFELTTREQELLT-TTAVLGQIAGALGGGILANAIGR-KKSVVLIVAGYAVFALL 134
                                    578999999999997.567889999*9999999886653.34444555555555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00075
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 132 vllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslll 192
                                    v ++++a lllG+   + + +   Y+ +++       ++ +++ +++ G ++G+l+G+ll+
  gi|121639259|ref|YP_979483.1| 141 VPMLVVARLLLGVTIGLSVVVVPVYVAESAPAAVRGSLVTAYQLATLSGIVVGYLVGYLLA 201
                                    55899****************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3150.06
//
Query:       gi|121639260|ref|YP_979484.1|  [L=383]
Description: N-acetylglucosamine-6-phosphate deacetylase nagA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-39  135.4   6.0    3.6e-39  135.1   6.0    1.1  1  Amidohydro_1  Amidohydrolase family
    7.1e-09   35.6  11.1    5.6e-07   29.4   0.5    2.9  3  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
       0.04   14.0   1.0         10    6.2   0.0    2.8  2  2CSK_N        Two-component sensor kinase N-terminal


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   6.0     6e-43   3.6e-39       1     342 [.      48     379 ..      48     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 6e-43
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT.SS CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee.lp 74 
                                    iv+PG++D+HvH+ +++             +  a+ ++++++ +l++Gttt++++  t+ +     ++ al+ea+++ ++
  gi|121639260|ref|YP_979484.1|  48 IVVPGFVDMHVHGGGGA----------SFADGNAADIARAAEFHLRHGTTTTLASLVTAGPaellsAVGALAEATRDgVV 117
                                    79************998..........6888999*************************99******************* PP

                                    SEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEET CS
                   Amidohydro_1  75 lglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHal 153
                                     g++++g+++s++ +++ ++++++++ ++ + e++++ adg+v  v+lap+ + +   ++++         d+ v++ ++
  gi|121639260|ref|YP_979484.1| 118 AGIHLEGPWLSPA-RCGAHDHTRMRAPDPAEIESVLAAADGAVRmVTLAPELPGSD--AAIRRFR------DAEVVVAVG 188
                                    *************.*************************************88876..5998888......9******** PP

                                    SSCHHHHHHHHHHTTTEEEETTTTSTCC.............HHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHH CS
                   Amidohydro_1 154 etkgevedaeaafgetiehgthlevaes.............lglldeiklilahgvhltpteaellkerlkeagvahcpf 220
                                    +t++++ ++++a++ +++ gthl +a+              l+ ++++  i+a+gvh++p+ +  ++e++  ++va    
  gi|121639260|ref|YP_979484.1| 189 HTDATYTQTRHAIDLGATVGTHLFNAMPpldhrapgpvlalLCDPRVTVEIIADGVHVHPAVVHAVIEAVGPDRVA---- 264
                                    ***********************************************************99999999*********.... PP

                                    HHHHSEHHHHHHHHHHHHTSC....EEEEEECT.........TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHH CS
                   Amidohydro_1 221 snsilrsgrealrkaldeGvk....vglgtDga.........asgnslnlleelrlalklqrgllye.deegglslkeal 286
                                        + ++ +a++ + d G++    + + + +           +g++     ++ +++ +  gl  + d++g++ l+ a+
  gi|121639260|ref|YP_979484.1| 265 ----VVTDAIAAAGCGD-GAFrlgtMPIEVESSvarvagastLAGSTT----TMDQLFRTVAGLGSKsDSAGDVALAAAV 335
                                    ....9999999999988.888888877777755678655444444444....467777777788888************* PP

                                    HHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTE CS
                   Amidohydro_1 287 rmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGk 342
                                    ++++  +A+algl+  vG++++G+ A+lvv+            +d  v+ v+v+ +
  gi|121639260|ref|YP_979484.1| 336 QVTSATPARALGLT-GVGRLAAGYAANLVVL-----------DRDLRVTAVMVNDD 379
                                    *************7.****************...........89999999999865 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.2     3e-05      0.18       8      25 ..      47      62 ..      45      91 .. 0.76
   2 ?   -2.0   0.0      0.32   1.9e+03      29      75 ..     138     198 ..     119     205 .. 0.61
   3 !   29.4   0.5   9.4e-11   5.6e-07     406     449 ..     327     369 ..     299     378 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                   Amidohydro_3  8 rlvlPGFvDsHtHlaggg 25
                                   ++v+PGFvD+H H  ggg
  gi|121639260|ref|YP_979484.1| 47 AIVVPGFVDMHVH--GGG 62
                                   58***********..444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.32
                   Amidohydro_3  29 rllrlpdarvtslegvltavrdqagtt................pkgrwivgeGwdeaqfaeer 75 
                                    +++r pd  +  +e vl+a+++ +                   ++ +++v++G+++a  +++r
  gi|121639260|ref|YP_979484.1| 138 TRMRAPD--PAEIESVLAAADGAVRMVtlapelpgsdaairrfRDAEVVVAVGHTDATYTQTR 198
                                    4455555..666666666665555433566666666666666666666677777666666665 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 9.4e-11
                   Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvldadp 449
                                     ++ l +a++ ++++pA+algl+   G+L++G+ A+lvvld+d+
  gi|121639260|ref|YP_979484.1| 327 GDVALAAAVQVTSATPARALGLTGV-GRLAAGYAANLVVLDRDL 369
                                    568899******************9.***************986 PP

>> 2CSK_N  Two-component sensor kinase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0017        10      70     101 ..      21      60 ..      20      62 .. 0.85
   2 ?    5.4   0.2     0.003        18     101     137 ..     156     199 ..     141     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                         2CSK_N  70 VsdadgrllaGdadlplpp.......a.aeprfydaeyrg 101
                                    V++adgr+l+G a++p++p       a   p+f d++++g
  gi|121639260|ref|YP_979484.1|  21 VHTADGRILSGGAGAPPMPadaefpdAiVVPGFVDMHVHG 60 
                                    899************8666688898877889999998887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.003
                         2CSK_N 101 gepvRvaalarplag.......agr.gpvlVqVAetlekRdalar 137
                                    + +vR+++la +l+g         r  +v+V+V++t +  ++  +
  gi|121639260|ref|YP_979484.1| 156 DGAVRMVTLAPELPGsdaairrF-RdAEVVVAVGHTDATYTQTRH 199
                                    568***********999887642.249999999999887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2827.36
//
Query:       gi|121639261|ref|YP_979485.1|  [L=281]
Description: hypothetical protein BCG_3403c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-24   83.7   0.0    2.2e-23   82.5   0.0    1.6  2  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   1.2e-27   2.2e-23       2      94 ..      16     120 ..      15     121 .. 0.97
   2 ?   -2.6   0.0      0.41   7.4e+03      51      68 ..     147     164 ..     131     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.2e-27
                         DUF732   2 aaallaaalllaapAaAd.saddaFlaalnqagi.aygspdaaialGkavCkkldsGksaeavvaevkndnsglsp.... 75 
                                    +++l++aa+l+ +pAaAd ++dd+Fla l++++i a+++  ++i ++++vC+kld G++ +++v++++nd ++++p    
  gi|121639261|ref|YP_979485.1|  16 LVVLIGAAILHDGPAAADpNQDDRFLALLEKKEIpAVANVPRVIDAAHKVCRKLDGGMPVNDIVDGLRNDAYNIDPvmrl 95 
                                    7899**************999999**********9999********************************99*999**** PP

                         DUF732  76 ......eqaaqfvgaAvsayCPeql 94 
                                          +++++f+ aAv+ yCP+++
  gi|121639261|ref|YP_979485.1|  96 ypvrltTTMTRFISAAVEIYCPNHH 120
                                    ***********************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.41
                         DUF732  51 kkldsGksaeavvaevkn 68 
                                    ++++sG +  a+v++++ 
  gi|121639261|ref|YP_979485.1| 147 SAVNSGSDLRASVSDMTI 164
                                    445666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1879.66
//
Query:       gi|121639262|ref|YP_979486.1|  [L=103]
Description: hypothetical protein BCG_3404 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 772.72
//
Query:       gi|121639263|ref|YP_979487.1|  [L=146]
Description: MerR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-18   67.5   4.9    1.5e-18   67.0   4.9    1.2  1  MerR-DNA-bind   MerR, DNA binding
    1.3e-18   66.8   0.0    2.3e-18   66.0   0.0    1.3  1  MerR_1          MerR HTH family regulatory protein
    4.8e-16   58.2   0.1      8e-16   57.5   0.1    1.4  1  MerR            MerR family regulatory protein
  ------ inclusion threshold ------
       0.14   12.3   0.0        0.5   10.6   0.0    2.0  2  HTH_17          Helix-turn-helix domain
       0.36   10.6   1.2       0.53   10.0   0.1    1.8  2  SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain


Domain annotation for each model (and alignments):
>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   4.9   4.3e-22   1.5e-18       1      65 []      44     108 ..      44     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4.3e-22
                                    HHHHHHHHHHHHTT--HHHHHHHHHHHHSTTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind   1 leRLkfIrrarrlGFsLdeIrelLalyddrappcqdvrallarklaeleeriaeLqalraeLaal 65 
                                    ++RL+fI r++++G+ L+e+r++La++d++++pc++vr+ll  +++e++++iaeL al+ +L++l
  gi|121639263|ref|YP_979487.1|  44 VDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVRQLLSTRIDEVRAQIAELIALEGHLQTL 108
                                    78************************************************************986 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   6.4e-22   2.3e-18       1      66 [.       1      67 [.       1      68 [. 0.98

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 6.4e-22
                                   EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE.-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XX CS
                         MerR_1  1 ysigevakilgvtthtlrywekegllkpkr.teggrryYtdedierLklikyLlkrGltlkgikkll 66
                                   ++i+eva +++++t+tlr++e+ gll+p+  t  g+r Y++e ++rL++i + + +Gl l++++++l
  gi|121639263|ref|YP_979487.1|  1 MKISEVAALTNTSTKTLRFYENSGLLPPPArTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL 67
                                   89***********************999999**********************************98 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   2.2e-19     8e-16       1      38 []       2      39 ..       2      39 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.2e-19
                                   EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEEE CS
                           MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyRlY 38
                                   +I+evA lt+ s++tLR+YE  GL+ppp Rt++GyR Y
  gi|121639263|ref|YP_979487.1|  2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNY 39
                                   6***********************************88 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014       0.5       2      29 ..       1      28 [.       1      37 [. 0.91
   2 ?   -2.3   0.0       1.5   5.2e+03       6      15 ..      62      71 ..      60      88 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                         HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpa 29
                                   ++++E+A+l + s +t++ + ++g lp+
  gi|121639263|ref|YP_979487.1|  1 MKISEVAALTNTSTKTLRFYENSGLLPP 28
                                   799***************9999999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                         HTH_17  6 EaAelLgvsr 15
                                   E+ ++L +++
  gi|121639263|ref|YP_979487.1| 62 EVRQILAIHD 71
                                   6666666654 PP

>> SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.3   8.2e+03      25      33 ..      57      65 ..      53      71 .. 0.63
   2 ?   10.0   0.1   0.00015      0.53      20      38 ..      93     111 ..      89     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                 SNCAIP_SNCA_bd 25 RInlQkhlQ 33
                                    ++lQ+  Q
  gi|121639263|ref|YP_979487.1| 57 GLALQEVRQ 65
                                   567776544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00015
                 SNCAIP_SNCA_bd  20 EQTaeRInlQkhlQrLlea 38 
                                     Q ae I+l  hlQ Ll+ 
  gi|121639263|ref|YP_979487.1|  93 AQIAELIALEGHLQTLLDH 111
                                    699**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1065.46
//
Query:       gi|121639264|ref|YP_979488.1|  [L=289]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-39  135.3  26.5    3.1e-39  135.2  26.5    1.0  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2  26.5   1.7e-43   3.1e-39       2     254 ..      32     287 ..      31     289 .] 0.91

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 1.7e-43
                 Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgl.lglddelqeqlldllaevlpegaaevvedil.qrllnqaslgllgla 79 
                                    ++++sl+Aa+l+yyt++++fPll+v ++v g+ l+  +el  +l + ++  + + + +++ d++ +++  +as+g++gla
  gi|121639264|ref|YP_979488.1|  32 DRNGSLFAAGLTYYTIFAIFPLLMVGFGVGGFaLSRRPELLTTLEERIRTSVSGVVGQQLVDLMnSAIDARASVGVIGLA 111
                                    6899***************************98888999999999999999998666899999945777778******** PP

                 Virul_fac_BrkB  80 vllwsasggvsalrralnkiygv.eesrsflrkrllsllllllllvllllslvlsvflqslllasa.pllglglelsell 157
                                    +  w ++g++ +lr+al +++ +   + ++lr++l +l++++++ v+++++++l+v++++  +a + ++l++++++  ++
  gi|121639264|ref|YP_979488.1| 112 TAAWVGLGWMWHLREALSQMWAHpVAPAGYLRTKLSDLAAMVGTFVVIVATIALTVLGHARPMAAVlRWLEIPQFS--VF 189
                                    *********************99755789*****************************997776669999999876..34 PP

                 Virul_fac_BrkB 158 ..llqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYG.slgaliill 234
                                      +++ +++lv++l+ +++f+++   lp++ v l  a+ ++l+aa++++l+k++ ++yl+ +    +  G  +g +++l+
  gi|121639264|ref|YP_979488.1| 190 deIFRGISVLVSVLVSWVLFTWMIGRLPREPVGLVTAARAGLMAAVGFELFKQVGAIYLQIVL--RSPAGaVFGPVLGLM 267
                                    58***********************************************************87..5666659******** PP

                 Virul_fac_BrkB 235 lWlylsalilLlGaelnael 254
                                    ++ +++a+++L+  +++a+ 
  gi|121639264|ref|YP_979488.1| 268 VFAFVTAWLILFATAWAATA 287
                                    *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2026.86
//
Query:       gi|121639265|ref|YP_979489.1|  [L=336]
Description: tryptophanyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-81  272.8   0.0    4.1e-81  272.5   0.0    1.0  1  tRNA-synt_1b     tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.058   13.2   0.0    1.6  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.5   0.0   4.6e-85   4.1e-81       5     292 ..       7     289 ..       3     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 4.6e-85
                                    --EEEEEEETSSS.-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHT CS
                   tRNA-synt_1b   5 plrvysGidPTgk.lHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldp 82 
                                      r++sG++PT++ lHlG  l+++ ++v lq + h++ff+++DlhAi+ +++   ++ lr r+  ++++   +la g+dp
  gi|121639265|ref|YP_979489.1|   7 SRRIFSGVQPTSDsLHLGnALGAVAQWVGLQ-DDHDAFFCVVDLHAITIPQD---PEALRRRTLITAAQ---YLALGIDP 79 
                                    5699***************************.********************...**************...******** PP

                                    TTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.SC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGH CS
                   tRNA-synt_1b  83 ekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.gegislgeftYplLqaaDilllkadlvpgGsDQk 161
                                     +a++++qs++++h++la++l +++ +g+ +rm+qfk+  k++++ +e  ++g+ftYp+LqaaD+l+++++lvp+G+DQ+
  gi|121639265|ref|YP_979489.1|  80 GRATIFVQSQVPAHTQLAWVLGCFTGFGQASRMTQFKD--KSARQgSEATTVGLFTYPVLQAADVLAYDTELVPVGEDQR 157
                                    **************************************..777775699******************************* PP

                                    HHHHHHHHHHHHHHHH..STTSS-EEEEET....-BBSTTSSSBTTCETTC..GC-BTTCCHHHHHHHHHHCHCSTTCSH CS
                   tRNA-synt_1b 162 qnielgrdlarrfnkk..evfkkpegltvp....lltgldGekKmSKSagn..saIfLddekesvkkkiqkavtdsdeev 233
                                    q++el+rd+a+rfn++   ++  p++l+++    + ++ d+++KmSKSag   + I+L+d+++   kki++avtds++++
  gi|121639265|ref|YP_979489.1| 158 QHLELARDVAQRFNSRfpGTLVVPDVLIPKmtakIYDLQDPTSKMSKSAGTdaGLINLLDDPALSAKKIRSAVTDSERDI 237
                                    ****************9999999**999999999*****************999************************** PP

                                    HHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 234 ekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                    ++++ +k+++sn l+++ +av+g++       l+  ++ +  ++gdlkk++aea+ e+ 
  gi|121639265|ref|YP_979489.1| 238 RYDPDVKPGVSN-LLNIQSAVTGTDI----DVLVDGYAGH--GYGDLKKDTAEAVVEFV 289
                                    ************.**********998....8888889999..*************9985 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-06     0.058      31      70 ..      87     130 ..      81     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-06
                                    HHS-----.-SEEEEESTSSHHHHHHHHH......HHHSS--EEEE CS
                Eno-Rase_NADH_b  31 ksqkkiekgpkkvLviGaStGYGLAsria......aafgagadtig 70 
                                    +sq +++  ++ + v+G+ tG+G Asr++      a  g++a+t+g
  gi|121639265|ref|YP_979489.1|  87 QSQVPAH--TQLAWVLGCFTGFGQASRMTqfkdksARQGSEATTVG 130
                                    4554444..58899*************9833222123446666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2567.16
//
Query:       gi|121639266|ref|YP_979490.1|  [L=297]
Description: hypothetical protein BCG_3408 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-15   58.7   8.7    1.5e-15   58.4   8.7    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.4e-12   47.9   0.0      2e-11   44.1   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
      5e-06   25.9   0.0    9.7e-06   25.0   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0059   16.6   0.0      0.017   15.1   0.0    1.6  2  UPF0227        Uncharacterised protein family (UPF0227)
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.25   11.4   0.0    1.3  1  Thioesterase   Thioesterase domain


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   8.7   4.2e-19   1.5e-15       1     218 [.      37     280 ..      37     282 .. 0.60

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.2e-19
                                    EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTS.TS-GGCS--HHH..CHHH.HHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGh.Grsdpppldled..ladl.aalldelaagggpvvlvGHSl 74 
                                    vlllH + +s+++W   + +L  + +++++v+ap   Gh G++ +    l+   lad  +++ldel+      ++vG+Sl
  gi|121639266|ref|YP_979490.1|  37 VLLLHPFLMSQTVWEkvAQQL--ADTGRFEVFAPTMAGHnGGPASGTRFLSSavLADHvERQLDELG--WETSHIVGNSL 112
                                    89************6345566..44555888********9756555555555333444488888885..9999******* PP

                                    HHHHHHHHHHCC..EE.EEES-..........----TTT.............S----TTHHHHHHTT-CCCCHCCH...S CS
                  Abhydrolase_6  75 GGalalaaaplalvvg.vlldp........pptalpagl.............laaalelllallallrllawlsre...p 129
                                    GG++a ++ +  + ++   ++p        p                     + a++ +l ++  +l++ ++l++    +
  gi|121639266|ref|YP_979490.1| 113 GGWVAFELERRGRARSvTGIAPaggwtrwsP-------VkfeviakfiagapILAVAHILGQRALRLPFSRLLATLpisA 185
                                    *******777775555455555223333331.......022222222221212222222223333333333332112211 PP

                                    -HSCCCCHHH.....CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHH.....HCHHCCCHSTTEEE CS
                  Abhydrolase_6 130 lprlfladed.....adaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvp.....rllerllaqagarl 198
                                     p++  + e      + a+  a+++ l + l  +g   +++++++ vp +v+ +++D++vp     r++ + l  ag rl
  gi|121639266|ref|YP_979490.1| 186 TPDGVSERELsgiidDAAHCPAYFQLLVKALVLPG---LQELEHTAVPSHVVlCEQDRVVPpsrfsRHFTDSLP-AGHRL 261
                                    11122221111111134555555555555555555...889999999997776*****8887766666778888.***** PP

                                    TCE...SSS-HHHHSHHHHH CS
                  Abhydrolase_6 199 pvvlpgaGHlphleepdeva 218
                                     +vl g GH+p++e+p ++ 
  gi|121639266|ref|YP_979490.1| 262 -TVLDGVGHVPMFEAPGRIT 280
                                    .************9998765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   5.5e-15     2e-11       2     257 .]      36     276 ..      35     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.5e-15
                                    EEEEE-STTTCGGGGTTGHHHHHHHHT.TSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakd.gfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    ++++lh +++s  vw +  +a+ La++ +f+v+++ + G+  ++++ +      + a +ad ++r ld lg++  ++vG 
  gi|121639266|ref|YP_979490.1|  36 PVLLLHPFLMSQTVWEK--VAQQLADTgRFEVFAPTMAGHNGGPASGTRF---LSSAVLADHVERQLDELGWETSHIVGN 110
                                    89***************..************************9999753...48899********************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHH CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvda 160
                                    S+GG +a+++  +   r ++++ +++   a  + ++ +   +        +a +    +a  l+++ l++ ++r+ ++  
  gi|121639266|ref|YP_979490.1| 111 SLGGWVAFELERR--GRARSVTGIAP---AGGWTRWSPVKFEVIA---KFIAGAPILAVAHILGQRALRLPFSRLLAT-- 180
                                    ********99776..78888888888...6667777666555554...456667778899999999999999999887.. PP

                                    HHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS CS
                  Abhydrolase_1 161 lkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvpp.kaledlaqllpk 239
                                          s +++  + +  s+    a+ +  +++ + +a +l  l+el    +p+ v+  ++D++vpp + ++ +++ lp 
  gi|121639266|ref|YP_979490.1| 181 ---LPISATPDGVSERELSGIIDDAAHCPAYFQLLVKALVLPGLQELEHTAVPSHVVLCEQDRVVPPsRFSRHFTDSLPA 257
                                    ...5668888889999999999999999999999999999999999666666*************************999 PP

                                    .EEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 240 .krlvvisdagHlaflegp 257
                                     +rl v+++ gH   +e p
  gi|121639266|ref|YP_979490.1| 258 gHRLTVLDGVGHVPMFEAP 276
                                    9************999875 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.7e-09   9.7e-06       7     237 ..      37     274 ..      35     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.7e-09
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqG.favyalDhrGhGrse..gkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                    v+l+H +  +    +++a++La+ G f+v+a    Gh   +  g r      + +   la +ve+  +e + +   ++G 
  gi|121639266|ref|YP_979490.1|  37 VLLLHPFLMSQTVWEKVAQQLADTGrFEVFAPTMAGHNGGPasGTRF---LSSAV---LADHVERQLDELGWETSHIVGN 110
                                    77888888888899999999999998899999999996663224444...22333...444566677777788889**** PP

                    Hydrolase_4  84 SmGGliallyllrypd.kvaglilsaPalkikakl......kappllkl........llkllgkllpklqvsnnlkadsl 148
                                    S+GG +a+++  r ++ +v+g+  ++ + ++ + +      k      +        ++ +lg+ + +l++s+ l +  +
  gi|121639266|ref|YP_979490.1| 111 SLGGWVAFELERRGRArSVTGIAPAGGWTRWSP-VkfeviaK------FiagapilaVAHILGQRALRLPFSRLLATLPI 183
                                    **********96665536778888888877765.33554441......34445556689************9999999** PP

                    Hydrolase_4 149 srdpevvaayeadplv..hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeas.relyerlgskdktlk 225
                                    s  p+ v + e   ++    ++ + + l +  ++   +++ ++  +P  ++  e+D+vv+p+   r++ ++l++   +l+
  gi|121639266|ref|YP_979490.1| 184 SATPDGVSERELSGIIddAAHCPAYFQLLVKALVLPGLQELEHTAVPSHVVLCEQDRVVPPSRFsRHFTDSLPA-GHRLT 262
                                    ****************63333334333444455667788888888***************99865999999996.***** PP

                    Hydrolase_4 226 lypglyHellnE 237
                                    + +g  H  ++E
  gi|121639266|ref|YP_979490.1| 263 VLDGVGHVPMFE 274
                                    ********9999 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.7e-06     0.017      43      90 ..      87     135 ..      82     142 .. 0.86
   2 ?   -2.1   0.0      0.85     3e+03     135     159 ..     229     253 ..     194     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
                        UPF0227  43 qqalkeleklvaelgddnillvGssLGGyyatrlgerfglrqvl.lnPa 90 
                                    + ++ ++e+++ elg +++ +vG sLGG++a  l  r   r+v  ++Pa
  gi|121639266|ref|YP_979490.1|  87 AVLADHVERQLDELGWETSHIVGNSLGGWVAFELERRGRARSVTgIAPA 135
                                    567899**************************99999888886436665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.85
                        UPF0227 135 erilvllskqDevldyrravaefra 159
                                    ++  v+l  qD v++ +r   +f +
  gi|121639266|ref|YP_979490.1| 229 VPSHVVLCEQDRVVPPSRFSRHFTD 253
                                    5566788888888888888888764 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.1e-05      0.25       2      89 ..      36     126 ..      35     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                                    EEEEE--TTCCSGGGHHHHHHCTTC.EEEEEEECSTTST....SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHH CS
                   Thioesterase   2 pLflfppagGsasvfrslasklsdp.vvevlavqlpgre....rdepplesieelaaeyaealrqiqpegPyalfGhSlG 76 
                                    p+ l++p   s +v  + a++l d+   ev+a + +g++    +++++l+s + la+ +  +l +   e   +++G SlG
  gi|121639266|ref|YP_979490.1|  36 PVLLLHPFLMSQTVWEKVAQQLADTgRFEVFAPTMAGHNggpaSGTRFLSS-AVLADHVERQLDELGWE-TSHIVGNSLG 113
                                    6889999999999999********998999999999998888777777766.56777777777777777.889******* PP

                                    HHHHHHHHHHHHH CS
                   Thioesterase  77 gllAfevArqLes 89 
                                    g +Afe+ r+ ++
  gi|121639266|ref|YP_979490.1| 114 GWVAFELERRGRA 126
                                    ******8776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2195.93
//
Query:       gi|121639267|ref|YP_979491.1|  [L=409]
Description: isocitrate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-73  246.7   0.0    4.2e-73  246.5   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.5   0.0   2.3e-77   4.2e-73       5     348 .]      12     399 ..       8     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 246.5 bits;  conditional E-value: 2.3e-77
                                    EEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSHHH. CS
                         Iso_dh   5 legdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrpen. 83 
                                    + ++ +G+e++++++k++k++   ++l++ + ++d+G + +d+t+++++ +++ aik+  v +++a++tp+  e+r+e+ 
  gi|121639267|ref|YP_979491.1|  12 PVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAYAIKKHGVGVKCATITPD--EARVEEf 89 
                                    668999*****************************************************************..7777777 PP

                                    HHHHHHHHTT.EEEEEEEEE-BCCTTCCSSBTHHHHCT.-EEEEEEE-SSCGGCSSEEEEET.................. CS
                         Iso_dh  84 gLlaLrkeld.lfanlrpvkvfeklkvksplkrevvee.vdlvivReltggiYfgeekekkg.................. 143
                                     L++++ +++ +++n++ +++f +  v s + r v+++ + +vi R+++g++Y++++ + ++                  
  gi|121639267|ref|YP_979491.1|  90 NLKKMWLSPNgTIRNILGGTIFREPIVISNVPRLVPGWtKPIVIGRHAFGDQYRATNFKVDQpgtvtltftpadgsapiv 169
                                    7********99***********666666666668****899****************999999***************** PP

                                    ....TG.GGGEEEEEEEEEHHH.HHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC......TTTTS CS
                         Iso_dh 144 ....sifteevavdtklyseee.ieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee......eypdi 211
                                        s  +e+ +v + +y+ +e i+ +ar++f + l+  k++v+l++K+++lk+++ ++++++e+v+ee      e++++
  gi|121639267|ref|YP_979491.1| 170 hemvS-IPEDGGVVLGMYNFKEsIRDFARVSFSYGLNA-KWPVYLSTKNTILKAYDgMFKDEFERVYEEefkaqfEAAGL 247
                                    *9743.799**********9998999************.******************************9********** PP

                                    EEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEET.SS-EEEEESS---CCCTTSS-... CS
                         Iso_dh 212 elehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslge.kkvaifEavHGsapdiagkdk... 287
                                    ++eh+l+D++++  +k +    V+++kN++GD++SD +a+  GslGl++S+ + + +k++ +Ea+HG+++++ ++ +   
  gi|121639267|ref|YP_979491.1| 248 TYEHRLIDDMVAACLKWE-GGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTAdGKTVEAEAAHGTVTRHYRQYQagk 326
                                    ******************.445*******************************99899**************99999999 PP

                                    ...S-THHHHHHHHHHHHHTTT-HHHH......HHHHHHHHHHHHHTSCCHHHCTTS...TCCCHHHHHHHHH CS
                         Iso_dh 288 ...aNpiavilSaalmLryslgleeaA......dkiekAvekvleagivTkDlagea...akevstsefgdav 348
                                       +Npia+i+++++ L+++ +l+ +       +k+e+ v +++e+g++TkDla      +  ++ +ef da+
  gi|121639267|ref|YP_979491.1| 327 ptsTNPIASIFAWTRGLQHRGKLDGTPevidfaHKLESVVIATVESGKMTKDLAILIgpeQDWLNSEEFLDAI 399
                                    999****************88776543444444********************98877777888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3162.60
//
Query:       gi|121639268|ref|YP_979492.1|  [L=449]
Description: O-acetylhomoserine aminocarboxypropyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.3e-137  456.2   0.0   7.3e-137  456.0   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00041   19.4   0.0    0.00077   18.5   0.0    1.5  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.64    9.2   0.0    2.2  2  Beta_elim_lyase  Beta-eliminating lyase
        0.8   10.3   2.7        9.9    6.8   0.2    2.8  3  MccV             Microcin V bacteriocin


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.0   0.0  1.6e-140  7.3e-137       1     381 [.      19     433 ..      19     434 .. 0.97

  Alignments for each domain:
  == domain 1  score: 456.0 bits;  conditional E-value: 1.6e-140
                                    HHHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHH CS
                Cys_Met_Meta_PP   1 eTllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavssGm 77 
                                    eT+++hagq++d++t+a+a piy+t++y+f+d+++a   f+ e  g++Y+R+gnpt++v+e+ri aLegg aal +ssG+
  gi|121639268|ref|YP_979492.1|  19 ETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAaalFGLEIPGNIYTRIGNPTTDVVEQRIGALEGGVAALFLSSGQ 98 
                                    69*********************************9999***************************************** PP

                                    HHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEEEEESS-TTTT----H CS
                Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.sdleelekaikentklvylEtptnpllkvvDi 156
                                    aA + ail+l+ aGd+iv+s  lYggt++l+++ l klgiev+fvd  +dl+ +++a+++ntk+++ Et++np ++++D 
  gi|121639268|ref|YP_979492.1|  99 AAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLGIEVSFVDDpDDLDTWQAAVRPNTKAFFAETISNPQIDLLDT 178
                                    *********************************************75499****************************** PP

                                    HHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH......... CS
                Cys_Met_Meta_PP 157 ekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq......... 227
                                    ++++++a+ +gv+++vDnt+a+p+l++pl+ gaDivvhSaTKylgGh+ ++aGviv+ g++++++  +f +         
  gi|121639268|ref|YP_979492.1| 179 PAVSEVAHRNGVPLIVDNTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWTQG-RF-Pgfttpdpsy 256
                                    ***************************************************************996.43.34779***** PP

                                    ......................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTST CS
                Cys_Met_Meta_PP 228 ......................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshp 285
                                                          ++ G++ spf+a+l+++Gl+TLslR+erh +nA++vAefL++ + v +v+Y+glps+p
  gi|121639268|ref|YP_979492.1| 257 hgvvfaelgppafalkarvqllRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVAEFLAARDDVLSVNYAGLPSSP 336
                                    ******************************************************************************** PP

                                    THHHHHHHS.SSG-SEEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE CS
                Cys_Met_Meta_PP 286 qhelakkql.kgaggvlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRls 364
                                     he ak+ + kg+g+vlsFel ++ e+ k+fv++lkl s+ +++G+v sl+++pas+tha++++ e+ a+gv+++l+Rl+
  gi|121639268|ref|YP_979492.1| 337 WHERAKRLApKGTGAVLSFELAGGIEAGKAFVNALKLHSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLA 416
                                    *******88255566***************************************************************** PP

                                    --SS-HHHHHHHHHHHH CS
                Cys_Met_Meta_PP 365 vGiEdvdDliaDlkqal 381
                                    vGiE +dD++aDl+ ++
  gi|121639268|ref|YP_979492.1| 417 VGIEGIDDILADLELGF 433
                                    *************9887 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-07   0.00077      65     209 ..      92     228 ..      67     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-07
                                    EEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEE CS
                    Aminotran_5  65 iftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklva 144
                                    +f+s++  a + ++l+l     +gd+iv +   + ++ +  +    + g++v ++        dld+ +++++++tk+ +
  gi|121639268|ref|YP_979492.1|  92 LFLSSGQAAETFAILNL---AGAGDHIVSSPRLYGGTYNLFHYSLAKLGIEVSFVDD----PDDLDTWQAAVRPNTKAFF 164
                                    66666666666677777...6677777777766666665555444466777766544....45789999*********** PP

                                    EESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-E CS
                    Aminotran_5 145 ithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiG 209
                                       +sn    + +++++ ++a+++g+ ++vD + a +   i+  ++g+D+++ s+ K+lg  G  
  gi|121639268|ref|YP_979492.1| 165 AETISNPQIDLLDTPAVSEVAHRNGVPLIVDNTIATPYL-IQPLAQGADIVVHSATKYLGGHGAA 228
                                    ********9***********************9988865.667788**************99965 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00014      0.64      30      75 ..      71     116 ..      52     133 .. 0.90
   2 ?    3.5   0.0    0.0082        37     152     201 ..     180     223 ..     172     327 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                                    --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEE CS
                Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevi 75 
                                    +++t+ ++e+++ +l g  aalf+ +G aA+ +++  l+  g+ ++
  gi|121639268|ref|YP_979492.1|  71 GNPTTDVVEQRIGALEGGVAALFLSSGQAAETFAILNLAGAGDHIV 116
                                    6899*******************************99987777665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0082
                                    HHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT- CS
                Beta_elim_lyase 152 evaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdll 201
                                    +v+++a+++g+pl++D      +  +    ++ +++++D+v+ s++K l+
  gi|121639268|ref|YP_979492.1| 180 AVSEVAHRNGVPLIVD------NTIATPYLIQPLAQGADIVVHSATKYLG 223
                                    7999999999999988......6678888888899999999999999554 PP

>> MccV  Microcin V bacteriocin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.046   2.1e+02      22      75 ..      65     117 ..      44     123 .. 0.76
   2 ?    6.8   0.2    0.0022       9.9      27      58 ..     214     245 ..     206     259 .. 0.78
   3 ?   -2.4   0.0       1.5   6.9e+03      80      92 ..     332     344 ..     324     383 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
                           MccV  22 diakgigaaagtfvaGaiGaivggivagavydvastktpdaalspsGlggtlkq 75 
                                    +i   ig  ++ +v   iGa  gg++a      + ++++ a+l+ +G g+ +  
  gi|121639268|ref|YP_979492.1|  65 NIYTRIGNPTTDVVEQRIGALEGGVAA-LFLSSGQAAETFAILNLAGAGDHIVS 117
                                    567778999999*********999875.44556666666778888888877655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                           MccV  27 igaaagtfvaGaiGaivggivagavydvastk 58 
                                    +  +a+++++G   ai+g iv g+ +d++  +
  gi|121639268|ref|YP_979492.1| 214 VVHSATKYLGGHGAAIAGVIVDGGNFDWTQGR 245
                                    455677888888888999999*******9765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                           MccV  80 lPseawnyaeGrl 92 
                                    lPs  w   + rl
  gi|121639268|ref|YP_979492.1| 332 LPSSPWHERAKRL 344
                                    5555554433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3283.78
//
Query:       gi|121639269|ref|YP_979493.1|  [L=379]
Description: homoserine O-acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-29  101.3   0.0    7.8e-29  101.1   0.0    1.0  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.018   14.3   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
       0.21   11.7   0.0       0.48   10.5   0.0    1.5  1  DUF4884        Domain of unknown function (DUF4884)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   1.3e-32   7.8e-29       1     256 [.      52     356 ..      52     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 1.3e-32
                                    SEEEEE-STTTCGGG............GTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB........CHHSHHHH CS
                  Abhydrolase_1   1 pvlvilhGlpgssdv............waerglapaLakd..gfdvillDlrGvgySspapacin.......ddygtasv 59 
                                    +v+v+lh+l+g s++            w+    +p+ + d  +++ ++++++G +++s++p++         ++++++s+
  gi|121639269|ref|YP_979493.1|  52 NVVVVLHALTGDSHItgpagpghptpgWWDGVAGPGAPIDttRWCAVATNVLGGCRGSTGPSSLArdgkpwgSRFPLISI 131
                                    79*************************999888888888899********************999*************** PP

                                    HHHHH...HHHHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHHHCHHCHH CS
                  Abhydrolase_1  60 addld...rildalgddklt.lvGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksfpdffdgy 131
                                    +d ++   ++l+alg+ +++ +vG+SmGG+ al++   yp+rV+a  ll+      ++ + +  +q  ++k +pd+  g+
  gi|121639269|ref|YP_979493.1| 132 RDQVQadvAALAALGITEVAaVVGGSMGGARALEWVVGYPDRVRAGLLLAVgaraTADQIGTQTTQIAAIKADPDWQSGD 211
                                    ******7666********************************************************************** PP

                                    HHHHHHHH.HHHHHHCCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC.... CS
                  Abhydrolase_1 132 aadcarnp.agplladelaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre.... 206
                                    + +  r p ag+ la++ a+l++r +        + + rf ++++ n+  +a g  ++++++ +++ +kll r++     
  gi|121639269|ref|YP_979493.1| 212 YHETGRAPdAGLRLARRFAHLTYRGE-------IELDTRFANHNQGNEDPTAGGR-YAVQSYLEHQGDKLLSRFDAgsyv 283
                                    9988875527899***********99.......799********77777766666.*******************9**** PP

                                    .....................THHHHS....EEEEEEETTCSSSCHHHHHHHHHCHTS..EEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 207 .....................lknvla....ptlvisgtsDplvppkaledlaqllpk..krlvvisdagHlafleg 256
                                                         l         p++v ++tsD+l p + + +la+llp+   ++vv+s +gH+ fl++
  gi|121639269|ref|YP_979493.1| 284 iltealnshdvgrgrggvsaaL----RacpvPVVVGGITSDRLYPLRLQQELADLLPGcaGLRVVESVYGHDGFLVE 356
                                    *******999999999965554....34555************************998888*************987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-06     0.018      77     112 ..     150     186 ..     130     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-06
                    Hydrolase_4  77 plfllGhSmGGliallyllrypdkva.glilsaPalk 112
                                       ++G SmGG+ al+++  ypd+v+ gl l+  a +
  gi|121639269|ref|YP_979493.1| 150 VAAVVGGSMGGARALEWVVGYPDRVRaGLLLAVGARA 186
                                    46799*********************67766554444 PP

>> DUF4884  Domain of unknown function (DUF4884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     8e-05      0.48       5      32 ..     260     287 ..     257     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8e-05
                        DUF4884   5 YtveYLFeHeGvkVYRFyDmgsYvYFTt 32 
                                    Y v+   eH+G k    +D gsYv  T 
  gi|121639269|ref|YP_979493.1| 260 YAVQSYLEHQGDKLLSRFDAGSYVILTE 287
                                    8998889********99*******9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2749.70
//
Query:       gi|121639270|ref|YP_979494.1|  [L=243]
Description: methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-22   77.5   0.0    1.9e-21   76.5   0.0    1.5  2  Methyltransf_11  Methyltransferase domain
    2.8e-18   66.4   0.0    2.4e-17   63.4   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    1.1e-10   42.2   0.0    7.3e-10   39.5   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
    1.4e-08   34.7   0.0    3.2e-08   33.5   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
    4.9e-07   29.7   0.0    7.2e-07   29.2   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    5.1e-07   29.3   0.0    7.8e-07   28.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00052   19.9   0.0     0.0013   18.6   0.0    1.5  1  Methyltransf_8   Hypothetical methyltransferase
     0.0019   17.8   0.0      0.036   13.6   0.0    2.2  1  MTS              Methyltransferase small domain
     0.0048   16.0   0.0     0.0069   15.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.063   13.0   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.042   12.4   0.0      0.052   12.1   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.11   12.0   0.0       0.16   11.5   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.23   10.5   0.0       0.28   10.2   0.0    1.2  1  DREV             DREV methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.4e-24   1.9e-21       1      94 [.      43     131 ..      43     133 .. 0.97
   2 ?   -3.0   0.0       8.8   1.2e+04      62      81 ..     189     210 ..     171     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.4e-24
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ld+G+GtG+l+  l +rg +vv+vD+ +eml++ +++ ++       + ++ae++p+ dns+D+v++ +++h+v dp++a
  gi|121639270|ref|YP_979494.1|  43 LDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVLRAALPQTVA----LLGTAEEIPLDDNSVDAVLVAQAWHWV-DPARA 117
                                    8*************************************99874....9**************************.7**** PP

                                    HHHHHHHEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGll 94 
                                    + e+aRvL+pgG+l
  gi|121639270|ref|YP_979494.1| 118 IPEVARVLRPGGRL 131
                                    ************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.8
                                    EEEEEEES-CCC-..CCHHHHH CS
                Methyltransf_11  62 fDlvvssevlhhv..edpekal 81 
                                    +Dlv s++   +   + + k+l
  gi|121639270|ref|YP_979494.1| 189 IDLVASRSYCITSpaQVRTKTL 210
                                    5666666544444334444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   1.7e-20   2.4e-17       1      97 []      42     129 ..      42     129 .. 0.95
   2 ?    0.8   0.0      0.59   8.1e+02      47      94 ..     171     218 ..     159     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.7e-20
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLdlG+GtG+lt +l +r+   +v++vD+ +eml+  r+ +    ++   + g ae++p++d+s+D+v++++a+h+++  
  gi|121639270|ref|YP_979494.1|  42 VLDLGAGTGKLTTRLVERG--LDVVAVDPIPEMLDVLRAAL----PQTVALLGTAEEIPLDDNSVDAVLVAQAWHWVD-- 113
                                    9*****************5..********************....8889999******************98899986.. PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                      ++a+ e+arvL+pgG
  gi|121639270|ref|YP_979494.1| 114 -PARAIPEVARVLRPGG 129
                                    .568************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.59
                                    TEEEEESBCCGBSSSTTTEEEEEEESTGGG.SSHHHHHHHHHHHHHHEE CS
                Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssgalhh.lsdedlekalkeiarvLk 94 
                                     v+ +q + +++  +++ +Dlv s+ ++++  + + + k+l++++++L 
  gi|121639270|ref|YP_979494.1| 171 TVQRHQVEWTNYLTPQALIDLVASR-SYCItSPAQVRTKTLDRVRQLLA 218
                                    5566677777877888999999995.54441455667789999999886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   5.3e-13   7.3e-10       1      99 []      43     131 ..      43     131 .. 0.88
   2 ?    0.3   0.0      0.88   1.2e+03      68      94 ..     190     218 ..     169     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 5.3e-13
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L++G+GtG l+ +l e+  ++++++vD+ p++++  ++ l +  ++  +  e+  +d       +s+D+v+++++ h++ 
  gi|121639270|ref|YP_979494.1|  43 LDLGAGTGKLTTRLVER--GLDVVAVDPIPEMLDVLRAALPQTVALLGTAEEIPLDD-------NSVDAVLVAQAWHWV- 112
                                    8****************..**************888888888886555555555444.......3*************9. PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d+++++ +++++L+pgGrl
  gi|121639270|ref|YP_979494.1| 113 DPARAIPEVARVLRPGGRL 131
                                    *****************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.88
                Methyltransf_12  68 Dlvvas.nvlhhl.kdir.evldnirklLk 94 
                                    Dlv +   ++    +++r ++ld++r+lL+
  gi|121639270|ref|YP_979494.1| 190 DLVASRsYCIT-SpAQVRtKTLDRVRQLLA 218
                                    55555523333.245555599*****9996 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.3e-11   3.2e-08       5     107 ..      40     131 ..      36     154 .. 0.92
   2 ?   -2.2   0.0       2.3   3.2e+03      55      91 ..     171     205 ..     167     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.3e-11
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                     rvlDlG+GtG+lt +l e+   + +vv +D  +e++ + r+      l       g +ee++  l d+++D +l  ++ 
  gi|121639270|ref|YP_979494.1|  40 RRVLDLGAGTGKLTTRLVER---GLDVVAVDPIPEMLDVLRAA-----LPQTVALLGTAEEIP--LDDNSVDAVLVAQAW 109
                                    68****************76...467****************5.....55678899*******..99*********9998 PP

                Methyltransf_31  85 naladpdkileeiervlkpggil 107
                                     +  dp+ ++ e+ rvl+pgg+l
  gi|121639270|ref|YP_979494.1| 110 -HWVDPARAIPEVARVLRPGGRL 131
                                    .9*******************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                Methyltransf_31  55 nveFeqgdiee.leklledekfDlilsnevlnaladpd 91 
                                     v+ +q ++++ l     ++ +Dl+ s++ + + +++ 
  gi|121639270|ref|YP_979494.1| 171 TVQRHQVEWTNyLTP---QALIDLVASRSYCITSPAQV 205
                                    556666777775552...36677777776665544443 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.2e-10   7.2e-07       9     124 ..      27     139 ..      19     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.2e-10
                Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlI 86 
                                    + ++++ llp   a  rvLd+G+GtG l+  l e+g +v++vD+ pe+ + ++    ++ +     ++e++ ++++ d +
  gi|121639270|ref|YP_979494.1|  27 PPEAIDWLLP--AAARRVLDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVLRaaL-PQTVALLGTAEEIPLDDNSVDAV 103
                                    5555666663..6788********************************99987742.333333333556666889***** PP

                Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                       +  ++v+ p++++  +a+ l+pgG+l l  ++ ++
  gi|121639270|ref|YP_979494.1| 104 LVAQAWHWVD-PARAIPEVARVLRPGGRLGLV-WNTRD 139
                                    ******9995.69**************98443.33333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   5.6e-10   7.8e-07      48     150 ..      39     132 ..      30     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.6e-10
                                    TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GG CS
                Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlr 127
                                    +++vlD+ +Gtg l+ +l   v++  +vv +D  ++mL+v ++ l +        l + aee+p +d+s D v v+    
  gi|121639270|ref|YP_979494.1|  39 ARRVLDLGAGTGKLTTRL---VERGLDVVAVDPIPEMLDVLRAALPQ-----TVALLGTAEEIPLDDNSVDAVLVAQAWH 110
                                    5689***********887...567789************98876654.....445789******************9876 PP

                                    G-S-HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 128 nvtDklkaLkeayrvlkpGGrlv 150
                                       D  +a+ e+ rvl+pGGrl 
  gi|121639270|ref|YP_979494.1| 111 -WVDPARAIPEVARVLRPGGRLG 132
                                    .5699***************986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.7e-07    0.0013      75     154 ..      41     131 ..      29     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.7e-07
                                    -EEEES-TT-HHHHH.--S-..EEEEE........S.S-SSTTEEES-T.TS-S--TT-EEEEEEES---SS-HHHHHHH CS
                 Methyltransf_8  75 vvadlGcGeakiaea.vrekekvrsfd........l.vavnervvacdl.akvPledesvdvavfclslmgtnladflke 143
                                     v dlG G  k++++ v++  +v ++d        l +a+ + v       ++Pl+d+svd +++  +    + a  + e
  gi|121639270|ref|YP_979494.1|  41 RVLDLGAGTGKLTTRlVERGLDVVAVDpipemldvLrAALPQTVALLGTaEEIPLDDNSVDAVLVAQAWHWVDPARAIPE 120
                                    5889999999998652556677877773222222211234444444444468**************************** PP

                                    HHHHEEEEEEE CS
                 Methyltransf_8 144 anrvlkvGGll 154
                                    + rvl++GG l
  gi|121639270|ref|YP_979494.1| 121 VARVLRPGGRL 131
                                    *********87 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.6e-05     0.036      29     140 ..      37     136 ..      28     154 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                    CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---ST CS
                            MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfh 108
                                    + ++++vlDlG+G+G l++ l ++  +  v++vd   + l++ ++ l ++ + + + +      ++++++d+++     h
  gi|121639270|ref|YP_979494.1|  37 A-AARRVLDLGAGTGKLTTRLVERGLD--VVAVDPIPEMLDVLRAALPQTVALLGTAE---EIPLDDNSVDAVLVAQAWH 110
                                    4.7789**************9998766..88888877777777777665544322222...2233445566666544444 PP

                                    TTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEE CS
                            MTS 109 agkatelavaeeliaeAkeaLkegGeLliVan 140
                                               + i e +++L++gG+L +V+n
  gi|121639270|ref|YP_979494.1| 111 WVDP------ARAIPEVARVLRPGGRLGLVWN 136
                                    4333......3344455566666666666666 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     5e-06    0.0069      31      72 ..      39      80 ..      28      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5e-06
                                   TSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHT CS
                         RrnaAD 31 kltvleigpGkGilTeeLakrakqvvvlElderLakllqkkl 72
                                      vl++g+G+G lT++L++r   vv++   ++++ +l+++l
  gi|121639270|ref|YP_979494.1| 39 ARRVLDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVLRAAL 80
                                   568*************************99999999998865 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.6e-05     0.063      65     113 ..      30      75 ..      15      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                    HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHH CS
                           PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelvee 113
                                    a+++l   +  rvL++G+G+G lt   +rlv++   vv+++ i+e+ + 
  gi|121639270|ref|YP_979494.1|  30 AIDWLLPAAARRVLDLGAGTGKLT---TRLVERGLDVVAVDPIPEMLDV 75 
                                    67888888899**********998...5999*************99765 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05     0.052     117     214 ..      38     130 ..      10     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                Methyltransf_29 117 kvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgt.krlpyPsrsfdlihCsrCridwt 195
                                      r vlD+G g   +++ l++r++  +++ p  e  + +  aL    p ++a+lgt + +p   +s d +  ++    w+
  gi|121639270|ref|YP_979494.1|  38 AARRVLDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVLRAAL----PQTVALLGTaEEIPLDDNSVDAVLVAQA---WH 110
                                    6799*************************99999888877775....8899999983579**********99985...55 PP

                Methyltransf_29 196 eed.gilllevdRvlRpgGy 214
                                      d +  + ev RvlRpgG 
  gi|121639270|ref|YP_979494.1| 111 WVDpARAIPEVARVLRPGGR 130
                                    544267899*********95 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.16      57     115 ..      40      97 ..      35     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                Methyltransf_PK  57 kvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqe 115
                                    +++ld GaG G++t +l+ + l  v  v+p+ ++l+ ++  l +     g   +++l++
  gi|121639270|ref|YP_979494.1|  40 RRVLDLGAGTGKLTTRLVERGLDVV-AVDPIPEMLDVLRAALPQTVALLGTAEEIPLDD 97 
                                    679***************9999877.589******999999888666666666666665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.28      94     132 ..      38      76 ..      29     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                           DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrdrl 132
                                      +++ldlGaG G++t r+ +   +v a +   +m d l
  gi|121639270|ref|YP_979494.1|  38 AARRVLDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVL 76 
                                    5789**************998888888877777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1776.00
//
Query:       gi|121639271|ref|YP_979495.1|  [L=1338]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-89  292.5 416.2    8.2e-11   41.6  18.7   17.6 17  Pentapeptide_2  Pentapeptide repeats (8 copies)
    2.3e-59  200.0  20.2    2.3e-59  200.0  20.2    1.7  2  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5  16.7   1.3e-11   1.1e-07       6      39 ..     187     220 ..     186     221 .. 0.94
   2 !   20.0  26.2     5e-08   0.00045       1      35 [.     212     246 ..     212     247 .. 0.92
   3 !   36.7  24.2   3.2e-13   2.9e-09       1      39 [.     254     292 ..     254     293 .. 0.98
   4 !   31.7  29.5   1.1e-11     1e-07       2      40 .]     297     335 ..     296     335 .. 0.96
   5 !   36.5  19.4   3.7e-13   3.3e-09       2      39 ..     337     374 ..     336     375 .. 0.98
   6 !   41.6  18.7   9.1e-15   8.2e-11       1      40 []     376     415 ..     376     415 .. 0.98
   7 ?   -0.1  13.3     0.097   8.7e+02       4      35 ..     655     688 ..     654     691 .. 0.75
   8 !   10.7   8.4     4e-05      0.36       1      29 [.     699     727 ..     699     734 .. 0.86
   9 !   26.1  15.9   6.6e-10   5.9e-06       6      39 ..     763     796 ..     762     796 .. 0.97
  10 !   15.5  30.0   1.3e-06     0.012       1      35 [.     788     822 ..     788     824 .. 0.94
  11 !   36.7  24.2   3.2e-13   2.9e-09       1      39 [.     830     868 ..     830     869 .. 0.98
  12 !   31.7  29.5   1.1e-11     1e-07       2      40 .]     873     911 ..     872     911 .. 0.96
  13 !   36.5  19.4   3.7e-13   3.3e-09       2      39 ..     913     950 ..     912     951 .. 0.98
  14 !   41.6  18.7   9.1e-15   8.2e-11       1      40 []     952     991 ..     952     991 .. 0.98
  15 ?   -0.9  11.7      0.17   1.5e+03      12      37 ..    1244    1271 ..    1234    1273 .. 0.77
  16 !    7.5   2.3   0.00041       3.6       4      30 ..    1283    1309 ..    1281    1312 .. 0.73
  17 ?    0.2   0.7     0.081   7.3e+02      19      27 ..    1320    1328 ..    1318    1337 .. 0.50

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-11
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +N+G +N+G+fN GsgN+Gs+N+G gN+Gs n+G
  gi|121639271|ref|YP_979495.1| 187 VNLGLANVGLFNAGSGNVGSYNVGAGNVGSYNVG 220
                                    799*****************************99 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5e-08
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGs 35 
                                    gN+Gs+N+G gN+G  N+G gN+G++N+G +N+G 
  gi|121639271|ref|YP_979495.1| 212 GNVGSYNVGGGNIGGNNVGLGNVGFGNVGLANSGL 246
                                    8999*************************999996 PP

  == domain 3  score: 36.7 bits;  conditional E-value: 3.2e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+Gs N+G++N+G gN+G++N+GsgN+G+g tG
  gi|121639271|ref|YP_979495.1| 254 GNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTG 292
                                    8************************************99 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 1.1e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                     +G +N+GsgN+G+fN+G+gN+G+fN+G+gN G +n+Gs
  gi|121639271|ref|YP_979495.1| 297 GFGGFNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGS 335
                                    68************************************6 PP

  == domain 5  score: 36.5 bits;  conditional E-value: 3.7e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++NsG + tG+fN G  NtG  N+Gs+NtGs+n+G
  gi|121639271|ref|YP_979495.1| 337 NTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAG 374
                                    *************************************9 PP

  == domain 6  score: 41.6 bits;  conditional E-value: 9.1e-15
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG +N Gs+NtG++N+G +NtG +N+G++NtG++ +G+
  gi|121639271|ref|YP_979495.1| 376 ANTGGFNPGSVNTGWLNTGDTNTGVANSGDVNTGAFISGN 415
                                    6*************************************96 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.097
                 Pentapeptide_2   4 GslN.sGsgNtGffNlGsgNt.GsfNlGsgNtGs 35 
                                    G++N +G   +GffN+G g + G++N+G   +G 
  gi|121639271|ref|YP_979495.1| 655 GFGNtTGAPSSGFFNSGAGGVsGFGNVGAMVSGG 688
                                    6677348888999999998855999999877775 PP

  == domain 8  score: 10.7 bits;  conditional E-value: 4e-05
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlG 29 
                                    g +G++N+G+ ++G +N Gsg  G fN+ 
  gi|121639271|ref|YP_979495.1| 699 GGSGVFNAGTLHSGVLNFGSGMSGLFNTS 727
                                    5689***********************85 PP

  == domain 9  score: 26.1 bits;  conditional E-value: 6.6e-10
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    lN+G + +G++N+G gN+G+fNlG gN+G +n+G
  gi|121639271|ref|YP_979495.1| 763 LNFGLADVGLGNVGLGNVGDFNLGAGNVGGFNVG 796
                                    8*******************************99 PP

  == domain 10  score: 15.5 bits;  conditional E-value: 1.3e-06
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGs 35 
                                    gN+G +N+G gN+G  N+G gN+G++N+G gN+G 
  gi|121639271|ref|YP_979495.1| 788 GNVGGFNVGGGNIGGNNVGLGNVGWGNFGLGNSGL 822
                                    89******************************996 PP

  == domain 11  score: 36.7 bits;  conditional E-value: 3.2e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G++N+Gs N+G++N+G gN+G++N+GsgN+G+g tG
  gi|121639271|ref|YP_979495.1| 830 GNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTG 868
                                    8************************************99 PP

  == domain 12  score: 31.7 bits;  conditional E-value: 1.1e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                     +G +N+GsgN+G+fN+G+gN+G+fN+G+gN G +n+Gs
  gi|121639271|ref|YP_979495.1| 873 GFGGFNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGS 911
                                    68************************************6 PP

  == domain 13  score: 36.5 bits;  conditional E-value: 3.7e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++NsG + tG+fN G  NtG  N+Gs+NtGs+n+G
  gi|121639271|ref|YP_979495.1| 913 NTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAG 950
                                    *************************************9 PP

  == domain 14  score: 41.6 bits;  conditional E-value: 9.1e-15
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG +N Gs+NtG++N+G +NtG +N+G++NtG++ +G+
  gi|121639271|ref|YP_979495.1| 952 ANTGGFNPGSVNTGWLNTGDTNTGVANSGDVNTGAFISGN 991
                                    6*************************************96 PP

  == domain 15  score: -0.9 bits;  conditional E-value: 0.17
                 Pentapeptide_2   12 NtGffNlGsgN..tGsfNlGsgNtGsgn 37  
                                      +GffN+G g    G+ NlG g +G +n
  gi|121639271|ref|YP_979495.1| 1244 SSGFFNIGGGGglSGFHNLGAGMSGVLN 1271
                                     5799**99887668******99999988 PP

  == domain 16  score: 7.5 bits;  conditional E-value: 0.00041
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNlGs 30  
                                     G++N+G+  +G +N G    G +N+G 
  gi|121639271|ref|YP_979495.1| 1283 GFANFGTQLSGILNRGADISGVYNTGA 1309
                                     777777777777777777777777775 PP

  == domain 17  score: 0.2 bits;  conditional E-value: 0.081
                 Pentapeptide_2   19 GsgNtGsfN 27  
                                     G+gN+G + 
  gi|121639271|ref|YP_979495.1| 1320 GFGNVGQQL 1328
                                     445555443 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0  20.2   2.6e-63   2.3e-59       1     158 []       5     162 ..       5     162 .. 0.99
   2 ?   -4.3   0.3       1.9   1.7e+04      18      37 ..     173     192 ..     169     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 2.6e-63
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    ++pPE+ns l+y+G+g+gpllaAaaaWd+Laael saaa++ sv+++l ++ WqGpss amaaaaapy+ WLsaaaa+ae
  gi|121639271|ref|YP_979495.1|   5 VMPPEINSLLIYTGAGPGPLLAAAAAWDELAAELGSAAAAFGSVTSGLVGGIWQGPSSVAMAAAAAPYAGWLSAAAASAE 84 
                                    58****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     aA qa+a++ ++eaAlaa+v+p +iaanr +l++l+ +n+fGqntpaIaa+e +ye mwaqd+aam +Y++ ++aaa
  gi|121639271|ref|YP_979495.1|  85 SAAGQARAVVGVFEAALAATVDPFVIAANRSRLVSLALSNLFGQNTPAIAAAEFDYELMWAQDVAAMLGYHTGASAAA 162
                                    *************************************************************************99985 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHHHHHHH CS
                            PPE  18 gpllaAaaaWdgLaaelasa 37 
                                    ++l aAa+  ++La +l  a
  gi|121639271|ref|YP_979495.1| 173 ASLAAAAEPAKSLAVNLGLA 192
                                    68889999999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.24s 00:00:00.99 Elapsed: 00:00:00.41
# Mc/sec: 9719.87
//
Query:       gi|121639272|ref|YP_979496.1|  [L=1876]
Description: hypothetical protein BCG_3414c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-33  112.7  20.9    1.3e-32  112.0  20.9    1.3  1  PE             PE family
  ------ inclusion threshold ------
      0.087   13.3  12.2       0.16   12.5  12.2    1.4  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0  20.9   1.4e-36   1.3e-32       4      93 .]       5      94 ..       2      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1.4e-36
                                   XXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  4 vvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaag 85
                                   ++vaPe++aaaaadl+gig+a+saanaaaa+ptt+vlaaa DeVSaaiAalf++haqeyqalsa++a+fheqfv++l+aa++
  gi|121639272|ref|YP_979496.1|  5 LMVAPELVAAAAADLTGIGQAISAANAAAAGPTTQVLAAAGDEVSAAIAALFGTHAQEYQALSARVATFHEQFVRSLTAAGS 86
                                   899******************************************************************************* PP

                                   HHHS--XX CS
                             PE 86 sYaaaEaa 93
                                   +Ya+aEaa
  gi|121639272|ref|YP_979496.1| 87 AYATAEAA 94
                                   ******97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  12.2   1.7e-05      0.16       1      99 [.       1     100 [.       1     101 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                  T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaar.raagealaaasteLadk 79 
                                    m  +L V p+ + ++aa+++++ + i++a+aaaag +++vl   G   +a  +a+   +a   +a  +++a+ ++++ + 
  gi|121639272|ref|YP_979496.1|   1 MVMSLMVAPELVAAAAADLTGIGQAISAANAAAAGPTTQVLAAAGDEVSAAIAALFGTHAQEyQALSARVATFHEQFVRS 80 
                                    566799*************************************9965544444444444444044445678889999999 PP

                  T7SS_ESX_EspC  80 LraAAaaYeatDeeaagald 99 
                                    L+aA  aY  ++ ++a+ l+
  gi|121639272|ref|YP_979496.1|  81 LTAAGSAYATAEAANASPLQ 100
                                    ***************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.66u 0.33s 00:00:01.99 Elapsed: 00:00:00.61
# Mc/sec: 9319.36
//
Query:       gi|121639273|ref|YP_979497.1|  [L=85]
Description: hypothetical protein BCG_3415c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-19   69.8   9.2    1.8e-19   69.8   9.2    1.5  2  DUF3017   Protein of unknown function (DUF3017)
  ------ inclusion threshold ------
       0.23   11.5   2.5         35    4.5   0.0    2.9  3  DUF2109   Predicted membrane protein (DUF2109)


Domain annotation for each model (and alignments):
>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.23   2.1e+03      32      42 ..       2      12 ..       1      19 [. 0.69
   2 !   69.8   9.2     2e-23   1.8e-19      13      74 .]      17      78 ..      10      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                        DUF3017 32 llaAvlRlvlp 42
                                    + AvlR ++ 
  gi|121639273|ref|YP_979497.1|  2 TVRAVLRRTVG 12
                                   56678887765 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 2e-23
                        DUF3017 13 llvaldhwRrGalllGvalllaAvlRlvlpsrrvGlLaVRsRafDvllllvlGaaivvlalt 74
                                   +l++++ wRrGall+G+++ +aAvlRlvl+++r+GlL+VRs+ +D++++++++aa+v++a t
  gi|121639273|ref|YP_979497.1| 17 ILAGVNFWRRGALLIGIGVGVAAVLRLVLSEERAGLLVVRSKGIDFVTTVTVAAAMVYIAST 78
                                   5688999****************************************************975 PP

>> DUF2109  Predicted membrane protein (DUF2109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0039        35      12      38 ..       1      27 [.       1      41 [. 0.81
   2 ?    2.6   0.0     0.016   1.4e+02      32      47 ..      33      48 ..      24      56 .. 0.58
   3 ?    4.1   0.5    0.0051        46      50      63 ..      67      80 ..      60      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0039
                        DUF2109 12 aairilleknraekLlylnvlnFaiaa 38
                                   +++r++l +   ++ ++l  +nF   +
  gi|121639273|ref|YP_979497.1|  1 MTVRAVLRRTVGAQWPILAGVNFWRRG 27
                                   789*******************96555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.016
                        DUF2109 32 lnFaiaalialliktp 47
                                   ++ ++aa++ l+++++
  gi|121639273|ref|YP_979497.1| 33 IGVGVAAVLRLVLSEE 48
                                   4555555555555433 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0051
                        DUF2109 50 liaAiayFvgsTle 63
                                    +aA++++++sT++
  gi|121639273|ref|YP_979497.1| 67 TVAAAMVYIASTID 80
                                   57899999****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 635.77
//
Query:       gi|121639274|ref|YP_979498.1|  [L=2096]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.5e-135  439.3 723.5      9e-10   38.3  24.0   29.3 32  Pentapeptide_2  Pentapeptide repeats (8 copies)
    1.6e-53  181.0  35.1    2.9e-53  180.2  35.1    1.4  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6  15.4   1.1e-10   9.6e-07       6      39 ..     196     229 ..     195     230 .. 0.96
   2 !   22.3  23.8   9.6e-09   8.6e-05       7      39 ..     222     254 ..     222     257 .. 0.53
   3 !   35.0  22.6   1.1e-12   9.9e-09       1      39 [.     262     300 ..     262     301 .. 0.98
   4 !   32.3  28.8   7.7e-12   6.9e-08       2      40 .]     305     343 ..     304     343 .. 0.96
   5 !   35.5  22.7   7.4e-13   6.6e-09       2      40 .]     345     383 ..     344     383 .. 0.98
   6 !   34.8  27.4   1.2e-12   1.1e-08       1      40 []     384     423 ..     384     423 .. 0.98
   7 !    4.6  11.2    0.0032        29       4      37 ..     666     701 ..     665     704 .. 0.81
   8 !    8.5  11.6    0.0002       1.8       3      30 ..     712     739 ..     709     744 .. 0.58
   9 ?   -2.2   0.4      0.43   3.9e+03      29      34 ..     750     755 ..     749     766 .. 0.45
  10 !   32.0   9.3   8.9e-12     8e-08       6      39 ..     774     807 ..     773     807 .. 0.94
  11 !   25.8  20.7   7.7e-10   6.9e-06       1      34 [.     799     832 ..     799     835 .. 0.85
  12 !   29.2  30.0     7e-11   6.3e-07       1      39 [.     841     879 ..     841     880 .. 0.98
  13 !   28.1  28.5   1.6e-10   1.4e-06       2      39 ..     884     921 ..     883     922 .. 0.97
  14 !   33.0  23.1   4.4e-12     4e-08       2      39 ..     924     961 ..     923     962 .. 0.98
  15 !   38.3  24.0     1e-13     9e-10       1      40 []     963    1002 ..     963    1002 .. 0.98
  16 ?   -3.1   0.1      0.88   7.9e+03       9      15 ..    1058    1064 ..    1057    1065 .. 0.39
  17 ?   -1.4  12.7      0.24   2.2e+03      13      37 ..    1259    1284 ..    1249    1287 .. 0.79
  18 !    6.4   4.2   0.00091       8.2       4      28 ..    1296    1320 ..    1295    1326 .. 0.82
  19 ?    0.1   0.6     0.087   7.8e+02      24      30 ..    1332    1338 ..    1328    1344 .. 0.50
  20 !   27.4  22.6   2.5e-10   2.2e-06       1      39 [.    1385    1423 ..    1382    1423 .. 0.97
  21 !   25.6  28.6   8.9e-10     8e-06       2      39 ..    1411    1448 ..    1410    1449 .. 0.98
  22 !   26.6  30.1   4.4e-10     4e-06       1      39 [.    1456    1494 ..    1456    1495 .. 0.98
  23 !   32.0  26.5   9.3e-12   8.4e-08       2      40 .]    1499    1537 ..    1498    1537 .. 0.96
  24 !   33.6  22.8   2.9e-12   2.6e-08       1      40 []    1528    1567 ..    1528    1567 .. 0.98
  25 !   35.6  22.5   6.8e-13   6.1e-09       2      40 .]    1539    1577 ..    1538    1577 .. 0.98
  26 !   31.9  26.3     1e-11   9.1e-08       1      40 []    1578    1617 ..    1578    1617 .. 0.98
  27 !   22.7  20.6   7.5e-09   6.7e-05       2      39 ..    1589    1626 ..    1588    1627 .. 0.94
  28 !    3.2  11.3    0.0091        82      11      37 ..    1884    1911 ..    1875    1913 .. 0.74
  29 !   13.5   6.9   5.7e-06     0.051       3      28 ..    1922    1947 ..    1920    1955 .. 0.81
  30 ?   -1.6   0.2       0.3   2.7e+03      29      36 ..    1960    1967 ..    1958    1976 .. 0.55
  31 !   29.3   9.1   6.6e-11     6e-07       6      39 ..    1984    2017 ..    1982    2017 .. 0.95
  32 !   26.4  22.6   5.2e-10   4.6e-06       2      34 ..    2010    2042 ..    2009    2045 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.1e-10
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    lN+G gN+G++N+G gN+G fNlG +N+G+ n+G
  gi|121639274|ref|YP_979498.1| 196 LNAGLGNVGNYNVGLGNVGIFNLGAANVGAQNLG 229
                                    7*******************************99 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9.6e-09
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N+G  N+G +N GsgN+G++N+G++N+G+gn+G
  gi|121639274|ref|YP_979498.1| 222 NVGAQNLGAANAGSGNFGFGNIGNANFGFGNSG 254
                                    555555555555555555555555555555555 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 1.1e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G +N+Gs N+G++NlG gN+G++N+Gs+N+G+g tG
  gi|121639274|ref|YP_979498.1| 262 GNIGLGNAGSSNYGLANLGVGNIGFANTGSNNIGIGLTG 300
                                    8************************************99 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 7.7e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                     +G lNsG+gN+G+fN+G+gN+G+fN+G+gN+G +n+Gs
  gi|121639274|ref|YP_979498.1| 305 GIGGLNSGTGNLGLFNSGTGNIGFFNSGTGNFGVFNSGS 343
                                    68************************************6 PP

  == domain 5  score: 35.5 bits;  conditional E-value: 7.4e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG++N+G++ tG+fN+G  NtG +N+Gs+NtGs+n+G+
  gi|121639274|ref|YP_979498.1| 345 NTGVGNAGTASTGLFNVGGFNTGVANVGSYNTGSFNAGN 383
                                    *************************************96 PP

  == domain 6  score: 34.8 bits;  conditional E-value: 1.2e-12
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG +N G++NtG++N+G++NtG +N+G++NtG++ +G+
  gi|121639274|ref|YP_979498.1| 384 TNTGGFNPGNVNTGWLNTGNTNTGIANSGNVNTGAFISGN 423
                                    6*************************************96 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.0032
                 Pentapeptide_2   4 GslNsGsg.NtGffNlGsgNt.GsfNlGsgNtGsgn 37 
                                    G++N+ ++  +GffN+G g + G++N+G g +G  n
  gi|121639274|ref|YP_979498.1| 666 GFGNTTTApSSGFFNSGDGGVsGFGNFGAGSSGWWN 701
                                    67777766468******99855*******9999766 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0002
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGs 30 
                                    +G++N+Gs  +G +N Gsg  G +N+G 
  gi|121639274|ref|YP_979498.1| 712 SGFANFGSLGSGVLNFGSGVSGLYNTGG 739
                                    4666666666666666666666666654 PP

  == domain 9  score: -2.2 bits;  conditional E-value: 0.43
                 Pentapeptide_2  29 GsgNtG 34 
                                    G gN+G
  gi|121639274|ref|YP_979498.1| 750 GIGNVG 755
                                    222222 PP

  == domain 10  score: 32.0 bits;  conditional E-value: 8.9e-12
                 Pentapeptide_2   6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                     N+G + +G++N+G+gN+G+fNlG +N+G++n+G
  gi|121639274|ref|YP_979498.1| 774 INLGLADVGSVNVGFGNVGDFNLGAANIGDLNVG 807
                                    699*****************************98 PP

  == domain 11  score: 25.8 bits;  conditional E-value: 7.7e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtG 34 
                                    +N+G+lN+G gN+G +N+G+gN+G++N+G gN G
  gi|121639274|ref|YP_979498.1| 799 ANIGDLNVGLGNVGGGNVGFGNIGDANFGLGNAG 832
                                    6999999999999999999999999999999988 PP

  == domain 12  score: 29.2 bits;  conditional E-value: 7e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G +N+GsgN+Gf+N+G gN+G++N+G++N G+g tG
  gi|121639274|ref|YP_979498.1| 841 GNIGLGNAGSGNVGFGNMGVGNIGFGNTGTNNLGIGLTG 879
                                    8************************************99 PP

  == domain 13  score: 28.1 bits;  conditional E-value: 1.6e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                     +G lNsG gN+G+fN+G+gN+G fN+G+gN+G +n+G
  gi|121639274|ref|YP_979498.1| 884 GIGGLNSGAGNIGLFNSGTGNVGLFNSGTGNFGLFNSG 921
                                    68***********************************9 PP

  == domain 14  score: 33.0 bits;  conditional E-value: 4.4e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N G+g tG+fN G+ NtG +N Gs+NtGs+n+G
  gi|121639274|ref|YP_979498.1| 924 NTGIGNGGTGSTGLFNAGNFNTGVANPGSYNTGSFNVG 961
                                    *************************************9 PP

  == domain 15  score: 38.3 bits;  conditional E-value: 1e-13
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +NtG +N Gs NtG+fN+G++NtG +N+G++NtG++ tG+
  gi|121639274|ref|YP_979498.1|  963 TNTGGFNPGSINTGWFNTGNANTGVANSGTVNTGAFITGN 1002
                                     6*************************************96 PP

  == domain 16  score: -3.1 bits;  conditional E-value: 0.88
                 Pentapeptide_2    9 GsgNtGf 15  
                                     G +N+Gf
  gi|121639274|ref|YP_979498.1| 1058 GQANYGF 1064
                                     4444443 PP

  == domain 17  score: -1.4 bits;  conditional E-value: 0.24
                 Pentapeptide_2   13 tGffNlGs.gNtGsfNlGsgNtGsgn 37  
                                     +GffN+G  g  G +N+G g +G +n
  gi|121639274|ref|YP_979498.1| 1259 SGFFNTGGgGGSGIANFGAGVSGLLN 1284
                                     79***9862679********999988 PP

  == domain 18  score: 6.4 bits;  conditional E-value: 0.00091
                 Pentapeptide_2    4 GslNsGsgNtGffNlGsgNtGsfNl 28  
                                     G +N+Gs  +G +N+G    G fN+
  gi|121639274|ref|YP_979498.1| 1296 GLGNAGSLASGVLNSGVDISGMFNV 1320
                                     8888888888888888888888886 PP

  == domain 19  score: 0.1 bits;  conditional E-value: 0.087
                 Pentapeptide_2   24 GsfNlGs 30  
                                     G++NlG+
  gi|121639274|ref|YP_979498.1| 1332 GFGNLGN 1338
                                     3333333 PP

  == domain 20  score: 27.4 bits;  conditional E-value: 2.5e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gN+Gs+N+G +N+G++NlG gN G+ NlG gN G  n+G
  gi|121639274|ref|YP_979498.1| 1385 GNVGSYNLGFANVGDVNLGAGNLGNLNLGGGNLGGQNLG 1423
                                     8************************************98 PP

  == domain 21  score: 25.6 bits;  conditional E-value: 8.9e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     N G +N+G  N+G++NlG gN+G++NlG+gN+G+gn+G
  gi|121639274|ref|YP_979498.1| 1411 NLGGGNLGGQNLGLGNLGDGNVGFGNLGHGNVGFGNSG 1448
                                     99***********************************9 PP

  == domain 22  score: 26.6 bits;  conditional E-value: 4.4e-10
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     gN+G +N+Gs N+Gf+N+G gN+G++N+G++N G+g tG
  gi|121639274|ref|YP_979498.1| 1456 GNIGLGNAGSNNVGFGNMGLGNIGFGNTGTNNLGIGLTG 1494
                                     8************************************99 PP

  == domain 23  score: 32.0 bits;  conditional E-value: 9.3e-12
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                      +G lNsG gN+G+fN+G+gN+G+fN+G+gN G +n+Gs
  gi|121639274|ref|YP_979498.1| 1499 GFGGLNSGAGNLGLFNSGTGNIGFFNTGTGNWGLFNSGS 1537
                                     68************************************6 PP

  == domain 24  score: 33.6 bits;  conditional E-value: 2.9e-12
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     gN G +NsGs NtG +N+G+g+tG fN+Gs+NtG  n+Gs
  gi|121639274|ref|YP_979498.1| 1528 GNWGLFNSGSYNTGIGNSGTGSTGLFNAGSFNTGLANAGS 1567
                                     8*************************************96 PP

  == domain 25  score: 35.6 bits;  conditional E-value: 6.8e-13
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     NtG++NsG+g tG+fN Gs NtG +N+Gs+NtGs+n+G+
  gi|121639274|ref|YP_979498.1| 1539 NTGIGNSGTGSTGLFNAGSFNTGLANAGSYNTGSLNAGN 1577
                                     *************************************96 PP

  == domain 26  score: 31.9 bits;  conditional E-value: 1e-11
                 Pentapeptide_2    1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40  
                                     +NtG +N G++NtG+fN G +NtG fN+G++Nt ++n+Gs
  gi|121639274|ref|YP_979498.1| 1578 TNTGGFNPGNVNTGWFNAGHTNTGGFNTGNVNTAAFNSGS 1617
                                     6*************************************96 PP

  == domain 27  score: 22.7 bits;  conditional E-value: 7.5e-09
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                     NtG +N+G +NtG fN+G++Nt  fN+Gs+N G++ tG
  gi|121639274|ref|YP_979498.1| 1589 NTGWFNAGHTNTGGFNTGNVNTAAFNSGSFNNGALWTG 1626
                                     9********************************99888 PP

  == domain 28  score: 3.2 bits;  conditional E-value: 0.0091
                 Pentapeptide_2   11 gNtGffNlGsgNt.GsfNlGsgNtGsgn 37  
                                       +GffN+G g + G++N+G g +G  n
  gi|121639274|ref|YP_979498.1| 1884 PSSGFFNSGAGGVsGFGNFGAGSSGWWN 1911
                                     4689999999885599999999999766 PP

  == domain 29  score: 13.5 bits;  conditional E-value: 5.7e-06
                 Pentapeptide_2    3 tGslNsGsgNtGffNlGsgNtGsfNl 28  
                                     +G+lN+G+ N+G +N+Gsg  G +N+
  gi|121639274|ref|YP_979498.1| 1922 SGVLNVGTLNSGVLNVGSGISGLYNT 1947
                                     79999999999999999999999997 PP

  == domain 30  score: -1.6 bits;  conditional E-value: 0.3
                 Pentapeptide_2   29 GsgNtGsg 36  
                                     G gN+G  
  gi|121639274|ref|YP_979498.1| 1960 GAGNVGQQ 1967
                                     44444444 PP

  == domain 31  score: 29.3 bits;  conditional E-value: 6.6e-11
                 Pentapeptide_2    6 lNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39  
                                      N+G + +G++NlG gN+G+fNlG +N G++n+G
  gi|121639274|ref|YP_979498.1| 1984 INLGLADVGNYNLGLGNVGDFNLGAANLGDLNLG 2017
                                     69******************************98 PP

  == domain 32  score: 26.4 bits;  conditional E-value: 5.2e-10
                 Pentapeptide_2    2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtG 34  
                                     N G+lN+G gN+G++N+G+gN+G +N+G+gN+G
  gi|121639274|ref|YP_979498.1| 2010 NLGDLNLGLGNIGNANVGFGNIGHGNVGFGNSG 2042
                                     666666666666666666666666666666666 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2  35.1   3.2e-57   2.9e-53       1     158 []       5     162 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 3.2e-57
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns l+y+G+gs pllaAaaaWdgLa+el saa ++ +v+++l+a+ WqG+++aamaaaaapy+ WL   aaqa 
  gi|121639274|ref|YP_979498.1|   5 VLPPEINSVLMYSGAGSSPLLAAAAAWDGLAEELGSAAVSFGQVTSGLTAGVWQGAAAAAMAAAAAPYAGWLGSVAAQAV 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                    ++A qa+aa+aa+eaAlaa+v+pa +a nr++++al+++n++Gqn++aIaa+eaeye mwa+d+aama+Y++ ++aaa
  gi|121639274|ref|YP_979498.1|  85 AVAGQARAAVAAFEAALAATVDPAAVAVNRMAMRALAMSNLLGQNAAAIAAVEAEYELMWAADVAAMAGYHSGASAAA 162
                                    *************************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2096 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.98u 0.28s 00:00:01.26 Elapsed: 00:00:00.46
# Mc/sec: 13637.66
//
Query:       gi|121639275|ref|YP_979499.1|  [L=163]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-14   52.0   0.0    8.2e-14   51.8   0.0    1.0  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   4.6e-18   8.2e-14       1     148 [.      14     160 ..      14     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.6e-18
                 DEDD_Tnp_IS110   1 vGiDvakdk.hdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvnpl 79 
                                    vGiD a +  h++++ d+ g + ++++v+ + +gl++l +k ++  +++   ve t+  + +l  ++++ag t+++  ++
  gi|121639275|ref|YP_979499.1|  14 VGIDAAITAcHHIAIRDDVGARSIRFSVEPTLAGLRTLTDK-LSGYDDIDATVEPTSMTWLPLTIAVENAGDTMHMAGAR 92 
                                    8*****998899999**************************.99******************9999************** PP

                 DEDD_Tnp_IS110  80 avkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlra 148
                                    +  rlr +  +k+K+D +DA+v+ ++     +l+pl+l++ a  +Lr+ + +r   v + +r  +rl +
  gi|121639275|ref|YP_979499.1|  93 HCARLRGAIVGKSKSDVIDAEVLTRASE-VFDLTPLTLPTPAQLALRRSVIRRAGAVIDANRSWRRLMS 160
                                    **************************99.9***********************9999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1250.50
//
Query:       gi|121639276|ref|YP_979500.1|  [L=246]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-18   67.2   0.0    2.1e-18   66.9   0.0    1.1  1  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   1.2e-22   2.1e-18      59     173 ..       2     128 ..       1     142 [. 0.83

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.2e-22
                   DDE_Tnp_ISL3  59 vmDmsaayksavke..alPnAkivvDrFHvvklanealdevRrreqkel...reekrkklkrsrrlllknpenlteeqkq 133
                                    ++D +aay+sa+++  +lPnAk+vvD+FHv+ lan+al+ vRrr+ + +   r++k ++ + +rr ll+ +e+l+++  +
  gi|121639276|ref|YP_979500.1|   2 AIDPAAAYASAIRTpgLLPNAKLVVDHFHVTTLANDALTAVRRRVTWAFhdrRGRKIDPQWANRRRLLTARERLSDKSFA 81 
                                    79***********8668********************************66555888899999***************** PP

                   DDE_Tnp_ISL3 134 rlde.ll..easpelekaYelkeelrevfrkk....dkeearkalke 173
                                    ++++ +   +   ++ +a+  keelr+++ +     d++ ar  l++
  gi|121639276|ref|YP_979500.1|  82 KMRNrINavDPRAQILSAWIAKEELRTLLSTVrtggDPHLARHHLHR 128
                                    *999544335566999***********99633334556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1788.63
//
Query:       gi|121639277|ref|YP_979501.1|  [L=432]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-57  191.6  29.0    1.3e-56  191.1  29.0    1.2  1  PPE             PPE family
    1.7e-42  143.0 187.4    1.2e-10   41.1  20.1    6.6  6  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.1  29.0   1.4e-60   1.3e-56       1     158 []       5     162 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.1 bits;  conditional E-value: 1.4e-60
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns l+y+G+gs pllaAaaaWdgLa+el saa ++ +v+++l+a+ WqG+++aamaaaaapy+ WL   aa ae
  gi|121639277|ref|YP_979501.1|   5 VLPPEINSVLMYSGAGSSPLLAAAAAWDGLAEELGSAAVSFGQVTSGLTAGVWQGAAAAAMAAAAAPYAGWLGSVAAAAE 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                    ++A qa++++ ++eaAlaa+v+pa++aanra+l+al+ +n++GqntpaIaa+eaeye mwa+d+aama+Y++ ++aaa
  gi|121639277|ref|YP_979501.1|  85 AVAGQARVVVGVFEAALAATVDPALVAANRARLVALAVSNLLGQNTPAIAAAEAEYELMWAADVAAMAGYHSGASAAA 162
                                    **************************************************************************9985 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  19.8   2.1e-10   1.9e-06       5      39 ..     195     229 ..     195     229 .. 0.96
   2 !   20.8  24.6   2.9e-08   0.00026       2      31 ..     227     256 ..     226     258 .. 0.77
   3 !   21.3  25.2     2e-08   0.00018       1      39 [.     263     299 ..     263     304 .. 0.85
   4 !   33.5  30.2   3.1e-12   2.8e-08       2      40 .]     304     342 ..     303     342 .. 0.96
   5 !   41.1  20.1   1.3e-14   1.2e-10       2      39 ..     344     381 ..     343     382 .. 0.98
   6 !   31.8  30.6   1.1e-11   9.8e-08       1      40 []     383     422 ..     383     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-10
                 Pentapeptide_2   5 slNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    slN+G gN+G++N+G gN+G fNlG gN+G  n+G
  gi|121639277|ref|YP_979501.1| 195 SLNAGLGNVGNYNVGLGNVGVFNLGAGNVGGQNLG 229
                                    68*******************************98 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.9e-08
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsg 31 
                                    N G++N+G +N+Gf+NlG+gN+G++N+G g
  gi|121639277|ref|YP_979501.1| 227 NLGFGNAGGTNVGFGNLGNGNVGFGNSGLG 256
                                    788888888888888888888888888865 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2e-08
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G +N+Gs N+Gf+NlG gN+G++N+  +N+G g tG
  gi|121639277|ref|YP_979501.1| 263 GNIGLGNAGSSNYGFANLGVGNIGFGNT--NNVGVGLTG 299
                                    8*************************97..555555555 PP

  == domain 4  score: 33.5 bits;  conditional E-value: 3.1e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                     +G lNsG+gN+G+fN+G+gN+G+fN+G+gN+G +n+G+
  gi|121639277|ref|YP_979501.1| 304 GIGGLNSGTGNIGLFNSGTGNVGFFNSGTGNFGVFNSGN 342
                                    68************************************6 PP

  == domain 5  score: 41.1 bits;  conditional E-value: 1.3e-14
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N+G++ tG+fN G+ NtG  N+Gs+NtGs+n+G
  gi|121639277|ref|YP_979501.1| 344 NTGVGNAGTASTGLFNAGNFNTGVVNVGSYNTGSFNAG 381
                                    *************************************9 PP

  == domain 6  score: 31.8 bits;  conditional E-value: 1.1e-11
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG +N G +NtG++N+G++NtG +N+G++NtG++ +G+
  gi|121639277|ref|YP_979501.1| 383 TNTGGFNPGGVNTGWLNTGNTNTGIANSGNVNTGAFISGN 422
                                    6*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2966.82
//
Query:       gi|121639278|ref|YP_979502.1|  [L=264]
Description: hypothetical protein BCG_3423c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-07   30.1   0.1    6.7e-07   29.3   0.1    1.4  1  BBE           Berberine and berberine like
  ------ inclusion threshold ------
      0.077   12.4   0.0        0.1   12.0   0.0    1.1  1  Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin bi


Domain annotation for each model (and alignments):
>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   7.4e-11   6.7e-07       2      37 ..     150     182 ..     149     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.4e-11
                                    -TTS--GGG-HHHHHHHHGGGHHHHHHHHHHH-TT- CS
                            BBE   2 YvNyrdldlgkewgerYFggNferLvkvKtkyDPdN 37 
                                    YvNy     +     +YFg+N++rL  v++kyDPd 
  gi|121639278|ref|YP_979502.1| 150 YVNYLEANAA---ASQYFGANLSRLTTVRRKYDPDR 182
                                    *********9...*********************96 PP

>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.1e-05       0.1     233     277 ..     143     187 ..     120     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                                    TT--EEESS---SSHHHHHHHHGHHHHHHHHHHHHH-TT--B-GG CS
                   Cytokin-bind 233 agikvkqYlphyesqeeWkkhfGakWerfverKakyDPkaiLspG 277
                                    ++++v  Y+ + e+++  ++ fGa+ +r+++ ++kyDP +i+  G
  gi|121639278|ref|YP_979502.1| 143 QHFSVGGYVNYLEANAAASQYFGANLSRLTTVRRKYDPDRIMYSG 187
                                    4677788999999999*************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1846.28
//
Query:       gi|121639279|ref|YP_979503.1|  [L=123]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-08   34.2   1.1    2.6e-08   33.7   1.1    1.3  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   1.1   1.4e-12   2.6e-08      70     137 ..       3      68 ..       1      70 [. 0.93

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.4e-12
                                    TTSBHHHHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEE CS
                  FAD_binding_4  70 aGvtlgdlvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvr 137
                                    a + l ++++ala + ++++  +gs+ +++v+G++++++ G  s+ +Gl++d +++++vvl+ G  v 
  gi|121639279|ref|YP_979503.1|   3 AATDLYAVHQALAGESRAIP--TGSCPTVGVAGLTLGGGLGADSRHAGLTCDALKSATVVLPGGDAVS 68 
                                    5677899*************..9*****************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 878.77
//
Query:       gi|121639280|ref|YP_979504.1|  [L=86]
Description: hypothetical protein BCG_3425c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 645.58
//
Query:       gi|121639281|ref|YP_979505.1|  [L=129]
Description: hypothetical protein BCG_3426 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-24   84.8   7.2    4.7e-24   84.6   7.2    1.1  1  DUF732    Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   7.2   2.6e-28   4.7e-24       1      93 [.      15     108 ..      15     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.6e-28
                         DUF732   1 aaaallaaalllaapAaAdsaddaFlaalnqagiaygspdaaialGkavCkkl.dsGksaeavvaevkndnsglspeqaa 79 
                                    aa a+++ a+++aapA+A++ ddaF+aaln+ag++yg+p +a alG++vC+ l + G s+++ va+v ++ +g+s+++a+
  gi|121639281|ref|YP_979505.1|  15 AASAGILSAAAFAAPAQANPVDDAFIAALNNAGVNYGDPVDAKALGQSVCPILaEPGGSFNTAVASVVARAQGMSQDMAQ 94 
                                    57899999*********************************************88*******99999888********** PP

                         DUF732  80 qfvgaAvsayCPeq 93 
                                    +f+ +A+s+yCP  
  gi|121639281|ref|YP_979505.1|  95 TFTSIAISMYCPSV 108
                                    ************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 997.40
//
Query:       gi|121639282|ref|YP_979506.1|  [L=97]
Description: hypothetical protein BCG_3427c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-22   77.7  13.9    5.9e-22   77.7  13.9    1.4  2  DUF3017   Protein of unknown function (DUF3017)
  ------ inclusion threshold ------
       0.82   10.1   4.2        1.2    9.6   4.2    1.4  1  DUF2628   Protein of unknown function (DUF2628)


Domain annotation for each model (and alignments):
>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.86   7.7e+03      33      41 ..       3      11 ..       1      14 [. 0.62
   2 !   77.7  13.9   6.6e-26   5.9e-22       1      74 []      17      90 ..      17      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.86
                        DUF3017 33 laAvlRlvl 41
                                   + Av+R ++
  gi|121639282|ref|YP_979506.1|  3 VRAVFRRTV 11
                                   557777665 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 6.6e-26
                        DUF3017  1 lllvllvvavglllvaldhwRrGalllGvalllaAvlRlvlpsrrvGlLaVRsRafDvllllvlGaaivvlalt 74
                                   +llv  ++avg++l++++ wRrGall+G+++ +aAvlRlvl+++r+GlL+VRs+ +D++++++++aa+v++a t
  gi|121639282|ref|YP_979506.1| 17 ILLVGSIFAVGFVLAGANFWRRGALLIGIGVGVAAVLRLVLSEERAGLLVVRSKGIDFVTTVTVAAAMVYIAST 90
                                   6899*******************************************************************975 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.2   0.00013       1.2      34      70 ..      28      74 ..       3      91 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                        DUF2628 34 iwLlyrklwlkalvllviavavsvvlavl..........gfsdavrl 70
                                   + L+    w+ +++l++i v v++vl ++            s+++ +
  gi|121639282|ref|YP_979506.1| 28 FVLAGANFWRRGALLIGIGVGVAAVLRLVlseeragllvVRSKGIDF 74
                                   34677889******************999775555555422222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 707.21
//
Query:       gi|121639283|ref|YP_979507.1|  [L=281]
Description: bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-60  202.1   0.2    4.8e-60  201.5   0.2    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    1.7e-33  115.3   0.0    2.3e-33  114.9   0.0    1.2  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.5   0.2   5.3e-64   4.8e-60       1     158 [.     123     280 ..     123     281 .] 0.98

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 5.3e-64
                                    SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT..T-EEEEE-TTSCCHHHHHC CS
                  THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLlek..natVtvchsktkdlaeitr 78 
                                    hp+nlgrlv+g++a lpctp+g+v+ll++++i+++g++vvv+Gr+ +vg+pl llL+++  natVt+ch+ t+dl+++tr
  gi|121639283|ref|YP_979507.1| 123 HPTNLGRLVLGTPAPLPCTPRGIVHLLRRYDISIAGAHVVVIGRGVTVGRPLGLLLTRRseNATVTLCHTGTRDLPALTR 202
                                    89*******************************************************9777******************* PP

                                    CSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHHC CS
                  THF_DHG_CYH_C  79 eadivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaakr 158
                                    +adivv+avG+++l++a+mv++ga+viDvG++r+ ++ lvGDv+  +v e+a++++P+pgGVGp+T a ll+n++e a+r
  gi|121639283|ref|YP_979507.1| 203 QADIVVAAVGVAHLLTADMVRPGAAVIDVGVSRT-DDGLVGDVH-PDVWELAGHVSPNPGGVGPLTRAFLLTNVVELAER 280
                                    **********************************.999******.99*****************************9987 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   2.6e-37   2.3e-33       2     116 .]       6     120 ..       5     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 2.6e-37
                                    --HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHH CS
                    THF_DHG_CYH   2 ldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieel 81 
                                    ldGka+++ei  +lk +v++l + g++p+L +ilvgddp s++Yvr k+  c++vGi+s  ++lp+d+s+++l ++i+el
  gi|121639283|ref|YP_979507.1|   6 LDGKATRDEIFGDLKPRVAALDAAGRTPGLGTILVGDDPGSQAYVRGKHADCAKVGITSIRRDLPADISTATLNETIDEL 85 
                                    9**********************9******************************************************** PP

                                    HH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                    THF_DHG_CYH  82 neddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                    n++++++G +vqlPlpkh+de+a+le+++p+KD D
  gi|121639283|ref|YP_979507.1|  86 NANPDCTGYIVQLPLPKHLDENAALERVDPAKDAD 120
                                    *********************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1960.06
//
Query:       gi|121639284|ref|YP_979508.1|  [L=91]
Description: hypothetical protein BCG_3429 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-20   71.2   0.1      6e-20   70.8   0.1    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.037   14.1   0.0    1.3  1  PHD_like         Antitoxin of toxin-antitoxin, RelE / RelB, T
       0.12   12.3   0.0       0.15   12.0   0.0    1.1  1  Imm31            Immunity protein 31
       0.15   12.3   0.0       0.16   12.1   0.0    1.2  1  ArlS_N           ArlS sensor domain


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.1   1.3e-23     6e-20       3      74 ..       2      71 ..       1      72 [. 0.96

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.3e-23
                                   EEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHHHHHHHC CS
                PhdYeFM_antitox  3 ivsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslplnaerlaesgaever 74
                                   ++s+sea+++l  l+++v+++++pv It+r ++ aVl+s+++y+++qe t +ll++p+na+rl e+ a+ ++
  gi|121639284|ref|YP_979508.1|  2 SISASEARQRLFPLIEQVNTDHQPVRITSRAGD-AVLMSADDYDAWQE-TVYLLRSPENARRLMEAVARDKA 71
                                   69******************************6.**************.****************9998887 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.2e-06     0.037       4      55 ..       2      51 ..       1      84 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-06
                                   EEEHHHHHHTHHHHHHHHHHT.--EEEEETT..EEEEEEEHHHHHHHT...T CS
                       PHD_like  4 elsitearkefsalidqvvkeykpvlvkrnrkkekvsiistdllkelldrgy 55
                                    +s++ear+ +  li+qv  +++pv ++  r + +  ++s+d  + + +  y
  gi|121639284|ref|YP_979508.1|  2 SISASEARQRLFPLIEQVNTDHQPVRITS-R-AGDAVLMSADDYDAWQETVY 51
                                   5799***********************99.4.66777889998888876666 PP

>> Imm31  Immunity protein 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.15       8      57 ..      15      64 ..       9      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                          Imm31  8 vvrvlstdailaelhGerGvvlGrseddqGefeyavfiyadeniCWslee 57
                                   ++  + td ++ ++    G  + +s dd   ++ +v++ +  +   +l e
  gi|121639284|ref|YP_979508.1| 15 LIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLME 64
                                   677799******************************99987555555555 PP

>> ArlS_N  ArlS sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.16      40      77 ..      13      50 ..       2      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                         ArlS_N 40 dsllekinekdqtirildkdgkevlevsndspeikftv 77
                                    +l+e++n ++q +ri  + g+ vl +++d ++ + tv
  gi|121639284|ref|YP_979508.1| 13 FPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETV 50
                                   589************************99877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 705.46
//
Query:       gi|121639285|ref|YP_979509.1|  [L=85]
Description: hypothetical protein BCG_3430 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-39  134.3   0.1    1.2e-39  134.2   0.1    1.0  1  YoeB_toxin       YoeB-like toxin of bacterial type II toxin-a
     0.0045   17.6   0.0     0.0054   17.3   0.0    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
  ------ inclusion threshold ------
       0.14   12.6   0.0        0.2   12.1   0.0    1.2  1  HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin s


Domain annotation for each model (and alignments):
>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.1     2e-43   1.2e-39       1      80 []       6      85 .]       6      85 .] 0.99

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 2e-43
                                   E-HHHHHHHHHHHCC-HHHHHHHHHHHHHHHHSTTSSTT--EE-SGGGTTEEEEESSSSEEEEEEEESSEEEEEESSST- CS
                     YoeB_toxin  1 fteeaweDylywqeadkkilkkineLikeikRdpfeGiGkPepLkedlsglwsRRideehRlvYlveddeltilsaryHY 80
                                   f+++aweD+l+w +ad+k++++i++Li ei+Rdpf+GiGkPepL+++lsg+wsRRid+ehRlvY++ dde+t+l+aryHY
  gi|121639285|ref|YP_979509.1|  6 FDPDAWEDFLFWLAADRKTARRITRLIGEIQRDPFSGIGKPEPLQGELSGYWSRRIDDEHRLVYRAGDDEVTMLKARYHY 85
                                   899****************************************************************************9 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     9e-07    0.0054      24      78 ..      20      77 ..       5      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9e-07
                                   HHHHHHHHHHHHHHHHHHHTTTSEECTSTC...CTTEEEEEEC.TEEEEEEEETSTTEE CS
                     ParE_toxin 24 aakrfldaleealellaenpalgrprrelg...lkglrririg.dyriiYriddeelvv 78
                                   a ++   ++++ + ++ ++p +g   +e +   l+g+++ ri+  +r++Yr  ++++v+
  gi|121639285|ref|YP_979509.1| 20 ADRKTARRITRLIGEIQRDPFSGIGKPEPLqgeLSGYWSRRIDdEHRLVYRA-GDDEVT 77
                                   46677777777777777777777775555567999********99******7.455665 PP

>> HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin system HigB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.4e-05       0.2      54      87 ..      47      78 ..      41      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                HigB-like_toxin 54 ekLkgdlkglySirvNkqyrlifkfkaeeaevvd 87
                                   e L+g+l g++S r+ +++rl+++   +++ev+ 
  gi|121639285|ref|YP_979509.1| 47 EPLQGELSGYWSRRIDDEHRLVYRA--GDDEVTM 78
                                   779*******************887..6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.18s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 729.14
//
Query:       gi|121639286|ref|YP_979510.1|  [L=396]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-47  162.4   0.0    3.5e-41  141.6   0.0    2.0  2  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
    0.00021   20.5   1.3       0.14   11.2   0.0    2.9  3  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.23   10.9   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   5.8e-45   3.5e-41       2     249 ..      11     248 ..      10     260 .. 0.90
   2 !   18.8   0.0   1.3e-07   0.00076     287     337 ..     316     365 ..     299     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 5.8e-45
                                    CCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSG.GGHH CS
                   Oxidored_FMN   2 LFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwde.eqie 80 
                                    +F+P k+g+ tL+nR++ a+    r   ++  ++d ++ey +  a ++v++  +++++v+p +++  n  +iw     ++
  gi|121639286|ref|YP_979510.1|  11 VFNPAKLGPLTLRNRVIKAATFEART--PDALVTDDLIEYHRLPAAGGVAMTTVAYCAVSPGGRTGGN--QIWMRpHAVP 86 
                                    7***************9987544443..444678899************************9887555..577661569* PP

                                    HHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHHHHHHH CS
                   Oxidored_FMN  81 ewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefveAAkr 160
                                    ++r ltea+h++g+ +  q+ h+G  a  + + +q   ++ +pv + +++      +++++ t e+i ++  ++++AA++
  gi|121639286|ref|YP_979510.1|  87 GLRRLTEAIHAEGAAISAQIGHAGPVA--DARSNQA--TALAPVRFFNPIA----MRFAQKATREDIDDVLAAHAHAARL 158
                                    ************************999..7777777..8999999999966....6678899****************** PP

                                    HHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE--STTS--HHH CS
                   Oxidored_FMN 161 aieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedvvekgldfae 239
                                    a++AgfD Veih  + YL   Flsp  n+r De+gGsl+nRa+ ++ +v aV++av ++  v  +l + d +  g+++ e
  gi|121639286|ref|YP_979510.1| 159 AVDAGFDAVEIHLGHNYLASAFLSPLLNRRDDEFGGSLQNRAKVARGLVMAVRRAVRQQVaVTAKLNMTDGIRGGITVDE 238
                                    ***********************************************************99****************999 PP

                                    HHHHHHHHCH CS
                   Oxidored_FMN 240 taqkivllke 249
                                    +  ++ +l++
  gi|121639286|ref|YP_979510.1| 239 ALTTARWLQD 248
                                    9888877765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.3e-07
                                    HCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHC CS
                   Oxidored_FMN 287 vkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkk 337
                                     +     pli  g+i++ ++++ ++aeg  + vam+R++la+pdlv++++ 
  gi|121639286|ref|YP_979510.1| 316 FRAELTIPLILLGGITNRTTMDLAMAEG-FEFVAMARALLAEPDLVNRIAA 365
                                    5667788************999999886.689****************975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.011        68     129     158 ..     141     170 ..     137     174 .. 0.88
   2 !    5.3   0.8    0.0015       8.8      69     135 ..     153     228 ..     149     256 .. 0.69
   3 !   11.2   0.0   2.4e-05      0.14     179     246 ..     317     383 ..     303     393 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.011
                                    EESESSTTTC.HHHHHHHHHHCT-SEEEEE CS
                            Dus 129 irigiddeeenalelakiveaaGaqaltvH 158
                                    +r  idd    + ++a+ + +aG +a+ +H
  gi|121639286|ref|YP_979510.1| 141 TREDIDDVLAAHAHAARLAVDAGFDAVEIH 170
                                    677899999999999999999999999999 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0015
                                    HHHHHHHHHTT-SCEEEEES.........STTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESST CS
                            Dus  69 aeaAklvadlgadeIdlNvG.........CPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigidd 135
                                    a+aA+l++d g d++++ +G          P  +    ++G +L + ++++  +v av++av   v v  ++ + d
  gi|121639286|ref|YP_979510.1| 153 AHAARLAVDAGFDAVEIHLGhnylasaflSPLLNRRDDEFGGSLQNRAKVARGLVMAVRRAVRQQVAVTAKLNMTD 228
                                    6677777777777777777744444444447777788899***********************5555555554443 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 2.4e-05
                                    HHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHSC------HHHH.HHH CS
                            Dus 179 kqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktgeaepapplaee.aei 246
                                    + +++ip+i  G+I+++  ++ +++e G + v ++r+ l +P l+++  a++ ++ ++a++ +++ +++
  gi|121639286|ref|YP_979510.1| 317 RAELTIPLILLGGITNRTTMDLAMAE-GFEFVAMARALLAEPDLVNRI-AAEGSQVRSACTHCNQcMAT 383
                                    67899*********************.******************954.66666666666644443444 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.9e-05      0.23      69     118 ..     317     366 ..     309     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                                    HHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                   His_biosynth  69 aeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                    + e++ip+ + GGI +  +++ ++  g + v ++ a + +p+l++++a +
  gi|121639286|ref|YP_979510.1| 317 RAELTIPLILLGGITNRTTMDLAMAEGFEFVAMARALLAEPDLVNRIAAE 366
                                    45667777777777777777777777777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2579.02
//
Query:       gi|121639287|ref|YP_979511.1|  [L=122]
Description: hypothetical protein BCG_3432 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-10   41.0   0.1    2.8e-10   40.4   0.1    1.3  1  FHA           FHA domain
    2.8e-09   37.1   0.0    4.3e-09   36.6   0.0    1.2  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d


Domain annotation for each model (and alignments):
>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   3.1e-14   2.8e-10       1      69 []      26      89 ..      23      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.1e-14
                                   EEEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA  1 vtiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69
                                   v++G + ++d+++ +p i r H+l++fd g  ++  +D +S  G fv+gqr++    v++ +g +i++G
  gi|121639287|ref|YP_979511.1| 26 VVVGSDLRADMRVAHPLIARAHLLLRFDRG--NWIAIDNDSQSGMFVDGQRVSE---VDIYDGLTINIG 89
                                   57899999**********************..*********************8...*********998 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   4.8e-13   4.3e-09      15      82 ..      22      89 ..      13      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.8e-13
                                   TTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-SECC--TTSEEEET CS
                   Yop-YscD_cpl 15 eegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerveelelrpgdvlelG 82
                                   ++++vv+Gsd ++D+ +  + ++r+hl L+++  ++ + d +s+ g++v+g+rv+e  + +g  +++G
  gi|121639287|ref|YP_979511.1| 22 AGRDVVVGSDLRADMRVAHPLIARAHLLLRFDRGNWIAIDNDSQSGMFVDGQRVSEVDIYDGLTINIG 89
                                   6789***************************************************9999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 865.10
//
Query:       gi|121639288|ref|YP_979512.1|  [L=183]
Description: hypothetical protein BCG_3433c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-22   78.0  29.8    7.4e-09   35.1   0.4    4.5  6  Pentapeptide    Pentapeptide repeats (8 copies)
    3.9e-20   71.8   0.1    6.9e-11   42.2   0.4    3.1  3  Pentapeptide_4  Pentapeptide repeats (9 copies)
    9.5e-14   51.3  11.3    8.1e-06   25.9   4.3    4.4  5  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.13   12.2   4.6       0.25   11.4   0.3    3.1  3  Zap1_zf2        Zap1 zinc finger 2


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   4.3e-06     0.019       5      38 ..       6      39 ..       5      40 .. 0.95
   2 !   21.1   0.6   3.9e-08   0.00017       1      38 [.      32      69 ..      32      71 .. 0.96
   3 !   10.8   0.2   6.4e-05      0.29       3      33 ..      49      79 ..      45      80 .. 0.65
   4 !   16.4   0.6   1.2e-06    0.0052       6      39 ..      77     110 ..      72     110 .. 0.84
   5 !   30.6   0.5   4.1e-11   1.8e-07       2      40 .]      88     126 ..      88     126 .. 0.97
   6 !   35.1   0.4   1.7e-12   7.4e-09       2      36 ..     113     147 ..     112     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-06
                                   T-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide  5 gAnLsganLsganlsgAnLtgAnlsgAdLsganL 38
                                   ++ ++g ++++ +ls+    +A +s +d+sg+nL
  gi|121639288|ref|YP_979512.1|  6 DCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNL 39
                                   799*****************************98 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.9e-08
                                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide  1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38
                                   +++sg+nL ++  +g+ ++++++ +++l ++ + ++ +
  gi|121639288|ref|YP_979512.1| 32 CDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSM 69
                                   9******************************9999975 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 6.4e-05
                                   -TT-B-CCSCCEECCCESEEECT-B-TT-EE CS
                   Pentapeptide  3 LsgAnLsganLsganlsgAnLtgAnlsgAdL 33
                                   ++++ ++ + L ++ + ++++ g+ +  ++L
  gi|121639288|ref|YP_979512.1| 49 FRNCTFERTTLWHSTFAQCSMLGSVFVACRL 79
                                   5677777777777777777776666666665 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1.2e-06
                                    -B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                    ++L+   L++++++ A+L g +l+g +L+g++L+
  gi|121639288|ref|YP_979512.1|  77 CRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLR 110
                                    5566667999*********************997 PP

  == domain 5  score: 30.6 bits;  conditional E-value: 4.1e-11
                                    B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    +++ A L g +L+g nl+g+ L++++l ++dL+ + L+g
  gi|121639288|ref|YP_979512.1|  88 DFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRG 126
                                    68899********************************98 PP

  == domain 6  score: 35.1 bits;  conditional E-value: 1.7e-12
                                    B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCE CS
                   Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsga 36 
                                    +L +++L+ + L+ga+lsgA  tgA l +AdL+ga
  gi|121639288|ref|YP_979512.1| 113 SLVDTDLRKCVLRGADLSGARTTGARLDDADLRGA 147
                                    699*******************************9 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.2e-06    0.0098      35      71 ..       6      43 ..       2      49 .. 0.75
   2 !   42.2   0.4   1.5e-14   6.9e-11       2      75 ..      48     122 ..      47     122 .. 0.96
   3 !   22.2   0.0   2.7e-08   0.00012       3      60 ..     104     161 ..     103     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                 Pentapeptide_4 35 nvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.k 71
                                   +++F+  +++d d++  +  ra Fs+c++++vn+ + +
  gi|121639288|ref|YP_979512.1|  6 DCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAEsQ 43
                                   67888888888888888888888888888888884424 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 1.5e-14
                 Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkdi 75 
                                     f++c+f++++l   +F+++ + ++ F++crl   ++d+ ++  + + ++dl+ ++++gc+l+++ + ++ l+++
  gi|121639288|ref|YP_979512.1|  48 AFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLvDTDLRKC 122
                                    69*****************************************************************77789876 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 2.7e-08
                 Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsg 60 
                                    +t c ++++ l +++++++ lr+++++++r + +++d+++l+ + + +v +++as+ g
  gi|121639288|ref|YP_979512.1| 104 LTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVG 161
                                    5678888888888888888888888888888888888888888888888888887766 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.5   1.1e-05     0.049      14      47 ..       6      37 ..       5      43 .. 0.84
   2 !   25.9   4.3   1.8e-09   8.1e-06       1      46 [.      29      71 ..      29      81 .. 0.95
   3 !    7.8   0.1   0.00081       3.6      11      39 ..      63      90 ..      61     101 .. 0.89
   4 !   21.1   0.0   5.9e-08   0.00026       2      48 .]     105     148 ..      84     148 .. 0.91
   5 ?   -3.2   0.0       2.2     1e+04      30      38 ..     156     164 ..     153     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                 Pentapeptide_3 14 gatFsgaasFsnadFgsadFsgarFtgdvdFsga 47
                                   ++ F+g  +F++ d+++ + ++a F+ ++dFsg+
  gi|121639288|ref|YP_979512.1|  6 DCEFTGR-DFRDEDLSRLHTERAMFS-ECDFSGV 37
                                   7******.*******88888888888.8888876 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.8e-09
                 Pentapeptide_3  1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46
                                   Fs++ Fsg  ++ ++  +g+a F+n++F++ ++ +++F   +++ g
  gi|121639288|ref|YP_979512.1| 29 FSECDFSGV-NLAESQHRGSA-FRNCTFERTTLWHSTFA-QCSMLG 71
                                   9********.**********8.****************9.998766 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00081
                 Pentapeptide_3 11 dFrgatFsgaasFsnadFgsadFsgarFt 39
                                   +F  +   g++ F  ++++  +++++ Ft
  gi|121639288|ref|YP_979512.1| 63 TFAQCSMLGSV-FVACRLRPLTLDDVDFT 90
                                   79999999996.******99999999998 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 5.9e-08
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                                    +g++++ + ++ ++  ++++  ++ad+++a+  gar + d+d++gat
  gi|121639288|ref|YP_979512.1| 105 TGCRLRET-SLVDTDLRKCV-LRGADLSGARTTGARLD-DADLRGAT 148
                                    78999999.99999999996.99999999999999999.99999986 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 2.2
                 Pentapeptide_3  30 sadFsgarF 38 
                                    +a++ gar 
  gi|121639288|ref|YP_979512.1| 156 TASLVGARV 164
                                    677777775 PP

>> Zap1_zf2  Zap1 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.5e-05      0.25       2      12 ..       3      13 ..       3      15 .. 0.92
   2 ?    0.8   0.1      0.12   5.2e+02       5      10 ..      31      36 ..      30      39 .. 0.85
   3 ?   -2.1   0.1      0.92   4.1e+03       5       9 ..      51      55 ..      50      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                       Zap1_zf2  2 nWkDCdFegeD 12
                                   +W DC+F g D
  gi|121639288|ref|YP_979512.1|  3 QWVDCEFTGRD 13
                                   7********99 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                       Zap1_zf2  5 DCdFeg 10
                                   +CdF g
  gi|121639288|ref|YP_979512.1| 31 ECDFSG 36
                                   8***88 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.92
                       Zap1_zf2  5 DCdFe 9 
                                   +C Fe
  gi|121639288|ref|YP_979512.1| 51 NCTFE 55
                                   8*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1266.09
//
Query:       gi|121639289|ref|YP_979513.1|  [L=193]
Description: ATP/GTP-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-29  103.8   0.2    4.3e-28   98.7   0.2    2.5  1  ATP_bind_1  Conserved hypothetical ATP binding protein
    8.1e-05   22.2   0.0     0.0001   21.9   0.0    1.1  1  GTP_EFTU    Elongation factor Tu GTP binding domain
     0.0048   16.0   0.4     0.0072   15.4   0.4    1.2  1  T2SSE       Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.02   14.6   0.3      0.036   13.8   0.3    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.029   14.1   0.1       0.04   13.6   0.1    1.2  1  AAA_24      AAA domain
      0.043   13.4   0.1       0.25   10.9   0.1    1.9  1  Ras         Ras family
      0.097   12.7   0.1       0.14   12.1   0.1    1.4  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
       0.13   12.5   0.1        0.2   11.9   0.1    1.4  1  AAA_28      AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.2   1.9e-31   4.3e-28       1     239 [.      18     185 ..      18     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.9e-31
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmed..lglgpngalvvaleflres 78 
                                    ++G++GsGKttfvga+sei++lr                       ++ ++t +++ +d    + ++++++va++f+r++
  gi|121639289|ref|YP_979513.1|  18 IAGGFGSGKTTFVGAVSEIMPLR-----------------------TEAMVTDASAGVDmlEATPDKRSTTVAMDFGRIT 74 
                                    79*********************.......................*************9889999************** PP

                     ATP_bind_1  79 ldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltd...ptkfisgllsalsamlrl 155
                                    l    e+l      ++lf+tPGQ ++++++++l+        ++a+++++LvD++rl+d   +++f+++           
  gi|121639289|ref|YP_979513.1|  75 L---GEDL-----VLYLFGTPGQRRFWFMWDDLV--------RGAIGAIVLVDCRRLQDsfaAVDFFEH----------R 128
                                    9...9***.....*********************........*****************9*99******..........* PP

                     ATP_bind_1 156 elPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllsli 235
                                    +lP+++++n+fD  +                          +++  +a++++l+++a+++++ ++++++++++++l+++ 
  gi|121639289|ref|YP_979513.1| 129 NLPFLIAINEFDS-A--------------------------PRYPVSAVRDALTLPAHIPVINVDARNRRSATDALIAVS 181
                                    *************.4..........................689999999999999999999999999999999999998 PP

                     ATP_bind_1 236 deal 239
                                    ++al
  gi|121639289|ref|YP_979513.1| 182 EYAL 185
                                    8876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.6e-08    0.0001       5     135 ..      15     142 ..      12     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.6e-08
                                    EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG CS
                       GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgeka...eeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv 81 
                                    +i+i+g   +GKtT+++++ +     ++ ++++    +  +l  +++ r   + ++   i+l    ++  + l  tPG +
  gi|121639289|ref|YP_979513.1|  15 KIVIAGGFGSGKTTFVGAVSEIMPLRTE-AMVTdasAGVDMLEATPDKRSTTVAMDFGRITLG---EDLVLYLFGTPGQR 90 
                                    689****************988777776.4455132224456666667777777777777776...99************ PP

                                    GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST CS
                       GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl 135
                                     F       +r + ga+++vd++    + +   +     +++p+ ++iN  D +
  gi|121639289|ref|YP_979513.1|  91 RFWFMWDDLVRGAIGAIVLVDCR--RLQDSFAAVDFFEHRNLPFLIAINEFDSA 142
                                    **********************9..56677788888999999999999999977 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   3.2e-06    0.0072     129     162 ..      13      46 ..       6      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
                          T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivt 162
                                       i+++Gg gsGKtt++ a+ ++++ ++e +vt
  gi|121639289|ref|YP_979513.1|  13 STKIVIAGGFGSGKTTFVGAVSEIMPLRTEAMVT 46 
                                    5689*******************99999888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.6e-05     0.036      24      46 ..      15      37 ..       4      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                         AAA_29 24 atlltGpsGsGKSTllDAiqalL 46
                                    ++++G  GsGK+T++ A++ ++
  gi|121639289|ref|YP_979513.1| 15 KIVIAGGFGSGKTTFVGAVSEIM 37
                                   5789***************9988 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.8e-05      0.04       2      39 ..      13      56 ..      12      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                         AAA_24  2 klkiliyGpsgiGKTtlakel......gpkplfidtekGlksld 39
                                   + ki+i G  g+GKTt++           ++ + d  +G++ l+
  gi|121639289|ref|YP_979513.1| 13 STKIVIAGGFGSGKTTFVGAVseimplRTEAMVTDASAGVDMLE 56
                                   579**************998854555444555555555555554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00011      0.25      36      91 ..      61     123 ..      15     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                    EEEEEEEET......TEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTB.HHHHHTHH CS
                            Ras  36 fytkeievd......gkevkleiwDTAGqeefkslrelyyrdaegillvydits.resfenvk 91 
                                    + ++++ +d      g+++ l ++ T Gq +f  + +  +r+a g++++ d  + ++sf  v+
  gi|121639289|ref|YP_979513.1|  61 KRSTTVAMDfgritlGEDLVLYLFGTPGQRRFWFMWDDLVRGAIGAIVLVDCRRlQDSFAAVD 123
                                    34444444466666789999*****************************99986467888775 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.4e-05      0.14      19      43 ..      13      37 ..       2      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                   TEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglakal 43
                                   ++ i++ G  G+GKTt+v ++ + +
  gi|121639289|ref|YP_979513.1| 13 STKIVIAGGFGSGKTTFVGAVSEIM 37
                                   45599*************9887766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     9e-05       0.2       1      22 [.      15      36 ..      15      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-05
                         AAA_28  1 kivitGgestGKTtlleaLaar 22
                                   kivi Gg ++GKTt + a ++ 
  gi|121639289|ref|YP_979513.1| 15 KIVIAGGFGSGKTTFVGAVSEI 36
                                   79*************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1544.60
//
Query:       gi|121639290|ref|YP_979514.1|  [L=122]
Description: hypothetical protein BCG_3435c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-35  120.6   0.3    3.1e-35  120.4   0.3    1.0  1  DUF742    Protein of unknown function (DUF742)
      0.007   16.1   0.0      0.012   15.4   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.041   13.8   0.5      0.069   13.0   0.2    1.6  2  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.3   5.2e-39   3.1e-35       3     114 .]      10     122 .]       8     122 .] 0.97

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 5.2e-39
                         DUF742   3 kgalvRpyaltgGrtrpeedldletlvvaeagape.aarlqpehrailrLcreplsVaelaAelklPvgvvrvLlsdLld 81 
                                    k+ lvRpy+lt+Grt ++ dl l++ v++ ++ p     +++++r+il+Lc  + sVae++A+l+lPvgv+rvL++dL++
  gi|121639290|ref|YP_979514.1|  10 KAGLVRPYTLTAGRTGTDVDLPLQAPVQTLPAGPAgRWPAYDMRRRILQLCIGSPSVAEISARLDLPVGVARVLVGDLVT 89 
                                    6789******************************768899**************************************** PP

                         DUF742  82 aglltvrapvtdraaeqpdrelLeevlsGLrrl 114
                                    +g+l+v+a+ tdr+++++++el+ ++l+GL++l
  gi|121639290|ref|YP_979514.1|  90 SGYLRVHATLTDRSTRDERHELIGRTLRGLKAL 122
                                    ******************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-06     0.012      19      49 ..      64      94 ..      55      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                                   -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                    +++e+++r++lp   ++ l+  Lv  Gy++
  gi|121639290|ref|YP_979514.1| 64 PSVAEISARLDLPVGVARVLVGDLVTSGYLR 94
                                   489***************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   6.9e+03      47      53 ..      10      16 ..      10      23 .. 0.67
   2 ?   13.0   0.2   1.2e-05     0.069      16      60 ..      62     102 ..      50     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                   HTTSEEE CS
                         MarR_2 47 aaGLver 53
                                   +aGLv+ 
  gi|121639290|ref|YP_979514.1| 10 KAGLVRP 16
                                   5899875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.2e-05
                                    CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                         MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60 
                                     +p    +v+e+ +rl+l+ + +  ++ +Lv  G+++  + ++D+
  gi|121639290|ref|YP_979514.1|  62 GSP----SVAEISARLDLPVGVARVLVGDLVTSGYLRVHATLTDR 102
                                    444....9****************************988777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 982.95
//
Query:       gi|121639291|ref|YP_979515.1|  [L=130]
Description: hypothetical protein BCG_3436c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-22   78.8   0.9    2.6e-22   78.4   0.9    1.2  1  Robl_LC7  Roadblock/LC7 domain


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.9   1.5e-26   2.6e-22       1      90 [.      10     100 ..      10     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.5e-26
                                    HHHHHHHHCCHHCTECEEEEEETTS-EEEE.CCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEE CS
                       Robl_LC7   1 lveelleelqsvpgvrgalvvskdGlviat.stldnddadqlAalasgllsaakaaarelgegelkelliegkkgelylt 79 
                                    l++++ +    v gv +al+vs dGl++a+ ++l++++adqlAa++sgl+s+a +aa+ +++g++ ++++e+++g+l+l+
  gi|121639291|ref|YP_979515.1|  10 LDWLVSKFAREVLGVAHALLVSVDGLPVAAsEHLPRERADQLAAVTSGLASLAGGAAQLFDGGQVLQSVVEMQNGYLLLM 89 
                                    5899**************************************************************************** PP

                                    ECTTTEEEEEE CS
                       Robl_LC7  80 pagegalLvvl 90 
                                    ++g+g+ L+ l
  gi|121639291|ref|YP_979515.1|  90 QVGDGSALAAL 100
                                    *******9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 987.03
//
Query:       gi|121639292|ref|YP_979516.1|  [L=876]
Description: hypothetical protein BCG_3437c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-08   35.5   0.0    2.6e-08   34.4   0.0    1.6  1  HATPase_c   Histidine kinase-, DNA gyrase B-, and HSP90-like 
    1.1e-05   25.7   0.2    5.9e-05   23.4   0.2    2.3  1  HAMP        HAMP domain
  ------ inclusion threshold ------
      0.051   14.1   0.0        0.2   12.2   0.0    2.0  1  ATPgrasp_N  ATP-grasp N-terminal domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   4.3e-12   2.6e-08       5     111 ..     523     633 ..     520     634 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.3e-12
                                    HHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHH CS
                      HATPase_c   5 rLrqiisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkk 83 
                                    ++ +++ +l+dNa++++++++ ++v     se+ + ++++D+G G++ +d+ +  +++   +++ +  + +++Gl +v +
  gi|121639292|ref|YP_979516.1| 523 GVIHLLAELIDNALRYSSPTTPVRVAAAIgSEGSVLLRISDSGLGMTDADRRMANMRLRA-GGEVTPDSARHMGLFVVGR 601
                                    6789************77888887777766669*******************66667776.888888899999******* PP

                                    HHHHTTTEEEE....EEETTTEEEEEEEEESS CS
                      HATPase_c  84 lvelmgGeiwv....esepgrGttftftlple 111
                                    l+ ++g ++ +    + e+g Gtt  ++lpl+
  gi|121639292|ref|YP_979516.1| 602 LAGRHGIRVGLrgpvTGEQGTGTTAEVYLPLA 633
                                    **99**766668887777799********985 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   9.9e-09   5.9e-05       1      50 [.     338     401 ..     338     403 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.9e-09
                                    HHHHTTHHHHHHHHHHHHHHTTTBTSST..............CCTTSSSHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaaGdldtr..............lpvsgrDEiGeLarafNaMldr 50 
                                    ++ar+++ P+r L++ a ++a+ dld                l v++  EiG++a+a++++++r
  gi|121639292|ref|YP_979516.1| 338 VVARTLVGPMRVLRDGALKVAHTDLDGEiaavragdepipepLAVYTTEEIGQVAHAVDELHTR 401
                                    68*******************998888888888888888888******************9998 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.3e-05       0.2      29      76 ..     175     222 ..     158     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                                    EEEEEEE-TTT-HHHHHHHHHHHHHHS--SEEE---GGGHHHHHHHHH CS
                     ATPgrasp_N  29 vekfipldlaqdpdaaleavralsrerpvdGivtftdlavplvArlae 76 
                                     +++i  ++  d++++ + v+ lsr+ + +G +t+++++v   A+lae
  gi|121639292|ref|YP_979516.1| 175 AQNVIDASVRVDSEQIRTQVQGLSRAVGARGQMTMQEILVTRGADLAE 222
                                    4899999***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5677.57
//
Query:       gi|121639293|ref|YP_979517.1|  [L=154]
Description: tRNA/rRNA methylase spoU [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-30  103.9   0.0    8.7e-30  103.7   0.0    1.0  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   4.9e-34   8.7e-30       2     142 .]       2     142 ..       1     142 [. 0.95

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 4.9e-34
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvat 81 
                                    +++++v ++++ N+G+++Rt++a+g+ el+lv+p ++dl +p+++ra+++++++  ++v++sl++a ++l  +  +++a+
  gi|121639293|ref|YP_979517.1|   2 FRLLFVSPRIAPNTGNAIRTCAATGC-ELHLVEPLGFDLSEPKLRRAGLDYHDLASVTVHASLAHAWEALSPA--RVFAF 78 
                                    68999*********************.********************************************99..***** PP

                                    STT-SEGC.CSHHHTTEEEEEEBTTTBS-HHHHCTSS..EEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  82 slkgksls.eidlkekvalvfGnEdkGlsnellelad..rlvkIpmsgeveSLNvavAvailly 142
                                    ++++++l  ++ ++   +l+fG+E +Gl++ +l+  +    v+Ipm    +SLN+++A+a+++y
  gi|121639293|ref|YP_979517.1|  79 TAQATTLFtNVGYRAGDVLMFGPEPTGLDEATLADTHitGQVRIPMLAGRRSLNLSNAAAVAVY 142
                                    **888777699**********************88885579********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1260.71
//
Query:       gi|121639294|ref|YP_979518.1|  [L=591]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-33  113.5  21.2      7e-33  112.8  21.2    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8  21.2   3.9e-37     7e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 3.9e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv++Pealaaaa+d+a+igsalsaanaaaaa tt++laa+aDeVSaa A+lfs ha +yq+++aqa+a h+qfvqal++
  gi|121639294|ref|YP_979518.1|  1 MSFVVAVPEALAAAASDVANIGSALSAANAAAAAGTTGLLAAGADEVSAALASLFSGHAVSYQQVAAQATALHDQFVQALTG 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   a+gsYa +Eaa
  gi|121639294|ref|YP_979518.1| 83 AGGSYALTEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.26s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 3859.51
//
Query:       gi|121639295|ref|YP_979519.1|  [L=214]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-23   82.4   0.0      5e-23   82.0   0.0    1.2  1  Nitroreductase  Nitroreductase family
    0.00095   18.8   0.0        0.2   11.2   0.0    2.2  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   5.5e-27     5e-23       4     168 ..      14     189 ..      11     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 5.5e-27
                                    --B--.-B-S--.--HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-.SS-GGGGGG... CS
                 Nitroreductase   4 RrSiR.kFddep.vpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqa.elaqryrke... 77 
                                     rS+R  +d ++ vp+++l ++le a +aP+++n+q w+ v v+d ++++++a+  l++++        + ++       
  gi|121639295|ref|YP_979519.1|  14 TRSVRkRLDFDKpVPRDVLMECLELALQAPTGSNSQGWQWVFVEDAAKKKAIADVYLANARGYLSGPaPEYPD---Gdtr 90 
                                    6999989997777******************************999999777766555555443333033333...1334 PP

                                    ........HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH. CS
                 Nitroreductase  78 ........elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae. 148
                                            ++  + ++++++apvl++    + k ++++++ +    ++++  a++ + La++++Glgsc+++    +++ 
  gi|121639295|ref|YP_979519.1|  91 germgrvrDSATYLAEHMHRAPVLLIP---CLKGREDESAVGGVSFWASLFPAVWSFCLALRSRGLGSCWTTLHLLDNGe 167
                                    77889999*******************...*******************************************9966666 PP

                                    .HHHHHHT-S...SEEEEEEEE CS
                 Nitroreductase 149 .evrkllglp.deeeivvliav 168
                                     +v+++lg+p de++  +l+++
  gi|121639295|ref|YP_979519.1| 168 hKVADVLGIPyDEYSQGGLLPI 189
                                    69********877777777776 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   2.3e-05       0.2     157     186 ..      29      58 ..      10      74 .. 0.78
   2 !    5.8   0.0   0.00099       8.8      91     107 ..     144     160 ..     141     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                                    -HHHHHHHHHHHTS--GGG----EEE.E-S CS
                 TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkdd 186
                                    ++ ++e le+a+ AP+  N+q w+  +++d
  gi|121639295|ref|YP_979519.1|  29 RDVLMECLELALQAPTGSNSQGWQWVFVED 58 
                                    456799***************999887775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00099
                                    HHHHHHHTT-EEEEES- CS
                 TM1586_NiRdase  91 lvLkltalGlgtcWvgg 107
                                    + L l ++Glg+cW  +
  gi|121639295|ref|YP_979519.1| 144 FCLALRSRGLGSCWTTL 160
                                    579999********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1551.88
//
Query:       gi|121639296|ref|YP_979520.1|  [L=144]
Description: hypothetical protein BCG_3441 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-12   46.0   0.0    6.2e-12   45.5   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   3.4e-16   6.2e-12       1      85 [.      13      96 ..      13      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.4e-16
                                   HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEE.EEEEEE CS
                 Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgv.rieGta 81
                                   l++e+ + l +  +++l+Tv ++G+P  ++v++ ++  +  +++++  +++k++++ ++p+v+l +++d++g g+  + Gta
  gi|121639296|ref|YP_979520.1| 13 LTQEVSARLTSDLYGWLTTVARSGQPVPRLVWFYFDGTD--LTVYSMPQAAKVAHITAHPQVSLNLDSDGNGAGIiVVGGTA 92
                                   5778888899999*********************77777..*****************************665550557777 PP

                                   EEES CS
                 Putative_PNPOx 82 elvs 85
                                   ++v 
  gi|121639296|ref|YP_979520.1| 93 AVVA 96
                                   7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 933.55
//
Query:       gi|121639297|ref|YP_979521.1|  [L=1079]
Description: error-prone DNA polymerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-78  262.6   0.0    8.3e-78  261.5   0.0    1.6  1  DNA_pol3_alpha   Bacterial DNA polymerase III alpha NTPase do
    1.1e-55  187.4   0.0    1.9e-55  186.7   0.0    1.4  1  DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit f
    2.2e-30  106.2   0.0    3.7e-30  105.4   0.0    1.4  1  PHP              PHP domain
    2.9e-26   91.5   0.0    2.4e-25   88.6   0.0    2.5  3  HHH_6            Helix-hairpin-helix motif
      3e-05   23.9   0.0    7.5e-05   22.6   0.0    1.7  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00011   22.3   0.0    0.00032   20.9   0.0    1.7  1  HHH_3            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.058   13.7   0.0       0.18   12.1   0.0    1.9  1  HTH_Tnp_1        Transposase
       0.18   12.5   1.6         12    6.7   0.0    3.8  3  SnoaL_2          SnoaL-like domain


Domain annotation for each model (and alignments):
>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   3.7e-81   8.3e-78       2     260 .]     338     582 ..     337     582 .. 0.95

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 3.7e-81
                                    HHHHHHHHHHHHHS.TT---TTHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHTT--B-S--GGGGG-HHHHHTTS-- CS
                 DNA_pol3_alpha   2 yLrklveeglkerl.keelpeevkerlekElevIekmgfadyflivadlvkaakkkgilvGpgRGSaagslvayllgiTe 80 
                                    +Lr+lv+ g++er+ + +   +  +++e+El+vI++++f++yfl+v+d+++++++++il+ +gRGSaa+s v+y+lg+T 
  gi|121639297|ref|YP_979521.1| 338 WLRSLVMAGARERYgPPKSAPRAYSQIEHELKVIAQLRFPGYFLVVHDITRFCRDNDILC-QGRGSAANSAVCYALGVTA 416
                                    89************54447778999***********************************.******************* PP

                                    --HHHHT--HHHHS-TTS-------EEEEGGGHHHHHHHHHHHH-TTTEEEEEEEEE--HHHHHHHHHHHH-GGHHHHHH CS
                 DNA_pol3_alpha  81 idPlkydllFerFlnpervsmPDiDidfekerreevidyvkekyGkenvaqiitfgtlaakaairdvgralglplkevdk 160
                                    +dP+ ++llFerFl+p r+ +PDiDid+e+++re+vi+yv++kyG++++aq++++ t++ ++a+rd++ralg++  + d+
  gi|121639297|ref|YP_979521.1| 417 VDPVANELLFERFLSPARDGPPDIDIDIESDQREKVIQYVYHKYGRDYAAQVANVITYRGRSAVRDMARALGFSPGQQDA 496
                                    ******************************************************************************** PP

                                    HHHTS---SS--GGGG-----SHHHHHHH-HHHHHHHHHHHTTTT-EEEEEEEEEEEEE-SS-GGGTS-EEE-TTT--EE CS
                 DNA_pol3_alpha 161 laklipkelgitlekaleeekelkelieedeevkrlvelakkleglkrntgqHaaGvvispkeltdlvPlqkaekeeevv 240
                                    ++k++++++g              + ++ d   +++++la++++ l+r++g+H +G+vi+++++ d++P++ a++ +++v
  gi|121639297|ref|YP_979521.1| 497 WSKQVSHWTG--------------QADDVDGIPEQVIDLATQIRSLPRHLGIHSGGMVICDRPIADVCPVEWARMANRSV 562
                                    *****99977..............223445566899******************************************** PP

                                    ESS-HHHHHTTT-EEEEEEE CS
                 DNA_pol3_alpha 241 tqfdmedledlgllKlDfLG 260
                                     q+d++d+ ++gl+K+D+LG
  gi|121639297|ref|YP_979521.1| 563 LQWDKDDCAAIGLVKFDLLG 582
                                    *******************9 PP

>> DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.7   0.0   8.5e-59   1.9e-55       1     164 [.     585     749 ..     585     751 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 8.5e-59
                                    HHHHHHHHHHHHHHHH-----GGG--S--HHHHHHHHHT--TTSTT--SHHHHHHHHHH---SHHHHHHHHHHSSHHHHH CS
                DNA_pol3_finger   1 tltiirralklikekkgkeidleeipleDkkvykllskgdtlGvfqlesrgmrqllkrlkPktfeDlvalvaLyRpgpvq 80 
                                    +l++++ a +l+ e+kg+e+dl++++l++++vy++l+++d++Gvfq+esr+++ +l+rlkP+ f+Dlv+ vaL+Rpgp+q
  gi|121639297|ref|YP_979521.1| 585 MLSALHYAKDLVAEHKGIEVDLARLDLSEPAVYEMLARADSVGVFQVESRAQMATLPRLKPRVFYDLVVEVALIRPGPIQ 664
                                    799***************************************************************************** PP

                                    TTHHHHHHHHHTTSS----SSHHHTTTTTTTTT---BHHHHHHHHHHHH---HHHHHHHHHHHHH.--HHHHHHHHHHHH CS
                DNA_pol3_finger  81 ggnvddyikrkngeekveyihpeleeiLketygvivyQEqvmqiaqvlagfslgeAdllrramgk.kkeeeleklkekfi 159
                                    gg v++yi+r+ng ++v y hp++++ L++t gv+++QEq mq+a ++agfs++eAd+lrramg  + +e +++l+ +f 
  gi|121639297|ref|YP_979521.1| 665 GGSVHPYIRRRNGVDPVIYEHPSMAPALRKTLGVPLFQEQLMQLAVDCAGFSAAEADQLRRAMGSkRSTERMRRLRGRFY 744
                                    ****************************************************************98899*********** PP

                                    HHHHH CS
                DNA_pol3_finger 160 egake 164
                                    +g+++
  gi|121639297|ref|YP_979521.1| 745 DGMRA 749
                                    **985 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   1.7e-33   3.7e-30       1     167 []      48     219 ..      48     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.7e-33
                                    EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
                            PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse....ker 76 
                                    +lH+H+ ys+ldga ++eelv++a++lgl a+a+TDh++l+g+v+f++aa    + +++ ++G+e+++    +    +  
  gi|121639297|ref|YP_979521.1|  48 ELHAHSAYSFLDGASTPEELVEEAARLGLCALALTDHDGLYGAVRFAEAA---AELDVRTVFGAELSLGATARterpDPP 124
                                    79************************************************...6667*********99999884444555 PP

                                    .......E....EHHHHHHHHHHHHH...........HHHHHH....S..................TTGGHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  77 pshltllaknqeGyknllkllskaylegf.yrkpridkellek....hsegLivlsgclkGevfealdlieveekaeeal 151
                                      hl++la+  eGy++l ++l +a+l g  ++kpr d + l +    h   + +l+gc+kG+v +al ++  ++ a++al
  gi|121639297|ref|YP_979521.1| 125 GPHLLVLARGPEGYRRLSRQLAAAHLAGGeKGKPRYDFDALTEaaggH---WHILTGCRKGHVRQALSQGGPAA-AQRAL 200
                                    67************************9999***********9987764...77*********************.***** PP

                                    HHHHHC....T-EEEEEGC CS
                                    xxxxxxx...xxxxxxxxx RF
                            PHP 152 eelakif...gdyiEints 167
                                      l ++f   ++ iE+ ++
  gi|121639297|ref|YP_979521.1| 201 ADLVDRFtpsRVSIELTHH 219
                                    ***************9876 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.1   1.1e+04      67      89 ..     613     636 ..     605     637 .. 0.67
   2 ?   -1.5   0.0       1.3     3e+03      27      47 ..     745     765 ..     729     771 .. 0.80
   3 !   88.6   0.0     1e-28   2.4e-25       1      90 []     825     913 ..     825     913 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.1
                          HHH_6  67 nkrqleaLakaGaldslgl.nRrq 89 
                                    + ++ e La+a+    ++  +R+q
  gi|121639297|ref|YP_979521.1| 613 EPAVYEMLARADSVGVFQVeSRAQ 636
                                    456789999999988885536665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                          HHH_6  27 lGLaaikglgeaaaerivaeR 47 
                                     G++a++g  +++++ri ++ 
  gi|121639297|ref|YP_979521.1| 745 DGMRALHGAPDEVIDRIYEKL 765
                                    599**************9964 PP

  == domain 3  score: 88.6 bits;  conditional E-value: 1e-28
                          HHH_6   1 gvevlppdvnrSeadftveeedgairlGLaaikglgeaaaerivaeRekegpfksledlarrvdslnkrqleaLakaGal 80 
                                    gv v+ p+vn+S a++t e++++++rlGL+a++ lg++ ae++vaeR+++gpf+sl dl++rv+ l++ q+eaLa+aGal
  gi|121639297|ref|YP_979521.1| 825 GVAVHGPCVNASLAHATCENAGTEVRLGLGAVRYLGAELAEKLVAERTANGPFTSLPDLTSRVQ-LSVPQVEALATAGAL 903
                                    899****************77777****************************************.*************** PP

                          HHH_6  81 dslglnRrql 90 
                                     ++g +Rr++
  gi|121639297|ref|YP_979521.1| 904 GCFGMSRREA 913
                                    ********86 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.6   1.2e+04      23      36 ..     880     893 ..     877     899 .. 0.72
   2 !   22.6   0.0   3.4e-08   7.5e-05       1      72 [.     992    1063 ..     992    1067 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.6
                                    EEETTEEEEEEEET CS
                tRNA_anti-codon  23 lrDgtgriqvvlfr 36 
                                    l D t r+q+++  
  gi|121639297|ref|YP_979521.1| 880 LPDLTSRVQLSVPQ 893
                                    66889999998765 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.4e-08
                                     EEEEEEEEEEE.EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                tRNA_anti-codon    1 VtvaGrvtsis.drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72  
                                     V +aG vt ++ +   ++v fi l+D+tg+++v ++++   +  +       + ++G+v+   g  +++++e+
  gi|121639297|ref|YP_979521.1|  992 VLIAGAVTHRQrPATAQGVTFINLEDETGMVNVLCTPGVWARHRKLAHTAPALLIRGQVQNASGA-ITVVAER 1063
                                     6799*******99999*********************7777777777799999999****99999.9999886 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00032      18      54 ..     855     891 ..     852     899 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                          HHH_3  18 klpGlgpklAknIvayReknGpfksreeLlkvkglgp 54 
                                     +  lg+ lA+++va R++nGpf+s+ +L++   l+ 
  gi|121639297|ref|YP_979521.1| 855 AVRYLGAELAEKLVAERTANGPFTSLPDLTSRVQLSV 891
                                    6889*************************98666665 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.2e-05      0.18      22      72 ..     476     530 ..     465     533 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                      HTH_Tnp_1  22 pgksvsevArrhgvspnqLykWrrqyregeeaspae....feltaleeenrelkr 72 
                                    +   v++ Ar +g+sp q  +W +q++   +++++      ++ +l+ ++r l r
  gi|121639297|ref|YP_979521.1| 476 GRSAVRDMARALGFSPGQQDAWSKQVSHWTGQADDVdgipEQVIDLATQIRSLPR 530
                                    556799********************94444444444567889999999998876 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.53   1.2e+03      29      74 ..     123     181 ..      92     211 .. 0.62
   2 ?    1.0   0.1      0.29   6.5e+02      29      48 ..     469     489 ..     454     511 .. 0.70
   3 ?    6.7   0.0    0.0052        12      53      86 ..     978    1012 ..     963    1026 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.53
                                    TTSE.....EESHHHHHHHHHHHHH........HEEEEEEEEEEEEEETTEEEEEEEEE CS
                        SnoaL_2  29 pgge.....lrGreairaffralfa........afpdlrfeihdvvadgdrvavewtvt 74 
                                    p+g+      rG+e++r+  r+l a        ++p+++f+    +a g++ ++ +  +
  gi|121639297|ref|YP_979521.1| 123 PPGPhllvlARGPEGYRRLSRQLAAahlaggekGKPRYDFDALTEAAGGHWHILTGCRK 181
                                    44556777788999888855554443334453355555555555577777666664444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.29
                                    T.TSEEESHHHHHHHHHHHHH CS
                        SnoaL_2  29 p.ggelrGreairaffralfa 48 
                                    + + ++rGr a+r++ ral  
  gi|121639297|ref|YP_979521.1| 469 AnVITYRGRSAVRDMARALGF 489
                                    334459*********999864 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0052
                                     EEEEEEEEEEETTEEEEEEEEEEE.EETTSSEEEE CS
                        SnoaL_2   53 lrfeihdvvadgdrvavewtvtgt.ipatgrgvtv 86  
                                     l  e    v dgdrv++ + vt++ +pat +gvt+
  gi|121639297|ref|YP_979521.1|  978 LPAERLGSVSDGDRVLIAGAVTHRqRPATAQGVTF 1012
                                     5556667799************9888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1079 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 6743.11
//
Query:       gi|121639298|ref|YP_979522.1|  [L=446]
Description: hypothetical protein BCG_3443 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-42  143.7   2.3    1.3e-40  139.9   2.3    2.4  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    1.3e-15   57.6   0.0    2.6e-15   56.7   0.0    1.4  1  DUF1298         Protein of unknown function (DUF1298)


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   2.3   1.4e-44   1.3e-40       1     264 []       4     237 ..       4     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.4e-44
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    L++lDa fl++ ++e+  h g ++ + +  +ga++ ++++l + + +r + +pr  q        + a  W++ + fDl+
  gi|121639298|ref|YP_979522.1|   4 LTALDAGFLKSRDPER--HPGLAIGAVAVVNGAAP-SYDQLKTVLTERIKSIPRCTQ--------VLATEWIDYPGFDLT 72 
                                    6889*******99999..99999999999999999.799999999999999999999........55678********** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                     HvRrvalp+PG+e+el+ +++   ++pLD +rPlWe+++iEGl+g+r+Ail+k+HH+++  +++++llarl+d+ +  +
  gi|121639298|ref|YP_979522.1|  73 QHVRRVALPRPGDEAELFRAIALALERPLDPDRPLWECWIIEGLNGNRWAILIKIHHCMAGAMSAAHLLARLCDDADGSA 152
                                    **************************************************************************998888 PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrfa 240
                                     ++++    ++    + +++s      +++l ++  s+ag+v +a+    +a++  ++++p          p++ +Rr++
  gi|121639298|ref|YP_979522.1| 153 FANNVDI--KQI-PPYGDARS-----WAETLWRMSVSIAGAVCTAAA---RAVSWPAVTSP--------AGPVTTRRRYQ 213
                                    7766543..222.12334443.....488888998888888766532...22222333333........467999***** PP

                 WES_acyltransf 241 aaslpLadvkavakalgvtiNDvv 264
                                    a+++p + v av++++gvt NDv+
  gi|121639298|ref|YP_979522.1| 214 AVRVPRDAVDAVCHKFGVTANDVA 237
                                    **********************95 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   2.8e-19   2.6e-15       6     139 ..     271     400 ..     270     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.8e-19
                        DUF1298   6 gvvllpLpidladPlerlrkakkamdrk.KrsleavltylllelllkllpakvaaalikrllsnttlviSNvpGPqeely 84 
                                    +++l  Lp++ +dP+ rlr+++++ +++ +r++++++ y  l l      ak+  al++  ++ + ++ ++ pGP+ +l 
  gi|121639298|ref|YP_979522.1| 271 SAMLPYLPVEYDDPVRRLRTVHNRSQQSgRRQPDSLSDYTPLML-----CAKMIHALARLPQQGIVTLATSAPGPRHQLR 345
                                    578888****************9887652666666666555555.....5566666655568889999999********* PP

                        DUF1298  85 laGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddlee 139
                                    l+G++++++ p+ p + + + +++vlSy ++l +g+++d d+ +++q+l++ +e 
  gi|121639298|ref|YP_979522.1| 346 LMGQKMDQVLPIPPTALQLSTGVAVLSYGDELVFGITADYDAASEMQQLVNGIEL 400
                                    **************************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2711.60
//
Query:       gi|121639299|ref|YP_979523.1|  [L=391]
Description: trehalose 6-phosphate phosphatase otsB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-72  243.4   0.0    2.2e-72  243.0   0.0    1.2  1  Trehalose_PPase  Trehalose-phosphatase


Domain annotation for each model (and alignments):
>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.0   0.0   1.2e-76   2.2e-72       1     232 [.     145     369 ..     145     370 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 1.2e-76
                                    EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-H CS
                Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenq 80 
                                    f+D+dGTls+ivedpdaa++ + +l++L+kLa++++  +a++SGr+l+++ ++v++p++++a++HG+e+++p+g++++n+
  gi|121639299|ref|YP_979523.1| 145 FFDFDGTLSDIVEDPDAAWLAPGALEALQKLAARCP--IAVLSGRDLADVTQRVGLPGIWYAGSHGFELTAPDGTHHQND 222
                                    89**********************************..****************************************** PP

                                    HHHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT..THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S CS
                Trehalose_PPase  81 aevedlewlkevkeileektertpGsyiEekkfalsvHyrnaddeelqakelaehlesvltdkpdlevtqgkkvvevrpq 160
                                    a+++++++lk++++ l++++  +pG+++E+k+f ++vHyrna+++  ++ e+a++++++ +++  l+vt+g++v+e+rp+
  gi|121639299|ref|YP_979523.1| 223 AAAAAIPVLKQAAAELRQQLGPFPGVVVEHKRFGVAVHYRNAARD--RVGEVAAAVRTAEQRH-ALRVTTGREVIELRPD 299
                                    *********************************************..****************.**************** PP

                                    ---.HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT...-EEEEE--TTS---EES-SEEESSH CS
                Trehalose_PPase 161 gvs.KGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktkesgvsievsavevgskpskakysldsk 232
                                    +++ KGk++ ++l++l++++s++ +++++GDd+tDed+F+v+ ++   gv+i+v+++++g+++++a ++lds+
  gi|121639299|ref|YP_979523.1| 300 VDWdKGKTLLWVLDHLPHSGSAPLVPIYLGDDITDEDAFDVVGPH---GVPIVVRHTDDGDRATAALFALDSP 369
                                    ********************************************8...*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3018.16
//
Query:       gi|121639300|ref|YP_979524.1|  [L=296]
Description: enoyl-CoA hydratase echA18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-51  173.5   0.1    5.7e-51  173.2   0.1    1.1  1  ECH_1     Enoyl-CoA hydratase/isomerase
    6.9e-28   98.1   0.5    8.8e-28   97.8   0.5    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   0.1   6.4e-55   5.7e-51       3     250 ..      46     296 .]      44     296 .] 0.95

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 6.4e-55
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC..HHHHHHHCCHHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek..akqallkeevle 79 
                                    + +va+i+l  P+a+Nal+ +    l   l +l  +  +ravvL G gdkaFaaGad+ke  +  +  a++a+++e++  
  gi|121639300|ref|YP_979524.1|  46 HRNVALITLSHPQAQNALNLASWRRLKRLLDDLAGESGLRAVVLRGaGDKAFAAGADIKEFPNTRMsaADAAEYNESLAV 125
                                    679*********************************************************99877667999********* PP

                                    HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EE CS
                          ECH_1  80 lwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkki 159
                                     +++l+t+p+pviaav+G a+gGG+ela acD+ ia d+a+fg +  klG++ g+   +++ar +G ++ +++l  g+ i
  gi|121639300|ref|YP_979524.1| 126 CLRALTTMPIPVIAAVRGLAVGGGCELATACDVCIATDDARFGIPLGKLGVTTGFTEADTVARLIGPAALKYLLFSGELI 205
                                    ******************************************************************************** PP

                                    EHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHH CS
                          ECH_1 160 saqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqa 239
                                    + +ea+++Glv+kvv+ ++l   + +l+ ++ ++s   +r++k   n + +    +  +a ++   +  + +d +eG+ a
  gi|121639300|ref|YP_979524.1| 206 GIEEAARWGLVQKVVAPQDLAAATAKLVGQVCRQSAVTMRAAKVVANMHGRALTGADTDALIRFGVEAYEGADLREGVAA 285
                                    ***********************************9999999988887777666777888889999999999******** PP

                                    HHTCSH----- CS
                          ECH_1 240 flEkrkpefed 250
                                    f   r+p+f+d
  gi|121639300|ref|YP_979524.1| 286 FSQGRPPKFDD 296
                                    *******9975 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.5   9.8e-32   8.8e-28       2     195 ..      50     246 ..      49     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 9.8e-32
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    ++itL  p+a NaL+l+  r+lk+ l++ + ++  ++vvl+gag+kaf AG D++++ +++ + +++ +e+ ++   +  
  gi|121639300|ref|YP_979524.1|  50 ALITLSHPQAQNALNLASWRRLKRLLDDLAGESGLRAVVLRGAGDKAFAAGADIKEFPNTRMSAADA-AEYNESLAVCLR 128
                                    68********************************************************999997755.79999999999* PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkga 160
                                    ++ t+p pv+a + G+++GgG+ l++ + + ++t++++f +P  ++G+++        +rl g +  +yl  +G+ ++ +
  gi|121639300|ref|YP_979524.1| 129 ALTTMPIPVIAAVRGLAVGGGCELATACDVCIATDDARFGIPLGKLGVTTGFTEADTVARLIGpAALKYLLFSGELIGIE 208
                                    *************************************************************8846668************ PP

                                    HHHHTTS--EE--GGGHHHHHHHHHTT........... CS
                          ECH_2 161 dalaaglathyvpseklealeeaLaelessd...eeav 195
                                    +a   gl +++v  ++l+a +++L  +  ++   + + 
  gi|121639300|ref|YP_979524.1| 209 EAARWGLVQKVVAPQDLAAATAKLVGQVCRQsavTMRA 246
                                    ************************98655543332233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2158.37
//
Query:       gi|121639301|ref|YP_979525.1|  [L=475]
Description: amidase amiD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-115  386.5   0.2   2.1e-115  386.3   0.2    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.3   0.2  1.2e-119  2.1e-115       1     450 [.      38     455 ..      38     456 .. 0.96

  Alignments for each domain:
  == domain 1  score: 386.3 bits;  conditional E-value: 1.2e-119
                                    HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS CS
                        Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaek 80 
                                    e++e+ l+rie+++++l+++++v++e+ala+A+++d+++arg+ +g+LhGvPi vKD + + + pt+aG+ ++ ++++ +
  gi|121639301|ref|YP_979525.1|  38 EVTESTLRRIERLDPQLKSYAFVMPETALAAARAADADIARGHYEGVLHGVPIGVKDLCYTVDAPTAAGTTIFRDFRPAY 117
                                    79****************************************************************************** PP

                                    --HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHH CS
                        Amidase  81 DatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPA 160
                                    Datvv+rL++aGavi+gk  m+e a+  ++ +  + + +NPwd++ ++G SS+G+++a+Aagl+  +iG+DtGGSiR+P 
  gi|121639301|ref|YP_979525.1| 118 DATVVARLRAAGAVIIGKLAMTEGAYLGYHPS--LPTPVNPWDPTAWAGVSSSGCGVATAAGLCFGSIGSDTGGSIRFPT 195
                                    *************************9988766..9999****************************************** PP

                                    HHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EE CS
                        Amidase 161 sfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglri 240
                                    s+cg++G+KPt+grvSr+gvv+l++s d+vGp++rs++d+a+ll+vi+g+d +d+++s   e+++d+a+ l+ + +  r+
  gi|121639301|ref|YP_979525.1| 196 SMCGVTGIKPTWGRVSRHGVVELAASYDHVGPITRSAHDAAVLLSVIAGSDIHDPSCSA--EPVPDYAADLALT-RIPRV 272
                                    **********************************************************9..7899999999988.9**** PP

                                    EEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHH.HHHHHHHHHHHHHTTT-SSSSS---SS-SCCCC CS
                        Amidase 241 GvvkedgvasldpevqravekalkaLeeaGhevvevelpsleeals.lyylilvaeassnlarylgvryerlsetkvlse 319
                                    Gv +++  +s+d++ ++++++++k+L + G+ v++v+lp+l+ +++ +  + +v+ a ++                  ++
  gi|121639301|ref|YP_979525.1| 273 GVDWSQT-TSFDEDTTAMLADVVKTLDDIGWPVIDVKLPALAPMVAaFGKMRAVETAIAH------------------AD 333
                                    *******.7*************************************55555555555544..................68 PP

                                    CCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSH CS
                        Amidase 320 llpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsy 399
                                    ++p  ra+++g++++++i+ g++  + e     y++ +++r +++r+++++f+++D+ll+P+a ++ p+l+ ++ ++ ++
  gi|121639301|ref|YP_979525.1| 334 TYP-ARADEYGPIMRAMIDAGHRLAAVE-----YQTLTERRLEFTRSLRRVFHDVDILLMPSAGIASPTLETMRGLG-QD 406
                                    888.78999*************877777.....9***************************************9986.99 PP

                                    HHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                        Amidase 400 tvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                     +l++ l+++  ++p+n+ g+pa+++pag++++g+P+Gvq+ig++f+e+ l
  gi|121639301|ref|YP_979525.1| 407 PELTARLAMP--TAPFNVSGNPAICLPAGTTARGTPLGVQFIGREFDEHLL 455
                                    9999999999..9***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3436.59
//
Query:       gi|121639302|ref|YP_979526.1|  [L=217]
Description: hypothetical protein BCG_3447 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-14   53.8   0.1    3.4e-13   50.4   0.1    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    6.7e-13   49.1   0.0    1.5e-12   48.0   0.0    1.7  1  HAD_2           Haloacid dehalogenase-like hydrolase
    0.00019   21.4   0.0    0.00032   20.7   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
     0.0022   18.1   0.0      0.032   14.3   0.0    2.7  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.006   16.4   0.0      0.011   15.6   0.0    1.4  1  Acid_PPase      Acid Phosphatase
  ------ inclusion threshold ------
      0.075   12.9   0.0       0.19   11.6   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   1.1e-16   3.4e-13       1     210 []       3     185 ..       3     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.1e-16
                                    SSEEEEESBTTTBCHH.HHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttge.psvedvivsaalalaaaletgsehpigkal.vaaakarsgaltgfatfigrgayaigkpewlt 78 
                                    i +vvfD dG+Lt     + e+ ++++                   l  ++ + r+g   +  t+ +  +      e+l 
  gi|121639302|ref|YP_979526.1|   3 ISAVVFDRDGVLTSFDwTRAEEDVRRI-----------------TGLpLEEIERRWGGWLNGLTIDDAFVETQPISEFLS 65 
                                    679**********88865555555555.................334356666664444333333333344666778888 PP

                                    HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx. RF
                      Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG. 156
                                    +l       a+  ++ s++r++ +     l + ++a+    +p+a+ a+++ +++g++v++lt+++     r + q +  
  gi|121639302|ref|YP_979526.1|  66 SL-------ARELELGSKARDELVR----LDYMAFAQG---YPDARPALEEARRRGLKVGVLTNNSLLVSARSLLQcAAl 131
                                    88.......8999999999999999....999999977...************************999988888884668 PP

                                    GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    +d +d+v++s   + akp+p++++a+++ L+++   +++++D +  +++++ Ag
  gi|121639302|ref|YP_979526.1| 132 HDLVDVVLSSQMIGAAKPDPRAYQAIAEALGVSTTSCLFFDDIADWVEGARCAG 185
                                    9999**************************************999999999887 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   4.9e-16   1.5e-12      76     177 ..      88     190 ..       6     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.9e-16
                          HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveek.leqlgiesyFdvivtsedvekkKPdpeviekaleklklkkee 154
                                     + + y++++ +Lee +++g+k+g+ T++s  +  ++ l+   ++++ dv+++s++++  KPdp+ ++++ e l+++  +
  gi|121639302|ref|YP_979526.1|  88 AFAQGYPDARPALEEARRRGLKVGVLTNNSLLVSARSlLQCAALHDLVDVVLSSQMIGAAKPDPRAYQAIAEALGVSTTS 167
                                    67788************************7766665505556789*********************************** PP

                          HAD_2 155 viyvGDsptDieaakkagikvia 177
                                    ++++ D    +e+a+ ag+++  
  gi|121639302|ref|YP_979526.1| 168 CLFFDDIADWVEGARCAGMRAYL 190
                                    *******************9865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-07   0.00032       3      56 ..     147     200 ..     145     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                                    STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS.SSS-TT CS
                 Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt.Gvtrpe 56 
                                     KP p +y +++e+lg+    +l+  D  a+ ++gA+ aG++  LV + G tr++
  gi|121639302|ref|YP_979526.1| 147 AKPDPRAYQAIAEALGVSTTSCLFFDDI-ADWVEGARCAGMRAYLVDRsGQTRDG 200
                                    6************************999.999**************765877775 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.032       2      42 ..       7     119 ..       6     148 .. 0.72
   2 ?   -1.8   0.0       1.1   3.4e+03      38      55 ..     192     209 ..     171     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                    EEESTTTSE....................................................................... CS
                    Hydrolase_6   2 lfDidGvLw....................................................................... 10 
                                    +fD dGvL                                                                        
  gi|121639302|ref|YP_979526.1|   7 VFDRDGVLTsfdwtraeedvrritglpleeierrwggwlngltiddafvetqpiseflsslarelelgskardelvrldy 86 
                                    66666666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                    .ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS CS
                    Hydrolase_6  11 .rgdkaipgaaealnalraagkpvvllTNnssk 42 
                                      + + +p a  al+  r++g +v +lTNns  
  gi|121639302|ref|YP_979526.1|  87 mAFAQGYPDARPALEEARRRGLKVGVLTNNSLL 119
                                    6677889***********************965 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                    ---SS-HHHHHHHHHHTT CS
                    Hydrolase_6  38 Nnsskseeeyakkleklg 55 
                                     +s++++++++ +l++lg
  gi|121639302|ref|YP_979526.1| 192 DRSGQTRDGVVRDLSSLG 209
                                    568889999999999988 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.6e-06     0.011      46     163 ..      92     205 ..      75     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                                    --TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEEEESSS-H..HHHHHHHHHHH--- CS
                     Acid_PPase  46 lypdveeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddveiykgsk..tkhfeklkkktgie 123
                                     ypd++ +lee ++++ k+ v    +    ar+lL+  +++        l dv+ + ++  + k   + +++++++ g++
  gi|121639302|ref|YP_979526.1|  92 GYPDARPALEEARRRGLKVGVLTNNSLLVSARSLLQCAALH-------DLVDVVLSSQMIGAAKpdPRAYQAIAEALGVS 164
                                    59999999999999999999999999999999999999999.......899999998887766522689*********** PP

                                    GGGEEEEES-HHHHHHHHTTT-EEEE-SS.S--HHHHHHHH CS
                     Acid_PPase 124 yedmlfFDdesrnievesrlgvtfvlvpd.Gltreefekgl 163
                                     ++ lfFDd ++ +e  +  g+  +lv++ G tr+ + + l
  gi|121639302|ref|YP_979526.1| 165 TTSCLFFDDIADWVEGARCAGMRAYLVDRsGQTRDGVVRDL 205
                                    ***********999999999****99977799998877766 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.4e-05      0.19      18      35 ..     152     169 ..     150     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                  HTH_AsnC-type  18 isyaeLAervGlSestvl 35 
                                    + y+++Ae++G+S++ +l
  gi|121639302|ref|YP_979526.1| 152 RAYQAIAEALGVSTTSCL 169
                                    679************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1669.99
//
Query:       gi|121639303|ref|YP_979527.1|  [L=483]
Description: cyclase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-06   25.1   0.0      0.023   13.8   0.0    2.5  2  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
    8.8e-05   21.7   0.0       0.51    9.4   0.0    2.7  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
    0.00083   19.1   0.2      0.019   14.7   0.2    3.1  3  Prenyltrans      Prenyltransferase and squalene oxidase repea


Domain annotation for each model (and alignments):
>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00015      0.87     207     236 ..      36      66 ..      12      92 .. 0.74
   2 !   13.8   0.0   3.8e-06     0.023     142     201 ..     339     399 ..     332     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHTT--TTSSBB--G.GGGT-G CS
                SQHop_cyclase_C 207 pvirkavdWlksvqnedGGWGesa.esykdp 236
                                    ++   a++Wl ++q +dG WG +    y+d+
  gi|121639303|ref|YP_979527.1|  36 ELSDLALNWLCERQLPDGSWGAEFpFCYEDR 66 
                                    4455688899999999999985541456665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.8e-06
                                    HHHHHHHHHHHT--TTSHHHHHHHHHHHHHS-TT.S----SSBSSHHHHHHHHHHHHHHTT CS
                SQHop_cyclase_C 142 tarvlellaqlgeeedsealkraveylkkeqepd.GsWfGrWGvnyiyGtwsvlsalaavg 201
                                      +vl +l q g+++ ++ +++ +e++++ +ep   +W  +W     y t + ++a ++ +
  gi|121639303|ref|YP_979527.1| 339 NVHVLGALKQAGYDKCHPRVRKVLEFIRSSKEPGrFCWRDKWHRSAYYTTAHLICAASNYD 399
                                    568999*************************996259**************9999977655 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   8.6e-05      0.51      28      66 ..      19      57 ..      10      77 .. 0.82
   2 ?   -2.1   0.0      0.27   1.6e+03      72      86 ..     196     210 ..     191     235 .. 0.68
   3 !    9.2   0.0   9.5e-05      0.57      65     105 ..     327     367 ..     316     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 8.6e-05
                SQHop_cyclase_N 28 itaeyillreflgeddeeeeekiakylrsqqredGgWel 66
                                    ta +      lg+ d+e+ + + ++l+++q +dG+W+ 
  gi|121639303|ref|YP_979527.1| 19 STAYDTAWVAKLGQLDDELSDLALNWLCERQLPDGSWGA 57
                                   566666666778899999999999************975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.27
                SQHop_cyclase_N  72 gdlsttveaYlALkl 86 
                                     + s +  aY+AL +
  gi|121639303|ref|YP_979527.1| 196 VKYSPSASAYFALHV 210
                                    56688999****987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 9.5e-05
                SQHop_cyclase_N  65 elypggpgdlsttveaYlALkllGdspdapalarArefila 105
                                      +++    +st v    ALk +G+++ +p+ ++  efi++
  gi|121639303|ref|YP_979527.1| 327 TYFHEVGPSISTNVHVLGALKQAGYDKCHPRVRKVLEFIRS 367
                                    356888899*****************************997 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.1e-06     0.019       5      21 ..      40      56 ..      38      57 .. 0.92
   2 ?   -1.5   0.0      0.37   2.2e+03       5      19 ..     216     231 ..     215     231 .. 0.83
   3 ?   -0.3   0.0      0.16   9.5e+02       2      14 ..     357     369 ..     356     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHHHSHTTS-BB CS
                    Prenyltrans  5 kavefLlscQnedGGwg 21
                                    a+++L+ +Q +dG+wg
  gi|121639303|ref|YP_979527.1| 40 LALNWLCERQLPDGSWG 56
                                   689*************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.37
                                    HHHHHHHHHSH.TTS- CS
                    Prenyltrans   5 kavefLlscQn.edGG 19 
                                    +a+ ++ s+ +  dGG
  gi|121639303|ref|YP_979527.1| 216 RALAYISSIIQaGDGG 231
                                    6899*****9977777 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHS CS
                    Prenyltrans   2 dvekavefLlscQ 14 
                                     v+k++ef++s  
  gi|121639303|ref|YP_979527.1| 357 RVRKVLEFIRSSK 369
                                    689*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2924.22
//
Query:       gi|121639304|ref|YP_979528.1|  [L=296]
Description: hypothetical protein BCG_3449c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0019   17.7   0.0     0.0022   17.6   0.0    1.1  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-07    0.0022       3     123 ..      34     158 ..      33     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-07
                                    --HHHHHHHTT.S-HHHHHHH.HHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-H.HHHHHHHHHHHHHHHHHHHHHHH CS
                   Prenyltransf   3 DGNrRwAkkrgleereeGhka.GaealkeilelclelgvkvvtvYafSteNfkRsk.eevdalmellkeellkeelkell 80 
                                    DG rRw + +  +++ + +++  +++  +il++  e+g+++v    fS + + R + + v+al  ++   + +ee+ ++ 
  gi|121639304|ref|YP_979528.1|  34 DGTRRWFHLEC-NPQYDDYQQaALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDrYIVQALEGMALL-ANDEEILSFY 111
                                    9*******999.6666677651668999**************************751567777666632.3445555666 PP

                                    HT.TEEEEEESSGG.GS-HHHH..HHHHHHHHHHT.TTTSEEEEEEE CS
                   Prenyltransf  81 ke.gvrvrviGdle.llpedvl..ealekaeeatkknnkklvlniav 123
                                    ke +v+v + Gd + +lp++ +  +a+++  + t ++++++   +++
  gi|121639304|ref|YP_979528.1| 112 KEhEVHVLFYGDYKkRLPSTAQgaAAVKSFDDLTISTSSNTEHRLCF 158
                                    665********976378877762234555555565544445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2273.15
//
Query:       gi|229576790|ref|YP_979529.2|  [L=612]
Description: 1-deoxy-D-xylulose-5-phosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-88  296.4   0.0    2.3e-76  256.6   0.0    2.4  3  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    6.4e-36  123.7   0.0    2.1e-35  122.0   0.0    1.9  2  Transket_pyr     Transketolase, pyrimidine binding domain
    2.1e-23   82.5   0.0    4.8e-23   81.4   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain
    9.2e-06   25.5   0.0    3.8e-05   23.5   0.0    2.1  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
      0.052   13.9   0.0       0.16   12.3   0.0    1.9  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
      0.067   12.1   0.0       0.11   11.5   0.0    1.2  1  E1_dh            Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   0.0   7.6e-80   2.3e-76       3     191 ..      15     204 ..      13     209 .. 0.97
   2 !   37.5   0.0   5.1e-13   1.5e-09     232     273 .]     211     252 ..     205     252 .. 0.95
   3 ?   -3.5   0.0       1.5   4.6e+03      52      69 ..     359     377 ..     357     389 .. 0.70

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 7.6e-80
                 DXP_synthase_N   3 kinspedlkklskeeleelaeelrefliesvsktggHlasnLgvveLtlalhyvfdtpkDklvwDvgHqaYvhKiltgRk 82 
                                     i  p d+++l +++l+ela ++r+ lie+v++tggHl+++Lg+veLt+alh+vf +p+D +v+D+gHq+Y+hK+ltgR 
  gi|229576790|ref|YP_979529.2|  15 AIGGPCDVQALPESQLPELAVQMRRRLIETVTATGGHLGAGLGMVELTIALHRVFTSPHDIVVFDTGHQTYPHKLLTGRG 94 
                                    678899************************************************************************** PP

                 DXP_synthase_N  83 dkfktlrqkgGlsgfpkrsEseyDafeagHsstsisaalGlavardlkge.kkkvvaviGDgaltgGmafealnnigelk 161
                                    ++f+tlrq++Glsg+p+r+Es++D++e++H+s s+++  G+a+a  l+g+ +++v+aviGDgaltgG+a+e+lnn+g+ +
  gi|229576790|ref|YP_979529.2|  95 KDFATLRQADGLSGYPNRHESPHDWVENSHASVSLAWVDGIAKALALQGQcDRRVIAVIGDGALTGGVAWEGLNNLGAAT 174
                                    ************************************************96489*************************** PP

                 DXP_synthase_N 162 kkllvilNdNemsisknvGalskylsklls 191
                                    + ++v+lNdN +s++++ Gal+++l++l+ 
  gi|229576790|ref|YP_979529.2| 175 RPVIVVLNDNGRSYDPTAGALAAHLEELRV 204
                                    *************************99986 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 5.1e-13
                 DXP_synthase_N 232 tlfeelgfkYlGpidGhdleelikvleevkklkgpvllhvvt 273
                                    +lfe++gf+Y+Gp+dGh++ + + vl+++ ++ +pv++h vt
  gi|229576790|ref|YP_979529.2| 211 NLFENMGFTYIGPVDGHNIPDTCAVLRKAAAAARPVVVHAVT 252
                                    79*************************************997 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.5
                 DXP_synthase_N  52 alhyvf.dtpkDklvwDvg 69 
                                    a++  f +   D+l++D+g
  gi|229576790|ref|YP_979529.2| 359 AVYSTFlHRAFDQLLFDIG 377
                                    666655245679******9 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.97   2.9e+03       3      29 ..     129     155 ..     128     165 .. 0.78
   2 !  122.0   0.0     7e-39   2.1e-35       3     174 ..     288     448 ..     286     452 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.97
                                    EEHHHHHHHHHHHHHCTTTTEEEEESS CS
                   Transket_pyr   3 iawrkaeaealaellkedpevvligaD 29 
                                    +aw +++a+ala  ++ d +v+++  D
  gi|229576790|ref|YP_979529.2| 129 LAWVDGIAKALALQGQCDRRVIAVIGD 155
                                    689999999**9999999999876555 PP

  == domain 2  score: 122.0 bits;  conditional E-value: 7e-39
                                    EEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEH CS
                   Transket_pyr   3 iawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFg 82 
                                     +w++++++ +a+++++  +vv+++a+++  t++   + ++++   rv+dsgi+Eq++l+ a+G+a+ag  +++v+a ++
  gi|229576790|ref|YP_979529.2| 288 RSWTDVFEDEIARIADDRSDVVGLTAAMRLPTGLGALSRRYPH---RVFDSGIAEQHLLASAAGLAAAG--THPVVAVYS 362
                                    68*****************************************...***********************..9******** PP

                                    HHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSS CS
                   Transket_pyr  83 dFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairre 161
                                    +F+     +a++++  +  +++l+v+ v++r+++ +g dGp+h++++++a+l+++pg+++++P d+  +++ lr+ai+  
  gi|229576790|ref|YP_979529.2| 363 TFLH----RAFDQLLFDIGLHRLPVTlVLDRAGV-TGPDGPSHHGLWDLALLACVPGFQIACPRDAPRLRQQLRTAIA-- 435
                                    ****....**************************.*******************************************.. PP

                                    S.SEEEEEE-SSE CS
                   Transket_pyr 162 drkPvvlrlpksl 174
                                    +  P+++r+pk++
  gi|229576790|ref|YP_979529.2| 436 TAAPTAVRFPKGA 448
                                    678********86 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.0   1.6e-26   4.8e-23       8     124 .]     472     585 ..     467     585 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.6e-26
                                    TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHC CS
                Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaee 87 
                                    + +dv+lva+G+m + +++Aa  L++e+i+++Vvd+++v+p+  ++ + ++ +++  v+ve+a   +Gig+++++ + + 
  gi|229576790|ref|YP_979529.2| 472 WRPDVLLVAVGAMSRPCMDAARCLSEEQIGVTVVDPQWVWPISPALTE-LAGRHRITVCVEDAIADVGIGAHLSHHIGR- 549
                                    579****************************************99986.******************************. PP

                                    CCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
                Transketolase_C  88 afdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                      ++  ++  ++g+p + i+++s+++++  +gl+  +i
  gi|229576790|ref|YP_979529.2| 550 --THPRTRTYTLGLPPAyIPHASRDHILSSHGLTGPAI 585
                                    ..*******************************98766 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.3e-08   3.8e-05      16     152 ..     114     249 ..     105     250 .. 0.81
   2 ?   -2.2   0.0       1.1   3.2e+03     112     151 ..     405     442 ..     394     444 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                                    SSSSEEEC.ETTTS-TTTHHHHHHHHHHHST.TSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-.SBCCCHHH CS
                   TPP_enzyme_C  16 krprsylt.sgglgtmGyglpaAiGaklakp.drevvaivGDGgflmi..lqelatavrrnlpitvvvlnN.egygmtgg 90 
                                    ++p  ++  s   +++ +  ++A +++l+ + dr+v+a++GDG++      + l +      p++vv+ +N ++y  t g
  gi|229576790|ref|YP_979529.2| 114 ESPHDWVEnSHASVSLAWVDGIAKALALQGQcDRRVIAVIGDGALTGGvaWEGLNNLGAATRPVIVVLNDNgRSYDPTAG 193
                                    446777776667777777777777777743349***********6554457889999999889******99779****** PP

                                    HHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEE.EESSH.HHHHHHHHHHHHCSSSEEEEE CS
                   TPP_enzyme_C  91 qqepfggkrksgpagkdlkpvdfaklaealGakga.rvekadveeleealkealekkgpalie 152
                                        + ++ ++g+      p    +l e +G + +  v+ +++ ++ ++l++a +  +p++++
  gi|229576790|ref|YP_979529.2| 194 ALAAHLEELRVGTP---RGP----NLFENMGFTYIgPVDGHNIPDTCAVLRKAAAAARPVVVH 249
                                    *9999999988866...333....799******66699************************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                    -HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                   TPP_enzyme_C 112 dfaklaealGakgarvekadveeleealkealekkgpali 151
                                    d+a la   G + a   ++d   l+++l++a+++  p+ +
  gi|229576790|ref|YP_979529.2| 405 DLALLACVPGFQIAC--PRDAPRLRQQLRTAIATAAPTAV 442
                                    555556566777555..45558999999999998888876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.8   1.1e+04      72     100 ..     428     456 ..     423     457 .. 0.78
   2 ?   12.3   0.0   5.5e-05      0.16       2      70 ..     475     543 ..     474     558 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.8
                                    HHHHHHTGGGTSEEEEEE--GGG----HH CS
                        PFOR_II  72 eevkaalkkskvkvvnfvaglgGrditve 100
                                    +  ++a+   ++++v+f +g+ G+ it+e
  gi|229576790|ref|YP_979529.2| 428 QQLRTAIATAAPTAVRFPKGAPGEPITAE 456
                                    56677777778899999999999999887 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.5e-05
                                    SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HH CS
                        PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGql 70 
                                    +v++va+G++++ + +a++ l ee i v ++ +++++P   +  + + ++   v+v d  +++g+   l
  gi|229576790|ref|YP_979529.2| 475 DVLLVAVGAMSRPCMDAARCLSEEQIGVTVVDPQWVWPISPALTELAGRHRITVCVEDAIADVGIGAHL 543
                                    89************************************8544444444444455555555556655555 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.11     107     162 ..     129     185 ..     101     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                    HHHHHHHHHHHHHHTS.---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEES CS
                          E1_dh 107 vplvaGialaakiegk.kevailliGDgAanqGdvyealnlaalwklpvifvveNNk 162
                                       v Gia a   +g+ ++ +i++iGDgA   G ++e+ln   +   pvi v + N+
  gi|229576790|ref|YP_979529.2| 129 LAWVDGIAKALALQGQcDRRVIAVIGDGALTGGVAWEGLNNLGAATRPVIVVLNDNG 185
                                    335669999999887647899********999********9999999***9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4765.90
//
Query:       gi|121639306|ref|YP_979530.1|  [L=329]
Description: lytB-related protein lytB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-85  285.5   0.0    3.8e-85  285.3   0.0    1.0  1  LYTB          LytB protein
  ------ inclusion threshold ------
      0.074   13.2   0.0       0.16   12.1   0.0    1.5  1  DUF2325       Uncharacterized protein conserved in bacteria (
      0.087   12.6   0.0        4.9    6.9   0.0    2.4  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   0.0   6.4e-89   3.8e-85       1     263 [.      20     300 ..      20     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 6.4e-89
                                    EEE-TT-SS-HHHHHHHHHHHHHHCCC-S.EEECS-SSS-HHHHHHHHHCTEEEESSSSTE.........EEE-TT---H CS
                           LYTB   1 illaksaGfCfGVerAieiaeealeekke.vyvlgeivHNeqvverLeekgvkfieeleev.........viirAhGvsk 70 
                                    +lla+++ fC+GVerAie++++ l+ +++ vyv+++ivHN+ vv++L+++g+ f+e+l+e+         v+++AhGvs+
  gi|121639306|ref|YP_979530.1|  20 VLLASPRSFCAGVERAIETVKRVLDVAEGpVYVRKQIVHNTVVVAELRDRGAVFVEDLDEIpdppppgavVVFSAHGVSP 99 
                                    689**********************9999**************************996542333344444********** PP

                                    HHHHHHHHTTEEEEE---HHHHHHHHHHHHHHHCT-EEEEES-TT-HHHHHHHCCT--TEEEESSCHHHHHG......CE CS
                           LYTB  71 eveeelkekglevvDatCplVkkvqkevkklakegyeiviiGkkkHpEvegilgqaeekvvvveeseevekl......kv 144
                                    +v++ ++e+gl+vvDatCplV+kv+ e++++a++g ++v+iG+++H+E+eg+lg a++++++v++ ++v++l      ++
  gi|121639306|ref|YP_979530.1| 100 AVRAGADERGLQVVDATCPLVAKVHAEAARFAARGDTVVFIGHAGHEETEGTLGVAPRSTLLVQTPADVAALnlpegtQL 179
                                    **********************************************************9****8888877778899999* PP

                                    EEEE-TTS-HHHHHHHHHHHHHHSTCEEE..C-S--CHHHHHHHHHHHHHGHSSEEEEES-TT-HHHHHHHHHHHHCSCT CS
                           LYTB 145 alvsQTTlsveefeeivealkkklkelev..kdtiCkatqeRqeavkelakevdlvivvGgknSsNtkkLveiakeknkk 222
                                     +++QTTl  +e++++++al++++++l +  +++iC+at++Rq+a+++++ e+d+v+v+G+ nSsN+++Lve+a++++++
  gi|121639306|ref|YP_979530.1| 180 SYLTQTTLALDETADVIDALRARFPTLGQppSEDICYATTNRQRALQSMVGECDVVLVIGSCNSSNSRRLVELAQRSGTP 259
                                    **************************99999************************************************* PP

                                    EEEESSGGG--HHHHTT-SEEEEEE-TTS-HHHHHHHHHHH CS
                           LYTB 223 tyliesaeeldeewlegvkkvgitaGaStpeelieeviekl 263
                                    +yli+  +++++ewl++v+++g+taGaS+p +l+ +vi++l
  gi|121639306|ref|YP_979530.1| 260 AYLIDGPDDIEPEWLSSVSTIGVTAGASAPPRLVGQVIDAL 300
                                    **************************************988 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05      0.16      34      79 ..     219     263 ..     214     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                        DUF2325  34 ekkkkkleskigkaDlvvlftdtvsHkavkkvkkeakkkgkpvvrl 79 
                                    +++++ l+s++g++D+v+++ +++s ++ +++ ++a+++g+p +++
  gi|121639306|ref|YP_979530.1| 219 TNRQRALQSMVGECDVVLVIGSCNSSNS-RRLVELAQRSGTPAYLI 263
                                    345669*******************998.77889999999998765 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.011        63      48      95 ..     109     150 ..     106     191 .. 0.70
   2 ?    6.9   0.0   0.00082       4.9      65      86 ..     219     240 ..     205     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                                    GTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTT CS
                   TPP_enzyme_M  48 gkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddirttg 95 
                                    g  v++ ++pl +    +  +++a + +++ D+v+++G   ++  t g
  gi|121639306|ref|YP_979530.1| 109 GLQVVDATCPLVA---KV--HAEAARFAARGDTVVFIGHAGHE-ETEG 150
                                    6778888888773...33..5677777799********76655.4444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00082
                                    GGSCHHHHHHHHH-SEEEEES- CS
                   TPP_enzyme_M  65 lhgskaanealeeaDlvlalGa 86 
                                      +++a + ++ e+D+vl++G+
  gi|121639306|ref|YP_979530.1| 219 TNRQRALQSMVGECDVVLVIGS 240
                                    55678889999**********4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2516.85
//
Query:       gi|121639307|ref|YP_979531.1|  [L=350]
Description: polyprenyl synthetase idsB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-58  197.5   0.0    2.6e-58  197.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   0.0   1.5e-62   2.6e-58      14     254 ..      67     303 ..      58     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 1.5e-62
                                    SSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHH CS
                polyprenyl_synt  14 agGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllar 93 
                                    ++GK++R++lv +aa a++    ++ +a  + ++vel+h+++L+hDD+mD + tRRG+p++ +++G+  Ai+ gd+l a+
  gi|121639307|ref|YP_979531.1|  67 SSGKYFRAALVYAAAAACG---GDVGDATPVSAAVELVHNFTLLHDDVMDGDATRRGRPTVWSVWGVGGAILLGDALHAT 143
                                    78*****************...35799***************************************************** PP

                                    HHHHHHHHHSTT..HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHH CS
                polyprenyl_synt  94 afellaklfeks..lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasde 171
                                    a+++l+ l +++  +++++ ++  +l++++Gq+ d+  e +++++   +++yl++   KTa+l  +++al+al+a+a+d+
  gi|121639307|ref|YP_979531.1| 144 AVRILTGLTDECvaVRAIRRLQMSCLDLCIGQFEDCLLEGQPEVT---VDDYLRMAAGKTAALTGCCCALGALVANADDA 220
                                    ********9666689********************9888889999...*****************************99* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTT.SSHHHHHHHH CS
                polyprenyl_synt 172 elealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilg.kkaekeedvk 250
                                    +++al+++g+elGlaFQ +DD++ + gdp v+gKp+g+D++  k+tlp++ al+ + +e +++l ++++   a + +dv+
  gi|121639307|ref|YP_979531.1| 221 TIAALERFGHELGLAFQCVDDLIGIWGDPGVTGKPVGNDLARRKATLPVVAALN-SRSEAATELAALYQaPAAMTASDVE 299
                                    ******************************************************.5556678*******77778888888 PP

                                    HHHH CS
                polyprenyl_synt 251 eale 254
                                    +a +
  gi|121639307|ref|YP_979531.1| 300 RATA 303
                                    8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2652.67
//
Query:       gi|121639308|ref|YP_979532.1|  [L=130]
Description: hypothetical protein BCG_3453c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-15   55.9   0.3    6.3e-15   55.8   0.3    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.057   13.4   0.6       0.75    9.8   0.6    2.3  2  ALF       Short repeats of unknown function


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3     7e-19   6.3e-15       1     121 [.       4     120 ..       4     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7e-19
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                    i+lD+s++++l  +e++++a+r+ l      v+sal+ aE+++ l       + + ++++ +  l+ l +l +d+++++ 
  gi|121639308|ref|YP_979532.1|   4 IYLDSSAIVKLAVREPESDALRRYLRTRHPRVSSALARAEVMRALLD-----KGESARKAGRRALAHLDLLRVDKRVLDL 78 
                                    79************************99*******************.....88888889999999************** PP

                                    HHHHHHHHHSBHHHHHHHHHHHHHT-E..EE.ESSTHHHHHHH CS
                            PIN  81 aaeialkygllpnDaliaAtAkehgik..liatfDedfrrvak 121
                                    a+ +    +l+++Da+++AtA++ g +   ++t+D+++r++ak
  gi|121639308|ref|YP_979532.1|  79 AGGLLP-FELRTLDAIHLATAQRLGVDlgRLCTYDDRMRDAAK 120
                                    ***999.56******************88899*******9986 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.047   4.2e+02      28      39 ..      21      32 ..      15      34 .. 0.84
   2 ?    9.8   0.6   8.3e-05      0.75       1      24 [.      41      64 ..      41      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.047
                            ALF 28 paalraFLetGq 39
                                    +alr +L+t +
  gi|121639308|ref|YP_979532.1| 21 SDALRRYLRTRH 32
                                   589******975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 8.3e-05
                            ALF  1 RvavarllatgGpaVraAAqaALd 24
                                   R++v+r+l + G   r+A+++AL+
  gi|121639308|ref|YP_979532.1| 41 RAEVMRALLDKGESARKAGRRALA 64
                                   899********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1055.99
//
Query:       gi|121639309|ref|YP_979533.1|  [L=102]
Description: hypothetical protein BCG_3454c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-11   41.8   0.0    8.9e-11   41.5   0.0    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0     5e-15   8.9e-11       1      50 [.      12      63 ..      12      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 5e-15
                                   CEEEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEH...HHHHHHHH CS
                PhdYeFM_antitox  1 mkivsiseakanlselldeveegeepviItrrGkpvaVlvsl...eeyerlqe 50
                                   m++v+++ +++++sell++ve+ge+ + It+rG+pva l +l     ye+l++
  gi|121639309|ref|YP_979533.1| 12 MTSVGVRALRQRASELLRRVEAGET-IEITDRGRPVALLSPLpqgGPYEQLLA 63
                                   99**********************9.*********999988877777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 768.81
//
Query:       gi|121639310|ref|YP_979534.1|  [L=234]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-15   56.0   0.1    5.8e-15   55.1   0.1    1.5  1  DUF772    Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   3.2e-19   5.8e-15       1      66 [.      52     118 ..      52     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.2e-19
                         DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee..l 66 
                                    Grp++p e+ l+l++l++ y+l  + l++++ +++++r+f+++ le  +vp+++tl +  +r +e  +
  gi|121639310|ref|YP_979534.1|  52 GRPSIPMETYLRLMFLKFRYRLGYESLCREVTDSITWRRFCRIPLE-GSVPHPTTLMKLTTRCGEdaV 118
                                    9********************************************9.99*********9999887651 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1753.36
//
Query:       gi|121639311|ref|YP_979535.1|  [L=225]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-08   32.9   0.5    1.7e-07   31.1   0.1    2.0  2  DDE_Tnp_1    Transposase DDE domain
    0.00034   20.8   1.0    0.00036   20.7   0.1    1.5  2  DDE_Tnp_1_6  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.16   1.4e+03     121     143 ..      11      33 ..       5      54 .. 0.80
   2 !   31.1   0.1   1.9e-11   1.7e-07      22     191 ..      63     194 ..      43     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.16
                      DDE_Tnp_1 121 rrgrlrkhdrnkiltksqkrrnk 143
                                    r++ +rk++ +++++  +k+ ++
  gi|121639311|ref|YP_979535.1|  11 RASGRRKAWLRQAINHLEKLIGR 33 
                                    66778999999999999999998 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.9e-11
                      DDE_Tnp_1  22 darwgykggk...ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr...kgklvlaDaGYasaelldtl 95 
                                    dar+  kg      ++gyk++++ ++  g+il+  +  gn +d ++l + ++++ +r    ++ v+aD+G + a++ d+l
  gi|121639311|ref|YP_979535.1|  63 DARPIRKGRLgkpVEFGYKAQVVDNAD-GVILDHSVELGNPADAPQLAPAIERISRRtgrPPRAVTADRGCGDASVEDDL 141
                                    4555333333335789*****999999.9*************************************************** PP

                      DDE_Tnp_1  96 eekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRw 175
                                    ++ gv  + +++k +             ++r   ++++++                                    + R 
  gi|121639311|ref|YP_979535.1| 142 HQLGVRNVAIPRKSK----------PSATRRAFEHRRAFRD---------------------------------KIKWRT 178
                                    *99997776663322..........2222222223333322.................................244444 PP

                      DDE_Tnp_1 176 qiErvFkwlkrkfgld 191
                                    + E  +  lkr++g++
  gi|121639311|ref|YP_979535.1| 179 GSEGRINHLKRSYGWN 194
                                    4444444444444444 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.85   7.6e+03      74     101 ..      17      44 ..       4      48 .. 0.48
   2 !   20.7   0.1     4e-08   0.00036      58     124 ..     155     220 ..     141     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.85
                    DDE_Tnp_1_6  74 kaeykkRaitvEgvfaqikrnlglrrfr 101
                                    ka  ++     E+ ++ + r     r r
  gi|121639311|ref|YP_979535.1|  17 KAWLRQAINHLEKLIGRTERVVDQARSR 44 
                                    3333333344555555555555555555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4e-08
                    DDE_Tnp_1_6  58 selaekarerikseegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    s+  ++ r+  + ++++++ k R  + Eg +  +kr++g +r+ l+G+  +++++   ++a+Nl k+
  gi|121639311|ref|YP_979535.1| 155 SKPSATRRAFEHRRAFRDKIKWR-TGSEGRINHLKRSYGWNRTELTGITGARTWCGHGVFAHNLVKI 220
                                    44555555555555666666666.5***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1478.10
//
Query:       gi|121639312|ref|YP_979536.1|  [L=750]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-34  117.8  17.5    3.4e-34  117.0  17.5    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0  17.5   1.9e-38   3.4e-34       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.9e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pe+laaaa+dlagi+sa+saa+aaaaapt +v+aa+aDeVS ai+alf++haq+yqalsaqa+ fh+qfvqal++
  gi|121639312|ref|YP_979536.1|  1 MSFVIANPEMLAAAATDLAGIRSAISAATAAAAAPTIQVAAAGADEVSLAISALFGQHAQAYQALSAQATIFHDQFVQALTS 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +++ YaaaE 
  gi|121639312|ref|YP_979536.1| 83 GGNLYAAAES 92
                                   ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.02u 0.26s 00:00:01.28 Elapsed: 00:00:00.47
# Mc/sec: 4821.47
//
Query:       gi|121639313|ref|YP_979537.1|  [L=290]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-33  113.3   0.0    8.5e-33  112.5   0.0    1.3  1  MaoC_dehydratas  MaoC like domain
    9.3e-08   32.3   0.0    2.6e-07   30.9   0.0    1.7  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.0   9.4e-37   8.5e-33       6     116 ..     161     271 ..     157     278 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 9.4e-37
                                    TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HH.HHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEE CS
                MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpe.fAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvr 84 
                                    ++++++++ ++++ e+++ +y+l sgD np+H dp+ + ++agf++pI+hG++t++++ +++++elg +v+a++++i++r
  gi|121639313|ref|YP_979537.1| 161 PDRHPDARIDMPTREDQALIYRL-SGDRNPLHSDPWfATQLAGFPKPILHGLCTYGVAGRALVAELGGGVAANITSIAAR 239
                                    799********************.************55688*************************************** PP

                                    E-S--BTTCEEEEEEEEEE.EEEEEEEEEEEEE CS
                MaoC_dehydratas  85 FtkpVlpgdtlkvelevvg.krdvrktkkvevt 116
                                    FtkpV+pg+tl + +++++  r+v++t +v+ +
  gi|121639313|ref|YP_979537.1| 240 FTKPVFPGETLSTVIWRTEpGRAVFRT-EVAGS 271
                                    ******************988888877.55555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.8e-11   2.6e-07       3     123 ..       8     125 ..       6     135 .. 0.79
   2 ?   -1.7   0.0      0.32   2.9e+03      79      95 ..     235     251 ..     182     254 .. 0.45

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.8e-11
                MaoC_dehydrat_N   3 iGaefepvkaevereavrefakavge.tnpayldeeaaraagyrsliaPptflivlat.kapellealg.idlsrllhge 79 
                                    iGa++ep  +e++ ++   +a  vg+ t  + +  e+    g ++ + P   +i+     a     ++g  + + llhg+
  gi|121639313|ref|YP_979537.1|   8 IGAVTEPMLFEWTDRDTLLYAIGVGAgTGDLAFTTENS--HGIDQQVLPTYAVICCPAfGA---AAKVGtFNPAALLHGS 82 
                                    89999*******************88666665555554..477776666666665554255...67775499******** PP

                MaoC_dehydrat_N  80 qefeyhepiraGDelttesriadvydkkgvGalefivvettvtn 123
                                    q +++h+p+ a ++l++++++ad++dk g G+ +++v + +  +
  gi|121639313|ref|YP_979537.1|  83 QGIRLHAPLPAAGKLSVVTEVADIQDK-GEGKNAIVVLRGRGCD 125
                                    **************************8.6899999987776655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.32
                MaoC_dehydrat_N  79 eqefeyhepiraGDelt 95 
                                    +   ++ +p+ +G++l+
  gi|121639313|ref|YP_979537.1| 235 SIAARFTKPVFPGETLS 251
                                    33345556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2132.53
//
Query:       gi|121639314|ref|YP_979538.1|  [L=236]
Description: lipoprotein lpqD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-21   76.2   0.0    3.2e-21   75.9   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   1.8e-25   3.2e-21       1     191 [.      37     229 ..      37     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.8e-25
                                    EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS- CS
                     His_Phos_1   1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrE 79 
                                    l ++R +++++na+g+       + L+++G+++A+++a+ ++++++d iysSp+   +qTa ++a++lg +ve+ +gL+ 
  gi|121639314|ref|YP_979538.1|  37 LTFIRNAQSQANADGIiDTDMPGSGLSADGKAEAQQVAHQVSRRDVDSIYSSPMAADQQTAGPLAGELGKQVEILPGLQA 116
                                    579***********98444567888******************************************************* PP

                                    ---GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHH.HHHHH CS
                     His_Phos_1  80 idfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvira.llarl 158
                                    i+ G + g++ + ++++y  ++++wl+++ ++++pg  s  ++ +  +aa++++ ++ ++   +v+s g +i +  l+ +
  gi|121639314|ref|YP_979538.1| 117 INAGWFNGKPESMANSTYMLAPADWLAGDVHNTIPGSISGTEFNSQFSAAVRKIYDSGHNT-PVVFSQGVAIMIwTLMNA 195
                                    *********************************************************9986.777777776655145666 PP

                                    HT--GGGGGGB---TT-EEEEEE-S.S-EEEEEE CS
                     His_Phos_1 159 lglpleelrrleldnaslsvlefde.ggwrlvrl 191
                                     +   + l  ++l+n + +v++ ++  gwrlv++
  gi|121639314|ref|YP_979538.1| 196 RNSRDSLLTTHPLPNIGRVVITGNPvTGWRLVEW 229
                                    6666777777777998888888887556888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1797.30
//
Query:       gi|121639315|ref|YP_979539.1|  [L=650]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-50  171.9   0.1    1.1e-46  158.7   0.1    2.2  2  adh_short        short chain dehydrogenase
    3.4e-36  125.0   2.2      1e-33  116.9   1.0    2.3  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    3.5e-30  105.0   0.0    9.8e-29  100.3   0.0    2.8  2  NAD_binding_4    Male sterility protein
    2.8e-22   79.5   1.8    1.9e-14   54.0   0.4    2.3  2  KR               KR domain
    1.2e-19   70.8   0.4    1.6e-13   50.7   0.0    2.7  2  Epimerase        NAD dependent epimerase/dehydratase family
    1.7e-15   57.4   2.5    1.3e-09   38.3   0.0    2.4  2  NAD_binding_10   NAD(P)H-binding
    1.6e-09   37.6   0.1    1.4e-06   28.0   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.7e-05   22.0   0.0    0.00022   20.4   0.0    1.8  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.9e-05   22.3   1.1       0.21   11.1   0.5    2.3  2  NmrA             NmrA-like family
    0.00015   21.0   0.3       0.81    8.7   0.0    3.2  2  RmlD_sub_bind    RmlD substrate binding domain
    0.00019   20.7   0.0       0.03   13.4   0.0    2.2  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.054   13.3   0.0    1.5  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
       0.11   11.8   0.0       0.23   10.8   0.0    1.4  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00016      0.22       4      90 ..       4      87 ..       2     113 .. 0.74
   2 !  158.7   0.1   8.2e-50   1.1e-46       2     189 ..     354     543 ..     353     548 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                   EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE- CS
                      adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnN 84
                                   +vtG+++ IGr ++ +l+    +  + +   ++     + l  + g+++ ++ +D+t+ e    l e+ +++lg +d + ++
  gi|121639315|ref|YP_979539.1|  4 VVTGGTGFIGRHVVSRLLDGRPEARLWALVRRQSLSRFERLAGQwGDRVRPLVGDLTELE----LSERTIAELGDIDHVLHC 81
                                   8****************9876666664444444445566666666999*********776....556666777********* PP

                                   --SS-- CS
                      adh_short 85 AGitgs 90
                                   A+++ +
  gi|121639315|ref|YP_979539.1| 82 AAVHDT 87
                                   **9433 PP

  == domain 2  score: 158.7 bits;  conditional E-value: 8.2e-50
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                    +v++tGassGIGra a ++ak+Ga+v++++r+ ++l e+++e++++g +a+a+++Dvtd+++ve +v+++  +++++d L
  gi|121639315|ref|YP_979539.1| 354 HVIITGASSGIGRASAIAVAKRGATVFALARNGNALDELVTEIRAHGGQAHAFTCDVTDSASVEHTVKDILGRFDHVDYL 433
                                    89****************************************************************************** PP

                                    EE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                    vnNAG    +s+  s     ++erv++vN++g++ ++ a+lp++ +++ G++vnvsS   + +++ +++Y  +Kaa++++
  gi|121639315|ref|YP_979539.1| 434 VNNAGRsiRRSVVNSTDRLHDYERVMAVNYFGAVRMVLALLPHWRERRFGHVVNVSSAGVQARNPKYSSYLPTKAALDAF 513
                                    ******744555555556667*********************************************************** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdmake 189
                                    ++ +a e  ++ i+ ++++ +lv+T+m  +
  gi|121639315|ref|YP_979539.1| 514 ADVVASETLSDHITFTNIHMPLVATPMIVP 543
                                    **************************9765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0     0.003       4.1      21      93 ..      29      95 ..      12     123 .. 0.67
   2 !  116.9   1.0   7.2e-37     1e-33       1     193 [.     359     555 ..     359     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                                   EEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HH CS
                   adh_short_C2 21 vvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsre 93
                                   +++  +++++ +r e+la + g +v  l  D t+ e      e++ +++g +D ++++a++ ++     ++++r+
  gi|121639315|ref|YP_979539.1| 29 LWALVRRQSL-SRFERLAGQWGDRVrpLVGDLTELEL----SERTIAELGDIDHVLHCAAVHDT---TWADATRA 95
                                   4444444444.78889999999888778888887765....5556667899*********9998...33333333 PP

  == domain 2  score: 116.9 bits;  conditional E-value: 7.2e-37
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIGra A a+a++Ga+v +  +n +a ++ v+e+ + +g++ ++ cDVtd ++ve++v+++  +f+++D+lvnnag
  gi|121639315|ref|YP_979539.1| 359 GASSGIGRASAIAVAKRGATVFALARNGNAlDELVTEIRAHGGQAhAFTCDVTDSASVEHTVKDILGRFDHVDYLVNNAG 438
                                    899*******************999999999*********9997758********************************* PP

                                    --EGCSS-GGGH..-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpflet..sreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtry 154
                                     + +   ++++      +++r+++vn  ++++++ a+lp+ +e+  g +vn+ss g +   p+y+ y  +Kaal a++  
  gi|121639315|ref|YP_979539.1| 439 RSIR--RSVVNStdRLHDYERVMAVNYFGAVRMVLALLPHWRERrfGHVVNVSSAGVQARNPKYSSYLPTKAALDAFADV 516
                                    ****..66666524569**********************8888889********************************** PP

                                    HHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHH CS
                   adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgikgfdelleele 193
                                    +A e  ++ i+   ++  +++T++    ++ + +++ ++
  gi|121639315|ref|YP_979539.1| 517 VASETLSDHITFTNIHMPLVATPMIVPSRRLNPVRAISA 555
                                    ************************655555444444443 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   7.1e-32   9.8e-29       1     256 [.       5     218 ..       5     219 .. 0.86
   2 ?    1.2   0.0      0.12   1.6e+02      99     144 ..     450     498 ..     426     530 .. 0.73

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 7.1e-32
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG+TGF+G++++ +LL+ +pe ++++lvR +s  s  eRl       +        + +r+++++GDl+e  l Lse++
  gi|121639315|ref|YP_979539.1|   5 VTGGTGFIGRHVVSRLLDGRPEARLWALVRRQSL-SRFERL------AGQ-------WGDRVRPLVGDLTE--LELSERT 68 
                                    7*****************************9976.666666......222.......3789********97..669**** PP

                                    HHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                    + el   +d+++h+aA  +          +  ++tr v+ela++l ++  ++hvS+ +v+g+  g+              
  gi|121639315|ref|YP_979539.1|  69 IAEL-GDIDHVLHCAAVHD---------TTWADATRAVIELAARLDAT--FHHVSSIAVAGDFAGH-------------- 122
                                    ****.99*********876.........566789*********99777..******8899999988.............. PP

                                    HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHH.H-EEES-SB CS
                  NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllglia.kgvlpeilg 239
                                      e + + ++ lp+ Y +  ++aE+lvr++    gl+  i+Rp +++g+s tG +++ d g++ l+g+ a   vlp++++
  gi|121639315|ref|YP_979539.1| 123 YTEADFDVGQRLPTPYHRMTFEAERLVRSTP---GLRYRIYRPAVVVGDSRTGEMDTID-GPYYLFGVLAkLAVLPSFTP 198
                                    5788999***********************9...9************************.77777776661566777777 PP

                                    ---TT...--EEEHHHHHHH CS
                  NAD_binding_4 240 dkeav...ldlvpvDyvana 256
                                    +        ++vpvDyva+a
  gi|121639315|ref|YP_979539.1| 199 MLLPDigrTNIVPVDYVADA 218
                                    64322344**********98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                    S.STTSSEEHHHHHHHHHH.HHHHHTSSS--...-EEEEEEGGGTTS-T CS
                  NAD_binding_4  99 nfdepykellrvNveGtre.vlelakklkkl..kvllhvSTayvngere 144
                                    +  ++y+++++vN  G+++ vl l    ++    +++ vS+a v+  + 
  gi|121639315|ref|YP_979539.1| 450 DRLHDYERVMAVNYFGAVRmVLALLPHWRERrfGHVVNVSSAGVQARNP 498
                                    45568999*****999765166777766665335777788877766555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.6e-08   2.2e-05       3      96 ..       3      89 ..       2     101 .. 0.87
   2 !   54.0   0.4   1.4e-17   1.9e-14       3     168 ..     355     522 ..     354     537 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-08
                                   EEEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR  3 ylitGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppi 82
                                   y++tGG+G +G++++  l++   +++l  l R+     +s +++++l+ + g +v+ +  D+++ +  e++++e+      i
  gi|121639315|ref|YP_979539.1|  3 YVVTGGTGFIGRHVVSRLLDGRpEARLWALVRR-----QSLSRFERLAGQwGDRVRPLVGDLTELELSERTIAELG----DI 75
                                   9****************99855599*******9.....4556778888877**********************996....9* PP

                                   -EEEE--------- CS
                             KR 83 kGvihaAgvlrdkl 96
                                     v+h+A v +++ 
  gi|121639315|ref|YP_979539.1| 76 DHVLHCAAVHDTTW 89
                                   *******9987654 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1.4e-17
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                    ++itG+  g+G++ a   a++ga+    l+R+    ++ ++l++e++a+g + +++ +Dv+d+++ve+++++i  +++ +
  gi|121639315|ref|YP_979539.1| 355 VIITGASSGIGRASAIAVAKRGATV-FALARN---GNALDELVTEIRAHGGQAHAFTCDVTDSASVEHTVKDILGRFDHV 430
                                    68********************975.566888...3456679************************************** PP

                                    -EEEE---------TTT--H..HHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  83 kGvihaAgvlrdklleemta..edleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNafl 156
                                       ++ Ag +  + + + t+   d+e+v+a    Ga  +  +l +    ++  ++v +SS++    +++ ++Y  + a l
  gi|121639315|ref|YP_979539.1| 431 DYLVNNAGRSIRRSVVNSTDrlHDYERVMAVNYFGAVRMVLALLPhwreRRFGHVVNVSSAGVQARNPKYSSYLPTKAAL 510
                                    ********9888888877753379********99998766555444666999**************************** PP

                                    HHHHHHHHHHHH CS
                             KR 157 Dalaeyrrsqgl 168
                                    Da+a+  +s+ l
  gi|121639315|ref|YP_979539.1| 511 DAFADVVASETL 522
                                    ****98887766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.2e-16   1.6e-13       2     176 ..       4     169 ..       3     178 .. 0.89
   2 !   17.1   0.2   2.1e-06    0.0029       1     118 [.     355     493 ..     355     510 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.2e-16
                                    EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHH.T-SEEEE--S CS
                      Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl.....elveldltdrsalerlfkee.qpdavihlAa 73 
                                    +VtG+tGfiG+++v +ll+     ++++l r++s s+++rl+       +   +dlt+ +  er ++e  ++d+v+h+Aa
  gi|121639315|ref|YP_979539.1|   4 VVTGGTGFIGRHVVSRLLDGRpeARLWALVRRQSLSRFERLAGQwgdrvRPLVGDLTELELSERTIAELgDIDHVLHCAA 83 
                                    7*****************9887677*****************99***99999**************************99 PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS--..--SSHHHHHHHHHHH CS
                      Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl..kpnspYaaaKlagek 151
                                    v +  +            +  t+ ++e a + ++  ++++sS +v G+ a   +e +     +  +  +pY +    +e+
  gi|121639315|ref|YP_979539.1|  84 VHDTTW------------ADATRAVIELAARLDA-TFHHVSSIAVAGDFAGHYTEADF---DVgqRLPTPYHRMTFEAER 147
                                    988888............456889**********.****************6455555...44457789*********** PP

                                    HHHHHHHHHT-EEEEEEESEEESTT CS
                      Epimerase 152 lveayaaqyglnaiilrlfnlyGpr 176
                                    lv++   + gl++ i r+  ++G  
  gi|121639315|ref|YP_979539.1| 148 LVRS---TPGLRYRIYRPAVVVGDS 169
                                    9997...589***********9987 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.1e-06
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHH....H.T-SEEE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfke....e.qpdavi 69 
                                    +++tGa+  iG+a + a++++g +v +l+r+ +a  +   e        +  ++d+td++++e  +k+    + ++d+ +
  gi|121639315|ref|YP_979539.1| 355 VIITGASSGIGRASAIAVAKRGATVFALARNGNALDELVTEIRahggqaHAFTCDVTDSASVEHTVKDilgrFdHVDYLV 434
                                    68*****************************66666555444499***************88777765332244777888 PP

                                    E--S---HHHHHHSHHHHHHHHTHHHHHHHHHHH..........HHTCTEEEEEEEGGG CS
                      Epimerase  70 hlAavggvaassedpadfieknlqgtlnlleaar..........kagvkrllflsSsev 118
                                    + A+ +  +  +++  ++ +   ++++n + a+r          ++    ++++sS+ v
  gi|121639315|ref|YP_979539.1| 435 NNAGRSIRRSVVNSTDRLHDYERVMAVNYFGAVRmvlallphwrERRFGHVVNVSSAGV 493
                                    88774433333333333333333344444444433333334443445556777777665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   9.2e-13   1.3e-09       1     152 [.       7     172 ..       7     181 .. 0.80
   2 !   18.2   1.0   1.3e-06    0.0018       1     120 [.     359     485 ..     359     526 .. 0.63

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 9.2e-13
                                    TTTSHHHHHHHHHHHHC-.T-EEEEEETTH..HHCHHHHCT..TTCEEEE--TT-CCHHHHHHT...T-SEEEES---TC CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnp..eklaeleae..eglevvegdvtdvedlaealk...gadaVvsalgggg 72 
                                    G+tG +Gr++v++ll+ + + ++ alvR++  +++++l+ +  ++++ ++gd+t+ e  +++++   ++d V+ +++ ++
  gi|121639315|ref|YP_979539.1|   7 GGTGFIGRHVVSRLLDGRpEARLWALVRRQslSRFERLAGQwgDRVRPLVGDLTELELSERTIAelgDIDHVLHCAAVHD 86 
                                    9***************999999******963369999986655899********976666666545499*9999998888 PP

                                    C.HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHH....HHHHCCHHHHHHHHHHHHHHHHS.SSEEEEEEE-CE CS
                 NAD_binding_10  73 k.deegaknivdaakeagvkRfvlvsaigvgdevpgefge....wnkellkaylaakraaeellras.gldwTivrpggL 146
                                    +  +++++++++ a + +   f  vs+i v  + +g+  e    + ++l  +y++   +ae+l+r++ gl + i rp+  
  gi|121639315|ref|YP_979539.1|  87 TtWADATRAVIELAARLDA-TFHHVSSIAVAGDFAGHYTEadfdVGQRLPTPYHRMTFEAERLVRSTpGLRYRIYRPAVV 165
                                    867789******9999888.789999999887777664431111567899****************77**********98 PP

                                    E-ST.-- CS
                 NAD_binding_10 147 tdep.tt 152
                                      +  t+
  gi|121639315|ref|YP_979539.1| 166 VGDSrTG 172
                                    7665254 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH....HHHCT.TTCEEEE--TT-CCHHHHHHT.......T-SEEEES- CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla....eleae.eglevvegdvtdvedlaealk.......gadaVvsal 68 
                                    GA+ ++Gr+ +   ++r g +v al+Rn + l+    e++a+  ++++++ dvtd++++++++k       ++d  v ++
  gi|121639315|ref|YP_979539.1| 359 GASSGIGRASAIAVAKR-GATVFALARNGNALDelvtEIRAHgGQAHAFTCDVTDSASVEHTVKdilgrfdHVDYLVNNA 437
                                    9********99888888.6*********888872222556666899******************5555444444444444 PP

                                    --TCCHHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHH CS
                 NAD_binding_10  69 ggggkdeegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkay 120
                                    g++ +  ++++n  d +  ++ +R+  v ++g+ + v   ++ w ++ ++++
  gi|121639315|ref|YP_979539.1| 438 GRSIR--RSVVNSTDRL--HDYERVMAVNYFGAVRMVLALLPHWRERRFGHV 485
                                    43333..2322222222..445555555555555444444444444444433 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     1e-09   1.4e-06       2      85 ..       5      84 ..       4      89 .. 0.84
   2 !    7.5   0.1    0.0017       2.3       2     119 ..     357     479 ..     356     493 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-09
                                   EETTTSHHHHHHHHHHHHC..T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.T-SEEE CS
                  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlek..gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.qpdevy 80
                                   +TG++GfiG +++ +Ll+   + + + +vrr+s+ +++r++           ++++   gDlt+ +  er +ae  ++d v+
  gi|121639315|ref|YP_979539.1|  5 VTGGTGFIGRHVVSRLLDGrpEARLWALVRRQSLSRFERLAGQ-------WGDRVRPLVGDLTELELSERTIAELgDIDHVL 79
                                   9****************98345667889999998766666542.......35689999****************989***** PP

                                   E--S- CS
                  GDP_Man_Dehyd 81 nLAAq 85
                                   + AA 
  gi|121639315|ref|YP_979539.1| 80 HCAAV 84
                                   **995 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0017
                                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.....T- CS
                  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.....qp 76 
                                    iTG +  iG   a    ++g +v+ + r+ ++     +++l ++ +++  ++ + + +D+tDs+s+e+ ++++     ++
  gi|121639315|ref|YP_979539.1| 357 ITGASSGIGRASAIAVAKRGATVFALARNGNA-----LDELVTEIRAH-GGQAHAFTCDVTDSASVEHTVKDIlgrfdHV 430
                                    89999999999999999*****9999887666.....55555555555.5789999***************998844445 PP

                                    SEEEE--S---...HHHHT...TSHHHHHHHHTHHHHHHHHHHHHCT.. CS
                  GDP_Man_Dehyd  77 devynLAAqsh...Vdvsf...ekPeytaevnvlGtlrLLeairalgle 119
                                    d  +n A+ s    V +s    ++ e+++ vn  G++r++ a   +++e
  gi|121639315|ref|YP_979539.1| 431 DYLVNNAGRSIrrsVVNSTdrlHDYERVMAVNYFGAVRMVLALLPHWRE 479
                                    5556666665422233332111334566777777777776666666654 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00022       1      81 [.       4      89 ..       4     155 .. 0.78
   2 ?   -1.8   0.0       0.9   1.2e+03      46      67 ..     402     423 ..     374     447 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                      3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.....viegDvtdkdkleeale...gvdvvihla 74
                                   vvtGg+GF+Gr++v++L++     e r   l+ +++l ++++++  +       + gD+t+ +  e+ +    ++d v+h a
  gi|121639315|ref|YP_979539.1|  4 VVTGGTGFIGRHVVSRLLDGR--PEARLWALVRRQSL-SRFERLAGQWgdrvrPLVGDLTELELSERTIAelgDIDHVLHCA 82
                                   8*****************998..58899888888887.445444333224556999**999877776654122789999999 PP

                      3Beta_HSD 75 slvdvag 81
                                   ++ d + 
  gi|121639315|ref|YP_979539.1| 83 AVHDTTW 89
                                   9988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.9
                      3Beta_HSD  46 vkkviegDvtdkdkleealegv 67 
                                     ++  ++Dvtd +++e+ ++++
  gi|121639315|ref|YP_979539.1| 402 QAHAFTCDVTDSASVEHTVKDI 423
                                    344789*******999988775 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00046      0.63       2      40 ..       4      44 ..       3      70 .. 0.87
   2 !   11.1   0.5   0.00015      0.21       1      64 [.     355     422 ..     355     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                                   EESSTTSHHHHHHHHHHHH..HT-EEEEEES-S-SHHHHHH CS
                           NmrA  2 lviGaTGrqGksvvrallk..aghkvralvRdtkselaksl 40
                                   +v+G+TG +G++vv+ ll+   + +  alvR ++  + + l
  gi|121639315|ref|YP_979539.1|  4 VVTGGTGFIGRHVVSRLLDgrPEARLWALVRRQSLSRFERL 44
                                   69****************988999999****9876666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                                    EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvealkg 64 
                                    ++++Ga+  +G++ + a++k+g +v+al R+     el++++ + G +      d+ d +s+++ +k+
  gi|121639315|ref|YP_979539.1| 355 VIITGASSGIGRASAIAVAKRGATVFALARNGnaLDELVTEIRAHGGQAHafTCDVTDSASVEHTVKD 422
                                    6799**************************98667899999999997654358888899998888876 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00059      0.81       1     104 [.       1     115 [.       1     177 [. 0.63
   2 !    7.9   0.0     0.001       1.4       2      50 ..     354     423 ..     353     437 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00059
                                    EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT....................T--TTSHHHHHHHHHHH.--SEEEE CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae..eglevlaltre....................eldltdaeavaellkea.kpdvvvn 57 
                                    m+ +vtG++G +G++++ +l     ++ + al r+                      dlt+ e  +++++e  + d v +
  gi|121639315|ref|YP_979539.1|   1 MRYVVTGGTGFIGRHVVSRLLDgrPEARLWALVRRqslsrferlagqwgdrvrplVGDLTELELSERTIAELgDIDHVLH 80 
                                    77888888888888887766543456778888666688888888888888888777788888877777777535678888 PP

                                    ------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGG CS
                  RmlD_sub_bind  58 aAAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyV 104
                                    +AA ++   a            +a++a+ e+aa+ +a++ hvS+  V
  gi|121639315|ref|YP_979539.1|  81 CAAVHDTTWA------------DATRAVIELAARLDATFHHVSSIAV 115
                                    8887776555............3455555555555555555555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkea 50 
                                    ++++tGa+  +G++ a ++a++g+ v al r+                     ++d+td+++v++++k++
  gi|121639315|ref|YP_979539.1| 354 HVIITGASSGIGRASAIAVAKRGATVFALARNgnaldelvteirahggqahafTCDVTDSASVEHTVKDI 423
                                    689****************************9***********************************986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.2e-05      0.03       2      88 ..       4      85 ..       3      95 .. 0.81
   2 !    5.0   0.0    0.0081        11       1      75 [.     355     422 ..     355     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT...T-SEEE CS
                Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.kvdvvf 82
                                   +vtG++G iG+++v+++l+ +p+  +      ++l ++e+    +  +     ++ p++gd+++ e  e+++ el ++d v+
  gi|121639315|ref|YP_979539.1|  4 VVTGGTGFIGRHVVSRLLDGRPEARLWALVRRQSLSRFERLA-GQWGD-----RVRPLVGDLTELELSERTIAELgDIDHVL 79
                                   69******************9988777777777888888755.34444.....34599********999999886379**** PP

                                   E----- CS
                Polysacc_synt_2 83 haAAlK 88
                                   h+AA+ 
  gi|121639315|ref|YP_979539.1| 80 HCAAVH 85
                                   ****86 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0081
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT. CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekalee 75 
                                    v++tGa+  iG++    ++k+ + +++ l r+ ++l+e+ +e++++  + +      ++ +dv+d++++e+++++
  gi|121639315|ref|YP_979539.1| 355 VIITGASSGIGRASAIAVAKRGA-TVFALARNGNALDELVTEIRAHGGQAH------AFTCDVTDSASVEHTVKD 422
                                    79**********99998888765.6788899999********976555532......34799*999999998874 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.9e-05     0.054      40      63 ..     352     375 ..     337     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-05
                                    -SEEEEESTSSHHHHHHHHHHHHS CS
                Eno-Rase_NADH_b  40 pkkvLviGaStGYGLAsriaaafg 63 
                                     ++v++ GaS+G G As ia+a  
  gi|121639315|ref|YP_979539.1| 352 GRHVIITGASSGIGRASAIAVAKR 375
                                    489*****************8754 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.23      31      77 ..     347     393 ..     344     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                    T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHH CS
                  THF_DHG_CYH_C  31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeit 77 
                                    +  l g++v++ G+s+ +g++ a+ +++++atV  + ++ + l+e++
  gi|121639315|ref|YP_979539.1| 347 NDPLLGRHVIITGASSGIGRASAIAVAKRGATVFALARNGNALDELV 393
                                    56788*****************************9999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 4723.05
//
Query:       gi|121639316|ref|YP_979540.1|  [L=287]
Description: cyclopropane-fatty-acyl-phospholipid synthase 1 cmaA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-126  421.4   0.0   1.6e-126  421.2   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    9.3e-10   39.1   0.0    1.8e-09   38.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.5e-08   34.7   0.0    2.4e-08   34.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    3.8e-08   33.9   0.0    7.9e-08   32.8   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.6e-06   28.8   0.0    2.7e-06   28.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0037   17.1   0.0     0.0063   16.3   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.019   13.9   0.0    1.4  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.016   14.8   0.0      0.027   14.0   0.0    1.4  1  MTS              Methyltransferase small domain
      0.022   14.5   0.0      0.031   14.0   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.16   11.6   0.1       0.29   10.7   0.1    1.4  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.2   0.0  8.7e-130  1.6e-126       3     273 .]       5     283 ..       3     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.2 bits;  conditional E-value: 8.7e-130
                                    SXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                           CMAS   3 kkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrrave 82 
                                     k++++n++ahYDls+dff+lfldpt+tYsCAyferddmtL+eAq+aK+dl+l+kl+l+pGmtlLd+GcGWG++++rave
  gi|121639316|ref|YP_979540.1|   5 LKPHFANVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVE 84 
                                    68899*************************************************************************** PP

                                    HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EE CS
                           CMAS  83 rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGll 162
                                    +ydv+vvglTlSk+qa+++++ v++ ++ r+++v+l+++e++de+vdr+vs+gafeh+g+e+yd+ff+ +++ll++dG++
  gi|121639316|ref|YP_979540.1|  85 KYDVNVVGLTLSKNQANHVQQLVANSESLRSKRVLLAGWEQFDEPVDRIVSIGAFEHFGHERYDAFFSLAHRLLPADGVM 164
                                    ******************************************************************************** PP

                                    EEEEEEE--HHHHHCTTCCC........HHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHH CS
                           CMAS 163 llhtitslhkkelaerglkl........kfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealq 234
                                    llhtit lh+ke++ergl++        kfi +eiFPgG+lpsi +++e++s++gftv++v+sl++hYakTL++W++alq
  gi|121639316|ref|YP_979540.1| 165 LLHTITGLHPKEIHERGLPMsftfarflKFIVTEIFPGGRLPSIPMVQECASANGFTVTRVQSLQPHYAKTLDLWSAALQ 244
                                    *******************9************************************************************ PP

                                    HTHHHHHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEEE CS
                           CMAS 235 enkdeaialvseevarmyelYLagcaeaFrkgyidvaql 273
                                    +nk +aial+seev+++y++YL+gcae+Fr gyidv+q+
  gi|121639316|ref|YP_979540.1| 245 ANKGQAIALQSEEVYERYMKYLTGCAEMFRIGYIDVNQF 283
                                    *************************************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0     1e-12   1.8e-09       2      97 .]      69     162 ..      68     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1e-12
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    Ld+GcG G +++++ +++ + +v+g+ +s+++ +++++ +++++ +++  +  +  +++ d+ +D +vs+ga++h+ +e+
  gi|121639316|ref|YP_979540.1|  69 LDVGCGWGATMMRAVEKY-DVNVVGLTLSKNQANHVQQLVANSE-SLRSKRVLLAGWEQFDEPVDRIVSIGAFEHFGHER 146
                                    9****************8.7********************7765.77777777788888899********99******** PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    ++++++ ++r+L  +G
  gi|121639316|ref|YP_979540.1| 147 YDAFFSLAHRLLPADG 162
                                    ***********98776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.3e-11   2.4e-08      11     124 ..      51     173 ..      40     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.3e-11
                Methyltransf_23  11 dklerllpk..lraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkf 83 
                                    +k++ +l+k  l++g+ +Ld+GcG G ++++  +++ ++v+g  ls ++ + ++    +    +++ +    +++ ++  
  gi|121639316|ref|YP_979540.1|  51 AKIDLALGKlgLQPGMTLLDVGCGWGaTMMRAVEKYDVNVVGLTLSKNQANHVQqlvaNSESLRSKRVLLAGWEQFDEPV 130
                                    66776776666899************8899999**************9999886666644444444444558889999** PP

                Methyltransf_23  84 dlIvlrevlehvpd..ppellrqiatllkpgGylllseplasl 124
                                    d Iv++  +eh+ +  + + ++ +++ll  +G++ll++++  +
  gi|121639316|ref|YP_979540.1| 131 DRIVSIGAFEHFGHerYDAFFSLAHRLLPADGVMLLHTITGLH 173
                                    *************76799********************87555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   4.4e-11   7.9e-08       1      95 [.      69     165 ..      69     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.4e-11
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                    LdvGcG G+ +    +++  +vvg+ lsk++ + +++ + +++   + +++ a  e+  f d+ +D +vs  +++h+  e
  gi|121639316|ref|YP_979540.1|  69 LDVGCGWGATMMRAVEKYdVNVVGLTLSKNQANHVQQLVANSESlrSKRVLLAGWEQ--F-DEPVDRIVSIGAFEHFghE 145
                                    8*******99998888888*************9999999999877744667777776..4.77***************99 PP

                                    CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                    + +++++ ++R+L  +G+++
  gi|121639316|ref|YP_979540.1| 146 RYDAFFSLAHRLLPADGVML 165
                                    9999**********999876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.5e-09   2.7e-06       1      98 [.      69     163 ..      69     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG G+++++  ek  d++++g+ +s+++ ++ ++  a  e ++ ++v l   + +d+     +D +v++++++h+ 
  gi|121639316|ref|YP_979540.1|  69 LDVGCGWGATMMRAVEK-YDVNVVGLTLSKNQANHVQQLVANSESLRSKRVLLAGWEQFDE----PVDRIVSIGAFEHFg 143
                                    8****************.9**************9999999999999999999999997766....9*************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGr 98 
                                     +  +++++ +++lL  +G+
  gi|121639316|ref|YP_979540.1| 144 hERYDAFFSLAHRLLPADGV 163
                                    88888999999999988886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.5e-06    0.0063       2     113 ..      63     170 ..      62     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre...naqklgldnveFeqgdieeleklledekfDli 78 
                                    + g+++lD+GCG G+   ++ e+   + +vvG+  s++  ++ ++   n+++l +   ++  + +e+++     e++D i
  gi|121639316|ref|YP_979540.1|  63 QPGMTLLDVGCGWGATMMRAVEK--YDVNVVGLTLSKNQANHVQQlvaNSESLRS--KRVLLAGWEQFD-----EPVDRI 133
                                    5789*****************64..3799*****999999998885335555555..588899999988.....789*** PP

                Methyltransf_31  79 lsnevlnaladp..dkileeiervlkpggilliedpr 113
                                    +s +++ ++ +   d+++  ++r+l  +g++l+ ++ 
  gi|121639316|ref|YP_979540.1| 134 VSIGAFEHFGHEryDAFFSLAHRLLPADGVMLLHTIT 170
                                    **99997776643389999999999999999888776 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.019     116     219 ..      65     168 ..      50     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                    T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTT...SSEEEE---GGGS-T---EEEEEEES-G CS
                 Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllged...qrahllplgieqlpeleafdtvfsmGvl 192
                                    g t+ldvGcg G  ++r v +    vvG+  s+      + v++l+++    + + +l  g eq++  e  d + s+G +
  gi|121639316|ref|YP_979540.1|  65 GMTLLDVGCGWGATMMRAVEKYDVNVVGLTLSKNQ---ANHVQQLVANSeslRSKRVLLAGWEQFD--EPVDRIVSIGAF 139
                                    6789************************9877654...4444454444311144455556888876..467888888888 PP

                                    GG-.S-HHHHHHHHHCTEE.EEEEEEEEE CS
                 Methyltransf_9 193 yhr.rsPldhllqlkdqlv.kgGelvlet 219
                                     h  +   d +  l + l  ++G ++l t
  gi|121639316|ref|YP_979540.1| 140 EHFgHERYDAFFSLAHRLLpADGVMLLHT 168
                                    77424556777777665541466666655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05     0.027      32     137 ..      65     166 ..      54     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTC CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagk 111
                                      ++lD+GcG+G+  + + ++++ + v l+  + +A ++ +  ++++ l+ + v   + e+++ + +d ivs   f +  
  gi|121639316|ref|YP_979540.1|  65 GMTLLDVGCGWGATMMRAVEKYDVNVVGLTLSKNQANHVQQLVANSESLRSKRVLLAGWEQFD-EPVDRIVSIGAFEHFG 143
                                    5678*********99999999988888888888999999999999999999999999999999.99*****988886655 PP

                                    HCHHHHHHHHHHHHHHHEEEEEEEEE CS
                            MTS 112 atelavaeeliaeAkeaLkegGeLli 137
                                    +   +  ++++  A++ L  +G +l+
  gi|121639316|ref|YP_979540.1| 144 H---ERYDAFFSLAHRLLPADGVMLL 166
                                    5...5777899999999999998876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.031      64     122 ..      55     111 ..      35     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCT CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkld 122
                                    lal  l l++g+  L+vG+G G  + ++  + + + +vv++  +k+ +++ ++ + +++
  gi|121639316|ref|YP_979540.1|  55 LALGKLGLQPGMTLLDVGCGWG--ATMMRAVEKYDVNVVGLTLSKNQANHVQQLVANSE 111
                                    5667789**********99887..56677777778899998877776666666555554 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00016      0.29      11      51 ..      62     102 ..      53     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                           MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvae 51 
                                    ++pg ++ld+GcG G  +    e+ +v+  Gl l+++  ++
  gi|121639316|ref|YP_979540.1|  62 LQPGMTLLDVGCGWGATMMRAVEKYDVNVVGLTLSKNQANH 102
                                    578999*********988888899********999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1981.78
//
Query:       gi|121639317|ref|YP_979541.1|  [L=308]
Description: nucleoside hydrolase iunH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-73  247.5   0.0    2.5e-73  247.3   0.0    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.3   0.0   1.4e-77   2.5e-73       3     305 .]       4     295 ..       2     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 1.4e-77
                                    EEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S-SHHHH CS
                   IU_nuc_hydro   3 vilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.kaaaeih 81 
                                    v  D+D+GiDDalA++++la+ p+ +l+gi ++ Gn  + q+++n l++l +l+g+ dipv +Ga++pl  + ++++++h
  gi|121639317|ref|YP_979541.1|   4 VFADVDTGIDDALAVIYLLAS-PDADLVGIASTGGNIAVGQVCANNLSLL-ELCGAADIPVSKGADEPLGGRwPDHPKFH 81 
                                    678************999995.99**************************.9999999**********9888999999** PP

                                    TTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE---SSS--S CS
                   IU_nuc_hydro  82 GedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGGaftarGN 161
                                    G +G+g ++lp+++r+ ++ +a  a+i a+   +++ g++  ++tGplTN+Alalr +p l+++++rlviMGG f+++  
  gi|121639317|ref|YP_979541.1|  82 GPKGIGYAELPASNRRLTDYDATTAWIAAA---HSHAGDLIGLVTGPLTNLALALRAEPALPRLLRRLVIMGGMFDGQ-- 156
                                    ***********************9999888...888878*************************************88.. PP

                                    SSSSS-HHHHHSHHHHHHHHHT...S-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHH..HHHHHHHHHHHHHHHH CS
                   IU_nuc_hydro 162 vtpvaEfNifvDPeAAkiVles...apvkitlvpldvthkvqalltseeveelaalekglga..fladllefyikaykea 236
                                      p  E+Ni vDPeAA+ V+++   +++  ++++ld+t+  ++++t++ +++la++  ++++  +++d+l+fy+++++ +
  gi|121639317|ref|YP_979541.1| 157 --PITEWNIRVDPEAASEVFTAwagQRQLPIVCGLDLTR--RVAMTPDILARLASVCGSSPVmrVIEDALRFYFESHEAR 232
                                    ..9*****************99865333679********..8889*******877754444467***********99999 PP

                                    HHSSEEE-HHHHHHHHHH-GGGEEEEEEEEEEESSSSTTTTEEEEETSTTTTS--EEEEEEE-HHHHHH CS
                   IU_nuc_hydro 237 egsdgaplhDplavavaldpelvttkrlavdveleggltrGrtvvdlrrlkkaknvkvatevdverfle 305
                                     +++ a++hDpla+ava+dpel+tt++++vdv+      +G+tv  +++ k+++n+++ ++vd + f++
  gi|121639317|ref|YP_979541.1| 233 GHGYLAYMHDPLAAAVAMDPELLTTRTATVDVDP-----TGATVT-DWSGKRNPNARIGMSVDPAVFFD 295
                                    99******************************66.....578966.66669*************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2273.37
//
Query:       gi|121639318|ref|YP_979542.1|  [L=527]
Description: hypothetical protein BCG_3463c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-11   42.1   0.1    1.5e-10   41.3   0.1    1.3  1  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   8.2e-15   1.5e-10      12     146 ..      20     148 ..      14     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.2e-15
                                    HHHT.T-.TTS-EEEEET....TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHHHHHHHHHHHH-S. CS
                            IMS  12 rardpeL.kgkPvvvaqgsekrgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrraskkileilkrfisp 90 
                                    +a+  +L  + Pv+v       + via+s  Ara+Gv+rg r +ea + cp+l ++ +d ++  r+ + +++ + +  +p
  gi|121639318|ref|YP_979542.1|  20 AAAAAGLsATAPVAVTLA----NRVIACSATARAAGVRRGLRRREAAARCPQLFIATADADRDARLFEGVIAAVDDL-VP 94 
                                    45556888999******9....99*****************************************************.66 PP

                                    .EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHH CS
                            IMS  91 kvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAK 146
                                    + e + +  ++l + g ++ ++se +  a++l +a+++  g ++ +Gia+   +A 
  gi|121639318|ref|YP_979542.1|  95 RAELLRPGLLVLPVRGPARFFGSE-QMAAERLIDAVAAA-GAECQVGIADRLSTAV 148
                                    ***********************7.77888888887766.5********9888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 4043.79
//
Query:       gi|121639319|ref|YP_979543.1|  [L=204]
Description: hypothetical protein BCG_3464c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1446.19
//
Query:       gi|121639320|ref|YP_979544.1|  [L=208]
Description: hypothetical protein BCG_3465 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.6   0.1      0.021   15.2   0.1    1.7  1  Ank_5     Ankyrin repeats (many copies)


Domain annotation for each model (and alignments):
>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.2e-06     0.021      11      46 ..     158     198 ..     152     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                          Ank_5  11 rldgggn....tpLhvAakygaadvvrlLl.argadlnltd 46 
                                    rl+gg++    + L++ a +g +dv+r+L+ + g d+n+t+
  gi|121639320|ref|YP_979544.1| 158 RLRGGSVttadHTLILVAGNGDLDVARRLVeEAGGDWNATT 198
                                    6666666666699*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1505.83
//
Query:       gi|121639321|ref|YP_979545.1|  [L=525]
Description: GMP synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-40  134.6   0.0      2e-39  133.5   0.0    1.6  1  GMP_synt_C     GMP synthase C terminal domain
    2.4e-37  128.6   0.0    3.4e-37  128.1   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    2.2e-09   36.8   0.2    1.1e-05   24.7   0.1    2.2  2  NAD_synthase   NAD synthase
    3.7e-09   36.6   0.3    2.6e-08   33.9   0.3    2.3  1  Peptidase_C26  Peptidase C26
     0.0022   16.9   0.1     0.0036   16.1   0.1    1.3  1  tRNA_Me_trans  tRNA methyl transferase
      0.008   15.7   0.0      0.099   12.1   0.0    2.1  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.015   14.9   0.0       0.04   13.5   0.0    1.7  2  ThiI           Thiamine biosynthesis protein (ThiI)
      0.017   14.8   0.4        0.1   12.2   0.3    2.0  2  Asn_synthase   Asparagine synthase
      0.097   12.8   0.0       0.35   11.0   0.0    1.9  1  HHH_2          Helix-hairpin-helix motif
       0.14   11.9   0.0       0.23   11.2   0.0    1.3  1  ATP_bind_3     PP-loop family
       0.17   11.7   0.3        1.7    8.4   0.0    2.3  2  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.0   1.2e-42     2e-39       1      92 []     432     524 ..     432     524 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 1.2e-42
                                    CCCCTTT-GGGSSEEEEEEEE.EEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EE CS
                     GMP_synt_C   1 eelkkaglykkiwQafavllp.vksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvv 79 
                                    eel++agl+++iwQ+ +vll  v+svGv+gd Rty++ ++lR v+seDamtad++++pyevLe+is+ri+nev +vnrvv
  gi|121639321|ref|YP_979545.1| 432 EELTAAGLDNQIWQCPVVLLAdVRSVGVQGDGRTYGHPIVLRPVSSEDAMTADWTRVPYEVLERISTRITNEVAEVNRVV 511
                                    7999***********9998755********************************************************** PP

                                    EE---TTTS-S-- CS
                     GMP_synt_C  80 yditskPpatiEw 92 
                                    +ditskPpatiEw
  gi|121639321|ref|YP_979545.1| 512 LDITSKPPATIEW 524
                                    ************* PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.0   2.1e-40   3.4e-37       2     188 ..      19     197 ..      18     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 2.1e-40
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHH CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGm 81 
                                    ++D+++++ + ++++++e++v  ev+p++as+eei+  + +p ++++sgGp s++++g++++   +++ ++P+LGIC+G+
  gi|121639321|ref|YP_979545.1|  19 VVDFGAQYAQLIARRVREARVFSEVIPHTASIEEIR--ARQPVALVLSGGPASVYADGAPKLDPALLDLGVPVLGICYGF 96 
                                    89*********************************5..79**************************************** PP

                                    HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEET CS
                         GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekk 161
                                    Q++a+++g+ v +  ++e+   + ++     +l ++l+++  ++++H+++v+     p+g++v+a s+     ++++e  
  gi|121639321|ref|YP_979545.1|  97 QAMAQALGGIVAHTGTREYGRTELKVLG--GKLHSDLPEVQPVWMSHGDAVTA---APDGFDVVASSAGA--PVAAFEAF 169
                                    ***************8888888888888..78999*****************9...*******9999554..66666666 PP

                                    T.TEEEESSBTTSTTSTTHHHHHHHHHH CS
                         GATase 162 n.pfvgvQFHPEststpegpellfnfli 188
                                    + ++ gvQ+HPE+ +tp+g+++l +fl+
  gi|121639321|ref|YP_979545.1| 170 DrRLAGVQYHPEVMHTPHGQQVLSRFLH 197
                                    626*********************9986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   6.8e-09   1.1e-05       9      51 ..     215     257 ..     209     307 .. 0.69
   2 !    9.9   0.0   0.00022      0.37     148     177 ..     372     401 ..     366     410 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.8e-09
                                    HHHHHH.HCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE CS
                   NAD_synthase   9 lkeyvk.kagakgvvlGlSGGvDSslvaalavkalgkenvlall 51 
                                    l e+v+ + g   ++ GlSGGvDS+++aal ++a+g+ + + + 
  gi|121639321|ref|YP_979545.1| 215 LIEQVRtQIGDGHAICGLSGGVDSAVAAALVQRAIGD-RLTCVF 257
                                    44444404566789*********************65.455554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                    BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                   NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                    ++p+  l+K ev++  +el+ Pe+++ ++P
  gi|121639321|ref|YP_979545.1| 372 VEPLRLLFKDEVRAVGRELGLPEEIVARQP 401
                                    689*************************99 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.3   1.6e-11   2.6e-08     100     216 .]      81     181 ..      76     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.6e-11
                  Peptidase_C26 100 aalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaik 179
                                    a l+ gvP+lgiC G+q ++ alGG ++               + +  + ++kv  g+l ++l +     v   H  a++
  gi|121639321|ref|YP_979545.1|  81 ALLDLGVPVLGICYGFQAMAQALGGIVAHTGT-----------R-EYGRTELKVLGGKLHSDLPE--VQPVWMSHGDAVT 146
                                    567889*******************7654433...........3.34488899998888888887..6678889****** PP

                  Peptidase_C26 180 elaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +++ v+A ++   + a+e+ +++  + gvQ+HPE
  gi|121639321|ref|YP_979545.1| 147 AAPDGFDVVASSAGAPVAAFEAFDRR--LAGVQYHPE 181
                                    ***********************966..9*******9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.2e-06    0.0036       4      24 ..     229     249 ..     226     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                  tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqg 24 
                                    +++lSgGVDS+vaaal++++ 
  gi|121639321|ref|YP_979545.1| 229 ICGLSGGVDSAVAAALVQRAI 249
                                    89**************99875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   6.1e-05     0.099       2      61 ..     228     288 ..     227     312 .. 0.72
   2 ?    0.9   0.0      0.16   2.7e+02     147     177 ..     361     394 ..     334     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                                    EEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE- CS
                           QueC   2 avvllSGGlDSttvlalakke.gkevealtfdYgqr.hkkeleaakkiakelgveehkildl 61 
                                    a++ lSGG+DS++++al++++ g++++++ +d g   + +  ++ +++++++g  +  ++d 
  gi|121639321|ref|YP_979545.1| 228 AICGLSGGVDSAVAAALVQRAiGDRLTCVFVDHGLLrAGERAQVQRDFVAATGA-NLVTVDA 288
                                    8999**********9998877259999999999976255556666777777776.5555544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                                    H...HTS--EEE-TTTT--HHHHHHHHHHTTHHH CS
                           QueC 147 g...edkkieieaPlidlsKaeivklgkelgvpl 177
                                    g    d k++++ Pl  l K e+ ++g elg+p 
  gi|121639321|ref|YP_979545.1| 361 GglpDDLKFTLVEPLRLLFKDEVRAVGRELGLPE 394
                                    3343778999*********************976 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   4.8e+03      16      49 ..     161     192 ..     149     203 .. 0.70
   2 ?   13.5   0.0   2.5e-05      0.04       4      51 ..     226     274 ..     223     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                           ThiI  16 SpVaaylllkRGcrvvlvhlknepgtseeaiekv 49 
                                    +pVaa+ ++ R +    v  + e +++++ ++++
  gi|121639321|ref|YP_979545.1| 161 APVAAFEAFDRRLA--GVQYHPEVMHTPHGQQVL 192
                                    69999999998544..444445677777766655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.5e-05
                           ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekvek 51 
                                    g++++ lSgG+DS Vaa l+ +  G r  +v+++  +  + e  ++ ++
  gi|121639321|ref|YP_979545.1| 226 GHAICGLSGGVDSAVAAALVQRAiGDRLTCVFVDHGLLRAGERAQVQRD 274
                                    8899*************98866458899999998776666665555544 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.33   5.4e+02      13      27 ..      52      66 ..      47      69 .. 0.86
   2 ?   12.2   0.3   6.3e-05       0.1       3      46 ..     212     254 ..     210     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.33
                   Asn_synthase 13 rlradvpvGalLSGG 27
                                     ra+ pv+++LSGG
  gi|121639321|ref|YP_979545.1| 52 EIRARQPVALVLSGG 66
                                   67999*********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.3e-05
                   Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplk 46 
                                    + +L + V+ +  +d    + LSGG+DS++ aal +r    +l+
  gi|121639321|ref|YP_979545.1| 212 ANALIEQVRTQI-GDGHAICGLSGGVDSAVAAALVQRAIGDRLT 254
                                    667788888776.89999999**************997655555 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.35       5      19 ..     406     420 ..     405     435 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                          HHH_2   5 aLGIrhVGektAklL 19 
                                    +LGIr VGe tAk L
  gi|121639321|ref|YP_979545.1| 406 GLGIRIVGEVTAKRL 420
                                    7************98 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.23       2      48 ..     228     270 ..     227     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                    EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHH CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeae 48 
                                    ++ ++SgG+DS +   l+++     g +l+++ vdhgl    ++ a+
  gi|121639321|ref|YP_979545.1| 228 AICGLSGGVDSAVAAALVQRA---IGDRLTCVFVDHGLLRAGER-AQ 270
                                    5789*******9988888777...4569*********9754433.23 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.001       1.7      48     110 ..      44     102 ..      19     149 .. 0.81
   2 ?    0.6   0.1      0.27   4.4e+02      81     154 ..     213     291 ..     203     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                                    EE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                      DJ-1_PfpI  48 vtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                    ++ +as+++++a +  alvl GG a + +      + +l    ++ g +v  IC g q +a+a
  gi|121639321|ref|YP_979545.1|  44 IPHTASIEEIRARQPVALVLSGGPA-SVYADG---APKLDPALLDLGVPVLGICYGFQAMAQA 102
                                    56789******************88.555555...5555566788999999999999888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTT...TSEE--SGGGHHHHHHTTSEE-SSSEE..EETTEEEESSGGG CS
                      DJ-1_PfpI  81 ekvvelvkefaekgklvaaICagpqlLaaagvlk...grrvTsypavkdklekagakyvdkrvv..vdgnlvTsrgpga 154
                                    ++++e v+++  +g  ++ ++ g    +aa +++   g r+T+++     l+++  + v + +v  + +nlvT  ++++
  gi|121639321|ref|YP_979545.1| 213 NALIEQVRTQIGDGHAICGLSGGVDSAVAAALVQraiGDRLTCVFVDHGLLRAGERAQVQRDFVaaTGANLVTVDAAET 291
                                    4789999999999999999999998888888877455789999999777776666666777555114566888666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 3926.71
//
Query:       gi|121639322|ref|YP_979546.1|  [L=302]
Description: phytoene synthase phyA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-58  198.7   3.4    1.4e-58  198.5   3.4    1.0  1  SQS_PSY   Squalene/phytoene synthase
  ------ inclusion threshold ------
      0.027   14.3   0.5        0.1   12.4   0.5    1.9  1  TruB_C    tRNA Pseudouridine synthase II, C terminal
      0.049   13.4   0.3        1.4    8.7   0.2    2.4  2  MdcG      Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   3.4   2.4e-62   1.4e-58       2     261 ..      16     268 ..      15     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 2.4e-62
                                    XHH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----........------------..---------THHHHHHHH CS
                        SQS_PSY   2 raasksfylaslllppelRdalgalYafcreaddlvDdvseplqararldwwrdavdavyaedklkpprepvlralaqli 81 
                                    r a+++fy+ ++llp+e+R al a+Ya+ r +dd++D +  p+ +  +ld+ r+++d++       ++ +pvl ala+++
  gi|121639322|ref|YP_979546.1|  16 RTAARNFYYGIRLLPREKRAALSAVYALGRRIDDVADGELAPETKITELDAIRKSLDNID------DSSDPVLVALADAA 89 
                                    8899************************************99999999*********877......367*********** PP

                                    HHHT--HHHHHHHHHHTS--SS-..--SHHHHHHHHHHHHHHHHHHHHHHH-S.S-HHHHHHHHHHHHHHHHHHHHHT-- CS
                        SQS_PSY  82 rtyklpkellleliegmeadleftryetlddLeeYcyrvagvVgelclrllgarrsdralaeaarrlGkalQltnilRdv 161
                                    r++ +p +++ eli+g ++ ++ t  +++d+L  Yc+r ag++g lcl ++g   s+ a+ ++a++lG+alQ tnilRdv
  gi|121639322|ref|YP_979546.1|  90 RRFPVPIAMFAELIDGARMEIDWTGCRDFDELIVYCRRGAGTIGKLCLSIFGP-VST-ATSRYAEQLGIALQQTNILRDV 167
                                    *****************************************************.444.57******************** PP

                                    -SHHHHTT..S-HHHHHHHT--HH..HHHHT-....-SHHHHHHHHHHHHHHHHHHHHHHHTGGGS.-HHHHHHHHHHHH CS
                        SQS_PSY 162 peDaergrvyLPadvlkefgvsee..dllrkg...vrsaelrallrrlaerArelldearellkqlpdrrarpalllava 236
                                    +eD  +gr+yLP+d l++ gv+    d    g    ++ +l allr+ a+rA +++  + +l+ +l drr+ ++++++  
  gi|121639322|ref|YP_979546.1| 168 REDFLNGRIYLPRDELDRLGVRLRldDT---GaldDPDGRLAALLRFSADRAADWYSLGLRLIPHL-DRRSAACCAAMSG 243
                                    ********************99874433...234356888**************************.************* PP

                                    HHHHHHHHHHHTTT-TTT------H CS
                        SQS_PSY 237 lyrailerieaadydvlsrrvklsl 261
                                    +yr+ l  i+a ++ v +rr++ls 
  gi|121639322|ref|YP_979546.1| 244 IYRRQLALIRASPAVVYDRRISLSG 268
                                    **************87679999875 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   1.7e-05       0.1      17      49 ..     187     216 ..     185     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                    T---B-----S-EEEE-TTS-EEEEEEEETTEE CS
                         TruB_C  17 GrrLeaagikgvvAaiaPdGrliALleerggra 49 
                                    G rL++   +++ A  +PdGrl ALl++ ++ra
  gi|121639322|ref|YP_979546.1| 187 GVRLRL---DDTGALDDPDGRLAALLRFSADRA 216
                                    555555...77778889*************998 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.02   1.2e+02      30      63 ..     119     151 ..      71     167 .. 0.76
   2 ?    8.7   0.2   0.00023       1.4      37      80 ..     210     251 ..     197     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.02
                           MdcG  30 glpvvvrRakaedagaevplGlrlppaarkqRla 63 
                                    +  +v +R+ a   g+ ++l + +p ++++ R+a
  gi|121639322|ref|YP_979546.1| 119 DELIVYCRRGAGTIGK-LCLSIFGPVSTATSRYA 151
                                    4567889999989999.*******9999998887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00023
                           MdcG  37 RakaedagaevplGlrlppaarkqRlalavapsaiarvveplaL 80 
                                    R +a++a+++  lGlrl p+  ++ +a+++a+s i r++    L
  gi|121639322|ref|YP_979546.1| 210 RFSADRAADWYSLGLRLIPHLDRRSAACCAAMSGIYRRQLA--L 251
                                    5556677778*************************876643..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2353.78
//
Query:       gi|121639323|ref|YP_979547.1|  [L=359]
Description: multifunctional geranylgeranyl pyrophosphate synthetase idsA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-53  181.4   0.0      2e-53  181.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.034   13.7   0.0    1.4  1  CobU             Cobinamide kinase / cobinamide phosphate gua


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.0   2.3e-57     2e-53       9     237 ..      68     287 ..      61     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 2.3e-57
                                    HHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHH CS
                polyprenyl_synt   9 eylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgd 88 
                                    + ++   GK +Rp+lv+ aaea +    + ++a   a+ vel+h++sLvhDD+mD +e RR +p++ +l+G ++A+++gd
  gi|121639323|ref|YP_979547.1|  68 NNNC---GKAIRPALVFVAAEAAGA---DPHSAIPGAVSVELVHNFSLVHDDLMDRDEHRRHRPTVWALWGDAMALLAGD 141
                                    4555...*****************3...4599************************************************ PP

                                    HHHHHHHHHHHHHHSTT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTT CS
                polyprenyl_synt  89 fllarafellaklfeks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallag 167
                                    ++l++a e+l ++ +++   +l+ +se++ ++++Gq+ d+  e+++d++   l+e l++ + KTa+l+a++++++allag
  gi|121639323|ref|YP_979547.1| 142 AMLSLAHEVLLDCDSPHvGAALRAISEATRELIRGQAADTAFESRTDVA---LDECLKMAEGKTAALMAASAEVGALLAG 218
                                    *************76667899*******************999999999...**************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHH CS
                polyprenyl_synt 168 asdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlke 237
                                    a +++ eal  +g+++GlaFQ++DD+l + g pe +gKp+ +D++  k tlp+  ++ +  ++ r +l +
  gi|121639323|ref|YP_979547.1| 219 APRSVREALVAYGRHIGLAFQLVDDLLGIWGRPEITGKPVYSDLRSRKKTLPVTWTVAHGGSAGR-RLAA 287
                                    *88999***********************************************998887666655.5554 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-06     0.034      44     130 ..     118     216 ..     109     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-06
                           CobU  44 arHrerRpaeWetveepldlaealkeeekkevvLvDcltlwltnllleeeaek............veekleeeveellea 111
                                    ++Hr++Rp+ W ++    +l +  +  + ++ vL+Dc +  +  +l + ++++             e++++ +++e l++
  gi|121639323|ref|YP_979547.1| 118 DEHRRHRPTVWALWGDAMALLAGDAMLSLAHEVLLDCDSPHVGAALRAISEATrelirgqaadtaFESRTDVALDECLKM 197
                                    58************998888765555555789**************998866699******999999999999******* PP

                           CobU 112 lkelkatvvlVsnEvglgv 130
                                    ++ ++a ++  s Evg  +
  gi|121639323|ref|YP_979547.1| 198 AEGKTAALMAASAEVGALL 216
                                    ***************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2413.15
//
Query:       gi|121639324|ref|YP_979548.1|  [L=348]
Description: hypothetical protein BCG_3469 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-65  220.0   0.0    4.4e-65  219.2   0.0    1.4  2  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   0.0   2.4e-69   4.4e-65       1     188 []      61     244 ..      61     244 .. 0.97
   2 ?   -3.6   0.0      0.52   9.3e+03      28      67 ..     263     280 ..     250     294 .. 0.49

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 2.4e-69
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal 80 
                                    a++ a aral+sr++ ++li+Dp+ae+lv+a+g +l++r a +el  e+   ++++  + + + ia+Rt+f+dd++ +a+
  gi|121639324|ref|YP_979548.1|  61 ATMIATARALASRAE-NPLINDPFAEPLVRAVGIDLFTRLASGELRLED-IGDHATGGRWMIDNIAIRTKFYDDFFGDAT 138
                                    799**********98.*******************************98.4577899*********************** PP

                                    HCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT-T CS
                            LCM  81 saagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfdp 160
                                     +agirqvViL+AGlDtrayRlpw+ g++v+E+Dqp+v++fK++ l++l+aep+ae++ v+vDlr +dwp+aL++agfdp
  gi|121639324|ref|YP_979548.1| 139 -TAGIRQVVILAAGLDTRAYRLPWPPGTVVYEIDQPAVIKFKTRALANLNAEPNAERHAVAVDLR-NDWPTALKNAGFDP 216
                                    .8***************************************************************.************** PP

                                    TSEEEEEEESSGGGS-HHHHHHHHHHHH CS
                            LCM 161 ekptawvaeGvlvYLtpeasdalleaia 188
                                    ++pta++aeG+l YL+p+ +d+ll+ai+
  gi|121639324|ref|YP_979548.1| 217 ARPTAFSAEGLLSYLPPQGQDRLLDAIT 244
                                    *************************985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.52
                                    CCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHH CS
                            LCM  28 lvsaaglellerkadkelekekeeekkekkapelnrgiav 67 
                                    l++++++++                      +  ++  a 
  gi|121639324|ref|YP_979548.1| 263 LAEEDEKKM----------------------RMKSAAEAW 280
                                    444444433......................222233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2605.44
//
Query:       gi|121639325|ref|YP_979549.1|  [L=262]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   55.0   0.0    2.2e-14   54.0   0.0    1.4  1  HAD_2           Haloacid dehalogenase-like hydrolase
    9.2e-13   49.0   0.3    1.3e-12   48.5   0.3    1.2  1  Hydrolase       haloacid dehalogenase-like hydrolase
      1e-05   25.5   0.3    2.1e-05   24.5   0.3    1.5  1  Hydrolase_like  HAD-hyrolase-like
     0.0014   19.0   1.4     0.0068   16.8   1.4    2.0  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.11   12.7   0.1         14    5.9   0.0    2.3  2  TrkA_N          TrkA-N domain
       0.14   12.3   0.0         14    5.9   0.0    2.6  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   7.2e-18   2.2e-14       1     175 [.      26     230 ..      26     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7.2e-18
                          HAD_2   1 iiFDlDgTlldteeliiqafnelleey.......................gls.elseeelrkliglslrellrklgese 56 
                                    ++FDlDg+l dt  l+ +a++ +++ y                        ++ +  e+ +r+++     e+ + + ++ 
  gi|121639325|ref|YP_979549.1|  26 CLFDLDGVLTDTASLHTKAWKAMFDAYlaeraertgekfvpfdpaadyhtYVDgKKREDGVRSFLSSRAIEIPDGSPDDP 105
                                    69*************************99999999998776666666665444455566666666666666666666666 PP

                          HAD_2  57 eeee....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyF....dvivts 128
                                       e    + ++  +  ++ + ++  +++dg + +Le +++ag+ +++v+s+  +++++ l+ +g++++     d +   
  gi|121639325|ref|YP_979549.1| 106 GAAEtvygLGNRKNDMLHKLLRDDGAQVFDGSRRYLEAVTAAGLGVAVVSSS--ANTRDVLATTGLDRFVqqrvDGVTLR 183
                                    6555777655555455555555599************************996..44555566666555550000556666 PP

                          HAD_2 129 edvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikv 175
                                    e+    KP+p+++++a e l+++++ + +++D  +++ a+++ +  v
  gi|121639325|ref|YP_979549.1| 184 EEHIAGKPAPDSFLRAAELLGVTPDAAAVFEDALSGVAAGRAGNFAV 230
                                    666667*******************************9999876655 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.3   4.3e-16   1.3e-12       1     209 [.      23     226 ..      23     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.3e-16
                                    SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.......HHHHHHHHHETTTEHHHHTH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.......sgaltgfatfigrgayaigk 73 
                                    +++++fD+dG+Lt++ + ++++++                  + a+ a+  +r         + ++++t+ +  +   g 
  gi|121639325|ref|YP_979549.1|  23 VRACLFDLDGVLTDTASLHTKAWKAM----------------FDAYLAERAERtgekfvpFDPAADYHTYVDGKKREDGV 86 
                                    589***********************................77776666666677777655558888855555788888 PP

                                    HHHHHHH.....HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHH CS
                                    xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  74 pewltal.....dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpeta 148
                                    + +l +      d +pd   a ++  + g        + l+ +   d  +v+++ +  +++  aag+ v++++++  ++ 
  gi|121639325|ref|YP_979549.1|  87 RSFLSSRaieipDGSPDDPGAAETVYGLGNRKN----DMLHKLLRDDGAQVFDGSRRYLEAVTAAGLGVAVVSSS--ANT 160
                                    889988878566555555555555555555544....4478888888889*****************99999944..455 PP

                                    HHHHHHTT.....GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 149 eraanqlG.....ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                    + ++   G     ++ +d+v  ++++  +kp p+ +++a++ L++ p   a+++D + ++aa++a 
  gi|121639325|ref|YP_979549.1| 161 RDVLATTGldrfvQQRVDGVTLREEHIAGKPAPDSFLRAAELLGVTPDAAAVFEDALSGVAAGRAG 226
                                    555555665255444445555555555************************************986 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.3     7e-09   2.1e-05       2      75 .]     188     261 ..     187     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7e-09
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEE.E.SSSSS-TTTHHHHHHHHT---SEEES- CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvL.V.ltGvtrpedleepehkptyvaddlaea 75 
                                    +gKP+p ++ +a+e lg++p++  +  D   + +a++++     v  + +tG  ++++ ++  h++++v+ dlae+
  gi|121639325|ref|YP_979549.1| 188 AGKPAPDSFLRAAELLGVTPDAAAVFEDA-LSGVAAGRAGNFAVVVgInRTGRAAQAA-QLRRHGADVVVTDLAEL 261
                                    69***************************.********99988753233678877766.55779*********986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.4   2.3e-06    0.0068       2     157 ..      27     195 ..      26     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                            HAD   2 lfDfDgTLldgdsle.....lllrfllrrgaprlwralrek..lllalfrellrldraglaellea.............. 60 
                                    lfD+Dg L+d+ sl+     ++++++l+++a+r+++   ++  +  ++ +  ++ +++g++ +l++              
  gi|121639325|ref|YP_979549.1|  27 LFDLDGVLTDTASLHtkawkAMFDAYLAERAERTGEKFVPFdpAADYHTYVDGKKREDGVRSFLSSraieipdgspddpg 106
                                    8*******************99999********99999999854445577778888999999999988887777777777 PP

                            HAD  61 ...llaglseelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddr 137
                                       +  gl  + ++ l +++++  ++ ++  g +++l+a+ aaG  v+vvS++   +++ +la  g d+++        r
  gi|121639325|ref|YP_979549.1| 107 aaeTVYGLGNRKNDMLHKLLRDDGAQ-VF-DGSRRYLEAVTAAGLGVAVVSSS--ANTRDVLATTGLDRFVQQ------R 176
                                    77733333333333333333222233.35.79******************987..588999999998888888......7 PP

                            HAD 138 ltgelglegkpvrgegkvaa 157
                                    ++g   l++  ++g+  +++
  gi|121639325|ref|YP_979549.1| 177 VDGV-TLREEHIAGKPAPDS 195
                                    7777.566666666554444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        35       4      63 ..     112     172 ..     110     174 .. 0.80
   2 ?    5.9   0.0    0.0048        14       2      28 ..     230     257 ..     184     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                                    ES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGE CS
                         TrkA_N   4 iGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagieka 63 
                                     GlG+    ++++L + +g    v d +++ +e +++ g  + vv  +a  ++vL+  g++++
  gi|121639325|ref|YP_979549.1| 112 YGLGNRKNDMLHKLLRdDG--AQVFDGSRRYLEAVTAAGlgVAVVSSSANTRDVLATTGLDRF 172
                                    5667766777777777344..6799999999999999987788999***********999986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0048
                                    EEES-SHHHHHH.HHHHHHTTEEEEEEE CS
                         TrkA_N   2 iiiGlGrvGrsl.aeeLseggkdvvvid 28 
                                    +++G +r+Gr+  a +L+++g dvvv d
  gi|121639325|ref|YP_979549.1| 230 VVVGINRTGRAAqAAQLRRHGADVVVTD 257
                                    6788888887654666666554677655 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0047        14       2      22 ..      27      47 ..      26      63 .. 0.85
   2 ?    3.8   0.0     0.021        63      11      41 ..     129     159 ..     107     187 .. 0.87
   3 ?   -2.6   0.0         2   5.9e+03      29      55 ..     226     250 ..     202     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0047
                                   EEESTTTSEETTEE-TTHHHH CS
                    Hydrolase_6  2 lfDidGvLwrgdkaipgaaea 22
                                   lfD+dGvL +  ++  +a +a
  gi|121639325|ref|YP_979549.1| 27 LFDLDGVLTDTASLHTKAWKA 47
                                   8********998887777655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                                    ETTEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                    Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnss 41 
                                    +g ++++g+ + l+a++aag  v++++ +++
  gi|121639325|ref|YP_979549.1| 129 DGAQVFDGSRRYLEAVTAAGLGVAVVSSSAN 159
                                    478899******************9998654 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2
                                    TT-EEEEEE---SS-HHHHHHHHHHTT CS
                    Hydrolase_6  29 agkpvvllTNnsskseeeyakkleklg 55 
                                     +  vv+  N++++   + a++l++ g
  gi|121639325|ref|YP_979549.1| 226 GNFAVVVGINRTGRA--AQAAQLRRHG 250
                                    444555555555554..4444555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1829.87
//
Query:       gi|121639326|ref|YP_979550.1|  [L=786]
Description: hypothetical protein BCG_3471 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-142  474.8   0.4   2.2e-142  474.5   0.4    1.1  1  Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalyt
    6.2e-59  199.4   0.0    1.2e-58  198.4   0.0    1.5  2  Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal dom
    2.7e-13   49.6   0.0      1e-12   47.8   0.0    2.1  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.5   0.4  3.7e-146  2.2e-142       1     386 [.     327     693 ..     327     694 .. 0.99

  Alignments for each domain:
  == domain 1  score: 474.5 bits;  conditional E-value: 3.7e-146
                Glyco_hydro_65m   1 rlalfhllqtlaaadarldvgakGltGegYrGhvfWDtElfvlPlylltepevarnlLeyRynrleaArekAkekglkGA 80 
                                    r+ lfhllq++a+a++r ++++kGltG+gY+Gh+fWDtE fvlP++++t+p++++++L++R+++l+ A+e+A+e gl+GA
  gi|121639326|ref|YP_979550.1| 327 RFGLFHLLQASARAERR-AIPSKGLTGTGYDGHAFWDTEGFVLPVLTYTAPHAVADALRWRASTLDLAKERAAELGLEGA 405
                                    799************99.************************************************************** PP

                Glyco_hydro_65m  81 lyPwesasdGeEesqelhlnirsgewepdaseeeiHvnaaiayavvqYveatgDeefleeeglellvetarfWasraeld 160
                                    ++Pw++++ G+E+s         ++w+  a+++++H+na+ia+a+ +Y  +tgD +++ee+gl++l+etar+W+s++++d
  gi|121639326|ref|YP_979550.1| 406 AFPWRTIR-GQESS---------AYWP--AGTAAWHINADIAMAFERYRIVTGDGSLEEECGLAVLIETARLWLSLGHHD 473
                                    ********.****9.........****..*************************************************** PP

                Glyco_hydro_65m 161 kdkgryeidgviGPdEYeenvdnNaytnliaawnlelalealeeleeeaeklevkeeelekwekvleklylpideelgvi 240
                                    + +g++++dgv+GPdEY+++v++N++tnl+aa+nl++a++a+ +++e+ae+++v++ee+++w++++++ ++p+deelgv+
  gi|121639326|ref|YP_979550.1| 474 R-HGVWHLDGVTGPDEYTAVVRDNVFTNLMAAHNLHTAADACLRHPEAAEAMGVTTEEMAAWRDAADAANIPYDEELGVH 552
                                    8.8***************************************************************************** PP

                Glyco_hydro_65m 241 aqkdgflelaeldleeykalagdetdlllkaegdkvlesqviKQaDvllllyllkeefseeqikanldfYeprtvhdSsl 320
                                    +q++gf++lae+d+e+     +++++lll+ ++ +++ +qviKQaD++l++++++++f++eq+++n+d+Ye+r+v+dSsl
  gi|121639326|ref|YP_979550.1| 553 QQCEGFTTLAEWDFEA-----NTTYPLLLHEAYVRLYPAQVIKQADLVLAMQWQSHAFTPEQKARNVDYYERRMVRDSSL 627
                                    ****************.....9999******************************************************* PP

                Glyco_hydro_65m 321 SalvhaivaaelgklekalelfkeaariDldaqerstedGiHiaslagtleaivqgfaglrlrege 386
                                    Sa+++a+++ae+g+le a+++++eaa iDl++ +r+t+dG+H+aslag+++a+v gf+glr +eg 
  gi|121639326|ref|YP_979550.1| 628 SACTQAVMCAEVGHLELAHDYAYEAALIDLRDLHRNTRDGLHMASLAGAWTALVVGFGGLRDDEGI 693
                                    *************************************************************99986 PP

>> Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   2.1e-62   1.2e-58       2     227 ..      16     270 ..      15     271 .. 0.89
   2 ?   -3.9   0.0       1.4   8.6e+03      28      58 ..     296     321 ..     291     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 2.1e-62
                                    ......S--HHHHHHT-EE-SSEEE----TTTT--....-EEETT-EE-T...........TSSS-EE----EEEEEEEE CS
                Glyco_hydro_65N   2 etgfdpeeeglrEslftlGNGylGtRgafeeeysd...pgtyiaGvYdreis...eeanGypeeneelvnlpdwlglrlr 75 
                                    et+++ + ++++Eslf+l+NG++G+Rg+++e + +   pgty++ +Y+ ++    e+++Gype ++++v +++ +  rl 
  gi|121639326|ref|YP_979550.1|  16 ETKLNLNLLAQSESLFALSNGHIGLRGNLDEGE-PfglPGTYLNSFYEIRPLpyaEAGYGYPEAGQTVVDVTNGKIFRLL 94 
                                    8999999************************33.24477********99966778************************* PP

                                    ETTEE--GGGSEEEEEEEEEETTTTEEEEEEEEE-TTS-EEEEEEEEEE-SSSTTEEEEEEEEEESS--EEEEEEEEEET CS
                Glyco_hydro_65N  76 vdgeeldldegeildyereLdlreGvltrsltwrspagkevrveserfvsladrhlaairlevtplnfsgevevesgldg 155
                                    v++e++d+++ge+ ++er Ldlr+G+ltr+ +wrspagk+v+v+s+r+vsla+r +aai++ v++++   +v+v+s+l  
  gi|121639326|ref|YP_979550.1|  95 VGDEPFDVRYGELISHERILDLRAGTLTRRAHWRSPAGKQVKVTSTRLVSLAHRSVAAIEYVVEAIEEFVRVTVQSELVT 174
                                    ******************************************************************************** PP

                                    T--B.....................................EEEEETTSS-EEEEEEEEEEEETTEE--SEE...SEEEE CS
                Glyco_hydro_65N 156 dvan.................ekhkdprka...........levrtresgitvavaartrveasgeklevee...ekiaq 204
                                    ++++                 +       a           l +rtr s + +a++++++ve++g+ + +++   + +++
  gi|121639326|ref|YP_979550.1| 175 NEDVpetsadprvsaildrplQ-------AvehertergalLMHRTRASALMMAAGMEHEVEVPGRVEITTDarpDLART 247
                                    ****877666555544443330.......14444445667**************************7766559*999999 PP

                                    EEEEEE-TT-EEEEEEEEEEEET CS
                Glyco_hydro_65N 205 tlsvelkagetvtleKyvavats 227
                                    t+ + l++g+++++ Ky a+ +s
  gi|121639326|ref|YP_979550.1| 248 TVICGLRPGQKLRIVKYLAYGWS 270
                                    999*****************998 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.4
                                    ---TTTT--.-EEETT-EE-T........TS CS
                Glyco_hydro_65N  28 gafeeeysdpgtyiaGvYdreiseeanGype 58 
                                    g ++     + +y+ +++d++   e++G pe
  gi|121639326|ref|YP_979550.1| 296 GLLDA----QRAYLDDFWDSA-DVEVEGDPE 321
                                    55555....56899****999.446667665 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.7e-16     1e-12       1      51 []     698     750 ..     698     750 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.7e-16
                                    ----TT-SEEEEEEEETTEEEEEEEESSEEEEEEES..SSTEEEEETTEEEEE CS
                Glyco_hydro_65C   1 PrLPeeWdglsFrlryRGrrLrVrvtpeevtvtles..gepltievyGeevtL 51 
                                    P+LP+++++l+Frlr+RG rL V+ +++ vt+ l +  g+ lt++++G+++tL
  gi|121639326|ref|YP_979550.1| 698 PQLPDGISRLRFRLRWRGFRLIVDANHTDVTFILGDgpGTQLTMRHAGQDLTL 750
                                    99*********************************98899**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5312.72
//
Query:       gi|121639327|ref|YP_979551.1|  [L=350]
Description: hypothetical protein BCG_3472c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-78  263.9   0.0    2.9e-78  263.7   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.7   0.0   1.6e-82   2.9e-78       5     307 ..      50     350 .]      47     350 .] 0.96

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 1.6e-82
                                    HHHHHHHHHHTSS-SSS.SHHHHHHHHHHHHHHT.-SEEEEESSHHHHHHHHHHH.TTTT.TT-EEEEESSS-THHHHHH CS
                DegT_DnrJ_EryC1   5 eeleaveevlksgwlts.gpeveeFEkafaaylg.vkhaiavssGtaAlhlaLra.lgvg.pgdeVIvpsltFvatanav 80 
                                    e  e++ ++++++w+t+ gp++++F++a+++ylg + h+ ++++Gt Al+ aL++ +g+g +++++++ps+tFv+ a+a+
  gi|121639327|ref|YP_979551.1|  50 ELAEDFVQIAQANWYTNfGPNERRFARALRDYLGpHLHVATLANGTLALLAALHVsFGAGtRDRYLLMPSFTFVGVAQAA 129
                                    6778999***************************99***********************977789*************** PP

                                    HHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE...EEEEEB-GGGB--.-HHHHHHHHHHCT-EEEEE-TT-TT-EETT. CS
                DegT_DnrJ_EryC1  81 lelgakpvfvDvdpdtynidpaaieaaitert...kaIlpVhlyGqva.dmdalkaiaakhglkvieDaAhAlGatykg. 155
                                    l++g++p+f+D+d++t+++++++++a+i++ +   ++Il+++++G  + +++ ++++aa+++l+++ D+A ++G+ty++ 
  gi|121639327|ref|YP_979551.1| 130 LWTGYRPWFIDIDANTWQPCVHSARAVIERFRdriAGILLANVFGVGNpQISVWEELAAEWELPIVLDSAAGFGSTYADg 209
                                    *****************************9998889************9*************************999754 PP

                                    EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHC CS
                DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLe 235
                                    +++G  g++++fSF++tK++++GeGGa+v++d++l e+a++++n+Gl+     +++++++lG+n +l+ei+AAigl+qL 
  gi|121639327|ref|YP_979551.1| 210 ERLGGRGACEIFSFHATKPFAVGEGGALVSRDPRLVEHAYKFQNFGLV-----QTRESIQLGMNGKLSEISAAIGLRQLV 284
                                    ************************************************.....8999999******************** PP

                                    THHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-S CS
                DegT_DnrJ_EryC1 236 rldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvh 307
                                     ld+ +a+Rr+++e+y++++a+++    ++++++++  a +++a  ++++a+ ++++++ +l+++ i++r +
  gi|121639327|ref|YP_979551.1| 285 GLDRRLASRRKVLECYRTGMADAG----VRFQDNAN-VASLCFASACCTSAD-HKAAVLGSLRRHAIEARDY 350
                                    **********************99....68999999.8**********9999.9*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2562.45
//
Query:       gi|121639328|ref|YP_979552.1|  [L=533]
Description: hypothetical protein BCG_3473c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-10   39.6   0.0    1.8e-09   37.7   0.0    2.0  2  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.036   14.5   0.1    1.7  1  BMFP           Membrane fusogenic activity
      0.075   12.3   0.0       0.24   10.6   0.0    1.9  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.081   13.0   0.0       0.18   11.9   0.0    1.5  1  BCL_N          BCL7, N-terminal conserver region


Domain annotation for each model (and alignments):
>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   4.1e-13   1.8e-09       1     155 [.      19     205 ..      19     206 .. 0.77
   2 ?   -1.8   0.0      0.62   2.8e+03     106     135 ..     386     417 ..     383     442 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.1e-13
                  NAD_binding_9   1 aivGaGprGlavlerLlara....kkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslftddp..ptfaeWl 73 
                                    a +G G+++ ++l ++++      + + +l+i ++++ ++++ g ++ ++     +  ++ +++  f+d+p    ++ Wl
  gi|121639328|ref|YP_979552.1|  19 AFIGSGAACSMTLLEMADALlsspSASPKLRIAVVERdEQFWCGIPYGQRS---SIGSLAIQKLDDFADEPekAAYRIWL 95 
                                    689******99999888888776577788********77779777777774...477899999999***99996677777 PP

                  NAD_binding_9  74 rerga.....................lee..aeeldpddfvpRalyGrYlrdlfeellarl..pegvtvevhraevvdle 128
                                    +++++                       +    +  ++ ++pR l+G +l++++ +++a+l  ++  ++  +rae+ + +
  gi|121639328|ref|YP_979552.1|  96 EQNKQrwlaffqaeggaaaarwicdnR-DalDGNQWGELYLPRFLFGVFLSEQMIAAIAALgeRDLAEIVTIRAEAMSAH 174
                                    777666766666666665555554321.13434556779*********************965556799999******** PP

                  NAD_binding_9 129 eradgqavll...adg.aslaadaVvLAlGh 155
                                     +++++++ l    +g + +aa +Vv+A+G 
  gi|121639328|ref|YP_979552.1| 175 SADGHYRIGLrpsGNGpTAIAAGKVVVAIGS 205
                                    **999998886543333568*********96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.62
                  NAD_binding_9 106 ellarlpegvtvevhraevvdleeradgq..a 135
                                    ++ ++l ++ t++++ +ev++++  a+gq  a
  gi|121639328|ref|YP_979552.1| 386 QASEELAADGTLSLLAGEVLRVDACASGQpfA 417
                                    56677778889999999999999999987422 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   8.1e-06     0.036      25      51 ..     339     365 ..     317     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.1e-06
                           BMFP  25 reeieknvravlqealsklDLVtREEF 51 
                                      ++  +v a + +al+k+DLV+ EEF
  gi|121639328|ref|YP_979552.1| 339 LADLYDAVAALFGQALHKMDLVQQEEF 365
                                    578889999****************** PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.4e-05      0.24      93     157 ..     189     265 ..      16     292 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.4e-05
                                    TCEEEEEESEEEE---EEE-BCTCTTC.................TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  93 gdeekiaydklvlAtGssprdlgipGv................aenvgklvrtldsaealklkllpkrivvvGgGyiGvE 156
                                    +  + ia++k+v+A+Gs p +  +  +                +     +v  l++     + + +++++vvG+ ++++E
  gi|121639328|ref|YP_979552.1| 189 NGPTAIAAGKVVVAIGSPPTKAILASDsepaftyindfyspggE----SNVARLRDSLDRVESWEKRNVLVVGSNATSLE 264
                                    4446899**********998885554455778888888844433....4444444444444555557999*********9 PP

                                    H CS
                                    x RF
                    Pyr_redox_2 157 l 157
                                     
  gi|121639328|ref|YP_979552.1| 265 A 265
                                    5 PP

>> BCL_N  BCL7, N-terminal conserver region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     4e-05      0.18      15      36 ..     234     255 ..     231     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                          BCL_N  15 dlkrvikslekVrkWEKkWVtv 36 
                                    ++ r+  sl++V +WEK+ V v
  gi|121639328|ref|YP_979552.1| 234 NVARLRDSLDRVESWEKRNVLV 255
                                    6789999************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3990.44
//
Query:       gi|121639329|ref|YP_979553.1|  [L=234]
Description: hypothetical protein BCG_3474c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-18   64.4   0.7    1.8e-17   62.7   0.0    2.2  3  N_formyltrans_C  N-formyltransferase dimerization C-terminal 
    2.4e-15   56.8   0.0    3.1e-15   56.4   0.0    1.2  1  Formyl_trans_N   Formyl transferase


Domain annotation for each model (and alignments):
>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         1     9e+03      39      48 ..     100     108 ..      95     109 .. 0.75
   2 ?   -1.3   0.0       0.2   1.8e+03      16      34 ..     149     167 ..     146     168 .. 0.84
   3 !   62.7   0.0     2e-21   1.8e-17       1      51 [.     177     227 ..     177     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                                    TTS-EEEEEE CS
                N_formyltrans_C  39 dtGekvFvsl 48 
                                    d G+kv v++
  gi|121639329|ref|YP_979553.1| 100 D-GQKVGVTI 108
                                    6.99998887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHT--TT---E CS
                N_formyltrans_C  16 lrElidlLRAltfgpyknA 34 
                                    + E+ d +R  ++  +++A
  gi|121639329|ref|YP_979553.1| 149 VLEHFDAIRDGSYTAKSPA 167
                                    57999****9999888877 PP

  == domain 3  score: 62.7 bits;  conditional E-value: 2e-21
                                    HHHHHHB--TT-EEEHHHHHHHHHHT--TT---EEEE-TTS-EEEEEEEEE CS
                N_formyltrans_C   1 DykelceidLdkkvtlrElidlLRAltfgpyknAyfiddtGekvFvsleLt 51 
                                    D+++l ++dL++  t++ ++++LRAlt++++ nA+f+d  G+kvFv++ L+
  gi|121639329|ref|YP_979553.1| 177 DFEQLRRLDLNERGTFGHFLNRLRALTHDDFRNAWFVDASGRKVFVRVVLE 227
                                    9*************************************99********996 PP

>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   3.5e-19   3.1e-15      81     179 ..      56     151 ..      42     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 3.5e-19
                                    SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT- CS
                 Formyl_trans_N  81 dlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaed 160
                                    dl++   + +  p +l++ v  +++n+Hp + P  +G  ++  +++ G+k  Gvtih +d++lD+G+i+aq ++ i   d
  gi|121639329|ref|YP_979553.1|  56 DLVLSFHCKQRFPAALIDGV--RCVNVHPGFNPYNRGWFPQVFSIIDGQK-VGVTIHEIDDQLDHGPIIAQRECAIESWD 132
                                    55666666666677777765..67************************97.5**************************** PP

                                    -HHHHHHHHHHHHHHHHHH CS
                 Formyl_trans_N 161 tkeeleqrvadaehkalve 179
                                    +++++++r+ d e ++++e
  gi|121639329|ref|YP_979553.1| 133 SSGSVYARLMDIERELVLE 151
                                    *************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1600.19
//
Query:       gi|121639330|ref|YP_979554.1|  [L=188]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-18   63.9   0.0    8.9e-17   60.6   0.1    2.4  2  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1     5e-21   8.9e-17       1      47 []      23      69 ..      23      69 .. 0.98
   2 ?    0.1   0.0     0.041   7.3e+02      30      47 .]     111     128 ..     108     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 5e-21
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   Il aA  lfaerG +at++r+IA+r +v+ g+++r+F++K++L+ a+
  gi|121639330|ref|YP_979554.1| 23 ILQAATDLFAERGPAATSIRDIAARSKVNHGLVFRHFGTKDQLVGAV 69
                                   9******************************************9886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.041
                                    HHHHHHHTSSHHHHHHHH CS
                         TetR_N  30 kgalYryFpsKeeLleal 47 
                                     g l ++Fp+ +eLl+a+
  gi|121639330|ref|YP_979554.1| 111 VGQLQQRFPNVAELLDAV 128
                                    6667789********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1392.30
//
Query:       gi|121639331|ref|YP_979555.1|  [L=295]
Description: dioxygenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-49  167.0   0.5    8.2e-49  166.8   0.5    1.0  1  TauD      Taurine catabolism dioxygenase TauD, TfdA family


Domain annotation for each model (and alignments):
>> TauD  Taurine catabolism dioxygenase TauD, TfdA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.5   4.6e-53   8.2e-49       2     268 .]       7     269 ..       6     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 4.6e-53
                           TauD   2 vkpltpkfgae..gvdlsdleslddelkeelrellaeygvvvfrgfpl.speqqlefarrfGplygtpgrgtntkygevl 78 
                                    vk+l + +ga+  gv l     ld++ + e+r++l+ ++vv+frg++  ++++ql+fa  +G  +g+p  ++ ++   + 
  gi|121639331|ref|YP_979555.1|   7 VKKLGSRIGAQidGVRLGGD--LDPAAVNEIRAALLAHKVVFFRGQHQlDDAEQLAFAGLLGTPIGHPAAIALADDAPII 84 
                                    7899999****666666664..77777******************9666*************999999777666666666 PP

                           TauD  79 d.vssvyesadianlayttllwHtDlsylesppgiqlLhcleapatGGetpfvDgraaynaLpeelpellegltavrvyy 157
                                    +  +s   +  +an      +wHtD ++  + p +++L+++  p+ GG t++++++aay +Lpe l+ l e+l a ++++
  gi|121639331|ref|YP_979555.1|  85 TpINS---EFGKAN------RWHTDVTFAANYPAASVLRAVSLPSYGGSTLWANTAAAYAELPEPLKCLTENLWALHTNR 155
                                    63444...444444......5**********************************************************9 PP

                           TauD 158 hyrg.....gglrteqelpavdkhprtghpvvrthpvltgrkallvnppfatrieglgtpeskelldaleelledpefty 232
                                     ++         +  +++   + + rt+hpvvr+hp+ tg+++ll    f ++++gl++ es+ l++ l++ ++ pe+t+
  gi|121639331|ref|YP_979555.1| 156 YDYVttkplTAAQRAFRQVFEKPDFRTEHPVVRVHPE-TGERTLLAG-DFVRSFVGLDSHESRVLFEVLQRRITMPENTI 233
                                    99999999877777777777788899**********7.*********.******************************** PP

                           TauD 233 rfqwqeGdlvifdNrrvlHgrt.afdegeeRhllrcy 268
                                    r+ w +Gd++i+dNr+++H++  ++ ++++R ++r++
  gi|121639331|ref|YP_979555.1| 234 RWNWAPGDVAIWDNRATQHRAIdDY-DDQHRLMHRVT 269
                                    **********************99*.788******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2038.61
//
Query:       gi|121639332|ref|YP_979556.1|  [L=99]
Description: hypothetical protein BCG_3477 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-10   40.7   0.3      3e-10   39.7   0.2    1.6  2  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.28   11.1   0.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   3.4e-14     3e-10       3      62 ..      10      69 ..       8      81 .. 0.84
   2 ?   -1.9   0.0      0.34   3.1e+03      10      23 ..      85      98 ..      80      99 .] 0.77

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.4e-14
                                   EEEHHHHHHTHHHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH..HHHHHCSHHHH CS
                PhdYeFM_antitox  3 ivsiseakanlselldeveegeepviItrrGkpvaVlvsleeyerlqel.tekllslplna 62
                                   +++i+e+++++s++l +ve+gee + +t++G+ va+l++++  er  e+ +e+   +p+ +
  gi|121639332|ref|YP_979556.1| 10 AIGIRELRQHASRYLARVEAGEE-LGVTNKGRLVARLIPVQAAERSREAlIESGVLIPARR 69
                                   799********************.****************999987775455555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.34
                                   HHTHHHHHHHHHHH CS
                PhdYeFM_antitox 10 kanlselldeveeg 23
                                   k+ ls++l+e +++
  gi|121639332|ref|YP_979556.1| 85 KRTLSDVLNEMRDE 98
                                   66788888887775 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.1e-05      0.28       4      28 ..      46      70 ..      45      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.1e-05
                                   EEGGGHHHHHHHHHHTT-B-TTS-- CS
                         Trm5_N  4 VpkkegEkvRkkLlekglLdrnyKI 28
                                   +p + +E+ R +L+e g+L + +++
  gi|121639332|ref|YP_979556.1| 46 IPVQAAERSREALIESGVLIPARRP 70
                                   899****************888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 789.12
//
Query:       gi|121639333|ref|YP_979557.1|  [L=136]
Description: hypothetical protein BCG_3478 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   51.0   0.0    2.3e-13   50.7   0.0    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.3e-17   2.3e-13       1     116 [.       2     118 ..       2     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.3e-17
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                    i+ DTs+l +ll +e+++ ++r +l ++    e+ +ts l   El++v+ar     +   + ++++ ll++l ilp++++
  gi|121639333|ref|YP_979557.1|   2 IYMDTSALTKLLISEPETTELRTWLTAQsgqgEDAATSTLGRVELMRVVAR----YGQPGQTERARYLLDGLDILPLTEP 77 
                                    799************************************************....77777777888889*********** PP

                                    HHHHHHHHHHHHHSBHHHHHHHHHH..HHHT-EEE.ESSTHH CS
                            PIN  77 iaeeaaeialkygllpnDaliaAtA..kehgikliatfDedf 116
                                    +   a+ i     l+++Da+++A A  +++ +++++t+D ++
  gi|121639333|ref|YP_979557.1|  78 VIGLAETIGPAT-LRSLDAIHLAAAaqIKRELTAFVTYDHRL 118
                                    *****9999999.************77777777999***985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 962.36
//
Query:       gi|121639334|ref|YP_979558.1|  [L=578]
Description: cholesterol oxidase precursor choD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-13   49.8   0.0    9.1e-13   48.9   0.0    1.5  1  GMC_oxred_C    GMC oxidoreductase
    1.2e-12   48.2   0.1    1.5e-05   24.8   0.0    2.4  2  DAO            FAD dependent oxidoreductase
    5.2e-09   35.9   0.1    0.00045   19.7   0.1    2.2  2  GMC_oxred_N    GMC oxidoreductase
    3.8e-07   29.5   0.0    0.00016   20.9   0.0    2.3  2  FAD_binding_2  FAD binding domain
    4.8e-06   26.7   0.1      5e-05   23.5   0.1    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    7.7e-05   22.1   0.0    0.00042   19.6   0.0    1.9  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00086   18.6   0.0     0.0049   16.2   0.0    2.0  2  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.032   14.8   0.1       0.25   11.9   0.0    2.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.061   12.0   0.0       0.42    9.3   0.0    2.0  2  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   4.6e-16   9.1e-13      87     144 .]     468     525 ..     373     525 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.6e-16
                                    -S--B-TT-B-STCGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                    GMC_oxred_C  87 saHplGtcrMGadpkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                    +aH lG++ +G+dp+++V+D++ rv+g + L+VvD++++  ++g+np+l+i+a Ae+a
  gi|121639334|ref|YP_979558.1| 468 TAHFLGGAVIGDDPEHGVIDPYHRVYGYPTLYVVDGAAISANLGVNPSLSIAAQAERA 525
                                    68******************************************************97 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     1e-07    0.0002       1      33 [.       6      40 ..       6      70 .. 0.88
   2 !   24.8   0.0   7.5e-09   1.5e-05     148     234 ..     209     304 ..     185     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   dv+iiG+G  G+ tA+ L+++g  V +le+g++++
  gi|121639334|ref|YP_979558.1|  6 DVLIIGSGFGGSVTALRLTEKGyrVGVLEAGRRFS 40
                                   8******************************9987 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 7.5e-09
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.......EECTEEEE......EEEEEEE--GGGHH..HH.HTT. CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve.......rttpgend......aadavVnaaGawsd..ll.gll. 210
                                    l++ ++  ae++G++++  t+v+g+e++++++w+v+              +      +a+++V+aaG w +  ll ++  
  gi|121639334|ref|YP_979558.1| 209 LVKNYLGLAESAGAQVIPMTTVKGFERRSDGLWEVRtvrtgswL------RrdrrtfTATQLVLAAGTWGTqhLLfKMRd 282
                                    88999********************9999999***775444431......23455556789********87765555554 PP

                                    .CTTTSEEEEEEEEEEEEEECCTHS CS
                            DAO 211 .keldlpispvrgqvlvlkplsekl 234
                                     ++l + +s + g   ++   se+ 
  gi|121639334|ref|YP_979558.1| 283 rGRL-PGLSKRLGVLTRT--NSESI 304
                                    4444.2334444444444..34433 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.3e-05     0.025       1      85 [.       5      87 ..       5     132 .. 0.77
   2 !   19.7   0.1   2.3e-07   0.00045     173     263 ..     190     277 ..     186     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                    GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggreknrl..imvlalalklidkklntayetepekalngrrlilpaGktl 80
                                   +d l++g+G  gsv+A RL+e++  +v vleag r ++ +  ++   l+  l   +l  +  ++ ++   ++++il aG+++
  gi|121639334|ref|YP_979558.1|  5 YDVLIIGSGFGGSVTALRLTEKG-YRVGVLEAGRRFSDEEfaKTSWDLRKFLWAPRLGCYGIQRIHP--LRNVMIL-AGAGV 82
                                   689******************97.68*******9988877434444444444444444444444444..4556777.9**** PP

                    GMC_oxred_N 81 GGgsv 85
                                   GGgs+
  gi|121639334|ref|YP_979558.1| 83 GGGSL 87
                                   ***96 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.3e-07
                    GMC_oxred_N 173 gkhqcGvcllgvtcrtgarqstarawLrpalerpnleiltgakaekiilegrkkravGVeasdkkgt..vkrlvvaakev 250
                                    g+ +cG c++g  cr ga++   +++L  a ++ +++++  ++++ +  e r++    V++ ++++   + r++  a + 
  gi|121639334|ref|YP_979558.1| 190 GCLECGCCMTG--CRHGAKNTLVKNYLGLAESA-GAQVIPMTTVKGF--ERRSDGLWEVRTVRTGSWlrRDRRTFTATQL 264
                                    6789*******..***************99999.*************..9899999999999998888878888899*** PP

                    GMC_oxred_N 251 vvaaGalnsPqlL 263
                                    v+aaG+  + +lL
  gi|121639334|ref|YP_979558.1| 265 VLAAGTWGTQHLL 277
                                    *********9999 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   8.2e-08   0.00016       1      34 [.       6      39 ..       6      47 .. 0.94
   2 !    6.5   0.0     0.002       3.9     137     212 ..     203     282 ..      76     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.2e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqef 34
                                   Dv++iGsG++G + Al+++e+G +v v+e + +f
  gi|121639334|ref|YP_979558.1|  6 DVLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRF 39
                                   9****************************99876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.002
                                    ..HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT...EEEEEEEEETTTTCEEEEEESEEEE-----GG......... CS
                  FAD_binding_2 137 lvtghallarlvesarkagvdfqerteadeLivedg...rvtGavvenpesgrevrirakavvlatgGfgr.allkellg 212
                                     +  ++l++  +  a++ag ++ + t ++ + ++++   +v+++         +++++a+++vla+g +g  +ll+++++
  gi|121639334|ref|YP_979558.1| 203 HGAKNTLVKNYLGLAESAGAQVIPMTTVKGFERRSDglwEVRTVRTGSWLRRDRRTFTATQLVLAAGTWGTqHLLFKMRD 282
                                    4677888888888888889999999999999997555998888877766566667889************9888877766 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.5e-08     5e-05       1      31 [.       9      39 ..       9      49 .. 0.96
   2 ?   -0.2   0.0      0.62   1.2e+03      18      40 ..     405     427 ..     396     445 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.5e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                   I+G+G++G+v+A +L+++g++v +le+++r+
  gi|121639334|ref|YP_979558.1|  9 IIGSGFGGSVTALRLTEKGYRVGVLEAGRRF 39
                                   9**************************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.62
                                    CTEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8  18 agfdvlllekrdrlGGraasyev 40 
                                     + +++ + kr +lG r++s + 
  gi|121639334|ref|YP_979558.1| 405 LDNSITTFTKRGKLGIRWYSSKQ 427
                                    367899999**********9877 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00042       1      35 [.       5      39 ..       5      49 .. 0.90
   2 ?   -0.4   0.0      0.27   5.3e+02      93     110 ..     254     271 ..     202     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                   +dv++iG+G++G  +al+l ++g++v ++e+++ +
  gi|121639334|ref|YP_979558.1|  5 YDVLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRF 39
                                   69***************************977765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                                    TCEEEEEESEEEE---EE CS
                                    xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  93 gdeekiaydklvlAtGss 110
                                     d +++++ +lvlA G +
  gi|121639334|ref|YP_979558.1| 254 RDRRTFTATQLVLAAGTW 271
                                    345566666666666643 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.5e-06    0.0049       2      38 ..       5      41 ..       4      48 .. 0.89
   2 ?    0.0   0.0       0.2   3.9e+02     172     278 ..     293     399 ..     207     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38
                                   +dVlI+G+G  G ++al L+e+G rv ++e  ++ ++
  gi|121639334|ref|YP_979558.1|  5 YDVLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRFSD 41
                                   79***************************98877665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.2
                                    HTGG.EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCE.TEEEEEEEEECCE-GGGSCCCHHHHHHH CS
                  FAD_binding_3 172 lgie.fegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlen.tlerfyvqvearaekeersekfteeevk 249
                                    lg+  ++ +e+++ a  l+v++d dl++ v+  +  +++  +   + P++  + ++++ ++++  ++++ ++ ++  + +
  gi|121639334|ref|YP_979558.1| 293 LGVLtRTNSESIVGAATLKVNPDLDLTHGVAI-TSSIHPTADT-HIEPVRYgKGSNAMGLLQTLMTDGSGPQGTDVPRWR 370
                                    45443555566666666677766666633333.2222333332.688888877888888888888888888888999999 PP

                                    HHHHHHHTTSSCEEEEEEEEEEEEEEEEE CS
                  FAD_binding_3 250 arlreivgektldveieevsawtvaqrva 278
                                    + l++++++++ + ++ + ++w  ++ +a
  gi|121639334|ref|YP_979558.1| 371 QLLQTASQDPRGTIRMLNPRQWSERTVIA 399
                                    99999999999888888888888777666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.25       2      44 ..       7      46 ..       6      51 .. 0.92
   2 ?   -0.3   0.0      0.82   1.6e+03      45      77 ..     212     244 ..     204     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeask 44
                                   v+++G+G+ g   A  l+e g +V v+e++ ++    Dee++k
  gi|121639334|ref|YP_979558.1|  7 VLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRFS---DEEFAK 46
                                   89****************************9999...888877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.82
                                    HHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                      Pyr_redox  45 ilqeklekngievllntkveeiegsedg.vesvk 77 
                                    +     e  g +v+  t+v+ +e  +dg +e v+
  gi|121639334|ref|YP_979558.1| 212 NYLGLAESAGAQVIPMTTVKGFERRSDGlWE-VR 244
                                    55556688899*************9999554.65 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00021      0.42       1      35 [.       5      39 ..       5      42 .. 0.94
   2 ?    0.3   0.0      0.11   2.2e+02     110     164 ..     208     270 ..     201     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                   +dv++iG G  G  +A+++ ++g rV +le+++++
  gi|121639334|ref|YP_979558.1|  5 YDVLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRF 39
                                   59****************************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.........TTEEEEESEEEE---- CS
                    HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.k.......seeeleadklvlAtGG 164
                                    ++v+ +l  +++ag ++   t+vk++e+++dg  +v+t +       ++++++a++lvlA G 
  gi|121639334|ref|YP_979558.1| 208 TLVKNYLGLAESAGAQVIPMTTVKGFERRSDGLWEVRTvRtgswlrrDRRTFTATQLVLAAGT 270
                                    677777888899999999999999999999999999985467888888999*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4054.05
//
Query:       gi|121639335|ref|YP_979559.1|  [L=375]
Description: inosine 5-monophosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-32  112.5   1.4    2.8e-31  108.8   0.5    2.0  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    1.2e-08   34.4   4.6    1.2e-08   34.4   4.6    1.6  2  FMN_dh        FMN-dependent dehydrogenase
    0.00077   18.7   1.2     0.0012   18.0   1.2    1.3  1  Glu_synthase  Conserved region in glutamate synthase
     0.0011   18.4  12.0      0.014   14.8   2.1    3.0  3  NMO           Nitronate monooxygenase
     0.0038   16.4   0.4       0.12   11.5   0.0    2.3  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.023   14.0   7.1       0.89    8.8   1.1    2.5  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.5   9.2e-35   2.8e-31       5     249 ..      17     302 ..      13     310 .. 0.85
   2 ?    2.4   0.0     0.022        65     305     327 ..     346     368 ..     345     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 9.2e-35
                                    GGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          IMPDH   5 ddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkrs.. 82 
                                     ++ +vp++ +  +k+v+++ +l    + +iP+v+ + d+    e Ai+l r Gg+gv+  +  i ++ +  +k+ +   
  gi|121639335|ref|YP_979559.1|  17 SEISIVPSRRTRSSKDVSTAWQLD-AYRFEIPVVAHPTDALVSPEFAIELGRLGGLGVLNGEGLIGRHLDVEAKIAQLle 95 
                                    578999****99******999997.67*******************************9999888888777777776677 PP

                                    ...........................TTSXBXTTSXB-EEEEE-SSTTHHHH.HHHHHHTT-SEEEEE-STSSSHHHHH CS
                                    ...........................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  83 ...........................pnaakdekgrllvgaavgvkedaler.vkalveagvdvlvvdsahghsekvle 134
                                                                 aa  + ++  v+ av v+ ++ +     lv+ag+d+lv+  +    e+v +
  gi|121639335|ref|YP_979559.1|  96 aaaadpepstairllqelhaaplnpdlLGAAVARIREAGVTTAVRVSPQNAQWlTPVLVAAGIDLLVIQGTIVSAERVAS 175
                                    7899********************8774455556666678889998887766515789**********988888888877 PP

                                    HHHHH..HHHTT..TSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-S.TTBHHHHHCSB---HHHHHHHHHHHHCTC.T. CS
                                    xxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x. RF
                          IMPDH 135 avkei..kkkve..eveviaGnvataegakaLieagadavkvGiGpG.siCttrvvagvGvpqltAvaevaeaakka.g. 207
                                      + +  k+ ++  ++ v+aG v ++  a +L+++ga +v vG G+   + tt +v g+ vp +tA+a++a+a +++ + 
  gi|121639335|ref|YP_979559.1| 176 DGEPLnlKTFISelDIPVVAGGVLDHRTALHLMRTGAAGVIVGYGSTqGVTTTDEVLGISVPMATAIADAAAARRDYlDe 255
                                    65543003333322699****************************863799********************999887436 PP

                                    .....-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEE CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 208 .....vpviaDGGikysgdivkAlaaGadavmlGsllagteEspgev 249
                                         v+v+aDG i++sg+++kA+a+Gadav+lG  la   E+ ge 
  gi|121639335|ref|YP_979559.1| 256 tggryVHVLADGDIHTSGELAKAIACGADAVVLGTPLAESAEALGEG 302
                                    78999**************************************9985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.022
                                    HHHHHHHHHHHHHT-SSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 305 qlvgglrsgmgylGaktieelke 327
                                    +lvgglr +m ++G  +++e+++
  gi|121639335|ref|YP_979559.1| 346 NLVGGLRRSMAKAGYCDLKEFQK 368
                                    589*****************997 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   3.2e+03      29      66 ..      15      53 ..       8      56 .. 0.74
   2 !   34.4   4.6   4.1e-12   1.2e-08     206     312 ..     180     301 ..     126     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                   GGGGEEE--.-SSSS-SS-B--EEETTEEESSSEEE--B CS
                         FMN_dh 29 aferirlrp.rvlrdvskvdlsttllGqklslPvliaPv 66
                                   ++++i ++p r  r+ ++v+++ +l  +++++Pv++ P+
  gi|121639335|ref|YP_979559.1| 15 ELSEISIVPsRRTRSSKDVSTAWQLDAYRFEIPVVAHPT 53
                                   566777777356677778899999999999999998886 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 4.1e-12
                                    HHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE...--GGGTSSTT---.HHHCHHHHHHHH............S CS
                         FMN_dh 206 ddikwlreqtklplvvKGvltaedakraveaGvdgivv...SNHGGRqldgapa.tidvLpeiveav..........ggr 271
                                     ++k++ +++++p+v  Gvl++++a  +++ G+ g++v   S  G    d +   ++ +  +i++a+          ggr
  gi|121639335|ref|YP_979559.1| 180 LNLKTFISELDIPVVAGGVLDHRTALHLMRTGAAGVIVgygSTQGVTTTDEVLGiSVPMATAIADAAaarrdyldetGGR 259
                                    5789999*******************************444455555555444323334466655556667777666445 PP

                                    .S-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHH CS
                         FMN_dh 272 .ievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGe 312
                                     + vl+Dg i +    +kA+a+GAdav+lG p++  + a Ge
  gi|121639335|ref|YP_979559.1| 260 yVHVLADGDIHTSGELAKAIACGADAVVLGTPLAESAEALGE 301
                                    5*******************************9988888876 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   4.1e-07    0.0012     251     304 ..     234     290 ..     186     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.1e-07
                                    B---HHHHHHHHH...HHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                   Glu_synthase 251 aGlPlelalaevd...qtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                      +P+ +a+a +    +   +e   + v++ adG+++t+ +++ka+a GAdav +gt
  gi|121639335|ref|YP_979559.1| 234 ISVPMATAIADAAaarRDYLDETGGRYVHVLADGDIHTSGELAKAIACGADAVVLGT 290
                                    456888888765411134455666778****************************99 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.052   1.6e+02      10      42 ..      44      76 ..      37     119 .. 0.81
   2 !   14.8   2.1   4.6e-06     0.014     151     222 ..     152     218 ..     123     231 .. 0.77
   3 !    6.9   1.6    0.0012       3.5     193     225 ..     254     292 ..     219     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.052
                            NMO 10 ikppvvqpgmggiskarLaaavsnaGgLGvlas 42
                                    + pvv+ +      +++a      GgLGvl +
  gi|121639335|ref|YP_979559.1| 44 FEIPVVAHPTDALVSPEFAIELGRLGGLGVLNG 76
                                   577999999999999***************984 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.6e-06
                            NMO 151 kvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqig 222
                                    ++ a+G D l++qG      +     +  g+   +++  + +diPv+A GG+ d+r     ++ GA+gv +g
  gi|121639335|ref|YP_979559.1| 152 VLVAAGIDLLVIQGTIVSAERV----ASDGEPLNLKTFISELDIPVVA-GGVLDHRTALHLMRTGAAGVIVG 218
                                    5678999999999988766555....445677777888899*****96.9*******************998 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0012
                            NMO 193 d......iPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                    d      + v+A G i +  ++a a+a GA +v +gt +
  gi|121639335|ref|YP_979559.1| 254 DetggryVHVLADGDIHTSGELAKAIACGADAVVLGTPL 292
                                    1555566889***************************76 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.019        57     130     177 ..     176     222 ..     124     232 .. 0.77
   2 !   11.5   0.0   4.1e-05      0.12     145     178 ..     261     294 ..     241     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.019
                                    SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                           NanE 130 aepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsait 177
                                    + + ++l   +se ++ v+a G ++    a + +++G++ v+vG   t
  gi|121639335|ref|YP_979559.1| 176 DGEPLNLKTFISELDIPVVAGGVLDH-RTALHLMRTGAAGVIVGYGST 222
                                    44456666667888999999998886.68999***********96555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                                    --EEEES---SHHHHHHHHTT--SEEEE-HHHH- CS
                           NanE 145 lkviaeGrintPekakkaieiGvdavvvGsaitr 178
                                    ++v+a+G i+t  + +kai +G+davv+G+ ++ 
  gi|121639335|ref|YP_979559.1| 261 VHVLADGDIHTSGELAKAIACGADAVVLGTPLAE 294
                                    689**************************98865 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1    0.0003      0.89     164     226 ..     179     244 ..     153     256 .. 0.75
   2 ?    8.0   0.4   0.00055       1.6     176     212 ..     261     297 ..     257     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                                    HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEE....SHHHHTSSSHHHHHHHHHHHHHH CS
                           ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavll....ntavaeakdpvamArafklavea 226
                                    + +lk++i+e+++Pv+   G+     a + m  Ga +v++       v+++++   +   +++a+  
  gi|121639335|ref|YP_979559.1| 179 PLNLKTFISELDIPVV-AGGVLDHRTALHLMRTGAAGVIVgygsTQGVTTTDEVLGISVPMATAIAD 244
                                    679***********86.689*9*****************9433224577777765544444444433 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00055
                                    S-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                           ThiG 176 vPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                    v v+ D  i ++ + a+a+  Gadav+l t +ae+++
  gi|121639335|ref|YP_979559.1| 261 VHVLADGDIHTSGELAKAIACGADAVVLGTPLAESAE 297
                                    67899999*************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2842.34
//
Query:       gi|121639336|ref|YP_979560.1|  [L=529]
Description: inosine 5'-monophosphate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   9.5e-152  504.9   8.0   1.1e-151  504.7   8.0    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    9.6e-21   74.0   0.3    2.9e-09   37.2   0.1    2.9  2  CBS           CBS domain
    1.8e-08   34.2  15.4    0.00035   20.0  11.7    2.4  2  NMO           Nitronate monooxygenase
    3.2e-06   26.4  11.7    9.8e-06   24.8  11.1    2.0  2  FMN_dh        FMN-dependent dehydrogenase
    0.00025   20.6   2.9       0.31   10.5   0.1    2.3  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.077   12.1   7.2       0.14   11.3   7.2    1.4  1  Glu_synthase  Conserved region in glutamate synthase
        1.3    8.2   5.5       0.81    8.8   0.9    2.1  2  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.7   8.0  4.3e-155  1.1e-151       1     345 []      44     515 ..      44     515 .. 0.97

  Alignments for each domain:
  == domain 1  score: 504.7 bits;  conditional E-value: 4.3e-155
                                    E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvk 80 
                                    gltfddvll+pa+s+v+p+++d++++ltkki+l++Plvs+amdtvtes+mAia+ar+Gg+gv+h+nl + eqa +v+ vk
  gi|121639336|ref|YP_979560.1|  44 GLTFDDVLLLPAASDVVPATADTSSQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLHRNLPVAEQAGQVEMVK 123
                                    79****************************************************************************** PP

                                    TS.............................................................................. CS
                                    xx.............................................................................. RF
                          IMPDH  81 rs.............................................................................. 82 
                                    rs                                                                              
  gi|121639336|ref|YP_979560.1| 124 RSeagmvtdpvtcrpdntlaqvdalcarfrisglpvvdddgalvgiitnrdmrfevdqskqvaevmtkaplitaqegvsa 203
                                    ******************************************************************************** PP

                                    .......................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE CS
                                    .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  83 .......................................pnaakdekgrllvgaavgvkedalervkalveagvdvlvvd 123
                                                                           p a+kd++grllvgaavgv  da  r+ +lv+agvdvlvvd
  gi|121639336|ref|YP_979560.1| 204 saalgllrrnkieklpvvdgrgrltglitvkdfvkteqhPLATKDSDGRLLVGAAVGVGGDAWVRAMMLVDAGVDVLVVD 283
                                    ******************************************************************************** PP

                                    -STSSSHHHHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 124 sahghsekvleavkeikkkvee.veviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaea 202
                                    +ah+h++ vl++v ++k++v + vev++Gnvat+++a+aL++agadavkvG+GpGsiCttrvvagvG pq+tA++e+++a
  gi|121639336|ref|YP_979560.1| 284 TAHAHNRLVLDMVGKLKSEVGDrVEVVGGNVATRSAAAALVDAGADAVKVGVGPGSICTTRVVAGVGAPQITAILEAVAA 363
                                    ********************999********************************************************* PP

                                    HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH....-..SS-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x..xxxx RF
                          IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkk....g..skdr 276
                                    ++ agvpviaDGG++ysgdi+kAlaaGa++ mlGsllagt E+pge+i+++g++yK+yrGmgslgam+     +  skdr
  gi|121639336|ref|YP_979560.1| 364 CRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLLAGTAEAPGELIFVNGKQYKSYRGMGSLGAMRGrggaTsySKDR 443
                                    *******************************************************************4445541569*** PP

                                    TS-......--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                    xxx..x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 277 yfq..k..keklvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                    yf   +  ++klvpeG+egrvp++g++++v++ql+gglr++mgy+G+ tie l+ +a+fvrit aglkesh+H
  gi|121639336|ref|YP_979560.1| 444 YFAddAlsEDKLVPEGIEGRVPFRGPLSSVIHQLTGGLRAAMGYTGSPTIEVLQ-QAQFVRITPAGLKESHPH 515
                                    **84314355*******************************************6.79***************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   1.1e-12   2.9e-09       5      52 ..     129     176 ..     116     180 .. 0.88
   2 !   33.9   0.0   1.3e-11   3.3e-08       1      53 [.     185     238 ..     185     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.1e-12
                                    SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                    m +d+vt++pd tl+++  l ++ ++s+lPVVd+dg lvGi+t rD  
  gi|121639336|ref|YP_979560.1| 129 MVTDPVTCRPDNTLAQVDALCARFRISGLPVVDDDGALVGIITNRDMR 176
                                    889********99999999976777*********************86 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 1.3e-11
                                    HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    V+++mt+ +++t+ +  + + al l+r++++  lPVVd+ g+l G++t +D ++
  gi|121639336|ref|YP_979560.1| 185 VAEVMTKaPLITAQEGVSASAALGLLRRNKIEKLPVVDGRGRLTGLITVKDFVK 238
                                    789****8889***************9999*********************986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.9e-06      0.01       2      41 ..      68     107 ..      67     125 .. 0.91
   2 !   20.0  11.7   1.4e-07   0.00035     138     232 ..     309     407 ..     253     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-06
                            NMO   2 slltellkikppvvqpgmggiskarLaaavsnaGgLGvla 41 
                                    s+lt+++  k p+v + m  +++ r+a a + aGg+Gvl 
  gi|121639336|ref|YP_979560.1|  68 SQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLH 107
                                    679999********************************95 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.4e-07
                            NMO 138 vliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd......iPviAaGGiidrrgvaaa 211
                                    v+ + +++  +a ++  +GaDa+ v G   G    t+ v+++g  ++   +l+av+      +PviA GG+    ++a a
  gi|121639336|ref|YP_979560.1| 309 VVGGNVATRSAAAALVDAGADAVKV-GVGPGSICTTRVVAGVGAPQIT-AILEAVAacrpagVPVIADGGLQYSGDIAKA 386
                                    4556788889999999*****9766.7777777778888888877765.56677777889******************** PP

                            NMO 212 LalGAsgvqigtrfLltkesd 232
                                    La+GAs + +g+ + +t e++
  gi|121639336|ref|YP_979560.1| 387 LAAGASTAMLGSLLAGTAEAP 407
                                    **************9999987 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  11.1   3.8e-09   9.8e-06     206     303 ..     294     400 ..     253     410 .. 0.80
   2 ?   -1.0   0.0      0.26   6.8e+02     317     344 ..     472     499 ..     470     503 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.8e-09
                                    HHHHHHHHHHSSEEEEEE..E-SHHHHHHHHHTTESEEEE--GGG.....TSSTT---H.HHCHHHHHHHH..S.S-EEE CS
                         FMN_dh 206 ddikwlreqtklplvvKG..vltaedakraveaGvdgivvSNHGG.....Rqldgapat.idvLpeiveavggr.ievlv 276
                                    d + +l++++  ++ v G  v t   a  +v+aG+d++ v    G     R + g+ a+ i ++ e v+a++   ++v++
  gi|121639336|ref|YP_979560.1| 294 DMVGKLKSEVGDRVEVVGgnVATRSAAAALVDAGADAVKVGVGPGsicttRVVAGVGAPqITAILEAVAACRPAgVPVIA 373
                                    55566666665433333223889999**************98888899999999987765999999999999755***** PP

                                    ESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 277 DgGirrGsDvlkAlalGAdavllGRpf 303
                                    DgG +   D++kAla GA+  +lG  +
  gi|121639336|ref|YP_979560.1| 374 DGGLQYSGDIAKALAAGASTAMLGSLL 400
                                    ***********************9765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                                    HHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                         FMN_dh 317 rvleilraelertmallGvksvaeldrs 344
                                    +v++ l+  l+++m  +G  +++ l+++
  gi|121639336|ref|YP_979560.1| 472 SVIHQLTGGLRAAMGYTGSPTIEVLQQA 499
                                    78999*****************999876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   0.00014      0.35      39     102 ..     273     334 ..     260     342 .. 0.83
   2 !   10.5   0.1   0.00012      0.31     187     223 ..     364     400 ..     345     410 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                    HHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS.SSSHHHHHHHHHCT-SEEEES CS
                   His_biosynth  39 eeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG.Irsledveelleagadkviig 102
                                     ++g+d l+ v  d a+++++  ld+v ++ +ev   v+v GG + + +++++l++agad v +g
  gi|121639336|ref|YP_979560.1| 273 VDAGVDVLV-V--DTAHAHNRLVLDMVGKLKSEVGDRVEVVGGnVATRSAAAALVDAGADAVKVG 334
                                    556666554.3..568999999*****************99999****************99876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00012
                                    HHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                   His_biosynth 187 aeavkipviasGGvgsledlkelksegvdavivgsal 223
                                    ++   +pvia GG +   d++++ ++g++ +++gs+l
  gi|121639336|ref|YP_979560.1| 364 CRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLL 400
                                    3334455555555555555555555555555555544 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.2   5.5e-05      0.14     212     304 ..     311     398 ..     291     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                                    -STTHH.HHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHH CS
                   Glu_synthase 212 aeagve.tiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvv 290
                                     ++++    aa +++a+ad++++ G+  G     + ++  +G P ++a+ e++ + +  g    v +iadGgl+ + d++
  gi|121639336|ref|YP_979560.1| 311 GGNVATrSAAAALVDAGADAVKV-GVGPGS-ICTTRVVAGVGAPQITAILEAVAACRPAG----VPVIADGGLQYSGDIA 384
                                    444433034556899******99.554443.456678899*************9998877....89************** PP

                                    HHHHHT-SEEE-SH CS
                   Glu_synthase 291 kalalGAdavgigt 304
                                    kala GA +  +g+
  gi|121639336|ref|YP_979560.1| 385 KALAAGASTAMLGS 398
                                    *******9988876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.065   1.7e+02     231     274 ..     293     335 ..     287     347 .. 0.89
   2 ?    8.8   0.9   0.00032      0.81     236     276 ..     360     400 ..     347     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESH CS
                         DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvyt 274
                                    l ++ +l++++ +++ ++g G + +   a   + aGA +v+v+ 
  gi|121639336|ref|YP_979560.1| 293 LDMVGKLKSEVGDRVEVVG-GNVATRSAAAALVDAGADAVKVGV 335
                                    678999999********98.99******************9986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00032
                                    HHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                         DHO_dh 236 elykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                    ++++     +p+I+ GG++ + D    + aGAs   +++ l
  gi|121639336|ref|YP_979560.1| 360 AVAACRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLL 400
                                    5555555679***********************99999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4056.24
//
Query:       gi|121639337|ref|YP_979561.1|  [L=136]
Description: hypothetical protein BCG_3482 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-50  169.4   1.7    3.7e-50  169.2   1.7    1.0  1  DUF5319   Family of unknown function (DUF5319)


Domain annotation for each model (and alignments):
>> DUF5319  Family of unknown function (DUF5319)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   1.7   2.1e-54   3.7e-50       5     118 ..       9     122 ..       5     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 2.1e-54
                        DUF5319   5 lPrdPfaddPndPasfleeeeeleplseeereevledLadveefkalLeprGirGivllCedCeeehyydWdllaanlka 84 
                                    lP+dPfaddP dP+++le+ e+ +pl+++er +v++dLad+++++alL+++GirG+v++C++C+++hy+dWd+l++nl +
  gi|121639337|ref|YP_979561.1|   9 LPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKGIRGLVVCCDECQQDHYHDWDMLRSNLLQ 88 
                                    8******************************************************************************* PP

                        DUF5319  85 lledelarvhePaadpdpeayvsWdyalGyldgl 118
                                    ll d+++r+hePa+dp+p++yv+Wdy++Gy+d+ 
  gi|121639337|ref|YP_979561.1|  89 LLIDGTVRPHEPAYDPEPDSYVTWDYCRGYADAS 122
                                    ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 982.61
//
Query:       gi|121639338|ref|YP_979562.1|  [L=299]
Description: hypothetical protein BCG_3483c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-17   63.7  11.3    3.4e-17   62.4  11.3    1.8  1  RsdA_SigD_bd  Anti-sigma-D factor RsdA to sigma factor bindin
  ------ inclusion threshold ------
       0.28   11.6   1.4       0.61   10.5   0.2    1.9  2  Chibby        Chibby family


Domain annotation for each model (and alignments):
>> RsdA_SigD_bd  Anti-sigma-D factor RsdA to sigma factor binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4  11.3   3.8e-21   3.4e-17       2      46 .]      14      58 ..      13      58 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3.8e-21
                                   CHHHHHHHHHHHHHHTT-----SSHHHHHHHHHHHHHHHHHHS-X CS
                   RsdA_SigD_bd  2 LaavardDaLLDALAgrgpvdtddpdeyeLAaLLadWRddvraeP 46
                                   L+++ar+D+LLDALA+r++vd +dp++++LAaLL +WRdd+r++P
  gi|121639338|ref|YP_979562.1| 14 LDELARTDLLLDALAEREEVDFADPRDDALAALLGQWRDDLRWPP 58
                                   9*******************************************9 PP

>> Chibby  Chibby family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.19   1.7e+03      94     105 ..      19      30 ..      18      33 .. 0.87
   2 ?   10.5   0.2   6.8e-05      0.61      44      96 ..     138     191 ..     122     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                         Chibby  94 klevLLDmLtet 105
                                    ++++LLD L+e+
  gi|121639338|ref|YP_979562.1|  19 RTDLLLDALAER 30 
                                    579*******96 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.8e-05
                         Chibby  44 klkLgdqelvFedGqWvsesggaggasskeslrlk..kenkqLeeEnnllklkle 96 
                                    k +L + e + ++GqW  ++++++++ss   +++    + + L +E nll+ k+e
  gi|121639338|ref|YP_979562.1| 138 KANLAKVEQMIAQGQWAEAQDELAEVSS-TVQAVTdgSRRQDLINEVNLLNTKVE 191
                                    78899999999********999999876.3333331267899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2032.77
//
Query:       gi|121639339|ref|YP_979563.1|  [L=212]
Description: RNA polymerase sigma factor SigD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   49.5   1.0    4.8e-13   48.7   0.2    1.8  2  Sigma70_r2    Sigma-70 region 2
      3e-10   39.6   0.5      3e-10   39.6   0.5    2.2  2  Sigma70_r4_2  Sigma-70, region 4
    4.8e-10   38.8   0.6      1e-09   37.8   0.6    1.6  1  Sigma70_r4    Sigma-70, region 4
    0.00043   20.2   0.1    0.00074   19.5   0.1    1.3  1  Sigma70_ECF   ECF sigma factor
    0.00053   20.0   0.0    0.00086   19.3   0.0    1.4  1  HTH_16        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.2   1.3e-16   4.8e-13       3      70 ..      49     119 ..      47     120 .. 0.93
   2 ?   -1.7   0.1      0.71   2.5e+03      53      67 ..     189     203 ..     189     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.3e-16
                                    HHHHHHHHHHHHHC....T-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS
                     Sigma70_r2   3 erylplvkrlarrl....lgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 
                                    e  +p v+r++r +     +sg++a+D++Qe++l+ + a++r++ +rg+ f a+l+ ia +++ d++R ++r
  gi|121639339|ref|YP_979563.1|  49 ETIRPIVVRYCRARvgtvERSGLSADDVAQEVCLATITALPRYR-DRGRPFLAFLYGIAAHKVADAHRAAGR 119
                                    67789999****9988888899**********************.***********************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHHHHHT CS
                     Sigma70_r2  53 llriarnaaidrlRk 67 
                                    ++r+a ++a+ rl++
  gi|121639339|ref|YP_979563.1| 189 AVRVAQHRALQRLKD 203
                                    578999999999886 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.97   3.5e+03      46      51 ..      57      62 ..      56      63 .. 0.86
   2 !   39.6   0.5   8.4e-14     3e-10       5      54 .]     152     201 ..     149     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.97
                                   HHHHHH CS
                   Sigma70_r4_2 46 rlsRAr 51
                                   r++RAr
  gi|121639339|ref|YP_979563.1| 57 RYCRAR 62
                                   89***9 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 8.4e-14
                                    HHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   5 realaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                     e+l+ Lp +qrei++lr + gls +E+A+  g + g+V+ + +RA+++L
  gi|121639339|ref|YP_979563.1| 152 NELLEILPAKQREILILRVVVGLSAEETAAAVGSTTGAVRVAQHRALQRL 201
                                    589********************************************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.6   2.8e-13     1e-09       2      49 ..     155     202 ..     154     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.8e-13
                                    HHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     Sigma70_r4   2 LasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                    L+ Lp+++re+l lr + gl+ eE+++  g + ++Vr  ++rAl++L+
  gi|121639339|ref|YP_979563.1| 155 LEILPAKQREILILRVVVGLSAEETAAAVGSTTGAVRVAQHRALQRLK 202
                                    889********************************************9 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   2.1e-07   0.00074      12     169 ..      37     191 ..      28     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                    Sigma70_ECF  12 kdGdaeaaeqllelvydeLrrlagskl.knerreetledtaLvfeaflrlvdkekfpdlsgrdh.lfalaaeamrrilid 89 
                                      Gd +a  ++le++   ++r  ++++   er +   +d+  + e +l+ +   ++p + +r+  + a +  + + ++ d
  gi|121639339|ref|YP_979563.1|  37 VAGDRNALREVLETIRPIVVRYCRARVgTVERSGLSADDV--AQEVCLATIT--ALPRYRDRGRpFLAFLYGIAAHKVAD 112
                                    579************************6666666555555..6899999998..999**9998736688999******** PP

                    Sigma70_ECF  90 haRrrkrqkRGGdvvraeldeeedsvdsdspdelleLdea..lerlls.ldpeqarlvelrkleGlsveEiAeklgvskr 166
                                    + R+  r +    +  + l e+  s d+ ++++ +e d+   +++ll+ l+ +q++ + lr++ Gls eE+A+++g  + 
  gi|121639339|ref|YP_979563.1| 113 AHRAAGRDRA---YPAETLPERW-SADAGPEQMAIEADSVtrMNELLEiLPAKQREILILRVVVGLSAEETAAAVGSTTG 188
                                    *****99986...4555555555.4455555555554442113444454788999999****************998877 PP

                    Sigma70_ECF 167 tve 169
                                    +v+
  gi|121639339|ref|YP_979563.1| 189 AVR 191
                                    765 PP

>> HTH_16  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.4e-07   0.00086       3      65 .]      32      92 ..      30      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.4e-07
                         HTH_16  3 vieaAvnGDeeAieeiLkhYegyIrklSlrklydedgnvngyvdedlkqeleiklieaIlkFk 65
                                   v+  Av+GD+ A+ e+L+  ++   ++++   +    + +g   +d+ qe++++ i+a+ +++
  gi|121639339|ref|YP_979563.1| 32 VVAEAVAGDRNALREVLETIRPIVVRYCRA--RVGTVERSGLSADDVAQEVCLATITALPRYR 92
                                   8899*************************4..44444568899***************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1457.00
//
Query:       gi|121639340|ref|YP_979564.1|  [L=275]
Description: hypothetical protein BCG_3485c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.1    8.7  21.6       0.21   11.9   6.1    3.6  4  TPR_12    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       0.4   7.3e+03      58      63 ..      47      52 ..      37      61 .. 0.47
   2 ?   11.9   6.1   1.2e-05      0.21       5      71 ..      73     135 ..      69     135 .. 0.91
   3 ?    3.5   2.8    0.0048        86      10      72 ..     157     219 ..     154     222 .. 0.66
   4 ?    2.3   0.5     0.012   2.1e+02       9      35 ..     198     224 ..     190     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.4
                         TPR_12 58 lgryee 63
                                   +gry+ 
  gi|121639340|ref|YP_979564.1| 47 QGRYAH 52
                                   222222 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.2e-05
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                    a++  +++lr+lg ++ A+ +  +al++a    G d+++ a +l++L+   +  gr+++A +ll +a
  gi|121639340|ref|YP_979564.1|  73 AHSTQGSLLRQLGWHTLARGWDGRALALA----GADREAGADALIGLAADALGVGRFAAAGALLDRA 135
                                    44569************************....9**************************8888776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0048
                         TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                    a++ ++ g+ + A ++ e+a+e+ ++         + +   L+ ++  +g  + A++  eeal
  gi|121639340|ref|YP_979564.1| 157 AELAMATGDGATAVRHAEEAVELTQAMAVASARHRVKSDVVLAAALCSAGAVARARAVGEEAL 219
                                    778899999999999999999998754333333355555555555555566666666666655 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.012
                         TPR_12   9 laavlrrlgrydeAlellekaleiarr 35 
                                    laa+l+ +g  + A++  e+al++  r
  gi|121639340|ref|YP_979564.1| 198 LAAALCSAGAVARARAVGEEALDATAR 224
                                    677788888888888888888877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2118.91
//
Query:       gi|121639341|ref|YP_979565.1|  [L=102]
Description: transcriptional regulatory protein whiB-like whib3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-25   87.5   1.4    8.3e-25   87.2   1.4    1.1  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   1.4   4.6e-29   8.3e-25       1      62 [.      17      85 ..      17      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 4.6e-29
                           Whib  1 WreraaCrgedpelffpekg.......dreeeAkavCarCpVrreCleealeegeeyGvwGGltereRr 62
                                   W+ ++ Crg+d+++ff+++g       +re++Ak++C+rCpV ++C+ +ale ge+yGvwGGl+e+eR+
  gi|121639341|ref|YP_979565.1| 17 WQLQGLCRGMDSSMFFHPDGergrartQREQRAKEMCRRCPVIEACRSHALEVGEPYGVWGGLSESERD 85
                                   ******************999***********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 812.58
//
Query:       gi|121639342|ref|YP_979566.1|  [L=539]
Description: chaperonin GroEL [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-87  294.2   9.4    4.7e-87  292.7   9.4    1.6  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.7   9.4   2.6e-91   4.7e-87       1     491 []      22     525 ..      22     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 292.7 bits;  conditional E-value: 2.6e-91
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHH....HHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPa....akllveaaesqdeevGDGTttvviLageLlee 76 
                                    lad+v++tlGP+G+ ++l +++g ++vTnDG+t+++e+e+e+P     a+l+ ++a+++++ +GDGTtt++iLa++L++ 
  gi|121639342|ref|YP_979566.1|  22 LADTVRVTLGPRGRHVVLAKAFGGPTVTNDGVTVAREIELEDPFedlgAQLVKSVATKTNDVAGDGTTTATILAQALIKG 101
                                    79****************************************************************************** PP

                                    HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCC CS
                     Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieen 156
                                    + +l+aagv+p+++  g+ ka++++ eaL + a  +s +    + +++va++s +        e++++lv +A+      
  gi|121639342|ref|YP_979566.1| 102 GLRLVAAGVNPIALGVGIGKAADAVSEALLASATPVSGK----TGIAQVATVSSRD-------EQIGDLVGEAM------ 164
                                    *****************************8885555554....7888888776554.......6**********...... PP

                                    SEECSCCCEECCCCEECEC..TTSEEESEEEESS--SST.......TSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                     Cpn60_TCP1 157 ekeldlgrikvvkieggsl..edselveGlvldkgvlsp.......dmpkklenakvllldvsLeiektetkttvvlsda 227
                                        ++g  +vv++e++s   ++ e+ eG+ +dkg+ls+       + +  le+a +ll + +++   +           
  gi|121639342|ref|YP_979566.1| 165 ---SKVGHDGVVSVEESSTlgTELEFTEGIGFDKGFLSAyfvtdfdNQQAVLEDALILLHQDKISSLPD----------- 230
                                    ...89*************955555566************888877666677799999999999999888........... PP

                                    CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S-...........-HHHHHHHHHHHT-- CS
                     Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrv...........kkkdlerlakatGat 296
                                                 l++llek++ +g+++++++++++ +al++l+ n i+   ++           +k+ le+la +tG++
  gi|121639342|ref|YP_979566.1| 231 -------------LLPLLEKVAGTGKPLLIVAEDVEGEALATLVVNAIRKTLKAvavkgpyfgdrRKAFLEDLAVVTGGQ 297
                                    .............***********************************9988888************************* PP

                                    EBSCGGGGGCGC.....-EEEEEEEECCETTCCEEEEE...................................CESSSSX CS
                     Cpn60_TCP1 297 avssledltpee.....lGtakkveeekigsekttiie...................................evksgki 336
                                    +v+  + +   e     lG+a++v    +++++t+i++                                     + g++
  gi|121639342|ref|YP_979566.1| 298 VVNPDAGMVLREvglevLGSARRV---VVSKDDTVIVDgggtaeavanrakhlraeidksdsdwdreklgerlAKLAGGV 374
                                    *****666654445666*******...9**********88887777777777777666666666665555554339**** PP

                                    EEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHH.HHHHCCCCTSXCCHHHHHHHHHHHHTHHHHH CS
                     Cpn60_TCP1 337 atillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelela.kklkeyaksvsgeeqlaieafakALevipkt 415
                                    a+i++++at+t l+e+++++edA+ ++k+a+e e++vpGGGa++++ a k+l e   s++g+e l++++f++AL +++  
  gi|121639342|ref|YP_979566.1| 375 AVIKVGAATETALKERKESVEDAVAAAKAAVE-EGIVPGGGASLIHQArKALTELRASLTGDEVLGVDVFSEALAAPLFW 453
                                    ********************************.***********98772579999************************* PP

                                    HHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXXX CS
                     Cpn60_TCP1 416 LaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiikakk 491
                                    +a NaGld+  v++k+ +        +g++v++ ++ dl ++gv+Dp+kv+r+a+ +A+++a+++L+++ ++++k+
  gi|121639342|ref|YP_979566.1| 454 IAANAGLDGSVVVNKVSE----LPAGHGLNVNTLSYGDLAADGVIDPVKVTRSAVLNASSVARMVLTTETVVVDKP 525
                                    ****************88....33377**********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4154.58
//
Query:       gi|121639343|ref|YP_979567.1|  [L=100]
Description: co-chaperonin GroES [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-35  119.2   0.2    6.5e-35  119.1   0.2    1.0  1  Cpn10     Chaperonin 10 Kd subunit


Domain annotation for each model (and alignments):
>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.2   3.6e-39   6.5e-35       1      93 []       5      98 ..       5      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 3.6e-39
                                   S-EE-TTEEEEEESGG-TTS-TT----HHHHHSEEEEEEEEE-T.........TS-TTS--T-EEEEEGGGTSS-GG---.E CS
                          Cpn10  1 kikplgdrVlvkraeeeekteggiilpdsakekpeqGvVvaVGegarnekge.dvplevkvgdkVlfpkyagtkvkvdgkey 81
                                   +ikpl+d++lv+ +e+e++t++g+++pd+akekp++G+VvaVG+g+ +e+ge ++pl+v +gd+V+++ky+gt++k++g+ey
  gi|121639343|ref|YP_979567.1|  5 NIKPLEDKILVQANEAETTTASGLVIPDTAKEKPQEGTVVAVGPGRWDEDGEkRIPLDVAEGDTVIYSKYGGTEIKYNGEEY 86
                                   69**********************************************999879**************************** PP

                                   EEEEGGG--EE- CS
                          Cpn10 82 lilkekdIlavi 93
                                   lil+++d+lav+
  gi|121639343|ref|YP_979567.1| 87 LILSARDVLAVV 98
                                   **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 711.74
//
Query:       gi|121639344|ref|YP_979568.1|  [L=344]
Description: DNA-binding/iron metalloprotein/AP endonuclease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-86  289.4   0.4    3.8e-86  289.2   0.4    1.0  1  Peptidase_M22   Glycoprotease family
    0.00044   20.0   0.0    0.00064   19.5   0.0    1.2  1  Carbam_trans_N  Carbamoyltransferase N-terminus


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.2   0.4   4.2e-90   3.8e-86       2     270 ..      29     312 ..      28     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 289.2 bits;  conditional E-value: 4.2e-90
                                    CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT CS
                  Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalaln 81 
                                    +la++vas+ + h ++GGvvPe+asraH e+l p++++ala+agl+  + d +a+t gPGl+++L+vGv++Ak+++ a++
  gi|121639344|ref|YP_979568.1|  29 LLADEVASSVDEHVRFGGVVPEIASRAHLEALGPAMRRALAAAGLK--QPDIVAATIGPGLAGALLVGVAAAKAYSAAWG 106
                                    78999****************************************9..6799**************************** PP

                                    --EEEEEHHHHHHHCCHCTSECSSC..EEEEESSSTEEEEEECT..TEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHH CS
                  Peptidase_M22  82 kPlvgVnhleahalaarleekeefP..vvllvsGghtqvylvke..gryeilgetlddaagealdkvarllglpypggpk 157
                                    +P+++Vnhl +h++a  +e+++  P  v+llvsGght+++ v++  + +  lg+t+ddaagea+dkvarllgl+ypgg++
  gi|121639344|ref|YP_979568.1| 107 VPFYAVNHLGGHLAADVYEHGP-LPecVALLVSGGHTHLLHVRSlgEPIIELGSTVDDAAGEAYDKVARLLGLGYPGGKA 185
                                    ****************988765.7999******************778999***************************** PP

                                    HHHHHCTC..S.......EET.....TEEE.CHHHHHHHHHHST.T......HHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                  Peptidase_M22 158 ieklakeg..kkiefprplkg.....ldfsfsGlktavlkelek.e......vedlaasfqeavvdhlvekteralklpk 223
                                    ++ la+ g  ++i fpr + g     + fsfsGlktav++ +e+ +      ++d+aa fqeav+d+l+ k+ ra+   +
  gi|121639344|ref|YP_979568.1| 186 LDDLARTGdrDAIVFPRGMSGpaddrYAFSFSGLKTAVARYVEShAadpgfrTADIAAGFQEAVADVLTMKAVRAATALG 265
                                    ********9777******************************55435799****************************** PP

                                    BSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                  Peptidase_M22 224 akelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamia 270
                                    +++l+i+GGvaan+rLre  ++ + e+g +l iP++++ctdn+amia
  gi|121639344|ref|YP_979568.1| 266 VSTLLIAGGVAANSRLRELATQRCGEAGRTLRIPSPRLCTDNGAMIA 312
                                    **********************************************8 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.2e-08   0.00064     127     306 ..     112     279 ..      92     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-08
                 Carbam_trans_N 127 yeHhlsH.aaSaystSpFakkeklvlcldgdGdiaprllaveketelkikslvsfsesiGhlYaaateylGfkknsdegK 205
                                    ++H  +H aa +y   p     + v  l+  G   ++ll+v + +e  i+   +  +  G +Y  + + lG         
  gi|121639344|ref|YP_979568.1| 112 VNHLGGHlAADVYEHGPL--P-ECVALLVSGG--HTHLLHVRSLGEPIIELGSTVDDAAGEAYDKVARLLGLGYPG-GKA 185
                                    678888833457888888..3.4444455556..478999999888888777777789999999999999998776.344 PP

                 Carbam_trans_N 206 lmalaayGkpkeriveelyellkkagyrinlennieiskkkvhdffeasalrlkearekdedlaAsiqvflErlvvevln 285
                                    l  la +G+ +  ++   +   ++ +y        + +k +v++++e+ a      r+   d+aA +q+++ +++     
  gi|121639344|ref|YP_979568.1| 186 LDDLARTGDRDAIVFPRGMSGPADDRYAFS----FSGLKTAVARYVESHA-ADPGFRTA--DIAAGFQEAVADVLTMKAV 258
                                    789999999997777666665556577777....4667777889999888.55566666..**************99999 PP

                 Carbam_trans_N 286 ivyeklkirnLclaGGvalNi 306
                                     +   l++  L +aGGva+N 
  gi|121639344|ref|YP_979568.1| 259 RAATALGVSTLLIAGGVAANS 279
                                    99999*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2542.81
//
Query:       gi|121639345|ref|YP_979569.1|  [L=158]
Description: ribosomal-protein-alanine acetyltransferase rimI [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-21   76.0   0.0    3.3e-21   75.7   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.4e-16   58.2   0.0    8.5e-16   58.0   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.1e-13   48.8   0.1      1e-12   48.3   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.3e-06   26.6   0.1    5.8e-06   26.2   0.1    1.3  1  FR47             FR47-like protein
    4.6e-05   23.5   0.0    8.5e-05   22.6   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    8.8e-05   22.6   0.0    0.00041   20.4   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00014   21.6   0.0    0.00023   20.9   0.0    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    0.00022   21.9   0.0    0.00026   21.7   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00071   19.4   0.0      0.014   15.2   0.0    2.0  2  Acetyltransf_18  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.04   13.4   0.0        1.1    8.7   0.0    2.0  2  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   1.9e-24   3.3e-21      14     117 .]      33     130 ..      17     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.9e-24
                                    HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                 Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                     p++ a + +   s   ++++++ a+ +g+l+G+++++    + + +++++ + V+p+y+g+G+G++Ll++l+++ar   
  gi|121639345|ref|YP_979569.1|  33 DPWPPAAFNRELAS---PHNHYVGARSGGTLVGYAGISRLGRTPPFEYEVHTIGVDPAYQGRGIGRRLLRELLDFARGG- 108
                                    67777788887777...9999999******************999*****************************99988. PP

                                    ESEE.EEEEETTEHHHHHHHHH.TTE CS
                 Acetyltransf_1  94 ikki.vlaveedndaairlYek.lGF 117
                                       + +l+v+ dndaa +lY + +GF
  gi|121639345|ref|YP_979569.1| 109 ---VvYLEVRTDNDAALALY-RsVGF 130
                                    ...44***************.65**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   4.8e-19   8.5e-16      19     124 ..      37     151 ..      18     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 4.8e-19
                Acetyltransf_10  19 pealrerieegealllvaeeggkivGviel.rdgs......hisllfVdpeyrgqGigkaLleaveeeaekdgikleltv 91 
                                    p+a++++++++++++++a  gg++vG++++ r g+      +++ + Vdp+y+g+Gig++Ll ++++ a + g    l+v
  gi|121639345|ref|YP_979569.1|  37 PAAFNRELASPHNHYVGARSGGTLVGYAGIsRLGRtppfeyEVHTIGVDPAYQGRGIGRRLLRELLDFA-RGGVV-YLEV 114
                                    5889999*********************9955555889******************************9.44433.**** PP

                Acetyltransf_10  92 nasp.yavpfYeklGFkav...geeqeenGirfvpMe 124
                                    + ++ +a ++Y+++GF++v    +    +G   + M+
  gi|121639345|ref|YP_979569.1| 115 RTDNdAALALYRSVGFQRVglrRRYYRVSGADAYTMR 151
                                    *******************554444556677777666 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   5.7e-16     1e-12       3      76 .]      49     132 ..      46     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 5.7e-16
                                    EEEEEEEETTEEEEEEEEEEES......TCTEEEEE-GGGTTSSHHHHHHHHTT...SE.EEEE.EEEETHHHHHHHHHH CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld......aeitrlaVdpeyrgkGiGraLleaae...kg.iile.qlelnaekaikfYek 71 
                                    +++  a+ +g  vG++++s+l+      +e + + Vdp+y+g+GiGr+Ll+      +g +  + ++++++++a+++Y++
  gi|121639345|ref|YP_979569.1|  49 NHYVGARSGGTLVGYAGISRLGrtppfeYEVHTIGVDPAYQGRGIGRRLLRELLdfaRGgVV-YlEVRTDNDAALALYRS 127
                                    455568888999****999999*9998555555*****************952234444322.2334444449999**** PP

                                    TTEEE CS
                 Acetyltransf_7  72 lGFee 76 
                                     GF++
  gi|121639345|ref|YP_979569.1| 128 VGFQR 132
                                    ***85 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   3.2e-09   5.8e-06      24      80 ..      79     133 ..      51     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.2e-09
                                    EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                    +  + v+p  ++rG g+rl ++l     +rg  v l v+++N+++ +ly ++Gf+  
  gi|121639345|ref|YP_979569.1|  79 VHTIGVDPAYQGRGIGRRLLRELLD--FARGGVVYLEVRTDNDAALALYRSVGFQRV 133
                                    567889****************987..579************************987 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.7e-08   8.5e-05      24      54 ..      76     106 ..      51     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.7e-08
                Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaalddar 54 
                                    +++++ + V+++++G+Gi+++L ++ ld+ar
  gi|121639345|ref|YP_979569.1|  76 EYEVHTIGVDPAYQGRGIGRRLLRELLDFAR 106
                                    78888899*********************98 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-07   0.00041       4     125 ..      12     130 ..       9     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                    EE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHT.TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEE.EEEEEEEE CS
                 Acetyltransf_9   4 elteedldevlellkyaFqdeespleeireyfrklle.esrvlgaedngelvgqlallplelnvpGktlka.agvtgVav 81 
                                     lt +d + ++el ++ F  +++      ++ r+l + +++++ga+++g+lvg +++ +l     G+t +  + v  ++v
  gi|121639345|ref|YP_979569.1|  12 ALTRADAQRCAELEAQLFVGDDPWP-P-AAFNRELASpHNHYVGARSGGTLVGYAGISRL-----GRTPPFeYEVHTIGV 84 
                                    68999*************9999976.2.3455666663478999999******8887665.....66666634577899* PP

                                    -CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT- CS
                 Acetyltransf_9  82 apehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGy 125
                                    +p ++grg+ ++Ll+++l+ +r   + l + +   ++ ++Yr+ G+
  gi|121639345|ref|YP_979569.1|  85 DPAYQGRGIGRRLLRELLDFARGGVVYLEVRTDndAALALYRSVGF 130
                                    ******************9998633333333335555566666666 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.3e-07   0.00023      33     141 ..      39     134 ..      28     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                                    HHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCT CS
                 Acetyltransf_8  33 ellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttallralvhylfadp 112
                                    ++ ++l+ +ph + + ++  g+ vgy+ i +  +         +p+   +H +  ++++ g+g++++llr+l++++    
  gi|121639345|ref|YP_979569.1|  39 AFNRELA-SPHNHYVGARSGGTLVGYAGISRLGRT--------PPFEYEVHTIGVDPAYQGRGIGRRLLRELLDFARGG- 108
                                    5666664.777777777777777777777666666........899999999999*******************97555. PP

                                    T--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                 Acetyltransf_8 113 rtrrvvvEPdvrNerairllekaGfekek 141
                                        v +E + +N +a++l++++Gf++++
  gi|121639345|ref|YP_979569.1| 109 ---VVYLEVRTDNDAALALYRSVGFQRVG 134
                                    ...9**********************986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.5e-07   0.00026      60     138 .]      54     131 ..       7     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-07
                 Acetyltransf_3  60 lkdtgv.iGsvglrdleeedee.aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklG 136
                                     +++g  +G++g+ +l + + +  e+  + ++p+++g+G+++  +r ll++a    +   ++ ++ ++N a  ++++++G
  gi|121639345|ref|YP_979569.1|  54 ARSGGTlVGYAGISRLGRTPPFeYEVHtIGVDPAYQGRGIGRRLLRELLDFA----RGGVVYLEVRTDNDAALALYRSVG 129
                                    3556655999999988887765677765778999******************....344588888999************ PP

                 Acetyltransf_3 137 fe 138
                                    f+
  gi|121639345|ref|YP_979569.1| 130 FQ 131
                                    *6 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.084   1.5e+02      18      45 ..      41      68 ..      37      73 .. 0.82
   2 !   15.2   0.0   8.1e-06     0.014      62     109 ..      93     140 ..      87     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.084
                Acetyltransf_18 18 krrlkqaeqklvvveedgeivGyglark 45
                                   +r l  +++++v   ++g++vGy+ + +
  gi|121639345|ref|YP_979569.1| 41 NRELASPHNHYVGARSGGTLVGYAGISR 68
                                   66788899999************97655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.1e-06
                Acetyltransf_18  62 iAeaLlkalvanaegkkvridvpeenkalielleklgfkevfecarmv 109
                                    i ++Ll++l+  a+g  v++ v + n+a+ +l +++gf++v    r +
  gi|121639345|ref|YP_979569.1|  93 IGRRLLRELLDFARGGVVYLEVRTDNDAALALYRSVGFQRVGLRRRYY 140
                                    6789************************************98666555 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00061       1.1      74      98 ..      78     102 ..      63     108 .. 0.91
   2 ?    2.8   0.0     0.039        70     126     140 ..     120     134 ..     112     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00061
                Acetyltransf_15  74 eiYtlyvsekyrgkGlakklLeesl 98 
                                    e+ t+ v++ y+g+G+ ++lL e l
  gi|121639345|ref|YP_979569.1|  78 EVHTIGVDPAYQGRGIGRRLLRELL 102
                                    7899*****************9865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.039
                Acetyltransf_15 126 isfalYyslgFrkgl 140
                                     + alY+s+gF++++
  gi|121639345|ref|YP_979569.1| 120 AALALYRSVGFQRVG 134
                                    5789********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1200.05
//
Query:       gi|121639346|ref|YP_979570.1|  [L=211]
Description: hypothetical protein BCG_3491c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-25   90.2   0.8    2.1e-25   89.9   0.8    1.1  1  Peptidase_M22  Glycoprotease family
      0.002   18.0   0.3      0.003   17.5   0.3    1.3  1  Mycobact_memb  Mycobacterium membrane protein
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.025   14.3   0.0    1.2  1  GATase         Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.8   3.6e-29   2.1e-25      26     144 ..      40     145 ..      32     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 3.6e-29
                                    HHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHHHHHHCCHCTSECSS CS
                  Peptidase_M22  26 sraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhleahalaarleekeef 105
                                    +raH+erl+p + +ala+a l+++dlda++v++gPG ftgLr G++ A ++ +al++P++gV++l+a+  ++  +     
  gi|121639346|ref|YP_979570.1|  40 ARAHAERLTPNVLAALADAALTMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGD----- 114
                                    89*******************************************************************999644..... PP

                                    CEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHH CS
                  Peptidase_M22 106 PvvllvsGghtqvylvkegryeilgetlddaagealdkv 144
                                      ++++++++ +vy++   ry  + +t+  a+     + 
  gi|121639346|ref|YP_979570.1| 115 -TLVVTDARRREVYWA---RYCDGIRTVGPAV----NAA 145
                                    .79*************...5555555543333....222 PP

>> Mycobact_memb  Mycobacterium membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   5.1e-07     0.003      81     130 ..       4      53 ..       1      63 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.1e-07
                                    -SS--B--EE-SSS------B--SS-S------BBTTB---------S-T CS
                  Mycobact_memb  81 aalPWsltikttlaavvgnvvaqgnsdsigCriivdgvvkdervsnevna 130
                                    +++   l i t+++av++ +v + +  ++g r++vd   ++er + +v a
  gi|121639346|ref|YP_979570.1|   4 VQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLA 53 
                                    56677899***********************************9866544 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-06     0.025      39      78 ..      61     102 ..      26     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-06
                                    THHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEET CS
                         GATase  39 llknpdgilvsgGpgspg..vegkieaikearenkiPiLGIC 78 
                                       + d+++v  Gpg  +  + g+ +a+ +    +iP+ G+C
  gi|121639346|ref|YP_979570.1|  61 TMADLDAVVVGCGPGPFTglRAGMASAAAYGHALGIPVYGVC 102
                                    35789************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1713.91
//
Query:       gi|121639347|ref|YP_979571.1|  [L=168]
Description: hypothetical protein BCG_3492c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-29  101.1   0.0    4.9e-29  100.9   0.0    1.0  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
     0.0028   17.4   0.1     0.0051   16.6   0.1    1.4  1  RuvB_N      Holliday junction DNA helicase RuvB P-loop domain
     0.0042   17.0   0.0     0.0054   16.7   0.0    1.2  1  NACHT       NACHT domain
      0.007   16.8   0.1      0.011   16.1   0.1    1.4  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.017   15.7   0.0      0.019   15.5   0.0    1.3  1  ABC_tran    ABC transporter
      0.029   14.1   0.0      0.035   13.8   0.0    1.3  1  AAA_30      AAA domain
      0.046   12.9   0.1      0.064   12.5   0.1    1.1  1  TIP49       TIP49 P-loop domain
      0.055   12.9   0.0      0.079   12.4   0.0    1.2  1  PhoH        PhoH-like protein
      0.055   13.0   1.0      0.063   12.9   0.6    1.6  1  AAA_25      AAA domain
      0.056   13.0   0.0        0.1   12.1   0.0    1.4  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
      0.057   13.6   0.1       0.14   12.3   0.0    1.7  2  AAA_33      AAA domain
      0.096   13.0   0.0       0.13   12.5   0.0    1.3  1  AAA_22      AAA domain
       0.16   11.7   0.1       0.29   10.9   0.1    1.4  1  IstB_IS21   IstB-like ATP binding protein
       0.16   12.5   0.0       0.31   11.6   0.0    1.6  1  AAA_18      AAA domain
       0.16   11.2   0.1       0.33   10.2   0.1    1.4  1  Zeta_toxin  Zeta toxin
       0.18   10.9   0.1       0.26   10.4   0.1    1.2  1  NB-ARC      NB-ARC domain


Domain annotation for each model (and alignments):
>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   4.4e-32   4.9e-29       3     120 ..      26     154 ..      24     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 4.4e-32
                                    SHHHHHHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT--.----TTTTSEEEEEE..SS...EEEEE-TT-SS CS
                           TsaE   3 seeetealgkklakal..gdvilLeGdLGaGKTtlvrglakalgve.evkSPTFtlveeYelekeg...lyHfDlYRled 76 
                                    + e+t +lg++l+++l  gdv++L+G+LGaGKT+l++g+a a++ve +++SPTF+l++ ++ ++ g   ++H+D+YRl d
  gi|121639347|ref|YP_979571.1|  26 RVEDTLTLGSRLGEQLcaGDVVVLSGPLGAGKTVLAKGIAMAMDVEgPITSPTFVLARMHRPRRPGtpaMVHVDVYRLLD 105
                                    57899*********99999*****************************************9987779***********44 PP

                                    ......THHHHHCTTCCCCSTSCEEEEETGGGGCCCS-S-CEEEEEEEET CS
                           TsaE  77 ......eeeleelgleeyleeeavvlvEWpekleellpeedleieleeee 120
                                           +el++l+l++ l e+avv+vEW+e l+e l++++l+++le+ +
  gi|121639347|ref|YP_979571.1| 106 hnsadlLSELDSLDLDTDL-EDAVVVVEWGEGLAERLSQRHLDVRLERVS 154
                                    3334447789999999999.557**************9999*99997754 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.5e-06    0.0051      33      66 ..      44      77 ..      30      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                         RuvB_N 33 ldhvllyGpPGlGkttlakiiakelgvklkitsg 66
                                    d v+l+Gp G Gkt lak ia  ++v+  its 
  gi|121639347|ref|YP_979571.1| 44 GDVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSP 77
                                   589************************9999885 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.8e-06    0.0054       1      31 [.      45      75 ..      45     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-06
                                   SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpq 31
                                   ++v+l G+ G GKT+L++++a+a+  + +  
  gi|121639347|ref|YP_979571.1| 45 DVVVLSGPLGAGKTVLAKGIAMAMDVEGPIT 75
                                   589*******************998887666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     1e-05     0.011       1      25 [.      47      71 ..      47     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                                   EEEESSTTSSHHHHHHHHHHHHTHE CS
                            AAA  1 vllyGppGtGKTllakavakelgve 25
                                   v+l+Gp G GKT lak +a  ++ve
  gi|121639347|ref|YP_979571.1| 47 VVLSGPLGAGKTVLAKGIAMAMDVE 71
                                   689****************998754 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.7e-05     0.019       8      42 ..      41      74 ..      36     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGei 42
                                   l +g +v++ G+ GaGK+ L+k +a  ++  eG i
  gi|121639347|ref|YP_979571.1| 41 LCAGDVVVLSGPLGAGKTVLAKGIAMAMD-VEGPI 74
                                   66899*******************99887.57777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.035      12      52 ..      40      81 ..      35     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                         AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaweaag...grvigl 52
                                   +l++++  v+vl Gp G+GKt + k+++ a++ +g    + ++l
  gi|121639347|ref|YP_979571.1| 40 QLCAGD--VVVLSGPLGAGKTVLAKGIAMAMDVEGpitSPTFVL 81
                                   555544..9*******************9999887555444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.7e-05     0.064      47      79 ..      41      73 ..      32      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 47 klaGravLlaGpsgtGktalaiaiskelgedvp 79
                                     aG +v+l+Gp g+Gkt la +i+ ++  + p
  gi|121639347|ref|YP_979571.1| 41 LCAGDVVVLSGPLGAGKTVLAKGIAMAMDVEGP 73
                                   56899*******************998876655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     7e-05     0.079      15      46 ..      40      71 ..      34      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                                   HHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                           PhoH 15 alkkndivfaiGpaGtGKtylavalavealkk 46
                                   +l + d+v+  Gp G+GKt la  +a+++  +
  gi|121639347|ref|YP_979571.1| 40 QLCAGDVVVLSGPLGAGKTVLAKGIAMAMDVE 71
                                   566789****************8888776554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   5.6e-05     0.063      30      58 ..      41      69 ..       8     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                         AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                   l ag++++l G+ g+GKt+la  +a a+ 
  gi|121639347|ref|YP_979571.1| 41 LCAGDVVVLSGPLGAGKTVLAKGIAMAMD 69
                                   568******************99999885 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-05       0.1       2      18 ..      46      62 ..      45      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                                   EEEEEESTTCCHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLln 18
                                   v+vl+G+lG+GKT L +
  gi|121639347|ref|YP_979571.1| 46 VVVLSGPLGAGKTVLAK 62
                                   79***********9966 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.14       1      33 [.      46      79 ..      46     115 .. 0.76
   2 ?   -1.6   0.0       2.4   2.7e+03      98     119 ..     125     145 ..     102     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                         AAA_33  1 lvllvGlpGsGKstlaerllkklgavl.lssdtl 33
                                   +v+l G+ G+GK+ la++++ + +++  ++s+t+
  gi|121639347|ref|YP_979571.1| 46 VVVLSGPLGAGKTVLAKGIAMAMDVEGpITSPTF 79
                                   899**************99877665555666664 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                         AAA_33  98 pvrivvvetdeetlkeRlakRa 119
                                    ++++vvve  e  l+eRl +R 
  gi|121639347|ref|YP_979571.1| 125 EDAVVVVEWGE-GLAERLSQRH 145
                                    45555555443.3566777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.13       7      66 ..      46     106 ..      43     160 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst.sskdllrellralgl 66 
                                    ++v+ G+ G+GKT+l++ +++  d e  ++  +p++v  ++  p    +++ +  ++ r l++
  gi|121639347|ref|YP_979571.1|  46 VVVLSGPLGAGKTVLAKGIAMAMDVEGPIT--SPTFVlaRMHRPRRPgTPAMVHVDVYRLLDH 106
                                    6899*************9999987543333..3333313222222223555555555555554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00026      0.29      47      70 ..      44      67 ..      30      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                      IstB_IS21 47 kenivllGpsGvGKshlaialgve 70
                                    + +vl Gp G+GK+ la  ++++
  gi|121639347|ref|YP_979571.1| 44 GDVVVLSGPLGAGKTVLAKGIAMA 67
                                   5789**************988876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027      0.31       1      25 [.      47      78 ..      47     157 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf.......g 25
                                   ++l+G+ G+GKt lak ++  + +        
  gi|121639347|ref|YP_979571.1| 47 VVLSGPLGAGKTVLAKGIAMAMDVegpitspT 78
                                   789*************9977765564444441 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0003      0.33      18      42 ..      46      70 ..      39      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                     Zeta_toxin 18 lillgGqpGAGKselaellkdeler 42
                                   +++l+G  GAGK+ la+ ++ +++ 
  gi|121639347|ref|YP_979571.1| 46 VVVLSGPLGAGKTVLAKGIAMAMDV 70
                                   799***************9999974 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00024      0.26      21      43 ..      45      67 ..      30      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                                   EEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                   +vv l+G  G GKt+lak i   
  gi|121639347|ref|YP_979571.1| 45 DVVVLSGPLGAGKTVLAKGIAMA 67
                                   599***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1129.01
//
Query:       gi|121639348|ref|YP_979572.1|  [L=408]
Description: alanine racemase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-67  225.4   2.1    7.8e-67  225.1   2.1    1.1  1  Ala_racemase_N  Alanine racemase, N-terminal domain
      1e-43  148.1   0.1    4.3e-43  146.0   0.0    1.9  2  Ala_racemase_C  Alanine racemase, C-terminal domain


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   2.1   8.7e-71   7.8e-67       1     219 []      40     262 ..      40     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 8.7e-71
                                    EEHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESCSTGG CS
                 Ala_racemase_N   1 idldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvlegfspe 80 
                                    +dl a++hN+r+lr++a ++a+lmavvKa++yghga +va++++ +ga  +gvat++Eal+lr+ gitap+l + + +  
  gi|121639348|ref|YP_979572.1|  40 VDLGAIEHNVRVLREHA-GHAQLMAVVKADGYGHGATRVAQTALGAGAAELGVATVDEALALRADGITAPVLAWLHPPGI 118
                                    79***************.6777********************************************************** PP

                                    GHHHHHHTTEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSSSSSBSCHHHHHHHHHHHH...TTTEEEEEEE-S-S CS
                 Ala_racemase_N  81 elaalaeydltvtvdsleqlealaaaareagkplrvhlkidtgmgRlGftpeeleellealaa...lpglrleglmtHfa 157
                                    ++  ++ +d++v+v+sl ql++l +a r++g++++v +k+dtg++R+G+ p++++++l al++   ++ +rl+glm+H+ 
  gi|121639348|ref|YP_979572.1| 119 DFGPALLADVQVAVSSLRQLDELLHAVRRTGRTATVTVKVDTGLNRNGVGPAQFPAMLTALRQamaEDAVRLRGLMSHMV 198
                                    ********************************************************9999999443455*********** PP

                                    STTSTSHHHHH.HHHHHHHHHHHHHHTTGGGSEEEEESHHHHHHSG.GGTTEEEESGGGGT-SS CS
                 Ala_racemase_N 158 sadepdeetea.qlarfeealeelekaglrppvvslanSaaillaa.ahfdmvRpGialyGlsp 219
                                     ad+pd+ ++  q +rf+++l++ +++g+r +v +l+nS+a+++++   fd+vRpGia+yGlsp
  gi|121639348|ref|YP_979572.1| 199 YADKPDDSINDvQAQRFTAFLAQAREQGVRFEVAHLSNSSATMARPdLTFDLVRPGIAVYGLSP 262
                                    ******999999*********************************8567*************98 PP

>> Ala_racemase_C  Alanine racemase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.16   1.4e+03      32      50 ..      60      79 ..      53      96 .. 0.70
   2 !  146.0   0.0   4.8e-47   4.3e-43       1     124 []     274     402 ..     274     402 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.16
                                   EEEEEES-.-GGGTCGGGGT CS
                 Ala_racemase_C 32 triavvpi.GYaDGlprals 50
                                   + +avv++ GY+ G +r ++
  gi|121639348|ref|YP_979572.1| 60 QLMAVVKAdGYGHGATRVAQ 79
                                   56677765599999999764 PP

  == domain 2  score: 146.0 bits;  conditional E-value: 4.8e-47
                                    SEEEEEEEEEEEEESTTSEESGGGSEE-SSSEEEEEES--GGGTCGGGGTT..EEEETTEEEEEESEE-SSEEEEEECTS CS
                 Ala_racemase_C   1 vmtlkarviqvkevkagegvgYgatyvaerdtriavvpiGYaDGlpralsg..evlingkrvpvvGrvcMDqlmvdltev 78 
                                    +mt+k  v+ vk+++agegv+Yg+t++a+rdt++a++piGYaDG+ r+l g  evling+r+p vGr+cMDq+mvdl+  
  gi|121639348|ref|YP_979572.1| 274 AMTVKCAVALVKSIRAGEGVSYGHTWIAPRDTNLALLPIGYADGVFRSLGGrlEVLINGRRCPGVGRICMDQFMVDLGPG 353
                                    79***********************************************9556************************965 PP

                                    TT.--TT-EEEEEEET..EEEEHHHHHHHHTSEHHHHHHTSHTTSEEEE CS
                 Ala_racemase_C  79 ee.vkvgdevvllgeg..eeitveelaeaagtisyeiltrlskrvprvy 124
                                    +  v++gde++l+g+g   e+t++++a+ +gti+ye++t+ + r++r+y
  gi|121639348|ref|YP_979572.1| 354 PLdVAEGDEAILFGPGirGEPTAQDWADLVGTIHYEVVTSPRGRITRTY 402
                                    5469**********9999*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2617.99
//
Query:       gi|121639349|ref|YP_979573.1|  [L=120]
Description: hypothetical protein BCG_3494c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 963.31
//
Query:       gi|121639350|ref|YP_979574.1|  [L=178]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-50  169.2   0.5    7.8e-50  169.1   0.5    1.0  1  PPE        PPE family
    2.1e-05   24.7   0.8    2.1e-05   24.7   0.8    1.7  2  WXG100     Proteins of 100 residues with WXG
  ------ inclusion threshold ------
       0.05   13.5   0.0        2.1    8.3   0.0    2.2  2  CI-B14_5a  NADH:ubiquinone oxidoreductase subunit B14.5a (Com
       0.11   12.9   0.6       0.31   11.4   0.6    1.7  1  Nnf1       Nnf1


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.5   1.7e-53   7.8e-50       1     155 [.       4     157 ..       4     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.7e-53
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    ++p+E++s+ +y+Gpg+++l+ A  ++++La +++++a++le+ l+el  e+W+G+ss+ +a+a+ +yl+WLs+++ q +
  gi|121639350|ref|YP_979574.1|   4 MIPAEYISNIIYEGPGADSLFFASGQLRELAYSVETTAESLEDELDELD-ENWKGSSSDLLADAVERYLQWLSKHSSQLK 82 
                                    79***********************************************.****************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasa 155
                                    +aA +++ +a+aY+ ++ ++vpp+eiaanr+e+++l+a+n++G+ntpaIa ++a+y+++ aq++a+m++Y+++++
  gi|121639350|ref|YP_979574.1|  83 HAAWVINGLANAYNDTRRKVVPPEEIAANREEVHRLIASNVAGVNTPAIAGLDAQYQQYRAQNIAVMNDYQSTAR 157
                                    ***********************************************************************9986 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.8   4.6e-09   2.1e-05      12      84 ..      26      98 ..      20      99 .. 0.95
   2 ?   -2.0   0.1      0.99   4.4e+03      51      70 ..     136     155 ..     132     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.6e-09
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 12 aaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84
                                   a+ ++++ a ++e+  ++l+ e+d+l ++W+G+++d  +++ e++ q + k   +L+  +  ++  ana+ d+
  gi|121639350|ref|YP_979574.1| 26 ASGQLRELAYSVETTAESLEDELDELDENWKGSSSDLLADAVERYLQWLSKHSSQLKHAAWVINGLANAYNDT 98
                                   788999999*************************************************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.99
                                    HHHHHHHHHHHHHHHHHHHH CS
                         WXG100  51 aefeewkqaaqklvdaLeei 70 
                                    a++++++++   + + ++++
  gi|121639350|ref|YP_979574.1| 136 AQYQQYRAQNIAVMNDYQST 155
                                    56666666665555555555 PP

>> CI-B14_5a  NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00047       2.1      52      72 ..      96     116 ..      89     131 .. 0.80
   2 ?    2.9   0.0     0.022     1e+02       8      39 ..     144     175 ..     141     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00047
                      CI-B14_5a  52 RDaRRevappivvvssqkkll 72 
                                     D RR+v pp +++ ++++ +
  gi|121639350|ref|YP_979574.1|  96 NDTRRKVVPPEEIAANREEVH 116
                                    69***********99988655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.022
                      CI-B14_5a   8 rdfllgrklklalRyedeiakRtqppPklPdG 39 
                                    ++++++++++++ R+   + +R q pP++  G
  gi|121639350|ref|YP_979574.1| 144 QNIAVMNDYQSTARFILAYLPRWQEPPQIYGG 175
                                    6899999*********************9887 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   6.9e-05      0.31      29     104 ..      42     151 ..      39     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                                    TTHHHHHHHHH........HHHHHHHCCHH-T.....................................TTSSTTTHHHH CS
                           Nnf1  29 rdvvekLneLD........dlieeAkerreegeeeasrpe...........................vpphtLpPeelia 73 
                                    ++++++L+eLD        dl+++A er  +  +++s  +                           ++++  +   lia
  gi|121639350|ref|YP_979574.1|  42 ESLEDELDELDenwkgsssDLLADAVERYLQWLSKHSS-QlkhaawvinglanayndtrrkvvppeeIAANREEVHRLIA 120
                                    679999*****999999999999999888884443333.13566677778888888888888666665555556778999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  74 ahlapakkeeqeeLearlqeleaenaelaee 104
                                    +++a     + + L+a++q+ +a+n + ++ 
  gi|121639350|ref|YP_979574.1| 121 SNVAGVNTPAIAGLDAQYQQYRAQNIAVMND 151
                                    9999999******************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 960.61
//
Query:       gi|121639351|ref|YP_979575.1|  [L=387]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-24   84.5   0.1    1.7e-23   83.1   0.0    1.8  2  rve            Integrase core domain
    5.1e-14   51.8   0.2      1e-13   50.8   0.2    1.6  1  rve_3          Integrase core domain
    1.5e-05   25.2   0.0    2.1e-05   24.7   0.0    1.2  1  DDE_Tnp_IS240  DDE domain
     0.0029   18.2   5.1      0.004   17.7   0.0    3.3  4  HTH_32         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   3.7e-27   1.7e-23       2     117 ..     136     252 ..     135     253 .. 0.98
   2 ?   -2.2   0.0      0.98   4.4e+03      67      84 ..     291     315 ..     260     333 .. 0.54

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.7e-27
                            rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve.pervlsDngseyts 80 
                                    ++p+++w+ D+t++r p +++ +yl+v++d fsr+++++ + +++++ ++ +l+ + +a ++ +   ++++ D+gs++ s
  gi|121639351|ref|YP_979575.1| 136 HQPNSVWSWDITKLRGPAKWSYYYLYVILDIFSRYVVGWMVASRESKVLAERLIAQTLAAQHISAdQLTLHADRGSSMSS 215
                                    89*************************************************************999************** PP

                            rve  81 kafrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                    k ++ +ladlg++ s++rp+ ++dn + E  ++tlk 
  gi|121639351|ref|YP_979575.1| 216 KPVALLLADLGVTKSHSRPHTSNDNPLSEAQFKTLKY 252
                                    ***********************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.98
                            rve  67 pervlsDngseytsk.......afr 84 
                                    p  v++ ++ +++ +       a+r
  gi|121639351|ref|YP_979575.1| 291 PADVHYGRADQIRRHratvldtAYR 315
                                    5555555555555444444444444 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.2   2.3e-17     1e-13       2      67 .]     226     291 ..     225     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.3e-17
                          rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLgykTP 67 
                                    g++ s+++p++ ++N l E  ++tl+++  + + f+s++ ar ++++++ +YN+e+ Hs++g  TP
  gi|121639351|ref|YP_979575.1| 226 GVTKSHSRPHTSNDNPLSEAQFKTLKYRPDFPKRFESIEAARVHCDRFFGWYNHEHKHSGIGLHTP 291
                                    899************************************************************999 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.8e-09   2.1e-05       3     139 ..     141     283 ..     139     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.8e-09
                  DDE_Tnp_IS240   3 swrvDETyvkikGkw..aYlyravDkegr.ildflvskrRdtkaakaflrkalkkek..lepeeivtD.kasayasalke 76 
                                    +w  D T ++   kw  +Yly ++D  +r +++++v  r  +  a +++ ++l  ++      ++ +D ++s   + ++ 
  gi|121639351|ref|YP_979575.1| 141 VWSWDITKLRGPAKWsyYYLYVILDIFSRyVVGWMVASRESKVLAERLIAQTLAAQHisADQLTLHADrGSSMSSKPVAL 220
                                    5666666666666662257999*****************************99998877888999999445556677888 PP

                  DDE_Tnp_IS240  77 lkregelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                    l ++   +++ s+ ++   n   E++++tlK r    + f+s++ a+   + f   +n+  +h
  gi|121639351|ref|YP_979575.1| 221 LLADLGVTKSHSRPHTSNDNPLSEAQFKTLKYRPDFPKRFESIEAARVHCDRFFGWYNHEHKH 283
                                    8888888999999999999*******************************9999999998877 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     9e-07     0.004      22      73 .]      56     110 ..      43     110 .. 0.81
   2 ?   -1.5   0.2      0.89     4e+03      19      35 ..     118     135 ..     111     143 .. 0.62
   3 ?   -2.4   0.0       1.7   7.7e+03      36      53 ..     187     204 ..     181     213 .. 0.55
   4 ?    0.5   0.3      0.22   9.9e+02      19      44 ..     300     325 ..     293     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9e-07
                         HTH_32  22 rrg.rprklsdevrariiallreep..rWsprqlaarlaeregvkvShstvyriL 73 
                                    r    pr ls+++r++++a+l +++  ++ p  + a l +++ +  S+st yr+L
  gi|121639351|ref|YP_979575.1|  56 RESaQPRALSAAEREHVLAVLNSQRfaDMAPAVVYATLLDEGIYLCSESTMYRLL 110
                                    33237889*************556577889999999887888999********98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.89
                         HTH_32  19 drprrg.rprklsdevra 35 
                                    dr+r+  +p  + +e++a
  gi|121639351|ref|YP_979575.1| 118 DRRRQAtHPAAVKPELVA 135
                                    554553366666666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.7
                         HTH_32  36 riiallreeprWsprqla 53 
                                    r+ia +  + + s++ql 
  gi|121639351|ref|YP_979575.1| 187 RLIAQTLAAQHISADQLT 204
                                    333333233366666665 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.22
                         HTH_32  19 drprrgrprklsdevrariiallree 44 
                                    d+ rr r   l+ + r+++ +++ + 
  gi|121639351|ref|YP_979575.1| 300 DQIRRHRATVLDTAYRDHLERIRSQT 325
                                    56566666679999999999999433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2376.31
//
Query:       gi|121639352|ref|YP_979576.1|  [L=281]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-107  359.4   0.0   2.2e-107  359.2   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
    1.3e-08   35.2   0.0    2.4e-08   34.3   0.0    1.5  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.013   15.5   0.1        2.3    8.2   0.0    2.4  2  FTR_C            FTR, proximal lobe


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.2   0.0  3.6e-111  2.2e-107      27     302 ..       3     278 ..       1     281 [] 0.98

  Alignments for each domain:
  == domain 1  score: 359.2 bits;  conditional E-value: 3.6e-111
                Transposase_mut  27 kellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRrekaleav 106
                                     el+++ l++l+eae++ea+ga ryers+ r  +RnG+r +++sT+ag++e++iP++R+GsF+p ller++R +kal av
  gi|121639352|ref|YP_979576.1|   3 AELIRAGLQALIEAEATEAIGAGRYERSDGRIVHRNGHRPKTVSTTAGDIEVQIPKLRAGSFFPSLLERRRRIDKALHAV 82 
                                    6789999************************************************************************* PP

                Transposase_mut 107 vielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvskavl 186
                                    ++e+yv+Gvstr v++lv++++++++vSksevS+i++ ld+++eafr+RsL ++e+p++f+Da+ +kvR    vvs+a +
  gi|121639352|ref|YP_979576.1|  83 IMEAYVHGVSTRSVDDLVAAMGVQAGVSKSEVSRICAGLDTEIEAFRTRSLTHTEFPYVFCDATFCKVRVGAHVVSQALV 162
                                    ******************************************************************************** PP

                Transposase_mut 187 iaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHllrnllak 266
                                    +a+gv  dG+re+Lg  v+dsEs +fW+++l sLk+rGl+gv+lv+sDah+GL++a+ + f +a++QrCrvH++rnl ++
  gi|121639352|ref|YP_979576.1| 163 VATGVSIDGTREVLGTAVGDSESYEFWREFLASLKARGLTGVHLVISDAHAGLKAAVAQQFSGASWQRCRVHFMRNLYTA 242
                                    ******************************************************************************** PP

                Transposase_mut 267 vpkkkadkvaealksiykaedaeearealeeflekl 302
                                    v  k+a  v+ a+k+i++++d ee+ ++++++++ l
  gi|121639352|ref|YP_979576.1| 243 VAAKHAPAVTVAVKTIFAHTDPEEVGAQWDRVADPL 278
                                    *******************************99865 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   3.9e-12   2.4e-08       3      96 .]     142     238 ..     140     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.9e-12
                           MULE   3 vlDgTyktnkykl.....plltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnal 77 
                                    + D+T+ + +         l+ ++gv   g+  +l+ a+ +se+ e ++ +l++l+++       + +i+D +++l+ a+
  gi|121639352|ref|YP_979576.1| 142 FCDATFCKVRVGAhvvsqALVVATGVSIDGTREVLGTAVGDSESYEFWREFLASLKARGL--TGVHLVISDAHAGLKAAV 219
                                    56777766665431111168889********************************99644..59**************** PP

                           MULE  78 eevfpeakhrlClfHiakn 96 
                                    +++f +a  + C  H+++n
  gi|121639352|ref|YP_979576.1| 220 AQQFSGASWQRCRVHFMRN 238
                                    ****************987 PP

>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0039        23     112     140 ..       4      32 ..       1      37 [. 0.86
   2 ?    8.2   0.0   0.00039       2.3      78     133 ..      65     120 ..      45     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0039
                                    HHHHHHHHHHTTSTTEEEEE---STTSS- CS
                          FTR_C 112 eamkagieaavkvegvlkisAgNygGkLG 140
                                    e ++ag++a++++e   +i Ag y+ + G
  gi|121639352|ref|YP_979576.1|   4 ELIRAGLQALIEAEATEAIGAGRYERSDG 32 
                                    5689********************86555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00039
                                    -TTSTT....----TT--.EEEEEEEEESSHHHHHHHHH.HHHHHHTTSTTEEEEE-- CS
                          FTR_C  78 cptlkekveeselpedve.avlEiVidgldeeavaeamk.agieaavkvegvlkisAg 133
                                     p+l e+    ++++  + +++E  + g+++++v++ +  +g++a v++++v++i Ag
  gi|121639352|ref|YP_979576.1|  65 FPSLLERR--RRIDKALHaVIMEAYVHGVSTRSVDDLVAaMGVQAGVSKSEVSRICAG 120
                                    56666554..455555541579************9977527***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1930.74
//
Query:       gi|121639353|ref|YP_979577.1|  [L=460]
Description: glutamate decarboxylase gadB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-71  238.6   0.0    1.1e-70  238.3   0.0    1.1  1  Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved do
  ------ inclusion threshold ------
      0.017   14.1   0.0       0.03   13.3   0.0    1.5  1  Aminotran_5    Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.3   0.0   1.2e-74   1.1e-70      11     374 ..      41     380 ..      32     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.3 bits;  conditional E-value: 1.2e-74
                                    SHHSSHH.HHHHHHHHHHCTGGGS--TTSTTBHCSSH....HHHHHHHHHHHHHT-BTSSTTTSHHHHHHHHHHHHHHHH CS
                  Pyridoxal_deC  11 aapekaesleqilediekilapgvttwhspefhkllpagnslisllgdlLadainkngftweesPaltelevvvldwlae 90 
                                    a+  + + + ++++  + +la++vttw++pe  kl+               ++  kn+++++e+Pa++++e +++ ++a+
  gi|121639353|ref|YP_979577.1|  41 AYRFIHD-ELMLDGSSRLNLATFVTTWMDPEAEKLMA--------------ETFDKNMIDKDEYPATAAIEARCVSMVAD 105
                                    3444444.89**************************9..............9**************************** PP

                                    HTT--GGGTCCT..-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHHHHT-E CS
                  Pyridoxal_deC  91 llglpeefleke..gggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqahssvekaalvlgvk 168
                                    l+++     +    + gv ++gsse+++l++lA ++++++++   + +         ++l+ ++++++ +ek+ ++++v+
  gi|121639353|ref|YP_979577.1| 106 LFHAEGLRDHDPtsATGVSTIGSSEAVMLGGLALKWRWRQRVGSWKGR--------MPNLVMGSNVQVVWEKFCRYFDVE 177
                                    ***99666665357****************************998856........799********************* PP

                                    EEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHH......CT-EEEEE-TTGGGGG CS
                  Pyridoxal_deC 169 lrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicek......ydlwlHvDAAyaGsaf 242
                                     r++p++  g  ++ ++e+ + +++e+  ++  vva+lGtt++g+ + + e+  +++k       d+++HvDAA++G  f
  gi|121639353|ref|YP_979577.1| 178 PRYLPMER-G-RYVITPEQVLAAVDEN--TI-GVVAILGTTYTGELEPIAEICAALDKlaagggVDVPVHVDAASGG--F 250
                                    *******7.7.78899***********..87.9********************************************..* PP

                                    GSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCCGSSSSSG..H CS
                  Pyridoxal_deC 243 icpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgtkaiplsr..r 317
                                    + p+  +   ++++++r+ Si+v++hK++l + +++ ++++  e+l++ l++ ++YL+        d++t+++++sr  +
  gi|121639353|ref|YP_979577.1| 251 VVPFLHPdlvWDFRLPRVVSINVSGHKYGLTYPGVGFVVWRGPEHLPEDLVFRVNYLG-------GDMPTFTLNFSRpgN 323
                                    **********************************************************.......9************99 PP

                                    HTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECS.TTBSSEEEEEE CS
                  Pyridoxal_deC 318 vrilklwfvlralGveglqnqirksvelakyleklirkderfeiva.evelglVcFrl 374
                                    +++ +++ +lr lG+ g+++++++  + a+ l +++r+  + e+++    ++ V+Frl
  gi|121639353|ref|YP_979577.1| 324 QVVGQYYNFLR-LGRDGYTKVMQALSHTARWLGDQLREVDHCEVISdGSAIPVVSFRL 380
                                    9999*******.*****************************999996789******98 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-06      0.03     103     214 ..     165     291 ..     157     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                                    HHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH..T....T-EEEEE CS
                    Aminotran_5 103 vpwqelakrtgakvkvipldeeg.eldldelekllnektklvaithvsnvtGtiqpveeigklakk..k....galvlvD 175
                                    v w++ ++   ++ +++p++++   ++++++ ++++e+t  v      + tG ++p++ei++++ k  +    ++ v+vD
  gi|121639353|ref|YP_979577.1| 165 VVWEKFCRYFDVEPRYLPMERGRyVITPEQVLAAVDENTIGVVAILGTTYTGELEPIAEICAALDKlaAgggvDVPVHVD 244
                                    689****************77652578************9999999**************98877643222235789*** PP

                                    -TTTTTTS---HHHHTESE.......EEEETTT.TTSSTT-EEEEEE CS
                    Aminotran_5 176 aaqavghipidvkklgvDf.......lafsghK.llgPtGiGvlyvr 214
                                    aa++    p+   +l  Df       + +sghK  l  +G+G+++ r
  gi|121639353|ref|YP_979577.1| 245 AASGGFVVPFLHPDLVWDFrlprvvsINVSGHKyGLTYPGVGFVVWR 291
                                    ****9999999999999996666666679999987899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3389.84
//
Query:       gi|121639354|ref|YP_979578.1|  [L=472]
Description: hypothetical protein BCG_3499c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-71  240.0   3.7    3.9e-71  239.4   3.7    1.2  1  Carb_kinase   Carbohydrate kinase
    6.9e-36  123.7   4.1    1.4e-35  122.7   4.1    1.6  1  YjeF_N        YjeF-related protein N-terminus
      4e-05   23.1   0.0    0.00011   21.7   0.0    1.7  2  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.4   3.7   6.6e-75   3.9e-71       2     241 ..     234     461 ..     233     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 6.6e-75
                                    EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSH CS
                    Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrde 81 
                                    +v++Gs++y+GAa+l++ aa+++++g+v++a   +a+a++ +++pevi++p++        +++ r++a+v+GpGLg+de
  gi|121639354|ref|YP_979578.1| 234 GVLAGSSTYPGAAVLCTGAAVAATSGMVRYAG--TAHAEVLAHWPEVIASPTP--------AAAGRVQAWVVGPGLGTDE 303
                                    69******************************..9******************........5789*************** PP

                                    CHHHHCHHHCCCCS-EEEEGGGGGSGGGG....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEE CS
                    Carb_kinase  82 kikklleevlekdeplviDAdgLnllaqkne.lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvll 160
                                    +++++l+++l++d p+++DAdgL++la++ + ++ r+a+++LTPh++Ef+rL++a+   +ddr+ ++r+la++l+a+vll
  gi|121639354|ref|YP_979578.1| 304 AGAAALWFALDTDLPVLVDADGLTMLADHPDlVAGRNAPTVLTPHAGEFARLAGAPP--GDDRVGACRQLADALGATVLL 381
                                    *********************************************************..********************* PP

                                    ESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHHH CS
                    Carb_kinase 161 kgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatelsk 240
                                    kg+++vi++p+g+v++n++g+s++a++GsGDvL+G+igalLa+  +s ea +aaa++h++a+++aa++ g g ++t++s+
  gi|121639354|ref|YP_979578.1| 382 KGNVTVIADPGGPVYLNPAGQSWAATAGSGDVLSGMIGALLASGLPSGEA-AAAAFVHARAAAAAAADPGPGDAPTSASR 460
                                    *********************************************66665.57889****************99999987 PP

                                    H CS
                    Carb_kinase 241 i 241
                                    i
  gi|121639354|ref|YP_979578.1| 461 I 461
                                    6 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   4.1   2.4e-39   1.4e-35       3     170 ..      25     182 ..      23     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 2.4e-39
                         YjeF_N   3 eLmenagravaevlrallg...nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellk 79 
                                    +Lm++a+ ++a  + + l+   + + +++v+ +vGsg+nGgd+l+aA +L+++ga ++++ll++    d+ +++al++++
  gi|121639354|ref|YP_979578.1|  25 ALMRRAAFGLATEIGRELTartGGVVGRRVCAVVGSGDNGGDALWAATFLRRRGAAADAVLLNP----DRTHRKALAAFT 100
                                    69**********9999999899999*************************************88....79********** PP

                         YjeF_N  80 kaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavka 159
                                    k gg++ve+ +++          dlviD+++Gi+ +g+lr ++a+++  ++++  pv+avDiPSG+d+ tGa++g+av+a
  gi|121639354|ref|YP_979578.1| 101 KSGGRLVESVSAA---------TDLVIDGVVGISGSGPLRPAAAQVFAAVQAAAIPVVAVDIPSGIDVATGAITGPAVHA 171
                                    *******755555.........79******************************************************** PP

                         YjeF_N 160 dvtvtfgapkr 170
                                     +tvtfg +k+
  gi|121639354|ref|YP_979578.1| 172 ALTVTFGGLKP 182
                                    *********97 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.4   2.4e+03     206     228 ..      95     117 ..      91     122 .. 0.85
   2 !   21.7   0.0   1.8e-08   0.00011     120     245 ..     342     456 ..     317     457 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.4
                                    HHHHHHHCTSSHHHHHHHHHHHH CS
                   Phos_pyr_kin 206 aiaaelakgesleeAvkkAkeyv 228
                                    a+aa    g +l e+v+ A++ v
  gi|121639354|ref|YP_979578.1|  95 ALAAFTKSGGRLVESVSAATDLV 117
                                    899999999*******9999877 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.8e-08
                                    -SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTH CS
                   Phos_pyr_kin 120 atvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGt 199
                                     tv+tP   E ++L+g  +   +d   a+++l++    +Vl+kG            v+ d ++ + l+    +   t G+
  gi|121639354|ref|YP_979578.1| 342 PTVLTPHAGEFARLAG--APPGDDRVGACRQLADALGATVLLKGNV---------TVIADPGGPVYLNPAGQSWAATAGS 410
                                    48**************..4456788899999*9988899*****86.........46777777777777777779***** PP

                                    HHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS-B- CS
                   Phos_pyr_kin 200 GCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkgagpv 245
                                    G++ls +i a la g +  eA + A    ++a ++a + g g  p+
  gi|121639354|ref|YP_979578.1| 411 GDVLSGMIGALLASGLPSGEAAAAAFVHARAAAAAAADPGPGDAPT 456
                                    *********************9999998889999999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3583.38
//
Query:       gi|121639355|ref|YP_979579.1|  [L=237]
Description: hypothetical protein BCG_3500c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1626.32
//
Query:       gi|121639356|ref|YP_979580.1|  [L=284]
Description: hypothetical protein BCG_3501c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.8e-101  337.3   4.1   6.9e-101  336.8   4.1    1.2  1  DUF4436       Domain of unknown function (DUF4436)
  ------ inclusion threshold ------
      0.017   15.4   6.2      0.017   15.4   6.2    2.3  3  TctB          Tripartite tricarboxylate transporter TctB fami
       0.27   11.0  10.3        1.7    8.4   0.9    2.5  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
          7    7.0   6.0       0.87    9.9   0.8    2.1  2  DUF4536       Domain of unknown function (DUF4536)


Domain annotation for each model (and alignments):
>> DUF4436  Domain of unknown function (DUF4436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.8   4.1  1.5e-104  6.9e-101       2     255 .]      24     275 ..      23     275 .. 0.99

  Alignments for each domain:
  == domain 1  score: 336.8 bits;  conditional E-value: 1.5e-104
                        DUF4436   2 laeskglgrpvdlsedadtpdrtsvtltvekldavanrLtvkvlvtpeealldekgevlkedlavrvsslaektdltypa 81 
                                    l++s+glgrp++++++++t+d t+vtl+ve+l+++++ L+++++v+p+++lld++++ lk+dl+v+v+s++++t++t+++
  gi|121639356|ref|YP_979580.1|  24 LYHSTGLGRPHEVAHGRPTADGTTVTLHVEQLQTIKGVLVANLAVSPGTELLDSQTQGLKDDLTVTVTSVVTPTKRTWSS 103
                                    67999*************************************************************************** PP

                        DUF4436  82 gklpaavevtveltGdiedwPFdrYrtgsltaevvvgagsdaapvpvrveltgrlegwdltvkrseeadkaaavevtlaR 161
                                    g+lp++++v+++++Gd+++wPFd+Yr+g++t++++ g  + +ap++v+v++++rl+gw+++++ +++a+  a+++v l+R
  gi|121639356|ref|YP_979580.1| 104 GSLPGVFPVPLTISGDPANWPFDHYRSGPITVQLYRG--AAHAPERVSVTFVDRLPGWNVDISGVGDANVPAPYRVGLHR 181
                                    ************************************9..8899************************************* PP

                        DUF4436 162 skstlifalvivlvlialpvlalivaiqvlrgrrkleppaltwmAAmLFAvvplRnalPgsPPiGswiDvavvlwvlval 241
                                    s+s+++f++viv+vlial+ ++l+va+q++rgrr+++pp++tw+AAmLFAv+plRnalP++PPiG+wiDv+vvlwv+val
  gi|121639356|ref|YP_979580.1| 182 SPSSVAFGTVIVGVLIALAGVGLFVAVQTARGRRQFQPPMTTWYAAMLFAVIPLRNALPDAPPIGFWIDVTVVLWVVVAL 261
                                    ******************************************************************************** PP

                        DUF4436 242 vaslvvyvvawvrr 255
                                    v+s+v+y+++w+++
  gi|121639356|ref|YP_979580.1| 262 VTSMVLYILCWWWH 275
                                    ************97 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.074   3.3e+02      35      49 ..       9      30 ..       3      72 .. 0.55
   2 ?   -3.5   0.0       2.6   1.2e+04      21      32 ..      98     111 ..      86     116 .. 0.54
   3 ?   15.4   6.2   3.8e-06     0.017      33     124 ..     191     273 ..     158     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.074
                           TctB 35 lgvllallgllllv.......a 49
                                   +g++l++++ ++++        
  gi|121639356|ref|YP_979580.1|  9 VGLVLVIAAYVTVIalyhstgL 30
                                   3444444443333344444440 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                           TctB  21 d.tg.arvgpgffP 32 
                                    + t+ ++  pg+fP
  gi|121639356|ref|YP_979580.1|  98 KrTWsSGSLPGVFP 111
                                    34444444588888 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.8e-06
                           TctB  33 lllgvllallgllllvaadgekeekearedwrkllklvlallaalll..yal.lleplGfilatalflllllgreerkwl 109
                                     ++gvl+al+g+ l+v   + ++++ +r+++++  ++ +a+l+a++    al   +p+Gf++ ++++l    +     ++
  gi|121639356|ref|YP_979580.1| 191 VIVGVLIALAGVGLFV---AVQTARGRRQFQPPMTTWYAAMLFAVIPlrNALpDAPPIGFWIDVTVVL----W-----VV 258
                                    4579999999999999...444555555666666667777333333355666666778**********....8.....99 PP

                           TctB 110 kalilavvlallvyl 124
                                    +al++++vl +l+++
  gi|121639356|ref|YP_979580.1| 259 VALVTSMVLYILCWW 273
                                    999*****9999997 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.9   0.00038       1.7      63     114 ..       2      56 ..       1      75 [. 0.53
   2 ?    7.0   2.7    0.0011       4.7      66     131 ..     189     269 ..     184     284 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00038
                   Trp_oprn_chp  63 rglgrrvvgvllalagagaavaals..lltdpadaaraaa.aaatgvasaaaave 114
                                    ++++r+vvg++l++a+ ++++a  +  +l  p+++a ++  a+ t+v+  +++ +
  gi|121639356|ref|YP_979580.1|   2 GRILRVVVGLVLVIAAYVTVIALYHstGLGRPHEVAHGRPtADGTTVTLHVEQLQ 56 
                                    6899******999999766655443003333333333333233333333333333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                   Trp_oprn_chp  66 grrvvgvllalagagaavaalslltdpadaaraaa.aaatgvasaaaavelta..............wpvlalaggvlll 130
                                    g ++vgvl+alag+g+ va+ ++   ++ +   ++  aa ++a    + +l++              w+v+al+  ++l 
  gi|121639356|ref|YP_979580.1| 189 GTVIVGVLIALAGVGLFVAVQTARGRRQFQPPMTTwYAAMLFAVIPLRNALPDappigfwidvtvvlWVVVALVTSMVLY 268
                                    66899********9998876666555555555555444444444444444444555666666666666666666666665 PP

                   Trp_oprn_chp 131 l 131
                                    +
  gi|121639356|ref|YP_979580.1| 269 I 269
                                    5 PP

>> DUF4536  Domain of unknown function (DUF4536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4      0.78   3.5e+03       6      24 ..       6      23 ..       6      33 .. 0.68
   2 ?    9.9   0.8   0.00019      0.87      12      45 ..     198     231 ..     195     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.78
                        DUF4536  6 RlvSGsGLigaGvYvyvqa 24
                                   R+v G+ L+ +++Yv v a
  gi|121639356|ref|YP_979580.1|  6 RVVVGLVLV-IAAYVTVIA 23
                                   555555444.788998866 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00019
                        DUF4536  12 GLigaGvYvyvqarrrlklggkfgmltiaqvafa 45 
                                    +L g+G++v+vq  r  ++++++     a+++fa
  gi|121639356|ref|YP_979580.1| 198 ALAGVGLFVAVQTARGRRQFQPPMTTWYAAMLFA 231
                                    899************9999999988777888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1972.68
//
Query:       gi|121639357|ref|YP_979581.1|  [L=624]
Description: glucosamine--fructose-6-phosphate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-58  196.7   0.1    1.8e-35  121.6   0.0    2.6  2  SIS       SIS domain
    7.4e-21   74.8   0.3    1.6e-20   73.6   0.3    1.6  1  GATase_6  Glutamine amidotransferase domain
    5.6e-15   55.3   0.0    1.1e-14   54.4   0.0    1.6  1  GATase_7  Glutamine amidotransferase domain
     0.0023   18.0   0.0     0.0061   16.6   0.0    1.8  1  SIS_2     SIS domain
      0.003   16.5   0.0     0.0078   15.1   0.1    1.6  2  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   0.0   5.1e-39   1.8e-35       2     128 ..     301     426 ..     300     429 .. 0.97
   2 !   72.4   0.0   8.4e-24     3e-20       2     127 ..     473     603 ..     472     606 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 5.1e-39
                                    HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                            SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerga 81 
                                    L++ ++++v+++Gt y++++ +++++e+++  +veve+ase++++  +++d+ +lv++is+sget+d+++a+++ake++a
  gi|121639357|ref|YP_979581.1| 301 LREIDKVFVVACGTAYHSGLLAKYAIEHWTRLPVEVELASEFRYR-DPVLDRSTLVVAISQSGETADTLEAVRHAKEQKA 379
                                    88899****************************************.********************************** PP

                                    EEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                            SIS  82 kiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                    k++aI++ +gs++ re+d +ly++a+pe++vastk+++aq aa ++l
  gi|121639357|ref|YP_979581.1| 380 KVLAICNTNGSQIPRECDAVLYTRAGPEIGVASTKTFLAQIAANYLL 426
                                    ******************************************99887 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 8.4e-24
                                    HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHH.....HHHH CS
                            SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaa.....aela 76 
                                    +a++ ++++lG+   y++a+e+alkl+e++++++e+ +a+elkhg++ali+++ +vi++ +s+  + +++a     +++ 
  gi|121639357|ref|YP_979581.1| 473 FAQSSTVLFLGRHVGYPVALEGALKLKELAYMHAEGFAAGELKHGPIALIEDGLPVIVVMPSPKGSATLHAkllsnIREI 552
                                    578999******************************************************9998766544322222779* PP

                                    HHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHH CS
                            SIS  77 kergakiiaITdskgsplareadlalyinaepetlvastksltaqlaalda 127
                                    + rga +i+I+ + + ++  +ad+ ++i+a+   l+++++++++q +a ++
  gi|121639357|ref|YP_979581.1| 553 QTRGAVTIVIAEEGDETVRPYADHLIEIPAVSTLLQPLLSTIPLQVFAASV 603
                                    **********************************************99765 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.3   4.6e-24   1.6e-20      10     133 ..      66     199 ..      54     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 4.6e-24
                       GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.....eel 84 
                                     +++++l+H+R+a++g +++  a+P   ++g++++vhNG i+n+  lr+el+  +g++f+s++Dtev ++l+     +  
  gi|121639357|ref|YP_979581.1|  66 LSGTTGLGHTRWATHGRPTDRNAHPHRDAAGKIAVVHNGIIENFAVLRRELET-AGVEFASDTDTEVAAHLVarayrH-- 142
                                    46789*************77666******************************.****************87788650.. PP

                       GATase_6  85 G..........eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                    G           +vl+rl+G f+ +++++ +++tl+ ar    + pl+ ++ ++ + ++s
  gi|121639357|ref|YP_979581.1| 143 GetaddfvgsvLAVLRRLEGHFTLVFANAdDPGTLVAARR---STPLVLGIGDNEMFVGS 199
                                    3444566668667779*************88888888854...47999999888888887 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   3.2e-18   1.1e-14       9     121 ..      84     204 ..      74     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 3.2e-18
                       GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea............ewgeealerlnG 76 
                                    ++++a P   ++ g++++v+nG i N+  lr+eLe++g++f++++Dtev ++l+++              + ++l+rl+G
  gi|121639357|ref|YP_979581.1|  84 TDRNAHPHR-DAAGKIAVVHNGIIENFAVLRRELETAGVEFASDTDTEVAAHLVARayrhgetaddfvGSVLAVLRRLEG 162
                                    566777888.699****************************************9999999****999888999******* PP

                       GATase_7  77 mfAfaiwdeeek.rlllaRDrlGikPLyygedkgdallfaSelkal 121
                                     f ++  ++++  +l++aR     +PL +g  + ++++++S + a+
  gi|121639357|ref|YP_979581.1| 163 HFTLVFANADDPgTLVAARR---STPLVLGIGD-NEMFVGSDVAAF 204
                                    *******9777659999999...6********6.7******99887 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0061     104     137 ..     352     385 ..     307     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                    T-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2 104 gDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                    + + + iS+sG+ a  +ea+++ake+ +kv A++
  gi|121639357|ref|YP_979581.1| 352 STLVVAISQSGETADTLEAVRHAKEQKAKVLAIC 385
                                    4455679*************************97 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.2e-06    0.0078      69     180 ..      66     172 ..      28     188 .. 0.68
   2 ?   -2.6   0.0      0.58   2.1e+03     153     178 ..     539     564 ..     534     580 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                       GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasr 144
                                    +  +  + H R at+G+ +++n+hp  R+ +g+ +   HnG +++++  +    +   e   +TD+E+a  +l+ +  ++
  gi|121639357|ref|YP_979581.1|  66 LSGTTGLGHTRWATHGRPTDRNAHPH-RDAAGK-IAVVHNGIIENFAVLRreleTAGVEFASDTDTEVAA-HLVARAYRH 142
                                    55566678*****************6.888886.5667*****99765553345556677789****985.444433333 PP

                       GATase_4 145 fekaepsaeeleralaelakeiaelGvfnlllsdgr 180
                                     e+   + + + ++l ++++++  +G f+l++++++
  gi|121639357|ref|YP_979581.1| 143 GET---ADDFVGSVL-AVLRRL--EGHFTLVFANAD 172
                                    323...333333333.333333..588888888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.58
                       GATase_4 153 eeleralaelakeiaelGvfnlllsd 178
                                    ++l++ l   ++ei+++G +++++++
  gi|121639357|ref|YP_979581.1| 539 ATLHAKLLSNIREIQTRGAVTIVIAE 564
                                    56788888889999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4358.84
//
Query:       gi|121639358|ref|YP_979582.1|  [L=158]
Description: hypothetical protein BCG_3503 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-09   36.0  14.2    1.1e-08   34.7  14.2    1.8  1  DUF2510   Protein of unknown function (DUF2510)


Domain annotation for each model (and alignments):
>> DUF2510  Protein of unknown function (DUF2510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7  14.2   5.9e-13   1.1e-08       1      30 [.     129     156 ..     129     158 .] 0.93

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.9e-13
                        DUF2510   1 pGWYpDPsgtpgllRyWDGarWTehtapap 30 
                                    +GWYpDP ++ g lRyWDGa WT  t+p+ 
  gi|121639358|ref|YP_979582.1| 129 AGWYPDP-SGAG-LRYWDGATWTHWTHPPR 156
                                    8******.8889.**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1103.65
//
Query:       gi|121639359|ref|YP_979583.1|  [L=280]
Description: hypothetical protein BCG_3504 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-06   26.8   0.0    3.5e-06   26.1   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme
    0.00022   20.3   0.2    0.00033   19.8   0.2    1.2  1  Chlorophyllase   Chlorophyllase
    0.00027   20.6   0.0     0.0051   16.4   0.0    2.0  1  DLH              Dienelactone hydrolase family
  ------ inclusion threshold ------
       0.25    9.8   0.2         12    4.2   0.0    2.0  2  PAF-AH_p_II      Platelet-activating factor acetylhydrolase, 


Domain annotation for each model (and alignments):
>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   7.9e-10   3.5e-06       6     123 ..      31     147 ..      27     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.9e-10
                Chlorophyllase2   6 llvvaPteageYpvllflhGylllnslYsqlLkhiashgfivvapqlykvaeadakeiksaakvlnWlakgLesvlpeev 85 
                                     +v++P+   + p + f h +l  +s Ys lL+h+as+g ++ ap   +   +++ ++     v+  + +g++   p ++
  gi|121639359|ref|YP_979583.1|  31 GVVYTPEAGLHLPGVAFGHDWLTGTSRYSGLLEHLASWGIVAAAPDSERGLAPSVLNLAFDLGVALDIVAGVR-LGPGKI 109
                                    57999*9999************************************999888988888888888888888877.447999 PP

                Chlorophyllase2  86 epdlsklalsgHSrGgktafalalgkaktslkfsalig 123
                                    + +  kl+l+gH  Gg +a+  a g + t++k+ a+i+
  gi|121639359|ref|YP_979583.1| 110 SVHPAKLGLVGHGFGGSAAVFAAAGLTGTHVKSVAAIF 147
                                    9999**********************999999999886 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   7.3e-08   0.00033      36     146 ..      32     141 ..      25     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.3e-08
                 Chlorophyllase  36 iivtPaeaGtypvvlflhGtllsnkfyskllnhiashGfivvaPqlykllpPsaqdeidsaaevieWlseglkavlptsv 115
                                    ++ tP      p v f h +l   + ys ll+h+as+G +  aP   + l+Ps  +   + +  ++ ++ g++   p ++
  gi|121639359|ref|YP_979583.1|  32 VVYTPEAGLHLPGVAFGHDWLTGTSRYSGLLEHLASWGIVAAAPDSERGLAPSVLNLAFDLGVALDIVA-GVR-LGPGKI 109
                                    5778877778899***************************************99875555554444433.332.347889 PP

                 Chlorophyllase 116 eanlsklalvGhsrGGktafalalgys.selt 146
                                         kl lvGh  GG +a   a g + ++++
  gi|121639359|ref|YP_979583.1| 110 SVHPAKLGLVGHGFGGSAAVFAAAGLTgTHVK 141
                                    99999***********9985444444325554 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-06    0.0051      84     170 ..     100     189 ..      29     199 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                            DLH  84 aavaylksvpevstkkvgvvGfCmGGalalllaaev..pevdaavafYG.lspekeleeaakikapilalfgeeDefipa 160
                                    a v+    + +v + k+g+vG  +GG  a+  aa      v+ ++a ++ ++++   + aa + +p l+l +  D+    
  gi|121639359|ref|YP_979583.1| 100 AGVRLGPGKISVHPAKLGLVGHGFGGSAAVFAAAGLtgTHVKSVAAIFPtVTNPAAEQPAATLDVPGLILTAPGDPKTLT 179
                                    55555556667889**************999998776789*********667777778889999********99998777 PP

                            DLH 161 devekleeal 170
                                    +++  l  a 
  gi|121639359|ref|YP_979583.1| 180 SNALGLSRAW 189
                                    7666666655 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0028        12      99     133 ..      41      75 ..      30      80 .. 0.86
   2 ?    3.6   0.1    0.0042        19     224     245 ..     110     131 ..     102     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0028
                                    -EEEEEEE--TT--TTTTHHHHHHHHHTT-EEEEE CS
                    PAF-AH_p_II  99 kyPlivFsHGLgafRtlYsalcielAskGfvvaav 133
                                     +P + F H   +  + Ys l  +lAs G+v aa 
  gi|121639359|ref|YP_979583.1|  41 HLPGVAFGHDWLTGTSRYSGLLEHLASWGIVAAAP 75 
                                    47889999998888889**************9997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0042
                                    -EEEEEEEEEEETHHHHHHHHH CS
                    PAF-AH_p_II 224 nldtskvaviGHsFGgAtviks 245
                                    +++ +k+ ++GH FGg  ++ +
  gi|121639359|ref|YP_979583.1| 110 SVHPAKLGLVGHGFGGSAAVFA 131
                                    67789999*******9887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1942.48
//
Query:       gi|121639360|ref|YP_979584.1|  [L=467]
Description: hypothetical protein BCG_3505c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   16.0   2.5      0.012   15.8   0.8    2.0  2  WXG100       Proteins of 100 residues with WXG
        2.4    7.6   9.6        3.8    6.9   9.6    1.2  1  Osteopontin  Osteopontin


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.8   1.3e-06     0.012       7      73 ..      58     124 ..      55     137 .. 0.85
   2 ?   -3.2   0.0       1.2     1e+04      29      40 ..     197     208 ..     192     218 .. 0.44

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisea 73 
                                     +l++  a+++++a+ l+++l+  +++v+ l+++W G+ ada   + ++  ++ + +v++    ++ 
  gi|121639360|ref|YP_979584.1|  58 HALDADCAQLRAAASVLMEALRMERSQVAVLAAAWTGSGADAAVHFVQRHCETGNSVVTEVRAAAQR 124
                                    5777888999***********************************9999888888888777666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                    HHHHHHHHCGCG CS
                         WXG100  29 rlkaevdalqsg 40 
                                    +++++ + ++++
  gi|121639360|ref|YP_979584.1| 197 TMRSTTAGVAAS 208
                                    333333333222 PP

>> Osteopontin  Osteopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.6   0.00043       3.8      66     120 ..     352     404 ..     346     420 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00043
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                    Osteopontin  66 DdvDddddddhvdsqdsvdsddsdetddsdksdeshhsDesDelv.tdfptdvpat 120
                                    D +D+ dd+d++      ++d++ e+ ++ + de+++ D++De v  + ++dv++ 
  gi|121639360|ref|YP_979584.1| 352 DAADNADDGDDAH---PEEADEAAEPKEATEPDEADEVDDADESVpAERAQDVAEE 404
                                    4445555555333...3445555556666666666666666666623344454444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2977.29
//
Query:       gi|121639361|ref|YP_979585.1|  [L=103]
Description: hypothetical protein BCG_3506c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0039   17.6   2.4     0.0044   17.5   2.4    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.4   2.4e-07    0.0044       6      98 ..      10     102 ..       5     103 .] 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-07
                  T7SS_ESX_EspC   6 sVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAa 85 
                                     +d +++ ++a+++ ++a+ i++a   ++ + a      G  +a   da++  ++  +++++ + +a+ ++a  Lra A 
  gi|121639361|ref|YP_979585.1|  10 GIDIAAVYAVADRFSAAAELIDDAIGNHLTRLAFGGACAGRGHASRGDALRCRLDRLAGELSVWSRAAVQIAFALRAGAN 89 
                                    578999************************************************************************** PP

                  T7SS_ESX_EspC  86 aYeatDeeaagal 98 
                                    +Y ++D  aa ++
  gi|121639361|ref|YP_979585.1|  90 RYAEADLCAAARI 102
                                    ******9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 751.13
//
Query:       gi|121639362|ref|YP_979586.1|  [L=448]
Description: phosphoglucosamine mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-41  141.3   0.0    4.4e-41  139.8   0.0    1.8  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.1e-27   96.5   0.8    2.1e-27   95.6   0.8    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    6.2e-18   65.3   0.4    1.7e-17   63.9   0.4    1.8  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.6e-15   56.3   1.0    8.5e-15   54.7   1.0    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   9.9e-45   4.4e-41       2     131 ..       3     133 ..       2     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 9.9e-45
                                    GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHC..STS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                      PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkae..akkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                    ++fgt+G+Rg+++  elt+el+++lg+a+a+ l+++   +++  v+GrD R+s+++l++a++agl+++Gv+++++g+lpt
  gi|121639362|ref|YP_979586.1|   3 RLFGTDGVRGVAN-RELTAELALALGAAAARRLSRSgaPGRRVAVLGRDPRASGEMLEAAVIAGLTSEGVDALRVGVLPT 81 
                                    68***********.77********************9667777789********************************** PP

                                    HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHH CS
                      PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaii 131
                                    Pav++++ +++ad g+mi+aSHnp  +ngiK++ + G ++++++e++Ie+ +
  gi|121639362|ref|YP_979586.1|  82 PAVAYLTGAYDADFGVMISASHNPMPDNGIKIFGPGGHKLDDDTEDQIEDLV 133
                                    *************************************************976 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.8   4.7e-31   2.1e-27       1     109 [.     260     368 ..     260     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 4.7e-31
                                    HHHHHHHHHHHHHHCH.CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTT CS
                    PGM_PMM_III   1 dgdqllallakyllee.klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiiflde 79 
                                    dgd+++++la +++e+ +l+ ++ +v+tvm++l+l+ +++++g+++  t+vGd+yvlee+++++++lGgE+Sghi+++  
  gi|121639362|ref|YP_979586.1| 260 DGDAIMVVLALAMKEAgELACNT-LVATVMSNLGLHLAMRSAGVTVRTTAVGDRYVLEELRAGDYSLGGEQSGHIVMPAL 338
                                    79***********9998888776.******************************************************** PP

                                    BSS--HHHHHHHHHHHHHHHTS-HHHHHHH CS
                    PGM_PMM_III  80 attkDGilaallvleilaetgkslsellee 109
                                      t+DGi++ l+++  + +tg sls+l+++
  gi|121639362|ref|YP_979586.1| 339 GSTGDGIVTGLRLMTRMVQTGSSLSDLASA 368
                                    ***************************944 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.4   3.7e-21   1.7e-17       2     103 .]     161     256 ..     160     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.7e-21
                                    HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----T.T-TTTTHHHHGGG CS
                     PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpee.kealkllielvkk 80 
                                    +Y++++++++     + ++l vv+d++hGa++  ++++ + +g++v+ +naep++       n  + + +l+ l ++v +
  gi|121639362|ref|YP_979586.1| 161 RYLRHVAKAAT---ARLDDLAVVVDCAHGAASSAAPRAYRAAGARVIAINAEPNGRNI----NDGCgSTHLDPLRAAVLA 233
                                    68888877776...78899************************************555....5555468999******** PP

                                    GG-SEEEEE-TTS-BEEEEETTE CS
                     PGM_PMM_II  81 egadlglafDgDaDRlgvvderG 103
                                    ++adlgla+DgDaDR+ +vd +G
  gi|121639362|ref|YP_979586.1| 234 HRADLGLAHDGDADRCLAVDANG 256
                                    ********************998 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   1.0   1.9e-18   8.5e-15       1      73 [.     376     444 ..     376     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.9e-18
                                    CCCCCHCC-TT..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                     PGM_PMM_IV   1 linvrveekakvvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                    linv+v +ka+  aa + +  +    ++++ l+  Gr+l +RpSGTep++rv+vEa ++  ++rla+ va+++
  gi|121639362|ref|YP_979586.1| 376 LINVEVVDKAT-AAAAPSVRTA--VEQAAAELGDTGRIL-LRPSGTEPMIRVMVEAADEGVAQRLAATVADAV 444
                                    8*******988.8888888888..9**************.*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2786.75
//
Query:       gi|121639363|ref|YP_979587.1|  [L=151]
Description: 30S ribosomal protein S9 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-43  147.6   0.0    2.7e-43  147.4   0.0    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   1.5e-47   2.7e-43       1     121 []      31     151 .]      31     151 .] 0.99

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.5e-47
                                    EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSSEEEEEEEESS-HHHHHHHHHHHHHHHHHH CS
                   Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgkfdvfvkvkgGGlsgqaeAirlgiaraLva 80 
                                    GrrKe+v rv++++g+gk+  ng+sle+Yf+++ +++ +++pl +++ +++fd+f++  gGG sgqa+A+rlgiaraL+ 
  gi|121639363|ref|YP_979587.1|  31 GRRKEAVVRVRLVPGTGKFDLNGRSLEDYFPNKVHQQLIKAPLVTVDRVESFDIFAHLGGGGPSGQAGALRLGIARALIL 110
                                    9******************************************************************************* PP

                                    HHHHHHHHHCTCCCTS-B--------TTSSCTTB----S-- CS
                   Ribosomal_S9  81 lekeekkeLkkaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                    +++e +++Lkkag+ltrDpR +ErkK+g+kkARk++q+skR
  gi|121639363|ref|YP_979587.1| 111 VSPEDRPALKKAGFLTRDPRATERKKYGLKKARKAPQYSKR 151
                                    ***88***********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 812.10
//
Query:       gi|121639364|ref|YP_979588.1|  [L=147]
Description: 50S ribosomal protein L13 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-53  180.4   0.0    1.7e-53  180.2   0.0    1.0  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2   0.0   9.4e-58   1.7e-53       2     124 ..      15     137 ..      14     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 9.4e-58
                                    EEEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHC CS
                  Ribosomal_L13   2 WyviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakelle 81 
                                    WyviDA++ vlgrla  +a++LrGkhkpt+ p+vd Gd+v+vina+kva++g+kl++k+ yrh+gypggl+++t+ el++
  gi|121639364|ref|YP_979588.1|  15 WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQ 94 
                                    ******************************************************************************** PP

                                    CSHHHHHHHHHHCCS-SSHHHHHHGCTEEEESSSTTSGGGGSC CS
                  Ribosomal_L13  82 kkpeeilekaVkgmLpknklgrrrlkrLkvyageehpheaqkp 124
                                    ++p++++eka+ gmLpkn+l+r+  ++L+vyag+ehph+aq+p
  gi|121639364|ref|YP_979588.1|  95 RHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSAQQP 137
                                    *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 806.20
//
Query:       gi|121639365|ref|YP_979589.1|  [L=100]
Description: hypothetical protein BCG_3510c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.6   2.0    2.4e-10   40.5   2.0    1.1  1  WXG100    Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.022   14.6   0.6      0.036   13.9   0.6    1.4  1  DUF5315   Disordered region of unknown function (DUF5315)


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   2.0   2.6e-14   2.4e-10      11      86 .]      17      92 ..       6      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.6e-14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         WXG100 11 qaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaDe 86
                                   ++ +++ ++a++  ++lq+l+++++ lq+ W  +aa a++ae+ +w+qaa  l++ L ++++a+++ a+ +++aD+
  gi|121639365|ref|YP_979589.1| 17 SVRQEIHTTAARFNAALQELRSQIAPLQQLWTREAAAAYHAEQLKWHQAASALNEILIDLGNAVRHGADDVAHADR 92
                                   566889999*****************************************************************95 PP

>> DUF5315  Disordered region of unknown function (DUF5315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6     4e-06     0.036      26      71 ..      14      57 ..      10      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-06
                        DUF5315 26 VklsAeegkkthvFgeehekaLeelReaqikLaqawrrseadekle 71
                                   ++ s +++   h     ++ aL+elR++ + L q w r+ a +  +
  gi|121639365|ref|YP_979589.1| 14 IEYSVRQE--IHTTAARFNAALQELRSQIAPLQQLWTREAAAAYHA 57
                                   66666666..7777789*******************9996655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 550.32
//
Query:       gi|121639366|ref|YP_979590.1|  [L=125]
Description: hypothetical protein BCG_3511c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   51.0   0.0    1.6e-13   50.7   0.0    1.1  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   8.8e-18   1.6e-13       2      85 ..      27     111 ..      26     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.8e-18
                                    HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                    +++d++ +r++a   ++ +ee++++lq+  + ++ +  s W G aa +fq++ ++w+++ ++l++ L+ i+++++++ +a
  gi|121639366|ref|YP_979590.1|  27 LNADFDLMRSVAGITDARNEEIRAMLQAFIGRMSGVpPSVWGGLAAARFQDVVDRWNAESTRLYHVLHAIADTIRHNEAA 106
                                    689***************************************************************************** PP

                                    HHHHH CS
                         WXG100  81 fedaD 85 
                                    +++a 
  gi|121639366|ref|YP_979590.1| 107 LREAG 111
                                    **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 701.73
//
Query:       gi|121639367|ref|YP_979591.1|  [L=404]
Description: hypothetical protein BCG_3512c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2243.37
//
Query:       gi|121639368|ref|YP_979592.1|  [L=1236]
Description: hypothetical protein BCG_3513c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.6e-118  392.4   1.6    6.4e-76  254.9   0.0    5.4  5  FtsK_SpoIIIE     FtsK/SpoIIIE family
    4.7e-10   39.9   0.0      0.012   15.8   0.0    3.7  3  AAA_22           AAA domain
    1.3e-08   35.4   9.6      0.092   13.1   0.1    4.5  3  AAA_16           AAA ATPase domain
    5.7e-08   32.9   0.4        0.4   10.6   0.0    4.0  3  NACHT            NACHT domain
      3e-06   27.6   0.2       0.42   10.9   0.0    3.7  3  AAA_19           AAA domain
      2e-05   24.8   0.2       0.47   10.5   0.0    3.2  3  DUF87            Helicase HerA, central domain
    8.9e-05   22.5   0.0       0.14   12.3   0.0    3.6  3  MMR_HSR1         50S ribosome-binding GTPase
     0.0001   22.8   0.0        4.9    7.7   0.1    3.3  3  ABC_tran         ABC transporter
    0.00011   22.6   0.0        3.2    8.2   0.0    3.3  3  RNA_helicase     RNA helicase
    0.00035   20.2   0.1        2.1    8.2   0.0    3.4  3  AAA_29           P-loop containing region of AAA domain
     0.0014   19.1   0.0        1.4    9.4   0.0    3.0  3  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.017   13.7   1.6      0.057   12.0   0.1    2.2  3  DUF853           Bacterial protein of unknown function (DUF85
      0.022   13.7   0.0        9.8    5.0   0.0    3.0  3  AAA_10           AAA-like domain
      0.026   13.4   0.4        2.8    6.8   0.0    3.0  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.054   12.9   0.0        3.2    7.1   0.0    3.3  4  TniB             Bacterial TniB protein
      0.071   12.8   0.3       0.31   10.7   0.2    2.0  2  LRR_RI_capping   Capping Ribonuclease inhibitor Leucine Rich 
      0.085   13.0   1.1         21    5.3   0.0    2.9  3  AAA_33           AAA domain
      0.093   12.4   0.0         13    5.4   0.0    3.1  3  AAA_24           AAA domain
        0.1   12.8   0.0         10    6.4   0.0    3.0  3  Roc              Ras of Complex, Roc, domain of DAPkinase
        0.1   12.6   0.0         18    5.3   0.0    2.7  3  AAA_14           AAA domain
       0.17   12.1   0.0        5.7    7.2   0.0    2.6  2  AAA_28           AAA domain
       0.27   10.9   0.3         32    4.1   0.0    2.9  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.11        89      56      72 ..     219     235 ..     217     283 .. 0.92
   2 !   80.6   0.1   1.4e-25   1.1e-22       7     128 ..     388     515 ..     385     531 .. 0.92
   3 !   16.2   0.0   6.1e-06     0.005     184     241 ..     528     580 ..     522     582 .. 0.91
   4 !  254.9   0.0   7.8e-79   6.4e-76       2     240 ..     721     967 ..     720     970 .. 0.98
   5 !   32.4   0.0   6.9e-11   5.6e-08      20     120 ..    1009    1106 ..    1003    1170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                                    HHHHHHHHHTT--TTTE CS
                   FtsK_SpoIIIE  56 lntLilSlatthtPeeV 72 
                                    l+++i+ la+ h+Pee+
  gi|121639368|ref|YP_979592.1| 219 LRAMICQLAVWHSPEEL 235
                                    89*************96 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 1.4e-25
                                    TSHHHHT---TTEEEEEEETTS-EEEEEGGGS-......SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTS CS
                   FtsK_SpoIIIE   7 eskkfrtessqlpvalgkeisgnplvldlkkma.....shllvaGatgsGKStalntLilSlatthtPeeVqliliDykg 81 
                                    +++  + ++ ++p+ + ++  g ++ ld+k++a     +h+l +GatgsGKS+ l+t+ l+++++++Pe ++l+l+D+kg
  gi|121639368|ref|YP_979592.1| 388 WRNVNQHDRLRVPIGVTPD--GTAVQLDIKEAAeqgmgPHGLCVGATGSGKSELLRTIALGMMARNSPEVLNLLLVDFKG 465
                                    6667788888899999999..99999999999999999****************************************** PP

                                    S.SCGGGTT-TTBSS...S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                   FtsK_SpoIIIE  82 v.elsalediphlls..vavatdperalraleeLvkemeeryalfreagv 128
                                    + ++  l + ph+++  ++ a+++  ++r+ ++L  em +r++l+r+ag 
  gi|121639368|ref|YP_979592.1| 466 GaTFLDLAGAPHVAAviTNLAEEAPLVARMQDALAGEMSRRQQLLRMAGH 515
                                    ***************999*****************************996 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 6.1e-06
                                    ---B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                   FtsK_SpoIIIE 184 agrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrl 241
                                    +g++l  +p l+ +vde+ eL  ++p+       d++  ++r gr+ g+Hllla qrl
  gi|121639368|ref|YP_979592.1| 528 TGAQLPCLPILFIVVDEFSELLSQHPEF-----VDVFLAIGRVGRSLGMHLLLASQRL 580
                                    5666778999******************.....999999*****************97 PP

  == domain 4  score: 254.9 bits;  conditional E-value: 7.8e-79
                                    HHHHHTSHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTS CS
                   FtsK_SpoIIIE   2 LlevleskkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykg 81 
                                    Ll+++e+++++ + + ++v++++e+s+ pl++dl+++a+++ v+Ga+++GKStal+tLi++la+th++ +Vq++++D++g
  gi|121639368|ref|YP_979592.1| 721 LLRDAEPAQAELAVPIGIVDRPFEQSRVPLTIDLSGAAGNVAVVGAPQTGKSTALRTLIMALAATHDAGRVQFYCLDFGG 800
                                    788999************************************************************************** PP

                                    SSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-........ CS
                   FtsK_SpoIIIE  82 velsalediphllsvavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddlaa 161
                                    ++l++++++ph+++va++++p+ a+r+l+eL+++++ r+a+fr++g++s+a+y++  a++++++f+d+flv+D++++l++
  gi|121639368|ref|YP_979592.1| 801 GALAQVDELPHVGAVAGRAQPQLASRMLAELESAVRFREAFFRDHGIDSVARYRQLRAKSAAESFADIFLVIDGWASLRQ 880
                                    ******************************************************************************** PP

                                    ..................-----------B-----EEEEEEC-HHHHHHHHHHH........HHHHHHHHHHHCGGGTEE CS
                   FtsK_SpoIIIE 162 ene....ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkds....svlvedaivRlarkgraaglH 233
                                    e++    +i++L++qg+s+gvhv+++a+r++e+rpsl++++++rieLrla+p+ds    +++++ +++R++r+ +++g+H
  gi|121639368|ref|YP_979592.1| 881 EFAaleeSIVALAAQGLSFGVHVALSAARWAEIRPSLRDQIGSRIELRLADPADSeldrRQAQRVPVDRPGRGLSRDGMH 960
                                    **********************************************************99******************** PP

                                    EEEEES- CS
                   FtsK_SpoIIIE 234 lllatqr 240
                                    +++a + 
  gi|121639368|ref|YP_979592.1| 961 MVIALPD 967
                                    ****875 PP

  == domain 5  score: 32.4 bits;  conditional E-value: 6.9e-11
                                     EEEEEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS. CS
                   FtsK_SpoIIIE   20 valgkei.sgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykgvelsalediphllsv 96  
                                     ++lg e  +g+p+ +d   ++ hllv+G  + GK+ al+tL   ++ tht+ + ql+++D+  + l  + +  h++  
  gi|121639368|ref|YP_979592.1| 1009 ILLGLEErRGQPVAVDFGRHP-HLLVLGDNECGKTAALRTLCREIVRTHTAARAQLLIVDFRHTLLD-VIESEHMGG- 1083
                                     778888879************.***************************************965554.445577777. PP

                                     S-B-SHHHHHHHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE   97 avatdperalraleeLvkemeery 120 
                                       +++p    + l  Lv++++ r 
  gi|121639368|ref|YP_979592.1| 1084 -YVSSPAALGAKLSSLVDLLQARM 1106
                                     .67777777777777887777775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05     0.012       7     103 ..     425     548 ..     420     578 .. 0.68
   2 !   15.0   0.0   2.8e-05     0.023       5     111 ..     758     887 ..     754     912 .. 0.63
   3 ?    4.3   0.0     0.056        46       6      40 ..    1029    1061 ..    1024    1163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdllrellralglelk 69 
                                    +++++G +G+GK+ llr+++    +++++e                  ++++ v   ++++ + + l  ++  al  e +
  gi|121639368|ref|YP_979592.1| 425 HGLCVGATGSGKSELLRTIALGMMARNSPEVlnlllvdfkggatfldlAGAPHVAAVITNLAEEAPLVARMQDALAGEMS 504
                                    89*******************99766655556677777666666666655555555555555555555555555555555 PP

                         AAA_22  70 aerlsseell.ealeqalrarav..........ielliiDEaqhl 103
                                    + r+++ ++  +++   + +ra+          i ++++DE+  l
  gi|121639368|ref|YP_979592.1| 505 R-RQQLLRMAgHLVSVTAYQRARqtgaqlpclpILFIVVDEFSEL 548
                                    5.6666666644444444444446777888899999999998875 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka 70 
                                    ag ++v+G + tGK+t lr+l + l +  +a +              + +e+ +v + ++  + +l++++l +l++    
  gi|121639368|ref|YP_979592.1| 758 AGNVAVVGAPQTGKSTALRTLIMALAATHDAGRvqfycldfgggalaQVDELPHVGAVAGRAQPQLASRMLAELESAVRF 837
                                    78899*******************96554444499999998888887444444555555555555555555555555544 PP

                         AAA_22  71 erlsseellealeqalrarav...........ielliiDEaqhlr.seealee 111
                                       ++  ++++  + + +++              +l+iD    lr + +alee
  gi|121639368|ref|YP_979592.1| 838 ---REAFFRDHGIDSVARYRQlraksaaesfaDIFLVIDGWASLRqEFAALEE 887
                                    ...33333344444444444444444444446788888888888644555555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.056
                         AAA_22    6 gilvvtGesGtGKTtllrrlleqldeeakaeeerp 40  
                                      +l+v G   +GKT  lr+l ++ ++   a++  +
  gi|121639368|ref|YP_979592.1| 1029 PHLLVLGDNECGKTAALRTLCREIVRTHTAAR--A 1061
                                     68999*************99998754443333..3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00011     0.092      17     144 ..     416     545 ..     409     574 .. 0.62
   2 !   12.9   0.9   0.00014      0.11      21     114 ..     755     859 ..     750     969 .. 0.73
   3 !   12.0   0.1   0.00025       0.2      22     167 ..    1026    1162 ..    1018    1165 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                         AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaele 95 
                                    e++ +g ++  l++G+ G+GKs l+r+++  + +++   +l+   ++++ +++++ la a     +++ l++e  + +++
  gi|121639368|ref|YP_979592.1| 416 EAAEQGMGPHGLCVGATGSGKSELLRTIALGMMARNsPEVLNLLLVDFKGGATFLDLAGAPHVAAVITNLAEE--APLVA 493
                                    57888999*******************9964444422555555555555556666666666555566666555..45566 PP

                         AAA_16  96 awrekleealaavpelagaeasrllellkrllallsrder.......p.lvlvlDdl 144
                                    + +++l ++++     ++++  r++ +l +  a+ + ++        p l +v+D++
  gi|121639368|ref|YP_979592.1| 494 RMQDALAGEMS-----RRQQLLRMAGHLVSVTAYQRARQTgaqlpclPiLFIVVDEF 545
                                    66666666666.....23333333333333332222222233444444466666665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                    sg  ++v ++G++ +GKs+ +r+l  al +++ +  ++  c +++ +      + + ++   + +++ +a+ +++++  +
  gi|121639368|ref|YP_979592.1| 755 SGAAGNVAVVGAPQTGKSTALRTLIMALAATHdAGRVQFYCLDFGGG-----ALAQVDELPHVGAVAGRAQPQLASRMLA 829
                                    677799***************99999888886688889999888333.....3333335455566666655555555555 PP

                         AAA_16 100 kleeala...............avpelaga 114
                                    +le+a++                 ++l+++
  gi|121639368|ref|YP_979592.1| 830 ELESAVRfreaffrdhgidsvaRYRQLRAK 859
                                    555555555555555545544423333333 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00025
                         AAA_16   22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde......aesae 93  
                                     gr + +l+ G+  +GK++ +r+l r++ +++   ++++++ l         +  + r++ll  +++e      ++ a+
  gi|121639368|ref|YP_979592.1| 1026 GRHPHLLVLGDNECGKTAALRTLCREIVRTH---TAARAQLL---------IVDF-RHTLLDVIESEhmggyvSSPAA 1090
                                     66799***********************995...44444444.........3333.3333333333322222211233 PP

                         AAA_16   94 leawrekleealaavpelagaeasrllellkrllallsrderp.lvlvlDdlqwade...aslql.laaLlrllesk. 165 
                                     l+a    l + l+        ++    ++ ++ l+  s  + p +++v+Dd + +      +l++ l++L ++++ + 
  gi|121639368|ref|YP_979592.1| 1091 LGAKLSSLVDLLQ--------ARMPAPDVSQAQLRARSWWSGPdIYVVVDDYDLVAVssgNPLMVlLEYLPHARDLGl 1160
                                     3333333333333........223344444444433333333447777777774444222455555555555555544 PP

                         AAA_16  166 pl 167 
                                     +l
  gi|121639368|ref|YP_979592.1| 1161 HL 1162
                                     55 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00088      0.72       6      95 ..     429     550 ..     427     596 .. 0.63
   2 !    7.7   0.0    0.0037         3       3      39 ..     761     794 ..     760     929 .. 0.74
   3 !   10.6   0.0   0.00049       0.4       3     132 ..    1031    1171 ..    1030    1188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00088
                                    EC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-......-HCHHHCCCCTS--SSS-CCHHHHCCSCC CS
                          NACHT   6 qGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgna...rsladllfsqlpepaapvsevwavllelpe 81 
                                     G+ GsGK+ Ll+ +al + +++ p++    lv f   +++ +   a     +++ l+++ p  a+ ++   a  +++++
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIALGMMARNSPEVLnLLLVDFKGGATFLDLAGAphvAAVITNLAEEAPLVARMQDA-LAGEMSRRQ 507
                                    69****************9999999875233333333334444444433334444444444444444444.333333444 PP

                                    CEE.............................EEEE-STT-SS CS
                          NACHT  82 rlL.............................lilDglDelvt 95 
                                    +lL                             +++D + el +
  gi|121639368|ref|YP_979592.1| 508 QLLrmaghlvsvtayqrarqtgaqlpclpilfIVVDEFSELLS 550
                                    4444444444666666666666666666666555566666555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0037
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEE CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFf 39 
                                    v++ G++  GK+t l+ l++a+a+ ++ +    + F+
  gi|121639368|ref|YP_979592.1| 761 VAVVGAPQTGKSTALRTLIMALAATHDAGR---VQFY 794
                                    68999999******************8884...3333 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00049
                                     EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....................-HCHHHCCCCT CS
                          NACHT    3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.................rsladllfsqlp 63  
                                     +++ G++ +GKT+ l+ l++++ + +  + a +l+++ + ++l +  ++                  sl dll + +p
  gi|121639368|ref|YP_979592.1| 1031 LLVLGDNECGKTAALRTLCREIVRTHTAARA-QLLIVDFRHTLLDVIESehmggyvsspaalgaklSSLVDLLQARMP 1107
                                     5799**********************99986.888877777777665556789999999999999999********** PP

                                     S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                          NACHT   64 epaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132 
                                     +p   + + +a  +     +  ++D++D ++   g+    p+ +lL e ++ +   + +l+++ r+++ 
  gi|121639368|ref|YP_979592.1| 1108 APDVSQAQLRARSWWSGPDIYVVVDDYDLVAVSSGN----PLMVLL-EYLPHARDLGLHLVVARRSGGA 1171
                                     **9999998888888888888*******99987777....444444.7777766667777777666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.032        26       4     114 ..     417     548 ..     415     561 .. 0.55
   2 !   10.9   0.0   0.00052      0.42      10      61 ..     758     809 ..     752     889 .. 0.86
   3 !    7.0   0.0    0.0084       6.9       9      50 ..    1027    1068 ..    1019    1106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                         AAA_19   4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAak.elrerlaalgaeatTiHrlal..... 77 
                                    a+e+   ++ l ++  G+GK+++l++i   + ++++ ++ ++llv f g A+   l+ +     + a  i +la+     
  gi|121639368|ref|YP_979592.1| 417 AAEQGMGPHGLCVGATGSGKSELLRTIALGMMARNSPEVLNLLLVDFKGGATFlDLAGA----PHVAAVITNLAEeaplv 492
                                    5555566777889999**********999999999888888888888777652122222....22233344443344444 PP

                         AAA_19  78 .................ldfddlltealelle...............eaeeekklqeeellivDEfqdv 114
                                                     l             +               ++  + +      ++vDEf+++
  gi|121639368|ref|YP_979592.1| 493 armqdalagemsrrqqlL-------------RmaghlvsvtayqrarQTGAQLPCLPILFIVVDEFSEL 548
                                    444433333432222221.............22222233555444433333334434446777777766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00052
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrer 61 
                                    +++++v++ p tGK++ l++ +  l ++++    +++++ f g A  ++ e 
  gi|121639368|ref|YP_979592.1| 758 AGNVAVVGAPQTGKSTALRTLIMALAATHDAGRVQFYCLDFGGGALAQVDEL 809
                                    67899************************9999999*999999999988874 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0084
                         AAA_19    9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaf 50  
                                     ++++llv++   +GKT  l++ ++++v++++ + +++l+v f
  gi|121639368|ref|YP_979592.1| 1027 RHPHLLVLGDNECGKTAALRTLCREIVRTHTAARAQLLIVDF 1068
                                     678899************************999999999876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00058      0.47      12      60 ..     408     463 ..     399     484 .. 0.74
   2 ?    3.8   0.0     0.066        54       8      51 ..     744     786 ..     736     791 .. 0.85
   3 !    6.7   0.0    0.0084       6.9      11      59 ..    1018    1067 ..    1005    1070 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                          DUF87  12 vpvyldlnklvtr....HlAilgsTGsGKSntvavLleelle..kkga.tililDp 60 
                                    + v ld++++ ++    H + +g TGsGKS + + +   +++  ++ + ++l++D 
  gi|121639368|ref|YP_979592.1| 408 TAVQLDIKEAAEQgmgpHGLCVGATGSGKSELLRTIALGMMArnSPEVlNLLLVDF 463
                                    4566666666554333388899**************99999755444456666665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
                          DUF87   8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekk 51 
                                    ++s+vp+ +dl+ +    +A++g   +GKS+  + L+  l++++
  gi|121639368|ref|YP_979592.1| 744 EQSRVPLTIDLSGA-AGNVAVVGAPQTGKSTALRTLIMALAATH 786
                                    5688999****777.999*******************9998744 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0084
                          DUF87   11 evpvyldlnklvtrHlAilgsTGsGKSntvavLleelle...kkgatililD 59  
                                     + pv +d  +    Hl++lg    GK+   + L++e+++     +a++li+D
  gi|121639368|ref|YP_979592.1| 1018 GQPVAVDFGRH--PHLLVLGDNECGKTAALRTLCREIVRthtAARAQLLIVD 1067
                                     56666676554..8*************************9888888999999 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.067        55       4      20 ..     428     444 ..     426     527 .. 0.81
   2 !   12.3   0.0   0.00017      0.14       1      27 [.     760     786 ..     760     800 .. 0.86
   3 ?    1.7   0.0      0.33   2.7e+02       3      27 ..    1032    1056 ..    1030    1072 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.067
                                    EEESTTSSHHHHHHHHH CS
                       MMR_HSR1   4 ivGrpNvGKStLinalt 20 
                                    +vG + +GKS L++++ 
  gi|121639368|ref|YP_979592.1| 428 CVGATGSGKSELLRTIA 444
                                    69************996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                                    EEEEEESTTSSHHHHHHHHHTSTEEES CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivs 27 
                                    +va+vG p +GKSt +++l+ + a + 
  gi|121639368|ref|YP_979592.1| 760 NVAVVGAPQTGKSTALRTLIMALAATH 786
                                    59*****************98866554 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.33
                                     EEEESTTSSHHHHHHHHHTSTEEES CS
                       MMR_HSR1    3 aivGrpNvGKStLinaltgekaivs 27  
                                     +++G    GK+  +++l++e +++ 
  gi|121639368|ref|YP_979592.1| 1032 LVLGDNECGKTAALRTLCREIVRTH 1056
                                     6899999************966554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1     0.006       4.9      17      32 ..     429     444 ..     422     455 .. 0.87
   2 ?    5.6   0.0     0.027        22      13      43 ..     760     792 ..     751     909 .. 0.84
   3 ?    5.4   0.0     0.029        24       5      35 ..    1022    1052 ..    1019    1074 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                                    EESTTSSHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxx RF
                       ABC_tran  17 vGenGaGKStLlklla 32 
                                    vG +G+GKS Ll+++a
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIA 444
                                    8*************97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                                    EEEEEESTTSSHHHHHHHHTTSS--..SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllkp..teGeil 43 
                                     va+vG   +GKSt l++l+  l    ++G+++
  gi|121639368|ref|YP_979592.1| 760 NVAVVGAPQTGKSTALRTLIMALAAthDAGRVQ 792
                                    589**************9998876644666664 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.029
                                     EEEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran    5 slklkegekvaivGenGaGKStLlkllagll 35  
                                      +++ +   + ++G+n +GK+  l++l+++ 
  gi|121639368|ref|YP_979592.1| 1022 AVDFGRHPHLLVLGDNECGKTAALRTLCREI 1052
                                     566667778899****************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.13   1.1e+02       4      23 ..     429     448 ..     427     458 .. 0.83
   2 !    8.2   0.0    0.0039       3.2       2      26 ..     762     786 ..     761     798 .. 0.82
   3 !    7.0   0.0    0.0091       7.4       2      26 ..    1032    1056 ..    1031    1090 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                   RNA_helicase   4 yGpsgeGKStlakeLakall 23 
                                    +G++g GKS l +++a  ++
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIALGMM 448
                                    79***********9987766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                     ++G++++GKSt+ ++L+ al+ + 
  gi|121639368|ref|YP_979592.1| 762 AVVGAPQTGKSTALRTLIMALAATH 786
                                    689******************9766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0091
                   RNA_helicase    2 wlyGpsgeGKStlakeLakallkkl 26  
                                     ++ G++ +GK+ + ++L++++ ++ 
  gi|121639368|ref|YP_979592.1| 1032 LVLGDNECGKTAALRTLCREIVRTH 1056
                                     689******************9766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0025       2.1      24      48 ..     425     449 ..     413     455 .. 0.77
   2 !    6.6   0.1    0.0081       6.6      23      49 ..     756     785 ..     745     793 .. 0.76
   3 ?    0.8   0.0      0.52   4.2e+02      21      38 ..    1027    1044 ..    1018    1048 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                         AAA_29  24 atlltGpsGsGKSTllDAiqalLvp 48 
                                      l +G++GsGKS ll  i+  +++
  gi|121639368|ref|YP_979592.1| 425 HGLCVGATGSGKSELLRTIALGMMA 449
                                    45999********999777665555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0081
                         AAA_29  23 g...atlltGpsGsGKSTllDAiqalLvpa 49 
                                    g   ++ ++G+  +GKST l  +++ L ++
  gi|121639368|ref|YP_979592.1| 756 GaagNVAVVGAPQTGKSTALRTLIMALAAT 785
                                    433599************997777777665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.52
                         AAA_29   21 lkgatlltGpsGsGKSTl 38  
                                     ++   l+ G+++ GK++ 
  gi|121639368|ref|YP_979592.1| 1027 RHPHLLVLGDNECGKTAA 1044
                                     444789*********975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0       0.1        84      25      44 ..     429     448 ..     427     457 .. 0.85
   2 ?    2.1   0.0       0.3   2.4e+02      13      44 ..     750     783 ..     741     874 .. 0.86
   3 !    9.4   0.0    0.0017       1.4      15      40 ..    1023    1049 ..    1015    1050 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                         AAA_23  25 tGpNGaGKTTildAiklaLy 44 
                                    +G +G+GK+ +l+ i l++ 
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIALGMM 448
                                    79***********9998875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                         AAA_23  13 qeidF..skgltlItGpNGaGKTTildAiklaLy 44 
                                     +id+    g ++++G   +GK+T l+ +  aL 
  gi|121639368|ref|YP_979592.1| 750 LTIDLsgAAGNVAVVGAPQTGKSTALRTLIMALA 783
                                    578886555999999************9999984 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0017
                         AAA_23   15 idF.skgltlItGpNGaGKTTildAik 40  
                                     +dF  ++  l+ G+N++GKT+ l+ ++
  gi|121639368|ref|YP_979592.1| 1023 VDFgRHPHLLVLGDNECGKTAALRTLC 1049
                                     799777999************998877 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.1e-05     0.057      22      70 ..     424     476 ..     408     500 .. 0.76
   2 ?   -0.3   0.0      0.37     3e+02      22      58 ..     759     799 ..     742     834 .. 0.66
   3 ?   -3.2   0.0       2.8   2.3e+03      23      45 ..    1030    1052 ..    1019    1067 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                         DUF853  22 rhGliaGatGtGktvtLqvlaesl....seaGvpvfladvkGdLsgiakaGev 70 
                                     hGl  GatG Gk   L+++a ++    s      +l+d kG  + +  aG +
  gi|121639368|ref|YP_979592.1| 424 PHGLCVGATGSGKSELLRTIALGMmarnSPEVLNLLLVDFKGGATFLDLAGAP 476
                                    6******************9988722223344567899999988877777765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                         DUF853  22 rhGliaGatGtGktvtLqvlaeslse...aG.vpvfladvk 58 
                                        + Ga  tGk  +L++l  +l++   aG v  ++ d  
  gi|121639368|ref|YP_979592.1| 759 GNVAVVGAPQTGKSTALRTLIMALAAthdAGrVQFYCLDFG 799
                                    444678*************9888864111343556666655 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                         DUF853   23 hGliaGatGtGktvtLqvlaesl 45  
                                     h l+ G    Gkt +L++l+ ++
  gi|121639368|ref|YP_979592.1| 1030 HLLVLGDNECGKTAALRTLCREI 1052
                                     77999999**********98776 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        14      21      58 ..     423     464 ..     412     482 .. 0.84
   2 ?    5.0   0.0     0.012       9.8     245     313 ..     541     610 ..     532     614 .. 0.86
   3 ?   -0.8   0.0      0.71   5.8e+02      21      47 ..     758     784 ..     754     791 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                         AAA_10  21 asasliiGdlGnGKSvlakllvlyisllg....gkaliiDpk 58 
                                     ++ l +G +G GKS l +++ l +++++      +l++D k
  gi|121639368|ref|YP_979592.1| 423 GPHGLCVGATGSGKSELLRTIALGMMARNspevLNLLLVDFK 464
                                    578899****************99999986665566677765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                         AAA_10 245 ifDE.awiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvL 313
                                    ++DE +  + + +e   +   + R GRs    ++l++q  d     +l++ ++++++ +    +e ++vL
  gi|121639368|ref|YP_979592.1| 541 VVDEfSELLSQHPEFVDVFLAIGRVGRSLGMHLLLASQRLDEGRLRGLETHLSYRMCLKTWSASESRNVL 610
                                    56662334566777788888999************************************99999988887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.71
                         AAA_10  21 asasliiGdlGnGKSvlakllvlyisl 47 
                                    a +++++G +  GKS   ++l++ +++
  gi|121639368|ref|YP_979592.1| 758 AGNVAVVGAPQTGKSTALRTLIMALAA 784
                                    6788*****************998765 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0034       2.8      17      54 ..     425     466 ..     412     477 .. 0.82
   2 ?    2.4   0.0     0.075        61      16      44 ..     759     787 ..     744     804 .. 0.82
   3 ?   -0.2   0.0      0.44   3.6e+02      17      50 ..    1030    1067 ..    1026    1075 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0034
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairarg....draivlDltGa 54 
                                    h l vG+tGsGK++ l+ +  ++ ar+       + +D++G 
  gi|121639368|ref|YP_979592.1| 425 HGLCVGATGSGKSELLRTIALGMMARNspevLNLLLVDFKGG 466
                                    8899**************999999998544445666777775 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.075
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargd 44 
                                      +++vG+  +GK++al+ l+ a+ a  d
  gi|121639368|ref|YP_979592.1| 759 GNVAVVGAPQTGKSTALRTLIMALAATHD 787
                                    57899****************99877665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.44
                  TrwB_AAD_bind   17 hilivGttGsGKtqalekllrairarg....draivlD 50  
                                     h+l++G    GKt al+ l r+i +       + +++D
  gi|121639368|ref|YP_979592.1| 1030 HLLVLGDNECGKTAALRTLCREIVRTHtaarAQLLIVD 1067
                                     99999**************9998655433334556666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.97   7.9e+02      35      55 ..     422     443 ..     413     460 .. 0.79
   2 ?   -2.5   0.0       3.4   2.8e+03     114     136 ..     531     553 ..     516     564 .. 0.71
   3 ?    0.3   0.0      0.49     4e+02      37      54 ..     760     777 ..     755     793 .. 0.82
   4 ?    7.1   0.0    0.0039       3.2      34      65 ..    1027    1058 ..    1021    1071 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.97
                           TniB  35 m.pnlllvGdsnnGKtmivekF 55 
                                    m p+ l vG +  GK+ +++  
  gi|121639368|ref|YP_979592.1| 422 MgPHGLCVGATGSGKSELLRTI 443
                                    4488899*********999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                           TniB 114 llrelkvrvLiiDEihnllagsa 136
                                     l  l +  +++DE+ +ll+ + 
  gi|121639368|ref|YP_979592.1| 531 QLPCLPILFIVVDEFSELLSQHP 553
                                    55566667799*****9997655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.49
                           TniB  37 nlllvGdsnnGKtmivek 54 
                                    n+ +vG +++GK++ ++ 
  gi|121639368|ref|YP_979592.1| 760 NVAVVGAPQTGKSTALRT 777
                                    889**********99876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0039
                           TniB   34 rmpnlllvGdsnnGKtmivekFarlhppekde 65  
                                     r p+ll++Gd ++GKt+ ++  +r+  +++ +
  gi|121639368|ref|YP_979592.1| 1027 RHPHLLVLGDNECGKTAALRTLCREIVRTHTA 1058
                                     89***************999988876665544 PP

>> LRR_RI_capping  Capping Ribonuclease inhibitor Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         3   2.4e+03      13      19 ..     368     374 ..     367     375 .. 0.83
   2 ?   10.7   0.2   0.00038      0.31      10      24 ..     905     919 ..     904     920 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                 LRR_RI_capping  13 sRWtELL 19 
                                    s W+EL+
  gi|121639368|ref|YP_979592.1| 368 SGWAELV 374
                                    67****8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                 LRR_RI_capping  10 LSdsRWtELLplmqq 24 
                                    LS++RW+E+ p++++
  gi|121639368|ref|YP_979592.1| 905 LSAARWAEIRPSLRD 919
                                    9********999975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        22       3      24 ..     427     446 ..     427     516 .. 0.84
   2 ?    5.3   0.0     0.025        21       2      26 ..     761     785 ..     761     792 .. 0.87
   3 ?   -3.0   0.1       9.4   7.7e+03      81     118 ..     906     944 ..     879     947 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                         AAA_33   3 llvGlpGsGKstlaerllkklg 24 
                                    l+vG+ GsGKs l++ ++  lg
  gi|121639368|ref|YP_979592.1| 427 LCVGATGSGKSELLRTIA--LG 446
                                    589**********99886..55 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                         AAA_33   2 vllvGlpGsGKstlaerllkklgav 26 
                                    v +vG+p +GKst ++ l+ +l+a+
  gi|121639368|ref|YP_979592.1| 761 VAVVGAPQTGKSTALRTLIMALAAT 785
                                    568**************99888765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.4
                         AAA_33  81 srrerarflklar.rlgvpvrivvvetdeetlkeRlakR 118
                                    s++++a+++  +r ++g+++++   ++ +++l +R a+R
  gi|121639368|ref|YP_979592.1| 906 SAARWAEIRPSLRdQIGSRIELRLADPADSELDRRQAQR 944
                                    455666666555557888888888889999999999988 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.12        97       4      46 ..     425     478 ..     422     500 .. 0.77
   2 ?    5.4   0.0     0.016        13       4      23 ..     760     790 ..     757     817 .. 0.73
   3 ?   -0.2   0.0      0.86     7e+02       4      22 ..    1030    1048 ..    1027    1075 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                         AAA_24   4 kiliyGpsgiGKTtlakel...........gpkplfidtekGlksldadkfpdi 46 
                                      l++G  g+GK+ l++++             + l++d+ +G+  ld +  p +
  gi|121639368|ref|YP_979592.1| 425 HGLCVGATGSGKSELLRTIalgmmarnspeVLNLLLVDFKGGATFLDLAGAPHV 478
                                    56899*************999999988655556667788888877777666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
                         AAA_24   4 kiliyGpsgiGKTtlakel...........g 23 
                                    +++++G + +GK+t +++l            
  gi|121639368|ref|YP_979592.1| 760 NVAVVGAPQTGKSTALRTLimalaathdagR 790
                                    689**************99555555555444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.86
                         AAA_24    4 kiliyGpsgiGKTtlakel 22  
                                      +l+ G+++ GKT  +++l
  gi|121639368|ref|YP_979592.1| 1030 HLLVLGDNECGKTAALRTL 1048
                                     5799*********999998 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.45   3.7e+02       4      23 ..     428     447 ..     427     461 .. 0.81
   2 ?    0.6   0.0      0.76   6.2e+02       2      21 ..     761     780 ..     760     794 .. 0.85
   3 ?    6.4   0.0     0.013        10       2      32 ..    1031    1061 ..    1030    1081 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.45
                                    EESSTTSSHHHHHHCHCT-C CS
                            Roc   4 lvGdsgvGKtsllkrfvedk 23 
                                    +vG +g+GK+ ll+ +  + 
  gi|121639368|ref|YP_979592.1| 428 CVGATGSGKSELLRTIALGM 447
                                    79***********9887655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.76
                                    EEEESSTTSSHHHHHHCHCT CS
                            Roc   2 vvlvGdsgvGKtsllkrfve 21 
                                    v +vG  ++GK++ l+ ++ 
  gi|121639368|ref|YP_979592.1| 761 VAVVGAPQTGKSTALRTLIM 780
                                    789**********9998875 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.013
                                     EEEESSTTSSHHHHHHCHCT-CCC-EEETTT CS
                            Roc    2 vvlvGdsgvGKtsllkrfvedkfsekeksti 32  
                                     ++++Gd++ GKt  l+ ++++ +++++ +  
  gi|121639368|ref|YP_979592.1| 1031 LLVLGDNECGKTAALRTLCREIVRTHTAARA 1061
                                     689****************998877766554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.9     4e+03       8      23 ..     429     444 ..     427     463 .. 0.77
   2 ?    5.3   0.0     0.023        18       5      27 ..     761     783 ..     758     798 .. 0.82
   3 ?    4.0   0.0      0.06        49       4      41 ..    1030    1071 ..    1027    1089 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                         AAA_14   8 tGaRrvGKTtllkqli 23 
                                    +Ga  +GK+ ll++++
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIA 444
                                    5888899999999887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                         AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                    ++++Ga ++GK+t l++li  l 
  gi|121639368|ref|YP_979592.1| 761 VAVVGAPQTGKSTALRTLIMALA 783
                                    7899*************996655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.06
                         AAA_14    4 ilvitGaRrvGKTtllkqlikell....vkkesilyinldde 41  
                                      l++ G   +GKT  l++l +e      + + + l +++ + 
  gi|121639368|ref|YP_979592.1| 1030 HLLVLGDNECGKTAALRTLCREIVrthtAARAQLLIVDFRHT 1071
                                     57889999*****99999988877777678888888888765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.27   2.2e+02       5      20 ..     429     444 ..     427     463 .. 0.79
   2 ?    7.2   0.0     0.007       5.7       1      19 [.     760     778 ..     760     867 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                         AAA_28   5 tGgestGKTtlleaLa 20 
                                    +G+ ++GK+ ll+ +a
  gi|121639368|ref|YP_979592.1| 429 VGATGSGKSELLRTIA 444
                                    7***********9988 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.007
                         AAA_28   1 kivitGgestGKTtlleaL 19 
                                    +++++G++ tGK+t l+ L
  gi|121639368|ref|YP_979592.1| 760 NVAVVGAPQTGKSTALRTL 778
                                    589***********99887 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.04        32       5      20 ..     430     445 ..     426     460 .. 0.80
   2 ?    0.1   0.0      0.67   5.5e+02       3      20 ..     763     780 ..     761     790 .. 0.82
   3 ?    2.4   0.0      0.13   1.1e+02       9      30 ..    1039    1058 ..    1038    1074 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.04
                Viral_helicase1   5 GvpGcGKStlirkllr 20 
                                    G+ G+GKS l+r+++ 
  gi|121639368|ref|YP_979592.1| 430 GATGSGKSELLRTIAL 445
                                    99**********9985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.67
                Viral_helicase1   3 vhGvpGcGKStlirkllr 20 
                                    v G+p  GKSt++r+l+ 
  gi|121639368|ref|YP_979592.1| 763 VVGAPQTGKSTALRTLIM 780
                                    6788999********985 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.13
                Viral_helicase1    9 cGKStlirkllrtsliltvnrp 30  
                                     cGK+ ++r+l+r+  i+++++ 
  gi|121639368|ref|YP_979592.1| 1039 CGKTAALRTLCRE--IVRTHTA 1058
                                     *************..4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 1.04u 0.39s 00:00:01.43 Elapsed: 00:00:00.58
# Mc/sec: 6367.80
//
Query:       gi|121639369|ref|YP_979593.1|  [L=467]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-20   73.1   2.0    4.3e-20   72.2   1.0    2.1  2  YukD      WXG100 protein secretion system (Wss), protein YukD


Domain annotation for each model (and alignments):
>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   1.0   2.4e-24   4.3e-20       2      76 .]       9      83 ..       8      83 .. 0.98
   2 ?   -2.7   0.0      0.56     1e+04      32      57 ..     337     362 ..     322     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.4e-24
                                   EEEEEE-TTTEEEEEEETTSBTTHHHHHHHHHS-...--S---TT-EEEEGGGEEEETTSBCGGGT--TT-EEEE CS
                           YukD  2 vrVtvlagnrrvDlaLPadvpvaellpalvrllgepddeagrpggwsLarvggapLsgdrtLaeagVrDGdlLvL 76
                                    rVtv+ag++ vDl LPa+vpva+l+p++v++lg+ +++++ +++++L+ +g ++L+   tLa++g+rDG++LvL
  gi|121639369|ref|YP_979593.1|  9 RRVTVHAGAQAVDLTLPAAVPVATLIPSIVDILGDRGASPATAARYQLSALGAPALPNATTLAQCGIRDGAVLVL 83
                                   69***********************************************************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.56
                                    HHS-...--S---TT-EEEEGGGEEE CS
                           YukD  32 rllgepddeagrpggwsLarvggapL 57 
                                    +++++ ++ +   gg +La v+ga L
  gi|121639369|ref|YP_979593.1| 337 TAVATHGIHRSSMGGIALAAVTGALL 362
                                    44445667777788888998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.37s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 2545.59
//
Query:       gi|121639370|ref|YP_979594.1|  [L=455]
Description: serine protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-32  112.1   5.3    5.5e-32  111.2   5.3    1.5  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   5.3   3.1e-36   5.5e-32       1     298 []      89     376 ..      89     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 3.1e-36
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B...SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.apee 79 
                                    g g  vav+DtGv   h +l        k+          ++g+d+  t +  a+ d      HGt vAGi+aa  ++++
  gi|121639370|ref|YP_979594.1|  89 GAGQRVAVIDTGV-ARHRRLP-------KV----------VAGGDYVFTGDGTADCDA-----HGTLVAGIIAAApDAQS 145
                                    67899********.7777777.......55..........566666655555555543.....************9**** PP

                                    SSSB-SSTTSEEE........EEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH...HHH CS
                                    xxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                   Peptidase_S8  80 gekngvapgakil........svkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal...ain 148
                                     +++gvap+++++         + v+d+s++   + +++++a++ aa  ++ vin+s      +p        +   a+ 
  gi|121639370|ref|YP_979594.1| 146 DNFSGVAPDVTLIsirqssskFAPVGDPSSTGVGDVDTMAKAVRTAADLGASVINISSI--ACVPAAAAPDDRAlgaALA 223
                                    *************7777765444577777777766699*******************99..3333333332223377*** PP

                                    HHH.CCT-EEEEE--SS-T-HH.......EEE-TTCEEC.TTTST.TCEEEEEESTTSSB-TT--B-TT.......-EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 149 ravnkkgvlvviSaGNngktgs.......slqagspvgt.pstsk.nvitvgayttegkiapfSsrGpssdgklkpdiva 219
                                    +av+ k+ ++v++aGN g  ++        + ++ +v   p+ ++  v+tvg+++ +g+ + f+  Gp +      d++a
  gi|121639370|ref|YP_979594.1| 224 YAVDVKNAVIVAAAGNTGGAAQcppqapgVTRDSVTVAVsPAWYDdYVLTVGSVNAQGEPSAFTLAGPWV------DVAA 297
                                    ***99*************555566666653344444443466666799********************87......7*** PP

                                    E-S-CCCCCCCCCHHHTTTHH....EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 220 pGgnivstwsrqsnnsaglss....yqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaq 295
                                     G++ v + s  +  + ++ +       +sGTS A+P+++g aAl++ ++p lt+++v + ++ tA     ++++++  +
  gi|121639370|ref|YP_979594.1| 298 TGEA-VTSLSPFGDGTVNRLGgqhgSIPISGTSYAAPVVSGLAALIRARFPTLTARQVMQRIESTA---HHPPAGWDPLV 373
                                    ***9.55555555444444445668999**************************************...88999999999 PP

                                    STT CS
                                    xxx RF
                   Peptidase_S8 296 GaG 298
                                    G+G
  gi|121639370|ref|YP_979594.1| 374 GNG 376
                                    988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3068.96
//
Query:       gi|121639371|ref|YP_979595.1|  [L=470]
Description: hypothetical protein BCG_3516c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.1e-154  514.7   7.9   2.4e-154  514.5   7.9    1.0  1  T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM
  ------ inclusion threshold ------
      0.065   13.4   4.0       0.13   12.4   1.6    2.5  2  DUF4232         Protein of unknown function (DUF4232)


Domain annotation for each model (and alignments):
>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.5   7.9  2.6e-158  2.4e-154       3     474 .]       5     468 ..       3     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 514.5 bits;  conditional E-value: 2.6e-158
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSSEEEETTT--E CS
                 T7SS_ESX1_EccB   3 lttrdqvsgyrFllrRlehAlvrrdvrmlddplrsqsrallvGvvlavvvlagaavlallkPqgkvgdskivadkesgal 82 
                                     tt+ +vsgyrFllrR+e+Al+  dv + +  lr+++++l++G+vla+v+++g+a +all+Pq+++g++ iv+++esgal
  gi|121639371|ref|YP_979595.1|   5 ATTWLHVSGYRFLLRRIECALLFGDVCAATGALRARTTSLALGCVLAIVAAMGCAFVALLRPQSALGQAPIVMGRESGAL 84 
                                    59****************************************************************************** PP

                                    EEEETTEEEEES-HHHHHHHCTS-B--EEE-HHHHHTS-B--EBS-TTS-S---B-SS.SSCEEEEEEEECSTTSS-EEE CS
                 T7SS_ESX1_EccB  83 YvvvdgtLhPvlNlaSArLilgkaakpttvkdseLdklprGplvGIpgAPealpqsadldeskWtvCDtvssaasasave 162
                                    Yv+vd+ +hPvlNlaSArLi+ ++a+p+ v++seL +++rGpl+GIpgAP+ l q+ + +es+W++CD+       +  +
  gi|121639371|ref|YP_979595.1|  85 YVRVDDVWHPVLNLASARLIAATNANPQPVSESELGHTKRGPLLGIPGAPQLLDQPLAGAESAWAICDSD------NGGS 158
                                    ********************************************************************95......6789 PP

                                    EEEEES----BTTEEE--TTEEEEEEE..TTEEEEEETTEEEEE-TTSHHHHHCCT--TS--EE--HHHHHHS-EEEESS CS
                 T7SS_ESX1_EccB 163 ttviagklalgaraaelaadqavLvsa..dgktyLvydgkraeidladravtrAlglegakprpvsagllnalpevpplk 240
                                    ttv++g +a++++a++l+a+q +Lv++  ++ tyL+y g+ra +dlad+av+ Al+l+g+ p+ v+++llna+pe+p+++
  gi|121639371|ref|YP_979595.1| 159 TTVVVG-PAEDSSAQVLTAEQMILVATesGSPTYLLYGGRRAVVDLADPAVVWALRLQGRVPHVVAQSLLNAVPEAPRIT 237
                                    ******.999***************9998999************************************************ PP

                                    ----TTTTSB-TTSS-TTSBTT-EEEEEET.TEEEEEEEETTEEEEE-HHHHHHHHHHT-TT-SS--EE-CCHCCCS-E- CS
                 T7SS_ESX1_EccB 241 aPaipgaGkpaglelggkarvGsvvkvsdadgeeeyYvvlsdglqrvtevvadllrnansqgltepptvepdvlaklpvv 320
                                    aP+i+g G+ a++ l+g+  vG vv++++a+ ++eyYvvl+dg+qr+ +v+adllr+ +sqg+ ++ptv+pdv++ +p+v
  gi|121639371|ref|YP_979595.1| 238 APRIRGGGR-ASVGLPGFL-VGGVVRITRAS-GDEYYVVLEDGVQRIGQVAADLLRFGDSQGSVNVPTVAPDVIRVAPIV 314
                                    ******999.9999***99.*********97.8*********************************************** PP

                                    ----...--SS--EEE-TT...TS-EEEEEEEE-STTSS-EEEEEEESS-SS-GCCGEEE-TTSSEE......EEESSBE CS
                 T7SS_ESX1_EccB 321 eelpvdayPekppkivdvk...eapvlCaswekgagdarakvallagaalPvpekaktvelvsadgsgatvdavylppgt 397
                                    ++lpv+a+P++pp+ vd +   + ++lC++w++++ + +a+va+lag+  Pvp ++ +v+l++adg+g+++davylppg+
  gi|121639371|ref|YP_979595.1| 315 NTLPVSAFPDRPPTPVDGSpgrAVTTLCVTWTPAQPG-AARVAFLAGSGPPVPLGGVPVTLAQADGRGPALDAVYLPPGR 393
                                    *****************988778899*****999655.9***************************************** PP

                                    ..EEEEEECSTT..CEEEEEEEETTSEEEEE-SHHHHHHCT--S.-EE--HHHHTTSEEEEEE-CCCCT-EESSXXX CS
                 T7SS_ESX1_EccB 398 galvqatgaepaseargslfyvsdtGvRYgipdeetakaLGlkeepepaPwsilkllpaGPtLsradAlvahDglpp 474
                                    +a+v a + +++   +g+ ++v+dtGvR+ i+d+++a+ LGl +++ paPw++l++lp+GP+Lsra+A+va+D+++p
  gi|121639371|ref|YP_979595.1| 394 SAYVAARSLSGG--GTGTRYLVTDTGVRFAIHDDDVAHDLGLPTAAIPAPWPVLATLPSGPELSRANASVARDTVAP 468
                                    **********99..8***********************************************************986 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.14   1.2e+03      83     109 ..     152     175 ..     136     203 .. 0.64
   2 ?   12.4   1.6   1.5e-05      0.13      37     101 ..     351     426 ..     348     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                        DUF4232  83 ggdgdgectaaglrvtppdgtksvtvp 109
                                    ++d +g    ++++v p+++ +++ ++
  gi|121639371|ref|YP_979595.1| 152 DSDNGGS---TTVVVGPAEDSSAQVLT 175
                                    4444433...44566677666666665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.5e-05
                        DUF4232  37 GyPgVslldadgqqvgaaaeregpaavp........vtLapGesAyaglrwtnaggdgdgecta.aglrvt.pp.d 101
                                    G + V++l ++g +v++  +    a+++        v L pG sAy++ r  + gg+g++  ++ +g+r +  + d
  gi|121639371|ref|YP_979595.1| 351 GAARVAFLAGSGPPVPLGGVPVTLAQADgrgpaldaVYLPPGRSAYVAARSLSGGGTGTRYLVTdTGVRFAiHDdD 426
                                    667788887778666654444333333334455666*************************999999999855533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3003.65
//
Query:       gi|121639372|ref|YP_979596.1|  [L=261]
Description: cutinase precursor cut3 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-56  189.2   0.0      7e-56  189.0   0.0    1.1  1  Cutinase  Cutinase


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.0   3.9e-60     7e-56       2     178 .]      44     226 ..      43     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 3.9e-60
                                    --SEEEEEE--TT--TTTSSHHHHHHHHHHHH.TTT-EEEEE------CGGSTTSS-HHHHHHHHHHHHHHHHH-TT-EE CS
                       Cutinase   2 ckdvevifArgttepgglgsvGeavvsalesavgsksvavqgvnYpAdleqlyegseeagakeaaalvqslaskCPdtki 81 
                                    c+d+ev+fArgt+ep+g+g+vG+a+v++l++++g ++++v++vnY A++ ql   +  +ga++a ++++s+as+CP+tk+
  gi|121639372|ref|YP_979596.1|  44 CPDAEVTFARGTGEPPGIGRVGQAFVDSLRQQTG-MEIGVYPVNYAASRLQL---HGGDGANDAISHIKSMASSCPNTKL 119
                                    **********************************.**************994...7789********************* PP

                                    EEEEETHHHHHHHHHHTT..........S-HHHHHHEEEEEEES-TTC..CCCTTS-TTS-GGGEEEE--TT-GGG..TS CS
                       Cutinase  82 vlgGYSqGaqvidnaiegga...tat..lpaavadkvaavvlfGdpsn..vaglpevsklyaskikslCdagDpiC..gs 152
                                    vlgGYSqGa+vid ++ ++    ++   lpaa+ad+vaav++fG+psn  +++l+++s+l++sk ++lC+++DpiC  g 
  gi|121639372|ref|YP_979596.1| 120 VLGGYSQGATVIDIVAGVPLgsiSFGspLPAAYADNVAAVAVFGNPSNraGGSLSSLSPLFGSKAIDLCNPTDPIChvGP 199
                                    *****************99987733356********************7788899*********************9999 PP

                                    ----GGGG.-GGGG.HHHHHHHHHHH- CS
                       Cutinase 153 gneleaHl.sYvseyttqaakFvvskl 178
                                    gne++ H+ +Y+ +yttqaa+Fvv++l
  gi|121639372|ref|YP_979596.1| 200 GNEFSGHIdGYIPTYTTQAASFVVQRL 226
                                    ********99**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1752.39
//
Query:       gi|121639373|ref|YP_979597.1|  [L=226]
Description: cutinase precursor cut4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-54  183.5   0.0      4e-54  183.3   0.0    1.1  1  Cutinase  Cutinase
     0.0042   16.7   0.0     0.0068   16.0   0.0    1.3  1  PE-PPE    PE-PPE domain
  ------ inclusion threshold ------
      0.062   13.2   0.0      0.077   12.9   0.0    1.2  1  VirJ      Bacterial virulence protein (VirJ)


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   6.7e-58     4e-54       2     177 ..      47     225 ..      46     226 .] 0.95

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 6.7e-58
                                    --SEEEEEE--TT--TTTSSHHHHHHHHHHHH.TTT-EEEEE------CGGSTTSS-HHHHHHHHHHHHHHHHH-TT-EE CS
                       Cutinase   2 ckdvevifArgttepgglgsvGeavvsalesavgsksvavqgvnYpAdleqlyegseeagakeaaalvqslaskCPdtki 81 
                                    c+d+ev+fArgt+ep+glg+vG+a+vs+l+++++ ks++ +gvnYpA+ +      +++ga++a+ ++q++as+C  t++
  gi|121639373|ref|YP_979597.1|  47 CPDAEVVFARGTGEPPGLGRVGQAFVSSLRQQTN-KSIGTYGVNYPANGDF---LAAADGANDASDHIQQMASACRATRL 122
                                    ********************************99.**************97...47899********************* PP

                                    EEEEETHHHHHHHHHHTT..........S-HHHHHHEEEEEEES-TTC..CCCTTS-TTS-GGGEEEE--TT-GGGTS-- CS
                       Cutinase  82 vlgGYSqGaqvidnaiegga...tat..lpaavadkvaavvlfGdpsn..vaglpevsklyaskikslCdagDpiCgsgn 154
                                    vlgGYSqGa+vid +++++    ++t  lp+a++d++aa++lfG+ps   ++ ++++++ ++sk+++lC++gDpiC +gn
  gi|121639373|ref|YP_979597.1| 123 VLGGYSQGAAVIDIVTAAPLpglGFTqpLPPAADDHIAAIALFGNPSGraGGLMSALTPQFGSKTINLCNNGDPICSDGN 202
                                    ******************9999966668******************985566789************************* PP

                                    --GGGG-GGGG.HHHHHHHHHHH CS
                       Cutinase 155 eleaHlsYvseyttqaakFvvsk 177
                                     + aHl+Yv   t+qaa Fv+s+
  gi|121639373|ref|YP_979597.1| 203 RWRAHLGYVPGMTNQAARFVASR 225
                                    ********************998 PP

>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-06    0.0068      30     102 ..     100     181 ..      84     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                         PE-PPE  30 aeGtenLeaairaela..agekvvvfGySqgalvasnekar......laalsepaapdql.sfvlvgnpnrpnggllarf 100
                                    a+G++   + i++  +   + ++v  GySqga+v++   a        ++   paa d++   +l+gnp+++ ggl++ +
  gi|121639373|ref|YP_979597.1| 100 ADGANDASDHIQQMASacRATRLVLGGYSQGAAVIDIVTAAplpglgFTQPLPPAADDHIaAIALFGNPSGRAGGLMSAL 179
                                    56666666667665543356669999*********998776222211233333444555525789************988 PP

                         PE-PPE 101 pg 102
                                     +
  gi|121639373|ref|YP_979597.1| 180 TP 181
                                    76 PP

>> VirJ  Bacterial virulence protein (VirJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.077      49      85 ..     101     137 ..      60     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                           VirJ  49 evaaDldrlikkyakrwkkkkvvliGysfGaDvlPaa 85 
                                    + a+D +  i++ a+  +++++vl Gys+Ga v+ ++
  gi|121639373|ref|YP_979597.1| 101 DGANDASDHIQQMASACRATRLVLGGYSQGAAVIDIV 137
                                    568999999**********************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1580.35
//
Query:       gi|121639374|ref|YP_979598.1|  [L=561]
Description: hypothetical protein BCG_3519 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3619.44
//
Query:       gi|121639375|ref|YP_979599.1|  [L=256]
Description: tRNA pseudouridine synthase A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-28   97.1   0.0    1.4e-23   83.4   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   1.5e-05      0.26      29      70 ..      10      47 ..       2      61 .. 0.78
   2 !   83.4   0.0     8e-28   1.4e-23       1     108 []     137     238 ..     137     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                PseudoU_synth_1 29 leaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgq 70
                                   l+aa++ + ++      v+++++g++d++V+a ++v+ ++v  
  gi|121639375|ref|YP_979599.1| 10 LDAALTTIFRT-----PVRLRAAGRTDAGVHASGQVAhVDVPA 47
                                   55666666666.....89******************9777754 PP

  == domain 2  score: 83.4 bits;  conditional E-value: 8e-28
                PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvke 80 
                                    A++ l G hdf++fc +++e+ +t+r + + +++    ++++l++++v++++F++++VR +vg+l+avg+ ++++ + +e
  gi|121639375|ref|YP_979599.1| 137 ASRDLMGLHDFAAFC-RHREGATTIRDLQRLDWS----RAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRE 211
                                    7889**********9.888999************....88999************************************* PP

                PseudoU_synth_1  81 llnakkrkkiavetapavglvlfhvrYd 108
                                    ll a+ r++  + +apa+gl+l +v+Y+
  gi|121639375|ref|YP_979599.1| 212 LLTATGRSS-DFAVAPAHGLTLIQVDYP 238
                                    *******99.*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1908.95
//
Query:       gi|121639376|ref|YP_979600.1|  [L=180]
Description: 50S ribosomal protein L17 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-35  122.3   0.1    1.2e-35  122.3   0.1    1.7  2  Ribosomal_L17  Ribosomal protein L17


Domain annotation for each model (and alignments):
>> Ribosomal_L17  Ribosomal protein L17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.1   6.8e-40   1.2e-35       2      94 .]      21     116 ..      20     116 .. 0.97
   2 ?   -1.3   0.4      0.24   4.4e+03      12      27 ..     128     143 ..     119     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 6.8e-40
                                    HHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHHH-SHHHHHHHHHHS-...HHHHHHHTHHHHTSS--S--EEEEEE CS
                  Ribosomal_L17   2 lrnlvtsLleherIetTlakAkelrklaeklitlakkgelaarrkalayla...lvkkLfeelapryadrngGYtRilkl 78 
                                    l nl+tsL+eh+rI+tT++kA++lr++aeklit akkg l++rr++l++l+   +v+ Lf e+ p +adr+gGYtRi+k+
  gi|121639376|ref|YP_979600.1|  21 LANLATSLFEHGRITTTEPKARALRPYAEKLITHAKKGALHNRREVLKKLRdkdVVHTLFAEIGPFFADRDGGYTRIIKI 100
                                    78************************************************66669************************* PP

                                    EE-TTTH-EEEEEEE- CS
                  Ribosomal_L17  79 gprrgDaaemailelV 94 
                                    + r+gD+a+ma++elV
  gi|121639376|ref|YP_979600.1| 101 EARKGDNAPMAVIELV 116
                                    ***************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                                    HSEEEEEHHHHHHHHH CS
                  Ribosomal_L17  12 herIetTlakAkelrk 27 
                                      r+   +akAk+++ 
  gi|121639376|ref|YP_979600.1| 128 ARRVAAAQAKAKKAAA 143
                                    4567777788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1228.00
//
Query:       gi|121639377|ref|YP_979601.1|  [L=347]
Description: DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-26   91.6   0.0    3.3e-26   90.8   0.0    1.4  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
    6.8e-26   90.9   0.0    1.5e-25   89.7   0.0    1.5  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    7.2e-21   73.4   0.0    1.3e-20   72.6   0.0    1.5  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.037   13.8   0.0        1.6    8.6   0.0    2.4  2  RNA_pol_L_2    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   7.3e-30   3.3e-26       5      66 ..     241     302 ..     237     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 7.3e-30
                                    XXXXXXX--BHHHHT--HHHHHHHHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHH CS
                  RNA_pol_A_CTD   5 eeelkklsisIeeLeLSvRslNcLkragiktvgeLvklseeeLlkikNlGkKSleEIkekLe 66 
                                     ++ ++++ +I++L+L+vRs+NcLkr+g++tvgeLv+++e++Ll i+N+G+KS++E+k kL+
  gi|121639377|ref|YP_979601.1| 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLH 302
                                    45788999****************************************************97 PP

>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   3.4e-29   1.5e-25       6     109 ..      57     149 ..      52     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 3.4e-29
                                    CTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEESSTTSEE CS
                  RNA_pol_A_bac   6 ntsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadveivnpdilI 85 
                                    ++       v+H+++++p+v+edv+ei+lnlk lv     +ee++ v+++L+++gpgevtagd++  +a v++ np+++I
  gi|121639377|ref|YP_979601.1|  57 DG-------VLHEFTTVPGVKEDVTEIILNLKSLVV---SSEEDEPVTMYLRKQGPGEVTAGDIVP-PAGVTVHNPGMHI 125
                                    44.......99***********************85...45555568*******************.************* PP

                                    EEEETT-EEEEEEEEEEESSEECT CS
                  RNA_pol_A_bac  86 akLrkgqeleleakvkkGiGkeha 109
                                    a+L+++ +le+e+ v++G+G+++a
  gi|121639377|ref|YP_979601.1| 126 ATLNDKGKLEVELVVERGRGYVPA 149
                                    **********************98 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   2.9e-24   1.3e-20       1      68 [.      24     218 ..      24     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 2.9e-24
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                      RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea.................................................. 30 
                                    e+l+ g+++tlgN+LRr+lls++pg+a+++                                                  
  gi|121639377|ref|YP_979601.1|  24 EPLEPGFGYTLGNSLRRTLLSSIPGAAVTSiridgvlhefttvpgvkedvteiilnlkslvvsseedepvtmylrkqgpg 103
                                    79******************************************************************999999999999 PP

                                    ..................................................................xxxxxx........ RF
                      RNA_pol_L  31 ..................................................................pvvkvn........ 36 
                                                                                                      pv kv+        
  gi|121639377|ref|YP_979601.1| 104 evtagdivppagvtvhnpgmhiatlndkgklevelvvergrgyvpavqnrasgaeigripvdsiysPVLKVTykvdatrv 183
                                    99999999999999999999998888888888888888888888888888888888888777777766555555666677 PP

                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  37 ...tdkdklilevetdgslkPeealkeAlkiLkek 68 
                                       td+dklil+vet+ s++P++al++A k L+e 
  gi|121639377|ref|YP_979601.1| 184 eqrTDFDKLILDVETKNSISPRDALASAGKTLVEL 218
                                    788****************************9986 PP

>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.028   1.2e+02      11      23 ..      32      44 ..      29      54 .. 0.87
   2 ?    8.6   0.0   0.00035       1.6      40      69 ..     190     219 ..     171     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.028
                                   HHHHHHHHHHHTT CS
                    RNA_pol_L_2 11 hTLgnlLrhlllk 23
                                    TLgn Lr  ll+
  gi|121639377|ref|YP_979601.1| 32 YTLGNSLRRTLLS 44
                                   6*******99986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00035
                                    SEEEEEEEESTSS-HHHHHHHHHHHHHHHH CS
                    RNA_pol_L_2  40 pkmnlriqtkssnnpleaLkkalkdlldic 69 
                                    +k+ l ++tk+s++p++aL  a k+l +++
  gi|121639377|ref|YP_979601.1| 190 DKLILDVETKNSISPRDALASAGKTLVELF 219
                                    6899*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2619.07
//
Query:       gi|121639378|ref|YP_979602.1|  [L=201]
Description: 30S ribosomal protein S4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-28   98.6   3.5    5.8e-28   97.6   3.2    1.6  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
    2.4e-16   59.2   0.3    4.3e-16   58.3   0.3    1.5  1  S4            S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   3.2   6.5e-32   5.8e-28       1      83 []       3      90 ..       3      90 .. 0.98
   2 ?   -2.3   0.0      0.99   8.9e+03      11      44 ..     106     141 ..     103     145 .. 0.60

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 6.5e-32
                                   TT-S-CHHHHCHCTS-STSSS.....S-S-SSTTTTS-----CHCHHHHHHHHHHHHHT-SHHHHHHHHHHHHHCCSHHHHH CS
                   Ribosomal_S4  1 rykgpkckllRrvgfklflkg.....reyppGqhgkrrkklseYgkqlrekqklkrrYgllekqfrryfkearrirGktgen 77
                                   ry+gp+++++Rr+ ++l++ +     r+yppGqhg++r k+seY  ql+ekqk++++Yg++ekqfrry++ea r +Gktge+
  gi|121639378|ref|YP_979602.1|  3 RYTGPVTRKSRRLRTDLVGGDqafekRPYPPGQHGRARIKESEYLLQLQEKQKARFTYGVMEKQFRRYYEEAVRQPGKTGEE 84
                                   8***************99888************************************************************* PP

                                   HHHHHH CS
                   Ribosomal_S4 78 LlqlLE 83
                                   Ll++LE
  gi|121639378|ref|YP_979602.1| 85 LLKILE 90
                                   *****9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.99
                                    CHCTS-STSSSS-S-SSTTTTS.-----CHCH.HHH CS
                   Ribosomal_S4  11 RrvgfklflkgreyppGqhgkr.rkklseYgk.qlr 44 
                                    Rr+  +l+ +g+ +  G h +  + + s+Y +   r
  gi|121639378|ref|YP_979602.1| 106 RRMARQLVSHGHFNVNGVHVNVpSYRVSQYDIvDVR 141
                                    555555555565556666665566777777765555 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.3   4.8e-20   4.3e-16       2      47 ..      92     137 ..      91     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 4.8e-20
                                    EHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                             S4   2 RLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                    RLd+v++r+gla +rr Arql++hG++ VNG  v+ psyrV+  D+
  gi|121639378|ref|YP_979602.1|  92 RLDNVIYRAGLARTRRMARQLVSHGHFNVNGVHVNVPSYRVSQYDI 137
                                    9****************************************87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1465.36
//
Query:       gi|121639379|ref|YP_979603.1|  [L=139]
Description: 30S ribosomal protein S11 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-48  162.4   1.3    5.1e-48  162.0   1.3    1.1  1  Ribosomal_S11   Ribosomal protein S11
     0.0059   16.4   0.1       0.16   11.6   0.0    2.0  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
  ------ inclusion threshold ------
      0.012   16.0   0.2      0.015   15.7   0.2    1.3  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   1.3   8.6e-52   5.1e-48       1     110 []      29     138 ..      29     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 8.6e-52
                  Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasrkssPyaaqlaaekaaekvldkGikavevkvkgpGpGreaalr 80 
                                    G ahi+++fnnti+titd +G++++++s+G +g+k+srks+P+aaqlaae+aa+k+ d+G+++v+v vkgpG+Gre+a+r
  gi|121639379|ref|YP_979603.1|  29 GAAHIKSTFNNTIVTITDPQGNVIAWASSGHVGFKGSRKSTPFAAQLAAENAARKAQDHGVRKVDVFVKGPGSGRETAIR 108
                                    88****************************************************************************** PP

                  Ribosomal_S11  81 alaraGlkigriedvtPiPhdgirrpkkrr 110
                                    +l++aGl++g+i dvtP Ph+g+r+p++rr
  gi|121639379|ref|YP_979603.1| 109 SLQAAGLEVGAISDVTPQPHNGVRPPNRRR 138
                                    ****************************98 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.014        84      42      69 ..      25      52 ..      25      58 .. 0.84
   2 !   11.6   0.0   2.7e-05      0.16       3      64 ..      62     123 ..      61     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHCT-EEEEEEESSEEEE CS
                  ELFV_dehydrog 42 nvgsyaallltelgakvvavsDssGviy 69
                                   nv + aa + ++ ++++v++ D +G ++
  gi|121639379|ref|YP_979603.1| 25 NVPHGAAHIKSTFNNTIVTITDPQGNVI 52
                                   5666778888899************997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.7e-05
                                    -TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEES CS
                  ELFV_dehydrog   3 sldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDs 64 
                                     ++  ++T + +  ++e++++k++ + +++  v + G+G     a++ l+ +g +v a+sD 
  gi|121639379|ref|YP_979603.1|  62 FKGSRKSTPFAAQLAAENAARKAQDHGVRKVDVFVKGPGSGRETAIRSLQAAGLEVGAISDV 123
                                    567788899999999*******9999***********************************7 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.2   2.5e-06     0.015      35      91 ..      38      95 ..       9     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-06
                                   -EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHHCHHCHTC-.EE CS
                 Ribosomal_L18p 35 hiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAerakekgiekv.vf 91
                                   +  +  i d +g+++a as+ +  +k++ +++  aa+  +e+ A++a++ g++kv vf
  gi|121639379|ref|YP_979603.1| 38 NNTIVTITDPQGNVIAWASSGHVGFKGSRKSTPFAAQLAAENAARKAQDHGVRKVdVF 95
                                   33444577889***************9999999999999**************99566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 958.54
//
Query:       gi|121639380|ref|YP_979604.1|  [L=124]
Description: 30S ribosomal protein S13 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-37  127.6   5.8    1.5e-35  122.4   5.8    2.0  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.035   12.9   0.0      0.038   12.7   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   5.8   1.7e-39   1.5e-35       1     128 []       3     109 ..       3     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 1.7e-39
                  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdikdGk 80 
                                    R++g+d++++k++e+alt+i GiGr+++++il+++++d+d r+++ltee++ ++++++e                     
  gi|121639380|ref|YP_979604.1|   3 RLVGVDLPRDKRMEVALTYIFGIGRTRSNEILAATGIDRDLRTRDLTEEQLIHLRDYIEA-------------------- 62 
                                    89*********************************************************9.................... PP

                  Ribosomal_S13  81 dshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                     + +ve+dlrr++++di+R+++i++y+GlRH+rG++vRGQrTkt++Rt
  gi|121639380|ref|YP_979604.1|  63 -NLKVEGDLRREVQADIRRKIEIGCYQGLRHRRGMPVRGQRTKTNART 109
                                    .799*******************************************8 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-06     0.038     186     239 ..      12      64 ..       5      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-06
                                    .XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHH CS
                           FbpA 186 ekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqell 239
                                    +k+++ aL   f G++++ ++e+l+ +g+d++ ++++l+ee+l +l++ ++  l
  gi|121639380|ref|YP_979604.1|  12 DKRMEVALTYIF-GIGRTRSNEILAATGIDRDLRTRDLTEEQLIHLRDYIEANL 64 
                                    566777888888.*******************************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 936.67
//
Query:       gi|121639381|ref|YP_979605.1|  [L=37]
Description: 50S ribosomal protein L36 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-18   65.7   6.4    3.4e-18   65.6   6.4    1.0  1  Ribosomal_L36  Ribosomal protein L36


Domain annotation for each model (and alignments):
>> Ribosomal_L36  Ribosomal protein L36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   6.4   1.9e-22   3.4e-18       1      38 []       1      37 []       1      37 [] 0.99

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.9e-22
                  Ribosomal_L36  1 MKVrssvkkmcegCkvvrRkgrvyviCkknPrhKqRQG 38
                                   MKV  svk +c++C+++rR+grv+viC ++PrhKqRQG
  gi|121639381|ref|YP_979605.1|  1 MKVNPSVKPICDKCRLIRRHGRVMVIC-SDPRHKQRQG 37
                                   ***************************.*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 286.59
//
Query:       gi|121639382|ref|YP_979606.1|  [L=73]
Description: translation initiation factor IF-1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-28   98.9   0.1    1.1e-28   98.8   0.1    1.0  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.1   6.3e-33   1.1e-28       1      64 []       8      71 ..       8      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 6.3e-33
                                   EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHH.CT----TT-EEEEEE-TT-TTEEEEES- CS
                         eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfR.nkiwikrGdyVlVelspydltkGrIvyr 64
                                   +ev+g+V+e l+n++fr+el +ng++vla+i+gk+R ++i+i++ d+V+Velspydl++GrIvyr
  gi|121639382|ref|YP_979606.1|  8 IEVEGRVVEPLPNAMFRIEL-ENGHKVLAHISGKMRqHYIRILPEDRVVVELSPYDLSRGRIVYR 71
                                   69******************.59*****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 555.12
//
Query:       gi|121639383|ref|YP_979607.1|  [L=285]
Description: hypothetical protein BCG_3528 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-15   56.8   3.6    4.1e-12   46.2   0.1    2.6  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   2.3e-16   4.1e-12      27     133 ..      28     123 ..      14     128 .. 0.93
   2 !   10.6   0.6   1.5e-05      0.27     170     313 ..     136     258 ..     130     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.3e-16
                 Bac_luciferase  27 elaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglg 106
                                    ++a ++E+lG+ avwv+ +       + a+++   +++aT+++ + t+++++++    ++A+++  ++  ++GRf lg+g
  gi|121639383|ref|YP_979607.1|  28 QQATEIEALGYGAVWVGGSP------PAALSWVEPILQATTTLCVATGIVNIWSAPAQRVAESFHRIEAAYPGRFLLGIG 101
                                    899***************99......99*************************555569********************* PP

                 Bac_luciferase 107 tggpaveerrfGvdhderyarlrEfve 133
                                     g+++ +      +++++y+ l E+++
  gi|121639383|ref|YP_979607.1| 102 VGHAEMI-----SEYRKPYNALVEYLD 123
                                    ******9.....488999999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.5e-05
                 Bac_luciferase 170 yvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagld 249
                                    +vaa +p+ l l ar+  g ++ + +pe+ a++ e +            ++ +++   v+++ +++ Ar   r+ +    
  gi|121639383|ref|YP_979607.1| 136 VVAALGPRVLGLSARRSAGAHPYLTTPEHTARARELIGP----------SAFLAPEHKVVLTTDSARARTVGRQAL---- 201
                                    689*********************999999999998884..........455567888999988888887776666.... PP

                 Bac_luciferase 250 fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                            + +  ++ ++  +  +   +++ +  +d+lv+a ++ Gtp+ +a+rl +   ag+d
  gi|121639383|ref|YP_979607.1| 202 -------DMYFNLANYRNNWKRLGFTDDEVSRPGSDRLVDAVVAYGTPDAIAARLNEHLLAGAD 258
                                    .......222343444444445555555555555778889999************997667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2121.54
//
Query:       gi|121639384|ref|YP_979608.1|  [L=331]
Description: dTDP-glucose 4,6-dehydratase rmlB1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-75  254.2   0.0    2.8e-75  253.8   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.9e-62  209.5   0.1    6.2e-62  209.2   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.1e-19   68.4   0.0    6.4e-19   68.0   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.9e-18   66.5   0.0      3e-18   65.9   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    9.8e-15   54.4   0.0      2e-13   50.1   0.0    2.1  1  NAD_binding_4    Male sterility protein
    1.6e-12   47.2   0.0      3e-12   46.3   0.0    1.4  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.1e-08   35.2   0.2    1.7e-08   34.6   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
    3.2e-05   23.5   0.9      0.083   12.3   0.2    2.4  2  adh_short        short chain dehydrogenase
     0.0021   18.3   0.2     0.0074   16.5   0.2    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.016   15.1   2.2      0.023   14.5   0.4    2.3  2  VbhA             Antitoxin VbhA
      0.019   14.9   0.0      0.037   13.9   0.0    1.4  1  KR               KR domain
      0.028   14.0   0.3       0.06   12.9   0.2    1.6  2  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.8   0.0   1.9e-78   2.8e-75       1     331 [.       4     303 ..       4     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 253.8 bits;  conditional E-value: 1.9e-78
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGfiG ++++  ++++ +  ++  +++++++gr e+la+     +e+ ++l++gD+tD++ + +l+ae   d+v+
  gi|121639384|ref|YP_979608.1|   4 LVTGGAGFIGTNFVHSAVREHPDDAVT-VLDALTYAGRRESLAD-----VEDAIRLVQGDITDAELVSQLVAES--DAVV 75 
                                    9*******************9988665.688999********96.....45789*******************9..9*** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S...SSSB-TTS-----SHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq...evpqtEttpfyPrsPYaaaK 157
                                    ++AA+shVd+ +++Pe ++ +nv+Gt+++Lea+r++g    vr++++St+EvYG+++   ++ +tE+tp++P sPY+a+K
  gi|121639384|ref|YP_979608.1|  76 HFAAESHVDNALDNPEPFLHTNVIGTFTILEAVRRHG----VRLHHISTDEVYGDLElddRARFTESTPYNPSSPYSATK 151
                                    ***********************************98....59*************7655778***************** PP

                                    HHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHH CS
                  GDP_Man_Dehyd 158 lyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlml 237
                                    + ad++v+++ ++yg+ a++++++n+++p++    v++ i+r++++++ g++++l +G + ++Rdw hv+D+ +a++++l
  gi|121639384|ref|YP_979608.1| 152 AGADMLVRAWVRSYGVRATISNCSNNYGPYQ---HVEKFIPRQITNVLTGRRPKL-YGAGANVRDWIHVDDHNSAVRRIL 227
                                    ******************************6...799*****************9.8*********************** PP

                                    HCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH CS
                  GDP_Man_Dehyd 238 qqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeL 317
                                     +++        g+t+ + +  e+ +l + +t+   ++            ++   +d +++r g++ ++++d+s +  eL
  gi|121639384|ref|YP_979608.1| 228 DRGR-------IGRTYLISSEGERDNLTVLRTLLRLMD------------RDPDDFDHVTDRVGHDLRYAIDPSTLYDEL 288
                                    ***9.......799999999999999999998765432............2334688999******************** PP

                                    ----S.S-HHHHHHH CS
                  GDP_Man_Dehyd 318 gWkpk.vsfeelvre 331
                                     W pk ++fee++r 
  gi|121639384|ref|YP_979608.1| 289 CWAPKhTDFEEGLRT 303
                                    ****9789****986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.2   0.1   4.1e-65   6.2e-62       2     240 ..       4     238 ..       3     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 4.1e-65
                                    EEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                      Epimerase   2 lVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavg 75 
                                    lVtG++GfiG+++v+   +++  + v++ld l++a+++++l+d+    +lv++d+td++ + +l++  + dav+h+Aa++
  gi|121639384|ref|YP_979608.1|   4 LVTGGAGFIGTNFVHSAVREHpDDaVTVLDALTYAGRRESLADVedaiRLVQGDITDAELVSQLVA--ESDAVVHFAAES 81 
                                    9**************9999996557*****************************************..79********** PP

                                    -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                      Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                    +v++  ++p+ f+++n++gt ++lea+r++gv rl+++s++evYG+ +   +   t+++p++p+spY+a+K+ ++ lv+a
  gi|121639384|ref|YP_979608.1|  82 HVDNALDNPEPFLHTNVIGTFTILEAVRRHGV-RLHHISTDEVYGDLELDDRARFTESTPYNPSSPYSATKAGADMLVRA 160
                                    ********************************.************99997799999999********************* PP

                                    HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STT CS
                      Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkg 235
                                    + ++yg++a+i +++n+yGp+   ++v+++ip+ i+++l+g+   +l+g g ++Rd+++v+D+  a+ ++l++   g+ g
  gi|121639384|ref|YP_979608.1| 161 WVRSYGVRATISNCSNNYGPY---QHVEKFIPRQITNVLTGR-RPKLYGAGANVRDWIHVDDHNSAVRRILDR---GRIG 233
                                    *********************...99****************.*****************************9...7778 PP

                                    EEEEE CS
                      Epimerase 236 eiyni 240
                                    ++y i
  gi|121639384|ref|YP_979608.1| 234 RTYLI 238
                                    88866 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   4.3e-22   6.4e-19       1     159 [.       4     160 ..       4     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.3e-22
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegvdvvihlaslvdv 79 
                                    +vtGgaGF+G + v++ vr+++   v vlD  +    +e+l  v+ +  +++gD+td++ +++ + ++d+v+h a+ + v
  gi|121639384|ref|YP_979608.1|   4 LVTGGAGFIGTNFVHSAVREHPDDAVTVLDALTYAGRRESLADVEDAIrLVQGDITDAELVSQLVAESDAVVHFAAESHV 83 
                                    69****************************9999999999999987666******************************* PP

                      3Beta_HSD  80 ag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                     +  ++ + + + nv GT ++lea +++gvr l + S+ ev g+  + ++  +  E+++y+  ++++y+ +Ka a+ lv 
  gi|121639384|ref|YP_979608.1|  84 DNaLDNPEPFLHTNVIGTFTILEAVRRHGVR-LHHISTDEVYGD-LELDDRARFTESTPYN--PSSPYSATKAGADMLVR 159
                                    996678899*********************8.6799********.5555555588888885..789*********99986 PP

                      3Beta_HSD 159 k 159
                                    +
  gi|121639384|ref|YP_979608.1| 160 A 160
                                    4 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0     2e-21     3e-18       1     143 [.       1     169 [.       1     193 [. 0.85

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2e-21
                                    EEEEEESTTSHHHHHHHHHCTTTSEE..EEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeegle..vlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                    m++lvtG+ G +G++ ++++ +e+ +  v+ l+ +                    + d+tdae v +l++e   d+vv+ 
  gi|121639384|ref|YP_979608.1|   1 MRLLVTGGAGFIGTNFVHSAVREHPDdaVTVLD-AltyagrresladvedairlvQGDITDAELVSQLVAE--SDAVVHF 77 
                                    89****************998866431144333.24788999***************************99..899**** PP

                                    -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-...TTS-B-TTS----SSHHHHHHHHHHHH CS
                  RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe...kkrpYeeddetsPlnvYGrtKlaGEqa 135
                                    AA   vD+a +++e   + n+ ++ ++ ea +++g+ L h+StD V+          ++e+ + +P + Y +tK+     
  gi|121639384|ref|YP_979608.1|  78 AAESHVDNALDNPEPFLHTNVIGTFTILEAVRRHGVRLHHISTDEVYGDLeldDRARFTESTPYNPSSPYSATKAGADML 157
                                    **********************************************96546745566******************99998 PP

                                    HHH....H-SSE CS
                  RmlD_sub_bind 136 vla....agkka 143
                                    v+a    +g +a
  gi|121639384|ref|YP_979608.1| 158 VRAwvrsYGVRA 169
                                    887333244444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.3e-16     2e-13       1     204 [.       5     175 ..       5     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.3e-16
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG+ GF+G+ +++  +r++p+          +  ++++ l+ + ++ +l ++     ++ i+ v+GD+++ +       
  gi|121639384|ref|YP_979608.1|   5 VTGGAGFIGTNFVHSAVREHPD----------DAVTVLDALTYAGRRESLADV-----EDAIRLVQGDITDAE------L 63 
                                    7******************996..........555555666666666666555.....589*********876......5 PP

                                    HHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    + +l++e d+++h aA  ++d+ +++   +l +Nv Gt  +le  ++      l+h+ST  v+g+ e             
  gi|121639384|ref|YP_979608.1|  64 VSQLVAESDAVVHFAAESHVDNALDNpepFLHTNVIGTFTILEAVRRH-GV-RLHHISTDEVYGDLELD----------- 130
                                    89********************999988899************88844.44.7******8888887732........... PP

                                    ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE- CS
                  NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRps 204
                                           ++++  + +  Y+ +Ka a++lvr++ r+ g++++i  +s
  gi|121639384|ref|YP_979608.1| 131 --DRARFTESTPYNPSSPYSATKAGADMLVRAWVRSYGVRATISNCS 175
                                    ..2577889999999**************************998877 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0     2e-15     3e-12       1     130 [.       3     122 ..       3     127 .. 0.84
   2 ?   -4.0   0.0       4.1   6.1e+03     133     152 ..     142     161 ..     141     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2e-15
                                    EEEETTTSHHHHHHHHHHHHHB-SE.EEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkk.iillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                    +lvtG++G iG ++v+  ++++p   + +l+      y+ ++e  +++++      i  v gd++d+e +++++   + d
  gi|121639384|ref|YP_979608.1|   3 LLVTGGAGFIGTNFVHSAVREHPDDaVTVLDAL---TYAGRRESLADVED-----AIRLVQGDITDAELVSQLVA--ESD 72 
                                    59*******************997615566554...45555555445554.....344568**************..9** PP

                                    EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGG CS
                Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDK 130
                                    +v+h AA  hV  +  np   ++tNv+gt +++ea  ++gv+ +  iStD 
  gi|121639384|ref|YP_979608.1|  73 AVVHFAAESHVDNALDNPEPFLHTNVIGTFTILEAVRRHGVR-LHHISTDE 122
                                    ****************************************96.67899995 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.1
                                    S--SHHHHHHHHHHHHHHHG CS
                Polysacc_synt_2 133 nPtnvmGatKrlaekllqal 152
                                    nP + + atK+ a++l+ a 
  gi|121639384|ref|YP_979608.1| 142 NPSSPYSATKAGADMLVRAW 161
                                    78889999999999999876 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.2   1.1e-11   1.7e-08       1     133 [.       7     160 ..       7     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-11
                                    TTTSHHHHHHHHHHHHC-.T-EEEEE.....ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCH CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtal.....vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkd 74 
                                    G+ G +G   v+ +++++ + +vt+l     + + e+la++e  +++++v+gd+td+e + + ++  daVv  ++ ++ d
  gi|121639384|ref|YP_979608.1|   7 GGAGFIGTNFVHSAVREHpDDAVTVLdaltyAGRRESLADVE--DAIRLVQGDITDAELVSQLVAESDAVVHFAAESHVD 84 
                                    999***************987888754322234577777786..79**********************998777766665 PP

                                    HHH.............HHHHHHHHHHCT--EEEEEEETTTTS.....GCGCHHHHHHHHCCHHHHHHHHHHHHHHHH CS
                 NAD_binding_10  75 eeg.............aknivdaakeagvkRfvlvsaigvgd.....evpgefgewnkellkaylaakraaeellra 133
                                    +               + +i++a++++gv R+  +s+  v+      + ++ ++++ ++  ++y a k+ a+ l+ra
  gi|121639384|ref|YP_979608.1|  85 NALdnpepflhtnvigTFTILEAVRRHGV-RLHHISTDEVYGdleldDRARFTESTPYNPSSPYSATKAGADMLVRA 160
                                    5555666788888899*************.99999999998522111222222333334557777888888888876 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   5.5e-05     0.083       4      71 ..       4      71 ..       2     114 .. 0.84
   2 !    9.3   0.0   0.00047      0.71     142     168 ..     140     166 ..     136     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                   EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                      adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                   lvtG+++ IG ++++  ++e  + +v+   + + +   ++l + ++ +  +q+D+td+e v++lv++ 
  gi|121639384|ref|YP_979608.1|  4 LVTGGAGFIGTNFVHSAVREHPDDAVTVLDALTYAGRRESLADVEDAIRLVQGDITDAELVSQLVAES 71
                                   8*******************988888777777788888888888999******************986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00047
                                    B-TTBHHHHHHHHHHHHHHHHHHHHHG CS
                      adh_short 142 pvagvaaYsAsKaavagltrslakela 168
                                    p++  ++YsA+Ka+ ++l+r++ + + 
  gi|121639384|ref|YP_979608.1| 140 PYNPSSPYSATKAGADMLVRAWVRSYG 166
                                    6777899*************9987765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2     5e-06    0.0074       5      77 ..       8      78 ..       3      87 .. 0.88
   2 ?   -1.5   0.0       1.9   2.8e+03      84      99 ..     103     118 ..      98     174 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-06
                                   --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                   GaG++G  +++  +r+++ d  +tv d      +++  +  +  +  ++ d+ + e  +++l++e d+vv+ +
  gi|121639384|ref|YP_979608.1|  8 GAGFIGTNFVHSAVREHPDD-AVTVLDALTYAGRRESLADVEDAIRLVQGDITDAEL-VSQLVAESDAVVHFA 78
                                   67***************986.9***99988888888877799999999******998.************987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                    HHHHHHHHHT-EEEES CS
                Sacchrp_dh_NADP  84 dvlkaCietgvhyvdt 99 
                                    ++l+a +++gv+   +
  gi|121639384|ref|YP_979608.1| 103 TILEAVRRHGVRLHHI 118
                                    4444444444443322 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   1.6e-05     0.023      22      44 ..      45      67 ..      39      69 .. 0.88
   2 ?   -2.1   0.1       2.4   3.6e+03      15      39 ..     299     323 ..     299     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                           VbhA 22 etvadleayvrGeIdadElvrrv 44
                                   ++v+d+ ++v G+I+ +Elv ++
  gi|121639384|ref|YP_979608.1| 45 ADVEDAIRLVQGDITDAELVSQL 67
                                   89******************886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                           VbhA  15 EGlepsaetvadleayvrGeIdadE 39 
                                    EGl+ + ++ +d+e + r   da+E
  gi|121639384|ref|YP_979608.1| 299 EGLRTTIDWYRDNESWWRPLKDATE 323
                                    8999999999999999775555555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.037       4      77 ..       4      73 ..       2      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                   EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77
                                   l+tGG+G +G+ +++  ++++    + +l     + +      ++l++ +  +++v+ D++d++ v++l++e +a
  gi|121639384|ref|YP_979608.1|  4 LVTGGAGFIGTNFVHSAVREHpDDAVTVLDAL--TYAGR---RESLADVEDAIRLVQGDITDAELVSQLVAESDA 73
                                   9***************9998845555555544..33333...3567777779*****************999873 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2     4e-05      0.06       2      73 ..       4      79 ..       3     114 .. 0.82
   2 ?   -2.3   0.0       1.7   2.5e+03     124     141 ..     157     174 ..     136     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                   EESSTTSHHHHHHHHHHHH.....HT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                           NmrA  2 lviGaTGrqGksvvrallk.....aghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                   lv+G++G +G  +v+ +++     a     al+   ++e ++ +++a   lv+gd+ d e++++++ ++d+v    +
  gi|121639384|ref|YP_979608.1|  4 LVTGGAGFIGTNFVHSAVRehpddAVTVLDALTYAGRRESLADVEDA-IRLVQGDITDAELVSQLVAESDAVVHFAA 79
                                   8*************999995543222223455655588888888775.99********************9976655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                    HHHHHHHHCTS-EEEEEE CS
                           NmrA 124 eieeyvralgipytfvya 141
                                     ++  vr+ g+++t+  +
  gi|121639384|ref|YP_979608.1| 157 LVRAWVRSYGVRATISNC 174
                                    588888888999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2600.70
//
Query:       gi|121639385|ref|YP_979609.1|  [L=202]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase rmlC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-61  207.2   0.0    1.5e-61  207.0   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.017   14.8   0.0    1.2  1  FdtA             WxcM-like, C-terminal


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   0.0   1.7e-65   1.5e-61       2     169 .]       6     179 ..       5     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 1.7e-65
                                    -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHH.TS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEE CS
                dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaea.gleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldva 80 
                                    ++++g+++i+p+++ D+RG+f+e+ +++ f++  g + ++ q n+svs++gvlRGlHf++ p++qak+v++v+G+v+dv+
  gi|121639385|ref|YP_979609.1|   6 LDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFaGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVV 85 
                                    689****************************76589999***************************************** PP

                                    EE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---.....SS. CS
                dTDP_sugar_isom  81 VDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw.....eel 155
                                    VD+R+gSptfg+w +v L+++++r++y++eg+ahGfl+l+d+++v+Y++++ y+p++e++i  +Dp+l++dw      ++
  gi|121639385|ref|YP_979609.1|  86 VDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWplvdgAAP 165
                                    **************************************************99*************************889 PP

                                    B--HHHHT-B-HHH CS
                dTDP_sugar_isom 156 ilSekDkaapslae 169
                                     lS++D+aaps+++
  gi|121639385|ref|YP_979609.1| 166 SLSDRDAAAPSFED 179
                                    **********9975 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.9e-06     0.017      44     117 ..      57     141 ..      46     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-06
                                    TEEEEEEES...S--EEEEEEES-E.EEEEE..-SS-E....EEEEE-STT.EEEEE-TT-EEEEE---TT-EEEEEESS CS
                           FdtA  44 eerGeHahk...kleqllialsGsv.evlld..dgkkk....keilldsps.kglyipkmiWrelinfsedavllvlase 112
                                    + rG H  +   ++ + + ++sGsv +v++d  +g+       ++lld+++   +y+ +++ +    ++ ++ ++ l+s 
  gi|121639385|ref|YP_979609.1|  57 VLRGLHFAQlppSQAKYVTCVSGSVfDVVVDirEGSPTfgrwDSVLLDDQDrRTIYVSEGLAHGFLALQDNSTVMYLCSA 136
                                    5566665543335678899****963666662244432333478999988879*************************** PP

                                    ---GG CS
                           FdtA 113 sydee 117
                                    +y+++
  gi|121639385|ref|YP_979609.1| 137 EYNPQ 141
                                    **985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1463.89
//
Query:       gi|121639386|ref|YP_979610.1|  [L=222]
Description: hypothetical protein BCG_3531 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-19   70.4   2.5    2.1e-19   70.2   2.5    1.2  1  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   2.5   1.1e-23   2.1e-19       3      98 ..      38     143 ..      36     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.1e-23
                         DUF222   3 aaleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlAralrer...........Lpa 71 
                                    + le+le + rrl+av+++l+++l+ ++s+ee g++ ++ ++a+rlri+  +A+ r++ A++l++r           L+a
  gi|121639386|ref|YP_979610.1|  38 RSLERLECLVRRLPAVGHTLINQLDTQASEEELGGT-LCCALANRLRITKPDAALRIADAADLGPRraltgeplapqLTA 116
                                    6799********************************.******************************************* PP

                         DUF222  72 vaaalraGdidlrqvrvIaartdllpd 98 
                                    +a+a+r+G i++ +++vI+a ++   +
  gi|121639386|ref|YP_979610.1| 117 TATAQRQGLIGEAHIKVIRALFRPPAR 143
                                    *******************99886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1860.53
//
Query:       gi|121639387|ref|YP_979611.1|  [L=317]
Description: hypothetical protein BCG_3532 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-64  217.2   3.4    4.3e-64  216.9   3.4    1.1  1  DUF222    Domain of unknown function (DUF222)
  ------ inclusion threshold ------
      0.042   14.0   0.1      0.042   14.0   0.1    2.2  3  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   3.4   4.8e-68   4.3e-64     103     301 .]       2     223 ..       1     223 [. 0.97

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 4.8e-68
                         DUF222 103 atvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltk.dedGmsrisgeldaeaaaaldavLd 181
                                    +t+++aea+l+++aa+++p+eLa+ ++r++++l+pDg+ +d+e+ar+r++tl++ + dGmsr+sg+l+++a+a+++avL+
  gi|121639387|ref|YP_979611.1|   2 STRQAAEADLAGKAAQYRPDELARYAQRVMDWLHPDGDLTDTERARKRGITLSNqQYDGMSRLSGYLTPQARATFEAVLA 81 
                                    799***************************************************9************************* PP

                         DUF222 182 slaap.vcap..............dgtkDpRspaqrraDALlallrlalaagaldchagvpatvvvhvtaeeltaaagga 246
                                    +laap   +p              ++++D+Rs+aqr++D+Lla+lr+++a+g+l++h+g+p+++vv++t+++l++ ag+ 
  gi|121639387|ref|YP_979611.1|  82 KLAAPgATNPddhtpvidttpdaaAIDRDTRSQAQRNHDGLLAGLRALIASGELGQHNGLPVSIVVTTTLTDLQTGAGK- 160
                                    *****88888*********************************************************************. PP

                         DUF222 247 altgggglLpasdvrrLAkdAt..........laifdepagrpldlgrtkrtasaalrralraRD 301
                                    + tggg+lLp++dv+r+ ++A+           aifd+  g+pl+l++tkr+as+a+r++l a D
  gi|121639387|ref|YP_979611.1| 161 GFTGGGTLLPMADVIRMTSHAHhyspasgrypQAIFDH--GTPLALYHTKRLASPAQRIMLFAND 223
                                    **************************999986668888..*********************9877 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.61   5.5e+03      14      23 ..     179     188 ..     173     203 .. 0.65
   2 ?   14.0   0.1   4.7e-06     0.042       4      42 ..     226     266 ..     224     271 .. 0.85
   3 ?   -3.8   0.8       1.7   1.5e+04      13      18 ..     297     302 ..     289     314 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.61
                            HNH  14 levdHiipis 23 
                                    ++ +H  p s
  gi|121639387|ref|YP_979611.1| 179 SHAHHYSPAS 188
                                    5667765544 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.7e-06
                            HNH   4 Cgrkfhks..ealevdHiipisqggaddieNlqllCksCHn 42 
                                    C +++ +   + ++ +H+  +   g++di  l+l+C   ++
  gi|121639387|ref|YP_979611.1| 226 CTKPGCDApaYHSQAHHVTGWTSTGRTDITELTLACDPDNR 266
                                    6666666666889***********************98887 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.7
                            HNH  13 alevdH 18 
                                     ++ +H
  gi|121639387|ref|YP_979611.1| 297 TNTFHH 302
                                    466677 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2680.20
//
Query:       gi|121639388|ref|YP_979612.1|  [L=364]
Description: dTDP-glucose 4,6-dehydratase rmlB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-27   95.9   0.0    4.6e-27   95.0   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-16   61.2   0.0    9.8e-14   51.5   0.0    3.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.9e-16   58.5   0.0    8.5e-16   57.8   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-15   56.5   1.0    3.2e-11   42.9   0.2    3.0  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.6e-14   53.0   0.0    3.7e-14   52.5   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-10   40.6   0.0    1.5e-08   34.1   0.0    2.2  2  NAD_binding_4    Male sterility protein
    2.1e-10   40.8   0.1    3.4e-10   40.1   0.1    1.4  1  NAD_binding_10   NAD(P)H-binding
     0.0086   16.0   1.1       0.11   12.3   0.1    2.3  2  KR               KR domain
  ------ inclusion threshold ------
      0.019   14.5   0.3       0.15   11.6   0.3    1.9  1  NmrA             NmrA-like family
      0.029   14.2   0.3      0.049   13.4   0.3    1.3  1  DFP              DNA / pantothenate metabolism flavoprotein
      0.033   13.6   0.0      0.059   12.8   0.0    1.4  1  adh_short        short chain dehydrogenase
       0.27    9.8   0.1       0.55    8.8   0.1    1.4  1  UPF0236          Uncharacterised protein family (UPF0236)


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.0   3.1e-30   4.6e-27       2     176 ..      39     207 ..      38     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 3.1e-30
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                    lVtG +G +G alv+ l ++g +v+ ld+++s+         + + + + dr+ l+++++  ++++v+h+Aa   ++  +
  gi|121639388|ref|YP_979612.1|  39 LVTGSSGHLGEALVRTLRARGADVVSLDSRPSRY--------TNIVGCVSDRALLRDVMA--GVEVVFHAAAHHKPQLAF 108
                                    8*****************************6655........45789*************..9***************** PP

                                    HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS....SS....BSTCSTTS----SSHHHHHHHHHHHHH CS
                      Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae....qp....keettltgplkpnspYaaaKlageklv 153
                                      +++f+++n++gt+++l+aa +a+v+ ++  sS++v+G+  +    qp    +e++t   p+ p + Y+++K+ +e l+
  gi|121639388|ref|YP_979612.1| 109 LPRQAFLDTNIIGTQTVLDAAVAANVRAFVMTSSTTVFGDALTppadQPaawiDESVT---PI-PKNIYGVTKASSEDLC 184
                                    ***************************************7665444466888666666...77.**************** PP

                                    HHHHHHHT-EEEEEEESEEESTT CS
                      Epimerase 154 eayaaqyglnaiilrlfnlyGpr 176
                                    + +++  gl +++lr+   + ++
  gi|121639388|ref|YP_979612.1| 185 QLAHRNDGLACVVLRVARFFVEG 207
                                    ***************98777555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   6.5e-17   9.8e-14       1     179 [.      39     199 ..      39     208 .. 0.87
   2 ?    3.8   0.0     0.021        31     307     329 ..     305     327 ..     289     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 6.5e-17
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG +G  G  l++ L ++g +v+ ++ r s ++     +               + g ++D++ l++++a v  + v+
  gi|121639388|ref|YP_979612.1|  39 LVTGSSGHLGEALVRTLRARGADVVSLDSRPSRYT-----N---------------IVGCVSDRALLRDVMAGV--EVVF 96 
                                    8***********************99988887633.....2...............346689***********9..79** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB.......-TTS-----SHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpq.......tEttpfyPrsPY 153
                                    + AA    +  f   ++++++n++Gt+++L+a+ a++++    f+ +S+ +v+G++   p        +E+    P++ Y
  gi|121639388|ref|YP_979612.1|  97 HAAAHHKPQLAFLPRQAFLDTNIIGTQTVLDAAVAANVR---AFVMTSSTTVFGDALTPPAdqpaawiDESVTPIPKNIY 173
                                    *********************************999986...7************96444311222337999999***** PP

                                    HHHHHHHHHHHHHHHHHH---EEEEE CS
                  GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngi 179
                                    +++K++++ +++  +++ gl +v+ +
  gi|121639388|ref|YP_979612.1| 174 GVTKASSEDLCQLAHRNDGLACVVLR 199
                                    ********************999876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                                    -B-THHHHHHH----SS-HHHHH CS
                  GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelv 329
                                    +  +s+a+++L+W+p+++++ + 
  gi|121639388|ref|YP_979612.1| 305 VYVNSRARRDLNWRPRFDLNAVA 327
                                    556799**********9998765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   5.7e-19   8.5e-16       1     188 [.      39     210 ..      39     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 5.7e-19
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +vtG++G lG+alv++L  ++   +v +lD r s  +            i g v d + l++++ gv+vv+h a+  + +
  gi|121639388|ref|YP_979612.1|  39 LVTGSSGHLGEALVRTLRARGA--DVVSLDSRPSRYT-----------NIVGCVSDRALLRDVMAGVEVVFHAAAHHKPQ 105
                                    69***************98884..7777776655554...........35689********************9988765 PP

                      3Beta_HSD  81 g.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnsl...geeilngdEeleyeslhqdaypesKalaEkl 156
                                       l ++ + + n+ GT++vl+a+v a+vr++v tSs  v g+  +    ++    dE   + + ++++y  +Ka +E+l
  gi|121639388|ref|YP_979612.1| 106 LaFLPRQAFLDTNIIGTQTVLDAAVAANVRAFVMTSSTTVFGDALTppaDQPAAWIDE--SVTPIPKNIYGVTKASSEDL 183
                                    538899************************************9543111233333333..456679************** PP

                      3Beta_HSD 157 vlkaNgrtlknggrlyTcaLRpagiyGegdkl 188
                                       a     ++g  l  + LR a  + egd++
  gi|121639388|ref|YP_979612.1| 184 CQLAHR---NDG--LACVVLRVARFFVEGDDM 210
                                    ***998...677..99999****999999875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.019        29       2      26 ..      39      63 ..      38      69 .. 0.83
   2 !   42.9   0.2   2.1e-14   3.2e-11      56     128 ..      72     142 ..      63     146 .. 0.88
   3 !    7.2   0.0    0.0017       2.5     134     167 ..     169     202 ..     161     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.019
                                   EEETTTSHHHHHHHHHHHHHB-SEE CS
                Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkki 26
                                   lvtG++G +G++lvr++ ++ +  +
  gi|121639388|ref|YP_979612.1| 39 LVTGSSGHLGEALVRTLRARGADVV 63
                                   8**************9987766655 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 2.1e-14
                                    ....E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHH.HHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  56 ivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenplea.iktNvlgtenvieaaieagvkkvvliSt 128
                                    +++++g v d++ l++++   +v+vvfhaAA+ h P + + p +a ++tN++gt++v++aa++a+v+++v+ S+
  gi|121639388|ref|YP_979612.1|  72 YTNIVGCVSDRALLRDVMA--GVEVVFHAAAH-HKPQLAFLPRQAfLDTNIIGTQTVLDAAVAANVRAFVMTSS 142
                                    46899**************..*********98.567777777765379***********************996 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0017
                                    --SHHHHHHHHHHHHHHHGGG--SSS--EEEEEE CS
                Polysacc_synt_2 134 PtnvmGatKrlaekllqalakeseekktkfvvvR 167
                                    P n++G+tK+ +e l+q ++++ + +   + v R
  gi|121639388|ref|YP_979612.1| 169 PKNIYGVTKASSEDLCQLAHRNDGLACVVLRVAR 202
                                    67***************99999866555555555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   2.5e-17   3.7e-14       1     153 [.      36     205 ..      36     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.5e-17
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...T--TTSHHHHHHHHHHH-..-SEEEE------HHHHHHSHHHHH CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...eldltdaeavaellkeak..pdvvvnaAAytavDkaEseeeaay 75 
                                    m+ lvtG++G lG +L++ l+++g++v++l+++    +++    + ++ll+++    +vv +aAA+++   a   ++a  
  gi|121639388|ref|YP_979612.1|  36 MRTLVTGSSGHLGEALVRTLRARGADVVSLDSRpsrYTNIVGCVSDRALLRDVMagVEVVFHAAAHHKPQLAFLPRQAFL 115
                                    899***************************88867756666666666777765411679********************* PP

                                    HHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-......TTS-B-.TTS----SSHHHHHHHHHHHHHHH....H-SSE CS
                  RmlD_sub_bind  76 avnaeavealAeaaaavga.lLihvStDyVFdGe......kkrpYe.eddetsPlnvYGrtKlaGEqavla....agkka 143
                                      n  +++++ +aa a+++  ++  S+  VF  +      ++ ++  e+ ++ P+n+YG tK+  E   +     +g  +
  gi|121639388|ref|YP_979612.1| 116 DTNIIGTQTVLDAAVAANVrAFVMTSSTTVFGDAltppadQPAAWIdESVTPIPKNIYGVTKASSEDLCQLahrnDGLAC 195
                                    **********999988887358999999***7778888777777751556789*************98765333367789 PP

                                    EEEEE-SEES CS
                  RmlD_sub_bind 144 livRtswvyg 153
                                    +++R++  + 
  gi|121639388|ref|YP_979612.1| 196 VVLRVARFFV 205
                                    9***998875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        19       1      20 [.      40      59 ..      40      73 .. 0.84
   2 !   34.1   0.0     1e-11   1.5e-08      81     204 ..      85     201 ..      80     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                                   EE-TTSHHHHHHHHHHHHHS CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                                   +TG++G LG+ L++ L  + 
  gi|121639388|ref|YP_979612.1| 40 VTGSSGHLGEALVRTLRARG 59
                                   7*************986555 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1e-11
                                    HHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    l+++++ v+v++h aA  + +    p + +l++N+ Gt+ vl+ a + +   +++  S+ +v g+  +   +        
  gi|121639388|ref|YP_979612.1|  85 LRDVMAGVEVVFHAAAHHKPQLaflPRQAFLDTNIIGTQTVLDAAVAANVR-AFVMTSSTTVFGDALTPPAD-------- 155
                                    6788999*********9997765558899****************977666.99999997777777766644........ PP

                                    ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE- CS
                  NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRps 204
                                     + +   +++     +n Y  +Ka +E+l++ a+r++gl +v++R+ 
  gi|121639388|ref|YP_979612.1| 156 -QPAAWIDESVTPIPKNIYGVTKASSEDLCQLAHRNDGLACVVLRVA 201
                                    .4677888888889999****************************86 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   2.3e-13   3.4e-10       1     147 [.      42     204 ..      42     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.3e-13
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC....... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk....... 73 
                                    G +G+ G +lv+ l arg  +v+ l  +p++ +          ++g v+d + l+++++g+++V+ a+++++        
  gi|121639388|ref|YP_979612.1|  42 GSSGHLGEALVRTLRARG-ADVVSLDSRPSRYT---------NIVGCVSDRALLRDVMAGVEVVFHAAAHHKPqlaflpr 111
                                    899**************5.99999977777776.........47899*********************999987777654 PP

                                    HHHH........HHHHHHHHHHCT--EEEEEEETTTTSG....CGCHHHHHHHH....CCHHHH.HHHHHHHHHH....H CS
                 NAD_binding_10  74 deeg........aknivdaakeagvkRfvlvsaigvgde....vpgefgewnke....llkayl.aakraaeell....r 132
                                    +  +        +++++daa +a+v+ fv+ s+  v  +     +++   w +e    + k+++   k+ +e+l     r
  gi|121639388|ref|YP_979612.1| 112 Q--AfldtniigTQTVLDAAVAANVRAFVMTSSTTVFGDaltpPADQPAAWIDEsvtpIPKNIYgVTKASSEDLCqlahR 189
                                    0..156666699*********************99965312112233444555423334566663334444444233446 PP

                                    HSSSEEEEEEE-CEE CS
                 NAD_binding_10 133 asgldwTivrpggLt 147
                                    + gl  +++r +++ 
  gi|121639388|ref|YP_979612.1| 190 NDGLACVVLRVARFF 204
                                    789999999988874 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   7.7e-05      0.11       4      35 ..      39      70 ..      37      99 .. 0.85
   2 ?    2.4   0.1     0.088   1.3e+02     108     138 ..     114     144 ..      79     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS. CS
                             KR  4 litGGlGgLGlelarwlaekgarhlvllsRsa 35
                                   l+tG  G+LG +l+r+l ++ga  + l sR +
  gi|121639388|ref|YP_979612.1| 39 LVTGSSGHLGEALVRTLRARGADVVSLDSRPS 70
                                   9**************************99975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.088
                                    HHTTTTHHHHHHHHHTTTS--SEEEEEEEHH CS
                             KR 108 vlapKvkGawnLhelledesldffvlfSSia 138
                                     l   + G++ +  +    ++  fv++SS  
  gi|121639388|ref|YP_979612.1| 114 FLDTNIIGTQTVLDAAVAANVRAFVMTSSTT 144
                                    45556677777777777789******99975 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3    0.0001      0.15       9     101 ..      46     141 ..      36     147 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                    HHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT............-HHHHHHHHTT-SEEEE---GG. CS
                           NmrA   9 rqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld............dkeslvealkgvdvvfsvtgfy. 75 
                                    ++G+++vr l ++g                        +v+ d              d+++l+ ++ gv+vvf + +   
  gi|121639388|ref|YP_979612.1|  46 HLGEALVRTLRARGA----------------------DVVSLDSRpsrytnivgcvsDRALLRDVMAGVEVVFHAAAHHk 103
                                    333333333333333......................3333333333333333333388888888888888888887667 PP

                                    ............S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                           NmrA  76 ............skeiedgkklvdAakeaGvkhfiySs 101
                                                +++i   +++ dAa++a v+ f+  s
  gi|121639388|ref|YP_979612.1| 104 pqlaflprqaflDTNIIGTQTVLDAAVAANVRAFVMTS 141
                                    78888888887777777777888999999999998755 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   3.3e-05     0.049      20      91 ..      36     100 ..      23     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                    TEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE--- CS
                            DFP  20 VRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAA 91 
                                    +R++   SSG+ G al + ++arGa+V    +       + +++v   s + +l+ v++ +   ++v++aAA
  gi|121639388|ref|YP_979612.1|  36 MRTLVTGSSGHLGEALVRTLRARGADVVSLDSRP----SRYTNIVGCVSDRALLRDVMAGV---EVVFHAAA 100
                                    6899999********************9988872....33567888888888888887764...46666666 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.9e-05     0.059       4      41 ..      39      76 ..      37     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                   EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHH CS
                      adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleeva 41
                                   lvtG s+ +G a++++l ++Ga+vv +d+++++  +++
  gi|121639388|ref|YP_979612.1| 39 LVTGSSGHLGEALVRTLRARGADVVSLDSRPSRYTNIV 76
                                   8***************************9999887665 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00037      0.55     377     433 ..     276     332 ..     269     338 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                        UPF0236 377 vverfsaRlkkrgrsWseeGLkamlkvlaasidGidlreveweekknisavsaklke 433
                                    + ++f+ R+   +  W ++G +   ++  ++++   +r+ +w  + + +av+a+l  
  gi|121639388|ref|YP_979612.1| 276 AASVFARRVPLAAAVWTQRGWRFPDRLDRVYVNSRARRDLNWRPRFDLNAVAARLAR 332
                                    789*************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2642.71
//
Query:       gi|121639389|ref|YP_979613.1|  [L=336]
Description: 4-hydroxy-2-ketovalerate aldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-39  134.1   0.9    7.3e-38  130.6   0.7    2.4  2  HMGL-like  HMGL-like
    0.00051   19.6   0.0       0.27   10.7   0.0    2.9  3  ComA       (2R)-phospho-3-sulfolactate synthase (ComA)
  ------ inclusion threshold ------
       0.25   10.7   0.0       0.35   10.2   0.0    1.1  1  LETM1      LETM1-like protein


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.7   1.2e-41   7.3e-38       3     261 ..      11     261 ..       9     263 .. 0.92
   2 ?   -1.3   0.0      0.22   1.3e+03      36      63 ..     274     303 ..     271     320 .. 0.59

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.2e-41
                                    EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--............TSGGGT.THHHHHHHS---TT-B..... CS
                      HMGL-like   3 kivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEv............gfpaaseddfevvraiakavkkar...i 67 
                                    +++dtt RDG+ a + +++ +++++i+  Ld+ag+ +iE+            g +a+  +d e  ra+ ++v +ar   +
  gi|121639389|ref|YP_979613.1|  11 IVLDTTVRDGSYAVNFQYTDDDVRRIVGDLDAAGIPYIEIghgvtigaaaaqGPAAH--TDEEYFRAARSVVRNARlgaV 88 
                                    689*****************************************9998886544444..599999999999999986667 PP

                                    --EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHH CS
                      HMGL-like  68 lalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdlef 147
                                    ++++ ar++ ++ a +       + +++ + ++e              ++ +   v++a+s+g +v++ l  ++  +++ 
  gi|121639389|ref|YP_979613.1|  89 IVPALARIETVDLAGD-----YLDFLRICVIATE--------------FELVMPFVERAQSKGLEVSIQLVKSHLFEPDV 149
                                    7777777777777777.....8999999999999..............999***************************** PP

                                    HHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS- CS
                      HMGL-like 148 laevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGl 227
                                    la   ++a+++G++++++ Dt G   P++a++ ++al+   +  v + +H+Hn+l +Avantl+A  aGad +dgt+ G 
  gi|121639389|ref|YP_979613.1| 150 LAAAGKRARDVGVRIVYVVDTTGTFLPEDARRYVEALRGASD--VSVGFHGHNNLAMAVANTLEAFDAGADFLDGTLMGF 227
                                    ******************************************..************************************ PP

                                    -SSBBB-BHHHHHHHHHHTT-B----HHHHHHHH CS
                      HMGL-like 228 GeraGnaaleelvaalealgvdtgldlqklrsia 261
                                    G +aGn+ +e lvaal+++g    + l ++ ++a
  gi|121639389|ref|YP_979613.1| 228 GRGAGNCQIECLVAALQRRGHLAAVGLDRIFDAA 261
                                    ********************99999888888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                                    T-SEE--TSGGGT.THH..HHHHHS---TT CS
                      HMGL-like  36 gvdeiEvgfpaaseddf..evvraiakavk 63 
                                    g+d  E++f++++ d++  e +ra+a++++
  gi|121639389|ref|YP_979613.1| 274 GIDPWEISFGFHGLDSLqvEHLRAAAQQAG 303
                                    777778888888866541144555555543 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.042   2.5e+02      76     105 ..      25      54 ..      13      60 .. 0.82
   2 !   10.7   0.0   4.5e-05      0.27      28     123 ..      98     189 ..      90     221 .. 0.85
   3 !    4.3   0.0    0.0039        23      91     135 ..     270     314 ..     204     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.042
                                    HHHHHTT-HHHHHHHHHHCT-SEEEE--SS CS
                           ComA  76 EaalaqgkvdeyleeckelgfdviEvsdgt 105
                                    +  ++ + v++ + ++++ g+ +iE+  g+
  gi|121639389|ref|YP_979613.1|  25 NFQYTDDDVRRIVGDLDAAGIPYIEIGHGV 54 
                                    4556777999****************9996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.5e-05
                                    HHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHHHHHHHHCT-SEEEE--SSS- CS
                           ComA  28 lletageyiDglKlgggtsallpeeilrekielahehgvyvstGgtlfEaalaqgkvdeyleeckelgfdviEvsdgtle 107
                                     ++ ag+y+D+l+++   ++ ++ e++  ++e a++ g +vs    +  +++  + + +  ++++++g++++ v d+t +
  gi|121639389|ref|YP_979613.1|  98 TVDLAGDYLDFLRIC---VIATEFELVMPFVERAQSKGLEVSIQL-VKSHLFEPDVLAAAGKRARDVGVRIVYVVDTTGT 173
                                    5678999****9998...67778889*****************99.999999999************************* PP

                                    --HHHHHHHHHHHCCT CS
                           ComA 108 lpeeeklrliekakke 123
                                    + +e+ +r++e ++ +
  gi|121639389|ref|YP_979613.1| 174 FLPEDARRYVEALRGA 189
                                    9999999***998765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0039
                                    HHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SS CS
                           ComA  91 ckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkd 135
                                     +++g+d  E+s g+  l+  +  +l   a+++gl v   + +  
  gi|121639389|ref|YP_979613.1| 270 PQSYGIDPWEISFGFHGLDSLQVEHLRAAAQQAGLSVSHVIRQTA 314
                                    5789*******************************9977665544 PP

>> LETM1  LETM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.9e-05      0.35     215     253 ..     285     323 ..     279     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.9e-05
                          LETM1 215 eGvdsLseeeLqeacrsRGlraaglseeelreqLeqWle 253
                                     G+dsL++e L+ a+++ Gl++ ++ +++ +++  qWl+
  gi|121639389|ref|YP_979613.1| 285 HGLDSLQVEHLRAAAQQAGLSVSHVIRQTAKSHAGQWLS 323
                                    69***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2582.48
//
Query:       gi|121639390|ref|YP_979614.1|  [L=552]
Description: acetolactate synthase large subunit IlvB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-45  154.7   0.4    1.1e-44  152.0   0.2    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    2.2e-30  105.5   0.2    2.2e-30  105.5   0.2    1.6  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.8e-28   97.6   0.0    9.7e-28   96.6   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.067   13.0   0.2      0.067   13.0   0.2    2.7  3  DUF4774       Domain of unknown function (DUF4774)
       0.11   12.2   0.2       0.17   11.6   0.2    1.3  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.2   3.2e-48   1.1e-44       1     169 [.       1     172 [.       1     175 [. 0.96
   2 ?   -0.0   0.0      0.16   5.8e+02     115     162 ..     498     540 ..     480     541 .. 0.80

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 3.2e-48
                                    EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                   TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                    mtv++ lv +++a+g+ +v+g+p sr+ +ll +ls+  g+++vlarhE+ga++ Adg+ara+gk ++v+v +gpGatn++
  gi|121639390|ref|YP_979614.1|   1 MTVGDHLVARMRAAGISVVCGLPTSRLDSLLVRLSRDAGFQIVLARHEGGAGYLADGFARASGKSAAVFV-AGPGATNVI 79 
                                    89********************************************************************.9******** PP

                                    HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T.-CCHH...HCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEE CS
                   TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqel.dqlal...frpvtkyaervtspeelpealrrAirtalsgrpgPvy 156
                                     a+a+A+v+++P+l+l+g++++ + g + +q++  d l+l   fr ++++++ ++s +++++ ++ A+r+++s ++gPv+
  gi|121639390|ref|YP_979614.1|  80 SAVANASVNQVPMLILTGEVAVGEFGLHSQQDTSdDGLGLgatFRRFCRCSVSIESIANARSKIDSAFRALASIPRGPVH 159
                                    **************************99999666777777888************************************* PP

                                    EEEEHHHCC-EEE CS
                   TPP_enzyme_N 157 lelpkdvlleevd 169
                                    ++lp+d+++e  +
  gi|121639390|ref|YP_979614.1| 160 IALPRDLVDERLP 172
                                    ********99876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.16
                                    -CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                   TPP_enzyme_N 115 dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                    d +a++r +  +  rv++  el+  +++A+++      gP +l+++ d
  gi|121639390|ref|YP_979614.1| 498 DLAAMARALGAEGIRVDTRCELRAGVQKALAAT-----GPCVLDIAID 540
                                    777888888888888888888888888888777.....9999998765 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       2.4   8.7e+03      41      77 ..      59      94 ..      48      95 .. 0.56
   2 !  105.5   0.2   6.1e-34   2.2e-30       1     153 []     391     537 ..     391     537 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                                   HHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                   TPP_enzyme_C 41 klakpdrevvaivGDGgflmilqelatavrrnlpitv 77
                                   ++a  ++  v ++G G++   ++++a+a  +++p+++
  gi|121639390|ref|YP_979614.1| 59 ARASGKSAAVFVAGPGATNV-ISAVANASVNQVPMLI 94
                                   44433444566666666544.4666666666666665 PP

  == domain 2  score: 105.5 bits;  conditional E-value: 6.1e-34
                                    ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEE CS
                   TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvl 80 
                                    d+G++  w+ r ++v+rp++++    ++ mG g+++AiG++la+p+++v++i+GDG+flm+++e++tav +++ +t+ vl
  gi|121639390|ref|YP_979614.1| 391 DVGTCISWTFRGIPVRRPGRFFATVDFSPMGCGIAGAIGVALARPEEHVICIAGDGAFLMHGTEISTAVAHGIRVTWAVL 470
                                    89****************************************************************************** PP

                                    E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                    n++ + +  g  + + + + ++   +++ + d+a++a+alGa+g+rv+++   el++ +++al+  gp+++++
  gi|121639390|ref|YP_979614.1| 471 NDGQMSASAGPVSGRMDPSPVA---RIGAN-DLAAMARALGAEGIRVDTR--CELRAGVQKALAATGPCVLDI 537
                                    *******999866666544444...34556.*******************..******************996 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   2.7e-31   9.7e-28       2     137 .]     198     336 ..     197     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.7e-31
                                    HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHH..HH-S CS
                   TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaaneal..eeaD 79 
                                    ++++ +l +++ p++++G+g++ +g  e++++++ek g+P++tt++g+g++ e+hpl+lg+lg++g+  a+e l    +D
  gi|121639390|ref|YP_979614.1| 198 DEVIGRLDRSRAPMLVLGNGCRLDGIGEQIVAFCEKAGLPFATTPNGRGIVAETHPLSLGVLGIFGDGRADEYLfdTPCD 277
                                    689999********************************************************************6555** PP

                                    EEEEES-SSSTCCCTTTTT.TTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                   TPP_enzyme_M  80 lvlalGarfddirttgsep.efapea.kiihididpaeigknyqvdlaivgdvketleaL 137
                                    l++a+G+ f    +t s++ ++   +  ++h+d+dp+ +g+ + ++l+i    +++++aL
  gi|121639390|ref|YP_979614.1| 278 LLIAVGVSFGG-LVTRSFSpRWRGLKaDVVHVDPDPSAVGRFVATSLGITTSGRAFVNAL 336
                                    ***********.5666555499888889*********************99999998887 PP

>> DUF4774  Domain of unknown function (DUF4774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.7   6.1e+03      44      51 ..      68      75 ..      57      80 .. 0.63
   2 ?   -3.0   0.1       1.9   6.7e+03       8      18 ..     176     186 ..     171     193 .. 0.67
   3 ?   13.0   0.2   1.9e-05     0.067       6      38 ..     418     450 ..     413     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                        DUF4774 44 vAiaGPgg 51
                                   v +aGPg+
  gi|121639390|ref|YP_979614.1| 68 VFVAGPGA 75
                                   33566665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                        DUF4774   8 vGkAvaGkgGv 18 
                                     G A aG gG+
  gi|121639390|ref|YP_979614.1| 176 LGTAAAGLGGL 186
                                    46677777775 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.9e-05
                        DUF4774   6 kpvGkAvaGkgGvAisaPvgtaivkkGkkglal 38 
                                     p+G  +aG  GvA ++P  ++i   G +++++
  gi|121639390|ref|YP_979614.1| 418 SPMGCGIAGAIGVALARPEEHVICIAGDGAFLM 450
                                    69*********************9888877765 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.8e-05      0.17      39     111 ..      41     114 ..      23     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                                    EEEE-SSHHHHHHHHHH.HHCTT-EEEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TT CS
                          POR_N  39 evvqmesEigaisaviG.AaaaGaraaTaTSgqGllLmienlglaageelPvvivvvaRalpstglsirtdqsD 111
                                    ++v +  E ga   + G A a+G  aa++ +g+G    i ++  a+ +++P++i     a+   gl  ++d sD
  gi|121639390|ref|YP_979614.1|  41 QIVLARHEGGAGYLADGfARASGKSAAVFVAGPGATNVISAVANASVNQVPMLILTGEVAVGEFGLHSQQDTSD 114
                                    6777888999988888868899**********************************999999999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3767.99
//
Query:       gi|121639391|ref|YP_979615.1|  [L=177]
Description: hypothetical protein BCG_3536c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-14   51.6   0.0    7.9e-14   51.1   0.0    1.3  1  Cupin_2          Cupin domain
    3.7e-05   23.3   0.1    6.6e-05   22.5   0.1    1.4  1  Cupin_3          Protein of unknown function (DUF861)
    0.00012   21.7   0.0    0.00016   21.3   0.0    1.2  1  Cupin_1          Cupin
    0.00021   21.0   0.3    0.00043   20.0   0.3    1.5  1  AraC_binding_2   AraC-binding-like domain
    0.00057   19.8   0.0    0.00095   19.1   0.0    1.4  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.036   14.0   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   2.6e-17   7.9e-14       3      70 ..      87     154 ..      85     155 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.6e-17
                                    EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                        Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                     +++ G+++ +hr + +de+++Vl+G+g + v++e  e+++Gd+v +pag+p ++r  g+ p+ +l+ 
  gi|121639391|ref|YP_979615.1|  87 ATVAAGAETVWHRLQATDEIYFVLSGRGLVSVGDESGEVGPGDAVWIPAGVPQKIRALGSVPLTFLCA 154
                                    6899*********77778***********************************************996 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.2e-08   6.6e-05      20      64 ..      98     141 ..      85     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.2e-08
                                    EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEECC CS
                        Cupin_3  20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkglsgtw 64 
                                    +    +dE+ ++l+G+  v + g e  e+++GD+v +p+g  ++ 
  gi|121639391|ref|YP_979615.1|  98 HRLQATDEIYFVLSGRGLVSV-GDESGEVGPGDAVWIPAGVPQKI 141
                                    555567***************.******************98776 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   5.4e-08   0.00016      32     108 ..      81     150 ..      52     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.4e-08
                                    TEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEE CS
                        Cupin_1  32 gisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepav 108
                                     +s+a   +++g+    h    + ei +vl G+g+   v+ g    d++ ++ +Gd++++Pag+++ + + g  p+ 
  gi|121639391|ref|YP_979615.1|  81 SVSLAHATVAAGAETVWHRLQATDEIYFVLSGRGL---VSVG----DESGEVGPGDAVWIPAGVPQKIRALGSVPLT 150
                                    566666667888888888889999***********...5555....6789*****************9999977665 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   1.4e-07   0.00043      39     102 ..      89     150 ..      65     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                 AraC_binding_2  39 lrygaavsi.rpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsadceql 102
                                    + +ga+++  r ++ d    + + lsGr+ v++g++  ++gpgdav + +g p+++r  + +  +
  gi|121639391|ref|YP_979615.1|  89 VAAGAETVWhRLQATD---EIYFVLSGRGLVSVGDESGEVGPGDAVWIPAGVPQKIRALGSVPLT 150
                                    3344444331444434...58899********************************998776655 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.2e-07   0.00095      25      70 ..     105     150 ..      84     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.2e-07
                                    EEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEE CS
                   AraC_binding  25 vihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwe 70 
                                    +i  v++G+g ++++++  ++gpGd +++p g+p  +++ ++ +++
  gi|121639391|ref|YP_979615.1| 105 EIYFVLSGRGLVSVGDESGEVGPGDAVWIPAGVPQKIRALGSVPLT 150
                                    799*******************************999987766655 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.036      68     145 ..      87     164 ..      78     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                MannoseP_isomer  68 itvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgedd 145
                                     tv  g++ + ++ +   e + v++G   v+v+de+ ++   + ++ip+g+  ++   G +pl+++     +yl e d
  gi|121639391|ref|YP_979615.1|  87 ATVAAGAETVWHRLQATDEIYFVLSGRGLVSVGDESGEVGPGDAVWIPAGVPQKIRALGSVPLTFLCACGPAYLPERD 164
                                    56777777777777888899********************************************99988889998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1230.00
//
Query:       gi|121639392|ref|YP_979616.1|  [L=168]
Description: hypothetical protein BCG_3537 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-25   89.6   1.0    1.7e-25   89.6   1.0    1.7  2  SnoaL_4          SnoaL-like domain
    3.7e-06   27.3   1.6    2.2e-05   24.8   0.4    2.0  2  DUF4440          Domain of unknown function (DUF4440)
     0.0002   22.0   2.0    0.00021   21.9   1.0    1.6  2  SnoaL_2          SnoaL-like domain
  ------ inclusion threshold ------
      0.075   13.1   0.1        1.9    8.5   0.1    2.2  2  Ring_hydroxyl_B  Ring hydroxylating beta subunit


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.0   3.7e-29   1.7e-25       7     127 .]      12     126 ..       7     126 .. 0.93
   2 ?    0.2   0.1      0.17   7.6e+02      67      96 ..     128     160 ..     124     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.7e-29
                                    HHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEETTEEEE CS
                        SnoaL_4   7 eaIrdlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldgdtAtg 86 
                                      I+ l ary+  +Dt+d e +a +Fted+ ++++g+   v++gr a+r++  ++ ++ ++ +Hl+++ l e+dgd Atg
  gi|121639392|ref|YP_979616.1|  12 LRIQALCARYCLTIDTQDGEGWAGCFTEDGAFEFDGW---VIRGRPALREYADAH-ARVVRGRHLTTDLLYEVDGDVATG 87 
                                    679********************************98...**********88886.6999******************** PP

                                    EEEEEEEEEETTEEEEEE..EEEEEEEEEEETTEEEEEEEE CS
                        SnoaL_4  87 rayllatlvrdgdggrqvlaggryedelvredggWrisrrk 127
                                    r+ +++tl  ++ +g + l +g y+d+l+++dg+Wri+ r+
  gi|121639392|ref|YP_979616.1|  88 RSASVVTL--ATAAGYKILGSGEYQDRLIKQDGQWRIAYRR 126
                                    *******6..4456789********************9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                                    -EEEEE---EEEE...ETTEEEEEEEEEEEEEE CS
                        SnoaL_4  67 ltqHllsnpliel...dgdtAtgrayllatlvr 96 
                                    +++ l+s+p + +   d d A ++++lla  +r
  gi|121639392|ref|YP_979616.1| 128 RNDRLVSDPSVAVnvaDADVAAVVGHLLAAARR 160
                                    678889999999988888999999999987655 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.4     5e-09   2.2e-05       1     107 []      14     122 ..      14     122 .. 0.90
   2 ?    1.9   0.0     0.064   2.9e+02      62      87 ..     138     164 ..     125     168 .] 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5e-09
                                    HHHHHHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEE.EEEEEETTEEEEEEEEEE CS
                        DUF4440   1 iaaleealeeafvagdaealaallapdavlvgpsgtvldkeellealeagfaagrslelte.eevrvlgdlAvvtgrytf 79 
                                    i+al +++  ++ + d e +a ++++d  +  ++  ++++++l e   a +   r  +lt+ + ++v gd+A+ +    +
  gi|121639392|ref|YP_979616.1|  14 IQALCARYCLTIDTQDGEGWAGCFTEDGAFEFDGWVIRGRPALREYADAHARVVRGRHLTTdLLYEVDGDVATGRSASVV 93 
                                    778889999999**********************999*****99999887777888888553888888*********999 PP

                                    EECC.TTEEEEEEEEEEEEEEEETTEEEE CS
                        DUF4440  80 egrg.dgepvegrgrftsvwrkegggWri 107
                                    +    +g ++ g+g +   + k++g+Wri
  gi|121639392|ref|YP_979616.1|  94 TLATaAGYKILGSGEYQDRLIKQDGQWRI 122
                                    9966489999******************8 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.064
                                    EEEEEE.TTEEEEEEEEEEEECCTTEE CS
                        DUF4440  62 eevrvl.gdlAvvtgrytfegrgdgep 87 
                                    ++v v   d+A+v+g+  +++r+ g +
  gi|121639392|ref|YP_979616.1| 138 VAVNVAdADVAAVVGHLLAAARRLGTQ 164
                                    677777789*******99999987754 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.0   4.7e-08   0.00021       4      98 ..      21     119 ..      18     134 .. 0.78
   2 ?   -1.4   0.0      0.86   3.9e+03      60      73 ..     138     154 ..     114     163 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.7e-08
                                    HHHHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSE CS
                        SnoaL_2   4 flaalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrg 83 
                                    +   ++++d +++a +f++d  +e  g  +rGr a+r++  a  + + +++ + + +++ +  va+   +++ + at +g
  gi|121639392|ref|YP_979616.1|  21 YCLTIDTQDGEGWAGCFTEDGAFEFDGWVIRGRPALREYADAHARVVRGRHLTTDLLYEVDGDVATGRSASVVTLATAAG 100
                                    5556789*******************999**********99999988888888888866666666654455556789988 PP

                                    EEE....EEEEEEEEETTE CS
                        SnoaL_2  84 vtv....rgvdvfrvrdGk 98 
                                    + +    ++ d +  +dG+
  gi|121639392|ref|YP_979616.1| 101 YKIlgsgEYQDRLIKQDGQ 119
                                    8886666555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.86
                                    E...EEETTEEEEEEEE CS
                        SnoaL_2  60 v...vadgdrvavewtv 73 
                                    v   vad d +av +++
  gi|121639392|ref|YP_979616.1| 138 VavnVADADVAAVVGHL 154
                                    33445666666665554 PP

>> Ring_hydroxyl_B  Ring hydroxylating beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.028   1.2e+02       6      32 ..      25      51 ..      21      66 .. 0.81
   2 ?    8.5   0.1   0.00043       1.9     111     136 ..     103     128 ..      62     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.028
                                   HHTT-HHHHHCTEEEEEEEEEE-B--- CS
                Ring_hydroxyl_B  6 LDdrdydaWlallaedihYwmpareer 32
                                   +D +d ++W  +++ed ++    +  r
  gi|121639392|ref|YP_979616.1| 25 IDTQDGEGWAGCFTEDGAFEFDGWVIR 51
                                   699999**********99987777655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00043
                                    EEEEEEEEEEEEE-SSTEEEEEEEEE CS
                Ring_hydroxyl_B 111 difaGeredvlrrsddsfkiarrtil 136
                                     + +Ge++d+l ++d++++ia r+  
  gi|121639392|ref|YP_979616.1| 103 ILGSGEYQDRLIKQDGQWRIAYRRLR 128
                                    4568******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1219.34
//
Query:       gi|121639393|ref|YP_979617.1|  [L=261]
Description: peroxidase bpoA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-17   65.5  11.1    1.3e-17   65.2  11.1    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
      2e-16   60.4   0.2    9.4e-14   51.7   0.3    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      3e-13   49.6   0.3    1.3e-12   47.5   0.3    1.8  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0038   17.3   0.0      0.012   15.7   0.0    1.7  2  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.19   11.6   0.0    1.3  1  UPF0227        Uncharacterised protein family (UPF0227)


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2  11.1   3.6e-21   1.3e-17       2     219 ..       2     248 ..       1     249 [. 0.59

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 3.6e-21
                                    EEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTST.S-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETCHH CS
                  Abhydrolase_6   2 lllHGagssassWlvapLaallaag.vhvlapDlpGhG.rsdpppldled...ladlaalldelaagggpvvlvGHSlGG 76 
                                    ++lHG+g +++sW   + aa+ a++ ++ +++Dl+GhG +++++  d++    + d+ ++l+ l   +g++ lvG SlGG
  gi|121639393|ref|YP_979617.1|   2 VFLHGGGQTRRSWG--RAAAAVAERgWQAVTIDLRGHGeSDWSSEGDYRLvsfAGDIQEVLRNL---PGQPALVGASLGG 76 
                                    9************4..44444466667779*******966677778887744457779999999...8************ PP

                                    HHHHHHHHCC.....EE..EEES-..----TTT...S----TTHHHHHH......TT-C.....CCCHCCH........S CS
                  Abhydrolase_6  77 alalaaapla...lvvg..vlldppptalpagl...laaalelllalla......llrl.....lawlsre........p 129
                                    + a+++a  +   + ++  vl+d     +p  +   +++++++++ +                 +     +        +
  gi|121639393|ref|YP_979617.1|  77 FAAMLLAGELspgI-ASavVLVDI----VPNMDlagASRIHAFMAERVEsgfgslD--EvadviA-----NynphrprpS 144
                                    *****444448854.334455555....3333313322222222222222222221..1222222.....0233334444 PP

                                    -HSCCCCHHH.C....CCCHCHCCCGHHHHCCHHC.......HTTCCHHTT-TTGCEEE.C.TT-CHHHHCHHCCCH.ST CS
                  Abhydrolase_6 130 lprlfladed.a....daawrarlarlaallaglg.......llpaaawadlpvpllvl.g.geDplvprllerlla.qa 194
                                    +p++++a++       + +w + + ++ a +++++         ++a + +  vp+l++ g  +D + ++ ++++l   +
  gi|121639393|ref|YP_979617.1| 145 DPDGLVANLRrRgdrwYWHWDPQFIGGIAAFPPVEvtdvdrmNAAVATILRDEVPVLLVrGqVSDIVRQESADQFLSrFP 224
                                    44466665554134455555555555556666555222211111244555555555776764555566677889999877 PP

                                    TEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 195 garlpvvlpgaGHlphleepdevae 219
                                     +++ + ++gaGH++  +++d++a 
  gi|121639393|ref|YP_979617.1| 225 QVEF-TDVRGAGHMVAGDRNDAFAG 248
                                    7777.99**********999**995 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.3   2.6e-17   9.4e-14       3     109 ..       1     101 [.       1     123 [. 0.91
   2 !    7.0   0.0    0.0011         4     209     253 ..     192     239 ..     112     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.6e-17
                                    EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETH CS
                  Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSm 82 
                                    +v+lhG++ +  +w +   a a a++g++ +++DlrG+g+S+ +++    dy+++s+a d++ +l  l+ ++  lvG S+
  gi|121639393|ref|YP_979617.1|   1 MVFLHGGGQTRRSWGR--AAAAVAERGWQAVTIDLRGHGESDWSSE---GDYRLVSFAGDIQEVLRNLPGQPA-LVGASL 74 
                                    59**************..999*********************9999...9***************99998887.****** PP

                                    HHHHHHHHHHHH.GGGEEEEEEESECSS CS
                  Abhydrolase_1  83 GGmialayaaey.perVkalvllgaidp 109
                                    GG+ a+ +a e  p   +a+vl++   p
  gi|121639393|ref|YP_979617.1|  75 GGFAAMLLAGELsPGIASAVVLVDI-VP 101
                                    ************8998899999887.33 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                                    HHHS...EEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHH CS
                  Abhydrolase_1 209 nvla...ptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaf 253
                                     +l    p+l++ g+   +v  ++ +++ + +p+++   + +agH++ 
  gi|121639393|ref|YP_979617.1| 192 TILRdevPVLLVRGQVSDIVRQESADQFLSRFPQVEFTDVRGAGHMVA 239
                                    3333555***************999999999**************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.3   3.7e-16   1.3e-12       8     238 ..       2     242 ..       1     243 [. 0.80

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.7e-16
                    Hydrolase_4   8 vlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    v++HG +++ +   + a+a a++G++ +++D rGhG+s+    g   ++ ++  D++++++++    p++p  l+G S+G
  gi|121639393|ref|YP_979617.1|   2 VFLHGGGQTRRSWGRAAAAVAERGWQAVTIDLRGHGESDwSSEG-DYRLVSFAGDIQEVLRNL----PGQP-ALVGASLG 75 
                                    89************************************965555.456777889998887554....5776.89****** PP

                    Hydrolase_4  87 Gliallyllrypdkva.glilsaPalkikaklk.appllklllkllgkllpklqv............snnlkadslsrdp 152
                                    G+ a+l++ + ++ +a +++l+  + +++  l  a+++ +++++ + + + +l              ++++++d l  + 
  gi|121639393|ref|YP_979617.1|  76 GFAAMLLAGELSPGIAsAVVLVDIVPNMD--LAgASRIHAFMAERVESGFGSLDEvadvianynphrPRPSDPDGLVANL 153
                                    ********766666775888875443333..3447777777777777777777667788888888887778888888777 PP

                    Hydrolase_4 153 evva..ay.eadplvhgkitvrlllel..ldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlkly 227
                                    +++    y + dp  +g+i +   +e+  +d m+++++   + ++P+ll+ G+   +v +e + +++ r +  +++++  
  gi|121639393|ref|YP_979617.1| 154 RRRGdrWYwHWDPQFIGGIAAFPPVEVtdVDRMNAAVATILRDEVPVLLVRGQVSDIVRQESADQFLSRFP--QVEFTDV 231
                                    66642244156999999999988887722567888888888889***************************..7****** PP

                    Hydrolase_4 228 pglyHellnEp 238
                                     g+ H++ +++
  gi|121639393|ref|YP_979617.1| 232 RGAGHMVAGDR 242
                                    ******99886 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   3.6e+03      48      76 ..      10      39 ..       8      44 .. 0.71
   2 !   15.7   0.0   3.4e-06     0.012      31      92 ..     194     255 ..     165     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                  Abhydrolase_4 48 TPyegakklakalgga.vlvtvegeGHgal 76
                                   T  ++++++a   +++ + vt +  GHg +
  gi|121639393|ref|YP_979617.1| 10 TRRSWGRAAAAVAERGwQAVTIDLRGHGES 39
                                   666777777777776558889999999876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.4e-06
                  Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                     ++++pvLl+ ++   ++  e+a ++ +++++ +   v+g+GH +  + n++   av ++L+
  gi|121639393|ref|YP_979617.1| 194 LRDEVPVLLVRGQVSDIVRQESADQFLSRFPQVEFTDVRGAGHMVAGDRNDAFAGAVLDFLA 255
                                    2457*****************************************99************996 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.19      52      78 ..      58      84 ..      50     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                        UPF0227 52 lvaelgddnillvGssLGGyyatrlge 78
                                    v  + + +++lvG sLGG+ a  l+ 
  gi|121639393|ref|YP_979617.1| 58 EVLRNLPGQPALVGASLGGFAAMLLAG 84
                                   455556667*************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1671.89
//
Query:       gi|121639394|ref|YP_979618.1|  [L=449]
Description: dicarboxylic acid transport integral membrane protein kgtP [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-38  132.2  20.4    6.7e-25   87.9   5.6    2.0  2  Sugar_tr      Sugar (and other) transporter
    1.6e-22   80.0  28.2    1.6e-22   80.0  28.2    1.6  2  MFS_1         Major Facilitator Superfamily
     0.0072   16.5  23.1       0.21   11.8   0.2    4.3  4  DUF3792       Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
       0.54   10.5  20.1       0.73   10.0   0.1    4.5  6  AzlD          Branched-chain amino acid transport protein (Az


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   5.6   1.5e-28   6.7e-25       7     194 ..      28     219 ..      22     224 .. 0.92
   2 !   51.1   6.3   2.1e-17   9.5e-14     226     444 ..     223     435 ..     220     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.5e-28
                                    HHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                       Sugar_tr   7 lggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlf 86 
                                     g l+++Yd++v+ +f+t  + +++  ++++++      v++ +i+++++v + +Gs f+g ++dr GR+ +l +++ l+
  gi|121639394|ref|YP_979618.1|  28 SGNLVEWYDVYVYTVFATYFEDQFFDRADRNST------VYVYAIFAVTFVTRPVGSWFFGRFADRRGRRAALTFSVSLM 101
                                    56699************9999666666665554......5678************************************* PP

                                    HHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  87 vigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl 161
                                     +++++ a+ +++      +  +li++R++ G++ G++++++ +y+sE A+ + Rg++ s++ + ++ G ++a+++ l++
  gi|121639394|ref|YP_979618.1| 102 AACSLIVALVPSRssigvAAPILLILCRLVQGFATGGEYGTSVTYMSEAATRERRGYFSSFQYVTLVGGHVLAQFTLLVI 181
                                    ***********99999999999*******************************************************999 PP

                                    .HTSS-....TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                       Sugar_tr 162 .nktsn....adgwrillglqlvpallllilllflPES 194
                                     + ++     + gwri +++    a++++ l+ +++ES
  gi|121639394|ref|YP_979618.1| 182 lAVFTReqvhEFGWRIGFAVGGGAAIVVFWLRRTMDES 219
                                    666555899999********************999999 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 2.1e-17
                                    HHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...HHHHHHHHHHHHH CS
                       Sugar_tr 226 eekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks...llvtiivgvvnfv 302
                                    e  ++++a+++  + s++el +   + ++ll+++++ ++  +  + +  + +p i +++  s+     +++++  ++ ++
  gi|121639394|ref|YP_979618.1| 223 ERLTAIKAGRDHDSGSLRELATH--YWKPLLLCFLVTLGGTVAFYTYSVN-APAIVKSVYGSQAmtaTWINLVGLILLMM 299
                                    66677888877777788888877..8888888888877766666555555.78899999888886777788888888999 PP

                                    HHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTT CS
                       Sugar_tr 303 atfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqs 382
                                       ++ +++d++GR++lll+ ++g++i + +l  v++l +++s  +s+++++  ++ +    +g  ++ +++ sElfp +
  gi|121639394|ref|YP_979618.1| 300 LQPIGGMISDKIGRKPLLLWFGVGGLIYTYVL--VTYLPETRSPTMSFLLVAVGYVIL----TGYCSINALVKSELFPAH 373
                                    999999**************************..588888886666666666666665....5555888888******** PP

                                    THHHHHHHHHH.HHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT-- CS
                       Sugar_tr 383 vRskalaiava.vnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrt 444
                                    vR+++  + +a +n ++     l+++ + e+ +  ++f+ ++  ++++ ++v++f++  k  t
  gi|121639394|ref|YP_979618.1| 374 VRALGVGVGYAlANSVFGGTAPLIYQALKERDQ-VPMFIAYVTACIAVSLIVYVFFIKNKADT 435
                                    ********9873688999999999999999999.*******************9999877665 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0  28.2   3.5e-26   1.6e-22      37     349 ..      66     391 ..      56     396 .. 0.77
   2 ?   -0.1   0.7     0.076   3.4e+02     143     177 ..     396     433 ..     376     443 .. 0.40

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.5e-26
                          MFS_1  37 lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.......sslw.lllvlrvlqGlgagalfpagaa 108
                                    ++++ +++  v+s ++Gr++dr Grr  l +++ l+a+++l+ +++          + ll+++r++qG+++g+ + ++++
  gi|121639394|ref|YP_979618.1|  66 IFAVTFVTRPVGSWFFGRFADRRGRRAALTFSVSLMAACSLIVALVpsrssigVAAPiLLILCRLVQGFATGGEYGTSVT 145
                                    56677777799****************************77777643453334226667********************* PP

                          MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslg........Wravfyilaivsllafvlfllllpeepperk 180
                                    ++++ +++e+rg   ++ +++   G +l+     ++++ +         Wr  f + +++++++f+l     ++e  + +
  gi|121639394|ref|YP_979618.1| 146 YMSEAATRERRGYFSSFQYVTLVGGHVLAQFTLLVILAVFTreqvhefgWRIGFAVGGGAAIVVFWL--RRTMDESLSQE 223
                                    ********************88888888866666666677778888999**************9332..33344444444 PP

                          MFS_1 181 rkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                    r + ++ +  +   +l+++ ++ +k+  l  ++++ l+++++f+++++  p ++++v+g     ++++ + l++l+ +++
  gi|121639394|ref|YP_979618.1| 224 RLTAIKAGRDHDSGSLRELATHYWKPLLL--CFLVTLGGTVAFYTYSVNAPAIVKSVYGSQ--AMTATWINLVGLILLMM 299
                                    44444443333333333345566666644..9999999999********************..55555666666666666 PP

                          MFS_1 261 .allagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllala.sdlappeeagtas 338
                                     ++++g +sd++gr++ ll++++++l+ +  l+   + + ++ + ++lv +G    + ++s++al+ s+l+p++ ++  +
  gi|121639394|ref|YP_979618.1| 300 lQPIGGMISDKIGRKPLLLWFGVGGLIYTYVLVTYLPETRSPTMSFLLVAVGYVILTGYCSINALVkSELFPAHVRALGV 379
                                    6****************999999999999999999888888888888888888555556666665526777******999 PP

                          MFS_1 339 glfn.tagslgg 349
                                    g+   +a+s+ g
  gi|121639394|ref|YP_979618.1| 380 GVGYaLANSVFG 391
                                    998866666555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.076
                          MFS_1 143 llasslg.....Wravfyilaivsllafvlfllllpeepp 177
                                    l++++l         + y+ a +++ +  ++++++  ++ 
  gi|121639394|ref|YP_979618.1| 396 LIYQALKerdqvPMFIAYVTACIAVSL--IVYVFFIKNKA 433
                                    333333354432222233333333333..55566665555 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   4.6e-05      0.21      34     106 ..      59     130 ..      39     141 .. 0.75
   2 ?    3.0   1.1     0.025   1.1e+02      46      90 ..     176     220 ..     158     263 .. 0.73
   3 !   10.9   6.1   8.4e-05      0.38      27     105 ..     279     354 ..     243     363 .. 0.69
   4 ?    0.9   0.3      0.11     5e+02       8      51 ..     378     422 ..     372     437 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                        DUF3792  34 ekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllslli.kksgsafslkllikllllll 106
                                    ++v+ ++i++++++   +g++++g+ a+++g    l + + +++ + l+  l+ ++s+    +++ i l+l+ l
  gi|121639394|ref|YP_979618.1|  59 STVYVYAIFAVTFVTRPVGSWFFGRFADRRGRRAALTFSVSLMAACSLIVALVpSRSSI--GVAAPILLILCRL 130
                                    566677888888888899***********************999988888888344444..4444455555543 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.025
                        DUF3792  46 ilsvfigGflagkkakkkgllnGllvGllyflillllsllikksg 90 
                                    +  ++i ++++  +  + g+  G++vG    ++++ l   + +s 
  gi|121639394|ref|YP_979618.1| 176 FTLLVILAVFTREQVHEFGWRIGFAVGGGAAIVVFWLRRTMDESL 220
                                    556678889999999999*********999999887777664444 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 8.4e-05
                        DUF3792  27 lyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllslli.kksgsafslklliklllll 105
                                    +   +++ + ++++ li+l++   igG+++ k+ +k  ll+ ++ Gl+y+ +  l+++l  ++s ++    ll+++  ++
  gi|121639394|ref|YP_979618.1| 279 YGSQAMTATWINLVGLILLMMLQPIGGMISDKIGRKPLLLWFGVGGLIYTYV--LVTYLPeTRSPTM--SFLLVAVGYVI 354
                                    334678899999999******99*************************9999..5666662333332..22333333333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.11
                        DUF3792   8 gllialvitlilllilalllyftslsekvlsililiili.lsvfi 51 
                                    g++++++++  ++   a l+y+   + ++++++i ++++ ++v +
  gi|121639394|ref|YP_979618.1| 378 GVGVGYALANSVFGGTAPLIYQALKERDQVPMFIAYVTAcIAVSL 422
                                    566666666666666666666665555556555544443033322 PP

>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.7   0.00078       3.5       5      56 ..      63     113 ..      60     133 .. 0.72
   2 ?   10.0   0.1   0.00016      0.73      42      84 ..     174     216 ..     161     217 .. 0.92
   3 ?   -2.0   0.1      0.91   4.1e+03      78      96 ..     245     265 ..     241     268 .. 0.64
   4 ?   -2.7   0.1       1.5   6.7e+03      63      76 ..     286     299 ..     262     304 .. 0.57
   5 ?   -1.6   0.0      0.68     3e+03      31      46 ..     342     357 ..     316     394 .. 0.60
   6 ?    3.4   0.1      0.02        88      23      57 ..     398     432 ..     376     444 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00078
                           AzlD   5 illmalvtyltRylplllfrrlklppwlqrllryvPiavLaaliapellaet 56 
                                    + ++++vt++tR ++ ++f+r   +++ +r+  + +++++aa  +   l + 
  gi|121639394|ref|YP_979618.1|  63 VYAIFAVTFVTRPVGSWFFGRFA-DRRGRRAALTFSVSLMAACSLIVALVPS 113
                                    56899****************88.6777777777788888876555544453 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                           AzlD  42 avLaaliapellaetgklsaslglarllaalvavlvalltrnl 84 
                                    a +++l++ ++++ ++ +++ + +   +++ +a++v++l+r +
  gi|121639394|ref|YP_979618.1| 174 AQFTLLVILAVFTREQVHEFGWRIGFAVGGGAAIVVFWLRRTM 216
                                    66899***********************************975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.91
                           AzlD  78 alltrn..lllsilvGmavya 96 
                                    ++++     +l++l+G+++++
  gi|121639394|ref|YP_979618.1| 245 HYWKPLllCFLVTLGGTVAFY 265
                                    566653124678888888886 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.5
                           AzlD  63 lglarllaalvavl 76 
                                      + +l+++++ ++
  gi|121639394|ref|YP_979618.1| 286 ATWINLVGLILLMM 299
                                    25555555555444 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 0.68
                           AzlD  31 wlqrllryvPiavLaa 46 
                                     +  ll +v++ +L+ 
  gi|121639394|ref|YP_979618.1| 342 TMSFLLVAVGYVILTG 357
                                    4444444444444443 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.02
                           AzlD  23 frrlklppwlqrllryvPiavLaaliapellaetg 57 
                                     + lk  + +  ++ yv +++ + li++ ++ +++
  gi|121639394|ref|YP_979618.1| 398 YQALKERDQVPMFIAYVTACIAVSLIVYVFFIKNK 432
                                    44556667777788899999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2903.08
//
Query:       gi|121639395|ref|YP_979619.1|  [L=98]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-30  103.9  15.4    4.6e-30  103.8  15.4    1.0  1  PE             PE family
  ------ inclusion threshold ------
       0.22   12.0   9.2       0.27   11.7   9.2    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8  15.4   5.1e-34   4.6e-30       5      93 .]       4      92 ..       1      92 [. 0.98

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 5.1e-34
                                   XX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  5 vvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaaaags 86
                                   +++Pe+laaaa++l ++g++l+a naaaa ptt+v+++aaDeVS   A++f +ha++yq++sa+aa  heqfv +la++a+s
  gi|121639395|ref|YP_979619.1|  4 TAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHAATYQTASAKAAVIHEQFVTTLATSASS 85
                                   79******************************************************************************** PP

                                   HHS--XX CS
                             PE 87 YaaaEaa 93
                                   Ya++Eaa
  gi|121639395|ref|YP_979619.1| 86 YADTEAA 92
                                   *****97 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   9.2     3e-05      0.27       6      95 ..       4      94 ..       1      96 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                  T7SS_ESX_EspC  6 sVdpdhlrelaakhdevaaeiasavaaa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLraAAaa 86
                                   + +p+ l ++a ++++  a++++++aaa ++++  v +    +++ +++ ++   a+ ++a ++ a  ++++ + L ++A  
  gi|121639395|ref|YP_979619.1|  4 TAQPEMLAAAAGELRSLGATLKASNAAAaVPTTGVVPPAADEVSLLLATQFRTHAATYQTASAKAAVIHEQFVTTLATSASS 85
                                   789********************9999978888889999999**************************************** PP

                  T7SS_ESX_EspC 87 YeatDeeaa 95
                                   Y +t+ ++a
  gi|121639395|ref|YP_979619.1| 86 YADTEAANA 94
                                   ****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 721.85
//
Query:       gi|121639396|ref|YP_979620.1|  [L=393]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-56  190.7  24.8    1.7e-56  190.7  24.8    2.6  2  PPE       PPE family
    3.8e-15   56.6  13.1    3.8e-15   56.6  13.1    5.0  2  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7  24.8   1.9e-60   1.7e-56       1     157 [.       6     162 ..       6     163 .. 0.99
   2 ?    1.1   0.4     0.042   3.8e+02      58      89 ..     255     286 ..     223     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 1.9e-60
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    alpPE+nsa++yaGpgs++l+aAa+ Wd++a++l saa++++sv+ +l+ ++W G+s+  maaaa py+aW+s +a qa+
  gi|121639396|ref|YP_979620.1|   6 ALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGSWIGSSAGLMAAAASPYVAWMSVTAGQAQ 85 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                     +Aaq+++aaaaYe+A+  +vpp++ia+nr+el++l+atn++GqntpaI+a+ a+y++mw qda+am++Y+a++a+a
  gi|121639396|ref|YP_979620.1|  86 LTAAQVRVAAAAYETAYRLTVPPPVIAENRTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATA 162
                                    *************************************************************************9987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.042
                                    HHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  58 saamaaaaapylaWLsaaaaqaeeaAaqaeaa 89 
                                      +m++    +l+ L+ aaaqa e+Aa+  + 
  gi|121639396|ref|YP_979620.1| 255 GVSMTNTLHSMLKGLAPAAAQAVETAAENGVW 286
                                    45788888889999999999999999987665 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -28.9  35.3         2   1.8e+04      69      69 ..     103     103 ..      16     307 .. 0.71
   2 !   56.6  13.1   4.2e-19   3.8e-15       1      79 [.     309     388 ..     309     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: -28.9 bits;  conditional E-value: 2
                       PE_PPE_C  69 r 69 
                                    r
  gi|121639396|ref|YP_979620.1| 103 R 103
                                    2 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 4.2e-19
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaa.aaaaaagaalggmPlaaagaggaaggaaprygfrptvmpr 79 
                                    +A lG+Aa+vG+LSVPp+Waaa++a+++aa+al+ t  + aa+ a+g++lgg+Pl+ + ++g++ ++a+r+  r+  +pr
  gi|121639396|ref|YP_979620.1| 309 AANLGRAASVGSLSVPPAWAAANQAVTPAARALPLTSLTsAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPR 388
                                    69*******************************888765155567778888****9999999989************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3012.76
//
Query:       gi|121639397|ref|YP_979621.1|  [L=433]
Description: hypothetical protein BCG_3542 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   63.5   2.3    2.9e-17   63.5   2.3    1.8  2  Patatin   Patatin-like phospholipase
  ------ inclusion threshold ------
      0.041   13.9   0.1       0.16   12.1   0.0    1.9  2  DUF4128   Bacteriophage related domain of unknown function


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   2.3   3.2e-21   2.9e-17      23     203 ..      49     257 ..      34     258 .. 0.68
   2 ?   -1.1   0.0       0.2   1.8e+03      79     110 ..     342     373 ..     290     407 .. 0.53

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 3.2e-21
                        Patatin  23 elgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdl..................lirelaanlaarls 84 
                                    + + ++di+sGtSaG+i+a+lla+ r  +     +r+l+l++ +   l                  +   la++l+++ +
  gi|121639397|ref|YP_979621.1|  49 DMVVDVDILSGTSAGGINAALLASSRVTGSDLGGIRDLWLDLGALTELlrdprdkktpsllygderIFAALAKRLPKLAT 128
                                    77899***************************************999655556666666666666544444444444444 PP

                        Patatin  85 gllgkgglfd...aealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglytedddd 161
                                    g++ ++++ +   +++ + +++++l +++++r++  +g+l                  +  +++   ++ + +  +++d+
  gi|121639397|ref|YP_979621.1| 129 GPFPPTTFPEaarTPSTTLYITTTLLAGETSRFTDSFGTL------------------VQDVDRRGLFTFTETDLARPDT 190
                                    4444444332000233333334555555666666666655..................7888888888888888899999 PP

                        Patatin 162 dvdladavraSsafPglfppvsl........dge.................lyvDGGilsNvPilaa 203
                                    +  la a+r S++fP++f+p  l        +ge                 +  DGG+l+N Pi ++
  gi|121639397|ref|YP_979621.1| 191 APALALAARSSASFPLAFEPSFLpftkgtakKGEvparpamapftsltrphWVSDGGLLDNRPIGVL 257
                                    ******************77777666555552224444444444444555688**********9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                        Patatin  79 laarlsgllgkgglfdaealrellrkvladkt 110
                                    la++   l+++++l+++  l+++ ++  ++++
  gi|121639397|ref|YP_979621.1| 342 LAELAATLRNGTRLLTPSLLTDYRTREATKQA 373
                                    33333333333333333333333333333333 PP

>> DUF4128  Bacteriophage related domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.16       2      56 ..     115     168 ..     114     205 .. 0.86
   2 ?   -1.2   0.0      0.22     2e+03      83     102 ..     343     362 ..     333     408 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                        DUF4128   2 iraalkarlealakapalpvawpnvkftpptgepYLrvsvvpadtepltlggddd 56 
                                    i aal++rl +la  p +p+  p  + tp t+  Y+  +++ ++t + t ++++ 
  gi|121639397|ref|YP_979621.1| 115 IFAALAKRLPKLATGPFPPTTFPEAARTPSTTL-YITTTLLAGETSRFTDSFGTL 168
                                    789**********99*****************9.***********9988665544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.22
                        DUF4128  83 deiaalFpdglrlaegglvv 102
                                    +e+aa + +g+rl    l  
  gi|121639397|ref|YP_979621.1| 343 AELAATLRNGTRLLTPSLLT 362
                                    56666666666665333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3118.92
//
Query:       gi|121639398|ref|YP_979622.1|  [L=348]
Description: hypothetical protein BCG_3543 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   33.5   4.2    9.9e-08   31.4   4.2    1.9  1  DUF3376   Protein of unknown function (DUF3376)
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.11   12.4   0.0    1.4  1  GFRP      GTP cyclohydrolase I feedback regulatory protein (G


Domain annotation for each model (and alignments):
>> DUF3376  Protein of unknown function (DUF3376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   4.2   1.1e-11   9.9e-08     372     494 ..       1     118 [.       1     190 [. 0.75

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-11
                        DUF3376 372 mWGRLDGAerlvraLldeetkprRlvllreaqraige.......lreaLae..............vaaaPaarel..... 425
                                    mWGRLDGA++lv +Lld    prR  ++    +  +        +  +L+e               ++++ a+ l     
  gi|121639398|ref|YP_979622.1|   1 MWGRLDGAGWLVHVLLD----PRRVRWIVGERADTNGpqsgaqwFLGKLKElgapdfpspgyplpAVGGGPAQHLtedml 76 
                                    9****************....99888763322222223468999555555544457777777775333333333323334 PP

                        DUF3376 426 LdelralletvaqslvgkdkadteskelrafledpdaPvaprlpetatwvavGieravdivakelsela 494
                                    Ldel                          fl+dp +P +++ p ta w +   +    ++++el++la
  gi|121639398|ref|YP_979622.1|  77 LDEL-------------------------GFLDDPAKPLPASIPWTALWLSQAWQQ--RVLEEELDGLA 118
                                    4555.........................8************************98..9********98 PP

>> GFRP  GTP cyclohydrolase I feedback regulatory protein (GFRP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05      0.11      30      71 ..     182     223 ..     161     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                           GFRP  30 eLgaklrkvlgnkfkeylvedpprvvLnkLekkGykvvamtg 71 
                                    +  a+    +g+ ++  +v +pp + L  L   Gy+vv+ t+
  gi|121639398|ref|YP_979622.1| 182 KAAATAAGAAGSVRQLPSVLKPPLITLRTLTLSGYRVVSLTK 223
                                    4455566677888999999********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2456.37
//
Query:       gi|121639399|ref|YP_979623.1|  [L=497]
Description: hypothetical protein BCG_3544c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.9e-104  348.1   0.0   1.1e-103  346.6   0.0    1.7  2  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
      2e-35  121.9   0.0    3.3e-35  121.2   0.0    1.4  1  DUF1298         Protein of unknown function (DUF1298)


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.6   0.0  1.3e-107  1.1e-103       1     264 []       8     298 ..       8     298 .. 0.99
   2 ?   -1.6   0.0       0.2   1.8e+03     182     216 ..     343     378 ..     310     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 346.6 bits;  conditional E-value: 1.3e-107
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    L+p+D++fl++es++t+mhvgal++++pp +ga+++llr+l+++++++e ++p++ + +++e l++++++Wv+d++fDld
  gi|121639399|ref|YP_979623.1|   8 LGPQDMFFLYSESSTTMMHVGALMPFTPP-SGAPPDLLRQLVDESKASEVVEPWSLRLSHPELLYHPTQSWVVDDNFDLD 86 
                                    789**************************.************************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yHvRr+al++PG+erel+ +vsrL+s++LD++rP+Wevh+iEGleggr+Ai++k+HH+liDG++g+k+lar+l++dp+d+
  gi|121639399|ref|YP_979623.1|  87 YHVRRSALASPGDERELGIPVSRLHSHALDLRRPPWEVHFIEGLEGGRFAIYIKMHHSLIDGYTGQKMLARSLSTDPHDT 166
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdr..srtqlrasg..................alvglvaglgkvlgsvagvvssagrlleaal....... 213
                                    ++p ++++p+++r  ++tq++++g                   l glv+g+g+vlgsvag+ +s+++l++a++       
  gi|121639399|ref|YP_979623.1| 167 THPLFFNIPTPGRspADTQDSVGGgliagagnvldglgnvvrGLGGLVSGVGSVLGSVAGAGRSTFELTKALVnaqlrsd 246
                                    ************999999**9999************************************************9******* PP

                 WES_acyltransf 214 .earslvlpfaaprtplntplsraRrfaaaslpLadvkavakalgvtiNDvv 264
                                     e+r+lv +++ap+++lnt++sr+Rrfa++++pL+++ka+ +++++tiNDv+
  gi|121639399|ref|YP_979623.1| 247 hEYRNLVGSVQAPHCILNTRISRNRRFATQQYPLDRLKAIGAQYDATINDVA 298
                                    **************************************************95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.2
                 WES_acyltransf 182 galvglvaglgkvlgsvagvvssagrlleaal.ear 216
                                     +l++l   +   ++++a+v++s++ + ++++  ++
  gi|121639399|ref|YP_979623.1| 343 TILATLGTDVADPVQRLAAVTASTRAAKAQLRsMDK 378
                                    356666666666777777777777666666664333 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   3.7e-39   3.3e-35       2     144 ..     338     486 ..     337     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 3.7e-39
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl.......lsnttlviS 74 
                                    GN ++++l+ L++d+adP++rl++++++++++K +l+++ + ++l++ ++ l+a+++ +l++ l       +  ++l++S
  gi|121639399|ref|YP_979623.1| 338 GNAVATILATLGTDVADPVQRLAAVTASTRAAKAQLRSMDKDAILAY-SAALMAPYGVQLASTLsgvkppwPYTFNLCVS 416
                                    9**********************************************.9999999999998888888999999******* PP

                        DUF1298  75 NvpGPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    NvpGP++ lyl G++++a ypv++++++qaln+t++Syag+l++g+++++d++p++q+l+ +  eal++l
  gi|121639399|ref|YP_979623.1| 417 NVPGPEDVLYLRGSRMEASYPVSLVAHSQALNVTLQSYAGTLNFGFIGCRDTLPHLQRLAVYTGEALDQL 486
                                    *******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3970.51
//
Query:       gi|121639400|ref|YP_979624.1|  [L=229]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-60  203.5  25.3    3.1e-60  203.3  25.3    1.0  1  SfLAP          Sap, sulfolipid-1-addressing protein
  ------ inclusion threshold ------
       0.43   10.2   2.0        1.3    8.5   0.2    2.2  2  Saf_2TM        SAVED-fused 2TM effector domain
       0.72   10.2   4.1        7.9    6.8   0.1    2.8  4  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
        8.8    6.0   9.2       0.67    9.6   2.6    2.3  2  Tetraspanin    Tetraspanin family


Domain annotation for each model (and alignments):
>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3  25.3     7e-64   3.1e-60       1     214 []      18     227 ..      18     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 7e-64
                          SfLAP   1 llvlAlvvalsPlrlgvavlllsrprpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlll 80 
                                    l++lAlv+alsPl++++avl++++p+p++++laFl+gwl++l+++++++++++++l+ g+s++ ++++++l++vlG++l+
  gi|121639400|ref|YP_979624.1|  18 LVPLALVIALSPLSVIPAVLVVHSPQPRPSSLAFLGGWLLGLAVVTAVFVAASGALG-GLSTTSPAWASWLRVVLGSALI 96 
                                    799******************************************************.999999**************** PP

                          SfLAP  81 llaaveavrrpkassrselprllsrleslleggalwvAlvlgllsakplllylaalaaigasgasvgtqvvalvvFvvva 160
                                    +++++++++r   ++++e+p +++ ++s+++++a +v++vl+++++++l++++aa++aig+ g+ ++ +++ +++F ++a
  gi|121639400|ref|YP_979624.1|  97 VFGVLRWLTR---HRHTEMPGWMRAFASFTPARAGLVGAVLVVVRPEVLIICAAAGLAIGSGGHGAAGSWIYTAFFAMLA 173
                                    **********...******************************************************************* PP

                          SfLAP 161 lavveipllaylvapertqavlerlkdwlrsnrrlilavilgvvGllllakGls 214
                                    +++v+ip+lay++a++r+++ lerlkdw+++n++ ++a+il+v+Gllll++G++
  gi|121639400|ref|YP_979624.1| 174 ASTVAIPILAYVAAGDRLDDSLERLKDWMEKNHAGMVAAILVVIGLLLLYNGVH 227
                                    ****************************************************96 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0003       1.3      60      88 ..      77     104 ..      48     118 .. 0.70
   2 ?    0.9   0.1     0.068     3e+02      51      87 ..     188     223 ..     159     227 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0003
                        Saf_2TM  60 sseipeivlaiilvigvllivvGavllil 88 
                                    s  +p++ +++ +v+g++liv+G vl +l
  gi|121639400|ref|YP_979624.1|  77 STTSPAWASWLRVVLGSALIVFG-VLRWL 104
                                    33479******************.55554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.068
                        Saf_2TM  51 ggslevsfssseipeivlaiilvigvllivvGavlli 87 
                                    g++l++s++  +  ++    + +++ +l+v+G++ll+
  gi|121639400|ref|YP_979624.1| 188 GDRLDDSLERLK-DWMEKNHAGMVAAILVVIGLLLLY 223
                                    555555555444.122223334566666666666655 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.34   1.5e+03      67      83 ..      55      71 ..      13      92 .. 0.53
   2 ?    3.6   0.4     0.018        79      35      56 ..      89     110 ..      32     124 .. 0.72
   3 ?    3.3   0.1     0.023     1e+02      35      58 ..      89     112 ..      82     137 .. 0.78
   4 ?    6.8   0.1    0.0018       7.9      14      47 ..     162     222 ..     157     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHHHH CS
                  Cytochrom_B_C 67 vllallvvsfvvLgylG 83
                                   +ll l vv++v+++  G
  gi|121639400|ref|YP_979624.1| 55 WLLGLAVVTAVFVAASG 71
                                   33344444444333333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                                    HHHHHHHHGGGCHHHH---SSS CS
                  Cytochrom_B_C  35 vamgaaivilfllpwldrskvk 56 
                                    v++g a++++ +l wl r++ +
  gi|121639400|ref|YP_979624.1|  89 VVLGSALIVFGVLRWLTRHRHT 110
                                    4556666666666666665544 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.023
                                    HHHHHHHHGGGCHHHH---SSSSS CS
                  Cytochrom_B_C  35 vamgaaivilfllpwldrskvksi 58 
                                    v++g a++++ +l wl r++ +++
  gi|121639400|ref|YP_979624.1|  89 VVLGSALIVFGVLRWLTRHRHTEM 112
                                    678888889999999988876544 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0018
                                    -GGGHHHHHHHHCSS...........................SHHHHHHHHHHHHHGGGCH CS
                  Cytochrom_B_C  14 eWYflpfYaiLraip...........................akllGvvamgaaivilfll 47 
                                     W +++f+a+L a                             ++ +G+va +  ++ l+ll
  gi|121639400|ref|YP_979624.1| 162 SWIYTAFFAMLAASTvaipilayvaagdrlddslerlkdwmeKNHAGMVAAILVVIGLLLL 222
                                    69*********99644455666777777777777777777777888888888777777665 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.9     0.014        63      13      66 ..      55     101 ..      48     105 .. 0.72
   2 ?    9.6   2.6   0.00015      0.67       7     129 ..      83     204 ..      77     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.014
                                    XXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Tetraspanin  13 wligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgfl 66 
                                    wl+g++++   v +      aa  +l   s+++pa++++l +v+G++l+++g+l
  gi|121639400|ref|YP_979624.1|  55 WLLGLAVVTA-VFV------AASGALGGLSTTSPAWASWLRVVLGSALIVFGVL 101
                                    6666666655.333......44555566688999999999******99999975 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                                    XXXXXXXXXXXXXXXXXXXXXX...XXX.....................XXXXXX...XXXXXXXXX.XXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxxxxxxxxx RF
                    Tetraspanin   7 ffnllfwligivllavGvwlrl...khaeaalacllsesaedpailaillivvGv...llfllgflG.cigalkenkcll 79 
                                    + ++l +++g +l+++Gv  +l   +h+e      + +s +++++  ++ ++v v   +l++ + +G  ig+        
  gi|121639400|ref|YP_979624.1|  83 WASWLRVVLGSALIVFGVLRWLtrhRHTEMPGWMRAFASFTPARAGLVGAVLVVVrpeVLIICAAAGlAIGSGGHGAAGS 162
                                    678999***********766667785555544444455555555554555555555689999999997799********* PP

                                    XXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Tetraspanin  80 ltfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldl 129
                                    +++  +  +l +  +a+ il++v   ++       +++++ ++++d+ + 
  gi|121639400|ref|YP_979624.1| 163 WIYTAFFAMLAASTVAIPILAYVAAGDR-------LDDSL-ERLKDWMEK 204
                                    ***********************99995.......55555.455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1608.14
//
Query:       gi|121639401|ref|YP_979625.1|  [L=496]
Description: hypothetical protein BCG_3546c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-12   45.2  12.1    2.1e-11   43.4  12.1    2.1  1  DUF2510   Protein of unknown function (DUF2510)


Domain annotation for each model (and alignments):
>> DUF2510  Protein of unknown function (DUF2510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4  12.1   1.2e-15   2.1e-11       1      34 [.      11      43 ..      11      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-15
                        DUF2510  1 pGWYpDPsgtpgllRyWDGarWTehtapapaapp 34
                                   +GWY DP+g+ g +RyWDG rWT+h +p+p+ap+
  gi|121639401|ref|YP_979625.1| 11 AGWYTDPDGSAG-QRYWDGDRWTRHRRPNPSAPR 43
                                   8***********.*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3609.17
//
Query:       gi|121639402|ref|YP_979626.1|  [L=220]
Description: hypothetical protein BCG_3547c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-23   82.9   0.1    2.1e-23   82.2   0.1    1.3  1  Lipoprotein_21  LppP/LprE lipoprotein
  ------ inclusion threshold ------
       0.03   14.5   2.1       0.05   13.8   2.1    1.4  1  DUF4381         Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> Lipoprotein_21  LppP/LprE lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.1   2.3e-27   2.1e-23       1      87 []     118     204 ..     118     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 2.3e-27
                 Lipoprotein_21   1 sgydpcaaLswvvistegatasspqqallFhdgeflGtatpepyasip.rvlrsdddtVtVeYrwykpddplccpsgtat 79 
                                    s+ydpca+Ls+v++++++at+ssp+qal+Fh+g+f+Gtatp++y++++    +s++d V++ Yr +++++  c++   + 
  gi|121639402|ref|YP_979626.1| 118 SNYDPCADLSAVLVTVQDATNSSPDQALMFHRGTFVGTATPRAYPFTNlIGPASTNDIVVLSYR-TRQSCDGCQDGILTI 196
                                    69*********************************************98889999*********.6778889******** PP

                 Lipoprotein_21  80 vtFrwdgd 87 
                                    v F w+gd
  gi|121639402|ref|YP_979626.1| 197 VGFAWRGD 204
                                    ******97 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.1   5.6e-06      0.05       5      43 ..      21      62 ..      20     119 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-06
                        DUF4381  5 DihlPepvswwPpapGwwlllaalll.llllvlalwllr..r 43
                                   D   P+p + wP a+   l+++a+++ +++++++++++r   
  gi|121639402|ref|YP_979626.1| 21 DTTPPAPGGSWPTAWLVALVVLACVAaAVVAYAGMHRVRpgA 62
                                   66779999******8877777777775555555555555321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1790.71
//
Query:       gi|121639403|ref|YP_979627.1|  [L=512]
Description: protein cpsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-43  146.7   0.0    1.1e-42  145.8   0.0    1.5  1  LytR_cpsA_psr  Cell envelope-related transcriptional attenuat
    3.6e-11   43.9   0.3    3.6e-11   43.9   0.3    2.6  3  LytR_C         LytR cell envelope-related transcriptional att
  ------ inclusion threshold ------
        3.4    8.2   9.3       0.43   11.1   0.6    2.4  2  Alpha_GJ       Alphavirus glycoprotein J


Domain annotation for each model (and alignments):
>> LytR_cpsA_psr  Cell envelope-related transcriptional attenuator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   0.0   1.8e-46   1.1e-42       1     151 [.     109     281 ..     109     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 1.8e-46
                                    --SEEEEEEEEGGGTEEEEEEE-TTBEE-----.......--...---EES-TTTTT.................-HHHHH CS
                  LytR_cpsA_psr   1 rsDtimlvtvnakkkkvklvSipRDtlveipgg....eskat...gekkinsayalg.................gaellv 56 
                                    +++t++lv+v a + kv+++SipRD +v ++g+    + k++   g +k++ a++l+                 ++++++
  gi|121639403|ref|YP_979627.1| 109 NTNTLILVHVGA-DGKVVAFSIPRDDWVPFTGVpgynHIKIKeayGLTKQYVAEQLAnqgvsdrkeletrgreaARAATL 187
                                    69*********9.999**************977554533333445777777777777999**********9*99999*** PP

                                    HHHHHHHTS---EEEEE-HHHHHHHHHHHT---B--------------------B---HHHHHH-------------SHH CS
                  LytR_cpsA_psr  57 ktvekllginidyYvevdfegfaklvdalgGvevdvkedvkdkeeselklkaGeqkldGeqalayvRfRkddeegDlgRi 136
                                    ++v++l+g++idy++e++++gf++l+++lgGv+v+++++v+d+  s+++++aG+q+l++ qala+vR+R+++++gDl+R+
  gi|121639403|ref|YP_979627.1| 188 RAVRSLTGVPIDYFAEINLAGFYDLAQTLGGVDVCLNHAVYDS-YSGADFPAGRQRLNAAQALAFVRQRHGLDNGDLDRT 266
                                    ****************************************997.************************************ PP

                                    HHHHHHHHHHHHTT- CS
                  LytR_cpsA_psr 137 krQqqvleallkklk 151
                                    +rQq++l++++++l+
  gi|121639403|ref|YP_979627.1| 267 HRQQAFLSSVMRELQ 281
                                    ************987 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.73   4.4e+03      19      31 ..     159     172 ..     153     218 .. 0.68
   2 ?   -2.9   0.0       2.3   1.4e+04      43      65 ..     349     362 ..     331     372 .. 0.55
   3 !   43.9   0.3     6e-15   3.6e-11       3      84 ..     379     463 ..     377     464 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.73
                         LytR_C  19 vadaLeerGf.tvg 31 
                                    va++L+++G  +  
  gi|121639403|ref|YP_979627.1| 159 VAEQLANQGVsDRK 172
                                    77888888863333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                         LytR_C  43 ttivyreaaaaaakalaaalglg 65 
                                    t i++         ++aaa+g +
  gi|121639403|ref|YP_979627.1| 349 TAIRA---------EVAAAFGSA 362
                                    44443.........788888744 PP

  == domain 3  score: 43.9 bits;  conditional E-value: 6e-15
                         LytR_C   3 kVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee....ttivyreaaaaaakalaaalglgelqedsvkdas.. 76 
                                     V+V+N+ ++sGlA++v+ aL +rG+t+g+v + ++        t i y+++a+ +a+ +a++lg+ + ++ + ++a+  
  gi|121639403|ref|YP_979627.1| 379 VVDVVNAGSISGLASQVSGALLKRGYTAGQVRDRES---GdpftTAIEYGAGAETDAQNVADLLGIDAPNHPDPAVAPgh 455
                                    59****************************775333...234569999*666668**********888566555555589 PP

                         LytR_C  77 vtvvlGkd 84 
                                    ++v++ ++
  gi|121639403|ref|YP_979627.1| 456 IRVTVDTN 463
                                    88888666 PP

>> Alpha_GJ  Alphavirus glycoprotein J
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   7.2e-05      0.43      54     110 ..     352     403 ..     337     415 .. 0.78
   2 ?    0.6   2.5      0.13   7.6e+02      21      76 ..     447     502 ..     432     510 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.2e-05
                       Alpha_GJ  54 aastiaatvgapptdstvaaetPgpflptdfalPlviGGlcaltlaamGaGallrrc 110
                                     a  +aa  +appt  t+aa  P p+  +d+     i Gl     a+  +Gall+r 
  gi|121639403|ref|YP_979627.1| 352 RAEVAAAFGSAPPTSQTAAAAKPNPSTVVDVVNAGSISGL-----ASQVSGALLKRG 403
                                    4566788899********************9988888886.....566678888875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                       Alpha_GJ  21 pkaalatgttatvgaana.aavanatganatsaaaastiaatvgapptdstvaaetP 76 
                                    p+ a+a g    +  +n    +++ + a ats+  +st +   g  +td+t+ +++P
  gi|121639403|ref|YP_979627.1| 447 PDPAVAPGHIRVTVDTNFsLPAPDEATAAATST-ETSTYPLYGGGTTTDPTPDQGAP 502
                                    566666665544444444145666667777776.55677776777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3569.60
//
Query:       gi|121639404|ref|YP_979628.1|  [L=314]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-59  198.8   0.6    1.2e-58  198.4   0.6    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.8e-44  151.6   0.2    2.2e-44  151.3   0.2    1.1  1  adh_short        short chain dehydrogenase
    2.6e-18   66.6   0.5    3.9e-18   66.0   0.5    1.2  1  KR               KR domain
    0.00024   20.7   0.2    0.00054   19.5   0.0    1.6  2  Epimerase        NAD dependent epimerase/dehydratase family
    0.00037   19.7   0.0     0.0005   19.3   0.0    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0055   17.3   0.2      0.011   16.4   0.2    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.049   13.5   0.5      0.075   12.9   0.5    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.05   13.9   0.1      0.071   13.4   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.11   12.5   0.0       0.25   11.4   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.6   6.2e-62   1.2e-58       4     232 ..      55     287 ..      51     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 6.2e-62
                                    TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                   adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    sgIG+++A  l ++Ga v+++ +n ++ +++v+++++    ++   ++D+tdeeq  ++v+++++ +g+l+++v++ag +
  gi|121639404|ref|YP_979628.1|  55 SGIGKGVAAGLVAAGAAVMIVGRNPDKlAAAVKDIEALKTGAIgyEPADITDEEQTLRVVDAATAWHGRLHGVVHCAGGS 134
                                    8**************************8999999887544554669********************************** PP

                                    EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    ++  gp+++++ + ++r++d n++++++++k+a++ l++ g gs v +ss++a+ +     ayg++K a+ ++++ +A e
  gi|121639404|ref|YP_979628.1| 135 QT-IGPITQIDSQAWRRTVDLNVNGTMYVLKHAAReLVRGGgGSFVGISSIAASNTHRWFGAYGVTKSAVDHMMKLAADE 213
                                    *9.********************************7666558************************************** PP

                                    HGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    lgp  +RvN++ pg+i+T+++  +++++el +  +  +pl r+g++e+va++a+fL+sd+as+itGq++ vDgG
  gi|121639404|ref|YP_979628.1| 214 LGPSWVRVNSIRPGLIRTDLVVPVTESPELSADYRVCTPLPRVGEVEDVANLAMFLLSDAASWITGQVINVDGG 287
                                    ************************************************************************** PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.3   0.2   1.1e-47   2.2e-44       3     192 ..      48     239 ..      46     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 1.1e-47
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvL 81 
                                     lvtG++sGIG+ +a  l+++Ga v++v+r+++kl++++k ++++    + + ++D+td+e++ ++v++a + +g+l+ +
  gi|121639404|ref|YP_979628.1|  48 YLVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKLAAAVKDIEALkTGAIGYEPADITDEEQTLRVVDAATAWHGRLHGV 127
                                    69*******************************************666677778************************** PP

                                    EE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  82 vnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    v++AG  +  gp+ ++++++w+r++++N++g++ + ++++++++++ +G+ v +sS+a+ +   ++ aY+ +K av++++
  gi|121639404|ref|YP_979628.1| 128 VHCAGGsQTIGPITQIDSQAWRRTVDLNVNGTMYVLKHAARELVRGGGGSFVGISSIAASNTHRWFGAYGVTKSAVDHMM 207
                                    ******8889********************************************************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmakelre 192
                                    + +a+el p+ +rvn++ PGl++Td++ +++e
  gi|121639404|ref|YP_979628.1| 208 KLAADELGPSWVRVNSIRPGLIRTDLVVPVTE 239
                                    *************************9887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.5     2e-21   3.9e-18       2     163 ..      47     210 ..      46     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2e-21
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHHSS CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikaeep 80 
                                    tyl+tGG  g+G+ +a  l++ ga+ +++++R++ + ++    ++ +eal +  + + +aD++d+++  +++++++a ++
  gi|121639404|ref|YP_979628.1|  47 TYLVTGGGSGIGKGVAAGLVAAGAA-VMIVGRNPDKLAA---AVKDIEALKTgAIGYEPADITDEEQTLRVVDAATAWHG 122
                                    8**********************96.6789***444444...5666666644389************************* PP

                                    ---EEEE------.---TTT--HHHHHHHHTTTTHHHHH.HHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                             KR  81 pikGvihaAgvlr.dklleemtaedleqvlapKvkGawn.Lhelled...esldffvlfSSiagllgsagqanYaaaNaf 155
                                    +++Gv+h+Ag ++  +++++ +++++++ +   v+G+   L+++ ++        fv +SSia+   ++  ++Y  + + 
  gi|121639404|ref|YP_979628.1| 123 RLHGVVHCAGGSQtIGPITQIDSQAWRRTVDLNVNGTMYvLKHAARElvrGGGGSFVGISSIAASNTHRWFGAYGVTKSA 202
                                    **********998459********************9862566666666667789************************* PP

                                    HHHHHHHH CS
                             KR 156 lDalaeyr 163
                                    +D +++  
  gi|121639404|ref|YP_979628.1| 203 VDHMMKLA 210
                                    **999865 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.7e-07   0.00054       2     161 ..      49     215 ..      48     226 .. 0.82
   2 ?   -2.3   0.0       1.2   2.5e+03     215     240 ..     259     284 ..     257     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH....H.T-SEEE CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke....e.qpdavi 69 
                                    lVtG+   iG+ ++  l ++g  v+ + r++++ + a ++             +d+td++++ r+++     + + + v+
  gi|121639404|ref|YP_979628.1|  49 LVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKLAAAVKDIEalktgaiGYEPADITDEEQTLRVVDAatawHgRLHGVV 128
                                    8********************99999988877666655544478***998999*******766666642222567899** PP

                                    E--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                      Epimerase  70 hlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                    h+A+  ++++   +  ++ +++++ +++n   ++ k+ ++ l+  +  +  G +      ++t     +   +Y+++K a
  gi|121639404|ref|YP_979628.1| 129 HCAGgSQTIGPITQIDSQAWRRTVDLNVNGTMYVLKHAARELVRGGGGSFVGISSI--AASNT----HRWFGAYGVTKSA 202
                                    ****9*****999999999****************************999996665..33333....36689******** PP

                                    HHHHHHHHHHHHT CS
                      Epimerase 149 geklveayaaqyg 161
                                    ++++++ +a++ g
  gi|121639404|ref|YP_979628.1| 203 VDHMMKLAADELG 215
                                    ****998877765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHTT-STTEEEEE CS
                      Epimerase 215 veDvaeaillvlehvdagdkgeiyni 240
                                    veDva++ +++l   ++  +g+++n+
  gi|121639404|ref|YP_979628.1| 259 VEDVANLAMFLLSDAASWITGQVINV 284
                                    89**********99888888888886 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07    0.0005       2     167 ..      49     225 ..      48     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                    EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT....... CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel..... 76 
                                    lvtG+g  iG+ +   +++  +  ++++ r+  kl +  k++ e lk+  + +e     +d++d+e+  +++++      
  gi|121639404|ref|YP_979628.1|  49 LVTGGGSGIGKGVAAGLVAAGA-AVMIVGRNPDKLAAAVKDI-EALKTGAIGYE----PADITDEEQTLRVVDAAtawhg 122
                                    8*************99998876.5777888888888888887.45666677666....5666666655555543311133 PP

                                    T-SEEEE------H..HHHH...HSHHHHHHHHHHHHHHHHHHHHHTT-S....EEEEEEEGGGSS--...SHHHHHHHH CS
                Polysacc_synt_2  77 kvdvvfhaAAlKhV..Plve...enpleaiktNvlgtenvieaaieagvk....kvvliStDKAvnPt...nvmGatKrl 144
                                    + + v+h+A   +   P+ +   + +  +++ Nv gt+ v++ a +  v+    ++v iS+  A n      ++G+tK +
  gi|121639404|ref|YP_979628.1| 123 RLHGVVHCAGGSQTigPITQidsQAWRRTVDLNVNGTMYVLKHAARELVRggggSFVGISSIAASNTHrwfGAYGVTKSA 202
                                    5789*****8776434666522245678999*************99988644448******999987622268999**** PP

                                    HHHHHHHGGG--SSS--EEEEEE CS
                Polysacc_synt_2 145 aekllqalakeseekktkfvvvR 167
                                     + ++  +a+e + +  ++  +R
  gi|121639404|ref|YP_979628.1| 203 VDHMMKLAADELGPSWVRVNSIR 225
                                    ****9999988877666666666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   5.3e-06     0.011       7      48 ..      53      91 ..      49     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.3e-06
                                   TSH.HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                  F420_oxidored  7 aGn.mgealasgllaagaqpheivvansrnpekaeelaeelgv 48
                                   +G+ +g+++a gl+aag     ++++  rnp+k++++ +++++
  gi|121639404|ref|YP_979628.1| 53 GGSgIGKGVAAGLVAAG---AAVMIV-GRNPDKLAAAVKDIEA 91
                                   44339************...9***88.*********9999883 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   3.8e-05     0.075       6      46 ..      52      93 ..      49     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                                   --SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHH CS
                        3HCDH_N  6 GaGt.mGagiaavfasagleVvlvdiseealekalekieksl 46
                                   G G  +G+g+aa +++ag  V +v +++++l++a + ie+  
  gi|121639404|ref|YP_979628.1| 52 GGGSgIGKGVAAGLVAAGAAVMIVGRNPDKLAAAVKDIEALK 93
                                   555449*******************************99843 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.6e-05     0.071       4      66 ..      51     110 ..      48     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                    E--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH CS
                Sacchrp_dh_NADP   4 iGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal 66 
                                     G+  ++G++va  l++ +     +++++r+ +kl+a+++++   +  ai   ++++++  ++ 
  gi|121639404|ref|YP_979628.1|  51 TGGgSGIGKGVAAGLVAAGAA---VMIVGRNPDKLAAAVKDIEALKTGAIGYEPADITD-EEQT 110
                                    566247************986...******************77666666666666655.3333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.25       9      60 ..      42      93 ..      36     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                   ..TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET CS
                   Shikimate_DH  9 slkekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkgee 60
                                   s+++++ l+ G G  +++ va  L+a+g+  v++++R+ ++ ++ ++++++ +
  gi|121639404|ref|YP_979628.1| 42 SFQDRTYLVTGGGSgIGKGVAAGLVAAGAA-VMIVGRNPDKLAAAVKDIEALK 93
                                   5789999999999758999**********9.**********999888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2484.77
//
Query:       gi|121639405|ref|YP_979629.1|  [L=149]
Description: hypothetical protein BCG_3550 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-14   53.6   3.2    2.6e-14   53.6   3.2    1.5  2  DoxX      DoxX
    3.3e-08   33.6   1.9    4.7e-08   33.1   1.9    1.4  1  DoxX_2    DoxX-like family
    2.4e-05   24.3   2.5     0.0061   16.5   1.4    2.6  2  DoxD      TQO small subunit DoxD
  ------ inclusion threshold ------
        3.9    7.6   8.7        2.3    8.3   1.9    2.9  3  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   3.2   5.8e-18   2.6e-14       4      83 ..      11      89 ..       8      91 .. 0.91
   2 ?   -2.9   0.1       2.4   1.1e+04       8       8 ..     119     119 ..      99     129 .. 0.61

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 5.8e-18
                           DoxX  4 llRlllgvlfiahGlqkltgfgleg.taaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvatltv 83
                                    +Rll+g++f+  G+qk++   +++   + ++ +g+p+++++a l ++vE+v+g l+llGlltR+aA+ l++ +++a+++ 
  gi|121639405|ref|YP_979629.1| 11 CIRLLVGLVFLSEGIQKFM--YPDQlGPGRFERIGIPAATFFADLDGVVEIVCGTLVLLGLLTRVAAVPLLIDMVGAIVLT 89
                                   68*****************..455536678889*********************************************975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                           DoxX   8 l 8  
                                    l
  gi|121639405|ref|YP_979629.1| 119 L 119
                                    1 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   1.9   1.1e-11   4.7e-08       3      87 ..      13      96 ..      11     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.1e-11
                         DoxX_2  3 tvllalffllsGvakllraeevv.akfaqlgfp..ssfvrllGvvellgalgLllplvtaprltplAavglallmvgAiath 81
                                    +l+ l+fl +G+ k++ ++++    f+++g+p    f  l Gvve++++ ++ll+l     lt +Aav l++ mvgAi+  
  gi|121639405|ref|YP_979629.1| 13 RLLVGLVFLSEGIQKFMYPDQLGpGRFERIGIPaaTFFADLDGVVEIVCGTLVLLGL-----LTRVAAVPLLIDMVGAIVLT 89
                                   57999***********9998886269*****99523347789**************7.....9***************9854 PP

                         DoxX_2 82 .lrrgdp 87
                                    lr+ +p
  gi|121639405|ref|YP_979629.1| 90 kLRALQP 96
                                   3676666 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0     0.002       8.8       4      43 ..      11      49 ..       9      55 .. 0.78
   2 !   16.5   1.4   1.4e-06    0.0061      72     102 ..      55      85 ..      48     147 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                           DoxD  4 ilRlalgliflsagirkkvlkpakLdPnsssyvGgklief 43
                                   ++Rl +gl+fls gi k +  p +L P   + +G+   +f
  gi|121639405|ref|YP_979629.1| 11 CIRLLVGLVFLSEGIQKFMY-PDQLGPGRFERIGIPAATF 49
                                   79*************88665.5589888777777765555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-06
                           DoxD  72 tlvEiivGlllliGlltRlsslvafalalgi 102
                                    ++vEi+ G l+l+GlltR++++ ++   +g 
  gi|121639405|ref|YP_979629.1|  55 GVVEIVCGTLVLLGLLTRVAAVPLLIDMVGA 85 
                                    689*****************98765443332 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.1   4.6e+02      12      46 ..      12      23 ..       7      28 .. 0.61
   2 ?    8.3   1.9   0.00051       2.3       8      44 ..      53      88 ..      51      90 .. 0.83
   3 ?    0.7   0.1      0.12   5.4e+02      13      23 ..     117     127 ..      97     140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                        DUF2892 12 lrivvGlvllllallglsggwgwllglvGavlllt 46
                                   +r++vGlv                       +l +
  gi|121639405|ref|YP_979629.1| 12 IRLLVGLV-----------------------FLSE 23
                                   45555555.......................5444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                        DUF2892  8 ldRilrivvGlvllllallglsggwgwllglvGavll 44
                                   ld ++ iv+G ++ll++l++++++  +l  +vGa+ l
  gi|121639405|ref|YP_979629.1| 53 LDGVVEIVCGTLVLLGLLTRVAAV-PLLIDMVGAIVL 88
                                   678999***************776.777788888765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.12
                        DUF2892  13 rivvGlvllll 23 
                                    ++++Gl++ll+
  gi|121639405|ref|YP_979629.1| 117 SMLLGLIFLLW 127
                                    33444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1016.99
//
Query:       gi|121639406|ref|YP_979630.1|  [L=277]
Description: esterase/lipase lipF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-42  146.1   0.4    1.6e-42  145.8   0.4    1.1  1  Abhydrolase_3    alpha/beta hydrolase fold
    1.2e-09   37.5   0.0    1.6e-09   37.1   0.0    1.1  1  Say1_Mug180      Steryl acetyl hydrolase
    9.6e-05   23.1   6.5    0.00013   22.6   6.5    1.2  1  Abhydrolase_6    Alpha/beta hydrolase family
    0.00019   21.0   0.0    0.00053   19.5   0.0    1.7  2  Peptidase_S9     Prolyl oligopeptidase family
    0.00041   19.7   0.0    0.00067   19.0   0.0    1.3  1  Hydrolase_4      Serine aminopeptidase, S33
     0.0081   16.1   0.0      0.012   15.6   0.0    1.2  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.034   14.1   0.0    1.3  1  UPF0227          Uncharacterised protein family (UPF0227)
      0.026   13.5   0.0      0.042   12.8   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme
       0.06   13.5   0.0        0.1   12.7   0.0    1.3  1  Thioesterase     Thioesterase domain
      0.084   12.4   0.0        4.5    6.8   0.0    2.1  2  DLH              Dienelactone hydrolase family
       0.12   12.2   0.0       0.31   10.9   0.0    1.7  2  BTRD1            Bacterial tandem repeat domain 1


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   0.4   9.8e-46   1.6e-42       1     210 [.      16     222 ..      16     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 9.8e-46
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETH CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSa 80 
                                    ++y+HGG+fv++++++h ++++ l+  ++  v+ vdYrl P+h + +a++d+ +a++wl+++    g+ p++ivlaGdSa
  gi|121639406|ref|YP_979630.1|  16 VLYLHGGAFVMCGPNSHSRIVNALSGFAESPVLIVDYRLIPKHSLGMALDDCHDAYQWLRAR----GYRPEQIVLAGDSA 91 
                                    79***********************************************************9....8************* PP

                                    HHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS......GGGGGSTT CS
                  Abhydrolase_3  81 GGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp......eadrddpl 154
                                    GG la+a+a+r++ +   k+a++v i+P+++l   ++++++   +  ++++++++a+d+++  + +       + r + l
  gi|121639406|ref|YP_979630.1|  92 GGYLALALAQRLQCD-DEKPAAIVAISPLLQL--AKGPKQDHP-NIGTDAMFPARAFDALAAWVRAaaaknmVDGRPEDL 167
                                    ***********9998.689*********9966..667888544.446668888777775444333212212333333448 PP

                                    TSGGGCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                  Abhydrolase_3 155 aspllaedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                    ++pl +   s lpptl+ v + ++l ++++  a +l+aagv +e+++++g+ H f+
  gi|121639406|ref|YP_979630.1| 168 YEPLDH-IESSLPPTLIHVSGSEVLLHDAQLGAGKLAAAGVCAEVRVWPGQAHLFQ 222
                                    888866.4566******************************************996 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   9.9e-13   1.6e-09     123     239 ..      14     124 ..       3     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 9.9e-13
                    Say1_Mug180 123 pvllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvkskgfk..nvvvl 200
                                    +v+lylHGG f++   p + + + n    f + ++l++DY ++   ++s    l   ++   y++l  + g++  ++v+ 
  gi|121639406|ref|YP_979630.1|  14 RVVLYLHGGAFVM-CGPNSHSRIVNALSGFAESPVLIVDYRLIP--KHSLGMALD--DCHDAYQWLR-ARGYRpeQIVLA 87 
                                    79*********97.689999***********************9..677766666..*********9.88886558**** PP

                    Say1_Mug180 201 GdSaGGnlvLslllklsklnkvvlPkkaiaiSPWlnlti 239
                                    GdSaGG l L l  +l+  +    P  ++aiSP l+l+ 
  gi|121639406|ref|YP_979630.1|  88 GDSAGGYLALALAQRLQCDDE--KPAAIVAISPLLQLAK 124
                                    ************999876444..6*********999875 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   6.5   8.1e-08   0.00013       1     212 [.      16     224 ..      16     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.1e-08
                                    EEEE--GC.....G.....C.HHHHHHHHCCT....CEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT.....TTS CS
                  Abhydrolase_6   1 vlllHGagssassW.....l.vapLaallaag....vhvlapDlpGhGrsdpppldled.ladlaalldelaa...gggp 66 
                                    vl lHG+      +       +++++++l++     v  l++D++       p ++l   l+d++++ + l+a   ++ +
  gi|121639406|ref|YP_979630.1|  16 VLYLHGGA-----FvmcgpNsHSRIVNALSGFaespV--LIVDYR-----LIPKHSLGMaLDDCHDAYQWLRArgyRPEQ 83 
                                    56789866.....655543245566555555555447..999998.....667777777335669999999998888888 PP

                                    EEEEEETCHHHHHHHHHHCC........EE.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHH CS
                  Abhydrolase_6  67 vvlvGHSlGGalalaaapla......lvvg.vlldppptalpagllaaalelllallallrllawlsreplprlfladed 139
                                    +vl G S GG+lala+a  +      + ++ v+++p         l  +++ +++  ++  ++a++     +r f a  +
  gi|121639406|ref|YP_979630.1|  84 IVLAGDSAGGYLALALAQRLqcddekP-AAiVAISP---------LLQLAKGPKQDHPNIGTDAMFP----ARAFDALAA 149
                                    9**************555558866643.33588888.........5566666666666666666663....323333222 PP

                                    CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-C.....HHHHCHHCCCH.STTEEETCE...SSS-HHHH CS
                  Abhydrolase_6 140 adaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDp.....lvprllerlla.qagarlpvvlpgaGHlphle 212
                                         +a+   + + ++ + + p+++++  ++p+l++  g++       +   + +l+a    a++  v+pg  Hl++l+
  gi|121639406|ref|YP_979630.1| 150 --WVRAAAAKNMVDGRPEDLYEPLDHIESSLPPTLIHvSGSEVllhdaQLG--AGKLAAaGVCAEV-RVWPGQAHLFQLA 224
                                    ..4445555555566666667778888888888866433443321100333..3333333344555.8888888877764 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.3e-07   0.00053      44      83 ..      63     101 ..      53     124 .. 0.90
   2 ?   -1.7   0.0      0.99   1.6e+03     156     186 ..     189     219 ..     141     233 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.3e-07
                                    HHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH CS
                   Peptidase_S9  44 efdDfiaaaealakegyvdserlaitGgSyGGyltgaaln 83 
                                     +dD+ +a ++l ++gy  +e++++ G S+GGyl++a++ 
  gi|121639406|ref|YP_979630.1|  63 ALDDCHDAYQWLRARGYR-PEQIVLAGDSAGGYLALALAQ 101
                                    579*************97.****************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.99
                                    SS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                   Peptidase_S9 156 rvppaealklvaaLqkkgknvlllifpdegH 186
                                     v +  a   + +L  +g+ +++++ p++ H
  gi|121639406|ref|YP_979630.1| 189 EVLLHDAQLGAGKLAAAGVCAEVRVWPGQAH 219
                                    4444445555566667777777777777777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.1e-07   0.00067      55     118 ..      60     140 ..      51     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.1e-07
                    Hydrolase_4  55 fddyvdDlaafvekvkeehpel.plfllGhSmGGliallyllrypd...kvaglilsaPalkikakl............. 117
                                    +   +dD++ +++ ++++  +  +++l G S GG++al++++r +    k a+++ ++P+l++++               
  gi|121639406|ref|YP_979630.1|  60 LGMALDDCHDAYQWLRARGYRPeQIVLAGDSAGGYLALALAQRLQCddeKPAAIVAISPLLQLAKGPkqdhpnigtdamf 139
                                    556799**********77777669*****************55444445889*********9987655555555555543 PP

                    Hydrolase_4 118 k 118
                                    +
  gi|121639406|ref|YP_979630.1| 140 P 140
                                    3 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.2e-06     0.012       8      68 ..      69     132 ..      65     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                                    HHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS....SEEEEEEES--SB--SSEEEETTE CS
                         BAAT_C   8 eainyllrhpkvkkdkigllGiSkGgelalllasflk....kisavvlingsavvvegklvykde 68 
                                    +a+++l+ +     ++i l G S Gg lal+la +l+    k+ a+v+i++     +g++  + +
  gi|121639406|ref|YP_979630.1|  69 DAYQWLRAR-GYRPEQIVLAGDSAGGYLALALAQRLQcddeKPAAIVAISPLLQLAKGPKQDHPN 132
                                    799****99.6677**********************98888999****99987777777666555 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.034       2      82 ..      16     105 ..      15     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                        UPF0227   2 llYlHG..FdS.SPlshka..qllsqfiaedvlaielsvlklkedpqqalkeleklvaelgddn.....illvGssLGGy 71 
                                    +lYlHG  F    P+sh    + ls f ++ vl ++++ l +k++   al   + + + l+++      i+l G s GGy
  gi|121639406|ref|YP_979630.1|  16 VLYLHGgaFVMcGPNSHSRivNALSGFAESPVLIVDYR-LIPKHSLGMALDDCHDAYQWLRARGyrpeqIVLAGDSAGGY 94 
                                    69***96666579*999873234555666666666665.679999999999999988876655455566*********** PP

                        UPF0227  72 yatrlgerfgl 82 
                                    +a  l++r + 
  gi|121639406|ref|YP_979630.1|  95 LALALAQRLQC 105
                                    *******9765 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05     0.042      90     140 ..      82     133 ..      58     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                Chlorophyllase2  90 sklalsgHSrGgktafalalgkaktslkfsaligvdPvag.askskqtepki 140
                                    ++++l+g S+Gg+ a+ala   +  + k +a++++ P+   a+  kq +p+i
  gi|121639406|ref|YP_979630.1|  82 EQIVLAGDSAGGYLALALAQRLQCDDEKPAAIVAISPLLQlAKGPKQDHPNI 133
                                    5799****************9999999**********988344457777877 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05       0.1      68     100 ..      84     116 ..      73     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                    EEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEE CS
                   Thioesterase  68 yalfGhSlGgllAfevArqLesqGlavkslfli 100
                                     +l+G S+Gg+lA ++A++L+   +++++++ i
  gi|121639406|ref|YP_979630.1|  84 IVLAGDSAGGYLALALAQRLQCDDEKPAAIVAI 116
                                    689********************9999999987 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0028       4.5      77     119 ..      62     103 ..      52     158 .. 0.89
   2 ?    3.8   0.0     0.022        36     136     190 ..     170     222 ..     145     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                            DLH  77 kvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                      ldd ++a ++l++++ + ++++++ G   GG lal+la++ 
  gi|121639406|ref|YP_979630.1|  62 MALDDCHDAYQWLRARG-YRPEQIVLAGDSAGGYLALALAQRL 103
                                    5789999**********.999*******************986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                            DLH 136 eleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFa 190
                                    +l++++ +  p l+++ +       +  +  + +l+aa+v +e+ v+pg +H F 
  gi|121639406|ref|YP_979630.1| 170 PLDHIESSLPPTLIHVSGSEVLLHDA--QLGAGKLAAAGVCAEVRVWPGQAHLFQ 222
                                    56666666667777777766665555..57788999****************996 PP

>> BTRD1  Bacterial tandem repeat domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.31       9      32 ..      61      84 ..      59      92 .. 0.93
   2 ?   -3.4   0.0       5.7   9.2e+03      29      35 ..     182     188 ..     182     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                          BTRD1  9 GltaaqyqakfdklkakGYrpvhv 32
                                   G+  ++++ ++  l+a+GYrp ++
  gi|121639406|ref|YP_979630.1| 61 GMALDDCHDAYQWLRARGYRPEQI 84
                                   9999*****************875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.7
                          BTRD1  29 pvhvsgY 35 
                                    ++hvsg 
  gi|121639406|ref|YP_979630.1| 182 LIHVSGS 188
                                    79***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2085.75
//
Query:       gi|121639407|ref|YP_979631.1|  [L=107]
Description: hypothetical protein BCG_3552 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-22   78.1   0.1    4.9e-22   77.7   0.1    1.2  1  PadR          Transcriptional regulator PadR-like family
    1.9e-05   24.8   0.0    2.3e-05   24.5   0.0    1.2  1  HTH_34        Winged helix DNA-binding domain
    0.00087   19.9   0.0     0.0011   19.6   0.0    1.3  1  RTP           Replication terminator protein
     0.0055   16.6   0.0      0.016   15.1   0.0    1.8  2  MarR          MarR family
     0.0075   16.3   0.6     0.0086   16.2   0.6    1.2  1  Replic_Relax  Replication-relaxation
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.017   15.0   0.0    1.2  1  HxlR          HxlR-like helix-turn-helix
      0.041   14.4   0.1      0.084   13.4   0.1    1.7  1  HTH_27        Winged helix DNA-binding domain
      0.056   13.1   0.9       0.28   10.9   0.0    2.1  2  GntR          Bacterial regulatory proteins, gntR family
       0.13   10.6   0.0       0.15   10.4   0.0    1.1  1  DUF505        Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.1   2.4e-25   4.9e-22       1      75 []      13      83 ..      13      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.4e-25
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                   iL+++++++ +G ++++el+++  g +++s+G+lYp+L+rLe++gl++se++  ++g++r++Yr T+aGr++l+e
  gi|121639407|ref|YP_979631.1| 13 ILHHAADNEVHGAWLTQELSRH--G-YRVSPGTLYPTLHRLEADGLLVSEQRV-VDGRARRVYRATPAGRAALTE 83
                                   8*********************..9.9***********************998.6****************9975 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.2e-08   2.3e-05      21      79 ..      33      91 ..       9      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                         HTH_34 21 kealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                   +   +++ g L+  l+ Le+ g ++ +  +++++ r ++r Tp+Gr+a  +  +aL++l
  gi|121639407|ref|YP_979631.1| 33 RHGYRVSPGTLYPTLHRLEADGLLVSEQRVVDGRARRVYRATPAGRAALTEDRRALEEL 91
                                   45578999***********************************************9986 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.5e-07    0.0011       6      74 ..       5      69 ..       3     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.5e-07
                                   HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSS CS
                            RTP  6 qrAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklq 74
                                   qrA ++l++++ ++ ++ +g  l +el     + gy+ ++ ++y +lh l  dg+l  ++++ ++  ++
  gi|121639407|ref|YP_979631.1|  5 QRAAVRLHILHHAADNEVHGAWLTQEL----SRHGYRVSPGTLYPTLHRLEADGLLVSEQRVVDGRARR 69
                                   899**************9999877666....678**********************9988877554443 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.2e-06     0.016      28      57 ..      37      66 ..       8      67 .. 0.82
   2 ?   -1.7   0.0       1.5   2.9e+03      51      58 ..      80      87 ..      78      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.2e-06
                                   TS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                           MarR 28 gvskstvtrvldrLekkGlieRskspeDrR 57
                                    vs++t+  +l+rLe +Gl+ +++   D R
  gi|121639407|ref|YP_979631.1| 37 RVSPGTLYPTLHRLEADGLLVSEQRVVDGR 66
                                   589*************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   EETTSTTS CS
                           MarR 51 kspeDrRe 58
                                     +eDrR+
  gi|121639407|ref|YP_979631.1| 80 ALTEDRRA 87
                                   5689**96 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   4.3e-06    0.0086      22      81 ..      34      95 ..      11     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                   Replic_Relax 22 shra....tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra..epeprsk 81
                                   ++ +    t++  L rL++ gll + ++ v+g+++     vY  tp+G+++l+++r+  e+ +r  
  gi|121639407|ref|YP_979631.1| 34 HGYRvspgTLYPTLHRLEADGLLVSEQRVVDGRAR----RVYRATPAGRAALTEDRRalEELAREV 95
                                   344466688999*************6666555444....6************76666553322333 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.5e-06     0.017      17      83 ..      24      92 ..      10     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.5e-06
                                   S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSE.EEEEESSSS-EEEEEE-TCGGG.GHHHHHHHHHHH CS
                           HxlR 17 gkkRfselkralpkisqkmLaqrLreLeqdgli.erevypevPpkveYsltekGrs.lepvlqelkkwg 83
                                   g   ++el+r+   +s  +L  +L++Le+dgl+ + + +     +  Y+ t++Gr+ l++   +l++++
  gi|121639407|ref|YP_979631.1| 24 GAWLTQELSRHGYRVSPGTLYPTLHRLEADGLLvSEQRVVDGRARRVYRATPAGRAaLTEDRRALEELA 92
                                   5566899999999******************8615556666678899*******962555555555555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.2e-05     0.084      37      68 .]      45      77 ..       7      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                         HTH_27 37 yslkkLtekGLvertgdeadrre.krvrlTdkG 68
                                     l +L++ GL+++++   d+r+ + +r+T++G
  gi|121639407|ref|YP_979631.1| 45 PTLHRLEADGLLVSEQRVVDGRArRVYRATPAG 77
                                   5789********999999****96678****99 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.28      34      60 ..      36      62 ..      23      63 .. 0.90
   2 ?    0.3   0.3      0.28   5.5e+02      42      51 ..      85      94 ..      85     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                   HTS-HHHHHHHHHHHHHTTSEEEETTC CS
                           GntR 34 fgVsrttvReALrrLeaeglverrqgr 60
                                   + Vs  t+   L rLea+gl++++q++
  gi|121639407|ref|YP_979631.1| 36 YRVSPGTLYPTLHRLEADGLLVSEQRV 62
                                   889********************9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.28
                                   HHHHHHHHHT CS
                           GntR 42 ReALrrLeae 51
                                   R+AL +L++e
  gi|121639407|ref|YP_979631.1| 85 RRALEELARE 94
                                   89*****998 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.7e-05      0.15     367     410 ..      44      90 ..      27      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.7e-05
                         DUF505 367 reaLysLesfeLiesev...eekgkevyvlTeyGekvledqekklre 410
                                       L++Le+ +L+ se    +   ++vy  T+ G+  l + ++ l+e
  gi|121639407|ref|YP_979631.1|  44 YPTLHRLEADGLLVSEQrvvDGRARRVYRATPAGRAALTEDRRALEE 90 
                                    568********99888766677889*************988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 838.30
//
Query:       gi|121639408|ref|YP_979632.1|  [L=54]
Description: hypothetical protein BCG_3553 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 428.09
//
Query:       gi|121639409|ref|YP_979633.1|  [L=500]
Description: alpha, alpha-trehalose-phosphate synthase OtsA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.9e-162  539.4   0.0   7.8e-162  539.2   0.0    1.0  1  Glyco_transf_20  Glycosyltransferase family 20
    2.7e-05   23.7   0.0       0.22   11.1   0.0    2.2  2  Glycos_transf_1  Glycosyl transferases group 1
     0.0032   17.9   0.0     0.0071   16.8   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.38   11.2   0.1       0.38   11.2   0.1    2.3  3  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.2   0.0  1.7e-165  7.8e-162       2     472 ..      21     491 ..      20     493 .. 0.97

  Alignments for each domain:
  == domain 1  score: 539.2 bits;  conditional E-value: 1.7e-165
                                    -EEEEEEE-SECEEE-S.SCG..EEECCGSSHHHHHCCCHHCCC-EEEEEEECCES-CCC...HCCCCHHHCCCCCEEEE CS
                Glyco_transf_20   2 klvvvsnrlplklereseeekeeyelkkssgglvsalkglkeetevvwvgwlgvevdesee.akekvskeleekfsvvpv 80 
                                    ++vvv+nrlp++ler   +++  +++k+s+gglv+al+++ ++++++wvgw+gv+ d  e+  +    + ++++++++pv
  gi|121639409|ref|YP_979633.1|  21 DFVVVANRLPVDLERLP-DGS--TTWKRSPGGLVTALEPVLRRRRGAWVGWPGVNDDGAEPdLHVLDGPIIQDELELHPV 97 
                                    689*************9.777..8999********************************9866666679*********** PP

                                    EE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHH CS
                Glyco_transf_20  81 flsdekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLmllPellR 160
                                     ls++++ +yy+gfs+++LWpl+H    d   +  ++r++wd+Yv+vn++FA+++ + + +g+++wv+DY+L l+P++lR
  gi|121639409|ref|YP_979633.1|  98 RLSTTDIAQYYEGFSNATLWPLYH----DVIVKPLYHREWWDRYVDVNQRFAEAASRAAAHGATVWVQDYQLQLVPKMLR 173
                                    ************************....7778************************************************ PP

                                    HCCTTSEEEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSS.......EEEECTTEEEEE CS
                Glyco_transf_20 161 kkledakigfflHiPFPsseifriLpvreeilegllgadliGFhtedyarhFlsccsrllg.......leveskrggvey 233
                                    +  +d++igfflHiPFP++e+f+ +p+r+ei++gllgadl+GFh +  a++Fl  ++rl+g       + v+s+ g+  +
  gi|121639409|ref|YP_979633.1| 174 MLRPDLTIGFFLHIPFPPVELFMQMPWRTEIIQGLLGADLVGFHLPGGAQNFLILSRRLVGtdtsrgtVGVRSRFGAAVL 253
                                    *************************************************************888888888888888999* PP

                                    TTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEE CS
                Glyco_transf_20 234 kgrkvsvkalpigidverlesalkkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvv 313
                                    ++r+++v+a+pi++d+++l++a+++++++++++e++++++n +k++lgvDrlDy+kG++ +l+af+++L+e + +r+++v
  gi|121639409|ref|YP_979633.1| 254 GSRTIRVGAFPISVDSGALDHAARDRNIRRRAREIRTELGNPRKILLGVDRLDYTKGIDVRLKAFSELLAEGRVKRDDTV 333
                                    ******************************************************************************** PP

                                    EEEEEEB-STTSHHHHHHHHHHHHHHHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHH CS
                Glyco_transf_20 314 lvqiavpsredveeyqelekeveelvgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvakeyv 393
                                    lvq+a+psre+ve+yq+l++++e++vg+INge+g++++  v+yl+r+++++elia+++a+dv+lvt+lRdGmnlvakeyv
  gi|121639409|ref|YP_979633.1| 334 LVQLATPSRERVESYQTLRNDIERQVGHINGEYGEVGHPVVHYLHRPAPRDELIAFFVASDVMLVTPLRDGMNLVAKEYV 413
                                    ******************************************************************************** PP

                                    HCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHH CS
                Glyco_transf_20 394 vcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieevaeaikeaLkmseeerkkrekkllkqvskhdvqsWaesflsel 472
                                    +c+++  g+L+LSeF+Gaa++L+ +a+lvNP+d+e v++ i+eaL+ +ee  ++r+++l +qv+ hdv++Wa+sfl+ l
  gi|121639409|ref|YP_979633.1| 414 ACRSDLGGALVLSEFTGAAAELR-HAYLVNPHDLEGVKDGIEEALNQTEEAGRRRMRSLRRQVLAHDVDRWAQSFLDAL 491
                                    ***********************.57**************************************************988 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   4.8e-05      0.22      11      50 ..     292     334 ..     284     359 .. 0.84
   2 !   10.5   0.0   7.4e-05      0.33      78     162 ..     377     463 ..     366     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                                    TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCC...HCSCEEE CS
                Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkq...lnpnvkl 50 
                                    + + +ki+l v rl+++Kg+d+ +kaf +l ++   ++++++l
  gi|121639409|ref|YP_979633.1| 292 LGNPRKILLGVDRLDYTKGIDVRLKAFSELLAEgrvKRDDTVL 334
                                    4567899**********************99876665555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.4e-05
                                    EECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHT....T--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHH CS
                Glycos_transf_1  78 lgevs.redleellknadifvlpsisEgfGivllEAmaa....glpviasnaggpaevvkdgetGllvkpnnaealaeai 152
                                    l +   r++l++++ ++d+++++  ++g+ +v+ E+ a+    g + + s   g+a  ++++    lv p++ e  +++i
  gi|121639409|ref|YP_979633.1| 377 LHRPApRDELIAFFVASDVMLVTPLRDGMNLVAKEYVACrsdlGGALVLSEFTGAAAELRHAY---LVNPHDLEGVKDGI 453
                                    44444599******************************9666678999999999988888887...9************* PP

                                    HHHHHSHHHH CS
                Glycos_transf_1 153 rklledeelr 162
                                    +++l++ e++
  gi|121639409|ref|YP_979633.1| 454 EEALNQTEEA 463
                                    ****998654 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.6e-06    0.0071       2     133 ..     297     458 ..     296     459 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                                    EEEEEES---GG.GTHHHHHHHHHHHH......HH..EEEEEES---............HHHHHHHTT-........... CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllr.....kkd..vrlvivGdgp.rp.........eeleelaagl........... 53 
                                    +++l v rl +  kg+d+ l+a+ +l+     k+d  v + ++   p r+         +++e++   +           
  gi|121639409|ref|YP_979633.1| 297 KILLGVDRL-DYTKGIDVRLKAFSELLaegrvKRDdtVLVQLAT--PsRErvesyqtlrNDIERQ---Vghingeygevg 370
                                    567777789.5669*********666635444332654444444..3233244453333333333...144455555544 PP

                                    T.TEEEE---...THHHHHHHH-SEE.EE--.---SHHHHHHHHT....T-EEEE-TGGG.TTT--TTSSEE--TT-HHH CS
                Glyco_trans_1_4  54 eerveftGfv...edlaellaaadvf.vaPs.egfglkllEamaa....glpvVatdvgg.iaevvgengllvppgdpea 123
                                    ++ v+++ +    ++l +++ a+dv+ v P+  g++l++ E+ a+    g + V ++  g +ae   ++++lv+p+d e 
  gi|121639409|ref|YP_979633.1| 371 HPVVHYLHRPaprDELIAFFVASDVMlVTPLrDGMNLVAKEYVACrsdlGGALVLSEFTGaAAE--LRHAYLVNPHDLEG 448
                                    466888877788677**********94556677***********96666678899988661566..6999*********9 PP

                                    HHHHHHHHHH CS
                Glyco_trans_1_4 124 laeailrLle 133
                                      + i++ l+
  gi|121639409|ref|YP_979633.1| 449 VKDGIEEALN 458
                                    9999999886 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   6.8e+03       8      20 ..     137     149 ..     132     161 .. 0.75
   2 ?   -3.8   0.8         4   1.8e+04      60      75 ..     272     287 ..     270     289 .. 0.63
   3 ?   11.2   0.1   8.4e-05      0.38       3      91 ..     397     488 ..     392     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                Glyco_trans_1_2   8 sespnlrlfEaaa 20 
                                    + ++n+r+ Eaa 
  gi|121639409|ref|YP_979633.1| 137 YVDVNQRFAEAAS 149
                                    5678888888875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                Glyco_trans_1_2  60 lanpeerraiaeaare 75 
                                    l++ ++ r i+++are
  gi|121639409|ref|YP_979633.1| 272 LDHAARDRNIRRRARE 287
                                    5666666667777665 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 8.4e-05
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaac.....Gafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaare 75 
                                    L +  ++++nl+  E+ ac     Ga++l++  +g +  +   +++ l+   dle + + i+++l++ ee+ +++ +  +
  gi|121639409|ref|YP_979633.1| 397 LVTPLRDGMNLVAKEYVACrsdlgGALVLSE-FTGAAAEL---RHAYLVNphDLEGVKDGIEEALNQTEEAGRRRMRSLR 472
                                    5566678888888888888555533344444.44444444...566666668**************99999999999888 PP

                Glyco_trans_1_2  76 rvlaehtydhraeqll 91 
                                    r    h++d+ a+ +l
  gi|121639409|ref|YP_979633.1| 473 RQVLAHDVDRWAQSFL 488
                                    8888999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3612.61
//
Query:       gi|121639410|ref|YP_979634.1|  [L=192]
Description: hypothetical protein BCG_3555 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1382.08
//
Query:       gi|121639411|ref|YP_979635.1|  [L=160]
Description: Mce-associated protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.015   15.4   0.0    1.4  1  SnoaL_4          SnoaL-like domain
      0.059   13.2   0.3      0.098   12.5   0.3    1.3  1  VirB8            VirB8 protein
      0.078   12.5   0.0       0.11   11.9   0.0    1.2  1  T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane c
       0.12   12.0   0.5       0.13   12.0   0.5    1.3  1  TPR_21           Tetratricopeptide repeat-like domain


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   3.3e-06     0.015      81     126 ..     114     157 ..      67     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                                    TTEEEEEEEEEEEEEETT..EEEEEE...EEEEEEEEEEETTEEEEEEE CS
                        SnoaL_4  81 gdtAtgrayllatlvrdg..dggrqvl.aggryedelvredggWrisrr 126
                                     d A++  yl       +  d++rq l  g r++++++r dg+W i+ +
  gi|121639411|ref|YP_979635.1| 114 RDCASVMVYLNR-----TvtDKTRQPLyDGSRLRVDFQRIDGKWLIAYI 157
                                    233444444444.....2334555555499****************976 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.2e-05     0.098      93     171 ..      57     134 ..      54     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                    B-TTTH.HHHHHHHHHTB-HHHHHHHHHHHSTT-TTSHHHHTTTSEEE.EEEEEEE.EEEET...TEEEEEEEEEEE.ET CS
                          VirB8  93 yddaalvqdnydkvyllstgsaakelneyarsnnensPfaqlgketelveveiksv.vlasp...ntaqvrfkettrred 168
                                    yd++++ +++ ++vy l t++ ++e+++ a+    ++    ++k+  +v+++++ v v++ +    +++v +++t+++++
  gi|121639411|ref|YP_979635.1|  57 YDYQTV-ERSLTAVYPLLTPDYRQEFQKSAN----AQIIPEAKKREVVVQANVVGVgVMDAKrdcASVMVYLNRTVTDKT 131
                                    99****.**********************77....46777777777678*******888855555899999999998777 PP

                                    TS- CS
                          VirB8 169 gtl 171
                                     ++
  gi|121639411|ref|YP_979635.1| 132 RQP 134
                                    665 PP

>> T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.11      53     121 ..      44     111 ..      36     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                T4BSS_DotI_IcmL  53 laWaakavlkaytldfvnYrsqLqkaseefteegwesfaqslkssgnlkavkdkklvltavptgapvir 121
                                     + a++ + +++ +d++  ++ L+++    t++  ++f++s ++  ++   k+ ++v++a+++g +v  
  gi|121639411|ref|YP_979635.1|  44 PKLAMQEIPQVFGYDYQTVERSLTAVYPLLTPDYRQEFQKSANA-QIIPEAKKREVVVQANVVGVGVMD 111
                                    467899*********************************99765.6899999999*******9998875 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   2.9e-05      0.13      10      47 ..      10      47 ..       6     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                         TPR_21 10 lilvgvvlalvglaGwqgwqdyqeeqaeeAsalYqqlq 47
                                   +++v+ +++l +  Gw +w   q+  +++A al  +l 
  gi|121639411|ref|YP_979635.1| 10 ALMVATIVGLSAAGGWFYWDRVQTGGEASARALLPKLA 47
                                   78999************************999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1192.22
//
Query:       gi|121639412|ref|YP_979636.1|  [L=242]
Description: Mce-associated protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.7   0.2        0.5   10.4   0.1    2.0  2  AvrPto    Central core of the bacterial effector protein AvrP
       0.25   11.6   2.6       0.82    9.9   0.4    2.3  2  SepZ      SepZ


Domain annotation for each model (and alignments):
>> AvrPto  Central core of the bacterial effector protein AvrPto
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   5.6e-05       0.5      40      85 ..     123     167 ..     101     183 .. 0.78
   2 ?   -0.5   0.0      0.14   1.2e+03       5      23 ..     193     211 ..     190     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.6e-05
                         AvrPto  40 rynnlyshtqrtldmadmqhrymtgasginpgmlp.henvddmrsai 85 
                                       n++s+t  t+d      r++ g+sg   gml   +nvd+++   
  gi|121639412|ref|YP_979636.1| 123 TVVNMFSYTPDTIDE--SVNRFVNGTSGPLRGMLNaNNNVDNLKGLF 167
                                    456899999999995..578**************7256899988655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                         AvrPto   5 ssqllsvrhqlaesagvpr 23 
                                    +s l+svr  +a+  gv +
  gi|121639412|ref|YP_979636.1| 193 ASVLVSVRVTVADIDGVNK 211
                                    68899*******9999976 PP

>> SepZ  SepZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.051   4.6e+02      48      70 ..      80     104 ..      69     111 .. 0.67
   2 ?    9.9   0.4   9.2e-05      0.82       8      42 ..     143     177 ..     136     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.051
                           SepZ  48 valatt..alaalGaGiaalcvens 70 
                                    + la++  a+aal  G++al ++n 
  gi|121639412|ref|YP_979636.1|  80 LSLAAGllAIAALAWGVTALVMQNR 104
                                    4455542377899999999888775 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.2e-05
                           SepZ   8 psGavlplaatinGnnsvdektGvlkpenGtsrtv 42 
                                      G+  pl   +n nn+vd+  G++++ n ts +v
  gi|121639412|ref|YP_979636.1| 143 VNGTSGPLRGMLNANNNVDNLKGLFRATNATSEAV 177
                                    5678889************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1591.75
//
Query:       gi|121639413|ref|YP_979637.1|  [L=564]
Description: Mce-family protein mce4F [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-18   65.1   0.1      2e-17   63.2   0.3    1.9  2  MlaD      MlaD protein


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.3   1.1e-21     2e-17       2      81 .]      39     114 ..      38     114 .. 0.95
   2 ?   -3.0   0.0      0.51   9.1e+03      40      65 ..     309     355 ..     305     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.1e-21
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdpg 81 
                                    +y v a f   +gL ++a+V+yrGv vGrV+s+ l  + ++vt++++l+  s+t ip++++a+v++ + +ge+yi+l+p+
  gi|121639413|ref|YP_979637.1|  39 TYGVSADFVAGGGLYKNANVTYRGVAVGRVESVGL--NPNGVTAHMRLN--SGTAIPSNVTATVRSVSAIGEQYIDLVPP 114
                                    577889999999***********************..889999******..**************************995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.51
                           MlaD  40 trrvtvtvdld.....................kksetsipedsraqv 65 
                                    + ++++++++d                      +s ++ip+d++ + 
  gi|121639413|ref|YP_979637.1| 309 DEGAKLDFKIDlhdpppcmtgflppplvrspaDESVREIPRDMYCKT 355
                                    56677777777777777777777777777777788888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3913.80
//
Query:       gi|121639414|ref|YP_979638.1|  [L=384]
Description: mce family lipoprotein LprN [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-12   45.9   0.1      1e-11   44.9   0.1    1.5  1  MlaD          MlaD protein
     0.0026   17.2   1.4     0.0051   16.3   1.3    1.5  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.02   15.5   0.0    1.3  1  DUF2645       Protein of unknown function (DUF2645)
       0.04   13.9   1.8       0.17   11.9   0.3    2.1  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.1   2.3e-15     1e-11       2      80 ..      41     120 ..      40     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.3e-15
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsi.tldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                     y vt+++ ++  L +++pV++  vtvG+V+ i  ++  + ++ + v+ld ++++++p+++ a+vs+++llg+  ++l p
  gi|121639414|ref|YP_979638.1|  41 AYSVTVEMADVATLPQNSPVMVDDVTVGSVAGIvAVQRPDGSFYAAVKLDLDKNVLLPANAVAKVSQTSLLGSLHVELAP 120
                                    699******************************6666666666666666666*************************988 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.3   1.1e-06    0.0051      15     127 ..     166     278 ..     157     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                      Mce4_CUP1  15 LnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqa 94 
                                    L +++  + +A++Gr  ++ + + +l e+ + lN+++ ++ + +  l++++++ a   ++l +aLd +    r ++++++
  gi|121639414|ref|YP_979638.1| 166 LEEIIDETHQAVAGRQAQFVNLVPRLAELTAGLNRQVHDIIDALDGLNRVSAILARDKDNLGRALDTLPDAVRVLNQNRD 245
                                    5566666789********************************************************************** PP

                      Mce4_CUP1  95 eLdalllaavglsntgadllerngdnLirlaad 127
                                    ++ ++++a+  l   ++++l++ + ++ + ++d
  gi|121639414|ref|YP_979638.1| 246 HIVDAFAALKRLTMVTSHVLAETKVDFGEDLKD 278
                                    ************999999999988766555555 PP

>> DUF2645  Protein of unknown function (DUF2645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   4.6e-06      0.02      17      80 ..     260     323 ..     247     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-06
                        DUF2645  17 llSildkewmid.gsdiknlCsvlrelelddsrdvaviaalllliPlllvlvkkklksaflvvia 80 
                                    ++S    e+ +d g+d+k+l s++++l +dd++d+++   lll +P+  + +k+ ++  +l+v +
  gi|121639414|ref|YP_979638.1| 260 VTSHVLAETKVDfGEDLKDLYSIVKAL-NDDRKDFVTSLQLLLTFPFPNFGIKQAVRGDYLNVFT 323
                                    5666667777775789**********8.9****************************99999876 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   3.7e-05      0.17      46     120 ..     165     242 ..     149     253 .. 0.72
   2 ?    2.4   0.3     0.032   1.4e+02      45      90 ..     252     297 ..     215     302 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                   Baculo_PEP_C  46 qLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnldl 120
                                     L+++ ++ ++++a  ++++ +l+ +L +  + l+    ++  +L++ln + + L+ +  N+  +L  l  a+  l++
  gi|121639414|ref|YP_979638.1| 165 ALEEIIDETHQAVAGRQAQFVNLVPRLAELTAGLNrqvHDIIDALDGLNRVSAILARDKDNLGRALDTLPDAVRVLNQ 242
                                    577777777777777777777777777777777776666666777777777777777777777777777777766654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.032
                   Baculo_PEP_C  45 tqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnl 90 
                                      L+ l+   +++lae + ++ + l+ L + ++al+d+ +   t+l
  gi|121639414|ref|YP_979638.1| 252 AALKRLTMVTSHVLAETKVDFGEDLKDLYSIVKALNDDRKDFVTSL 297
                                    2244444444455555555666666666666666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2745.51
//
Query:       gi|121639415|ref|YP_979639.1|  [L=451]
Description: Mce-family protein mce4D [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-13   50.7   0.5    3.5e-13   49.7   0.5    1.6  1  MlaD            MlaD protein
    2.2e-08   33.9   3.3    3.3e-08   33.3   3.3    1.2  1  Mce4_CUP1       Cholesterol uptake porter CUP1 of Mce4, putat
    1.5e-05   25.1   4.4        0.1   12.6   4.9    2.2  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
     0.0005   20.5   3.1       0.25   11.8   0.7    2.3  2  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 
    0.00057   19.9   0.3    0.00095   19.2   0.3    1.3  1  Serine_rich     Serine rich protein interaction domain
     0.0067   16.3   0.6      0.039   13.8   0.6    2.0  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.01   16.1   1.9        2.9    8.2   0.8    2.6  2  DUF948          Bacterial protein of unknown function (DUF948
  ------ inclusion threshold ------
      0.012   15.8   5.0         10    6.5   0.5    4.0  3  WXG100          Proteins of 100 residues with WXG
      0.015   15.1   1.3       0.22   11.3   1.3    2.2  1  Mer2            Mer2
        0.1   12.7   0.6          2    8.5   0.4    2.2  2  DUF1664         Protein of unknown function (DUF1664)
        0.1   13.2   0.4        8.1    7.0   0.1    2.6  2  HisKA_3         Histidine kinase
       0.14   12.2   0.1        0.2   11.7   0.1    1.1  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.16   11.0   0.0       0.26   10.4   0.0    1.3  1  APG17           Autophagy protein Apg17
       0.36   10.3   1.5          1    8.9   1.3    1.5  1  Vps5            Vps5 C terminal like
       0.56   10.6   5.8        8.6    6.8   0.0    2.6  3  Flagellin_C     Bacterial flagellin C-terminal helical region
       0.69    9.0   2.3        7.4    5.6   0.6    2.5  3  RmuC            RmuC family
        2.3    8.2   4.8        3.1    7.7   0.1    2.7  2  Flg_hook        Flagellar hook-length control protein FliK


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.5   3.3e-16   3.5e-13       2      80 ..      39     113 ..      38     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.3e-16
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    ++t++ +f++a+gL +g++Vr+ Gv+vG+++ i  +p +  v++t+++   +++++p d++a + + +l+ +++i+l+p
  gi|121639415|ref|YP_979639.1|  39 KRTIVGYFTSAVGLYPGDQVRVLGVPVGEIDMI--EPRSSDVKITMSVS--KDVKVPVDVQAVIMSPNLVAARFIQLTP 113
                                    6899*****************************..77999999999999..**************************98 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   3.3   3.2e-11   3.3e-08      15     141 ..     163     289 ..     145     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.2e-11
                      Mce4_CUP1  15 LnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqa 94 
                                    L a ++ +a+ L+G G+ l ++l +l +v  +l ++  ++   +++l+ l d+ +++ ++++++  +++  s+ +++ +a
  gi|121639415|ref|YP_979639.1| 163 LGAAINQAADTLDGNGDSLHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDALSESDEQIVQFAGHVASVSQVLADSSA 242
                                    55677889************************************************************************ PP

                      Mce4_CUP1  95 eLdalllaavglsntgadllerngdnLirlaadlrptlelLakYspe 141
                                    +Ld+ l ++ ++ ++ + +l++n+  Li+++++l+  ++ L + s++
  gi|121639415|ref|YP_979639.1| 243 NLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQSEN 289
                                    ************************************99999877766 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00047       0.5      40     118 ..     138     216 ..     127     238 .. 0.72
   2 !   12.6   4.9   9.8e-05       0.1      30     112 ..     234     319 ..     221     326 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                   Baculo_PEP_C  40 ldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl 118
                                     d++++ L+ l++dl+ +  el+  l +++++  d+l    d+l+n+L  l ++   L  s + i  t++nl   +++l
  gi|121639415|ref|YP_979639.1| 138 WDEVKEGLTRLAADLSPAAGELQGPLGAAINQAADTLDGNGDSLHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDAL 216
                                    5677777777777887777777777777777777777777799999999998888888888888888888887777666 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.8e-05
                   Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNins 106
                                    +q+la+ ++ ld+  ++Ln+  +d++  l e ++ l +++++L+d  ++l+   +++++ L      +tn  +     + 
  gi|121639415|ref|YP_979639.1| 234 SQVLADSSANLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSdqsENIEQVLHVAGPGITNFYNIYDPAQG 313
                                    45555555666666666666666666666666666666666666666666555555555555555555555555555566 PP

                   Baculo_PEP_C 107 tLnnll 112
                                    tLn+ll
  gi|121639415|ref|YP_979639.1| 314 TLNGLL 319
                                    666666 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0021       2.3      35      78 ..     147     190 ..     136     194 .. 0.90
   2 !   11.8   0.7   0.00024      0.25       3      80 ..     207     283 ..     205     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                  T7SS_ESX_EspC  35 gasaavldshGpicaatndavaaaeaarraagealaaasteLad 78 
                                    + +a++++  G +  ++ +a+++a ++ ++ g++l+ a++eLa+
  gi|121639415|ref|YP_979639.1| 147 RLAADLSPAAGELQGPLGAAINQAADTLDGNGDSLHNALRELAQ 190
                                    5678899999********************************98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00024
                  T7SS_ESX_EspC   3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkL 80 
                                    +nL+V  d+l e  ++  + a+ +as+ +  a+ sa++ ++ G++ +a+  +++ +++  ++++ ++  +++++a+ L
  gi|121639415|ref|YP_979639.1| 207 KNLQVLVDALSESDEQIVQFAGHVASVSQVLADSSANLDQTLGTLNQALS-DIRGFLRENNSTLIETVNQLNDFAQTL 283
                                    79*******************************************98875.577777777777777777777777776 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3     9e-07   0.00095       4     132 ..     168     297 ..     166     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9e-07
                    Serine_rich   4 dsAletlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsd..knlqtk 81 
                                    ++A +tl+   +++++a+ +L +++ +   s+  +  ++++++  vd+l++s +++++Fa  +++ ++ l d   nl + 
  gi|121639415|ref|YP_979639.1| 168 NQAADTLDGNGDSLHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDALSESDEQIVQFAGHVASVSQVLADssANLDQT 247
                                    6788888888889999999999999999999999999******************************999997779**** PP

                    Serine_rich  82 LrkqlqkledsdqilqetsqeLdsceWslealasdkkqekpddlDrlvmva 132
                                    L  + q+l+d +  l e  ++L ++  +l+ +a++ +++ ++++++++ va
  gi|121639415|ref|YP_979639.1| 248 LGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQ-SENIEQVLHVA 297
                                    ***********************9999999999998876.88888888776 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.6   3.7e-05     0.039      64     181 ..     141     255 ..     137     297 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                                    CCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH---- CS
                 Apolipoprotein  64 lgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslap 143
                                    +++ l  l ++l+p++ el+  l a+++++ ++l+ +++ l++ l++ + ++  rl+  + +++    ++l+ l + l +
  gi|121639415|ref|YP_979639.1| 141 VKEGLTRLAADLSPAAGELQGPLGAAINQAADTLDGNGDSLHNALRE-LAQVAGRLGDSRGDIFG-TVKNLQVLVDALSE 218
                                    45556667788888888888888888888888888888888776654.47777777777777775.66667777777776 PP

                                    -..-----SSSHHHHHHHTS-TTSHHHHHS--XXXXXX CS
                 Apolipoprotein 144 haeeveerlssrveelrekleeqaeelrerleanleel 181
                                    + e++  +++ +v  +++ l++  ++l + l +  + l
  gi|121639415|ref|YP_979639.1| 219 SDEQIV-QFAGHVASVSQVLADSSANLDQTLGTLNQAL 255
                                    655555.6666666666666666666666555444433 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0081       8.5      25      84 ..     164     223 ..     154     239 .. 0.76
   2 !    8.2   0.8    0.0028       2.9      15      73 ..     231     293 ..     224     299 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0081
                         DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                    +  +++aa+t+++ ++ +++ l+e++++     +   d+ + +++++ l++a+ +  e++
  gi|121639415|ref|YP_979639.1| 164 GAAINQAADTLDGNGDSLHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDALSESDEQI 223
                                    566778888888888888888888888888888888888888888888888777665555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                         DUF948  15 iflivvllklkktldeaaatieelekqvdpilkeve....dllakvnelledvneklekvdpl 73 
                                    + +  vl   +  ld++  t+++  +++++ l+e +    +++++ n+ ++ +++++e+++++
  gi|121639415|ref|YP_979639.1| 231 ASVSQVLADSSANLDQTLGTLNQALSDIRGFLRENNstliETVNQLNDFAQTLSDQSENIEQV 293
                                    444444444444445555555555555555555444101133344444555555566666555 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.017        18       7      39 ..     165     197 ..     163     200 .. 0.89
   2 ?    6.5   0.5    0.0095        10       8      78 ..     187     266 ..     184     274 .. 0.58
   3 ?    3.5   0.1      0.08        85       6      27 ..     273     294 ..     268     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                         WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                    +++ qaa +++++ ++l+++l++l++    l++
  gi|121639415|ref|YP_979639.1| 165 AAINQAADTLDGNGDSLHNALRELAQVAGRLGD 197
                                    5799*********************99888754 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0095
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GC.....GCTHHHCHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   8 elrqaaarfqkqaeeledelqrlkaevdal.qs.....gWsGaaadafq...aefeewkqaaqklvdaLeeisealkqaa 78 
                                    el+q+a r++++++++ + +++l+  vdal +s     ++ G  a+  q   +  ++++q++ +l++aL++i+  l++++
  gi|121639415|ref|YP_979639.1| 187 ELAQVAGRLGDSRGDIFGTVKNLQVLVDALsESdeqivQFAGHVASVSQvlaDSSANLDQTLGTLNQALSDIRGFLRENN 266
                                    57777777777777777777777777777744455555455443333221113334566666666666666666666555 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.08
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   6 peelrqaaarfqkqaeeledel 27 
                                     ++l + a+++++q+e++e++l
  gi|121639415|ref|YP_979639.1| 273 VNQLNDFAQTLSDQSENIEQVL 294
                                    5788899999999999999887 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3   0.00021      0.22      19     107 ..     214     292 ..     202     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                           Mer2  19 kklsEaDKqILeWAgKLELEsvdLrEksskLinvlkenskeLlkvisklnellidlke.eesdnskekeikdlikdLsvk 97 
                                    ++lsE+D qI++ Ag                ++vl  +s +L + + +ln+ l d+++    +ns+  e +++++d + +
  gi|121639415|ref|YP_979639.1| 214 DALSESDEQIVQFAGHVAS-----------VSQVLADSSANLDQTLGTLNQALSDIRGfLRENNSTLIETVNQLNDFAQT 282
                                    6799999999999998654...........45666666666666666666666666664344556666666666777777 PP

                           Mer2  98 ienqlskvsk 107
                                    + +q++++++
  gi|121639415|ref|YP_979639.1| 283 LSDQSENIEQ 292
                                    7777766655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.21   2.2e+02      41      99 ..     165     223 ..     160     230 .. 0.77
   2 ?    8.5   0.4    0.0019         2      42     107 ..     229     294 ..     225     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.21
                        DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlsei 99 
                                     a+++ +  l+   +sl+++ r+L++   r++++  +   + k+++  v++++e  ++i
  gi|121639415|ref|YP_979639.1| 165 AAINQAADTLDGNGDSLHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDALSESDEQI 223
                                    67788888889999999999999999888888888777777777777777777665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                        DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                     v+svs+ l + s++l +t   L++ +  +   l e++ +  e+ +++++  + ls+ +e++e+v 
  gi|121639415|ref|YP_979639.1| 229 HVASVSQVLADSSANLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQSENIEQVL 294
                                    689999****************************99999999999999999999999888888875 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0077       8.1      11      63 ..     139     195 ..     138     199 .. 0.81
   2 ?    3.8   0.0     0.079        84      38      62 ..     240     264 ..     208     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0077
                                    HHHHHHHHHHHHHHHHHHHHTTT-HH....HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  11 DsvgqsLsaiklqlelakrllekdpe....kaaeqlreieelarealqevRrllhnL 63 
                                    D+v   L+ +++ l+ a+++l+ + +    +aa++l+   + +++al+e+ ++ ++L
  gi|121639415|ref|YP_979639.1| 139 DEVKEGLTRLAADLSPAAGELQGPLGaainQAADTLDGNGDSLHNALRELAQVAGRL 195
                                    9999*****************887777777888888888888888888877766665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.079
                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  38 aaeqlreieelarealqevRrllhn 62 
                                      + l++   ++++al+++R +l++
  gi|121639415|ref|YP_979639.1| 240 SSANLDQTLGTLNQALSDIRGFLRE 264
                                    5567888888888888888887765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00019       0.2      83     167 ..     208     292 ..     181     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                        UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqr 162
                                    +l++  +al e+ e+  + + ++++ ++ l+    +  q    l+++  d+  +++e +++L e  ++l+++++t+++q 
  gi|121639415|ref|YP_979639.1| 208 NLQVLVDALSESDEQIVQFAGHVASVSQVLADSSANLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQS 287
                                    56777788888889999999999999999988887766666699999********************************* PP

                        UPF0242 163 svlek 167
                                    + +e+
  gi|121639415|ref|YP_979639.1| 288 ENIEQ 292
                                    99985 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.26     254     319 ..     226     296 ..     200     315 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                                    H....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHH CS
                          APG17 254 m....ekakkllsekkeeiekllsalkkaleeleev.gkklpeylaifkaeeeflerweeekekieeklee 319
                                          ++++ l +  ++++++l +l++al++++ + +++ +  ++++++ ++f ++ +++ e+ie+ l+ 
  gi|121639415|ref|YP_979639.1| 226 FaghvASVSQVLADSSANLDQTLGTLNQALSDIRGFlRENNSTLIETVNQLNDFAQTLSDQSENIEQVLHV 296
                                    14444888999999999*******************99999****************99999999987765 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.3   0.00095         1      41     116 ..     207     286 ..     204     296 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00095
                           Vps5  41 kkLykaiellvsqrkelasataelakslesLaslels..kslsralsqlaeveerikellerqae..qdvltLgetidey 116
                                    k+L+  +++l+++++++++ ++ +a++ + La+++ +  ++l ++ ++l+++   ++e+ +   e  + + ++++t++++
  gi|121639415|ref|YP_979639.1| 207 KNLQVLVDALSESDEQIVQFAGHVASVSQVLADSSANldQTLGTLNQALSDIRGFLRENNSTLIEtvNQLNDFAQTLSDQ 286
                                    7777888888999999999999999999999877655559************9888887665433114555666666665 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.9   7.3e+03      13      29 ..     158     174 ..     150     176 .. 0.79
   2 ?    6.8   0.0    0.0082       8.6       4      48 ..     181     225 ..     179     234 .. 0.92
   3 ?    6.4   3.6     0.011        11       2      80 ..     214     292 ..     213     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.9
                                    HHHHHHHHHHHHHHHHH CS
                    Flagellin_C  13 kvrselGavqnRlesai 29 
                                    + +  lGa+ n+  ++ 
  gi|121639415|ref|YP_979639.1| 158 ELQGPLGAAINQAADTL 174
                                    67888999999988775 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0082
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                    Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                    + +a+ +l++v+  lG +   +  +++nl+  ++ l+++ +++ +
  gi|121639415|ref|YP_979639.1| 181 LHNALRELAQVAGRLGDSRGDIFGTVKNLQVLVDALSESDEQIVQ 225
                                    67899**********************************999965 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCHH CS
                    Flagellin_C   2 divdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrledvDpaeestrvtklqiliqasyallaqanqlpq 80 
                                    d+++e  +++ + +  + +v++ l ++++nl+++   l++a s++++    + st +++ ++l + +++l  q  +++q
  gi|121639415|ref|YP_979639.1| 214 DALSESDEQIVQFAGHVASVSQVLADSSANLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQSENIEQ 292
                                    5677778899999999999***********************************************9999888888765 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.16   1.7e+02      41      71 ..     166     197 ..     133     200 .. 0.74
   2 ?    4.5   0.1     0.015        16     227     274 ..     208     255 ..     203     280 .. 0.68
   3 ?    5.6   0.6     0.007       7.4       8      61 ..     242     295 ..     235     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                           RmuC  41 elqelneqlgdeaenLtkaLk.nsktrGnwGE 71 
                                     +++ +  l+ + ++L++aL+   ++ G++G+
  gi|121639415|ref|YP_979639.1| 166 AINQAADTLDGNGDSLHNALReLAQVAGRLGD 197
                                    35566677788888999999999999999996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                           RmuC 227 naeeiaellgelydkfekfgedleklgkklekaqksydkavkklegni 274
                                    n + ++++l+e  +++++f+ ++ ++ + l +++ ++d++ ++l++ +
  gi|121639415|ref|YP_979639.1| 208 NLQVLVDALSESDEQIVQFAGHVASVSQVLADSSANLDQTLGTLNQAL 255
                                    566666666777777777777777777777777777777777776433 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.007
                           RmuC   8 kplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61 
                                      l+++l ++++++++      e+ ++l e +++l++ ++ l+d+ en++++L 
  gi|121639415|ref|YP_979639.1| 242 ANLDQTLGTLNQALSDIRGFLRENNSTLIETVNQLNDFAQTLSDQSENIEQVLH 295
                                    556777777777777777777777788888888888888888888888888875 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0029       3.1      24      66 ..     145     187 ..     143     200 .. 0.88
   2 ?    1.5   0.2      0.26   2.7e+02      40      72 ..     224     256 ..     210     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                                    CEEEEEEEEEETTEEEEEEEE-SCHHHHHHHHTHHHHHHHHHC CS
                       Flg_hook  24 LGkvevkltlrggqlsvqltaenpetrelLeqnlprLreaLaa 66 
                                    L ++ + l+ ++g+l+  l a+ +++++ L+ n ++L++aL++
  gi|121639415|ref|YP_979639.1| 145 LTRLAADLSPAAGELQGPLGAAINQAADTLDGNGDSLHNALRE 187
                                    55788899999999***************************98 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                    EEEEE-SCHHHHHHHHTHHHHHHHHHCCTTCCE CS
                       Flg_hook  40 vqltaenpetrelLeqnlprLreaLaaaGlkld 72 
                                    vq++ + + + + L ++++ L + L   +  l+
  gi|121639415|ref|YP_979639.1| 224 VQFAGHVASVSQVLADSSANLDQTLGTLNQALS 256
                                    566666666666666666666666655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3101.73
//
Query:       gi|121639416|ref|YP_979640.1|  [L=357]
Description: Mce-family protein mce4C [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-16   59.4   0.3    5.1e-16   58.7   0.3    1.3  1  MlaD           MlaD protein
    1.4e-06   27.9   1.0     0.0026   17.3   0.5    2.2  2  Mce4_CUP1      Cholesterol uptake porter CUP1 of Mce4, putati
     0.0019   18.2   1.3       0.89    9.6   0.2    2.4  2  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
     0.0079   16.4   0.2      0.019   15.3   0.2    1.6  1  DUF4164        Domain of unknown function (DUF4164)
  ------ inclusion threshold ------
      0.018   14.6   0.1      0.036   13.7   0.1    1.4  2  HAUS-augmin3   HAUS augmin-like complex subunit 3
       0.02   15.1   0.5       0.15   12.2   0.4    2.5  2  RPN13_C        UCH-binding domain
       0.14   12.7   2.5          6    7.4   2.7    2.3  2  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
       0.19   11.1   3.9        2.9    7.3   2.2    2.7  3  MttA_Hcf106    mttA/Hcf106 family
       0.27   10.9   0.0        0.5   10.0   0.0    1.4  2  BAR_3          BAR domain of APPL family
       0.27   11.5   5.2        1.4    9.2   0.1    3.5  4  DUF948         Bacterial protein of unknown function (DUF948)
       0.29    9.1   0.0        1.1    7.1   0.0    1.7  2  Prominin       Prominin


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.3   3.1e-19   5.1e-16       2      80 ..      44     118 ..      43     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.1e-19
                           MlaD   2 gytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                    g+ + a+f++a+g+++g+ V ++G++vG V++++l   +++++vt+++d   ++ + ++s a ++t ++lge+ ia++p
  gi|121639416|ref|YP_979640.1|  44 GKPYDAYFTDAGGITPGNSVYVSGLKVGAVSAVSL--AGNSAKVTFSVD--RSIVVGDQSLAAIRTDTILGERSIAVSP 118
                                    78899******************************..************..999**********************998 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   1.6e-06    0.0026      39     158 ..     137     254 ..     132     262 .. 0.85
   2 !    9.2   0.0   0.00047      0.76      32      69 ..     262     299 ..     258     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                      Mce4_CUP1  39 dlnevLdelNprlpqlredi..reladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadller 116
                                    +ln vL++l ++ ++l++    ++l+ ++++ +da p++  a+d ++  sr+++ + ++L+ ll++    +++++++l++
  gi|121639416|ref|YP_979640.1| 137 TLNGVLQDLGRNANDLNRPQfeQALNVFTQALHDATPQVRGAVDGLTSLSRALNRRDEALQGLLAH----AKSVTSVLSE 212
                                    5788999999999999876433789999****************************9999998876....5788999999 PP

                      Mce4_CUP1 117 ngdnLirlaadlrptlelLakYspeltCllrnladvepkvak 158
                                      +++ +l++d +   + L+    +l  l+++++dv+ +++ 
  gi|121639416|ref|YP_979640.1| 213 RAEQVNKLVEDGNQLFAALDARRAALSALISGIDDVAAQISG 254
                                    999999999999999999999999999999999998877765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00047
                      Mce4_CUP1  32 rlGesltdlnevLdelNprlpqlredireladladvYa 69 
                                    ++G +l++ln vL++lN+r + ++e +++l + a++ +
  gi|121639416|ref|YP_979640.1| 262 EFGPALSKLNLVLANLNERRDYITEALKRLPTYATTLG 299
                                    79***************************999988865 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.6    0.0032       5.1      43     116 ..     138     218 ..     125     226 .. 0.58
   2 !    9.6   0.2   0.00055      0.89      38      97 ..     236     298 ..     193     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0032
                   Baculo_PEP_C  43 ietqLnalsedlksll.aeldtrldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                    ++++L++l  + ++l  ++++++l+ ++++L+da  ++       ++l+ +L+  +  l  Ll+    + s L+   + +
  gi|121639416|ref|YP_979640.1| 138 LNGVLQDLGRNANDLNrPQFEQALNVFTQALHDATPQVRgavdglTSLSRALNRRDEALQGLLAHAKSVTSVLSERAEQV 217
                                    33344444433333321455667777777777777777766666666666666666666666666666666665555555 PP

                   Baculo_PEP_C 116 n 116
                                    n
  gi|121639416|ref|YP_979640.1| 218 N 218
                                    5 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00055
                   Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnL 97 
                                    ++l a+ + +++++++++  +a+ ++++  +l++L+  l++l+   d ++++L+ l +  t+L
  gi|121639416|ref|YP_979640.1| 236 AALSALISGIDDVAAQISGFVADNRKEFGPALSKLNLVLANLNerrDYITEALKRLPTYATTL 298
                                    334445556667777777777777778888888888888888877777777777776666665 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.1e-05     0.019       7      75 ..     169     251 ..     163     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                        DUF4164   7 eaaltrLeaald...sLEkavdrrleaerkr...........deleaeiealgedrsRLaeeLdqaearaarleevnrEv 72 
                                     +a+ + ++a+d   sL +a++rr ea +             +e+++++++l ed ++L ++Ld+++a +++l ++ ++v
  gi|121639416|ref|YP_979640.1| 169 HDATPQVRGAVDgltSLSRALNRRDEALQGLlahaksvtsvlSERAEQVNKLVEDGNQLFAALDARRAALSALISGIDDV 248
                                    555556666554111556667777777776678888889******************************99999988888 PP

                        DUF4164  73 srr 75 
                                    + +
  gi|121639416|ref|YP_979640.1| 249 AAQ 251
                                    766 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.2e-05     0.036      49     166 ..     138     261 ..     136     291 .. 0.79
   2 ?   -0.9   0.0      0.62     1e+03      74     111 ..     261     298 ..     255     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                   HAUS-augmin3  49 LeeaLktie..psdlkq.edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekea 125
                                    L+ +L+ ++   +dl+  + +++l+v+++++ +++ + +  ++ L +  + +++r + Lq + a ++++ + l+e+ +++
  gi|121639416|ref|YP_979640.1| 138 LNGVLQDLGrnANDLNRpQFEQALNVFTQALHDATPQVRGAVDGLTSLSRALNRRDEALQGLLAHAKSVTSVLSERAEQV 217
                                    6667888887667777789999*****************************************************99999 PP

                   HAUS-augmin3 126 kkklkeaqeelraenae...tnavLqqlteeakqlaeyfeeaek 166
                                    +k +++ ++ ++a  a+   ++a+ + + + a q++ +  +++k
  gi|121639416|ref|YP_979640.1| 218 NKLVEDGNQLFAALDARraaLSALISGIDDVAAQISGFVADNRK 261
                                    99999999877665554111666666666666666666666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
                   HAUS-augmin3  74 eeeeesleaLeqelqeLqkekalklkrlnkLqvqaasl 111
                                    +e + +l +L+  l +L + ++ +++ l++L   a++l
  gi|121639416|ref|YP_979640.1| 261 KEFGPALSKLNLVLANLNERRDYITEALKRLPTYATTL 298
                                    56677888888888999999999999998888888876 PP

>> RPN13_C  UCH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.4   3.9e+03      12      36 ..     120     144 ..     115     153 .. 0.78
   2 ?   12.2   0.4   9.4e-05      0.15      62      89 ..     152     181 ..     147     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                        RPN13_C  12 aaaqepevsLsdiltpealspllsd 36 
                                    ++++++++ Ls   tp +l+ +l+d
  gi|121639416|ref|YP_979640.1| 120 GSGKSTTIPLSRTTTPYTLNGVLQD 144
                                    4455889999999999999999977 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.4e-05
                        RPN13_C  62 lrSPqfrqalsslsqAL..qsgqlgpvlsq 89 
                                    l+ Pqf+qal+ ++qAL   + q+++ +++
  gi|121639416|ref|YP_979640.1| 152 LNRPQFEQALNVFTQALhdATPQVRGAVDG 181
                                    778**************5545666666655 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.7    0.0037         6       4      82 ..     160     233 ..     158     240 .. 0.88
   2 ?    2.7   0.0      0.11   1.8e+02      25      64 ..     244     283 ..     235     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                  T7SS_ESX_EspC   4 nLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLra 82 
                                     L+V +++l  +  ++++++++++s+ +a +++ +a++       +a++++v++++  r++++++l +++++L + L+a
  gi|121639416|ref|YP_979640.1| 160 ALNVFTQALHDATPQVRGAVDGLTSLSRALNRRDEALQGL-----LAHAKSVTSVLSERAEQVNKLVEDGNQLFAALDA 233
                                    599***************************6666666665.....9*************************99888875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                  T7SS_ESX_EspC  25 eiasavaaaagasaavldshGpicaatndavaaaeaarra 64 
                                    +i++++a  +g +a++ + +Gp  +++n+ +a++ + r+ 
  gi|121639416|ref|YP_979640.1| 244 GIDDVAAQISGFVADNRKEFGPALSKLNLVLANLNERRDY 283
                                    5677777777888888999999999999999999888753 PP

>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.2    0.0018       2.9       1      23 [.      17      39 ..      17      40 .. 0.93
   2 ?   -3.7   0.0       4.7   7.7e+03      20      31 ..     289     300 ..     289     300 .. 0.88
   3 ?    2.3   0.0     0.066   1.1e+02       9      24 ..     321     336 ..     319     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0018
                                   S-HHHHHHHHHHHHHHS-TTTHH CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLP 23
                                   +g+  l+++  V+l+ FG ++LP
  gi|121639416|ref|YP_979640.1| 17 TGIFGLVLVICVVLIAFGYSGLP 39
                                   588899***************99 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.7
                                    TTHHHHHHHHHH CS
                    MttA_Hcf106  20 kkLPEvaraLGk 31 
                                    k+LP  a  LG+
  gi|121639416|ref|YP_979640.1| 289 KRLPTYATTLGE 300
                                    89**99999995 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.066
                                    HHHHHHHHS-TTTHHH CS
                    MttA_Hcf106   9 IlvValllFGpkkLPE 24 
                                    ++ V  l+F p kLP+
  gi|121639416|ref|YP_979640.1| 321 VATVFDLVFQPGKLPD 336
                                    777888*********8 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       5.3   8.6e+03      13      25 ..     157     169 ..     152     192 .. 0.57
   2 ?   10.0   0.0   0.00031       0.5      24      99 ..     210     290 ..     201     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.3
                          BAR_3  13 fResleevEaele 25 
                                    f ++l+++ + l+
  gi|121639416|ref|YP_979640.1| 157 FEQALNVFTQALH 169
                                    3333333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00031
                          BAR_3  24 leelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkes.....kgdeetdesLkkfsellqelenehtilldqaq 98 
                                    l+e  ++++kl+ ++++l++a  a  aa +++++++ +++ +       + +e   +L k++ +l +l++ ++ + + ++
  gi|121639416|ref|YP_979640.1| 210 LSERAEQVNKLVEDGNQLFAALDARRAALSALISGIDDVAAQIsgfvaDNRKEFGPALSKLNLVLANLNERRDYITEALK 289
                                    56667899*******************************99987885444555559*************99998888776 PP

                          BAR_3  99 r 99 
                                    r
  gi|121639416|ref|YP_979640.1| 290 R 290
                                    6 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.8       5.2   8.4e+03      13      23 ..      22      32 ..      18      34 .. 0.72
   2 ?    5.5   0.1     0.012        20      31      85 ..     157     211 ..     141     214 .. 0.86
   3 ?    9.2   0.1   0.00088       1.4      20      85 ..     188     253 ..     182     257 .. 0.81
   4 ?    3.9   0.0     0.039        63      24      77 ..     245     298 ..     236     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.2
                         DUF948 13 Lviflivvllk 23
                                   Lv++++vvl+ 
  gi|121639416|ref|YP_979640.1| 22 LVLVICVVLIA 32
                                   78888888865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                         DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    +++++++ ++ ++  + +v+++++    l   +n++ e+++ l ++++ ++  +s
  gi|121639416|ref|YP_979640.1| 157 FEQALNVFTQALHDATPQVRGAVDGLTSLSRALNRRDEALQGLLAHAKSVTSVLS 211
                                    56778888888888888999999999999999999********999999998876 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00088
                         DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    +l++  + l+ + a+ +++++ + +  ++v++l++  n+l + +  + +++ +l++ + d+++++s
  gi|121639416|ref|YP_979640.1| 188 ALNRRDEALQGLLAHAKSVTSVLSERAEQVNKLVEDGNQLFAALDARRAALSALISGIDDVAAQIS 253
                                    555666777788888888888999999999999999999999999999999999999999999887 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.039
                         DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                    + +++ +++ ++++ +k+ +p l +++ +la+ ne  + ++e l+++ +  + +
  gi|121639416|ref|YP_979640.1| 245 IDDVAAQISGFVADNRKEFGPALSKLNLVLANLNERRDYITEALKRLPTYATTL 298
                                    5566777777888888999999************98888888888877666555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.15   2.5e+02     129     156 ..       7      34 ..       3      36 .. 0.87
   2 ?    7.1   0.0   0.00066       1.1     610     721 ..     138     269 ..     129     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                       Prominin 129 qkqkksdacrRktlgvllllltlllliG 156
                                      ++++d+ r  ++g++l++ ++l+ +G
  gi|121639416|ref|YP_979640.1|   7 SSKHERDPLRTGIFGLVLVICVVLIAFG 34 
                                    567899999****************999 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00066
                       Prominin 610 sslyleqlckkltkvnletlaekleelanelsngk....................knlkqslkneaqdlraiqqelvlpl 669
                                     + +l++l ++ +++n +++++ l+ + ++l+ ++                    +++ q l  +a+++ ++ +e+++++
  gi|121639416|ref|YP_979640.1| 138 LNGVLQDLGRNANDLNRPQFEQALNVFTQALHDATpqvrgavdgltslsralnrrDEALQGLLAHAKSVTSVLSERAEQV 217
                                    556677777777777777777777777777777667777888888888888777799999999***************** PP

                       Prominin 670 essvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinnesk 721
                                    +++v++ ++   +ld++   l++ i+ + + + +   f+ +n +e+  ++sk
  gi|121639416|ref|YP_979640.1| 218 NKLVEDGNQLFAALDARRAALSALISGIDDVAAQISGFVADNRKEFGPALSK 269
                                    *****************************99999999999999887655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2362.30
//
Query:       gi|121639417|ref|YP_979641.1|  [L=350]
Description: Mce-family protein mce4B [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-17   61.7   0.1    1.3e-16   60.7   0.1    1.5  1  MlaD          MlaD protein
    3.3e-06   26.7   3.4    5.7e-06   26.0   3.1    1.5  1  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
  ------ inclusion threshold ------
      0.034   14.2   3.0      0.066   13.3   2.8    1.6  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
      0.046   13.7   0.3      0.084   12.9   0.3    1.3  1  CcmE          CcmE
      0.057   12.7   0.1      0.098   12.0   0.1    1.3  1  CorA          CorA-like Mg2+ transporter protein
      0.082   11.6   0.0       0.11   11.2   0.0    1.0  1  MAP65_ASE1    Microtubule associated protein (MAP65/ASE1 fami
       0.17   12.0   0.1       0.24   11.5   0.1    1.2  1  Mod_r         Modifier of rudimentary (Mod(r)) protein


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1     5e-20   1.3e-16       3      81 .]      43     118 ..      41     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5e-20
                           MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdpg 81 
                                      ++a+f++a++Lk+g++Vr++Gv+vG+V++++l+pd   + v + +d   +  +++++ra ++ ++l+g+++++++ g
  gi|121639417|ref|YP_979641.1|  43 TVYHATFTDASRLKAGQKVRIAGVPVGSVKAVKLNPDHS-IDVAFAID--RSYTLYSSTRAVIRYENLVGDRFLEITSG 118
                                    5699******************************99887.7*******..*************************9875 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   3.1   2.2e-09   5.7e-06       4     136 ..     150     282 ..     148     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.2e-09
                      Mce4_CUP1   4 lplleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnav 83 
                                     p+l+  d  k+n++ sAv e L+G+G  l + l+d  ++ ++l +r   + e i++l+++ ++ ++ + ++   +d++ 
  gi|121639417|ref|YP_979641.1| 150 RPVLKGFDADKINTITSAVIELLQGQGGPLANVLADTGAFSAALGARDQLIGEVITNLNAVLATVDAKSAQFSASVDQLQ 229
                                    6899999************************************************************************* PP

                      Mce4_CUP1  84 ttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLa 136
                                    +  + ++++++ ++ +++ ++++ +++++ll++++  L+ +++++rp ++ L+
  gi|121639417|ref|YP_979641.1| 230 QLVSGLAKNRDPIAGAISPLASTTTDLTELLRNSRRPLQGILENARPLATELD 282
                                    ***********************************************887665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.8   2.6e-05     0.066      17     120 ..     178     279 ..     165     297 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                   Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsi 93 
                                     L nvL++  + ++ + ++  +l+ ++ t+Lna+ + + + +a    ++++++++L++ +  l+   d +  ++  l s 
  gi|121639417|ref|YP_979641.1| 178 PLANVLADTGAFSAAL-GARDQLIGEVITNLNAVLATVDAKSA----QFSASVDQLQQLVSGLAknrDPIAGAISPLAST 252
                                    4788888884444444.55555555555555555555555444....8888888888888888888899*********** PP

                   Baculo_PEP_C  94 ltnLlssvtNinstLnnllqalnnldl 120
                                     t+L+  + N    L+++l+    l++
  gi|121639417|ref|YP_979641.1| 253 TTDLTELLRNSRRPLQGILENARPLAT 279
                                    ****99999999999999987766644 PP

>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.3e-05     0.084       7      96 ..      19     114 ..      13     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXSSSXXBXTTTTTS--S-TTSEEEEEEEE-TTT-...EE-T.TSSEEEEEEE-..... CS
                           CcmE   7 klivllllvlaavvvlvlsalqenlvyfltpsevlekkaeegrrlrvgGlVkegsv...krdp.esleveFvvtd..... 77 
                                      +v+ll++ ++vvv+    +  ++vy  t +++   + ++g+++r+ G+   gsv   k +p +s +v F +       
  gi|121639417|ref|YP_979641.1|  19 FAVVMLLVAAGLVVVFGDFRFGPTTVYHATFTDAS--RLKAGQKVRIAGV-PVGSVkavKLNPdHSIDVAFAIDRsytly 95 
                                    33444444444445555566778889999999985..4689******994.44554111445557889999999877766 PP

                                    T.-EEEEEEES---TT--T CS
                           CcmE  78 lekelkVeYegilPdlFre 96 
                                     +++  ++Ye+ + d F e
  gi|121639417|ref|YP_979641.1|  96 SSTRAVIRYENLVGDRFLE 114
                                    578999*******999966 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.8e-05     0.098     116     206 ..     207     297 ..     190     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                           CorA 116 ldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkey 193
                                    l++++ ++++   + ++ +d+l++ +    +++++i++ ++ l  + + l + l+++r+ l+ +l+ +  +l ++ d ++
  gi|121639417|ref|YP_979641.1| 207 LNAVLATVDAKSAQFSASVDQLQQLVsgLAKNRDPIAGAISPLASTTTDLTELLRNSRRPLQGILE-NARPLATELD-NR 284
                                    56677778888888899999999999***********************************99999.6666666555.67 PP

                           CorA 194 lrdlldelerlle 206
                                      ++ +++e+l e
  gi|121639417|ref|YP_979641.1| 285 KAEVNNDIEQLGE 297
                                    8999999999765 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.3e-05      0.11      75     154 ..     205     298 ..     198     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---SS--TSS--HHHHHHHHHHHHHHHH..............HHHHH CS
                     MAP65_ASE1  75 taleelrkekaerlaeflelleqlqklceelgeeplsllidslpkleeleslrkhleelke..............ekerR 140
                                    t+l+ +++  + + a+f+ +++qlq+l++ l ++ ++++ +  p  +++++l + l + +               e ++R
  gi|121639417|ref|YP_979641.1| 205 TNLNAVLATVDAKSAQFSASVDQLQQLVSGLAKNRDPIAGAISPLASTTTDLTELLRNSRRplqgilenarplatELDNR 284
                                    678899999************************99999888888888888888888888888888886555555566666 PP

                                    HHHHHHHHHHHHHH CS
                     MAP65_ASE1 141 leeikelkkqIksl 154
                                     +e+++  +q+ ++
  gi|121639417|ref|YP_979641.1| 285 KAEVNNDIEQLGED 298
                                    66666666665544 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.5e-05      0.24      15      97 ..     218     301 ..     206     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                          Mod_r  15 eeklealvktlpe.vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                      +++a v++l++ v  l ++++ +  ++  la+   +l + l++ r  lq  le+++ l +e+++ ++e ++ ++++++
  gi|121639417|ref|YP_979641.1| 218 SAQFSASVDQLQQlVSGLAKNRDPIAGAISPLASTTTDLTELLRNSRRPLQGILENARPLATELDNRKAEVNNDIEQLGE 297
                                    46788888888555999999******************************************************999999 PP

                          Mod_r  94 dall 97 
                                    d l+
  gi|121639417|ref|YP_979641.1| 298 DYLR 301
                                    9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2387.05
//
Query:       gi|121639418|ref|YP_979642.1|  [L=400]
Description: Mce-family protein mce4A [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-50  169.6   0.0    1.1e-49  169.3   0.0    1.1  1  Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
      1e-14   54.6   0.2    2.6e-14   53.2   0.2    1.8  2  MlaD       MlaD protein


Domain annotation for each model (and alignments):
>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.0   1.2e-53   1.1e-49       1     245 [.     146     389 ..     146     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 1.2e-53
                      Mce4_CUP1   1 enllplleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLd 80 
                                    + l++ll+++dP + natLsA++e+L+G G+ lG  l+ ln++ ++ Np+lp l+ed+r+ a +a+vYadaa dl ++ d
  gi|121639418|ref|YP_979642.1| 146 QSLIDLLHKIDPLETNATLSALSEGLRGHGDDLGALLSGLNTLTRQANPKLPALQEDFRKAAVVANVYADAAGDLNTVFD 225
                                    57999*************************************************************************** PP

                      Mce4_CUP1  81 navttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptlelLakYspeltCllrnladvepkvakal 160
                                    n+ t ++Tiv+q+++L++ lla++glsn++ + l+  ++n+i++++ lr+ l++  +Ysp + Cl++++a+ ++++a   
  gi|121639418|ref|YP_979642.1| 226 NLPTINKTIVDQKDNLNDTLLATIGLSNNAYETLAPAEQNFIDAINRLRAPLKVTSDYSPVFGCLFKGIARGVKEFAPLI 305
                                    *************************************************************************9998876 PP

                      Mce4_CUP1 161 ggtngyslrldatlllgarnpYvypedlPrvnakgGP..ggapgcgslqditrd.wperelvsdtlapagvsiaphleig 237
                                     g ++ +l +++  +lga   Y+ype lP vna+gGP  +g p  ++ q+     ++++ lv+d  a    ++ ++l+++
  gi|121639418|ref|YP_979642.1| 306 -GVRKAGLFTSSSFVLGA-PSYTYPESLPIVNASGGPncRGLPDIPTKQTGG-SfYRAPFLVTDN-ALIPYQPFTELQVD 381
                                    .668999*9*******99.9****************9555888887744444.4599999*9998.33355555588888 PP

                      Mce4_CUP1 238 vPawaeYv 245
                                     P  ++++
  gi|121639418|ref|YP_979642.1| 382 APSTLQFL 389
                                    88887776 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.2   2.9e-18   2.6e-14       3      80 ..      41     117 ..      39     118 .. 0.96
   2 ?   -3.1   0.0       1.2     1e+04      47      61 ..     139     162 ..     126     173 .. 0.44

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.9e-18
                           MlaD   3 ytvtaqfdnang.LkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggllgekyialdp 80 
                                     tvt+  ++a+  +++ga+V+yrG++vG+Vt+i++   ++++++++ +d+ +  +ip+++++ + +++++g+k ++++p
  gi|121639418|ref|YP_979642.1|  41 DTVTVSSPRAGLvMEKGAKVKYRGIQVGKVTDISY--SGNQARLKLAIDSGEMGFIPSNATVRIAGNTIFGAKSVEFIP 117
                                    699******************************66..***************************************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                           MlaD  47 vdld.........kksetsipeds 61 
                                    ++++          ++++++++++
  gi|121639418|ref|YP_979642.1| 139 LEVNtlfqslidlLHKIDPLETNA 162
                                    222233333333334555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.58
# Mc/sec: 2070.14
//
Query:       gi|121639419|ref|YP_979643.1|  [L=280]
Description: integral membrane protein YrbE4b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-50  171.4  29.6    2.6e-50  171.1  29.6    1.1  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1  29.6   1.4e-54   2.6e-50       8     211 ..      64     267 ..      58     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 1.4e-54
                           MlaE   8 vgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtmrvteeid 87 
                                    +++++++++++++l  G v+a+qg+s l ++g+e+l+g+l a+  vr ++Pv++++ +a+ +G++ +A+lG+mrv+eeid
  gi|121639419|ref|YP_979643.1|  64 MIGGTVGVAAFLTLASGGVIAVQGYSSLGDIGIEALTGFLSAFLNVRVVAPVIAGIALAATIGAGATAQLGAMRVSEEID 143
                                    78899*************************************************************************** PP

                           MlaE  88 AlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllKalvfGl 167
                                    A e+m++ +++ylv +r++A+++a++ L+ +++l++++++++++v++ g+s+g y +++ ++l ++dll+++++a+ + +
  gi|121639419|ref|YP_979643.1| 144 AVECMAVHSVSYLVSTRLIAGLVAIIPLYSLSVLAAFFAARFTTVFVNGQSAGLYDHYFNTFLIPSDLLWSFMQAIAMSI 223
                                    ******************************************************************************** PP

                           MlaE 168 iialiacyqGltakggaegvgrattravvtsivlilvvdlvltl 211
                                    +++l+++y+G++a+gg+ gvg a+ +av ts+++++v+ l+++l
  gi|121639419|ref|YP_979643.1| 224 AVMLVHTYYGYNASGGSVGVGVAVGQAVRTSLIVVVVITLFISL 267
                                    ****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1560.87
//
Query:       gi|121639420|ref|YP_979644.1|  [L=254]
Description: integral membrane protein YrbE4a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-60  204.5  19.2    1.7e-60  204.3  19.2    1.0  1  MlaE      Permease MlaE


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3  19.2   9.5e-65   1.7e-60       1     212 []      36     247 ..      36     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 9.5e-65
                           MlaE   1 lveqlefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtm 80 
                                    +++q++ v+  sl+++ll+++++++++a+ +  +l+++ga +l g+ +a+ ++ +lgPv+t l+vag+ ++ai+A+lG++
  gi|121639420|ref|YP_979644.1|  36 FLDQTWMVARVSLVPTLLVSIPFTVLVAFTLNILLREIGAADLSGAGTAFGTITQLGPVVTVLVVAGAGATAICADLGAR 115
                                    679***************************************************************************** PP

                           MlaE  81 rvteeidAlevmgidpikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgll 160
                                    +++eeidA++v+gidpi++lvvPrvlA++++++lL+ +++++g+ ggy ++v+l+g++pga++++++  + l++l+ + +
  gi|121639420|ref|YP_979644.1| 116 TIREEIDAMRVLGIDPIQRLVVPRVLASTLVALLLNGLVCAIGLSGGYAFSVFLQGVNPGAFINGLTVLTGLRELILAEI 195
                                    ******************************************************************************** PP

                           MlaE 161 KalvfGliialiacyqGltakggaegvgrattravvtsivlilvvdlvltll 212
                                    Kal+fG++ +l++cy+Glt+kgg++gvg+a++++vv+++++++v+++v+t++
  gi|121639420|ref|YP_979644.1| 196 KALLFGVMAGLVGCYRGLTVKGGPKGVGNAVNETVVYAFICLFVINVVMTAI 247
                                    *************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1419.02
//
Query:       gi|121639421|ref|YP_979645.1|  [L=317]
Description: 3-ketoacyl-ACP reductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-38  131.8   5.5    2.7e-38  131.4   5.5    1.1  1  adh_short     short chain dehydrogenase
    1.3e-33  116.5   9.7    1.8e-33  116.1   9.7    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    5.8e-15   55.7   6.8    1.5e-14   54.4   6.8    1.5  1  KR            KR domain
  ------ inclusion threshold ------
      0.022   13.8   0.0      0.031   13.2   0.0    1.1  1  Omp_AT        Solitary outer membrane autotransporter beta-ba


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   5.5     6e-42   2.7e-38       1     187 [.      21     218 ..      21     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 6e-42
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHH.HHHHHHHHHHHT....TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrsee.kleevakelkee....gakalaiqvDvtdreevealvekavkkl 75 
                                    kv++vtGa++G+Gra a  la+ Ga+vvv d  ++ ++  v++e++++    gaka+a+++D+++r+ +++l++ a   l
  gi|121639421|ref|YP_979645.1|  21 KVAVVTGAAAGLGRAEALGLARLGATVVVNDVASAlDASDVVDEIGAAaadaGAKAVAVAGDISQRATADELLASA-VGL 99 
                                    89***************************76654427889******998888999********************9.789 PP

                                    SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH........HCTTEEEEEEEEGGGTSB-TTBH CS
                      adh_short  76 gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml........kqssGrIvnvsSvagkvpvagva 147
                                    g+ld++vnNAGit++++  ++s+eew++vi+v l g flltr ++ ++          +  Gr vn+sS ag+v+  g+a
  gi|121639421|ref|YP_979645.1| 100 GGLDIVVNNAGITRDRMLFNMSDEEWDAVIAVHLRGHFLLTRNAAAYWRdkakdaegGSVFGRLVNTSSEAGLVGPVGQA 179
                                    ***********************************************99888765544455899**************** PP

                                    HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                      adh_short 148 aYsAsKaavagltrslakelaptgirvnavaPGlvdTdma 187
                                     Y+A+Ka++++lt s+a+ l ++g+  n+++P + +T+m+
  gi|121639421|ref|YP_979645.1| 180 NYAAAKAGITALTLSAARALGRYGVCANVICPRA-RTAMT 218
                                    *******************************964.55555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   9.7     4e-37   1.8e-33       1     229 [.      27     263 ..      27     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 4e-37
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHH...HHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveel...aeelgae.v.lecDVtdeeqvealveevvekfgklDil 73 
                                    Gaa g+Gra A  la+ Ga+vv+ d+  ++   + v+e+   a++ ga+ v ++ D++++++ ++l + +v  +g+lDi+
  gi|121639421|ref|YP_979645.1|  27 GAAAGLGRAEALGLARLGATVVVNDVASALdaSDVVDEIgaaAADAGAKaVaVAGDISQRATADELLASAVG-LGGLDIV 105
                                    9**************************9997445555541114455666447*****************996.7****** PP

                                    EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..........CEEEEEEEGGGTSBSTTTTHHHH CS
                   adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..........gsivnlssvgaervvpnynayga 143
                                    vnnagi+++    + ++s+ee+d +++v l++ fll++ a+ + +++          g++vn+ss ++ ++  +++ y+a
  gi|121639421|ref|YP_979645.1| 106 VNNAGITRD--RMLFNMSDEEWDAVIAVHLRGHFLLTRNAAAYWRDKakdaeggsvfGRLVNTSSEAGLVGPVGQANYAA 183
                                    *********..*******************************77665567788999999********************* PP

                                    HHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGS.TTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT- CS
                   adh_short_C2 144 aKaalealtrylAvelgpkgiRvNavspgpikTlaasgi.kgfdelleelearaplgrlgtpeevaeaalfLasdeasyi 222
                                    aKa++ alt ++A+ lg++g+  N+++p +  T +++++   ++++++            +p++v +++ fLas++a+ +
  gi|121639421|ref|YP_979645.1| 184 AKAGITALTLSAARALGRYGVCANVICPRAR-TAMTADVfGAAPDVEAGQ------IDPLSPQHVVSLVQFLASPAAAEV 256
                                    ****************************975.556555504444443332......345689****************** PP

                                    -SEEEEE CS
                   adh_short_C2 223 tGqtlvv 229
                                    +Gq+++v
  gi|121639421|ref|YP_979645.1| 257 NGQVFIV 263
                                    ****998 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   6.8   3.2e-18   1.5e-14       4     160 ..      24     192 ..      22     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 3.2e-18
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHH.HHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskali.aelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                    ++tG++ gLG++ a  la+ ga+ +v    sa   +d  ++i a+ ++ ga+  +va D+s+++   +ll+++    + +
  gi|121639421|ref|YP_979645.1|  24 VVTGAAAGLGRAEALGLARLGATVVVNDVASALDASDVVDEIgAAAADAGAKAVAVAGDISQRATADELLASAVGL-GGL 102
                                    89***********************987777655555555551556667***********************9854.69* PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT............S--SEEEEEEEHHHHH--TT-HHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled............esldffvlfSSiagllgsagqanYa 150
                                      v++ Ag++rd++l +m++e++++v+a  ++G   L +  +             +    +v +SS agl+g  gqanYa
  gi|121639421|ref|YP_979645.1| 103 DIVVNNAGITRDRMLFNMSDEEWDAVIAVHLRGHFLLTRNAAAywrdkakdaeggSVFGRLVNTSSEAGLVGPVGQANYA 182
                                    **********************************999987766666666555554455679******************* PP

                                    HHHHHHHHHH CS
                             KR 151 aaNaflDala 160
                                    aa a + al 
  gi|121639421|ref|YP_979645.1| 183 AAKAGITALT 192
                                    **99998886 PP

>> Omp_AT  Solitary outer membrane autotransporter beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-06     0.031     147     208 ..     123     187 ..     111     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-06
                         Omp_AT 147 enWtls..vgigaqllyyrnkytYnsdvlkslk.svlDgllvNtsanAliiepnvklkYeeekdw 208
                                    e+W +   v +  ++l  rn   Y  d+ k+ + + + g+lvNts+ A ++ p  +++Y   k +
  gi|121639421|ref|YP_979645.1| 123 EEWDAViaVHLRGHFLLTRNAAAYWRDKAKDAEgGSVFGRLVNTSSEAGLVGPVGQANYAAAKAG 187
                                    7898651155679***************9999735799*********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.59
# Mc/sec: 1624.92
//
Query:       gi|121639422|ref|YP_979646.1|  [L=63]
Description: ferredoxin fdxD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.6   3.8    1.4e-13   51.4   3.8    1.0  1  Fer4_15   4Fe-4S single cluster domain
    2.4e-13   50.4   1.6      3e-13   50.1   1.6    1.0  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      1e-05   25.5   0.0    1.3e-05   25.2   0.0    1.1  1  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   3.8   2.3e-17   1.4e-13       1      64 [.       3      59 ..       3      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.3e-17
                        Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                   V vDrd+C+g ++C+  ap++f ld++++a+v++       +++p d+e+ a++A ++CP +A+
  gi|121639422|ref|YP_979646.1|  3 VIVDRDRCEGNAVCLGIAPDIFDLDDEDYAVVKT-------DPIPVDQEDLAEQAIAECPRAAL 59
                                   78****************************7774.......69******************997 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   1.6   4.9e-17     3e-13       1      55 [.       5      58 ..       5      60 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 4.9e-17
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPves 55
                                   VDrd+C + ++C  +aPd+F+ dde+ ++vv+ +p + +++++ae+A+++CP ++
  gi|121639422|ref|YP_979646.1|  5 VDRDRCEGNAVCLGIAPDIFDLDDED-YAVVKTDPIPVDQEDLAEQAIAECPRAA 58
                                   9***********************95.88999********************987 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.2e-09   1.3e-05       7      60 ..       2      60 ..       1      62 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.2e-09
                        Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrkpwi..kpdeast...eeiievverCPSGALs 60
                                   ++  +r+ C++ ++C   +p++Fd++++ +   k d   +   + +++++++CP  ALs
  gi|121639422|ref|YP_979646.1|  2 RVIVDRDRCEGNAVCLGIAPDIFDLDDEDYAvvKTDPIPVdqeDLAEQAIAECPRAALS 60
                                   78899**********************9765455555444334567899*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 347.05
//
Query:       gi|121639423|ref|YP_979647.1|  [L=400]
Description: acyl-CoA dehydrogenase fadE26 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-41  140.4   0.1    7.7e-41  139.8   0.1    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.7e-23   81.7   0.1    1.3e-22   80.6   0.1    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    6.1e-20   71.2   0.0    1.1e-19   70.4   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    0.00011   22.5   0.0     0.0002   21.6   0.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.17   12.4   0.0        0.4   11.2   0.0    1.6  1  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.1   2.1e-44   7.7e-41       1     149 [.     234     392 ..     234     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 2.1e-44
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC.-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafg.kplidhqlvreklaemaaeleaarllvyraae... 76 
                                    + G+++++++lnheR+a++  + + +  +l+e++e+a+++k+ g ++lid+++v+ +la+++a++e+++l+++++a+   
  gi|121639423|ref|YP_979647.1| 234 NAGWKLVTNQLNHERVALV--SPAPIFGCLREVREWAQNTKDAGgTRLIDSEWVQLNLARVHAKAEVLKLINWELASsqs 311
                                    78****************8..9******************99998*******************************9777 PP

                                    --------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT........SGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  77 aldagkpdraeasmaKlfaselaqevadlamqllGgaGy........leeypverlyrdarvlrigeGtseiqrniiarr 148
                                    ++++++p++a+as+aK+f++ela+e+++l m++lG+a++        l +++ver++r++++l++g+Gt+e+qr+ii+++
  gi|121639423|ref|YP_979647.1| 312 GPKDAGPSPADASAAKVFGTELATEAYRLLMEVLGTAATlrqnspgaLLRGRVERMHRACLILTFGGGTNEVQRDIIGMV 391
                                    88999999*******************************8888888668888*************************997 PP

                                    H CS
                  Acyl-CoA_dh_1 149 l 149
                                    +
  gi|121639423|ref|YP_979647.1| 392 A 392
                                    6 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.1   3.6e-26   1.3e-22       1     113 []       6     122 ..       6     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 3.6e-26
                                    THHHHHHHHHHHHHHHHHTHHHHHHHH..HHTS.....GHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewd..eege.....fprelwkklaelGllgitvpeeygGagldyleaaivaeelar 73 
                                    t++qe+lr+++r+++++ + p  +e+    +ge     + re++ ++++ G+l++ +p+eygG+g ++++++i+++e a 
  gi|121639423|ref|YP_979647.1|   6 TPQQEELRRELRSYFATLMTPERREALssVQGEygvgnVYRETIAQMGRDGWLALGWPKEYGGQGRSAMDQLIFTDEAAI 85 
                                    789****************998887754433344555566999************************************* PP

                                    H-HHHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  74 adaglalllgvhsslvapailrfGteeqkrryLpklasge 113
                                    a+a++  +l ++   vap+i+++Gt+eqkr +Lp++a+g+
  gi|121639423|ref|YP_979647.1|  86 AGAPVP-FLTIN--SVAPTIMAYGTDEQKRFFLPRIAAGD 122
                                    ***953.45554..3569*******************996 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   3.2e-23   1.1e-19       2      92 ..     127     217 ..     126     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 3.2e-23
                                    EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---....----EEEEEEE..GGGEE CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd....rarglslflvprdapgvs 74 
                                    ++ +Ep+aG+d+a+++t +a rdg++yv+nG+K+w +  ++a+++ + +r   +   +    ++rg+s+++vp+ a+g+s
  gi|121639423|ref|YP_979647.1| 127 IGYSEPGAGTDLANLRT-TAVRDGDDYVVNGQKMWTSLIQYADYVWLAVRtnpE---SsgakKHRGISVLIVPTTAEGFS 202
                                    789**************.77777778************************7552...234579***************** PP

                                    E-----BSS-TTS-EEEE CS
                  Acyl-CoA_dh_M  75 vrrieeklGlrglptgel 92 
                                    ++++++  G +   t+  
  gi|121639423|ref|YP_979647.1| 203 WTPVHTMAGPD---TSAT 217
                                    ****8755544...3333 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.6e-08    0.0002      13     113 ..     259     353 ..     258     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.6e-08
                                    HHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  13 aalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalave 92 
                                    ++l e+ e+a++ +  ++g++l d++ +ql la++ a+ + ++++  + a++     +ag        a+a++a+++ +e
  gi|121639423|ref|YP_979647.1| 259 GCLREVREWAQNTKD-AGGTRLIDSEWVQLNLARVHAKAEVLKLINWELASSQSGPKDAGP-----SPADASAAKVFGTE 332
                                    689999999997776.7****************************9999999444444444.....46************ PP

                                    HHHHHHHHHHHHCGGGGGBTT CS
                  Acyl-CoA_dh_2  93 laiaavdalfeaaGgsalrke 113
                                    la++a + l+e+ G+ a++ +
  gi|121639423|ref|YP_979647.1| 333 LATEAYRLLMEVLGTAATLRQ 353
                                    ****************98765 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011       0.4      99     120 ..      98     119 ..      67     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                    HHHHHHHHS-HHHHHHHHHHHH CS
                  Acyl-CoA_ox_N  99 FlptlkgqgteeQqakWlprae 120
                                    + pt++  gt+eQ++ +lpr+ 
  gi|121639423|ref|YP_979647.1|  98 VAPTIMAYGTDEQKRFFLPRIA 119
                                    679****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2204.39
//
Query:       gi|121639424|ref|YP_979648.1|  [L=373]
Description: acyl-CoA dehydrogenase fadE27 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-22   80.3   0.3    2.6e-22   79.7   0.3    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.7e-13   49.3   1.0    1.3e-12   48.1   1.0    1.6  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.5e-12   47.4   0.0    5.8e-12   46.3   0.0    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
     0.0023   18.1   0.0     0.0043   17.2   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.3   5.8e-26   2.6e-22      16     148 ..     227     367 ..     213     369 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 5.8e-26
                                    ----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------........HHH CS
                  Acyl-CoA_dh_1  16 lavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd........rae 87 
                                    l+  a +lg+++r l+ ++eyar+r++f +p++++q+v ++la+ ++++ ++rl++ +aa+++ ++  +          +
  gi|121639424|ref|YP_979648.1| 227 LSRTAFQLGVLERGLQMTAEYARTREQFDRPIGSFQAVGQRLADGYIDVKGLRLTLTQAAWRVAEDSLAsrecpqpaDID 306
                                    6667899******************************************************8888887778888888888 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  88 asmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                    ++ a ++a+e+ ++va+  ++++Gg G+ +++pv+r++ +a+ ++++ G    q++ i+r 
  gi|121639424|ref|YP_979648.1| 307 VATAGFWAAEAGHRVAHTIVHVHGGVGVDTDHPVHRYFLAAKQTEFALGGATGQLRRIGRE 367
                                    888*******************************************999888888888886 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   1.0     3e-16   1.3e-12       4     120 ..     230     344 ..     227     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                  Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                    +a+ lG++++ l+ ++e+ar+r +  + +++  ++a+ ++la+   +++ +r++l +aa+r+ + + a++e++     + 
  gi|121639424|ref|YP_979648.1| 230 TAFQLGVLERGLQMTAEYARTREQ--FDRPIGSFQAVGQRLADGYIDVKGLRLTLTQAAWRVAEDSLASRECPQPADIDV 307
                                    7999********************..************************************999*******99999999 PP

                                    HHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHH CS
                  Acyl-CoA_dh_2  84 rraaalavelaiaavdalfeaaGgsalrkesplqRlw 120
                                    ++a  +a+e   +++  ++ ++Gg ++++++p+ R++
  gi|121639424|ref|YP_979648.1| 308 ATAGFWAAEAGHRVAHTIVHVHGGVGVDTDHPVHRYF 344
                                    9**********************************98 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.3e-15   5.8e-12       4     112 ..       9     117 ..       6     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.3e-15
                                    HHHHHHHHHHHHHHHT.HHHHHHHHHHT.SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                  Acyl-CoA_dh_N   4 qealrdtvrefaeeel.aphaaewdeeg.efprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                     ++l   v   ++  + ++h +e d+ + +f+relw+kl ++G+l  + pe  gG g+++le++ v+  l++  a++  l
  gi|121639424|ref|YP_979648.1|   9 AQDLGGLVDTIVDAVCtPEHQRELDKLEqRFDRELWRKLIDAGILSSAAPESLGGDGFGVLEQVAVLVALGHQLAAVPYL 88 
                                    556666788889999956688888977769*****************************************988886554 PP

                                    HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasg 112
                                     +v   l+a a++rfG++e ++ +    +sg
  gi|121639424|ref|YP_979648.1|  89 ESV--VLAAGALARFGSPELQQGWGVSAVSG 117
                                    444..455579***********998777777 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.6e-07    0.0043      23      92 ..     138     201 ..     130     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.6e-07
                                    ETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----BSS-TTS-EEEE CS
                  Acyl-CoA_dh_M  23 rdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieeklGlrglptgel 92 
                                    + g +y+l+G+ + ++ ++ a+ +lv a      ++ g  +flv +++pgv v+ + +++Gl ++ + el
  gi|121639424|ref|YP_979648.1| 138 GTGHGYRLTGTRTQVGYGPVADAFLVPAE-----TDSGAAVFLVAAGDPGVAVTAL-ATTGLGSVGHLEL 201
                                    55677************************.....367999**************99.5788887665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 2039.84
//
Query:       gi|121639425|ref|YP_979649.1|  [L=502]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-58  198.7   0.0    1.5e-58  198.4   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    2.8e-07   31.4   0.0    7.3e-07   30.1   0.0    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   1.6e-62   1.5e-58      15     422 ..      24     394 ..      16     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 1.6e-62
                                    EECCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                    AMP-binding  15 vdsgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                    ++  e+   ++r+  ++  ++Aa+Lr +l+  +  +V++ll+n+p + ++l+a +  G+v+v lnp  + ++la  ++++
  gi|121639425|ref|YP_979649.1|  24 YF--EDSFTSWRDHIRHGAAIAAALReRLDPARPPHVGVLLQNTPFFSATLVAGALSGIVPVGLNPVRRGAALAGDIAKA 101
                                    45..67778999999999********999*************************************************** PP

                                    TESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS CS
                    AMP-binding  94 eakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGk 173
                                    ++++++  + s   +++       +a  + i +d+ e+ +e  + ++    +    +++ ++++  dl ++i+TSGT G 
  gi|121639425|ref|YP_979649.1| 102 DCQLVL--TGSGS-AEV-------PADVEHINVDSPEWTDE--VAAHR---DT---EVRFRSADLADLFMLIFTSGTSGD 163
                                    ******..43222.222.......22223444554444433..43333...22...33566789**************** PP

                                    -EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT CS
                    AMP-binding 174 PKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklk 253
                                    PK+V  shr ++ +  ++  ++rf+l++ddv+++ +pl+h+ ++ ++  +a ++ +++ l +k++a    ++l+++++++
  gi|121639425|ref|YP_979649.1| 164 PKAVKCSHRKVAIAGVTI--TQRFSLGRDDVCYVSMPLFHSNAVLVGWAVAAACQGSMALRRKFSAS---QFLADVRRYG 238
                                    ***********9998885..7889999****************99999999999999***9*99983...468******* PP

                                    -SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTT CS
                    AMP-binding 254 vtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleed 332
                                    +t+ ++v   l ++l+ ++l       d    lr v  g e ++ ++ rf  ++fg+ v++g+G TE ++++t  +l+++
  gi|121639425|ref|YP_979649.1| 239 ATYANYVGKPLSYVLATPELP-----DDADNpLRAV-YGNEGVPGDIDRF-GRRFGCVVMDGFGSTEGGVAIT-RTLDTP 310
                                    ****************87777.....267777**95.799**99999855.5556677**************9.666666 PP

                                    CTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEE.EEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEE CS
                    AMP-binding 333 kkklgsvGkplpgvevkivDeetgepvpdgeeGell.vrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyle 411
                                       +g  G+  pg  + ivD++tgep+p+g++Gel+   gpg ++gY+++++a ae++   g+ +++GDl+++d+ Gy +
  gi|121639425|ref|YP_979649.1| 311 ---AGALGPL-PG-GIQIVDPDTGEPCPTGVVGELVnTAGPGGFEGYYNDEAAEAERMA--GGVYHSGDLAYRDDAGYAY 383
                                    ...6766755.77.8*********************889*******************8..57***********99**** PP

                                    EEEECCCEEEE CS
                    AMP-binding 412 ivgRkkdlikl 422
                                    + gR+ d + +
  gi|121639425|ref|YP_979649.1| 384 FAGRLGDWMRV 394
                                    *****998865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   8.2e-11   7.3e-07       2      76 .]     404     480 ..     403     480 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 8.2e-11
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH..HT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk..elgpyavpkkvvfvdelpktrsGK 76 
                                    +E +l++ p+  e+aV+ vpd+v G  ++a  vl++g++  +++ +a++++   lg+   p++v++ + lp+t + K
  gi|121639425|ref|YP_979649.1| 404 IERVLMRYPDATEVAVYPVPDPVVGDQVMAALVLAPGTKFDADKFRAFLTEqpDLGHKQWPSYVRVSAGLPRTMTFK 480
                                    8********************************988864468*******88789999889*****999*****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2694.45
//
Query:       gi|121639426|ref|YP_979650.1|  [L=1372]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-31  106.5  23.5    1.2e-30  105.7  23.5    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7  23.5   6.5e-35   1.2e-30       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 6.5e-35
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv v+Pe++aa+a+dl++ig++l+  na aaa+ttav++aaaDeVS+a+Aalfs+haq yqa++aq+aafh +fvqal+a
  gi|121639426|ref|YP_979650.1|  1 MSFVLVSPETVAAVATDLKRIGASLAHENASAAASTTAVVSAAADEVSTAVAALFSQHAQGYQAAAAQVAAFHSRFVQALTA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya aEaa
  gi|121639426|ref|YP_979650.1| 83 GAGAYAFAEAA 93
                                   *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.64u 0.37s 00:00:02.00 Elapsed: 00:00:00.63
# Mc/sec: 6522.10
//
Query:       gi|121639427|ref|YP_979651.1|  [L=2094]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-33  115.2  13.9    2.2e-33  114.4  13.9    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4  13.9   1.2e-37   2.2e-33       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.2e-37
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv +aPe ++aaa+dl+++gs++saana aa++tt+vlaa+aDeVSa+iAalf+  + eyqa+saq+aa h++fvqal++
  gi|121639427|ref|YP_979651.1|  1 MSFVLIAPEFVTAAAGDLTNLGSSISAANASAASATTQVLAAGADEVSARIAALFGGFGLEYQAISAQVAAYHQRFVQALST 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEa+
  gi|121639427|ref|YP_979651.1| 83 GAGAYASAEAT 93
                                   *********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2094 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      116  (0.00646996); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 2.55u 0.38s 00:00:02.93 Elapsed: 00:00:00.80
# Mc/sec: 7902.27
//
Query:       gi|121639428|ref|YP_979652.1|  [L=515]
Description: hypothetical protein BCG_3573c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-35  122.1   3.2      6e-34  117.1   2.1    2.6  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    6.1e-31  107.3   0.1    2.9e-29  101.8   0.0    2.4  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   2.1   6.7e-38     6e-34       1     166 [.       1     164 [.       1     169 [. 0.94
   2 !    3.2   0.0    0.0065        58     112     146 ..     466     500 ..     385     509 .. 0.55

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 6.7e-38
                                    EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                   TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                    m++a+al+ +L + gv+++f++pG+++++++ al++ +++r +l++ E++a++aAdgyar+ g+p++vl++ gpG+ n+l
  gi|121639428|ref|YP_979652.1|   1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARIAGRPAAVLLHLGPGLGNGL 80 
                                    89****************************************************************************** PP

                                    HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                   TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                     +l++A+++r+P++v++gd++t++ + +++  e d+ a++  v  +++r + ++++    + Ai+++ sg +  + l lp
  gi|121639428|ref|YP_979652.1|  81 ANLHNARRARVPMVVVVGDHATYHKKYDAPL-ESDIDAVAGTVSGWVRRTEAAADVGADAEAAIAASRSGSQ-IATLILP 158
                                    **************************77777.889999999**************************77666.5667799 PP

                                    HHHCC- CS
                   TPP_enzyme_N 161 kdvlle 166
                                    +dv ++
  gi|121639428|ref|YP_979652.1| 159 ADVCWS 164
                                    999776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0065
                                    --T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHH CS
                   TPP_enzyme_N 112 qeldqlalfrpvtkyaervtspeelpealrrAirt 146
                                    +++d +++++ +   a+rvt+ ee++ alr A+++
  gi|121639428|ref|YP_979652.1| 466 PTMDFVKIAEGMGVPARRVTTCEEFADALRAAFAE 500
                                    23455555555555599999999999999999874 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.0    0.0085        76      60      85 ..      77     103 ..      44     147 .. 0.77
   2 !  101.8   0.0   3.2e-33   2.9e-29      21     153 .]     374     508 ..     359     508 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0085
                                    HT.GGGHHHHHHTT-SEEEEEEE-SBC CS
                   TPP_enzyme_C  60 mi.lqelatavrrnlpitvvvlnNegy 85 
                                     + l  l +a r ++p++vvv + ++y
  gi|121639428|ref|YP_979652.1|  77 GNgLANLHNARRARVPMVVVVGDHATY 103
                                    454677888888888888888777666 PP

  == domain 2  score: 101.8 bits;  conditional E-value: 3.2e-33
                                    EECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTT CS
                   TPP_enzyme_C  21 yltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrk 100
                                    +lt  + g++Gyg+paA+Ga++a+pdr+v ++  DG+ +++++ l+  +r+nl++t+v++nN++y   + + ++ g+++ 
  gi|121639428|ref|YP_979652.1| 374 WLT-LTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSD 452
                                    444.56799**************************************************************999999999 PP

                                    TTSBB......BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C 101 sgpagk.....dlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                     gp+         + +df+k+ae++G+++ rv++   ee+++al++a+++ gp li+v
  gi|121639428|ref|YP_979652.1| 453 PGPKALdlldiSRPTMDFVKIAEGMGVPARRVTTC--EEFADALRAAFAEPGPHLIDV 508
                                    9998779**97799**************99*9999..*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3473.34
//
Query:       gi|121639429|ref|YP_979653.1|  [L=278]
Description: hypothetical protein BCG_3574c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-38  131.4   0.3    6.7e-38  131.1   0.3    1.1  1  Amidohydro_2  Amidohydrolase
    6.6e-06   26.1   0.0        0.2   11.7   0.0    2.7  3  TruB-C_2      Pseudouridine synthase II TruB, C-terminal


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.3   7.5e-42   6.7e-38      70     291 .]      69     270 ..      31     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 7.5e-42
                                    HHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE. CS
                   Amidohydro_2  70 nnrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdiht 149
                                    n+ v++++  +p rf+g+aav++  p +a++el+r+v   gf+G+r+ p  +g +++++r++ p+f+ ++   +p+  ++
  gi|121639429|ref|YP_979653.1|  69 NDAVAEWVRLYPNRFAGLAAVDLDRPMAAVRELRRRV-GEGFVGLRVVPWLWGAPPTDRRYY-PLFAECVQSAVPFCTQV 146
                                    5556666666999999**9999999************.9***********************.****************9 PP

                                    ...CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHC CS
                   Amidohydro_2 150 GpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdsplad 229
                                    G    +++  p+et r+  +++++ va +fP+l iv  H G+p  + +++++ +++++nvy+++s+         + +  
  gi|121639429|ref|YP_979653.1| 147 G---HTGPLRPSETGRP--IPYIDQVALDFPELVIVCGHVGYP--WTEEMVAVARKHENVYIDTSA--------YTIKRL 211
                                    9...7788888888866..6***********************..*********************........466777 PP

                                    HHHHHHHHHH.H-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCTB CS
                   Amidohydro_2 230 ppalarliea.vgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarlygl 291
                                    p  l+r  ++ +g+ ++lfG++yP+++ ++ ++ l++l l    sde+r+++l+gNA+r+++l
  gi|121639429|ref|YP_979653.1| 212 PGKLVRFMKTdTGQRKVLFGTNYPMIAHTHALTGLDELGL----SDEARRDFLHGNAVRVFKL 270
                                    777666655538**************************99....*****************86 PP

>> TruB-C_2  Pseudouridine synthase II TruB, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.4   1.2e+04      10      16 ..      11      17 ..       9      18 .. 0.83
   2 !   11.7   0.0   2.3e-05       0.2      15      47 ..      62      90 ..      50      97 .. 0.87
   3 !   11.5   0.0   2.6e-05      0.23       3      32 ..     249     277 ..     248     278 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                       TruB-C_2 10 akrflqG 16
                                   ++rfl+G
  gi|121639429|ref|YP_979653.1| 11 TQRFLHG 17
                                   6899999 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.3e-05
                       TruB-C_2 15 qGQrvklaaglpaeglVRvydeegrFlGvGeit 47
                                   +GQ + + ++++ +++VR+y   +rF G++ ++
  gi|121639429|ref|YP_979653.1| 62 NGQDL-I-SNDAVAEWVRLY--PNRFAGLAAVD 90
                                   89**9.6.7888888*****..********987 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 2.6e-05
                       TruB-C_2   3 veLseesakrflqGQrvklaaglpaeglVR 32 
                                    + Ls+e+ + fl+G++v++  +l+++g+V+
  gi|121639429|ref|YP_979653.1| 249 LGLSDEARRDFLHGNAVRV-FKLDPRGKVQ 277
                                    679**************76.8999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 1447.44
//
Query:       gi|121639430|ref|YP_979654.1|  [L=1810]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-34  116.1  14.9    1.2e-33  115.3  14.9    1.4  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3  14.9   6.5e-38   1.2e-33       1      92 [.       1      92 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 6.5e-38
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv ++Pe+++aaa+dla++gs++saan+aaaa+tt+vlaa+aDeVSa+iAalf+ ++ eyqa+saq+aa h+qfvq+l++
  gi|121639430|ref|YP_979654.1|  1 MSFVLISPEVVSAAAGDLANVGSTISAANKAAAAATTQVLAAGADEVSARIAALFGMYGLEYQAISAQVAAYHQQFVQTLRT 82
                                   9********************************************************************************* PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                   +a+sY+ aEa
  gi|121639430|ref|YP_979654.1| 83 GAASYMLAEA 92
                                   *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 2.88u 0.40s 00:00:03.28 Elapsed: 00:00:00.79
# Mc/sec: 6924.63
//
Query:       gi|121639431|ref|YP_979655.1|  [L=218]
Description: fatty-acid-CoA ligase fadD18 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-17   61.9   0.1    2.4e-16   60.4   0.1    1.7  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    0.00026   19.7   0.1    0.00041   19.1   0.1    1.2  1  AMP-binding    AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.78     7e+03      23      35 ..      52      64 ..      47      77 .. 0.73
   2 !   60.4   0.1   2.7e-20   2.4e-16       1      76 []     116     191 ..     116     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.78
                                   -TTS---EEEEEE CS
                  AMP-binding_C 23 evkGealvafVvl 35
                                   ++kG+++v+++  
  gi|121639431|ref|YP_979655.1| 52 AKKGNIPVGYYKD 64
                                   6799999999865 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 2.7e-20
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE+al  hp+V +a VvGvpd++ G+ ++a+V  ++g  +    +eL ++vr+e++ y+vp+ + fvde+ +   GK
  gi|121639431|ref|YP_979655.1| 116 EVEAALKGHPDVFDALVVGVPDPRYGQQVAAVVQARPGcrP--SLAELDSFVRSEIAGYKVPRSLWFVDEVKRSPAGK 191
                                    8*********************************9988642..46*****************************9998 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.5e-08   0.00041     376     415 ..      59     100 ..      49     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-08
                                    SEBTT-HHHHHHHEEE.T.CCEEEEEEEEEEETTSEEEEEEE CS
                    AMP-binding 376 kgYlkkpeataeafds.e.grwlrTGDlgrldedGyleivgR 415
                                     gY+k++++tae+f + +  r+   GD + ++edG++  +gR
  gi|121639431|ref|YP_979655.1|  59 VGYYKDEKKTAETFRTiNgVRYAIPGDYAQVEEDGTVTMLGR 100
                                    69************9773356********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1189.44
//
Query:       gi|121639432|ref|YP_979656.1|  [L=1075]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  112.0  14.4      2e-32  111.4  14.4    1.3  1  PE              PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4  14.4   1.1e-36     2e-32       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.1e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv +aPe ++aaa+dl+++gs++saana aa++tt+vlaa+aDeVSa+iAalf+  + eyqa+saq+aa h++fvqa ++
  gi|121639432|ref|YP_979656.1|  1 MSFVLIAPEFVTAAAGDLTNLGSSISAANASAASATTQVLAAGADEVSARIAALFGGFGLEYQAISAQVAAYHQRFVQASST 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEa+
  gi|121639432|ref|YP_979656.1| 83 GAGAYASAEAT 93
                                   *********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1075 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.79u 0.42s 00:00:02.21 Elapsed: 00:00:00.75
# Mc/sec: 4327.36
//
Query:       gi|121639433|ref|YP_979657.1|  [L=548]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-66  222.6   0.0      9e-66  222.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.6e-16   59.9   0.1    1.2e-15   58.2   0.1    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.0     1e-69     9e-66       3     415 ..      13     430 ..      11     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 1e-69
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                    ++ +  pd+va++   ++++lTY++l++++nrlA++L   Gv+k+d+V+++++n++e v+a+l+i+kaGa++v +n ++ 
  gi|121639433|ref|YP_979657.1|  13 HAIDAVPDRVAVIC--GDEQLTYAQLEDKANRLAHHLIDQGVQKDDKVGLYCRNRIEIVIAMLGIVKAGAILVNVNFRYV 90 
                                    5567789*******..9*********************88**************************************** PP

                                    HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT.S-TSCCCS-BTTSE CS
                    AMP-binding  83 aeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseeka.ekpeeeeelkpddl 161
                                    + el+y++++s++ +l+   +++ +++++++ ++ ++v++++v+++++ +++++  + e  ++ a + pe++   ++ d 
  gi|121639433|ref|YP_979657.1|  91 EGELRYLFDNSDMVALV--HERRYADRVANVLPDTPHVRTILVVEDGSDQDYRRYGGVEFYSAIAaGSPERDFGERSADA 168
                                    *****************..666669***********************999999999998887775234455578899** PP

                                    EEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.......HHHCSCCTT..........T-EE..EESS-TTSCHHHHHHHH CS
                    AMP-binding 162 ayiiYTSGTTGkPKGVmlshrnlvanvaslk.......letrfklke..........ddvv..lsilplahifglilell 222
                                    +y++YT+GTTG PKGVm +h+ +   +           ++      +          +  +  + i p+ h + + ++++
  gi|121639433|ref|YP_979657.1| 169 IYLLYTGGTTGFPKGVMWRHEDIYRVLFGGTdfatgefVK------DeydlakaaaaNPPMirYPIPPMIHGATQ-SATW 241
                                    ***********************77776654432222222......234555667785555236679*******9.**** PP

                                    HHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHH.HHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHH CS
                    AMP-binding 223 lallsGatvvllpkdaaldpklllelieklkvtviagvPrvle.allesgalkaakkakdlsslrlvllggeplspellr 301
                                    +al+sG t vl+p+++a  ++ ++++i+k+kv++++ +  ++   l+++   k   +++dlssl l+ + ++  sp++ +
  gi|121639433|ref|YP_979657.1| 242 MALFSGQTTVLAPEFNA--DE-VWRTIHKHKVNLLFFTGDAMArPLVDAL-VK--GNDYDLSSLFLLASTAALFSPSIKE 315
                                    *************9988..34.56***************99993455543.44..3466*******99************ PP

                                    HHHHHHTC.EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-T.TEEEEEE-TTTSCBEETTSE..EEEEEEETTS-S CS
                    AMP-binding 302 ffralfge.evlegYGlTEttgvvtv.lpleedkkklgsvGkplp.gvevkivDeetgepvpdgee..Gellvrgpgvmk 376
                                    ++ +l+++  + ++ G +Et+   t  +   ++ +     G+ ++ + +  ++D++ g++v++g    G +  +g+ +  
  gi|121639433|ref|YP_979657.1| 316 KLLELLPNrVITDSIGSSETGFGGTSvVA-AGQ-AHG--GGPRVRiDHRTVVLDDD-GNEVKPGSGmrGVIAKKGN-IPV 389
                                    ********889************974222.233.223..477788899*******9.8888877766688877775.999 PP

                                    EBTT-HHHHHHHEEE.T.CCEEEEEEEEEEETTSEEEEEEE CS
                    AMP-binding 377 gYlkkpeataeafds.e.grwlrTGDlgrldedGyleivgR 415
                                    gY+k++++tae+f + +  r+   GD + ++edG++  +gR
  gi|121639433|ref|YP_979657.1| 390 GYYKDEKKTAETFRTiNgVRYAIPGDYAQVEEDGTVTMLGR 430
                                    *************9773356********************9 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.1   1.3e-19   1.2e-15       1      76 []     446     521 ..     446     521 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.3e-19
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE+al  hp+V +a VvGvpd++ G+ ++a+V  ++g  +    +eL ++vr+e++ y+vp+ + fvde+ +   GK
  gi|121639433|ref|YP_979657.1| 446 EVEAALKGHPDVFDALVVGVPDPRYGQQVAAVVQARPGcrP--SLAELDSFVRSEIAGYKVPRSLWFVDEVKRSPAGK 521
                                    8*********************************9988642..46*****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 2792.03
//
Query:       gi|121639434|ref|YP_979658.1|  [L=263]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-56  191.2   0.0    2.2e-56  191.0   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    3.1e-32  112.4   0.0    1.4e-27   97.1   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.0   0.0   2.4e-60   2.2e-56       7     250 ..      16     262 ..      10     263 .] 0.97

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 2.4e-60
                                    EEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC...HHHHHHHCCHHHHHHH CS
                          ECH_1   7 aviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek...akqallkeevlelwtk 83 
                                    + +++nrP a Nals e++  ++qa  ++++d+ +r  +LtG +++F+aG+dlk+++++ +    k+ ++  +  + + k
  gi|121639434|ref|YP_979658.1|  16 LIVTMNRPAARNALSTEMMRIMVQAWDRVDNDPDIRCCILTGAGGYFCAGMDLKAATQKPPgdsFKDGSYDPSRIDALLK 95 
                                    579*******************************************************98777678999*********** PP

                                    HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHH CS
                          ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqe 163
                                     + + kp+iaav+G ai+GG e+   +Di++a+++a+fg +e+k  l+p  g   +l+r+++  +A  +ll+g++i+a+e
  gi|121639434|ref|YP_979658.1|  96 GRRLTKPLIAAVEGPAIAGGTEILQGTDIRVAGESAKFGISEAKWSLYPMGGSAVRLVRQIPYTLACDLLLTGRHITAAE 175
                                    *************************************************99999************************** PP

                                    HHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                          ECH_1 164 alkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                    a+++Gl+ +vvp+ q l +alela  +  ++p+a++++  +++++  + + e+++++ ++  ++f +dd keG  af+Ek
  gi|121639434|ref|YP_979658.1| 176 AKEMGLIGHVVPDGQALTKALELADAISANGPLAVQAILRSIRETECMPENEAFKIDTQIGIKVFLSDDAKEGPRAFAEK 255
                                    ******************************************99999********************************* PP

                                    SH----- CS
                          ECH_1 244 rkpefed 250
                                    r p+f++
  gi|121639434|ref|YP_979658.1| 256 RAPNFQN 262
                                    *****86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   1.6e-31   1.4e-27       3     179 ..      17     191 ..      15     199 .. 0.91
   2 !   14.5   0.0   2.1e-06     0.018     249     318 ..     195     261 ..     188     263 .] 0.87

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.6e-31
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                    ++t+nrp+a NaLs+em+r + +a +++++d+++++ +l+gag   fCAG D++a +++   ++ +  +   +  ++++l
  gi|121639434|ref|YP_979658.1|  17 IVTMNRPAARNALSTEMMRIMVQAWDRVDNDPDIRCCILTGAG-GYFCAGMDLKAATQKPPGDSFK--DGSYDPSRIDAL 93 
                                    79***************************************99.89*********99988876544..567778889999 PP

                                    HH..C-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHC.SSTTHHHHHHHH---B-H CS
                          ECH_2  83 ia..typkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsr.lpgelGlylalTGarlkg 159
                                    ++  +++kp++a ++G ++ gG+ + +++ +rv+ e+++f + E +  l+P  G    L r +p  l+  l lTG+++++
  gi|121639434|ref|YP_979658.1|  94 LKgrRLTKPLIAAVEGPAIAGGTEILQGTDIRVAGESAKFGISEAKWSLYPMGGSAVRLVRqIPYTLACDLLLTGRHITA 173
                                    8644899***********************************************99999984599*************** PP

                                    HHHHHTTS--EE--GGGHHH CS
                          ECH_2 160 adalaaglathyvpseklea 179
                                    a+a ++gl  h+vp+ +  a
  gi|121639434|ref|YP_979658.1| 174 AEAKEMGLIGHVVPDGQ--A 191
                                    *************9875..4 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.1e-06
                                    HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                          ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                    a + +++++++ P++++++l+++r+++ +   +e+++ + ++  +++ ++D  eG ra   +  ++P+++
  gi|121639434|ref|YP_979658.1| 195 ALELADAISANGPLAVQAILRSIRETECMP-ENEAFKIDTQIGIKVFLSDDAKEGPRAFAEK--RAPNFQ 261
                                    56778999*********************7.9************************997533..566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1442.21
//
Query:       gi|121639435|ref|YP_979659.1|  [L=279]
Description: hypothetical protein BCG_3580 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-05   22.8   0.0    0.00019   21.5   0.0    1.6  1  MTES_1575  REase_MTES_1575
      0.007   16.7   2.1      0.042   14.2   2.1    2.1  1  AbiEi_1    AbiEi antitoxin C-terminal domain
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.26   11.2   0.0    1.3  1  DUF559     Protein of unknown function (DUF559)


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.2e-08   0.00019      25      78 ..     211     261 ..     185     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-08
                      MTES_1575  25 friDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwss 78 
                                      iD+ +    + ++++  +gd++ ++++  ++di+r e L +lGW+ +R++ +
  gi|121639435|ref|YP_979659.1| 211 AVIDMGW---AGIKVGVDYEGDHHRTDRRTFNKDIKRAEALTELGWTDVRVTVE 261
                                    3344444...5569************************************9865 PP

>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.1     7e-06     0.042      19     130 ..      57     157 ..      46     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                        AbiEi_1  19 yyagllsAawlhGaahrqp.qriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeatavdlatrp 97 
                                     ++ ++sAa +hGa+   + q  + l++   ++ p+g+         +++++ ++d   +  g+ +++P++ta+dla+r 
  gi|121639435|ref|YP_979659.1|  57 GVIAGQSAAAMHGAKWVDArQAAELLYD--HRRPPAGIH--------TWSDRVADDEIQPISGMNTTTPARTALDLARRY 126
                                    4555788999999876666577777777..444444443........33444455555899****************997 PP

                        AbiEi_1  98 savggldnvlevLdelaee..vkpeeLeellsgrp 130
                                    +      +++++ d+la +  +k +++e l++ ++
  gi|121639435|ref|YP_979659.1| 127 P----VGKAVAAIDALARAtdLKLADVEMLAERYR 157
                                    5....566789999999875566777777777666 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.3e-05      0.26      45      89 ..     212     259 ..     197     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                    EEEEEETTTTEEEEEE-------...----HHHHHHHHHTT-EEEEEE CS
                         DUF559  45 ivDfvclkaklivelDGaqhdee...eeyDaeRtelLeslGftvlRfk 89 
                                    ++D   +  k+ v+ +G +h  +    ++D +R+e+L++lG+t +R  
  gi|121639435|ref|YP_979659.1| 212 VIDMGWAGIKVGVDYEGDHHRTDrrtFNKDIKRAEALTELGWTDVRVT 259
                                    567777778999999*****887445689**************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1579.74
//
Query:       gi|121639436|ref|YP_979660.1|  [L=193]
Description: cytochrome P450 monooxygenase 142 cyp142b [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-24   84.7   0.7    3.3e-21   75.6   0.7    2.1  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.7   1.8e-25   3.3e-21     251     432 ..       4     155 ..       1     168 [. 0.93

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.8e-25
                                    TCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHH CS
                           p450 251 ekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikE 330
                                    e +ge  lsd+el++++l +l++G +Tt +tls +  +L++n +  + l+ +     +              +l  +i+E
  gi|121639436|ref|YP_979660.1|   4 EVDGE-RLSDDELVMETLLILIGGDETTRHTLSGGTEQLLRNRDQWDLLQRD-----P-------------SLLPGAIEE 64 
                                    56676.9***********************************9999999988.....2.............49999**** PP

                                    HHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGG CS
                           p450 331 tLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGpR 410
                                    +LR   +v  ++ R++t d+++ g  + +G ++++   + + d++vf +Pe+Fd +R          ++ ++l+FG+G +
  gi|121639436|ref|YP_979660.1|  65 MLRWTAPVK-NMCRVLTADTEFHGTALCAGEKMMLLFESANFDEAVFCEPEKFDVQR----------NPNSHLAFGFGTH 133
                                    *********.********************************************987..........35569******** PP

                                    S-TTHHHHHHHHHHHHHHHHHH CS
                           p450 411 nCiGerlArmelklflatlLqn 432
                                     C+G +lAr+el+l+  ++L++
  gi|121639436|ref|YP_979660.1| 134 FCLGNQLARLELSLMTERVLRR 155
                                    ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1077.05
//
Query:       gi|121639437|ref|YP_979661.1|  [L=205]
Description: cytochrome P450 monooxygenase 142 cyp142a [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.1   0.0     0.0057   16.5   0.0    1.2  1  malic     Malic enzyme, N-terminal domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.2e-07    0.0057      97     157 ..      57     120 ..      48     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-07
                                    HHHHHHHS-EGGG.EEEEEECS-BS.HHHHC.TT..S.SSB...SHHH..HHHHHHHHHHHHHH CS
                          malic  97 aLytalagidPek.vlpvvldvgtnneelledplYlGlrkkRvkgeey..defvdefveavkel 157
                                     L++ ++gi+P++ +lp+++d+    + l++  +  G  +kRvk++e    ++ d +++av e+
  gi|121639437|ref|YP_979661.1|  57 ELFSNAGGIRPDQpALPMMIDMDDPAHLLRRKLVNAGFTRKRVKDKEAsiAALCDTLIDAVCER 120
                                    69*********8769********5555555566789*******998752268899999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1127.96
//
Query:       gi|121639438|ref|YP_979662.1|  [L=236]
Description: hypothetical protein BCG_3583 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-38  131.1   0.1    5.3e-38  130.9   0.1    1.0  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.1   2.9e-42   5.3e-38       1     225 [.      14     228 ..       1     234 [. 0.86

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 2.9e-42
                                    SSSTCTSSSCTTSSSEEEEEEEEEEEEE-HHHHHTTSBT.TEEECS....TSEEEEEEEEEEEECTTTCEEEEEEEEEEE CS
                            ADC   1 tmPlaitpsgksalvpynaealtvsyrtdpeaaaallPe.pLelae....rplvavyfaeypdssfgggqYneagivvpv 75 
                                    tmP++i+          +a+ +++++++ ++ a++l+++ +L+++e    +++v+ ++++y d+++g   Y+e+g++++v
  gi|121639438|ref|YP_979662.1|  14 TMPVRIR----------TANLHSAMFSVPADPAQRLIDYsGLRVCEylpgKAIVMQMLVRYVDGDLG--RYHEYGTAIMV 81 
                                    4555555..........899**********************************************9..*********** PP

                                    E.ET.........TEEEEEEEEEEESSHHHHHHHHHHTT--EEE-EEEEEEETTEEEEEEEETTEEEEEEEEEEEEEE-H CS
                            ADC  76 r.yg.........gkegayilvlwvdkeaalaaGRElwGfPKklAditltregdtlggtverggkrlaeltvelkerapd 145
                                    + +g          + +a+i++l+vd+ ++l aGR +wGfPK++Ad+ +t  g+++g++v+++g+ +a ++++ + ++  
  gi|121639438|ref|YP_979662.1|  82 NpPGtqrrgpralTRAAAFIHHLPVDQVFTLEAGRTIWGFPKIMADFNVTD-GRRFGFDVSADGRLIAGIEFSTGLPV-- 158
                                    *655555555555447**********************************9.**************************.. PP

                                    HHHHHHHHTSEEEEEEEEE-...TTSTSEEEEEEEEEEEEEEEEEEEEEEEEEEEE.-SSTTCCGGGSCC.SEEEEEEEE CS
                            ADC 146 deealpslkaptfllkiips...vdggkadvtelvryelsdtrvgeawtGpaslel.epsaddpladlpv.levlsayyi 220
                                              pt+++  + +    dg    vt+ +++e++ +++ +a+ G a+l+l +++++ +la+l++ +++l + ++
  gi|121639438|ref|YP_979662.1| 159 ----------PTLGWQMLKTyshHDG----VTREIPWEMKVSGL-RARLGGARLRLgDHPYAKELASLGLpKRALLSQSA 223
                                    ..........4444444444200444....**************.***********999999********9999877666 PP

                                    EEEEE CS
                            ADC 221 kadlt 225
                                    ++  +
  gi|121639438|ref|YP_979662.1| 224 ANVEM 228
                                    66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.59
# Mc/sec: 1213.90
//
Query:       gi|121639439|ref|YP_979663.1|  [L=347]
Description: coenzyme F420-dependent oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-71  240.8   5.5    2.9e-71  240.5   5.5    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.5   5.5   1.6e-75   2.9e-71      20     313 ..      17     328 ..       1     329 [. 0.93

  Alignments for each domain:
  == domain 1  score: 240.5 bits;  conditional E-value: 1.6e-75
                 Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgG 99 
                                    +++++ +el+ aaE++Gfd+v++ae++g     +da+t+la+  + T+r+rlgt+v +l +r+P++ A++a tLdhlsgG
  gi|121639439|ref|YP_979663.1|  17 QPPQNHAELVAAAEDAGFDTVFTAEAWG-----SDAYTPLAWWGSSTQRVRLGTSVIQLSARTPTACAMAALTLDHLSGG 91 
                                    47899***********************.....9********************************************** PP

                 Bac_luciferase 100 RfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeev.dfeGeffsv.......kgalllprpgqgp....i 167
                                    R +lglg +gp+v+e+++G+++++++ar+rE+++++r++w++e + + +G ++++        g+    +p  +p    i
  gi|121639439|ref|YP_979663.1|  92 RHILGLGVSGPQVVEGWYGQRFPKPLARTREYIDIVRQVWARESPvTSAGPHYRLpltgegtTGLGKALKPITHPlradI 171
                                    ****************************************998888*******99999999977777778877778999* PP

                 Bac_luciferase 168 Pvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpa..dirvgisltvivadteeeAraearali 245
                                    P++++a +p++++laa+++dg+l+   +p  a  + e l++g a+ g++++  d+++++ + v+++d++++A a ++ ++
  gi|121639439|ref|YP_979663.1| 172 PIMLGAEGPKNVALAAEICDGWLPIFYSPRMAGMYNEWLDEGFARPGARRSreDFEICATAQVVITDDRAAAFAGIKPFL 251
                                    *********************************************66555555***********************6666 PP

                 Bac_luciferase 246 agld.........fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                    a ++         f a+  +++g+ +  +e ++ ++++++++aa+ +pdelv+ +++vG+ ++v++++a +++agv+
  gi|121639439|ref|YP_979663.1| 252 ALYMggmgaeetnFHADVYRRMGYTQVVDEVTKLFRSGRKDEAAEIIPDELVDDAVIVGDIDHVRKQMAVWEAAGVT 328
                                    5555666********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1893.21
//
Query:       gi|121639440|ref|YP_979664.1|  [L=303]
Description: hypothetical protein BCG_3585 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-25   89.5   1.9    3.1e-13   49.5   0.2    2.4  2  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    0.00041   20.2   0.2      0.031   14.2   0.0    2.3  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   4.7e-14   4.2e-10       2      64 ..      46     111 ..      45     112 .. 0.86
   2 !   49.5   0.2   3.5e-17   3.1e-13       2      65 .]     207     271 ..     206     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4.7e-14
                                    EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEE...EES..TT-B-EEE- CS
                  OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvd...pdevriGmrVravf 64 
                                    v++s  Gtv s+t++ ++  g++ ++P+++++++Ld+  +++++ v+v    p +++ G+rV a +
  gi|121639440|ref|YP_979664.1|  46 VPVSSVGTVASWTWQPEPLAGQPLDRPFAWALIKLDGADTLLMHAVDVGtagPSAIHTGARVHAHW 111
                                    899**********************************888666666665344555*******9988 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 3.5e-17
                                    EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEEEES..TT-B-EEE-S CS
                  OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvr.imarlvgvdpdevriGmrVravfr 65 
                                    vel+++Gtv +f +v+ ++ g++ ++Pyv ++V Ld+     ++ + +vd+ +vr GmrV+av++
  gi|121639440|ref|YP_979664.1| 207 VELPDKGTVTTFAIVNIPFLGQRIKPPYVAAYVLLDGADIpFLHLVSDVDAHQVRMGMRVEAVWK 271
                                    89***********************************4445999999999999**********96 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.1    0.0062        55       2      24 ..      10      31 ..       9      34 .. 0.85
   2 !   14.2   0.0   3.5e-06     0.031       3      25 ..     171     193 ..     170     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0062
                        DUF35_N  2 daaaegrLvgqrCpdCGtvqfPP 24
                                    a++  r+vg r +d G+v++PP
  gi|121639440|ref|YP_979664.1| 10 TALRARRIVGVRGSD-GRVHVPP 31
                                   578888999999998.******9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.5e-06
                        DUF35_N   3 aaaegrLvgqrCpdCGtvqfPPr 25 
                                    a a+g+Lvg r  ++G+v+fPP 
  gi|121639440|ref|YP_979664.1| 171 AIAQGKLVGARTGKTGKVYFPPH 193
                                    569*******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1711.53
//
Query:       gi|121639441|ref|YP_979665.1|  [L=354]
Description: lipid-transfer protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00044   19.9   0.0    0.00078   19.1   0.0    1.4  1  Thiolase_C  Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.3e-08   0.00078      35      86 ..     262     313 ..     237     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.3e-08
                                    HT--GGGESEEEE--SBHHHHHHHHHHHT--G.GGBSTT--HHHH-B-TTTHH CS
                     Thiolase_C  35 agltvedidlfEinEAFaaqaLavakaldldl.ekvNvnGGaialGHPlGasG 86 
                                    +g ++ did+ Ei+  F+ q L va+a+ +    kvN  GG +a   P+ a+G
  gi|121639441|ref|YP_979665.1| 262 TGGHTGDIDVAEIHGPFTHQHLIVAEAIRIPGkTKVNPSGGPLAA-NPMFAAG 313
                                    456779************************8538*******9995.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1959.82
//
Query:       gi|121639442|ref|YP_979666.1|  [L=394]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00017   21.4   0.1    0.00025   20.9   0.1    1.2  1  Peptidase_M22  Glycoprotease family
    0.00033   20.1   0.2     0.0018   17.7   0.1    1.9  2  Thiolase_N     Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.014   15.2   0.1        3.7    7.5   0.0    2.5  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   4.1e-08   0.00025      35      90 ..      31      86 ..      26     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.1e-08
                                   HHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHH CS
                  Peptidase_M22 35 plieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhl 90
                                   ++i++ala++g +++d+da++v+k P  f g+++   f      a +kPl+ V++ 
  gi|121639442|ref|YP_979666.1| 31 EAIDRALADSGSTFDDIDAVVVGKAPDFFEGVMMPELFMADAMGATGKPLIRVHTA 86
                                   79*********************************9999999999********986 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     3e-07    0.0018      15     120 ..      17     122 ..       6     130 .. 0.86
   2 ?   -0.1   0.0     0.079   4.7e+02     244     259 ..     206     221 ..     200     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-07
                                    TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHH CS
                     Thiolase_N  15 ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagipeevpavtvnkvcsSglkava 93 
                                        +d+s++ L +ea+ ++l++ g + +++d v+vG+    +eg + ++  +a ++g     p ++v  + s g ++ +
  gi|121639442|ref|YP_979666.1|  17 VAKRQDVSMNGLVREAIDRALADSGSTFDDIDAVVVGKAPDFFEGVMmPELFMADAMGA-TGKPLIRVHTAGSVGGSTGV 95 
                                    347899*****************************************555555555566.999************99999 PP

                                    HHHHHHHTTSHSEEEEEEEEESTTS-E CS
                     Thiolase_N  94 laaqsiaageadvvvagGvEsmsnapt 120
                                     aa  +++g++  v+a   E+ s+++ 
  gi|121639442|ref|YP_979666.1|  96 VAASLVQSGKYRRVLALAWEKQSESNA 122
                                    9*****************999998765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.079
                                    B--BEEEEEEEEEEEH CS
                     Thiolase_N 244 asqisDGaaavllmse 259
                                     ++ sDGa av++  e
  gi|121639442|ref|YP_979666.1| 206 TCPSSDGACAVVVGDE 221
                                    6999********9766 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00063       3.7      16      38 ..      96     118 ..      89     129 .. 0.90
   2 ?    5.0   0.0    0.0036        22      53      68 ..     210     225 ..     194     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00063
                                    HHHHHHHTTS-SEEEEEEEEEGG CS
                    ACP_syn_III  16 vAdaliesgaakrvLvigaetls 38 
                                    vA++l++sg+++rvL  + e+ s
  gi|121639442|ref|YP_979666.1|  96 VAASLVQSGKYRRVLALAWEKQS 118
                                    89*************99888877 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                                    -EEEEEEEEEEESSSS CS
                    ACP_syn_III  53 GDGAgAvvleaseeeg 68 
                                    +DGA+Avv++ +e  +
  gi|121639442|ref|YP_979666.1| 210 SDGACAVVVGDEEIAD 225
                                    7********9986444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2454.61
//
Query:       gi|121639443|ref|YP_979667.1|  [L=343]
Description: hypothetical protein BCG_3588 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-32  109.3  20.1    4.1e-06   26.5   0.1    6.3  6  NHL       NHL repeat
    9.2e-07   28.7   0.7     0.0098   15.5   0.1    3.6  3  SGL       SMP-30/Gluconolactonase/LRE-like region
     0.0022   18.2   8.8        7.5    6.8   0.1    5.1  4  US22      US22 like
     0.0058   16.6  18.1        3.4    7.7   0.0    5.7  6  SBBP      Beta-propeller repeat
  ------ inclusion threshold ------
      0.014   15.1   0.0       0.77    9.4   0.0    2.2  2  DUF4988   Domain of unknown function
      0.017   15.0   0.0      0.062   13.2   0.0    1.9  2  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.5e-06    0.0075       1      27 [.     104     130 ..     104     131 .. 0.93
   2 !   21.5   0.4   5.4e-08   0.00016       4      27 ..     149     172 ..     148     173 .. 0.93
   3 !   17.6   0.1   9.5e-07    0.0028       2      26 ..     189     213 ..     188     215 .. 0.89
   4 !   21.3   0.5   6.5e-08    0.0002       2      26 ..     231     255 ..     230     257 .. 0.92
   5 !   26.5   0.1   1.4e-09   4.1e-06       1      27 [.     272     298 ..     272     299 .. 0.94
   6 !   16.9   0.2   1.6e-06    0.0047       4      22 ..     317     335 ..     316     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +++P Gv+vd  + +yVaDs++ r+ +
  gi|121639443|ref|YP_979667.1| 104 LWNPDGVTVDLADAVYVADSGHKRLLK 130
                                    789*********************975 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.4e-08
                                    EEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   4 PhGvavdsnGdiyVaDsenhrvqv 27 
                                    P Gvav+sn d+yV D  +h+v +
  gi|121639443|ref|YP_979667.1| 149 PGGVAVNSNRDVYVIDEDSHHVLK 172
                                    99*******************976 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 9.5e-07
                                    SSEEEEEEETTTEEEEEECCCTEEE CS
                            NHL   2 nyPhGvavdsnGdiyVaDsenhrvq 26 
                                     ++hG+avd ++ +yV D+ n  v 
  gi|121639443|ref|YP_979667.1| 189 GDAHGLAVDRSDSVYVVDYDNAKVL 213
                                    679******************9886 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 6.5e-08
                                    SSEEEEEEETTTEEEEEECCCTEEE CS
                            NHL   2 nyPhGvavdsnGdiyVaDsenhrvq 26 
                                     +P +vavd  G +yV+Ds+++rv+
  gi|121639443|ref|YP_979667.1| 231 DHPYDVAVDGAGTVYVTDSGHNRVV 255
                                    67889******************97 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 1.4e-09
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +++P+Gv+vd ++ +yVaD +n+rv +
  gi|121639443|ref|YP_979667.1| 272 LSFPAGVTVDRDDSVYVADLNNNRVLK 298
                                    689*********************976 PP

  == domain 6  score: 16.9 bits;  conditional E-value: 1.6e-06
                                    EEEEEEETTTEEEEEECCC CS
                            NHL   4 PhGvavdsnGdiyVaDsen 22 
                                    P++vavd++G +yV D++n
  gi|121639443|ref|YP_979667.1| 317 PTDVAVDNDGAVYVIDFYN 335
                                    9***************777 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0018       5.4     185     209 ..     106     130 ..      81     147 .. 0.80
   2 ?    2.5   0.0     0.031        91     186     212 ..     191     217 ..     155     227 .. 0.80
   3 !   15.5   0.1   3.3e-06    0.0098      11     101 ..     241     330 ..     235     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                            SGL 185 epDGlavDaeGnvwvAvwgggkvvr 209
                                    +pDG++vD  + v+vA  g++++ +
  gi|121639443|ref|YP_979667.1| 106 NPDGVTVDLADAVYVADSGHKRLLK 130
                                    5***************998887765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.031
                            SGL 186 pDGlavDaeGnvwvAvwgggkvvrfdp 212
                                      GlavD ++ v+v  +++ kv ++ p
  gi|121639443|ref|YP_979667.1| 191 AHGLAVDRSDSVYVVDYDNAKVLKLPP 217
                                    459999999999999999999998766 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 3.3e-06
                            SGL  11 egaLlwvDilgqrihrldpatgketvldtpe...svGaiaprkdgrlvvasksglalldlasgeletladeeedekpllr 87 
                                     g+++ +D  ++r+ +l++ +++ ++l++ +   ++G++++ +d+ ++va  ++ ++l+la g+  +   ++   + l +
  gi|121639443|ref|YP_979667.1| 241 AGTVYVTDSGHNRVVALTAGSATPVHLPFADlsfPAGVTVD-RDDSVYVADLNNNRVLKLAAGSNAQSQLPF---TGLFS 316
                                    56777777777777777777777777666666667777777.777777777777777777777666666665...24577 PP

                            SGL  88 fNDgvvdpdGrlwf 101
                                    + D++vd dG++++
  gi|121639443|ref|YP_979667.1| 317 PTDVAVDNDGAVYV 330
                                    77777777777776 PP

>> US22  US22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0025       7.5      85     110 ..     152     177 ..      88     179 .. 0.86
   2 ?    0.3   0.1      0.27   8.2e+02      85     106 ..     194     215 ..     189     221 .. 0.84
   3 !    5.7   0.8    0.0057        17      83     108 ..     276     301 ..     212     304 .. 0.71
   4 ?    3.2   0.0     0.034     1e+02      85     101 ..     320     336 ..     310     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                           US22  85 vlldelgaVygydplddevyrlAasL 110
                                    v +     Vy++d ++++v +lAa +
  gi|121639443|ref|YP_979667.1| 152 VAVNSNRDVYVIDEDSHHVLKLAAGI 177
                                    67788889***************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                           US22  85 vlldelgaVygydplddevyrl 106
                                    + +d++  Vy++d ++ +v +l
  gi|121639443|ref|YP_979667.1| 194 LAVDRSDSVYVVDYDNAKVLKL 215
                                    5799*********888888765 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0057
                           US22  83 lvvlldelgaVygydplddevyrlAa 108
                                      v +d++  Vy+ d  ++ v +lAa
  gi|121639443|ref|YP_979667.1| 276 AGVTVDRDDSVYVADLNNNRVLKLAA 301
                                    45888888889999888888888886 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.034
                           US22  85 vlldelgaVygydpldd 101
                                    v +d +gaVy++d +++
  gi|121639443|ref|YP_979667.1| 320 VAVDNDGAVYVIDFYNR 336
                                    89**********98776 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.83   2.5e+03      15      29 ..     107     121 ..     105     121 .. 0.81
   2 ?   -0.3   0.7      0.37   1.1e+03      15      29 ..     149     163 ..     144     163 .. 0.84
   3 !    5.8   0.0    0.0047        14      15      29 ..     191     205 ..     185     205 .. 0.90
   4 !    6.0   0.3    0.0039        12      15      29 ..     233     247 ..     229     250 .. 0.92
   5 !    7.7   0.0    0.0011       3.4      14      29 ..     274     289 ..     268     289 .. 0.88
   6 !    5.6   0.2    0.0052        16      14      28 ..     316     330 ..     311     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.83
                           SBBP  15 gngIavDsnGNiYvt 29 
                                    + g++vD    +Yv+
  gi|121639443|ref|YP_979667.1| 107 PDGVTVDLADAVYVA 121
                                    5699***98888886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                           SBBP  15 gngIavDsnGNiYvt 29 
                                    + g+av sn  +Yv+
  gi|121639443|ref|YP_979667.1| 149 PGGVAVNSNRDVYVI 163
                                    6699*********95 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0047
                           SBBP  15 gngIavDsnGNiYvt 29 
                                    ++g+avD++  +Yv+
  gi|121639443|ref|YP_979667.1| 191 AHGLAVDRSDSVYVV 205
                                    68***********96 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0039
                           SBBP  15 gngIavDsnGNiYvt 29 
                                    ++++avD  G +Yvt
  gi|121639443|ref|YP_979667.1| 233 PYDVAVDGAGTVYVT 247
                                    89************8 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0011
                           SBBP  14 ygngIavDsnGNiYvt 29 
                                    ++ g++vD++  +Yv+
  gi|121639443|ref|YP_979667.1| 274 FPAGVTVDRDDSVYVA 289
                                    899***********97 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.0052
                           SBBP  14 ygngIavDsnGNiYv 28 
                                    +++++avD +G +Yv
  gi|121639443|ref|YP_979667.1| 316 SPTDVAVDNDGAVYV 330
                                    589***********9 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00026      0.77      45     112 ..     198     265 ..     194     267 .. 0.84
   2 ?    3.3   0.0     0.019        58      44      77 ..     282     314 ..     277     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                        DUF4988  45 nsdgsyvltlsdgktitltqgkdgeakaPvigvdeegyWtvtlnget.eelk.adgekvkavgedgktPe 112
                                    +sd+ yv+ + + k ++l  g d+  + P +g d+     v  +g+   +++ +  ++v a  + ++tP+
  gi|121639443|ref|YP_979667.1| 198 RSDSVYVVDYDNAKVLKLPPGADTPTELPFVGLDHPYDVAV--DGAGtVYVTdSGHNRVVALTAGSATPV 265
                                    4899*****************************98766566..776657899777889999988889986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.019
                        DUF4988  44 ensdgsyvltlsdgktitltqgkdgeakaPvigv 77 
                                    +  d+ yv  l++++ ++l++g++++ + P  g 
  gi|121639443|ref|YP_979667.1| 282 R-DDSVYVADLNNNRVLKLAAGSNAQSQLPFTGL 314
                                    3.6889**********************998775 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.062      10      43 ..      39      72 ..      36      72 .. 0.90
   2 ?   -2.8   0.0       2.2   6.5e+03      40      52 ..     118     130 ..     117     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                   HHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecE 10 ElkKVtWPtrkEllkttvvVlvfvvimglflflv 43
                                   E ++  WP  + +l +t++ +v+vv ++++++l+
  gi|121639443|ref|YP_979667.1| 39 ERRRYGWPRNRRTLAITGAAVVVVVTLAAIGYLI 72
                                   566667**************************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHH CS
                           SecE  40 lflvDlvfsklin 52 
                                    +++ D+++++l++
  gi|121639443|ref|YP_979667.1| 118 VYVADSGHKRLLK 130
                                    7999****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2335.67
//
Query:       gi|121639444|ref|YP_979668.1|  [L=174]
Description: siderophore-binding protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-13   48.1   6.3    1.9e-06   27.3   0.7    4.1  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
      0.036   13.8   8.9        1.9    8.3   0.6    4.2  6  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.5e-06     0.023       4      36 .]      13      45 ..      10      45 .. 0.88
   2 ?    1.8   0.0     0.025   2.3e+02      19      35 ..      49      65 ..      47      66 .. 0.69
   3 !    5.1   0.2    0.0022        19      20      36 .]      72      88 ..      71      88 .. 0.72
   4 !   27.3   0.7   2.2e-10   1.9e-06       1      34 [.      88     121 ..      88     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-06
                                   EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                   I   +++ p a++ g+V+I  ++ ++ ++v++g
  gi|121639444|ref|YP_979668.1| 13 IDPTAFVAPTATLIGDVTIEAGASVWFNAVLRG 45
                                   666688999*********************986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.025
                                   TEEE-TTEEEETTEEEE CS
                        Hexapep 19 nVkIGdnvkIgagvvig 35
                                   +V++ +++ +  g+v++
  gi|121639444|ref|YP_979668.1| 49 PVVVREGANVQDGAVLH 65
                                   67777777777777765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0022
                                   EEE-TTEEEETTEEEES CS
                        Hexapep 20 VkIGdnvkIgagvvigg 36
                                   V IG+++++++ +vi+g
  gi|121639444|ref|YP_979668.1| 72 VDIGPGATVAHLCVIHG 88
                                   66888888888888765 PP

  == domain 4  score: 27.3 bits;  conditional E-value: 2.2e-10
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    ++++Gs +lI + a+++++++IG ++ I+ag+ +
  gi|121639444|ref|YP_979668.1|  88 GVHVGSEALIANHATVLDGAVIGARCMIAAGALV 121
                                    589****************************987 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.2   1.8e+03      23      30 ..      28      35 ..      24      37 .. 0.70
   2 ?    0.4   0.0     0.062   5.5e+02      17      27 ..      55      65 ..      47      66 .. 0.59
   3 ?    3.9   0.0     0.005        45       8      27 ..      62      81 ..      60      82 .. 0.84
   4 ?    5.5   0.3    0.0016        14      14      28 ..      84      99 ..      74     104 .. 0.82
   5 ?    8.3   0.6   0.00021       1.9       2      30 ..      89     119 ..      89     123 .. 0.79
   6 ?    7.0   0.3   0.00055       4.9       3      20 ..     108     127 ..     105     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.2
                                   T-EE-TT- CS
                      Hexapep_2 23 ncvvgaGv 30
                                   +++++aG 
  gi|121639444|ref|YP_979668.1| 28 DVTIEAGA 35
                                   57788886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.062
                                   SEEE-TT-EE- CS
                      Hexapep_2 17 GvslGdncvvg 27
                                   G ++ d++v+ 
  gi|121639444|ref|YP_979668.1| 55 GANVQDGAVLH 65
                                   66677777764 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.005
                                   -EE-TT-EESEEE-TT-EE- CS
                      Hexapep_2  8 CliGanagiGvslGdncvvg 27
                                    +++a  gi+v++G +++v+
  gi|121639444|ref|YP_979668.1| 62 AVLHAPPGIPVDIGPGATVA 81
                                   67888889********9996 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0016
                                   -EE.SEEE-TT-EE-T CS
                      Hexapep_2 14 agi.GvslGdncvvga 28
                                   ++i Gv++G ++ +++
  gi|121639444|ref|YP_979668.1| 84 CVIhGVHVGSEALIAN 99
                                   6679********9987 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.00021
                                    EEE-TT-EE-TT-EE..SEEE-TT-EE-TT- CS
                      Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGv 30 
                                    v++G   li   a++  G  +G +c ++aG 
  gi|121639444|ref|YP_979668.1|  89 VHVGSEALIANHATVldGAVIGARCMIAAGA 119
                                    67777777755599889999********996 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.00055
                                    EE-TT-EE-TT-EE..SEEE CS
                      Hexapep_2   3 iIGdnCliGanagi..Gvsl 20 
                                     IG++C+i a a +  G+++
  gi|121639444|ref|YP_979668.1| 108 VIGARCMIAAGALVvaGTQI 127
                                    58888888888775578776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1229.19
//
Query:       gi|121639445|ref|YP_979669.1|  [L=386]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-17   61.7   0.1    8.5e-17   60.9   0.1    1.4  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   4.7e-21   8.5e-17       2      86 ..      26     109 ..      25     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.7e-21
                                    EEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEETTSBEEE-TT CS
                         Rieske   2 wvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwaydadGkvikgPa 81 
                                    w+++  ++d  eg+p++v+ +g++lvv+ d++g++++l+++C+H+g  lseg+++ + ++ Cp+H w++  dG+++ +P 
  gi|121639445|ref|YP_979669.1|  26 WHCLGVAKDYLEGKPHGVEAFGTKLVVFADSHGDLKVLDGYCRHMGGDLSEGTVK-GDEVACPFHDWRWGGDGRCKLVPY 104
                                    88888999999*******************************************5.55*********************9 PP

                                    HHHEE CS
                         Rieske  82 prpla 86 
                                     r+ +
  gi|121639445|ref|YP_979669.1| 105 ARRTP 109
                                    98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2583.40
//
Query:       gi|121639446|ref|YP_979670.1|  [L=149]
Description: hypothetical protein BCG_3591 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1096.45
//
Query:       gi|121639447|ref|YP_979671.1|  [L=237]
Description: hypothetical protein BCG_3592c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.009   15.3   0.0      0.013   14.8   0.0    1.1  1  Methyltransf_2  O-methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.2e-07     0.013      52     138 ..      22     109 ..      15     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.2e-07
                                    HHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE...-HHHHHHHHHHS-----TTEEEEES-TTT....S- CS
                 Methyltransf_2  52 kkvleafdleglkslvDvGGGtGalakaivsayPtikvivfD...lpeVveaAkehlsageeervefvgGdffk....ds 124
                                    ++++++  +e++  l  v G  Ga    +  +yP  ++++ D    p+V+++A+++      +++++++G+f +    d+
  gi|121639447|ref|YP_979671.1|  22 DRAFTSCRIESFADLGAVWGVEGAYTFRALDKYPVKEAVLVDgriTPTVAARANSY------PQLRVIEGNFGDqeiaDK 95 
                                    566677778888888888899*********************88779*********......99******9987112245 PP

                                    ----SEEEEESSGG CS
                 Methyltransf_2 125 lPeaDaillkrvlh 138
                                    + + Da++l  vl 
  gi|121639447|ref|YP_979671.1|  96 VGNVDALFLFDVLL 109
                                    56889999988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1768.31
//
Query:       gi|121639448|ref|YP_979672.1|  [L=384]
Description: hypothetical protein BCG_3593c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-65  219.6   0.6    9.2e-65  219.0   0.6    1.2  1  Sulfotransfer_3  Sulfotransferase family
    6.5e-07   29.1   0.0    1.1e-06   28.4   0.0    1.4  1  Sulfotransfer_1  Sulfotransferase domain
    1.1e-05   25.3   2.1    0.00035   20.5   2.1    2.3  1  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.6   1.5e-68   9.2e-65       1     217 []      93     341 ..      93     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.5e-68
                                    -EEEE--TTSSHHHHHHHHHTSTTEE--S--.--TT.-SBHHHHHHHHTT-S...TTTHHHHHHHHHH.....T--HHHH CS
                Sulfotransfer_3   1 PifivGlpRSGTTlLhrlLaahpdvripeetlfvaprllalleawskdgrelrrlldagltqeeaelp.....hledaee 75 
                                    Pif++Gl R+GTT+LhrlL+a+p+ +    +l   p+ +  +e+w  ++++l+r+lda++tq++ae+p     h+++a+e
  gi|121639448|ref|YP_979672.1|  93 PIFVTGLVRTGTTALHRLLGADPAHQGLHMWLAEYPQPRPPRETW--ESNPLYRQLDAQFTQHHAENPgytglHFMAAYE 170
                                    9********************999888888877777666666644..55678999************************* PP

                                    HHHHHHHHHTT-BHHHHHHHHHHHTTTSEEEE............................EESSGGG-HHHHHHHBSSEE CS
                Sulfotransfer_3  76 peedlqllraalasvilealarvpsyarwlvd............................KsPshlfrldlllelfPdAk 127
                                    +ee++qllr++l+sv++eala+vpsya+wl +                            K+Pshlf+ld+l++++PdA 
  gi|121639448|ref|YP_979672.1| 171 LEECWQLLRQSLHSVSYEALAHVPSYADWLSRqdwtpsycrhrrnlqliglndaekrwvlKNPSHLFALDALMATYPDAL 250
                                    ******************************999*********************************************** PP

                                    EEEEE--H.HHHHHHHHHTT----------..-.HHH.HHHHHHHHHHHHHHHHHHHS-TTSEEEEEHHHHHH-HHHHHH CS
                Sulfotransfer_3 128 fihlvRdpvdtvlssyvslfgkkresysedsld.ele.daleewarayerllaararlppdrfldvrYedLvadpegtlr 205
                                    ++ ++R pv+t+++s++sl+++++e +s+++++ +++ da+++w+r++er++aara+++ ++f+dv+Y+dL+adp gt+ 
  gi|121639448|ref|YP_979672.1| 251 VVQTHR-PVETIMASMCSLAQHTTEGWSTKFVGaQIGaDAMDTWSRGLERFNAARAKYDSAQFYDVDYHDLIADPLGTVA 329
                                    ******.99*********************************************************************** PP

                                    HHHHHHT----G CS
                Sulfotransfer_3 206 riyeflglpwdd 217
                                     iy+++gl+++d
  gi|121639448|ref|YP_979672.1| 330 DIYRHFGLTLSD 341
                                    ********9876 PP

>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.8e-10   1.1e-06       2     216 ..      92     356 ..      91     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.8e-10
                                    TSEEEEESTTSSHHHHHHHHHH............................HHTTTCC.HHHTSSGHCT-.HHHSCBTTHE CS
                Sulfotransfer_1   2 ddvlivtypKSGTtwlqellsl............................itsegdf.ekaeepalfna.rdrspfLely 51 
                                    + +++ ++ ++GTt+l++ll +                            +   ++  +++++ +  n+ ++ ++f+  y
  gi|121639448|ref|YP_979672.1|  92 RPIFVTGLVRTGTTALHRLLGAdpahqglhmwlaeypqprppretwesnpL--YRQLdAQFTQHHAENPgYTGLHFMAAY 169
                                    679*******************99999999999999999999888777442..333345677777777777777777776 PP

                                    CCTSG.CCGTTECCC..........................HHHTTTEEHHHHHHHSTSS.EEE..E....GGGS.CHHH CS
                Sulfotransfer_1  52 dlyfp.nslkppdhl..........................rsyshvaekvvrlralesprllk..tHlp.lkllpksll 101
                                     l    + l ++  l                          + +++ + +   l++ e++ +lk  +Hl+ l+ l     
  gi|121639448|ref|YP_979672.1| 170 ELEECwQLLRQS--LhsvsyealahvpsyadwlsrqdwtpsYCRHRRNLQLIGLNDAEKRWVLKnpSHLFaLDALMA--T 245
                                    444444444444..145788999999*************98677777888999999999999999999972455533..4 PP

                                    HTT-EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S-HHHHHHHHHTTHSTTC-HHHHHHHHHH...HTTTTTEEEEEHHH CS
                Sulfotransfer_1 102 dsnlKiiylvRnpkdvavSryhfsrslkklkepetpfeeffdlflegrvvcgsyfdhvkswlk...lrkkgnvlflrYEd 178
                                     +++ +++  R   ++++S+    + +++    +    +f+ +++ g   +  +++ ++++     +++  +++ ++Y d
  gi|121639448|ref|YP_979672.1| 246 YPDALVVQTHRPVETIMASMCSLAQHTTE----GW-STKFVGAQI-GADAMDTWSRGLERFNAaraKYDSAQFYDVDYHD 319
                                    899******************99966653....22.236888899.***************9999899999********* PP

                                    HHHHHHHHHHHHHHHTT--..HHHHHHHHHHTSHHHHH CS
                Sulfotransfer_1 179 lkkdpakeikkiaeFlGiplteeelekivkhlsfenmk 216
                                    l++dp +++  i++  G++l++e  +  +++   e+ +
  gi|121639448|ref|YP_979672.1| 320 LIADPLGTVADIYRHFGLTLSDEARQA-MTTVHAESQS 356
                                    *******************88665554.4555555555 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.1   5.9e-08   0.00035       2     151 ..      94     304 ..      93     352 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.9e-08
                Sulfotransfer_4   2 ViglGlpRtGTkSlkaALei.Lgykpvyhmeevien..............................gsdlkewaealeak 50 
                                    +++ Gl RtGT+    AL++ Lg  p +++ ++                                 +             
  gi|121639448|ref|YP_979672.1|  94 IFVTGLVRTGTT----ALHRlLGADPAHQGLHMWLAeypqprppretwesnplyrqldaqftqhhaE------------- 156
                                    678888888888....444315667766666666665566666555555444444444444444440............. PP

                Sulfotransfer_4  51 kegk.........kpitredfdkllggy.............................................davvdvp 76 
                                       +         + ++ e+  +ll++                                              + v+  p
  gi|121639448|ref|YP_979672.1| 157 ---NpgytglhfmAAYELEECWQLLRQSlhsvsyealahvpsyadwlsrqdwtpsycrhrrnlqliglndaekRWVLKNP 233
                                    ...04444444443333333333333223333334444444444444444444444555666666666666667788888 PP

                Sulfotransfer_4  77 aalfa.eelleayPdakvIlteRdpekWlksmkktllalrsetlsrllalldpllellaklvellralvrrlfgag 151
                                    + lfa + l++ yPda v+ t+R++e+ ++sm ++ +++++ +  +++       ++ a+ ++++ + ++r+  a+
  gi|121639448|ref|YP_979672.1| 234 SHLFAlDALMATYPDALVVQTHRPVETIMASMCSLAQHTTEGWSTKFVG---A--QIGADAMDTWSRGLERFNAAR 304
                                    88775378999***********************999999875444333...2..355666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2619.56
//
Query:       gi|121639449|ref|YP_979673.1|  [L=260]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-54  183.4   0.7    6.7e-54  182.9   0.7    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.8e-40  138.5   0.1    2.2e-40  138.2   0.1    1.1  1  adh_short        short chain dehydrogenase
    2.6e-08   34.0   0.3    3.5e-08   33.6   0.3    1.2  1  KR               KR domain
     0.0027   17.9   0.1     0.0052   17.0   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9   0.7   1.5e-57   6.7e-54       1     232 [.      14     256 ..      14     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 1.5e-57
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    G+  g+G  +A+++a+ Ga++vl+ ++ e+ ++ ++++ + + ++v +++D+td+++v +lv+++ + +gk D+l+nna 
  gi|121639449|ref|YP_979673.1|  14 GVGPGLGTTLAHRCARDGADLVLAARSAERlDDVAKQIIDTGRRAVaVRTDITDDDDVSNLVQATLAAYGKADVLINNAF 93 
                                    67789*************************77777777777777767********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                     +p+  +p++ t+ e++++a++ ++ ++++l++a+ p l++++g+ivn+ s+  + + p+y  y +aK  l a++++lA 
  gi|121639449|ref|YP_979673.1|  94 RVPS-MKPLAGTTFEHIRDAIELSALGTLRLIQAFTPaLAQSHGAIVNVNSMVIRHSQPKYGTYKMAKSVLLAMSHSLAT 172
                                    ***9.********************************666666************************************* PP

                                    HHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEE CS
                   adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlv 228
                                    elg++giRvN+v+pg+i  +  +++ +          d+++++ +a++ l+rl t +eva+a+lfLasd+as+itGqtl 
  gi|121639449|ref|YP_979673.1| 173 ELGEQGIRVNSVAPGYIWGDTLKSYFDhqagkygttVDQIYQATAANSDLKRLPTEDEVASAILFLASDLASGITGQTLD 252
                                    *****************8776554433233345555788***************************************** PP

                                    ESTT CS
                   adh_short_C2 229 vDgG 232
                                    v++G
  gi|121639449|ref|YP_979673.1| 253 VNCG 256
                                    **99 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.1   4.9e-44   2.2e-40       1     192 [.       8     199 ..       8     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 4.9e-44
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    kv++v G + G+G  +a+++a++Ga++v+++rs+e+l  vak++ ++g++a+a+++D+td ++v++lv++  + +gk dv
  gi|121639449|ref|YP_979673.1|   8 KVIVVSGVGPGLGTTLAHRCARDGADLVLAARSAERLDDVAKQIIDTGRRAVAVRTDITDDDDVSNLVQATLAAYGKADV 87 
                                    89****************************************************************************** PP

                                    EEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                    L+nNA     ++p + ++ e +++ ie+   g++ l++a++pa l+qs G+Ivnv S++ + + + +  Y  +K  + ++
  gi|121639449|ref|YP_979673.1|  88 LINNAFRvPSMKPLAGTTFEHIRDAIELSALGTLRLIQAFTPA-LAQSHGAIVNVNSMVIRHSQPKYGTYKMAKSVLLAM 166
                                    *****988999********************************.55********************************** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdmakelre 192
                                    ++sla el ++girvn+vaPG++  d+ k+  +
  gi|121639449|ref|YP_979673.1| 167 SHSLATELGEQGIRVNSVAPGYIWGDTLKSYFD 199
                                    ***********************9888877766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.3   7.9e-12   3.5e-08       4     164 ..      11     171 ..       8     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 7.9e-12
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    ++ G   gLG++la+  a++ga  lvl +Rsa+  +   +  +++ ++g +  +v+ D++d d+v++l+++  a  ++  
  gi|121639449|ref|YP_979673.1|  11 VVSGVGPGLGTTLAHRCARDGA-DLVLAARSAERLD---DVAKQIIDTGRRAVAVRTDITDDDDVSNLVQATLAAYGKAD 86 
                                    6677777**************8.69******55444...46689999*****************************9999 PP

                                    EEEE---.------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                             KR  84 GvihaAg.vlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaaNaflDal 159
                                      i+ A  v   k+l+ +t e+++ +++    G+  L +++++   +s   +v + S+     +++ ++Y  a ++l a+
  gi|121639449|ref|YP_979673.1|  87 VLINNAFrVPSMKPLAGTTFEHIRDAIELSALGTLRLIQAFTPalaQSHGAIVNVNSMVIRHSQPKYGTYKMAKSVLLAM 166
                                    999999735679*****************************998989999***********************9998776 PP

                                    HHHHH CS
                             KR 160 aeyrr 164
                                     ++ +
  gi|121639449|ref|YP_979673.1| 167 SHSLA 171
                                    66543 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.2e-06    0.0052       4      80 ..      13      95 ..      10     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                                   E--S.HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEEE CS
                Sacchrp_dh_NADP  4 iGaG.svGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkeg.......dlvvn 75
                                    G G + G  +a+ +ar +    ++++a rs e+l+ +a+++  +g r+ a+  d+ ++++ ++ l++ +       d+++n
  gi|121639449|ref|YP_979673.1| 13 SGVGpGLGTTLAHRCARDGA---DLVLAARSAERLDDVAKQIidTGRRAVAVRTDITDDDD-VSNLVQATlaaygkaDVLIN 90
                                   56643689999******997...59**************999**77777777777777777.66666655555588899999 PP

                                   -SSGG CS
                Sacchrp_dh_NADP 76 lsppi 80
                                    +  +
  gi|121639449|ref|YP_979673.1| 91 NAFRV 95
                                   87766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1817.23
//
Query:       gi|121639450|ref|YP_979674.1|  [L=375]
Description: hypothetical protein BCG_3595c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00036   21.0   0.2       0.12   12.8   0.1    2.3  2  DUF1214   Protein of unknown function (DUF1214)


Domain annotation for each model (and alignments):
>> DUF1214  Protein of unknown function (DUF1214)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0     0.001        18      13      82 ..      78     142 ..      73     154 .. 0.78
   2 !   12.8   0.1   6.9e-06      0.12      57     104 ..     274     317 ..     261     321 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.001
                                    S-B-BTTSEEEEEE-SS-S.EEEEEEEEEEETTT-.SB---TTS--EEETTS...BTTTSEEEEEEESS-T CS
                        DUF1214  13 gqpldgsktYrltfpadlPpaaafWSltlydaetr.ylvanplnryslgsrselkrnaDGsldillqpepp 82 
                                    g +l+++++Y++++ ++   +++  S  l + e   y v+ +  ++++++r+ l  +aDGs++  l p++p
  gi|121639450|ref|YP_979674.1|  78 GTRLQANRDYVVSGRRG---TTTDLSFQLLGGEYTdYNVPAS--QAAFDDRE-LDIAADGSFEWRLRPSAP 142
                                    67899999999999999...6777788777533333555555..58999999.689*******99999998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.9e-06
                                    -EEETTS...BTTTSEEEEEEESS-TTTST.TSEEE-TTT-BEEEEEE CS
                        DUF1214  57 yslgsrselkrnaDGsldillqpeppekekeanWLptpaggefslvlR 104
                                     sl+ ++  + ++DG++ i++++++p     +nW+ t ++++ +l +R
  gi|121639450|ref|YP_979674.1| 274 TSLNASQ-AQADPDGKVRIVVAEQNP---GVTNWVETLGHRRGFLQFR 317
                                    5555555.4899**************...778*****99888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:01.09
# Mc/sec: 1043.54
//
Query:       gi|121639451|ref|YP_979675.1|  [L=406]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-64  214.6  24.3    7.4e-64  214.6  24.3    1.7  2  PPE       PPE family
    6.9e-15   55.7  16.4    6.9e-15   55.7  16.4    4.8  4  PE_PPE_C  Polymorphic PE/PPE proteins C terminal
  ------ inclusion threshold ------
        6.3    7.1  11.2       0.48   10.7   5.9    1.9  2  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6  24.3   1.2e-67   7.4e-64       1     157 [.       7     163 ..       7     164 .. 0.99
   2 ?   -3.6   0.3       1.8   1.1e+04      95     107 ..     287     299 ..     286     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 1.2e-67
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPEvns+++y+Gpg+g+l+aAaaaWd+++ael+saa++++sv+a+l++ +W Gpss +m aa++py++WL+++aaqa+
  gi|121639451|ref|YP_979675.1|   7 MLPPEVNSTRMYSGPGAGSLWAAAAAWDQVSAELQSAAETYRSVIASLTGWQWLGPSSVRMGAAVTPYVEWLTTTAAQAR 86 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    ++A+q++aaa+ +e+A+a++vpp+ i+anra++ +l+atnffGqnt+aIaa+e +y+emw qda+am++Y+a+saaa
  gi|121639451|ref|YP_979675.1|  87 QTATQITAAATGFEQAFAMTVPPPAIMANRAQVLSLIATNFFGQNTAAIAALETQYAEMWEQDATAMYDYAATSAAA 163
                                    **************************************************************************987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                                    HHHHHS--HHHHH CS
                            PPE  95 aAlaamvppaeia 107
                                    aA aa +ppa ia
  gi|121639451|ref|YP_979675.1| 287 AAAAAAPPPADIA 299
                                    6888888888887 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.2  12.3         3   1.8e+04      26      59 ..      80     114 ..      24     133 .. 0.70
   2 ?    0.4   4.5      0.21   1.3e+03      26      66 ..     156     195 ..     143     201 .. 0.53
   3 ?   -0.7   1.4      0.46   2.7e+03      36      59 ..     287     311 ..     273     321 .. 0.53
   4 !   55.7  16.4   1.2e-18   6.9e-15       1      80 []     325     402 ..     325     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: -8.2 bits;  conditional E-value: 3
                       PE_PPE_C  26 asaaaaalsgttaaaaaaaagaalg.gmPlaaaga 59 
                                    ++aa a  ++t+ +aaa ++++a++  +P  a  a
  gi|121639451|ref|YP_979675.1|  80 TTAAQARQTATQITAAATGFEQAFAmTVPPPAIMA 114
                                    34444444555566666666655554444444443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                       PE_PPE_C  26 asaaaaal.sgttaaaaaaaagaalggmPlaaagaggaagga 66 
                                     +a++aa+ + t+ ++ ++  ++a  g+P+++a  ++a+++a
  gi|121639451|ref|YP_979675.1| 156 YAATSAAArTLTPFTSPQQDTNSA--GLPAQSAEVSRATANA 195
                                    333333332444444444444444..9999888887774443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.46
                       PE_PPE_C  36 ttaaaaaaaagaalg..gmPlaaaga 59 
                                    + aaaaa  ++  ++   +Pl+++++
  gi|121639451|ref|YP_979675.1| 287 A-AAAAAPPPADIAPafLAPLTSMAK 311
                                    2.222222222222244566666655 PP

  == domain 4  score: 55.7 bits;  conditional E-value: 1.2e-18
                       PE_PPE_C   1 sAglGqAatvGaLSVPpsWaaaapaasaaaaalsgttaaaaaaaagaalggmPlaaagaggaaggaaprygfrptvmprp 80 
                                    sA++  A t+G++SVPp+W+a+a ++  a  a++ tt  ++  a++a+++g+P+++a+++g+ +g++pryg+r tvm+rp
  gi|121639451|ref|YP_979675.1| 325 SAAMRGAGTIGQMSVPPAWKAPAVTTVRAFDATPMTTL-PGGDAPAAGVPGLPGMPASGAGR-AGVVPRYGVRLTVMTRP 402
                                    799****************9999999999999999988.55577888999*********999.9***************8 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.9     8e-05      0.48      11      84 ..      28     102 ..      23     102 .. 0.96
   2 ?   -3.0   0.2       1.5   8.7e+03      51      56 ..     144     149 ..     131     165 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  11 qaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                    +aaa+ ++ ++el+++ ++ ++ +++l + +W G ++++  a+ + + + +++ +++  +++ ++++aa+ fe+a
  gi|121639451|ref|YP_979675.1|  28 AAAAAWDQVSAELQSAAETYRSVIASLtGWQWLGPSSVRMGAAVTPYVEWLTTTAAQARQTATQITAAATGFEQA 102
                                    79999**********************777*******************************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                    HHHHHH CS
                         WXG100  51 aefeew 56 
                                    +++e+ 
  gi|121639451|ref|YP_979675.1| 144 EMWEQD 149
                                    222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2616.98
//
Query:       gi|121639452|ref|YP_979676.1|  [L=582]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-62  207.4 334.7    1.2e-09   37.9  18.8   11.7 13  Pentapeptide_2  Pentapeptide repeats (8 copies)
      2e-57  193.7  32.6    3.2e-57  193.0  32.6    1.3  1  PPE             PPE family


Domain annotation for each model (and alignments):
>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7  26.1   8.5e-10   7.6e-06       7      40 .]     177     210 ..     175     210 .. 0.94
   2 !   26.2  37.3     6e-10   5.3e-06       1      40 []     201     240 ..     201     244 .. 0.98
   3 !   23.5  39.5   4.3e-09   3.9e-05       1      40 []     251     290 ..     251     290 .. 0.98
   4 !   22.6  40.5     8e-09   7.2e-05       1      39 [.     291     329 ..     286     330 .. 0.67
   5 !   31.9  28.5   9.6e-12   8.6e-08       3      39 ..     335     371 ..     333     372 .. 0.95
   6 !    9.1   8.2   0.00013       1.2       1      20 [.     363     382 ..     363     385 .. 0.74
   7 !   30.0  29.7   3.9e-11   3.5e-07       2      39 ..     392     429 ..     391     430 .. 0.98
   8 !   33.8  26.7   2.5e-12   2.2e-08       2      39 ..     412     449 ..     411     450 .. 0.98
   9 !   37.2  23.9   2.2e-13   1.9e-09       2      39 ..     422     459 ..     421     459 .. 0.98
  10 !   36.6  21.6   3.3e-13   2.9e-09       2      39 ..     432     469 ..     431     469 .. 0.98
  11 !   37.9  18.8   1.3e-13   1.2e-09       1      39 [.     451     489 ..     451     490 .. 0.98
  12 !   25.9  23.9   7.4e-10   6.6e-06       2      38 ..     495     531 ..     494     532 .. 0.97
  13 !   22.2  16.9   1.1e-08   9.6e-05       4      38 ..     539     573 ..     537     575 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.5e-10
                 Pentapeptide_2   7 NsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N+G gN+G++NlG gNtG+ N+G+gN+G++n+Gs
  gi|121639452|ref|YP_979676.1| 177 NLGIGNIGNANLGGGNTGDLNTGNGNIGNTNLGS 210
                                    99*****************************996 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6e-10
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+GsgN G++NlGsgN+G+ N+G gN+G+gn+Gs
  gi|121639452|ref|YP_979676.1| 201 GNIGNTNLGSGNRGDANLGSGNIGNSNVGGGNVGNGNFGS 240
                                    8*************************************96 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 4.3e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    gN+G++N+G+ N+G++N+G+ N+G++N+G++N+G gn+Gs
  gi|121639452|ref|YP_979676.1| 251 GNVGNGNLGNSNLGSGNTGNSNVGFGNTGNNNVGTGNAGS 290
                                    8*************************************96 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 8e-09
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gN+G +N+Gs N+Gf+N G gN+G++N+G+gN+G+g tG
  gi|121639452|ref|YP_979676.1| 291 GNIGAGNTGSSNWGFGNNGIGNIGFGNTGNGNIGFGLTG 329
                                    577777777777777777777777777777777777766 PP

  == domain 5  score: 31.9 bits;  conditional E-value: 9.6e-12
                 Pentapeptide_2   3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    +G lNsGsgN+G+fN+G+ N+G+fN+G+gN G+gn++
  gi|121639452|ref|YP_979676.1| 335 IGGLNSGSGNIGLFNSGTNNVGFFNSGNGNLGIGNSS 371
                                    89*********************************96 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.00013
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGs 20 
                                    gN G++Ns+ +N+G +N+G 
  gi|121639452|ref|YP_979676.1| 363 GNLGIGNSSDANVGIGNSGA 382
                                    67777777777777777775 PP

  == domain 7  score: 30.0 bits;  conditional E-value: 3.9e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++NsGs NtG++N G +NtG++N G +N G+gn+G
  gi|121639452|ref|YP_979676.1| 392 NTGFGNSGSLNTGMGNAGGVNTGFGNGGAINLGFGNSG 429
                                    *************************************9 PP

  == domain 8  score: 33.8 bits;  conditional E-value: 2.5e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    NtG++N G  N+Gf+N+G  N GsfN+Gs+NtG++n+G
  gi|121639452|ref|YP_979676.1| 412 NTGFGNGGAINLGFGNSGQLNAGSFNAGSINTGNFNSG 449
                                    *************************************9 PP

  == domain 9  score: 37.2 bits;  conditional E-value: 2.2e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N G++NsG  N G+fN Gs NtG+fN+G gNtG++n+G
  gi|121639452|ref|YP_979676.1| 422 NLGFGNSGQLNAGSFNAGSINTGNFNSGQGNTGDFNAG 459
                                    9***********************************99 PP

  == domain 10  score: 36.6 bits;  conditional E-value: 3.3e-13
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N Gs+N+Gs NtG+fN+G gNtG+fN+G  NtG  n+G
  gi|121639452|ref|YP_979676.1| 432 NAGSFNAGSINTGNFNSGQGNTGDFNAGVRNTGWSNSG 469
                                    99**********************************99 PP

  == domain 11  score: 37.9 bits;  conditional E-value: 1.3e-13
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    gNtG++N+G  NtG+ N+G +NtG fN+Gs NtG+g +G
  gi|121639452|ref|YP_979676.1| 451 GNTGDFNAGVRNTGWSNSGLTNTGAFNAGSLNTGFGAVG 489
                                    8***********************************998 PP

  == domain 12  score: 25.9 bits;  conditional E-value: 7.4e-10
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    N+G++N+G+ N+GffN+G g+ G++N Gs+N+G  n+
  gi|121639452|ref|YP_979676.1| 495 NSGFGNAGTNNSGFFNTGVGSSGFQNGGSNNSGLQNA 531
                                    9********************************9995 PP

  == domain 13  score: 22.2 bits;  conditional E-value: 1.1e-08
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    G++N+G   +G +N+G  N G+fN+G  N+G +n+
  gi|121639452|ref|YP_979676.1| 539 GFGNTGAQTVGIANSGVLNSGFFNSGVHNSGGFNS 573
                                    9********************************97 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0  32.6   3.6e-61   3.2e-57       1     158 []       5     162 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 3.6e-61
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE ns ++++G+gs+p+laAa aWdgLaael saa+++ sv++ la++aWqGp++aamaaaaapy+ WLsaaaa+a+
  gi|121639452|ref|YP_979676.1|   5 VLPPELNSLRMFTGAGSAPMLAAAVAWDGLAAELGSAASSFGSVTSDLASQAWQGPAAAAMAAAAAPYAGWLSAAAARAA 84 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     aAaqa+a+a+a+eaA+aa+v+p ++aanr+++a+lv++n+fG n+p Iaa+e +ye+mwa+d+aam +Y++ ++aaa
  gi|121639452|ref|YP_979676.1|  85 GAAAQAKAVASAFEAARAATVHPLLVAANRNAFAQLVMSNWFGLNAPLIAAVEGAYEQMWAADVAAMVGYHSGASAAA 162
                                    *************************************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3650.53
//
Query:       gi|121639453|ref|YP_979677.1|  [L=346]
Description: 4-hydroxy-2-ketovalerate aldolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-49  169.2   3.3    1.5e-49  168.9   3.3    1.1  1  HMGL-like  HMGL-like
    3.7e-28   96.8   0.1    9.6e-28   95.5   0.1    1.7  1  DmpG_comm  DmpG-like communication domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   3.3   1.7e-53   1.5e-49       2     264 .]       7     265 ..       6     265 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.7e-53
                                    -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--.............TSGGGT.THHHHHHHS---TT-B... CS
                      HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEv.............gfpaaseddfevvraiakavkkar.. 66 
                                    v+i+dt+LRDG++  +++++ +e+ ai++aLd+agv +iEv             gf+     + e ++ +a+++k+ar  
  gi|121639453|ref|YP_979677.1|   7 VRITDTSLRDGSHHKRHQFTKDEVGAIVAALDAAGVPVIEVthgdglggssfnyGFSKTP--EQELIKLAAATAKEARia 84 
                                    89************************************************9977777777..777888888888888877 PP

                                    ..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--H CS
                      HMGL-like  67 .ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdl 145
                                     ++++   +++dik a +    +g  + +++++++e              a+ + ++  +ar+lg +++ +l++a+ + +
  gi|121639453|ref|YP_979677.1|  85 fLMLPGVGTKDDIKEARD----NGGSICRIATHCTE--------------ADVSIQHFGLARELGLETVGFLMMAHTIAP 146
                                    899999************....**************..............9***************************** PP

                                    HHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTT CS
                      HMGL-like 146 eflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvn 225
                                    e+la ++  +++aG++++++ D+ G+l  + +a+++sal++++ + +++ +H+H++lGl+van++aAv+aGa+++dg+  
  gi|121639453|ref|YP_979677.1| 147 EKLAAQARIMADAGCQCVYVVDSAGALVLDGVADRVSALVAELGEDAQVGFHGHENLGLGVANSVAAVRAGAKQIDGSCR 226
                                    ******************************************************************************** PP

                                    S--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                      HMGL-like 226 GlGeraGnaaleelvaalealgvdtgldlqklrsiaalv 264
                                      G++aGna++e+l+    + gv+tg+d+ ++ ++a++v
  gi|121639453|ref|YP_979677.1| 227 RFGAGAGNAPVEALIGVFDKIGVKTGIDFFDIADAAEDV 265
                                    ***********************************9986 PP

>> DmpG_comm  DmpG-like communication domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.1   1.1e-31   9.6e-28       2      62 ..     275     335 ..     274     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 1.1e-31
                      DmpG_comm   2 ridreslvlGyaGVYSsFllhaeraaerygvdardilvelGrrklvgGQEDliidvAleLa 62 
                                     +dr++l++Gy+GVYSsFl+ha r+aerygv+a ++l ++G+rkl+gGQED++id+Ale++
  gi|121639453|ref|YP_979677.1| 275 LLDRNALIMGYSGVYSSFLKHAVRQAERYGVPASALLHRAGQRKLIGGQEDQLIDIALEIK 335
                                    68*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2564.59
//
Query:       gi|121639454|ref|YP_979678.1|  [L=303]
Description: acetaldehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-63  213.3   0.6    1.9e-63  212.8   0.6    1.3  1  AcetDehyd-dimer  Prokaryotic acetaldehyde dehydrogenase, dime
    1.9e-10   41.2   0.0    1.1e-09   38.8   0.0    2.1  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00094   20.0   0.0     0.0017   19.1   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0074   16.9   0.0      0.017   15.8   0.0    1.6  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> AcetDehyd-dimer  Prokaryotic acetaldehyde dehydrogenase, dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.8   0.6   4.2e-67   1.9e-63       1     138 []     127     272 ..     127     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 4.2e-67
                AcetDehyd-dimer   1 CgGQAtiPivaavsrvaeveyaeivasiasksaGpgtranideftetTakaieevggakkgkaiiilnpaepplimrdtv 80 
                                    CgGQAtiPiv+avsr++ev yaeivas+as saGpgtranideft+tTa++++++gga++gkaiiilnpa+pp+imrdt+
  gi|121639454|ref|YP_979678.1| 127 CGGQATIPIVYAVSRIVEVPYAEIVASVASVSAGPGTRANIDEFTKTTARGVQTIGGAARGKAIIILNPADPPMIMRDTI 206
                                    ******************************************************************************** PP

                AcetDehyd-dimer  81 yalveeeadeeaieesveemveevqeyvPGYrlkqevqfd........eekvsvllevegagdylP 138
                                    ++++ ++ad+eai++s++++v+evq+yvPGYrl +e+qfd        ++ v++++evegagdylP
  gi|121639454|ref|YP_979678.1| 207 FCAIPTDADREAIAASIHDVVKEVQTYVPGYRLLNEPQFDepsinsggQALVTTFVEVEGAGDYLP 272
                                    ****************************************88888887799**************9 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   2.4e-13   1.1e-09       1     118 [.       6     117 ..       6     119 .. 0.87
   2 ?   -0.4   0.0      0.32   1.5e+03      58      81 ..     195     217 ..     138     228 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.4e-13
                                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSG..GGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssr.saGkklaeavk..aleegkdlkvedvdeeelkevdivflalpag 77 
                                    kvaivG +G++ ++ll  L ++ ++e  ++++ +  s+G + a++ +  ++ eg d+ + +      ++ d+vf a++a 
  gi|121639454|ref|YP_979678.1|   6 KVAIVG-SGNISTDLLYKLLRSEWLEPRWMVGIDPeSDGLARAAKLGleTTHEGVDWLLAQ-----PDKPDLVFEATSAY 79 
                                    7*****.************************999889999999998865555555555555.....57889********* PP

                                    HHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHH.GGGG CS
                 Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkddavyvlpevn.reai 118
                                    v+++ apk+aeag++ iDl+++       + v+p+ n re++
  gi|121639454|ref|YP_979678.1|  80 VHRDAAPKYAEAGIRAIDLTPAA----VGPAVIPPANlREHL 117
                                    **********************9....899999999866665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.32
                                    EGGGGGCTT-SEEEE-SCHHHHHH CS
                 Semialdhyde_dh  58 dvdeeelkevdivflalpagvske 81 
                                    ++d+  +   d +f+a p ++ +e
  gi|121639454|ref|YP_979678.1| 195 PADP-PMIMRDTIFCAIPTDADRE 217
                                    2333.3335677777777776655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.9e-07    0.0017       2      87 ..       6      93 ..       5      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.9e-07
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHEEESS.HHHHHTCT.TESEEEE-S-GGGHHHHHH CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.aesfgveaysd.leelladp.eidavivatpngtheelak 80
                                   +vai+G+G+i ++ l +l +s +++e    + +d+e+   + a+++g+e  ++ ++ lla+p ++d+v+ at ++ h++ a 
  gi|121639454|ref|YP_979678.1|  6 KVAIVGSGNISTDLLYKLLRS-EWLEPRWMVGIDPESDGLArAAKLGLETTHEgVDWLLAQPdKPDLVFEATSAYVHRDAAP 86
                                   79*************999999.77766666666666555445899****66655********99****************** PP

                                   HHHHTT- CS
                   GFO_IDH_MocA 81 aaleagk 87
                                   + +eag+
  gi|121639454|ref|YP_979678.1| 87 KYAEAGI 93
                                   *****98 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.7e-06     0.017       1      88 [.      11      97 ..      11     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                                   --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHHS.-EEEEE-S--HHHHTTHHHHH CS
                  NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahld.pdvvVEcasseavaelvlkaL 80
                                   G G+i +++l +l+r++     e +  +  d      +r+a+l+ e++++ +d l+a++d pd+v E++s    ++ ++k  
  gi|121639454|ref|YP_979678.1| 11 GSGNISTDLLYKLLRSEWL---EPRWMVGIDpESDGLARAAKLGLETTHEGVDWLLAQPDkPDLVFEATSAYVHRDAAPKYA 89
                                   7788888888888888853...33333333322244558899*****************55********************* PP

                                   HTTEEEE- CS
                  NAD_binding_3 81 kagkdvvt 88
                                   +ag+  + 
  gi|121639454|ref|YP_979678.1| 90 EAGIRAID 97
                                   ***98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2327.45
//
Query:       gi|121639455|ref|YP_979679.1|  [L=261]
Description: hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-12   45.0   0.1    1.3e-11   44.6   0.1    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1   7.5e-16   1.3e-11      46     214 ..      92     257 ..      68     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 7.5e-16
                                    TTSSSS-EE......EEEEEEEESS-B--T.--HHHHHTTEEEEEEEEEEE-SBGGG---.HH.HHHHTGGGEEEEEE-B CS
                  FAA_hydrolase  46 gdpirrPagsekldyEvELavvigkplrev.lsveeAedaiaGytllnDvsaRdlqaeekapl.gwflgksfdtftpiGp 123
                                    ++p+++ +   ++ +EvE+++++ ++l ++  + +++  a  +++ + ++    +++++  ++ ++++++++    ++G+
  gi|121639455|ref|YP_979679.1|  92 DTPVQASRY-LSPRVEVEVGFILAADLPGAgCTEDDVLAATEALVPAIELIDTRIKDWQI-KIcDTIADNASAAGFVLGA 169
                                    566776666.45799**********99999889**************************9.555999999999999**** PP

                                    --B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHHHHHHHHHHH.....-B-TT-EEEEEES........S--EE- CS
                  FAA_hydrolase 124 wivtpdeledpedlelrlrvngeevqdsntkdmifspaeliahlsagl.....tLepGdliltGTps.gvgaeeeslkfl 197
                                      v+p++l d ++++ +l+ nge+v +++ +  + +pa  +a+l+  +      L+ Gd++l G+++ +        +  
  gi|121639455|ref|YP_979679.1| 170 ARVPPADL-DVRAIDAKLTRNGEVVAEGRSDAVLGNPATAVAWLAGKVesfgvRLRKGDIVLPGSCTfA--------VEA 240
                                    ********.579*******************************8887778888*************634........447 PP

                                    -TT-EEEEEETTTEEEE CS
                  FAA_hydrolase 198 kdgDeveveieglGelr 214
                                    ++gDe +++ +glG +r
  gi|121639455|ref|YP_979679.1| 241 RAGDEFVADFTGLGLVR 257
                                    99999999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1937.25
//
Query:       gi|121639456|ref|YP_979680.1|  [L=563]
Description: 3-ketosteroid-delta-1-dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-90  304.7   1.0    1.3e-90  304.5   1.0    1.0  1  FAD_binding_2  FAD binding domain
    2.5e-11   43.6   1.0    4.4e-11   42.8   1.0    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    7.8e-08   31.4   0.3    1.3e-07   30.7   0.3    1.3  1  HI0933_like    HI0933-like protein
    3.4e-07   30.2   8.2    7.1e-06   25.8   4.8    2.5  2  DAO            FAD dependent oxidoreductase
    2.8e-06   27.5   1.5    8.6e-06   25.9   1.5    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    8.8e-06   25.1   0.8    5.4e-05   22.5   0.5    2.3  3  Thi4           Thi4 family
    1.7e-05   24.3   0.1    2.4e-05   23.7   0.1    1.2  1  FAD_binding_3  FAD binding domain
    2.9e-05   23.4   2.6    9.2e-05   21.8   0.5    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0021   17.3   0.4      0.021   14.1   0.3    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0057   15.8   5.5      0.014   14.5   4.5    1.9  2  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.058   12.4   0.5      0.089   11.8   0.5    1.3  1  Lycopene_cycl  Lycopene cyclase protein
      0.087   13.4   1.1       0.19   12.3   0.8    1.7  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.24    9.9   0.0       0.37    9.3   0.0    1.2  1  GDI            GDP dissociation inhibitor
          1    8.6   3.0        1.9    7.7   3.0    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.5   1.0     1e-93   1.3e-90       1     416 [.       7     541 ..       7     542 .. 0.94

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 1e-93
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HH CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqp 80 
                                    Dv+V+GsG+AG++AAl aa++Gl+++vvek++  gg+ta s+Gg+++++++  k+ g++d+pe++rt++ + ++e  +++
  gi|121639456|ref|YP_979680.1|   7 DVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTARSGGGVWIPNNEVLKRRGVRDTPEAARTYLHGIVGEIVEPE 86 
                                    9******************************************************************************* PP

                                    HHHHHHHTHHHHHHHHHHT...T----B............CCTS........SB-EEE-TT-SST............... CS
                  FAD_binding_2  81 lveafveaapeavdeLeel...gvpfsr............tedg........pvdvrelGglsat............... 122
                                    +++a+++++pe++++  ++    + + +            +           p+++r+lG+  a                
  gi|121639456|ref|YP_979680.1|  87 RIDAYLDRGPEMLSFVLKHtplKMCWVPgysdyypeapggR--PggrsiepkPFNARKLGADMAGlepaygkvplnvvvm 164
                                    ***************99999**7777776778888766553..0457777889999999999999*************** PP

                                    ........................EEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEE CS
                  FAD_binding_2 123 ........................artlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGav 178
                                                            art++ a +  ++ ++ g+al+ +l  ++++agv +  +t+ ++L ve+g v+G++
  gi|121639456|ref|YP_979680.1| 165 qqdyvrlnqlkrhprgvlrsmkvgARTMW-AKATGKNLVGMGRALIGPLRIGLQRAGVPVELNTAFTDLFVENGVVSGVY 243
                                    *****************************.5554569******************************************* PP

                                    EEET...TTTCEEEEEES.EEEE-----GG.............GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEE CS
                  FAD_binding_2 179 venp...esgrevrirak.avvlatgGfgr...allkellgaaaeaettnapavtGdglalalragaalnddrmeevqfh 251
                                    v+++   es + + ira+ +v+la+gGf++     +k  ++++ +++t++a a+tGdg+ +a+  gaal    m+ ++++
  gi|121639456|ref|YP_979680.1| 244 VRDSheaESAEPQLIRARrGVILACGGFEHneqMRIKYQRAPITTEWTVGASANTGDGILAAEKLGAALDL--MDDAWWG 321
                                    **99998888889******************9877788889999***********************9877..******* PP

                                    EEEET....TTTBB--THHHHTT-EEE-TTSSBTHGGGS-HHHHHHHHH.HHHHTTTS...CCBEEEE-TT......... CS
                  FAD_binding_2 252 PtslvpirdgsgiLitealrgeGgilvdkdGrrFmnelasrdvvsrailekeiaeggs...eanvyldash......... 319
                                    Pt  + ++++  +    ++  +G+i+v+ +G+rFmne+ ++ +  + +   e+ +g +   +   +l++++         
  gi|121639456|ref|YP_979680.1| 322 PTVPL-VGKPWFA--LSERNSPGSIIVNMSGKRFMNESMPYVEACHHMYGGEHGQGPGpgeNIPAWLVFDQryrdryifa 398
                                    **988.6666666..56*******************************98888888878875556*************** PP

                                    ................................SSHHHHHHHSHHHHHHHHHCCT......S-TTTS........EEE... CS
                  FAD_binding_2 320 ...............................gldaegleatleaineeaangldkdfgrgidpadr........pip... 357
                                                                   gl+a+ l at++++n  a+ g+d+d +rg +++dr        p+p   
  gi|121639456|ref|YP_979680.1| 399 glqpgqripsrwldsgvivqadtlaelagkaGLPADELTATVQRFNAFARSGVDEDYHRGESAYDRyygdpsnkPNPnlg 478
                                    ************************************************************************99777889 PP

                                    ...........EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
                  FAD_binding_2 358 ....gpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                                         p+y +k+vp++++t gG++td ngr+l++dg++i+GLYAaG+v a  ++++++++G +
  gi|121639456|ref|YP_979680.1| 479 evghPPYYGAKMVPGDLGTKGGIRTDVNGRALRDDGSIIDGLYAAGNVSAPVMGHTYPGPGGT 541
                                    99888*******************************************************987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   1.0   3.4e-14   4.4e-11       1      50 [.       7      56 ..       7      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.4e-14
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignk 50
                                   DvvVvG+g+aG++AA+ Aa +G ++++ve+ ++ GG +++ +++ +i n+
  gi|121639456|ref|YP_979680.1|  7 DVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTARSGGGVWIPNN 56
                                   9**************************************99998888876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.3     1e-10   1.3e-07       1      45 [.       6      50 ..       6      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1e-10
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGG CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgG 45
                                   +dv+v+G GaAG+ aA+ aa+rg +++++eka++ g   + sGgG
  gi|121639456|ref|YP_979680.1|  6 FDVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTARSGGG 50
                                   59*****************************************99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   4.8   5.6e-09   7.1e-06       1      45 [.       7      52 ..       7      77 .. 0.89
   2 ?    4.7   0.0     0.015        19     152     203 ..     212     271 ..     195     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.6e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllh 45
                                   dvv++G+G +G+ +A+ +a rg  ++++ek++  g g++ r++g ++
  gi|121639456|ref|YP_979680.1|  7 DVVVVGSGAAGMVAALVAAHRGlsTVVVEKAPHYG-GSTARSGGGVW 52
                                   9**********************************.*******9985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEE.....EECTEEEE......EEEE.EEE--GGG CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgve.....rttpgend......aada.vVnaaGaw 203
                                    l+  ++++Gv + ++t  t+l  e+g v+gv+     +    +++      +a+  v++a+G +
  gi|121639456|ref|YP_979680.1| 212 LRIGLQRAGVPVELNTAFTDLFVENGVVSGVYvrdshE----AESaepqliRARRgVILACGGF 271
                                    5566899*************978889*****9865531....22223445433448*****976 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.5   6.7e-09   8.6e-06       1      36 [.      10      45 ..      10      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.7e-09
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                   +vG+G++G+vaA  +a +g++ +++ek+++ GG  a
  gi|121639456|ref|YP_979680.1| 10 VVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTA 45
                                   8********************************765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.5   4.2e-08   5.4e-05      15      60 ..       3      49 ..       1      66 [. 0.84
   2 ?   -0.9   0.0      0.62   7.9e+02     111     167 ..     219     270 ..     214     285 .. 0.60
   3 ?   -3.0   0.0       2.8   3.5e+03     206     229 ..     511     534 ..     501     538 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.2e-08
                                   HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT..TT CS
                           Thi4 15 yaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw..lG 60
                                     e Dvv+vG+G++G+ aa + a++ +l ++++e+   +GG +   +G
  gi|121639456|ref|YP_979680.1|  3 VQEFDVVVVGSGAAGMVAALVAAHR-GLSTVVVEKAPHYGGSTArsGG 49
                                   5689*****************9999.**********999998642133 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
                                    TTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEE..EEEE--G CS
                           Thi4 111 anvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirak..vvvdatG 167
                                    a+v +   +a  Dl v +   v+Gv      v  +h+ +s  +P++ira+  v++   G
  gi|121639456|ref|YP_979680.1| 219 AGVPVELNTAFTDLFVEN-GVVSGV-----YVRDSHEAES-AEPQLIRARrgVILACGG 270
                                    555555566666666666.233333.....4666775554.588888887544444444 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.8
                                    HHECEEETTEEE-THHHHHHHT-E CS
                           Thi4 206 kktrevvpnlyvaGmevaevdgan 229
                                    ++   ++++ly+aG  +a v g  
  gi|121639456|ref|YP_979680.1| 511 RDDGSIIDGLYAAGNVSAPVMGHT 534
                                    556789999999999888887765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.9e-08   2.4e-05       2      79 ..       6      86 ..       5     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS..S--EEEHHHHHHHHHTT-HHHHHHH.SEECCCCEEEEEEE CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp..radglnqrtmellrqlGledrilae.gapnelmgealyne 79
                                    dV++VG+G aG+++al+ + +G ++v+vek       +   ++g+     e+l+ +G+ d+ +a  ++ + ++ge+++ e
  gi|121639456|ref|YP_979680.1|  6 FDVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTarSGGGVWIPNNEVLKRRGVRDTPEAArTYLHGIVGEIVEPE 86
                                   79*****************************87654444425567777788999999998886654144555555555555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.5   7.2e-08   9.2e-05       1      37 [.       6      40 ..       6      78 .. 0.86
   2 ?    0.9   0.1      0.16   2.1e+02     246     278 ..     497     527 ..     487     543 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.2e-08
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcln 37
                                   +dvvv+G+G+AG+ aal +a+ g+ +++ve  ++ ++
  gi|121639456|ref|YP_979680.1|  6 FDVVVVGSGAAGMVAALVAAHRGLSTVVVE--KAPHY 40
                                   69***************************4..33344 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                                    HCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 246 eklglelderggivvdeflrtnvpgiyaiGDva 278
                                     k g+ +d +g+ + d+ +   ++g+ya+G v 
  gi|121639456|ref|YP_979680.1| 497 TKGGIRTDVNGRALRDDGS--IIDGLYAAGNVS 527
                                    4566777777777777766..69********98 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3   1.6e-05     0.021       1      30 [.       9      37 ..       9      46 .. 0.87
   2 ?    1.1   0.0      0.15   1.9e+02     124     147 ..     259     283 ..     235     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                   +++G G+aG+ aa+ + + gl + +++Ek+
  gi|121639456|ref|YP_979680.1|  9 VVVGSGAAGMVAALVAAHRGL-STVVVEKA 37
                                   79*******************.689****8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                    Pyr_redox_3 124 eAkk.viiAtGefdkPnklnipGee 147
                                    +A++ vi+A G f++ ++++i+ + 
  gi|121639456|ref|YP_979680.1| 259 RARRgVILACGGFEHNEQMRIKYQR 283
                                    554339**************99876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   4.5   1.1e-05     0.014       1      29 [.       7      35 ..       7      51 .. 0.88
   2 ?   -0.6   0.0      0.42   5.3e+02     117     159 ..     228     279 ..     224     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                   dv+V+G G AG+ AAl aa +G++++ + 
  gi|121639456|ref|YP_979680.1|  7 DVVVVGSGAAGMVAALVAAHRGLSTVVVE 35
                                   79***********************9983 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.42
                                    -EEEEEECTTEEEEEEETTS-EEEEC.........EEEE--TT-BT-EEEET CS
                           GIDA 117 eveeliveekkvkgvvtedgetikak.........avviatGtflkgkihig 159
                                      ++l ve++ v+gv+ +d ++ ++           v++a G f + + + +
  gi|121639456|ref|YP_979680.1| 228 AFTDLFVENGVVSGVYVRDSHEAESAepqlirarrGVILACGGFEHNEQMRI 279
                                    5678889999999999888877766666777777889999999987766554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   6.9e-05     0.089       1      35 [.       7      39 ..       7      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                   Dvvv+G+G+Ag+  A    +a+ gl+ v++e +p+
  gi|121639456|ref|YP_979680.1|  7 DVVVVGSGAAGMVAALV--AAHRGLSTVVVEKAPH 39
                                   9**********976654..59*********99886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   0.00014      0.19       2      34 ..       8      40 ..       7      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                   vvvvG+G  g+ +A ++a+ g ++ vve +++ 
  gi|121639456|ref|YP_979680.1|  8 VVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHY 40
                                   8***************************99875 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00029      0.37       3      44 ..       4      45 ..       2      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00029
                                   XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG- CS
                            GDI  3 eeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesa 44
                                   +e+dv+v+G+G    + + + ++ g   +++++ ++yGg +a
  gi|121639456|ref|YP_979680.1|  4 QEFDVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTA 45
                                   79************99999999*****************987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.0    0.0015       1.9      26      61 ..       3      38 ..       1      50 [. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                   B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                    AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                   v++  v+v+G G aG+ A+ +a+  g +++v+++ p
  gi|121639456|ref|YP_979680.1|  3 VQEFDVVVVGSGAAGMVAALVAAHRGLSTVVVEKAP 38
                                   56779******************9999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3771.70
//
Query:       gi|121639457|ref|YP_979681.1|  [L=286]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-26   91.7   0.0    3.5e-26   91.2   0.0    1.2  1  MaoC_dehydratas  MaoC like domain
    3.4e-14   53.1   0.0    8.1e-12   45.4   0.0    2.3  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   3.9e-30   3.5e-26       5     114 ..     163     271 ..     160     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 3.9e-30
                                    CTTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEE CS
                MaoC_dehydratas   5 aigekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvr 84 
                                    a+++ ++ +  +++ ++++ ly+l  gD np+H dpefA++agf+ pI+hG++t+++  k++++ l d+ ++ v ++ +r
  gi|121639457|ref|YP_979681.1| 163 APERAPDLQVAMPILPQQALLYRL-CGDRNPLHSDPEFAAAAGFPRPILHGLCTYGMTCKAIVDALLDSDATAVAGYGAR 241
                                    58999*******************.******************************************************* PP

                                    E-S--BTTCEEEEEEEEEEEEEEEEEEEEE CS
                MaoC_dehydratas  85 FtkpVlpgdtlkvelevvgkrdvrktkkve 114
                                    F+++ +pg+tl+v +++ g r v  ++  +
  gi|121639457|ref|YP_979681.1| 242 FAGVAYPGETLTVNVWKDGRRLVASVVAPT 271
                                    *******************99887775555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   9.1e-16   8.1e-12       3     131 ..       9     138 ..       7     139 .. 0.86
   2 !    5.6   0.0    0.0018        16      26      49 ..     187     210 ..     183     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 9.1e-16
                MaoC_dehydrat_N   3 iGaefepvkaevereavrefakavge.tnpa.yldeeaaraagyrsliaPptflivlat....kap..ellealgidlsr 74 
                                    +Ga++ pv+++++ ++v+ +   +g+ ++p+   + ++      +++++ ptf  v+at    + p  + ++ ++i+ls+
  gi|121639457|ref|YP_979681.1|   9 LGAQLPPVEFSWTSTDVQLYQLGLGAgSDPMnPRELSYL---ADDTPQVLPTFGNVAATfhltT-PptVQFPGIDIELSK 84 
                                    7999********************996334444444443...3589*******99999865532.256778999****** PP

                MaoC_dehydrat_N  75 llhgeqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                    +lh+++++e+ +p+ ++++ + ++r +d++dk   G++++i  ett t+ +G  ++t
  gi|121639457|ref|YP_979681.1|  85 VLHASERVEVPAPLPPSGSARAVTRFTDIWDK---GKAAVICSETTATTPDGLLLWT 138
                                    *******************************9...9***************988887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0018
                MaoC_dehydrat_N  26 vgetnpayldeeaaraagyrslia 49 
                                     g+ np++ d+e a+aag+  +i 
  gi|121639457|ref|YP_979681.1| 187 CGDRNPLHSDPEFAAAAGFPRPIL 210
                                    6899***************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2110.85
//
Query:       gi|121639458|ref|YP_979682.1|  [L=479]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-65  220.2   2.2    4.6e-65  219.4   2.2    1.4  1  PE-PPE    PE-PPE domain
    5.9e-57  192.2  31.5      1e-56  191.4  29.8    2.0  2  PPE       PPE family


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.4   2.2   5.1e-69   4.6e-65       1     227 []     240     462 ..     240     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 5.1e-69
                         PE-PPE   1 PgadaelvsyPasflpvtg.lksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa.. 77 
                                    Pg+++e+vsyPa++ +++g l++++ ++S+a G+++L+++i a++a g++v+v+G+S+g++v+++e+a+la   +p+a  
  gi|121639458|ref|YP_979682.1| 240 PGTTPEVVSYPATIGVLSGsLGAVDANQSIAIGQQMLHNEILAATASGQPVTVAGLSMGSMVIDRELAYLAI--DPNApp 317
                                    8999*******************************************************************9..888877 PP

                         PE-PPE  78 pdqlsfvlvgnpnrpnggllarfpg.gltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNailGia 156
                                    ++ l+fv +++p   + gl++++ + g+tipi    +t+++  +sqy+T+ v++qYD +ad Pd+p+NllA +Na++G+a
  gi|121639458|ref|YP_979682.1| 318 SSALTFVELAGP---ERGLAQTYLPvGTTIPI--AGYTVGNAPESQYNTSVVYSQYDIWADPPDRPWNLLAGANALMGAA 392
                                    899********9...66788877666******..9********************************************* PP

                         PE-PPE 157 lvHtnyetevaeqlpanirttvnsrgakttyylipteelPLlqplrslgvpeplvdaldavLrvlvdlgYd 227
                                    ++H+ + +  a+q+  +i+ +++s g++tt+y+ip+++lPLl+pl+++gvp+++v  l++vL++lvd+gY+
  gi|121639458|ref|YP_979682.1| 393 YFHDLT-AYAAPQQGIEIAAVTSSLGGTTTTYMIPSPTLPLLLPLKQIGVPDWIVGGLNNVLKPLVDAGYS 462
                                    ***766.88999**********************************************************6 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4  29.8   1.2e-60     1e-56       2     157 ..       7     162 ..       6     163 .. 0.99
   2 ?   -0.3   0.0      0.12     1e+03     105     133 ..     222     250 ..     210     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 1.2e-60
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                    l PEvnsa++yaG g+g+l+aAaaaWd+Laael  aaa++esv+++la+  WqGpss++maa+aa+++ WL+aaa+qae 
  gi|121639458|ref|YP_979682.1|   7 LSPEVNSARMYAGGGPGSLSAAAAAWDELAAELWLAAASFESVCSGLADRWWQGPSSRMMAAQAARHTGWLAAAATQAEG 86 
                                    78****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaa 157
                                    aA+qa+++a aYeaA+aa+v+pa++aanra +a+l+ +n+fGqntpaIaa+ea ye+mwaqd+ am +Y+a+++a+
  gi|121639458|ref|YP_979682.1|  87 AASQAQTMALAYEAAFAATVHPALVAANRALVAWLAGSNVFGQNTPAIAAAEAIYEQMWAQDVVAMLNYHAVASAV 162
                                    ************************************************************************9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHT-TTSTTHHHHHHHH CS
                            PPE 105 eiaanraelaalvatnffGqntpaIaate 133
                                    ++aa  ael +++ tn+f   tp + + +
  gi|121639458|ref|YP_979682.1| 222 LLAARYAELNTAIGTNWFPGTTPEVVSYP 250
                                    5788899999********99999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3414.18
//
Query:       gi|121639459|ref|YP_979683.1|  [L=386]
Description: lipid-transfer protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.1   1.6      6e-06   25.8   1.6    1.7  1  Thiolase_N       Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.075   12.9   0.0    1.9  2  Peptidase_M23_N  Peptidase family M23 N-terminal domain
      0.027   15.0   0.0       0.05   14.1   0.0    1.4  1  DUF4473          Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.6     1e-09     6e-06       3     258 ..       8     226 ..       6     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1e-09
                                    EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEE CS
                     Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvn 82 
                                    iv+   t + k     +  s   L+aea+ ++l++ag++p +vd +   ++     + n + ++a +agi e + ++ + 
  gi|121639459|ref|YP_979683.1|   8 IVGIGATDFSK----NSGRSELRLAAEAVLDALADAGLSPTDVDGLTTFTM-----DTNTEIAVARAAGIGELTFFSKIH 78 
                                    55555666666....445566789********************9877666.....455667788899************ PP

                                    HGGGHHHHHHHHHHHHHHTTSHSEEEEEEE..EESTTS-EEETCTTTTGGSSS.SEEEEEHHHHHHTEETTTTSEHHHHH CS
                     Thiolase_N  83 kvcsSglkavalaaqsiaageadvvvagGv..Esmsnaptaestdvrsglklg.dekakdllipdgladafneehmGlta 159
                                       + + ++v +aa ++a+g advvva  +  E+ + +  +++   r   + + +   + +  p+gl       ++++ a
  gi|121639459|ref|YP_979683.1|  79 YGGGAACATVQHAAMAVATGVADVVVAYRAfnERSGMRFGQVQ--TRLTENADsTGVDNSFSYPHGLSTPA--AQVAMIA 154
                                    ***************************7542244333333333..33222233033334455566666554..567889* PP

                                    HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS- CS
                     Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtv 239
                                    +++ +  +++ ++  ++ v+  ++aa+++ka  + + i              + +++ +s+  ae+L+ l          
  gi|121639459|ref|YP_979683.1| 155 RRYMHLSGATSRDFGAVSVADRKHAANNPKAYFYGKPI--------------TIEDHQNSRWIAEPLRLL---------- 210
                                    ********************************888866..............566777888999999999.......... PP

                                    BTTSB--BEEEEEEEEEEE CS
                     Thiolase_N 240 tAgnasqisDGaaavllms 258
                                       +++q +DGa a++++s
  gi|121639459|ref|YP_979683.1| 211 ---DCCQETDGAVAIVVTS 226
                                    ...9999999999999887 PP

>> Peptidase_M23_N  Peptidase family M23 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.85   5.1e+03      41      48 ..       7      14 ..       5      30 .. 0.66
   2 ?   12.9   0.0   1.3e-05     0.075       6      41 ..     169     204 ..     168     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.85
                                   EEEE--TT CS
                Peptidase_M23_N 41 aiVGipLk 48
                                   aiVGi+ +
  gi|121639459|ref|YP_979683.1|  7 AIVGIGAT 14
                                   89999743 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                                    TSEEEEE-S--SS--EEEETTEEEEEEESTTSSEEE CS
                Peptidase_M23_N   6 GGvaviplgakaqaPevtyqgkrvlvvkeeknqwla 41 
                                    G v v + +++a++P++++ gk++ +  +++++w+a
  gi|121639459|ref|YP_979683.1| 169 GAVSVADRKHAANNPKAYFYGKPITIEDHQNSRWIA 204
                                    567788888999**********************97 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.4e-06      0.05       4      53 ..      29      78 ..      26      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-06
                        DUF4473  4 aeeakaeLvaaGlsekaadglvkiaekfksefakakgdkeaakkafeklk 53
                                   ae +++ L +aGls++ +dgl  ++ + ++e+a a     +  ++f k++
  gi|121639459|ref|YP_979683.1| 29 AEAVLDALADAGLSPTDVDGLTTFTMDTNTEIAVARAAGIGELTFFSKIH 78
                                   677999*********************99999998777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2677.12
//
Query:       gi|121639460|ref|YP_979684.1|  [L=129]
Description: hypothetical protein BCG_3605c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.7   0.0     0.0012   18.4   0.0    1.1  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.7e-08    0.0012      27     117 ..      24     112 ..       7     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.7e-08
                                    HHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEE CS
                MaoC_dehydratas  27 alvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrd 106
                                    al++ D++ +H d++ A + g + + ++ +  +++v ++v++++g    a +++i +r   p ++ dt++++ ev++++d
  gi|121639460|ref|YP_979684.1|  24 ALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGP--SALIKSIGLRLGVPWYAYDTVTFSGEVTAVND 101
                                    899*******************************************..899**************************999 PP

                                    EEEEEEEEEEE CS
                MaoC_dehydratas 107 vrktkkvevtk 117
                                    +  t+kv  ++
  gi|121639460|ref|YP_979684.1| 102 GLITVKVVGRN 112
                                    99777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 966.50
//
Query:       gi|121639461|ref|YP_979685.1|  [L=311]
Description: hypothetical protein BCG_3606c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-20   73.0   2.9    3.1e-20   71.9   2.9    1.6  1  OB_aCoA_assoc    DUF35 OB-fold domain, acyl-CoA-associated
    1.5e-16   60.8   0.0    2.4e-16   60.1   0.0    1.3  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.021   14.4   0.0    1.4  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   2.9   5.2e-24   3.1e-20       1      63 [.     234     295 ..     234     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 5.2e-24
                                    EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE CS
                  OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVrav 63 
                                    +v +sgrGtv+sf+ vh+ap   + ++P+v+++VeL+egvr++++l g+dp++v iGm+Vra+
  gi|121639461|ref|YP_979685.1| 234 YVVSSGRGTVFSFV-VHHAPKVPGRTVPFVIALVELEEGVRMLGELRGADPARVAIGMPVRAT 295
                                    6889*********9.555555999*************************************97 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0     4e-20   2.4e-16      11     131 ..      26     159 ..      18     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4e-20
                MaoC_dehydrat_N  11 kaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlat......kap......elleal.gidlsrllh 77 
                                    + +v++ +++ +++a+g+ np+y+d++aaraag+ +++aPp    v+ +      + p       +++ + +  + +++ 
  gi|121639461|ref|YP_979685.1|  26 RDPVNQPMINNWVEAIGDRNPIYVDDAAARAAGHPGIVAPPAMIQVWTMmglggvR-PkddplgPIIKLFdDAGYIGVVA 104
                                    67999*******************************************96666541.145456666666656889***** PP

                MaoC_dehydrat_N  78 geqefeyhepiraGDelttesriadvyd.kkg.vGalefivvettvtnqrGepvat 131
                                    ++ e +yh+ + +G+++++++++ dv   k++  G++ fi +  ++    +e va+
  gi|121639461|ref|YP_979685.1| 105 TNCEQTYHRYLLPGEQVSISAELGDVVGpKQTaLGEGWFINQHIVWQ-VGDEDVAE 159
                                    ***************************99999********9877665.66666665 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-06     0.021      15      53 ..      26      64 ..      15      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-06
                                   EEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB- CS
                MaoC_dehydratas 15 eitvteadialyalvsgDlnpiHvdpefAkkagfggpIa 53
                                   + +v++ +i+++  + gD npi vd+++A++ag +g++a
  gi|121639461|ref|YP_979685.1| 26 RDPVNQPMINNWVEAIGDRNPIYVDDAAARAAGHPGIVA 64
                                   6678888899998999********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2143.80
//
Query:       gi|121639462|ref|YP_979686.1|  [L=387]
Description: acyl-CoA dehydrogenase fadE29 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-26   93.0   0.2    2.6e-26   92.6   0.2    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.8e-22   80.1   0.0    4.1e-22   79.0   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.2e-20   72.6   0.0    4.3e-20   71.7   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.2   4.4e-30   2.6e-26       1     148 [.     228     378 ..     228     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 4.4e-30
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++G+r+++++ln+eR++++   +g +++++++++++a     +g + idh+ v++ l+e++a ++   ll++++a+a ++
  gi|121639462|ref|YP_979686.1| 228 NDGWRLITTQLNNERVMLG--PAGRFASIYDRVHAWASVPGGNGVTPIDHDDVKRALGEIRAIWRINELLNWQVASAGED 305
                                    79****************7..99*****************************************************9999 PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT.....SGGGH..HHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGy.....leeyp..verlyrdarvlrigeGtseiqrniiarr 148
                                     +++  +a+++K+f++e +q++ +la +++G++G      ++e    +++  ++ +v ++g+G +e++r++ia++
  gi|121639462|ref|YP_979686.1| 306 INMA--DAAATKVFGTERVQRAGRLAEEIVGKYGNpaepdTAELLrwLDAQTKRNLVITFGGGVNEVMREMIAAS 378
                                    9998..*****************************8877633322569999999******************986 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   6.9e-26   4.1e-22       1     113 []       6     118 ..       6     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 6.9e-26
                                    THHHHHHHHHHHHHHHHHTHHHHHHHHHHT.SGH..HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeeg.efp..relwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                    t+eq++l++++r+++++ + p ++   e++ + p  r++++++++ G lg+ +p+e+gG+g++++e+ i++ e  rad++
  gi|121639462|ref|YP_979686.1|   6 TPEQRQLQAEIRQYFSNLISPDERTEMEKDrHGPayRAVIRRMGRDGRLGVGWPKEFGGLGFGPIEQQIFVNEAHRADVP 85 
                                    79*****************88665555555477766778***************************************** PP

                                    HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       l++v  + v+p++ ++G+e qk+++Lp +++ge
  gi|121639462|ref|YP_979686.1|  86 ---LPAVTLQTVGPTLQAHGSELQKKKFLPAILAGE 118
                                    ...56666777889********************98 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   7.2e-24   4.3e-20       1      88 [.     122     209 ..     122     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 7.2e-24
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    a++ TEp+aG+d+as++t +a rdg++y++nG+K++ t+a++a+++ + +rt+ ++ +++g+s+++v++++pg s+++i 
  gi|121639462|ref|YP_979686.1| 122 AIGYTEPEAGTDLASLRT-TAVRDGDHYIVNGQKVFTTGAHDADYIWLACRTDPNAaKHKGISILIVDTKDPGYSWTPII 200
                                    6899**************.77777778************************5555589******************9998 PP

                                    -BSS-TTS- CS
                  Acyl-CoA_dh_M  80 eklGlrglp 88 
                                       G + ++
  gi|121639462|ref|YP_979686.1| 201 LADGAHHTN 209
                                    766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2793.36
//
Query:       gi|121639463|ref|YP_979687.1|  [L=339]
Description: acyl-CoA dehydrogenase fadE28 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-15   55.3   0.0    1.6e-14   54.4   0.0    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.7e-10   39.8   0.1    1.3e-09   38.7   0.1    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.1e-05   23.9   0.0    0.00014   22.2   0.0    1.9  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   2.6e-18   1.6e-14      17     139 ..     204     327 ..     190     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.6e-18
                                    ---..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  17 avaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlfas 96 
                                    +++a a gl + al+ +++y+ +rk+fgkpl  +q v+ +lae+++  + + l +  ++++l ++ +++ +  ++ ++++
  gi|121639463|ref|YP_979687.1| 204 VMGAYADGLVAGALRLTADYVANRKQFGKPLSTFQTVAAQLAEVYIASRTIDLVAKSVIWRLAEDLDAGDDLGVLGYWVT 283
                                    456788899*********************************************************************** PP

                                    HHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTH.HHHHSSS-HH CS
                  Acyl-CoA_dh_1  97 elaqevadlamqllGgaGyleeypverlyrdar.vlrigeGtse 139
                                      a  +++ + +l+Gg+G+   yp++r+y  ++ ++r+++G+s 
  gi|121639463|ref|YP_979687.1| 284 SQAPPAMQICHHLHGGMGMDVTYPMHRYYSTIKdLTRLLGGPSH 327
                                    *****************************999856777888775 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   2.1e-13   1.3e-09      32     112 ..      20      99 ..       4     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.1e-13
                                    GHHHH.HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_N  32 fprel.wkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrfGteeqkrryLpkla 110
                                     +r++ w++l   G+++++vpe  gG g++ +e   ++ e++r++a++ +l  ++ ++v  ++l+ +++eq++r+L  +a
  gi|121639463|ref|YP_979687.1|  20 LERDIsWEALVCGGVTALPVPERLGGDGVGLFEVGALLTEVGRHGAVTPALATLGLGVV--PLLELASAEQQDRFLAGVA 97 
                                    346667****999*********************************9988777777777..9****************** PP

                                    TT CS
                  Acyl-CoA_dh_N 111 sg 112
                                    +g
  gi|121639463|ref|YP_979687.1|  98 KG 99 
                                    98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.3e-08   0.00014       3     120 ..     205     312 ..     203     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-08
                                    HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                  Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    ++a a G+  +al  +++++++r++  +g++l+ ++++ ++lae+  + ++  ++ +++++r  +  +ag+ +       
  gi|121639463|ref|YP_979687.1| 205 MGAYADGLVAGALRLTADYVANRKQ--FGKPLSTFQTVAAQLAEVYIASRTIDLVAKSVIWRLAEDLDAGDDL------- 275
                                    677888999****************..***********************************77766666665....... PP

                                    HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHH CS
                  Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlw 120
                                      +   ++++ a  a++ ++ ++Gg++++  +p+ R++
  gi|121639463|ref|YP_979687.1| 276 -GVLGYWVTSQAPPAMQICHHLHGGMGMDVTYPMHRYY 312
                                    .788999****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2432.42
//
Query:       gi|121639464|ref|YP_979688.1|  [L=433]
Description: cytochrome P450 125 cyp125 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-18   66.8   0.8    3.9e-13   49.0   0.1    2.7  3  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0     0.045   8.1e+02      86     114 ..     115     143 ..      72     171 .. 0.63
   2 !   15.5   0.0     3e-07    0.0053     215     294 ..     219     289 ..     209     303 .. 0.75
   3 !   49.0   0.1   2.2e-17   3.9e-13     329     427 ..     304     392 ..     300     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.045
                                    SSTTCGHHHHHHHHHHHHHHHTSH..STTTH CS
                           p450  86 gvlfangekwkklRrfltptltsf..gklsl 114
                                     +l+++ +++++lR+++ + +t    g  +l
  gi|121639464|ref|YP_979688.1| 115 VMLNMDAPHHTRLRKIISRGFTPRavG--RL 143
                                    356667799999999999999988432..22 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3e-07
                                    HHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHH CS
                           p450 215 klkdlldklieerretldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPe 294
                                    +l+++++k+ ee+ ++  ++       +  l++a+   +ge klsd+e    v  l +aG +Tt + ++ +++  a++P+
  gi|121639464|ref|YP_979688.1| 219 ELIGYAMKMAEEKAKNPADD------IVTQLIQAD--IDGE-KLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPD 289
                                    55666666666666666666......445555553..4444.9************************************7 PP

  == domain 3  score: 49.0 bits;  conditional E-value: 2.2e-17
                                    HHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTE.E CS
                           p450 329 kEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFG.a 407
                                     E+ R  ++v    +R +++d++++g+ i+kG++v+++  + + d+evf++P +F++ R          ++  +++FG +
  gi|121639464|ref|YP_979688.1| 304 DEIVRWATPVT-AFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILR----------NPNPHVGFGgT 372
                                    6999*******.999****************************************9976..........45568999648 PP

                                    GGGS-TTHHHHHHHHHHHHH CS
                           p450 408 GpRnCiGerlArmelklfla 427
                                    G++ CiG +lArm ++l++ 
  gi|121639464|ref|YP_979688.1| 373 GAHYCIGANLARMTINLIFN 392
                                    *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3093.46
//
Query:       gi|121639465|ref|YP_979689.1|  [L=391]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-53  179.6   0.0    1.3e-52  178.7   0.0    1.4  1  Thiolase_N     Thiolase, N-terminal domain
      1e-40  138.2   0.1    4.2e-39  133.0   0.1    2.4  2  Thiolase_C     Thiolase, C-terminal domain
  ------ inclusion threshold ------
      0.033   14.3   0.1       0.16   12.2   0.0    2.2  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7   0.0   2.2e-56   1.3e-52       2     259 ..       5     260 ..       4     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 2.2e-56
                                    EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHT....S-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-TTS CS
                     Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekag....vdpeevdevivGnvlqagegqn.iarqaalkagipeev 76 
                                    viv+a+r+pigk +g l+ l a+eLl ++ ka+++kag    +++ +v++vi G+v q ge +n i+r a l ag+pe+v
  gi|121639465|ref|YP_979689.1|   5 VIVEATRSPIGKRNGWLSGLHATELLGAVQKAVVDKAGiqsgLHAGDVEQVIGGCVTQFGEQSNnISRVAWLTAGLPEHV 84 
                                    8************************************944445677*************887777*************** PP

                                    EEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHH CS
                     Thiolase_N  77 pavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmG 156
                                     a+tv+ +c+Sg +a +l+a+ iaag++dv +a+G E ms++   ++  +    +l +++  d+ +p+            
  gi|121639465|ref|YP_979689.1|  85 GATTVDCQCGSGQQANHLIAGLIAAGAIDVGIACGIEAMSRVGLGAN--AGPDRSLIRAQSWDIDLPN----------QF 152
                                    ******************************************99997..6677788888888888888..........23 PP

                                    HHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSE.E......EE-S-TTS-TT--HHHHHTS CS
                     Thiolase_N 157 ltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgk.k......tvdkdeairsevtaekLakl 229
                                     +ae++ak+ +i+Re+ d f ++s+++a+ a+++g+F++ei P++ ++ +++ +       v +d+++r+ +t+  L +l
  gi|121639465|ref|YP_979689.1| 153 EAAERIAKRRGITREDVDVFGLESQRRAQRAWAEGRFDREISPIQAPVLDEQnQptgerrLVFRDQGLRE-TTMAGLGEL 231
                                    579********************************************9999955899999999******9.99******* PP

                                    -BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                     Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmse 259
                                    kp+ +  G  tAg++sqisDGaaavl m e
  gi|121639465|ref|YP_979689.1| 232 KPVLE-GGIHTAGTSSQISDGAAAVLWMDE 260
                                    ***97.7999*****************987 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.016        96      26      47 ..     153     174 ..     147     183 .. 0.87
   2 !  133.0   0.1   7.1e-43   4.2e-39       2     123 .]     269     390 ..     268     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHT--GGGESEEEE CS
                     Thiolase_C  26 yaikkvlkkagltvedidlfEi 47 
                                     a++++ k+ g+t ed+d+f +
  gi|121639465|ref|YP_979689.1| 153 EAAERIAKRRGITREDVDVFGL 174
                                    5788999************975 PP

  == domain 2  score: 133.0 bits;  conditional E-value: 7.1e-43
                                    --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                     Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                    +p a+i++ a vg +p     gP+  + kvl+kag+++ did++EinEAFa+++L+ a+  + d+++vNvnGGaialGHP
  gi|121639465|ref|YP_979689.1| 269 TPRARIVAQALVGAEPYYHLDGPVQSTAKVLEKAGMKIGDIDIVEINEAFASVVLSWARVHEPDMDRVNVNGGAIALGHP 348
                                    799***************************************************************************** PP

                                    TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                     Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                    +G++G+R+++t+l+el++ ++ l+++++C+gg+ +++++ie+
  gi|121639465|ref|YP_979689.1| 349 VGCTGSRLITTALHELERTDQSLALITMCAGGALSTGTIIER 390
                                    ***************************************985 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.62   3.7e+03       3      16 ..     161     174 ..     159     185 .. 0.82
   2 ?   12.2   0.0   2.6e-05      0.16       1      83 [.     299     384 ..     299     391 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                                    HTT--GGG-SEEEE CS
                  ACP_syn_III_C   3 kagltpedidalvp 16 
                                    + g+t ed+d++ +
  gi|121639465|ref|YP_979689.1| 161 RRGITREDVDVFGL 174
                                    67999*****9965 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.6e-05
                                    HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--T.....H.HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEE CS
                  ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvn.....l.deyGntsaasiplaLdeaveegklkpgdlvll 74 
                                    Lekag++  did + ++ a ++++ ++a+  + ++++v vn     l + +G t++  i  aL+e+ ++   ++  l+ +
  gi|121639465|ref|YP_979689.1| 299 LEKAGMKIGDIDIVEINEAFASVVLSWARVHEPDMDRVNVNggaiaLgHPVGCTGSRLITTALHELERTD--QSLALITM 376
                                    89**********************************9987733333446789999999999999999955..33333333 PP

                                    EEEETTTEE CS
                  ACP_syn_III_C  75 vgfGaGltw 83 
                                    ++ G+ l+ 
  gi|121639465|ref|YP_979689.1| 377 CA-GGALST 384
                                    33.333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3034.84
//
Query:       gi|121639466|ref|YP_979690.1|  [L=151]
Description: hypothetical protein BCG_3611 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-58  196.0   0.1    2.5e-58  195.8   0.1    1.0  1  F420H2_quin_red  F420H(2)-dependent quinone reductase
      0.005   17.0   0.0     0.0088   16.2   0.0    1.3  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.1   2.8e-62   2.5e-58       2     130 .]      22     151 .]      20     151 .] 0.98

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 2.8e-62
                                    XXXXXXXXXXXXX.XXTTXTTS---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEE CS
                F420H2_quin_red   2 lReqvaiyrrteg.kvgrrlegvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevq 80 
                                    +R+++++yrr++g  +g++++++pv+lLtttGrktg+pr +pl+f rdg++++v+askgGa+k+p+wylNlkanP+v+vq
  gi|121639466|ref|YP_979690.1|  22 SRINTWMYRRNDGeGLGGTFQKIPVALLTTTGRKTGQPRVNPLYFLRDGGRVIVAASKGGAEKNPMWYLNLKANPKVQVQ 101
                                    49***********99***************************************************************** PP

                                    ETTEEEEEEEEE--HHHHHHHHHHHHHH-THHHHHHHHHSSTS-EEEEE- CS
                F420H2_quin_red  81 vgakkldvtAreveddekarlwklvvenspsYadyqsktdreipvvVlep 130
                                    +++++ld+tAr+++d+e+a++w ++v+++psY+dyqs+tdr+ip+vV+ep
  gi|121639466|ref|YP_979690.1| 102 IKKEVLDLTARDATDEERAEYWPQLVTMYPSYQDYQSWTDRTIPIVVCEP 151
                                    ************************************************96 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.8e-07    0.0088      11      64 ..      43     100 ..      39     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-07
                                    HSSEEEEEEEE.TTSEEEEEEEEEEEETTTTEEEEEEETTSHH....HHHHHHH-EEEE CS
                 Putative_PNPOx  11 eskavvlATvd.edGrPnvspvllkagdgrdgivfatnadsrk....lrnleenprval 64 
                                    + +++ l+T + + G+P v p+ + ++ gr +iv a+   ++k    + nl++np+v +
  gi|121639466|ref|YP_979690.1|  43 KIPVALLTTTGrKTGQPRVNPLYFLRDGGR-VIVAASKGGAEKnpmwYLNLKANPKVQV 100
                                    56788899987688****************.999999999966555589*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1173.30
//
Query:       gi|121639467|ref|YP_979691.1|  [L=304]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-42  142.6   8.5    2.2e-41  141.5   8.5    1.5  1  adh_short      short chain dehydrogenase
    1.7e-36  126.0  12.5    3.7e-36  124.8  12.5    1.5  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    2.8e-14   53.4   7.1    8.3e-14   51.9   7.1    1.7  1  KR             KR domain
  ------ inclusion threshold ------
       0.57   10.2   6.4        1.7    8.7   1.7    2.4  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   8.5   4.8e-45   2.2e-41       1     190 [.       7     214 ..       7     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 4.8e-45
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEES..........CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdr..........seekleevakelkeegakalaiqvDvtdreevealvek 70 
                                    +vv+vtGa++GIGra a ++a+eGa+vvv d+            ++++ v++e+ ++g +a+a   D++d++++ +l+++
  gi|121639467|ref|YP_979691.1|   7 RVVIVTGAGGGIGRAHALAFAAEGARVVVNDIgvgldgspasGGSAAQDVVDEILAAGGQAVADGSDISDWDQAANLIQA 86 
                                    59**************************98752222221111356789999999999*********************** PP

                                    HHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.........HCTTEEEEEEEEGGGTS CS
                      adh_short  71 avkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.........kqssGrIvnvsSvagkv 141
                                    av+ +g++dvLvnNAGi ++++++++seee+++vi+v l+g f ++r+++ ++          k   +rI+n+sS ag++
  gi|121639467|ref|YP_979691.1|  87 AVETYGGVDVLVNNAGIVRDRMIANTSEEEFDAVIAVHLKGHFATMRHAASHWRglskagkapKDIDARIINTSSGAGLQ 166
                                    ****************************************************999999999999999************* PP

                                    B-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 142 pvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                    ++ g+  YsA+Ka++a+lt   a e++++g++vna+aP++ +T m++++
  gi|121639467|ref|YP_979691.1| 167 GSVGQGNYSAAKAGIAALTLVGAAEMRRYGVTVNAIAPAA-RTRMTETV 214
                                    **************************************75.67777665 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8  12.5   8.3e-40   3.7e-36       1     233 [.      13     260 ..      13     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 8.3e-40
                                    TTTTSHHHHHHHHHHHTT-EEEEEESS...........GGHHHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHS CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdln...........eeakkrveelaeelgaev.lecDVtdeeqvealveevvekfg 68 
                                    Ga  gIGra A a+a+eGa+vv+ d++            +a++ v+e+ +++g++v    D++d +q ++l++++ve++g
  gi|121639467|ref|YP_979691.1|  13 GAGGGIGRAHALAFAAEGARVVVNDIGvgldgspasggSAAQDVVDEILAAGGQAVaDGSDISDWDQAANLIQAAVETYG 92 
                                    7889*********************96333333222213347888999999898865889******************** PP

                                    SEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH....HCTSC.......CEEEEEEEGGGTSBSTT CS
                   adh_short_C2  69 klDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp....lmkeg.......gsivnlssvgaervvpn 137
                                    ++D+lvnnagi+++    +++ts+eefd +++v l++ f+++++a+     l k+g       ++i+n+ss ++ ++  +
  gi|121639467|ref|YP_979691.1|  93 GVDVLVNNAGIVRD--RMIANTSEEEFDAVIAVHLKGHFATMRHAAShwrgLSKAGkapkdidARIINTSSGAGLQGSVG 170
                                    **************..******************************977766666688899999**************** PP

                                    TTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSG CS
                   adh_short_C2 138 ynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasd 217
                                    +  y+aaKa++ alt   A+e+ ++g++vNa++p + +T++++ +  f e++++ ++      ++ pe+v  ++++L s 
  gi|121639467|ref|YP_979691.1| 171 QGNYSAAKAGIAALTLVGAAEMRRYGVTVNAIAPAA-RTRMTETV--FAEVMAKPQEG---FDAMAPENVSPLVVWLGSA 244
                                    **********************************75.89999988..45555555444...45678************** PP

                                    GGTT--SEEEEESTTG CS
                   adh_short_C2 218 easyitGqtlvvDgGl 233
                                    e++ +tG+++ v gG+
  gi|121639467|ref|YP_979691.1| 245 ESRDVTGKVFEVEGGI 260
                                    ***************6 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   7.1   1.8e-17   8.3e-14       3     160 ..       9     185 ..       7     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.8e-17
                                    EEEETTTSHHHHHHHHHHHHHHS-EEE......EE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlv......llsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76 
                                    +++tG+ Gg+G++ a   a++gar +v      l +  a+  +++++ ++e+ a g +  +   D+sd d+ ++l++++ 
  gi|121639467|ref|YP_979691.1|   9 VIVTGAGGGIGRAHALAFAAEGARVVVndigvgLDGSPASGGSAAQDVVDEILAAGGQAVADGSDISDWDQAANLIQAAV 88 
                                    79**********************99833322233333477888999********************************* PP

                                    HHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHH.HHHHTTT...........S--SE.EEEEEEHHHHH-- CS
                             KR  77 aeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawn.Lhelled...........esldf.fvlfSSiagllgs 143
                                    ++ + +   ++ Ag++rd++++++++e++++v+a  +kG    + ++ ++           +++d  ++ +SS agl gs
  gi|121639467|ref|YP_979691.1|  89 ETYGGVDVLVNNAGIVRDRMIANTSEEEFDAVIAVHLKGHFAtMRHAASHwrglskagkapKDIDArIINTSSGAGLQGS 168
                                    ***************************************7541444444467777778778889974667999******* PP

                                    TT-HHHHHHHHHHHHHH CS
                             KR 144 agqanYaaaNaflDala 160
                                     gq+nY+aa a + al 
  gi|121639467|ref|YP_979691.1| 169 VGQGNYSAAKAGIAALT 185
                                    *********99888774 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.7   0.00037       1.7      20      54 ..       3      38 ..       2      42 .. 0.89
   2 ?    3.6   0.3     0.014        62      54      95 ..      57     100 ..      37     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00037
                                   --TTSEEEEE--S.HHHHHHHHHHHHCT-EEEEE-S CS
                  AdoHcyase_NAD 20 llaGkvavvaGyG.dvGkGcaaslkglGarvivtev 54
                                   l+ G+v++v+G G  +G+  a ++ + Garv+v ++
  gi|121639467|ref|YP_979691.1|  3 LVDGRVVIVTGAGgGIGRAHALAFAAEGARVVVNDI 38
                                   6789*******86379*****************987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                                    S-HHHHH..HHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HH CS
                  AdoHcyase_NAD  54 vdPical..qaameGfevvtleevvkkadivvtttGnkdiitle 95 
                                    vd i a   qa+ +G ++   +++++  +  v t G  d++ ++
  gi|121639467|ref|YP_979691.1|  57 VDEILAAggQAVADGSDISDWDQAANLIQAAVETYGGVDVLVNN 100
                                    5555554349****************************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2270.13
//
Query:       gi|121639468|ref|YP_979692.1|  [L=259]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-53  180.0   1.0    8.5e-53  179.3   1.0    1.3  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    9.5e-44  149.2   1.0      2e-43  148.1   1.0    1.4  1  adh_short      short chain dehydrogenase
    1.4e-06   28.3   0.4    4.7e-05   23.4   0.4    2.3  1  KR             KR domain
    5.5e-05   22.7   0.1     0.0001   21.9   0.1    1.6  1  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.019   14.1   0.3      0.033   13.3   0.0    1.5  2  RmlD_sub_bind  RmlD substrate binding domain
      0.078   12.3   0.0       0.18   11.1   0.0    1.6  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   1.0   2.9e-56   8.5e-53       3     232 ..      25     245 ..      22     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 2.9e-56
                                    TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                   adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                     +g+G++i   +ae+Ga+v+ + ++  +           + e+ +cD++de++v++lv e+ e++g+lD+lvnnag +p 
  gi|121639468|ref|YP_979692.1|  25 VRGVGAGISSVFAEQGATVITCARRAVD---------GQPYEFHRCDIRDEDSVKRLVGEIGERHGRLDMLVNNAGGSPY 95 
                                    58******************99766555.........4566799************************************ PP

                                    CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalealtrylAvel 159
                                      + ++e++ +  +++++ n+ + +l++++a  lm+++   gsivn+ sv+++r +p+++aygaaKa+le+lt +lAve+
  gi|121639468|ref|YP_979692.1|  96 --ALAAEATHNFHRKIVELNVLAPLLVSQHANVLMQAQpngGSIVNICSVSGRRPTPGTAAYGAAKAGLENLTTTLAVEW 173
                                    ..9999*****************************988889*************************************** PP

                                    GGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                   adh_short_C2 160 gpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    +p ++RvNav  g+++T+ ++ + g  e +++++a  plgrl++p +++ aa+fLasd+asyi+G+tl v gG
  gi|121639468|ref|YP_979692.1| 174 AP-KVRVNAVVVGMVETERSELFYGDAESIARVAATVPLGRLARPADIGWAAAFLASDAASYISGATLEVHGG 245
                                    **.9*******************************************************************99 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   1.0   6.7e-47     2e-43       1     186 [.      17     191 ..      17     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 6.7e-47
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                    +vvlvtG+ +G+G  i+  +a++Ga+v+ ++r++ +            + + + ++D++d+++v++lv ++ +++g+ld+
  gi|121639468|ref|YP_979692.1|  17 RVVLVTGGVRGVGAGISSVFAEQGATVITCARRAVDG-----------QPYEFHRCDIRDEDSVKRLVGEIGERHGRLDM 85 
                                    59*******************************7766...........347799************************** PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                    LvnNAG +  + ++e + +  ++++e+N+ +++l+++++   m  + ++G+Ivn++Sv g+ p +g+aaY+A+Ka+++ l
  gi|121639468|ref|YP_979692.1|  86 LVNNAGGSPYALAAEATHNFHRKIVELNVLAPLLVSQHANVLMQaQPNGGSIVNICSVSGRRPTPGTAAYGAAKAGLENL 165
                                    *******************************************9777899****************************** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHH CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdm 186
                                    t +la e+ap+ +rvnav+ G+v+T+ 
  gi|121639468|ref|YP_979692.1| 166 TTTLAVEWAPK-VRVNAVVVGMVETER 191
                                    **********8.*************86 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   1.6e-08   4.7e-05       2     171 ..      18     177 ..      17     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeepp 81 
                                    ++l+tGG+ g+G  ++   ae+ga+  + ++R+ a+d             g   e+ ++D+ d+d+v++l+ ei +++++
  gi|121639468|ref|YP_979692.1|  18 VVLVTGGVRGVGAGISSVFAEQGATV-ITCARR-AVD-------------GQPYEFHRCDIRDEDSVKRLVGEIGERHGR 82 
                                    579********************975.566777.222.............45568899********************** PP

                                    --EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaaNafl 156
                                    +   ++ Ag +  +l +e t +  +++++  v +   + +  +       +   +v + S++g   ++g a+Y aa a l
  gi|121639468|ref|YP_979692.1|  83 LDMLVNNAGGSPYALAAEATHNFHRKIVELNVLAPLLVSQHANVlmqaqPNGGSIVNICSVSGRRPTPGTAAYGAAKAGL 162
                                    ********************99999988888887766665443332233577899***********************99 PP

                                    HHHHHHHHHHHHTEE CS
                             KR 157 Dalaeyrrsqglpav 171
                                    + l ++ + + +p v
  gi|121639468|ref|YP_979692.1| 163 ENLTTTLAVEWAPKV 177
                                    999887766666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   3.4e-08    0.0001       1      62 [.      19      75 ..      19     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.4e-08
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHH CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfke 62
                                   +lVtG+   +G+ +   ++e+g +vi+ +r+  +++       e++++d++d+++++rl+ e
  gi|121639468|ref|YP_979692.1| 19 VLVTGGVRGVGAGISSVFAEQGATVITCARRAVDGQPY-----EFHRCDIRDEDSVKRLVGE 75
                                   79*****************************5555544.....9**********99998754 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.033       3      59 ..      19      90 ..      17     127 .. 0.79
   2 ?   -3.4   0.0       1.3   3.9e+03      39      67 ..     198     232 ..     179     234 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHH.....HHH--SEEEE-- CS
                  RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaell.....keakpdvvvnaA 59
                                   +lvtG+   +G  +   +ae+g+ v+++ r+          ++d++d+++v++l+     ++ + d++vn A
  gi|121639468|ref|YP_979692.1| 19 VLVTGGVRGVGAGISSVFAEQGATVITCARRavdgqpyefhRCDIRDEDSVKRLVgeigeRHGRLDMLVNNA 90
                                   89**************************9999***********************66666566677777766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                    SHHHHHHHH......HHH--SEEEE------HHHH CS
                  RmlD_sub_bind  39 daeavaell......keakpdvvvnaAAytavDka 67 
                                    dae++a++       + a+p+ +  aAA+ a D+a
  gi|121639468|ref|YP_979692.1| 198 DAESIARVAatvplgRLARPADIGWAAAFLASDAA 232
                                    44444444333344456677777777777777766 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.9e-05      0.18      31      72 ..      11      52 ..       2      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.9e-05
                                   T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCC CS
                  THF_DHG_CYH_C 31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkd 72
                                   +  l+g+ v+v G  + vg  ++ +++e++atV +c +++ d
  gi|121639468|ref|YP_979692.1| 11 NFGLAGRVVLVTGGVRGVGAGISSVFAEQGATVITCARRAVD 52
                                   566899******************************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1956.63
//
Query:       gi|121639469|ref|YP_979693.1|  [L=247]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-37  126.6   0.3    1.1e-36  126.4   0.3    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    8.7e-20   71.5   0.1    1.1e-19   71.2   0.1    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.3   1.3e-40   1.1e-36       4     206 ..      10     209 ..       7     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.3e-40
                                    TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHHHHH CS
                          ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeevlelwt 82 
                                     g++ ++ + P +vNa+  +  ++l++a   +  +   rav+L   ++ F aG d+kem++ e      + +   ++ ++
  gi|121639469|ref|YP_979693.1|  10 PGIVAVTVDYP-PVNAIPSKAWFDLADAVTAAGANSDTRAVILRAEGRGFNAGVDIKEMQRTEGfTALIDANRGCFAAFR 88 
                                    5899*******.*************************************************874344445667799**** PP

                                    HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                          ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                    ++y++ +pviaavnG+++gGG+ l+   D+++a+++a fgl+e+  G +    +   l r v++++ +++  ++  + a+
  gi|121639469|ref|YP_979693.1|  89 AVYECAVPVIAAVNGFCVGGGIGLVGNSDVIVASEDATFGLPEVERGALG---AATHLSRLVPQHLMRRLFFTAATVDAA 165
                                    ***********************************************876...77889999******************* PP

                                    HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHH CS
                          ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealn 206
                                     +++ G v +vv+++ql e al +a+ +a k   ++r++kealn
  gi|121639469|ref|YP_979693.1| 166 TLQHFGSVHEVVSRDQLDEAALRVARDIAAKDTRVIRAAKEALN 209
                                    ******************************************98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.1   1.2e-23   1.1e-19      12     195 ..      22     200 ..      15     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.2e-23
                                    TT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHHHC-SS-EE CS
                          ECH_2  12 lNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyliatypkpvv 91 
                                    +Na+  +   +l++a+++  +++++++v+l+++g ++f AG D++++++++  ++    +  r  ++   ++ ++  pv+
  gi|121639469|ref|YP_979693.1|  22 VNAIPSKAWFDLADAVTAAGANSDTRAVILRAEG-RGFNAGVDIKEMQRTEGFTAL--IDANRGCFAAFRAVYECAVPVI 98 
                                    5888888899999*******************88.************988777543..578899999999********** PP

                                    EEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCS.STTHHHHHHHH---B-HHHHHHTTS--E CS
                          ECH_2  92 almdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrl.pgelGlylalTGarlkgadalaaglath 170
                                    a ++G+++GgG+Gl  ++ + v++e+++f  PE++ G     G+   Lsrl p++l + l  T+a++++a + ++g    
  gi|121639469|ref|YP_979693.1|  99 AAVNGFCVGGGIGLVGNSDVIVASEDATFGLPEVERGA---LGAATHLSRLvPQHLMRRLFFTAATVDAATLQHFGSVHE 175
                                    *************************************8...59*******88**************************** PP

                                    E--GGGHHHHHHHHHTT........ CS
                          ECH_2 171 yvpseklealeeaLaelessdeeav 195
                                    +v++++l++ + ++a+   +++++v
  gi|121639469|ref|YP_979693.1| 176 VVSRDQLDEAALRVARDIAAKDTRV 200
                                    *******999888877544433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1314.44
//
Query:       gi|121639470|ref|YP_979694.1|  [L=292]
Description: CoA-transferase subunit alpha [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-49  167.7   0.0    2.9e-49  167.4   0.0    1.1  1  CoA_trans  Coenzyme A transferase


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   0.0   1.6e-53   2.9e-49       2     217 .]       6     233 ..       5     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 1.6e-53
                                    CHHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBC.... CS
                      CoA_trans   2 etaaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetv.... 77 
                                    +++++ava ++++Gmt+ + G+g+ ++P+a+++a++rs+v+dltv+++ +    lg+l+++g+vk+v++++++ ++    
  gi|121639470|ref|YP_979694.1|   6 TSLDDAVA-QLRSGMTIGIAGWGSRRKPMAFVRAILRSDVTDLTVVTYGGPD--LGLLCSAGKVKRVYYGFVSLDSppfy 82 
                                    6899****.***************************************8887..********************999*** PP

                                    EHHHHHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTT.SHGGTT.......ESEEEEETTEEEEEEESSSE CS
                      CoA_trans  78 nprfgkqflsgelefellpqgtlaerlraGgaglpelgfltntgig.tlvapk.......lkkvpgfgGaeyilepalka 149
                                    +p+f+++ +sg++e++++ +g+l + l+a++++lp+l++++  g+  ++++ +       +++ pg+g++++i++pal+ 
  gi|121639470|ref|YP_979694.1|  83 DPWFAHARTSGAIEAREMDEGMLRCGLQAAAQRLPFLPIRAGLGSSvPQFWAGelqtvtsPYPAPGGGYETLIAMPALRL 162
                                    ************************************************************99****************** PP

                                    EEEEEECCEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEEEEEE....CTTSSECCCESBTGGGHSEEEET CS
                      CoA_trans 150 dvalikaskadeegnlvfeksagnfnkpaiaeaakvtileveeiv....ekgkldpekvliPgvlvdavvea 217
                                    d a+ + + +d++gn++++++ ++f++++++ aa++ +l+ve+iv     +++++p++ l+++++vda+vea
  gi|121639470|ref|YP_979694.1| 163 DAAFAHLNLGDSHGNAAYTGIDPYFDDLFLM-AAERRFLSVERIVateeLVKSVPPQALLVNRMMVDAIVEA 233
                                    *****************************99.*************9998899******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1525.95
//
Query:       gi|121639471|ref|YP_979695.1|  [L=250]
Description: CoA-transferase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1347.49
//
Query:       gi|121639472|ref|YP_979696.1|  [L=355]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-113  379.3   6.2   4.7e-113  377.9   6.2    1.6  1  NMO       Nitronate monooxygenase
    7.9e-11   41.5   8.9    1.6e-10   40.6   8.8    1.5  1  IMPDH     IMP dehydrogenase / GMP reductase domain
    1.1e-06   27.9   8.0    1.1e-06   27.9   6.9    1.6  1  FMN_dh    FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.9   6.2  7.9e-117  4.7e-113       2     330 ..       5     341 ..       4     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 377.9 bits;  conditional E-value: 7.9e-117
                            NMO   2 slltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdkPfgvnlflpkkdaadrae 81 
                                    ++ltel++i++pvvq+gmg++++arL++a++naGgLG+las+++t+D+la++i+kvka+tdkPfgvn++++++da+dr  
  gi|121639472|ref|YP_979696.1|   5 TPLTELIGIEHPVVQTGMGWVAGARLVSATANAGGLGILASATMTLDELAAAITKVKAVTDKPFGVNIRADAADAGDR-- 82 
                                    789***************************************************************************.. PP

                            NMO  82 kykkeleeaalelnieegvrfyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDali 161
                                              +el+i+egvr              v+sf+++++ ++++arlkeag+v+ip+i+++k+arkv+a+GaDa+i
  gi|121639472|ref|YP_979696.1|  83 ----------VELMIREGVR--------------VASFALAPK-QQLIARLKEAGAVVIPSIGAAKHARKVAAWGADAMI 137
                                    ..........99********..............*******99.************************************ PP

                            NMO 162 vqGpeaGGhqGtpevgdkglfaLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahk 238
                                    vqG+e+GGh+G  +v+   ++ L+p+vldav+   iPviAaGG++d+rg+aaaL++GA+gv++gtrfLlt++s+++da+k
  gi|121639472|ref|YP_979696.1| 138 VQGGEGGGHTG--PVA---TTLLLPSVLDAVAgtgIPVIAAGGFFDGRGLAAALCYGAAGVAMGTRFLLTSDSTVPDAVK 212
                                    ***********..776...9************************************************************ PP

                            NMO 239 kklleaklddteltsavsGrpaRalatelleelee...akiatlalpeah.............................. 285
                                    +++l+a+ld+t++t++v+G+p+R+l+tel+e+le+   a+++++al++a+                              
  gi|121639472|ref|YP_979696.1| 213 RRYLQAGLDGTVVTTRVDGMPHRVLRTELVEKLESgsrARGFAAALRNAGkfrrmsqmtwrsmirdgltmrhgkeltwsq 292
                                    ************************************9******************************************9 PP

                            NMO 286 .elakk....iraalveagnteegllwagqgidrldkiisvkeLiesLve 330
                                      +a++    ++a+lv++ nte+g+l++gq++++ld+++s+keLies+v 
  gi|121639472|ref|YP_979696.1| 293 vLMAANtpmlLKAGLVDG-NTEAGVLASGQVAGILDDLPSCKELIESIVL 341
                                    9888889999********.*****************************97 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   8.8   2.6e-14   1.6e-10      22     245 ..       2     205 ..       1     213 [. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.6e-14
                                    B--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SS.S-HHHHHHHHHHHHTSTTSXBXTTSXB-EEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  22 dlktkltkkiklniPlvsaamdtvtesemAialareGgigvihkn.lsieeqaeevkkvkrspnaakdekgrllvgaavg 100
                                    +l+t lt+ i ++ P+v + m +v+++++  a a++Gg+g++    ++ +e a+ ++kvk    a++d+   + + a   
  gi|121639472|ref|YP_979696.1|   2 RLRTPLTELIGIEHPVVQTGMGWVAGARLVSATANAGGLGILASAtMTLDELAAAITKVK----AVTDKPFGVNIRADA- 76 
                                    689***************************************86449*************....667766555554432. PP

                                    SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 101 vkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiC 180
                                      +da +rv+ ++++gv v     a        + ++++k++     v+  ++  a+ a+++++ gada+ v  G G   
  gi|121639472|ref|YP_979696.1|  77 --ADAGDRVELMIREGVRVASFALAP-----KQQLIARLKEAG---AVVIPSIGAAKHARKVAAWGADAMIVQGGEGGGH 146
                                    ..35679*********9987666554.....345678888777...58899*********************99999977 PP

                                    HHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 181 ttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEs 245
                                    t  v + +  p      +v +a++ +g+pvia GG    + ++ Al+ Ga  v +G  +  t++s
  gi|121639472|ref|YP_979696.1| 147 TGPVATTLLLP------SVLDAVAGTGIPVIAAGGFFDGRGLAAALCYGAAGVAMGTRFLLTSDS 205
                                    77776666655......57788899*******************************988766665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   6.9   1.9e-10   1.1e-06     208     305 ..     105     201 ..      44     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.9e-10
                                    HHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..S.S-EEEESS--SHHHH CS
                         FMN_dh 208 ikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggr.ievlvDgGirrGsDv 286
                                    i++l+e   + +v+  +  a+ a+++++ G+d+ +v    G    g +at   Lp++ +av+g  i+v++ gG+  G   
  gi|121639472|ref|YP_979696.1| 105 IARLKE--AGAVVIPSIGAAKHARKVAAWGADAMIVQGGEGGGHTGPVATTLLLPSVLDAVAGTgIPVIAAGGFFDGRGL 182
                                    444444..5889999999******************9988888999****************966*************** PP

                                    HHHHHTT-SEEEESHHHHH CS
                         FMN_dh 287 lkAlalGAdavllGRpfly 305
                                    + Al+ GA +v++G  fl 
  gi|121639472|ref|YP_979696.1| 183 AAALCYGAAGVAMGTRFLL 201
                                    **************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2288.20
//
Query:       gi|121639473|ref|YP_979697.1|  [L=685]
Description: electron transfer protein fdxB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-36  124.4  23.9      1e-35  123.8  23.9    1.3  1  FA_desaturase  Fatty acid desaturase
    1.1e-15   58.2   0.0    2.1e-15   57.3   0.0    1.5  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    5.2e-13   48.7   0.0    8.6e-13   48.0   0.0    1.4  1  Fer2           2Fe-2S iron-sulfur cluster binding domain
    1.2e-12   48.1   0.0    2.2e-12   47.2   0.0    1.4  1  FAD_binding_6  Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
        0.2   11.8   0.0       0.61   10.2   0.0    1.7  2  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8  23.9   2.9e-39     1e-35       2     251 ..      67     299 ..      66     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 2.9e-39
                  FA_desaturase   2 swlallla.lllglfllgitgslaHeaaHgalfkkrklnrwlndllgallglplgi..sysawrisHlrHHaytngpdeD 78 
                                    +w++++++  + +++  ++ + ++H+a+H+a++      rw+n l+g+l++l++g    + a+ + H++HH++ n++++D
  gi|121639473|ref|YP_979697.1|  67 GWIPFWVTiPVNAAV-TFVMFTVVHDASHYAIS----SIRWVNGLFGRLAWLFVGPvvAFPAFGYIHIQHHRHSNDDEQD 141
                                    899999998999999.67768************....9***********888887667********************** PP

                  FA_desaturase  79 pdlaplalsrfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllll 158
                                    pd++    +++++l+   lr+ + +++           +++ +  r++++++++   +l+++ l+l ++  +++ + + +
  gi|121639473|ref|YP_979697.1| 142 PDTF----ASHGSLWVLPLRWSMVEYF-----------YIKYYLPRGRSRPVIEVAETLVMMTLFLTGL--IVAIVTG-N 203
                                    ****....****************999...........5577777788888888778888888888733..3333333.3 PP

                  FA_desaturase 159 glall.lwlvplllllfllalvlnyveHyggdwgerqvetsasir..saswllnlltgnlnyHieHHlfPgvpwyrLpel 235
                                    ++ l+ ++l+p +++l++la++++++ H+g ++ +r  +++a+ +   a wl++ +++  nyH++HHl+P+vp+yr+ + 
  gi|121639473|ref|YP_979697.1| 204 FWTLAiVFLIPQRIGLTVLAWWFDWLPHHGLEDTQRSNRYRATRNrvGAEWLFTPVLLSQNYHLVHHLHPSVPFYRYLRT 283
                                    333334************************999999999999999999******************************** PP

                  FA_desaturase 236 hrrlrellpehglpyr 251
                                    +rr++e++ e +++++
  gi|121639473|ref|YP_979697.1| 284 WRRNEEAYLERNAAIS 299
                                    ******9999888765 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   5.8e-19   2.1e-15       4     108 ..     456     562 ..     454     563 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 5.8e-19
                                    EGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHHH CS
                  NAD_binding_1   4 gGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdalle 83 
                                    +G+Gi+Pv+s+l + le  + + + +l+yGnrt+e+ ++r+el++l++++ +rl++++v+s e+    + +gr++ + l 
  gi|121639473|ref|YP_979697.1| 456 AGSGITPVLSILATTLEI-ETESRFTLIYGNRTKESTMFRAELDRLESRYADRLEILHVLSSEPLHTPELRGRIDRDKLT 534
                                    8****************8.889*************************************888888888********9999 PP

                                    HHHH...HSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  84 ells...lkkeethvyvCGppgMikavr 108
                                     +l     + + +  ++CGp +M++avr
  gi|121639473|ref|YP_979697.1| 535 RWLTstlRPAGVDEWFICGPLAMATAVR 562
                                    999988777888899**********997 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.4e-16   8.6e-13       2      78 .]     601     675 ..     600     675 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.4e-16
                                    ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTT.SSSSTHHHHHTTEEEEGGGSEES CS
                           Fer2   2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsd.etelegeeldegklrlaCqtivt 78 
                                    t+ g++  ++ ++g++ +l+ a      d py+C gg+CgtC++++ eg+v   d + +l+++eld+g+  l+Cq+ +t
  gi|121639473|ref|YP_979697.1| 601 TLSGQRAIFDLVPGDS-ILEGALGL-RSDAPYACMGGACGTCRAKLIEGNVeM-DhNFALRKAELDAGYI-LTCQSHPT 675
                                    678999**********.99999988.9************************54.5599*******99988.****9886 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   6.2e-16   2.2e-12       3      97 ..     344     439 ..     342     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 6.2e-16
                                    EEEEEEECCTTEEEEEEEESTT.TS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH.H CS
                  FAD_binding_6   3 kltekeevsedtrifrfklpse.kqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaL.d 80 
                                    +++++  ++ d   ++f++p++  + +++ +Gqhv +r++  g+ + R+Y+ i ++ ++ +l + vk++pgG++s    +
  gi|121639473|ref|YP_979697.1| 344 PVASVDPITADATLVTFAVPEAlRDAFRFEPGQHVTVRTDLGGQGIRRNYS-ICAPATRAQLRIAVKHIPGGAFSTFVaN 422
                                    67888999***********987346799***********************.8889999*******************88 PP

                                    CS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  81 elkigdtleikGPlGkf 97 
                                    elk gd+le+  P+G+f
  gi|121639473|ref|YP_979697.1| 423 ELKAGDVLELMTPTGRF 439
                                    8**************98 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.61       7      62 ..     454     503 ..     449     533 .. 0.81
   2 ?   -1.9   0.0       0.9   3.2e+03     140     153 ..     550     563 ..     548     565 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6   7 vagGiGitpfisilkdllkkskkealktkkikliwvvressslewfkdvLneleee 62 
                                    + +G+Gitp++sil  +l+ +        + +li  +r ++s  +f+  L+ le++
  gi|121639473|ref|YP_979697.1| 454 LVAGSGITPVLSILATTLEIET-----ESRFTLIYGNRTKES-TMFRAELDRLESR 503
                                    4479*************99997.....889999999998766.5788777777765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.9
                                    xxxxxxxxxxxxxx RF
                  NAD_binding_6 140 fvCGppklvkevkk 153
                                    f+CGp +++  v++
  gi|121639473|ref|YP_979697.1| 550 FICGPLAMATAVRE 563
                                    89*******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4442.60
//
Query:       gi|121639474|ref|YP_979698.1|  [L=289]
Description: hypothetical protein BCG_3619c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-09   37.5   0.0    3.4e-09   36.8   0.0    1.4  1  MTES_1575  REase_MTES_1575
     0.0001   22.1   0.0    0.00017   21.4   0.0    1.3  1  DUF559     Protein of unknown function (DUF559)
      0.009   16.3   2.4      0.019   15.3   2.4    1.5  1  AbiEi_1    AbiEi antitoxin C-terminal domain
  ------ inclusion threshold ------
      0.094   13.1   0.0       0.19   12.2   0.0    1.5  1  RAMA       Restriction Enzyme Adenine Methylase Associated


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   7.6e-13   3.4e-09      18      83 ..     208     270 ..     191     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 7.6e-13
                      MTES_1575  18 pqvgvggfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwssdwyrn 83 
                                      +g    riDl  e+    ++++e dg+++ +++ +r+rdier + L  lGW+i+R++s+   ++
  gi|121639474|ref|YP_979698.1| 208 DDYGDFVARIDLGYEQL---RVGVEYDGPQHWTDPAQRARDIERSTALLDLGWTIIRVTSELLRYR 270
                                    34444456788877777...**************************************99866555 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.9e-08   0.00017      46      97 ..     217     271 ..     206     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.9e-08
                                    EEEEETTTTEEEEEE-------...----HHHHHHHHHTT-EEEEEEHHHHHH-H CS
                         DUF559  46 vDfvclkaklivelDGaqhdee...eeyDaeRtelLeslGftvlRfkndevlkni 97 
                                    +D   ++ ++ ve DG qh  +   +++D eR+++L  lG+t++R   + ++   
  gi|121639474|ref|YP_979698.1| 217 IDLGYEQLRVGVEYDGPQHWTDpaqRARDIERSTALLDLGWTIIRVTSELLRYRR 271
                                    566778999**********87655599******************9987766555 PP

>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.4   4.3e-06     0.019      16     137 ..      57     169 ..      46     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-06
                        AbiEi_1  16 ardyyagllsAawlhGaahrqp.qriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeatavdla 94 
                                     r  ++ ++sAa l+Ga+  +p    + +++ ++k  p+  +  ++        +p + v   ++gv v++P++ta+d+ 
  gi|121639474|ref|YP_979698.1|  57 RRRAVVAGNSAAALLGAKWVNPaLDAELVHA-NRKPPPRIVVHTDRL-------APHETV--AVDGVAVTTPARTAFDIG 126
                                    5667777899999999999999445555555.888888888888888.......776666..789**************9 PP

                        AbiEi_1  95 trpsavggldnvlevLdelaee..vkpeeLeellsgrp.asvlqRl 137
                                    +r ++   l ++++ Ld+la++  vk ++++++++    a+ l Rl
  gi|121639474|ref|YP_979698.1| 127 RRTPSR--L-QAVQRLDALANStdVKVADVQAVIAEHTgARGLVRL 169
                                    998864..4.66899****998667777777766655556655555 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.19      25     101 ..     187     273 ..     174     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                           RAMA  25 vtlkdLleagllepGekll.ieykgrthkAdl.ladGkIk.gqefgspsaaa...kalvGnp.s....gnGWaswkykgk 93 
                                     t   L++agl +p ++++ ++  g  ++A++ l   +++ g e++ p  +    +++++ + s    + GW+ ++++ +
  gi|121639474|ref|YP_979698.1| 187 WTRLVLIDAGLPKPQTQIRvFDDYGD-FVARIdLGYEQLRvGVEYDGPQHWTdpaQRARDIErStallDLGWTIIRVTSE 265
                                    566679*************9999998.*****88888999***********988744444443246779******99777 PP

                           RAMA  94 kLddlrqe 101
                                     L++ r +
  gi|121639474|ref|YP_979698.1| 266 LLRYRRGT 273
                                    77776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1983.25
//
Query:       gi|121639475|ref|YP_979699.1|  [L=386]
Description: acetyl-CoA acetyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-57  193.7   0.0    5.3e-57  193.1   0.0    1.2  1  Thiolase_N     Thiolase, N-terminal domain
    2.3e-41  140.3   0.3    8.6e-41  138.4   0.0    2.0  2  Thiolase_C     Thiolase, C-terminal domain
    3.8e-06   26.7   0.7    1.8e-05   24.5   0.2    2.1  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.1   0.0   8.8e-61   5.3e-57       2     259 ..       5     255 ..       4     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 193.1 bits;  conditional E-value: 8.8e-61
                                    EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEEEE CS
                     Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqniarqaalkagipeevpavt 80 
                                    ++++a+rt++gk gg+l+ +  ++L+a a ++ll+++ +dp++vd+vi G+v +  g+  niar   l+ag peevp vt
  gi|121639475|ref|YP_979699.1|   5 YVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIgGQAGNIARLSWLAAGYPEEVPGVT 84 
                                    79**************************************************998788889******************* PP

                                    EEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHHH CS
                     Thiolase_N  81 vnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGlt 158
                                    v+++c+S+ +a+  +aq+i++g+adv+vagGv +ms+ p++ +++v    g + ++++ k+ l +    d+   ++ G  
  gi|121639475|ref|YP_979699.1|  85 VDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMSQIPISSAMTVGeqFGFTSPTNESKQWLHRY--GDQEISQFRG-- 160
                                    ****************************************99877654466777777888887776..4555556666.. PP

                                    HHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS CS
                     Thiolase_N 159 aenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGt 238
                                    +e +a+k+++sRee +++ + sh++a aa+ ag+F++ei  ++v++++g   +  de++r+ +++ek+a l+p  +  G 
  gi|121639475|ref|YP_979699.1| 161 SELIAEKWNLSREEMERYSLTSHERAFAAIRAGHFENEI--ITVETESGP--FRVDEGPRE-SSLEKMAGLQPLVE-GGR 234
                                    79*************************************..555555554..9*******9.9********99865.8** PP

                                    -BTTSB--BEEEEEEEEEEEH CS
                     Thiolase_N 239 vtAgnasqisDGaaavllmse 259
                                     tA+ asqisDGa+avll+se
  gi|121639475|ref|YP_979699.1| 235 LTAAMASQISDGASAVLLASE 255
                                    ******************998 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.29   1.8e+03      68      82 ..      13      27 ..       4      41 .. 0.78
   2 !  138.4   0.0   1.4e-44   8.6e-41       2     123 .]     264     385 ..     263     385 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.29
                                   GBSTT--HHHH-B-T CS
                     Thiolase_C 68 kvNvnGGaialGHPl 82
                                    v  +GGa+a  HP+
  gi|121639475|ref|YP_979699.1| 13 AVGKRGGALAGIHPV 27
                                   566789****99996 PP

  == domain 2  score: 138.4 bits;  conditional E-value: 1.4e-44
                                    --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                     Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                    +p a+i++++  + dp  + +gP++a++ +l+k+gl ++did +EinEAFa +++a +k+++ d+ kvN nGGaialGHP
  gi|121639475|ref|YP_979699.1| 264 RPRARIHHISARAADPVFMLTGPIPATRYALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHP 343
                                    789***************************************************************************** PP

                                    TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                     Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                    lGa+Ga++++t+l el++ gg++g+ ++C ggg+++ ++ie+
  gi|121639475|ref|YP_979699.1| 344 LGATGAKLFTTMLGELERIGGRYGLQTMCEGGGTANVTIIER 385
                                    **************************************9985 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2     3e-09   1.8e-05     167     207 ..      81     121 ..      79     145 .. 0.83
   2 ?   -0.3   0.0      0.11   6.5e+02      78     108 ..     236     266 ..     220     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-09
                                    SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                  ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                    p vtvd  C Ss  a+    q+++sg adv++aGGv+ + +
  gi|121639475|ref|YP_979699.1|  81 PGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMSQ 121
                                    5689********************************97754 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.11
                                    HHHHHCTS-HHHHHHHHHHHHHHHHHTS-HH CS
                  ketoacyl-synt  78 spreaeamdpqqrllleaawealedagltpe 108
                                    ++ +a +++  +  +l a+++a++d gl p+
  gi|121639475|ref|YP_979699.1| 236 TAAMASQISDGASAVLLASERAVKDHGLRPR 266
                                    5667788888888889999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2595.89
//
Query:       gi|121639476|ref|YP_979700.1|  [L=200]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-20   71.5   0.1    1.1e-19   70.8   0.1    1.3  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    1.3e-17   63.3   0.4      2e-17   62.7   0.4    1.3  1  TetR_N     Bacterial regulatory proteins, tetR family
    1.8e-05   24.8   0.0      3e-05   24.1   0.0    1.3  1  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
    7.3e-05   22.8   0.0    0.00014   21.9   0.0    1.5  1  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
     0.0007   19.9   0.6     0.0068   16.7   0.0    2.4  2  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
     0.0054   16.9   0.0     0.0084   16.3   0.0    1.3  1  TetR_C_4   YsiA-like protein, C-terminal region


Domain annotation for each model (and alignments):
>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.1   3.6e-23   1.1e-19       2     114 .]      81     195 ..      80     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 3.6e-23
                                    SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HH.HHHHHHHHHHHHHHHHHHHHHHHHHTTSB.-SS-HHHHHHH CS
                      TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelraLspe.hreeiralrreyerllrdlieeGvaagef.edldpklaala 79 
                                    ++p erL+ l  a  e+i ++++++++++ e + L  + + + i ++ ++ ++++ d++++G+++g f  dld++l+ ++
  gi|121639476|ref|YP_979700.1|  81 ANPLERLQGLFMASFEAIEHHHAQVVIYQDEAQRLASQpRFSYIEDRNKQQRKMWVDVLNQGIEEGYFrPDLDVDLVYRF 160
                                    689****************************9998665155666666778889*************************** PP

                                    HHHHHHCHHHC--TTSSS-HHHHHHHHHHHHHH-S CS
                      TetR_C_24  80 ilgmlnwvyrWyrpdGplspeeiadqyadlllrgl 114
                                    i  ++  + rWyrp+Gpl+++++++qy  ++l g+
  gi|121639476|ref|YP_979700.1| 161 IRDTTWVSVRWYRPGGPLTAQQVGQQYLAIVLGGI 195
                                    ********************************986 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.4   6.7e-21     2e-17       1      47 []      15      61 ..      15      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.7e-21
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                   +l+ A+++faerG +attvr+IA+ AG+  g+lY++F+sKee++++l
  gi|121639476|ref|YP_979700.1| 15 LLELAAAMFAERGLRATTVRDIADGAGILSGSLYHHFASKEEMVDEL 61
                                   7999****************************************986 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     1e-08     3e-05       1      84 [.      83     165 ..      83     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHS-TT--TTS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHH CS
                      TetR_C_29   1 PvealrrlveftfdyhaanpefvrLvsiEnlhrgrhlkksesirelnspliekleeilerGqaagvFrpgvdaldlylli 80 
                                    P e l+ l+ + f+  +++ + v + + E+   +++  + + i++ n++  ++  ++l++G ++g Frp++d+  +y  i
  gi|121639476|ref|YP_979700.1|  83 PLERLQGLFMASFEAIEHHHAQVVIYQDEAQRLASQP-RFSYIEDRNKQQRKMWVDVLNQGIEEGYFRPDLDVDLVYRFI 161
                                    8999*************************88777777.7888**********************************9988 PP

                                    HHHH CS
                      TetR_C_29  81 sslc 84 
                                       +
  gi|121639476|ref|YP_979700.1| 162 RDTT 165
                                    6655 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.5e-08   0.00014      32      78 ..     115     161 ..      89     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.5e-08
                                    GG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHH CS
                      TetR_C_17  32 yreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakyl 78 
                                     + + r++y+e+R ++  +  +++l++G+e+g f+P l+++ + +++
  gi|121639476|ref|YP_979700.1| 115 LASQPRFSYIEDRNKQQRKMWVDVLNQGIEEGYFRPDLDVDLVYRFI 161
                                    4567899**********************************999987 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17   4.9e+02      80      93 ..      37      50 ..       9      82 .. 0.51
   2 !   16.7   0.0   2.3e-06    0.0068      54     104 ..     129     181 ..      84     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                      TetR_C_11 80 elvldlllgpllyr 93
                                   +  + +l g l+++
  gi|121639476|ref|YP_979700.1| 37 ADGAGILSGSLYHH 50
                                   22222333333333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.3e-06
                      TetR_C_11  54 eprraalravlrrAvarGelradadvelvldlllgpll..yrllltgepldda 104
                                     ++r+ + +vl ++++ G  r+d+dv+lv   + +  +   r+   g+pl+++
  gi|121639476|ref|YP_979700.1| 129 KQQRKMWVDVLNQGIEEGYFRPDLDVDLVYRFIRDTTWvsVRWYRPGGPLTAQ 181
                                    456888999*********************99999888555677777777766 PP

>> TetR_C_4  YsiA-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.8e-06    0.0084      10     100 ..      71     162 ..      58     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                                    HHHHHHHTT-SSHHHHHHHHHHHHHHHHHC-HHHHHHHHTTCCGSSHHHH.HHHHHHHHHHHHHHHHHHHHHHHTTSC-T CS
                       TetR_C_4  10 ekikeeikekesaeeklkllvekhfsqlsadkelaivtqlelrqsnlelr.lkinevlkgyltlldeiiaeGkekGefke 88 
                                     + ++ +++++++ e+l+ l    f+++++++   ++ q e ++  ++ r   i++  k   ++  +++++G+e+G+f+ 
  gi|121639476|ref|YP_979700.1|  71 ARYRDIVDSTANPLERLQGLFMASFEAIEHHHAQVVIYQDEAQRLASQPRfSYIEDRNKQQRKMWVDVLNQGIEEGYFRP 150
                                    5667778889999***************************997777777625799999********************** PP

                                    T--HHHHHHHHH CS
                       TetR_C_4  89 eldvrlarqlif 100
                                    +ldv l+ ++i 
  gi|121639476|ref|YP_979700.1| 151 DLDVDLVYRFIR 162
                                    *****9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1408.70
//
Query:       gi|121639477|ref|YP_979701.1|  [L=552]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-55  187.4  27.8    2.5e-55  186.9  27.8    1.2  1  PPE             PPE family
    3.3e-39  132.5 283.8    8.4e-09   35.2  29.7   11.6 11  Pentapeptide_2  Pentapeptide repeats (8 copies)
  ------ inclusion threshold ------
        2.3    8.5   6.1        5.1    7.4   6.1    1.5  1  WXG100          Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.9  27.8   4.2e-59   2.5e-55       1     158 []       6     163 ..       6     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 4.2e-59
                                    GS-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHH CS
                            PPE   1 alpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqae 80 
                                    +lpPE+ns ++y G+gs+p+l+AaaaWdgLaael +aa++++sv+++l+++aWqGp+saamaaaaapy+ +L++a+aqa+
  gi|121639477|ref|YP_979701.1|   6 VLPPEINSLRMYLGAGSAPMLQAAAAWDGLAAELGTAASSFSSVTTGLTGQAWQGPASAAMAAAAAPYAGFLTTASAQAQ 85 
                                    59****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE  81 eaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqntpaIaateaeyeemwaqdaaamaaYeaasaaaa 158
                                     aA qa+a+a+++eaA aa+vppa +aanr+++ al+ +n++G n+p Iaa+e  yee+wa+d+aam++Y+a +++aa
  gi|121639477|ref|YP_979701.1|  86 LAAGQAKAVASVFEAAKAAIVPPAAVAANREAFLALIRSNWLGLNAPWIAAVESLYEEYWAADVAAMTGYHAGASQAA 163
                                    *************************************************************************99875 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  33.9   1.5e-07   0.00091       2      40 .]     181     219 ..     179     219 .. 0.64
   2 !   21.7  31.0   2.3e-08   0.00014       2      39 ..     211     248 ..     210     249 .. 0.96
   3 !   20.3  27.0   6.4e-08   0.00038       4      35 ..     259     290 ..     256     290 .. 0.53
   4 !   15.1  45.5   2.6e-06     0.016       1      40 []     281     320 ..     281     324 .. 0.97
   5 !   33.9  24.8   3.6e-12   2.2e-08       4      39 ..     329     364 ..     326     365 .. 0.97
   6 !   21.5  17.6   2.6e-08   0.00016      12      38 ..     375     401 ..     373     403 .. 0.72
   7 !   35.2  29.7   1.4e-12   8.4e-09       2      40 .]     405     443 ..     404     443 .. 0.98
   8 !   31.5  27.7     2e-11   1.2e-07       2      38 ..     425     461 ..     424     463 .. 0.96
   9 !   14.7  20.6   3.5e-06     0.021       2      38 ..     445     484 ..     444     487 .. 0.93
  10 ?   -3.5   5.2       1.7   9.9e+03      14      23 ..     495     504 ..     493     521 .. 0.53
  11 !   10.1   1.4   9.5e-05      0.57       2      17 ..     531     546 ..     523     548 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    N G++N G++N+G +N+GsgN+G++N Gs N G gn+G+
  gi|121639477|ref|YP_979701.1| 181 NLGIGNQGNANLGGGNTGSGNIGNGNKGSSNLGGGNIGN 219
                                    666666666666666666666666666666666666664 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.3e-08
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    N G +N+G+ N+G++N Gs N+G +N+G+gN+G+gn G
  gi|121639477|ref|YP_979701.1| 211 NLGGGNIGNNNIGSGNRGSDNFGAGNVGTGNIGFGNQG 248
                                    99**********************************98 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 6.4e-08
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGs 35 
                                    G  N+G gN+G+ N+G+gNtG++N+G gNtG+
  gi|121639477|ref|YP_979701.1| 259 GQNNVGLGNIGNNNMGFGNTGDANTGGGNTGN 290
                                    44455555555555555555555555555554 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 2.6e-06
                 Pentapeptide_2   1 gNtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    +NtG +N+G+gN+G +N+G+ N+G++N+G++N+G+g tG+
  gi|121639477|ref|YP_979701.1| 281 ANTGGGNTGNGNIGGGNTGNNNFGFGNTGNNNIGIGLTGN 320
                                    6************************************996 PP

  == domain 5  score: 33.9 bits;  conditional E-value: 3.6e-12
                 Pentapeptide_2   4 GslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39 
                                    G lNsGsgN+G +N+G+ N+G fN+GsgN+G +ntG
  gi|121639477|ref|YP_979701.1| 329 GLLNSGSGNIGIGNSGTNNIGLFNSGSGNIGVFNTG 364
                                    99*********************************9 PP

  == domain 6  score: 21.5 bits;  conditional E-value: 2.6e-08
                 Pentapeptide_2  12 NtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    N+G +N+G++N+G++N+G  NtG+gn+
  gi|121639477|ref|YP_979701.1| 375 NLGVGNSGNANIGFGNAGVLNTGFGNA 401
                                    777777777777777777777777775 PP

  == domain 7  score: 35.2 bits;  conditional E-value: 1.4e-12
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntGs 40 
                                    NtG +N+G  NtGf+N G++NtG+ N+G++NtG+gn+G+
  gi|121639477|ref|YP_979701.1| 405 NTGLGNAGELNTGFGNAGFVNTGFDNSGNVNTGNGNSGN 443
                                    **************************************6 PP

  == domain 8  score: 31.5 bits;  conditional E-value: 2e-11
                 Pentapeptide_2   2 NtGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgnt 38 
                                    NtG+ NsG++NtG++N+G+ NtGs N+G++NtG+g +
  gi|121639477|ref|YP_979701.1| 425 NTGFDNSGNVNTGNGNSGNINTGSWNAGNVNTGFGII 461
                                    **********************************976 PP

  == domain 9  score: 14.7 bits;  conditional E-value: 3.5e-06
                 Pentapeptide_2   2 NtGslNsGsgNtGff...NlGsgNtGsfNlGsgNtGsgnt 38 
                                    NtGs N+G++NtGf+   ++G +N G++N+G+  +G++nt
  gi|121639477|ref|YP_979701.1| 445 NTGSWNAGNVNTGFGiitDSGLTNSGFGNTGTDVSGFFNT 484
                                    *************96666*********************7 PP

  == domain 10  score: -3.5 bits;  conditional E-value: 1.7
                 Pentapeptide_2  14 GffNlGsgNt 23 
                                    GffN+ sg t
  gi|121639477|ref|YP_979701.1| 495 GFFNTASGGT 504
                                    6666655554 PP

  == domain 11  score: 10.1 bits;  conditional E-value: 9.5e-05
                 Pentapeptide_2   2 NtGslNsGsgNtGffN 17 
                                    NtG +N+G++ +G+fN
  gi|121639477|ref|YP_979701.1| 531 NTGLFNMGTAISGLFN 546
                                    4555555555555555 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.1   0.00085       5.1       9      84 ..      25     101 ..      21     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00085
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   9 lrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                    + qaaa+ ++ a+el ++ ++  +    l +++W+G a+ a +a+ + +   +++  ++ +  + + k++a+ fe a
  gi|121639477|ref|YP_979701.1|  25 MLQAAAAWDGLAAELGTAASSFSSVTTGLtGQAWQGPASAAMAAAAAPYAGFLTTASAQAQLAAGQAKAVASVFEAA 101
                                    89***************************999*************99999999999999999999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3855.77
//
Query:       gi|121639478|ref|YP_979702.1|  [L=262]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-59  201.2   5.1    2.1e-59  200.9   5.1    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      5e-50  169.7   1.5      6e-50  169.4   1.5    1.1  1  adh_short     short chain dehydrogenase
      3e-11   43.5   2.1    4.5e-11   43.0   2.1    1.3  1  KR            KR domain
  ------ inclusion threshold ------
      0.026   13.9   0.1      0.049   13.0   0.1    1.4  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
       0.18   11.2   1.7       0.35   10.3   0.3    1.9  2  Epimerase     NAD dependent epimerase/dehydratase family
       0.41   10.6   3.2       0.26   11.3   0.8    2.1  2  ADH_zinc_N    Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.9   5.1   6.9e-63   2.1e-59       2     229 ..      26     257 ..      25     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 6.9e-63
                                    TT.TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                   adh_short_C2   2 aa.sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                    aa  gIG a+A+++ +eGa+vv++d +e++  ++++el + +  +v  + cDVt+++qv+al++ +++++g+lD+lvnna
  gi|121639478|ref|YP_979702.1|  26 AAgTGIGSATARRALAEGADVVISDHHERRlGETAAELSALGLGRVehVVCDVTSTAQVDALIDSTTARMGRLDVLVNNA 105
                                    4579**************************877788877754466667******************************** PP

                                    ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                   adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalealtry 154
                                    g   +  +p+++++++e+dr+ldv+l+s+f+ ++aal+++++    g ivn +sv + r+  ++++y+aaKa++ altr+
  gi|121639478|ref|YP_979702.1| 106 GLGGQ--TPVADMTDDEWDRVLDVSLTSVFRATRAALRYFRDAphgGVIVNNASVLGWRAQHSQSHYAAAKAGVMALTRC 183
                                    *****..*******************************99877777********************************** PP

                                    HHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                   adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                     A e +++g+R+Navsp++ + +  ++ + + ell++l a   +gr+++p eva++++fLasd +sy tG+++ v
  gi|121639478|ref|YP_979702.1| 184 SAIEAAEYGVRINAVSPSIARHKFLDKTA-SAELLDRLVAGEAFGRAAEPWEVAATIAFLASDYSSYLTGEVISV 257
                                    ************************99998.799****************************************98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   1.5     2e-53     6e-50       1     185 [.      19     206 ..      19     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 2e-53
                                    SEEEEESTT.SHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short   1 kvvlvtGas.sGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkl 78 
                                    kvv+vt a+  GIG a+a++ ++eGa+vv+ d +e++l e+a+el ++   ++ ++ +Dvt+ ++v+al++   +++g+l
  gi|121639478|ref|YP_979702.1|  19 KVVVVTAAAgTGIGSATARRALAEGADVVISDHHERRLGETAAELSALgLGRVEHVVCDVTSTAQVDALIDSTTARMGRL 98 
                                    79999986527*************************************9899**************************** PP

                                    SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
                      adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                                    dvLvnNAG+ g++p+++++++ew+rv++v lt+vf +tra+l+++  + ++G Ivn +Sv g  +  +++ Y+A+Ka+v 
  gi|121639478|ref|YP_979702.1|  99 DVLVNNAGLGGQTPVADMTDDEWDRVLDVSLTSVFRATRAALRYFRdAPHGGVIVNNASVLGWRAQHSQSHYAAAKAGVM 178
                                    *********************************************988999***************************** PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSH CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTd 185
                                    +ltr+ a e a++g+r+nav P + + +
  gi|121639478|ref|YP_979702.1| 179 ALTRCSAIEAAEYGVRINAVSPSIARHK 206
                                    **********************987655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   2.1   1.5e-14   4.5e-11       4     161 ..      22     182 ..      19     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.5e-14
                                    EEETTTS.HHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   4 litGGlG.gLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikaeepp 81 
                                    ++t ++G g+G ++ar  +++ga  +  +s +   +++  ++ ael+alg  +ve v +Dv++ ++v al+++ +a++++
  gi|121639478|ref|YP_979702.1|  22 VVTAAAGtGIGSATARRALAEGADVV--ISDH--HERRLGETAAELSALGLgRVEHVVCDVTSTAQVDALIDSTTARMGR 97 
                                    5565555489******9999999955..4666..4455566899*****9889*************************** PP

                                    --EEEE---------TTT--HHHHHHHHTTTTH....HHHHHHHHTTT.S--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvk....GawnLhelled.esldffvlfSSiagllgsagqanYaaaNafl 156
                                    +   ++ Ag+  ++++++mt++++++vl   ++    +++   ++++d  +  ++v  +S+ g   +  q++Yaaa a +
  gi|121639478|ref|YP_979702.1|  98 LDVLVNNAGLGGQTPVADMTDDEWDRVLDVSLTsvfrATRAALRYFRDaPHGGVIVNNASVLGWRAQHSQSHYAAAKAGV 177
                                    ***************************9877651111566666667774456788899******************9877 PP

                                    HHHHH CS
                             KR 157 Dalae 161
                                     al +
  gi|121639478|ref|YP_979702.1| 178 MALTR 182
                                    77655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.6e-05     0.049      43     127 ..      28     105 ..       5     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                    S-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHH.HHH-SEEEE-S--STTTTTSBSHHHHHCSTTTE CS
                   2-Hacid_dh_C  43 GlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleel.laesDivslhlpltpetrhlinaeelakmkkga 121
                                    G+G IG+a+a+r+ a g++v++ d++++      +lg + ++l +l l + + v++ +  t++   li++++ a+m +  
  gi|121639478|ref|YP_979702.1|  28 GTG-IGSATARRALAEGADVVISDHHER------RLGETAAELSALgLGRVEHVVCDVTSTAQVDALIDSTT-ARMGRLD 99 
                                    343.**********************66......455566788887799*******************9876.6777777 PP

                                    EEEESS CS
                   2-Hacid_dh_C 122 iliNta 127
                                    +l+N a
  gi|121639478|ref|YP_979702.1| 100 VLVNNA 105
                                    777754 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00012      0.35       6      63 ..      26      91 ..      21     118 .. 0.78
   2 ?    0.1   0.1      0.15   4.6e+02      67     104 ..     151     188 ..     116     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                                   TTSH.HHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHH CS
                      Epimerase  6 atGf.iGsalvkallekgyevigldrlssasntarledl...........elveldltdrsalerlfkee 63
                                   a+G  iGsa++++ l++g +v+  d+ +++  +     +           e v +d+t  +++++l++++
  gi|121639478|ref|YP_979702.1| 26 AAGTgIGSATARRALAEGADVVISDHHERRLGET----AaelsalglgrvEHVVCDVTSTAQVDALIDST 91
                                   555449**************99999993333222....1234689***999999*******999999865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                                    EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHH CS
                      Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaark 104
                                    ++++ A v g++a++++  + + k  +++l+ ++a+ +
  gi|121639478|ref|YP_979702.1| 151 VIVNNASVLGWRAQHSQSHYAAAKAGVMALTRCSAIEA 188
                                    55555555566665555555555555555555444443 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   8.8e-05      0.26       1      67 [.      30     106 ..      30     173 .. 0.77
   2 ?   -2.4   0.1       1.4   4.2e+03      10      33 ..     188     211 ..     176     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHHT.....T.ESEEEET.TTC.HHHHHHHHHTT.TSSEEEEEESSC CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseekl.elakkl.....G.adeviny.kea.dlverikeltg.gegvdvvfecvG 67 
                                    g+G+a+   A a Ga v+  d+ e++l e a++l     G +++v+   +++ ++++ i + t   + +dv ++ +G
  gi|121639478|ref|YP_979702.1|  30 GIGSATARRALAEGADVVISDHHERRLgETAAELsalglGrVEHVVCDvTSTaQVDALIDSTTArMGRLDVLVNNAG 106
                                    89************************997777775555556555554444443444444444433445566555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                    HHHTT-EEEEEESSHHHHHHHHHT CS
                     ADH_zinc_N  10 AkalGaeviavdsseeklelakkl 33 
                                    A+ +G+++ av++s  + +++ k 
  gi|121639478|ref|YP_979702.1| 188 AAEYGVRINAVSPSIARHKFLDKT 211
                                    334555888888887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1907.49
//
Query:       gi|121639479|ref|YP_979703.1|  [L=385]
Description: acyl-CoA dehydrogenase fadE30 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-31  109.8   0.3    2.3e-31  109.0   0.3    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-24   86.4   0.0    2.4e-24   85.3   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.6e-20   72.7   0.2    8.7e-20   71.5   0.2    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.3   3.9e-35   2.3e-31       1     150 []     231     377 ..     231     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 3.9e-35
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g+G+rvam tl++eR +  +++  +++r l +++e+arr++a     +d++l+re+l + ++ l+a+r+++++++e++  
  gi|121639479|ref|YP_979703.1| 231 GDGWRVAMATLTFERGVSTLGQQIVYARELSNLVELARRTAA-----ADDPLIRERLTRAWTGLRAMRSYALATMEGPAV 305
                                    79***************************************9.....89******************************* PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTS.GGGH...HHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyl.eeyp...verlyrdarvlrigeGtseiqrniiarrll 150
                                    ++p   + ++ Kl+++++++++ +lam+++G+ G++  +++   ++rly  +r+++i++G++eiqrniia+r+l
  gi|121639479|ref|YP_979703.1| 306 EQPG--QDNVSKLLWANWHRNLGELAMDVIGKPGMTmPDGEfdeWQRLYLFTRADTIYGGSNEIQRNIIAERVL 377
                                    9999..*****************************778888888***************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   4.1e-28   2.4e-24       1      96 [.     125     218 ..     125     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 4.1e-28
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    + + +Ep+aGsd+asv+t +ae dg+++v+nG+K+w + a+ +++++vlartek + r+ gls +lvp d+pgv++r+i 
  gi|121639479|ref|YP_979703.1| 125 CQGYSEPGAGSDLASVAT-TAELDGDQWVINGQKVWTSLAHLSQWCFVLARTEKGSqRHAGLSYLLVPLDQPGVQIRPIV 203
                                    7899**************.89999999************************8888899*********************9 PP

                                    -BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfed 96 
                                    + +G+   ++ e++f+d
  gi|121639479|ref|YP_979703.1| 204 QITGTA--EFNEVFFDD 218
                                    877766..567888887 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.2   1.5e-23   8.7e-20       3     109 ..       3     117 ..       1     120 [. 0.83

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.5e-23
                                    HHHHHHHHHHHHHHHHTHHHHHHH.......HHHTSGH..HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHH CS
                  Acyl-CoA_dh_N   3 eqealrdtvrefaeeelaphaaew.......deegefp..relwkklaelGllgitvpeeygGagldyleaaivaeelar 73 
                                    + e++r++vr +++++la   a         +e+++f+  r++ ++la++Gl+++ +pee+gG+gl++ + + ++ee ar
  gi|121639479|ref|YP_979703.1|   3 DVEEFRAQVRGWLADNLAGEFAALkglggpgREHEAFEerRAWNQRLAAAGLTCLGWPEEHGGRGLSTAHRVAFYEEYAR 82 
                                    5689*************987777744444333444777423357889********************************* PP

                                    H-HHHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_N  74 adaglalllgvhsslvapailrfGteeqkrryLpkl 109
                                    ada+  +    +  l +p++++fGt++q+rr+Lp++
  gi|121639479|ref|YP_979703.1|  83 ADAPDKV-NHFGEELLGPTLIAFGTPQQQRRFLPRI 117
                                    ****887.445667888*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2734.57
//
Query:       gi|121639480|ref|YP_979704.1|  [L=507]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-91  306.6   0.1    2.5e-91  306.4   0.1    1.0  1  AMP-binding      AMP-binding enzyme
    3.6e-19   69.5   0.2      9e-19   68.2   0.2    1.7  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.16   12.3   0.0        0.4   11.0   0.0    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   0.1   4.1e-95   2.5e-91       3     421 ..      14     412 ..      12     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 4.1e-95
                                    HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                    AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                    + +++ pd++al+   e++++T  el+++v  +Aa+L +lGv++ drVai++pn+++wvva lai  aGa+vvpln+++t
  gi|121639480|ref|YP_979704.1|  14 RLVRQLPDHTALIA--EDRRFTSTELRDAVYGAAAALIALGVEPADRVAIWSPNTWHWVVACLAIHHAGAAVVPLNTRYT 91 
                                    668899*******9..**************************************************************** PP

                                    HHHHHHHHHHHTESEEE.....ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS- CS
                    AMP-binding  83 aeelayiledseakvli.....atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeel 156
                                    a e   il+ ++a vl+        d+++ l+++  a   l+a ++v+ +  ++ + ++++ +++++ + +    +++++
  gi|121639480|ref|YP_979704.1|  92 ATEATDILDRAGAPVLFaaglfLGADRAAgLDRA--A---LPALRHVVRVPVEADDGTWDEFIATGAGALDAVAARAAAV 166
                                    *****************86654133344433332..2...3333333333333333333333333333222113356689 PP

                                    BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                    AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllp 235
                                     p+d+  i++TSGTTG+ KGV   h ++l+a+++++      k+++dd++l+i p++h fg+ +++l++l  Gat++   
  gi|121639480|ref|YP_979704.1| 167 APQDVSDILFTSGTTGRSKGVLCAHrQSLSASASWA---ANGKITSDDRYLCINPFFHNFGYKAGILACLQTGATLIPHV 243
                                    *************************55555554443...3467889*****************************99877 PP

                                    TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEE CS
                    AMP-binding 236 kdaaldpklllelieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfge.evle 313
                                    ++++l+    l++ie++++tv++g+P++++ ll+++a+k +     dlsslr++++g++ ++  l++++++ +    vl 
  gi|121639480|ref|YP_979704.1| 244 TFDPLH---ALRAIERHRITVLPGPPTIYQSLLDHPARKdF-----DLSSLRFAVTGAATVPVVLVERMQSELDIdIVLT 315
                                    776655...58************************999844.....**************************98889*** PP

                                    EEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEET CS
                    AMP-binding 314 gYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdse 392
                                    +YGlTE+ g+ t+  p+++  +++ ++G+p+++ e++i+D+           Ge+l+rgp+vm gYl + eata a+d  
  gi|121639480|ref|YP_979704.1| 316 AYGLTEANGMGTMcRPEDDAVTVATTCGRPFADFELRIADD-----------GEVLLRGPNVMVGYLDDTEATAAAID-A 383
                                    ***********765666777788899**************8...........9************************9.6 PP

                                    CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                    AMP-binding 393 grwlrTGDlgrldedGyleivgRkkdlik 421
                                    ++wl+TGD+g +d+ G+l+i +R+kd+ +
  gi|121639480|ref|YP_979704.1| 384 DGWLHTGDIGAVDQAGNLRINDRLKDMYI 412
                                    57************************965 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.2   1.5e-22     9e-19       1      76 []     422     497 ..     422     497 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.5e-22
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evE++l+++++Va+aaV+Gvpd++ Ge+  afVv ++g+ + e+ ++a+ r++l+ +++p+ v+fvd lp+++ GK
  gi|121639480|ref|YP_979704.1| 422 EVEQVLARMDGVADAAVIGVPDQRLGEVGRAFVVARPGTGLDEASVIAYTREHLANFKTPRSVRFVDVLPRNAAGK 497
                                    8*********************************998965568********************************9 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.8e-05       0.4       1      22 [.     415     436 ..     415     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.8e-05
                                    TEEE-HHHHHHHHHT-TTEEEE CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepe 22 
                                    G nv+P ++e+vl ++++v++ 
  gi|121639480|ref|YP_979704.1| 415 GFNVYPAEVEQVLARMDGVADA 436
                                    89***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3626.18
//
Query:       gi|121639481|ref|YP_979705.1|  [L=377]
Description: acyl-CoA dehydrogenase fadE31 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-20   72.4   0.0    8.4e-20   71.5   0.0    1.5  1  Acyl-CoA_dh_N   Acyl-CoA dehydrogenase, N-terminal domain
    7.4e-19   68.4   0.0    1.2e-18   67.8   0.0    1.3  1  Acyl-CoA_dh_1   Acyl-CoA dehydrogenase, C-terminal domain
    2.7e-18   66.0   0.0    1.1e-17   64.0   0.0    1.9  2  Acyl-CoA_dh_M   Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.069   12.5   1.6        7.1    6.1   0.0    3.2  3  Enolase_like_N  Enolase N-terminal domain-like


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   1.9e-23   8.4e-20       2     113 .]       7     120 ..       6     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.9e-23
                                    HHHHHHHHHHHHHHHHHTHHHHHHHHHHT.SGHHHH.HHHH.HHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeeg.efprel.wkkl.aelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                    +e  a++++vref++ ++a   ++ ++++  f +++ w+++  ++Gl  it+p +ygG+++  l+ +++ ee  ra+a++
  gi|121639481|ref|YP_979705.1|   7 DETLAFQAEVREFLAANAASIPTKSYDNAeGFAQHRyWDRVlFDAGLSVITWPAKYGGRDAPLLHWIVFEEEYFRAGAPG 86 
                                    7899**************9988888755547887766999879************************************8 PP

                                    HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                    +++ + ++s+ ap+++++Gt+eq +r Lpk+asge
  gi|121639481|ref|YP_979705.1|  87 RASAN-GTSMLAPTLFAHGTAEQLDRILPKMASGE 120
                                    87554.566777**********************8 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   2.6e-22   1.2e-18       1     150 []     230     370 ..     230     370 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.6e-22
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++G+r+am+t  +eR +  +++ + + +  e+++++ ++r +        +  ++++a+ +++++a rl ++ ++ +l a
  gi|121639481|ref|YP_979705.1| 230 NDGWRAAMSTSSNERGMS-LRSPARFLASAERLVQLWKDRGS-------PPEFADRVADAWIKAQAYRLQTFGTVTRLAA 301
                                    79**************99.5999999999999****999988.......5889*************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                    g++ +ae+s++K+f+sel + +++ a++l G++G l++ + e l   a+  +i++Gt+eiqrniia+rll
  gi|121639481|ref|YP_979705.1| 302 GGELGAESSVTKVFWSELDVHLHQTALDLRGADGELAGPWTEGL-LFALGGPIYAGTNEIQRNIIAERLL 370
                                    **********************************9988877775.9**********************86 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.49   2.2e+03      70      95 ..      50      76 ..      34      77 .. 0.84
   2 !   64.0   0.0   2.4e-21   1.1e-17       2      97 .]     125     218 ..     124     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.49
                                   GGGEEE-----BSS-TTS-.EEEEEEE CS
                  Acyl-CoA_dh_M 70 apgvsvrrieeklGlrglp.tgelvfe 95
                                   + g+sv  +++k+G r++p  +++vfe
  gi|121639481|ref|YP_979705.1| 50 DAGLSVITWPAKYGGRDAPlLHWIVFE 76
                                   56999*9*******9999966667776 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 2.4e-21
                                    EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvrrie 79 
                                     a++Ep++Gsd+as+++ +a++ +g++ lnG+Kiw+++a+ a++ + l+r+ +p+  r+rgl+ f+ + +a+gv+vr+i 
  gi|121639481|ref|YP_979705.1| 125 QAWSEPESGSDLASLRS-TASKVDGGWLLNGQKIWSSRAPFADMGFGLFRS-DPAveRHRGLTYFMFDLKAKGVTVRPI- 201
                                    689**************.55566669************************4.44458**********************. PP

                                    -BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfedv 97 
                                    ++lG + + +ge++++dv
  gi|121639481|ref|YP_979705.1| 202 AQLGGD-TGFGEIFLDDV 218
                                    689987.68899999987 PP

>> Enolase_like_N  Enolase N-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.012        52      19      35 ..     150     166 ..     145     169 .. 0.89
   2 ?    6.1   0.0    0.0016       7.1      11      30 ..     194     213 ..     189     215 .. 0.91
   3 ?   -0.4   0.1      0.17   7.8e+02      34      47 ..     272     285 ..     265     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.012
                 Enolase_like_N  19 vlleGpaGwgEfspFle 35 
                                     ll+G++ w+  +pF++
  gi|121639481|ref|YP_979705.1| 150 WLLNGQKIWSSRAPFAD 166
                                    699************97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0016
                 Enolase_like_N  11 RgitvReavlleGpaGwgEf 30 
                                    +g+tvR ++ l G+ G+gE 
  gi|121639481|ref|YP_979705.1| 194 KGVTVRPIAQLGGDTGFGEI 213
                                    79*****************5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.17
                 Enolase_like_N  34 leYddaeaarWlaa 47 
                                    +e+ d+ a +W++a
  gi|121639481|ref|YP_979705.1| 272 PEFADRVADAWIKA 285
                                    6999*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2795.72
//
Query:       gi|121639482|ref|YP_979706.1|  [L=319]
Description: acyl-CoA dehydrogenase fadE32 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-22   80.5   5.1    2.2e-22   79.9   5.1    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      4e-09   37.1   0.2    3.6e-08   34.0   0.0    2.3  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.8e-05   24.4   8.2    0.00013   22.3   8.2    2.1  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   5.1   3.7e-26   2.2e-22       8     148 ..     183     318 ..     180     319 .] 0.94

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 3.7e-26
                                    TTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHH CS
                  Acyl-CoA_dh_1   8 metlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdrae 87 
                                     ++ +++ la+aa+ +g+ ++ le a++ya++r++fg++++++q++++kla++++ +e a  lvy aa        ++ +
  gi|121639482|ref|YP_979706.1| 183 ARAYEFGALATAAQLVGAGQALLEAAVNYAKQRTQFGRAIGSYQAIKHKLADVHIAIELACPLVYGAAV-----SLEPRD 257
                                    556678899***********************************************************7.....556779 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1  88 asmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                    +s+aK+ ase+a  +a++a+q +G+ G++ e+ ++ ++ ++++l  + Gt + +r+ + ++
  gi|121639482|ref|YP_979706.1| 258 VSAAKAAASEAALLAARSALQTHGAIGFTCEHDLSLWLLRVQALHSAWGTPQEHRRRVLEA 318
                                    9*************************************************99999998876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   6.1e-12   3.6e-08       2      94 ..       9     100 ..       8     113 .. 0.77
   2 ?    0.1   0.0      0.21   1.2e+03      31      66 ..     176     209 ..     158     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.1e-12
                                    HHHHHHHHHHHHHHHH.HTHHHHHHHHHHTSGH.HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaee.elaphaaewdeegefp.relwkklaelGllgitvpeeygGagldyleaaivaeelaradagla 79 
                                    e+q+++ +++ + +    l+ +++ w + +  p r++w++la lG++++ v e++ G+g+++++ ++++e l+r ++++ 
  gi|121639482|ref|YP_979706.1|   9 EQQRDFAASIDAALGAaDLPGVVRAWAAGDVAPgRKVWQQLANLGVTALGVAEKFDGLGASPVDLVVALERLGRWCVPGP 88 
                                    7888999998887766255666777755555566889**************************************99954 PP

                                    HHHHHHHHTTHHHHH CS
                  Acyl-CoA_dh_N  80 lllgvhsslvapail 94 
                                    +   + s  vap++l
  gi|121639482|ref|YP_979706.1|  89 V---TESIAVAPILL 100
                                    4...33333445444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.21
                                    SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHH CS
                  Acyl-CoA_dh_N  31 efprelwkklaelGllgitvpeeygGagldyleaai 66 
                                    + p++++ ++ e G l+ +   +  Gag   leaa+
  gi|121639482|ref|YP_979706.1| 176 RAPKDVVARAYEFGALATAA--QLVGAGQALLEAAV 209
                                    35888999999988875554..66777755565554 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   8.2   2.1e-08   0.00013       2     101 ..     192     276 ..     191     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-08
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                      aa+ +Ga +a l+++v +a++r++  +g+++   +a++++la++  +++ A+ l++ aa + e               
  gi|121639482|ref|YP_979706.1| 192 ATAAQLVGAGQALLEAAVNYAKQRTQ--FGRAIGSYQAIKHKLADVHIAIELACPLVYGAAVSLEPRDVS---------- 259
                                    5799**********************..*******************************99995544222.......... PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdal 101
                                       +a+a+a+e a  a++++
  gi|121639482|ref|YP_979706.1| 260 ---AAKAAASEAALLAARSA 276
                                    ...22222233333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2250.61
//
Query:       gi|121639483|ref|YP_979707.1|  [L=318]
Description: acyl-CoA dehydrogenase fadE33 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   74.3   7.6    1.5e-20   73.9   4.7    2.5  3  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.9e-14   54.3   0.5    4.9e-14   53.0   0.5    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.6e-08   33.8   7.1    3.6e-08   33.8   7.1    2.3  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.25   1.5e+03      33      64 ..      67      98 ..      51     111 .. 0.78
   2 ?   -2.3   0.0      0.78   4.6e+03      52      81 ..     126     155 ..     121     165 .. 0.78
   3 !   73.9   4.7   2.5e-24   1.5e-20      15     129 ..     185     294 ..     181     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                                   HHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1 33 aleyarrrkafgkplidhqlvreklaemaael 64
                                   +++ a   ++ g++l+ ++l+   lae+a  +
  gi|121639483|ref|YP_979707.1| 67 LADAAIVVQELGRALVPSPLLGTTLAELALLA 98
                                   45556666778899999999999999988655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.78
                                    HHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                  Acyl-CoA_dh_1  52 lvreklaemaaeleaarllvyraaealdag 81 
                                    +v   +a++ + +++ +l+ ++  +a+  +
  gi|121639483|ref|YP_979707.1| 126 VVNGDIADIVVAATSGQLTRWTRFSAQPVA 155
                                    577889999999999999999888776555 PP

  == domain 3  score: 73.9 bits;  conditional E-value: 2.5e-24
                                    -----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHH CS
                  Acyl-CoA_dh_1  15 RlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlf 94 
                                     +++aa ++g+a+r+l+ ++eya++r +fg+p++++q++++++a++++ ++aar+ v +a +     +p++  a+ a l 
  gi|121639483|ref|YP_979707.1| 185 AILLAAEQIGAAERCLQLTVEYAKSRVQFGRPIGSFQALKHRMADLYVTIAAARAVVADACH-----APTPTNAATARLA 259
                                    5889********************************************************97.....78889******** PP

                                    HHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTH CS
                  Acyl-CoA_dh_1  95 aselaqevadlamqllGgaGyleeypverlyrdar 129
                                    ase++ ++a++ +ql+Gg ++++e+ ++ ++++a 
  gi|121639483|ref|YP_979707.1| 260 ASEALSTAAAEGIQLHGGIAITWEHDMHLYFKRAH 294
                                    ************************99888877664 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.5   8.2e-18   4.9e-14       2     100 ..       5     103 ..       4     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 8.2e-18
                                    HHHHHHHHHHHHHHHHHTHHHHHHHH.HHT.SGHHHHHHHHHH.TTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                  Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewd.eeg.efprelwkklae.lGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                    ee ++lr+tv++++++++ p a ++  +++  ++++lw+ l+e  G +++ +pee gGag++  +aaiv++el+ra ++ 
  gi|121639483|ref|YP_979707.1|   5 EERQMLRETVASLVAKHAGPAAVRAAmASDrGYDESLWRLLCEqVGAAALVIPEELGGAGGELADAAIVVQELGRALVP- 83 
                                    899***************8876666654444688999****9736******************************9999. PP

                                    HHHHHHHHHTTHHHHHHHS-HH CS
                  Acyl-CoA_dh_N  79 alllgvhsslvapailrfGtee 100
                                      ++ ++++l+  a+l+ + ++
  gi|121639483|ref|YP_979707.1|  84 --SPLLGTTLAELALLAAAKPD 103
                                    ..45567788877777777665 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.75   4.5e+03      49      58 ..      99     108 ..      65     146 .. 0.58
   2 !   33.8   7.1     6e-12   3.6e-08       2     101 ..     187     271 ..     186     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.75
                                    HHHHHHHHHH CS
                  Acyl-CoA_dh_2  49 arldAArall 58 
                                    a+   A+al+
  gi|121639483|ref|YP_979707.1|  99 AAKPDAQALT 108
                                    2222222222 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 6e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                    ++aa  +GaA+++l+ +ve+a+ rv+  +g+++  ++a++++ a++   + AAra++++a+ + +              a
  gi|121639483|ref|YP_979707.1| 187 LLAAEQIGAAERCLQLTVEYAKSRVQ--FGRPIGSFQALKHRMADLYVTIAAARAVVADACHAPTPTN----------AA 254
                                    679999********************..*********************************9933332..........33 PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdal 101
                                     ar+   +a+e    a+ + 
  gi|121639483|ref|YP_979707.1| 255 TARL---AASEALSTAAAEG 271
                                    3333...3333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2244.68
//
Query:       gi|121639484|ref|YP_979708.1|  [L=388]
Description: aspartate aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-55  188.1   0.0    2.9e-55  187.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00031   19.6   0.0    0.00051   18.9   0.0    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
       0.04   12.8   0.0      0.058   12.3   0.0    1.2  1  Alliinase_C      Allinase
      0.049   12.6   0.0      0.094   11.6   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
      0.049   12.3   0.0       0.07   11.8   0.0    1.3  1  Aminotran_3      Aminotransferase class-III
       0.16    9.4   0.0       0.22    9.0   0.0    1.0  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
       0.19   10.9   0.0       0.34   10.2   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.0   1.1e-58   2.9e-55       2     363 .]      32     381 ..      31     381 .. 0.90

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 1.1e-58
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    d++nL++++++ +     ++ v+ a++   + + +   y+   g pel+ a+a  ++r+++++++++ avv ++G++ + 
  gi|121639484|ref|YP_979708.1|  32 DLVNLSAGQPSAG----APEPVRAAAAA--ALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPD-AVVITTGSSGGF 104
                                    689********99....55555555543..44566678999999***********************.999999999776 PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                     +++ ++ +++gd++ + +p y+ y nil + g+evv++p+ ++  f+ +++ l e ++       + ++++v+sp NPt
  gi|121639484|ref|YP_979708.1| 105 LLAFLAC-FDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDP------PLRGVVVASPANPT 176
                                    6666666.99****************************************999988.999......99************ PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    Gtv+++eel ++++ +++  ++l++De+Y g+v++  +a +t +  ++  n ++v+s+sK ++++G+R+G++l+   +++
  gi|121639484|ref|YP_979708.1| 177 GTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQ--GAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRR 254
                                    ***********************************..566775666666677**************************** PP

                                    HHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHH..CH CS
                  Aminotran_1_2 242 qlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsae..ta 317
                                    ++  l  +f++ + +l++++a ++ +++ +  e + + + ++ +r  l d+L+++g++ la+  ++++++ d+s    + 
  gi|121639484|ref|YP_979708.1| 255 AVDCLTGNFTIcPPVLSQIAAVSAFTPEAT-AEADGNLASYAINRSLLLDGLRRIGIDRLAPTdGAFYVYADVSDFtsDS 333
                                    ***********9777777777777777766.4*****************************999*********9988889 PP

                                    HHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 318 kelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelveal 363
                                     +++ kLl   gv++ pg  f +    +++Ri++ ++++ ++ee+++++
  gi|121639484|ref|YP_979708.1| 334 LAFCSKLLADTGVAIAPGIDFDTargGSFVRISF-AGPSGDIEEALRRI 381
                                    99****99999**********99**999******.99*********998 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-07   0.00051     128     217 ..     119     206 ..     112     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                                    EEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT CS
                 Aminotran_MocR 128 lvtvpGydrhfllleelGielltvdlqddGpdvdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaapd 207
                                     +++pGy  +  +l  lG e++ ++  ++     + + l+  d+ ++G++ v   +nptG++i +e    +a+  + a d
  gi|121639484|ref|YP_979708.1| 119 AMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVV-VASPANPTGTVIPPEELAAIASW-CDASD 196
                                    5789**********************999999999999**********86.77889**********99999987.5678* PP

                                    -EEEEE-TTS CS
                 Aminotran_MocR 208 frifaddaya 217
                                     r+  d+ y 
  gi|121639484|ref|YP_979708.1| 197 VRLISDEVYH 206
                                    *******995 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05     0.058     142     209 ..     168     249 ..     110     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                                    EEESS-TTT----..----......-TT-EEEEEE-TT-......STTTS---S-B--SEEEEEHHHHHS-GGG-EEEEE CS
                    Alliinase_C 142 lvtsPnnPdgllr..eavv......kgseakviyDlayY......WPhytpitskadedimLftlskltGhaGsrlGWal 207
                                    +v+sP nP g++   e++       + s++++i D +y+       P+ +   + + + +++ ++sk+   +G rlGW l
  gi|121639484|ref|YP_979708.1| 168 VVASPANPTGTVIppEELAaiaswcDASDVRLISDEVYHglvyqgAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247
                                    799*******984222222225666889999****999733223347777777889999*******************99 PP

                                    ES CS
                    Alliinase_C 208 vk 209
                                    v 
  gi|121639484|ref|YP_979708.1| 248 VP 249
                                    94 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05     0.094      58     165 ..      89     189 ..      78     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                                    -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE.GGGHHHH- CS
                    Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld.ldelekll 136
                                    +e  + ++ t G++ ++ l+ l+    +++gd++ + + ++ + +    ++  + g +v+ ip  ++ + + + ++ + +
  gi|121639484|ref|YP_979708.1|  89 VEP-DAVVITTGSSGGFLLAFLAC---FDAGDRVAMASPGYPCYR----NILSALGCEVVEIPCGPQTRFQpTAQMLAEI 160
                                    554.88999999999999999999...9**************999....6666789*************9977899**** PP

                                    -TTEEEEEEESBETTTTEB--HHHHHHHH CS
                    Aminotran_5 137 nektklvaithvsnvtGtiqpveeigkla 165
                                    ++  + v ++   n tGt+ p ee++++a
  gi|121639484|ref|YP_979708.1| 161 DPPLRGVVVASPANPTGTVIPPEELAAIA 189
                                    *********************99999876 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.07     187     239 ..     158     209 ..      86     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                    CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                    Aminotran_3 187 kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                    +++++ + +v+v       G v++++e la+++++c+  dv li DEv  G+ 
  gi|121639484|ref|YP_979708.1| 158 AEIDPPLRGVVVASPANPTGTVIPPEE-LAAIASWCDASDVRLISDEVYHGLV 209
                                    556666666666555555676666555.899*****************99985 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   8.7e-05      0.22     766     806 ..      93     135 ..      90     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 8.7e-05
                        Bac_GDH 766 avIVPvGaKGGFvvkrlp..kaadreallaegiacYktfirgL 806
                                    av++ +G+ GGF++  l+  +a+dr a+ + g  cY++++++L
  gi|121639484|ref|YP_979708.1|  93 AVVITTGSSGGFLLAFLAcfDAGDRVAMASPGYPCYRNILSAL 135
                                    89************9999889*******************997 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013      0.34     129     167 ..     166     202 ..     149     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                    EEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 129 klisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    ++++   +n t  G+v+++eel+++a ++++ +++l+ D
  gi|121639484|ref|YP_979708.1| 166 GVVVASPANPT--GTVIPPEELAAIASWCDASDVRLISD 202
                                    45566666666..**********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2617.03
//
Query:       gi|121639485|ref|YP_979709.1|  [L=283]
Description: arylamine n-acetyltransferase nat [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-80  270.5   0.0    1.8e-80  270.2   0.0    1.0  1  Acetyltransf_2  N-acetyltransferase


Domain annotation for each model (and alignments):
>> Acetyltransf_2  N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   0.0   9.9e-85   1.8e-80       1     236 [.      21     258 ..      21     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 9.9e-85
                                    SHHHHHHHHHHHHHHS-EE-HHHHTT---.--SHHHHHHHHTTST--B-HHHHHHHHHHHHHHTT-EEEEEEEEEETTGG CS
                 Acetyltransf_2   1 dLetLrellqahlraiPFENldvllgeei.eldlealfdklVkkkRGGyCyelNgLlarvLkelGFevtllagrvvvkae 79 
                                    +L++L++l++ h r+iPFENld+llg ++ +l+ +al dklV ++RGGyC+e+NgL+++vL+elG++v+++a+rvv+k +
  gi|121639485|ref|YP_979709.1|  21 TLDVLQDLVTVHSRTIPFENLDPLLGVPVdDLSPQALADKLVLRRRGGYCFEHNGLMGYVLAELGYRVRRFAARVVWKLA 100
                                    79***************************99************************************************* PP

                                    SSS.SSSCEEEEEEEEETTE..EEEE-SSSSCG.-SS-EESSTTCEEEESSEEEEEEEETTCEEEEEEEETTEEEEEEEE CS
                 Acetyltransf_2  80 eaa.stertHllllVtidge..tylvDvGFGgstltaplelesgkdqqtthgifrlveeeenewvlekkkreewvklYsf 156
                                    ++a ++++tH+ll Vt+ g+   ylvDvGFGg+t+t+pl+le+g +q+tth+++rl ++ +  +vl+++ r++w++lY+f
  gi|121639485|ref|YP_979709.1| 101 PDApLPPQTHTLLGVTFPGSggCYLVDVGFGGQTPTSPLRLETGAVQPTTHEPYRLEDRVD-GFVLQAMVRDTWQTLYEF 179
                                    **99*************99988**********************************88888.****************** PP

                                    EEEEB-HHHHHHHHHHHHHSTT-HHHCS-EEEEEETTEEEEEETTEEEEEETTSEEEEEEE-SHHHHHHHHHHTT----S CS
                 Acetyltransf_2 157 tleprqiedfeeandylstspdsvftkkllcslatpdgrltLvgrtlterekdgaleeiklltdeeleevlkekFgiele 236
                                    t+++r ++d+++a++y st+p+s f++ l+++++t+d+r++L+gr+l+++ + g +e+i+l +++++ ++l+e+Fgi+++
  gi|121639485|ref|YP_979709.1| 180 TTQTRPQIDLKVASWYASTHPASKFVTGLTAAVITDDARWNLSGRDLAVH-RAGGTEKIRLADAAAVVDTLSERFGINVA 258
                                    **************************************************.7777***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2398.64
//
Query:       gi|121639486|ref|YP_979710.1|  [L=88]
Description: hypothetical protein BCG_3631c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 677.08
//
Query:       gi|121639487|ref|YP_979711.1|  [L=187]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-37  128.8   0.0    2.2e-37  128.5   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.041   13.7   0.0    1.2  1  DUF447         Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   0.0   2.4e-41   2.2e-37       2     154 ..      15     160 ..      14     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 2.4e-41
                                    TTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SC CS
                  Flavin_Reduct   2 rrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgpr 81 
                                    ++++++++v+tt v+++ p g+ + sf +lsl+Pplv+f+  + s++++a++++g+f++n+l e+q+++ ++f++    +
  gi|121639487|ref|YP_979711.1|  15 GQFCTGITVITT-VHDDVPVGFACQSFAALSLEPPLVLFCPTKVSRSWQAIEASGRFCVNVLTEKQKDVSARFGS----K 89 
                                    689*********.**************************************************************....5 PP

                                    CCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEEEE CS
                  Flavin_Reduct  82 tddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrryagl 154
                                    + dk  fag++w++s+ g+p+++g+la+++C+v + ++ gdh ++ g V++ +     +  pLl++r+ y g+
  gi|121639487|ref|YP_979711.1|  90 EPDK--FAGIDWRPSELGSPIIEGSLAYIDCTVASVHDGGDHFVVFGAVESLSEVPAVKPRPLLFYRGDYTGI 160
                                    6799..**********************************************999999989*********986 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-06     0.041      27     132 ..      50     161 ..      22     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                                    EEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTTC.TT...EETT-SEEEEEEEEEE.CTCEC CS
                         DUF447  27 vvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkpa.kia..vlksaeawveveveev.egdse 102
                                    v++ + k sr+++ ++++g++ +nv +  +  + a +g  e ++f   +    ++   +++++ a++ ++v +v  g ++
  gi|121639487|ref|YP_979711.1|  50 VLFCPTKVSRSWQAIEASGRFCVNVLTEKQKDVSARFGSKEPDKFAGIDWRPsELGspIIEGSLAYIDCTVASVhDGGDH 129
                                    445555779*********************************9996555422233345***************9444455 PP

                                    CEEEEEEEEEEEEETTB---B..-HHHHHHHH CS
                         DUF447 103 alelelepvkeeileervkpf..nRgdaaviE 132
                                     +++ +    +e+ + +++p+   Rgd+  iE
  gi|121639487|ref|YP_979711.1| 130 FVVFGAVESLSEVPAVKPRPLlfYRGDYTGIE 161
                                    55555555567777777777777999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1389.04
//
Query:       gi|121639488|ref|YP_979712.1|  [L=300]
Description: biphenyl-2,3-diol 1,2-dioxygenase bphC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-22   78.4   0.0    1.1e-20   74.2   0.0    2.3  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    3.2e-05   24.7   0.1     0.0012   19.7   0.0    2.6  2  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.023   2.1e+02     106     127 ..      98     116 ..       6     117 .. 0.79
   2 !   74.2   0.0   1.2e-24   1.1e-20       1     128 []     142     267 ..     142     267 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.023
                                    ECHHCTEEEEEEEEETTSEEEE CS
                     Glyoxalase 106 grhyfgalysfyfrDpdGille 127
                                    +r++ +++    f Dp+G+ le
  gi|121639488|ref|YP_979712.1|  98 DRRVDEMIR---FADPSGNCLE 116
                                    445555555...9999999888 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 1.2e-24
                                    EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.......EEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC CS
                     Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdn.......teet.eglriaffhaggghielvlneapsgaakhvkkiee 72 
                                    g++hv+l ++d +++l FY++vLGf+l +              + + ++ +ff ++ +h++l+  + p ++   +     
  gi|121639488|ref|YP_979712.1| 142 GMGHVVLSTRDDAEALHFYRDVLGFRLRDSMRLppqmvgrPA-DgPPAWLRFFGCNPRHHSLAFLPMPTSSGIVH----- 215
                                    689********************************9998544.45999********************9999887..... PP

                                    TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                     Glyoxalase  73 tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                        +++ +   +dvg  ldr+ +++v+ +a++grh+++ + sfy ++p+G+ +e+
  gi|121639488|ref|YP_979712.1| 216 ----LMVEVEQADDVGLCLDRALRRKVPMSATLGRHVNDLMLSFYMKTPGGFDIEF 267
                                    ....**************************************************98 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.029   2.6e+02      84     106 ..      96     117 ..      53     118 .. 0.75
   2 !   19.7   0.0   1.3e-07    0.0012       2      90 ..     146     251 ..     145     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.029
                   Glyoxalase_6  84 lreprdgthgr..vlaDPeGneFcv 106
                                    l + r +   +   +aDP+Gn   v
  gi|121639488|ref|YP_979712.1|  96 LADRRVD---EmiRFADPSGNCLEV 117
                                    3333332...24589*****97766 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.3e-07
                   Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe...........paknrvHldlavedld 70 
                                    vvl ++d a++  F++++lg+++++    l+++ +++pa++  a+l f                +    vHl ++ve++d
  gi|121639488|ref|YP_979712.1| 146 VVLSTRDDAEALHFYRDVLGFRLRDSM-RLPPQMVGRPADGPPAWLRFFGCNPrhhslaflpmpTSSGIVHLMVEVEQAD 224
                                    8999*********************99.67777777777777777766554444777777777545557*******8887 PP

                   Glyoxalase_6  71 .......aevarlvalGArvlreprdg 90 
                                           ++ +r v + A+  r+ +d 
  gi|121639488|ref|YP_979712.1| 225 dvglcldRALRRKVPMSATLGRHVNDL 251
                                    666777788888888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2027.94
//
Query:       gi|121639489|ref|YP_979713.1|  [L=291]
Description: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-24   84.8   0.5    7.8e-22   78.2   0.5    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    5.5e-21   76.2   3.3    6.3e-21   76.0   3.3    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    6.2e-15   55.1   0.1    1.3e-14   54.1   0.1    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.011   14.4   0.0      0.017   13.8   0.0    1.2  1  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.5   1.7e-25   7.8e-22       2     256 ..      38     275 ..      37     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.7e-25
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH.HHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld.rildalgddkltlvGh 80 
                                    ++v+lhG++ ++ +w +++   a   ++f+v+++D++G+g+S+++ +    +++   +a++    + d+lg++++ lvG 
  gi|121639489|ref|YP_979713.1|  38 TVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEH--GQFNR--YAAMALkGLFDQLGLGRVPLVGN 113
                                    588889888889999995555555555*******************86..55554..666666477************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHH CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvda 160
                                    S+GG +a  +a++yp r  +lvl+g+       + +  +  + +p+   +   ++ + p+   l+  l+   +  +l   
  gi|121639489|ref|YP_979713.1| 114 SLGGGTAVRFALDYPARAGRLVLMGP-------GGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLIT- 185
                                    **************************.......6666666666666666666666666555555555555555544433. PP

                                    HHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS CS
                  Abhydrolase_1 161 lkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvpp.kaledlaqllpk 239
                                       p+ ++++    s+++s +at a    ++++  d+ +   + re+    +p+l+i+g++D++ p  +al+ l+  +p+
  gi|121639489|ref|YP_979713.1| 186 ---PELVDQRFALASTPESLTATRA-M-GKSFAGADFEAGMMW-REVYRLRQPVLLIWGREDRVNPLdGALVALK-TIPR 258
                                    ...7777777777766666555555.3.333333333333333.33455566***************99999997.8899 PP

                                    EEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 240 krlvvisdagHlafleg 256
                                    ++l+v+ ++gH+++ e+
  gi|121639489|ref|YP_979713.1| 259 AQLHVFGQCGHWVQVEK 275
                                    9*************997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   3.3   1.4e-24   6.3e-21       1     218 [.      39     280 ..      39     282 .. 0.60

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.4e-24
                                    EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS..--HHHCHHH..HHHHCCTT..TTSEEEEEETCH CS
                  Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdppp..ldledladl..aalldelaagggpvvlvGHSlG 75 
                                    v+llHG+g +a sW  +++  a la+++hvla+D pG+G+sd ++    ++++a+     l d l  g g+v lvG+SlG
  gi|121639489|ref|YP_979713.1|  39 VVLLHGGGPGAASWTnFSRNIAVLARHFHVLAVDQPGYGHSDKRAehGQFNRYAAMalKGLFDQL--GLGRVPLVGNSLG 116
                                    8*************65666679999999***********77555522444444444334455555..6888889****** PP

                                    HHHHHH.HHHCC..EE..EEES-......----TTT..S----TTHHHHHH..TT-CCCCHCCH..S-HSCCCCHHHC.. CS
                  Abhydrolase_6  76 Galala.aaplalvvg..vlldppp....talpagl..laaalelllalla..llrllawlsre..plprlfladeda.. 140
                                    G  a + a++++ ++g  vl+ p +    +++p++   + ++ ++  a+++  l+++l+ ++++  + +++++++  a  
  gi|121639489|ref|YP_979713.1| 117 GGTAVRfALDYPARAGrlVLMGPGGlsinLFAPDPTegVKRLSKFSVAPTRenLEAFLRVMVYDknLITPELVDQRFAla 196
                                    998888677777878899*****444444222222233333333322222222333344444333422223333333311 PP

                                    .CCCHCHCCCGHHHHCCHHCHTT...CCHHTT-TTGCEEEC.TT-CHHHHCHHCCCH....STTEEETCE...SSS-HHH CS
                  Abhydrolase_6 141 .daawrarlarlaallaglgllp...aaawadlpvpllvlg.geDplvprllerlla....qagarlpvvlpgaGHlphl 211
                                      ++  ++ +++ +++ag ++ +   ++++ +l+ p+l+++  eD++ p  l+ +l+    +++a+l +v+ ++GH+++ 
  gi|121639489|ref|YP_979713.1| 197 sTPESLTATRAMGKSFAGADFEAgmmWREVYRLRQPVLLIWgREDRVNP--LDGALValktIPRAQL-HVFGQCGHWVQV 273
                                    2344444444444444433322233377777777777777549999999..8877874556677777.************ PP

                                    HSHHHHH CS
                  Abhydrolase_6 212 eepdeva 218
                                    e+ de++
  gi|121639489|ref|YP_979713.1| 274 EKFDEFN 280
                                    7778886 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   2.8e-18   1.3e-14       4     237 ..      36     274 ..      34     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.8e-18
                    Hydrolase_4   4 kavvvlvHGlaehsgryaelaeaLa..aqGfavyalDhrGhGrsegkrghvpsfddyvd.Dlaafvekvkeehpelplfl 80 
                                    +++vvl+HG +  +    ++ ++ a  a+ f+v+a+D+ G+G+s  kr++  +f++y +  l+ +++++       ++ l
  gi|121639489|ref|YP_979713.1|  36 DQTVVLLHGGGPGAASWTNFSRNIAvlARHFHVLAVDQPGYGHS-DKRAEHGQFNRYAAmALKGLFDQLG----LGRVPL 110
                                    689*******99999999998876544899**************.7888888999986525666777766....446789 PP

                    Hydrolase_4  81 lGhSmGGliallyllrypdkvaglilsaPalkikakl.....kappllklllkllgkllpklqv.......snnlkadsl 148
                                    +G S+GG +a++++l+yp++  +l+l++P     + +     +   +++l    ++++  +l+         +nl +  l
  gi|121639489|ref|YP_979713.1| 111 VGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFapdptE--GVKRLSKFSVAPTRENLEAflrvmvyDKNLITPEL 188
                                    *****************************84443333554331..33333223334444444446666775555555555 PP

                    Hydrolase_4 149 srdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlkly 227
                                     +++  +a++  ++l+ ++++  +++   ++a++ +++++ +++ P+ll+ G +D+v + +++  ++++++  + +l+++
  gi|121639489|ref|YP_979713.1| 189 VDQRFALAST-PESLTaTRAMGKSFAGADFEAGM-MWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIP--RAQLHVF 264
                                    5555555555.55555599999999988898887.7889999*********************99999999..6999999 PP

                    Hydrolase_4 228 pglyHellnE 237
                                     ++ H +  E
  gi|121639489|ref|YP_979713.1| 265 GQCGHWVQVE 274
                                    9999977666 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-06     0.017      47     132 ..      57     139 ..      50     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-06
                                    HHHHHHHTTSEEEEEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEE CS
                            Ndr  47 esmaeilekfvilhvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveg 126
                                     ++a ++ +f +l vd PG  +  +   ++ qf     +   l+ + d++ l  v  +G   G    +rfal +p r   
  gi|121639489|ref|YP_979713.1|  57 RNIAVLARHFHVLAVDQPGYGHSDKRAEHG-QFNRYAAM--ALKGLFDQLGLGRVPLVGNSLGGGTAVRFALDYPARAGR 133
                                    678999************998877777666.66665544..5999*********************************** PP

                                    EEEES- CS
                            Ndr 127 lvLini 132
                                    lvL+ +
  gi|121639489|ref|YP_979713.1| 134 LVLMGP 139
                                    ***965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2173.04
//
Query:       gi|121639490|ref|YP_979714.1|  [L=394]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-41  140.9   6.9    2.9e-41  140.9   6.9    1.9  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    6.2e-05   23.6   0.0    0.00027   21.6   0.0    1.9  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
     0.0013   18.8   0.0     0.0025   18.0   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.022   15.0   3.1      0.039   14.2   2.5    1.7  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.61   2.8e+03      96     112 ..      70      86 ..      66      88 .. 0.86
   2 !  140.9   6.9   6.5e-45   2.9e-41       2     133 ..     240     372 ..     239     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                                    HHHHHHHHHCGGGGGBT CS
                  Acyl-CoA_dh_2  96 aavdalfeaaGgsalrk 112
                                    +a+++l +++G++++ +
  gi|121639490|ref|YP_979714.1|  70 EATRRLASVCGSTGWVS 86 
                                    7999**********976 PP

  == domain 2  score: 140.9 bits;  conditional E-value: 6.5e-45
                                    HHHHHHHHHHHHHHHHHHHHHHHHHC.TTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervr.assgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    +i+a+++G+A +a+a++ve++++rvr a +gek++ddp +++++aeaa+++dAA++ l  ++++ +al aagke+++e+r
  gi|121639490|ref|YP_979714.1| 240 TISAPIVGMAYGAYAAHVEHQGKRVRaAFAGEKAKDDPFAKVRIAEAASDIDAAWRQLIGNVSDEYALLAAGKEIPFELR 319
                                    699***********************9999************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    a+arr++++a+ ++ia +d+lfea+G++al +e+p+qR+wRDaha+++Haa++
  gi|121639490|ref|YP_979714.1| 320 ARARRDQVRATGRSIASIDRLFEASGATALSNEAPIQRFWRDAHAGRVHAAND 372
                                    **************************************************998 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   6.1e-08   0.00027      18      84 ..      22      88 ..       5     108 .. 0.76
   2 ?   -1.2   0.0      0.71   3.2e+03      59      84 ..     275     300 ..     254     313 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.1e-08
                                   HTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHH CS
                  Acyl-CoA_dh_N 18 elaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgv 84
                                   e++++a+  ++ ++ p+e++k+l + G++ +  p+++gG+++d+     ++  la ++ +++ + ++
  gi|121639490|ref|YP_979714.1| 22 EIRDRAQATEDLRRLPDETVKALDDVGFFTLLQPQQWGGLQCDPALFFEATRRLASVCGSTGWVSSI 88
                                   566677777777789***************************9999999999999999987764433 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.71
                                    S-HHHHHHHHHHHHHH-HHHHHHHHH CS
                  Acyl-CoA_dh_N  59 ldyleaaivaeelaradaglalllgv 84 
                                     d+++ + +ae  +  da+++ l+g 
  gi|121639490|ref|YP_979714.1| 275 DDPFAKVRIAEAASDIDAAWRQLIGN 300
                                    46888999999999999988874433 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.6e-07    0.0025      25      97 .]     130     200 ..     119     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.6e-07
                                    T.EEEEEEEEEEEETTTT-SEEEEEEE.TS---.----EEEEEEE..GGGEEE-----BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  25 ggeyvlnGeKiwitnaaiatlalvlar.tekpd.rarglslflvprdapgvsvrrieeklGlrglptgelvfedv 97 
                                    +g+y +nG+ +w+++  +a++++v +     +d r  ++  fl+pr+  + ++++++  +Glrg+ +  lv +dv
  gi|121639490|ref|YP_979714.1| 130 DGGYLVNGSWNWSSGCDHASWTFVGGPvI--KDgRPVDFGSFLIPRS--EYEIKDVWYVVGLRGTGSNTLVVKDV 200
                                    568**********************9942..2335788999****75..55999*****************9997 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         1   4.7e+03      68      98 ..     206     236 ..     204     243 .. 0.84
   2 ?   14.2   2.5   8.7e-06     0.039      18     132 ..     245     366 ..     236     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                                    HHHHHHHHH--------HHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  68 rllvyraaealdagkpdraeasmaKlfasel 98 
                                    r l y+a++   ag+ ++  a + K+ +  +
  gi|121639490|ref|YP_979714.1| 206 RFLSYKAMNDHTAGGLATNSAPVYKMPWGTM 236
                                    7788999999999999999999999988766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.7e-06
                                    --..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHH.HHHHHHHHH...--------.....HHHH CS
                  Acyl-CoA_dh_1  18 vaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaa.rllvyraae...aldagkpd.....raea 88 
                                    ++ +a+g++++ +e+  +++r   a g++  d+++ + ++ae a +++aa r l+ ++     +l agk +     ra+a
  gi|121639490|ref|YP_979714.1| 245 IVGMAYGAYAAHVEHQGKRVRAAFA-GEKAKDDPFAKVRIAEAASDIDAAwRQLIGNVSDeyaLLAAGK-EipfelRARA 322
                                    5678889999999966666555555.5899*******************99999999987774444555.4599999999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHH CS
                  Acyl-CoA_dh_1  89 smaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlr 132
                                        ++a+      +d+  +  G+ ++++e p++r++rda + r
  gi|121639490|ref|YP_979714.1| 323 RRDQVRATGRSIASIDRLFEASGATALSNEAPIQRFWRDAHAGR 366
                                    9999************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2909.02
//
Query:       gi|121639491|ref|YP_979715.1|  [L=358]
Description: hemoglobine-related protein hmp [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-14   53.6   0.5    4.8e-14   52.1   0.5    1.9  1  Fer2           2Fe-2S iron-sulfur cluster binding domain
      8e-13   49.0   0.0    2.2e-12   47.6   0.0    1.7  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    2.1e-09   37.6   0.0    3.4e-09   36.9   0.0    1.4  1  FAD_binding_6  Oxidoreductase FAD-binding domain
     0.0027   17.9   0.0      0.017   15.3   0.0    2.0  2  NAD_binding_6  Ferric reductase NAD binding domain
  ------ inclusion threshold ------
      0.024   14.8   0.0      0.046   13.9   0.0    1.4  1  FAD_binding_9  Siderophore-interacting FAD-binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.5   1.3e-17   4.8e-14       2      77 ..     274     347 ..     273     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.3e-17
                                    ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCECTT.SSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2   2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegevqsd.etelegeeldegklrlaCqtiv 77 
                                    ++dg++++v+ + + + lld++  + g+d p+sC++g Cg+C++++ +g+v  + +  le ++ldeg l+laCq+++
  gi|121639491|ref|YP_979715.1| 274 ELDGQTHTVSWPRTAK-LLDVLLAA-GLDAPFSCREGHCGACACTLRAGKVNMGvNDVLEQQDLDEG-LILACQSRP 347
                                    689********99999.******99.*************************5556899****99886.66*****98 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0     6e-16   2.2e-12       1     108 [.     132     229 ..     132     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6e-16
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqda 80 
                                    ++a+G+Gi+P++s+ + +l+e    ++v+l+y+nr ++++++ + l+ela+k+p+rl+v+++++  +  +       +++
  gi|121639491|ref|YP_979715.1| 132 LLAAGSGITPIMSICKSALAE--GGGQVTLLYANRDDRSVIFGDALRELAAKYPDRLTVLHWLESLQGLP-------SAS 202
                                    79******************8..78*************************************66666665.......444 PP

                                    HHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  81 lleellslkkeethvyvCGppgMikavr 108
                                     l +l+  +  +  v++CGp ++++a+r
  gi|121639491|ref|YP_979715.1| 203 ALAKLVA-PYTDRPVFICGPGPFMQAAR 229
                                    4444444.477789**********9987 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   9.6e-13   3.4e-09      25      97 ..      47     121 ..      16     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.6e-13
                                    TS-----TT-EEEEEEC.ETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH.HCS-TT-EEEEEEEE-SE CS
                  FAD_binding_6  25 kqklglpvGqhvflrlk.ikgeaviRsYtpissenekGelellvkvypgGkmsqaL.delkigdtleikGPlGkf 97 
                                      +l++ +Gq++ lr++   + +v R Y+++ss+ ++  l + vk+ ++G  s+ L d++++g+ +++ +P G+f
  gi|121639491|ref|YP_979715.1|  47 PRRLRYAPGQFLTLRVPsERTGSVARCYSLCSSPYTDDALAVTVKRTADGYASNWLcDHAQVGMRIHVLAPSGNF 121
                                    46799************53455799************************************************99 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.7e-06     0.017       5      49 ..     131     169 ..     128     189 .. 0.76
   2 ?    0.3   0.0      0.19   6.9e+02     138     152 ..     215     229 ..     183     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.7e-06
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_6   5 llvagGiGitpfisilkdllkkskkealktkkikliwvvresssl 49 
                                    ll+a+G+Gitp++si+k  l++         +++l  ++r+  s+
  gi|121639491|ref|YP_979715.1| 131 LLLAAGSGITPIMSICKSALAEGG------GQVTLLYANRDDRSV 169
                                    89***************9998775......667777777776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                                    xxxxxxxxxxxxxxx RF
                  NAD_binding_6 138 gvfvCGppklvkevk 152
                                     vf+CGp  +++  +
  gi|121639491|ref|YP_979715.1| 215 PVFICGPGPFMQAAR 229
                                    69*****99998876 PP

>> FAD_binding_9  Siderophore-interacting FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.046      29     120 ..      25     120 ..      16     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                  FAD_binding_9  29 gtDqhikLll.pepgqtepelppe...lteeglqeweelpederpvmRtYtvraldaeaeeldidfvlHgdegpaarw.A 103
                                     tD+  +L++ +++g+++pe+pp    +++ ++ + + ++e +  v R Y++++   +++ l++     +d g a++w  
  gi|121639491|ref|YP_979715.1|  25 ETDEARSLVFaVPDGSDDPEIPPRrlrYAPGQFLTLRVPSERTGSVARCYSLCSSPYTDDALAVTVKRTAD-GYASNWlC 103
                                    455555666614567788888665211455666667778888999*******************9888888.******55 PP

                  FAD_binding_9 104 aqAqpGdelaivgPgga 120
                                     +Aq+G ++++++P+g+
  gi|121639491|ref|YP_979715.1| 104 DHAQVGMRIHVLAPSGN 120
                                    68************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2473.97
//
Query:       gi|121639492|ref|YP_979716.1|  [L=176]
Description: hypothetical protein BCG_3637 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1279.76
//
Query:       gi|121639493|ref|YP_979717.1|  [L=711]
Description: acyl-CoA dehydrogenase fadE34 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   99.5  22.8    4.7e-18   65.8   6.8    3.3  3  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.5e-22   79.2   4.4    1.7e-10   41.6   0.4    2.8  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.3e-19   70.2   0.0    3.1e-19   69.0   0.0    1.7  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.43   2.6e+03      48      81 ..       6      39 ..       3      47 .. 0.77
   2 !   65.8   6.8   7.8e-22   4.7e-18      16     130 ..     212     328 ..     208     347 .. 0.90
   3 !   42.9   2.7   9.3e-15   5.6e-11       1     150 []     568     707 ..     568     707 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.43
                                   GGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                  Acyl-CoA_dh_1 48 idhqlvreklaemaaeleaarllvyraaealdag 81
                                    d q+ +++l++ +a+++a+ +++ +a++ ++ g
  gi|121639493|ref|YP_979717.1|  6 TDEQSAARELVRGWARTAASGAAATAAVRDMEYG 39
                                   5788888999999999999999988888877766 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 7.8e-22
                                    ----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------..HHHHHHHHH CS
                  Acyl-CoA_dh_1  16 lavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd..raeasmaKl 93 
                                     ++aa a+g+ar  l++a++ya+ r++fgkp++++q+v++ +a+m +++e+a  ++ +aa+a+ + + +  + +a++a  
  gi|121639493|ref|YP_979717.1| 212 TVLAAEAAGVARWTLDTAVAYAKVREQFGKPIGSFQAVKHLCAQMLCRAEQADVAAADAARAAADSDGTqlSIAAAVAAS 291
                                    5789********************************************************987777766699******** PP

                                    HHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHH CS
                  Acyl-CoA_dh_1  94 faselaqevadlamqllGgaGyleeypverlyrdarv 130
                                     + ++a   a++++q+lGg G+++e+  + ++r+a  
  gi|121639493|ref|YP_979717.1| 292 IGIDAAKANAKDCIQVLGGIGCTWEHDAHLYLRRAHG 328
                                    *****************************99999864 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 9.3e-15
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    ++G+r+a +tl++eR+a+a     ++ + +ee+l+ + + +        + + +++l+++   ++a  ll +r+ae++  
  gi|121639493|ref|YP_979717.1| 568 NDGWRLARTTLANERVAMA--TGTALGNPMEELLKVLGDMEL-------DVAQQDRLGRLILLAQAGALLDRRIAELAVG 638
                                    79****************8..6688999**********9999.......5578*************************** PP

                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                  Acyl-CoA_dh_1  81 gkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                    g++++a++s+ Kl + +  q +a+  m++  g G+ e  +v  +  ++r+l+i++Gt++i++ + a+rll
  gi|121639493|ref|YP_979717.1| 639 GQDPGAQSSVRKLIGVRYRQALAEYLMEVSDGGGLVENRAVYDF-LNTRCLTIAGGTEQILLTVAAERLL 707
                                    *******************************************6.89********************985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.3   2.9e-13   1.8e-09       1      89 [.       6     105 ..       6     113 .. 0.75
   2 !   41.6   0.4   2.8e-14   1.7e-10      22     113 .]     369     458 ..     359     458 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.9e-13
                                    THHHHHHHHHHHHHHHHHTHHHHHHHH.HHTS.......GH..HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewd.eege.......fp..relwkklaelGllgitvpeeygGagldyleaaivaee 70 
                                    t+eq a r+ vr +a++ +   aa +  ++ e        +  r ++  la lGl+g++vpe+ gGag+++ + + +++e
  gi|121639493|ref|YP_979717.1|   6 TDEQSAARELVRGWARTAASGAAATAAvRDMEygfeegnADawRPVFAGLAGLGLFGVAVPEDCGGAGGSIEDLCAMVDE 85 
                                    79***************88655444432222322222222222446********************************** PP

                                    HHHH-HHHHH.HHHHHHHTT CS
                  Acyl-CoA_dh_N  71 laradaglal.llgvhsslv 89 
                                     ara +++ + + +v + +v
  gi|121639493|ref|YP_979717.1|  86 AARALVPGPVaTTAVATLVV 105
                                    ******98885555555554 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 2.8e-14
                                    HHHHHHHHTSGHHHH.HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-HH CS
                  Acyl-CoA_dh_N  22 haaewdeegefprel.wkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrfGtee 100
                                     aa + e ++ p+e  + +la+ Gll+ ++p  y G+g+++ e++++ +ela+a +  ++ l ++   +ap+il++Gt+e
  gi|121639493|ref|YP_979717.1| 369 IAAAVAEVAALPEEKrQVALADTGLLAPHWPAPY-GRGASPAEQLLIDQELAAAKVE-RPDLVIGW-WAAPTILEHGTPE 445
                                    34444455678988537777**************.69999*************9997.45444544.5569********* PP

                                    HHHHHHHHHHTTS CS
                  Acyl-CoA_dh_N 101 qkrryLpklasge 113
                                    q +r++p  ++ge
  gi|121639493|ref|YP_979717.1| 446 QIERFVPATMRGE 458
                                    ***********98 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   5.2e-23   3.1e-19       1      83 [.     462     544 ..     462     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.2e-23
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    +  ++Ep+aGsd+as++t+a++ dg ++ l+G+K+w + a++a + ++lart+ ++ +++g++ flv+  +pg+++r+++
  gi|121639493|ref|YP_979717.1| 462 CQLFSEPGAGSDLASLRTKAVRADG-GWLLTGQKVWTSAAHKARWGVCLARTDPDApKHKGITYFLVDMTTPGIEIRPLR 540
                                    67789*************9999999.8************************6555599*********************9 PP

                                    -BSS CS
                  Acyl-CoA_dh_M  80 eklG 83 
                                    e +G
  gi|121639493|ref|YP_979717.1| 541 EITG 544
                                    8554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4556.67
//
Query:       gi|121639494|ref|YP_979718.1|  [L=199]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-38  131.9   1.5    2.1e-38  130.9   1.5    1.5  1  TetR_C_20  Tetracyclin repressor-like, C-terminal domain
    3.9e-16   58.6   0.1    8.7e-16   57.5   0.1    1.6  1  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.048   13.7   0.0    1.9  1  HTH_7      Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> TetR_C_20  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   1.5   3.5e-42   2.1e-38       1     107 []      86     192 ..      86     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 3.5e-42
                                    S-SHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHH--TTT-GGGHHHHHHHHHHHHHHHT-SS--HHHHHHHHHHHHHHH CS
                      TetR_C_20   1 GespaerlaevLrratralqrePaLaeAmvrAlsaadasaaaevdrvaavvealllralgeeePteedadlarvlsdvwl 80 
                                    G +p +rl+ ++++++ra+qr+P L+eAm+rA ++adasaa+evd+v+++++++++ra++ +ePte++ ++arv+sdvwl
  gi|121639494|ref|YP_979718.1|  86 GATPFQRLNFMVGKLNRAMQRNPLLTEAMTRAYVFADASAASEVDQVEKLIDSMFARAMANGEPTEDQYHIARVISDVWL 165
                                    89****************************************************************************** PP

                                    HHHHHHHTTSS-HHHHHHHHHHHHHHH CS
                      TetR_C_20  81 glLvawlngrasitdveadleravrlL 107
                                    ++L awl++ras+tdv ++l++avrlL
  gi|121639494|ref|YP_979718.1| 166 SNLLAWLTRRASATDVSKRLDLAVRLL 192
                                    **************************8 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   1.5e-19   8.7e-16       1      45 [.      21      65 ..      21      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.5e-19
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   Ilda+++  ++ Gy+a+++r++A+rA v+ g+lYryFpsK  Ll 
  gi|121639494|ref|YP_979718.1| 21 ILDATMAIASKGGYEAVQMRAVADRADVAVGTLYRYFPSKVHLLV 65
                                   9***************************************99986 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.1e-06     0.048      24      44 ..      39      59 ..      33      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-06
                                   STTTSSSS---SSSS--SS-- CS
                          HTH_7 24 iskIAkevnisRsTvYRylad 44
                                    +++A++ ++++ T+YRy++ 
  gi|121639494|ref|YP_979718.1| 39 MRAVADRADVAVGTLYRYFPS 59
                                   578***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1473.06
//
Query:       gi|121639495|ref|YP_979719.1|  [L=359]
Description: LacI family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-17   63.2   0.5    1.1e-16   61.6   0.2    2.0  2  Peripla_BP_3   Periplasmic binding protein-like domain
    1.3e-09   37.9   0.0    5.6e-09   35.8   0.0    1.8  1  Peripla_BP_1   Periplasmic binding proteins and sugar binding
    3.4e-07   29.9   0.0    1.1e-06   28.3   0.0    1.9  1  LacI           Bacterial regulatory proteins, lacI family
  ------ inclusion threshold ------
      0.032   14.2   0.0      0.072   13.0   0.0    1.6  1  HTH_11         HTH domain
      0.046   13.5   0.1       0.19   11.6   0.0    2.0  2  HTH_10         HTH DNA binding domain
      0.047   13.3   0.1       0.18   11.5   0.1    2.0  1  GntR           Bacterial regulatory proteins, gntR family
       0.16   12.0   0.1       0.32   11.0   0.1    1.5  1  HTH_35         Winged helix-turn-helix DNA-binding
       0.18   11.7   3.3       0.69    9.8   0.3    3.1  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.95   2.1e+03      28      60 ..      38      70 ..      16     123 .. 0.56
   2 !   61.6   0.2   5.1e-20   1.1e-16       4     142 ..     183     333 ..     180     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.95
                                   HHHHHHHHHHTTSSS-EEEEE-S-SS-SSHHHH CS
                   Peripla_BP_3 28 erergfrqaleelglplnetvvaaddpaaaaaa 60
                                   ++++++  ++++lg+  ++ v+++ +   a+a+
  gi|121639495|ref|YP_979719.1| 38 DLRERVLATAKRLGYAGPDPVARSLRTRKAGAV 70
                                   455555555555555544444444443333333 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 5.1e-20
                                    HHHCS--EEEEEE...............--TTSS-HHHHHHHHHHHHHHTTSSS-EEEEE-S-SS-SSHHHHH.....HH CS
                   Peripla_BP_3   4 LvelGhrriafig...............gegdrgasasderergfrqaleelglplnetvvaaddpaaaaaaraalllqa 68 
                                     + lGhr++++++                  + +   ++er  g+ +a+ ++g++++   v +  +++ ++   a    +
  gi|121639495|ref|YP_979719.1| 183 VLGLGHRELGLLTmrlgrdrrqdlvdaeRLRSPTFDVQRERIVGVWEAMTAAGVDPDSLTVVESYEHLPTSGGTAA---K 259
                                    5789999999999999666666665555333344445556666699999999999999999888888877766665...2 PP

                                    HHHCC-S..EEEEESSCCHHHHHHHHHCCTT--TTTTEEEEBSS--SCCCSSSS--EEEE--HHHHHHHHHHHHHH CS
                   Peripla_BP_3  69 lklaalP..tAviaasDelAlgvlqalreaglrvPedlsvigfddselaalssPplTtvrqpleelGraaaellld 142
                                    ++l+a+P  tA++++ D lAl ++ +lr++g+ vP +  v+gfd+  + + +s  lTtv+qp    G++a elll+
  gi|121639495|ref|YP_979719.1| 260 VALQANPrlTALMCTADILALSAMDYLRAHGIYVPGQMTVTGFDG--VPEALSRGLTTVAQPSLHKGHRAGELLLK 333
                                    2444456448**********************************6..55577777*******************96 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.5e-12   5.6e-09       3     224 ..      69     305 ..      67     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.5e-12
                                    EEEEEES-T.....TSHHHHHHHHHHHHHHHHHTEEEEEEE-SSHHHHHHHHHHHHHTT-SEEEEE-S-GGHHHHHHHHH CS
                   Peripla_BP_1   3 klglvlpql.....dePffldlvkgitkaakehgvdvlllaageeedlakaidllkakgidgliiatsdtsfdditakae 77 
                                    ++glv++++     ++P   d v+g+ +  +e+g  + l+ +g+   la     ++  g+dg+++ + +++ + ++   +
  gi|121639495|ref|YP_979719.1|  69 AVGLVMAEPltyffSDPAARDFVAGVAQSCEELGQGLQLVSVGSSRSLADGTAAVLGAGVDGFVVYSVGDDDPYLQVVLQ 148
                                    7889999984444455556789*************************************************999998877 PP

                                    HT-EEEEESS--B-TTTS-EEEE-HHHHHHHHHHHHHHHHHHHTG..............EE.EEEE-TTS..HHHHHHHH CS
                   Peripla_BP_1  78 sgipvialedaidapdgvPcvipddtqageestqkLiaeghkrpi..............al.legpesal..takervqG 140
                                      +pv+ +++  d   gv  v  dd  a  e   + +  gh++                ++  e  +s+    ++er  G
  gi|121639495|ref|YP_979719.1| 149 RRLPVVVVDQPKDLS-GVSRVGIDDRAAMRELAGYVLGLGHRE-LglltmrlgrdrrqdLVdAERLRSPTfdVQRERIVG 226
                                    789********9999.***************************.55567788888888744133345665556789999* PP

                                    HHHHHHHTT-GGGEEEEE-SSSSH.HHHHHHHHHHHTT-TT-SEEE-SSHHHHHHHHHHHHHTT..--GGGEEEEEESSG CS
                   Peripla_BP_1 141 flaalaeaGlevkdvhvalgsndi.edaaealnelleshPeidaivaindeaalGavlalkkeGr.lkikeevdsfiesv 218
                                      +a+ +aG +  +  v +  ++  + +  a++  l+ +P + a+++ +d  al a+  l+++G  + ++ +v       
  gi|121639495|ref|YP_979719.1| 227 VWEAMTAAGVDPDSLTVVESYEHLpTSGGTAAKVALQANPRLTALMCTADILALSAMDYLRAHGIyVPGQMTV------- 299
                                    **********666666666666652568899*********************************555555555....... PP

                                    GGHHHH CS
                   Peripla_BP_1 219 vvydgL 224
                                     ++dg 
  gi|121639495|ref|YP_979719.1| 300 TGFDGV 305
                                    444444 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   4.8e-10   1.1e-06       3      44 ..      12      53 ..      10      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.8e-10
                                   HHHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHHHHHTTB- CS
                           LacI  3 kDVArlAGVSkaTVSrvLnnkerVseetrerVeaameelnYi 44
                                     +A + +VS +TVS   n +++ s+++rerV+a ++ l+Y+
  gi|121639495|ref|YP_979719.1| 12 ASLAAELKVSRTTVSNAFNRPDQLSADLRERVLATAKRLGYA 53
                                   55677779*********************************6 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.072      16      36 ..       9      29 ..       5      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                         HTH_11 16 isgeeLAeeLnvSrrtvrrdI 36
                                    + + LA eL+vSr+tv +  
  gi|121639495|ref|YP_979719.1|  9 ATLASLAAELKVSRTTVSNAF 29
                                   58899************9975 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.19      22      43 ..       7      28 ..       4      33 .. 0.89
   2 ?   -1.7   0.0       1.2   2.7e+03       7      17 ..      42      52 ..      38      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                         HTH_10 22 RrvtlkeLAkelGIskstlseh 43
                                   Rr+tl++LA el +s++t+s+ 
  gi|121639495|ref|YP_979719.1|  7 RRATLASLAAELKVSRTTVSNA 28
                                   89*****************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                         HTH_10  7 evlklAyemGY 17
                                   +vl++A ++GY
  gi|121639495|ref|YP_979719.1| 42 RVLATAKRLGY 52
                                   7999******9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.9e-05      0.18      28      47 ..      12      31 ..       9      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHTS-HHHHHHHHHH CS
                           GntR 28 reLaaefgVsrttvReALrr 47
                                    +Laae++Vsrttv  A +r
  gi|121639495|ref|YP_979719.1| 12 ASLAAELKVSRTTVSNAFNR 31
                                   68**************9987 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00014      0.32      13      40 ..       6      33 ..       4      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                         HTH_35 13 krgttLaalsreaglssstlsnaltrpw 40
                                   +r+ tLa+l+ e+  s+ t+sna++rp 
  gi|121639495|ref|YP_979719.1|  6 RRRATLASLAAELKVSRTTVSNAFNRPD 33
                                   7999**********************94 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00031      0.69      17      36 ..       8      27 ..       7      31 .. 0.90
   2 ?   -1.1   0.0      0.77   1.7e+03      15      25 ..     171     181 ..     169     186 .. 0.79
   3 ?    0.3   0.0      0.28   6.3e+02      11      19 ..     261     269 ..     260     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                  HTH_AsnC-type 17 RisyaeLAervGlSestvlr 36
                                   R++ a LA+++ +S++tv +
  gi|121639495|ref|YP_979719.1|  8 RATLASLAAELKVSRTTVSN 27
                                   99****************86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                  HTH_AsnC-type  15 daRisyaeLAe 25 
                                    d R+ ++eLA 
  gi|121639495|ref|YP_979719.1| 171 DDRAAMRELAG 181
                                    6799*****96 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.28
                  HTH_AsnC-type  11 aLqedaRis 19 
                                    aLq+++R++
  gi|121639495|ref|YP_979719.1| 261 ALQANPRLT 269
                                    8******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2347.45
//
Query:       gi|121639496|ref|YP_979720.1|  [L=237]
Description: lipoprotein lppH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-52  177.6   3.8      3e-52  177.3   3.8    1.1  1  PknH_C    PknH-like extracellular domain


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   3.8   1.7e-56     3e-52       2     189 .]      44     233 ..      43     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 1.7e-56
                                    -GGGGGGGS--HHHHHHHHT-S.--EE-S-B-S-B-S--EESSGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT-SE CS
                         PknH_C   2 paaaldslLltpaelaailGtpeaasatesdttppdtaasvdppeClgvasageesvYggsgvtavagqtlrdsaddgas 81 
                                    p +al++lLl+ ++++a+lG++ +++++ +  +++d++ sv +++Cl++ ++++e+vY+g+g+ta++gq l+ds  d+++
  gi|121639496|ref|YP_979720.1|  44 PVSALEGLLLDLSQINAALGAT-SMKVWFNAKAMWDWSKSVADKNCLAIDGPAQEKVYAGTGWTAMRGQRLDDSINDSKK 122
                                    789*******************.***************************************************999999 PP

                                    E...EEEEEEE-SSHHHHHHHHHHHHHHHHTTTT.-EEEEEETTEEEEEEE---B--TT-EEEEEE.ESSTT--EEEEEE CS
                         PknH_C  82 l...vsqavvafptadaAqaffaalaaqwrrCag.vttttdsggatetwtvgdvsdddgvltatvtvtsggdgarcqral 157
                                        + qavv fpta++A++f+++++++w +C++ + ++ ++g++++ wtv dv++d+g+l+ +++ ++ggdg++cqral
  gi|121639496|ref|YP_979720.1| 123 RdhyAIQAVVGFPTAHDAEEFYSSSVQSWSSCSNrRFVEVTPGQDDAAWTVADVVNDNGMLSSSQV-QEGGDGWTCQRAL 201
                                    999********************************99***************************99.************* PP

                                    EEETTEEEEEEEEE.SS-SSHHHHHHHHHHHH CS
                         PknH_C 158 avranvvvdvevcgfedggdaaaeiadaildk 189
                                    ++r+nv++d+ +c++++++  a+ ia++i++k
  gi|121639496|ref|YP_979720.1| 202 TARNNVTIDIVTCAYSQPDLVAIGIANQIAAK 233
                                    ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1661.98
//
Query:       gi|121639497|ref|YP_979721.1|  [L=288]
Description: hypothetical protein BCG_3642 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00012   21.7   0.5     0.0011   18.5   0.5    2.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0065   16.5   0.1      0.011   15.7   0.1    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.5   1.2e-07    0.0011      24     201 .]      60     236 ..      44     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-07
                                    SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTE CS
                  Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggl 103
                                    +r++++++ aV+  h H+DH  +   ++ +++  ++l++ ++ + v +  + +       +++++   +ge+++lg   +
  gi|121639497|ref|YP_979721.1|  60 ARANVSRLTAVIPVHTHIDHAMDSALVADRTG--AQLVGGESAANVGRGYGLP-------EESLVVAVPGEPIQLG--AF 128
                                    688999***************99888888544..5677666666666666543.......457777999******9..56 PP

                                    EEEEEEE-EE--C...............TCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-S CS
                  Lactamase_B_2 104 eitatparhksgr...............rldrnagdtlGlrie.gggkrvyyigDtgyipeeigerlggadllllditay 167
                                    ++t+++ +h  +                + + + g++ + ++  ++  r + i D++ +   + + +  ad + l ++ +
  gi|121639497|ref|YP_979721.1| 129 DVTLVESHHCPPDrfpgvisapltppvkASAYRCGEAWSTLVHhRPSGRRLLIQDSAGFVSGALAGY-RADAAYLSVGQL 207
                                    79*9999887777666666665555544222223333333333466666666666666653333222.266666666655 PP

                                    STTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 168 eddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                      +          +e   e ++ +g++r++liH+
  gi|121639497|ref|YP_979721.1| 208 GLQP-----PSYLLEYWTETVRTVGVRRVILIHW 236
                                    5533.....3455666777777777777777776 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.3e-06     0.011      38     122 ..      60     131 ..      13     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                    HTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECC CS
                    Lactamase_B  38 lglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgna 117
                                    ++ +  +++avi  H H+DH+ + + ++++t++  +  + +a ++++ ++               +  +++++ e    +
  gi|121639497|ref|YP_979721.1|  60 ARANVSRLTAVIPVHTHIDHAMDSALVADRTGAQLVGGESAANVGRGYGLP-------------EESLVVAVPGEPIQLG 126
                                    567778999************************************999993.............3333333333333333 PP

                                    CTEEE CS
                    Lactamase_B 118 ggrra 122
                                    +++++
  gi|121639497|ref|YP_979721.1| 127 AFDVT 131
                                    33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1939.62
//
Query:       gi|121639498|ref|YP_979722.1|  [L=413]
Description: arsenical pump integral membrane protein arsB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-23   82.6  24.4    4.6e-23   82.2  24.4    1.1  1  ArsB      Arsenical pump membrane protein
      1e-16   61.0  39.0    1.8e-16   60.2  39.0    1.4  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  24.4   5.1e-27   4.6e-23       1     415 [.       3     399 ..       3     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 5.1e-27
                           ArsB   1 lavfiflltlvl..viwqpknlsigwsacggavlaliagvvnfhdvl.tvtgivwnatlafv.aiilislildnigffew 76 
                                    lav ++ll++vl   + +p+      +a+  av+ l  g +  ++ +  v+g+     +af+ a+++++ + d+ g+fe 
  gi|121639498|ref|YP_979722.1|   3 LAVALILLAVVLgfAVARPRGWPEAAAAVPAAVILLAIGAISPQQAMaQVSGLAR--VVAFLgAVLVLAKLCDDEGLFEA 80 
                                    6788888888873357889999999999999999999999987776615777654..456652677788999******** PP

                           ArsB  77 aalhmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsn 156
                                    a   ma+a+     r++  v  + a ++a ++ d + ++ltp+vla vr l+     v p+  a+  +a+++sl + vsn
  gi|121639498|ref|YP_979722.1|  81 AGAAMARASA-ESHRLLRQVFAVSAAITAALCLDATVVLLTPVVLATVRRLRT---PVRPYAYATAHLANAASLLLPVSN 156
                                    ******9875.467888888888877777788999***************985...589********************* PP

                           ArsB 157 lvnivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkrydltevkkpveaikdqnmfrlswyilgllligy 236
                                    l n+++     i+f  ++  m +p+l ++ a  +v+  ff + +    d  ++k p        mf l   ++ l l g+
  gi|121639498|ref|YP_979722.1| 157 LTNLLAYHGAGISFTKFTLLMALPWLSAVAAVYVVFRWFFARDLRVVPDRQQLK-PAP---RLPMFVLV--VVALTLGGF 230
                                    **************************9999999999999988776666665554.443...45788875..677788888 PP

                           ArsB 237 faseffsipvsvvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdviqaaadqglf 316
                                      +e + +  +  a + a ++ + + +       ++ +    + ++f + + vvv+ v   g++  +s v+ +    gl 
  gi|121639498|ref|YP_979722.1| 231 AVAESVGLAPTWAALAGAAVLALRSLRRGHTSVLRIARAVNVSFLVFVLALGVVVHAVMLNGMAARMSAVLPTG--SGLP 308
                                    8899888877666666666666666666666777899999999999************************9875..5765 PP

                           ArsB 317 agtigmgfiaailssimnnlptvmida.laiagtdthgmmrealiyanvigsdlgpkitpigslatllwlhvlshkgmki 395
                                    a  +g+  +a++l++++nnlp+ ++   l  ag         a + a ++g ++gp++t  gsl+ llw  vl ++ +  
  gi|121639498|ref|YP_979722.1| 309 A-LLGIAALASVLANVVNNLPATLVLVpLVAAGG-------PAAVLAVLLGVNIGPNLTYAGSLSNLLWRGVLRRHNVDA 380
                                    5.799****************8766541555554.......46788999******************************* PP

                           ArsB 396 swgtyfktgiiltiptllit 415
                                    s g y + g+  t+p+ l  
  gi|121639498|ref|YP_979722.1| 381 SVGEYTRLGLC-TVPAALAM 399
                                    *********75.67765543 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2  39.0     2e-20   1.8e-16      11     284 ..      29     343 ..       4     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2e-20
                                    xxxxxxxxxxxx.xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  11 ldvvallvlvll.vltieealsgias..piillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltallsa 87 
                                     +v+a ++l++   +++++a++ ++    ++++l+++ ++++++++ Glf+  +a ++r++ ++ +ll  +++++a ++a
  gi|121639498|ref|YP_979722.1|  29 AAVPAAVILLAIgAISPQQAMAQVSGlaRVVAFLGAVLVLAKLCDDEGLFEAAGAAMARASAESHRLLRQVFAVSAAITA 108
                                    5566666666668999999999987511568********************************99988888888888889 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  88 fvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraa.....arpglslpnllllalllvgl 161
                                     + +d++v++++p+vl+ ++r  ++p++ ++ + a  an+ ++l+p+ + t + a      ++ ++ + ++l++l +v++
  gi|121639498|ref|YP_979722.1| 109 ALCLDATVVLLTPVVLATVRR-LRTPVRpYAYATAHLANAASLLLPVSNLTNLLAyhgagISFTKFTLLMALPWLSAVAA 187
                                    998*****************9.899999*999******************777777777744444444444444444433 PP

                                    ...........................xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         CitMHS 162 ...........................lplvllfmfgvalalpvnap......kvkkqkaiieaiarsllpvatillla. 207
                                                               lp+++l+                     +  + +  a ++++l  a++l+l  
  gi|121639498|ref|YP_979722.1| 188 vyvvfrwffardlrvvpdrqqlkpaprLPMFVLV------------VvaltlgGFAVAESVGLAPTWAALAGAAVLALRs 255
                                    1222233333333333333333333332222222............0111111222222233333344444444443338 PP

                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 208 ...........ykkveWsvlllfaGvfllvgaleqtGilealadllga.ggplvalalvlgliallsafisnvavaalma 275
                                                ++v+ s l+++ +++++v a+   G++  ++++l + +g+  al+ +++l ++l ++++n +++++++
  gi|121639498|ref|YP_979722.1| 256 lrrghtsvlriARAVNVSFLVFVLALGVVVHAVMLNGMAARMSAVLPTgSGLP-ALLGIAALASVLANVVNNLPATLVLV 334
                                    888888888889999999999*************************4433443.34678999999*************** PP

                                    xxxxxxxxx RF
                         CitMHS 276 pialgmapa 284
                                    p++++  pa
  gi|121639498|ref|YP_979722.1| 335 PLVAAGGPA 343
                                    ***996664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2792.73
//
Query:       gi|121639499|ref|YP_979723.1|  [L=322]
Description: tRNA/rRNA methyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-34  119.6   0.1    2.5e-34  118.5   0.0    1.5  2  SpoU_methylase  SpoU rRNA Methylase family
    1.8e-15   57.0   0.0    3.4e-15   56.1   0.0    1.5  1  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.092   12.8   0.0    2.1  2  TSNR_N          Thiostrepton-resistance methylase, N terminus


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   6.8e+03      29      60 ..     112     143 ..      99     154 .. 0.53
   2 !  118.5   0.0   4.1e-38   2.5e-34       2     141 ..     161     300 ..     160     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                    EEEEESGSSCTCGSHHHHHHCTTHHHHHHEEE CS
                 SpoU_methylase  29 elvlvkprsadllnpeakraaagalevlelkv 60 
                                    ++ +v+  +adl+  +a ++ +g + +++ + 
  gi|121639499|ref|YP_979723.1| 112 GIAIVELLRADLDRMTANHLHQGIALQVPPYN 143
                                    34444555555555555555555555555555 PP

  == domain 2  score: 118.5 bits;  conditional E-value: 4.1e-38
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvat 81 
                                    l v+l++++dp+NlGai+R+++afg +++++ ++rsa   +  a r++aga+  ++++++++l ++lk + ++g++++++
  gi|121639499|ref|YP_979723.1| 161 LLVALDNLSDPRNLGAIVRSVAAFGGHGVLIPQRRSA-SVTAVAWRTSAGAAARIPVARATNLTRTLKGWADRGVRVIGL 239
                                    679****************************998887.9999************************************** PP

                                    ST.T-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS
                 SpoU_methylase  82 sl.kgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141
                                    ++ +g+ l+++d +++ ++v+G+E+kGls+ +++++d++v+Ipm+ ++eSLN +vA++++l
  gi|121639499|ref|YP_979723.1| 240 DAgGGTALDDVDGTDSLVVVVGSEGKGLSRLVRQNCDEVVSIPMAAQAESLNASVAAGVVL 300
                                    **9********************************************************98 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   5.8e-19   3.4e-15       2      75 ..      70     144 ..      69     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 5.8e-19
                  SpoU_sub_bind   2 iyGlhaVleaLksgrriekllvteg.radkrleellklakkrgikvelvdkekLdklsgtanHQGvvaevkpley 75 
                                    + G+++Vle+L++g + ++l+v+ g +ad+rl+e +++a++ gi + +  +++Ld+++ +  HQG++++v p++y
  gi|121639499|ref|YP_979723.1|  70 VLGRNPVLECLRAGVPATALYVALGtEADERLTECVARAADSGIAIVELLRADLDRMTANHLHQGIALQVPPYNY 144
                                    78***********************************************************************99 PP

>> TSNR_N  Thiostrepton-resistance methylase, N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.092       7      68 ..      45     108 ..      43     132 .. 0.75
   2 ?   -0.7   0.0      0.24   1.4e+03      33      57 ..     286     310 ..     270     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                         TSNR_N   7 psdPavrRilDvvkrs.raaiktiLieDleplvqairaGvevieiYilegrdvsaklee.laek 68 
                                    p +Pa++R     +r+ + a +t  +   +p+ +++raGv    +Y+  g++ +++l+e +a+ 
  gi|121639499|ref|YP_979723.1|  45 PHHPAAKRARAQPRRPvKRADETETVLGRNPVLECLRAGVPATALYVALGTEADERLTEcVARA 108
                                    679999999888776525566777888999*****************99999999886624443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.24
                         TSNR_N  33 DleplvqairaGvevieiYilegrd 57 
                                     +e l  ++ aGv +  i     r+
  gi|121639499|ref|YP_979723.1| 286 QAESLNASVAAGVVLAAIARQRRRP 310
                                    6899999999999988876655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2721.97
//
Query:       gi|121639500|ref|YP_979724.1|  [L=469]
Description: cysteinyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.6e-126  421.0   0.0   3.2e-126  420.7   0.0    1.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    6.1e-13   48.3   0.0    6.4e-06   25.2   0.0    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    5.8e-07   29.9   0.0    1.5e-06   28.6   0.0    1.7  1  DALR_2        DALR domain
    2.9e-06   26.5   0.0     0.0034   16.4   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)
    6.8e-05   21.3   0.0      0.011   14.0   0.0    2.1  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.7   0.0    9e-130  3.2e-126       3     300 ..      21     314 ..      19     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 420.7 bits;  conditional E-value: 9e-130
                                    --SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHH CS
                   tRNA-synt_1e   3 kpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfiee 82 
                                    +pl+ ++v++Y+CG+tv+   h+Gh+Rs vafDilrr+l a+gYdv+f++nvtDi+Dki+++a+++++ ++e+a++++++
  gi|121639500|ref|YP_979724.1|  21 VPLRPGHVSIYLCGATVQGLPHIGHVRSGVAFDILRRWLLARGYDVAFIRNVTDIEDKILAKAAAAGRPWWEWAATHERA 100
                                    678999************************************************************************** PP

                                    HHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S- CS
                   tRNA-synt_1e  83 fkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseek 162
                                    f+++++aL+vl+p++epr++ +++++ie++e+li+ g+aY+   gdvyfdv +++eYg+ls ++++++++g+ +++  +k
  gi|121639500|ref|YP_979724.1| 101 FTAAYDALDVLPPSAEPRATGHITQMIEMIERLIQAGHAYTGG-GDVYFDVLSYPEYGQLSGHKIDDVHQGEGVAA--GK 177
                                    *****************************************99.*************************9998866..8* PP

                                    SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEE CS
                   tRNA-synt_1e 163 kdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafdkqlvkyfl 242
                                    +d++Df+LWk +k+gepsw++Pwg+GRPGWh+eCs+ma+++lg e+dih+GG+DL+fPhhene+aqs+aa d  +++y+l
  gi|121639500|ref|YP_979724.1| 178 RDQRDFTLWKGEKPGEPSWPTPWGRGRPGWHLECSAMARSYLGPEFDIHCGGMDLVFPHHENEIAQSRAAGD-GFARYWL 256
                                    *********************************************************************999.9****** PP

                                    EE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                   tRNA-synt_1e 243 hnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                    hng++++ gekmsksL+n++++ ++l++++p++lR++l sahyrs+l+f+e+++++a+
  gi|121639500|ref|YP_979724.1| 257 HNGWVTMGGEKMSKSLGNVLSMPAMLQRVRPAELRYYLGSAHYRSMLEFSETAMQDAV 314
                                    ******************************************************9986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.3e-08   0.00012      10      83 ..      37     110 ..      33     150 .. 0.87
   2 !   25.2   0.0   1.8e-09   6.4e-06     317     369 ..     257     308 ..     233     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-08
                                    -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT- CS
                   tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklni 83 
                                    ++g +H+Gh+++ ++ Di+ R+  +rg++v f+        +i  kA+++g    e +++ ++++++ ++ l++
  gi|121639500|ref|YP_979724.1|  37 VQGLPHIGHVRSGVAFDILRRWLLARGYDVAFIRNVTDIEDKILAKAAAAGRPWWEWAATHERAFTAAYDALDV 110
                                    6789*****************************99999999**********99999999999999999998887 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.8e-09
                                    EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                   tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                                     ++++t+ g+K+SkS g+v  +  +l+r+ +  lRYyl +++   + l+fs++
  gi|121639500|ref|YP_979724.1| 257 HNGWVTMGGEKMSKSLGNVLSMPAMLQRVRPAELRYYLGSAHY-RSMLEFSET 308
                                    689***********************************87543.334555555 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   4.2e-10   1.5e-06       1      53 [.     342     394 ..     342     404 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.2e-10
                                    HHHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT CS
                         DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalkallrelaevLG 53 
                                    +F ea+dDD+  + A+a ++ +  e Nral++ d++ a + ++++r++ ++LG
  gi|121639500|ref|YP_979724.1| 342 RFAEALDDDLSVPIALAEIHHVRAEGNRALDAGDHDGALRSASAIRAMMGILG 394
                                    79**************************************************9 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00036       1.3      29      70 ..      33      74 ..      23      79 .. 0.89
   2 !   16.4   0.0   9.4e-07    0.0034     276     338 ..     263     323 ..     256     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00036
                   tRNA-synt_1f 29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                    G+++ Gl+HiG +r  +  d+++r l +rg +v +i  + d
  gi|121639500|ref|YP_979724.1| 33 CGATVQGLPHIGHVRSGVAFDILRRWLLARGYDVAFIRNVTD 74
                                   699******************************999976665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9.4e-07
                   tRNA-synt_1f 276 lkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerk 338
                                    + ggekms+S Gnvl++  +l+ + p  lr+++ +++ ++ ++++    ++++v  Y  le+ 
  gi|121639500|ref|YP_979724.1| 263 M-GGEKMSKSLGNVLSMPAMLQRVRPAELRYYLGSAHYRSMLEFSET-AMQDAVKAYVGLEDF 323
                                    3.566******************************999999999998.999999999988875 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0015       5.2      33      65 ..      36      68 ..      27      74 .. 0.90
   2 !   14.0   0.0   3.1e-06     0.011     559     599 ..     263     303 ..     226     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0015
                    tRNA-synt_1 33 yvtGslHiGhalaktlkdivirykrmkGkevly 65
                                    v G +HiGh+   +  di+ r+   +G++v +
  gi|121639500|ref|YP_979724.1| 36 TVQGLPHIGHVRSGVAFDILRRWLLARGYDVAF 68
                                   589***************************988 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.1e-06
                    tRNA-synt_1 559 eeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                      G KmSKslgNv++   +++++    lR++l ++++ + +
  gi|121639500|ref|YP_979724.1| 263 MGGEKMSKSLGNVLSMPAMLQRVRPAELRYYLGSAHYRSML 303
                                    569*****************************998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3502.08
//
Query:       gi|121639501|ref|YP_979725.1|  [L=159]
Description: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-48  164.6   0.0    2.2e-48  164.4   0.0    1.0  1  YgbB      YgbB family


Domain annotation for each model (and alignments):
>> YgbB  YgbB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.0   1.3e-52   2.2e-48       2     154 ..       6     155 ..       5     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 1.3e-52
                                    EEEEEEEEEEEEEECEEEETTEEEEESEEEESSSTCHHHHHHHHHHHHHHTT--SHHHHSTTTCGGCTTTCHHHHHHHHH CS
                           YgbB   2 riGlGyDvHrlaegrklvlgGveieaekgllahSDgDvllhAlvDAllGalalgdigelfpdtdpkykgadSaelLeevl 81 
                                    r+GlG+DvH +++gr+++l G+ +++  g+++hSDgDv++hAl+DA+l+a++lgdige+f  +dp+++g+++a++L++v+
  gi|121639501|ref|YP_979725.1|   6 RVGLGTDVHPIEPGRPCWLVGLLFPSADGCAGHSDGDVAVHALCDAVLSAAGLGDIGEVFGVDDPRWQGVSGADMLRHVV 85 
                                    89****************************************************************************** PP

                                    HHHHHTTEEEEEEEEEEECSSSTCGGGHHHHHHHHHHHHTS-GGGEEEEEEETTTSHHHHTTSEEEEEEEEEE CS
                           YgbB  82 ellkekgykivnvdvtiiaekpklapykeamrenlakllgleeeqvsvkattteklgfvGrgegiaalavvll 154
                                     l++++gy+++n+ v++i ++pk+  ++ + ++ l++ll+   + vsv+attt++lg +Grgeg+aa+a++l+
  gi|121639501|ref|YP_979725.1|  86 VLITQHGYRVGNAVVQVIGNRPKIGWRRLEAQAVLSRLLN---APVSVSATTTDGLGLTGRGEGLAAIATALV 155
                                    ***************************************8...9**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1079.45
//
Query:       gi|121639502|ref|YP_979726.1|  [L=231]
Description: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-87  292.3   3.6    2.8e-87  292.1   3.6    1.0  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    1.1e-10   42.1   4.4    1.4e-10   41.7   4.4    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      2e-05   24.6   0.0    2.5e-05   24.3   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
       0.21   11.2   0.0       0.25   10.9   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.1   3.6   6.2e-91   2.8e-87       1     220 [.       8     230 ..       8     231 .] 0.99

  Alignments for each domain:
  == domain 1  score: 292.1 bits;  conditional E-value: 6.2e-91
                                    EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE--SSHHHH CS
                           IspD   1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaGGdeRaes 80 
                                    vv+++pAAGsG+R+++g+pK+f++l+gqtl+e++vd+ll+s++vd++vv+v++d+t+e++q+l+++ +++vaGG++R+++
  gi|121639502|ref|YP_979726.1|   8 VVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHR-AMIVAGGSNRTDT 86 
                                    799**************************************************************6.************* PP

                                    HHHHHHTTSSTT..SEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEEEETTTBEEEEETGTTEEEEEEE CS
                           IspD  81 Vlnglkalegea..kfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikrveadglvaetedRegLwaaqtP 158
                                    V+ +l++l+g+a  +fVLvHDaAR+l+++a +a++++a+++++++++++lp++Dtik+v+a+g+v++t++R+gL+a+qtP
  gi|121639502|ref|YP_979726.1|  87 VNLALTVLSGTAepEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTP 166
                                    ***********9999***************************************************************** PP

                                    EEEEHHHHHHHHHHH..HHCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHHHHHH CS
                           IspD 159 qgFrvdlllaahakg..eqegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAeailr 220
                                    qgF++dlll+++++g  + ++ae+tDdaslve+iG++v+vV+G++ ++Kitt+ Dl+lA+ai+r
  gi|121639502|ref|YP_979726.1| 167 QGFTTDLLLRSYQRGslDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVR 230
                                    ***************88899******************************************97 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   4.4   3.2e-14   1.4e-10       1     122 [.      10     135 ..      10     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.2e-14
                                    EEEEEESS-TTTT.T.THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHC..HHHHHHTTCTS-EEE-TTSS-SHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmg.g.dKallplggkpllervldalraag.vdevvvvggde..evlaalarlgvrvvededpgkgplas 75 
                                    a++ A+G + R+  g +Ka+++l+g++l+er++d l ++g vd vvv+++++  + ++++ ++++ +v+     + ++  
  gi|121639502|ref|YP_979726.1|  10 AIVPAAGSGERLAvGvPKAFYQLDGQTLIERAVDGLLDSGvVDTVVVAVPADrtDEARQILGHRAMIVAGGSNRTDTVNL 89 
                                    6788********8447***********************94599999998852233345667777788877777777777 PP

                                    HHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                   NTP_transf_3  76 laaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                     ++ l+  a+ + vlv  +  +l +p+lv+r+++a++ +g+++vvp+
  gi|121639502|ref|YP_979726.1|  90 ALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALR-DGYAAVVPV 135
                                    777777766889999999999**************97.899999986 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.5e-09   2.5e-05       1     125 [.       9     133 ..       9     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.5e-09
                                    EEEEEE-SSSSSST...TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHH CS
                   CTP_transf_3   1 iaIipARsgSkRlp...gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterf 77 
                                    +aI+pA  + +Rl     K+  +l g++li++ ++ +l+s++++ v+va   ++++++ + +g+  +   +  ++ t+++
  gi|121639502|ref|YP_979726.1|   9 VAIVPAAGSGERLAvgvPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGG-SNRTDTV 87 
                                    589999999999974336***************************************999999776655554.4446777 PP

                                    HHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEE CS
                   CTP_transf_3  78 levvkaflmseneeiivnlqGdnPllqeevikkaietlkenqedylst 125
                                    + ++  ++   + e ++   ++ +l+++ ++++++e+l++   +  + 
  gi|121639502|ref|YP_979726.1|  88 NLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDG--YAAVV 133
                                    777777777766889999999*****************987..34444 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.7e-05      0.25       2      66 ..      10      70 ..       9     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHT CS
                NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlk 66
                                   a++ a GsG+RL        +k++  l++++li+  +  l++sg+ +++vv  + +++  ++q+ 
  gi|121639502|ref|YP_979726.1| 10 AIVPAAGSGERL----AVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQIL 70
                                   678899*****9....5899********************************9999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1627.06
//
Query:       gi|121639503|ref|YP_979727.1|  [L=162]
Description: transcription factor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-20   71.9   0.1    7.1e-20   71.5   0.1    1.2  1  CarD_CdnL_TRCF  CarD-like/TRCF domain
  ------ inclusion threshold ------
       0.06   13.8   0.0      0.091   13.2   0.0    1.2  1  DUF4012         Protein of unknown function (DUF4012)


Domain annotation for each model (and alignments):
>> CarD_CdnL_TRCF  CarD-like/TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.1   7.9e-24   7.1e-20       1      96 []       3     111 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 7.9e-24
                 CarD_CdnL_TRCF   1 lkvGDyVvhedhGiGriegiekrevegaekeylvleyadkkgdklyvPvdqldl..irkyiskeepkldklg........ 70 
                                    +kvGD Vv+++hG++ +e+ie+r+++g++keylvl++a+ +  ++ vP+++++   +r ++++e   ldk++        
  gi|121639503|ref|YP_979727.1|   3 FKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGD-LTVRVPAENAEYvgVRDVVGQE--GLDKVFqvlrapht 79 
                                    89*************************************87.9*******************99..************** PP

                 CarD_CdnL_TRCF  71 ......gkrwektkekakkgvkeeaaelvkly 96 
                                          ++r++++ ek+ +g+ +++ae+v+++
  gi|121639503|ref|YP_979727.1|  80 eeptnwSRRYKANLEKLASGDVNKVAEVVRDL 111
                                    *****************************985 PP

>> DUF4012  Protein of unknown function (DUF4012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05     0.091      15      97 ..      23     116 ..      17     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                        DUF4012  15 ElRatgGlvgavglltvdnGklelgdqasaadls...........vkktpvlp.ltpeeaalygerlglylrda..nltp 80 
                                    E R   G    +++l+v +G l+++  a++a++             k  +vl   + ee    ++++++y +++    + 
  gi|121639503|ref|YP_979727.1|  23 ETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVgvrdvvgqeglDKVFQVLRaPHTEEP---TNWSRRYKANLekLASG 99 
                                    8899999999*****************977777435676666544333333332333333...33344444443116899 PP

                        DUF4012  81 dfpraaelakelweaqt 97 
                                    d++++ae++++lw++++
  gi|121639503|ref|YP_979727.1| 100 DVNKVAEVVRDLWRRDQ 116
                                    **************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1265.13
//
Query:       gi|121639504|ref|YP_979728.1|  [L=182]
Description: lipoprotein lpqE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.3   0.1        6.1    6.7   0.0    2.5  2  PCuAC     Copper chaperone PCu(A)C
       0.12   12.9   0.1       0.58   10.7   0.4    2.1  2  PQQ_3     PQQ-like domain
        2.1    8.3   5.6        4.7    7.2   5.6    1.6  1  LPAM_2    Prokaryotic lipoprotein-attachment site


Domain annotation for each model (and alignments):
>> PCuAC  Copper chaperone PCu(A)C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.013        80      11      40 ..      73     102 ..      32     117 .. 0.78
   2 ?    6.7   0.0     0.001       6.1      83     107 ..     143     167 ..     140     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.013
                                    TS-SEEEEEEEEEECSSSEEEEEEEE-TTC CS
                          PCuAC  11 pgakvsaaymtirNtgdeddkLvaassdva 40 
                                    pg++v  + + ++ + d  d+Lv+++sd+ 
  gi|121639504|ref|YP_979728.1|  73 PGKAVDLVLVAVNQSPDVSDRLVGITSDIG 102
                                    556666666677777788999999999974 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.001
                                    ECESS-B-TTEEEEEEEEETTTEEE CS
                          PCuAC  83 iglkrdlkaGdevtltLtfekggti 107
                                    ++l+++++ G + ++t++fek+g+ 
  gi|121639504|ref|YP_979728.1| 143 VNLTKPIANGLTYNFTFKFEKAGQG 167
                                    589*******************985 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   7.5e+03      15      24 ..      41      50 ..      34      52 .. 0.74
   2 ?   10.7   0.4   9.7e-05      0.58      10      35 ..      98     129 ..      83     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                          PQQ_3 15 sspavdgglv 24
                                     pav g+++
  gi|121639504|ref|YP_979728.1| 41 QKPAVNGNRL 50
                                   5689999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.7e-05
                          PQQ_3  10 pgpvnsspavdggl.......vyvgtgdGtlyA 35 
                                     +++ +s++v+g+        ++vgt+dG ++A
  gi|121639504|ref|YP_979728.1|  98 TSDI-GSVTVAGDArlpasgmLFVGTPDGQIVA 129
                                    5566.6777776633344444**********98 PP

>> LPAM_2  Prokaryotic lipoprotein-attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.6   0.00079       4.7       2      15 ..      18      31 ..      17      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                         LPAM_2  2 llllallllLaGCG 15
                                   + +++l+++L+GCG
  gi|121639504|ref|YP_979728.1| 18 ASIALLAAALSGCG 31
                                   5799*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1336.94
//
Query:       gi|121639505|ref|YP_979729.1|  [L=480]
Description: DNA repair protein RadA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-17   62.5   2.7    1.2e-16   60.8   2.7    1.9  1  AAA_25           AAA domain
    1.7e-16   60.3   0.1    9.8e-14   51.2   0.1    2.1  1  ATPase           KaiC
    3.1e-10   39.6   4.8      5e-10   38.9   4.8    1.4  1  Rubredoxin_2     Rubredoxin metal binding domain
    4.2e-09   36.1   0.0    6.4e-06   25.7   0.0    2.1  2  DnaB_C           DnaB-like helicase C terminal domain
    3.6e-08   33.3   0.6    1.8e-07   31.0   0.1    2.3  3  ChlI             Subunit ChlI of Mg-chelatase
    3.2e-06   26.8   3.9    7.8e-05   22.3   0.1    2.7  2  Lon_C            Lon protease (S16) C-terminal proteolytic do
    1.9e-05   25.1   0.4    6.5e-05   23.4   0.4    1.9  1  AAA_16           AAA ATPase domain
    2.2e-05   24.9   0.0    4.2e-05   24.0   0.0    1.4  1  AAA              ATPase family associated with various cellul
    4.3e-05   23.3   5.5    4.6e-05   23.2   2.5    2.4  2  AAA_30           AAA domain
    4.4e-05   22.9   0.4    0.00079   18.8   0.4    2.2  1  Rad51            Rad51
    8.2e-05   22.9   0.0    0.00016   22.0   0.0    1.4  1  AAA_22           AAA domain
     0.0003   20.7   0.1    0.00064   19.7   0.1    1.5  1  NACHT            NACHT domain
     0.0019   18.2   0.1     0.0038   17.2   0.1    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0068   16.2   0.0      0.012   15.3   0.0    1.4  1  AAA_24           AAA domain
     0.0073   16.0   0.1      0.031   14.0   0.1    2.1  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.1   0.8      0.021   14.3   0.8    1.4  1  RecA             recA bacterial DNA recombination protein
      0.029   13.5   0.0       0.07   12.2   0.0    1.6  1  MCM              MCM P-loop domain
      0.039   14.5   0.0      0.096   13.2   0.0    1.7  1  ABC_tran         ABC transporter
      0.041   14.6   1.0      0.094   13.4   1.0    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
       0.07   12.4   0.0      0.094   11.9   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.074   13.0   0.0       0.14   12.1   0.0    1.6  1  NTPase_1         NTPase
      0.077   12.9   0.0       0.15   12.0   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
       0.11   12.6   0.0       0.18   11.9   0.0    1.3  1  AAA_14           AAA domain
       0.15   11.8   0.1       0.46   10.2   0.1    1.8  1  IstB_IS21        IstB-like ATP binding protein
       0.24   10.3   0.0       0.35    9.7   0.0    1.2  1  AAA_10           AAA-like domain
       0.95    9.4   3.1         32    4.5   0.0    2.8  3  L_biotic_typeA   Type-A lantibiotic


Domain annotation for each model (and alignments):
>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   2.7   1.8e-19   1.2e-16      20     193 ..      75     221 ..      57     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.8e-19
                         AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealr 98 
                                     +++ +++g ++ g+++llaG+pg+GK+tl+l++a+ +a +G           ++ lyvs+E+s+ ++r R+ ++g    
  gi|121639505|ref|YP_979729.1|  75 DELDRVLGGGIVPGSVTLLAGDPGVGKSTLLLEVAHRWAqSG-----------RRALYVSGEESAGQIRLRADRIGCGT- 142
                                    5666777777788**************************444...........489********************886. PP

                         AAA_25  99 ddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd....vgalvealer 174
                                    + ++ ++                     ++dv+ + ++ie v +++lv++D+++ +   + +  +     v+a+ +al  
  gi|121639505|ref|YP_979729.1| 143 EVEEIYLAA-------------------QSDVHTVLDQIETV-QPALVIVDSVQTMSTSEADGVTGgvtqVRAVTAALTA 202
                                    334444442...................4899999******7.5***********9999655555444448********* PP

                         AAA_25 175 iarrtgaavllvhHvgKes 193
                                     a++  +a++lv Hv K++
  gi|121639505|ref|YP_979729.1| 203 AAKANEVALILVGHVTKDG 221
                                    *****************97 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1   1.4e-16   9.8e-14       1     198 [.      70     251 ..      70     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.4e-16
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                    ++tgI +lD++l gGi  g+v+l++G+pG GK+++ l+ + + a++ g++ ++v+ ee+a ++r +a ++G  +e +ee 
  gi|121639505|ref|YP_979729.1|  70 CPTGIDELDRVLGGGIVPGSVTLLAGDPGVGKSTLLLEVAHRWAQS-GRRALYVSGEESAGQIRLRADRIGCGTE-VEEI 147
                                    69*****************************************999.**********************998764.3322 PP

                         ATPase  81 gklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeav......aReilrqlvrvlkkl 154
                                       + + a            ++d++ ++    + i++++   v++Ds+++++++e + v      +R+    l+   k +
  gi|121639505|ref|YP_979729.1| 148 ---Y-LAA------------QSDVHTVL----DQIETVQPALVIVDSVQTMSTSEADGVtggvtqVRAVTAALTAAAKAN 207
                                    ...1.222............23344444....446677888899999999955555443122222677777777777888 PP

                         ATPase 155 gvTailvsekssseeaaggygveefivdgvivLdlkeiee.elvR 198
                                    +v  ilv  ++++   ag   +e+ +vd v++ + +++   ++vR
  gi|121639505|ref|YP_979729.1| 208 EVALILVGHVTKDGAIAGPRSLEH-LVDVVLHFEGDRNGAlRMVR 251
                                    888888888777655566666777.99988888877776655555 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   4.8   7.2e-13     5e-10       1      28 []       8      35 ..       8      35 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.2e-13
                   Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgsWntlke 28
                                   Y+Cs+C ++sakw+GrC +Cg W+t++e
  gi|121639505|ref|YP_979729.1|  8 YRCSECRHVSAKWVGRCLECGRWGTVDE 35
                                   9************************987 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   9.3e-09   6.4e-06       3      67 ..      71     135 ..      70     166 .. 0.81
   2 !    8.5   0.0    0.0016       1.1     129     175 ..     166     214 ..     144     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.3e-09
                                    XSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHH CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C   3 stgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRl 67 
                                    +tg ++LD++++ G+ +g ++++A+ p++Gk++l l++a++ a+ +  + +++s e sa q+  R 
  gi|121639505|ref|YP_979729.1|  71 PTGIDELDRVLGgGIVPGSVTLLAGDPGVGKSTLLLEVAHRWAQ-SGRRALYVSGEESAGQIRLRA 135
                                    799*****9886279**************************997.55589999*****99998775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                    TEEEEEEEEGGGTBTSCS..SSCCCHHHHHHHHHHHHHHHHCTSXEEEE CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 129 glgliviDyLqlmegsee..kenreqevseisrsLkalakelnvpvial 175
                                    +  l+++D +q m++se+   +  +++v +++ +L a ak  +v +i +
  gi|121639505|ref|YP_979729.1| 166 QPALVIVDSVQTMSTSEAdgVTGGVTQVRAVTAALTAAAKANEVALILV 214
                                    5589**********874435568899******************99986 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.8     2e+03      91     115 ..     187     211 ..     185     216 .. 0.71
   2 ?   -1.8   0.0         4   2.8e+03      76      96 ..     205     225 ..     193     242 .. 0.64
   3 !   31.0   0.1   2.6e-10   1.8e-07      59     119 ..     367     427 ..     320     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.8
                           ChlI  91 dGslrpvkgvlpialaakkegikkv 115
                                    +G + +v+ v++++ aa+k++   +
  gi|121639505|ref|YP_979729.1| 187 TGGVTQVRAVTAALTAAAKANEVAL 211
                                    7888888888888888877765444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                           ChlI  76 ieaeeetlflGeLsldGslrp 96 
                                    +++e  ++++G + +dG +  
  gi|121639505|ref|YP_979729.1| 205 KANEVALILVGHVTKDGAIAG 225
                                    233346788899999998865 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 2.6e-10
                           ChlI  59 safDLpiAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                    ++ DL++Ai++ +a+ + +  ++ +++Ge++l G++r+v+g+   + +a+++g++ ++vp 
  gi|121639505|ref|YP_979729.1| 367 PSADLAVAIALASAYANLPLPTTAVMIGEVGLAGDIRRVNGMARRLSEAARQGFTIALVPP 427
                                    667********************************************************96 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.025        17     107     145 ..     183     223 ..     126     226 .. 0.91
   2 !   22.3   0.1   1.1e-07   7.8e-05     109     170 ..     366     427 ..     352     432 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.025
                                    GGGGGGHHHHHHHHHHHHTS--B-TTBEE..--EE-TT-BE CS
                          Lon_C 107 kdGPsaGvtlatalvslltgkkvrkdvam..tGeitLrGrv 145
                                     dG   Gvt + a++++lt  +  ++va+   G +t  G +
  gi|121639505|ref|YP_979729.1| 183 ADGVTGGVTQVRAVTAALTAAAKANEVALilVGHVTKDGAI 223
                                    59999**********************96336888888765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
                                    GGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEG CS
                          Lon_C 109 GPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPk 170
                                     Psa +++a al s+ ++ +  +   m Ge+ L G +  + G+  +l  a r+g +  ++P 
  gi|121639505|ref|YP_979729.1| 366 EPSADLAVAIALASAYANLPLPTTAVMIGEVGLAGDIRRVNGMARRLSEAARQGFTIALVPP 427
                                    6******************************************************9999985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   9.4e-08   6.5e-05      16      63 ..      77     127 ..      74     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.4e-08
                         AAA_16  16 lervrsgrp...elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    l+rv  g+    +++ll G++GvGKs+l+ e+++++ ++g  +l+   +++
  gi|121639505|ref|YP_979729.1|  77 LDRVLGGGIvpgSVTLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEES 127
                                    45555555566689*************************766666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.1e-08   4.2e-05       2      87 ..      92     194 ..      91     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.1e-08
                                    EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTSTSEEE CS
                            AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk................yvgesekkirelfkeakekakpsil 62 
                                    ll G pG+GK++l   va+ +   g++ l +sg e   +                +  +++++++ +++++++ + p  +
  gi|121639505|ref|YP_979729.1|  92 LLAGDPGVGKSTLLLEVAHRWaqsGRRALYVSGEESAGQirlradrigcgteveeIYLAAQSDVHTVLDQIETVQ-PALV 170
                                    89******************655467777777777776677777888888888889999***************8.**** PP

                                    EEETGGGHHHHH.TTCCCHHHHHHHH CS
                            AAA  63 fiDEidalaksr.sgseseeeervvn 87 
                                    ++D +  + +s+ +g   + + + v 
  gi|121639505|ref|YP_979729.1| 171 IVDSVQTMSTSEaDGV--TGGVTQVR 194
                                    ********99994222..22222222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   2.5   6.6e-08   4.6e-05      19     116 ..      89     194 ..      85     236 .. 0.75
   2 ?   -1.2   0.1       2.1   1.4e+03      81     114 ..     369     414 ..     311     425 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-08
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Lae...elgieastiakllkrlk......grarlep 88 
                                     v++l G +G GK+t+l ++++ w+++g+r + ++ ++ a +  L++   ++g+e + i   l ++       ++ +  +
  gi|121639505|ref|YP_979729.1|  89 SVTLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIrLRAdriGCGTEVEEIY--LAAQSdvhtvlDQIETVQ 166
                                    5899************************99999999988888668843222222222222..222223455554445556 PP

                         AAA_30  89 gtllivDEagmvdtkqlaallkaaekag 116
                                      l+ivD +  ++t++++ ++  +++  
  gi|121639505|ref|YP_979729.1| 167 PALVIVDSVQTMSTSEADGVTGGVTQVR 194
                                    79**********9999988887777644 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                         AAA_30  81 k..........grarlepg.tllivDEagmv.dtkqlaallkaaek 114
                                    +          + a+l    t +++ E+g++ d++ ++ +++++++
  gi|121639505|ref|YP_979729.1| 369 AdlavaialasAYANLPLPtTAVMIGEVGLAgDIRRVNGMARRLSE 414
                                    0444444444422333333377888888888644444444333333 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   1.1e-06   0.00079      20      82 ..      71     127 ..      58     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                    --S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS- CS
                          Rad51  20 ttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegt 82 
                                     tG  +lD++LgGGi  gs+t + G+ + Gk+ l  +++           + ++a+y++ e +
  gi|121639505|ref|YP_979729.1|  71 PTGIDELDRVLGGGIVPGSVTLLAGDPGVGKSTLLLEVAH------RWAQSGRRALYVSGEES 127
                                    59******************************87655442......22223345666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.3e-07   0.00016       6     129 ..      89     215 ..      86     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.3e-07
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseellealeq 84 
                                    +++++ G +G+GK+tll +++++  +       +++ ++v   +s ++  l + ++   +++e  +  l  +  ++++ +
  gi|121639505|ref|YP_979729.1|  89 SVTLLAGDPGVGKSTLLLEVAHRWAQS------GRRALYVSGEESAGQIRLrADRIGCGTEVEEIY--LAAQSDVHTVLD 160
                                    67899***************9997554......9999******99977777699999999999999..99********** PP

                         AAA_22  85 alraravielliiDEaqhlr.s........eealeeLrsllnl.....srkgvqliLvG 129
                                    ++++ +  +l+i+D +q ++ s         ++++ +           +   v+liLvG
  gi|121639505|ref|YP_979729.1| 161 QIETVQP-ALVIVDSVQTMStSeadgvtggVTQVRAV---TAAltaaaKANEVALILVG 215
                                    *******.**********9652555554442222222...1112223456677777776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   9.2e-07   0.00064       2      31 ..      90     119 ..      89     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.2e-07
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpq 31 
                                    + +l G++G+GK+tLl ++a+ wa++   +
  gi|121639505|ref|YP_979729.1|  90 VTLLAGDPGVGKSTLLLEVAHRWAQSGRRA 119
                                    6799*********************98555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.5e-06    0.0038       3      80 ..      92     168 ..      90     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                                    EEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--H CS
                          AAA_5   3 lLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraes 79 
                                    lL G+pG+gKs+l  ++a++    +r+ +yv + ++  +  l+  r   + +t+ ++   + aa++  ++vlD +e++++
  gi|121639505|ref|YP_979729.1|  92 LLAGDPGVGKSTLLLEVAHRWaqsGRRALYVSGEESAGQIRLRADRI--GCGTEVEEI--YLAAQSDVHTVLDQIETVQP 167
                                    89********************9999*****9999777666666666..445554443..33688888888888887665 PP

                                    H CS
                          AAA_5  80 e 80 
                                    +
  gi|121639505|ref|YP_979729.1| 168 A 168
                                    4 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.012       5      76 ..      91     177 ..      88     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                         AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksl..dadkfpdieswedfldevvel......aaeladyktl 69 
                                     l+ G++g+GK+tl++e        g ++l++  e+++ ++   ad++ + + +e+++ +++++      + e  +   +
  gi|121639505|ref|YP_979729.1|  91 TLLAGDPGVGKSTLLLEVahrwaqsGRRALYVSGEESAGQIrlRADRIGCGTEVEEIYLAAQSDvhtvldQIETVQPALV 170
                                    6899********************************66655005555555444444444444445444442222233556 PP

                         AAA_24  70 viDtide 76 
                                    ++D+++ 
  gi|121639505|ref|YP_979729.1| 171 IVDSVQT 177
                                    7777765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   4.5e-05     0.031      23      39 ..      88     105 ..      84     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                         AAA_29  23 g.atlltGpsGsGKSTll 39 
                                    g +tll+G+ G+GKSTll
  gi|121639505|ref|YP_979729.1|  88 GsVTLLAGDPGVGKSTLL 105
                                    448*************97 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   3.1e-05     0.021      33     155 ..      69     189 ..      57     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                    EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HH..HHHHT..T--GGG- CS
                           RecA  33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpk..yakkl..Gvdidel 108
                                      ++G   ld  lG GG+  G ++ + G    Gk+tl l++  +  ++g  a ++  e +       a ++  G +++e+
  gi|121639505|ref|YP_979729.1|  69 PCPTGIDELDRVLG-GGIVPGSVTLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIrlRADRIgcGTEVEEI 147
                                    57899999******.99999*************************************99887651146666225789999 PP

                                    EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT------- CS
                           RecA 109 lvsqpdtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgd 155
                                    +++        l+ ++++       l++vdsv ++   +e +G  g 
  gi|121639505|ref|YP_979729.1| 148 YLAAQSDVHTVLDQIETVQ----PALVIVDSVQTMS-TSEADGVTGG 189
                                    9987777778888877764....3599*****9875.4566665543 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.07      61      93 ..      92     128 ..      86     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                    EEEESSTSTHHHHHHHHHH....HSSSEEEEESSSSS CS
                            MCM  61 llvgdpgtaKsqlLkyvek....lapravytsgkgss 93 
                                    ll gdpg++Ks+lL +v++       ra y+sg+ s 
  gi|121639505|ref|YP_979729.1|  92 LLAGDPGVGKSTLLLEVAHrwaqSGRRALYVSGEESA 128
                                    899**********998864111144678999998775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014     0.096       8      40 ..      85     116 ..      80     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteG 40 
                                    + +g+++ + G+ G GKStLl  +a+    ++G
  gi|121639505|ref|YP_979729.1|  85 IVPGSVTLLAGDPGVGKSTLLLEVAHRWA-QSG 116
                                    679*****************987776654.344 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.0   0.00014     0.094      30     104 ..     149     222 ..     141     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                                    EEESSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--SSGGGH CS
                DXP_reductoisom  30 laagsnvellaeqakefkpklvavadeeaaeelkealkekelktevlvGeealkelaeeeeadvvvaaivGaaGL 104
                                    laa+s+v+++++q+++++p+lv+v + +++++ ++    ++  t+v + ++al+++a+++e+ +++ + v   G 
  gi|121639505|ref|YP_979729.1| 149 LAAQSDVHTVLDQIETVQPALVIVDSVQTMSTSEADG-VTGGVTQVRAVTAALTAAAKANEVALILVGHVTKDGA 222
                                    899*********************9988888777766.5788999*********************999887775 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014     0.094       3      41 ..      90     126 ..      88     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                        DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNh 41 
                                    v l  G++G GK+ +ll++++++   +++r+a y+s+ +
  gi|121639505|ref|YP_979729.1|  90 VTLLAGDPGVGKSTLLLEVAHRW--AQSGRRALYVSGEE 126
                                    77889******************..99999999999876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.14       3      29 ..      92     118 ..      90     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                    EEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvk 29 
                                    ++ G pGvGK+Tl+  v++  ++sg +
  gi|121639505|ref|YP_979729.1|  92 LLAGDPGVGKSTLLLEVAHRWAQSGRR 118
                                    689***************999888765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.15      99     121 ..      88     110 ..      69     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                    TSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                    +++++l+G  GvGKStL+ +++ 
  gi|121639505|ref|YP_979729.1|  88 GSVTLLAGDPGVGKSTLLLEVAH 110
                                    6799*************977665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.18       5      83 ..      91     172 ..      88     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe......kllelileklkeekktylflDEiqevpe 78 
                                     ++ G   vGK+tll +++++   + ++ ly++ ++   + +   +      +++e++l+    + +   +lD i  v+ 
  gi|121639505|ref|YP_979729.1|  91 TLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIRLRADrigcgtEVEEIYLAA---QSDVHTVLDQIETVQP 167
                                    67778889***********99889999********97774433333344444556666664...3456677887777765 PP

                         AAA_14  79 wekal 83 
                                    +  ++
  gi|121639505|ref|YP_979729.1| 168 ALVIV 172
                                    54444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00067      0.46      50      91 ..      91     132 ..      85     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00067
                      IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelk 91 
                                     +l G +GvGKs l   ++++ +++g + l+v+ e+   +++
  gi|121639505|ref|YP_979729.1|  91 TLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIR 132
                                    5799***************************99877666665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00051      0.35      24      98 ..      91     167 ..      81     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                         AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe..iakkinvvtLdseeenegvLdPlvllke 98 
                                    +l+ Gd+G GKS l   + +  +  g +al++   +   + + ++    +  +++ + L  +++ + vLd +  ++ 
  gi|121639505|ref|YP_979729.1|  91 TLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIRLRADRigCGTEVEEIYLAAQSDVHTVLDQIETVQP 167
                                    699*****************************99999999988886666889999****999999****98876654 PP

>> L_biotic_typeA  Type-A lantibiotic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4         6   4.1e+03      37      50 ..      11      24 ..      10      25 .. 0.88
   2 ?    4.5   0.1     0.047        32      18      28 ..      75      84 ..      72      91 .. 0.83
   3 ?    4.5   0.0     0.046        32       9      27 ..     172     190 ..     164     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6
                 L_biotic_typeA 37 heCrmnSwqfvftC 50
                                   +eCr  S + v+ C
  gi|121639505|ref|YP_979729.1| 11 SECRHVSAKWVGRC 24
                                   69*****9999998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.047
                 L_biotic_typeA 18 eELdqilGGkg 28
                                   +ELd +lGG g
  gi|121639505|ref|YP_979729.1| 75 DELDRVLGG-G 84
                                   8********.3 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.046
                 L_biotic_typeA   9 lnslqevseeELdqilGGk 27 
                                    + s+q++s +E d + GG 
  gi|121639505|ref|YP_979729.1| 172 VDSVQTMSTSEADGVTGGV 190
                                    789***************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 3375.76
//
Query:       gi|121639506|ref|YP_979730.1|  [L=358]
Description: DNA integrity scanning protein DisA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-47  159.4   0.2    6.4e-47  158.9   0.2    1.2  1  DisA-linker  DisA bacterial checkpoint controller linker regi
      1e-24   86.4   0.0    1.9e-24   85.5   0.0    1.5  1  DisA_N       DisA bacterial checkpoint controller nucleotide-
    3.5e-07   30.2   0.7    2.3e-06   27.6   0.0    2.6  3  HHH_2        Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.011   15.6   0.0        1.9    8.5   0.0    2.5  2  HHH          Helix-hairpin-helix motif
       0.11   10.9   0.1       0.16   10.4   0.1    1.1  1  BicD         Microtubule-associated protein Bicaudal-D
       0.21   11.8   0.1       0.35   11.1   0.1    1.3  1  Spc24        Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> DisA-linker  DisA bacterial checkpoint controller linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.2   2.1e-50   6.4e-47       1     141 [.     141     284 ..     141     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 2.1e-50
                                    .--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EBHHHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGHHHHHH CS
                    DisA-linker   1 LedievilakanqalqTLekYrsvldevlsnLsalEfedlVtlsdVaeviqrlemvlrikeeiekyiveLGteGrlislq 80 
                                    L d+++il++anqa++TLe+Y+++ldev ++Ls +E+ed+Vtl+dV++v+qrle+v+ri   i+  +veLGt+Gr+++lq
  gi|121639506|ref|YP_979730.1| 141 LTDSATILSRANQAIATLERYKTRLDEVSRQLSRAEIEDFVTLRDVMTVVQRLELVRRIGLVIDYDVVELGTDGRQLRLQ 220
                                    689***************************************************************************** PP

                                    HHHHHTTHHHHHHHHHHHHSSS--...HHHHHHHHHHH...HTTS---HHHHHHHTT---SSGG CS
                    DisA-linker  81 leeLlanveeeeellikDYlkeek...eeeaeeileelkelsseelldlskiaklLGyekssea 141
                                    l+eLl++ ++ +el+++DY+++ +   + +++++l+el++ls+ +lld +++ak++Gy++++ea
  gi|121639506|ref|YP_979730.1| 221 LDELLGGNDTARELIVRDYHANPEppsTGQINATLDELDALSDGDLLDFTALAKVFGYPTTTEA 284
                                    **********************9999999******************************99875 PP

>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.0   6.5e-28   1.9e-24       2     118 ..      24     137 ..      23     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 6.5e-28
                                    HHHHHHHHHT--EEEEEESSSCCCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.E.TTEEEEEEEEE--TT-TT CS
                         DisA_N   2 eaveelskkkiGaliviereeelkeiietgvkldaevskellkeifekksplhDGAvii.r.dgrivaagviLplsenke 79 
                                    +++e++ + ++Galiv++++e+++ i+++g++ld ++ ++ l+e+      ++DGAv++   ++riv+a+v+L +  +  
  gi|121639506|ref|YP_979730.1|  24 DGLERILRGRTGALIVLGHDENVEAICDGGFSLDVRYAATRLREL-----CKMDGAVVLsTdGSRIVRANVQLVPDPSIP 98 
                                    68999****************************************.....*********74699***********55434 PP

                                    SST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                         DisA_N  80 lkelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                    ++e GtRHr+A++ + +t   vi VS +++ ++++ +g+
  gi|121639506|ref|YP_979730.1|  99 TDESGTRHRSAERAAIQTGYPVISVSHSMNIVTVYVRGE 137
                                    57*********************************9996 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.44   1.3e+03      28      45 ..     171     188 ..     165     209 .. 0.80
   2 ?   -4.0   0.0       5.7   1.7e+04      32      41 ..     253     262 ..     252     267 .. 0.65
   3 !   27.6   0.0   7.6e-10   2.3e-06       7      55 ..     299     347 ..     295     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                          HHH_2  28 aLkkasleeLlevddiGe 45 
                                    +L++a++e+ ++++d+ +
  gi|121639506|ref|YP_979730.1| 171 QLSRAEIEDFVTLRDVMT 188
                                    688888888888888755 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.7
                          HHH_2  32 asleeLlevd 41 
                                    a+l+eL ++ 
  gi|121639506|ref|YP_979730.1| 253 ATLDELDALS 262
                                    6666666654 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 7.6e-10
                          HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefF 55 
                                    GI+    + A lL+++F++l+ L +as+ +L++vd+iG   A+ +++ +
  gi|121639506|ref|YP_979730.1| 299 GIPRLQFAHADLLVRAFGTLQGLLAASAGDLQSVDGIGAMWARHVRDGL 347
                                    666666678***********************************99865 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.012        35       4      17 ..     249     262 ..     249     263 .. 0.88
   2 ?    8.5   0.0   0.00063       1.9       1      21 [.     317     337 ..     317     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                                    HHHTSSHHHHHTST CS
                            HHH   4 glipasreeLlalP 17 
                                    g i+a+++eL al+
  gi|121639506|ref|YP_979730.1| 249 GQINATLDELDALS 262
                                    689*******9996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00063
                                    SHHHHHTSSHHHHHTSTT-SH CS
                            HHH   1 sleglipasreeLlalPGVGp 21 
                                    +l+gl +as  +L+++ G+G 
  gi|121639506|ref|YP_979730.1| 317 TLQGLLAASAGDLQSVDGIGA 337
                                    589*****************6 PP

>> BicD  Microtubule-associated protein Bicaudal-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   5.4e-05      0.16     649     714 ..     136     199 ..     125     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.4e-05
                           BicD 649 neLkaLkeDaatfssLRamfatRCdeYvtqldelqrqLaaaedek.ktLnsLLRlaiqqkLaLtqrL 714
                                     e ++L  D+at  s      +  + Y t lde+ rqL+ ae e   tL  +  + + q+L L  r+
  gi|121639506|ref|YP_979730.1| 136 GERHVLT-DSATILSRANQAIATLERYKTRLDEVSRQLSRAEIEDfVTLRDV--MTVVQRLELVRRI 199
                                    5555554.55555554444445679*****************7752688776..7888999998876 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.35      14      70 ..     149     206 ..     139     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                          Spc24  14 sdleselesleselaelkeeleeleeesee....keserve.detllklklYrsLGielekd 70 
                                    s +++++    ++l++ k++l+e++++ ++    +  ++ +  +++++l+l r +G+ +++d
  gi|121639506|ref|YP_979730.1| 149 SRANQAI----ATLERYKTRLDEVSRQLSRaeieDFVTLRDvMTVVQRLELVRRIGLVIDYD 206
                                    3444444....45555555555555555552111333447779999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2458.16
//
Query:       gi|121639507|ref|YP_979731.1|  [L=263]
Description: hypothetical protein BCG_3652c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1780.33
//
Query:       gi|121639508|ref|YP_979732.1|  [L=207]
Description: carbonic anhydrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  133.0   0.2    1.4e-38  132.7   0.2    1.1  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.2   7.6e-43   1.4e-38       1     155 [.      46     193 ..      46     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 7.6e-43
                                    EEEEEETTTTS-HHHHTTS-TTSEEEEEETTG---TT-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHS..HHCCS CS
                         Pro_CA   1 alvigCsDSRvppelitdagpGdlFvvrnvgnlvppadssvlaaleyAvevlkvkhivVlGHskCGavkaalk..aekse 78 
                                    a+++gC+DSRv +e+i+d+g+Gd+Fvvr++g+++   ds+vl+++eyAv+vl+v+ ivVlGH++CGav+aal+  + + +
  gi|121639508|ref|YP_979732.1|  46 AVIFGCADSRVAAEIIFDQGLGDMFVVRTAGHVI---DSAVLGSIEYAVTVLNVPLIVVLGHDSCGAVNAALAaiN-DGT 121
                                    689*******************************...**********************************99854.446 PP

                                    TTSSHHHHHHHHHHHHHHHCHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHTTS-EEEEEEEETTTTE CS
                         Pro_CA  79 eeagaidkwlekirealekveeelesekekearerlleeenVaeqlenLlek.pvvreavekgklkvhGlvydletGe 155
                                       g++++++e++++++   +++        +r + +e+++V+e+++ L+++ ++++e+++ g+l+++G+ y+l++G+
  gi|121639508|ref|YP_979732.1| 122 LPGGYVRDVVERVAPSVLLGRRD------GLSRVDEFEQRHVHETVAILMARsSAISERIAGGSLAIVGVTYQLDDGR 193
                                    6699***********99887753......34566666*************9999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1713.52
//
Query:       gi|121639509|ref|YP_979733.1|  [L=304]
Description: adenine glycosylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-16   58.8   0.0      1e-15   58.1   0.0    1.3  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    7.4e-08   31.9   0.0    3.8e-07   29.6   0.0    2.3  2  HHH            Helix-hairpin-helix motif
     0.0012   19.1   5.2     0.0025   18.1   5.2    1.5  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.7e-19     1e-15       1      88 [.      46     161 ..      46     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.7e-19
                                    HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.............. 66 
                                    vs+ + qqt+ +r+ +i++++++r+  ptp + a a+ +++  ++ +lG++ r+ak+++e+A  ++              
  gi|121639509|ref|YP_979733.1|  46 VSEFMLQQTPAARVLAIWPDWVRRW--PTPSATATASTADVLRAWGKLGYP-RRAKRLHECATVIArdhndvvpddieil 122
                                    7899********************8..9*********************99.**************************** PP

                                    .................S-SSS--TTSHHHHHHHHHHTT CS
                                    .................xxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 .................gkpdvlivvDvhvrrilkrlrs 88 
                                                     ++ + ++vvD++vrr++ r   
  gi|121639509|ref|YP_979733.1| 123 vtlpgvgsytaravacfAYRQRVPVVDTNVRRVVARAVH 161
                                    *****************77789************99755 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   6.4e-11   3.8e-07       2      30 .]     111     139 ..     110     139 .. 0.94
   2 ?   -2.1   0.0      0.74   4.4e+03       5      13 ..     257     265 ..     256     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.4e-11
                                    HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                            HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                                    ++ ++p+++e L++lPGVG +tA+a++++
  gi|121639509|ref|YP_979733.1| 111 HNDVVPDDIEILVTLPGVGSYTARAVACF 139
                                    7889**********************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.74
                                    HHTSSHHHH CS
                            HHH   5 lipasreeL 13 
                                    ++p +r+eL
  gi|121639509|ref|YP_979733.1| 257 EFPVTRAEL 265
                                    6899****9 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   5.2   4.2e-07    0.0025       1      13 [.     203     215 ..     203     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-07
                  EndIII_4Fe-2S   1 CTARkPkCeaCPL 13 
                                    CTAR P+C+ CPL
  gi|121639509|ref|YP_979733.1| 203 CTARTPRCGLCPL 215
                                    ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1980.05
//
Query:       gi|121639510|ref|YP_979734.1|  [L=584]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-35  121.3  22.0    2.4e-35  120.7  22.0    1.3  1  PE              PE family
  ------ inclusion threshold ------
       0.21   12.1   1.0       0.29   11.6   1.0    1.1  1  DUF3526         Domain of unknown function (DUF3526)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7  22.0   2.6e-39   2.4e-35       1      93 []       1      93 [.       1      93 [. 0.99

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.6e-39
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+vaPeal ++a+++agigsal+aanaaaaaptt+vlaaaaDeVSaa+Aalf+ahaqeyq+lsaqaa fh+qfvqal+a
  gi|121639510|ref|YP_979734.1|  1 MSFVIVAPEALMSVASEVAGIGSALNAANAAAAAPTTGVLAAAADEVSAAMAALFGAHAQEYQRLSAQAAGFHAQFVQALNA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   + +sYa+aEaa
  gi|121639510|ref|YP_979734.1| 83 GVNSYASAEAA 93
                                   *********97 PP

>> DUF3526  Domain of unknown function (DUF3526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   3.2e-05      0.29      92     143 ..      49     100 ..      41     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                        DUF3526  92 slsmalAgTDlaayldFqdqaeayrrdlvqqLnedlraffypklfedrrvta 143
                                    +++ al g  ++ y++  +qa  ++ ++vq+Ln+ ++ +  +++ ++ +++a
  gi|121639510|ref|YP_979734.1|  49 AAMAALFGAHAQEYQRLSAQAAGFHAQFVQALNAGVNSYASAEAANASPLQA 100
                                    5667777899999********************9999999888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 3456.49
//
Query:       gi|121639511|ref|YP_979735.1|  [L=257]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-16   59.5  19.9    7.9e-16   59.3  19.9    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.5e-12   45.3   0.2    9.2e-07   28.8   0.2    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.9e-06   26.0   0.0    1.5e-05   24.4   0.0    1.6  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.03   14.2   0.1    1.8  2  Ser_hydrolase  Serine hydrolase
      0.093   12.4   0.2        0.2   11.2   0.2    1.7  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3  19.9   2.2e-19   7.9e-16       1     218 [.      19     245 ..      19     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.2e-19
                                    EEEE--GC.....GCHHHH..HHHHCCTCEEEEE--TTS.TS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassWlvapL..aallaagvhvlapDlpGh.Grsdpppldled...ladlaalldelaagggpvvlvGHSl 74 
                                    ++l+HG+ + +s W +++L  + ll+a    +++D+p h Gr+  +p+  +    +adl +++ +l   g p   vGHS+
  gi|121639511|ref|YP_979735.1|  19 LVLVHGLMGRGSTW-ARQLpwLTLLGAV---YTYDAPWHrGRDVADPHPISTerfVADLGDAVSAL---GAPTRMVGHSM 91 
                                    79****8888999*.3455215555554...7*********9988888887766789999999999...7899******* PP

                                    HHHHHHHHHHCC.......EEEEES-..----TTT..S----TTHHHHHHTT-CCCCHCCH........S-HSCCCCHHH CS
                  Abhydrolase_6  75 GGalalaaapla.....lvvgvlldppptalpagl..laaalelllallallrllawlsre........plprlfladed 139
                                    G++ ++    la     lv++++++    ++p+       ++e++l++l+     +++s+e         ++r fl+  d
  gi|121639511|ref|YP_979735.1|  92 GALHSWC---LAaerpeLVSALVVED---MAPDFRgrTTGPWEPWLRALP----VEFDSAEqvfaefgpVAGRYFLDAFD 161
                                    ***8888...3333355555599999...555555587777777777777....33333222222224333334444333 PP

                                    .CCCCHCHCCCGHH..HHCCHHCHTT.CCHHTT-TTGCEEECTT-C.HHHHCHHCCCH.STTEEET.CE...SSS-HHHH CS
                  Abhydrolase_6 140 .adaawrarlarla..allaglgllp.aaawadlpvpllvlggeDp.lvprllerlla.qagarlp.vvlpgaGHlphle 212
                                     + + wr   ++++    +a +g++  +a w+++++p l++ ++D  + p  +++++        +   +p+aGHl+h+e
  gi|121639511|ref|YP_979735.1| 162 rTATGWRLHGRTARwiEIAAEWGTRDyWAQWRAVRSPALLIEAGDGvTPPGQMRAMAErDYPT--AyLRVPDAGHLVHDE 239
                                    11233333333333443333444332499*********9995555524444455555533333..2599**********8 PP

                                    SHHHHH CS
                  Abhydrolase_6 213 epdeva 218
                                    +p+ + 
  gi|121639511|ref|YP_979735.1| 240 APQVYR 245
                                    887665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   2.6e-10   9.2e-07       2     104 ..      18     113 ..      17     148 .. 0.86
   2 !   14.7   0.0     5e-06     0.018     206     256 ..     189     240 ..     152     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.6e-10
                                    EEEEE-STTTCGGGGTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakd..gfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvG 79 
                                    +lv++hGl g +  wa+    p L      +++ ++ +rG +  +p+p       +t  + +dl  ++ alg     +vG
  gi|121639511|ref|YP_979735.1|  18 PLVLVHGLMGRGSTWAR--QLPWLTLLgaVYTYDAPWHRGRDVADPHPI------STERFVADLGDAVSALGAPTR-MVG 88 
                                    89********9999*99..666555544488888888888888888885......789999***********9999.*** PP

                                    ETHHHHHHHHHHHHHGGGEEEEEEE CS
                  Abhydrolase_1  80 hSmGGmialayaaeyperVkalvll 104
                                    hSmG + ++ +aae pe V+alv  
  gi|121639511|ref|YP_979735.1|  89 HSMGALHSWCLAAERPELVSALVVE 113
                                    **********************975 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5e-06
                                    C..THHHHSEEEEEEETTCSSSCHHHHHHHHHC.HTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 206 e..lknvlaptlvisgtsDplvppkaledlaql.lpkkrlvvisdagHlafleg 256
                                    +   ++v +p+l+i +  D+++pp++++ +a+   p   +++++dagHl++ e 
  gi|121639511|ref|YP_979735.1| 189 WaqWRAVRSPALLIEA-GDGVTPPGQMRAMAERdYPT-AYLRVPDAGHLVHDEA 240
                                    133356888****966.*******9999999988999.9***********9987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   4.1e-09   1.5e-05       7     124 ..      19     132 ..      16     150 .. 0.87
   2 ?   -1.2   0.0      0.27   9.8e+02     180     216 ..     185     220 ..     167     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.1e-09
                    Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmG 86 
                                    +vlvHGl    +  a+   +L+  G avy++D+  h   + +  h  s++++v+Dl  +v+++      +p  ++GhSmG
  gi|121639511|ref|YP_979735.1|  19 LVLVHGLMGRGSTWARQLPWLTLLG-AVYTYDAPWHRGRDVADPHPISTERFVADLGDAVSALG-----APTRMVGHSMG 92 
                                    799*********************9.8*****988877778888888************99888.....7889******* PP

                    Hydrolase_4  87 Gliallyllrypdkvaglil..saPalkikaklkappllk 124
                                    +l +  +++++p+ v++l++  +aP ++ ++  +  p+l+
  gi|121639511|ref|YP_979735.1|  93 ALHSWCLAAERPELVSALVVedMAPDFRGRTTGPWEPWLR 132
                                    *************999***966788888887655445544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                    Hydrolase_4 180 mkrleeraakitlPllllhGeaDkvvdpeasrelyer 216
                                    + + +++  +++ P ll+ ++ D v++p++ r+++er
  gi|121639511|ref|YP_979735.1| 185 TRDYWAQWRAVRSPALLIEAG-DGVTPPGQMRAMAER 220
                                    556777778888898888876.788888888877765 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   8.4e-06      0.03      30      88 ..      54     113 ..      19     148 .. 0.71
   2 ?   -1.6   0.0      0.59   2.1e+03     125     157 ..     206     239 ..     188     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.4e-06
                                    EEC--TS-...-HHHHHHHHHHHHHC-STTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET CS
                  Ser_hydrolase  30 eqadwlkP...dledWvaaleaaveaaeekvvlvAHSlgclavlhaaelqlakkvagalLVa 88 
                                    + +d+ +P     e+ va l  av+a+ +++ +v HS+g+l +  +a  +++ ++  al V 
  gi|121639511|ref|YP_979735.1|  54 RGRDVADPhpiSTERFVADLGDAVSALGAPTRMVGHSMGALHSWCLA--AERPELVSALVVE 113
                                    444444441125799*************************9887777..5555566666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
                                    BTTC-HHHHHHHHH.HCT-EEEEETT-TTSSGGG CS
                  Ser_hydrolase 125 Dpyvsfeeaeelae.awgaelvdlgeaGHinads 157
                                    D + +  + +++ae ++  +   ++ aGH+  d+
  gi|121639511|ref|YP_979735.1| 206 DGVTPPGQMRAMAErDYPTAYLRVPDAGHLVHDE 239
                                    5666667777777525777888899999987765 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   5.7e-05       0.2     117     141 ..      84     108 ..      73     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
                                    EEEEEETHHHHHHHHHHHCSTTTCC CS
                       Esterase 117 ravaGqSmGGlgALilalkhpdrFg 141
                                    +  +G+SmG+l + +la+++p++ +
  gi|121639511|ref|YP_979735.1|  84 TRMVGHSMGALHSWCLAAERPELVS 108
                                    6689******************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1694.28
//
Query:       gi|121639512|ref|YP_979736.1|  [L=105]
Description: hypothetical protein BCG_3657 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-18   65.9   0.1    3.6e-18   65.5   0.1    1.3  1  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1     2e-22   3.6e-18       2      74 ..       3      74 ..       2      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2e-22
                                   EEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHH CS
                            ABM  2 viviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfka 74
                                   v+ i+ i+v+ g+  +++++fa+++ ++ ++ pG+lg++llr+ +++++++v+++Wes +a++a+ + p+  a
  gi|121639512|ref|YP_979736.1|  3 VVKINAIEVPAGAGPELEKRFAHRAHAV-ENSPGFLGFQLLRPVKGEERYFVVTHWESDEAFQAWANGPAIAA 74
                                   7889**********************99.9**************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 736.40
//
Query:       gi|121639513|ref|YP_979737.1|  [L=452]
Description: lipoprotein lpqF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-22   80.1   0.0    3.5e-22   79.0   0.0    1.5  1  Beta-lactamase2  Beta-lactamase enzyme family
    1.1e-18   67.5   0.3    2.7e-18   66.1   0.3    1.8  1  ORF_12_N         ORF 12 gene product N-terminal
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.027   13.9   0.0    1.3  1  Peptidase_S11    D-alanyl-D-alanine carboxypeptidase
       0.13   11.3   0.1       0.21   10.6   0.1    1.2  1  YdfA_immunity    SigmaW regulon antibacterial


Domain annotation for each model (and alignments):
>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   7.7e-26   3.5e-22      12     169 ..     188     391 ..     180     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 7.7e-26
                                    TS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGHHHHTSSSTSGGGSTTSEEEHHHHHHHHHHTT-HHHHHHHHHHH CS
                Beta-lactamase2  12 deefpaaStiKvpillalleavlegklslderltltaedivggsgilqklpgktlslrdlltlmiavSDNtAtnlLidrl 91 
                                     e++p+aS++K+++l al  av+++++s+d+ lt+ta+ ++ gs  l+   g ++s+r+ +++mia SDN At+lLi+rl
  gi|121639513|ref|YP_979737.1| 188 GESLPLASIFKLYVLHALAGAVQHNTVSWDDLLTVTAKSKAVGSSGLELPVGARVSVRTAAEKMIATSDNMATDLLIERL 267
                                    5789********************************99999999889655588*************************** PP

                                    THHHHHHHHHHCTHTTSB--SHTT..............................................CCHHHTTSST CS
                Beta-lactamase2  92 gleavnawlkelglretrlrrklp..............................................dleaadkdkr 125
                                    g  a+++ l+++g ++ +  +++p                                               + a   + +
  gi|121639513|ref|YP_979737.1| 268 GTRAIEEALASAGHHDPASMTPFPtmyelfsvgwgkpdlrdqwkhatqqvraqilrqtnstpyqpdptraHTPASNYGAE 347
                                    **************999988888899999999999999999999999999999999999888888766653334444555 PP

                                    TEE-HHHHHHHHHHHHHTTSSHHHHHHHHHHT-STTTTTTTTTT CS
                Beta-lactamase2 126 ntttardlarllealargellspeelleilsnqqfrdrlaaglp 169
                                     + +a+d  r ++al  + +  ++ +++i+s+    ++ ++ +p
  gi|121639513|ref|YP_979737.1| 348 WYGSAEDICRVHAALRADAVGPASPVRQIMSAVPGIQLDRSVWP 391
                                    69999999999999988877666667888776555554444444 PP

>> ORF_12_N  ORF 12 gene product N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.3   6.1e-22   2.7e-18       2      94 .]      51     138 ..      49     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 6.1e-22
                       ORF_12_N   2 pdtpaGeqarWvldalnsdapiaaeevaerfsaeflaevpaeelaevlaqlraagPftvtsyegvesaavvtlesstgee 81 
                                    ++tp+G +a++++d+lnsd+pi + +v + +++ +++      ++++++ l++++Pf + +++ ++s a+++l ss+g++
  gi|121639513|ref|YP_979737.1|  51 TRTPPGLRAQQTMDMLNSDWPIGEIGVGTLAAPGQVDT-----VKTTMEALWWDRPFALAGVDIGASVAALHLISSYGAQ 125
                                    68***********************************9.....************************************* PP

                       ORF_12_N  82 ldlqlvvdddglI 94 
                                    +d+++++dddg++
  gi|121639513|ref|YP_979737.1| 126 QDIRIHTDDDGWV 138
                                    ***********97 PP

>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.1e-06     0.027      34     109 ..     189     260 ..     183     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-06
                                    S-BE-GGGHHHHHHHHHHHHHHTTSS-TTSEEE--GGGHGCCSGTTSSTTS-TTT-EEEHHHHHHHHHCC--HHHH CS
                  Peptidase_S11  34 evveiASltKlmTaylvlealkkgklkeddkvtisedayalgnnkevsniflkkgskvsvkdLlegllvssgNdAa 109
                                    e ++ AS+ Kl     +  a++++ + +dd +t+ +++ a g    +s + l  g +vsv+   e ++  s+N A+
  gi|121639513|ref|YP_979737.1| 189 ESLPLASIFKLYVLHALAGAVQHNTVSWDDLLTVTAKSKAVG----SSGLELPVGARVSVRTAAEKMIATSDNMAT 260
                                    67899*********************************9999....89999999*******************998 PP

>> YdfA_immunity  SigmaW regulon antibacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   4.6e-05      0.21     128     183 ..     223     282 ..     203     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.6e-05
                  YdfA_immunity 128 tpkvaavakdGiqlkvkarvtvranierlvGgage...etiiarvGe.givttiGsaesh 183
                                    t k +av   G++l v arv vr+  e+++  + +   + +i r+G  +i +++ sa +h
  gi|121639513|ref|YP_979737.1| 223 TAKSKAVGSSGLELPVGARVSVRTAAEKMIATSDNmatDLLIERLGTrAIEEALASAGHH 282
                                    567789************************987542226689999962455566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3006.75
//
Query:       gi|121639514|ref|YP_979738.1|  [L=275]
Description: hypothetical protein BCG_3659 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-13   51.2   0.1    2.1e-13   50.8   0.1    1.2  1  Amidase_2  N-acetylmuramoyl-L-alanine amidase
  ------ inclusion threshold ------
       0.13   12.5   0.3       0.32   11.3   0.3    1.7  1  DUF3618    Protein of unknown function (DUF3618)


Domain annotation for each model (and alignments):
>> Amidase_2  N-acetylmuramoyl-L-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.1   2.4e-17   2.1e-13       3     125 ..      37     172 ..      35     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.4e-17
                                    ESEEEEEEEEBSS.-HHHHHHH.HHHSHHHHTTTS.S..-SEEE-SSSSEEESS-TTCEESSSSS........EHCHHGE CS
                      Amidase_2   3 rpidfiviHhtagssaagalav.aaaeyaastngsig..yhylidkdGtiyqlvdengrawHagd........kggNdns 71 
                                    r+i++++ Hht++s  + a+++ + +++       +g  +++ i   G ++  v   g++wHag+        +++N + 
  gi|121639514|ref|YP_979738.1|  37 RDIRGVMWHHTGNSRET-AKSIaRGRPD------LPGplANLHIAHSGVVTI-V-AVGVCWHAGRgsypwlptDNANWHM 107
                                    689********997554.3333233333......345679********6555.3.589********************** PP

                                    EEEEESSTTE.......EESCHHHHHHHHHHHHHHHHHHHHTEEEGGGEEEHHHH.....TB-TTC CS
                      Amidase_2  72 igIElvgngd.......gkeppteaqyealakLvaallkrygippdrrvvgHsdi.....rktdPg 125
                                    ig+E++            +e++++aq+ ++ +++aal  + g  p+r  +gH+++     +k+dPg
  gi|121639514|ref|YP_979738.1| 108 IGVECAWPTIrrdgsydAGERWPDAQIVSMRDVAAALTLKLGYGPER-NIGHKEYagaaqGKWDPG 172
                                    *******9889******************************999988.559*644456789****9 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   3.5e-05      0.32      16      33 ..     249     266 ..     249     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                        DUF3618  16 aeLaeTvdeLaaradPkr 33 
                                    aeL++ vd+Laa++d ++
  gi|121639514|ref|YP_979738.1| 249 AELGNKVDALAAKLDARE 266
                                    79*************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1977.32
//
Query:       gi|121639515|ref|YP_979739.1|  [L=492]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-36  124.1  19.4    2.2e-36  124.1  19.4    3.7  4  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1  19.4   1.2e-40   2.2e-36       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?  -15.2  17.1         1   1.8e+04      13      35 ..     316     338 ..     302     383 .. 0.55
   3 ?   -5.4   7.4         1   1.8e+04       3      30 ..     365     393 ..     354     407 .. 0.51
   4 ?   -2.9   1.0      0.49   8.8e+03      13      27 ..     422     436 ..     415     454 .. 0.51

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.2e-40
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv+++Pe l+aaa+dla++gs++saanaaa+ ptt+vlaa+aD+VSaaiAalf+ahaq+yq++saqaa+fh+qfvq+l+a
  gi|121639515|ref|YP_979739.1|  1 MSFVIAVPEFLSAAATDLANLGSTISAANAAASIPTTGVLAAGADDVSAAIAALFGAHAQAYQTISAQAATFHAQFVQTLSA 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +ag+Ya+aEaa
  gi|121639515|ref|YP_979739.1| 83 GAGAYANAEAA 93
                                   *********97 PP

  == domain 2  score: -15.2 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  13 aaaadlagigsalsaanaaaaap 35 
                                    a+aa++a+ ++  +aa+a  aap
  gi|121639515|ref|YP_979739.1| 316 ATAAQVASGAQGAKAASAPGAAP 338
                                    44444444444444444433332 PP

  == domain 3  score: -5.4 bits;  conditional E-value: 1
                                    XXXX-HHHHHHHHHHHHHHH.HHHHHHHH CS
                             PE   3 fvvvaPealaaaaadlagig.salsaana 30 
                                     v++aP + aa aa+ a+ + sa   a  
  gi|121639515|ref|YP_979739.1| 365 AVTAAPAETAARAARAARAAcSASPVAPG 393
                                    45555544444333333332033333444 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.49
                                    HHHHHHHHHHHHHHH CS
                             PE  13 aaaadlagigsalsa 27 
                                    a+aa  ++  sal+ 
  gi|121639515|ref|YP_979739.1| 422 AVAATATSASSALKV 436
                                    333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3286.70
//
Query:       gi|121639516|ref|YP_979740.1|  [L=848]
Description: ATP-dependent Clp protease ATP-binding subunit clpC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-52  176.7   0.0    2.9e-50  170.7   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    6.4e-35  119.2   2.0    1.5e-34  118.0   2.0    1.6  1  AAA_lid_9        AAA lid domain
    1.4e-33  114.7  11.2    8.9e-18   64.2   0.6    3.0  2  Clp_N            Clp amino terminal domain, pathogenicity isl
      1e-24   86.4   0.4    3.9e-24   84.5   0.4    2.1  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    7.9e-22   78.1   0.0    6.6e-12   46.0   0.0    2.7  2  AAA              ATPase family associated with various cellul
    6.1e-17   61.9   0.0    1.3e-10   41.4   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    5.5e-13   49.7   2.1    1.9e-06   28.3   0.0    4.2  4  AAA_16           AAA ATPase domain
    2.8e-10   40.2   0.1    2.6e-07   30.5   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-08   35.2   0.1     0.0033   17.7   0.1    4.5  3  AAA_22           AAA domain
    1.2e-07   31.2   6.6    3.3e-07   29.8   6.6    1.8  1  UVR              UvrB/uvrC motif
    1.2e-07   31.3   0.0    0.00011   21.6   0.0    3.8  2  TniB             Bacterial TniB protein
    1.1e-06   28.7   1.8      0.039   13.9   0.1    4.0  3  ATPase_2         ATPase domain predominantly from Archaea
    1.2e-05   25.1   0.0      0.093   12.5   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    2.3e-05   25.0   0.5       0.19   12.3   0.0    3.3  3  AAA_18           AAA domain
    0.00011   22.2   0.0       0.32   10.9   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    0.00011   22.0   0.2        2.1    8.1   0.0    4.4  4  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00027   20.9   0.0       0.28   11.2   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00029   21.2   0.0          1    9.8   0.0    2.7  2  RNA_helicase     RNA helicase
    0.00033   20.4   0.0       0.22   11.2   0.0    2.9  2  AAA_24           AAA domain
     0.0004   20.6   0.3        2.2    8.4   0.0    3.8  4  AAA_33           AAA domain
    0.00083   19.2   0.1       0.57   10.0   0.0    3.1  2  AAA_3            ATPase family associated with various cellul
     0.0014   18.9   0.4        5.5    7.2   0.0    3.6  3  AAA_28           AAA domain
     0.0016   17.9   0.0        5.7    6.3   0.0    3.4  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0017   18.2   0.0        2.2    8.0   0.0    2.7  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0024   17.8   0.0       0.11   12.4   0.0    2.5  2  NACHT            NACHT domain
      0.003   18.1   2.6       0.36   11.3   0.0    3.2  2  AAA_23           AAA domain
     0.0075   16.0   0.0        2.4    8.0   0.0    2.6  2  AAA_29           P-loop containing region of AAA domain
     0.0087   15.2   0.4        2.2    7.4   0.0    3.4  3  DUF815           Protein of unknown function (DUF815)
     0.0089   16.2   0.0        4.5    7.5   0.0    2.8  2  Roc              Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.011   15.8   0.0        6.3    6.8   0.0    4.0  4  ResIII           Type III restriction enzyme, res subunit
      0.012   15.1   0.0        1.9    8.0   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
      0.017   14.7   0.0        2.8    7.5   0.0    2.8  2  AAA_25           AAA domain
      0.024   14.4   0.0        2.6    7.7   0.0    3.4  3  AAA_30           AAA domain
      0.026   14.6   0.0       0.45   10.6   0.0    2.7  3  Torsin           Torsin
      0.029   13.7   0.2        2.9    7.1   0.0    2.9  2  Zeta_toxin       Zeta toxin
      0.029   14.4   0.1        5.9    7.0   0.0    3.4  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.034   14.5   0.5       0.83   10.0   0.2    3.2  2  AAA_19           AAA domain
      0.052   13.4   0.1        8.7    6.2   0.0    3.0  2  NTPase_1         NTPase
      0.061   12.7   0.0        8.6    5.7   0.0    2.5  2  DUF99            Protein of unknown function DUF99
      0.073   12.3   0.0         15    4.7   0.0    2.6  2  TIP49            TIP49 P-loop domain
      0.084   13.4   0.0        6.9    7.2   0.0    2.7  2  ABC_tran         ABC transporter
       0.17   10.5   0.0       0.31    9.7   0.0    1.3  1  PEPCK_ATP        Phosphoenolpyruvate carboxykinase


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.19        80       6      55 ..     212     258 ..     207     297 .. 0.62
   2 !  170.7   0.0   6.8e-53   2.9e-50       1     171 []     544     716 ..     544     716 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHH CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsr 55 
                                      l+g+ gvGkt + + la+ +  + e + + +d + ++   ++ +lv+ 
  gi|121639516|ref|YP_979740.1| 212 PVLIGEPGVGKTAVVEGLAQAIV-HGEVPETLKDKQLYTL--DLGSLVAG 258
                                    5689999*************997.6666666666666665..44554443 PP

  == domain 2  score: 170.7 bits;  conditional E-value: 6.8e-53
                                    -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                          AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                    rp +s++++gp+gvGktel+kala++lf +++++li +d+ e+      + + srl gappgyvg+eegG          
  gi|121639516|ref|YP_979740.1| 544 RPSGSFIFAGPSGVGKTELSKALANFLF-GDDDALIQIDMGEFHD----RFTASRLFGAPPGYVGYEEGGqltekvrrkp 618
                                    6889************************.9***************....******************************* PP

                                    ..EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-S......T CS
                          AAA_2  71 ..ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrsk......e 142
                                      +vl+DEi+K+h+           ++++ LLq+le+g+ltd qgr+vd+kn+++I+t+++g+s+is+    +      e
  gi|121639516|ref|YP_979740.1| 619 fsVVLFDEIEKAHQ-----------EIYNSLLQVLEDGRLTDGQGRTVDFKNTVLIFTSNLGTSDISKPVGLGfskgggE 687
                                    **************...........*******************************************88887******* PP

                                    TTTSGGG--HHHHHHTT--HHHHTT--EE CS
                          AAA_2 143 eeeekkkeeveeelkkglipEllgRlpei 171
                                    +++e +k++v++elkk+++pE+l+R+++i
  gi|121639516|ref|YP_979740.1| 688 NDYERMKQKVNDELKKHFRPEFLNRIDDI 716
                                    **************************976 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   2.0   3.6e-37   1.5e-34       1     102 [.     351     452 ..     351     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 3.6e-37
                      AAA_lid_9   1 seeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklekelak 80 
                                    ++e+tieiL+gl+++ye+hH+v+i+d+a++aa++l++rYi+drflPdkAIDl+Dea+ar+r+++ + p +l+++++++a+
  gi|121639516|ref|YP_979740.1| 351 TVEHTIEILKGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPDLREFDEKIAE 430
                                    5799**************************************************************************** PP

                      AAA_lid_9  81 lekekealekeeekekaerlke 102
                                     ++eke++++++++eka+ l++
  gi|121639516|ref|YP_979740.1| 431 ARREKESAIDAQDFEKAASLRD 452
                                    *****************99986 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.6   2.1e-20   8.9e-18       1      53 []      16      68 ..      16      68 .. 0.99
   2 !   57.0   1.1   3.7e-18   1.6e-15       3      52 ..      93     142 ..      91     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.1e-20
                                   HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
                          Clp_N  1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekllg 53
                                   Aqe+A+ l+h+yi+tEH+Ll+L+ e++G+aa+ L+ +G++l+ +r+++e+++g
  gi|121639516|ref|YP_979740.1| 16 AQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIG 68
                                   9*************************************************997 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 3.7e-18
                                    HHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHH CS
                          Clp_N   3 elAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekll 52 
                                    ++A++lgh+yi+tEH+Ll+L++e++G+aa++L k+G+ l ++r+++ +ll
  gi|121639516|ref|YP_979740.1|  93 REALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLL 142
                                    79********************************************9987 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.4   9.1e-27   3.9e-24       1      81 []     722     802 ..     722     802 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 9.1e-27
                                    SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTSEEE CS
                  ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegdtvr 80 
                                    Lt+ee+ + vdl++ +++ +lk++++ l +td+a++ la++g+dp+ GARpLrr+iqreied+l+e+il++e+ +g+ v+
  gi|121639516|ref|YP_979740.1| 722 LTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQREIEDQLSEKILFEEVGPGQVVT 801
                                    89**************************************************************************9998 PP

                                    E CS
                  ClpB_D2-small  81 v 81 
                                    v
  gi|121639516|ref|YP_979740.1| 802 V 802
                                    6 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.5e-14   6.6e-12       2     111 ..     213     325 ..     212     347 .. 0.81
   2 !   29.2   0.0   2.4e-09     1e-06       2     115 ..     550     673 ..     549     679 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.5e-14
                                    EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGG CS
                            AAA   2 llyGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDEida 69 
                                    +l+G pG+GKT++++ +a+ +          + +++++++ +l+  s y g+ e+++++++ke+ +     ilfiDE++ 
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIvhgevpetlkDKQLYTLDLGSLVagSRYRGDFEERLKKVLKEINTRG-DIILFIDELHT 291
                                    599*****************76665555554478999**999997677****************9997.8********** PP

                                    HHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  70 laksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                    l+++    + e + ++++ L ++l + +        igat+ 
  gi|121639516|ref|YP_979740.1| 292 LVGAG---AAEGAIDAASILKPKLARGEL-----QTIGATTL 325
                                    ****9...888899999999999988877.....36888776 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.4e-09
                                    EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTSTS.EEEEEE CS
                            AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesekkirelfkeakekakp.silfiD 65 
                                    ++ Gp G+GKT l ka+a+ l   +  +++i++ e+ +             yvg  e    +l +++++k  p s++++D
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALANFLfgdDDALIQIDMGEFHDRftasrlfgappgYVGYEEGG--QLTEKVRRK--PfSVVLFD 625
                                    799*****************9765588**********889****999999988866654..455565555..66****** PP

                                    TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.GGGS CS
                            AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.pdkl 115
                                    Ei++ +++             n Ll++l++ +           +++++i ++n   +++
  gi|121639516|ref|YP_979740.1| 626 EIEKAHQEI-----------YNSLLQVLEDGRLTdgqgrtvdFKNTVLIFTSNLgTSDI 673
                                    *****8777...........9*******9999888999999955588999988755555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.7e-06    0.0033       3      75 ..     213     290 ..     211     296 .. 0.73
   2 !   41.4   0.0   3.1e-13   1.3e-10       2     123 ..     549     669 ..     548     677 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.7e-06
                                    EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH...HH--B--.........--------G-SEE.EEESGG CS
                          AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteed...lkgrreikngttslvdsplvraaregeil.vlDEve 75 
                                    +L+G+pG+gK+ ++e la+a+   ev + +  +++ + d   l+ + +++++ +++ +++l++  ++g+i+ ++DE++
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIvHGEVPETLKDKQLYTLDlgsLVAGSRYRGDFEERLKKVLKEINTRGDIIlFIDELH 290
                                    79*******************977777766666666665111455556657777777777777777777642788876 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 3.1e-13
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--............--------..G-SEEEEESGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik...ngttslvdsplvraar..egeilvlDEve 75 
                                    ++  Gp+G+gK+el++ la +l ++    +q+  +   + ++ +r +    +     + + l++++r    +++++DE+e
  gi|121639516|ref|YP_979740.1| 549 FIFAGPSGVGKTELSKALANFLfGDDDALIQIDMGEFHDRFTASRLFGappGYVGYEEGGQLTEKVRrkPFSVVLFDEIE 628
                                    6889*******************77777777777777777777777766645666667789******655589******* PP

                                    G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                          AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                    +a++e+ nsLl++le+ rl  +  g+ v++kn      + +i+t+n  
  gi|121639516|ref|YP_979740.1| 629 KAHQEIYNSLLQVLEDGRLT-DGQGRTVDFKN------TVLIFTSNLG 669
                                    ********************.45555566777......8999999965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   4.5e-09   1.9e-06       2      49 ..     190     234 ..     189     249 .. 0.89
   2 ?    3.6   0.0      0.18        78     117     146 ..     263     291 ..     235     323 .. 0.78
   3 ?   -1.7   0.2       7.5   3.2e+03      89     127 ..     416     458 ..     301     486 .. 0.60
   4 !   14.5   0.0   7.9e-05     0.034       3      51 ..     519     573 ..     517     646 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.5e-09
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellrale 49 
                                    ++GRe+e+e++ ++l+r  ++ p   +l+Ge+GvGK+++v+ l++a+ 
  gi|121639516|ref|YP_979740.1| 190 VIGREKEIERVMQVLSRRTKNNP---VLIGEPGVGKTAVVEGLAQAIV 234
                                    78**************8888766...899************9998775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.18
                         AAA_16 117 srllellkrllallsrderplvlvlDdlqw 146
                                     ++ e lk+ l+ + ++++ ++l++D+l+ 
  gi|121639516|ref|YP_979740.1| 263 GDFEERLKKVLKEINTRGD-IILFIDELHT 291
                                    5678888899977778688.********93 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.5
                         AAA_16  89 aesaeleawrekleeala....avpelagaeasrllellkrll 127
                                    ++  +l++++ek+ ea +    a+++ + ++a +l++  k l+
  gi|121639516|ref|YP_979740.1| 416 TAPPDLREFDEKIAEARRekesAIDAQDFEKAASLRDREKTLV 458
                                    3333333333333333334333444444444455555555555 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 7.9e-05
                         AAA_16   3 vGReeeleqLlsalervrsgrp......elvllsGesGvGKsslvrellralekd 51 
                                    +G e+ ++++  a++r+r+g        ++ ++ G+sGvGK+ l ++l++ l +d
  gi|121639516|ref|YP_979740.1| 519 IGQEDAVKAVSKAIRRTRAGLKdpkrpsGSFIFAGPSGVGKTELSKALANFLFGD 573
                                    7889999999999999999877778889*****************9999876665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0097       4.1       2      44 ..     191     231 ..     190     295 .. 0.76
   2 !   30.5   0.0   6.2e-10   2.6e-07       8     124 ..     532     649 ..     518     674 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0097
                                    ---SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat   2 igesealkelleqikkvaktdlsvlitGesGtGKellaraihe 44 
                                    ig++++++++++ +++ +k + +v + Ge G+GK+ + + + +
  gi|121639516|ref|YP_979740.1| 191 IGREKEIERVMQVLSRRTK-NNPV-LIGEPGVGKTAVVEGLAQ 231
                                    7788888888888877544.3455.56*******999876655 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 6.2e-10
                                    HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE. CS
                Sigma54_activat   8 lkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk. 86 
                                    ++++++ +k   + + s +  G sG+GK+ l++a+ +    ++  +++++++++ ++  +s+LFG   G + G e+  + 
  gi|121639516|ref|YP_979740.1| 532 IRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPG-YVGYEEGGQl 610
                                    333333333333444788999*********************************************999.8888777665 PP

                                    .HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEES CS
                Sigma54_activat  87 .GlfekadgGtlfLDeigelplelQekLlrvlqegever 124
                                      ++++   +++++Dei++   e+ + Ll+vl++g+++ 
  gi|121639516|ref|YP_979740.1| 611 tEKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLEDGRLTD 649
                                    5788899999************************99875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   7.8e-06    0.0033       4     104 ..     208     293 ..     205     320 .. 0.82
   2 !    9.2   0.0    0.0033       1.4       6      29 ..     547     570 ..     543     592 .. 0.88
   3 ?    2.1   0.0      0.51   2.2e+02      81     118 ..     609     644 ..     605     668 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.8e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                    t++  v++Ge+G+GKT +++ l++               v+ ++p+  + k+l++  l  l  +  + r++ ee l+++ 
  gi|121639516|ref|YP_979740.1| 208 TKNNPVLIGEPGVGKTAVVEGLAQAI-------------VHGEVPETLKDKQLYTLDLGSLVAGSRY-RGDFEERLKKVL 273
                                    778889****************9985.............7888888888888877666666655555.799999999999 PP

                         AAA_22  84 qalraravielliiDEaqhlr 104
                                    + +++r++  +l iDE + l 
  gi|121639516|ref|YP_979740.1| 274 KEINTRGD-IILFIDELHTLV 293
                                    99999999.999999999984 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0033
                         AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                    g+ +  G+sG+GKT l + l++ l
  gi|121639516|ref|YP_979740.1| 547 GSFIFAGPSGVGKTELSKALANFL 570
                                    677889*************99976 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.51
                         AAA_22  81 aleqalraravielliiDEaqhlrseealeeLrsllnl 118
                                    +l++ +r++   ++++ DE+++  ++e+++ L + l++
  gi|121639516|ref|YP_979740.1| 609 QLTEKVRRKPF-SVVLFDEIEKA-HQEIYNSLLQVLED 644
                                    78889999999.9**********.99999999776664 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   6.6   7.7e-10   3.3e-07       1      33 [.     425     457 ..     425     460 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.7e-10
                            UVR   1 kklikeLeeemeeAaenedFEkAAklRDqinal 33 
                                    +++i e ++e+e A++++dFEkAA lRD+++ l
  gi|121639516|ref|YP_979740.1| 425 DEKIAEARREKESAIDAQDFEKAASLRDREKTL 457
                                    689**************************9977 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.7e-07   0.00011      22     184 ..     196     347 ..     193     350 .. 0.83
   2 ?    1.8   0.0      0.31   1.3e+02      17      54 ..     529     565 ..     509     570 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-07
                           TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkar 101
                                    ++e+++++ +r   +n +l+G++ +GKt++ve  a+              +++ ++p++ ++k+ly+  L +l a  + r
  gi|121639516|ref|YP_979740.1| 196 EIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQ-------------AIVHGEVPETLKDKQLYTLDLGSLVAGSRYR 262
                                    567778887777778889999999999999987664.............489999*********************9999 PP

                           TniB 102 arvskleqqvlrllrelkvrvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGt.eealralrtDpqlasRF 179
                                     + ++  ++vl+ +++ +  +L iDE+h l+ ag a+    +  +lk    + ++  +++ t +e  + +++D+ l++RF
  gi|121639516|ref|YP_979740.1| 263 GDFEERLKKVLKEINTRGDIILFIDELHTLVgAGAAEGAIDAASILKPKLARGELQTIGATTlDEYRKYIEKDAALERRF 342
                                    99999999998888888889*********9846777777888899997666777777777762567789*********** PP

                           TniB 180 epial 184
                                    +p+++
  gi|121639516|ref|YP_979740.1| 343 QPVQV 347
                                    *9976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                           TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmivek 54 
                                     ++++r ++ l+ pkr    + +++G+s +GKt + + 
  gi|121639516|ref|YP_979740.1| 529 SKAIRRTRAGLKDPKRPS-GSFIFAGPSGVGKTELSKA 565
                                    455566667777777776.789999********99875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   9.2e-05     0.039       4      41 ..     193     230 ..     191     253 .. 0.90
   2 !    7.5   0.0    0.0081       3.4     101     134 ..     264     296 ..     246     361 .. 0.87
   3 ?    3.7   0.0      0.11        49      25      49 ..     550     575 ..     541     646 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-05
                       ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeii 41 
                                    Reke++++ ++l+r +++  ++ G  g+GKta++  ++
  gi|121639516|ref|YP_979740.1| 193 REKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLA 230
                                    ********************************987655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0081
                       ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlg 134
                                    + ++ ++++l++i+ +g  ii++iDel  l+  g
  gi|121639516|ref|YP_979740.1| 264 DFEERLKKVLKEINTRGD-IILFIDELHTLVGAG 296
                                    66889999******9987.*********999444 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.11
                       ATPase_2  25 iY.GpegsGKtaLlkeiienledkdk 49 
                                    i+ Gp g+GKt L k +++ l   d+
  gi|121639516|ref|YP_979740.1| 550 IFaGPSGVGKTELSKALANFLFGDDD 575
                                    5559*********9999987755444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00022     0.093      45     107 ..     207     273 ..     192     293 .. 0.69
   2 !    9.6   0.0    0.0016       0.7      49      69 ..     548     568 ..     531     586 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavr....aglsvlfvrvedLveelkrarrdgklaralkrll 107
                                    ++k+n vl+G +GvGK+ +   l+++ v+    + l+   + + dL + ++  r  g ++++lk++l
  gi|121639516|ref|YP_979740.1| 207 RTKNNPVLIGEPGVGKTAVVEGLAQAIVHgevpETLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVL 273
                                    6899*************97777776665411114555555666777777777777777777776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                      IstB_IS21  49 nivllGpsGvGKshlaialgv 69 
                                    ++++ GpsGvGK+ l+ al+ 
  gi|121639516|ref|YP_979740.1| 548 SFIFAGPSGVGKTELSKALAN 568
                                    6899**************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0047         2       3      44 ..     214     254 ..     213     293 .. 0.66
   2 ?   -1.8   0.3       9.8   4.2e+03      69     112 ..     459     512 ..     421     523 .. 0.60
   3 !   12.3   0.0   0.00044      0.19       2      20 ..     550     568 ..     550     592 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0047
                         AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                    l G pGvGKt + + L++   ++ ++ +++k+++l++ +   
  gi|121639516|ref|YP_979740.1| 214 LIGEPGVGKTAVVEGLAQAI-VHGEVPETLKDKQLYTLDLGS 254
                                    8899************9883.477777777777777766665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.8
                         AAA_18  69 s.......aleegknlvidghlaeleseaakdikk...vvLtaspeelleRlek 112
                                    +        +++g+  v+  +  e + e +  + +   + Lt  + ++l R+e+
  gi|121639516|ref|YP_979740.1| 459 AqraerekQWRSGDLDVVAEVDDEQIAEVLGNWTGipvFKLTEAETTRLLRMEE 512
                                    122333345666777777777777776666666666666666666666666665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00044
                         AAA_18   2 lltGtpGvGKttlakeLsk 20 
                                    + +G++GvGKt+l+k+L++
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALAN 568
                                    579**************86 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0035       1.5      88     122 ..     195     232 ..     177     246 .. 0.71
   2 !   10.9   0.0   0.00076      0.32      77     120 ..     523     567 ..     474     581 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0035
                                    TTHHHHHHHCTT...SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  88 egleelkellkd...ktsvlvGqSGvGKStLinallpe 122
                                    +++e++ ++l+    +  vl+G+ GvGK+++++ l++ 
  gi|121639516|ref|YP_979740.1| 195 KEIERVMQVLSRrtkNNPVLIGEPGVGKTAVVEGLAQA 232
                                    444555555544111567**************999875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00076
                                    SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                     +v +vs+  +++ + lk+  +     +++G+SGvGK+ L +al+
  gi|121639516|ref|YP_979740.1| 523 DAVKAVSKAIRRTRAGLKDPKRPsGSFIFAGPSGVGKTELSKALA 567
                                    5555555555556666665555546789**********9998886 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.06        26      35      56 ..     211     232 ..     186     245 .. 0.75
   2 ?    2.5   0.0      0.26   1.1e+02      77      96 ..     271     292 ..     263     300 .. 0.73
   3 !    8.1   0.0     0.005       2.1       9      55 ..     518     568 ..     510     574 .. 0.73
   4 ?   -0.0   0.0       1.5   6.5e+02      85     113 ..     619     647 ..     609     661 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.06
                         RuvB_N  35 hvllyGpPGlGkttlakiiake 56 
                                      +l+G PG+Gkt++ + +a+ 
  gi|121639516|ref|YP_979740.1| 211 NPVLIGEPGVGKTAVVEGLAQA 232
                                    34688*********98877765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.26
                         RuvB_N  77 alltnleek.d.vlfideihrl 96 
                                     +l++++++ d +lfide+h l
  gi|121639516|ref|YP_979740.1| 271 KVLKEINTRgDiILFIDELHTL 292
                                    56666665324379******98 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.005
                         RuvB_N   9 yigqekvkeklkifieaak....kreealdhvllyGpPGlGkttlakiiak 55 
                                     igqe+  + ++ +i+ ++      +++    +++Gp G+Gkt l+k +a+
  gi|121639516|ref|YP_979740.1| 518 IIGQEDAVKAVSKAIRRTRaglkDPKRPSGSFIFAGPSGVGKTELSKALAN 568
                                    678877777777777655411114466778899**************9998 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.5
                         RuvB_N  85 kdvlfideihrlsraveevlysamedfrl 113
                                      v++ dei + ++++ + l + +ed rl
  gi|121639516|ref|YP_979740.1| 619 FSVVLFDEIEKAHQEIYNSLLQVLEDGRL 647
                                    568899********************876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00065      0.28       4      47 ..     194     237 ..     191     241 .. 0.85
   2 ?    7.1   0.0     0.012       5.1       6      43 ..     524     570 ..     519     576 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00065
                                    HHHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--- CS
                           TsaE   4 eeetealgkklakalgdvilLeGdLGaGKTtlvrglakalgvee 47 
                                    e+e+e++ + l + +++  +L G+ G+GKT+ v gla+a+ + e
  gi|121639516|ref|YP_979740.1| 194 EKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGE 237
                                    6788888888988888899*******************986645 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHCH...TEE.......EEEEESTTSSHHHHHHHHHHHT CS
                           TsaE   6 etealgkklakal...gdv.......ilLeGdLGaGKTtlvrglakal 43 
                                    +++a+ k++ ++    +         +++ G+ G+GKT l+++la+ l
  gi|121639516|ref|YP_979740.1| 524 AVKAVSKAIRRTRaglK-DpkrpsgsFIFAGPSGVGKTELSKALANFL 570
                                    55555555555333331.03444555999**************99865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0024         1       3      36 ..     214     249 ..     213     263 .. 0.77
   2 !    8.3   0.0    0.0069       2.9       2      22 ..     550     570 ..     549     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkkl..klkkkdsvys 36 
                                    l G++g+GK+ +++ La+a+      ++ k++++y+
  gi|121639516|ref|YP_979740.1| 214 LIGEPGVGKTAVVEGLAQAIVHGEvpETLKDKQLYT 249
                                    78*****************99322345555566665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0069
                   RNA_helicase   2 wlyGpsgeGKStlakeLakal 22 
                                    ++ Gpsg+GK+ l+k La+ l
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALANFL 570
                                    689*************99765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.021         9       3      22 ..     210     229 ..     208     292 .. 0.85
   2 !   11.2   0.0   0.00052      0.22       7      86 ..     551     639 ..     547     659 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    ++ +++G++g+GKT ++  l
  gi|121639516|ref|YP_979740.1| 210 NNPVLIGEPGVGKTAVVEGL 229
                                    56699*********998877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00052
                         AAA_24   7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel....................aaelady 66 
                                      Gpsg+GKT l k l  ++lf d ++ l ++d  +f          d +++                     +   +++
  gi|121639516|ref|YP_979740.1| 551 FAGPSGVGKTELSKAL-ANFLFGDDDA-LIQIDMGEFH---------DRFTASrlfgappgyvgyeeggqlteKVRRKPF 619
                                    67**************.*****99888.6666666665.........444444555666666777777777766677788 PP

                         AAA_24  67 ktlviDtideleelclaevi 86 
                                    +++ +D i+++ + + + + 
  gi|121639516|ref|YP_979740.1| 620 SVVLFDEIEKAHQEIYNSLL 639
                                    88888888888776666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.9   3.4e+03      39      74 ..      65     103 ..      44     104 .. 0.81
   2 ?    7.1   0.0     0.013       5.7       4      22 ..     214     232 ..     213     281 .. 0.86
   3 ?   -1.3   0.2       5.3   2.3e+03      54     110 ..     354     421 ..     323     451 .. 0.59
   4 !    8.4   0.0    0.0052       2.2       3      21 ..     550     568 ..     549     597 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.9
                         AAA_33  39 g...tdqqsktdytrvldrlyqilnelarkalsagrnvi 74 
                                    +   ++qq ++  + +++r+++ l+  +r+al+ g n+i
  gi|121639516|ref|YP_979740.1|  65 EiigQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYI 103
                                    4444778888888999999****************9998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                         AAA_33   4 lvGlpGsGKstlaerllkk 22 
                                    l+G pG+GK+ ++e+l+++
  gi|121639516|ref|YP_979740.1| 214 LIGEPGVGKTAVVEGLAQA 232
                                    89**************976 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.3
                         AAA_33  54 rlyqilnelarkalsagrnvildatnlsrrer...........arflklarrlgvpvrivvvetdeet 110
                                    ++++il++l +++ ++ r  i+da ++ +++            ++ + l  ++g++ ri  +++++++
  gi|121639516|ref|YP_979740.1| 354 HTIEILKGLRDRYEAHHRVSITDAAMVAAATLadryindrflpDKAIDLIDEAGARMRIRRMTAPPDL 421
                                    45556666666666666666666665554443333333336667777777777777777666665554 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0052
                         AAA_33   3 llvGlpGsGKstlaerllk 21 
                                    ++ G++G+GK+ l++ l++
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALAN 568
                                    899************9984 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.047        20       4      23 ..     214     233 ..     212     239 .. 0.88
   2 !   10.0   0.0    0.0013      0.57       8     106 ..     555     663 ..     549     671 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.047
                          AAA_3   4 legvPGlaktllvkalakal 23 
                                    l g PG++kt +v+ la+a+
  gi|121639516|ref|YP_979740.1| 214 LIGEPGVGKTAVVEGLAQAI 233
                                    6789*************987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                          AAA_3   8 PGlaktllvkalakal.dlefkriqftpdllPsdilGtevfeekekefefkkGpvfa........nllladeinrappkt 78 
                                     G++kt l kala+ l + +   iq+    +    + +++f +    + +++G  ++        +++l dei++a   +
  gi|121639516|ref|YP_979740.1| 555 SGVGKTELSKALANFLfGDDDALIQIDMGEFHDRFTASRLFGAPPGYVGYEEGGQLTekvrrkpfSVVLFDEIEKAHQEI 634
                                    57777777777776652333344554444444444444444333333333333322211111111699************ PP

                          AAA_3  79 qsalleameerqvtve.gethklpepflv 106
                                      +ll+++e+ ++t + g+t +++++ l+
  gi|121639516|ref|YP_979740.1| 635 YNSLLQVLEDGRLTDGqGRTVDFKNTVLI 663
                                    ************99641566666665554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.022       9.2       3      22 ..     213     232 ..     211     244 .. 0.82
   2 ?    0.4   0.4       1.6   6.8e+02      18      70 ..     384     439 ..     317     464 .. 0.76
   3 ?    7.2   0.0     0.013       5.5       2      21 ..     549     568 ..     548     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                         AAA_28   3 vitGgestGKTtlleaLaar 22 
                                    v++G ++ GKT ++e La+ 
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQA 232
                                    89****************86 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                         AAA_28  18 aLaar..gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa 70 
                                     La+r  + + +p+ a ++++e +a+ +     +  dl +f e++ e+++e+e a 
  gi|121639516|ref|YP_979740.1| 384 TLADRyiNDRFLPDKAIDLIDEAGARMRIRRMTApPDLREFDEKIAEARREKESAI 439
                                    45555334445566666677777766654444444688888888888877777554 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.013
                         AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                    +++ G+++ GKT l++aLa+
  gi|121639516|ref|YP_979740.1| 549 FIFAGPSGVGKTELSKALAN 568
                                    5799**************96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.013       5.7      12      58 ..     198     245 ..     186     264 .. 0.71
   2 ?    5.6   0.0     0.021       9.1      24      46 ..     548     570 ..     516     581 .. 0.85
   3 ?    1.6   0.0      0.36   1.5e+02     109     147 ..     621     658 ..     606     714 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                   Mg_chelatase  12 kralei.aaaGgHnlllvGppGsGKtmlakrlpsllpplseeealeva 58 
                                    +r++++ +   + n +l+G pG GKt + + l++ + + +  e+l+ +
  gi|121639516|ref|YP_979740.1| 198 ERVMQVlSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPETLKDK 245
                                    4555541445667889***********999998877766666666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsll 46 
                                    +++++Gp+G GKt l k+l++ l
  gi|121639516|ref|YP_979740.1| 548 SFIFAGPSGVGKTELSKALANFL 570
                                    689***************99876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.36
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefp 147
                                    v+++DE+ + ++++ ++L + ledg++t   + ++v+f 
  gi|121639516|ref|YP_979740.1| 621 VVLFDEIEKAHQEIYNSLLQVLEDGRLTDG-QGRTVDFK 658
                                    7889*********************98743.34455665 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.012         5      17      47 ..     544     574 ..     526     588 .. 0.88
   2 !    8.0   0.0    0.0052       2.2      97     129 ..     612     644 ..     602     647 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                DNA_pol3_delta2  17 rlahayLfeGdegigkkelalnlakallcee 47 
                                    r + +++f+G++g+gk el ++la+ l+ ++
  gi|121639516|ref|YP_979740.1| 544 RPSGSFIFAGPSGVGKTELSKALANFLFGDD 574
                                    667799*******************999765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0052
                DNA_pol3_delta2  97 rkpreskkkiiiiedaekmtksAaNalLktlEE 129
                                    +k r     +++ +++ek +++  N+lL++lE+
  gi|121639516|ref|YP_979740.1| 612 EKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLED 644
                                    5555666789**********************7 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00027      0.11       4      31 ..     213     240 ..     212     256 .. 0.89
   2 ?    2.6   0.0      0.27   1.2e+02       4      22 ..     550     568 ..     548     576 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                                    EEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT   4 ilqGeaGsGKTtLlqklalawaegklpq 31 
                                    +l Ge+G+GKT+ +++la+a+ +g+ p+
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIVHGEVPE 240
                                    689******************9999887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
                                    EEEC-TTTCHHHHHHHHHH CS
                          NACHT   4 ilqGeaGsGKTtLlqklal 22 
                                    i  G++G+GKT L + la 
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALAN 568
                                    678*********9998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.3      0.13        56      23      55 ..     213     253 ..     208     470 .. 0.67
   2 !   11.3   0.0   0.00083      0.36      19     169 ..     546     788 ..     541     794 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                         AAA_23  23 lItGpNGaGKTTildAiklaL.ygetprlsrks.......g 55 
                                    +++G+ G GKT++++ +  a   ge+p++ +++       g
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIvHGEVPETLKDKqlytldlG 253
                                    678999************99856888777665534444441 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00083
                         AAA_23  19 kgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese..............gkvkayvelt...... 78 
                                    +g +++ Gp G GKT +  A+   L+g+   l   +  g +++ ++ + +              g+  + v+++      
  gi|121639516|ref|YP_979740.1| 546 SGSFIFAGPSGVGKTELSKALANFLFGDDDALIQID-MGEFHDRFTAS-RlfgappgyvgyeegGQLTEKVRRKpfsvvl 623
                                    5899***********************876665544.34444444422.1355566666666765555556666766667 PP

                         AAA_23  79 fenkdgry............trsiererelskkkgkttkkaklellei.........................deleqfi 121
                                    f  + +              +        l++++g+t++++++ l+ +                         +  +q++
  gi|121639516|ref|YP_979740.1| 624 FDEIEKAHqeiynsllqvleD------GRLTDGQGRTVDFKNTVLIFTsnlgtsdiskpvglgfskgggendyERMKQKV 697
                                    444444334445664333330......33444444444333222222212222222223333333344443447777888 PP

                         AAA_23 122 sellgskki......ilnlilflgqerfeefel...........kdkke.............................rl 155
                                    +++l++ ++      i ++i+f++  r+e ++                +                               
  gi|121639516|ref|YP_979740.1| 698 NDELKKHFRpeflnrIDDIIVFHQLTREEIIRMvdlmisrvagqL---KskdmalvltdaakallakrgfdpvlgarpLR 774
                                    888887777887775557777777777544443433443332221...12234444444444444555555555555544 PP

                         AAA_23 156 eelekeleeledek 169
                                    + +++e+e++  ek
  gi|121639516|ref|YP_979740.1| 775 RTIQREIEDQLSEK 788
                                    44555555554444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.044        19      20      44 ..     207     231 ..     199     238 .. 0.78
   2 !    8.0   0.0    0.0056       2.4      21      49 ..     545     573 ..     539     577 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.044
                         AAA_29  20 dlkgatlltGpsGsGKSTllDAiqa 44 
                                    ++k++ +l+G+ G+GK++++  ++ 
  gi|121639516|ref|YP_979740.1| 207 RTKNNPVLIGEPGVGKTAVVEGLAQ 231
                                    4556789***********9987765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0056
                         AAA_29  21 lkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                    ++g+++++GpsG+GK+ l  A++  L ++
  gi|121639516|ref|YP_979740.1| 545 PSGSFIFAGPSGVGKTELSKALANFLFGD 573
                                    67899***********9999998888775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0051       2.2      42      79 ..     198     235 ..     181     289 .. 0.85
   2 ?    3.1   0.0       0.1        43      29      90 ..     517     583 ..     497     589 .. 0.74
   3 ?   -0.2   0.0       1.1   4.6e+02     189     219 ..     716     746 ..     709     762 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                         DUF815  42 enteqfleglpannvLLwGarGtGKSslvkallneyae 79 
                                    e + q l+ ++ nn +L+G+ G+GK ++v  l +++ +
  gi|121639516|ref|YP_979740.1| 198 ERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVH 235
                                    455677888899999***************99998765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                         DUF815  29 dLvgidkqkealventeqfleg.....lpannvLLwGarGtGKSslvkallneyaeegLrlieveke 90 
                                    +++g ++  +a+ + +++  +g     +p+   ++ G  G+GK  l kal n +  +  +li+++  
  gi|121639516|ref|YP_979740.1| 517 RIIGQEDAVKAVSKAIRRTRAGlkdpkRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMG 583
                                    56666666666666555555551112246778999*****************999999999999865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                         DUF815 189 wlgFykldqeeYleiveklakklglelekee 219
                                     + F++l++ee +++v+ +++++  +l++++
  gi|121639516|ref|YP_979740.1| 716 IIVFHQLTREEIIRMVDLMISRVAGQLKSKD 746
                                    589*****************99988777654 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.011       4.5       3      27 ..     213     237 ..     212     250 .. 0.81
   2 ?    5.6   0.0     0.043        18       3      26 ..     550     573 ..     548     590 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                                    EEESSTTSSHHHHHHCHCT-CCC-E CS
                            Roc   3 vlvGdsgvGKtsllkrfvedkfsek 27 
                                    vl+G+ gvGKt  ++ + +  ++ +
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIVHGE 237
                                    79***********999887766655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.043
                                    EEESSTTSSHHHHHHCHCT-CCC- CS
                            Roc   3 vlvGdsgvGKtsllkrfvedkfse 26 
                                    ++ G sgvGKt l k + +  f +
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALANFLFGD 573
                                    688***********9998776644 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.54   2.3e+02      11      47 ..     196     232 ..     189     242 .. 0.77
   2 ?    0.4   0.0       1.3   5.5e+02     129     149 ..     277     297 ..     243     313 .. 0.70
   3 ?    6.8   0.0     0.015       6.3      10      46 ..     530     568 ..     517     577 .. 0.68
   4 ?   -0.4   0.0       2.3   9.8e+02     123     154 ..     609     639 ..     590     648 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.54
                                    HHHHHT......TTSEEEEEESTTSTHHHHHHHHHHH CS
                         ResIII  11 aienlleklkskrdkrglikmaTGtGKTlvaaklier 47 
                                     ie++++ l+ + +++ ++  + G+GKT v   l+++
  gi|121639516|ref|YP_979740.1| 196 EIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQA 232
                                    5677777777666778889999*******98666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                                    HTTT-SEEEEETGGGTTS.TT CS
                         ResIII 129 lrdrfdviiiDEaHrlgakks 149
                                          +++iDE H l ++ +
  gi|121639516|ref|YP_979740.1| 277 NTRGDIILFIDELHTLVGAGA 297
                                    333344899*****9988544 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.015
                                    HHHHHHT.......TTS..EEEEEESTTSTHHHHHHHHHH CS
                         ResIII  10 eaienlleklks.krdk..rglikmaTGtGKTlvaaklie 46 
                                    +ai+++++ lk+ kr     ++++ + G+GKT ++ +l+ 
  gi|121639516|ref|YP_979740.1| 530 KAIRRTRAGLKDpKR-PsgSFIFAGPSGVGKTELSKALAN 568
                                    455555555554433.246889**********99977766 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.3
                                    ....HHHTTT-SEEEEETGGGTTS.TTTHHHH CS
                         ResIII 123 eeseellrdrfdviiiDEaHrlgakkswreil 154
                                    + +e+ +r+ f v+++DE  ++++ + ++++l
  gi|121639516|ref|YP_979740.1| 609 QLTEKVRRKPFSVVLFDEIEKAHQ-EIYNSLL 639
                                    677888999999******877777.5555554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0045       1.9      32      56 ..     208     232 ..     194     243 .. 0.75
   2 ?    4.3   0.0     0.057        25      35      57 ..     548     570 ..     539     595 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                          AAA_7  32 nkkpvllvGptGtGKtviikdllkk 56 
                                     k++ +l+G+ G+GKt++++ l ++
  gi|121639516|ref|YP_979740.1| 208 TKNNPVLIGEPGVGKTAVVEGLAQA 232
                                    45567899***********987765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.057
                          AAA_7  35 pvllvGptGtGKtviikdllkkl 57 
                                    ++++ Gp+G+GKt + k l + l
  gi|121639516|ref|YP_979740.1| 548 SFIFAGPSGVGKTELSKALANFL 570
                                    5789*********9999877665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0066       2.8      37      65 ..     213     240 ..     193     305 .. 0.76
   2 ?    4.0   0.0     0.078        33      32      54 ..     545     567 ..     521     577 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                         AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg 65 
                                    +l+G pg+GKt+++  la a++ G+ +++
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIVHGE-VPE 240
                                    699*******************998.444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.078
                         AAA_25  32 agelallaGapgtGKttlaldla 54 
                                      +  ++aG++g+GKt l   la
  gi|121639516|ref|YP_979740.1| 545 PSGSFIFAGPSGVGKTELSKALA 567
                                    4566799*********9876666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0062       2.6      20      42 ..     211     233 ..     198     242 .. 0.81
   2 ?    2.0   0.0      0.33   1.4e+02      22      40 ..     550     568 ..     544     578 .. 0.86
   3 ?   -2.7   0.0       9.6   4.1e+03      84     114 ..     614     644 ..     604     649 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                         AAA_30  20 vavltGpAGtGKttalkalreaw 42 
                                      vl G +G GKt ++++l++a+
  gi|121639516|ref|YP_979740.1| 211 NPVLIGEPGVGKTAVVEGLAQAI 233
                                    46899**************9987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    +  Gp G GKt + kal++
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALAN 568
                                    778**********999986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.6
                         AAA_30  84 arlepgtllivDEagmvdtkqlaallkaaek 114
                                    +r +p ++++ DE+  + ++  ++ll+ +e+
  gi|121639516|ref|YP_979740.1| 614 VRRKPFSVVLFDEIEKAHQEIYNSLLQVLED 644
                                    3444457777788888777777777777665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.8   1.6e+03      47      77 ..      81     112 ..      72     122 .. 0.77
   2 ?   -1.1   0.0       4.4   1.9e+03      59     111 ..     215     267 ..     205     282 .. 0.71
   3 ?   10.6   0.0    0.0011      0.45      15      79 ..     506     572 ..     499     582 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                                    -SS-SS-EEEEEEE-TTSSHHHH.HHHHHHHH CS
                         Torsin  47 nekpkkpLvlsfhGwtGtGknfv.aeiiaenl 77 
                                    ++++kk L ls+      G n++ +e i   l
  gi|121639516|ref|YP_979740.1|  81 TPRAKKVLELSLREALQLGHNYIgTEHILLGL 112
                                    57899*****************9445555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.4
                                    EE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEHHHHS--GGGHHHHHHHHHH CS
                         Torsin  59 hGwtGtGknfvaeiiaenlyrdGlrsdyvkkfvatadfPkkkkveeykeelke 111
                                     G +G Gk  v e +a+++ +  +  +   k + t d+      ++y+ +++e
  gi|121639516|ref|YP_979740.1| 215 IGEPGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEE 267
                                    5999********99999987766666555555556555555555555555555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0011
                                    -HHHHHHHHHHH--S-HHHHHHHHHHHHHHHT-.SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHST CS
                         Torsin  15 nleeLekdlekklfGqhlvkklvvksvkaylen.ekpkkpL.vlsfhGwtGtGknfvaeiiaenlyr 79 
                                    +l  +e++l+k+++Gq  + k v k+++   +  ++pk+p   + f G +G Gk  +++ +a+ l+ 
  gi|121639516|ref|YP_979740.1| 506 RLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGlKDPKRPSgSFIFAGPSGVGKTELSKALANFLFG 572
                                    6678999********************87655414666664267899***************99985 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.1        44      15      40 ..     208     233 ..     195     241 .. 0.77
   2 ?    7.1   0.0    0.0068       2.9      11      56 ..     540     587 ..     529     602 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdel 40 
                                    ++   +l G pG GK+++ e l++++
  gi|121639516|ref|YP_979740.1| 208 TKNNPVLIGEPGVGKTAVVEGLAQAI 233
                                    44455677***********9999876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0068
                     Zeta_toxin  11 psqerPk.lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                    ++ +rP  + + +G +G GK+el+++l++ l   ++  +++d  ++  
  gi|121639516|ref|YP_979740.1| 540 KDPKRPSgSFIFAGPSGVGKTELSKALANFLFgDDDALIQIDMGEFHD 587
                                    455777635677*****************9987888888998777655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.28   1.2e+02       9      24 ..     219     234 ..     213     242 .. 0.87
   2 ?    7.0   0.0     0.014       5.9       3     110 ..     550     711 ..     549     726 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.28
                                    TSSHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLarala 24 
                                    GvGKT ++ +La+a+ 
  gi|121639516|ref|YP_979740.1| 219 GVGKTAVVEGLAQAIV 234
                                    9************976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                    EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.......................... RF
                           CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep.......................... 54 
                                    i ++ +GvGKT l+ +La  l  +    + +D++      +   l+g  +                              
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTAsrLFGAPPGYVGyeeggqltekvrrkpfsvvlfdeiek 629
                                    677889************99887555555555543322211123333333333355666666666666666666666666 PP

                                    ..........................CCHCCCHHH.HHHCHCHHHH...EEEEEEEEESS...-TTCHHHHHHHHHHC.T CS
                                    ..........................xxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                           CbiA  55 ..........................dlkrllell.ealgkkkall.lkiagvvlnrvdgeneetllkealeelkqry.g 105
                                                              d k  + ++ ++lg++      k++g+++ + +gen ++++k+ + ++++++ +
  gi|121639516|ref|YP_979740.1| 630 ahqeiynsllqvledgrltdgqgrtvDFKNTVLIFtSNLGTS---DiSKPVGLGFSKGGGENDYERMKQKVNDELKKHfR 706
                                    666666666666666666666655555555444443444433...13666666666666666666666666666666666 PP

                                    S-EEE CS
                                    xxxxx RF
                           CbiA 106 vpvlg 110
                                    +++l+
  gi|121639516|ref|YP_979740.1| 707 PEFLN 711
                                    66655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2    0.0019      0.83      10      38 ..     209     237 ..     201     406 .. 0.80
   2 ?    0.4   0.0       1.7   7.3e+02      13      30 ..     549     566 ..     540     579 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0019
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelg 38 
                                    +++ ++++ pG GKT v+++  + +v+ +
  gi|121639516|ref|YP_979740.1| 209 KNNPVLIGEPGVGKTAVVEGLAQAIVHGE 237
                                    5667899************9998887655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                         AAA_19  13 llvtaGpGtGKTrvlkhi 30 
                                    ++  ++ G GKT++ k+ 
  gi|121639516|ref|YP_979740.1| 549 FIFAGPSGVGKTELSKAL 566
                                    4455556*****976655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.02       8.7       4      25 ..     214     235 ..     211     241 .. 0.84
   2 ?    3.8   0.0      0.12        50       2      23 ..     549     570 ..     548     574 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.02
                                    EE--TTSSHHHHHHHHHHHH.. CS
                       NTPase_1   4 iTGppGvGKtTlvkkvlellks 25 
                                    + G+pGvGKt +v+ +++++ +
  gi|121639516|ref|YP_979740.1| 214 LIGEPGVGKTAVVEGLAQAIVH 235
                                    67************99999865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                                    EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                    ++  Gp+GvGKt l k +++ l
  gi|121639516|ref|YP_979740.1| 549 FIFAGPSGVGKTELSKALANFL 570
                                    5678**********99888765 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.064        27     121     173 ..     192     243 ..     172     247 .. 0.85
   2 ?    5.7   0.0      0.02       8.6      89     162 ..     490     569 ..     482     572 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.064
                                    HHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC-SSSSS-HHHH CS
                          DUF99 121 eRlelieklgerieevektgeelyvravGieleeaaklvrkltlegriPEPlR 173
                                     R + ie++ +++  ++++++++ +   G+ ++ + + + + +++g++PE l+
  gi|121639516|ref|YP_979740.1| 192 GREKEIERV-MQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPETLK 243
                                    577888999.66666667799*****************************986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                                    HHH---EEEEESS--.-HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT.........EEEEEESS-HHHHHHHHHHC CS
                          DUF99  89 eetglPviavtreep.dlgklekaLrkhfpdeeeRlelieklgerieevek.....tgeelyvravGieleeaaklvrkl 162
                                    + tg+Pv  +t+ e  +l ++e++L+k++ ++e+ +++++k+++r++   k     +g+ ++    G+ ++e +k++ ++
  gi|121639516|ref|YP_979740.1| 490 NWTGIPVFKLTEAETtRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLKdpkrpSGSFIFAGPSGVGKTELSKALANF 569
                                    679********977615789**********************99998877766665566677777777777777777665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.04        17      54      92 ..     213     251 ..     183     256 .. 0.79
   2 ?    4.7   0.0     0.034        15      21      74 ..     513     570 ..     496     587 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.04
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  54 LlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                    +l G++g Gkta+  ++++++ +     +l+  ++y+l+
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLD 251
                                    467*****************9854444566777777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.034
                                    XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  21 keeeglvGqkkareaagvivel....ikekklaGravLlaGpsgtGktalaiaiskel 74 
                                    + ++ ++Gq++a +a++  ++     +k+ k    + ++aGpsg Gkt l+ a+++ l
  gi|121639516|ref|YP_979740.1| 513 ELHKRIIGQEDAVKAVSKAIRRtragLKDPKRPSGSFIFAGPSGVGKTELSKALANFL 570
                                    456689999999999887666511123444444557889***********99998765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.27   1.1e+02      15      34 ..     213     232 ..     204     275 .. 0.84
   2 ?    7.2   0.0     0.016       6.9      15      46 ..     550     582 ..     544     661 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.27
                                    EEEESTTSSHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllagl 34 
                                    +++Ge G GK+ +++ la+ 
  gi|121639516|ref|YP_979740.1| 213 VLIGEPGVGKTAVVEGLAQA 232
                                    79**********99888765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.016
                                    EEEESTTSSHHHHHHHHTTSS--.SEEEEEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllagllkp.teGeilldg 46 
                                     + G++G GK+ L k+la+ l   +   i++d+
  gi|121639516|ref|YP_979740.1| 550 IFAGPSGVGKTELSKALANFLFGdDDALIQIDM 582
                                    578**************9876551333355555 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00072      0.31     213     243 ..     549     579 ..     537     586 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00072
                                    EEEEE-TTSSHHHHH-BTTB-EEESSEEEE- CS
                      PEPCK_ATP 213 alfFGLSGtGKTtLsadperkligdDehgws 243
                                     +f G SG GKT Ls+   + l gdD+  ++
  gi|121639516|ref|YP_979740.1| 549 FIFAGPSGVGKTELSKALANFLFGDDDALIQ 579
                                    4999**********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.89u 0.29s 00:00:01.18 Elapsed: 00:00:00.45
# Mc/sec: 5693.43
//
Query:       gi|121639517|ref|YP_979741.1|  [L=112]
Description: lsr2 protein precursor [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-43  147.9   0.3    1.1e-43  147.8   0.3    1.0  1  Lsr2      Lsr2
  ------ inclusion threshold ------
      0.076   13.0   0.0       0.13   12.3   0.0    1.2  1  Pou       Pou domain - N-terminal to homeobox domain


Domain annotation for each model (and alignments):
>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   0.3   1.3e-47   1.1e-43       1     110 []       1     111 [.       1     111 [. 0.98

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 1.3e-47
                           Lsr2   1 mArkvvvtlvDDldg.seadetvefgldgveYeiDLseenaeklrdaLapyieaarrvggrkkkrrarrkaaaaasreqa 79 
                                    mA+kv+vtlvDD+dg ++adetvefgldgv+YeiDLs++na+klr  L+++++a+rrvggr+++r+++ + + a +req+
  gi|121639517|ref|YP_979741.1|   1 MAKKVTVTLVDDFDGsGAADETVEFGLDGVTYEIDLSTKNATKLRGDLKQWVAAGRRVGGRRRGRSGSGRGRGAIDREQS 80 
                                    9**************667888*********************************************************** PP

                           Lsr2  80 aaiReWakengievserGripaevieaYeaA 110
                                    aaiReWa++ng++vs+rGripa+vi+aY+aA
  gi|121639517|ref|YP_979741.1|  81 AAIREWARRNGHNVSTRGRIPADVIDAYHAA 111
                                    *****************************98 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05      0.13      50      69 ..      34      53 ..      33      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                            Pou 50 LdlslknmlklkplLekWLe 69
                                    dls kn+ kl+  L++W+ 
  gi|121639517|ref|YP_979741.1| 34 IDLSTKNATKLRGDLKQWVA 53
                                   69****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 826.05
//
Query:       gi|121639518|ref|YP_979742.1|  [L=505]
Description: lysyl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-69  232.0   0.0      1e-68  231.7   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.3e-11   44.3   0.1    2.6e-11   43.4   0.1    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    2.8e-05   23.7   0.2     0.0035   16.9   0.0    2.3  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.7   0.0   1.7e-72     1e-68       1     312 [.     156     499 ..     156     501 .. 0.92

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 1.7e-72
                                    .CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   1 seelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79 
                                    see r+++ry+dl  +++ ++v rlr  v++a+r+ l+++gf+e+etP+L++ +++++ar+F ++s++ + +++ L+++p
  gi|121639518|ref|YP_979742.1| 156 SEESRVRQRYVDLiVRPEARAVARLRIAVVRAIRTALQRRGFLEVETPVLQTLAGGAAARPFATHSNALDIDLY-LRIAP 234
                                    5899*****************************************************************88999.***** PP

                                    HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirr 159
                                    +l+l+++iv+g+d+vf+++r+FR+E  ++++ + EF ++e +  + +++d   v+ eli+++++e++ +  +      + 
  gi|121639518|ref|YP_979742.1| 235 ELFLKRCIVGGFDKVFELNRVFRNEGADSTHSP-EFSMLETYQTYGTYDDSAVVTRELIQEVADEAIGTR-QLP--LPDG 310
                                    *********************************.********************************5444.333..3333 PP

                                    TSEE-SSS-EEEEHHHHHHHHHTS..................................-SS--HHHHHHHHHHS--SEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx..................................xxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 160 nskdlkkpfkrltykeaieklnei..................................gkdldkaderalvkkeknepvf 205
                                       d+  ++  +++  +++ + ++                                  gk +++  er   k + + p+f
  gi|121639518|ref|YP_979742.1| 311 SVYDIDGEWATIQMYPSLSVALGEeitpqttvdrlrgiadslglekdpaihdnrgfghGKLIEELWERTVGK-SLSAPTF 389
                                    44799999********99998777788888888888888888888888888888887766677777777777.99***** PP

                                    EEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH.....SSSGGGGHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 206 vtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld.....eeaeekfswylealeyG 280
                                    v dfP +++p+++++++  + +te++Dl+++g+El++G++++ dp +++e++ ++        +ea+  ++++l aleyG
  gi|121639518|ref|YP_979742.1| 390 VKDFPVQTTPLTRQHRSI-PGVTEKWDLYLRGIELATGYSELSDPVVQRERFADQARAaaagdDEAMVLDEDFLAALEYG 468
                                    *****************9.9***********************************99999999***************** PP

                                    --SEEEEEEEHHHHHHHHCT-SSGGGCSSS-X CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 281 apphgGlglGldRlvmlllgsesIrdviaFPk 312
                                    +pp  G g+G+dRl+m l+g+ sIr++++FP 
  gi|121639518|ref|YP_979742.1| 469 MPPCTGTGMGIDRLLMSLTGL-SIRETVLFPI 499
                                    ********************9.9********6 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   4.3e-15   2.6e-11       3      74 ..      64     139 ..      62     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 4.3e-15
                                    EEEEEEEEEEEEETTEEEEEEEETT.EEEEEEEET.....HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgt.griqvvlfr.....eeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                    vaGrv+    r++gk++f++l+Dg   ++qv++       ++ ++++ +++ Gd+v+v G v ++++gel++ ++ ++
  gi|121639518|ref|YP_979742.1|  64 VAGRVIFA--RNSGKLCFATLQDGDgTQLQVMISLdkvgqAALDAWKADVDLGDIVYVHGAVISSRRGELSVLADCWR 139
                                    9*******..***************669999999999***********************************998765 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.8e-07    0.0035     103     151 ..     248     294 ..     246     306 .. 0.73
   2 !    4.6   0.0    0.0033        20     209     229 ..     470     490 ..     454     496 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-07
                                    EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHH CS
                   tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkk 151
                                    k++ ++rvfR++  D+th++eF  +e     +  + +d  +v +el+++
  gi|121639518|ref|YP_979742.1| 248 KVFELNRVFRNEGADSTHSPEFSMLETYQ--TYGTYDDSAVVTRELIQE 294
                                    7999*******************999753..334455555555555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0033
                                    SEEEEEEEEHHHHHHHHHT-S CS
                   tRNA-synt_2d 209 vsgfafGlGveRlamlkygie 229
                                     ++ + G+G++Rl m  +g++
  gi|121639518|ref|YP_979742.1| 470 PPCTGTGMGIDRLLMSLTGLS 490
                                    578899*********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3689.74
//
Query:       gi|121639519|ref|YP_979743.1|  [L=272]
Description: pantothenate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-55  187.6   0.1    2.9e-55  187.3   0.1    1.1  1  Pan_kinase  Type III pantothenate kinase


Domain annotation for each model (and alignments):
>> Pan_kinase  Type III pantothenate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.1   1.6e-59   2.9e-55       1     206 [.       2     206 ..       2     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 1.6e-59
                                    EEEEEE-SSEEEEEEEETT....CCEETEEEEEEEEESCHHHHHHHHHHCHCCCCEGCEEEEEEESSCHHHHHHHHHHHH CS
                     Pan_kinase   1 lLliDiGNtrikwalfege....ellaswriastaasrtadelaellesllkaagleieaviissVvpaavaalleallk 76 
                                    lL+iD+ Nt+++++l++g     +++++wri +t+++ tadela  + +l+ +++ ++++ +  s+vp++ ++++ +l +
  gi|121639519|ref|YP_979743.1|   2 LLAIDVRNTHTVVGLLSGMkehaKVVQQWRI-RTESEVTADELALTIDGLIGEDSERLTGTAALSTVPSVLHEVRIMLDQ 80 
                                    69**************88777888999****.***********************999********************** PP

                                    HHSS-EEEES.CSSECTCEE-SSSGGGS-HHHHHHHHHHHHHCTTSEEEEEEESSEEEEEEEETTSEEEEEEEEE-HHHH CS
                     Pan_kinase  77 yfkveplvvrssaaklgltngydnpkelGaDRwvaavaarellpgkpllvvdfGTAttfdavsadgeylGGlIaPGlalm 156
                                    y+   p+v+ ++++++g+++ +dnpke+GaDR+v+++aa+ ++ +k+++vvdfG  + +d+vsa+ge+lGG+IaPG++++
  gi|121639519|ref|YP_979743.1|  81 YWPSVPHVLIEPGVRTGIPLLVDNPKEVGADRIVNCLAAYDRF-RKAAIVVDFGSSICVDVVSAKGEFLGGAIAPGVQVS 159
                                    ***99************************************99.78********************************** PP

                                    HHHHHHCSSS----HHCCHHSC.SSSBSSHHHHHHHHHHHHHHHHHHHHH CS
                     Pan_kinase 157 leaLaektakLprvelakpaeaesvigknTveaiqsGilyglagliegii 206
                                     +a a + a L+rvela+p +  sv+gknTve++q+G ++g+agl++g++
  gi|121639519|ref|YP_979743.1| 160 SDAAAARSAALRRVELARP-R--SVVGKNTVECMQAGAVFGFAGLVDGLV 206
                                    *******************.6..8***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1966.06
//
Query:       gi|121639520|ref|YP_979744.1|  [L=139]
Description: aspartate alpha-decarboxylase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-50  170.3   0.1    1.3e-50  170.2   0.1    1.0  1  Asp_decarbox  Aspartate decarboxylase
  ------ inclusion threshold ------
      0.099   12.8   0.1       0.17   12.1   0.1    1.4  1  CDC48_N       Cell division protein 48 (CDC48), N-terminal do


Domain annotation for each model (and alignments):
>> Asp_decarbox  Aspartate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.1   1.4e-54   1.3e-50       1     113 [.       1     113 [.       1     115 [. 0.99

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.4e-54
                                    XEEEEEEEEEEEEEXXEEETTXXXXEEEEHHHHHHCT--TTBEEEEEETTT--EEEEEEEEESTTTT-EEEEGGGGGG-- CS
                   Asp_decarbox   1 mlrtllksKihratvteaelnYeGSitideelleaagileyekvqvvnvnngeRletYvikgergsgviclnGaaarlvq 80 
                                    mlrt+lksKihratvt a+l+Y+GS+tid++l++aa++le+e+v++v+++ng+Rl tY+i+gergsgvi +nGaaa+lv+
  gi|121639520|ref|YP_979744.1|   1 MLRTMLKSKIHRATVTCADLHYVGSVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVH 80 
                                    89****************************************************************************** PP

                                    TT-EEEEEEEEEEEHHHHHH---EEEEE-TTS- CS
                   Asp_decarbox  81 vgdkviiiayaqleeeeakelkpkvvlvdeknr 113
                                    +gd vi+iaya++++++a++++p++v+vd+ n+
  gi|121639520|ref|YP_979744.1|  81 PGDLVILIAYATMDDARARTYQPRIVFVDAYNK 113
                                    ******************************997 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.9e-05      0.17      15      65 ..      24      74 ..      13      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                                   TEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HH CS
                        CDC48_N 15 givridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgv 65
                                   g v id + m++ +l +g+ v+i+   + + +v  a + ++g g+I ++g 
  gi|121639520|ref|YP_979744.1| 24 GSVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGA 74
                                   6799*******************9966677788888888899*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 941.92
//
Query:       gi|121639521|ref|YP_979745.1|  [L=309]
Description: pantoate--beta-alanine ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-91  306.0   0.0    2.1e-91  305.9   0.0    1.0  1  Pantoate_ligase  Pantoate-beta-alanine ligase
  ------ inclusion threshold ------
        2.2    8.6   6.5         56    4.1   5.4    3.1  2  Se-cys_synth_N   Selenocysteine synthase N terminal


Domain annotation for each model (and alignments):
>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.9   0.0   2.3e-95   2.1e-91       8     265 ..      19     283 ..      12     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 305.9 bits;  conditional E-value: 2.3e-95
                                    HHHHHHHHHHHTT-EEEEEEE-SS-GHHHHHHHHHHHHH.SSEEEEEEEEEGGGSSTTSCTTTSEEEHHHHHHHHHHTT- CS
                Pantoate_ligase   8 elrellkelrkegkkvglVpTmGaLHeGHlsLvkaakee.ndvvvvSiFvNplqFgpkedlekYPrtleaDlelleeagv 86 
                                    ++ ++ ++lr +g++v lVpTmGaLHeGHl+Lv+aak+   +vvvvSiFvNp+qFg+ edl++YPrt ++Dl++l+++gv
  gi|121639521|ref|YP_979745.1|  19 DVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVpGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGV 98 
                                    566777788889999*********************99637899************************************ PP

                                    SEEE---HHHHST....EEEEECSGGCSTHHHHSTTHHHHHHHHHHHHHHHHT-SEEEEEGGGHHHHHHHHHHHHHTT-S CS
                Pantoate_ligase  87 dlvFaPsveemyp....ttvevkelsevlegasrpghFrGVatvvtkLfnivqpdrayfGqKDaqqlavirrlvkdlnlp 162
                                    ++ F+P+++ myp    ttv++  l+ +leg  rp+hF GV+tvv kL++iv+pdr++fG+KD+qql++ir+lv+d+nl+
  gi|121639521|ref|YP_979745.1|  99 EIAFTPTTAAMYPdglrTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLD 178
                                    ****************999*999********************************************************* PP

                                    SEEEEEEEEBETTSEBTTGGGGGS-HHHHHHTTHHHHHHHHHH.....BHHHHHHHHHHHHHTHTTEEEEEEEEEETTTS CS
                Pantoate_ligase 163 veivavpivReedgLAlSSRNkyLseeerkaAlvlykaLkaak.....eaealkeaakeeleeeelekadyveivdaetl 237
                                    v +v+vp+vRe+dgLA+SSRN+yL++++r+aA++l++aL+aa+      a+a+ +aa++ l++++   +dy+e++d   l
  gi|121639521|ref|YP_979745.1| 179 VAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAhaataGAQAALDAARAVLDAAPGVAVDYLELRDIG-L 257
                                    *******************************************55433223333667777888887788*******96.5 PP

                                    S..BSSB.SEEEEEEEEEETTEEEEEEE CS
                Pantoate_ligase 238 eeleleeekkavllvaakvgkvrLiDni 265
                                     +++l  + + +llvaa++g++rL+Dni
  gi|121639521|ref|YP_979745.1| 258 GPMPL--NGSGRLLVAARLGTTRLLDNI 283
                                    47664..46689***************8 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.029   2.6e+02      16      26 ..      75      85 ..      47      86 .. 0.84
   2 ?    4.1   5.4    0.0063        56      13      39 ..     216     242 ..     212     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.029
                 Se-cys_synth_N 16 arallaalpRa 26
                                   a+++l+a+pR+
  gi|121639521|ref|YP_979745.1| 75 AGEDLDAYPRT 85
                                   789*******7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0063
                 Se-cys_synth_N  13 alearallaalpRalvrdavrafLdrc 39 
                                    al a+a +a  + ++ +da ra+Ld++
  gi|121639521|ref|YP_979745.1| 216 ALTAAAHAATAGAQAALDAARAVLDAA 242
                                    78899999*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2224.47
//
Query:       gi|121639522|ref|YP_979746.1|  [L=303]
Description: hypothetical protein BCG_3667c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-57  191.8   5.9    3.3e-57  191.8   5.9    2.7  3  Rossmann-like  Rossmann-like domain
    7.1e-38  129.2   1.1    1.2e-37  128.5   1.1    1.4  1  DUF2520        Domain of unknown function (DUF2520)
      2e-05   25.1   1.6    7.2e-05   23.3   0.1    2.4  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8   5.9   5.5e-61   3.3e-57       7     127 .]       8     128 ..       1     128 [. 0.98
   2 ?    0.2   0.0       0.1   6.2e+02      11      29 ..     145     163 ..     133     169 .. 0.80
   3 ?   -2.7   0.2      0.85   5.1e+03      34      34 ..     265     265 ..     235     292 .. 0.56

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 5.5e-61
                  Rossmann-like   7 rsarlsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvk 86 
                                    r+arl+vGiisaGrvGtalg+al+ra+hvvv++sais+asr+ra+rrlPd+pvl+  dvaa aellllav d+el+glv+
  gi|121639522|ref|YP_979746.1|   8 RPARLKVGIISAGRVGTALGVALQRADHVVVACSAISHASRRRAQRRLPDTPVLPPLDVAASAELLLLAVTDSELAGLVS 87 
                                    99****************************************************************************** PP

                  Rossmann-like  87 glaatgavraGtivahtsganGveilaPlteqGalPlaihP 127
                                    glaat+avr+ tivahtsganG++ilaPl++qG++PlaihP
  gi|121639522|ref|YP_979746.1|  88 GLAATSAVRPQTIVAHTSGANGIGILAPLAQQGCIPLAIHP 128
                                    ****************************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                  Rossmann-like  11 lsvGiisaGrvGtalgaal 29 
                                       Gi +a  vG a+g++l
  gi|121639522|ref|YP_979746.1| 145 TCFGITAADDVGYAIGQSL 163
                                    4679***********9987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.85
                  Rossmann-like  34 h 34 
                                    h
  gi|121639522|ref|YP_979746.1| 265 H 265
                                    2 PP

>> DUF2520  Domain of unknown function (DUF2520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   1.1     2e-41   1.2e-37       1     126 [.     145     286 ..     145     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 2e-41
                                    --EEEEE.SCCCHHHHHHHHHCCSS-EEE--HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCT.............T-S- CS
                        DUF2520   1 ipfaieg.deealaiaeelaeelggevvvideedralyHaAavlasNflvtlvalaaellrea.............glde 66 
                                    ++f+i++ d+ ++ai+++l+ e+gge+++++e++r lyHaA+++asN++vt++a+a e+lr+a             +   
  gi|121639522|ref|YP_979746.1| 145 TCFGITAaDDVGYAIGQSLVLEMGGEPFCVREDARILYHAALAHASNHIVTVLADALEALRAAlsggellgqqtvdD--- 221
                                    58*************************************************************99999887664430... PP

                                    ..H.....HHHHHHHHHHHHHHHHHS-HHHH--SCCCCT-HHHHHHHHHT.....HHHHHHCCHCHHH CS
                        DUF2520  67 kda.....akallpLleatlenalkagpkaalTGPvaRgDaetvakhlaal...apelaelYralara 126
                                      +     +++++pL++a+len+l++g+ aalTGPvaRgDa++va hlaal   +  la++Yr  a +
  gi|121639522|ref|YP_979746.1| 222 --QpggivERIVGPLARAALENTLQRGQ-AALTGPVARGDAAAVADHLAALadvDAALAQAYRINALR 286
                                    ..14556699*****************8.********************999889999*****99876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   1.2e-08   7.2e-05       1      85 [.      13      94 ..      13     106 .. 0.82
   2 ?    0.4   0.1      0.17     1e+03      40      65 ..     274     298 ..     240     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC. CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel. 81
                                   k+gii aG++g al   l++a+    ++vva+s   +  +  a++  +++   +  ++a++a+ ++lav  + ++ ++s l 
  gi|121639522|ref|YP_979746.1| 13 KVGIISAGRVGTALGVALQRAD----HVVVACSAISHASRRRAQRRLPDTPVLPPLDVAASAELLLLAVTDSELAGLVSGLa 90
                                   79*******************9....566699987777777777777788888************************99994 PP

                                   GHHH CS
                  F420_oxidored 82 akda 85
                                   a +a
  gi|121639522|ref|YP_979746.1| 91 ATSA 94
                                   3334 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                    HHHHHHHC-EEECECHHHHHHH-SEE CS
                  F420_oxidored  40 eelaeelgvkvtavdneeaaeeadvv 65 
                                    ++la+++ +++   +++ a + advv
  gi|121639522|ref|YP_979746.1| 274 AALAQAYRINALR-TAQRAHAPADVV 298
                                    5789999999999.999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2100.55
//
Query:       gi|121639523|ref|YP_979747.1|  [L=397]
Description: transmembrane protein rich in alanine and arginine and proline [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.021   14.6   4.1      0.041   13.7   4.1    1.5  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.1   2.3e-06     0.041      44     125 ..      21     123 ..      12     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-06
                   Trp_oprn_chp  44 altalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaavelta...... 117
                                    +ltal ++++ a  A++ + ++ +  ++vllal +a+a++ +  l + ++d+++a++++ ++v   + + e++a      
  gi|121639523|ref|YP_979747.1|  21 LLTALLVLAIGASSALVFTDRVELLKLAVLLALWAAVAGAFVSVLYRRQSDVDQARVRDLKLVYDLQLDREISArreyel 100
                                    47899999999***************************999999999999999999999999988888888766666666 PP

                   Trp_oprn_chp 118 ...............wpvlalag 125
                                                   +p++  ++
  gi|121639523|ref|YP_979747.1| 101 tlesqlrrelaselrAPAADEVA 123
                                    66666666666666644444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2830.61
//
Query:       gi|121639524|ref|YP_979748.1|  [L=158]
Description: hypothetical protein BCG_3669c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-39  134.4  22.2    3.1e-39  134.2  22.2    1.0  1  DUF3180        Protein of unknown function (DUF3180)
  ------ inclusion threshold ------
      0.017   14.8   7.7       0.73    9.5   1.6    2.1  2  DUF4131        Domain of unknown function (DUF4131)
      0.018   15.0   1.4      0.025   14.5   1.2    1.4  1  NiFe-hyd_HybE  [NiFe]-hydrogenase assembly, chaperone, HybE
       0.71   10.6   3.6          5    7.9   0.7    2.2  2  PrgI           PrgI family protein


Domain annotation for each model (and alignments):
>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2  22.2     7e-43   3.1e-39       1     134 [.       9     146 ..       9     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 7e-43
                        DUF3180   1 LvaaavvaavagwllvrvsygslpplpwlaavvllvlavvelvlAlqvrrrirgr...pgarqlepltaarllvlAkAsa 77 
                                    L aa+v aa++g+llv v y+++pp++++++++ll++av+e+++A++vr +i +    +g  +l+pl++ar l++AkAsa
  gi|121639524|ref|YP_979748.1|   9 LTAAVVGAAAVGYLLVAVLYRWFPPITVWTGLSLLAVAVAEALWARYVRVKISDGeigDGPGWLHPLVVARSLMVAKASA 88 
                                    78999***********************************************655555555******************* PP

                        DUF3180  78 lvGAllaGvyaGllvyll.ragelpaaaedllaavvavlaavalvvaglwlErlCrvP 134
                                    +vGAl++G+++G+l+y+l r++ l+aaaed++++vva+ +a+alvva+lwl+++C+ P
  gi|121639524|ref|YP_979748.1|  89 WVGALVTGWWIGVLAYFLpRRSWLRAAAEDTTGTVVAAGSALALVVAALWLQHCCKSP 146
                                    ********************************************************99 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.6   0.00016      0.73       6      55 ..      12      59 ..       8      64 .. 0.70
   2 ?    9.1   0.5   0.00021      0.95       4      57 ..      87     151 ..      84     158 .] 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                        DUF4131  6 alvllalllllllllllllrrrprrrvllllllllllallgfalrapqpn 55
                                   a+v  a+++ ll++ l+++   p  +v+++l+ll+++++  +++r+ +  
  gi|121639524|ref|YP_979748.1| 12 AVVGAAAVGYLLVAVLYRW--FPPITVWTGLSLLAVAVAEALWARYVRVK 59
                                   4444455555555555554..899999*********99999999887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00021
                        DUF4131   4 plalvllalllllllllllllrr....rprrrv...........llllllllllallgfalrapqpnan 57 
                                    + ++ +l+++ ++ +l+++l rr    +                  +l+l+ ++++l+ ++ +pq +++
  gi|121639524|ref|YP_979748.1|  87 SAWVGALVTGWWIGVLAYFLPRRswlrA----AaedttgtvvaaGSALALVVAALWLQHCCKSPQDPTE 151
                                    6788889999999999999886544440....1555555544435555555555555555555555555 PP

>> NiFe-hyd_HybE  [NiFe]-hydrogenase assembly, chaperone, HybE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.2   5.5e-06     0.025      39      80 ..      86     127 ..      47     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-06
                  NiFe-hyd_HybE  39 egqwlGvlvTPWflnlvllpgpeedwsalpagekeelelPsg 80 
                                     + w+G+lvT W + ++    p++ w +++a +++   + +g
  gi|121639524|ref|YP_979748.1|  86 ASAWVGALVTGWWIGVLAYFLPRRSWLRAAAEDTTGTVVAAG 127
                                    458**************************9999988777665 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0011         5      24      64 ..      12      53 ..       6      62 .. 0.63
   2 ?    3.4   0.1     0.028   1.3e+02      24      62 ..      92     136 ..      85     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                           PrgI 24 flvlallvaiglylllrafleelasvl.villavPvaalgfy 64
                                    +v+a++v+++l+ +l++++ +++++  + llav va   ++
  gi|121639524|ref|YP_979748.1| 12 AVVGAAAVGYLLVAVLYRWFPPITVWTgLSLLAVAVAEALWA 53
                                   57788889************4444443123334444444454 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.028
                           PrgI  24 flvlallvaiglylllrafl......eelasvlvillavPvaalg 62 
                                     lv +  +++++y+l r++       +++++v++   a+ +++ +
  gi|121639524|ref|YP_979748.1|  92 ALVTGWWIGVLAYFLPRRSWlraaaeDTTGTVVAAGSALALVVAA 136
                                    455555589999999998887777766666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1091.20
//
Query:       gi|121639525|ref|YP_979749.1|  [L=188]
Description: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-29  100.7   0.0    7.9e-29  100.4   0.0    1.1  1  HPPK      7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase


Domain annotation for each model (and alignments):
>> HPPK  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   4.4e-33   7.9e-29       1     112 []       5     139 ..       5     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 4.4e-33
                                    EEEEEE-SSSHHHHHHHHHHHHHHEEEEE---EEE--S...SS-GEEEEEEEEEE.SS-HHHHHHHHHHHHHHTT--C.. CS
                           HPPK   1 ylalGsNlgdreanleealealeekvvkvSslyetepv...dqpdFlNavvevet.elspeellealkeiEkelgrer.. 74 
                                    +l++GsNlgdr a l+++ + l ++++++S++ye++p+   +q +FlNav+ ++  +++p+e+l++ +e E+++gr+r  
  gi|121639525|ref|YP_979749.1|   5 VLSVGSNLGDRLARLRSVADGLGDALIAASPIYEADPWggvEQGQFLNAVLIADDpTCEPREWLRRAEEFERAAGRVRgq 84 
                                    589*******************999*************9888999*******987589*******************776 PP

                                    STS-BS-EEEEEEET.................EEES-TTGGG-HHHHHHHHHHCT CS
                           HPPK  75 rwgpRtlDlDillyg.................ltlPhprlaeraFvlvplaelap 112
                                    rwgpR+lD+D++++                  ltlPhp ++ raFvl p++ ++p
  gi|121639525|ref|YP_979749.1|  85 RWGPRNLDVDLIACYqtsatealvevtarenhLTLPHPLAHLRAFVLIPWIAVDP 139
                                    7************888**********************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1484.75
//
Query:       gi|121639526|ref|YP_979750.1|  [L=133]
Description: dihydroneopterin aldolase folB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-35  120.3   0.2    5.9e-35  120.2   0.2    1.0  1  FolB      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.2   3.3e-39   5.9e-35       1     111 []       5     116 ..       5     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.3e-39
                                    EEEEEEEEEEEESSSHHHHHC-EEEEEEEEEEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHH CS
                           FolB   1 ieikglrvpaiiGvnpeErelkQrvvvdleleldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaeal 80 
                                    ie++gl+v++++Gv+++Er ++Qr+v+d+++++dl++aa+sddl+dt dY +la+++ e+v++ + kl+E++ ++ia+++
  gi|121639526|ref|YP_979750.1|   5 IELRGLTVHGRHGVYDHERVAGQRFVIDVTVWIDLAEAANSDDLADTYDYVRLASRAAEIVAGPPRKLIETVGAEIADHV 84 
                                    79****************************************************************************** PP

                                    HCHSTESEEEEEEEETTSSS.TCESEEEEEEE CS
                           FolB  81 leefpvekvevrveKpnapi.gaadavgveit 111
                                    +++ +v++vev v+Kp+api +++d+v+v i+
  gi|121639526|ref|YP_979750.1|  85 MDDQRVHAVEVAVHKPQAPIpQTFDDVAVVIR 116
                                    **999***************888******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1147.84
//
Query:       gi|121639527|ref|YP_979751.1|  [L=280]
Description: dihydropteroate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-85  286.9   0.1    1.5e-85  286.7   0.1    1.0  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.7   0.1   8.6e-90   1.5e-85       1     244 []       9     255 ..       9     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 286.7 bits;  conditional E-value: 8.6e-90
                                    EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE- CS
                    Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDt 80 
                                    mg+lNvt+dsfsdgg ++dld+a+++  +m ++GA i+D+gges+rPga+rvd++ e +rv+pv+++l+++ ++++siDt
  gi|121639527|ref|YP_979751.1|   9 MGVLNVTDDSFSDGGCYLDLDDAVKHGLAMAAAGAGIVDVGGESSRPGATRVDPAVETSRVIPVVKELAAQ-GITVSIDT 87 
                                    9*********************************************************************9.9******* PP

                                    S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHT CS
                    Pterin_bind  81 tkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeea 160
                                    ++a+va+aAl++ga++vNdvsg+++dp+m +l+aea++++v+mh+r  ++++ +++++y +vv+ev+a l a+v++a++a
  gi|121639527|ref|YP_979751.1|  88 MRADVARAALQNGAQMVNDVSGGRADPAMGPLLAEADVPWVLMHWRAVSADTPHVPVRYGNVVAEVRADLLASVADAVAA 167
                                    ******************************************************************************** PP

                                    T--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHH.CTTC......HGHHHHHHHHHHHHH CS
                    Pterin_bind 161 GvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrll.elgk......aeeRdagtaaflala 233
                                    Gv+p r++lDpg+gf+kt++hn+++l++l+el +a+++pvl+G+Srk+flg+ll           ++ Rd++ta+++ala
  gi|121639527|ref|YP_979751.1| 168 GVDPARLVLDPGLGFAKTAQHNWAILHALPEL-VATGIPVLVGASRKRFLGALLaG--PdgvmrpTDGRDTATAVISALA 244
                                    ********************************.*******************9952..23579999************** PP

                                    HHTT-SEEEES CS
                    Pterin_bind 234 aaaGadivrVh 244
                                    a +Ga+ vrVh
  gi|121639527|ref|YP_979751.1| 245 ALHGAWGVRVH 255
                                    **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.18s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2464.78
//
Query:       gi|121639528|ref|YP_979752.1|  [L=202]
Description: GTP cyclohydrolase I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-76  255.0   0.0    3.2e-76  254.8   0.0    1.0  1  GTP_cyclohydroI  GTP cyclohydrolase I
  ------ inclusion threshold ------
      0.057   13.2   0.0      0.079   12.7   0.0    1.2  1  DUF2785          Protein of unknown function (DUF2785)
      0.095   13.0   0.0       0.15   12.3   0.0    1.4  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.8   0.0   5.3e-80   3.2e-76       2     178 ..      22     199 ..      21     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 254.8 bits;  conditional E-value: 5.3e-80
                                    HHHHHHHHHHTT--TTSTTTTTHHHHHHHHHHHHTGGGGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEE CS
                GTP_cyclohydroI   2 eeavreiLealgedpereglketpkRvakayeelfkgleedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigk 81 
                                    e+avre+L a+gedp+r+gl  tp+Rva+ y+e+f+gl +dp ++vl+++f+e++de+vlvk+i+++S+CeHHl+ f g+
  gi|121639528|ref|YP_979752.1|  22 EAAVRELLYAIGEDPDRDGLVATPSRVARSYREMFAGLYTDP-DSVLNTMFDEDHDELVLVKEIPMYSTCEHHLVAFHGV 100
                                    799***************************************.8************************************ PP

                                    EEEEEE-..TTEEE-HHHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHHHSSTT--TT-EEEEEE CS
                GTP_cyclohydroI  82 ahvaYiP..kkkviGlSklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCmtmrgvkkkesktvtsa 159
                                    ahv+YiP  +++v+GlSk+aR+vd++a+r+qvQErlt+qiadal+++l+p+gv+vvieaehlCm+mrgv+k++s t+tsa
  gi|121639528|ref|YP_979752.1| 101 AHVGYIPgdDGRVTGLSKIARLVDLYAKRPQVQERLTSQIADALMKKLDPRGVIVVIEAEHLCMAMRGVRKPGSVTTTSA 180
                                    *******8779********************************************************************* PP

                                    EEEHHHH-HHHHHHHHHHH CS
                GTP_cyclohydroI 160 lrGefkedaalreefleli 178
                                    +rG fk++aa r+e l+li
  gi|121639528|ref|YP_979752.1| 181 VRGLFKTNAASRAEALDLI 199
                                    **************99986 PP

>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05     0.079      15     125 ..      49     169 ..      40     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                        DUF2785  15 arsFsalllAlileadrrkpflteaeldel..vdalaeylkleqDvRGy.........veekGWaHafahiadlldellk 83 
                                    ars++ ++  l  + d+  + + +++ del  v+++++y   e+ +  +          ++ G +  +++ia l+d  +k
  gi|121639528|ref|YP_979752.1|  49 ARSYREMFAGLYTDPDSVLNTMFDEDHDELvlVKEIPMYSTCEHHLVAFhgvahvgyiPGDDGRVTGLSKIARLVDLYAK 128
                                    79999999999999999988887887777522689999999999988888888888855566****************** PP

                        DUF2785  84 epelkradailllelivkkltrtqsvlaadEdeRlatailal 125
                                     p+++++ + ++ ++++kkl     v +  E e+l++a+  +
  gi|121639528|ref|YP_979752.1| 129 RPQVQERLTSQIADALMKKLDP-RGVIVVIEAEHLCMAMRGV 169
                                    *********************9.7777788999997776554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      55     103 ..     114     162 ..      78     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                         AAA_22  55 dllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhl 103
                                    + l++++r ++l +k+ ++ +e+l +++++al ++ + ++++++ Ea+hl
  gi|121639528|ref|YP_979752.1| 114 TGLSKIARLVDLYAKR-PQVQERLTSQIADALMKKLDpRGVIVVIEAEHL 162
                                    4578999999998888.99999999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1407.20
//
Query:       gi|121639529|ref|YP_979753.1|  [L=760]
Description: membrane-bound protease ftsH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-71  238.6   0.3    7.1e-71  238.0   0.3    1.3  1  Peptidase_M41    Peptidase family M41
    2.4e-46  157.4   0.0    1.5e-45  154.9   0.0    2.2  2  AAA              ATPase family associated with various cellul
    1.5e-10   40.7   0.2    3.3e-10   39.6   0.2    1.6  1  AAA_lid_3        AAA+ lid domain
    3.2e-06   27.5   1.5    0.00011   22.5   1.1    2.5  2  FtsH_ext         FtsH Extracellular
    1.4e-05   25.1   0.0    5.1e-05   23.3   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    4.9e-05   23.8   0.4     0.0015   18.9   0.1    2.6  2  AAA_16           AAA ATPase domain
     0.0002   21.1   0.0    0.00056   19.7   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00028   20.2   0.1    0.00053   19.3   0.1    1.3  1  TIP49            TIP49 P-loop domain
     0.0022   18.3   0.1      0.054   13.8   0.1    2.4  2  AAA_22           AAA domain
     0.0067   16.6   0.0      0.021   15.0   0.0    1.9  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.049   13.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.027   13.9   0.1      0.049   13.0   0.1    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.034   14.1   0.0      0.069   13.2   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.062   13.0   0.0       0.14   11.8   0.0    1.6  1  AAA_24           AAA domain
      0.077   13.2   0.3        0.2   11.9   0.0    1.8  1  AAA_28           AAA domain
      0.092   12.3   0.2       0.49   10.0   0.0    2.3  2  AAA_25           AAA domain
       0.12   12.8   0.4       0.45   10.9   0.0    2.2  2  AAA_17           AAA domain
       0.12   12.5   0.0       0.32   11.1   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.14   11.8   0.0       0.46   10.2   0.0    1.8  1  Sigma54_activat  Sigma-54 interaction domain
       0.15   12.6   0.0       0.36   11.4   0.0    1.7  1  AAA_18           AAA domain
       0.19   12.1   0.1        0.4   11.1   0.1    1.5  1  CttA_N           Cellulose-binding protein CttA N-terminal do
       0.21   12.0   0.0       0.97    9.9   0.0    2.1  2  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0   0.3   8.7e-74   7.1e-71       1     191 []     412     601 ..     412     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 8.7e-74
                                    XX--HHHHHHHHHHHHHHHHHHCCSSS-S-B--EES--TTS-----------TSS--BHHHHHHHHHHHHHHHHHHHHHH CS
                  Peptidase_M41   1 rvisekekklvAyHEaGHalvglllkeadpveKvtiiPRgqalGltlslPeedklsltkeellarlavllGGraaEelif 80 
                                    r+ise+ekk++AyHE+GH+l ++ +++ +p++Kvti++Rg+++G+++++Peedk   t++e++a+l++++GGraaEel+f
  gi|121639529|ref|YP_979753.1| 412 RIISEQEKKITAYHEGGHTLAAWAMPDIEPIYKVTILARGRTGGHAVAVPEEDKGLRTRSEMIAQLVFAMGGRAAEELVF 491
                                    589***************************************************************************** PP

                                    HS-BGGGHHHHHHHHHHHHHHHHTS---TTT-S--------..----.------SS-HHHHHHHHHHHHHHHHHHHHHHH CS
                  Peptidase_M41  81 gevttGasnDlekatkiarkmvtefGmsdklGpvsleeeeeeevflgkelkkekelseetaeeideevkelveeayerak 160
                                     e ttGa +D+e+atkiar+mvtefGms+klG v++ +e++ ++flg+++ ++ ++s+e+a+eideev++l+e+a+++a+
  gi|121639529|ref|YP_979753.1| 492 REPTTGAVSDIEQATKIARSMVTEFGMSSKLGAVKYGSEHG-DPFLGRTMGTQPDYSHEVAREIDEEVRKLIEAAHTEAW 570
                                    **************************************999.89************************************ PP

                                    HHHHHTHHHHHHHHHHHHHHSEE-HHHHHHH CS
                  Peptidase_M41 161 eileekreelealaeaLlekEtldaeeieel 191
                                    eil+e+r+ l++la +LlekEtl++ e+e++
  gi|121639529|ref|YP_979753.1| 571 EILTEYRDVLDTLAGELLEKETLHRPELESI 601
                                    ***************************9876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.1   1.7e+03      23      57 ..      39      73 ..       7      81 .. 0.78
   2 !  154.9   0.0   1.8e-48   1.5e-45       1     131 [.     199     331 ..     199     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                                   THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                            AAA 23 gvefleisgsellskyvgesekkirelfkeakeka 57
                                   +v + +i+g ++ s  + ++e+++r ++k+  ++ 
  gi|121639529|ref|YP_979753.1| 39 SVAITQINGDNVKSAQIDDREQQLRLILKKGNNET 73
                                   5678999999999999*********9999876554 PP

  == domain 2  score: 154.9 bits;  conditional E-value: 1.8e-48
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyGppGtGKTlla+ava e+gv+f++isgs++++++vg +++++r+lf++ak+++ p+i+f+DEida++++r    g+
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAGEAGVPFFTISGSDFVEMFVGVGASRVRDLFEQAKQNS-PCIIFVDEIDAVGRQRgagLGG 277
                                    79******************************************************9.****************999889 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                     ++e+e+++nqLl e+dg+ ++ + vi+i+atnrpd ldpallr gRfdr+i ++
  gi|121639529|ref|YP_979753.1| 278 GHDEREQTLNQLLVEMDGFGDRAG-VILIAATNRPDILDPALLRpGRFDRQIPVS 331
                                    9********************755.**************************9875 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.2     4e-13   3.3e-10       1      39 [.     354     392 ..     354     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4e-13
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeit 39 
                                    d dl+ LA+rT G++GADla++++eAall+ r++ + it
  gi|121639529|ref|YP_979753.1| 354 DADLDGLAKRTVGMTGADLANVINEAALLTARENGTVIT 392
                                    669******************************987766 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.1   1.4e-07   0.00011       5     107 ..      12     105 ..       9     107 .. 0.64
   2 ?    2.6   0.0      0.21   1.7e+02       2      35 ..     116     162 ..     115     180 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-07
                       FtsH_ext   5 lllallllllllslfggsgtgstkeisyseFledleqgnvekvvvqestisalirrptgdgvsttkkgnstttystptlg 84 
                                    ++++++ll+  +++f +  t  +k ++ s  +++++ +nv+++++++ +++     +++ +  ++++ +++  + t +  
  gi|121639529|ref|YP_979753.1|  12 AIAVVVLLGWSFFYF-SDDTRGYKPVDTSVAITQINGDNVKSAQIDDREQQ-----LRLILKKGNNETDGSEKVITKY-- 83 
                                    333444444444444.99****************************88888.....4444444444444444444444.. PP

                       FtsH_ext  85 svesleekLeealkskgvdvess 107
                                      +    +L +al +k+++v+++
  gi|121639529|ref|YP_979753.1|  84 -PTGYAVDLFNALSAKNAKVSTV 105
                                    .3334444777888888777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.21
                       FtsH_ext   2 llwlllallllllllslfg.............gsgtgstkeisyseF 35 
                                    l+++l +lll++l+ +++              ++ ++ +k+++ ++F
  gi|121639529|ref|YP_979753.1| 116 LVYVLPLLLLVGLFVMFSRmqggarmgfgfgkSRAKQLSKDMPKTTF 162
                                    67777777777777777655557777665555555557777777777 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.3e-08   5.1e-05       1     134 [.     198     318 ..     198     321 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.3e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ la+ +a   + +++++ ++++ +    +g  ++           l ++a+  +++i+++DE++ + 
  gi|121639529|ref|YP_979753.1| 198 GVLLYGPPGTGKTLLARAVAGEAGVPFFTISGSDFVEMFVGVGASRV---------RDLFEQAKqnSPCIIFVDEIDAVG 268
                                    59********************************9876666666666.........777778877899*********999 PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHH CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspal 134
                                    ++  + L    +er+  l+++  +++   d    r  + +ia++n++d     l+pal
  gi|121639529|ref|YP_979753.1| 269 RQRGAGLGGGHDEREQTLNQLLVEMDGFGD----RagVILIAATNRPD----ILDPAL 318
                                    999999988888888887777666654332....23488888888888....666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.9e-06    0.0015      19      47 ..     191     219 ..     173     237 .. 0.76
   2 ?    1.6   0.0       0.4   3.3e+02     123     147 ..     244     267 ..     238     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellra 47 
                                    + +  p  vll+G++G+GK+ l+r+++ +
  gi|121639529|ref|YP_979753.1| 191 LGAKIPKGVLLYGPPGTGKTLLARAVAGE 219
                                    44445699****************99854 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.4
                         AAA_16 123 lkrllallsrderplvlvlDdlqwa 147
                                    +++l++++++  +p ++++D+++ +
  gi|121639529|ref|YP_979753.1| 244 VRDLFEQAKQ-NSPCIIFVDEIDAV 267
                                    5666778888.7889*****99954 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.9e-07   0.00056      35      94 ..     198     265 ..     182     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.9e-07
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgP.vlek.....agdlaalltnleekd..vlfideih 94 
                                     vllyGpPG Gkt la+ +a e gv + + sg   +e      a+ +  l+ + +++   ++f+dei 
  gi|121639529|ref|YP_979753.1| 198 GVLLYGPPGTGKTLLARAVAGEAGVPFFTISGSdFVEMfvgvgASRVRDLFEQAKQNSpcIIFVDEID 265
                                    59***********************9998888623443111112222333333333323367777765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.5e-07   0.00053      51      88 ..     197     232 ..     191     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.5e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                    ++vLl Gp+gtGkt la a++ e g  vpf ++sgs++
  gi|121639529|ref|YP_979753.1| 197 KGVLLYGPPGTGKTLLARAVAGEAG--VPFFTISGSDF 232
                                    89*********************98..*********86 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   6.6e-05     0.054       8      29 ..     199     220 ..     196     253 .. 0.80
   2 ?    2.1   0.0      0.26   2.1e+02      85     131 ..     247     308 ..     238     314 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+l+r ++ ++
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAGEA 220
                                    589*************998776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                         AAA_22  85 alrarav..ielliiDEaqhlr..s...........eealeeLrsllnl..srkgvqliLvGtp 131
                                     +++++   + ++ +DE++ +   +           e+ l++L          +   +iL+  +
  gi|121639529|ref|YP_979753.1| 247 LFEQAKQnsPCIIFVDEIDAVGrqRgaglggghderEQTLNQLLVE--MdgFGDRAGVILIAAT 308
                                    33333334557*********97651555666676667777777333..3336666666666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.021       2      39 ..     199     238 ..     199     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                    vll G+pG+GK+ la+ ++ + g  ++++s  ++ ++ +g
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAGEAGvpFFTISGSDFVEMFVG 238
                                    7899******************999999998887766665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-05     0.049      49      71 ..     198     220 ..     193     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                      IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                    +++l Gp+G+GK+ la a++ ea
  gi|121639529|ref|YP_979753.1| 198 GVLLYGPPGTGKTLLARAVAGEA 220
                                    789***************99876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     6e-05     0.049      25      43 ..     199     217 ..     187     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+la++++
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVA 217
                                    89*************9875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.4e-05     0.069       4      46 ..     185     223 ..     182     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                                    HHHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE   4 eeetealgkklakalgdvilLeGdLGaGKTtlvrglakalgve 46 
                                    ++  +alg+k+ k     +lL+G+ G+GKT l+r++a + gv 
  gi|121639529|ref|YP_979753.1| 185 PSRYQALGAKIPK----GVLLYGPPGTGKTLLARAVAGEAGVP 223
                                    5566777777766....8*******************999885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.14       5      22 ..     199     216 ..     196     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g+GKT la+  
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAV 216
                                    89************9987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025       0.2       2      33 ..     199     231 ..     198     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                         AAA_28   2 ivitGgestGKTtlleaLa.argypvvpEaare 33 
                                    + + G+++tGKT l++a a + g+p ++ ++ +
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAgEAGVPFFTISGSD 231
                                    6799***************55599877655555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0006      0.49      36      54 ..     199     217 ..     177     234 .. 0.78
   2 ?   -2.3   0.1       3.3   2.7e+03      60     140 ..     532     608 ..     530     617 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0006
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt la  +a
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVA 217
                                    68**********9986554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                         AAA_25  60 Gkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaai 137
                                    G+p+lg  + +++     v+ E +e e+r+ ++a+++++    ++ ++ + +v + l   ++  ++tl  ++++ + a++
  gi|121639529|ref|YP_979753.1| 532 GDPFLGrTMGTQPDYSHEVAREIDE-EVRKLIEAAHTEA----WEILTEYRDVlDTL-AGELLEKETLHRPELESIFADV 605
                                    5566664444444444445555555.6666666665554....44444444432221.1122234455566667777777 PP

                         AAA_25 138 eev 140
                                    e++
  gi|121639529|ref|YP_979753.1| 606 EKR 608
                                    764 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00055      0.45       1      52 [.     202     254 ..     202     316 .. 0.80
   2 ?   -2.3   0.0       6.7   5.4e+03      41      66 ..     542     567 ..     535     592 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklple 52 
                                    +G+PG GK+ +++ ++ + g+++++  G+ + e+    g+++ rd +++++++
  gi|121639529|ref|YP_979753.1| 202 YGPPGTGKTLLARAVAGEAGVPFFTIsGSDFVEMFVGVGASRVRDLFEQAKQN 254
                                    7*******************999765455566777777776677776666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.7
                                    SSHHHHCTSHHHHHHHHHHHHHHHHH CS
                         AAA_17  41 kardemrklpleekkelqkeaaekia 66 
                                    ++ d+ +++  e+++e++k+++++  
  gi|121639529|ref|YP_979753.1| 542 TQPDYSHEVAREIDEEVRKLIEAAHT 567
                                    56677788888888888888776554 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.32       6      83 ..     199     270 ..     196     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+la+a+a    v    ++ ++  s++ e   +   v    + ++   +a+++   i+++DEid + ++
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAGEAGV----PFFTISGSDFVE---MFVGVGASRV-RDLFEQAKQNSpcIIFVDEIDAVGRQ 270
                                    5789******************98....************...3334444444.4444445555468********99885 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00056      0.46      19      43 ..     193     217 ..     177     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                                    CTSSS-EEEECSTTSSHHHHHHHHH CS
                Sigma54_activat  19 aktdlsvlitGesGtGKellaraih 43 
                                    ak +  vl+ G  GtGK+llara+ 
  gi|121639529|ref|YP_979753.1| 193 AKIPKGVLLYGPPGTGKTLLARAVA 217
                                    567788****************985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00044      0.36       1      24 [.     199     222 ..     199     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf 24 
                                    +ll G+pG+GKt la++++ + g+
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVAGEAGV 222
                                    799*************99876544 PP

>> CttA_N  Cellulose-binding protein CttA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00049       0.4       4      35 ..      24      56 ..      22      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                         CttA_N  4 fYfseddreFnkaqlikviliidttk.keteie 35
                                   fYfs d+r+++  + ++ i+ i+ ++ k  +i+
  gi|121639529|ref|YP_979753.1| 24 FYFSDDTRGYKPVDTSVAITQINGDNvKSAQID 56
                                   9*************8888888865541334555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0012      0.97       1      19 [.     199     217 ..     199     255 .. 0.89
   2 ?   -1.8   0.0       4.9     4e+03      41      61 ..     600     620 ..     575     628 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                   RNA_helicase   1 iwlyGpsgeGKStlakeLa 19 
                                    ++lyGp+g+GK++la+ +a
  gi|121639529|ref|YP_979753.1| 199 VLLYGPPGTGKTLLARAVA 217
                                    689************9866 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                   RNA_helicase  41 ddfwdgYtgqevvvidDfgqv 61 
                                    + f d  +++  +++dDfg +
  gi|121639529|ref|YP_979753.1| 600 SIFADVEKRPRLTMFDDFGGR 620
                                    33445556899999***9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.88u 0.34s 00:00:01.22 Elapsed: 00:00:00.56
# Mc/sec: 4110.86
//
Query:       gi|121639530|ref|YP_979754.1|  [L=217]
Description: hypothetical protein BCG_3675 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-05   23.9  16.9        9.7    6.6   0.2    5.4  5  Kelch_3      Galactose oxidase, central domain


Domain annotation for each model (and alignments):
>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2   0.00054       9.7      30      47 ..      26      43 ..      19      44 .. 0.90
   2 !    6.6   0.2   0.00056        10      30      47 ..      63      80 ..      57      81 .. 0.90
   3 !    6.6   0.2   0.00056        10      30      47 ..     100     117 ..      94     118 .. 0.90
   4 !    6.6   0.2   0.00056        10      30      47 ..     137     154 ..     131     155 .. 0.90
   5 !    6.6   0.2   0.00056        10      30      47 ..     174     191 ..     168     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00054
                        Kelch_3 30 tWaeiaslppaRaghaat 47
                                    W+++++ +++R++ a+t
  gi|121639530|ref|YP_979754.1| 26 AWRQCGPQNGPRRSQAIT 43
                                   6*************9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00056
                        Kelch_3 30 tWaeiaslppaRaghaat 47
                                    W+++++ +++R++ a+t
  gi|121639530|ref|YP_979754.1| 63 AWRQCGPQNGPRRSQAIT 80
                                   6*************9987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00056
                        Kelch_3  30 tWaeiaslppaRaghaat 47 
                                     W+++++ +++R++ a+t
  gi|121639530|ref|YP_979754.1| 100 AWRQCGPQNGPRRSQAIT 117
                                    6*************9987 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.00056
                        Kelch_3  30 tWaeiaslppaRaghaat 47 
                                     W+++++ +++R++ a+t
  gi|121639530|ref|YP_979754.1| 137 AWRQCGPQNGPRRSQAIT 154
                                    6*************9987 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.00056
                        Kelch_3  30 tWaeiaslppaRaghaat 47 
                                     W+++++ +++R++ a+t
  gi|121639530|ref|YP_979754.1| 174 AWRQCGPQNGPRRSQAIT 191
                                    6*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        56  (0.00312343); expected 358.6 (0.02)
Passed bias filter:                       24  (0.00133861); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 1432.62
//
Query:       gi|121639531|ref|YP_979755.1|  [L=109]
Description: hypothetical protein BCG_3676c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 799.19
//
Query:       gi|121639532|ref|YP_979756.1|  [L=53]
Description: hypothetical protein BCG_3677c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       123  (0.00686039); expected 358.6 (0.02)
Passed bias filter:                       90  (0.0050198); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 398.18
//
Query:       gi|121639533|ref|YP_979757.1|  [L=184]
Description: hypothetical protein BCG_3678c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1330.15
//
Query:       gi|121639534|ref|YP_979758.1|  [L=103]
Description: hypothetical protein BCG_3679c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-30  105.8   0.9    1.5e-30  105.6   0.9    1.0  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
      0.004   17.6   0.1     0.0066   16.9   0.1    1.5  1  EspB_PE        ESX-1 secreted protein B PE domain


Domain annotation for each model (and alignments):
>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.9   1.7e-34   1.5e-30       1     100 []       1     100 [.       1     100 [. 0.99

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.7e-34
                  T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkL 80 
                                    mt+nL+V+p++l  la++hd++a +++s v+aaag +++v+ +hGp+c+++nd+++ +++a++a g++l++a+ +La+ L
  gi|121639534|ref|YP_979758.1|   1 MTENLTVQPERLGVLASHHDNAAVDASSGVEAAAGLGESVAITHGPYCSQFNDTLNVYLTAHNALGSSLHTAGVDLAKSL 80 
                                    9******************************************************************************* PP

                  T7SS_ESX_EspC  81 raAAaaYeatDeeaagaldk 100
                                    r AA+ Y+++De++ +a+d+
  gi|121639534|ref|YP_979758.1|  81 RIAAKIYSEADEAWRKAIDG 100
                                    ******************95 PP

>> EspB_PE  ESX-1 secreted protein B PE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   7.4e-07    0.0066      56      77 .]      73      94 ..      53      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-07
                                   HHHHHHHHHHHHHHHHHHHHCH CS
                        EspB_PE 56 rerLAesLrnaAkaYeevDeaa 77
                                   +  LA+sLr aAk Y+e+Dea+
  gi|121639534|ref|YP_979758.1| 73 GVDLAKSLRIAAKIYSEADEAW 94
                                   667*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 736.98
//
Query:       gi|121639535|ref|YP_979759.1|  [L=392]
Description: hypothetical protein BCG_3680c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.6   1.8        4.1    7.7   0.8    2.4  2  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0   0.00066        12      34      74 ..      76     116 ..      68     128 .. 0.91
   2 ?    7.7   0.8   0.00023       4.1       2      55 ..     141     202 ..     139     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00066
                         DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                     +++l +q+ +++++ ++++++++++le+ ++ le v p+ 
  gi|121639535|ref|YP_979759.1|  76 ELADLDRQLISLIHDQANAVQTTRDILEGAKKGLEFVRPVA 116
                                    678999*****************************999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00023
                         DUF948   2 AglIaAiAFvvLviflivvllkl........kktldeaaatieelekqvdpilkevedllak 55 
                                    A++++ +A++ Lv+   +   +l        + ++ ++a+ i ++ + +++il ev + +++
  gi|121639535|ref|YP_979759.1| 141 AMAVVGGALAYLVVKTLINATQLlkllaklaELVAAAIADIISDVADIIKGILGEVWEFITN 202
                                    67788889988888777776666555533333333333444444445555666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2986.24
//
Query:       gi|121639536|ref|YP_979760.1|  [L=171]
Description: lipoprotein lpqG [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-33  115.3   0.3    5.3e-33  115.2   0.3    1.0  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.3     3e-37   5.3e-33      34     200 .]       2     168 ..       1     168 [. 0.89

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 3e-37
                          SIMPL  34 aevaekmnavlealkklgikekdiqtsslslkpeysy..engknkitgyeasqsltvkfrdldklgevldaavka.an.. 108
                                    ++ +++ +av++al  +g+++kdi+t+++++ p+ys+    g+++itgy+a + ++vk++ +d+++++l+ +v+  ++  
  gi|121639536|ref|YP_979760.1|   2 NQTNDRQQAVIDALVGAGLDRKDIRTTRVTVAPQYSNpePAGTATITGYRADNDIEVKIHPTDAASRLLALVVSTgGDat 81 
                                    68999**********779********************99**********************************998887 PP

                          SIMPL 109 eingvsfslsdedelrdeareeAvkdArakAealAkalgvklgkvvsise...sgsnpyappapamaaaaaaaasaatpf 185
                                    +i++vs+s+ d+++l ++ar++A +dA+++A+++A+ +g++lgkv+sise   ++++++ap++p           +a p+
  gi|121639536|ref|YP_979760.1|  82 RISSVSYSIGDDSQLVKDARARAFQDAKNRADQYAQLSGLRLGKVISISEasgAAPTHEAPAPP--------RGLSAVPL 153
                                    8*************************************************64322233333322........3346789* PP

                          SIMPL 186 epgeievtasVtvvf 200
                                    epg+++v  sVtvv+
  gi|121639536|ref|YP_979760.1| 154 EPGQQTVGFSVTVVW 168
                                    *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1352.10
//
Query:       gi|121639537|ref|YP_979761.1|  [L=216]
Description: hypoxanthine-guanine phosphoribosyltransferase hpt [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-18   66.3   0.0    2.8e-18   65.9   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
      0.009   15.5   0.0       0.01   15.3   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   3.2e-22   2.8e-18      25     158 ..      64     197 ..      39     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3.2e-22
                                    E...--GGGEEEEEEETTTHHHHHHHHHHSTT-..EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESS CS
                   Pribosyltran  25 e...yngkpdvvvgiargGvpfakiladeLevp..layvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildt 99 
                                    e     g+  +++++++g+v f+++la+++ vp  + ++ +++y ++ s++ +  + ++  l +d+ g+ VliV+D++d+
  gi|121639537|ref|YP_979761.1|  64 ElsaTTGQDLLLITVLKGAVLFVTDLARAIPVPtqFEFMAVSSYGSSASSSGVVRILKN--LDRDIHGRDVLIVEDVVDS 141
                                    1333467888********************8887788************9999999887..******************* PP

                                    SHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-SEE-T CS
                   Pribosyltran 100 GgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgfelds 158
                                    G Tl    + L +++p ++r+++l++kp+ +      a+++f +    + +vvg++ld+
  gi|121639537|ref|YP_979761.1| 142 GLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFDIP---NDFVVGYGLDY 197
                                    ******************************************888...99999999887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06      0.01      51     168 ..      54     174 ..      16     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                        UPRTase  51 vttplgkeysg.elldeekialVpilRaGegmeealrellpea.rvghlglqr..ee.etlepveyynkLPkkiaertvl 125
                                       ++g+ y +   ++ ++++l+ +l +   ++  l +++p + ++  + +    +  ++   v ++++L ++i+ r vl
  gi|121639537|ref|YP_979761.1|  54 LGEQIGNDYRElSATTGQDLLLITVLKGAVLFVTDLARAIPVPtQFEFMAVSSygSSaSSSGVVRILKNLDRDIHGRDVL 133
                                    5556677776655566678999999999999999999998887655544444411331334557899************* PP

                        UPRTase 126 llDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkr 168
                                    +++ v+ +G ++    + L++r  + ++ +v+++l  + +v++
  gi|121639537|ref|YP_979761.1| 134 IVEDVVDSGLTLSWLSRNLTSR--NPRSLRVCTLLRKPDAVHA 174
                                    *********************5..5689999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1574.11
//
Query:       gi|121639538|ref|YP_979762.1|  [L=323]
Description: cell cycle protein mesJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.9e-29  100.4   0.0    1.3e-28  100.0   0.0    1.2  1  ATP_bind_3  PP-loop family
    4.5e-10   39.9   0.5    4.5e-10   39.9   0.5    2.4  3  TilS        TilS substrate binding domain


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   1.5e-32   1.3e-28       3     181 ..      29     193 ..      27     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.5e-32
                                    EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT.-EEEEEE--HHHCTTSTCCCHHH CS
                     ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckkln.ikleiekvdvakkkgknleeaAR 81 
                                     v++SgG+DS+aL+ ++a+l     +  +a+ vdhgl++ s+  ae+ +  + +l+ ++ ++  v+v++    + e+aAR
  gi|121639538|ref|YP_979762.1|  29 SVGLSGGPDSLALTAVAARL-----WPTTALIVDHGLQPGSATVAETARIQAISLGcVDARVLCVQVGA--AGGREAAAR 101
                                    69****************99.....679**********9998888877666666654788888888776..6999***** PP

                                    HHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT- CS
                     ATP_bind_3  82 elRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvskeeleeylkekki 161
                                     +RY +l+e+        +llAh+ dDqaEt+ll l rgsg +++ag++++        +RPlL v+++  ++ ++e ++
  gi|121639538|ref|YP_979762.1| 102 SARYSALEEHRDG----PVLLAHTLDDQAETVLLGLGRGSGARSIAGMRPYD----PPWCRPLLGVRRSVTHAACRELGL 173
                                    *******997655....59*******************************88....99********************** PP

                                    --B--CGGGCTTSHHHHHHH CS
                     ATP_bind_3 162 kwveDesNadekyeRnriRk 181
                                    +  +D+ N+d++++R r+R+
  gi|121639538|ref|YP_979762.1| 174 TAWQDPHNTDRRFTRTRLRT 193
                                    *******************8 PP

>> TilS  TilS substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       1.2   1.1e+04      40      48 ..       8      15 ..       4      28 .. 0.50
   2 ?   -2.8   0.1       1.1   9.5e+03      14      31 ..     160     177 ..     159     181 .. 0.67
   3 !   39.9   0.5   5.1e-14   4.5e-10       1      57 [.     246     304 ..     246     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                   HHHH.H-S- CS
                           TilS 40 rqlllaaed 48
                                    ql+ aa  
  gi|121639538|ref|YP_979762.1|  8 AQLRAAA-E 15
                                   4444222.2 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHTTTT--H CS
                           TilS  14 qrrlLRrWLaqlglpmps 31 
                                    +r + +++ ++lgl ++ 
  gi|121639538|ref|YP_979762.1| 160 RRSVTHAACRELGLTAWQ 177
                                    677778888888866554 PP

  == domain 3  score: 39.9 bits;  conditional E-value: 5.1e-14
                                    E-HHHHHHS-HHHHHHHHHHHHHHTTTT--HHHHHHH.HHHHH.H-S-SEEEEE-S....T CS
                           TilS   1 LsiaaLaaLsparqrrlLRrWLaqlglpmpsaahLeellrqlllaaedaqpqldlp....g 57 
                                    Ls +aL aL++a +rr++R WL + g+  ++ ++++  +++l+ +a+++q+ ++++    g
  gi|121639538|ref|YP_979762.1| 246 LSTSALTALPDAVRRRVIRGWLLAGGATGLTDRQIRG-VDRLV-TAWRGQGGVAVGstlrG 304
                                    7899*********************************.*****.***********953331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2392.91
//
Query:       gi|121639539|ref|YP_979763.1|  [L=350]
Description: hypothetical protein BCG_3684c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-100  336.1   0.1     3e-100  335.7   0.1    1.1  1  Zincin_2  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.7   0.1  1.7e-104    3e-100       1     332 []      13     346 ..      13     346 .. 0.93

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 1.7e-104
                                    --HHHHHHHHHHHHTGG.GS--S-HHHHHHHHHHHHHHHHHHHHHHHT---SS-.-EEEE--HHHHHHHHHHHHHHTTHH CS
                       Zincin_2   1 VdwdlaarvArrlarag.evdrseaaaavaelreaarlAelwldevtglpaaag.sevevvdraeWveatleswrrllep 78 
                                    Vdw++aa+v++rlar++ + ++++++++ +el+ aa++Ae  +++vtgl a++  ++++vvdr+ W+++++es+r++++ 
  gi|121639539|ref|YP_979763.1|  13 VDWEFAASVGERLARPApPSTEYTRRQVIDELTVAAEKAEPPVRDVTGLIADGVvPPARVVDRPAWIRSAAESMRAMTHG 92 
                                    9*****************99*******************************9999**********************765 PP

                                    HHHHHH---------------HHHHHHHHHHHHHHHHTT--BTTSSH---.---EEEE-HHHHHHHHHHTT--HHHHHHH CS
                       Zincin_2  79 vaeklaealaeelaallrqvggavfgaqvGqalgeLssevlgqtdvglplapegrllLvapnvaaverelevdpedvrlw 158
                                     a+         ++++   ++g+++gaq+G++l++++s +lgq+d++  +a eg llLv pnv aver+l+v+p+d+rlw
  gi|121639539|ref|YP_979763.1|  93 SAK---------PRGF---LTGRITGAQTGAVLAFVASGILGQYDPF-GAAGEGCLLLVYPNVIAVERQLRVEPSDFRLW 159
                                    433.........3444...556*************************.788999************************** PP

                                    HHHHHHHHHHHHHTSTHHHHHHHHHHHHHHT---...-----.---........................--------HH CS
                       Zincin_2 159 valrEaaharlFaavpWLrehllsaveeyargitidtsalle.leealr.......qealeg........gllelvqtpe 222
                                    v+l+E++h+++F+a+pWL  ++++a++ ++ +   d  ++++ l++ +r       +    +        gl+++vq++ 
  gi|121639539|ref|YP_979763.1| 160 VCLHEVTHRVQFTANPWLSGYMSQALNLLTFEPVDDIGRVVSrLADFIRsrghgtdD----SevnpsgilGLVRAVQSEP 235
                                    *****************************9999989999888999988865555442....044456789********** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHH.HHHHHHHHHHHHTT-------SSHHHHHHHHHH CS
                       Zincin_2 223 qraaldrLeallaLlEGwvdvVmdavgpevlpsvaalrerfrrrra.tggpaerllrrllGlelklrqyreaaalvravv 301
                                    qr+ald+L +l +LlEG++++Vmdavgp v+psva++r+rf+ rr+ ++ p++rl+r+llG+++kl+qy++++a+v++vv
  gi|121639539|ref|YP_979763.1| 236 QRKALDQLLVLGTLLEGHAEHVMDAVGPMVVPSVATIRRRFDDRRHhKQPPLQRLVRALLGFDAKLSQYTRGKAFVDHVV 315
                                    *********************************************977778***************************** PP

                                    HHH-HHHHGGGGS-GGGS--HHHHH-HHHHH CS
                       Zincin_2 302 eavGmegrdavWehPdlLPtaeelddpaawv 332
                                    +++Gm+ ++++W++P++LP ++e+++p++w+
  gi|121639539|ref|YP_979763.1| 316 DRAGMKLFNTIWSGPETLPLPAEIENPQRWI 346
                                    ******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2393.88
//
Query:       gi|121639540|ref|YP_979764.1|  [L=461]
Description: hypothetical protein BCG_3685c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.5e-131  437.6   7.5    4.7e-78  262.9   2.2    2.0  2  Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family


Domain annotation for each model (and alignments):
>> Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.4   6.8e-57   1.2e-52       2     163 ..      73     238 ..      72     240 .. 0.98
   2 !  262.9   2.2   2.6e-82   4.7e-78     224     443 ..     238     453 ..     235     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 6.8e-57
                                    HHHHHHHHTTGCGTTSEEEEEEEETTTTEEEEEESTTSEB--GGGHHHHHHHHHHHHT-TT-EEEEEEEESSEEETTEEE CS
                  Peptidase_S13   2 aanldeiladpeLegavagvvvqdaetgkelydhqgdtpllPAStqKllTAaaAlltLganfrftTevvaegtvenrnle 81 
                                    +a+l+ ++ dp+L g+ ag+ ++da tg+el+++ +d+pl+PASt+K+lTAaaAlltL++++r++T+vva+g    +n +
  gi|121639540|ref|YP_979764.1|  73 TAALAVVAVDPDL-GKLAGR-ITDALTGQELWQRLDDVPLVPASTNKILTAAAALLTLDRQARISTRVVAGG----QNPQ 146
                                    68999********.******.*************************************************99....**** PP

                                    SCEEEEECSBTTBBHHH............HHHHHHHHHHTT-SEESS-EEEE-TTC-S-SS-TTSBGGGTTBGGG----S CS
                  Peptidase_S13  82 gnlvlvgsGDPtLsaed............ldalaeelkksGvtkiegelvvDdslfaserlapgwewaDltsgysapiea 149
                                    g++vlvg+GDPtLsa+             + +l+e++++sGvt++  +++vD+s+f+++++apgw++aD+++g++apiea
  gi|121639540|ref|YP_979764.1| 147 GPVVLVGAGDPTLSAAPpgqdtwyhgaarIGDLVEQIRRSGVTPT--AVQVDASAFSGPTMAPGWDPADIDNGDIAPIEA 224
                                    *********************************************..********************************* PP

                                    S-SGGGEEEEEEE- CS
                  Peptidase_S13 150 aiidagvvivevtp 163
                                    a+idag++++++++
  gi|121639540|ref|YP_979764.1| 225 AMIDAGRIQPTTVN 238
                                    **********9986 PP

  == domain 2  score: 262.9 bits;  conditional E-value: 2.6e-82
                                    EEEE-SSHHHHHHHHHHHHHHHTT-EESS-EEEESS-TTSEEEEEEEECEHHHHHHHHHHHT-HHHHHHHHHHHHHHHCS CS
                  Peptidase_S13 224 lslavqdpaayagallkkkLkeqGitvsgevgiaeapesaevlashqSaPLsellkkmmkkSdNliAesllrevakeikr 303
                                     s+++++pa +ag++l+k+L+ +    +++v+ia+ap++a++la++qSaPL+++l++mm++SdN++Ae+++reva++i+r
  gi|121639540|ref|YP_979764.1| 238 NSRRSRTPALDAGRELAKALGLD----PAAVTIASAPAGARQLAVVQSAPLIQRLSQMMNASDNVMAECIGREVAVAINR 313
                                    5899*******************....***************************************************** PP

                                    -BSHHHHHHHHHHHHHHTT--CTTSB-S-SSS-STT-BBEHHHHHHHHHHHH..CTCCHHHHHHCS-BTTTSGGGTTSST CS
                  Peptidase_S13 304 pgsfeagldavrerLskagidtanlvLeDgSGLSrknlvtaktlaqlLeaia..dqpalqalldsLPvAGesGtlenrfk 381
                                    p+sf++++dav++rL++a+idta+++L+D+SGLS +n++ta+tl+++++a+a  dqpal+ lld+LP+AG+sGtl +rf 
  gi|121639540|ref|YP_979764.1| 314 PQSFSGAVDAVTSRLNTAHIDTAGAALVDSSGLSLDNRLTARTLDATMQAAAgpDQPALRPLLDLLPIAGGSGTLGERFL 393
                                    *******************************************************************************9 PP

                                    ..HCTTTTTTTEEEEEEEETTEEEEEEEEESTTSEEEEEEEEEESSSCCCTHHHHHHHHHHHHH CS
                  Peptidase_S13 382 ..ltstpavGkvraKTGsLtgvssLaGyvttasGeklaFsfllngldeedgknirdaldellae 443
                                      +t+++++G++raKTGsLt+++sL+G++t++sG++l+F+f++n    e+g+n+r+a+d+l+++
  gi|121639540|ref|YP_979764.1| 394 daATDQGPAGWLRAKTGSLTAINSLVGVLTDRSGRVLTFAFISN----EAGPNGRNAMDALATK 453
                                    999*****************************************....9***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3295.14
//
Query:       gi|121639541|ref|YP_979765.1|  [L=162]
Description: inorganic pyrophosphatase ppa [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-55  185.2   0.0    7.8e-55  185.0   0.0    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.055   13.2   0.0    1.7  1  InPase           Inorganic Pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0   0.0   8.7e-59   7.8e-55       1     160 []       5     158 ..       5     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 8.7e-59
                                    EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEE CS
                Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGv 80 
                                    v++Eip+g+++Kye+d+e+g++rldr l+t + yp++YGfi++Tl d     DgDPlD+lvl  +p++pg++v ++++G+
  gi|121639541|ref|YP_979765.1|   5 VTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTLGD-----DGDPLDALVLLPQPVFPGVLVAARPVGM 79 
                                    68*********************************************.....**************************** PP

                                    EEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHHHH CS
                Pyrophosphatase  81 lamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeaheryk 160
                                    ++m+De++ DdK+++vp+ dpr+++++di d+p   l++i+hfF +ykdle ++k vk  +w d++eAe+++++++er+k
  gi|121639541|ref|YP_979765.1|  80 FRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAFELDAIKHFFVHYKDLE-PGKFVKAADWVDRAEAEAEVQRSVERFK 158
                                    ***************************************************.77999*******************9975 PP

>> InPase  Inorganic Pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.2e-06     0.055      21      69 ..       3      60 ..       1      87 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-06
                         InPase 21 ldiaiEnpkgseRkG.tdkd.GkeWs.....semk..ahYGyikgtkgaDgdhvDvfl 69
                                   +d++iE pkg   k  +d++ G+        + m+  ++YG i+ t g Dgd +D  +
  gi|121639541|ref|YP_979765.1|  3 FDVTIEIPKGQRNKYeVDHEtGRVRLdrylyTPMAypTDYGFIEDTLGDDGDPLDALV 60
                                   789999999975554134444543221111133433379****************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1137.76
//
Query:       gi|121639542|ref|YP_979766.1|  [L=365]
Description: hypothetical protein BCG_3687c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.8e-143  475.3   7.2   1.2e-142  475.0   7.2    1.1  1  DUF475    Protein of unknown function (DUF475)
    7.3e-18   64.9   9.7    9.5e-16   58.0   9.7    2.5  1  TerC      Integral membrane protein TerC family
  ------ inclusion threshold ------
        1.9    6.5   5.5        4.5    5.3   0.4    2.1  2  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> DUF475  Protein of unknown function (DUF475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.0   7.2  2.1e-146  1.2e-142       1     294 [.      45     355 ..      45     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.0 bits;  conditional E-value: 2.1e-146
                         DUF475   1 fdnavvnaailkklsefWqklfltlGiliavfGmrlvfPlvivavsakldpiealklalek...........kdsyeell 69 
                                    fdna++naail+++s+fWq++flt+GiliavfGmrlvfPl+i++++a+ldp++a++lal++           ++sye+l+
  gi|121639542|ref|YP_979766.1|  45 FDNAIINAAILQRMSPFWQRMFLTIGILIAVFGMRLVFPLAIIWTTAGLDPVRAMELALRPpahgalefadgSPSYEKLI 124
                                    9******************************************************************************* PP

                         DUF475  70 taahpsiaafGgmflllvfldfllddrdikWlkwiekplaklgkldavsvvivlvlllllaallakkaeqrqkvllagll 149
                                    taahp+iaafGgmfll++fldf+++drdikWlkwie p+a++g+l++v v++++v l+l++all+++++qr++vl+agll
  gi|121639542|ref|YP_979766.1| 125 TAAHPQIAAFGGMFLLMLFLDFVVHDRDIKWLKWIEVPFARIGRLGQVPVIVASVGLVLAGALLTHSSDQRGTVLIAGLL 204
                                    ******************************************************************************** PP

                         DUF475 150 glltyllvdglerlfekdeaakaa....avraagkaglalflylevldasfsfdGviGafaitkdivlialGlg.igamf 224
                                    g++tyl+v+g++r+f++++  +a+    a++aagkag+alflylevlda+fsfdGv+Gafait+d+++ialGlg +gamf
  gi|121639542|ref|YP_979766.1| 205 GMVTYLVVNGISRAFRPAGLGEATpgvqARQAAGKAGCALFLYLEVLDAAFSFDGVTGAFAITTDPIIIALGLGvVGAMF 284
                                    *****************99665555668999*******************************************99**** PP

                         DUF475 225 vrsltvylvrkgtldeyvylehGahyaigalavilllsie.ryeipevvtglvGvvfigaslvssvirnrr 294
                                    vrs+t+ylvr++tld+yvylehGah+aigala+illlsi+ r+++pe+vt++vGvvfiga++++sv+rnr 
  gi|121639542|ref|YP_979766.1| 285 VRSITIYLVRQDTLDRYVYLEHGAHWAIGALAIILLLSIDhRFAVPEWVTASVGVVFIGAAFTESVRRNRL 355
                                    ****************************************9****************************95 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   9.7   1.6e-19   9.5e-16       3     179 ..      36     321 ..      34     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.6e-19
                           TerC   3 lvlleivLsiDNlvviallvkklpeeqqkkalllGilgAlv.lRillillavallel....................... 58 
                                    l+lle++Ls+DN+++ a + +++ +  q+  l++Gil+A++ +R+++ l++++  +                        
  gi|121639542|ref|YP_979766.1|  36 LALLEVSLSFDNAIINAAILQRMSPFWQRMFLTIGILIAVFgMRLVFPLAIIWTTAGldpvramelalrppahgalefad 115
                                    789***********************************9744***********99999********************** PP

                           TerC  59 ............fdlilligglfLlytavkellekr.lenklvkeekkkkkktkst........................ 101
                                                 + i ++gg+fLl++ ++ ++++r +  k  k+ +    +  +                         
  gi|121639542|ref|YP_979766.1| 116 gspsyeklitaaHPQIAAFGGMFLLMLFLDFVVHDRdI--KWLKWIEVPFARIGRLgqvpvivasvglvlagallthssd 193
                                    *******988765********************98751..3334433333333333555777777889999999999999 PP

                           TerC 102 ...............................................llavviqielaDlvfslDSvlaavaitsdlfiv 134
                                                                                     a  + +e++D +fs+D v+ a+ait+d++i+
  gi|121639542|ref|YP_979766.1| 194 qrgtvliagllgmvtylvvngisrafrpaglgeatpgvqarqaagkaGCALFLYLEVLDAAFSFDGVTGAFAITTDPIII 273
                                    9999******************************************866677889************************* PP

                           TerC 135 itav.ilsilvlrflaklla..kllerfptlkylalalllligvklvl 179
                                     +++ +++ +++r++  +l+  + l+r+ +l+++a + ++ +++ l+l
  gi|121639542|ref|YP_979766.1| 274 ALGLgVVGAMFVRSITIYLVrqDTLDRYVYLEHGAHWAIGALAIILLL 321
                                    **9658999999998887762269********************9987 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4   0.00076       4.5       5     116 ..      29     159 ..      26     167 .. 0.71
   2 ?    3.7   0.7    0.0023        14     125     226 ..     252     349 ..     247     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00076
                        UPF0182   5 lavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerl......ell...... 72 
                                    +++l+++l+lle+ +++   ++    l+  s f++r+++ ++++++vf + +++ l+ +++++ l      e l      
  gi|121639542|ref|YP_979766.1|  29 ALFLLAVLALLEVSLSFDNAIINAAILQRMSPFWQRMFLTIGILIAVFGMRLVFPLAIIWTTAGLdpvramE-Lalrppa 107
                                    566777788899999999999999999*********************999999888888877664444440.0444444 PP

                        UPF0182  73 .......eklerlre.alekklkllllaialvlsllvglvassqwekvllfl 116
                                           +   ++++ +++ ++++++++  ++l l++ +v+ ++  k+l+++
  gi|121639542|ref|YP_979766.1| 108 hgalefaDGSPSYEKlITAAHPQIAAFGGMFLLMLFLDFVVHDRDIKWLKWI 159
                                    5555556334444440445566777777777777777777777766666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0023
                        UPF0182 125 DpifgkDisFYvFklPflelllslllalvllaliavllvyllsgeslgirlkfaelskaarrhlsvllallllllalsyw 204
                                    D+ f+ D    +F +    ++  l l++v ++++ ++++yl+ +++l    +   +  +  +h ++ + +++lll++++ 
  gi|121639542|ref|YP_979766.1| 252 DAAFSFDGVTGAFAITTDPIIIALGLGVVGAMFVRSITIYLVRQDTL---DR--YVYLEHGAHWAIGALAIILLLSIDHR 326
                                    56666666666677777777888888889999999999999999777...23..45556667777777778888899999 PP

                        UPF0182 205 Ldryellyskrg.vvtGagYtdv 226
                                    ++  e ++++ g v++Ga +t+ 
  gi|121639542|ref|YP_979766.1| 327 FAVPEWVTASVGvVFIGAAFTES 349
                                    9999999998886899****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2499.63
//
Query:       gi|121639543|ref|YP_979767.1|  [L=431]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3107.93
//
Query:       gi|121639544|ref|YP_979768.1|  [L=241]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-25   88.6   0.0    5.6e-25   88.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00013   21.9   0.8     0.0071   16.2   0.1    2.2  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00013   22.4   0.0     0.0002   21.8   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   9.4e-29   5.6e-25       2     133 ..      16     149 ..      15     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 9.4e-29
                                    EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
                Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                    vvip++Ne++ + ++++ +++      +++++vDDgStD+t +i+++      + +++r++ n G+++a+ +g+++a+ +
  gi|121639544|ref|YP_979768.1|  16 VVIPAFNEAAVIGKVVTDVRSV----FDHVVCVDDGSTDGTGDIARRS-----GAHLVRHPINLGQGAAIQTGIEYARKQ 86 
                                    9*********************....**********************.....9************************** PP

                                    ....EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.......E CS
                Glycos_transf_2  82 ....yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.......g 133
                                        +++++D D ++  +++  +v++l ++++dvv+g+r+ +++++   +r+  +       g
  gi|121639544|ref|YP_979768.1|  87 pgaqVFATFDGDGQHRVKDVAAMVDRLGAGDVDVVIGTRFGRPVGKASASRPPLMkrivlqtG 149
                                    ***********************************************9999988755444331 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-06    0.0071       3      77 ..      13      77 ..      11      98 .. 0.72
   2 !    4.7   0.0    0.0039        24      32      76 ..      89     133 ..      80     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                Glyco_tranf_2_3  3 dlavlVptfneedvlgevlesllaqeypr.vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77
                                   d+ v++p+fne++v+g+v++++ +      ++vv v+d+s+++t + a+     +++   ++v+ + nlg +++++
  gi|121639544|ref|YP_979768.1| 13 DVWVVIPAFNEAAVIGKVVTDVRS----VfDHVVCVDDGSTDGTGDIARR----SGA---HLVRHPINLGQGAAIQ 77
                                   588******************998....51555555599*****998875....433...5666666677655554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0039
                Glyco_tranf_2_3  32 vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                     +v+   d++ ++ ++++ +++++l++ +v+vv+ +r +++ gk+
  gi|121639544|ref|YP_979768.1|  89 AQVFATFDGDGQHRVKDVAAMVDRLGAGDVDVVIGTRFGRPVGKA 133
                                    5666666888889899999*****************988888886 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.3e-08    0.0002       2      48 ..      22      66 ..      21     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.3e-08
                Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhv 48
                                   nea++++++++  +++ fd+++++d++stDgt +i ++   + l+++
  gi|121639544|ref|YP_979768.1| 22 NEAAVIGKVVTDVRSV-FDHVVCVDDGSTDGTGDIARRS-GAHLVRH 66
                                   9***************.******************9984.3344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1922.67
//
Query:       gi|121639545|ref|YP_979769.1|  [L=114]
Description: hypothetical protein BCG_3690 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-26   92.6   2.4    1.8e-26   92.4   2.4    1.0  1  DUF2304          Uncharacterized conserved protein (DUF2304)
  ------ inclusion threshold ------
      0.024   14.0   0.1      0.038   13.3   0.1    1.3  1  Sugar_transport  Sugar transport protein
      0.038   14.0   4.0        1.2    9.2   0.1    2.9  3  DUF2269          Predicted integral membrane protein (DUF2269
       0.14   10.7   2.1       0.16   10.5   2.1    1.0  1  ATG22            Vacuole effluxer Atg22 like
       0.19   11.5   6.4        1.9    8.3   0.2    2.1  2  DUF2157          Predicted membrane protein (DUF2157)
       0.21   10.0   3.8      0.072   11.5   0.9    1.6  1  ABC_export       Putative ABC exporter
       0.36   10.5   5.9       0.19   11.4   4.1    1.4  1  DUF4131          Domain of unknown function (DUF4131)
       0.57   10.1   5.9       0.35   10.8   2.0    2.4  3  PLDc_N           Phospholipase_D-nuclease N-terminal
        1.1    9.7   8.4       0.49   10.7   4.2    2.3  3  DUF308           Short repeat of unknown function (DUF308)
        2.3    8.3   6.1         24    5.0   6.1    2.0  1  GWT1             GWT1


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   2.4     1e-29   1.8e-26       1     104 [.       3     106 ..       3     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1e-29
                        DUF2304   1 llqiiliivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilf 80 
                                    ++q++li+ ++ ll++++r++r+++ +++ ++ ++l++l+ i+++l+p+ +tv+an++Gv rgt+l+++++++++ ++++
  gi|121639545|ref|YP_979769.1|   3 WIQVLLIASIIGLLFYLLRSRRSARSRAWVKVGYVLFVLAGIYAVLRPDDTTVVANWFGVRRGTDLMLYALVMAFSFTTL 82 
                                    69****************************************************************************** PP

                        DUF2304  81 slslklskleekikeLaqeiAlle 104
                                    s+++++++le ++ ++a+++Al+ 
  gi|121639545|ref|YP_979769.1|  83 STYMRFKDLELRYARIARALALEG 106
                                    *********************986 PP

>> Sugar_transport  Sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.038     238     279 ..       5      47 ..       2      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                Sugar_transport 238 qlsvvistlggi.llLkekktkkelvlviiGivlilvgavlla 279
                                    q+ ++ s++g + +lL+ +++ ++  +v +G vl++++++  +
  gi|121639545|ref|YP_979769.1|   5 QVLLIASIIGLLfYLLRSRRSARSRAWVKVGYVLFVLAGIYAV 47 
                                    778889999987357899********************99765 PP

>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00068       1.2      12      38 ..       6      32 ..       5      35 .. 0.88
   2 ?    3.6   0.4     0.034        61      76      92 ..      29      45 ..      26      49 .. 0.86
   3 ?    3.1   0.0     0.051        91      83     107 ..      68      92 ..      64     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00068
                        DUF2269 12 vlllgtgigiafyllrasrtrdaavia 38
                                   vll++++ig+ fyllr++r+ + ++ +
  gi|121639545|ref|YP_979769.1|  6 VLLIASIIGLLFYLLRSRRSARSRAWV 32
                                   89*****************99887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.034
                        DUF2269 76 qsWlllslvLyllagal 92
                                     W+ +++vL++lag+ 
  gi|121639545|ref|YP_979769.1| 29 RAWVKVGYVLFVLAGIY 45
                                   68************986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.051
                        DUF2269  83 lvLyllagalwlpVvwlqirlrrla 107
                                    l+Ly+l++a+ ++ ++  +r ++l 
  gi|121639545|ref|YP_979769.1|  68 LMLYALVMAFSFTTLSTYMRFKDLE 92 
                                    689********99999999998875 PP

>> ATG22  Vacuole effluxer Atg22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.1     9e-05      0.16     326     403 ..       6      87 ..       1      89 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9e-05
                          ATG22 326 vaviaavlGaflwplvsrrlnlktkktllaiivlfeliplyGllGii.....lgkiGlkqpwEfyvlavvyglvlgglss 400
                                    v  ia+++G +l++l+ +r +++++ ++ +  vlf+l+ +y++l         + +G++   +++++a+v+ +++  ls+
  gi|121639545|ref|YP_979769.1|   6 VLLIASIIG-LLFYLLRSRRSARSRAWVKVGYVLFVLAGIYAVLRPDdttvvANWFGVRRGTDLMLYALVMAFSFTTLST 84 
                                    567889999.56666666669999*******************943355566999************************* PP

                          ATG22 401 ysR 403
                                    y R
  gi|121639545|ref|YP_979769.1|  85 YMR 87 
                                    *88 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.5    0.0044       7.9      70     108 ..       4      41 ..       1      49 [. 0.64
   2 ?    8.3   0.2    0.0011       1.9      54     100 ..      55     104 ..      52     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0044
                        DUF2157  70 llvllllslllg.avlwrdrrvpprlgeallllaalllga 108
                                    + vll++s+++  ++l+r r  +++ ++a++ ++ +l++ 
  gi|121639545|ref|YP_979769.1|   4 IQVLLIASIIGLlFYLLRSR--RSARSRAWVKVGYVLFVL 41 
                                    6789999999999***9954..344444444444444433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                        DUF2157  54 vAanWqglsrlvkfllllvllllslllg.avlwrdr..rvpprlgealll 100
                                    v anW g+ r + ++l ++++++s+ +   ++  +    +++r+++al+l
  gi|121639545|ref|YP_979769.1|  55 VVANWFGVRRGTDLMLYALVMAFSFTTLsTYMRFKDleLRYARIARALAL 104
                                    779**********************9998888776677558888888876 PP

>> ABC_export  Putative ABC exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9     4e-05     0.072     158     205 ..       5      47 ..       1      62 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                     ABC_export 158 lllialllsvillliYllsskekklkkivkaiivlvlvlllvavvlai 205
                                     +l  l++s+i+ll+Yll s++  +++++ ++ +++ ++l  a ++a+
  gi|121639545|ref|YP_979769.1|   5 QVL--LIASIIGLLFYLLRSRRSARSRAWVKVGYVL-FVL--AGIYAV 47 
                                    444..9****************99998888877775.444..555444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.1    0.0001      0.19       5      52 ..       4      51 ..       2      72 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                        DUF4131  5 lalvllalllllllllllllrrrprrrvlllll.lllllallgfalrap 52
                                   ++++l+a+++ ll++ll   r   r r ++ ++ +l++la+++++lr +
  gi|121639545|ref|YP_979769.1|  4 IQVLLIASIIGLLFYLLRSRR-SARSRAWVKVGyVLFVLAGIYAVLRPD 51
                                   456666666666666666554.555555555550556677777777655 PP

>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0    0.0002      0.35      22      39 ..       3      20 ..       2      23 .. 0.94
   2 ?    0.7   0.2      0.29   5.2e+02      14      27 ..      23      41 ..      19      45 .. 0.57
   3 ?   -1.4   0.0       1.3   2.3e+03       2      15 ..      38      50 ..      37      56 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                         PLDc_N 22 WllvilflPvlGailYll 39
                                   W+ v+l+  ++G+++Yll
  gi|121639545|ref|YP_979769.1|  3 WIQVLLIASIIGLLFYLL 20
                                   *****************8 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                         PLDc_N 14 rnpss.....klaWllvil 27
                                   r++++     k+  +l++l
  gi|121639545|ref|YP_979769.1| 23 RRSARsrawvKVGYVLFVL 41
                                   3333324567777777776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                         PLDc_N  2 lwiialidiirdrn 15
                                   l ++a i+ ++ r+
  gi|121639545|ref|YP_979769.1| 38 LFVLAGIYAVL-RP 50
                                   66677777666.44 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.2   0.00027      0.49      31      72 ..       6      47 ..       5      48 .. 0.77
   2 ?    7.5   0.3    0.0028       5.1       4      25 ..      37      58 ..      36      62 .. 0.86
   3 ?   -0.6   0.1      0.93   1.7e+03      12      26 ..      71      85 ..      67      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                         DUF308 31 lllvsGivqiiaaf.aarkknrggrwlglllGilyliaGllll 72
                                   +ll+++i++++ ++ ++r++ r++ w++ +  +l+++aG++++
  gi|121639545|ref|YP_979769.1|  6 VLLIASIIGLLFYLlRSRRSARSRAWVK-VGYVLFVLAGIYAV 47
                                   5889999999877746666666666655.5**********986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                         DUF308  4 illivlGilalllPvaallalv 25
                                   +l++++Gi+a+l P+ ++++  
  gi|121639545|ref|YP_979769.1| 37 VLFVLAGIYAVLRPDDTTVVAN 58
                                   89************99998754 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.93
                         DUF308 12 lalllPvaallalvl 26
                                   +al++ + +++ +++
  gi|121639545|ref|YP_979769.1| 71 YALVMAFSFTTLSTY 85
                                   677777777777777 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.1     0.014        24      55      96 ..       5      45 ..       1     108 [. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                           GWT1 55 ikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnl 96
                                   + ll++si+ l l++ll++  +  SR  + ++Yvl+v+a   
  gi|121639545|ref|YP_979769.1|  5 QVLLIASIIGL-LFYLLRSRRSARSRAWVKVGYVLFVLAGIY 45
                                   34444444444.446777777778888888888888887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 885.11
//
Query:       gi|121639546|ref|YP_979770.1|  [L=291]
Description: hypothetical protein BCG_3691 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-38  130.8   0.0      1e-37  130.5   0.0    1.1  1  PhyH            Phytanoyl-CoA dioxygenase (PhyH)
  ------ inclusion threshold ------
      0.045   14.2   0.0      0.072   13.5   0.0    1.3  1  2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
      0.083   12.6   0.0       0.16   11.7   0.0    1.4  1  Cupin_2         Cupin domain


Domain annotation for each model (and alignments):
>> PhyH  Phytanoyl-CoA dioxygenase (PhyH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.0   1.7e-41     1e-37       2     211 .]      15     213 ..      14     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1.7e-41
                                    HHHSEEEETTSS-HHHHHHHHHHHHHHHHHCHTTCCSEEEEECEEESTTCCCEE...CCCHHCHHHHTTH.......HHH CS
                           PhyH   2 eedGylviegflsaeevealraeiealldralesgdkidfffeekaaadedgll...eksinkvghflhp.......rkv 71 
                                    +e Gy+v+e++l+a++v+a++a++++l +r+l +  ++++   ++ a+  ++++   +++ + +     +       r+ 
  gi|121639546|ref|YP_979770.1|  15 DEFGYTVVEDVLDADSVAAYLADTRRL-ERELPTVIANSTTVVKGLARPGHVPVdrvDHDWVRI-----DnlllhgtRYE 88 
                                    789***********************9.*********************999993332333333.....13344467555 PP

                                    HHHHHHHHTSCEEEE...EEEEEEEEEEEE-TTTCB-EEEEE-SGGGST.EES.GCCEEEEEEESS-B-TTBT-EEEETT CS
                           PhyH  72 adlvrailgqdvyva...avlqsmyqdifkqpkiGgevqpwHqDstflp.tdp.eesvvgvwialedateenGclrfiPG 146
                                    a  v+  l +    +    +l s+   ++ ++ +G+ +q++H+D++++p  +p +++++++ ial+d+t++nG+++++PG
  gi|121639546|ref|YP_979770.1|  89 ALPVHPKLLPVIEGVlgrDCLLSWC--MTSNQLPGAVAQRLHCDDEMYPlPRPhQPLLCNALIALCDFTADNGATQVVPG 166
                                    5555555554443322222233444..*********99***********866689************************* PP

                                    GGGS-CCGTCCHHCSGCCTTSCCCTTTGHGSCEEEE.BTTTEEEEEETTSEEEE-TB.SSSXEEE CS
                           PhyH 147 SHkweegplrrrlpeddteaeddeakkedeeeavpvevkaGdavlfhgrllHgsgaNrsdksRra 211
                                    SH+w+e       p+++++++             pve++aGda++++g+l+H ++aNr+d++R a
  gi|121639546|ref|YP_979770.1| 167 SHRWPER------PSPPYPEG------------KPVEINAGDALIWNGSLWHTAAANRTDAPRPA 213
                                    ****666......799***99............*****************************975 PP

>> 2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.2e-05     0.072      68     101 .]     184     217 ..     153     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                 2OG-FeII_Oxy_5  68 vkpkeGdlvlFPswlrHevlpnegeeeRisisfn 101
                                    v+ ++Gd +++  +l+H++ +n+++++R  + +n
  gi|121639546|ref|YP_979770.1| 184 VEINAGDALIWNGSLWHTAAANRTDAPRPALTIN 217
                                    78899***********************877665 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.6e-05      0.16      35      64 ..     180     210 ..     179     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                                    CTEEEEEETTEEEEE-TT-EEEE.EE-SSS- CS
                        Cupin_2  35 dgeeveleaGdsvyfpagtpHrf.rNtgdep 64 
                                    +g++ve++aGd+++ +   +H+  +N++d+p
  gi|121639546|ref|YP_979770.1| 180 EGKPVEINAGDALIWNGSLWHTAaANRTDAP 210
                                    5899******************988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2495.65
//
Query:       gi|121639547|ref|YP_979771.1|  [L=314]
Description: UDP-glucose 4-epimerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-59  201.3   0.0    3.1e-58  197.7   0.0    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.2e-57  195.2   0.0    1.4e-57  194.9   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.5e-17   62.8   0.0    4.2e-17   62.1   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.8e-16   60.1   0.1    3.6e-16   59.1   0.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
    8.8e-11   41.5   0.1    1.4e-10   40.8   0.1    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.9e-09   37.1   0.1      8e-05   21.9   0.0    2.5  2  NAD_binding_4    Male sterility protein
    2.5e-09   37.3   0.1    3.6e-09   36.8   0.1    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00018   21.0   0.9    0.00079   18.9   0.9    2.2  1  adh_short        short chain dehydrogenase
     0.0013   18.7   0.1     0.0027   17.6   0.1    1.5  1  KR               KR domain
  ------ inclusion threshold ------
      0.033   13.8   1.2      0.058   13.0   1.2    1.4  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.0   1.7e-61   3.1e-58       1     332 []       4     304 ..       4     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 1.7e-61
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG aGfiGs l+++Ll+ g+ v+g+++ ++  +++++ehla++  ++      ++++D+   + l+ +l++++p+ v+
  gi|121639547|ref|YP_979771.1|   4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFAT-GRATNLEHLADNS-AH-----VFVEADIVT-ADLHAILEQHRPEVVF 75 
                                    9*************************988765.68899****9754.44.....6*******8.56************** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEE.GGGG-S-SSSSB-TTS-----SHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSt.sEvYGkvqevpqtEttpfyPrsPYaaaKly 159
                                    +LAAq  V++s+ +P+  a vnv+Gt+rL ea+r++g++   +++++S+   +YG++ e p  Et p++P sPYaa K++
  gi|121639547|ref|YP_979771.1|  76 HLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVR---KIVHTSSgGSIYGTPPEYPTPETAPTDPASPYAAGKVA 152
                                    *************************************96...5555555279**************************** PP

                                    HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                  GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq 239
                                     +     +r+ ygl ++     n ++pr+ ++     +  +++  + g +++ ++G++ ++Rd+ +v+D+v+a++++   
  gi|121639547|ref|YP_979771.1| 153 GEIYLNTFRHLYGLDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSG-KPTRVFGDGTNTRDYVFVDDVVDAFVRVSAD 231
                                    *****************************9997766666555555555.577789********************98865 PP

                                    .SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH- CS
                  GDP_Man_Dehyd 240 .dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLg 318
                                     +    ++i+tg+++s r++  + ++++g                          ++++ r g+ ++ + d+  a++ Lg
  gi|121639547|ref|YP_979771.1| 232 vGGGLRFNIGTGKETSDRQLHSAVAAAVGGP-----------------D----DPEFHPPRLGDLKRSCLDIGLAERVLG 290
                                    3556789999999999999999888888741.................1....234667899****************** PP

                                    ---SS-HHHHHHHH CS
                  GDP_Man_Dehyd 319 Wkpkvsfeelvrem 332
                                    W+p++++ ++vr++
  gi|121639547|ref|YP_979771.1| 291 WRPQIELADGVRRT 304
                                    ***********986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.0   7.9e-61   1.4e-57       1     241 []       3     241 ..       3     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 7.9e-61
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavg 75 
                                    +lVtGa+GfiGs lv++ll+ g+ v+gld+  ++++t++++ +      +ve+d+  ++ l++++++++p++v+hlAa+ 
  gi|121639547|ref|YP_979771.1|   3 ALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLAdnsahVFVEADIVTAD-LHAILEQHRPEVVFHLAAQI 81 
                                    59*****************************99988887666599***********866.******************** PP

                                    -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                      Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                    +v++s+ dp+  +  n++gt++l+eaar++gv+++++ sS  ++YG ++e p+ et+   p+ p spYaa K+age ++ 
  gi|121639547|ref|YP_979771.1|  82 DVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSSgGSIYGTPPEYPTPETA---PTDPASPYAAGKVAGEIYLN 158
                                    ****************************************99******999988999...******************** PP

                                    HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-ST CS
                      Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdk 234
                                     +++ ygl++  + + n+yGpr+ ++ +++v++ +++ +l+gk +  ++gdgt+ Rd+++v+Dv++a+++v +       
  gi|121639547|ref|YP_979771.1| 159 TFRHLYGLDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSGK-PTRVFGDGTNTRDYVFVDDVVDAFVRVSAD---VGG 234
                                    **********************55555****************.***************************999...445 PP

                                    TEEEEES CS
                      Epimerase 235 geiyniG 241
                                    g  +niG
  gi|121639547|ref|YP_979771.1| 235 GLRFNIG 241
                                    5689998 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   2.3e-20   4.2e-17       1     226 [.       4     226 ..       4     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.3e-20
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlas 75 
                                    +vtG+aGF+G++lv +L+  ++   v  lD       ++l   + ++    ++e+D+   ++l++ le+   +vv+hla+
  gi|121639547|ref|YP_979771.1|   4 LVTGAAGFIGSTLVDRLLADGH--SVVGLDnfaTGRATNLEHLADNSAHV-FVEADIVT-ADLHAILEQHrpEVVFHLAA 79 
                                    69****************9996..66666643144445554444444444.******96.5799999876347******* PP

                      3Beta_HSD  76 lvdvagkltedei.mkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaE 154
                                     +dv+  + + ++   vnv GT  + ea++++gvr++v+tSs + +++     +     E+ +  + + ++y+  K   E
  gi|121639547|ref|YP_979771.1|  80 QIDVRRSVADPQFdAAVNVIGTVRLAEAARQTGVRKIVHTSSGGSIYG---TPPEYPTPETAP--TDPASPYAAGKVAGE 154
                                    ****996555544168*******************************9...444444556665..55789******9999 PP

                      3Beta_HSD 155 klvlkaNgrtlknggrlyTcaLRpagiyGegdkll.....vpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                     ++   N   ++    l    + pa +yG++++ +     v+ + q++ +g+     gd  ++ d+v+v+ v++a +
  gi|121639547|ref|YP_979771.1| 155 IYL---NT--FRHLYGLDCSHIAPANVYGPRQDPHgeagvVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFV 226
                                    776...44..66666789999*********876542222277889999999999********************988 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0     2e-19   3.6e-16       1     134 [.       1     155 [.       1     164 [. 0.92

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2e-19
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE--- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAA 60 
                                    m+ lvtGa G +Gs L+++l ++g++v++l++                     e+d+  a  ++++l++++p+vv ++AA
  gi|121639547|ref|YP_979771.1|   1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFatgratnlehladnsahvfvEADIVTA-DLHAILEQHRPEVVFHLAA 79 
                                    899**************************977679999**************99999875.699**************** PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-.TTS-B-TTS----SSHHHHHHHHHHH CS
                  RmlD_sub_bind  61 ytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGe.kkrpYeeddetsPlnvYGrtKlaGEq 134
                                      +v +   +++ ++avn+ ++ +lAeaa+++g+ +++h S+     G+  + p  e+++t+P + Y++ K+aGE 
  gi|121639547|ref|YP_979771.1|  80 QIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVrKIVHTSSGGSIYGTpPEYPTPETAPTDPASPYAAGKVAGEI 155
                                    *********************************9569***9986666662666789*******************6 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1     8e-14   1.4e-10       2     128 ..       4     121 ..       3     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8e-14
                                    EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                    lvtGa+G iGs+lv+++l+   + + l + +  +  ++e+       +++ +v+   v +d+   + l+ +le+++++vv
  gi|121639547|ref|YP_979771.1|   4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLA-----DNSAHVF---VEADIVT-ADLHAILEQHRPEVV 74 
                                    8*****************999887777666666666666543.....3333334...4577765.5699*********** PP

                                    EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                    fh AA   V      p      Nv+gt  ++eaa ++gv+k+v  S+
  gi|121639547|ref|YP_979771.1|  75 FHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSS 121
                                    **********9999999999***********************9997 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   2.9e-05     0.051       1      21 [.       5      25 ..       5      68 .. 0.86
   2 !   21.9   0.0   4.4e-08     8e-05      89     256 ..      72     224 ..      59     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                   EE-TTSHHHHHHHHHHHHHS- CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                   +TGa GF+G+ L+ +LL +  
  gi|121639547|ref|YP_979771.1|  5 VTGAAGFIGSTLVDRLLADGH 25
                                   7****************8765 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4.4e-08
                                    -EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HHH-- CS
                  NAD_binding_4  89 dviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeeklded 164
                                    +v++h aA++++ +++ +     +vNv Gt+++ e a+++     ++h S+ + ++g+                  ++ +
  gi|121639547|ref|YP_979771.1|  72 EVVFHLAAQIDVRRSVADpqfDAAVNVIGTVRLAEAARQTGVR-KIVHTSSgGSIYGTPP----------------EYPT 134
                                    79************9999554579**************99888.7888887788888777................3445 PP

                                    EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-..-SSST---TTSHHHHHHHHHHHH-EEES-SB--- CS
                  NAD_binding_4 165 eraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg..esktGwingsdlgirgllgliakgvlpeilgdke 242
                                     ++  ++ +  Y   K+++E  +++ r+  gl ++ + p +++g  +     ++g   +++ +  +   g+ ++++gd  
  gi|121639547|ref|YP_979771.1| 135 PETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANVYGprQ--D--PHGEAGVVAIFAQALLSGKPTRVFGDGT 210
                                    56667778889**************9999999999999999999442..3..3444444555555555555555666666 PP

                                    TT--EEEHHHHHHH CS
                  NAD_binding_4 243 avldlvpvDyvana 256
                                    ++ d+v vD v++a
  gi|121639547|ref|YP_979771.1| 211 NTRDYVFVDDVVDA 224
                                    66788888888776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1     2e-12   3.6e-09       1     144 [.       7     174 ..       7     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2e-12
                                    TTTSHHHHHHHHHHHHC-T-EEEEE....ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S.EEEES---TCCHH CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtal....vRnpeklaeleaeeglevvegdvtdvedlaealkgad.aVvsalggggkde 75 
                                    GA G +G+ lv++lla+g h+v+ l    + ++  l++l+++++   ve+d+  ++dl + l+++   Vv+ l+++ + +
  gi|121639547|ref|YP_979771.1|   7 GAAGFIGSTLVDRLLADG-HSVVGLdnfaTGRATNLEHLADNSAHVFVEADIV-TADLHAILEQHRpEVVFHLAAQIDVR 84 
                                    9****************5.9998763222334667777888899999*****9.899******99966999998887733 PP

                                    HH..............HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH...HCCHHHHHHHHHHHHHHHH....S CS
                 NAD_binding_10  76 eg..............aknivdaakeagvkRfvlvsaigvgdevpgefgewnk...ellkaylaakraaeellra....s 134
                                    ++              ++++++aa+++gv+++v  s+ g+   +p e ++  +   +  ++y+a k a e +l++     
  gi|121639547|ref|YP_979771.1|  85 RSvadpqfdaavnvigTVRLAEAARQTGVRKIVHTSSGGSIYGTPPEYPTPETaptDPASPYAAGKVAGEIYLNTfrhlY 164
                                    33455556777899999999*****************9975555555443322111466788888888888877655555 PP

                                    SSEEEEEEE- CS
                 NAD_binding_10 135 gldwTivrpg 144
                                    gld   + p+
  gi|121639547|ref|YP_979771.1| 165 GLDCSHIAPA 174
                                    6666666665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.9   4.4e-07   0.00079       3      60 ..       3      59 ..       1     179 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTS CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtd 60
                                   +lvtGa++ IG  ++++l+++G +vv +d+ +   ++ +++l ++ +  +++++D+ +
  gi|121639547|ref|YP_979771.1|  3 ALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADN-SAHVFVEADIVT 59
                                   89*******************************999999999987.456677888763 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.5e-06    0.0027       4     144 ..       4     129 ..       2     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    l+tG++G +G +l++ l+++g + + l           ++++++l+++ a+v  v+aD+   ++++a+le+ + e     
  gi|121639547|ref|YP_979771.1|   4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFA----TGRATNLEHLADNSAHVF-VEADIVT-ADLHAILEQHRPEV---- 73 
                                    9********************9877664443....44456899****999995.6779976.56889999988444.... PP

                                    EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                             KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                     v+h A  ++ +   ++ + ++++  a  v G+  L e+ +++ +  +v +SS ++++g++
  gi|121639547|ref|YP_979771.1|  74 -VFHLAAQIDVRR--SVADPQFDA--AVNVIGTVRLAEAARQTGVRKIVHTSSGGSIYGTP 129
                                    .****99888542..334444444..44588***************************987 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   3.2e-05     0.058       2     102 ..       4     121 ..       3     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                    EESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE.ES-TT...........-HHHHHHHHTT-SE CS
                           NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv.kgdld...........dkeslvealkgvdv 67 
                                    lv+Ga+G +G+ +v+ ll++gh+v  l      +  ++++l+++ + +  ++d+              e++ ++  + dv
  gi|121639547|ref|YP_979771.1|   4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFAtgRATNLEHLADNSAHVFvEADIVtadlhaileqhRPEVVFHLAAQIDV 83 
                                    79**********************99865556788889999999988765888664555555555544555555555555 PP

                                    EEE---GG...S-HHHHHHHHHHHHHHHS-SEEEEEE- CS
                           NmrA  68 vfsvtgfy...skeiedgkklvdAakeaGvkhfiySsl 102
                                      sv   +     ++   ++l++Aa + Gv++++  s 
  gi|121639547|ref|YP_979771.1|  84 RRSVADPQfdaAVNVIGTVRLAEAARQTGVRKIVHTSS 121
                                    55555444876677777889999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2286.02
//
Query:       gi|121639548|ref|YP_979772.1|  [L=591]
Description: hypothetical protein BCG_3693 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3787.33
//
Query:       gi|121639549|ref|YP_979773.1|  [L=115]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-06   26.7   1.8     0.0041   16.9   0.3    2.5  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    1.5e-05   24.6   0.0    4.6e-05   23.0   0.0    1.8  1  Sigma70_r4_2   Sigma-70, region 4
    2.4e-05   23.8   0.8      0.013   15.1   0.4    2.4  2  HTH_24         Winged helix-turn-helix DNA-binding
    3.8e-05   23.7   0.1    0.00015   21.8   0.0    2.0  2  HTH_7          Helix-turn-helix domain of resolvase
    0.00019   21.1   0.7    0.00057   19.6   0.1    2.0  2  HTH_23         Homeodomain-like domain
    0.00055   19.4   0.2     0.0012   18.3   0.2    1.6  1  Sigma70_r4     Sigma-70, region 4
     0.0013   18.5   1.6     0.0017   18.1   0.4    1.8  2  HTH_38         Helix-turn-helix domain
     0.0035   17.2   0.6      0.068   13.1   0.5    2.1  2  HTH_11         HTH domain
     0.0062   16.4   0.4      0.038   13.9   0.1    2.1  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.057   13.6   0.0    2.2  2  HTH_17         Helix-turn-helix domain
      0.013   15.5   0.0       0.86    9.7   0.0    2.3  2  HTH_20         Helix-turn-helix domain
      0.014   16.0   5.4       0.55   10.9   0.3    2.2  2  HTH_32         Homeodomain-like domain
      0.019   14.8   0.1       0.83    9.5   0.1    2.2  2  HTH_IclR       IclR helix-turn-helix domain
      0.025   14.2   0.9       0.05   13.3   0.1    1.9  2  GntR           Bacterial regulatory proteins, gntR family
      0.037   13.6   0.1       0.06   12.9   0.1    1.3  1  GerE           Bacterial regulatory proteins, luxR family
       0.04   14.0   0.1      0.072   13.2   0.1    1.4  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
      0.043   13.9   2.1      0.069   13.3   0.1    2.0  2  HTH_28         Helix-turn-helix domain
      0.067   12.2   0.0      0.075   12.0   0.0    1.0  1  TnsD           Tn7-like transposition protein D
      0.082   12.9   0.0       0.22   11.5   0.0    1.7  2  MarR           MarR family
      0.086   13.1   0.1       0.24   11.7   0.1    1.7  2  NUMOD1         NUMOD1 domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   4.5e-06    0.0041       9      35 ..      10      36 ..       6      41 .. 0.92
   2 !    9.1   0.1    0.0012       1.1      10      29 ..      65      84 ..      62      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                  HTH_AsnC-type  9 LeaLqedaRisyaeLAervGlSestvl 35
                                   ++ L++  R++ +e+A+ + +S++tv 
  gi|121639549|ref|YP_979773.1| 10 IRRLRRSERLPISEIARVLKISRNTVK 36
                                   68899********************97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                  HTH_AsnC-type 10 eaLqedaRisyaeLAervGl 29
                                   e+L + +R++ + +Aer+G+
  gi|121639549|ref|YP_979773.1| 65 ELLAAYPRMPATVIAERIGW 84
                                   567777************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.2e-08   4.6e-05      21      47 ..      13      39 ..      12      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.2e-08
                                   HHHTS---HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrl 47
                                   lr+ e l++ EIA++l+is +tVks+l
  gi|121639549|ref|YP_979773.1| 13 LRRSERLPISEIARVLKISRNTVKSAL 39
                                   6778999******************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   1.4e-05     0.013      11      38 ..      12      39 ..      10      41 .. 0.88
   2 !    7.0   0.0    0.0049       4.4      10      28 ..      65      83 ..      57      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                         HTH_24 11 lLqknprisqreLAerlglSpstvnrrl 38
                                    L++  r++++e+A+ l +S++tv+  l
  gi|121639549|ref|YP_979773.1| 12 RLRRSERLPISEIARVLKISRNTVKSAL 39
                                   588889******************9876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0049
                         HTH_24 10 elLqknprisqreLAerlg 28
                                   elL + pr++ + +Aer+g
  gi|121639549|ref|YP_979773.1| 65 ELLAAYPRMPATVIAERIG 83
                                   788999************9 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.7e-07   0.00015       7      39 ..       3      36 ..       1      42 [. 0.91
   2 ?   -0.4   0.0       1.4   1.3e+03      13      30 ..      62      81 ..      44      83 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                                   -HHHHGGGGSSTTTT.--STTTSSSS---SSSS- CS
                          HTH_7  7 skndinrvvkLleeG.isiskIAkevnisRsTvY 39
                                   s +d++++++L+++   +is+IA+ ++isR Tv+
  gi|121639549|ref|YP_979773.1|  3 SVEDWAEIRRLRRSErLPISEIARVLKISRNTVK 36
                                   5689*********999****************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                                   GGGSSTTT.T.--STTTSSS CS
                          HTH_7 13 rvvkLlee.G.isiskIAke 30
                                   r+++Ll++ + ++++ IA++
  gi|121639549|ref|YP_979773.1| 62 RIRELLAAyPrMPATVIAER 81
                                   45555554235666667766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   6.3e-07   0.00057      11      35 ..      11      36 ..       1      43 [. 0.79
   2 ?   -0.4   0.0       1.2   1.1e+03      16      28 ..      69      83 ..      62      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                         HTH_23 11 llllae.GlsvreIAreLgvsrrTvy 35
                                    +l +  +l+++eIAr L +sr+Tv 
  gi|121639549|ref|YP_979773.1| 11 RRLRRSeRLPISEIARVLKISRNTVK 36
                                   4555546******************7 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         HTH_23 16 e..GlsvreIAreLg 28
                                      +++ + IA++ g
  gi|121639549|ref|YP_979773.1| 69 AypRMPATVIAERIG 83
                                   355788888999888 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.4e-06    0.0012      14      40 ..      12      38 ..       8      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                                   HHHHTTT--HHHHHHHHTS-HHHHHHH CS
                     Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrqi 40
                                   +lr+ e l+ +EI+++l iSr +V++ 
  gi|121639549|ref|YP_979773.1| 12 RLRRSERLPISEIARVLKISRNTVKSA 38
                                   689999*******************85 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   1.9e-06    0.0017       5      37 ..       2      35 ..       1      38 [. 0.92
   2 ?   -2.0   0.0       3.5   3.2e+03      24      31 ..      76      83 ..      63      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                         HTH_38  5 LsleeReeIerll.aeGlslreIArrLgrspsTI 37
                                   Ls e+  eI rl+ +e l ++eIAr L+ s++T+
  gi|121639549|ref|YP_979773.1|  2 LSVEDWAEIRRLRrSERLPISEIARVLKISRNTV 35
                                   899999******63799****************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                         HTH_38 24 reIArrLg 31
                                     IA r+g
  gi|121639549|ref|YP_979773.1| 76 TVIAERIG 83
                                   46888876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.5   7.6e-05     0.068       7      36 ..      11      39 ..       8      41 .. 0.80
   2 ?    2.2   0.0       0.2   1.8e+02       8      40 ..      65      99 ..      62     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-05
                         HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdI 36
                                   ++L++++  ++++e+A+ L++Sr tv   +
  gi|121639549|ref|YP_979773.1| 11 RRLRRSER-LPISEIARVLKISRNTVKSAL 39
                                   56755554.*****************8766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                         HTH_11  8 lLleargpisgeeLAeeLnv..SrrtvrrdIkaLe 40
                                    Ll+a + +++  +Ae+++   S rt   ++++L+
  gi|121639549|ref|YP_979773.1| 65 ELLAAYPRMPATVIAERIGWwySIRTLSGRVRELR 99
                                   4557777799999****997778888888777775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.3e-05     0.038      12      42 ..      11      39 ..       2      41 .. 0.83
   2 ?    0.4   0.0      0.71   6.4e+02      14      32 ..      67      83 ..      55      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                   HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHH CS
                         MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsril 42
                                     L+r+++  l ++e+ar l++s+ +v  +l
  gi|121639549|ref|YP_979773.1| 11 RRLRRSER--LPISEIARVLKISRNTVKSAL 39
                                   55888887..**************9998776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.71
                                   HHCTTTSEEEHHHHHHHHT CS
                         MarR_2 14 Lgrrpgrdltvgelarrlg 32
                                   L++ p+  + ++ +a+r g
  gi|121639549|ref|YP_979773.1| 67 LAAYPR--MPATVIAERIG 83
                                   555665..99999999976 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.66   5.9e+02      18      28 ..      10      20 ..       8      22 .. 0.86
   2 ?   13.6   0.0   6.4e-05     0.057       2      25 ..      19      43 ..      18      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.66
                         HTH_17 18 vyrlirrgelp 28
                                   ++rl+r+ +lp
  gi|121639549|ref|YP_979773.1| 10 IRRLRRSERLP 20
                                   89*****9996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.4e-05
                         HTH_17  2 ltveEaAelLgvsrstvy.rlirrg 25
                                   l ++E+A+ L++sr+tv   l+++g
  gi|121639549|ref|YP_979773.1| 19 LPISEIARVLKISRNTVKsALASDG 43
                                   6699*************95566666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00096      0.86      17      42 ..      11      36 ..      10      40 .. 0.89
   2 ?    3.6   0.0      0.08        71      22      48 ..      70      98 ..      55      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                                   HHHSTCTTB-HHHHHHHHTS-HHHHH CS
                         HTH_20 17 raLaraegltaselaerldlskntls 42
                                   r L+r e l  se+a+ l +s+nt+ 
  gi|121639549|ref|YP_979773.1| 11 RRLRRSERLPISEIARVLKISRNTVK 36
                                   78999999****************96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.08
                                   CTTB-HHHHHHHHT..S-HHHHHHHHHHH CS
                         HTH_20 22 aegltaselaerld..lskntlsyHLrvL 48
                                      + a+ +aer++   s  tls ++r+L
  gi|121639549|ref|YP_979773.1| 70 YPRMPATVIAERIGwwYSIRTLSGRVREL 98
                                   5568999******9999999999999998 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9     0.006       5.4      33      72 ..       6      38 ..       2      39 .. 0.82
   2 ?   10.9   0.3   0.00061      0.55      23      68 ..      49      90 ..      37      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                         HTH_32 33 vrariiallreeprWsprqlaarlaeregvkvShstvyri 72
                                     a+i++l+r+e r+  +++a+ l      k+S+ tv   
  gi|121639549|ref|YP_979773.1|  6 DWAEIRRLRRSE-RLPISEIARVL------KISRNTVKSA 38
                                   558999***555.***********......9*****9765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00061
                         HTH_32 23 rgrprklsdevrariiallreeprWsprqlaarlaeregvkvShst 68
                                   r ++  + de + ri++ll   pr+ +  +a+r+    g  +S +t
  gi|121639549|ref|YP_979773.1| 49 RAAKGSVADEAEPRIRELLAAYPRMPATVIAERI----GWWYSIRT 90
                                   2234479************889**********99....33366665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00092      0.83      15      39 ..      15      39 ..      10      41 .. 0.81
   2 ?    3.2   0.0     0.084        75      10      30 ..      65      84 ..      62      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00092
                                   TBSS-BHHHHHHHHTS-HHHHHHHH CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlL 39
                                   + ++l +se+Ar + +++ tv   L
  gi|121639549|ref|YP_979773.1| 15 RSERLPISEIARVLKISRNTVKSAL 39
                                   45669***************97655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.084
                                   CT-CTTBSS-BHHHHHHHHTS CS
                       HTH_IclR 10 dalaeapqeltlselArrtgl 30
                                   ++la+ p+ +  + +A+r+g+
  gi|121639549|ref|YP_979773.1| 65 ELLAAYPR-MPATVIAERIGW 84
                                   68899999.9********996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.6e-05      0.05      17      46 ..      12      40 ..       2      41 .. 0.90
   2 ?   -1.6   0.0       2.4   2.1e+03      25      34 ..      61      70 ..      56      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                                   SS-TTSB---HHHHHHHHTS-HHHHHHHHH CS
                           GntR 17 elrpGdkLPsereLaaefgVsrttvReALr 46
                                   +lr  ++L + +e+a  +++sr+tv  AL 
  gi|121639549|ref|YP_979773.1| 12 RLRRSERL-PISEIARVLKISRNTVKSALA 40
                                   788899**.9******************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                   --HHHHHHHH CS
                           GntR 25 PsereLaaef 34
                                   P+ reL a++
  gi|121639549|ref|YP_979773.1| 61 PRIRELLAAY 70
                                   7788887776 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.7e-05      0.06      21      38 ..      22      39 ..      19      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                                   HHHHHHHTS-HHHHHHHH CS
                           GerE 21 keIAeelniSekTVkvhk 38
                                    eIA+ l iS +TVk+ +
  gi|121639549|ref|YP_979773.1| 22 SEIARVLKISRNTVKSAL 39
                                   69*************866 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     8e-05     0.072      22      50 ..      13      41 ..      10      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                                   HHHHSSBEHHHHHHHHSSTHHHHHHHHHH CS
                          HTH_9 22 LlrkgrltlrelvkktkLsldqVkksLvv 50
                                   L r+ rl+++e+++ +k+s++ Vk++L++
  gi|121639549|ref|YP_979773.1| 13 LRRSERLPISEIARVLKISRNTVKSALAS 41
                                   567889*********************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.7e-05     0.069       8      33 ..      12      39 ..      10      40 .. 0.80
   2 ?   -0.1   0.2       1.2   1.1e+03      13      34 ..      73      96 ..      63      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.7e-05
                         HTH_28  8 lla.aGh.svreaArelgisrrtvyrWi 33
                                   +l  + + +++e+Ar l isr tv++ +
  gi|121639549|ref|YP_979773.1| 12 RLRrSERlPISEIARVLKISRNTVKSAL 39
                                   555246689***************9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                         HTH_28 13 hsvreaArelgi..srrtvyrWik 34
                                   ++++ +A++ g   s rt+++ ++
  gi|121639549|ref|YP_979773.1| 73 MPATVIAERIGWwySIRTLSGRVR 96
                                   577889999887766688877776 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.3e-05     0.075     190     264 ..       9      76 ..       6     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-05
                           TnsD 190 rlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskdrekkrkewleliksypdlgkt 264
                                    ++++L  +e l + eiA+ l+++ +tV++ + + g  k   +++++ ++      ++++ + +el+++yp++  t
  gi|121639549|ref|YP_979773.1|   9 EIRRLRRSERLPISEIARVLKISRNTVKSALASDGPPK--YQRAAKGSV-----ADEAEPRIRELLAAYPRMPAT 76 
                                    5788889999********************99998554..455555555.....566666666666666655544 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.22       4      35 ..       5      36 ..       2      41 .. 0.84
   2 ?   -1.4   0.0       2.5   2.2e+03      12      28 ..      67      83 ..      65      98 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHH CS
                           MarR  4 tqfviLrilyeqgplsvseLakklgvskstvt 35
                                     +  +r l++++ l +se+a+ l++s+ tv 
  gi|121639549|ref|YP_979773.1|  5 EDWAEIRRLRRSERLPISEIARVLKISRNTVK 36
                                   56666899********************9995 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                                   HHHSTTEEHHHHHHHHT CS
                           MarR 12 lyeqgplsvseLakklg 28
                                   l+  + +  + +a+++g
  gi|121639549|ref|YP_979773.1| 67 LAAYPRMPATVIAERIG 83
                                   66677788888888876 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026      0.24      19      37 .]      21      39 ..      21      39 .. 0.92
   2 ?   -2.2   0.0       6.3   5.7e+03      13      23 ..      82      92 ..      80      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                         NUMOD1 19 ireAakyLgishntInkyl 37
                                   i+e a+ L+is+nt++ +l
  gi|121639549|ref|YP_979773.1| 21 ISEIARVLKISRNTVKSAL 39
                                   89*************9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.3
                         NUMOD1 13 igkFsSireAa 23
                                   ig+ +Sir ++
  gi|121639549|ref|YP_979773.1| 82 IGWWYSIRTLS 92
                                   67889999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 856.87
//
Query:       gi|121639550|ref|YP_979774.1|  [L=166]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1138.42
//
Query:       gi|121639551|ref|YP_979775.1|  [L=248]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-44  152.4   0.0    2.1e-38  131.8   0.0    2.1  2  IstB_IS21  IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.043   14.0   0.3      0.043   14.0   0.3    2.5  3  ParB_C     Centromere-binding protein ParB C-terminal
       0.16   11.8   0.0       0.26   11.1   0.0    1.3  1  Bac_DnaA   Bacterial dnaA  protein


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-07   0.00078       7      45 ..      69     107 ..      66     108 .. 0.95
   2 !  131.8   0.0   3.6e-42   2.1e-38      63     178 .]     108     223 ..     106     223 .. 0.99

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-07
                      IstB_IS21   7 rlrlaklpaqktledidfraarsldkrkvkeLatlsfie 45 
                                    r+r+a++p +k le++df++ar+l++ ++++L tl+f++
  gi|121639551|ref|YP_979775.1|  69 RIRAARFPSRKSLEEFDFDHARGLKRDTIAHLGTLDFVT 107
                                    799**********************************96 PP

  == domain 2  score: 131.8 bits;  conditional E-value: 3.6e-42
                      IstB_IS21  63 laialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrs 142
                                    lai ++ +a++ag++vlf ++++ v +l++a++ g l+++l rl++  ll++D++g+ p++ ++a+l+f+++++ryer+s
  gi|121639551|ref|YP_979775.1| 108 LAIGIAIRACQAGHRVLFATASQWVDRLAAAHHSGTLQSELIRLARYPLLVVDEVGYIPFEPEAANLFFQLVSSRYERAS 187
                                    899***************************************************************************** PP

                      IstB_IS21 143 iiitsnlpfaewdevlgdatlatAilDRlvHhahvv 178
                                    +i+tsn+pf++w+ev+gd+++a A++DRlvHha+v+
  gi|121639551|ref|YP_979775.1| 188 LIVTSNKPFGRWGEVFGDDVVAAAMIDRLVHHAEVI 223
                                    *********************************986 PP

>> ParB_C  Centromere-binding protein ParB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   7.2e-06     0.043       6      39 ..      28      63 ..      24      70 .. 0.93
   2 ?   -2.9   0.0       1.3     8e+03       4       9 ..      68      73 ..      65      73 .. 0.86
   3 ?   -1.3   0.2      0.42   2.5e+03      26      38 ..     209     221 ..     206     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-06
                         ParB_C  6 vRaAflatrhleGdqtlS..dfiaaAvmaeVerlEr 39
                                   +R+A+++     + +t+S  +f aa +++eV ++E 
  gi|121639551|ref|YP_979775.1| 28 LRGAIEQLADRARTKTWSyeEFLAACLQREVSARES 63
                                   7*****************999*************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                         ParB_C  4 aRvRaA 9 
                                   +R+RaA
  gi|121639551|ref|YP_979775.1| 68 GRIRAA 73
                                   79**98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.42
                         ParB_C  26 iaaAvmaeVerlE 38 
                                    +aa ++++V + E
  gi|121639551|ref|YP_979775.1| 209 AAAMIDRLVHHAE 221
                                    467799***9987 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.3e-05      0.26      53     137 ..     109     192 ..     100     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-E CS
                       Bac_DnaA  53 aignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkq 132
                                    aig ++++ +  +rv++ ta +++ +l+ a ++ ++++   +l +  +L++D++ ++    +  + +f+++ + +e +  
  gi|121639551|ref|YP_979775.1| 109 AIGIAIRACQAGHRVLFATASQWVDRLAAAHHSGTLQSELIRLARYPLLVVDEVGYIPFEPEAANLFFQLVSSRYERASL 188
                                    89999999*************************999999999999**************************999998876 PP

                                    EEEEE CS
                       Bac_DnaA 133 vvlss 137
                                    +v +s
  gi|121639551|ref|YP_979775.1| 189 IV-TS 192
                                    55.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1874.97
//
Query:       gi|121639552|ref|YP_979776.1|  [L=188]
Description: hypothetical protein BCG_3697c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1406.93
//
Query:       gi|121639553|ref|YP_979777.1|  [L=409]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.1e-160  532.8   0.0   4.6e-160  532.6   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
      7e-08   32.8   0.0    1.6e-07   31.6   0.0    1.7  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.054   13.6   0.4          6    7.0   0.0    2.5  2  SnoaL_4          SnoaL-like domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.6   0.0  7.7e-164  4.6e-160       7     380 ..       6     379 ..       1     380 [. 0.98

  Alignments for each domain:
  == domain 1  score: 532.6 bits;  conditional E-value: 7.7e-164
                Transposase_mut   7 llelealkaieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsG 86 
                                    ++ +e l+a+++ +g  dl+++++++vl+el e e++e++ga+ryers++r ++RnG+r+r lsT+ag++elriP++R+G
  gi|121639553|ref|YP_979777.1|   6 SALSELLDAFRTGDGV-DLIRDAVRLVLQELSELEATERIGAARYERSDTRVTDRNGARSRVLSTQAGDVELRIPKLRKG 84 
                                    5667888999999999.9************************************************************** PP

                Transposase_mut  87 sFspallerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllf 166
                                    sF+pa+le ++R ++al+avv+e+yv+G+str+v++lve++++e+++SksevS+i++ lde+v+afr+R+L++ e+p+++
  gi|121639553|ref|YP_979777.1|  85 SFFPAILEPRRRIDQALYAVVMEAYVHGISTRAVDDLVEAMGVETGISKSEVSRICAGLDEIVGAFRTRTLGHIEFPYVY 164
                                    ******************************************************************************** PP

                Transposase_mut 167 lDalylkvR.eegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisa 245
                                    lDa+yl+vR  +g+vvs+av++a g++adGsreiLgl+v+dsE+e+fW+ +l+sLk+rGl gv+lv+sD+h+GLvka+++
  gi|121639553|ref|YP_979777.1| 165 LDATYLNVRnGTGQVVSMAVIVASGIAADGSREILGLDVGDSEDETFWRGFLTSLKGRGLGGVRLVISDQHAGLVKALKR 244
                                    *********7789******************************************************************* PP

                Transposase_mut 246 vfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlafla 325
                                    +f++a +QrCrvH++rnlla+vpk+kad+va+++++i++a+dae++++++ee++++l++++pk+  l+d+a+++vlaf+a
  gi|121639553|ref|YP_979777.1| 245 CFQGAGHQRCRVHFARNLLAHVPKDKADMVASMFRMIFSAPDAEAVHATWEEVRDRLAASFPKIGPLMDDARAEVLAFTA 324
                                    ******************************************************************************** PP

                Transposase_mut 326 fpeqirrkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                    fp+++++ki+stN+lEr+Nkei+Rr+rvvgiFPn+++++rlvgavla++hdew++
  gi|121639553|ref|YP_979777.1| 325 FPKAHWQKIWSTNPLERINKEIKRRSRVVGIFPNPAAVIRLVGAVLADMHDEWQA 379
                                    *****************************************************97 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.7e-11   1.6e-07       2      96 .]     163     261 ..     162     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.7e-11
                           MULE   2 vvlDgTyktnk......yklplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekalln 75 
                                    v lD+Ty+  +        +  + + g+ + g+  +l++ + +se+e  ++ +l++l+ +  g    + +i+D++++l +
  gi|121639553|ref|YP_979777.1| 163 VYLDATYLNVRngtgqvVSMAVIVASGIAADGSREILGLDVGDSEDETFWRGFLTSLKGRGLG--GVRLVISDQHAGLVK 240
                                    67899998654111112455666669999*****************************98777..9************** PP

                           MULE  76 aleevfpeakhrlClfHiakn 96 
                                    al+++f++a h+ C  H+a+n
  gi|121639553|ref|YP_979777.1| 241 ALKRCFQGAGHQRCRVHFARN 261
                                    ******************987 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1    0.0069        41      12     104 ..     105     212 ..      94     222 .. 0.76
   2 ?    7.0   0.0     0.001         6      56     114 ..     240     301 ..     223     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0069
                                    HHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH................-EEEEE--- CS
                        SnoaL_4  12 lvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfa................ltqHllsnp 75 
                                    ++ +y++ + t+  ++l++    +  +   +v +    g d+i+ a+r+++ g++                 t  ++s+ 
  gi|121639553|ref|YP_979777.1| 105 VMEAYVHGISTRAVDDLVEAMGVETGISKSEV-SRICAGLDEIVGAFRTRTLGHIefpyvyldatylnvrnGTGQVVSMA 183
                                    67789999999999999988877766677766.79999***********6655555444444444455555778888888 PP

                                    EEEEETTEEEEEEEEEEEEEETTEEEEEE CS
                        SnoaL_4  76 lieldgdtAtgrayllatlvrdgdggrqv 104
                                    +i   g  A g+   l+ +v+d ++++++
  gi|121639553|ref|YP_979777.1| 184 VIVASGIAADGSREILGLDVGDSEDETFW 212
                                    88889999999999999988888887554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                                    HHHHSHHHHHH...-EEEEE---EEEEETTEEEEEEEEEEEEEETTEEEEEE..EEEEEEEE CS
                        SnoaL_4  56 aalrealdgfa...ltqHllsnplieldgdtAtgrayllatlvrdgdggrqvlaggryedel 114
                                    +al++ ++g        H+  n l +++ d+A ++a+++ + + + d++  +  ++ ++d+l
  gi|121639553|ref|YP_979777.1| 240 KALKRCFQGAGhqrCRVHFARNLLAHVPKDKADMVASMFRMIFSAPDAEAVHATWEEVRDRL 301
                                    44444444333333668************************888777765555777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2436.75
//
Query:       gi|121639554|ref|YP_979778.1|  [L=211]
Description: cell filamentation protein fic [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-15   57.0   0.0    4.8e-15   56.2   0.0    1.4  1  Fic       Fic/DOC family


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   2.7e-19   4.8e-15       3      97 .]      64     162 ..      62     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2.7e-19
                                    SHHHHHHHHCHS-S------TS--SS-ST..EEEE---SCCCHHHHHHHHHHHHC......HHT-S-HHHHHHHHHHHHH CS
                            Fic   3 tledllelhrlllqdigeeagefrdeevsegklesalappeevpaeleelleyln......elekeeplekaaalhyefe 76 
                                    +l++l+++hr+l+qdi+ +ag++r++ +  +k + ++++p  ++  +e++ +++       + ++ +++ ++a+ + +++
  gi|121639554|ref|YP_979778.1|  64 DLAYLRAIHRQLFQDIYVWAGDLRTVGI--EKEDESFCAPGGISRPMEHVAAEIYqldrlrAVGEGDLAGQVAYRYDYVN 141
                                    6889*********************777..********************99999777777777777************* PP

                                    HH--SSS-HHHHHHHHHHHHH CS
                            Fic  77 kiHPFaDGNgRtarlllnllL 97 
                                    + HPF++GNgR  r +++llL
  gi|121639554|ref|YP_979778.1| 142 YAHPFREGNGRSTREFFDLLL 162
                                    *****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1167.45
//
Query:       gi|121639555|ref|YP_979779.1|  [L=64]
Description: hypothetical protein BCG_3700c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-16   58.3   7.1    6.3e-16   58.0   7.1    1.1  1  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   7.1   3.5e-20   6.3e-16       1      47 []      14      60 ..      14      60 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.5e-20
                           VbhA  1 RrraVrqAlAsnelEGlepsaetvadleayvrGeIdadElvrrvraR 47
                                   R r+Vr  ++++elEG +++a+t+ad+++y+rG+I+a+El +rvr+R
  gi|121639555|ref|YP_979779.1| 14 RFRNVRATRRNTELEGTRSTAATRADQNDYARGKITAAELGERVRRR 60
                                   88********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.57
# Mc/sec: 340.06
//
Query:       gi|121639556|ref|YP_979780.1|  [L=63]
Description: hypothetical protein BCG_3701 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 420.11
//
Query:       gi|121639557|ref|YP_979781.1|  [L=401]
Description: DNA polymerase III subunit delta' [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-35  121.4   0.0    4.4e-35  120.9   0.0    1.2  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    5.1e-05   23.7   0.0    0.00021   21.7   0.0    2.1  1  AAA              ATPase family associated with various cellul
     0.0004   20.9   0.0    0.00088   19.8   0.0    1.5  1  DNApol3-delta_C  DNA polymerase III, delta subunit, C termina
     0.0021   18.3   0.0     0.0061   16.8   0.0    1.8  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.044   13.8   0.3       0.64   10.0   0.3    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
        2.4    8.5  13.5          1    9.7   0.6    4.0  2  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   1.5e-38   4.4e-35      16     159 ..      37     179 ..      30     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.5e-38
                DNA_pol3_delta2  16 grlahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivieteekersikldqirelieel 95 
                                    g+++ha+L++G+ g+g+  +al++a al c+++ e   cg+c++c +   g+h Dv  + +e+   si +d+ r + + +
  gi|121639557|ref|YP_979781.1|  37 GTMTHAWLLTGPPGSGRSVAALCFAAALQCTSGGEP-GCGRCRACTTTLAGTHADVRRVIPEGL--SIGVDEMRAIVQIA 113
                                    7899*****************************988.***************************..************** PP

                DNA_pol3_delta2  96 srkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLits..dtnklLktirSRcqelkf 159
                                     r+p+ ++++i++ieda+++t+ AaNalLk++EEP+ +++f+L++   d++ +  t+rSRc ++ +
  gi|121639557|ref|YP_979781.1| 114 ARRPTTGHWQIVVIEDADRLTEGAANALLKVVEEPPPSTVFLLCAPsvDPEDIAVTLRSRCRHVAL 179
                                    *******************************************97633799***********9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.2e-08   0.00021       2     128 ..      44     178 ..      43     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.2e-08
                                    EEESSTTSSHHHHHHHHHHHHTHE..................EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TS.E CS
                            AAA   2 llyGppGtGKTllakavakelgve..................fleisgsellskyvgesekkirelfkeakeka..kp.s 60 
                                    ll+GppG G++ +a   a  l+ +                      ++ +++ + ++ + +++r++++ a +    ++  
  gi|121639557|ref|YP_979781.1|  44 LLTGPPGSGRSVAALCFAAALQCTsggepgcgrcractttlaGTHADVRRVIPEGLSIGVDEMRAIVQIAARRPttGHwQ 123
                                    89******************85333344444444444333323444444444446677777777777775444447566* PP

                                    EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                            AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                    i++i+++d+l++             +n+Ll+++++   +   +++++ + +p+++   l+ +R+ ++ 
  gi|121639557|ref|YP_979781.1| 124 IVVIEDADRLTEGA-----------ANALLKVVEEPPPS-TVFLLCAPSVDPEDIAVTLR-SRCRHVA 178
                                    **********9888...........***********995.32555555666999999999.9*98765 PP

>> DNApol3-delta_C  DNA polymerase III, delta subunit, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     3e-07   0.00088      43      97 ..     325     380 ..     311     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3e-07
                                    HHHHHHHHHHHTTT-S..--S-TT-HHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH CS
                DNApol3-delta_C  43 LlslLlDalklqqgaqe.qlvnqdqlplikqlakrlsiekLlkilqkllelreqLl 97 
                                    L++ + Dal +  +a      ++d+++ +++la + ++e+Ll+ ++++l +re L 
  gi|121639557|ref|YP_979781.1| 325 LATYFRDALLVAAHAGGvRANHPDMADRVAALAAHAPPERLLRCIEAVLACREALA 380
                                    8999*************99999*******************************996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     2e-06    0.0061       9     117 ..      44     146 ..      40     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2e-06
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalra 88 
                                    ++tG++G+G+++ +  ++  l+  +  e  + ++  +t +  ++ +d++r + + l  +        +e+++ ++ a+r+
  gi|121639557|ref|YP_979781.1|  44 LLTGPPGSGRSVAALCFAAALQCTSGGEPGCGRCRACTTTLAGTHADVRRVIPEGLSIG-------VDEMRAIVQIAARR 116
                                    79*******************7666666677777789999999**************74.......55587888877777 PP

                         AAA_22  89 rav..ielliiDEaqhlrseealeeLrslln 117
                                      +   ++++i++a++l +e a + L + ++
  gi|121639557|ref|YP_979781.1| 117 PTTghWQIVVIEDADRL-TEGAANALLKVVE 146
                                    777999***********.8888888876665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00021      0.64       3      24 ..      44      74 ..      42     152 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                   EEE--SSSSHHHHHHHGGGGB.........S CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.........n 24
                                   lL GppG+g+s  a  +aaal         +
  gi|121639557|ref|YP_979781.1| 44 LLTGPPGSGRSVAALCFAAALqctsggepgC 74
                                   8********************6655555441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00034         1      24      51 ..      36      67 ..       7     157 .. 0.64
   2 ?   -3.1   6.5       3.1   9.2e+03       6      34 ..     269     297 ..     167     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                         AAA_16 24 p....elvllsGesGvGKsslvrellralekd 51
                                   +    ++ ll+G++G+G s  + +++ al+ +
  gi|121639557|ref|YP_979781.1| 36 GgtmtHAWLLTGPPGSGRSVAALCFAAALQCT 67
                                   13466888999999999999999999766533 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.1
                         AAA_16   6 eeeleqLlsalervrsgrpelvllsGesG 34 
                                    e+e+e+L++al++  +g +    l+G+ G
  gi|121639557|ref|YP_979781.1| 269 EAETEELRTALGAGGTGKGTGAALRGATG 297
                                    34555555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2825.61
//
Query:       gi|121639558|ref|YP_979782.1|  [L=549]
Description: hypothetical protein BCG_3703 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-20   73.7   0.0    2.3e-20   73.0   0.0    1.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
    1.4e-09   38.2   0.1    4.1e-09   36.7   0.1    1.9  1  HAMP           HAMP domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   2.5e-24   2.3e-20       7     174 ..     359     526 ..     356     532 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 2.5e-24
                  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdml 86 
                                    ++v++lF d+vg+t+l++   p evv+lLne +  + e ++++++   k+ Gda ++++g+p e+++ a  +++ a ++ 
  gi|121639558|ref|YP_979782.1| 359 RDVAVLFVDLVGSTQLAATRPPAEVVQLLNEFFRVVVETVARHGGFVNKFQGDAALAIFGAPIEHPDGAGAALSAARELH 438
                                    78************************************************************999998888888888887 PP

                  Guanylate_cyc  87 ealeevaveskeglkvrvGihtGpvvagviG.akkprydvwGntvnlAsrmestgkagkiqvseetyellk...eeqfel 162
                                    ++l  v  +     + ++G++ G+ +ag+iG + +++y+v+G+ vn A+r+  ++k ++ +v +++ ++      e   +
  gi|121639558|ref|YP_979782.1| 439 DELIPVLGSA----EFGIGVSAGRAIAGHIGaQARFEYTVIGDPVNEAARLTELAKLEDGHVLASAIAVSGaldAEALCW 514
                                    7775555444....89***************999**********************999999766666554443555555 PP

                  Guanylate_cyc 163 tergevevkGkg 174
                                    +  + ve++G+ 
  gi|121639558|ref|YP_979782.1| 515 DVGEVVELRGRA 526
                                    555667777764 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   4.5e-13   4.1e-09       1      52 [.     275     326 ..     275     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 4.5e-13
                                    HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    l+a +i  PLr+L+ a  ++++G+++++  ++   E+G L + fN+M+++L 
  gi|121639558|ref|YP_979782.1| 275 LVAMSIADPLRQLRWALSEVQRGNYNAHMQIYDASELGLLQAGFNDMVRELS 326
                                    6899*********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3853.21
//
Query:       gi|121639559|ref|YP_979783.1|  [L=934]
Description: DNA topoisomerase I [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.9e-115  386.2   0.0   2.4e-115  385.9   0.0    1.1  1  Topoisom_bac  DNA topoisomerase
    6.7e-64  211.7   1.9    3.4e-21   75.0   0.0    4.5  4  Toprim_C_rpt  Topoisomerase C-terminal repeat
    2.5e-28   98.3   0.0    6.2e-28   97.0   0.0    1.7  1  Toprim        Toprim domain
      5e-06   26.9   0.0    3.3e-05   24.3   0.0    2.5  2  Toprim_4      Toprim domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.9   0.0  5.4e-119  2.4e-115       2     412 ..     156     604 ..     155     605 .. 0.92

  Alignments for each domain:
  == domain 1  score: 385.9 bits;  conditional E-value: 5.4e-119
                   Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatl.kkekkek 80 
                                    ++ +lvda+e+Rr+lD+l+G+++s++l+kk+     lsaGRVq+++ ++iv Rer++ +F+++ yw++ a+l ++ +++ 
  gi|121639559|ref|YP_979783.1| 156 LDIDLVDAQETRRILDRLYGYEVSPVLWKKVA--PKLSAGRVQSVATRIIVARERDRMAFRSAAYWDILAKLdASVSDPD 233
                                    6789*************************999..9************************************964444444 PP

                   Topoisom_bac  81 e...........................kkkkkkkerikdkeeaeaileklkkkeakvesvekkekkk.ppplpfdtttL 132
                                    +                              k ++  + d+  a+a+++ l+ ++++v s e+k   + p p pf t+tL
  gi|121639559|ref|YP_979783.1| 234 AapptfsarltavagrrvatgrdfdslgTLRKGDEVIVLDEGSATALAAGLDGTQLTVASAEEKPYARrPYP-PFMTSTL 312
                                    48************************99888999999**************7779***********995666.******* PP

                   Topoisom_bac 133 qkeasrklglsakktlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknk 212
                                    q+easrkl++sa++t+siaq+LYe+ g+itY+RTdst+lse+a ++a++++ ++ yg+ey + a+++++ +k    vkn+
  gi|121639559|ref|YP_979783.1| 313 QQEASRKLRFSAERTMSIAQRLYEN-GYITYMRTDSTTLSESA-INAARTQARQLYGDEYVAPAPRQYT-RK----VKNA 385
                                    ************************7.*****************.9*********************997.44....5699 PP

                   Topoisom_bac 213 kveaHeAIrPteelp.klkels.........ddekklYelIvrrflaslmkdakyeettvklev....eeeefkasgkti 278
                                    + eaHeAIrP +e   + ++           dd + lYelI++r++as+m+da+  + +++++     +e  f+a+g+t+
  gi|121639559|ref|YP_979783.1| 386 Q-EAHEAIRPAGETFaT-PDAVrreldgpniDDFR-LYELIWQRTVASQMADARGMTLSLRITGmsghQEVVFSATGRTL 462
                                    9.***********9954.44445677799966666.**************************666777999********* PP

                   Topoisom_bac 279 lekGfkkvy.......keekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiie 351
                                    +++Gf+k+y          ++++ e++lp+l+ g+++++ e++ + ++T+pp+ryteasL+ka+e+ giG+p+T+++ii+
  gi|121639559|ref|YP_979783.1| 463 TFPGFLKAYvetvdelVGGEADDAERRLPHLTPGQRLDIVELTPDGHATNPPARYTEASLVKALEELGIGRPSTYSSIIK 542
                                    *********888777634445555559***************************************************** PP

                   Topoisom_bac 352 klvergYverkkkslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevl 412
                                    ++++rgYv++k+++lvp+  ++a++ ll ++f +lv++++Ta +e++LdeIa g++ + ++l
  gi|121639559|ref|YP_979783.1| 543 TIQDRGYVHKKGSALVPSWVAFAVTGLLeQHFGRLVDYDFTAAMEDELDEIAAGNERRTNWL 604
                                    **********98****************7778***********************9988776 PP

>> Toprim_C_rpt  Topoisomerase C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     3e-09   1.4e-05       4      52 ..     651     708 ..     648     711 .. 0.86
   2 !   46.8   0.0     5e-16   2.2e-12       1      50 [.     714     788 ..     714     791 .. 0.83
   3 !   61.2   0.0   1.5e-20   6.9e-17       1      54 [.     793     846 ..     793     848 .. 0.96
   4 !   75.0   0.0   7.5e-25   3.4e-21       1      53 [.     860     912 ..     860     915 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3e-09
                   Toprim_C_rpt   4 tgepikvkeGRfGPYvkh......gk...knasLpkgddvetitleeAlellaekral 52 
                                     g+pi+v+ G+ GPY+        g+    +a+L +  +++++tl+ A el+a +++ 
  gi|121639559|ref|YP_979783.1| 651 HGRPIYVRVGKNGPYLERlvagdtGEptpQRANLSDSITPDELTLQVAEELFATPQQG 708
                                    69***************777766622667*************************9865 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 5e-16
                   Toprim_C_rpt   1 hPetgepikvkeGRfGPYvkhgk...........................knasLpkgddvetitleeAlellaekr 50 
                                    +Petg++i+++eGRfGPYv+  +                           +  sL + +d +t+tle+Al ll+++r
  gi|121639559|ref|YP_979783.1| 714 DPETGHEIVAREGRFGPYVT--EilpepaadaaaaaqgvkkrqkaagpkpRTGSLLRSMDLQTVTLEDALRLLSLPR 788
                                    8*******************..3344555555555666666777888888*************************98 PP

  == domain 3  score: 61.2 bits;  conditional E-value: 1.5e-20
                   Toprim_C_rpt   1 hPetgepikvkeGRfGPYvkhgkknasLpkgddvetitleeAlellaekralgk 54 
                                    +P++ge+i++++GR+GPY+k g + +sL  +d+++titl+eAl++ ae++++g+
  gi|121639559|ref|YP_979783.1| 793 DPASGEEITAQNGRYGPYLKRGNDSRSLVTEDQIFTITLDEALKIYAEPKRRGR 846
                                    8************************************************98775 PP

  == domain 4  score: 75.0 bits;  conditional E-value: 7.5e-25
                   Toprim_C_rpt   1 hPetgepikvkeGRfGPYvkhgkknasLpkgddvetitleeAlellaekralg 53 
                                    +P++g+p+++k+GRfGPYv++g++nasL+kgddv++it e+A ella++ra+g
  gi|121639559|ref|YP_979783.1| 860 DPASGKPMVIKDGRFGPYVTDGETNASLRKGDDVASITDERAAELLADRRARG 912
                                    8*************************************************877 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   1.4e-31   6.2e-28       2     103 .]      20     141 ..      19     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 1.4e-31
                                    EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.......................TTEEEEEECTTTHHHHHHHHH CS
                         Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildlet.......................efkpvyeeiedkkkvlkalke 58 
                                    lvivE+p++a+++a++lg ++++v +s+Ghi+dl+                        +f+p y++ ++k++++++l+ 
  gi|121639559|ref|YP_979783.1|  20 LVIVESPTKARKLASYLG-SGYIVESSRGHIRDLPRaasdvpakyksqpwarlgvnvdaDFEPLYIISPEKRSTVSELRG 98 
                                    9*****************.************************************************************* PP

                                    HHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESSS CS
                         Toprim  59 lakradeiilatDpDreGeaiawellevlkellenkigrvefsei 103
                                    l+k++de++latD+DreGeaiaw+lle lk+ ++   +r++f+ei
  gi|121639559|ref|YP_979783.1|  99 LLKDVDELYLATDGDREGEAIAWHLLETLKPRIPV--KRMVFHEI 141
                                    **************************988866666..******98 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.3e-09   3.3e-05      29      87 ..      77     135 ..      18     137 .. 0.87
   2 ?   -2.1   0.0       1.3   5.6e+03       4      35 ..     202     233 ..     200     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.3e-09
                       Toprim_4  29 galspldgirpeklkt.enlveaekkvkevilaldgDaeGeataerlaellleegvkvtr 87 
                                     +++pl  i+pek+ t  +l+  +k v+e++la+dgD eGea a +l+e+l ++ + v+r
  gi|121639559|ref|YP_979783.1|  77 ADFEPLYIISPEKRSTvSELRGLLKDVDELYLATDGDREGEAIAWHLLETL-KPRIPVKR 135
                                    57899999********888888***************************77.56666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                       Toprim_4   4 iiVEgyaDvlalekagiknvvavlggalspld 35 
                                    iiV  + D +a+ +a +  + a l+ ++s +d
  gi|121639559|ref|YP_979783.1| 202 IIVARERDRMAFRSAAYWDILAKLDASVSDPD 233
                                    8999*********9999888887777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.57
# Mc/sec: 4920.10
//
Query:       gi|121639560|ref|YP_979784.1|  [L=192]
Description: hypothetical protein BCG_3705c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 1035.48
//
Query:       gi|121639561|ref|YP_979785.1|  [L=67]
Description: cold shock protein A cspA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-31  107.2   0.1    2.9e-31  107.1   0.1    1.0  1  CSD       'Cold-shock' DNA-binding domain
    0.00015   21.3   0.1     0.0002   21.0   0.1    1.3  1  OB_RNB    Ribonuclease B OB domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.1   3.3e-35   2.9e-31       2      65 ..       3      66 ..       2      67 .] 0.98

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 3.3e-35
                                   EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                            CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                   +GtVkwfna+kgfGFI++edg++dvFvH+++iqg+gfr+L+e+q+VeFe+ ++ kgp+A+ V+ 
  gi|121639561|ref|YP_979785.1|  3 QGTVKWFNAEKGFGFIAPEDGSADVFVHYTEIQGTGFRTLEENQKVEFEIGHSPKGPQATGVRS 66
                                   8***********************************************************9975 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.3e-08    0.0002       7      30 ..      12      35 ..       4      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-08
                                   SSS-EEEEECT.TEEEEE-HHHHT CS
                         OB_RNB  7 kkGFGFlipdegkeDifippeqmk 30
                                   +kGFGF+ p++g+ D+f++ ++++
  gi|121639561|ref|YP_979785.1| 12 EKGFGFIAPEDGSADVFVHYTEIQ 35
                                   79****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 375.11
//
Query:       gi|121639562|ref|YP_979786.1|  [L=771]
Description: helicase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-20   72.0   0.0    7.8e-20   71.4   0.0    1.2  1  DEAD        DEAD/DEAH box helicase
      2e-19   70.1   0.1    7.4e-19   68.3   0.1    2.0  2  DUF1998     Domain of unknown function (DUF1998)
    1.2e-09   38.4   0.0    2.2e-09   37.6   0.0    1.4  1  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.3e-23   7.8e-20       3     170 ..      62     232 ..      60     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.3e-23
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEE. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx. RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvl. 79 
                                     Qaea +l++ g++v++    +sGK+la+++pvl++++   ++++ +al+++Pt++L +++l+ +  +   +     v  
  gi|121639562|ref|YP_979786.1|  62 HQAEAAELAYAGRHVVIGTGPASGKSLAYQLPVLNALA---TDSRARALYLSPTKALGHDQLRAAHALAAAVPrlADVAp 138
                                    7************************************5...79999************************7444444555 PP

                                    EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  80 liiggvaardqlskldngvdivvgtpgrlddll....stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                      + g++ ++ ++  +++ + ++++p++ +  +     +  + l+++rf+++DE++ +    f+  +  +l++l + +++
  gi|121639562|ref|YP_979786.1| 139 TAYDGDSPDEVRRFARERSRWLFSNPEMTHLSVlrnhARWAVLLRNLRFVIVDECHYYRGV-FGSNVAMVLRRLLRLCAR 217
                                    6799****8888888899**********999775654344455*****************9.************999999 PP

                                    STTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxx RF
                           DEAD 156 gklqrqvivlSATlp 170
                                     +++ +vi+ SAT  
  gi|121639562|ref|YP_979786.1| 218 YSAHPTVIFASATTA 232
                                    888889*******75 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   7.8e+03       1      27 [.     122     148 ..     122     165 .. 0.69
   2 !   68.3   0.1   1.2e-22   7.4e-19       1      83 []     660     738 ..     660     738 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                        DUF1998   1 lehalinalplflqcdesdlgteckap 27 
                                    ++hal  a+p  +++ +   ++ +  +
  gi|121639562|ref|YP_979786.1| 122 AAHALAAAVPRLADVAPTAYDGDSPDE 148
                                    689999999999999888777777633 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 1.2e-22
                        DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaGCp 80 
                                    +eha i +lpl++ cd++d+g+ ++a+     +  + +++yd++pgGaG+ae++++ + ++l a+ e ie+c+C  +GCp
  gi|121639562|ref|YP_979786.1| 660 AEHAAIGLLPLVASCDRDDIGGMSTATGP---EGLPSVFVYDGYPGGAGFAERGFRRARTWLGATAEAIEACECP-SGCP 735
                                    69**********************97766...59****************************************8.**** PP

                        DUF1998  81 aCl 83 
                                    +C+
  gi|121639562|ref|YP_979786.1| 736 SCV 738
                                    **8 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   3.7e-13   2.2e-09       9     111 .]     295     402 ..     287     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.7e-13
                                    HHHHTTTTSEEEEEESSHHHHHH......HHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                     Helicase_C   9 llkleeeggkilifvntidrlek......vklllekk.....gikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                    l    +eg ++l fv++++ +e       ++l+         + +va + +   +++r +  ++  +g+ + L +t+++e
  gi|121639562|ref|YP_979786.1| 295 L---IVEGAQTLTFVRSRRAAELtalgarARLV---DiapelSDTVASYRAGYLAEDRSALHQALAEGQLRGLATTNALE 368
                                    3...48999**********77544455542333...0233456889999999**************************** PP

                                    SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                     G+di +++ V+  ++p +v+s++q++GR gR g
  gi|121639562|ref|YP_979786.1| 369 LGVDIAGLDAVVLAGFPGTVASFWQQAGRSGRRG 402
                                    ********************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 4218.76
//
Query:       gi|121639563|ref|YP_979787.1|  [L=94]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-29  101.1  17.2    3.8e-29  100.8  17.2    1.0  1  PE          PE family
  ------ inclusion threshold ------
      0.023   14.7   2.7      0.027   14.4   2.7    1.3  1  LacAB_rpiB  Ribose/Galactose Isomerase


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8  17.2   4.3e-33   3.8e-29       1      82 [.       1      82 [.       1      86 [. 0.97

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 4.3e-33
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfv++aPeal +aa+dl  +gs+l aa+aaaaa tt+++aaa DeVSaaiAalfsah+q+yqa+saqaaafh++f++a ++
  gi|121639563|ref|YP_979787.1|  1 MSFVIAAPEALDSAATDLVVLGSTLGAATAAAAAQTTGIVAAAHDEVSAAIAALFSAHGQAYQAASAQAAAFHTRFIRARSR 82
                                   9****************************************************************************99665 PP

>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.7   3.1e-06     0.027      43      92 ..       3      52 ..       1      86 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHHHHTTSSSEEEEEESSSHHHHHHHHTSTT--EEE-SSHHHHHH CS
                     LacAB_rpiB 43 fakkvaeavasgeadlgiliCgtGiGmsiaaNkvkgiraalchdeesAkl 92
                                   f +++ ea+ s + dl++l+ + G   + aa +  gi+aa   + + A  
  gi|121639563|ref|YP_979787.1|  3 FVIAAPEALDSAATDLVVLGSTLGAATAAAAAQTTGIVAAAHDEVSAAIA 52
                                   67888899*******************************97665544332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 530.86
//
Query:       gi|121639564|ref|YP_979788.1|  [L=345]
Description: hypothetical protein BCG_3709 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-53  180.4   0.0    2.2e-53  179.4   0.0    1.6  1  DUF5628   Family of unknown function (DUF5628)
    1.5e-33  115.3   0.2    4.7e-33  113.8   0.2    1.8  2  DUF5593   Domain of unknown function (DUF5593)
  ------ inclusion threshold ------
      0.094   12.8   0.3          6    7.0   0.0    2.4  2  DUF3489   Protein of unknown function (DUF3489)


Domain annotation for each model (and alignments):
>> DUF5628  Family of unknown function (DUF5628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.0   3.7e-57   2.2e-53       1     110 []      99     208 ..      99     208 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 3.7e-57
                        DUF5628   1 ipGplkWdltsGvatdtpeslansGldpeaeathgrafaedlptrdlnpseakvlslaikpepgktlcstWdvtdarGep 80 
                                    ipGplkWdlt+Gvatdtpesl+nsG++pe+e t+grafaedlp+r+lnp+e++vl++a+k++pgktlcs Wd+td++G+p
  gi|121639564|ref|YP_979788.1|  99 IPGPLKWDLTRGVATDTPESLTNSGKNPEVEITYGRAFAEDLPARELNPNETQVLAMAVKAKPGKTLCSIWDLTDWQGTP 178
                                    79****************************************************************************** PP

                        DUF5628  81 itvGfvarvvleaqedgserlicramnwra 110
                                    i++Gfvar++le   +g+++l++ramnwra
  gi|121639564|ref|YP_979788.1| 179 IRIGFVARSALEPGPNGRDHLVARAMNWRA 208
                                    *****************************7 PP

>> DUF5593  Domain of unknown function (DUF5593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.2   7.8e-37   4.7e-33       1      93 []       4      96 ..       4      96 .. 0.99
   2 ?   -1.9   0.0      0.96   5.7e+03       9      32 ..     286     309 ..     274     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 7.8e-37
                        DUF5593  1 dWlLvEtlgneptVvakggrpkewtplasllrrkaalaavrsaiaevvrsgepvsritpksdrviraepVlgpdgrvhgVqv 82
                                   dWlLvEtlg+ep+Vva+g++ k+++p++++lrr++ laavr+aiae+ ++g+++++itpk+drvir+epV ++dgr+hgVqv
  gi|121639564|ref|YP_979788.1|  4 DWLLVETLGDEPAVVARGRELKKLVPITTFLRRSPYLAAVRTAIAETLQTGQSLTSITPKHDRVIRTEPVIMTDGRMHGVQV 85
                                   7********************************************************************************* PP

                        DUF5593 83 WvGtedeepPp 93
                                   W G+ d+epP+
  gi|121639564|ref|YP_979788.1| 86 WSGPTDAEPPD 96
                                   **********6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                        DUF5593   9 gneptVvakggrpkewtplasllr 32 
                                    g++  V+   g+  +w+p++  + 
  gi|121639564|ref|YP_979788.1| 286 GSASHVLRLPGHDVDWVPVHVTVN 309
                                    556677777788888888875544 PP

>> DUF3489  Protein of unknown function (DUF3489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.015        91      37      61 ..      42      66 ..      40      70 .. 0.88
   2 ?    7.0   0.0     0.001         6      10      39 ..     150     180 ..     144     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.015
                        DUF3489 37 tvRgalagalkkklgltltsekveg 61
                                   +vR a+a +l+ + +lt   +k + 
  gi|121639564|ref|YP_979788.1| 42 AVRTAIAETLQTGQSLTSITPKHDR 66
                                   79***************99999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                        DUF3489  10 arlial.LrrpeGatiaeimeatgWqahtvR 39 
                                     +++a+ ++++ G t+  i   t+Wq   +R
  gi|121639564|ref|YP_979788.1| 150 TQVLAMaVKAKPGKTLCSIWDLTDWQGTPIR 180
                                    578888678999**************99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1905.46
//
Query:       gi|121639565|ref|YP_979789.1|  [L=104]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-19   68.0   9.1    7.8e-19   67.8   9.1    1.1  1  PE        PE family
  ------ inclusion threshold ------
      0.074   12.4   3.2      0.084   12.3   3.2    1.1  1  DUF3482   Domain of unknown function (DUF3482)


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   9.1   8.7e-23   7.8e-19       1      60 [.       1      60 [.       1      67 [. 0.94

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 8.7e-23
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaq 60
                                   Ms+v++aPeal aaa+dla++gs++ aanaaaa++tta+l a+aDeVSaaiAa  +  a+
  gi|121639565|ref|YP_979789.1|  1 MSYVIAAPEALVAAATDLATLGSTIGAANAAAAGSTTALLTAGADEVSAAIAAYSECTAR 60
                                   9****************************************************8877665 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.2   9.3e-06     0.084     158     207 ..      10      57 ..       5      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-06
                        DUF3482 158 AaaGagiDlavgGltLGaaaaiGalaGglaatlkrygkrllaklkGarel 207
                                    A++ a+ Dla++G t+Gaa a  a+aG++ a+l++  +++ a +  + e 
  gi|121639565|ref|YP_979789.1|  10 ALVAAATDLATLGSTIGAANA--AAAGSTTALLTAGADEVSAAIAAYSEC 57 
                                    778899**********99876..788999999988888888887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 585.52
//
Query:       gi|121639566|ref|YP_979790.1|  [L=231]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                       72  (0.00401584); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 1251.01
//
Query:       gi|121639567|ref|YP_979791.1|  [L=84]
Description: hypothetical protein BCG_3712c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0074   16.6  11.3     0.0074   16.6  11.3    3.0  3  Tad       Putative Flp pilus-assembly TadE/G-like


Domain annotation for each model (and alignments):
>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  11.3   4.1e-07    0.0074      28      47 ..       1      20 [.       1      21 [. 0.92
   2 ?   -0.3   1.4     0.075   1.3e+03      37      45 ..      26      34 ..      24      46 .. 0.64
   3 ?    2.3   0.9     0.012   2.1e+02      13      27 ..      60      74 ..      54      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.1e-07
                            Tad 28 vlartrlQnAADaAALAaAq 47
                                   ++ar+r+Q+AAD+A+LAaA+
  gi|121639567|ref|YP_979791.1|  1 MVARHRAQAAADLASLAAAA 20
                                   689**************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.075
                            Tad 37 AADaAALAa 45
                                   +A a+A+A 
  gi|121639567|ref|YP_979791.1| 26 LAAACARAT 34
                                   466666663 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.012
                            Tad 13 pllllvglavDvgra 27
                                   ++++++g+a++++ra
  gi|121639567|ref|YP_979791.1| 60 VAVAFAGVATATARA 74
                                   456688888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 477.95
//
Query:       gi|121639568|ref|YP_979792.1|  [L=99]
Description: hypothetical protein BCG_3713c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   15.4   4.1      0.017   15.4   4.1    1.9  2  TadE            TadE-like protein
      0.059   12.4   1.7      0.073   12.1   1.7    1.1  1  NPDC1           Neural proliferation differentiation control-
        2.5    8.4   6.3          2    8.7   2.9    2.0  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> TadE  TadE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   4.1   2.9e-06     0.017       6      43 .]       2      39 ..       1      39 [. 0.94
   2 ?   -3.3   0.1       1.9   1.1e+04      34      40 ..      86      92 ..      85      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                           TadE  6 EFALvlPlllllllgiiefgrylyarqtlnnAAreaAR 43
                                   E+AL++  l+l+l +++    +++ + ++ +AAreaAR
  gi|121639568|ref|YP_979792.1|  2 EAALAIATLVLVLVLCLAGVTAVSMQVRCIDAAREAAR 39
                                   9****9999999999999999****************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                           TadE 34 lnnAAre 40
                                   l+ AAr+
  gi|121639568|ref|YP_979792.1| 86 LDIAARA 92
                                   6678886 PP

>> NPDC1  Neural proliferation differentiation control-1 protein (NPDC1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   1.2e-05     0.073     199     250 ..       9      59 ..       5      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                          NPDC1 199 alvlilafclasaaalavaalcwcrlqreirltqkadyaatakaptspaapr 250
                                    +lvl+l +cla+ +a+++   c    +   rl+ + d   +a   +   apr
  gi|121639568|ref|YP_979792.1|   9 TLVLVLVLCLAGVTAVSMQVRCIDAAREAARLAARGDVR-SATDVARSIAPR 59 
                                    89********************99999999*****9984.444444444555 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.9   0.00034         2      18      63 ..       3      56 ..       3      58 .. 0.80
   2 ?    0.9   0.1     0.092   5.5e+02      20      32 ..      71      83 ..      70      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHT..TEH.HHH....HHHHHHHHHHHHHHH.HHSHHHHHHH CS
                 GHMP_kinases_N 18 AAlavalvaAllall..gls.lee....aklaleaerlaqggn.gsggDvaasv 63
                                   AAla a+++ +l l+  g+  +++     + a ea rla++g   s  Dva s+
  gi|121639568|ref|YP_979792.1|  3 AALAIATLVLVLVLClaGVTaVSMqvrcIDAAREAARLAARGDvRSATDVARSI 56
                                   89999999999999955544335577899*******99977766******9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.092
                                   HHHHHHHHHHHHT CS
                 GHMP_kinases_N 20 lavalvaAllall 32
                                   ++va+v+A  +ll
  gi|121639568|ref|YP_979792.1| 71 FVVATVTAHSNLL 83
                                   5899999988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 566.24
//
Query:       gi|121639569|ref|YP_979793.1|  [L=68]
Description: hypothetical protein BCG_3714c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-23   79.9   4.7      8e-23   79.6   4.7    1.1  1  DUF4244   Protein of unknown function (DUF4244)


Domain annotation for each model (and alignments):
>> DUF4244  Protein of unknown function (DUF4244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   4.7   4.4e-27     8e-23       2      54 .]      13      65 ..      12      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.4e-27
                        DUF4244  2 rlrarlredaGmsTaEYAvgtlAAvafAavLykvvtsdsVrsaLtgiiekALs 54
                                   r++a++ +++GmsT+EYA+gt+AA+af+a+Ly+vvt+ds+ saL+ ii +ALs
  gi|121639569|ref|YP_979793.1| 13 RMTALAVDESGMSTVEYAIGTIAAAAFGAILYTVVTGDSIVSALNRIIGRALS 65
                                   67888999********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 477.90
//
Query:       gi|121639570|ref|YP_979794.1|  [L=191]
Description: alanine rich membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-14   53.0   0.6    4.1e-14   52.6   0.6    1.1  1  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.6   2.3e-18   4.1e-14       2     122 ..      46     172 ..      45     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.3e-18
                                    HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC.......T-TT.TS-HHHHHHHHHHHHH CS
                          T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale.......rtpssefpelvvqlirageeg 74 
                                    l+ la++l+aG+ + +a  + a++a +++la++l+r+a+ l+ G +++ a++        t + + + +++   r++ +g
  gi|121639570|ref|YP_979794.1|  46 LDVLAVCLAAGMAVSTAAAATAAVA-PPRLARVLRRAADLLALGADPNIAWSrppdlppGTHDAQTDAVLRLARRSAASG 124
                                    789**********************.**************************66666664444899************** PP

                                    T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                          T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                      La+ +  la +++ ++++++  +a+++++l+  +++l++l+++l +
  gi|121639570|ref|YP_979794.1| 125 AALADGIVELAVQVRHDAAQAAAAAAERAGVLIAGPLGLCFLPAFLCV 172
                                    ********************************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1363.28
//
Query:       gi|121639571|ref|YP_979795.1|  [L=266]
Description: hypothetical protein BCG_3716c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-09   36.7   4.4    3.3e-09   36.7   4.4    2.2  2  T2SSF         Type II secretion system (T2SS), protein F
    5.6e-05   23.3   0.1    0.00015   21.9   0.0    1.7  2  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.049   4.4e+02      87     112 ..      77     102 ..      73     103 .. 0.75
   2 !   36.7   4.4   3.7e-13   3.3e-09       2     120 ..      97     219 ..      96     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.049
                                    HHHHHHHHHHHHHHHHHTTXXXXXXX CS
                          T2SSF  87 yleeerelrrkllaallepllllvva 112
                                    y +++r lrr +  + le +l+lvv+
  gi|121639571|ref|YP_979795.1|  77 YRRRRRYLRRSREGQALEAALELVVG 102
                                    56777777788888888888887775 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 3.7e-13
                                    HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT- CS
                          T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeggn 76 
                                    l++++  l+aG+ +v+a++++a+e+  gp+a +l+++a+r r G ++ + l     ++  + +  +l+v +    ++g  
  gi|121639571|ref|YP_979795.1|  97 LELVVGELRAGAHPVRAFSIAADET-GGPVAVALRAVAARARLGADVTAGLLaaarSSALPAYwERLAVCWQLGSDHGLA 175
                                    6778889******************.*******************9997777776666668999**************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXX CS
                          T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllill 120
                                    +a  ++++++++ e+++  +++ a +++ +++++++++++l+ +
  gi|121639571|ref|YP_979795.1| 176 IASLMRAAQRDVAERQRFSARVSAGMAGARASAAILAILPLLGV 219
                                    **************************************999865 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-08   0.00015       3      78 ..      63     137 ..      62     165 .. 0.89
   2 ?   -2.3   0.0      0.46   4.1e+03       7      27 ..     244     264 ..     240     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-08
                                    XXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH CS
                   Spore_III_AB   3 igallillactgiGfalakrlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerle 78 
                                    + a+ +l a+ g+ + + +r+ rr +e ++l+ alel+ ge+r ga p   a++  a ++++p++  ++ va r +
  gi|121639571|ref|YP_979795.1|  63 VVAVAVLGATLGLRYRRRRRYLRRSREGQALEAALELVVGELRAGAHPV-RAFSIAADETGGPVAVALRAVAARAR 137
                                    67999*******************************************6.99*******************99854 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.46
                                    XXXXXXXXXXXXXXXXXXHHH CS
                   Spore_III_AB   7 lillactgiGfalakrlkrrl 27 
                                    ++ l+ +++G+++++r+++r+
  gi|121639571|ref|YP_979795.1| 244 VVGLTLACAGLLWSDRITDRP 264
                                    455667889999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1862.88
//
Query:       gi|121639572|ref|YP_979796.1|  [L=352]
Description: hypothetical protein BCG_3717c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-70  236.2   0.1    4.1e-70  235.9   0.1    1.1  1  T2SSE          Type II/IV secretion system protein
    0.00046   19.5   0.0     0.0008   18.7   0.0    1.3  1  Zeta_toxin     Zeta toxin
    0.00074   20.0   0.0     0.0011   19.4   0.0    1.5  1  ABC_tran       ABC transporter
      0.004   17.5   1.1     0.0087   16.5   0.3    2.0  2  AAA_16         AAA ATPase domain
     0.0055   16.4   0.0      0.011   15.5   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
     0.0067   17.0   0.1       0.01   16.3   0.1    1.2  1  AAA_23         AAA domain
  ------ inclusion threshold ------
       0.02   14.3   0.3      0.075   12.4   0.3    1.9  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.042   13.4   0.0      0.073   12.6   0.0    1.3  1  AAA_7          P-loop containing dynein motor region
      0.043   14.1   0.0      0.099   12.9   0.0    1.6  1  AAA_22         AAA domain
       0.05   13.2   0.0      0.091   12.3   0.0    1.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.093   12.8   0.0       0.13   12.3   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.094   11.6   0.1       0.19   10.6   0.0    1.5  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.094   12.5   0.1       0.18   11.6   0.1    1.4  1  MukB           MukB N-terminal
       0.11   12.7   1.1       0.44   10.8   0.0    2.4  3  AAA_28         AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.9   0.1   3.2e-73   4.1e-70       3     272 ..      22     303 ..      20     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.9 bits;  conditional E-value: 3.2e-73
                          T2SSE   3 illeallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlp.....ekg 77 
                                     +le+ll +++ +d++v  p++v+v +  +g++ +++++ +++a++rl++r+a +a++++++ +p++d++l+     + +
  gi|121639572|ref|YP_979796.1|  22 GILEPLLSADGTTDVLVTAPDSVWV-DDGNGLRRSQIRFADESAVRRLAQRLALAAGRRLDDAQPWVDGQLTgigvgGFA 100
                                    57899********************.889999******************************************999999 PP

                          T2SSE  78 vrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                    vrl++vl+Pv+ + ++l++R  +++  +l+ l+a++a +++ a++++  v++r  +lv GgTg GKttll a+l  +  +
  gi|121639572|ref|YP_979796.1| 101 VRLHAVLPPVATQgTCLSLRVLRPATQDLAALAAAGAIDPAAAALVADIVTARLAFLVCGGTGAGKTTLLAAMLGAVSPD 180
                                    ***********999******99999999**************************************************99 PP

                          T2SSE 157 derivtvEDpvEiqleganqvqlnak......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsT 230
                                     eriv vED++E+ +++++ v+l+a+       ++vt+++l+r+aLR+rPDri+vGE+R++e++++l A+nTGH+g+ +T
  gi|121639572|ref|YP_979796.1| 181 -ERIVCVEDAAELAPRHPHLVKLVARranvegIGEVTVRQLVRQALRMRPDRIVVGEVRGAEVVDLLAALNTGHEGGAGT 259
                                    .*************************999999899********************************************* PP

                          T2SSE 231 lHansaagalerLeqlgae..veaaelkssilavvdivvrlvrk 272
                                    +Han++ ++  r+e lga   + +a+l+s+++a+v+++ +++r+
  gi|121639572|ref|YP_979796.1| 260 VHANNPGEVPARMEALGALggLDRAALHSQLAAAVQVLLHVARD 303
                                    *****************98******************9999885 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.3e-07    0.0008      18      67 ..     155     205 ..     149     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.3e-07
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrl.dpDdlRelhPeyeeilka 67 
                                    + l+ G++GAGK++l++++  ++ +++++v + d+ +l ++hP+  ++ + 
  gi|121639572|ref|YP_979796.1| 155 AFLVCGGTGAGKTTLLAAMLGAVSPDERIVCVeDAAELAPRHPHLVKLVAR 205
                                    7899********************9999999857899*******9987763 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.8e-07    0.0011      16      45 ..     158     187 ..     150     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.8e-07
                                    EEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  16 ivGenGaGKStLlkllagllkpteGeilld 45 
                                    + G +GaGK+tLl++++g ++p+e  + ++
  gi|121639572|ref|YP_979796.1| 158 VCGGTGAGKTTLLAAMLGAVSPDERIVCVE 187
                                    68********************99888666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.5   5.8e+03     117     128 ..      66      78 ..      19      92 .. 0.62
   2 !   16.5   0.3   6.8e-06    0.0087      25     120 ..     154     246 ..     141     311 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.5
                         AAA_16 117 srllellkrll.a 128
                                    +rl++ l+ ++ +
  gi|121639572|ref|YP_979796.1|  66 RRLAQRLALAAgR 78 
                                    4444444444433 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.8e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekle 102
                                     + l+ G  G GK++l+ + l a++ d+ i+ ++  ++      p+ + l+++ ar+  ++ +++ +    ++  r++l+
  gi|121639572|ref|YP_979796.1| 154 LAFLVCGGTGAGKTTLLAAMLGAVSPDERIVcVEDAAELA----PRHPhLVKLVARRANVEGIGEVT---VRQLVRQALR 226
                                    6789***********************8555255555555....66555666666655555555552...2333333333 PP

                         AAA_16 103 eala..avpelagaeasrll 120
                                     +     v+e++gae  +ll
  gi|121639572|ref|YP_979796.1| 227 MRPDriVVGEVRGAEVVDLL 246
                                    32223323333333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.5e-06     0.011      23      50 ..     153     181 ..     143     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.5e-06
                         AAA_29  23 g.atlltGpsGsGKSTllDAiqalLvpak 50 
                                      a+l+ G +G+GK+Tll A+     p++
  gi|121639572|ref|YP_979796.1| 153 RlAFLVCGGTGAGKTTLLAAMLGAVSPDE 181
                                    4479***************9998888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.1e-06      0.01      22      40 ..     156     174 ..     153     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                         AAA_23  22 tlItGpNGaGKTTildAik 40 
                                    +l++G +GaGKTT+l A+ 
  gi|121639572|ref|YP_979796.1| 156 FLVCGGTGAGKTTLLAAML 174
                                    89**************986 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   5.9e-05     0.075      32      60 ..     146     174 ..     141     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                                    EEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE  32 vldlkkmashllvaGatgsGKStalntLi 60 
                                    v+d++++    lv+G+tg GK+t l +++
  gi|121639572|ref|YP_979796.1| 146 VADIVTARLAFLVCGGTGAGKTTLLAAML 174
                                    56666666668****************97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.073      24      62 ..     144     182 ..     141     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                          AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                     l+  +++++  +l++G tG GKt+++  +l ++++++ 
  gi|121639572|ref|YP_979796.1| 144 ALVADIVTARLAFLVCGGTGAGKTTLLAAMLGAVSPDER 182
                                    577889999********************9998887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-05     0.099       7      30 ..     155     178 ..     150     244 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                      +v+G +G+GKTtll+ +l    
  gi|121639572|ref|YP_979796.1| 155 AFLVCGGTGAGKTTLLAAMLGAVS 178
                                    679*************99998774 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05     0.091       3      30 ..     156     184 ..     154     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                    EEEEESTTCCHHHHHHHHH.CT--SS-EE CS
                           cobW   3 tvltGflGsGKTtLlnhll.enraglkla 30 
                                    ++++G  G+GKTtLl ++l + + ++++ 
  gi|121639572|ref|YP_979796.1| 156 FLVCGGTGAGKTTLLAAMLgAVSPDERIV 184
                                    679999************97666666654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.13       6      87 ..     160     240 ..     156     319 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                    SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHHCCHCCCHHH.HHHCHCHHHH..EEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiepdlkrllell.ealgkkkalllkiagvvlnrv 84 
                                    +  G+GKTtl+a+++ a + +++ V + Da   a+   +l +l+ ++++ ++ ++e+  ++l++ +al +++ ++v+  v
  gi|121639572|ref|YP_979796.1| 160 GGTGAGKTTLLAAMLGAVSPDERIVCVEDAAELAPRHPHLVKLVARRAN-VEGIGEVTvRQLVR-QALRMRPDRIVVGEV 237
                                    6689****************88888888988888887766666666665.44444444233332.244455555555555 PP

                                    SS. CS
                                    xxx RF
                           CbiA  85 dge 87 
                                    +g 
  gi|121639572|ref|YP_979796.1| 238 RGA 240
                                    544 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.19      17      46 ..     155     184 ..     142     197 .. 0.80
   2 ?   -3.8   0.1       3.5   4.5e+03      31      54 ..     216     240 ..     214     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargdra 46 
                                     +l+ G+tG+GKt+ l ++l a+   +  +
  gi|121639572|ref|YP_979796.1| 155 AFLVCGGTGAGKTTLLAAMLGAVSPDERIV 184
                                    68999***************9987655444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.5
                  TrwB_AAD_bind  31 alekllrai.rargdraivlDltGa 54 
                                    ++++l+r++ r r dr++v    Ga
  gi|121639572|ref|YP_979796.1| 216 TVRQLVRQAlRMRPDRIVVGEVRGA 240
                                    5678887643889999999888886 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.18      31      59 ..     158     186 ..     146     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                    HHS--SHHHHHHHHHHHHHHS--TTT--- CS
                           MukB  31 lsGgnGaGksttmaafvtaliPdlsllhf 59 
                                    + Gg GaGk+t +aa++ a+ Pd  ++  
  gi|121639572|ref|YP_979796.1| 158 VCGGTGAGKTTLLAAMLGAVSPDERIVCV 186
                                    579********************877655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.5e+03     107     132 ..      31      58 ..       5      80 .. 0.69
   2 ?   10.8   0.0   0.00034      0.44       3      31 ..     157     190 ..     155     196 .. 0.73
   3 ?   -2.5   0.1         4   5.1e+03      63      89 ..     314     342 ..     283     348 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                         AAA_28 107 krydlvfllppap.ei.dddgeRredle 132
                                    +  + v++++p+  ++ d +g Rr + +
  gi|121639572|ref|YP_979796.1|  31 DGTTDVLVTAPDSvWVdDGNGLRRSQIR 58 
                                    4556688888866366555666765433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00034
                         AAA_28   3 vitGgestGKTtlleaLaar.....gypvvpEaa 31 
                                     + Gg ++GKTtll+a+         +++v++aa
  gi|121639572|ref|YP_979796.1| 157 LVCGGTGAGKTTLLAAMLGAvspdeRIVCVEDAA 190
                                    689***********99873324444677777766 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4
                         AAA_28  63 qleeeaaa....aankvlfcDrglldtlaYa 89 
                                    ++  +++a    +a  v   Drg+ d +a +
  gi|121639572|ref|YP_979796.1| 314 AV--LRQAegrvQAVTVWHADRGMSDDAAAL 342
                                    22..222222345566666677777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2347.26
//
Query:       gi|121639573|ref|YP_979797.1|  [L=350]
Description: hypothetical protein BCG_3718c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.046   13.8   0.1    1.8  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
      0.045   13.7   1.7        6.8    6.6   0.1    2.1  2  AAA_31    AAA domain
       0.58    9.6   2.9        9.9    5.6   0.5    2.3  2  CBP_BcsQ  Cellulose biosynthesis protein BcsQ


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.7e-06     0.046       1      37 [.     118     150 ..     118     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-06
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDp 37 
                                    +a++++ GG+G + +a++La+a a+     llvD+Dp
  gi|121639573|ref|YP_979797.1| 118 VAVIGGRGGAGASLFAVALAQAAAD----ALLVDLDP 150
                                    699*********************9....9******9 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0011       6.8       3      40 ..     117     150 ..     115     154 .. 0.76
   2 ?    6.4   0.1    0.0013       7.5     121     166 ..     225     270 ..     224     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0011
                         AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                    v+a++  +GG G +  +v+la+a a      LlvDlDp
  gi|121639573|ref|YP_979797.1| 117 VVAVIGGRGGAGASLFAVALAQAAA----DALLVDLDP 150
                                    7888989999997777766666665....56******9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                         AAA_31 121 iiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                    ++ D p  L   t+ aL a+d v+ +  ++ +a   ++ +   ++ 
  gi|121639573|ref|YP_979797.1| 225 VVCDLPRRLTDATQAALDAADLVVLVSPCDVRACAAAATMAPVLTA 270
                                    78899999*********************99999988877766555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0016       9.9       3      26 ..     117     140 ..     116     151 .. 0.78
   2 ?    3.8   0.1    0.0057        34     119     150 ..     225     256 ..     220     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0016
                       CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawal 26 
                                    v+a+ G RGG+G++  ++aLa+a 
  gi|121639573|ref|YP_979797.1| 117 VVAVIGGRGGAGASLFAVALAQAA 140
                                    78999********99999999874 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0057
                       CBP_BcsQ 119 illDlpagasaltrellaladlvllvvepdan 150
                                    ++ Dlp+  ++ t+++l  adlv+lv   d+ 
  gi|121639573|ref|YP_979797.1| 225 VVCDLPRRLTDATQAALDAADLVVLVSPCDVR 256
                                    789***********************988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2578.90
//
Query:       gi|121639574|ref|YP_979798.1|  [L=287]
Description: hypothetical protein BCG_3719 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-32  112.4   0.1    4.2e-32  112.1   0.1    1.1  1  HAD          haloacid dehalogenase-like hydrolase
    1.2e-07   32.2   0.1    2.1e-07   31.4   0.1    1.5  1  Hydrolase    haloacid dehalogenase-like hydrolase
     0.0012   18.6   0.0     0.0025   17.6   0.0    1.5  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.21   11.4   0.0       0.32   10.8   0.0    1.2  1  PH_4         Pleckstrin homology domain


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.1   9.3e-36   4.2e-32       1     188 []      28     213 ..      28     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 9.3e-36
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv... 77 
                                    a+fD+D+T++++ s  ++ + + ++g + +++ l+   +++++  l+  d+++ +++  +l    ++ + a+++ +v   
  gi|121639574|ref|YP_979798.1|  28 AFFDLDKTIIAKPSTLAFSKPFFAQGLLNRRAVLKSS-YAQFIFLLSGADHDQMDRMRTHLTNMCAGWDVAQVRSIVnet 106
                                    8*******************9****999965555555.555557777777888888888888888888888888888555 PP

                            HAD  78 .aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkv 155
                                     +++++p ++  +a +l+aah+  G  vvvvS++ +++v p++++lga + +at++ v+d ++tge       ++gegk+
  gi|121639574|ref|YP_979798.1| 107 lHDIVTPLVF-AEAADLIAAHKLCGRDVVVVSASGEEIVGPIARALGATHAMATRMIVEDgKYTGE---VAFYCYGEGKA 182
                                    5666666655.8******************************************************...999******** PP

                            HAD 156 aalrewlaaegegidleevvayGDspsDlpllr 188
                                    +a+re +a eg+++  e+++ay+Ds++Dlp+l+
  gi|121639574|ref|YP_979798.1| 183 QAIRELAASEGYPL--EHCYAYSDSITDLPMLE 213
                                    *****666666666..66*************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   4.8e-11   2.1e-07     118     210 .]     114     216 ..      26     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.8e-11
                                    HBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE.SEEEEHHCES.STTT....SHHHHHHHHHHHT... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx.xxxx....xxxxxxxxxxxxx... RF
                      Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf.daviasdiet.vakp....spegkvaaireLq... 187
                                     v+ eaa+++a+ k  g +vv+++ + +e +  +a+ lG  +++    i  d  +  +++      egk +aireL    
  gi|121639574|ref|YP_979798.1| 114 LVFAEAADLIAAHKLCGRDVVVVSASGEEIVGPIARALGaTHAMaTRMIVEDG-KyTGEVafycYGEGKAQAIRELAase 192
                                    5999**********99***********************64444233333333.2577778888************7555 PP

                                    .STGGGEEEEESSHHHHHHHHHTT CS
                                    .xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 188 .gkpeevamVGDgvnDaaalaaAg 210
                                      + e++ +  D+++D+++l+a+g
  gi|121639574|ref|YP_979798.1| 193 gYPLEHCYAYSDSITDLPMLEAVG 216
                                    456999***************987 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         2     9e+03       2      11 ..      29      38 ..      29      42 .. 0.83
   2 !   17.6   0.0   5.6e-07    0.0025     185     228 ..     178     221 ..     147     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2
                                   EEEIIIIIS- CS
                    Hydrolase_3  2 alDlDGTLln 11
                                   ++DlD T++ 
  gi|121639574|ref|YP_979798.1| 29 FFDLDKTIIA 38
                                   79*****986 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.6e-07
                                    T-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEE CS
                    Hydrolase_3 185 gvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAm 228
                                    g  K++a+++la   +++le+++a  D+  D++MLea+g++  +
  gi|121639574|ref|YP_979798.1| 178 GEGKAQAIRELAASEGYPLEHCYAYSDSITDLPMLEAVGHASVV 221
                                    556************************************98655 PP

>> PH_4  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.1e-05      0.32      54      83 ..     195     224 ..     176     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.1e-05
                           PH_4  54 plkdcYvysGkltelDLlernktfdeanpg 83 
                                    pl++cY ys+++t+l +le   +   +np+
  gi|121639574|ref|YP_979798.1| 195 PLEHCYAYSDSITDLPMLEAVGHASVVNPD 224
                                    8*****************988888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1942.46
//
Query:       gi|121639575|ref|YP_979799.1|  [L=256]
Description: hypothetical protein BCG_3720c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1939.10
//
Query:       gi|121639576|ref|YP_979800.1|  [L=548]
Description: dipeptide-transport ATP-binding protein ABC transporter dppD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-57  193.5   0.0    5.9e-29  101.3   0.0    2.2  2  ABC_tran         ABC transporter
    1.3e-12   48.1   0.3    6.8e-05   23.3   0.0    2.4  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    3.6e-11   43.5   1.8    3.9e-05   23.9   0.0    3.6  2  AAA_22           AAA domain
    2.6e-09   37.5   0.1     0.0017   18.5   0.0    2.3  2  DUF87            Helicase HerA, central domain
    3.2e-09   37.4   7.1    6.8e-05   23.3   0.5    2.7  2  AAA_16           AAA ATPase domain
    1.3e-08   34.4   1.7     0.0015   18.2   0.0    2.3  2  AAA_29           P-loop containing region of AAA domain
    2.3e-08   34.2   8.1      0.042   13.7   0.1    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.9e-08   32.7   0.4     0.0076   15.7   0.0    3.7  3  SMC_N            RecF/RecN/SMC N terminal domain
      2e-05   24.6   1.9       0.11   12.4   0.2    2.5  2  NACHT            NACHT domain
    2.5e-05   24.2   0.4      0.084   12.8   0.0    2.3  2  RsgA_GTPase      RsgA GTPase
    2.7e-05   23.7   0.1       0.32   10.4   0.0    2.8  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.3e-05   24.1   0.2       0.31   11.2   0.0    3.3  3  AAA_33           AAA domain
    5.5e-05   23.0   0.2       0.28   10.9   0.0    2.3  2  AAA_24           AAA domain
    0.00014   21.6   0.2       0.75    9.5   0.0    2.8  2  Sigma54_activat  Sigma-54 interaction domain
    0.00027   21.0   0.6       0.88    9.7   0.1    2.5  2  MMR_HSR1         50S ribosome-binding GTPase
    0.00028   21.4   0.2        1.1    9.7   0.0    2.2  2  AAA_23           AAA domain
    0.00029   20.8   0.4       0.51   10.3   0.0    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00034   20.0   1.4      0.085   12.1   0.0    2.4  2  Zeta_toxin       Zeta toxin
    0.00034   20.2   0.2        1.2    8.6   0.0    3.6  3  AAA_25           AAA domain
    0.00042   19.6   0.1       0.16   11.2   0.0    2.2  2  NB-ARC           NB-ARC domain
    0.00099   18.5   0.3       0.73    9.1   0.0    2.5  2  ATPase           KaiC
     0.0012   18.4   0.4       0.34   10.4   0.1    2.2  2  AAA_7            P-loop containing dynein motor region
     0.0012   18.7   0.2        1.4    8.8   0.0    2.5  2  APS_kinase       Adenylylsulphate kinase
     0.0014   18.3   0.2        1.4    8.6   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
     0.0015   17.9   0.6        1.6    8.0   0.1    2.4  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0018   17.4   0.9       0.22   10.6   0.1    2.4  2  T2SSE            Type II/IV secretion system protein
      0.002   18.2   1.9        1.3    9.0   1.2    2.6  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.002   17.9   1.0        1.2    8.8   0.0    2.6  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0024   17.3   2.6          3    7.2   0.1    4.0  4  TniB             Bacterial TniB protein
      0.003   16.7   1.1       0.52    9.3   0.0    2.3  2  DUF3987          Protein of unknown function (DUF3987)
     0.0062   17.0   0.5        4.9    7.6   0.0    3.2  2  AAA              ATPase family associated with various cellul
     0.0074   16.2   0.6          2    8.3   0.0    2.4  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.013   15.9   0.3        4.8    7.6   0.0    2.3  2  RNA_helicase     RNA helicase
      0.021   13.7   0.0        1.2    8.0   0.0    2.1  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.025   14.2   0.1        3.9    7.0   0.0    2.3  2  SRP54            SRP54-type protein, GTPase domain
      0.026   15.1   0.0        9.7    6.8   0.0    2.8  2  AAA_18           AAA domain
      0.055   13.5   4.5        1.3    9.0   0.5    2.3  2  Dynamin_N        Dynamin family
      0.061   12.5   0.0        3.5    6.7   0.0    2.1  2  G-alpha          G-protein alpha subunit
      0.064   12.0   2.4        3.9    6.2   0.1    3.9  4  ABC_ATPase       Predicted ATPase of the ABC class
      0.084   12.6  16.2        4.4    7.0   5.2    4.7  5  AAA_30           AAA domain
      0.096   12.6   0.6        4.6    7.1   0.1    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.096   11.6   0.5        3.4    6.5   0.0    2.1  2  AAA_10           AAA-like domain
       0.19   10.5   0.1         11    4.7   0.0    2.2  2  DLIC             Dynein light intermediate chain (DLIC)
        0.2   11.7   0.4        9.9    6.2   0.0    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
        0.2   10.9   4.9       0.32   10.3   0.5    2.3  2  AIG1             AIG1 family
       0.22   11.2   0.0         24    4.5   0.0    2.1  2  AAA_15           AAA ATPase domain
       0.26   11.6   2.5         19    5.5   0.2    3.7  4  AAA_19           AAA domain
       0.26   10.5   1.2        8.3    5.6   0.1    2.1  2  Septin           Septin
       0.31   10.8   2.4         24    4.6   0.3    2.9  3  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.63   10.3   1.6         11    6.3   0.1    2.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
        1.8    8.2   6.0        8.4    6.1   0.1    3.3  3  Cytidylate_kin   Cytidylate kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   4.5e-28   1.6e-25       3     137 .]      27     182 ..      25     182 .. 0.91
   2 !  101.3   0.0   1.7e-31   5.9e-29       2     136 ..     308     459 ..     307     460 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 4.5e-28
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..pqlfp 72 
                                     v+l ++ g++va+vGe+G+GKSt +++++gll      t+G++ +dg+d++     + +++  +eig++pq+  ++l+p
  gi|121639576|ref|YP_979800.1|  27 GVDLAVRSGQTVAVVGESGSGKSTTAAAILGLLPAggriTAGRVVFDGRDITGadakRLRSIRGREIGYVPQDpmTNLNP 106
                                    58999****************************9899999************9777555666678********8878888 PP

                                    TSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  73 eltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                      +v+ +            ++++++ ++l++ gl++ +++ +++ p++LSgG+ qr  +a  l+ +p+ll++DEpt+
  gi|121639576|ref|YP_979800.1| 107 VWKVGFQvtealrantdgrAARRRAVELLAEAGLPD-PAKQAGRYPHQLSGGMCQRALIAIGLAGRPRLLIADEPTS 182
                                    77777668999***9999999999************.777778********************************96 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 1.7e-31
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTC.EGGG...B-HHHCCHCEEEE-SS..--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxx..xxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgk.dlke...qeleslrkeigvlpqe..pqlfpelt 75 
                                    + vs+ l + +++aivGe+G+GKStL+++++gll+pt+G++ +dg+ d+     ++   +r++++ ++q+  ++l+p ++
  gi|121639576|ref|YP_979800.1| 308 DGVSFRLPRASTLAIVGESGSGKSTLARMVLGLLQPTSGTVVFDGTyDVGAlarDQVLAFRRRVQPVFQNpySSLDPMYS 387
                                    789**************************************88854244446669999************999******* PP

                                    HHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    v +            +++++  ++++ ++++ l+ ++++++p++LSgGq+qrva+aral+ +p++l++DE+ 
  gi|121639576|ref|YP_979800.1| 388 VFRAieeplrvhhvgDRRQRQRAVRELVDQVALPSSILGRRPRELSGGQRQRVAIARALALRPEVLVCDEAV 459
                                    99999********9888888889999999999999***********************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.9e-07   6.8e-05       1      35 [.     233     267 ..     233     280 .. 0.83
   2 !   22.5   0.1   3.4e-07   0.00012       1      27 [.     511     537 ..     511     545 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.9e-07
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdkl 35 
                                    vE g ++ ++++p+H YT+ L++++p+l+++ ++ 
  gi|121639576|ref|YP_979800.1| 233 VESGAAQSILQSPQHEYTRRLVAAAPSLTARSRRP 267
                                    8****************************999922 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.4e-07
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvpr 27 
                                    vE ++++++f++p+H YT+ Ll+++p 
  gi|121639576|ref|YP_979800.1| 511 VEHASTEEVFSRPRHEYTRQLLQAIPG 537
                                    8************************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   5.8e-05      0.02       5      38 ..      35      83 ..      32     216 .. 0.54
   2 !   23.9   0.0   1.1e-07   3.9e-05       5     117 ..     317     479 ..     315     496 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee...............e 38
                                    + ++v+GesG+GK+t+++ +l  l++   ++                +
  gi|121639576|ref|YP_979800.1| 35 GQTVAVVGESGSGKSTTAAAILGLLPAGGRITAgrvvfdgrditgadaK 83
                                   66789***************99998876555556666666666665551 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.1e-07
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............erpevv....fvtlpsst..sskdllrellral 64 
                                    a+ l+++GesG+GK+tl+r++l  l+                     +r++v+    +v++  ++  ss d +  ++ra+
  gi|121639576|ref|YP_979800.1| 317 ASTLAIVGESGSGKSTLARMVLGLLQP--T--SgtvvfdgtydvgalARDQVLafrrRVQPVFQNpySSLDPMYSVFRAI 392
                                    67799*******************952..2..245778888888888666666666655555555556666677777777 PP

                         AAA_22  65 glelka..........................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seeale 110
                                    +++l                             + + +el   + ++ + ara    +e+l+ DEa   l+   ++++l 
  gi|121639576|ref|YP_979800.1| 393 EEPLRVhhvgdrrqrqravrelvdqvalpssiLGRRPRELSgGQRQRVAIARALalrPEVLVCDEAVSaLDvlvQAQILD 472
                                    77777788999888888888888888888888444444444344444444444467889******999887777688888 PP

                         AAA_22 111 eLrslln 117
                                     L +l+ 
  gi|121639576|ref|YP_979800.1| 473 LLADLQA 479
                                    8877765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   2.2e-05    0.0077      26      59 ..      38      73 ..      26      74 .. 0.80
   2 !   18.5   0.0   4.7e-06    0.0017      26      82 ..     320     370 ..     303     422 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-05
                          DUF87 26 lAilgsTGsGKSntvavLleelle..kkgatililD 59
                                   +A++g++GsGKS+t+a +l  l +  +  a  +++D
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGLLPAggRITAGRVVFD 73
                                   8*****************987776555555666666 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.7e-06
                          DUF87  26 lAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitps 82 
                                    lAi+g++GsGKS++++  l  ll ++ + ++++D   + g++     +++v  ++ +
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVL-GLL-QPTSGTVVFDGTYDVGALA----RDQVLAFRRR 370
                                    8***********9998666.677.7*********777666666....6666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.1     2e-05    0.0069      19     107 ..      32     136 ..      28     227 .. 0.62
   2 !   23.3   0.5   1.9e-07   6.8e-05      22     162 ..     315     478 ..     294     488 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2e-05
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.sa.laqalareellrqlldeaesaelea 96 
                                    vrsg  + v ++GesG+GKs+ + ++l  l  +gg  ++g+ +  +++i+  +a  ++ + r + +  + +++ +++ + 
  gi|121639576|ref|YP_979800.1|  32 VRSG--QTVAVVGESGSGKSTTAAAIL-GLLPAGGRITAGRVVFDGRDITGaDAkRLRSI-RGREIGYVPQDPMTNLNPV 107
                                    5666..57*******************.56666566665555555555444333356666.4466677777777766666 PP

                         AAA_16  97 wrekleeala..................a 107
                                    w+  ++ + a                  a
  gi|121639576|ref|YP_979800.1| 108 WKVGFQVTEAlrantdgraarrravellA 136
                                    66666665554333333333333333330 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.9e-07
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql..esa..............ipy......salaqalar 78 
                                    +r + + ++GesG+GKs+l+r++l  l+ + g +++ g++d     ++               py      + + +a+ +
  gi|121639576|ref|YP_979800.1| 315 PRASTLAIVGESGSGKSTLARMVLGLLQPTsGTVVFDGTYDVGalARDqvlafrrrvqpvfqNPYssldpmYSVFRAI-E 393
                                    3448999*****************988888545557777777744222555555556655664442222223344444.2 PP

                         AAA_16  79 eellrqlldeaesaeleawrekleeala........avpelagaeasrllellkrllallsrderplvlvlDdlqwade. 149
                                    e l      +   ++++++ ++l +++a          +el+g   +r + +++r+lal      p vlv+D++  a + 
  gi|121639576|ref|YP_979800.1| 394 EPLRVHHVGD--RRQRQRAVRELVDQVAlpssilgrRPRELSGG--QRQRVAIARALALR-----PEVLVCDEAVSALDv 464
                                    2333333333..22233333333333335566443333333333..66666666777444.....448888887755553 PP

                         AAA_16 150 .aslqllaaLlrll 162
                                      ++q+l++L++l+
  gi|121639576|ref|YP_979800.1| 465 lVQAQILDLLADLQ 478
                                    33333355555444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   4.1e-05     0.014      20      47 ..      33      60 ..      26      66 .. 0.78
   2 !   18.2   0.0   4.4e-06    0.0015      13      49 ..     308     344 ..     303     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-05
                         AAA_29 20 dlkg.atlltGpsGsGKSTllDAiqalLv 47
                                   + +g ++ ++G+sGsGKST   Ai  lL 
  gi|121639576|ref|YP_979800.1| 33 R-SGqTVAVVGESGSGKSTTAAAILGLLP 60
                                   4.455899***********9988887775 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.4e-06
                         AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                    dg ++++ ++++  ++G+sGsGKSTl   +  lL p+
  gi|121639576|ref|YP_979800.1| 308 DGVSFRLPRASTLAIVGESGSGKSTLARMVLGLLQPT 344
                                    67788888888999***********976666666665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.014         5       3      47 ..      39      90 ..      38     107 .. 0.65
   2 !   13.7   0.1   0.00012     0.042     233     301 ..     150     216 ..     125     218 .. 0.85
   3 ?    6.5   0.1     0.018       6.3       3      24 ..     321     342 ..     320     379 .. 0.82
   4 !    9.5   0.1    0.0022      0.76     233     302 ..     428     495 ..     403     496 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.014
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl.......drdvegltdelsggggirkips 47
                                   +++G  gsGKS+   a+ +l  +       +  ++g+ ++  + + +r+i++
  gi|121639576|ref|YP_979800.1| 39 AVVGESGSGKSTTAAAILGLLPAggritagRVVFDGRDITGADAKRLRSIRG 90
                                   69***************99976655555554444444444444444444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                     +++lS G+ +  al+++ l+ ++  +ll+ DEp + L+  ++r +l+ l  ++ + g+ ++l TH+  l
  gi|121639576|ref|YP_979800.1| 150 YPHQLSGGMCQR-ALIAIGLAGRP--RLLIADEPTSALDVTVQRQVLDHLqGLTDELGTALLLITHDLAL 216
                                    67999*******.77777776665..9********************8885444448899*******887 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                         AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                    +++G  gsGKS+L +   +l +
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMVLGLLQ 342
                                    79***********998888865 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0022
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                     +relS G+++  a++ al+ ++    +l+ DE  + L+  +++ +l+ll +l++  g   ++ +H+  ++
  gi|121639576|ref|YP_979800.1| 428 RPRELSGGQRQRVAIARALALRP---EVLVCDEAVSALDVLVQAQILDLLADLQAdLGLTYLFISHDLAVI 495
                                    67999******999999999999...9***********************888888***********8876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0038       1.3      25      45 ..      36      56 ..      28      64 .. 0.84
   2 ?    4.0   0.0     0.082        29     133     205 ..     150     220 ..     112     233 .. 0.75
   3 !   15.7   0.0   2.1e-05    0.0076      26     203 ..     319     496 ..     311     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
                                   SEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                   +  a+vG+ GSGKs    Ail
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTAAAIL 56
                                   5679***************95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.082
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                    ++++LSgG   ++  aL+ Ai  + +  l + De  +aLD +  ++v + l+  +++  + ++ i+++  + ++ 
  gi|121639576|ref|YP_979800.1| 150 YPHQLSGG---MCQRALI-AIGLAGRPRLLIADEPTSALDVTVQRQVLDHLQGLTDElgTALLLITHDLALAAQR 220
                                    55688998...4555665.666677788999********************988887556677777766555443 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.1e-05
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                      aivG+ GSGKs l   +l +L  +s  ++  + + d+    +++  + + +v+ +f+n+ ++    ++ +s+ r +++
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQPTSG-TVVFDGTYDVGALARDQVLAFRRRVQPVFQNPYSS---LDPMYSVFRAIEE 394
                                    569************9999777776666.566666666655556777778899*******9998...7899999999999 PP

                                    TSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 106 kgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                      +  +++ +++ +++ v+el+ ++ + ++       +LSgG+++ va+a  +A++   p+   + De  +aLD    ++
  gi|121639576|ref|YP_979800.1| 395 PLR-VHHVGDRRQRQRAVRELVDQVALPSSilgrrprELSGGQRQRVAIARALALR---PEV-LVCDEAVSALDVLVQAQ 469
                                    888.778888999999*******99999888888898*************999974...554.578********999999 PP

                                    HHHHHHHHCTT..SEEEEE-SSHHHCC CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxx RF
                          SMC_N 179 vaellkekskn..aQfivislreemle 203
                                    + +ll   + +    ++ is++  +++
  gi|121639576|ref|YP_979800.1| 470 ILDLLADLQADlgLTYLFISHDLAVIR 496
                                    999999777663455666666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00074      0.26       2      28 ..      37      63 ..      36      73 .. 0.79
   2 !   12.4   0.2   0.00031      0.11       2      21 ..     319     338 ..     318     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00074
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                   +v++ Ge+GsGK+t ++ +  ++ +g 
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAAAILGLLPAGG 63
                                   89***************9988776655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00031
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    ++++ Ge+GsGK+tL++ + 
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVL 338
                                    799*************9876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0031       1.1      98     120 ..      34      56 ..      23      65 .. 0.85
   2 !   12.8   0.0   0.00024     0.084      90     121 ..     307     339 ..     285     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0031
                                    TTSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                    +++t+++vG+SG GKSt   a+l
  gi|121639576|ref|YP_979800.1|  34 SGQTVAVVGESGSGKSTTAAAIL 56 
                                    4699*************877665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00024
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    ++ ++ +l   +t ++vG+SG GKStL  ++l+
  gi|121639576|ref|YP_979800.1| 307 VDGVSFRLPRaSTLAIVGESGSGKSTLARMVLG 339
                                    55666666665899*************988776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2    0.0013      0.44      15      48 ..      28      61 ..      19      67 .. 0.88
   2 ?   -2.8   0.0       9.7   3.4e+03     176     197 ..     145     166 ..     143     176 .. 0.80
   3 !   10.4   0.0    0.0009      0.32      25      56 ..     320     351 ..     316     384 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                   Mg_chelatase 15 leiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                   +++a+  g  + +vG +GsGK+  a+++ +llp+
  gi|121639576|ref|YP_979800.1| 28 VDLAVRSGQTVAVVGESGSGKSTTAAAILGLLPA 61
                                   677888889999********************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.7
                   Mg_chelatase 176 keierYlsklsgplldRidlqv 197
                                    k+  rY ++lsg +  R  + +
  gi|121639576|ref|YP_979800.1| 145 KQAGRYPHQLSGGMCQRALIAI 166
                                    6778999999999999977766 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0009
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeeale 56 
                                    l +vG +GsGK+ la+ + +ll p s + +++
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLGLLQPTSGTVVFD 351
                                    6789******************9988766555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0048       1.7       2      24 ..      38      60 ..      38     143 .. 0.88
   2 ?   -0.5   0.1       3.7   1.3e+03      53     107 ..     205     259 ..     179     278 .. 0.72
   3 !   11.2   0.0   0.00087      0.31       4      23 ..     322     341 ..     320     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0048
                         AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                   v +vG +GsGKst a  +l  l+
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGLLP 60
                                   5689***********99886665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.7
                         AAA_33  53 drlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetd 107
                                    + l  i+++la  a++a++ v+++ + + ++  a+ +   +++++ +r+v+  ++
  gi|121639576|ref|YP_979800.1| 205 TALLLITHDLALAAQRAEAVVVVRRGVVVESGAAQSILQSPQHEYTRRLVAAAPS 259
                                    5566688899988999999999988887776666555555566666666665555 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00087
                         AAA_33   4 lvGlpGsGKstlaerllkkl 23 
                                    +vG +GsGKstla+ +l  l
  gi|121639576|ref|YP_979800.1| 322 IVGESGSGKSTLARMVLGLL 341
                                    79************986544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0015      0.53       2      22 ..      35      55 ..      34      77 .. 0.88
   2 !   10.9   0.0    0.0008      0.28       4      23 ..     319     344 ..     316     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                         AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                   ++ ++++G+sg+GK+t+a+ +
  gi|121639576|ref|YP_979800.1| 35 GQTVAVVGESGSGKSTTAAAI 55
                                   57899************9876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0008
                         AAA_24   4 kiliyGpsgiGKTtlakel......g 23 
                                     ++i+G+sg+GK+tla++       +
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVlgllqpT 344
                                    689*************9886655443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1     0.003         1      17      42 ..      30      55 ..      23      64 .. 0.86
   2 !    9.5   0.0    0.0021      0.75      22      44 ..     317     339 ..     303     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.003
                                   HHCTSSS-EEEECSTTSSHHHHHHHH CS
                Sigma54_activat 17 kvaktdlsvlitGesGtGKellarai 42
                                    ++++  +v ++GesG+GK++ a ai
  gi|121639576|ref|YP_979800.1| 30 LAVRSGQTVAVVGESGSGKSTTAAAI 55
                                   56778899***************998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                                    SS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraihe 44 
                                     +++ i+GesG+GK++lar++  
  gi|121639576|ref|YP_979800.1| 317 ASTLAIVGESGSGKSTLARMVLG 339
                                    56788**************9865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0025      0.88       2      21 ..      38      57 ..      37      95 .. 0.73
   2 !    9.3   0.1    0.0033       1.2       2      21 ..     320     339 ..     319     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0025
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   va+vG + +GKSt   a++g
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILG 57
                                   9****************997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0033
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                     aivG + +GKStL +  +g
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLG 339
                                    69************998776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0033       1.2      20      41 ..      36      57 ..      10      84 .. 0.84
   2 !    9.7   0.0    0.0031       1.1      23      37 ..     321     335 ..     307     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0033
                         AAA_23 20 gltlItGpNGaGKTTildAikl 41
                                     ++++G+ G+GK+T   Ai  
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTAAAILG 57
                                   56789**************965 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0031
                         AAA_23  23 lItGpNGaGKTTild 37 
                                    +I+G+ G+GK+T+ +
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLAR 335
                                    7***********976 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0      0.01       3.5       3      26 ..      39      62 ..      37     106 .. 0.74
   2 !   10.3   0.0    0.0014      0.51       3      28 ..     321     346 ..     319     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                   EEE--SSSSHHHHHHHGGGGBS-- CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnre 26
                                    +vG++G+gKs+ a  ++ +l + 
  gi|121639576|ref|YP_979800.1| 39 AVVGESGSGKSTTAAAILGLLPAG 62
                                   679**************9999443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
                                    EEE--SSSSHHHHHHHGGGGBS--EE CS
                          AAA_5   3 lLvGppGtgKselaerlaaalnreve 28 
                                     +vG++G+gKs+la+ ++ +l+ +  
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMVLGLLQPTSG 346
                                    589**************999954444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6     0.017       6.1      19      40 ..      38      59 ..      32      71 .. 0.83
   2 !   12.1   0.0   0.00024     0.085      20      51 ..     321     352 ..     311     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                     Zeta_toxin 19 illgGqpGAGKselaellkdel 40
                                   + ++G +G+GKs++a+++   l
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGLL 59
                                   6799***********9997666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00024
                     Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrldp 51 
                                     ++G +G+GKs+la+++   l+++++ v++d+
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMVLGLLQPTSGTVVFDG 352
                                    578********************999999986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.027       9.5      31      52 ..      33      54 ..      28      87 .. 0.84
   2 ?    1.1   0.0       0.7   2.5e+02     163     188 ..     184     212 ..     171     213 .. 0.80
   3 !    8.6   0.0    0.0035       1.2      29      50 ..     313     334 ..     301     419 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                         AAA_25 31 pagelallaGapgtGKttlald 52
                                   + g +++++G +g+GK+t a  
  gi|121639576|ref|YP_979800.1| 33 RSGQTVAVVGESGSGKSTTAAA 54
                                   568899***********98865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.7
                         AAA_25 163 sdv...galvealeriarrtgaavllvhH 188
                                     dv   ++++++l+ + +++g a+ll+ H
  gi|121639576|ref|YP_979800.1| 184 LDVtvqRQVLDHLQGLTDELGTALLLITH 212
                                    44334799********************9 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0035
                         AAA_25  29 llpagelallaGapgtGKttla 50 
                                     lp+ ++ +++G +g+GK+tla
  gi|121639576|ref|YP_979800.1| 313 RLPRASTLAIVGESGSGKSTLA 334
                                    58999***************98 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.016       5.7      22      41 ..      37      56 ..      30      59 .. 0.88
   2 !   11.2   0.0   0.00045      0.16      22      55 ..     319     354 ..     310     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                   EEEEEESTTSSHHHHHHHHC CS
                         NB-ARC 22 vvalvGmgGvGKttlakqil 41
                                    va+vG  G+GK+t a+ il
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAAAIL 56
                                   799***********999885 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00045
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCC..CBTEEE CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg..rFdsva 55 
                                     +a+vG  G+GK+tla+ +l  ++ + g   Fd+  
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQPTSGtvVFDGTY 354
                                    689**************9987776666644566655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.012       4.1      17      37 ..      33      53 ..      24      56 .. 0.89
   2 !    9.1   0.0    0.0021      0.73      15      36 ..     313     334 ..     307     338 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                         ATPase 17 pegrvvlitGepGtGKtifal 37
                                    +g++v ++Ge+G+GK++ a+
  gi|121639576|ref|YP_979800.1| 33 RSGQTVAVVGESGSGKSTTAA 53
                                   5799*************9886 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                         ATPase  15 GipegrvvlitGepGtGKtifa 36 
                                     +p++++  i+Ge+G+GK+++a
  gi|121639576|ref|YP_979800.1| 313 RLPRASTLAIVGESGSGKSTLA 334
                                    589*****************98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00097      0.34      27      57 ..      29      59 ..      25      67 .. 0.87
   2 ?    5.9   0.0     0.024       8.3      35      58 ..     319     342 ..     311     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                          AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkl 57
                                   +l +++++ v +vG++G+GK++++  +l  l
  gi|121639576|ref|YP_979800.1| 29 DLAVRSGQTVAVVGESGSGKSTTAAAILGLL 59
                                   788999*****************99877655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                          AAA_7  35 pvllvGptGtGKtviikdllkkld 58 
                                     + +vG++G+GK+++++ +l  l+
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQ 342
                                    5679***********999887666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0091       3.2       2      31 ..      35      64 ..      34     117 .. 0.77
   2 !    8.8   0.0     0.004       1.4       2      38 ..     317     352 ..     316     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0091
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT- CS
                     APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgi 31
                                   g +v + G sgsGKst a a+   L + g+
  gi|121639576|ref|YP_979800.1| 35 GQTVAVVGESGSGKSTTAAAILGLLPAGGR 64
                                   6789999************99888877664 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.004
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEH CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdG 38 
                                    + ++ + G sgsGKst+a+++   L+     +++ dG
  gi|121639576|ref|YP_979800.1| 317 ASTLAIVGESGSGKSTLARMVLGLLQP-TSGTVVFDG 352
                                    5688999***********999865543.444455555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.014       4.8      44      67 ..      32      55 ..      27      64 .. 0.90
   2 !    8.6   0.0    0.0041       1.4      24      65 ..     291     335 ..     282     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                      IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                   +++ + ++++G sG GKs  a+a+
  gi|121639576|ref|YP_979800.1| 32 VRSGQTVAVVGESGSGKSTTAAAI 55
                                   577899*************99996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0041
                      IstB_IS21  24 fraarsldkrkvk..eLatlsf.iekkenivllGpsGvGKshlai 65 
                                    +r++r++  r+v+  ++ + sf + ++  ++++G sG GKs la 
  gi|121639576|ref|YP_979800.1| 291 YRESRGAPWRRVEsrAVDGVSFrLPRASTLAIVGESGSGKSTLAR 335
                                    66777777777764466777885678999**************95 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0053       1.9      40      59 ..      36      55 ..      14      61 .. 0.77
   2 !    8.0   0.1    0.0047       1.6      40      64 ..     318     341 ..     301     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0053
                                   .SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE 40 shllvaGatgsGKStalntL 59
                                   + + v+G +gsGKSt+  ++
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTAAAI 55
                                   4689***********97765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0047
                                    .SEEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  40 shllvaGatgsGKStalntLilSla 64 
                                    s l ++G +gsGKSt    ++l+l+
  gi|121639576|ref|YP_979800.1| 318 STLAIVGESGSGKSTL-ARMVLGLL 341
                                    5799**********85.55666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00062      0.22     124     160 ..      30      65 ..      14      82 .. 0.90
   2 ?    4.9   0.1     0.032        11     131     158 ..     319     346 ..     308     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00062
                          T2SSE 124 kavrerglilvsGgTgsGKttllyallkeinksderi 160
                                     avr+ +++ v G  gsGK+t++ a+l  +++   ri
  gi|121639576|ref|YP_979800.1|  30 LAVRSGQTVAVVGESGSGKSTTAAAILGLLPAG-GRI 65 
                                    588999999*******************99987.555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                          T2SSE 131 lilvsGgTgsGKttllyallkeinksde 158
                                    ++ + G  gsGK+tl+ ++l  ++ ++ 
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQPTSG 346
                                    56688***************99987755 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   1.2    0.0038       1.3       4      27 ..      40      63 ..      37      70 .. 0.82
   2 ?    7.0   0.0     0.016       5.6       6      69 ..     324     395 ..     320     467 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                                   EESSTTSSHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  4 astkGGvGKTtlaanLaralarrg 27
                                   + + +G+GK+t+aa+++ +l  +g
  gi|121639576|ref|YP_979800.1| 40 VVGESGSGKSTTAAAILGLLPAGG 63
                                   5689************99998744 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                                    SSTTSSHHHHHHHHHHHHHHTT--EEEEE..EEESSCCCCHHTTEB-HHHH.......CCHCCCHHHHHHCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF
                           CbiA   6 tkGGvGKTtlaanLaralarrglrVllvD..aDpqannlaileglendiep.......dlkrllellealgkk 69 
                                    + +G+GK+tla   + +l+     ++++D   D+ a +   +   + +++p       +l+ +  +++a+ ++
  gi|121639576|ref|YP_979800.1| 324 GESGSGKSTLARMVLGLLQP-TSGTVVFDgtYDVGALARDQVLAFRRRVQPvfqnpysSLDPMYSVFRAIEEP 395
                                    78**********99999998.7777778755566655544333333333336666666444444444444444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.017       5.8       2      20 ..      38      56 ..      37      71 .. 0.87
   2 !    8.8   0.0    0.0035       1.2       3      72 ..     321     390 ..     319     417 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                            PRK  2 IgvagsSGaGkttvarkle 20
                                   ++v g+SG+Gk+t+a+++ 
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAIL 56
                                   689***********99885 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0035
                            PRK   3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleer.krakekevsflspeandfd 72 
                                    ++ g+SG+Gk+t+ar +  +++  +  +++ +g+ ++     ++ l+ ++r +  +++ +s l+p    f 
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMVLGLLQ-PTSGTVVFDGTYDVGALARDQVLAFRRRvQPVFQNPYSSLDPMYSVFR 390
                                    899***********99888887.333324444444444444444444443312234444444444444444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0         1   3.5e+02      36      52 ..      36      52 ..      31      56 .. 0.85
   2 !    7.2   0.1    0.0087         3     119     168 ..     171     218 ..     157     228 .. 0.85
   3 ?    4.7   0.0     0.051        18      34      53 ..     316     335 ..     312     345 .. 0.88
   4 ?    1.2   0.1       0.6   2.1e+02     114     156 ..     444     484 ..     405     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                           TniB 36 pnlllvGdsnnGKtmiv 52
                                   + + +vG+s  GK++ +
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTA 52
                                   6789**********965 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0087
                           TniB 119 kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealra 168
                                    ++r+Li DE  ++l   ++ qr++l  l+ L++el  ++ l+  + al+a
  gi|121639576|ref|YP_979800.1| 171 RPRLLIADEPTSAL--DVTVQRQVLDHLQGLTDELGTALLLITHDLALAA 218
                                    689***********..77889**************999998877766665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.051
                           TniB  34 rmpnlllvGdsnnGKtmive 53 
                                    r + l +vG+s  GK+++++
  gi|121639576|ref|YP_979800.1| 316 RASTLAIVGESGSGKSTLAR 335
                                    77899************986 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.6
                           TniB 114 llrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                       +l+++vL+ DE  ++l   +  q ++l +l  L+ +l ++
  gi|121639576|ref|YP_979800.1| 444 RALALRPEVLVCDEAVSAL--DVLVQAQILDLLADLQADLGLT 484
                                    44467889*******9999..6777788888888888887765 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.018       6.3      39      59 ..      38      58 ..      34      61 .. 0.86
   2 !    9.3   0.0    0.0015      0.52      39      62 ..     320     343 ..     308     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                        DUF3987 39 tlvvapsGerKSpvdklvlrp 59
                                   ++vv++sG++KS+++ ++l +
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGL 58
                                   689***********9887766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                        DUF3987  39 tlvvapsGerKSpvdklvlrplee 62 
                                    +++v++sG++KS+++++vl +l++
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLGLLQP 343
                                    689****************99986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.038        13       2      22 ..      39      59 ..      38      92 .. 0.67
   2 ?    7.6   0.0     0.014       4.9       3      23 ..     322     342 ..     320     495 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.038
                                   EEESSTTSSHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakel 22
                                    ++G  G GK+++a a+   l
  gi|121639576|ref|YP_979800.1| 39 AVVGESGSGKSTTAAAILGLL 59
                                   589**************9876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.014
                                    EESSTTSSHHHHHHHHHHHHT CS
                            AAA   3 lyGppGtGKTllakavakelg 23 
                                    ++G  G GK++la+ v   l+
  gi|121639576|ref|YP_979800.1| 322 IVGESGSGKSTLARMVLGLLQ 342
                                    79**************98875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.028       9.9       2      33 ..      38      69 ..      37      86 .. 0.84
   2 !    8.3   0.0    0.0056         2       2      26 ..     320     344 ..     319     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf 33
                                   v++ G++G+GK+T    +l ll   g   +G 
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGLLPAGGRITAGR 69
                                   7899***************9998777777765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0056
                                    EEEE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                    ++i G++G+GK+Tl + vl ll+  
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLGLLQPT 344
                                    6799***************999754 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.041        14       2      18 ..      39      55 ..      38      71 .. 0.86
   2 ?    7.6   0.0     0.014       4.8       2      18 ..     321     337 ..     320     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.041
                   RNA_helicase  2 wlyGpsgeGKStlakeL 18
                                    ++G+sg GKSt+a  +
  gi|121639576|ref|YP_979800.1| 39 AVVGESGSGKSTTAAAI 55
                                   689*********99874 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.014
                   RNA_helicase   2 wlyGpsgeGKStlakeL 18 
                                     ++G+sg GKStla+ +
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMV 337
                                    589**********9974 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.075        26      16      43 ..      36      63 ..      24      82 .. 0.76
   2 ?    8.0   0.0    0.0034       1.2      16      91 ..     318     399 ..     304     405 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.075
                  TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairarg 43
                                   q +++vG  GsGK++++ ++l  + a g
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTAAAILGLLPAGG 63
                                   67899***********999987665555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0034
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlDlt...Gaf....vsrfydegkdillnPlDaRsaaWsvfaeikeks 88 
                                    + ++ivG  GsGK++ ++ ++ ++ +     +v+D t   Ga+    v +f +  +++  nP+ +  +  svf+ i+e+ 
  gi|121639576|ref|YP_979800.1| 318 STLAIVGESGSGKSTLAR-MVLGLLQPTSGTVVFDGTydvGALardqVLAFRRRVQPVFQNPYSSLDPMYSVFRAIEEPL 396
                                    5679**********8665.5567777888999999764445552222446888999999999999999999999888876 PP

                  TrwB_AAD_bind  89 dfa 91 
                                     ++
  gi|121639576|ref|YP_979800.1| 397 RVH 399
                                    665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.069        24       3      21 ..      37      55 ..      35      64 .. 0.86
   2 ?    7.0   0.0     0.011       3.9       3      78 ..     319     394 ..     317     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.069
                                   EEEEEESTTSSHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKL 21
                                    +++vG  G+GK tt+a +
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAAAI 55
                                   5789***********9865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTS.CHHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeea.dpaavakeavek 78 
                                     +++vG  G+GK t +  +  ll+    +v++  +    a A +Q+ ++ ++++ pv+++   + dp+  +++a+e+
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQPTSGTVVFDGTYDVGALARDQVLAFRRRVQ-PVFQNPYSSlDPMYSVFRAIEE 394
                                    5789********998877777888777777777766667778899999999999.89986666569*9999999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.061        21       1      18 [.      38      55 ..      38     131 .. 0.86
   2 ?    6.8   0.0     0.027       9.7       3      17 ..     322     336 ..     320     419 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.061
                         AAA_18  1 IlltGtpGvGKttlakeL 18
                                   +++ G +G+GK+t a ++
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAI 55
                                   6899*********99876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.027
                         AAA_18   3 ltGtpGvGKttlake 17 
                                    + G +G+GK+tla+ 
  gi|121639576|ref|YP_979800.1| 322 IVGESGSGKSTLARM 336
                                    8899*********96 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0038       1.3       1      33 [.      38      68 ..      38      72 .. 0.81
   2 ?    6.0   0.3     0.031        11       1      20 [.     320     339 ..     320     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                   +avvG+  sGKS+ + a+lg  +lp g  +t  
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILG--LLPAGGRITAG 68
                                   89*****************9..45776666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                                    EEEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlg 20 
                                    +a+vG+  sGKS+++  +lg
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLG 339
                                    589***********999998 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.089        31      25      41 ..      37      53 ..      30      62 .. 0.84
   2 ?    6.7   0.0    0.0098       3.5      25      47 ..     319     341 ..     304     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.089
                                   EEEEEESTTSSHHHHHH CS
                        G-alpha 25 kllllGqseSGKsTilk 41
                                   ++ ++G+s+SGKsT+  
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAA 53
                                   57789*********975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0098
                                    EEEEEESTTSSHHHHHHHHHHHC CS
                        G-alpha  25 kllllGqseSGKsTilkqlklly 47 
                                    +l ++G+s+SGKsT+ + +  l 
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLL 341
                                    7899***********99876555 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.63   2.2e+02     224     264 ..      13      55 ..       4      99 .. 0.74
   2 ?    0.7   0.0       0.5   1.8e+02     321     366 ..     152     197 ..     115     265 .. 0.78
   3 ?   -0.2   0.0      0.94   3.3e+02     246     262 ..     319     335 ..     303     338 .. 0.77
   4 ?    6.2   0.1     0.011       3.9     324     419 ..     433     513 ..     429     535 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.63
                                    GGEEEEEETTTEEEEE..EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 224 sleveielpngkkvsG..mgipkG.vtlIvGggfhGKsTLLeAl 264
                                     lev++ +    +v G  ++++ G  +++vG    GKsT   A+
  gi|121639576|ref|YP_979800.1|  13 GLEVTFGTDA-PAVCGvdLAVRSGqTVAVVGESGSGKSTTAAAI 55 
                                    5566665554.455553367889966679999999999988887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.5
                                    SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS CS
                     ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelv 366
                                    ++ SG + q a i+  l  + +ll+ DE tsA    ++ + +++l 
  gi|121639576|ref|YP_979800.1| 152 HQLSGGMCQRALIAIGLAGRPRLLIADEPTSALDVTVQRQVLDHLQ 197
                                    56799999999999999999999999*****998887766666665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.94
                                    EEEEEE-TTSSHHHHHH CS
                     ABC_ATPase 246 vtlIvGggfhGKsTLLe 262
                                      +IvG    GKsTL +
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLAR 335
                                    457************76 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.011
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTT CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyld 403
                                    SG   q ++i++al ++ ++l+ DE  sA   ++     q+           ++d++++l ++lg++ + ++  +    +
  gi|121639576|ref|YP_979800.1| 433 SGGQRQRVAIARALALRPEVLVCDEAVSALDVLV-----QAQ----------ILDLLADLQADLGLTYLFISHDLAVIRQ 497
                                    8999999999999999999999999999999988.....222..........3677778888888888888888888888 PP

                                    T-SEEEEEETTEEEE- CS
                     ABC_ATPase 404 vAdtvilmeeykpkdv 419
                                    +Ad v++m++ ++ + 
  gi|121639576|ref|YP_979800.1| 498 IADDVLVMRAGRVVEH 513
                                    8888888877666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.2     0.013       4.4      13      63 ..      31      86 ..      27     227 .. 0.81
   2 ?    1.0   0.4      0.84     3e+02      47      99 ..     212     289 ..     181     308 .. 0.77
   3 ?    6.5   0.0     0.018       6.2      20      49 ..     319     348 ..     312     367 .. 0.77
   4 ?    2.1   0.0      0.38   1.3e+02     105     129 ..     385     408 ..     380     450 .. 0.80
   5 ?   -1.3   0.1       4.4   1.6e+03      81     115 ..     433     477 ..     407     483 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                         AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaag....grvi..glAptgkaAkvLa 63
                                   ++ sg+ +++++G  G+GK+t+ +a+  ++ a g    grv+  g   tg+ Ak+L+
  gi|121639576|ref|YP_979800.1| 31 AVRSGQ-TVAVVGESGSGKSTTAAAILGLLPAGGritaGRVVfdGRDITGADAKRLR 86
                                   556664.999****************9999988877776665445556666666666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.84
                         AAA_30  47 grviglAptgkaAkvLaeelgieastiakllkrlk.........................grarlepgtllivDEagm 99 
                                    ++++++A  ++a  v+++++ +e+   +++l++ +                         +ra+ ++g++l+v E   
  gi|121639576|ref|YP_979800.1| 212 HDLALAAQRAEAVVVVRRGVVVESGAAQSILQSPQheytrrlvaaapsltarsrrppesrSRATTQAGDILVVSELTK 289
                                    667788888999999999999999888888877778888888888888888888998887667777779999888765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                         AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                    + +++G  G+GK+t+ + +  +++   g+v
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLGLLQPTSGTV 348
                                    5689***********999988888774444 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.38
                         AAA_30 105 laallkaaekagakvilvGDerQla 129
                                    + ++++a+e+   +v  vGD+rQ +
  gi|121639576|ref|YP_979800.1| 385 MYSVFRAIEE-PLRVHHVGDRRQRQ 408
                                    6778888988.99**********86 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4.4
                         AAA_30  81 k.........grarlepg.tllivDEagmv.dtkqlaallkaaeka 115
                                              +  +l+ + ++l+ DEa  + d    a++l+ +++ 
  gi|121639576|ref|YP_979800.1| 433 SggqrqrvaiA-RALALRpEVLVCDEAVSAlDVLVQAQILDLLADL 477
                                    34444555543.2344444899999985443777777777776665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.2        69       2      26 ..      38      62 ..      37      86 .. 0.86
   2 ?    7.1   0.1     0.013       4.6       2      24 ..     320     342 ..     319     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.2
                           MobB  2 lgivgksgsGKTtLleklipelkar 26
                                   +++vg sgsGK t    ++  l a 
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAAILGLLPAG 62
                                   789**********999988877655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                           MobB   2 lgivgksgsGKTtLleklipelk 24 
                                    l+ivg sgsGK tL   ++  l+
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLGLLQ 342
                                    89************999988876 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1       0.1        36      22      41 ..      36      55 ..      24      68 .. 0.81
   2 ?    6.5   0.0    0.0097       3.4      20      42 ..     316     338 ..     303     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
                         AAA_10 22 sasliiGdlGnGKSvlakll 41
                                     ++++G+ G GKS +a  +
  gi|121639576|ref|YP_979800.1| 36 QTVAVVGESGSGKSTTAAAI 55
                                   4569**********998766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0097
                         AAA_10  20 nasasliiGdlGnGKSvlakllv 42 
                                    +as  +i+G+ G GKS la+++ 
  gi|121639576|ref|YP_979800.1| 316 RASTLAIVGESGSGKSTLARMVL 338
                                    67888*************99875 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.087        31      23      47 ..      33      57 ..      29      64 .. 0.88
   2 ?    4.7   0.0      0.03        11      19      54 ..     311     346 ..     297     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.087
                           DLIC 23 PsgksvlvlGedgsGkttliaklqG 47
                                    sg++v v+Ge+gsGk+t  a + G
  gi|121639576|ref|YP_979800.1| 33 RSGQTVAVVGESGSGKSTTAAAILG 57
                                   5899*************99888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                           DLIC  19 ssklPsgksvlvlGedgsGkttliaklqGveeekkG 54 
                                    s +lP + ++ ++Ge+gsGk+tl   + G+ ++  G
  gi|121639576|ref|YP_979800.1| 311 SFRLPRASTLAIVGESGSGKSTLARMVLGLLQPTSG 346
                                    5689*******************9888887776666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.22        76      13      41 ..      29      57 ..      20      67 .. 0.79
   2 ?    6.2   0.0     0.028       9.9      19      44 ..     317     342 ..     301     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                                   HHHHCHTEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 13 klakalgdvilLeGdLGaGKTtlvrglak 41
                                   +la   g++++  G+ G+GK+t + +++ 
  gi|121639576|ref|YP_979800.1| 29 DLAVRSGQTVAVVGESGSGKSTTAAAILG 57
                                   555555889*************9988875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.028
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    ++++++ G+ G+GK+tl+r ++  l+
  gi|121639576|ref|YP_979800.1| 317 ASTLAIVGESGSGKSTLARMVLGLLQ 342
                                    4568999************9987664 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5    0.0009      0.32       2      22 ..      37      57 ..      36      68 .. 0.94
   2 ?    2.1   0.3      0.28     1e+02       2      22 ..     319     339 ..     318     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0009
                                   EEEEESSTTSSHHHHHHHHHT CS
                           AIG1  2 tivlvGktgnGkSaTgNsilg 22
                                   t+ +vG +g+GkS+T+ +ilg
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAAAILG 57
                                   7889***************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                                    EEEEESSTTSSHHHHHHHHHT CS
                           AIG1   2 tivlvGktgnGkSaTgNsilg 22 
                                    t+ +vG +g+GkS+ +  +lg
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLARMVLG 339
                                    6789*********98877776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.067        24      25      44 ..      37      56 ..      28      75 .. 0.89
   2 ?    4.4   0.0     0.074        26      26      47 ..     320     341 ..     311     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.067
                         AAA_15 25 ltvliGkNnsGKSsileald 44
                                   +  ++G+ +sGKS+ + a+ 
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTAAAIL 56
                                   5689************9995 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.074
                         AAA_15  26 tvliGkNnsGKSsilealdlFl 47 
                                      ++G+ +sGKS+++++   +l
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARMVLGLL 341
                                    689***********98865555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.055        19       9      40 ..      34      65 ..      29      87 .. 0.82
   2 ?    2.9   0.0      0.36   1.3e+02      10      36 ..     317     343 ..     310     365 .. 0.86
   3 ?   -1.2   0.0       6.8   2.4e+03     118     141 ..     385     407 ..     379     412 .. 0.79
   4 ?   -1.5   0.1       8.2   2.9e+03     100     127 ..     448     476 ..     432     483 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.055
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggv 40
                                   + ++++v++  G+GK+++  +i+ ll + g++
  gi|121639576|ref|YP_979800.1| 34 SGQTVAVVGESGSGKSTTAAAILGLLPAGGRI 65
                                   568999************99999888776665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.36
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallve 36 
                                    +++l++++  G+GK+++ ++++ ll+ 
  gi|121639576|ref|YP_979800.1| 317 ASTLAIVGESGSGKSTLARMVLGLLQP 343
                                    67899***********99998887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 6.8
                         AAA_19 118 qyrLlkallgekkklllvGDpdQl 141
                                    +y++++a+ ++   +  vGD+ Q 
  gi|121639576|ref|YP_979800.1| 385 MYSVFRAIEEPLR-VHHVGDRRQR 407
                                    7899999994445.9******996 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 8.2
                         AAA_19 100 lqeeellivDE.fqdvd.elqyrLlkallg 127
                                    l + e+l+ DE ++ +d  +q ++l+ l++
  gi|121639576|ref|YP_979800.1| 448 L-RPEVLVCDEaVSALDvLVQAQILDLLAD 476
                                    3.6679999995589999999999998875 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.097        34       6      21 ..      37      52 ..      34      58 .. 0.85
   2 ?    5.6   0.1     0.024       8.3       6      22 ..     319     335 ..     316     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.097
                                   EEEEEEBTTSSCCCCC CS
                         Septin  6 tlmvvGesglGkttli 21
                                   t+ vvGesg Gk+t  
  gi|121639576|ref|YP_979800.1| 37 TVAVVGESGSGKSTTA 52
                                   789**********965 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                                    EEEEEEBTTSSCCCCCC CS
                         Septin   6 tlmvvGesglGkttlin 22 
                                    tl +vGesg Gk+tl +
  gi|121639576|ref|YP_979800.1| 319 TLAIVGESGSGKSTLAR 335
                                    899***********976 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.067        24       1      22 [.      40      61 ..      40      67 .. 0.83
   2 ?    4.5   0.1     0.073        26       1      20 [.     322     341 ..     322     351 .. 0.81
   3 ?   -0.9   0.0       3.3   1.2e+03     200     235 ..     384     418 ..     368     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.067
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilel 22
                                   vvG  GsGK+t   a+  +l++
  gi|121639576|ref|YP_979800.1| 40 VVGESGSGKSTTAAAILGLLPA 61
                                   89*********99988777766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.073
                     ATP_bind_1   1 vvGpaGsGKttfvgalseil 20 
                                    +vG  GsGK+t+ + +  +l
  gi|121639576|ref|YP_979800.1| 322 IVGESGSGKSTLARMVLGLL 341
                                    79*********998776555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.3
                     ATP_bind_1 200 laeaiaelleefalvlrflplssekeesiedllsli 235
                                     ++++ +++ee+ +v   + + ++++ ++ +l++++
  gi|121639576|ref|YP_979800.1| 384 PMYSVFRAIEEPLRV-HHVGDRRQRQRAVRELVDQV 418
                                    6789999********.9999********99999887 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.34   1.2e+02       2      16 ..      38      52 ..      37      57 .. 0.84
   2 ?    6.3   0.1     0.031        11       2      18 ..     320     336 ..     319     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.34
                                   EEEESSTTSSHHHHH CS
                            Roc  2 vvlvGdsgvGKtsll 16
                                   v +vG+sg+GK++ +
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTA 52
                                   689*********966 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                                    EEEESSTTSSHHHHHHC CS
                            Roc   2 vvlvGdsgvGKtsllkr 18 
                                    + +vG+sg+GK++l++ 
  gi|121639576|ref|YP_979800.1| 320 LAIVGESGSGKSTLARM 336
                                    679***********875 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.62   2.2e+02       1      17 [.      38      54 ..      38      59 .. 0.85
   2 ?    1.8   0.2      0.48   1.7e+02     112     123 ..      67      78 ..      63      82 .. 0.86
   3 ?    6.1   0.1     0.024       8.4       2      18 ..     321     337 ..     320     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.62
                                   EEEE-STTSSHHHHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvara 17
                                   +a+ G +gsGKs+ a a
  gi|121639576|ref|YP_979800.1| 38 VAVVGESGSGKSTTAAA 54
                                   68899********9876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.48
                                    SSBEEEEESSII CS
                 Cytidylate_kin 112 karvvveGRDig 123
                                     +rvv++GRDi+
  gi|121639576|ref|YP_979800.1|  67 AGRVVFDGRDIT 78 
                                    689********8 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                                    EEE-STTSSHHHHHHHH CS
                 Cytidylate_kin   2 aiDGPagsGKssvaral 18 
                                    ai G +gsGKs++ar++
  gi|121639576|ref|YP_979800.1| 321 AIVGESGSGKSTLARMV 337
                                    899************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              51  [number of targets reported over threshold]
# CPU time: 0.76u 0.27s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 3575.37
//
Query:       gi|121639577|ref|YP_979801.1|  [L=266]
Description: dipeptide-transport integral membrane protein ABC transporter dppC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-30  104.8  13.9    4.4e-30  104.8  13.9    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.7     0.071   1.3e+03     159     177 ..       3      21 ..       1      29 [. 0.51
   2 !  104.8  13.9   2.5e-34   4.4e-30       2     183 ..      79     261 ..      78     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.071
                   BPD_transp_1 159 lalviavlllnlvadilqr 177
                                    +a++i+++l+++++  l +
  gi|121639577|ref|YP_979801.1|   3 AAALILLILVVAAFPSLFT 21 
                                    3444444444444444444 PP

  == domain 2  score: 104.8 bits;  conditional E-value: 2.5e-34
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilp.viillllsaapyvrlirraalrsl 79 
                                      lG+la+ ++++++d +++++++v+l+lP ++ ai+l       ++ +  +++  ++il+l++++ ++r+ r a+l+++
  gi|121639577|ref|YP_979801.1|  79 GALGALAG-FYGSWIDAVVSRVTDVFLGLPLLLAAIVLM------QVMHhRTVWTvIAILALFGWPQVARIARGAVLEVR 151
                                    679*****.************************999999......677646777789*********************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                     +d+v aa+alG++r+qi+ +++lPna+ p+i+ + +a+g+++   + l++lg    +g+++  +++g d++ ++     
  gi|121639577|ref|YP_979801.1| 152 ASDYVLAAKALGLNRFQILLRHALPNAVGPVIAVATVALGIFIVTEATLSYLG----VGLPTSVVSWGGDINVAQtrlrs 227
                                    *****************************************************....*********************** PP

                   BPD_transp_1 155 .....nggvlalviavlllnlvadilqrlldprv 183
                                         + ++ al+i vl+++   d+l ++ldp  
  gi|121639577|ref|YP_979801.1| 228 gspilFYPAGALAITVLAFMMMGDALRDALDPAS 261
                                    *******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1749.22
//
Query:       gi|121639578|ref|YP_979802.1|  [L=308]
Description: dipeptide-transport integral membrane protein ABC transporter dppB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-34  119.9  15.8      1e-34  119.9  15.8    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.3       0.2   3.6e+03      29      43 ..      12      26 ..       8     108 .. 0.51
   2 !  119.9  15.8   5.7e-39     1e-34       1     185 []     113     307 ..     113     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.2
                   BPD_transp_1 29 slPsfvlaillvlvf 43
                                   ++P+f+ a ll++  
  gi|121639578|ref|YP_979802.1| 12 MVPVFLGATLLIYGM 26
                                   566666444433322 PP

  == domain 2  score: 119.9 bits;  conditional E-value: 5.7e-39
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaapyvr 69 
                                    gi++G++a+l++++++d ++++   v+ ++P+fvl++l +++f               ++g l lp+i+l+++s+a +vr
  gi|121639578|ref|YP_979802.1| 113 GIGFGVIAGLRQGGIFDSAVLVTGLVIIAIPIFVLGFLAQFLFgvqleiapvtvGERASVGRLLLPGIVLGAMSFAYVVR 192
                                    89**************************************999***********99************************ PP

                   BPD_transp_1  70 lirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgyd 149
                                    l+r+a+  +   d+v++a+a+G+sr +++  ++l+n+l+p++t+l+  +g+l+gga+++e +++ +G+g +l +a   + 
  gi|121639578|ref|YP_979802.1| 193 LTRSAVAANAHADYVRTATAKGLSRPRVVTVHILRNSLIPVVTFLGADLGALMGGAIVTEGIFNIHGVGGVLYQAVTRQE 272
                                    ******************************************************************************** PP

                   BPD_transp_1 150 yseisnggvlalviavlllnlvadilqrlldprvrk 185
                                    ++     +v +lv+++l+ nl++d+l+++ldpr+r+
  gi|121639578|ref|YP_979802.1| 273 TPTVV-SIVTVLVLIYLITNLLVDLLYAALDPRIRY 307
                                    **999.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1972.73
//
Query:       gi|121639579|ref|YP_979803.1|  [L=541]
Description: periplasmic dipeptide-binding lipoprotein dppA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-46  159.0   0.3      2e-46  158.7   0.3    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.3   1.1e-50     2e-46       5     375 ..      79     462 ..      75     464 .. 0.91

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 1.1e-50
                                    SSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC...............TCTEEE CS
                      SBP_bac_5   5 aLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee...............dqdikk 69 
                                     +A+s+ e s+D+  y+++ ++g kF+DG+p+tA+ +v ++++ +   +a+  + ++++                ++  +
  gi|121639579|ref|YP_979803.1|  79 EVAQSI-E-SADNVNYRITVKPGWKFTDGSPVTAHSFVDAWNYGALSTNAQLQQHFFSPiegfddvagapgdksRTTMSG 156
                                    679995.5.9*******************************************999999***************99**** PP

                                    EEEEETTEEEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEE......EETTTEEEEEE-TT CS
                      SBP_bac_5  70 veavddytvrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklke......fkpgqkivlernpd 143
                                      +v+d++++++lk+p+ +f   l + +  +     + +  + + + ++p+g+GPYkl++      ++++ +i l+ npd
  gi|121639579|ref|YP_979803.1| 157 LRVVNDLEFTVRLKAPTIDFTLRLGHSSFYPL---PDSAFRDMAAFGRNPIGNGPYKLADgpagpaWEHNVRIDLVPNPD 233
                                    ******************99999999999888...3566666889*********************************** PP

                                    STTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGS... CS
                      SBP_bac_5 144 YwgggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfdd... 220
                                    Y g++kp+ + ++f+++++ d++ a l+sG++d+   +pps +  ++ + g     ++p +  + l    + p f     
  gi|121639579|ref|YP_979803.1| 234 YHGNRKPRNKGLRFEFYANLDTAYADLLSGNLDVLDTIPPSALTVYQRDLGDHA-TSGPAAINQTLDTPLRLPHFGGeeg 312
                                    **99****************************9999999999999988888888.8888888888888888777755555 PP

                                    HHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH...SHHHHHHHHHHHTT-BCSSTSCEETCEE CS
                      SBP_bac_5 221 krvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka...ydpekAkklLkeaGykdgdggglrekkl 297
                                       R Als Ai+r +i ++++ g+  pa  +++ s+pg+d++ + +  +   ydp+ A++l+++a     + g       
  gi|121639579|ref|YP_979803.1| 313 RLRRLALSAAINRPQICQQIFAGTRSPARDFTARSLPGFDPNLPGN--EvldYDPQRARRLWAQADAISPWSG------- 383
                                    67788*************************************9997..3458*******************98....... PP

                                    EEEEEEETTSHHHHHHHHHHHHHHHH.TTEEEEEEEE.CHHHHHHHHHHCTTESEEEE.EEECTTSTTHHHHHHHHSTTC CS
                      SBP_bac_5 298 kltlllasgspaekaiaeliqqqlkk.iGikvevktv.dwaatylervkdgdfdmill.gwgadypdpdnflnpflsssg 374
                                        ++++ ++ +++++++++++ k+ +Gi++   +   + a + ++ +++  d ++  gw +dyp+  +fl p+++ ++
  gi|121639579|ref|YP_979803.1| 384 -RYAIAYNADAGHRDWVDAVANSIKNvLGIDAVAAPQpTF-AGFRTQITNRAIDSAFRaGWQGDYPSMIEFLAPLFTAGA 461
                                    .569999******************************566.888888888888766555****************99886 PP

                                    T CS
                      SBP_bac_5 375 a 375
                                     
  gi|121639579|ref|YP_979803.1| 462 G 462
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3752.10
//
Query:       gi|121639580|ref|YP_979804.1|  [L=651]
Description: acetyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-96  322.7   0.0      4e-96  322.2   0.0    1.2  1  AMP-binding    AMP-binding enzyme
    3.8e-27   95.1   2.3    9.2e-27   93.8   2.3    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.7e-22   78.0   0.9    3.7e-22   78.0   0.9    2.3  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.2   0.0  6.7e-100     4e-96       5     422 ..      85     530 ..      80     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 322.2 bits;  conditional E-value: 6.7e-100
                                    HHHSTTSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   5 aaktpdkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                     a + d+va+++     g+ +tlTY++l ++v+++A++L+ lG+  gdrVai+lp  pe v+a+la++++G++++++  +
  gi|121639580|ref|YP_979804.1|  85 EAGHGDRVAIHWegepVGDRRTLTYSDLLAEVSKAANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGG 164
                                    46788*****999999889************************************************************* PP

                                    S-HHHHHHHHHHHTESEEE...........E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                    AMP-binding  81 ltaeelayiledseakvli...........a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                    +ta++l+  + d++ak+li           +  +   ++++++l+a + + +v++v+v+ + +++ ++ +  +  + ++ 
  gi|121639580|ref|YP_979804.1| 165 FTAAALQARIVDAQAKLLItadgqfrrgkpSplK---AAADEALAAIP-DCSVEHVLVVRRTGIEMAWSEGRDLWWHHVV 240
                                    *********************9999866441221...22344444444.3688899999999988887666666555554 PP

                                    S...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTT.T-EEEESS-TTSCHHHHHHHHH CS
                    AMP-binding 148 e...kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklke.ddvvlsilplahifglilelll 223
                                    +     +++e+ +++++++++YTSGTTGkPKG+m++ + ++++++   ++t f++k+ +dv+++++++ +++g+++++++
  gi|121639580|ref|YP_979804.1| 241 GsasPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYT-MRTIFDVKPdSDVFWCTADIGWVTGHTYGVYG 319
                                    26674557889**************************8888887775.78789988878999****************** PP

                                    HHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHH CS
                    AMP-binding 224 allsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellr 301
                                    +l++G t vl++++++ +d ++ ++ iek++vt+ +++P++++++++  +++    +++dlsslrl+ ++gep++pe++r
  gi|121639580|ref|YP_979804.1| 320 PLCNGVTEVLYEGTPDtPDRHRHFQIIEKYGVTIYYTAPTLIRMFMKwGREIP---DSHDLSSLRLLGSVGEPINPEAWR 396
                                    ****************8889999************************998888...778********************* PP

                                    HHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE......TTSEEEEEEEET CS
                    AMP-binding 302 ffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvp......dgeeGellvrgp 372
                                    ++r++ g+   ++++++++TEt+ +++ + +    +k+gs+ +plpg+ +kivD++ g p+p      ++++G l++ +p
  gi|121639580|ref|YP_979804.1| 397 WYRDVIGGgrtPLVDTWWQTETGSAMISPLPGIAAAKPGSAMTPLPGISAKIVDDH-GDPLPphtegaQHVTGYLVLDQP 475
                                    ******99******************77555777899******************9.99999566555555589999998 PP

                                    ..TS-SEBTT-HHHHHHHEEE..T.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 373 ..gvmkgYlkkpeataeafds..e.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                      ++ +g +++p++  ++++s  + ++++  GD +r+d+dG ++++gR++d++++
  gi|121639580|ref|YP_979804.1| 476 wpSMLRGIWGDPARYWHSYWSkfSdKGYYFAGDGARIDPDGAIWVLGRIDDVMNV 530
                                    778*****************8663456*************************997 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   2.3   1.5e-30   9.2e-27       1      76 []     539     617 ..     539     617 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.5e-30
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsalv+h +VaeaaVvGv+de++ +a++afVvl++++++   ++eeL+  v++ + p+a+p++v++v+elpktrsGK
  gi|121639580|ref|YP_979804.1| 539 EVESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAPhdrTAEELRTEVARVISPIARPRDVHVVPELPKTRSGK 617
                                    8**********************************988533357**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.9   6.2e-26   3.7e-22       2      55 .]      26      79 ..      25      79 .. 0.98
   2 ?   -0.9   0.1      0.26   1.6e+03      11      23 ..     486     498 ..     478     504 .. 0.66

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 6.2e-26
                                   HHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  2 kelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   +ely+e+ ed  aFWa+qa++l+W +pf++vld+s +pf+kWF+GG+lN++yNc
  gi|121639580|ref|YP_979804.1| 26 AELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAKWFVGGELNVAYNC 79
                                   58**************************************************** PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                                    -HHHHHHHHHCCS CS
                         ACAS_N  11 dpeaFWaeqakel 23 
                                    dp+++W + ++++
  gi|121639580|ref|YP_979804.1| 486 DPARYWHSYWSKF 498
                                    6666776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4557.43
//
Query:       gi|121639581|ref|YP_979805.1|  [L=232]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   13.1   6.3       0.28   12.1   6.3    1.6  1  Trypsin_2  Trypsin-like peptidase domain


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.3   1.6e-05      0.28       1     149 [.      38     181 ..      38     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                      Trypsin_2   1 GsGflvgsdg...............lilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssd 65 
                                    G G++v++d                +  T aH+ ++ ++ a+        e +++   v   v + d +lD+A++k+   
  gi|121639581|ref|YP_979805.1|  38 GAGIVVNGDTmctlttighdkngdlIGFTSAHCGGPGAQIAA--------EGAENAGPVGIMVAGND-GLDYAVIKF--- 105
                                    567777777665556666666666566788888888888888........56666666666699999.*********... PP

                      Trypsin_2  66 eraglpplplgpsealkggepvyvvGy.plggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsd 144
                                    ++a++ p+ + +      g   ++ G  p+ + ++ ++ +G+ +g + + ++ +ge+++ l  ++   pG SG+p+   d
  gi|121639581|ref|YP_979805.1| 106 DPAKVTPVAVFN------G--FAINGIgPDPSFGQIACKQGRTTGNSCGVTWGPGESPGTLVMQVCGGPGDSGAPVT-VD 176
                                    999999999999......5..334455335555555888999988888888899999999988888888******97.55 PP

                      Trypsin_2 145 GrvvG 149
                                      +vG
  gi|121639581|ref|YP_979805.1| 177 NLLVG 181
                                    55666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1627.59
//
Query:       gi|121639582|ref|YP_979806.1|  [L=172]
Description: hypothetical protein BCG_3727 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-30  103.6   7.2      7e-30  103.4   7.2    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
     0.0048   16.0   0.6     0.0065   15.6   0.6    1.1  1  DUF973           Protein of unknown function (DUF973)
     0.0049   15.9   0.0     0.0058   15.7   0.0    1.1  1  Tmp39            Putative transmembrane protein
  ------ inclusion threshold ------
      0.019   14.9   0.9      0.024   14.5   0.9    1.1  1  VIT1             VIT family
       0.12   12.3   8.7       0.18   11.8   8.7    1.1  1  Colicin_V        Colicin V production protein
       0.19   10.4   2.6       0.22   10.2   2.6    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.38    9.4   3.5       0.45    9.1   3.5    1.1  1  Ndc1_Nup         Nucleoporin protein Ndc1-Nup
       0.41   10.4   1.7       0.51   10.1   1.7    1.2  1  S_2TMBeta        SMODS-associating 2TM, beta-strand rich effe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   7.2   3.1e-33     7e-30       1     112 [.      32     145 ..      32     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 3.1e-33
                Phage_holin_3_6   1 gelvrrltaqlssLvrteleLakaElkeeakragsgagllgaagvlallalllllvalalala.a..lwlaalivaavll 77 
                                    g+l++++t+q+s+Lvr+e+eLa+aE+++++k+ ++g ++++  +v+++++ +++++++a +l+ +  +w+a+l+v+a+++
  gi|121639582|ref|YP_979806.1|  32 GDLIKDATTQMSTLVRAEVELARAEITRDVKKGLTGSVFFISSLVVGFYSTFFFFFFVAELLDtWiwRWVAFLLVFAIMV 111
                                    69*********************************************************99*98899************* PP

                Phage_holin_3_6  78 vlagvlalvglkklkkakplpertieelkedvaal 112
                                    v+++vlal+g  k+++ ++ p++ti+++ke++ al
  gi|121639582|ref|YP_979806.1| 112 VVTAVLALLGFLKVRRIRG-PRQTIASVKETRTAL 145
                                    ****************999.************998 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   2.9e-06    0.0065      89     158 ..      56     125 ..      45     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                         DUF973  89 stgrdvgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilaliGqillglsfykl 158
                                    +++rdv++G tg++ ++ ++++ + ++    +++ +l  + i   v++ll+ +i+++++ +l  l+f k+
  gi|121639582|ref|YP_979806.1|  56 EITRDVKKGLTGSVFFISSLVVGFYSTFFFFFFVAELLDTWIWRWVAFLLVFAIMVVVTAVLALLGFLKV 125
                                    5689******************9999998888888999999999999999999*********99999886 PP

>> Tmp39  Putative transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-06    0.0058     209     279 ..      33     109 ..      13     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                          Tmp39 209 llpthscslspdlireevellkldfnlrikevlfss......llsayyvalvplifvkktvyydll...wscqllilvll 279
                                    +l + + ++ ++l+r evel ++++ + +k+ l  s      l+  +y+++  ++fv +  ++d++   w + ll++  +
  gi|121639582|ref|YP_979806.1|  33 DLIKDATTQMSTLVRAEVELARAEITRDVKKGLTGSvffissLVVGFYSTFFFFFFVAE--LLDTWiwrWVAFLLVFA-I 109
                                    556777889999******************9887665655569999*****99999944..45544211333333221.1 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   1.1e-05     0.024     112     190 ..      39     130 ..      22     145 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                           VIT1 112 dallelmlreelgpsaseel.asplkaAls...salsfliGgliPllpylf.ve.......s...vglalvvsiavtlla 176
                                     +  ++++r e ++   +++ ++ +k++l+    ++s l+ g+ + + ++f v+           + l++++ ++v++++
  gi|121639582|ref|YP_979806.1|  39 TTQMSTLVRAEVELA--RAEiTRDVKKGLTgsvFFISSLVVGFYSTFFFFFfVAelldtwiWrwvAFLLVFAIMVVVTAV 116
                                    333344444444433..222245555555511166777889999999987635555544331332222222333444555 PP

                           VIT1 177 lllfGavkalltgs 190
                                    l+l+G++k +  + 
  gi|121639582|ref|YP_979806.1| 117 LALLGFLKVRRIRG 130
                                    66666666554444 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.7     8e-05      0.18      18      81 ..      62     120 ..      61     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-05
                      Colicin_V  18 rrGfvrevlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgal 81 
                                     +G+  +v+ + ++vv+f+ ++++   +aell +     ++ +++afll+f ++++++++l+ l
  gi|121639582|ref|YP_979806.1|  62 KKGLTGSVFFISSLVVGFYSTFFFFFFVAELLDT-----WIWRWVAFLLVFAIMVVVTAVLALL 120
                                    589999****************************.....4666666666666666665555443 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.6    0.0001      0.22     381     427 ..      61     119 ..      30     141 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0001
                        DUF2207 381 kklsalglgliilglilillallllvll............lvfllilllillliaiivl 427
                                     k ++ g +++i +l++++++ ++++++            + fll++++++++ a+++l
  gi|121639582|ref|YP_979806.1|  61 VKKGLTGSVFFISSLVVGFYSTFFFFFFvaelldtwiwrwVAFLLVFAIMVVVTAVLAL 119
                                    33444455555555555555555555555556788755443333333333333333333 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.5    0.0002      0.45     175     218 ..      59     107 ..      38     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                       Ndc1_Nup 175 krlpsilkksl..ilslvlllvspiiyyll....lrsfiwslalillrlf 218
                                    + +++ l+ s+  i+slv+ ++s+++++++    l ++iw++ +++l +f
  gi|121639582|ref|YP_979806.1|  59 RDVKKGLTGSVffISSLVVGFYSTFFFFFFvaelLDTWIWRW-VAFLLVF 107
                                    4455555555555777777799999988889999*******8.4444444 PP

>> S_2TMBeta  SMODS-associating 2TM, beta-strand rich effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.7   0.00023      0.51      29      59 ..      76     106 ..      40     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                      S_2TMBeta  29 alsvigtaviflllyllfdkklWklklfrki 59 
                                    +    +t+ +f+++  l+d+++W++ +f  +
  gi|121639582|ref|YP_979806.1|  76 VVGFYSTFFFFFFVAELLDTWIWRWVAFLLV 106
                                    3334448889***************999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1235.51
//
Query:       gi|121639583|ref|YP_979807.1|  [L=327]
Description: epoxide hydrolase ephE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-20   74.3  12.9      3e-20   73.8  12.9    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
      1e-19   71.2   0.2    1.8e-19   70.4   0.2    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
    2.3e-08   33.6   0.2    9.8e-08   31.5   0.2    1.9  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8  12.9     5e-24     3e-20       1     219 [.      57     314 ..      57     315 .. 0.58

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5e-24
                                    EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH..CHHH.HHHHCCTT..TTSE.EEEEETCH CS
                  Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhGrsdpppldled..ladl.aalldelaagggpv.vlvGHSlG 75 
                                    v+llHG+gs  +sW +  +L  l +a+v  +a+Dl+G+G+sd pp +++   la + a l+++l   g+p   lvGH  G
  gi|121639583|ref|YP_979807.1|  57 VILLHGFGSFWWSWrH--QLCGLTGARV--VAVDLRGYGGSDKPPRGYDGwtLAGDtAGLIRAL---GHPSaTLVGHADG 129
                                    79************88..**9999***9..********98*****88888664444599*****...45555******** PP

                                    HHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHHHTT-C......CCCH....CCH..........S CS
                  Abhydrolase_6  76 Galalaaapla.....lvvg.vlldppptalpagllaaalelllallallrl......lawl....sre..........p 129
                                    G+  +     a     lv++  l+++     pa+l++  l+  +++ all++      + w+    +r+          +
  gi|121639583|ref|YP_979807.1| 130 GLACWT---TAllhsrLVRAiALISS---PHPAALRRSTLTRRDQRHALLPTllryqlPIWPerllTRNnaaeierlvrA 203
                                    **7777...44444545455788888...445555444444444444444433222333333222211133334434221 PP

                                    -HS...CCCCHHH...CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC..............EEE..CTT-C...HHH CS
                  Abhydrolase_6 130 lpr...lfladed...adaawrarlarlaallaglgllpaaawadlpvpl..............lvl..ggeDp...lvp 184
                                      r    +la ed   a  + r++ + +aa  ++l++ ++a   +l++                l++  g++Dp   + p
  gi|121639583|ref|YP_979807.1| 204 --RgcaKWLASEDfsqAIDHLRQAIQIPAAAHCALEYQRWAVRSQLRSEGrrfiramtqqlgmpLLHlrGDADPyvlADP 281
                                    ..122444443333332333333333333333333322222222222222333444444446553433578888755444 PP

                                    HCHHCCCH.STTEEETCE...SSS-HHHHSHHHHHH CS
                  Abhydrolase_6 185 rllerlla.qagarlpvvlpgaGHlphleepdevae 219
                                      +er  + +++ r+ + ++gaGH+ h+e+p+ev++
  gi|121639583|ref|YP_979807.1| 282 --VERTQRyAPHGRY-ISIAGAGHFSHEEAPEEVNR 314
                                    ..666666669****.******************87 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.2   3.1e-23   1.8e-19       1     257 []      55     309 ..      55     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 3.1e-23
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                    p++++lhG++  +++w+      +L   g++v+++DlrG+g S+++p+     y  +++a d   +  alg  + tlvGh
  gi|121639583|ref|YP_979807.1|  55 PLVILLHGFGSFWWSWRH--QLCGLT--GARVVAVDLRGYGGSDKPPR----GYDGWTLAGDTAGLIRALGHPSATLVGH 126
                                    78****************..554455..*******************7....6*************************** PP

                                    THHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHH CS
                  Abhydrolase_1  81 SmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvda 160
                                      GG+ +++ a+++   V+a++l+++++paa  +++  + ++++       ++    +p+ +l  + +a +e   r+   
  gi|121639583|ref|YP_979807.1| 127 ADGGLACWTTALLHSRLVRAIALISSPHPAALRRSTLTRRDQRHALLPTLLRYQLPIWPERLLTRNNAAEIERLVRARG- 205
                                    **************************99999999999999999999999999999999999999999999988877643. PP

                                    HHH.....HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHS....EEEEEEETTCSSSCHHHHH CS
                  Abhydrolase_1 161 lkf.....pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvla....ptlvisgtsDplvppkale 231
                                     +      +d+s+ ++  ++++++  a+  ++  ++w+++    + +r+ + +++++    p l + g+ Dp+v  +  e
  gi|121639583|ref|YP_979807.1| 206 -CAkwlasEDFSQAIDHLRQAIQIPAAAHCALEYQRWAVRSQLRSEGRRFI-RAMTQqlgmPLLHLRGDADPYVLADPVE 283
                                    .3367888******************************9999888777665.888889999******************* PP

                                    HHHHCHTSEEEEEEETCSSSHHHHSH CS
                  Abhydrolase_1 232 dlaqllpkkrlvvisdagHlaflegp 257
                                    + ++  p+ r++ i++agH+++ e p
  gi|121639583|ref|YP_979807.1| 284 RTQRYAPHGRYISIAGAGHFSHEEAP 309
                                    *********************99875 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   1.6e-11   9.8e-08       4     237 ..      54     307 ..      51     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.6e-11
                    Hydrolase_4   4 kavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                    + +v+l+HG+++  +   +    L   G  v+a+D rG+G s+ + rg  + + ++  D a +++++   hp +  +l+G
  gi|121639583|ref|YP_979807.1|  54 RPLVILLHGFGSFWWSWRHQLCGL--TGARVVAVDLRGYGGSDkPPRG-YDGW-TLAGDTAGLIRALG--HPSA--TLVG 125
                                    7789**********9999977777..599**************76666.6666.5889*****99998..6666..89** PP

                    Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPalkikakl.......kappllklllkllgkllpklqv................ 139
                                    h  GGl   + +l +++ v+++ l+++    + +        + ++ll  ll+   +++p+  +                
  gi|121639583|ref|YP_979807.1| 126 HADGGLACWTTALLHSRLVRAIALISSPHPAALRRstltrrdQRHALLPTLLRYQLPIWPERLLtrnnaaeierlvrarg 205
                                    *****************999888777544333322344555324445555788888888888889999999999999999 PP

                    Hydrolase_4 140 ....snnlkadslsrdpevvaayeadplv.hgkitvrlllelldam.krleeraakitlPllllhGeaDkvvdpeasrel 213
                                         ++ ++++  ++ ++  ++ a  ++  +  ++ +  +l   +  ++++ ++++ +Pll l G+aD+ v  ++ +++
  gi|121639583|ref|YP_979807.1| 206 cakwLASEDFSQAIDHLRQAIQIPAAAHCaLEYQRWAVRSQLRSEGrRFIRAMTQQLGMPLLHLRGDADPYVLADPVERT 285
                                    9877444555555555555555566666657788888888887655155777788899*******************999 PP

                    Hydrolase_4 214 yerlgskdktlklypglyHellnE 237
                                     + ++  + ++  ++g+ H  + E
  gi|121639583|ref|YP_979807.1| 286 QRYAP--HGRYISIAGAGHFSHEE 307
                                    99999..69999999999977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2382.53
//
Query:       gi|121639584|ref|YP_979808.1|  [L=397]
Description: membrane-associated serine protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-23   83.0   4.6    4.2e-23   82.9   1.5    2.3  2  Trypsin_2     Trypsin-like peptidase domain
    1.1e-12   48.1  11.4    1.9e-12   47.4  11.4    1.4  1  Colicin_V     Colicin V production protein
    7.2e-11   42.3   0.1      1e-09   38.6   0.1    2.3  1  Trypsin       Trypsin
      0.005   16.7   0.2      0.011   15.5   0.2    1.6  1  Peptidase_S3  Alphavirus core protein


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.26   1.2e+03      11      90 ..     111     199 ..      80     209 .. 0.61
   2 !   82.9   1.5   9.3e-27   4.2e-23       1     150 []     220     357 ..     220     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.26
                      Trypsin_2  11 lilTnaHvvdsadgaav....kaikkkveeagadgrevpakvvaadpelDlAllkv.....ssderaglpplplgpseal 81 
                                    ++lT+a ++++  + ++     a ++k + + a  +e + +++++ p +  All         ++ +  p++p+++ +++
  gi|121639584|ref|YP_979808.1| 111 VVLTAAWLLAMPLTQSKeqpeLAAAVKGSRVLARVNEAAPTWLKTVPKRLSALLTTsglpaVLEPFSRTPVIPVASPDPA 190
                                    68888888876666666333333444444444444444444444443445566666555555555566666666666666 PP

                      Trypsin_2  82 kggepvyvv 90 
                                     + +pv++ 
  gi|121639584|ref|YP_979808.1| 191 LVNNPVVAA 199
                                    666677765 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 9.3e-27
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsea 80 
                                    G+Gf++++d  ++TnaHvv+++++++v           a ++ ++a+vv +dp+ D+A+l v   +  + ppl ++  e+
  gi|121639584|ref|YP_979808.1| 220 GTGFVISPDR-VMTNAHVVAGSNNVTV----------YAGDKPFEATVVSYDPSVDVAILAV---PHLPPPPLVFAA-EP 284
                                    9*********.****************..........9**************999*******...666666666666.67 PP

                      Trypsin_2  81 lkggepvyvvGyplggeksgsvssGivsgvve.....sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                    +k+g +v+v+Gyp+gg+   +++  +++   +      ++  +   +++ +  a++ +G SGGpl+d +G+v+G+
  gi|121639584|ref|YP_979808.1| 285 AKTGADVVVLGYPGGGNF--TATPARIREAIRlsgpdIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGV 357
                                    78888*******888888..99999999999977775444444444555599999999****************8 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4  11.4   4.2e-16   1.9e-12       1     142 [.       7     148 ..       7     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 4.2e-16
                      Colicin_V   1 lDliillilllsallGlrrGfvrevlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllga 80 
                                    lD+++l++ +++a+ G+r G++ ++ls+ g+++++ +++ll+p ++ ++      + +aa++ +l+l++++ +++ +lg+
  gi|121639584|ref|YP_979808.1|   7 LDIAVLAVAFIAAISGWRAGALGSMLSFGGVLLGATAGVLLAPHIVSQISAP-RAKLFAALFLILALVVVGEVAGVVLGR 85 
                                    7**************************************************4.8999999999999************** PP

                      Colicin_V  81 llsklvsktglglldrllGaifGllkglllvv.llllllalvplpkvqewlqnSvlapllesl 142
                                     ++++++   ++l+d+++G+ + l+ +l  ++ l++ l +  + p+ + +++ S+++  ++++
  gi|121639584|ref|YP_979808.1|  86 AVRGAIRNRPIRLIDSVIGVGVQLVVVLTAAWlLAMPLTQSKEQPELAAAVKGSRVLARVNEA 148
                                    ********************************8888888888888888899999998877665 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   2.2e-13     1e-09      28     199 ..     221     361 ..     199     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.2e-13
                                    EEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCC CS
                        Trypsin  28 gGslisenwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpi 107
                                    +G++is++ v+T+aH+v ++++v+v++g+   k  e+     +   v++   y+ps    D+a+l +           p+
  gi|121639584|ref|YP_979808.1| 221 TGFVISPDRVMTNAHVVAGSNNVTVYAGD---KPFEA-----T---VVS---YDPSV---DVAILAVPHL-----PPPPL 278
                                    8*****************98888888886...22333.....2...334...99*98...*****99998.....33455 PP

                                    BBCSTTHTTSTTTEEEEEESSBSSTSS.BSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEE CS
                        Trypsin 108 clpaassslpvgttclvsGwgrtkekg.ksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPlv 186
                                      +a+ +  + g+ ++v G++   ++  ++ +++e+     ++   +   ++ vt++   + a     d +qGDSGGPl+
  gi|121639584|ref|YP_979808.1| 279 VFAAEPA--KTGADVVVLGYPGGGNFTaTPARIREAIRLSGPDIYGD---PEPVTRDVYTIRA-----DVEQGDSGGPLI 348
                                    5555333..899**********8888867777775543333333333...457**********.....************ PP

                                    ETTTEEEEEEEEE CS
                        Trypsin 187 csdgelvGivswg 199
                                      +g++ G+v + 
  gi|121639584|ref|YP_979808.1| 349 DLNGQVLGVVLGA 361
                                    *********9876 PP

>> Peptidase_S3  Alphavirus core protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.5e-06     0.011     102     139 ..     337     373 ..     328     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                                    TS--TT-TT-EEE-TTS-EEEEEEEEEEETTEEEEEEE CS
                   Peptidase_S3 102 gvgkrgdsgrpildnkgrvvaivlggadegsrtalsvv 139
                                       ++gdsg p++d +g+v+ +vlg a + + t + + 
  gi|121639584|ref|YP_979808.1| 337 D-VEQGDSGGPLIDLNGQVLGVVLGAAVDDAETGFVLT 373
                                    4.368**********************99998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2935.78
//
Query:       gi|121639585|ref|YP_979809.1|  [L=273]
Description: hypothetical protein BCG_3730c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.7   0.0    2.3e-12   47.1   0.0    1.4  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.3e-16   2.3e-12      13     115 ..      99     200 ..      74     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.3e-16
                                    TTSEEEEEEES..SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX  13 ekgevLlvrrs..kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvf 88 
                                     +  +Ll+ r+   ++++g  ++PgG v+p +  p ++A+RE++EEtG+++  l+ l+ ++ ++  +   +  h + ++ 
  gi|121639585|ref|YP_979809.1|  99 AD--LLLTVRAstLRHHAGqAAFPGGVVDPADdGPVATALREANEETGIDPSRLHPLATMERTFIAP--SR-FHVVPVLA 173
                                    23..888888879999999456**********9************************9555444333..33.33444444 PP

                                    EEEECSGCSSTSTTTEEEEEEEEHHHH CS
                          NUDIX  89 leevegelepndenevsevrwvpleel 115
                                      ++ g +++ +e+e++ v  vp+ ++
  gi|121639585|ref|YP_979809.1| 174 YSPDPGPVAVVNEAETAIVARVPVRAF 200
                                    477777777777777766666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1874.50
//
Query:       gi|121639586|ref|YP_979810.1|  [L=227]
Description: membrane-anchored thioredoxin-like protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-10   39.8   0.0    4.8e-10   39.3   0.0    1.2  1  Redoxin        Redoxin
    5.3e-10   39.3   0.0    7.5e-10   38.8   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    5.2e-07   29.9   0.0    7.3e-07   29.4   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
    0.00061   19.7   0.0      0.001   19.0   0.0    1.4  1  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.052   13.6   0.5          1    9.4   0.0    2.6  3  CIDE-N         CIDE-N domain
        0.3   11.4   7.0       0.35   11.2   1.5    2.4  2  DUF2568        Protein of unknown function (DUF2568)


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.6e-13   4.8e-10      14     129 ..      99     206 ..      86     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.6e-13
                                    ETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHHTT-TSEEEE CS
                        Redoxin  14 aatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgkeglkfpvls 91 
                                    +a dg++v+++  ++g++vv+n ++  +c +C++e+p +++++++    +v vv v   +++  + + ++++g+  p l 
  gi|121639586|ref|YP_979810.1|  99 CAGDGSAVDVARaLAGRRVVINLWAH-WCAPCMTELPVMAEYQRR-VGPAVLVVTVHQGQNEAaALSRLADLGVRLPTLQ 176
                                    789***********************.******************.666687877777666666**************** PP

                                    -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEE CS
                        Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvy 129
                                    D    +++al ++          +p+++v+  dg v +
  gi|121639586|ref|YP_979810.1| 177 DDRRRVAAALRVA--------NVMPATVVLRPDGSVAQ 206
                                    ***********77........29*******99999976 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   2.5e-13   7.5e-10      13     123 ..     101     206 ..      91     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.5e-13
                                    TTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES.SSCHHHHHHHHH-H.SSEEEE-T CS
                       AhpC-TSA  13 adgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv.dspeshkkfiekeslnfpllsDe 90 
                                    +dg  v+++   +g+ vv++ +++ wc +C telp +a++  +   + v v+ v   +++++  +  ++ ++ +p l D 
  gi|121639586|ref|YP_979810.1| 101 GDGSAVDVARAlAGRRVVINLWAH-WCAPCMTELPVMAEYQRRVGPA-VLVVTVHQgQNEAAALSRLADLGVRLPTLQDD 178
                                    5677777755559***********.**************99999865.5566666647777999**************** PP

                                    TSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  91 egkvakaygvlkeekglalratfvidkegkiry 123
                                     + va a+ v        ++at+v+ ++g +++
  gi|121639586|ref|YP_979810.1| 179 RRRVAAALRVA-----NVMPATVVLRPDGSVAQ 206
                                    ***********.....589**********9975 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.4e-10   7.3e-07       3      95 .]     116     204 ..     114     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.4e-10
                                    EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT CS
                  Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvka 82 
                                     v++  +a+wc+pc++ +p + e+++++   + v +v v+  ++e +  + l++     +++p+ +++r  ++  ++v +
  gi|121639586|ref|YP_979810.1| 116 RVVINLWAHWCAPCMTELPVMAEYQRRVG--PAVLVVTVHQGQNEAAALSRLADL---GVRLPTLQDDRRRVAAALRVAN 190
                                    68999***********************9..*************99999999999...9999999999999999999988 PP

                                    -.SEEEEE-TT-BE CS
                  Thioredoxin_8  83 i.Ptlvvldkngev 95 
                                    + P +vvl+++g+v
  gi|121639586|ref|YP_979810.1| 191 VmPATVVLRPDGSV 204
                                    55**********97 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.4e-07     0.001      19      65 ..     115     161 ..     104     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.4e-07
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHH CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedla 65 
                                    + v+++ +A wC++C    P++++ ++++   v ++ v   +ne  a
  gi|121639586|ref|YP_979810.1| 115 RRVVINLWAHWCAPCMTELPVMAEYQRRVGPAVLVVTVHQGQNEAAA 161
                                    789************************99999999999888777655 PP

>> CIDE-N  CIDE-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.1   3.3e+03      60      77 .]       6      23 ..       4      23 .. 0.87
   2 ?    1.2   0.0      0.13   3.8e+02      39      53 ..      93     107 ..      88     112 .. 0.85
   3 ?    9.4   0.0   0.00035         1      11      51 ..     164     204 ..     160     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                                   CS-TTEEEEEE-TT---- CS
                         CIDE-N 60 tLpdnTelmllekgekWt 77
                                   t p++T +  l+ + +Wt
  gi|121639586|ref|YP_979810.1|  6 TTPAETAMTTLTGKTRWT 23
                                   67999*******999996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                    TT-EEEETTTT-EE. CS
                         CIDE-N  39 eevtlvLeeDGTeVd 53 
                                    + v +v++ DG++Vd
  gi|121639586|ref|YP_979810.1|  93 RGVVVVCAGDGSAVD 107
                                    57899*********7 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00035
                                    SS-EEEEEESSHHHHHHHHHHHCT-S.STT-EEEETTTT-E CS
                         CIDE-N  11 rekkkgvaakslkeLlekgaeklklssseevtlvLeeDGTe 51 
                                    r    gv   +l++ ++++a +l + +  ++t+vL  DG++
  gi|121639586|ref|YP_979810.1| 164 RLADLGVRLPTLQDDRRRVAAALRVANVMPATVVLRPDGSV 204
                                    56677999999****************************86 PP

>> DUF2568  Protein of unknown function (DUF2568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.043   1.3e+02      55      75 ..      16      36 ..       7      48 .. 0.50
   2 ?   11.2   1.5   0.00012      0.35      12      50 ..      91     136 ..      88     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.043
                        DUF2568 55 lpgpvrlllellvfalaalal 75
                                   l+g +r  + +l  ++a +a+
  gi|121639586|ref|YP_979810.1| 16 LTGKTRWTIAILAVVAALMAA 36
                                   333333333333333333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                        DUF2568  12 aalgvwGfrlgkgallkivlavllpllaavlWglfaaP.......k 50 
                                    a+ gv+ +++g+g ++ ++ a++   +++ lW+ ++aP        
  gi|121639586|ref|YP_979810.1|  91 ALRGVVVVCAGDGSAVDVARALAGRRVVINLWAHWCAPcmtelpvM 136
                                    556778889999**************************76555442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1696.68
//
Query:       gi|121639587|ref|YP_979811.1|  [L=245]
Description: endonuclease III nth [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-22   79.5   0.0    3.2e-22   79.0   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    9.1e-10   37.9   0.4    2.9e-09   36.3   0.0    2.1  2  HHH            Helix-hairpin-helix motif
    9.6e-05   22.6   5.1    0.00017   21.8   5.1    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
  ------ inclusion threshold ------
       0.11   13.1   0.1       0.87   10.2   0.0    2.3  2  HHH_5          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   7.2e-26   3.2e-22       1     107 [.      45     179 ..      45     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 7.2e-26
                                    HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.............. 66 
                                    v++ils+q +d+r+n  ++ lf+r+   t+ d a+ad ++L++lir++Gfyr+Ka  ++ l ++lv              
  gi|121639587|ref|YP_979811.1|  45 VATILSAQSTDKRVNLTTPALFARYR--TARDYAQADRTELESLIRPTGFYRNKAASLIGLGQALVerfggevpatmdkl 122
                                    789*********************97..**************************************************** PP

                                    ...................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                    ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ...................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                       g   ++i vD+h+ r+++r+r++ + +++ kve++  el+e
  gi|121639587|ref|YP_979811.1| 123 vtlpgvgrktanvilgnafG--IPGITVDTHFGRLVRRWRWTTA-EDPVKVEQAVGELIE 179
                                    ****************9554..799*****************99.7********999886 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.91   4.1e+03       7      16 ..      77      86 ..      76      86 .. 0.84
   2 !   36.3   0.0   6.5e-13   2.9e-09       1      28 [.     110     137 ..     110     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.91
                                   TSSHHHHHTS CS
                            HHH  7 pasreeLlal 16
                                    a+r eL++l
  gi|121639587|ref|YP_979811.1| 77 QADRTELESL 86
                                   59999**987 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 6.5e-13
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIl 28 
                                    +++g++pa+++ L++lPGVG+ktA++Il
  gi|121639587|ref|YP_979811.1| 110 RFGGEVPATMDKLVTLPGVGRKTANVIL 137
                                    699************************8 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   5.1   3.7e-08   0.00017       1      17 []     198     214 ..     198     214 .. 0.99

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.7e-08
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                    C AR+P+C+ C+La  C
  gi|121639587|ref|YP_979811.1| 198 CHARRPACGVCVLAKDC 214
                                    ***************99 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   1.6e+03      23      40 ..      69      86 ..      64     110 .. 0.75
   2 ?   10.2   0.0   0.00019      0.87      35      51 ..     120     136 ..     114     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                   --SHHHHHHS-HHHHHTS CS
                          HHH_5 23 iesvedlaaadveeLaki 40
                                   +++  d a+ad+ eL ++
  gi|121639587|ref|YP_979811.1| 69 YRTARDYAQADRTELESL 86
                                   678888899999888775 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                                    HHHHTSTTS-HHHHHHH CS
                          HHH_5  35 eeLakipGiGkktAeri 51 
                                    ++L ++pG+G ktA  i
  gi|121639587|ref|YP_979811.1| 120 DKLVTLPGVGRKTANVI 136
                                    67778888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2078.92
//
Query:       gi|121639588|ref|YP_979812.1|  [L=125]
Description: hypothetical protein BCG_3733 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 902.59
//
Query:       gi|121639589|ref|YP_979813.1|  [L=224]
Description: CRP/FNR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-23   80.9   0.0      9e-23   80.2   0.0    1.4  1  cNMP_binding    Cyclic nucleotide-binding domain
    2.3e-17   62.7   2.0      3e-17   62.4   0.7    1.9  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      4e-05   23.2   0.0    9.9e-05   21.9   0.0    1.7  2  Crp             Bacterial regulatory proteins, crp family
    5.2e-05   23.1   0.3     0.0002   21.2   0.3    2.1  1  MarR_2          MarR family
    0.00019   21.0   0.3    0.00061   19.4   0.1    2.0  2  GntR            Bacterial regulatory proteins, gntR family
     0.0002   20.8   0.0    0.00048   19.6   0.0    1.7  1  Sigma70_r4      Sigma-70, region 4
    0.00051   19.5   0.2     0.0027   17.2   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0011   18.9   0.5      0.011   15.8   0.0    2.3  2  HTH_29          Winged helix-turn helix
     0.0016   18.5   0.1      0.079   13.0   0.0    2.5  2  HTH_3           Helix-turn-helix
     0.0022   17.6   0.0     0.0056   16.3   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
     0.0046   17.0   1.4      0.029   14.5   0.1    2.5  2  HTH_28          Helix-turn-helix domain
     0.0054   16.7   0.0      0.011   15.7   0.0    1.6  1  HTH_36          Helix-turn-helix domain
     0.0056   16.4   0.0      0.019   14.7   0.0    1.9  1  HTH_23          Homeodomain-like domain
     0.0066   16.8   2.1       0.35   11.3   0.0    2.7  2  HTH_31          Helix-turn-helix domain
     0.0095   15.7   0.6      0.057   13.2   0.0    2.3  2  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.1   0.0       0.11   12.4   0.0    2.3  3  MarR            MarR family
      0.019   15.3   0.1       0.76   10.2   0.0    2.5  2  Rrf2            Transcriptional regulator
      0.026   14.4   2.1        2.2    8.2   0.1    2.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.04   13.7   0.5        0.2   11.5   0.0    2.3  2  HTH_38          Helix-turn-helix domain
      0.055   13.4   0.0      0.095   12.6   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.081   11.8   0.0       0.12   11.3   0.0    1.2  1  Phage_min_cap2  Phage minor capsid protein 2


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   1.1e-25     9e-23       2      87 ..      29     114 ..      28     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.1e-25
                                    EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    + f++g+++f +G+p+d+ yi++sG+v++ r+++dg+e++l+++gp d+fGel++++ +prt +++++t+++ ++++rd+
  gi|121639589|ref|YP_979813.1|  29 VDFPRGHTVFAEGEPGDRPYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDA 108
                                    679***************************************************************************** PP

                                    HHHHHH CS
                   cNMP_binding  82 flellq 87 
                                    +++ ++
  gi|121639589|ref|YP_979813.1| 109 LRSWIA 114
                                    *98765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         4   3.5e+03      19      30 ..     130     141 ..     113     144 .. 0.65
   2 !   62.4   0.7   3.5e-20     3e-17       1      67 [.     148     221 ..     148     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4
                                    EEEHHHHHHHHH CS
                      HTH_Crp_2  19 elpltqeelAsm 30 
                                    +l+ t+  lA++
  gi|121639589|ref|YP_979813.1| 130 RLRRTNNNLADL 141
                                    466677777776 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 3.5e-20
                                    HHHHHHHHHHHCT...TTC...EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES-HHHHHH CS
                      HTH_Crp_2   1 qRlArfLlrlaer...agg...eielpltqeelAsmlGltretvsrilseLkreglis.rgrririldleaLra 67 
                                    +R+A+ Ll+la+r   ++g   +++ +ltq+e+A+++G++retv+++l+++  +g+i+  g+ + i d e+L++
  gi|121639589|ref|YP_979813.1| 148 GRVAKQLLQLAQRfgtQEGgalRVTHDLTQKEIAQLVGASRETVNKALADFAHRGWIRlEGKSVLISDSERLAR 221
                                    6*********99855422247999**********************************55644*********97 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.4   5.5e+03       4      12 ..     134     142 ..     131     142 .. 0.79
   2 !   21.9   0.0   1.2e-07   9.9e-05       3      32 .]     175     204 ..     174     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.4
                                    -HHHHHHHH CS
                            Crp   4 SRqdIAdyl 12 
                                    +++ +Ad++
  gi|121639589|ref|YP_979813.1| 134 TNNNLADLI 142
                                    789999986 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.2e-07
                                    --HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                            Crp   3 mSRqdIAdylGlTrETVSRlLtrLrekGLI 32 
                                    ++  +IA ++G++rETV+  L +++ +G I
  gi|121639589|ref|YP_979813.1| 175 LTQKEIAQLVGASRETVNKALADFAHRGWI 204
                                    7889********************999865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   2.3e-07    0.0002      20      54 ..     163     207 ..     122     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                                    S..........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  20 r..........dltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                               dlt++e+a+  g s+ +v+++l+++  +G+++ +
  gi|121639589|ref|YP_979813.1| 163 TqeggalrvthDLTQKEIAQLVGASRETVNKALADFAHRGWIRLE 207
                                    355557888889******************************976 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.1   4.3e+03      50      62 ..     151     163 ..     150     164 .. 0.63
   2 !   19.4   0.1   7.2e-07   0.00061      16      58 ..     167     208 ..     165     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.1
                                    HTTSEEEETTCEE CS
                           GntR  50 aeglverrqgrGt 62 
                                    a++l++  q+ Gt
  gi|121639589|ref|YP_979813.1| 151 AKQLLQLAQRFGT 163
                                    5667777776665 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.2e-07
                                    TSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           GntR  16 gelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58 
                                    g lr    L +++e+a+  g sr tv++AL   + +g++  + 
  gi|121639589|ref|YP_979813.1| 167 GALRVTHDL-TQKEIAQLVGASRETVNKALADFAHRGWIRLEG 208
                                    667777889.****************************98765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.7e-07   0.00048      15      38 ..     169     192 ..     153     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.7e-07
                                    HHHTTT--HHHHHHHHTS-HHHHH CS
                     Sigma70_r4  15 lrfgeglTleEIgerlgiSrerVr 38 
                                    lr  ++lT++EI++  g Sre+V 
  gi|121639589|ref|YP_979813.1| 169 LRVTHDLTQKEIAQLVGASRETVN 192
                                    6779*******************7 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.5   1.3e+03       6      25 ..     121     140 ..     117     145 .. 0.71
   2 !   17.2   0.0   3.1e-06    0.0027      17      48 .]     174     205 ..     168     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                         HTH_24   6 rkILelLqknprisqreLAe 25 
                                     ++L++L +  r +++ LA+
  gi|121639589|ref|YP_979813.1| 121 EQLLRVLARRLRRTNNNLAD 140
                                    56777777777777777776 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.1e-06
                         HTH_24  17 risqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    +++q+e+A+ +g S+ tvn+ l  +   G+I+
  gi|121639589|ref|YP_979813.1| 174 DLTQKEIAQLVGASRETVNKALADFAHRGWIR 205
                                    58********************9999888886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.57   4.8e+02      20      45 ..     100     125 ..      96     140 .. 0.70
   2 !   15.8   0.0   1.3e-05     0.011      14      44 ..     176     206 ..     164     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                         HTH_29  20 kllglsrrtvyrwlkrfeegGlaall 45 
                                    +++ ++r+  + w+ +  e  ++ l+
  gi|121639589|ref|YP_979813.1| 100 RAVSMDRDALRSWIADRPEISEQLLR 125
                                    6778999******9876666655544 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                         HTH_29  14 tvsqiAkllglsrrtvyrwlkrfeegGlaal 44 
                                    t ++iA+l+g sr tv+++l +f   G+  l
  gi|121639589|ref|YP_979813.1| 176 TQKEIAQLVGASRETVNKALADFAHRGWIRL 206
                                    899**********************998766 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.17   1.4e+02      19      49 ..     102     132 ..      94     134 .. 0.87
   2 !   13.0   0.0   9.3e-05     0.079       4      28 ..     169     193 ..     168     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                                    HTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                          HTH_3  19 lGvsrstisriEnGernPsletlkklakaLg 49 
                                    + + r +++ ++ ++ ++s + l  la+ L 
  gi|121639589|ref|YP_979813.1| 102 VSMDRDALRSWIADRPEISEQLLRVLARRLR 132
                                    5578999********************9986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.3e-05
                                    HHHHTTHHHHHHHHHHTSSHHHHHH CS
                          HTH_3   4 lRkqlglsqeeLAeklGvsrstisr 28 
                                    lR  ++l+q+e+A+++G sr t+++
  gi|121639589|ref|YP_979813.1| 169 LRVTHDLTQKEIAQLVGASRETVNK 193
                                    78889******************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.6e-06    0.0056      21      47 ..     169     195 ..     168     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-06
                                    HHHTS---HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2  21 lryleglsykEIAellgisegtVksrl 47 
                                    lr  ++l++kEIA+l g s  tV+++l
  gi|121639589|ref|YP_979813.1| 169 LRVTHDLTQKEIAQLVGASRETVNKAL 195
                                    78899*******************988 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2         1   8.8e+02      25      34 ..     105     114 ..      99     133 .. 0.63
   2 !   14.5   0.1   3.4e-05     0.029      13      44 ..     174     206 ..     168     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1
                         HTH_28  25 srrtvyrWik 34 
                                    +r+ +++Wi 
  gi|121639589|ref|YP_979813.1| 105 DRDALRSWIA 114
                                    5666666664 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.4e-05
                         HTH_28  13 h.svreaArelgisrrtvyrWikryeegGiagL 44 
                                    + +++e+A+++g sr+tv + +  + + G+  L
  gi|121639589|ref|YP_979813.1| 174 DlTQKEIAQLVGASRETVNKALADFAHRGWIRL 206
                                    359************************998655 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05     0.011      27      55 .]     176     204 ..     150     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                         HTH_36  27 sqetlakrlglsknTvsraikeLeqlGyi 55 
                                    +q+ +a++ g s++Tv +a++  +  G+i
  gi|121639589|ref|YP_979813.1| 176 TQKEIAQLVGASRETVNKALADFAHRGWI 204
                                    699*************************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.3e-05     0.019      17      45 ..     174     202 ..     168     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                         HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                     l+++eIA++ g sr Tv + l  ++  G
  gi|121639589|ref|YP_979813.1| 174 DLTQKEIAQLVGASRETVNKALADFAHRG 202
                                    579*******************9997566 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.066        56      22      62 ..     100     139 ..      92     141 .. 0.84
   2 !   11.3   0.0   0.00041      0.35       8      33 ..     168     193 ..     167     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.066
                         HTH_31  22 erlgvsestlsrlEqGrrgrpspavlealaralgldpaera 62 
                                    +++ + ++ l+ +   r  + s++ l+ lar l+ + + +a
  gi|121639589|ref|YP_979813.1| 100 RAVSMDRDALRSWIADRP-EISEQLLRVLARRLRRTNNNLA 139
                                    678899999999999999.8***********9987766555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00041
                         HTH_31   8 alReraGLsqeevAerlgvsestlsr 33 
                                    alR  + L+q+e A+++g s+ t+++
  gi|121639589|ref|YP_979813.1| 168 ALRVTHDLTQKEIAQLVGASRETVNK 193
                                    79999****************99987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.2     1e+03       7      26 ..     122     140 ..     120     142 .. 0.79
   2 !   13.2   0.0   6.6e-05     0.057      17      51 ..     173     207 ..     154     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                    HHHCT-CTTBSS-BHHHHHH CS
                       HTH_IclR   7 aiLdalaeapqeltlselAr 26 
                                    ++L+ la++ ++ t+  lA+
  gi|121639589|ref|YP_979813.1| 122 QLLRVLARRLRR-TNNNLAD 140
                                    799999999888.6777765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.6e-05
                                    SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                     +lt +e+A+  g ++ tv   L+ + ++G+++ +
  gi|121639589|ref|YP_979813.1| 173 HDLTQKEIAQLVGASRETVNKALADFAHRGWIRLE 207
                                    4599****************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.2   2.8e+03      28      41 ..      13      26 ..      11      27 .. 0.85
   2 ?   -2.2   0.0       4.7     4e+03      12      33 ..     113     137 ..     111     142 .. 0.63
   3 ?   12.4   0.0   0.00013      0.11      16      48 ..     173     205 ..     168     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                                   TS-HHHHHHHHHHH CS
                           MarR 28 gvskstvtrvldrL 41
                                   gv++s++  ++++L
  gi|121639589|ref|YP_979813.1| 13 GVEPSAIAALTKQL 26
                                   68999999999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.7
                                    HHHSTTEEHH...HHHHHHTS-HHH CS
                           MarR  12 lyeqgplsvs...eLakklgvskst 33 
                                    +++++++s +    La++l  ++ +
  gi|121639589|ref|YP_979813.1| 113 IADRPEISEQllrVLARRLRRTNNN 137
                                    6666666666666677777766555 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00013
                                    TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  16 gplsvseLakklgvskstvtrvldrLekkGlie 48 
                                     +l+++e+a  +g s+ tv ++l    ++G+i+
  gi|121639589|ref|YP_979813.1| 173 HDLTQKEIAQLVGASRETVNKALADFAHRGWIR 205
                                    679*****************************7 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.22   1.8e+02      29      52 ..     111     134 ..      90     136 .. 0.84
   2 ?   10.2   0.0   0.00089      0.76      25      56 ..     174     205 ..     150     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.22
                                    HHHHHHHTS-HHHHHHHHHHHHHT CS
                           Rrf2  29 eeiaerqnispsylekilakLrka 52 
                                    + ia+r +is++ l+ + ++Lr+ 
  gi|121639589|ref|YP_979813.1| 111 SWIADRPEISEQLLRVLARRLRRT 134
                                    579******************986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00089
                                    -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           Rrf2  25 pvsseeiaerqnispsylekilakLrkaglvk 56 
                                     ++ +eia+ ++ s++ + k la  ++ g+++
  gi|121639589|ref|YP_979813.1| 174 DLTQKEIAQLVGASRETVNKALADFAHRGWIR 205
                                    3899**************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.031        27       4      27 ..     119     142 ..     118     146 .. 0.88
   2 ?    8.2   0.1    0.0025       2.2      18      35 ..     175     192 ..     167     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                  HTH_AsnC-type   4 iDrkILeaLqedaRisyaeLAerv 27 
                                    i  ++L+ L +  R+++  LA+ +
  gi|121639589|ref|YP_979813.1| 119 ISEQLLRVLARRLRRTNNNLADLI 142
                                    6679*****************865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                  HTH_AsnC-type  18 isyaeLAervGlSestvl 35 
                                    ++ +e+A+ vG S++tv 
  gi|121639589|ref|YP_979813.1| 175 LTQKEIAQLVGASRETVN 192
                                    6889************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.9   1.6e+03      24      33 ..     125     134 ..     124     136 .. 0.80
   2 ?   11.5   0.0   0.00023       0.2      20      41 ..     174     195 ..     168     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                         HTH_38  24 reIArrLgrs 33 
                                    r  ArrL r 
  gi|121639589|ref|YP_979813.1| 125 RVLARRLRRT 134
                                    7789**9995 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00023
                         HTH_38  20 GlslreIArrLgrspsTIsREl 41 
                                    +l+++eIA+++g s+ T+++ l
  gi|121639589|ref|YP_979813.1| 174 DLTQKEIAQLVGASRETVNKAL 195
                                    689***************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.095      22      55 ..     174     207 ..     168     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                    CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                           TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVere 55 
                                     +t +eia+ +g +r +v+++L     +G+++ e
  gi|121639589|ref|YP_979813.1| 174 DLTQKEIAQLVGASRETVNKALADFAHRGWIRLE 207
                                    57999*************************9876 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.12      21      89 ..     120     206 ..     116     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                 Phage_min_cap2  21 eqeiiediarrikktge......ltntaewqieklaelgll............nreilkliskltgksekelrkllkeag 82 
                                     +++++ +arr+++t++      +t+++   +++l +l +             ++ ++k i++l+g s+++++k+l++ +
  gi|121639589|ref|YP_979813.1| 120 SEQLLRVLARRLRRTNNnladliFTDVPGRVAKQLLQLAQRfgtqeggalrvtHDLTQKEIAQLVGASRETVNKALADFA 199
                                    567888888888888888888888888888888888888888888888888889************************** PP

                 Phage_min_cap2  83 dkaiksd 89 
                                     +++ + 
  gi|121639589|ref|YP_979813.1| 200 HRGWIRL 206
                                    9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1641.06
//
Query:       gi|121639590|ref|YP_979814.1|  [L=264]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-14   54.6  10.4    5.2e-13   49.4  10.4    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-06   27.8   2.7    5.6e-06   26.0   2.7    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.6e-06   26.5   0.9    9.7e-06   25.5   0.1    2.1  3  BLACT_WH       Beta-lactamase associated winged helix domain
    0.00034   20.5   0.0    0.00056   19.8   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4  10.4   1.2e-16   5.2e-13       2     197 .]      35     193 ..      34     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.2e-16
                                    CCCSSEEEEEEET..TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                    Lactamase_B   2 gpdpvnsyliegd..ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                    ++d++n+++++g+  ++++++D+G + ++ +a      +   + ++  v+++H H DH++g ++lv  t++pv+a     
  gi|121639590|ref|YP_979814.1|  35 TLDGTNTWVLRGPlsDELVVVDPGPDDDEHLA------RVAALGRIALVLISHRHGDHTSGIDKLVALTGAPVRAADPQ- 107
                                    6799*******5555****************9......7*********************************9876554. PP

                                    HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                    Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                      ++++ +                      e  +dg++ ++ +l +t+  ++gh+  ++++  ++ ++t D++l + t  
  gi|121639590|ref|YP_979814.1| 108 --FLRRDG----------------------ETLTDGEVIDVAGLTITVLATPGHTADSLSFVLDDAVLTADTVLGCGTTV 163
                                    ..444444......................4458888888888888888888888888899999**************** PP

                                    CCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 160 idltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                    id+         +++ ++yl+sl +l+gl   +++pgH
  gi|121639590|ref|YP_979814.1| 164 IDK--------EDGSLADYLESLHRLRGLGRRTVLPGH 193
                                    ***........*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   2.7   1.2e-09   5.6e-06       3     115 ..      53     139 ..      52     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.2e-09
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                    +++D+gpd  ++++r       ++ l +i++Vl++h H DH+ g++ l +l++  +p+       a   a  ++l ++ e
  gi|121639590|ref|YP_979814.1|  53 VVVDPGPDDDEHLAR-------VAALGRIALVLISHRHGDHTSGIDKLVALTG--APVR------A---ADPQFLRRDGE 114
                                    789*****4444222.......45799***********************654..2322......1...12222222333 PP

                                    TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE-- CS
                  Lactamase_B_2  83 pavnvheldwgesfelgdggleitatparhksg 115
                                          +l+ ge ++++  gl+it+ + ++ ++
  gi|121639590|ref|YP_979814.1| 115 ------TLTDGEVIDVA--GLTITVLATPGHTA 139
                                    ......56666666665..45555555555555 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   8.7e+03       1      12 [.       4      15 ..       3      18 .. 0.50
   2 ?   -3.7   0.1       2.8   1.3e+04      15      24 ..      63      72 ..      62      75 .. 0.55
   3 !   25.5   0.1   2.2e-09   9.7e-06       1      33 [.     230     262 ..     230     264 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                       BLACT_WH  1 TveelVkviYkd 12
                                   T+e l+   Y +
  gi|121639590|ref|YP_979814.1|  4 TAESLTHPAYGQ 15
                                   455555555544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.8
                       BLACT_WH 15 eslhpaAerg 24
                                   e+l + A+ g
  gi|121639590|ref|YP_979814.1| 63 EHLARVAALG 72
                                   5566666544 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 2.2e-09
                       BLACT_WH   1 TveelVkviYkdvpeslhpaAergvlahLeKLe 33 
                                    Tv e+V+++Y dv+e+l+ aAe +v+a L+ L+
  gi|121639590|ref|YP_979814.1| 230 TVREVVEHVYLDVDEKLWNAAEWSVQAQLDYLR 262
                                    899************************998776 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.2e-07   0.00056       6      83 ..      38     134 ..      34     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.2e-07
                  Lactamase_B_3   6 ghnsfllet..agarilvDPfka...nlgyeppa..eeaDlvlisqaledHah.letlkql.............aenvkv 64 
                                    g n+++l++  ++  ++vDP+     +l     a   ++ lvlis+++ dH   +++l +l              ++ ++
  gi|121639590|ref|YP_979814.1|  38 GTNTWVLRGplSDELVVVDPGPDddeHLARV--AalGRIALVLISHRHGDHTSgIDKLVALtgapvraadpqflRRDGET 115
                                    89*******5459********6542233333..25599************975355555559999995555555555555 PP

                  Lactamase_B_3  65 leegeslevggleiravat 83 
                                    l++ge ++v+gl i+  at
  gi|121639590|ref|YP_979814.1| 116 LTDGEVIDVAGLTITVLAT 134
                                    5556667777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1940.16
//
Query:       gi|121639591|ref|YP_979815.1|  [L=151]
Description: hypothetical protein BCG_3736c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-32  112.1   0.3    2.8e-32  111.9   0.3    1.0  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori
    1.3e-28   99.4   0.1    1.6e-28   99.1   0.1    1.1  1  Ribonuc_L-PSP    Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.3   3.1e-36   2.8e-32       2     148 .]       5     150 ..       4     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 3.1e-36
                                    HHHHHTT---------SSSS-SEEEETTEEEE--B--EETTEE--BS-BTTTB-HHHHHHHHHHHHHHHHHHHHHHHSSG CS
                YjgF_endoribonc   2 srlvalGlelpkvaaalGayepyaivasflttsfqlpylqekllyvGllGddvsvseGiaaarlaalnalaqlkeaaGel 81 
                                    +rl  lG+ lp+vaa l ay p  + ++ + t++qlp + +kl   G+lG+dv  +eG + ar++alnala +     +l
  gi|121639591|ref|YP_979815.1|   5 ARLGQLGVTLPQVAAPLAAYVPAVRTGNLVYTAGQLPLEAGKLVRTGKLGADVNPEEGKTLARICALNALAAVDS-LVDL 83 
                                    69999******************************************************************9865.6799 PP

                                    GG-SEEEEEEEEE-B-TT---HHHHHHHHHHHHHHHHGGGG--EEEEEE-SS-GGGBSEEEEEEEE- CS
                YjgF_endoribonc  82 arvkrlirleGvlnvtqdyiempkvldaasdlllevlGeaGrhartiltnhvmplnalvllylfael 148
                                      v r++++ G ++    +  +p v+++asdll ev+G++G har +++   +pl+a+v + l  e+
  gi|121639591|ref|YP_979815.1|  84 DAVTRVVKVVGFVASAPGFHGQPSVINGASDLLAEVFGDSGAHARSAVGVSELPLDAPVEVELIVEV 150
                                    9************************************************************999885 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.1   1.8e-32   1.6e-28       6     121 .]      19     150 ..      15     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 1.8e-32
                                    TTSSS-BSEEEETTEEEEEEE-SB-T....TTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGG......EEEEEEEES CS
                  Ribonuc_L-PSP   6 aaaapYsqavkagnlvyvsGqlpldp....etgelv.egdveeqtrqalenlkavLaaagaslsd......vVkvtvFla 74 
                                    a++a+Y++av++gnlvy++Gqlpl++    +tg+l+ + ++ee+++ a+ ++ ++Laa+++ l d      vVkv  F+a
  gi|121639591|ref|YP_979815.1|  19 APLAAYVPAVRTGNLVYTAGQLPLEAgklvRTGKLGaDVNPEEGKTLARICALNALAAVDS-LVDldavtrVVKVVGFVA 97 
                                    479*********************************************************5.555588999********* PP

                                    SGGGHHHHHHHHHHHSSSS.....T.S--EEEEEE-SBSGGG-SEEEEEEEE- CS
                  Ribonuc_L-PSP  75 diedfaevnevyaeafdel.....k.eaParsaveVaaLpkgakvEIeaiavv 121
                                    +++ f+ + +v+++a+d l     + +a+arsav+V++Lp +a vE+e+i++v
  gi|121639591|ref|YP_979815.1|  98 SAPGFHGQPSVINGASDLLaevfgDsGAHARSAVGVSELPLDAPVEVELIVEV 150
                                    ******************999998469***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1210.28
//
Query:       gi|121639592|ref|YP_979816.1|  [L=53]
Description: hypothetical protein BCG_3737c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-06   27.2   0.0    5.6e-06   26.5   0.0    1.4  1  DUF4177   Domain of unknown function (DUF4177)


Domain annotation for each model (and alignments):
>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.1e-10   5.6e-06       1      47 [.       7      42 ..       7      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.1e-10
                        DUF4177  1 YEYkvvevkegglgngkieeeeleeyqeilnelAkeGWrlvsii..pvk 47
                                   +EY +v      l   +      ++   il++++++GW+lv+++  p+ 
  gi|121639592|ref|YP_979816.1|  7 WEYATVP-----LL-THAT----KQ---ILDQWGADGWELVAVLpgPTG 42
                                   8999999.....44.2233....56...**************9965433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 365.62
//
Query:       gi|121639593|ref|YP_979817.1|  [L=340]
Description: anion transporter atpase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-23   81.0   0.0    1.5e-15   57.2   0.0    2.1  2  ArsA_ATPase    Anion-transporting ATPase
    1.4e-08   34.8   0.0    4.2e-08   33.3   0.0    1.9  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      1e-06   28.8   1.3    1.1e-05   25.4   1.3    2.2  1  AAA_31         AAA domain
    6.8e-06   25.7   1.5    1.3e-05   24.7   0.0    2.1  2  ParA           NUBPL iron-transfer P-loop NTPase
    4.7e-05   23.0   0.5    0.00012   21.7   0.5    1.6  1  AAA_25         AAA domain
    0.00042   19.7   0.3    0.00042   19.7   0.3    2.3  3  MipZ           ATPase MipZ
     0.0012   18.3   0.2     0.0026   17.2   0.1    1.6  2  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
     0.0027   17.2   0.1     0.0048   16.4   0.1    1.4  1  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
     0.0042   16.8   1.4      0.013   15.3   1.4    1.8  1  AAA_30         AAA domain
     0.0058   16.4   0.4      0.014   15.2   0.4    1.6  1  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.024   14.0   0.0    1.3  1  ATPase         KaiC
      0.018   14.7   0.4      0.039   13.7   0.4    1.4  1  IstB_IS21      IstB-like ATP binding protein
      0.033   14.1   0.2      0.078   12.9   0.2    1.6  1  APS_kinase     Adenylylsulphate kinase
      0.047   14.1   0.4      0.047   14.1   0.4    2.0  2  AAA_16         AAA ATPase domain
      0.052   12.5   1.7       0.07   12.1   0.8    1.6  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.086   13.1   0.1       0.25   11.6   0.1    1.7  1  AAA_22         AAA domain
      0.095   12.5   0.0       0.65    9.8   0.0    2.0  2  Helicase_RecD  Helicase
        0.1   12.5   0.6       0.19   11.6   0.6    1.4  1  NACHT          NACHT domain
       0.12   12.0   1.2       0.22   11.1   0.7    1.7  2  SRP54          SRP54-type protein, GTPase domain
       0.15   12.6   0.2       0.28   11.7   0.2    1.4  1  AAA_23         AAA domain
       0.18   11.5   0.2       0.32   10.7   0.2    1.5  1  AAA_24         AAA domain
       0.23   10.7   0.5       0.32   10.2   0.5    1.2  1  DUF2075        Uncharacterized conserved protein (DUF2075)
       0.32   11.5   1.3        1.1    9.8   0.9    2.0  2  AAA_18         AAA domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.9e-18   1.5e-15       2     150 ..      22     181 ..      21     188 .. 0.84
   2 !   21.8   0.1   1.2e-07   9.1e-05     201     250 ..     198     247 ..     187     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.9e-18
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS.....--BSS-EEET.....SSEEEEE--HHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq.....klgkeptkvk.....eNLsavEidpev 71 
                                    ++ lv+GKGG GK+t++aa+a+ l+  g+kvll+ +     ++  fd      +    + k+          a  id+e 
  gi|121639593|ref|YP_979817.1|  22 RLHLVTGKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLFDVpplpyQ----ELKIAtaergGQVNALAIDIEA 97 
                                    56689******************************************9755443....4444444446788999999999 PP

                                    HHHHHHCCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH......CSSSSEEEEESBSCCHTCGGGGHH CS
                    ArsA_ATPase  72 eleeakqevqkeeeallgleeledvlaeelaslPGideilsfeellkyvk......eeeydvvvlDtaPTGhtlrllslp 145
                                    +  e+ + +++       +    ++++ ++++ PG+ ++l   ++++ v          yd++v+D +PTG   r+l++ 
  gi|121639593|ref|YP_979817.1|  98 AFLEYLDMFYNLGI-AGRAMRRIGAVEFATTIAPGLRDVLLTGKIKETVVrldknkLPVYDAIVVDAPPTGRIARFLDVT 176
                                    99999998887655.4555778999****************999999887676655567*******************99 PP

                                    HHHHH CS
                    ArsA_ATPase 146 evlek 150
                                    + ++ 
  gi|121639593|ref|YP_979817.1| 177 KAVSD 181
                                    88765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.2e-07
                                    HTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCS CS
                    ArsA_ATPase 201 ltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeee 250
                                    l   ++t++ lV+  E l+++Et  ai+eL+++++ + +vivN+ +p++ 
  gi|121639593|ref|YP_979817.1| 198 LLHSNQTAIHLVTLLEALPVQETLEAIEELAQMELPIGSVIVNRNIPAHL 247
                                    4567899*************************************999864 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   5.4e-11   4.2e-08       4      55 ..      26     204 ..      23     260 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.4e-11
                                    EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.....HTTEB-HHHH........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxx........................ RF
                           CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.....leglendiep........................ 54 
                                    + +kGG+GK+t+aa+La  la +g++Vllv +      + +     l        p                        
  gi|121639593|ref|YP_979817.1|  26 VTGKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLfdvppL--------Pyqelkiataerggqvnalaidiea 97 
                                    789***************************97654333332222220........0223344444455555555666666 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121639593|ref|YP_979817.1|  98 afleyldmfynlgiagramrrigavefattiapglrdvlltgkiketvvrldknklpvydaivvdapptgriarfldvtk 177
                                    66666666666666666666666666666666666666665555555555555555555555555555555555555555 PP

                                    ..........................C CS
                                    ..........................x RF
                           CbiA  55 ..........................d 55 
                                                              +
  gi|121639593|ref|YP_979817.1| 178 avsdlakggpvhaqsegvvkllhsnqT 204
                                    555555555555555555555555552 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.3   1.4e-08   1.1e-05       7     127 ..      26     165 ..      23     183 .. 0.55

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.4e-08
                         AAA_31   7 anqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgie.kneiektlyevl......ieeknikeaiiktkve 79 
                                    +  KGG GK+T + +la +la  g kvLlv++   +  ++ +++      e ++ ++       +  ++i+ a  +   +
  gi|121639593|ref|YP_979817.1|  26 VTGKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLFDVPpLPYQELKIATAErggqvnALAIDIEAAFLEY-LD 104
                                    567*****************************988888875555312223334444321111111122233322211.11 PP

                         AAA_31  80 nl.dlipssidLaea.eielvelekk.......eeilkellekvkde....YDyiiiDcpP 127
                                    +  +l  +   + ++  +e++++          +  +ke++ +++++    YD i++D+pP
  gi|121639593|ref|YP_979817.1| 105 MFyNLGIAGRAMRRIgAVEFATTIAPglrdvllTGKIKETVVRLDKNklpvYDAIVVDAPP 165
                                    1122323333333321223333333334333333335555555555555567777777777 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.7e-08   1.3e-05       8      40 ..      25      57 ..      21      84 .. 0.90
   2 ?   -0.6   0.3      0.94   7.4e+02     112     122 ..     156     166 ..     132     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                           ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDa 40
                                    + gKGG GKSt+a+ lAl+La+ g kv l+ +
  gi|121639593|ref|YP_979817.1| 25 LVTGKGGTGKSTIAAALALTLAAGGRKVLLVEV 57
                                   678************************988764 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.94
                           ParA 112 lDyLiiDlPPG 122
                                     D +++D PP 
  gi|121639593|ref|YP_979817.1| 156 YDAIVVDAPPT 166
                                    47777777773 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.5   1.5e-07   0.00012      34      83 ..      22      61 ..      14      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-07
                         AAA_25 34 elallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdse 83
                                    l+l++G +gtGK+t+a  lal++a G           +kVl+v  E+++
  gi|121639593|ref|YP_979817.1| 22 RLHLVTGKGGTGKSTIAAALALTLAAGG----------RKVLLVEVEGRQ 61
                                   5899*********************765..........478888888877 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   5.4e-07   0.00042       8      42 ..      28      62 ..      22      68 .. 0.90
   2 ?   -1.5   0.0       1.6   1.3e+03      94     108 ..     150     164 ..      76     181 .. 0.59
   3 ?   -1.4   0.0       1.5   1.2e+03     225     261 ..     272     311 ..     266     312 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.4e-07
                                   SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                           MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqr 42
                                    kGG+Gkst+a  +a +L++ G +v  ++++ rq 
  gi|121639593|ref|YP_979817.1| 28 GKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQG 62
                                   69******************************995 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                    HHHHHH-SEEEEE-- CS
                           MipZ  94 adleaeldfividtP 108
                                    ++    +d iv+d+P
  gi|121639593|ref|YP_979817.1| 150 KNKLPVYDAIVVDAP 164
                                    333445677777776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                                    GT--GGGSSSS--S---CHH...HHHHHHHHHHHHHTT-G CS
                           MipZ 225 sGltlldlkelgleelnlsh...vaarqelrdLlaalkLp 261
                                     G+ l d + +gl + +++h   ++ar e+ + l al++p
  gi|121639593|ref|YP_979817.1| 272 AGVKLPDADFAGLLTETIQHatrITARAEIAQQLDALQVP 311
                                    56666666666655444444333899***99999999876 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.3e-06    0.0026       5      36 ..      26      57 ..      22      67 .. 0.89
   2 ?   -3.8   0.0       8.5   6.6e+03      45      62 ..     135     152 ..     134     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-06
                      Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGC 36
                                   + GkGG Gkst ++ l+ +la+ g+kvl+v  
  gi|121639593|ref|YP_979817.1| 26 VTGKGGTGKSTIAAALALTLAAGGRKVLLVEV 57
                                   67**************************9865 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.5
                      Fer4_NifH  45 lllggkaqetvldtlrek 62 
                                    +ll+gk++etv+ + ++k
  gi|121639593|ref|YP_979817.1| 135 VLLTGKIKETVVRLDKNK 152
                                    589999999999887766 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.1e-06    0.0048      10      51 ..      29      70 ..      19     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.1e-06
                       CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvd 51
                                   +GG+G+++++aaLa  l + g +vl++++   + ++  F+v+
  gi|121639593|ref|YP_979817.1| 29 KGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLFDVP 70
                                   7**************************998777666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.4   1.6e-05     0.013      16      52 ..      19      55 ..      16      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   sg r++++tG  GtGK+t+ +al+ +++a g++v+++
  gi|121639593|ref|YP_979817.1| 19 SGVRLHLVTGKGGTGKSTIAAALALTLAAGGRKVLLV 55
                                   566899***************************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.7e-05     0.014      20      48 ..      17      47 ..      10      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                         AAA_29 20 dlkg..atlltGpsGsGKSTllDAiqalLvp 48
                                   +l+g   +l+tG+ G+GKST+  A++  L +
  gi|121639593|ref|YP_979817.1| 17 RLSGvrLHLVTGKGGTGKSTIAAALALTLAA 47
                                   55666679*************9888766654 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.1e-05     0.024      20      59 ..      22      60 ..      16      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                         ATPase 20 rvvlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                   r  l+tG+ GtGK+++a+  +++ a+  g+++++v ve +
  gi|121639593|ref|YP_979817.1| 22 RLHLVTGKGGTGKSTIAAALALTLAAG-GRKVLLVEVEGR 60
                                   6789********************999.*******99976 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   5.1e-05     0.039      51      83 ..      25      57 ..      20      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                      IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrv 83
                                   +++G  G+GKs +a+al+   ++ g +vl v v
  gi|121639593|ref|YP_979817.1| 25 LVTGKGGTGKSTIAAALALTLAAGGRKVLLVEV 57
                                   689*************************98877 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2    0.0001     0.078       6      36 ..      25      55 ..      20      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                     APS_kinase  6 wltGlsgsGKstianalekkLvekgisvylL 36
                                   ++tG  g+GKstia al+ +L + g++v l+
  gi|121639593|ref|YP_979817.1| 25 LVTGKGGTGKSTIAAALALTLAAGGRKVLLV 55
                                   57**********************9998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4     6e-05     0.047      25      63 ..      22      62 ..      15     188 .. 0.76
   2 ?   -0.7   0.1         2   1.6e+03      94      94 ..     249     249 ..     175     315 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63
                                   +l l++G  G+GKs+++ +l+  l +   ++++++ + +q 
  gi|121639593|ref|YP_979817.1| 22 RLHLVTGKGGTGKSTIAAALALTLAAGgrKVLLVEVEGRQG 62
                                   7789*************999865554421344444444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                         AAA_16  94 l 94 
                                    +
  gi|121639593|ref|YP_979817.1| 249 P 249
                                    1 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8     9e-05      0.07      34      66 ..      26      58 ..      19      63 .. 0.91
   2 ?   -3.1   0.0       3.9     3e+03      50      67 ..      78      95 ..      75      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                                   EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   +tG  G+Gkst+  al+l+l++ G++v ++ v+
  gi|121639593|ref|YP_979817.1| 26 VTGKGGTGKSTIAAALALTLAAGGRKVLLVEVE 58
                                   7**************************988775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                                   HHHHHCTT--EEEEEE-- CS
                           MeaB 50 glelrrrGkrvavlavDP 67
                                    +  ++rG +v  la+D 
  gi|121639593|ref|YP_979817.1| 78 KIATAERGGQVNALAIDI 95
                                   566789999******995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00031      0.25       8      52 ..      24      62 ..      19      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpssts 52
                                    +vtG  GtGK+t ++ l+ +l +       +++v++v++ +  +
  gi|121639593|ref|YP_979817.1| 24 HLVTGKGGTGKSTIAAALALTLAAG------GRKVLLVEVEGRQG 62
                                   589******************9766......77777777766655 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00084      0.65       2      79 ..      26     103 ..      25     112 .. 0.84
   2 ?    0.2   0.0      0.77     6e+02      28     110 ..     158     238 ..     139     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00084
                  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyi 79 
                                    +t++ G+GKS++++ ++  l+a g++ +lv    ++ +++lf+      ++l++ + e+  + +  ++ ++   +ey+
  gi|121639593|ref|YP_979817.1|  26 VTGKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLFDVPPLPYQELKIATAERGGQVNALAIDIEAAFLEYL 103
                                    79999*********99999999999999999999999****9999888888888877777777777777777777776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.77
                  Helicase_RecD  28 nilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyiapdellklkeqadllvvDEAAaiplpll 107
                                     i+v ap    ++++++  ++  +  +    + ++++  + l+++++ i+ ++  e+l  +  + l  ++E A+++lp+ 
  gi|121639593|ref|YP_979817.1| 158 AIVVDAPPTGRIARFLDVTKAVSDLAKGGPVHAQSEGVVKLLHSNQTAIHLVTLLEALPVQ--ETLEAIEELAQMELPIG 235
                                    6788888888888888877444443333335666666666666677777777777777765..57888999999999876 PP

                  Helicase_RecD 108 kkl 110
                                    + +
  gi|121639593|ref|YP_979817.1| 236 SVI 238
                                    555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00024      0.19       2      28 ..      23      49 ..      22      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                   l +++G+ G GK+t ++ lal++a+g 
  gi|121639593|ref|YP_979817.1| 23 LHLVTGKGGTGKSTIAAALALTLAAGG 49
                                   6789********************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00028      0.22       4      35 ..      24      55 ..      21      61 .. 0.92
   2 ?   -2.0   0.0       2.9   2.3e+03      78      95 ..     150     169 ..     109     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                    l+ G  G+GK t +a La  l + g+kvllv
  gi|121639593|ref|YP_979817.1| 24 HLVTGKGGTGKSTIAAALALTLAAGGRKVLLV 55
                                   6899**************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                                    HHHHTTSSEEEEEE..--SS CS
                          SRP54  78 kakeekidvvlvDT..aGrl 95 
                                    k k   +d+++vD   +Gr 
  gi|121639593|ref|YP_979817.1| 150 KNKLPVYDAIVVDAppTGRI 169
                                    44445566666664223444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00036      0.28      21      43 ..      23      45 ..      19      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                         AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                   l l+tG+ G+GK+Ti  A+ l L
  gi|121639593|ref|YP_979817.1| 23 LHLVTGKGGTGKSTIAAALALTL 45
                                   6799**************99877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00041      0.32       6      33 ..      25      59 ..      22     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                         AAA_24  6 liyGpsgiGKTtlakel.......gpkplfidtek 33
                                   l++G+ g+GK+t+a+ l       g k+l++ +e+
  gi|121639593|ref|YP_979817.1| 25 LVTGKGGTGKSTIAAALaltlaagGRKVLLVEVEG 59
                                   799*************9999999999999999998 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00041      0.32       3      30 ..      23      47 ..      21      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                        DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddee 30
                                   + lVtG+ GtGK+ ++ +l+ +l   + 
  gi|121639593|ref|YP_979817.1| 23 LHLVTGKGGTGKSTIAAALALTL---AA 47
                                   679****************9998...33 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9    0.0014       1.1       2      19 ..      25      42 ..      25      63 .. 0.86
   2 ?   -1.4   0.0       4.2   3.3e+03      96     111 ..     153     173 ..     134     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                         AAA_18  2 lltGtpGvGKttlakeLs 19
                                   l+tG+ G+GK+t+a +L+
  gi|121639593|ref|YP_979817.1| 25 LVTGKGGTGKSTIAAALA 42
                                   69*************996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                         AAA_18  96 k.....vvLtaspeelleRle 111
                                          +v++a+p  ++ R+ 
  gi|121639593|ref|YP_979817.1| 153 LpvydaIVVDAPPTGRIARFL 173
                                    245566999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2434.04
//
Query:       gi|121639594|ref|YP_979818.1|  [L=386]
Description: anion transporter atpase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-26   91.8   0.0    8.3e-26   90.9   0.0    1.4  1  ArsA_ATPase     Anion-transporting ATPase
    5.7e-11   42.6   0.0    9.5e-11   41.9   0.0    1.3  1  AAA_31          AAA domain
    2.4e-08   34.1   0.0    1.5e-07   31.6   0.0    2.2  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    3.3e-08   33.3   0.1    3.4e-06   26.7   0.1    2.7  2  ParA            NUBPL iron-transfer P-loop NTPase
    0.00023   20.8   0.4    0.00058   19.5   0.2    1.8  2  SRP54           SRP54-type protein, GTPase domain
    0.00031   20.5   1.2    0.00049   19.9   0.2    1.8  2  AAA_30          AAA domain
    0.00043   19.3   1.0     0.0021   17.1   0.3    2.1  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
     0.0016   18.7   0.1     0.0051   17.1   0.0    1.9  2  AAA_22          AAA domain
     0.0018   18.0   0.1     0.0039   16.9   0.1    1.5  1  IstB_IS21       IstB-like ATP binding protein
     0.0029   17.9   0.2      0.011   16.0   0.1    2.0  2  AAA_28          AAA domain
     0.0029   17.1   0.0     0.0048   16.4   0.0    1.4  1  PhoH            PhoH-like protein
     0.0037   17.4   0.2       0.01   16.0   0.0    1.9  1  AAA_33          AAA domain
     0.0059   17.0   0.3      0.039   14.3   0.0    2.3  2  AAA_16          AAA ATPase domain
     0.0061   16.8   0.9       0.04   14.2   0.6    2.1  2  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
     0.0091   15.8   0.0       0.33   10.8   0.0    2.3  2  AAA_26          AAA domain
     0.0097   15.7   0.1      0.034   13.9   0.1    1.8  2  ATP_bind_1      Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.011   15.1   0.4       0.47    9.7   0.2    2.3  2  MipZ            ATPase MipZ
      0.016   14.7   0.0      0.039   13.4   0.1    1.6  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
      0.044   13.7   0.2        0.1   12.5   0.2    1.5  1  YjeF_N          YjeF-related protein N-terminus
      0.052   13.8   0.1         33    4.8   0.0    3.3  3  TrkA_N          TrkA-N domain
       0.12   11.7   0.0       0.26   10.6   0.0    1.4  1  ATPase          KaiC
       0.14   12.2   0.3       0.25   11.4   0.3    1.3  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
       0.15   11.8   0.0       0.29   10.9   0.0    1.4  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
        1.2    8.7   8.2       0.61    9.6   4.3    2.5  2  AAA_25          AAA domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   1.1e-28   8.3e-26       2     245 ..      20     285 ..      19     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.1e-28
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS.--BSS-EEET......SSEEEEE--HHHHHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq.klgkeptkvk......eNLsavEidpevele 74 
                                    +v++  G GGVGKtt +aa+a++ +e g+ v++++ DPA  l+ ++   +lg++p++v         L+a+ +d++   +
  gi|121639594|ref|YP_979818.1|  20 RVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKRLAQALGInDLGNTPQRVPlapevpGELHAMMLDMRRTFD 99 
                                    78999*****************************************97689*****99888878789*********9999 PP

                                    HHHCCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHH. CS
                    ArsA_ATPase  75 eakqevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklle. 153
                                    e+  + +  e+a+      +++ +  ++sl G++e +++e+l ++++++ +d +v+Dt+P  ++l +l+ p+ l+++++ 
  gi|121639594|ref|YP_979818.1| 100 EMVMQYSGPERAQSI--LDNQFYQTVATSLAGTQEYMAMEKLGQLLSQDRWDLIVVDTPPSRNALDFLDAPKRLGSFMDs 177
                                    999998888886555..6789999**************************************************999973 PP

                                    HHHHHHH........HHHHHHHHHCC.CSHCHHHHHH....HHHHHHHHHHHHHHHHHH...HHTSTTTEEEEEEEESSH CS
                    ArsA_ATPase 154 klvklke........klsplakqlvk.llglggvsie....ealeeleetkeeikkvee...iltdpertsfrlVvipEk 217
                                    +l +l           ++ ++   +k l+++ g+++       +++l++t+  +++  +    l     t f++V+ +E 
  gi|121639594|ref|YP_979818.1| 178 RLWRLLLapgrgigrLITGVMGLAMKaLSTVLGSQMLadaaAFVQSLDATFGGFREKADrtyALLKRRGTQFVVVSAAEP 257
                                    4444432344544442222222222202222222222334566777777777665443322257788999********** PP

                                    HHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                    ArsA_ATPase 218 lslkEteRaikeLkkygikvdavivNkl 245
                                     +l+E    +  L++ ++    ++ N+ 
  gi|121639594|ref|YP_979818.1| 258 DALREASFFVDRLSQESMPLAGLVFNRT 285
                                    ******************9999999985 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.3e-13   9.5e-11      10     132 ..      27     162 ..       8     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.3e-13
                         AAA_31  10 KGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgie.kne.iek..........tlyevli.eeknikeaiikt 76 
                                     GGvGKTTt+ +la   a++g  v +  +Dp + ++++lgi+   +   +          +l+ +++  + + +e++++ 
  gi|121639594|ref|YP_979818.1|  27 AGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKRLAQALGINdLGNtP-QrvplapevpgELHAMMLdMRRTFDEMVMQY 105
                                    5***************************************95233341.2344455555588888877888999999977 PP

                         AAA_31  77 k.venldlipssidLaeaeielvelekkeei..lkellekvkdeYDyiiiDcpPsLgll 132
                                    +  e+ + i  +   + + ++l+++++   +  l +ll+  +d++D+i++D+pPs + l
  gi|121639594|ref|YP_979818.1| 106 SgPERAQSILDNQFYQTVATSLAGTQEYMAMekLGQLLS--QDRWDLIVVDTPPSRNAL 162
                                    755666777777778999999998887744411444444..588***********8865 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.9e-10   1.5e-07       1      83 [.      21     284 ..      21     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.9e-10
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH...................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx...................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep...................... 54 
                                    ++++ + GGvGKTt+aa+La   a+ g+ V+++  Dp   ++        g      +                      
  gi|121639594|ref|YP_979818.1|  21 VVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKRLAQAlginDLG------Ntpqrvplapevpgelhammldm 94 
                                    578999********************************9999854433333......23455669999999999988888 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121639594|ref|YP_979818.1|  95 rrtfdemvmqysgperaqsildnqfyqtvatslagtqeymameklgqllsqdrwdlivvdtppsrnaldfldapkrlgsf 174
                                    88888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|121639594|ref|YP_979818.1| 175 mdsrlwrlllapgrgigrlitgvmglamkalstvlgsqmladaaafvqsldatfggfrekadrtyallkrrgtqfvvvsa 254
                                    88888888888888777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ....CCHCCCHHHHHHCHCHHHH..EEEEEEEE CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ....dlkrllellealgkkkalllkiagvvlnr 83 
                                         l   + ++ +l+++    + +ag+v+nr
  gi|121639594|ref|YP_979818.1| 255 aepdALREASFFVDRLSQES---MPLAGLVFNR 284
                                    77763333333334444332...3444444444 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   4.6e-09   3.4e-06       3     107 ..      18     123 ..      16     163 .. 0.85
   2 ?   -1.1   0.0       1.4   1.1e+03     139     175 ..     249     285 ..     239     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.6e-09
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfll 82 
                                    ++ ++v+ g GGVGK+t+a+ lAl  a+ g +v +l +D     +++ lg+++   + ++  l P    ++++m +++  
  gi|121639594|ref|YP_979818.1|  18 SNRVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDP-AKRLAQALGINDLGNTPQRVPLAPEVPGELHAMMLDMRR 96 
                                    57899**********************************6.578999999999666666656888888999999999999 PP

                           ParA  83 esedeavvwrGpmkskai..kqllkdv 107
                                    + ++  + + Gp  ++ i  +q++++v
  gi|121639594|ref|YP_979818.1|  97 TFDEMVMQYSGPERAQSIldNQFYQTV 123
                                    888888889999887776445666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                           ParA 139 aviVttpqevaladvkkaiemfkkvkvkvlGvveNms 175
                                     v+V+  +  al +++  ++ +++ ++++ G+v N +
  gi|121639594|ref|YP_979818.1| 249 FVVVSAAEPDALREASFFVDRLSQESMPLAGLVFNRT 285
                                    5666666666666666666666666666666666643 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   7.8e-07   0.00058       2      39 ..      20      57 ..      19      75 .. 0.90
   2 ?   -2.9   0.0         6   4.5e+03      77      91 ..     141     155 ..     121     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.8e-07
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   +v++ +G  G+GKTtt+a La +  + g++v++ + D 
  gi|121639594|ref|YP_979818.1| 20 RVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDP 57
                                   58999*****************************9995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6
                                    HHHHHTTSSEEEEEE CS
                          SRP54  77 ekakeekidvvlvDT 91 
                                    +   +++ d+++vDT
  gi|121639594|ref|YP_979818.1| 141 QLLSQDRWDLIVVDT 155
                                    445667789999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   6.6e-07   0.00049      13      68 ..      14      67 ..       8      97 .. 0.84
   2 ?   -3.4   0.1       9.2   6.9e+03      51      81 ..     213     246 ..     197     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.6e-07
                         AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi 68
                                   l+ +++rv+v  G+ G GKtt+ +al+  +++ g++v++l+     Ak+La++lgi
  gi|121639594|ref|YP_979818.1| 14 LADTSNRVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTI--DPAKRLAQALGI 67
                                   4567778*******************9999999*****9974..445666666665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.2
                         AAA_30  51 glAptgkaAkvLaeelgi...eastiakllkrlk 81 
                                    +lA  ++  + L + +g    +a+++  llkr +
  gi|121639594|ref|YP_979818.1| 213 MLADAAAFVQSLDATFGGfreKADRTYALLKRRG 246
                                    5666666666666666644556666666665544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.7e-06    0.0021      23      69 ..      14      59 ..       5      66 .. 0.84
   2 ?   -0.3   0.0      0.55   4.1e+02      85     127 ..     212     252 ..     204     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                                   GGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB 23 lakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                   la++ + +vv   G  G+Gk t+  al+l+ ++ G+ v vl +DP+ 
  gi|121639594|ref|YP_979818.1| 14 LADTSN-RVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAK 59
                                   555554.455678********************************86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.55
                                    CCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEE CS
                           MeaB  85 elavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvli 127
                                    ++ +d+++f++sl +  + GG  +k+  + +ll   G   v++
  gi|121639594|ref|YP_979818.1| 212 QMLADAAAFVQSLDA--TFGGFREKADRTYALLKRRGTQFVVV 252
                                    566888999988865..78999999999999999998888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.9e-06    0.0051       4      43 ..      18      51 ..      15      78 .. 0.82
   2 ?   -2.8   0.0       9.6   7.2e+03      68      98 ..     127     154 ..      85     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.9e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                   + +++v++G  G+GKTt+++ l+ ++ e+      +++vv
  gi|121639594|ref|YP_979818.1| 18 SNRVVVCCGAGGVGKTTTAAALALRAAEY------GRTVV 51
                                   57899*******************99665......55555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.6
                         AAA_22  68 lkaerlsseell.ealeqalraravielliiD 98 
                                    l +   ++e +  e+l q l++ +   l+++D
  gi|121639594|ref|YP_979818.1| 127 LAG---TQEYMAmEKLGQLLSQDRW-DLIVVD 154
                                    222...2222222555555555555.666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.2e-06    0.0039      47      84 ..      19      56 ..       6      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.2e-06
                      IstB_IS21 47 kenivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                   +  +v +G  GvGK+  a+al+ +a++ g  v+ ++++
  gi|121639594|ref|YP_979818.1| 19 NRVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTID 56
                                   4457889************************9988864 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.4e-05     0.011       2     117 ..      22     157 ..      21     180 .. 0.60
   2 ?   -2.5   0.0         7   5.2e+03     139     156 ..     236     253 ..     231     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                         AAA_28   2 ivitGgestGKTtlleaLa..ar..gypvv...pEaareileeklakgedalpwve......dllafaervleeqleeea 68 
                                    +v  G+ + GKTt+++aLa  a   g +vv    ++a ++ + ++ ++ ++ p+ +       + ++ +++l++++    
  gi|121639594|ref|YP_979818.1|  22 VVCCGAGGVGKTTTAAALAlrAAeyGRTVVvltIDPAKRLAQALGINDLGNTPQ-RvplapeVPGELHAMMLDMRRT-FD 99 
                                    7889***************76115665544378888888888888444333332.1112232344444455544432.21 PP

                         AAA_28  69 aa......aankvlfcDrglldtlaYaraygge..aeaeleaaarekrydl.vfllpp 117
                                    +        ++   ++D ++  t+a + a  +e  a+++l + + ++r+dl v+ +pp
  gi|121639594|ref|YP_979818.1| 100 EMvmqysgPERAQSILDNQFYQTVATSLAGTQEymAMEKLGQLLSQDRWDLiVVDTPP 157
                                    1122333345666677777777777666666664334456667777777775555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7
                         AAA_28 139 erlrealrelgipviivp 156
                                    +r+ ++l+++g ++++v+
  gi|121639594|ref|YP_979818.1| 236 DRTYALLKRRGTQFVVVS 253
                                    677789999999999994 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.4e-06    0.0048      18      91 ..      18      91 ..       3     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                   H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS CS
                           PhoH 18 kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrplydaLkdll 91
                                   +n +v++ G  G GKt  a ala++a + ++   ++ + pa    + lG+ +   + +  p    +  +L+ ++
  gi|121639594|ref|YP_979818.1| 18 SNRVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKRLAQALGINDLGNTPQRVPLAPEVPGELHAMM 91
                                   789*****************************9999999*9999999999887666555566666666666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05      0.01       1      33 [.      21      82 ..      21     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg.....avllssdt........................l 33
                                   +v+++G+ G+GK+t a  l+ + +     +v+l+ d                         +
  gi|121639594|ref|YP_979818.1| 21 VVVCCGAGGVGKTTTAAALALRAAeygrtVVVLTIDPakrlaqalgindlgntpqrvplapE 82
                                   89****************96554457798888888884444444444444444444443330 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.3e-05     0.039      24      76 ..      18      65 ..       9     144 .. 0.71
   2 ?    0.0   0.2       1.3   9.8e+02      57     118 ..     284     333 ..     261     378 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-05
                         AAA_16 24 p.elvllsGesGvGKsslvrellralekd.g.giflrgkcdqlesaipysalaqal 76
                                   + ++v++ G+ GvGK++ + +l+ ++ +  + +++l+ +  +         laqal
  gi|121639594|ref|YP_979818.1| 18 SnRVVVCCGAGGVGKTTTAAALALRAAEYgRtVVVLTIDPAKR--------LAQAL 65
                                   3489***************888744444324355566666666........56655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
                         AAA_16  57 rgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasr 118
                                    r++   +  a   +++ +a+++ e l ++ +++++++l+a+  +++++ +       + a+r
  gi|121639594|ref|YP_979818.1| 284 RTHPMLC--A---LPIERAIDAAETLDAETTDSDATSLAAAVLRIHAERG-------QTAKR 333
                                    4444455..2...2355555555667777777777666666666666544.......22222 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.6   5.4e-05      0.04       4      36 ..      20      53 ..      17      60 .. 0.88
   2 ?    0.2   0.0       1.1     8e+02      82     104 ..     133     155 ..      93     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                 CobA_CobO_BtuR  4 lihvytGdG.KGKttAAlGlalRalgaglkvlvv 36
                                    + v +G G  GKtt A  lalRa+  g  v+v+
  gi|121639594|ref|YP_979818.1| 20 RVVVCCGAGgVGKTTTAAALALRAAEYGRTVVVL 53
                                   57899998537********************987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                 CobA_CobO_BtuR  82 kealekakealaseeydlvvlDE 104
                                      a+ek+ ++l+++++dl+v+D 
  gi|121639594|ref|YP_979818.1| 133 YMAMEKLGQLLSQDRWDLIVVDT 155
                                    45678888999999999999995 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12        90     100     124 ..      20      44 ..       4      68 .. 0.66
   2 !   10.8   0.0   0.00044      0.33     102     171 ..     219     299 ..     200     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                         AAA_26 100 divvVEGagglgvpiteellnadia 124
                                    ++vv+ Gagg+g+ +t+ +l  + a
  gi|121639594|ref|YP_979818.1|  20 RVVVCCGAGGVGKTTTAAALALRAA 44 
                                    5566666666666666665555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00044
                         AAA_26 102 vvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp.......... 170
                                     +V  ++ +  +  e+ + ++ + k+ g + ++V +++ +++  +   ++ l q+  +++G+++N++ +p          
  gi|121639594|ref|YP_979818.1| 219 AFVQSLDATFGGFREKaDRTYALLKRRGTQFVVVSAAEPDALREASFFVDRLSQESMPLAGLVFNRT-HPmlcalpiera 297
                                    57888888888888888999**********************************************5.664665555433 PP

                         AAA_26 171 .e 171
                                     +
  gi|121639594|ref|YP_979818.1| 298 iD 299
                                    32 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.5e-05     0.034       2      37 ..      25      60 ..      24      64 .. 0.94
   2 ?   -2.0   0.0       3.4   2.5e+03      79      99 ..     136     156 ..     120     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                   +G  G+GKtt   al+  + + gr+v v+ +DPA +
  gi|121639594|ref|YP_979818.1| 25 CGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKR 60
                                   7999******************************75 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                     ATP_bind_1  79 ldwldeelekeeddyllfDtP 99 
                                    +++l + l++ + d++++DtP
  gi|121639594|ref|YP_979818.1| 136 MEKLGQLLSQDRWDLIVVDTP 156
                                    456677774445599999999 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00063      0.47       2      42 ..      20      60 ..      19      80 .. 0.90
   2 ?    3.1   0.0     0.065        48      86     113 ..     133     161 ..      92     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                           MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqr 42
                                   ++v+    GG Gk+tta  +a   ++ G  v ++ +d  +r
  gi|121639594|ref|YP_979818.1| 20 RVVVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPAKR 60
                                   6899999*************************999997665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHHH.HH-SEEEEE--SS--H CS
                           MipZ  86 vaeleelvadle.aeldfividtPGsdsa 113
                                     +++e+l + l+  + d+iv+dtP s +a
  gi|121639594|ref|YP_979818.1| 133 YMAMEKLGQLLSqDRWDLIVVDTPPSRNA 161
                                    3445555555441579********88766 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.2e-05     0.039       3      39 ..      22      58 ..      20      67 .. 0.90
   2 ?   -3.2   0.0       6.2   4.6e+03     171     184 ..     272     284 ..     243     311 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                      Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                   +   G GG+Gk+tt++ l+   ae g+ v+++  DP 
  gi|121639594|ref|YP_979818.1| 22 VVCCGAGGVGKTTTAAALALRAAEYGRTVVVLTIDPA 58
                                   56679******************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.2
                      Fer4_NifH 171 sggvrlgGliinsr 184
                                    ++++ l+Gl+ n r
  gi|121639594|ref|YP_979818.1| 272 QESMPLAGLVFN-R 284
                                    445667777777.3 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00013       0.1      23      65 ..      15      59 ..       4      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                         YjeF_N 23 spaekkvlvlvGsgnnGgdglaaArhLaqegak..Vtvllleeee 65
                                   ++ +++v+v++G g  G    aaA  L+ +++   V vl++ + +
  gi|121639594|ref|YP_979818.1| 15 ADTSNRVVVCCGAGGVGKTTTAAALALRAAEYGrtVVVLTIDPAK 59
                                   567899****************99999666665226666665544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.062        47       4      33 ..      25      59 ..      22      69 .. 0.60
   2 ?   -0.3   0.0       1.7   1.2e+03      13      33 ..     139     159 ..     137     163 .. 0.81
   3 ?    4.8   0.0     0.044        33      30      59 ..     235     264 ..     233     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                                   ES-SHHHHHHHHHHHH.TT....EEEEEEESSHHH CS
                         TrkA_N  4 iGlGrvGrslaeeLse.gg....kdvvvidkdeer 33
                                   +G+G vG++ +    + +     + vvv   d+++
  gi|121639594|ref|YP_979818.1| 25 CGAGGVGKTTTAAALAlRAaeygRTVVVLTIDPAK 59
                                   66666666554443333333468669999999854 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                    HHHHHHHTTEEEEEEESSHHH CS
                         TrkA_N  13 laeeLseggkdvvvidkdeer 33 
                                    l + Ls++ +d +v+d+ ++r
  gi|121639594|ref|YP_979818.1| 139 LGQLLSQDRWDLIVVDTPPSR 159
                                    56788998889*****98865 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.044
                                    SHHHHHHHHHTTSEEEES-TTSHHHHHHTT CS
                         TrkA_N  30 deerveelreeglevvvgdatdeevLeeag 59 
                                     +++ + l+++g+++vv +a+++++L+ea 
  gi|121639594|ref|YP_979818.1| 235 ADRTYALLKRRGTQFVVVSAAEPDALREAS 264
                                    5667788999******************95 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.26      19      59 ..      19      58 ..      14      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                         ATPase 19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                   +rvv  +G  G GKt+ a+  +++ ae  g+ +v  t++  
  gi|121639594|ref|YP_979818.1| 19 NRVVVCCGAGGVGKTTTAAALALRAAEY-GRTVVVLTIDPA 58
                                   789999*****************99665.********9855 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00033      0.25      23      61 ..      19      62 ..      12      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                   TSEEEEE--SHHHHHHHHH...HHH..CT-EEEEE-S-HHHHHH CS
                  AdoHcyase_NAD 23 GkvavvaGyGdvGkGcaas...lkg..lGarvivtevdPicalq 61
                                    +v+v +G G vGk ++a+   l++   G  v+v  +dP   l 
  gi|121639594|ref|YP_979818.1| 19 NRVVVCCGAGGVGKTTTAAalaLRAaeYGRTVVVLTIDPAKRLA 62
                                   578999********86543122554226999********98775 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00039      0.29       1      33 [.      26      58 ..      26      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                   G+  +GK+T a+ L+ +a++ gr++v++ +D+ 
  gi|121639594|ref|YP_979818.1| 26 GAGGVGKTTTAAALALRAAEYGRTVVVLTIDPA 58
                                   67789**************************96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.3   0.00082      0.61      34      61 ..      20      48 ..      16     163 .. 0.86
   2 ?   -3.5   0.1       8.5   6.4e+03     159     180 ..     307     328 ..     297     332 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00082
                         AAA_25 34 elallaGapgtGKttlaldlalava.tGk 61
                                    +++ +Ga+g+GKtt a  lal  a  G+
  gi|121639594|ref|YP_979818.1| 20 RVVVCCGAGGVGKTTTAAALALRAAeYGR 48
                                   68899*****************9995444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.5
                         AAA_25 159 ensnsdvgalvealeriarrtg 180
                                    e+ +sd+++l +a+ ri ++ g
  gi|121639594|ref|YP_979818.1| 307 ETTDSDATSLAAAVLRIHAERG 328
                                    5666777777777777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 2743.02
//
Query:       gi|121639595|ref|YP_979819.1|  [L=118]
Description: transcriptional regulatory protein whiB-like whiB4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-22   80.0   2.4    2.3e-22   79.4   2.4    1.3  1  Whib      Transcription factor WhiB
  ------ inclusion threshold ------
      0.025   13.8   0.2      0.026   13.8   0.2    1.0  1  DUF2800   Protein of unknown function (DUF2800)
       0.12   12.3   3.3       0.78    9.6   0.0    3.3  4  DUF1289   Protein of unknown function (DUF1289)


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   2.4   3.8e-26   2.3e-22       1      64 []      31      93 ..      31      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.8e-26
                           Whib  1 WreraaCrgedpelffpekgdreeeAkavCarCpVrreCleealeegeeyGvwGGltereRraL 64
                                   W ++a Cr++dp+  f ++ +++++A  +C++CpV++eC+++al++++e+GvwGG+ter+RraL
  gi|121639595|ref|YP_979819.1| 31 WVSKALCRTTDPDELFVRG-AAQRKAAVICRHCPVMQECAADALDNKVEFGVWGGMTERQRRAL 93
                                   9***********9999886.9*****************************************97 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.4e-06     0.026     190     275 ..      28     112 ..      10     118 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                        DUF2800 190 Llewaeevlkpka...ekaaegegefvpgehcrFCkakatCraraekalklakddfkeptlltdeeiaevlskvdelksw 266
                                      +w+ + l  +    e+ ++g+ + +++  cr C + ++C a a ++    k +f     +t+ +  ++l++ +e+ sw
  gi|121639595|ref|YP_979819.1|  28 RIAWVSKALCRTTdpdELFVRGAAQRKAAVICRHCPVMQECAADALDN----KVEFGVWGGMTERQRRALLKQHPEVVSW 103
                                    4455554443332111444899999999999**********9776655....468999999******************* PP

                        DUF2800 267 akdveeyal 275
                                     + +e++  
  gi|121639595|ref|YP_979819.1| 104 SDYLEKRKR 112
                                    *99998765 PP

>> DUF1289  Protein of unknown function (DUF1289)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.34     2e+03      24      31 ..      26      33 ..      22      41 .. 0.71
   2 ?   -3.3   0.1       1.4   8.4e+03      14      19 ..      57      62 ..      52      63 .. 0.63
   3 ?    9.6   0.0   0.00013      0.78      25      45 ..      78      98 ..      75     100 .. 0.86
   4 ?    3.3   0.1     0.012        73      23      39 ..      97     113 ..      94     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
                        DUF1289 24 dEiaaWss 31
                                   +E++aW s
  gi|121639595|ref|YP_979819.1| 26 EERIAWVS 33
                                   67777754 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                        DUF1289 14 glClGC 19
                                    +C+ C
  gi|121639595|ref|YP_979819.1| 57 VICRHC 62
                                   466666 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00013
                        DUF1289 25 EiaaWssmsdeerravlarle 45
                                   E   W  m++++rra+l++ +
  gi|121639595|ref|YP_979819.1| 78 EFGVWGGMTERQRRALLKQHP 98
                                   7889************99866 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.012
                        DUF1289  23 ldEiaaWssmsdeerra 39 
                                      E+  Ws++ ++++r+
  gi|121639595|ref|YP_979819.1|  97 HPEVVSWSDYLEKRKRR 113
                                    679*******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 854.70
//
Query:       gi|121639596|ref|YP_979820.1|  [L=810]
Description: bifunctional membrane-associated penicillin-binding protein 1A/1B ponA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-54  181.7   0.1    1.4e-53  181.0   0.1    1.3  1  Transgly        Transglycosylase
    1.9e-20   73.3   0.0    3.6e-20   72.4   0.0    1.4  1  Transpeptidase  Penicillin binding protein transpeptidase dom
    7.1e-10   38.6   0.8    2.7e-09   36.7   0.8    2.1  1  PASTA           PASTA domain
  ------ inclusion threshold ------
        2.2    7.9   5.1        4.9    6.8   5.1    1.5  1  CLLAC           CLLAC-motif containing domain


Domain annotation for each model (and alignments):
>> Transgly  Transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.1   3.1e-57   1.4e-53       2     177 ..      70     256 ..      69     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 3.1e-57
                       Transgly   2 gellaeleeeenrelvkleeippalkkavvaiEDrrFyehkGvdlkgiarAvlknlksgkssqGgSTitqQlvknlfl.. 79 
                                    g+++a+l ++++r  v+ ++i++++k a+v+iED+rF +h+Gvd+kg++  ++  +++   ++GgST+ qQ+vkn+ l  
  gi|121639596|ref|YP_979820.1|  70 GNTIAWL-YSQRRFEVPSDKIANTMKLAIVSIEDKRFADHSGVDWKGTLTGLAGYASGDLDTRGGSTLEQQYVKNYQLlv 148
                                    6788899.799*********************************************999999*************86667 PP

                       Transgly  80 ......see.....rtlerKlkeavlAlklekklsKdeILeaYlNsvylgrevyGieaAarayFgkdakdLtlaeaalLa 148
                                          + +     +t +rKl+e+ +Al l+k+++K+eIL+ YlN v +g++ +G+++Aa++yFg +a+dL++++aalLa
  gi|121639596|ref|YP_979820.1| 149 taqtdaE-KraaveTTPARKLREIRMALTLDKTFTKSEILTRYLNLVSFGNNSFGVQDAAQTYFGINASDLNWQQAALLA 227
                                    7765441.145566889*************************************************************** PP

                       Transgly 149 gllkaPsrynplenpeeakkrrkvvlerm 177
                                    g++++ s++np++np+ a +rr+vvl++m
  gi|121639596|ref|YP_979820.1| 228 GMVQSTSTLNPYTNPDGALARRNVVLDTM 256
                                    ***************************99 PP

>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0     8e-24   3.6e-20      12     252 ..     364     620 ..     360     640 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 8e-24
                                    BEEEEEEESE-TTTHHCC.TCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS.........E CS
                 Transpeptidase  12 evlamaskpsydpnakvg.kneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqs........i 82 
                                    +vlamas+++y  + ++g   +p    +v +    GS+fK++t+aaal+ g +  + +ld ++  + +g           
  gi|121639596|ref|YP_979820.1| 364 KVLAMASNRKYGLDLEAGeTMRPQPFSLVGDG--AGSIFKIFTTAAALDMG-MGINAQLDVPPRFQAKGLGsggakgcpK 440
                                    79999999999888887742333333334444..4****************.6668889888876665443333346778 PP

                                    CTCCCC-..SSSSEEEHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--B--SSH.......HHH CS
                 Transpeptidase  83 kdweqdn..kgsegitlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaGvptrkw.......leg 153
                                    + w + n  +  + +++++al+ S nt+f+kl  ++g  ++ +++ k+gl +   + +pg+   +++++          +
  gi|121639596|ref|YP_979820.1| 441 ETWCVVNagNYRGSMNVTDALATSPNTAFAKLISQVGVGRAVDMAIKLGLRS---YANPGTARDYNPDSNesladfvKRQ 517
                                    889999998888899*************************************...8888888885555444666665559 PP

                                    HHHHHTTT.SBB-HHHHHHHHHHHHTTTEEE--BSEEEEEECTTEEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTT CS
                 Transpeptidase 154 atisfgiG.ltvtplqlaqayaaiangGklvkPhlvkaivdpdgvrkvkpkelnklpisketaekvkeglkgvvsrgsgt 232
                                    ++ sf+ G +++++l+l +++a++a+gG+  +P  ++++ d +g++   ++e   +++ +  a+++ +++ + +    gt
  gi|121639596|ref|YP_979820.1| 518 NLGSFTLGpIELNALELSNVAATLASGGVWCPPNPIDQLIDRNGNEVAVTTETCDQVVPAGLANTLANAMSKDAVGS-GT 596
                                    999*****************************************99999999******************8877665.66 PP

                                    GCG..TCTTS..--EEEEEEEEEC CS
                 Transpeptidase 233 ata..avegy..kvagKTGTAeva 252
                                    a++    +g+  +++gKTGT+e  
  gi|121639596|ref|YP_979820.1| 597 AAGsaGAAGWdlPMSGKTGTTEAH 620
                                    666667777777********9965 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.8     6e-13   2.7e-09       2      62 ..     702     761 ..     701     762 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6e-13
                                    E--TTTTSBHHHHHHHHHHTT--CCCEEE.ECTCCGTTBEEEECS-TTSEECTTS-EEEEEE CS
                          PASTA   2 tvPdvtGmsvdeAkatLkalGlkiktvee.tsddvpeGtVisQsPeaGtevskgskvtltvs 62 
                                    +vP+v+G++vd A++ Lk++G+++  ++  ++++   G V+++sP+ G+++ +gs vt+ +s
  gi|121639596|ref|YP_979820.1| 702 RVPSVAGLDVDAARQRLKDAGFQVADQTNsVNSSAKYGEVVGTSPS-GQTI-PGSIVTIQIS 761
                                    69********************999999989999999*********.9**9.*******998 PP

>> CLLAC  CLLAC-motif containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.1    0.0011       4.9      11      22 ..      18      29 ..      17      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                          CLLAC 11 CLLACiitTaig 22
                                   CLLA++++Ta++
  gi|121639596|ref|YP_979820.1| 18 CLLASVVATALT 29
                                   **********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 5749.65
//
Query:       gi|121639597|ref|YP_979821.1|  [L=319]
Description: hypothetical protein BCG_3742 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-11   42.5   0.0    2.6e-10   40.8   0.0    1.7  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    7.1e-07   29.9   0.2    1.4e-06   28.9   0.2    1.5  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.9e-14   2.6e-10       2     128 ..      52     233 ..      51     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.9e-14
                  Metallophos_2   2 klaiiSDlH..snldaleavlealkevgvdaiihaGDleeeepe....vleellela..pvlaVrGNnD........... 62 
                                    ++++iSDlH   n ++ +a+l++l++ ++d+++++GD + ++p+    v+++l +l+  p + V+G nD           
  gi|121639597|ref|YP_979821.1|  52 RVLHISDLHmlPNQHRKQAWLRELASWEPDLVVNTGD-NLAHPKavpaVVQTLSDLLsrPGVFVFGSNDyfgprlknpmn 130
                                    89*******9999************************.667775223377777777799****************99999 PP

                  Metallophos_2  63 ...................................eev.veedvlreaaelgtdlpeeaelel........agekvlliH 98 
                                                                         + ++  ++ +aa++++ + ++++ +         a+ +++l+H
  gi|121639597|ref|YP_979821.1| 131 yltspdhrvrgaalpwqdlraaftergwldlthtrR-EfEVAGLHIAAAGVDDPHIDRDRYDTiagpaspaANLRLGLTH 209
                                    999998888888888887777777666666655432.1244444444444444444555555345555555666688888 PP

                  Metallophos_2  99 gdplgvkdalaellkeaeegsdvvvcGHtH 128
                                    + +++v d++a++ ++      +v++GHtH
  gi|121639597|ref|YP_979821.1| 210 SPEPRVLDRFAADGYQ------LVLAGHTH 233
                                    8866666666666666......******** PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   1.6e-10   1.4e-06       1     202 [.      51     233 ..      51     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.6e-10
                                    EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEEST.SSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                    Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGD.lvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                    lr+l+i+DlH      + ++ +++l++l++  +pdlv+ +GD l +   ++  ++ l + l++   p +++ G  + +  
  gi|121639597|ref|YP_979821.1|  51 LRVLHISDLH---MLPNQHRKQAWLRELASW-EPDLVVNTGDnLAHPKAVPAVVQTL-SDLLS--RPGVFVFGSND-YFG 122
                                    69********...899999999******888.**********666667777755555.66666..399********.444 PP

                                    .HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE........THHHHHHHHHHHSCHHHHCCHHH CS
                    Metallophos  80 .ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel........lvsldklgslnleleapepgdew 150
                                      l+n+  yl+  s+++r  +  + +  l +  +   + +l+  ++ ++             +  ++++++      ++ 
  gi|121639597|ref|YP_979821.1| 123 pRLKNPMNYLT--SPDHRVRGAALPWQDLRAAFTE--RGWLDLTHTRREfevaglhiAAAGVDDPHIDRDR------YDT 192
                                    45555555444..5555444434444444443333..4444444422222111111111112222222222......444 PP

                                    HHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                    Metallophos 151 lkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtH 202
                                    ++   +   a   + l+Hsp +          ++ d +   g +lv+ GHtH
  gi|121639597|ref|YP_979821.1| 193 IAG-PASPAANLRLGLTHSPEP----------RVLDRFAADGYQLVLAGHTH 233
                                    444.566666666666777777..........4445566677899******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2231.18
//
Query:       gi|121639598|ref|YP_979822.1|  [L=346]
Description: lyase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-49  168.2   0.2    3.2e-49  167.9   0.2    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.2   1.8e-53   3.2e-49      18     292 ..      25     305 ..      10     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.8e-53
                                    CCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHH CS
                           PALP  18 kelgvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaallGlkvtivvpadaspekv 94 
                                     ++ v+l+lK+E ++ tgS K R a +l+++ l +g  ++++tvveassG ++++ A+ aallGl+++ v+pa +s++k+
  gi|121639598|ref|YP_979822.1|  25 TDVDVELYLKDETTHITGSLKHRLARSLFLYaLCNGwiNENTTVVEASSGSTAVSEAYFAALLGLPFIAVMPAATSASKI 104
                                    467788********************9988867777**99**************************************** PP

                                    HHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT...SHHHHHHHHTHHHHHHHHTT....TTEEEEEEE-SS CS
                           PALP  95 allrllGaevvevggdydeavaaaaelaaegegaylvsqfd...nptviegygtiglEileqlg....gkpdavvvpvGg 167
                                    al+++ G ++++v ++  +  a a+++a+e +g ++++qf      t + g + i+  i+ q+     + p+++vv++G+
  gi|121639598|ref|YP_979822.1| 105 ALIESQGGRCHFV-QNSSQVYAEAERVAKE-TGGHYLDQFTnaeRATDWRGNNNIAESIYVQMReekhPTPEWIVVGAGT 182
                                    *************.66888888889*****.**********555555************96665566699********** PP

                                    SHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHH CS
                           PALP 168 GgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsdee 247
                                    Gg+ a i++++++rr  +r+++v+pe+s+ + ++  +gr++ v ++++ ++g++ +   +   + l + vd++v+v+d++
  gi|121639598|ref|YP_979822.1| 183 GGTSATIGRYIRYRRHATRLCVVDPENSAFFPAYS-EGRYDIVMPTSSRIEGIGRP---RVEPSFLPGVVDRMVAVPDAA 258
                                    **************************777777777.********************...7777788899999999***** PP

                                    HHHHHHHHHHHHSB-B-HHHHHHHHHH..HHHHHHCCTTCEEEEEEE CS
                           PALP 248 aleamrllarregivvepssaaalaal..klreagelkegdrvvvil 292
                                     ++a+r++    g  v+ps++++l ++   l+e  + +++ +vv++l
  gi|121639598|ref|YP_979822.1| 259 SIAAARHVSAVLGRRVGPSTGTNLWGAfgLLAEMVKQGRSGSVVTLL 305
                                    ***************************88555555555555788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2500.99
//
Query:       gi|121639599|ref|YP_979823.1|  [L=476]
Description: cytochrome P450 137 cyp137 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-63  212.9   0.0      1e-62  212.4   0.0    1.2  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.0   5.8e-67     1e-62      27     457 ..      71     466 ..      60     472 .. 0.90

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 5.8e-67
                                    HHHHHHH-SEEEEEETT.EEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHH CS
                           p450  27 rklqkkygpifrlklgs.kpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltpt 105
                                     +l ++ygpi+++ + s  +v+++s++ ++kev+ + ++   g   e +   ++  +   ++++++ +++ + R++ltp 
  gi|121639599|ref|YP_979823.1|  71 LRLIRRYGPIMTMPILSlGDVAIVSDSALAKEVFTAPTDVLLG--GEGVGP-AAAIYGSGSMFVQEEPQHLRRRKLLTPP 147
                                    567789*******998868999***************866666..333333.455799999999999************* PP

                                    HTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHHHHHHSSHHHTTTSSHHHHHHHHHHHHHHHH CS
                           p450 106 ltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvigsilFgarfdlledeklselvkaveelssll 184
                                    l++  +l ++++++e +++  ++++  ++ ++    + ++    +ldvi +++Fg+     + e+  +l + +e+l++l 
  gi|121639599|ref|YP_979823.1| 148 LHGA-ALdRYVPIIENSTRAAMHTWPVDRPFA----MLTVARSLMLDVIVKVIFGVD----DPEEVRRLGRPFERLLNLG 218
                                    ****.999*****************9888888....********************6....4555668899999997655 PP

                                    HCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHH CS
                           p450 185 skssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsakksrrdfldalllakkekkgesklsdeela 264
                                       s ql   + l +    + +    +a  +++d++++li +rr++ +    +r d l++l++a+  ++ge +lsd e++
  gi|121639599|ref|YP_979823.1| 219 --VSEQLTVRYALRRLGALRVWPARARANTEIDDVVMALIAQRRADPRLG--ERHDVLSLLVSAR-GESGE-QLSDSEIR 292
                                    ..345788888889999999******************************..9***********8.77776.9******* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEE CS
                           p450 265 atvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlgdkreptyddlqklpyldavikEtLRlhpvvplllpR 344
                                      +++l +aG++Tt++tl+wa+ +L+++P++ +++r E   ++g+ +           +++avi+EtLR +p++p l+ R
  gi|121639599|ref|YP_979823.1| 293 DDLITLVLAGHETTATTLAWAFDLLLHHPDALRRVRAE---AVGGGE----------AFTTAVINETLRVRPPAP-LTAR 358
                                    **************************************...887766..........79****************.99** PP

                                    ESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHH CS
                           p450 345 evtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGerlArmelkl 424
                                    ++ ++++i+gy +++Gt+++v + a++r+ ev+++P+eF+peRFl ++     + +a++PFG G++ C+G ++ + el  
  gi|121639599|ref|YP_979823.1| 359 VAAQPLTIGGYRVEAGTRIVVHIIAINRSAEVYEHPHEFRPERFLGTRP----QTYAWVPFGGGVKRCLGANFSMRELIT 434
                                    ***********************************************75....79************************* PP

                                    HHHHHHHHEEEEESTSTSGGEEESSCSSEEESS CS
                           p450 425 flatlLqnFevelqpetdpppileksglllppk 457
                                    +l+ lL++ e++   +++p+ i ++s +l+p +
  gi|121639599|ref|YP_979823.1| 435 VLHVLLREGEFTA-VDDEPERIVRRSIMLVPRR 466
                                    ************8.5688888888875555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3330.78
//
Query:       gi|121639600|ref|YP_979824.1|  [L=110]
Description: hypothetical protein BCG_3745c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.3   1.2       0.07   12.5   1.2    1.4  1  GETHR     GETHR pentapeptide repeat (5 copies)


Domain annotation for each model (and alignments):
>> GETHR  GETHR pentapeptide repeat (5 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   3.9e-06      0.07       9      23 ..      82      95 ..      81      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-06
                          GETHR  9 vRGETvRGEThRGeT 23
                                   v+GET RG T+ GeT
  gi|121639600|ref|YP_979824.1| 82 VCGETLRG-TPAGET 95
                                   69999999.999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 766.10
//
Query:       gi|121639601|ref|YP_979825.1|  [L=81]
Description: hypothetical protein BCG_3746c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-08   34.6   0.0    1.5e-08   34.3   0.0    1.0  1  STAS      STAS domain
      8e-05   22.9   0.0    0.00011   22.4   0.0    1.3  1  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.6e-12   1.5e-08      47     117 .]       4      70 ..       2      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.6e-12
                                    .-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                           STAS  47 slkslildlsavsfiDssGvraLkeilkelkrigvevvlvnikpevreklektgffdeveeeklfltvhdA 117
                                    +++ l++dlsav+f+ s+G++ L  + +++  + v++ +v   +  r+ ++ +g+++ +   +lf+t+hdA
  gi|121639601|ref|YP_979825.1|   4 NPTALVIDLSAVEFLGSVGLKILAATSEKIG-QSVKFGVVARGSVTRRPIHLMGLDKTF---RLFSTLHDA 70 
                                    5789***************************.***************************...********8 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-08   0.00011      26      80 .]       5      58 ..       1      58 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-08
                         STAS_2 26 gaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlldlyGld 80
                                   ++++v+Dls ve++ s +l  L+a  +  +++  ++ +++ ++  rr  +l+Gld
  gi|121639601|ref|YP_979825.1|  5 PTALVIDLSAVEFLGSVGLKILAATSEKIGQS-VKFGVVARGSVTRRPIHLMGLD 58
                                   5799*************************555.99999999999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 581.19
//
Query:       gi|121639602|ref|YP_979826.1|  [L=154]
Description: hypothetical protein BCG_3747c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-45  154.8   5.3    1.7e-45  154.6   5.3    1.0  1  YqeY       Yqey-like protein
     0.0079   16.1   1.9      0.065   13.1   1.9    2.0  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
       0.43    9.9   4.5         10    5.4   4.5    2.0  1  GlnE       Glutamate-ammonia ligase adenylyltransferase


Domain annotation for each model (and alignments):
>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   5.3   2.8e-49   1.7e-45       1     143 []       5     154 .]       5     154 .] 0.98

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 2.8e-49
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTTS..S--HHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHH CS
                           YqeY   1 keklkedlkeamkakdkerlstlrllkaaikqeevderk..elsdeevlkvlakevkqRresieefekagRedlaekeka 78 
                                    k++l++dl++amk +dk r++t+r+l+aai++eev+ ++  elsd+ev+kvla+e ++R e++e+++++gR +la++e+a
  gi|121639602|ref|YP_979826.1|   5 KSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQarELSDDEVIKVLARESRKRGEAAEIYTQNGRGELAATEHA 84 
                                    679*********************************999889************************************** PP

                                    HHHHHGGGS-----HHHHHHHHHHHHHHTT--.....BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                           YqeY  79 EievleeYlPeqlseeeiealvkeaiaevgae.....smkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                    E+++++eYlP++l+e e++++ ++aiaev +e     smk+mG vmka++  ++GkaDg+++sa+vke+L
  gi|121639602|ref|YP_979826.1|  85 EARIIDEYLPTPLTEGELADVADTAIAEVAEElghrpSMKQMGLVMKAATVIAAGKADGARLSAAVKERL 154
                                    *****************************88888889*******************************98 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.9   1.1e-05     0.065      35     148 .]      19     154 .]       1     154 [] 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                    TTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHH.HHHH....HHTXXH......................HHHHHHCTXXX CS
                      GatB_Yqey  35 ieelkltpeqlaellkliaegkIskkiakevl.eell....eegksp......................eeiieekgLkq 87 
                                     +  kl+ + +  ll+ i+ +++s+k+a+e+  +e++     e+++                       + ii+e+  ++
  gi|121639602|ref|YP_979826.1|  19 QD--KLRTATIRMLLAAIQTEEVSGKQARELSdDEVIkvlaRESRKRgeaaeiytqngrgelaatehaeARIIDEYLPTP 96 
                                    22..5889999999**************9765333332221333222678899999999999999999999999998888 PP

                                    XXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHT....TSSXSXHHHHHHHHHHHS CS
                      GatB_Yqey  88 isdeeeleklveeviaenpkavedyksgkekalkflvGqvMkk....tkGkadpklvnellkekL 148
                                    +++ +el ++ + +iae ++++    s k+      +G vMk+      Gkad+++++  +ke+L
  gi|121639602|ref|YP_979826.1|  97 LTE-GELADVADTAIAEVAEELGHRPSMKQ------MGLVMKAatviAAGKADGARLSAAVKERL 154
                                    886.**************666666666665......7888887444468************9987 PP

>> GlnE  Glutamate-ammonia ligase adenylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.5    0.0017        10      37      91 ..      16      71 ..       2     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0017
                                   GGGCCCH.HHHHHHHTTTS-TCHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHH CS
                           GlnE 37 pkeleaa.aaelaealaavedeeqliealRqfkreellriavadllglltveevsr 91
                                   +k+ +++ +a ++  laa++ ee   +++R++  +e++++ ++++ +  +++e+  
  gi|121639602|ref|YP_979826.1| 16 MKTQDKLrTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARESRKRGEAAEIYT 71
                                   34444441345677789999999999*************99999999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1169.01
//
Query:       gi|121639603|ref|YP_979827.1|  [L=451]
Description: hypothetical protein BCG_3748 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0002   20.3   6.8     0.0002   20.3   6.8    2.0  3  GPDPase_memb  Membrane domain of glycerophosphoryl diester ph
  ------ inclusion threshold ------
       0.35   10.6   4.3       0.75    9.5   4.3    1.5  1  UPF0259       Uncharacterised protein family (UPF0259)


Domain annotation for each model (and alignments):
>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.1      0.66     6e+03      64     266 ..     160     168 ..     148     174 .. 0.41
   2 ?   -0.9   0.0     0.061   5.4e+02     202     238 ..     238     273 ..     234     289 .. 0.61
   3 !   20.3   6.8   2.2e-08    0.0002     168     284 ..     292     412 ..     286     420 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 0.66
                   GPDPase_memb  64 lvlllLillllllllliylefalLilgiqeilkkekislkalfketfkklkklrgvsllflliYflLiiPflnlvlsssL 143
                                    +v++                                                                            
  gi|121639603|ref|YP_979827.1| 160 MVVV---------------------------------------------------------------------------- 163
                                    2222............................................................................ PP

                   GPDPase_memb 144 lnkikIPeFIvdellkttilivllylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllkllllil 223
                                                                                                                    
  gi|121639603|ref|YP_979827.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                   GPDPase_memb 224 iivivltvilsllllllqllldklpkkvslilaiinltllqii 266
                                                                          +lqii
  gi|121639603|ref|YP_979827.1| 164 --------------------------------------TLQII 168
                                    ......................................22222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.061
                   GPDPase_memb 202 eSwqltkknflrlllklllliliivivltvilsllll 238
                                    e w ++++++l+l ++l ll  + v+ +  + +++l 
  gi|121639603|ref|YP_979827.1| 238 EAWAKVRGRLLAL-FGLALLEAAGVVAVLGLAVVILS 273
                                    7899999998888.44444444444443333333333 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 2.2e-08
                   GPDPase_memb 168 ylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllklllliliivivltvilsllllllqllldkl 247
                                    +l++ + ++yl + l+f+  li+le+ ++ eA+++S+ l+++ f+r+l ++ll +l++++v  +i    ++++  +++ +
  gi|121639603|ref|YP_979827.1| 292 LLVVGVSLAYLYVVLLFAPVLIVLERLPIVEAITRSFALVRHGFWRVLGIRLLTVLVVGVVGNAIA-APFMIVGEIVTAV 370
                                    56777899999*******99***************************6666666666655555554.4444444555554 PP

                   GPDPase_memb 248 .pkkvs....lilaiinltllqiisliilvlsivlitqllvk 284
                                       + s    l+ a+++   + i  ++++++s  +++ l+++
  gi|121639603|ref|YP_979827.1| 371 tASDGSvtmrLVGATLSAIGVTIGQIVTAPFSAGVVVLLYTD 412
                                    333222235578888877777778888888777777777765 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.3   8.4e-05      0.75     146     225 ..     287     370 ..     282     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.4e-05
                        UPF0259 146 lGllllliPGiiva...illslsPiillkekksildsikasvnit.fknikliaPavllWllvklllllliskfsllskk 221
                                    lG+ lll+ G+ +a   ++l ++P++++ e+  i+++i  s  +  +   ++++  +l  l+v ++   +++ f ++ + 
  gi|121639603|ref|YP_979827.1| 287 LGFPLLLVVGVSLAylyVVLLFAPVLIVLERLPIVEAITRSFALVrHGFWRVLGIRLLTVLVVGVVGNAIAAPFMIVGEI 366
                                    799*******98653337899*******************9987615566888888888888888878888877777666 PP

                        UPF0259 222 iafl 225
                                    ++++
  gi|121639603|ref|YP_979827.1| 367 VTAV 370
                                    6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 3668.45
//
Query:       gi|121639604|ref|YP_979828.1|  [L=217]
Description: hypothetical protein BCG_3749 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-11   44.4   2.8    1.9e-11   44.0   1.2    2.1  2  DUF4129     Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.097   12.0   0.0       0.13   11.6   0.0    1.2  1  Bestrophin  Bestrophin, RFP-TM, chloride channel
       0.43   10.8   6.6        0.9    9.8   6.6    1.6  1  HemY_N      HemY protein N-terminus


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   8.2e+03      15      15 ..      20      20 ..       8      43 .. 0.44
   2 !   44.0   1.2   3.2e-15   1.9e-11       1      68 [.     121     190 ..     121     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                        DUF4129 15 d 15
                                   d
  gi|121639604|ref|YP_979828.1| 20 D 20
                                   1 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 3.2e-15
                        DUF4129   1 ayrallraLaer.gldrrpgeTprEyarrv.riapspaaalaalaelfeearYGgrpasaeeyrrlveal 68 
                                    +++a+ r L+e   l +++g+T+ E+a  + ++ p++a +l ++a++f+++ YG rp++ + y+   +++
  gi|121639604|ref|YP_979828.1| 121 RLQAVARELEETgMLNPAAGRTANELASDAgEVLPHLAGELTQAATAFNDVTYGERPGTQGAYQMIADLD 190
                                    68999**********************************************************9877765 PP

>> Bestrophin  Bestrophin, RFP-TM, chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.2e-05      0.13     115     190 ..      61     139 ..      33     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                     Bestrophin 115 ylvlllvlffralssrvrkrfptle...hlleagllteeeakilenkywvplqWavsllrrlaerlkelakegrikddq 190
                                     l+ll+++++ a++ + r +  +     +l +ag lt ++++   ++y    +Wa+++ +rl++  +el++ g+++   
  gi|121639604|ref|YP_979828.1|  61 LLILLMIAVTAAVQIARRTMRTNRGgdyQLFDAGQLTAAQHRSTAESYAAEGNWAAAIRHRLQAVARELEETGMLNPAA 139
                                    2455555555555555444444444889*************9999****************998888888888887755 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.6   0.00015       0.9      19      96 ..      58     136 ..      51     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                         HemY_N  19 avlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAekaaaka.aklseapllay 96 
                                      +ll+ll++++ +++++ r+++r+ +          +  a ++ s++    aeG++a+A ++  +a a+ +e+ ++ +
  gi|121639604|ref|YP_979828.1|  58 ITVLLILLMIAVTAAVQIARRTMRTNRGGDYQLFDAGQLTAAQHRSTAESYAAEGNWAAAIRHRLQAvARELEETGMLN 136
                                    6799*********************999998888889999999999**************8776544044445544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1460.51
//
Query:       gi|121639605|ref|YP_979829.1|  [L=333]
Description: hypothetical protein BCG_3750 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-08   33.2   0.9    1.4e-07   31.8   0.9    1.8  1  DUF4350   Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
       0.17   12.4   0.5       0.79   10.2   0.1    2.0  2  XdhC_C    XdhC Rossmann domain


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.9   1.6e-11   1.4e-07       1      69 []       5      72 ..       5      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.6e-11
                        DUF4350  1 skspnGtralaelLeaqGvevrrvrkpfd.alegedgtllvvapdlrlteeelaallewva.rGntlvlaa 69
                                   s+s  G +ala+lL ++Gvev ++++ +d + +++++ ll+va++ +l +   +all+++a + ++l+l+a
  gi|121639605|ref|YP_979829.1|  5 STSSTGGHALATLLGNHGVEVVVADSIADvEAAARPDSLLLVAQTQYLVD---NALLDRLAkAPGDLLLVA 72
                                   67899**********************99999999999999999999999...788888886779999986 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   8.9e-05      0.79      10      80 ..      11      76 ..       7      93 .. 0.75
   2 ?   -0.3   0.1      0.16   1.5e+03      82     117 ..     253     287 ..     247     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.9e-05
                                   HHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-HHH CS
                         XdhC_C 10 aqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGSrkk 80
                                   ++ala+l+ + g++v+v+d+ +++++++r      + ++v+  ++  D ++l+++ +   + + l++++++
  gi|121639605|ref|YP_979829.1| 11 GHALATLLGNHGVEVVVADSIADVEAAARPD----SLLLVAQTQYLVDNALLDRLAKA-PGDLLLVAPTSR 76
                                   789******************9966555554....99*****************9943.334444444433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                                    HHHCTTS.--.......TTEESS-S--S---SHHHH CS
                         XdhC_C  82 arrlerlraaglseeelarlhaPiGldigaktpeeI 117
                                    +r ++r  a+ l  + l+rl+   G+  ga  p+ +
  gi|121639605|ref|YP_979829.1| 253 RRARDRA-ADALRTATLQRLRPRLGVGAGAPAPAVV 287
                                    3333333.4578899999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2257.28
//
Query:       gi|121639606|ref|YP_979830.1|  [L=358]
Description: methanol dehydrogenase transcriptional regulatory protein moxR2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-63  211.4   0.1    4.5e-63  210.9   0.1    1.2  1  AAA_3            ATPase family associated with various cellul
    3.2e-22   78.1   0.0    9.4e-22   76.6   0.0    1.9  1  AAA_lid_2        AAA lid domain
    1.5e-14   54.2   0.0    2.4e-14   53.5   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    7.2e-06   25.3   0.0    1.4e-05   24.3   0.0    1.4  1  MCM              MCM P-loop domain
    2.7e-05   23.9   0.0     0.0016   18.2   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
    0.00025   21.5   0.0    0.00061   20.2   0.0    1.7  1  AAA              ATPase family associated with various cellul
    0.00058   19.6   0.0     0.0038   17.0   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0018   17.7   0.9      0.021   14.2   0.2    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   0.1     2e-66   4.5e-63       1     131 []      82     212 ..      82     212 .. 1.00

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 2e-66
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqs 80 
                                    hvllegvPG+aktl+v+a++ al+lefkr+qftpdl+P+d++G+ v+++++ ef f++Gpvf+nllladeinr+ppktq+
  gi|121639606|ref|YP_979830.1|  82 HVLLEGVPGVAKTLIVRAMSAALQLEFKRVQFTPDLMPGDVTGSLVYDARTAEFVFRPGPVFTNLLLADEINRTPPKTQA 161
                                    9******************************************************************************* PP

                          AAA_3  81 alleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                    alleameerqv+vege ++lp+pf+v atqnPie+eGty+lpeaqldrfll
  gi|121639606|ref|YP_979830.1| 162 ALLEAMEERQVSVEGEPKPLPNPFIVAATQNPIEYEGTYQLPEAQLDRFLL 212
                                    *************************************************96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   4.2e-25   9.4e-22       2      68 ..     278     345 ..     277     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 4.2e-25
                      AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegettee 68 
                                    atr+++a++lgvs+r ++ all +Ar +A+l grdyVtp+Dvk++a++ L+HR+   +e+e eg t + 
  gi|121639606|ref|YP_979830.1| 278 ATRSSPALQLGVSPR-GATALLGTARSWAWLSGRDYVTPDDVKAMARPTLRHRVMlrPEAELEGATPDG 345
                                    79*************.***************************************88888888876665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.1e-17   2.4e-14       1     138 []      82     210 ..      82     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.1e-17
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEverae 78 
                                    +vlL G pG++K+ +++ ++aal+ e+  vq+t d+ + d++g++ ++    + +++++p+        +l+ DE++r +
  gi|121639606|ref|YP_979830.1|  82 HVLLEGVPGVAKTLIVRAMSAALQLEFKRVQFTPDLMPGDVTGSLVYDarTAEFVFRPGPVF-----TNLLLADEINRTP 156
                                    79*********************************************966677778999999.....6899********* PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    ++++++Ll  +eer+++    ge    +n+     f v at np +  +  +l +a ++Rf
  gi|121639606|ref|YP_979830.1| 157 PKTQAALLEAMEERQVS--VEGEPKPLPNP-----FIVAATQNPIEyEGTYQLPEAQLDRF 210
                                    *****************..33444444444.....9********99655666666777776 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   6.1e-09   1.4e-05      57     153 ..      80     175 ..      49     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.1e-09
                                    S-EEEEEESSTSTHHHHHHHHHHHSSSEEE..EESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGST CS
                            MCM  57 dinvllvgdpgtaKsqlLkyveklapravy..tsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmk 134
                                    + +vll g pg+aK+ +++++++ ++               + t + v d +t efv+  G + +    +++ De+++  
  gi|121639606|ref|YP_979830.1|  80 RGHVLLEGVPGVAKTLIVRAMSAALQLEFKrvQFTPDLMPGDVTGSLVYDARTAEFVFRPGPVFTN---LLLADEINRTP 156
                                    559****************999766554331022334455678******************99865...89********* PP

                                    CHHHHHHHHHHHHSEEEEE CS
                            MCM 135 eedrsalhEamEqqtisia 153
                                     +++ al+EamE+ ++s+ 
  gi|121639606|ref|YP_979830.1| 157 PKTQAALLEAMEERQVSVE 175
                                    ****************995 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.023        53      22      45 ..      80     103 ..      67     115 .. 0.82
   2 !   18.2   0.0     7e-07    0.0016      96     146 ..     146     195 ..     143     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.023
                                    SS-EEEECSTTSSHHHHHHHHHHH CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraihea 45 
                                    + +vl++G  G+ K+l+ ra+ +a
  gi|121639606|ref|YP_979830.1|  80 RGHVLLEGVPGVAKTLIVRAMSAA 103
                                    679****************99764 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7e-07
                                    EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                     l+ Dei++ p+++Q+ Ll++++e++v+  G+ k+ +    i+aat++ +e
  gi|121639606|ref|YP_979830.1| 146 LLLADEINRTPPKTQAALLEAMEERQVSVEGEPKPLPN-PFIVAATQNPIE 195
                                    5778****************************999985.558999988776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.7e-07   0.00061       1     127 [.      83     213 ..      83     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETT.TCS.SS...STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHT CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgs.ell.sk...yvgesekkirelfkeakekakpsilfiDEidalaksrs 75 
                                    vll G pG+ KTl+++a+   l+ ef +++ + +l+  +    +   ++  + +f+       +  l+ DEi +  ++  
  gi|121639606|ref|YP_979830.1|  83 VLLEGVPGVAKTLIVRAMSAALQLEFKRVQFTpDLMpGDvtgSLVYDARTAEFVFRPGPV--FTNLLLADEINRTPPKT- 159
                                    79************************9999751555333333222233333334443332..348999*******9999. PP

                                    TCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS......GGGSTHHHHSTTSSEE CS
                            AAA  76 gseseeeervvnqLlteldgvkkk........eskvivigatnr......pdkldpallrgRfdrk 127
                                              +++Ll+++++ + +         +  ++++at++        +l++a l +Rf  k
  gi|121639606|ref|YP_979830.1| 160 ----------QAALLEAMEERQVSvegepkplPN-PFIVAATQNpieyegTYQLPEAQL-DRFLLK 213
                                    ..........***********9999999999544.466666665344444445566666.666555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.7e-06    0.0038      34     115 ..      81     174 ..      55     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkits.gPvlekagdlaallt.nlee...........kdvlfideihrlsrav 100
                                     hvll G PG+ kt + + +++ l+ ++k    +P l  +gd+++ l+ + ++           +++l+ dei r  +++
  gi|121639606|ref|YP_979830.1|  81 GHVLLEGVPGVAKTLIVRAMSAALQLEFKRVQfTPDL-MPGDVTGSLVyDARTaefvfrpgpvfTNLLLADEINRTPPKT 159
                                    6**************************9876526776.57888875542444311111122222356789********** PP

                         RuvB_N 101 eevlysamedfrldi 115
                                    +  l  ame+ ++ +
  gi|121639606|ref|YP_979830.1| 160 QAALLEAMEERQVSV 174
                                    *********998865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   9.3e-06     0.021       3      46 ..      61     104 ..      60     111 .. 0.92
   2 ?    1.7   0.0     0.065   1.5e+02     109     158 ..     146     193 ..     138     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-06
                   Mg_chelatase   3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsll 46 
                                    k v+Gq+     l ia   + ++ll G pG  Kt++ +++++ l
  gi|121639606|ref|YP_979830.1|  61 KAVVGQDGVISGLVIALLCRGHVLLEGVPGVAKTLIVRAMSAAL 104
                                    5799**********************************998765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.065
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    +L+ DE+     k+  +L e +e+++v+++   +    p  f + a+ Np
  gi|121639606|ref|YP_979830.1| 146 LLLADEINRTPPKTQAALLEAMEERQVSVEGEPKP--LPNPFIVAATQNP 193
                                    6888***********************99765544..3555555555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2245.40
//
Query:       gi|121639607|ref|YP_979831.1|  [L=440]
Description: hypothetical protein BCG_3752 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-18   66.5   3.0    1.9e-18   66.5   0.9    2.2  2  DUF58     Protein of unknown function DUF58
     0.0037   17.5   0.1      0.014   15.6   0.0    2.0  1  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.95   8.5e+03      21      37 ..      90     105 ..      89     126 .. 0.56
   2 !   66.5   0.9   2.2e-22   1.9e-18       1      85 [.     187     280 ..     187     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.95
                          DUF58  21 WkatARtgelyvrefea 37 
                                    W+ +AR +++++++ + 
  gi|121639607|ref|YP_979831.1|  90 WPPSAR-AQPHTHDVDV 105
                                    777777.4444444433 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 2.2e-22
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..........dekletavsaa 70 
                                    g++f++lReYv gD++r+IdW+a+AR+++++vr    er+r+v++vld+ + +  g  g             l+ +++aa
  gi|121639607|ref|YP_979831.1| 187 GTEFDSLREYVVGDDVRSIDWRASARRADVMVRTWRPERDRRVVIVLDTGRMA-AGRVGvdptaadpagWPRLDWSMDAA 265
                                    689**********************************************9986.45555799****999999******** PP

                          DUF58  71 aslarqlldegdrvg 85 
                                    + la+ + ++gd+v 
  gi|121639607|ref|YP_979831.1| 266 LLLAALASRAGDHVD 280
                                    **********99986 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-06     0.014      10      86 ..      62     127 ..      53     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                          DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasga 86 
                                    +r G+ v+  l + N g +   + +v+D +P++ +++++++            +++ag++ ++ +++r+ r++++ a
  gi|121639607|ref|YP_979831.1|  62 ARLGQPVDASLLLCNGGRRRF-RGQVRDAWPPSARAQPHTHD----------VDVAAGQRQQVHTALRPVRRGDQRA 127
                                    677777777777777777777.89******************..........79*****************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3262.53
//
Query:       gi|121639608|ref|YP_979832.1|  [L=330]
Description: hypothetical protein BCG_3753c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-35  121.8   8.0      4e-35  121.2   8.0    1.3  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
      0.053   13.9   0.1      0.053   13.9   0.1    2.0  3  DUF3619   Protein of unknown function (DUF3619)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   8.0   4.4e-39     4e-35       2     156 .]     108     281 ..     107     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 4.4e-39
                         SpoIIM   2 lllflvgillgallaa.............snfaeqis........seskensalslflaifanNlrvalllfllGllllg 60 
                                    +++f+v +l+g+++a                     +        s+++e++a+s++l++++nN +va +++++ + +lg
  gi|121639608|ref|YP_979832.1| 108 VAFFAVVVLIGFWVAGshevqsaigtpteI------DelvshdvqSYYSEHPAASFALQVWVNNSWVATTCIAMSV-VLG 180
                                    789*************88877777544330......1334467779*****************************7.*** PP

                         SpoIIM  61 iptilvllinGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellk 135
                                    +p+ lvl+ n++++G++a+l+++ g++ ++l+l+lPhg+lel+a+++a+a+g+rlg+++     r r++ l+e +r ++ 
  gi|121639608|ref|YP_979832.1| 181 LPIPLVLFDNAANVGLIAGLMFQAGKGDFLLGLLLPHGLLELTAVFLAAAIGMRLGWSVisagnRPRGQVLAEQGRGVVS 260
                                    ****************************************************************99************** PP

                         SpoIIM 136 lllllvpllliAaliEafvtp 156
                                    ++++lv ++l+A+liEa vtp
  gi|121639608|ref|YP_979832.1| 261 VAVGLVGVFLVAGLIEAVVTP 281
                                    ********************8 PP

>> DUF3619  Protein of unknown function (DUF3619)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.9e-06     0.053      10     109 ..      39     140 ..      35     145 .. 0.77
   2 ?   -3.4   0.0       1.3   1.1e+04      68      89 ..     164     186 ..     149     193 .. 0.60
   3 ?   -3.7   0.0       1.6   1.4e+04      78      90 ..     258     270 ..     238     275 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                        DUF3619  10 aaaLdegaadlpediaeRLaaAReqAlarkkpeaaaravaaalalagagaslt..lgeeeagswlrrlalalpllalvvg 87 
                                     ++ +++ + l ++ ++ L   R  +l ++ ++a + a+a+ + +  +  ++   + + ++ +w+ + a+a+ ++++++g
  gi|121639608|ref|YP_979832.1|  39 YQRVSTHLSMLRSASSDQLMTGRLSSLVARARSAVTGAHAPLTRTFIRFWTVSfpVVAYRTWRWWLATAVAFFAVVVLIG 118
                                    56778889999999999******9999988866555555555444444444444433344889999999999999999** PP

                        DUF3619  88 LvgiaywqdqqrvaelaeiDaa 109
                                    +++   ++ q+ + +  eiD  
  gi|121639608|ref|YP_979832.1| 119 FWVAGSHEVQSAIGTPTEIDEL 140
                                    **************99999965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                        DUF3619  68 agswlrrlalalpllalv.vgLv 89 
                                    ++sw+++   a+++++ + + Lv
  gi|121639608|ref|YP_979832.1| 164 NNSWVATTCIAMSVVLGLpIPLV 186
                                    45677666666666665555555 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.6
                        DUF3619  78 alpllalvvgLvg 90 
                                    ++++++ +vg+++
  gi|121639608|ref|YP_979832.1| 258 VVSVAVGLVGVFL 270
                                    4444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2283.65
//
Query:       gi|121639609|ref|YP_979833.1|  [L=310]
Description: hypothetical protein BCG_3754 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   53.1   4.9    5.3e-14   52.6   4.9    1.3  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   4.9     3e-18   5.3e-14       3     134 ..      18     137 ..      16     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3e-18
                            RDD   3 slgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllglk 82 
                                    +l  R ++++iD+++++i ++l  +l +      a ++ ++a + ++l+++ +l++ ++  ++ ++++g ++Gk ++gl+
  gi|121639609|ref|YP_979833.1|  18 QLPVRAVSAVIDITIIFIGYILGLMLWAT-----ALTQFDEALTTAFLIIFTVLALVGYPLVWETATRGRSVGKIVMGLR 92 
                                    556799**********9988876666666.....578888888888888999999999999999999************* PP

                            RDD  83 vvdedgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqa 134
                                    vv++dg +  + qal+Ral  ++ +    +l++  + ++++l    s+k ++
  gi|121639609|ref|YP_979833.1|  93 VVSDDGGPERFRQALFRALASVVEI---WMLLGSPAVICSML----SPKAKR 137
                                    ******************9654443...44444444444444....444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2561.73
//
Query:       gi|121639610|ref|YP_979834.1|  [L=518]
Description: glycerol kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-69  234.4   0.0    1.8e-69  234.0   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom
    6.7e-65  218.5   1.1    3.2e-64  216.3   1.2    1.9  2  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.0     2e-73   1.8e-69       2     245 .]      17     269 ..      16     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 2e-73
                                    EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                    i ++D+Gttst+ +++d++g  va++q+e+e++ p+ gw+e++p eiw+++a+++ +vl++ ++s+k+i+a+gi++qre+
  gi|121639610|ref|YP_979834.1|  17 IAAIDQGTTSTRCMIFDHHGAEVARHQLEHEQILPRAGWVEHNPVEIWERTASVLISVLNATNLSPKDIAALGITNQRET 96 
                                    579***************************************************************************** PP

                                    EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC....EEEEH CS
                         FGGY_N  82 lvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie....kflli 156
                                    + ++++++ +p ynai+w+d+rt  i+  l ++g+ + ++ k gl+  t+f++ kl+W++en+ +v++++e    +f+++
  gi|121639610|ref|YP_979834.1|  97 TLVWNRHTgRPYYNAIVWQDTRTDRIASALDRDGRGNLIRRKAGLPPATYFSGGKLQWILENVDGVRAAAEngdaLFGTP 176
                                    ******************************************************************************** PP

                                    HHHHHHHHCT......--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-T..CCEEEEEECCCCCCTT.S- CS
                         FGGY_N 157 ddyLiwrLtg......qfvtdvtnasesmlfnikklewdeellailgipeelLPklves..seiigelkpelaaklGlke 228
                                    d+++ w Ltg      ++vtdvtnas++ml+++++l+wd+ell ++ ip+++LP++ +s  se +g + +     +G   
  gi|121639610|ref|YP_979834.1| 177 DTWVLWNLTGgprgggVHVTDVTNASRTMLMDLETLDWDDELLSLFSIPRAMLPEIASSapSEPYGVTLA--TGPVG--G 252
                                    ********************************************************99833566776655..55566..5 PP

                                    EEEEEEEEEHHHHHHHH CS
                         FGGY_N 229 gvpvvggggDqqaaalG 245
                                    +vp+ g +gDq aa++G
  gi|121639610|ref|YP_979834.1| 253 EVPITGVLGDQHAAMVG 269
                                    9*************998 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.11     1e+03      39      67 ..     140     168 ..     117     208 .. 0.66
   2 !  216.3   1.2   3.5e-68   3.2e-64       1     197 [.     278     468 ..     278     469 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.11
                         FGGY_C  39 alegsiavagslvawlldnl.glreeirda 67 
                                    +l  ++++ g+ ++w+l+n  g+r +  ++
  gi|121639610|ref|YP_979834.1| 140 GLPPATYFSGGKLQWILENVdGVRAAA-EN 168
                                    5666788899999******75443333.22 PP

  == domain 2  score: 216.3 bits;  conditional E-value: 3.5e-68
                         FGGY_C   1 akvslGTssflll.vgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveeslael 77 
                                    ak+++GT+ flll +g++ v+s +gllt+v    +++kp+yalegsiav+gs+v+wl+d+lg+   i+ a++  e la  
  gi|121639610|ref|YP_979834.1| 278 AKNTYGTGNFLLLnTGETIVRSNNGLLTTVCyqFGNAKPVYALEGSIAVTGSAVQWLRDQLGI---ISGAAQS-EALA-- 351
                                    79***********8888888*********98766669**************************...9888886.8999.. PP

                         FGGY_C  78 aaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdG 157
                                       ++v+d+gg++fvpafsgl+apyw++darg+i+gls+ +t ah+arA+lea+++q r++++a+e+dsg+ l+ l vdG
  gi|121639610|ref|YP_979834.1| 352 ---RQVPDNGGMYFVPAFSGLFAPYWRSDARGAIVGLSRFNTNAHLARATLEAICYQSRDVVDAMEADSGVRLQVLKVDG 428
                                    ...9**************************************************************************** PP

                         FGGY_C 158 GgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                    G + ndl+mq++Ad+lgv+V+rp  ae+talGaA++A++a
  gi|121639610|ref|YP_979834.1| 429 GITGNDLCMQIQADVLGVDVVRPVVAETTALGAAYAAGLA 468
                                    **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 4248.13
//
Query:       gi|121639611|ref|YP_979835.1|  [L=145]
Description: hypothetical protein BCG_3756c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-07   31.1   0.0    4.3e-07   30.5   0.0    1.4  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.4e-11   4.3e-07       4     120 ..       6     135 ..       4     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.4e-11
                                    -HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEEB CS
                            PIN   4 DTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkilpi 73 
                                    D  vl+++  r ++++++a+ l+e+     + +++   v+   l+v++       ++  e a e+ e++  ++ ++ +  
  gi|121639611|ref|YP_979835.1|   6 DVDVLVHAThRASPFHDKAKTLVERFlarpGLVYLLWPVALGYLRVVTHptllgAPLAPEVAVENIEQFTSRPHVRQVGE 85 
                                    56688888888899999999988888778788888888888888888889999977777777777777777777777776 PP

                                    CHHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  74 daeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrva 120
                                      + +  ++++a+  +    l+ Da+++A++++hgi+ i++ D+dfr+ +
  gi|121639611|ref|YP_979835.1|  86 ANGFWPVYRRVADPVKprgNLVPDAHLVALMRHHGIATIWSHDRDFRKFE 135
                                    6666666666666666666****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 980.25
//
Query:       gi|121639612|ref|YP_979836.1|  [L=74]
Description: antitoxin [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.026   14.5   2.2      0.056   13.4   2.2    1.6  1  RHH_1           Ribbon-helix-helix protein, copG family
      0.048   13.6   0.3      0.068   13.1   0.3    1.2  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
       0.13   12.2   0.1       0.24   11.3   0.0    1.5  2  RHH_4           Ribbon-helix-helix domain
        1.9    8.5   7.7       0.19   11.7   2.6    2.1  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.2   1.3e-05     0.056       1      37 [.       2      38 ..       2      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   r++i ld+++l++L ++ r+++++ ++l  e+l+++l
  gi|121639612|ref|YP_979836.1|  2 RTTIDLDDDILRALKRRQREERKTLGQLASELLAQAL 38
                                   89**********************9999999888887 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.5e-05     0.068       3      41 ..       2      40 ..       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                          RHH_5  3 RvnvtLPeelleeLeewAdeegRsvSnlaafLvekalre 41
                                   R+++ L +++l +L++   ee+ ++ +la+ L+ +al +
  gi|121639612|ref|YP_979836.1|  2 RTTIDLDDDILRALKRRQREERKTLGQLASELLAQALAA 40
                                   77788889*****************************87 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-05      0.24      12      43 ..       2      33 ..       1      46 [. 0.90
   2 ?   -2.2   0.0      0.87   3.9e+03      19      26 ..      65      72 ..      64      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                                   EEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH CS
                          RHH_4 12 rTSirLEpafWdaLeeiArregltvnaLiaei 43
                                   rT+i L + + +aL++  r+e  t+ +L +e+
  gi|121639612|ref|YP_979836.1|  2 RTTIDLDDDILRALKRRQREERKTLGQLASEL 33
                                   9****************************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.87
                                   HHHHHHHH CS
                          RHH_4 19 pafWdaLe 26
                                   +a+W++L+
  gi|121639612|ref|YP_979836.1| 65 DAVWAILD 72
                                   679*9998 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.6   4.3e-05      0.19       1      13 [.       1      13 [.       1      26 [. 0.86
   2 ?   -1.9   0.2      0.72   3.2e+03      10      16 ..      32      38 ..      28      40 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                   XXXXXXXXXXXXX CS
                 VapB_antitoxin  1 MrtnIeiDDeLla 13
                                   Mrt+I++DD+ l+
  gi|121639612|ref|YP_979836.1|  1 MRTTIDLDDDILR 13
                                   9*********986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.72
                                   XXXXXXX CS
                 VapB_antitoxin 10 eLlaeAi 16
                                   eLla+A+
  gi|121639612|ref|YP_979836.1| 32 ELLAQAL 38
                                   5677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 553.12
//
Query:       gi|121639613|ref|YP_979837.1|  [L=509]
Description: hypothetical protein BCG_3757 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-05   24.8   0.2     0.0049   16.3   0.3    2.4  2  GCS2      Glutamate-cysteine ligase family 2(GCS2)


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0   0.00032       5.7       3      95 ..      66     156 ..      64     180 .. 0.71
   2 !   16.3   0.3   2.7e-07    0.0049     121     191 ..     204     271 ..     195     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00032
                                    EEEEEEEEETTTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--....SBSSHHHHHHHHHHHHHHHHHHHHHT CS
                           GCS2   3 vEeeflvvdlatgdlrgwseiledeaiiglseggsvvkelpegqvElsta....pleslaeaaeeisadleelrsvadel 78 
                                    +E e  +vd+        +++++++ +++   ++  ++el   ++E+  +    p ++  e+++e++a l+ + + a+  
  gi|121639613|ref|YP_979837.1|  66 IEIECNLVDADY------QPAMSNRYVLDAIADPAYQTELGAYNIEFNVPprplPGRTCLELEDEVRASLNDAETKASCS 139
                                    555555555433......355666666666666678888888888887652222669*********************** PP

                                    T-EEE--SB-SS----- CS
                           GCS2  79 GlellglGthPfalrse 95 
                                    G  ++++G  P   ++ 
  gi|121639613|ref|YP_979837.1| 140 GAHIVMIGILPTLMPEH 156
                                    ***********655544 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.7e-07
                                    --B-EEEEEEE-SSHHHHH.HHHHHHHTTHHHHHHHH--B-EETTEE-S-SB-GGGCCTTSTT-CS----S CS
                           GCS2 121 mmvaglhvqvnidssseedVevlrlvrallPvllAlsAnSPfleGrdtgyaStRariftqtpqagelplaf 191
                                    + + ++  ++ ++   + + + ++ + +l+   lAl AnSP+  G+   ++ tR ++ftq  +a + +l +
  gi|121639613|ref|YP_979837.1| 204 SACTSVQLHLQLAP-ADFP-ANWNAAQVLAGRQLALGANSPYFFGH-QLWSETRIELFTQSTDARPEELKS 271
                                    55666666667766.4555.899***********************.9***********987744444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3859.09
//
Query:       gi|121639614|ref|YP_979838.1|  [L=233]
Description: hypothetical protein BCG_3758 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-15   56.3   0.0    5.8e-15   55.8   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    5.9e-14   52.2   0.0    7.9e-14   51.8   0.0    1.1  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    6.4e-14   52.0   0.0    7.8e-14   51.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.7e-12   47.8   0.0    2.4e-12   47.3   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.7e-11   44.2   0.0    2.2e-11   43.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.6e-08   35.2   0.0    2.3e-08   34.7   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    6.8e-05   22.9   0.0    8.8e-05   22.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00013   21.5   0.1    0.00019   21.0   0.1    1.2  1  MTS              Methyltransferase small domain
     0.0012   18.3   0.3     0.0019   17.6   0.3    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0016   17.9   0.0     0.0018   17.7   0.0    1.1  1  TehB             Tellurite resistance protein TehB
     0.0075   15.6   0.0      0.011   15.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.014   14.4   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.013   14.8   0.0      0.018   14.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.11   11.9   0.0       0.17   11.3   0.0    1.2  1  adh_short        short chain dehydrogenase
       0.14   11.6   0.0       0.19   11.2   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
       0.17   10.9   0.1       0.28   10.3   0.1    1.2  1  ECSIT            Evolutionarily conserved signalling intermed


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   5.2e-18   5.8e-15       1      96 [.      46     144 ..      46     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.2e-18
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS....STTTEEEEEEESTGG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf....edgsfDlvvssgalh 75 
                                    vLd+GcG  +l+lala+ +  ++v+g+D+++++++aa + aee+gl  ++fvq+d++++       +g+f  v+ s  +h
  gi|121639614|ref|YP_979838.1|  46 VLDAGCGYAELSLALAADG--YTVVGIDLTPTAVAAATKAAEERGLtTASFVQADITEFAAypagSAGRFSTVIDSTLFH 123
                                    9*****************5..***********************************997633335788*******87799 PP

                                    GSSHHHHHHHHHHHHHHEEEE CS
                Methyltransf_25  76 hlsdedlekalkeiarvLkpg 96 
                                     l+ + ++++l+ ++r+  pg
  gi|121639614|ref|YP_979838.1| 124 SLPVDSRDRYLSSVHRAAAPG 144
                                    9****************9997 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   7.1e-17   7.9e-14      15     188 ..      22     186 ..       5     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.1e-17
                                    -TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--. CS
                           TPMT  15 ipfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkey 94 
                                     p++ +e +p l  ++ a   k    vl  +CG a+   +lA+ g++vvG++l + Av+++ ++a +e  +++ s+v+  
  gi|121639614|ref|YP_979838.1|  22 PPWNIGEPQPELATLIAA--GKVRSDVLDAGCGYAELSLALAADGYTVVGIDLTPTAVAAA-TKAAEERGLTTASFVQA- 97 
                                    589999999999999999..455556*********************************95.55666677888888888. PP

                                    ..........-TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEEEE-.-.-S----SS----H CS
                           TPMT  95 sageiellcgdvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdgeglLvtldy.p.qaeheGPPfsvpe 172
                                       +i    +++ +++a + g+f ++ d   +  lp + r+ry +s+++   p+++++ ++    + +ae e  P +v+e
  gi|121639614|ref|YP_979838.1|  98 ---DI----TEFAAYPAGSAGRFSTVIDSTLFHSLPVDSRDRYLSSVHRAAAPGASYYVLVFAKgAfPAELEVKPNEVDE 170
                                    ...44....47888999**************************************96655555413379999******** PP

                                    HHHHHHHGGTEEEEEE CS
                           TPMT 173 aeleallsagfkvael 188
                                    +el+a +s+ +k+ e+
  gi|121639614|ref|YP_979838.1| 171 DELRAAVSKYWKIDEI 186
                                    ************9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0     7e-17   7.8e-14       6     110 ..      45     150 ..      41     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 7e-17
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekfDlilsne 82 
                                     vlD+GCG  el+++la    ++ +vvGiD +++a+  A++ a++ gl+ ++F q+di+e+   +      +f  +++  
  gi|121639614|ref|YP_979838.1|  45 DVLDAGCGYAELSLALA---ADGYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITEFAA-YPAgsaGRFSTVIDST 120
                                    69***************...45678***********************************663.44466899***99977 PP

                Methyltransf_31  83 vl..naladpdkileeiervlkpggillie 110
                                    ++    + + d +l +++r+  pg  + + 
  gi|121639614|ref|YP_979838.1| 121 LFhsLPVDSRDRYLSSVHRAAAPGASYYVL 150
                                    777667778899999999999998766665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   2.1e-15   2.4e-12       1      94 [.      47     147 ..      47     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.1e-15
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT...-EEEEEEES-CCC-. CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaekl.pfedn...sfDlvvssevlhhv. 74 
                                    Ld+GcG   l+ ala  g++vvg+Dl+++++++a ++a+e+gl + +fv+ad++++  ++ +    f  v+ s  +h + 
  gi|121639614|ref|YP_979838.1|  47 LDAGCGYAELSLALAADGYTVVGIDLTPTAVAAATKAAEERGLtTASFVQADITEFaAYPAGsagRFSTVIDSTLFHSLp 126
                                    8*******************************************999*******97567765334899***********9 PP

                                    .CCHHHHHHHHHHHEEEEEEE CS
                Methyltransf_11  75 .edpekalkeiaRvLkpgGll 94 
                                     + ++++l+ ++R   pg   
  gi|121639614|ref|YP_979838.1| 127 vDSRDRYLSSVHRAAAPGASY 147
                                    99***************9765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0     2e-14   2.2e-11      10     123 ..      30     155 ..      24     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2e-14
                Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae.. 78 
                                    + +l+ l +  + ++ vLd GcG+ +l+  l++ g++v+g+Dl p av+ a          +a++ q d +  ++aa+  
  gi|121639614|ref|YP_979838.1|  30 QPELATLIAAGKVRSDVLDAGCGYAELSLALAADGYTVVGIDLTPTAVAAATkaaeergltTASFVQADIT--EFAAYpa 107
                                    56777788889999***********************************9999998885553333333333..3444444 PP

                Methyltransf_23  79 .pqgkfdlIvlrevlehvp..dppellrqiatllkpgGylllseplas 123
                                     ++g+f +++ + +++++p  +  ++l+++++  +pg+  +++++++ 
  gi|121639614|ref|YP_979838.1| 108 gSAGRFSTVIDSTLFHSLPvdSRDRYLSSVHRAAAPGASYYVLVFAKG 155
                                    4666***************85588*************98888888654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0     2e-11   2.3e-08       1      97 [.      47     145 ..      47     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2e-11
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnvlhh 78 
                                    L+ GcG ++l+ al+++  + +++g+D+ p a+++a +   +r+   +++v+ + ++ +  + g  + f +v+ s ++h 
  gi|121639614|ref|YP_979838.1|  47 LDAGCGYAELSLALAAD--GYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITEFAAYPAGsaGRFSTVIDSTLFHS 124
                                    89***************..**************77777777777777777777777776666669*************** PP

                Methyltransf_12  79 l..kdirevldnirklLkpgG 97 
                                    l  + ++++l++++++ +pg+
  gi|121639614|ref|YP_979838.1| 125 LpvDSRDRYLSSVHRAAAPGA 145
                                    **99999************97 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.9e-08   8.8e-05      24      92 ..      41     102 ..      32     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.9e-08
                Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                                    + + +v+D+G+G + Ls +la    + ++ vvgid+    v++a k ae+ g  + +  sf +++i+e 
  gi|121639614|ref|YP_979838.1|  41 KVRSDVLDAGCGYAELSLALAA---D-GYTVVGIDLTPTAVAAATKAAEERG--L-TTASFVQADITEF 102
                                    55678*****************...5.9************************..6.7788888887765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.7e-07   0.00019      31      91 ..      42     101 ..      33     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle 91 
                                     + +vlD GcG+  l++ala+     +v+ +d    A+++a++ +e+ +l  +++v+ d++e
  gi|121639614|ref|YP_979838.1|  42 VRSDVLDAGCGYAELSLALAADGY--TVVGIDLTPTAVAAATKAAEERGLTtASFVQADITE 101
                                    5668***************99655..59**********************999999999986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   1.7e-06    0.0019     160     211 ..      41      91 ..      32     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                           PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea 211
                                    k ++ vlD G+G + L++a a  g  +vv++D+ + Av +a + ae  ++++
  gi|121639614|ref|YP_979838.1|  41 KVRSDVLDAGCGYAELSLALAADG-YTVVGIDLTPTAVAAATKAAEERGLTT 91 
                                    45579*************988766.689*************99888766555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.6e-06    0.0018      32      89 ..      44     101 ..      32     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-06
                                    -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG CS
                           TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydine 89 
                                    + vld gcg    sl l++ gy v  +d   +++a   + +e   l++ s    di e
  gi|121639614|ref|YP_979838.1|  44 SDVLDAGCGYAELSLALAADGYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITE 101
                                    469***********************************99999999976666666655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.011      43     157 ..      38     155 ..      32     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-....T-EE CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed....dsfD 118
                                     a+k  ++vlD  +G ++l+++l+    + ++vv++D+ ++ +  + k ++e+g +   f+qa+  e+        + f 
  gi|121639614|ref|YP_979838.1|  38 AAGKVRSDVLDAGCGYAELSLALAA---DGYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITEFAAYPagsaGRFS 114
                                    56677789***********999864...6789*******************************98877543221124444 PP

                                    EEEEE..S-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
                Ubie_methyltran 119 vvtvs..fGlrnvtDklkaLkeayrvlkpGGrlvvlefskv 157
                                    +v  s  f    v  +++ L +++r   pG   +vl f+k 
  gi|121639614|ref|YP_979838.1| 115 TVIDStlFHSLPVDSRDRYLSSVHRAAAPGASYYVLVFAKG 155
                                    44333224444566788889999999999999999988875 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.014     199     262 ..      40     103 ..       5     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                tRNA_U5-meth_tr 199 qeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeelt 262
                                     + ++d+l+  cG+ ++slala     v+  +++ ++v+aa +  ++  ++  ++++    e++
  gi|121639614|ref|YP_979838.1|  40 GKVRSDVLDAGCGYAELSLALAADGYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITEFA 103
                                    45667***************************************99999999998888777775 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.018      65     158 ..      45     143 ..      37     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                    EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-..EEEEES-GGG---....--SEEEEES-GG CS
                           CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk..vevklldyedlde....kvdrvvsvgafe 138
                                     +Ld GcG+ +l    ++  +  vvg+ l     + a k+ +e++l+    v+ +++++   +     ++  v+   +f 
  gi|121639614|ref|YP_979838.1|  45 DVLDAGCGYAELSLALAAD-GYTVVGIDLTPTAVAAATKAAEERGLTTAsfVQADITEFAAYPAgsagRFSTVIDSTLFH 123
                                    69***********999999.99*********************9987651256667777777657777999999999999 PP

                                    GTSGGGHHHHHHHHHHHS-T CS
                           CMAS 139 hvgkenydtffkklkkllke 158
                                     + +++ d++ + ++++  +
  gi|121639614|ref|YP_979838.1| 124 SLPVDSRDRYLSSVHRAAAP 143
                                    99999999999998887655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.17      15      63 ..      55     104 ..      48     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                    HHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHH CS
                      adh_short  15 aiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdree 63 
                                    +++ +la++G++vv +d ++ +++++ k  +e   ++a ++q+D+t+ ++
  gi|121639614|ref|YP_979838.1|  55 ELSLALAADGYTVVGIDLTPTAVAAATKAAEERgLTTASFVQADITEFAA 104
                                    68899******************99999999998889*********8776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.19       4      62 ..      45     101 ..      42     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62 
                                     vl+ GcG+ e+ +alA +    +++Gi++  + va++ k++e+++l+    ++ d ++
  gi|121639614|ref|YP_979838.1|  45 DVLDAGCGYAELSLALAAD--GYTVVGIDLTPTAVAAATKAAEERGLTTASFVQADITE 101
                                    689********99999887..5889********************99988888888765 PP

>> ECSIT  Evolutionarily conserved signalling intermediate in Toll pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.28     151     184 ..     176     209 ..     172     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                          ECSIT 151 plrkyvrlmyWlpkfknlnPfpvPkdlpedpvdl 184
                                    ++ ky+++    p f ++nP ++P +l   pv++
  gi|121639614|ref|YP_979838.1| 176 AVSKYWKIDEIRPAFIHVNPVTIPPQLAGAPVEF 209
                                    789************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1680.41
//
Query:       gi|121639615|ref|YP_979839.1|  [L=390]
Description: hypothetical protein BCG_3759c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-32  113.0   0.0    1.9e-32  112.6   0.0    1.1  1  Aminotran_5  Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.0   1.1e-36   1.9e-32       3     371 .]      30     375 ..      28     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.1e-36
                                    EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCC CS
                    Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsla 82 
                                    ldsaA ++   ++lda++++  ++ a v  + + +++ a++ +++ r+ va+l + ++  e++ft G+ +a+ l + s+ 
  gi|121639615|ref|YP_979839.1|  30 LDSAACSRQSFAALDAAAQH-ARHEAEV--GGYVAAEAAAAVLDAGRAAVAALSGLPD-AEVVFTTGSLHALDLLLGSW- 104
                                    9*****************99.7899999..9999***********************7.********************. PP

                                    CC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHH CS
                    Aminotran_5  83 rslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveei 161
                                        + ++      e+  nl  ++++a  +g++v+ +p  ++g++ ld+++  l+ + ++lv++t v +  G+ qp++ +
  gi|121639615|ref|YP_979839.1| 105 --PGENRTLACLPGEYGPNL--AVMAA--HGFDVRPLPTLQDGRVALDDAAFMLAdDPPDLVHLTVVASHRGVAQPLAMV 178
                                    ..99****************..66665..9********************999974778********************* PP

                                    HHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEE CS
                    Aminotran_5 162 gklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eet 239
                                    ++l+ + +  ++vDaaq++gh       +g+D+ ++s+ K + gP G+Gvl vr+el e+l+  l+  + +   ++ ++ 
  gi|121639615|ref|YP_979839.1| 179 AQLCTELKLPLVVDAAQGLGHVDCA---VGADVTYASSRKwIAGPRGVGVLAVRPELMERLRARLPAPDWMPPLTVaQQL 255
                                    *********************9875...69*******************************9999999966666665555 PP

                                    EEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTC CS
                    Aminotran_5 240 tfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgv 319
                                    +          G  nva+ +g++ al    + g +ai+++ +el + ++  l+++ g r+++ +++e +a ++  +++g 
  gi|121639615|ref|YP_979839.1| 256 G---------FGEANVAARVGFSVALGEHLACGPQAIRARLAELGDIARTVLADVSGWRVVE-AVDEPSAITTLAPIDGA 325
                                    5.........3678************8888******************************77.67777777777789*** PP

                                    SHHHHHHHHHHT.TEEEEE.E-TTTHHHHHHTT.S.-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 320 haedvatlLdee.gIavrs.Ghhcaqplmkrlale.gtvRaSlyiynteeevdrl 371
                                    +++ v+  L ++  I  +  G + a      l+l+  ++R+S ++ nt++++d++
  gi|121639615|ref|YP_979839.1| 326 DPAAVRAWLLSQrRIVTTYaGVERA-----PLELPaPVLRISPHVDNTADDLDAF 375
                                    *****987766646665546***99.....66676689**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 3287.95
//
Query:       gi|121639616|ref|YP_979840.1|  [L=321]
Description: hypothetical protein BCG_3760c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.4e-114  380.0   0.0   8.4e-114  379.9   0.0    1.0  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
  ------ inclusion threshold ------
      0.072   13.8   0.0       0.76   10.5   0.0    2.4  2  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.9   0.0  9.4e-118  8.4e-114       1     308 [.      18     320 ..      18     321 .] 0.98

  Alignments for each domain:
  == domain 1  score: 379.9 bits;  conditional E-value: 9.4e-118
                Methyltransf_33   1 laedvlagLsskpktlpskllYDarGselFeeitelpeYyptrtEiaiLqehaaeiaaaipaatlvelGsGsseKtrlLL 80 
                                    l++dv +gL+++pk+lp+k++YD+ GselF++it+lpeYyptr+E++iL++++ae+a+a++a+tlvelGsG+seKtr+LL
  gi|121639616|ref|YP_979840.1|  18 LRRDVYSGLQKTPKSLPPKWFYDTVGSELFDQITRLPEYYPTRAEAEILRARSAEVASACRADTLVELGSGTSEKTRMLL 97 
                                    5789**************************************************************************** PP

                Methyltransf_33  81 ealeaaekeltYvplDvseeaLeealealaaeypsleveglvgdyedglewlaslpeaederrlvlflGssigNlepeea 160
                                    +al+++++ +++vp+Dv++++L+++++a+++ey+++e+++++gd+e++   l+++p+   +rrl++flGs+igNl+p  +
  gi|121639616|ref|YP_979840.1|  98 DALRHRGSLRRFVPFDVDASVLSATATAIQREYSGVEINAVCGDFEEH---LTEIPR--GGRRLFVFLGSTIGNLTPGPR 172
                                    ****9******************************************8...888985..89******************* PP

                Methyltransf_33 161 aafLrklraalgpgdllLlGvDlvkdeekleaAYndsagvtaaFnlnllerinrelgadfdledfehvaewnaeegriem 240
                                    a+fL++l+  ++pgd lLlG+Dlvkd ++l++AY+d+ gvta+Fn+n+l++inrel+adfd ++f+hva+wn++e+riem
  gi|121639616|ref|YP_979840.1| 173 AQFLTALAGVMRPGDSLLLGTDLVKDAARLVRAYDDPGGVTAQFNRNVLAVINRELEADFDVDAFQHVARWNSAEERIEM 252
                                    ******************************************************************************** PP

                Methyltransf_33 241 ylrskrdqtvrvealdltvafkagekirteiSyKyteeevrelleaaglevlkvWtdeksdfalyllq 308
                                    +lr+  +q+vrv+aldltv+f+age++ te S+K+++++v ++l+aagl+  ++Wtde +df+l l+ 
  gi|121639616|ref|YP_979840.1| 253 WLRADGRQRVRVGALDLTVDFDAGEEMLTEVSCKFRPQAVGAELAAAGLHRIRWWTDEAGDFGLSLAA 320
                                    ****************************************************************9975 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.4e-05      0.76       2      91 ..      84     186 ..      83     191 .. 0.77
   2 ?    1.3   0.0     0.061   5.5e+02      62      93 ..     228     259 ..     170     262 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
                                    EET-TTSHHHHHHH....HTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.T.SS-T.T-EEEEEEES- CS
                Methyltransf_11   2 dvGcGtGrlaeala....krg..arvvgvDlskemlklakekaseegl..kvefvvadaek.l.pfed.nsfDlvvssev 70 
                                    ++G+Gt   ++ l     +rg  +r v +D+++ +l +  +++++e+   +++ v++d+e+ l  ++  +   +v++ ++
  gi|121639616|ref|YP_979840.1|  84 ELGSGTSEKTRMLLdalrHRGslRRFVPFDVDASVLSATATAIQREYSgvEINAVCGDFEEhLtEIPRgGRRLFVFLGST 163
                                    79999999999999766555599*************999999999999888999*****975445666346667777777 PP

                                    CCC-..CCHHHHHHHHHHHEEEE CS
                Methyltransf_11  71 lhhv..edpekalkeiaRvLkpg 91 
                                    + ++    ++++l  +a v++pg
  gi|121639616|ref|YP_979840.1| 164 IGNLtpGPRAQFLTALAGVMRPG 186
                                    77776546777777777777777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.061
                                    EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEE CS
                Methyltransf_11  62 fDlvvssevlhhvedpekalkeiaRvLkpgGl 93 
                                      + +   +++hv+++++a + i  +L+ +G+
  gi|121639616|ref|YP_979840.1| 228 LEADFDVDAFQHVARWNSAEERIEMWLRADGR 259
                                    44445557888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2388.99
//
Query:       gi|121639617|ref|YP_979841.1|  [L=233]
Description: hypothetical protein BCG_3761c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-14   52.4   0.1    8.1e-14   52.0   0.1    1.2  1  GATase_6  Glutamine amidotransferase domain
    1.3e-10   40.6   0.0    4.5e-09   35.6   0.0    2.5  3  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1     9e-18   8.1e-14       2     134 .]      69     197 ..      68     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 9e-18
                       GATase_6   2 dasglaslvedevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllal 80 
                                    ++ ++a + +++++la+vR+a+vg++ e +a  Pf  +dg++ll+hNG ++ +      lpa  g a +s +D+++l+a 
  gi|121639617|ref|YP_979841.1|  69 SFHSVAPALRSHCILAAVRSATVGMPIEVSAtPPF--TDGHWLLAHNGVVDRAV-----LPA--GPAAESVCDSAILAAT 139
                                    5677888999*********************9999..****************8.....998..88889**********8 PP

                       GATase_6  81 leelG....eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafase 134
                                    +  +G     +++ ++  + + a  +  ++n+  l++ ++g ++l++    +g++ ase
  gi|121639617|ref|YP_979841.1| 140 IFAHGldalGDTIVKVGAADPNARLNIlAANGSRLIATTWG-DTLSILRRADGVVLASE 197
                                    86666445555556888899999999999999999999***.99999999*******98 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0     5e-13   4.5e-09      21     113 ..      29     118 ..      16     133 .. 0.82
   2 ?   -0.1   0.0     0.039   3.5e+02     171     196 ..     163     188 ..     137     195 .. 0.77
   3 ?    1.6   0.0     0.012     1e+02     222     253 ..     190     221 ..     185     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 5e-13
                       GATase_4  21 gfaarggltd.ahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGe.vklenthpFvRel 98 
                                    ++a r+++ +   adGwG++f++g   r    p+p    +  + v    ++s+ ++a +R at G  ++ + t pF+   
  gi|121639617|ref|YP_979841.1|  29 SYAPRRQKHGlMNADGWGVGFFDGAIPRRWRSPAPLWGDTSFHSVAP-ALRSHCILAAVRSATVGMpIEVSATPPFT--- 104
                                    56665554432789*********************987766666654.5****************746778899986... PP

                       GATase_4  99 wgrewifAHnGdlke 113
                                     + +w++AHnG +++
  gi|121639617|ref|YP_979841.1| 105 -DGHWLLAHNGVVDR 118
                                    .789*******9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.039
                       GATase_4 171 vfnlllsdgralfahastrLvyilRk 196
                                     +n+l ++g  l+a +  +   ilR+
  gi|121639617|ref|YP_979841.1| 163 RLNILAANGSRLIATTWGDTLSILRR 188
                                    6899********99988665555565 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.012
                       GATase_4 222 rvavvatepLtrdetWkklepGellvfrdGal 253
                                      +v+a+ep  +d  W +++  +l+ +++  +
  gi|121639617|ref|YP_979841.1| 190 DGVVLASEPYDDDSGWGDVPDRHLVEVTQKGV 221
                                    5789****************999986554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1749.31
//
Query:       gi|121639618|ref|YP_979842.1|  [L=425]
Description: hypothetical protein BCG_3762c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-63  214.6   5.6    2.2e-63  214.3   5.6    1.1  1  FGE-sulfatase  Sulfatase-modifying factor enzyme 1
    3.5e-17   63.1   4.1    3.5e-17   63.1   4.1    2.3  2  DinB_2         DinB superfamily


Domain annotation for each model (and alignments):
>> FGE-sulfatase  Sulfatase-modifying factor enzyme 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   5.6   2.5e-67   2.2e-63       4     259 ..     166     422 ..     163     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 2.5e-67
                                    TEEEE-SEEEEES-...TSTTGGCCC-S-EEEEES-EEEESS--BHHHHHHHHHHH....H................SSE CS
                  FGE-sulfatase   4 emvlipgGsfemGs...eektandeeapahevtvraFaidkteVTnaqyaafveatgyete................aas 64 
                                    + vl++gG+f +G    +e+++ d+e+pah v+v+aF+i++++VTn+++++f+++ gy+++                +a+
  gi|121639618|ref|YP_979842.1| 166 TSVLVAGGPFVLGVdaaDEPCSLDNERPAHVVDVPAFRIGRVPVTNGEWQDFIDDGGYTQSrwwsergwqhrqraglTAP 245
                                    689*********************************************************9***************9999 PP

                                    TTEEEEETSCTTBCCTTC-SSTT-TTSB--S--HHHHHHHHHHHCHHHTS-EE---HHHHHHHHHTT-...SSSSCTTBS CS
                  FGE-sulfatase  65 qwwaeveganvrhpegrksdikkradhPvvhVsweDavaYArwlgkktgegyrLPteaEweyAArggk...kgreypwgd 141
                                    q+w++  ++++r  +     ++ +ad+Pv+hVs+++a+aYA+w+g       rLPte+Ewe+A+ ++    ++r+ypwg 
  gi|121639618|ref|YP_979842.1| 246 QFWRSGGRTRTRFGHV----EDIPADEPVQHVSYFEAEAYAAWAGA------RLPTEVEWEKACAWDPatgSRRRYPWGT 315
                                    ****999999998886....899***********************......**************9999999******* PP

                                    TTSCCGB...SSTTTTB--TTCGGS-SS.---TT-S-B..-TTS-B-TTCSSEEEEEEE--...THCCH-SSCS----SS CS
                  FGE-sulfatase 142 elkpakniwqGslakfekeaaaadsqngrtspvgsfpp..nalGlyDmaGNvwEWtsdwyk...kyalapaeelsqeaek 216
                                    e+              ++++a+ ++q+ r++pvg++p+  +a+G  +m+G+vwEWt++ ++   ++ ++ +e++sq++++
  gi|121639618|ref|YP_979842.1| 316 EEP-------------TDTYANLGGQTLRPAPVGAYPAgaSACGAEQMLGDVWEWTTSPLRpwpGFVPMVYERYSQPFFG 382
                                    *55.............78899999**************99**********************999*************** PP

                                    -SSEEEEC--TTS.TTGGCTSTT-E.EEE-TT--BTTEEE--E CS
                  FGE-sulfatase 217 gelrvvkGgswlkaelssllraafrasaetpdtaasdvGfRlv 259
                                    g++rv++Ggsw+ +  +  lr++fr ++++p +++++ G+Rl+
  gi|121639618|ref|YP_979842.1| 383 GDYRVLRGGSWAVE--PAILRPSFR-NWDHPYRRQIFAGVRLA 422
                                    *************8..8********.****************8 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   4.1   3.9e-21   3.5e-17       2     128 .]      11     137 ..      10     137 .. 0.85
   2 ?   -2.9   0.0         1   9.2e+03      37      57 ..     271     301 ..     247     330 .. 0.64

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 3.9e-21
                         DinB_2   2 lerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlrgeeap.................rpgldplt 64 
                                    l+rarar+l l+ d++++el  q++p++++++w+laH+g +eel+l+r  ++ +p                 r+++ +l+
  gi|121639618|ref|YP_979842.1|  11 LARARARTLRLV-DFDDAELCCQYDPLMSPLVWDLAHIGQQEELWLLRGGDPGQPgllppaveglydafehsRASRVELP 89 
                                    89**********.*************************************666666664455555555544455555555 PP

                         DinB_2  65 ppsaaealaylaevrarllallealtdadldrpltaphpglgkltlgdvllfvlqHeqhHleqi 128
                                     +s+a a+ y a vr ++l+ l+al++ d d                +v+++v+ He++H+e++
  gi|121639618|ref|YP_979842.1|  90 LLSPARARSYCATVRSAALDALAALPE-DGD---------------SFVFAMVISHENQHDETM 137
                                    5*************************9.344...............69**************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                         DinB_2  37 aHlgnveelllerlrgeeap..........r 57 
                                    +H+  +e  + +++ g++ p          +
  gi|121639618|ref|YP_979842.1| 271 QHVSYFEAEAYAAWAGARLPtevewekacaW 301
                                    5666666666666666555544444333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3313.11
//
Query:       gi|121639619|ref|YP_979843.1|  [L=432]
Description: glutamate--cysteine ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-96  321.5   0.2      6e-96  321.2   0.2    1.1  1  GCS2      Glutamate-cysteine ligase family 2(GCS2)


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.2   0.2  3.3e-100     6e-96       1     290 [.      46     354 ..      46     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 321.2 bits;  conditional E-value: 3.3e-100
                                    EEEEEEEEEEETTTTEE-.S-HHHHHCCCTTT-S...SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHH CS
                           GCS2   1 lgvEeeflvvdlatgdlr.gwseiledeaiigls..eggsvvkelpegqvElstapleslaeaaeeisadleelrsvade 77 
                                    +g+E+e++++d+a++++r +w+ei+e  ++++ls  +ggsvv+++p+g+vEls++p++++ +a++++++d+++lrs++++
  gi|121639619|ref|YP_979843.1|  46 VGLEMEAHCFDPADPFRRpSWEEITE--VLEWLSplPGGSVVSVEPGGAVELSGPPADGVLAAIGAMTRDQAVLRSALAN 123
                                    79************************..99***999******************************************** PP

                                    TT-EEE--SB-SS---------------THHHHHGG....G.G-S--B-EEEEEEE-SSHHHHH..HHHHHHHTTHHHHH CS
                           GCS2  78 lGlellglGthPfalrsedevtpkaryrrmleymdr..vGvlgrqmmvaglhvqvnidssseed.VevlrlvrallPvll 154
                                    +Gl+l++lG++P  lrs+++v+p aryr+m++++++  +Gv+g++mm++++++qvn+d++++e+ +e++rl++al+P+++
  gi|121639619|ref|YP_979843.1| 124 AGLGLVFLGADP--LRSPVRVNPGARYRAMEQFFAAshSGVPGAAMMTSTAAIQVNLDAGPQEGwAERVRLAHALGPTMI 201
                                    ************..**********************99****************************************** PP

                                    HHH--B-EETTEE-S-SB-GGGCCTTSTT..-CS----SSHHH.HHHHHHHHTTSTT-SSGG...............G-- CS
                           GCS2 155 AlsAnSPfleGrdtgyaStRariftqtpq..agelplafedgaaferyaryaldvpvidvrr..............frlw 218
                                    A++AnSP+l+Gr++g++StR+r+++q+++  +g++  a+ d++ + ++a+yal++pv++vr+              f++w
  gi|121639619|ref|YP_979843.1| 202 AIAANSPMLGGRFSGWQSTRQRVWGQMDSarCGPILGASGDHP-GIDWAKYALKAPVMMVRSpdtqdtravtdyvpFTDW 280
                                    *****************************************97.7*********************************** PP

                                    BSEEEETTTT....EEEEEEEE--...SSHHHHHHHHHHHHHHHHHHHHH------GGGGTT..HHHHHHHHHHHG CS
                           GCS2 219 ldirpsslpg...ttlelrihdttlfPevrlrallearlldaqpadrldalpaavlvalldd.eaeenawdavrsg 290
                                    +d+r+  l+g   t+++l++h+ttlfP+vr+r++le+r+ld+ p d+++++++++lv+lldd +a+++a+dav+++
  gi|121639619|ref|YP_979843.1| 281 VDGRVL-LDGrraTVADLVYHLTTLFPPVRPRQWLEIRYLDSVP-DEVWPAVVFTLVTLLDDpVAADLAVDAVEPV 354
                                    ******.888889*******************************.9***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3223.00
//
Query:       gi|121639620|ref|YP_979844.1|  [L=214]
Description: hypothetical protein BCG_3764c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-38  132.7   6.1    1.6e-38  132.5   6.1    1.0  1  PknH_C    PknH-like extracellular domain


Domain annotation for each model (and alignments):
>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   6.1   8.9e-43   1.6e-38       3     187 ..      30     210 ..      28     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 8.9e-43
                                    GGGGGGGS--HHHHHHHHT-S.--EE-S-B-S-B-S--EESSGGGHHHH-SSBHHHHTTS---EEEEEEEE-SSTT-SEE CS
                         PknH_C   3 aaaldslLltpaelaailGtpeaasatesdttppdtaasvdppeClgvasageesvYggsgvtavagqtlrdsaddgasl 82 
                                    ++ ++ ++l + ++ +i+G+p     +e+  t+p++a+ v+ p+C+++++ g ++vY+++++++++g+t ++sa+d+++l
  gi|121639620|ref|YP_979844.1|  30 PGVVSYAVLGKGSVGNIVGAP---MGWEAVFTRPFQAFWVELPACNNWVDIGLPEVYDDPDLASFNGATTQTSATDQTHL 106
                                    6778999**************...9******************************************************* PP

                                    EEEEEEE-SSHHHHHHHHHHHHHHHHTTTT.-EEEEEETTEEEEEEE---B--..TT-EEEEEE.ESSTT--EEEEEEEE CS
                         PknH_C  83 vsqavvafptadaAqaffaalaaqwrrCag.vttttdsggatetwtvgdvsdd..dgvltatvtvtsggdgarcqralav 159
                                    v+qav +f++ daA+++f+++++++ +C+g +t+ + ++g+t+ w + + +++  d+++t     +++g+++rc+ + ++
  gi|121639620|ref|YP_979844.1| 107 VKQAVGVFASNDAADRAFHRVVDRTVGCSGqTTAIHLDDGTTQVWSFAGGPSTgtDEAWTK----QEAGTDRRCFVQTRL 182
                                    ***********************************************99999988888888....999************ PP

                                    ETTEEEEEEEEE.SS-SSHHHHHHHHHH CS
                         PknH_C 160 ranvvvdvevcgfedggdaaaeiadail 187
                                    r+nv+++++vc+ +++g+a++++a a+ 
  gi|121639620|ref|YP_979844.1| 183 RENVLLQAKVCQSGNAGPAVNVLAGAMQ 210
                                    **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1540.32
//
Query:       gi|121639621|ref|YP_979845.1|  [L=129]
Description: hypothetical protein BCG_3765c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 912.63
//
Query:       gi|121639622|ref|YP_979846.1|  [L=106]
Description: hypothetical protein BCG_3766c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 815.94
//
Query:       gi|121639623|ref|YP_979847.1|  [L=336]
Description: hypothetical protein BCG_3767c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-47  161.5   0.1    3.1e-47  161.3   0.1    1.0  1  DUF4185   Domain of unknown function (DUF4185)


Domain annotation for each model (and alignments):
>> DUF4185  Domain of unknown function (DUF4185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   0.1   1.7e-51   3.1e-47       7     312 ..      14     325 ..       8     326 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 1.7e-51
                        DUF4185   7 dsrfgvsgTDLGimwdngkgrvlivfGDtfgekavgsgkgdWrsnvllrssdrdls..dgltfdgavgdaggkakqlips 84 
                                    + ++g+++TDL+ +++  ++++l v+GD+f ++ vg g  +W  +v l+ ++++++   g++++g++g        l++ 
  gi|121639623|ref|YP_979847.1|  14 TGDYGIGATDLCEFVEF-PSQLLQVCGDSFAGQGVGFG--GWYAPVALHVDTESIDdpAGVRYTGVTG----VGTPLLAD 86 
                                    679*************9.79***********9999998..9**************9556899999997....44555555 PP

                        DUF4185  85 eklkgvevtviPtagisvggtqylsymsvrswgapgewttnysaiaksdDngetWekvpesvrtnsdtagnenfqqvafv 164
                                     + ++   + +P+ ++++++++yl ++++++++++       s++++++     W++v +s+r ++++ g +  q + ++
  gi|121639623|ref|YP_979847.1|  87 PT-PP-GDSQLPAGVVQINRRNYLMVTTTKDLQPQN------SRLVRAEAARGGWQTVSGSRRNAAYQDGRQT-QISGYY 157
                                    43.33.3379**********************9999......9******************999999767655.999999 PP

                        DUF4185 165 k.......ddgyvYvfgtpngRsgaayLarvpeadildlsayeywkgggea.WvkaeeaaatpvlagpvgElSvqynekl 236
                                              g+vY+++  + R+++a L+r  +++++d+s+++ w gg +  W+k     +tp+++++ gE+S++ +  +
  gi|121639623|ref|YP_979847.1| 158 DpvptpdsPTGWVYIVADSFTRGEPAVLYRATPESFTDRSRWQGWAGGPDGgWNKP----PTPLWPDQLGEMSIRQI--D 231
                                    66777777999**********************************8777778***9....*****************..9 PP

                        DUF4185 237 gkwvllyldeeknsivlrtadspegpwsepktl.................vssaqvpglYgpyihPwstlksktgkdlyf 299
                                    g+ vl+y++++++++++r+a++p++   +p t+                   ++++++ Yg+yi P+st+++     l +
  gi|121639623|ref|YP_979847.1| 232 GQTVLSYFNASTGNMEVRVAHHPTSLGAAPVTTvvrhdewpepaeslpppY-DNRLAQPYGGYISPGSTIDE-----LRI 305
                                    ******************************999889888888887777742.37*************88888.....*** PP

                        DUF4185 300 llSqWnt.......Ynvmlm 312
                                    ++SqW+t       Y+v+++
  gi|121639623|ref|YP_979847.1| 306 FVSQWDTrarqngpYRVIQF 325
                                    *****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2496.71
//
Query:       gi|121639624|ref|YP_979848.1|  [L=345]
Description: aspartate-semialdehyde dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-46  156.2   0.0    1.4e-45  155.7   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    2.8e-29  102.0   0.0    7.3e-29  100.7   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0   1.5e-49   1.4e-45       1     184 []     139     328 ..     139     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 1.5e-49
                                    HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHH...........HHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTT CS
                Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkq...........vaelqrsdeakpgvfgvpiagNlipyidkeedk 69 
                                    Lk L+d+ ++l r++v++yqavSG+G +gv+eL++q           v +  + + ++p+++ +pia+N++p++++ +d+
  gi|121639624|ref|YP_979848.1| 139 LKVLHDE-ARLVRLVVSSYQAVSGSGLAGVAELAEQaraviggaeqlVYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDD 217
                                    788***9.9*********************************************************************** PP

                                    TCHCBHHHHHHHHHHHHHCTESC.SEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCSTTEEEEESSHCHHSSH CS
                Semialdhyde_dhC  70 gepetreelkavaetkkilefte.kvsatcvrVPvlrGhseavtiklklkdveveeveellaaapevkvvvneeedrPtp 148
                                    g+ et+e +k + e++kil+ ++  vs+tcvrVPv++Ghs ++++++ +++ + e+++ell  a +v +v+      Ptp
  gi|121639624|ref|YP_979848.1| 218 GSGETDEDQKLRFESRKILGIPDlLVSGTCVRVPVFTGHSLSINAEF-AQPLSPERARELLDGATGVQLVDV-----PTP 291
                                    ***********************************************.5******************99999.....9** PP

                                    HHHTTCSSSEEEEEEEEETTCTT..EEEEEEEEETTTT CS
                Semialdhyde_dhC 149 aavaggtnsvsVGRirkdemgde..glklvvvgDNllk 184
                                    +a+ag  ++  VGRir d+ +++  gl+l+v+gDNl+k
  gi|121639624|ref|YP_979848.1| 292 LAAAG-VDESLVGRIRRDPGVPDgrGLALFVSGDNLRK 328
                                    ****9.7*************998779**********97 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   8.2e-33   7.3e-29       2     116 ..       5     114 ..       4     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 8.2e-33
                                    EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                 Semialdhyde_dh   2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80 
                                    ++ivGatG vGq++ +lL+e +++++ v++++s+rs+G+kla++      g++++ved+++++ +++di+++++++ +sk
  gi|121639624|ref|YP_979848.1|   5 IGIVGATGQVGQVMRTLLDErDFPASAVRFFASARSQGRKLAFR------GQEIEVEDAETADPSGLDIALFSAGSAMSK 78 
                                    89******************************************......78**************************** PP

                                    HHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGG CS
                 Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkddavyvlpevnre 116
                                      ap++a+agv+viD+ss++R ++d+++v++evn e
  gi|121639624|ref|YP_979848.1|  79 VQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFE 114
                                    **********************************66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2536.95
//
Query:       gi|121639625|ref|YP_979849.1|  [L=421]
Description: aspartate kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-54  184.9   3.0    3.3e-54  184.0   2.5    1.6  2  AA_kinase  Amino acid kinase family
    3.1e-18   65.2   0.6    5.4e-11   42.1   0.1    2.8  2  ACT        ACT domain
    9.3e-17   60.6   0.1    1.3e-12   47.3   0.0    2.8  3  ACT_7      ACT domain
  ------ inclusion threshold ------
      0.025   14.6   0.2        6.3    6.9   0.0    2.7  2  ACT_6      ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   2.5   7.4e-58   3.3e-54       2     241 .]       3     231 ..       2     231 .. 0.96
   2 ?   -1.5   0.0      0.35   1.6e+03      90     115 ..     360     385 ..     325     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 7.4e-58
                                    EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHH CS
                      AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaaglrstleeagevatrd 80 
                                    +vV K GGss++d+e+  +rr+ae i a k++gn++vvV+++ g +td ll+l++++ + +                + d
  gi|121639625|ref|YP_979849.1|   3 LVVQKYGGSSVADAER--IRRVAERIVATKKQGNDVVVVVSAmGDTTDDLLDLAQQVCPAPPP-------------RELD 67 
                                    69**************..***********************************8888888777.............344* PP

                                    HHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.....HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE... CS
                      AA_kinase  81 alaslgerlvaallaaglpavglsaaaldateagr...degsdgnvesvdaeaieelleagvvpvltgfigldeege... 154
                                    +l++ ger++ al+a ++++ g +a++++ ++ag     ++ ++++  v+   +++ le+g v+ ++gf+g++++ +   
  gi|121639625|ref|YP_979849.1|  68 MLLTAGERISNALVAMAIESLGAHARSFTGSQAGVittGTHGNAKIIDVTPGRLQTALEEGRVVLVAGFQGVSQDTKdvt 147
                                    ************************************99889999999999****************************** PP

                                    .EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCT CS
                      AA_kinase 155 .lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrg 233
                                     lgrg+sDt+a++ A+algAd ++i+tdVdG+++adp++v +ar+l++++++e++e    +a  G+kv+++++++ arr+
  gi|121639625|ref|YP_979849.1| 148 tLGRGGSDTTAVAMAAALGADVCEIYTDVDGIFSADPRIVRNARKLDTVTFEEMLE----MAACGAKVLMLRCVEYARRH 223
                                    ********************************************************....******************** PP

                                    T-EEEEEE CS
                      AA_kinase 234 gipvvItn 241
                                    +ipv++++
  gi|121639625|ref|YP_979849.1| 224 NIPVHVRS 231
                                    *****985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                                    HHHHHHTTHGEEEE-GGGTCEECCCE CS
                      AA_kinase  90 vaallaaglpavglsaaaldateagr 115
                                    v+a + ++l+avg++ + + ++e ++
  gi|121639625|ref|YP_979849.1| 360 VTATFCEALAAVGVNIELISTSEIRI 385
                                    77888999999999999999888777 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   1.2e-14   5.4e-11       3      66 ..     268     330 ..     266     331 .. 0.95
   2 !   20.6   0.1   6.2e-08   0.00028       3      38 ..     350     385 ..     348     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-14
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                     +vg+pD PG +a+vf+a+ad+++Nid++ q  s+ +  g ++++++ + ++ ++++e+l +l 
  gi|121639625|ref|YP_979849.1| 268 TIVGLPDIPGYAAKVFRAVADADVNIDMVLQNVSKVE-DGKTDITFTCSRDVGPAAVEKLDSLR 330
                                    578**********************************.**********************9986 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.2e-08
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEEST CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssed 38 
                                    +  g++ +PG+ a ++ ala  g+Ni+ i++++ + 
  gi|121639625|ref|YP_979849.1| 350 IGAGMRSHPGVTATFCEALAAVGVNIELISTSEIRI 385
                                    5668999*************************9965 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   5.7e+03      33      45 ..     222     234 ..     221     235 .. 0.86
   2 !   10.2   0.0   0.00011       0.5       8      40 ..     266     295 ..     261     298 .. 0.84
   3 !   47.3   0.0   2.9e-16   1.3e-12       3      65 .]     341     403 ..     339     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                    TTT---EEEE-SS CS
                          ACT_7  33 eagIsifqiStyr 45 
                                    +++I++ + S+y 
  gi|121639625|ref|YP_979849.1| 222 RHNIPVHVRSSYS 234
                                    689*****99996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                                    EEEE-S-.---SS--HHHHHHHHHHTTT---EE CS
                          ACT_7   8 klsvvgsglpfdvtGivaklaspLaeagIsifq 40 
                                    k+++vg   p d++G +ak++++ a+a+++i +
  gi|121639625|ref|YP_979849.1| 266 KVTIVGL--P-DIPGYAAKVFRAVADADVNIDM 295
                                    6777776..3.7******************966 PP

  == domain 3  score: 47.3 bits;  conditional E-value: 2.9e-16
                                    EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHHH CS
                          ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLhe 65 
                                    +d++ k+s++g+g+++ ++G++a+ +++La+ g++i  iS +++ +++L ++ +l+kAv aLhe
  gi|121639625|ref|YP_979849.1| 341 DDHIGKVSLIGAGMRS-HPGVTATFCEALAAVGVNIELIStSEIRISVLCRDTELDKAVVALHE 403
                                    78999***********.**********************************************6 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.006        27       6      31 ..     268     294 ..     267     302 .. 0.81
   2 ?    6.9   0.0    0.0014       6.3      12      34 ..     357     379 ..     349     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.006
                          ACT_6   6 tvtG.pdrpGltasLtsvlaefgvnil 31 
                                    t++G pd pG  a++++++a+ +vni 
  gi|121639625|ref|YP_979849.1| 268 TIVGlPDIPGYAAKVFRAVADADVNID 294
                                    56665899*****************95 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                          ACT_6  12 rpGltasLtsvlaefgvnilDie 34 
                                    +pG+ta ++++la  gvni  i 
  gi|121639625|ref|YP_979849.1| 357 HPGVTATFCEALAAVGVNIELIS 379
                                    7******************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2942.00
//
Query:       gi|121639626|ref|YP_979850.1|  [L=834]
Description: 2-isopropylmalate synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-76  256.1   0.0    1.4e-75  254.3   0.0    1.8  2  HMGL-like   HMGL-like
    5.9e-27   94.2   0.8    1.1e-18   67.4   0.1    2.4  2  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.3   0.0   1.5e-79   1.4e-75       3     264 .]      73     352 ..      71     352 .. 0.94
   2 ?   -1.2   0.1      0.14   1.2e+03     216     250 ..     510     549 ..     508     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 254.3 bits;  conditional E-value: 1.5e-79
                                    EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B.....--EE-SSHHHHH CS
                      HMGL-like   3 kivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar...ilalvrarekdik 79 
                                     ++ ++LRDG+qal +++s ++k+++++ L+++g++eiEvgfp+as++df++vr+i++++ +++   i++l ++r ++i+
  gi|121639626|ref|YP_979850.1|  73 LWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDdvtIQVLTQCRPELIE 152
                                    69*************************************************************9999************* PP

                                    HHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHH....HHHHHHHTT-E......TTT-BTTTBS--HHHHH CS
                      HMGL-like  80 aavealkgagakrvhvfiatselhlkaklkkdreevakkaee....avkaarslgkd......velsledasrtdlefla 149
                                    ++++a+ ga  ++vh++++ts l+++++++ +r+ev ++a++    +v+ a +           e+s+e+ + t+le++ 
  gi|121639626|ref|YP_979850.1| 153 RTFQACSGAHRAIVHFYNSTSILQRRVVFRANRAEVQAIATDgarkCVEQAAK---YpgtqwrFEYSPESYTGTELEYAK 229
                                    ***********************************988765411115554444...244468999*************** PP

                                    HHHHHHHHH......T-SEEEEEETTS---HHHHHHHHHHHHHHS-...GGGEEEEEB-TTS-HHHHHHHHHHTT--EEE CS
                      HMGL-like 150 evveaaeea......GatriniaDtvGvltPneaaelisalkervk..dkvilsvHcHndlGlAvantlaAveaGadrvd 221
                                    +v++a+ e+       ++++n+++tv+++tPn++a++i+++++++   ++vils+H+Hnd+G+Ava+++++  aGadr++
  gi|121639626|ref|YP_979850.1| 230 QVCDAVGEViaptpeRPIIFNLPATVEMTTPNVYADSIEWMSRNLAnrESVILSLHPHNDRGTAVAAAELGFAAGADRIE 309
                                    *************999******************************99******************************** PP

                                    EBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                      HMGL-like 222 gtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaalv 264
                                    g+++G+Ger+Gn++l++l ++l  +gvd+++d++++ +i+++v
  gi|121639626|ref|YP_979850.1| 310 GCLFGNGERTGNVCLVTLGLNLFSRGVDPQIDFSNIDEIRRTV 352
                                    ***************************************9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                                    T--EEEEBTTS--.....SSBBB-BHHHHHHHHHHTT-B- CS
                      HMGL-like 216 GadrvdgtvnGlG.....eraGnaaleelvaalealgvdt 250
                                    G + + +tv  +G      ++Gn +l ++v al+  g d 
  gi|121639626|ref|YP_979850.1| 510 GTTSITATVKINGveteiSGSGNGPLAAFVHALADVGFDV 549
                                    778888888888887888899***********99888664 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.1   1.2e-22   1.1e-18       1     102 [.     474     575 ..     474     599 .. 0.89
   2 !   25.0   0.1   1.6e-09   1.4e-05     106     132 ..     806     832 ..     791     833 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.2e-22
                                    XXXXXXXXXXXXXXXXXXX--EEEEEEEEEEETTCEEEEEEEEEE..TTEEEEEEEE-SSHHHHHHHHHHHHHHHT-EEE CS
                     LeuA_dimer   1 evtdedlealvkdelleaeerlkleklqvssgedelstatvklevk.dgeekeasaeGnGpvdAllnAlrkalgvdikLl 79 
                                    ev+++++++ + +e+l + ++l+    +v  ++d++ t++++++vk +g e+e+s++GnGp++A+++Al   +g d+ +l
  gi|121639626|ref|YP_979850.1| 474 EVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKiNGVETEISGSGNGPLAAFVHALAD-VGFDVAVL 552
                                    7999*************************************999999************************.******** PP

                                    EEEEE--TT-TT--EEEEEEEE- CS
                     LeuA_dimer  80 dYsvhaitegtdaqaevrVelev 102
                                    dY +ha+++g+daqa+++Ve +v
  gi|121639626|ref|YP_979850.1| 553 DYYEHAMSAGDDAQAAAYVEASV 575
                                    ********************997 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.6e-09
                                    GEEEEEEEESSHHHHHHHHHHHHHHHH CS
                     LeuA_dimer 106 kkvsgvGvdsdiveASlkAlisalnrl 132
                                    k+v+gvG++++i++ASl+A++sa+nr+
  gi|121639626|ref|YP_979850.1| 806 KTVWGVGIAPSITTASLRAVVSAVNRA 832
                                    56***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 5248.64
//
Query:       gi|121639627|ref|YP_979851.1|  [L=329]
Description: DNA polymerase III subunit epsilon [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-19   70.6   0.0    3.1e-19   70.1   0.0    1.2  1  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   1.7e-23   3.1e-19       2     162 ..      18     168 ..      17     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.7e-23
                                    EEEEEESSSTTCTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHHH CS
                        RNase_T   2 viDlEttgldakekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevleefkell 81 
                                    viD+Et g+ +  + +ii++a   +d+  +  +++++++ +p+ +    +  t ++g t +mld++p f +++ e+ ++l
  gi|121639627|ref|YP_979851.1|  18 VIDVETSGFRP-GQARIISLAVLGLDAAGR-LEQSVVSLLNPKVD----PGPTHVHGLTAAMLDDQPQFADIAGEVVDVL 91 
                                    8**********.8**************996.77779999999988....9****************************** PP

                                    HHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHCHHHHHHHHHTTCHSSSSTSSHHHHHHHH CS
                        RNase_T  82 rklallvahnaafdvgflraadkrilkkevpkrnqfldtlildkatlkelartsldklaeklgleedgraHrAldDaeat 161
                                    r ++ lvahn+afd+ fl a+ + i  +e+p  + + +t++l+++   +  + +l+ la++ g++++   H+A dDa+ +
  gi|121639627|ref|YP_979851.1|  92 R-GRTLVAHNVAFDYAFLAAEAE-IAEAELP-VDFVMCTVELARRLQLGVDNLRLETLAAHWGVPQQRP-HDAFDDARVL 167
                                    *.99***************9999.6699999.999***********999999**************885.*******987 PP

                                    H CS
                        RNase_T 162 a 162
                                     
  gi|121639627|ref|YP_979851.1| 168 T 168
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2160.19
//
Query:       gi|121639628|ref|YP_979852.1|  [L=413]
Description: ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-25   86.6   0.0    5.2e-24   84.3   0.0    2.0  2  DUF1727       Domain of unknown function (DUF1727)
    1.5e-16   61.0   0.0    6.7e-16   58.9   0.0    1.9  1  Mur_ligase_M  Mur ligase middle domain


Domain annotation for each model (and alignments):
>> DUF1727  Domain of unknown function (DUF1727)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.13   1.2e+03      55      76 ..      52      73 ..      43     107 .. 0.79
   2 !   84.3   0.0   5.8e-28   5.2e-24       1     110 []     303     402 ..     303     402 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.13
                        DUF1727 55 kkvvvsGeraeDmalRLkyagv 76
                                   ++vvv+G+  + +  R++ a +
  gi|121639628|ref|YP_979852.1| 52 RTVVVTGTNGKSTTTRMTAAAL 73
                                   68999*****999999998876 PP

  == domain 2  score: 84.3 bits;  conditional E-value: 5.8e-28
                        DUF1727   1 LvkNPvglnetlrllaedkekkellillndraadgtdvsWlwDvdfeklaeskvkkvvvsGeraeDmalRLkyagveeek 80 
                                    L+kNP+g++e+l ++++  ++  ++i++n r +dg+d sWlwDv fe++++   ++vv++Ger +D+a+RL yagve++ 
  gi|121639628|ref|YP_979852.1| 303 LAKNPAGWQEALAMVDK--HADGVVIAVNGRVPDGEDLSWLWDVRFEHFET---TRVVAAGERGTDLAVRLGYAGVEHTL 377
                                    79*************99..8899**************************97...59********************7766 PP

                        DUF1727  81 ieieedleealeaekkeeetlyilatYtam 110
                                    ++    + +a++  + +  ++ ++a+Yta+
  gi|121639628|ref|YP_979852.1| 378 VHD---TVAAIA--SCPPGRVEVVANYTAF 402
                                    655...778888..9999**********95 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   7.4e-20   6.7e-16       1     190 [.      56     263 ..      56     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 7.4e-20
                                    EESSS-HHHHHHHHHHHHHCTEEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE--- CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvgttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitni 80 
                                    vTGtnGK+Ttt+++aa+l + g+v++ ++  n + gl ++la  ++  ae+avlEv + ++   +++++++p+v+v++n+
  gi|121639628|ref|YP_979852.1|  56 VTGTNGKSTTTRMTAAALGTLGAVATNAEGANMDAGLVAALAAHRD--AELAVLEVDEMHVP--HISDAVDPAVVVLLNL 131
                                    9********************9999999999999**9999966665..*********99554..5666699********* PP

                                    TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEE CS
                   Mur_ligase_M  81 spdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegtei 160
                                    s+d ld+ g++  + ++ +  ++r+++ +++v n dd     l+  ++ ++ +vv +   +       ++++  ++++ i
  gi|121639628|ref|YP_979852.1| 132 SRDQLDRVGEINVIERTLRAGLARHPD-AVVVANCDDV----LMTSAAYDSPNVVWVAAGGAW---SNDSVSCPRSSEVI 203
                                    ***************999999999985.6********9....444444443444433333321...11222222222222 PP

                                    ..............................EEEEETTEEEEEEESSCSCHHHHHHHHHHH CS
                   Mur_ligase_M 161 ..............................ellevkggeleieipllGkhnvyNalaaia 190
                                                                  +l  ++g  l ++++l+G+ n  Na+ a+a
  gi|121639628|ref|YP_979852.1| 204 vrkapsqedhwystgadfkrpaphwwfddaTLYGPDGLALPMRLALPGSVNRGNAAQAVA 263
                                    233333333334444555555555555554444445555556666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3028.49
//
Query:       gi|121639629|ref|YP_979853.1|  [L=231]
Description: cobyric acid synthase cobQ2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-35  122.9   0.0    1.3e-35  122.7   0.0    1.0  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   7.5e-40   1.3e-35       1     195 [.       3     197 ..       3     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 7.5e-40
                       GATase_3   1 kiavirlpaisnyt...dldpLeaepevrvrfvplkdeslg....edadlvilpGgkdtiqdlallresgldeaikeaae 73 
                                    +i+++ ++ + +y+   +  +L+++   r++ +++ + +l+    +++dl+ l+G +d++q+la+ +  +    +++aa 
  gi|121639629|ref|YP_979853.1|   3 RIGLVLPDVMGTYGdggNAVVLRQRLLLRGIAAEIVEITLAdpvpDSLDLYTLGGAEDYAQRLATRHL-RRYPGLQRAAG 81 
                                    69999*****************************9999999999988********************9.8899******* PP

                       GATase_3  74 aggpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevelaaegeevkGyEiHsGrtilke 153
                                    +g+pvl+iC+  q+LG+++e+++g      +v+g+glLd++t  ++ +++g+ +++  la  +++++G+E+H+G t+l++
  gi|121639629|ref|YP_979853.1|  82 RGAPVLAICAAIQVLGHWYETSSGD-----RVDGVGLLDVTTSPQDARTIGELVSKPLLAGLTQPLTGFENHRGGTVLGP 156
                                    ************************9.....*************************95555556***************** PP

                       GATase_3 154 kakpllkvkv.ggnng..ekdGavkksedgnvlGtYlHglfdnrn 195
                                    +++pl++v++  gn+   + dGav +    +v++tY+Hg++++rn
  gi|121639629|ref|YP_979853.1| 157 GTSPLGAVVKgAGNRAgdGFDGAVAG----SVVATYMHGPCLARN 197
                                    ********9964444479******66....***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1576.77
//
Query:       gi|121639630|ref|YP_979854.1|  [L=296]
Description: hypothetical protein BCG_3774c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-06   27.2   0.1    5.2e-06   26.5   0.1    1.3  1  MTES_1575  REase_MTES_1575
     0.0012   18.7   0.1      0.002   18.0   0.1    1.3  1  DUF559     Protein of unknown function (DUF559)


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   5.8e-10   5.2e-06      18      93 ..     213     287 ..     199     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.8e-10
                      MTES_1575  18 pqvgvggfriDlvvedp..gkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwssdwyrnpeeeleklve 93 
                                    +q+ v +    + v d   +ky++a e dgd++ s++ ++ +d +r + L +lGW ++R+  +d   np+++++++++
  gi|121639630|ref|YP_979854.1| 213 TQIPVVHRWRNVGVLDMgwEKYMVAAEYDGDQHRSDRGRYVKDQRRLRKLAELGWIVIRVIAED---NPDDVVNRVRA 287
                                    566666666667777777899***************************************9876...66666666655 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.2e-07     0.002      46     105 ..     227     286 ..     220     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-07
                                    EEEEETTTTEEEEEE-------...----HHHHHHHHHTT-EEEEEEHHHHHH-HHHHHHHHH CS
                         DUF559  46 vDfvclkaklivelDGaqhdee...eeyDaeRtelLeslGftvlRfkndevlknieevleeil 105
                                    +D   +k  +  e DG qh ++     +D++R + L++lG+ v+R   ++   n+++v++++ 
  gi|121639630|ref|YP_979854.1| 227 LDMGWEKYMVAAEYDGDQHRSDrgrYVKDQRRLRKLAELGWIVIRVIAED---NPDDVVNRVR 286
                                    566667778889*******987555789*****************98764...5677766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2089.85
//
Query:       gi|121639631|ref|YP_979855.1|  [L=203]
Description: recombination protein RecR [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-22   79.3   0.0    3.2e-22   78.8   0.0    1.3  1  Toprim_4       Toprim domain
    2.9e-13   49.1   3.5    5.5e-13   48.2   3.5    1.5  1  RecR           RecR protein
    2.2e-11   43.9   0.0    5.8e-11   42.5   0.0    1.6  2  Toprim         Toprim domain
    7.3e-06   25.6   0.8    3.1e-05   23.6   0.0    2.4  2  HHH            Helix-hairpin-helix motif
    9.1e-05   23.0   0.3     0.0031   18.1   0.0    2.7  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.051   13.9   0.0    1.9  2  HHH_8          Helix-hairpin-helix domain
       0.05   14.0   0.1       0.33   11.4   0.0    2.4  2  IMS_HHH        IMS family HHH motif
      0.078   12.7   0.1       0.15   11.9   0.1    1.5  1  zinc_ribbon_2  zinc-ribbon domain
      0.083   13.2   0.0        0.3   11.4   0.0    1.9  2  HHH_3          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   1.6e-25   3.2e-22       1      89 []      79     175 ..      79     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.6e-25
                       Toprim_4   1 seiiiVEgyaDvlaleka.giknvvavlggalspldgirpeklktenlve......aekkvkevilaldgDaeGeataer 73 
                                    s ++iVE + D  a+e++ ++++ ++vlggal+pl+gi+p++l++++l+        +  v+evi+a+d+  eGeata +
  gi|121639631|ref|YP_979855.1|  79 SVVCIVEEPKDIQAVERTrEFRGRYHVLGGALDPLSGIGPDQLRIRELLSrigervDDVDVTEVIIATDPNTEGEATATY 158
                                    579******************************************888888***999999******************** PP

                       Toprim_4  74 laelll.eegvkvtrla 89 
                                    l+++l+  +g++vtr+a
  gi|121639631|ref|YP_979855.1| 159 LVRMLRdIPGLTVTRIA 175
                                    ***99989******996 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   3.5   2.8e-16   5.5e-13       2      40 .]      39      77 ..      38      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.8e-16
                                   HHHHHHHHHHHHHH-EE-TTT--EESSSS-CCCCSTTSE CS
                           RecR  2 aeeLaeaLqeakekvrhCsrCgnlteedlCaICsdprRD 40
                                   +++L + L +++++vr+C +Cgn+++++ C+ICsd rRD
  gi|121639631|ref|YP_979855.1| 39 IDRLTGVLAKVRDGVRFCAVCGNVSDNERCRICSDIRRD 77
                                   689***********************************9 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   4.5e+03      14      35 ..      46      65 ..      24      70 .. 0.65
   2 !   42.5   0.0   2.9e-14   5.8e-11       1      88 [.      80     164 ..      80     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                   HHHTHTSTEEEEEEESSSSEEE CS
                         Toprim 14 iakalgsgfqavtaslGhildl 35
                                   +ak+  +++++  a++G++ d 
  gi|121639631|ref|YP_979855.1| 46 LAKV--RDGVRFCAVCGNVSDN 65
                                   3333..4566777777777665 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 2.9e-14
                                    EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHH.HHHS.....EEEEECSSSH CS
                         Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkela.krad.....eiilatDpDr 74 
                                    +++ivE p+d ++++++  ++f   +++lG +ld  +        i +++  + +l ++  +r+d     e+i+atDp +
  gi|121639631|ref|YP_979855.1|  80 VVCIVEEPKDIQAVERT--REFRGRYHVLGGALDPLS-------GIGPDQLRIRELLSRIgERVDdvdvtEVIIATDPNT 150
                                    68***************..568888888888888888.......67777766666444434666666688********** PP

                                    HHHHHHHHHHHHHT CS
                         Toprim  75 eGeaiawellevlk 88 
                                    eGea+a++l+ +l+
  gi|121639631|ref|YP_979855.1| 151 EGEATATYLVRMLR 164
                                    **********7777 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.5e-08   3.1e-05       8      27 ..       8      27 ..       2      28 .. 0.87
   2 ?   -1.4   0.1       1.3   2.6e+03      16      21 ..     113     118 ..     111     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-08
                                   SSHHHHHTSTT-SHHHHHHH CS
                            HHH  8 asreeLlalPGVGpktAeaI 27
                                   + ++eL +lPG+Gpk A++I
  gi|121639631|ref|YP_979855.1|  8 DLIDELGKLPGIGPKSAQRI 27
                                   669****************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                                    STT-SH CS
                            HHH  16 lPGVGp 21 
                                    l+G+Gp
  gi|121639631|ref|YP_979855.1| 113 LSGIGP 118
                                    79***9 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-06    0.0031      34      53 ..      10      29 ..       6      31 .. 0.88
   2 ?    2.1   0.1      0.16   3.1e+02       7      28 ..     113     136 ..     109     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                   HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5 34 veeLakipGiGkktAeriil 53
                                   ++eL k+pGiG+k A+ri  
  gi|121639631|ref|YP_979855.1| 10 IDELGKLPGIGPKSAQRIAF 29
                                   689**************965 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                                    STT--HH..HHHHHHTTT--S.HHH CS
                          HHH_5   7 vsGiGpk..tAlallsaGies.ved 28 
                                    +sGiGp   +++ lls  i+  v+d
  gi|121639631|ref|YP_979855.1| 113 LSGIGPDqlRIRELLSR-IGErVDD 136
                                    78999986666777777.6532444 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.051      41      64 ..       5      28 ..       2      31 .. 0.87
   2 ?   -3.2   0.0       5.7   1.1e+04      52      58 ..     113     119 ..     106     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                   -HHHH.TTHCTTSTT--HHHHHHHH CS
                          HHH_8 41 eitsl.eeeltklpgiGkkiaakie 64
                                   ++++l +e l klpgiG+k a++i+
  gi|121639631|ref|YP_979855.1|  5 PVQDLiDE-LGKLPGIGPKSAQRIA 28
                                   78899677.**************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.7
                                    STT--HH CS
                          HHH_8  52 lpgiGkk 58 
                                    l giG++
  gi|121639631|ref|YP_979855.1| 113 LSGIGPD 119
                                    7888865 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.33      12      27 ..      12      27 ..      10      30 .. 0.89
   2 ?   -1.8   0.0       2.5   5.1e+03      13      19 ..     163     169 ..     163     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                        IMS_HHH 12 pitkipGiGgklgekL 27
                                   +++k+pGiG+k ++++
  gi|121639631|ref|YP_979855.1| 12 ELGKLPGIGPKSAQRI 27
                                   589**********985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                        IMS_HHH  13 itkipGi 19 
                                    +++ipG+
  gi|121639631|ref|YP_979855.1| 163 LRDIPGL 169
                                    79***96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.3e-05      0.15       7      20 ..      47      60 ..      47      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                  zinc_ribbon_2  7 aelqdnakFCpyCG 20
                                   a++ d+++FC  CG
  gi|121639631|ref|YP_979855.1| 47 AKVRDGVRFCAVCG 60
                                   6899********** PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015       0.3      14      30 ..      11      27 ..      10      30 .. 0.90
   2 ?   -3.5   0.0       6.5   1.3e+04      16      24 ..     110     118 ..     109     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                          HHH_3 14 eeLqklpGlgpklAknI 30
                                   +eL klpG+gpk A++I
  gi|121639631|ref|YP_979855.1| 11 DELGKLPGIGPKSAQRI 27
                                   6999************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.5
                          HHH_3  16 LqklpGlgp 24 
                                    L+ l+G+gp
  gi|121639631|ref|YP_979855.1| 110 LDPLSGIGP 118
                                    666888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1499.81
//
Query:       gi|121639632|ref|YP_979856.1|  [L=133]
Description: hypothetical protein BCG_3776c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-31  108.9   5.4    1.3e-31  108.7   5.4    1.0  1  YbaB_DNA_bd  YbaB/EbfC DNA-binding family
  ------ inclusion threshold ------
      0.018   14.8   6.4      0.032   14.0   6.4    1.4  1  Collagen     Collagen triple helix repeat (20 copies)
       0.11   12.8   0.3       0.13   12.6   0.3    1.1  1  HutP         HutP


Domain annotation for each model (and alignments):
>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   5.4   2.1e-35   1.3e-31       2      90 ..      12     100 ..      11     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.1e-35
                                    HHHHHHHHHHHHHHHHHTTSEEEEEETTTTEEEEEETT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                    YbaB_DNA_bd   2 kqaqkmqkkmeeaqeelaekevegssggglVkVtvngkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaee 81 
                                     qaq+mq+k+ eaq++la+ ev+g++ggglVkV+v+g+gev  ++Idp+++dp+d+e+L+dliv A++dA ++++++a+e
  gi|121639632|ref|YP_979856.1|  12 AQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQE 91 
                                    69****************************************************************************** PP

                                    HHHHHT--X CS
                    YbaB_DNA_bd  82 emskltggl 90 
                                    ++++l+g +
  gi|121639632|ref|YP_979856.1|  92 RLGALAGAM 100
                                    *****9977 PP

>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.4   5.4e-06     0.032      29      48 ..     109     128 ..      98     133 .] 0.41

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                                    EEE-TTSS------------ CS
                       Collagen  29 ekGpaGekGppGaaGkpGap 48 
                                    ++G++G +G pG +G+pGap
  gi|121639632|ref|YP_979856.1| 109 PPGAPGMPGMPGMPGAPGAP 128
                                    22222222222222222222 PP

>> HutP  HutP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.2e-05      0.13       8      87 ..      11      90 ..       5     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                   HHH-SSSCH.HHHH.HHHHTTEEEEEEEEEESS...HHHHHHHHHHHHHHTTSS-SS..SHHHHHHHHHHHHHHHHHHTTSH CS
                           HutP  8 lalsesreeeeelkeklkkegikvaavevggeaeelskkivesavvaAkregvikee..hreehavahAvleAlsqvtrkav 87
                                   la  + ++++++l e+ ++     + +++gg   +++ k   +++   +  +v++ +   + +  +++A+++A +qvt+ a 
  gi|121639632|ref|YP_979856.1| 11 LA--QAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDdiETLQDLIVGAMRDASQQVTKMAQ 90
                                   33..345666677777777778889999999999********************988545667889***********87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 967.38
//
Query:       gi|121639633|ref|YP_979857.1|  [L=241]
Description: hypothetical protein BCG_3777 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-31  108.9   0.0    3.7e-31  108.6   0.0    1.1  1  Amidase_3  N-acetylmuramoyl-L-alanine amidase


Domain annotation for each model (and alignments):
>> Amidase_3  N-acetylmuramoyl-L-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.0   2.1e-35   3.7e-31       1     173 [.      29     230 ..      29     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 2.1e-35
                      Amidase_3   1 ividpGHGgkdp....................GavgknglkEkdlnlkvalklaklLeakgaeVvltrdddksv..slke 58 
                                    ++idpGH+g +                     G+  ++g+ E+++++++ l+l++ L+a g++  l+r +d  +  +++e
  gi|121639633|ref|YP_979857.1|  29 VFIDPGHNGANDasigrqvptgrggtkncqasGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDNALgpCVDE 108
                                    89*****7776669*******9998888888888779*********************************966667**** PP

                      Amidase_3  59 ranianksradlfvsiHadsaanssasGvevfy...leknekkaeskrlaksiqkelkkklglk.....nrgvkeannly 130
                                    ran+an+ r++++vs+Had+ + s+ +G++v y     ++ ++  s ++a+ + ++l++ +  k     + g+  +++l+
  gi|121639633|ref|YP_979857.1| 109 RANMANALRPNAIVSLHADGGPASG-RGFHVNYsapPLNAIQAGPSVQFARIMRDQLQASGIPKanyigQDGLYGRSDLA 187
                                    ***********************99.*******8888888999999*********9998887777788888888888*** PP

                      Amidase_3 131 vlrktkipavlvElgfisnpedakllkseeyqeklakaiaegi 173
                                     l+ ++ p++lvElg+++np+d +l++s e ++k+a+a+++g+
  gi|121639633|ref|YP_979857.1| 188 GLNLAQYPSILVELGNMKNPADSALMESAEGRQKYANALVRGV 230
                                    ****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1682.51
//
Query:       gi|121639634|ref|YP_979858.1|  [L=147]
Description: hypothetical protein BCG_3778c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-23   81.5   0.7    7.6e-23   81.4   0.7    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.7   4.3e-27   7.6e-23       2     143 .]       4     144 ..       3     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 4.3e-27
                                    EEEEEEEEESS-HHHHHHHHTTTTGGG.G.T-TTEEEEECSE.STSSSTTTEEEEECCCSSEEEEEEEEEE.TTTTEEEE CS
                Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwp.r.Whpevarveleg.gggpargvegtvrvggrgtvreelvevd.pegrllsy 77 
                                    v++ +++ i+a p +  ++++d+e+++ +  +p ++++++ + g+g++++++++++++  ++vr++ v vd + +++++ 
  gi|121639634|ref|YP_979858.1|   4 VSAASTILINAEPTATLDALADYETVRpKiLSPHYSEYQVLEgGKGRGTVAKWRLQATQ-SRVRDVQVNVDvAGHTVIEK 82 
                                    67889**********************64469999999876624444467778888888.99*********77******* PP

                                    EEE.SSS-TSEEEEEEEEECCET....EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  78 rivkpvpvanyvatwtvtpdggg....trvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                    +++     +++v++wtv+p+g+g     ++twtg   ag+++g+fek++a+ ++k+++ + L +Lk++le
  gi|121639634|ref|YP_979858.1|  83 DMN-----SSMVTNWTVAPAGPGssvtVKTTWTG---AGGVKGFFEKTFAPLGLKKIQAEVLSNLKTELE 144
                                    **7.....889************66644477999...6789***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 972.35
//
Query:       gi|121639635|ref|YP_979859.1|  [L=470]
Description: hypothetical protein BCG_3779 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-09   38.2   0.1    1.7e-09   37.5   0.1    1.3  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   9.8e-14   1.7e-09      34     139 .]      50     154 ..      42     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 9.8e-14
                                    TTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTE CS
                  FAD_binding_4  34 ssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaakglllglepgsgipgtvGGaiatnagGygs 113
                                    s+l ++ v+ ++  ld s l++++ id+e++ta v + +t++dl +a+  + +l +l    + + t+GGa+ + ++ + s
  gi|121639635|ref|YP_979859.1|  50 SNLFRARVKHDARGLDASGLTGVIGIDPEARTADVAGMCTYEDLIAAT-LHYGLSPLVVPQLRTITLGGAVTGLGIESAS 128
                                    5555666677778899999*****************************.7777777787778899*************** PP

                                    EGG--HHGTEEEEEEEETTSEEEEEE CS
                  FAD_binding_4 114 ekyGlirdnvlglevvladGevvrls 139
                                     + Gl ++ vl+++++++ Ge++++s
  gi|121639635|ref|YP_979859.1| 129 FRNGLPHESVLEMDILTGAGELLTVS 154
                                    **********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3339.33
//
Query:       gi|121639636|ref|YP_979860.1|  [L=420]
Description: fatty acid synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-99  333.0   0.0    1.5e-99  332.8   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    2.1e-10   41.1   0.0    5.1e-10   39.9   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    3.3e-09   36.8   0.0    5.7e-09   36.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    3.7e-09   37.2   0.0    1.2e-08   35.6   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
    2.4e-05   25.0   0.0      6e-05   23.7   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.024   14.3   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.015   14.9   0.0      0.025   14.1   0.0    1.3  1  MTS              Methyltransferase small domain
      0.075   12.8   0.0       0.14   11.9   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.093   12.5   0.0        0.3   10.9   0.0    1.8  1  Methyltransf_31  Methyltransferase domain
       0.12   12.0   0.0        0.2   11.2   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.8   0.0  8.2e-103   1.5e-99       1     272 [.     130     398 ..     130     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 332.8 bits;  conditional E-value: 8.2e-103
                                    .XSXXXHHHHHHHHTS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHH CS
                           CMAS   1 qkkkkevenikahYDlsndffalfldptmtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrra 80 
                                    ++k++++e+i++hYD+sn+f++++l+p+mtY+CA+f +++++Le+Aq++K++li+ekl+l+pG++lLd+GcGWG++vr+a
  gi|121639636|ref|YP_979860.1| 130 HSKTRDAEAIHHHYDVSNNFYEWVLGPSMTYTCAVFPNAEASLEQAQENKYRLIFEKLRLEPGDRLLDVGCGWGGMVRYA 209
                                    6899**************************************************************************** PP

                                    HHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT CS
                           CMAS  81 verydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsvgafehvgkenydtffkklkkllked 159
                                    ++r +v+v+g TlS+eqak+ +k+v++++l++ ++v+ +dy+d++e  +d+v+s+g++eh+g++ny+ +f +lk++l+++
  gi|121639636|ref|YP_979860.1| 210 ARR-GVRVIGATLSAEQAKWGQKAVEDEGLSDLAQVRHSDYRDVAEtGFDAVSSIGLTEHIGVKNYPFYFGFLKSKLRTG 288
                                    ***.******************************************89******************************** PP

                                    -EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHHHTHHH CS
                           CMAS 160 GllllhtitslhkkelaerglklkfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealqenkde 239
                                    Glll+h+it+ ++++++ +g    f+d+++FP+Gel+ + +i++ei+++g++v++ e++r+hYa+TL++W+ +l e++d+
  gi|121639636|ref|YP_979860.1| 289 GLLLNHCITRHDNRSTSFAG---GFTDRYVFPDGELTGSGRITTEIQQVGLEVLHEENFRHHYAMTLRDWCGNLVEHWDD 365
                                    *****************777...9******************************************************** PP

                                    HHHHSHHHHHHHHHHHHHHHHHHHHTTSCEEEE CS
                           CMAS 240 aialvseevarmyelYLagcaeaFrkgyidvaq 272
                                    a+a v+  +a+++ lY+a+++ aF+++++++++
  gi|121639636|ref|YP_979860.1| 366 AVAEVGLPTAKVWGLYMAASRVAFERNNLQLHH 398
                                    ******************************997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.8e-13   5.1e-10       1      94 [.     196     291 ..     196     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.8e-13
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv..ed 76 
                                    LdvGcG G ++++ a+rg rv+g  ls+e+ k+ ++++++egl    +++++d ++  +++  fD+v s    +h+  ++
  gi|121639636|ref|YP_979860.1| 196 LDVGCGWGGMVRYAARRGVRVIGATLSAEQAKWGQKAVEDEGLsdLAQVRHSDYRD--VAETGFDAVSSIGLTEHIgvKN 273
                                    8*****************************************98866778888887..999***************9999 PP

                                    HHHHHHHHHHHEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGll 94 
                                       ++  ++  L+ gGll
  gi|121639636|ref|YP_979860.1| 274 YPFYFGFLKSKLRTGGLL 291
                                    999999999999999998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   3.2e-12   5.7e-09      14     126 ..     181     302 ..     168     361 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.2e-12
                Methyltransf_23  14 erllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgk 82 
                                      +++k  l++g r+Ld+GcG G + ++++++g+ v+g  ls e+ ++ +            + +++      +++ +  
  gi|121639636|ref|YP_979860.1| 181 RLIFEKlrLEPGDRLLDVGCGWGGMVRYAARRGVRVIGATLSAEQAKWGQkavedeglsDLAQVRHSD----YRDVAETG 256
                                    3344444479999*****************************99888876666665553222222222....3555777* PP

                Methyltransf_23  83 fdlIvlrevlehvp..dppellrqiatllkpgGylllseplaslke 126
                                    fd ++++ ++eh+   ++p ++  +++ l+ gG+ll + +++ + +
  gi|121639636|ref|YP_979860.1| 257 FDAVSSIGLTEHIGvkNYPFYFGFLKSKLRTGGLLLNHCITRHDNR 302
                                    ************98779*******************9998876532 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.6e-12   1.2e-08       2      97 .]     196     289 ..     195     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.6e-12
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    Ld+GcG G +++++a+r+   +v+g  +s+e+ +  ++ +e+egl   +++++ d +d+ +    fD+v s+g  +h+  
  gi|121639636|ref|YP_979860.1| 196 LDVGCGWGGMVRYAARRG--VRVIGATLSAEQAKWGQKAVEDEGLsdLAQVRHSDYRDVAE--TGFDAVSSIGLTEHIGV 271
                                    9****************5..*************************98899999****9985..56******988*****9 PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                    ++++ ++  +++ L+ gG
  gi|121639636|ref|YP_979860.1| 272 KNYPFYFGFLKSKLRTGG 289
                                    999999999999888888 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.4e-08     6e-05       1      99 []     196     291 ..     196     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.4e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG G ++r+ +++  +++++g  +s+++ +  ++   +++  + ++v+  +  +  +     fD+v ++++ +h+ 
  gi|121639636|ref|YP_979860.1| 196 LDVGCGWGGMVRYAARR--GVRVIGATLSAEQAKWGQKAVEDEGLSDLAQVRHSDYRDVAET---GFDAVSSIGLTEHIg 270
                                    8****************..***********************************99987664...8*************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGrl 99 
                                     k+  +++  +++ L+ gG l
  gi|121639636|ref|YP_979860.1| 271 vKNYPFYFGFLKSKLRTGGLL 291
                                    888889988888888888865 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.024      31     108 ..     182     259 ..     177     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                          GCD14  31 liimkLelkpGsvvvesGtGsgslshaia.rtvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfde 108
                                    li  kL+l+pG + ++ G G g +  + a r v   G   + e  ++  +ka+e+    +l+q+ +   rDv ++Gfd+
  gi|121639636|ref|YP_979860.1| 182 LIFEKLRLEPGDRLLDVGCGWGGMVRYAArRGVRVIGATLSAEQ-AKWGQKAVEDEGLSDLAQVRHSDYRDVAETGFDA 259
                                    8999*****************99988765268999999888874.556788888888888888888889********54 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.025      21     101 ..     181     260 ..     177     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                    HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-E CS
                            MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkf 98 
                                    +l+ e+l  e  +++lD+GcG+G +   +a++  +  v     +a+  +  ++ +e+++l+  ++v++sd  + +e   f
  gi|121639636|ref|YP_979860.1| 181 RLIFEKLRLEPGDRLLDVGCGWGGMVRYAARRGVR--VIGATLSAEQAKWGQKAVEDEGLSdlAQVRHSDYRDVAE-TGF 257
                                    57788899999999*********999999887766..677777778889999999999999999999999766555.888 PP

                                    EEE CS
                            MTS  99 dli 101
                                    d++
  gi|121639636|ref|YP_979860.1| 258 DAV 260
                                    876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.9e-05      0.14      64     126 ..     182     241 ..     166     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSE CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenv 126
                                    l+ e l+l++g+r L+vG+G G          ++  rv++   ++e ++  ++ ++ ++l+++
  gi|121639636|ref|YP_979860.1| 182 LIFEKLRLEPGDRLLDVGCGWGGMV---RYAARRGVRVIGATLSAEQAKWGQKAVEDEGLSDL 241
                                    567899**************99543...33345555788888888888888888888877755 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017       0.3       3     107 ..     191     291 ..     189     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlils 80 
                                     g r+lD+GCG G  +  +a++   + +v+G   s+e  +  ++  ++ gl+  ++++++d  + +e       fD + s
  gi|121639636|ref|YP_979860.1| 191 PGDRLLDVGCGWGGMVRYAARR---GVRVIGATLSAEQAKWGQKAVEDEGLSdLAQVRHSDYRDvAE-----TGFDAVSS 262
                                    57899***************54...788**********************99778999999999555.....57999988 PP

                Methyltransf_31  81 nevl..naladpdkileeiervlkpggil 107
                                     ++     +++ + +++ +++ l++gg l
  gi|121639636|ref|YP_979860.1| 263 IGLTehIGVKNYPFYFGFLKSKLRTGGLL 291
                                    87775555555555666666666666555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011       0.2      11      79 ..     189     260 ..     178     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                           MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegv....aecvakGlsviqgdldkdlenfedksfdyv 79 
                                    ++pg r+ld+GcG G ++++ + +++v+  G  l++e      +++   Gls + +   +d    ++  fd v
  gi|121639636|ref|YP_979860.1| 189 LEPGDRLLDVGCGWGGMVRYAA-RRGVRVIGATLSAEQAkwgqKAVEDEGLSDLAQVRHSDYRDVAETGFDAV 260
                                    5899**************9985.58888888766655431111445567777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3223.66
//
Query:       gi|121639637|ref|YP_979861.1|  [L=578]
Description: DNA polymerase III subunits gamma and tau [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-38  129.5   0.0    1.4e-37  129.0   0.0    1.2  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    6.2e-15   55.4   0.4    1.2e-14   54.4   0.4    1.5  1  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
    1.8e-10   41.3   0.0    5.4e-10   39.8   0.0    1.8  2  AAA              ATPase family associated with various cellul
    5.4e-07   30.0   0.0    4.8e-06   26.9   0.0    2.6  3  AAA_22           AAA domain
    1.7e-06   27.9   0.0    4.1e-06   26.6   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.9e-05   23.4   0.0    0.00014   21.6   0.0    1.9  2  AAA_30           AAA domain
     0.0011   19.4   0.1     0.0087   16.4   0.0    2.5  2  AAA_19           AAA domain
     0.0011   18.4   0.0     0.0033   16.8   0.0    1.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0029   18.0   5.1     0.0049   17.3   0.0    3.5  2  AAA_16           AAA ATPase domain
     0.0048   16.8   0.0     0.0088   16.0   0.0    1.3  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.014   15.4   0.0        4.3    7.3   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
       0.04   13.9   0.0       0.18   11.8   0.0    1.9  1  AAA_14           AAA domain
       0.19   12.3   0.0       0.68   10.5   0.0    2.0  2  AAA_18           AAA domain
       0.54   10.2   6.8       0.21   11.6   0.6    2.3  2  CHAD             CHAD domain


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   1.1e-40   1.4e-37       1     160 [.      17     175 ..      17     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 1.1e-40
                DNA_pol3_delta2   1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivieteeke 80 
                                    gqe++   ls al  gr++hayLf+G++g+gk ++a  la++l+c ++ + +pcg c+sc  ++ +    + v+e + + 
  gi|121639637|ref|YP_979861.1|  17 GQEHVTAPLSVALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTANPCGVCESCVSLAPNAPGSIDVVELDAA- 95 
                                    588889999*******************************************************999999999999888. PP

                DNA_pol3_delta2  81 rsikldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfs 160
                                    ++  +d+ rel +++   p++s+++++i+++a ++t++  NalLk++EEP+e+ ifi+ t++++k+L+tirSR+ ++ f+
  gi|121639637|ref|YP_979861.1|  96 SHGGVDDTRELRDRAFYAPVQSRYRVFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFR 175
                                    7899************************************************************************9997 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.4   9.3e-18   1.2e-14       4     129 ..     235     362 ..     232     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 9.3e-18
                DNA_pol3_gamma3   4 aqVrdmLGladrarlldlleallegdaaaalaelreqyaaGadpvvvlrdLlellhqltllkvlpeaaedls..lpeeer 81 
                                    +++  +LG++d a + d ++al++ daaa++  ++++++ G dp+ + +dLle ++ l++l+ +p+aa       pe+  
  gi|121639637|ref|YP_979861.1| 235 TRALGLLGVTDVALIDDAVDALAACDAAALFGAIESVIDGGHDPRRFATDLLERFRDLIVLQSVPDAASRGVvdAPEDAL 314
                                    556679***********************************************************777665424889999 PP

                DNA_pol3_gamma3  82 erlkelaeklsleqLqrlWqlllkgieevknapdpraaaEmvLlRlaa 129
                                     r++e a ++  ++L+r+ +++  g+ e + a+ pr+ +E+v  Rl+ 
  gi|121639637|ref|YP_979861.1| 315 DRMREQAARIGRATLTRYAEVVQAGLGEMRGATAPRLLLEVVCARLLL 362
                                    9*******************************************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   4.2e-13   5.4e-10       2     124 ..      39     169 ..      38     174 .. 0.78
   2 ?   -3.3   0.0       9.1   1.2e+04      46      92 ..     182     226 ..     179     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.2e-13
                                    EEESSTTSSHHHHHHHHHHHHTHE..........................EEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgve..........................fleisgsellskyvgesekkirelfkeake 55 
                                    l++Gp G+GKT+ a+ +a++l+                            ++e+++++     v ++ +     f  a  
  gi|121639637|ref|YP_979861.1|  39 LFSGPRGCGKTSSARILARSLNCAqgptanpcgvcescvslapnapgsidVVELDAASHG--GVDDTRELRDRAFY-APV 115
                                    89******************9533344555666666666666666665558888888888..55555555555553.444 PP

                                    TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
                            AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                                    +++  ++++DE++ ++++             n+Ll+ +++  +   ++i+i at++p+k+ p ++ +R 
  gi|121639637|ref|YP_979861.1| 116 QSRYRVFIVDEAHMVTTAG-----------FNALLKIVEEPPE---HLIFIFATTEPEKVLPTIR-SRT 169
                                    4446***************...........***********99...5******************.886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.1
                                    HHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                            AAA  46 irelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                    +r+l++++ e++   +++ D ++ l+ +  g++ +++ +v++qLl+ 
  gi|121639637|ref|YP_979861.1| 182 MRALLARICEQE--GVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAG 226
                                    566666666665..777777777777777777777777888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.7e-09   4.8e-06       9     130 ..      39     154 ..      35     162 .. 0.72
   2 ?   -2.5   0.0       4.5   5.8e+03      57      71 ..     186     213 ..     171     266 .. 0.50
   3 ?   -1.4   0.0       2.1   2.6e+03      41      86 ..     334     380 ..     313     388 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.7e-09
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee....erpevvfvtlpsstsskdl.lrellralglelkaerlsseell.eal 82 
                                    +  G+ G+GKT ++r l+++l+ ++ ++      + ++v+  +++++   ++   el  a +  + +   +++el+ +a+
  gi|121639637|ref|YP_979861.1|  39 LFSGPRGCGKTSSARILARSLNCAQGPTAnpcgVCESCVSLAPNAPG---SIdVVELDAASHG-GVD---DTRELRdRAF 111
                                    567******************76555555444444444444444444...4424455555554.333...699******* PP

                         AAA_22  83 eqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGt 130
                                    +  +++r++  ++i+DEa+ + + + ++ L ++++  + + +li++  
  gi|121639637|ref|YP_979861.1| 112 YAPVQSRYR--VFIVDEAHMV-TTAGFNALLKIVE--EPPEHLIFIFA 154
                                    *********..**********.9999999999999..66666666654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                         AAA_22  57 lrellralglelka.............e 71 
                                    l +++++ g+  ++             +
  gi|121639637|ref|YP_979861.1| 186 LARICEQEGVVVDDavyplviragggsP 213
                                    4444444433333334444444433322 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.1
                         AAA_22  41 evv...fvtlpsstsskdllrellralglelkaerlsseellealeqal 86 
                                    evv   + ++ + t ++ ll+ ++  l l+  +  + +++ll+++e+  
  gi|121639637|ref|YP_979861.1| 334 EVVqagLGEMRGATAPRLLLEVVCARLLLPSAS--DAESALLQRVERIE 380
                                    455445556777788999999999999999988..88888889888765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.2e-09   4.1e-06       2      67 ..       8      69 ..       7      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.2e-09
                         RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgP 67
                                   rP s++e +gqe+v++ l+++++a +  +      l++Gp G Gkt+ a+i+a+ l+     t+ P
  gi|121639637|ref|YP_979861.1|  8 RPASFAEVVGQEHVTAPLSVALDAGRINHA----YLFSGPRGCGKTSSARILARSLNCAQGPTANP 69
                                   9***********************986543....589*******************9988888777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.1e-07   0.00014      22     115 ..      39     145 ..      30     152 .. 0.73
   2 ?   -3.0   0.1         4   5.1e+03      72     100 ..     446     473 ..     426     502 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                         AAA_30  22 vltGpAGtGKttalkalreaweaa.g.........grviglAptgkaAkv...Laeelgieastiakllkrlk.grarle 87 
                                    +  Gp G GKt + + l++ ++ a g         ++ + lAp++  + +   L +++    + + +l +r +   a ++
  gi|121639637|ref|YP_979861.1|  39 LFSGPRGCGKTSSARILARSLNCAqGptanpcgvcESCVSLAPNAPGSIDvveLDAASHGGVDDTRELRDR-AfY-APVQ 116
                                    678**************8888777579********666666666665544100555544455555544433.343.4567 PP

                         AAA_30  88 pg.tllivDEagmvdtkqlaallkaaeka 115
                                    ++ +++ivDEa mv t+ ++allk++e+ 
  gi|121639637|ref|YP_979861.1| 117 SRyRVFIVDEAHMVTTAGFNALLKIVEEP 145
                                    777**********************9985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                         AAA_30  72 tiakllkrlkgrarlepgtllivDEagmv 100
                                    t++ +l   +   +le++tl++  E++ +
  gi|121639637|ref|YP_979861.1| 446 TTEVMLAGATV-RALEDNTLVLTHESAPL 473
                                    44444433332.33444455544444433 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.8e-06    0.0087      82     135 ..     102     152 ..      28     153 .. 0.64
   2 ?   -2.9   0.1         6   7.7e+03      50      84 ..     434     466 ..     425     490 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.8e-06
                         AAA_19  82 dlltealelleeaeeekklqeee.llivDEfqdvd.elqyrLlkallgekkklllv 135
                                    d+       l++++   ++q+++ ++ivDE+ +v+    ++Llk + ++ ++l+++
  gi|121639637|ref|YP_979861.1| 102 DTR-----ELRDRAFYAPVQSRYrVFIVDEAHMVTtAGFNALLKIVEEPPEHLIFI 152
                                    222.....3456677789999**9***********9**********9888889886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6
                         AAA_19  50 ftgrAakelrerlaalgaeatTiHrlalldfddll 84 
                                    +t r   +lr r++++ ++  T+ +l   d++  l
  gi|121639637|ref|YP_979861.1| 434 PTVRDKVRLRSRTTEVMLAGATVRAL--EDNTLVL 466
                                    56666667777777777777777766..4444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.6e-06    0.0033       2      44 ..      12      57 ..      11      78 .. 0.87
   2 ?   -2.4   0.0         2   2.6e+03     148     169 ..     518     539 ..     513     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                   Mg_chelatase  2 lkdvkGqeeakraleiaa.aG..gHnlllvGppGsGKtmlakrlps 44
                                   +++v+Gqe+    l +a  aG  +H  l+ Gp G+GKt  a+ l+ 
  gi|121639637|ref|YP_979861.1| 12 FAEVVGQEHVTAPLSVALdAGriNHAYLFSGPRGCGKTSSARILAR 57
                                   789**************7577445**************99998865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                   Mg_chelatase 148 arfqlvaamNpcpcgklkdkek 169
                                    a++    a+Np+p+++ +++++
  gi|121639637|ref|YP_979861.1| 518 ANVATAKAVNPAPTANSTQRDE 539
                                    66777789*****999887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.8e-06    0.0049       2      49 ..      15      60 ..      14     152 .. 0.87
   2 ?   -1.2   2.0       1.9   2.4e+03     117     117 ..     330     330 ..     218     508 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                         AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellrale 49
                                   +vG e+ ++ L  al++ r +  ++ l+sG++G+GK+s +r l+r+l+
  gi|121639637|ref|YP_979861.1| 15 VVGQEHVTAPLSVALDAGRIN--HAYLFSGPRGCGKTSSARILARSLN 60
                                   577777777777788766665..89******************99986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                         AAA_16 117 s 117
                                    +
  gi|121639637|ref|YP_979861.1| 330 T 330
                                    0 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.9e-06    0.0088      10      79 ..       4      69 ..       2      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.9e-06
                          Rad17 10 fekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnp 79
                                   + ky+P   +e+    +    +  +l+a  ++++     L sGP GCgk+   ++L++ l        np
  gi|121639637|ref|YP_979861.1|  4 YRKYRPASFAEVVGQEHVTAPLSVALDAGRINHA----YLFSGPRGCGKTSSARILARSLNCAQGPTANP 69
                                   6788888888887777777778888888888888....99******************998776666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0034       4.3       3      25 ..      39      61 ..      37      69 .. 0.87
   2 ?    5.4   0.0     0.013        17      49      93 ..     101     146 ..      89     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                                   EEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnr 25
                                   l  Gp G+gK++ a+ la+ ln+
  gi|121639637|ref|YP_979861.1| 39 LFSGPRGCGKTSSARILARSLNC 61
                                   678***************99965 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                                    ........--------.G-SEEEEESGGG--HHHHHHHHHHHHSSE CS
                          AAA_5  49 ngttslvdsplvraar.egeilvlDEveraesevlnsLlslleerr 93 
                                    ++t++l+d +++  ++ + +++++DE +++ ++ +n+Ll++ ee  
  gi|121639637|ref|YP_979861.1| 101 DDTRELRDRAFYAPVQsRYRVFIVDEAHMVTTAGFNALLKIVEEPP 146
                                    67899999999999998889*********************99865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.18       3      91 ..      36     146 ..      35     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell.....................vkkesilyinldderdkkladpekll.elilekl 60 
                                    ++++ +G+R +GKT  ++ l+++l                        + si  ++ld  +    +d+++l  +++ + +
  gi|121639637|ref|YP_979861.1|  36 HAYLFSGPRGCGKTSSARILARSLNcaqgptanpcgvcescvslapNAPGSIDVVELDAASHGGVDDTRELRdRAFYAPV 115
                                    578899***********999999889888888888877777776666666777777777666555544333314444444 PP

                         AAA_14  61 keekktylflDEiqevpew.ekalkslvdegk 91 
                                    ++ + ++++ DE+++v+++ ++al ++v+e +
  gi|121639637|ref|YP_979861.1| 116 QS-RYRVFIVDEAHMVTTAgFNALLKIVEEPP 146
                                    44.67778888888887753567777777664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00053      0.68       3      25 ..      40      71 ..      39     155 .. 0.80
   2 ?   -2.9   0.0       7.2   9.2e+03      95     115 ..     463     482 ..     452     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf.........g 25
                                    +G+ G+GKt+ a+ L+++l++         g
  gi|121639637|ref|YP_979861.1| 40 FSGPRGCGKTSSARILARSLNCaqgptanpcG 71
                                   68*****************9998766666661 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.2
                         AAA_18  95 kkvvLtaspeelleRlekRgy 115
                                       vLt +   l++Rl+++++
  gi|121639637|ref|YP_979861.1| 463 T-LVLTHESAPLARRLSEQRN 482
                                    3.7888888999999998775 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.9      0.16     2e+02      63     156 ..     284     382 ..     216     411 .. 0.63
   2 ?   11.6   0.6   0.00016      0.21      44      84 ..     457     535 ..     423     575 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHTHHHHH.HTS-TTTCGGGHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHT--S--.... CS
                           CHAD  63 raLGeaRDldVllerllsrleerlpaaeqealerllkrlekerkrararvlaaLdsaryqalldaldallaaerle.... 138
                                      L + RDl Vl+ +         +aa++  +++ +++l++ r++a +    + +  ry ++++a    ++ + ++    
  gi|121639637|ref|YP_979861.1| 284 DLLERFRDLIVLQ-S-------VPDAASRGVVDAPEDALDRMREQAARI--GRATLTRYAEVVQAGLGEMRGATAPrlll 353
                                    5566677777766.2.......223334444555555555555554444..33333444444444333332222223555 PP

                                    ...........TSBHHHHHHHHHHHHHHH CS
                           CHAD 139 ...........aepaaaalekrlrkayrk 156
                                               a +a+ al +r+++  ++
  gi|121639637|ref|YP_979861.1| 354 evvcarlllpsASDAESALLQRVERIETR 382
                                    66666664444444444444444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                                    TSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH........................................H CS
                           CHAD  44 pvldkeeaaalekelrwlaraLGeaRDldVllerllsrle.......................................e 84 
                                    ++l ++++  l  e + lar+L+e R++dVl e l+++l                                         
  gi|121639637|ref|YP_979861.1| 457 RAL-EDNTLVLTHESAPLARRLSEQRNADVLAEALKDALGvnwrvrcetgepaaaaspvggganvatakavnpaptansT 535
                                    455.677788889999********************99988888888877777777777755555555555444444430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3880.00
//
Query:       gi|121639638|ref|YP_979862.1|  [L=435]
Description: hypothetical protein BCG_3782c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.1e-180  598.5   0.0   6.9e-180  598.3   0.0    1.0  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase


Domain annotation for each model (and alignments):
>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.3   0.0  3.9e-184  6.9e-180       1     420 [.       6     425 ..       6     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 598.3 bits;  conditional E-value: 3.9e-184
                                    XXX---HHHHHHHHHHHHHHHCC---EES------HHHHHGGGGGGGS--CCC-EE.TTEETTSSS-TT--HHHHHHHHH CS
                 Aminotran_MocR   1 lskealadvlaeleaayealkarGlkldltrGkpadedldlsnallallGeedlraadGtdlrnyGGlaGlpelralfae 80 
                                    ls+++la ++a+ ++ y+al+   l ldltrGkp+ e+ldlsn ll+l+G+ d+r  +Gtd+rnyGG  Glp lra+fae
  gi|121639638|ref|YP_979862.1|   6 LSPQELAALHARHQQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPEGTDTRNYGGQHGLPGLRAIFAE 84 
                                    68899*********************************************5.89999*********************** PP

                                    HTTS-GGGEEE-SS-HHHHHHHHHHHHHHC--TT-SS-GGGG..--EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE- CS
                 Aminotran_MocR  81 lldvkaenvlvqnnsslelqglvltlallhGvrdsegpwvke.ekvkllvtvpGydrhfllleelGielltvdlqddGpd 159
                                    ll++   n+++ nnsslel+++++++++l+G +ds +pw++e + +k+l++vpGydrhf+++e++Gie++ +++ +dGpd
  gi|121639638|ref|YP_979862.1|  85 LLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWIQEqDGIKFLCPVPGYDRHFAITETMGIEMIPIPMLQDGPD 164
                                    ***************************************9862579********************************** PP

                                    HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT CS
                 Aminotran_MocR 160 vdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaapdfrifaddayavhdlvaeedkdanivalardaG 239
                                    vd +e+lva d+++kG+++vp + np+G t+s e +rrl+ +++aapdfr+f+d+ayavh l  + ++++++++la++aG
  gi|121639638|ref|YP_979862.1| 165 VDLIEELVAVDPAIKGMWTVPVFGNPSGVTYSWETVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAG 244
                                    ******************************************************************************** PP

                                    -TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_MocR 240 hpdrafvlastskitfaGaGvafvassedniawlkkylGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfea 319
                                     p+r++v+astskitfaG Gv+f++ s  niaw+ +y G +siGpdkv+qlrh++f+ d++G++ +m ++++++apkf+ 
  gi|121639638|ref|YP_979862.1| 245 NPNRPYVFASTSKITFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDADGVRLHMLRYQQILAPKFAL 324
                                    ******************************************************************************** PP

                                    HHHHHHHHHTTTSSEEE---SBSS-EEEEESSS-HHHHHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHH CS
                 Aminotran_MocR 320 vlevleaelggaevatwteprGGyfisldtldgvakrvvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleeve 399
                                    v evl+++l+ +++a+wtep+GGyfisld+l g+a r+v+la++ G+++t aGa++p+ +dp d+nir+ap++p++ +++
  gi|121639638|ref|YP_979862.1| 325 VAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVALAKDVGIAVTEAGASFPYRKDPDDKNIRIAPSFPSVPDLR 404
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHTT. CS
                 Aminotran_MocR 400 tamdvvatcvklaseeklagq 420
                                    +a+d++atc  la++e l +q
  gi|121639638|ref|YP_979862.1| 405 NAVDGLATCALLAATETLLNQ 425
                                    ***************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2980.71
//
Query:       gi|121639639|ref|YP_979863.1|  [L=254]
Description: hypothetical protein BCG_3783 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   20.1   0.6     0.0096   16.2   0.0    2.1  2  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.7     0.016   2.9e+02      42      83 ..      13      64 ..       2      68 .. 0.58
   2 !   16.2   0.0   5.3e-07    0.0096      24     102 ..      79     172 ..      63     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.016
                        DUF1772 42 lallsalafayla..........araasrgarllylaaaal.lllsivpyTll 83
                                   +++++ ++++y++            ++  +  ++  ++a++ l++  v++Tll
  gi|121639639|ref|YP_979863.1| 13 FSIGAGVLYFYFVlprwpelmgdTGHSLGTGLRIA-TGALVgLAALPVVFTLL 64
                                   35555566665557888888875444444444444.55666566556666665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.3e-07
                        DUF1772  24 llkqwrrlfkrgkavfpplallsalafaylaaraasrgarllylaaaallllsivpyTllvm........vPtN...... 89 
                                     ++ w+ +    +++ ++l +++a++ ++l+ +aa++  +++y aaaa+++l+ + + l ++        +P+       
  gi|121639639|ref|YP_979863.1|  79 SMRIWSIMA---HVLAGALIVGTAISEVWLSLDAAGQWLFGIYGAAAAIAVLGFFGFYLSFVaelpppppKPLKpkkpkq 155
                                    455554444...77788899999999999**************7777779999999888888788888884444444443 PP

                        DUF1772  90 nkLaal...k.eedake 102
                                    ++L ++   k +e++ e
  gi|121639639|ref|YP_979863.1| 156 RRLRRKktaKgDEAEPE 172
                                    55555543311222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1837.36
//
Query:       gi|121639640|ref|YP_979864.1|  [L=233]
Description: cutinase precursor cut5 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-46  158.0   0.3    2.7e-46  157.8   0.3    1.1  1  Cutinase       Cutinase
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.16   11.8   0.0    1.2  1  Abhydrolase_2  Phospholipase/Carboxylesterase
       0.19   11.3   0.0       0.26   10.8   0.0    1.2  1  DUF2974        Protein of unknown function (DUF2974)


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.3   4.5e-50   2.7e-46       1     178 []      37     233 .]      37     233 .] 0.91

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 4.5e-50
                                    ---SEEEEEE--TT--TTTSSHHHHHHHHHHHH.TTT-EEEEE------CGG...STTSS-HHHHHHHHHHHHHHHHH-T CS
                       Cutinase   1 sckdvevifArgttepgglgsvGeavvsalesavgsksvavqgvnYpAdleq...lyegseeagakeaaalvqslaskCP 77 
                                    +c+dvev+fArgt+ep+g+gsvG ++v+al+s+vg+ks++v++vnYpA+++     + ++  +g+++a +++qs+a +CP
  gi|121639640|ref|YP_979864.1|  37 PCPDVEVVFARGTGEPPGIGSVGGLFVDALRSQVGAKSLGVYAVNYPASNDFassDFPKTVIDGIRDAGSHIQSMAMSCP 116
                                    6************************************************9976666678899****************** PP

                                    T-EEEEEEETHHHHHHHHHHTT..............S-HHHHHHEEEEEEES-TTC......CCCTTS-TTS-GGGEEEE CS
                       Cutinase  78 dtkivlgGYSqGaqvidnaiegga......tat...lpaavadkvaavvlfGdpsn......vaglpevsklyaskiksl 142
                                    +t+ vlgGYSqGa+v+  ++++ +      +a    + ++va++vaav lfG ps+      +a+  ++ +ly+ k+ +l
  gi|121639640|ref|YP_979864.1| 117 QTRQVLGGYSQGAAVAGYVTSAVVppavpvQAVpapMAPEVANHVAAVTLFGAPSAqflgqyGAPPIAIGPLYQPKTLQL 196
                                    ***************988887755777998433567*******************9887654444449************ PP

                                    --TT-GGGTS----GGGG-GGGG..HHHHHHHHHHH- CS
                       Cutinase 143 CdagDpiCgsgneleaHlsYvsey.ttqaakFvvskl 178
                                    C++gD iCg+gn+  aH  Y+ ++ + q a+F++s+l
  gi|121639640|ref|YP_979864.1| 197 CADGDSICGDGNSPVAHGLYAVNGmVGQGANFAASRL 233
                                    *********************99999******99985 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.16      98     124 ..     111     137 ..      96     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                    HHTT--GGGEEEEEETHHHHHHHHHHH CS
                  Abhydrolase_2  98 lkkgipssriiigGFSqGaalalylal 124
                                    ++ + p+ r ++gG+SqGaa+a y + 
  gi|121639640|ref|YP_979864.1| 111 MAMSCPQTRQVLGGYSQGAAVAGYVTS 137
                                    5667899999***********988765 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.3e-05      0.26      68     105 ..     101     139 ..      87     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.3e-05
                        DUF2974  68 qesAlkYlnkileesegk.iylgGhSkGGnlAvyaamna 105
                                     ++A + +++++   +++  +lgG+S+G+ +A y+   +
  gi|121639640|ref|YP_979864.1| 101 IRDAGSHIQSMAMSCPQTrQVLGGYSQGAAVAGYVTSAV 139
                                    57788999999999999879**************98873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1765.59
//
Query:       gi|121639641|ref|YP_979865.1|  [L=333]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-20   72.4   0.0    8.9e-20   71.2   0.0    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.2e-14   54.1   0.0    1.7e-14   53.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-14   54.3   0.7    2.9e-14   53.4   0.7    1.5  1  NAD_binding_10   NAD(P)H-binding
    3.2e-12   46.2   0.8    4.5e-10   39.1   0.8    2.7  1  NAD_binding_4    Male sterility protein
    4.9e-10   39.3   0.0    6.2e-10   39.0   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.5e-09   37.1   0.0    1.1e-08   34.9   0.2    1.8  2  NmrA             NmrA-like family
    1.3e-08   34.4   0.0    2.2e-08   33.6   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.8e-07   30.2   0.4    1.3e-06   28.0   0.4    1.9  1  adh_short        short chain dehydrogenase
    4.6e-07   29.2   0.1    6.4e-07   28.8   0.1    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    7.2e-06   26.0   0.5    1.9e-05   24.7   0.5    1.6  1  KR               KR domain
      0.004   16.7   0.8       0.01   15.4   0.8    1.7  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
      0.021   14.5   0.1      0.034   13.8   0.1    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.038   14.4   4.2       0.45   10.9   0.3    2.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
        0.1   12.5   0.1       0.15   11.9   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0     7e-23   8.9e-20       1     232 [.       8     227 ..       8     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 7e-23
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S.- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAa.v 74 
                                    +lVtG+tGf+G  ++ka++++g+ v  l r++ + +t+  + l     ++  +d+ dr++++++++  ++dav+h Aa v
  gi|121639641|ref|YP_979865.1|   8 VLVTGGTGFVGGWTAKAIADAGHSVRFLVRNPARLKTSVAK-LgvdvsDFAVADISDRDSVREALN--GCDAVVHSAAlV 84 
                                    79****************************96666655443.36999*******************..**********99 PP

                                    --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSCSSSSBSTCSTTS--.--SSHHHHHHHHHHHH CS
                      Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkdaeqpkeettltgpl.kpnspYaaaKlagekl 152
                                    ++ +++ ++   ++ +n++g++n+l  a + g++ ++++sS ++++ ++  +  + ++   p+   +  Y+ +K+ +e +
  gi|121639641|ref|YP_979865.1|  85 ATDPRETSR---MLSTNMAGAQNVLGQAVELGMDPIVHVSSfTALFRPNLAT-LSADL---PVaGGTDGYGQSKAQIEIY 157
                                    999997666...777**************************76666555553.77777...9999*************** PP

                                    HHHHHHHHT-EEEEEEESEEESTTS-TTS...TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHH CS
                      Epimerase 153 veayaaqyglnaiilrlfnlyGprngege...vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehv 229
                                    ++ +++++  ++ i+ +  + Gp  g+++    ++v +al  +        ++ g g a +  ++v+Dva ++ ++le  
  gi|121639641|ref|YP_979865.1| 158 ARGLQDAG-APVNITYPGMVLGPPVGDQFgeaGEGVRSALWMH--------VIPGRGAA-WLIVDVRDVAALHAALLES- 226
                                    **997777.899999999****995554420133333333222........33344433.4456666666666666666. PP

                                    TT- CS
                      Epimerase 230 dag 232
                                      g
  gi|121639641|ref|YP_979865.1| 227 --G 227
                                    ..4 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.3e-17   1.7e-14       1     122 [.       9     128 ..       9     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.3e-17
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvd 78 
                                    +vtGg+GF+G    k++ ++++   vr l +r+  +l+ ++ k++v+   +  +D+ d d+++eal+g d+v+h a+lv 
  gi|121639641|ref|YP_979865.1|   9 LVTGGTGFVGGWTAKAIADAGH--SVRFL-VRNPARLKTSVAKLGVDVsdFAVADISDRDSVREALNGCDAVVHSAALVA 85 
                                    69*******************5..99987.88889999999998887666*************************99999 PP

                      3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                         ++ ++ + n+ G +nvl  +v+ g+  +v++Ss  + + 
  gi|121639641|ref|YP_979865.1|  86 TDP-RETSRMLSTNMAGAQNVLGQAVELGMDPIVHVSSFTALFR 128
                                    888.566679*****************************99985 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.7   2.3e-17   2.9e-14       1     102 [.      12     126 ..      12     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.3e-17
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEE...EE--TT-CCHHHHHHTT-SEEEES-...--TCC. CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglev...vegdvtdvedlaealkgadaVvsal...ggggk. 73 
                                    G+tG vG   +k ++++ gh+v+ lvRnp++l+   a+ g++v    ++d++d ++++eal+g+daVv ++   +   + 
  gi|121639641|ref|YP_979865.1|  12 GGTGFVGGWTAKAIADA-GHSVRFLVRNPARLKTSVAKLGVDVsdfAVADISDRDSVREALNGCDAVVHSAalvA---Td 87 
                                    9***********99999.5*************977678888872225589999*************988885652...32 PP

                                    ...HHHH.........HHHHHHHHHHCT--EEEEEEETTTT CS
                 NAD_binding_10  74 ...deeg.........aknivdaakeagvkRfvlvsaigvg 102
                                       +  +         a+n++  a e g+  +v vs++ + 
  gi|121639641|ref|YP_979865.1|  88 preT--SrmlstnmagAQNVLGQAVELGMDPIVHVSSFTAL 126
                                    2232..2346666677*********************9986 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.8   3.5e-13   4.5e-10      71     211 ..      63     181 ..      10     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.5e-13
                                    SGGGG--HHHHHHHHHH--EEEE--SS-S.ST.TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT- CS
                  NAD_binding_4  71 eprlGLseedlqelaeevdviihsaAtvnfde.pykellrvNveGtrevlelakklkklkvllhvST..ayvngeregev 147
                                    +       ++++e  + +d+++hsaA v  d  +++++l++N+ G+++vl  a +l    +++hvS+  a ++++  +  
  gi|121639641|ref|YP_979865.1|  63 D------RDSVREALNGCDAVVHSAALVATDPrETSRMLSTNMAGAQNVLGQAVELGMD-PIVHVSSftALFRPNLATL- 134
                                    3......35788999***************9857899*******************999.******8655555555532. PP

                                    -SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SS CS
                  NAD_binding_4 148 eekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesk 211
                                                     +    +g +++Y qsKa  E   r  ++  g pv+i  p++++g ++
  gi|121639641|ref|YP_979865.1| 135 ----------------SADLPVAGGTDGYGQSKAQIEIYARGLQDA-GAPVNITYPGMVLGPPV 181
                                    ................23344567889*****************88.*************9543 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   4.9e-13   6.2e-10       1     129 [.       9     122 ..       9     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 4.9e-13
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG++Gf+G ++a+ + + g+ v  +vr+ + ++t ++++l  d          +  +D++D++s++++l+ +  d+v+
  gi|121639641|ref|YP_979865.1|   9 LVTGGTGFVGGWTAKAIADAGHSVRFLVRNPARLKT-SVAKLGVDV-------SDFAVADISDRDSVREALNGC--DAVV 78 
                                    9*****************************999985.577887655.......36999**************98..9*** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEE CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSt 129
                                    + AA  +  +   +  +++ +n+ G++++L  + +lg+++   ++++S+
  gi|121639641|ref|YP_979865.1|  79 HSAALVA--TDPRETSRMLSTNMAGAQNVLGQAVELGMDP---IVHVSS 122
                                    ***9855..55577889**************999999874...566665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   8.5e-12   1.1e-08       1      72 [.       8      81 ..       8     102 .. 0.84
   2 ?   -0.9   0.0      0.78     1e+03     121     196 ..     150     226 ..     149     256 .. 0.55

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.5e-12
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEE...EES-TT-HHHHHHHHTT-SEEEE-- CS
                           NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvel...vkgdlddkeslvealkgvdvvfsvt 72
                                   +lv+G+TG  G+  ++a+++agh+vr lvR++ + l +s+++ Gv +     +d+ d++s++eal+g d+v  + 
  gi|121639641|ref|YP_979865.1|  8 VLVTGGTGFVGGWTAKAIADAGHSVRFLVRNPAR-LKTSVAKLGVDVsdfAVADISDRDSVREALNGCDAVVHSA 81
                                   79******************************54.446777777766222689****************998665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                                    HHHHHHHHHHHC...TS-EEEEEE-EEGGG-BSSS-SS-BEEE-TTS...-EEEEESS-TTS-EE-HHHHHHHHHHHHHH CS
                           NmrA 121 sKaeieeyvral...gipytfvyagffmenflsllaqlkvgdtapped..kvtllgpgnpkavlldaeeDiGafvikilk 195
                                    sKa+ie y r l   g p  + y+g+  +   +     ++g+  ++     +    pg   a l+++++D++a  +++l+
  gi|121639641|ref|YP_979865.1| 150 SKAQIEIYARGLqdaGAPVNITYPGMVLGPPVGD----QFGEAGEGVRsaLWMHVIPGRGAAWLIVDVRDVAALHAALLE 225
                                    6777777777666666666666666533333222....222222222200333345666556666777777777777666 PP

                                    H CS
                           NmrA 196 d 196
                                     
  gi|121639641|ref|YP_979865.1| 226 S 226
                                    4 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.7e-11   2.2e-08       1     131 [.       8     125 ..       8     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.7e-11
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    vlvtG++G +G    + i++   ++++ l r+  +l +   +l  ++++    +     ++d+ d++++++al+  ++d+
  gi|121639641|ref|YP_979865.1|   8 VLVTGGTGFVGGWTAKAIADAG-HSVRFLVRNPARLKTSVAKLGVDVSD----F----AVADISDRDSVREALN--GCDA 76 
                                    89*********99999888875.45666666666666655556333333....3....59**************..**** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA 131
                                    v+h+AAl  V +  +++  +++tN+ g++nv+  a+e g++ +v +S+  A
  gi|121639641|ref|YP_979865.1|  77 VVHSAAL--VATDPRETSRMLSTNMAGAQNVLGQAVELGMDPIVHVSSFTA 125
                                    ******9..55666667889***************************8655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.4   1.1e-09   1.3e-06       3     170 ..       8     168 ..       6     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-09
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    vlvtG+++ +G  +ak++a +G +v ++ r++++l++ +++l+ +     ++ +D++dr++v+++++ +       d++v
  gi|121639641|ref|YP_979865.1|   8 VLVTGGTGFVGGWTAKAIADAGHSVRFLVRNPARLKTSVAKLGVD--VSDFAVADISDRDSVREALNGC-------DAVV 78 
                                    9******************************************75..578999*********9999988.......**** PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH.HHHCTTEEEEEEEEGGGTSB-TTBHH............H CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpa.mlkqssGrIvnvsSvagkvpvagvaa............Y 149
                                    + A++        ++ +e+ r++++N+ g+ ++  ++++  m+      Iv vsS +++ + +  +             Y
  gi|121639641|ref|YP_979865.1|  79 HSAAL------VATDPRETSRMLSTNMAGAQNVLGQAVELgMD-----PIVHVSSFTALFRPNLATLsadlpvaggtdgY 147
                                    *****......5678889************9999999888344.....78888888774332211110111111222226 PP

                                    HHHHHHHHHHHHHHHHHHGGG CS
                      adh_short 150 sAsKaavagltrslakelapt 170
                                    + sKa ++ ++r l++  ap 
  gi|121639641|ref|YP_979865.1| 148 GQSKAQIEIYARGLQDAGAPV 168
                                    666666666666666666664 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1     5e-10   6.4e-07       1     101 [.       6     122 ..       6     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5e-10
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE---- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...................eldltdaeavaellkeakpdvvvnaAAy 61 
                                    m++lvtG++G +G   ak++a +g++v  l r+                    +d++d+++v+e+l+   +d+vv+ AA 
  gi|121639641|ref|YP_979865.1|   6 MRVLVTGGTGFVGGWTAKAIADAGHSVRFLVRNparlktsvaklgvdvsdfaVADISDRDSVREALNG--CDAVVHSAAL 83 
                                    89**********************9999999999*****************99*************99..99******** PP

                                    --HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEE CS
                  RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaavga.lLihvSt 101
                                     a D  E+ + +    n+ +++++  +a + g+ +++hvS+
  gi|121639641|ref|YP_979865.1|  84 VATDPRETSRML--STNMAGAQNVLGQAVELGMdPIVHVSS 122
                                    *****9988765..6799999999999999997689***98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   1.5e-08   1.9e-05       3     141 ..       8     127 ..       7     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.5e-08
                                    EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEE.E----TT-HHHHHHHHHHHHHHSS- CS
                             KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaeve.vvaaDvsdkdavealleeikaeepp 81 
                                    +l+tGG+G +G  +a+ +a+ g + + +l R++      ++l +++++lg++v+ ++ aD+sd+d+v+++l+ ++     
  gi|121639641|ref|YP_979865.1|   8 VLVTGGTGFVGGWTAKAIADAGHS-VRFLVRNP------ARLKTSVAKLGVDVSdFAVADISDRDSVREALNGCD----- 75 
                                    69******************9964.66777882......2344567889**99725568**************98..... PP

                                    --EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagll 141
                                       v+h+A +++      ++  +  ++l+  ++Ga+n+     +  +d +v +SS  +l+
  gi|121639641|ref|YP_979865.1|  76 --AVVHSAALVA------TDPRETSRMLSTNMAGAQNVLGQAVELGMDPIVHVSSFTALF 127
                                    ..8999997665......567788899999999999988888889999999999999886 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   7.9e-06      0.01       9     115 ..      20     111 ..      17     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.9e-06
                                    HHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE...EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG... CS
                   adh_short_C2   9 aiAkalaeeGaevvltdlneeakkrveelaeelgaev...lecDVtdeeqvealveevvekfgklDilvnnagiapk... 82 
                                     +Aka+a++G +v +  +n ++   +++ +++lg +v     +D++d+++v+++       +++ D +v++a+ + +   
  gi|121639641|ref|YP_979865.1|  20 WTAKAIADAGHSVRFLVRNPAR---LKTSVAKLGVDVsdfAVADISDRDSVREA-------LNGCDAVVHSAALVATdpr 89 
                                    58*******************9...55555556655433399999999988766.......56799*******9998444 PP

                                    CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH CS
                   adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaalp 115
                                     ++++l+t+ ++ ++           ++ +a++
  gi|121639641|ref|YP_979865.1|  90 ETSRMLSTNMAGAQN-----------VLGQAVE 111
                                    444444444444444...........4444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-05     0.034       5      47 ..      13      57 ..       9      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                   S-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT CS
                           ApbA  5 GaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg 47
                                   G+G +G+  a  +a ag+ v +++r++ rl++ + k G+++++  
  gi|121639641|ref|YP_979865.1| 13 GTGFVGGWTAKAIADAGHSVRFLVRNPaRLKTsVAKLGVDVSDFA 57
                                   99*****************************99999999998765 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00035      0.45       1      98 [.      12     139 ..      12     142 .. 0.55
   2 ?    4.4   0.3     0.036        46      11      68 ..     158     225 ..     151     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg.........................apeleedgvrvhrlpvprrpspla 55 
                                    gG g +   +a+a a++Gh+V+ l+++pa+                          +++l++  + vh+  + ++  p+ 
  gi|121639641|ref|YP_979865.1|  12 GGTGFVGGWTAKAIADAGHSVRFLVRNPARLktsvaklgvdvsdfavadisdrdsvREALNGCDAVVHSAALVATD-PRE 90 
                                    67777777899**************999999555555555555555555554333333344445555555444332.122 PP

                Glyco_trans_4_4  56 dlaal....ralrrll.rqrrerpd.vvhahsptaglaarlarrrrgip 98 
                                    + ++l    ++++ +l ++ + + d +vh+ s+ta +   la + +++p
  gi|121639641|ref|YP_979865.1|  91 TSRMLstnmAGAQNVLgQAVELGMDpIVHVSSFTALFRPNLATLSADLP 139
                                    1111122223444444422344444577777777666555665555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                Glyco_trans_4_4  11 araLaarGheVtvlt.....papapgapeleedgvr....vhrlpvprrpspladlaalralrrll.r 68 
                                    ar+L+++G+ V +        +p ++++ + ++gvr     h +p + + ++  d++ ++al ++l +
  gi|121639641|ref|YP_979865.1| 158 ARGLQDAGAPVNITYpgmvlGPPVGDQFGEAGEGVRsalwMHVIPGRGAAWLIVDVRDVAALHAALlE 225
                                    8999*****99997655554333333444555555533227788888888999999999999999842 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00012      0.15       6      75 ..      13      82 ..       7     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                   --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHH CS
                        3HCDH_N  6 GaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdlee 75
                                   G+G +G   a+++a ag++V+ + +++++l+++ +k+   ++ ++ +   ++++v++al+   +  + ++
  gi|121639641|ref|YP_979865.1| 13 GTGFVGGWTAKAIADAGHSVRFLVRNPARLKTSVAKLGVDVSDFAVADISDRDSVREALNGCDAVVHSAA 82
                                   78***********************************999999988888888888887776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2502.32
//
Query:       gi|121639642|ref|YP_979866.1|  [L=397]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-11   43.2   0.2    5.8e-10   39.2   0.1    2.5  2  ADH_zinc_N   Zinc-binding dehydrogenase
      1e-10   41.5   0.1    1.1e-09   38.1   0.0    2.5  2  ADH_N        Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.056   12.9   0.0       0.18   11.3   0.0    1.8  2  Glu_dehyd_C  Glucose dehydrogenase C-terminus


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   9.8e-14   5.8e-10       1     129 [.     175     345 ..     175     346 .. 0.84
   2 ?   -3.8   0.0         2   1.2e+04      58      70 ..     363     375 ..     360     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 9.8e-14
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET...........TTCHHHHHHHHHT.............. CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadeviny...........keadlverikelt.............. 54 
                                    ++Gla++ ++k  G+ +via d s+ +++la   Gad v+++                                      
  gi|121639642|ref|YP_979866.1| 175 PIGLAVICMLKSRGVhTVIASDFSPGRRALATACGADSVVDPvqdspyavaagL-----------Gqgnrhlqsildafd 243
                                    79****************************************765555555550...........444555555555556 PP

                                    ............................TTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEEEHHHHHHTT CS
                     ADH_zinc_N  55 ............................ggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeeefdlrnlllke 106
                                                                 + +  v+fecvG++  ++  ++++    r+vvvG+ +g +++++++ + ke
  gi|121639642|ref|YP_979866.1| 244 lavgtveslqrlrlpwwhlwraaeaagaATPKRPVIFECVGVPGIIDGIIASAPLFSRVVVVGVCMGSDHIRPAMAINKE 323
                                    77777777777778888888999888663447789*****************************999999********** PP

                                    -EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N 107 ksilGsllgslreefkealdlla 129
                                    ++++ +l+++ + ef++ l++la
  gi|121639642|ref|YP_979866.1| 324 INLRFVLGYT-PLEFRDTLHMLA 345
                                    *********9.999999998876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                                    SEEEEEESSCSHH CS
                     ADH_zinc_N  58 gvdvvfecvGsga 70 
                                    gv ++f+++G+++
  gi|121639642|ref|YP_979866.1| 363 GVAAAFDALGDPE 375
                                    7899999999876 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.8e-13   1.1e-09       2      66 ..      24     102 ..      23     135 .. 0.88
   2 ?   -3.4   0.0       1.5   8.9e+03       8      19 ..     302     314 ..     301     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.8e-13
                                    TEEEEEEEEEEE-HHHHHHHTTS.............TTTTSSSSEE---EEEEEEEEESTT-CS.--TT-EEEE-SEEE CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkgg.............kelevklplilGHEivGeveevgpevkk.lkvGdrVvveplis 66 
                                    g++l++v  +giCgsDlh   +              + ++ ++ +++GHE++Gev++ gp++++  + G+ Vv+ pl  
  gi|121639642|ref|YP_979866.1|  24 GQLLLDVLRCGICGSDLHARLHCdeladvmaesgyhAFMRSNQQVVFGHEFCGEVVDYGPGTRRtPRRGTPVVAMPLLR 102
                                    68899*************998878999****9999889999999*****************9996789****9988765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                    EEEEEE-.HHHHH CS
                          ADH_N   8 vkaagiC.gsDlh 19 
                                    v ++g+C gsD  
  gi|121639642|ref|YP_979866.1| 302 VVVVGVCmGSDHI 314
                                    7788999455553 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     3e-05      0.18      30      61 ..     164     193 ..     142     224 .. 0.70
   2 ?   -1.7   0.0      0.27   1.6e+03     169     200 ..     339     369 ..     269     381 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                    Glu_dehyd_C  30 epesalvlGaGslGLLalalleaeerglervy 61 
                                    + + a+v+G G++GL  + +l++  rg+++v 
  gi|121639642|ref|YP_979866.1| 164 KGDVAIVIGCGPIGLAVICMLKS--RGVHTVI 193
                                    4578*************999985..7877553 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.27
                    Glu_dehyd_C 169 aavdtLaalpeslldelvtkvvdldeleeAfe 200
                                     +++ La  + +  + l+t+ v+l  +++Af+
  gi|121639642|ref|YP_979866.1| 339 DTLHMLADGKVN-AAPLITGTVGLPGVAAAFD 369
                                    333333333222.4557777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2888.85
//
Query:       gi|121639643|ref|YP_979867.1|  [L=602]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-17   62.7   0.0      2e-16   60.4   0.0    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
    5.4e-12   45.3   0.0    0.00064   18.6   0.1    3.1  3  MCRA            MCRA family
    1.5e-11   44.3   0.2    3.5e-11   43.2   0.2    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-10   41.1   0.1    1.5e-06   28.0   0.2    2.2  2  DAO             FAD dependent oxidoreductase
      3e-09   36.6   0.0    0.00032   20.0   0.1    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.8e-08   32.9   0.5     0.0042   15.8   4.0    2.3  2  HI0933_like     HI0933-like protein
    3.4e-08   33.1   0.3    7.9e-06   25.4   1.1    2.2  2  FAD_binding_3   FAD binding domain
    1.8e-07   30.6   6.8    0.00034   19.8   6.4    2.3  2  FAD_binding_2   FAD binding domain
    8.5e-07   29.4   0.3      0.002   18.6   0.9    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.9e-05   24.2   0.5    5.3e-05   22.7   0.9    1.5  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00052   19.3   1.3    0.00088   18.6   1.3    1.3  1  Thi4            Thi4 family
     0.0022   17.1   3.2     0.0045   16.1   3.2    1.5  1  GIDA            Glucose inhibited division protein A
     0.0038   16.6   0.1     0.0061   15.9   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.026   14.5   0.0         11    5.9   0.1    2.9  3  NAD_binding_9   FAD-NAD(P)-binding
      0.029   14.2   0.0      0.046   13.6   0.0    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.11   13.0   0.1       0.21   12.1   0.1    1.5  1  XdhC_C          XdhC Rossmann domain
       0.55    9.0   4.2       0.81    8.5   3.3    1.6  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   1.9e-19     2e-16       1     267 [.      17     324 ..      17     376 .. 0.69
   2 ?   -2.6   0.0       2.4   2.6e+03     435     451 ..     521     537 ..     490     538 .. 0.67

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.9e-19
                                    HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET.TEEEESS--EEETTTHHHHHHHHHTTCCCCEE..EESCC...G CS
                  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsd.GylielGamwftgagnpllellkelgledsls..lpdpg...a 74 
                                    +aGLaaA  L++aG++Vt+ Ea + +GG++ + r+  G++ e    ++t++++ ll+l+ ++  e++++      +   +
  gi|121639643|ref|YP_979867.1|  17 IAGLAAAMILAEAGVRVTLCEAASEAGGKAKSLRLAdGHPTEHSLRVYTDTYQTLLTLFSRIPTEHDRTmlD---NlvgV 93 
                                    8***********************************9*****************************999542...22233 PP

                                    CEEEEETTEECC.............................TTEECHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHHHHH CS
                  Amino_oxidase  75 pkrvlskggref.............................pgdlspvpaewealleqgals.aellsleeklrlgleal 124
                                         +++g +                                +l + p+ + +l++ g  + + l+ l ++lrl +   
  gi|121639643|ref|YP_979867.1|  94 SMVSATAQGVIGriaapvalqrrrptfariigkvvepprqlVRILLRGPMVIVGLAQRGVPAtDVLHYLYAHLRLLWMCR 173
                                    33333333443377799999999888889974444444444333333344444444422222544444444444444333 PP

                                    H.......HHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTT..TTCBHHHHTCCCCHH CS
                  Amino_oxidase 125 l.......qktldeldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdp..selsaklalpllwel 195
                                            +  +++  +   ++a++ e++++  p   +v  r   + +  +  ++ glf+ +   ++++ +++lp+ + +
  gi|121639643|ref|YP_979867.1| 174 ErllaelgDISYADYLQLGCKSAQAQEFFSA-VPRI-YVAARTSAEAAAIAPIVLKGLFRLKSncPSALNDAKLPAIMMM 251
                                    3666777633333333333333334344444.4444.4666666667777777777777765555**************9 PP

                                    HHHTSCCCEETTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEET.TSTEEEESEEEE-S-HHHHH.......S CS
                  Amino_oxidase 196 egfggslllprgGlsqlpealaeelrgldirlntrVkeikregdgvtvtle.dgevveaDaVvvTvplgvlk.......a 267
                                     g  ++ +      +  +++l++  +g+di++ntrV +++ +++ vt  ++ dg+ + +D+ +++vp  +l+        
  gi|121639643|ref|YP_979867.1| 252 DGPTSERM-----VDPWIRHLTR--LGVDIHFNTRVGDLEFDDGRVTALISsDGRRFACDYALLAVPYLTLRelaksahV 324
                                    99999955.....59********..****************66665555444****************999955543222 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                    TSHHHHHHHHHHHHHHH CS
                  Amino_oxidase 435 gtvegAilSGlraAari 451
                                     t+e+A  SG  aA++i
  gi|121639643|ref|YP_979867.1| 521 PTMEKAACSGYLAARQI 537
                                    47999999999999998 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   6.1e-07   0.00064       3      90 ..       9      90 ..       7     102 .. 0.82
   2 !   12.7   0.0   3.9e-05     0.041     206     237 ..     257     288 ..     243     301 .. 0.85
   3 !   10.3   0.0   0.00021      0.22     355     424 ..     365     437 ..     345     450 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.1e-07
                                   EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B.-TT-HHHHHHHTTSB-SSSTT CS
                           MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggrel.eehyeclwdLlssipSleepg 83
                                   ++ + G+Gia+LaaA+ L +     g ++++ e+ + agg+ ++ + ++ G+ ++    + + +y++l  L+s+ip+   ++
  gi|121639643|ref|YP_979867.1|  9 HVVIAGAGIAGLAAAMILAEA----GVRVTLCEAASEAGGKAKSLRLAD-GHPTEHSLRVyTDTYQTLLTLFSRIPTE--HD 83
                                   67899***********99764....679**************9998888.87776655444***************95..45 PP

                                   SBHHHHH CS
                           MCRA 84 asvldei 90
                                   +++ld++
  gi|121639643|ref|YP_979867.1| 84 RTMLDNL 90
                                   6777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.9e-05
                                    HHCCHHHHHHHHHTT-EEE-SEEEEEEEEEEE CS
                           MCRA 206 eslilPlvkyLkeqgVdfqfntkVtdiefeee 237
                                    e ++ P +++L++ gVd++fnt+V d+ef++ 
  gi|121639643|ref|YP_979867.1| 257 ERMVDPWIRHLTRLGVDIHFNTRVGDLEFDDG 288
                                    889**************************943 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00021
                                    -EEETT-TT-EEEE--SS-SSTT-..-TT-.EEEEEEES-SSSB-SSS-SBGGG--HHHHHHHHHHHHT--HH CS
                           MCRA 355 lvtlkdSnwllsivvnrqphfkeQ..pedv.tvlwgYglfpekeGdyvkKpmlectGeEileEllyhLgvpee 424
                                    + t  +S+w l +v++    +k+   pe++  vl +    +e++G   ++p++ect +Eil+E l + g++++
  gi|121639643|ref|YP_979867.1| 365 VTTHLQSQWSLVCVLQGEGFWKNVrlPEGTrYVLSITWSDVETPGPVFDRPLSECTPDEILTECLTQCGLDKS 437
                                    5566788888888888888888752234331466666677899************************999754 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2   3.3e-14   3.5e-11       1      66 [.      12      76 ..      12      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.3e-14
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TTCEECTS---EEETTHHHHCHHHHC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pgvrvdygahifhgsgyypnvrrllr 66
                                   I GaG++Gl+aA  La+ag++v+l e+++  GG+a+s ++ +g++ ++  ++++++  y+ + +l+ 
  gi|121639643|ref|YP_979867.1| 12 IAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKAKSLRLaDGHPTEHSLRVYTDT--YQTLLTLFS 76
                                   67**************************************889************5..788888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.2   1.4e-09   1.5e-06       1      34 [.       9      44 ..       9      87 .. 0.88
   2 !   11.1   0.0    0.0002      0.21     152     205 ..     263     314 ..     156     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.4e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                   +vvi G+Gi+Gl++A+ La++g  Vtl+e++++ag 
  gi|121639643|ref|YP_979867.1|  9 HVVIAGAGIAGLAAAMILAEAGvrVTLCEAASEAGG 44
                                   79*****************************99994 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                      r + +lGv+i+++t+v +le +dg+v+ +   ++ g+++a+d+  +a  ++ +
  gi|121639643|ref|YP_979867.1| 263 WIRHLTRLGVDIHFNTRVGDLEFDDGRVTAL--ISSdGRRFACDYALLAV-PYLT 314
                                    6788999**************9999*****9..55559888889999998.6654 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1     3e-07   0.00032       2      31 ..       9      38 ..       8      82 .. 0.86
   2 !   14.0   0.0   2.1e-05     0.022     185     235 ..     259     310 ..     243     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvel 31
                                   +vv+ G+G+AGlaaa+ la+ag++vtl+e+
  gi|121639643|ref|YP_979867.1|  9 HVVIAGAGIAGLAAAMILAEAGVRVTLCEA 38
                                   79999********************99973 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvav 235
                                    + +   ++l++ Gv+++++t+v +++ ++ +++ ++ +dg+++++d+ ++av
  gi|121639643|ref|YP_979867.1| 259 MVDPWIRHLTRLGVDIHFNTRVGDLEFDDGRVTaLISSDGRRFACDYALLAV 310
                                    445556899*****************99998888***************998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   4.0     4e-06    0.0042       2      38 ..       9      45 ..       8      48 .. 0.94
   2 !   11.1   0.0   0.00011      0.11     107     162 ..     255     310 ..     249     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                   +v++ G+G AGl aA+ +a++g rV+l e+a+++g K
  gi|121639643|ref|YP_979867.1|  9 HVVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGK 45
                                   79*******************************9998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                    -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                    HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                    ++e++vd ++++l++ gv+++ +t+v ++e +++++  +  ++++++++d+ +lA+
  gi|121639643|ref|YP_979867.1| 255 TSERMVDPWIRHLTRLGVDIHFNTRVGDLEFDDGRVTALISSDGRRFACDYALLAV 310
                                    68999**************************99998888889*********99995 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.1   7.5e-09   7.9e-06       1      40 [.       7      46 ..       7      54 .. 0.87
   2 ?    4.7   0.0     0.014        15     112     157 ..     264     305 ..     212     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.5e-09
                                   EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp 40
                                   +t V+I GaG aGl +a++L+eaGvrv+l e  s++  + 
  gi|121639643|ref|YP_979867.1|  7 DTHVVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKA 46
                                   689***************************9998876555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                                    HHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEE CS
                  FAD_binding_3 112 vehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakY 157
                                    + h+++ g++++f+t+v  le d+  vta + +   g  +++ ++Y
  gi|121639643|ref|YP_979867.1| 264 IRHLTRLGVDIHFNTRVGDLEFDDGRVTALISSD--G--RRFACDY 305
                                    45789************************88754..2..3466666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   6.4   3.2e-07   0.00034       2      38 ..      10      46 ..       9      54 .. 0.91
   2 !    9.0   0.0    0.0006      0.63     138     187 ..     254     300 ..     212     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.2e-07
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                   v++ G+G+AGLaAA+ +aeaG +v++ e ++e gg +
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKA 46
                                   9******************************999954 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0006
                                    .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCE CS
                  FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgre 187
                                     t  +++ + ++++ ++gvd++++t++ +L  +dgrvt  + +   +gr+
  gi|121639643|ref|YP_979867.1| 254 PTSERMVDPWIRHLTRLGVDIHFNTRVGDLEFDDGRVTALISS---DGRR 300
                                    477899*******************************987655...5555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.9   1.9e-06     0.002       1      35 [.       9      43 ..       9      53 .. 0.93
   2 !    7.8   0.0    0.0047         5      42      76 ..     259     293 ..     246     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +vv+ G+G  gl +A +lae g +Vt++e++++  
  gi|121639643|ref|YP_979867.1|  9 HVVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAG 43
                                   89***************************998765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0047
                                    HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                      Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesv 76 
                                    + + + ++l+++g+++++nt+v  +e ++  v+++
  gi|121639643|ref|YP_979867.1| 259 MVDPWIRHLTRLGVDIHFNTRVGDLEFDDGRVTAL 293
                                    45556899*****************9777657665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.9   5.1e-08   5.3e-05       2      63 ..      10      71 ..       9     105 .. 0.80
   2 ?   -3.5   0.0       4.7   4.9e+03      98     125 ..     268     295 ..     253     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.1e-08
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiaref 63
                                   vv+ G+g+aG+aAA+  a+aG +v L e     GG +   l+ +d +++ ++ +v t +++ +
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKAK-SLRLADGHPTEHSlRVYTDTYQTL 71
                                   9**********************************975.455666665544455555555555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                   FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtv 125
                                    ++ gv++ +ntr+ + e +++r+++++ 
  gi|121639643|ref|YP_979867.1| 268 TRLGVDIHFNTRVGDLEFDDGRVTALIS 295
                                    56699999*****999999999998765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.3   8.4e-07   0.00088      16      55 ..       6      44 ..       4      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.4e-07
                                   TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                   a++ vvi GaG +GL+aa +la++ +++v++ e+    GG
  gi|121639643|ref|YP_979867.1|  6 ADTHVVIAGAGIAGLAAAMILAEA-GVRVTLCEAASEAGG 44
                                   5688********************.********9988887 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.2   4.2e-06    0.0045       2      30 ..      10      38 ..       9      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLith 30
                                   v++ G+G AG++AA+ +a++G++v+L+  
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAGVRVTLCEA 38
                                   8999**********************944 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.8e-06    0.0061      29      69 ..       8      48 ..       3      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                    +v++ G+G+aGl+A+ + ++ g +Vt+++  +++  + +s
  gi|121639643|ref|YP_979867.1|  8 THVVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKAKS 48
                                   68**************************9998877666665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.011        11       1      41 [.      11      46 ..      11      71 .. 0.79
   2 ?    4.8   0.0     0.025        26     116     153 ..     271     310 ..     257     312 .. 0.78
   3 ?   -1.2   0.0       1.7   1.8e+03       8      36 ..     529     558 ..     528     566 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.011
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrv 41
                                   +i GaG++Gla++  L++       +++tl +  se+g g++
  gi|121639643|ref|YP_979867.1| 11 VIAGAGIAGLAAAMILAEA-----GVRVTLCEAaSEAG-GKA 46
                                   699********99888877.....6*******966666.544 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                  NAD_binding_9 116 tvevh.raevvdleeradgq.avlladgaslaadaVvLAl 153
                                     v++h +++v dle +++++ a++ +dg+++a+d+  LA+
  gi|121639643|ref|YP_979867.1| 271 GVDIHfNTRVGDLEFDDGRVtALISSDGRRFACDYALLAV 310
                                    44544499*********998578889************96 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                  NAD_binding_9   8 rGlavlerLlara.kkkspleitlfdpsep 36 
                                    +G ++++++++   ++++pl+i+  dp+++
  gi|121639643|ref|YP_979867.1| 529 SGYLAARQIMNMVaSHAAPLRIDFRDPAPF 558
                                    6777888888887778999****9999987 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.3e-05     0.046       2      39 ..      10      47 ..       9      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekal 39
                                   v + GaG+ G   a+++a+ag++V+l++ ++ea  ka+
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGGKAK 47
                                   8899*************************999877765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0002      0.21       1      65 [.      10      91 ..      10     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.......-GGG-TT-SE................-EEEE--S-H.HHHH CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa.......tkerfpeade................tavvvlthdh.klDa 58
                                   +vi Gag  + a a ++a++g+rvt++++ +e+               a +                t + + ++ + ++D+
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAGVRVTLCEAASEAGgkakslrL------A-DghptehslrvytdtyqTLLTLFSRIPtEHDR 84
                                   68***************************9975454443331......2.12344555666666553333333332246666 PP

                                   HHHHHHS CS
                         XdhC_C 59 ealeaal 65
                                    +l++++
  gi|121639643|ref|YP_979867.1| 85 TMLDNLV 91
                                   6666666 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3   0.00076      0.81       2      34 ..      10      39 ..       9      43 .. 0.93
   2 ?   -2.4   0.0       1.6   1.7e+03     183     202 ..     286     305 ..     268     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00076
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvese 34
                                   +vi+G+G+aG  aA++la+a+   ++vtl e++
  gi|121639643|ref|YP_979867.1| 10 VVIAGAGIAGLAAAMILAEAG---VRVTLCEAA 39
                                   9********************...99***9975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                                    TTS-EEEEEETTS-EEE-SE CS
                 Trp_halogenase 183 edgrveslrledgreveadl 202
                                    +dgrv++l  +dgr++  d 
  gi|121639643|ref|YP_979867.1| 286 DDGRVTALISSDGRRFACDY 305
                                    49************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3696.13
//
Query:       gi|121639644|ref|YP_979868.1|  [L=1065]
Description: hypothetical protein BCG_3788 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-46  157.3  68.9      8e-40  136.8  34.4    2.8  3  MFS_1         Major Facilitator Superfamily
    8.4e-25   88.1   1.0      4e-24   85.9   1.0    2.2  1  Patatin       Patatin-like phospholipase
    9.1e-20   70.5   0.1    2.3e-19   69.2   0.1    1.7  1  cNMP_binding  Cyclic nucleotide-binding domain
    4.1e-08   32.5   6.3    4.1e-08   32.5   6.3    2.4  2  Sugar_tr      Sugar (and other) transporter
    0.00068   18.7  11.0    0.00068   18.7  11.0    3.6  4  PUCC          PUCC protein
     0.0014   17.6   3.1     0.0014   17.6   3.1    2.2  2  MFS_1_like    MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8  34.4   2.7e-43     8e-40       2     260 ..      47     346 ..      46     348 .. 0.89
   2 !   35.7  26.5   1.5e-12   4.6e-09       6     184 ..     304     495 ..     300     538 .. 0.73
   3 ?   -5.1   1.1       3.8   1.1e+04     128     144 ..     836     852 ..     835     855 .. 0.77

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 2.7e-43
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                    +++afl++l+++i+++a+p  ++++++++ s ++++l +y +++a++ + +Grl+d +Gr+rv++lg++lf ++ +l+++
  gi|121639644|ref|YP_979868.1|  47 AFGAFLAFLDSTIVNVAFP-DIQRHFHSDISDLSWMLNAYNIVFAAFLVAAGRLADLMGRKRVFILGVALFTVAsGLCAI 125
                                    79*****************.******************************************************666666 PP

                          MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                     a s+  l+++rvlqG+ga++l+pa++ l+++ fp e+r+ ++ l++a+ +++a lgp++gg+l+++ gWr+vf+++ ++
  gi|121639644|ref|YP_979868.1| 126 -AESVGELVAFRVLQGIGAAVLVPASLGLVVEAFPAERRAHGVNLWGAAGAIAAGLGPPIGGALIEADGWRWVFLVNLPL 204
                                    .57777************************************************************************** PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeee.............................................kgtgpap 195
                                    +++a++ +   l+e++ + +r  p  ++                                             +++ pap
  gi|121639644|ref|YP_979868.1| 205 GVFAVLAARRALVENRAAGRRRVPDVRGavllafalglltlglikgpdwgwaslptsgsllaaavamvgfvmsSRHHPAP 284
                                    ****9988888888888777777766668*************************************************** PP

                          MFS_1 196 lvpawkallkdpvlw.illialllfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                    +v+  ++l+ + ++    l+a+++++ ++++llt++ + l+ v g++ ll+ag+++a +alv+a++
  gi|121639644|ref|YP_979868.1| 285 MVE-PTLLRIQSFVAgTGLTAVASAG-FYAYLLTHVLF-LNYVWGYT-LLEAGMAVAPAALVAAVV 346
                                    ***.7777777755433555555553.34444444444.6*******.*****9999999888665 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 1.5e-12
                          MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa.. 82 
                                    +++++++++++++  l+l+   g++  e+g++++  al+aav + +lGr++dr+G r ++ +g+l++a++ll+ l ++  
  gi|121639644|ref|YP_979868.1| 304 AVASAGFYAYLLTHVLFLNYVWGYTLLEAGMAVAPAALVAAVVAAVLGRVADRHGYRFIVGIGALIWAASLLWYLkVVgs 383
                                    44455555555555558899999***********************************************4444444356 PP

                          MFS_1  83 .sslw.lllvlrvlqGlgagalfpa.gaaliadwfpkeergraigllsagfslGailgpllggllasslg.......... 149
                                     + +   +l + +lqG+g ga fp+ g a++a+++++   + a ++ ++  ++Ga++g ++  +l+   g          
  gi|121639644|ref|YP_979868.1| 384 qPDFLgEWLPGQILQGIGVGATFPLlGSAALARLAKGGSYATASAVTGTIRQVGAVIGVAVLVILV---Gtpapgaaeea 460
                                    7888889************888886267888999999*********************99999999...43446799898 PP

                          MFS_1 150 ....Wravfyilaivsllafvlfllllpeepperkrksp 184
                                        W ++ + + +v++ a  l   l + +p++ + ++p
  gi|121639644|ref|YP_979868.1| 461 lrhrWALAAICFVAVGIGA--L--SLGRIRPVPAAVEPP 495
                                    8855544444444444444..4..344333333333222 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 3.8
                          MFS_1 128 agfslGailgpllggll 144
                                    ag+s+Gai+++l+++ l
  gi|121639644|ref|YP_979868.1| 836 AGTSMGAIIAALAASGL 852
                                    68888888888888766 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   1.0   1.3e-27     4e-24       1     201 [.     806     962 ..     806     965 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.3e-27
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanla 80 
                                    LvlsGG +r+ ++lg+l++L +++g  +d ++GtS GAiia+l a+g d+a+ ++++++ + +k+  +            
  gi|121639644|ref|YP_979868.1| 806 LVLSGGAARACAHLGVLEEL-EAAGVTVDRFAGTSMGAIIAALAASGLDAAGVDAQIYEHFVRKSHGDY----------- 873
                                    8*******************.************************************************........... PP

                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglyteddd 160
                                         +l  +gl  ++  +++lr++++d+ +++l ++++++                             +  + +    
  gi|121639644|ref|YP_979868.1| 874 -----TLPSKGLIRGKRTQSTLRTIFGDHLVEELPKHFRCV---------------------------SVDLLARRPVVH 921
                                    .....999*********************************...........................567777777778 PP

                        Patatin 161 ddvdladavraSsafPglfppvsldgelyvDGGilsNvPil 201
                                    ++++lad+v +S+ +P+l+ p  ++g+l vDGG+l+NvP+ 
  gi|121639644|ref|YP_979868.1| 922 RQGPLADVVGCSMRLPFLYAPLPYGGTLHVDGGVLDNVPVT 962
                                    8**************************************97 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.1   7.7e-23   2.3e-19       3      86 ..     548     630 ..     546     632 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 7.7e-23
                                    EE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.E.EEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   3 sfkagevifrqGdpadslyivlsGevrvyrlsedgke.vvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    +++ag+++f++Gd  d ly+v+sG+++v  l++dg++  v+a+lg+G+++Gel++l ++pr+a+v+A+ ds l+++++++
  gi|121639644|ref|YP_979868.1| 548 ELQAGSYLFHAGDVSDALYVVRSGRLQV--LAGDGAKdEVVAELGRGQVVGELGVLLDAPRSASVRAVRDSSLMRVTKAE 625
                                    799*************************..999997668*****************99********************** PP

                                    HHHHH CS
                   cNMP_binding  82 flell 86 
                                    f ++ 
  gi|121639644|ref|YP_979868.1| 626 FAKIA 630
                                    *9986 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   6.3   1.4e-11   4.1e-08       3     185 ..      44     209 ..      42     213 .. 0.81
   2 ?   -2.4   7.4      0.53   1.6e+03      46     121 ..     330     407 ..     296     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.4e-11
                                    HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                       Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                    lvaa+g +l   d+ +++++   ++  ++f+ + s+         +++++++++++ ++  + ag l+d +GRk +++ +
  gi|121639644|ref|YP_979868.1|  44 LVAAFGAFLAFLDSTIVNVAFPDIQ--RHFHSDISD---------LSWMLNAYNIVFAAFLVAAGRLADLMGRKRVFILG 112
                                    7888888888888888887766666..666666665.........479999*****99999******************* PP

                                    HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgln 162
                                    ++lf +++ l+a+a+   sv  l++ Rvl Gig+ +    +  ++ E  p++ R   v l+  a ++   ++  +g   +
  gi|121639644|ref|YP_979868.1| 113 VALFTVASGLCAIAE---SVGELVAFRVLQGIGAAVLVPASLGLVVEAFPAERRAHGVNLWGAAGAIAAGLGPPIGG--A 187
                                    ***************...********************99999****99*999988776655554444444444444..5 PP

                                    TSS-TTHHHHHHHCCHHHHHHHH CS
                       Sugar_tr 163 ktsnadgwrillglqlvpallll 185
                                     +++ dgwr+ + ++l + ++ +
  gi|121639644|ref|YP_979868.1| 188 LIEA-DGWRWVFLVNLPLGVFAV 209
                                    5555.77*****99999998765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.53
                                    .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT...SS-TGGGGGHHHHHHHHHHHHH CS
                       Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk...nsvevlivgRvlvGigvGlasv 121
                                    +  g+ v+ + ++a++ + ++g ++dr G++ +  i+a++  ++ +l ++   +     +   + g++l GigvG++  
  gi|121639644|ref|YP_979868.1| 330 LEAGMAVAPAALVAAVVAAVLGRVADRHGYRFIVGIGALIWAAS-LLWYLKVVGsqpDFLGEWLPGQILQGIGVGATFP 407
                                    55688899999999999999999999999997766666665554.444444434355667778888*********8754 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  11.0   2.3e-07   0.00068     256     360 ..      88     189 ..      71     210 .. 0.89
   2 ?   -1.4   0.2      0.29   8.7e+02      42     103 ..     220     277 ..     199     286 .. 0.67
   3 ?   -6.1  10.2         6   1.8e+04     340     399 ..     324     383 ..     239     385 .. 0.72
   4 ?   -1.0   1.4      0.23   6.8e+02      53     102 ..     429     479 ..     414     483 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                           PUCC 256 tlvGlllaglvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeerag 335
                                    +++ +l+a+  l+  ++ +r+  lgv+l  +++ l  +a  +++ +++    +l G+++ ++  a+l+l+++  ++er +
  gi|121639644|ref|YP_979868.1|  88 VFAAFLVAAGRLADLMGRKRVFILGVALFTVASGLCAIAESVGELVAF---RVLQGIGAAVLVPASLGLVVEAFPAERRA 164
                                    678899999999*9********************99999988886666...5788999********************** PP

                           PUCC 336 lalGaWGaaQaiaaglavllggalr 360
                                      + +WGaa aiaagl+  +ggal 
  gi|121639644|ref|YP_979868.1| 165 HGVNLWGAAGAIAAGLGPPIGGALI 189
                                    **********************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.29
                           PUCC  42 ralGwkRvpyiwlGslalalglaiaplalivlsgkgeaeaaatwaglilaavafllvGlgvs 103
                                    ra G++Rvp + +G+++la+ l +++l+li          a   ++ +l+a+a ++vG+ +s
  gi|121639644|ref|YP_979868.1| 220 RAAGRRRVPDV-RGAVLLAFALGLLTLGLIKGPD---WGWASLPTSGSLLAAAVAMVGFVMS 277
                                    47788888865.6777777755555555554333...3344444555666677788888776 PP

  == domain 3  score: -6.1 bits;  conditional E-value: 6
                           PUCC 340 aWGaaQaiaaglavllggalrdllkalaan.daalayglVfaleavlliisilvlnklvrr 399
                                    +WG    + ag+av+ ++ ++ +++a+++   +  +y ++  + a++  +s+l  +k+v +
  gi|121639644|ref|YP_979868.1| 324 VWGYT-LLEAGMAVAPAALVAAVVAAVLGRvADRHGYRFIVGIGALIWAASLLWYLKVVGS 383
                                    67765.4789***********9999999884589999999999999999999999999876 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.23
                           PUCC  53 wlGslalalglaiaplalivlsgkgeae.aaatwaglilaavafllvGlgv 102
                                    ++G++ +++ +  +++ +i++++ +    ++a     +laa+ f++vG+g+
  gi|121639644|ref|YP_979868.1| 429 VTGTIRQVGAVIGVAVLVILVGTPAPGAaEEALRHRWALAAICFVAVGIGA 479
                                    6799999986666666666666644433466666777889999****9985 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.1   4.6e-07    0.0014     275     384 ..      91     199 ..      69     200 .. 0.93
   2 ?   -3.0   7.9      0.84   2.5e+03     241     357 ..     307     433 ..     290     451 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.6e-07
                     MFS_1_like 275 plfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgll 354
                                     +++ a +l + +G  ++ i+++ ++++   l ai e++  ++ + vL+gi  ++l  a    v +++p + +a g  l 
  gi|121639644|ref|YP_979868.1|  91 AFLVAAGRLADLMGRKRVFILGVALFTVASGLCAIAESVGELVAFRVLQGIGAAVLVPASLGLVVEAFPAERRAHGVNLW 170
                                    589999************************************************************************99 PP

                     MFS_1_like 355 sglyfglGralGsliGGllwdlksaiflFr 384
                                     ++   +  +lG  iGG+l++ ++ +++F 
  gi|121639644|ref|YP_979868.1| 171 GAA-GAIAAGLGPPIGGALIEADGWRWVFL 199
                                    877.78999*****************9997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.84
                     MFS_1_like 241 wgiienF...lflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii..enaw 314
                                    ++ ++++   + l+L    g++   +G++va  ++   ++  +  ++ ++ G ++++ i+ l+ ++ +l+y  +  +++ 
  gi|121639644|ref|YP_979868.1| 307 SAGFYAYlltHVLFLnYVWGYTLLEAGMAVAPAALVAAVVAAVLGRVADRHGYRFIVGIGALIWAASLLWYLKVvgSQPD 386
                                    44455554544566644568888888888888888888999999999**********99999888887777655586666 PP

                     MFS_1_like 315 lv...lpievLhgisfgllwaaa.veyvskiapksleatgqgllsgl 357
                                    ++   lp ++L+gi +g+++  +     +++a  +  at  ++  ++
  gi|121639644|ref|YP_979868.1| 387 FLgewLPGQILQGIGVGATFPLLgSAALARLAKGGSYATASAVTGTI 433
                                    64333999999999999998554144556667777777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.43
# Mc/sec: 7382.32
//
Query:       gi|121639645|ref|YP_979869.1|  [L=776]
Description: transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-19   69.7   0.0    2.8e-18   66.4   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
      8e-19   68.1   0.1    2.9e-18   66.4   0.1    2.0  1  Methyltransf_25  Methyltransferase domain
    2.6e-17   63.7   2.2    4.3e-17   63.0   0.1    2.4  2  Radical_SAM      Radical SAM superfamily
    5.6e-17   61.9   0.0      1e-16   61.1   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    3.1e-11   43.4   0.0    6.8e-11   42.3   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    2.3e-09   36.9   0.0    4.3e-09   36.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.7e-08   34.0   0.0    9.3e-08   32.7   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    2.3e-07   31.1   0.0    5.7e-07   29.9   0.0    1.6  1  Fer4_12          4Fe-4S single cluster domain
    3.9e-06   27.0   1.1    6.5e-06   26.3   0.0    1.9  1  Fer4_14          4Fe-4S single cluster domain
    3.2e-05   23.4   0.0    5.6e-05   22.6   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    5.4e-05   22.5   0.0     0.0042   16.3   0.0    2.3  2  Methyltransf_20  Putative methyltransferase
  ------ inclusion threshold ------
      0.024   15.7   0.0       0.36   11.9   0.0    2.8  3  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.73   1.1e+03      23      95 ..     376     446 ..     361     446 .. 0.58
   2 !   66.4   0.0   1.8e-21   2.8e-18       2      93 ..     567     661 ..     566     664 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                                    EEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  23 gvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllv 95 
                                    g+D+ +++l++a ++ + ++    +     e l  + d  f +v+  +   +  ++++++k +++   p+G+l+
  gi|121639645|ref|YP_979869.1| 376 GTDTMTAQLQRATAALNCAEG---CGINLPEALtHLTDRVFAIVIQDFQDPYTLNVKQLMKCCVQQITPDGRLI 446
                                    555555555555544444432...22222222223555555555555544455689999999999999999986 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 1.8e-21
                                    EET-TTSHHHHHHH.HTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   2 dvGcGtGrlaeala.krgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                    d+++G G+ a+ la ++g  v gvD+s+  +k+a++++ + gl  +v+f+ +dae++p++d++fD+ v+  ++++++d +
  gi|121639645|ref|YP_979869.1| 567 DIAAGPGASARLLAsDYGVAVDGVDISEINVKRAQAAVAQTGLteRVRFHLGDAESVPLPDDTFDALVCECAFCTFPDKN 646
                                    899***********6666************************************************************** PP

                                    HHHHHHHHHEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGl 93 
                                    +a +++aR+L+pgGl
  gi|121639645|ref|YP_979869.1| 647 AAAQQFARILRPGGL 661
                                    **************8 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   1.9e-21   2.9e-18       1      97 []     565     660 ..     565     660 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.9e-21
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                    v d+++G+G  ++ la  +g   v gvDise  +++a++ +++ gl  +v+f+ gdae++p++d++fD+ v+  a++ ++
  gi|121639645|ref|YP_979869.1| 565 VADIAAGPGASARLLASDYG-VAVDGVDISEINVKRAQAAVAQTGLteRVRFHLGDAESVPLPDDTFDALVCECAFCTFP 643
                                    78****************98.***********************99**************************65588887 PP

                                    HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                      d  +a +++ar+L+pgG
  gi|121639645|ref|YP_979869.1| 644 --DKNAAAQQFARILRPGG 660
                                    ..56699***********9 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.1   2.9e-20   4.3e-17       5     164 ..      98     258 ..      94     260 .. 0.92
   2 ?   -0.6   0.0         1   1.5e+03      11      20 ..     637     650 ..     636     762 .. 0.77

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.9e-20
                                    SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritve 83 
                                      Cnl+C+ C   +     ++g+ ++  + ++ ++ l a  g  ++v+++ggep+ ++ + e+++++ ++  p  +i + 
  gi|121639645|ref|YP_979869.1|  98 THCNLDCPICFADSG--HQPDGYAITAAQCERMLDTLVAAEGePEVVMFSGGEPTIHKQLLEFVDAAQAR--PVKTIIIN 173
                                    67***********96..*********************77788***************************..9******* PP

                                    ECSSCHG..HHHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHH.HHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxx..xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  84 tngtlpd..eeklerllelg....vdrvslgleaaddekvlklmnrghtfeevl.ealeklreagikrvvdrivglpGen 156
                                    tng+++   +++++ l+ ++    + +++l  + +d+  +++++ rgh++ +v+ +al+++++ag+  v+ +  + +G n
  gi|121639645|ref|YP_979869.1| 174 TNGIRLAsdRRFVDQLATRNrpghPVHIYLQFDGLDEA-THRRI-RGHDLRDVKqRALDNCAAAGLT-VSLVAAVERGLN 250
                                    *********999999999888999**************.*****.7777766652799*********.9*********** PP

                                    HHHHHHHH CS
                                    xxxxxxxx RF
                    Radical_SAM 157 deeleell 164
                                    ++el +++
  gi|121639645|ref|YP_979869.1| 251 EHELGAVI 258
                                    *9998776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                    -TTTSCCTT....H CS
                                    xxxxxxxxx....x RF
                    Radical_SAM  11 CsfCarpet....v 20 
                                    C fC++p +    +
  gi|121639645|ref|YP_979869.1| 637 CAFCTFPDKnaaaQ 650
                                    99999997544440 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   6.9e-20     1e-16       6     113 ..     564     668 ..     560     707 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 6.9e-20
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevl 84 
                                    rv D+++G G+ +  la+  g    v G+Dise  +++A++  ++ gl+ +v+F+ gd+e+ +  l d++fD +++ +++
  gi|121639645|ref|YP_979869.1| 564 RVADIAAGPGASARLLASDYG--VAVDGVDISEINVKRAQAAVAQTGLTeRVRFHLGDAESVP--LPDDTFDALVCECAF 639
                                    799**************7654..5677*********************99*************..9************** PP

                Methyltransf_31  85 naladpdkileeiervlkpggilliedpr 113
                                    ++++d++++ ++  r l+pgg   i+d+ 
  gi|121639645|ref|YP_979869.1| 640 CTFPDKNAAAQQFARILRPGGLAGITDVT 668
                                    *********************98888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   4.6e-14   6.8e-11      21     160 ..     560     706 ..     537     711 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 4.6e-14
                Methyltransf_23  21 raggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                      + rv di++G G  +++l +++g+ v+gvD+s+++v++a+        +   +++  d+++ + p+++fd  v+   +
  gi|121639645|ref|YP_979869.1| 560 GDPRRVADIAAGPGASARLLaSDYGVAVDGVDISEINVKRAQaavaqtgLTERVRFHLGDAESVPLPDDTFDALVCECAF 639
                                    45669*********9999998999****************9888777763333333333355666699************ PP

                Methyltransf_23  93 ehvpdppellrqiatllkpgGylllseplasl....kedrllldw.lylvpagrhisffsarslkelleeaGl 160
                                    +++pd  ++ +q+a++l+pgG++ ++++++ +    +e+  l  w +++++a       + +++ ++le+aGl
  gi|121639645|ref|YP_979869.1| 640 CTFPDKNAAAQQFARILRPGGLAGITDVTVGDgglpAELTPLAAWvACIADAR------TVTDYTDILEGAGL 706
                                    ***************************98877777656666666656777662......33445556666666 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.9e-12   4.3e-09      47     148 ..     561     661 ..     548     668 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.9e-12
                                    -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES- CS
                Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsfG 125
                                     +++v D+a+G g  a  l++  g    v+++Di+e  +k +++ + ++g + +++f  ++ae +p  dd+fD +     
  gi|121639645|ref|YP_979869.1| 561 DPRRVADIAAGPGASARLLASDYG--VAVDGVDISEINVKRAQAAVAQTGLTeRVRFHLGDAESVPLPDDTFDALVCECA 638
                                    466889999999988877776655..579*********************9989************************** PP

                                    GGG-S-HHHHHHHHHHHEEEEEE CS
                Ubie_methyltran 126 lrnvtDklkaLkeayrvlkpGGr 148
                                    +  ++Dk+ a ++  r+l+pGG 
  gi|121639645|ref|YP_979869.1| 639 FCTFPDKNAAAQQFARILRPGGL 661
                                    *********************96 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   6.3e-11   9.3e-08       2      98 ..     567     661 ..     566     662 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.3e-11
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlk 80 
                                    +i +G G+ +r l+ +  ++ + gvDis+  +++a++  a+ +     +v++   d+++ + + ++fD+ v+ ++++ ++
  gi|121639645|ref|YP_979869.1| 567 DIAAGPGASARLLASD-YGVAVDGVDISEINVKRAQAAVAQTGLTE--RVRFHLGDAESVPLPdDTFDALVCECAFCTFP 643
                                    8999999888888888.9**************99999999999866..66666556555555568*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    d++++ +++++ L+pgG 
  gi|121639645|ref|YP_979869.1| 644 DKNAAAQQFARILRPGGL 661
                                    *****************6 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.8e-10   5.7e-07      14     100 ..      99     183 ..      93     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.8e-10
                        Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.egltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                     Cnl C+ Cf+ + +++++   +  + ++ + + ++ e   e + ++GGEP      ++lle+v+  +++ ++  i+ ++
  gi|121639645|ref|YP_979869.1|  99 HCNLDCPICFADSGHQPDGYAITAAQCERMLDTLVAAEGEpEVVMFSGGEPTI---HKQLLEFVDAAQARPVKTIIINTN 175
                                    6***************998777766665555555555554578899*******...999*************999999** PP

                        Fer4_12  93 gytleels 100
                                    g  l   +
  gi|121639645|ref|YP_979869.1| 176 GIRLASDR 183
                                    99887665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.3e-09   6.5e-06       7      90 ..      99     177 ..      95     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.3e-09
                        Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                     Cnl C+ C+  +  + +   + + +  e++l+ l + e +++ + ++GGeP ++   k+ll++v+  + +   k i ++
  gi|121639645|ref|YP_979869.1|  99 HCNLDCPICFADSGHQPDGYAITAAQ-CERMLDTLVAAEGEPEVVMFSGGEPTIH---KQLLEFVDAAQARP-VKTIIIN 173
                                    7*********9997776555554444.44778877788888999*********99...999****9998886.899999* PP

                        Fer4_14  87 tngt 90 
                                    tng 
  gi|121639645|ref|YP_979869.1| 174 TNGI 177
                                    *996 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.8e-08   5.6e-05      64     162 ..     563     662 ..     545     678 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.8e-08
                                    -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES-GGGT CS
                           CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvgafehv 140
                                     ++ di +G G+ +r  ++ y+v v g+ +S+ + k+a+++v++++l+++v+ +l d e ++     +d++v   af  +
  gi|121639645|ref|YP_979869.1| 563 RRVADIAAGPGASARLLASDYGVAVDGVDISEINVKRAQAAVAQTGLTERVRFHLGDAESVPLpddTFDALVCECAFCTF 642
                                    4799*****************************************************99985444599999999999999 PP

                                    SGGGHHHHHHHHHHHS-TT-EE CS
                           CMAS 141 gkenydtffkklkkllkedGll 162
                                      +n ++  +++ ++l+++Gl 
  gi|121639645|ref|YP_979869.1| 643 PDKNAAA--QQFARILRPGGLA 662
                                    8887664..6777788888765 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.018        26     130     174 ..     383     430 ..     319     439 .. 0.82
   2 !   16.3   0.0   2.8e-06    0.0042     128     195 ..     556     620 ..     545     650 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                Methyltransf_20 130 aegrpvrildiaaGhGryvldalekaeervesillrdyse...lnveq 174
                                    + +r++  l+ a G+G  + +al++ ++rv +i+++d+ +   lnv+q
  gi|121639645|ref|YP_979869.1| 383 QLQRATAALNCAEGCGINLPEALTHLTDRVFAIVIQDFQDpytLNVKQ 430
                                    4467788899****************************8722245554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.8e-06
                Methyltransf_20 128 lkaegrpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgda 195
                                    l+++g+p r+ diaaG G         a++   ++   d se+nv++ +a +a+ gl + +rf+ gda
  gi|121639645|ref|YP_979869.1| 556 LRSTGDPRRVADIAAGPGASAR---LLASDYGVAVDGVDISEINVKRAQAAVAQTGLTERVRFHLGDA 620
                                    68899999**********7542...2233334667778*****************************9 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.8   1.5e+04      67      80 ..     322     335 ..     240     355 .. 0.66
   2 ?   -0.5   0.0       1.7   2.5e+03      58     101 ..     401     445 ..     363     446 .. 0.80
   3 ?   11.9   0.0   0.00024      0.36      28     100 ..     589     661 ..     567     667 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.8
                Methyltransf_24  67 agsiDllfiDggha 80 
                                     +si  l+ Dg+h+
  gi|121639645|ref|YP_979869.1| 322 CRSITYLLTDGEHV 335
                                    45666777777775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                Methyltransf_24  58 seealaslaagsiDllfiDgghaae.avledleallprlapggvv 101
                                    ++eal++l ++ + +++ D++  ++  v++ ++ + ++++p+g +
  gi|121639645|ref|YP_979869.1| 401 LPEALTHLTDRVFAIVIQDFQDPYTlNVKQLMKCCVQQITPDGRL 445
                                    5899999999999******98777658999999999999999865 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                Methyltransf_24  28 avdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDggh.aaeavledleallprlapggv 100
                                     vd  +   ++a+a ++++gl++rvr++ +d+e++   l ++++D l++ +   +  +  ++ + + ++l+pgg+
  gi|121639645|ref|YP_979869.1| 589 GVDISEInVKRAQAAVAQTGLTERVRFHLGDAESV--PLPDDTFDALVCECAFcTFPDKNAAAQQFARILRPGGL 661
                                    4555444545567777788***************9..677899**999998541557788888889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.41
# Mc/sec: 5658.64
//
Query:       gi|121639646|ref|YP_979870.1|  [L=346]
Description: hypothetical protein BCG_3790c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-07   31.1   0.0    5.5e-06   26.5   0.0    2.5  2  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.1e-10   5.5e-06       2     177 .]     139     260 ..     138     260 .. 0.92
   2 ?    1.2   0.0     0.018   3.3e+02      97     148 ..     273     326 ..     263     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.1e-10
                                    EEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH.... CS
                  DNA_primase_S   2 DiDmddyddcseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnly 81 
                                    D+D+++  +         +++  +vav vl+++l +d+g     + +sg+rG+H+  +  + +++ + +ra i+      
  gi|121639646|ref|YP_979870.1| 139 DLDPQPGTG---------FVEARTVAVDVLRSVL-DDLGLV-GYPKTSGGRGIHVFLRIATDWDFVEVRRAGIA------ 201
                                    444444444.........67779***********.****96.********************************...... PP

                                    ..............................HCHHHHCT--------..................---------------- CS
                  DNA_primase_S  82 rplhpflsrsmlkivkpvveeiileeqdpfeikkllrllpdkslrekkkweakedivlvllyprldeqvtkgikhllkap 161
                                                                    +++ r++pd++ ++     ++++++ ++++++++++   ++++++++ 
  gi|121639646|ref|YP_979870.1| 202 ------------------------------LAREVERRAPDAVTTS-----WWKEERGARIFIDFNQN---ARDRTMASA 243
                                    ..............................99**************.....9**************99...9******** PP

                                    -....---.------.. CS
                  DNA_primase_S 162 fcihgktg.nvcvpldv 177
                                    +++++ +   v+ pl++
  gi|121639646|ref|YP_979870.1| 244 YSVRPTPIaTVSMPLTW 260
                                    ***************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.018
                                    .......................HCHHHHCT--------..................--- CS
                  DNA_primase_S  97 kpvveeiileeqdpf........eikkllrllpdkslrekkkweakedivlvllyprlde 148
                                    ++ v e +++ +dp+        +i+ ll+l+  ++ r       + d ++   yp+++ 
  gi|121639646|ref|YP_979870.1| 273 MTTVPELVKIRDDPWagmddvaqSIAPLLDLAAADEERG------LGDMPYPPNYPKMPG 326
                                    67789999********99999999999999999999988......777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2388.17
//
Query:       gi|121639647|ref|YP_979871.1|  [L=358]
Description: ATP-dependent DNA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-39  135.2   0.0    3.4e-39  134.6   0.0    1.2  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    5.6e-15   55.8   0.0    1.3e-14   54.6   0.0    1.6  2  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.021   15.1   0.0    1.3  1  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   5.7e-43   3.4e-39       1     204 []      11     201 ..      11     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 5.7e-43
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLA+s+++i          ++ +E K+DG R  + ++gd+v+l SR+++++t+++pelv a+++ ++++   +++DGE+
  gi|121639647|ref|YP_979871.1|  11 PMLAKSVTAI--------PPDASYEPKWDGFRSICFRDGDQVELGSRNERPMTRYFPELVAAIRAELPHR---CVIDGEI 79 
                                    8999999977........78889*********88888**************************9999886...******* PP

                                    EEEETTTTCBEHHHHHCHHH.HCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB..--BTTTEEE-- CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrk.kkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil..kesedrvelae 157
                                    ++   +t+++l+f+ l++r+  ++++v+ +++++++++++FD+L+l ++++t +p++eRr+ L +++  +  + +++++ 
  gi|121639647|ref|YP_979871.1|  80 II---ATDHGLDFEALQQRIhPAESRVRMLADRTPASFIAFDLLALGDDDYTGRPFSERRAALVDAVtgSGADADLSIHV 156
                                    **...799************999999*****************************************7777899999*** PP

                                    EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 158 slevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                    +  ++d+ +++++++e+  +gl+G+++K p+ +Y+p+kr   ++K+K
  gi|121639647|ref|YP_979871.1| 157 TPATTDMATAQRWFSEFEGAGLDGVIAKPPHITYQPDKR--VMFKIK 201
                                    ***************************************..9***99 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   1.8e+04      62      74 ..      56      67 ..      46      68 .. 0.66
   2 !   54.6   0.0   2.1e-18   1.3e-14       3      99 .]     221     332 ..     219     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                                   EEE-TT-EEEEEE CS
                 DNA_ligase_A_C 62 vWvePelvveVkf 74
                                   +++ Pelv+ +++
  gi|121639647|ref|YP_979871.1| 56 RYF-PELVAAIRA 67
                                   565.999998876 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.1e-18
                                    GSEEEEEEEEEE.TTEEEEEEEE-SS--HHHHHHHHHHHG..GGEECTTCE......SS---HHHHTT.....EE..... CS
                 DNA_ligase_A_C   3 glvgslllgvyd.dgkleyvgkvgtGfsdaeleelrkklk..elerkkppf......aekvpeeekrd.....vW..... 63 
                                    +++gslllg+y+ dg+l +vg++g+ f +ae+++l ++l+    + +++p+      a     +++++     +W     
  gi|121639647|ref|YP_979871.1| 221 DAIGSLLLGLYQeDGQLASVGVIGA-FPMAERRRLLTELQplVTSFDDHPWnwaahvA----GQRTPRknefsRWnvgkd 295
                                    689**********************.**************554445599997654321....2222224567799***** PP

                                    .....E-TT-EEEEEESEEECTSSSTTEECT-E.EEEE-TTS CS
                 DNA_ligase_A_C  64 .....vePelvveVkfaeitasgkykaslRfPr.fkrlReDk 99 
                                         ++Pe vveV++++++       ++R+++ f r+R+D+
  gi|121639647|ref|YP_979871.1| 296 lsfvpLRPERVVEVRYDHMEGA-----RFRHTAqFNRWRPDR 332
                                    ****************888887.....6*****9******96 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.5e-06     0.021      41     161 .]      54     201 ..      29     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                                    HTHHHHHHHHHHHHH..ECCEEEEEEEES....SS..TTSS...................EEEEEEEEEEE.CTTBECE- CS
                     RNA_ligase  41 fkrwaaalrkklkeklaneelilyGElig...hsikygglpk..................efyvFdifdir.dkeeqryl 98 
                                     +r+  +l +++++ l  ++ ++ GE+i    h    ++l++                   f++Fd++++  d+ ++r  
  gi|121639647|ref|YP_979871.1|  54 MTRYFPELVAAIRAELP-HRCVIDGEIIIatdHGLDFEALQQrihpaesrvrmladrtpaSFIAFDLLALGdDDYTGRPF 132
                                    44555555567788888.67*********7774443233222344556666667777777********999988899988 PP

                                    -HHHHHHHHHCCT.........B..EEEEE.SSHHHHHCCC.HHHHTC--EEEEEESSSSBE.TTEBSEEEEE CS
                     RNA_ligase  99 spdevealakglg.........tvpvlyegkflaaeellelllskgnkrEGlVikpeselyk.nkgraifKvk 161
                                    s +++  + + +g         +v  +++  ++a + + e+   +g    G++ kp++ +y+ +k r +fK+k
  gi|121639647|ref|YP_979871.1| 133 SERRAALVDAVTGsgadadlsiHVTPATTDMATAQRWFSEF---EGAGLDGVIAKPPHITYQpDK-RVMFKIK 201
                                    88888888885545566666554444422222233333333...677999*********999775.9***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2612.29
//
Query:       gi|121639648|ref|YP_979872.1|  [L=352]
Description: hypothetical protein BCG_3792 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-75  253.3   0.3    1.6e-68  231.1   0.2    2.1  2  DUF2330   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2330  Uncharacterized protein conserved in bacteria (DUF2330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.2   8.8e-73   1.6e-68       1     226 [.      29     246 ..      29     249 .. 0.95
   2 !   21.7   0.0     5e-09     9e-05     256     308 ..     246     298 ..     244     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 8.8e-73
                        DUF2330   1 paaaaaCGayvlkaddklrneaekvvlarDgdkttilmrldlkgdakefAlvvPvPtvaqvsvgekktfdeLdeltaPrl 80 
                                    p++a+aCGa v+  +++++ ++e+++l +Dg ++ti+m+l++++d++++AlvvP+Pt+a v+ ++++tf eLd+l+aP +
  gi|121639648|ref|YP_979872.1|  29 PSYACACGAAVTAHGSQATLNHEVALLHWDGTTETIVMQLAMNADTDNVALVVPTPTPAIVTTADQSTFGELDTLSAPLI 108
                                    79****************************************************************************** PP

                        DUF2330  81 aeesdpepcaavapgaaavgsaaakaagvtvlaqvqvgpydvvilsatdsdgLetWLkdngYrlpaeleaaLapYirqgm 160
                                    + +++++ + +      a+g   a+a ++ vl+qv++gp+++++l+++d+ gL+tWL dngY++++ ++aaL+pY+r+g+
  gi|121639648|ref|YP_979872.1| 109 EHQRHWSLRRG----VGASGPQEAAARAPHVLNQVRLGPLEATTLTGGDLSGLQTWLSDNGYAIRPAVSAALDPYVRDGW 184
                                    *********44....44444445566779*************************************************** PP

                        DUF2330 161 kfvaaklnleeakkadtgqlrPlqlsfeseklvlPlRlsalaatgqqdliiYiLtehrveaanart 226
                                     fva++l+  +   +  g l+P++++f s +lv+P+Rls +a+++q  ++i++L+ hr ++++a+ 
  gi|121639648|ref|YP_979872.1| 185 AFVAIRLTSTD---LIVGGLDPVRMTFRSSRLVYPMRLSVAAQEPQ-HVTIFTLSDHRQQRTDADA 246
                                    ********996...89*****************************9.***************9984 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 5e-09
                        DUF2330 256 eavkavfveyagdvaaadpcaeeLreltaaweaylTrlhvei.epesiteDlef 308
                                    +a++++ v +agd+++a   + +Lrel  ++ +ylT+++v i + ++i++D++f
  gi|121639648|ref|YP_979872.1| 246 AATQTTHVRFAGDMSTAV-RDPLLRELIGNHGSYLTKVEVDIyQTSRISSDFTF 298
                                    7889999*******9987.899*******************99**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1948.37
//
Query:       gi|121639649|ref|YP_979873.1|  [L=166]
Description: hypothetical protein BCG_3793c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.7   0.0    2.5e-14   53.4   0.0    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   1.4e-18   2.5e-14       2     130 ..       2     147 ..       1     148 [. 0.81

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.4e-18
                                    EEEEEEEEEEETTSE...EEEEEES....SSSTTT.....EESSEEECBTTSHHHHHHHHHHHHHHS..EEE.EEEEEEE CS
                          NUDIX   2 lrravgvvllnekge...vLlvrrs....kkpfpg.....WelPgGkvepgEtpeeAArREleEEtG..lea.ellellg 66 
                                    ++ ++gv+l++ +     vLl++           g     W++P+G+   gE+p+ AArRE+ EE+G  ++  + +++ +
  gi|121639649|ref|YP_979873.1|   2 PKLSAGVLLYRARAGvvdVLLAHPGgpfwA----GkddgaWSIPKGEYTGGEDPWLAARREFSEEIGlcVPDgPRIDFGS 77 
                                    56799********77898999986655553....344458***************************4445556777777 PP

                                    EEEEEEEEEEEEEE......EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                          NUDIX  67 rlhylapydgpygd......eheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                      ++  ++ +++g       ++  + +f+ + ++g  + ++ +ev+ v w+p++ + ++kl +++r +l++
  gi|121639649|ref|YP_979873.1|  78 LKQSGGKVVTVFGVradldiTDARSSTFElDWPKGSGKMRKFPEVDRVSWFPVARA-RTKLLKGQRGFLDR 147
                                    666666666666668878887777788889**************************.99999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 885.29
//
Query:       gi|121639650|ref|YP_979874.1|  [L=454]
Description: hypothetical protein BCG_3794c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-99  333.3   0.6    1.8e-99  332.8   0.6    1.2  1  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    9.2e-36  123.0   0.0    1.2e-34  119.4   0.0    2.1  2  DUF1298         Protein of unknown function (DUF1298)
     0.0028   16.4   0.3      0.043   12.5   0.2    2.1  2  Condensation    Condensation domain
  ------ inclusion threshold ------
      0.083   11.4   0.0       0.12   10.9   0.0    1.1  1  AATase          Alcohol acetyltransferase


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.8   0.6  4.1e-103   1.8e-99       1     264 []       4     262 ..       4     262 .. 0.99

  Alignments for each domain:
  == domain 1  score: 332.8 bits;  conditional E-value: 4.1e-103
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    ++p D +fl +es+e+pmhvg l+++epp +gag++++r+++e++ +++e +p++r+++++  +g+a+++W  d+d+D+d
  gi|121639650|ref|YP_979874.1|   4 MMPNDSMFLFIESREHPMHVGGLSLFEPP-QGAGPEFVREFTERLVANDEFQPMFRKHPATIGGGIARVAWAYDDDIDID 82 
                                    789**************************.************************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yHvRr+alp+PG+ r+llel+srL++s+LDr+rPlWe+hv+EGl++gr+A+++k+HHAliDGv+++kl++r+l++dpdd+
  gi|121639650|ref|YP_979874.1|  83 YHVRRSALPSPGRVRDLLELTSRLHTSLLDRHRPLWELHVVEGLNDGRFAMYTKMHHALIDGVSAMKLAQRTLSADPDDA 162
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrfa 240
                                    +++++++ ppr   rt++ ++g  ++l+++l k++gsv g++ s+ +l++aal +++l+lpfaap++++n ++++aRr+a
  gi|121639650|ref|YP_979874.1| 163 EVRAIWNLPPRP--RTRPPSDG--SSLLDALFKMAGSVVGLAPSTLKLARAALLEQQLTLPFAAPHSMFNVKVGGARRCA 238
                                    *******99999..99999999..9******************************************************* PP

                 WES_acyltransf 241 aaslpLadvkavakalgvtiNDvv 264
                                    a+s++L+++k+v++a+gvt+ND+v
  gi|121639650|ref|YP_979874.1| 239 AQSWSLDRIKSVKQAAGVTVNDAV 262
                                    **********************97 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.075   3.4e+02     108     138 ..      71     101 ..      52     104 .. 0.86
   2 !  119.4   0.0   2.6e-38   1.2e-34       2     144 ..     303     448 ..     302     449 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.075
                        DUF1298 108 tvlSyagklriglavdkdlvpdpqkllddle 138
                                      + y+++++i   v ++++p+p ++ d le
  gi|121639650|ref|YP_979874.1|  71 VAWAYDDDIDIDYHVRRSALPSPGRVRDLLE 101
                                    5688*******************99988776 PP

  == domain 2  score: 119.4 bits;  conditional E-value: 2.6e-38
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaalikrl....lsnttlviSNvp 77 
                                    GN +g vl++L+++++dP++r++++ ++md  K+ l+++++ ++l+l ++l +a+++ a + ++    ++ +++viSNvp
  gi|121639650|ref|YP_979874.1| 303 GNLVGSVLCNLATHVDDPAQRIQTISASMDGNKKVLSELPQLQVLAL-SALNMAPLTLAGVPGFlsavPPPFNIVISNVP 381
                                    9**********************************************.******99999966666666************ PP

                        DUF1298  78 GPqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                    GP+++ly   a+l++ yp++ + +gqalnit++  ag+l++gl+++++ vp++q+ll +le +l+ l
  gi|121639650|ref|YP_979874.1| 382 GPVDPLYYGTARLDGSYPLSNIPDGQALNITLVNNAGNLDFGLVGCRRSVPHLQRLLAHLESSLKDL 448
                                    ****************************************************************987 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   9.6e-06     0.043     116     150 ..     115     150 ..     100     157 .. 0.81
   2 ?    1.7   0.0     0.018        79     226     265 ..     233     272 ..     209     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-06
                                    S-SEEEEEEE.SSTTEEEEEEEEECCT--TTTHHHH CS
                   Condensation 116 gpLfraalfk.iaenrlllllsvHHiivDGvSlgil 150
                                     pL+  ++++ +++ r+ ++ ++HH ++DGvS   l
  gi|121639650|ref|YP_979874.1| 115 RPLWELHVVEgLNDGRFAMYTKMHHALIDGVSAMKL 150
                                    4888888886478999****************7655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.018
                                    -EEEEEEEE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHHH CS
                   Condensation 226 drlsikldeeteeklrklakeqgvtlndvllaalgllLsk 265
                                       + + +++  ++++++ ++ gvt+nd  la+ + +L  
  gi|121639650|ref|YP_979874.1| 233 GARRCAAQSWSLDRIKSVKQAAGVTVNDAVLAMCAGALRY 272
                                    5555666788999*******************98877765 PP

>> AATase  Alcohol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.6e-05      0.12     122     178 ..      98     152 ..      96     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                         AATase 122 elnellselvipvgdpkkPlwrlivlpsaddkkkwkkfvf.itdHllfDGisgvnffk 178
                                    +l+el+s l  ++ d ++Plw l v++  +d+   +  ++  + H l DG+s++++ +
  gi|121639650|ref|YP_979874.1|  98 DLLELTSRLHTSLLDRHRPLWELHVVEGLNDG---RFAMYtKMHHALIDGVSAMKLAQ 152
                                    5789999999******************8776...44445157899*******99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2473.30
//
Query:       gi|121639651|ref|YP_979875.1|  [L=162]
Description: hypothetical protein BCG_3795 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-73  243.2   0.0      1e-72  243.0   0.0    1.0  1  Adenosine_kin  Adenosine specific kinase
  ------ inclusion threshold ------
       0.24   11.4   1.5          2    8.5   0.1    2.3  2  FliMN_C        Type III flagellar switch regulator (C-ring) F


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.0   0.0   1.1e-76     1e-72       1     154 []       8     161 ..       8     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 1.1e-76
                                    EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEE CS
                  Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvil 80 
                                    v+++kp++vnv++gq+hfik+vedl+ea+v  +p+++fglafcEasg+rLvr++gnd +lvela+++alai+agh+fvi+
  gi|121639651|ref|YP_979875.1|   8 VSVDKPDDVNVVIGQAHFIKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDGDLVELATRTALAIAAGHSFVIF 87 
                                    789***************************************************************************** PP

                                    EEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                  Adenosine_kin  81 lknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                    l+++fPin+ln +++vpev++i++Atanp++v+va t +grg++gvvDG++p+gve+++d+++r++llr igYk
  gi|121639651|ref|YP_979875.1|  88 LREGFPINILNPVQAVPEVCTIYCATANPVDVVVAVTPHGRGIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYK 161
                                    *************************************************************************9 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.032   2.8e+02      31      52 ..       6      25 ..       6      29 .. 0.82
   2 ?    8.5   0.1   0.00022         2      41      63 ..     115     137 ..     110     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.032
                                   SEEE--TTGGGCEEEEETTEEE CS
                        FliMN_C 31 dvipLdkpadepvevyvngkpi 52
                                   dv+ +dkp  ++v v +++  +
  gi|121639651|ref|YP_979875.1|  6 DVVSVDKP--DDVNVVIGQAHF 25
                                   8999****..999999988655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00022
                                    GCEEEEETTEEEEEEEEEEETTE CS
                        FliMN_C  41 epvevyvngkpiarGelgvvggr 63 
                                     pv+v v   p +rG +gvv+g+
  gi|121639651|ref|YP_979875.1| 115 NPVDVVVAVTPHGRGIVGVVDGQ 137
                                    79*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 919.59
//
Query:       gi|121639652|ref|YP_979876.1|  [L=353]
Description: AraC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-36  123.8   4.8    8.6e-36  123.8   4.8    2.0  2  Arabinose_bd  Arabinose-binding domain of AraC transcription 
    4.8e-14   52.4   0.2    9.2e-14   51.5   0.2    1.5  1  HTH_18        Helix-turn-helix domain
    1.5e-06   28.1   0.0    0.00049   20.1   0.0    2.5  2  HTH_AraC      Bacterial regulatory helix-turn-helix proteins,
    0.00042   20.4   0.7       0.69   10.1   0.0    2.5  2  HTH_28        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.061   12.7   0.0       0.19   11.1   0.0    1.9  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
       0.11   12.3   0.1       0.38   10.6   0.1    1.9  1  HTH_30        PucR C-terminal helix-turn-helix domain
       0.12   13.3   0.5       0.94   10.5   0.4    2.5  2  LytR_C        LytR cell envelope-related transcriptional atte


Domain annotation for each model (and alignments):
>> Arabinose_bd  Arabinose-binding domain of AraC transcription regulator, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   4.8   3.4e-39   8.6e-36       1     187 []      20     204 ..      20     204 .. 0.94
   2 ?    1.7   0.2     0.095   2.4e+02      70     134 ..     241     300 ..     240     312 .. 0.65

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 3.4e-39
                   Arabinose_bd   1 GldpdallrragldpalladpdarvplaqyarlweaaaralgdpalGlrlgrrlrpgslgllgyaalssptlgeAlqrlv 80 
                                    G+dp++llr+ag+  +++ + da +++++  r +e aa+++   ++G rl++r+ +  lg++g+aa++++t+g+Al+ + 
  gi|121639652|ref|YP_979876.1|  20 GGDPATLLRAAGVRDQDVGNYDAFISIRAAIRAIESAAAVTATMDFGRRLAQRQGIKILGPVGVAARTAATVGDALAIFN 99 
                                    99****************************************************************************** PP

                   Arabinose_bd  81 rylrllsdalelrle..egegdlarlrlevaeilaalrafl.evlelllaallrllrwllgrrlpllrVefehpapadaa 157
                                     +++ +s  +++r++   g+++ + l +  +e    +++   +++el+l++ l+++r llg+++++l+V+++h++   +a
  gi|121639652|ref|YP_979876.1| 100 TFMAAYSPVIAIRITplAGQRSFIALEFLLDE----PAS-YpQTMELALGVALGVIRLLLGADYAPLAVHLPHDPLTPEA 174
                                    **************546777777888887776....333.3377*********************************99* PP

                   Arabinose_bd 158 eyrrlFgcpvrFgapanalvfdaadldlpl 187
                                     y ++Fgc + F +   ++++++adl++pl
  gi|121639652|ref|YP_979876.1| 175 FYLQYFGCRPYFAERVGGFTMRTADLSRPL 204
                                    *****************************7 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.095
                   Arabinose_bd  70 ptlgeAlqrlvrylrllsdalelrleegegdlarlrlevaeilaalraflevlelllaallrllr 134
                                    pt ++ l  ++  ++l+   l+ rl e++ + + l+ +v++++a++      l ++  +l +l+r
  gi|121639652|ref|YP_979876.1| 241 PTGAATLNVVAEQFHLHPKTLQRRLAEENTTFVILVDRVRKDVADR-----YLRTTGIGLTHLAR 300
                                    56777888999999***********655566566666666533332.....23344444555555 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.2   3.6e-17   9.2e-14       1      81 []     250     328 ..     250     328 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 3.6e-17
                                    HHHHHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHHHH CS
                         HTH_18   1 laaalgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPseyrr 80 
                                    +a++++++++tLqr++ +  ++t++ +++r+R + A r L+ +tg  ++++A +lG++++s ++r ++++fg+ P++yr+
  gi|121639652|ref|YP_979876.1| 250 VAEQFHLHPKTLQRRLAE-ENTTFVILVDRVRKDVADRYLR-TTGIGLTHLARELGYAEQSVLTRSCKRWFGTGPAAYRN 327
                                    599***************.9********************5.7************************************8 PP

                                    H CS
                         HTH_18  81 r 81 
                                    +
  gi|121639652|ref|YP_979876.1| 328 Q 328
                                    5 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0079        20      10      32 ..     246     268 ..     241     272 .. 0.84
   2 !   20.1   0.0   1.9e-07   0.00049       7      42 .]     291     327 ..     288     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0079
                                    -HHHHHHHTTSSHHHHHHHHHHH CS
                       HTH_AraC  10 tiediAdelgfSrsyFsrlFkke 32 
                                    t++ +A+++++++ +++r++ +e
  gi|121639652|ref|YP_979876.1| 246 TLNVVAEQFHLHPKTLQRRLAEE 268
                                    8899**************98665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.9e-07
                                    CT--HHHHHHHTTS.SHHHHHHHHHHHSSS-HHHHHH CS
                       HTH_AraC   7 tnltiediAdelgf.SrsyFsrlFkketGmtPsqyrt 42 
                                    t++ ++ +A elg+  +s ++r +k+++G  P +yr+
  gi|121639652|ref|YP_979876.1| 291 TGIGLTHLARELGYaEQSVLTRSCKRWFGTGPAAYRN 327
                                    55556779****************************7 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00027      0.69       4      36 ..     234     268 ..     233     278 .. 0.87
   2 !    8.1   0.3    0.0011       2.8       2      49 ..     280     330 ..     279     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                         HTH_28   4 eiiklla.aGh.svreaArelgisrrtvyrWikry 36 
                                    +i+++l+  G  + + +A+++++++ t++r +   
  gi|121639652|ref|YP_979876.1| 234 TIVRQLLpTGAaTLNVVAEQFHLHPKTLQRRLAEE 268
                                    6899999788899****************988765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                         HTH_28   2 RleiikllaaGh..svreaArelgisrrtv.yrWikryeegGiagLvprrr 49 
                                    R+ +  ++++      + +Arelg  +++v  r +kr+   G a+ +++ r
  gi|121639652|ref|YP_979876.1| 280 RKDVADRYLRTTgiGLTHLARELGYAEQSVlTRSCKRWFGTGPAAYRNQAR 330
                                    778888899854469999*********99999999999999**99998865 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.6e-05      0.19      23      48 ..     239     265 ..     233     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.6e-05
                   HTH_Tnp_ISL3  23 llles.rsvkavArqlgvSwtTVwril 48 
                                    ll  + ++   vA+q++++++T++r+l
  gi|121639652|ref|YP_979876.1| 239 LLPTGaATLNVVAEQFHLHPKTLQRRL 265
                                    55555678888**************98 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.38      15      34 ..     247     266 ..     235     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                    HHHHHHHHTS-HHHHHHHHH CS
                         HTH_30  15 isatAkaLhvHrnTlryRLr 34 
                                    ++ +A++ h+H+ Tl+ RL 
  gi|121639652|ref|YP_979876.1| 247 LNVVAEQFHLHPKTLQRRLA 266
                                    5678**************96 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00037      0.94      12      66 ..      16      67 ..      10      99 .. 0.76
   2 ?   -1.1   0.0       1.5   3.9e+03      76      85 .]     144     158 ..     121     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                         LytR_C 12 vsGlAarvadaLeerGftvgevgnagnadeettivyreaaa..aaakalaaalglge 66
                                   v+Gl ++ a++L+++G +  +   +gn+d+  +i++  a +  ++a a+ a++ +g+
  gi|121639652|ref|YP_979876.1| 16 VAGLGGDPATLLRAAGVRDQD---VGNYDAFISIRA--AIRaiESAAAVTATMDFGR 67
                                   79**************99999...677755556664..2223367888888888777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                         LytR_C  76 s.....vtvvlGkdf 85 
                                    +     ++++lG+d+
  gi|121639652|ref|YP_979876.1| 144 GvalgvIRLLLGADY 158
                                    033445999****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1958.75
//
Query:       gi|121639653|ref|YP_979877.1|  [L=529]
Description: hypothetical protein BCG_3797 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-68  228.7  37.4    4.3e-63  212.9  12.0    2.0  2  ThrE      Putative threonine/serine exporter
    1.6e-13   50.9  12.3    1.6e-13   50.9  12.3    2.4  3  ThrE_2    Threonine/Serine exporter, ThrE


Domain annotation for each model (and alignments):
>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.9  12.0   4.8e-67   4.3e-63       1     238 [.      49     287 ..      49     289 .. 0.98
   2 !   22.0  17.4     1e-08     9e-05     105     237 ..     313     445 ..     295     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 212.9 bits;  conditional E-value: 4.8e-67
                           ThrE   1 dlilrlGeiLlesGaetyrvedtmkriaralgleevevfvtptsiivsv.d.eeeesittvrrvrsrgvnleklsevnel 78 
                                    dl++rl+e++l+sG++t++v++t + +a+a++l+++ v++t+t+iivs+   ++  ++t +r vr+r++++++l+e+++l
  gi|121639653|ref|YP_979877.1|  49 DLTIRLAEVMLSSGSGTADVVATAQDVAQAYQLTDCVVDITVTTIIVSAlAtTDTPPVTIMRSVRTRSTDYSRLAELDRL 128
                                    5789*********************************************76888999999******************** PP

                           ThrE  79 sreiaageisleeaeerLdeIerskpryprwlvvlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsf 158
                                    +++i++g + +++a+e++de+++++++yprwl++++a+ +a ++a+l+gg+w+ +++a+++++++++l +ll+++g++ f
  gi|121639653|ref|YP_979877.1| 129 VQRITSGGVAVDQAHEAMDELTERPHPYPRWLATAGAAGFALGVAMLLGGTWLTCVLAAVTSGVIDRLGRLLNRIGTPLF 208
                                    ******************************************************************************** PP

                           ThrE 159 vleavaaflasllallavslglglnpdaiiigsillLvPGlpltnavrDllsgdlvsGlaRlveailialaiafGivlal 238
                                    ++ +++a +a+l+a++a+ +  g++p+a+++ +i++L++G++l+ +++D+++g+++++laRl +a++++++i++Gi+++l
  gi|121639653|ref|YP_979877.1| 209 FQRVFGAGIATLVAVAAYLI-AGQDPTALVATGIVVLLSGMTLVGSMQDAVTGYMLTALARLGDALFLTAGIVVGILISL 287
                                    *******************7.4899****************************************************987 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1e-08
                           ThrE 105 ryprwlvvlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallavslglglnp 184
                                    + p +++v +a+l+++++++   + +  ++ a l ++l+ l+   l   g+ ++v++ +aa+ +++la l+     +  +
  gi|121639653|ref|YP_979877.1| 313 PLPILVAVSGAALSGVCLTIASYAPLRSVATAGLSAGLAELVLIGLGAAGFGRVVATWTAAIGVGFLATLISI-RRQAPA 391
                                    678899999***********************************************************66655.434445 PP

                           ThrE 185 daiiigsillLvPGlpltnavrDllsgd.lvsGlaRlveailialaiafGivla 237
                                       ++++i++++PGl++  av   + +d +  Gl+ l+ea+ +ala++ G+vl+
  gi|121639653|ref|YP_979877.1| 392 LVTATAGIMPMLPGLAVFRAVFAFAVNDtPDGGLTQLLEAAATALALGSGVVLG 445
                                    888999***************998877625679******************997 PP

>> ThrE_2  Threonine/Serine exporter, ThrE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       1.7   1.5e+04     102     120 ..      81      99 ..      71     100 .. 0.58
   2 !    9.3  12.5   0.00014       1.2       5     126 ..     165     286 ..     160     288 .. 0.91
   3 !   50.9  12.3   1.8e-17   1.6e-13       5     128 ..     323     447 ..     319     448 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.7
                         ThrE_2 102 leeavengiealliagala 120
                                    l+++v  ++ + +i+ ala
  gi|121639653|ref|YP_979877.1|  81 LTDCVVDITVTTIIVSALA 99 
                                    4445555555555555555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00014
                         ThrE_2   5 afiaalgfavifnvpkrallvagllGavgwlvylllmelgvsialasflaalaigllsellArriktPvtvflipgllpl 84 
                                    a+ +alg a+++   +   ++a+++ +v   +  ll  +g ++ ++ +++a + +l++  +  +     t ++  g++ l
  gi|121639653|ref|YP_979877.1| 165 AAGFALGVAMLLGGTWLTCVLAAVTSGVIDRLGRLLNRIGTPLFFQRVFGAGIATLVAVAAYLIAGQDPTALVATGIVVL 244
                                    67789999999999998888888888777777888999**************99999999999999999*********** PP

                         ThrE_2  85 vPGlaaYktvlslvqgnleeavengiealliagalavGlvlv 126
                                      G+ +  +++  v+g++ +a+  +  al+ +++++vG++++
  gi|121639653|ref|YP_979877.1| 245 LSGMTLVGSMQDAVTGYMLTALARLGDALFLTAGIVVGILIS 286
                                    ***************************************987 PP

  == domain 3  score: 50.9 bits;  conditional E-value: 1.8e-17
                         ThrE_2   5 afiaalgfavifnvpkrallvagllGavgwlvylllmelgvsialasflaalaigllsellArriktPvtvflipgllpl 84 
                                    a++  +++ +++ +p r +  agl ++++ lv + l + g + ++a+ +aa+ +g+l++l++ r ++P+ v + +g++p+
  gi|121639653|ref|YP_979877.1| 323 AALSGVCLTIASYAPLRSVATAGLSAGLAELVLIGLGAAGFGRVVATWTAAIGVGFLATLISIRRQAPALVTATAGIMPM 402
                                    788999************************************************************************** PP

                         ThrE_2  85 vPGlaaYktvlslvqgn.leeavengiealliagalavGlvlvsl 128
                                     PGla++++v++++ ++  +  +++++ea ++a+al  G+vl ++
  gi|121639653|ref|YP_979877.1| 403 LPGLAVFRAVFAFAVNDtPDGGLTQLLEAAATALALGSGVVLGEF 447
                                    ************9876648999*******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.54
# Mc/sec: 2943.15
//
Query:       gi|121639654|ref|YP_979878.1|  [L=448]
Description: hypothetical protein BCG_3799c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-97  324.8   2.4    1.6e-96  323.2   1.3    1.9  2  WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransfer
    2.6e-39  134.5   0.0    7.1e-39  133.0   0.0    1.8  2  DUF1298         Protein of unknown function (DUF1298)
    0.00015   20.6   0.1      0.017   13.8   0.1    2.1  2  Condensation    Condensation domain


Domain annotation for each model (and alignments):
>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.2   1.3  2.6e-100   1.6e-96       1     264 []       1     257 [.       1     257 [. 0.98
   2 ?    0.5   0.0     0.069   4.1e+02     149     219 ..     265     346 ..     261     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 323.2 bits;  conditional E-value: 2.6e-100
                 WES_acyltransf   1 LsplDalflelesaetpmhvgalavleppskgagelllrrlreaieqreeraprlrqkvveeplglaapvWvededfDld 80 
                                    +sp+Dalfl++es+e+p+hvgal+++epp +gag+ ++r++++a+ q++e ap +r+++++ +++l +  W +d d+Dl+
  gi|121639654|ref|YP_979878.1|   1 MSPIDALFLSAESREHPLHVGALQLFEPP-AGAGRGFVRETYQAMLQCREIAPLFRKRPTSLHGALINLGWSTDADVDLG 79 
                                    89***************************.************************************************** PP

                 WES_acyltransf  81 yHvRrvalpaPGterellelvsrLasspLDrsrPlWevhviEGleggriAillkvHHAliDGvgglkllarlldldpddp 160
                                    yH Rr+alpaPG+ rellel+srL+s++LDr+rPlWe+hviEGl++gr+Ai+ k+HHAl+DGv+gl+l+++ +++dp + 
  gi|121639654|ref|YP_979878.1|  80 YHARRSALPAPGRVRELLELTSRLHSNLLDRHRPLWETHVIEGLRDGRFAIYSKMHHALVDGVSGLTLMRQPMTTDPIEG 159
                                    ******************************************************************************** PP

                 WES_acyltransf 161 prpeppqvpprdrsrtqlrasgalvglvaglgkvlgsvagvvssagrlleaalearslvlpfaaprtplntplsraRrfa 240
                                    ++++ ++ p+++  +t+++++   +g +++lg++lgsvag++ s+ rl+++al++++l+lpf ap+t+ln ++++aRr+a
  gi|121639654|ref|YP_979878.1| 160 KLRTAWS-PATQ--HTAIKRR---RGRLQQLGGMLGSVAGLAPSTLRLARSALIEQQLTLPFGAPHTMLNVAVGGARRCA 233
                                    *******.7777..7888874...699***************************************************** PP

                 WES_acyltransf 241 aaslpLadvkavakalgvtiNDvv 264
                                    a+s+pL++vkav++a+gv++NDvv
  gi|121639654|ref|YP_979878.1| 234 AQSWPLDRVKAVKDAAGVSLNDVV 257
                                    ***********************7 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.069
                 WES_acyltransf 149 larlldldpddpprpeppqvpprdrsrtqlrasg.............alvglvaglgkvlgsvagvvssagrlleaalea 215
                                    l++ ld+++  p  p + +vp +   rt++++ g              l +++++l ++ +s++g ++++ +l +a + a
  gi|121639654|ref|YP_979878.1| 265 LREYLDDNDALPDTPLVAMVPVSL--RTDRDSVGgnmvgavlcnlatHLDDPADRLNAIHASMRGNKNVLSQLPRAQALA 342
                                    667777777778888888888887..666666556888898888888888999999999999999988888888877666 PP

                 WES_acyltransf 216 rslv 219
                                    +sl+
  gi|121639654|ref|YP_979878.1| 343 VSLL 346
                                    6554 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.5   9.2e+03     110     136 ..      70      96 ..      58      98 .. 0.78
   2 !  133.0   0.0   1.2e-42   7.1e-39       2     144 ..     297     442 ..     296     443 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                        DUF1298 110 lSyagklriglavdkdlvpdpqklldd 136
                                    +S + ++++g  + ++++p p ++ + 
  gi|121639654|ref|YP_979878.1|  70 WSTDADVDLGYHARRSALPAPGRVREL 96 
                                    788889999999999999999887665 PP

  == domain 2  score: 133.0 bits;  conditional E-value: 1.2e-42
                        DUF1298   2 GNqigvvllpLpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaal...ikrllsnttlviSNvpG 78 
                                    GN +g+vl++L+++l+dP++rl++++++m+  K+ l++++  ++l++ l ll ++++ +l   +k +++ ++++iSNvpG
  gi|121639654|ref|YP_979878.1| 297 GNMVGAVLCNLATHLDDPADRLNAIHASMRGNKNVLSQLPRAQALAVSLLLLSPAALNTLpglAKATPPPFNVCISNVPG 376
                                    9**********************************************77777777777777777777************* PP

                        DUF1298  79 PqeelylaGaplkaiypvvpglpgqalnitvlSyagklriglavdkdlvpdpqkllddleealeel 144
                                     +e+ly++Ga++++ yp++++l+gqalnit++S a++l++g++++ + vp++q++l++le++l+el
  gi|121639654|ref|YP_979878.1| 377 AREPLYFNGARMVGNYPMSLVLDGQALNITLTSTADSLDFGVVGCCRSVPHVQRVLSHLETSLKEL 442
                                    ****************************************************************98 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.8e-06     0.017     116     153 ..     112     150 ..      93     154 .. 0.83
   2 !    4.7   0.0    0.0017        10     232     295 ..     234     303 ..     205     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-06
                                    S-SEEEEEEE.SSTTEEEEEEEEECCT--TTTHHHHHHH CS
                   Condensation 116 gpLfraalfk.iaenrlllllsvHHiivDGvSlgillrd 153
                                     pL+  ++++ + + r+ ++ ++HH +vDGvS  +l+r+
  gi|121639654|ref|YP_979878.1| 112 RPLWETHVIEgLRDGRFAIYSKMHHALVDGVSGLTLMRQ 150
                                    4888888886478999****************9999997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0017
                                    EEE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-SEE......EEEEEEESSTTCSTCHHC--SS- CS
                   Condensation 232 ldeeteeklrklakeqgvtlndvllaalgllLskytgqddi......vvgteisgReseikdiermvGlF 295
                                     +++  ++++ +  + gv+lndv la+ + +L +y   +d+      v  +++s R++ ++   +mvG  
  gi|121639654|ref|YP_979878.1| 234 AQSWPLDRVKAVKDAAGVSLNDVVLAMCAGALREYLDDNDAlpdtplVAMVPVSLRTDRDSVGGNMVGAV 303
                                    5666778899999**********************99988622222245555666666655556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2455.02
//
Query:       gi|121639655|ref|YP_979879.1|  [L=224]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1244.41
//
Query:       gi|121639656|ref|YP_979880.1|  [L=131]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-05   24.1   0.1    2.4e-05   24.1   0.1    1.6  2  DAO            FAD dependent oxidoreductase
    9.6e-05   21.7   0.1    0.00035   19.9   0.0    1.7  2  Thi4           Thi4 family
    0.00018   20.9   1.0      0.039   13.2   0.1    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00056   18.6   0.0     0.0046   15.6   0.0    1.9  2  Mqo            Malate:quinone oxidoreductase (Mqo)
      0.001   19.3   1.3     0.0087   16.3   0.0    2.3  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0028   16.8   0.2        1.2    8.2   0.0    2.0  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0035   17.9   0.6        1.8    9.2   0.0    2.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0043   17.1   0.1        2.2    8.3   0.0    2.1  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.041   13.2   0.2      0.085   12.1   0.0    1.7  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.15   11.4   0.3       0.99    8.7   0.1    2.3  2  ThiF           ThiF family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.4e-08   2.4e-05       1      33 [.      13      48 ..      13     104 .. 0.80
   2 ?   -1.9   0.1       1.1     2e+03       3      13 ..     105     115 ..     103     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                                   EEEEECTSHHHHHHHHHHHHT.T...EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarr.g...Vtllekgdiag 33
                                   dv+i+G+Gi G ++Ay+L +  +    +++e++  ++
  gi|121639656|ref|YP_979880.1| 13 DVLIVGAGISGTGAAYYLKTMqPaktFAIVEAR-YPA 48
                                   8*****************543347799****99.766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    EEECTSHHHHH CS
                            DAO   3 viiGGGiiGls 13 
                                    viiG+G + ++
  gi|121639656|ref|YP_979880.1| 105 VIIGSGATAVT 115
                                    88888887665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.9e-07   0.00035      14      50 ..       8      45 ..       2      48 .. 0.86
   2 ?   -0.9   0.0      0.44   7.8e+02      17      38 ..     101     122 ..      91     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.9e-07
                                   HHTEEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESS CS
                           Thi4 14 kyaesDvvivGaGssGLtaayylakk.pdlkvailers 50
                                   ++   Dv+ivGaG sG  aayyl +  p    ai+e++
  gi|121639656|ref|YP_979880.1|  8 SIEHVDVLIVGAGISGTGAAYYLKTMqPAKTFAIVEAR 45
                                   56679******************998798888999976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.44
                                    EEEEEEE--SHHHHHHHHHHHH CS
                           Thi4  17 esDvvivGaGssGLtaayylak 38 
                                    e  +vi+G+G++ +t    +a+
  gi|121639656|ref|YP_979880.1| 101 ELRMVIIGSGATAVTLVPAMAQ 122
                                    6678999999998887666665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   2.2e-05     0.039       2      29 ..      13      41 ..      12      75 .. 0.84
   2 !    7.1   0.1    0.0015       2.7     142     165 ..      98     124 ..      62     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                   SEEEE--SHHHHHHHHHHHH.HTS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq.agakvtlv 29
                                   dv+++G+G+ G+ aa +l++ + ak+  +
  gi|121639656|ref|YP_979880.1| 13 DVLIVGAGISGTGAAYYLKTmQPAKTFAI 41
                                   89*****************9767777766 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0015
                                    T...SEEEEES-SHHHHHHHHHHHHHT CS
                                    x...xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 142 p...krivvvGgGyiGvElAaalaklg 165
                                    +    r+v++G+G+++v l  a+a+ +
  gi|121639656|ref|YP_979880.1|  98 RhheLRMVIIGSGATAVTLVPAMAQTA 124
                                    233356899999999998766655554 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-06    0.0046       2      36 ..      11      45 ..      10      57 .. 0.88
   2 ?    1.0   0.0     0.067   1.2e+02     223     247 ..      93     117 ..      87     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                            Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerl 36
                                   +vdv+++GaGi  +  + +lk+++p  + +++e  
  gi|121639656|ref|YP_979880.1| 11 HVDVLIVGAGISGTGAAYYLKTMQPAKTFAIVEAR 45
                                   79******************************975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.067
                            Mqo 223 ktgekkkvkakfvfiGaGGgalklL 247
                                    +++++++++ ++v iG+G +a++l+
  gi|121639656|ref|YP_979880.1|  93 RHRRTRHHELRMVIIGSGATAVTLV 117
                                    5667888999999999999999986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.8e-06    0.0087       1      27 [.      16      44 ..      16      62 .. 0.83
   2 ?    1.5   0.6       0.2   3.5e+02       1      12 [.     106     117 ..     106     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                                   EE--SHHHHHHHHHHHCC..TEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllek 27
                                   IvGaG+sG  aAy+L+     +   ++e+
  gi|121639656|ref|YP_979880.1| 16 IVGAGISGTGAAYYLKTMqpAKTFAIVEA 44
                                   9**************97433556666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                    EE--SHHHHHHH CS
                  NAD_binding_8   1 IvGaGlsGlvaA 12 
                                    I+G+G+++ ++ 
  gi|121639656|ref|YP_979880.1| 106 IIGSGATAVTLV 117
                                    9*****999876 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00066       1.2     186     230 ..       6      50 ..       1      75 [. 0.76
   2 !    7.0   0.0    0.0015       2.7     179     214 ..      89     124 ..      75     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00066
                    K_oxygenase 186 eellakkriaVvGsGqSaaeifedllrrqkkvelklvtrsealep 230
                                    +++ ++ ++++vG+G S+   ++ l + q++++ ++v  +     
  gi|121639656|ref|YP_979880.1|   6 SASIEHVDVLIVGAGISGTGAAYYLKTMQPAKTFAIVEARYPAIR 50 
                                    446677899******************999998888866654444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0015
                    K_oxygenase 179 seylerkeellakkriaVvGsGqSaaeifedllrrq 214
                                    +++l++++ ++++ r++++GsG +a  ++  +++++
  gi|121639656|ref|YP_979880.1|  89 DRTLRHRRTRHHELRMVIIGSGATAVTLVPAMAQTA 124
                                    56778888899999***********99988887765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.001       1.8       2      23 ..      14      36 ..      13      57 .. 0.78
   2 ?   -3.0   0.0       6.4   1.1e+04      27      45 ..      78      95 ..      73     101 .. 0.55
   3 !    6.8   0.2    0.0056        10       1      26 [.     103     128 ..     103     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                                   EEEECSSHHHHHHHHHHHHTT.S CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg.k 23
                                   v++vG+G +g  +A +l+ ++ +
  gi|121639656|ref|YP_979880.1| 14 VLIVGAGISGTGAAYYLKTMQpA 36
                                   89***************987753 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                                   EEESSSSSSTTSSHHHHHH CS
                      Pyr_redox 27 vversdkllrllDeeaski 45
                                   +v+r+  l  + D++++ +
  gi|121639656|ref|YP_979880.1| 78 MVHRGRSLA-GGDRTLRHR 95
                                   455554444.556665555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0056
                                    EEEEECSSHHHHHHHHHHHHTTSEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVt 26 
                                    ++v++G+G +++ l  a+a+ +  Vt
  gi|121639656|ref|YP_979880.1| 103 RMVIIGSGATAVTLVPAMAQTAGAVT 128
                                    68**********99999999888877 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0012       2.2       9      37 ..       8      36 ..       2      53 .. 0.81
   2 !    6.9   0.1    0.0035       6.2       9      34 ..      98     123 ..      91     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvk 37
                                   s+++  vl++GaG  ++ +a +L + +  
  gi|121639656|ref|YP_979880.1|  8 SIEHVDVLIVGAGISGTGAAYYLKTMQPA 36
                                   678899****************9887543 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0035
                                    ..TT-EEEEES-SHHHHHHHHHHHCC CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlak 34 
                                    +++e ++++iG G +a  ++ ++++ 
  gi|121639656|ref|YP_979880.1|  98 RHHELRMVIIGSGATAVTLVPAMAQT 123
                                    567899*************9999864 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.7e-05     0.085      26      51 ..       9      34 ..       4      79 .. 0.80
   2 ?   -1.2   0.1      0.59   1.1e+03      30      44 ..     103     117 ..      86     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                                   B---EEEEESTSHHHHHHHHHHHHTT CS
                    AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakglg 51
                                   +e+  vl++G+G+ G+ A+   k ++
  gi|121639656|ref|YP_979880.1|  9 IEHVDVLIVGAGISGTGAAYYLKTMQ 34
                                   66889**************9999986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.59
                                    EEEEESTSHHHHHHH CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAi 44 
                                    ++++iG G   +  +
  gi|121639656|ref|YP_979880.1| 103 RMVIIGSGATAVTLV 117
                                    678888886655443 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00055      0.99      12      42 ..       5      35 ..       1      83 [. 0.68
   2 ?   -0.4   0.0      0.33   5.8e+02      18      34 ..     101     117 ..      85     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                                   HHHHHHTSEEEEE--SHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 12 gqekLrdskvllvGaGglGsellknLalsGv 42
                                     + ++++ vl+vGaG  G  ++ +L  +  
  gi|121639656|ref|YP_979880.1|  5 QSASIEHVDVLIVGAGISGTGAAYYLKTMQP 35
                                   5678999****************99988766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                                    TSEEEEE--SHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                           ThiF  18 dskvllvGaGglGsell 34 
                                    + +++++G G+    l+
  gi|121639656|ref|YP_979880.1| 101 ELRMVIIGSGATAVTLV 117
                                    36667777776554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 727.34
//
Query:       gi|121639657|ref|YP_979881.1|  [L=660]
Description: cation transporter P-type atpase ctpJ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-47  159.4   1.8    6.5e-47  159.4   1.8    2.0  2  E1-E2_ATPase  E1-E2 ATPase
    3.7e-39  135.2   3.6    6.7e-39  134.3   3.6    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
     0.0015   18.4   0.1     0.0026   17.6   0.1    1.3  1  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.051   14.0   0.5       0.39   11.1   0.2    2.6  2  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   1.8   1.5e-50   6.5e-47       2     180 ..     138     317 ..     137     318 .. 0.97
   2 ?   -2.3   0.2      0.61   2.7e+03     110     137 ..     586     613 ..     568     626 .. 0.63

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 1.5e-50
                                    SS--EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                   E1-E2_ATPase   2 llpptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                    l p ta+++  +g ee+++a++l++GDivl+++g+r++aD+ ++ g +evd++ +TGE lpv+k+ gd+vf+Gtv+  g 
  gi|121639657|ref|YP_979881.1| 138 LAPGTATRVgAGGGEETVNAADLRIGDIVLVRPGERISADATVLAGGSEVDQATVTGEPLPVDKSIGDQVFAGTVNGTGA 217
                                    5677888888999******************************************************************* PP

                                    EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiP 160
                                    ++++V ++++d+ +++ia+lve+a+++k+++q +++k+ + +++ +++++l+vf++ +l+g++l++allra++++++a P
  gi|121639657|ref|YP_979881.1| 218 LRIRVDRLARDSVVARIATLVEQASQTKARTQLFIEKVEQRYSIGMVAVTLAVFAVPPLWGETLQRALLRAMTFMIVASP 297
                                    ******************************************************************************** PP

                                    TTHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 161 caLplavplalalgarrlak 180
                                    ca +la+   l+++++++ +
  gi|121639657|ref|YP_979881.1| 298 CAVVLATMPPLLAAIANAGR 317
                                    ********999999998766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.61
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase 110 plqkkldklgkvlvpvvlliallvflia 137
                                    p++  +++ ++ +v++ l++a+++++ +
  gi|121639657|ref|YP_979881.1| 586 PTVIAMSRRARRIVVANLIVAVTFIAGL 613
                                    5555666666666666666555555444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   3.6   1.5e-42   6.7e-39       4     209 ..     337     555 ..     334     556 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.5e-42
                                    EEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx...... RF
                      Hydrolase   4 vvfDkdGTLttgepsvedvivsa.......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg...... 67 
                                    ++fDk+GTLt+g+p++  ++v+         l laaa e+ sehp+g+a+v+aa+ r    + + +f++ +g+       
  gi|121639657|ref|YP_979881.1| 337 IAFDKTGTLTRGTPELAGIWVYErrftddeLLRLAAAAEYPSEHPLGAAIVKAAQSRrirLPTVGEFTAHPGCRvtarvd 416
                                    89**********************99998888888999999****************67555559999999999****** PP

                                    ..HHHHTHHHHHHHH....HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT.TEEEE CS
                                    ..xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      Hydrolase  68 ..ayaigkpewltal....dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaa.gievv 138
                                      ++a+g+   l         +  +  a++ +q++g tv+++  + + +++++i d+  ++peaa a+ +  +  g + v
  gi|121639657|ref|YP_979881.1| 417 ghVIAVGSATALLGTagaaALEASMITAVDFLQGEGYTVVVVvcDSHPVGLLAITDQ--LRPEAAAAISAATKLtGAKPV 494
                                    *9777777765555556666667789999*********999999*************..***********99999***** PP

                                    EEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 139 lltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                    lltgdn++ta+r+  q+G          ++++ a+ +p++kvaa+r+Lq+ +++  +VGDg+nDa+alaaA
  gi|121639657|ref|YP_979881.1| 495 LLTGDNRATADRLGVQVG----------IDDVRAGLLPDDKVAAVRQLQAGGARLTVVGDGINDAPALAAA 555
                                    ******************..........6666**************************************9 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.7e-07    0.0026     198     236 ..     531     569 ..     524     583 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.7e-07
                                    HCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHH CS
                    Hydrolase_3 198 elnisleeviafGDgeNDieMLeaaglgvAmgnaseevk 236
                                    +l+   ++  ++GDg ND + L aa +g+Amg+a+ e+ 
  gi|121639657|ref|YP_979881.1| 531 QLQAGGARLTVVGDGINDAPALAAAHVGIAMGSARSELT 569
                                    56677788899***********************99875 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1     5e+03       3      12 ..     339     348 ..     297     398 .. 0.60
   2 ?   11.1   0.2   8.6e-05      0.39      84     187 ..     473     552 ..     463     553 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                            HAD   3 fDfDgTLldg 12 
                                    fD  gTL++g
  gi|121639657|ref|YP_979881.1| 339 FDKTGTLTRG 348
                                    4444555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.6e-05
                            HAD  84 klldpgalella.ahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewl 162
                                    + l+p+a ++++ a +  G + v+++g +r  + +l  ++g    ++        + ++          ++kvaa+r+  
  gi|121639657|ref|YP_979881.1| 473 Q-LRPEAAAAISaATKLTGAKPVLLTGDNRATADRLGVQVG----IDD-------VRAG-------LLPDDKVAAVRQ-- 531
                                    4.569999999978889999**********99999999999....777.......5555.......333455566666.. PP

                            HAD 163 aaegegidleevvayGDspsDlpll 187
                                          +  +++ ++GD+++D p+l
  gi|121639657|ref|YP_979881.1| 532 ----LQAGGARLTVVGDGINDAPAL 552
                                    ....334667799**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 3593.31
//
Query:       gi|121639658|ref|YP_979882.1|  [L=120]
Description: ArsR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-16   58.8   0.1    6.7e-16   57.9   0.1    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    3.6e-12   46.1   0.5    5.7e-12   45.5   0.5    1.3  1  HTH_20          Helix-turn-helix domain
      1e-07   31.8   0.5    1.8e-07   30.9   0.3    1.5  1  MarR_2          MarR family
    7.6e-06   25.6   0.2    1.5e-05   24.7   0.2    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    4.1e-05   23.1   0.0    6.4e-05   22.4   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    4.7e-05   23.2   0.0    7.4e-05   22.6   0.0    1.3  1  MarR            MarR family
    0.00013   21.9   0.2    0.00019   21.3   0.2    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0003   20.6   0.0    0.00048   20.0   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00069   20.1   0.0     0.0011   19.4   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
     0.0038   17.3   0.1      0.013   15.5   0.0    1.9  2  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
     0.0097   15.7   0.0      0.019   14.8   0.0    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.4   3.7      0.043   13.9   3.7    1.8  1  DprA_WH         DprA winged helix domain
      0.024   14.6   0.0      0.024   14.6   0.0    1.6  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.026   14.5   0.1      0.035   14.1   0.1    1.2  1  Dimerisation2   Dimerisation domain
      0.026   14.8   0.1      0.034   14.5   0.1    1.3  1  Rrf2            Transcriptional regulator
      0.043   14.0   0.0      0.088   13.0   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.055   13.3   0.0      0.077   12.8   0.0    1.3  1  HxlR            HxlR-like helix-turn-helix
      0.063   12.9   0.0      0.089   12.5   0.0    1.3  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.079   12.9   0.0       0.13   12.2   0.0    1.3  1  HTH_11          HTH domain
        0.1   12.9   0.0       0.14   12.4   0.0    1.2  1  PaaX            PaaX-like protein
       0.13   11.9   0.0       0.14   11.7   0.0    1.2  1  CheW            CheW-like domain
       0.17   12.0   0.0       0.27   11.3   0.0    1.3  1  Cro             Cro


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.1   8.2e-19   6.7e-16       2      45 ..      33      76 ..      32      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 8.2e-19
                                   HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   p Rl IL +L++g+l v++lae++g+ qs+vSh+L++Lr++GLV
  gi|121639658|ref|YP_979882.1| 33 PSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLV 76
                                   99*****************************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.5     7e-15   5.7e-12       3      61 .]      26      83 ..      21      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7e-15
                                   HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                    + ALa P+R++il  L r+++l +++lae++++ ++ +s++LrvL+  gLv + r gr
  gi|121639658|ref|YP_979882.1| 26 TLQALATPSRLMILTQL-RNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGR 83
                                   4689*************.***********************************999886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.3   2.3e-10   1.8e-07       4      52 ..      32      77 ..      28      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.3e-10
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   tp+ +++L  L+++p   l v++la++ g+++savs  l+ L   GLv+
  gi|121639658|ref|YP_979882.1| 32 TPSRLMILTQLRNGP---LPVTDLAEAIGMEQSAVSHQLRVLRNLGLVV 77
                                   899********9999...9*****************************6 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.2   1.9e-08   1.5e-05       6      50 ..      36      78 ..      35      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   l+iL +l+ +p    +++lA+++g+  S+v++ L+ L +lG+v  
  gi|121639658|ref|YP_979882.1| 36 LMILTQLRNGPL--PVTDLAEAIGMEQSAVSHQLRVLRNLGLVVG 78
                                   567777766665..5***************************975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.9e-08   6.4e-05      14      47 ..      43      76 ..      33      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-08
                         HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +n+ ++ ++LAe++g+ +s+v+ +l+ L + Gl+
  gi|121639658|ref|YP_979882.1| 43 RNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLV 76
                                   47******************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   9.1e-08   7.4e-05       2      47 ..      32      76 ..      31      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.1e-08
                                   -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                   t+++++iL++l+ +gpl v++La+++g+++s+v+ +l+ L   Gl+
  gi|121639658|ref|YP_979882.1| 32 TPSRLMILTQLR-NGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLV 76
                                   788999999997.5***********************999877776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   2.4e-07   0.00019       3      57 ..      23      85 ..      21      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHCTTTC.....EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EE.E CS
                      HTH_Crp_2  3 lArfLlrlaeragg.....eielpltqeelAsmlGltretvsrilseLkreglis.rg.rr.i 57
                                   +A++L  la  ++        + pl  ++lA+ +G+ ++ vs  l+ L++ gl+   + +r i
  gi|121639658|ref|YP_979882.1| 23 VASTLQALATPSRLmiltqLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVgDRaGRsI 85
                                   788888886653312322223459999***************************963323334 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.9e-07   0.00048      18      65 ..      42      90 ..      37      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.9e-07
                                   HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE- CS
                           TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYrav 65
                                   l++gp+ ++++ae++g ++s v   Lr L + GlV   + gr  +Y+  
  gi|121639658|ref|YP_979882.1| 42 LRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRaGRSIVYSLY 90
                                   789*******************************987774556677655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-06    0.0011       2      59 ..      32      84 ..      31      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                         HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                   t++  ++L ++r  +++   +dl+++  +e+s++s  l+ L + GLv   gd+  +r+
  gi|121639658|ref|YP_979882.1| 32 TPSRLMILTQLR--NGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLV--VGDR-AGRS 84
                                   677789******..*********************************..6664.4444 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.013      23      57 ..      42      76 ..      34      77 .. 0.94
   2 ?   -2.9   0.0       9.3   7.6e+03       5      17 ..      84      96 ..      83      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                                   HHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                          HTH_9 23 lrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                   lr+g l++++l++++++  + V + L vL +++lV
  gi|121639658|ref|YP_979882.1| 42 LRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLV 76
                                   89****************************99998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.3
                                   HHHHHCSTTHHHH CS
                          HTH_9  5 eiieehFGevvak 17
                                   +i+ +++++ va+
  gi|121639658|ref|YP_979882.1| 84 SIVYSLYDTHVAQ 96
                                   5777788877765 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.4e-05     0.019      14      35 ..      43      64 ..      37      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                  HTH_AsnC-type 14 edaRisyaeLAervGlSestvl 35
                                   +++ +++++LAe++G+ +s+v 
  gi|121639658|ref|YP_979882.1| 43 RNGPLPVTDLAEAIGMEQSAVS 64
                                   69******************96 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.7   5.3e-05     0.043       7      46 ..      28      67 ..       8      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                        DprA_WH  7 epplddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaL 46
                                   ++ +++ +  +L++L + P++v +L+++ g++ ++vs++L
  gi|121639658|ref|YP_979882.1| 28 QALATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQL 67
                                   344599999*****************************99 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.9e-05     0.024      20      40 ..      53      73 ..      49      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                                   HHHHTS-HHHHHHHHHHHHHH CS
                          HTH_1 20 AeeLglsqpavsrqikrLEee 40
                                   Ae+ g+ q+avs+q++ L+++
  gi|121639658|ref|YP_979882.1| 53 AEAIGMEQSAVSHQLRVLRNL 73
                                   99****************984 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.3e-05     0.035      13      78 ..      28      91 ..      17     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                  Dimerisation2 13 kaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsnte 78
                                   +aL t ++L +   L++ +pl + ++ae++g++ ++++  l+++  LgL   ++  +++ +Ys  +
  gi|121639658|ref|YP_979882.1| 28 QALATPSRLMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRA-GRSIVYSLYD 91
                                   799999*********99.*******************************997744.4467887544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.2e-05     0.034      14      57 ..      36      78 ..      22      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                                   HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   l++L++ ++ +p+ ++++ae  ++++s +++ l+ Lr+ glv  
  gi|121639658|ref|YP_979882.1| 36 LMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVG 78
                                   455555555.57*****************************965 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.088      23      53 ..      47      77 ..      38      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyve 53
                                     ++dlae+++ + s Vs  l+ L++ G+v+
  gi|121639658|ref|YP_979882.1| 47 LPVTDLAEAIGMEQSAVSHQLRVLRNLGLVV 77
                                   5689*************************96 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05     0.077       8      50 ..      36      77 ..      33     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                                   HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEE CS
                           HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglie 50
                                   l+il++l +g+   ++l++a+ ++ q+  +++Lr L + gl+ 
  gi|121639658|ref|YP_979882.1| 36 LMILTQLRNGPLPVTDLAEAI-GMEQSAVSHQLRVLRNLGLVV 77
                                   68*******************.89*************999984 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.089      21      55 ..      44      78 ..      26      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                   HrcA_DNA-bdg 21 kravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                   + ++  +++Ae+++ ++  v  ql +L+ lgLv g
  gi|121639658|ref|YP_979882.1| 44 NGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVG 78
                                   55666789*************************87 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.13       5      46 ..      38      77 ..      35      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                         HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                   il++L   +gp++  +LAe +++  ++v   ++ L+ lg+ +
  gi|121639658|ref|YP_979882.1| 38 ILTQL--RNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVV 77
                                   67777..3345***************************9655 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.14      28      68 ..      51      91 ..      40      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                           PaaX 28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsd 68
                                    l +++G+++s+v   l  l + G++v+ + gr  +Y+L d
  gi|121639658|ref|YP_979882.1| 51 DLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYD 91
                                   46789**********************************87 PP

>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.14      34      72 ..      32      70 ..      20     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                   SSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEE CS
                           CheW 34 apgavlgvinlrGevipvidLrellglgpeesrentrvi 72
                                   +p+ ++ + +lr+  +pv dL+e +g++++  +++ rv+
  gi|121639658|ref|YP_979882.1| 32 TPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVL 70
                                   6788888999*******************9986665554 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.27      19      43 ..      53      77 ..      49      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                   HHHHTS-HHHHHHHHHCT-EEEEEE CS
                            Cro 19 AkdlgvkqsaIsKAlkakRnIyliv 43
                                   A+++g++qsa+s  l++ Rn+ l+v
  gi|121639658|ref|YP_979882.1| 53 AEAIGMEQSAVSHQLRVLRNLGLVV 77
                                   99******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 684.42
//
Query:       gi|121639659|ref|YP_979883.1|  [L=70]
Description: hypothetical protein BCG_3804c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   82.0   0.0    3.2e-23   81.9   0.0    1.0  1  DUF2237   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2237  Uncharacterized protein conserved in bacteria (DUF2237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.8e-27   3.2e-23       2      61 ..       5      64 ..       4      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-27
                                   BTTSSB---S-TTTT-STTSSSS----TT-TT-EEEEEE--HHHHHHHHHCT---SS-BC CS
                        DUF2237  2 nvlgeeLelcstdpltGfyrdglCetseeDlGshtvcavvteeFLefskskGndLstpvp 61
                                   nvlg++Le+ +tdpltGfyrdg+C t++eDlG ht+cav+t+eFL++++s GndLs ++p
  gi|121639659|ref|YP_979883.1|  5 NVLGGALEQGGTDPLTGFYRDGCCATGPEDLGWHTICAVMTTEFLAHQRSVGNDLSIARP 64
                                   9******************************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 399.05
//
Query:       gi|121639660|ref|YP_979884.1|  [L=111]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.3   5.9    1.8e-10   41.0   5.9    1.1  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   5.9     1e-14   1.8e-10       1      92 [.       1      91 [.       1      92 [. 0.93

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1e-14
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   M+ ++++P +   +++ +++  + l+a + a  + ++++l+a+a+eVSa + ++f++ a+   al++ a+++++++++ ++a
  gi|121639660|ref|YP_979884.1|  1 MQSMSFDPAVADIGSQVVNNAFQGLQAGAVAWVS-LSSLLPAGAEEVSAWAVTAFTTAATGLLALNQAAQEELRKAGEVFTA 81
                                   89999********************988666665.566******************************************** PP

                                   HHHHHHS--X CS
                             PE 83 aagsYaaaEa 92
                                    a+ Y++a+ 
  gi|121639660|ref|YP_979884.1| 82 IARMYSDADV 91
                                   *******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 712.83
//
Query:       gi|121639661|ref|YP_979885.1|  [L=127]
Description: hypothetical protein BCG_3806 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 946.24
//
Query:       gi|121639662|ref|YP_979886.1|  [L=119]
Description: hypothetical protein BCG_3807 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.24   12.1   0.0    1.6  1  YtkA      YtkA-like
       0.15   12.2   0.0       0.21   11.7   0.0    1.2  1  DUF4232   Protein of unknown function (DUF4232)


Domain annotation for each model (and alignments):
>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05      0.24      27      85 ..      42     104 ..      26     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                           YtkA  27 tvtqggkpVedadvkvefwmpameGmeemttkv......elkesedGvYeaevnfsmeGtWqvql 85 
                                    + tq ++  +d  v+ve+w p   G++ ++ +        + e +   +++evn++ +G+W++ +
  gi|121639662|ref|YP_979886.1|  42 VLTQAETDDPDRRVDVEVWPPT--GDDAHHIEFelpeaaVAAEVGFAIFRIEVNLPVDGRWVLVV 104
                                    4666666667889********6..888887777334332122245568*************9866 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.21      51     114 ..      14      77 ..       5      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                        DUF4232  51 vgaaaeregpaavpvtLapGesAyaglrwtnaggdgdgectaaglrvtpp..dgtksvtvpdlgat 114
                                    v+ +   +g+   +++++p  sA++ l + + ++++d+++ +  ++v pp  d++++++++ l+ +
  gi|121639662|ref|YP_979886.1|  14 VDNKLNVSGGVLYRFAVDPDRSAQFLLVVLTQAETDDPDRRV-DVEVWPPtgDDAHHIEFE-LPEA 77 
                                    555555555555558999*******99887777777777776.7****6626666666666.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 840.69
//
Query:       gi|121639663|ref|YP_979887.1|  [L=169]
Description: hypothetical protein BCG_3808c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   18.0   0.2     0.0073   17.1   0.2    1.5  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   4.1e-07    0.0073      93     116 .]      58      81 ..      49      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-07
                          PIN_3  93 pdDqkvlelAlaaradvlVTkdra 116
                                     +D +vl++A+ +ra+v+VT++ +
  gi|121639663|ref|YP_979887.1|  58 YKDRHVLAAAVRERAEVIVTTNLK 81 
                                    58********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1123.45
//
Query:       gi|121639664|ref|YP_979888.1|  [L=130]
Description: excisionase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-13   49.8   0.0    4.1e-13   49.3   0.0    1.2  1  HTH_17     Helix-turn-helix domain
    7.6e-05   22.6   0.1    0.00052   19.9   0.1    2.2  1  HTH_37     Helix-turn-helix domain
     0.0016   18.3   0.0     0.0036   17.2   0.0    1.5  1  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0041   17.1   0.0      0.009   16.0   0.0    1.7  1  HTH_29     Winged helix-turn helix
     0.0049   16.6   0.0      0.012   15.4   0.0    1.6  1  HTH_8      Bacterial regulatory protein, Fis family
     0.0057   16.4   0.0      0.013   15.3   0.0    1.7  1  HTH_23     Homeodomain-like domain
     0.0078   16.7   0.0      0.012   16.1   0.0    1.3  1  DUF134     Protein of unknown function  DUF134
  ------ inclusion threshold ------
      0.011   16.0   1.8      0.091   13.1   0.3    2.7  3  HTH_31     Helix-turn-helix domain
      0.066   13.3   0.0       0.16   12.1   0.0    1.6  1  HTH_3      Helix-turn-helix
      0.071   13.3   0.1       0.18   12.0   0.0    1.7  2  AbiEi_4    Transcriptional regulator, AbiEi antitoxin
      0.092   12.5   0.1      0.092   12.5   0.1    2.0  3  MerR       MerR family regulatory protein


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   2.5e-16   4.1e-13       2      49 ..      55     102 ..      55     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.5e-16
                         HTH_17   2 ltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdleewlek 49 
                                    lt++EaA+lL++sr t+ rl+ +g++p+ k Gr++r++ ++l e+ ++
  gi|121639664|ref|YP_979888.1|  55 LTTQEAADLLNISRPTLVRLLEDGRIPFEKPGRHRRVSLDALLEYQQE 102
                                    8*************************777****************997 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.2e-07   0.00052      28      65 ..      51      97 ..      36     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                                   HHCT--HHHHHHHHT--HHHHHHHHT.........T--TT--HHHHH CS
                         HTH_37 28 ekrelsqseaaqllgiaqPkvsrllr.........gklsrfsldkLl 65
                                   ++++l+++eaa ll+i++P ++rll          g+ +r+sld+Ll
  gi|121639664|ref|YP_979888.1| 51 RHLKLTTQEAADLLNISRPTLVRLLEdgripfekpGRHRRVSLDALL 97
                                   799********************985333333333555666666665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0036       7      43 ..      37      76 ..      31      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                                   HHHHHCTTTC....EEEEEHHHHHHHHHTTSSHHHHHHHHH CS
                      HTH_Crp_2  7 Llrlaeragg....eielpltqeelAsmlGltretvsrils 43
                                    l l++++ g      +l+lt +e A++l+++r t+ r+l 
  gi|121639664|ref|YP_979888.1| 37 VLALSQGK-GislvPRHLKLTTQEAADLLNISRPTLVRLLE 76
                                   55666653.333444589********************996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.5e-06     0.009       4      35 ..      36      77 ..      34     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.5e-06
                         HTH_29  4 allllaeGvs..........tvsqiAkllglsrrtvyrwlkr 35
                                   ++l+l++G +          t++++A ll++sr+t  r l++
  gi|121639664|ref|YP_979888.1| 36 VVLALSQGKGislvprhlklTTQEAADLLNISRPTLVRLLED 77
                                   68899999889999999999*******************987 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.4e-06     0.012      22      37 ..      58      73 ..      56      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-06
                                   HHHHHHHTS-HHHHHH CS
                          HTH_8 22 skAArlLGisRrtLyr 37
                                   ++AA+lL+isR tL r
  gi|121639664|ref|YP_979888.1| 58 QEAADLLNISRPTLVR 73
                                   79************87 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.9e-06     0.013      17      38 ..      54      75 ..      34      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.9e-06
                         HTH_23 17 GlsvreIAreLgvsrrTvyrwl 38
                                   +l+++e+A++L++sr T+ r l
  gi|121639664|ref|YP_979888.1| 54 KLTTQEAADLLNISRPTLVRLL 75
                                   799**************99987 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.6e-06     0.012      32      75 ..      35      79 ..       8      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.6e-06
                         DUF134 32 kvaisldeleairlvd.yedlkqeeaaklmGiskatlwrlltear 75
                                    v+++l +   i lv  + +l+ +eaa+l+ is++tl rll+++r
  gi|121639664|ref|YP_979888.1| 35 NVVLALSQGKGISLVPrHLKLTTQEAADLLNISRPTLVRLLEDGR 79
                                   599999999999999625699*********************999 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.9e+03      48      59 ..       2      13 ..       1      15 [. 0.82
   2 ?   13.1   0.3   5.6e-05     0.091      14      43 ..      54      86 ..      46     110 .. 0.72
   3 ?    0.4   0.3      0.54   8.8e+02       9      23 ..     107     122 ..     101     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                         HTH_31 48 ealaralgldpa 59
                                   ++l+++lg+++ 
  gi|121639664|ref|YP_979888.1|  2 TSLLEVLGAPEV 13
                                   689******975 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-05
                         HTH_31 14 GLsqeevAerlgvsestlsrlEqGrrgrp....s 43
                                    L+ +e+A++l++s+ tl rl    r +p     
  gi|121639664|ref|YP_979888.1| 54 KLTTQEAADLLNISRPTLVRLLEDGR-IPfekpG 86
                                   699***************99987544.3434432 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.54
                         HTH_31   9 lReraG.LsqeevAer 23 
                                    +R++ G Ls+++++e+
  gi|121639664|ref|YP_979888.1| 107 RRAALGeLSRDALGEL 122
                                    6777777999999875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.8e-05      0.16       8      36 ..      53      81 ..      51      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                                   TTHHHHHHHHHHTSSHHHHHHHHTTSSCS CS
                          HTH_3  8 lglsqeeLAeklGvsrstisriEnGernP 36
                                   l+l+ +e+A++l++sr t+ r+  + r+P
  gi|121639664|ref|YP_979888.1| 53 LKLTTQEAADLLNISRPTLVRLLEDGRIP 81
                                   577788***************99988876 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.18      14      38 ..      55      80 ..      55      80 .. 0.95
   2 ?   -3.2   0.0       6.2     1e+04      20      27 ..      83      90 ..      81      97 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                        AbiEi_4 14 fttrelea.aGispsalrrLvrkGwL 38
                                   +tt+e++  ++is+ +l rL++ G++
  gi|121639664|ref|YP_979888.1| 55 LTTQEAADlLNISRPTLVRLLEDGRI 80
                                   59**********************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.2
                        AbiEi_4 20 eaaGisps 27
                                   e+ G++++
  gi|121639664|ref|YP_979888.1| 83 EKPGRHRR 90
                                   66788884 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         3     5e+03      25      32 ..      25      32 ..      25      32 .. 0.84
   2 ?   12.5   0.1   5.6e-05     0.092       1      36 [.      56      89 ..      56      91 .. 0.81
   3 ?   -3.1   0.1       4.3   6.9e+03      29      36 ..     101     108 ..      96     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                                   STSEEETT CS
                           MerR 25 ipppeRte 32
                                   +p+p+R++
  gi|121639664|ref|YP_979888.1| 25 LPEPVRDA 32
                                   799**985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.6e-05
                                   EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSE CS
                           MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyR 36
                                   t+ e+A+l+++s  tL ++ + G ip  e  +g++R
  gi|121639664|ref|YP_979888.1| 56 TTQEAADLLNISRPTLVRLLEDGRIPF-E-KPGRHR 89
                                   788**********************63.3.344555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.3
                                    EETTTSSE CS
                           MerR  29 eRtegGyR 36 
                                    + t +++R
  gi|121639664|ref|YP_979888.1| 101 QETRSNRR 108
                                    66888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 854.88
//
Query:       gi|121639665|ref|YP_979889.1|  [L=71]
Description: integrase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-10   41.1   0.1    1.7e-10   40.9   0.1    1.1  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.025   13.5   0.0      0.029   13.3   0.0    1.0  1  DUF3435          Protein of unknown function (DUF3435)


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   1.9e-14   1.7e-10     120     171 ..       2      53 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.9e-14
                                    HHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH.HHHHCCCH CS
                Phage_integrase 120 eeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssistt.qiYthvak 171
                                    ++a+++ ++tpH+lRh++a+  + agv++ ++q++lGH+s + t  +Y+++++
  gi|121639665|ref|YP_979889.1|   2 KRAKVQ-QITPHDLRHTAASLAVSAGVNVLALQRILGHKSAKVTlDTYADLFD 53 
                                    556666.9****************************************99875 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-06     0.029     193     253 ..       7      65 ..       3      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                        DUF3435 193 epitpYklRrgaakalneSgevseaqrnlilqHassrtFlkhYlsqkvdkdvqavvlglpp 253
                                    ++itp+ lR  aa    +   v     + il+H+s+++ l+ Y  + +d d+ av   l  
  gi|121639665|ref|YP_979889.1|   7 QQITPHDLRHTAASLAVS-AGVNVLALQRILGHKSAKVTLDTY-ADLFDADLDAVAVTLGK 65 
                                    679******998876555.6777777889**************.66668888887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 551.61
//
Query:       gi|121639666|ref|YP_979890.1|  [L=152]
Description: cytidine/deoxycytidylate deaminase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-23   81.8   0.0    3.2e-23   81.5   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    9.6e-20   70.7   0.0      1e-19   70.7   0.0    1.0  1  MafB19-deam      MafB19-like deaminase
     0.0042   17.2   4.0       0.02   14.9   0.6    2.1  2  Bd3614-deam      Bd3614-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   5.4e-27   3.2e-23       1     100 [.       1     102 [.       1     103 [. 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.4e-27
                                    HHHHHHHHHHHHHHHHHHHTTTSCSEEEEEEE.TTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHH.T.SSCETTEEEEE CS
                dCMP_cyt_deam_1   1 mekdekllelalkaakeaqkcsnfkVGavivk.ngeiistgyngepaggsktiHAEvnAilkaakn.g.gsklegatlyv 77 
                                    m++de l++ al++a +a     ++VGav+v  +g  +++++n ++a g++t+HAE++A++ aa   g g++leg+tl+v
  gi|121639666|ref|YP_979890.1|   1 MTTDEDLIRAALAVAATA-GPRDVPVGAVVVGaDGTELARAVNAREALGDPTAHAEILAMRLAAGVlGdGWRLEGTTLAV 79 
                                    6789**************.999********************************************************** PP

                                    EE--BHHHHHHHHHHT-SEEEEE CS
                dCMP_cyt_deam_1  78 tlePCsmCakaiiqsgikkvvvg 100
                                    t+ePC+mCa a++ +++ ++v+g
  gi|121639666|ref|YP_979890.1|  80 TVEPCTMCAGALVLARVARLVFG 102
                                    *********************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   1.7e-23     1e-19      18     134 ..      18     146 ..       2     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.7e-23
                    MafB19-deam  18 tkikedkigaviv.kdkkviargsnekelnakataHaEiaalqqAakklk.skrlddatlyvtlepCdmCagaivqaglk 95 
                                    +   ++++gav+v  d+  +ar+ n +e   ++taHaEi a++ Aa  l+ ++rl+++tl vt+epC mCaga+v a++ 
  gi|121639666|ref|YP_979890.1|  18 AGPRDVPVGAVVVgADGTELARAVNAREALGDPTAHAEILAMRLAAGVLGdGWRLEGTTLAVTVEPCTMCAGALVLARVA 97 
                                    345789******989999***************************9987627**************************** PP

                    MafB19-deam  96 klvygagnpks......lnkLkvkekngrvelv....eddckeilkgff 134
                                    +lv+ga +pk+        ++   + n+r e+       +c++ l+ ff
  gi|121639666|ref|YP_979890.1|  98 RLVFGAWEPKTgavgslWDVVRDRRLNHRPEVRggvlARECAAPLEAFF 146
                                    **********999888767777778888888776666667776666666 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.015        89       6      39 ..      21      56 ..      16      70 .. 0.76
   2 !   14.9   0.6   3.4e-06      0.02      76      97 ..      73      94 ..      70     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.015
                    Bd3614-deam  6 rDRkvvAalvsdqGelldaavntna..enkvLHAEv 39
                                   rD  v A++v  +G+ l+ avn+    +  + HAE+
  gi|121639666|ref|YP_979890.1| 21 RDVPVGAVVVGADGTELARAVNAREalGDPTAHAEI 56
                                   788899********9999999975422567888886 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-06
                    Bd3614-deam 76 egarllvtlqcCkmCAalvvaa 97
                                   eg++l vt ++C mCA+ +v a
  gi|121639666|ref|YP_979890.1| 73 EGTTLAVTVEPCTMCAGALVLA 94
                                   79**************877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1074.64
//
Query:       gi|121639667|ref|YP_979891.1|  [L=173]
Description: hypothetical protein BCG_3812c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.024   14.1   0.0    1.3  1  MauJ      Methylamine utilization protein MauJ


Domain annotation for each model (and alignments):
>> MauJ  Methylamine utilization protein MauJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-06     0.024     122     148 ..      18      44 ..      13     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-06
                           MauJ 122 GWRvaDveheaRWRcvPfRPsaleldl 148
                                    G+ va v++e RWRc P  P al    
  gi|121639667|ref|YP_979891.1|  18 GFGVAVVREEGRWRCSPMGPKALTSLR 44 
                                    7889******************97543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1136.91
//
Query:       gi|121639668|ref|YP_979892.1|  [L=301]
Description: prephenate dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-40  138.2   0.0    3.1e-40  137.8   0.0    1.1  1  PDH            Prephenate dehydrogenase
  ------ inclusion threshold ------
       0.07   13.7   0.1       0.27   11.8   0.0    2.1  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   0.0   3.4e-44   3.1e-40      13     246 ..      10     240 ..       2     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 3.4e-44
                                    EEEEE-SSHHHHHHHHHTT..SSSEEES-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHH CS
                            PDH  13 tvigydideekaeaalelg..lvdeatdd.ieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvrel 89 
                                     v gy+++ e a+ a+  g  ++ + ++   +a+ + +++vlavP+ ++  +l+ + +   +++ +tDv+svK +v +e+
  gi|121639668|ref|YP_979892.1|  10 EVFGYNRSVEGAHGARSDGfdAITDLNQTlTRAAATEALIVLAVPMPALPGMLAHIRK-SAPGCPLTDVTSVKCAVLDEV 88 
                                    56777777766666654432244455555467778889****************9999.899****************** PP

                                    HHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHT CS
                            PDH  90 eellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvs 169
                                     +    ++++vgghPm Gt++sG  a++  lf++a+++   +++ d+    +v+ l  ++ga v+  +++eHD + a vs
  gi|121639668|ref|YP_979892.1|  89 TAAGL-QARYVGGHPMTGTAHSGWTAGHGGLFNRAPWVVSVDDHVDPTVWSMVMTLALDCGAMVVPAKSDEHDAAAAAVS 167
                                    **999.9************************************************************************* PP

                                    HHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHHCGGGS-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHT CS
                            PDH 170 hlphvvaialaatlkekkndekeirklasggfrdvtRiaksnPelwadilleNkeavlealdkfikelkklkelien 246
                                    hlph++a ala        + ++++ la+g+frd+tR+a+  P l + +  +N+ ++++a d  i  l +++  +++
  gi|121639668|ref|YP_979892.1| 168 HLPHLLAEALAV----TAAEVPLAFALAAGSFRDATRVAATAPDLVRAMCEANTGQLAPAADRIIDLLSRARDSLQS 240
                                    **********99....55678899***************************************99999988887765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.1e-05      0.27      17      84 ..       3      68 ..       1      79 [. 0.74
   2 ?   -2.9   0.0       1.2     1e+04      56      56 ..     179     179 ..     147     210 .. 0.59
   3 ?   -2.4   0.0      0.85   7.6e+03      34      52 ..     196     214 ..     171     233 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                                   HHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE...CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHH CS
                  F420_oxidored 17 gllaagaqpheivvansrnpekaeelaeelgvkvtav...dneeaaeeadvvvlavkpedveevlselakd 84
                                    ++aag   +e+  + +r+ e a  ++++ g ++++    +   aa+    +vlav++ +++ +l+ ++k+
  gi|121639668|ref|YP_979892.1|  3 AAAAAG---REVF-GYNRSVEGAHGARSD-GFDAITDlnqTLTRAAATEALIVLAVPMPALPGMLAHIRKS 68
                                   578889...9999.999999999887766.54555540004455777889****************99443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                                    H CS
                  F420_oxidored  56 e 56 
                                     
  gi|121639668|ref|YP_979892.1| 179 V 179
                                    1 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.85
                                    SSCCCHHHHHHHHC-EEEC CS
                  F420_oxidored  34 rnpekaeelaeelgvkvta 52 
                                    r+  +++++a +l + +++
  gi|121639668|ref|YP_979892.1| 196 RDATRVAATAPDLVRAMCE 214
                                    4444444554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2015.26
//
Query:       gi|121639669|ref|YP_979893.1|  [L=199]
Description: hypothetical protein BCG_3814c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-56  188.8   0.0    6.4e-56  188.7   0.0    1.0  1  Glycolipid_bind  Putative glycolipid-binding


Domain annotation for each model (and alignments):
>> Glycolipid_bind  Putative glycolipid-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.7   0.0   3.6e-60   6.4e-56       1     178 []      16     198 ..      16     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.7 bits;  conditional E-value: 3.6e-60
                                    ..EEEE-EE--EEEEEE-S....SEEEEEEEEE-TTT--E..EEEEEEE-TTS-EEEEEEEEEETTEEEEEEEEE-SSS- CS
                Glycolipid_bind   1 tvtWrrldgeglehlrleeseegiraegvvvgaeegeala..lsYeletdadwrtrrlsvkvataeeerslslerdeege 78 
                                    ++tWr++d +++e++r++ s+++ira+g++v+a++ +++a  ++Y+l+td++++t+r+ ++v+ ae+er+l+++rdee++
  gi|121639669|ref|YP_979893.1|  16 MLTWRAQDISRMESVRVQLSGKRIRANGRIVAAATANNPAfgAHYDLQTDETGATKRFGLTVTLAERERQLAIARDEENM 95 
                                    69*******************************999998889************************************** PP

                                    EEETT-..-B-GGGTT--EEEEET-GGGGHHHHHHH---TT-EEE.EEEEEEETTTT--EEEEEEEEEEET.TEEEEEE- CS
                Glycolipid_bind  79 Wlvdag..eerpdldgcldvDlslsPftNtlpIrRlglaegesae.ipvvyvslpdleveraeqrYtrleeesvyryese 155
                                    Wlv+++  e+r++++g+ld+Dl +sPf+N+lpIrRlgl+e++++  +pvvyv++p+++v++a+ +Yt+  + + ++ +s+
  gi|121639669|ref|YP_979893.1|  96 WLVTDHqgERRAAYNGALDIDLVFSPFFNALPIRRLGLHERAESIaLPVVYVNVPEMSVDAATVSYTSEGRLDGIKLRSP 175
                                    **99987789*********************************988*************************999999999 PP

                                    S-EEEEEE-TTS-EEEETTTEEE CS
                Glycolipid_bind 156 dfsadLtvDedGlVldYpglarR 178
                                       +++tvD+dG+++dYpgla+R
  gi|121639669|ref|YP_979893.1| 176 VADTTVTVDSDGFIVDYPGLAER 198
                                    999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1491.86
//
Query:       gi|121639670|ref|YP_979894.1|  [L=239]
Description: osmoprotectant (glycine betaine/carnitine/choline/l-proline) transport integral membrane protein ABC transporter proZ [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-15   55.5  13.9      6e-15   55.5  13.9    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5  13.9   3.3e-19     6e-15       1     174 [.      45     204 ..      45     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.3e-19
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslp 80 
                                    ++++G+l++  + ++++ l+ + ++ l++lP++ +++l v        +g +  p +++l+l  +p  +  ++a++ s++
  gi|121639670|ref|YP_979894.1|  45 AVPVGLLIG--HTGRGTLLVVGAVNGLRALPTLGVLLLGV------LLFGLGLGPPLVALMLLGIPSLLASTYAGIASVD 116
                                    5899*****..99***************************......99******************************** PP

                   BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvla 160
                                       v aara+G+++ q++ +v +Pnalp ++ gl+ a   ++  a+++ +    +Glg  l++ i ++ ++ ++     +
  gi|121639670|ref|YP_979894.1| 117 PLVVDAARAMGMTESQVLLRVEVPNALPLMLGGLRSATLQVVATATVAAYAS-LGGLGGYLIDGIKERRFHIAL-----V 190
                                    *****************************************99999988876.668***************555.....4 PP

                   BPD_transp_1 161 lviavlllnlvadi 174
                                    ++ +v++l l +d 
  gi|121639670|ref|YP_979894.1| 191 GAMMVAALALTLDG 204
                                    44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1558.15
//
Query:       gi|121639671|ref|YP_979895.1|  [L=229]
Description: osmoprotectant (glycine betaine/carnitine/choline/l-proline) transport integral membrane protein ABC transporter proW [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-17   63.1  18.9    3.5e-17   62.7  18.9    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7  18.9   1.9e-21   3.5e-17       2     181 ..      34     206 ..      19     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.9e-21
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslp 80 
                                    ++lG+l+   r   l++l +    v++++Ps++l+++l l+     +   l  + vi++l+ +++++ ++ + +al+++p
  gi|121639671|ref|YP_979895.1|  34 VPLGLLVQ--RAPLLRRLTTATASVIFTIPSLALFVVLPLI----IGTRILDEAnVIVALAAYTTALLVRAVLEALDAVP 107
                                    45555555..999********************88887732....4555555566************************* PP

                   BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvla 160
                                     +   aa+a G sr+  + kv lP+++p++++gl+++++ ++   ++ + +g  +Glgt+++  ++ +  ++i  +gv+a
  gi|121639671|ref|YP_979895.1| 108 AQVHDAATAIGYSRIAQMLKVELPLSIPVLVAGLRVVAVTNIAMVSVGSVIG-IGGLGTWFTAGYQTNKSDQIV-AGVVA 185
                                    ****************************************************.899******************.99999 PP

                   BPD_transp_1 161 lviavlllnlvadilqrlldp 181
                                    + ++ +++ +v+++  rl  p
  gi|121639671|ref|YP_979895.1| 186 MFLLAIVVDVVINLAGRLATP 206
                                    999999999999998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1617.18
//
Query:       gi|121639672|ref|YP_979896.1|  [L=376]
Description: osmoprotectant (glycine betaine/carnitine/choline/l-proline) transport ATP-binding protein ABC transporter proV [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-31  108.7   0.0    4.5e-31  108.2   0.0    1.2  1  ABC_tran     ABC transporter
    4.5e-08   33.3   0.1      0.002   18.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0017   18.1   0.0     0.0023   17.7   0.0    1.1  1  AAA_15       AAA ATPase domain
     0.0038   17.0   0.1     0.0089   15.8   0.1    1.6  1  AAA_30       AAA domain
     0.0055   17.0   0.0      0.013   15.8   0.0    1.5  1  AAA_22       AAA domain
     0.0071   16.7   0.5      0.015   15.6   0.1    2.0  2  AAA_16       AAA ATPase domain
     0.0087   16.6   0.0      0.014   15.9   0.0    1.2  1  AAA_23       AAA domain
     0.0098   16.3   0.1      0.043   14.2   0.1    2.0  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   14.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.013   15.5   0.0      0.021   14.7   0.0    1.2  1  Rad17        Rad17 P-loop domain
      0.018   13.9   0.2        1.1    8.0   0.0    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.037   13.3   0.1      0.081   12.2   0.0    1.5  2  Zeta_toxin   Zeta toxin
      0.038   14.1   0.4       0.11   12.7   0.4    2.0  1  AAA_33       AAA domain
      0.051   13.8   0.2       0.34   11.1   0.1    2.4  2  AAA_28       AAA domain
       0.12   12.2   0.0       0.26   11.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.0   3.8e-34   4.5e-31       2     136 ..      19     163 ..      18     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 3.8e-34
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++++l++ +g ++++vG++G+GK+t l+++ ++++pt+G+i++dg+d+++ +  +lr  ig++ q++ l p+ +v +n  
  gi|121639672|ref|YP_979896.1|  19 DRLTLEVPNGMLTVFVGPSGCGKTTALRMINRMVDPTSGTITVDGTDVSTVNAVKLRLGIGYVIQNAGLMPHQRVIDNva 98 
                                    7899**************************************************************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               ++++  +++l+++gl+    +v+++ p++LSgG++qrv +aral+ +p++ll+DEp+
  gi|121639672|ref|YP_979896.1|  99 tvpvlkgqprrAARKAGYEVLERVGLDP---KVATRYPAQLSGGEQQRVGVARALAADPPILLMDEPF 163
                                    *****99887666666899999999888...5666669*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.8e-05     0.057       1      22 [.      30      51 ..      30      70 .. 0.83
   2 !   18.0   0.0   1.7e-06     0.002     233     298 ..     132     195 ..     121     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   l+v++Gp g+GK++ L+ +  +
  gi|121639672|ref|YP_979896.1| 30 LTVFVGPSGCGKTTALRMINRM 51
                                   79***************99655 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.7e-06
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHS 298
                                     +++lS G ++  +++ al++++   ++ll DEp +  +P    +l+ ++l+l  el++    ++++TH+
  gi|121639672|ref|YP_979896.1| 132 YPAQLSGGEQQRVGVARALAADP---PILLMDEPFSAVDPvvrhELQNEILRLQAELHK---TIVFVTHD 195
                                    56788999888889999999988...**************5555555555555555555...9******8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     2e-06    0.0023      25      67 ..      30      68 ..      19      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                         AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedlei 67
                                   ltv++G+ ++GK+++l++++ + + +    + +i+++  d+++
  gi|121639672|ref|YP_979896.1| 30 LTVFVGPSGCGKTTALRMINRMVDPT----SGTITVDGTDVST 68
                                   9*********************9987....5666666666554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.5e-06    0.0089      18      67 ..      28      79 ..      15     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-06
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelg 67
                                    +++v +Gp G GKttal+ ++++++   g  +v g   +   A +L+ ++g
  gi|121639672|ref|YP_979896.1| 28 GMLTVFVGPSGCGKTTALRMINRMVDPTsGtITVDGTDVSTVNAVKLRLGIG 79
                                   46899****************9988877444666677667777766665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.013       7      49 ..      30      65 ..      26      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                   ++v +G+sG+GKTt lr++ +  d         +++++v+ + 
  gi|121639672|ref|YP_979896.1| 30 LTVFVGPSGCGKTTALRMINRMVDP-------TSGTITVDGTD 65
                                   6899***************999874.......56666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.3e-05     0.015      25      59 ..      29      64 ..      15     230 .. 0.63
   2 ?   -2.8   0.0       5.9     7e+03     135     151 ..     277     297 ..     246     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekd.ggiflrgk 59
                                    l++++G+sG+GK++ +r++ r +  + g i++ g+
  gi|121639672|ref|YP_979896.1| 29 MLTVFVGPSGCGKTTALRMINRMVDPTsGTITVDGT 64
                                   57899***************9766666322333333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.9
                         AAA_16 135 rplvlvlDdlq....wadeas 151
                                    + +vlv+D +     w+d++ 
  gi|121639672|ref|YP_979896.1| 277 DGWVLVVDGAGaplgWIDADG 297
                                    237888887766666777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05     0.014      19      39 ..      28      48 ..      15      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                         AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                     lt+++Gp G+GKTT l+ i
  gi|121639672|ref|YP_979896.1| 28 GMLTVFVGPSGCGKTTALRMI 48
                                   459**************9988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   3.6e-05     0.043       2      35 ..      32      67 ..      31     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                            AAA  2 llyGppGtGKTllakavakelg..vefleisgsell 35
                                   +++Gp G+GKT++ + + + ++  +  ++++g+++ 
  gi|121639672|ref|YP_979896.1| 32 VFVGPSGCGKTTALRMINRMVDptSGTITVDGTDVS 67
                                   689*************99997433334555554443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.019      85     124 ..      13      53 ..       6      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                    TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                    +  +++++l+ ++ +  ++v+vG+SG GK+t + +++   +
  gi|121639672|ref|YP_979896.1|  13 HGATAVDRLTLEVPNgMLTVFVGPSGCGKTTALRMINRMVD 53 
                                    555677778777776699*************8887766544 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.8e-05     0.021      40      68 ..      23      51 ..      12      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                          Rad17 40 LesrkkriLLisGPsGCgkstvvkvLske 68
                                   Le  +  + +  GPsGCgk+t+++++ + 
  gi|121639672|ref|YP_979896.1| 23 LEVPNGMLTVFVGPSGCGKTTALRMINRM 51
                                   555555677889***********998765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.016        19     241     270 ..      24      54 ..      21      86 .. 0.85
   2 ?    8.0   0.0   0.00093       1.1     324     390 ..     137     203 ..     129     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                                    EE-SS.EEEEEE-TTSSHHHHHHHHHHCCSE CS
                     ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlekGvyn 270
                                     +p+G +t+ vG+   GK+T L+ +++ v++
  gi|121639672|ref|YP_979896.1|  24 EVPNGmLTVFVGPSGCGKTTALRMINRMVDP 54 
                                    5899999******************998875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00093
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--E CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvs 390
                                    SG   q + +++al a+ ++lL+DE  sA+  ++r e+ +e++  ++e  +++v   +++ + l + 
  gi|121639672|ref|YP_979896.1| 137 SGGEQQRVGVARALAADPPILLMDEPFSAVDPVVRHELQNEILRLQAELHKTIVFVTHDIDEALKLA 203
                                    89999999********************************999888877777776666665555544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05     0.081      19      54 ..      31      66 ..      19      70 .. 0.89
   2 ?   -3.8   0.0       5.4   6.4e+03     114     124 ..     108     118 ..     104     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                     Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                    + +G +G+GK+++++++++ ++++++ +++d++d+
  gi|121639672|ref|YP_979896.1| 31 TVFVGPSGCGKTTALRMINRMVDPTSGTITVDGTDV 66
                                   567899**************************9986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.4
                     Zeta_toxin 114 aealkkaGYev 124
                                     +a++kaGYev
  gi|121639672|ref|YP_979896.1| 108 RRAARKAGYEV 118
                                    5789999**98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4     9e-05      0.11       1      18 [.      30      47 ..      30     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9e-05
                         AAA_33  1 lvllvGlpGsGKstlaer 18
                                   l+++vG++G+GK+t ++ 
  gi|121639672|ref|YP_979896.1| 30 LTVFVGPSGCGKTTALRM 47
                                   689***********9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00028      0.34       3      23 ..      32      57 ..      30     196 .. 0.86
   2 ?   -0.5   0.0       1.1   1.3e+03     103     130 ..     270     302 ..     251     311 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                         AAA_28  3 vitGgestGKTtlleaLaar.....g 23
                                   v++G++++GKTt l+ ++++     g
  gi|121639672|ref|YP_979896.1| 32 VFVGPSGCGKTTALRMINRMvdptsG 57
                                   99************998865444444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                         AAA_28 103 aarekrydlvfllpp.ap....eidddgeRred 130
                                    a  ++  d ++l+   a+    +id dg Rr++
  gi|121639672|ref|YP_979896.1| 270 ARDRQVRDGWVLVVDgAGaplgWIDADGRRRHR 302
                                    445555666555554244777799999999985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.26      16      39 ..      22      45 ..      15      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                         AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                   t+e+  +g  t+++GpsG GK+T l
  gi|121639672|ref|YP_979896.1| 22 TLEVP-NGmLTVFVGPSGCGKTTAL 45
                                   55664.6779*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2904.23
//
Query:       gi|121639673|ref|YP_979897.1|  [L=315]
Description: osmoprotectant (glycine betaine/carnitine/choline/l-proline) binding lipoprotein proX [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-51  175.3   0.0    1.9e-51  175.1   0.0    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain
  ------ inclusion threshold ------
      0.011   15.6   0.1       0.02   14.7   0.1    1.4  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC
       0.14   11.4   0.9        2.2    7.6   0.0    2.5  3  AvrD      Pseudomonas avirulence D protein (AvrD)


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.0   3.2e-55   1.9e-51       1     256 [.      41     305 ..      41     306 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 3.2e-55
                                    CEEEEEEESSHHHHHHHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH................H CS
                          OpuAC   1 ktivigsknwteqevlaeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta................y 63 
                                    k+iv+gs +++e++v+aei++q+l+++G+ + +++++gs+++++ al++ +iD++p e+ g++                +
  gi|121639673|ref|YP_979897.1|  41 KSIVVGSGDFPESQVIAEIYAQVLQANGFdVGRRLGIGSRETYIPALKDHSIDLVP-EYIGNLllyfqpdatvtmldavE 119
                                    68******************************************************.**********************7 PP

                                    HHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHH CS
                          OpuAC  64 eaykkaveekkglevlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaY 143
                                     +++k+++   +l +l p++a +t++++v++++a ++++k+i+DL+ ++ d++++a + f++rp+g++      gl  +Y
  gi|121639673|ref|YP_979897.1| 120 LELYKRLP--GDLSILTPSPASDTDTVTVTAATAARWNLKTIADLAPHSADVKFAAPSVFQTRPSGLP------GLRHKY 191
                                    78888899..6666669***************************************************......****** PP

                                    T-TTCEEE.GSCEEEEHH....HHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCT CS
                          OpuAC 144 gldkvelv.egseaamda....elyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPe 218
                                     l    ++ +g++ ++ +     + +a+ +g++ ++ ++++++ai++ +lvvLedp++ f +  n+vp+v++  ++++  
  gi|121639673|ref|YP_979897.1| 192 SL----DIaPGNFVTINDgggaVTVRALVEGTATAANLFSTSAAIPQNHLVVLEDPEHNFLA-GNIVPLVNSRKKSDH-- 264
                                    **....7889999999999999****************************************.***************.. PP

                                    HHHHHHHHC..--HHHHHHHHHHHHT.TTT-HHHHHHHHHH CS
                          OpuAC 219 vaafLekls..ldtetlnelnaqvdv.egkdpeevAkawla 256
                                    ++++L+++s  l+t+ l+elna+v+  +g dp+++A++w++
  gi|121639673|ref|YP_979897.1| 265 LKDVLDAVSakLTTAGLAELNAAVSGnSGVDPDQAARKWVR 305
                                    **************************9************97 PP

>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.4e-06      0.02      24      86 ..     214     274 ..     213     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
                       PvlArgDC  24 ALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrliaaavgv 86 
                                    AL ++     NL + S  +P++   v  e+  +++ +G+iv+ v +r++s++ ++ +  av+ 
  gi|121639673|ref|YP_979897.1| 214 ALVEGTATAANLFSTSAAIPQNHL-VVLEDPEHNFLAGNIVPLVNSRKKSDHLKD-VLDAVSA 274
                                    99999999************9987.77788889*****************99887.6666665 PP

>> AvrD  Pseudomonas avirulence D protein (AvrD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.29   1.8e+03      79     118 ..      14      54 ..      10      68 .. 0.70
   2 ?    1.5   0.1     0.025   1.5e+02      43      73 ..     138     168 ..     128     172 .. 0.74
   3 ?    7.6   0.0   0.00036       2.2      56     106 ..     254     306 ..     242     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.29
                           AvrD  79 lavqLseaal.aralgleaeerarmrlrrvvvkAGsaPeed 118
                                     av L+ + l a   + ++  +a + ++++vv  G  Pe +
  gi|121639673|ref|YP_979897.1|  14 AAVWLATVCLvASCANADPLGSATGSVKSIVVGSGDFPESQ 54 
                                    56777777651445578899999999999999999999755 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.025
                           AvrD  43 akaaaratldvvYPadWSrKkdadlrPHlSs 73 
                                    a+ +  +t++    a W  K  adl PH + 
  gi|121639673|ref|YP_979897.1| 138 ASDTDTVTVTAATAARWNLKTIADLAPHSAD 168
                                    34444566777789**************765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00036
                           AvrD  56 PadWSrKkdadlrPHlSsvDalvlavqLsea..alaralgleaeerarmrlrr 106
                                    P   SrKk   l+  l +v a + ++ L+e+  a++   g++++++ar ++r 
  gi|121639673|ref|YP_979897.1| 254 PLVNSRKKSDHLKDVLDAVSAKLTTAGLAELnaAVSGNSGVDPDQAARKWVRD 306
                                    55669**999*************9****99622688899************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2424.89
//
Query:       gi|121639674|ref|YP_979898.1|  [L=100]
Description: hypothetical protein BCG_3819 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-10   39.6   0.7    3.4e-10   39.6   0.7    2.0  2  LapA_dom  Lipopolysaccharide assembly protein A domain
  ------ inclusion threshold ------
        1.9    7.1   3.3        2.1    7.0   3.3    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
        2.5    7.7   8.8        3.1    7.4   8.8    1.1  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   5.2      0.53   3.2e+03      26      39 ..      26      39 ..      20      42 .. 0.74
   2 !   39.6   0.7   5.8e-14   3.4e-10       1      52 [.      43      94 ..      43      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.53
                       LapA_dom 26 afgiGallgwllsl 39
                                   a+++G+l+ +ll +
  gi|121639674|ref|YP_979898.1| 26 ALIVGFLILILLLI 39
                                   78899977777766 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 5.8e-14
                       LapA_dom  1 qNtqpVtvnflfaqvelpLsllllvafgiGallgwllslwsylrlrrelrrl 52
                                   qNt++ ++ f+ ++++lpL++ +l+a++ G l+++++++ ++l+lrr++++ 
  gi|121639674|ref|YP_979898.1| 43 QNTASAQFAFFGWRWSLPLGVAILLAAVGGGLITVFAGTARILQLRRAAKKT 94
                                   9***********************************************9985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.3   0.00035       2.1     382     426 ..      19      72 ..      11      97 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00035
                        DUF2207 382 klsalglgliilglilillallllvll.........lvfllilllillliaiiv 426
                                    +  a++ +li+ +lilill+++ ++ +         + + l l++++ll+a++ 
  gi|121639674|ref|YP_979898.1|  19 RAAAVWSALIVGFLILILLLIFIAQNTasaqfaffgWRWSLPLGVAILLAAVGG 72 
                                    444444444444444444444444444566677777333333333333333333 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   8.8   0.00051       3.1       5      49 ..      23      77 ..      20      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00051
                        DUF4131  5 lalvllalllllllllllllrr..........rprrrvllllllllllallgfal 49
                                   ++  l++ +l+l+lll+++ ++           ++   l++++ll++++++ +++
  gi|121639674|ref|YP_979898.1| 23 VWSALIVGFLILILLLIFIAQNtasaqfaffgWRWSLPLGVAILLAAVGGGLITV 77
                                   5667777777777777777777899999976333333344444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 546.70
//
Query:       gi|121639675|ref|YP_979899.1|  [L=351]
Description: acyl-CoA dehydrogenase fadE36 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-41  141.7   4.9    5.2e-41  141.1   4.9    1.3  1  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   4.9   2.9e-45   5.2e-41       4     228 ..      34     268 ..      31     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.9e-45
                                    EE--.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-...B--B-CTTBS-EEETTEEEEEEE----E CS
                            APH   4 elsggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagv...pvPevlagdtddeeigllfalieyvpgr 80 
                                     +sgg sn t++v ++a ++++rr+p   + ++++++++++r++a++g    pv++ + +++dd ++g +f+++e+v g+
  gi|121639675|ref|YP_979899.1|  34 LISGGRSNLTFRVYDDASSWLVRRPPLHGLTPSAHDMAREYRVVAALGDtpvPVARTISLCQDDSVLGAPFQVVEFVAGQ 113
                                    689*************************88888888888888888887776799999*********************** PP

                                    E-SS......HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC..HHHHHHHHH CS
                            APH  81 sllr......klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselld..lleeleeqv 152
                                    +++r        s ++++  ++al+++l +lh++dp a +l+df+++d +l+rq+ ++  ++   +l+d  + +++ + +
  gi|121639675|ref|YP_979899.1| 114 VVRRraeleaLGSRSVIEGCVDALIRVLVDLHSIDPKAVGLSDFGKPDGYLERQVRRWGSQWELVRLPDdhRDADISR-L 192
                                    ******999977899*******************************************99*********987888888.9 PP

                                    HHHHHHH--SSS-EEEE-SS-SGGGEEEC...TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHH CS
                            APH 153 laalaallpgelptvllHgDlhpgNllvd.pddgrvtGviDfedaglgpplyDlavllrswtseldpeflaallray 228
                                      al +  p +++t+++HgD++ +N ++d +d+ +v++v+D+e+++lg+pl D a ++  +++++ +  ++a ++  
  gi|121639675|ref|YP_979899.1| 193 HLALQQAIPQQSRTSIVHGDYRIDNTILDtDDPCHVRAVVDWELSTLGDPLSDAALMC-VYRDPALDLIVHAQAAWT 268
                                    9999999999************************************************.667777666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.59
# Mc/sec: 1802.61
//
Query:       gi|121639676|ref|YP_979900.1|  [L=626]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-58  195.3   0.0    9.1e-58  194.6   0.0    1.3  1  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    1.7e-43  148.9   4.9    4.1e-43  147.7   4.9    1.7  1  Lactamase_B      Metallo-beta-lactamase superfamily
    1.1e-32  113.0   0.0    1.9e-32  112.2   0.0    1.4  1  Alkyl_sulf_C     Alkyl sulfatase C-terminal
    2.6e-07   30.4   0.2    7.1e-07   28.9   0.2    1.9  1  Lactamase_B_2    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.68   10.6  12.8      0.082   13.6   6.3    2.4  2  TPR_16           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.6   0.0   2.5e-61   9.1e-58       1     138 [.     361     498 ..     361     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 2.5e-61
                                    -CCCHHHC----HHHHTSGGGSSSSS-HHHHHHHHHHHHH-S--S-GGGTS---HHHHHHHHHHHTTSHHHHHHHHHHHH CS
                Alkyl_sulf_dimr   1 tpdeiaekvklPeslanepylreyYGtvehnvraiyqrylGWfdgnPanLnplppeekakrlvelmGgaekvlekakeal 80 
                                    t+ eiae+++lP++l++++++++yYG+v+hnv+aiyqry+GWfdgnP  L+p+ppe+ a r+v+++Gg ++vle a+ea+
  gi|121639676|ref|YP_979900.1| 361 TGVEIAEMFQLPPALQRAWHTHGYYGSVSHNVKAIYQRYMGWFDGNPGWLWPHPPEALAPRYVDALGGIDRVLELAREAF 440
                                    678***************************************************************************** PP

                                    HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHH CS
                Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsgakelrn 138
                                    ++gd+rwaa+ll+h+vfad+e+a+a+ l ad+leql+y+ae+atwRn++l+ga elr+
  gi|121639676|ref|YP_979900.1| 441 DAGDFRWAATLLDHAVFADSEHAAARGLYADTLEQLAYGAECATWRNFFLTGAAELRD 498
                                    ********************************************************97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   4.9   1.1e-46   4.1e-43       1     197 []      97     324 ..      97     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 1.1e-46
                                    ECCCSSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                    Lactamase_B   1 rgpdpvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                    rg+d++n+ ++egd+g+i+iD+++ste a aal +++a++  +++v avi+TH+H+DH+Gg+ g++ ++dv  g+va  a
  gi|121639676|ref|YP_979900.1|  97 RGFDISNISFVEGDTGLIVIDPLVSTEVAAAALdLYRAHRGADRPVVAVIYTHSHVDHFGGVLGVTTQADVDAGKVAVLA 176
                                    699******************************77777788899************************************ PP

                                    HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                    Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                    p++f+ +a                    v+e++++g a++rra+y++g+ +  ++ g+v++g g++l tG ++l+ +t++
  gi|121639676|ref|YP_979900.1| 177 PEGFTAHA--------------------VQENIYAGSAMMRRAGYMYGTVLARGLRGHVGCGLGQTLSTGEVSLVVPTVD 236
                                    ********....................**************************************************** PP

                                    CCC...................................................TTCEEE-SHCHHHHHHHHHHHHHHHC CS
                    Lactamase_B 160 idl..................................................tlrgaevrdpsdaekyldsllklaglk 189
                                    i++                                                  tlrga vrdp  ++ yl ++++ ++++
  gi|121639676|ref|YP_979900.1| 237 ITEtgethtidgveiefqmapgteapaemhfyfprfralcmaenathnlhnllTLRGALVRDPRAWSGYLTEAIDTFADR 316
                                    ******************************************************************************** PP

                                    HSEEEESS CS
                    Lactamase_B 190 aevlvpgH 197
                                    ++v++++H
  gi|121639676|ref|YP_979900.1| 317 TDVVFASH 324
                                    *******9 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   5.3e-36   1.9e-32       5     126 .]     510     626 .]     506     626 .] 0.93

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 5.3e-36
                                    HHCCCCS-HHHHHHHHHHHB-HHHHTT-EEEEEEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE.-HHHHHHHH CS
                   Alkyl_sulf_C   5 pdvlaalsleqlfDylAirvdgpkaadkdltinlvvtDvdekyllrlsngvLthtrkaaqaddadltvtl.treqLvall 83 
                                    p + a+l+++q+fD+lAi+++gp+a+d dl+i++++t+ d +y+l+l+ngvL+h++ +a+ ++a++tvt+ ++ +Lva++
  gi|121639676|ref|YP_979900.1| 510 PTFFAQLTPDQIFDVLAISINGPRAWDLDLAIDFTFTEPDVNYRLTLRNGVLIHRKLPADPATANATVTVgDKVRLVAAA 589
                                    77899*************************************************4444555********9999******9 PP

                                    TTSS-HHHHHHTTTEEEEE-TCHHHHHHCTB----TT--SSSS CS
                   Alkyl_sulf_C  84 lgkatlgkevaagklkieGdaealakllslldefdpaFnIVtP 126
                                    lg+      +++ ++++ Gd+++l+++ls+ld++d aFnIVtP
  gi|121639676|ref|YP_979900.1| 590 LGD------ISSPGFEVFGDRTVLQTFLSVLDRPDSAFNIVTP 626
                                    877......9999*****************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2     2e-10   7.1e-07       3      79 ..     114     193 ..     113     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2e-10
                                    EEES--TT..HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEEEHHHHHHCCTTCGHH CS
                  Lactamase_B_2   3 iLiDagpd..lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkklplyapkgvlavleanfvyl 77 
                                    i+iD+  +  +++ al +  ++++ ++ +p+ aV++th+H+DH+ g+l + +     + k+ ++ap+g  a+  ++ +y+
  gi|121639676|ref|YP_979900.1| 114 IVIDPLVSteVAAAALDL-YRAHRGAD-RPVVAVIYTHSHVDHFGGVLGVTTqadVDAGKVAVLAPEGFTAHAVQENIYA 191
                                    899999996633332222.34444455.8*******************99997665555699******999999888887 PP

                                    HC CS
                  Lactamase_B_2  78 al 79 
                                     +
  gi|121639676|ref|YP_979900.1| 192 GS 193
                                    65 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4      0.41   1.5e+03      50      63 ..     124     138 ..     122     141 .. 0.73
   2 ?   13.6   6.3   2.3e-05     0.082       1      46 [.     433     475 ..     433     479 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.41
                         TPR_16  50 laeAa.alyraalra 63 
                                    +a+Aa +lyra+ +a
  gi|121639676|ref|YP_979900.1| 124 VAAAAlDLYRAHRGA 138
                                    567777999998765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.3e-05
                         TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46 
                                    l+lar+a++agd++ Aa +l+ a+ +d   +++a+A+ l++d + +
  gi|121639676|ref|YP_979900.1| 433 LELAREAFDAGDFRWAATLLDHAVFAD---SEHAAARGLYADTLEQ 475
                                    689************************...************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4111.72
//
Query:       gi|121639677|ref|YP_979901.1|  [L=159]
Description: 19 kDa lipoprotein antigen precursor lpqH [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-37  126.0   6.6    8.2e-37  126.0   6.6    1.4  1  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
  ------ inclusion threshold ------
      0.046   14.1   0.8       0.67   10.4   0.2    2.2  2  PilX         Type IV pilus assembly protein PilX C-term


Domain annotation for each model (and alignments):
>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   6.6   9.2e-41   8.2e-37       5     116 .]      47     158 ..      41     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 9.2e-41
                    Myco_19_kDa   5 agtatvtvdGqdlqttgsvtCtqaggaltiaigdgasgvsavltdgdeptvesvgigdvdGftltyaegtgggsaevtkd 84 
                                    a+  +v++dG+d++ tgsv Ct+a+g+++iaig +a+g++avltdg++p+v+svg+g+v+G+tl+y++gtg+g+a +tkd
  gi|121639677|ref|YP_979901.1|  47 ASGPKVVIDGKDQNVTGSVVCTTAAGNVNIAIGGAATGIAAVLTDGNPPEVKSVGLGNVNGVTLGYTSGTGQGNASATKD 126
                                    55679*******777*****************978********************************************* PP

                    Myco_19_kDa  85 gntYtitGtaegadsanpaqpvtktFeievtC 116
                                    g++Y+itGta+g+d+anp+ pv+k+FeievtC
  gi|121639677|ref|YP_979901.1| 127 GSHYKITGTATGVDMANPMSPVNKSFEIEVTC 158
                                    ******************************** PP

>> PilX  Type IV pilus assembly protein PilX C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.025   2.3e+02      21      50 ..      34      63 ..      17      89 .. 0.75
   2 ?   10.4   0.2   7.4e-05      0.67      44      75 ..     110     140 ..     105     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
                           PilX 21 ataataatglaavakqPrYiIEylgdnaag 50
                                   +t+a + t++++ a+ P+ +I   ++n  g
  gi|121639677|ref|YP_979901.1| 34 TTTAAGTTASPGAASGPKVVIDGKDQNVTG 63
                                   457777888888888999999865555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.4e-05
                           PilX  44 lgdnaagssenltsatsaayvYRITArgfGas 75 
                                    lg++++ +++n +sat+++  Y+IT+ ++G +
  gi|121639677|ref|YP_979901.1| 110 LGYTSGTGQGN-ASATKDGSHYKITGTATGVD 140
                                    67888888888.9*****************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1156.28
//
Query:       gi|121639678|ref|YP_979902.1|  [L=475]
Description: two component sensor kinase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-23   81.9   0.0    7.2e-23   81.2   0.0    1.3  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-18   66.7   0.5    5.4e-18   64.8   0.5    2.0  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.5e-08   34.8   2.4      2e-08   34.5   0.2    2.5  3  HAMP         HAMP domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.073   13.0   0.0    1.9  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.038   13.9   0.0      0.073   13.0   0.0    1.5  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0     2e-26   7.2e-23       1     111 [.     355     465 ..     355     466 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2e-26
                                    EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                      HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                    gd  rL+q++ nl+ Na  ++++++ ++ ++++   ++v++v DnG+Gip + + ++fe+f + d s++r+ g tGlGl+
  gi|121639678|ref|YP_979902.1| 355 GDAARLHQVVTNLLANARVHTGPGTIVTTRLSTGPTHVVLQVIDNGPGIPAALQSEVFERFARgDTSRSRQAGSTGLGLA 434
                                    7999****************6677777888886458***************************999999999******** PP

                                    HHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlple 111
                                    iv ++v+ ++G+i+v+s+p + t+f ++lpl+
  gi|121639678|ref|YP_979902.1| 435 IVSAVVKAHNGTITVSSSP-GYTEFAVRLPLD 465
                                    ***************8888.7888*****986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.5   1.5e-21   5.4e-18       3      67 .]     248     312 ..     246     312 .. 0.97
   2 ?   -2.2   0.0       1.3   4.6e+03      47      64 ..     356     373 ..     352     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.5e-21
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                    ++f+a+ +HELrtPL+ai+g++e+ +r g+ +e ++ +  ++ se++r+++lvedlL l+r+++g
  gi|121639678|ref|YP_979902.1| 248 RQFVADASHELRTPLAAIRGYTELTQRIGDDPEAVAHAMSRVASETERITRLVEDLLLLARLDSG 312
                                    79*************************98889*******************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHHHCCH CS
                          HisKA  47 earrldhlvedlLdlsri 64 
                                     a rl ++v +lL  +r 
  gi|121639678|ref|YP_979902.1| 356 DAARLHQVVTNLLANARV 373
                                    688999999999876665 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.2   5.7e-12     2e-08       1      51 [.     173     233 ..     173     235 .. 0.81
   2 ?   -2.4   0.1       1.8   6.4e+03      14      22 ..     283     291 ..     281     303 .. 0.62
   3 ?   -3.5   0.0       3.9   1.4e+04      16      26 ..     411     421 ..     409     423 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.7e-12
                                    HHHHTTHHHHHHHHHHHHHHTT.....T..BTSST.....CCTTSSSHHHHHHHHHHHHHHHH CS
                           HAMP   1 llarrilrPLrrLaraarriaa.....G..dldtr.....lpvsgrDEiGeLarafNaMldrL 51 
                                    ++++r l+PLrr+a++a ++ +     G      +     ++ ++  E+G+L+ a+N+Mld++
  gi|121639678|ref|YP_979902.1| 173 VIIKRALAPLRRVAQTASEVVDlpldrGevK--LPvrvpePDANPSTEVGQLGSALNRMLDHI 233
                                    5899*****************7555556552..33557767779*****************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                    HHHHHHHTT CS
                           HAMP  14 araarriaa 22 
                                    a a+ r+a+
  gi|121639678|ref|YP_979902.1| 283 AHAMSRVAS 291
                                    667777775 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.9
                                    HHHHHTTTBTS CS
                           HAMP  16 aarriaaGdld 26 
                                    + +r a+Gd +
  gi|121639678|ref|YP_979902.1| 411 VFERFARGDTS 421
                                    67899999987 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.073      31     110 ..     359     441 ..     346     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                    HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGl 102
                                    +++ +v+ +++Na  h  +      v+ rl+ +++ ++++v D+Gpg +++ + +  e           + ++ + G+Gl
  gi|121639678|ref|YP_979902.1| 359 RLHQVVTNLLANARVHTGP---GTIVTTRLSTGPTHVVLQVIDNGPGIPAALQSEVFE--RfargdtsrSRQAGSTGLGL 433
                                    5566666667777666665...5679999******************66654433322..234677887999999***** PP

                    HATPase_c_2 103 alikglvD 110
                                    a++ ++v 
  gi|121639678|ref|YP_979902.1| 434 AIVSAVVK 441
                                    **998875 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.073      55     100 ..     417     462 ..     358     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                    HATPase_c_5  55 kklesskskkeehGiGlksireivkkykgnlsieaedglFtlsvll 100
                                    +   s++++ +  G+Gl  ++ +vk ++g+++++ + g+ +  v l
  gi|121639678|ref|YP_979902.1| 417 RGDTSRSRQAGSTGLGLAIVSAVVKAHNGTITVSSSPGYTEFAVRL 462
                                    34447789999**********************9988876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3408.74
//
Query:       gi|121639679|ref|YP_979903.1|  [L=234]
Description: two component transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-29  101.6   0.0    4.6e-29  100.8   0.0    1.4  1  Response_reg  Response regulator receiver domain
    6.8e-25   87.0   0.0    4.4e-24   84.4   0.0    2.0  2  Trans_reg_C   Transcriptional regulatory protein, C terminal
    0.00048   20.5   0.0    0.00083   19.7   0.0    1.4  1  FleQ          Flagellar regulatory protein FleQ
  ------ inclusion threshold ------
      0.022   15.2   0.9       0.39   11.2   0.2    2.5  2  3HCDH_RFF     3-hydroxybutyryl-CoA dehydrogenase reduced Ross
       0.03   14.4   0.1      0.072   13.1   0.0    1.6  2  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   1.3e-32   4.6e-29       1     111 [.      11     120 ..      11     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.3e-32
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl+vdD+p+++e ++ +l+ eg  ++++a dg++a++ ++++++d+++lD+++p+m+Gl++l ++r e+p lpv++lta+
  gi|121639679|ref|YP_979903.1|  11 VLVVDDEPVLAEMVSMALRYEGW-NITTAGDGSSAIAAARRQRPDVVVLDVMLPDMSGLDVLHKLRSENPGLPVLLLTAK 89 
                                    8**********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++ ed++++l ag dd+++Kpf++ee++ +l
  gi|121639679|ref|YP_979903.1|  90 DAVEDRIAGLTAGGDDYVTKPFSIEEVVLRL 120
                                    *************************998776 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.25     9e+02      37      60 ..     104     127 ..     100     134 .. 0.75
   2 !   84.4   0.0   1.2e-27   4.4e-24       1      77 []     156     230 ..     156     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.25
                                    TTSTSHTHHHHHHHHHHHHHHHTT CS
                    Trans_reg_C  37 ededvddrtvdvhisrLRkkLedd 60 
                                    +d+ +   +++  + rLR  L+ +
  gi|121639679|ref|YP_979903.1| 104 DDYVTKPFSIEEVVLRLRALLRRT 127
                                    566666678899999***999984 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 1.2e-27
                                    TEEEE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
                    Trans_reg_C   1 geeveltpkefklLelLlenpgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                                    ge+v+lt++ef+lL+++++n++rv+s++++l++vw +d+ + ++ v+ +is+LRkk+++ +++p +I+t+rg GY+l
  gi|121639679|ref|YP_979903.1| 156 GEPVSLTSTEFELLRFMMHNSKRVLSKAQILDRVWSYDFGGRSNIVELYISYLRKKIDN-GREP-MIHTLRGAGYVL 230
                                    789********************************************************.8888.**********87 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07   0.00083       1      82 [.      10      94 ..      10     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                           FleQ  1 kiLvidddaerrrdletiLeFlgeeveavsseel.saaleessseala..vilgsvssleealealaekdphlPvlllgesd 79
                                   ++Lv+dd+   ++ +++ L++ g ++ + ++ +   aa+++++ ++++  v+l ++ s  + l++l +++p lPvlll+ +d
  gi|121639679|ref|YP_979903.1| 10 TVLVVDDEPVLAEMVSMALRYEGWNITTAGDGSSaIAAARRQRPDVVVldVMLPDM-SGLDVLHKLRSENPGLPVLLLTAKD 90
                                   59***********************9999998875444444444444412444444.599*******************999 PP

                           FleQ 80 ea.e 82
                                   +  +
  gi|121639679|ref|YP_979903.1| 91 AVeD 94
                                   8744 PP

>> 3HCDH_RFF  3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00011      0.39       5      27 ..      40      62 ..      37      70 .. 0.87
   2 ?    1.8   0.0     0.092   3.3e+02      15      32 ..     133     150 ..     124     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                      3HCDH_RFF  5 dGrtAtqraaeegrpvvlfDlal 27
                                   dG +A   a++++ +vv++D +l
  gi|121639679|ref|YP_979903.1| 40 DGSSAIAAARRQRPDVVVLDVML 62
                                   9******9999999******987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.092
                      3HCDH_RFF  15 eegrpvvlfDlaldyraa 32 
                                    ++g+++v+ Dl+ld ++ 
  gi|121639679|ref|YP_979903.1| 133 DSGAQLVVGDLVLDEDSH 150
                                    56799********98875 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.072      13      85 ..      17      84 ..       9      85 .. 0.80
   2 ?   -3.1   0.0       2.1   7.7e+03      73      87 ..     125     141 ..     119     156 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                    B12-binding 13 hplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvv 85
                                    p+ + ++  alr +g++++  g        +aa+r+ +pdvv+l + +   +++   l + l++++p+++v+
  gi|121639679|ref|YP_979903.1| 17 EPVLAEMVSMALRYEGWNITTAGDGS---SAIAAARRQRPDVVVLDV-MLPDMSGLDVL-HKLRSENPGLPVL 84
                                   567788999**********9998888...67899*************.99988886554.5555667888876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                    B12-binding  73 el..lkrirprvkvvvG 87 
                                    ++  + ++++++ +vvG
  gi|121639679|ref|YP_979903.1| 125 RRtgVTTVDSGAQLVVG 141
                                    33344445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1809.46
//
Query:       gi|121639680|ref|YP_979904.1|  [L=229]
Description: hypothetical protein BCG_3825 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1669.83
//
Query:       gi|121639681|ref|YP_979905.1|  [L=314]
Description: hypothetical protein BCG_3826c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-62  209.1   0.1      8e-62  208.5   0.1    1.3  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.5   0.1   4.5e-66     8e-62       1     187 [.      19     204 ..      19     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 4.5e-66
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHG.C.HCCCCT--HHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekek.e.eekkekkapelnrgiavRtrffddllka 78 
                                    algvaaara+e++++ ++li+Dp+a+ +v+aag+ +++ + +++l +   + +++ ++  +++ +++a+Rt+ffd+++ a
  gi|121639681|ref|YP_979905.1|  19 ALGVAAARAAETESD-NPLINDPFARIFVDAAGDGIWSMYTNRTLLAGAtDlDPDLRAPIQQMIDFMAARTAFFDEYFLA 97 
                                    789***********9.*******************9966666666555544699************************** PP

                                    HHHCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT CS
                            LCM  79 alsaagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagf 158
                                     + +ag+rqvViL++GlD+ra+Rlpw++g++v+E+Dqp+vlefK +tl+++ga+p  +l  vp+Dlr +dwp+aL++agf
  gi|121639681|ref|YP_979905.1|  98 TA-DAGVRQVVILASGLDSRAWRLPWPDGTVVYELDQPKVLEFKSATLRQHGAQPASQLVNVPIDLR-QDWPKALQKAGF 175
                                    **.7***************************************************************.************ PP

                                    -TTSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 159 dpekptawvaeGvlvYLtpeasdalleai 187
                                    dp+kp aw+aeG++ YL++ a+d l+e+i
  gi|121639681|ref|YP_979905.1| 176 DPSKPCAWLAEGLVRYLPARAQDLLFERI 204
                                    **************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1666.61
//
Query:       gi|121639682|ref|YP_979906.1|  [L=119]
Description: hypothetical protein BCG_3827 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-12   46.9   0.8    4.3e-12   46.6   0.8    1.1  1  SnoaL_2       SnoaL-like domain
    3.6e-05   23.5   0.0    4.9e-05   23.1   0.0    1.3  1  SnoaL         SnoaL-like polyketide cyclase
     0.0006   20.2   0.1     0.0007   20.0   0.1    1.1  1  DUF4440       Domain of unknown function (DUF4440)
     0.0068   16.3   0.4      0.013   15.4   0.4    1.5  1  HCBP_related  Haemolysin-type calcium binding protein related
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.023   15.0   0.0    1.3  1  SnoaL_3       SnoaL-like domain
      0.062   13.4   0.0       0.16   12.1   0.0    1.6  1  LEH           Limonene-1,2-epoxide hydrolase catalytic domain


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.8   1.4e-15   4.3e-12       6     102 .]      18     109 ..      13     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.4e-15
                                    HHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEE CS
                        SnoaL_2   6 aalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvt 85 
                                    +al+agdld+++a +a+d  +  p+g  rG+e+ir+ f +l++ +p   ++++  + +gd  ++ewt+        +  +
  gi|121639682|ref|YP_979906.1|  18 QALAAGDLDEIVADYADDSFVITPAGIARGKEGIRQLFVKLLDDIPNALWDLKTQIFEGDILFLEWTAN------SAVSR 91 
                                    69****************************************************************995......56666 PP

                                    E.EEEEEEEEETTEEEEE CS
                        SnoaL_2  86 v.rgvdvfrvrdGkiveh 102
                                    v +gvd+f +rdG i++h
  gi|121639682|ref|YP_979906.1|  92 VdDGVDTFVFRDGTIWAH 109
                                    78************9876 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.6e-08   4.9e-05      11      79 ..      20      87 ..      11     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-08
                                   HHTT-HHH.HHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEE CS
                          SnoaL 11 wnsgdlda.ldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftG 79
                                   +  gdld+ +++++++++v    +++ arG+eg+r+ +++l++++P+   + + ++ egd   +++t++ 
  gi|121639682|ref|YP_979906.1| 20 LAAGDLDEiVADYADDSFVIT--PAGIARGKEGIRQLFVKLLDDIPNALWDLKTQIFEGDILFLEWTANS 87
                                   567888661566666667766..55******************************************875 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.3e-07    0.0007       9      93 ..      17     102 ..      10     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                    HHHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEE.TTEEEEEEEEEEEECC.TTE CS
                        DUF4440   9 eeafvagdaealaallapdavlvgpsgtvldkeellealeagfaagrslelteeevrvl.gdlAvvtgrytfegrg.dge 86 
                                     +a++agd++++ a +a+d  +++p g +  ++e + +l+ + +++   +l ++++++  gd+ ++ ++ + ++ + d++
  gi|121639682|ref|YP_979906.1|  17 GQALAAGDLDEIVADYADDSFVITPAG-IARGKEGIRQLFVKLLDDIPNALWDLKTQIFeGDILFLEWTANSAVSRvDDG 95 
                                    689************************.655555788889999999999**********99*999998877665332433 PP

                                    EEEEEEE CS
                        DUF4440  87 pvegrgr 93 
                                      ++ +r
  gi|121639682|ref|YP_979906.1|  96 VDTFVFR 102
                                    2233444 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   4.3e-06     0.013      24      38 ..      93     107 ..      81     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-06
                   HCBP_related  24 syrieqieFaDGtvW 38 
                                    + ++++++F DGt+W
  gi|121639682|ref|YP_979906.1|  93 DDGVDTFVFRDGTIW 107
                                    45799********** PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   7.6e-06     0.023       4      57 ..      12      63 ..      10     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                        SnoaL_3  4 lldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakge 57
                                   ++++  +a+a+gd+d+++a +add + i   +   ++g+e +r+ + + +++++
  gi|121639682|ref|YP_979906.1| 12 VFAHHGQALAAGDLDEIVADYADDSFVIT--PAGIARGKEGIRQLFVKLLDDIP 63
                                   56666799*********************..5569***********99999874 PP

>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.3e-05      0.16       2      91 ..       8     107 ..       7     112 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHHHHHHT-HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT..........TTT-EEEEEEEEE...E CS
                            LEH   2 epirvVeaFlaalqeddydaavrrlatdlevyeneglstihGraeaiallerl.........sadilavevkilri...a 69 
                                    +p +v  +  +al   d+d  v+++a+d  v ++ g+++  G+++ ++l+ +l           ++  +e +il     a
  gi|121639682|ref|YP_979906.1|   8 TPQEVFAHHGQALAAGDLDEIVADYADDSFVITPAGIAR--GKEGIRQLFVKLlddipnalwDLKTQIFEGDILFLewtA 85 
                                    56778888899******************9999999985..666666666655221133333222333444443321112 PP

                                    EETTEEEEEEEEEEEE..TTEE CS
                            LEH  70 adgsaVltERlDrliladGpli 91 
                                      +   + + +D ++++dG+ +
  gi|121639682|ref|YP_979906.1|  86 NSAVSRVDDGVDTFVFRDGTIW 107
                                    2223334556666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 659.00
//
Query:       gi|121639683|ref|YP_979907.1|  [L=90]
Description: hypothetical protein BCG_3828 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0074   16.2   1.2      0.013   15.4   0.6    1.6  1  BAT           GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.015   15.5   4.1      0.068   13.5   4.1    2.1  1  DUF4164       Domain of unknown function (DUF4164)
      0.018   15.1   0.1      0.093   12.8   0.1    1.8  2  DUF1664       Protein of unknown function (DUF1664)
      0.069   13.4   0.3       0.11   12.8   0.3    1.5  1  DUF948        Bacterial protein of unknown function (DUF948)
        0.1   12.9   0.3        1.6    9.0   0.3    2.2  1  ABC_tran_CTD  ABC transporter C-terminal domain
       0.11   12.7   0.3        1.4    9.1   0.2    2.0  2  XhlA          Haemolysin XhlA


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   4.4e-06     0.013      91     137 ..       2      50 ..       1      56 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.4e-06
                            BAT  91 stlaehGgtvrsaeae..dgrarlvvevPpgadvRsvvealeerypdve 137
                                    +tl e G++v ++ea+  d ra l +  Ppga+ R+++ +++e+  + +
  gi|121639683|ref|YP_979907.1|   2 TTLKELGARVAALEANqaDYRAVLAAVNPPGANQREIATTVREHTGRLD 50 
                                    79*************9444455555567**************9987765 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.1   2.3e-05     0.068      35      79 ..      43      87 ..       3      90 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                        DUF4164 35 deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79
                                   +e   ++ +++    +La++ d+++ar ++lee+++E+++ L +a
  gi|121639683|ref|YP_979907.1| 43 REHTGRLDRVTTKVGQLAAKSDDTNARVRSLEEGQAEIKDLLLRA 87
                                   677778889999999************************988766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.23   6.8e+02      61      81 ..       4      24 ..       1      30 [. 0.64
   2 ?   12.8   0.1   3.1e-05     0.093      55     101 ..      36      82 ..      32      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                        DUF1664 61 krhLssridrvdkkldeqkei 81
                                    ++L +r++ +++++ +  ++
  gi|121639683|ref|YP_979907.1|  4 LKELGARVAALEANQADYRAV 24
                                   567777777777777666655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.1e-05
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                     ++a+t r+ + r+drv +k+ + ++ s ++++ v +++e+ +ei++
  gi|121639683|ref|YP_979907.1|  36 REIATTVREHTGRLDRVTTKVGQLAAKSDDTNARVRSLEEGQAEIKD 82 
                                    68999***********************************9999986 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.7e-05      0.11      27      84 ..       3      63 ..       1      83 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                         DUF948 27 tldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84
                                   tl+e+ a+++ le    + +++l  v+   a+ +e++  v+e++ ++d++t++v++l+++ 
  gi|121639683|ref|YP_979907.1|  3 TLKELGARVAALEanqADYRAVLAAVNPPGANQREIATTVREHTGRLDRVTTKVGQLAAKS 63
                                   5666666666666544667777777777788888888888888888888888888887764 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00055       1.6      10      36 ..       4      30 ..       2      90 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00055
                   ABC_tran_CTD 10 leeleaeIeaLEeeiaeleaeladpel 36
                                   l+el a+ +aLE+ +a+  a la+ + 
  gi|121639683|ref|YP_979907.1|  4 LKELGARVAALEANQADYRAVLAAVNP 30
                                   78999999********99998886543 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.09   2.7e+02      11      29 ..       2      20 ..       1      29 [. 0.74
   2 ?    9.1   0.2   0.00048       1.4       2      45 ..      38      81 ..      37      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.09
                           XhlA 11 tkldnleervdkleekaae 29
                                   t l++l+ rv  le ++a 
  gi|121639683|ref|YP_979907.1|  2 TTLKELGARVAALEANQAD 20
                                   5678888888888888775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00048
                           XhlA  2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkle 45
                                   i   + ++ ++ld   ++v +l  k++ + +++ +lee  ++++
  gi|121639683|ref|YP_979907.1| 38 IATTVREHTGRLDRVTTKVGQLAAKSDDTNARVRSLEEGQAEIK 81
                                   66677788888888888888888888888888888877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 498.03
//
Query:       gi|121639684|ref|YP_979908.1|  [L=191]
Description: hypothetical protein BCG_3829c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1036.39
//
Query:       gi|121639685|ref|YP_979909.1|  [L=60]
Description: remnant of a transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 338.90
//
Query:       gi|121639686|ref|YP_979910.1|  [L=63]
Description: remnant of a transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00039   20.1   4.6    0.00087   19.0   0.4    2.1  2  HTH_23    Homeodomain-like domain
     0.0086   16.2   2.9      0.059   13.5   2.6    2.3  1  HTH_28    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.8   0.4      0.034   14.3   0.4    1.5  1  HTH_17    Helix-turn-helix domain
       0.17   12.0   0.2       0.76   10.0   0.2    1.8  1  U-box     U-box domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4     0.016        71       6      26 ..       4      23 ..       2      25 .. 0.86
   2 !   19.0   0.4   1.9e-07   0.00087       3      39 ..      26      62 ..      24      63 .] 0.92

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                         HTH_23  6 eRlrillllaeGlsvreIAre 26
                                   eR+r++ l++  + +re+A++
  gi|121639686|ref|YP_979910.1|  4 ERARAIGLFR-YQLIREAADA 23
                                   8*******99.8999999986 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.9e-07
                         HTH_23  3 sereRlrillllaeGlsvreIAreLgvsrrTvyrwlk 39
                                   s +eR ++++ la +  +    r+  +sr+T++rw++
  gi|121639686|ref|YP_979910.1| 26 STKERGKMVRELASREHTDPFGRKVRISRHTIDRWIR 62
                                   6789999****************************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.6   1.3e-05     0.059       1      34 [.      29      62 ..       4      63 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                         HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWik 34
                                   +R +++++la+ +  +   r++ isr t+ rWi+
  gi|121639686|ref|YP_979910.1| 29 ERGKMVRELASREHTDPFGRKVRISRHTIDRWIR 62
                                   578999*****99********************8 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   7.6e-06     0.034      20      48 ..      36      62 ..      14      63 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.6e-06
                         HTH_17 20 rlirrgelpaakiGrrwriprsdleewle 48
                                   +l++r    ++  Gr++ri+r  +++w++
  gi|121639686|ref|YP_979910.1| 36 ELASREHTDPF--GRKVRISRHTIDRWIR 62
                                   44444444444..899***********98 PP

>> U-box  U-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00017      0.76      25      51 ..      27      53 ..      21      63 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                                   EEEHHHHHHHHTT.SSB-TTT-SB--G CS
                          U-box 25 vvdrstiekhllsrdktdPftrepltq 51
                                   + +r  + + l sr++tdPf r++  +
  gi|121639686|ref|YP_979910.1| 27 TKERGKMVRELASREHTDPFGRKVRIS 53
                                   668999999***********9987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 358.07
//
Query:       gi|121639687|ref|YP_979911.1|  [L=108]
Description: hypothetical protein BCG_3832c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   16.8   0.2     0.0072   16.1   0.2    1.4  1  HTH_23    Homeodomain-like domain
      0.008   16.3   0.5      0.016   15.3   0.5    1.5  1  HTH_28    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     8e-07    0.0072      21      48 ..      15      41 ..       7      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8e-07
                         HTH_23 21 reIAreLgvsrrTvyrwlkryreeGleg 48
                                   r+IA+ L ++  Tv+ wl+r+ +e +e+
  gi|121639687|ref|YP_979911.1| 15 RRIAADLARPAETVRGWLRRF-AERAEA 41
                                   89*******************.565555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   1.8e-06     0.016       9      38 ..       8      37 ..       5      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                         HTH_28  9 laaGhsvreaArelgisrrtvyrWikryee 38
                                   +++++  r +A+ l    +tv++W++r+ e
  gi|121639687|ref|YP_979911.1|  8 ALSQVGFRRIAADLARPAETVRGWLRRFAE 37
                                   6789999*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 571.27
//
Query:       gi|121639688|ref|YP_979912.1|  [L=353]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-48  164.2   0.0    5.6e-48  163.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      0.009   14.6   0.0      0.016   13.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.051   12.9   0.0       0.08   12.2   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.21   10.5   0.2       0.68    8.7   0.0    1.9  2  Alliinase_C      Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.0   1.3e-51   5.6e-48       4     353 ..      25     338 ..      22     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1.3e-51
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    i+L+sne  ++    +lp+v+ a  +   a+ t+n+y+++    +l+ ala+ lg     ++ +e  v vg G+ +l + 
  gi|121639688|ref|YP_979912.1|  25 IKLASNETVFG----PLPSVRAAIDR---ATDTVNRYPDNG-CVQLKAALARHLG----PDFAPE-HVAVGCGSVSLCQQ 91 
                                    89*********....****8888866...**********99.*************....789999.************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    l +++ +  gde++    +++ y + +r +g+  +++pl+   d + dl a+++a+++      +t++i+v++p+NPt t
  gi|121639688|ref|YP_979912.1|  92 LVQVT-ASVGDEVVFGWRSFELYPPQVRVAGAIPIQVPLT---DHTFDLYAMLAAVTD------RTRLIFVCNPNNPTST 161
                                    *****.9*******************************99...99*************......**************** PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsql 243
                                    v  ++ l   ++ + + ++l+ +DeaY +   + +++ + + +v ++ n+++++++sKa+GlaG+R+Gy++g+++v+ +l
  gi|121639688|ref|YP_979912.1| 162 VVGPDALARFVEAVPA-HILIAIDEAYVEYIRDGMRPDS-LGLVRAHNNVVVLRTFSKAYGLAGLRIGYAIGHPDVITAL 239
                                    ***************8.9***************998777.999999999******************************* PP

                                    HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHH CS
                  Aminotran_1_2 244 rklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskk 323
                                     k+  pf++ss++qaa+ a+l++a+    el ++ +++ ++r ++ +eL+++g++  +sq++++ l ++s+   +++ ++
  gi|121639688|ref|YP_979912.1| 240 DKVYVPFTVSSIGQAAAIASLDAAD----ELLARTDTVVAERARVSAELRAAGFTLPPSQANFVWLPLGSRT--QDFVEQ 313
                                    *************************....9****************************************99..9***** PP

                                    HHHTCTEEEEEGGGGTSTTEEEEECTTS-H CS
                  Aminotran_1_2 324 LleevgvyvtpgtsftvpgrlRitvAglte 353
                                     ++   ++v+p   +++ g +R+tvA+  e
  gi|121639688|ref|YP_979912.1| 314 AADA-RIVVRP---YGTDG-VRVTVAAPEE 338
                                    ****.******...66677.*****65443 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.5e-06     0.016      70     176 ..      78     187 ..      70     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                                    EEEESSHHHHHHHHHHTTS-T.TEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTT.SHHHHHHHCCTTEEEEEEESS- CS
                Cys_Met_Meta_PP  70 alavssGmaAiaaailallka.GdeivvsddlYggtqrllkkvlkklgievkfvdts.dleelekaikentklvylEtpt 147
                                     +av +G  ++ + ++++  + Gde+v     ++    +++ v+  + i+v  +d + dl ++ +a++++t+l+++  p 
  gi|121639688|ref|YP_979912.1|  78 HVAVGCGSVSLCQQLVQVTASvGDEVVFGWRSFELYPPQVR-VAGAIPIQVPLTDHTfDLYAMLAAVTDRTRLIFVCNPN 156
                                    67888998888777776655559999998887776555554.5666778888877643789999**************** PP

                                    TTTT----HHHHHHHHHHTT..-EEEEEGTT CS
                Cys_Met_Meta_PP 148 npllkvvDiekiaklakkag..vlvvvDntf 176
                                    np+  vv   ++a+++ ++   +l+ +D ++
  gi|121639688|ref|YP_979912.1| 157 NPTSTVVGPDALARFVEAVPahILIAIDEAY 187
                                    ********99999999998666999999865 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.8e-05      0.08      26     117 ..      60     152 ..      39     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHT...-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GG CS
                DegT_DnrJ_EryC1  26 eeFEkafaaylg...vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpa 102
                                     ++ +a+a++lg   +   +av  G+ +l   L  + ++ gdeV+    +F      v+ +ga p+ v  + +t+  d  
  gi|121639688|ref|YP_979912.1|  60 VQLKAALARHLGpdfAPEHVAVGCGSVSLCQQLVQVTASVGDEVVFGWRSFELYPPQVRVAGAIPIQVPLTDHTF--DLY 137
                                    57788899999944445559*********************************************9999886665..677 PP

                                    GCGGG--TTEEEEEE CS
                DegT_DnrJ_EryC1 103 aieaaitertkaIlp 117
                                    a+ aa+t rt+ I++
  gi|121639688|ref|YP_979912.1| 138 AMLAAVTDRTRLIFV 152
                                    8899********987 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.21   9.6e+02      67      87 ..      77      97 ..      74     105 .. 0.83
   2 ?    8.7   0.0   0.00015      0.68     180     212 ..     203     235 ..     143     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.21
                                   SEEEEECHHHHHHHHHHHHHH CS
                    Alliinase_C 67 ryivvGtGstqLlqalvyals 87
                                    ++ vG Gs  L+q lv   +
  gi|121639688|ref|YP_979912.1| 77 EHVAVGCGSVSLCQQLVQVTA 97
                                   5899**********9997655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00015
                                    -S-B--SEEEEEHHHHHS-GGG-EEEEEES-HH CS
                    Alliinase_C 180 tskadedimLftlskltGhaGsrlGWalvkdke 212
                                     ++ ++ ++L t+sk  G aG r+G+a+ +   
  gi|121639688|ref|YP_979912.1| 203 VRAHNNVVVLRTFSKAYGLAGLRIGYAIGHPDV 235
                                    55666778999****************865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2410.63
//
Query:       gi|121639689|ref|YP_979913.1|  [L=114]
Description: hypothetical protein BCG_3834c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 880.54
//
Query:       gi|121639690|ref|YP_979914.1|  [L=78]
Description: hypothetical protein BCG_3835c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 589.99
//
Query:       gi|121639691|ref|YP_979915.1|  [L=274]
Description: enoyl-CoA hydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-40  138.6   0.0      4e-40  137.7   0.0    1.4  1  ECH_1     Enoyl-CoA hydratase/isomerase
      3e-19   69.7   0.1    4.7e-16   59.2   0.1    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   4.4e-44     4e-40       1     250 [.      11     273 ..      11     274 .] 0.91

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 4.4e-44
                                    EEETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.........HHHH CS
                          ECH_1   1 eieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.........akqa 71 
                                    e+++ va+++l  P + Na+ +++  E+ ++++ l+ d++vra+v+tG++k F+ G+d+ +m +            +  +
  gi|121639691|ref|YP_979915.1|  11 ETKDQVAQVTLIGPGKGNAMGPAFWSEMPEVFHALDADREVRAIVITGSGKNFSYGLDVPAMGGMFApliadgalaRPRT 90 
                                    57889******************************************************999764333432222355666 PP

                                    HHHCCH...HHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHH CS
                          ECH_1  72 llkeev...lelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGksk 148
                                    +++ e+   ++  +++ ++  p+iaav+G +igG + l +a Di++a+ +a+f+  e+kl +++++g   +l+ ++    
  gi|121639691|ref|YP_979915.1|  91 DFHTEIlrmQKAINAVADCRTPTIAAVQGWCIGGAVDLISAVDIRYASADAKFSVREVKLAIVADMGSLARLPLILSDGH 170
                                    666665111555667789************************************************************** PP

                                    HHHHHHHT-EEEHHHHHHCTSSSEEESG.GGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ECH_1 149 AeeilllgkkisaqealkvGlvdkvvpe.eqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfest 227
                                     +e++l+gk+i a+ a+k+Glv+ v  + +q l  a + a+++a ++p+a+  +k+ l+++ ++a  e l   a    ++
  gi|121639691|ref|YP_979915.1| 171 LRELALTGKNIDAARAEKIGLVNDVYDDaDQTLAAAHATAAEIAANPPLAVYGIKDVLDQQRTSAVSENLRYVAAWNAAF 250
                                    *************************99989*********************************99999999999999999 PP

                                    CTSHHHHHHHHHHHTCSH----- CS
                          ECH_1 228 fskddikeGlqaflEkrkpefed 250
                                      ++d  eG+ a   kr+p+f++
  gi|121639691|ref|YP_979915.1| 251 LPSKDLTEGISATFAKRPPQFTG 273
                                    9999*****************86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   5.2e-20   4.7e-16       3     175 ..      18     199 ..      16     204 .. 0.87
   2 !    9.4   0.0   7.4e-05      0.66     246     311 ..     203     267 ..     195     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5.2e-20
                                    EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS......-THH..HHHHH CS
                          ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakeg......kkee..eeffr 74 
                                     +tL  p + Na+  +  +++ e +++ ++d ev+++v++g+g k f+ G Dv a+             +  +  ++f +
  gi|121639691|ref|YP_979915.1|  18 QVTLIGPGKGNAMGPAFWSEMPEVFHALDADREVRAIVITGSG-KNFSYGLDVPAMGGMFAPLiadgalA--RprTDFHT 94 
                                    6899999**********************************88.**********9877665544434432..23489999 PP

                                    HHHHHHHHH...HC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCS.STTHHHHH CS
                          ECH_2  75 eeYklnyli...atypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrl.pgelGlyl 150
                                    e  +++++i   a++++p++a ++G ++Gg v l     +r ++ +++f++ E+++ ++ D G    L+ + +    + l
  gi|121639691|ref|YP_979915.1|  95 EILRMQKAInavADCRTPTIAAVQGWCIGGAVDLISAVDIRYASADAKFSVREVKLAIVADMGSLARLPLIlSDGHLREL 174
                                    99999877622267899***************************************************99645566678* PP

                                    HHH---B-HHHHHHTTS--EE--GG CS
                          ECH_2 151 alTGarlkgadalaaglathyvpse 175
                                    alTG+++++a a ++gl + + +++
  gi|121639691|ref|YP_979915.1| 175 ALTGKNIDAARAEKIGLVNDVYDDA 199
                                    *****************99887766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 7.4e-05
                                    SHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS- CS
                          ECH_2 246 dewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdk 311
                                     + a++t+++++++ P+++  +   l++ r+ + ++e lr   +  +++l +kD++eG+ a++ ++
  gi|121639691|ref|YP_979915.1| 203 LAAAHATAAEIAANPPLAVYGIKDVLDQQRTSA-VSENLRYVAAWNAAFLPSKDLTEGISATFAKR 267
                                    4578999************************96.***************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1705.94
//
Query:       gi|121639692|ref|YP_979916.1|  [L=415]
Description: lipase lipE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-69  232.4   0.3    1.1e-68  232.0   0.3    1.0  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.0   0.3   5.9e-73   1.1e-68       4     324 ..      43     398 ..      40     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 5.9e-73
                                    HHHHHHHHTTESEEEEEEEETTEEEEEEEEEE.........EETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSC CS
                 Beta-lactamase   4 lvrelmaqggipGvavavvrdgkvvldkggGv.........adleggrpvtadtlfriaSvtKtftaaavlqlveeGkld 74 
                                    + r++m+    p +++++ ++g+vvl++++G+         ad+e+  pvt+dt+f ++S+ K++ta++v++lve+G++ 
  gi|121639692|ref|YP_979916.1|  43 WYRAGMH----PAIQLCIRHHGRVVLNRAIGHgwgnaptdeADAEKI-PVTTDTPFCVYSAAKAITATVVHMLVERGHFA 117
                                    5677777....*******************99889999886777666.******************************** PP

                                    TTSBGGGTSTTCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSSTTSCEE-SHHHHH.HHH CS
                 Beta-lactamase  75 LddpVskylPefagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkyapGtkwgYsntgyg.llg 153
                                    Ldd+V++ylP ++++gk++ T+r++ltH++G+p  + ++   ++a+d++ ++++l +l+p y pG  ++Y++++ g l+ 
  gi|121639692|ref|YP_979916.1| 118 LDDRVCEYLPSYTSHGKHRTTIRHVLTHSAGVPFPTGPRPDVRRADDHEYAVERLGELRPLYRPGLVHIYHALTWGpLMR 197
                                    ******************************************************************************** PP

                                    HHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC................. CS
                 Beta-lactamase 154 ellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae................. 216
                                    e++ ++tg+ ++++l +eil+pLg + t +g++e + p +a ++++ ++ +++ +a ++++ +                 
  gi|121639692|ref|YP_979916.1| 198 EIVYAATGKEIREILATEILDPLGFRWTNFGVAERDVPLVAPSHATGRQLPPVIAAVFRKAIGgtvheiipytntpffls 277
                                    ********************************************9999999999999999988***************** PP

                                    ...TTTBEEEEHHHHHHHH.....HHHHHCCSSSSHHHHHHH..HHHHTSEEEECTTEEEECECSSEEEEECCH...... CS
                 Beta-lactamase 217 ...gagglistardlarfl.....glalegglllsaetlaql..taklssgttrpagiraglglGwvladktga...... 280
                                       ++ + +sta+ l rf+     g++l+g ++ls+etl+ +    ++ ++  ++++++ ++g G++l+  + +      
  gi|121639692|ref|YP_979916.1| 278 tilPSSNTVSTANELSRFMeilrrGGELDGVRVLSPETLRGAvtECRRLRPDFATGLMPLRWGTGFMLGSAKYGpfgrna 357
                                    *******************9999999999999999999988877999********************************* PP

                                    TEEEEEEESTEEEEEEEECGGTEEEEEEESBCSSHHHHHHHHHH CS
                 Beta-lactamase 281 pgtfghtGggygtyvfvdpeanlvvavltnrdppnedaaedarl 324
                                    p +fgh G   + +v++dpe+ l   + ++++p+ + ++e+ r+
  gi|121639692|ref|YP_979916.1| 358 PAAFGHLG-LVNIAVWADPERALSGGLISSGKPG-R-DPEAGRY 398
                                    ********.************************7.3.3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3133.22
//
Query:       gi|121639693|ref|YP_979917.1|  [L=519]
Description: hypothetical protein BCG_3838 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-56  192.5  20.0    1.9e-56  191.8  20.0    1.3  1  DUF222    Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8  20.0   1.1e-60   1.9e-56       4     301 .]      28     355 ..      26     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.1e-60
                         DUF222   4 aleeleaaarrlaavevllvael..aeresaeedgaeavaalvaarlrisraeAsrrvrlAralrerLpavaaalraGdi 81 
                                    a++e +a arrl a+++l  ++   ++r++++ dg++  aa+vaa+l +s  +As +++l  +l+  Lp+vaa + aG++
  gi|121639693|ref|YP_979917.1|  28 ARAEVAAGARRLSAIAELTSRRTgnDQRADWACDGWDCAAAEVAAALTVSHRKASGQMHLSLTLNR-LPQVAALFLAGQL 106
                                    799********************99***************************************97.************* PP

                         DUF222  82 dlrqvrvIaartdllpdavdlatvdkaeaallrraakldpaeLaklvdrlvarldpDgvrrdeeaarrreltltk..ded 159
                                    ++r v +Ia rt l+ d ++l+ +d+a+a+ ++ +  l+  +L+k++d +++r+dp + rr++ +ar+r l +++  ++ 
  gi|121639693|ref|YP_979917.1| 107 SARLVSIIAWRTYLVRDPEALSLLDAALAKHATAWGPLSAPKLEKAIDSWIDRYDPAALRRTRISARSRDLCIGDpdEDA 186
                                    **************************************************************************998888 PP

                         DUF222 160 GmsrisgeldaeaaaaldavLdslaapvcapdgtkDpRspaqrraDALlall....rlalaagaldchagvp.....atv 230
                                    G +++ g l a++aa ld++L +la  vc +    DpR+ aqrraDAL+al+    rl++++g+ dc++ +      + v
  gi|121639693|ref|YP_979917.1| 187 GTAALWGRLFATDAAMLDKRLTQLAHGVCDD----DPRTIAQRRADALGALAagadRLTCGCGNSDCPSSAGnhrqaTGV 262
                                    *******************************....********************************988777799899* PP

                         DUF222 231 vvhvtaeeltaaagg........................aaltgggglLpasdvrrLAkdAt.laifdepagrpld.lgr 284
                                    v+hv+a+ +   a++                        aal +ggg++pa   ++L +  + l+    ++ +p d   +
  gi|121639693|ref|YP_979917.1| 263 VIHVVADAAALGAAPdprlsgpepalapeapatpavkppAALISGGGVVPAPLLAELIRGGAaLS----RVRHPGDlRSE 338
                                    ***********9999*******************************************9755499....9******8899 PP

                         DUF222 285 tkrtasaalrralraRD 301
                                      +++sa+l++++r RD
  gi|121639693|ref|YP_979917.1| 339 PHYRPSAKLAEFVRIRD 355
                                    ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3665.68
//
Query:       gi|121639694|ref|YP_979918.1|  [L=328]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-26   91.9   0.5    4.8e-26   91.3   0.5    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    8.7e-21   75.4   0.7    1.7e-20   74.4   0.1    1.8  3  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.7e-12   47.2   0.3    3.2e-10   39.9   0.1    2.4  2  ADH_N         Alcohol dehydrogenase GroES-like domain
    0.00045   19.6   0.1    0.00086   18.7   0.1    1.4  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.05   13.6   0.0    2.0  2  YAcAr         YspA, cpYpsA-related SLOG family


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.5   1.3e-29   4.8e-26       1     116 [.     151     266 ..     151     283 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 1.3e-29
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                    g+G++a+q+A+al a+v  +++s+eklel+++lGa  +iny+++d+v+r+k+ t+g g+d++++  G  + l++ +++l+
  gi|121639694|ref|YP_979918.1| 151 GIGSHAIQVARALAARVAITAGSPEKLELCRDLGAQITINYRDEDFVARLKQETDGSGADIILDIMG-ASYLDRNIDALA 229
                                    8****************************************444***********************.************ PP

                                    EEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSC CS
                     ADH_zinc_N  81 pgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgs 116
                                     +G+l v+G+ g+ + e++l++ll k+ +++G++l  
  gi|121639694|ref|YP_979918.1| 230 TDGQLIVIGMqGGVKAELNLGKLLTKRARVIGTTLRA 266
                                    *********98888888***************99865 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.8   6.5e+03      27      54 ..      69      99 ..      55     149 .. 0.56
   2 ?   -3.3   0.0       4.9   1.8e+04      42      53 ..     136     146 ..     102     167 .. 0.67
   3 !   74.4   0.1   4.8e-24   1.7e-20       1     133 []     183     326 ..     183     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                                   EES-H.....HHHH.HHHHHHEEEEEEEEE--- CS
                   ADH_zinc_N_2 27 ldtvg.....gealleaslkvlpggGrlvsigg 54
                                   + +vg     + a  ++++++l+g G + ++ +
  gi|121639694|ref|YP_979918.1| 69 VAAVGpgvteWSAG-QEVCALLAG-GGYAEYVA 99
                                   55555544443333.344445555.55544442 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                    HEEEEEEEEE-- CS
                   ADH_zinc_N_2  42 vlpggGrlvsig 53 
                                    +l++ G+lv i 
  gi|121639694|ref|YP_979918.1| 136 HLRP-GQLVLIH 146
                                    3455.6666655 PP

  == domain 3  score: 74.4 bits;  conditional E-value: 4.8e-24
                                    TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE CS
                   ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvky 75 
                                    lGA+  i+yr+edf+    ++t+g g D++ld +g  +l ++ +++l+  G+l++ig +  ++a+l+  ++  k+++v  
  gi|121639694|ref|YP_979918.1| 183 LGAQITINYRDEDFVarlkQETDGSGADIILDIMGASYL-DRNIDALATDGQLIVIGmQGGVKAELNLGKLLTKRARVIG 261
                                    8********************************997777.*******888*******66657777777777666666666 PP

                                    --GGG...-.........-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  76 eflfsmkas........aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                    ++l  +++         + + + + +  +i+++++rpv++ ++p+++aa+Ah+++ sg+++GKi l
  gi|121639694|ref|YP_979918.1| 262 TTLR-ARPVsgphgkaaIAQAVAASVWPMIAANRVRPVIGTRLPIQQAAQAHELMLSGKTFGKILL 326
                                    6666.56668998888855555899***************************************86 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   8.9e-14   3.2e-10       1      61 [.      27      87 ..      27      91 .. 0.95
   2 !    5.5   0.0    0.0043        15      92     109 .]      91     108 ..      86     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.9e-14
                                   TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                          ADH_N  1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvv 61
                                   pgevlikv+a+g+++ D+  + g+  ++     i+G E++G+v++vgp+v++++ G++V++
  gi|121639694|ref|YP_979918.1| 27 PGEVLIKVAASGVNRADVLQAAGKYPPPPGVSDIIGLEVSGIVAAVGPGVTEWSAGQEVCA 87
                                   689********************999999999***************************86 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                                    -SSSBSEEEECGGGEEEE CS
                          ADH_N  92 dGgfaeyvvvpekklvkl 109
                                     Gg+aeyv vp+++++++
  gi|121639694|ref|YP_979918.1|  91 GGGYAEYVAVPADQVLPI 108
                                    6************99875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.4e-07   0.00086      26      93 ..     137     205 ..     126     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                                    B---EEEEESTSHH..HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-S CS
                    AlaDh_PNT_C  26 vepakvlviGgGva..GlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkead 93 
                                     +p++ + i gG    G +Ai++a++l a+V ++  +p++le  ++lga+ +++ +++e+ +a+  +e+d
  gi|121639694|ref|YP_979918.1| 137 LRPGQLVLIHGGASgiGSHAIQVARALAARVAITAGSPEKLELCRDLGAQ-ITINYRDEDFVARLKQETD 205
                                    4589999998887622679*******************************.***9999999888777666 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   5.6e+03      17      44 ..      16      41 ..      12      42 .. 0.65
   2 ?   13.6   0.0   1.4e-05      0.05      16      51 ..     126     161 ..      87     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                          YAcAr 17 iwatLdklhaeapidmvlvhGgakGaDr 44
                                   +w++   + a  +   vl++ +a+G++r
  gi|121639694|ref|YP_979918.1| 16 VWQEVPDVSAGPG--EVLIKVAASGVNR 41
                                   5555555555443..6899999999876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.4e-05
                          YAcAr  16 liwatLdklhaeapidmvlvhGgakGaDrlAarWAa 51 
                                    ++w  L    +  p ++vl+hGga+G+ ++A + A+
  gi|121639694|ref|YP_979918.1| 126 TVWSNLVMTAHLRPGQLVLIHGGASGIGSHAIQVAR 161
                                    5777777777777889***************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2535.77
//
Query:       gi|121639695|ref|YP_979919.1|  [L=398]
Description: aminotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-37  129.0   0.0    1.7e-36  126.0   0.0    1.9  1  Aminotran_5      Aminotransferase class-V
    2.8e-06   26.1   0.0    4.2e-06   25.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.003   16.9   0.1     0.0052   16.1   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   2.8e-40   1.7e-36       2     371 .]      21     390 ..      20     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 2.8e-40
                                    EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                    Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                     +d +A   +p++V ++++  ++++ a++  ++h  + + ++ +++are va+l+na+    ++     +  ++l a + 
  gi|121639695|ref|YP_979919.1|  21 HFDAPAGMLIPDSVATTVSTAFRRSGAST-VGAHPSARRSAAVLDAAREAVADLVNADP-GGVVLGADRAVLLSLLAEAS 98 
                                    589999999************99877766.799999**********************7.77776444444556666666 PP

                                    CCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE.TTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHH CS
                    Aminotran_5  82 arslkpgdeivvteaehhanlvpwqelakrtgakvkvipld.eegeldldelekllnektklvaithvsnvtGtiqpvee 160
                                      +   g e++v++++  an+ pw ++a+r gakvk++++d e+gel + + e+l+++ t+lva++ +s ++G + ++ +
  gi|121639695|ref|YP_979919.1|  99 SSRAGLGYEVIVSRLDDEANIAPWLRAAHRYGAKVKWAEVDiETGELPTWQWESLISKSTRLVAVNSASGTLGGVTDLRA 178
                                    555999**********************************9788************************************ PP

                                    HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEE CS
                    Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleett 240
                                    ++kl++++galv+vD ++a++ + +d++++++D++++ +h   gP+ iG++++r+    ++        m +  s+ +  
  gi|121639695|ref|YP_979919.1| 179 MTKLVHDVGALVVVDHSAAAPYRLLDIRETDADVVTVNAHAWGGPP-IGAMVFRD---PSV--------MNSFGSVSTNP 246
                                    *****************************************99999.********...333........56666777788 PP

                                    EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHH..............HHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-C CS
                    Aminotran_5 241 faeapskfeaGTpnvagiiglgaaleyleeig..............leaiekhekelaeyllerlkslpgvrlygpdkae 306
                                    +a+ p ++e G  +   + g+ a +eyl++++              +++++++ ++  +yl+  l+slp v l+g    e
  gi|121639695|ref|YP_979919.1| 247 YATGPARLEIGVHQFGLLAGVVASIEYLAALDesargsrrerlavsMQSADAYLNRVFDYLMVSLRSLPLVMLIGR--PE 324
                                    8899************************876522222222232222677777888888999************994..59 PP

                                    TCBSEEEEEETTCSHHHHHHHHHHTTEEEEE..E-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 307 rrasivsfnfkgvhaedvatlLdeegIavrs..GhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                    ++  +vsf++++v a+ v++ L+++gI   +  G++++  ++ + ++ g+v ++l++y+t +evd+l
  gi|121639695|ref|YP_979919.1| 325 AQIPVVSFAVHKVPADRVVQRLADNGILAIAntGSRVL-DVLGVNDVGGAVTVGLAHYSTMAEVDQL 390
                                    999**********************99887778*****.555566677*****************97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.1e-10   4.2e-06     128     195 ..     148     216 ..     123     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.1e-10
                                    HHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEE CS
                Cys_Met_Meta_PP 128 eelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhS 195
                                     ++e+ i++ t+lv + + +  l  v+D+++++kl++++g+lvvvD + a+p+    + + +aD+v+  
  gi|121639695|ref|YP_979919.1| 148 WQWESLISKSTRLVAVNSASGTLGGVTDLRAMTKLVHDVGALVVVDHSAAAPYRLLDIrETDADVVTVN 216
                                    47999***********************************************8766662678**99865 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   8.8e-07    0.0052      48     149 ..      86     198 ..      65     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-07
                                    HHHHHHHHHH....TTTTTT-EEEEESS...S-THHH.HHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB- CS
                DegT_DnrJ_EryC1  48 taAlhlaLra....lgvgpgdeVIvpsl...tFvata.navlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh 119
                                      A++l+L a      +g g eVIv  l    ++a +  a+ + gak+  ++vd++t  +   + e++i + t+ + +  
  gi|121639695|ref|YP_979919.1|  86 DRAVLLSLLAeassSRAGLGYEVIVSRLddeANIAPWlRAAHRYGAKVKWAEVDIETGELPTWQWESLISKSTRLVAVNS 165
                                    5677777777766666778899999876333456654268999******************************9887765 PP

                                    ...GGGB---HHHHHHHHHHCT-EEEEE-TT-T CS
                DegT_DnrJ_EryC1 120 ...lyGqvadmdalkaiaakhglkvieDaAhAl 149
                                       ++G v d+ a++++ ++ g  v+ D + A 
  gi|121639695|ref|YP_979919.1| 166 asgTLGGVTDLRAMTKLVHDVGALVVVDHSAAA 198
                                    112566788***************999987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2845.29
//
Query:       gi|121639696|ref|YP_979920.1|  [L=666]
Description: transmembrane protein alanine and leucine rich [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.043   13.8   0.3       0.57   10.2   0.0    2.8  2  Cuticle_2  Cuticle protein 7 isoform family


Domain annotation for each model (and alignments):
>> Cuticle_2  Cuticle protein 7 isoform family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.2e-05      0.57       2      36 ..     133     167 ..     132     180 .. 0.89
   2 ?   -0.3   0.1     0.063   1.1e+03      22      51 ..     561     589 ..     550     595 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.2e-05
                      Cuticle_2   2 avryanGytydietGqvsspytGrvyetkGkapfy 36 
                                    av +an   + ++tGq ss + G + +    ap+y
  gi|121639696|ref|YP_979920.1| 133 AVWHANTVRFILDTGQASSTHMGELRNVETHAPLY 167
                                    89999****************************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.063
                      Cuticle_2  22 ytGrvyetkGkapfyGfGfeypyhyypGyy 51 
                                     t  +y   G  p++   ++yp    pGy+
  gi|121639696|ref|YP_979920.1| 561 GTAWMYAVAGLHPLWT-HYDYPLQQGPGYH 589
                                    4566677777777776.4889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4462.04
//
Query:       gi|121639697|ref|YP_979921.1|  [L=178]
Description: hypothetical protein BCG_3842 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-78  260.9   1.7    3.4e-78  260.7   1.7    1.0  1  DUF2587   Protein of unknown function (DUF2587)


Domain annotation for each model (and alignments):
>> DUF2587  Protein of unknown function (DUF2587)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.7   1.7   1.9e-82   3.4e-78       6     144 ..      32     171 ..      28     178 .] 0.93

  Alignments for each domain:
  == domain 1  score: 260.7 bits;  conditional E-value: 1.9e-82
                        DUF2587   6 deeeeeeeevaelveePakvmrigtmikqlleevraapldeasrerlkeihersikeleeglaPelveelerlslpfted 85 
                                    +e++++e+++++lve+Pakvmrigtmikqlleevraapldeasr+rl++ih++si+ele+glaPel+eel+rl+lpf+ed
  gi|121639697|ref|YP_979921.1|  32 QENDSDESSLTDLVEQPAKVMRIGTMIKQLLEEVRAAPLDEASRNRLRDIHATSIRELEDGLAPELREELDRLTLPFNED 111
                                    67888999************************************************************************ PP

                        DUF2587  86 evPsdaelriaqaqlvGWleGlfhGiqtalvaqqmaaraqleqlrr.alPpggkaaeeeg 144
                                    +vPsdaelriaqaqlvGWleGlfhGiqtal+aqqmaaraql+q+r+ alPpg  ++ ++g
  gi|121639697|ref|YP_979921.1| 112 AVPSDAELRIAQAQLVGWLEGLFHGIQTALFAQQMAARAQLQQMRQgALPPGVGKSGQHG 171
                                    **********************************************99****54444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1402.79
//
Query:       gi|121639698|ref|YP_979922.1|  [L=273]
Description: O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter rfbE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-18   66.7   0.0    1.4e-17   64.5   0.0    1.9  1  ABC_tran     ABC transporter
    0.00049   20.0   0.7     0.0016   18.3   0.1    2.0  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0015   16.2   0.1     0.0021   15.7   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
     0.0052   16.9   0.0      0.012   15.7   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
      0.007   16.1   0.0      0.013   15.2   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.019   15.5   0.0      0.037   14.5   0.0    1.4  1  AAA_23       AAA domain
      0.032   14.2   0.0      0.047   13.6   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.038   14.4   0.1      0.053   13.9   0.1    1.5  1  AAA_16       AAA ATPase domain
       0.05   13.3   0.0      0.077   12.7   0.0    1.2  1  AAA_15       AAA ATPase domain
       0.07   12.1   0.4       0.28   10.1   0.1    2.1  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   7.7e-21   1.4e-17       1     134 [.      53     183 ..      53     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 7.7e-21
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l++++++l+ g +v++vG+nGaGKStLl+ll+g ++pt G               ++  +++ ++     ++pe++ +en
  gi|121639698|ref|YP_979922.1|  53 LRDITMELNLGDRVGLVGHNGAGKSTLLRLLSGIYEPTRGWA-------------KVTGRVAPVFDLgIGMDPEISGYEN 119
                                    689*************************************99.............3344444444444555666666666 PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                 +++++++++++  +l e    ++    +++S G+++r+a+  +   +p++lllDE
  gi|121639698|ref|YP_979922.1| 120 iiirglflgqtrkQMQAKVDEIAEFTELGEYLSMPL----RTYSTGMRVRLAMGVVTSIDPEILLLDE 183
                                    666666999888888888999999999999888888....***************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   8.9e-07    0.0016       3      24 ..      67      88 ..      66     141 .. 0.79
   2 ?   -0.1   0.1      0.37   6.7e+02     289     302 ..     206     220 ..     129     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.9e-07
                         AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                   +l+G Ng+GKS+LL++l+++  
  gi|121639698|ref|YP_979922.1| 67 GLVGHNGAGKSTLLRLLSGIYE 88
                                   69***************99854 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.37
                         AAA_21 289 gaQv.iltTHSplll 302
                                    ++ + ++++HS+++l
  gi|121639698|ref|YP_979922.1| 206 RSGIlVFASHSNEFL 220
                                    333338888887776 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.2e-06    0.0021      12      37 ..      58      83 ..      52      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                        DUF3584 12 aeldldghtnieGtNaaGKTtLlrLi 37
                                    el+l +++ ++G N+aGK tLlrL+
  gi|121639698|ref|YP_979922.1| 58 MELNLGDRVGLVGHNGAGKSTLLRLL 83
                                   69***********************8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.6e-06     0.012       1      27 [.      65      91 ..      65     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-06
                                   EEEEEESTTSSHHHHHHHHHTSTEEES CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltgekaivs 27
                                   +v++vG+  +GKStL++ l+g    + 
  gi|121639698|ref|YP_979922.1| 65 RVGLVGHNGAGKSTLLRLLSGIYEPTR 91
                                   69*****************98544444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.5e-06     0.013      16      39 ..      57      80 ..      51      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-06
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   t+e++l + + l+G++G+GKSTll
  gi|121639698|ref|YP_979922.1| 57 TMELNLGDRVGLVGHNGAGKSTLL 80
                                   677777778889***********8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.1e-05     0.037      24      39 ..      68      83 ..      52      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                         AAA_23 24 ItGpNGaGKTTildAi 39
                                   ++G+NGaGK+T+l+ +
  gi|121639698|ref|YP_979922.1| 68 LVGHNGAGKSTLLRLL 83
                                   79***********876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.047      90     121 ..      53      85 ..      34     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    l++++ +l+  + + lvG+ G+GKStL+  l +
  gi|121639698|ref|YP_979922.1|  53 LRDITMELNLgDRVGLVGHNGAGKSTLLRLLSG 85 
                                    5666666665577889************99976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.9e-05     0.053      27      60 ..      66     100 ..      49     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                         AAA_16  27 vllsGesGvGKsslvrellralekdggif.lrgkc 60 
                                    v l+G+ G GKs+l+r l   +e ++g++ ++g+ 
  gi|121639698|ref|YP_979922.1|  66 VGLVGHNGAGKSTLLRLLSGIYEPTRGWAkVTGRV 100
                                    6689**************98888876555566554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.077      17      44 ..      58      84 ..      48     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                         AAA_15 17 veidlseeltvliGkNnsGKSsileald 44
                                   +e++l +    l+G+N++GKS++l++l 
  gi|121639698|ref|YP_979922.1| 58 MELNLGD-RVGLVGHNGAGKSTLLRLLS 84
                                   4666777.888*************9985 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00015      0.28      19      49 ..      53      83 ..      38      96 .. 0.82
   2 ?   -2.0   0.0      0.79   1.4e+03     120     145 ..     115     140 ..     112     145 .. 0.81
   3 ?   -2.0   0.0      0.79   1.4e+03     197     234 ..     213     250 ..     187     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                                   HHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB 19 lerllakaGraqvvGltGvPGaGkstlveal 49
                                   l+ ++ +     +vGl G  GaGkstl+  l
  gi|121639698|ref|YP_979922.1| 53 LRDITMELNLGDRVGLVGHNGAGKSTLLRLL 83
                                   666777777789**************99765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.79
                                    TT-SEEEEEEESSTTHHHHHHTT-SE CS
                           MeaB 120 aGfDvvlietvGvGqsevdvaevvdt 145
                                     G++ ++i     Gq   ++ + vd 
  gi|121639698|ref|YP_979922.1| 115 SGYENIIIRGLFLGQTRKQMQAKVDE 140
                                    69999999999999998888777775 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.79
                                    STTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHH CS
                           MeaB 197 eekekeWrpkvlktsavegeGidelvdaieehrevlkk 234
                                     ++++e+ +++ kt+    +G+ +l+  iee  ++ + 
  gi|121639698|ref|YP_979922.1| 213 ASHSNEFLARLCKTAIWIDHGVIRLAGGIEEVVRAYEG 250
                                    33567777777777777788888887777777665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1458.40
//
Query:       gi|121639699|ref|YP_979923.1|  [L=304]
Description: L-rhamnosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.5   0.0      2e-09   37.7   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.9e-08   33.3   0.0    6.7e-08   32.5   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.3e-13     2e-09       5     209 ..       6     213 ..       3     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.3e-13
                Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnl.gstgksralnea 82 
                                      +V+t +++d+l + l+ l aq++ +++++vv+ d+  ++  + ++el+a  p +  +++   rnl g +g++ ++ +a
  gi|121639699|ref|YP_979923.1|   6 FAVVVTHRRPDELAKSLDVLTAQTRLPDHLIVVDnDG--CGDSP-VRELVAGQPIA-TTYLGSRRNLgGAGGFALGMLHA 81 
                                    45677779**********************9988444..44444.45666666643.25555556666*******99999 PP

                Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdt.lkrllqffltpkvgavgtpvflln.rs..tlvsalgalefaerhl...rflaarral 155
                                    l + + d+v+l DdD   ++   l+ ll+ +  +k+  + ++ ++ n ++  +l  +l +  + +r +   r+ a ++ l
  gi|121639699|ref|YP_979923.1|  82 LAQGA-DWVWLADDDGHAQDARvLATLLACA--EKYSLAEVSPMVCNiDDptRLAFPLRRGLVWRRRAselRTEAGQELL 158
                                    99886.8***********6654166666665..99999996665544233223322222222233333011455555555 PP

                Glyco_tranf_2_3 156 gvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaav 209
                                      +++  +g l+r++ l++++ +d  lf+ +d +e+ +rl r g +  ++ +aa 
  gi|121639699|ref|YP_979923.1| 159 PGIASLFNGALFRASTLAAIGVPDLrLFIRGDEVEMHRRLIRSGLPFGTCLDAAY 213
                                    33333338899************************************99999983 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.4e-12   6.7e-08       2     106 ..       7     113 ..       6     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.4e-12
                                    EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgS.tDetveileelak.edprvrvirreenvGkagalnaglraat 79 
                                    +v++t+ ++++l+++l+ l aq +++ +++ivvD+    D   + ++el++ ++   +++   +n G ag++  g+ +a 
  gi|121639699|ref|YP_979923.1|   7 AVVVTHRRPDELAKSLDVLTAQ-TRLPDHLIVVDNDGcGD---SPVRELVAgQPIATTYLGSRRNLGGAGGFALGMLHAL 82 
                                    59********************.************99455...55555555467899999999999************99 PP

                                    SS...EEEEEESSEEE-TT.HHHHHHHHHHH CS
                Glycos_transf_2  80 gd...yilflDaDdepdpd.wleklvealek 106
                                     +   ++++ D+D   ++   l  l++ +ek
  gi|121639699|ref|YP_979923.1|  83 AQgadWVWLADDDGHAQDArVLATLLACAEK 113
                                    98889*********99999666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1675.31
//
Query:       gi|121639700|ref|YP_979924.1|  [L=280]
Description: O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter rfbD [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-25   89.7   9.8    1.7e-25   89.7   9.8    1.9  2  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   9.8   9.7e-30   1.7e-25       2     209 ..      33     241 ..      32     242 .. 0.91
   2 !    1.5   0.1    0.0095   1.7e+02     138     159 ..     251     272 ..     248     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 9.7e-30
                  ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.......pgllffsvlflafsaltsvapv 74 
                                    +++ l +++++qr+r+++lg +w +i +  +a+ +g ++++l        r       p++  ++++++ ++a++  ++ 
  gi|121639700|ref|YP_979924.1|  33 LWLHLGWQDIKQRYRRSVLGPFWITIATGTTAVAMGGLYSKLF-------RlelsehlPYVTLGLIVWNLINAAILDGAE 105
                                    578899**********************************864.......12345566********************** PP

                  ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisal 154
                                    +++ ++ l ++l++pl+ +   ++++ ++++++++++ +++ +i+  + ++     + fl++l l++l +++++l++++l
  gi|121639700|ref|YP_979924.1| 106 VFVANEGLIKQLPAPLSVHVYRLVWRQMIFFAHNIVIYFVIAIIFPKPWSWAD---LSFLPALALIFLNCVWVSLCFGIL 182
                                    ****************999999*************999999995555436665...9*********************** PP

                  ABC2_membrane 155 apsfedasqlaslvllpllllsGffipidsm....pkwlqwiaylnPltyavealrsnl 209
                                    a+ ++d++ l + v+++l+++++++++ +++     + +  i +lnPl ++++++r+ l
  gi|121639700|ref|YP_979924.1| 183 ATRYRDIGPLLFSVVQLLFFMTPIIWNDETLrrqgAGRWSSIVELNPLLHYLDIVRAPL 241
                                    *******************************9853257777***************976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.0095
                  ABC2_membrane 138 lltalaasslgllisalapsfe 159
                                    +l++l+++ +g++++a+a+ + 
  gi|121639700|ref|YP_979924.1| 251 WLVVLVLTVVGWMLAAFAMRQY 272
                                    7899999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1707.70
//
Query:       gi|121639701|ref|YP_979925.1|  [L=326]
Description: dTDP-glucose 4,6-dehydratase rfbB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-59  202.3   0.0    8.1e-59  199.7   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.7e-59  199.3   0.1    8.2e-59  199.0   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      5e-25   88.1   0.0    6.2e-25   87.7   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.3e-18   66.3   0.0    7.8e-17   61.3   0.0    2.1  1  NAD_binding_4    Male sterility protein
    1.3e-16   60.6   0.0    1.8e-16   60.1   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      1e-14   54.4   0.0    4.1e-11   42.6   0.0    2.0  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.1e-13   51.5   0.0    1.5e-13   51.0   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    1.8e-05   24.4   0.2    3.4e-05   23.5   0.2    1.4  1  NmrA             NmrA-like family
    2.9e-05   23.6   0.1     0.0029   17.1   0.0    2.6  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.079   13.2   0.1       0.13   12.5   0.1    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.14   12.5   0.0       0.23   11.8   0.0    1.3  1  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.0     5e-62   8.1e-59       1     313 [.       4     285 ..       4     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 5e-62
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGf Gs+l+e Ll++g+ v+++++  s  ++++++  ++      +++  +++g +tD + ++r+++++  + v+
  gi|121639701|ref|YP_979925.1|   4 LVTGGAGFQGSHLTESLLANGHWVTVLDKS-SRNAVRNMQGFRS------HDRAAFISGSVTDGQTIDRAVRDH--HVVF 74 
                                    9***********************988755.4557788887764......45789*******************..79** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S...SSS.B-TTS-----SHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq...evp.qtEttpfyPrsPYaaa 156
                                    +LAA   Vd+s+ +Pe ++e+nv+Gt+r+Lea+r++      r++ +St EvYG+     e    +E+  ++P+sPY+a+
  gi|121639701|ref|YP_979925.1|  75 HLAAHVNVDQSLGDPESFLETNVMGTYRVLEAVRRYR----NRLIYVSTCEVYGDGHnlkEGErLDEHAELKPNSPYGAS 150
                                    ***********************************96....49***********9752224433799************* PP

                                    HHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHH CS
                  GDP_Man_Dehyd 157 KlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlm 236
                                    K++ad ++ +y ++ygl +++ + fn  + r+++     +i+r v +  +g+   +++G ++a+Rd+++v+D+v a+ l+
  gi|121639701|ref|YP_979925.1| 151 KAAADRLCYSYFRSYGLDVTIVRPFNIFGVRQKAGRFGALIPRLVRQGINGE-GLTIFGAGSATRDYLYVSDIVGAYNLV 229
                                    *********************************99999*********99998.56679********************** PP

                                    HHCSS-..--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHH CS
                  GDP_Man_Dehyd 237 lqqdkp..edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaska 313
                                    l+  +   + +++a+g+ ++vr++ve  + + g +ie +  +  ev                       ++  +d+s a
  gi|121639701|ref|YP_979925.1| 230 LRTPTLrgQAINFASGKDTRVRDIVEYVADKFGARIEHRDARPGEV-----------------------QRFPADISLA 285
                                    *996642278999*************99999998776665555554.......................4444444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.0   0.1     5e-62   8.2e-59       1     230 [.       3     234 ..       3     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 5e-62
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkeeqpdavihlAa 73 
                                    ilVtG++Gf Gs+l++ ll++g+ v++ld+ s++  ++ +           ++ + +td++ ++r+++  + ++v+hlAa
  gi|121639701|ref|YP_979925.1|   3 ILVTGGAGFQGSHLTESLLANGHWVTVLDKSSRNAVRNMQ--GfrshdraAFISGSVTDGQTIDRAVR--DHHVVFHLAA 78 
                                    8*****************************9444333332..24689999******************..569******* PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS.SSBSTCSTTS----SSHHHHHHHHHHHH CS
                      Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae.qpkeettltgplkpnspYaaaKlagekl 152
                                      +v++s  dp+ f+e+n++gt+++lea+r++   rl+++s++evYG++++ +  e   +  +lkpnspY+a+K+a+++l
  gi|121639701|ref|YP_979925.1|  79 HVNVDQSLGDPESFLETNVMGTYRVLEAVRRYRN-RLIYVSTCEVYGDGHNlKEGERLDEHAELKPNSPYGASKAAADRL 157
                                    ********************************99.****************4347777777788**************** PP

                                    HHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                      Epimerase 153 veayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                    + +y ++ygl+++i+r+fn++G r+  g+   +ip+l+r+  +g+  +t++g g+a Rd+lyv+D++ a+ lvl+ + 
  gi|121639701|ref|YP_979925.1| 158 CYSYFRSYGLDVTIVRPFNIFGVRQKAGRFGALIPRLVRQGINGE-GLTIFGAGSATRDYLYVSDIVGAYNLVLRTPT 234
                                    ************************999******************.****************************9965 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   3.8e-28   6.2e-25       1     227 [.       4     228 ..       4     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 3.8e-28
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespellee..lskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                    +vtGgaGF G++l ++L+  ++   v vlD+  ++ +++   +++ +++ +i g vtd +++++a+++ +vv+hla+ v+
  gi|121639701|ref|YP_979925.1|   4 LVTGGAGFQGSHLTESLLANGH--WVTVLDKSSRNAVRNMqgFRSHDRAAFISGSVTDGQTIDRAVRDHHVVFHLAAHVN 81 
                                    69*****************995..899***99999887641156666666****************************** PP

                      3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeley.eslhqdaypesKalaEkl 156
                                    v +     +++ + nv GT  vlea ++   ++l+Y+S++ev g+   g+++ +g+   e+ e +++++y  sKa a++l
  gi|121639701|ref|YP_979925.1|  82 VDQsLGDPESFLETNVMGTYRVLEAVRRYR-NRLIYVSTCEVYGD---GHNLKEGERLDEHaELKPNSPYGASKAAADRL 157
                                    *984567899**************988776.89************...8888888776555155699************* PP

                      3Beta_HSD 157 vlkaNgrtlknggrlyTcaLRpagiyGegdkl.....lvpllkqlaklglalfkigdeevlsdrvYvgNvawahil 227
                                      +           l    +Rp  i+G ++k      l p+l++   +g+ l   g  +++ d+ Yv  ++ a+ l
  gi|121639701|ref|YP_979925.1| 158 CYSYFR----SY-GLDVTIVRPFNIFGVRQKAgrfgaLIPRLVRQGINGEGLTIFGAGSATRDYLYVSDIVGAYNL 228
                                    987555....44.3777789*******998743322256666666667889*****************99887655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   4.8e-20   7.8e-17       1     209 [.       5     181 ..       5     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.8e-20
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG+ GF G++L e LL +    ++++l ++++         +++++++ f+       +r  +++G +++ +      +
  gi|121639701|ref|YP_979925.1|   5 VTGGAGFQGSHLTESLLANGH--WVTVLDKSSR---------NAVRNMQGFRSH-----DRAAFISGSVTDGQ------T 62 
                                    7*****************998..8888866663.........355666666555.....7999******9876......8 PP

                                    HHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    +++ ++  +v++h aA vn+d+++ +   +l++Nv+Gt +vle  ++ ++   l++vST  v+g+ ++ ++e        
  gi|121639701|ref|YP_979925.1|  63 IDRAVRDHHVVFHLAAHVNVDQSLGDpesFLETNVMGTYRVLEAVRRYRNR--LIYVSTCEVYGDGHN-LKE-------- 131
                                    999999999*************98766669*************99988777..******666666553.322........ PP

                                    ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.- CS
                  NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.e 209
                                        + +++  + + +  Y  sKa+a++l+ +++r+ gl v+ivRp +i g +
  gi|121639701|ref|YP_979925.1| 132 ---GERLDEHAELKPNSPYGASKAAADRLCYSYFRSYGLDVTIVRPFNIFGvR 181
                                    ...233333334445569****************************9998843 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   1.1e-19   1.8e-16       1     155 [.       1     181 [.       1     198 [. 0.90

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-19
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE--- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAA 60 
                                    m+ilvtG+ G  Gs+L+++l ++g+ v+ l+++                    +  +td +++++++++   +vv ++AA
  gi|121639701|ref|YP_979925.1|   1 MEILVTGGAGFQGSHLTESLLANGHWVTVLDKSsrnavrnmqgfrshdraafiSGSVTDGQTIDRAVRD--HHVVFHLAA 78 
                                    89**********************99***999999******************99**************..789****** PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS.-S-...TTS-B-TTS----SSHHHHHHHHHHHHH CS
                  RmlD_sub_bind  61 ytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVF.dGe...kkrpYeeddetsPlnvYGrtKlaGEqav 136
                                    + +vD+   ++e+  + n+ ++ ++ ea +++   Li+vSt  V+ dG+   + +   e++e +P + YG++K+a  +  
  gi|121639701|ref|YP_979925.1|  79 HVNVDQSLGDPESFLETNVMGTYRVLEAVRRYRNRLIYVSTCEVYgDGHnlkEGERLDEHAELKPNSPYGASKAAADRLC 158
                                    ********************************************9778888666679*******************9987 PP

                                    HH....H-SSEEEEEE-SEESSS CS
                  RmlD_sub_bind 137 la....agkkalivRtswvygek 155
                                     +    +g +++ivR   ++g +
  gi|121639701|ref|YP_979925.1| 159 YSyfrsYGLDVTIVRPFNIFGVR 181
                                    65444377788999988888764 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   2.5e-14   4.1e-11       1     128 [.       3     119 ..       3     123 .. 0.82
   2 !    9.9   0.0   0.00023      0.37     133     252 ..     142     266 ..     138     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.5e-14
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-.HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerd.Elklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                    +lvtG++G  Gs+l++ +l++    + +l+++  +++ +++       ++++     + + g+v+d +++++a++  + +
  gi|121639701|ref|YP_979925.1|   3 ILVTGGAGFQGSHLTESLLANGHW-VTVLDKSsRNAVRNMQGFR----SHDRA----AFISGSVTDGQTIDRAVR--DHH 71 
                                    89***************9998765.5555555055555555543....22233....2358**************..889 PP

                                    EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                    vvfh AA+ +V      p + ++tNv+gt  v+ea  +++ ++++++St
  gi|121639701|ref|YP_979925.1|  72 VVFHLAAHVNVDQSLGDPESFLETNVMGTYRVLEAVRRYR-NRLIYVST 119
                                    9*********************************988776.78888888 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                                    S--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT......TSSHHHHHHHHHTTSSEEES-T.T-EE...E CS
                Polysacc_synt_2 133 nPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSr......GSviplFkkqikeggpvtvTdp.emtR...y 202
                                    +P + +Ga+K++a+ l+ ++ ++       +++vR  N++g r      G +ip   +q  +g+ +t+  + + tR   y
  gi|121639701|ref|YP_979925.1| 142 KPNSPYGASKAAADRLCYSYFRSY---GLDVTIVRPFNIFGVRqkagrfGALIPRLVRQGINGEGLTIFGAgSATRdylY 218
                                    78999**************99998...899999**999998776666679*****************9754278884444 PP

                                    EE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                Polysacc_synt_2 203 fmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                    +  i  a +Lvl + +l  +g+      G+ ++++d+++ + + +g + +
  gi|121639701|ref|YP_979925.1| 219 VSDIVGAYNLVLRTPTL--RGQAINFASGKDTRVRDIVEYVADKFGARIE 266
                                    45566688999987654..4555556678888888888888777765554 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   9.4e-17   1.5e-13       1     145 [.       7     176 ..       7     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.4e-17
                                    TTTSHHHHHHHHHHHHC-T-EEEEE...ETTH.HHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHH CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtal...vRnp.eklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdee 76 
                                    G+ G  G++l++ lla+g h vt+l    Rn+   ++ +++++++  ++g+vtd +++ +a++++ +V+  +++ + d+ 
  gi|121639701|ref|YP_979925.1|   7 GGAGFQGSHLTESLLANG-HWVTVLdksSRNAvRNMQGFRSHDRAAFISGSVTDGQTIDRAVRDHHVVFHLAAHVNVDQS 85 
                                    999**************5.999999555566424557799****************************999876666444 PP

                                    H.............HHHHHHHHHHCT--EEEEEEETTTTSGCGCH.....HHHHHH.HCCHHHHHHHHHHHHH....HHH CS
                 NAD_binding_10  77 g.............aknivdaakeagvkRfvlvsaigvgdevpge.....fgewnk.ellkaylaakraaeel....lra 133
                                                  + ++++a+++    R+++vs+  v+ + ++      ++e ++ +  ++y a k+aa++l     r+
  gi|121639701|ref|YP_979925.1|  86 LgdpesfletnvmgTYRVLEAVRRYRN-RLIYVSTCEVYGDGHNLkegerLDEHAElKPNSPYGASKAAADRLcysyFRS 164
                                    45556677778899********99875.**********964222111111222222122345557777777763333677 PP

                                    SSSEEEEEEE-C CS
                 NAD_binding_10 134 sgldwTivrpgg 145
                                     gld Tivrp  
  gi|121639701|ref|YP_979925.1| 165 YGLDVTIVRPFN 176
                                    8*********65 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   2.1e-08   3.4e-05       1      73 [.       3      78 ..       3      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.1e-08
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHS.TTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                           NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkea.Gvelvkgdlddkeslvealkgvdvvfsvtg 73
                                   Ilv+G++G qG+++++ ll++gh v +l + +     +++ + +   + +++g++ d + +++a+++ +vvf   +
  gi|121639701|ref|YP_979925.1|  3 ILVTGGAGFQGSHLTESLLANGHWVTVLDKSSrnAVRNMQGFRSHdRAAFISGSVTDGQTIDRAVRDHHVVFHLAA 78
                                   9***************************99884444567788665158889*********************8776 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-06    0.0029       3      70 ..       3      69 ..       2     113 .. 0.91
   2 ?    3.7   0.0     0.023        38     146     162 ..     144     160 ..     138     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvek 70
                                   +lvtG+++  G  + + l+++G  v+v+d+s++++ + ++ ++++ ++a +i++ vtd + ++++v++
  gi|121639701|ref|YP_979925.1|  3 ILVTGGAGFQGSHLTESLLANGHWVTVLDKSSRNAVRNMQGFRSH-DRAAFISGSVTDGQTIDRAVRD 69
                                   89*****999*************************9999999985.99****************9986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.023
                                    BHHHHHHHHHHHHHHHH CS
                      adh_short 146 vaaYsAsKaavagltrs 162
                                     ++Y+AsKaa + l  s
  gi|121639701|ref|YP_979925.1| 144 NSPYGASKAAADRLCYS 160
                                    689*******9988765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.9e-05      0.13       3      78 ..       5      78 ..       3      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                                   EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                   + G+ G+ G+ ++e l++++++   +tv d+s +++ +  +   ++ r+ +i+  + + +  ++++++++ +v +l+ 
  gi|121639701|ref|YP_979925.1|  5 VTGGaGFQGSHLTESLLANGHW---VTVLDKSSRNAVRNMQGFrSHDRAAFISGSVTDGQT-IDRAVRDHHVVFHLAA 78
                                   55555****************9...********9987777666778888888888999888.9999999999999886 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.23       5      58 ..       8      66 ..       3      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                   S-SHHHHHHHHHHHH.TTEEEEEEESSHHH.HHHH...HHTT.SEEEES-TTSHHHHHHT CS
                         TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeer.veel...reeg.levvvgdatdeevLeea 58
                                   G+G  G++l+e L + g++ v+v dk+ ++ v+++   r +  + ++ g++td +++++a
  gi|121639701|ref|YP_979925.1|  8 GAGFQGSHLTESLLAnGHW-VTVLDKSSRNaVRNMqgfRSHDrAAFISGSVTDGQTIDRA 66
                                   78999**********7789.******9976344442224444455999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2109.25
//
Query:       gi|121639702|ref|YP_979926.1|  [L=357]
Description: hypothetical protein BCG_3847 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2288.19
//
Query:       gi|121639703|ref|YP_979927.1|  [L=407]
Description: hypothetical protein BCG_3848c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.4   0.0    1.9e-15   56.8   0.0    1.3  1  Peptidase_M23    Peptidase family M23
    1.5e-09   38.2   0.2    2.7e-09   37.4   0.2    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    6.2e-07   29.4   0.3    0.00016   21.5   0.1    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
     0.0021   18.0   0.0     0.0035   17.3   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   4.3e-19   1.9e-15       2      96 .]     275     369 ..     274     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.3e-19
                                    EESSEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEEEEBSTSSCSSS CS
                  Peptidase_M23   2 fhkGidiaapkgtpVlAaadGtVvfagkkegyGnvviidhgdgystlyahlskisvkegqkVkaGqvIGtvgstgrstgp 81 
                                    fh G+d+a+ +gtpV+A+a+G V  +++ +g+  ++i + +  ++ ++   ++ ++  g++++aG+++Gt+g++g+s+  
  gi|121639703|ref|YP_979927.1| 275 FHPGVDFATDPGTPVYAVASGAVSAIDEVDGLVSLTIARCELDVVYVFRPGDEGRLVLGDRIAAGAQLGTIGAQGESADG 354
                                    8***************************999************************************************* PP

                                    EEEEEEEETTEEE-C CS
                  Peptidase_M23  82 hLhfeirkngkavdp 96 
                                     Lhfe+r+++ +v+p
  gi|121639703|ref|YP_979927.1| 355 YLHFEVRTQDGHVNP 369
                                    *******99999998 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   6.1e-13   2.7e-09       2      94 ..      11     106 ..      10     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.1e-13
                Glyco_tranf_2_4   2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevk.llhvd.....ksy..ederrqvellkallaryaead 73 
                                    n+  +L ++l+ +  +  d+i+v+d+ stD+t++il+++p+v+ +++ +     +++    e  + ell +++ + ++ d
  gi|121639703|ref|YP_979927.1|  11 NAGRTLAATLDSLAVF-SDDIYVIDDRSTDDTAEILANHPAVTnVVRARpdlppTPWliP-ESAGLELLYRMA-DFCRPD 87 
                                    7777888888888555.9***********************9966666656655555542.456677777777.669*** PP

                Glyco_tranf_2_4  74 wvlvvDaDEflvvpdsrslra 94 
                                    wv++vDaD ++ ++   +lra
  gi|121639703|ref|YP_979927.1|  88 WVMMVDADWLVETDI--DLRA 106
                                    ********8877777..6665 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   3.5e-08   0.00016       6      49 ..       9      48 ..       6      60 .. 0.91
   2 !    5.8   0.0    0.0024        11      75     129 ..      81     134 ..      74     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.5e-08
                                   ESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGG CS
                Glycos_transf_2  6 tyNeektlletlesllaqdpypdfeiivvDDgStDetveileel 49
                                   ++N   tl++tl+sl+       ++i+v+DD StD+t+eil ++
  gi|121639703|ref|YP_979927.1|  9 AHNAGRTLAATLDSLAVF----SDDIYVIDDRSTDDTAEILANH 48
                                   69999*************....*******************987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0024
                                    HHH--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                Glycos_transf_2  75 lraatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiern 129
                                    ++ ++ d+++ +DaD  ++ d +l+ ++++  +  + v+l++++++++++ e++  
  gi|121639703|ref|YP_979927.1|  81 ADFCRPDWVMMVDADWLVETDiDLRAVLARTPD--DIVALMCPMVSRWDDPEYPDL 134
                                    677899***************999999988777..446888888888888777765 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.8e-07    0.0035      13     111 ..       8     110 ..       3     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.8e-07
                Glyco_tranf_2_3  13 eedvlgevlesllaq.eyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn......a..rnlgstgksralneal 83 
                                    ++   g++l+++l + +  +++++v++d+s+++t+e +     ++p+v  +vv+       +   +++s g  + l+++ 
  gi|121639703|ref|YP_979927.1|   8 RAHNAGRTLAATLDSlAVFSDDIYVIDDRSTDDTAEILA----NHPAV-TNVVRArpdlppTpwLIPESAGL-ELLYRMA 81 
                                    55567788888885425689***************9885....58875.24444443444312233333332.3466666 PP

                Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdt.lkrllqf 111
                                    + +++d+v +vD+D +ve d+ l+++l+ 
  gi|121639703|ref|YP_979927.1|  82 DFCRPDWVMMVDADWLVETDIdLRAVLAR 110
                                    6789*************998867766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3075.83
//
Query:       gi|121639704|ref|YP_979928.1|  [L=308]
Description: hypothetical protein BCG_3849c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-65  220.8   0.4    1.7e-65  220.5   0.4    1.1  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.5   0.4   9.5e-70   1.7e-65       1     187 [.      19     203 ..      19     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.5 bits;  conditional E-value: 9.5e-70
                                    HHHHHHHHHHHHHHHHHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHG.CHCCCCT--HHHHHHHHHHHHHHHHHHHHH CS
                            LCM   1 algvaaaralesrraadglidDplaeslvsaaglellerkadkelekek.eeekkekkapelnrgiavRtrffddllkaa 79 
                                    a+ vaa+ra ++r+a ++lidDp+ae+lv+a+g+e+l+r+a++el++++ +++++++  ++++  ++vRtr+fd+++ +a
  gi|121639704|ref|YP_979928.1|  19 ATLVAAGRARAARAA-QPLIDDPFAEPLVRAVGVEFLTRWATGELDAADvDDPDAAWGLQRMTTELVVRTRYFDQFFLDA 97 
                                    789********9998.*********************************99***************************** PP

                                    HHCTTESEEEEET-TT--HHHHHHHTTTEEEEEEE-HHHHHHHHHHHHHSHHHHHEECSEEE--TTSHHHHHHHHHHTT- CS
                            LCM  80 lsaagirqvViLGAGlDtrayRlpwlaglkvfEvDqpevlefKretlkelgaepkaelryvpvDlrdddwpeaLaaagfd 159
                                    + aag+rq+ViL++GlD+r yRlpw+a+++vfEvDqp+vlefK++tl+ lga+p+a+lr+vp+Dlr +dwp+aL++ gfd
  gi|121639704|ref|YP_979928.1|  98 A-AAGVRQAVILASGLDARGYRLPWPADTTVFEVDQPRVLEFKAQTLAGLGAQPTADLRMVPADLR-HDWPDALRRGGFD 175
                                    *.7***************************************************************.************* PP

                                    TTSEEEEEEESSGGGS-HHHHHHHHHHH CS
                            LCM 160 pekptawvaeGvlvYLtpeasdalleai 187
                                    +++p+aw+aeG+  YL+p+a+++ll+++
  gi|121639704|ref|YP_979928.1| 176 AAEPAAWIAEGLFGYLPPDAQNRLLDHV 203
                                    *************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2209.59
//
Query:       gi|121639705|ref|YP_979929.1|  [L=161]
Description: nucleoside diphosphate kinase regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-10   40.8   0.0    2.5e-10   40.1   0.0    1.3  1  GreA_GreB    Transcription elongation factor, GreA/GreB, C-te
  ------ inclusion threshold ------
       0.06   13.5   3.5      0.087   13.0   3.5    1.2  1  GreA_GreB_N  Transcription elongation factor, N-terminal
      0.076   12.8   1.0       0.11   12.3   0.1    1.7  2  DivIC        Septum formation initiator


Domain annotation for each model (and alignments):
>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   4.2e-14   2.5e-10       9      76 ..      89     158 ..      85     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.2e-14
                                    T-EEEEE-.SS--EEEE----TTT-BS...-SSB--TTSHHHHHHTT--TT-EE---BTTB---EEEEEEX CS
                      GreA_GreB   9 GstVtledldtgeeetytiVgpdeadp...skgkiSveSPlGkaLlgkkvGdevevkapsgkikveIlkie 76 
                                    G+ Vtl+   +ge +t+++++  e  p   ++  +   SPlG+aL g++ Gd+v++ +p+g  +v+ l+++
  gi|121639705|ref|YP_979929.1|  89 GTEVTLRF-PDGEVVTMHVISVVEETPvgrEAETLTARSPLGQALAGHQPGDTVTYSTPQGPNQVQLLAVK 158
                                    899*****.******************887777****************************9999999886 PP

>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.5   1.5e-05     0.087       7      67 ..      14      74 ..      10      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHXHHHHHHHHHHHHHHH.SSSTSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    GreA_GreB_N  7 gyekleeeLeelktverpeiaeaikearee.GDlsENaeYdaAkeeqaeiearIreLedkLa 67
                                   + + l +eL +l++ +r +   ++k+ r   GD  + ae  ++ +e+a +  rI+eL ++L+
  gi|121639705|ref|YP_979929.1| 14 ARDHLAAELARLRQ-RRDRLEVEVKNDRGMiGDHGDAAEAIQRADELAILGDRINELDRRLR 74
                                   67899*********.***********99755999999***********************98 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.8e-05      0.11      26      49 ..      15      38 ..      10      46 .. 0.76
   2 ?   -2.3   0.1      0.66     4e+03      27      45 ..      53      71 ..      48      74 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHCC CS
                          DivIC 26 iaalqaelaklkaeneeLeaevkd 49
                                   ++ l aela+l++++++Le evk+
  gi|121639705|ref|YP_979929.1| 15 RDHLAAELARLRQRRDRLEVEVKN 38
                                   456788888888888888888886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.66
                                   HHHHHHHHHHHHHHHHHHH CS
                          DivIC 27 aalqaelaklkaeneeLea 45
                                    +  +ela l ++++eL++
  gi|121639705|ref|YP_979929.1| 53 IQRADELAILGDRINELDR 71
                                   4555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1159.16
//
Query:       gi|121639706|ref|YP_979930.1|  [L=121]
Description: hypothetical protein BCG_3851 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-19   70.9  12.4    1.2e-19   70.7  12.4    1.1  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7  12.4   6.7e-24   1.2e-19       1     117 []       2     118 ..       2     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 6.7e-24
                           GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglllnll 80 
                                    rF++ G+l+ +vd++l+++l++++gl++ l++ai+fiv++++++++nrrwtF+++ ++    +f+  +l+++++++++++
  gi|121639706|ref|YP_979930.1|   2 RFVVTGGLAGIVDFGLYVVLYKVAGLQVDLSKAISFIVGTITAYLINRRWTFQAEPST---ARFVAVMLLYGITFAVQVG 78 
                                    8*****************************************************9996...5777777777777777777 PP

                           GtrA  81 ilwllveklgleall...aklvgiivalvlnyvlsklfvF 117
                                    + +l++  l+  a+    a +++++ a+v+n+++++ ++F
  gi|121639706|ref|YP_979930.1|  79 LNHLCLALLHYRAWAipvAFVIAQGTATVINFIVQRAVIF 118
                                    7777777777755556669999***************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1081.52
//
Query:       gi|121639707|ref|YP_979931.1|  [L=461]
Description: oxidoreductase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   89.6   1.0    1.4e-25   89.6   1.0    1.5  2  FAD_binding_4  FAD binding domain
    3.3e-07   30.4   0.0    5.5e-07   29.7   0.0    1.3  1  ALO            D-arabinono-1,4-lactone oxidase


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.0   1.6e-29   1.4e-25       7     138 ..      30     161 ..      24     162 .. 0.89
   2 ?   -4.2   0.1       1.5   1.3e+04      97     108 ..     172     183 ..     169     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.6e-29
                                    ESSHHHHHHHHHHHHHC.TSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHT CS
                  FAD_binding_4   7 peseeevaaalrlanea.glpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaakg 85 
                                    p  e  v+a+ r+a++  g+  ++rG G s++++a++ gg+v+d++ ln+i++id++++ + + aGv+l++l +a+ + g
  gi|121639707|ref|YP_979931.1|  30 PDAEMIVKAVARVAESGgGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFG 109
                                    55555566666667666556699*********9998899******99********************************* PP

                                    TECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                  FAD_binding_4  86 lllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                    l++++ pg+  ++tvGGaia  ++G + + +G++ ++v+++++++adGe+++l
  gi|121639707|ref|YP_979931.1| 110 LWVPVLPGTR-QVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHL 161
                                    *********7.77*************************************997 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.5
                                    GSBHHHTTTTT- CS
                  FAD_binding_4  97 pgtvGGaiatna 108
                                     +tvGG+ +t++
  gi|121639707|ref|YP_979931.1| 172 WATVGGNGLTGI 183
                                    689999988876 PP

>> ALO  D-arabinono-1,4-lactone oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.1e-11   5.5e-07     200     259 ..     398     457 ..     387     458 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.1e-11
                            ALO 200 kyfkafedimkkagGrPHWaKnflltaedlkelYpdlkkflkvRkklDPegvFlnewler 259
                                    k+  ++++ + ++gGr   aK    tae+++ +Yp+ +++ +vR+k+DP +vF++++++r
  gi|121639707|ref|YP_979931.1| 398 KFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARR 457
                                    5666777778899********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3121.70
//
Query:       gi|121639708|ref|YP_979932.1|  [L=254]
Description: short chain dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-28   98.4   0.0    4.2e-28   98.1   0.0    1.1  1  adh_short       short chain dehydrogenase
    8.1e-20   71.4   0.7    9.9e-20   71.1   0.7    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    2.1e-05   24.5   0.3    3.8e-05   23.7   0.3    1.4  1  KR              KR domain
  ------ inclusion threshold ------
      0.027   14.3   0.2        5.1    6.9   0.0    2.2  2  YjeF_N          YjeF-related protein N-terminus
      0.064   12.8   0.1      0.094   12.3   0.1    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   1.2e-31   4.2e-28       1     192 [.      10     203 ..      10     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 1.2e-31
                                    SEEEEESTTSHHHHHHHHHHHHTT-EEEE..EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                      adh_short   1 kvvlvtGassGIGraiakelakeGakvvv..vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgk 77 
                                    ++vl  G++s IG+ai+++++ + a  +v  +   + + e +a+ +k++ ++++  i +D  d +++ +++e+a    g 
  gi|121639708|ref|YP_979932.1|  10 QTVLLLGGTSEIGLAICERYLHNSAARIVlaCLPDDPRREDAAAAMKQAgARSVELIDFDALDTDSHPKMIEAAF-SGGD 88 
                                    589****************9988765444378889999999999999998899*******************995.45** PP

                                    ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
                      adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                                    +dv +   G+ g+++    ++++  ++ e+N+t+++++  +++++m +q  G+I+ +sS ag+       +Y+++Ka+++
  gi|121639708|ref|YP_979932.1|  89 VDVAIVAFGLLGDAEELWQNQRKAVQIAEINYTAAVSVGVLLAEKMRAQGFGQIIAMSSAAGERVRRANFVYGSTKAGLD 168
                                    **********88888888888889999***************************************************** PP

                                    HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakelre 192
                                    g+   l++ l+++g+rv ++ PG v+T m + l+e
  gi|121639708|ref|YP_979932.1| 169 GFYLGLSEALREYGVRVLVIRPGQVRTRMSAHLKE 203
                                    *****************************998876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.7   2.8e-23   9.9e-20       5     187 ..      20     206 ..      16     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.8e-23
                                    SHHHHHHHH.HHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   5 gIGraiAka.laeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                     IG ai ++ l++  a++vl+ l ++  +++++++ ++ ga+ v  +  D+ d+++  +++e++ +  g +D+++ + g 
  gi|121639708|ref|YP_979932.1|  20 EIGLAICERyLHNSAARIVLACLPDDPrREDAAAAMKQAGARsVelIDFDALDTDSHPKMIEAAFSG-GDVDVAIVAFGL 98 
                                    59999998736788899******99999888998889999776678***************998865.9*********** PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                      +  +++ + +r +  ++ ++n ++++++   +++ m+++  g+i+++ss ++erv   + +yg +Ka+l ++   l  
  gi|121639708|ref|YP_979932.1|  99 LGD-AEELWQNQR-KAVQIAEINYTAAVSVGVLLAEKMRAQgfGQIIAMSSAAGERVRRANFVYGSTKAGLDGFYLGLSE 176
                                    *99.555555555.555889*********9999999776666******************9******************* PP

                                    HHGGGTEEEEEEEE--BHCTGGGGSTTHHH CS
                   adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikgfde 187
                                     l ++g+Rv ++ pg ++T++++++k+++ 
  gi|121639708|ref|YP_979932.1| 177 ALREYGVRVLVIRPGQVRTRMSAHLKEAPL 206
                                    ************************998653 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   1.1e-08   3.8e-05       2     160 ..      11     171 ..      10     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHHSS CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikaeep 80 
                                    t+l+ GG+  +Gl++++  +++ a+++vl       d++ ++  a++++ ga +ve+++ D  d d+  +++e++  +++
  gi|121639708|ref|YP_979932.1|  11 TVLLLGGTSEIGLAICERYLHNSAARIVLACLP--DDPRREDAAAAMKQAGArSVELIDFDALDTDSHPKMIEAAF-SGG 87 
                                    6899***********************999887..67888888999****9978*******************997.667 PP

                                    ---EEEE---------TTT--HHHHHHH....HTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR  81 pikGvihaAgvlrdklleemtaedleqv....lapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156
                                     +   i a g+l d+    +++ +  q+    + + v+    L e ++ +    ++ +SS+ag    +    Y ++ a l
  gi|121639708|ref|YP_979932.1|  88 DVDVAIVAFGLLGDAEELWQNQRKAVQIaeinYTAAVSVGVLLAEKMRAQGFGQIIAMSSAAGERVRRANFVYGSTKAGL 167
                                    88888888888887654444444433331122678888888999999999**************************9999 PP

                                    HHHH CS
                             KR 157 Dala 160
                                    D++ 
  gi|121639708|ref|YP_979932.1| 168 DGFY 171
                                    9875 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0044        16      45     100 ..      26      87 ..       3     128 .. 0.62
   2 ?    6.9   0.0    0.0014       5.1      27      70 ..     154     197 ..     130     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0044
                         YjeF_N  45 aArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedleekls.......a 100
                                    + r+L++  a++ + +l ++++++eda++a++++ +  ++++  +  + ++   +        
  gi|121639708|ref|YP_979932.1|  26 CERYLHNSAARIVLACL-PDDPRREDAAAAMKQAGARSVELIDFDALDTDSHPKMieaafsgG 87 
                                    45999999999777555.778899999998887777666666544433332222245666553 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                         YjeF_N  27 kkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeeklded 70 
                                    ++  ++ Gs++ G dg++++   a +++ V+vl++++ + ++++
  gi|121639708|ref|YP_979932.1| 154 RRANFVYGSTKAGLDGFYLGLSEALREYGVRVLVIRPGQVRTRM 197
                                    5566889*************888888888888878887665554 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.6e-05     0.094     126     201 ..      55     134 ..      50     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                                    TCCCCT--HHH..HSSEEEE--HHHHHH.HHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEE..EEEEEEEE--EEEEET CS
                 Phosphonate-bd 126 Lvkeagldped..dfsevfsgshdaavl.avlsgdadaaavsadaledlvaegpedkdelrv..iassppipndpvvvrk 200
                                    + k+ag ++ +  df++  ++sh+++++ a   gd+d+a v  + l d ++ ++++++++++  i+ ++++   ++++ k
  gi|121639708|ref|YP_979932.1|  55 M-KQAGARSVEliDFDALDTDSHPKMIEaAFSGGDVDVAIVAFGLLGDAEELWQNQRKAVQIaeINYTAAVSVGVLLAEK 133
                                    5.78888888744689999********8355679********************99999999666777777555555554 PP

                                    T CS
                 Phosphonate-bd 201 e 201
                                    +
  gi|121639708|ref|YP_979932.1| 134 M 134
                                    4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1899.82
//
Query:       gi|121639709|ref|YP_979933.1|  [L=643]
Description: hypothetical protein BCG_3854 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.6e-169  562.0  44.8   9.5e-169  561.7  44.8    1.0  1  AftA_N    Arabinofuranosyltransferase N terminal
    2.5e-72  242.2   0.1    3.3e-72  241.8   0.1    1.2  1  AftA_C    Arabinofuranosyltransferase A C terminal


Domain annotation for each model (and alignments):
>> AftA_N  Arabinofuranosyltransferase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.7  44.8  1.1e-172  9.5e-169       1     422 [.      31     453 ..      31     458 .. 0.97

  Alignments for each domain:
  == domain 1  score: 561.7 bits;  conditional E-value: 1.1e-172
                         AftA_N   1 elvlaavvaavvalvallalkrvelpafnsSnvtkalatvgqvlvlvvvaalllllrrerkrllakllsllalaglvvat 80 
                                    +l++a+vva+ va+v+lla++rve+paf sSn+++al+tvgqv +l+ ++ + +l+r++r r+la+l  l+ +++++v+t
  gi|121639709|ref|YP_979933.1|  31 QLAAAVVVAVGVAVVSLLAIARVEWPAFPSSNQLHALTTVGQVGCLAGLVGIGWLWRHGRFRRLARLGGLVLVSAFTVVT 110
                                    5889**************************************************************************** PP

                         AftA_N  81 lgiPLsatrLYLdGisvDqeFRtqfLtrltdsaalaDmtYadlppfYpagWFwlGGrlanllglpgWeafkPwaiislav 160
                                    lg+PL+at+LYL+GisvDq+FRt++Ltrltd+aal+DmtY++lppfYp+gWFw+GGr a+l+g+p+We+fkPwai+s+a+
  gi|121639709|ref|YP_979933.1| 111 LGMPLGATKLYLFGISVDQQFRTEYLTRLTDTAALRDMTYIGLPPFYPPGWFWIGGRAAALTGTPAWEMFKPWAITSMAI 190
                                    ******************************************************************************** PP

                         AftA_N 161 aaavlvvlwqrlvgsevalavalattavtlvlaseEpYaavialllpavlvlarralrg....sraavvgvgvflGlsat 236
                                    a+av++vlw+r++++e+al+v++at+av+l+++s+EpYaa+i++llp++lvl++++l +    ++aavvg+gvflG++at
  gi|121639709|ref|YP_979933.1| 191 AVAVALVLWWRMIRFEYALLVTVATAAVMLAYSSPEPYAAMITVLLPPMLVLTWSGLGArdrqGWAAVVGAGVFLGFAAT 270
                                    *********************************************************988999***************** PP

                         AftA_N 237 lYtLytgvaalavvlvalvvavarvra..erslkpllrllvigvisilialivwgPYllavltgeeassgtAqhyLpeeg 314
                                    +YtL++++ a++vvl+al++a +r ++  + +++pl+rl+v+g+i+++i +++w+PYll++++++ +++g+AqhyLp++g
  gi|121639709|ref|YP_979933.1| 271 WYTLLVAYGAFTVVLMALLLAGSRLQSgiKAAVDPLCRLAVVGAIAAAIGSTTWLPYLLRAARDPVSDTGSAQHYLPADG 350
                                    ***********************9998777788*********************************************** PP

                         AftA_N 315 aelplPmlelsllgvlcliglvwlvvrarsseearalliavvavYlwvllSmlatlagtTLLgFRlevvltvlLataGvl 394
                                    a l++Pml++sllg++cl+g++wlv+rarss  a al+i+v+avYlw+llSmlatla+tTLL+FRl+++l+vlL++aG++
  gi|121639709|ref|YP_979933.1| 351 AALTFPMLQFSLLGAICLLGTLWLVMRARSSAPAGALAIGVLAVYLWSLLSMLATLARTTLLSFRLQPTLSVLLVAAGAF 430
                                    ******************************************************************************** PP

                         AftA_N 395 glaelarllaerlseetarrvtavlvav 422
                                    g++e+ ++l +r      r v  +++a+
  gi|121639709|ref|YP_979933.1| 431 GFVEAVQALGKRG-----RGVIPMAAAI 453
                                    *****99998873.....3355555555 PP

>> AftA_C  Arabinofuranosyltransferase A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8   0.1   3.7e-76   3.3e-72       1     176 []     465     637 ..     465     637 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 3.7e-76
                         AftA_C   1 ipaeleeeidlAytdtdGdgeradrrpadaakyyaevdeaikektgkp.adtvvltdeksflsyypYlgfqaltshYanp 79 
                                    ip++l+ ++++AytdtdG+g+r+drrp++++kyy ++d+ai++ tgk+ + tvvlt+++sflsyypY+gfq+lt+hYanp
  gi|121639709|ref|YP_979933.1| 465 IPDVLRPDLTIAYTDTDGYGQRGDRRPPGSEKYYPAIDAAIRRVTGKRrDRTVVLTADYSFLSYYPYWGFQGLTPHYANP 544
                                    899******************************************999899***************************** PP

                         AftA_C  80 LgefekRnaeieswselkdpeellaaldeapwraPdvlvlRgsleeeeeeeyklrlaediyPnqPnvrfrtvkfdaevFd 159
                                    L++f+kR+++i+sws l++++e++aald++pw+ P+v+++R+ +    +++y+lrla+d+yPnqPnvr++tv ++ ++F+
  gi|121639709|ref|YP_979933.1| 545 LAQFDKRATQIDSWSGLSTADEFIAALDKLPWQPPTVFLMRHGA----HNSYTLRLAQDVYPNQPNVRRYTVDLRTALFA 620
                                    *******************************************4....678***************************** PP

                         AftA_C 160 deefeveqvGPfvvvvr 176
                                    d++f ve++GPfv+++r
  gi|121639709|ref|YP_979933.1| 621 DPRFVVEDIGPFVLAIR 637
                                    **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 4289.73
//
Query:       gi|121639710|ref|YP_979934.1|  [L=1094]
Description: integral membrane indolylacetylinositol arabinosyltransferase embC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-204  679.7  39.5   2.9e-204  679.1  39.5    1.3  1  Arabinose_trans  Mycobacterial cell wall arabinan synthesis p
   1.5e-150  501.5   0.6   1.9e-150  501.2   0.6    1.1  1  Arabino_trans_C  EmbC C-terminal domain
      5e-49  166.5   0.2    8.7e-49  165.7   0.2    1.4  1  Arabino_trans_N  Arabinosyltransferase concanavalin like doma


Domain annotation for each model (and alignments):
>> Arabinose_trans  Mycobacterial cell wall arabinan synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.1  39.5  4.9e-208  2.9e-204       1     458 [.     225     681 ..     225     682 .. 1.00

  Alignments for each domain:
  == domain 1  score: 679.1 bits;  conditional E-value: 4.9e-208
                Arabinose_trans   1 tptalkllviilgvlavlvslvaLarldradgrrhrrllparwlklrlvDvvvvavLvvWhviGantsDDgYiltmarva 80 
                                    +pt+lk++++ilgv+++ ++lvaL++ld+adg+rhrr+lparw+++  +D+ v+avLv+Wh++GantsDDgYiltmarv+
  gi|121639710|ref|YP_979934.1| 225 SPTPLKMAAMILGVALTGAALVALHILDTADGMRHRRFLPARWWSIGGLDTLVIAVLVWWHFVGANTSDDGYILTMARVS 304
                                    69****************************************************************************** PP

                Arabinose_trans  81 keagYlanyyrwfgvpeaPfgwyydllallaqvstaslwlRlpalllglvtWllisrevlpRLgravrrskvalwtaalv 160
                                    ++agY+anyyrwfg+peaPfgwyydllal+a+vstas+w+Rlp+l ++l++W++isrev+pRLg+av++s++a+wtaa +
  gi|121639710|ref|YP_979934.1| 305 EHAGYMANYYRWFGTPEAPFGWYYDLLALWAHVSTASIWMRLPTLAMALTCWWVISREVIPRLGHAVKTSRAAAWTAAGM 384
                                    ******************************************************************************** PP

                Arabinose_trans 161 flafwlpynnGLRpEpvialgalltwvsveraiatrrllPaavavvvAaltlaaaPtGliavaallaalrpllrilvkra 240
                                    fla+wlp++nGLRpEp+ialg+lltw+svera+at+rllP+a+a++++altl  +PtG+ ++ all+a+ pl +il++r+
  gi|121639710|ref|YP_979934.1| 385 FLAVWLPLDNGLRPEPIIALGILLTWCSVERAVATSRLLPVAIACIIGALTLFSGPTGIASIGALLVAIGPLRTILHRRS 464
                                    ******************************************************************************** PP

                Arabinose_trans 241 kelgllallapllAagtlvllvvfadqtlaavleatrvrsavGpslewyeellRYeaLleetadGslaRRfavlllllcl 320
                                    ++ g+l+l+ap+lAa+t+  + +f+dqt+a+ ++a+ +++avGpsl+w++e++RYe+L+++++dGs+aRRfavl+l+l+l
  gi|121639710|ref|YP_979934.1| 465 RRFGVLPLVAPILAAATVTAIPIFRDQTFAGEIQANLLKRAVGPSLKWFDEHIRYERLFMASPDGSIARRFAVLALVLAL 544
                                    ******************************************************************************** PP

                Arabinose_trans 321 vvvlavllrrkripgvaagptrRlvavtalsllllaftPTKwthhfGvfAglaaalaalaavavaeaalrsarnralfla 400
                                    +v++a+ lr++ripg+aagp+rR++++t++s+l+++ftPTKwthhfGvfAgla++l alaavav+ aa+rs+rnr++f+a
  gi|121639710|ref|YP_979934.1| 545 AVSVAMSLRKGRIPGTAAGPSRRIIGITIISFLAMMFTPTKWTHHFGVFAGLAGSLGALAAVAVTGAAMRSRRNRTVFAA 624
                                    ******************************************************************************** PP

                Arabinose_trans 401 avlfvlalalagtngwwyvssygvpwsdkapsiagvklstvllvlavlllavaawlhl 458
                                    +v+fvlal++a++ngwwyvs++gvpws++ p+++ ++l+t+ll l+vl+l++aaw+h+
  gi|121639710|ref|YP_979934.1| 625 VVVFVLALSFASVNGWWYVSNFGVPWSNSFPKWR-WSLTTALLELTVLVLLLAAWFHF 681
                                    *********************************6.**********************8 PP

>> Arabino_trans_C  EmbC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.2   0.6  3.2e-154  1.9e-150       1     385 []     720    1092 ..     720    1092 .. 0.98

  Alignments for each domain:
  == domain 1  score: 501.2 bits;  conditional E-value: 3.2e-154
                                     XXXXXXXXXXXXXXX-HHHHHHHHHHHSTTGGGGTEEEES-GGGGB--BS.SS-HHHHTTSSEEES-BTT-S-S---- CS
                Arabino_trans_C    1 vaslakgavsqypaysvaksNlealagnscglAddvlvEedpnaglLtpleeadaaeaLageestgFtpngvaedlsa 78  
                                     v+sl+++++sqypa+sv++sNl+alag++cglA+dvlvE dpnag+L+p+ +a +a+aL++  s++Ftpng++ d++a
  gi|121639710|ref|YP_979934.1|  720 VVSLTQAMISQYPAWSVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPV-TAPLADALGAGLSEAFTPNGIPADVTA 796 
                                     689***********************************************.*************************** PP

                                     -----------...------------------B-SS--TTS--B--STT--GGG---EE---SSS---EEEE---EE- CS
                Arabino_trans_C   79 deeeeksgaantsasaeeeeatteeeagteggteaeagvngstvaLPfgLdparvPvlGsysegeqeeaeltsswYeL 156 
                                     d+++e++g  +     +++  +t++e+gteggt+a++g+ngs+++LP++Ldpar+PvlGs+++g q +a l+s+wY+L
  gi|121639710|ref|YP_979934.1|  797 DPVMERPGDRS---FLNDDGLITGSEPGTEGGTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRL 871 
                                     ********999...7899999********************************************************* PP

                                     --..TTB-.SEEEEEEEE--...-G.......GGEEEEEE-HHHHHTT--SEEEE-EEES-SSS-EEEEEEGGGS-TT CS
                Arabino_trans_C  157 pe..rsddapllvvsaAGriasvdedgvvtegqeleleygtreadgsvealgevepiDigpapsWRnLRvpldelpae 232 
                                     p+  ++d+apllvv+aAGr+           ++e++l+++t+e++++ ++ g++e++D+g+ap+WRnLR pl+++p++
  gi|121639710|ref|YP_979934.1|  872 PTneQRDRAPLLVVTAAGRFD----------SREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPST 939 
                                     *85577889**********94..........489******************************************** PP

                                     --EEEEEEEE---STT--EEE---B--B-EEHHHHHTTTSEEE--HHHHTT-TTSEE---GGG------EEEE----- CS
                Arabino_trans_C  233 anvvRivaedkdlaedqwlavtPPRvpkletlqdvvgsedPvllDwavglaFpcQrpfdhrnGvaevPkyrilpdrkg 310 
                                     a++vR+va+d+dla+++w+a+tPPR+p+++tlq+vvg  dPv+lDw vglaFpcQrpf h++Gv e+Pk+rilpdr g
  gi|121639710|ref|YP_979934.1|  940 ATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDRFG 1017
                                     ****************************************************************************** PP

                                     ------------------TTTTEEEEEEEEEETT-TT----EEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXX CS
                Arabino_trans_C  311 akasstwqdaegGGplgitelllsattvptYlkndwarDWGslerytplvpsaepAelelgtatrsGlwspgpir 385 
                                     a+a+s+++d++gGGplgitell++attv++Ylk+dw rDWG+l+r+tp++p+a+pA+l+lgt+trsGlwsp+p+r
  gi|121639710|ref|YP_979934.1| 1018 AEANSPVMDHNGGGPLGITELLMRATTVASYLKDDWFRDWGALQRLTPYYPDAQPADLNLGTVTRSGLWSPAPLR 1092
                                     *************************************************************************97 PP

>> Arabino_trans_N  Arabinosyltransferase concanavalin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.2   1.4e-52   8.7e-49       1     157 []      53     221 ..      53     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.4e-52
                                    XXXEEEEEESBTTB---EE--BSSBB-SEEEEEEEGGGGGGB-TT--....EEEESS-TTSTTHHHHSEEEEEETTEEEE CS
                Arabino_trans_N   1 kqttatlsWPqngslssvtaPLvsyvPvsldvtvpcaavaelpaegg....vvlsTvPkeakdaakrGLfvrvtadsvev 76 
                                    +qtta+l+WPqng+++sv+aPL+ yv+++l++tvpc+a+a l+ +++    v+lsTvPk+a++a +rGL+++  +d++ +
  gi|121639710|ref|YP_979934.1|  53 NQTTAQLNWPQNGTFASVEAPLIGYVATDLNITVPCQAAAGLAGSQNtgktVLLSTVPKQAPKAVDRGLLLQRANDDLVL 132
                                    79***************************************99777777789**************************** PP

                                    EETTEEEEEEEHHHHHT-TT-EEEEEEESS-EEEEETT-T...........TT-EEESS-----BSEEB--B-GGGHHTT CS
                Arabino_trans_N  77 vvrnvvllsapreelaspecaeltvtsdsegttaefvglte.........ekasgtlegdlrPqvvGvftdLesgaapag 147
                                    vvrnv+l++ap++++ +p+c++lt+t++++++ aefvgl +         + + ++   d+rPq+vGvftdL+ g+ap g
  gi|121639710|ref|YP_979934.1| 133 VVRNVPLVTAPLSQVLGPTCQRLTFTAHADRVAAEFVGLVQgpnaehpgaPLRGERSGYDFRPQIVGVFTDLA-GPAPPG 211
                                    ****************************************999988888666666777***************.****** PP

                                    -EEEEEEE-B CS
                Arabino_trans_N 148 lsvsvevDsR 157
                                    ls+s++vD+R
  gi|121639710|ref|YP_979934.1| 212 LSFSASVDTR 221
                                    *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1094 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.23s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 7541.68
//
Query:       gi|121639711|ref|YP_979935.1|  [L=1094]
Description: integral membrane indolylacetylinositol arabinosyltransferase embA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.9e-171  569.3  40.9   9.1e-171  568.7  40.9    1.3  1  Arabinose_trans  Mycobacterial cell wall arabinan synthesis p
   2.8e-149  497.3   0.1   3.7e-149  496.9   0.1    1.2  1  Arabino_trans_C  EmbC C-terminal domain
    8.9e-49  165.7   0.0    1.5e-48  164.9   0.0    1.4  1  Arabino_trans_N  Arabinosyltransferase concanavalin like doma


Domain annotation for each model (and alignments):
>> Arabinose_trans  Mycobacterial cell wall arabinan synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.7  40.9  1.5e-174  9.1e-171       1     459 []     198     667 ..     198     667 .. 0.96

  Alignments for each domain:
  == domain 1  score: 568.7 bits;  conditional E-value: 1.5e-174
                Arabinose_trans   1 tptalkllviilgvlavlvslvaLarldradgrrhrrllparwl.......klrlvDvvvvavLvvWhviGantsDDgYi 73 
                                    tp alk +v++lgvlavlv++v La+ldr+++ r+ r   +r++         rl+D++v+a+L++WhviGa++sDDgY+
  gi|121639711|ref|YP_979935.1| 198 TPGALKKAVMLLGVLAVLVAMVGLAALDRLSRGRTLRDWLTRYRprvrvgfASRLADAAVIATLLLWHVIGATSSDDGYL 277
                                    6999************************998776655555555444444556789************************* PP

                Arabinose_trans  74 ltmarvakeagYlanyyrwfgvpeaPfgwyydllallaqvstaslwlRlpalllglvtWllisrevlpRLg...ravrrs 150
                                    lt+arva +agY+anyyr+fg+ eaPf+wy ++la+la+vsta +w+Rlpa l+g+++Wl++sr+vl+RLg      +++
  gi|121639711|ref|YP_979935.1| 278 LTVARVAPKAGYVANYYRYFGTTEAPFDWYTSVLAQLAAVSTAGVWMRLPATLAGIACWLIVSRFVLRRLGpgpGGLASN 357
                                    ***********************************************************************65556889* PP

                Arabinose_trans 151 kvalwtaalvflafwlpynnGLRpEpvialgalltwvsveraiatrrllPaavavvvAaltlaaaPtGliavaallaalr 230
                                    +va++ta++vfl +wlp+nnGLRpEp+ialg+l+twv+ver+ia +rl+Paava++vA+lt ++aP+Glia+a+ll ++r
  gi|121639711|ref|YP_979935.1| 358 RVAVFTAGAVFLSAWLPFNNGLRPEPLIALGVLVTWVLVERSIALGRLAPAAVAIIVATLTATLAPQGLIALAPLLTGAR 437
                                    ******************************************************************************** PP

                Arabinose_trans 231 pllrilvkrakelgllallapllAagtlvllvvfadqtlaavleatrvrsavGpslewyeellRYeaLleeta.dGslaR 309
                                    ++++++++r++++glla la+l+Aa  l+ +vvf+dqtla+v+e++r++++vGp+++wy+++lRY+ L+ e++ +Gs++R
  gi|121639711|ref|YP_979935.1| 438 AIAQRIRRRRATDGLLAPLAVLAAALSLITVVVFRDQTLATVAESARIKYKVGPTIAWYQDFLRYYFLTVESNvEGSMSR 517
                                    ********************************************************************988766****** PP

                Arabinose_trans 310 RfavlllllclvvvlavllrrkripgvaagptrRlvavtalsllllaftPTKwthhfGvfAglaaalaalaavavaeaal 389
                                    Rfavl+ll+cl+ vl+vllrr+r++g+a+gp++Rl+++ta++llll+ftPTKw+ +fG+fAgla++l a++a+++a+  l
  gi|121639711|ref|YP_979935.1| 518 RFAVLVLLFCLFGVLFVLLRRGRVAGLASGPAWRLIGTTAVGLLLLTFTPTKWAVQFGAFAGLAGVLGAVTAFTFARIGL 597
                                    ******************************************************************************** PP

                Arabinose_trans 390 rsarnralflaavlfvlalalagtngwwyvssygvpwsdkapsiagvklstvllvlavlllavaawlhlr 459
                                    +s+rn +l+++a+lfvla+a++g+ngw+yv++ygvpw+d +p ia+  +++++l+l++l+ ++aaw h+r
  gi|121639711|ref|YP_979935.1| 598 HSRRNLTLYVTALLFVLAWATSGINGWFYVGNYGVPWYDIQPVIASHPVTSMFLTLSILTGLLAAWYHFR 667
                                    ********************************************************************97 PP

>> Arabino_trans_C  EmbC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.9   0.1  6.2e-153  3.7e-149       1     385 []     702    1091 ..     702    1091 .. 0.98

  Alignments for each domain:
  == domain 1  score: 496.9 bits;  conditional E-value: 6.2e-153
                                     XXXXXXXXXXXXXXX-HHHHHHHHH.HH.STTGGGGTEEEES-GGGGB--BS...SS-HHHHTTSSEEES-BTT-S-S CS
                Arabino_trans_C    1 vaslakgavsqypaysvaksNleal.ag.nscglAddvlvEedpnaglLtpl..eeadaaeaLageestgFtpngvae 74  
                                     v s+ak+av +yp y++ak+Nl+al +g +sc++Addvl E+dpnag+L+p+  ++ ++  +L+g +++gF+p+gv e
  gi|121639711|ref|YP_979935.1|  702 VGSMAKAAVFRYPLYTTAKANLTALsTGlSSCAMADDVLAEPDPNAGMLQPVpgQAFGPDGPLGGISPVGFKPEGVGE 779 
                                     579**********************644479*********************8888999******************* PP

                                     ---------------...------------------B-SS--TTS--B--STT--GGG---EE---SSS---EEEE-- CS
                Arabino_trans_C   75 dlsadeeeeksgaantsasaeeeeatteeeagteggteaeagvngstvaLPfgLdparvPvlGsysegeqeeaeltss 152 
                                     dl++d++ +k+g  n++as ++++a+ +++agt+gg+ ++ g+ngs++aLPfgLdpar+Pv+Gsy ++++ +a++ts+
  gi|121639711|ref|YP_979935.1|  780 DLKSDPVVSKPGLVNSDASPNKPNAAITDSAGTAGGK-GPVGINGSHAALPFGLDPARTPVMGSY-GENNLAATATSA 855 
                                     ************************************9.***************************.9999******** PP

                                     -EE---TTB-.SEEEEEEEE--...-G.......GGEEEEEE-HHHHHTT--SEEEE-EEES-SSS-EEEEEEGGGS- CS
                Arabino_trans_C  153 wYeLpersddapllvvsaAGriasvdedgvvtegqeleleygtreadgsvealgevepiDigpapsWRnLRvpldelp 230 
                                     wY+Lp+rs d+pl+vvsaAG+i+s++edg + +gq+l+l++g +++dg++++lg+v piDigp+p+WRnLR+pl+++p
  gi|121639711|ref|YP_979935.1|  856 WYQLPPRSPDRPLVVVSAAGAIWSYKEDGDFIYGQSLKLQWGVTGPDGRIQPLGQVFPIDIGPQPAWRNLRFPLAWAP 933 
                                     ****************************************************************************** PP

                                     TT--EEEEEEEE---STT--EEE---B--B-EEHHHHHTTTSEEE--HHHHTT-TTSEE---GGG------EEEE--- CS
                Arabino_trans_C  231 aeanvvRivaedkdlaedqwlavtPPRvpkletlqdvvgsedPvllDwavglaFpcQrpfdhrnGvaevPkyrilpdr 308 
                                     +ea+v Riva d++l+++qw+a+tPPRvp le+lq ++gs +Pvl+D+a++++FpcQrpf+++ G+ae+P+yrilpd+
  gi|121639711|ref|YP_979935.1|  934 PEADVARIVAYDPNLSPEQWFAFTPPRVPVLESLQRLIGSATPVLMDIATAANFPCQRPFSEHLGIAELPQYRILPDH 1011
                                     ****************************************************************************** PP

                                     ---.-----------------TTTTEEEEEEEEEETT-TT----EEEEEEE--XX..XXXXXXXXXXXXXXXXXXXXX CS
                Arabino_trans_C  309 kga.kasstwqdaegGGplgitelllsattvptYlkndwarDWGslerytplvps..aepAelelgtatrsGlwspgp 383 
                                     k++ ++s+ wq++++GGp+ +t++ll+++t++tYl++dw+rDWGs+e+y++lvp+  a++A +e g  t  G+ +pgp
  gi|121639711|ref|YP_979935.1| 1012 KQTaASSNLWQSSSTGGPFLFTQALLRTSTIATYLRGDWYRDWGSVEQYHRLVPAdqAPDAVVEEGVITVPGWGRPGP 1089
                                     **9999**********************************************99865666****************** PP

                                     XX CS
                Arabino_trans_C  384 ir 385 
                                     ir
  gi|121639711|ref|YP_979935.1| 1090 IR 1091
                                     98 PP

>> Arabino_trans_N  Arabinosyltransferase concanavalin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.9   0.0   2.5e-52   1.5e-48       1     157 []      37     194 ..      37     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 2.5e-52
                                    XXXEEEEEESBTTB....---EE--BSSBB-SEEEEEEEGGGGGGB-TT--EEEESS-TTSTTHHHHSEEEEEETTEEEE CS
                Arabino_trans_N   1 kqttatlsWPqngs....lssvtaPLvsyvPvsldvtvpcaavaelpaeggvvlsTvPkeakdaakrGLfvrvtadsvev 76 
                                    +qttat+ WPq+ +    ++++taPLvs +P+ ld+++pc+a+a+lpa+gg+vlsT+P+++ d+ k GLfvr+++d+v v
  gi|121639711|ref|YP_979935.1|  37 NQTTATIFWPQGSTadgnITQITAPLVSGAPRALDISIPCSAIATLPANGGLVLSTLPAGGVDTGKAGLFVRANQDTVVV 116
                                    79*********9888888************************************************************** PP

                                    EETTEEEEEEEHHHHHT-TT-EEEEEEESS-EEEEETT-T..TT-EEESS-----BSEEB--B-GGGHHTT-EEEEEEE- CS
                Arabino_trans_N  77 vvrnvvllsapreelaspecaeltvtsdsegttaefvglteekasgtlegdlrPqvvGvftdLesgaapaglsvsvevDs 156
                                    ++r++v++ a r+++a+++c++l++++d+ g+ a+f g++    +gtl ++++Pqv G+ftdL+ ga+  gls++v++D+
  gi|121639711|ref|YP_979935.1| 117 AFRDSVAAVAARSTIAAGGCSALHIWADTGGAGADFMGIP--GGAGTLPPEKKPQVGGIFTDLKVGAQ-PGLSARVDIDT 193
                                    ***************************************8..89********************9888.5********** PP

                                    B CS
                Arabino_trans_N 157 R 157
                                    R
  gi|121639711|ref|YP_979935.1| 194 R 194
                                    9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1094 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 6287.00
//
Query:       gi|121639712|ref|YP_979936.1|  [L=1098]
Description: integral membrane indolylacetylinositol arabinosyltransferase embB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-194  647.5  36.9   1.6e-194  647.0  36.9    1.2  1  Arabinose_trans  Mycobacterial cell wall arabinan synthesis p
   6.6e-137  456.6   0.4   1.1e-136  455.9   0.4    1.4  1  Arabino_trans_C  EmbC C-terminal domain
      4e-56  189.5   1.6    6.5e-56  188.9   1.6    1.3  1  Arabino_trans_N  Arabinosyltransferase concanavalin like doma
  ------ inclusion threshold ------
        1.5    7.0   6.1        2.3    6.3   6.1    1.2  1  YfhO             Bacterial membrane protein YfhO


Domain annotation for each model (and alignments):
>> Arabinose_trans  Mycobacterial cell wall arabinan synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.0  36.9  3.7e-198  1.6e-194       2     458 ..     214     688 ..     213     689 .. 1.00

  Alignments for each domain:
  == domain 1  score: 647.0 bits;  conditional E-value: 3.7e-198
                Arabinose_trans   2 ptalkllviilgvlavlvslvaLarldradgr..................rhrrllparwlklrlvDvvvvavLvvWhvi 63 
                                    pt+lkll+ii +++a++v+l+aL+rld++dgr                   +rrl+pa+w++++l+D+vv+  +++Whvi
  gi|121639712|ref|YP_979936.1| 214 PTTLKLLAIIGAIVATVVALIALWRLDQLDGRgsiaqlllrpfrpasspgGMRRLIPASWRTFTLTDAVVIFGFLLWHVI 293
                                    9************************************************99***************************** PP

                Arabinose_trans  64 GantsDDgYiltmarvakeagYlanyyrwfgvpeaPfgwyydllallaqvstaslwlRlpalllglvtWllisrevlpRL 143
                                    Gan+sDDgYil+marva++agY++ny+rwfg pe+Pfgwyy+llal+++vs aslw+Rlp+l +glv+Wll+srevlpRL
  gi|121639712|ref|YP_979936.1| 294 GANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRL 373
                                    ******************************************************************************** PP

                Arabinose_trans 144 gravrrskvalwtaalvflafwlpynnGLRpEpvialgalltwvsveraiatrrllPaavavvvAaltlaaaPtGliava 223
                                    g av+ sk a+w+aa+v+l++w+p+nnGLRpE +ialg+l+t+v++er++  +rl+Paa+avv Aa+tl+++PtGliava
  gi|121639712|ref|YP_979936.1| 374 GPAVAASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVA 453
                                    ******************************************************************************** PP

                Arabinose_trans 224 allaalrpllrilvkrakelgllallapllAagtlvllvvfadqtlaavleatrvrsavGpslewyeellRYeaLleeta 303
                                    al+a+ rp+lrilv+r++ +g+l+l+ p+lAagt++l+vvfadqtl++vleatrvr ++Gps++wy+e lRY++L+ +t+
  gi|121639712|ref|YP_979936.1| 454 ALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTV 533
                                    ******************************************************************************** PP

                Arabinose_trans 304 dGslaRRfavlllllclvvvlavllrrkripgvaagptrRlvavtalsllllaftPTKwthhfGvfAglaaalaalaava 383
                                    dGsl+RRf++l++ lcl+++++++lrrkrip va+gp++Rl++v+++++++l+ftPTKw+hhfG+fA+++aa+aal++v 
  gi|121639712|ref|YP_979936.1| 534 DGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVL 613
                                    ******************************************************************************** PP

                Arabinose_trans 384 vaeaalrsarnralflaavlfvlalalagtngwwyvssygvpwsdkapsiagvklstvllvlavlllavaawlhl 458
                                    v++++lr +rnr+ flaa++f+lal+ a+tngwwyvssygvp+++ +p+i g+++st++++l+++++ +aawlh+
  gi|121639712|ref|YP_979936.1| 614 VSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHF 688
                                    **************************************************************************8 PP

>> Arabino_trans_C  EmbC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.9   0.4  2.5e-140  1.1e-136       1     385 []     719    1095 ..     719    1095 .. 0.93

  Alignments for each domain:
  == domain 1  score: 455.9 bits;  conditional E-value: 2.5e-140
                                     XXXXXXXXXXXXXXX-HHHHHHHHHHHSTTGGGGTEEEES-GGGGB--BS.....SS-HHHHTTSSEEES-BTT-S-S CS
                Arabino_trans_C    1 vaslakgavsqypaysvaksNlealagnscglAddvlvEedpnaglLtpl....eeadaaeaLageestgFtpngvae 74  
                                     vas+++g+v+qyp+ys+++sN++a+ g  cglAddvlvE+d+nag+++pl    ++ ++  +L+g++++gFtpngv+e
  gi|121639712|ref|YP_979936.1|  719 VASMVAGIVRQYPTYSNGWSNVRAFVG-GCGLADDVLVEPDTNAGFMKPLdgdsGSWGPLGPLGGVNPVGFTPNGVPE 795 
                                     789************************.9*********************8765566788999*************** PP

                                     ---------------...------------------B-SS--TTS--B--STT--GGG---EE---SSS---EEEE-- CS
                Arabino_trans_C   75 dlsadeeeeksgaantsasaeeeeatteeeagteggteaeagvngstvaLPfgLdparvPvlGsysegeqeeaeltss 152 
                                     +  a++   k+         +++ +  + +a t+    +++g+ngstv+LP+gLdparvP+ G+y++g+q++++l+s+
  gi|121639712|ref|YP_979936.1|  796 HTVAEAIVMKP---------NQPGTDYDWDAPTKL---TSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSA 861 
                                     99999433333.........333333333333333...569************************************* PP

                                     -EE---TTB-.SEEEEEEEE--...-G.......GGEEEEEE-HHHHHTT--SEEEE-EEE.S-SSS.-EEEEEEGGG CS
                Arabino_trans_C  153 wYeLpersddapllvvsaAGriasvdedgvvtegqeleleygtreadgsvealgevepiDi.gpaps.WRnLRvplde 228 
                                     wY Lp+++d +pl+vv+aAG+ia  +     t+gq+++ley+  +  g++ ++g+++p D+ g++p+ WRnLR+++++
  gi|121639712|ref|YP_979936.1|  862 WYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPG-PGALVPAGRMVPDDLyGEQPKaWRNLRFARAK 938 
                                     ************************9998888************96.67999*********96555544********** PP

                                     S-TT--EEEEEEEE---STT--EEE---B--B-EEHHHHHTTTSEEE--HHHHTT-TTSEE---GGG------EEEE- CS
                Arabino_trans_C  229 lpaeanvvRivaedkdlaedqwlavtPPRvpkletlqdvvgsedPvllDwavglaFpcQrpfdhrnGvaevPkyrilp 306 
                                     +pa+a +vR+vaed +l++++w+avtPPRvp l++lq++vgs++PvllDwavglaFpcQ+p+ h+nG+ae+Pk+ri+p
  gi|121639712|ref|YP_979936.1|  939 MPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITP 1016
                                     ****************************************************************************** PP

                                     -----.-----------------TTTTEEEEEEEEEETT-TT----EEEEEEE--XXXXXXXXXXXXXXXXXXXXXXX CS
                Arabino_trans_C  307 drkga.kasstwqdaegGGplgitelllsattvptYlkndwarDWGslerytplvpsaepAelelgtatrsGlwspgp 383 
                                     d++++  +++tw+d+++GG+lgit+lll+a++++tYl++dwarDWGsl+++++lv+ a+pA+lelgtatrsGlwspg+
  gi|121639712|ref|YP_979936.1| 1017 DYSAKkLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVD-APPAQLELGTATRSGLWSPGK 1093
                                     *****89************************************************8.********************* PP

                                     XX CS
                Arabino_trans_C  384 ir 385 
                                     ir
  gi|121639712|ref|YP_979936.1| 1094 IR 1095
                                     98 PP

>> Arabino_trans_N  Arabinosyltransferase concanavalin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.9   1.6   1.4e-59   6.5e-56       2     157 .]      51     209 ..      50     209 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 1.4e-59
                                    XXEEEEEESBTTB---EE--BSSBB-SEEEEEEEGGGGGGB-TT--EEEESS-TTSTTHHHHSEEEEEETTEEEEEETTE CS
                Arabino_trans_N   2 qttatlsWPqngslssvtaPLvsyvPvsldvtvpcaavaelpaeggvvlsTvPkeakdaakrGLfvrvtadsvevvvrnv 81 
                                    qtta l+WPq+g+l svtaPL+s +Pv++++tvpc +v+++p+ ggvvl+T+Pk++kda+ ++Lfv v+a++v+v++rnv
  gi|121639712|ref|YP_979936.1|  51 QTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNV 130
                                    99****************************************************************************** PP

                                    EEEEEEHHHHHT-TT-EEEEEEESS-EEEEETT-T......TT-EEESS-----BSEEB--B-GGGHHTT-EEEEEEE-B CS
                Arabino_trans_N  82 vllsapreelaspecaeltvtsdsegttaefvglte....ekasgtlegdlrPqvvGvftdLesgaapaglsvsvevDsR 157
                                    v+ls+pre+++sp+c++++vts+++gt a+fvgl++    + +sg  +++lrPq+vGvftdL+ g+ap gl+vs+++D+R
  gi|121639712|ref|YP_979936.1| 131 VILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDpsgaPLRSGFPDPNLRPQIVGVFTDLT-GPAPPGLAVSATIDTR 209
                                    **********************************99999888999******************.***************9 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.1   0.00052       2.3     340     451 ..     539     653 ..     537     662 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00052
                           YfhO 340 yRfsfilsflllllaaealkelkql.k.klkllaailllvlllliilllknkksynfltssqll..lgllllllalllll 415
                                     Rf f+++ l+l++a+ ++ ++k++ +  ++ ++ ++ ++ + +++l++ ++k+   + +  l+  +g+ +  l+++l++
  gi|121639712|ref|YP_979936.1| 539 RRFGFLITALCLFTAVFIMLRRKRIpSvARGPAWRLMGVIFGTMFFLMFTPTKW---VHHFGLFaaVGAAMAALTTVLVS 615
                                    6*******************9999942355555555555555555555555555...44444440045555555666666 PP

                           YfhO 416 llll.kkkkkklvl.lllllvlvlelggnaylslnkis 451
                                    + +l +++++ ++l +l +l++++ +++n+++ +++ +
  gi|121639712|ref|YP_979936.1| 616 PSVLrWSRNRMAFLaALFFLLALCWATTNGWWYVSSYG 653
                                    55557555555554045555666677788887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1098 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 6864.66
//
Query:       gi|121639713|ref|YP_979937.1|  [L=375]
Description: hypothetical protein BCG_3858 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-13   48.1   0.0      1e-07   31.7   0.0    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-05   25.2   0.2    4.2e-05   23.7   0.0    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.4e-06     0.021       4      47 ..      92     129 ..      90     149 .. 0.82
   2 !   31.7   0.0   1.1e-11     1e-07      94     201 .]     232     342 ..     192     342 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-06
                                    EES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGG CS
                  Lactamase_B_2   4 LiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlagl 47 
                                    +iD+g++ +  ++ a        ++++++a ++th H DH+ ++
  gi|121639713|ref|YP_979937.1|  92 VIDCGLGSLNAFTNA------GLQFDDLKAMFITHLHTDHIVDY 129
                                    799999966663433......346889**************775 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1.1e-11
                                    SEEEE.CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE..CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTT CS
                  Lactamase_B_2  94 esfel.gdggleitatparhksgrrldrnagdtlGlrie..gggkrvyyigDtgyipeeigerlggadllllditayedd 170
                                     +f++  d ++++tat ++h           +++G+r++  ++g +v ++gDt   +  i  + +g d+l++++ +  d 
  gi|121639713|ref|YP_979937.1| 232 SPFSVaSDDNVSVTATLVSHYDVY-------PAFGFRFDlkKSGVSVTFSGDTTKSDNLIT-LAQGTDILVHEAVFSLDT 303
                                    567776445789999999999999.......9********9*************8886655.***********9998887 PP

                                    HHHH........HHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 171 emir........hmgHltpeeaveaaadlgakrlvliHi 201
                                     +           ++H++ e+  e+aa++++k+l+l H+
  gi|121639713|ref|YP_979937.1| 304 AYFGnafppnylVNSHISAEQVGEVAAAAKPKQLILSHY 342
                                    76558*********************************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.6e-09   4.2e-05       8      58 ..      81     126 ..      63     158 .. 0.94
   2 ?   -3.4   0.0      0.93   8.3e+03     144     156 ..     270     282 ..     268     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.6e-09
                                    EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHH CS
                    Lactamase_B   8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHi 58 
                                    s ++  + ++++iD+G+++ +a        +gl+ +d++a ++THlH+DHi
  gi|121639713|ref|YP_979937.1|  81 SSVLKIGRDLYVIDCGLGSLNAFTN-----AGLQFDDLKAMFITHLHTDHI 126
                                    67888999***************96.....9*******************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.93
                                    CEEEECTTTSSHH CS
                    Lactamase_B 144 kvlftGDallage 156
                                    +v f+GD++ + +
  gi|121639713|ref|YP_979937.1| 270 SVTFSGDTTKSDN 282
                                    6889***997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2591.45
//
Query:       gi|121639714|ref|YP_979938.1|  [L=593]
Description: acyl-CoA dehydrogenase fadE35 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-42  143.6   2.9      3e-41  141.1   0.2    2.5  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    6.2e-16   58.4   0.0    1.2e-15   57.4   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      9e-14   51.9   2.7    1.3e-13   51.3   0.0    2.5  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.2e-13   50.4   0.0    3.9e-13   49.6   0.0    1.4  1  AidB_N         Adaptive response protein AidB N-terminal doma
  ------ inclusion threshold ------
       0.25   11.9   4.1       0.24   11.9   2.0    2.1  2  MerR-DNA-bind  MerR, DNA binding


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.2   8.4e-45     3e-41       1     149 [.     309     461 ..     309     462 .. 0.98
   2 ?    2.2   0.3     0.052   1.9e+02      56      97 ..     518     558 ..     502     562 .. 0.82

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 8.4e-45
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    gkG++ +me  n  Rl++a  alg arral e+l ya +r+afg++lid++l+r+klaem +++eaa ++v++   a+++
  gi|121639714|ref|YP_979938.1| 309 GKGLTRMMELTNRLRLGTASFALGNARRALVESLCYAGQRRAFGGALIDKPLMRRKLAEMVVDVEAALAMVFDGFGAANH 388
                                    79****************************************************************************** PP

                                    ----....HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd....raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                     +p+    r ++ ++Kl++++l  +va++a++++Gg+Gy e +pv+rl+rda+v++i+eG+++i+++++ r++
  gi|121639714|ref|YP_979938.1| 389 RQPRclpqRIAVPVTKLKTCRLGITVASDAIEIHGGNGYIETWPVARLLRDAQVNTIWEGPDNILCLDVRRGI 461
                                    ******9999**********************************************************99875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.052
                                    HHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  56 klaemaaeleaarllvyraaealdagkpdraeasmaKlfase 97 
                                     la+++ ++ a  ll+++aa+   + + d  +a +a l+a +
  gi|121639714|ref|YP_979938.1| 518 PLAQFMGDVYAGALLTEQAAWERATRGTD-RKALVARLYARR 558
                                    589999999************88888888.666777777655 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   3.4e-19   1.2e-15       3      96 ..     193     290 ..     191     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.4e-19
                                    E---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS-------EEEEEEE..GG.....GEEE- CS
                  Acyl-CoA_dh_M   3 alTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpdrarglslflvprdap.....gvsvr 76 
                                     lTE+ +Gsd+ +++t +a+r+g+ + lnG K++ +n    + ++vla+ ++ pd +rg+ +flv r +      gv++r
  gi|121639714|ref|YP_979938.1| 193 LLTERAGGSDLGALET-TATRSGDVWLLNGFKWFASNC-AGEAFVVLAKpEGAPDSTRGVATFLVLRTRRdgsrnGVRIR 270
                                    69**************.88888889************9.568899999986666679******999444346788***** PP

                                    ----BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  77 rieeklGlrglptgelvfed 96 
                                    r+++klG+r++++ge++f d
  gi|121639714|ref|YP_979938.1| 271 RLKDKLGTRSVASGEIEFVD 290
                                    ****************9965 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   3.7e-17   1.3e-13       2     129 ..     325     446 ..     324     450 .. 0.93
   2 ?   -1.4   0.8      0.71   2.6e+03      42      73 ..     517     545 ..     484     561 .. 0.65

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.7e-17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                    g a +alG+Ar+al e + +a++r    +g +l d+p +  +lae+  +++AA a++ + + +    a+ +++    +r 
  gi|121639714|ref|YP_979938.1| 325 GTASFALGNARRALVESLCYAGQRRA--FGGALIDKPLMRRKLAEMVVDVEAALAMVFDGFGA----ANHRQPRCLPQRI 398
                                    6799*********************9..**********************************9....55555556899** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTS CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaH 129
                                       ++++ + +l i ++++++e++Gg+++ +  p+ Rl+RDa++ +++
  gi|121639714|ref|YP_979938.1| 399 AVPVTKLKTCRLGITVASDAIEIHGGNGYIETWPVARLLRDAQVNTIW 446
                                    ******************************************998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                  Acyl-CoA_dh_2  42 lalaeaaarldAAralleraaaraealaaagk 73 
                                    + la+   ++ A  +l+e+aa++      +g+
  gi|121639714|ref|YP_979938.1| 517 FPLAQFMGDVYAGALLTEQAAWERAT---RGT 545
                                    44788888888888888888877222...222 PP

>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.1e-16   3.9e-13       8     155 ..      33     187 ..      28     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.1e-16
                         AidB_N   8 dvnlfasdpaLqeavaregaaea....aeelaalGellgsaevlelarlanrnpPrlrthDrfGrRiDevefhpayhalm 83 
                                      n + +dp Lq ++a +++ ++    + +l+++Gel+g   v ++a++ +rnpPrl+++Dr+G+ i +v   +++ +  
  gi|121639714|ref|YP_979938.1|  33 GLNWYLTDPTLQFIMAYYLRPDElafaEPHLTRIGELTGG-PVTRWAEETDRNPPRLERYDRWGHDISRVVLPESFIQSK 111
                                    5799****************9888898*************.*************************************** PP

                         AidB_N  84 aaaveaglhasawe.earegahvaraallyllaqveaGhlCPltmThAavpaL.k..aepalaeewlpkllsrdYd 155
                                    +a +ea+ +    + +a+ +  +a +a+ yll+q++ G++C l+     v+ L +  a p+++e +l kl s ++d
  gi|121639714|ref|YP_979938.1| 112 RAVIEARQAVRDDAaRAGVKPSLALFAADYLLNQADIGMACALATGGNMVRSLvTayAPPDVREFVLGKLNSGEWD 187
                                    *9999886655444467889999********************999999998864344677777777887777766 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.1   1.1e+04      40      53 ..     107     120 ..     103     121 .. 0.80
   2 ?   11.9   2.0   6.8e-05      0.24      24      64 ..     471     513 ..     467     514 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                                    HHHHHHHHHHHHHH CS
                  MerR-DNA-bind  40 llarklaeleeria 53 
                                     ++ k+a +e+r+a
  gi|121639714|ref|YP_979938.1| 107 FIQSKRAVIEARQA 120
                                    57889999999986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.8e-05
                                    H.HHHHS.TTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  24 L.alydd.rappcqdvrallarklaeleeriaeLqalraeLaa 64 
                                    L  l+d  + ++ +d  +l+ r++++l++ i ++++l ++La+
  gi|121639714|ref|YP_979938.1| 471 LaRLRDAvSVSDDDDTTRLVSRRIEDLDAAITAWTKLDRQLAE 513
                                    44677777788889999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4294.92
//
Query:       gi|121639715|ref|YP_979939.1|  [L=444]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-71  239.5   0.0    5.1e-71  239.2   0.0    1.1  1  DDE_Tnp_ISL3  Transposase
    5.5e-12   44.9   3.3    5.5e-12   44.9   3.3    2.8  3  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    2.3e-09   37.8   0.4    5.6e-09   36.5   0.4    1.7  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.2   0.0   8.6e-75   5.1e-71       1     238 [.     163     420 ..     163     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 8.6e-75
                   DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsekerekveavvmDmsaayksavkealPnAkiv 80 
                                    +giDEis+k++h+y+tvvvd+  d grl++++pg +k+tl  f+++l++++++++++v++D + +++++v e++P+A  +
  gi|121639715|ref|YP_979939.1| 163 IGIDEISYKRHHRYLTVVVDH--DSGRLVWAAPGHDKATLGLFFDALGAERAAQITHVSADAADWIADVVTERCPDAIQC 240
                                    8********************..********************************************************* PP

                   DDE_Tnp_ISL3  81 vDrFHvvklanealdevRrreqkelre.......................ekrkklkrsrrlllknpenlteeqkqrlde 137
                                    +D+FHvv++a+eald  Rrr ++++r+                       e++++lk++r++l+knpe+lte+q ++l +
  gi|121639715|ref|YP_979939.1| 241 ADPFHVVAWATEALDVERRRAWNDARAiartepkwgrgrpgknaaprpgrERARRLKGARYALWKNPEDLTERQSAKLAW 320
                                    *************************7777788999999***********999999************************* PP

                   DDE_Tnp_ISL3 138 lleaspelekaYelkeelrevfrkkdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiN 217
                                    +++++p+l +aY lke+lr+vf   + ee+++al++wi++a+r++++ f +la+ +k+hr  I +++d++ls+g +E++N
  gi|121639715|ref|YP_979939.1| 321 IAKTDPRLYRAYLLKESLRHVFS-VKGEEGKQALDRWISWAQRCRIPVFVELAARIKRHRVAIDAALDHGLSQGLIESTN 399
                                    **********************9.78****************************************************** PP

                   DDE_Tnp_ISL3 218 nkikaikrrayGfrnfenfrl 238
                                    +ki++++r+a+Gfr+++++++
  gi|121639715|ref|YP_979939.1| 400 TKIRLLTRIAFGFRSPQALIA 420
                                    *****************9987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.48   2.9e+03      29      44 ..       3      18 ..       1      19 [. 0.77
   2 !   44.9   3.3   9.1e-16   5.5e-12       2      52 .]      98     147 ..      97     147 .. 0.96
   3 ?   -1.7   0.1      0.34   2.1e+03      10      24 ..     213     230 ..     209     233 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.48
                   HTH_Tnp_ISL3 29 svkavArqlgvSwtTV 44
                                   +v+   ++lgv+ +TV
  gi|121639715|ref|YP_979939.1|  3 NVRLFRALLGVDKRTV 18
                                   666667899*****99 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 9.1e-16
                   HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                    ++Pwar+++++T ++++ +++l+  + s +av++++++ w+TV  i+ r++
  gi|121639715|ref|YP_979939.1|  98 AVPWARHHAGHTYAFDDTVAWLAVAC-SKTAVCELMRIAWRTVGAIVARVW 147
                                    79************************.*******************99875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.34
                   HTH_Tnp_ISL3  10 sriTl...rleayilell 24 
                                    ++iT+   +++++i+  +
  gi|121639715|ref|YP_979939.1| 213 AQITHvsaDAADWIADVV 230
                                    444444446666666555 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.4   9.5e-13   5.6e-09       3      47 .]      47      92 ..      46      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 9.5e-13
                        zf-ISL3  3 hrCPnCgsk.tvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                   +rC +Cg+k +++++g   r++r l++g  +v+L+++ +R+ C+++
  gi|121639715|ref|YP_979939.1| 47 RRCGRCGRKaSWYDRGAGLRQWRSLDWGTVEVFLEAEAPRVNCPTH 92
                                   69*******999*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2473.98
//
Query:       gi|121639716|ref|YP_979940.1|  [L=522]
Description: propionyl-CoA carboxylase beta chain 4 accD4 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.4e-138  461.0   0.0     5e-138  460.8   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.8   0.0  2.8e-142    5e-138       4     493 ..      39     519 ..      36     520 .. 0.97

  Alignments for each domain:
  == domain 1  score: 460.8 bits;  conditional E-value: 2.8e-142
                                    TTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEEC CS
                 Carboxyl_trans   4 prGkltareridllldpgsFgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekll 83 
                                    ++G   ar ri  l+dpgsF+e+ +l +     ++    l++dgvvtg G ++Gr v v+++d+tv+gg++g++ g+k+ 
  gi|121639716|ref|YP_979940.1|  39 KKGIPSARARIYELVDPGSFMEIGALCRTPGDPNA----LYGDGVVTGHGLINGRPVGVFSHDQTVFGGTVGEMFGRKVA 114
                                    6777789**********************999999....79*************************************** PP

                                    HHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTE CS
                 Carboxyl_trans  84 kaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveet 163
                                    + +e  +  g+p++gindsgGa  riq+ v sl+ ++++ ++  ++sg +pqis+++g+caGg++Y+p+ +d v++v+++
  gi|121639716|ref|YP_979940.1| 115 RLMEWCAMVGCPIVGINDSGGA--RIQDAVTSLAWYAELGRRHELLSGLVPQISIILGKCAGGAVYSPIQTDLVVAVRDQ 192
                                    **********************..******************************************************** PP

                                    EEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSS CS
                 Carboxyl_trans 164 skifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepd 243
                                    +++f+tGpdvik v+g e+v+ +elgGa+ h +  G++h ++e++ +a + +r++ls+lP   sn ++++P+v++  ep+
  gi|121639716|ref|YP_979940.1| 193 GYMFVTGPDVIKDVTG-EDVSLDELGGAD-HQASYGNIHQVVESEAAAYQYVRDFLSFLP---SNCFDKPPVVNPGLEPE 267
                                    ****************.*******99997.88999*************************...9999*******999998 PP

                                    SH.......HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHH CS
                 Carboxyl_trans 244 rd.....lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavK 318
                                           l++ivPd+++ +yD++ev+ r++d+g+Fl++ ++ ++ +++G+Ar++G++vGvvAn++ +++G  +++++++K
  gi|121639716|ref|YP_979940.1| 268 ITghdleLDSIVPDSDNMAYDMHEVLLRIFDDGDFLDVAAQAGQAIITGYARVDGRTVGVVANQPMHMSG-AIDNEASDK 346
                                    888888788*************************************************************.********* PP

                                    HHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEE CS
                 Carboxyl_trans 319 aarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlva 398
                                    aarfir+ da+++Plv+++d++Gfl+G +qe++gi+k+G   ++a++ea+vPk+t+++rk+yGGay vm+sk++ adl++
  gi|121639716|ref|YP_979940.1| 347 AARFIRFSDAFDIPLVFVVDTPGFLPGVEQEKNGIIKRGGRFLYAVVEADVPKVTITIRKSYGGAYAVMGSKQLTADLNF 426
                                    ******************************************************************************** PP

                                    ETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEE CS
                 Carboxyl_trans 399 awptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvialel 478
                                    awptariaV+g++ga++ l ++    ++    + +a rk+ +++y+ +++ p  aa+rgf+Davidp etr  l ++ +l
  gi|121639716|ref|YP_979940.1| 427 AWPTARIAVIGADGAAQLLMKRFPDPNA---PEAQAIRKSFVENYNLNMAIPWIAAERGFIDAVIDPHETRLLLRKSMHL 503
                                    ********************99977776...567888******************************************* PP

                                    HGGGHH.HHHHHHHHH CS
                 Carboxyl_trans 479 ewkkar.klparkrrn 493
                                    + +k+   ++ rk++ 
  gi|121639716|ref|YP_979940.1| 504 LRDKQLwWRVGRKHGL 519
                                    *999997788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2829.76
//
Query:       gi|121639717|ref|YP_979941.1|  [L=1733]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-84  283.6   0.2    3.3e-83  279.1   0.1    2.9  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    7.2e-53  180.1   0.0    1.3e-52  179.3   0.0    1.4  1  Acyl_transf_1    Acyl transferase domain
    1.4e-44  150.8   0.1    3.1e-44  149.8   0.1    1.6  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      6e-21   74.6   0.2    1.2e-09   38.3   0.0    4.1  3  PP-binding       Phosphopantetheine attachment site
    9.7e-18   65.1   0.4    3.1e-17   63.5   0.0    2.1  3  Thioesterase     Thioesterase domain
    3.3e-11   43.6   0.0    9.8e-11   42.1   0.0    1.8  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    6.3e-08   32.3   0.2    2.1e-07   30.6   0.1    1.8  2  Thiolase_N       Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.014   16.1   0.1      0.014   16.1   0.1    4.7  4  Abhydrolase_6    Alpha/beta hydrolase family
      0.085   13.5   0.0       0.19   12.3   0.0    1.6  1  Adaptin_binding  Alpha and gamma adaptin binding protein p34
       0.14   12.0   0.0       0.81    9.5   0.0    2.1  2  Lipase_3         Lipase (class 3)


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.1   1.8e-86   3.3e-83       3     253 .]     118     366 ..     116     366 .. 0.95
   2 ?   -0.4   0.0       0.4   7.1e+02      93     121 ..     400     431 ..     389     462 .. 0.78
   3 ?   -0.5   0.0      0.42   7.6e+02      89     126 ..     995    1033 ..     987    1067 .. 0.79

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 1.8e-86
                                    -EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSB.TSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadkly.dpparaagkiktklggfld.vddfdpeffgisp 79 
                                    ++aivG++ rfPg  + +e++w++Llegrd+i++lp+ rw++   +  ++ar+ag  +   gg+l+ ++ fd eff + +
  gi|121639717|ref|YP_979941.1| 118 DIAIVGLSTRFPGEMNtPEQTWQALLEGRDGITDLPDGRWSEFLEEpRLAARVAGARTR--GGYLKdIKGFDSEFFAVAK 195
                                    79***********9999************************999987888888888665..99***9************* PP

                                    HHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
                  ketoacyl-synt  80 reaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagris 159
                                     ea+++dpqqr++le +weale+a +++ +l+g++vgv+iG++ +dy+ la++d++      +  ++g+ ++++ia+r+s
  gi|121639717|ref|YP_979941.1| 196 TEADNIDPQQRMALELTWEALEHARIPASSLRGQAVGVYIGSSTNDYSFLAVSDPTV--AHPYA-ITGT-SSSIIANRVS 271
                                    ***********************************************9887777555..45555.7777.********** PP

                                    HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TTSGGGTTBTTB-SB-B CS
                  ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag.llspdgrckafdpkadGfvl 238
                                    y+++++Gpsvt+dtACsSslva+h+ vq+lr+geadv++aGGv++l+tp+ + gf+++g +l+pdgr+k+f+++adG+++
  gi|121639717|ref|YP_979941.1| 272 YFYDFHGPSVTIDTACSSSLVAIHQGVQALRNGEADVVVAGGVNALITPMVTLGFDEIGaVLAPDGRIKSFSADADGYTR 351
                                    ******************************************************************************** PP

                                    B-EEEEEEEEECHHH CS
                  ketoacyl-synt 239 GEGvGavvLkrleda 253
                                    +EG G++vLkr +da
  gi|121639717|ref|YP_979941.1| 352 SEGGGMLVLKRVDDA 366
                                    ***********9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHTS-HHTC...TTGGEEEEEEE CS
                  ketoacyl-synt  93 leaawealedagltpeel...dgsrvgvfiGv 121
                                     ++ ++a +dag++p+++   +   +g ++G 
  gi|121639717|ref|YP_979941.1| 400 ADVLRRAYKDAGIDPRTVdyiEAHGTGTILGD 431
                                    567899**********9955555559998885 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.42
                                     HHHHHHHHHHHHHHHTS-HHTCTTGG.EEEEEEESSTHH CS
                  ketoacyl-synt   89 qrllleaawealedagltpeeldgsr.vgvfiGvgagdy 126 
                                      +++l++a+  l+da l p+  ++++ v  ++ ++a+ y
  gi|121639717|ref|YP_979941.1|  995 MQVALTTADAGLHDAQLIPTLARKQDeVSSMVSTMAQLY 1033
                                     6789***************77766667999999999977 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.0   7.4e-56   1.3e-52       1     314 [.     713    1034 ..     713    1038 .. 0.91

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 7.4e-56
                                     EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHH CS
                  Acyl_transf_1    1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellk 78  
                                     v+v  G G+Q + MG +L+  +++faa i++ d  ++++ g+svl+++++    +  +i+ +q+ ++a+qial ell+
  gi|121639717|ref|YP_979941.1|  713 VWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDA--QDYGIETTQVTIFAIQIALGELLR 788 
                                     79**********************************************9999..999********************* PP

                                     HTT-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHT..S-....EECCEECS...HHHHHHH..TT.E CS
                  Acyl_transf_1   79 skGvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqla..gp....gdmaavel..aeeeeklrcqddvv 148 
                                       G +paav+G SlGE A+a+ ag ls+ +a +a++ rs lm + +  +     + ma ve   +e++e   +++d+ 
  gi|121639717|ref|YP_979941.1|  789 HHGAKPAAVIGQSLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEamLFgeyiRLMALVEYsaDEIREVFSDFPDLE 866 
                                     ******************************************875422321233779999996556666666****** PP

                                     EEEEEECCCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHH CS
                  Acyl_transf_1  149 gavansprrvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstslde 226 
                                     + v++ p ++vi+g++e+++++ +r ++eg +a++ +   a+h  q+d++  +l ++l+ i p  p+    s++    
  gi|121639717|ref|YP_979941.1|  867 VCVYAAPTQTVIGGPPEQVDAILARAEAEGKFARKFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGR 944 
                                     *******************************************************************99998876555 PP

                                     H....HHHCHHHHHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS- CS
                  Acyl_transf_1  227 s....serelsaeywvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltd 300 
                                           e+  + eyw++ lr  v f   +++a+++++ +f+e++p ++ l+ +  t  + ++ ++a+l+++l r +++
  gi|121639717|ref|YP_979941.1|  945 YikpgGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALTTAD-AGLHDAQLIPTLARKQDE 1021
                                     55555999*********************************************999994.9***************99 PP

                                     HHHCHHHHHHHHHH CS
                  Acyl_transf_1  301 flvtflyllakahl 314 
                                      ++ +   +a++ +
  gi|121639717|ref|YP_979941.1| 1022 -VSSMVSTMAQLYV 1034
                                     .6666666666655 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.1   1.7e-47   3.1e-44       1     117 [.     374     491 ..     374     492 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.7e-47
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGG.SCTSE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekar.kqpla 79 
                                    +avi+gsavn+dg++n+l apn++aqa+++++a+++ag+dp++vdy+eahgtgt lgDpiE+eal +v+g+++  ++p  
  gi|121639717|ref|YP_979941.1| 374 LAVIAGSAVNHDGRSNGLIAPNQDAQADVLRRAYKDAGIDPRTVDYIEAHGTGTILGDPIEAEALGRVVGRGRPaDRPAL 453
                                    69**********************************************************************99*99*** PP

                                    EE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  80 vgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                    +g+vK+n+GHle+AaG+a+++kvvlal+h+++pp++n+
  gi|121639717|ref|YP_979941.1| 454 LGAVKTNVGHLESAAGAASMAKVVLALQHDKLPPSINF 491
                                    ************************************98 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   6.8e-13   1.2e-09       1      67 []      25      91 ..      25      91 .. 0.96
   2 !   25.6   0.0   6.7e-09   1.2e-05       6      50 ..    1241    1283 ..    1236    1304 .. 0.85
   3 !    5.9   0.0    0.0093        17      34      65 ..    1410    1441 ..    1405    1443 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 6.8e-13
                     PP-binding  1 eklrelvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                   ++lr+ v ++ g ++++id + +  +lGl S +av+++a +e+  gv++++++ f+hpt+++la ++
  gi|121639717|ref|YP_979941.1| 25 QWLRNWVGKAVGKAPDSIDESVPMVELGLSSRDAVAMAADIEDLTGVTLSVAVAFAHPTIESLATRI 91
                                   68999999*******************************************************9876 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 6.7e-09
                     PP-binding    6 lvaevlgvpleeidpdtdlfdlGlDSllavellaaleeefgveip 50  
                                     +v +++g ++e++ ++ +l +lGlDSl+av++ +++e  f++  p
  gi|121639717|ref|YP_979941.1| 1241 IVGSAMGYEPEDLPWEVPLIELGLDSLMAVRIKNRVEYDFDL--P 1283
                                     78999******************************9988854..3 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0093
                     PP-binding   34 avellaaleeefgveiplsdlfehptlaelaa 65  
                                     a++++ +l+e+ + +i+ +d+++ +++++la+
  gi|121639717|ref|YP_979941.1| 1410 AAKIAQRLSERAEGPITAEDVLTSSNIEALAD 1441
                                     7899**************************98 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       7.2   1.3e+04     125     162 ..     603     639 ..     590     685 .. 0.63
   2 ?   -3.5   0.0       5.1   9.1e+03      57      76 ..     784     803 ..     782     805 .. 0.91
   3 !   63.5   0.0   1.7e-20   3.1e-17       2     106 ..    1470    1565 ..    1469    1668 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.2
                                    HHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHHHHTCCS CS
                   Thioesterase 125 eltdlggtepeelledeellsellpalradyraleqys 162
                                    e  +l+++ + e l+ +e+++ l+p++ +++++  ++ 
  gi|121639717|ref|YP_979941.1| 603 EALRLKEA-ALEELAAQEVTAPLVPLAVSAFLTSRKKA 639
                                    44445554.55555555666666666666665544443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.1
                                    HHHHHH-SSSSEEEEEETHH CS
                   Thioesterase  57 ealrqiqpegPyalfGhSlG 76 
                                     +l++++  +P a++G SlG
  gi|121639717|ref|YP_979941.1| 784 GELLRHHGAKPAAVIGQSLG 803
                                    689999************99 PP

  == domain 3  score: 63.5 bits;  conditional E-value: 1.7e-20
                                     EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTSTSHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHH CS
                   Thioesterase    2 pLflfppagGsasvfrslasklsdpvvevlavqlpgrerdepplesieelaaeyaealrqiqpegPyalfGhSlGgll 79  
                                     p+f+f+pagGs+ v+  l  +l+++   +++ +            siee a++y+  l + q +gPy+l+G+SlGg l
  gi|121639717|ref|YP_979941.1| 1470 PVFVFHPAGGSTVVYEPLLGRLPAD-TPMYGFERVEG--------SIEERAQQYVPKLIEMQGDGPYVLVGWSLGGVL 1538
                                     79**********************8.77777766666........9******************************** PP

                                     HHHHHHHHHHCT-SEEEEEEESCCCCC CS
                   Thioesterase   80 AfevArqLesqGlavkslflidssaps 106 
                                     A++ A  L++ G  v++++lid+    
  gi|121639717|ref|YP_979941.1| 1539 AYACAIGLRRLGKDVRFVGLIDAVRAG 1565
                                     **********************86544 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   5.4e-14   9.8e-11       1      56 [.     494     552 ..     494     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 5.4e-14
                 KAsynt_C_assoc   1 PnpeipaleegrlkVvteptpwpggi....vgvNsfGfGGsnvHviLksnkkekrkeesk 56 
                                    P+p i+ ++ +rlk++t+pt+wp+       gv+sfGfGG+n+Hv++++   ++  e+++
  gi|121639717|ref|YP_979941.1| 494 PSPYID-FDAMRLKMITTPTDWPRYGgyalGGVSSFGFGGANAHVVVREVLPRDVVEKEP 552
                                    99****.****************98888999*****************988555555544 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   1.2e-10   2.1e-07      75     114 ..     277     316 ..     256     326 .. 0.85
   2 ?   -2.7   0.0       1.7   3.1e+03      25      48 ..     397     420 ..     391     423 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.2e-10
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEE CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEs 114
                                    + p+vt++ +csS+l a+++++q+++ geadvvvagGv  
  gi|121639717|ref|YP_979941.1| 277 HGPSVTIDTACSSSLVAIHQGVQALRNGEADVVVAGGVNA 316
                                    56899********************************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHTS-GGGCCEE CS
                     Thiolase_N  25 eLlaealkallekagvdpeevdev 48 
                                    + +a +l+++ ++ag+dp +vd++
  gi|121639717|ref|YP_979941.1| 397 DAQADVLRRAYKDAGIDPRTVDYI 420
                                    66789999*************987 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.1   3.8e+03     150     174 ..     163     234 ..      56     260 .. 0.49
   2 ?   -3.0   3.0       4.9   8.9e+03     135     135 ..     616     616 ..     462     740 .. 0.47
   3 ?    1.4   4.4      0.23     4e+02      53     152 ..     783     893 ..     715    1140 .. 0.70
   4 ?   16.1   0.1   7.6e-06     0.014      52     121 ..    1510    1584 ..    1451    1706 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                                    GHH.....................................HHCCHHCHTTCCHHTT-TTGC..........E CS
                  Abhydrolase_6 150 rla.....................................allaglgllpaaawadlpvpl..........l 174
                                    +++                                     +++ +  +l+++a+++++ p           +
  gi|121639717|ref|YP_979941.1| 163 EPRlaarvagartrggylkdikgfdseffavakteadnidPQQRMALELTWEALEHARIPAsslrgqavgvY 234
                                    111111111111222223333333332222222222222222223333346666666655555555544442 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                                    C CS
                  Abhydrolase_6 135 l 135
                                     
  gi|121639717|ref|YP_979941.1| 616 A 616
                                    1 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.23
                                    HHHHHCCTT..TTSEEEEEETCH.HHHHHHHHHCC...EE.EEES-.........----TTTS----TTHHHHHHTT-C. CS
                  Abhydrolase_6  53 laalldelaagggpvvlvGHSlG.Galalaaapla.lvvg.vlldp.......pptalpagllaaalelllallallrl. 121
                                    l +ll++   g++p+ ++G SlG +a a +a+ l  +  +  ++++          a  +g+  ++++l++   +  r  
  gi|121639717|ref|YP_979941.1| 783 LGELLRHH--GAKPAAVIGQSLGeAASAYFAGGLSlR-DAtRAICSrshlmgeG-EAMLFGEYIRLMALVEYSADEIREv 858
                                    24455555..68999*********8877776666643.3336666622221110.2222222333333333333322222 PP

                                    .CCCHCCH.....S-HSCCCCHHHCCCCHCHCCCGHH CS
                  Abhydrolase_6 122 .lawlsre.....plprlfladedadaawrarlarla 152
                                       ++ +e     +++++ +++++  + + a lar+ 
  gi|121639717|ref|YP_979941.1| 859 fSDFPDLEvcvyaAPTQTVIGGPP--EQVDAILARAE 893
                                    233333223333333335555555..33333333333 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 7.6e-06
                                     HHHHHHCCTT....TTSEEEEEETCHHHHHHHHHHCC......EE..EEES-..----TTTS----TTHHHHHHTT-C CS
                  Abhydrolase_6   52 dlaalldelaa..gggpvvlvGHSlGGalalaaapla....lvvg..vlldppptalpagllaaalelllallallrl 121 
                                     +  +++ +l++  g+gp vlvG+SlGG+la a a ++     +v+   l+d+   +    +++   e ++++++++++
  gi|121639717|ref|YP_979941.1| 1510 RAQQYVPKLIEmqGDGPYVLVGWSLGGVLAYACAIGLrrlgKDVRfvGLIDA---VRAGEEIPQTKEEIRKRWDRYAA 1584
                                     334455666668778888************9944433555533444355555...44444455555555555554444 PP

>> Adaptin_binding  Alpha and gamma adaptin binding protein p34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.19      82     120 ..    1291    1329 ..    1188    1330 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                Adaptin_binding   82 eaarledlesllsklqqakdnvrnlpdeeRkkeAakval 120 
                                      +a+l ++e+l++   +++d+v++l ++++ + A+++a+
  gi|121639717|ref|YP_979941.1| 1291 RDANLYNVEKLIEYAVEHRDEVQQLHEHQKTQTAEEIAR 1329
                                     455666*******************************97 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.1e+03      50      89 ..     778     817 ..     738     831 .. 0.79
   2 ?    9.5   0.0   0.00045      0.81      40      90 ..    1501    1550 ..    1484    1559 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHHHHT CS
                       Lipase_3  50 qvlkelkrllekypeysivvtGHSLGgalAlLaaldlven 89 
                                    +++  l +ll+ +     +v G SLG a ++ +a  l  +
  gi|121639717|ref|YP_979941.1| 778 AIQIALGELLRHHGAKPAAVIGQSLGEAASAYFAGGLSLR 817
                                    566678888888988889999*****99888777666555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00045
                                     HHHHHS-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHHHHTT CS
                       Lipase_3   40 leayeeslreqvlkelkrllekypeysivvtGHSLGgalAlLaaldlveng 90  
                                      ++ + s++e  ++ + +l+e + +   v++G SLGg lA  +a+ l++ g
  gi|121639717|ref|YP_979941.1| 1501 ERVEG-SIEERAQQYVPKLIEMQGDGPYVLVGWSLGGVLAYACAIGLRRLG 1550
                                     44445.889999999**************************9999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.13u 0.35s 00:00:01.48 Elapsed: 00:00:00.56
# Mc/sec: 9337.69
//
Query:       gi|121639718|ref|YP_979942.1|  [L=637]
Description: long-chain-fatty-acid--CoA ligase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-64  215.9   0.0    8.7e-64  215.7   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.7   0.0   4.9e-68   8.7e-64       2     422 ..      34     497 ..      33     498 .. 0.83

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 4.9e-68
                                    HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                    AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                    e++a+ + dk a+ +       +g  + + ++++ +r ++++a L++   ++gdrVail+p+ ++++++++++l+ G ++
  gi|121639718|ref|YP_979942.1|  34 EKWAKVRGDKLAYRFldfsterDGVARDILWSDFSARNRAVGARLQQ-VTQPGDRVAILCPQNLDYLISFFGALYSGRIA 112
                                    788999999**998899999999999*******************99.67****************************** PP

                                    EEEETTS-H...HHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-T CS
                    AMP-binding  75 vplnptlta...eelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekp 150
                                    vpl +   +    +l+ +l+d+ ++++++t+ds++ + k  +a++++   +   v+  d++++e        ++ ++  +
  gi|121639718|ref|YP_979942.1| 113 VPLFDPAEPghvGRLHAVLDDCAPSTILTTTDSAEgVRKFIRARSAK---ERPRVIAVDAVPTE-------VAATWQ--Q 180
                                    ****9777766689**************5555666666666666554...44444444455544.......222332..2 PP

                                    SCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                    AMP-binding 151 eeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGat 230
                                       +e++++++ay++YTSG+T  P GV+++h nl +nv ++ l+  +  +e+d+ +s+lp++h++gl + +lla + G++
  gi|121639718|ref|YP_979942.1| 181 ---PEANEETVAYLQYTSGSTRIPSGVQITHLNLPTNVVQV-LNALE-GQEGDRGVSWLPFFHDMGL-ITVLLASVLGHS 254
                                    ...24689*****************************9997.44444.4689**************9.999999999*** PP

                                    EEE-TTCGC.CHHHHHHHHHHH....HT-SEEEEEHHHHHHH.HH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHH CS
                    AMP-binding 231 vvllpkdaa.ldpkllleliek....lkvtviagvPrvleal.le.sgalkaakkakdlsslrlvllggeplspellrff 303
                                      ++++ a+ ++p+++++ +++     + t+ a+++ ++e+  ++    ++ ++   dls ++ +l g ep+sp+ +r+f
  gi|121639718|ref|YP_979942.1| 255 FTFMTPAAFvRRPGRWIRELARkpgeTGGTFSAAPNFAFEHAaVRgV--PRDDEPPLDLSNVKGILNGSEPVSPASMRKF 332
                                    *********888****9999841221455666666666664433322..22234445*********************** PP

                                    HHHHTC......EEEEEEEEGGGSSECEE..........................CHCTTTCTSTTS-BEE-TTEEEEEE CS
                    AMP-binding 304 ralfge......evlegYGlTEttgvvtv..........................lpleedkkklgsvGkplpgvevkiv 351
                                     + f +      +v  +YGl+E+t +v++                          + +  + + + s+Gk+     + iv
  gi|121639718|ref|YP_979942.1| 333 FEAFAPyglkqtAVKPSYGLAEATLFVSTtpmdevptvihvdrdelnnqrfvevaA-DAPNAVAQVSAGKVGVSEWAVIV 411
                                    *****9*****99**************66699999999***************963.34444566688888888889999 PP

                                    -TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE..............T.CC.EEEEEEEEEEETTSEEEEEEE CS
                    AMP-binding 352 DeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds..............e.gr.wlrTGDlgrldedGyleivgR 415
                                    D +t  ++pdg+ Ge++++g+++  gY++k+e+ a++f++              + +  w+rTGD g++  + +l+i gR
  gi|121639718|ref|YP_979942.1| 412 DADTASELPDGQIGEIWLHGNNLGTGYWGKEEESAQTFKNilksrisesraegaPdDAlWVRTGDYGTYF-KDHLYIAGR 490
                                    **************************************9788899******99845678*********86.35******* PP

                                    CCCEEEE CS
                    AMP-binding 416 kkdlikl 422
                                    +kdl+++
  gi|121639718|ref|YP_979942.1| 491 IKDLVII 497
                                    ****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.23s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4222.53
//
Query:       gi|121639719|ref|YP_979943.1|  [L=336]
Description: hypothetical protein BCG_3864c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-16   59.7   0.6    8.5e-16   58.4   0.6    1.7  1  Cutinase     Cutinase
    1.6e-09   37.7   0.1    2.5e-09   37.1   0.1    1.3  1  PE-PPE       PE-PPE domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.014   15.1   0.0    1.2  1  FSH1         Serine hydrolase (FSH1)
        0.2   10.9   0.0        0.3   10.3   0.0    1.2  1  IncFII_repA  IncFII RepA protein family
        0.3   11.3   2.0       0.62   10.2   2.0    1.5  1  CwsA         Cell wall synthesis protein CwsA


Domain annotation for each model (and alignments):
>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.6   2.4e-19   8.5e-16      30     154 ..     110     275 ..      71     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.4e-19
                                    HHHH.TTT-EEEEE------CGG........STTSS-HHHHHHHHHHHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.. CS
                       Cutinase  30 lesavgsksvavqgvnYpAdleq........lyegseeagakeaaalvqslaskCPdtkivlgGYSqGaqvidnaiegga 101
                                    +++++   +v+ ++v Y+A++++        +y++s ++g++++ a++++++++CP t  vl G+SqGa ++ +++++ +
  gi|121639719|ref|YP_979943.1| 110 IAQQFAPARVQTYTVAYTAQFHNplttdnqmSYNDSRAEGTRAMVAAMTDMNNRCPLTSYVLIGFSQGAVIAGDVASD-I 188
                                    56677778899999********99******99******************************************9999.7 PP

                                    ...S-HHHHHHEEEEEEES-TTCCCCTT...................................S-TTS-GGGEEEE--TT CS
                       Cutinase 102 tatlpaavadkvaavvlfGdpsnvaglp...................................evsklyaskikslCdag 146
                                    +    +  +d v +v l  d++ ++g++                                   ++ +    +++++C++g
  gi|121639719|ref|YP_979943.1| 189 GNGRGPVDEDLVLGVTLIADGRRQQGVGnqvppsprgegaeitlhevpvlsglgltmtgprpgGFGA-LDGRTNEICAQG 267
                                    77799999***************999999999*****************************976666.889********* PP

                                    -GGGTS-- CS
                       Cutinase 147 DpiCgsgn 154
                                    D+iC++  
  gi|121639719|ref|YP_979943.1| 268 DLICAAPA 275
                                    ****7654 PP

>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   6.9e-13   2.5e-09       4     162 ..     120     302 ..     116     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.9e-13
                         PE-PPE   4 daelvsyPasfl.pvtglksltvdeSvaeGtenLeaairaela..agekvvvfGySqgalvasnekarlaalsepaa.pd 79 
                                    +   v y a+f  p+t  +++++++S aeGt  + aa+   ++     ++v +G+Sqga++a +  ++  +   p++   
  gi|121639719|ref|YP_979943.1| 120 QTYTVAYTAQFHnPLTTDNQMSYNDSRAEGTRAMVAAMTDMNNrcPLTSYVLIGFSQGAVIAGDVASDIGNGRGPVDeDL 199
                                    66789999999625666*********************986655566779*********************999999555 PP

                         PE-PPE  80 qlsfvlvgnpnrp.............nggllarfpggltipi........lgitftgatptdsq...ydTvdvvaqYDgv 135
                                     l ++l+++  r+             +         g+ i +        lg+t tg++p   +     T+++ aq D +
  gi|121639719|ref|YP_979943.1| 200 VLGVTLIADGRRQqgvgnqvppsprgE---------GAEITLhevpvlsgLGLTMTGPRPGGFGaldGRTNEICAQGDLI 270
                                    6789******87733333333333211.........223332556667779*********988643356*********** PP

                         PE-PPE 136 adfPdy...plNllAdvNailGia..lvHtny 162
                                      +P     p Nl  ++N+++G a   vH  y
  gi|121639719|ref|YP_979943.1| 271 CAAPAQafsPANLPTTLNTLAGGAgqPVHAMY 302
                                    ****8644489**********96522678766 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.9e-06     0.014     102     128 ..     165     193 ..     113     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                           FSH1 102 p..fdGiiGFSqGaalaallaslleellk 128
                                    p     +iGFSqGa++a+ +as++ +++ 
  gi|121639719|ref|YP_979943.1| 165 PltSYVLIGFSQGAVIAGDVASDIGNGRG 193
                                    3445679***************9998876 PP

>> IncFII_repA  IncFII RepA protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.3e-05       0.3      27      84 ..     105     162 ..      86     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.3e-05
                    IncFII_repA  27 kyalkaakekdvarsellyilklkdvktglilkrerrlnehraralralveallyhln 84 
                                    k     a++ ++ar + + ++   +    l+++++   n+ ra   ra+v a+ +  n
  gi|121639719|ref|YP_979943.1| 105 KVTGPIAQQFAPARVQTYTVAYTAQFHNPLTTDNQMSYNDSRAEGTRAMVAAMTDMNN 162
                                    45556799********9999998888888889999999***************98766 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0   0.00017      0.62      84     126 ..       5      50 ..       1      55 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                           CwsA  84 krrrkrp...lllagvavavlaGGavafsivrrssrPePsslpPsv 126
                                    +rr+++    ++ ag  ++v+a   va+ i+ r  +  Ps+ pP v
  gi|121639719|ref|YP_979943.1|   5 SRRKRHRilaWIAAGAMASVVALVIVAVVIMLRGAESPPSAVPPGV 50 
                                    333333223488888889999999****9998886666******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2208.90
//
Query:       gi|121639720|ref|YP_979944.1|  [L=299]
Description: hypothetical protein BCG_3865c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-49  169.4   3.4    1.3e-49  169.1   3.4    1.0  1  Esterase      Putative esterase
  ------ inclusion threshold ------
      0.059   12.8   3.4      0.094   12.2   3.4    1.3  1  Peptidase_S9  Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   3.4   1.4e-53   1.3e-49       1     250 [.      43     293 ..      43     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.4e-53
                                    ETTTTEEEEEEEEE.CC.GGTTTEEEEEEE--T......THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSB CS
                       Esterase   1 SealgreikvqvyLPedyspgrkypvvylldGl......tgwdqnfrakelleslaregeiaeviivvvprggessfysd 74 
                                    S ++gr+i v+++       ++++++vylld++      ++w + ++a+ +l     +g     i vv p+gg++s+y++
  gi|121639720|ref|YP_979944.1|  43 SPSMGRDIPVAFL-------AGGPHAVYLLDAFnagpdvSNWVTAGNAMNTLA---GKG-----ISVVAPAGGAYSMYTN 107
                                    789**********.......99******************************4...444.....66************** PP

                                    TTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC. CS
                       Esterase  75 wdlgarfyenategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps. 153
                                    w+++           g+++++tfl++eL+++l+an+  ap g+a++G+ +GG+gA+ la+ hpdrFg+++s+S++++ps 
  gi|121639720|ref|YP_979944.1| 108 WEQD-----------GSKQWDTFLSAELPDWLAANRGLAPGGHAAVGAAQGGYGAMALAAFHPDRFGFAGSMSGFLYPSn 176
                                    **66...........***************************************************************** PP

                                    ...................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCC CS
                       Esterase 154 ...................namWgqeekeawqendpvllakelsaslkalriyldvGtseddlgeqlsveilevlarnre 214
                                                       n mWg+++ ++w+++dp+++a+ l++++++++++     +++   +  ++  ++  a+  +
  gi|121639720|ref|YP_979944.1| 177 tttngaiaagmqqfggvdtNGMWGAPQLGRWKWHDPWVHASLLAQNNTRVWVWSPTNPGAS---DPAAMIGQAAEAMGNS 253
                                    *****************************************************98754444...3456666666677777 PP

                                    HHHHCCCCCCTT-SCCCC....--SSHHHHHHHHHHCHHH CS
                       Esterase 215 lkeqlaargvegedheyd....GghsweyWraqLiaalad 250
                                    + ++ ++r+v+g+++++d    G++ w  W +qL a+ +d
  gi|121639720|ref|YP_979944.1| 254 RMFYNQYRSVGGHNGHFDfpasGDNGWGSWAPQLGAMSGD 293
                                    8889******************************999876 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.4     1e-05     0.094       9     109 ..      86     182 ..      78     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                                    HHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG CS
                   Peptidase_S9   9 lladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdl 88 
                                    +la +G+ vv++ + G   +  +++++g++++ +   + +    ++la++    +   a+ G+  GGy ++a+++ +pd+
  gi|121639720|ref|YP_979944.1|  86 TLAGKGISVVAPAG-GAYSMYTNWEQDGSKQWDTFLSAEL---PDWLAANRGLAPGGHAAVGAAQGGYGAMALAAFHPDR 161
                                    56566655555443.4444557788888888877655444...4566666767788899********************* PP

                                    -SEEEEESE---CCCHHCSTT CS
                   Peptidase_S9  89 Fkaavaevpvvdvlrydsdtd 109
                                    F+ a +  +++   ++ ++  
  gi|121639720|ref|YP_979944.1| 162 FGFAGSMSGFLYPSNTTTNGA 182
                                    *********999888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1972.76
//
Query:       gi|121639721|ref|YP_979945.1|  [L=338]
Description: hypothetical protein BCG_3866c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-78  262.0   0.3    6.7e-78  261.8   0.3    1.0  1  Esterase  Putative esterase


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.8   0.3   3.7e-82   6.7e-78       1     251 []      58     321 ..      58     321 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.8 bits;  conditional E-value: 3.7e-82
                                    ETTTTEEEEEEEEE.CC.GGTTTEEEEEEE--T......THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSB CS
                       Esterase   1 SealgreikvqvyLPedyspgrkypvvylldGl......tgwdqnfrakelleslaregeiaeviivvvprggessfysd 74 
                                    S ++gr+ikvq++     s g + p++ylldGl      +gwd+n++a+e++++++ +        vv+p+gg+ssfysd
  gi|121639721|ref|YP_979945.1|  58 SPSMGRDIKVQFQ-----SGGANSPALYLLDGLraqddfSGWDINTPAFEWYDQSGLS--------VVMPVGGQSSFYSD 124
                                    789**********.....99**************************************........************** PP

                                    TTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC. CS
                       Esterase  75 wdlgarfyenategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps. 153
                                    w+++    +++++g++++++etflt+eL+ +l+an++++p+g av+G Sm++++AL+la++hp++F +++++S++++ps 
  gi|121639721|ref|YP_979945.1| 125 WYQP----ACGKAGCQTYKWETFLTSELPGWLQANRHVKPTGSAVVGLSMAASSALTLAIYHPQQFVYAGAMSGLLDPSq 200
                                    ****....************************************************************************ PP

                                    ...................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCC CS
                       Esterase 154 ...................namWgqeekeawqendpvllakelsaslkalriyldvGtseddlgeqlsveilevlarnre 214
                                                       + mWg++e++awq+ndp+l++ +l+a+++++++y+ +G+++d +g++l++++le ++r+++
  gi|121639721|ref|YP_979945.1| 201 amgptliglamgdaggykaSDMWGPKEDPAWQRNDPLLNVGKLIANNTRVWVYCGNGKPSDLGGNNLPAKFLEGFVRTSN 280
                                    ******************************************************************************** PP

                                    HHHHCCCCCCTT-SCCCC....--SSHHHHHHHHHHCHHHH CS
                       Esterase 215 lkeqlaargvegedheyd....GghsweyWraqLiaaladl 251
                                    +k+q a+++ +g+++++d    G+hsweyW aqL+a+++dl
  gi|121639721|ref|YP_979945.1| 281 IKFQDAYNAGGGHNGVFDfpdsGTHSWEYWGAQLNAMKPDL 321
                                    *************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2553.03
//
Query:       gi|121639722|ref|YP_979946.1|  [L=627]
Description: hypothetical protein BCG_3867c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.15   11.2   1.1       0.29   10.3   1.1    1.4  1  Glyco_transf_22  Alg9-like mannosyltransferase family


Domain annotation for each model (and alignments):
>> Glyco_transf_22  Alg9-like mannosyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   1.6e-05      0.29     135     206 ..     137     212 ..      83     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.6e-05
                Glyco_transf_22 135 nslemlltsialyllsellsrenksss.....nekylvavlliavlavliRptsallwlplvlflllrlvkkrsktf 206
                                    + le  l++  l ll++++    ++       ++  l a++++a  +vl Rp++al++ + ++ +l+ ++  r+ ++
  gi|121639722|ref|YP_979946.1| 137 SGLESGLVLAYLGLLWWMMVCW-SQPLrarpdSQMFLGALAFVAGCSVLVRPEFALIGGLALIMMLIAARTWRRRVL 212
                                    5567777777777777755222.222234445555678899999999*******************66665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4084.12
//
Query:       gi|121639723|ref|YP_979947.1|  [L=302]
Description: phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-19   69.8  18.7    2.2e-19   69.8  18.7    1.4  1  UbiA       UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.023   15.0   0.4      0.071   13.4   0.4    1.8  1  Cornichon  Cornichon protein


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8  18.7   2.4e-23   2.2e-19      19     234 ..      48     266 ..      30     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.4e-23
                           UbiA  19 l....llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltal 94 
                                         + +  +++ + laa+a++++Nd+ D+e D+ ++ ++ RP+++G +  + a+++a+vl++ +l+ + ++l p +al
  gi|121639723|ref|YP_979947.1|  48 YievlSKVSMAFVVFSLAASAVYLVNDVRDVEADREHPTKRFRPIAAGVVPEWLAYTVAVVLGVTSLAGA-WMLTPNLAL 126
                                    2544455666666666******************************************************.********* PP

                           UbiA  95 lgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrka 174
                                    +++++l++ ++Y  + lK   ++++ v++ a+ + +++g +a+   ls ++ll++++  l+ +a   +  l+  e   +a
  gi|121639723|ref|YP_979947.1| 127 VMVVYLAMQLAYC-FGLKHQAVVDICVVSSAYLIRAIAGGVATKIPLSKWFLLIMAFGSLFMVAGKRYAELHLAERTGAA 205
                                    *************.9********************************999999999989999999999899988888899 PP

                           UbiA 175 giktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlv 234
                                     +k+l         +++ ++++av+l++ l+++   ++++ +++++++ +++a+lr a  v
  gi|121639723|ref|YP_979947.1| 206 IRKSLESYTSTYLRFVWTLSATAVVLCYgLWAFERDGYSGSWFAVSMIPFTIAILRYAVDV 266
                                    999988877777777666667777777777888888999999*****99999999987666 PP

>> Cornichon  Cornichon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   7.9e-06     0.071       9      83 ..      59     141 ..      53     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                      Cornichon   9 iltaallflsvyfiialsDleadyinpidlcsklNplvlpelilhafltl..lfllsgewilf.llnlpllayniyr... 82 
                                    ++   l + +vy +  + D+ead   p++  + +   v+pe ++ ++ ++  ++ l+g w+l   l+l++++y +++   
  gi|121639723|ref|YP_979947.1|  59 FVVFSLAASAVYLVNDVRDVEADREHPTKRFRPIAAGVVPEWLAYTVAVVlgVTSLAGAWMLTpNLALVMVVYLAMQlay 138
                                    4556677889********************************99999888345667789998866788888888777555 PP

                      Cornichon  83 ..v 83 
                                       
  gi|121639723|ref|YP_979947.1| 139 cfG 141
                                    541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2203.28
//
Query:       gi|121639724|ref|YP_979948.1|  [L=165]
Description: hypothetical protein BCG_3869c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   53.8   6.5      2e-14   53.5   4.2    2.1  2  PAP2      PAP2 superfamily
    8.5e-08   32.1   7.5    1.7e-07   31.1   7.5    1.5  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
      0.045   13.9   2.0      0.046   13.9   0.1    1.9  2  CwsA      Cell wall synthesis protein CwsA
      0.068   13.3   0.8        1.3    9.2   0.1    2.2  2  DUF212    Divergent PAP2 family
       0.38    8.6   0.9       0.46    8.3   0.9    1.1  1  DUF4175   Domain of unknown function (DUF4175)


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3     0.089   3.2e+02      59      99 ..      26      59 ..      15      65 .. 0.67
   2 !   53.5   4.2   5.5e-18     2e-14       6     127 ..      53     152 ..      48     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.089
                           PAP2 59 gHsafafalalllalllrrkrkkiglvllalillllavlva 99
                                    H++  + lall a  l+r+r+        ++++ + ++va
  gi|121639724|ref|YP_979948.1| 26 EHCIGWLILALLGAIALPRRRRE-------WLVAGAGAFVA 59
                                   57777778888888888888888.......44444444444 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 5.5e-18
                           PAP2   6 llalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkiglv 85 
                                    + + ++a ++ +++K lv+r+RP++ a     dt  +            sfPS H++ ++a+all+    +   +     
  gi|121639724|ref|YP_979948.1|  53 GAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQ-----------LSFPSAHATSTTAAALLMGRATGLPLPV---- 117
                                    44555677778899*******************9944...........4********9999999998888877766.... PP

                           PAP2  86 llalillllavlvalsRlylgvHflsDvlaGlliGialaala 127
                                           +l+  +alsR+ lgvH++sDv +G+++G++++a++
  gi|121639724|ref|YP_979948.1| 118 -------VLVPPMALSRILLGVHYPSDVAVGVALGATVGAIV 152
                                    .......89999*************************99875 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   7.5   4.8e-11   1.7e-07      69     187 ..      30     148 ..      16     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.8e-11
                         PAP2_3  69 atll.gllvyalfPaagPrll.eeagfvdtvaaaslag.alrdgasravllrgtieng.laafPSlHvawallvalalwr 144
                                     +l+ +ll+++++P+ +  +l + ag+  ++a a l +   r +   ++++  ++  +   +fPS H++ ++  al+   
  gi|121639724|ref|YP_979948.1|  30 GWLIlALLGAIALPRRRREWLvAGAGAFVAHAIAVLIKrLVRRQRPDHPAIAVNVDTPsQLSFPSAHATSTTAAALL--- 106
                                    44444777777777766644435555555555555555645555555555555555440467***************... PP

                         PAP2_3 145 lrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                    + r +   +l ++l+  m+++ + +g HY  Dv++Gval++ +
  gi|121639724|ref|YP_979948.1| 107 MGRAT-GLPLPVVLVPPMALSRILLGVHYPSDVAVGVALGATV 148
                                    66666.456777777789********************99865 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.3e-05     0.046      76     127 ..      34      85 ..      16      89 .. 0.75
   2 ?   -1.0   0.2       0.5   1.8e+03      12      35 ..     133     157 ..     119     165 .] 0.48

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                           CwsA  76 qaledarkkrrrkrplllagvavavlaGGavafsivrrssrPePsslpPsvd 127
                                     al +a +  rr+r++l+ag ++ v    av +    r++rP+ ++ +  vd
  gi|121639724|ref|YP_979948.1|  34 LALLGAIALPRRRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVD 85 
                                    5777888889************999887777765444556887666665555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                           CwsA  12 kysavGPvdvtrGv.vglgvesaqs 35 
                                    +y +   v v+ G+ vg  v+s+  
  gi|121639724|ref|YP_979948.1| 133 HYPSDVAVGVALGAtVGAIVDSVGG 157
                                    4444444444444334444444443 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00036       1.3      11      65 ..      54     115 ..      48     130 .. 0.64
   2 ?    2.6   0.0      0.04   1.4e+02     113     127 ..     133     147 ..     124     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00036
                         DUF212  11 lawlvaqllKvliellkek.kld...lkllv...stGgmPSsHsalvtalatavgleeglds 65 
                                    ++++va ++ vli+ l+++ + d   + + v   s+  +PS+H++  ta a+ +g  +gl  
  gi|121639724|ref|YP_979948.1|  54 AGAFVAHAIAVLIKRLVRRqRPDhpaIAVNVdtpSQLSFPSAHATSTTAAALLMGRATGLPL 115
                                    555666666666664444422223222222211145689**************999998765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.04
                         DUF212 113 HtpleVlvGallGii 127
                                    H p +V+vG+ lG++
  gi|121639724|ref|YP_979948.1| 133 HYPSDVAVGVALGAT 147
                                    99***********86 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.9   0.00013      0.46      21      87 ..      38     103 ..      19     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00013
                        DUF4175  21 sllglwqllpdllrlalllafalallaalvlplrrfrwPtraealrrlerasglphrPltaleDtla 87 
                                     ++ l++   +++ +a++ af++ ++a+l+++l+r ++P++ ++   ++  s+l    ++a + t a
  gi|121639724|ref|YP_979948.1|  38 GAIALPR-RRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAA 103
                                    2233333.345677889999******************************99998777777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1118.34
//
Query:       gi|121639725|ref|YP_979949.1|  [L=637]
Description: galactofuranosyl transferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-63  211.1   0.1    9.1e-63  210.4   0.1    1.4  1  Glft2_N          Galactofuranosyltransferase 2 N-terminal
    4.3e-50  170.7   0.0      7e-50  170.0   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0045   16.8   0.0      0.018   14.8   0.0    2.0  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.13   13.0   0.0       0.29   11.8   0.0    1.5  1  PglD_N           PglD N-terminal domain
        0.5   10.3   5.0        2.4    8.0   0.1    2.8  4  Glyco_trans_2_3  Glycosyl transferase family group 2


Domain annotation for each model (and alignments):
>> Glft2_N  Galactofuranosyltransferase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.1   2.5e-66   9.1e-63       1     140 [.       9     152 ..       9     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 2.5e-66
                        Glft2_N   1 lqrvllPregepldvrsLylveseenkerakassrtsvtipaesevsfetyfnafpasyWrrwsqldsvvLrleveGear 80 
                                    l+rv+lPr gepldvr+Lyl+es++n++ra+a++rts++i+aesevsf+tyfnafpasyWrrw++ +svvLr++v+G++r
  gi|121639725|ref|YP_979949.1|   9 LSRVILPRPGEPLDVRKLYLEESTTNARRAHAPTRTSLQIGAESEVSFATYFNAFPASYWRRWTTCKSVVLRVQVTGAGR 88 
                                    79****************************************************************************** PP

                        Glft2_N  81 vdvyrskadgsriavegkevede....eaveleldLkpfedGGwlWfdvtaetdveleeagWya 140
                                    vdvyr+ka+g+ri veg+ ++ +    +ave e+ L+pfedGGw+Wfd+t++t v+l+++gWya
  gi|121639725|ref|YP_979949.1|  89 VDVYRTKATGARIFVEGHDFTGTedqpAAVETEVVLQPFEDGGWVWFDITTDTAVTLHSGGWYA 152
                                    *******************9988788899**********************************8 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0     2e-53     7e-50       4     229 ..     162     420 ..     159     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 2e-53
                Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey.pr.vevvvvvdesdaetle..vaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                    +av +ptfn+++++++ l++l a++  +  +  v+v d++++++++  ++ ++aa+l+  r+++  +++ +gs+g+sr +
  gi|121639725|ref|YP_979949.1| 162 IAVGIPTFNRPADCVNALRELTADPLvDQvIGAVIVPDQGERKVRDhpDFPAAAARLGS-RLSIHDQPNLGGSGGYSRVM 240
                                    89***********************656636666666*******96558********99.9**87777888********* PP

                Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrstl..............vsalgalefaer 144
                                    +eal++++++ +l++DdD ++ePd++ r+l+   +++ ++ vg+++++l++ ++              ++a+   e++++
  gi|121639725|ref|YP_979949.1| 241 YEALKNTDCQQILFMDDDIRLEPDSILRVLAMHrFAKAPMLVGGQMLNLQEPSHlhimgevvdrsifmWTAAPHAEYDHD 320
                                    ********************************999999********88875555599***********9999888***** PP

                Glyco_tranf_2_3 145 hlrflaar.........ralgvltlnG.sgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfp 214
                                    +++ ++ +         r+++v+ +nG ++++i+r+v +el+++ plf+++dD+++glr+ ++g++t+++pgaa++++ +
  gi|121639725|ref|YP_979949.1| 321 FAEYPLNDnnsrskllhRRIDVD-YNGwWTCMIPRQVAEELGQPLPLFIKWDDADYGLRAAEHGYPTVTLPGAAIWHMAW 399
                                    **888888777777765777777.6**999************************************************88 PP

                Glyco_tranf_2_3 215 ss......lkayikqrnRwvy 229
                                    s+      ++ay+++rnR v+
  gi|121639725|ref|YP_979949.1| 400 SDkddaidWQAYFHLRNRLVV 420
                                    55566666**********997 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.1e-06     0.018      66     105 ..     235     274 ..     163     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHH CS
                Glycos_transf_2  66 GkagalnaglraatgdyilflDaDdepdpdwleklveale 105
                                    G+++ + ++l++++ + ilf+D+D   +pd + ++++   
  gi|121639725|ref|YP_979949.1| 235 GYSRVMYEALKNTDCQQILFMDDDIRLEPDSILRVLAMHR 274
                                    8888999*************************99997655 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.2e-05      0.29       6      35 ..     232     260 ..     230     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.2e-05
                         PglD_N   6 GaGGhgkvvadiieangeyeiigflDdnkk 35 
                                    G GG+++v ++ +++++  + i f+Dd+  
  gi|121639725|ref|YP_979949.1| 232 GSGGYSRVMYEALKNTD-CQQILFMDDDIR 260
                                    99*************99.89999***9874 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.4   8.7e+03      12      38 ..     172     198 ..     172     206 .. 0.77
   2 ?    3.7   0.1     0.014        49       2      34 ..     252     284 ..     251     323 .. 0.75
   3 ?    8.0   0.1   0.00067       2.4      77     154 ..     350     437 ..     348     465 .. 0.71
   4 ?   -3.0   0.1       1.7   5.9e+03     136     166 ..     551     591 ..     548     599 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                Glyco_trans_2_3  12 ppdclreiaaelaspevaivqgpvlvm 38 
                                    p+dc++ ++++ a+p v+ v g v+v 
  gi|121639725|ref|YP_979949.1| 172 PADCVNALRELTADPLVDQVIGAVIVP 198
                                    789999999999999999888887764 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgp 34 
                                    il++D+D +l pd++++++a+ +  ++ ++ g 
  gi|121639725|ref|YP_979949.1| 252 ILFMDDDIRLEPDSILRVLAMHRFAKAPMLVGG 284
                                    89**************99887666677766654 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00067
                Glyco_trans_2_3  77 aflrrsalqevg.....gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksplt......lraalrQrkRwayGc. 144
                                    ++++r++++e+g     +         +D d glr++++Gy ++  p+++++    ++      ++a++  r R +  + 
  gi|121639725|ref|YP_979949.1| 350 CMIPRQVAEELGqplplF------IKWDDADYGLRAAEHGYPTVTLPGAAIWHMAWSDkddaidWQAYFHLRNRLVVAAm 423
                                    678999999999855543......4457*********************8876655554566667777778888777765 PP

                Glyco_trans_2_3 145 .el...eklillvr 154
                                     ++    ++i lvr
  gi|121639725|ref|YP_979949.1| 424 hWDgpkAQVIGLVR 437
                                    54445444444444 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.7
                Glyco_trans_2_3 136 QrkRwayGc.....el.....eklillvrllgylgsllwsa 166
                                    Q +Rw++ c            + +++++r ++ ++ llw +
  gi|121639725|ref|YP_979949.1| 551 QDARWFLLCtvdgaTVttadgCGVVYRQRDRAKMFALLWQS 591
                                    66777777765443113334433333555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4173.65
//
Query:       gi|121639726|ref|YP_979950.1|  [L=399]
Description: UDP-galactopyranose mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-80  267.1   0.1    1.3e-79  266.6   0.1    1.2  1  GLF            UDP-galactopyranose mutase
    1.8e-18   66.6   0.0    3.8e-18   65.5   0.0    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    7.1e-06   25.6   0.0    1.2e-05   24.9   0.0    1.5  1  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0005   19.5   0.0     0.0011   18.4   0.0    1.5  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00076   19.5   0.0     0.0017   18.4   0.0    1.6  1  NAD_binding_9  FAD-NAD(P)-binding
     0.0013   18.4   0.1      0.003   17.2   0.1    1.8  1  DAO            FAD dependent oxidoreductase
     0.0015   17.8   0.0     0.0024   17.2   0.0    1.2  1  Thi4           Thi4 family
     0.0024   18.4   0.0      0.028   15.0   0.0    2.3  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.016   14.4   0.0       0.03   13.5   0.0    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.095   12.1   0.0       0.14   11.5   0.0    1.2  1  GMC_oxred_N    GMC oxidoreductase


Domain annotation for each model (and alignments):
>> GLF  UDP-galactopyranose mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.6   0.1   7.5e-83   1.3e-79       1     204 []     156     366 ..     156     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 266.6 bits;  conditional E-value: 7.5e-83
                                    HHTHHHHHHHHTSSGGGSBGGGGCGS-B-SSS--BS--SSEEEEBTTHHHHHHHHHTTSTTEEEESS--HHHHHH.HHHH CS
                            GLF   1 klfkgYtkKqWglkpeeldasvlkrvpvrlsyddrYfndkyqglPkeGYtklfekmldhenievrlntdffdvke.aeek 79 
                                    +++kgYt+KqW+++p+el+a+ ++r+pvr+++d+rYf+d+y+glP++GYt+++++m ++++ievrlntd+fdv+   +  
  gi|121639726|ref|YP_979950.1| 156 AFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGqLRPG 235
                                    599**********************************************************************9955566 PP

                                    TTEEEEEE-S-HHHHTTTTTS---EEEEEEEEEEESSS-SSSSSEEEESSTTSSSSEEEEGGGGCTC..S.SSSEEEEEE CS
                            GLF  80 eeakkvvytgpideyFdyklgeLeYrsldfeketldeekfqenavvnYpdeevpytrivEykhltkq..k.skktvivre 156
                                    + a++vvytgp+d+yFdy++g+L +r+ldfe e+l   +fq++av+nY+d +vpytri+E++h++++    ++ktvi+re
  gi|121639726|ref|YP_979950.1| 236 SPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPErdYpTDKTVIMRE 315
                                    7788***************************************************************76369******** PP

                                    EEEE.STTS.--EE--SHHHHHHHHHHHHHHHHCT...TEEE-HHHHTTS- CS
                            GLF 157 ypkeaeegdepyYpinteenrelyekYkelakkee...kvlfvGRLaeYkY 204
                                    y++ ae++depyYpinte++r+l++ Y+++ak+e+   kvlf+GRL++Y+Y
  gi|121639726|ref|YP_979950.1| 316 YSRFAEDDDEPYYPINTEADRALLATYRARAKSETassKVLFGGRLGTYQY 366
                                    *******************************99877779***********9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   2.1e-21   3.8e-18       1      68 []      12      81 ..      12      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.1e-21
                                   EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSSSGGG-EECETT...CEECTS---EEETTHHHHCHHHHCCC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrlGGraasyevpg...vrvdygahifhgsgyypnvrrllrel 68
                                   +vG+G++Gl++A + a + +++vl+le+r+++GG+a+s+  p+    +++ygah fh+s  +++v++++r++
  gi|121639726|ref|YP_979950.1| 12 VVGSGFFGLTIAERVATQlDKRVLVLERRPHIGGNAYSEAEPQtgiEVHKYGAHLFHTS--NKRVWDYVRQF 81
                                   8*************99888********************9976679************6..7*******986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   6.5e-09   1.2e-05       3      80 ..      19      95 ..      19     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.5e-09
                                   HHHHHHHHHHTT.EEEEEEESSSSSBTTS-EEEET..TEEEES...S--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEEE CS
                  Amino_oxidase  3 GLaaArqLlsaG.fdVtvlEardrvGGRirtvrsd..Gyliel...Gamwftgagnpllellkelgledslslpdpgapkrv 78
                                   GL+ A + +++   +V+vlE r+++GG ++++  +  G  ie+   Ga+ f+ ++  ++ +++++   d   + d+ ++ ++
  gi|121639726|ref|YP_979950.1| 19 GLTIAERVATQLdKRVLVLERRPHIGGNAYSEAEPqtG--IEVhkyGAHLFHTSNKRVWDYVRQFT--D---FTDYRHRVFA 93
                                   88888888888889*********************666..444446******************42..2...3344433333 PP

                                   EE CS
                  Amino_oxidase 79 ls 80
                                    +
  gi|121639726|ref|YP_979950.1| 94 MH 95
                                   44 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.2e-07    0.0011       1      95 [.       9     128 ..       9     148 .. 0.60
   2 ?   -2.3   0.0       1.2   2.1e+03      88     113 ..     203     228 ..     135     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.2e-07
                   FAD_oxidored   1 DvvVvGGgpaGvaAA.iaAaraGakvlLveergvlGGlltsglvatdignkaee......qvvtgiareflerlrqrgga 73 
                                    D+ VvG+g  G++ A   A + +++vl++e+r+++GG++ s++  + +g + ++      +  ++ +++++++ ++ +++
  gi|121639726|ref|YP_979950.1|   9 DLFVVGSGFFGLTIAeRVATQLDKRVLVLERRPHIGGNAYSEAE-PQTGIEVHKygahlfHTSNKRVWDYVRQFTDFTDY 87 
                                    899********87552779999*****************99995.33333333334556633333333444444342222 PP

                   FAD_oxidored  74 .......rlkkrskwn................tfepevakavlee 95 
                                           ++++    +                 f pe a++++ e
  gi|121639726|ref|YP_979950.1|  88 rhrvfamHNGQ----AyqfpmglglvsqffgkYFTPEQARQLIAE 128
                                    12223222122....122344556666666666666666666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                   FAD_oxidored  88 vakavleemlaeagvtvllntrlvev 113
                                     ++a l++m a+++++v lnt+  +v
  gi|121639726|ref|YP_979950.1| 203 GYTAWLQNMAADHRIEVRLNTDWFDV 228
                                    45566677777777777777776665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.3e-07    0.0017       2      91 ..      12     103 ..      11     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.3e-07
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerga... 78 
                                    +vG G+ Gl+++er++ +     + ++ + +++++  g +++++ +++  + v+    +lf+  ++  ++++r+  +   
  gi|121639726|ref|YP_979950.1|  12 VVGSGFFGLTIAERVATQL----DKRVLVLERRPHIGGNAYSEA-EPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDftd 86 
                                    8*****************7....889******999627666666.788999***********999666666666555332 PP

                  NAD_binding_9  79 .lee....aeeldpddfv 91 
                                            +++ + ++f+
  gi|121639726|ref|YP_979950.1|  87 yR-HrvfaMHNGQAYQFP 103
                                    21.023444555555554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.7e-06     0.003       1      37 [.       9      47 ..       9     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                                   EEEEECTSHHHHHHHHHHHHT.T..EEEEESSSSTTSSGG CS
                            DAO  1 dvviiGGGiiGlstAyeLarr.g..VtllekgdiagsgaS 37
                                   d+ ++G+G +Gl++A   a++    V++le+++ +g g  
  gi|121639726|ref|YP_979950.1|  9 DLFVVGSGFFGLTIAERVATQlDkrVLVLERRPHIG-GNA 47
                                   678***************9776469*******9999.433 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-06    0.0024      16      58 ..       6      48 ..       3      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                   TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                           Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                   a  D+ +vG+G  GLt a  +a++ d +v++ler+  +GG a+
  gi|121639726|ref|YP_979950.1|  6 ARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAY 48
                                   56799**********************************9876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.028       2      36 ..      10      46 ..       9      61 .. 0.83
   2 ?    0.4   0.0      0.53   9.6e+02      44      62 ..     206     224 ..     200     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                   EEEECSSHHHHHHHHHH.HHTTSEEEEEESSSSSS.T CS
                      Pyr_redox  2 vvvvGgGyiglElAgal.aelgkkVtvversdkll.r 36
                                   + vvG+G+ gl  A+   ++l k+V v+er++++  +
  gi|121639726|ref|YP_979950.1| 10 LFVVGSGFFGLTIAERVaTQLDKRVLVLERRPHIGgN 46
                                   57************987477*************9933 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.53
                                    HHHHHHHHHTTEEEECSEE CS
                      Pyr_redox  44 kilqeklekngievllntk 62 
                                    ++lq+   ++ iev+lnt 
  gi|121639726|ref|YP_979950.1| 206 AWLQNMAADHRIEVRLNTD 224
                                    7899999**********96 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05      0.03     144     192 ..       9      51 ..       2      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                    EEEEES-SHHHHHHHHH.HHHHT-EEEEEESSSSSSTTS-HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaa.laklgkevtlveardrllraldkelsaaleea 192
                                    ++ vvG+G+ G+ +A   +++l k+v ++e+r+++        ++a+ ea
  gi|121639726|ref|YP_979950.1|   9 DLFVVGSGFFGLTIAERvATQLDKRVLVLERRPHIG-------GNAYSEA 51 
                                    578************9868999************98.......3444444 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.7e-05      0.14       2      56 ..       9      71 ..       8      97 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                    GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvle....aggreknrl....imvlalalklidkkln 56
                                   d  v+g+G +g ++A+R +++ +++vlvle    +gg+ ++ +     +++ +   ++++ +n
  gi|121639726|ref|YP_979950.1|  9 DLFVVGSGFFGLTIAERVATQLDKRVLVLErrphIGGNAYSEAepqtGIEVHKYGAHLFHTSN 71
                                   66799************************9444345554444445452233333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2701.45
//
Query:       gi|121639727|ref|YP_979951.1|  [L=284]
Description: hypothetical protein BCG_3872 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.1  20.2    7.2e-06   25.6   7.7    3.5  4  GLTT      GLTT repeat (6 copies)


Domain annotation for each model (and alignments):
>> GLTT  GLTT repeat (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0      0.87   1.6e+04      15      17 ..      64      66 ..      63      70 .. 0.47
   2 !   17.7   4.6   1.2e-07    0.0022       8      28 .]      85     105 ..      85     105 .. 0.92
   3 !   25.6   7.7     4e-10   7.2e-06       1      28 []      93     120 ..      93     120 .. 0.98
   4 ?   -0.0   0.1     0.045   8.1e+02      14      19 ..     158     163 ..     157     164 .. 0.36

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.87
                           GLTT 15 mGL 17
                                   +GL
  gi|121639727|ref|YP_979951.1| 64 QGL 66
                                   233 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.2e-07
                           GLTT   8 vslGLvtmGLvtlGLvtmGLv 28 
                                    +s GL+ +GL+++GL+++GL+
  gi|121639727|ref|YP_979951.1|  85 ASTGLTGPGLTSPGLTSPGLT 105
                                    589****************96 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 4e-10
                           GLTT   1 GLvtlGLvslGLvtmGLvtlGLvtmGLv 28 
                                    GL+++GL+s+GL+++GL+ + L+++GL+
  gi|121639727|ref|YP_979951.1|  93 GLTSPGLTSPGLTSPGLTDPALTSPGLT 120
                                    9**************************7 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.045
                           GLTT  14 tmGLvt 19 
                                    t+GL++
  gi|121639727|ref|YP_979951.1| 158 TPGLTS 163
                                    333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1974.84
//
Query:       gi|121639728|ref|YP_979952.1|  [L=539]
Description: hypothetical protein BCG_3873 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-19   69.3   8.9    9.9e-16   58.0   0.9    4.9  4  LGFP       LGFP repeat
    3.5e-15   56.6   0.0    6.5e-15   55.7   0.0    1.4  1  Amidase_2  N-acetylmuramoyl-L-alanine amidase


Domain annotation for each model (and alignments):
>> LGFP  LGFP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.053   4.8e+02      16      42 ..     343     384 ..     336     386 .. 0.55
   2 !    7.1   0.2   0.00091       8.2      38      52 ..     403     417 ..     399     418 .. 0.85
   3 !   58.0   0.9   1.1e-19   9.9e-16       1      53 []     420     471 ..     420     471 .. 0.93
   4 !    3.9   0.0    0.0086        77       1      32 [.     473     502 ..     473     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.053
                           LGFP  16 G.ryqhFegGsi......yWspatG........ahavkgaIr 42 
                                    G  y +F gG+i      + + + G        a+av+ +Ir
  gi|121639728|ref|YP_979952.1| 343 GsSYTTFPGGAIarlpaiFTHRDVGntdcpgnaAYAVMDEIR 384
                                    448999999966222222444444444444444566665555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00091
                           LGFP  38 kgaIrdkWaalGwer 52 
                                     gaI+++W+alG+ +
  gi|121639728|ref|YP_979952.1| 403 GGAIYQRWQALGGMN 417
                                    58**********965 PP

  == domain 3  score: 58.0 bits;  conditional E-value: 1.1e-19
                           LGFP   1 LGyPttdetatpdggGryqhFegGsiyWspatGahavkgaIrdkWaalGwerG 53 
                                    LG+Pt++e++ +++g ry +F +G++yWsp t a++++gaI+++Wa++ +erG
  gi|121639728|ref|YP_979952.1| 420 LGAPTSPEAD-AADGARYATFAKGAMYWSPVTDAQPITGAIYEAWASQSYERG 471
                                    9*******88.44455************************************8 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.0086
                           LGFP   1 LGyPttdetatpdggGryqhFegGsiyWspat 32 
                                    LG Pt+ e + p      q+F++G++     t
  gi|121639728|ref|YP_979952.1| 473 LGLPTSAEIQEPLQ--ITQNFQHGTLNFERLT 502
                                    8*******996665..6999999987655555 PP

>> Amidase_2  N-acetylmuramoyl-L-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   7.3e-19   6.5e-15       5     125 ..     221     373 ..     217     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 7.3e-19
                                    EEEEEEEEBSS.-HHHHHHHHHHSHHHH........TTTS...S-SEEE-SSSSEEESS-TTCEES.........SSSSE CS
                      Amidase_2   5 idfiviHhtagssaagalavaaaeyaas........tngs..igyhylidkdGtiyqlvdengraw.........Hagdk 65 
                                    +++ v+Hhtags++ + l++a      +        t g+  i y+ l+dk+G++++     g a+         H+g  
  gi|121639728|ref|YP_979952.1| 221 VRAAVVHHTAGSNDYSPLESAGIV---KaiytyhskTLGWcdIAYNALVDKYGQVFE-----GSAGgltkpvegfHTG-- 290
                                    8999*******9887666553322...13445666667777777*************.....8888888899999*99.. PP

                                    HCHHGEEEEEESSTTEEESCHHHHHHHHHHHHHHHHHHHHTEEEGGG.......................EEEHHHH.TB CS
                      Amidase_2  66 ggNdnsigIElvgngdgkeppteaqyealakLvaallkrygippdrr.......................vvgHsdi.rk 121
                                    g+N+n+ g++++gn+ ++ +pt+ q++++ +L+ + l   +++p++                        +  H+d+ ++
  gi|121639728|ref|YP_979952.1| 291 GFNRNTWGVAMIGNF-DDVAPTPIQIRTVGRLLGWRLGMDDVDPRSMvdlqsagssyttfpggaiarlpaIFTHRDVgNT 369
                                    ***************.********************99999998777999999**********9999999999*9999** PP

                                    -TTC CS
                      Amidase_2 122 tdPg 125
                                    ++Pg
  gi|121639728|ref|YP_979952.1| 370 DCPG 373
                                    ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3442.13
//
Query:       gi|121639729|ref|YP_979953.1|  [L=504]
Description: PE-PGRS family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-32  111.3  11.3      2e-32  111.3  11.3    4.1  5  PE             PE family
  ------ inclusion threshold ------
        1.6    9.2  15.0      0.051   14.0   6.4    3.0  3  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3  11.3   2.3e-36     2e-32       1      93 []       1      93 [.       1      93 [. 0.99
   2 ?    3.0   0.8     0.014   1.3e+02      40      76 ..     102     135 ..      95     142 .. 0.72
   3 ?    1.3   2.7     0.047   4.2e+02      50      87 ..     160     197 ..     157     203 .. 0.86
   4 ?   -3.2   0.0       1.2   1.1e+04       8      35 ..     315     342 ..     313     350 .. 0.73
   5 ?   -2.9   0.3         1   9.2e+03      11      29 ..     374     392 ..     371     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 2.3e-36
                                   XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  1 MsfvvvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqfvqalaa 82
                                   Msfvv++Pea+aaaa+dla+igs+l++a+aaaa+ptt+++aaaaD+VS+a+++lf+ ++qe+q++s q aafh++fv++l++
  gi|121639729|ref|YP_979953.1|  1 MSFVVTVPEAVAAAAGDLAAIGSTLREATAAAAGPTTGLAAAAADDVSIAVSQLFGRYGQEFQTVSNQLAAFHTEFVRTLNR 82
                                   9********************************************************************************* PP

                                   HHHHHHS--XX CS
                             PE 83 aagsYaaaEaa 93
                                   +a++Y ++E a
  gi|121639729|ref|YP_979953.1| 83 GAAAYLNTESA 93
                                   ********975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                                    --SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  40 laaaaDeVSaaiAalfsahaqeyqalsaqaaafheqf 76 
                                    + a++  VSaa+Aa   a + +y +l a  a+ +e +
  gi|121639729|ref|YP_979953.1| 102 IEAGQRAVSAAAAA---APGGAYGQLVANTATNLESL 135
                                    56888999999998...66677777777777666655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.047
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  50 aiAalfsahaqeyqalsaqaaafheqfvqalaaaagsY 87 
                                    +iAa++++  q++ al a   a ++ +vq++ a  ++Y
  gi|121639729|ref|YP_979953.1| 160 QIAAALANAVQNFPALVANLPAAIDAAVQQFLAFNAAY 197
                                    79999999999999***999999999999887776666 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE   8 Pealaaaaadlagigsalsaanaaaaap 35 
                                    P +l++ +++ +++ ++ls  n +a a+
  gi|121639729|ref|YP_979953.1| 315 PSILRDMSQNFTNVLTTLSNPNIQAVAS 342
                                    7788888888888888888877776665 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHH CS
                             PE  11 laaaaadlagigsalsaan 29 
                                    l a a+  ++i +al a n
  gi|121639729|ref|YP_979953.1| 374 LNAIATSAETIEQALLAGN 392
                                    6677788888888877766 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.4   5.7e-06     0.051       8      98 ..       7      98 ..       1     100 [. 0.90
   2 ?   -1.8   0.1      0.49   4.4e+03      32      48 ..     108     125 ..      99     141 .. 0.42
   3 ?   -1.7   0.2      0.46   4.1e+03      48      58 ..     162     172 ..     147     197 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-06
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaaagasaavlds.hGpicaatndavaaaeaarraagealaaasteLadkLraAAaaYe 88
                                   +p+++ ++a ++ ++ ++++ a+aaaag ++ ++      ++ a+ + +  + +  ++  ++laa +te+ + L+  AaaY 
  gi|121639729|ref|YP_979953.1|  7 VPEAVAAAAGDLAAIGSTLREATAAAAGPTTGLAAAaADDVSIAVSQLFGRYGQEFQTVSNQLAAFHTEFVRTLNRGAAAYL 88
                                   79************************887777665504579999999*********************************** PP

                  T7SS_ESX_EspC 89 atDeeaagal 98
                                   +t+++++g+l
  gi|121639729|ref|YP_979953.1| 89 NTESANGGQL 98
                                   *******998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
                  T7SS_ESX_EspC  32 aa.agasaavldshGpic 48 
                                    a+ a a+aa    +G + 
  gi|121639729|ref|YP_979953.1| 108 AVsAAAAAAPGGAYGQLV 125
                                    331222222222333333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.46
                  T7SS_ESX_EspC  48 caatndavaaa 58 
                                     aa+++av+++
  gi|121639729|ref|YP_979953.1| 162 AAALANAVQNF 172
                                    22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3474.42
//
Query:       gi|121639730|ref|YP_979954.1|  [L=273]
Description: hypothetical protein BCG_3875c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-56  191.8   0.0      2e-56  191.6   0.0    1.0  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
    4.8e-11   42.7   0.0    2.8e-06   27.0   0.0    2.1  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    8.4e-09   36.1   3.5     0.0046   17.4   0.0    3.2  3  HAD          haloacid dehalogenase-like hydrolase
      1e-07   32.5   4.2    0.00011   22.6   0.1    2.9  2  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.07   13.2   0.0       0.25   11.5   0.0    1.9  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
       0.13   12.3   0.1        5.2    7.1   0.0    2.2  2  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0   6.8e-60     2e-56       1     255 []       9     268 ..       9     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 6.8e-60
                                    EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEEEE--B CS
                    Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkilyksti 79 
                                    +a+D+DGTLl+++++++++t++a++ + ++g ++++ATGR++r+v+p++++lg+  +++++NGa+i d  ++++ + +t+
  gi|121639730|ref|YP_979954.1|   9 VACDVDGTLLDDGETVTKRTRDAVHAAVDAGTHFILATGRPPRWVRPIVDALGFAPMAVCANGAVIyDPGTDRVTSVRTL 88 
                                    79****************************************************************999*********** PP

                                    -HHHHHHHHHHHHHTT..CEEEEEESSEEEESTT..THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HHHHHH CS
                    Hydrolase_3  80 skedvkeiikllkenn..veillytedkvyvlnk.eksekkkkeeektkkkkeeidseeeledeeiakililkdkeklde 156
                                    + +++  + + +        +++++  +    ++  ++ ++  +e+ + + +++  s + l + +++k+li k    + +
  gi|121639730|ref|YP_979954.1|  89 PVDALATLAEVATRVIpgAGLAVERIGERAHDTAtPQFVSSPGYEHAWLNPDNTEVSIDHLLSAPAIKLLIRKAGAASAD 168
                                    ************99988877777775555555555788****************************************** PP

                                    HHHHHHHHCTTTE.EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHH CS
                    Hydrolase_3 157 lekelksklnkll.titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseev 235
                                    +++el+++++ +   ++s+++g +ei+p g+sK+t++ ++a  l+is +ev+afGD+ ND++ML +aglgvAmgna++ +
  gi|121639730|ref|YP_979954.1| 169 MAAELAKHVGFEGdITYSTNNGLVEIVPLGISKATGVDEIARPLGISDAEVVAFGDMPNDVPMLLRAGLGVAMGNAHPDA 248
                                    ********9988866677788999******************************************************** PP

                                    HHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 236 kkaAdyvtksnnedGVakal 255
                                     ++Ad vt+ n+edGVa++l
  gi|121639730|ref|YP_979954.1| 249 LAVADEVTAPNSEDGVARVL 268
                                    *****************997 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.1e-05     0.033       3      74 ..       7      76 ..       5      86 .. 0.83
   2 !   27.0   0.0   9.4e-10   2.8e-06     137     222 ..     170     257 ..     158     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                   EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE CS
                           S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyy 74
                                    l++ d+D+tl+d  +  ++r ++ ++a+ +  + +++aTGR +  ++ ++       P +++++ G+ iy+
  gi|121639730|ref|YP_979954.1|  7 ALVACDVDGTLLDDGETVTKRTRDAVHAAVDAGTHFILATGRPPRWVRPIVDALGFA-P-MAVCANGAVIYD 76
                                   68899*******8888899999*****9*****************999998876653.3.667777777776 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 9.4e-10
                                    HHHHHTT.TS-EEEEEETTT.EEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHH CS
                           S6PP 137 eqlLekr.eldvkviyssgk.dlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeell 214
                                     ++L k+ + + ++ ys ++  + ++P + sk+  +  +a+ l++   +++  Gd  nD  +l+   lgV +gna++  l
  gi|121639730|ref|YP_979954.1| 170 AAELAKHvGFEGDITYSTNNgLVEIVPLGISKATGVDEIARPLGISDAEVVAFGDMPNDVPMLLRAGLGVAMGNAHPDAL 249
                                    44454433678889999765278******************************************************988 PP

                                    HHHHHH-- CS
                           S6PP 215 qwllenak 222
                                    + ++e ++
  gi|121639730|ref|YP_979954.1| 250 AVADEVTA 257
                                    87776555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.9     0.024        71       1      13 [.       9      21 ..       9      29 .. 0.82
   2 !   14.3   0.0   1.4e-05     0.041      90     130 ..      28      70 ..      22     101 .. 0.75
   3 !   17.4   0.0   1.5e-06    0.0046     143     187 ..     190     232 ..     154     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.024
                            HAD  1 alfDfDgTLldgd 13
                                   + +D+DgTLld+ 
  gi|121639730|ref|YP_979954.1|  9 VACDVDGTLLDDG 21
                                   579*******983 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.4e-05
                            HAD  90 alellaahraaGdrvvvvSgglrplvepllaelg..adevlat 130
                                     +++++a+ +aG ++++ +g + ++v+p+ ++lg  + +v a+
  gi|121639730|ref|YP_979954.1|  28 TRDAVHAAVDAGTHFILATGRPPRWVRPIVDALGfaPMAVCAN 70 
                                    5678887779************************744444444 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1.5e-06
                            HAD 143 glegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                    gl + +  g  k++ ++e   a++ gi+ +evva+GD p+D+p+l
  gi|121639730|ref|YP_979954.1| 190 GLVEIVPLGISKATGVDE--IARPLGISDAEVVAFGDMPNDVPML 232
                                    455555566678888999..999*********************8 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.5    0.0014       4.1       3      35 ..       8      45 ..       6      60 .. 0.57
   2 !   22.6   0.1   3.5e-08   0.00011     146     210 .]     168     236 ..     151     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                   EEEEESBTTTB.CHH...HHHHHHHHHH.CHHHHHHHH CS
                                   xxxxxxxxxxx.xxx...xxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase  3 tvvfDkdGTLt.tge...psvedvivsa.alalaaale 35
                                   +v+ D+dGTL+ +ge   ++ +d++  a +     +l+
  gi|121639730|ref|YP_979954.1|  8 LVACDVDGTLLdDGEtvtKRTRDAVHAAvDAGTHFILA 45
                                   689999****9555544444444444444333444444 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.5e-08
                                    HHHHHHHHHTT...GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxx...xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 146 etaeraanqlG...ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                     +a ++a+++G   d ++  ++  ++i+  +  +  g+ +++r L+++ +ev+++GD +nD+++l +Ag
  gi|121639730|ref|YP_979954.1| 168 DMAAELAKHVGfegDITYsTNNGLVEIVPLGISKATGVDEIARPLGISDAEVVAFGDMPNDVPMLLRAG 236
                                    578899*****6653333355556666669999********************************9997 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.2e-05      0.25       1      39 [.       9      48 ..       9      69 .. 0.85
   2 ?   -2.4   0.0       1.8   5.3e+03      14      29 ..     102     117 ..      99     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                                   EEEESTTTSEE.TTEE-TTHHHHHHHHHHTT-EEEEEE-- CS
                    Hydrolase_6  1 flfDidGvLwr.gdkaipgaaealnalraagkpvvllTNn 39
                                   +++D+dG+L++ g+++ +   +a++a  +ag +++l T +
  gi|121639730|ref|YP_979954.1|  9 VACDVDGTLLDdGETVTKRTRDAVHAAVDAGTHFILATGR 48
                                   579*******847778999*****************9964 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                    EE-TTHHHHHHHHHHT CS
                    Hydrolase_6  14 kaipgaaealnalraa 29 
                                    ++ipga  a++++ ++
  gi|121639730|ref|YP_979954.1| 102 RVIPGAGLAVERIGER 117
                                    7899999999998776 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.033        99       4      22 ..      12      30 ..       9      41 .. 0.84
   2 ?    7.1   0.0    0.0017       5.2     138     176 ..     202     240 ..     196     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.033
                          HAD_2  4 DlDgTlldteeliiqafne 22
                                   D+DgTlld  e++ + ++ 
  gi|121639730|ref|YP_979954.1| 12 DVDGTLLDDGETVTKRTRD 30
                                   9*******99999887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0017
                          HAD_2 138 peviekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                    ++ + ++ + l+++ +ev+ +GD p+D+    +ag+ v+
  gi|121639730|ref|YP_979954.1| 202 ATGVDEIARPLGISDAEVVAFGDMPNDVPMLLRAGLGVA 240
                                    5678899999******************99999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1974.38
//
Query:       gi|121639731|ref|YP_979955.1|  [L=261]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-30  104.7   0.0    3.6e-30  104.3   0.0    1.2  1  Acyltransferase  Acyltransferase
  ------ inclusion threshold ------
      0.092   11.9   0.1       0.19   10.8   0.1    1.5  1  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   4.1e-34   3.6e-30       1     134 [.      23     149 ..      23     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 4.1e-34
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraag 80 
                                    k++++glen+pe g+a+++ NH+sy+D++  + ++++++  r+++++ k+e+++++ ++ ++++++ i++dR   +++a 
  gi|121639731|ref|YP_979955.1|  23 KITFEGLENIPERGGALIALNHTSYVDWVPASIAAHHRR--RRLRFMIKAEMQDVRAVNYVIKHAQLIPVDR---SVGAD 97 
                                    5899*******************************8888..9******************************...999** PP

                Acyltransferase  81 sleniselleegklvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                    +++ ++++l++g+lv++ PE t sr+ el++fk+G++r+a++a  +vpi+P+ +
  gi|121639731|ref|YP_979955.1|  98 AYAVAVQRLRAGELVGLHPEATISRSLELREFKTGAARMALEA--QVPIIPMIV 149
                                    *******************************************..******986 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.1e-05      0.19     104     240 ..      23     150 ..       8     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.1e-05
                Lip_A_acyltrans 104 rveviglehikealaeeegvilllpHfanwelaglvlakqyp....glavvaenkknpllnqliislRerfggkllprkn 179
                                    +++++gle+i     e  g++++l H  +++ +   +a ++      + + ae +  + +n++i +       + +   +
  gi|121639731|ref|YP_979955.1|  23 KITFEGLENIP----ERGGALIALNHTSYVDWVPASIAAHHRrrrlRFMIKAEMQDVRAVNYVIKHAQLIPVDRSVGADA 98 
                                    57799999999....8899************9999999999866544555566677788888887776666666665555 PP

                Lip_A_acyltrans 180 aikelikalrkgevvvllpDqdlgrkdsvfvpfFgepaatttspaklalktkaavipvaii 240
                                        ++++lr ge+v+l p+  + r+         e     t++a++al+ + ++ip+ ++
  gi|121639731|ref|YP_979955.1|  99 -YAVAVQRLRAGELVGLHPEATISRS--L------ELREFKTGAARMALEAQVPIIPMIVW 150
                                    .9*********************999..3......33445789999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2184.19
//
Query:       gi|121639732|ref|YP_979956.1|  [L=251]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-32  112.6   0.0    1.4e-32  112.1   0.0    1.2  1  Acyltransferase  Acyltransferase
     0.0076   15.5   0.0      0.012   14.8   0.0    1.2  1  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   1.6e-36   1.4e-32       1     134 [.      23     149 ..      23     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1.6e-36
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraag 80 
                                    ++++ g+en+p +g+a+++ NH+sy+D+l  +l++++++  r+++++ k+e+++++l++fl+r++++i++dR   + + +
  gi|121639732|ref|YP_979956.1|  23 RITYVGEENVPDQGGAVVAINHTSYVDWLPAALAMHRRR--RRMRFMIKAEMQRVRLVNFLIRHTRTIPVDR---GAGGS 97 
                                    578899***************************997777..9******************************...77788 PP

                Acyltransferase  81 sleniselleegklvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                    +++ ++++l+eg+lv+++PE t sr++el  fk+G++r+aa+a  +vpivPv++
  gi|121639732|ref|YP_979956.1|  98 AYAVAVQRLREGELVGVYPEATISRSFELKGFKTGAARMAAEA--DVPIVPVVV 149
                                    9999999************************************..*******97 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.3e-06     0.012     105     241 ..      24     151 ..      20     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
                Lip_A_acyltrans 105 veviglehikealaeeegvilllpHfanwel..aglvlakqypglavv..aenkknpllnqliislRerfggkllprkna 180
                                    ++  g+e++      + g+++++ H  +++   a+l ++ +   + ++  ae ++ +l+n li ++R     +     +a
  gi|121639732|ref|YP_979956.1|  24 ITYVGEENVP----DQGGAVVAINHTSYVDWlpAALAMHRRRRRMRFMikAEMQRVRLVNFLIRHTRTIPVDRGAG-GSA 98 
                                    5566677776....7899*********9996446677888777777772256677888888888888765444443.444 PP

                Lip_A_acyltrans 181 ikelikalrkgevvvllpDqdlgrkdsvfvpfFgepaatttspaklalktkaavipvaiir 241
                                       ++++lr+ge+v++ p+  + r+       F   +   t++a++a++   +++pv+++ 
  gi|121639732|ref|YP_979956.1|  99 YAVAVQRLREGELVGVYPEATISRS-------FEL-KGFKTGAARMAAEADVPIVPVVVWG 151
                                    ************************9.......443.445689999***********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1995.34
//
Query:       gi|121639733|ref|YP_979957.1|  [L=259]
Description: acyltransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-34  117.1   0.0    5.4e-34  116.7   0.0    1.2  1  Acyltransferase  Acyltransferase
    0.00018   20.8   0.0    0.00024   20.4   0.0    1.1  1  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera
  ------ inclusion threshold ------
       0.14   12.3   0.3          1    9.5   0.0    2.4  2  THDPS_M          Tetrahydrodipicolinate N-succinyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   9.1e-38   5.4e-34       1     134 [.      22     150 ..      22     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 9.1e-38
                Acyltransferase   1 kvrvtglenlpekgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnaraa 79 
                                    k++vtg +nlp++g+a+++ NH+sylD+ +  l +y+++ g r+v+++ak+e+++ +++g++mr+l++i++dR   +++ 
  gi|121639733|ref|YP_979957.1|  22 KITVTGVDNLPTSGGAVVAINHTSYLDFTFAGLPAYQQGlG-RKVRFMAKQEVFDHKITGPIMRSLRHIPVDR---QDGS 97 
                                    689************************************88.*******************************...9999 PP

                Acyltransferase  80 gsleniselleegklvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                    +s++ ++++l++g+lv+++PE t sr++e+ +fk+G++r+a++a  gvpivP  +
  gi|121639733|ref|YP_979957.1|  98 ASYDAAVRMLKAGELVGVYPEATISRSFEIKEFKTGAARMAIEA--GVPIVPHIV 150
                                    ********************************************..******865 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     4e-08   0.00024     110     245 ..      28     156 ..       9     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4e-08
                Lip_A_acyltrans 110 lehikealaeeegvilllpHfanwelaglvlakqypglav.vaenkknpllnqliislRerfggkl.lprkna...ikel 184
                                     +++        g+++++ H  +++  +  l  +++gl+  v+  +k ++++++i+   +r+  ++ ++r+++      +
  gi|121639733|ref|YP_979957.1|  28 VDNLP----TSGGAVVAINHTSYLDFTFAGLPAYQQGLGRkVRFMAKQEVFDHKITGPIMRSLRHIpVDRQDGsasYDAA 103
                                    55555....7789***********************999636667889********9887776666599***99999*** PP

                Lip_A_acyltrans 185 ikalrkgevvvllpDqdlgrkdsvfvpfFgepaatttspaklalktkaavipvaiirkkdg 245
                                    +++l+ ge+v++ p+  + r+       F  +++  t++a++a++ + +++p  ++  ++ 
  gi|121639733|ref|YP_979957.1| 104 VRMLKAGELVGVYPEATISRS-------FEIKEF-KTGAARMAIEAGVPIVPHIVWGAQRI 156
                                    ********************9.......555444.67899999999999999888755554 PP

>> THDPS_M  Tetrahydrodipicolinate N-succinyltransferase middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017         1      17      40 ..       9      32 ..       2      33 .. 0.89
   2 ?   -1.0   0.6      0.32   1.9e+03      15      29 ..     233     247 ..     230     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHTT------EEESS- CS
                        THDPS_M 17 feerrlrlraagrsvtVlsVDKFP 40
                                    ++ rl+ r++g  +tV++VD +P
  gi|121639733|ref|YP_979957.1|  9 IRLARLSWRIQGLKITVTGVDNLP 32
                                   5789*****************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHTT- CS
                        THDPS_M  15 edfeerrlrlraagr 29 
                                    + +++ ++++raa+r
  gi|121639733|ref|YP_979957.1| 233 ARLDAQEAAVRAARR 247
                                    678899999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1675.03
//
Query:       gi|121639734|ref|YP_979958.1|  [L=251]
Description: phosphotransferase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-15   57.2   9.6    5.2e-10   39.7   2.7    2.1  2  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.18   11.4   0.0    1.1  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.3   9.5e-09   8.5e-05      26     134 ..      50     153 ..      33     160 .. 0.82
   2 !   39.7   2.7   5.8e-14   5.2e-10     154     240 .]     151     239 ..     146     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.5e-09
                                    EEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----.EE-SSHHHHHHHHHHHHHHHHHHCC CS
                            APH  26 rrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpg.rsllrklsaaqlpellealgeflaa 104
                                    ++++ +   +++++e++ lr+ a   + vP+vl  + d++ ++l+  +++++ + ++++r    a  + ++ alg+ l+ 
  gi|121639734|ref|YP_979958.1|  50 KVARRG--TADFANEARRLRWAAPYLA-VPRVLGVGVDGDWAWLHTDALPGLSAvHPRWR----ASPQVAVPALGAGLRT 122
                                    666666..7889999999999999855.************************98345556....77888899******** PP

                                    HHCH..-STTTB-SHHCHTCCHHHHHHCHHH CS
                            APH 105 lhqvd.paalpladflaqdlellrqlesata 134
                                    lh+     ++p+++ +a++l+ l+   +a  
  gi|121639734|ref|YP_979958.1| 123 LHDSLpVHSCPFDWSTASRLAKLAPARRAEL 153
                                    ****9788*********99998887777654 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 5.8e-14
                                    HHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH....HHCSCHCCCHCHHHHHHHHC CS
                            APH 154 aalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll....rswtseldpeflaallraye 229
                                    a+l +  p  ++ v++HgD +++N ++d d gr+ G +Df+ +g++++ +Dlav+     +++++  +   ++++++ay+
  gi|121639734|ref|YP_979958.1| 151 AELGDSPPV-DRLVVCHGDACSPNTILD-DTGRCCGHVDFGNLGVADRWADLAVATlslqWNFPDYPGQVRDDEFFAAYG 228
                                    455666664.899***************.88*********************9999999888999999************ PP

                                    S-HHHHCCCGH CS
                            APH 230 qeaglarlael 240
                                     ++++ar++ +
  gi|121639734|ref|YP_979958.1| 229 VAPDPARIDYY 239
                                    99****99865 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     2e-05      0.18     144     185 ..     161     202 ..     134     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                                    -EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHHHH CS
                 Choline_kinase 144 pvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDlan 185
                                     +v cH D  + N +l+++ ++   +DF   g+  r  Dla 
  gi|121639734|ref|YP_979958.1| 161 RLVVCHGDACSPNTILDDTGRCCGHVDFGNLGVADRWADLAV 202
                                    39***************************9999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1825.72
//
Query:       gi|121639735|ref|YP_979959.1|  [L=516]
Description: hypothetical protein BCG_3880 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-07   31.3   0.1      3e-07   30.3   0.1    1.4  1  Rieske         Rieske [2Fe-2S] domain
    7.1e-07   29.3   0.0    1.1e-06   28.6   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0031   17.1   0.1     0.0058   16.2   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1     5e-11     3e-07      40      79 ..     466     506 ..     464     513 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5e-11
                                    ESC-TTTT-BCGG.SEEETT.EEE-TTT--EEE.TTSBEEE- CS
                         Rieske  40 sdvCtHrgaplse.gkidekgvleCpcHgwayd.adGkvikg 79 
                                    + +C+H++a ls+ g + e+++l+C++Hgw+++  dG+++++
  gi|121639735|ref|YP_979959.1| 466 QRRCPHLKADLSKfGVV-EGNTLTCNLHGWQWRlDDGRCLTA 506
                                    679**********9999.666*****************9876 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.8e-10   1.1e-06       1      58 [.       2      72 ..       2     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.8e-10
                  Lactamase_B_3  1 eltwlghnsflletagarilvDPfkanlgyeppa..............eeaDlvlisqaledHahletlkql 58
                                   ++t +gh+ fl++t+  +il+DP+  n  y +++               e D + +s+ ++dH+++e+l++ 
  gi|121639735|ref|YP_979959.1|  2 QVTSVGHAGFLIQTQAGSILCDPWV-NPAYFASWfpfpdnsgldwgalGECDYLYVSHLHKDHFDAENLRAH 72
                                   6899********************5.55555555566677777778889********************994 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.7e-07    0.0058       3     163 ..      20     175 ..      19     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.7e-07
                                    EEES--TT...HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                  Lactamase_B_2   3 iLiDagpd...lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                    iL+D++ +   ++    +   +    +  l + d + ++h H DH+ ++  lr+  +k++ ++ p+    +l+++++ l 
  gi|121639735|ref|YP_979959.1|  20 ILCDPWVNpayFA-SWFPFPDNSGlDWGALGECDYLYVSHLHKDHF-DAENLRAHVNKDAVVLLPDFPVPDLRNELQKL- 96 
                                    7888888877433.33555544556899999***************.9******8888877889999999999996544. PP

                                    CHTTTTEEEEEE-TTSEEEE....CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHH CS
                  Lactamase_B_2  79 leeepavnvheldwgesfel....gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeiger 153
                                     + +   ++ e +   +++l    gd ++ i a  a+ +++           +l++++g+ +++ + D   ++ + ++ +
  gi|121639735|ref|YP_979959.1|  97 -GFH---RFFETTDSVKHRLrgpnGDLDVMIIALRAPADGPI-------GDSALVVADGETTAFNMNDARPVDlDVLASE 165
                                    .333...55666666666667766666666666667777777.......5678999999999999999999998889999 PP

                                    HCT-SEEEEE CS
                  Lactamase_B_2 154 lggadlllld 163
                                    +g +d+ +l+
  gi|121639735|ref|YP_979959.1| 166 FGHIDVHMLQ 175
                                    9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3641.61
//
Query:       gi|121639736|ref|YP_979960.1|  [L=111]
Description: hypothetical protein BCG_3881 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 790.82
//
Query:       gi|121639737|ref|YP_979961.1|  [L=468]
Description: polyketide synthase associated protein papA2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-15   54.2   0.0    1.4e-14   53.7   0.0    1.1  1  Condensation  Condensation domain


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   7.7e-19   1.4e-14      34     333 ..      70     360 ..      62     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 7.7e-19
                                    EEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSSSHHHHHHHHHHHHHTC--SC CS
                   Condensation  34 klegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdleeseeeeaieefaqkdlqepfdL 113
                                     l g+ ++ +++ a+++ ++rhd+    f+ + n e + + + ++++++ev++++++++++      + ++ +++ p  L
  gi|121639737|ref|YP_979961.1|  70 DLPGRCNIRAMNYAINAHLRRHDTYHSWFEFD-NAEHIVRHTIADPADIEVVQAEHQNMTS------AELRHHIATPQPL 142
                                    678999***********************777.7777778888999999999999877776......4444456668888 PP

                                    CCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT---.----S--HHHHHHHHHHHHCSHHHH CS
                   Condensation 114 ekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekgeel.plpqktpYkdyaeweqqyleskdle 192
                                    +   +f +++++ +++++++++s+ H++vD + +g+l+ +++ +Y +l  g+++ +lp+   Y d+ ++  qy+  ++l 
  gi|121639737|ref|YP_979961.1| 143 QW-DCFLFGIIQ-SDDHFTFYASIAHLCVDPMIVGVLFIEIHMMYSALVGGDPPiELPPAGRYDDHCVR--QYADTAALT 218
                                    75.5999*****.************************************99986145555559888888..444444444 PP

                                    HHH...HHHHHHH...H......S---BSS---SS---S-EEEEEEEE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHH CS
                   Condensation 193 kee...aYWseql...egelpvlqLpkdkarpakrsfkadrlsikldeeteeklrklakeqgvtlndvllaalgllLsky 266
                                     ++   + W e     +g+lp+  Lp    ++ +  + +  ++  +de+  e+++ ++ + g+       a+ +l+  ++
  gi|121639737|ref|YP_979961.1| 219 LDSarvRRWVEFAannDGTLPHFPLPLG--DLSVPHTGKLLTETLMDEQQGERFEAACVAAGARFSGGVFACAALAEREL 296
                                    3331124577555111566777777776..3333333323444455********************************** PP

                                    HT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHHHHHHHHHHHCCTTS-H CS
                   Condensation 267 tgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfselikrvkedllkaephqgypl 333
                                    t+ + + v t++  R  +  +  r++G+F+  +P+ + v+ +  f ++ +  +    + ++   +p+
  gi|121639737|ref|YP_979961.1| 297 TNCETFDVVTTTDTRRTP--TELRTTGWFTGLVPITVPVASGL-FDSAARVAQISFDSGKDLATVPF 360
                                    ******************..*****************996655.66665555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3258.42
//
Query:       gi|121639738|ref|YP_979962.1|  [L=237]
Description: integral membrane protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-59  200.1  22.1    3.2e-59  199.9  22.1    1.0  1  SfLAP     Sap, sulfolipid-1-addressing protein


Domain annotation for each model (and alignments):
>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9  22.1   1.8e-63   3.2e-59       1     214 []       5     235 ..       5     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 1.8e-63
                          SfLAP   1 llvlAlvvalsPlrlgvavlllsrprpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlll 80 
                                    +lvlAl v+++P+r+g++vl+l+r+rp+l+ll+Fl+g+++++ +++++ l+vl++++  a   +++++ ++qi++G+++l
  gi|121639738|ref|YP_979962.1|   5 VLVLALSVICEPVRIGLVVLMLNRRRPLLHLLTFLCGGYTMAGGVAMVTLVVLGATP-LA---GHFSVAEVQIGTGLIAL 80 
                                    79*******************************************************.55...7999************* PP

                          SfLAP  81 llaaveavrr.....................pkassrselprllsrleslleggalwvAlvlgllsakplllylaalaai 139
                                    l+a+  ++++                     +++  +s++++l+ r++++l+g++l+vA+v gl+ a p+ +y+ a+aai
  gi|121639738|ref|YP_979962.1|  81 LIAFALTTNVigkhvrratharvgdnggrvlRESVPPSGTHKLAVRARCFLQGDSLYVAGVSGLGAALPSANYMGAMAAI 160
                                    ******************************************************************************** PP

                          SfLAP 140 gasgasvgtqvvalvvFvvvalavveipllaylvapertqavlerlkdwlrsnrrlilavilgvvGllllakGls 214
                                    +asga+++tq +a+v F+vva++v+e+pl++yl+ap++t+a++++l++wlrs++r+  a+++++ G+l+l+ Gls
  gi|121639738|ref|YP_979962.1| 161 LASGATPATQALAVVTFNVVAFTVAEVPLVSYLAAPRKTRAFMAALQSWLRSRSRRDAALLVAAGGCLMLTLGLS 235
                                    ************************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1581.62
//
Query:       gi|121639739|ref|YP_979963.1|  [L=122]
Description: hypothetical protein BCG_3884 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 901.48
//
Query:       gi|121639740|ref|YP_979964.1|  [L=282]
Description: hypothetical protein BCG_3885 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-62  211.7   1.1      1e-62  211.7   1.1    1.3  2  PE-PPE    PE-PPE domain


Domain annotation for each model (and alignments):
>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   1.1   5.7e-67     1e-62      21     227 .]       2     203 ..       1     203 [. 0.96
   2 ?   -3.6   0.1      0.38   6.8e+03      19      40 ..     235     256 ..     225     262 .. 0.51

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 5.7e-67
                         PE-PPE  21 ksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaalsepaa..pdqlsfvlvgnpnrpngglla 98 
                                    +s+tv++Sv++Gt+nL+aair+   ++ +++v+G+Sqg+lv+++e+arla+  +p+a  p ql+f+ +g+p   n+ l++
  gi|121639740|ref|YP_979964.1|   2 NSPTVGSSVSAGTNNLDAAIRS---TDGPIFVAGLSQGTLVLDREQARLAN--DPTAppPGQLTFIKAGDP---NNLLWR 73 
                                    689*******************...99************************..8888889***********...789*** PP

                         PE-PPE  99 rfpggltipilgitftgatptdsqydTvdvvaqYDgvadfPdyplNllAdvNail.GialvHt..nyetevaeqlpanir 175
                                     f++g+++pi  i++t++ p++sqydT+++v qYD ++d P++p+NllAd+Nai+ G +++H+  ++ +++a++ p++i+
  gi|121639740|ref|YP_979964.1|  74 AFRPGTHVPI--IDYTVPAPVESQYDTINIVGQYDIFSDPPNRPGNLLADLNAIAaGGYYGHSatAF-SDPARVAPRDIT 150
                                    **********..*****************************************97269*****8556.8999******** PP

                         PE-PPE 176 ttvnsrgakttyylipteelPLlqplrslg.vpeplvdaldavLrvlvdlgYd 227
                                    tt+ns ga+tt+y+i+t++lPL++ l +++ +p + + ++da+Lr+++d +Y+
  gi|121639740|ref|YP_979964.1| 151 TTTNSLGATTTTYFIRTDQLPLVRALVDMAgLPPQAAGTVDAALRPIIDRAYQ 203
                                    *****************************77*********************6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.38
                         PE-PPE  19 glksltvdeSvaeGtenLeaai 40 
                                    + +  +   S+a++t+   +a+
  gi|121639740|ref|YP_979964.1| 235 STTGASAATSTAAATAAATNAL 256
                                    3444445555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1965.82
//
Query:       gi|121639741|ref|YP_979965.1|  [L=1089]
Description: integral membrane transport protein mmpL8 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.7e-207  687.9  39.9   9.5e-106  353.5  15.1    2.5  2  MMPL            MMPL family
    9.6e-06   25.5   2.6    9.6e-06   25.5   2.6    2.4  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
     0.0049   16.7   5.1     0.0049   16.7   5.1    2.8  3  PhageMin_Tail   Phage-related minor tail protein
  ------ inclusion threshold ------
      0.054   11.6   1.7         11    4.0   0.0    2.5  2  Patched         Patched family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.9  16.8  2.8e-105  1.3e-101       2     332 ..      75     401 ..      74     402 .. 0.99
   2 !  353.5  15.1  2.1e-109  9.5e-106       2     331 ..     677    1047 ..     676    1049 .. 0.93

  Alignments for each domain:
  == domain 1  score: 339.9 bits;  conditional E-value: 2.8e-105
                           MMPL   2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpdvaaafv 81 
                                    ++p+da++ +++++++aaf+e a+ ++++vvvl  +++ lg+ a+e+ ++elvd+l++dt++v +++df+++p ++++++
  gi|121639741|ref|YP_979965.1|  75 ILPSDAPVLVSTRQMTAAFRE-AGLQSVAVVVL-SDAKGLGA-ADERSYKELVDALRRDTRDVVMLQDFVTTPPLRELMT 151
                                    6899*****************.***********.********.************************************* PP

                           MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                    SkD++a++++v l gd gst++++++a+++++ve++++ + l++++tGpaat+adl+ +++rd+  ie+++ +++lviLl
  gi|121639741|ref|YP_979965.1| 152 SKDNQAWILPVGLPGDLGSTQSKQAYARVADIVEHQVAGSTLTANLTGPAATVADLNLTGQRDRSRIEFAITILLLVILL 231
                                    ******************************************************************************** PP

                           MMPL 162 ivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavi 241
                                    i+yr++++++lpl+t+++s+++a+ lv+ +a l+gl+++++++ +++ +++++GtDYa++L+sRy+++l++g d+++av 
  gi|121639741|ref|YP_979965.1| 232 IIYRNPITMVLPLITIGMSVVVAQRLVA-IAGLAGLGIANQSIIFMSGMMVGAGTDYAVFLISRYHDYLRQGADSDQAVK 310
                                    **************************77.67788********************************************** PP

                           MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrkkrwWrr 321
                                    +a++s+gkv++a+++tvai++lg+v+++l++l++vG++++++v+v++++++TllPAl+vl+Gr+++++prr++++r+Wr+
  gi|121639741|ref|YP_979965.1| 311 KALTSIGKVIAASAATVAITFLGMVFTQLGILKTVGPMLGISVAVVFFAAVTLLPALMVLTGRRGWIAPRRDLTRRFWRS 390
                                    ******************************************************************************** PP

                           MMPL 322 lgrlvvrrPlp 332
                                    +g+++vrrP++
  gi|121639741|ref|YP_979965.1| 391 SGVHIVRRPKT 401
                                    *********86 PP

  == domain 2  score: 353.5 bits;  conditional E-value: 2.1e-109
                           MMPL    2 lspadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf......... 70  
                                     l+ a+a++++am +l++++p+ +  +ki++v+++ +d a+gs++ +++v+ lvd++kk++ ++ge+s+f         
  gi|121639741|ref|YP_979965.1|  677 LRGALATVIRAMGSLGMSSPG-GVRSKINLVNKGVNDLADGSRQLAEGVQLLVDQVKKMGFGLGEASAFllamkdtat 753 
                                     57899****************.6667*******************************************988888888 PP

                           MMPL   71 .......................................lsdpd....vaaafvSkDgkaaralvtlegdpgsteade 105 
                                                                            +   d    vaaaf+S+Dg+++r+l++++++p+st+a++
  gi|121639741|ref|YP_979965.1|  754 tpamagfyippellsyatgesvkaetmpseyrdllgglnV---DqlkkVAAAFISPDGHSIRYLIQTDLNPFSTAAMD 828 
                                     8888777777777777776666666666666666555332...22457****************************** PP

                           MMPL  106 svaairaaveear...pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvs 180 
                                     +++ai+aa++ a+   +l+++kv+v+G +++l+d+rd+sd+dl+li+++t++++l+iL++++r++va+l+++++v+vs
  gi|121639741|ref|YP_979965.1|  829 QIDAITAAARGAQpntALADAKVSVVGLPVVLKDTRDYSDHDLRLIIAMTVCIVLLILIVLLRAIVAPLYLIGSVIVS 906 
                                     *************999************************************************************** PP

                           MMPL  181 llaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGlt 257 
                                     +laalg+ v+++++llg+e++++++gl++v+l+avG+DY++lL+sR+ree+  g ++  +vir+vastg+v+taaGl+
  gi|121639741|ref|YP_979965.1|  907 YLAALGIgVIVFQFLLGQEMHWSIPGLTFVILVAVGADYNMLLISRLREEAVLGVRS--GVIRTVASTGGVITAAGLI 982 
                                     *********************************************************..******************* PP

                           MMPL  258 vaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraalakprrkrkkrwW.rrlgrlvvrrPl 331 
                                     +a++m+gLv+a+l+++ q ++++++G+l+d+++v+T++ PA++vl+G+a           +wW ++++r+++++Pl
  gi|121639741|ref|YP_979965.1|  983 MAASMYGLVFASLGSVVQGAFVLGTGLLLDTFLVRTVTvPAIAVLVGQA-----------NWWlPSSWRPATWWPL 1047
                                     *************************************************...........***************7 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   2.6   2.1e-09   9.6e-06       9     140 ..     240     375 ..     234     386 .. 0.88
   2 ?   -2.7   5.3       1.1   4.8e+03      15     124 ..     902    1015 ..     890    1030 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.1e-09
                                    HHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHH...HHHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCC CS
                 Sterol-sensing   9 glagviivllsvasslgllaylgltltliilevlPfl...vlavgvd.nifvlvkavqrtsrsldeseriaealgevgps 84 
                                    ++  +i++++sv+++  l+a+ gl    i  + + f+    +  g+d  +f++ + ++ + +  d ++ +++al+++g  
  gi|121639741|ref|YP_979965.1| 240 MVLPLITIGMSVVVAQRLVAIAGLAGLGIANQSIIFMsgmMVGAGTDyAVFLISRYHDYLRQGADSDQAVKKALTSIGKV 319
                                    567789*****************9999999999999643378889994478888888888888999************** PP

                                    CHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                 Sterol-sensing  85 illtsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre 140
                                    i ++++t ++++l  ++t++  +++      ++v+v F+  +t+  a++ l  rr 
  gi|121639741|ref|YP_979965.1| 320 IAASAATVAITFLGMVFTQLGILKTVGPMLGISVAVVFFAAVTLLPALMVLTGRRG 375
                                    ***********99667************************************9996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                     HHHCCHHHHCCH....HHHHHHHHHHHHHHHHHHHHH.HHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCH CS
                 Sterol-sensing   15 ivllsvasslgl....laylgltltliilevlPflvl.avgvd.nifvlvkavqrtsrsldeseriaealgevgpsil 86  
                                      v++s++++lg+    + +l  +  ++++  l f++l avg d n+++ +  + r +  l + + + +++ ++g  i+
  gi|121639741|ref|YP_979965.1|  902 SVIVSYLAALGIgvivFQFLLGQEMHWSIPGLTFVILvAVGADyNMLL-ISRL-REEAVLGVRSGVIRTVASTGGVIT 977 
                                     455555555555211134444444555556677776538999945544.4443.445666777777777777777777 PP

                                     HCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                 Sterol-sensing   87 ltsltellall.lgaltdvpavqeFclfaavavlvdFll 124 
                                     +  l  +++++ l  + ++  v + ++    ++l+d +l
  gi|121639741|ref|YP_979965.1|  978 AAGLIMAASMYgLV-FASLGSVVQGAFVLGTGLLLDTFL 1015
                                     76665555555344.444444444555555555555555 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3         1   4.6e+03     132     145 ..     303     316 ..     258     344 .. 0.56
   2 ?   -0.5   1.1      0.21   9.4e+02      29     111 ..     507     596 ..     498     614 .. 0.59
   3 !   16.7   5.1   1.1e-06    0.0049      36     135 ..     661     759 ..     633     761 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                  PhageMin_Tail 132 seAgtalknllsrl 145
                                    +++ +a+k++l+++
  gi|121639741|ref|YP_979965.1| 303 ADSDQAVKKALTSI 316
                                    22222333333332 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.21
                  PhageMin_Tail  29 Gvsteeilnll.egaaklataggadd.....leeaaeilstalnafglsaadaeeaaDvlaaaann.gatsvedlaealk 101
                                     ++++e+ + l eg+ ++a+ +g+ d     ++ +a+ l+++  + + + + ++ + D+la++++  g + v +  e+  
  gi|121639741|ref|YP_979965.1| 507 SWQAGEVGSKLdEGSKQIAAHTGDIDklaggANLMASKLGDVRAQVNRAISTVGGLIDALAYLQDLlGGNRVLGELEGAE 586
                                    56667777777777777777777444532223333333333333333333388888888888887655555555556666 PP

                  PhageMin_Tail 102 evgavakaaG 111
                                    ++ ++++a+G
  gi|121639741|ref|YP_979965.1| 587 KLIGSMRALG 596
                                    6666666666 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.1e-06
                  PhageMin_Tail  36 lnllegaaklataggaddleeaaeilstalnafglsaa..daeeaaDvlaaaanngatsvedlaealkevgavakaaGls 113
                                    l++++++ +la+++    l  a  +++ a++ +g+s +   +    +++++++n  a+ +++lae+ + +  + k++G+ 
  gi|121639741|ref|YP_979965.1| 661 LQATRAVQTLAATVS-G-LRGALATVIRAMGSLGMS-SpgGVRSKINLVNKGVNDLADGSRQLAEGVQLLVDQVKKMGFG 737
                                    677889999999998.7.9*****************.559**************************************** PP

                  PhageMin_Tail 114 feetaaalallaaagikgseAg 135
                                    + e++a+l ++ ++  ++++Ag
  gi|121639741|ref|YP_979965.1| 738 LGEASAFLLAMKDTATTPAMAG 759
                                    *************888888887 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   5.7     0.021        96     222     384 ..     218     372 ..     146     376 .. 0.61
   2 ?    4.0   0.0    0.0024        11     427     533 ..     382     486 ..     377     492 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.021
                        Patched 222 lvvtiaiLlvfsiivsvvlssdalkidwvrskpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdm 301
                                    +  +i+iLl+  ++++++           ++   l  +g+ + v+  + ++  l  lG+  +si  ++  + ++ G D +
  gi|121639741|ref|YP_979965.1| 218 IEFAITILLLVILLIIYRNPI--------TMVLPLITIGMSVVVAQRLVAIAGLAGLGIANQSIIFMSGMM-VGAGTDYA 288
                                    444444444433333322222........223333333443444444444445556666666666655544.46677765 PP

                        Patched 302 flmvaawkr.teaklsvkkrigealseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavl 380
                                      ++ ++++ +++  +  + +++al   g  i+    T +++F   + t+l  ++    + ++++++ f+  +t++ a++
  gi|121639741|ref|YP_979965.1| 289 VFLISRYHDyLRQGADSDQAVKKALTSIGKVIAASAATVAITFLGMVFTQLGILKTVGPMLGISVAVVFFAAVTLLPALM 368
                                    44444444404445567777778888888888888888888887667777777777788888888888888888888888 PP

                        Patched 381 aiaa 384
                                    ++++
  gi|121639741|ref|YP_979965.1| 369 VLTG 372
                                    7765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0024
                        Patched 427 elkskffreiyapfllnksvrlvvlllfvvylaiaiyGcvnikegLepkklvledsplvevlkliekeiwkeglqve.vv 505
                                    +l+++f+r++ +  + +++++l++  l +v la +  G    + + +  k + ++ + +  +  ++k++  +    e  +
  gi|121639741|ref|YP_979965.1| 382 DLTRRFWRSSGVHIVRRPKTHLLASALVLVILAGCA-GLA--RYNYDDRKTLPASVESSIGYAALDKHFPSNLIIPEyLF 458
                                    57899******************9999998887653.554..5689999******999999999*9*9988766544389 PP

                        Patched 506 vnNppdltikesrdrleelveefentpy 533
                                    ++ + dl++++  + le++v++  ++p 
  gi|121639741|ref|YP_979965.1| 459 IQSSTDLRTPKALADLEQMVQRVSQVPG 486
                                    *********************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1089 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.83u 0.26s 00:00:01.08 Elapsed: 00:00:00.43
# Mc/sec: 7557.54
//
Query:       gi|121639742|ref|YP_979966.1|  [L=511]
Description: polyketide synthase associated protein papA1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-15   54.2   0.0    1.4e-14   53.7   0.0    1.2  1  Condensation  Condensation domain


Domain annotation for each model (and alignments):
>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   7.7e-19   1.4e-14      31     355 ..      71     384 ..      44     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 7.7e-19
                                    EEEEEES---HHHHHHHHHHHHHH-SSCCEEEEE..TTEEEEEE-TT-----EEEE-T..TSSSHHHHHHHHHHHHHTC- CS
                   Condensation  31 avlklegeldlerlekalqelierhdaLRtvfleeengepvQvileerevelevleisdleeseeeeaieefaqkdlqep 110
                                    a++++ g  dl ++  ++++ ++rhd+ R  f+   +++ + + + ++++++e++  ++ e+++  +++ + +      +
  gi|121639742|ref|YP_979966.1|  71 ASVEVFGHCDLRAMTYVINAHLRRHDTYRSWFELR-DTDHIVRHSIADPADIEFVPTTHGEMTS--ADLRQHIV----AT 143
                                    567778999999********************887.6666666677888899889888766665..33333333....24 PP

                                    -SCCCS-SEEEEEEESSTTEEEEEEEEECCT--TTTHHHHHHHHHHHHHHHHTT-------S--.HHHHHHHHHHHHCSH CS
                   Condensation 111 fdLekgpLfraalfkiaenrlllllsvHHiivDGvSlgillrdlaklYqqlekgeelplpqktp.Ykdyaeweqqylesk 189
                                     d     +f +++++  ++++++++s+ H+ +DG  +g+ l +++++Y++l  ge++  +++   Y d+ +++ +y    
  gi|121639742|ref|YP_979966.1| 144 PDSLHWDCFSFGVIQ-RADSFTFYASIDHLHADGQFVGVGLMEFQSMYTALIMGEPPIGLSEAGsYVDFCVRQHEYTSAL 222
                                    4555668********.999************************************9776666667**********98887 PP

                                    HHHH.HHHHHH...HHHH......S---BSS---SS---S-EEEEEE.EE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHH CS
                   Condensation 190 dlek.eeaYWs...eqlegelpvlqLpkdkarpakrsfkadrlsikl.deeteeklrklakeqgvtlndvllaalgllLs 264
                                     + + e + W    e+ +g+ p+  Lp      ++ +  +d ls+ l de+ ++++++++ + ++     +la+ +++++
  gi|121639742|ref|YP_979966.1| 223 TVDSpEVRAWIdfaEINNGTFPEFPLPLG---DPSVRCGGDLLSMMLmDEQQTQRFESACMAANARFIGGMLACIAIAIH 299
                                    77662447797444666676666666666...4555566778887778******************************** PP

                                    HHHT-SEEEEEEEEESSTTCSTCHHC--SS-EEEEEEEEE--TT-BHHHHHHHHHHHHHHHHCCTTS-HHHHHHCSS.SS CS
                   Condensation 265 kytgqddivvgteisgReseikdiermvGlFvntlPlridvkeaktfselikrvkedllkaephqgypleeLvkdlelqr 344
                                    ++tg d +   t+   R+ +  d+  + G+F+  +P+ + v ++ +f+e+ +  ++   +  +  ++p+e++v+ +   r
  gi|121639742|ref|YP_979966.1| 300 ELTGADTYFGITPKDIRTPA--DL-MTQGWFTGQIPVTVPV-AGLSFNEIARIAQTSFDTGADLAKVPFERVVELSPSLR 375
                                    ******999999******99..65.578*************.7778****************************999877 PP

                                    -SSSS-S-SEE CS
                   Condensation 345 kesrspLfdpv 355
                                        +pLf+ v
  gi|121639742|ref|YP_979966.1| 376 R--PQPLFSLV 384
                                    5..67777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3675.73
//
Query:       gi|121639743|ref|YP_979967.1|  [L=2126]
Description: polyketide synthase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-97  324.8   2.2    1.5e-96  323.7   2.2    1.6  1  Acyl_transf_1    Acyl transferase domain
    1.5e-93  313.0   0.2    1.5e-93  313.0   0.2    2.4  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    3.9e-59  199.6   0.6    3.9e-59  199.6   0.6    2.6  2  KR               KR domain
    1.3e-49  169.1   5.7    2.5e-49  168.1   5.7    1.5  1  PS-DH            Polyketide synthase dehydratase
    1.1e-34  119.0   3.7    1.1e-34  118.9   1.1    2.6  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.6e-22   79.8   0.4    5.6e-22   78.1   0.0    2.2  2  ADH_zinc_N       Zinc-binding dehydrogenase
      3e-19   70.4   0.1    6.6e-18   66.1   0.0    3.0  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    4.4e-15   56.1   0.0    9.5e-15   55.0   0.0    1.5  1  KAsynt_C_assoc   Ketoacyl-synthetase C-terminal extension
    1.5e-09   38.1   0.1    9.9e-09   35.4   0.0    2.4  2  PP-binding       Phosphopantetheine attachment site
    1.9e-09   37.3   0.6    1.6e-08   34.2   0.0    2.8  3  adh_short        short chain dehydrogenase
    4.5e-07   29.5   0.3    4.5e-07   29.5   0.3    2.2  2  Thiolase_N       Thiolase, N-terminal domain
    6.1e-06   26.1   0.7    1.8e-05   24.6   0.1    2.2  2  ADH_N            Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.042   13.2   0.4       0.89    8.9   0.1    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.7   2.2   1.1e-99   1.5e-96       1     318 [.     553     869 ..     553     870 .. 0.98

  Alignments for each domain:
  == domain 1  score: 323.7 bits;  conditional E-value: 1.1e-99
                                    EEEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHHHT CS
                  Acyl_transf_1   1 vfvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellksk 80 
                                    v++fsGqGsQwa+MG++Ll ++ +faa++a++++ +++++gfsv++++++ +  ++++i+ vqp ++a+q+ala+++ ++
  gi|121639743|ref|YP_979967.1| 553 VWLFSGQGSQWAAMGADLLTNESVFAATVAELEPLIAAESGFSVTEAMTAPE--TVTGIDRVQPTIFAMQVALAATMAAY 630
                                    79**************************************************..************************** PP

                                    T-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHTS-EECCEECS.....HHHHHHH..TT.EEEEEEECC CS
                  Acyl_transf_1  81 GvrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqlagpgdmaavel....aeeeeklrcqddvvgavanspr 156
                                    Gvrp+av+GHS+GE+Aaavvag ls+e++++++++rs+lm+ +ag  +ma+vel    +++e+ +  +ddvv+av+  p+
  gi|121639743|ref|YP_979967.1| 631 GVRPGAVIGHSMGESAAAVVAGVLSAEDGVRVICRRSKLMATIAGSAAMASVELpalaVQSELTALGIDDVVVAVVTAPQ 710
                                    *******************************************************99778888888************** PP

                                    CCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHH CS
                  Acyl_transf_1 157 rvvisgsqealrelvervskegvgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaey 236
                                    ++vi+g +e++r+lv  +++++v a+ ++v+va+hspqvd+i d+l +alad+ p+ p+++++s+t +d+++++ ++a+y
  gi|121639743|ref|YP_979967.1| 711 STVIAGGTESVRKLVDIWERRDVLARAVAVDVASHSPQVDPILDELIAALADLNPKAPEIPYYSATLFDPREAPACDARY 790
                                    ******************************************************************************** PP

                                    HHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCCCCCHHGGG-TCCCCCCTEETTSS-HHHCHHHHHHHHHHCT CS
                  Acyl_transf_1 237 wvanlrspvrfaeavlsaaetiplvfveispHslllaalektlksaedvksatlvGklkrdltdflvtflyllakahltg 316
                                    w++nlr +vrf +av+sa++++++vf+e+spH+ll++a+ +   s  ++++a+l+G ++r++      +++ll+ +h +g
  gi|121639743|ref|YP_979967.1| 791 WADNLRHTVRFSAAVRSALDDGYRVFAELSPHPLLTHAGDQIAGS-VGMPVAALAG-MRREQPL-PLGLRRLLTDLHNAG 867
                                    *****************************************9996.9*********.*******.9*******9999999 PP

                                    -H CS
                  Acyl_transf_1 317 se 318
                                    ++
  gi|121639743|ref|YP_979967.1| 868 AA 869
                                    86 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.0   0.2   1.1e-96   1.5e-93       3     253 .]      26     274 ..      24     274 .. 0.96
   2 ?   -2.8   0.7       2.7   3.7e+03     168     194 ..    1543    1568 ..    1540    1586 .. 0.85

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 1.1e-96
                                    -EEEEEEEEEBTTBSS.HHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHH CS
                  ketoacyl-synt   3 pvaivGmgarfPggnd.veefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispr 80 
                                    pva++Gm++r+Pgg d +e +w++Ll+g d i+e+p drwd+d++ydp++ ++g++ +k+ggfld  +dfd effgi +r
  gi|121639743|ref|YP_979967.1|  26 PVAVIGMACRLPGGIDsPELLWKALLRGDDLITEVPPDRWDCDEFYDPQPGVPGRTVCKWGGFLDnPADFDCEFFGIGER 105
                                    8***************9*************************************************************** PP

                                    HHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHH CS
                  ketoacyl-synt  81 eaeamdpqqrllleaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagrisy 160
                                    ea a+dpqqrllle++wea+e+aglt+++l gs++gvf+Gv++gdy  ++a d ++  ++ +   +g+ + ++++gr++y
  gi|121639743|ref|YP_979967.1| 106 EAIAIDPQQRLLLETSWEAMEHAGLTQQTLAGSATGVFAGVTHGDYT-MVAADAKQ-LEEPYG-YLGN-SFSMASGRVAY 181
                                    **********************************************5.45555455.678888.8899.9********** PP

                                    HHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TTSGGGTTBTTB-SB-BB- CS
                  ketoacyl-synt 161 alglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspdgrckafdpkadGfvlGE 240
                                    a+ l+Gp++tvdtACsS+l+avh+a++sl++ge+dvalaGGv l+l+p++ a+ sa+g+lsp+grc+afd +adGfv GE
  gi|121639743|ref|YP_979967.1| 182 AMRLHGPAITVDTACSSGLTAVHMACRSLHEGESDVALAGGVALMLEPRKAAAGSALGMLSPTGRCRAFDVAADGFVSGE 261
                                    ******************************************************************************** PP

                                    EEEEEEEEECHHH CS
                  ketoacyl-synt 241 GvGavvLkrleda 253
                                    G+++vvLkrl da
  gi|121639743|ref|YP_979967.1| 262 GCAVVVLKRLPDA 274
                                    **********887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                     EEEEESGGGHHHHHHHHHHHHHHTTS- CS
                  ketoacyl-synt  168 svtvdtACsSslvavhaavqslrsgea 194 
                                     + +v+tA +++   +h    ++r+g+ 
  gi|121639743|ref|YP_979967.1| 1543 AAAVTTAHATAWYGLHEL-ARIRAGDT 1568
                                     679********9999998.89**9987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.8   2.5e+03       2      26 ..    1568    1592 ..    1540    1628 .. 0.64
   2 !  199.6   0.6   2.9e-62   3.9e-59       1     180 []    1772    1950 ..    1772    1950 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                     EEEEETTTSHHHHHHHHHHHHHHS- CS
                             KR    2 tylitGGlGgLGlelarwlaekgar 26  
                                     t+li  G+Gg+G++ +    + ga+
  gi|121639743|ref|YP_979967.1| 1568 TVLIHSGTGGVGQAAIAIARAAGAE 1592
                                     4556666666665544433333333 PP

  == domain 2  score: 199.6 bits;  conditional E-value: 2.9e-62
                                     SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                             KR    1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78  
                                     g+y+itGGlGgLGl la+ +a+ g  ++vl sR+ +++++++++i++++a+g ev v   D++++   e+l++++ a+
  gi|121639743|ref|YP_979967.1| 1772 GSYIITGGLGGLGLFLAEKMAAAGCGRIVLNSRT-QPTQKMRETIEAIAAMGSEVVVECGDIAQPGTAERLVATAVAT 1848
                                     89********************************.89999999*********************************** PP

                                     SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                             KR   79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagqanYaaaNafl 156 
                                     + p++Gv+haA v++d++l++ t+e l++  apKv+Gaw Lhe+++ ++ld+f lfSS+a+l+gs+gq++Y+aaN++l
  gi|121639743|ref|YP_979967.1| 1849 GLPVRGVLHAAAVVEDATLANITDELLARDWAPKVHGAWELHEATSGQPLDWFCLFSSAAALTGSPGQSAYSAANSWL 1926
                                     ****************************************************************************** PP

                                     HHHHHHHHHHHHTEEEEEE--BTT CS
                             KR  157 Dalaeyrrsqglpavsinwglwae 180 
                                     Da+a++r++qglpa++i+wg+w++
  gi|121639743|ref|YP_979967.1| 1927 DAFAHWRQAQGLPATAIAWGAWSD 1950
                                     **********************86 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1   5.7   1.8e-52   2.5e-49       1     288 [.     914    1189 ..     914    1198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 1.8e-52
                                     BTTB.-EE--..-SS-EEEEEEE-S-SS.TTTSEEETTEEB--TTHHHHHHHHHHHHTS---.-EEEEEEEE----.B CS
                          PS-DH    1 hpllGsrvrsa.sdkevvfrnrlrlaelpwLrDHrvdgkvvlPgagylemaleAarqltgeskavelrdvsilkalvl 77  
                                     hpllG++vr + +++++ +++++ +a lpwL DHr+++ + lPga+y emal+Aar + ge+   e+rd +++++l l
  gi|121639743|ref|YP_979967.1|  914 HPLLGAHVRLPeEPERHAWQADVGTATLPWLGDHRIHNVAALPGAAYCEMALSAARAVLGEQ--SEVRDMRFEAMLLL 989 
                                     9**********99**********************************************999..9************* PP

                                     --SS-EEEEEEEEE-TTS-E....EEEEEEE-SS-TT.EEEEEEEEEE-----.--B--HHHHHHHS-SEE....E-H CS
                          PS-DH   78 pedepvevqlslepeedgadrawvefeifSregggeewtehatGtvrlaegaa.aaavdlealqarcaepaslrsvss 154 
                                     ++++pv  + +++    g     v+f + + ++g ++  + a++ ++   g+  ++a d+++l      +a++ +v++
  gi|121639743|ref|YP_979967.1|  990 DDQTPVSTVATVTSP--GV----VDFAVEALQEGVGHHLRRASAVLQQVSGECePPAYDMASL-----LEAHPCRVDG 1056
                                     *98877777777766..34....5999999999988779999999996655445677777777.....55556669** PP

                                     HHHHHHHHHHSEEE-GGG--EEEEEEE...TTEEEEEE---GGGSSTTTT-SB-HHHHHHHHHHG..GG--------- CS
                          PS-DH  155 aefYerlaargleyGpsFqglralwrg...dgealaelrlpeelaggesayvlhPallDaalQllaaalsaeaekada 229 
                                     +++ +++++ g++yGp+F gl  +++    +   lae++lp +++++++ y++hPallDa++Q+++a   + ++    
  gi|121639743|ref|YP_979967.1| 1057 EDLRRQFDKHGVQYGPAFTGLAVAYVAedaTATMLAEVALPGSIRSQQGLYAIHPALLDACFQSVGAHP-DSQSVGSG 1133
                                     **********************999985555589************9999*************987766.7899**** PP

                                     -EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEE CS
                          PS-DH  230 aylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrl 288 
                                     + +P+++ r+r y    + +   ++++r+++ +  +++ad++++d+ G+v++ + glr+
  gi|121639743|ref|YP_979967.1| 1134 LLVPLGVRRVRAYA---PVRTARYCYTRVTKVELVGVEADIDVLDAHGTVLLAVCGLRI 1189
                                     *************7...77888*********************************9985 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   1.1   8.2e-38   1.1e-34       1     117 [.     282     395 ..     282     396 .. 0.99
   2 ?   -2.9   0.1       4.9   6.7e+03      42      52 ..    1169    1179 ..    1161    1180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 8.2e-38
                                    SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEE CS
                Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplav 80 
                                    +avi+g+++n+dg++  + +p++ aq +a+++ala  gvd+++v++veahg gtp+gDpiE++++++v+g ++   p+a+
  gi|121639743|ref|YP_979967.1| 282 LAVIRGTSANQDGHTVNIATPSQPAQVAAYRAALAAGGVDAATVGMVEAHGPGTPIGDPIEYASVSEVYGVDG---PCAL 358
                                    69*********************************************************************98...9*** PP

                                    E-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                Ketoacyl-synt_C  81 gSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                     SvK+n GH+++ aGv++likvvlalkhgv+p +l++
  gi|121639743|ref|YP_979967.1| 359 ASVKTNFGHTQSTAGVLGLIKVVLALKHGVVPRNLHF 395
                                    ************************************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                                     GGEEEEE-SS- CS
                Ketoacyl-synt_C   42 edvdyveahgt 52  
                                     +d+d++ ahgt
  gi|121639743|ref|YP_979967.1| 1169 ADIDVLDAHGT 1179
                                     79********9 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   4.1e-25   5.6e-22       1     116 [.    1577    1692 ..    1577    1708 .. 0.87
   2 ?   -3.2   0.1       5.4   7.5e+03       1      24 [.    1782    1806 ..    1782    1829 .. 0.61

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.1e-25
                                     HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalk 77  
                                     gvG+aa+++A+a+Gae++a++++++++el++ +G ++v+++ +  ++ e+i++ t+g+gvdvv++ v  ga+  a lk
  gi|121639743|ref|YP_979967.1| 1577 GVGQAAIAIARAAGAEIFATAGTPQRRELLRNMGIEHVYDS-RSiEFAEQIRRDTNGRGVDVVLNSVT-GAAQLAGLK 1652
                                     9****************************************.666***********************.********* PP

                                     CEEEEEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSC CS
                     ADH_zinc_N   78 llkpgGrlvvvGg..gkgeeefdlrnlllkeksilGsllgs 116 
                                     ll+ +Gr+v +G    +g++++ l++ +++++s++ + lg 
  gi|121639743|ref|YP_979967.1| 1653 LLAFRGRFVEIGKrdIYGDTKLGLFP-FRRNLSFYAVDLGL 1692
                                     ***************99999977776.46666665555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                                     HHHHHHHHHHHHTT-.EEEEEESSH CS
                     ADH_zinc_N    1 gvGlaavqlAkalGa.eviavdsse 24  
                                     g+Gl++ +  +a+G+ +++  ++++
  gi|121639743|ref|YP_979967.1| 1782 GLGLFLAEKMAAAGCgRIVLNSRTQ 1806
                                     6777777777777777666544443 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1   1.5e+03      62     106 ..     453     499 ..     430     514 .. 0.70
   2 !   66.1   0.0   4.8e-21   6.6e-18       2     133 .]    1610    1748 ..    1609    1748 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                                    -CHHHCTTT-EEEE--GGG...-....-HHHHHHHHHHHHHHH----E CS
                   ADH_zinc_N_2  62 lkpakkrkgrsvkyeflfsmkas...aqadileelaalieeGklrpvv 106
                                    ++p + +++++  +  lf+++as   a +++ ++l+++i++++   v+
  gi|121639743|ref|YP_979967.1| 453 AQPHA-ASTPPTGTPALFTLSASsadALRQTAQRLTDWIQQHADSLVL 499
                                    44444.667777777888888886775566679999999988755555 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 4.8e-21
                                     T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--....S-EEE-CHHHCTTT- CS
                   ADH_zinc_N_2    2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp...lsaallkpakkrkgr 71  
                                     G ++v+d+r+ +f+    ++t+g+gvDvvl++v g+a   a lk+l+ +Gr+v+ig +++   ++ +l +    r++ 
  gi|121639743|ref|YP_979967.1| 1610 GIEHVYDSRSIEFAeqirRDTNGRGVDVVLNSVTGAAQ-LAGLKLLAFRGRFVEIGkRDIygdTKLGLFPF---RRNL 1683
                                     899*******************************9999.7777999888*******666664444444444...5555 PP

                                     EEEE--GGG...-....-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2   72 svkyeflfsmkas...aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133 
                                     s++++ l  ++a+   + +d+l ++ +l ++G+l ++ + ++pl eaa+A+r + ++ ++GK+Vl
  gi|121639743|ref|YP_979967.1| 1684 SFYAVDLGLLSAThpeELRDLLGTVYRLTAAGELPMPQSTHYPLVEAATAIRVMGNAEHTGKLVL 1748
                                     566555554444455689999*************9999999***********************8 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   6.9e-18   9.5e-15      12     108 ..     408     513 ..     401     520 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 6.9e-18
                 KAsynt_C_assoc  12 rlkVvteptpwpggi......vgvNsfGfGGsnvHviLksnkkekrkeesk...eeslprLlvlsgrteeaveallekle 82 
                                    +l V++ +tpwp +       ++v+s+Gf+G+nvH+++++++++++++ +     + +p L++ls+ +++a+++++++l 
  gi|121639743|ref|YP_979967.1| 408 NLFVPEVTTPWPTNGrqvprrAAVSSYGFSGTNVHAVVEQAPQTEAQPHAAstpPTGTPALFTLSASSADALRQTAQRLT 487
                                    678999999**9888899************************888777776667899*********************** PP

                 KAsynt_C_assoc  83 ehlldaellsllneilseeisrlpyR 108
                                    ++ +++++  +l++++ +  +r ++R
  gi|121639743|ref|YP_979967.1| 488 DWIQQHADSLVLSDLAYTLARRRTHR 513
                                    **555555554444444444444444 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.6   2.2e+03      13      35 ..     682     704 ..     674     708 .. 0.79
   2 !   35.4   0.0   7.2e-12   9.9e-09       2      67 .]    2045    2109 ..    2044    2109 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                     PP-binding  13 vpleeidpdtdlfdlGlDSllav 35 
                                    v+l ++++++ l  lG+D ++++
  gi|121639743|ref|YP_979967.1| 682 VELPALAVQSELTALGIDDVVVA 704
                                    56677889**********88776 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 7.2e-12
                     PP-binding    2 klrelvaevlgvplee.idpdtdlfdlGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67  
                                     +lr+lvae+  + l + +dpd +l ++GlDSl a+el  ++e e g+++ +  +    t++ la++l
  gi|121639743|ref|YP_979967.1| 2045 RLRQLVAEQVSLILRRtVDPDRPLPEYGLDSLGALELRTRIETETGIRLAPKNV--SATVRGLADHL 2109
                                     7999999999995555378*********************************99..79******997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8   3.9e+03      38      71 ..    1352    1385 ..    1343    1388 .. 0.81
   2 ?   -1.2   0.1      0.82   1.1e+03       2      37 ..    1568    1603 ..    1567    1626 .. 0.86
   3 !   34.2   0.0   1.2e-11   1.6e-08       4     160 ..    1775    1930 ..    1773    1940 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                     HHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                      adh_short   38 eevakelkeegakalaiqvDvtdreevealveka 71  
                                     + ++  +++e  ++ a q+Dv +++ ve+l ++ 
  gi|121639743|ref|YP_979967.1| 1352 RGLLRTIGAEHPHLRATQIDVDEQTGVEQLARQL 1385
                                     556778888899999**************99886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.82
                                     EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHH CS
                      adh_short    2 vvlvtGassGIGraiakelakeGakvvvvdrseekl 37  
                                     +vl+  +++G+G+a      ++Ga++++++ ++++ 
  gi|121639743|ref|YP_979967.1| 1568 TVLIHSGTGGVGQAAIAIARAAGAEIFATAGTPQRR 1603
                                     799999********9999999******999887766 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 1.2e-11
                                     EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT...TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                      adh_short    4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee...gakalaiqvDvtdreevealvekavkklgkl 78  
                                     ++tG+ +G+G+ +a+++a++G+  +v++++ ++ +++ + +++    g+++++  +D+++   +e+lv++av+   ++
  gi|121639743|ref|YP_979967.1| 1775 IITGGLGGLGLFLAEKMAAAGCGRIVLNSRTQPTQKMRETIEAIaamGSEVVVECGDIAQPGTAERLVATAVATGLPV 1852
                                     8*************************999999999999999988888999**************************** PP

                                     SEEEE---SS--SSGGGCSHHH.HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                      adh_short   79 dvLvnNAGitgsgpfselseee.wervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155 
                                       + + A++     +++ + ++ ++++++      ++ + ++ +a   q        sS a++ +++g++aYsA+   
  gi|121639743|ref|YP_979967.1| 1853 RGVLHAAAV-----VEDATLANiTDELLARDWAPKVHGAWELHEATSGQPLDWFCLFSSAAALTGSPGQSAYSAANSW 1925
                                     *********.....677777777888888899999999999888888889999999******************9777 PP

                                     HHHHH CS
                      adh_short  156 vaglt 160 
                                     +++++
  gi|121639743|ref|YP_979967.1| 1926 LDAFA 1930
                                     77665 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.3   3.3e-10   4.5e-07      75     116 ..     186     227 ..     174     243 .. 0.88
   2 ?   -2.4   2.0       1.8   2.4e+03      49     115 ..     649     721 ..     599     741 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.3e-10
                                    TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEEST CS
                     Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsms 116
                                    + pa+tv+ +csSgl+av++a++s+  ge+dv++agGv  m 
  gi|121639743|ref|YP_979967.1| 186 HGPAITVDTACSSGLTAVHMACRSLHEGESDVALAGGVALML 227
                                    5699**********************************9885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                    EEEHSSCTTSTSC.HHHHHHHHTTS-TTSEEEEEEH...GGGHHHHH..HHHHHHHHHTTSHSEEEEEEEEES CS
                     Thiolase_N  49 ivGnvlqagegqn.iarqaalkagipeevpavtvnk...vcsSglka..valaaqsiaageadvvvagGvEsm 115
                                    +v+ vl+a++g   i r   l+a i+ ++++  v+    +  S l+a  + +++ ++ +   + v+agG+Es 
  gi|121639743|ref|YP_979967.1| 649 VVAGVLSAEDGVRvICRRSKLMATIAGSAAMASVELpalAVQSELTAlgIDDVVVAVVTAPQSTVIAGGTESV 721
                                    56678888888777888888888888888888777522234555554227889999999999999****9996 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       8.3   1.1e+04      27      61 ..     630     664 ..     624     668 .. 0.79
   2 !   24.6   0.1   1.3e-08   1.8e-05       1      67 [.    1453    1519 ..    1453    1531 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.3
                                    TTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                          ADH_N  27 levklplilGHEivGeveevgpevkklkvGdrVvv 61 
                                    + v+++ ++GH +    ++v  +v + + G rV++
  gi|121639743|ref|YP_979967.1| 630 YGVRPGAVIGHSMGESAAAVVAGVLSAEDGVRVIC 664
                                    56778899999998888888888888888888876 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.3e-08
                                     TTEEEEEEEEEEE-HHHHHHHTTS.TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE- CS
                          ADH_N    1 pgevlikvkaagiCgsDlhilkgg.kelevklplilGHEivGeveevgpevkklkvGdrVvveplisc 67  
                                     pg++ + v+a++++  D+ i+ g+  ++e +lp  lG +++G+v +vgp+v++ kvGd+V       c
  gi|121639743|ref|YP_979967.1| 1453 PGQIEVAVRASSVNFADVLIAFGRyPSFEGHLP-QLGTDFAGVVTAVGPGVTDHKVGDHVGGMSPNGC 1519
                                     57999**************99998334444555.79************************98766666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00064      0.89      34      81 ..    1564    1612 ..    1542    1621 .. 0.77
   2 ?    1.7   0.0       0.1   1.4e+02      39      77 ..    1775    1813 ..    1760    1829 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00064
                                     GTTSEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                   2-Hacid_dh_C   34 lsgktvGii.GlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81  
                                      +g tv i  G+G +Gqa++ +++a g++++a+  +++++e  +++g+e
  gi|121639743|ref|YP_979967.1| 1564 RAGDTVLIHsGTGGVGQAAIAIARAAGAEIFATAGTPQRRELLRNMGIE 1612
                                     4567777744***********************9999988877776665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                                     EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                   2-Hacid_dh_C   39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77  
                                     +   GlG +G  +a++++a g+  i+ + + +++++++e
  gi|121639743|ref|YP_979967.1| 1775 IITGGLGGLGLFLAEKMAAAGCGRIVLNSRTQPTQKMRE 1813
                                     55569*****************88888877777774444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.08u 0.30s 00:00:01.38 Elapsed: 00:00:00.46
# Mc/sec: 13780.26
//
Query:       gi|121639744|ref|YP_979968.1|  [L=584]
Description: acyl-CoA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.7e-73  245.3   0.0    1.1e-72  245.0   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.0   6.1e-77   1.1e-72       4     422 ..      13     467 ..      10     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 6.1e-77
                                    HHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding   4 qaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                     ++ +pd +a+++       +g  ++lT++++++r+ ++Aa  r+  +  gdr +il+p++++++va+l++l+aG+++vp
  gi|121639744|ref|YP_979968.1|  13 CVNLHPDGTAFTYidyerdsEGISESLTWSQVYRRTLNVAAEVRR-HAAIGDRAVILAPQGLDYIVAFLGALQAGLIAVP 91 
                                    56779999999889999999999*********************8.799******************************* PP

                                    EET...TS-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSC CS
                    AMP-binding  77 lnp...tltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpee 152
                                    l++   + + e++  +++d+++ v++  + s+   + + ++++          + + +    ++l+ +++ ++       
  gi|121639744|ref|YP_979968.1|  92 LSAplgGASDERVDAVVRDAKPNVVL--TTSAImGDVVPRVTP-------PPGIASPPTVAVDQLDLDSPIRS------N 156
                                    ***8888999****************..555553444444443.......22333333333344444444442......2 PP

                                    CCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHCSCCTT....T-EEEESS-TTSCHHHHHHHHHHH CS
                    AMP-binding 153 eeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk...letrfklke....ddvvlsilplahifglilelllal 225
                                     +  + +++ay++YTSG+T +P GVm++ +n++an +++    + ++    +    d  ++s+lp++h++gl+l++++++
  gi|121639744|ref|YP_979968.1| 157 IVDDSLQTTAYLQYTSGSTRTPAGVMITYKNILANFQQMIsayFADTG---AvpplDLFIMSWLPFYHDMGLVLGVCAPI 233
                                    33467899***************************9998544333333...244677778******************** PP

                                    HTT-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                    AMP-binding 226 lsGatvvllpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                    ++G+  vl ++ a+l+ p+++l+l+++++   + ++P ++  l++++a++ + +  dl++++++l+g e++ p++l++f 
  gi|121639744|ref|YP_979968.1| 234 IVGCGAVLTSPVAFLQrPARWLQLMAREGQA-FSAAPNFAFELTAAKAIDDDLAGLDLGRIKTILCGSERVHPATLKRFV 312
                                    **************666*********77766.555555555555544565456677************************ PP

                                    HHHTC......EEEEEEEEGGGSSECEE.....................CHCTTTCTSTTS-B.......EE-T.TEEEE CS
                    AMP-binding 305 alfge......evlegYGlTEttgvvtv.....................lpleedkkklgsvG.......kplp.gvevk 349
                                    ++f +      ++  +YGl+E+t+ v++                     +++          G        plp    v+
  gi|121639744|ref|YP_979968.1| 313 DRFSRfnlrefAIRPAYGLAEATVYVATsqagqppeiryfephelsagqAKPCAT-------GagtalvsYPLPqSPIVR 385
                                    ***99*****99**************88899999999998887755433221222.......2445556699998999** PP

                                    EE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.........T.CCEEEEEEEEEEETTSEEEEEEECCCE CS
                    AMP-binding 350 ivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds.........e.grwlrTGDlgrldedGyleivgRkkdl 419
                                    ivD++t+ ++p+g+ Ge++v+g +v+ gY+ kp++t+++f           + g wlrTGD g++  +  ++i+gR+kdl
  gi|121639744|ref|YP_979968.1| 386 IVDPNTNTECPPGTIGEIWVHGDNVAGGYWEKPDETERTFGGalvapsagtPvGPWLRTGDSGFVS-EDKFFIIGRIKDL 464
                                    ****************************************956888999975555**********9.56**********9 PP

                                    EEE CS
                    AMP-binding 420 ikl 422
                                    +++
  gi|121639744|ref|YP_979968.1| 465 LIV 467
                                    986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3967.55
//
Query:       gi|121639745|ref|YP_979969.1|  [L=408]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-31  108.2   0.6    5.6e-31  107.2   0.6    1.5  1  OrfB_IS605      Probable transposase
    1.5e-10   40.4   0.1    4.2e-10   38.9   0.1    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.6   6.3e-35   5.6e-31       4     117 ..     206     321 ..     201     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 6.3e-35
                     OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtw..flykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                    v+ +++++++++++++g+D+G+++Latv++e g+   +++++r+l++++k+l+ + +  ++++k+s++y++++++++rlh
  gi|121639745|ref|YP_979969.1| 206 VQRPQQPNVAQPGSRVGVDVGVRRLATVANEAGAVleEVPNPRPLDAALKELRYASRARSRCTKGSRRYRERTTEISRLH 285
                                    4455569****************************99******************************************* PP

                     OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                    r++++ r+h+lh l+t+l++t+ +++ve L+ ++m 
  gi|121639745|ref|YP_979969.1| 286 RRVNDVRTHHLHVLTTRLAQTHGHIVVEGLDAAGML 321
                                    **********************************97 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   4.7e-14   4.2e-10       4      40 ..      14      50 ..      13      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 4.7e-14
                 HTH_OrfB_IS605  4 kaykyrlyPTpeQeeklartfGcvRfVYNkaLaerke 40
                                   +a+++ l PT+ Q+++lar+fG+ R +YN+a a  k 
  gi|121639745|ref|YP_979969.1| 14 QAFRFTLDPTEDQARALARHFGARRKAYNWAVATLKA 50
                                   69*****************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2627.51
//
Query:       gi|121639746|ref|YP_979970.1|  [L=203]
Description: resolvase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-09   38.7   0.1    1.4e-09   38.3   0.1    1.2  1  Resolvase  Resolvase, N terminal domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.1   7.5e-14   1.4e-09       2     133 ..      63     188 ..      62     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.5e-14
                                    EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                      Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                    ++YaRvS+++q+ +l+r++++++a+a++++l ++k++ +    + + +R+++ +ll +        +vve+ dR+    +
  gi|121639746|ref|YP_979970.1|  63 LVYARVSSADQRSDLDRRVARVTAWATSQHLSVDKVVAEG-GWALNGHRRKFFALLGDPVV---TRIVVEHRDRFCWFGS 138
                                    58***************************88887766665.89999899999999997666...789************* PP

                                    S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHHHHHHHHCT- CS
                      Resolvase  82 dlltlleelrekgvslvsldegidtstpm.grlllqilaalaeferelirert 133
                                    ++++    l ++g +lv++d   + +++  g ++  + +++a++  e+ +++ 
  gi|121639746|ref|YP_979970.1| 139 EYVEA--ALVAQGRELVVVDL-AEVDDDLvGDMTEILTSMCARLYGERAAQNG 188
                                    ****9..55556666666664.3344444477777777777777666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1480.06
//
Query:       gi|121639747|ref|YP_979971.1|  [L=536]
Description: dehydrogenase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-10   40.8   0.4    5.8e-10   39.3   0.4    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.4e-09   37.0   1.0    3.3e-08   33.2   1.0    2.0  1  Amino_oxidase  Flavin containing amine oxidoreductase
    8.4e-05   22.3   9.9      0.016   14.8   1.0    3.0  2  DAO            FAD dependent oxidoreductase
    8.7e-05   21.8   3.4    0.00015   21.0   1.7    1.9  2  FAD_binding_2  FAD binding domain
    0.00025   20.4   1.0     0.0034   16.7   0.3    2.2  2  FAD_binding_3  FAD binding domain
    0.00044   19.7   1.9    0.00066   19.1   0.8    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0022   17.3   0.2     0.0039   16.5   0.2    1.4  1  Thi4           Thi4 family
     0.0037   16.4   3.3     0.0079   15.3   0.9    2.0  2  GIDA           Glucose inhibited division protein A
     0.0057   15.9   0.3       0.05   12.8   0.2    2.0  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.04   12.6   0.6      0.073   11.8   0.2    1.5  2  HI0933_like    HI0933-like protein
      0.071   11.6   0.0       0.43    9.0   0.0    1.9  2  GDI            GDP dissociation inhibitor


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.4   3.6e-13   5.8e-10       1      54 [.       8      62 ..       8      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.6e-13
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TTCEECTS---EEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pgvrvdygahifhg 54
                                   ++GaG  Gl+aA lL++ag++  +l++ ++ GG a+++e+ +g+r+d   ++ ++
  gi|121639747|ref|YP_979971.1|  8 VIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGGMASTVELfDGYRFDIAGSVQFP 62
                                   8***************************************99*****87766544 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   1.0   2.1e-11   3.3e-08       3     293 ..      15     327 ..      15     358 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.1e-11
                                    HHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET.TEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEEEEET CS
                  Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardrvGGRirtvrsd.GylielGamwftgagnpllellkelgledslslpdpgapkrvlsk 81 
                                    GL+aA  L++aG+++  l a+  +GG ++tv++  Gy ++  +++ ++      ++  elgl++ +++++        s+
  gi|121639747|ref|YP_979971.1|  15 GLTAAVLLQRAGLRTACLDAKRYAGGMASTVELFdGYRFDIAGSVQFP---TSSAVSSELGLDSLPTVDLEV-----MSV 86 
                                    9*******************************9989999999999888...444556677777766633333.....221 PP

                                    TEECC.TTEECHHHHHHHHHHHHHHHH........CHHHHHHHHHHHHHHHHH........HHHCCCCHHHHHHHHHCHH CS
                  Amino_oxidase  82 ggref.pgdlspvpaewealleqgals........aellsleeklrlgleall........qktldeldldskslaesle 144
                                      r + + ++ ++  + ++l   ++++        a ll + +   ++l ++         ++++++  ++ +++a++ +
  gi|121639747|ref|YP_979971.1|  87 ALRGVgDDPVVQFTDPTKMLTHLHRVHgadavtgmAGLLAWSQAPTRALGRFEagtlpksfDEMYACATNEFERSAIDDM 166
                                    11111133333332222222222222222222233334444444444444444333333332222222222222222222 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE.................TT CS
                  Amino_oxidase 145 elgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp.................rg 207
                                     +g          +++ + e   +l  +  ++a +   l+ + a p   +          +                 rg
  gi|121639747|ref|YP_979971.1| 167 LFGSVTDVL---DRHFPDREKHGALRGSMTVLAVNT--LYRGPATPGSAAA---------LafglgvpegdfvrwkklRG 232
                                    222222222...222222222222222222222222..3333333333333.........133333335566667777** PP

                                    HTHHHHHHHHH..TTTTEEEETSEEEEEEEE.....ETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCC.SHHHH CS
                  Amino_oxidase 208 Glsqlpealae..elrgldirlntrVkeikr.....egdgvtvtledgevveaDaVvvTvplgvlkailfsPpl.pdeka 279
                                    G+++l  +l++  e+ g+++rl+++V+ei       ++   +v++  g++++   Vv+++ ++v  ++l +P + p e +
  gi|121639747|ref|YP_979971.1| 233 GIGALTTHLSQllERTGGEVRLRSKVTEIVVdnsrsSARVRGVRTAAGDTLTSPIVVSAIAPDVTINELIDPAVlPSEIR 312
                                    *******************************776655666999999****************999999999955587766 PP

                                    HHHHHS.EEEEEEEE CS
                  Amino_oxidase 280 eairnl.gfgsvnkv 293
                                    +   ++ + gs    
  gi|121639747|ref|YP_979971.1| 313 DRYLRIdHRGSYLQM 327
                                    655555555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.0   9.9e-06     0.016       1      34 [.       5      40 ..       5      45 .. 0.89
   2 !   10.0   2.2   0.00028      0.45     147     258 ..     236     360 ..     231     519 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.9e-06
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                   d ++iG+G  Gl++A  L+r+g  ++ l++++ ag 
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGlrTACLDAKRYAGG 40
                                   789***************999**********99884 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00028
                                    HHHHHHHHHHHHTT-EEEESECEEEEEEEE....TCEEEEEEECT.EEE.EEEEEEEE--GGGHH...HHHTTCTTTSEE CS
                            DAO 147 kltaalaraaealGveilegtevtgleeed....gkvwgverttp.gen.daadavVnaaGawsd...llgllkeldlpi 217
                                    +lt  l + +e+ G+e++++++vt++  ++     +v gv   t+ g + ++   vV a  + ++   l+      d+ +
  gi|121639747|ref|YP_979971.1| 236 ALTTHLSQLLERTGGEVRLRSKVTEIVVDNsrssARVRGV--RTAaGDTlTS-PIVVSAIAPDVTineLI------DPAV 306
                                    689999999****************955445567999999..5555877444.44666666665533222......2222 PP

                                    EE...........EEEEEEEE....EECCTHSTGSGCSEEEEEEEETTTTEEEEEE CS
                            DAO 218 sp...........vrgqvlvl....kplseklvspaailpvpetdddgrgvyvtpr 258
                                     p            rg++l +    +++  ++ +p++ l++p +   + g+++tp 
  gi|121639747|ref|YP_979971.1| 307 LPseirdrylridHRGSYLQMhfalAQP-PAFAAPYQALNDP-SMQASMGIFCTPE 360
                                    2222111111122333333221111221.1233334444444.6666666666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.7   9.1e-08   0.00015       1      36 [.       5      40 ..       5      45 .. 0.92
   2 ?   -0.5   0.0       0.3   4.9e+02     141     179 ..     234     277 ..     215     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.1e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   D+iViG+G  GL+AA+ +++aGl++a+++ + + gg
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGG 40
                                   89****************************999888 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHHHTCT.EEEEESEEEEEEEECTT....EEEEEEE CS
                  FAD_binding_2 141 hallarlvesarkag.vdfqerteadeLivedg....rvtGavv 179
                                     + l + + +++++   +++ r +++e++v++     rv+G+  
  gi|121639747|ref|YP_979971.1| 234 IGALTTHLSQLLERTgGEVRLRSKVTEIVVDNSrssaRVRGVRT 277
                                    44555555555555559999999999999987677889999865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   2.1e-06    0.0034       3      33 ..       5      35 ..       3      41 .. 0.91
   2 ?    1.9   0.0     0.065   1.1e+02     107     160 ..     237     290 ..     234     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   d +++GaG  Gl++a lL++aG r+ +++  
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGLRTACLDAK 35
                                   789************************9976 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE CS
                  FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvG 160
                                    l+  L++ +e++g +vr   +v+ +  d++  +a+vr+ +t +  t+++  +v 
  gi|121639747|ref|YP_979971.1| 237 LTTHLSQLLERTGGEVRLRSKVTEIVVDNSRSSARVRGVRTAAGDTLTSPIVVS 290
                                    567789999********************************9999999988876 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.8     4e-07   0.00066       1      40 [.       5      44 ..       5      60 .. 0.93
   2 ?   -1.5   0.0      0.74   1.2e+03      90     138 ..     238     287 ..     234     291 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4e-07
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                   D +V+G+g  G++AA+   raG +++ ++ +++ GG+++ 
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGGMAST 44
                                   679**********************************985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.74
                   FAD_oxidored  90 kavleemlaeagvtvllntrlvevekeg....kriesvtveskegrktirAkv 138
                                    ++ l ++l++ g +v l ++++e+++++     r+++v+++    + t+++++
  gi|121639747|ref|YP_979971.1| 238 TTHLSQLLERTGGEVRLRSKVTEIVVDNsrssARVRGVRTAA---GDTLTSPI 287
                                    5667899999999999*****999998744444477777643...55555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.4e-06    0.0039      18      55 ..       4      40 ..       1      50 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-06
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                    D +++GaG  GLtaa  l ++ +l++a l+++   GG
  gi|121639747|ref|YP_979971.1|  4 YDAIVIGAGHNGLTAAVLLQRA-GLRTACLDAKRYAGG 40
                                   599****************999.********9977766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   4.8e-06    0.0079       1      28 [.       5      32 ..       5      47 .. 0.87
   2 ?    1.1   0.1       0.1   1.7e+02     115     148 ..     255     292 ..     241     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.8e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   d iViG+Gh G+ AA+ + r+G++++ +
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGLRTACL 32
                                   579**********************876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.1
                                    ES-EEEEEECT....TEEEEEEETTS-EEEECEEEE-- CS
                           GIDA 115 eeeveelivee....kkvkgvvtedgetikakavviat 148
                                    + +v+e++v++     +v+gv+t+ g t+++ +vv a 
  gi|121639747|ref|YP_979971.1| 255 RSKVTEIVVDNsrssARVRGVRTAAGDTLTSPIVVSAI 292
                                    56899999988899999****************99886 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2     3e-05      0.05       1      33 [.       4      36 ..       4      61 .. 0.85
   2 ?    0.9   0.0      0.13   2.2e+02     188     235 ..     240     292 ..     235     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   +d +viG+G+ Gl+aa  l++ag++++++++++
  gi|121639747|ref|YP_979971.1|  4 YDAIVIGAGHNGLTAAVLLQRAGLRTACLDAKR 36
                                   5789*************************6433 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                    HHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 188 aleealekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvav 235
                                     l + le+ G ev+l+++v+ei  +++    +++ v +  g+++    vv a+
  gi|121639747|ref|YP_979971.1| 240 HLSQLLERTGGEVRLRSKVTEIVVDNSrssaRVRgVRTAAGDTLTSPIVVSAI 292
                                    56778899999***********9999988766668888888888888888776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   4.5e-05     0.073       2      35 ..       5      38 ..       4      40 .. 0.92
   2 ?   -2.8   0.0       1.2   1.9e+03     115     141 ..     241     267 ..     237     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                   d iviG+G  Gl aA+ ++++g r++ l++++ +
  gi|121639747|ref|YP_979971.1|  5 DAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYA 38
                                   89***************************98765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHT-EEE-S--EEEEECETTE CS
                    HI0933_like 115 llkelkeagvklrletevksvekeedg 141
                                    l + l+++g ++rl+++v+++  ++++
  gi|121639747|ref|YP_979971.1| 241 LSQLLERTGGEVRLRSKVTEIVVDNSR 267
                                    77788999999999**99999665554 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00027      0.43       5      53 ..       4      52 ..       1      82 [. 0.90
   2 ?    0.0   0.0      0.14   2.3e+02     229     278 ..     233     286 ..     230     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00027
                                   ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HHHHHH CS
                            GDI  5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltleqlye 53
                                   yd+iv+G+G +    + ll   g +   ld + y Gg +++++l + y+
  gi|121639747|ref|YP_979971.1|  4 YDAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGGMASTVELFDGYR 52
                                   *****************************************99988774 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.14
                                    -TTHHHHHHHHHHHHTT-EEETS--ECEEEE-TT...S-EEEEEE.TTEEEEEC CS
                            GDI 229 GlGelpqgfarlsaiyGGtymlnkpvdevvlded...gkvvGvks.eeevakak 278
                                    G+G l   +++l    GG   l  +v+e+v+d+    ++v Gv++  +++  + 
  gi|121639747|ref|YP_979971.1| 233 GIGALTTHLSQLLERTGGEVRLRSKVTEIVVDNSrssARVRGVRTaAGDTLTSP 286
                                    899999999999999****************98644467889988445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3404.29
//
Query:       gi|121639748|ref|YP_979972.1|  [L=209]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-12   46.0   0.5    6.6e-12   45.0   0.5    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
     0.0076   16.3   0.1      0.023   14.8   0.1    1.8  2  HTH_AraC     Bacterial regulatory helix-turn-helix proteins, 
  ------ inclusion threshold ------
      0.015   15.1   0.2      0.043   13.6   0.2    1.8  1  HTH_23       Homeodomain-like domain
      0.018   15.1   0.0      0.029   14.4   0.0    1.4  1  HTH_7        Helix-turn-helix domain of resolvase
      0.035   14.2   0.3        0.4   10.8   0.0    2.6  2  HTH_20       Helix-turn-helix domain
      0.038   13.9   0.0      0.074   13.0   0.0    1.5  1  HTH_11       HTH domain
      0.044   14.0   0.5       0.18   12.1   0.1    2.0  2  HTH_18       Helix-turn-helix domain
        0.1   12.7   0.3       0.41   10.8   0.1    2.1  2  HTH_28       Helix-turn-helix domain
       0.18   12.0   0.0       0.39   10.9   0.0    1.5  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.5   3.3e-15   6.6e-12       3      46 ..      19      62 ..      17      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 3.3e-15
                                   HHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                         TetR_N  3 daArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                    aA+  f  +G +at+ ++IA+ AGvs +++Yr+F+sK +Ll a
  gi|121639748|ref|YP_979972.1| 19 QAALVRFLAQGVEATSAEQIAEDAGVSLRTFYRHFRSKHDLLFA 62
                                   58888899*********************************976 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.1e-05     0.023      12      31 ..      36      55 ..      34      56 .. 0.94
   2 ?   -3.0   0.0       4.5     9e+03       9      19 ..     178     188 ..     175     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   HHHHHHTTSSHHHHHHHHHH CS
                       HTH_AraC 12 ediAdelgfSrsyFsrlFkk 31
                                   e+iA+ +g+S ++F+r F++
  gi|121639748|ref|YP_979972.1| 36 EQIAEDAGVSLRTFYRHFRS 55
                                   69****************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                                    --HHHHHHHTT CS
                       HTH_AraC   9 ltiediAdelg 19 
                                     +++++A  ++
  gi|121639748|ref|YP_979972.1| 178 RSLGELARVCH 188
                                    58999999887 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.2e-05     0.043       3      37 ..      14      52 ..      12      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                         HTH_23  3 sereRlrilllla.e...GlsvreIAreLgvsrrTvyrw 37
                                   +e  R+ +l  ++ +     s ++IA+  gvs rT yr 
  gi|121639748|ref|YP_979972.1| 14 REALRQAALVRFLaQgveATSAEQIAEDAGVSLRTFYRH 52
                                   555666655555524777899****************95 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.029      11      43 ..      19      54 ..       3      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   HGGGGSSTTTT...--STTTSSSS---SSSS--SS- CS
                          HTH_7 11 inrvvkLleeG...isiskIAkevnisRsTvYRyla 43
                                   ++ +v+ l++G   +s+ +IA+  ++s  T+YR ++
  gi|121639748|ref|YP_979972.1| 19 QAALVRFLAQGveaTSAEQIAEDAGVSLRTFYRHFR 54
                                   667777788887556899***************775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002       0.4      22      46 ..      30      54 ..      18      55 .. 0.83
   2 ?    0.1   0.1      0.42   8.5e+02      19      38 ..     173     191 ..     155     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                   CTTB-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_20 22 aegltaselaerldlskntlsyHLr 46
                                    e+ +a+++ae  ++s  t ++H+r
  gi|121639748|ref|YP_979972.1| 30 VEATSAEQIAEDAGVSLRTFYRHFR 54
                                   5899*******************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.42
                                    HSTCTTB-HHHHHHHHTS-H CS
                         HTH_20  19 Laraegltaselaerldlsk 38 
                                       +  ++++ela+ + ++ 
  gi|121639748|ref|YP_979972.1| 173 M-LGSDRSLGELARVCHVAL 191
                                    3.5777999****9987665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.074       1      35 [.      18      52 ..      18      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                         HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrd 35
                                   R+ +++++L +  +  s+e++Ae  +vS rt +r+
  gi|121639748|ref|YP_979972.1| 18 RQAALVRFLAQGVEATSAEQIAEDAGVSLRTFYRH 52
                                   788999999888888****************9998 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   9.1e-05      0.18       1      26 [.      38      63 ..       6      66 .. 0.66
   2 ?   12.1   0.1     9e-05      0.18       1      27 [.      38      64 ..      38      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                                   HHHHHT--HHHHHHHHHHHTSS-HHH CS
                         HTH_18  1 laaalgvsrrtLqrlfkrvlgltpke 26
                                   +a+ +gvs rt++r+f++ + l +++
  gi|121639748|ref|YP_979972.1| 38 IAEDAGVSLRTFYRHFRSKHDLLFAD 63
                                   35566666666666666665555544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9e-05
                                   HHHHHT--HHHHHHHHHHHTSS-HHHH CS
                         HTH_18  1 laaalgvsrrtLqrlfkrvlgltpkey 27
                                   +a+ +gvs rt++r+f++ + l +++y
  gi|121639748|ref|YP_979972.1| 38 IAEDAGVSLRTFYRHFRSKHDLLFADY 64
                                   6899**************999888877 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0002      0.41       4      31 ..      21      51 ..      18      54 .. 0.86
   2 ?   -1.6   0.0       1.6   3.2e+03      11      27 ..     176     192 ..     169     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                         HTH_28  4 eiikllaaGh...svreaArelgisrrtvyr 31
                                     ++ la+G+   s+ ++A+  g+s rt yr
  gi|121639748|ref|YP_979972.1| 21 ALVRFLAQGVeatSAEQIAEDAGVSLRTFYR 51
                                   568999***88878888*************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                         HTH_28  11 aGhsvreaArelgisrr 27 
                                    + +s  e+Ar  ++  +
  gi|121639748|ref|YP_979972.1| 176 SDRSLGELARVCHVALE 192
                                    56799999999888655 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.39      15      51 ..      22      57 ..       8      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHHH-HH CS
                    HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTlykWkkkke 51
                                   ++ +   +  e ++ ++iae+ gvs +T+y+  + k+
  gi|121639748|ref|YP_979972.1| 22 LVRF-LAQGVEATSAEQIAEDAGVSLRTFYRHFRSKH 57
                                   3333.34556889*****************9764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1646.37
//
Query:       gi|121639749|ref|YP_979973.1|  [L=160]
Description: hypothetical protein BCG_3894 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.2e-30  102.9   3.6    1.4e-29  102.3   3.6    1.3  1  DUF2834    Protein of unknown function (DUF2834)
     0.0062   16.5   1.2       0.21   11.6   0.0    2.2  2  Colicin_V  Colicin V production protein


Domain annotation for each model (and alignments):
>> DUF2834  Protein of unknown function (DUF2834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   3.6   1.6e-33   1.4e-29       1      96 []      41     147 ..      41     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.6e-33
                        DUF2834   1 vYlllailglvlpwyfnipfvaeng..........lslalfiqdafanpaasslslDlliaavall.vfivvegrrlgvk 69 
                                    vY++++i++++l+wyfni+fv+++           +s+a++++ +f+npaass+ +D++ia+v+ll +f+  +g+r+g++
  gi|121639749|ref|YP_979973.1|  41 VYYVVGIASIALGWYFNIRFVQQYAhgaanplwgpGSWAEYVRLMFTNPAASSAGQDYTIANVILLpLFSTTDGYRRGLR 120
                                    7***********************668***************************************************** PP

                        DUF2834  70 rrwlyilltllvgvsfalPlfLalrer 96 
                                    r+wly++++l+++++fa+++++a+ er
  gi|121639749|ref|YP_979973.1| 121 RPWLYFVSSLFTSFAFAFAFYFATIER 147
                                    ***********************9886 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.4    0.0067        60      40      85 ..      26      68 ..       2      81 .. 0.62
   2 !   11.6   0.0   2.3e-05      0.21       5      42 ..     103     141 ..     101     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0067
                      Colicin_V 40 llypslaellae..lilspalaaiiaflllfllvllivsllgallskl 85
                                   +  p          ++l++ ++++++++ + l+ ++ ++++  + +++
  gi|121639749|ref|YP_979973.1| 26 FTRPAG-----GswFSLPECVYYVVGIASIALGWYFNIRFVQQYAHGA 68
                                   222222.....1344457888888888888888888888887776664 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.3e-05
                      Colicin_V   5 illilllsallGlrrGfvrevlsllg.wvvafvvaslly 42 
                                    ++l+ l+s+  G+rrG+ r +l++++ ++ +f++a+ +y
  gi|121639749|ref|YP_979973.1| 103 VILLPLFSTTDGYRRGLRRPWLYFVSsLFTSFAFAFAFY 141
                                    78999**************99998862556777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1204.91
//
Query:       gi|121639750|ref|YP_979974.1|  [L=191]
Description: hypothetical protein BCG_3895c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   63.5   0.0    3.3e-17   62.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.1e-15   58.1   0.0    1.7e-15   57.5   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    3.1e-10   40.7   0.0    4.6e-10   40.1   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      4e-07   30.0   0.0    4.6e-07   29.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      4e-07   29.4   0.0    4.9e-07   29.1   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00046   19.9   0.0    0.00055   19.6   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0025   17.2   0.0      0.004   16.5   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0054   16.5   0.0     0.0072   16.1   0.0    1.1  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.5e-20   3.3e-17       1      95 [.      39     133 ..      39     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.5e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-...CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv...edp 77 
                                    L++G G G+ ++al    a++++v++++ m+++ ++++ ++    +++++d +++ ++d+ f  vv++ +lhhv   + +
  gi|121639750|ref|YP_979974.1|  39 LEIGPGYGATLQALLGLTASLTAVEVDNSMVERLNRRYGQRA---RIIRGDGTQTGLPDDHFTSVVCFTMLHHVasaQLQ 115
                                    89*************777********************9996...89***************************99989* PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                    +++++e++RvL+pgG+++
  gi|121639750|ref|YP_979974.1| 116 DQLFAEAYRVLQPGGVFA 133
                                    ***************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   7.6e-19   1.7e-15       2      97 .]      39     130 ..      38     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 7.6e-19
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    L++G G G +++al+     a++t+v+++ +m+e+ ++r+   g ++++++gd ++  ++d++f  vv++ +lhh+  ++
  gi|121639750|ref|YP_979974.1|  39 LEIGPGYGATLQALLGLT--ASLTAVEVDNSMVERLNRRY---GQRARIIRGDGTQTGLPDDHFTSVVCFTMLHHVASAQ 113
                                    89*************886..********************...679***********************888***76665 PP

                                    .HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 .lekalkeiarvLkpgG 97 
                                     ++++++e++rvL+pgG
  gi|121639750|ref|YP_979974.1| 114 lQDQLFAEAYRVLQPGG 130
                                    1579************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0     2e-13   4.6e-10       1      99 []      39     132 ..      39     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2e-13
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    LeiG G G++l+all    ++++t+v+++ s++    e+l++r ++++  ++ + ++ +  d+  +f  vv++  lhh+ 
  gi|121639750|ref|YP_979974.1|  39 LEIGPGYGATLQALLGL--TASLTAVEVDNSMV----ERLNRRYGQRARIIRGDGTQTGLPDD--HFTSVVCFTMLHHVa 110
                                    8****************..**************....89999998888899999998765554..*************** PP

                Methyltransf_12  80 .kdir.evldnirklLkpgGrl 99 
                                     ++++ +++++++++L pgG++
  gi|121639750|ref|YP_979974.1| 111 sAQLQdQLFAEAYRVLQPGGVF 132
                                    *88887**************86 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     2e-10   4.6e-07      21     119 ..      33     136 ..       7     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2e-10
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae......pqgkfdlIvlrevleh 94 
                                    + g r L+iG+G+G +l+ l    +s+t+v+ +  +ve++      +  q  ++ + +      p+++f  +v++ +l+h
  gi|121639750|ref|YP_979974.1|  33 ELGPRTLEIGPGYGATLQALLGLTASLTAVEVDNSMVERLN----RRYGQRARIIRGDgtqtglPDDHFTSVVCFTMLHH 108
                                    556699**************99999*************975....4444443332222333455889************* PP

                Methyltransf_23  95 vpd...ppellrqiatllkpgGylllse 119
                                    v +      l++ +++ l pgG++  s+
  gi|121639750|ref|YP_979974.1| 109 VASaqlQDQLFAEAYRVLQPGGVFAGSD 136
                                    **866677**************987665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.2e-10   4.9e-07      34     125 ..      38     121 ..      11     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.2e-10
                                    EEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TT CS
                         RrnaAD  34 vleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPye 113
                                     leigpG G++ + L+    +++++E d++++++l+   + +++  ++  D+ ++ +p +            ++  l + 
  gi|121639750|ref|YP_979974.1|  38 TLEIGPGYGATLQALLGLTASLTAVEVDNSMVERLNR--RYGQRARIIRGDGTQTGLPDDH------FTSVVCFTMLHHV 109
                                    49***********************************..889****************944......4778888889999 PP

                                    THHHHHHHHHHG CS
                         RrnaAD 114 istqlvkqllee 125
                                    +s ql +ql+ e
  gi|121639750|ref|YP_979974.1| 110 ASAQLQDQLFAE 121
                                    999998888864 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.5e-07   0.00055      22     138 ..      12     128 ..       7     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-07
                           NodS  22 danefeqerlaqilrlslaqgsia.dalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqq 100
                                    +++ +e+   +q+l  +l++ +++  +le+G   Ga  + l  ++ +lt v+v ++ ++r ++r  + + i+    d +q
  gi|121639750|ref|YP_979974.1|  12 SSAGWEKAVANQLLPWALQHVELGpRTLEIGPGYGATLQALLGLTASLTAVEVDNSMVERLNRRYGQRARII--RGDGTQ 89 
                                    6778999999************98469****************************************88886..556555 PP

                           NodS 101 fs.tdekfdlivvaevlyyiedvaelraavrnlvsllap 138
                                        d++f  +v+  +l+++   +       +  ++l+p
  gi|121639750|ref|YP_979974.1|  90 TGlPDDHFTSVVCFTMLHHVASAQLQDQLFAEAYRVLQP 128
                                    541688999999999999987655444444555555555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06     0.004      59     163 ..      31     133 ..      20     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                    T--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS..S-EEEEES-GGG..---.--SEEEE CS
                           CMAS  59 elkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle..rkvevklldyed..lde.kvdrvvs 133
                                    +++ G + L+iG G+G++++          +glT S    ++ + +v++l+ +  +++++   d  +  l++ ++ +vv 
  gi|121639750|ref|YP_979974.1|  31 HVELGPRTLEIGPGYGATLQA--------LLGLTASLTAVEVDNSMVERLNRRygQRARIIRGDGTQtgLPDdHFTSVVC 102
                                    57789999********99864........567777777777777777766654113333333333331255469****** PP

                                    ES-GGGTSGGGH.HHHHHHHHHHS-TT-EEE CS
                           CMAS 134 vgafehvgkeny.dtffkklkkllkedGlll 163
                                    + ++ hv  +++ d+ f++++++l+++G+++
  gi|121639750|ref|YP_979974.1| 103 FTMLHHVASAQLqDQLFAEAYRVLQPGGVFA 133
                                    *******998873679************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.2e-06    0.0072       6     112 ..      37     137 ..      34     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl. 84 
                                    r l++G G G+ + +l       a ++ ++ +  ++e+ + +      ++++  +gd ++    l d+ f  ++++  l 
  gi|121639750|ref|YP_979974.1|  37 RTLEIGPGYGATLQALLG---LTASLTAVEVDNSMVERLNRR----YGQRARIIRGDGTQTG--LPDDHFTSVVCFTMLh 107
                                    678999999999999984...468899999999999999887....45799********988..889************4 PP

                Methyltransf_31  85 ..naladpdkileeiervlkpggilliedp 112
                                      +    +d+ + e+ rvl+pgg+++ +d 
  gi|121639750|ref|YP_979974.1| 108 hvASAQLQDQLFAEAYRVLQPGGVFAGSDG 137
                                    4444445778888***********987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1043.58
//
Query:       gi|121639751|ref|YP_979975.1|  [L=263]
Description: AraC family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-21   75.9   0.1    2.2e-21   75.9   0.1    3.3  4  HTH_18        Helix-turn-helix domain
      8e-15   54.5   0.0    1.5e-08   34.5   0.0    2.3  2  HTH_AraC      Bacterial regulatory helix-turn-helix proteins,
    1.8e-07   30.8   1.3      3e-07   30.1   1.3    1.3  1  Cupin_2       Cupin domain
    6.7e-05   22.8   0.8    6.7e-05   22.8   0.8    1.7  2  AraC_binding  AraC-like ligand binding domain
     0.0046   17.3   0.5     0.0046   17.3   0.5    2.6  2  HTH_31        Helix-turn-helix domain
      0.009   15.8   0.1       0.83    9.5   0.0    2.6  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.037   14.0   0.1    1.6  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.045   13.3   0.0      0.088   12.3   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4
      0.099   12.7   0.0       0.22   11.6   0.0    1.5  1  HTH_3         Helix-turn-helix
       0.17   11.7   0.0       0.35   10.7   0.0    1.5  1  TetR_N        Bacterial regulatory proteins, tetR family
       0.24   10.6   0.0        2.3    7.4   0.0    1.9  2  FmiP_Thoc5    Fms-interacting protein/Thoc5


Domain annotation for each model (and alignments):
>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.2   1.9e+03       7      32 ..       1      26 [.       1      28 [. 0.90
   2 ?    1.5   0.1      0.23   3.7e+02      30      45 ..     146     161 ..     145     172 .. 0.69
   3 !   75.9   0.1   1.3e-24   2.2e-21       4      78 ..     172     244 ..     169     247 .. 0.95
   4 ?   -0.9   0.2       1.3   2.1e+03      23      38 ..     246     261 ..     243     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                                   --HHHHHHHHHHHTSS-HHHHHHHHH CS
                         HTH_18  7 vsrrtLqrlfkrvlgltpkeylrrlR 32
                                   +s+ + +rl ++ l l+p + + r+R
  gi|121639751|ref|YP_979975.1|  1 MSENSHHRLATTSLTLPPGARIERHR 26
                                   79999999999999999999999998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                                    HHHHHHHHHHHHSSS- CS
                         HTH_18  30 rlRlerArrlLlentg 45 
                                    ++Rl++A++l+++n  
  gi|121639751|ref|YP_979975.1| 146 DRRLRHACALIADNLT 161
                                    69*******9987433 PP

  == domain 3  score: 75.9 bits;  conditional E-value: 1.3e-24
                                    HHT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS---HHHHHHHTT-S-HHHHHHHHHHHHSS-HHHH CS
                         HTH_18   4 algvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLlentglsvaeiAlalGFsdlsrFsrafrklfgetPsey 78 
                                    + gvs+rtL+rlf ++lg+t+ +++++lRl++A  lL+e   ++v+ +A ++G++++s+F++ +r++fg tP++ 
  gi|121639751|ref|YP_979975.1| 172 RIGVSQRTLSRLFSDELGMTFPQWRTQLRLQHALVLLAE--RHDVTSVASECGWATPSAFIDTYRQAFGHTPGQA 244
                                    789********************************9975..*******************************986 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.3
                                    -HHHHHHHHHHHHHHH CS
                         HTH_18  23 tpkeylrrlRlerArr 38 
                                     p++  r  Rl+rAr+
  gi|121639751|ref|YP_979975.1| 246 KPMAATRLTRLRRARD 261
                                    5889999999999996 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   9.2e-12   1.5e-08       1      42 []     156     197 ..     156     197 .. 0.97
   2 !   17.8   0.0   1.6e-06    0.0026      11      39 ..     214     243 ..     208     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 9.2e-12
                                    HHCCCSCT--HHHHHHHTTSSHHHHHHHHHHHSSS-HHHHHH CS
                       HTH_AraC   1 LrenlstnltiediAdelgfSrsyFsrlFkketGmtPsqyrt 42 
                                    +++nl+++lt+ +i    g+S++++srlF+ e+Gmt+ q+rt
  gi|121639751|ref|YP_979975.1| 156 IADNLTQPLTLQQIGGRIGVSQRTLSRLFSDELGMTFPQWRT 197
                                    789*************************************96 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.6e-06
                                    HHHHHHHTTS.SHHHHHHHHHHHSSS-HHH CS
                       HTH_AraC  11 iediAdelgf.SrsyFsrlFkketGmtPsq 39 
                                    ++++A+e+g   +s F+ ++++++G tP q
  gi|121639751|ref|YP_979975.1| 214 VTSVASECGWaTPSAFIDTYRQAFGHTPGQ 243
                                    899*************************87 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   1.3   1.8e-10     3e-07       3      64 ..      14      74 ..      12      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.8e-10
                                   EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS- CS
                        Cupin_2  3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdep 64
                                    +lppG+ +++hrHp + +++y   G + +t    +++     ++ +pag +H+++ +g+++
  gi|121639751|ref|YP_979975.1| 14 LTLPPGARIERHRHPSH-QIVYPSAGAVSVTTHAGTWITPVNRAIWIPAGCWHQHKFHGHTQ 74
                                   589**************.*************99999********************999876 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.8   4.1e-08   6.7e-05      12      82 ..      18      86 ..      16     134 .. 0.83
   2 ?   -2.2   0.0       2.2   3.5e+03     119     132 ..     176     189 ..     145     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.1e-08
                                   TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE---GGG CS
                   AraC_binding 12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfegelle 82
                                   p+ + ++h+h+ ++i+y  +G+++++   +t+  + +  +++p g++H+   ++  + +++ + +++  ++
  gi|121639751|ref|YP_979975.1| 18 PGARIERHRHPSHQIVYPSAGAVSVTTHAGTWITPVNRAIWIPAGCWHQHKFHG--HTQFHGVALDPQRYR 86
                                   567889******************************************999998..777777777776555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                                    HHHT-SSTTHHHHH CS
                   AraC_binding 119 etrsgddllleall 132
                                    ++r  ++l++++l 
  gi|121639751|ref|YP_979975.1| 176 SQRTLSRLFSDELG 189
                                    33333444444433 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   2.8e-06    0.0046       7      54 ..     147     205 ..     147     225 .. 0.83
   2 ?   -3.2   2.7       6.7   1.1e+04       7      13 ..     254     260 ..     248     263 .] 0.53

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-06
                         HTH_31   7 ralRera.........GLsqeevAerlgvsestlsrlEqGrrg..rpspavlealaral 54 
                                    r+lR ++          L++++ ++r+gvs+ tlsrl + + g   p++++  +l +al
  gi|121639751|ref|YP_979975.1| 147 RRLRHACaliadnltqPLTLQQIGGRIGVSQRTLSRLFSDELGmtFPQWRTQLRLQHAL 205
                                    89999999999999988*********************976663356666666665555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.7
                         HTH_31   7 ralRera 13 
                                     +lR+++
  gi|121639751|ref|YP_979975.1| 254 TRLRRAR 260
                                    4555443 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00051      0.83      18      38 ..     164     184 ..     147     189 .. 0.88
   2 ?    3.7   0.0     0.033        54       4      30 ..     197     224 ..     194     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                         HTH_23  18 lsvreIAreLgvsrrTvyrwl 38 
                                    l+ ++I  + gvs+rT++r  
  gi|121639751|ref|YP_979975.1| 164 LTLQQIGGRIGVSQRTLSRLF 184
                                    5889**************986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                         HTH_23   4 ereRlr.illllaeGlsvreIAreLgvs 30 
                                     + Rl+ +l llae++ v+ +A e+g+ 
  gi|121639751|ref|YP_979975.1| 197 TQLRLQhALVLLAERHDVTSVASECGWA 224
                                    5677777******************976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.3e-05     0.037      17      43 ..     159     185 ..     146     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                    EEEEEHHHHHHHHHTTSSHHHHHHHHH CS
                      HTH_Crp_2  17 eielpltqeelAsmlGltretvsrils 43 
                                     ++ plt ++++ ++G+++ t+sr++s
  gi|121639751|ref|YP_979975.1| 159 NLTQPLTLQQIGGRIGVSQRTLSRLFS 185
                                    4678********************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05     0.088      19      40 ..     162     183 ..     148     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                                    TT--HHHHHHHHTS-HHHHHHH CS
                     Sigma70_r4  19 eglTleEIgerlgiSrerVrqi 40 
                                    ++lTl++Ig r g+S+ + +++
  gi|121639751|ref|YP_979975.1| 162 QPLTLQQIGGRIGVSQRTLSRL 183
                                    89**************997775 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.22      10      32 ..     164     186 ..     157     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHTSSHHHHHHHHTT CS
                          HTH_3  10 lsqeeLAeklGvsrstisriEnG 32 
                                    l+++++  ++Gvs++t+sr++++
  gi|121639751|ref|YP_979975.1| 164 LTLQQIGGRIGVSQRTLSRLFSD 186
                                    67799999************987 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.35       5      38 ..     152     185 ..     149     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                                    HHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTS CS
                         TetR_N   5 ArelfaerGydattvreIAkrAGvskgalYryFp 38 
                                    A +l+a++  + +t+++I  r Gvs+++l r F+
  gi|121639751|ref|YP_979975.1| 152 ACALIADNLTQPLTLQQIGGRIGVSQRTLSRLFS 185
                                    7777777778899******************997 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.12     2e+02      78     101 ..     109     130 ..      92     132 .. 0.77
   2 ?    7.4   0.0    0.0014       2.3     300     349 ..     170     221 ..     154     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                     FmiP_Thoc5  78 skpedtkkeadehelmlaRLewEl 101
                                    s+ + t++  deh +mla L+ +l
  gi|121639751|ref|YP_979975.1| 109 SQADRTDT--DEHHRMLAVLQDQL 130
                                    55556666..**********9987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                     FmiP_Thoc5 300 asdllsseslLsnLfpgDtGlesPnpankyqlqklgl..eslsslleeasel 349
                                    ++ +  s+  Ls Lf++  G + P+  ++++lq++ +   + +++++ ase 
  gi|121639751|ref|YP_979975.1| 170 GGRIGVSQRTLSRLFSDELGMTFPQWRTQLRLQHALVllAERHDVTSVASEC 221
                                    567788999************************7766676666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1438.32
//
Query:       gi|121639752|ref|YP_979976.1|  [L=419]
Description: seryl-tRNA synthetase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-25   89.6   0.3    1.9e-25   89.2   0.3    1.2  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
    1.3e-24   87.1   0.0    1.9e-24   86.6   0.0    1.1  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 


Domain annotation for each model (and alignments):
>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.3   2.1e-29   1.9e-25       1     107 [.       1     105 [.       1     106 [. 0.98

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 2.1e-29
                                    ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHH CS
                   Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelk 80 
                                    M+D+kl+renp+av++++ +Rged+a+vd+ll +d++rr++++++++l+ae++++sk++g a+   e++  l+ ++kel 
  gi|121639752|ref|YP_979976.1|   1 MIDLKLLRENPDAVRRSQLSRGEDPALVDALLTADAARRAVISTADSLRAEQKAASKSVGGASP--EERPPLLRRAKELA 78 
                                    9**************************************************************8..58************ PP

                                    HHHHHHHHHHHHHHHHHHHHHCTS--- CS
                   Seryl_tRNA_N  81 eelkaleaelkeleaeleklllaiPNi 107
                                    e++ka+ea++ e+ea+++++ lai N+
  gi|121639752|ref|YP_979976.1|  79 EQVKAAEADEVEAEAAFTAAHLAISNV 105
                                    **************************8 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   2.1e-28   1.9e-24       8     179 .]     218     393 ..     213     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2.1e-28
                                    SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                    ++ ++L  t+e +++  ++ e+l   r Pl+++  ++++R+E+     d+rG++Rv++F++ +g+v++++a+++ + + l
  gi|121639752|ref|YP_979976.1| 218 GDGLYLVGTSEVPLAGYHSGEILDLSRGPLRYAGWSSCFRREAGshgkDTRGIIRVHQFDKVEGFVYCTPADAEHEHERL 297
                                    45699****************8888999***************66999******************************** PP

                                    HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimic 163
                                    +    +++ r+ +++r+i    ++   +++ k + ea+ + +++++e+ + +++ t +++rl +++ d  ++ +   +++
  gi|121639752|ref|YP_979976.1| 298 LGWQRQMLARIEVPYRVIDVAAGDLGSSAARKFDCEAWIPTQGAYRELTSTSNCTTFQARRLATRYRDASGKPQIAATLN 377
                                    **************999999999999****************************************************** PP

                                    EEEEHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 164 aaigveRllsaileqn 179
                                     +++++R l aile++
  gi|121639752|ref|YP_979976.1| 378 GTLATTRWLVAILENH 393
                                    **************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2988.74
//
Query:       gi|121639753|ref|YP_979977.1|  [L=452]
Description: hypothetical protein BCG_3898 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-77  259.7   0.0    2.8e-77  259.3   0.0    1.2  1  Septum_form  Septum formation


Domain annotation for each model (and alignments):
>> Septum_form  Septum formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.3   0.0   1.6e-81   2.8e-77       2     226 .]      98     322 ..      97     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 259.3 bits;  conditional E-value: 1.6e-81
                    Septum_form   2 GdCltwdesadasdlekVdCaeehrfevvaredlsaypgsefgagapppseeraaelaeelCeqavaeylggkldpagrf 81 
                                    GdCl w + ++ ++++ V+Ca+ehrfev++++d++++pg e+g++a+pps +r+++++ee+Ce+av++ylg+k+dp+++f
  gi|121639753|ref|YP_979977.1|  98 GDCLMWPD-GTPESAAIVSCADEHRFEVAESIDMRTFPGMEYGQNAAPPSPARIQQISEEQCEAAVRRYLGTKFDPNSKF 176
                                    9******9.78********************************************************************* PP

                    Septum_form  82 sigvilPseaaW.aaGdRtlrCglqvtgssgklvertgkvaeqdqskvaeagtClaikedkkaev.dpVdCaepHaaevv 159
                                    +i++++P ++aW +aG+R+++Cglq +g+++++++++gkva+ dqskv++agtCl+i++++++++  pVdCa+pHa+ev 
  gi|121639753|ref|YP_979977.1| 177 TISMLWPGDRAWrQAGERRMLCGLQSPGPNNQQLAFKGKVADIDQSKVWPAGTCLGIDATTNQPIdVPVDCAAPHAMEVS 256
                                    ************999**************************************************9************** PP

                    Septum_form 160 gvvdladkfpdaypseeeqdeklekaCaaaaaeYlggpdklrkstltvfwstlseesWkaGsrkvnC 226
                                    g+v+la++fpda+pse eqd ++++aC++++++Yl  p klr++tlt++++tl+  sW+aGsr v C
  gi|121639753|ref|YP_979977.1| 257 GTVNLAERFPDALPSEPEQDGFIKDACTRMTDAYLA-PLKLRTTTLTLIYPTLTLPSWSAGSRVVAC 322
                                    ************************************.59**************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3368.16
//
Query:       gi|121639754|ref|YP_979978.1|  [L=116]
Description: hypothetical protein BCG_3899 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-30  104.3   0.4    3.7e-30  103.9   0.4    1.1  1  Zincin_1  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.4   2.1e-34   3.7e-30       1      96 []      29     115 ..      29     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 2.1e-34
                                    --EEEEESS--B-TTS.....TT-B-.-EEEE---S-BTTB-.-GGG--EEEEEHHHHHHH--TT--HHHHHHHHHHHHH CS
                       Zincin_1   1 lenvavlvedkpdeevleelledepellGlyegvpltersaedagslpdrivlyrrpllavaetreeleeevretllHEi 80 
                                    ++nv+vlv++++         +++++llG yegv+lter +++agslpd i++yr++ll+++++++e++++v+ t++HE+
  gi|121639754|ref|YP_979978.1|  29 MDNVVVLVANRH---------PQHENLLGQYEGVALTERGSDYAGSLPDAITIYREALLDACDSEDEVVDQVAITVIHEV 99 
                                    689999999999.........68899****************************************************** PP

                                    HHHHTT-HHHHHHH.. CS
                       Zincin_1  81 ghhfGlddedleelga 96 
                                    +hhfG+dde+l++lg+
  gi|121639754|ref|YP_979978.1| 100 AHHFGIDDERLDQLGW 115
                                    **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1008.46
//
Query:       gi|121639755|ref|YP_979979.1|  [L=232]
Description: phosphoglycerate mutase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-36  123.3   0.2    1.1e-35  123.1   0.2    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
       0.16   10.8   0.1       0.22   10.4   0.1    1.2  1  PALB2_WD40  Partner and localizer of BRCA2 WD40 domain


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.2   1.3e-39   1.1e-35       1     192 [.       5     202 ..       5     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1.3e-39
                                    EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS- CS
                     His_Phos_1   1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrE 79 
                                    l+L+RHG++  n+e+r       + Lt++Gr qA+a+a+   + +++ + +S   Ra+qTa+ +a++l++  ++ +g++E
  gi|121639755|ref|YP_979979.1|   5 LVLLRHGQSYGNVERRlDTLPPGTALTPLGRDQARAFARSGCR-RPALLAHSVAIRAYQTAAVVAAELDMVAHEVAGIHE 83 
                                    79************99555589999*************99888.677789****************************** PP

                                    ---GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSE.....EEEEE-HHHHHHH CS
                     His_Phos_1  80 idfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarheget.....vlvVsHggviral 154
                                    +++G++e+++ +e+ +e+++++ +w+r++ dv+ pggE+ +dv +R  ++l +l+ r+ ++      ++vVsH ++ir++
  gi|121639755|ref|YP_979979.1|  84 VQVGELENRNDDEAVAEFNATYSRWHRGELDVPLPGGETANDVLDRYLPVLADLRMRYLDDGdwdgdIVVVSHSAAIRLA 163
                                    ****************************************************999998877777788************* PP

                                    HHHHHT--GGGGGGB---TT-EEEE.EE-SS-EEEEEEE CS
                     His_Phos_1 155 larllglpleelrrleldnaslsvl.efdeggwrlvrln 192
                                    +a l g++ +++ + +l+n + +vl  +++g+w++v+++
  gi|121639755|ref|YP_979979.1| 164 AAVLAGVDGNFVLDNHLENVESVVLaPITDGRWSCVQWG 202
                                    *****************7776665526899*******97 PP

>> PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   2.5e-05      0.22     293     332 ..     161     202 ..     122     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.5e-05
                     PALB2_WD40 293 qlaaavlt..sGaiavWdlllghctalllpesdesWslvrWs 332
                                    +laaavl+   G  ++ + l    + +l+p +d +Ws v+W 
  gi|121639755|ref|YP_979979.1| 161 RLAAAVLAgvDGNFVLDNHLENVESVVLAPITDGRWSCVQWG 202
                                    468999973369999999999999*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1828.97
//
Query:       gi|121639756|ref|YP_979980.1|  [L=321]
Description: prephenate dehydratase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-43  147.0   0.0    6.7e-43  146.6   0.0    1.2  1  PDT        Prephenate dehydratase
    7.2e-11   41.7   0.1    1.5e-10   40.7   0.1    1.6  1  ACT        ACT domain
  ------ inclusion threshold ------
      0.023   14.1   0.3       0.22   10.9   0.2    2.2  2  SBP_bac_3  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   1.1e-46   6.7e-43       1     180 [.       4     189 ..       4     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 1.1e-46
                                    EEEES-TTSHHHHHHCCCS.............EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSE CS
                            PDT   1 vaylGpegtyshqAalkvf........kaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdl 72 
                                    +aylGpegt+++ A+ +++        + +  + +pv+s ++++ av++g adya+vPiENs++GsV  tlD L+   +l
  gi|121639756|ref|YP_979980.1|   4 IAYLGPEGTFTEAALVRMVaaglvpetGPDALQRMPVESAPAALAAVRDGGADYACVPIENSIDGSVLPTLDSLAIGVRL 83 
                                    8***************998899998877778899****************************************9989** PP

                                    EEEEEEEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHH CS
                            PDT  73 kivgEvvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiaseva 152
                                    ++++E++l++++++++kp+ + ++++++ + p a +Q+r++L++hlp +  ++++s+a+Aa++   ++    aa+ s +a
  gi|121639756|ref|YP_979980.1|  84 QVFAETTLDVTFSIVVKPGRNAADVRTLAAFPVAAAQVRQWLAAHLPAADLRPAYSNADAARQ--VADGLVDAAVTSPLA 161
                                    ***************************************************************..7778899******** PP

                                    HHHTT-EEEECS-SS-S--EEEEEEEEE CS
                            PDT 153 aelyglkvleeniedkknntTRFlvlak 180
                                    a + gl  l+  + d++n +TRF+++++
  gi|121639756|ref|YP_979980.1| 162 AARWGLAALADGVVDESNARTRFVLVGR 189
                                    *************************998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   2.5e-14   1.5e-10       6      66 ..     207     267 ..     202     268 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.5e-14
                                    EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                    +  ++PG+L + ++ ++ rgi +++ie+r+++ +++++ f+v+ v++ d+e+v ealk++ 
  gi|121639756|ref|YP_979980.1| 207 RIDNQPGALVAALAEFGIRGIDLTRIESRPTRTELGTYLFFVDCVGHIDDEAVAEALKAVH 267
                                    55689*****************************************************985 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.051     3e+02     136     156 ..      38      58 ..      10      63 .. 0.72
   2 ?   10.9   0.2   3.6e-05      0.22      84     166 ..      92     165 ..      82     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.051
                                    EEESSHHHHHHHHHTTSSSEE CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 136 vefdtleealqaLkngrvdav 156
                                     ++++ ++al+a+++g +d++
  gi|121639756|ref|YP_979980.1|  38 MPVESAPAALAAVRDGGADYA 58 
                                    368899999999999999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                                    EEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3  84 sagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivefdtleealqaLkngrvdavvadspvl 163
                                    + + +++v+ ++  +  +++    L+     v a+ + + +l+ +l+  a++++ +++++a +++++g vda+v++  ++
  gi|121639756|ref|YP_979980.1|  92 DVTFSIVVKPGR--NAADVR---TLAAF--PVAAAQVRQ-WLAAHLP-AADLRPAYSNADAARQVADGLVDAAVTSPLAA 162
                                    555566666443..223333...33332..233333444.6666555.99************************998888 PP

                                    HHH CS
                                    xxx RF
                      SBP_bac_3 164 ayl 166
                                    a +
  gi|121639756|ref|YP_979980.1| 163 ARW 165
                                    765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2231.09
//
Query:       gi|121639757|ref|YP_979981.1|  [L=258]
Description: hypothetical protein BCG_3902 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   22.4   0.0    0.00033   21.2   0.0    1.6  1  DUF2470   Protein of unknown function (DUF2470)


Domain annotation for each model (and alignments):
>> DUF2470  Protein of unknown function (DUF2470)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.8e-08   0.00033       5      72 ..     174     240 ..     170     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-08
                                    HHHHHHH-HHHHHHHHHHCST-TTC.CEEEEEEE-SSEEEEEEC.....CEEEEEE-SS---SCCHHHH CS
                        DUF2470   5 iaHMNkDHaddlllylrhygkvkea.ksarmtdidldgltlrlgakagsektvripFdpplkswaeare 72 
                                    + H+ + H d +++++ ++  ++    + r +++d++g ++r+ a++ ++ ++r+pF++p++++  + +
  gi|121639757|ref|YP_979981.1| 174 LWHLATAHDDVVARLVSRLP-APLRrGQIRPLGLDRYGVRFRIEARD-GDRDIRLPFHKPVDDMTGLSQ 240
                                    569999*************6.455536669************85444.369***********9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1724.35
//
Query:       gi|121639758|ref|YP_979982.1|  [L=137]
Description: transcriptional regulatory protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-22   80.7   0.0    1.1e-20   74.4   0.0    2.0  1  LytR_cpsA_psr  Cell envelope-related transcriptional attenuat


Domain annotation for each model (and alignments):
>> LytR_cpsA_psr  Cell envelope-related transcriptional attenuator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   6.1e-25   1.1e-20      13     133 ..      20     121 ..      18     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 6.1e-25
                                    GGTEEEEEEE-TTBEE-----...-----EES-TTTTT-HHHHHHHHHHHHTS---EEEEE-HHHHHHHHHHHT---B-- CS
                  LytR_cpsA_psr  13 kkkkvklvSipRDtlveipggeskatgekkinsayalggaellvktvekllginidyYvevdfegfaklvdalgGvevdv 92 
                                    +++ ++l+SipRD++v ipg+     g +kin+a+algg  ll++tve  +g++ d+Y+ev f+ fa+lvda        
  gi|121639758|ref|YP_979982.1|  20 SDNPTTLISIPRDSYVPIPGH-----GRDKINAAFALGGGRLLTQTVELATGLHLDHYAEVGFSEFADLVDAFDP----- 89 
                                    567799**************8.....799******************************************8643..... PP

                                    ------------------B---HHHHHH------------- CS
                  LytR_cpsA_psr  93 kedvkdkeeselklkaGeqkldGeqalayvRfRkddeegDl 133
                                              +++l+aG q+ldG+ al yvR+R +    Dl
  gi|121639758|ref|YP_979982.1|  90 --------LAGVDLPAGCQTLDGRAALGYVRTRATPR-ADL 121
                                    ........46899********************9876.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1037.07
//
Query:       gi|121639759|ref|YP_979983.1|  [L=181]
Description: bacterioferritin bfrB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-33  114.0   2.9    6.2e-33  113.7   2.9    1.1  1  Ferritin      Ferritin-like domain
    2.7e-05   24.6   0.0    3.5e-05   24.2   0.0    1.3  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.093   13.1   0.2       0.24   11.8   0.1    1.8  2  kleA_kleC     Uncharacterized KorC regulated protein A


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   2.9     1e-36   6.2e-33       3     137 ..      14     144 ..      12     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1e-36
                                    HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSSH CS
                       Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgsv 81 
                                    +++eq+ +e+taa+qy a+a y+++++l++la++f+ qa eer+ha++l +++l+++      r+e++ ++++ + f+ +
  gi|121639759|ref|YP_979983.1|  14 LMQEQIHNEFTAAQQYVAIAVYFDSEDLPQLAKHFYSQAVEERNHAMMLVQHLLDRDL-----RVEIPGVDTVRNqFDRP 88 
                                    789*******************************************************.....************999** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeehewelealle 137
                                    +e+l+ al++e++vt+++ +l ++a++egD+  ++f+++fl+eq e+++ +++l++
  gi|121639759|ref|YP_979983.1|  89 REALALALDQERTVTDQVGRLTAVARDEGDFLGEQFMQWFLQEQIEEVALMATLVR 144
                                    ***************************************************99986 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.9e-09   3.5e-05       7      79 ..      19      92 ..      14     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.9e-09
                                   HHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG CS
                   Rubrerythrin  7 iagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl 79
                                   i +E++a + Y ++a  ++ e +pq+a+ F   A eEr Ha +l + l ++++  e+   + vr+++ ++ + l
  gi|121639759|ref|YP_979983.1| 19 IHNEFTAAQQYVAIAVYFDsEDLPQLAKHFYSQAVEERNHAMMLVQHLLDRDLRVEIPGVDTVRNQFDRPREAL 92
                                   889***********************************************999999777788888777776654 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.76   4.5e+03      32      44 ..      37      49 ..      15      66 .. 0.52
   2 ?   11.8   0.1     4e-05      0.24      14      74 ..      80     140 ..      73     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                      kleA_kleC 32 eAeeLvrqaeeLR 44
                                   + e+L + a++  
  gi|121639759|ref|YP_979983.1| 37 DSEDLPQLAKHFY 49
                                   3444444444333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4e-05
                      kleA_kleC  14 evatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaLedrakkrWtleeveqAkarA 74 
                                     v +++   R+++A  l +    + q+ +L a ++ e+  L ++ ++ +  e++e  +  A
  gi|121639759|ref|YP_979983.1|  80 TVRNQFDRPREALALALDQERTVTDQVGRLTAVARDEGDFLGEQFMQWFLQEQIEEVALMA 140
                                    344789999************************************9988888999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1353.82
//
Query:       gi|121639760|ref|YP_979984.1|  [L=274]
Description: glycerophosphoryl diester phosphodiesterase glpQ1 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-51  175.9   0.0    1.4e-51  175.8   0.0    1.0  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
       0.06   13.9   0.0       0.11   13.1   0.0    1.4  1  AXH       Ataxin-1 and HBP1 module (AXH)


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.0   1.5e-55   1.4e-51       1     258 [.      17     258 ..      17     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.5e-55
                                    TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCC CS
                           GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaq 80 
                                    HRGas+ +pE+Tl++++ A+++Gad +E+Dv+lT+Dg++V++HD++ldrt ++ag   v+ +tl++l++l+ +++++  +
  gi|121639760|ref|YP_979984.1|  17 HRGASAARPEHTLAAYDLALKEGADGVECDVRLTRDGHLVCVHDRRLDRTSTGAG--LVSTMTLAQLRELE-YGAWH-DS 92 
                                    *******************************************************..**************.99**9.** PP

                                    SCCCSSGCCB...BHHHHHHH..HHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTH CS
                           GDPD  81 lsenrvrlefpfptleevlkk..pqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnp 158
                                    ++++  ++++++ tl+ +++   +++  ++i +++++ + +++  e  ++   l +++ i +     ad  + ++ sf++
  gi|121639760|ref|YP_979984.1|  93 WRPDGSHGDTSLLTLDALVSLvlDWHRPVKIFVETKHPVRYGSLVE--NKLLALLHRFGIAA--PASADRSRAVVMSFSA 168
                                    ********************************************99..66667777777775..47899999999***** PP

                                    HHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSH CS
                           GDPD 159 dilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnede 238
                                    ++++++r+++p lp+++l +++ + +       aa +++a a+ ++ +a++e    p+lV+r +++g +v+++ v+++  
  gi|121639760|ref|YP_979984.1| 169 AAVWRIRRAAPLLPTVLLGKTPRYLTSS-----AATAVGATAVGPSLPALKEY---PQLVDRSAAQGRAVYCWNVDEY-- 238
                                    ********************99999998.....********************...**********************.. PP

                                    HHHHHHHCCC-SEEEES-HH CS
                           GDPD 239 eemkrlleagvdgvitDfpd 258
                                    e++++++e+gv ++ t++p+
  gi|121639760|ref|YP_979984.1| 239 EDIDFCREVGVAWIGTHHPG 258
                                    ******************97 PP

>> AXH  Ataxin-1 and HBP1 module (AXH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05      0.11      73     102 ..       7      36 ..       3      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                            AXH  73 cslehPfFvkgkGWsSfsPsltvqryglkc 102
                                    +   hPf v ++G s  +P++t++ y+l  
  gi|121639760|ref|YP_979984.1|   7 VLAGHPFVVAHRGASAARPEHTLAAYDLAL 36 
                                    6678***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1990.66
//
Query:       gi|121639761|ref|YP_979985.1|  [L=342]
Description: hypothetical protein BCG_3906c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-29  101.5  24.1    3.6e-29  101.5  24.1    2.1  2  DUF4328        Domain of unknown function (DUF4328)
  ------ inclusion threshold ------
      0.021   15.2   0.4      0.057   13.8   0.4    1.7  1  DUF1180        Protein of unknown function (DUF1180)
      0.051   13.6   0.3      0.086   12.9   0.3    1.3  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.18   11.8   0.4       0.32   11.0   0.4    1.3  1  DZR            Double zinc ribbon
       0.37   10.7   1.8        1.4    8.9   1.8    1.9  1  zinc_ribbon_4  zinc-ribbon domain
        1.5    8.8   6.0        5.1    7.1   6.0    1.8  1  Nudix_N_2      Nudix N-terminal
        6.4    7.0   7.5        1.5    9.0   0.1    3.2  3  UPF0547        Uncharacterised protein family UPF0547
        7.2    7.1   0.0        7.2    7.1   0.0    3.4  4  DUF5447        Family of unknown function (DUF5447)


Domain annotation for each model (and alignments):
>> DUF4328  Domain of unknown function (DUF4328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9      0.11   2.4e+02      14      37 ..     120     143 ..     110     151 .. 0.76
   2 !  101.5  24.1   1.6e-32   3.6e-29       2     166 ..     153     305 ..     152     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                        DUF4328  14 dalvelagllalllllaaavvflv 37 
                                     a+v+++ l++ll++ +a+vvf+v
  gi|121639761|ref|YP_979985.1| 120 PAAVRTTLLVSLLVFSIAVVVFVV 143
                                    567788888888888888888875 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 1.6e-32
                        DUF4328   2 tllldeealrladalvelagllalllllaaavvflvWlrraranaealapgrhrrspgwavggwlvPvvnLvlPlqvvad 81 
                                    ++ll+  +++++ +l +l++l+a++++ ++ v++++Wl+++ra+a+ +++ ++rrs++++++g+l P+vnL++++ +v +
  gi|121639761|ref|YP_979985.1| 153 NTLLNSVVASASVWLGVLVSLAAIAAAGTTIVLLVRWLVARRAAAFMHQGLPERRSARELWAGCLLPMVNLLWAPLYVIE 232
                                    6789999************************************************************************* PP

                        DUF4328  82 lwrasapeaqaaadprparlsallgvWWaaWvlsllldavvvrlsladaadtlqeladsvalsivadllaiaaavlalll 161
                                    l         a  ++r++rl++ + vWW++W++s++++++++++s   + +++q +a+++ ++++a+l+a+aa ++a+++
  gi|121639761|ref|YP_979985.1| 233 L---------ALVEDRYTRLRRPIVVWWIVWIVSNAISMFAFATS---WVTDAQGIANNTTMMVLAYLCAAAAVAAAARV 300
                                    *.........6778889999***********************99...******************************** PP

                        DUF4328 162 vrrit 166
                                    ++ ++
  gi|121639761|ref|YP_979985.1| 301 FEGFE 305
                                    *9987 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   2.5e-05     0.057      23     124 ..      46     148 ..      26     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                        DUF1180  23 sralspaasspeaepP.lpp.gataaespgkata.ieaksaqaaeggngsspragsaadaggslavvpelssntdkpmtl 99 
                                    +r + p+as ++ +pP lpp     a  pg a+   + +  ++   + +  pr g+++     +a vp  ++    p ++
  gi|121639761|ref|YP_979985.1|  46 ARPQVPTASDTRRTPPrLPPgFRWIAVRPGAAPPpRHGPRLRGPTPHYAGIPRWGLTD--HVDQAPVPASAKAGPSPAAV 123
                                    4566677777777777345553445556777765123445677778888888888884..4566778878899999**** PP

                        DUF1180 100 qrallvlvvvsaavivylvvRtvrl 124
                                    + +llv + v ++++v++vvR v l
  gi|121639761|ref|YP_979985.1| 124 RTTLLVSLLVFSIAVVVFVVRYVLL 148
                                    *********************9866 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.8e-05     0.086      72      95 ..       4      28 ..       1      34 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                                   EETTTS-EEECHHH.HHS-TTTSSS CS
                           HypA 72 rCreCgkefeleek.alrCpkCgsa 95
                                    C++Cg++++++e+ ++ Cp+C + 
  gi|121639761|ref|YP_979985.1|  4 VCSQCGTRWNVRERqRVWCPRCRGM 28
                                   6*********88855899****875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00014      0.32      13      36 ..       3      27 ..       2      34 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                            DZR 13 rfCseCgtklkavaa.edrCpsCge 36
                                   ++Cs+Cgt+ +  ++    Cp+C  
  gi|121639761|ref|YP_979985.1|  3 QVCSQCGTRWNVRERqRVWCPRCRG 27
                                   5799999997644446888999975 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.8   0.00062       1.4       1      32 [.       1      26 [.       1      27 [. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00062
                  zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCg 32
                                   M+ +C +C+++ +++++      ++v C++C+
  gi|121639761|ref|YP_979985.1|  1 MIQVCSQCGTRWNVRER------QRVWCPRCR 26
                                   8889***********95......678888885 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.0    0.0023       5.1       3      29 ..       5      26 ..       4      27 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                                   -TTT--B-EEE--TT-SS-EEEETTTT CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCg 29
                                   CsqCGt+ + r     +r+R +Cp+C 
  gi|121639761|ref|YP_979985.1|  5 CSQCGTRWNVR-----ERQRVWCPRCR 26
                                   ******96555.....7*********5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00065       1.5      15      25 ..       3      13 ..       2      14 .. 0.91
   2 ?    0.9   0.3      0.22   4.9e+02       3       7 ..      22      26 ..      21      28 .. 0.90
   3 ?   -2.3   0.3       2.3   5.1e+03       8      15 ..     108     115 ..     107     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00065
                        UPF0547 15 qfCphCGyvFq 25
                                   q+C+ CG++++
  gi|121639761|ref|YP_979985.1|  3 QVCSQCGTRWN 13
                                   89********6 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                        UPF0547  3 CPeCe 7 
                                   CP+C+
  gi|121639761|ref|YP_979985.1| 22 CPRCR 26
                                   ****7 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                        UPF0547   8 akvPvaaq 15 
                                    a+vP++a+
  gi|121639761|ref|YP_979985.1| 108 APVPASAK 115
                                    78****98 PP

>> DUF5447  Family of unknown function (DUF5447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   4.4       1.3   2.9e+03      12      72 ..       5      72 ..       3      84 .. 0.55
   2 ?   -1.5   0.0       1.6   3.5e+03      38      66 ..     179     209 ..     172     216 .. 0.65
   3 ?   -1.3   0.1       1.4     3e+03      48      73 ..     229     254 ..     214     262 .. 0.77
   4 ?    7.1   0.0    0.0032       7.2      59      83 ..     306     330 ..     286     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                        DUF5447 12 csvcwsrrevakpvasrftpcaecrpa.....gilkvelgrwkv..e...pasicakhtpserpaky.wsvv 72
                                   cs c +r +v    + +   c+ cr +     + + +  +rw+   +   p++   + tp++ p+ + w  v
  gi|121639761|ref|YP_979985.1|  5 CSQCGTRWNVR---ERQRVWCPRCRGMllaplADMPA-EARWRTpaRpqvPTASDTRRTPPRLPPGFrWIAV 72
                                   77776666666...33346699999874443222222.3677642231113344457788888887645444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                        DUF5447  38 agilkvelgrwkvepas..icakhtpserpa 66 
                                    ag + v l rw+v  ++  + ++  p +r a
  gi|121639761|ref|YP_979985.1| 179 AGTTIVLLVRWLVARRAaaFMHQGLPERRSA 209
                                    5667788899999765500444445777766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.4
                        DUF5447  48 wkvepasicakhtpserpakywsvvy 73 
                                    + +e a + +++t  +rp   w +v+
  gi|121639761|ref|YP_979985.1| 229 YVIELALVEDRYTRLRRPIVVWWIVW 254
                                    55667777888999999998887775 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0032
                        DUF5447  59 htpserpakywsvvydsgkptpfvp 83 
                                     +p erpa+ w vv   g+ +p   
  gi|121639761|ref|YP_979985.1| 306 QKPVERPAHRWVVVNTDGRSAPASS 330
                                    679***************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1150  (0.0641419); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2115.74
//
Query:       gi|121639762|ref|YP_979986.1|  [L=163]
Description: transposase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-14   52.0   0.0    8.2e-14   51.8   0.0    1.0  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   4.6e-18   8.2e-14       1     148 [.      14     160 ..      14     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.6e-18
                 DEDD_Tnp_IS110   1 vGiDvakdk.hdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvnpl 79 
                                    vGiD a +  h++++ d+ g + ++++v+ + +gl++l +k ++  +++   ve t+  + +l  ++++ag t+++  ++
  gi|121639762|ref|YP_979986.1|  14 VGIDAAITAcHHIAIRDDVGARSIRFSVEPTLAGLRTLTDK-LSGYDDIDATVEPTSMTWLPLTIAVENAGDTMHMAGAR 92 
                                    8*****998899999**************************.99******************9999************** PP

                 DEDD_Tnp_IS110  80 avkrlrklylrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlra 148
                                    +  rlr +  +k+K+D +DA+v+ ++     +l+pl+l++ a  +Lr+ + +r   v + +r  +rl +
  gi|121639762|ref|YP_979986.1|  93 HCARLRGAIVGKSKSDVIDAEVLTRASE-VFDLTPLTLPTPAQLALRRSVIRRAGAVIDANRSWRRLMS 160
                                    **************************99.9***********************9999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1045.90
//
Query:       gi|121639763|ref|YP_979987.1|  [L=119]
Description: hypothetical protein BCG_3908 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.066   13.5   2.6       0.11   12.8   2.6    1.6  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.6   6.1e-06      0.11      15      67 ..       4      55 ..       1      94 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-06
                      TetR_C_11 15 lralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrA 67
                                   +r++++  +s  agal r  la  ++dp+la+ +++ ++++r+ + +a ++ A
  gi|121639763|ref|YP_979987.1|  4 VRRVVTDRDS-GAGALARHPLAGRRTDPQLAAFYHRLMTTQRHCHTQATIAVA 55
                                   5777777777.7************************99999998888877544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 797.09
//
Query:       gi|121639764|ref|YP_979988.1|  [L=207]
Description: superoxide dismutase [Fe] sodA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-34  116.3   0.2    9.6e-34  115.6   0.2    1.4  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    1.3e-30  105.7   3.6    1.3e-30  105.7   3.6    1.5  2  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.2   1.1e-37   9.6e-34       1     102 []      91     193 ..      91     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.1e-37
                                    --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHH CS
                       Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldy 79 
                                    p+gela+ai ++fgs++kf+++f+aaa++v+gsGwa L +d+  +kL i+++ ++++++  + +plL lD+wehA+yl+y
  gi|121639764|ref|YP_979988.1|  91 PTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLgNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQY 170
                                    89***************************************97679********************************** PP

                                    TT-HHHHHHHHGGGBBHHHHHHH CS
                       Sod_Fe_C  80 qnkradYieafwnvvnWkeveer 102
                                    +n + d+ +afwnvvnW +v++r
  gi|121639764|ref|YP_979988.1| 171 KNVKVDFAKAFWNVVNWADVQSR 193
                                    ********************986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   3.6   1.4e-34   1.3e-30       1      82 []       3      84 ..       3      84 .. 0.98
   2 ?   -3.7   0.2       1.9   1.7e+04      71      79 ..     161     169 ..     160     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1.4e-34
                                   S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTB- CS
                       Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwknls 82
                                   +y+Lp+L+++y aLePhis ++ elHh+kHh+tYv+++N+a++kleea++k ++ ++  +ek+l++n +ghvnH+++wknls
  gi|121639764|ref|YP_979988.1|  3 EYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLS 84
                                   69******************************************************************************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.9
                                    HHHHHHHHH CS
                       Sod_Fe_N  71 hvnHslfwk 79 
                                    ++ H+++ +
  gi|121639764|ref|YP_979988.1| 161 MWEHAFYLQ 169
                                    689999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1536.18
//
Query:       gi|121639765|ref|YP_979989.1|  [L=177]
Description: hypothetical protein BCG_3910 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1172.58
//
Query:       gi|121639766|ref|YP_979990.1|  [L=302]
Description: hypothetical protein BCG_3911 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-36  122.8  26.7    7.2e-20   71.1   4.3    3.0  3  UPF0016   Uncharacterized protein family UPF0016
  ------ inclusion threshold ------
      0.065   13.1   0.0         15    5.4   0.0    2.2  2  PaRep2a   PaRep2a protein


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   7.1   5.8e-21   5.2e-17       2      75 .]       7      80 ..       6      80 .. 0.97
   2 !   71.1   4.3     8e-24   7.2e-20       2      75 .]     107     180 ..     106     180 .. 0.97
   3 ?    0.7   0.7     0.074   6.6e+02      29      45 ..     195     210 ..     188     226 .. 0.55

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 5.8e-21
                        UPF0016  2 aaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                    +++++flaElGD++ql++++   ry+++ V++G+++A + +++++v++G++l++ +p r    v+a++Fl+f+
  gi|121639766|ref|YP_979990.1|  7 LSLGAVFLAELGDRSQLITMTYTLRYRWWVVLTGVAIAAFTVHGVAVAIGHFLGSTVPARPAACVSAIAFLIFA 80
                                   5889*********************************************************************7 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 8e-24
                        UPF0016   2 aaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                    ++++ ++laElGDkT la+++La+ +++ +V++G++l+++l+++l++ +G  l +rlperl+++++++lFllfG
  gi|121639766|ref|YP_979990.1| 107 TVVSSFALAELGDKTTLATVTLASDHHWAGVWIGTTLGMILADGLAIGAGLLLHRRLPERLLQVLTGLLFLLFG 180
                                    677899********************9999*******************************************9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.074
                        UPF0016  29 plpVflGavlAlalmtv 45 
                                    +++V++++vlA a  t+
  gi|121639766|ref|YP_979990.1| 195 AIAVTAAVVLAAAT-TA 210
                                    33455555555433.33 PP

>> PaRep2a  PaRep2a protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0017        15      35      62 ..       8      35 ..       3      56 .. 0.74
   2 ?    5.4   0.0    0.0017        15      36      78 ..     109     149 ..      98     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0017
                        PaRep2a 35 qlakaikrelGgkaellasefalrrafw 62
                                    l  +  +elG +++l+++ ++lr  +w
  gi|121639766|ref|YP_979990.1|  8 SLGAVFLAELGDRSQLITMTYTLRYRWW 35
                                   56667789***************98766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0017
                        PaRep2a  36 lakaikrelGgkaellasefalrrafwweGewrGkplscfvte 78 
                                    + +++ +elG k+    +  +l     w G w G +l  ++++
  gi|121639766|ref|YP_979990.1| 109 VSSFALAELGDKT--TLATVTLASDHHWAGVWIGTTLGMILAD 149
                                    4678899***994..4566889999*********998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2148.18
//
Query:       gi|121639767|ref|YP_979991.1|  [L=132]
Description: hypothetical protein BCG_3912 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.2   0.0    0.00043   20.3   0.0    1.5  1  HTH_3     Helix-turn-helix
    0.00048   20.4   0.2      0.022   15.1   0.0    2.5  2  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.19   10.0   0.0       0.23    9.8   0.0    1.1  1  ActA      ActA Protein
       0.28   11.2   2.9        1.8    8.6   0.3    2.6  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.6e-08   0.00043      16      55 .]      35      75 ..      32      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.6e-08
                                   HHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHHTSEHHHH CS
                          HTH_3 16 AeklGvsrstisriEnG.ernPsletlkklakaLgvsldel 55
                                   Ae + +s  ++s++ +G ++nPs  t+ +la+++ ++ +++
  gi|121639767|ref|YP_979991.1| 35 AEGITMSAPYLSQLRSGnRTNPSGATMAALANFFRIKAAYF 75
                                   5667799****************************998886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     5e-06     0.022      21      55 ..      35      69 ..       6      73 .. 0.86
   2 ?    3.0   0.1     0.029   1.3e+02      23      52 ..      91     120 ..      86     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                         HTH_31 21 AerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                   Ae + +s+ +ls+l +G r++ps a+ +ala+ ++
  gi|121639767|ref|YP_979991.1| 35 AEGITMSAPYLSQLRSGNRTNPSGATMAALANFFR 69
                                   34445**************************9876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.029
                         HTH_31  23 rlgvsestlsrlEqGrrgrpspavlealar 52 
                                    ++ +  + ++r+ q ++g+ps a+   l r
  gi|121639767|ref|YP_979991.1|  91 LCTMRDDGVRRIAQRAHGLPSAAQQKVLDR 120
                                    556667889999999999999995555544 PP

>> ActA  ActA Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.1e-05      0.23     393     438 ..      65     110 ..      47     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.1e-05
                           ActA 393 eefsslnsgdftddensetteeeidrladlrdrgtgkhsrnagflp 438
                                     +f  +++  ftdde  e  ++e++ l+ +rd g  + ++ a  lp
  gi|121639767|ref|YP_979991.1|  65 ANFFRIKAAYFTDDEYYEKLDKELQWLCTMRDDGVRRIAQRAHGLP 110
                                    4677889999*************************99988887777 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.048   2.1e+02       7      16 ..      77      86 ..      77      91 .. 0.87
   2 ?    8.6   0.3   0.00039       1.8       8      22 ..     115     129 ..     112     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.048
                                   EHHHHHHHHH CS
                          RHH_1  7 deellerLde 16
                                   d+e++e+Ld+
  gi|121639767|ref|YP_979991.1| 77 DDEYYEKLDK 86
                                   89*******8 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00039
                                    HHHHHHHHHHHHHHT CS
                          RHH_1   8 eellerLdelarrrg 22 
                                    +++l+r+del+r++g
  gi|121639767|ref|YP_979991.1| 115 QKVLDRIDELRRAEG 129
                                    789**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1040.76
//
Query:       gi|121639768|ref|YP_979992.1|  [L=218]
Description: hypothetical protein BCG_3913 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1597.42
//
Query:       gi|121639769|ref|YP_979993.1|  [L=94]
Description: hypothetical protein BCG_3914 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   14.1   0.5      0.058   13.7   0.5    1.3  1  DUF3239   Protein of unknown function (DUF3239)
       0.86    9.3   3.0        1.5    8.5   3.0    1.4  1  DotU      Type VI secretion system protein DotU


Domain annotation for each model (and alignments):
>> DUF3239  Protein of unknown function (DUF3239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   6.4e-06     0.058      32      79 ..      45      91 ..      30      94 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                                   EEEE-BSSTTS---EEEEEEEES--TT-S-STT-EEEEEEEEEEEECS CS
                        DUF3239 32 aLvdiakdeaaepeyalalrtvtalpgverkvGervpsvavtgerssr 79
                                   a++ +a+ ++a+p++a+a++  + +p  ++ vG+ v++vav++ +++r
  gi|121639769|ref|YP_979993.1| 45 AFAHTAQLSTATPAPAVAATDANDVPTWPFVVGT-VAAVAVAALWAVR 91
                                   788899999************************8.9*****9998887 PP

>> DotU  Type VI secretion system protein DotU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.0   0.00017       1.5     162     201 ..      45      90 ..      11      92 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00017
                           DotU 162 alsphwqagdeaarrll....rrelplw..vilalallvllllflg 201
                                    a+++ +q +++++ +++    ++++p w  v++++a++++++l+++
  gi|121639769|ref|YP_979993.1|  45 AFAHTAQLSTATPAPAVaatdANDVPTWpfVVGTVAAVAVAALWAV 90 
                                    3555555555555555533323499988767777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 691.01
//
Query:       gi|121639770|ref|YP_979994.1|  [L=134]
Description: histone-like protein hns [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.5  21.7     0.0051   16.9  21.7    1.2  1  HC2       Histone H1-like nucleoprotein HC2
     0.0073   16.7   7.5     0.0093   16.4   7.5    1.3  1  DUF1180   Protein of unknown function (DUF1180)
  ------ inclusion threshold ------
       0.19   11.9   0.2       0.28   11.4   0.2    1.3  1  MHYT      Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> HC2  Histone H1-like nucleoprotein HC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  21.7   8.5e-07    0.0051     105     175 ..      19      95 ..      11     111 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.5e-07
                            HC2 105 vakKtvakkaaaakKpaakkavakkaaarKaaak...KavaKkaast.....ckkkhkkkaackrvasssakraasgsK 175
                                     akK +akk  aakK+ a+k+ akka+a+K+ ak    a +K+a +         +  + aa+++ a+  ak +  g+ 
  gi|121639770|ref|YP_979994.1|  19 PAKKLPAKK--AAKKAPARKTPAKKAPAKKTPAKgakSAPPKPAEAPvslqqRIETNGQLAAAAKDAAAQAKSTVEGAN 95 
                                    466666666..66666666666666666665543110333444443333332112222233333333333333344443 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   7.5   1.6e-06    0.0093      18     124 ..      28     133 ..       4     134 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                        DUF1180  18 saadasralspaasspeaepPlppgataaespgkataieaksaqaaeggngsspragsaadaggslavvpelssntdkpm 97 
                                    +a++a   ++pa+++p  + P ++ ++a  +p +a++ + ++    +g+ +  ++ ++a+ ++++++    l+ n + p 
  gi|121639770|ref|YP_979994.1|  28 AAKKAPARKTPAKKAPAKKTPAKGAKSAPPKPAEAPV-SLQQRIETNGQLAAAAKDAAAQAKSTVEGANDALARNASVPA 106
                                    3444444556666666666777665555545777777.333333333333333344444456666666667777888888 PP

                        DUF1180  98 tlqrallvlvvvsaavivylvvRtvrl 124
                                      +  + ++v+v+ ++++ l++R +r 
  gi|121639770|ref|YP_979994.1| 107 PSHSPVPLIVAVTLSLLALLLIRQLRR 133
                                    8889999999*************9986 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   4.8e-05      0.28      29      51 ..     111     133 ..      97     134 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                           MHYT  29 alSlliaivasvlAlalavrrrd 51 
                                     + l++a+++s+lAl+l+++ r+
  gi|121639770|ref|YP_979994.1| 111 PVPLIVAVTLSLLALLLIRQLRR 133
                                    4559*************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 950.13
//
Query:       gi|121639771|ref|YP_979995.1|  [L=157]
Description: ribonuclease activity regulator protein RraA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-41  142.0   1.1    1.8e-41  141.8   1.1    1.0  1  RraA-like  Aldolase/RraA


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   1.1     1e-45   1.8e-41       1     150 []       8     156 ..       8     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 1e-45
                                    HHHHHHH...........CEE-SSBSTB.TT.EESEEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSEC CS
                      RraA-like   1 tadvsDa...........lkklggrsggirplersfvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraal 69 
                                    tad++D+           ++++ggrs+        f+Gp+ Tv++++ dn+l+k++l+++ +g vlV+dg g  sl++al
  gi|121639771|ref|YP_979995.1|   8 TADLVDDigpdvrscdlqFRQFGGRSQ--------FAGPISTVRCFQ-DNALLKSVLSQPSAGGVLVIDGAG--SLHTAL 76 
                                    788999988888888888999999999........************.************************..889*** PP

                                    E-HHHHHHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEE CS
                      RraA-like  70 lGgllataakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvv 149
                                    +G+++a++a++ g+ G++v+GavRD a+lr +d+++ a+g++prk++k+ g+ge +v++++ggvt+ pgd+ ++D+dG++
  gi|121639771|ref|YP_979995.1|  77 VGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKT-GAGERDVEITLGGVTFVPGDIAYSDDDGII 155
                                    ********************************************98888.*****************************9 PP

                                    E CS
                      RraA-like 150 v 150
                                    v
  gi|121639771|ref|YP_979995.1| 156 V 156
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1220.71
//
Query:       gi|121639772|ref|YP_979996.1|  [L=489]
Description: monooxygenase ethA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-13   48.4   0.0    8.6e-12   44.2   0.0    2.2  2  FMO-like        Flavin-binding monooxygenase-like
    2.2e-10   40.6   0.0      1e-07   32.1   0.0    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.4e-09   34.9   0.0    8.1e-07   28.5   0.0    2.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-08   34.6   0.0    3.7e-08   33.0   0.0    1.8  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   34.0   4.9      2e-06   27.7   0.1    3.6  4  DAO             FAD dependent oxidoreductase
    7.6e-07   28.6   0.0      2e-05   23.9   0.0    2.3  2  Thi4            Thi4 family
    1.2e-06   28.0   0.0     0.0016   17.7   0.0    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      6e-05   23.1   0.0     0.0075   16.3   0.0    2.8  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    0.00011   22.2   0.6        0.2   11.7   0.0    3.5  3  NAD_binding_9   FAD-NAD(P)-binding
    0.00014   22.3   0.1      0.066   13.8   0.0    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00056   19.1   0.5       0.22   10.6   0.0    2.5  2  GIDA            Glucose inhibited division protein A
    0.00084   18.5   0.1     0.0047   16.1   0.0    2.0  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
       0.05   12.6   0.2          3    6.8   0.0    2.8  3  Lycopene_cycl   Lycopene cyclase protein
      0.056   12.3   0.0        5.5    5.7   0.0    2.3  2  Trp_halogenase  Tryptophan halogenase
      0.078   12.3   0.0       0.22   10.8   0.0    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
      0.091   11.3   0.0        1.1    7.8   0.0    2.2  2  Mqo             Malate:quinone oxidoreductase (Mqo)
      0.097   11.4   0.0       0.14   10.9   0.0    1.2  1  MCRA            MCRA family
       0.15   12.5   0.0       0.47   10.9   0.0    1.8  1  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.091        90       4      41 ..       7      46 ..       5      52 .. 0.73
   2 !   44.2   0.0   8.6e-15   8.6e-12      85     332 ..      80     346 ..      74     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.091
                       FMO-like  4 vaviGaGvsGlasikcclee..gleptcfersddiGGlwr 41
                                   v ++GaG+sG+++     +       + +e+ + +GG w 
  gi|121639772|ref|YP_979996.1|  7 VVIVGAGISGVSAAWHLQDRcpTKSYAILEKRESMGGTWD 46
                                   789*******998766555411234457899999999996 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 8.6e-15
                       FMO-like  85 klleylklfakefdllkyiqfkttvcsvkkrpdfst.sGqwevvtekegkkesavfdavmvctGhhvnphlplesfpGie 163
                                     +ley+k  a  +++ ++i+f+ +v+s     d+st   +w v  +++g   +   + + +c+G++ + +     f G e
  gi|121639772|ref|YP_979996.1|  80 PILEYVKSTAAMYGIDRHIRFHHKVISA----DWSTaENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSE 155
                                    589**********************985....55551578*************9****************9999****** PP

                       FMO-like 164 kfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsr.taeqvllstrsGswvlsrvsdsG........ypwdmll 234
                                     f G ++h +++ e   ++ k ++viG G ++  +   l+   a++v +  rs ++++s+   +G         p  m +
  gi|121639772|ref|YP_979996.1| 156 DFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADsGAKHVTMLQRSPTYIVSQPDRDGiaeklnrwLPETMAY 235
                                    ********************************99998887516899************9977777222222224667765 PP

                       FMO-like 235 v.trfksllkni........lptalsnw...lvekklnkrfn.henyglkpkkralakepvlndelparilaGavkvkss 301
                                    +  r+k++l+++         p+++ ++   l++++l + ++  +++g + +   ++   v n +l  +i  G+v+v ++
  gi|121639772|ref|YP_979996.1| 236 TaVRWKNVLRQAavysacqkWPRRMRKMflsLIQRQLPEGYDvRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTD 315
                                    42699999997521111111455554433335788888888834567877777777777899*************99876 PP

                       FMO-like 302 .vkeltetsaifedgtveedidvvifatGytf 332
                                     ++++t t  i  ++ +e + d++i atG  +
  gi|121639772|ref|YP_979996.1| 316 tIERFTATG-IRLNSGRELPADIIITATGLNL 346
                                    155566665.5556668999*********865 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     1e-10     1e-07       1      46 [.       9      56 ..       9      70 .. 0.90
   2 ?    5.9   0.0     0.015        15       1      28 [.     180     208 ..     180     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-10
                                   EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSSGGG-EECETTCEEC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlGGraasyevpgvrvd 46
                                   IvGaG+sG +aA++L+++   ++  +lekr++ GG +  +++pg+r d
  gi|121639772|ref|YP_979996.1|  9 IVGAGISGVSAAWHLQDRcpTKSYAILEKRESMGGTWDLFRYPGIRSD 56
                                   9****************99899****************9999997655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                    EE--SHHHHHHHHHHHCCTE.EEEEE-SS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvlllekr 28 
                                    ++G+G+++ ++  +La+ g+ +v+ l+++
  gi|121639772|ref|YP_979996.1| 180 VIGSGATAVTLVPALADSGAkHVTMLQRS 208
                                    8*****************7758**99986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   8.2e-10   8.1e-07       2     178 ..       6     212 ..       5     231 .. 0.71
   2 ?    3.3   0.0     0.039        39     198     239 ..     310     346 ..     301     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 8.2e-10
                                    SEEEE--SHHHHHHHHHHHH.HTS-EEEE.E.TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq.agakvtlv.e.legtclnggcllskallgvaedaeias..................... 57 
                                    dvv++G+G+ G++aa +l+     k + + e +e +  +++ + ++ +++ ++ +                         
  gi|121639772|ref|YP_979996.1|   6 DVVIVGAGISGVSAAWHLQDrCPTKSYAIlEkRESMGGTWDLFRYPGIRSDSDMYTL-Gfrfrpwtgrqaiadgkpiley 84 
                                    8******************97577777772334444444555556666666666643.2588888899999999888878 PP

                                    ....HHHHCHHHHCCCCHCCTCEEEE..ESCEEEEETEEECTCEEEEEESEEEE---EEE-BC....TCTTC.TTBEECC CS
                                    ....xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ....evvkklnqgielllgeevvkid..pgkkkvklekkkegdeekiaydklvlAtGssprdl....gipGvaenvgklv 127
                                          +  +  +i++ ++  v++ d  +++ + ++  ++ g    ++++ l+l++G  + d        G ++ vg  +
  gi|121639772|ref|YP_979996.1|  85 vkstAAMYGIDRHIRFHHK--VISADwsTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEgyspRFAGSEDFVGPII 162
                                    8877444455566777777..888885533345555445669999************96666521115558877777776 PP

                                    SECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                    Pyr_redox_2 128 rtldsaealklkllpkrivvvGgGyiGvElAaalaklgke.vtlveardrll 178
                                    ++ +  e l ++ +  +ivv+G+G+++v l  ala+ g++ vt++++ ++  
  gi|121639772|ref|YP_979996.1| 163 HPQHWPEDLDYDAK--NIVVIGSGATAVTLVPALADSGAKhVTMLQRSPTYI 212
                                    66666666665555..5********************7766******99876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.039
                                    EEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 198 vevklgtsvkeidgngeklevvledgeeidadlvvvavGvrp 239
                                    vev+   +++++++ g      l++g+e++ad +++a+G+  
  gi|121639772|ref|YP_979996.1| 310 VEVV-TDTIERFTATG----IRLNSGRELPADIIITATGLNL 346
                                    4444.33455555555....5899999999999999999865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   3.7e-11   3.7e-08       1     199 [.       8     211 ..       8     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.7e-11
                    Pyr_redox_3   1 iIiGaGPaGlaaaielkk.agledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeekl 78 
                                    +I+GaG  G++aa +l++ +  ++y ilEk  ++g ++  ++      +++       +  l + +    p ++ ++  +
  gi|121639772|ref|YP_979996.1|   8 VIVGAGISGVSAAWHLQDrCPTKSYAILEKReSMGGTWDLFRYPGIRSDSD-------MYTLGFRF---RP-WTGRQAIA 76 
                                    7***************9725789*******989999998888777664433.......33333333...34.45567788 PP

                    Pyr_redox_3  79 srkealeYlrevaksfel..piklfeeVesvkk..edegfevetske....tyeAkkviiAtGef..dkPnklnipGeek 148
                                     +k +leY+++ a+ + +  +i+ +++V s +   +++  +v+ +++     ++++++++  G++  d  + +++ G+e+
  gi|121639772|ref|YP_979996.1|  77 DGKPILEYVKSTAAMYGIdrHIRFHHKVISADWstAENRWTVHIQSHgtlsALTCEFLFLCSGYYnyDEGYSPRFAGSED 156
                                    999*************9944699*****988764367889998666445667889********9722556899******8 PP

                    Pyr_redox_3 149 ...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkga.eVtvvtrgsei 199
                                         +h ++ +e  +y  +++vViG + +av     l++ ga +Vt++ r+ + 
  gi|121639772|ref|YP_979996.1| 157 fvgPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAkHVTMLQRSPTY 211
                                    554467998988888**************************8637*****98765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1     2e-09     2e-06       1      36 [.       6      44 ..       6      47 .. 0.88
   2 ?    2.3   0.2       0.1     1e+02       2      29 ..     178     208 ..     177     215 .. 0.90
   3 ?   -0.2   0.0      0.57   5.7e+02     243     271 ..     272     306 ..     248     321 .. 0.71
   4 ?    3.1   0.1     0.058        58     154     210 ..     303     353 ..     300     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-09
                                   EEEEECTSHHHHHHHHHHHHT.T...EEEEESSSSTTSSG CS
                            DAO  1 dvviiGGGiiGlstAyeLarr.g...Vtllekgdiagsga 36
                                   dvvi+G+Gi G+s+A++L+ r +    ++lek++  g g+
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDRcPtksYAILEKRESMG-GT 44
                                   9*****************87775789*******8777.65 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                                    EEEECTSHHHHHHHHHHHHTT...EEEEESS CS
                            DAO   2 vviiGGGiiGlstAyeLarrg...Vtllekg 29 
                                    +v+iG+G + ++   +La  g   Vt l ++
  gi|121639772|ref|YP_979996.1| 178 IVVIGSGATAVTLVPALADSGakhVTMLQRS 208
                                    9****************9988999**99887 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.57
                                    EEE..EEETTTTEEEEEETTSEEEEEESSE.....E CS
                            DAO 243 vpe..tdddgrgvyvtprkdgrvlvGgtad.....e 271
                                    +pe   ++ ++g+++ p+ d+r+++ +++d      
  gi|121639772|ref|YP_979996.1| 272 LPEgyDVRKHFGPHYNPW-DQRLCLVPNGDlfraiR 306
                                    3334489999*******9.699*9999987654431 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.058
                                    HHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH.HTT CS
                            DAO 154 raaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll.gll 210
                                    ra++ + ve+++  +++++      ++g+ r ++g++  ad ++ a+G+  +l+ g +
  gi|121639772|ref|YP_979996.1| 303 RAIRHGKVEVVTD-TIERFT-----ATGI-RLNSGRELPADIIITATGLNLQLFgGAT 353
                                    5556666888888.777773.....5677.444476645699********99773332 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     2e-08     2e-05      18      56 ..       5      44 ..       2      49 .. 0.92
   2 ?    1.9   0.0      0.11   1.1e+02      13      48 ..     171     206 ..     164     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2e-08
                                   EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS--TT CS
                           Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailersvspGGG 56
                                    DvvivGaG sG++aa  l  + p    aile++ s+GG 
  gi|121639772|ref|YP_979996.1|  5 LDVVIVGAGISGVSAAWHLQDRcPTKSYAILEKRESMGGT 44
                                   6*********************99999**********874 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                    HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4  13 lkyaesDvvivGaGssGLtaayylakkpdlkvaile 48 
                                    l+y   ++v++G+G++ +t    la +   +v++l 
  gi|121639772|ref|YP_979996.1| 171 LDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQ 206
                                    579999************999999988555555555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0018       1.8       2      39 ..       4      41 ..       3      46 .. 0.85
   2 !   17.7   0.0   1.6e-06    0.0016     108     228 ..      93     211 ..      83     224 .. 0.86
   3 ?   -3.0   0.0         3     3e+03     324     339 ..     328     343 ..     291     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                    K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerqpef 39
                                   +lD++++G+G s +s a +l+++  +++   le+++++
  gi|121639772|ref|YP_979996.1|  4 HLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESM 41
                                   78999999999999999999999988888999998765 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.6e-06
                    K_oxygenase 108 qleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvG....tepkiPevleklegkervvHsseyle 183
                                     ++ ++rf ++v + +++++e+  ++tv+  +++g+ + l+++ l l  G     e + P ++ + +    ++H ++  e
  gi|121639772|ref|YP_979996.1|  93 GIDRHIRFHHKVISADWSTAEN--RWTVHI-QSHGTLSALTCEFLFLCSGyynyDEGYSPRFAGSEDFVGPIIHPQHWPE 169
                                    567889************9975..577776.579***************9555557789**999999889*******999 PP

                    K_oxygenase 184 rkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrseal 228
                                    +   + ++k+i+V+GsG +a  ++  l+++ + ++++++ rs+ +
  gi|121639772|ref|YP_979996.1| 170 DL--DYDAKNIVVIGSGATAVTLVPALADSGA-KHVTMLQRSPTY 211
                                    98..7999***************999988866.899999999876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3
                    K_oxygenase 324 geeetlevdavvlATG 339
                                    ++ ++l +d++++ATG
  gi|121639772|ref|YP_979996.1| 328 NSGRELPADIIITATG 343
                                    5567888999999999 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.11     1e+02      14      34 ..       6      26 ..       2      36 .. 0.85
   2 !   16.3   0.0   7.5e-06    0.0075      10      46 ..     173     209 ..     168     214 .. 0.92
   3 ?   -1.2   0.0         2     2e+03      76      88 ..     335     347 ..     320     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                                   EEEEES-SHHHHHHHHHHHCC CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlak 34
                                    v+++GaG  +  +a hL ++
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDR 26
                                   79***************9876 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.5e-06
                                    .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                   Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                    ++ k++++iG G +a  ++ +L+++g+k+v+ + R+ 
  gi|121639772|ref|YP_979996.1| 173 YDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSP 209
                                    6789******************************986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                                    -SEEEE-SSSSS- CS
                   Shikimate_DH  76 advvisataseep 88 
                                    ad++i+at+ +  
  gi|121639772|ref|YP_979996.1| 335 ADIIITATGLNLQ 347
                                    8*******87655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002       0.2       1      36 [.       8      40 ..       8      49 .. 0.73
   2 ?   -2.1   0.0       3.3   3.3e+03     116     154 ..      97     139 ..      83     140 .. 0.63
   3 !    6.2   0.2    0.0096       9.5      67     154 ..     251     343 ..     179     345 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                   +ivGaG++G++++ +L +r+      +  + +++e+
  gi|121639772|ref|YP_979996.1|  8 VIVGAGISGVSAAWHLQDRC---PTKSYAILEKRES 40
                                   7***************9998...3333344555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                  NAD_binding_9 116 tvevhraevv.dleeradgqavlladgas...laadaVvLAlG 154
                                    ++++h++ +  d ++++++++v+ ++  +   l+++ ++L+ G
  gi|121639772|ref|YP_979996.1|  97 HIRFHHKVISaDWSTAENRWTVHIQSHGTlsaLTCEFLFLCSG 139
                                    4666666665356777777888887775523367777788877 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0096
                  NAD_binding_9  67 ptfaeWlrerga..lee.aeeldpddfvpRalyGrYlrdlfeellarlpegvtvevh.raevvdleeradgq...avlla 139
                                       ++W r+ ++  l + +++  p+ +  R+++G + +   ++l+  +p+g  ++ + +++v+ ++++ +++    ++l+
  gi|121639772|ref|YP_979996.1| 251 SACQKWPRRMRKmfL-SlIQRQLPEGYDVRKHFGPHYNPWDQRLC-LVPNGDLFRAIrHGKVEVVTDTIERFtatGIRLN 328
                                    455555555554332.14566666666667777766666666666.334444444441346666666555532225899* PP

                  NAD_binding_9 140 dgaslaadaVvLAlG 154
                                    +g++l ad ++ A+G
  gi|121639772|ref|YP_979996.1| 329 SGRELPADIIITATG 343
                                    ************999 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.017        17       2      19 ..       7      24 ..       6      44 .. 0.83
   2 !   13.8   0.0   6.6e-05     0.066       1      37 [.     177     215 ..     177     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                                   EEEECSSHHHHHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgala 19
                                   vv+vG+G +g+ +A  l+
  gi|121639772|ref|YP_979996.1|  7 VVIVGAGISGVSAAWHLQ 24
                                   8**********9997775 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.6e-05
                                    EEEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSS.TT CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelg.kkVtvversdkll.rl 37 
                                    ++vv+G+G +++ l  ala+ g k+Vt+++rs++   ++
  gi|121639772|ref|YP_979996.1| 177 NIVVIGSGATAVTLVPALADSGaKHVTMLQRSPTYIvSQ 215
                                    59******************8878********9876555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00022      0.22       1      19 [.       6      24 ..       6      32 .. 0.91
   2 !    6.3   0.1    0.0043       4.3     108     167 ..     307     359 ..     302     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                   CEEEE-SSHHHHHHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaaa 19
                                   dv+++G+G +G+ AA+++ 
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQ 24
                                   79**************975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0043
                                    STTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSC CS
                           GIDA 108 epnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGr 167
                                    + ++e++++++e+        +g+++++g+++ a++++ atG   + +   g +++  G+
  gi|121639772|ref|YP_979996.1| 307 HGKVEVVTDTIERFTA-----TGIRLNSGRELPADIIITATGL--NLQLFGGATATIDGQ 359
                                    5678888888888855.....9********************8..555555555555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.7e-06    0.0047       1      37 [.       6      44 ..       6      47 .. 0.89
   2 ?   -0.4   0.0      0.48   4.8e+02       2      27 ..     178     204 ..     177     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                                   SEEEE--SHHHHHHHHHHHH..TTT-EEEEESSSGGGSG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaae..aGlkvavvekeqefgga 37
                                   Dv+++G+G++G +AA  +++    ++ a++ek +++gg+
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDrcPTKSYAILEKRESMGGT 44
                                   9******************9633559*********9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                                    EEEE--SHHHHHHHHHHHHTTT.-EEE CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvav 27 
                                    ++ViGsG+   +   ++a+ G+  v++
  gi|121639772|ref|YP_979996.1| 178 IVVIGSGATAVTLVPALADSGAkHVTM 204
                                    79******9999888888888855555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.003         3       1      32 [.       6      37 ..       6      48 .. 0.82
   2 ?   -0.1   0.1      0.37   3.6e+02       2      36 ..     178     211 ..     177     216 .. 0.79
   3 ?    1.7   0.0      0.11   1.1e+02     105     154 ..     306     348 ..     296     387 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                   Dvv++GaG  g+s A +l +  p  +  ++e 
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDRCPTKSYAILEK 37
                                   9****************977777766666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.37
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                    +vviG+G+  + l   l+++  + +v++++ sp  
  gi|121639772|ref|YP_979996.1| 178 IVVIGSGATAVTLVPALADSG-AKHVTMLQRSPTY 211
                                    89***********99995554.4578888887765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                  Lycopene_cycl 105 leakvesveeeea..geslvvleggrkirarlvvdarglaslkkarrlglQt 154
                                    +++kve v++  +  + + + l+ gr+++a +++ a+gl          lQ 
  gi|121639772|ref|YP_979996.1| 306 RHGKVEVVTDTIErfTATGIRLNSGRELPADIIITATGLN---------LQL 348
                                    567888887754445889999*****************54.........333 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0055       5.5       1      24 [.       6      29 ..       6      40 .. 0.83
   2 ?    4.4   0.0     0.014        14     175     220 ..     309     353 ..     303     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                                   EEEEE--SHHHHHHHHHHHHHTTT CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkg 24
                                   ++vivG+G++G  aA +l+     
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDRCPT 29
                                   69***************9987755 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                                    -EEEEEE-T..TS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT-- CS
                 Trp_halogenase 175 kvvevqlde..dgrveslrledgreveadlfiDcsGfrgllieqaLkt 220
                                    kv ev++d   +   +++rl++gre+ ad++i ++G +  l + a  t
  gi|121639772|ref|YP_979996.1| 309 KV-EVVTDTieRFTATGIRLNSGRELPADIIITATGLNLQLFGGA--T 353
                                    44.3333332344567899999***************99998877..3 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.22       1      37 [.       6      44 ..       6      45 .. 0.82
   2 ?   -2.5   0.0       2.5   2.5e+03     120     145 ..     322     344 ..     291     407 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAara..GakvlLveergvlGGl 37
                                   Dvv+vG+g++Gv AA     +   ++ +++e+r+ +GG+
  gi|121639772|ref|YP_979996.1|  6 DVVIVGAGISGVSAAWHLQDRcpTKSYAILEKRESMGGT 44
                                   9**************877665336788888888888886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                   FAD_oxidored 120 iesvtveskegrktirAkvfiDATgd 145
                                     ++++++s   ++++ A+++i ATg 
  gi|121639772|ref|YP_979996.1| 322 ATGIRLNS---GRELPADIIITATGL 344
                                    44444433...888999999999986 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0011       1.1       2      40 ..       4      42 ..       3      44 .. 0.93
   2 ?    0.6   0.0      0.16   1.6e+02     197     240 ..      97     139 ..      83     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                            Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerldkva 40
                                   + dvv++GaGi   + +  l++  p+ s ++le+ ++++
  gi|121639772|ref|YP_979996.1|  4 HLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMG 42
                                   68*******************************998875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                            Mqo 197 elklkhevkdlk.reedgkWkvkvkdlktgekkkvkakfvfiGaG 240
                                    +++++h+v + +  +++++W+v+++  ++g+ + ++ +f+f+ +G
  gi|121639772|ref|YP_979996.1|  97 HIRFHHKVISADwSTAENRWTVHIQ--SHGTLSALTCEFLFLCSG 139
                                    6888899888762456789*****9..567888899999999887 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.14       4      47 ..       7      48 ..       4      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                   EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS---------- CS
                           MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga 47
                                   + +vG+Gi++ +aA +L      p +   ile+ +++gg++d  
  gi|121639772|ref|YP_979996.1|  7 VVIVGAGISGVSAAWHLQDR--CPTKSYAILEKRESMGGTWDLF 48
                                   679**************765..57788899*********99866 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00047      0.47       4      45 ..     172     214 ..     171     269 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                  NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagak.vtvvapevkeele 45 
                                    d + k+++v+G G  A + v  l+++gak vt++    +++++
  gi|121639772|ref|YP_979996.1| 172 DYDAKNIVVIGSGATAVTLVPALADSGAKhVTMLQRSPTYIVS 214
                                    67889**********************7637776555433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 3169.62
//
Query:       gi|121639773|ref|YP_979997.1|  [L=216]
Description: TetR family transcriptional regulator [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-13   50.3   0.1    4.8e-13   48.7   0.0    1.9  2  TetR_N     Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.029   14.2   0.0       0.37   10.6   0.0    2.5  3  HTH_10     HTH DNA binding domain
       0.09   12.7   0.1        0.2   11.6   0.1    1.6  1  TetR_C_36  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0     8e-17   4.8e-13       1      45 [.      29      73 ..      29      75 .. 0.97
   2 ?   -2.4   0.0       0.7   4.2e+03       2      12 ..     171     181 ..     171     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 8e-17
                                   HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                         TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                   Il++A++l+++r  +  +v+++Ak AG+s++++Y yFpsKe+ l+
  gi|121639773|ref|YP_979997.1| 29 ILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLL 73
                                   9*****************************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.7
                                    HHHHHHHHHHH CS
                         TetR_N   2 ldaArelfaer 12 
                                    l++A++l++er
  gi|121639773|ref|YP_979997.1| 171 LATALNLMNER 181
                                    67888888886 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.61   3.7e+03       3      12 ..      24      33 ..      24      36 .. 0.84
   2 ?   10.6   0.0   6.2e-05      0.37      23      43 ..      44      64 ..      39      73 .. 0.89
   3 ?   -0.0   0.0      0.13   7.8e+02      21      35 ..     163     177 ..     161     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.61
                         HTH_10  3 dkqlevlklA 12
                                   d++l++l++A
  gi|121639773|ref|YP_979997.1| 24 DRELAILATA 33
                                   7999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.2e-05
                         HTH_10 23 rvtlkeLAkelGIskstlseh 43
                                   ++++++LAk  GIs++t++ +
  gi|121639773|ref|YP_979997.1| 44 DISVDDLAKGAGISRPTFYFY 64
                                   6899**************876 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.13
                         HTH_10  21 PRrvtlkeLAkelGI 35 
                                    PR+  + eLA +l++
  gi|121639773|ref|YP_979997.1| 163 PRTLPAHELATALNL 177
                                    99999******9987 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.4e-05       0.2      44     103 ..     140     198 ..     121     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                      TetR_C_36  44 evqrrvvaavaelleeevaageleppldlddlAyllvRiaEsflYadliageepdidkae 103
                                    +  ++ +a +a+++++e ++g+   +l++++lA +l  + E +l+a   age+p++ +a+
  gi|121639773|ref|YP_979997.1| 140 TFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASF-AGEQPSVPEAR 198
                                    566788999************************************986.67777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1465.97
//
Query:       gi|121639774|ref|YP_979998.1|  [L=335]
Description: hypothetical protein BCG_3919c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-13   51.0   0.0    2.8e-13   50.0   0.0    1.5  1  HHH_8          Helix-hairpin-helix domain
    2.5e-10   40.9   0.0    4.6e-10   40.0   0.0    1.5  1  PHP            PHP domain
     0.0049   16.7   0.0      0.014   15.3   0.0    1.8  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.037   13.5   0.0       0.15   11.5   0.0    2.0  2  RNase_P_p30    RNase P subunit p30
      0.043   13.9   0.2       0.64   10.1   0.0    2.8  2  CMD            Carboxymuconolactone decarboxylase family
       0.18   12.3   1.3       0.86   10.2   0.7    2.4  2  HEPN_SAV_6107  SAV_6107-like HEPN


Domain annotation for each model (and alignments):
>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   9.5e-17   2.8e-13       6      66 ..       5      68 ..       2      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 9.5e-17
                                   HHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHHTT...HCTTSTT--HHHHHHHHHH CS
                          HHH_8  6 daLeeladllelkgedpfrvraYrrAaraiealpeeitslee...eltklpgiGkkiaakieei 66
                                    aL+++a + ++++ dp rv aYr+Aa+ ie l+++ ++ ++   ++++l giG+k+a++i++ 
  gi|121639774|ref|YP_979998.1|  5 TALRQIAYYKDRNRHDPRRVMAYRNAADIIEGLDDAARQRHGqanSWQSLAGIGPKTAKVIAQA 68
                                   79*********************************999984445899**************986 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   1.6e-13   4.6e-10       1      74 [.      99     218 ..      99     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.6e-13
                                    EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEEE.. CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGleay 67 
                                    dlH+H++ s ++ +++  ee++++a++lg++  a+TDh+++             + ++ + ++++k  a ++++ G+e++
  gi|121639774|ref|YP_979998.1|  99 DLHLHSNWSdGS-API--EEMMATAAALGHQYCALTDHSPRLtianglspdrlrKQLDVIDELREKF-APLRILTGIEVD 174
                                    89******9444.666..************************************9999999998888.8*********** PP

                                    ............................................ CS
                                    xxxxxx.....................................x RF
                            PHP  68 vaddse.....................................k 74 
                                    + +d+                                       
  gi|121639774|ref|YP_979998.1| 175 ILEDGSldqepemldrldivvasvhsklsmdsaamtrrmvravA 218
                                    **999866666666666665555555555555555555555550 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-06     0.014      13      29 ..      51      67 ..      49      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                                   HHTSTT-SHHHHHHHHH CS
                            HHH 13 LlalPGVGpktAeaIls 29
                                   +++l G+GpktA +I++
  gi|121639774|ref|YP_979998.1| 51 WQSLAGIGPKTAKVIAQ 67
                                   799***********975 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   3.3e+03      95     115 ..      57      77 ..      38      78 .. 0.81
   2 ?   11.5   0.0   4.9e-05      0.15      11     110 ..     108     211 ..      99     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                    EE--SHHHHHHHHHT.T-SEE CS
                    RNase_P_p30  95 vrPttekalraacenldvDii 115
                                    + P+t k++ +a +  + D++
  gi|121639774|ref|YP_979998.1|  57 IGPKTAKVIAQAWSGREPDLL 77 
                                    789999***999999999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.9e-05
                                    ........HHHHHHHHH-SEEEEEEEEEESS---HHHHH..........HHHHHHHH..HHSSEEEEEEES-H.HHHHHH CS
                    RNase_P_p30  11 dskkks.rtiktlaelgytgvainftveaekekkpnase...pikeelkelkkelsglkllsRvtlvvsdpsklqrlskv 86 
                                    d +++  +++ t+a+lg +  a++ +    + +   +++   ++   ++el++++  l++l+++++ + +  +l +  ++
  gi|121639774|ref|YP_979998.1| 108 DGSAPIeEMMATAAALGHQYCALTDHSPRLTIANGLSPDrlrKQLDVIDELREKFAPLRILTGIEVDILEDGSLDQEPEM 187
                                    333333579999999999999999998854444444444665555568999999999***********999999****** PP

                                    HHH--EEEEE--SHHHHHHHHHT. CS
                    RNase_P_p30  87 rqkfdllavrPttekalraacenl 110
                                     ++ d++++   ++  +  a+++ 
  gi|121639774|ref|YP_979998.1| 188 LDRLDIVVASVHSKLSMDSAAMTR 211
                                    *******99887777777777665 PP

>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.41   1.2e+03      60      81 ..      77      97 ..      70      98 .. 0.66
   2 ?   10.1   0.0   0.00021      0.64      31      62 ..     117     150 ..     116     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.41
                                   HHHHHHHHHHHHSHHHHHHHHH CS
                            CMD 60 iaevlaqaaayagwpaaraAla 81
                                   +ae+ a a++  g+ a+raAl+
  gi|121639774|ref|YP_979998.1| 77 LAELRADAEDL-GGGAIRAALR 97
                                   55555555555.5599999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00021
                                    HHHHHHTT-HHHH.HHHHHHHH.HTT--HHHHHH CS
                            CMD  31 lavsaangceyCv.daHtraAl.eaGvteeeiae 62 
                                    +a++aa+g +yC+   H  ++   +G+++++++ 
  gi|121639774|ref|YP_979998.1| 117 MATAAALGHQYCAlTDHSPRLTiANGLSPDRLRK 150
                                    79************666666666*******9975 PP

>> HEPN_SAV_6107  SAV_6107-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00029      0.86       9      56 ..      17      64 ..      11      97 .. 0.84
   2 ?   -1.1   0.0      0.92   2.7e+03      12      36 ..     247     271 ..     240     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                  HEPN_SAV_6107  9 eryaaahlaAlraAaAvLaargrperrrrrprsaWelLaevaPelaew 56
                                   +r     + A r Aa +++   + +r+r+++++ W+ La + P+ a++
  gi|121639774|ref|YP_979998.1| 17 NRHDPRRVMAYRNAADIIEGLDDAARQRHGQANSWQSLAGIGPKTAKV 64
                                   5666677889**********99999***************99987764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.92
                  HEPN_SAV_6107  12 aaahlaAlraAaAvLaargrperrr 36 
                                    a+a  +A r  + ++++++rperr 
  gi|121639774|ref|YP_979998.1| 247 AEAVFTACREHGTAVEINSRPERRD 271
                                    4577889999999999999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2315.76
//
Query:       gi|121639775|ref|YP_979999.1|  [L=65]
Description: hypothetical protein BCG_3920c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 523.87
//
Query:       gi|121639776|ref|YP_980000.1|  [L=488]
Description: glutamate synthase subunit beta [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-26   91.9   0.4      2e-25   89.6   0.4    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.4e-24   84.8   0.0    4.8e-24   84.3   0.0    1.2  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    1.2e-10   41.5   0.1    5.6e-10   39.3   0.0    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.3e-10   40.0   1.3    2.2e-05   24.9   0.1    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.3e-09   37.9   1.7    8.2e-09   35.3   0.2    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
    4.7e-08   32.6   0.0     0.0047   16.2   0.0    3.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.1e-08   32.6   3.4      2e-05   24.4   0.3    2.6  2  DAO             FAD dependent oxidoreductase
    2.4e-07   30.5   0.0    4.1e-07   29.7   0.0    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    1.3e-06   27.8   1.0    6.5e-06   25.5   0.0    2.4  3  FAD_binding_2   FAD binding domain
    3.7e-06   25.9   1.0    1.9e-05   23.6   0.1    2.3  2  HI0933_like     HI0933-like protein
    1.6e-05   25.3   1.5     0.0072   16.8   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    2.9e-05   23.5   0.2      0.025   13.9   0.0    3.2  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    4.2e-05   22.9   0.2    4.2e-05   22.9   0.2    2.0  2  FAD_binding_3   FAD binding domain
    0.00021   19.9   0.0      0.017   13.6   0.0    2.1  2  FMO-like        Flavin-binding monooxygenase-like
    0.00023   20.5   0.4    0.00073   18.8   0.0    1.9  2  Thi4            Thi4 family
     0.0015   17.9   1.9      0.072   12.4   0.3    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0021   18.6   0.0        1.8    9.2   0.1    2.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.003   16.7   0.0        1.2    8.3   0.0    2.7  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0038   16.4   0.0     0.0038   16.4   0.0    2.2  3  GIDA            Glucose inhibited division protein A
     0.0045   17.1   0.5        1.2    9.1   0.1    2.4  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0073   16.4   0.0       0.85    9.7   0.0    2.2  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.6   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.013   15.4   1.6      0.095   12.5   0.1    2.8  3  DJ-1_PfpI       DJ-1/PfpI family
      0.022   13.8   0.3      0.054   12.5   0.1    1.7  2  Lycopene_cycl   Lycopene cyclase protein
      0.025   14.6   4.5      0.049   13.6   0.1    3.3  4  NAD_binding_9   FAD-NAD(P)-binding
       0.03   14.3   0.0      0.057   13.4   0.0    1.4  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.033   14.1   0.1       0.46   10.3   0.0    2.2  2  YjeF_N          YjeF-related protein N-terminus
      0.055   13.0   1.2       0.18   11.4   0.0    2.0  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
        0.1   12.9   0.0        2.3    8.6   0.0    2.6  2  Kelch_3         Galactose oxidase, central domain
       0.12   12.0   0.0       0.22   11.1   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.13   12.0   0.1        2.1    8.0   0.0    2.1  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
       0.14   12.4   0.9       0.78   10.0   0.0    2.3  2  TrkA_N          TrkA-N domain
          5    5.9   6.3       0.34    9.7   0.1    2.0  3  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.4   3.7e-28     2e-25       2     294 .]     146     459 ..     145     459 .. 0.66

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.7e-28
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCT.CEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgee.vvkid 79 
                                     v+v+G+GpAGlaaa++l +ag+ vt++e+e+ +   g ll + + +++ +++ + + +++++++  e++ g++ +v+i 
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRI---GGLLRYGIPEFKMEKRHLDRRLDQMRSEgTEFRPGVNvGVDI- 221
                                    59**************************655544...457888888888888877755566665557777775544444. PP

                                    ESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC...............TTBEECCSECHHHHHHCCSS-TSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  80 pgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGv..............aenvgklvrtldsaealklkllpkr 144
                                      ++k+             ++d++vlA G+   r l+ipG               a+ v+++ + ld++ +     + k+
  gi|121639776|ref|YP_980000.1| 222 -SAEKLR-----------ADFDAVVLAGGAtAWRELPIPGRelegvhqameflpwANRVQEGDDVLDEDGQPPITAKGKK 289
                                    .333444...........589********9456777***998555555555555555555555555555555555555** PP

                                    EEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSS..TTS-.....HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                    Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgke.vtlveardrll..rald.....kelsaaleealekeGvevklgtsvkeidgnge.. 214
                                    +v++GgG +G ++ ++ ++ g+  v+  e ++r+   ra         l  ++ +a+e+ G e ++  + +++ g +   
  gi|121639776|ref|YP_980000.1| 290 VVIIGGGDTGADCLGTVHRQGAIaVHQFEIMPRPPdaRAEStpwptYPLMYRVSAAHEEGG-ERVFSVNTEAFVGTDGrv 368
                                    ********************99446655555555443222111222334444444544433.333344444455555444 PP

                                    ......EEEEEETTSCE.........EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                    ......xxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 215 ......klevvledgee.........idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDva 278
                                          +  v   dg+          ++adlv++a G+    +     +lg++ +e+g +   +   t+vpg++++GD+ 
  gi|121639776|ref|YP_980000.1| 369 salrahE--VNMLDGKFvkvegsdfeLEADLVLLAMGFVGPERAGLlTALGVKFTEHGNVARGDDFDTSVPGVFVAGDMG 446
                                    4443221..22222222334444456***********8655544235*******************************98 PP

                                    TECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 279 ggkggpelaqaAvqqG 294
                                       +g  l++ A+++G
  gi|121639776|ref|YP_980000.1| 447 ---RGQSLIVWAIAEG 459
                                    ...6767777666665 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   8.8e-27   4.8e-24       2     112 ..      25     132 ..      24     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 8.8e-27
                                    TTS-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GGGTG CS
                        Fer4_20   2 aknfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqeelC 81 
                                     ++++ev++++++e+  ++A+RC++C  + c++gCP+ + ipe+ + +++g++++a++ +++tn++p  +gr+Cp    C
  gi|121639776|ref|YP_980000.1|  25 LRDWREVYEEFDNESLRQQATRCMDCGIPFCHNGCPLGNLIPEWNDLVRRGRWRDAIERLHATNNFPDFTGRLCPAP--C 102
                                    57899**********************************************************************99..* PP

                                    CCS-GGGTTB.----HHHHHHHHHHHHHHT- CS
                        Fer4_20  82 egaCvlekkgkepvaigklerfvadaareeg 112
                                    e aCvl+ ++ +pv+i+++e  ++d+a +eg
  gi|121639776|ref|YP_980000.1| 103 EPACVLGINQ-DPVTIKQIELEIIDKAFDEG 132
                                    ******9766.9***********99998765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0     1e-12   5.6e-10       1      35 [.     149     183 ..     149     199 .. 0.93
   2 ?   -1.3   0.0       4.9   2.7e+03       1      26 [.     292     318 ..     292     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1e-12
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35 
                                    +vG+G +Gl+aA+ L++ag+ v+++e+ dr+GG +
  gi|121639776|ref|YP_980000.1| 149 VVGSGPAGLAAAQQLTRAGHTVTVFEREDRIGGLL 183
                                    8********************************65 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.9
                                    EE--SHHHHHHHHHHHCCTE.EEEEE- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvllle 26 
                                    I+G+G +G+ +  + +++g+  v+ +e
  gi|121639776|ref|YP_980000.1| 292 IIGGGDTGADCLGTVHRQGAiAVHQFE 318
                                    899999998777777776554566665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   4.1e-08   2.2e-05       2      35 ..     147     180 ..     146     190 .. 0.94
   2 !   10.4   0.0    0.0014      0.75       1      33 [.     289     322 ..     289     330 .. 0.80
   3 ?    1.3   0.0      0.93     5e+02       8      26 ..     403     421 ..     398     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.1e-08
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                    v+vvG+G  gl +A+ l++ g+ Vtv+er+d++ 
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIG 180
                                    89******************************97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0014
                                    EEEEECSSHHHHHHHHHHHHTTS.EEEEEESSSS CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgk.kVtvversdk 33 
                                    kvv++GgG++g ++ g+ ++ g+  V+ +e +++
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVHRQGAiAVHQFEIMPR 322
                                    79************99999977437777776666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.93
                                    SHHHHHHHHHHHHTTSEEE CS
                      Pyr_redox   8 GyiglElAgalaelgkkVt 26 
                                    G++g E Ag l++lg k t
  gi|121639776|ref|YP_980000.1| 403 GFVGPERAGLLTALGVKFT 421
                                    9**************9876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.2   1.5e-11   8.2e-09       2      30 ..     155     183 ..     154     185 .. 0.94
   2 ?   -0.9   0.0       1.4   7.6e+02     226     272 ..     196     248 ..     193     266 .. 0.60
   3 ?   -0.1   0.2      0.79   4.3e+02     418     451 ..     435     466 ..     419     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.5e-11
                                    HHHHHHHHHHHTTEEEEEEESSSSSBTTS CS
                  Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRi 30 
                                    aGLaaA+qL++aG+ Vtv+E +dr+GG +
  gi|121639776|ref|YP_980000.1| 155 AGLAAAQQLTRAGHTVTVFEREDRIGGLL 183
                                    9**************************76 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                    ETSEEEEEEEEETTC......EEEEETTSTEE.EESEEEE-S-HHHHHSSEEES CS
                  Amino_oxidase 226 rlntrVkeikregdg......vtvtledgevv.eaDaVvvTvplgvlkailfsP 272
                                    +l++r+ +++ eg +      v+v ++  + + ++DaVv++    + + +l  P
  gi|121639776|ref|YP_980000.1| 196 HLDRRLDQMRSEGTEfrpgvnVGVDISAEKLRaDFDAVVLAGGATAWR-ELPIP 248
                                    566666666664443344434555554444448999999999988888.55555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.79
                                    CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                  Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraAari 451
                                     +p++f+AG+       + +  Ai  G+ aAa++
  gi|121639776|ref|YP_980000.1| 435 SVPGVFVAGDMGR--GQSLIVWAIAEGRAAAAAV 466
                                    589********66..7777************987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.6e-06    0.0047       2      32 ..     149     179 ..     137     192 .. 0.77
   2 !   12.2   0.0   0.00015     0.082     162     305 .]     285     443 ..     273     443 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg.ni 32 
                                    ++G GPaGlaaa +l +ag  ++++ E++ +i
  gi|121639776|ref|YP_980000.1| 149 VVGSGPAGLAAAQQLTRAGH-TVTVFEREdRI 179
                                    78888888888888888887.68888887444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00015
                    Pyr_redox_3 162 yagqkvvViGgknSavDaAlelvrkga.eVt...vvtrgseiek.eesdpsyslkpdienrleelvke............ 224
                                     +g+kvv+iGg+++++D    + r+ga  V+   ++ r    ++ +   p y l  ++    ee+ ++            
  gi|121639776|ref|YP_980000.1| 285 AKGKKVVIIGGGDTGADCLGTVHRQGAiAVHqfeIMPRPPDARAeSTPWPTYPLMYRVSAAHEEGGERvfsvnteafvgt 364
                                    6799**************99999999733331113333332222022334444444444444443333433343333333 PP

                    Pyr_redox_3 225 .ekikvlfnaevkeikekeeey...kvktedgkkvevkddvvla.tGykpd..lsflkkslfeldedgrpvlteeteetn 297
                                     +        +v +++ +e+++   k  + +g+ +e + d vl+ +G+     + +l++ +++ +e g  v   ++ +t 
  gi|121639776|ref|YP_980000.1| 365 dG--------RVSALRAHEVNMldgKFVKVEGSDFELEADLVLLaMGFVGPerAGLLTALGVKFTEHGN-VARGDDFDTS 435
                                    33........444444444333222222334455566555554449*9876447789988998866665.5577899999 PP

                    Pyr_redox_3 298 vpglflaG 305
                                    vpg+f+aG
  gi|121639776|ref|YP_980000.1| 436 VPGVFVAG 443
                                    *****999 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3   3.6e-08     2e-05       2      33 ..     147     180 ..     146     190 .. 0.95
   2 !    8.3   0.2    0.0028       1.5     157     271 ..     205     301 ..     195     332 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.6e-08
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                    v+++G+G +Gl++A +L+r+g  Vt++e++d++g
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGhtVTVFEREDRIG 180
                                    99******************99********9998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                                    HHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTG CS
                            DAO 157 ealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvs 236
                                    ++ G e++ g +v g++     + ++      +   +davV+a Ga +  +   +el++p + + g + +++ l+    +
  gi|121639776|ref|YP_980000.1| 205 RSEGTEFRPGVNV-GVDI---SAEKL-----RAD--FDAVVLAGGATA--W---RELPIPGRELEGVHQAMEFLPW---A 265
                                    5555555555443.3322...13333.....332..699******997..8...8887777889999999955555...2 PP

                                    SGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE..E CS
                            DAO 237 paailpvpetdddgrgvyvtprkdgrvlvGgtad..e 271
                                    ++ +  + +  d+++ + +t+  +  v++Gg ++  +
  gi|121639776|ref|YP_980000.1| 266 NRVQEGD-DVLDEDGQPPITAKGKKVVIIGGGDTgaD 301
                                    3222222.37778888899998767677799875550 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   7.5e-10   4.1e-07       2      42 ..     147     187 ..     146     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.5e-10
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                    v VvG+gpaG+aAA +  raG +v + e+++++GGll  g+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIGGLLRYGI 187
                                    89*********************************997765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.2e-08   6.5e-06       2      36 ..     147     181 ..     146     211 .. 0.94
   2 ?   -0.8   0.3       1.1     6e+02     155     203 ..     349     406 ..     255     435 .. 0.68
   3 ?   -0.7   0.1       1.1   5.8e+02     371     401 ..     413     445 ..     405     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.2e-08
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                    v V+GsG AGLaAA ++++aG++v+v e e++ gg
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIGG 181
                                    89****************************99887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                    TEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE-----G CS
                  FAD_binding_2 155 gvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgGfg 203
                                    g +  ++ + ++++ +dgrv+   +++           +g++++++a+ v+la g +g
  gi|121639776|ref|YP_980000.1| 349 GGERVFSVNTEAFVGTDGRVSALRAHEVnmldgkfvkVEGSDFELEADLVLLAMGFVG 406
                                    3555555555566666666666555555555666666777777777777777777555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                                    EES-EEEBETTSBE..STTEEESSBTEEE-STC CS
                  FAD_binding_2 371 ytmgGvetdengrv..ldadgqpipGLYAaGev 401
                                     t+ Gv+ +e+g+v   d+ ++ +pG + aG +
  gi|121639776|ref|YP_980000.1| 413 LTALGVKFTEHGNVarGDDFDTSVPGVFVAGDM 445
                                    6899**********555555799*****99975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.5e-08   1.9e-05       2      36 ..     146     180 ..     145     185 .. 0.94
   2 ?    0.1   0.1      0.47   2.5e+02       2      23 ..     289     310 ..     288     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.5e-08
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                    +v+v+G G+AGl aA ++ ++g+ V+++e+++++g
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIG 180
                                    69*****************************9998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                                    SEEEE--SHHHHHHHHHHHHTT CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrg 23 
                                    +v++iGgG  G  +  +++++g
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVHRQG 310
                                    89*******9988877666555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0072       4      47 ..     141     182 ..     140     245 .. 0.72
   2 ?    7.2   0.4     0.012       6.8       5      30 ..     285     310 ..     283     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                  NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleel 47 
                                    +l+g++v vvG G+ ++  +++l +ag +vtv   e  + + +l
  gi|121639776|ref|YP_980000.1| 141 KLTGQTVAVVGSGPAGLAAAQQLTRAGHTVTVFERE--DRIGGL 182
                                    689*****************************9988..333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleag 30 
                                     kgkkv+++GgG+ +a  + ++ ++g
  gi|121639776|ref|YP_980000.1| 285 AKGKKVVIIGGGDTGADCLGTVHRQG 310
                                    689**********9997766666665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.7e-05     0.025      21      69 ..     132     177 ..     119     195 .. 0.85
   2 ?    5.3   0.0     0.021        11      13      63 ..     263     315 ..     255     335 .. 0.72
   3 ?   -0.9   0.0       1.7     9e+02      38      66 ..     396     424 ..     371     438 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                                    TCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                   2-Hacid_dh_C  21 gewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                    g w   +  + ++l+g+tv+++G G  G a+a+ l+  g  v++++r  
  gi|121639776|ref|YP_980000.1| 132 G-W--VQPRPPRKLTGQTVAVVGSGPAGLAAAQQLTRAGHTVTVFERED 177
                                    4.6..56678899******************************999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                                    HHHHHHHTTCC.HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEE CS
                   2-Hacid_dh_C  13 eadeevregew.ksekallgkelsgktvGiiGlGrIGqavakrlkafgm.kvi 63 
                                     + ++v+eg+   +e+  +  + +gk+v iiG G+ G     +++  g+  v 
  gi|121639776|ref|YP_980000.1| 263 PWANRVQEGDDvLDEDGQPPITAKGKKVVIIGGGDTGADCLGTVHRQGAiAVH 315
                                    55666777755466777778899**************9988777765553555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.7
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviayd 66 
                                     + ++ +G +G + a +l+a+g+k + + 
  gi|121639776|ref|YP_980000.1| 396 DLVLLAMGFVGPERAGLLTALGVKFTEHG 424
                                    56788999999999999999999987665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   7.8e-08   4.2e-05       3      34 ..     146     177 ..     145     184 .. 0.93
   2 ?   -0.9   0.3       1.3   7.3e+02       3      14 ..     289     300 ..     288     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.8e-08
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                    +V++VG+GpaGl +a+ L++aG  v++ e+ +
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFERED 177
                                    699*************************9976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                    EEEEE--SHHHH CS
                  FAD_binding_3   3 dVlIVGaGpaGl 14 
                                    +V+I+G+G +G+
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGA 300
                                    69********97 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   3.1e-05     0.017       3      42 ..     146     185 ..     144     193 .. 0.95
   2 ?    4.2   0.0     0.022        12     170     202 ..     274     306 ..     217     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                       FMO-like   3 kvaviGaGvsGlasikccleegleptcfersddiGGlwrf 42 
                                     vav+G+G +Gla+ +     g   t fer d iGGl r+
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIGGLLRY 185
                                    79***********************************997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                       FMO-like 170 fhsrdykepevfkgkrvlviGlGnsggdiavel 202
                                    +   d + p + kgk+v++iG G++g+d    +
  gi|121639776|ref|YP_980000.1| 274 VLDEDGQPPITAKGKKVVIIGGGDTGADCLGTV 306
                                    555666778889***************976555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06   0.00073      18      57 ..     145     183 ..     140     194 .. 0.87
   2 ?   -1.6   0.1       2.4   1.3e+03      19      37 ..     289     307 ..     284     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                    EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                           Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57 
                                    + v++vG+G++GL+aa+ l+++ +  v+++er+  +GG  
  gi|121639776|ref|YP_980000.1| 145 QTVAVVGSGPAGLAAAQQLTRA-GHTVTVFEREDRIGGLL 183
                                    5699******************.**********9999965 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                    EEEEE--SHHHHHHHHHHH CS
                           Thi4  19 DvvivGaGssGLtaayyla 37 
                                     vvi+G+G +G  +  ++ 
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVH 307
                                    69*******9987765555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   0.00013     0.072      30      60 ..     146     176 ..     141     187 .. 0.91
   2 ?    4.4   0.1     0.036        19      29      53 ..     288     312 ..     280     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                    EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                    +v v+G G aGl+A++  ++ g +Vtv++ +
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFERE 176
                                    699*************************976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                                    -EEEEESTSHHHHHHHHHHHHTT-E CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgak 53 
                                     kv++iGgG  G   + t ++ ga+
  gi|121639776|ref|YP_980000.1| 288 KKVVIIGGGDTGADCLGTVHRQGAI 312
                                    59***************99999986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0033       1.8       2      35 ..     147     176 ..     146     184 .. 0.88
   2 ?    6.2   0.0     0.029        16       1      40 [.     289     328 ..     289     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0033
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESS CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrn 35 
                                    ++++G+G  g a a++l++ag   h ++v  +r+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAG---HTVTVF-ERE 176
                                    89*******************...***976.554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
                                    EEEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaaga.qpheivvansrnpekae 40 
                                    k+ iiG+G+ g+  +  + ++ga + h++ +   r p+ ++
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVHRQGAiAVHQFEIM-PRPPDARA 328
                                    689********************999999866.55555443 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.016       8.9     154     218 ..     108     171 ..     104     183 .. 0.71
   2 ?   -2.9   0.0       5.2   2.8e+03     318     339 ..     217     238 ..     191     240 .. 0.66
   3 !    8.3   0.0    0.0021       1.2     187     215 ..     280     311 ..     255     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                    K_oxygenase 154 lgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkve 218
                                    lg+++ p   +++e le  ++ +    +  r +++l+++++aVvGsG  +   +++l+r  ++v+
  gi|121639776|ref|YP_980000.1| 108 LGINQDPVTIKQIE-LEIIDKAFDEGWVQPRPPRKLTGQTVAVVGSGPAGLAAAQQLTRAGHTVT 171
                                    55555555555554.333466677777777778899999********999999999988877443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                    K_oxygenase 318 lrneesgeeetlevdavvlATG 339
                                    +  + s e+ + ++davvlA G
  gi|121639776|ref|YP_980000.1| 217 VGVDISAEKLRADFDAVVLAGG 238
                                    444456677788999****988 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0021
                    K_oxygenase 187 e...llakkriaVvGsGqSaaeifedllrrqk 215
                                    +   ++++k+++++G+G ++a+ +  ++r+ +
  gi|121639776|ref|YP_980000.1| 280 QppiTAKGKKVVIIGGGDTGADCLGTVHRQGA 311
                                    45557899**************9999998843 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     7e-06    0.0038       2      36 ..     147     180 ..     146     206 .. 0.89
   2 ?   -1.6   1.7         2   1.1e+03       1      22 [.     289     310 ..     289     314 .. 0.82
   3 ?   -3.4   0.1       7.2   3.9e+03     355     388 ..     436     470 ..     433     473 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7e-06
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtia 36 
                                    v V+G G AG++AA ++ r+G+ v+ + ++ d+i+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVF-EREDRIG 180
                                    89**********************999.6666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                                    CEEEE-SSHHHHHHHHHHHHTT CS
                           GIDA   1 dviViGgGhAGceAAlaaarlG 22 
                                    +v++iGgG  G  +  ++ r G
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVHRQG 310
                                    69*********98877777766 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.2
                                    SBTEEE-CGG.GTB-SHHHHHHHHHHHHHHHHHHH CS
                           GIDA 355 vkgLflAGqi.nGteGYeEaaaqGllAGinaarka 388
                                    v+g+f+AG++  G +  + a+a G  A+  + r++
  gi|121639776|ref|YP_980000.1| 436 VPGVFVAGDMgRGQSLIVWAIAEGRAAAAAVDRYL 470
                                    78999999984477777888888888888777766 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.027        14      21      53 ..     142     174 ..     139     183 .. 0.91
   2 !    9.1   0.1    0.0023       1.2      22      49 ..     286     313 ..     280     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE- CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivte 53 
                                    l+G+++ v+G G  G  +a+ l  +G  v+v e
  gi|121639776|ref|YP_980000.1| 142 LTGQTVAVVGSGPAGLAAAQQLTRAGHTVTVFE 174
                                    689**************************9987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                                    TTSEEEEE--SHHHHHHHHHHHHCT-EE CS
                  AdoHcyase_NAD  22 aGkvavvaGyGdvGkGcaaslkglGarv 49 
                                     Gk++v++G Gd G  c  +++ +Ga+ 
  gi|121639776|ref|YP_980000.1| 286 KGKKVVIIGGGDTGADCLGTVHRQGAIA 313
                                    69***********************974 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0016      0.85       9      47 ..     141     178 ..     135     205 .. 0.83
   2 ?    4.3   0.0      0.07        38      10      37 ..     285     312 ..     280     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                                    ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                    +l++++v ++G G  +  +a++L ++g + v+v+ R+ +
  gi|121639776|ref|YP_980000.1| 141 KLTGQTVAVVGSGPAGLAAAQQLTRAGHT-VTVFEREDR 178
                                    68899**********************99.*****9865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.07
                                    .TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvk 37 
                                     k+kkv++iG G ++   +   +++g+ 
  gi|121639776|ref|YP_980000.1| 285 AKGKKVVIIGGGDTGADCLGTVHRQGAI 312
                                    5799***********9998888888765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.3e-05     0.023       1      34 [.     146     179 ..     146     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseea 34 
                                    +vav+G+G  G   a+++ +ag++V+++++++++
  gi|121639776|ref|YP_980000.1| 146 TVAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRI 179
                                    69**************************998765 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.5   2.7e+02      94     120 ..     144     170 ..     142     185 .. 0.82
   2 ?   12.5   0.1   0.00017     0.095      21      73 ..     161     241 ..     156     260 .. 0.75
   3 ?   -0.5   0.1       1.8   9.7e+02      63      82 ..     289     308 ..     281     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.5
                                    T-EEEEETTTHHHHHHTTTTTTSEE-- CS
                      DJ-1_PfpI  94 gklvaaICagpqlLaaagvlkgrrvTs 120
                                    g++va ++ gp  Laaa+ l++  +T 
  gi|121639776|ref|YP_980000.1| 144 GQTVAVVGSGPAGLAAAQQLTRAGHTV 170
                                    788999999999999999998776664 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00017
                                    HHHHHTTEEEEEEESS.............................TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BH CS
                      DJ-1_PfpI  21 dvlkragikvdvvsvd.............................keevkgsrGlkvtvdaslddvkaaeyDalvlpGGr 71 
                                    + l rag++v+v + +                             +e  +   G++v vd s ++++a+ +Da+vl GG 
  gi|121639776|ref|YP_980000.1| 161 QQLTRAGHTVTVFEREdriggllrygipefkmekrhldrrldqmrSEGTEFRPGVNVGVDISAEKLRAD-FDAVVLAGGA 239
                                    566677777777777777777777777777777777777766665555566789**********98887.*********8 PP

                                    HH CS
                      DJ-1_PfpI  72 ag 73 
                                    + 
  gi|121639776|ref|YP_980000.1| 240 TA 241
                                    74 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.8
                                    SEEEE--BHHHHHHHHTSHH CS
                      DJ-1_PfpI  63 DalvlpGGragperlrenek 82 
                                     ++++ GG++g+++l + ++
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGADCLGTVHR 308
                                    68999999999999876555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.9e-05     0.054       2      29 ..     147     172 ..     146     181 .. 0.79
   2 ?   -3.3   0.0       6.7   3.6e+03     120     154 ..     382     414 ..     359     422 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvl 29 
                                    v+v+G+GpAgl+ A++lt+a   +  ++
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTV--TV 172
                                    89***************6665554..44 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                  Lycopene_cycl 120 slvvleggr.kirarlvvdarglaslkkarrlglQt 154
                                    + v +eg   +++a lv+ a g     ++ r gl t
  gi|121639776|ref|YP_980000.1| 382 KFVKVEGSDfELEADLVLLAMG---FVGPERAGLLT 414
                                    3444555445666666666666...33444445555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     9e-05     0.049       1      39 [.     148     181 ..     148     190 .. 0.85
   2 ?   -0.6   0.0       2.1   1.1e+03     140     154 ..     224     238 ..     199     240 .. 0.81
   3 ?   -1.7   0.2       4.8   2.6e+03       1      19 [.     291     309 ..     291     322 .. 0.75
   4 ?   -0.2   0.0       1.6   8.6e+02     127     154 ..     376     403 ..     361     405 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-05
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39 
                                    a+vG Gp+Gla++++L +       +++t+f+++   g g
  gi|121639776|ref|YP_980000.1| 148 AVVGSGPAGLAAAQQLTRA-----GHTVTVFEREDRiG-G 181
                                    89***************99.....599******66524.3 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                  NAD_binding_9 140 dgaslaadaVvLAlG 154
                                    ++ + ++daVvLA G
  gi|121639776|ref|YP_980000.1| 224 EKLRADFDAVVLAGG 238
                                    455679*******88 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.8
                  NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                    +i+G+G +G+ +l  + ++
  gi|121639776|ref|YP_980000.1| 291 VIIGGGDTGADCLGTVHRQ 309
                                    69****9999887766665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                  NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlG 154
                                    ++  ++++  ++ ++ +l+ad V LA+G
  gi|121639776|ref|YP_980000.1| 376 VNMLDGKFVKVEGSDFELEADLVLLAMG 403
                                    444444444445566789*********9 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.057       2      32 ..     147     177 ..     146     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree 32 
                                    +av+G+G  G a A+ l+++gh+v+++ re+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVFERED 177
                                    9**************************9987 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00085      0.46      37      65 ..     151     177 ..     136     207 .. 0.83
   2 ?    1.1   0.1      0.59   3.2e+02      28      43 ..     288     303 ..     280     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00085
                         YjeF_N  37 nnGgdglaaArhLaqegakVtvllleeee 65 
                                     +G  glaaA++L ++g++Vtv  +e+e+
  gi|121639776|ref|YP_980000.1| 151 GSGPAGLAAAQQLTRAGHTVTV--FERED 177
                                    5799******************..45544 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.59
                         YjeF_N  28 kvlvlvGsgnnGgdgl 43 
                                    k +v++G+g++G+d+l
  gi|121639776|ref|YP_980000.1| 288 KKVVIIGGGDTGADCL 303
                                    557899********98 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033      0.18       2      37 ..     142     177 ..     141     180 .. 0.91
   2 ?   -0.1   0.2       1.1   5.9e+02       3      16 ..     286     299 ..     284     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglreg 37 
                                    l+g+++av+G G  G a a++l  +g  v+v  re+
  gi|121639776|ref|YP_980000.1| 142 LTGQTVAVVGSGPAGLAAAQQLTRAGHTVTVFERED 177
                                    7899*************************9987776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                                    HTS-EEEES-SHHH CS
                           IlvN   3 kgkkiaviGyGsqG 16 
                                    kgkk+++iG G  G
  gi|121639776|ref|YP_980000.1| 286 KGKKVVIIGGGDTG 299
                                    89*******99887 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.86   4.7e+02      37      49 .]     161     173 ..     142     173 .. 0.75
   2 ?    8.6   0.0    0.0042       2.3       1      24 [.     287     309 ..     287     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.86
                        Kelch_3  37 lppaRaghaatai 49 
                                     +  Ragh++t++
  gi|121639776|ref|YP_980000.1| 161 QQLTRAGHTVTVF 173
                                    4558*******86 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0042
                        Kelch_3   1 gdrlyifGGlgddgqdrlndvyvy 24 
                                    g +++i+GG + +g d+l++v++ 
  gi|121639776|ref|YP_980000.1| 287 GKKVVIIGGGD-TGADCLGTVHRQ 309
                                    5789*******.8********985 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.22       1      33 [.     147     179 ..     147     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHH CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrl 33 
                                    +a++G+G  G   a +L++ag++vt+  r++r+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRI 179
                                    69*************************999876 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0039       2.1      29      59 ..     141     171 ..     130     187 .. 0.89
   2 ?    1.5   0.0      0.38   2.1e+02      29      59 ..     284     314 ..     272     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                                    -STTEEEEEE--SHHHHHHHHHHHHCT-EEE CS
                  ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvv 59 
                                    +l+g++va+ GsG  g +aa+ lt++g++v+
  gi|121639776|ref|YP_980000.1| 141 KLTGQTVAVVGSGPAGLAAAQQLTRAGHTVT 171
                                    6899*******************99998775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.38
                                    -STTEEEEEE--SHHHHHHHHHHHHCT-EEE CS
                  ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvv 59 
                                    + +gk+v+i G G+ g  +   ++++ga  v
  gi|121639776|ref|YP_980000.1| 284 TAKGKKVVIIGGGDTGADCLGTVHRQGAIAV 314
                                    689**************99999999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0014      0.78       1      31 [.     147     177 ..     147     190 .. 0.85
   2 ?    0.1   0.3       1.7   9.5e+02       1      21 [.     290     310 ..     290     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkde 31 
                                    ++++G G  G + a++L++ g+  v+v ++++
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRaGH-TVTVFERED 177
                                    68*****************666.6***99864 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                                    EEEES-SHHHHHHHHHHHHTT CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLsegg 21 
                                    ++iiG G++G   + +++++g
  gi|121639776|ref|YP_980000.1| 290 VVIIGGGDTGADCLGTVHRQG 310
                                    79********98888777754 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00062      0.34       2      35 ..     147     177 ..     146     186 .. 0.91
   2 ?   -1.5   0.4       1.6   8.5e+02       1      12 [.     289     300 ..     289     319 .. 0.71
   3 ?   -3.7   0.1       7.5     4e+03     168     203 ..     349     384 ..     344     405 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00062
                                    EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                 Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlvesee 35 
                                    + +vG G+aG  aA  l +a+   ++vt+ e e+
  gi|121639776|ref|YP_980000.1| 147 VAVVGSGPAGLAAAQQLTRAG---HTVTVFERED 177
                                    89*******************...8899999875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                    EEEEE--SHHHH CS
                 Trp_halogenase   1 kivivGGGtaGw 12 
                                    k+vi+GGG  G 
  gi|121639776|ref|YP_980000.1| 289 KVVIIGGGDTGA 300
                                    79******9883 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.5
                                    T-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEE CS
                 Trp_halogenase 168 Gvtrvegkvvevqldedgrveslrledgreveadlf 203
                                    G +rv    +e+ +  dgrv++lr ++ + +++ ++
  gi|121639776|ref|YP_980000.1| 349 GGERVFSVNTEAFVGTDGRVSALRAHEVNMLDGKFV 384
                                    555555555666677788888888888777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.39
# Mc/sec: 3762.83
//
Query:       gi|121639777|ref|YP_980001.1|  [L=1527]
Description: ferredoxin-dependent glutamate synthase large subunit GltB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-180  599.4   0.0   3.9e-180  599.1   0.0    1.1  1  GATase_2         Glutamine amidotransferases class-II
   8.4e-152  505.6   0.0   1.5e-149  498.2   0.0    2.5  2  Glu_synthase     Conserved region in glutamate synthase
   6.7e-113  376.8   0.0   9.9e-113  376.2   0.0    1.3  1  Glu_syn_central  Glutamate synthase central domain
    2.5e-81  271.8   5.5    4.3e-81  271.1   5.5    1.3  1  GXGXG            GXGXG motif
  ------ inclusion threshold ------
        2.5    7.0   8.3       0.12   11.4   1.2    2.2  2  FMN_dh           FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.1   0.0  1.1e-183  3.9e-180       1     420 []      18     439 ..      18     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 599.1 bits;  conditional E-value: 1.1e-183
                                    -EEEEEE-SSS--BSHHHHHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEEEE- CS
                       GATase_2   1 CGvgfiaelkgkkshkivekalealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgmlflp 80 
                                    CGv+++++++g++s++iv+ka++al nleHRGa+ga++++GDGaGil+q+Pdeflr+++   ++elp+ g+ya+g++flp
  gi|121639777|ref|YP_980001.1|  18 CGVAMVVDMHGRRSRDIVDKAITALLNLEHRGAQGAEPRSGDGAGILIQVPDEFLREAV---DFELPAPGSYATGIAFLP 94 
                                    ********************************************************999...9***************** PP

                                    SSHHHHHHHHHHHHHHHHHTT-EEEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHHHGGG.. CS
                       GATase_2  81 kdeekaeeakkileeiveeeglevlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviRkriekeia 160
                                    +++++a++a +++++i+e+egl+vlgwR+vp+d+s+lg+ +++++P+++qvf++ ++     +ler+ yv+Rkr+e+e+ 
  gi|121639777|ref|YP_980001.1|  95 QSSKDAAAACAAVQKIAEAEGLQVLGWRSVPTDDSSLGALSRDAMPTFRQVFLAGAS---GMALERRCYVVRKRAEHELG 171
                                    *****************************************************9887...899****************9 PP

                                    .........-BTTBEEEEEESSEEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SSEEEEE- CS
                       GATase_2 161 kkk......aekefYicslssrtivYkglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRllaHnGE 234
                                    +k        ++++Y++sls +t+vYkg+lt+ qlk+fy dl+de+l+sal +vHsRfstntfPsW+la+P+R +aHnGE
  gi|121639777|ref|YP_980001.1| 172 TKGpgqdgpGRETVYFPSLSGQTLVYKGMLTTPQLKAFYLDLQDERLTSALGIVHSRFSTNTFPSWPLAHPFRRIAHNGE 251
                                    987888888899******************************************************************** PP

                                    -TTHHHHHHHHHHHCTT--BT-HH...HHHTC--S--TTS-HHHHHHHHHHHHHHTT--HHHHHHHHS----TT-GGGTH CS
                       GATase_2 235 intlrGnknwmkareaelksellgd..elekllPivneegsDsasldnvlellvlsgrslaealmlliPeawennksldk 312
                                    int++Gn+nwm+area +k++++g+  ++ekl Pi++ ++sD+a++d+vlell+l+grsla+a++++iPeawe+++s+d+
  gi|121639777|ref|YP_980001.1| 252 INTVTGNENWMRAREALIKTDIFGSaaDVEKLFPICTPGASDTARFDEVLELLHLGGRSLAHAVLMMIPEAWERHESMDP 331
                                    ***********************96569**************************************************** PP

                                    HHHHHHHHHTTT-----SSEEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EE CS
                       GATase_2 313 ekkafyeyasalmepWDGPalivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrml 392
                                     ++afy+y+++lmepWDGPa+++ftdG+vvgavLDRnGLRP+R++vt+d+lvv+asE+Gvldl++++vv+++rlqPGrm+
  gi|121639777|ref|YP_980001.1| 332 ARRAFYQYHASLMEPWDGPASMTFTDGTVVGAVLDRNGLRPSRIWVTDDGLVVMASEAGVLDLHPSTVVRRMRLQPGRMF 411
                                    ******************************************************************************** PP

                                    EEETTTTEEEEHHHHHHHHHTTS-HHHH CS
                       GATase_2 393 lvdleegriledeeikkkiaskkpykew 420
                                    lvd+++gri++deeik+++a+++py+ew
  gi|121639777|ref|YP_980001.1| 412 LVDTAQGRIVSDEEIKADLAAEHPYQEW 439
                                    ***************************9 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0039        14     249     299 ..     640     691 ..     633     694 .. 0.81
   2 !  498.2   0.0  4.1e-153  1.5e-149       3     368 .]     821    1190 ..     819    1190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0039
                                    HHB---HHHHHHHHHHHHHHTT-GGG-EEEE.ESS--SHHHHHHHHHHT-SE CS
                   Glu_synthase 249 khaGlPlelalaevdqtlkeeglrdrvslia.dGglktgadvvkalalGAda 299
                                    + a +P +la+a v++ l++e  r +v l + +G+ +  + ++  + +GA a
  gi|121639777|ref|YP_980001.1| 640 EMAPIPSLLAVAGVHHHLVRERTRTQVGLVVeSGDAREVHHMAALVGFGAAA 691
                                    56789**********************9988357777777777777777765 PP

  == domain 2  score: 498.2 bits;  conditional E-value: 4.1e-153
                                     S-HHHHHHHHHHHHH---HHHHHHHHHHHTS..-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-TTTS- CS
                   Glu_synthase    3 neievikllqkavqveskesidkyrekleer.evlkakrdlleldaaeealikleevepalkikkriltsamSyGals 79  
                                      ++e+   lq+++++++++ +++y++ ++++ e++ ++r ll++++  ++ ++l+evepa++i+kr+ t+amSyG++s
  gi|121639777|ref|YP_980001.1|  821 FNPETVFKLQHSTRTGQYKIFKEYTRLVDDQsERMASLRGLLKFRTGVRPPVPLDEVEPASEIVKRFSTGAMSYGSIS 898 
                                     567788899****************9998762678889*******999999*************************** PP

                                     HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----.....SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS-- CS
                   Glu_synthase   80 eeahealakamnrlgtksntGEGGedeerlktakdv.....aikQvasgrFGvteeyLnnakaleikiaQGakpgeGg 152 
                                      eahe+la+amnrlg+ sn+GEGGed +r+  + +      aikQvas+rFGvt++yL+n+  l+ik+aQGakpgeGg
  gi|121639777|ref|YP_980001.1|  899 AEAHETLAIAMNRLGARSNCGEGGEDVKRFDRDPNGdwrrsAIKQVASARFGVTSHYLTNCTDLQIKMAQGAKPGEGG 976 
                                     ********************************999999**************************************** PP

                                     EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SE CS
                   Glu_synthase  153 qlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvakanadi 230 
                                     qlpg+Kv++++a++R+++pgv+liSP+phhdiysiedlaqli+dLk++n++a+v vKlv+e+gv+t+aagv+ka+ad+
  gi|121639777|ref|YP_980001.1|  977 QLPGHKVYPWVAEVRHSTPGVGLISPPPHHDIYSIEDLAQLIHDLKNANPSARVHVKLVSENGVGTVAAGVSKAHADV 1054
                                     ****************************************************************************** PP

                                     EEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHH CS
                   Glu_synthase  231 ilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaali 308 
                                     +li+G++GGTGA+p +s+khaG P+el+lae++qtl  +glrdr+++++dG+lktg+dv++a +lGA+++g++ta+l+
  gi|121639777|ref|YP_980001.1| 1055 VLISGHDGGTGATPLTSMKHAGAPWELGLAETQQTLLLNGLRDRIVVQVDGQLKTGRDVMIATLLGAEEFGFATAPLV 1132
                                     ****************************************************************************** PP

                                     HTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                   Glu_synthase  309 algCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368 
                                       gCim+rvCh++tCpvGvatq+p Lr  +++++k+e v n+++++aeevre+la+lg++
  gi|121639777|ref|YP_980001.1| 1133 VAGCIMMRVCHLDTCPVGVATQNPLLR--ERFTGKPEFVENFFMFIAEEVREYLAQLGFR 1190
                                     ***************************..9****************************85 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.2   0.0  2.8e-116  9.9e-113       2     279 .]     466     757 ..     465     757 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.2 bits;  conditional E-value: 2.8e-116
                                    HHHHTT--HHHHHHTHHHHHHHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG-B--EEES-- CS
                Glu_syn_central   2 rqkafgyteedlelllepmakegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvmsletllGke 81 
                                    rq afgyt+e+l+ll++pma+ g+e+igsmG+Dtp+avLs++pr+lydYF+qlfAqVTNPp+D+iREe+v+sl+ + G e
  gi|121639777|ref|YP_980001.1| 466 RQLAFGYTYEELNLLVAPMARLGAEPIGSMGTDTPVAVLSQRPRMLYDYFHQLFAQVTNPPLDAIREEVVTSLQGTTGGE 545
                                    689***************************************************************************** PP

                                    --SSS--GGGG-EEEESSSB--HHHHHHH...........HHSSS-EEEEESEE.......SHHHHHHHHHHHHHHHHHT CS
                Glu_syn_central  82 gnlleeeeeqakrlklesPiLteeeleklkkl.......kekkefkaktlditfeae....aleealerlceeaeeavre 150
                                    ++ll+++e+++++++l +PiL ++el+kl +l        + +++++k+++++++++    +l++ale+++ +a++a+++
  gi|121639777|ref|YP_980001.1| 546 RDLLNPDENSCHQIVLPQPILRNHELAKLVSLdpndkvnGRPHGLRSKVIRCLYRVSeggaGLAAALEEVRGAAAAAIAD 625
                                    *****************************999999888744569**********98866655****************** PP

                                    T-SEEEEESS--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHHHHHH CS
                Glu_syn_central 151 gaeilvLsDrkvseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaletieklv 230
                                    ga+i++LsDr+ +ee +pipslLav+ vhhhLvr+++rt+v+lvvesg+arevhh+a+l+g+Ga+a+nPyl++e+ie++ 
  gi|121639777|ref|YP_980001.1| 626 GARIIILSDRESDEEMAPIPSLLAVAGVHHHLVRERTRTQVGLVVESGDAREVHHMAALVGFGAAAINPYLVFESIEDML 705
                                    ******************************************************************************** PP

                                    TTTS-...----HHHHHHHHHHHHHHHHHHHTT--BHHHHHHS--EEESSB- CS
                Glu_syn_central 231 eegal...aeeeleknyrkavekGllKimskmGistlqSYkgaqifeavGls 279
                                    ++g +   +++++ +ny+ka+ kG+lK+mskmGistl+SY+gaq+f+avG+s
  gi|121639777|ref|YP_980001.1| 706 DRGVIegiDRTAALNNYIKAAGKGVLKVMSKMGISTLASYTGAQLFQAVGIS 757
                                    ***88665666666************************************96 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.1   5.5   1.2e-84   4.3e-81       2     187 ..    1271    1458 ..    1270    1460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 271.1 bits;  conditional E-value: 1.2e-84
                                     EE-TT--STTHHHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--T CS
                          GXGXG    2 eirnldrsvgtilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpsk 79  
                                     +i n++r+vgt+l++e++k yg +glp++ti+i+++GsaG+s+gaf++kG+tl++ GdandyvGkglsgG+iv++ps+
  gi|121639777|ref|YP_980001.1| 1271 TIGNVNRTVGTMLGHELTKAYGGQGLPDGTIDITFDGSAGNSFGAFVPKGITLRVYGDANDYVGKGLSGGRIVVRPSD 1348
                                     688**************************************************************************9 PP

                                     T-S..S-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT- CS
                          GXGXG   80 esk..fkaeeniivGnvvlygatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGm 155 
                                     ++   + ae+nii Gnv+l+gat+G++++rg +geRfavrnsga+avvegvgdhgceYmtGG+vv+Lg+tgrnfaaGm
  gi|121639777|ref|YP_980001.1| 1349 DAPqdYVAEDNIIGGNVILFGATSGEVYLRGVVGERFAVRNSGAHAVVEGVGDHGCEYMTGGRVVILGRTGRNFAAGM 1426
                                     86433899********************************************************************** PP

                                     -EEEEEEE-SSSTHHHHB-TTT-EEEES-SHH CS
                          GXGXG  156 sgGiayvldedekfekklnkelvelekvedee 187 
                                     sgG+ayv+d d+++ ++ln e+vele++++++
  gi|121639777|ref|YP_980001.1| 1427 SGGVAYVYDPDGELPANLNSEMVELETLDEDD 1458
                                     ***************************98876 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.9       0.4   1.4e+03     230     282 ..     619     676 ..     616     693 .. 0.72
   2 ?   11.4   1.2   3.4e-05      0.12     234     300 ..    1048    1127 ..    1031    1136 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.4
                                    HHHHHHTTESEEEE--GGGTSSTT---HHHCHHHH........HHHH..SS-EEEESS--S CS
                         FMN_dh 230 akraveaGvdgivvSNHGGRqldgapatidvLpei........veavggrievlvDgGirr 282
                                    a  a++ G+ +i++S+   R+ d  +a+i  L ++        +e+ + ++ ++v +G  r
  gi|121639777|ref|YP_980001.1| 619 AAAAIADGARIIILSD---RESDEEMAPIPSLLAVagvhhhlvRERTRTQVGLVVESGDAR 676
                                    7789999********9...999**********99966665555555566777777777444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.4e-05
                                     HHTTESEEEE--GGG.......TSSTT---HHHC.HHHHHHHH.......SS-EEEESS--SHHHHHHHHHTT-SEEE CS
                         FMN_dh  234 veaGvdgivvSNHGG.......Rqldgapatidv.Lpeiveav.....ggrievlvDgGirrGsDvlkAlalGAdavl 298 
                                      +a +d +++S H G        ++ +a a+ +  L e ++ +     ++ri v vDg  ++G Dv+ A  lGA+  +
  gi|121639777|ref|YP_980001.1| 1048 SKAHADVVLISGHDGgtgatplTSMKHAGAPWELgLAETQQTLllnglRDRIVVQVDGQLKTGRDVMIATLLGAEEFG 1125
                                     56778999999998867777776666677776654566655544444478************************8766 PP

                                     ES CS
                         FMN_dh  299 lG 300 
                                     ++
  gi|121639777|ref|YP_980001.1| 1126 FA 1127
                                     55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.87u 0.26s 00:00:01.12 Elapsed: 00:00:00.43
# Mc/sec: 10580.63
//
Query:       gi|121639778|ref|YP_980002.1|  [L=353]
Description: hypothetical protein BCG_3923 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-07   30.8   0.0    4.7e-07   29.9   0.0    1.4  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00028   20.2   0.4    0.00042   19.6   0.4    1.1  1  ArsA_ATPase   Anion-transporting ATPase
    0.00035   20.0   0.0    0.00057   19.3   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00057   19.8   0.1      0.013   15.4   0.1    2.2  2  AAA_31        AAA domain
     0.0083   15.6   0.6      0.017   14.6   0.6    1.4  1  ParA          NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.011   16.1   0.5      0.037   14.4   0.2    1.6  1  AAA_16        AAA ATPase domain
      0.037   13.5   0.1      0.068   12.6   0.1    1.4  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
      0.058   13.1   0.0      0.071   12.8   0.0    1.2  1  AAA_24        AAA domain
       0.22   11.0   0.0       0.47    9.9   0.0    1.5  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.4e-10   4.7e-07       4     117 ..     139     345 ..     136     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.4e-10
                                    EESSTTSSHHHHHHHHHHHHHH..TT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           CbiA   4 astkGGvGKTtlaanLaralar..rglrVllvDaDpqannlaileglendiep........................... 54 
                                    + +kGGvGKT++aa  + +la+  ++ r++ +DaD+          l+ +i+p                           
  gi|121639778|ref|YP_980002.1| 139 VLGKGGVGKTSVAACVGSILAElrQQDRIVGIDADTAF------GRLSSRIDPraagsfwelttdtnlrsftditarlgr 212
                                    569******************98789**********94......44456666677999999999999************* PP

                                    .......................................................................CCHCCCHHH CS
                                    .......................................................................xxxxxxxxx RF
                           CbiA  55 .......................................................................dlkrllell 63 
                                                                                                           +++   +++
  gi|121639778|ref|YP_980002.1| 213 nsaglyvlagqpasgprraldpaiyreaalrldhhfaisvidcgssmeaavtqevlrdvdalivvsspwadGASAAANTI 292
                                    ***********************************************************************888888888 PP

                                    HHHCHCHHHH....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CC CS
                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  64 ealgkkkall..lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdea 117
                                    e l+    l   l+   vvln  dg  ++++ k+ l+++  ++g pv+ ++p+d +
  gi|121639778|ref|YP_980002.1| 293 EWLSDY-GLTglLRRSIVVLNDSDGH-ADKRTKSLLAQEFIDHGQPVV-EVPFDPH 345
                                    888865.33358***********997.7999999999999999*9998.6888765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.4   2.1e-07   0.00042       5      38 ..     138     171 ..     135     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                    EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                     v GKGGVGKt+v+a ++  l+e +++  ++  D
  gi|121639778|ref|YP_980002.1| 138 AVLGKGGVGKTSVAACVGSILAELRQQDRIVGID 171
                                    678********************99987777666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.9e-07   0.00057      14      55 ..     126     167 ..     116     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.9e-07
                   Mg_chelatase  14 aleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                    +++    G+H++ ++G  G GKt +a+++ s+l++l +++ +
  gi|121639778|ref|YP_980002.1| 126 TIRTVLHGNHKVAVLGKGGVGKTSVAACVGSILAELRQQDRI 167
                                    4566678******************************99875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.7e-06     0.013      10      40 ..     142     174 ..     136     188 .. 0.86
   2 ?    2.0   0.0     0.088   1.8e+02     109     164 ..     239     292 ..     228     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.7e-06
                         AAA_31  10 KGGvGKTTtsvnlaaala..klgkkvLlvDlDp 40 
                                    KGGvGKT  +  +++ la  +++ ++  +D+D+
  gi|121639778|ref|YP_980002.1| 142 KGGVGKTSVAACVGSILAelRQQDRIVGIDADT 174
                                    9*****************555677899999886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.088
                         AAA_31 109 ellekvkdeYDyiiiDcpPsLgl.ltenaLvasdsviipvqaeayaleGleqllkti 164
                                    e+  ++++++ + +iDc  s++  +t+  L   d +i++  +     +G+++  +ti
  gi|121639778|ref|YP_980002.1| 239 EAALRLDHHFAISVIDCGSSMEAaVTQEVLRDVDALIVVSSPW---ADGASAAANTI 292
                                    5556778889999********8637888999999999998872...34555555555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.6   8.4e-06     0.017       4      41 ..     135     173 ..     133     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                           ParA   4 kviavlSgKGGVGKStvavnlAlaLa...kkglkvgllDaD 41 
                                    +++avl gKGGVGK++va+ +   La   +++  vg+ DaD
  gi|121639778|ref|YP_980002.1| 135 HKVAVL-GKGGVGKTSVAACVGSILAelrQQDRIVGI-DAD 173
                                    556665.9***********998887744355555664.776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.9e-05     0.037       7      50 ..     118     159 ..     115     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                         AAA_16   7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralek 50 
                                    ++ +q+++++++v  g  + v + G  GvGK+s++ ++  ++ +
  gi|121639778|ref|YP_980002.1| 118 RQEAQFEATIRTVLHGN-HKVAVLGKGGVGKTSVAACVG-SILA 159
                                    56688999999999999.8999*************8877.3433 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.4e-05     0.068       2      39 ..     136     173 ..     135     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                      Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39 
                                    k+a+ GkGG+Gk+  ++ + + lae  ++  ivG D  
  gi|121639778|ref|YP_980002.1| 136 KVAVLGKGGVGKTSVAACVGSILAELRQQDRIVGIDAD 173
                                    89*************************99999999864 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05     0.071       3      48 ..     135     199 ..     133     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                         AAA_24   3 lkiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdie..........s 48 
                                     k+++ G+ g+GKT++a+           +++++ id +  + +l  +  p++           +
  gi|121639778|ref|YP_980002.1| 135 HKVAVLGKGGVGKTSVAACVgsilaelrqQDRIVGIDADTAFGRLSSRIDPRAAgsfwelttdtN 199
                                    699****************9888999998889999999998888888888877675555544441 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00024      0.47      20      53 ..     121     154 ..     117     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                          AAA_7  20 vrysyllelllknkkpvllvGptGtGKtviikdl 53 
                                    ++++  ++++l+ +++v + G+ G+GKt+++  +
  gi|121639778|ref|YP_980002.1| 121 AQFEATIRTVLHGNHKVAVLGKGGVGKTSVAACV 154
                                    56788999********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2445.63
//
Query:       gi|121639779|ref|YP_980003.1|  [L=108]
Description: hypothetical protein BCG_3924 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.085   13.3   0.6      0.085   13.3   0.6    1.2  1  HJURP_mid  Holliday junction recognition protein-associated r


Domain annotation for each model (and alignments):
>> HJURP_mid  Holliday junction recognition protein-associated repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   4.7e-06     0.085       5      54 ..      14      62 ..      10     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-06
                      HJURP_mid  5 LsakpsciistktfiaqnwssrrRhklksrmnrtyckgarrsqrssrerl 54
                                    +a  +c  s  + i+++w+++r  ++++r    +c +a + q  s    
  gi|121639779|ref|YP_980003.1| 14 ARA-QACKTSISAPIVESWRAQRGAQCGQREKSCRCSRAVHIQGISPPLF 62
                                   444.4688899999*************************99998775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 832.37
//
Query:       gi|121639780|ref|YP_980004.1|  [L=116]
Description: transcriptional regulatory protein whiB-like whiB6 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   31.9   1.1    2.3e-07   31.3   1.1    1.3  1  Whib      Transcription factor WhiB


Domain annotation for each model (and alignments):
>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   1.1   1.3e-11   2.3e-07      10      57 ..      36      82 ..      31      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.3e-11
                           Whib 10 edpelffpekgdreeeAkavCarCpVrreCleealeegeeyGvwGGl..t 57
                                   +dp+ +        +eAk++C++Cp r  C+++a+e+  + G w+G+   
  gi|121639780|ref|YP_980004.1| 36 QDPDRWTTT---PDDEAKTLCRACPRRWLCARDAVESAGAEGLWAGVviP 82
                                   566666644...689*******************************8443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 793.02
//
Query:       gi|121639781|ref|YP_980005.1|  [L=392]
Description: hypothetical protein BCG_3926 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00089   19.3   1.7      0.013   15.6   0.1    3.0  3  HTH_3     Helix-turn-helix
     0.0068   16.4   0.4          4    7.5   0.1    2.3  2  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.018   15.4   0.5      0.034   14.5   0.5    1.5  1  FHA       FHA domain
        1.1    9.7  15.0        0.3   11.5   2.6    3.1  2  HTH_31    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.9e-06     0.013       3      49 ..     172     218 ..     171     224 .. 0.94
   2 ?    3.9   0.1     0.013        57      11      35 ..     209     234 ..     206     237 .. 0.86
   3 ?    1.0   0.1     0.098   4.4e+02       1      26 [.     342     367 ..     342     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                                    HHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                          HTH_3   3 elRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                    ++R +l++sq+ LA+   +   ++ + E+G+++P+ +t  kl+++L+
  gi|121639781|ref|YP_980005.1| 172 ARRRELDISQRSLAADGIINAGALIAFEKGRSWPRERTRAKLEEVLQ 218
                                    5688**************************************99996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                    HHHHHHHHHTSSHHHHHHHHTT.SSC CS
                          HTH_3  11 sqeeLAeklGvsrstisriEnG.ern 35 
                                    ++++L e+l  +  ti+ri +G  ++
  gi|121639781|ref|YP_980005.1| 209 TRAKLEEVLQWPAGTIARIRRGePTE 234
                                    8999******************5555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.098
                                    HHHHHHHTTHHHHHHHHHHTSSHHHH CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrsti 26 
                                    l ++R  ++ls  e A+++Gv    i
  gi|121639781|ref|YP_980005.1| 342 LYAARRRANLSTLETAQAAGVAEEMI 367
                                    678999**************987665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1   0.00088         4       8      37 ..     174     203 ..     171     218 .. 0.84
   2 !    6.8   0.0    0.0015       6.9       2      29 ..     340     367 ..     339     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00088
                         HTH_19   8 ReelgltqeelaerlgisrskisaiEngkk 37 
                                    R+el ++q+ la + +i+ + ++a+E+g++
  gi|121639781|ref|YP_980005.1| 174 RRELDISQRSLAADGIINAGALIAFEKGRS 203
                                    899*************************86 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                         HTH_19   2 erLkeaReelgltqeelaerlgisrski 29 
                                    +rL +aR+ ++l+  e a+ +g+   +i
  gi|121639781|ref|YP_980005.1| 340 QRLYAARRRANLSTLETAQAAGVAEEMI 367
                                    8********************9977766 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   7.6e-06     0.034       3      69 .]      55     115 ..      53     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
                                    EESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEET CS
                            FHA   3 iGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdvielG 69 
                                    iG s +   ++dd++iS  H++ + d+g  +++++  +   G fv g+r ++   v +++++ i++G
  gi|121639781|ref|YP_980005.1|  55 IGHSCRVGTQIDDSRISQTHLRAVSDDG--RWRIVG-NIPRGMFVGGRRGSS---VTVSDKTLIRFG 115
                                    666666667999****************..******.779*******99998...**********98 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   4.8     0.041   1.8e+02       3      57 ..     167     220 ..     165     266 .. 0.82
   2 ?   11.5   2.6   6.6e-05       0.3       2      44 ..     338     379 ..     337     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.041
                         HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                    Ga  +a+R++  +sq+ +A+   + +  l   E Gr   p++++ ++l ++l+ +
  gi|121639781|ref|YP_980005.1| 167 GAAAAARRRELDISQRSLAADGIINAGALIAFEKGRS-WPRERTRAKLEEVLQWP 220
                                    5666788888888888888888888888888888888.58888888888888776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.6e-05
                         HTH_31   2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpsp 44 
                                    L+++L a+R+ra+Ls  e A+++gv e  +   E  ++ +p +
  gi|121639781|ref|YP_980005.1| 338 LAQRLYAARRRANLSTLETAQAAGVAEEMIVGAEAEEE-LPAE 379
                                    89***********************9988877777777.6744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2867.24
//
Query:       gi|121639782|ref|YP_980006.1|  [L=418]
Description: hypothetical protein BCG_3927 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 2140.03
//
Query:       gi|121639783|ref|YP_980007.1|  [L=103]
Description: hypothetical protein BCG_3928 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-27   94.0   0.0    6.8e-27   93.9   0.0    1.0  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   3.8e-31   6.8e-27       1     100 []       1     100 [.       1     100 [. 0.99

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 3.8e-31
                  T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkL 80 
                                    mt+ L V+p+ l+ la +h+e++++i++a++++ag s +v+ +hG++++++nd+++++e++r+++g++l++++++La++L
  gi|121639783|ref|YP_980007.1|   1 MTGFLGVVPSFLKVLAGMHNEIVGDIKRATDTVAGISGRVQLTHGSFTSKFNDTLQEFETTRSSTGTGLQGVTSGLANNL 80 
                                    9999**************************************************************************** PP

                  T7SS_ESX_EspC  81 raAAaaYeatDeeaagaldk 100
                                     aAA+aY ++D+  ag +dk
  gi|121639783|ref|YP_980007.1|  81 LAAAGAYLKADDGLAGVIDK 100
                                    *****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 570.97
//
Query:       gi|121639784|ref|YP_980008.1|  [L=283]
Description: hypothetical protein BCG_3929 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-54  185.0  13.2      2e-54  184.8  13.2    1.1  1  ESX-1_EspG  EspG family


Domain annotation for each model (and alignments):
>> ESX-1_EspG  EspG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8  13.2   1.1e-58     2e-54       1     244 [.      22     258 ..      22     259 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 1.1e-58
                                    EHHHHHHHHHHHT----CGGGCC--STSSHHHHHHHHHHHHHHHHHTTSBETT.EB-HHHHHHHHHHHS-SEEEEEEEEE CS
                     ESX-1_EspG   1 svdeldvlwealglgelPvpLevpspgataeeraalreraaaeLaerGLadgr.rvdpeladaLrlLarpdrevdarvvr 79 
                                    + d++ v++++l+l ++Pv L++++++++++ r+ ++e+++++L+++G++d + +++p +a+++++L rpdr++++r++r
  gi|121639784|ref|YP_980008.1|  22 TIDGMLVIADRLHLVDFPVTLGIRPNIPQEDLRDIVWEQVQRDLTAQGVLDLHgEPQPTVAEMVETLGRPDRTLEGRWWR 101
                                    67999*************************************************************************** PP

                                    --STTCEEEEEEEEETTEEEEEEEETTEEEEEEE-T.SGHHHHHHTTSH.--B-SS--EEEEHHHHHHHHHHHHTGHHHH CS
                     ESX-1_EspG  80 rdlgdeelralvarrgrqavlavrdgddvtlepvrp.dslaaalvalLpeappgrgrsvslpadeleeaaeraraalaaa 158
                                    rd+g+ ++r++v+rrg+++v+a+rdgd+++l+ v+p  +la++++a+L++a+p+++++++  a+el+e        +a++
  gi|121639784|ref|YP_980008.1| 102 RDIGGVMVRFVVCRRGDRHVIAARDGDMLVLQLVAPqVGLAGMVTAVLGPAEPANVEPLTGVATELAECT------TASQ 175
                                    ************************************999*****************************97......6789 PP

                                    HHHHT--CCCHHHHHHHTSSTSEEEEEEEEEEECCCECEEECESS-EEEEEETTEEEEEEEEEETTS--EEEEEE--HHH CS
                     ESX-1_EspG 159 lralgasaadaralarllasprsrvgqfivavardrggrrtradrplswfDteaGRylvspsraadgeewltvaPadpar 238
                                    l++ g+++a ar++a+++++p+ +v+  iva++r+ gg++t++d + +++D+  GR+++ p+r  +g+ + ++ P+++++
  gi|121639784|ref|YP_980008.1| 176 LTQYGIAPASARVYAEIVGNPTGWVE--IVASQRHPGGTTTQTDAAAGVLDSKLGRLVSLPRRV-GGDLYGSFLPGTQQN 252
                                    **************************..99999*****************************98.7899*********** PP

                                    HHHHHH CS
                     ESX-1_EspG 239 larale 244
                                    l ral+
  gi|121639784|ref|YP_980008.1| 253 LERALD 258
                                    ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1560.64
//
Query:       gi|121639785|ref|YP_980009.1|  [L=183]
Description: hypothetical protein BCG_3930 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0075   16.5   0.1      0.011   15.9   0.1    1.3  1  YbaB_DNA_bd   YbaB/EbfC DNA-binding family
  ------ inclusion threshold ------
      0.034   14.2   0.0       0.07   13.2   0.0    1.5  1  DUF2694       Protein of unknown function (DUF2694)
      0.098   12.7   0.4        3.5    7.7   0.1    2.5  2  Sox17_18_mid  Sox 17/18 central domain


Domain annotation for each model (and alignments):
>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-06     0.011      15      83 ..      58     125 ..      50     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                                    HHHHTTSEEEEEETTTTEEEEEETT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    YbaB_DNA_bd  15 qeelaekevegssggglVkVtvngkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaeeem 83 
                                     ee + + ++++  +g V+V+   +g+++ +++ +++ + +    L+d i    + A++ka++ +   m
  gi|121639785|ref|YP_980009.1|  58 DEEPELELFTVTNPQGSVSVSTLMDGRIQHVELTDKATSMS-EAQLADEIFVIADLARQKARASQYTFM 125
                                    566677789************************99996633.367****************99887666 PP

>> DUF2694  Protein of unknown function (DUF2694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05      0.07       8      60 ..      66     118 ..      58     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                        DUF2694   8 fdtvhpsgdvlvrscrggylhsvalseaameadaerlaeaillaadvsylkal 60 
                                    f  + p g v v +   g ++ v l++ a +    +la+ i + ad++  ka 
  gi|121639785|ref|YP_980009.1|  66 FTVTNPQGSVSVSTLMDGRIQHVELTDKATSMSEAQLADEIFVIADLARQKAR 118
                                    78899******************************************999885 PP

>> Sox17_18_mid  Sox 17/18 central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00059       3.5      19      30 ..      24      35 ..      23      44 .. 0.85
   2 ?    2.5   0.0     0.025   1.5e+02      15      21 ..     151     157 ..     136     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00059
                   Sox17_18_mid 19 TPEmSPLDavdp 30
                                   T E SPLDa+d+
  gi|121639785|ref|YP_980009.1| 24 TNEASPLDALDD 35
                                   5699******97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.025
                   Sox17_18_mid  15 YgLPTPE 21 
                                     +LPTPE
  gi|121639785|ref|YP_980009.1| 151 LNLPTPE 157
                                    58****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 958.73
//
Query:       gi|121639786|ref|YP_980010.1|  [L=573]
Description: hypothetical protein BCG_3931 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-22   79.8   0.0    7.6e-22   78.1   0.0    1.9  1  AAA              ATPase family associated with various cellul
    2.1e-07   31.0   3.3    8.1e-07   29.1   3.3    2.1  1  AAA_lid_6        AAA lid domain
    6.2e-06   26.0   0.2    1.8e-05   24.5   0.2    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.1e-06   25.6   0.6    6.8e-05   22.3   0.2    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.1e-05   24.2   0.6     0.0031   17.8   0.2    2.9  2  AAA_22           AAA domain
    0.00061   19.6   0.2    0.00061   19.6   0.2    2.2  2  AAA_30           AAA domain
    0.00072   19.6   0.2     0.0034   17.4   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0013   19.1   0.2     0.0033   17.8   0.2    1.8  1  AAA_19           AAA domain
     0.0014   19.2   0.1      0.005   17.4   0.0    2.1  1  AAA_18           AAA domain
     0.0017   18.5   1.1      0.022   14.9   0.1    2.8  2  AAA_33           AAA domain
     0.0018   18.2   0.1      0.005   16.8   0.1    1.7  2  NTPase_1         NTPase
     0.0021   18.5   5.7     0.0046   17.4   3.4    2.7  2  AAA_16           AAA ATPase domain
     0.0066   16.0   1.9      0.021   14.4   0.1    2.4  2  AAA_25           AAA domain
     0.0069   16.8   0.0      0.015   15.7   0.0    1.5  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.012   14.8   0.2        2.3    7.3   0.0    2.3  2  DUF815           Protein of unknown function (DUF815)
      0.017   15.7   2.4        3.8    8.4   0.0    3.7  2  TPR_6            Tetratricopeptide repeat
      0.018   14.8   0.2       0.57    9.9   0.2    2.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.031   14.4   0.0        0.2   11.7   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.042   14.1   0.1      0.042   14.1   0.1    3.2  3  AAA_28           AAA domain
      0.048   13.7   0.6        3.6    7.6   0.0    2.7  2  DUF218           DUF218 domain
      0.053   13.0   0.1      0.095   12.2   0.1    1.3  1  AAA_7            P-loop containing dynein motor region
      0.054   13.3   0.0        0.1   12.4   0.0    1.4  1  AAA_11           AAA domain
      0.056   13.2   0.0      0.097   12.4   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.3   0.0       0.21   11.5   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
       0.13   12.4   0.0       0.27   11.3   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.17   11.9   0.0       0.81    9.7   0.0    2.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.52   11.3   0.1       0.52   11.3   0.1    4.8  2  TPR_14           Tetratricopeptide repeat
        8.2    7.0  15.0       0.59   10.7   0.2    4.0  4  TPR_19           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   1.2e-24   7.6e-22       1     131 [.     330     464 ..     330     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.2e-24
                                    EEEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaks 73 
                                    ++++GppGtGKT++a+ va+ l       + +++e+s ++++ +y g+s+ k+++++++a       +lfiDE++al+++
  gi|121639786|ref|YP_980010.1| 330 MIFTGPPGTGKTTIARVVANILaglgviaEPKLVETSRKDFVAEYEGQSAVKTAKTIDQA--LG--GVLFIDEAYALVQE 405
                                    799******************75554444699*************************997..33..9************* PP

                                    HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..GGGSTHHHH.S.TTSSEEEETT CS
                            AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnr..pdkldpall.r.gRfdrkieie 131
                                    r+g+++ ++++++++Ll+ +++ ++   +++vi+a+++  +d+l +    + +Rf  +ie++
  gi|121639786|ref|YP_980010.1| 406 RDGRTDPFGQEALDTLLARMENDRD---RLVVIIAGYSsdIDRLLETNEgLrSRFATRIEFD 464
                                    *************************...4777777666558998888776559**9999986 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   3.3   1.3e-09   8.1e-07       3      62 .]     498     558 ..     490     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-09
                      AAA_lid_6   3 AeevlrellerrrrdenfGNARfVRnllekairrqadRlatt.ddseltredlmtLtaeDi 62 
                                    A++  + +l+ rr+ + +GN+R++R+l+e++++ +++Rla+  d + l+++ l  +  +D+
  gi|121639786|ref|YP_980010.1| 498 AKQLEQRMLRGRRALDVAGNGRYARQLVEASEQCRDMRLAQVlDIDTLDEDRLREINGSDM 558
                                    44455567778999***************************99999999999999999996 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   2.9e-08   1.8e-05      19      65 ..     311     358 ..     289     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.9e-08
                         RuvB_N  19 lkifieaakkr..eealdhvllyGpPGlGkttlakiiakelgvklkits 65 
                                    l   ++aak     ++  h++++GpPG Gktt+a+++a+ l   l + +
  gi|121639786|ref|YP_980010.1| 311 LMARVRAAKGMkvAQPSKHMIFTGPPGTGKTTIARVVANILA-GLGVIA 358
                                    555677777541156789********************9764.333334 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   1.1e-07   6.8e-05       9      50 ..     315     355 ..     309     384 .. 0.75
   2 ?    0.6   0.0      0.49   3.1e+02     101     116 ..     385     400 ..     375     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.1e-07
                   Mg_chelatase   9 eeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                     +a + +++a   +H ++++GppG+GKt +a+ ++++l+ l 
  gi|121639786|ref|YP_980010.1| 315 VRAAKGMKVAQPSKH-MIFTGPPGTGKTTIARVVANILAGLG 355
                                    567888999888776.889******************98763 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                   Mg_chelatase 101 eislahnGvLfLDElp 116
                                     i  a  GvLf+DE+ 
  gi|121639786|ref|YP_980010.1| 385 TIDQALGGVLFIDEAY 400
                                    5788999*******85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.9   5.1e+03      18      70 ..     253     300 ..     253     318 .. 0.49
   2 !   17.8   0.2   4.9e-06    0.0031       6     126 ..     328     435 ..     323     447 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.9
                         AAA_22  18 KTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka 70 
                                    KTt+++++++++d +      +p+ v  + ++ +  +++   el r++gl + +
  gi|121639786|ref|YP_980010.1| 253 KTTTAEQIASRADPW------DPGSVVTDNSGRErLLAEAQAELDRQIGLTRVK 300
                                    677777777766655......444444444443333333344444444444444 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.9e-06
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                    ++++ tG++GtGKTt +r +++ l         + +v+     ++ts+kd+  e   +  +++ +               
  gi|121639786|ref|YP_980010.1| 328 KHMIFTGPPGTGKTTIARVVANILA--------GLGVIAEPKLVETSRKDFVAEYEGQSAVKTAK--------------T 385
                                    7899******************995........55555555555555666655555555544433..............3 PP

                         AAA_22  86 lraravielliiDEaqhlr...s.......eealeeLrsllnlsrkgvqli 126
                                    ++++   ++l iDEa  l            +eal +L  +++++r+ + +i
  gi|121639786|ref|YP_980010.1| 386 IDQALG-GVLFIDEAYALVqerDgrtdpfgQEALDTLLARMENDRDRLVVI 435
                                    333333.34444444444333202233344444444444443344444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   9.5e-07   0.00061      17      97 ..     326     399 ..     316     438 .. 0.69
   2 ?   -1.6   0.5       2.9   1.9e+03     128     180 ..     512     564 ..     469     572 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.5e-07
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtll 92 
                                    + + ++ tGp+GtGKtt+ ++++++++  g     +++  + +  +A+  ++++  +a+ti++ l    g        +l
  gi|121639786|ref|YP_980010.1| 326 PSKHMIFTGPPGTGKTTIARVVANILAGLGviaePKLVETSRKDFVAEYEGQSAVKTAKTIDQAL----G-------GVL 394
                                    445899********************998877665666666666666655555555777777777....3.......456 PP

                         AAA_30  93 ivDEa 97 
                                     +DEa
  gi|121639786|ref|YP_980010.1| 395 FIDEA 399
                                    66665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                         AAA_30 128 lasVeaGgvlrdlveaa.gigtaeLtevvRqkeseeraaalalregdaeealea 180
                                    l+  ++G+  r+lvea+ + + ++L +v  + ++  ++  ++++  d++ea++a
  gi|121639786|ref|YP_980010.1| 512 LDVAGNGRYARQLVEASeQCRDMRLAQVLDI-DTLDEDRLREINGSDMAEAIAA 564
                                    4444556666666665413356666666666.4455555555555555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.3e-06    0.0034       1      73 [.     329     398 ..     329     405 .. 0.76
   2 ?   -2.4   0.0       6.9   4.4e+03      31      64 ..     496     532 ..     484     553 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.3e-06
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------.....G-SEEEEES CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraar.....egeilvlDE 73 
                                    +++  GppGtgK+++a+ +a  l +  v        t+++d++ ++e          +++v+ a+      g +l++DE
  gi|121639786|ref|YP_980010.1| 329 HMIFTGPPGTGKTTIARVVANILaGLGVIAEPKLVETSRKDFVAEYEG---------QSAVKTAKtidqaLGGVLFIDE 398
                                    6899*******************9777777777778899999999994.........3333333334445677788877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                    E--TT--HHHHH--B--............-------- CS
                          AAA_5  31 qltrdtteedlkgrreik...ngttslvdsplvraar 64 
                                    q  ++++++ l+grr ++   ng+++++  ++ +++r
  gi|121639786|ref|YP_980010.1| 496 QAAKQLEQRMLRGRRALDvagNGRYARQLVEASEQCR 532
                                    6677888888888888888776666666555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   5.1e-06    0.0033       7      46 ..     324     362 ..     317     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.1e-06
                         AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeil 46 
                                    a ++k+++ t++pGtGKT++ + + ++l  lg + +e+ l
  gi|121639786|ref|YP_980010.1| 324 AQPSKHMIFTGPPGTGKTTIARVVANILAGLGVI-AEPKL 362
                                    67899*************9999888888777654.34444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.7e-06     0.005       2      25 ..     331     359 ..     330     456 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.7e-06
                         AAA_18   2 lltGtpGvGKttlakeLskrl.gf....g 25 
                                    + tG+pG+GKtt+a+ +++ l g+     
  gi|121639786|ref|YP_980010.1| 331 IFTGPPGTGKTTIARVVANILaGLgviaE 359
                                    68***************998866643330 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       0.5   3.2e+02      12      63 ..     253     311 ..     253     326 .. 0.66
   2 !   14.9   0.1   3.5e-05     0.022       3      38 ..     331     367 ..     330     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.5
                         AAA_33  12 Kstlaerllkklg....avllssdtlrrrlfgtdqqskt...dytrvldrlyqilnela 63 
                                    K+t ae+++ + +    + +++ ++ r+rl ++ q  +     +trv++++ +  ++++
  gi|121639786|ref|YP_980010.1| 253 KTTTAEQIASRADpwdpGSVVTDNSGRERLLAEAQAELDrqiGLTRVKNQIERYRAATL 311
                                    9******99888899999*******9999999766655511134445555444333333 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.5e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlf 38 
                                    ++ G+pG+GK+t a+ +++ l+   ++++++l ++ +
  gi|121639786|ref|YP_980010.1| 331 IFTGPPGTGKTTIARVVANILAgLGVIAEPKLVETSR 367
                                    899************9998888767778877666544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.1   5.8e+03      49      77 ..     272     300 ..     245     318 .. 0.71
   2 !   16.8   0.1   7.8e-06     0.005       1      29 [.     329     357 ..     329     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.1
                                    EEET.T--EEEEEETT---SSEETTEEE- CS
                       NTPase_1  49 ivdlasgeegiLarveakreprvgkyvvd 77 
                                    +v+ +sg+e  La+ +a+   ++g   v+
  gi|121639786|ref|YP_980010.1| 272 VVTDNSGRERLLAEAQAELDRQIGLTRVK 300
                                    55556788888888876666666655555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.8e-06
                                    EEEEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvk 29 
                                    +++ TGppG+GKtT+ + v++ l+  gv 
  gi|121639786|ref|YP_980010.1| 329 HMIFTGPPGTGKTTIARVVANILAGLGVI 357
                                    6789*******************988886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.2   4.6e+03      37      37 ..     253     253 ..     166     311 .. 0.59
   2 !   17.4   3.4   7.1e-06    0.0046      19     141 ..     323     436 ..     305     561 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.2
                         AAA_16  37 K 37 
                                    K
  gi|121639786|ref|YP_980010.1| 253 K 253
                                    1 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 7.1e-06
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleaw 97 
                                    v++++   ++++G++G+GK++++r +++ l + g + ++ k ++ +++      +a++    + ++  ++    +++   
  gi|121639786|ref|YP_980010.1| 323 VAQPS-KHMIFTGPPGTGKTTIARVVANILAGLG-VIAEPKLVETSRK----DfVAEYE-GQSAVKTAKTI---DQALGG 392
                                    33333.8999*****************9888774.4444444444222....2133333.22444433333...333444 PP

                         AAA_16  98 rekleealaavpelagaeasrllellkrllallsrderplvlvl 141
                                      +++ea+a v+e +g       e+l  lla++++d++ lv+++
  gi|121639786|ref|YP_980010.1| 393 VLFIDEAYALVQERDGRTDPFGQEALDTLLARMENDRDRLVVII 436
                                    45556666666666666666666666666666677666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   3.3e-05     0.021      36     148 ..     330     435 ..     316     440 .. 0.73
   2 ?   -0.0   0.3      0.88   5.6e+02      98     153 ..     487     547 ..     447     571 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                         AAA_25  36 allaGapgtGKttlaldlalava.tGkpwlg.pvapeqgkVlyvsaEdsed.elrrRlravgealrddarllvldlagve 112
                                     +++G+pgtGKtt+a  +a  +a +G   ++ +++ + +k  +   E++ +  +++ + +++  +      l++d a   
  gi|121639786|ref|YP_980010.1| 330 MIFTGPPGTGKTTIARVVANILAgLGV-IAEpKLVETSRKDFVAEYEGQSAvKTAKTIDQALGGV------LFIDEAY-- 400
                                    689************999998886666.3347888899999999999996225556666555554......5555333.. PP

                         AAA_25 113 slpLfakdrggtl..ltadvdaleaaieevegvrlvvi 148
                                       L+++++g t    ++++d l a++e   + rlvvi
  gi|121639786|ref|YP_980010.1| 401 --ALVQERDGRTDpfGQEALDTLLARMEN-DRDRLVVI 435
                                    ..366655555554368889999999999.55777776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.88
                         AAA_25  98 rddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieeveg...vrlvviDplsr 153
                                    ++ a + +l++a++ e+++L+  ++ + +   +  ++l +a e++ +   ++++ iD+l++
  gi|121639786|ref|YP_980010.1| 487 TAEAAENFLQAAKQlEQRMLRGRRALDVAgNGRYARQLVEASEQCRDmrlAQVLDIDTLDE 547
                                    5556666777777777777776666666654455667777777766666677777777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05     0.015       2      53 ..     331     380 ..     330     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevv 53 
                                    +++Gp+g+GK+t+a+ +a+ l+  l+ + ++++ + ++++df+  Y+gq +v
  gi|121639786|ref|YP_980010.1| 331 IFTGPPGTGKTTIARVVANILA-GLGVIAEPKL-VETSRKDFVAEYEGQSAV 380
                                    689*************666666.5556665555.5899*********99877 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0036       2.3      50      92 ..     324     370 ..     294     398 .. 0.81
   2 ?    5.4   0.1     0.014       8.7     182     234 ..     453     510 ..     422     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                         DUF815  50 glpannvLLwGarGtGKSslvkallneyaeeg....Lrlievekedl 92 
                                     +p+++++++G  GtGK ++ + + n +a  g     +l+e +++d 
  gi|121639786|ref|YP_980010.1| 324 AQPSKHMIFTGPPGTGKTTIARVVANILAGLGviaePKLVETSRKDF 370
                                    57899*******************99999888655568888888876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                         DUF815 182 LsdRFGlwlgFykldqeeYleiveklakklglelek...eeleeeAlewa..lergsr 234
                                    L  RF   + F + + ee lei + +a+  + +l+    e++ ++A + +  + rg r
  gi|121639786|ref|YP_980010.1| 453 LRSRFATRIEFDTYSPEELLEIANVIAAADDSALTAeaaENFLQAAKQLEqrMLRGRR 510
                                    778*********************9998776666653344444555444311334444 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.7      0.11        67       8      25 ..     108     125 ..     105     126 .. 0.85
   2 ?    8.4   0.0    0.0059       3.8       4      31 ..     210     237 ..     207     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHH CS
                          TPR_6   8 lsyrklgdtdkAlealer 25 
                                     +  ++g++++A+eale 
  gi|121639786|ref|YP_980010.1| 108 ACEAAQGNYADAMEALEA 125
                                    577789**********95 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0059
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   4 yklalsyrklgdtdkAlealerlikeYP 31 
                                    ++la+++r++g+ ++A+++le l + +P
  gi|121639786|ref|YP_980010.1| 210 WYLAMARRSQGNESAAVALLEWLQTTHP 237
                                    79*****************986655555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00088      0.57      15      44 ..     320     349 ..     307     449 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                                    HHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraihe 44 
                                      kva+ + +++ tG  GtGK+++ar + +
  gi|121639786|ref|YP_980010.1| 320 GMKVAQPSKHMIFTGPPGTGKTTIARVVAN 349
                                    457788889999*************99865 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00032       0.2      18     106 ..     324     435 ..     311     455 .. 0.70
   2 ?   -2.5   0.0       8.2   5.3e+03      77      99 ..     462     484 ..     461     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00032
                                    HT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H................HHHHHHTTTSEEEEEE-TT- CS
                Sigma54_activ_2  18 aqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp................ldlleqakggtLylkdiadl 81 
                                    aq +  +  tG++G+gk+++Ar+ ++  ++   i++  +l++                  +++++qa gg+L++ +   l
  gi|121639786|ref|YP_980010.1| 324 AQPSKHMIFTGPPGTGKTTIARVVANILAGLGVIAEP-KLVETSrkdfvaeyegqsavktAKTIDQALGGVLFIDEAYAL 402
                                    4444445569*************99988774433333.3333223445667777777777999999*********98887 PP

                                    -HHH........HHHHHHHHHHHTTTT-EEEEE CS
                Sigma54_activ_2  82 skae........qkeLlellakaeksslrlVst 106
                                     ++         q  L  lla+ e+ + rlV +
  gi|121639786|ref|YP_980010.1| 403 VQERdgrtdpfgQEALDTLLARMENDRDRLVVI 435
                                    655333333444888888888888888777754 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.2
                                    E-TT--HHHHHHHHHHHHHHTTT CS
                Sigma54_activ_2  77 diadlskaeqkeLlellakaeks 99 
                                    +++ +s++e+ e+++++a+a+ s
  gi|121639786|ref|YP_980010.1| 462 EFDTYSPEELLEIANVIAAADDS 484
                                    67889999999999999998654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.36   2.3e+02      12      70 ..     253     309 ..     253     323 .. 0.63
   2 ?   14.1   0.1   6.6e-05     0.042       3      29 ..     331     359 ..     329     387 .. 0.87
   3 ?   -2.0   0.2       5.7   3.7e+03      29      48 ..     489     508 ..     465     553 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                         AAA_28  12 KTtlleaLaar......gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaa 70 
                                    KTt++e++a+r      g +v   ++re l  +++ + d         ++   ++++q+e+++aa
  gi|121639786|ref|YP_980010.1| 253 KTTTAEQIASRadpwdpGSVVTDNSGRERLLAEAQAELD--------RQIGLTRVKNQIERYRAA 309
                                    9********887788777777788888876544433222........234444445555544444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.6e-05
                         AAA_28   3 vitGgestGKTtlleaLaar..gypvvpE 29 
                                    ++tG+++tGKTt+++  a+   g  v++E
  gi|121639786|ref|YP_980010.1| 331 IFTGPPGTGKTTIARVVANIlaGLGVIAE 359
                                    89*************99986667777777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.7
                         AAA_28  29 Eaareileeklakgedalpw 48 
                                    Eaa  +l+   + ++++l+ 
  gi|121639786|ref|YP_980010.1| 489 EAAENFLQAAKQLEQRMLRG 508
                                    44444444444333333333 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0057       3.6      13      67 ..     313     368 ..     294     403 .. 0.79
   2 ?    3.7   0.1     0.094        60      38      81 ..     483     529 ..     433     540 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0057
                         DUF218  13 laeRldeaaelyrag.kiivsGggadedvseaeamaeylrelgvpeeailledrsr 67 
                                     + R+ +++++++   ++i++G  ++ +++ a+++a++l  lgv +e  l+e+  +
  gi|121639786|ref|YP_980010.1| 313 ARVRAAKGMKVAQPSkHMIFTGPPGTGKTTIARVVANILAGLGVIAEPKLVETSRK 368
                                    45678888888888855****985567999*************9865666666554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.094
                         DUF218  38 edvseaeamaeylrelgvpeeailledrsrnTeenarfskell...k 81 
                                    ++   aea++++l++    e+++l  +r+ + + n r++++l+   +
  gi|121639786|ref|YP_980010.1| 483 DSALTAEAAENFLQAAKQLEQRMLRGRRALDVAGNGRYARQLVeasE 529
                                    55667999******9887788********************996541 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00015     0.095      30      53 ..     324     347 ..     314     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                          AAA_7  30 lknkkpvllvGptGtGKtviikdl 53 
                                     + +k+++++Gp GtGKt+i++ +
  gi|121639786|ref|YP_980010.1| 324 AQPSKHMIFTGPPGTGKTTIARVV 347
                                    56789**************98765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016       0.1      13      41 ..     324     351 ..     315     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                         AAA_11  13 alseseitliqGPPGtgKTktivellsql 41 
                                    a  +++  ++ GPPGtgKT+    + + l
  gi|121639786|ref|YP_980010.1| 324 AQPSKH-MIFTGPPGTGKTTIARVVANIL 351
                                    445555.799*********6555544444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015     0.097       3      74 ..     332     402 ..     330     404 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                Viral_helicase1   3 vhGvpGcGKStlirkllrts..liltvnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                      G pG GK+t+ r +++    l + + ++  +  ++     ++++++ v+t++++ +al       +l++DE+++l
  gi|121639786|ref|YP_980010.1| 332 FTGPPGTGKTTIARVVANILagLGVIAEPK-LVETSRKDfvaEYEGQSAVKTAKTIDQALG-----GVLFIDEAYAL 402
                                    5799*******9998888877555444444.333333336999999999999999999884.....59*****9986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032      0.21      21     128 ..     328     440 ..     319     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk.. 96 
                                    + +  +Gp g GKt++ + +++ l  ++   +   +   r+++ ++++      + +k +++alg ++  +e+ ++++  
  gi|121639786|ref|YP_980010.1| 328 KHMIFTGPPGTGKTTIARVVANILAGLGViaEPKLVETSRKDFVAEYEGQ-SAVKTAKTIDQALGGVLFIDEAYALVQer 406
                                    555668******************77764333344445555555555554.48899999999999999999999999888 PP

                       ATPase_2  97 ..eksklvfkaielllekikkkgkkiiiiiDelq 128
                                      ++    ++a++ ll+ +++++ ++++ii    
  gi|121639786|ref|YP_980010.1| 407 dgRTDPFGQEALDTLLARMENDRDRLVVIIAGYS 440
                                    55555556799**************888885555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00042      0.27       4      80 ..     328     402 ..     325     428 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                                    --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---...----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                          AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselle...eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                      ++++gp g+Gkt +a+ +a++l       l ++   +l e   ++ v+++  +  ++    + ++ gG++++DE    
  gi|121639786|ref|YP_980010.1| 328 KHMIFTGPPGTGKTTIARVVANILA-----GLGVIAEPKLVEtsrKDFVAEYEGQSAVKTAKTIDQALGGVLFIDEAYAL 402
                                    5689********************8.....5666666666662223333444444445556667788899*****96555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.6   2.9e+03      92     116 ..     224     245 ..     213     258 .. 0.68
   2 ?    9.7   0.0    0.0013      0.81      18      43 ..     324     351 ..     304     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.6
                                    SCEEEEETGGGGCCCS-S-CEEEEE CS
                           TsaE  92 eavvlvEWpekleellpeedleiel 116
                                    +av l EW +    + pe ++ + l
  gi|121639786|ref|YP_980010.1| 224 AAVALLEWLQT---THPEPKVAVAL 245
                                    36999999998...44555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                    H..TEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE  18 l..gdvilLeGdLGaGKTtlvrglakal 43 
                                    +  ++ ++++G+ G+GKTt++r +a+ l
  gi|121639786|ref|YP_980010.1| 324 AqpSKHMIFTGPPGTGKTTIARVVANIL 351
                                    13456799**************998766 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00081      0.52      11      40 ..     110     139 ..     102     142 .. 0.87
   2 ?    7.4   0.5     0.014       8.9       5      38 ..     210     243 ..     205     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00081
                         TPR_14  11 llalGdpdeAiallrralalaPddaeawll 40 
                                    ++a+G++++A+++l++a  ++ ++++aw+ 
  gi|121639786|ref|YP_980010.1| 110 EAAQGNYADAMEALEAAPVAGSEHLVAWMK 139
                                    5789*************9999999999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                         TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeaw 38 
                                    + la a + +G+  +A+all+++  ++P++ +a 
  gi|121639786|ref|YP_980010.1| 210 WYLAMARRSQGNESAAVALLEWLQTTHPEPKVAV 243
                                    578889999**************99***987665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00092      0.59      26      52 ..     101     127 ..      99     136 .. 0.89
   2 ?    5.2   0.3     0.049        31       7      61 ..     185     241 ..     184     246 .. 0.76
   3 ?   -1.9   0.0       7.7   4.9e+03      30      38 ..     282     290 ..     254     298 .. 0.60
   4 ?   -1.9   0.3       7.9     5e+03       4      16 ..     491     503 ..     488     529 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00092
                         TPR_19  26 earllLAeallalgqldeAealLdalp 52 
                                    ++ ++ A +  a+g++++A+++L+a+p
  gi|121639786|ref|YP_980010.1| 101 AITMGFAACEAAQGNYADAMEALEAAP 127
                                    56789999***************9988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                         TPR_19   7 yaeAlalleqalqedpk....naearllLAeallalgqldeAealLdalpeedpddary 61 
                                    ++eA ++l++a  ++p       +++ +LA a  ++g+  +A alL+ l+   p  + +
  gi|121639786|ref|YP_980010.1| 185 FTEAERRLTEA-NDSPAgeacARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE-PKV 241
                                    57899999997.77777666534444469*****************988888887.555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.7
                         TPR_19  30 lLAeallal 38 
                                    lLAea+ +l
  gi|121639786|ref|YP_980010.1| 282 LLAEAQAEL 290
                                    444444443 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.9
                         TPR_19   4 egdyaeAlalleq 16 
                                    ++++ +A++ leq
  gi|121639786|ref|YP_980010.1| 491 AENFLQAAKQLEQ 503
                                    3334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 3396.30
//
Query:       gi|121639787|ref|YP_980011.1|  [L=480]
Description: hypothetical protein BCG_3932 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.2e-162  539.3   2.3   8.2e-162  539.2   2.3    1.0  1  T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM


Domain annotation for each model (and alignments):
>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.2   2.3  4.6e-166  8.2e-162       2     473 ..       4     464 ..       3     465 .. 0.96

  Alignments for each domain:
  == domain 1  score: 539.2 bits;  conditional E-value: 4.6e-166
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSSEEEETTT-- CS
                 T7SS_ESX1_EccB   2 qlttrdqvsgyrFllrRlehAlvrrdvrmlddplrsqsrallvGvvlavvvlagaavlallkPqgkvgdskivadkesga 81 
                                    +ltt+ qvsg+rFllrRlehA+vrrd+rm+ddpl+ +sr++++G+v+av++lagaa+la++kPqgk+g +++ +d+ +++
  gi|121639787|ref|YP_980011.1|   4 RLTTKVQVSGWRFLLRRLEHAIVRRDTRMFDDPLQFYSRSIALGIVVAVLILAGAALLAYFKPQGKLGGTSLFTDRATNQ 83 
                                    79****************************************************************************** PP

                                    EEEEETTEEEEES-HHHHHHHCTS-B--EEE-HHHHHTS-B--EBS-TTS-S---B-SS.SSCEEEEEEEECSTTSS.-E CS
                 T7SS_ESX1_EccB  82 lYvvvdgtLhPvlNlaSArLilgkaakpttvkdseLdklprGplvGIpgAPealpqsadldeskWtvCDtvssaasa.sa 160
                                    lYv+++g+LhPv+Nl+SArL+lg++a+p+tvk+seL+klp G++vGIpgAP+a+p sa  ++s Wt+CDtv++a+s+ + 
  gi|121639787|ref|YP_980011.1|  84 LYVLLSGQLHPVYNLTSARLVLGNPANPATVKSSELSKLPMGQTVGIPGAPYATPVSAG-STSIWTLCDTVARADSTsPV 162
                                    *********************************************************99.***********998887688 PP

                                    EEEEEEES----BTTEEE--TTEEEEEEETTEEEEEETTEEEEE-TTSHHHHHCCT--.TS--EE--HHHHHHS-EEEES CS
                 T7SS_ESX1_EccB 161 vettviagklalgaraaelaadqavLvsadgktyLvydgkraeidladravtrAlgle.gakprpvsagllnalpevppl 239
                                    v+t+via++l+ +a++++l++++avLvs++g+t++v+ + r++idl+dra+t+++g+  +a+p+p+s+g++nalp+++p+
  gi|121639787|ref|YP_980011.1| 163 VQTAVIAMPLEIDASIDPLQSHEAVLVSYQGETWIVTTKGRHAIDLTDRALTSSMGIPvTARPTPISEGMFNALPDMGPW 242
                                    99999999**************************************************9999****************** PP

                                    S----TTTTSB-TTSS-TTSBTT-EEEEEET.TEEEEEEEETTEEEEE-HHHHHHHHHHT-TT-SS--EE-CCHCCCS-. CS
                 T7SS_ESX1_EccB 240 kaPaipgaGkpaglelggkarvGsvvkvsdadgeeeyYvvlsdglqrvtevvadllrnansqgltepptvepdvlaklp. 318
                                    ++P ip+aG+p++l l+++ ++Gsv+++++  ++ +yYvvl+dg+++v++++a+ lr+++++gl +pp++ p+ + +++ 
  gi|121639787|ref|YP_980011.1| 243 QLPPIPAAGAPNSLGLPDDLVIGSVFQIHTD-KGPQYYVVLPDGIAQVNATTAAALRATQAHGLVAPPAMVPSLVVRIAe 321
                                    ******************************6.59****************************************999765 PP

                                    E-----...--SS--EEE-TTTS-EEEEEEEE-STTSS-EEEEEEESS-SS-..GCCGEEE-TTSSEE......EEESSB CS
                 T7SS_ESX1_EccB 319 vveelpvdayPekppkivdvkeapvlCaswekgagdarakvallagaalPvp..ekaktvelvsadgsgatvdavylppg 396
                                    +v+    + +P++p+kiv++ ++p lC+sw+++agd++++ ++l+g++lP++  +++  ++++++++      +vyl++g
  gi|121639787|ref|YP_980011.1| 322 RVYP---SPLPDEPLKIVSRPQDPALCWSWQRSAGDQSPQSTVLSGRHLPISpsAMNMGIKQIHGTA------TVYLDGG 392
                                    5555...55******************************************9777777788888855......5***999 PP

                                    E..EEEEEECSTT..CEEEEEEEETTSEEEEE-SHHHHHHCT--S.-EE--HHHHTTSEEEEEE-CCCCT-EESSXX CS
                 T7SS_ESX1_EccB 397 tgalvqatgaepaseargslfyvsdtGvRYgipdeetakaLGlkeepepaPwsilkllpaGPtLsradAlvahDglp 473
                                    +  +v  ++ +p+  +++s++y++++GvRYg+p++etak LGl++ p++aPw+i++ll++GP+Ls+++Al++hD+lp
  gi|121639787|ref|YP_980011.1| 393 K--FVALQSPDPR--YTESMYYIDPQGVRYGVPNAETAKSLGLSS-PQNAPWEIVRLLVDGPVLSKDAALLEHDTLP 464
                                    9..*********9..9***************************98.*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2784.34
//
Query:       gi|121639788|ref|YP_980012.1|  [L=747]
Description: hypothetical protein BCG_3933 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-49  167.2   0.0    7.4e-47  159.7   0.0    3.1  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
    0.00037   19.5   0.0       0.19   10.6   0.0    2.2  2  AAA_10         AAA-like domain
     0.0082   16.4   0.0      0.019   15.2   0.0    1.6  1  AAA_22         AAA domain
     0.0095   16.1   0.1      0.017   15.2   0.1    1.3  1  DUF87          Helicase HerA, central domain
  ------ inclusion threshold ------
       0.15   10.9   0.1       0.26   10.1   0.1    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
        0.3    9.9   0.0       0.45    9.2   0.0    1.1  1  Adeno_IVa2     Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.07   2.1e+02      27      75 ..     211     257 ..     200     291 .. 0.75
   2 !  159.7   0.0   2.5e-50   7.4e-47       4     242 ..     431     637 ..     428     638 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.07
                                    TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEE CS
                   FtsK_SpoIIIE  27 sgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqli 75 
                                     + p  l+l++ +  ++ +G+   G    + ++i+ la+ h P+ +q  
  gi|121639788|ref|YP_980012.1| 211 HDCPKLLQLRTFP--TIAIGGDLAGAAGLMTAMICHLAVFHPPDLLQIR 257
                                    5666677788888..8888888899999999************977764 PP

  == domain 2  score: 159.7 bits;  conditional E-value: 2.5e-50
                                    HHHTSHHHHT---TTEEEEEEET.TS-EEEEEGGGS-......SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE CS
                   FtsK_SpoIIIE   4 evleskkfrtessqlpvalgkei.sgnplvldlkkma.....shllvaGatgsGKStalntLilSlatthtPeeVqlili 77 
                                     + ++++++t++++l++ +g+e  +gn+++ld+k+ a     +h++++G+tgsGKS++l+tLilSl+++++P++V+l+l+
  gi|121639788|ref|YP_980012.1| 431 PSRWRMYTDTDRDRLKIPFGHELkTGNVMYLDIKEGAefgagPHGMLIGTTGSGKSEFLRTLILSLVAMTHPDQVNLLLT 510
                                    67899*************************************************************************** PP

                                    -TTSS.SCGGGTT-TTBSS...S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH.HHHHHHHHHHTT---B-TT- CS
                   FtsK_SpoIIIE  78 Dykgv.elsalediphlls..vavatdperalraleeLvkemeeryalfreagvrsiaa.ydgeiaedpldifgdvflvl 153
                                    D+kg+ ++  +e++ph+++  +++a+++e ++r+ e L+ e+++r++++r+ag++  aa + +++ae++++++       
  gi|121639788|ref|YP_980012.1| 511 DFKGGsTFLGMEKLPHTAAvvTNMAEEAELVSRMGEVLTGELDRRQSILRQAGMKVGAAgALSGVAEYEKYRE------- 583
                                    ******************9988************************************999**********74....... PP

                                    ......................-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEE CS
                   FtsK_SpoIIIE 154 DnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglH 233
                                                                  +g+ l ++p+l+v+vde++eL +++p+      +++++R++r gr+ ++H
  gi|121639788|ref|YP_980012.1| 584 ------------------------------RGADLPPLPTLFVVVDEFAELLQSHPDF-----IGLFDRICRVGRSLRVH 628
                                    ..............................89999***********************.....***************** PP

                                    EEEEES--- CS
                   FtsK_SpoIIIE 234 lllatqrls 242
                                    lllatq+l+
  gi|121639788|ref|YP_980012.1| 629 LLLATQSLQ 637
                                    ******976 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.001       3.1      22      58 ..     473     513 ..     465     544 .. 0.75
   2 !   10.6   0.0   6.5e-05      0.19     245     313 ..     597     668 ..     593     677 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.001
                         AAA_10  22 sasliiGdlGnGKSvlakllvlyisllg....gkaliiDpk 58 
                                    ++ ++iG +G GKS + ++l+l ++++       +l+ D k
  gi|121639788|ref|YP_980012.1| 473 PHGMLIGTTGSGKSEFLRTLILSLVAMThpdqVNLLLTDFK 513
                                    6789***************9998887764554455555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.5e-05
                         AAA_10 245 ifDE.awiftssaeGkkllkelvRiGRsynaavylvtqsad..DvlkeelknniglklaFretdkeeikkvL 313
                                    ++DE a  ++s ++   l + + R GRs    ++l+tqs +   v  ++l+ n+ +++a r t  +e k v+
  gi|121639788|ref|YP_980012.1| 597 VVDEfAELLQSHPDFIGLFDRICRVGRSLRVHLLLATQSLQtgGVRIDKLEPNLTYRIALRTTSSHESKAVI 668
                                    6677445667777888899*******************977225788999*************999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.3e-06     0.019       6     104 ..     473     605 ..     468     637 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-06
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...............................erpevvfvtlpsstssk 54 
                                     +++++G +G+GK+  lr+l  +l++  ++++                               e++e+v+    ++t+  
  gi|121639788|ref|YP_980012.1| 473 PHGMLIGTTGSGKSEFLRTLILSLVAMTHPDQvnllltdfkggstflgmeklphtaavvtnmaEEAELVSRMGEVLTGEL 552
                                    5899********************98888777999999999888888887776666666666666666666666666666 PP

                         AAA_22  55 dllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqhlr 104
                                    d ++ +lr+ g +  a  +     ++  e++ ++ a+     + ++++DE+  l 
  gi|121639788|ref|YP_980012.1| 553 DRRQSILRQAGMKVGA--AGALSGVAEYEKYRERGADlpplpTLFVVVDEFAELL 605
                                    6666666666665555..3444444444444444444777888888888888754 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.6e-06     0.017      27      62 ..     476     514 ..     470     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                          DUF87  27 AilgsTGsGKSntvavLleelle...kkgatililDpHG 62 
                                      +g+TGsGKS + + L+ +l++    +++++l+ D  G
  gi|121639788|ref|YP_980012.1| 476 MLIGTTGSGKSEFLRTLILSLVAmthPDQVNLLLTDFKG 514
                                    578*******************99876777888888776 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   8.8e-05      0.26      17      39 ..     474     496 ..     471     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.8e-05
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrai 39 
                                    h +++GttGsGK++ l+ l+ ++
  gi|121639788|ref|YP_980012.1| 474 HGMLIGTTGSGKSEFLRTLILSL 496
                                    889**************998655 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00015      0.45      90     120 ..     475     505 ..     468     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                     Adeno_IVa2  90 GviyGPtGsGksqllrnlissklisPiPetv 120
                                    G++ G tGsGks++lr+li s +    P+ v
  gi|121639788|ref|YP_980012.1| 475 GMLIGTTGSGKSEFLRTLILSLVAMTHPDQV 505
                                    8999***************987777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.83u 0.37s 00:00:01.20 Elapsed: 00:00:00.57
# Mc/sec: 3929.50
//
Query:       gi|121639789|ref|YP_980013.1|  [L=490]
Description: hypothetical protein BCG_3934 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-57  194.2   0.0    1.1e-43  149.3   0.0    2.1  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
    2.4e-07   31.3   0.0      0.022   15.1   0.0    2.5  2  AAA_16         AAA ATPase domain
    2.2e-05   24.8   0.0       0.38   11.0   0.0    2.6  2  AAA_22         AAA domain
    2.7e-05   23.8   0.1       0.16   11.7   0.0    3.0  3  AAA_29         P-loop containing region of AAA domain
    3.8e-05   23.7   0.0       0.79    9.6   0.0    3.2  3  NACHT          NACHT domain
      7e-05   22.5   0.2       0.21   11.1   0.1    2.7  2  AAA_25         AAA domain
    0.00024   21.7   0.0       0.48   11.0   0.0    2.5  2  AAA_18         AAA domain
     0.0009   19.6   0.0       0.61   10.5   0.0    2.7  2  RNA_helicase   RNA helicase
     0.0024   17.9   0.2       0.21   11.7   0.1    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
     0.0068   16.4   0.0        3.1    7.8   0.0    2.3  2  AAA_14         AAA domain
      0.007   16.1   0.0        2.9    7.5   0.0    2.2  2  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
  ------ inclusion threshold ------
      0.011   15.5   0.0        1.6    8.4   0.0    2.3  2  IstB_IS21      IstB-like ATP binding protein
       0.02   15.3   0.1        1.4    9.3   0.0    2.9  2  AAA            ATPase family associated with various cellular
      0.021   14.5   0.0          3    7.5   0.0    2.3  2  AAA_24         AAA domain
      0.041   14.1   0.0        8.6    6.6   0.0    2.4  2  AAA_28         AAA domain
      0.044   14.3   0.1       0.27   11.7   0.0    2.0  2  AAA_23         AAA domain
      0.044   14.1   0.1        9.9    6.5   0.0    2.4  2  AAA_19         AAA domain
      0.044   12.9   0.1        1.7    7.7   0.1    2.3  2  Parvo_NS1      Parvovirus non-structural protein NS1
      0.063   13.2   0.1         17    5.3   0.0    2.6  2  NTPase_1       NTPase
      0.066   13.0   0.0       0.14   12.0   0.0    1.5  1  Bac_DnaA       Bacterial dnaA  protein
      0.078   13.5   0.1         25    5.4   0.2    2.4  2  ABC_tran       ABC transporter
       0.13   11.7   0.0          1    8.7   0.0    2.1  2  TniB           Bacterial TniB protein
       0.19   11.2   0.0        2.5    7.6   0.0    2.3  2  GTP_EFTU       Elongation factor Tu GTP binding domain
       0.24   10.3   0.1        1.2    7.9   0.0    2.0  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
        0.4   10.4   2.3        3.1    7.5   0.0    2.6  3  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.0   1.6e-46   1.1e-43      26     240 ..      57     289 ..      43     291 .. 0.89
   2 !   42.7   0.0   5.6e-14     4e-11      30     119 ..     361     449 ..     344     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 1.6e-46
                                    TTS-EEEEEGGGS-........SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS.S- CS
                   FtsK_SpoIIIE  26 isgnplvldlkkma.......shllvaGatgsGKStalntLilSlatthtPeeVqliliDykgvelsalediphllsvav 98 
                                    i+++p  + + ++        +++ + Ga+++GKSt l+t+++S+a+th+P +Vq+++iD +g+ l  le++ph++ va 
  gi|121639789|ref|YP_980013.1|  57 IMDEPRRHLQDVWGvdvsgagGNIGIGGAPQTGKSTLLQTMVMSAAATHSPRNVQFYCIDLGGGGLIYLENLPHVGGVAN 136
                                    4566666666666566666679********************************************************** PP

                                    B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH....HHHHHHHHHHTT---B-TT-..................... CS
                   FtsK_SpoIIIE  99 atdperalraleeLvkemeeryalfreagvrsiaa....ydgeiaedpldifgdvflvlDnyddlaaene....ritsLs 170
                                    +++p+++ r+++e+ + m++r+  f+e++v si +     d+  ++++ d  gdvfl++D++  +  e++    ++  L+
  gi|121639789|ref|YP_980013.1| 137 RSEPDKVNRVVAEMQAVMRQRETTFKEHRVGSIGMyrqlRDDPSQPVASDPYGDVFLIIDGWPGFVGEFPdlegQVQDLA 216
                                    ***********************************666656666778888899*************************** PP

                                    .....-----------B-----EEEEEEC-HHHHHHHHHHH.......HHHHHHHHHHHCGGGTEEEEEEES- CS
                   FtsK_SpoIIIE 171 nqgpsygvhvlvtagrelekrpslvvivderieLrlaapkds...svlvedaivRlarkgraaglHlllatqr 240
                                    +qg+++gvhv+++++r+ e +  +++ ++  ie rl + ++    ++  e ++ R++r+++++  Hl++  +r
  gi|121639789|ref|YP_980013.1| 217 AQGLAFGVHVIISTPRWTELKSRVRDYLGTKIEFRLGDVNETqidRITREIPANRPGRAVSMEKHHLMIGVPR 289
                                    *****************************************87777788888899999999999999987766 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 5.6e-14
                                    EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS.S-B-SHHHHHHHH CS
                   FtsK_SpoIIIE  30 plvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykgvelsalediphllsvavatdperalral 109
                                    p  +   +++ hll+ Ga +sGK+t  +++  ++ ++++P++V+++l Dy ++ l a++d   l++ a+  +     +a+
  gi|121639789|ref|YP_980013.1| 361 PAHCHMHTNP-HLLIFGAAKSGKTTIAHAIARAICARNSPQQVRFMLADYRSGLLDAVPDTHLLGAGAINRNSASLDEAV 439
                                    5667778888.*************************************************88888877777777777777 PP

                                    HHHHHHHHHH CS
                   FtsK_SpoIIIE 110 eeLvkemeer 119
                                    ++L   +++r
  gi|121639789|ref|YP_980013.1| 440 QALAVNLKKR 449
                                    7777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0    0.0001     0.073       7      51 ..      60     104 ..      59     164 .. 0.81
   2 !   15.1   0.0   3.1e-05     0.022      22     106 ..     367     447 ..     356     482 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                         AAA_16   7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                    e +++L+++++   sg ++++ + G++ +GKs+l+++   ++ ++
  gi|121639789|ref|YP_980013.1|  60 EPRRHLQDVWGVDVSGAGGNIGIGGAPQTGKSTLLQTMVMSAAAT 104
                                    567899*****999*********************6654444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.1e-05
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                    ++ + +l+ G++ +GK++++ +++ra++++     + f+ +++++         l++a    +ll + + + +sa+l+++
  gi|121639789|ref|YP_980013.1| 367 HTNPHLLIFGAAKSGKTTIAHAIARAICARnspqQVRFMLADYRSG--------LLDAVPDTHLLGAGAINRNSASLDEA 438
                                    44589***********************995554344444444444........77777777777777666666666666 PP

                         AAA_16  98 rekleeala 106
                                     ++l  +l+
  gi|121639789|ref|YP_980013.1| 439 VQALAVNLK 447
                                    666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00054      0.38      10      88 ..      82     156 ..      75     166 .. 0.68
   2 !   11.0   0.0   0.00055      0.39       4      38 ..     368     416 ..     365     479 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.erlsseellealeqalra 88 
                                    + G + tGK+tll+++++++     a++++p+ v +++  +++   ++ e l  +g  +++ e+++  ++++ ++  +r+
  gi|121639789|ref|YP_980013.1|  82 IGGAPQTGKSTLLQTMVMSA-----AATHSPRNVQFYCIDLGGGGLIYLENLPHVGGVANRsEPDKVNRVVAEMQAVMRQ 156
                                    6799***************8.....4557777777777666666666555555555555544555555555666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00055
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............e 38 
                                    t  +l+++G + +GKTt +  +++  ++++++++              +
  gi|121639789|ref|YP_980013.1| 368 TNPHLLIFGAAKSGKTTIAHAIARAICARNSPQQvrfmladyrsglldA 416
                                    6779********************9998876666666665554444442 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0033       2.3      22      48 ..      76     101 ..      65     109 .. 0.73
   2 !   11.7   0.0   0.00022      0.16      19      50 ..     366     397 ..     359     405 .. 0.80
   3 ?   -0.6   0.0       1.6   1.2e+03      36      58 ..     411     434 ..     410     437 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                         AAA_29  22 kg.atlltGpsGsGKSTllDAiqalLvp 48 
                                    +g ++ + G+  +GKSTll  +++++ +
  gi|121639789|ref|YP_980013.1|  76 AGgNIGIGGAPQTGKSTLL--QTMVMSA 101
                                    34688899***********..5555554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00022
                         AAA_29  19 idlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                    ++++   l+ G+  sGK+T+  Ai+  +++++
  gi|121639789|ref|YP_980013.1| 366 MHTNPHLLIFGAAKSGKTTIAHAIARAICARN 397
                                    4444479*****************99998876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                         AAA_29  36 STllDAi.qalLvpakkvrfNkaa 58 
                                    S llDA+  + L++a  ++ N+a+
  gi|121639789|ref|YP_980013.1| 411 SGLLDAVpDTHLLGAGAINRNSAS 434
                                    889999954778888889999998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0061       4.4       7      35 ..      84     111 ..      80     115 .. 0.80
   2 ?    2.9   0.0      0.13        95      83     162 ..     191     267 ..     140     271 .. 0.83
   3 !    9.6   0.0    0.0011      0.79       4      37 ..     373     405 ..     371     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                                    C-TTTCHHHHHHHHHHHHCTS-SCCCC-S CS
                          NACHT   7 GeaGsGKTtLlqklalawaegklpqgafk 35 
                                    G++  GK+tLlq +++ +a+ + p++ ++
  gi|121639789|ref|YP_980013.1|  84 GAPQTGKSTLLQTMVMSAAATHSPRN-VQ 111
                                    66778***************999984.33 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                                    EEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH..HCTTSSCE..EEEE--TCCHHHHHHH CS
                          NACHT  83 lLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd..leeqleeaivlevegfsesrrkqlvr 160
                                    + li+Dg   +v +++      ++   ++l  + l  ++++++++   +  +  ++ +l ++i + +++ +e +++++ r
  gi|121639789|ref|YP_980013.1| 191 VFLIIDGWPGFVGEFPD-----LEGQVQDLAAQGLAFGVHVIISTPRWTELKsrVRDYLGTKIEFRLGDVNETQIDRITR 265
                                    56999999999999998.....8888999999999999999998754444335799999999***********9999998 PP

                                    HC CS
                          NACHT 161 ky 162
                                    + 
  gi|121639789|ref|YP_980013.1| 266 EI 267
                                    75 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0011
                                    EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEE CS
                          NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklv 37 
                                    ++ G+a sGKTt ++ +a+a+ +++ pq+ ++++
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARAICARNSPQQ-VRFM 405
                                    7889999*****************99996.4554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0003      0.21      16      59 ..      59     104 ..      45     157 .. 0.86
   2 !    8.5   0.0    0.0019       1.4      37      59 ..     373     396 ..     365     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                         AAA_25  16 aapppprrwlvk.gllpagelallaGapgtGKttlaldlalava.t 59 
                                    + p ++++++++ ++  ag+ + + Gap tGK+tl+  ++ + a t
  gi|121639789|ref|YP_980013.1|  59 DEPRRHLQDVWGvDVSGAGGNIGIGGAPQTGKSTLLQTMVMSAAaT 104
                                    5577778888888899999999***************999999843 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                         AAA_25  37 llaGapgtGKttlaldlalava.t 59 
                                    l++Ga ++GKtt+a  +a a++ +
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARAICaR 396
                                    899****************99944 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0035       2.5       1      19 [.      80     101 ..      80     249 .. 0.71
   2 !   11.0   0.0   0.00067      0.48       2      34 ..     373     408 ..     372     476 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                         AAA_18   1 IlltGtpGvGKttlakeL...s 19 
                                    I++ G+p +GK+tl +     +
  gi|121639789|ref|YP_980013.1|  80 IGIGGAPQTGKSTLLQTMvmsA 101
                                    89************99885441 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00067
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf....gvnlrdvake 34 
                                    l+ G++ +GKtt+a+++++   +     +++r+++++
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARAI-CarnsPQQVRFMLAD 408
                                    699**************9985.344673333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.018        13       3      32 ..      82     110 ..      80     118 .. 0.72
   2 !   10.5   0.0   0.00085      0.61       2      28 ..     373     398 ..     372     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkd 32 
                                    + G++++GKStl ++++ + + +  ++++ 
  gi|121639789|ref|YP_980013.1|  82 IGGAPQTGKSTLLQTMVMSAAATH-SPRNV 110
                                    5699***********877666444.34444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00085
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklkl 28 
                                    +++G++  GK+t+a+ +a+a++ +  +
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARAICARN-S 398
                                    799******************9655.3 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1    0.0003      0.21       1      26 [.      79     104 ..      79     119 .. 0.85
   2 ?    3.2   0.0      0.12        89       3      23 ..     373     393 ..     371     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                    EEEEEESTTSSHHHHHHHHHTSTEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaiv 26 
                                    +++i G p +GKStL+++++ ++a +
  gi|121639789|ref|YP_980013.1|  79 NIGIGGAPQTGKSTLLQTMVMSAAAT 104
                                    58999**************9885544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                                    EEEESTTSSHHHHHHHHHTST CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltgek 23 
                                    +i+G   +GK+t+  a+ ++ 
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARAI 393
                                    79**************99873 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.013       9.5       5      26 ..      80     101 ..      77     117 .. 0.78
   2 !    7.8   0.0    0.0043       3.1       3      33 ..     370     402 ..     368     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                         AAA_14   5 lvitGaRrvGKTtllkqlikel 26 
                                    + i Ga ++GK+tll++++ + 
  gi|121639789|ref|YP_980013.1|  80 IGIGGAPQTGKSTLLQTMVMSA 101
                                    568899*********9997554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0043
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell..vkkesi 33 
                                    + l+i Ga ++GKTt+++ +++      +++++
  gi|121639789|ref|YP_980013.1| 370 PHLLIFGAAKSGKTTIAHAIARAICarNSPQQV 402
                                    6689*************9999877663333333 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.004       2.9      12      40 ..      75     103 ..      73     244 .. 0.90
   2 !    6.4   0.0    0.0087       6.2      17      37 ..     372     392 ..     365     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.004
                                    BTT-EEEEEESTTSSHHHHHHHHHHHSST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  12 vqGqrtlipgafgvGktvisqslskqsns 40 
                                    + G++++i ga ++Gk++++q+++  + +
  gi|121639789|ref|YP_980013.1|  75 GAGGNIGIGGAPQTGKSTLLQTMVMSAAA 103
                                    579*****************999877544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0087
                                    EEEEESTTSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  17 tlipgafgvGktvisqslskq 37 
                                    +li+ga++ Gkt+i++++++ 
  gi|121639789|ref|YP_980013.1| 372 LLIFGAAKSGKTTIAHAIARA 392
                                    68***************9986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.037        27      31      81 ..      61     113 ..      55     117 .. 0.78
   2 ?    8.4   0.0    0.0023       1.6      45      81 ..     367     405 ..     355     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.037
                      IstB_IS21  31 dkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavr..aglsvlfv 81 
                                     +r+++++ + +   +  ni + G + +GKs l  ++ ++a++  +  +v f+
  gi|121639789|ref|YP_980013.1|  61 PRRHLQDVWGVDVSGAGGNIGIGGAPQTGKSTLLQTMVMSAAAthSPRNVQFY 113
                                    578888999999999999**************988777766542255667776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavrag..lsvlfv 81 
                                    +++  ++++G +  GK+ +a a++++ ++++   +v+f+
  gi|121639789|ref|YP_980013.1| 367 HTNPHLLIFGAAKSGKTTIAHAIARAICARNspQQVRFM 405
                                    5666799********************996622467765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.19   1.4e+02       5      30 ..      84     118 ..      80     252 .. 0.64
   2 ?    9.3   0.0     0.002       1.4       1      22 [.     372     393 ..     372     433 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                                    SSTTSSHHHHHHHHHHHH.........THEEEEEE CS
                            AAA   5 GppGtGKTllakavakel.........gvefleis 30 
                                    G p tGK++l + ++ ++         +++++ + 
  gi|121639789|ref|YP_980013.1|  84 GAPQTGKSTLLQTMVMSAaathsprnvQFYCIDLG 118
                                    77888887777766655423333331122233333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                                    EEEESSTTSSHHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel 22 
                                    +l++G    GKT++a+a+a+ +
  gi|121639789|ref|YP_980013.1| 372 LLIFGAAKSGKTTIAHAIARAI 393
                                    58999999***********986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.026        19       4      22 ..      79      97 ..      76     126 .. 0.80
   2 ?    7.5   0.0    0.0043         3       3      25 ..     370     391 ..     368     472 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   +i i G + +GK+tl+ ++
  gi|121639789|ref|YP_980013.1| 79 NIGIGGAPQTGKSTLLQTM 97
                                   68899***********999 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                         AAA_24   3 lkiliyGpsgiGKTtlakelgpk 25 
                                      +li+G +++GKTt+a  +  +
  gi|121639789|ref|YP_980013.1| 370 PHLLIFGAAKSGKTTIAHAI-AR 391
                                    6789************9887.44 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.033        24       2      19 ..      80      97 ..      79     120 .. 0.83
   2 ?    6.6   0.0     0.012       8.6       3      22 ..     373     392 ..     371     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                         AAA_28  2 ivitGgestGKTtlleaL 19
                                   i i G++ tGK+tll+ +
  gi|121639789|ref|YP_980013.1| 80 IGIGGAPQTGKSTLLQTM 97
                                   5578**********9876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                         AAA_28   3 vitGgestGKTtlleaLaar 22 
                                     i+G+  +GKTt++ a+a+ 
  gi|121639789|ref|YP_980013.1| 373 LIFGAAKSGKTTIAHAIARA 392
                                    699*************9964 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.8   1.3e+03      23      37 ..      81      95 ..      76     109 .. 0.84
   2 ?   11.7   0.0   0.00038      0.27      19      43 ..     369     393 ..     353     412 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.8
                         AAA_23 23 lItGpNGaGKTTild 37
                                    I G   +GK+T+l+
  gi|121639789|ref|YP_980013.1| 81 GIGGAPQTGKSTLLQ 95
                                   58888889*****97 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00038
                         AAA_23  19 kgltlItGpNGaGKTTildAiklaL 43 
                                    ++  lI+G   +GKTTi  Ai  a 
  gi|121639789|ref|YP_980013.1| 369 NPHLLIFGAAKSGKTTIAHAIARAI 393
                                    6777*****************9876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.037        27      11      44 ..      78     111 ..      71     119 .. 0.80
   2 ?    6.5   0.0     0.014       9.9       8      39 ..     367     398 ..     361     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpee 44 
                                    +++ + + p tGK+++l+++v  + ++++    +
  gi|121639789|ref|YP_980013.1|  78 GNIGIGGAPQTGKSTLLQTMVMSAAATHSPRNVQ 111
                                    56789999*************9999988654444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelgg 39 
                                    +++++ll+ + + +GKT++ ++i + + ++++
  gi|121639789|ref|YP_980013.1| 367 HTNPHLLIFGAAKSGKTTIAHAIARAICARNS 398
                                    678999***********988777776666553 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.084        60     117     165 ..      80     126 ..      54     160 .. 0.74
   2 ?    7.7   0.1    0.0023       1.7     117     138 ..     372     393 ..     364     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.084
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavplygcvnwtNenfpfndcfkklliwwe 165
                                    +++ G+++tGk+ l ++++     +     +N +f+  d +   li+ e
  gi|121639789|ref|YP_980013.1|  80 IGIGGAPQTGKSTLLQTMVMSAAATHS--PRNVQFYCIDLGGGGLIYLE 126
                                    6777************77644433332..55555555555555555444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    ++++G+a+ Gkt +a aIa+a+
  gi|121639789|ref|YP_980013.1| 372 LLIFGAAKSGKTTIAHAIARAI 393
                                    5789***************986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.023        17       2      20 ..      80      98 ..      79     110 .. 0.86
   2 ?    5.1   0.0     0.026        19       1      27 [.     371     397 ..     371     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                                   EEEE--TTSSHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvl 20
                                   + i G p++GK+Tl++ ++
  gi|121639789|ref|YP_980013.1| 80 IGIGGAPQTGKSTLLQTMV 98
                                   7899***********9876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                                    EEEEE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssg 27 
                                    +++i G   +GKtT+ + +++++  ++
  gi|121639789|ref|YP_980013.1| 371 HLLIFGAAKSGKTTIAHAIARAICARN 397
                                    67889999************9987665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.14      32      74 ..     366     409 ..     358     423 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                    T.S--.EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHH CS
                       Bac_DnaA  32 kkynP.lfiygevGlGktHLlkaignevlenapelrvvYltaee 74 
                                     + nP l+i+g    Gkt + +ai+ ++ ++++ ++v ++ a++
  gi|121639789|ref|YP_980013.1| 366 MHTNPhLLIFGAAKSGKTTIAHAIARAICARNSPQQVRFMLADY 409
                                    577986789*******************************9984 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.035        25      11      34 ..      77     100 ..      73     111 .. 0.85
   2 ?    5.3   0.0     0.036        26       7      34 ..     365     392 ..     359     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                                    TSEEEEEESTTSSHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  11 gekvaivGenGaGKStLlkllagl 34 
                                    g  ++i G   +GKStLl+++   
  gi|121639789|ref|YP_980013.1|  77 GGNIGIGGAPQTGKSTLLQTMVMS 100
                                    77899999999********99765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.036
                                    EEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagl 34 
                                    +++ +  + i+G   +GK+t++ ++a+ 
  gi|121639789|ref|YP_980013.1| 365 HMHTNPHLLIFGAAKSGKTTIAHAIARA 392
                                    5666778899**************9985 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.73   5.3e+02      37      61 ..      79     103 ..      62     114 .. 0.78
   2 ?    8.7   0.0    0.0015         1      33      66 ..     367     400 ..     358     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.73
                           TniB  37 nlllvGdsnnGKtmivekFarlhpp 61 
                                    n+ + G +++GK+++++    +  +
  gi|121639789|ref|YP_980013.1|  79 NIGIGGAPQTGKSTLLQTMVMSAAA 103
                                    6678899********9987665555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                           TniB  33 krmpnlllvGdsnnGKtmivekFarlhppekded 66 
                                    +  p+ll++G  + GKt+i++  ar   ++++++
  gi|121639789|ref|YP_980013.1| 367 HTNPHLLIFGAAKSGKTTIAHAIARAICARNSPQ 400
                                    45699***************99888776666555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0035       2.5       5      36 ..      79     110 ..      78     117 .. 0.88
   2 ?    0.7   0.0      0.45   3.2e+02       6      28 ..     372     394 ..     367     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0035
                                    EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHH CS
                       GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgek 36 
                                    nigi g   +GK+TL+ ++++++ a+++ +++
  gi|121639789|ref|YP_980013.1|  79 NIGIGGAPQTGKSTLLQTMVMSAAATHSPRNV 110
                                    8999******************9999886655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                                    EEEEESTTSSHHHHHHHHHHHTT CS
                       GTP_EFTU   6 igiighvDhGKtTLtdrLlyktg 28 
                                    + i g   +GKtT+  ++  +  
  gi|121639789|ref|YP_980013.1| 372 LLIFGAAKSGKTTIAHAIARAIC 394
                                    67899999******999876554 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.89   6.4e+02      18      41 ..      80     103 ..      76     118 .. 0.84
   2 ?    7.9   0.0    0.0017       1.2      15      43 ..     369     397 ..     362     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.89
                  TrwB_AAD_bind  18 ilivGttGsGKtqalekllraira 41 
                                    i i G+  +GK++ l+ ++ ++ a
  gi|121639789|ref|YP_980013.1|  80 IGIGGAPQTGKSTLLQTMVMSAAA 103
                                    67899999********99876654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0017
                  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairarg 43 
                                    + h+li+G++ sGKt+ ++++ rai ar+
  gi|121639789|ref|YP_980013.1| 369 NPHLLIFGAAKSGKTTIAHAIARAICARN 397
                                    569**********************9998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.22   1.6e+02      23      44 ..      82     103 ..      73     114 .. 0.70
   2 ?   -2.7   0.1       5.7   4.1e+03     148     163 ..     147     162 ..     141     165 .. 0.81
   3 ?    7.5   0.0    0.0043       3.1      11      47 ..     364     407 ..     360     477 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                         AAA_30  23 ltGpAGtGKttalkalreawea 44 
                                    + G++ tGK+t+l++++  ++a
  gi|121639789|ref|YP_980013.1|  82 IGGAPQTGKSTLLQTMVMSAAA 103
                                    567888*******998543333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                         AAA_30 148 taeLtevvRqkeseer 163
                                    +ae++ v+Rq+e++++
  gi|121639789|ref|YP_980013.1| 147 VAEMQAVMRQRETTFK 162
                                    789999****997765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0043
                         AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaweaag.........g 47 
                                     +++t+++   ++ G+A +GKtt+  a+++a+ a++          
  gi|121639789|ref|YP_980013.1| 364 CHMHTNPH--LLIFGAAKSGKTTIAHAIARAICARNspqqvrfmlA 407
                                    56666674..8899**************888877754554444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2603.50
//
Query:       gi|121639790|ref|YP_980014.1|  [L=115]
Description: hypothetical protein BCG_3935c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-12   45.3   0.7    9.4e-12   45.0   0.7    1.2  1  YbaB_DNA_bd      YbaB/EbfC DNA-binding family
     0.0028   17.3   1.1      0.003   17.2   1.1    1.1  1  ESX-1_EspG       EspG family
  ------ inclusion threshold ------
      0.044   13.0   0.5      0.063   12.4   0.3    1.3  1  Polysacc_deac_2  Divergent polysaccharide deacetylase
      0.092   13.2   2.6       0.11   13.0   2.6    1.2  1  SIMPL            Protein of unknown function (DUF541)
       0.38   10.2   7.3       0.42   10.0   5.4    1.8  2  DUF222           Domain of unknown function (DUF222)


Domain annotation for each model (and alignments):
>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.7   2.6e-15   9.4e-12       4      89 ..      17     102 ..      14     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.6e-15
                                    HHHHHHHHHHHHHHHTTSEEEEEETTTTEEEEEETT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    YbaB_DNA_bd   4 aqkmqkkmeeaqeelaekevegssggglVkVtvngkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaeeem 83 
                                    a ++q+ ++ + +++++ +++++ + ++V+Vt+ng++ ++ ++I++ ll++  +e +++ + +A+ +A+++a+++++++ 
  gi|121639790|ref|YP_980014.1|  17 AARFQSALDGTLNQMNNGSFRATDEAETVEVTINGHQWLTGLRIEDGLLKKLGAEAVAQRVNEALHNAQAAASAYNDAAG 96 
                                    77899999999*************************************999999*************************9 PP

                                    HHHT-- CS
                    YbaB_DNA_bd  84 skltgg 89 
                                    ++lt+ 
  gi|121639790|ref|YP_980014.1|  97 EQLTAA 102
                                    999975 PP

>> ESX-1_EspG  EspG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.1   8.4e-07     0.003      53     152 ..       4     107 ..       1     115 [] 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.4e-07
                                    TEB-HHHHHHHHHHHS-SEEEEEEEEE......--STTCEEEEEEEEETTEEEEEEE.ETTEEEEEEE-TSGHHHHHHTT CS
                     ESX-1_EspG  53 rrvdpeladaLrlLarpdrevdarvvr......rdlgdeelralvarrgrqavlavr.dgddvtlepvrpdslaaalval 125
                                    +++dp++a+aL+l ar + ++d+ +++      r ++de++ + v  +g+q++  +r +++   l  ++++++a+ + ++
  gi|121639790|ref|YP_980014.1|   4 DELDPHVARALTLAARFQSALDGTLNQmnngsfR-ATDEAETVEVTINGHQWLTGLRiEDGL--LKKLGAEAVAQRVNEA 80 
                                    79*****************************965.569999****************54444..4555555699999999 PP

                                    SH.--B-SS--EEEEHHHHHHHHHHHH CS
                     ESX-1_EspG 126 Lpeappgrgrsvslpadeleeaaerar 152
                                    L  a++++ +   +  ++l++a  +  
  gi|121639790|ref|YP_980014.1|  81 LHNAQAAASAYNDAAGEQLTAALSAMS 107
                                    998888888888888888888775543 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.8e-05     0.063      66     115 ..      62     112 ..      51     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                    T-B-TTS-HHHHHHHHHHHHCCST.T-SEEEEEE-CCHHC-HHHHHHHHHH CS
                Polysacc_deac_2  66 gaLlvsmseeeiekrleaalsrvp.gavgvnnhmGskftedeeameavlee 115
                                    ++Ll ++ +e +++r+++al +++  a   n+  G+++t+  +am+ +++e
  gi|121639790|ref|YP_980014.1|  62 DGLLKKLGAEAVAQRVNEALHNAQaAASAYNDAAGEQLTAALSAMSRAMNE 112
                                    67899999***************95577888999*************9986 PP

>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.6     3e-05      0.11     109     155 ..      48     104 ..      10     115 .] 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                          SIMPL 109 eingvsf.s...lsde..delrdearee....AvkdArakAealAkalgvklgkvvs 155
                                    +ing ++ +   ++d   ++l +ea ++    A+++A+a A a+ +a+g +l   +s
  gi|121639790|ref|YP_980014.1|  48 TINGHQWlTglrIEDGllKKLGAEAVAQrvneALHNAQAAASAYNDAAGEQLTAALS 104
                                    36666664354422224434444555555555*****************99974433 PP

>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.03   1.1e+02       4      42 ..       9      47 ..       6      56 .. 0.80
   2 ?   10.0   5.4   0.00012      0.42       4      80 ..      38     114 ..      35     115 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                         DUF222  4 aleeleaaarrlaavevllvaelaeresaeedgaeavaa 42
                                   +++++ ++a+r++++  +  +++++  + ++d ae v  
  gi|121639790|ref|YP_980014.1|  9 HVARALTLAARFQSALDGTLNQMNNGSFRATDEAETVEV 47
                                   678889999999999999999998888888888777665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                         DUF222   4 aleeleaaarrlaavevllvaelaeresaeedgaeavaalvaarlrisraeAsrrvrlA.ralrerLpavaaalraGd 80 
                                    a  e+e++  ++++ + l   ++ e++  ++ gaeava+ v ++l+  +a As + + A ++l   L a+ +a+ +G+
  gi|121639790|ref|YP_980014.1|  38 ATDEAETVEVTINGHQWLTGLRI-EDGLLKKLGAEAVAQRVNEALHNAQAAASAYNDAAgEQLTAALSAMSRAMNEGM 114
                                    55677777777777777777888.9******************************99996789999*******99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 659.12
//
Query:       gi|121639791|ref|YP_980015.1|  [L=460]
Description: hypothetical protein BCG_3936c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-30  103.3   6.1    2.2e-29  101.7   6.1    1.9  1  EspB_PE        ESX-1 secreted protein B PE domain
    0.00064   19.9   0.7    0.00064   19.9   0.7    2.4  2  PPE            PPE family
     0.0027   18.2   0.9     0.0027   18.2   0.9    2.7  3  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
  ------ inclusion threshold ------
        0.4   10.9  10.2       0.22   11.7   3.4    3.2  2  WXG100         Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> EspB_PE  ESX-1 secreted protein B PE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   6.1     5e-33   2.2e-29       1      77 []      12      88 ..      12      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 5e-33
                                   HHHHHHHHHCTS----------.-SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                        EspB_PE  1 eeLrarAaeleaplpeppsavpqaPdgLelakaaveqLnasAealrkylaageaErerLAesLrnaAkaYeevDeaa 77
                                   +e+ +rA+e+eap+++pp++vp++P++L++ak+a++qL +sA+++r+ylaag++Er+rLA+sLrnaAkaY evDe+a
  gi|121639791|ref|YP_980015.1| 12 QEILNRANEVEAPMADPPTDVPITPCELTAAKNAAQQLVLSADNMREYLAAGAKERQRLATSLRNAAKAYGEVDEEA 88
                                   699************************************************************************96 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.5     0.026   1.1e+02      57      95 ..      45      83 ..      39      94 .. 0.82
   2 !   19.9   0.7   1.4e-07   0.00064      51     106 ..     174     229 ..     137     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.026
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            PPE 57 ssaamaaaaapylaWLsaaaaqaeeaAaqaeaaaaaYea 95
                                   ++++++  a  + ++L+a a++ ++ A+ ++ aa+aY +
  gi|121639791|ref|YP_980015.1| 45 AAQQLVLSADNMREYLAAGAKERQRLATSLRNAAKAYGE 83
                                   677888888888999999999999999999999999975 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.4e-07
                                    TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--HHHH CS
                            PPE  51 eaWqGpssaamaaaaapylaWLsaaaaqaeeaAaqaeaaaaaYeaAlaamvppaei 106
                                    ++W+G +++a+ a   +  +W+ + a+ ++++A+qa+ +a+ +  A+ + ++ + i
  gi|121639791|ref|YP_980015.1| 174 DNWEGDAATACEASLDQQRQWILHMAKLSAAMAKQAQYVAQLHVWARREHPTYEDI 229
                                    69*********************************************999998766 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.9     6e-07    0.0027      62     100 .]      56      94 ..       7      94 .. 0.78
   2 ?   -1.7   0.6      0.92   4.1e+03      51      84 ..     180     213 ..     175     223 .. 0.62
   3 ?   -3.1   0.5       2.4   1.1e+04      22      40 ..     335     353 ..     333     361 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6e-07
                  T7SS_ESX_EspC  62 rraagealaaasteLadkLraAAaaYeatDeeaagaldk 100
                                     r+ ++a a+  + La+ Lr AA+aY ++Deeaa ald+
  gi|121639791|ref|YP_980015.1|  56 MREYLAAGAKERQRLATSLRNAAKAYGEVDEEAATALDN 94 
                                    45566777788899***********************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
                  T7SS_ESX_EspC  51 tndavaaaeaarraagealaaasteLadkLraAA 84 
                                     ++a++a ++ +r+ +  +a+ s+ +a++ +  A
  gi|121639791|ref|YP_980015.1| 180 AATACEASLDQQRQWILHMAKLSAAMAKQAQYVA 213
                                    5666666666666666666666666666554444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
                  T7SS_ESX_EspC  22 vaaeiasavaaaagasaav 40 
                                    +aa+++sa + aa  s +v
  gi|121639791|ref|YP_980015.1| 335 TAAQLTSAGREAAALSGDV 353
                                    5555666555554444444 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4     0.071   3.2e+02      64      85 ..      64      85 ..      40      86 .. 0.62
   2 ?   11.7   3.4     5e-05      0.22      39      76 ..     174     214 ..     147     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.071
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 64 vdaLeeisealkqaanafedaD 85
                                   +++ + ++ +l++aa+a+ ++D
  gi|121639791|ref|YP_980015.1| 64 AKERQRLATSLRNAAKAYGEVD 85
                                   4445678888888888888887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5e-05
                                    CGCTHHHCHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  39 sgWsGaaadafqaefe...ewkqaaqklvdaLeeisealkq 76 
                                    ++W+G+aa+a++a ++   +w  +++kl +a+++ ++ + q
  gi|121639791|ref|YP_980015.1| 174 DNWEGDAATACEASLDqqrQWILHMAKLSAAMAKQAQYVAQ 214
                                    59********9976542237888999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 2466.99
//
Query:       gi|121639792|ref|YP_980016.1|  [L=462]
Description: hypothetical protein BCG_3937c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-20   71.6   2.3      1e-19   70.6   2.3    1.5  1  EccE      Putative type VII ESX secretion system translocon, 
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.32   10.6   0.0    1.5  1  DUF2271   Predicted periplasmic protein (DUF2271)


Domain annotation for each model (and alignments):
>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   2.3   1.2e-23     1e-19       1      98 [.     177     266 ..     177     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.2e-23
                           EccE   1 aaaqRttWlalrldpeenvaalsaRgggtegaaraaaaaarRlakaLreqGirarvlea.eeldaalaalavglaaapad 79 
                                    a+a+R+tW++lr dpe++++++++R+ g+ g+ar+++a a+R+a++L+++G++a++ ++ +++d+a++  +v        
  gi|121639792|ref|YP_980016.1| 177 APANRRTWIVLRADPERTRKSAQRRDEGVAGLARYLVASATRIADRLASHGVDAVCGRSfDDYDHATDIGFV-------- 248
                                    79*********************************************************9*********998........ PP

                           EccE  80 vreewrtirtrdgylttYa 98 
                                     re+w++i++rd y+++Ya
  gi|121639792|ref|YP_980016.1| 249 -REKWSMIKGRDAYTAAYA 266
                                    .9****************8 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.6e-05      0.32      35      78 ..      49      93 ..      40     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.6e-05
                        DUF2271 35 tLavw.gegekwlkdlrqWwrksgrklkeeidgvsgaTrapGkyk 78
                                   t+    ++ + w+  +  W r+ +r  ++  + v gaT++pG++ 
  gi|121639792|ref|YP_980016.1| 49 TVTFYgRRITGWVAAVYAWLRRRRRPPDSSSEPVVGATVKPGDHV 93
                                   555554555789***************99*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2574.64
//
Query:       gi|121639793|ref|YP_980017.1|  [L=446]
Description: protease [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-34  118.5   3.9    4.6e-33  114.8   3.9    2.0  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   3.9   2.6e-37   4.6e-33       1     298 []      81     379 ..      81     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 2.6e-37
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeeg 80 
                                    g gv+vav+DtGvd s                          g+d  +   n  +d +     HGt +A+i+a+  + + 
  gi|121639793|ref|YP_980017.1|  81 GAGVTVAVIDTGVDASPRVPA-------------------EPGGDFVDQAGNGLSDCDA----HGTLTASIIAGRPAPTD 137
                                    789**********88776666...................3344444444444444444....***************** PP

                                    SSB-SSTTSEEE..............EEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH CS
                                    xxxxxxxxxxxx..............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  81 ekngvapgakil..............svkvldtsggsmetg.teliraieeaaedkvdvinmslgestslpktgrsieal 145
                                    +++gvap+a++l              +++  d++ + +  + + l+ra+  aa+ +v vin+s  + ++++++ +   + 
  gi|121639793|ref|YP_980017.1| 138 GFVGVAPDARLLslrqtseafepvgsQANPNDPNATPAAGSiRSLARAVVHAANLGVGVINISEAACYKVSRPID---ET 214
                                    ************999988888888754444444444444446777777888888888899999994444444444...44 PP

                                    ....HHHHHH.CCT-EEEEE--SS-...T-HH.............EEE-TTCEECTTTST.TCEEEEEESTTSSB-TT-- CS
                                    ....xxxxxxxxxxxxxxxxxxxxx...xxxx.............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 146 ....ainravnkkgvlvviSaGNng...ktgs.............slqagspvgtpstsk.nvitvgayttegkiapfSs 204
                                         i++avn kgv+vv++aGN g      +             + ++ ++v tp+ +   v++vg++ + g+ ++fS 
  gi|121639793|ref|YP_980017.1| 215 slgaSIDYAVNVKGVVVVVAAGNTGgdcV--QnpapdpstpgdprGWNNVQTVVTPAWYApLVLSVGGIGQTGMPSSFSM 292
                                    45789*******************95440..1566666677889999**********99899****************** PP

                                    B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHH..EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 205 rGpssdgklkpdivapGgnivstwsrqsnnsaglss..yqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAq 282
                                    +Gp +      d++ap++niv+  ++ +  +a +       + GTS+A++ ++g aAll++++p+ltp+++ + +  tA 
  gi|121639793|ref|YP_980017.1| 293 HGPWV------DVAAPAENIVALGDTGEPVNALQGRegPVPIAGTSFAAAYVSGLAALLRQRFPDLTPAQIIHRITATA- 365
                                    ***87......7*******7777666664443333366889**************************************. PP

                                    EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxx RF
                   Peptidase_S8 283 dlgkadniesfaqGaG 298
                                        +  +++  +GaG
  gi|121639793|ref|YP_980017.1| 366 --RHPGGGVDDLVGAG 379
                                    ..67888999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2459.07
//
Query:       gi|121639794|ref|YP_980018.1|  [L=619]
Description: hypothetical protein BCG_3939c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-19   69.5   0.0      9e-19   68.2   0.0    1.8  1  AAA           ATPase family associated with various cellular 
    6.9e-12   45.4   0.3    6.9e-12   45.4   0.3    2.7  2  AAA_lid_6     AAA lid domain
    0.00083   19.6   0.8     0.0057   16.9   0.3    2.5  1  AAA_22        AAA domain
     0.0011   19.4   0.1     0.0011   19.4   0.1    2.4  3  AAA_16        AAA ATPase domain
     0.0013   19.2   0.0     0.0062   17.1   0.0    2.2  2  AAA_18        AAA domain
     0.0021   18.3   0.2      0.012   15.9   0.0    2.3  2  AAA_28        AAA domain
     0.0024   17.9   0.0     0.0065   16.5   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0028   17.1   0.0     0.0053   16.2   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0039   17.0   0.0     0.0091   15.7   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
     0.0087   15.8   0.2      0.022   14.5   0.0    1.8  2  IstB_IS21     IstB-like ATP binding protein
     0.0092   16.1   0.2      0.039   14.1   0.0    2.0  2  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.016   15.5   0.2      0.053   13.9   0.2    1.8  1  AAA_19        AAA domain
       0.02   14.6   3.3      0.027   14.2   0.4    2.6  3  AAA_30        AAA domain
      0.033   14.1   0.0       0.06   13.3   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.052   13.3   0.1      0.095   12.4   0.1    1.4  1  AAA_24        AAA domain
      0.055   12.6   0.0       0.56    9.3   0.0    2.2  2  DUF815        Protein of unknown function (DUF815)
      0.065   12.7   0.1       0.13   11.8   0.1    1.4  1  AAA_7         P-loop containing dynein motor region
       0.11   12.1   0.6       0.21   11.2   0.6    1.4  1  SRP54         SRP54-type protein, GTPase domain
       0.17   11.6   0.1       0.32   10.7   0.1    1.4  1  AAA_11        AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   9.5e-22     9e-19       1     131 [.     369     504 ..     369     505 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 9.5e-22
                                    EEEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaks 73 
                                    +ll+GppGtGKT++a+a+ k         + e+ e+  s+++ +y+ges  k++el+++  +     i+f+DE+++l+++
  gi|121639794|ref|YP_980018.1| 369 MLLVGPPGTGKTTTAEALGKIYagmgivrHPEIREVRRSDFCGHYIGESGPKTNELIEK--SLG--RIIFMDEFYSLIER 444
                                    89*******************64444444588*************************75..444..9***********99 PP

                                    H.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..GGGSTHHHH.S.TTSSEEEETT CS
                            AAA  74 r.sgseseeeervvnqLlteldgvkkkeskvivigatnr..pdkldpall.r.gRfdrkieie 131
                                      +g+ +  ++++vnqLl +l+  +    ++++iga+++  +d++      + gRf+rk+++e
  gi|121639794|ref|YP_980018.1| 445 HqDGTPDMIGMEAVNQLLVQLETHRF---DFCFIGAGYEdqVDEFLTVNPgLaGRFNRKLRFE 504
                                    988889999****************9...6*******99886655544444459999999886 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.8       2.2   2.1e+03      31      54 ..     288     309 ..     288     317 .. 0.76
   2 !   45.4   0.3   7.4e-15   6.9e-12       1      62 []     528     600 ..     528     600 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                      AAA_lid_6  31 ekairrqadRlattddseltredl 54 
                                    e++i+ ++dR ++  ++  +r++l
  gi|121639794|ref|YP_980018.1| 288 ERTIASRSDRWDA--STAKSRDQL 309
                                    8999********9..555555555 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 7.4e-15
                      AAA_lid_6   1 eeAeevlrelle.........rrrrdenfGNARfVRnllekairrqadRlatt..ddseltredlmtLtaeDi 62 
                                    ++A+ev+ ++++          ++ ++ + N+Rf+Rn++e+a+  +++R++++   +++++ +dl+ +ta Di
  gi|121639794|ref|YP_980018.1| 528 DAAREVFLDAVTtirnyttpsGQHGIDAMQNGRFARNVIERAEGFRDTRVVAQkrAGQPVSVQDLQIITATDI 600
                                    6899999999998877777777778888********************************************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   6.1e-06    0.0057       4      28 ..     365     389 ..     362     482 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleq 28 
                                    + ++++++G++GtGKTt+++ l + 
  gi|121639794|ref|YP_980018.1| 365 QTNHMLLVGPPGTGKTTTAEALGKI 389
                                    67899***************99775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         5   4.7e+03      80      80 ..     143     143 ..      60     208 .. 0.59
   2 ?   -1.8   0.1       3.8   3.6e+03      83     118 ..     307     324 ..     247     362 .. 0.52
   3 !   19.4   0.1   1.2e-06    0.0011      20      50 ..     362     392 ..     348     547 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5
                         AAA_16  80 e 80 
                                    +
  gi|121639794|ref|YP_980018.1| 143 Q 143
                                    2 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                         AAA_16  83 rqlldeaesaeleawrekleealaavpelagaeasr 118
                                     ql+d+ +++ +++  +                   
  gi|121639794|ref|YP_980018.1| 307 DQLDDDNAAQRRGELLA------------------E 324
                                    22222222222222222..................2 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.2e-06
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralek 50 
                                     +g+++ +ll+G++G+GK++ +++l + + +
  gi|121639794|ref|YP_980018.1| 362 VEGQTNHMLLVGPPGTGKTTTAEALGKIYAG 392
                                    68999*****************999876654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.9   4.6e+03      29      61 ..     236     264 ..     233     290 .. 0.73
   2 !   17.1   0.0   6.6e-06    0.0062       2      31 ..     370     413 ..     369     470 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.9
                         AAA_18  29 rdvakenglllevdpealdeskrldedkldkll 61 
                                     d+a+ +g+++ + +e    +++++++  ++ +
  gi|121639794|ref|YP_980018.1| 236 ADLAYVRGMVYRQLHE----EDKAQIWLSKATI 264
                                    6899999999999999....5555555544444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.6e-06
                         AAA_18   2 lltGtpGvGKttlakeLskrl.gf.............gvnlrdv 31 
                                    ll G+pG+GKtt a++L k   g+             ++ ++++
  gi|121639794|ref|YP_980018.1| 370 LLVGPPGTGKTTTAEALGKIYaGMgivrhpeirevrrSDFCGHY 413
                                    689**************988655566665555555555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.2     2e+03      70     100 ..     225     258 ..     189     311 .. 0.67
   2 !   15.9   0.0   1.3e-05     0.012       3      29 ..     370     400 ..     368     408 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                         AAA_28  70 a...aankvlfcDrglldtlaYarayggeaeael 100
                                    a   a+ ++l+ D  ++  ++Y + +++++++ +
  gi|121639794|ref|YP_980018.1| 225 AigpADIPLLVADLAYVRGMVYRQLHEEDKAQIW 258
                                    3455677888889999999999888888733322 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.3e-05
                         AAA_28   3 vitGgestGKTtlleaLaar....gypvvpE 29 
                                     ++G+++tGKTt++eaL +     g++ +pE
  gi|121639794|ref|YP_980018.1| 370 LLVGPPGTGKTTTAEALGKIyagmGIVRHPE 400
                                    689**************97556344444465 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.9e-06    0.0065       1      23 [.     368     390 ..     368     441 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.9e-06
                                    EEEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal 23 
                                    ++lLvGppGtgK++ ae l + +
  gi|121639794|ref|YP_980018.1| 368 HMLLVGPPGTGKTTTAEALGKIY 390
                                    78***************998776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.6e-06    0.0053      23      49 ..     367     393 ..     359     409 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                   Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllppl 49 
                                     ++llvGppG+GKt  a++l ++ + +
  gi|121639794|ref|YP_980018.1| 367 NHMLLVGPPGTGKTTTAEALGKIYAGM 393
                                    589*****************9998766 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.7e-06    0.0091      30      54 ..     363     387 ..     340     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-06
                         RuvB_N  30 eealdhvllyGpPGlGkttlakiia 54 
                                    e + +h+ll+GpPG Gktt a+ + 
  gi|121639794|ref|YP_980018.1| 363 EGQTNHMLLVGPPGTGKTTTAEALG 387
                                    55789**************998775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.1   7.7e+03     159     171 ..      43      55 ..      36      56 .. 0.85
   2 !   14.5   0.0   2.3e-05     0.022      46      69 ..     365     388 ..     335     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.1
                      IstB_IS21 159 gdatlatAilDRl 171
                                    +d+ +a+A l R+
  gi|121639794|ref|YP_980018.1|  43 ADPSMADAWLGRI 55 
                                    699*******997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgv 69 
                                    + + ++l+Gp+G+GK+  a alg+
  gi|121639794|ref|YP_980018.1| 365 QTNHMLLVGPPGTGKTTTAEALGK 388
                                    4556899***************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7   2.6e+03      55      82 ..     264     294 ..     232     315 .. 0.56
   2 !   14.1   0.0   4.1e-05     0.039       3      32 ..     370     400 ..     369     428 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                         AAA_33  55 lyqilnelarkalsagrn.vil..datnlsr 82 
                                    +++ l + a++al+  +  +i+    t +sr
  gi|121639794|ref|YP_980018.1| 264 INGVLTDAAKEALADPNLrLIVtdERTIASR 294
                                    5555555555555555442333333344444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.1e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdt 32 
                                    llvG+pG+GK+t ae l k  + + +++ ++
  gi|121639794|ref|YP_980018.1| 370 LLVGPPGTGKTTTAEALGKIYAgMGIVRHPE 400
                                    79*************9966544455555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   5.6e-05     0.053       9      35 ..     365     391 ..     361     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv 35 
                                    + +++l++++pGtGKT++ ++  +++ 
  gi|121639794|ref|YP_980018.1| 365 QTNHMLLVGPPGTGKTTTAEALGKIYA 391
                                    56899*************988777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.6   1.5e+03      70     101 ..     261     293 ..     243     302 .. 0.76
   2 ?   -2.4   0.0       3.5   3.3e+03      50      73 ..     333     356 ..     321     362 .. 0.78
   3 ?   14.2   0.4   2.8e-05     0.027      19      44 ..     367     392 ..     360     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                         AAA_30  70 astiakllkrlkgrarlepg.tllivDEagmvd 101
                                     +ti+ +l+  +++a  +p+ +l++ DE   ++
  gi|121639794|ref|YP_980018.1| 261 KATINGVLTDAAKEALADPNlRLIVTDERTIAS 293
                                    568888887777778888999999999988776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                         AAA_30  50 iglAptgkaAkvLaeelgieasti 73 
                                    +glA  ++a  +L+++l+++ +++
  gi|121639794|ref|YP_980018.1| 333 VGLAAVKQAVSALEDQLEVRMMRL 356
                                    789999999999999999887766 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.8e-05
                         AAA_30  19 rvavltGpAGtGKttalkalreawea 44 
                                      ++l+Gp+GtGKtt+ +al ++++ 
  gi|121639794|ref|YP_980018.1| 367 NHMLLVGPPGTGKTTTAEALGKIYAG 392
                                    5689***************9998875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-05      0.06      21      70 ..     335     391 ..     330     416 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                          Rad17  21 lavhkkkieevkewlkadvLesrkkr........iLLisGPsGCgkstvvkvLskelg 70 
                                    la  k+ ++++++ l+  ++  ++           +L+ GP+G gk+t+ + L k+++
  gi|121639794|ref|YP_980018.1| 335 LAAVKQAVSALEDQLEVRMMRLEH-GlpvegqtnHMLLVGPPGTGKTTTAEALGKIYA 391
                                    566666666666666654433221.11222334468899****************974 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001     0.095       4      22 ..     368     386 ..     365     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     +l++Gp+g+GKTt+a  l
  gi|121639794|ref|YP_980018.1| 368 HMLLVGPPGTGKTTTAEAL 386
                                    689*************987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0006      0.56      52      82 ..     365     396 ..     340     436 .. 0.85
   2 ?    0.6   0.0      0.28   2.6e+02     181     219 ..     492     532 ..     479     566 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0006
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg.L 82 
                                    ++n++LL+G  GtGK ++  al + ya  g +
  gi|121639794|ref|YP_980018.1| 365 QTNHMLLVGPPGTGKTTTAEALGKIYAGMGiV 396
                                    579*******************9999887743 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                         DUF815 181 sLsdRFGlwlgFykldqeeYleiveklakklglelek..ee 219
                                     L+ RF  +l F++ +  e +ei +++a+ +  +l++  +e
  gi|121639794|ref|YP_980018.1| 492 GLAGRFNRKLRFESYSPVEIVEIGHRYATPRASQLDDaaRE 532
                                    489*************************9888877763344 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00013      0.13      32      52 ..     365     385 ..     360     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                          AAA_7  32 nkkpvllvGptGtGKtviikd 52 
                                    + +++llvGp GtGKt++++ 
  gi|121639794|ref|YP_980018.1| 365 QTNHMLLVGPPGTGKTTTAEA 385
                                    5689*************9876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00022      0.21       2      26 ..     367     391 ..     366     396 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                    EEEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallk 26 
                                    n +llvG+ G+GKTtt+  L +++ 
  gi|121639794|ref|YP_980018.1| 367 NHMLLVGPPGTGKTTTAEALGKIYA 391
                                    5789*************99999886 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00034      0.32      17      34 ..     367     383 ..     357     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                         AAA_11  17 seitliqGPPGtgKTkti 34 
                                    ++  l+ GPPGtgKT+t 
  gi|121639794|ref|YP_980018.1| 367 NH-MLLVGPPGTGKTTTA 383
                                    44.7999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.80u 0.40s 00:00:01.20 Elapsed: 00:00:00.60
# Mc/sec: 3120.72
//
Query:       gi|121639795|ref|YP_980019.1|  [L=537]
Description: hypothetical protein BCG_3940c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-18   66.8   5.8    1.6e-18   66.8   5.8    2.3  3  EccE      Putative type VII ESX secretion system translocon, 


Domain annotation for each model (and alignments):
>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   5.8   8.9e-23   1.6e-18       2      98 ..     173     262 ..     172     263 .. 0.95
   2 ?   -4.3   0.0         1   1.8e+04      16      21 ..     322     327 ..     312     332 .. 0.44
   3 ?   -2.8   0.0      0.45   8.1e+03      49      49 ..     401     401 ..     372     424 .. 0.50

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 8.9e-23
                           EccE   2 aaqRttWlalrldpeenvaalsaRgggtegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaapadvr 81 
                                    a++R+tWl++rl +  n++al++R    +++++aa+++a+R+a+ Lr qG+ra++++a++l++++++l+  + +a +  +
  gi|121639795|ref|YP_980019.1| 173 AGRRETWLIMRLPVIGNTQALRWR----TSVGAAAISVAQRVASSLRCQGLRAKLATATDLAELDRRLGSDA-VAGS--A 245
                                    799*********************....*****************************************976.5666..7 PP

                           EccE  82 eewrtirtrdgylttYa 98 
                                    ++w++ir++ g++ttYa
  gi|121639795|ref|YP_980019.1| 246 QRWKAIRGEAGWMTTYA 262
                                    ****************8 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1
                           EccE  16 eenvaa 21 
                                    e+++aa
  gi|121639795|ref|YP_980019.1| 322 EQAAAA 327
                                    222222 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.45
                           EccE  49 e 49 
                                    +
  gi|121639795|ref|YP_980019.1| 401 G 401
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3562.50
//
Query:       gi|121639796|ref|YP_980020.1|  [L=550]
Description: hypothetical protein BCG_3941c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-21   77.4   8.9    3.5e-20   72.5   1.5    3.0  2  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   1.0   0.00021       3.8       1      74 [.      94     143 ..      94     150 .. 0.62
   2 !   72.5   1.5     2e-24   3.5e-20      81     298 .]     236     482 ..     233     482 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00021
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaa 74 
                                    g+gv vav+DtGv+p+ p+l v                  + g+d+  +++  ++ d      HGt v +i+aa
  gi|121639796|ref|YP_980020.1|  94 GNGVPVAVIDTGVSPN-PRLPV------------------VPGGDYIMGEDGLSDCD-A----HGTVVSSIIAA 143
                                    78999********875.44441..................34444444443333333.2....77777777776 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 2e-24
                                    SSB-SSTTSEEE.............EEE-SSTTSB-HH....HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH CS
                                    xxxxxxxxxxxx.............xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  81 ekngvapgakil.............svkvldtsggsmetg..teliraieeaaedkvdvinmslgestslpktgrsieal 145
                                    +++gvap a+i+                ++++s+++ + g  + ++ra+  aa+ +++vin+s+++      +g++   +
  gi|121639796|ref|YP_980020.1| 236 GVVGVAPHATIIsirqssrafepvnPSSAGPNSDEKVKAGtlDSVARAVVHAANMGAKVINISVTACLPAAAPGDQR--V 313
                                    5789999999999999999999999555666666655555559999*******************555555555432..2 PP

                                    ...HHHHHH.CCT-EEEEE--SS-T-HH...............EEE-TTCEECTTTST.TCEEEEEESTTSSB-TT--B- CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 146 ...ainravnkkgvlvviSaGNngktgs...............slqagspvgtpstsk.nvitvgayttegkiapfSsrG 206
                                       a+ +a   k+ ++v++aGN+g+ g                + ++   v++ps +   v++vga++  g   + S +G
  gi|121639796|ref|YP_980020.1| 314 lgaALWYAATVKDAVIVAAAGNDGEAGCgnnpmydpldpsdprDWHQVTVVSSPSWFSdYVLSVGAVDAYGAALDKSMSG 393
                                    255666666678************5555778888888888889999999******99889******************** PP

                                    TT.......-EEEE-S-...CCCCCCCCCHHHTTTHH..........EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHH CS
                                    xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 207 pssdgklkpdivapGgn...ivstwsrqsnnsaglss..........yqsmsGTSmAsPnaagaaAlllsalpkltpetv 273
                                    p +       ++apG++   +    ++ +       +           + ++GTS++++ ++g+aAl++ ++p+lt+++v
  gi|121639796|ref|YP_980020.1| 394 PWV------GVAAPGTHimgL---SPQGG-GPV---NayppsrpgekNMPFWGTSFSAAYVSGVAALVRAKFPELTAYQV 460
                                    *87......7*******4422...32222.222...122355678887899***************************** PP

                                    HHHHHCCS-EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 274 raallntAqdlgkadniesfaqGaG 298
                                       ++++A    +++++++++ G+G
  gi|121639796|ref|YP_980020.1| 461 INRIVQSA---HNPPAGVDNKLGYG 482
                                    ********...9************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3615.89
//
Query:       gi|121639797|ref|YP_980021.1|  [L=509]
Description: hypothetical protein BCG_3942c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-12   46.0   0.0    2.5e-11   44.1   0.0    2.1  2  YukD      WXG100 protein secretion system (Wss), protein YukD
    4.9e-06   25.4  42.5    1.6e-05   23.7  22.6    2.0  2  DUF2339   Predicted membrane protein (DUF2339)
  ------ inclusion threshold ------
      0.019   15.3   0.0      0.041   14.2   0.0    1.5  1  DUF2604   Protein of Unknown function (DUF2604)


Domain annotation for each model (and alignments):
>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.2e-15   2.5e-11       2      76 .]      13      93 ..      12      93 .. 0.97
   2 ?   -2.6   0.0       1.6   9.5e+03      43      65 ..     114     137 ..     107     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.2e-15
                                   EEEEEE-TTTEEEEEEETTSBTTHHHHHHHHHS-.........--S---TT-EEEEGGGEEEETTSBCGGGT--TT-EEEE CS
                           YukD  2 vrVtvlagnrrvDlaLPadvpvaellpalvrllg......epddeagrpggwsLarvggapLsgdrtLaeagVrDGdlLvL 76
                                   + V++ ++++ +  + Pa +pv+ + + +v+l++      + d+ a ++g++ L++++g +L+ +++L+e+gV+DGd+LvL
  gi|121639797|ref|YP_980021.1| 13 CAVNICYDKHLCSQVFPAGIPVEGFFEGMVELFDadlkrkGFDGVALPAGSYELHKINGVRLDINKSLDELGVQDGDTLVL 93
                                   8899*****************************999999999*************************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                                    --TT-EEEEGGG.EEEETTSBCGG CS
                           YukD  43 rpggwsLarvgg.apLsgdrtLae 65 
                                    ++ g +L r gg + +++  +L++
  gi|121639797|ref|YP_980021.1| 114 AAMGKWLGRDGGdRMFAPVTSLTA 137
                                    567779999999999999999976 PP

>> DUF2339  Predicted membrane protein (DUF2339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  11.8   0.00028       1.7     257     343 ..     112     213 ..      96     217 .. 0.77
   2 !   23.7  22.6   2.7e-09   1.6e-05     137     315 ..     224     493 ..     218     508 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00028
                        DUF2339 257 lylalaawlarrkrekaralgeallll....avvfltlAlplaleaa...............wltvalAlegaalawlag 317
                                     ++a+  wl r + +++ a+  +l ++    a+++++++++lal  +                  v+  ++ga ++w +g
  gi|121639797|ref|YP_980021.1| 112 GLAAMGKWLGRDGGDRMFAPVTSLTAAhtamAIIAMAVGVVLALTLRtrtitdspvpaamagGIGVL-LVIGALVVW-WG 189
                                    5788899***********9999998889977666666777777666655666665555555444444.599999999.9* PP

                        DUF2339 318 lrqkrrlarlfgllalrlllaaalll 343
                                     r++r l + fg+la+ ll++aa  +
  gi|121639797|ref|YP_980021.1| 190 WRERRDLFSGFGWLAVVLLAVAA--A 213
                                    *************8888887774..3 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.7e-09
                        DUF2339 137 lvllfsYlallnaailavarrkrwrwLnllglagtfgiaalWgl.lnyapdlfastelflllfllly............. 202
                                    + l  + +++l a ++ va rkrw+   +++++   gi a+ ++ ++++p +++ + + +l+ ll+              
  gi|121639797|ref|YP_980021.1| 224 HALIGLVVVVLGAITIGVATRKRWQTAVVTAVVTVCGILAAVAAvRMFRPVSMQVLAICVLVGLLVLirmtptvalwvar 303
                                    44455556668888899*****************99985555445*****************99999************* PP

                        DUF2339 203 ..............................................................lalalllallfvaa.... 216
                                                                                                  + + + ++l+++aa    
  gi|121639797|ref|YP_980021.1| 304 vrpphfgsitgrdlfarragmpvdtvapvseadaddedneltditargtaiaasarlvnavqVGMCVGVSLVLPAAvwgv 383
                                    **********************************************9988888888888888444555555444446666 PP

                        DUF2339 217 ..rravdatlvfgaplvalvlqyalladleygwalaalalaalylalaawlarrkrekaralgeallll......avvfl 288
                                       r+ +a+l+++++ + ++l +   ++++   +++al+ +a  +++a +l  + + ++++  ++ ll+      a+++l
  gi|121639797|ref|YP_980021.1| 384 ltPRQPWAWLALLVAGLTVGLFITQGRGFAAKYQAVALVCGASAAVCAGVL--KYALDTPKGVQTGLLWpaifvaAFAAL 461
                                    664446677766666666666666677778888888888777777777777..344555555566666666665577777 PP

                        DUF2339 289 tlAlplaleaa......wltvalAlegaalawl 315
                                     lA++l++ a        ltv + le++a++ l
  gi|121639797|ref|YP_980021.1| 462 GLAVALVVPATrfrpiiRLTVEW-LEVLAMIAL 493
                                    77777777777888888455555.333333222 PP

>> DUF2604  Protein of Unknown function (DUF2604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.9e-06     0.041      31      68 ..      56      93 ..      50      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.9e-06
                        DUF2604 31 nvaqPaenwelkdeaGtlldvdkkvedlGiaaivklfl 68
                                    va Pa  +el   +G  ld++k +++lG+ ++ +l l
  gi|121639797|ref|YP_980021.1| 56 GVALPAGSYELHKINGVRLDINKSLDELGVQDGDTLVL 93
                                   5999*******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.89u 0.27s 00:00:01.16 Elapsed: 00:00:00.48
# Mc/sec: 3210.18
//
Query:       gi|121639798|ref|YP_980022.1|  [L=220]
Description: hypothetical protein BCG_3943c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.086   12.7   0.2       0.49   10.2   0.1    1.9  2  SIS       SIS domain
       0.12   11.3   0.1        0.5    9.3   0.0    1.8  2  PDH       Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0    0.0095        86      43      65 ..      70      92 ..      66     100 .. 0.83
   2 ?   10.2   0.1   5.5e-05      0.49      32     110 ..      84     165 ..      77     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0095
                                   HHHTGGGG-STTCEEEEEESSSH CS
                            SIS 43 lkhgvlalideddlvilisfsge 65
                                   + + vl+ +++ + vi+i++s+ 
  gi|121639798|ref|YP_980022.1| 70 MFSAVLSRLRRTHTVIVIDTSPD 92
                                   5677899************9986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.5e-05
                                    TSEEEEEEHHHHHHTGGGG-STTCEEEEEE..SSSHHHHHHHHHHHHHHTT.SEE....EEEESSTTSHHHHHSSEEEEE CS
                            SIS  32 givvevedaselkhgvlalideddlvilis..fsgetkdlvaaaelakerg.aki....iaITdskgsplareadlalyi 104
                                    +iv + +++ e ++ ++a++++ d ++++s  + ++++++++a+ +++++g +++     +I ++++s+  ++a   l+ 
  gi|121639798|ref|YP_980022.1|  84 VIVIDTSPDLE-HDVMKAVLQSTDTLVFVSgiTADRSRPVLRAVDYLRAQGyHELvsrsTVILNHTDSITDKDA---LAY 159
                                    55555555556.556678999*****************************954445666677777777777777...666 PP

                                    EEECHC CS
                            SIS 105 naepet 110
                                     +e+ t
  gi|121639798|ref|YP_980022.1| 160 LTERFT 165
                                    666666 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.044     4e+02     152     178 ..      85     112 ..      69     135 .. 0.67
   2 ?    9.3   0.0   5.5e-05       0.5     115     161 ..     132     179 ..     119     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.044
                                    EEEE--HH.HHHHHHHHHTHHHHHHHHH CS
                            PDH 152 rvilmspe.eHDrvvavvshlphvvaia 178
                                     vi +sp+ eHD + av +    +v+++
  gi|121639798|ref|YP_980022.1|  85 IVIDTSPDlEHDVMKAVLQSTDTLVFVS 112
                                    3455666547888888888877777766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 5.5e-05
                                    G--TTTTTT-EEEEEE-TT.S-HHHHHHHHHHHHHCT-EEEE--HHHH CS
                            PDH 115 aareelfenavviLtPtek.tdkealekvkelleevgarvilmspeeH 161
                                    ++ +el  +  viL  t+  tdk al+++ e + +vga v+ m+ + H
  gi|121639798|ref|YP_980022.1| 132 QGYHELVSRSTVILNHTDSiTDKDALAYLTERFTKVGAIVEAMPFDPH 179
                                    6678899999****999999*********************9987777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1520.35
//
Query:       gi|121639799|ref|YP_980023.1|  [L=121]
Description: hypothetical protein BCG_3944c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       167  (0.00931452); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 856.73
//
Query:       gi|121639800|ref|YP_980024.1|  [L=276]
Description: hypothetical protein BCG_3945c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-36  126.5  21.7    1.5e-36  126.3  21.7    1.0  1  ESX-1_EspG    EspG family
  ------ inclusion threshold ------
       0.19   12.4   0.0       0.29   11.8   0.0    1.3  1  SecA_PP_bind  SecA preprotein cross-linking domain


Domain annotation for each model (and alignments):
>> ESX-1_EspG  EspG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3  21.7   1.7e-40   1.5e-36       1     244 [.       5     257 ..       5     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.7e-40
                                    EHHHHHHHHHHHT---.-CGGGCC--STS.SHHHHHHHHHHHHHHHHHTTSBETT.EB-HHHHHHHHHHHS-SEEEEEEE CS
                     ESX-1_EspG   1 svdeldvlwealglge.lPvpLevpspga.taeeraalreraaaeLaerGLadgr.rvdpeladaLrlLarpdrevdarv 77 
                                    +vd+l+vl++ +g+++ +P  L++++  +  +++++alr+ +aaeL++ G +d+  + dp+++++L++L r d+ + + +
  gi|121639800|ref|YP_980024.1|   5 TVDGLWVLQAVTGVEQtCP-ELGLRPLLPrLDTAERALRHPVAAELMAVGALDQAgNADPMVREWLTVLLRRDLGLLVTI 83 
                                    79**************555.*****9999779999********************************************* PP

                                    EE--STTCEEEEEEEEETTEEEEEEEETTEEEEEEE-TSG........HHHHHHTTSH.--B-SS--EEEEHHHHHHHHH CS
                     ESX-1_EspG  78 vrrdlgdeelralvarrgrqavlavrdgddvtlepvrpds........laaalvalLpeappgrgrsvslpadeleeaae 149
                                     +   g+e++ra ++r + ++v++ r+g+ v+l p+++ s        +++++ +l++ a++++ r+v++ adel  a++
  gi|121639800|ref|YP_980024.1|  84 GV--PGGEPTRAAICRFATWWVVLERHGNLVRLYPAGTASdeagagelVVGQVERLCGVAEAAPLRPVTVDADELLHAVR 161
                                    **..6799******************************5559*************************************6 PP

                                    HHHTGHHHHHHHHT--CCCHHHHHHHTSSTSEEEEEEEEEEECCCECEEECE...SS-EEEEEETTEEEEEEEEEETTS- CS
                     ESX-1_EspG 150 raraalaaalralgasaadaralarllasprsrvgqfivavardrggrrtra...drplswfDteaGRylvspsraadge 226
                                    +a+  l++ l +  ++ ++++++  + + +rs+ +++++ +a+ + ++ +r    d+ ++++Dt+aGR++v++ ++ +++
  gi|121639800|ref|YP_980024.1| 162 DAG-TLRSYLLSQRLDVDQLQMVTMAADPTRSAHATLVALQAGVGPEKSARIlvgDSTVAIVDTAAGRICVESVTS-GQR 239
                                    654.67788888899*************************988888888888999*************99999987.567 PP

                                    -EEEEEE--HHHHHHHHH CS
                     ESX-1_EspG 227 ewltvaPadparlarale 244
                                    ++ +++P++++++  a++
  gi|121639800|ref|YP_980024.1| 240 RYQVLSPGSRSDIGGAVQ 257
                                    79************9997 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05      0.29      53      97 ..     186     230 ..     150     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                    SCCHCCHHHHHHHHHHHHHCSTTTTTEEECTTCEEEBSTTTSSEB CS
                   SecA_PP_bind  53 deenlelvhhvnqaLkAhtlferdvdYivkdgeviivDeftGRlm 97 
                                    +++ ++ +h+   aL+A    e+    +v d +v ivD   GR+ 
  gi|121639800|ref|YP_980024.1| 186 AADPTRSAHATLVALQAGVGPEKSARILVGDSTVAIVDTAAGRIC 230
                                    4455678899999******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2038.86
//
Query:       gi|121639801|ref|YP_980025.1|  [L=124]
Description: ESAT-6 like protein 11 esxC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0035   17.5   0.0     0.0045   17.2   0.0    1.1  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.5e-07    0.0045       1      52 [.       4      55 ..       4      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-07
                                   CHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHH CS
                         WXG100  1 qikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqae 52
                                   qi ++p ++ + a+++++ a++l+ + ++ +++ +alq+ + G  a+ f+++
  gi|121639801|ref|YP_980025.1|  4 QITYNPGAVSDFASDVGSRAGQLHMIYEDTASKTNALQEFFAGHGAQGFFDA 55
                                   6899*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 977.07
//
Query:       gi|121639802|ref|YP_980026.1|  [L=107]
Description: hypothetical protein BCG_3947c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.1   0.9    1.2e-13   51.1   0.9    1.4  2  WXG100         Proteins of 100 residues with WXG
    0.00077   17.6   1.5    0.00078   17.5   1.5    1.1  1  MTTB           Trimethylamine methyltransferase (MTTB)
     0.0049   17.3   5.2     0.0059   17.1   5.2    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.9     2e-17   1.2e-13       2      85 ..       5      90 ..       4      91 .. 0.97
   2 ?   -2.4   0.1      0.97   5.8e+03      44      53 ..      92     101 ..      92     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2e-17
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelq.rlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81
                                   i+v+p++lr++a+++q++ e+ +++ +  l+++ + +  ++WsGa  +a +++ +e++++++k+ ++ + ++e l qaa+ +
  gi|121639802|ref|YP_980026.1|  5 IQVTPQMLRSTANDIQANMEQAMGIAKgYLANQENVMnPATWSGAGVVASHMTATEITNELNKVLTGGTRLAEGLVQAAALM 86
                                   9**************************8999999999********************************************* PP

                                   HHHH CS
                         WXG100 82 edaD 85
                                   e ++
  gi|121639802|ref|YP_980026.1| 87 EGHE 90
                                   *998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.97
                                    HHCHHHHHHH CS
                         WXG100  44 aaadafqaef 53 
                                    ++++afqa f
  gi|121639802|ref|YP_980026.1|  92 DSQTAFQALF 101
                                    5789999876 PP

>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.5   1.3e-07   0.00078     340     404 ..      10      71 ..       5     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-07
                           MTTB 340 gltasklpDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarlleg 404
                                    ++  s ++D+Qa +e+a+ +++  la    v++ A w  +g vas+   ++ +++ +++ ++l+g
  gi|121639802|ref|YP_980026.1|  10 QMLRSTANDIQANMEQAMGIAKGYLANQENVMNPATWSGAGVVASH---MTATEITNELNKVLTG 71 
                                    5678999************************************997...5566677776666664 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   5.2   9.9e-07    0.0059       1      97 [.       1      96 [.       1      99 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.9e-07
                  T7SS_ESX_EspC  1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLra 82
                                   m+d+++V+p+ lr+ a + ++  +++   ++  + ++++v++   +++ a   a  +  +  + +++++ + +t La+ L +
  gi|121639802|ref|YP_980026.1|  1 MADTIQVTPQMLRSTANDIQANMEQAMGIAKGYLANQENVMNP-ATWSGAGVVASHMTATEITNELNKVLTGGTRLAEGLVQ 81
                                   99******************************97777777777.6899999999999999999******************* PP

                  T7SS_ESX_EspC 83 AAaaYeatDeeaaga 97
                                   AAa+ e ++ ++  a
  gi|121639802|ref|YP_980026.1| 82 AAALMEGHEADSQTA 96
                                   ****99999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 796.92
//
Query:       gi|121639803|ref|YP_980027.1|  [L=399]
Description: PPE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.6  12.3    1.5e-23   83.6  12.3    2.4  3  PPE       PPE family


Domain annotation for each model (and alignments):
>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6  12.3   8.6e-28   1.5e-23       2     157 ..       9     166 ..       8     167 .. 0.96
   2 ?   -9.0  10.4         1   1.8e+04      15      49 ..     181     214 ..     175     273 .. 0.56
   3 ?   -4.3   1.0      0.96   1.7e+04      17      33 ..     287     303 ..     280     308 .. 0.58

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 8.6e-28
                                    S-HHHHHHHHHHS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                            PPE   2 lpPEvnsallyaGpgsgpllaAaaaWdgLaaelasaaaelesvlaelaaeaWqGpssaamaaaaapylaWLsaaaaqaee 81 
                                     +PE n+ ll+aG g g++la+++aW++L a+++++  + +  +a++a ++W G  saa a ++++  a L+  a +++ 
  gi|121639803|ref|YP_980027.1|   9 RTPEANDLLLKAGTGVGTHLANQTAWTTLGASHHASGVASAINTAATA-ASWLGVGSAASALNVTMLNATLHGLAGWVDV 87 
                                    68***************************************9999999.******************************* PP

                                    HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHH..HHHT-TTSTTHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHH CS
                            PPE  82 aAaqaeaaaaaYeaAlaamvppaeiaanraelaa..lvatnffGqntpaIaateaey.eemwaqdaaamaaYeaasaaa 157
                                    + a++++a+aa+e+A aam p++e+++nr e  +  +++  ++   tp+I +++ ey   mw ++aa+ a+Y  + aa+
  gi|121639803|ref|YP_980027.1|  88 KPAVVSTAIAAFETANAAMRPAPECMENRDEWGVdnAINPSVLWTLTPRIVSLDVEYfGVMWPNNAAVGATYGGVLAAL 166
                                    *******************************99877899999******************************9998876 PP

  == domain 2  score: -9.0 bits;  conditional E-value: 1
                                    --SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT CS
                            PPE  15 pgsgpllaAaaaWdgLaaelasaaaelesvlaela 49 
                                    + ++   +Aaaa  + aae  +a + ++s  ++++
  gi|121639803|ref|YP_980027.1| 181 ASPAAPAQAAAAVGQAAAEA-AAGDGIRSAYQGVQ 214
                                    55555555555555555553.33444444444444 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 0.96
                                    SHHHHHHHHHHHHHHHH CS
                            PPE  17 sgpllaAaaaWdgLaae 33 
                                    ++p   Aa+a  g++a 
  gi|121639803|ref|YP_980027.1| 287 AAPGASAASAAGGISAA 303
                                    55555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2916.68
//
Query:       gi|121639804|ref|YP_980028.1|  [L=77]
Description: PE family protein [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   34.2   7.7    2.6e-08   34.0   7.7    1.0  1  PE        PE family


Domain annotation for each model (and alignments):
>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   7.7   1.5e-12   2.6e-08       5      76 ..       4      75 ..       2      77 .] 0.95

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.5e-12
                                   XX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----SSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             PE  5 vvaPealaaaaadlagigsalsaanaaaaapttavlaaaaDeVSaaiAalfsahaqeyqalsaqaaafheqf 76
                                   +v+Pea+ a aa   +i ++ +aa+a aa+++ +  +++ D  Sa+++a+++a +++y  + a+ a +   f
  gi|121639804|ref|YP_980028.1|  4 SVQPEAVLASAAAESAISAETEAAAAGAAPALLSTTPMGGDPDSAMFSAALNACGASYLGVVAEHASQRGLF 75
                                   69**************************************************************99887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 622.79
//
Query:       gi|121639805|ref|YP_980029.1|  [L=561]
Description: hypothetical protein BCG_3950c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-92  309.3   0.0    3.8e-84  281.8   0.0    2.7  3  FtsK_SpoIIIE   FtsK/SpoIIIE family
    4.9e-05   23.3   0.0      0.067   13.1   0.0    2.7  2  NACHT          NACHT domain
    6.7e-05   23.2   0.0      0.007   16.6   0.0    2.5  2  AAA_22         AAA domain
    0.00098   19.5   0.1       0.25   11.7   0.0    2.9  2  AAA_16         AAA ATPase domain
     0.0026   17.4   0.0        1.5    8.3   0.0    3.0  3  AAA_25         AAA domain
      0.004   17.2   0.1        1.9    8.5   0.0    2.8  2  AAA_14         AAA domain
  ------ inclusion threshold ------
      0.018   15.4   0.0        1.4    9.3   0.0    2.4  2  RNA_helicase   RNA helicase
      0.028   14.2   0.0        3.2    7.6   0.0    2.6  2  AAA_29         P-loop containing region of AAA domain
       0.03   14.8   0.0       0.18   12.3   0.0    2.2  2  ABC_tran       ABC transporter
      0.063   13.6   1.2         10    6.5   0.2    2.9  2  AAA_19         AAA domain
      0.096   12.3   0.5        4.4    6.9   0.0    2.5  2  SRP54          SRP54-type protein, GTPase domain
        0.1   13.1   0.0       0.55   10.7   0.0    2.0  2  AAA_23         AAA domain
        0.1   13.0   0.2        3.8    7.9   0.0    2.9  2  AAA            ATPase family associated with various cellular
       0.12   11.3   0.1        3.8    6.3   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.12   12.7   0.0       0.43   10.9   0.0    1.9  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I
       0.13   12.5   0.0         15    5.9   0.0    2.4  2  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.13   12.4   0.0         20    5.4   0.0    2.4  2  AAA_28         AAA domain
       0.14   11.2   0.0        1.5    7.8   0.0    2.1  2  T2SSE          Type II/IV secretion system protein
       0.16   11.7   0.6        5.8    6.7   0.0    2.3  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0   4.1e-87   3.8e-84       4     238 ..       2     261 ..       1     290 [. 0.97
   2 !   24.3   0.0   1.9e-08   1.8e-05      29      82 ..     333     385 ..     303     424 .. 0.80
   3 ?   -1.0   0.0      0.96   9.1e+02     151     234 ..     447     485 ..     425     526 .. 0.65

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 4.1e-87
                                    HHHTSHHHHT---TTEEEEEEET.TS-EEEEEGGGS-......SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE CS
                   FtsK_SpoIIIE   4 evleskkfrtessqlpvalgkei.sgnplvldlkkma.....shllvaGatgsGKStalntLilSlatthtPeeVqlili 77 
                                    +++++k+++++++q+p+++++++ +++p++++++++a     s+++v+Ga+++GK+t+l++L++S+at++tPe+V++++i
  gi|121639805|ref|YP_980029.1|   2 AAYRGKPWHVDYGQNPGLMFPVGvMDIPEESQQVVHAvdalrSNIIVVGAKQRGKTTTLMALMCSAATMYTPERVTFFCI 81 
                                    689***************************************************************************** PP

                                    -TTSS.SCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHH..HHHHHTT-SSHHH...HHHHHHHHHHTT---B-T CS
                   FtsK_SpoIIIE  78 Dykgv.elsalediphllsvavatdperalraleeLvkemeery..alfreagvrsiaa...ydgeiaedpldifgdvfl 151
                                    +++++ ++++l+++++++s+++a+++er+l+++++L++++ee++  a+++++g+r++++   +dg++++dp+d+fgdvf+
  gi|121639805|ref|YP_980029.1|  82 GGATMaQIGSLPHVTDIVSPKDAEGIERILSTMDALIDAREEAFrrAKIDMDGFRERRFgigGDGVGGTDPTDAFGDVFV 161
                                    ******************************************9999********************************** PP

                                    T-..........................-----------B--.---EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHH CS
                   FtsK_SpoIIIE 152 vlDnyddlaaene....ritsLsnqgpsygvhvlvtagrele.krpslvvivderieLrlaapkdssvlvedaivRlark 226
                                    vlD+yddl+a+++    ri+sLs++gp+ygvh++++ag++++ +r+sl+++v++ri+Lrla+p++s++++ ++++R+a++
  gi|121639805|ref|YP_980029.1| 162 VLDDYDDLYAKDTllgdRIISLSSRGPEYGVHLMCSAGGWIHgQRQSLLQNVTARIQLRLADPGESQMGHLSIESREAAR 241
                                    ******************************************************************************** PP

                                    ...CG.....GGTEEEEEEE CS
                   FtsK_SpoIIIE 227 ...gr.....aaglHlllat 238
                                       +r     +++lH+l+++
  gi|121639805|ref|YP_980029.1| 242 rtlNRpgfglTESLHELRIG 261
                                    9997888899*******998 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.9e-08
                                    -EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS CS
                   FtsK_SpoIIIE  29 nplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykgv 82 
                                     p+ + l++++  l+++G++g GK+tal ++  +++ + +P++ ql liD+k+ 
  gi|121639805|ref|YP_980029.1| 333 GPVPIKLRESP-GLMILGRQGCGKTTALVAIGEAVMNRFSPQQAQLTLIDPKTA 385
                                    57888999999.9***************************************86 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.96
                                    TT-......................-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGG CS
                   FtsK_SpoIIIE 151 lvlDnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraa 230
                                    ++                                             +d + +Lr a++  ++  v  a+ +l +++r+ 
  gi|121639805|ref|YP_980029.1| 447 VL---------------------------------------------IDDVQDLRPAQSYPQKPPVGAALWKLMERARQV 481
                                    44.............................................444444444444444444444455555555555 PP

                                    TEEE CS
                   FtsK_SpoIIIE 231 glHl 234
                                    glH 
  gi|121639805|ref|YP_980029.1| 482 GLHV 485
                                    5554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0047       4.4       3      94 ..      46     170 ..      44     211 .. 0.76
   2 !   13.1   0.0   7.1e-05     0.067       4     134 ..     346     496 ..     344     519 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0047
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelper 82 
                                    +i+ G+   GKTt l  l+  +a+ + p+     +F +  +++ ++g  +++ d++  +  e ++++   +  l+  +e 
  gi|121639805|ref|YP_980029.1|  46 IIVVGAKQRGKTTTLMALMCSAATMYTPER--VTFFCIGGATMAQIGSLPHVTDIVSPKDAEGIERILSTMDALIDAREE 123
                                    789999999*****************9993..455666778888888888888888877777777776666666666666 PP

                                    EE...................................EEEE-STT-S CS
                          NACHT  83 lL...................................lilDglDelv 94 
                                    +                                     +lD++D+l 
  gi|121639805|ref|YP_980029.1| 124 AFrrakidmdgfrerrfgiggdgvggtdptdafgdvfVVLDDYDDLY 170
                                    66666666666666666666666666666666666666666666665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.1e-05
                                    EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHH....HCCCCTS--SSS-CCHHHHCCS CS
                          NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladl....lfsqlpepaapvsevwavllel 79 
                                    ++ G++G+GKTt l  + +a   +  pq+a +l +    ++ ++     +l+dl     ++ +   +++++e   v++el
  gi|121639805|ref|YP_980029.1| 346 MILGRQGCGKTTALVAIGEAVMNRFSPQQA-QLTLI-DPKTAPH-----GLRDLhapgYVRAYAYDQDEIDE---VITEL 415
                                    799*************************86.66654.4444444.....44444111124445555555656...89999 PP

                                    CCCEE..........................EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHH CS
                          NACHT  80 perlL..........................lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralr 133
                                    ++++L                           ++D++ +l+   +  +k pv   L +l++++   + +++ t  + ++ 
  gi|121639805|ref|YP_980029.1| 416 AQQILlprlppkglsqeelralkpwegprhfVLIDDVQDLRPAQSYPQKPPVGAALWKLMERARQVGLHVFSTRNSANWA 495
                                    99999999999999999999999999999988999999999877778888999999999998777777777776666665 PP

                                    H CS
                          NACHT 134 d 134
                                     
  gi|121639805|ref|YP_980029.1| 496 T 496
                                    5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.07        66       5      28 ..      43      66 ..      40     124 .. 0.83
   2 !   16.6   0.0   7.5e-06     0.007       8     105 ..     345     460 ..     340     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                         AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                   ++ ++v+G +  GKTt+l  l+ +
  gi|121639805|ref|YP_980029.1| 43 RSNIIVVGAKQRGKTTTLMALMCS 66
                                   5779*************9887655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.5e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..................erpevvfvtlpsstsskdllrellralglelk 69 
                                    l++ G  G+GKTt l  + e   ++ ++++                  + p++v+ ++  + + +++ +el++++ l++ 
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIGEAVMNRFSPQQaqltlidpktaphglrdlHAPGYVRAYAYDQDEIDEVITELAQQILLPRL 424
                                    6899****************9999998888999*******************************************9888 PP

                         AAA_22  70 a.erlsseellealeqalraravielliiDEaqhlr...s 105
                                      ++ls+eel+++      ++    +++iD++q lr   s
  gi|121639805|ref|YP_980029.1| 425 PpKGLSQEELRALKPWEGPRH----FVLIDDVQDLRpaqS 460
                                    866677777766665555555....66********75531 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.04        38      10      48 ..      33      67 ..      30     134 .. 0.83
   2 !   11.7   0.0   0.00026      0.25      24     150 ..     342     458 ..     336     486 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellral 48
                                   +q+ +a++++r    ++++++G++  GK++ + +l+ ++
  gi|121639805|ref|YP_980029.1| 33 QQVVHAVDALR----SNIIVVGAKQRGKTTTLMALMCSA 67
                                   55666666665....6899*************9988555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                    ++ +++ G +G+GK++ + ++ +a+  +   f  ++++          l++  ++ + lr+l+++   ++ ++++++++e
  gi|121639805|ref|YP_980029.1| 342 SPGLMILGRQGCGKTTALVAIGEAVMNR---FSPQQAQLT--------LIDPKTAPHGLRDLHAPGYVRAYAYDQDEIDE 410
                                    47899*************8888766666...666666666........66666666899999999999999999999999 PP

                         AAA_16 104 alaavpelagaea...srllellkrllallsrderp.lvlvlDdlqwadea 150
                                    +++   ela ++         l ++ l+ l++ e p   +++Dd+q++++a
  gi|121639805|ref|YP_980029.1| 411 VIT---ELAQQILlprLPPKGLSQEELRALKPWEGPrHFVLIDDVQDLRPA 458
                                    988...444444455433334444444444444555468888999988875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0016       1.5      19      59 ..      29      69 ..      24      78 .. 0.86
   2 ?    4.7   0.0     0.021        20      37      58 ..     346     367 ..     339     387 .. 0.87
   3 ?   -0.4   0.0      0.74     7e+02     144     184 ..     445     486 ..     401     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                         AAA_25 19 ppprrwlvkgllpagelallaGapgtGKttlaldlalavat 59
                                   p++ +++v+ + ++ + ++++Ga   GKtt ++ l+++ at
  gi|121639805|ref|YP_980029.1| 29 PEESQQVVHAVDALRSNIIVVGAKQRGKTTTLMALMCSAAT 69
                                   566677788887888999********************997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                         AAA_25  37 llaGapgtGKttlaldlalava 58 
                                    ++ G++g+GKtt+++ ++ av+
  gi|121639805|ref|YP_980029.1| 346 MILGRQGCGKTTALVAIGEAVM 367
                                    6789**********99877765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.74
                         AAA_25 144 rlvviDplsralggdensn.sdvgalvealeriarrtgaavl 184
                                    ++v iD ++ + ++++  +   vga++++l + ar+ g +v+
  gi|121639805|ref|YP_980029.1| 445 HFVLIDDVQDLRPAQSYPQkPPVGAALWKLMERARQVGLHVF 486
                                    578999999999995555515589999999999999999996 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0021       1.9       5      24 ..      46      65 ..      43      81 .. 0.79
   2 ?    5.6   0.0     0.016        15       5      28 ..     345     369 ..     341     488 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                         AAA_14  5 lvitGaRrvGKTtllkqlik 24
                                   ++++Ga++ GKTt l  l+ 
  gi|121639805|ref|YP_980029.1| 46 IIVVGAKQRGKTTTLMALMC 65
                                   89***********9998875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                         AAA_14   5 lvitGaRrvGKTtllkqlikell.v 28 
                                    l+i G   +GKTt l  + +  +  
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIGEAVMnR 369
                                    6899*********998887665551 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.087        82       1      24 [.      46      69 ..      46      86 .. 0.77
   2 ?    9.3   0.0    0.0015       1.4       2      32 ..     346     376 ..     345     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.087
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallk 24
                                   i+++G+++ GK+t+   L+ + ++
  gi|121639805|ref|YP_980029.1| 46 IIVVGAKQRGKTTTLMALMCSAAT 69
                                   6899********999997766654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkd 32 
                                    ++ G++g+GK+t+   + +a+++++  ++++
  gi|121639805|ref|YP_980029.1| 346 MILGRQGCGKTTALVAIGEAVMNRFSPQQAQ 376
                                    799*******************999444433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.056        53      22      47 ..      43      65 ..      32      78 .. 0.73
   2 ?    7.6   0.0    0.0034       3.2      22      42 ..     340     362 ..     330     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.056
                         AAA_29 22 kgatlltGpsGsGKSTllDAiqalLv 47
                                   +++++++G+   GK+T l A+   ++
  gi|121639805|ref|YP_980029.1| 43 RSNIIVVGAKQRGKTTTLMAL---MC 65
                                   33799***********98444...43 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0034
                         AAA_29  22 kg..atlltGpsGsGKSTllDAi 42 
                                    ++    ++ G++G GK+T l Ai
  gi|121639805|ref|YP_980029.1| 340 REspGLMILGRQGCGKTTALVAI 362
                                    3334799***********98776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.9   1.8e+03      14      32 ..      46      64 ..      42      76 .. 0.82
   2 ?   12.3   0.0   0.00019      0.18       4      32 ..     335     363 ..     332     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.9
                                   EEEEESTTSSHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlklla 32
                                   + +vG    GK+t l++l+
  gi|121639805|ref|YP_980029.1| 46 IIVVGAKQRGKTTTLMALM 64
                                   678899999***9998886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00019
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlklla 32 
                                    v +kl+e+  + i+G+ G+GK+t l ++ 
  gi|121639805|ref|YP_980029.1| 335 VPIKLRESPGLMILGRQGCGKTTALVAIG 363
                                    55688888899************998875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.033        31       4      52 ..      38      83 ..      33     136 .. 0.79
   2 ?    6.5   0.2     0.011        10      10      43 ..     342     375 ..     336     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.033
                         AAA_19  4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftg 52
                                   av ++ +++++v++    GKT++l++ +  +  +    pe+++  +  g
  gi|121639805|ref|YP_980029.1| 38 AV-DALRSNIIVVGAKQRGKTTTLMALMCSAATMY--TPERVTFFCIGG 83
                                   55.66678889999999********9998877776..456666666555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpe 43 
                                    ++ l++++  G+GKT+ l++i + + ++ + + +
  gi|121639805|ref|YP_980029.1| 342 SPGLMILGRQGCGKTTALVAIGEAVMNRFSPQQA 375
                                    556789999**********999888776654444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.07        66       3      22 ..      45      64 ..      43      84 .. 0.83
   2 ?    6.9   0.0    0.0046       4.4       4      26 ..     345     367 ..     343     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.07
                                   EEEEEESTTSSHHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKLa 22
                                    i++vG +  GKTttl  L 
  gi|121639805|ref|YP_980029.1| 45 NIIVVGAKQRGKTTTLMALM 64
                                   689************97765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0046
                                    EEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   4 illvGlqGaGKTttlaKLaallk 26 
                                    ++++G qG GKTt+l  + + ++
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIGEAVM 367
                                    699**********9977766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   1.4e+03      23      39 ..      47      63 ..      43      77 .. 0.83
   2 ?   10.7   0.0   0.00058      0.55      19      48 ..     343     371 ..     320     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                   +++G    GKTT l A+
  gi|121639805|ref|YP_980029.1| 47 IVVGAKQRGKTTTLMAL 63
                                   56788889****99997 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                         AAA_23  19 kgltlItGpNGaGKTTildAiklaLygetp 48 
                                    +gl  I G  G+GKTT l Ai  a  ++++
  gi|121639805|ref|YP_980029.1| 343 PGL-MILGRQGCGKTTALVAIGEAVMNRFS 371
                                    444.8***************9877666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.4   3.7e+02       2      31 ..      47      83 ..      46     122 .. 0.76
   2 ?    7.9   0.0     0.004       3.8       2      23 ..     346     367 ..     345     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.4
                                   EEESSTTSSHHHHHHHHHHHH.......THEEEEEET CS
                            AAA  2 llyGppGtGKTllakavakel.......gvefleisg 31
                                   +++G +  GKT++  a++ ++        v+f+ i g
  gi|121639805|ref|YP_980029.1| 47 IVVGAKQRGKTTTLMALMCSAatmytpeRVTFFCIGG 83
                                   78999999*****999998863333333355555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.004
                                    EEESSTTSSHHHHHHHHHHHHT CS
                            AAA   2 llyGppGtGKTllakavakelg 23 
                                    ++ G  G+GKT++  a+ + + 
  gi|121639805|ref|YP_980029.1| 346 MILGRQGCGKTTALVAIGEAVM 367
                                    688*********9999988753 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.055        52      15      40 ..      43      68 ..      34     106 .. 0.79
   2 ?    6.3   0.0     0.004       3.8       5      39 ..     333     366 ..     329     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.055
                  TrwB_AAD_bind 15 tqhilivGttGsGKtqalekllrair 40
                                   ++ i++vG+   GKt++l +l+ ++ 
  gi|121639805|ref|YP_980029.1| 43 RSNIIVVGAKQRGKTTTLMALMCSAA 68
                                   568999***************98765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.004
                  TrwB_AAD_bind   5 agvplpkeretqhilivGttGsGKtqalekllrai 39 
                                    + vp++  re   ++i+G +G GKt+al ++ +a+
  gi|121639805|ref|YP_980029.1| 333 GPVPIK-LRESPGLMILGRQGCGKTTALVAIGEAV 366
                                    566665.479999**************98765554 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00046      0.43      23      65 ..     118     154 ..     106     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                  Lambda_tail_I  23 vktleeairalssqldafkellqrskfavrvagvdVgesvpvd 65 
                                     +  eea r+  +++d+f+e     +f+++ +gv+ g+  p+d
  gi|121639805|ref|YP_980029.1| 118 IDAREEAFRRAKIDMDGFRER----RFGIGGDGVG-GT-DPTD 154
                                    57789**************99....9999999999.65.4555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.055        52       2      22 ..      46      66 ..      45      80 .. 0.84
   2 ?    5.9   0.0     0.015        15       2      33 ..     345     379 ..     344     392 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.055
                                   EEEESSTTSSHHHHHHCHCT- CS
                            Roc  2 vvlvGdsgvGKtsllkrfved 22
                                   +++vG ++ GKt+ l  ++ +
  gi|121639805|ref|YP_980029.1| 46 IIVVGAKQRGKTTTLMALMCS 66
                                   89**********999888854 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                    EEEESSTTSSHHHHHHCH...CT-CCC-EEETTTT CS
                            Roc   2 vvlvGdsgvGKtsllkrf...vedkfsekekstig 33 
                                    ++++G +g GKt+ l  +   v ++fs+++ + + 
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIgeaVMNRFSPQQAQLTL 379
                                    79**********98765511155777777766554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.021        20       1      29 [.      45      74 ..      45     128 .. 0.82
   2 ?    4.8   0.0     0.033        31       3      21 ..     346     364 ..     345     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.021
                         AAA_28  1 kivitGgestGKTtlleaLa.argypvvpE 29
                                   +i+++G+   GKTt+l aL  +  + + pE
  gi|121639805|ref|YP_980029.1| 45 NIIVVGAKQRGKTTTLMALMcSAATMYTPE 74
                                   599**************9984335555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                         AAA_28   3 vitGgestGKTtlleaLaa 21 
                                    +i+G +++GKTt l a+ +
  gi|121639805|ref|YP_980029.1| 346 MILGRQGCGKTTALVAIGE 364
                                    58999*******9987765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0016       1.5     118     151 ..      35      65 ..      24      77 .. 0.77
   2 ?    0.7   0.0      0.24   2.3e+02     132     154 ..     345     367 ..     336     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallk 151
                                    + +++ +    r +i+v G+   GKtt+l al+ 
  gi|121639805|ref|YP_980029.1|  35 VVHAVDAL---RSNIIVVGAKQRGKTTTLMALMC 65 
                                    34444444...99****************99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                          T2SSE 132 ilvsGgTgsGKttllyallkein 154
                                    +++ G  g GKtt l a+ + + 
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIGEAVM 367
                                    5677999********88766554 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.083        78       3      21 ..      45      63 ..      43      72 .. 0.82
   2 ?    6.7   0.0    0.0061       5.8       4      26 ..     345     367 ..     343     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.083
                      PduV-EutP  3 killiGkvgsGKttLtqal 21
                                   +i+++G+ + GKtt   al
  gi|121639805|ref|YP_980029.1| 45 NIIVVGAKQRGKTTTLMAL 63
                                   79**********9966555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                      PduV-EutP   4 illiGkvgsGKttLtqalkgeel 26 
                                    ++++G+ g+GKtt   a+ +  +
  gi|121639805|ref|YP_980029.1| 345 LMILGRQGCGKTTALVAIGEAVM 367
                                    699**********8877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4237.88
//
Query:       gi|121639806|ref|YP_980030.1|  [L=833]
Description: hypothetical protein BCG_3951c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-18   65.7   0.0    5.7e-16   58.6   0.0    2.3  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.25   11.6   0.0    1.6  1  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.1     0.002        18      56      76 ..     233     253 ..     231     257 .. 0.89
   2 !   58.6   0.0   6.4e-20   5.7e-16      41     215 ..     518     702 ..     484     714 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.002
                                    HHHHHHHHHTT--TTTEEEEE CS
                   FtsK_SpoIIIE  56 lntLilSlatthtPeeVqlil 76 
                                    +++ ++Sla+ h+P +V+l++
  gi|121639806|ref|YP_980030.1| 233 MRSVLCSLAVFHNPRDVKLMV 253
                                    6789***************97 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 6.4e-20
                                    SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS.SCGGGTT-TTBSS....S-B-SHHHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  41 hllvaGatgsGKStalntLilSlatthtPeeVqliliDykgv.elsalediphlls...vavatdperalraleeLvkem 116
                                    h +v+G++gsGKS+   +L+ ++a+th+Pe  + i +D+k   + + + +iph+++     + ++   a r+ + +  e+
  gi|121639806|ref|YP_980030.1| 518 HSVVIGTSGSGKSELFLSLVYGIALTHSPETFNVIFVDMKFEsAAQDILGIPHVVAalsNLGKDERHLAERMRRVIDGEI 597
                                    99**************************************9999************7733345555666666666667** PP

                                    HHHHHHHHHTT-SSHHHHHHHHHHHHHTT..---B-TT-..........................-----------B--. CS
                   FtsK_SpoIIIE 117 eeryalfreagvrsiaaydgeiaedpldi..fgdvflvlDnyddlaaene....ritsLsnqgpsygvhvlvtagrele. 189
                                    ++ry+lf++ g+r+ ++y++ i  +  d+   +++ +++D+y +l a  +     i+ + ++g    v  ++  +r +  
  gi|121639806|ref|YP_980030.1| 598 KQRYELFKSVGARDANDYEE-IRLAGRDLppVPVLLVIVDEYLELFANHKkwidLIIHIGQEGRGANVFFMLGGQRLDLs 676
                                    *****************554.333333330036777889*****9999988999999**999999999999998887767 PP

                                    ---EEEEEEC-HHHHHHHHHHH.... CS
                   FtsK_SpoIIIE 190 krpslvvivderieLrlaapkdssvl 215
                                     ++ + ++++ ri+Lr   ++ds+  
  gi|121639806|ref|YP_980030.1| 677 SLQKVKSNIAFRIALRAESGDDSREV 702
                                    **********************8543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.25       8      86 ..     519     593 ..     517     675 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl..lrellralglelkaerlsseellealeqa 85 
                                     vv+G sG+GK+ l   l++    +  +  e   v+fv+++ ++  +d+    +++ al + +k+    +++l e++++ 
  gi|121639806|ref|YP_980030.1| 519 SVVIGTSGSGKSELFLSLVYGI--ALTHSPETFNVIFVDMKFESAAQDIlgIPHVVAALSNLGKD----ERHLAERMRRV 592
                                    58******************97..34444488889999999999888875667888888764444....45555555444 PP

                         AAA_22  86 l 86 
                                    +
  gi|121639806|ref|YP_980030.1| 593 I 593
                                    4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (833 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 5756.83
//
Query:       gi|121639807|ref|YP_980031.1|  [L=495]
Description: hypothetical protein BCG_3952c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.1e-153  511.4   6.4   2.3e-153  511.3   6.4    1.0  1  T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM


Domain annotation for each model (and alignments):
>> T7SS_ESX1_EccB  Type VII secretion system ESX-1, transport TM domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.3   6.4  1.3e-157  2.3e-153       3     473 ..       5     479 ..       3     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 511.3 bits;  conditional E-value: 1.3e-157
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSSEEEETTT--E CS
                 T7SS_ESX1_EccB   3 lttrdqvsgyrFllrRlehAlvrrdvrmlddplrsqsrallvGvvlavvvlagaavlallkPqgkvgdskivadkesgal 82 
                                    l++rdq sg+ F+ rRl++A +r  vrm +d+ r+q+ al++++vl++++++++++l +lkP g vgds+i+ d++sgal
  gi|121639807|ref|YP_980031.1|   5 LSNRDQNSGHLFYNRRLRAATTRFSVRMKHDD-RKQTAALALSMVLVAIAAGWMMLLNVLKPTGIVGDSAIIGDRDSGAL 83 
                                    789*****************************.*********************************************** PP

                                    EEEETTEEEEES-HHHHHHHCTS-B--EEE-HHHHHTS-B--EBS-TTS-S---B-SS.SSCEEEEEEEECSTTSS-EEE CS
                 T7SS_ESX1_EccB  83 YvvvdgtLhPvlNlaSArLilgkaakpttvkdseLdklprGplvGIpgAPealpqsadldeskWtvCDtvssaasasave 162
                                    Y ++dg+L+P+lNl+SArL++g+a +pt+vk +e++k+p GplvGIpgAP+a+p +   + s+W+vCDt+++++sa++  
  gi|121639807|ref|YP_980031.1|  84 YARIDGRLYPALNLTSARLATGTAGQPTWVKPAEIAKYPTGPLVGIPGAPAAMPVNRG-AVSAWAVCDTAGRPRSADKPV 162
                                    *********************************************************9.9******************** PP

                                    EEEEES----BTTEEE--TTEEEEEEETTEEEEEETTEEEEE-TTSHHHHHCCT--..TS--EE--HHHHHHS-EEEESS CS
                 T7SS_ESX1_EccB 163 ttviagklalgaraaelaadqavLvsadgktyLvydgkraeidladravtrAlgle..gakprpvsagllnalpevpplk 240
                                    +t iag+ ++g ra++l++d  +Lv+ dg+ty+++ gkr++id+++ravt +lgl+   ++p ++s++l++ lp+++pl+
  gi|121639807|ref|YP_980031.1| 163 VTSIAGPITGGGRATHLRDDAGLLVTFDGSTYVIWGGKRSQIDPTNRAVTLSLGLDpgVTSPIQISRALFDGLPATEPLR 242
                                    ********************************************************98899******************* PP

                                    ----TTTTSB-TTSS-TTSBTT-EEEEEET.TEEEEEEEETTEEEEE-HHHHHHHHHHT-TT-SS--EE-CCHCCCS-E- CS
                 T7SS_ESX1_EccB 241 aPaipgaGkpaglelggkarvGsvvkvsdadgeeeyYvvlsdglqrvtevvadllrnansqgltepptvepdvlaklpvv 320
                                    +Pa+p+aG+p+++ ++g++ vGsv+++++a+g++++Yv+l+dg+q+++++vadllr ans+g+++p++v+pdvl ++p+v
  gi|121639807|ref|YP_980031.1| 243 VPAVPEAGTPSTW-VPGAR-VGSVLQAQTAGGGSQFYVLLPDGVQKISSFVADLLRSANSYGAAAPRVVTPDVLVHTPQV 320
                                    *********9988.66655.************************************************************ PP

                                    ----...--SS--EEE-TTTS-EEEEEEEE-STTSS-EEEEEEESS-SS-..GCCGEEE-TTSSEE........EEESSB CS
                 T7SS_ESX1_EccB 321 eelpvdayPekppkivdvkeapvlCaswekgagdarakvallagaalPvp..ekaktvelvsadgs..gatvdavylppg 396
                                    ++lpv++yP+ ++++vd++++p++C+swek++++++a+va++ g+ lPvp   +++ v+lv+ d++  +  +++v + pg
  gi|121639807|ref|YP_980031.1| 321 TSLPVEYYPAGRLNFVDTAADPTTCVSWEKASTGPQARVAVYNGRGLPVPpsMDSRIVRLVRDDRApaSVVATQVLVLPG 400
                                    **************************************************9999999*******99878888******** PP

                                    E..EEEEEECSTT..CEEEEEEEETTSEEEEE-SH.HHHHHCT--S..-EE--HHHHTTSEEEEEE-CCCCT-EESSXX CS
                 T7SS_ESX1_EccB 397 tgalvqatgaepaseargslfyvsdtGvRYgipde.etakaLGlkee.pepaPwsilkllpaGPtLsradAlvahDglp 473
                                     +++v++t+   ++e+r+slf+vs +GvR+gi+++ +t++aLGl+   +++aPw++l++++aGP+Lsr++Al+a+D++p
  gi|121639807|ref|YP_980031.1| 401 AANFVTSTSGVITAESRESLFWVSGNGVRFGIANDeATLRALGLDPGaAVQAPWPLLRTFAAGPALSRDAALLARDTVP 479
                                    ********************************9986899*****9888999**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3582.95
//
Query:       gi|121639808|ref|YP_980032.1|  [L=288]
Description: hypothetical protein BCG_3953c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00099   18.8   0.0      0.002   17.8   0.0    1.5  1  SLT       Transglycosylase SLT domain


Domain annotation for each model (and alignments):
>> SLT  Transglycosylase SLT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-07     0.002      18      65 ..     209     264 ..     199     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-07
                                    HHHHHHHHTT-TT-B-........TTSEBTTTTBETTTHHHHHHHHT-SHHHHCSH CS
                            SLT  18 aaiaqvESgfnpkAvs........ksgavGLmQimpstakrlglrvklsedelldP 65 
                                      +a+ ES++n +A++        ++ + G +Q++  t+ ++  r ++ ++ +  P
  gi|121639808|ref|YP_980032.1| 209 DLVARRESNYNANAINhwdsnaarGTPSRGVWQFIAPTFAAITSRARRPTSTIWSP 264
                                    579*************99776666666**************999888777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1500.61
//
Query:       gi|121639809|ref|YP_980033.1|  [L=329]
Description: hypothetical protein BCG_3954c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1774.08
//
Query:       gi|121639810|ref|YP_980034.1|  [L=293]
Description: hypothetical protein BCG_3955c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-36  124.7   2.1    2.6e-36  123.5   2.1    1.6  1  DUF5632    Family of unknown function (DUF5632)
    1.9e-34  117.9   2.5    2.2e-34  117.7   0.4    2.1  2  DUF5631    Family of unknown function (DUF5631)
     0.0012   18.9   0.1     0.0031   17.6   0.1    1.6  2  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> DUF5632  Family of unknown function (DUF5632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   2.1   4.3e-40   2.6e-36       2      80 ..      78     159 ..      77     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 4.3e-40
                        DUF5632   2 seeqrLqRlldavaRqeprLaWavGeraDg.ttllvtDlasGWiPpgvelpagvtLlePa..rrsgeleallGevavaaa 78 
                                    +e+qrLqR++davaRqepr++Wa+G r+Dg ttllvtDla+GWiPp+v+lpa+vtLleP+  rr++++ +llG+v+++aa
  gi|121639810|ref|YP_980034.1|  78 AEQQRLQRIVDAVARQEPRISWAAGLRDDGtTTLLVTDLAGGWIPPHVRLPANVTLLEPTarRRDADVIDLLGAVVAVAA 157
                                    689***************************999**************************998999*************** PP

                        DUF5632  79 ye 80 
                                    +e
  gi|121639810|ref|YP_980034.1| 158 HE 159
                                    97 PP

>> DUF5631  Family of unknown function (DUF5631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.46   2.7e+03      11      27 ..      76      92 ..      62     101 .. 0.70
   2 !  117.7   0.4   3.6e-38   2.2e-34       1      94 [.     187     280 ..     187     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.46
                        DUF5631 11 atrrrdgLPrlvhtlak 27
                                    +  +++L r+v+++a+
  gi|121639810|ref|YP_980034.1| 76 RAAEQQRLQRIVDAVAR 92
                                   44556677777777775 PP

  == domain 2  score: 117.7 bits;  conditional E-value: 3.6e-38
                        DUF5631   1 idelgvelseatrrrdgLPrlvhtlakaaaagtgvldeEvdllrehldtirkqvlaaYPdvdaalvlnwlLLAaiealva 80 
                                    +de+g++l+ea+rrrd LPr+++++a  a+++tgvl++E +ll+ +++ ++++vl+aYP+++ ++v++w+LLAaieal++
  gi|121639810|ref|YP_980034.1| 187 VDEFGPTLVEAVRRRDSLPRIAQAIALPAVRKTGVLENEAELLHGCITAVKESVLKAYPSHELTAVGDWMLLAAIEALID 266
                                    79****************************************************************************** PP

                        DUF5631  81 gdevaAnYHlaWfr 94 
                                     +++ AnYHlaW+ 
  gi|121639810|ref|YP_980034.1| 267 EQDYLANYHLAWYA 280
                                    ************96 PP

>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.2e-07    0.0031      43     110 ..      38     105 ..      32     117 .. 0.85
   2 ?   -2.9   0.0       1.2     7e+03      62      94 ..     236     267 ..     227     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.2e-07
                      tRNA_edit  43 reldlkklakllgakklrlaseeelrellgvepGgvgPlglkaagvpvllDeslkeyptvvvgageng 110
                                     ++  k++a + ga++ ++a +  l +  g  +G+v+  ++++++++ ++D+ ++++p++  +ag ++
  gi|121639810|ref|YP_980034.1|  38 ERAASKAVAGQAGASSSTMAGASALSATAGATAGAVSARAAEQQRLQRIVDAVARQEPRISWAAGLRD 105
                                    566789***********************************9****************9877777554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                      tRNA_edit  62 aseeelrellgvepGgvgPlglkaagvpvllDe 94 
                                    ++e  l+++  +e  +vg   l  a ++ l+De
  gi|121639810|ref|YP_980034.1| 236 VKESVLKAYPSHELTAVGDWML-LAAIEALIDE 267
                                    5677777788888888888887.6888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1529.84
//
Query:       gi|121639811|ref|YP_980035.1|  [L=311]
Description: hypothetical protein BCG_3957c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 1581.45
//
Query:       gi|121639812|ref|YP_980036.1|  [L=131]
Description: hypothetical protein BCG_3958c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.7    7.5  16.6        5.8    7.2  16.3    1.4  1  RskA      Anti-sigma-K factor rskA


Domain annotation for each model (and alignments):
>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  16.3   0.00033       5.8      25      86 ..      15      86 ..       2     126 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00033
                                   ..................XXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXX...........X CS
                           RskA 25 aaaaapppaaapaararrlaaaaAaalllvlgqlavasaaldplrqsaaqaeavvavlaap...........d 86
                                   + a+ap+p ++++ +++ ++aa+Aa++++++   + +++a+ ++  ++++ ++++a  +a+           +
  gi|121639812|ref|YP_980036.1| 15 VTAPAPWPIPRTRSWPAIVVAAIAAVVAVAAL-IVALTNARPAATPATTSVPTYTAAQTAAaqrqlcdtyklV 86
                                   45566666666666665566666666665544.3444444444444444444444444444223444443330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 865.91
//
Query:       gi|121639813|ref|YP_980037.1|  [L=176]
Description: hypothetical protein BCG_3959c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-57  192.1   0.0    5.8e-57  191.9   0.0    1.0  1  Imm61     Immunity protein 61


Domain annotation for each model (and alignments):
>> Imm61  Immunity protein 61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0   3.2e-61   5.8e-57       1     154 []      14     167 ..      14     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 3.2e-61
                                    HHHHTT-EEE-GGGS..--EEEE-GGGSEEEEEEEETTEEEEEEEETT---EEEEEESSHHHHHHHHHHHHHHHHHHHTT CS
                          Imm61   1 waklagyrltpssds..grlilvdeggeirliieakedrylltkaeraeeeevvlaAasldvverylwgllgddvrekre 78 
                                    w++l+g+++ + s++  gr+il+++gge+r++i++ +++y++t+++r+++e +++aAas++v+e+yl+g++g +vr++re
  gi|121639813|ref|YP_980037.1|  14 WIRLSGMNMIQGSETndGRTILWNKGGEVRYFIDRLAGWYVITSSDRMSREGYEFAAASMSVIEKYLYGYFGGSVRSERE 93 
                                    **************999*************************************************************** PP

                                    ---EE---SGGGS-TT-EEEEEEET...EEEEE-TTS-EEEES-HHH.....HHHHHHHHHS-HHHHHHHHHSTT-TTT CS
                          Imm61  79 LprlklPvsaediasgysletreea...rlalvdsdgnllAkgeadstdlaklvklshlLavsldelkaSfldpdGkPL 154
                                    Lp++++P++ e+++++ys+ t+++a   r++l+ds+g+++A+++ad+     lv+lsh+L+vs++ +k+Sfld++GkPL
  gi|121639813|ref|YP_980037.1|  94 LPAIRAPFQPEELMPEYSIGTMTFAgrqRDTLIDSSGTVVAITAADR-----LVELSHYLDVSVNVIKDSFLDSEGKPL 167
                                    ***********************999999******************.....**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.89
# Mc/sec: 596.83
//
Query:       gi|121639814|ref|YP_980038.1|  [L=846]
Description: hypothetical protein BCG_3960c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-16   58.4   0.0    2.8e-15   56.7   0.0    1.9  2  TNT            Tuberculosis necrotizing toxin


Domain annotation for each model (and alignments):
>> TNT  Tuberculosis necrotizing toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.91   1.6e+04      39      59 ..      84     104 ..      79     111 .. 0.82
   2 !   56.7   0.0   1.5e-19   2.8e-15       4      87 ..     751     846 .]     750     846 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.91
                                    -EEEEEE.----EEEEEB--B CS
                            TNT  39 nyhvYevlkpleveaGeiapw 59 
                                    + h Y + + +   aG++ap 
  gi|121639814|ref|YP_980038.1|  84 SAHNYSLAEAMSDVAGRAAPL 104
                                    579999999999999999986 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 1.5e-19
                                    H-SEEEEES-TT-S-EE..EGG---..GGGT--GGGGGS-EEEEEE.----....EEEEEB--BTTB----EEEEEE... CS
                            TNT   4 pGtlldRfGseeGrfla..pagtpy..eeRaLppsnlnknyhvYevlkple....veaGeiapwfgqpGgGvqyelv... 72 
                                    +G +ldR+G+++G++la  ++g p   e+RaL+ ++l+++yh+Y++ ++l+    +e +e+ap +gqpGg +q+++    
  gi|121639814|ref|YP_980038.1| 751 YGPQLDRIGGDQGKYLAimEHGRPAswEQRALHVTSLRDPYHAYTI-DWLPegwfIEVSEVAPGCGQPGGSIQVRIFdhq 829
                                    5899************95558888777*****************99.67777899*********************9776 PP

                                    --..-HHHHHHTTSEE- CS
                            TNT  73 ks..svkellengyLee 87 
                                    ++  +v+el+++g+L++
  gi|121639814|ref|YP_980038.1| 830 NEmrKVEELIRRGVLRQ 846
                                    22678**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (846 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 5339.42
//
Query:       gi|121639815|ref|YP_980039.1|  [L=90]
Description: ESAT-6 like protein 12 esxE [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-09   36.4   3.1    5.1e-09   36.3   3.1    1.0  1  WXG100    Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   3.1   2.8e-13   5.1e-09       4      84 ..       1      81 [.       1      83 [. 0.97

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.8e-13
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  4 vdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84
                                   +dp +l++a ar+++   ++e++++++++ v  l+ +W G+ a a ++++  w ++ + + +aL++++ a ++a+++++ a
  gi|121639815|ref|YP_980039.1|  1 MDPTVLADAVARMAEFGRHVEELVAEIESLVTRLHVTWTGEGAAAHAEAQRHWAAGEAMMRQALAQLTAAGQSAHANYTGA 81
                                   6999************************************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 670.19
//
Query:       gi|121639816|ref|YP_980040.1|  [L=57]
Description: ESAT-6 like protein 13 esxF [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   37.7   0.2    1.9e-09   37.6   0.2    1.0  1  WXG100         Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.034   14.4   0.0      0.045   14.0   0.0    1.2  1  RMF            Ribosome modulation factor
      0.045   14.2   0.1      0.045   14.2   0.1    1.1  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.2   3.2e-13   1.9e-09       2      51 ..       7      56 ..       6      57 .] 0.96

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.2e-13
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqa 51
                                   ++v+p++++  aa+++++ae+l  +l++l+a+v ++ +gW+Ga+++a+ +
  gi|121639816|ref|YP_980040.1|  7 LRVEPAVMQGFAASLDGAAEHLAVQLAELDAQVGQMLGGWRGASGSAYGS 56
                                   79*********************************************976 PP

>> RMF  Ribosome modulation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.6e-06     0.045       9      48 ..       9      50 ..       5      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                            RMF  9 lerAfsrGYqaGleGrskelcPyq.tlda.rseWLgGWRear 48
                                   +e A  +G+ a l+G    l+    +lda   + LgGWR a 
  gi|121639816|ref|YP_980040.1|  9 VEPAVMQGFAASLDGAAEHLAVQLaELDAqVGQMLGGWRGAS 50
                                   67899***********998885434778734799*****986 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   7.5e-06     0.045       3      48 ..       5      47 ..       1      57 [] 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                  T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpic 48
                                   d+L+V+p++++ +aa +d++a+ +a  +a      a+v +  G + 
  gi|121639816|ref|YP_980040.1|  5 DTLRVEPAVMQGFAASLDGAAEHLAVQLAEL---DAQVGQMLGGWR 47
                                   78********************997655544...555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 403.91
//
Query:       gi|121639817|ref|YP_980041.1|  [L=169]
Description: hypothetical protein BCG_3963c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.096   13.1   0.4        3.5    8.1   0.0    2.3  2  DUF5060    Domain of unknown function (DUF5060)
        4.2    7.0  36.4        1.5    8.4   1.4    6.9  7  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> DUF5060  Domain of unknown function (DUF5060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.016   1.4e+02      24      53 ..      53      82 ..      44      92 .. 0.80
   2 ?    8.1   0.0   0.00039       3.5      38      56 ..     135     155 ..     132     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.016
                                   G--EEEEEEET.TEEEEEE-EE..-STTEEEE CS
                        DUF5060 24 dvelsatFtspsgksltvpGFY..dGdgayrv 53
                                   dv+ +a+F  +     t + ++  dG+g++ v
  gi|121639817|ref|YP_980041.1| 53 DVADHAVFDVD--NDGTPESYFidDGSGTWAV 82
                                   67777777777..55667789999999***98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00039
                                    EEEEE-EE..-STTEEEEEE- CS
                        DUF5060  38 sltvpGFY..dGdgayrvrFa 56 
                                    +++v G+   dGdg++ vr +
  gi|121639817|ref|YP_980041.1| 135 EQRVTGYVdtDGDGRWDVRLT 155
                                    689*****99999******86 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4   0.00017       1.5       8      18 ..      21      31 ..      20      31 .. 0.90
   2 ?    3.1   0.7    0.0081        72       8      14 ..      34      40 ..      34      41 .. 0.91
   3 ?   -2.6   0.2      0.53   4.8e+03       8      13 ..      47      52 ..      45      52 .. 0.69
   4 ?    4.4   0.2    0.0031        28       7      15 ..      59      67 ..      58      67 .. 0.87
   5 ?    5.5   0.2    0.0014        13       7      14 ..     118     125 ..     117     126 .. 0.87
   6 ?    5.7   0.3    0.0013        11       8      15 ..     142     149 ..     141     149 .. 0.90
   7 ?    3.3   0.5     0.007        63       9      15 ..     156     162 ..     154     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00017
                                   H-SS-SSCE-H CS
                      EF-hand_5  8 iDlNgDGkIsk 18
                                   +Dl+gDG++++
  gi|121639817|ref|YP_980041.1| 21 VDLDGDGRLDA 31
                                   7*******995 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0081
                                   H-SS-SS CS
                      EF-hand_5  8 iDlNgDG 14
                                   +Dl+gDG
  gi|121639817|ref|YP_980041.1| 34 LDLDGDG 40
                                   6*****9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.53
                                   H-SS-S CS
                      EF-hand_5  8 iDlNgD 13
                                   +D +gD
  gi|121639817|ref|YP_980041.1| 47 ADFDGD 52
                                   577777 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0031
                                   HH-SS-SSC CS
                      EF-hand_5  7 aiDlNgDGk 15
                                    +D+++DG+
  gi|121639817|ref|YP_980041.1| 59 VFDVDNDGT 67
                                   59******6 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0014
                                    HH-SS-SS CS
                      EF-hand_5   7 aiDlNgDG 14 
                                     +D++gDG
  gi|121639817|ref|YP_980041.1| 118 LLDTDGDG 125
                                    69*****9 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.0013
                                    H-SS-SSC CS
                      EF-hand_5   8 iDlNgDGk 15 
                                    +D++gDG+
  gi|121639817|ref|YP_980041.1| 142 VDTDGDGR 149
                                    7******7 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.007
                                    -SS-SSC CS
                      EF-hand_5   9 DlNgDGk 15 
                                    D++gDG+
  gi|121639817|ref|YP_980041.1| 156 DTDGDGT 162
                                    9*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1248.56
//
Query:       gi|121639818|ref|YP_980042.1|  [L=480]
Description: poly(A) polymerase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-32  111.0   0.0    9.7e-32  110.1   0.0    1.5  1  PolyA_pol        Poly A polymerase head domain
    2.7e-18   65.5   0.0    6.2e-18   64.3   0.0    1.6  1  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym
    1.6e-14   54.2   0.9    3.2e-14   53.2   0.9    1.6  1  HD               HD domain
    8.7e-06   25.8   0.0    1.9e-05   24.7   0.0    1.5  1  tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putativ


Domain annotation for each model (and alignments):
>> PolyA_pol  Poly A polymerase head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   2.2e-35   9.7e-32       1     125 [.      39     165 ..      39     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 2.2e-35
                                    EEEETHHHHHHHTT---CEEEEEECS-HHHHHHHHHHHHT-EEEEETTTTCCCCEECCEEEEECCEECEEEEEE---SSH CS
                      PolyA_pol   1 lylvGGaVRDlllgkepkDvDlatdaapeelakllrkkvkeallsgeefqtiavlekkqllevatfRlekdesdarnpes 80 
                                    lylvGG+VRD+llg+ + D+D++tda+pe+++++ r +++ ++ +g+ef+t+ v ++++++e++tfR++++ + +r+pe 
  gi|121639818|ref|YP_980042.1|  39 LYLVGGSVRDALLGRLSPDLDFTTDARPERVQEIVRPWADAVWDTGIEFGTVGVGKSDHRMEITTFRADSYDRVSRHPE- 117
                                    7*********************************************************************999999995. PP

                                    HH...HHHHHHCTSSBGGGS-EEE...CTTTCEE-TTSHHHHHHTTEE CS
                      PolyA_pol  81 ekstesleeDlkrRDftiNalayn...lnkgkvlDlfgGikdLkskvi 125
                                    +++ + le Dl+rRDft Na+a++     +g++lD++gG+++L+ kv+
  gi|121639818|ref|YP_980042.1| 118 VRFGDCLEGDLVRRDFTTNAMAVRvtaTGPGEFLDPLGGLAALRAKVL 165
                                    8999********************8878899*************9987 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   1.4e-21   6.2e-18       1      60 [.     193     252 ..     193     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.4e-21
                PolyA_pol_RNAbd   1 gFtIepeTaaairklaplLkkispeRifeEllKlLlsghpeaglelLretgLlkylfPel 60 
                                    gF ++p+++aai+++ap+L++is+eR++ El+KlL +++p+ag++l++++g+ ++++Pe+
  gi|121639818|ref|YP_980042.1| 193 GFAVAPRVRAAIEEMAPQLARISAERVAAELDKLLVGEDPAAGIDLMVQSGMGAVVLPEI 252
                                    8*********************************************************98 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.9   7.1e-18   3.2e-14       1      99 [.     268     368 ..     268     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 7.1e-18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH... CS
                             HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld... 77 
                                    +++Hsl V++ a  l +d        +l++aaLlHDiGk+ +++     ++   +f+ He+vga+++r++   l+++   
  gi|121639818|ref|YP_980042.1| 268 VYQHSLTVLRQAIALEDDGP----DLVLRWAALLHDIGKPATRR---HEPDGGVSFHHHEVVGAKMVRKRMRALKYSkqm 340
                                    69**********88888866....999**************997...33444889999****************999*** PP

                                    HHHHHHHHHTTCCHHHHHHHH.......H CS
                             HD  78 ledvaklirehheswegkkrp.......r 99 
                                    ++d+++l+  h++ +  ++         r
  gi|121639818|ref|YP_980042.1| 341 IDDISQLVYLHLRFHG-YGDGkwtdsavR 368
                                    *************994.444455544441 PP

>> tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.1e-09   1.9e-05      22     131 ..     325     453 ..     316     469 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.1e-09
                tRNA_NucTran2_2  22 eqarsfLkswkfsnklikavtallkllekrk...naeltklelykageealllaeelaqaqgqa......edlqaldeiy 92 
                                    + +r+ ++++k+s+++i+++++l+ l+ +     ++++t+  ++++  +a  l+ +l+++ + +         ++l+ +y
  gi|121639818|ref|YP_980042.1| 325 KMVRKRMRALKYSKQMIDDISQLVYLHLRFHgygDGKWTDSAVRRYVTDAGALLPRLHKLVRADcttrnkRRAARLQASY 404
                                    668999******************9998888999*********9999998888777755544444445556777788888 PP

                tRNA_NucTran2_2  93 qaLpIk............skkeLaitGkdLlealgvkpGpwlgeiLkeleq 131
                                    ++L+ +             +   +++G++ ++ l++++Gp++ge+ + l++
  gi|121639818|ref|YP_980042.1| 405 DRLEERiaelaaqedldrVRP--DLDGNQIMAVLDIPAGPQVGEAWRYLKE 453
                                    888655557774455533333..46*******************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2507.15
//
Query:       gi|121639819|ref|YP_980043.1|  [L=248]
Description: hypothetical protein BCG_3965 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-20   71.4   0.2    9.9e-20   70.9   0.2    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.2   5.5e-24   9.9e-20      20     124 ..      87     190 ..      69     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 5.5e-24
                                    EEESSSSTTT...EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEECSG CS
                          NUDIX  20 vrrskkpfpg...WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfl.eevege 95 
                                    + r +++  g   W+lP+G++e gEt+e++A+RE++EEtG++   l  lgr++y++ +dg+       ++ +l + + ge
  gi|121639819|ref|YP_980043.1|  87 IGRVDRR--GrllWSLPKGHIELGETAEQTAIREVAEETGIRGSVLAALGRIDYWFVTDGRRVH--KTVHHYLmRFLGGE 162
                                    5555333..3358****************************99****************99884..33444441444555 PP

                                    CSSTSTTTEEEEEEEEHHHHHHHHTHCTH CS
                          NUDIX  96 lepndenevsevrwvpleellkeklaaes 124
                                    l  +++ ev+ev wvp+ el    ++a+ 
  gi|121639819|ref|YP_980043.1| 163 LS-DEDLEVAEVAWVPIRELPSRLAYADE 190
                                    55.45999************444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1346.62
//
Query:       gi|121639820|ref|YP_980044.1|  [L=802]
Description: hypothetical protein BCG_3966 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   11.9   0.8        2.9    7.6   0.2    2.4  2  RecC_C           RecC C-terminal domain
       0.23   11.5   0.0       0.37   10.8   0.0    1.2  1  DUF2393          Protein of unknown function (DUF2393)
          3    8.2   7.1       0.63   10.3   1.2    3.0  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> RecC_C  RecC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.02   1.2e+02     159     188 ..     286     340 ..     198     348 .. 0.80
   2 ?    7.6   0.2   0.00048       2.9     159     197 ..     495     547 ..     436     549 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                         RecC_C 159 a.........................lpaeeArelLaellalyrqGlrqpLpffp 188
                                    a                           +++A ++L  l +l ++   +pLpf+ 
  gi|121639820|ref|YP_980044.1| 286 AmtggyvvsdspdgaaqlpgtpthpgTGQAAASSWLDRLRTLVHRTCVTPLPFAQ 340
                                    0555555555555555556666666656889**********************85 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00048
                         RecC_C 159 a..............lpaeeArelLaellalyrqGlrqpLpffpktalaylea 197
                                    a              l++++A+ +L++l+++ r+Gl  p p+++ +a a +++
  gi|121639820|ref|YP_980044.1| 495 AaprtqilvppaswsLASDDAQVILTALATAIRSGLAVPRPLPVVIADAAART 547
                                    155555556666777889**************************999998875 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.2e-05      0.37      61      89 ..      66      94 ..      54     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                        DUF2393 61 eafvvdgtitNeGkftikeCkleiklvnk 89
                                     + v+gt+tN+G+++++ ++++++   +
  gi|121639820|ref|YP_980044.1| 66 PHVTVSGTVTNTGDRPVRDVMVRLEHAAA 94
                                   5789*******************987655 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.2   0.00011      0.63       1      32 [.      69     100 ..      69     108 .. 0.79
   2 ?   -1.9   0.1      0.69   4.1e+03      18      73 ..     400     454 ..     387     462 .. 0.64
   3 ?   -3.8   0.0       2.7   1.6e+04      31      42 ..     641     652 ..     628     654 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvast 32 
                                    t+sG+Vt++ ++p+  + V++++a+  t++++
  gi|121639820|ref|YP_980044.1|  69 TVSGTVTNTGDRPVRDVMVRLEHAAAVTSSTA 100
                                    79********************9766555443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.69
                CarboxypepD_reg  18 tVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                    tV+v++ad + + +  + + G+  l++ +p + s +v a+ +++a       +ag+
  gi|121639820|ref|YP_980044.1| 400 TVAVAAADFSPEEQQGSSQIGSALLPATAPRRLSPRVVAAPFDPAVGA-ALAAAGT 454
                                    555555555555555566667777777777888888888888877753.3333344 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.7
                CarboxypepD_reg  31 stttdadGafrl 42 
                                     t  ++ G+++l
  gi|121639820|ref|YP_980044.1| 641 VTIVNPGGSYTL 652
                                    466677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 4375.24
//
Query:       gi|121639821|ref|YP_980045.1|  [L=1184]
Description: hypothetical protein BCG_3967 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.7e-134  448.8  28.4   2.2e-134  448.5  28.4    1.1  1  MurJ            Lipid II flippase MurJ
  ------ inclusion threshold ------
        0.2   11.7   0.1       0.54   10.3   0.1    1.7  1  Coiled-coil_56  Coiled-coil domain-containing protein 56


Domain annotation for each model (and alignments):
>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.5  28.4  2.5e-138  2.2e-134       1     451 [.      48     521 ..      48     522 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.5 bits;  conditional E-value: 2.5e-138
                           MurJ   1 iaallGaglladaFnvAfklPnllrrlfaegalssaFvPvlaeakkkdeekaaefvrkvltllilvlllvtligilaapl 80 
                                    +aa+lGa+l+++ F+vA++lPnl+++l+ e++++++FvPvla+a+++d +++a+fvr+++tl++++ll++t++++laapl
  gi|121639821|ref|YP_980045.1|  48 LAAILGAALASS-FSVANQLPNLVAALVLEATFTAIFVPVLARAEQDDPDGGAAFVRRLVTLATTLLLGATTLSVLAAPL 126
                                    599****99998.******************************************************************* PP

                           MurJ  81 lirllatgfdeetlelavsllrillpylllvslsavfgavLnarkkFfapafsPvllNvsvIltllllanklgeeail.. 158
                                    l+rl+  ++++ ++ l+++++++llp++l+++ls+vf+a+Ln+r++F++pa++Pv++Nv++I+tl+++ ++ ge +++  
  gi|121639821|ref|YP_980045.1| 127 LVRLMLGTNPQVNEPLTTAFAYLLLPQVLVYGLSSVFMAILNTRNVFGPPAWAPVVNNVVAIATLAVYLAVPGELSVDpv 206
                                    *************************************************************************99999** PP

                           MurJ 159 ........aLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptllgvsvsqlnllvdtalAsflae 230
                                            +L+iG+++G+++q++v l+a+++++++l+p+++ +d++lk+f +++++++l+v++sql+l+v +++As++a+
  gi|121639821|ref|YP_980045.1| 207 rmgnakllVLGIGTTAGVFAQTAVLLVAIRREHISLRPLWG-IDQRLKRFGAMAAAMVLYVLISQLGLVVGNRIASTAAA 285
                                    **9999988********************************.9************************************* PP

                           MurJ 231 gsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllfer 310
                                    ++++i++y++++l+lP+g++gv+++tv++PrlSr+a+++d+++v ++ls a+rlt+++lip++++++v +++i s+lf++
  gi|121639821|ref|YP_980045.1| 286 SGPAIYNYTWLVLMLPFGMIGVTVLTVVMPRLSRNAAADDTPAVLADLSLATRLTMITLIPTVAFMTVGGPAIGSALFAY 365
                                    ******************************************************************************** PP

                           MurJ 311 GnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnills.....llllpplgvvglalat 385
                                    GnF++ d+ ++++++a++a++Lipyalv l+lrvfYAre+ +tP++i+++++ ++il s     +++ p+l +++l+la+
  gi|121639821|ref|YP_980045.1| 366 GNFGDVDAGYLGAAIALSAFTLIPYALVLLQLRVFYAREQPWTPITIIVVITGVKILGSllaphITGDPQLVAAYLGLAN 445
                                    ***********************************************************999999*************** PP

                           MurJ 386 slsaliglvllyvllrkrlk........lteargiktflak..lvvllalaavvilllssltqaewvvgslllilv 451
                                    +l++l+g+++ y++lr++l+        + ear+ ++++a+  l++lla++a+++l+ls+lt+++++vgsll+++v
  gi|121639821|ref|YP_980045.1| 446 GLGFLAGTIVGYYILRRALRpdggqligVGEARTALVTVAAslLAGLLAHVADRLLGLSELTAHAGSVGSLLRLSV 521
                                    ***************************999999999888888999***************************9876 PP

>> Coiled-coil_56  Coiled-coil domain-containing protein 56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   6.1e-05      0.54      47      77 ..     973    1003 ..     966    1013 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.1e-05
                 Coiled-coil_56   47 krrrrnlltGlaiGglvlgiygytfysvkqe 77  
                                      rrrrnll G++ G+ vl + +  + sv   
  gi|121639821|ref|YP_980045.1|  973 TRRRRNLLIGIGAGAAVLMVALLVLASVLSR 1003
                                     689*****************99999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 7148.31
//
Query:       gi|121639822|ref|YP_980046.1|  [L=196]
Description: RNA polymerase sigma factor SigM [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-16   59.7   3.0    3.6e-16   58.7   3.0    1.5  1  Sigma70_r2    Sigma-70 region 2
    1.3e-15   56.8   0.5    1.3e-15   56.8   0.5    2.2  3  Sigma70_r4_2  Sigma-70, region 4
    9.6e-09   35.4   4.3    3.1e-05   23.9   0.3    2.1  2  Sigma70_ECF   ECF sigma factor
    1.4e-07   30.9   0.1    3.6e-07   29.6   0.1    1.7  1  Sigma70_r4    Sigma-70, region 4
     0.0056   16.5   0.3      0.019   14.7   0.3    2.0  1  HTH_23        Homeodomain-like domain
     0.0056   16.8   1.5      0.011   15.8   0.3    2.2  2  HTH_28        Helix-turn-helix domain
     0.0084   16.0   0.0      0.021   14.7   0.0    1.7  1  Terminase_5   Putative ATPase subunit of terminase (gpP-like)
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.084   12.7   0.0    1.6  1  DUF746        Domain of Unknown Function (DUF746)
      0.064   12.8   0.0       0.21   11.1   0.0    1.8  2  GerE          Bacterial regulatory proteins, luxR family
      0.099   13.2   0.1       0.16   12.5   0.1    1.3  1  DUF134        Protein of unknown function  DUF134


Domain annotation for each model (and alignments):
>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   3.0     2e-19   3.6e-16       1      69 [.      39     105 ..      39     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2e-19
                                    HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSS CS
                     Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrr 69 
                                    l++r++++++rlar   + ++da+D +Q+a+l ++r++ +f+ + +  +s+wl+ri+ na++drlR+++
  gi|121639822|ref|YP_980046.1|  39 LFRRHHRQLHRLARLTSRTSEDADDALQDAMLSAHRGAGSFRYDAA--VSSWLHRIVVNACLDRLRRAK 105
                                    79************99**************************5555..*******************87 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1     2e+03      41      49 ..      83      91 ..      82      93 .. 0.85
   2 ?   -3.5   0.3         5   8.9e+03      46      53 ..     100     107 ..      99     107 .. 0.75
   3 !   56.8   0.5     7e-19   1.3e-15       3      54 .]     130     181 ..     128     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHH CS
                   Sigma70_r4_2 41 gtVksrlsR 49
                                   ++V s+l+R
  gi|121639822|ref|YP_980046.1| 83 AAVSSWLHR 91
                                   689*****9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                                    HHHHHHHH CS
                   Sigma70_r4_2  46 rlsRArkk 53 
                                    rl+RA+++
  gi|121639822|ref|YP_980046.1| 100 RLRRAKAH 107
                                    68888875 PP

  == domain 3  score: 56.8 bits;  conditional E-value: 7e-19
                                    HHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    a+++al +Lp +qr++++  +++g+s++++A++lg+ egtVksr +RAr++L
  gi|121639822|ref|YP_980046.1| 130 AVQRALMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    799***********************************************98 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   3.5e-05     0.062       5      54 ..      22      73 ..      18      81 .. 0.90
   2 !   23.9   0.3   1.7e-08   3.1e-05     129     181 ..     130     183 ..      98     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                    Sigma70_ECF  5 telleqvkdGdaeaaeqllelvydeLrrlagskl.knerreetledtaL.vf 54
                                   +ell +   Gd  a +ql+++ + +L rla+     +e +++ l+d  L ++
  gi|121639822|ref|YP_980046.1| 22 AELLAAHVAGDRYAFDQLFRRHHRQLHRLARLTSrTSEDADDALQDAMLsAH 73
                                   678999999**********************99989999*******999666 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.7e-08
                    Sigma70_ECF 129 aler.llsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawler 181
                                    a++r l++l++eq+  v    ++G+s++++A  lgv++ tv+ r a aRa+l+r
  gi|121639822|ref|YP_980046.1| 130 AVQRaLMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARLAR 183
                                    455426679*****************************************9976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1     2e-10   3.6e-07       1      48 [.     134     181 ..     134     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2e-10
                                    HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    aL +Lp ++r  ++ +  +g++ ++++++lg+ +++V+++ +rA+ +L
  gi|121639822|ref|YP_980046.1| 134 ALMRLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    799******************************************999 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.1e-05     0.019      10      40 ..     145     176 ..     133     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                         HTH_23  10 illlla.eGlsvreIAreLgvsrrTvyrwlkr 40 
                                    ++ +++ +G+s+++ Ar+Lgv + Tv     r
  gi|121639822|ref|YP_980046.1| 145 AVVAVDmQGYSIADTARMLGVAEGTVKSRCAR 176
                                    56666667******************855555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   4.5e+03      28      35 ..      84      91 ..      81      92 .. 0.83
   2 !   15.8   0.3   6.2e-06     0.011       6      40 ..     146     180 ..     129     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                         HTH_28 28 tvyrWikr 35
                                    v++W++r
  gi|121639822|ref|YP_980046.1| 84 AVSSWLHR 91
                                   6899*998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.2e-06
                         HTH_28   6 iklla.aGhsvreaArelgisrrtvyrWikryeegG 40 
                                    + ++  +G s++++Ar lg+ + tv++ + r ++  
  gi|121639822|ref|YP_980046.1| 146 VVAVDmQGYSIADTARMLGVAEGTVKSRCARARA-R 180
                                    455554788**********************998.4 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.021      12      38 ..     152     178 ..     142     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                    Terminase_5  12 qGyrvaeIAeelglkeatVysWkkrde 38 
                                    qGy++a+ A++lg+ e tV s + r +
  gi|121639822|ref|YP_980046.1| 152 QGYSIADTARMLGVAEGTVKSRCARAR 178
                                    9*******************9888866 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05     0.084      11      43 ..     152     184 ..     141     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                         DUF746  11 qplslaeaadllgtdegiiakwvreFrewllqL 43 
                                    q  s+a+ a++lg+ eg+++ + ++ r++l++L
  gi|121639822|ref|YP_980046.1| 152 QGYSIADTARMLGVAEGTVKSRCARARARLARL 184
                                    6679*************************9987 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.77   1.4e+03      39      55 ..     132     148 ..     129     150 .. 0.84
   2 ?   11.1   0.0   0.00012      0.21      15      45 ..     151     181 ..     142     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.77
                                    HHHHHHHT-SSHHHHHH CS
                           GerE  39 snimkKLnvksrvelvr 55 
                                    ++++++L v+ r+++v 
  gi|121639822|ref|YP_980046.1| 132 QRALMRLPVEQRAAVVA 148
                                    68999*****9999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                                    CTTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                           GerE  15 aeGksnkeIAeelniSekTVkvhksnimkKL 45 
                                    ++G+s  + A+ l+++e TVk+  +++  +L
  gi|121639822|ref|YP_980046.1| 151 MQGYSIADTARMLGVAEGTVKSRCARARARL 181
                                    79*********************99998887 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.9e-05      0.16      34      80 ..     137     183 ..     114     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                         DUF134  34 aisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiak 80 
                                     + +++  a+  vd + ++  ++a+++G+++ t+ +  + ar ++a 
  gi|121639822|ref|YP_980046.1| 137 RLPVEQRAAVVAVDMQGYSIADTARMLGVAEGTVKSRCARARARLAR 183
                                    566788889999********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1441.30
//
Query:       gi|121639823|ref|YP_980047.1|  [L=254]
Description: hypothetical protein BCG_3970 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1793.12
//
Query:       gi|121639824|ref|YP_980048.1|  [L=335]
Description: thioredoxin reductase trxB2 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-48  165.6   0.6    1.6e-48  165.4   0.6    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-23   83.7   0.0      2e-19   70.0   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.5e-20   72.3   1.3    5.6e-19   68.5   0.1    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   34.0   9.4     0.0056   16.3   0.0    4.1  4  DAO             FAD dependent oxidoreductase
      5e-08   32.5  11.9    7.8e-05   21.9   0.8    4.6  5  FAD_binding_2   FAD binding domain
    8.2e-08   31.7   1.7     0.0054   15.9   0.7    3.8  4  GIDA            Glucose inhibited division protein A
      4e-07   29.8   4.9    1.6e-06   27.7   0.7    3.0  3  FAD_oxidored    FAD dependent oxidoreductase
    1.7e-06   27.4   0.2     0.0039   16.4   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    7.8e-06   24.8   0.1     0.0035   16.1   0.1    3.4  4  HI0933_like     HI0933-like protein
    3.6e-05   23.1   0.0    0.00069   18.9   0.0    2.3  2  Thi4            Thi4 family
    0.00012   22.2   0.1     0.0081   16.4   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.001   18.2   2.4       0.77    8.7   0.0    3.0  4  Lycopene_cycl   Lycopene cyclase protein
     0.0094   16.4   0.2      0.088   13.3   0.0    2.2  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.011   15.0   1.8       0.96    8.6   0.1    2.9  3  FAD_binding_3   FAD binding domain
       0.02   13.7   0.3          1    8.1   0.1    2.8  3  Trp_halogenase  Tryptophan halogenase
      0.035   14.7   2.6        0.1   13.3   0.9    2.6  3  SnoaL_2         SnoaL-like domain
       0.11   12.5   7.4       0.76    9.8   0.0    3.5  4  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.6   1.6e-51   1.6e-48       2     294 .]      16     304 ..      15     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1.6e-51
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgielllg 72 
                                    dv+viG+GpAG++aal++a+a++  +++  egt ++g  + ++ +++++++++ ++         e+   l+ g +l+++
  gi|121639824|ref|YP_980048.1|  16 DVIVIGSGPAGYTAALYAARAQLAPLVF--EGTSFGGALMTTTGVENYPGFRNGITgpelmdemrEQ--ALRFGADLRME 91 
                                    8***************************..99999999********************666655444..23333333333 PP

                                    CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGy 152
                                      v ++   ++ +k    ++ d+++  + +++lA+G+ +r l++pG++e  g++v+++++++++    ++  i+v+GgG 
  gi|121639824|ref|YP_980048.1|  92 -DVESVSL-HGPLKS--VVTADGQTHRARAVILAMGAAARYLQVPGEQELLGRGVSSCATCDGFFFRDQD--IAVIGGGD 165
                                    .3333332.224444..4458999*****************************************99998..******** PP

                                    HHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxx RF
                    Pyr_redox_2 153 iGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle.vvledgeei 226
                                     ++E A +l++++  vtlv++rd++       +s+++ ++ +++ ++++ ++++v+++dg+++    +++ + ++ ++++
  gi|121639824|ref|YP_980048.1| 166 SAMEEATFLTRFARSVTLVHRRDEFR------ASKIMLDRARNNdKIRFLTNHTVVAVDGDTTvtglRVRdTNTGAETTL 239
                                    *************************7......9999999999988******************9966555899999999* PP

                                    EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    ++  v+va+G +p++ l+  +  + +d++g+++v  +   t+ pg++a+GD +  ++++++a++A  +G
  gi|121639824|ref|YP_980048.1| 240 PVTGVFVAIGHEPRSGLV--REAIDVDPDGYVLVQGRTtSTSLPGVFAAGDLV--DRTYRQAVTAAGSG 304
                                    **************9775..7778889*****9988874788***********..9********99876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1    0.0001      0.11       1      34 [.      18      50 ..      18      57 .. 0.89
   2 !   70.0   0.0   1.9e-22     2e-19     101     305 .]      90     287 ..      65     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                   i+iG GPaG +aa+ + +a+l   l+ E  + g 
  gi|121639824|ref|YP_980048.1| 18 IVIGSGPAGYTAALYAARAQL-APLVFEGTSFGG 50
                                   89*******************.689999887775 PP

  == domain 2  score: 70.0 bits;  conditional E-value: 1.9e-22
                    Pyr_redox_3 101 feeVesvkkedeg.fevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefh..kyagqkvvViGgknSa 176
                                     e+Vesv+ ++    +v+++ +t +A+ vi+A+G     ++l++pGe++ l    s    ++   +++q+++ViGg++Sa
  gi|121639824|ref|YP_980048.1|  90 MEDVESVSLHGPLkSVVTADGQTHRARAVILAMGA--AARYLQVPGEQElLGRGVSSCATCDgfFFRDQDIAVIGGGDSA 167
                                    4789999998755266777778************9..99********97555545555544400567************* PP

                    Pyr_redox_3 177 vDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkve 256
                                    ++ A+ l r   +Vt+v+r++e ++++   +   +++++++++ l +++ + v  +++v+ ++ +++    +t  ++++ 
  gi|121639824|ref|YP_980048.1| 168 MEEATFLTRFARSVTLVHRRDEFRASKIMLD---RARNNDKIRFLTNHTVVAVDGDTTVTGLRVRDT----NTGAETTLP 240
                                    *********************9888753333...677888888888888888888988888887654....344445555 PP

                    Pyr_redox_3 257 vkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    v + v++a+G +p   +++ + ++ d dg+++++  t +t +pg+f aG
  gi|121639824|ref|YP_980048.1| 241 V-TGVFVAIGHEPRSGLVR-EAIDVDPDGYVLVQGRTTSTSLPGVFAAG 287
                                    5.678889*********99.9999***********************99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.21   2.2e+02       2      21 ..      17      36 ..      16     109 .. 0.88
   2 !   68.5   0.1   5.3e-22   5.6e-19       2      80 ..     158     230 ..     157     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                                   EEEECSSHHHHHHHHHHHHT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalael 21
                                   v+v+G+G  g  +A ++a+ 
  gi|121639824|ref|YP_980048.1| 17 VIVIGSGPAGYTAALYAARA 36
                                   89******999999988765 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 5.3e-22
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklkd 80 
                                    ++v+GgG++++E+A++l++++ +Vt+v+r+d+++      aski+ ++ ++n +i++l+n++v++++g++  v++++++d
  gi|121639824|ref|YP_980048.1| 158 IAVIGGGDSAMEEATFLTRFARSVTLVHRRDEFR------ASKIMLDRARNNdKIRFLTNHTVVAVDGDTT-VTGLRVRD 230
                                    89********************************......***************************9998.99999985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   6.2e-05     0.066       1      42 [.      16      57 ..      16      67 .. 0.85
   2 !   16.3   0.0   5.3e-06    0.0056     147     206 ..      72     129 ..      63     146 .. 0.79
   3 ?    3.0   0.0      0.06        63       1      32 [.     157     190 ..     157     194 .. 0.84
   4 ?    5.3   0.1     0.012        12     152     207 ..     196     257 ..     188     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsg 42
                                   dv++iG+G +G ++A+++ar+    +++e    +g ga   ++g
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQlaPLVFEGT-SFG-GALMTTTG 57
                                   9*****************9998888888888.777.77655555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.3e-06
                                    HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.H CS
                            DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.l 206
                                    +l+  ++++a + G++++ +  v++++ ++  ++ v  +t+ g++++a+av++a+Ga ++ l
  gi|121639824|ref|YP_980048.1|  72 ELMDEMREQALRFGADLRME-DVESVSLHG-PLKSV--VTAdGQTHRARAVILAMGAAARyL 129
                                    69999**************9.****98864.45566..4555988777*********99842 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.06
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32 
                                    d+++iGGG   +  A +L+r    Vtl+ ++d++
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFArsVTLVHRRDEF 190
                                    8*****************874336****999876 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.012
                                    HHHHHHHTT.-EEEESECEEEEEEEETCEEEEE.EECT.EEEE..EEEEEEE--GGGHH..HH CS
                            DAO 152 laraaealG.veilegtevtgleeedgkvwgve.rttp.gend..aadavVnaaGawsd..ll 207
                                    ++++a+++  +++l++++v+++ + d  v+g++ r+t+ g+++   ++ v +a G+  +  l+
  gi|121639824|ref|YP_980048.1| 196 MLDRARNNDkIRFLTNHTVVAV-DGDTTVTGLRvRDTNtGAETtlPVTGVFVAIGHEPRsgLV 257
                                    67778777659**********9.4457788888988888887324555599999988665333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.8   7.4e-08   7.8e-05       1      40 [.      16      54 ..      16      63 .. 0.84
   2 !    8.4   1.1   0.00096         1     111     227 ..      43     150 ..      41     174 .. 0.67
   3 ?    2.3   0.0     0.067        71       1      35 [.     157     191 ..     157     196 .. 0.92
   4 !    5.7   0.5    0.0061       6.5     146     204 ..     195     253 ..     191     287 .. 0.82
   5 ?    1.2   0.0      0.14   1.5e+02     378     404 ..     263     292 ..     260     306 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.4e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataw 40
                                   DviViGsG AG++AAl aa+a l  +v e ++ fgga+  
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTS-FGGALMT 54
                                   9**********************988888877.5777655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00096
                                    B-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEEC..TTEEEEEEEEETTTTCEE CS
                  FAD_binding_2 111 vdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLive..dgrvtGavvenpesgrev 188
                                    + ++ +Gg   t  t+ +++   +++ +tg++l+  + e+a++ g d+    +++++      g    +v +   +g+++
  gi|121639824|ref|YP_980048.1|  43 FEGTSFGGALMT-TTGVENYP-GFRNGITGPELMDEMREQALRFGADL----RMEDVESVslHGPLKSVVTA---DGQTH 113
                                    668999999999.88886666.47999**************6666555....44444221116677776666...77766 PP

                                    EEEESEEEE-----GG..........GSSSBSSGTT-S- CS
                  FAD_binding_2 189 rirakavvlatgGfgrallkellgaaaeaettnapavtG 227
                                    r  a+av+la g++ r l  +  +++  + +++ ++++G
  gi|121639824|ref|YP_980048.1| 114 R--ARAVILAMGAAARYLQVPGEQELLGRGVSSCATCDG 150
                                    5..9***********933333345555666666666666 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.067
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                    D+ ViG+G + +  A+ +++  ++v++v   +ef+
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDEFR 191
                                    899*************************9998887 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0061
                                    HHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 146 rlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                     ++++ar+++ ++f++++ ++++   d  vtG  v++ ++g e+++  ++v +a g  +r
  gi|121639824|ref|YP_980048.1| 195 IMLDRARNNDkIRFLTNHTVVAV-DGDTTVTGLRVRDTNTGAETTLPVTGVFVAIGHEPR 253
                                    57788888888***********9.3355**************999988888888776555 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.14
                                    BETTSBE...STTEEESSBTEEE-STCEES CS
                  FAD_binding_2 378 tdengrv...ldadgqpipGLYAaGevaag 404
                                    +d++g v    + + + +pG +AaG     
  gi|121639824|ref|YP_980048.1| 263 VDPDGYVlvqGRTTSTSLPGVFAAGDLVDR 292
                                    66666665555668999********88754 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7   5.1e-06    0.0054       1      25 [.      16      40 ..      16      79 .. 0.86
   2 !    8.2   0.0    0.0011       1.1     113     156 ..      88     130 ..      75     149 .. 0.78
   3 ?    3.4   0.0     0.031        33       1      34 [.     157     189 ..     157     211 .. 0.85
   4 ?   -0.1   0.1      0.36   3.8e+02     354     388 ..     279     315 ..     270     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--E CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakv 25
                                   dviViG G AG+ AAl aar+ +  
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQLAP 40
                                   8*******************98765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                    EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EE CS
                           GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGtflkgki 156
                                    ++ e ve++++ ++ +k vvt+dg+t +a+av++a G+  +   
  gi|121639824|ref|YP_980048.1|  88 LRMEDVESVSL-HGPLKSVVTADGQTHRARAVILAMGAAARYLQ 130
                                    55677788866.8999*********************9444443 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.031
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                    d+ ViGgG + +e A  + r   +v+L+ h+ d+
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLV-HRRDE 189
                                    799************************9.44444 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.36
                                    SSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHH CS
                           GIDA 354 kvkgLflAGqinGteGY...eEaaaqGllAGinaarka 388
                                    + +g+f+AG++   + Y   + aa++G+ A+i a r +
  gi|121639824|ref|YP_980048.1| 279 SLPGVFAAGDLVDRT-YrqaVTAAGSGCAAAIDAERWL 315
                                    568899999988887.6222345669999999998765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.7   1.6e-09   1.6e-06       1      66 [.      16      80 ..      16     128 .. 0.82
   2 ?    0.9   0.0      0.22   2.3e+02       1      32 [.     157     188 ..     157     190 .. 0.94
   3 ?    1.2   0.0      0.18   1.9e+02      90     130 ..     194     234 ..     187     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.6e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtg..iarefler 66
                                   Dv+V+G+gpaG++AA+ Aara    l+ e + + G l+t  +v +  g++   + +tg  +++e++e+
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTSFGGALMTTTGVENYPGFR---NGITGpeLMDEMREQ 80
                                   9*******************************************999999...666663344444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                    D+ V+GGg + +  A    r  ++v Lv++r+
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRD 188
                                    9***************************9986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.18
                   FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske.g 130
                                    k +l+   ++++++ l+n+++v+v+ +  ++++++v++ + g
  gi|121639824|ref|YP_980048.1| 194 KIMLDRARNNDKIRFLTNHTVVAVDGDT-TVTGLRVRDTNtG 234
                                    45555556889**************985.8****99887755 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.27   2.8e+02       3      34 ..      15      44 ..      10      49 .. 0.72
   2 !   16.4   0.0   3.7e-06    0.0039     134     230 ..     104     192 ..      73     195 .. 0.66
   3 !    6.8   0.0     0.003       3.1     288     341 ..     199     251 ..     193     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                    K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalfle 34
                                    D+i iG Gp+  + a+ ++ ++  l+ l++e
  gi|121639824|ref|YP_980048.1| 15 RDVIVIGSGPAGYTAALYAARAQ--LAPLVFE 44
                                   58999999998877666665555..6666666 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.7e-06
                    K_oxygenase 134 tveskdaegeeeelearnlvlgvGtep...kiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                    +v     + + ++++ar+++l++G  +   ++P   e l    r v s  +        + ++iaV+G+G Sa e +  l
  gi|121639824|ref|YP_980048.1| 104 SVV----TADGQTHRARAVILAMGAAArylQVPGEQELLG---RGVSSCATCDGF--FFRDQDIAVIGGGDSAMEEATFL 174
                                    333....3467899**********7762224565555443...444444433333..67789*************99888 PP

                    K_oxygenase 211 lrrqkkvelklvtrsealep 230
                                    +r ++  +++lv r++++++
  gi|121639824|ref|YP_980048.1| 175 TRFAR--SVTLVHRRDEFRA 192
                                    87766..999*****99986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.003
                    K_oxygenase 288 kvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                    + ++++++r+l+n++v +++ +++  + l +r++++g+e+tl v  v++A G +
  gi|121639824|ref|YP_980048.1| 199 RARNNDKIRFLTNHTVVAVDGDTT-VTGLRVRDTNTGAETTLPVTGVFVAIGHE 251
                                    6677889**************996.999**********************9975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.3e-06    0.0035       2      36 ..      16      50 ..      15      59 .. 0.84
   2 ?    1.2   0.0      0.11   1.2e+02     130     165 ..      91     125 ..      71     127 .. 0.62
   3 ?    2.6   0.0     0.041        43       2      35 ..     157     190 ..     156     198 .. 0.86
   4 ?   -2.1   0.0       1.1   1.2e+03     372     386 ..     277     291 ..     271     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   dviviG G+AG  aA+ aa+++   l++e ++  g
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQLAPLVFEGTSFGG 50
                                   8***************************9875544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                    --EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 130 tevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    ++v+sv+ +   k  v+  ++++ +a++++lA+G +
  gi|121639824|ref|YP_980048.1|  91 EDVESVSLHGPLKSVVT-ADGQTHRARAVILAMGAA 125
                                    34555555555544455.59**************86 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.041
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                    d++viGgG + +  A  + +  ++V+l+ + +++
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDEF 190
                                    89************************99887765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.1
                                    BTTSTTEEE-GGGBS CS
                    HI0933_like 372 skkvpgLffaGEvlD 386
                                    s ++pg+f aG ++D
  gi|121639824|ref|YP_980048.1| 277 STSLPGVFAAGDLVD 291
                                    7889********999 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.6e-07   0.00069      13      56 ..      10      51 ..       1      59 [. 0.83
   2 ?    1.5   0.0      0.14   1.4e+02      15      38 ..     153     176 ..     142     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                                   HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                           Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                    ++ + Dv+++G+G++G taa y a++ +l  +++e   s+GG 
  gi|121639824|ref|YP_980048.1| 10 AHHPVRDVIVIGSGPAGYTAALYAARA-QLAPLVFEG-TSFGGA 51
                                   566689********************9.999999996.478875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                    HTEEEEEEE--SHHHHHHHHHHHH CS
                           Thi4  15 yaesDvvivGaGssGLtaayylak 38 
                                    + ++D++++G+G s +  a  l++
  gi|121639824|ref|YP_980048.1| 153 FRDQDIAVIGGGDSAMEEATFLTR 176
                                    5679**********9999988876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.7e-06    0.0081       1      37 [.      19      54 ..      19      80 .. 0.81
   2 ?    3.0   0.0      0.12   1.2e+02       1      30 [.     160     189 ..     160     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                   ++G+G +G +aA ++a+a++  l++e   ++GG + +
  gi|121639824|ref|YP_980048.1| 19 VIGSGPAGYTAALYAARAQLAPLVFEGT-SFGGALMT 54
                                   8************************865.55655444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    ++G+G s++  A +L++  ++v+l+ +rd 
  gi|121639824|ref|YP_980048.1| 160 VIGGGDSAMEEATFLTRFARSVTLVHRRDE 189
                                    8****************9999*99988876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0014       1.5       1      24 [.      16      39 ..      16      47 .. 0.80
   2 !    8.7   0.0   0.00073      0.77      88     157 ..      72     139 ..      64     147 .. 0.78
   3 ?   -1.1   0.0      0.71   7.4e+02       1      30 [.     157     184 ..     157     194 .. 0.78
   4 ?   -2.9   0.0       2.6   2.7e+03     119     157 ..     212     249 ..     196     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpg 24
                                   Dv+viG+GpAg   A   ++a+ +
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARAQLA 39
                                   9***********999888555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00073
                  Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyG 157
                                    +l  e+ e+    g+ l+   vesv  +    ++vv+++g++ rar+v+ a g a+++  +  g Q  +G
  gi|121639824|ref|YP_980048.1|  72 ELMDEMREQALRFGADLRMEDVESVSLHGP-LKSVVTADGQTHRARAVILAMG-AAARYLQVPGEQELLG 139
                                    677788888888899999999999987666.899*******************.5555444555555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.71
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                    D++viG+G   +  A  l   + + +v+l+
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFL--TRFARSVTLV 184
                                    99******9999888888..6666666666 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 2.6
                  Lycopene_cycl 119 eslvvleggrkirarlvvdarglaslkkarrlglQtfyG 157
                                    +++v+++g+ ++ +  v d    ++++  + +g+ ++ G
  gi|121639824|ref|YP_980048.1| 212 HTVVAVDGDTTVTGLRVRDTNT-GAETTLPVTGVFVAIG 249
                                    5567778888888888888776.5555555555555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.77   8.1e+02       8      29 ..      15      36 ..      13      54 .. 0.82
   2 !   13.3   0.0   8.4e-05     0.088       5      72 ..     153     221 ..     151     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.77
                  NAD_binding_7  8 kkvlvvGgGevAarkvrkllea 29
                                   + v+v+G G+ +++ +   ++a
  gi|121639824|ref|YP_980048.1| 15 RDVIVIGSGPAGYTAALYAARA 36
                                   6799******999877665555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.4e-05
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdle..gadlviaatddr 72 
                                    ++++ + v+GgG+ A++ +  l ++   vt+v  +  e+  +++ l +   ++++     ++v+a+  d+
  gi|121639824|ref|YP_980048.1| 153 FRDQDIAVIGGGDSAMEEATFLTRFARSVTLVHRR-DEFRASKIMLDRARNNDKIRflTNHTVVAVDGDT 221
                                    68999***************************999.6666666666655544443311344666655555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00091      0.96       3      19 ..      16      32 ..      15      42 .. 0.89
   2 ?    1.7   0.0      0.12   1.3e+02       3      35 ..     157     189 ..     155     193 .. 0.90
   3 ?    2.3   0.1     0.077        82     108     153 ..     193     239 ..     190     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00091
                                   EEEEE--SHHHHHHHHH CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlall 19
                                   dV+++G+GpaG ++al 
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALY 32
                                   8*************975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                    d++++G+G + +  a++L++   +v+lv +r++
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFARSVTLVHRRDE 189
                                    789******************889999999876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.077
                                    HHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                  FAD_binding_3 108 eriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetv 153
                                     +i++++a++   +++  ++ v+++  d++    +vrd +tg+e+t+
  gi|121639824|ref|YP_980048.1| 193 SKIMLDRARNNDkIRFLTNHTVVAVDGDTTVTGLRVRDTNTGAETTL 239
                                    689999999999899999999**999999999999*******99986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.001         1       1      21 [.      16      36 ..      16      43 .. 0.89
   2 ?   -0.1   0.0      0.31   3.3e+02     160     211 ..      77     126 ..      72     131 .. 0.84
   3 ?    1.7   0.0     0.089        93       1      33 [.     157     186 ..     157     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                                   EEEEE--SHHHHHHHHHHHHH CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalaka 21
                                   +++++G G+aG++aA + a+a
  gi|121639824|ref|YP_980048.1| 16 DVIVIGSGPAGYTAALYAARA 36
                                   699*************99887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                                    HHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG- CS
                 Trp_halogenase 160 LrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrg 211
                                    +r+ a + G + +  +v++v l+  g  +s+ ++dg++  a+ +i + G ++
  gi|121639824|ref|YP_980048.1|  77 MREQALRFGADLRMEDVESVSLH--GPLKSVVTADGQTHRARAVILAMGAAA 126
                                    78889999999999999999886..8999*********99999998888765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.089
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                    +i ++GGG ++   A+ l +      +vtlv  
  gi|121639824|ref|YP_980048.1| 157 DIAVIGGGDSAMEEATFLTRFA---RSVTLVHR 186
                                    699*****************99...56888875 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.8   5.1e+03      32      57 ..      16      45 ..       7      58 .. 0.72
   2 ?   -1.3   0.0       3.2   3.4e+03      62      62 ..      97      97 ..      50     160 .. 0.56
   3 ?   13.3   0.9   9.6e-05       0.1      32      92 ..     179     245 ..     153     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                                   E....EESHHHHHHHHHHHHHHEEEEEEEE CS
                        SnoaL_2 32 e....lrGreairaffralfaafpdlrfei 57
                                   +     +G++++ a++ a++a++  l fe 
  gi|121639824|ref|YP_980048.1| 16 DviviGSGPAGYTAALYAARAQLAPLVFEG 45
                                   344557889999998888888777777765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                                   E CS
                        SnoaL_2 62 a 62
                                    
  gi|121639824|ref|YP_980048.1| 97 S 97
                                   1 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 9.6e-05
                                    E....EESHHHHHH...HHHHHHHHEEEEEEE.EEEE.EEETTEEEEEEEEEEEEETTSSEEEEEEEEEE CS
                        SnoaL_2  32 e....lrGreaira...ffralfaafpdlrfe.ihdv.vadgdrvavewtvtgtipatgrgvtvrgvdvf 92 
                                    +    ++ r+++ra   ++ ++++  + +rf   h v ++dgd+ ++  +v+     tg+++t+++++vf
  gi|121639824|ref|YP_980048.1| 179 RsvtlVHRRDEFRAskiMLDRARN-NDKIRFLtNHTVvAVDGDTTVTGLRVRD--TNTGAETTLPVTGVF 245
                                    34556889999***9999999987.55555541555589************95..9**********9998 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.27   2.9e+02       2      19 ..      19      36 ..      18      59 .. 0.71
   2 ?    9.8   0.0   0.00072      0.76     122     155 ..      91     124 ..      72     125 .. 0.79
   3 ?   -2.5   0.0       4.2   4.4e+03       1      17 [.     159     175 ..     159     203 .. 0.68
   4 ?    3.7   0.3     0.052        55     108     155 ..     197     250 ..     189     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                  NAD_binding_9  2 ivGaGprGlavlerLlar 19
                                   ++G Gp+G +++   ++ 
  gi|121639824|ref|YP_980048.1| 19 VIGSGPAGYTAALYAARA 36
                                   8*******9998766555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                  NAD_binding_9 122 aevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    ++v++++ ++    v++adg++++a+aV+LA+G 
  gi|121639824|ref|YP_980048.1|  91 EDVESVSLHGPLKSVVTADGQTHRARAVILAMGA 124
                                    566677777777789*****************95 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.2
                  NAD_binding_9   1 aivGaGprGlavlerLl 17 
                                    a++G+G +++  ++ L 
  gi|121639824|ref|YP_980048.1| 159 AVIGGGDSAMEEATFLT 175
                                    67888877765544444 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.052
                  NAD_binding_9 108 larlpegvtvevh.raevvdleera..dgqavlladg...aslaadaVvLAlGh 155
                                    l+r++++ +++++ +++vv+++ +   +g +v+ ++    ++l +  V++A+Gh
  gi|121639824|ref|YP_980048.1| 197 LDRARNNDKIRFLtNHTVVAVDGDTtvTGLRVRDTNTgaeTTLPVTGVFVAIGH 250
                                    6778888899997355788777766335557776433233568**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2377.20
//
Query:       gi|121639825|ref|YP_980049.1|  [L=116]
Description: thioredoxin trxC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-33  113.3   0.0    5.1e-33  113.1   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.3e-09   38.5   0.1    1.7e-08   34.9   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    1.1e-06   28.8   0.0    0.00018   21.7   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    1.1e-05   25.0   0.0    1.7e-05   24.4   0.0    1.3  1  KaiB           KaiB domain
      5e-05   23.1   0.0    5.6e-05   22.9   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    7.9e-05   22.8   0.0    0.00012   22.1   0.0    1.3  1  Thioredoxin_7  Thioredoxin-like
    0.00011   21.9   0.1    0.00013   21.7   0.1    1.3  1  Redoxin        Redoxin
    0.00038   20.4   0.0     0.0015   18.4   0.0    1.7  2  AhpC-TSA       AhpC/TSA family
     0.0011   18.4   0.0     0.0012   18.3   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0015   18.5   0.0      0.002   18.1   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0021   17.9   0.0     0.0026   17.6   0.0    1.1  1  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.066   13.4   0.0       0.11   12.7   0.0    1.5  1  Glutaredoxin   Glutaredoxin
      0.083   13.3   0.0        0.1   13.0   0.0    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.0   3.7e-36   5.1e-33       2     101 ..       9     108 ..       8     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.7e-36
                                    EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEET CS
                    Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkn 81 
                                    ++++t+++F ++v +++k+vlv+F+A+wCg+Ck++aP+le++a+e + ++++ak+dvd+n+++a++++v +iPtl+lfk+
  gi|121639825|ref|YP_980049.1|   9 TIKVTDASFATDVLSSNKPVLVDFWATWCGPCKMVAPVLEEIATERATDLTVAKLDVDTNPETARNFQVVSIPTLILFKD 88 
                                    57899*************************************************************************** PP

                                    TEEEEEEESS-HHHHHHHHH CS
                    Thioredoxin  82 gkevkkyegarekeklaafl 101
                                    g+ vk+++ga+ k++l + l
  gi|121639825|ref|YP_980049.1|  89 GQPVKRIVGAKGKAALLREL 108
                                    ************99998766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.2e-11   1.7e-08       3     105 ..      23     104 ..      21     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.2e-11
                  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                    +++kpvlv+f++++C+ Ck    +l+e+               + + a+++  ak  +      ++n e ar ++v + P
  gi|121639825|ref|YP_980049.1|  23 SSNKPVLVDFWATWCGPCKMVAPVLEEI---------------ATERATDLTVAKLDV------DTNPETARNFQVVSIP 81 
                                    579*************************...............344455555555553......5666899********* PP

                  Thioredoxin_2  83 tiv.fldgkeivarlpGyvpaeel 105
                                    t++ f dg+ +v r++G+  ++ l
  gi|121639825|ref|YP_980049.1|  82 TLIlFKDGQ-PVKRIVGAKGKAAL 104
                                    *66599999.999****9866555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00018       1      28 [.      25      52 ..      25      68 .. 0.88
   2 ?    5.6   0.0     0.014        19      70      90 ..      67      87 ..      54      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                   .SEEEEEE--SSSHHHHHHHHHHHHHHH CS
                  Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelye 28
                                   +k vl+ f+a+wc pck + p l e+ +
  gi|121639825|ref|YP_980049.1| 25 NKPVLVDFWATWCGPCKMVAPVLEEIAT 52
                                   799********************99865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                                   -HHHHTT-S--TT-SEEEEE- CS
                  Thioredoxin_8 70 krnklkkkynvkaiPtlvvld 90
                                    + + +++++v +iPtl++ +
  gi|121639825|ref|YP_980049.1| 67 TNPETARNFQVVSIPTLILFK 87
                                   4557899**********9976 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.2e-08   1.7e-05      28      77 ..      56     106 ..      41     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                    TTEEEEEEETTTSHCHHCCTCEESCCCCCCC.CSCCHCCCCCCHHHCCHHC CS
                           KaiB  28 fqyeLqvvdvleqPelaeedrlvatPaLikl.sPePkqrlaGdlilqqlkl 77 
                                       ++  +dv ++Pe a+++++v +P+Li   + +P++r++G + ++ l +
  gi|121639825|ref|YP_980049.1|  56 TDLTVAKLDVDTNPETARNFQVVSIPTLILFkDGQPVKRIVGAKGKAALLR 106
                                    34555557*********************862579*******998776665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     4e-08   5.6e-05      48     107 ..      32      89 ..       6     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4e-08
                                    E--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                  Thioredoxin_9  48 ltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                    + + wCg + ++ Pvl++ia e + +++v  l  d n+e+ ++++     +iPtli+++++
  gi|121639825|ref|YP_980049.1|  32 FWATWCGPCKMVAPVLEEIAtERATDLTVAKLDVDTNPETARNFQV---VSIPTLILFKDG 89 
                                    5689***************9666779999999************66...9******98654 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     9e-08   0.00012      15      81 ..      23      86 ..      16      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                                   HHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                  Thioredoxin_7 15 ergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81
                                   +++kpvlv+f a+wc++C+ ++ ++++  +  +  a +  + ++dv+++ +  ++++   +P+++++
  gi|121639825|ref|YP_980049.1| 23 SSNKPVLVDFWATWCGPCKMVAPVLEEIAT--E-RATDLTVAKLDVDTNPETARNFQVVSIPTLILF 86
                                   689*****************9998877633..3.568888888888777776655555668888776 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   9.7e-08   0.00013      27      75 ..      24      70 ..       6     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.7e-08
                                   TTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                        Redoxin 27 kgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75
                                    +k+v+v f+++ +c++C+  +p le++a++ ++ + +v  + +d+++ 
  gi|121639825|ref|YP_980049.1| 24 SNKPVLVDFWAT-WCGPCKMVAPVLEEIATE-RATDLTVAKLDVDTNPE 70
                                   5899********.***************888.77777776666666665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0015      22      69 ..      20      67 ..       5      78 .. 0.74
   2 ?    1.6   0.0      0.17   2.4e+02      88     116 ..      65      87 ..      48      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                   HH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSS CS
                       AhpC-TSA 22 dy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvds 69
                                   d+  ++kpv++ f+++ wc +C+  +p l++ + e +  +++v  + vd+
  gi|121639825|ref|YP_980049.1| 20 DVlsSNKPVLVDFWAT-WCGPCKMVAPVLEEIATERA-TDLTVAKLDVDT 67
                                   4445779*********.**********9999886655.556666665554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                                    E-TTSHHHHHTT-EETTTTECSCEEEEE- CS
                       AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvid 116
                                     D++ ++a++++v+       +++ ++++
  gi|121639825|ref|YP_980049.1|  65 VDTNPETARNFQVV------SIPTLILFK 87 
                                    69999999999999......677766665 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.8e-07    0.0012      45     104 ..      36      88 ..       2     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.8e-07
                      OST3_OST6  45 kCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                     C +C+ ++p +e +a    +d       l  ak+d+d ++++ + +++ s+P l+lf+ 
  gi|121639825|ref|YP_980049.1|  36 WCGPCKMVAPVLEEIATERATD-------LTVAKLDVDTNPETARNFQVVSIPTLILFKD 88 
                                    4999999999999999888777.......99***************************87 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-06     0.002       9      55 ..      36      85 ..      28     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                   SSTTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEEC CS
                  Thioredoxin_3  9 gCakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvi 55
                                    C  C+ ++ +++e+a+e+ ++++v k    +++e   +++V s+P+l++
  gi|121639825|ref|YP_980049.1| 36 WCGPCKMVAPVLEEIATERATDLTVAKLdvDTNPETaRNFQVVSIPTLIL 85
                                   59*****************999988775446666667**********975 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0026     132     210 ..      28      97 ..      17     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                           TraF 132 gLlfFyrgkcpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpv 209
                                     L+ F +  c+ c++ ap+l+++a +    l+v   +vd +p   ++          +++v ++P+l+l++  +    +v
  gi|121639825|ref|YP_980049.1|  28 VLVDFWATWCGPCKMVAPVLEEIATERatDLTVAKLDVDTNPE--TAR---------NFQVVSIPTLILFKDGQPVKRIV 96 
                                    577788999**************98762267777777777766..666.........8************9997666666 PP

                           TraF 210 a 210
                                    +
  gi|121639825|ref|YP_980049.1|  97 G 97 
                                    5 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-05      0.11       5      41 ..      33      75 ..      26      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                                   ESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHH CS
                   Glutaredoxin  5 tkptCpyCkkakrlLkelg......vkfeeidvdkdeeireel 41
                                     ++C+ Ck++  +L+e        + ++  dvd ++e     
  gi|121639825|ref|YP_980049.1| 33 WATWCGPCKMVAPVLEEIAteratdLTVAKLDVDTNPETARNF 75
                                   5589***********8777444444669********9988776 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05       0.1      10      54 ..      37      84 ..      32     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                   -HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCT.TTTEEE CS
                         DUF836 10 ChlCeqakekLkelkleeg..leleviDIakdeeleakYgl.eipvla 54
                                   C+ C+ +  +L+e+++e    l++ + D+++++e  + +++  ip l 
  gi|121639825|ref|YP_980049.1| 37 CGPCKMVAPVLEEIATERAtdLTVAKLDVDTNPETARNFQVvSIPTLI 84
                                   9************77666656999************999953667665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 878.20
//
Query:       gi|121639826|ref|YP_980050.1|  [L=406]
Description: hydrolase [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-30  105.3   3.2    4.7e-16   58.7   0.1    3.0  3  PG_binding_1  Putative peptidoglycan binding domain
    1.2e-29  103.6   0.0      2e-29  103.0   0.0    1.3  1  Amidase_3     N-acetylmuramoyl-L-alanine amidase
    1.7e-08   34.6   0.1       0.12   12.7   0.0    3.5  3  PG_binding_3  Predicted Peptidoglycan domain
    1.9e-05   24.9   0.4    0.00042   20.6   0.1    2.8  2  PG_binding_2  Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> PG_binding_1  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.3   9.5e-16   4.3e-12       2      57 .]      18      83 ..      17      83 .. 0.87
   2 !   58.7   0.1   1.1e-19   4.7e-16       2      57 .]     105     160 ..     104     160 .. 0.97
   3 ?   -2.0   0.0      0.95   4.3e+03       7      26 ..     367     385 ..     355     386 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 9.5e-16
                                   SHHHHHHHHHHHHTT--..SSSS.........SB--HHHHHHHHHHHHHTTST-SSSBSHHHHHHH CS
                   PG_binding_1  2 gedvkelqryLsrlGyl.sgpad.........gtfgpateeaVkefQqffgLpvtGildpaTlaal 57
                                   +++v+e++ +L++lG l  +++d           f++++ +aV++fQq++gL v+Gi+++aT++al
  gi|121639826|ref|YP_980050.1| 18 SAAVTEIRAALTALGMLdHQEEDlttgrnvalELFDAQLDQAVRAFQQHRGLLVDGIVGEATYRAL 83
                                   689*************9844444445677777*******************************997 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 1.1e-19
                                    SHHHHHHHHHHHHTT--.SSSSSB--HHHHHHHHHHHHHTTST-SSSBSHHHHHHH CS
                   PG_binding_1   2 gedvkelqryLsrlGylsgpadgtfgpateeaVkefQqffgLpvtGildpaTlaal 57 
                                    g+dv +lq +L+ lG+++g +dg+fg +t +a+  +Q+ +gL ++Gi +p+Tl+ l
  gi|121639826|ref|YP_980050.1| 105 GDDVATLQARLQDLGFYTGLVDGHFGLQTHNALMSYQREYGLAADGICGPETLRSL 160
                                    79***************************************************976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.95
                                    HHHHHHHHTT--.SSSSSB- CS
                   PG_binding_1   7 elqryLsrlGylsgpadgtf 26 
                                    ++ ++L  lG + + ++gtf
  gi|121639826|ref|YP_980050.1| 367 AAVKRLYLLGKN-DRPTGTF 385
                                    455566666655.7777776 PP

>> Amidase_3  N-acetylmuramoyl-L-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   4.4e-33     2e-29       1     174 [.     193     370 ..     193     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 4.4e-33
                      Amidase_3   1 ividpGHGgkdpGavg...knglkEkdlnlkvalklaklLeakgaeVvltrdddksvslkeranianksradlfvsiHad 77 
                                    i+idpG Gg d G ++   ++ ++E+dl +++a +l+ +++a g+e +l+r +++s s  era+ an+ +adl++s+ + 
  gi|121639826|ref|YP_980050.1| 193 IIIDPGRGGVDHGLIAqgpAGPISEADLLWDLASRLEGRMAAIGMETHLSRPTNRSPSDAERAATANAVGADLMISLRCE 272
                                    89***********777667777********************************************************** PP

                      Amidase_3  78 saanssasGvevfy..leknekkaeskrlaksiqkelkkklglknrgvkeannlyvlrktkipavlvElgfisnpedakl 155
                                      ++ +a+Gv  f   + + + ++  ++la  iq+e+++++gl++  v+ ++ + +lr t++p v v++g+i+np d+ +
  gi|121639826|ref|YP_980050.1| 273 TQTSLAANGVASFHfgNSHGSVSTIGRNLADFIQREVVARTGLRDCRVHGRT-WDLLRLTRMPTVQVDIGYITNPHDRGM 351
                                    999999********98899999999***************************.*************************** PP

                      Amidase_3 156 lkseeyqeklakaiaegik 174
                                    l s+++++++a++i  ++k
  gi|121639826|ref|YP_980050.1| 352 LVSTQTRDAIAEGILAAVK 370
                                    ***************9986 PP

>> PG_binding_3  Predicted Peptidoglycan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.6e-05      0.12       2      32 ..      59      84 ..      58      97 .. 0.82
   2 !   10.3   0.0   0.00014      0.64       5      32 ..     110     138 ..     107     145 .. 0.75
   3 !    8.3   0.0   0.00061       2.7      13      31 ..     142     160 ..     138     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHT.....S---S---HHHHHHH. CS
                   PG_binding_3  2 aivilQriLgklgydvkvDGiiGpkTlaAve 32
                                   a++ +Q+  g     + vDGi+G +T +A++
  gi|121639826|ref|YP_980050.1| 59 AVRAFQQHRG-----LLVDGIVGEATYRALK 84
                                   6788888888.....9**************5 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                                    HHHHHHT......S---S---HHHHHHH. CS
                   PG_binding_3   5 ilQriLgklg.ydvkvDGiiGpkTlaAve 32 
                                     lQ  L +lg y+  vDG +G +T +A++
  gi|121639826|ref|YP_980050.1| 110 TLQARLQDLGfYTGLVDGHFGLQTHNALM 138
                                    57777755543899**************6 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00061
                                    ....S---S---HHHHHHH CS
                   PG_binding_3  13 lgydvkvDGiiGpkTlaAv 31 
                                    + y +++DGi Gp+Tl+ +
  gi|121639826|ref|YP_980050.1| 142 REYGLAADGICGPETLRSL 160
                                    567799**********988 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   5.1e+02      18      32 ..      21      35 ..       7      65 .. 0.77
   2 !   20.6   0.1   9.3e-08   0.00042      12      51 ..     102     141 ..      97     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                   PG_binding_2 18 aeevqaaLsrLGyyd 32
                                   + e++aaL +LG  d
  gi|121639826|ref|YP_980050.1| 21 VTEIRAALTALGMLD 35
                                   679999999999833 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 9.3e-08
                   PG_binding_2  12 vlaedvaeevqaaLsrLGyydgeaggafrealrdALrafi 51 
                                    +l +d +  +qa L+ LG+y g  +g f+ ++++AL +++
  gi|121639826|ref|YP_980050.1| 102 PLYGDDVATLQARLQDLGFYTGLVDGHFGLQTHNALMSYQ 141
                                    78899999******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 2459.71
//
Query:       gi|121639827|ref|YP_980051.1|  [L=244]
Description: hypothetical protein BCG_3974c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1312.03
//
Query:       gi|121639828|ref|YP_980052.1|  [L=344]
Description: chromosome partitioning protein parB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-26   91.4   0.2    6.4e-26   90.5   0.2    1.5  1  ParBc      ParB-like nuclease domain
    4.6e-16   58.3   0.4    9.8e-16   57.3   0.4    1.5  1  HTH_ParB   HTH domain found in ParB protein
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.056   13.3   0.0    1.6  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.076   13.4   0.1        7.1    7.1   0.1    2.5  2  HOASN      Haem-oxygenase-associated N-terminal helices
      0.084   12.9   0.3       0.64   10.0   0.1    2.6  2  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.11   12.6   0.0       0.25   11.5   0.0    1.5  1  SoPB_HTH   Centromere-binding protein HTH domain
       0.13   12.3   0.0        2.2    8.4   0.0    2.2  2  KorB       KorB domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.2   2.5e-29   6.4e-26       2      90 .]      62     155 ..      61     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.5e-29
                          ParBc   2 evplseirpnplqprkd.spekieelvasIkkkGllqPiivrktr....qgryeiiaGerRlrAakrlglkevpvivlei 76 
                                    e+p+s i+ np+qpr+  ++e+++elv+sI++ GllqPi+vr  +    + ry+i++GerR+rAa+++gl ++p+iv+e+
  gi|121639828|ref|YP_980052.1|  62 EIPPSAIEANPRQPRQVfDEEALAELVHSIREFGLLQPIVVRSLAgsqtGVRYQIVMGERRWRAAQEAGLATIPAIVRET 141
                                    8**********************************************9999***************************** PP

                          ParBc  77 ddeeamalslieni 90 
                                     d++ ++ +l eni
  gi|121639828|ref|YP_980052.1| 142 GDDNLLRDALLENI 155
                                    ************97 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.4   3.8e-19   9.8e-16       2      50 ..     206     255 ..     205     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.8e-19
                       HTH_ParB   2 evqeavsegkiseGHARaLlslkde.elqlqlaekiieegLsVRetEklv 50 
                                    +vq+ v +g +s+GHARaLlsl+   e q++la +i++egLsVR tE+ v
  gi|121639828|ref|YP_980052.1| 206 PVQRRVAAGVLSAGHARALLSLEAGpEAQEELASRIVAEGLSVRATEETV 255
                                    599*********************99*********************977 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056      10      46 ..     165     201 ..     162     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                                    CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHH CS
                           TrmB  10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsL 46 
                                    Ea +Y+ Ll +   t de+a ++g++r+ + +++r L
  gi|121639828|ref|YP_980052.1| 165 EAAAYQQLLDEFGVTHDELAARIGRSRPLITNMIRLL 201
                                    99**************************999998866 PP

>> HOASN  Haem-oxygenase-associated N-terminal helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.033        86      58      77 ..     167     186 ..     160     197 .. 0.85
   2 ?    7.1   0.1    0.0028       7.1      18      40 ..     238     260 ..     228     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                    HHHHHHHHHHHH---GGGHH CS
                          HOASN  58 aayqalllvlslsddvateq 77 
                                    aayq+ll ++ ++ d  +++
  gi|121639828|ref|YP_980052.1| 167 AAYQQLLDEFGVTHDELAAR 186
                                    89**********99976665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                                    HHHHHHHHTSTT--HHHHHHHHH CS
                          HOASN  18 eaalladalkvgasldqidlale 40 
                                    +++++a+ l v a+ + ++la +
  gi|121639828|ref|YP_980052.1| 238 ASRIVAEGLSVRATEETVTLANH 260
                                    79*****************9975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00025      0.64      17      46 ..     173     202 ..     150     203 .. 0.79
   2 ?   -1.4   0.0      0.94   2.4e+03       5      31 ..     222     241 ..     220     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                    EEEEEHHHHHHHHHTTSSHHHHHHHHHHHH CS
                      HTH_Crp_2  17 eielpltqeelAsmlGltretvsrilseLk 46 
                                      e+ +t++elA+++G +r  ++ +++ Lk
  gi|121639828|ref|YP_980052.1| 173 LDEFGVTHDELAARIGRSRPLITNMIRLLK 202
                                    346899**************9999999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                                    HHHHHHHCTTTCEEEEEHHHHHHHHHT CS
                      HTH_Crp_2   5 rfLlrlaeraggeielpltqeelAsml 31 
                                    r Ll l++++         qeelAs++
  gi|121639828|ref|YP_980052.1| 222 RALLSLEAGP-------EAQEELASRI 241
                                    6666664432.......2466666654 PP

>> SoPB_HTH  Centromere-binding protein HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.25       5      49 ..     164     207 ..     161     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                       SoPB_HTH   5 eRarrYalaLkdeyannlsalaeaeklskkilskmlrvaklPdav 49 
                                    e a  Y  +L de++     la +   s+ +++ m+r  klP  v
  gi|121639828|ref|YP_980052.1| 164 EEAAAYQ-QLLDEFGVTHDELAARIGRSRPLITNMIRLLKLPIPV 207
                                    5566664.6789*****************************9765 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   3.3e+02      26      84 ..     131     156 ..     123     173 .. 0.58
   2 ?    8.4   0.0   0.00087       2.2       3      77 ..     177     258 ..     175     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                           KorB  26 lldvpdylrelydseviadirtLyeLrraaekhpaevrafvaengeagltrsavrrflk 84 
                                    l+ +p+                                 +v+e g+++l r+a  +++ 
  gi|121639828|ref|YP_980052.1| 131 LATIPA---------------------------------IVRETGDDNLLRDALLENIH 156
                                    444455.................................55555555555555544443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00087
                           KorB   3 gvkqadIAkaLGksksfvslylklldvpdylrelydsevia..dirtLyeLrraaekhpaevrafv.....aengeaglt 75 
                                    gv+  + A++ G+s+  ++    ll++p  ++  +  +v +    r+L +L    e +++ ++++v      ++ e+++t
  gi|121639828|ref|YP_980052.1| 177 GVTHDELAARIGRSRPLITNMIRLLKLPIPVQRRVAAGVLSagHARALLSLEAGPEAQEELASRIVaeglsVRATEETVT 256
                                    78999**************************9999999975337999999999999999999999955544455555555 PP

                           KorB  76 rs 77 
                                    ++
  gi|121639828|ref|YP_980052.1| 257 LA 258
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1786.16
//
Query:       gi|121639829|ref|YP_980053.1|  [L=347]
Description: chromosome partitioning protein parA [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-58  195.5   0.0    9.4e-58  195.0   0.0    1.2  1  AAA_31       AAA domain
    1.8e-28   99.1   0.0    2.5e-28   98.7   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-10   40.6   2.0    3.1e-09   36.7   2.0    2.1  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.1e-09   38.0   0.2    1.5e-07   31.0   0.1    2.4  3  MipZ         ATPase MipZ
    1.4e-09   37.8   0.1    4.3e-05   23.1   0.2    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.3e-08   33.6   0.2    7.2e-08   32.0   0.2    1.7  1  ArsA_ATPase  Anion-transporting ATPase
    7.4e-05   22.3   0.1    0.00049   19.6   0.1    2.0  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0058   16.3   0.4       0.74    9.4   0.4    2.3  2  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.035   13.4   0.3      0.076   12.3   0.1    1.6  2  VirC1        VirC1 protein
      0.058   13.0   0.9       0.16   11.6   0.4    2.0  2  AAA_25       AAA domain
        0.1   11.6   0.2       0.24   10.4   0.2    1.6  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.17   11.7   0.6       0.57    9.9   0.0    2.1  3  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0   0.0   6.3e-61   9.4e-58       2     177 .]      85     263 ..      84     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 6.3e-61
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi.ekneiektlyevlieeknikeaiiktk.ve 79 
                                    +v++ianqKGGvGKTTt+vn+aaala +g k+L++DlDpQ+na+t+lgi ++++ + + ye+li e++++ a+ ++  +e
  gi|121639829|ref|YP_980053.1|  85 RVLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGItDRQSGTPSSYEMLIGEVSLHTALRRSPhSE 164
                                    799**********************************************66778999*****************998678 PP

                         AAA_31  80 nldlipssidLaeaeielvelekkeeilkellekvkd.eYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGle 158
                                    +l  ip++idLa+aeielv++  +e++l+++l ++++ ++Dy+++DcpPsLgllt+naLva+ +v+ip+q+e+yaleG++
  gi|121639829|ref|YP_980053.1| 165 RLFCIPATIDLAGAEIELVSMVARENRLRTALAALDNfDFDYVFVDCPPSLGLLTINALVAAPEVMIPIQCEYYALEGVS 244
                                    88*********************************9857***************************************** PP

                         AAA_31 159 qllktieevkkklnpklei 177
                                    ql+++ie vk +lnp+le+
  gi|121639829|ref|YP_980053.1| 245 QLMRNIEMVKAHLNPQLEV 263
                                    ****************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   1.7e-31   2.5e-28       1     127 [.      87     313 ..      87     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.7e-31
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    ++ia++kGGvGKTt+a+n+a+ala +gl++l++D+Dpq+n+++ + g   +  +                          
  gi|121639829|ref|YP_980053.1|  87 LTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNAST-ALGITDR--Qsgtpssyemligevslhtalrrsphs 163
                                    58****************************************9.3333333..2358999999***************** PP

                                    ..............................................................................CC CS
                                    ..............................................................................xx RF
                           CbiA  55 ..............................................................................dl 56 
                                                                                                                  ++
  gi|121639829|ref|YP_980053.1| 164 erlfcipatidlagaeielvsmvarenrlrtalaaldnfdfdyvfvdcppslglltinalvaapevmipiqceyyaleGV 243
                                    ******************************************************************************** PP

                                    HCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEE.EEE--CCHCCCCHHTS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxx RF
                           CbiA  57 krllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlg.viprdeavaeapargep 127
                                    ++l + +e+++ +++++l++  v+l+++dg+   t+l ++++++ ++y g +vl  vipr+++v+eap   ++
  gi|121639829|ref|YP_980053.1| 244 SQLMRNIEMVKAHLNPQLEVTTVILTMYDGR---TKLADQVADEVRQYfGSKVLRtVIPRSVKVSEAPGYSMT 313
                                    ******************************9...889999999999999******************987765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   2.0   2.1e-12   3.1e-09       3     151 ..      84     241 ..      82     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.1e-12
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.............ekpeqsekkliPve 69 
                                    ++v++++  KGGVGK+t+avn+A+aLa +glk+ ++D+D  G    + lg+++                         v+
  gi|121639829|ref|YP_980053.1|  84 RRVLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNA-STALGITDrqsgtpssyemliG----------EVS 152
                                    57899*************************************76.5566776623333322211110..........111 PP

                           ParA  70 a........kgikvmSigfllesedeavvwrGpm.kskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagav 140
                                             ++ ++  i   ++   + +   + +  ++ ++  l+  +  + Dy+++D+PP  g   lt+   +   +++
  gi|121639829|ref|YP_980053.1| 153 LhtalrrspHSERLFCIPATIDLAGAEIELVSMVaRENRLRTALAALDNFDFDYVFVDCPPSLG--LLTINALVAAPEVM 230
                                    1222333444444555555555444444443333134567777777777788888888888877..45555555555555 PP

                           ParA 141 iVttpqevala 151
                                    i    +  al+
  gi|121639829|ref|YP_980053.1| 231 IPIQCEYYALE 241
                                    55555555555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1     1e-10   1.5e-07       2      42 ..      86     126 ..      85     146 .. 0.89
   2 ?    4.7   0.0     0.011        16      74     133 ..     179     237 ..     158     270 .. 0.78
   3 ?   -3.6   0.0       3.5   5.2e+03      29      56 ..     309     336 ..     301     338 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1e-10
                                    EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                           MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqr 42 
                                    v+ ++n+kGG Gk+ttav +a aL+ +G++  +idld + +
  gi|121639829|ref|YP_980053.1|  86 VLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGN 126
                                    6789*********************************7654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                                    HHHHTTS-HHHHHHHHHHHHHHHHH.H-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSH CS
                           MipZ  74 eeaeveeeeeaevaeleelvadlea.eldfividtPGsdsalsrlahsladtlvtPlndsf 133
                                    e + v+  + +  ++l++++a+l + ++d++ +d+P s   l+  a   a  ++ P+   +
  gi|121639829|ref|YP_980053.1| 179 EIELVSMVARE--NRLRTALAALDNfDFDYVFVDCPPSLGLLTINALVAAPEVMIPIQCEY 237
                                    44444444444..488888888865389**********99999999999999999997665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                                    T--EEEEE--TTT-HHHHHHHHHHHHHH CS
                           MipZ  29 Garvaaidldlrqrtlarylenraatae 56 
                                    G +++ id d   r    yl+  ++ ae
  gi|121639829|ref|YP_980053.1| 309 GYSMTIIDYDPGSRGAMSYLDASRELAE 336
                                    6666677777777777777776666655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   2.9e-08   4.3e-05       8      45 ..      93     131 ..      87     140 .. 0.85
   2 !   12.6   0.0   4.6e-05     0.069     140     248 ..     225     338 ..     196     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.9e-08
                      Fer4_NifH   8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaD.strl 45 
                                    kGG+Gk+tt+ n++aala +g k l++  DP+ + st l
  gi|121639829|ref|YP_980053.1|  93 KGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNaSTAL 131
                                    9******************************97624544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.6e-05
                      Fer4_NifH 140 kaqevyivtsgelmalyaanniakgieky.aksgg.vrlgGliinsr..kvddereliekfaeelgtkvle.vvPrdeiv 214
                                     a ev+i  ++e  al    ++ + ie   a+ ++ ++++ +i      +++  ++++++  +  g+kvl  v+Pr+ +v
  gi|121639829|ref|YP_980053.1| 225 AAPEVMIPIQCEYYALEGVSQLMRNIEMVkAHLNPqLEVTTVILTMYdgRTKLADQVADEVRQYFGSKVLRtVIPRSVKV 304
                                    4778999999999999999999999986514444458899888763300355556666777777899*996368****** PP

                      Fer4_NifH 215 rkaelrkktvieyapeseqakeyrelarkilenk 248
                                     +a    +t+i+y+p s+ a  y + +r+++e +
  gi|121639829|ref|YP_980053.1| 305 SEAPGYSMTIIDYDPGSRGAMSYLDASRELAERD 338
                                    ***********************99999998877 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.2   4.8e-11   7.2e-08       8     144 ..      92     220 ..      85     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.8e-11
                                    ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSCC CS
                    ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeeal 87 
                                     KGGVGKtt +  +a+ l+ +g k+l+i +DP  + s ++     ++ t  +  + + E+  +++l++  ++   +    
  gi|121639829|ref|YP_980053.1|  92 QKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGITDRQSGTPSSYEMLIGEVSLHTALRRSPHSERLF---- 167
                                    59**************************************999999999888888899999998888877654433.... PP

                                    HHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGH CS
                    ArsA_ATPase  88 lgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllsl 144
                                      +  + d+   e + +  +     + + l  +++ ++d+v +D +P    l+ll +
  gi|121639829|ref|YP_980053.1| 168 -CIPATIDLAGAEIELVSMVARENRLRTALAALDNFDFDYVFVDCPPS---LGLLTI 220
                                    .33333333333333333445556677777778888888888888885...333333 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.3e-07   0.00049       4     138 ..      87     226 ..      85     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                       CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregw..araeldgapwrqaale..yapgl 79 
                                    l++   +GGvG+t+ ++ +a al  +g + lviDl p+    +   +  +q+ +    + ++ +  +++a  +    + l
  gi|121639829|ref|YP_980053.1|  87 LTIANQKGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNASTALGITDRQSGTPssYEMLIGEVSLHTALRRspHSERL 166
                                    6667779******************************9998888888744443331133444555555554442234557 PP

                       CBP_BcsQ  80 dllPfG.elnveekenlqqlaekaeallaalkelk.eqyrwillDlpagasaltrellala 138
                                      +P    l+ +e e l ++ +++++l +al++l   +++++++D+p     lt ++l  a
  gi|121639829|ref|YP_980053.1| 167 FCIPATiDLAGAEIE-LVSMVARENRLRTALAALDnFDFDYVFVDCPPSLGLLTINALVAA 226
                                    777876245555555.66788899999999999997899*******999888887776655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.4   0.00049      0.74      11      38 ..      95     122 ..      88     130 .. 0.91
   2 ?    4.3   0.0     0.019        28     135     156 ..     256     277 ..     223     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                                    TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54  11 GaGKTttlaKLaallkkegkkvllvaaD 38 
                                    G+GKTtt+  +aa l  +g k+l++ +D
  gi|121639829|ref|YP_980053.1|  95 GVGKTTTAVNIAAALAVQGLKTLVIDLD 122
                                    9**********************99888 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                                    HHHHHSSCSEEEEESTTSSSST CS
                          SRP54 135 aFkeavgitgviltklDgdakg 156
                                    + + ++++t+vilt  Dg++k 
  gi|121639829|ref|YP_980053.1| 256 HLNPQLEVTTVILTMYDGRTKL 277
                                    567789************9986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.1e-05     0.076       3      36 ..      86     119 ..      84     128 .. 0.86
   2 ?   -2.5   0.0       1.7   2.5e+03      82     114 ..     202     234 ..     187     285 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                          VirC1   3 litfcslkGGaGkttalmglcsalasdgkrvalf 36 
                                    ++t++  kGG Gktt+ + + +ala +g +  + 
  gi|121639829|ref|YP_980053.1|  86 VLTIANQKGGVGKTTTAVNIAAALAVQGLKTLVI 119
                                    799**********************999776555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                          VirC1  82 eGfdyaladtrg..GsselnntiiassdllliPtm 114
                                      fdy+++d     G   +n+ + a   +  iP  
  gi|121639829|ref|YP_980053.1| 202 FDFDYVFVDCPPslGLLTINALVAAPEVM--IPIQ 234
                                    55666666654311444444444433333..3333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4    0.0001      0.16      35      66 ..      87     120 ..      80     210 .. 0.75
   2 ?   -1.2   0.0      0.84   1.3e+03      76     107 ..     237     265 ..     215     316 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                         AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlg.p 66 
                                    l++    +g+GKtt a+++a+a+a +G + l  +
  gi|121639829|ref|YP_980053.1|  87 LTIANQKGGVGKTTTAVNIAAALAvQGLKTLViD 120
                                    56666679****************9998776554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.84
                         AAA_25  76 yvsaEdsedelrrRlravgealrddarllvld 107
                                    y+++E+   +l r ++ v ++l++  +l v++
  gi|121639829|ref|YP_980053.1| 237 YYALEGVS-QLMRNIEMVKAHLNP--QLEVTT 265
                                    66666666.666666666666622..222222 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00016      0.24      23      71 ..      78     127 ..      58     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                    GGG-S-SEEEEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEEEE------ CS
                           MeaB  23 lakaGraqvvGltGv.PGaGkstlvealglelrrrGkrvavlavDPsspf 71 
                                    l++ Gr +v+ +     G+Gk t+  ++++ l+ +G +  v+ +DP  + 
  gi|121639829|ref|YP_980053.1|  78 LQRPGRRRVLTIANQkGGVGKTTTAVNIAAALAVQGLKTLVIDLDPQGNA 127
                                    567899999999875268****************************8765 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00038      0.57       4      34 ..      95     125 ..      93     133 .. 0.89
   2 ?   -1.9   0.0       1.6   2.4e+03      26      52 ..     207     233 ..     200     267 .. 0.74
   3 ?   -3.9   0.0       6.8     1e+04      22      34 ..     309     321 ..     308     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                         CLP1_P   4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34 
                                     +GK+T a +++  ++ +g k++++DlD+  
  gi|121639829|ref|YP_980053.1|  95 GVGKTTTAVNIAAALAVQGLKTLVIDLDPQG 125
                                    59**************************964 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                         CLP1_P  26 vyvDlDvGqseispPgtislalverpi 52 
                                    v+vD+ +  + +++++ +++  v  pi
  gi|121639829|ref|YP_980053.1| 207 VFVDCPPSLGLLTINALVAAPEVMIPI 233
                                    788888888888888888887776666 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6.8
                         CLP1_P  22 grkpvyvDlDvGq 34 
                                    g++ +++D D+G 
  gi|121639829|ref|YP_980053.1| 309 GYSMTIIDYDPGS 321
                                    567899*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.68u 0.39s 00:00:01.07 Elapsed: 00:00:00.57
# Mc/sec: 1829.69
//
Query:       gi|121639830|ref|YP_980054.1|  [L=224]
Description: 16S rRNA methyltransferase GidB [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-55  187.9   0.0    1.3e-55  187.6   0.0    1.0  1  GidB             rRNA small subunit methyltransferase G
     0.0022   17.6   0.0     0.0036   16.9   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.08   12.0   0.0      0.098   11.8   0.0    1.1  1  VP40             Matrix protein VP40
       0.12   13.0   0.0       0.24   12.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
       0.15   11.7   0.0       0.21   11.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.16   11.0   0.0       0.23   10.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   4.4e-59   1.3e-55       5     179 ..      19     194 ..      15     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 4.4e-59
                                    HHHHHHHHHHHHHHS---S--SHHHHHHHCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHH CS
                           GidB   5 lkkYlelllkwNkkinLtsikepeellerhlldslsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekk 84 
                                    +++Y+e l+  + +++L++++e+ +l++rhll+++++ ell++ + +v+D+GsGaGlPG+pLaiarp+l+++Lle+l ++
  gi|121639830|ref|YP_980054.1|  19 ARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGD-RVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRR 97 
                                    689******************************************.9********************************* PP

                                    HHHHHHHHHHCT-SSEEEEES-CCC...TTTTT-EEEEEEC-SSSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCCHC CS
                           GidB  85 iaFLeevkeelklenveivearaee...kqeeekydvvtsRAlaslnelteillkllkegglilalKGksaedeleekek 161
                                    ++FL+e++++l+++ veiv+ raee   +++    d+++sRA+a+l++lt+++++l++++g++la+KG++a+de++e+++
  gi|121639830|ref|YP_980054.1|  98 TEFLREMVTDLGVA-VEIVRGRAEEswvQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRR 176
                                    **************.************999************************************************** PP

                                    CCCCCCEEEEEEEEEE-T CS
                           GidB 162 alqlskvevlsvkslkek 179
                                     +++s++++++v++++++
  gi|121639830|ref|YP_980054.1| 177 VMIASGAVDVRVVTCGAN 194
                                    *************99765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06    0.0036      31      93 ..      61     123 ..      51     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTS CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleev 93 
                                    + ++v+D+G+GaG+ g+ la + p+++v+l++   r  e+ +e +++ +++ve+v   + e +
  gi|121639830|ref|YP_980054.1|  61 RGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESW 123
                                    4678***************************************99999999999887766655 PP

>> VP40  Matrix protein VP40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05     0.098     118     218 ..      64     167 ..      49     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                    EEEEEEECS---TT-SSHHHHCSEEEEEHHHCS-CCG-STTEEEEEEEEEEEEEEE-TTBT---HHHHHTT..-EEEEEE CS
                           VP40 118 klvrvnrlGtGipdhplrllreGnqaflqelvlprvfltnqftydltalklivqklpddawrpsddkliGs..alrpavs 195
                                    ++v +   G+G+p  pl + r   q  l e +l r+   + +  dl   + iv+   +++w   +d+l Gs  a+  av+
  gi|121639830|ref|YP_980054.1|  64 RVVDIG-SGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESW--VQDQLGGSdaAVSRAVA 140
                                    444443.4899************************999999999*****************..9******9999999**9 PP

                                    SSTTS-....-EE---B-GGGGSS-S- CS
                           VP40 196 ihpklr....pillptvkkqayksgkk 218
                                       kl     p++ p+ +  a k ++ 
  gi|121639830|ref|YP_980054.1| 141 ALDKLTkwsmPLIRPNGRMLAIKGERA 167
                                    999996333477777766666654443 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.24       1      71 [.      65     137 ..      65     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvss 71 
                                    v+d+G G G     la + ++ +v+ +++  +  e  re + + g+ ve+v+g ae+  ++ + g  D+ vs+
  gi|121639830|ref|YP_980054.1|  65 VVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEEswVQDQLGGSDAAVSR 137
                                    89********99999988679**********************************983334455577777774 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.1e-05      0.21      47      75 ..      62      90 ..      43     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.1e-05
                Methyltransf_16 47 klsvlELGsGtGlvGlavaellpeakvil 75
                                   + +v+++GsG+Gl G+ +a + p+++v+l
  gi|121639830|ref|YP_980054.1| 62 GDRVVDIGSGAGLPGVPLAIARPDLQVVL 90
                                   678*****************999999986 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.8e-05      0.23      13      75 ..      44     109 ..      43     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                                    E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TC CS
                         RrnaAD  13 lknkkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kd 75 
                                    l+++ ++n ++    le  + v++ig+G G+  ++La      qvv+lE   r  ++l++ ++ ++
  gi|121639830|ref|YP_980054.1|  44 LWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARpdLQVVLLEPLLRRTEFLREMVTdLG 109
                                    78999999999999999*******************5444589******98888888888776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 1209.08
//
Query:       gi|121639831|ref|YP_980055.1|  [L=187]
Description: hypothetical protein BCG_3978c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-15   54.9   0.1    1.4e-14   53.8   0.1    1.6  2  R3H       R3H domain
    5.6e-07   29.3   0.0    9.3e-07   28.6   0.0    1.4  1  KH_4      KH domain


Domain annotation for each model (and alignments):
>> R3H  R3H domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   9.1e+03      29      36 ..      98     105 ..      91     105 .. 0.69
   2 !   53.8   0.1   1.5e-18   1.4e-14       2      59 ..     127     185 ..     126     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                                    HHHHHHHH CS
                            R3H  29 yeRriiHe 36 
                                      R+++H+
  gi|121639831|ref|YP_980055.1|  98 LTRLAVHQ 105
                                    56999996 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 1.5e-18
                                    HHHHHHHHHHHHHH-S--EEE-----SHHHHHHHHHHHHSS.EEEEEE--SS-SEEEEE CS
                            R3H   2 fllrvekklaefvkdtgrslefppmssyeRriiHelaeayg.leseSvGeepkRrvvvt 59 
                                     l ++++++a++v +tg + e+ pm+++eR+i+H++++a + ++seS+G ep+Rrvvv 
  gi|121639831|ref|YP_980055.1| 127 ELAALADEVARRVAETGDREELVPMTPFERKIVHDAVAAVPgVHSESEGVEPERRVVVL 185
                                    68899****************************************************95 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     1e-10   9.3e-07       6      65 ..      47     106 ..      43     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-10
                           KH_4   6 dilkalvddpe.evevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaaanke 65 
                                    d+l++l+d  + + +++++ e ++ ++ ++  ++dl +++G+ G++ldAlq l+ +a++++
  gi|121639831|ref|YP_980055.1|  47 DYLEELLDVLDfDGDIDLDVEGNRAVVSID-GSDDLNKLVGRGGEVLDALQELTRLAVHQK 106
                                    677777777766777777777888888888.7889**********************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1022.31
//
Query:       gi|121639832|ref|YP_980056.1|  [L=366]
Description: inner membrane protein translocase component YidC [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-49  165.6   0.4    1.2e-48  165.1   0.4    1.1  1  60KD_IMP        60Kd inner membrane protein
     0.0084   15.8   0.1       0.28   10.8   0.0    2.2  2  Wzy_C           O-Antigen ligase
  ------ inclusion threshold ------
      0.082   12.9   0.2       0.21   11.6   0.0    1.7  2  SicP-binding    SicP binding
       0.13   11.0   1.6        1.7    7.3   0.6    2.1  2  DUF2207         Predicted membrane protein (DUF2207)
       0.25   11.4   1.4       0.62   10.1   0.3    2.1  2  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
        2.9    7.8   7.4         36    4.3   3.3    3.0  2  LapA_dom        Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.4     4e-52   1.2e-48       1     164 [.      40     273 ..      40     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 4e-52
                       60KD_IMP   1 yglaIilltiivrlillpltlkqlkssakmqelqPelkeiqekykkdkqklqqemmklYkkegvnplaGclplLiqlpif 80 
                                    ++l++++l++++r++l++ +++q++++++mqelqP++k++q+ky kd+q+++ em+kl++++g+np+ Gclp+L q+p+f
  gi|121639832|ref|YP_980056.1|  40 WALSVMFLVFTLRALLYKPFVRQIRTTRQMQELQPQIKALQKKYGKDRQRMALEMQKLQREHGFNPILGCLPMLAQIPVF 119
                                    89****************************************************************************** PP

                       60KD_IMP  81 ialyrvlrsla....................................sfwikdLsapd...................... 102
                                    ++ly+vlrs++                                      ++++++a+                       
  gi|121639832|ref|YP_980056.1| 120 LGLYHVLRSFNrttggfgqphlsvienrltgnyvfspvdvghfldanL-FGAPIGAYMtqrsgldvfvdfsrpaliavgv 198
                                    *********999999999998888888888887777777775555530.3333333225566666777777777999999 PP

                       60KD_IMP 103 .lpillavttflqqkls...ksk..........kmqkmmlyvmplmilffslsfpaglvlYwlvsnllsiaqqlii 164
                                     ++il++++t+++++ s   + +          +m+k+ lyv+pl +++ + ++p +++lYw+ +n+++++qq+++
  gi|121639832|ref|YP_980056.1| 199 pVMILAGIATYFNSRASiarQ-SaeaaanpqtaMMNKLALYVFPLGVVVGGPFLPLAIILYWFSNNIWTFGQQHYV 273
                                    999**********99995541.134445555535599************************************986 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.028        83      18      59 ..      18      65 ..       2     132 .. 0.64
   2 !   10.8   0.0   9.4e-05      0.28      10      89 ..     184     290 ..     178     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.028
                          Wzy_C 18 giigllvalivlliifykrripfllllgilvgvilliilfv........l 59
                                   ++i  +   ++++++++ ++++++l   ++ +v +l +l++         
  gi|121639832|ref|YP_980056.1| 18 SWIMWVWYRLFAFVLGPSNFFAWALS--VMFLVFTLRALLYkpfvrqirT 65
                                   55555555666777777777744433..5555555555555555553331 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.4e-05
                          Wzy_C  10 lflstsRsgiigl.lvalivlliifykrri..........................pfllllgilvgvilliilfvlstn 62 
                                    +f+  sR ++i++ +  +i++ i++y + +                            l+++++   + l+iil ++s+n
  gi|121639832|ref|YP_980056.1| 184 VFVDFSRPALIAVgVPVMILAGIATYFNSRasiarqsaeaaanpqtammnklalyvFPLGVVVGGPFLPLAIILYWFSNN 263
                                    788899*******533466667777777777*****************98777555222222222224578888889999 PP

                          Wzy_C  63 letlknitkafgkldkkkgkdksgssR 89 
                                    + t++++ + fg  +k++++ k+   R
  gi|121639832|ref|YP_980056.1| 264 IWTFGQQHYVFGMIEKEEEAKKQEAVR 290
                                    999999999999999885554444443 PP

>> SicP-binding  SicP binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     7e-05      0.21      28      66 ..      59      98 ..      35     105 .. 0.82
   2 ?   -3.5   0.0       3.5     1e+04      20      30 ..     284     294 ..     272     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                                   HHHCS--S-H.HHHHHHHHHHHHTTSCHHHHHHHHHHHH- CS
                   SicP-binding 28 yaeqvrvedr.kiLevfllaLskkyGeeavkdaldysair 66
                                   +  q+r   + + L+  ++aL kkyG++  + al++ + +
  gi|121639832|ref|YP_980056.1| 59 FVRQIRTTRQmQELQPQIKALQKKYGKDRQRMALEMQKLQ 98
                                   6678997655378**********************98866 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                                    T-HHHHHHHHH CS
                   SicP-binding  20 kntevvrkyae 30 
                                    k+ e+vr+ a 
  gi|121639832|ref|YP_980056.1| 284 KKQEAVRRRAA 294
                                    77888888775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.6   0.00058       1.7     381     453 ..       8      81 ..       6      94 .. 0.72
   2 ?    2.7   0.0     0.014        43     184     231 ..     211     260 ..     172     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                        DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrr..teeGaellakwkgFkk 453
                                    ++l +++  + ++++++  l++++l++ ++f+++ l + +l++ + +ll++ ++++   t++ +el  ++k+++k
  gi|121639832|ref|YP_980056.1|   8 FSLDFIYYPVSWIMWVWYRLFAFVLGP-SNFFAWALSVMFLVFTLRALLYKPFVRQIrtTRQMQELQPQIKALQK 81 
                                    567777778889999999999999998.5555555555555555555555566666457*************965 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.014
                        DUF2207 184 nkldeilkeeqk..ntreraarlslallillilllillllllllllikll 231
                                    n++++i ++ ++  ++ + a  ++lal+++++ +++   +l+l ++++++
  gi|121639832|ref|YP_980056.1| 211 NSRASIARQSAEaaANPQTAMMNKLALYVFPLGVVVGGPFLPLAIILYWF 260
                                    56666666666666777778888888888888888888888888888843 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00021      0.62       6      91 ..      17      90 ..      12     101 .. 0.78
   2 ?   -0.9   0.0      0.48   1.4e+03      28      49 ..     194     217 ..     172     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                 Halogen_Hydrol  6 lsiliavivalvsffllgfsfflalliailggilvyvasrknkkkkhlkksglsrkelkyiretlkeakekikrlekalkrv 87
                                   +s++++v++ l++f+l   +ff++    +l+ +++ ++ r      ++k+     +++   +++++e + +ik+l+k + + 
  gi|121639832|ref|YP_980056.1| 17 VSWIMWVWYRLFAFVLGPSNFFAW----ALSVMFLVFTLR----ALLYKP---FVRQI-RTTRQMQELQPQIKALQKKYGKD 86
                                   899************999999999....999999999999....677777...34444.56789999999999999999887 PP

                 Halogen_Hydrol 88 rsle 91
                                   r++ 
  gi|121639832|ref|YP_980056.1| 87 RQRM 90
                                   7654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.48
                 Halogen_Hydrol  28 la..lliailggilvyvasrknkk 49 
                                    +a  + ++il+gi++y+ sr    
  gi|121639832|ref|YP_980056.1| 194 IAvgVPVMILAGIATYFNSRASIA 217
                                    342344569999999999883333 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.3     0.012        36      40      62 ..      60      82 ..      27      83 .. 0.69
   2 ?    4.0   0.0     0.015        43      27      57 ..     194     224 ..     192     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                       LapA_dom 40 wsylrlrrelrrlkkkikkleke 62
                                   ++++r+ r++++l+ +ik+l+k+
  gi|121639832|ref|YP_980056.1| 60 VRQIRTTRQMQELQPQIKALQKK 82
                                   56779****************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                       LapA_dom  27 fgiGallgwllslwsylrlrrelrrlkkkik 57 
                                    +++G+ +++l+++ +y+  r  + r+  + +
  gi|121639832|ref|YP_980056.1| 194 IAVGVPVMILAGIATYFNSRASIARQSAEAA 224
                                    689999******************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.39s 00:00:01.14 Elapsed: 00:00:00.59
# Mc/sec: 1861.16
//
Query:       gi|121639833|ref|YP_980057.1|  [L=120]
Description: hypothetical protein BCG_3980c [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-27   92.6   0.1    1.3e-26   92.2   0.1    1.2  1  YidD      Putative membrane protein insertion efficiency fact


Domain annotation for each model (and alignments):
>> YidD  Putative membrane protein insertion efficiency factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.1   7.3e-31   1.3e-26       4      65 ..      23      85 ..      20      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 7.3e-31
                           YidD  4 lialirlYqkvispll.ksCrfyptCSeYaleaiekyGllkGlllalkRilrCnplskgGyDp 65
                                   li++i++Y++++spl+ +sCrf+ptCS+Ya++a+++yGll+G++l++ R+++C p+++gG+Dp
  gi|121639833|ref|YP_980057.1| 23 LIFVIQVYRHMLSPLRpASCRFVPTCSQYAVDALTEYGLLRGSWLTMIRLAKCGPWHRGGWDP 85
                                   899***********7779********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 782.14
//
Query:       gi|121639834|ref|YP_980058.1|  [L=125]
Description: ribonuclease P [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-23   81.4   0.3    5.3e-23   81.2   0.3    1.0  1  Ribonuclease_P  Ribonuclease P


Domain annotation for each model (and alignments):
>> Ribonuclease_P  Ribonuclease P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.3     3e-27   5.3e-23       2     109 ..      12     117 ..      11     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 3e-27
                 Ribonuclease_P   2 pkkerLkkraeFqavfregkrvaskdlvlyalknsleksslrlGlsvskkvgkAvvRNrikRllReafrlnkdelpagld 81 
                                    + ++r++++a+F++++++g r  ++d+v+y++  s + +  r+Gl+++k vg+Av+R+r+ R+lR+++   ++el ++ +
  gi|121639834|ref|YP_980058.1|  12 RARNRMRRSADFETTVKHGMRTVRSDMVVYWWRGSGGGP--RVGLIIAKSVGSAVERHRVARRLRHVAGSIVKELHPSDH 89 
                                    6789*****************************666665..*************************************** PP

                 Ribonuclease_P  82 lvviakkgaaeadfaelekelekllkkl 109
                                    +v++a ++ + +++a+le++l+  l+++
  gi|121639834|ref|YP_980058.1|  90 VVIRALPSSRHVSSARLEQQLRCGLRRA 117
                                    ************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 937.10
//
Query:       gi|121639835|ref|YP_980059.1|  [L=47]
Description: 50S ribosomal protein L34 [Mycobacterium bovis BCG str. Pasteur 1173P2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-18   65.2  14.6      4e-18   65.1  14.6    1.0  1  Ribosomal_L34  Ribosomal protein L34


Domain annotation for each model (and alignments):
>> Ribosomal_L34  Ribosomal protein L34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1  14.6   2.2e-22     4e-18       2      44 .]       5      47 .]       4      47 .] 0.98

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.2e-22
                                   --S----HHHHHCSSSHHHHHHSHHHHHHHHHHHTTSSS-SCC CS
                  Ribosomal_L34  2 krtyqPskrkRkrkhGFraRmstknGrkvLkrRraKGRkrLsv 44
                                   krt+qP++r+R+r+hGFr Rm+t++Gr ++++Rr+KGR +Ls+
  gi|121639835|ref|YP_980059.1|  5 KRTFQPNNRRRARVHGFRLRMRTRAGRSIVSSRRRKGRRTLSA 47
                                   9****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 356.67
//
[ok]
